From a7d60f52e88dc009d25ef8f735ed4625c01baa43 Mon Sep 17 00:00:00 2001
From: bebatut <bebatut@users.noreply.github.com>
Date: Wed, 2 Oct 2024 15:01:20 +0000
Subject: [PATCH] Update resources

---
 communities/all/resources/tools.html          |   7379 +-
 communities/all/resources/tools.json          |  10368 +-
 communities/all/resources/tools.tsv           |   2933 +-
 communities/all/resources/tools_wordcloud.png |    Bin 315464 -> 327859 bytes
 communities/all/resources/tutorials.json      | 310896 ++++++++-------
 communities/assembly/resources/tools.html     |    772 +-
 communities/assembly/resources/tools.tsv      |    356 +-
 .../tools_filtered_by_ts_categories.tsv       |    356 +-
 communities/biodiversity/resources/tools.html |    590 +-
 communities/biodiversity/resources/tools.tsv  |    259 +-
 .../tools_filtered_by_ts_categories.tsv       |    259 +-
 communities/imaging/resources/tools.html      |    278 +-
 communities/imaging/resources/tools.tsv       |    140 +-
 .../tools_filtered_by_ts_categories.tsv       |    140 +-
 .../machine-learning/resources/tools.html     |     39 +-
 .../machine-learning/resources/tools.tsv      |     24 +-
 .../tools_filtered_by_ts_categories.tsv       |     24 +-
 communities/microgalaxy/resources/tools.html  |   1273 +-
 communities/microgalaxy/resources/tools.tsv   |    578 +-
 .../tools_filtered_by_ts_categories.tsv       |   1648 +-
 .../microgalaxy/resources/tools_wordcloud.png |    Bin 342126 -> 324410 bytes
 .../microgalaxy/resources/tutorials.html      |   1022 +-
 .../microgalaxy/resources/tutorials.tsv       |     98 +-
 communities/spoc/resources/tools.html         |   6565 +-
 communities/spoc/resources/tools.tsv          |    119 +-
 .../tools_filtered_by_ts_categories.tsv       |    119 +-
 .../spoc/resources/tools_wordcloud.png        |    Bin 238932 -> 119799 bytes
 27 files changed, 168872 insertions(+), 177363 deletions(-)

diff --git a/communities/all/resources/tools.html b/communities/all/resources/tools.html
index c5289334..1d53d59e 100644
--- a/communities/all/resources/tools.html
+++ b/communities/all/resources/tools.html
@@ -88,10 +88,8 @@
       <th>Tools available on UseGalaxy.eu</th>
       <th>Tools available on UseGalaxy.fr</th>
       <th>Tools available on APOSTL</th>
-      <th>Tools available on BF2I-MAP</th>
-      <th>Tools available on BioBix</th>
+      <th>Tools available on ARGs-OAP</th>
       <th>Tools available on CIRM-CFBP</th>
-      <th>Tools available on Center for Phage Technology (CPT)</th>
       <th>Tools available on ChemFlow</th>
       <th>Tools available on Coloc-stats</th>
       <th>Tools available on CoralSNP</th>
@@ -114,7 +112,6 @@
       <th>Tools available on Oqtans</th>
       <th>Tools available on Palfinder</th>
       <th>Tools available on PepSimili</th>
-      <th>Tools available on PhagePromotor</th>
       <th>Tools available on UseGalaxy.be</th>
       <th>Tools available on UseGalaxy.cz</th>
       <th>Tools available on UseGalaxy.no</th>
@@ -181,10 +178,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -248,10 +242,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -315,10 +306,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -382,10 +370,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -449,10 +434,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -522,9 +504,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -584,9 +563,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -651,9 +627,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -704,8 +677,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -720,7 +691,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -771,8 +741,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -792,7 +760,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -852,9 +819,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -919,9 +883,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -964,9 +925,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>8</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -1058,9 +1016,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -1125,9 +1080,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -1173,8 +1125,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1194,7 +1144,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -1259,9 +1208,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -1326,9 +1272,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -1374,8 +1317,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1395,7 +1336,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -1460,9 +1400,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -1527,9 +1464,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -1588,10 +1522,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1655,10 +1586,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1723,9 +1651,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1794,9 +1719,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>9</td>
     </tr>
     <tr>
@@ -1862,9 +1784,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -1929,9 +1848,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -1991,9 +1907,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2057,10 +1970,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2125,9 +2035,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2178,8 +2085,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2199,7 +2104,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -2258,10 +2162,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -2331,9 +2232,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -2398,9 +2296,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -2438,8 +2333,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -2461,8 +2354,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2527,9 +2419,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2599,9 +2488,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -2666,9 +2552,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -2733,9 +2616,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -2800,9 +2680,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -2862,9 +2739,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2934,9 +2808,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -2996,9 +2867,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3068,9 +2936,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -3129,10 +2994,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3197,9 +3059,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3250,8 +3109,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>20</td>
       <td>0</td>
       <td>0</td>
@@ -3271,7 +3128,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -3299,11 +3155,8 @@
       <td></td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -3398,9 +3251,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3465,9 +3315,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3518,8 +3365,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3534,7 +3379,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3599,9 +3443,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>7</td>
       <td>7</td>
       <td>0</td>
@@ -3671,9 +3512,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -3708,9 +3546,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -3775,10 +3610,8 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -3806,7 +3639,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>10</td>
     </tr>
     <tr>
@@ -3872,9 +3704,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -3939,9 +3768,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -4006,9 +3832,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -4054,8 +3877,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4075,7 +3896,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -4113,8 +3933,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -4136,8 +3954,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -4207,9 +4024,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -4274,9 +4088,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -4341,9 +4152,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -4403,9 +4211,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4475,9 +4280,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -4523,8 +4325,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4544,7 +4344,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -4609,9 +4408,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -4671,9 +4467,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4738,9 +4531,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4805,9 +4595,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4872,9 +4659,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4928,8 +4712,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4946,7 +4728,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -5005,10 +4786,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5078,9 +4856,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -5140,9 +4915,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5207,9 +4979,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5279,9 +5048,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -5346,9 +5112,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -5413,9 +5176,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -5475,9 +5235,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5547,9 +5304,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -5614,9 +5368,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -5681,9 +5432,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -5748,9 +5496,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -5815,9 +5560,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -5882,9 +5624,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -5949,9 +5688,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -6011,9 +5747,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -6078,9 +5811,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -6150,9 +5880,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -6211,10 +5938,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6279,9 +6003,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -6351,9 +6072,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -6418,9 +6136,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -6480,9 +6195,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -6547,9 +6259,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -6614,9 +6323,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6684,9 +6390,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>41</td>
       <td>6076</td>
     </tr>
@@ -6753,9 +6456,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -6820,9 +6520,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -6868,8 +6565,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -6884,7 +6579,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -6954,9 +6648,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -7001,8 +6692,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7017,8 +6706,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -7088,9 +6776,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -7150,9 +6835,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>10</td>
       <td>10</td>
       <td>0</td>
@@ -7222,9 +6904,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -7289,9 +6968,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -7356,9 +7032,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -7404,8 +7077,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7425,7 +7096,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -7485,9 +7155,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7557,9 +7224,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -7619,9 +7283,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -7686,9 +7347,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7758,9 +7416,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -7825,9 +7480,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -7887,9 +7539,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7940,8 +7589,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7955,8 +7602,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8026,9 +7672,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -8093,9 +7736,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -8155,9 +7795,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8227,9 +7864,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -8294,9 +7928,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -8361,9 +7992,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -8409,8 +8037,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8430,7 +8056,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -8495,9 +8120,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -8535,8 +8157,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -8564,7 +8184,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -8617,8 +8236,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8631,7 +8248,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -8696,9 +8312,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -8719,18 +8332,15 @@
       <td>imgteam</td>
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/</td>
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage</td>
-      <td>0.2</td>
+      <td>0.3</td>
       <td>scikit-image</td>
       <td></td>
       <td>Image analysis</td>
       <td>Imaging, Bioinformatics</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -8786,8 +8396,8 @@
       <td>imgteam</td>
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/</td>
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage</td>
-      <td>0.3-2</td>
-      <td>numpy</td>
+      <td>0.4</td>
+      <td>scikit-image</td>
       <td></td>
       <td>Image analysis</td>
       <td>Imaging, Bioinformatics</td>
@@ -8825,9 +8435,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8892,9 +8499,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8959,9 +8563,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -9026,9 +8627,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -9098,9 +8696,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -9165,9 +8760,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -9213,8 +8805,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>12</td>
       <td>0</td>
       <td>0</td>
@@ -9234,7 +8824,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -9299,9 +8888,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -9345,8 +8931,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>2</td>
@@ -9368,7 +8952,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -9433,9 +9016,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -9499,9 +9079,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>16</td>
     </tr>
     <tr>
@@ -9562,9 +9139,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -9633,9 +9207,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>7</td>
     </tr>
     <tr>
@@ -9701,9 +9272,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -9763,9 +9331,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -9835,9 +9400,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -9897,9 +9459,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9969,9 +9528,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -10017,8 +9573,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10033,7 +9587,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -10103,9 +9656,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -10165,9 +9715,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -10218,8 +9765,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10239,7 +9784,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -10304,9 +9848,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -10366,9 +9907,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -10438,9 +9976,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -10505,9 +10040,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -10567,9 +10099,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -10639,9 +10168,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -10662,9 +10188,9 @@
       <td>imgteam</td>
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/</td>
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d</td>
-      <td>0.0.3-2</td>
-      <td>imageio</td>
-      <td></td>
+      <td>0.1</td>
+      <td>giatools</td>
+      <td>0.3.1</td>
       <td>Image analysis</td>
       <td>Imaging, Bioinformatics</td>
       <td>0</td>
@@ -10701,9 +10227,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10754,8 +10277,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10770,7 +10291,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10819,8 +10339,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -10836,8 +10354,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -10888,8 +10405,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10909,7 +10424,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -10969,9 +10483,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -11036,9 +10547,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -11103,9 +10611,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -11170,9 +10675,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -11237,9 +10739,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -11304,9 +10803,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
       <td>0</td>
       <td>0</td>
@@ -11339,15 +10835,12 @@
       <td></td>
       <td>21</td>
       <td>21</td>
+      <td>22</td>
       <td>21</td>
       <td>21</td>
       <td>21</td>
+      <td>22</td>
       <td>21</td>
-      <td>21</td>
-      <td>21</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11438,9 +10931,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>12</td>
       <td>0</td>
       <td>0</td>
@@ -11505,9 +10995,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -11572,9 +11059,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>10</td>
       <td>0</td>
       <td>0</td>
@@ -11639,9 +11123,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>17</td>
       <td>0</td>
       <td>0</td>
@@ -11706,9 +11187,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -11773,9 +11251,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>11</td>
       <td>0</td>
       <td>0</td>
@@ -11840,9 +11315,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -11907,9 +11379,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>12</td>
       <td>0</td>
       <td>0</td>
@@ -11974,9 +11443,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
       <td>0</td>
       <td>0</td>
@@ -12041,9 +11507,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -12113,9 +11576,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -12175,9 +11635,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>15</td>
       <td>0</td>
       <td>0</td>
@@ -12242,9 +11699,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -12309,9 +11763,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>8</td>
       <td>0</td>
       <td>0</td>
@@ -12381,9 +11832,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -12443,9 +11891,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -12473,7 +11918,7 @@
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm</td>
       <td>0.2.0</td>
       <td>superdsm</td>
-      <td>0.3.0</td>
+      <td>0.4.0</td>
       <td>Image analysis</td>
       <td></td>
       <td>0</td>
@@ -12510,9 +11955,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -12552,9 +11994,6 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -12630,8 +12069,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -12651,7 +12088,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -12716,9 +12152,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -12764,8 +12197,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -12779,8 +12210,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -12845,9 +12275,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -12917,9 +12344,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -12979,9 +12403,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -13051,9 +12472,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -13113,9 +12531,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -13180,9 +12595,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -13252,9 +12664,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -13314,9 +12723,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -13349,17 +12755,139 @@
       <td>Data visualisation, Metabolomics</td>
       <td>9</td>
       <td>11</td>
-      <td>10</td>
-      <td>10</td>
+      <td>12</td>
+      <td>12</td>
       <td>9</td>
       <td>11</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
       <td>10</td>
-      <td>10</td>
+      <td>9</td>
+      <td>0</td>
+      <td>356</td>
+      <td>29809</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>10x_bamtofastq</td>
+      <td>10x_bamtofastq</td>
+      <td>Converts 10x Genomics BAM to FASTQ</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/10XGenomics/bamtofastq</td>
+      <td>Convert Formats</td>
+      <td>10x_bamtofastq</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq</td>
+      <td>1.4.1</td>
+      <td>10x_bamtofastq</td>
+      <td>1.4.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>46</td>
+      <td>228</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>AggregateAlignments</td>
+      <td>graphclust_aggregate_alignments</td>
+      <td>Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_aggregate_alignments</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments</td>
+      <td>0.6.0</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -13384,17 +12912,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>10</td>
-      <td>9</td>
       <td>0</td>
-      <td>356</td>
-      <td>29809</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6</td>
+      <td>116</td>
     </tr>
     <tr>
       <td></td>
-      <td>10x_bamtofastq</td>
-      <td>10x_bamtofastq</td>
-      <td>Converts 10x Genomics BAM to FASTQ</td>
+      <td>AlignCluster</td>
+      <td>graphclust_align_cluster</td>
+      <td>Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.</td>
       <td></td>
       <td></td>
       <td></td>
@@ -13403,27 +12934,24 @@
       <td></td>
       <td></td>
       <td>To update</td>
-      <td>https://github.com/10XGenomics/bamtofastq</td>
-      <td>Convert Formats</td>
-      <td>10x_bamtofastq</td>
-      <td>bgruening</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq</td>
-      <td>1.4.1</td>
-      <td>10x_bamtofastq</td>
       <td></td>
+      <td>RNA</td>
+      <td>graphclust_align_cluster</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster</td>
+      <td>0.1</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
       <td></td>
       <td></td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -13451,17 +12979,17 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
-      <td>46</td>
-      <td>228</td>
+      <td>10</td>
+      <td>3060</td>
     </tr>
     <tr>
       <td></td>
-      <td>AggregateAlignments</td>
-      <td>graphclust_aggregate_alignments</td>
-      <td>Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.</td>
+      <td>CMFinder</td>
+      <td>cmFinder</td>
+      <td>Determines consensus motives for sequences.</td>
       <td></td>
       <td></td>
       <td></td>
@@ -13469,14 +12997,14 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td></td>
       <td>RNA</td>
-      <td>graphclust_aggregate_alignments</td>
+      <td>graphclust_cmfinder</td>
       <td>rnateam</td>
-      <td>https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments</td>
-      <td>0.6.0</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder</td>
+      <td>0.4</td>
       <td>graphclust-wrappers</td>
       <td>0.6.0</td>
       <td></td>
@@ -13515,20 +13043,17 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>6</td>
-      <td>116</td>
+      <td>14</td>
+      <td>45191</td>
     </tr>
     <tr>
       <td></td>
-      <td>AlignCluster</td>
-      <td>graphclust_align_cluster</td>
-      <td>Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.</td>
+      <td>CollectResults</td>
+      <td>glob_report</td>
+      <td>Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.</td>
       <td></td>
       <td></td>
       <td></td>
@@ -13539,11 +13064,11 @@
       <td>To update</td>
       <td></td>
       <td>RNA</td>
-      <td>graphclust_align_cluster</td>
+      <td>graphclust_postprocessing</td>
       <td>rnateam</td>
-      <td>https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster</td>
-      <td>0.1</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults</td>
+      <td>0.5</td>
       <td>graphclust-wrappers</td>
       <td>0.6.0</td>
       <td></td>
@@ -13582,20 +13107,17 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>10</td>
-      <td>3060</td>
+      <td>14</td>
+      <td>1961</td>
     </tr>
     <tr>
       <td></td>
-      <td>CMFinder</td>
-      <td>cmFinder</td>
-      <td>Determines consensus motives for sequences.</td>
+      <td>CollectResultsNoAlign</td>
+      <td>graphclust_glob_report_no_align</td>
+      <td>Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.</td>
       <td></td>
       <td></td>
       <td></td>
@@ -13606,11 +13128,11 @@
       <td>To update</td>
       <td></td>
       <td>RNA</td>
-      <td>graphclust_cmfinder</td>
+      <td>graphclust_postprocessing_no_align</td>
       <td>rnateam</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder</td>
-      <td>0.4</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign</td>
+      <td>0.5</td>
       <td>graphclust-wrappers</td>
       <td>0.6.0</td>
       <td></td>
@@ -13649,20 +13171,17 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>14</td>
-      <td>45191</td>
+      <td>0</td>
+      <td>108</td>
     </tr>
     <tr>
       <td></td>
-      <td>CollectResults</td>
-      <td>glob_report</td>
-      <td>Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.</td>
+      <td>GSPAN</td>
+      <td>gspan</td>
+      <td>Second step of GraphClust</td>
       <td></td>
       <td></td>
       <td></td>
@@ -13673,11 +13192,11 @@
       <td>To update</td>
       <td></td>
       <td>RNA</td>
-      <td>graphclust_postprocessing</td>
+      <td>graphclust_fasta_to_gspan</td>
       <td>rnateam</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults</td>
-      <td>0.5</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN</td>
+      <td>0.4</td>
       <td>graphclust-wrappers</td>
       <td>0.6.0</td>
       <td></td>
@@ -13716,20 +13235,17 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>14</td>
-      <td>1961</td>
+      <td>4</td>
+      <td>133</td>
     </tr>
     <tr>
       <td></td>
-      <td>CollectResultsNoAlign</td>
-      <td>graphclust_glob_report_no_align</td>
-      <td>Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.</td>
+      <td>LocARNAGraphClust</td>
+      <td>locarna_best_subtree</td>
+      <td>MLocARNA computes a multiple sequence-structure alignment of RNA sequences.</td>
       <td></td>
       <td></td>
       <td></td>
@@ -13740,11 +13256,11 @@
       <td>To update</td>
       <td></td>
       <td>RNA</td>
-      <td>graphclust_postprocessing_no_align</td>
+      <td>graphclust_mlocarna</td>
       <td>rnateam</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign</td>
-      <td>0.5</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust</td>
+      <td>0.4</td>
       <td>graphclust-wrappers</td>
       <td>0.6.0</td>
       <td></td>
@@ -13783,20 +13299,17 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>0</td>
-      <td>108</td>
+      <td>13</td>
+      <td>45325</td>
     </tr>
     <tr>
       <td></td>
-      <td>GSPAN</td>
-      <td>gspan</td>
-      <td>Second step of GraphClust</td>
+      <td>NSPDK</td>
+      <td>NSPDK_candidateClust, nspdk_sparse</td>
+      <td>Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.</td>
       <td></td>
       <td></td>
       <td></td>
@@ -13807,25 +13320,22 @@
       <td>To update</td>
       <td></td>
       <td>RNA</td>
-      <td>graphclust_fasta_to_gspan</td>
+      <td>graphclust_nspdk</td>
       <td>rnateam</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN</td>
-      <td>0.4</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK</td>
+      <td>9.2.3.1</td>
       <td>graphclust-wrappers</td>
       <td>0.6.0</td>
       <td></td>
       <td></td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
+      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -13853,17 +13363,17 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
+      <td>2</td>
+      <td>2</td>
       <td>0</td>
-      <td>4</td>
-      <td>133</td>
+      <td>28</td>
+      <td>62388</td>
     </tr>
     <tr>
       <td></td>
-      <td>LocARNAGraphClust</td>
-      <td>locarna_best_subtree</td>
-      <td>MLocARNA computes a multiple sequence-structure alignment of RNA sequences.</td>
+      <td>Plotting</td>
+      <td>motifFinderPlot</td>
+      <td>Plotting results for GraphClust</td>
       <td></td>
       <td></td>
       <td></td>
@@ -13874,13 +13384,13 @@
       <td>To update</td>
       <td></td>
       <td>RNA</td>
-      <td>graphclust_mlocarna</td>
+      <td>graphclust_motif_finder_plot</td>
       <td>rnateam</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust</td>
+      <td>https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting</td>
       <td>0.4</td>
-      <td>graphclust-wrappers</td>
-      <td>0.6.0</td>
+      <td>seaborn</td>
+      <td></td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -13917,20 +13427,17 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>13</td>
-      <td>45325</td>
+      <td>3</td>
+      <td>68</td>
     </tr>
     <tr>
       <td></td>
-      <td>NSPDK</td>
-      <td>NSPDK_candidateClust, nspdk_sparse</td>
-      <td>Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.</td>
+      <td>PrepareForMlocarna</td>
+      <td>preMloc</td>
+      <td>This tool prepares files for locarna step.</td>
       <td></td>
       <td></td>
       <td></td>
@@ -13941,25 +13448,22 @@
       <td>To update</td>
       <td></td>
       <td>RNA</td>
-      <td>graphclust_nspdk</td>
+      <td>graphclust_prepocessing_for_mlocarna</td>
       <td>rnateam</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK</td>
-      <td>9.2.3.1</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna</td>
+      <td>0.4</td>
       <td>graphclust-wrappers</td>
       <td>0.6.0</td>
       <td></td>
       <td></td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -13987,17 +13491,17 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>2</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
-      <td>28</td>
-      <td>62388</td>
+      <td>15</td>
+      <td>1932</td>
     </tr>
     <tr>
       <td></td>
-      <td>Plotting</td>
-      <td>motifFinderPlot</td>
-      <td>Plotting results for GraphClust</td>
+      <td>Preprocessing</td>
+      <td>preproc</td>
+      <td>Preprocessing input for GraphClust</td>
       <td></td>
       <td></td>
       <td></td>
@@ -14008,13 +13512,13 @@
       <td>To update</td>
       <td></td>
       <td>RNA</td>
-      <td>graphclust_motif_finder_plot</td>
+      <td>graphclust_preprocessing</td>
       <td>rnateam</td>
-      <td>https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting</td>
-      <td>0.4</td>
-      <td>seaborn</td>
-      <td></td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing</td>
+      <td>0.5</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -14051,143 +13555,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>3</td>
-      <td>68</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>PrepareForMlocarna</td>
-      <td>preMloc</td>
-      <td>This tool prepares files for locarna step.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td></td>
-      <td>RNA</td>
-      <td>graphclust_prepocessing_for_mlocarna</td>
-      <td>rnateam</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna</td>
-      <td>0.4</td>
-      <td>graphclust-wrappers</td>
-      <td>0.6.0</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>15</td>
-      <td>1932</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>Preprocessing</td>
-      <td>preproc</td>
-      <td>Preprocessing input for GraphClust</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td></td>
-      <td>RNA</td>
-      <td>graphclust_preprocessing</td>
-      <td>rnateam</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing</td>
-      <td>0.5</td>
-      <td>graphclust-wrappers</td>
-      <td>0.6.0</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -14252,9 +13619,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -14318,10 +13682,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -14362,9 +13723,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
@@ -14388,7 +13747,6 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -14407,7 +13765,7 @@
       <td>Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.</td>
       <td>Data handling, Genome annotation</td>
       <td>Genomics</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/NBISweden/AGAT</td>
       <td>Convert Formats, Statistics, Fasta Manipulation</td>
       <td>agat</td>
@@ -14416,7 +13774,7 @@
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/agat</td>
       <td>1.4.0</td>
       <td>agat</td>
-      <td>1.4.0</td>
+      <td>1.4.1</td>
       <td>Data handling, Genome annotation</td>
       <td>Genomics</td>
       <td>0</td>
@@ -14453,9 +13811,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -14520,82 +13875,12 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>11</td>
       <td>329</td>
     </tr>
-    <tr>
-      <td></td>
-      <td>annotation_profiler</td>
-      <td>Annotation_Profiler_0</td>
-      <td>Profile Annotations for a set of genomic intervals</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td></td>
-      <td>Genomic Interval Operations</td>
-      <td>annotation_profiler</td>
-      <td>devteam</td>
-      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/annotation_profiler</td>
-      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/annotation_profiler</td>
-      <td>1.0.0</td>
-      <td>bx-python</td>
-      <td>0.12.0</td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
-    </tr>
     <tr>
       <td></td>
       <td>antarna</td>
@@ -14654,9 +13939,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -14703,8 +13985,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -14723,7 +14003,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -14788,9 +14067,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -14855,9 +14131,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -14907,8 +14180,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -14923,8 +14194,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -14989,9 +14259,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -15061,9 +14328,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -15086,7 +14350,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage</td>
       <td>1.0.0</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -15108,8 +14372,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -15124,8 +14386,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -15189,10 +14450,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -15261,9 +14519,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
     </tr>
     <tr>
@@ -15309,8 +14564,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -15326,7 +14579,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -15352,7 +14604,7 @@
       <td>bgruening</td>
       <td>https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging</td>
-      <td>2.3.1</td>
+      <td>2.4.0</td>
       <td>python</td>
       <td></td>
       <td></td>
@@ -15396,9 +14648,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -15462,9 +14711,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>13</td>
     </tr>
     <tr>
@@ -15525,9 +14771,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -15567,8 +14810,6 @@
       <td>4</td>
       <td>4</td>
       <td>0</td>
-      <td>4</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -15593,8 +14834,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>4</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
@@ -15664,9 +14904,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -15731,9 +14968,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -15793,9 +15027,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -15853,16 +15084,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -15920,16 +15148,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -15979,8 +15204,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -15995,8 +15218,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -16060,10 +15282,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -16103,8 +15322,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -16130,7 +15347,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -16194,10 +15410,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -16261,10 +15474,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -16315,8 +15525,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -16336,7 +15544,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -16401,9 +15608,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -16462,10 +15666,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>19</td>
       <td>23</td>
       <td>19</td>
       <td>0</td>
@@ -16516,8 +15717,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -16532,7 +15731,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -16573,9 +15771,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
@@ -16599,7 +15795,6 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -16669,9 +15864,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -16724,8 +15916,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -16733,7 +15923,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -16803,9 +15992,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -16865,9 +16051,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -16895,7 +16078,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell</td>
       <td>0.0.7</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -16937,9 +16120,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -17004,9 +16184,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -17029,7 +16206,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster</td>
       <td>1.0.0</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -17051,8 +16228,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -17067,8 +16242,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -17133,9 +16307,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -17200,9 +16371,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -17245,9 +16413,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -17320,11 +16485,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -17339,6 +16500,7 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>179</td>
       <td>3781</td>
@@ -17401,9 +16563,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -17468,9 +16627,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -17535,9 +16691,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -17565,7 +16718,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement</td>
       <td>1.0.0</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -17587,8 +16740,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -17603,8 +16754,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -17668,10 +16818,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -17735,10 +16882,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -17807,9 +16951,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>35</td>
     </tr>
     <tr>
@@ -17833,7 +16974,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat</td>
       <td>1.0.1</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -17845,8 +16986,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -17871,8 +17010,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -17912,8 +17050,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -17944,7 +17080,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -17980,14 +17115,12 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
@@ -18006,7 +17139,6 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -18076,9 +17208,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -18143,9 +17272,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -18204,10 +17330,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -18271,10 +17394,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -18302,7 +17422,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants</td>
       <td>0.0.6</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -18325,8 +17445,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -18346,7 +17464,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -18369,7 +17486,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage</td>
       <td>1.0.0</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -18391,8 +17508,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -18407,8 +17522,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -18436,7 +17550,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats</td>
       <td>0.1.0</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -18459,8 +17573,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -18480,7 +17592,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -18540,9 +17651,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -18593,8 +17701,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -18609,7 +17715,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -18673,10 +17778,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -18740,10 +17842,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -18807,10 +17906,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -18851,9 +17947,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
@@ -18877,7 +17971,6 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -18941,10 +18034,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -19009,9 +18099,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -19075,10 +18162,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -19142,10 +18226,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -19215,9 +18296,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -19276,10 +18354,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -19344,9 +18419,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -19416,9 +18488,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -19478,9 +18547,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -19531,8 +18597,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -19546,8 +18610,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -19617,9 +18680,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -19684,9 +18744,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -19751,9 +18808,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -19818,9 +18872,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -19879,10 +18930,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -19952,9 +19000,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -20014,9 +19059,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -20086,9 +19128,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -20148,9 +19187,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -20220,9 +19256,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -20257,8 +19290,6 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -20283,8 +19314,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -20324,10 +19354,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -20350,8 +19378,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -20379,7 +19406,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species</td>
       <td>0.0.1</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -20402,8 +19429,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -20417,8 +19442,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -20488,9 +19512,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -20528,8 +19549,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -20551,8 +19570,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -20592,10 +19610,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -20618,8 +19634,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -20689,9 +19704,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -20737,8 +19749,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -20753,7 +19763,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -20823,9 +19832,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -20890,9 +19896,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -20951,10 +19954,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -21024,9 +20024,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -21049,7 +20046,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter</td>
       <td>2.0.0</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -21072,8 +20069,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -21087,8 +20082,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -21139,8 +20133,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -21154,8 +20146,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -21219,10 +20210,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -21250,7 +20238,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits</td>
       <td>1.0.0</td>
       <td>taxonomy</td>
-      <td></td>
+      <td>0.10.0</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -21273,8 +20261,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -21288,8 +20274,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -21353,10 +20338,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -21384,7 +20366,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features</td>
       <td>4.0.1</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -21406,8 +20388,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -21422,8 +20402,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -21493,9 +20472,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -21509,14 +20485,14 @@
       <td>Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.</td>
       <td>Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly</td>
       <td>Sequence assembly, Metagenomics, Whole genome sequencing, Genomics</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/fenderglass/Flye/</td>
       <td>Assembly</td>
       <td>flye</td>
       <td>bgruening</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/flye</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/flye</td>
-      <td>2.9.4</td>
+      <td>2.9.5</td>
       <td>flye</td>
       <td>2.9.5</td>
       <td>Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly</td>
@@ -21540,8 +20516,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -21556,8 +20530,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -21622,9 +20595,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -21667,9 +20637,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -21742,8 +20709,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -21757,8 +20722,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -21822,10 +20786,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -21853,7 +20814,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks</td>
       <td>1.0.0</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -21865,10 +20826,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -21891,8 +20850,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -21935,8 +20893,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -21958,8 +20914,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -21987,7 +20942,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way</td>
       <td>1.0.0</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -22029,9 +20984,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -22096,9 +21048,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -22112,7 +21061,7 @@
       <td>gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.</td>
       <td>Data handling</td>
       <td>Computational biology</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/vgl-hub/gfastats</td>
       <td>Sequence Analysis</td>
       <td>gfastats</td>
@@ -22121,7 +21070,7 @@
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/gfastats</td>
       <td>1.3.6</td>
       <td>gfastats</td>
-      <td>1.3.6</td>
+      <td>1.3.7</td>
       <td>Data handling</td>
       <td>Computational biology</td>
       <td>1</td>
@@ -22144,8 +21093,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -22160,7 +21107,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -22210,8 +21156,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -22226,8 +21170,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -22297,9 +21240,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -22358,10 +21298,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -22426,9 +21363,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -22498,9 +21432,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -22564,9 +21495,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
     </tr>
     <tr>
@@ -22588,7 +21516,7 @@
       <td>bgruening</td>
       <td>https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick</td>
-      <td>1.3.44</td>
+      <td>1.3.45</td>
       <td>graphicsmagick</td>
       <td>1.3.26</td>
       <td></td>
@@ -22626,10 +21554,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -22657,7 +21582,7 @@
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/graphmap</td>
       <td>0.5.2</td>
       <td>graphmap</td>
-      <td>0.6.3</td>
+      <td>0.6.4</td>
       <td>Sequence trimming, EST assembly, Read mapping</td>
       <td>Gene transcripts, RNA-Seq, RNA splicing</td>
       <td>0</td>
@@ -22680,8 +21605,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -22695,8 +21618,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -22761,9 +21683,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -22833,9 +21752,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -22894,10 +21810,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -22961,10 +21874,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -23017,61 +21927,55 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>hicup</td>
-      <td>hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater</td>
-      <td>The HiCUP-Pipeline from the Bioinformatics Babraham Institute.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html</td>
-      <td>Epigenetics</td>
-      <td>hicup</td>
-      <td>bgruening</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/hicup</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/hicup</td>
-      <td>0.9.2</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>7</td>
-      <td>0</td>
-      <td>7</td>
-      <td>0</td>
-      <td>7</td>
-      <td>0</td>
-      <td>7</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hicup</td>
+      <td>hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater</td>
+      <td>The HiCUP-Pipeline from the Bioinformatics Babraham Institute.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html</td>
+      <td>Epigenetics</td>
+      <td>hicup</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/hicup</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/hicup</td>
+      <td>0.9.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>7</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>7</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -23149,8 +22053,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -23169,7 +22071,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>228</td>
     </tr>
     <tr>
@@ -23205,10 +22106,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -23235,6 +22132,7 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>242</td>
       <td>4350</td>
@@ -23302,9 +22200,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -23364,9 +22259,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -23436,14 +22328,11 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>imagej2</td>
-      <td>imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary</td>
+      <td>imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary</td>
       <td>ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.</td>
       <td>imagej</td>
       <td>imagej</td>
@@ -23459,7 +22348,7 @@
       <td>imgteam</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2</td>
-      <td>20170530</td>
+      <td>20240614</td>
       <td></td>
       <td></td>
       <td>Image analysis, Image annotation, Visualisation</td>
@@ -23498,9 +22387,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>27</td>
       <td>27</td>
       <td>0</td>
@@ -23570,9 +22456,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -23631,10 +22514,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -23699,9 +22579,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
       <td>6</td>
       <td>0</td>
@@ -23771,9 +22648,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -23833,9 +22707,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -23861,9 +22732,9 @@
       <td>rnateam</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna</td>
-      <td>3.4.0</td>
+      <td>3.4.1</td>
       <td>intarna</td>
-      <td>3.4.0</td>
+      <td>3.4.1</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -23900,9 +22771,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -23930,7 +22798,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect</td>
       <td>1.0.0</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -23942,8 +22810,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -23968,8 +22834,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -24039,9 +22904,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -24101,9 +22963,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -24122,16 +22981,16 @@
       <td>Modular genome browser with views of synteny and structural variation.</td>
       <td>Genome visualisation, Structure visualisation, Pathway visualisation</td>
       <td>Mapping, Structural variation, Genomics, Gene structure, Sequence assembly</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://jbrowse.org</td>
       <td>Sequence Analysis</td>
       <td>jbrowse2</td>
       <td>fubar</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2</td>
-      <td>2.13.1</td>
+      <td>2.15.4</td>
       <td>jbrowse2</td>
-      <td>2.14.0</td>
+      <td>2.15.4</td>
       <td>Genome visualisation, Structure visualisation, Pathway visualisation</td>
       <td>Mapping, Structural variation, Genomics, Gene structure, Sequence assembly</td>
       <td>1</td>
@@ -24153,10 +23012,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -24198,7 +23054,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join</td>
       <td>1.0.0</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -24210,8 +23066,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -24236,8 +23090,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -24288,8 +23141,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -24303,8 +23154,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -24372,9 +23222,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>30</td>
     </tr>
@@ -24435,10 +23282,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -24502,10 +23346,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -24575,9 +23416,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -24621,8 +23459,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -24638,8 +23474,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -24709,9 +23544,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -24770,10 +23602,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -24837,10 +23666,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -24904,10 +23730,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -24972,9 +23795,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -25044,9 +23864,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -25106,9 +23923,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -25178,9 +23992,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -25203,7 +24014,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter</td>
       <td>1.0.0</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -25245,9 +24056,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -25282,10 +24090,8 @@
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -25308,8 +24114,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -25379,9 +24184,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -25446,9 +24248,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -25508,9 +24307,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -25559,8 +24355,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -25576,8 +24370,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -25605,7 +24398,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge</td>
       <td>1.0.0</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -25628,8 +24421,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -25643,8 +24434,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -25685,9 +24475,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
@@ -25711,7 +24499,6 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -25780,9 +24567,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5461</td>
     </tr>
     <tr>
@@ -25832,8 +24616,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -25844,8 +24626,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -25894,8 +24675,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -25917,7 +24696,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -25961,8 +24739,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -25978,8 +24754,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -26049,9 +24824,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -26116,9 +24888,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -26183,9 +24952,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -26250,9 +25016,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -26275,7 +25038,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability</td>
       <td>1.1.0</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -26317,9 +25080,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -26379,9 +25139,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -26445,10 +25202,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -26499,8 +25253,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -26515,7 +25267,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -26566,8 +25317,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -26582,7 +25331,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -26652,6 +25400,67 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>motus</td>
+      <td>mereg_mOTUs_tables, motus_profiler</td>
+      <td>Tool for profiling the abundance of microbial taxa.</td>
+      <td>mOTUs</td>
+      <td>mOTUs</td>
+      <td></td>
+      <td>Metagenomic operational taxonomic units (mOTUs)</td>
+      <td>Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall.</td>
+      <td>Taxonomic classification</td>
+      <td>Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/motu-tool/mOTUs</td>
+      <td>Metagenomics</td>
+      <td>motus</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/motus</td>
+      <td>3.1.0</td>
+      <td>motus</td>
+      <td>3.1.0</td>
+      <td>Taxonomic classification</td>
+      <td>Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -26714,9 +25523,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -26786,9 +25592,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -26848,9 +25651,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -26915,9 +25715,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -26981,10 +25778,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -27027,8 +25821,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>3</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -27050,8 +25842,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>4</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
@@ -27116,9 +25907,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -27183,9 +25971,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -27250,9 +26035,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -27322,9 +26104,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -27384,9 +26163,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -27444,8 +26220,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -27457,7 +26231,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>486</td>
     </tr>
     <tr>
@@ -27481,7 +26254,7 @@
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/openms</td>
       <td>2.1.0</td>
       <td>openms</td>
-      <td>3.1.0</td>
+      <td>3.2.0</td>
       <td></td>
       <td></td>
       <td>7</td>
@@ -27517,10 +26290,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>19</td>
       <td>135</td>
       <td>134</td>
       <td>0</td>
@@ -27584,10 +26354,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -27652,9 +26419,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -27724,9 +26488,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -27785,10 +26546,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -27858,9 +26616,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -27925,9 +26680,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -27987,9 +26739,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -28059,9 +26808,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -28126,9 +26872,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -28188,9 +26931,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -28218,7 +26958,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval</td>
       <td>1.0.3</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -28233,8 +26973,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -28256,8 +26994,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -28297,8 +27034,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -28323,8 +27058,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -28389,9 +27123,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -28456,9 +27187,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -28528,9 +27256,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -28589,10 +27314,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -28656,10 +27378,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -28723,10 +27442,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -28790,10 +27506,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -28857,10 +27570,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -28930,9 +27640,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -28991,10 +27698,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -29059,9 +27763,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -29125,10 +27826,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>6</td>
       <td>6</td>
       <td>6</td>
       <td>0</td>
@@ -29193,9 +27891,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -29223,7 +27918,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter</td>
       <td>1.0.1</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -29265,9 +27960,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -29332,9 +28024,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -29380,8 +28069,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -29395,8 +28082,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -29424,7 +28110,7 @@
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench</td>
       <td>0.8.1</td>
       <td>rbpbench</td>
-      <td>0.9</td>
+      <td>1.0</td>
       <td></td>
       <td>RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis</td>
       <td>0</td>
@@ -29465,9 +28151,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>36</td>
     </tr>
     <tr>
@@ -29527,10 +28210,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -29600,9 +28280,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -29667,9 +28344,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -29705,9 +28379,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
@@ -29731,7 +28403,6 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -29796,9 +28467,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -29826,7 +28494,7 @@
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker</td>
       <td>0.1.2</td>
       <td>RepeatMasker</td>
-      <td>4.1.5</td>
+      <td>4.0.9_p2</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -29862,10 +28530,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -29916,8 +28581,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -29931,8 +28594,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -30002,9 +28664,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -30064,9 +28723,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -30136,9 +28792,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -30203,9 +28856,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -30265,9 +28915,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -30332,9 +28979,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -30399,9 +29043,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -30466,9 +29107,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -30538,9 +29176,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -30600,9 +29235,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -30667,9 +29299,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -30734,9 +29363,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
       <td>6</td>
       <td>0</td>
@@ -30790,8 +29416,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -30802,8 +29426,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -30853,8 +29476,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>1</td>
       <td>0</td>
@@ -30869,8 +29490,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -30934,10 +29554,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -31001,10 +29618,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -31074,9 +29688,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -31122,8 +29733,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -31138,7 +29747,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -31166,7 +29774,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad</td>
       <td>0.0.5</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -31208,9 +29816,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -31233,7 +29838,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth</td>
       <td>0.0.3</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -31254,8 +29859,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -31271,8 +29874,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -31300,7 +29902,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats</td>
       <td>0.0.6</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -31312,8 +29914,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -31338,8 +29938,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -31388,8 +29987,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -31405,8 +30002,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -31474,9 +30070,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>2276</td>
     </tr>
@@ -31538,9 +30131,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -31591,8 +30181,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -31607,7 +30195,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -31672,9 +30259,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -31725,8 +30309,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -31741,7 +30323,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -31792,8 +30373,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -31808,7 +30387,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -31859,8 +30437,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -31880,7 +30456,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -31945,9 +30520,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -31993,8 +30565,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -32010,7 +30580,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -32060,8 +30629,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -32081,7 +30648,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -32146,9 +30712,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -32208,9 +30771,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -32274,10 +30834,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -32318,9 +30875,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
@@ -32344,7 +30899,6 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -32384,10 +30938,8 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
@@ -32411,7 +30963,6 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -32460,8 +31011,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -32477,8 +31026,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -32542,10 +31090,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>29</td>
       <td>31</td>
       <td>27</td>
       <td>0</td>
@@ -32609,10 +31154,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -32652,8 +31194,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -32678,8 +31218,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -32730,8 +31269,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -32746,7 +31283,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -32797,8 +31333,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -32812,8 +31346,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -32864,8 +31397,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -32885,7 +31416,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -32923,8 +31453,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -32947,7 +31475,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -33012,9 +31539,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -33079,9 +31603,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -33150,9 +31671,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>47</td>
     </tr>
     <tr>
@@ -33218,9 +31736,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -33243,7 +31758,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions</td>
       <td>1.0.1</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -33285,9 +31800,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -33310,7 +31822,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract</td>
       <td>1.0.0</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -33332,8 +31844,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -33348,8 +31858,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -33377,7 +31886,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query</td>
       <td>0.1</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -33413,10 +31922,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -33467,8 +31973,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -33482,8 +31986,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -33534,8 +32037,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -33549,8 +32050,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -33614,10 +32114,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -33687,9 +32184,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -33742,16 +32236,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -33791,10 +32282,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -33817,8 +32306,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -33888,9 +32376,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -33950,9 +32435,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -34001,8 +32483,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>19</td>
       <td>1</td>
       <td>19</td>
@@ -34018,8 +32498,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>19</td>
       <td>19</td>
       <td>19</td>
       <td>0</td>
@@ -34084,9 +32563,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -34156,9 +32632,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -34217,10 +32690,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -34248,7 +32718,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat</td>
       <td>1.5.0</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -34281,8 +32751,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -34291,7 +32759,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
     </tr>
     <tr>
@@ -34327,8 +32794,6 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -34353,8 +32818,7 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -34418,10 +32882,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -34461,8 +32922,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -34487,8 +32946,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -34529,9 +32987,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
@@ -34555,7 +33011,6 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -34598,9 +33053,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -34609,6 +33061,7 @@
       <td>0</td>
       <td>0</td>
       <td>2</td>
+      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -34622,7 +33075,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -34662,10 +33114,6 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -34692,6 +33140,7 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>45</td>
       <td>394</td>
@@ -34753,10 +33202,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -34796,11 +33242,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -34887,10 +33330,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -34959,9 +33399,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
     </tr>
     <tr>
@@ -35008,8 +33445,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -35029,7 +33464,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -35088,10 +33522,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -35136,8 +33567,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -35162,7 +33591,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>19</td>
     </tr>
     <tr>
@@ -35201,10 +33629,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -35228,6 +33652,7 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>24</td>
       <td>171</td>
@@ -35268,10 +33693,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -35295,6 +33716,7 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>34</td>
       <td>531</td>
@@ -35320,7 +33742,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus</td>
       <td>0.1.11</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -35343,8 +33765,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -35364,7 +33784,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -35402,8 +33821,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -35425,8 +33842,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -35469,10 +33885,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -35496,6 +33908,7 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>68</td>
       <td>953</td>
@@ -35536,10 +33949,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -35563,6 +33972,7 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>24</td>
       <td>411</td>
@@ -35603,10 +34013,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -35630,6 +34036,7 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>17</td>
       <td>137</td>
@@ -35678,8 +34085,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -35694,7 +34099,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -35759,9 +34163,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>21</td>
       <td>21</td>
       <td>0</td>
@@ -35831,9 +34232,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -35898,9 +34296,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -35965,9 +34360,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -35990,7 +34382,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter</td>
       <td>1.0.1</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -36031,9 +34423,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>11</td>
     </tr>
     <tr>
@@ -36099,9 +34488,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -36147,8 +34533,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -36163,7 +34547,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -36209,8 +34592,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -36229,8 +34610,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -36295,9 +34675,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -36346,8 +34723,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>3</td>
@@ -36363,8 +34738,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -36383,14 +34757,14 @@
       <td>an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.</td>
       <td>Antimicrobial resistance prediction</td>
       <td>Microbiology, Public health and epidemiology, Infectious disease</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://zenodo.org/record/7370628</td>
       <td>Sequence Analysis</td>
       <td>abritamr</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr</td>
-      <td>1.0.14</td>
+      <td>1.0.19</td>
       <td>abritamr</td>
       <td>1.0.19</td>
       <td>Antimicrobial resistance prediction</td>
@@ -36434,9 +34808,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -36450,28 +34821,26 @@
       <td>De novo genome sequence assembler using short reads.</td>
       <td>Genome assembly, De-novo assembly, Scaffolding</td>
       <td>Sequence assembly</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://www.bcgsc.ca/platform/bioinfo/software/abyss</td>
       <td>Assembly</td>
       <td>abyss</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss</td>
-      <td>2.3.7</td>
+      <td>2.3.9</td>
       <td>abyss</td>
-      <td>2.3.8</td>
+      <td>2.3.9</td>
       <td>Genome assembly, De-novo assembly, Scaffolding</td>
       <td>Sequence assembly</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -36497,8 +34866,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -36563,9 +34931,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -36616,8 +34981,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -36632,7 +34995,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -36696,10 +35058,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -36764,9 +35123,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -36817,8 +35173,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -36838,7 +35192,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -36898,9 +35251,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -36965,9 +35315,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>19</td>
       <td>0</td>
       <td>0</td>
@@ -37036,9 +35383,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>591</td>
     </tr>
     <tr>
@@ -37099,9 +35443,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -37122,12 +35463,12 @@
       <td></td>
       <td>To update</td>
       <td>https://anndata.readthedocs.io</td>
-      <td>Transcriptomics, Sequence Analysis</td>
+      <td>Single Cell, Spatial Omics</td>
       <td>anndata</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata</td>
-      <td>0.10.3</td>
+      <td>0.10.9</td>
       <td>anndata</td>
       <td>0.6.22.post1</td>
       <td></td>
@@ -37165,10 +35506,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -37219,8 +35557,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -37234,8 +35570,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -37268,15 +35603,12 @@
       <td></td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -37367,9 +35699,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -37412,8 +35741,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>3</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -37441,7 +35768,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -37468,14 +35794,12 @@
       <td>Sequence alignment</td>
       <td>Genomics</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
+      <td>2</td>
+      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -37502,8 +35826,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>2</td>
       <td>1</td>
       <td>0</td>
@@ -37573,9 +35896,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -37624,8 +35944,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -37636,8 +35954,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -37687,8 +36004,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>2</td>
       <td>0</td>
@@ -37703,8 +36018,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -37768,10 +36082,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -37790,28 +36101,26 @@
       <td>Rapid &amp; standardized annotation of bacterial genomes, MAGs &amp; plasmids</td>
       <td>Genome annotation</td>
       <td>Genomics, Data submission, annotation and curation, Sequence analysis</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/oschwengers/bakta</td>
       <td>Sequence Analysis</td>
       <td>bakta</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta</td>
-      <td>1.9.3</td>
+      <td>1.9.4</td>
       <td>bakta</td>
       <td>1.9.4</td>
       <td>Genome annotation</td>
       <td>Genomics, Data submission, annotation and curation, Sequence analysis</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -37838,7 +36147,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -37902,10 +36210,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -37954,8 +36259,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -37971,8 +36274,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -38021,8 +36323,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -38038,8 +36338,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -38090,8 +36389,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -38106,7 +36403,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -38171,9 +36467,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -38216,8 +36509,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -38239,8 +36530,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -38310,9 +36600,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -38328,7 +36615,7 @@
       <td>RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability</td>
       <td>Up-to-date</td>
       <td>https://github.com/lldelisle/baredSC</td>
-      <td>Transcriptomics, Visualization</td>
+      <td>Single Cell, Transcriptomics, Visualization</td>
       <td>baredsc</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc</td>
@@ -38372,9 +36659,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -38414,8 +36698,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -38441,7 +36723,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -38492,8 +36773,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -38507,8 +36786,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -38572,10 +36850,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -38639,10 +36914,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -38712,9 +36984,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -38728,7 +36997,7 @@
       <td>BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.</td>
       <td>RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment</td>
       <td>Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://jgi.doe.gov/data-and-tools/bbtools/</td>
       <td>Sequence Analysis</td>
       <td>bbtools</td>
@@ -38737,15 +37006,15 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools</td>
       <td>39.08</td>
       <td>bbmap</td>
-      <td>39.08</td>
+      <td>39.09</td>
       <td>RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment</td>
       <td>RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq</td>
       <td>6</td>
-      <td>1</td>
+      <td>3</td>
       <td>5</td>
       <td>0</td>
       <td>6</td>
-      <td>1</td>
+      <td>3</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -38760,8 +37029,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -38776,7 +37043,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -38804,7 +37070,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools</td>
       <td>1.15.1</td>
       <td>bcftools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td>Data handling, Variant calling</td>
       <td>DNA polymorphism, GWAS study, Genotyping experiment</td>
       <td>0</td>
@@ -38846,9 +37112,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -38907,10 +37170,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>7</td>
       <td>7</td>
       <td>0</td>
@@ -38975,9 +37235,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -39003,9 +37260,9 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import</td>
-      <td>2.2.3</td>
+      <td>2.2.4</td>
       <td>beacon2-import</td>
-      <td>2.2.3</td>
+      <td>2.2.4</td>
       <td>Service discovery, Database search, Genetic variation analysis</td>
       <td>Genetic variation, Population genetics, Data security, Rare diseases</td>
       <td>0</td>
@@ -39047,9 +37304,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -39095,8 +37349,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -39111,7 +37363,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -39176,9 +37427,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -39218,10 +37466,8 @@
       <td>37</td>
       <td>37</td>
       <td>0</td>
-      <td>37</td>
       <td>0</td>
       <td>0</td>
-      <td>37</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -39244,8 +37490,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>37</td>
       <td>37</td>
       <td>37</td>
       <td>0</td>
@@ -39310,9 +37555,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -39382,9 +37624,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -39449,9 +37688,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -39477,16 +37713,13 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -39564,8 +37797,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -39580,7 +37811,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -39599,14 +37829,14 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://pypi.python.org/pypi/biopython-extensions/</td>
       <td>Next Gen Mappers</td>
       <td></td>
       <td>iuc</td>
       <td>https://github.com/davebx/bioext-gx/</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext</td>
-      <td>0.21.7</td>
+      <td>0.21.9</td>
       <td>python-bioext</td>
       <td>0.21.9</td>
       <td></td>
@@ -39631,8 +37861,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -39647,7 +37875,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -39712,9 +37939,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -39764,8 +37988,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -39780,8 +38002,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -39824,8 +38045,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -39848,7 +38067,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -39918,9 +38136,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -39980,9 +38195,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -40047,9 +38259,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -40092,9 +38301,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -40156,10 +38362,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -40182,8 +38386,7 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -40232,8 +38435,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -40250,7 +38451,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -40300,8 +38500,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -40317,7 +38515,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -40387,9 +38584,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -40435,8 +38629,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -40450,8 +38642,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -40491,10 +38682,8 @@
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -40503,7 +38692,7 @@
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>1</td>
+      <td>2</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -40517,8 +38706,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -40569,8 +38757,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -40585,7 +38771,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -40639,8 +38824,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -40651,8 +38834,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -40717,9 +38899,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -40789,9 +38968,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -40854,9 +39030,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>8</td>
       <td>1393</td>
     </tr>
@@ -40879,21 +39052,18 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber</td>
-      <td>2.0.6</td>
+      <td>2.0.7</td>
       <td>cami-amber</td>
-      <td>2.0.6</td>
+      <td>2.0.7</td>
       <td></td>
       <td></td>
       <td>0</td>
       <td>0</td>
-      <td>3</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>3</td>
+      <td>4</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>4</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -40971,8 +39141,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -40986,8 +39154,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -41036,8 +39203,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -41054,7 +39219,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -41119,9 +39283,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -41189,9 +39350,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>287</td>
       <td>3589</td>
     </tr>
@@ -41207,28 +39365,26 @@
       <td>CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.</td>
       <td>Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation</td>
       <td>Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/Ecogenomics/CheckM</td>
       <td>Metagenomics</td>
       <td>checkm</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm</td>
-      <td>1.2.0</td>
+      <td>1.2.3</td>
       <td>checkm-genome</td>
       <td>1.2.3</td>
       <td>Sequence assembly validation, Sequence composition calculation, Statistical calculation</td>
       <td>Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management</td>
       <td>0</td>
-      <td>0</td>
       <td>10</td>
       <td>10</td>
-      <td>0</td>
+      <td>10</td>
       <td>0</td>
       <td>10</td>
       <td>10</td>
-      <td>0</td>
-      <td>0</td>
+      <td>10</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -41255,7 +39411,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>10</td>
       <td>0</td>
       <td>0</td>
@@ -41320,9 +39475,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -41392,9 +39544,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -41453,10 +39602,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -41526,9 +39672,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -41574,8 +39717,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -41589,8 +39730,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -41655,9 +39795,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -41707,8 +39844,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>11</td>
       <td>11</td>
       <td>0</td>
@@ -41723,8 +39858,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>11</td>
       <td>11</td>
       <td>11</td>
       <td>0</td>
@@ -41745,7 +39879,7 @@
       <td>Transcriptomics, Immunoproteins and antigens</td>
       <td>To update</td>
       <td>https://github.com/Hoohm/CITE-seq-Count</td>
-      <td>Transcriptomics</td>
+      <td>Single Cell, Transcriptomics, Proteomics</td>
       <td>cite_seq_count</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count</td>
@@ -41789,9 +39923,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -41823,14 +39954,12 @@
       <td>Variant calling</td>
       <td>Molecular genetics</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -41858,7 +39987,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -41898,10 +40026,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -41924,8 +40050,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -41951,7 +40076,7 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat</td>
-      <td>1.1</td>
+      <td>1.1.1</td>
       <td>python</td>
       <td></td>
       <td></td>
@@ -41995,9 +40120,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -42062,9 +40184,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -42129,9 +40248,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -42191,9 +40307,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>17</td>
       <td>0</td>
       <td>0</td>
@@ -42257,10 +40370,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -42325,9 +40435,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -42397,9 +40504,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -42458,10 +40562,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -42512,8 +40613,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -42527,8 +40626,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -42577,8 +40675,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -42594,8 +40690,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -42635,8 +40730,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -42661,8 +40754,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -42726,10 +40818,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -42793,10 +40882,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -42828,15 +40914,13 @@
       <td>Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly</td>
       <td>Sequence assembly, Transcriptomics, Sequence analysis</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -42868,7 +40952,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -42917,8 +41000,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -42929,8 +41010,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -42995,9 +41075,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -43062,9 +41139,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -43085,7 +41159,7 @@
       <td></td>
       <td>Up-to-date</td>
       <td>https://github.com/genecell/COSG</td>
-      <td>Transcriptomics, Sequence Analysis</td>
+      <td>Transcriptomics, Sequence Analysis, Single Cell</td>
       <td>cosg</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/</td>
@@ -43097,14 +41171,11 @@
       <td></td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -43182,8 +41253,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -43203,7 +41272,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -43249,8 +41317,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -43265,7 +41331,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -43329,10 +41394,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -43396,10 +41458,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -43418,14 +41477,14 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://crossmap.sourceforge.net/</td>
       <td>Convert Formats, Genomic Interval Operations</td>
       <td>crossmap</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap</td>
-      <td>0.6.1</td>
+      <td>0.7.0</td>
       <td>crossmap</td>
       <td>0.7.0</td>
       <td></td>
@@ -43439,8 +41498,6 @@
       <td>6</td>
       <td>0</td>
       <td>0</td>
-      <td>4</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -43465,8 +41522,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>6</td>
       <td>5</td>
       <td>0</td>
@@ -43509,8 +41565,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -43532,8 +41586,7 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -43573,10 +41626,8 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -43599,8 +41650,7 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -43643,8 +41693,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -43666,8 +41714,7 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -43710,8 +41757,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -43733,8 +41778,7 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -43792,16 +41836,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -43859,16 +41900,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -43908,10 +41946,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -43934,8 +41970,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -43999,10 +42034,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -44072,9 +42104,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -44118,8 +42147,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>10</td>
       <td>0</td>
       <td>10</td>
@@ -44135,8 +42162,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>10</td>
       <td>10</td>
       <td>10</td>
       <td>0</td>
@@ -44201,9 +42227,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -44273,9 +42296,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -44319,8 +42339,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>3</td>
       <td>3</td>
@@ -44336,8 +42354,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -44402,9 +42419,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -44469,9 +42483,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -44540,9 +42551,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
     </tr>
     <tr>
@@ -44603,9 +42611,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -44654,8 +42659,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -44671,8 +42674,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -44700,7 +42702,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly</td>
       <td>0.9.1</td>
       <td>delly</td>
-      <td>1.2.6</td>
+      <td>1.2.9</td>
       <td>Indel detection, Structural variation detection, Genotyping</td>
       <td>Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases</td>
       <td>0</td>
@@ -44722,8 +42724,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -44738,8 +42738,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>6</td>
       <td>6</td>
       <td>0</td>
       <td>0</td>
@@ -44779,10 +42778,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -44805,8 +42802,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -44870,10 +42866,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -44916,8 +42909,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>3</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -44940,7 +42931,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -45005,9 +42995,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -45077,9 +43064,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -45125,8 +43109,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -45140,8 +43122,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -45211,9 +43192,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -45278,9 +43256,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -45340,9 +43315,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -45393,8 +43365,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -45408,8 +43378,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -45430,7 +43399,7 @@
       <td>Gene expression, RNA-seq, Sequencing, Transcriptomics</td>
       <td>To update</td>
       <td>https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html</td>
-      <td>Transcriptomics, Sequence Analysis</td>
+      <td>Single Cell, Sequence Analysis</td>
       <td>dropletutils</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/</td>
@@ -45463,8 +43432,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -45475,8 +43442,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -45540,10 +43506,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -45586,8 +43549,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -45609,8 +43570,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -45674,10 +43634,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -45720,8 +43677,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>107</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -45743,8 +43698,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>107</td>
       <td>107</td>
       <td>107</td>
       <td>0</td>
@@ -45763,7 +43717,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/usegalaxy-eu/ena-upload-cli</td>
       <td>Data Export</td>
       <td>ena_upload</td>
@@ -45772,7 +43726,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload</td>
       <td>0.7.3</td>
       <td>ena-upload-cli</td>
-      <td>0.7.3</td>
+      <td>0.7.4</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -45802,16 +43756,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -45861,8 +43812,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>4</td>
       <td>0</td>
@@ -45878,7 +43827,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -45897,14 +43845,14 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/Ensembl/ensembl-vep</td>
       <td>Variant Analysis</td>
       <td>ensembl_vep</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep</td>
-      <td>110.1</td>
+      <td>112.0</td>
       <td>ensembl-vep</td>
       <td>112.0</td>
       <td></td>
@@ -45943,9 +43891,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -45966,7 +43911,7 @@
       <td>Epigenomics, Cell biology, DNA</td>
       <td>To update</td>
       <td>https://github.com/colomemaria/epiScanpy</td>
-      <td>Epigenetics</td>
+      <td>Single Cell, Epigenetics</td>
       <td>episcanpy</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/</td>
@@ -46010,9 +43955,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -46021,34 +43963,34 @@
     </tr>
     <tr>
       <td></td>
-      <td>exomedepth</td>
-      <td>exomedepth</td>
-      <td>ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data</td>
-      <td>exomedepth</td>
-      <td>exomedepth</td>
+      <td>evidencemodeler</td>
+      <td>evidencemodeler</td>
+      <td>EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.</td>
+      <td>EvidenceModeler</td>
+      <td>EvidenceModeler</td>
       <td></td>
-      <td>ExomeDepth</td>
-      <td>Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.</td>
-      <td>Sequence analysis, Variant calling, Genotyping, Copy number estimation</td>
-      <td>Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases</td>
-      <td>To update</td>
-      <td>https://cran.r-project.org/package=ExomeDepth</td>
-      <td>Sequence Analysis, Variant Analysis</td>
-      <td>exomedepth</td>
-      <td>crs4</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth</td>
-      <td>1.1.0</td>
-      <td>r-exomedepth</td>
-      <td>1.1.16</td>
-      <td>Sequence analysis, Variant calling, Genotyping, Copy number estimation</td>
-      <td>Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases</td>
-      <td>1</td>
+      <td>EvidenceModeler</td>
+      <td>The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.</td>
+      <td>Gene prediction</td>
+      <td>Gene expression, Gene structure</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file</td>
+      <td>Genome annotation</td>
+      <td>evidencemodeler</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler</td>
+      <td>2.1.0</td>
+      <td>evidencemodeler</td>
+      <td>2.1.0</td>
+      <td>Gene prediction</td>
+      <td>Gene expression, Gene structure</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -46080,6 +44022,67 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>exomedepth</td>
+      <td>exomedepth</td>
+      <td>ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data</td>
+      <td>exomedepth</td>
+      <td>exomedepth</td>
+      <td></td>
+      <td>ExomeDepth</td>
+      <td>Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.</td>
+      <td>Sequence analysis, Variant calling, Genotyping, Copy number estimation</td>
+      <td>Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases</td>
+      <td>To update</td>
+      <td>https://cran.r-project.org/package=ExomeDepth</td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>exomedepth</td>
+      <td>crs4</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth</td>
+      <td>1.1.0</td>
+      <td>r-exomedepth</td>
+      <td>1.1.16</td>
+      <td>Sequence analysis, Variant calling, Genotyping, Copy number estimation</td>
+      <td>Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -46130,8 +44133,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -46145,8 +44146,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -46197,8 +44197,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -46212,8 +44210,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -46241,7 +44238,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna</td>
       <td>3.0.3+galaxy2</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -46253,10 +44250,8 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>1</td>
@@ -46279,8 +44274,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -46299,16 +44293,16 @@
       <td>A high-speed FastQC emulation for quality control of sequencing data.</td>
       <td>Sequencing quality control, Visualisation, Read mapping</td>
       <td>Workflows, Mapping, Imaging</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/smithlabcode/falco/</td>
       <td>Sequence Analysis</td>
       <td>falco</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco</td>
-      <td>1.2.2+galaxy1</td>
+      <td>1.2.4</td>
       <td>falco</td>
-      <td>1.2.3</td>
+      <td>1.2.4</td>
       <td>Sequencing quality control, Visualisation, Read mapping</td>
       <td>Workflows, Mapping, Imaging</td>
       <td>0</td>
@@ -46350,9 +44344,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -46398,8 +44389,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -46413,8 +44402,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -46433,14 +44421,14 @@
       <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
       <td></td>
       <td>Sequence analysis</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
       <td>Fasta Manipulation</td>
       <td>ucsc_fasplit</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit</td>
-      <td>377</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit</td>
+      <td>469</td>
       <td>ucsc-fasplit</td>
       <td>469</td>
       <td></td>
@@ -46465,8 +44453,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -46480,8 +44466,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -46514,13 +44499,11 @@
       <td></td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -46553,7 +44536,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -46588,10 +44570,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -46614,8 +44594,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -46666,8 +44645,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -46681,8 +44658,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -46746,10 +44722,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -46789,8 +44762,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -46815,8 +44786,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -46867,8 +44837,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -46882,8 +44850,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -46953,9 +44920,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -46999,8 +44963,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -47016,8 +44978,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -47060,8 +45021,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -47083,8 +45042,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -47135,8 +45093,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -47150,8 +45106,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -47191,10 +45146,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -47217,8 +45170,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -47282,10 +45234,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -47349,10 +45298,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -47410,16 +45356,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -47468,8 +45411,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -47485,8 +45426,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -47537,8 +45477,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -47552,8 +45490,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -47617,10 +45554,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -47671,8 +45605,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -47686,8 +45618,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -47738,8 +45669,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -47753,8 +45682,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -47804,8 +45732,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -47820,8 +45746,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -47875,8 +45800,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -47887,8 +45810,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -47928,8 +45850,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -47954,8 +45874,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -47995,8 +45914,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -48021,8 +45938,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -48080,16 +45996,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -48129,10 +46042,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -48155,8 +46066,7 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -48205,12 +46115,8 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -48226,6 +46132,7 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>1266</td>
       <td>4333</td>
@@ -48266,8 +46173,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -48289,8 +46194,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -48330,8 +46234,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -48356,8 +46258,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -48397,10 +46298,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -48423,8 +46322,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -48467,8 +46365,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -48490,8 +46386,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -48531,10 +46426,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -48557,8 +46450,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -48601,8 +46493,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -48624,8 +46514,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -48668,8 +46557,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -48691,8 +46578,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -48735,8 +46621,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -48758,8 +46642,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -48802,8 +46685,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -48825,8 +46706,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -48869,8 +46749,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -48892,8 +46770,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -48936,8 +46813,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -48959,8 +46834,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -48984,7 +46858,7 @@
       <td>Convert Formats</td>
       <td>ucsc_fatovcf</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fatovcf</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf</td>
       <td>448</td>
       <td>ucsc-fatovcf</td>
@@ -49025,9 +46899,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -49070,8 +46941,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -49093,8 +46962,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -49158,10 +47026,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -49231,9 +47096,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -49292,10 +47154,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -49345,8 +47204,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -49361,8 +47218,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -49426,10 +47282,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -49480,8 +47333,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -49495,8 +47346,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -49547,8 +47397,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -49562,8 +47410,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -49591,7 +47438,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes</td>
       <td>1.3.6</td>
       <td>freebayes</td>
-      <td>1.3.7</td>
+      <td>1.3.8</td>
       <td>Variant calling, Statistical calculation</td>
       <td>Genomics, Genetic variation, Rare diseases</td>
       <td>2</td>
@@ -49603,10 +47450,8 @@
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -49629,8 +47474,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -49694,10 +47538,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -49748,8 +47589,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -49764,7 +47603,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -49834,9 +47672,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -49895,10 +47730,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -49948,8 +47780,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -49964,8 +47794,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -50016,8 +47845,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -50031,8 +47858,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -50083,8 +47909,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -50098,8 +47922,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -50163,10 +47986,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -50207,9 +48027,7 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>1</td>
@@ -50232,8 +48050,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -50303,9 +48120,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -50365,9 +48179,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -50437,9 +48248,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -50485,8 +48293,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -50501,7 +48307,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -50566,9 +48371,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -50632,10 +48434,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -50700,9 +48499,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -50767,9 +48563,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -50833,10 +48626,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -50879,10 +48669,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -50906,6 +48692,7 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>12</td>
       <td>135</td>
@@ -50952,8 +48739,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -50969,8 +48754,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -51010,8 +48794,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -51036,8 +48818,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -51086,8 +48867,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>5</td>
@@ -51103,8 +48882,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -51174,9 +48952,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -51235,10 +49010,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>4</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -51289,8 +49061,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -51304,8 +49074,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -51354,8 +49123,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -51371,8 +49138,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -51436,10 +49202,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -51503,10 +49266,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -51557,8 +49317,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -51572,8 +49330,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -51606,14 +49363,11 @@
       <td>Computational biology</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -51659,14 +49413,14 @@
       <td>a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).</td>
       <td>Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval</td>
       <td>Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/Ecogenomics/GTDBTk</td>
       <td>Metagenomics</td>
       <td>gtdbtk</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk</td>
-      <td>2.3.2</td>
+      <td>2.4.0</td>
       <td>gtdbtk</td>
       <td>2.4.0</td>
       <td>Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval</td>
@@ -51691,8 +49445,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -51712,7 +49464,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -51756,8 +49507,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -51773,8 +49522,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -51825,8 +49573,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -51840,8 +49586,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -51911,9 +49656,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -51953,8 +49695,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -51976,7 +49716,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -52026,8 +49765,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -52042,7 +49779,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -52106,10 +49842,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -52179,9 +49912,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -52241,9 +49971,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -52313,9 +50040,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -52359,8 +50083,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -52376,8 +50098,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -52390,7 +50111,7 @@
       <td>heinz_bum, heinz, heinz_scoring, heinz_visualization</td>
       <td>An algorithm for identification of the optimal scoring subnetwork.</td>
       <td>heinz</td>
-      <td>bionet, heinz</td>
+      <td>heinz, bionet</td>
       <td></td>
       <td>Heinz</td>
       <td>Tool for single-species active module discovery.</td>
@@ -52441,10 +50162,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>4</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
@@ -52514,9 +50232,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -52569,16 +50284,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>13</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>33</td>
       <td>36</td>
       <td>33</td>
       <td>0</td>
@@ -52648,9 +50360,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -52696,8 +50405,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -52712,7 +50419,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -52777,9 +50483,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -52828,8 +50531,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -52845,8 +50546,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -52874,7 +50574,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering</td>
       <td>1.3.1</td>
       <td>python-hivclustering</td>
-      <td>1.6.8</td>
+      <td>1.8.0</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -52916,9 +50616,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -52956,8 +50653,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>12</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -52979,8 +50674,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>12</td>
       <td>12</td>
       <td>12</td>
       <td>0</td>
@@ -53034,8 +50728,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -53047,7 +50739,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -53087,8 +50778,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -53113,8 +50802,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -53124,7 +50812,7 @@
     <tr>
       <td></td>
       <td>humann</td>
-      <td>humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways</td>
+      <td>humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways</td>
       <td>HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution</td>
       <td>humann</td>
       <td>humann</td>
@@ -53133,30 +50821,26 @@
       <td>HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”</td>
       <td>Species frequency estimation, Taxonomic classification, Phylogenetic analysis</td>
       <td>Metagenomics, Phylogenomics</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://huttenhower.sph.harvard.edu/humann</td>
       <td>Metagenomics</td>
       <td>humann</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann</td>
-      <td>3.8</td>
+      <td>3.9</td>
       <td>humann</td>
       <td>3.9</td>
       <td>Species frequency estimation, Taxonomic classification, Phylogenetic analysis</td>
       <td>Metagenomics, Phylogenomics</td>
       <td>6</td>
-      <td>13</td>
-      <td>13</td>
-      <td>13</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
       <td>6</td>
-      <td>13</td>
-      <td>13</td>
-      <td>13</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -53167,9 +50851,9 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>13</td>
       <td>0</td>
       <td>0</td>
+      <td>10</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -53182,11 +50866,12 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>13</td>
-      <td>13</td>
+      <td>1</td>
+      <td>10</td>
+      <td>10</td>
       <td>0</td>
-      <td>1045</td>
-      <td>19521</td>
+      <td>1037</td>
+      <td>19490</td>
     </tr>
     <tr>
       <td></td>
@@ -53209,7 +50894,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper</td>
       <td>2.1.6</td>
       <td>hybpiper</td>
-      <td>2.2.0</td>
+      <td>2.3.0</td>
       <td>Sequence trimming, Sequence assembly, Read mapping</td>
       <td>Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics</td>
       <td>0</td>
@@ -53251,9 +50936,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -53306,16 +50988,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>12</td>
       <td>17</td>
       <td>12</td>
       <td>0</td>
@@ -53380,9 +51059,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -53433,8 +51109,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -53454,7 +51128,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -53513,10 +51186,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -53574,16 +51244,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -53609,7 +51276,7 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download</td>
-      <td>0.44.1</td>
+      <td>0.45</td>
       <td>omero-py</td>
       <td>5.11.1</td>
       <td></td>
@@ -53647,10 +51314,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -53714,10 +51378,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -53787,9 +51448,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -53849,9 +51507,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -53882,16 +51537,14 @@
       <td>2.0.5</td>
       <td>Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation</td>
       <td>Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -53918,7 +51571,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -53982,10 +51634,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -54025,10 +51674,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -54055,6 +51700,7 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>677</td>
       <td>35243</td>
@@ -54080,7 +51726,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf</td>
       <td>1.0.1+galaxy1</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td>Sequence analysis</td>
       <td>1</td>
@@ -54095,8 +51741,6 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -54118,8 +51762,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -54183,10 +51826,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -54235,8 +51875,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -54252,8 +51890,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -54281,7 +51918,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv</td>
       <td>1.0.5</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -54317,10 +51954,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -54351,16 +51985,14 @@
       <td>1.7.2.1</td>
       <td>Structural variation detection</td>
       <td>Genomics, Sequence analysis, Genetic variation</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -54387,7 +52019,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -54452,9 +52083,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -54505,8 +52133,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -54520,8 +52146,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -54585,10 +52210,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -54652,10 +52274,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -54704,10 +52323,8 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -54721,8 +52338,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -54786,10 +52402,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -54840,8 +52453,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -54856,7 +52467,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -54907,8 +52517,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -54928,7 +52536,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -54977,8 +52584,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -54989,8 +52594,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -55041,8 +52645,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -55057,7 +52659,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -55085,7 +52686,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto</td>
       <td>0.48.0</td>
       <td>kallisto</td>
-      <td>0.51.0</td>
+      <td>0.51.1</td>
       <td>Gene expression profiling</td>
       <td>Transcriptomics</td>
       <td>2</td>
@@ -55107,8 +52708,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -55123,8 +52722,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -55188,10 +52786,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -55241,8 +52836,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -55257,8 +52850,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>8</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
@@ -55323,9 +52915,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -55353,7 +52942,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate</td>
       <td>2.3.2</td>
       <td>kleborate</td>
-      <td>3.0.6</td>
+      <td>3.0.9</td>
       <td>Multilocus sequence typing, Genome assembly, Virulence prediction</td>
       <td>Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing</td>
       <td>0</td>
@@ -55376,8 +52965,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -55392,7 +52979,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -55456,10 +53042,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -55523,10 +53106,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -55573,8 +53153,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -55592,8 +53170,7 @@
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -55642,8 +53219,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -55659,8 +53234,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -55709,8 +53283,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -55727,7 +53299,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -55791,10 +53362,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -55843,12 +53411,9 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>4</td>
       <td>6</td>
-      <td>0</td>
+      <td>6</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -55912,8 +53477,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -55933,7 +53496,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -55956,7 +53518,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/last</td>
       <td>1205</td>
       <td>last</td>
-      <td>1574</td>
+      <td>1584</td>
       <td>Sequence alignment</td>
       <td>Comparative genomics</td>
       <td>0</td>
@@ -55992,10 +53554,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -56044,8 +53603,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>2</td>
@@ -56061,8 +53618,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -56132,9 +53688,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -56194,9 +53747,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -56245,8 +53795,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -56262,8 +53810,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -56327,10 +53874,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -56395,9 +53939,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -56448,8 +53989,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -56464,7 +54003,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -56515,8 +54053,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -56530,8 +54066,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -56596,9 +54131,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -56662,10 +54194,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -56734,9 +54263,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
     </tr>
     <tr>
@@ -56751,14 +54277,14 @@
       <td>MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.</td>
       <td>Filtering, Statistical calculation, Standardisation and normalisation, Visualisation</td>
       <td>Metagenomics, Statistics and probability</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://huttenhower.sph.harvard.edu/maaslin</td>
       <td>Metagenomics</td>
       <td>maaslin2</td>
       <td>iuc</td>
       <td>https://github.com/biobakery/Maaslin2</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2</td>
-      <td>1.16.0</td>
+      <td>1.18.0</td>
       <td>bioconductor-maaslin2</td>
       <td>1.18.0</td>
       <td>Filtering, Standardisation and normalisation, Visualisation</td>
@@ -56797,9 +54323,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -56839,8 +54362,6 @@
       <td>9</td>
       <td>9</td>
       <td>0</td>
-      <td>9</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -56865,8 +54386,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>9</td>
       <td>9</td>
       <td>9</td>
       <td>0</td>
@@ -56907,9 +54427,7 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>1</td>
@@ -56932,8 +54450,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -56952,14 +54469,14 @@
       <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
       <td></td>
       <td>Sequence analysis</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
       <td>Convert Formats</td>
       <td>ucsc_maftoaxt</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/maftoaxt</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt</td>
-      <td>377</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt</td>
+      <td>469</td>
       <td>ucsc-maftoaxt</td>
       <td>469</td>
       <td></td>
@@ -57003,9 +54520,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -57050,8 +54564,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -57066,8 +54578,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -57118,8 +54629,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -57133,8 +54642,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -57199,9 +54707,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -57269,9 +54774,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>9</td>
       <td>1528</td>
     </tr>
@@ -57319,8 +54821,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -57335,7 +54835,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -57386,8 +54885,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -57401,8 +54898,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -57472,9 +54968,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -57533,10 +55026,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -57587,8 +55077,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -57602,8 +55090,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -57668,9 +55155,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -57698,7 +55182,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka</td>
       <td>1.7.2</td>
       <td>medaka</td>
-      <td>1.11.3</td>
+      <td>2.0.0</td>
       <td>Base-calling, Variant calling, Sequence assembly</td>
       <td>Sequence assembly, Machine learning</td>
       <td>3</td>
@@ -57721,8 +55205,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -57736,8 +55218,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -57786,8 +55267,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -57803,8 +55282,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -57855,8 +55333,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -57871,7 +55347,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -57936,9 +55411,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>7</td>
       <td>0</td>
       <td>0</td>
@@ -57978,10 +55450,8 @@
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -58004,8 +55474,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
@@ -58054,8 +55523,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -58071,8 +55538,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -58142,9 +55608,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -58209,9 +55672,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -58271,9 +55731,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -58343,9 +55800,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -58391,8 +55845,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -58407,7 +55859,6 @@
       <td>0</td>
       <td>1</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -58426,7 +55877,7 @@
       <td>Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid</td>
       <td>Taxonomic classification</td>
       <td>Taxonomy</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/steineggerlab/Metabuli</td>
       <td>Sequence Analysis, Metagenomics</td>
       <td>metabuli</td>
@@ -58435,19 +55886,16 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli</td>
       <td>1.0.5</td>
       <td>metabuli</td>
-      <td>1.0.5</td>
+      <td>1.0.8</td>
       <td>Taxonomic classification</td>
       <td>Taxonomy</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -58538,10 +55986,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -58592,8 +56037,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -58607,8 +56050,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -58657,9 +56099,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
+      <td>2</td>
       <td>0</td>
       <td>4</td>
       <td>0</td>
@@ -58675,7 +56115,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
@@ -58745,9 +56184,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -58812,9 +56248,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -58835,7 +56268,7 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed</td>
-      <td>1.3.2</td>
+      <td>1.3.3</td>
       <td>python</td>
       <td></td>
       <td></td>
@@ -58879,9 +56312,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -58927,8 +56357,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -58942,8 +56370,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -58994,8 +56421,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -59009,8 +56434,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -59061,8 +56485,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -59076,8 +56498,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -59117,8 +56538,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -59143,8 +56562,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -59209,9 +56627,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -59281,9 +56696,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -59343,9 +56755,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -59396,8 +56805,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -59412,7 +56819,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -59463,8 +56869,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -59478,8 +56882,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>1</td>
       <td>0</td>
@@ -59530,8 +56933,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -59545,8 +56946,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -59610,10 +57010,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -59664,8 +57061,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -59680,7 +57075,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -59720,8 +57114,6 @@
       <td>129</td>
       <td>129</td>
       <td>0</td>
-      <td>3</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -59746,8 +57138,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>126</td>
       <td>129</td>
       <td>129</td>
       <td>0</td>
@@ -59811,10 +57202,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -59884,9 +57272,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -59946,9 +57331,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -59974,9 +57356,9 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc</td>
-      <td>1.11</td>
-      <td>multiqc</td>
       <td>1.24.1</td>
+      <td>multiqc</td>
+      <td>1.25.1</td>
       <td>Sequencing quality control</td>
       <td>Sequencing, Bioinformatics, Sequence analysis, Genomics</td>
       <td>1</td>
@@ -59991,8 +57373,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -60014,8 +57394,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -60065,8 +57444,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
       <td>3</td>
       <td>0</td>
@@ -60081,8 +57458,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>6</td>
       <td>6</td>
       <td>6</td>
       <td>0</td>
@@ -60152,9 +57528,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -60218,9 +57591,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
     </tr>
     <tr>
@@ -60286,9 +57656,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -60334,8 +57701,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -60349,8 +57714,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -60399,8 +57763,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -60416,8 +57778,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -60481,10 +57842,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -60535,8 +57893,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -60550,8 +57906,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -60602,8 +57957,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -60617,8 +57970,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -60669,8 +58021,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -60690,7 +58040,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -60728,8 +58077,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>8</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -60752,7 +58099,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
@@ -60803,8 +58149,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -60824,7 +58168,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -60884,9 +58227,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -60937,8 +58277,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -60952,8 +58290,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -61004,8 +58341,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -61020,7 +58355,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -61084,10 +58418,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -61151,10 +58482,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -61205,8 +58533,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -61220,8 +58546,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -61272,8 +58597,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -61287,8 +58610,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -61358,9 +58680,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -61420,9 +58739,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>10</td>
       <td>10</td>
       <td>0</td>
@@ -61473,8 +58789,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -61488,8 +58802,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -61553,10 +58866,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -61626,9 +58936,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -61674,8 +58981,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -61689,8 +58994,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>4</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
@@ -61755,9 +59059,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>17</td>
       <td>17</td>
       <td>0</td>
@@ -61827,9 +59128,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -61856,15 +59154,12 @@
       <td></td>
       <td></td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -61956,9 +59251,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -61998,10 +59290,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -62027,6 +59315,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>239</td>
@@ -62095,9 +59384,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -62162,9 +59448,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -62229,9 +59512,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -62277,8 +59557,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -62292,8 +59570,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -62358,9 +59635,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -62409,8 +59683,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -62426,8 +59698,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -62497,9 +59768,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -62564,9 +59832,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -62631,9 +59896,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -62682,8 +59944,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -62694,8 +59954,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -62765,9 +60024,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -62812,8 +60068,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -62828,8 +60082,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -62880,8 +60133,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -62896,7 +60147,6 @@
       <td>0</td>
       <td>1</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -62945,8 +60195,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -62963,7 +60211,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -63003,8 +60250,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -63029,8 +60274,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -63043,7 +60287,7 @@
       <td>picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile</td>
       <td>Picard SAM/BAM manipulation tools.</td>
       <td>picard_samtofastq</td>
-      <td>picard_reordersam, picard_replacesamheader, picard_fastqtosam, picard_samtofastq</td>
+      <td>picard_reordersam, picard_samtofastq, picard_fastqtosam, picard_replacesamheader</td>
       <td></td>
       <td>picard_samtofastq</td>
       <td>Create a FASTQ file.</td>
@@ -63070,10 +60314,8 @@
       <td>31</td>
       <td>31</td>
       <td>0</td>
-      <td>29</td>
       <td>0</td>
       <td>0</td>
-      <td>31</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -63096,8 +60338,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>31</td>
       <td>31</td>
       <td>31</td>
       <td>0</td>
@@ -63162,9 +60403,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -63215,8 +60453,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
       <td>0</td>
       <td>0</td>
@@ -63231,7 +60467,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -63296,9 +60531,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>7</td>
       <td>0</td>
       <td>0</td>
@@ -63349,8 +60581,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -63364,8 +60594,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -63416,8 +60645,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -63431,8 +60658,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -63497,9 +60723,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -63548,8 +60771,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -63565,8 +60786,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -63597,16 +60817,14 @@
       <td>2.1.6</td>
       <td>Genome assembly, Scaffolding, Multilocus sequence typing</td>
       <td>Whole genome sequencing, Sequence assembly, Mapping, Probes and primers</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -63633,7 +60851,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -63697,10 +60914,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -63751,8 +60965,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -63767,7 +60979,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -63817,9 +61028,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -63833,8 +61042,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -63877,8 +61085,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>13</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -63901,8 +61107,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>13</td>
+      <td>6</td>
       <td>13</td>
       <td>0</td>
       <td>409</td>
@@ -63971,9 +61176,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -64033,9 +61235,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -64086,8 +61285,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -64101,8 +61298,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -64134,15 +61330,13 @@
       <td>Genome annotation</td>
       <td>Genomics, Sequence analysis</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -64174,7 +61368,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -64212,8 +61405,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -64236,7 +61427,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -64285,8 +61475,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -64302,8 +61490,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -64368,9 +61555,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -64421,8 +61605,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -64436,8 +61618,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -64502,9 +61683,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -64569,9 +61747,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -64636,9 +61811,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -64687,12 +61859,9 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -64769,10 +61938,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -64821,8 +61987,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -64838,8 +62002,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -64890,8 +62053,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -64906,7 +62067,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -64976,9 +62136,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -65038,9 +62195,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -65089,8 +62243,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>31</td>
       <td>0</td>
       <td>1</td>
@@ -65107,7 +62259,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>31</td>
       <td>31</td>
       <td>0</td>
@@ -65177,9 +62328,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -65244,9 +62392,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -65292,8 +62437,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -65307,8 +62450,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>4</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
@@ -65351,8 +62493,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -65374,8 +62514,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -65444,9 +62583,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
     </tr>
     <tr>
@@ -65492,8 +62628,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>2</td>
       <td>0</td>
@@ -65508,8 +62642,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -65575,9 +62708,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -65597,7 +62727,7 @@
       <td></td>
       <td>To update</td>
       <td>https://github.com/dgrun/RaceID3_StemID2_package/</td>
-      <td>Transcriptomics</td>
+      <td>Single Cell, Transcriptomics</td>
       <td></td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3</td>
@@ -65640,10 +62770,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -65694,8 +62821,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -65710,7 +62835,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -65761,8 +62885,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -65777,7 +62899,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -65847,9 +62968,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -65895,8 +63013,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -65911,7 +63027,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -65954,8 +63069,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -65977,8 +63090,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -66043,9 +63155,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -66096,8 +63205,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -66112,7 +63219,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -66138,9 +63244,9 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge</td>
-      <td>1.14.1</td>
+      <td>1.15.0</td>
       <td>recentrifuge</td>
-      <td>1.14.1</td>
+      <td>1.15.0</td>
       <td>Taxonomic classification, Expression analysis, Cross-assembly</td>
       <td>Metagenomics, Microbial ecology, Metagenomic sequencing</td>
       <td>1</td>
@@ -66161,8 +63267,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -66179,7 +63283,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -66230,8 +63333,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -66246,7 +63347,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -66265,7 +63365,7 @@
       <td>A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).</td>
       <td>Genome annotation</td>
       <td>Sequence analysis, Sequence composition, complexity and repeats</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>http://www.repeatmasker.org/</td>
       <td>Sequence Analysis</td>
       <td>repeat_masker</td>
@@ -66274,7 +63374,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker</td>
       <td>4.1.5</td>
       <td>repeatmasker</td>
-      <td>4.1.5</td>
+      <td>4.0.9_p2</td>
       <td>Genome annotation</td>
       <td>Sequence composition, complexity and repeats</td>
       <td>1</td>
@@ -66310,10 +63410,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -66364,8 +63461,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -66380,7 +63475,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -66450,9 +63544,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -66498,8 +63589,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -66513,8 +63602,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -66578,10 +63666,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -66651,9 +63736,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -66713,9 +63795,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -66755,8 +63834,6 @@
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -66781,8 +63858,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -66847,9 +63923,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -66913,10 +63986,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -66967,8 +64037,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -66982,8 +64050,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -67053,9 +64120,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -67120,9 +64184,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -67187,9 +64248,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -67254,9 +64312,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -67321,9 +64376,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -67388,9 +64440,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -67434,8 +64483,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>22</td>
       <td>0</td>
       <td>0</td>
@@ -67451,8 +64498,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>22</td>
       <td>22</td>
       <td>22</td>
       <td>0</td>
@@ -67510,16 +64556,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -67570,8 +64613,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -67585,8 +64626,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -67656,9 +64696,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -67679,9 +64716,9 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools</td>
-      <td>1.15.1</td>
-      <td>samtools</td>
       <td>1.20</td>
+      <td>samtools</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -67723,9 +64760,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -67739,7 +64773,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/dellytools/sansa</td>
       <td>Variant Analysis</td>
       <td>sansa</td>
@@ -67748,7 +64782,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa</td>
       <td>0.2.1</td>
       <td>sansa</td>
-      <td>0.2.1</td>
+      <td>0.2.2</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -67784,10 +64818,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -67851,10 +64882,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -67918,10 +64946,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -67991,9 +65016,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -68009,12 +65031,12 @@
       <td>Gene expression, Cell biology, Genetics</td>
       <td>To update</td>
       <td>https://scanpy.readthedocs.io</td>
-      <td>Transcriptomics, Sequence Analysis</td>
+      <td>Single Cell, Spatial Omics, Transcriptomics</td>
       <td>scanpy</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy</td>
-      <td>1.9.6</td>
+      <td>1.10.2</td>
       <td>scanpy</td>
       <td>1.7.2</td>
       <td>Differential gene expression analysis</td>
@@ -68052,10 +65074,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>6</td>
       <td>6</td>
       <td>6</td>
       <td>0</td>
@@ -68076,7 +65095,7 @@
       <td>RNA-seq, Quality affairs, Molecular genetics</td>
       <td>To update</td>
       <td>http://bioconductor.org/packages/scater/</td>
-      <td>Transcriptomics, RNA, Visualization</td>
+      <td>Single Cell, Transcriptomics, Visualization</td>
       <td></td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater</td>
@@ -68119,10 +65138,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -68143,7 +65159,7 @@
       <td></td>
       <td>Up-to-date</td>
       <td>https://github.com/cellgeni/sceasy/</td>
-      <td>Transcriptomics</td>
+      <td>Single Cell, Spatial Omics, Convert Formats</td>
       <td>sceasy_convert</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/</td>
@@ -68180,8 +65196,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -68192,7 +65206,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>90</td>
       <td>721</td>
     </tr>
@@ -68210,7 +65223,7 @@
       <td></td>
       <td>To update</td>
       <td>https://github.com/joachimwolff/schicexplorer</td>
-      <td>Sequence Analysis, Transcriptomics, Visualization</td>
+      <td>Sequence Analysis, Transcriptomics, Visualization, Single Cell</td>
       <td>schicexplorer</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer</td>
@@ -68253,10 +65266,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>16</td>
       <td>16</td>
       <td>16</td>
       <td>0</td>
@@ -68325,9 +65335,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
     </tr>
     <tr>
@@ -68374,8 +65381,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -68390,7 +65395,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -68411,7 +65415,7 @@
       <td>Gene expression, RNA-Seq, Sequencing</td>
       <td>To update</td>
       <td>http://bioconductor.org/packages/release/bioc/html/scPipe.html</td>
-      <td>Transcriptomics, RNA, Statistics</td>
+      <td>Transcriptomics, Single Cell</td>
       <td>scpipe</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe</td>
@@ -68454,10 +65458,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -68521,10 +65522,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -68594,9 +65592,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -68656,9 +65651,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
       <td>0</td>
       <td>0</td>
@@ -68690,14 +65682,12 @@
       <td>Read mapping, Genetic variation analysis</td>
       <td>Transcriptomics, Mapping</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -68724,8 +65714,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -68779,8 +65768,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -68792,7 +65779,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -68826,13 +65812,11 @@
       <td>0</td>
       <td>2</td>
       <td>5</td>
-      <td>2</td>
+      <td>3</td>
       <td>0</td>
       <td>2</td>
       <td>5</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -68859,7 +65843,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -68929,9 +65912,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -68995,9 +65975,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>12</td>
     </tr>
     <tr>
@@ -69036,8 +66013,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>14</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -69059,8 +66034,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>14</td>
       <td>14</td>
       <td>14</td>
       <td>14</td>
@@ -69124,10 +66098,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -69137,8 +66108,8 @@
     <tr>
       <td></td>
       <td>seurat</td>
-      <td>seurat</td>
-      <td>A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data</td>
+      <td>seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension</td>
+      <td>Seurat - R toolkit for single cell genomics</td>
       <td></td>
       <td></td>
       <td></td>
@@ -69147,24 +66118,24 @@
       <td></td>
       <td></td>
       <td>To update</td>
-      <td>https://github.com/satijalab/seurat</td>
-      <td>Transcriptomics, RNA, Statistics</td>
+      <td>https://satijalab.org/seurat/</td>
+      <td>Single Cell, Transcriptomics, Sequence Analysis</td>
       <td>seurat</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat</td>
-      <td>4.3.0.1</td>
+      <td>5.0</td>
       <td>r-seurat</td>
       <td>3.0.2</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
+      <td>7</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>7</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -69185,9 +66156,10 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>7</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -69195,11 +66167,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>66</td>
-      <td>1543</td>
     </tr>
     <tr>
       <td></td>
@@ -69222,7 +66190,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta</td>
       <td>0.6.0</td>
       <td>shasta</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -69245,8 +66213,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -69260,8 +66226,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -69312,8 +66277,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -69333,7 +66296,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -69377,8 +66339,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -69394,8 +66354,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -69453,16 +66412,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -69527,9 +66483,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -69569,8 +66522,6 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -69595,8 +66546,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -69615,14 +66565,14 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/timoast/sinto</td>
-      <td>Sequence Analysis</td>
+      <td>Single Cell, Epigenetics</td>
       <td></td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto</td>
-      <td>0.9.0</td>
+      <td>0.10.1</td>
       <td>sinto</td>
       <td>0.10.1</td>
       <td></td>
@@ -69661,9 +66611,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -69727,10 +66674,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -69795,9 +66739,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -69862,9 +66803,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -69883,7 +66821,7 @@
       <td>Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568</td>
       <td>Sequence trimming, Genotyping, k-mer counting</td>
       <td>Sequence assembly, Genetic variation, Mathematics</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/KamilSJaron/smudgeplot</td>
       <td>Assembly</td>
       <td>smudgeplot</td>
@@ -69892,7 +66830,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot</td>
       <td>0.2.5</td>
       <td>smudgeplot</td>
-      <td>0.2.5</td>
+      <td>0.3.0</td>
       <td>Sequence trimming, Genotyping, k-mer counting</td>
       <td>Sequence assembly, Genetic variation, Mathematics</td>
       <td>1</td>
@@ -69929,9 +66867,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -69995,10 +66930,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -70019,7 +66951,7 @@
       <td></td>
       <td>To update</td>
       <td>https://kzhang.org/SnapATAC2/</td>
-      <td>Epigenetics, Sequence Analysis</td>
+      <td>Single Cell, Epigenetics</td>
       <td>snapatac2</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2</td>
@@ -70068,9 +67000,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -70084,14 +67013,14 @@
       <td>An algorithm for structural variation detection from third generation sequencing alignment.</td>
       <td>Sequence analysis, Structural variation detection</td>
       <td>DNA structural variation, Sequencing</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/fritzsedlazeck/Sniffles</td>
       <td>Sequence Analysis</td>
       <td>sniffles</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles</td>
-      <td>1.0.12</td>
+      <td>2.4</td>
       <td>sniffles</td>
       <td>2.4</td>
       <td>Sequence analysis, Structural variation detection</td>
@@ -70116,8 +67045,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -70131,8 +67058,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -70183,8 +67109,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -70199,7 +67123,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -70242,8 +67165,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -70265,8 +67186,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>2</td>
       <td>0</td>
@@ -70317,8 +67237,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -70332,8 +67250,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -70384,8 +67301,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -70399,8 +67314,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -70445,8 +67359,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -70466,8 +67378,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -70518,8 +67429,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -70533,8 +67442,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -70585,8 +67493,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -70601,7 +67507,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -70646,8 +67551,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>8</td>
       <td>0</td>
       <td>0</td>
@@ -70667,8 +67570,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>8</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
@@ -70733,9 +67635,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -70799,10 +67698,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -70853,8 +67749,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -70868,8 +67762,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -70920,8 +67813,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -70936,7 +67827,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -70949,7 +67839,7 @@
       <td>spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades</td>
       <td>SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.</td>
       <td>spades</td>
-      <td>coronaspades, biosyntheticspades, metaplasmidspades, plasmidspades, metaspades, rnaspades, metaviralspades, rnaviralspades, spades</td>
+      <td>spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades</td>
       <td></td>
       <td>SPAdes</td>
       <td>St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.</td>
@@ -70979,8 +67869,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -71002,8 +67890,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>9</td>
       <td>3</td>
       <td>0</td>
@@ -71054,8 +67941,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -71069,8 +67954,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -71080,7 +67964,7 @@
     <tr>
       <td></td>
       <td>spapros</td>
-      <td>spapros, spapros</td>
+      <td>spapros_evaluation, spapros_selection</td>
       <td>Select and evaluate probe sets for targeted spatial transcriptomics.</td>
       <td></td>
       <td></td>
@@ -71091,7 +67975,7 @@
       <td></td>
       <td>Up-to-date</td>
       <td>https://github.com/theislab/spapros</td>
-      <td>Transcriptomics, Sequence Analysis</td>
+      <td>Single Cell, Transcriptomics, Sequence Analysis</td>
       <td>spapros</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/</td>
@@ -71103,14 +67987,11 @@
       <td></td>
       <td>0</td>
       <td>0</td>
+      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -71202,9 +68083,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -71268,10 +68146,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -71320,8 +68195,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>3</td>
@@ -71337,8 +68210,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -71366,7 +68238,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2</td>
       <td>0.2.0</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td>Multilocus sequence typing</td>
       <td>Whole genome sequencing, Public health and epidemiology</td>
       <td>0</td>
@@ -71389,8 +68261,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -71405,7 +68275,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -71469,10 +68338,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>11</td>
       <td>13</td>
       <td>13</td>
       <td>0</td>
@@ -71537,9 +68403,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>12</td>
       <td>12</td>
       <td>0</td>
@@ -71588,8 +68451,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -71605,8 +68466,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -71676,9 +68536,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -71724,8 +68581,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -71739,8 +68594,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -71789,8 +68643,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -71806,8 +68658,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -71871,10 +68722,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -71944,9 +68792,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -72011,9 +68856,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -72073,9 +68915,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -72124,8 +68963,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -72141,8 +68978,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -72182,10 +69018,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -72212,6 +69044,7 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>200</td>
       <td>7388</td>
@@ -72260,8 +69093,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -72275,8 +69106,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -72346,9 +69176,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -72376,14 +69203,11 @@
       <td>Taxonomy, Biotechnology, Ecology</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -72461,8 +69285,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -72482,7 +69304,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -72526,8 +69347,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -72543,8 +69362,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -72614,9 +69432,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -72675,10 +69490,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -72742,10 +69554,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -72776,16 +69585,14 @@
       <td>0.6.6</td>
       <td></td>
       <td></td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -72812,7 +69619,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -72876,10 +69682,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -72907,7 +69710,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder</td>
       <td>1.0.1</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td>Genome indexing, Variant calling, PCR primer design</td>
       <td>Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation</td>
       <td>0</td>
@@ -72944,9 +69747,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -73016,9 +69816,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -73077,10 +69874,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -73131,8 +69925,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -73146,8 +69938,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -73166,14 +69957,14 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/veg/tn93/</td>
       <td>Sequence Analysis</td>
       <td>tn93</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93</td>
-      <td>1.0.6</td>
+      <td>1.0.14</td>
       <td>tn93</td>
       <td>1.0.14</td>
       <td></td>
@@ -73201,8 +69992,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -73214,7 +70003,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -73240,9 +70028,9 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator</td>
-      <td>0.9</td>
+      <td>0.9.1</td>
       <td>tooldistillator</td>
-      <td>0.9</td>
+      <td>0.9.1</td>
       <td>Parsing</td>
       <td>Microbiology, Bioinformatics, Sequence analysis</td>
       <td>2</td>
@@ -73284,9 +70072,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -73351,9 +70136,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -73376,7 +70158,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy</td>
       <td>0.6.1</td>
       <td>tracy</td>
-      <td>0.7.6</td>
+      <td>0.7.8</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -73413,9 +70195,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -73462,8 +70241,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -73481,8 +70258,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -73546,10 +70322,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -73613,10 +70386,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -73656,10 +70426,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -73682,8 +70450,7 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -73732,8 +70499,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>2</td>
       <td>1</td>
@@ -73749,8 +70514,7 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>11</td>
       <td>13</td>
       <td>12</td>
       <td>0</td>
@@ -73801,8 +70565,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -73816,8 +70578,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -73868,8 +70629,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -73884,7 +70643,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -73903,14 +70661,14 @@
       <td>TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.</td>
       <td>Homology-based gene prediction, Alternative splicing prediction</td>
       <td>Gene expression, RNA-Seq, Gene transcripts, Model organisms</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/Gaius-Augustus/TSEBRA</td>
       <td>Genome annotation</td>
       <td></td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra</td>
-      <td>1.1.2.4</td>
+      <td>1.1.2.5</td>
       <td>tsebra</td>
       <td>1.1.2.5</td>
       <td>Homology-based gene prediction, Alternative splicing prediction</td>
@@ -73953,9 +70711,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
     </tr>
     <tr>
@@ -74015,10 +70770,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -74037,14 +70789,14 @@
       <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
       <td></td>
       <td>Sequence analysis</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://genome.ucsc.edu/goldenpath/help/twoBit.html</td>
       <td>Convert Formats</td>
       <td>ucsc_twobittofa</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa</td>
-      <td>377</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa</td>
+      <td>469</td>
       <td>ucsc-twobittofa</td>
       <td>469</td>
       <td></td>
@@ -74076,16 +70828,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -74104,14 +70853,14 @@
       <td>An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.</td>
       <td>Pathway or network analysis, Formatting, RNA-Seq analysis</td>
       <td>Transcriptomics, Gene transcripts, Workflows</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://bioconductor.org/packages/tximport/</td>
       <td>Transcriptomics</td>
       <td>tximport</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport</td>
-      <td>1.22.0</td>
+      <td>1.30.0</td>
       <td>bioconductor-tximport</td>
       <td>1.30.0</td>
       <td>Pathway or network analysis, Formatting, RNA-Seq analysis</td>
@@ -74149,10 +70898,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -74171,20 +70917,84 @@
       <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
       <td></td>
       <td>Sequence analysis</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
       <td>Sequence Analysis</td>
       <td>ucsc_axtchain</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain</td>
-      <td>455</td>
+      <td>469</td>
       <td>ucsc-axtchain</td>
       <td>469</td>
       <td></td>
       <td>Sequence analysis</td>
       <td>1</td>
       <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_axttomaf</td>
+      <td>ucsc_axtomaf</td>
+      <td>Convert dataset from axt to MAF format.</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Convert Formats</td>
+      <td>ucsc_axttomaf</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf</td>
+      <td>469</td>
+      <td>ucsc-axttomaf</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>1</td>
@@ -74222,15 +71032,140 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_blat</td>
+      <td>ucsc_blat</td>
+      <td>Standalone blat sequence search command line tool</td>
+      <td>blat</td>
+      <td>blat</td>
+      <td></td>
+      <td>BLAT</td>
+      <td>Fast, accurate spliced alignment of DNA sequences.</td>
+      <td>Sequence alignment</td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://genome.ucsc.edu/goldenPath/help/blatSpec.html</td>
+      <td>Sequence Analysis</td>
+      <td>ucsc_blat</td>
+      <td>yating-l</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat</td>
+      <td>469</td>
+      <td>ucsc-blat</td>
+      <td>469</td>
+      <td>Sequence alignment</td>
+      <td>Sequence analysis</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_chainnet</td>
+      <td>ucsc_chainnet</td>
+      <td>Make alignment nets out of chains</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Sequence Analysis</td>
+      <td>ucsc_chainnet</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet</td>
+      <td>469</td>
+      <td>ucsc-chainnet</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
-      <td>ucsc_axttomaf</td>
-      <td>ucsc_axtomaf</td>
-      <td>Convert dataset from axt to MAF format.</td>
+      <td>ucsc_chainprenet</td>
+      <td>ucsc_chainprenet</td>
+      <td>Remove chains that don't have a chance of being netted</td>
       <td>UCSC_Genome_Browser_Utilities</td>
       <td>UCSC_Genome_Browser_Utilities</td>
       <td></td>
@@ -74238,15 +71173,15 @@
       <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
       <td></td>
       <td>Sequence analysis</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
-      <td>Convert Formats</td>
-      <td>ucsc_axttomaf</td>
+      <td>Sequence Analysis</td>
+      <td>ucsc_chainprenet</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf</td>
-      <td>377</td>
-      <td>ucsc-axttomaf</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet</td>
+      <td>469</td>
+      <td>ucsc-chainprenet</td>
       <td>469</td>
       <td></td>
       <td>Sequence analysis</td>
@@ -74289,37 +71224,36 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
-      <td>ucsc_blat</td>
-      <td>ucsc_blat</td>
-      <td>Standalone blat sequence search command line tool</td>
-      <td>blat</td>
-      <td>blat</td>
+      <td>ucsc_chainsort</td>
+      <td>ucsc_chainsort</td>
+      <td>Sort chains. By default sorts by score.</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
       <td></td>
-      <td>BLAT</td>
-      <td>Fast, accurate spliced alignment of DNA sequences.</td>
-      <td>Sequence alignment</td>
       <td>Sequence analysis</td>
-      <td>To update</td>
-      <td>http://genome.ucsc.edu/goldenPath/help/blatSpec.html</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
       <td>Sequence Analysis</td>
-      <td>ucsc_blat</td>
-      <td>yating-l</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat</td>
-      <td>377</td>
-      <td>ucsc-blat</td>
+      <td>ucsc_chainsort</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort</td>
       <td>469</td>
-      <td>Sequence alignment</td>
+      <td>ucsc-chainsort</td>
+      <td>469</td>
+      <td></td>
       <td>Sequence analysis</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -74346,11 +71280,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -74362,9 +71291,9 @@
     </tr>
     <tr>
       <td></td>
-      <td>ucsc_chainnet</td>
-      <td>ucsc_chainnet</td>
-      <td>Make alignment nets out of chains</td>
+      <td>ucsc_netfilter</td>
+      <td>ucsc_netfilter</td>
+      <td>Filter out parts of net</td>
       <td>UCSC_Genome_Browser_Utilities</td>
       <td>UCSC_Genome_Browser_Utilities</td>
       <td></td>
@@ -74375,25 +71304,22 @@
       <td>Up-to-date</td>
       <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
       <td>Sequence Analysis</td>
-      <td>ucsc_chainnet</td>
+      <td>ucsc_netfilter</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter</td>
       <td>469</td>
-      <td>ucsc-chainnet</td>
+      <td>ucsc-netfilter</td>
       <td>469</td>
       <td></td>
       <td>Sequence analysis</td>
+      <td>1</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -74429,9 +71355,9 @@
     </tr>
     <tr>
       <td></td>
-      <td>ucsc_chainprenet</td>
-      <td>ucsc_chainprenet</td>
-      <td>Remove chains that don't have a chance of being netted</td>
+      <td>ucsc_netsyntenic</td>
+      <td>ucsc_netsyntenic</td>
+      <td>Add synteny info to a net dataset</td>
       <td>UCSC_Genome_Browser_Utilities</td>
       <td>UCSC_Genome_Browser_Utilities</td>
       <td></td>
@@ -74439,15 +71365,15 @@
       <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
       <td></td>
       <td>Sequence analysis</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
       <td>Sequence Analysis</td>
-      <td>ucsc_chainprenet</td>
+      <td>ucsc_netsyntenic</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainprenet</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet</td>
-      <td>377</td>
-      <td>ucsc-chainprenet</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic</td>
+      <td>469</td>
+      <td>ucsc-netsyntenic</td>
       <td>469</td>
       <td></td>
       <td>Sequence analysis</td>
@@ -74490,15 +71416,12 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
-      <td>ucsc_chainsort</td>
-      <td>ucsc_chainsort</td>
-      <td>Sort chains. By default sorts by score.</td>
+      <td>ucsc_nettoaxt</td>
+      <td>ucsc_nettoaxt</td>
+      <td>Convert net (and chain) to axt format.</td>
       <td>UCSC_Genome_Browser_Utilities</td>
       <td>UCSC_Genome_Browser_Utilities</td>
       <td></td>
@@ -74506,28 +71429,25 @@
       <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
       <td></td>
       <td>Sequence analysis</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
-      <td>Sequence Analysis</td>
-      <td>ucsc_chainsort</td>
+      <td>Convert Formats</td>
+      <td>ucsc_nettoaxt</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort</td>
-      <td>455</td>
-      <td>ucsc-chainsort</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt</td>
+      <td>469</td>
+      <td>ucsc-nettoaxt</td>
       <td>469</td>
       <td></td>
       <td>Sequence analysis</td>
       <td>1</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -74573,14 +71493,14 @@
       <td>Tools for handling Unique Molecular Identifiers in NGS data sets.</td>
       <td>Sequencing quality control</td>
       <td>NGS, Sequence sites, features and motifs, Quality affairs</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/CGATOxford/UMI-tools</td>
-      <td>Sequence Analysis, Transcriptomics</td>
+      <td>Sequence Analysis, Transcriptomics, Single Cell</td>
       <td></td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools</td>
-      <td>1.1.2</td>
+      <td>1.1.5</td>
       <td>umi_tools</td>
       <td>1.1.5</td>
       <td>Sequencing quality control</td>
@@ -74605,8 +71525,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -74620,8 +71538,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -74671,8 +71588,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -74687,8 +71602,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -74753,9 +71667,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -74806,8 +71717,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -74821,8 +71730,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -74876,8 +71784,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -74889,7 +71795,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -74953,10 +71858,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -75020,10 +71922,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -75074,8 +71973,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -75089,8 +71986,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -75109,7 +72005,7 @@
       <td>variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.</td>
       <td>PCR primer design</td>
       <td>Virology, Probes and primers</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/jonas-fuchs/varVAMP/</td>
       <td>Sequence Analysis</td>
       <td>varvamp</td>
@@ -75118,7 +72014,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp</td>
       <td>1.2.0</td>
       <td>varvamp</td>
-      <td>1.2.0</td>
+      <td>1.2.1</td>
       <td>PCR primer design</td>
       <td>Virology, Probes and primers</td>
       <td>0</td>
@@ -75160,9 +72056,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -75207,8 +72100,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -75224,7 +72115,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -75252,7 +72142,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -75275,8 +72165,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -75290,8 +72178,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -75319,7 +72206,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -75342,8 +72229,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -75357,8 +72242,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -75386,7 +72270,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -75409,8 +72293,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -75424,8 +72306,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -75489,10 +72370,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -75520,7 +72398,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -75543,8 +72421,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -75558,8 +72434,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -75587,7 +72462,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -75610,8 +72485,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -75625,8 +72498,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -75654,7 +72526,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -75677,8 +72549,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -75692,8 +72562,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -75721,7 +72590,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -75744,8 +72613,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -75759,8 +72626,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -75788,7 +72654,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -75811,8 +72677,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -75826,8 +72690,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -75855,7 +72718,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -75878,8 +72741,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -75893,8 +72754,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -75922,7 +72782,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -75945,8 +72805,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -75960,8 +72818,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -75989,7 +72846,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -76012,8 +72869,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -76027,8 +72882,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -76056,7 +72910,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -76079,8 +72933,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -76094,8 +72946,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -76123,7 +72974,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -76146,8 +72997,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -76161,8 +73010,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -76190,7 +73038,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -76213,8 +73061,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -76228,8 +73074,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -76257,7 +73102,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -76280,8 +73125,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -76295,8 +73138,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -76324,7 +73166,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -76347,8 +73189,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -76362,8 +73202,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -76391,7 +73230,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -76414,8 +73253,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -76429,8 +73266,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -76458,7 +73294,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -76481,8 +73317,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -76496,8 +73330,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -76525,7 +73358,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -76548,8 +73381,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -76563,8 +73394,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -76592,7 +73422,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -76615,8 +73445,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -76630,8 +73458,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -76659,7 +73486,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -76682,8 +73509,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -76697,8 +73522,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -76726,7 +73550,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -76738,8 +73562,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -76764,8 +73586,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -76793,7 +73614,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect</td>
       <td></td>
       <td>vcflib</td>
-      <td>1.0.9</td>
+      <td>1.0.10</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -76816,8 +73637,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -76831,8 +73650,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -76883,8 +73701,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -76898,8 +73714,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -76920,7 +73735,7 @@
       <td></td>
       <td>Up-to-date</td>
       <td>http://velocyto.org/</td>
-      <td>Transcriptomics</td>
+      <td>Transcriptomics, Single Cell</td>
       <td>velocyto</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto</td>
@@ -76964,9 +73779,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -77015,8 +73827,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -77032,8 +73842,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -77073,8 +73882,6 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -77099,8 +73906,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -77128,19 +73934,16 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko</td>
       <td>1.3.1</td>
       <td>verkko</td>
-      <td>2.1</td>
+      <td>2.2</td>
       <td></td>
       <td></td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -77195,7 +73998,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg</td>
       <td>1.23.0</td>
       <td>vg</td>
-      <td>1.56.0</td>
+      <td>1.59.0</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -77231,10 +74034,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -77260,7 +74060,7 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot</td>
-      <td>1.0.1+galaxy0</td>
+      <td>1.1.0+galaxy0</td>
       <td>biopython</td>
       <td>1.70</td>
       <td>Sequence annotation, Sequence clustering, Sequence cluster visualisation</td>
@@ -77304,9 +74104,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -77371,9 +74168,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -77433,9 +74227,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -77484,8 +74275,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -77501,8 +74290,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -77530,7 +74318,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch</td>
       <td>2.8.3</td>
       <td>vsearch</td>
-      <td>2.28.1</td>
+      <td>2.29.0</td>
       <td>DNA mapping, Chimera detection</td>
       <td>Metagenomics, Sequence analysis</td>
       <td>8</td>
@@ -77552,8 +74340,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
@@ -77568,8 +74354,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>8</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
@@ -77639,9 +74424,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -77706,9 +74488,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -77743,10 +74522,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -77769,8 +74546,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -77789,14 +74565,14 @@
       <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
       <td></td>
       <td>Sequence analysis</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://genome.ucsc.edu/goldenPath/help/bigWig.html</td>
       <td>Convert Formats</td>
       <td>ucsc_wigtobigwig</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig</td>
-      <td>447</td>
+      <td>469</td>
       <td>ucsc-wigtobigwig</td>
       <td>469</td>
       <td></td>
@@ -77840,9 +74616,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -77906,9 +74679,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>85</td>
     </tr>
     <tr>
@@ -77969,9 +74739,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -78014,10 +74781,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -78041,6 +74804,7 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>3</td>
       <td>234</td>
@@ -78057,7 +74821,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/c-zhou/yahs</td>
       <td>Assembly</td>
       <td>yahs</td>
@@ -78066,7 +74830,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs</td>
       <td>1.2a.2</td>
       <td>yahs</td>
-      <td>1.2a.2</td>
+      <td>1.2.2</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -78103,9 +74867,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -78169,10 +74930,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -78182,7 +74940,7 @@
     <tr>
       <td></td>
       <td>EMLassemblyline</td>
-      <td>eal_table_template, eal_templates, eml2eal, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template</td>
+      <td>annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template</td>
       <td>Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa</td>
       <td></td>
       <td></td>
@@ -78198,22 +74956,19 @@
       <td>ecology</td>
       <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline</td>
       <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline</td>
-      <td>0.1.1+galaxy0</td>
-      <td>r-emlassemblyline</td>
+      <td>0.1.0+galaxy0</td>
+      <td>r-base</td>
       <td></td>
       <td></td>
       <td></td>
       <td>0</td>
       <td>0</td>
-      <td>9</td>
+      <td>11</td>
       <td>9</td>
       <td>0</td>
       <td>0</td>
+      <td>11</td>
       <td>9</td>
-      <td>9</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -78304,9 +75059,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -78376,9 +75128,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -78438,9 +75187,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>4</td>
       <td>0</td>
@@ -78505,9 +75251,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -78572,9 +75315,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -78623,8 +75363,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -78640,8 +75378,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>7</td>
       <td>5</td>
       <td>0</td>
@@ -78711,9 +75448,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -78778,9 +75512,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -78803,7 +75534,7 @@
       <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning</td>
       <td>1.10+galaxy0</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -78833,8 +75564,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -78847,7 +75576,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -78907,9 +75635,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -78967,8 +75692,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -78981,7 +75704,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -79046,9 +75768,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -79107,10 +75826,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -79160,8 +75876,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -79177,7 +75891,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -79235,8 +75948,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -79249,7 +75960,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -79293,8 +76003,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -79310,8 +76018,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>4</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -79376,9 +76083,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>3</td>
       <td>0</td>
@@ -79443,9 +76147,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -79485,9 +76186,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -79563,8 +76261,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -79584,7 +76280,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -79630,8 +76325,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -79646,7 +76339,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -79696,8 +76388,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -79718,7 +76408,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -79764,8 +76453,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -79785,7 +76472,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -79830,8 +76516,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -79852,7 +76536,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -79898,8 +76581,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -79919,7 +76600,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -79964,10 +76644,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -80046,9 +76723,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -80074,7 +76748,7 @@
       <td>climate</td>
       <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s</td>
       <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s</td>
-      <td>0.2.0</td>
+      <td>0.3.0</td>
       <td>python</td>
       <td></td>
       <td></td>
@@ -80113,9 +76787,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -80180,9 +76851,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -80247,9 +76915,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -80299,8 +76964,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -80316,7 +76979,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -80370,8 +77032,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>9</td>
       <td>0</td>
       <td>0</td>
@@ -80382,8 +77042,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>9</td>
       <td>11</td>
       <td>9</td>
       <td>0</td>
@@ -80448,9 +77107,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -80518,9 +77174,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>6</td>
     </tr>
@@ -80582,9 +77235,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -80649,15 +77299,76 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
       <td>19</td>
       <td>174</td>
     </tr>
+    <tr>
+      <td></td>
+      <td>checkv</td>
+      <td>checkv_end_to_end</td>
+      <td>Assess quality of single-contig viral genomes</td>
+      <td>checkv</td>
+      <td>checkv</td>
+      <td></td>
+      <td>CheckV</td>
+      <td>CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.</td>
+      <td>Sequence assembly, Validation, Read mapping</td>
+      <td>Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://bitbucket.org/berkeleylab/checkv/</td>
+      <td>Metagenomics</td>
+      <td>checkv</td>
+      <td>ufz</td>
+      <td>https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv</td>
+      <td>1.0.3</td>
+      <td>checkv</td>
+      <td>1.0.3</td>
+      <td>Sequence assembly, Validation, Read mapping</td>
+      <td>Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+    </tr>
     <tr>
       <td></td>
       <td>cherry_pick_fasta</td>
@@ -80701,8 +77412,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -80723,7 +77432,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -80783,9 +77491,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -80828,8 +77533,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -80852,7 +77555,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -80903,8 +77605,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -80919,7 +77619,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -80989,9 +77688,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -81014,7 +77710,7 @@
       <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler</td>
       <td>0.9.3</td>
       <td>htslib</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>4</td>
@@ -81051,9 +77747,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -81104,8 +77797,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -81125,7 +77816,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -81190,9 +77880,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -81251,10 +77938,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -81324,9 +78008,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -81386,9 +78067,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -81453,9 +78131,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -81520,9 +78195,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
       <td>0</td>
       <td>0</td>
@@ -81592,9 +78264,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -81659,9 +78328,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -81720,10 +78386,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -81792,9 +78455,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
     </tr>
     <tr>
@@ -81860,9 +78520,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -81911,8 +78568,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -81929,7 +78584,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -81989,9 +78643,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -82056,9 +78707,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -82123,9 +78771,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -82189,10 +78834,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -82257,9 +78899,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -82329,9 +78968,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -82396,9 +79032,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -82463,9 +79096,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -82528,9 +79158,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>95</td>
       <td>973</td>
     </tr>
@@ -82592,9 +79219,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -82657,11 +79281,8 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>3</td>
       <td>1</td>
       <td>0</td>
@@ -82731,9 +79352,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -82793,9 +79411,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>7</td>
       <td>0</td>
       <td>0</td>
@@ -82860,9 +79475,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -82927,9 +79539,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -82987,8 +79596,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -83001,7 +79608,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -83047,8 +79653,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -83062,8 +79666,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -83128,9 +79731,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -83200,9 +79800,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -83267,9 +79864,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -83334,9 +79928,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -83401,9 +79992,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -83463,9 +80051,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -83530,9 +80115,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -83582,8 +80164,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -83604,7 +80184,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -83657,8 +80236,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -83666,7 +80243,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -83736,9 +80312,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -83803,9 +80376,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -83870,9 +80440,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -83937,9 +80504,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -84004,9 +80568,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -84071,9 +80632,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -84132,10 +80690,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -84166,16 +80721,13 @@
       <td>20.0</td>
       <td></td>
       <td></td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -84272,9 +80824,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -84319,8 +80868,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>18</td>
       <td>18</td>
       <td>0</td>
@@ -84341,7 +80888,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -84406,9 +80952,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -84473,9 +81016,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -84538,9 +81078,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>27</td>
     </tr>
@@ -84607,9 +81144,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -84674,9 +81208,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -84736,9 +81267,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
@@ -84762,7 +81290,7 @@
       <td>Metagenomics</td>
       <td>genomad</td>
       <td>ufz</td>
-      <td>https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/</td>
+      <td>https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/</td>
       <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad</td>
       <td>1.8.0</td>
       <td>genomad</td>
@@ -84808,9 +81336,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -84875,9 +81400,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -84923,8 +81445,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -84944,7 +81464,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -85003,10 +81522,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -85055,8 +81571,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>13</td>
       <td>0</td>
       <td>0</td>
@@ -85072,8 +81586,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>6</td>
       <td>15</td>
       <td>9</td>
       <td>0</td>
@@ -85143,9 +81656,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -85210,9 +81720,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -85277,9 +81784,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -85344,9 +81848,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -85411,9 +81912,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -85478,9 +81976,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -85540,9 +82035,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -85612,9 +82104,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -85674,9 +82163,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -85727,8 +82213,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -85748,7 +82232,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -85808,9 +82291,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -85880,9 +82360,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -85928,8 +82405,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -85949,7 +82424,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -85970,7 +82444,7 @@
       <td>ecology</td>
       <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper</td>
       <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes</td>
-      <td>0.1.0</td>
+      <td>0.2.0</td>
       <td>r-base</td>
       <td></td>
       <td></td>
@@ -86014,9 +82488,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -86039,7 +82510,7 @@
       <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie</td>
       <td>20230328</td>
       <td>Fiji</td>
-      <td>20231211</td>
+      <td>20240614</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -86081,9 +82552,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -86143,9 +82611,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -86173,7 +82638,7 @@
       <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero</td>
       <td>20231221</td>
       <td>Fiji</td>
-      <td>20231211</td>
+      <td>20240614</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -86215,9 +82680,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -86282,9 +82744,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -86349,9 +82808,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -86404,8 +82860,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -86418,7 +82872,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -86464,8 +82917,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -86485,7 +82936,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -86545,9 +82995,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -86617,9 +83064,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -86684,9 +83128,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -86739,8 +83180,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -86753,7 +83192,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -86798,8 +83236,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -86820,7 +83256,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -86885,9 +83320,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -86936,8 +83368,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -86948,8 +83378,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -87007,8 +83436,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -87016,7 +83443,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -87081,9 +83507,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -87153,9 +83576,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -87182,15 +83602,12 @@
       <td></td>
       <td></td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -87282,9 +83699,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>9</td>
       <td>0</td>
       <td>0</td>
@@ -87334,8 +83748,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -87350,8 +83762,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -87400,8 +83811,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>10</td>
       <td>0</td>
       <td>0</td>
@@ -87417,8 +83826,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>10</td>
       <td>10</td>
       <td>0</td>
@@ -87482,10 +83890,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -87534,8 +83939,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -87552,7 +83955,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -87617,9 +84019,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -87661,10 +84060,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -87714,7 +84110,7 @@
       <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids</td>
       <td>20221216</td>
       <td>fiji</td>
-      <td>20231211</td>
+      <td>20240614</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -87756,9 +84152,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -87823,9 +84216,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -87871,8 +84261,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -87887,7 +84275,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -87936,8 +84323,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -87954,7 +84339,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -87986,15 +84370,12 @@
       <td>Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis</td>
       <td>Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -88085,10 +84466,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>6</td>
       <td>6</td>
       <td>6</td>
       <td>0</td>
@@ -88098,7 +84476,7 @@
     <tr>
       <td></td>
       <td>mfassignr</td>
-      <td>mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot</td>
+      <td>mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot</td>
       <td>The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements</td>
       <td>mfassignr</td>
       <td>mfassignr</td>
@@ -88114,21 +84492,18 @@
       <td>recetox</td>
       <td>https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr</td>
       <td>https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr</td>
-      <td>1.0.3</td>
+      <td>1.1.1</td>
       <td>r-mfassignr</td>
-      <td>1.0.3</td>
+      <td>1.1.1</td>
       <td>Visualisation</td>
       <td>Proteomics experiment, Molecular interactions, pathways and networks, Workflows</td>
       <td>0</td>
       <td>0</td>
-      <td>8</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>8</td>
+      <td>9</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>9</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -88225,9 +84600,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -88280,8 +84652,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -88294,12 +84664,11 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>misc</td>
-      <td>use_theoretical_mz_annotations</td>
+      <td>target_screen, use_theoretical_mz_annotations</td>
       <td></td>
       <td></td>
       <td></td>
@@ -88316,20 +84685,17 @@
       <td>https://github.com/RECETOX/galaxytools/tree/master/tools/misc</td>
       <td>https://github.com/RECETOX/galaxytools/tree/master/tools/misc</td>
       <td>1.0.0</td>
-      <td></td>
+      <td>pandas</td>
       <td></td>
       <td></td>
       <td></td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
+      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -88421,9 +84787,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -88491,9 +84854,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>264</td>
       <td>3266</td>
     </tr>
@@ -88555,9 +84915,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -88622,14 +84979,75 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>2</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ms2deepscore</td>
+      <td>ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training</td>
+      <td>Mass spectra similarity scoring using a trained ms2deepscore model.</td>
+      <td>ms2deepscore</td>
+      <td>ms2deepscore</td>
+      <td></td>
+      <td>MS2DeepScore</td>
+      <td>MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra.</td>
+      <td>Spectrum calculation, Spectral library search, Network analysis</td>
+      <td>Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/matchms/ms2deepscore</td>
+      <td>Metabolomics</td>
+      <td>ms2deepscore</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore</td>
+      <td>2.0.0</td>
+      <td>ms2deepscore</td>
+      <td>2.0.0</td>
+      <td>Spectrum calculation, Spectral library search, Network analysis</td>
+      <td>Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -88688,10 +85106,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -88756,9 +85171,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -88823,9 +85235,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -88874,8 +85283,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -88892,7 +85299,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -88962,9 +85368,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -89008,8 +85411,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -89025,8 +85426,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -89091,9 +85491,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -89158,9 +85555,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -89230,9 +85624,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -89291,10 +85682,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -89364,9 +85752,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -89401,10 +85786,8 @@
       <td>16</td>
       <td>16</td>
       <td>0</td>
-      <td>15</td>
       <td>0</td>
       <td>0</td>
-      <td>15</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -89427,8 +85810,7 @@
       <td>0</td>
       <td>0</td>
       <td>16</td>
-      <td>0</td>
-      <td>0</td>
+      <td>16</td>
       <td>16</td>
       <td>15</td>
       <td>0</td>
@@ -89478,8 +85860,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -89500,7 +85880,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -89560,9 +85939,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -89631,9 +86007,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
     </tr>
     <tr>
@@ -89699,9 +86072,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -89766,15 +86136,12 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>omero</td>
-      <td>omero_import, omero_metadata_import</td>
-      <td>Import images and metadata into an OMERO.server using omero-py</td>
+      <td>omero_import, omero_metadata_import, omero_roi_import</td>
+      <td>Import images, region of interest, metadata into an OMERO.server using omero-py</td>
       <td>omero</td>
       <td>omero</td>
       <td></td>
@@ -89833,9 +86200,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -89858,7 +86222,7 @@
       <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables</td>
       <td>20230623</td>
       <td>fiji</td>
-      <td>20231211</td>
+      <td>20240614</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -89900,9 +86264,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -89967,9 +86328,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -89992,7 +86350,7 @@
       <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images</td>
       <td>20240521</td>
       <td>fiji</td>
-      <td>20231211</td>
+      <td>20240614</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -90034,9 +86392,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -90059,7 +86414,7 @@
       <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid</td>
       <td>20230809</td>
       <td>fiji</td>
-      <td>20231211</td>
+      <td>20240614</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -90101,9 +86456,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -90126,7 +86478,7 @@
       <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements</td>
       <td>20240214</td>
       <td>fiji</td>
-      <td>20231211</td>
+      <td>20240614</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -90168,9 +86520,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -90230,9 +86579,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -90260,7 +86606,7 @@
       <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms</td>
       <td>3.1</td>
       <td>openms</td>
-      <td>3.1.0</td>
+      <td>3.2.0</td>
       <td></td>
       <td></td>
       <td>8</td>
@@ -90296,10 +86642,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>18</td>
       <td>141</td>
       <td>124</td>
       <td>0</td>
@@ -90364,9 +86707,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -90431,9 +86771,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -90498,9 +86835,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -90564,10 +86898,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -90632,9 +86963,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -90666,11 +86994,11 @@
       <td></td>
       <td></td>
       <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -90699,9 +87027,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -90765,10 +87090,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -90796,7 +87118,7 @@
       <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker</td>
       <td></td>
       <td>searchgui</td>
-      <td>4.3.9</td>
+      <td>4.3.11</td>
       <td></td>
       <td></td>
       <td>4</td>
@@ -90832,10 +87154,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>4</td>
       <td>2</td>
       <td>0</td>
@@ -90905,9 +87224,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -90930,7 +87246,7 @@
       <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator</td>
       <td>3.5</td>
       <td>percolator</td>
-      <td>3.6.5</td>
+      <td>3.7.1</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -90967,9 +87283,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
@@ -91039,9 +87352,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -91079,8 +87389,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -91108,7 +87416,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -91173,9 +87480,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -91240,9 +87544,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -91307,9 +87608,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -91362,8 +87660,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -91376,7 +87672,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -91441,9 +87736,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -91503,9 +87795,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -91570,9 +87859,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -91637,9 +87923,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -91704,9 +87987,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -91771,9 +88051,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -91838,9 +88115,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -91905,9 +88179,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -91972,9 +88243,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -92039,9 +88307,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -92110,9 +88375,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>15</td>
     </tr>
     <tr>
@@ -92178,9 +88440,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -92245,9 +88504,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -92312,9 +88568,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -92374,9 +88627,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -92402,7 +88652,7 @@
       <td>climate</td>
       <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps</td>
       <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps</td>
-      <td>1.2.1</td>
+      <td>1.3.1</td>
       <td>python</td>
       <td></td>
       <td></td>
@@ -92441,9 +88691,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -92507,10 +88754,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>6</td>
       <td>6</td>
       <td>0</td>
@@ -92520,7 +88764,7 @@
     <tr>
       <td></td>
       <td>pyscenic</td>
-      <td>pyscenic_aucell, pyscenic_ctx, pyscenic_grn</td>
+      <td>pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn</td>
       <td>PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/</td>
       <td></td>
       <td></td>
@@ -92580,9 +88824,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -92605,7 +88846,7 @@
       <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics</td>
       <td>4.4.1</td>
       <td>pyteomics</td>
-      <td>4.7.3</td>
+      <td>4.7.4</td>
       <td>Protein identification</td>
       <td>Proteomics, Proteomics experiment</td>
       <td>0</td>
@@ -92642,9 +88883,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -92709,9 +88947,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -92781,9 +89016,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -92843,9 +89075,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -92910,9 +89139,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -92982,9 +89208,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -93005,7 +89228,7 @@
       <td>galaxyp</td>
       <td>hhttps://github.com/npinter/ROIsplitter</td>
       <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter</td>
-      <td>0.3.1</td>
+      <td>0.3.2</td>
       <td>geojson</td>
       <td></td>
       <td></td>
@@ -93044,9 +89267,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -93111,9 +89331,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -93178,9 +89395,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -93250,9 +89464,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -93273,9 +89484,9 @@
       <td>recetox</td>
       <td>https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms</td>
       <td>https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms</td>
-      <td>0.13.2</td>
+      <td>0.13.3</td>
       <td>r-recetox-aplcms</td>
-      <td>0.13.2</td>
+      <td>0.13.3</td>
       <td>Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment</td>
       <td>Metabolomics</td>
       <td>0</td>
@@ -93312,9 +89523,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>8</td>
       <td>0</td>
       <td>0</td>
@@ -93384,9 +89592,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -93446,9 +89651,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -93488,10 +89690,8 @@
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -93514,8 +89714,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -93579,10 +89778,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>6</td>
       <td>7</td>
       <td>7</td>
       <td>0</td>
@@ -93652,9 +89848,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -93719,9 +89912,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -93774,8 +89964,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -93788,7 +89976,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -93853,9 +90040,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -93920,9 +90104,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -93987,9 +90168,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -94054,9 +90232,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -94079,7 +90254,7 @@
       <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam</td>
       <td>0.0.2</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -94116,9 +90291,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -94183,9 +90355,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -94250,9 +90419,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -94310,8 +90476,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -94319,7 +90483,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -94387,9 +90550,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>86</td>
       <td>561</td>
     </tr>
@@ -94444,8 +90604,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -94458,7 +90616,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -94504,8 +90661,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -94525,7 +90680,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -94588,9 +90742,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>9</td>
     </tr>
@@ -94657,9 +90808,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -94719,9 +90867,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>14</td>
       <td>13</td>
       <td>0</td>
@@ -94785,10 +90930,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -94856,9 +90998,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>110</td>
     </tr>
@@ -94913,8 +91052,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -94925,7 +91062,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>90</td>
       <td>721</td>
     </tr>
@@ -94987,9 +91123,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -95057,9 +91190,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>25</td>
     </tr>
@@ -95126,9 +91256,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -95193,9 +91320,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -95241,8 +91365,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -95262,7 +91384,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -95276,7 +91397,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
       <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
       <td>suite_seurat</td>
@@ -95285,7 +91406,7 @@
       <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat</td>
       <td>4.0.0</td>
       <td>seurat-scripts</td>
-      <td>4.0.0</td>
+      <td>4.4.0</td>
       <td></td>
       <td></td>
       <td>14</td>
@@ -95315,8 +91436,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>19</td>
       <td>0</td>
       <td>0</td>
@@ -95327,7 +91446,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>181</td>
       <td>1966</td>
     </tr>
@@ -95394,9 +91512,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -95456,9 +91571,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -95509,8 +91621,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -95525,7 +91635,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
@@ -95583,8 +91692,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -95597,7 +91704,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -95642,8 +91748,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -95664,7 +91768,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -95709,8 +91812,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -95731,7 +91832,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -95796,9 +91896,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -95863,9 +91960,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -95911,8 +92005,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -95932,7 +92024,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -95997,9 +92088,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -96064,9 +92152,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -96131,9 +92216,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -96192,10 +92274,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -96245,8 +92324,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -96267,7 +92344,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -96312,8 +92388,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -96334,7 +92408,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -96394,9 +92467,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>7</td>
       <td>0</td>
       <td>0</td>
@@ -96461,9 +92531,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -96533,9 +92600,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -96600,9 +92664,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -96646,8 +92707,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -96664,7 +92723,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -96728,10 +92786,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -96796,9 +92851,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -96863,9 +92915,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -96914,8 +92963,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -96931,8 +92978,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -96997,9 +93043,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -97069,9 +93112,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -97097,16 +93137,13 @@
       <td>1.0</td>
       <td></td>
       <td></td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -97203,9 +93240,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -97270,9 +93304,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -97337,6 +93368,67 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vibrant</td>
+      <td>vibrant</td>
+      <td>Virus Identification By iteRative ANnoTation</td>
+      <td>VIBRANT</td>
+      <td>VIBRANT</td>
+      <td></td>
+      <td>VIBRANT</td>
+      <td>Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions</td>
+      <td>Sequence trimming, Scaffolding, Genome annotation</td>
+      <td>Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/AnantharamanLab/VIBRANT</td>
+      <td>Metagenomics</td>
+      <td>vibrant</td>
+      <td>ufz</td>
+      <td>https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant</td>
+      <td>1.2.1</td>
+      <td>vibrant</td>
+      <td>1.2.1</td>
+      <td>Sequence trimming, Scaffolding, Genome annotation</td>
+      <td>Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -97399,9 +93491,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
@@ -97471,9 +93560,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -97538,9 +93624,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -97600,9 +93683,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -97667,9 +93747,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
       <td>2</td>
       <td>0</td>
@@ -97734,9 +93811,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -97806,9 +93880,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -97873,9 +93944,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -97920,8 +93988,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -97942,7 +94008,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -98007,9 +94072,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -98074,9 +94136,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
     </tr>
   </tbody>
 </table>
diff --git a/communities/all/resources/tools.json b/communities/all/resources/tools.json
index 733dcf0f..c1da03fe 100644
--- a/communities/all/resources/tools.json
+++ b/communities/all/resources/tools.json
@@ -35,10 +35,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -61,7 +59,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -106,10 +103,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -132,7 +127,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -176,10 +170,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -202,8 +194,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -264,10 +255,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -290,7 +279,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -334,10 +322,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -360,7 +346,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -404,10 +389,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -430,7 +413,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -474,10 +456,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -500,7 +480,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -558,10 +537,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -584,7 +561,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -628,10 +604,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -654,7 +628,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -698,10 +671,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -724,7 +695,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -768,10 +738,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -794,7 +762,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -838,10 +805,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -864,7 +829,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -911,10 +875,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 4,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -937,7 +899,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -983,10 +944,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -1009,7 +968,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 3,
@@ -1053,10 +1011,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -1079,7 +1035,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -1136,10 +1091,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -1162,7 +1115,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -1206,10 +1158,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -1232,7 +1182,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -1276,10 +1225,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -1302,7 +1249,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -1363,10 +1309,8 @@
     "Tools available on UseGalaxy.eu": 7,
     "Tools available on UseGalaxy.fr": 7,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -1389,7 +1333,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 7,
     "Tools available on UseGalaxy.no": 7,
@@ -1433,10 +1376,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -1459,7 +1400,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -1503,10 +1443,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -1529,8 +1467,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -1573,10 +1510,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -1599,7 +1534,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -1643,10 +1577,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -1669,7 +1601,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -1713,10 +1644,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -1739,7 +1668,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -1799,10 +1727,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -1825,8 +1751,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -1869,10 +1794,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -1895,7 +1818,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -1939,10 +1861,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -1965,7 +1885,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -2009,10 +1928,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -2035,7 +1952,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -2079,10 +1995,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -2105,7 +2019,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -2150,10 +2063,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -2176,7 +2087,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -2220,10 +2130,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -2246,7 +2154,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -2290,10 +2197,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -2316,7 +2221,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -2360,10 +2264,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -2386,7 +2288,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -2430,10 +2331,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -2456,7 +2355,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -2500,10 +2398,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -2526,7 +2422,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -2570,10 +2465,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -2596,7 +2489,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -2640,10 +2532,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -2666,7 +2556,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -2710,10 +2599,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -2736,7 +2623,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -2780,10 +2666,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -2806,7 +2690,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -2850,10 +2733,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -2876,7 +2757,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -2920,10 +2800,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -2946,8 +2824,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -2990,10 +2867,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -3016,7 +2891,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -3060,10 +2934,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -3086,7 +2958,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -3130,10 +3001,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -3156,7 +3025,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -3200,10 +3068,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -3226,7 +3092,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -3270,10 +3135,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -3296,7 +3159,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -3359,10 +3221,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -3385,7 +3245,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -3429,10 +3288,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -3455,7 +3312,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -3499,10 +3355,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -3525,7 +3379,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -3569,10 +3422,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -3595,7 +3446,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -3639,10 +3489,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -3665,7 +3513,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -3709,10 +3556,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -3735,7 +3580,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -3779,10 +3623,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -3805,7 +3647,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -3849,10 +3690,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -3875,7 +3714,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -3919,10 +3757,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -3945,7 +3781,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -3989,10 +3824,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -4015,7 +3848,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -4059,10 +3891,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -4085,7 +3915,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -4129,10 +3958,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -4155,7 +3982,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -4197,10 +4023,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -4223,7 +4047,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -4267,10 +4090,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -4293,7 +4114,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -4338,10 +4158,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -4364,7 +4182,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -4408,10 +4225,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -4434,8 +4249,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -4478,10 +4292,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -4504,7 +4316,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -4548,10 +4359,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -4574,8 +4383,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -4618,10 +4426,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -4644,7 +4450,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -4686,10 +4491,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -4712,7 +4515,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -4754,10 +4556,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -4780,7 +4580,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -4824,10 +4623,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -4850,7 +4647,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -4894,10 +4690,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -4920,7 +4714,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -4964,10 +4757,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -4990,7 +4781,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -5034,10 +4824,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -5060,7 +4848,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -5115,10 +4902,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 12,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -5141,7 +4926,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -5186,10 +4970,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -5212,7 +4994,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -5256,10 +5037,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -5282,7 +5061,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -5326,10 +5104,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -5352,7 +5128,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -5396,10 +5171,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -5422,7 +5195,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -5466,10 +5238,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -5492,7 +5262,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -5536,10 +5305,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -5562,7 +5329,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -5606,10 +5372,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -5632,7 +5396,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -5676,10 +5439,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -5702,7 +5463,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -5746,10 +5506,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -5772,8 +5530,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -5816,10 +5573,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -5842,7 +5597,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -5886,10 +5640,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -5912,7 +5664,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -5956,10 +5707,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -5982,7 +5731,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -6027,10 +5775,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -6053,8 +5799,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -6097,10 +5842,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -6123,7 +5866,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -6167,10 +5909,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -6193,7 +5933,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -6237,10 +5976,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -6263,7 +6000,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -6307,10 +6043,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -6333,7 +6067,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -6377,10 +6110,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -6403,7 +6134,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -6448,10 +6178,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -6474,7 +6202,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -6519,10 +6246,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -6545,7 +6270,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -6589,10 +6313,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -6615,7 +6337,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -6659,10 +6380,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -6685,7 +6404,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -6729,10 +6447,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -6755,7 +6471,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -6799,10 +6514,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -6825,7 +6538,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -6869,10 +6581,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -6895,7 +6605,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -6940,10 +6649,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -6966,7 +6673,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
@@ -7010,10 +6716,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -7036,7 +6740,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -7080,10 +6783,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -7106,7 +6807,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -7150,10 +6850,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -7176,7 +6874,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -7220,10 +6917,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -7246,7 +6941,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -7290,10 +6984,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -7316,7 +7008,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -7389,17 +7080,15 @@
     ],
     "Available on UseGalaxy.org (Main)": 9,
     "Available on UseGalaxy.org.au": 11,
-    "Available on UseGalaxy.eu": 10,
-    "Available on UseGalaxy.fr": 10,
+    "Available on UseGalaxy.eu": 12,
+    "Available on UseGalaxy.fr": 12,
     "Tools available on UseGalaxy.org (Main)": 9,
     "Tools available on UseGalaxy.org.au": 11,
-    "Tools available on UseGalaxy.eu": 10,
-    "Tools available on UseGalaxy.fr": 10,
+    "Tools available on UseGalaxy.eu": 12,
+    "Tools available on UseGalaxy.fr": 12,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -7422,8 +7111,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 6,
     "Tools available on UseGalaxy.cz": 10,
     "Tools available on UseGalaxy.no": 9,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -7466,10 +7154,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -7492,7 +7178,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -7536,10 +7221,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -7562,7 +7245,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -7606,10 +7288,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -7632,7 +7312,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -7686,10 +7365,8 @@
     "Tools available on UseGalaxy.eu": 10,
     "Tools available on UseGalaxy.fr": 11,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -7712,7 +7389,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 10,
     "Tools available on UseGalaxy.no": 10,
@@ -7756,10 +7432,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -7782,7 +7456,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -7834,10 +7507,8 @@
     "Tools available on UseGalaxy.eu": 9,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 8,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -7860,7 +7531,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 9,
     "Tools available on UseGalaxy.no": 9,
@@ -7904,10 +7574,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -7930,7 +7598,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -7999,10 +7666,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -8025,7 +7690,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -8069,10 +7733,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -8095,7 +7757,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -8139,10 +7800,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -8165,7 +7824,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -8209,10 +7867,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -8235,7 +7891,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -8300,10 +7955,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -8326,7 +7979,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -8370,10 +8022,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -8396,7 +8046,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -8440,10 +8089,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -8466,7 +8113,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -8510,10 +8156,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -8536,7 +8180,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -8600,10 +8243,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -8626,8 +8267,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -8690,10 +8330,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -8716,8 +8354,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -8772,10 +8409,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -8798,8 +8433,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -8862,10 +8496,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -8888,8 +8520,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -8932,10 +8563,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -8958,8 +8587,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -9002,10 +8630,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -9028,7 +8654,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -9072,10 +8697,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -9098,7 +8721,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -9142,10 +8764,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -9168,7 +8788,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -9213,10 +8832,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -9239,8 +8856,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -9295,10 +8911,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -9321,8 +8935,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -9377,10 +8990,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -9403,7 +9014,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -9448,10 +9058,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -9474,7 +9082,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -9530,10 +9137,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -9556,7 +9161,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -9600,10 +9204,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -9626,7 +9228,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -9682,10 +9283,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -9708,7 +9307,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -9764,10 +9362,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -9790,7 +9386,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -9846,10 +9441,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -9872,8 +9465,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -9910,17 +9502,15 @@
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
     "Available on UseGalaxy.org.au": 0,
-    "Available on UseGalaxy.eu": 1,
+    "Available on UseGalaxy.eu": 0,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
     "Tools available on UseGalaxy.org.au": 0,
-    "Tools available on UseGalaxy.eu": 1,
+    "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -9943,7 +9533,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -9999,10 +9588,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -10025,7 +9612,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -10081,10 +9667,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -10107,7 +9691,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -10151,10 +9734,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -10177,8 +9758,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -10221,10 +9801,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -10247,7 +9825,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -10303,10 +9880,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -10329,7 +9904,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -10385,10 +9959,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -10411,7 +9983,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -10467,10 +10038,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -10493,7 +10062,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -10549,10 +10117,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -10575,7 +10141,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -10631,10 +10196,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -10657,7 +10220,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -10701,10 +10263,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -10727,7 +10287,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -10783,10 +10342,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -10809,7 +10366,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -10853,10 +10409,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -10879,7 +10433,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -10923,10 +10476,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -10949,7 +10500,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -11005,10 +10555,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -11031,7 +10579,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -11087,10 +10634,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -11113,7 +10658,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -11179,10 +10723,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -11205,7 +10747,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -11242,7 +10783,7 @@
     "Galaxy wrapper owner": "imgteam",
     "Galaxy wrapper source": "https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/",
     "Galaxy wrapper parsed folder": "https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage",
-    "Galaxy wrapper version": "0.2",
+    "Galaxy wrapper version": "0.3",
     "Conda id": "scikit-image",
     "Conda version": null,
     "EDAM operation (no superclasses)": [
@@ -11254,17 +10795,15 @@
     ],
     "Available on UseGalaxy.org (Main)": 0,
     "Available on UseGalaxy.org.au": 0,
-    "Available on UseGalaxy.eu": 1,
+    "Available on UseGalaxy.eu": 0,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
     "Tools available on UseGalaxy.org.au": 0,
-    "Tools available on UseGalaxy.eu": 1,
+    "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -11287,7 +10826,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -11324,8 +10862,8 @@
     "Galaxy wrapper owner": "imgteam",
     "Galaxy wrapper source": "https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/",
     "Galaxy wrapper parsed folder": "https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage",
-    "Galaxy wrapper version": "0.3-2",
-    "Conda id": "numpy",
+    "Galaxy wrapper version": "0.4",
+    "Conda id": "scikit-image",
     "Conda version": null,
     "EDAM operation (no superclasses)": [
       "Image analysis"
@@ -11343,10 +10881,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -11369,7 +10905,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -11425,10 +10960,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -11451,7 +10984,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -11507,10 +11039,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -11533,7 +11063,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -11589,10 +11118,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -11615,7 +11142,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -11671,10 +11197,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -11697,7 +11221,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -11755,10 +11278,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -11781,7 +11302,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -11845,10 +11365,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -11871,7 +11389,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -11921,10 +11438,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -11947,7 +11462,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -12003,10 +11517,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -12029,7 +11541,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -12085,10 +11596,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -12111,7 +11620,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -12148,9 +11656,9 @@
     "Galaxy wrapper owner": "imgteam",
     "Galaxy wrapper source": "https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/",
     "Galaxy wrapper parsed folder": "https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d",
-    "Galaxy wrapper version": "0.0.3-2",
-    "Conda id": "imageio",
-    "Conda version": null,
+    "Galaxy wrapper version": "0.1",
+    "Conda id": "giatools",
+    "Conda version": "0.3.1",
     "EDAM operation (no superclasses)": [
       "Image analysis"
     ],
@@ -12167,10 +11675,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -12193,7 +11699,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -12229,7 +11734,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm",
     "Galaxy wrapper version": "0.2.0",
     "Conda id": "superdsm",
-    "Conda version": "0.3.0",
+    "Conda version": "0.4.0",
     "EDAM operation (no superclasses)": [
       "Image analysis"
     ],
@@ -12243,10 +11748,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -12269,7 +11772,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -12313,10 +11815,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -12339,8 +11839,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -12383,10 +11882,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -12409,7 +11906,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -12473,10 +11969,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -12499,7 +11993,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -12543,10 +12036,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -12569,7 +12060,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -12613,10 +12103,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -12639,7 +12127,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -12683,10 +12170,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -12709,7 +12194,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -12753,10 +12237,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -12779,7 +12261,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -12823,10 +12304,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -12849,7 +12328,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -12893,10 +12371,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -12919,7 +12395,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -12967,10 +12442,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -12993,7 +12466,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 0,
@@ -13043,10 +12515,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -13069,7 +12539,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 0,
@@ -13118,10 +12587,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 4,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -13144,7 +12611,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 0,
@@ -13193,10 +12659,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 4,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -13219,7 +12683,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 0,
@@ -13267,10 +12730,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -13293,7 +12754,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 0,
@@ -13347,10 +12807,8 @@
     "Tools available on UseGalaxy.eu": 6,
     "Tools available on UseGalaxy.fr": 6,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -13373,7 +12831,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 6,
     "Tools available on UseGalaxy.no": 0,
@@ -13434,17 +12891,15 @@
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 21,
     "Available on UseGalaxy.org.au": 21,
-    "Available on UseGalaxy.eu": 21,
+    "Available on UseGalaxy.eu": 22,
     "Available on UseGalaxy.fr": 21,
     "Tools available on UseGalaxy.org (Main)": 21,
     "Tools available on UseGalaxy.org.au": 21,
-    "Tools available on UseGalaxy.eu": 21,
+    "Tools available on UseGalaxy.eu": 22,
     "Tools available on UseGalaxy.fr": 21,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -13467,7 +12922,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 21,
     "Tools available on UseGalaxy.no": 0,
@@ -13524,10 +12978,8 @@
     "Tools available on UseGalaxy.eu": 12,
     "Tools available on UseGalaxy.fr": 12,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -13550,7 +13002,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 12,
     "Tools available on UseGalaxy.no": 0,
@@ -13598,10 +13049,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -13624,7 +13073,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 0,
@@ -13680,10 +13128,8 @@
     "Tools available on UseGalaxy.eu": 10,
     "Tools available on UseGalaxy.fr": 10,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -13706,7 +13152,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 10,
     "Tools available on UseGalaxy.no": 0,
@@ -13773,10 +13218,8 @@
     "Tools available on UseGalaxy.eu": 17,
     "Tools available on UseGalaxy.fr": 17,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -13799,7 +13242,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 17,
     "Tools available on UseGalaxy.no": 0,
@@ -13847,10 +13289,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -13873,7 +13313,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 0,
@@ -13929,10 +13368,8 @@
     "Tools available on UseGalaxy.eu": 11,
     "Tools available on UseGalaxy.fr": 11,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -13955,7 +13392,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 11,
     "Tools available on UseGalaxy.no": 0,
@@ -14004,10 +13440,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -14030,7 +13464,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 0,
@@ -14087,10 +13520,8 @@
     "Tools available on UseGalaxy.eu": 12,
     "Tools available on UseGalaxy.fr": 12,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -14113,7 +13544,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 12,
     "Tools available on UseGalaxy.no": 0,
@@ -14168,10 +13598,8 @@
     "Tools available on UseGalaxy.eu": 6,
     "Tools available on UseGalaxy.fr": 6,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -14194,7 +13622,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 6,
     "Tools available on UseGalaxy.no": 0,
@@ -14240,10 +13667,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -14266,7 +13691,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -14336,10 +13760,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -14362,7 +13784,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -14422,10 +13843,8 @@
     "Tools available on UseGalaxy.eu": 15,
     "Tools available on UseGalaxy.fr": 15,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -14448,7 +13867,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 15,
     "Tools available on UseGalaxy.no": 0,
@@ -14497,10 +13915,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 4,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -14523,7 +13939,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 0,
@@ -14576,10 +13991,8 @@
     "Tools available on UseGalaxy.eu": 8,
     "Tools available on UseGalaxy.fr": 7,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -14602,7 +14015,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 8,
     "Tools available on UseGalaxy.no": 0,
@@ -14650,10 +14062,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -14676,7 +14086,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -14720,10 +14129,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -14746,7 +14153,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -14790,10 +14196,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 1,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 1,
+    "Tools available on ARGs-OAP": 1,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 1,
     "Tools available on CoralSNP": 1,
@@ -14816,84 +14220,13 @@
     "Tools available on Oqtans": 1,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 1,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 1,
     "No. of tool users (2022-2023) (usegalaxy.eu)": 591,
     "Total tool usage (usegalaxy.eu)": 367167
   },
-  {
-    "Galaxy wrapper id": "annotation_profiler",
-    "Galaxy tool ids": [
-      "Annotation_Profiler_0"
-    ],
-    "Description": "Profile Annotations for a set of genomic intervals",
-    "bio.tool id": null,
-    "bio.tool ids": [],
-    "biii": null,
-    "bio.tool name": null,
-    "bio.tool description": null,
-    "EDAM operation": [],
-    "EDAM topic": [],
-    "Status": "To update",
-    "Source": null,
-    "ToolShed categories": [
-      "Genomic Interval Operations"
-    ],
-    "ToolShed id": "annotation_profiler",
-    "Galaxy wrapper owner": "devteam",
-    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/annotation_profiler",
-    "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/annotation_profiler",
-    "Galaxy wrapper version": "1.0.0",
-    "Conda id": "bx-python",
-    "Conda version": "0.12.0",
-    "EDAM operation (no superclasses)": [],
-    "EDAM topic (no superclasses)": [],
-    "Available on UseGalaxy.org (Main)": 1,
-    "Available on UseGalaxy.org.au": 0,
-    "Available on UseGalaxy.eu": 1,
-    "Available on UseGalaxy.fr": 0,
-    "Tools available on UseGalaxy.org (Main)": 1,
-    "Tools available on UseGalaxy.org.au": 0,
-    "Tools available on UseGalaxy.eu": 1,
-    "Tools available on UseGalaxy.fr": 0,
-    "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
-    "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
-    "Tools available on ChemFlow": 0,
-    "Tools available on Coloc-stats": 0,
-    "Tools available on CoralSNP": 0,
-    "Tools available on CropGalaxy": 0,
-    "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
-    "Tools available on GASLINI": 0,
-    "Tools available on Galaxy@AuBi": 0,
-    "Tools available on Galaxy@Pasteur": 0,
-    "Tools available on GalaxyTrakr": 0,
-    "Tools available on Genomic Hyperbrowser": 0,
-    "Tools available on GigaGalaxy": 0,
-    "Tools available on HyPhy HIV NGS Tools": 0,
-    "Tools available on IPK Galaxy Blast Suite": 0,
-    "Tools available on ImmPort Galaxy": 0,
-    "Tools available on InteractoMIX": 0,
-    "Tools available on MISSISSIPPI": 0,
-    "Tools available on Mandoiu Lab": 0,
-    "Tools available on MiModD NacreousMap": 0,
-    "Tools available on Oqtans": 0,
-    "Tools available on Palfinder": 0,
-    "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
-    "Tools available on UseGalaxy.cz": 1,
-    "Tools available on UseGalaxy.no": 1,
-    "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
-    "Total tool usage (usegalaxy.eu)": 2
-  },
   {
     "Galaxy wrapper id": "best_regression_subsets",
     "Galaxy tool ids": [
@@ -14931,10 +14264,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -14957,8 +14288,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -15002,10 +14332,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -15028,7 +14356,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -15073,10 +14400,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -15099,7 +14424,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -15143,10 +14467,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -15169,8 +14491,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -15213,10 +14534,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -15239,8 +14558,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -15283,10 +14601,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -15309,8 +14625,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -15353,10 +14668,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -15379,8 +14692,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -15424,10 +14736,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -15450,7 +14760,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -15494,10 +14803,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 1,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 1,
+    "Tools available on ARGs-OAP": 1,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 1,
     "Tools available on CoralSNP": 1,
@@ -15520,8 +14827,7 @@
     "Tools available on Oqtans": 1,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 1,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 1,
@@ -15565,10 +14871,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -15591,8 +14895,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -15636,10 +14939,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -15662,8 +14963,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -15706,10 +15006,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -15732,7 +15030,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -15776,10 +15073,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -15802,7 +15097,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -15846,10 +15140,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 1,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 1,
+    "Tools available on ARGs-OAP": 1,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 1,
     "Tools available on Coloc-stats": 1,
     "Tools available on CoralSNP": 1,
@@ -15872,8 +15164,7 @@
     "Tools available on Oqtans": 1,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 1,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 1,
@@ -15916,10 +15207,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -15942,7 +15231,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -15986,10 +15274,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -16012,8 +15298,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -16056,10 +15341,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -16082,8 +15365,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -16126,10 +15408,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -16152,8 +15432,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -16197,10 +15476,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -16223,8 +15500,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -16268,10 +15544,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -16294,8 +15568,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -16338,10 +15611,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 1,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 1,
+    "Tools available on ARGs-OAP": 1,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 1,
     "Tools available on CoralSNP": 1,
@@ -16364,8 +15635,7 @@
     "Tools available on Oqtans": 1,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 1,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 1,
@@ -16408,10 +15678,143 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
+    "Tools available on CIRM-CFBP": 0,
+    "Tools available on ChemFlow": 0,
+    "Tools available on Coloc-stats": 0,
+    "Tools available on CoralSNP": 0,
+    "Tools available on CropGalaxy": 0,
+    "Tools available on Dintor": 0,
+    "Tools available on FreeBioinfo": 0,
+    "Tools available on GASLINI": 0,
+    "Tools available on Galaxy@AuBi": 0,
+    "Tools available on Galaxy@Pasteur": 0,
+    "Tools available on GalaxyTrakr": 0,
+    "Tools available on Genomic Hyperbrowser": 0,
+    "Tools available on GigaGalaxy": 0,
+    "Tools available on HyPhy HIV NGS Tools": 0,
+    "Tools available on IPK Galaxy Blast Suite": 0,
+    "Tools available on ImmPort Galaxy": 0,
+    "Tools available on InteractoMIX": 0,
+    "Tools available on MISSISSIPPI": 0,
+    "Tools available on Mandoiu Lab": 0,
+    "Tools available on MiModD NacreousMap": 0,
+    "Tools available on Oqtans": 0,
+    "Tools available on Palfinder": 0,
+    "Tools available on PepSimili": 0,
+    "Tools available on UseGalaxy.be": 1,
+    "Tools available on UseGalaxy.cz": 1,
+    "Tools available on UseGalaxy.no": 1,
+    "Tools available on Viral Variant Visualizer (VVV)": 0,
+    "No. of tool users (2022-2023) (usegalaxy.eu)": 2,
+    "Total tool usage (usegalaxy.eu)": 39
+  },
+  {
+    "Galaxy wrapper id": "dgidb_annotator",
+    "Galaxy tool ids": [
+      "dgidb_annotate"
+    ],
+    "Description": "Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)",
+    "bio.tool id": null,
+    "bio.tool ids": [],
+    "biii": null,
+    "bio.tool name": null,
+    "bio.tool description": null,
+    "EDAM operation": [],
+    "EDAM topic": [],
+    "Status": "To update",
+    "Source": null,
+    "ToolShed categories": [
+      "Systems Biology",
+      "Variant Analysis"
+    ],
+    "ToolShed id": "dgidb_annotator",
+    "Galaxy wrapper owner": "devteam",
+    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator",
+    "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator",
+    "Galaxy wrapper version": "0.1",
+    "Conda id": null,
+    "Conda version": null,
+    "EDAM operation (no superclasses)": [],
+    "EDAM topic (no superclasses)": [],
+    "Available on UseGalaxy.org (Main)": 0,
+    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.eu": 1,
+    "Available on UseGalaxy.fr": 0,
+    "Tools available on UseGalaxy.org (Main)": 0,
+    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.eu": 1,
+    "Tools available on UseGalaxy.fr": 0,
+    "Tools available on APOSTL": 0,
+    "Tools available on ARGs-OAP": 0,
+    "Tools available on CIRM-CFBP": 0,
+    "Tools available on ChemFlow": 0,
+    "Tools available on Coloc-stats": 0,
+    "Tools available on CoralSNP": 0,
+    "Tools available on CropGalaxy": 0,
+    "Tools available on Dintor": 0,
+    "Tools available on FreeBioinfo": 0,
+    "Tools available on GASLINI": 0,
+    "Tools available on Galaxy@AuBi": 0,
+    "Tools available on Galaxy@Pasteur": 0,
+    "Tools available on GalaxyTrakr": 0,
+    "Tools available on Genomic Hyperbrowser": 0,
+    "Tools available on GigaGalaxy": 0,
+    "Tools available on HyPhy HIV NGS Tools": 0,
+    "Tools available on IPK Galaxy Blast Suite": 0,
+    "Tools available on ImmPort Galaxy": 0,
+    "Tools available on InteractoMIX": 0,
+    "Tools available on MISSISSIPPI": 0,
+    "Tools available on Mandoiu Lab": 0,
+    "Tools available on MiModD NacreousMap": 0,
+    "Tools available on Oqtans": 0,
+    "Tools available on Palfinder": 0,
+    "Tools available on PepSimili": 0,
+    "Tools available on UseGalaxy.be": 1,
+    "Tools available on UseGalaxy.cz": 1,
+    "Tools available on UseGalaxy.no": 1,
+    "Tools available on Viral Variant Visualizer (VVV)": 0,
+    "No. of tool users (2022-2023) (usegalaxy.eu)": 7,
+    "Total tool usage (usegalaxy.eu)": 65
+  },
+  {
+    "Galaxy wrapper id": "divide_pg_snp",
+    "Galaxy tool ids": [
+      "dividePgSnp"
+    ],
+    "Description": "Separate pgSnp alleles into columns",
+    "bio.tool id": null,
+    "bio.tool ids": [],
+    "biii": null,
+    "bio.tool name": null,
+    "bio.tool description": null,
+    "EDAM operation": [],
+    "EDAM topic": [],
+    "Status": "To update",
+    "Source": null,
+    "ToolShed categories": [
+      "Sequence Analysis"
+    ],
+    "ToolShed id": "divide_pg_snp",
+    "Galaxy wrapper owner": "devteam",
+    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp",
+    "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp",
+    "Galaxy wrapper version": "1.0.0",
+    "Conda id": null,
+    "Conda version": null,
+    "EDAM operation (no superclasses)": [],
+    "EDAM topic (no superclasses)": [],
+    "Available on UseGalaxy.org (Main)": 1,
+    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.eu": 1,
+    "Available on UseGalaxy.fr": 0,
+    "Tools available on UseGalaxy.org (Main)": 1,
+    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.eu": 1,
+    "Tools available on UseGalaxy.fr": 0,
+    "Tools available on APOSTL": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -16434,149 +15837,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
-    "Tools available on UseGalaxy.cz": 1,
-    "Tools available on UseGalaxy.no": 1,
-    "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 2,
-    "Total tool usage (usegalaxy.eu)": 39
-  },
-  {
-    "Galaxy wrapper id": "dgidb_annotator",
-    "Galaxy tool ids": [
-      "dgidb_annotate"
-    ],
-    "Description": "Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)",
-    "bio.tool id": null,
-    "bio.tool ids": [],
-    "biii": null,
-    "bio.tool name": null,
-    "bio.tool description": null,
-    "EDAM operation": [],
-    "EDAM topic": [],
-    "Status": "To update",
-    "Source": null,
-    "ToolShed categories": [
-      "Systems Biology",
-      "Variant Analysis"
-    ],
-    "ToolShed id": "dgidb_annotator",
-    "Galaxy wrapper owner": "devteam",
-    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator",
-    "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator",
-    "Galaxy wrapper version": "0.1",
-    "Conda id": null,
-    "Conda version": null,
-    "EDAM operation (no superclasses)": [],
-    "EDAM topic (no superclasses)": [],
-    "Available on UseGalaxy.org (Main)": 0,
-    "Available on UseGalaxy.org.au": 0,
-    "Available on UseGalaxy.eu": 1,
-    "Available on UseGalaxy.fr": 0,
-    "Tools available on UseGalaxy.org (Main)": 0,
-    "Tools available on UseGalaxy.org.au": 0,
-    "Tools available on UseGalaxy.eu": 1,
-    "Tools available on UseGalaxy.fr": 0,
-    "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
-    "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
-    "Tools available on ChemFlow": 0,
-    "Tools available on Coloc-stats": 0,
-    "Tools available on CoralSNP": 0,
-    "Tools available on CropGalaxy": 0,
-    "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
-    "Tools available on GASLINI": 0,
-    "Tools available on Galaxy@AuBi": 0,
-    "Tools available on Galaxy@Pasteur": 0,
-    "Tools available on GalaxyTrakr": 0,
-    "Tools available on Genomic Hyperbrowser": 0,
-    "Tools available on GigaGalaxy": 0,
-    "Tools available on HyPhy HIV NGS Tools": 0,
-    "Tools available on IPK Galaxy Blast Suite": 0,
-    "Tools available on ImmPort Galaxy": 0,
-    "Tools available on InteractoMIX": 0,
-    "Tools available on MISSISSIPPI": 0,
-    "Tools available on Mandoiu Lab": 0,
-    "Tools available on MiModD NacreousMap": 0,
-    "Tools available on Oqtans": 0,
-    "Tools available on Palfinder": 0,
-    "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
-    "Tools available on UseGalaxy.cz": 1,
-    "Tools available on UseGalaxy.no": 1,
-    "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 7,
-    "Total tool usage (usegalaxy.eu)": 65
-  },
-  {
-    "Galaxy wrapper id": "divide_pg_snp",
-    "Galaxy tool ids": [
-      "dividePgSnp"
-    ],
-    "Description": "Separate pgSnp alleles into columns",
-    "bio.tool id": null,
-    "bio.tool ids": [],
-    "biii": null,
-    "bio.tool name": null,
-    "bio.tool description": null,
-    "EDAM operation": [],
-    "EDAM topic": [],
-    "Status": "To update",
-    "Source": null,
-    "ToolShed categories": [
-      "Sequence Analysis"
-    ],
-    "ToolShed id": "divide_pg_snp",
-    "Galaxy wrapper owner": "devteam",
-    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp",
-    "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp",
-    "Galaxy wrapper version": "1.0.0",
-    "Conda id": null,
-    "Conda version": null,
-    "EDAM operation (no superclasses)": [],
-    "EDAM topic (no superclasses)": [],
-    "Available on UseGalaxy.org (Main)": 1,
-    "Available on UseGalaxy.org.au": 0,
-    "Available on UseGalaxy.eu": 1,
-    "Available on UseGalaxy.fr": 0,
-    "Tools available on UseGalaxy.org (Main)": 1,
-    "Tools available on UseGalaxy.org.au": 0,
-    "Tools available on UseGalaxy.eu": 1,
-    "Tools available on UseGalaxy.fr": 0,
-    "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
-    "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
-    "Tools available on ChemFlow": 0,
-    "Tools available on Coloc-stats": 0,
-    "Tools available on CoralSNP": 0,
-    "Tools available on CropGalaxy": 0,
-    "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
-    "Tools available on GASLINI": 0,
-    "Tools available on Galaxy@AuBi": 0,
-    "Tools available on Galaxy@Pasteur": 0,
-    "Tools available on GalaxyTrakr": 0,
-    "Tools available on Genomic Hyperbrowser": 0,
-    "Tools available on GigaGalaxy": 0,
-    "Tools available on HyPhy HIV NGS Tools": 0,
-    "Tools available on IPK Galaxy Blast Suite": 0,
-    "Tools available on ImmPort Galaxy": 0,
-    "Tools available on InteractoMIX": 0,
-    "Tools available on MISSISSIPPI": 0,
-    "Tools available on Mandoiu Lab": 0,
-    "Tools available on MiModD NacreousMap": 0,
-    "Tools available on Oqtans": 0,
-    "Tools available on Palfinder": 0,
-    "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -16620,10 +15881,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -16646,8 +15905,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -16690,10 +15948,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -16716,7 +15972,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -16760,10 +16015,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -16786,7 +16039,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -16830,10 +16082,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -16856,7 +16106,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -16900,10 +16149,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -16926,7 +16173,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -16970,10 +16216,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -16996,8 +16240,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -17040,10 +16283,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -17066,8 +16307,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -17110,10 +16350,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -17136,8 +16374,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -17168,7 +16405,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species",
     "Galaxy wrapper version": "0.0.1",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -17180,10 +16417,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -17206,8 +16441,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -17250,10 +16484,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -17276,8 +16508,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -17320,10 +16551,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -17346,8 +16575,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -17390,10 +16618,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -17416,8 +16642,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -17461,10 +16686,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -17487,7 +16710,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -17520,7 +16742,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter",
     "Galaxy wrapper version": "2.0.0",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -17532,10 +16754,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -17558,8 +16778,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -17602,10 +16821,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -17628,8 +16845,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -17672,10 +16888,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -17698,8 +16912,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -17731,7 +16944,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way",
     "Galaxy wrapper version": "1.0.0",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -17743,10 +16956,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -17769,7 +16980,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -17814,10 +17024,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -17840,7 +17048,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -17884,10 +17091,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -17910,8 +17115,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -17954,10 +17158,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -17980,7 +17182,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -18025,10 +17226,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -18051,8 +17250,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -18095,10 +17293,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -18121,8 +17317,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -18165,10 +17360,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -18191,8 +17384,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -18235,10 +17427,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -18261,8 +17451,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -18305,10 +17494,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -18331,8 +17518,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -18376,10 +17562,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -18402,8 +17586,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -18446,10 +17629,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -18472,7 +17653,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -18518,10 +17698,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -18544,7 +17722,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -18577,7 +17754,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter",
     "Galaxy wrapper version": "1.0.0",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -18589,10 +17766,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -18615,7 +17790,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -18661,10 +17835,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -18687,7 +17859,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -18732,10 +17903,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -18758,8 +17927,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -18802,10 +17970,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 1,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 1,
+    "Tools available on ARGs-OAP": 1,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 1,
     "Tools available on CoralSNP": 1,
@@ -18828,8 +17994,7 @@
     "Tools available on Oqtans": 1,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 1,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 1,
@@ -18872,10 +18037,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -18898,7 +18061,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -18943,10 +18105,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -18969,7 +18129,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -19002,7 +18161,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability",
     "Galaxy wrapper version": "1.1.0",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -19014,10 +18173,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -19040,7 +18197,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -19084,10 +18240,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -19110,8 +18264,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -19155,10 +18308,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -19181,7 +18332,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -19225,10 +18375,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -19251,8 +18399,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -19295,10 +18442,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -19321,7 +18466,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -19365,10 +18509,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -19391,7 +18533,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -19435,10 +18576,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -19461,7 +18600,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -19493,7 +18631,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval",
     "Galaxy wrapper version": "1.0.3",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -19505,10 +18643,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -19531,8 +18667,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -19575,10 +18710,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -19601,8 +18734,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -19646,10 +18778,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -19672,8 +18802,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -19716,10 +18845,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -19742,8 +18869,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -19775,7 +18901,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter",
     "Galaxy wrapper version": "1.0.1",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -19787,10 +18913,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -19813,7 +18937,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -19858,10 +18981,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -19884,7 +19005,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -19928,10 +19048,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 1,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 1,
+    "Tools available on ARGs-OAP": 1,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 1,
     "Tools available on CoralSNP": 1,
@@ -19954,8 +19072,7 @@
     "Tools available on Oqtans": 1,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 1,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 1,
@@ -19998,10 +19115,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -20024,7 +19139,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -20068,10 +19182,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -20094,7 +19206,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -20138,10 +19249,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -20164,8 +19273,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -20208,10 +19316,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -20234,8 +19340,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -20279,10 +19384,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -20305,8 +19408,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -20350,10 +19452,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -20376,7 +19476,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -20421,10 +19520,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -20447,7 +19544,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -20491,10 +19587,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -20517,8 +19611,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -20561,10 +19654,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 1,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 1,
+    "Tools available on ARGs-OAP": 1,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 1,
     "Tools available on CoralSNP": 1,
@@ -20587,8 +19678,7 @@
     "Tools available on Oqtans": 1,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 1,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 1,
@@ -20631,10 +19721,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 1,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 1,
+    "Tools available on ARGs-OAP": 1,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 1,
     "Tools available on CoralSNP": 1,
@@ -20657,8 +19745,7 @@
     "Tools available on Oqtans": 1,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 1,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 1,
@@ -20701,10 +19788,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -20727,8 +19812,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -20771,10 +19855,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -20797,7 +19879,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -20842,10 +19923,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -20868,7 +19947,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -20901,7 +19979,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions",
     "Galaxy wrapper version": "1.0.1",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -20913,10 +19991,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -20939,7 +20015,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -20983,10 +20058,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -21009,8 +20082,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -21053,10 +20125,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -21079,7 +20149,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -21123,10 +20192,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -21149,8 +20216,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -21182,7 +20248,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat",
     "Galaxy wrapper version": "1.5.0",
     "Conda id": "samtools",
-    "Conda version": "1.20",
+    "Conda version": "1.21",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -21194,10 +20260,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -21220,7 +20284,6 @@
     "Tools available on Oqtans": 1,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -21265,10 +20328,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -21291,8 +20352,7 @@
     "Tools available on Oqtans": 1,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -21335,10 +20395,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -21361,8 +20419,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -21405,10 +20462,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 1,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 1,
+    "Tools available on ARGs-OAP": 1,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 1,
     "Tools available on CoralSNP": 1,
@@ -21431,8 +20486,7 @@
     "Tools available on Oqtans": 1,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 1,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 1,
@@ -21475,10 +20529,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -21501,8 +20553,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -21545,10 +20596,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -21571,7 +20620,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -21615,10 +20663,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -21641,8 +20687,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -21685,10 +20730,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -21711,7 +20754,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -21755,10 +20797,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -21781,7 +20821,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -21825,10 +20864,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -21851,8 +20888,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -21895,10 +20931,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -21921,7 +20955,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -21966,10 +20999,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -21992,7 +21023,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -22025,7 +21055,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter",
     "Galaxy wrapper version": "1.0.1",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -22037,10 +21067,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -22063,7 +21091,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -22108,10 +21135,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -22134,8 +21159,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -22166,7 +21190,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage",
     "Galaxy wrapper version": "1.0.0",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -22178,10 +21202,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -22204,8 +21226,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -22236,7 +21257,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster",
     "Galaxy wrapper version": "1.0.0",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -22248,10 +21269,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -22274,8 +21293,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -22306,7 +21324,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement",
     "Galaxy wrapper version": "1.0.0",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -22318,10 +21336,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -22344,8 +21360,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -22376,7 +21391,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat",
     "Galaxy wrapper version": "1.0.1",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -22388,10 +21403,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -22414,8 +21427,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -22446,7 +21458,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage",
     "Galaxy wrapper version": "1.0.0",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -22458,10 +21470,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -22484,8 +21494,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -22516,7 +21525,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features",
     "Galaxy wrapper version": "4.0.1",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -22528,10 +21537,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -22554,8 +21561,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -22586,7 +21592,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks",
     "Galaxy wrapper version": "1.0.0",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -22598,10 +21604,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -22624,8 +21628,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -22656,7 +21659,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect",
     "Galaxy wrapper version": "1.0.0",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -22668,10 +21671,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -22694,8 +21695,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -22726,7 +21726,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join",
     "Galaxy wrapper version": "1.0.0",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -22738,10 +21738,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -22764,8 +21762,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -22796,7 +21793,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge",
     "Galaxy wrapper version": "1.0.0",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -22808,10 +21805,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -22834,8 +21829,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -22866,7 +21860,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract",
     "Galaxy wrapper version": "1.0.0",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -22878,10 +21872,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -22904,8 +21896,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -22936,7 +21927,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query",
     "Galaxy wrapper version": "0.1",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -22948,10 +21939,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -22974,8 +21963,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -23018,10 +22006,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -23044,8 +22030,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -23088,10 +22073,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -23114,8 +22097,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -23159,10 +22141,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -23185,8 +22165,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -23230,10 +22209,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -23256,8 +22233,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -23288,7 +22264,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits",
     "Galaxy wrapper version": "1.0.0",
     "Conda id": "taxonomy",
-    "Conda version": null,
+    "Conda version": "0.10.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -23300,10 +22276,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -23326,8 +22300,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -23382,10 +22355,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -23408,8 +22379,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -23452,10 +22422,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -23478,8 +22446,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -23522,10 +22489,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -23548,8 +22513,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -23593,10 +22557,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -23619,8 +22581,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -23673,10 +22634,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -23699,8 +22658,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -23743,10 +22701,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -23769,8 +22725,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -23813,10 +22768,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -23839,8 +22792,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -23883,10 +22835,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -23909,8 +22859,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -23941,7 +22890,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus",
     "Galaxy wrapper version": "0.1.11",
     "Conda id": "samtools",
-    "Conda version": "1.20",
+    "Conda version": "1.21",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -23953,10 +22902,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -23979,7 +22926,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -24023,10 +22969,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -24049,8 +22993,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -24093,10 +23036,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -24119,8 +23060,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -24163,10 +23103,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -24189,8 +23127,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -24233,10 +23170,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -24259,8 +23194,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -24280,7 +23214,7 @@
     "bio.tool description": null,
     "EDAM operation": [],
     "EDAM topic": [],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "https://github.com/10XGenomics/bamtofastq",
     "ToolShed categories": [
       "Convert Formats"
@@ -24291,7 +23225,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq",
     "Galaxy wrapper version": "1.4.1",
     "Conda id": "10x_bamtofastq",
-    "Conda version": null,
+    "Conda version": "1.4.1",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -24303,10 +23237,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -24329,7 +23261,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -24373,10 +23304,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -24399,7 +23328,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -24443,10 +23371,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -24469,7 +23395,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 1,
@@ -24513,10 +23438,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -24539,7 +23462,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -24583,10 +23505,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -24609,7 +23529,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -24653,10 +23572,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -24679,7 +23596,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -24723,10 +23639,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -24749,7 +23663,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -24793,10 +23706,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -24819,7 +23730,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -24864,10 +23774,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -24890,7 +23798,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
@@ -24934,10 +23841,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -24960,7 +23865,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -25004,10 +23908,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -25030,7 +23932,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -25074,10 +23975,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -25100,7 +23999,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -25144,10 +24042,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -25170,7 +24066,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -25198,7 +24093,7 @@
     "EDAM topic": [
       "Genomics"
     ],
-    "Status": "Up-to-date",
+    "Status": "To update",
     "Source": "https://github.com/NBISweden/AGAT",
     "ToolShed categories": [
       "Convert Formats",
@@ -25211,7 +24106,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/agat",
     "Galaxy wrapper version": "1.4.0",
     "Conda id": "agat",
-    "Conda version": "1.4.0",
+    "Conda version": "1.4.1",
     "EDAM operation (no superclasses)": [
       "Data handling",
       "Genome annotation"
@@ -25228,10 +24123,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -25254,7 +24147,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -25314,10 +24206,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -25340,7 +24230,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -25384,10 +24273,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -25410,7 +24297,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -25454,10 +24340,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -25480,8 +24364,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -25524,10 +24407,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -25550,7 +24431,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -25595,10 +24475,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -25621,7 +24499,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -25665,10 +24542,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -25691,7 +24566,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -25726,7 +24600,7 @@
     "Galaxy wrapper owner": "bgruening",
     "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging",
     "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging",
-    "Galaxy wrapper version": "2.3.1",
+    "Galaxy wrapper version": "2.4.0",
     "Conda id": "python",
     "Conda version": null,
     "EDAM operation (no superclasses)": [],
@@ -25742,10 +24616,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -25768,7 +24640,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -25813,10 +24684,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -25839,7 +24708,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -25883,10 +24751,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -25909,7 +24775,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -25957,10 +24822,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 4,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 4,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -25983,8 +24846,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 4,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 4,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -26028,10 +24890,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -26054,7 +24914,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -26099,10 +24958,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -26125,8 +24982,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -26177,10 +25033,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -26203,7 +25057,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -26247,10 +25100,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -26273,7 +25124,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -26357,10 +25207,8 @@
     "Tools available on UseGalaxy.eu": 23,
     "Tools available on UseGalaxy.fr": 19,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -26383,8 +25231,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 19,
     "Tools available on UseGalaxy.cz": 23,
     "Tools available on UseGalaxy.no": 19,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -26427,10 +25274,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -26453,7 +25298,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -26497,10 +25341,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -26523,7 +25365,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -26568,10 +25409,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -26594,7 +25433,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -26639,10 +25477,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -26665,7 +25501,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -26721,10 +25556,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -26747,7 +25580,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -26803,10 +25635,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -26829,7 +25659,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -26873,10 +25702,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -26899,7 +25726,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -26943,10 +25769,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -26969,7 +25793,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -27013,10 +25836,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -27039,8 +25860,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -27081,10 +25901,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -27107,7 +25925,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -27152,10 +25969,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -27178,7 +25993,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -27244,10 +26058,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -27270,7 +26082,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -27314,10 +26125,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -27340,7 +26149,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -27384,10 +26192,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -27410,7 +26216,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -27454,10 +26259,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -27480,8 +26283,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -27522,10 +26324,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -27548,8 +26348,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -27594,10 +26393,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -27620,7 +26417,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -27653,7 +26449,7 @@
       "Whole genome sequencing",
       "Genomics"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "https://github.com/fenderglass/Flye/",
     "ToolShed categories": [
       "Assembly"
@@ -27662,7 +26458,7 @@
     "Galaxy wrapper owner": "bgruening",
     "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/flye",
     "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/flye",
-    "Galaxy wrapper version": "2.9.4",
+    "Galaxy wrapper version": "2.9.5",
     "Conda id": "flye",
     "Conda version": "2.9.5",
     "EDAM operation (no superclasses)": [
@@ -27685,10 +26481,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -27711,8 +26505,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -27755,10 +26548,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -27781,7 +26572,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -27825,10 +26615,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -27851,7 +26639,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -27907,10 +26694,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -27933,8 +26718,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -27960,7 +26744,7 @@
     "EDAM topic": [
       "Computational biology"
     ],
-    "Status": "Up-to-date",
+    "Status": "To update",
     "Source": "https://github.com/vgl-hub/gfastats",
     "ToolShed categories": [
       "Sequence Analysis"
@@ -27971,7 +26755,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/gfastats",
     "Galaxy wrapper version": "1.3.6",
     "Conda id": "gfastats",
-    "Conda version": "1.3.6",
+    "Conda version": "1.3.7",
     "EDAM operation (no superclasses)": [
       "Data handling"
     ],
@@ -27987,10 +26771,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -28013,7 +26795,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -28055,10 +26836,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -28081,7 +26860,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -28125,10 +26903,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -28151,7 +26927,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -28195,10 +26970,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -28221,7 +26994,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -28265,10 +27037,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -28291,7 +27061,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -28334,7 +27103,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/graphmap",
     "Galaxy wrapper version": "0.5.2",
     "Conda id": "graphmap",
-    "Conda version": "0.6.3",
+    "Conda version": "0.6.4",
     "EDAM operation (no superclasses)": [
       "Sequence trimming",
       "EST assembly",
@@ -28354,10 +27123,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -28380,8 +27147,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -28424,10 +27190,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -28450,7 +27214,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -28495,10 +27258,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -28521,7 +27282,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -28571,10 +27331,8 @@
     "Tools available on UseGalaxy.eu": 7,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -28597,7 +27355,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 7,
     "Tools available on UseGalaxy.no": 6,
@@ -28639,10 +27396,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -28665,7 +27420,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -28709,10 +27463,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -28735,7 +27487,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -28779,10 +27530,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -28805,7 +27554,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -28837,7 +27585,7 @@
     "Galaxy wrapper owner": "bgruening",
     "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/",
     "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick",
-    "Galaxy wrapper version": "1.3.44",
+    "Galaxy wrapper version": "1.3.45",
     "Conda id": "graphicsmagick",
     "Conda version": "1.3.26",
     "EDAM operation (no superclasses)": [],
@@ -28851,10 +27599,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -28877,8 +27623,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -28904,7 +27649,9 @@
       "imagej2_bunwarpj_elastic_transform",
       "imagej2_bunwarpj_raw_transform",
       "imagej2_create_image",
+      "imagej2_crop",
       "imagej2_enhance_contrast",
+      "imagej2_filter",
       "imagej2_find_edges",
       "imagej2_find_maxima",
       "imagej2_make_binary",
@@ -28941,7 +27688,7 @@
     "Galaxy wrapper owner": "imgteam",
     "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2",
     "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2",
-    "Galaxy wrapper version": "20170530",
+    "Galaxy wrapper version": "20240614",
     "Conda id": null,
     "Conda version": null,
     "EDAM operation (no superclasses)": [
@@ -28961,10 +27708,8 @@
     "Tools available on UseGalaxy.eu": 27,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -28987,7 +27732,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 27,
     "Tools available on UseGalaxy.no": 27,
@@ -29031,10 +27775,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -29057,7 +27799,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -29125,10 +27866,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -29151,7 +27890,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -29193,10 +27931,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -29219,7 +27955,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -29275,10 +28010,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -29301,7 +28034,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -29334,7 +28066,7 @@
       "Gene structure",
       "Sequence assembly"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "https://jbrowse.org",
     "ToolShed categories": [
       "Sequence Analysis"
@@ -29343,9 +28075,9 @@
     "Galaxy wrapper owner": "fubar",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2",
     "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2",
-    "Galaxy wrapper version": "2.13.1",
+    "Galaxy wrapper version": "2.15.4",
     "Conda id": "jbrowse2",
-    "Conda version": "2.14.0",
+    "Conda version": "2.15.4",
     "EDAM operation (no superclasses)": [
       "Genome visualisation",
       "Structure visualisation",
@@ -29367,10 +28099,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -29379,7 +28109,7 @@
     "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
-    "Tools available on Galaxy@Pasteur": 0,
+    "Tools available on Galaxy@Pasteur": 1,
     "Tools available on GalaxyTrakr": 0,
     "Tools available on Genomic Hyperbrowser": 0,
     "Tools available on GigaGalaxy": 0,
@@ -29393,7 +28123,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -29437,10 +28166,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -29463,7 +28190,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -29507,10 +28233,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -29533,7 +28257,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -29599,10 +28322,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -29625,7 +28346,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -29680,10 +28400,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 2,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -29706,8 +28424,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -29750,10 +28467,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -29776,7 +28491,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -29827,10 +28541,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -29853,7 +28565,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -29897,10 +28608,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -29923,8 +28632,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -29967,10 +28675,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -29993,7 +28699,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -30038,10 +28743,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -30064,8 +28767,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -30125,10 +28827,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -30151,7 +28851,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -30195,10 +28894,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -30221,7 +28918,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -30265,10 +28961,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -30291,7 +28985,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -30349,10 +29042,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -30375,7 +29066,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -30419,10 +29109,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -30445,7 +29133,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -30489,10 +29176,86 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
+    "Tools available on CIRM-CFBP": 0,
+    "Tools available on ChemFlow": 0,
+    "Tools available on Coloc-stats": 0,
+    "Tools available on CoralSNP": 0,
+    "Tools available on CropGalaxy": 0,
+    "Tools available on Dintor": 0,
+    "Tools available on FreeBioinfo": 0,
+    "Tools available on GASLINI": 0,
+    "Tools available on Galaxy@AuBi": 0,
+    "Tools available on Galaxy@Pasteur": 0,
+    "Tools available on GalaxyTrakr": 0,
+    "Tools available on Genomic Hyperbrowser": 0,
+    "Tools available on GigaGalaxy": 0,
+    "Tools available on HyPhy HIV NGS Tools": 0,
+    "Tools available on IPK Galaxy Blast Suite": 0,
+    "Tools available on ImmPort Galaxy": 0,
+    "Tools available on InteractoMIX": 0,
+    "Tools available on MISSISSIPPI": 0,
+    "Tools available on Mandoiu Lab": 0,
+    "Tools available on MiModD NacreousMap": 0,
+    "Tools available on Oqtans": 0,
+    "Tools available on Palfinder": 0,
+    "Tools available on PepSimili": 0,
+    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.cz": 0,
+    "Tools available on UseGalaxy.no": 0,
+    "Tools available on Viral Variant Visualizer (VVV)": 0,
+    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+    "Total tool usage (usegalaxy.eu)": 0
+  },
+  {
+    "Galaxy wrapper id": "motus",
+    "Galaxy tool ids": [
+      "mereg_mOTUs_tables",
+      "motus_profiler"
+    ],
+    "Description": "Tool for profiling the abundance of microbial taxa.",
+    "bio.tool id": "mOTUs",
+    "bio.tool ids": [
+      "mOTUs"
+    ],
+    "biii": null,
+    "bio.tool name": "Metagenomic operational taxonomic units (mOTUs)",
+    "bio.tool description": "Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall.",
+    "EDAM operation": [
+      "Taxonomic classification"
+    ],
+    "EDAM topic": [
+      "Metagenomics"
+    ],
+    "Status": "Up-to-date",
+    "Source": "https://github.com/motu-tool/mOTUs",
+    "ToolShed categories": [
+      "Metagenomics"
+    ],
+    "ToolShed id": "motus",
+    "Galaxy wrapper owner": "bgruening",
+    "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs",
+    "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/motus",
+    "Galaxy wrapper version": "3.1.0",
+    "Conda id": "motus",
+    "Conda version": "3.1.0",
+    "EDAM operation (no superclasses)": [
+      "Taxonomic classification"
+    ],
+    "EDAM topic (no superclasses)": [
+      "Metagenomics"
+    ],
+    "Available on UseGalaxy.org (Main)": 0,
+    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.eu": 2,
+    "Available on UseGalaxy.fr": 0,
+    "Tools available on UseGalaxy.org (Main)": 0,
+    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.eu": 2,
+    "Tools available on UseGalaxy.fr": 0,
+    "Tools available on APOSTL": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -30515,7 +29278,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -30563,10 +29325,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -30589,7 +29349,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 0,
@@ -30634,10 +29393,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 4,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 3,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -30660,8 +29417,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 4,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 4,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -30704,10 +29460,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -30730,7 +29484,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -30788,10 +29541,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -30814,7 +29565,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -30874,10 +29624,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -30900,7 +29648,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -30944,10 +29691,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -30970,7 +29715,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -31141,7 +29885,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/openms",
     "Galaxy wrapper version": "2.1.0",
     "Conda id": "openms",
-    "Conda version": "3.1.0",
+    "Conda version": "3.2.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 7,
@@ -31153,10 +29897,8 @@
     "Tools available on UseGalaxy.eu": 135,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -31179,8 +29921,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 19,
     "Tools available on UseGalaxy.cz": 135,
     "Tools available on UseGalaxy.no": 134,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -31223,10 +29964,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -31249,8 +29988,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -31294,10 +30032,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -31320,8 +30056,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -31362,10 +30097,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -31388,7 +30121,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -31442,10 +30174,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -31468,7 +30198,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -31515,10 +30244,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -31541,7 +30268,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -31585,10 +30311,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -31611,7 +30335,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -31656,10 +30379,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -31682,7 +30403,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -31726,10 +30446,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -31752,7 +30470,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -31796,10 +30513,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -31822,8 +30537,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -31866,10 +30580,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -31892,8 +30604,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -31936,10 +30647,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -31962,8 +30671,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -32007,10 +30715,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -32033,7 +30739,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -32077,10 +30782,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -32103,7 +30806,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -32147,10 +30849,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -32173,7 +30873,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -32231,10 +30930,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -32257,8 +30954,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -32289,7 +30985,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker",
     "Galaxy wrapper version": "0.1.2",
     "Conda id": "RepeatMasker",
-    "Conda version": "4.1.5",
+    "Conda version": "4.0.9_p2",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -32301,10 +30997,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -32327,8 +31021,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -32371,10 +31064,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -32397,8 +31088,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -32441,10 +31131,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -32467,7 +31155,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -32511,10 +31198,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -32537,7 +31222,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -32583,10 +31267,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -32609,7 +31291,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -32653,10 +31334,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -32679,8 +31358,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -32737,10 +31415,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -32763,7 +31439,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -32810,10 +31485,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -32836,7 +31509,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
@@ -32880,10 +31552,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -32906,7 +31576,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -32951,10 +31620,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -32977,7 +31644,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -33022,10 +31688,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -33048,7 +31712,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -33094,10 +31757,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -33120,7 +31781,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -33165,10 +31825,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -33191,7 +31849,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -33236,10 +31893,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -33262,7 +31917,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -33307,10 +31961,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -33333,7 +31985,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -33377,10 +32028,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -33403,7 +32052,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -33449,10 +32097,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -33475,7 +32121,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -33521,10 +32166,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -33547,7 +32190,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -33608,10 +32250,8 @@
     "Tools available on UseGalaxy.eu": 6,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -33634,7 +32274,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 6,
     "Tools available on UseGalaxy.no": 6,
@@ -33676,10 +32315,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -33702,7 +32339,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -33732,9 +32368,9 @@
     "Galaxy wrapper owner": "rnateam",
     "Galaxy wrapper source": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna",
     "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna",
-    "Galaxy wrapper version": "3.4.0",
+    "Galaxy wrapper version": "3.4.1",
     "Conda id": "intarna",
-    "Conda version": "3.4.0",
+    "Conda version": "3.4.1",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -33746,10 +32382,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -33772,7 +32406,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -33814,10 +32447,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -33840,7 +32471,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -33888,10 +32518,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -33914,7 +32542,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -33958,10 +32585,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -33984,7 +32609,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -34028,10 +32652,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -34054,7 +32676,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -34098,10 +32719,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -34124,7 +32743,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -34168,10 +32786,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -34194,7 +32810,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -34238,10 +32853,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -34264,7 +32877,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -34308,10 +32920,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -34334,7 +32944,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -34376,7 +32985,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench",
     "Galaxy wrapper version": "0.8.1",
     "Conda id": "rbpbench",
-    "Conda version": "0.9",
+    "Conda version": "1.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [
       "RNA",
@@ -34394,10 +33003,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -34420,7 +33027,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -34464,10 +33070,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -34490,8 +33094,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -34551,10 +33154,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -34577,7 +33178,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -34621,10 +33221,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -34647,7 +33245,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -34703,10 +33300,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -34729,7 +33324,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 3,
@@ -34773,10 +33367,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -34799,7 +33391,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -34843,10 +33434,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -34869,7 +33458,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -34913,10 +33501,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -34939,7 +33525,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -34983,10 +33568,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -35009,7 +33592,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -35053,10 +33635,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -35079,7 +33659,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -35124,10 +33703,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -35150,7 +33727,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -35194,10 +33770,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -35220,7 +33794,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -35269,10 +33842,8 @@
     "Tools available on UseGalaxy.eu": 6,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -35295,7 +33866,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 6,
     "Tools available on UseGalaxy.no": 6,
@@ -35340,10 +33910,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -35366,7 +33934,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -35425,10 +33992,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -35451,8 +34016,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -35496,10 +34060,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -35522,7 +34084,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -35566,10 +34127,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -35592,7 +34151,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -35637,10 +34195,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 2,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -35649,7 +34205,7 @@
     "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
-    "Tools available on Galaxy@Pasteur": 0,
+    "Tools available on Galaxy@Pasteur": 2,
     "Tools available on GalaxyTrakr": 2,
     "Tools available on Genomic Hyperbrowser": 0,
     "Tools available on GigaGalaxy": 0,
@@ -35663,7 +34219,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
@@ -35729,10 +34284,8 @@
     "Tools available on UseGalaxy.eu": 21,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -35755,7 +34308,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 21,
     "Tools available on UseGalaxy.no": 21,
@@ -35800,10 +34352,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -35826,8 +34376,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -35891,10 +34440,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -35917,8 +34464,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 3,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 3,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -35964,10 +34510,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -35990,7 +34534,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -36034,10 +34577,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -36060,7 +34601,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -36104,10 +34644,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -36130,7 +34668,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -36207,10 +34744,8 @@
     "Tools available on UseGalaxy.eu": 31,
     "Tools available on UseGalaxy.fr": 16,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -36233,8 +34768,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 29,
     "Tools available on UseGalaxy.cz": 31,
     "Tools available on UseGalaxy.no": 27,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -36277,10 +34811,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -36303,7 +34835,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -36347,10 +34878,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -36373,7 +34902,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -36417,10 +34945,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -36443,7 +34969,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -36487,10 +35012,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -36513,7 +35036,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -36557,10 +35079,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -36583,8 +35103,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -36627,10 +35146,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -36640,7 +35157,7 @@
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
     "Tools available on Galaxy@Pasteur": 0,
-    "Tools available on GalaxyTrakr": 0,
+    "Tools available on GalaxyTrakr": 1,
     "Tools available on Genomic Hyperbrowser": 0,
     "Tools available on GigaGalaxy": 0,
     "Tools available on HyPhy HIV NGS Tools": 0,
@@ -36653,8 +35170,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -36697,10 +35213,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -36723,8 +35237,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -36767,10 +35280,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -36793,7 +35304,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -36837,10 +35347,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -36863,8 +35371,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -36926,10 +35433,8 @@
     "Tools available on UseGalaxy.eu": 20,
     "Tools available on UseGalaxy.fr": 20,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -36952,8 +35457,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 19,
     "Tools available on UseGalaxy.cz": 19,
     "Tools available on UseGalaxy.no": 19,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -37020,10 +35524,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -37046,7 +35548,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -37114,10 +35615,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -37140,7 +35639,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -37184,10 +35682,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -37210,8 +35706,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -37269,10 +35764,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -37295,8 +35788,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -37340,10 +35832,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -37366,8 +35856,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -37412,10 +35901,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -37438,7 +35925,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -37482,10 +35968,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -37508,7 +35992,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -37566,10 +36049,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -37592,7 +36073,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -37637,10 +36117,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -37663,7 +36141,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -37709,10 +36186,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -37735,7 +36210,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -37770,7 +36244,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell",
     "Galaxy wrapper version": "0.0.7",
     "Conda id": "samtools",
-    "Conda version": "1.20",
+    "Conda version": "1.21",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -37782,10 +36256,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -37808,7 +36280,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -37862,10 +36333,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -37888,7 +36357,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -37921,7 +36389,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants",
     "Galaxy wrapper version": "0.0.6",
     "Conda id": "samtools",
-    "Conda version": "1.20",
+    "Conda version": "1.21",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -37933,10 +36401,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -37959,7 +36425,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -37992,7 +36457,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats",
     "Galaxy wrapper version": "0.1.0",
     "Conda id": "samtools",
-    "Conda version": "1.20",
+    "Conda version": "1.21",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -38004,10 +36469,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -38030,7 +36493,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -38084,10 +36546,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -38110,7 +36570,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -38156,10 +36615,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -38182,7 +36639,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -38228,10 +36684,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -38254,7 +36708,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -38298,10 +36751,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -38324,7 +36775,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -38369,10 +36819,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -38395,7 +36843,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -38439,10 +36886,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -38465,8 +36910,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -38511,10 +36955,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -38537,7 +36979,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -38582,10 +37023,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -38608,7 +37047,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -38652,10 +37090,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -38678,7 +37114,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -38727,10 +37162,8 @@
     "Tools available on UseGalaxy.eu": 6,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -38753,8 +37186,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 6,
     "Tools available on UseGalaxy.cz": 6,
     "Tools available on UseGalaxy.no": 6,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -38800,10 +37232,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -38826,7 +37256,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -38860,7 +37289,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad",
     "Galaxy wrapper version": "0.0.5",
     "Conda id": "samtools",
-    "Conda version": "1.20",
+    "Conda version": "1.21",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -38872,10 +37301,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -38898,7 +37325,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -38932,7 +37358,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth",
     "Galaxy wrapper version": "0.0.3",
     "Conda id": "samtools",
-    "Conda version": "1.20",
+    "Conda version": "1.21",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -38944,10 +37370,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -38970,8 +37394,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 1,
@@ -39004,7 +37427,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats",
     "Galaxy wrapper version": "0.0.6",
     "Conda id": "samtools",
-    "Conda version": "1.20",
+    "Conda version": "1.21",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -39016,10 +37439,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -39042,8 +37463,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -39086,10 +37506,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -39112,7 +37530,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -39158,10 +37575,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -39184,7 +37599,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -39232,10 +37646,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -39258,7 +37670,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -39304,10 +37715,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -39330,7 +37739,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -39376,10 +37784,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -39402,7 +37808,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -39448,10 +37853,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -39474,7 +37877,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 1,
@@ -39520,10 +37922,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -39546,7 +37946,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -39592,10 +37991,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -39618,7 +38015,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -39662,10 +38058,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -39688,7 +38082,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -39746,10 +38139,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -39772,8 +38163,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 3,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -39801,7 +38191,7 @@
       "Public health and epidemiology",
       "Infectious disease"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "https://zenodo.org/record/7370628",
     "ToolShed categories": [
       "Sequence Analysis"
@@ -39810,7 +38200,7 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr",
-    "Galaxy wrapper version": "1.0.14",
+    "Galaxy wrapper version": "1.0.19",
     "Conda id": "abritamr",
     "Conda version": "1.0.19",
     "EDAM operation (no superclasses)": [
@@ -39830,10 +38220,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -39856,7 +38244,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -39885,7 +38272,7 @@
     "EDAM topic": [
       "Sequence assembly"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "http://www.bcgsc.ca/platform/bioinfo/software/abyss",
     "ToolShed categories": [
       "Assembly"
@@ -39894,9 +38281,9 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss",
-    "Galaxy wrapper version": "2.3.7",
+    "Galaxy wrapper version": "2.3.9",
     "Conda id": "abyss",
-    "Conda version": "2.3.8",
+    "Conda version": "2.3.9",
     "EDAM operation (no superclasses)": [
       "Genome assembly",
       "De-novo assembly",
@@ -39908,16 +38295,14 @@
     "Available on UseGalaxy.org (Main)": 0,
     "Available on UseGalaxy.org.au": 1,
     "Available on UseGalaxy.eu": 1,
-    "Available on UseGalaxy.fr": 0,
+    "Available on UseGalaxy.fr": 1,
     "Tools available on UseGalaxy.org (Main)": 0,
     "Tools available on UseGalaxy.org.au": 1,
     "Tools available on UseGalaxy.eu": 1,
-    "Tools available on UseGalaxy.fr": 0,
+    "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -39940,8 +38325,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -39995,10 +38379,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -40021,7 +38403,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -40065,10 +38446,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -40091,7 +38470,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -40151,10 +38529,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 4,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -40177,8 +38553,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -40233,10 +38608,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -40259,7 +38632,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -40317,10 +38689,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -40343,7 +38713,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -40401,10 +38770,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -40427,7 +38794,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -40501,10 +38867,8 @@
     "Tools available on UseGalaxy.eu": 19,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -40527,7 +38891,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 19,
     "Tools available on UseGalaxy.no": 0,
@@ -40585,10 +38948,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -40611,7 +38972,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -40669,10 +39029,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -40695,7 +39053,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -40723,14 +39080,14 @@
     "Status": "To update",
     "Source": "https://anndata.readthedocs.io",
     "ToolShed categories": [
-      "Transcriptomics",
-      "Sequence Analysis"
+      "Single Cell",
+      "Spatial Omics"
     ],
     "ToolShed id": "anndata",
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata",
-    "Galaxy wrapper version": "0.10.3",
+    "Galaxy wrapper version": "0.10.9",
     "Conda id": "anndata",
     "Conda version": "0.6.22.post1",
     "EDAM operation (no superclasses)": [],
@@ -40744,10 +39101,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -40770,8 +39125,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 5,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -40820,10 +39174,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -40846,8 +39198,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -40889,17 +39240,15 @@
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
     "Available on UseGalaxy.org.au": 0,
-    "Available on UseGalaxy.eu": 0,
+    "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 1,
     "Tools available on UseGalaxy.org (Main)": 0,
     "Tools available on UseGalaxy.org.au": 0,
-    "Tools available on UseGalaxy.eu": 0,
+    "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -40922,7 +39271,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -40969,10 +39317,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -40995,7 +39341,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 0,
@@ -41052,10 +39397,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 3,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -41078,7 +39421,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -41125,18 +39467,16 @@
       "Genomics"
     ],
     "Available on UseGalaxy.org (Main)": 0,
-    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.org.au": 2,
     "Available on UseGalaxy.eu": 2,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
-    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.org.au": 2,
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -41159,8 +39499,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -41203,10 +39542,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -41229,7 +39566,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -41273,10 +39609,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -41299,8 +39633,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -41363,10 +39696,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -41389,8 +39720,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -41446,10 +39776,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -41472,8 +39800,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -41501,7 +39828,7 @@
       "Data submission, annotation and curation",
       "Sequence analysis"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "https://github.com/oschwengers/bakta",
     "ToolShed categories": [
       "Sequence Analysis"
@@ -41510,7 +39837,7 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta",
-    "Galaxy wrapper version": "1.9.3",
+    "Galaxy wrapper version": "1.9.4",
     "Conda id": "bakta",
     "Conda version": "1.9.4",
     "EDAM operation (no superclasses)": [
@@ -41521,19 +39848,17 @@
       "Data submission, annotation and curation",
       "Sequence analysis"
     ],
-    "Available on UseGalaxy.org (Main)": 0,
+    "Available on UseGalaxy.org (Main)": 1,
     "Available on UseGalaxy.org.au": 1,
     "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 1,
-    "Tools available on UseGalaxy.org (Main)": 0,
+    "Tools available on UseGalaxy.org (Main)": 1,
     "Tools available on UseGalaxy.org.au": 1,
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -41556,7 +39881,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -41600,10 +39924,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -41626,8 +39948,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -41671,10 +39992,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -41697,7 +40016,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -41754,10 +40072,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 2,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -41780,8 +40096,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -41824,10 +40139,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -41850,7 +40163,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -41889,6 +40201,7 @@
     "Status": "Up-to-date",
     "Source": "https://github.com/lldelisle/baredSC",
     "ToolShed categories": [
+      "Single Cell",
       "Transcriptomics",
       "Visualization"
     ],
@@ -41920,10 +40233,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -41946,7 +40257,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 0,
@@ -42004,10 +40314,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -42030,7 +40338,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -42074,10 +40381,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -42100,8 +40405,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -42145,10 +40449,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -42171,8 +40473,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -42231,10 +40532,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -42257,8 +40556,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -42307,10 +40605,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -42333,7 +40629,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -42376,7 +40671,7 @@
       "Metagenomics",
       "RNA-Seq"
     ],
-    "Status": "Up-to-date",
+    "Status": "To update",
     "Source": "https://jgi.doe.gov/data-and-tools/bbtools/",
     "ToolShed categories": [
       "Sequence Analysis"
@@ -42387,7 +40682,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools",
     "Galaxy wrapper version": "39.08",
     "Conda id": "bbmap",
-    "Conda version": "39.08",
+    "Conda version": "39.09",
     "EDAM operation (no superclasses)": [
       "RNA-Seq analysis",
       "Sequence trimming",
@@ -42404,18 +40699,16 @@
       "RNA-Seq"
     ],
     "Available on UseGalaxy.org (Main)": 6,
-    "Available on UseGalaxy.org.au": 1,
+    "Available on UseGalaxy.org.au": 3,
     "Available on UseGalaxy.eu": 5,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 6,
-    "Tools available on UseGalaxy.org.au": 1,
+    "Tools available on UseGalaxy.org.au": 3,
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -42438,7 +40731,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 0,
@@ -42512,7 +40804,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools",
     "Galaxy wrapper version": "1.15.1",
     "Conda id": "bcftools",
-    "Conda version": "1.20",
+    "Conda version": "1.21",
     "EDAM operation (no superclasses)": [
       "Data handling",
       "Variant calling"
@@ -42531,10 +40823,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -42557,7 +40847,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -42608,10 +40897,8 @@
     "Tools available on UseGalaxy.eu": 7,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -42634,8 +40921,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 7,
     "Tools available on UseGalaxy.no": 7,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -42686,9 +40972,9 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import",
-    "Galaxy wrapper version": "2.2.3",
+    "Galaxy wrapper version": "2.2.4",
     "Conda id": "beacon2-import",
-    "Conda version": "2.2.3",
+    "Conda version": "2.2.4",
     "EDAM operation (no superclasses)": [
       "Service discovery",
       "Database search",
@@ -42709,10 +40995,8 @@
     "Tools available on UseGalaxy.eu": 12,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -42735,7 +41019,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -42801,10 +41084,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -42827,7 +41108,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 0,
@@ -42871,10 +41151,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -42897,7 +41175,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -42941,10 +41218,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -42967,7 +41242,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -43058,10 +41332,8 @@
     "Tools available on UseGalaxy.eu": 37,
     "Tools available on UseGalaxy.fr": 37,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 37,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 37,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -43084,8 +41356,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 37,
     "Tools available on UseGalaxy.cz": 37,
     "Tools available on UseGalaxy.no": 37,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -43128,10 +41399,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -43154,7 +41423,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -43198,10 +41466,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -43224,7 +41490,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -43292,10 +41557,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -43318,7 +41581,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -43355,19 +41617,17 @@
     "Conda version": null,
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
-    "Available on UseGalaxy.org (Main)": 0,
+    "Available on UseGalaxy.org (Main)": 1,
     "Available on UseGalaxy.org.au": 0,
     "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 0,
-    "Tools available on UseGalaxy.org (Main)": 0,
+    "Tools available on UseGalaxy.org (Main)": 1,
     "Tools available on UseGalaxy.org.au": 0,
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -43390,7 +41650,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -43450,10 +41709,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -43476,7 +41733,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -43498,7 +41754,7 @@
     "bio.tool description": null,
     "EDAM operation": [],
     "EDAM topic": [],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "https://pypi.python.org/pypi/biopython-extensions/",
     "ToolShed categories": [
       "Next Gen Mappers"
@@ -43507,7 +41763,7 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/davebx/bioext-gx/",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext",
-    "Galaxy wrapper version": "0.21.7",
+    "Galaxy wrapper version": "0.21.9",
     "Conda id": "python-bioext",
     "Conda version": "0.21.9",
     "EDAM operation (no superclasses)": [],
@@ -43521,10 +41777,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -43547,7 +41801,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -43591,10 +41844,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -43617,7 +41868,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -43678,10 +41928,8 @@
     "Tools available on UseGalaxy.eu": 6,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -43704,8 +41952,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -43763,10 +42010,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -43789,7 +42034,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -43833,10 +42077,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -43859,7 +42101,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -43903,10 +42144,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -43929,7 +42168,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -43974,10 +42212,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -44000,7 +42236,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -44058,10 +42293,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -44084,8 +42317,7 @@
     "Tools available on Oqtans": 1,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -44141,10 +42373,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -44167,7 +42397,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -44225,10 +42454,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -44251,7 +42478,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -44307,10 +42533,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -44333,7 +42557,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -44398,10 +42621,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -44424,8 +42645,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -44495,10 +42715,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 2,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -44507,7 +42725,7 @@
     "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 2,
-    "Tools available on Galaxy@Pasteur": 1,
+    "Tools available on Galaxy@Pasteur": 2,
     "Tools available on GalaxyTrakr": 2,
     "Tools available on Genomic Hyperbrowser": 0,
     "Tools available on GigaGalaxy": 0,
@@ -44521,8 +42739,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 2,
@@ -44575,10 +42792,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -44601,7 +42816,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -44646,10 +42860,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -44672,8 +42884,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -44737,10 +42948,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -44763,7 +42972,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
@@ -44809,10 +43017,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -44835,7 +43041,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -44879,10 +43084,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -44905,7 +43108,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -44938,24 +43140,22 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber",
-    "Galaxy wrapper version": "2.0.6",
+    "Galaxy wrapper version": "2.0.7",
     "Conda id": "cami-amber",
-    "Conda version": "2.0.6",
+    "Conda version": "2.0.7",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
     "Available on UseGalaxy.org.au": 0,
-    "Available on UseGalaxy.eu": 3,
+    "Available on UseGalaxy.eu": 4,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
     "Tools available on UseGalaxy.org.au": 0,
-    "Tools available on UseGalaxy.eu": 3,
+    "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -44978,7 +43178,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -45046,10 +43245,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -45072,8 +43269,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 5,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -45127,10 +43323,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -45153,7 +43347,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -45214,10 +43407,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -45240,7 +43431,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -45284,10 +43474,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -45310,7 +43498,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -45355,7 +43542,7 @@
       "Metagenomics",
       "Data quality management"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "https://github.com/Ecogenomics/CheckM",
     "ToolShed categories": [
       "Metagenomics"
@@ -45364,7 +43551,7 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm",
-    "Galaxy wrapper version": "1.2.0",
+    "Galaxy wrapper version": "1.2.3",
     "Conda id": "checkm-genome",
     "Conda version": "1.2.3",
     "EDAM operation (no superclasses)": [
@@ -45380,18 +43567,16 @@
       "Data quality management"
     ],
     "Available on UseGalaxy.org (Main)": 0,
-    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.org.au": 10,
     "Available on UseGalaxy.eu": 10,
     "Available on UseGalaxy.fr": 10,
     "Tools available on UseGalaxy.org (Main)": 0,
-    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.org.au": 10,
     "Tools available on UseGalaxy.eu": 10,
     "Tools available on UseGalaxy.fr": 10,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -45414,7 +43599,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 10,
     "Tools available on UseGalaxy.no": 0,
@@ -45470,10 +43654,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -45496,7 +43678,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -45547,10 +43728,8 @@
     "Tools available on UseGalaxy.eu": 8,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -45573,7 +43752,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -45632,10 +43810,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -45658,8 +43834,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 5,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -45702,10 +43877,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -45728,7 +43901,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -45772,10 +43944,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -45798,8 +43968,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -45853,10 +44022,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -45879,7 +44046,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -45939,10 +44105,8 @@
     "Tools available on UseGalaxy.eu": 11,
     "Tools available on UseGalaxy.fr": 11,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -45965,8 +44129,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 11,
     "Tools available on UseGalaxy.cz": 11,
     "Tools available on UseGalaxy.no": 11,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -45996,7 +44159,9 @@
     "Status": "To update",
     "Source": "https://github.com/Hoohm/CITE-seq-Count",
     "ToolShed categories": [
-      "Transcriptomics"
+      "Single Cell",
+      "Transcriptomics",
+      "Proteomics"
     ],
     "ToolShed id": "cite_seq_count",
     "Galaxy wrapper owner": "iuc",
@@ -46021,10 +44186,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -46047,7 +44210,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -46094,18 +44256,16 @@
       "Molecular genetics"
     ],
     "Available on UseGalaxy.org (Main)": 0,
-    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.org.au": 1,
     "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
-    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.org.au": 1,
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -46128,7 +44288,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -46185,10 +44344,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -46211,8 +44368,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -46241,7 +44397,7 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat",
-    "Galaxy wrapper version": "1.1",
+    "Galaxy wrapper version": "1.1.1",
     "Conda id": "python",
     "Conda version": null,
     "EDAM operation (no superclasses)": [],
@@ -46255,10 +44411,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -46281,7 +44435,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -46325,10 +44478,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -46351,7 +44502,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -46395,10 +44545,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -46421,7 +44569,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -46489,10 +44636,8 @@
     "Tools available on UseGalaxy.eu": 17,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -46515,7 +44660,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 17,
     "Tools available on UseGalaxy.no": 0,
@@ -46572,10 +44716,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -46598,8 +44740,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -46651,10 +44792,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -46677,7 +44816,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 0,
@@ -46745,10 +44883,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -46771,7 +44907,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -46822,10 +44957,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -46848,8 +44981,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -46892,10 +45024,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -46918,8 +45048,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -46962,10 +45091,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -46988,8 +45115,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -47032,10 +45158,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -47058,8 +45182,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -47102,10 +45225,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -47128,8 +45249,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -47172,10 +45292,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -47198,8 +45316,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -47255,18 +45372,16 @@
       "Sequence analysis"
     ],
     "Available on UseGalaxy.org (Main)": 1,
-    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.org.au": 1,
     "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 1,
     "Tools available on UseGalaxy.org (Main)": 1,
-    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.org.au": 1,
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -47289,7 +45404,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -47333,10 +45447,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -47359,8 +45471,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -47403,10 +45514,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -47429,7 +45538,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -47489,10 +45597,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 5,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -47515,7 +45621,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 0,
@@ -47540,7 +45645,8 @@
     "Source": "https://github.com/genecell/COSG",
     "ToolShed categories": [
       "Transcriptomics",
-      "Sequence Analysis"
+      "Sequence Analysis",
+      "Single Cell"
     ],
     "ToolShed id": "cosg",
     "Galaxy wrapper owner": "iuc",
@@ -47553,17 +45659,15 @@
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
     "Available on UseGalaxy.org.au": 0,
-    "Available on UseGalaxy.eu": 0,
+    "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
     "Tools available on UseGalaxy.org.au": 0,
-    "Tools available on UseGalaxy.eu": 0,
+    "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -47586,7 +45690,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -47630,10 +45733,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -47656,7 +45757,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -47711,10 +45811,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -47737,7 +45835,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -47795,10 +45892,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -47821,8 +45916,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -47866,10 +45960,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -47892,8 +45984,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -47919,7 +46010,7 @@
     "bio.tool description": null,
     "EDAM operation": [],
     "EDAM topic": [],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "http://crossmap.sourceforge.net/",
     "ToolShed categories": [
       "Convert Formats",
@@ -47929,7 +46020,7 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap",
-    "Galaxy wrapper version": "0.6.1",
+    "Galaxy wrapper version": "0.7.0",
     "Conda id": "crossmap",
     "Conda version": "0.7.0",
     "EDAM operation (no superclasses)": [],
@@ -47943,10 +46034,8 @@
     "Tools available on UseGalaxy.eu": 6,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 4,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -47969,8 +46058,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 5,
     "Tools available on UseGalaxy.cz": 6,
     "Tools available on UseGalaxy.no": 5,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -48033,10 +46121,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -48059,8 +46145,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -48120,10 +46205,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -48146,8 +46229,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -48190,10 +46272,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -48216,7 +46296,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -48287,10 +46366,8 @@
     "Tools available on UseGalaxy.eu": 10,
     "Tools available on UseGalaxy.fr": 10,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -48313,8 +46390,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 10,
     "Tools available on UseGalaxy.cz": 10,
     "Tools available on UseGalaxy.no": 10,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -48368,10 +46444,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -48394,7 +46468,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -48438,10 +46511,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -48464,7 +46535,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -48510,10 +46580,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -48536,8 +46604,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 3,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 3,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -48590,10 +46657,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -48616,7 +46681,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -48681,10 +46745,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -48707,7 +46769,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -48751,10 +46812,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -48777,7 +46836,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -48821,10 +46879,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -48847,7 +46903,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -48891,10 +46946,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -48917,8 +46970,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -48971,7 +47023,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly",
     "Galaxy wrapper version": "0.9.1",
     "Conda id": "delly",
-    "Conda version": "1.2.6",
+    "Conda version": "1.2.9",
     "EDAM operation (no superclasses)": [
       "Indel detection",
       "Structural variation detection",
@@ -48993,10 +47045,8 @@
     "Tools available on UseGalaxy.eu": 6,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -49019,8 +47069,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 6,
     "Tools available on UseGalaxy.cz": 6,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -49077,10 +47126,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -49103,8 +47150,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -49163,10 +47209,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -49189,8 +47233,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 3,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 3,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -49247,10 +47290,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 3,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -49273,7 +47314,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 3,
@@ -49327,10 +47367,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -49353,7 +47391,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -49406,10 +47443,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -49432,7 +47467,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -49487,10 +47521,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -49513,8 +47545,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -49557,10 +47588,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -49583,7 +47612,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -49627,10 +47655,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -49653,7 +47679,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -49715,10 +47740,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -49741,7 +47764,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 0,
@@ -49799,10 +47821,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -49825,8 +47845,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -49859,7 +47878,7 @@
     "Status": "To update",
     "Source": "https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html",
     "ToolShed categories": [
-      "Transcriptomics",
+      "Single Cell",
       "Sequence Analysis"
     ],
     "ToolShed id": "dropletutils",
@@ -49883,10 +47902,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -49909,8 +47926,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -49954,10 +47970,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -49980,8 +47994,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -50040,10 +48053,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -50066,8 +48077,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -50122,10 +48132,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -50148,8 +48156,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -50320,10 +48327,8 @@
     "Tools available on UseGalaxy.eu": 107,
     "Tools available on UseGalaxy.fr": 107,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 107,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -50346,8 +48351,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 107,
     "Tools available on UseGalaxy.cz": 107,
     "Tools available on UseGalaxy.no": 107,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -50367,7 +48371,7 @@
     "bio.tool description": null,
     "EDAM operation": [],
     "EDAM topic": [],
-    "Status": "Up-to-date",
+    "Status": "To update",
     "Source": "https://github.com/usegalaxy-eu/ena-upload-cli",
     "ToolShed categories": [
       "Data Export"
@@ -50378,7 +48382,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload",
     "Galaxy wrapper version": "0.7.3",
     "Conda id": "ena-upload-cli",
-    "Conda version": "0.7.3",
+    "Conda version": "0.7.4",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -50390,10 +48394,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -50416,8 +48418,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -50464,10 +48465,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -50490,7 +48489,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
@@ -50511,7 +48509,7 @@
     "bio.tool description": null,
     "EDAM operation": [],
     "EDAM topic": [],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "https://github.com/Ensembl/ensembl-vep",
     "ToolShed categories": [
       "Variant Analysis"
@@ -50520,7 +48518,7 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep",
-    "Galaxy wrapper version": "110.1",
+    "Galaxy wrapper version": "112.0",
     "Conda id": "ensembl-vep",
     "Conda version": "112.0",
     "EDAM operation (no superclasses)": [],
@@ -50534,10 +48532,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -50560,7 +48556,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -50595,6 +48590,7 @@
     "Status": "To update",
     "Source": "https://github.com/colomemaria/epiScanpy",
     "ToolShed categories": [
+      "Single Cell",
       "Epigenetics"
     ],
     "ToolShed id": "episcanpy",
@@ -50622,10 +48618,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -50648,7 +48642,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 0,
@@ -50656,6 +48649,85 @@
     "No. of tool users (2022-2023) (usegalaxy.eu)": 20,
     "Total tool usage (usegalaxy.eu)": 736
   },
+  {
+    "Galaxy wrapper id": "evidencemodeler",
+    "Galaxy tool ids": [
+      "evidencemodeler"
+    ],
+    "Description": "EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.",
+    "bio.tool id": "EvidenceModeler",
+    "bio.tool ids": [
+      "EvidenceModeler"
+    ],
+    "biii": null,
+    "bio.tool name": "EvidenceModeler",
+    "bio.tool description": "The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.",
+    "EDAM operation": [
+      "Gene prediction"
+    ],
+    "EDAM topic": [
+      "Gene expression",
+      "Gene structure"
+    ],
+    "Status": "Up-to-date",
+    "Source": "https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file",
+    "ToolShed categories": [
+      "Genome annotation"
+    ],
+    "ToolShed id": "evidencemodeler",
+    "Galaxy wrapper owner": "iuc",
+    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler",
+    "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler",
+    "Galaxy wrapper version": "2.1.0",
+    "Conda id": "evidencemodeler",
+    "Conda version": "2.1.0",
+    "EDAM operation (no superclasses)": [
+      "Gene prediction"
+    ],
+    "EDAM topic (no superclasses)": [
+      "Gene expression",
+      "Gene structure"
+    ],
+    "Available on UseGalaxy.org (Main)": 0,
+    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.eu": 1,
+    "Available on UseGalaxy.fr": 0,
+    "Tools available on UseGalaxy.org (Main)": 0,
+    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.eu": 1,
+    "Tools available on UseGalaxy.fr": 0,
+    "Tools available on APOSTL": 0,
+    "Tools available on ARGs-OAP": 0,
+    "Tools available on CIRM-CFBP": 0,
+    "Tools available on ChemFlow": 0,
+    "Tools available on Coloc-stats": 0,
+    "Tools available on CoralSNP": 0,
+    "Tools available on CropGalaxy": 0,
+    "Tools available on Dintor": 0,
+    "Tools available on FreeBioinfo": 0,
+    "Tools available on GASLINI": 0,
+    "Tools available on Galaxy@AuBi": 0,
+    "Tools available on Galaxy@Pasteur": 0,
+    "Tools available on GalaxyTrakr": 0,
+    "Tools available on Genomic Hyperbrowser": 0,
+    "Tools available on GigaGalaxy": 0,
+    "Tools available on HyPhy HIV NGS Tools": 0,
+    "Tools available on IPK Galaxy Blast Suite": 0,
+    "Tools available on ImmPort Galaxy": 0,
+    "Tools available on InteractoMIX": 0,
+    "Tools available on MISSISSIPPI": 0,
+    "Tools available on Mandoiu Lab": 0,
+    "Tools available on MiModD NacreousMap": 0,
+    "Tools available on Oqtans": 0,
+    "Tools available on Palfinder": 0,
+    "Tools available on PepSimili": 0,
+    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.cz": 0,
+    "Tools available on UseGalaxy.no": 0,
+    "Tools available on Viral Variant Visualizer (VVV)": 0,
+    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+    "Total tool usage (usegalaxy.eu)": 0
+  },
   {
     "Galaxy wrapper id": "exomedepth",
     "Galaxy tool ids": [
@@ -50718,10 +48790,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -50744,7 +48814,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -50806,10 +48875,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -50832,8 +48899,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -50890,10 +48956,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -50916,8 +48980,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -50948,7 +49011,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna",
     "Galaxy wrapper version": "3.0.3+galaxy2",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -50960,10 +49023,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 1,
@@ -50986,8 +49047,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -51017,7 +49077,7 @@
       "Mapping",
       "Imaging"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "https://github.com/smithlabcode/falco/",
     "ToolShed categories": [
       "Sequence Analysis"
@@ -51026,9 +49086,9 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco",
-    "Galaxy wrapper version": "1.2.2+galaxy1",
+    "Galaxy wrapper version": "1.2.4",
     "Conda id": "falco",
-    "Conda version": "1.2.3",
+    "Conda version": "1.2.4",
     "EDAM operation (no superclasses)": [
       "Sequencing quality control",
       "Visualisation",
@@ -51048,10 +49108,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -51074,7 +49132,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -51132,10 +49189,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -51158,8 +49213,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -51202,10 +49256,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -51228,8 +49280,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -51272,10 +49323,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -51298,8 +49347,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -51356,10 +49404,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -51382,8 +49428,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -51426,10 +49471,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -51452,7 +49495,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -51508,10 +49550,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -51534,8 +49574,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 1,
@@ -51596,10 +49635,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 1,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -51622,8 +49659,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 1,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -51678,10 +49714,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -51690,7 +49724,7 @@
     "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 1,
-    "Tools available on Galaxy@Pasteur": 0,
+    "Tools available on Galaxy@Pasteur": 1,
     "Tools available on GalaxyTrakr": 0,
     "Tools available on Genomic Hyperbrowser": 0,
     "Tools available on GigaGalaxy": 0,
@@ -51704,8 +49738,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -51758,10 +49791,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -51784,8 +49815,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -51842,10 +49872,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -51868,8 +49896,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -51925,10 +49952,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -51951,8 +49976,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -51997,10 +50021,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -52023,7 +50045,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -52079,10 +50100,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -52105,8 +50124,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -52158,10 +50176,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -52184,8 +50200,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -52229,10 +50244,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -52255,8 +50268,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -52316,10 +50328,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -52342,8 +50352,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -52398,10 +50407,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -52424,8 +50431,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -52466,7 +50472,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes",
     "Galaxy wrapper version": "1.3.6",
     "Conda id": "freebayes",
-    "Conda version": "1.3.7",
+    "Conda version": "1.3.8",
     "EDAM operation (no superclasses)": [
       "Variant calling",
       "Statistical calculation"
@@ -52485,10 +50491,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 2,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 2,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -52511,8 +50515,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -52574,10 +50577,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -52600,8 +50601,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -52658,10 +50658,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -52684,7 +50682,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 0,
@@ -52731,10 +50728,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -52757,7 +50752,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -52815,10 +50809,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 5,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -52841,8 +50833,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 5,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -52885,10 +50876,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -52911,8 +50900,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -52956,10 +50944,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -52982,8 +50968,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -53026,10 +51011,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -53052,8 +51035,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -53126,10 +51108,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -53152,8 +51132,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -53196,10 +51175,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 1,
+    "Tools available on ARGs-OAP": 1,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 1,
@@ -53222,8 +51199,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -53266,10 +51242,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -53292,7 +51266,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -53336,10 +51309,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -53362,7 +51333,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -53406,10 +51376,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -53432,7 +51400,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -53476,10 +51443,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -53502,7 +51467,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -53574,10 +51538,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -53600,7 +51562,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -53644,10 +51605,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -53670,8 +51629,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -53714,10 +51672,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -53740,7 +51696,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -53811,10 +51766,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -53837,7 +51790,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -53881,10 +51833,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -53907,8 +51857,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -53951,10 +51900,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -53977,8 +51924,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -54033,10 +51979,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -54059,8 +52003,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -54115,10 +52058,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -54141,8 +52082,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -54199,10 +52139,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 5,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -54225,8 +52163,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 5,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -54269,10 +52206,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -54295,7 +52230,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -54358,10 +52292,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -54384,8 +52316,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 4,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -54439,10 +52370,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -54465,8 +52394,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -54521,10 +52449,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -54547,8 +52473,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -54596,10 +52521,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -54622,8 +52545,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 5,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -54667,10 +52589,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -54693,8 +52613,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -54762,10 +52681,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -54788,8 +52705,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -54839,17 +52755,15 @@
     ],
     "Available on UseGalaxy.org (Main)": 0,
     "Available on UseGalaxy.org.au": 0,
-    "Available on UseGalaxy.eu": 0,
+    "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
     "Tools available on UseGalaxy.org.au": 0,
-    "Tools available on UseGalaxy.eu": 0,
+    "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -54872,7 +52786,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -54906,7 +52819,7 @@
       "Database management",
       "Proteins"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "https://github.com/Ecogenomics/GTDBTk",
     "ToolShed categories": [
       "Metagenomics"
@@ -54915,7 +52828,7 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk",
-    "Galaxy wrapper version": "2.3.2",
+    "Galaxy wrapper version": "2.4.0",
     "Conda id": "gtdbtk",
     "Conda version": "2.4.0",
     "EDAM operation (no superclasses)": [
@@ -54940,10 +52853,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -54966,7 +52877,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -55016,10 +52926,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -55042,8 +52950,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -55104,10 +53011,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -55130,8 +53035,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -55174,10 +53078,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -55200,7 +53102,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -55259,10 +53160,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -55285,7 +53184,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 1,
@@ -55347,10 +53245,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -55373,7 +53269,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -55439,10 +53334,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -55465,8 +53358,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -55517,10 +53409,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -55543,7 +53433,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -55601,10 +53490,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -55627,7 +53514,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -55687,10 +53573,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -55713,7 +53597,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -55757,10 +53640,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -55783,8 +53664,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -55802,8 +53682,8 @@
     "Description": "An algorithm for identification of the optimal scoring subnetwork.",
     "bio.tool id": "heinz",
     "bio.tool ids": [
-      "bionet",
-      "heinz"
+      "heinz",
+      "bionet"
     ],
     "biii": null,
     "bio.tool name": "Heinz",
@@ -55847,10 +53727,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -55873,8 +53751,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 4,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 4,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -55917,10 +53794,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -55943,7 +53818,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -56025,10 +53899,8 @@
     "Tools available on UseGalaxy.eu": 38,
     "Tools available on UseGalaxy.fr": 4,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -56051,8 +53923,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 33,
     "Tools available on UseGalaxy.cz": 36,
     "Tools available on UseGalaxy.no": 33,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -56095,10 +53966,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -56121,7 +53990,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -56165,10 +54033,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -56191,7 +54057,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -56247,10 +54112,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -56273,7 +54136,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -56325,10 +54187,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -56351,8 +54211,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -56383,7 +54242,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering",
     "Galaxy wrapper version": "1.3.1",
     "Conda id": "python-hivclustering",
-    "Conda version": "1.6.8",
+    "Conda version": "1.8.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -56395,10 +54254,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -56421,7 +54278,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -56523,10 +54379,8 @@
     "Tools available on UseGalaxy.eu": 12,
     "Tools available on UseGalaxy.fr": 12,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 12,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -56549,8 +54403,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 12,
     "Tools available on UseGalaxy.cz": 12,
     "Tools available on UseGalaxy.no": 12,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -56603,10 +54456,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 4,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -56629,7 +54480,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 0,
@@ -56686,10 +54536,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -56712,8 +54560,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -56724,17 +54571,14 @@
     "Galaxy wrapper id": "humann",
     "Galaxy tool ids": [
       "humann",
-      "humann_associate",
       "humann_barplot",
       "humann_join_tables",
       "humann_reduce_table",
       "humann_regroup_table",
       "humann_rename_table",
       "humann_renorm_table",
-      "humann_rna_dna_norm",
       "humann_split_stratified_table",
       "humann_split_table",
-      "humann_strain_profiler",
       "humann_unpack_pathways"
     ],
     "Description": "HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution",
@@ -56754,7 +54598,7 @@
       "Metagenomics",
       "Phylogenomics"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "http://huttenhower.sph.harvard.edu/humann",
     "ToolShed categories": [
       "Metagenomics"
@@ -56763,7 +54607,7 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann",
-    "Galaxy wrapper version": "3.8",
+    "Galaxy wrapper version": "3.9",
     "Conda id": "humann",
     "Conda version": "3.9",
     "EDAM operation (no superclasses)": [
@@ -56776,18 +54620,16 @@
       "Phylogenomics"
     ],
     "Available on UseGalaxy.org (Main)": 6,
-    "Available on UseGalaxy.org.au": 13,
-    "Available on UseGalaxy.eu": 13,
-    "Available on UseGalaxy.fr": 13,
+    "Available on UseGalaxy.org.au": 10,
+    "Available on UseGalaxy.eu": 10,
+    "Available on UseGalaxy.fr": 10,
     "Tools available on UseGalaxy.org (Main)": 6,
-    "Tools available on UseGalaxy.org.au": 13,
-    "Tools available on UseGalaxy.eu": 13,
-    "Tools available on UseGalaxy.fr": 13,
+    "Tools available on UseGalaxy.org.au": 10,
+    "Tools available on UseGalaxy.eu": 10,
+    "Tools available on UseGalaxy.fr": 10,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -56797,7 +54639,7 @@
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
     "Tools available on Galaxy@Pasteur": 0,
-    "Tools available on GalaxyTrakr": 13,
+    "Tools available on GalaxyTrakr": 10,
     "Tools available on Genomic Hyperbrowser": 0,
     "Tools available on GigaGalaxy": 0,
     "Tools available on HyPhy HIV NGS Tools": 0,
@@ -56810,13 +54652,12 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
-    "Tools available on UseGalaxy.cz": 13,
-    "Tools available on UseGalaxy.no": 13,
+    "Tools available on UseGalaxy.be": 1,
+    "Tools available on UseGalaxy.cz": 10,
+    "Tools available on UseGalaxy.no": 10,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 1045,
-    "Total tool usage (usegalaxy.eu)": 19521
+    "No. of tool users (2022-2023) (usegalaxy.eu)": 1037,
+    "Total tool usage (usegalaxy.eu)": 19490
   },
   {
     "Galaxy wrapper id": "hybpiper",
@@ -56855,7 +54696,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper",
     "Galaxy wrapper version": "2.1.6",
     "Conda id": "hybpiper",
-    "Conda version": "2.2.0",
+    "Conda version": "2.3.0",
     "EDAM operation (no superclasses)": [
       "Sequence trimming",
       "Sequence assembly",
@@ -56877,10 +54718,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -56903,7 +54742,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -56977,10 +54815,8 @@
     "Tools available on UseGalaxy.eu": 17,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -57003,8 +54839,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 12,
     "Tools available on UseGalaxy.cz": 17,
     "Tools available on UseGalaxy.no": 12,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -57061,10 +54896,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -57087,7 +54920,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -57151,10 +54983,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -57177,7 +55007,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -57233,10 +55062,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -57259,8 +55086,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 3,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 3,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -57303,10 +55129,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -57329,8 +55153,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -57359,7 +55182,7 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download",
-    "Galaxy wrapper version": "0.44.1",
+    "Galaxy wrapper version": "0.45",
     "Conda id": "omero-py",
     "Conda version": "5.11.1",
     "EDAM operation (no superclasses)": [],
@@ -57373,10 +55196,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -57399,8 +55220,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -57444,10 +55264,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -57470,8 +55288,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -57515,10 +55332,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -57541,7 +55356,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -57600,10 +55414,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -57626,7 +55438,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -57683,19 +55494,17 @@
       "Molecular biology",
       "Sequence analysis"
     ],
-    "Available on UseGalaxy.org (Main)": 0,
+    "Available on UseGalaxy.org (Main)": 1,
     "Available on UseGalaxy.org.au": 1,
     "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 1,
-    "Tools available on UseGalaxy.org (Main)": 0,
+    "Tools available on UseGalaxy.org (Main)": 1,
     "Tools available on UseGalaxy.org.au": 1,
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -57718,7 +55527,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -57762,10 +55570,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -57788,8 +55594,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -57846,10 +55651,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -57872,8 +55675,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -57908,7 +55710,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf",
     "Galaxy wrapper version": "1.0.1+galaxy1",
     "Conda id": "bx-python",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [
       "Sequence analysis"
@@ -57922,10 +55724,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 1,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -57948,8 +55748,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -58005,10 +55804,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -58031,8 +55828,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -58087,10 +55883,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -58113,8 +55907,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -58145,7 +55938,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv",
     "Galaxy wrapper version": "1.0.5",
     "Conda id": "samtools",
-    "Conda version": "1.20",
+    "Conda version": "1.21",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -58157,10 +55950,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -58183,8 +55974,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -58233,19 +56023,17 @@
       "Sequence analysis",
       "Genetic variation"
     ],
-    "Available on UseGalaxy.org (Main)": 0,
+    "Available on UseGalaxy.org (Main)": 1,
     "Available on UseGalaxy.org.au": 1,
     "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 1,
-    "Tools available on UseGalaxy.org (Main)": 0,
+    "Tools available on UseGalaxy.org (Main)": 1,
     "Tools available on UseGalaxy.org.au": 1,
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -58268,7 +56056,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -58328,10 +56115,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -58354,7 +56139,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -58402,10 +56186,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 5,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -58428,8 +56210,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 5,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -58491,10 +56272,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -58517,8 +56296,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 3,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 3,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -58561,10 +56339,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -58587,8 +56363,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -58642,10 +56417,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -58654,7 +56427,7 @@
     "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 2,
-    "Tools available on Galaxy@Pasteur": 0,
+    "Tools available on Galaxy@Pasteur": 2,
     "Tools available on GalaxyTrakr": 2,
     "Tools available on Genomic Hyperbrowser": 0,
     "Tools available on GigaGalaxy": 0,
@@ -58668,8 +56441,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -58712,10 +56484,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -58738,8 +56508,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -58794,10 +56563,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -58820,7 +56587,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -58864,10 +56630,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -58890,7 +56654,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -58934,10 +56697,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -58960,8 +56721,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -59004,10 +56764,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -59030,7 +56788,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -59071,7 +56828,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto",
     "Galaxy wrapper version": "0.48.0",
     "Conda id": "kallisto",
-    "Conda version": "0.51.0",
+    "Conda version": "0.51.1",
     "EDAM operation (no superclasses)": [
       "Gene expression profiling"
     ],
@@ -59087,10 +56844,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -59113,8 +56868,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -59167,10 +56921,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -59193,8 +56945,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -59257,10 +57008,8 @@
     "Tools available on UseGalaxy.eu": 8,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -59283,8 +57032,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 8,
     "Tools available on UseGalaxy.cz": 8,
     "Tools available on UseGalaxy.no": 8,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -59327,10 +57075,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -59353,7 +57099,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -59397,7 +57142,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate",
     "Galaxy wrapper version": "2.3.2",
     "Conda id": "kleborate",
-    "Conda version": "3.0.6",
+    "Conda version": "3.0.9",
     "EDAM operation (no superclasses)": [
       "Multilocus sequence typing",
       "Genome assembly",
@@ -59419,10 +57164,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -59445,7 +57188,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -59489,10 +57231,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -59515,8 +57255,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -59571,10 +57310,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -59597,8 +57334,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -59641,10 +57377,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -59667,7 +57401,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -59725,10 +57458,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -59751,8 +57482,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -59814,10 +57544,8 @@
     "Tools available on UseGalaxy.eu": 6,
     "Tools available on UseGalaxy.fr": 6,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -59826,7 +57554,7 @@
     "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 1,
-    "Tools available on Galaxy@Pasteur": 4,
+    "Tools available on Galaxy@Pasteur": 6,
     "Tools available on GalaxyTrakr": 6,
     "Tools available on Genomic Hyperbrowser": 0,
     "Tools available on GigaGalaxy": 0,
@@ -59840,7 +57568,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 6,
     "Tools available on UseGalaxy.no": 0,
@@ -59896,10 +57623,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -59922,7 +57647,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -59965,7 +57689,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/last",
     "Galaxy wrapper version": "1205",
     "Conda id": "last",
-    "Conda version": "1574",
+    "Conda version": "1584",
     "EDAM operation (no superclasses)": [
       "Sequence alignment"
     ],
@@ -59981,10 +57705,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 5,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -60007,8 +57729,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 5,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -60064,10 +57785,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -60090,8 +57809,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -60134,10 +57852,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -60160,7 +57876,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -60214,10 +57929,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -60240,7 +57953,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -60287,10 +57999,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -60313,8 +58023,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -60371,10 +58080,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -60397,8 +58104,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -60460,10 +58166,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -60486,7 +58190,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -60552,10 +58255,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -60578,7 +58279,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -60626,10 +58326,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 4,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -60652,8 +58350,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 5,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -60708,10 +58405,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -60734,7 +58429,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -60779,10 +58473,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -60805,8 +58497,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -60869,10 +58560,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -60895,7 +58584,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -60926,7 +58614,7 @@
       "Metagenomics",
       "Statistics and probability"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "http://huttenhower.sph.harvard.edu/maaslin",
     "ToolShed categories": [
       "Metagenomics"
@@ -60935,7 +58623,7 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/biobakery/Maaslin2",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2",
-    "Galaxy wrapper version": "1.16.0",
+    "Galaxy wrapper version": "1.18.0",
     "Conda id": "bioconductor-maaslin2",
     "Conda version": "1.18.0",
     "EDAM operation (no superclasses)": [
@@ -60956,10 +58644,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -60982,7 +58668,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -61053,10 +58738,8 @@
     "Tools available on UseGalaxy.eu": 9,
     "Tools available on UseGalaxy.fr": 9,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 9,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -61079,8 +58762,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 9,
     "Tools available on UseGalaxy.cz": 9,
     "Tools available on UseGalaxy.no": 9,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -61123,10 +58805,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 1,
+    "Tools available on ARGs-OAP": 1,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 1,
@@ -61149,8 +58829,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -61211,10 +58890,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 5,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -61237,8 +58914,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 5,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -61296,10 +58972,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -61322,8 +58996,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -61366,10 +59039,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -61392,7 +59063,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -61436,10 +59106,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -61462,7 +59130,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -61520,10 +59187,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -61546,7 +59211,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -61608,10 +59272,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -61634,8 +59296,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -61678,10 +59339,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -61704,7 +59363,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -61765,10 +59423,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -61791,8 +59447,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -61849,10 +59504,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -61875,8 +59528,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -61932,10 +59584,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -61958,7 +59608,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -62002,7 +59651,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka",
     "Galaxy wrapper version": "1.7.2",
     "Conda id": "medaka",
-    "Conda version": "1.11.3",
+    "Conda version": "2.0.0",
     "EDAM operation (no superclasses)": [
       "Base-calling",
       "Variant calling",
@@ -62021,10 +59670,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -62047,8 +59694,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 3,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 3,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -62108,10 +59754,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -62134,8 +59778,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -62195,10 +59838,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -62221,7 +59862,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -62283,10 +59923,8 @@
     "Tools available on UseGalaxy.eu": 7,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -62309,7 +59947,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 7,
     "Tools available on UseGalaxy.no": 0,
@@ -62377,10 +60014,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 2,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 2,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -62403,8 +60038,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 3,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 4,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -62447,10 +60081,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -62473,8 +60105,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -62530,10 +60161,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -62556,7 +60185,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -62613,10 +60241,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -62639,7 +60265,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -62706,10 +60331,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -62732,7 +60355,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -62797,10 +60419,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -62823,7 +60443,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -62886,10 +60505,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -62912,7 +60529,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -62939,7 +60555,7 @@
     "EDAM topic": [
       "Taxonomy"
     ],
-    "Status": "Up-to-date",
+    "Status": "To update",
     "Source": "https://github.com/steineggerlab/Metabuli",
     "ToolShed categories": [
       "Sequence Analysis",
@@ -62951,7 +60567,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli",
     "Galaxy wrapper version": "1.0.5",
     "Conda id": "metabuli",
-    "Conda version": "1.0.5",
+    "Conda version": "1.0.8",
     "EDAM operation (no superclasses)": [
       "Taxonomic classification"
     ],
@@ -62960,17 +60576,15 @@
     ],
     "Available on UseGalaxy.org (Main)": 0,
     "Available on UseGalaxy.org.au": 0,
-    "Available on UseGalaxy.eu": 0,
+    "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
     "Tools available on UseGalaxy.org.au": 0,
-    "Tools available on UseGalaxy.eu": 0,
+    "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -62993,7 +60607,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -63050,10 +60663,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -63076,8 +60687,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -63134,10 +60744,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -63160,8 +60768,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -63220,10 +60827,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 4,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -63231,7 +60836,7 @@
     "Tools available on Dintor": 0,
     "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
-    "Tools available on Galaxy@AuBi": 1,
+    "Tools available on Galaxy@AuBi": 2,
     "Tools available on Galaxy@Pasteur": 0,
     "Tools available on GalaxyTrakr": 4,
     "Tools available on Genomic Hyperbrowser": 0,
@@ -63246,7 +60851,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 4,
@@ -63312,10 +60916,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -63338,7 +60940,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -63393,10 +60994,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -63419,7 +61018,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -63449,7 +61047,7 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed",
-    "Galaxy wrapper version": "1.3.2",
+    "Galaxy wrapper version": "1.3.3",
     "Conda id": "python",
     "Conda version": null,
     "EDAM operation (no superclasses)": [],
@@ -63463,10 +61061,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -63489,7 +61085,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -63547,10 +61142,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -63573,8 +61166,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -63627,10 +61219,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -63653,8 +61243,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -63709,10 +61298,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -63735,8 +61322,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -63789,10 +61375,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -63815,8 +61399,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -63874,10 +61457,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -63900,7 +61481,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -63944,10 +61524,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -63970,7 +61548,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -64015,10 +61592,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -64041,7 +61616,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -64085,10 +61659,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -64111,7 +61683,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -64168,10 +61739,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -64194,8 +61763,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -64249,10 +61817,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -64275,8 +61841,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -64319,10 +61884,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -64345,8 +61908,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -64389,10 +61951,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -64415,7 +61975,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -64615,10 +62174,8 @@
     "Tools available on UseGalaxy.eu": 129,
     "Tools available on UseGalaxy.fr": 129,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 3,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -64641,8 +62198,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 126,
     "Tools available on UseGalaxy.cz": 129,
     "Tools available on UseGalaxy.no": 129,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -64685,10 +62241,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -64711,8 +62265,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -64755,10 +62308,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -64781,7 +62332,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -64849,10 +62399,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -64875,7 +62423,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -64917,9 +62464,9 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc",
-    "Galaxy wrapper version": "1.11",
+    "Galaxy wrapper version": "1.24.1",
     "Conda id": "multiqc",
-    "Conda version": "1.24.1",
+    "Conda version": "1.25.1",
     "EDAM operation (no superclasses)": [
       "Sequencing quality control"
     ],
@@ -64938,10 +62485,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -64964,8 +62509,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -65015,10 +62559,8 @@
     "Tools available on UseGalaxy.eu": 6,
     "Tools available on UseGalaxy.fr": 6,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -65041,8 +62583,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 6,
     "Tools available on UseGalaxy.cz": 6,
     "Tools available on UseGalaxy.no": 6,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -65109,10 +62650,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -65135,7 +62674,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -65221,10 +62759,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -65247,7 +62783,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -65293,10 +62828,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -65319,7 +62852,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -65387,10 +62919,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -65413,8 +62943,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -65469,10 +62998,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -65495,8 +63022,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -65556,10 +63082,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -65582,8 +63106,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -65626,10 +63149,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -65652,8 +63173,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -65711,10 +63231,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -65737,8 +63255,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -65783,10 +63300,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -65809,7 +63324,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -65860,10 +63374,8 @@
     "Tools available on UseGalaxy.eu": 8,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 8,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -65886,7 +63398,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 8,
     "Tools available on UseGalaxy.no": 8,
@@ -65946,10 +63457,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -65972,7 +63481,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -66026,10 +63534,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -66052,7 +63558,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -66111,10 +63616,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -66137,8 +63640,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -66197,10 +63699,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -66223,7 +63723,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -66284,10 +63783,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -66310,8 +63807,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -66372,10 +63868,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -66398,8 +63892,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -66448,10 +63941,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -66474,8 +63965,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -66518,10 +64008,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -66544,8 +64032,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -66601,10 +64088,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -66627,7 +64112,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -66696,10 +64180,8 @@
     "Tools available on UseGalaxy.eu": 10,
     "Tools available on UseGalaxy.fr": 10,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -66722,7 +64204,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 10,
     "Tools available on UseGalaxy.no": 10,
@@ -66766,10 +64247,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -66792,8 +64271,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -66837,10 +64315,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -66863,8 +64339,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -66923,10 +64398,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -66949,7 +64422,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -66996,10 +64468,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -67022,8 +64492,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 4,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 4,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -67084,10 +64553,8 @@
     "Tools available on UseGalaxy.eu": 17,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -67110,7 +64577,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 17,
     "Tools available on UseGalaxy.no": 17,
@@ -67154,10 +64620,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -67180,7 +64644,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -67216,18 +64679,16 @@
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
-    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.org.au": 1,
     "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
-    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.org.au": 1,
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -67250,7 +64711,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -67316,10 +64776,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -67342,7 +64800,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -67408,10 +64865,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -67434,8 +64889,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -67478,10 +64932,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -67504,7 +64956,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -67561,10 +65012,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -67587,7 +65036,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -67635,10 +65083,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -67661,7 +65107,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -67717,10 +65162,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -67743,8 +65186,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -67787,10 +65229,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -67813,7 +65253,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -67875,10 +65314,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -67901,8 +65338,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -67955,10 +65391,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -67981,7 +65415,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -68037,10 +65470,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -68063,7 +65494,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -68109,10 +65539,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -68135,7 +65563,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -68179,10 +65606,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -68205,8 +65630,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -68249,10 +65673,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -68275,7 +65697,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -68329,10 +65750,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -68355,8 +65774,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -68423,10 +65841,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -68449,7 +65865,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -68514,10 +65929,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 4,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -68540,7 +65953,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 3,
@@ -68596,10 +66008,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -68622,8 +66032,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -68669,9 +66078,9 @@
     "bio.tool id": "picard_samtofastq",
     "bio.tool ids": [
       "picard_reordersam",
-      "picard_replacesamheader",
+      "picard_samtofastq",
       "picard_fastqtosam",
-      "picard_samtofastq"
+      "picard_replacesamheader"
     ],
     "biii": null,
     "bio.tool name": "picard_samtofastq",
@@ -68709,10 +66118,8 @@
     "Tools available on UseGalaxy.eu": 31,
     "Tools available on UseGalaxy.fr": 31,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 29,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 31,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -68735,8 +66142,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 31,
     "Tools available on UseGalaxy.cz": 31,
     "Tools available on UseGalaxy.no": 31,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -68779,10 +66185,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -68805,7 +66209,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -68876,10 +66279,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 6,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -68902,7 +66303,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
@@ -68974,10 +66374,8 @@
     "Tools available on UseGalaxy.eu": 7,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -69000,7 +66398,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 7,
     "Tools available on UseGalaxy.no": 0,
@@ -69057,10 +66454,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -69083,8 +66478,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -69127,10 +66521,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -69153,8 +66545,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -69197,10 +66588,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -69223,7 +66612,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -69277,10 +66665,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -69303,8 +66689,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -69358,19 +66743,17 @@
       "Mapping",
       "Probes and primers"
     ],
-    "Available on UseGalaxy.org (Main)": 0,
+    "Available on UseGalaxy.org (Main)": 1,
     "Available on UseGalaxy.org.au": 1,
     "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 1,
-    "Tools available on UseGalaxy.org (Main)": 0,
+    "Tools available on UseGalaxy.org (Main)": 1,
     "Tools available on UseGalaxy.org.au": 1,
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -69393,7 +66776,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -69447,10 +66829,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -69473,8 +66853,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -69537,10 +66916,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -69563,7 +66940,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -69608,10 +66984,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -69620,7 +66994,7 @@
     "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
-    "Tools available on Galaxy@Pasteur": 0,
+    "Tools available on Galaxy@Pasteur": 1,
     "Tools available on GalaxyTrakr": 1,
     "Tools available on Genomic Hyperbrowser": 0,
     "Tools available on GigaGalaxy": 0,
@@ -69634,8 +67008,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -69703,10 +67076,8 @@
     "Tools available on UseGalaxy.eu": 13,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 13,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -69729,9 +67100,8 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
-    "Tools available on UseGalaxy.cz": 13,
+    "Tools available on UseGalaxy.cz": 6,
     "Tools available on UseGalaxy.no": 13,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
     "No. of tool users (2022-2023) (usegalaxy.eu)": 409,
@@ -69797,10 +67167,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -69823,7 +67191,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -69869,10 +67236,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -69895,7 +67260,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -69957,10 +67321,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -69983,8 +67345,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -70031,18 +67392,16 @@
       "Sequence analysis"
     ],
     "Available on UseGalaxy.org (Main)": 0,
-    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.org.au": 1,
     "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 1,
     "Tools available on UseGalaxy.org (Main)": 0,
-    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.org.au": 1,
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -70065,7 +67424,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -70110,10 +67468,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 2,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -70136,7 +67492,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
@@ -70197,10 +67552,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -70223,8 +67576,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -70267,10 +67619,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -70293,7 +67643,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -70351,10 +67700,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -70377,8 +67724,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 3,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 3,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -70431,10 +67777,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -70457,7 +67801,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -70503,10 +67846,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -70529,7 +67870,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -70587,10 +67927,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -70613,7 +67951,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -70673,10 +68010,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -70685,7 +68020,7 @@
     "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 1,
-    "Tools available on Galaxy@Pasteur": 0,
+    "Tools available on Galaxy@Pasteur": 1,
     "Tools available on GalaxyTrakr": 1,
     "Tools available on Genomic Hyperbrowser": 0,
     "Tools available on GigaGalaxy": 0,
@@ -70699,7 +68034,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -70743,10 +68077,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -70769,8 +68101,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -70829,10 +68160,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -70855,8 +68184,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -70915,10 +68243,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -70941,7 +68267,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -70985,10 +68310,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -71011,7 +68334,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -71081,10 +68403,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -71107,7 +68427,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
@@ -71206,10 +68525,8 @@
     "Tools available on UseGalaxy.eu": 32,
     "Tools available on UseGalaxy.fr": 32,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -71232,7 +68549,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 31,
     "Tools available on UseGalaxy.no": 31,
@@ -71276,10 +68592,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -71302,7 +68616,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -71347,10 +68660,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -71373,7 +68684,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -71432,10 +68742,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -71458,8 +68766,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 4,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 4,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -71514,10 +68821,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -71540,8 +68845,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -71585,10 +68889,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -71611,7 +68913,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -71657,10 +68958,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -71683,8 +68982,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 3,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 3,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -71751,84 +69049,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
-    "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
-    "Tools available on ChemFlow": 0,
-    "Tools available on Coloc-stats": 0,
-    "Tools available on CoralSNP": 0,
-    "Tools available on CropGalaxy": 0,
-    "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
-    "Tools available on GASLINI": 0,
-    "Tools available on Galaxy@AuBi": 0,
-    "Tools available on Galaxy@Pasteur": 0,
-    "Tools available on GalaxyTrakr": 0,
-    "Tools available on Genomic Hyperbrowser": 0,
-    "Tools available on GigaGalaxy": 0,
-    "Tools available on HyPhy HIV NGS Tools": 0,
-    "Tools available on IPK Galaxy Blast Suite": 0,
-    "Tools available on ImmPort Galaxy": 0,
-    "Tools available on InteractoMIX": 0,
-    "Tools available on MISSISSIPPI": 0,
-    "Tools available on Mandoiu Lab": 0,
-    "Tools available on MiModD NacreousMap": 0,
-    "Tools available on Oqtans": 0,
-    "Tools available on Palfinder": 0,
-    "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
-    "Tools available on UseGalaxy.cz": 0,
-    "Tools available on UseGalaxy.no": 1,
-    "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
-    "Total tool usage (usegalaxy.eu)": 0
-  },
-  {
-    "Galaxy wrapper id": "raceid",
-    "Galaxy tool ids": [
-      "raceid_clustering",
-      "raceid_filtnormconf",
-      "raceid_inspectclusters",
-      "raceid_inspecttrajectory",
-      "raceid_trajectory"
-    ],
-    "Description": "RaceID3, StemID2, FateID - scRNA analysis",
-    "bio.tool id": null,
-    "bio.tool ids": [],
-    "biii": null,
-    "bio.tool name": null,
-    "bio.tool description": null,
-    "EDAM operation": [],
-    "EDAM topic": [],
-    "Status": "To update",
-    "Source": "https://github.com/dgrun/RaceID3_StemID2_package/",
-    "ToolShed categories": [
-      "Transcriptomics"
-    ],
-    "ToolShed id": null,
-    "Galaxy wrapper owner": "iuc",
-    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3",
-    "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid",
-    "Galaxy wrapper version": "0.2.3",
-    "Conda id": "r-raceid",
-    "Conda version": "0.1.3",
-    "EDAM operation (no superclasses)": [],
-    "EDAM topic (no superclasses)": [],
-    "Available on UseGalaxy.org (Main)": 5,
-    "Available on UseGalaxy.org.au": 5,
-    "Available on UseGalaxy.eu": 5,
-    "Available on UseGalaxy.fr": 1,
-    "Tools available on UseGalaxy.org (Main)": 5,
-    "Tools available on UseGalaxy.org.au": 5,
-    "Tools available on UseGalaxy.eu": 5,
-    "Tools available on UseGalaxy.fr": 1,
-    "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -71851,8 +69073,79 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.cz": 0,
+    "Tools available on UseGalaxy.no": 1,
+    "Tools available on Viral Variant Visualizer (VVV)": 0,
+    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+    "Total tool usage (usegalaxy.eu)": 0
+  },
+  {
+    "Galaxy wrapper id": "raceid",
+    "Galaxy tool ids": [
+      "raceid_clustering",
+      "raceid_filtnormconf",
+      "raceid_inspectclusters",
+      "raceid_inspecttrajectory",
+      "raceid_trajectory"
+    ],
+    "Description": "RaceID3, StemID2, FateID - scRNA analysis",
+    "bio.tool id": null,
+    "bio.tool ids": [],
+    "biii": null,
+    "bio.tool name": null,
+    "bio.tool description": null,
+    "EDAM operation": [],
+    "EDAM topic": [],
+    "Status": "To update",
+    "Source": "https://github.com/dgrun/RaceID3_StemID2_package/",
+    "ToolShed categories": [
+      "Single Cell",
+      "Transcriptomics"
+    ],
+    "ToolShed id": null,
+    "Galaxy wrapper owner": "iuc",
+    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3",
+    "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid",
+    "Galaxy wrapper version": "0.2.3",
+    "Conda id": "r-raceid",
+    "Conda version": "0.1.3",
+    "EDAM operation (no superclasses)": [],
+    "EDAM topic (no superclasses)": [],
+    "Available on UseGalaxy.org (Main)": 5,
+    "Available on UseGalaxy.org.au": 5,
+    "Available on UseGalaxy.eu": 5,
+    "Available on UseGalaxy.fr": 1,
+    "Tools available on UseGalaxy.org (Main)": 5,
+    "Tools available on UseGalaxy.org.au": 5,
+    "Tools available on UseGalaxy.eu": 5,
+    "Tools available on UseGalaxy.fr": 1,
+    "Tools available on APOSTL": 0,
+    "Tools available on ARGs-OAP": 0,
+    "Tools available on CIRM-CFBP": 0,
+    "Tools available on ChemFlow": 0,
+    "Tools available on Coloc-stats": 0,
+    "Tools available on CoralSNP": 0,
+    "Tools available on CropGalaxy": 0,
+    "Tools available on Dintor": 0,
+    "Tools available on FreeBioinfo": 0,
+    "Tools available on GASLINI": 0,
+    "Tools available on Galaxy@AuBi": 0,
+    "Tools available on Galaxy@Pasteur": 0,
+    "Tools available on GalaxyTrakr": 0,
+    "Tools available on Genomic Hyperbrowser": 0,
+    "Tools available on GigaGalaxy": 0,
+    "Tools available on HyPhy HIV NGS Tools": 0,
+    "Tools available on IPK Galaxy Blast Suite": 0,
+    "Tools available on ImmPort Galaxy": 0,
+    "Tools available on InteractoMIX": 0,
+    "Tools available on MISSISSIPPI": 0,
+    "Tools available on Mandoiu Lab": 0,
+    "Tools available on MiModD NacreousMap": 0,
+    "Tools available on Oqtans": 0,
+    "Tools available on Palfinder": 0,
+    "Tools available on PepSimili": 0,
+    "Tools available on UseGalaxy.be": 5,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -71905,10 +69198,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -71931,7 +69222,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -71983,10 +69273,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -72009,7 +69297,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -72055,10 +69342,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -72081,7 +69366,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -72125,10 +69409,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -72151,7 +69433,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -72207,10 +69488,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -72233,8 +69512,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -72290,10 +69568,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -72316,7 +69592,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -72374,10 +69649,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -72400,7 +69673,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -72440,9 +69712,9 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge",
-    "Galaxy wrapper version": "1.14.1",
+    "Galaxy wrapper version": "1.15.0",
     "Conda id": "recentrifuge",
-    "Conda version": "1.14.1",
+    "Conda version": "1.15.0",
     "EDAM operation (no superclasses)": [
       "Taxonomic classification",
       "Expression analysis",
@@ -72462,10 +69734,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -72488,7 +69758,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -72548,10 +69817,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -72574,7 +69841,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -72602,7 +69868,7 @@
       "Sequence analysis",
       "Sequence composition, complexity and repeats"
     ],
-    "Status": "Up-to-date",
+    "Status": "To update",
     "Source": "http://www.repeatmasker.org/",
     "ToolShed categories": [
       "Sequence Analysis"
@@ -72613,7 +69879,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker",
     "Galaxy wrapper version": "4.1.5",
     "Conda id": "repeatmasker",
-    "Conda version": "4.1.5",
+    "Conda version": "4.0.9_p2",
     "EDAM operation (no superclasses)": [
       "Genome annotation"
     ],
@@ -72629,10 +69895,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -72655,8 +69919,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -72711,10 +69974,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -72737,7 +69998,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -72781,10 +70041,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -72807,7 +70065,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -72852,10 +70109,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -72878,8 +70133,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -72922,10 +70176,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -72948,8 +70200,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -73005,10 +70256,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -73031,7 +70280,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -73075,10 +70323,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -73101,7 +70347,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -73159,10 +70404,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -73185,8 +70428,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -73237,10 +70479,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -73263,7 +70503,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -73325,10 +70564,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -73351,8 +70588,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -73409,10 +70645,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -73435,8 +70669,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -73479,10 +70712,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -73505,7 +70736,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -73549,10 +70779,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -73575,7 +70803,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -73619,10 +70846,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -73645,7 +70870,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -73689,10 +70913,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -73715,7 +70937,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -73763,10 +70984,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -73789,7 +71008,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -73833,10 +71051,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -73859,7 +71075,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -73938,10 +71153,8 @@
     "Tools available on UseGalaxy.eu": 22,
     "Tools available on UseGalaxy.fr": 22,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -73964,8 +71177,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 22,
     "Tools available on UseGalaxy.cz": 22,
     "Tools available on UseGalaxy.no": 22,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -74021,10 +71233,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -74047,8 +71257,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -74109,10 +71318,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -74135,8 +71342,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -74195,10 +71401,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -74221,7 +71425,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -74242,7 +71445,7 @@
     "bio.tool description": null,
     "EDAM operation": [],
     "EDAM topic": [],
-    "Status": "Up-to-date",
+    "Status": "To update",
     "Source": "https://github.com/dellytools/sansa",
     "ToolShed categories": [
       "Variant Analysis"
@@ -74253,7 +71456,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa",
     "Galaxy wrapper version": "0.2.1",
     "Conda id": "sansa",
-    "Conda version": "0.2.1",
+    "Conda version": "0.2.2",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -74265,10 +71468,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -74291,8 +71492,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -74335,10 +71535,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -74361,8 +71559,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -74405,10 +71602,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -74431,8 +71626,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -74475,10 +71669,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -74501,7 +71693,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -74538,14 +71729,15 @@
     "Status": "To update",
     "Source": "https://scanpy.readthedocs.io",
     "ToolShed categories": [
-      "Transcriptomics",
-      "Sequence Analysis"
+      "Single Cell",
+      "Spatial Omics",
+      "Transcriptomics"
     ],
     "ToolShed id": "scanpy",
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy",
-    "Galaxy wrapper version": "1.9.6",
+    "Galaxy wrapper version": "1.10.2",
     "Conda id": "scanpy",
     "Conda version": "1.7.2",
     "EDAM operation (no superclasses)": [
@@ -74565,10 +71757,8 @@
     "Tools available on UseGalaxy.eu": 6,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -74591,8 +71781,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 6,
     "Tools available on UseGalaxy.cz": 6,
     "Tools available on UseGalaxy.no": 6,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -74629,8 +71818,8 @@
     "Status": "To update",
     "Source": "http://bioconductor.org/packages/scater/",
     "ToolShed categories": [
+      "Single Cell",
       "Transcriptomics",
-      "RNA",
       "Visualization"
     ],
     "ToolShed id": null,
@@ -74657,10 +71846,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -74683,8 +71870,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 5,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -74707,7 +71893,9 @@
     "Status": "Up-to-date",
     "Source": "https://github.com/cellgeni/sceasy/",
     "ToolShed categories": [
-      "Transcriptomics"
+      "Single Cell",
+      "Spatial Omics",
+      "Convert Formats"
     ],
     "ToolShed id": "sceasy_convert",
     "Galaxy wrapper owner": "iuc",
@@ -74727,10 +71915,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -74753,7 +71939,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -74794,7 +71979,8 @@
     "ToolShed categories": [
       "Sequence Analysis",
       "Transcriptomics",
-      "Visualization"
+      "Visualization",
+      "Single Cell"
     ],
     "ToolShed id": "schicexplorer",
     "Galaxy wrapper owner": "iuc",
@@ -74814,10 +72000,8 @@
     "Tools available on UseGalaxy.eu": 16,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -74840,8 +72024,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 16,
     "Tools available on UseGalaxy.cz": 16,
     "Tools available on UseGalaxy.no": 16,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -74884,10 +72067,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -74910,7 +72091,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -74970,10 +72150,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -74996,7 +72174,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -75032,8 +72209,7 @@
     "Source": "http://bioconductor.org/packages/release/bioc/html/scPipe.html",
     "ToolShed categories": [
       "Transcriptomics",
-      "RNA",
-      "Statistics"
+      "Single Cell"
     ],
     "ToolShed id": "scpipe",
     "Galaxy wrapper owner": "iuc",
@@ -75061,10 +72237,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -75087,8 +72261,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -75132,10 +72305,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -75158,8 +72329,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -75202,10 +72372,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -75228,7 +72396,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -75295,10 +72462,8 @@
     "Tools available on UseGalaxy.eu": 6,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -75321,7 +72486,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 6,
     "Tools available on UseGalaxy.no": 0,
@@ -75371,18 +72535,16 @@
       "Mapping"
     ],
     "Available on UseGalaxy.org (Main)": 0,
-    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.org.au": 1,
     "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
-    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.org.au": 1,
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -75405,8 +72567,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -75449,10 +72610,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -75475,7 +72634,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -75534,16 +72692,14 @@
     "Available on UseGalaxy.org (Main)": 0,
     "Available on UseGalaxy.org.au": 2,
     "Available on UseGalaxy.eu": 5,
-    "Available on UseGalaxy.fr": 2,
+    "Available on UseGalaxy.fr": 3,
     "Tools available on UseGalaxy.org (Main)": 0,
     "Tools available on UseGalaxy.org.au": 2,
     "Tools available on UseGalaxy.eu": 5,
-    "Tools available on UseGalaxy.fr": 2,
+    "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -75566,7 +72722,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 0,
@@ -75627,10 +72782,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -75653,7 +72806,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -75715,10 +72867,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -75741,7 +72891,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -75809,10 +72958,8 @@
     "Tools available on UseGalaxy.eu": 15,
     "Tools available on UseGalaxy.fr": 15,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 14,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -75835,8 +72982,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 14,
     "Tools available on UseGalaxy.cz": 14,
     "Tools available on UseGalaxy.no": 14,
     "Tools available on Viral Variant Visualizer (VVV)": 14,
@@ -75880,10 +73026,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -75906,8 +73050,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -75917,9 +73060,15 @@
   {
     "Galaxy wrapper id": "seurat",
     "Galaxy tool ids": [
-      "seurat"
+      "seurat_create",
+      "seurat_data",
+      "seurat_integrate",
+      "seurat_clustering",
+      "seurat_preprocessing",
+      "seurat_plot",
+      "seurat_reduce_dimension"
     ],
-    "Description": "A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data",
+    "Description": "Seurat - R toolkit for single cell genomics",
     "bio.tool id": null,
     "bio.tool ids": [],
     "biii": null,
@@ -75928,34 +73077,32 @@
     "EDAM operation": [],
     "EDAM topic": [],
     "Status": "To update",
-    "Source": "https://github.com/satijalab/seurat",
+    "Source": "https://satijalab.org/seurat/",
     "ToolShed categories": [
+      "Single Cell",
       "Transcriptomics",
-      "RNA",
-      "Statistics"
+      "Sequence Analysis"
     ],
     "ToolShed id": "seurat",
     "Galaxy wrapper owner": "iuc",
-    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat",
+    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat",
-    "Galaxy wrapper version": "4.3.0.1",
+    "Galaxy wrapper version": "5.0",
     "Conda id": "r-seurat",
     "Conda version": "3.0.2",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
     "Available on UseGalaxy.org.au": 1,
-    "Available on UseGalaxy.eu": 1,
+    "Available on UseGalaxy.eu": 7,
     "Available on UseGalaxy.fr": 1,
     "Tools available on UseGalaxy.org (Main)": 1,
     "Tools available on UseGalaxy.org.au": 1,
-    "Tools available on UseGalaxy.eu": 1,
+    "Tools available on UseGalaxy.eu": 7,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -75972,19 +73119,18 @@
     "Tools available on IPK Galaxy Blast Suite": 0,
     "Tools available on ImmPort Galaxy": 0,
     "Tools available on InteractoMIX": 0,
-    "Tools available on MISSISSIPPI": 1,
+    "Tools available on MISSISSIPPI": 7,
     "Tools available on Mandoiu Lab": 0,
     "Tools available on MiModD NacreousMap": 0,
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
-    "Tools available on UseGalaxy.cz": 1,
-    "Tools available on UseGalaxy.no": 1,
+    "Tools available on UseGalaxy.cz": 0,
+    "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 66,
-    "Total tool usage (usegalaxy.eu)": 1543
+    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+    "Total tool usage (usegalaxy.eu)": 0
   },
   {
     "Galaxy wrapper id": "shasta",
@@ -76011,7 +73157,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta",
     "Galaxy wrapper version": "0.6.0",
     "Conda id": "shasta",
-    "Conda version": "0.12.0",
+    "Conda version": "0.13.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -76023,10 +73169,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -76049,8 +73193,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -76109,10 +73252,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -76135,7 +73276,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -76193,10 +73333,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -76219,8 +73357,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -76274,10 +73411,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -76300,8 +73435,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -76347,10 +73481,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -76373,7 +73505,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 0,
@@ -76443,10 +73574,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -76469,8 +73598,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -76491,16 +73619,17 @@
     "bio.tool description": null,
     "EDAM operation": [],
     "EDAM topic": [],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "https://github.com/timoast/sinto",
     "ToolShed categories": [
-      "Sequence Analysis"
+      "Single Cell",
+      "Epigenetics"
     ],
     "ToolShed id": null,
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto",
-    "Galaxy wrapper version": "0.9.0",
+    "Galaxy wrapper version": "0.10.1",
     "Conda id": "sinto",
     "Conda version": "0.10.1",
     "EDAM operation (no superclasses)": [],
@@ -76514,10 +73643,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -76540,7 +73667,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -76588,10 +73714,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -76614,8 +73738,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -76679,10 +73802,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -76705,7 +73826,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -76771,10 +73891,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -76797,7 +73915,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -76828,7 +73945,7 @@
       "Genetic variation",
       "Mathematics"
     ],
-    "Status": "Up-to-date",
+    "Status": "To update",
     "Source": "https://github.com/KamilSJaron/smudgeplot",
     "ToolShed categories": [
       "Assembly"
@@ -76839,7 +73956,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot",
     "Galaxy wrapper version": "0.2.5",
     "Conda id": "smudgeplot",
-    "Conda version": "0.2.5",
+    "Conda version": "0.3.0",
     "EDAM operation (no superclasses)": [
       "Sequence trimming",
       "Genotyping",
@@ -76859,10 +73976,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -76885,7 +74000,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -76943,10 +74057,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -76969,8 +74081,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -76996,8 +74107,8 @@
     "Status": "To update",
     "Source": "https://kzhang.org/SnapATAC2/",
     "ToolShed categories": [
-      "Epigenetics",
-      "Sequence Analysis"
+      "Single Cell",
+      "Epigenetics"
     ],
     "ToolShed id": "snapatac2",
     "Galaxy wrapper owner": "iuc",
@@ -77017,10 +74128,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -77043,7 +74152,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -77072,7 +74180,7 @@
       "DNA structural variation",
       "Sequencing"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "https://github.com/fritzsedlazeck/Sniffles",
     "ToolShed categories": [
       "Sequence Analysis"
@@ -77081,7 +74189,7 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles",
-    "Galaxy wrapper version": "1.0.12",
+    "Galaxy wrapper version": "2.4",
     "Conda id": "sniffles",
     "Conda version": "2.4",
     "EDAM operation (no superclasses)": [
@@ -77100,10 +74208,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -77126,8 +74232,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -77181,10 +74286,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -77207,7 +74310,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -77272,10 +74374,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 2,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -77298,8 +74398,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 3,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -77342,10 +74441,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -77368,8 +74465,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -77412,10 +74508,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -77438,8 +74532,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -77496,10 +74589,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -77522,8 +74613,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -77566,10 +74656,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -77592,7 +74680,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -77636,10 +74723,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -77662,8 +74747,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -77726,10 +74810,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -77752,7 +74834,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -77776,15 +74857,15 @@
     "Description": "SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.",
     "bio.tool id": "spades",
     "bio.tool ids": [
-      "coronaspades",
-      "biosyntheticspades",
-      "metaplasmidspades",
+      "spades",
       "plasmidspades",
-      "metaspades",
       "rnaspades",
+      "metaplasmidspades",
+      "metaspades",
       "metaviralspades",
+      "biosyntheticspades",
       "rnaviralspades",
-      "spades"
+      "coronaspades"
     ],
     "biii": null,
     "bio.tool name": "SPAdes",
@@ -77824,10 +74905,8 @@
     "Tools available on UseGalaxy.eu": 9,
     "Tools available on UseGalaxy.fr": 9,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -77850,8 +74929,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 3,
     "Tools available on UseGalaxy.cz": 9,
     "Tools available on UseGalaxy.no": 3,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -77896,10 +74974,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -77922,8 +74998,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -77933,8 +75008,8 @@
   {
     "Galaxy wrapper id": "spapros",
     "Galaxy tool ids": [
-      "spapros",
-      "spapros"
+      "spapros_evaluation",
+      "spapros_selection"
     ],
     "Description": "Select and evaluate probe sets for targeted spatial transcriptomics.",
     "bio.tool id": null,
@@ -77947,6 +75022,7 @@
     "Status": "Up-to-date",
     "Source": "https://github.com/theislab/spapros",
     "ToolShed categories": [
+      "Single Cell",
       "Transcriptomics",
       "Sequence Analysis"
     ],
@@ -77961,17 +75037,15 @@
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
     "Available on UseGalaxy.org.au": 0,
-    "Available on UseGalaxy.eu": 0,
+    "Available on UseGalaxy.eu": 2,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
     "Tools available on UseGalaxy.org.au": 0,
-    "Tools available on UseGalaxy.eu": 0,
+    "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -77994,7 +75068,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -78054,10 +75127,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -78080,7 +75151,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -78125,10 +75195,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -78151,8 +75219,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -78212,10 +75279,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -78238,8 +75303,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 3,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 3,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -78277,7 +75341,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2",
     "Galaxy wrapper version": "0.2.0",
     "Conda id": "samtools",
-    "Conda version": "1.20",
+    "Conda version": "1.21",
     "EDAM operation (no superclasses)": [
       "Multilocus sequence typing"
     ],
@@ -78294,10 +75358,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -78320,7 +75382,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -78388,10 +75449,8 @@
     "Tools available on UseGalaxy.eu": 13,
     "Tools available on UseGalaxy.fr": 12,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -78414,8 +75473,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 11,
     "Tools available on UseGalaxy.cz": 13,
     "Tools available on UseGalaxy.no": 13,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -78469,10 +75527,8 @@
     "Tools available on UseGalaxy.eu": 12,
     "Tools available on UseGalaxy.fr": 12,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -78495,7 +75551,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 12,
     "Tools available on UseGalaxy.no": 12,
@@ -78540,10 +75595,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -78566,8 +75619,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -78613,10 +75665,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -78639,7 +75689,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -78684,10 +75733,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -78710,8 +75757,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -78768,10 +75814,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -78794,8 +75838,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -78849,10 +75892,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -78875,8 +75916,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -78920,10 +75960,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -78946,7 +75984,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -78990,10 +76027,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -79016,7 +76051,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -79060,10 +76094,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -79086,7 +76118,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -79130,10 +76161,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -79156,8 +76185,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -79202,10 +76230,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -79228,8 +76254,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -79272,10 +76297,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -79298,7 +76321,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -79352,17 +76374,15 @@
     ],
     "Available on UseGalaxy.org (Main)": 0,
     "Available on UseGalaxy.org.au": 0,
-    "Available on UseGalaxy.eu": 0,
+    "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
     "Tools available on UseGalaxy.org.au": 0,
-    "Tools available on UseGalaxy.eu": 0,
+    "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -79385,7 +76405,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -79430,10 +76449,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -79456,7 +76473,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -79510,10 +76526,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -79536,8 +76550,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -79598,10 +76611,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -79624,7 +76635,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -79674,10 +76684,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -79700,8 +76708,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -79744,10 +76751,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -79770,8 +76775,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -79806,19 +76810,17 @@
     "Conda version": "0.6.6",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
-    "Available on UseGalaxy.org (Main)": 0,
+    "Available on UseGalaxy.org (Main)": 1,
     "Available on UseGalaxy.org.au": 1,
     "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 1,
-    "Tools available on UseGalaxy.org (Main)": 0,
+    "Tools available on UseGalaxy.org (Main)": 1,
     "Tools available on UseGalaxy.org.au": 1,
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -79841,7 +76843,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -79885,10 +76886,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -79911,8 +76910,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -79955,7 +76953,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder",
     "Galaxy wrapper version": "1.0.1",
     "Conda id": "samtools",
-    "Conda version": "1.20",
+    "Conda version": "1.21",
     "EDAM operation (no superclasses)": [
       "Genome indexing",
       "Variant calling",
@@ -79977,10 +76975,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -80003,7 +76999,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -80073,80 +77068,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
-    "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
-    "Tools available on ChemFlow": 0,
-    "Tools available on Coloc-stats": 0,
-    "Tools available on CoralSNP": 0,
-    "Tools available on CropGalaxy": 0,
-    "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
-    "Tools available on GASLINI": 0,
-    "Tools available on Galaxy@AuBi": 0,
-    "Tools available on Galaxy@Pasteur": 0,
-    "Tools available on GalaxyTrakr": 0,
-    "Tools available on Genomic Hyperbrowser": 0,
-    "Tools available on GigaGalaxy": 0,
-    "Tools available on HyPhy HIV NGS Tools": 0,
-    "Tools available on IPK Galaxy Blast Suite": 0,
-    "Tools available on ImmPort Galaxy": 0,
-    "Tools available on InteractoMIX": 0,
-    "Tools available on MISSISSIPPI": 0,
-    "Tools available on Mandoiu Lab": 0,
-    "Tools available on MiModD NacreousMap": 0,
-    "Tools available on Oqtans": 0,
-    "Tools available on Palfinder": 0,
-    "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
-    "Tools available on UseGalaxy.cz": 0,
-    "Tools available on UseGalaxy.no": 0,
-    "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
-    "Total tool usage (usegalaxy.eu)": 0
-  },
-  {
-    "Galaxy wrapper id": "tetoolkit",
-    "Galaxy tool ids": [
-      "tetoolkit_tetranscripts"
-    ],
-    "Description": "The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.",
-    "bio.tool id": null,
-    "bio.tool ids": [],
-    "biii": null,
-    "bio.tool name": null,
-    "bio.tool description": null,
-    "EDAM operation": [],
-    "EDAM topic": [],
-    "Status": "Up-to-date",
-    "Source": "http://hammelllab.labsites.cshl.edu/software/",
-    "ToolShed categories": [
-      "Sequence Analysis"
-    ],
-    "ToolShed id": "tetoolkit",
-    "Galaxy wrapper owner": "iuc",
-    "Galaxy wrapper source": "https://github.com/mhammell-laboratory/TEtranscripts",
-    "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit",
-    "Galaxy wrapper version": "2.2.3",
-    "Conda id": "tetranscripts",
-    "Conda version": "2.2.3",
-    "EDAM operation (no superclasses)": [],
-    "EDAM topic (no superclasses)": [],
-    "Available on UseGalaxy.org (Main)": 0,
-    "Available on UseGalaxy.org.au": 1,
-    "Available on UseGalaxy.eu": 1,
-    "Available on UseGalaxy.fr": 0,
-    "Tools available on UseGalaxy.org (Main)": 0,
-    "Tools available on UseGalaxy.org.au": 1,
-    "Tools available on UseGalaxy.eu": 1,
-    "Tools available on UseGalaxy.fr": 0,
-    "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -80169,8 +77092,74 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.cz": 0,
+    "Tools available on UseGalaxy.no": 0,
+    "Tools available on Viral Variant Visualizer (VVV)": 0,
+    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+    "Total tool usage (usegalaxy.eu)": 0
+  },
+  {
+    "Galaxy wrapper id": "tetoolkit",
+    "Galaxy tool ids": [
+      "tetoolkit_tetranscripts"
+    ],
+    "Description": "The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.",
+    "bio.tool id": null,
+    "bio.tool ids": [],
+    "biii": null,
+    "bio.tool name": null,
+    "bio.tool description": null,
+    "EDAM operation": [],
+    "EDAM topic": [],
+    "Status": "Up-to-date",
+    "Source": "http://hammelllab.labsites.cshl.edu/software/",
+    "ToolShed categories": [
+      "Sequence Analysis"
+    ],
+    "ToolShed id": "tetoolkit",
+    "Galaxy wrapper owner": "iuc",
+    "Galaxy wrapper source": "https://github.com/mhammell-laboratory/TEtranscripts",
+    "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit",
+    "Galaxy wrapper version": "2.2.3",
+    "Conda id": "tetranscripts",
+    "Conda version": "2.2.3",
+    "EDAM operation (no superclasses)": [],
+    "EDAM topic (no superclasses)": [],
+    "Available on UseGalaxy.org (Main)": 0,
+    "Available on UseGalaxy.org.au": 1,
+    "Available on UseGalaxy.eu": 1,
+    "Available on UseGalaxy.fr": 0,
+    "Tools available on UseGalaxy.org (Main)": 0,
+    "Tools available on UseGalaxy.org.au": 1,
+    "Tools available on UseGalaxy.eu": 1,
+    "Tools available on UseGalaxy.fr": 0,
+    "Tools available on APOSTL": 0,
+    "Tools available on ARGs-OAP": 0,
+    "Tools available on CIRM-CFBP": 0,
+    "Tools available on ChemFlow": 0,
+    "Tools available on Coloc-stats": 0,
+    "Tools available on CoralSNP": 0,
+    "Tools available on CropGalaxy": 0,
+    "Tools available on Dintor": 0,
+    "Tools available on FreeBioinfo": 0,
+    "Tools available on GASLINI": 0,
+    "Tools available on Galaxy@AuBi": 0,
+    "Tools available on Galaxy@Pasteur": 0,
+    "Tools available on GalaxyTrakr": 0,
+    "Tools available on Genomic Hyperbrowser": 0,
+    "Tools available on GigaGalaxy": 0,
+    "Tools available on HyPhy HIV NGS Tools": 0,
+    "Tools available on IPK Galaxy Blast Suite": 0,
+    "Tools available on ImmPort Galaxy": 0,
+    "Tools available on InteractoMIX": 0,
+    "Tools available on MISSISSIPPI": 0,
+    "Tools available on Mandoiu Lab": 0,
+    "Tools available on MiModD NacreousMap": 0,
+    "Tools available on Oqtans": 0,
+    "Tools available on Palfinder": 0,
+    "Tools available on PepSimili": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -80213,10 +77202,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -80239,8 +77226,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -80263,7 +77249,7 @@
     "bio.tool description": null,
     "EDAM operation": [],
     "EDAM topic": [],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "https://github.com/veg/tn93/",
     "ToolShed categories": [
       "Sequence Analysis"
@@ -80272,7 +77258,7 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93",
-    "Galaxy wrapper version": "1.0.6",
+    "Galaxy wrapper version": "1.0.14",
     "Conda id": "tn93",
     "Conda version": "1.0.14",
     "EDAM operation (no superclasses)": [],
@@ -80286,10 +77272,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -80312,7 +77296,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 0,
@@ -80352,9 +77335,9 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator",
-    "Galaxy wrapper version": "0.9",
+    "Galaxy wrapper version": "0.9.1",
     "Conda id": "tooldistillator",
-    "Conda version": "0.9",
+    "Conda version": "0.9.1",
     "EDAM operation (no superclasses)": [
       "Parsing"
     ],
@@ -80372,10 +77355,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -80398,7 +77379,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -80442,10 +77422,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -80468,7 +77446,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -80501,7 +77478,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy",
     "Galaxy wrapper version": "0.6.1",
     "Conda id": "tracy",
-    "Conda version": "0.7.6",
+    "Conda version": "0.7.8",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -80513,10 +77490,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -80539,7 +77514,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 0,
@@ -80608,10 +77582,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -80634,8 +77606,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -80696,10 +77667,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -80722,8 +77691,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -80776,10 +77744,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -80802,8 +77768,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -80846,10 +77811,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -80872,8 +77835,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 1,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -80942,10 +77904,8 @@
     "Tools available on UseGalaxy.eu": 13,
     "Tools available on UseGalaxy.fr": 13,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -80968,8 +77928,7 @@
     "Tools available on Oqtans": 1,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 11,
     "Tools available on UseGalaxy.cz": 13,
     "Tools available on UseGalaxy.no": 12,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -81024,10 +77983,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -81050,8 +78007,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -81098,10 +78054,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 5,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -81124,7 +78078,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 0,
@@ -81155,7 +78108,7 @@
       "Gene transcripts",
       "Model organisms"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "https://github.com/Gaius-Augustus/TSEBRA",
     "ToolShed categories": [
       "Genome annotation"
@@ -81164,7 +78117,7 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra",
-    "Galaxy wrapper version": "1.1.2.4",
+    "Galaxy wrapper version": "1.1.2.5",
     "Conda id": "tsebra",
     "Conda version": "1.1.2.5",
     "EDAM operation (no superclasses)": [
@@ -81186,10 +78139,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -81212,7 +78163,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -81256,10 +78206,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -81282,8 +78230,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -81313,7 +78260,7 @@
       "Gene transcripts",
       "Workflows"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "http://bioconductor.org/packages/tximport/",
     "ToolShed categories": [
       "Transcriptomics"
@@ -81322,7 +78269,7 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport",
-    "Galaxy wrapper version": "1.22.0",
+    "Galaxy wrapper version": "1.30.0",
     "Conda id": "bioconductor-tximport",
     "Conda version": "1.30.0",
     "EDAM operation (no superclasses)": [
@@ -81344,10 +78291,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -81370,8 +78315,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -81397,7 +78341,7 @@
     "EDAM topic": [
       "Sequence analysis"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "http://genome.ucsc.edu/goldenPath/help/blatSpec.html",
     "ToolShed categories": [
       "Sequence Analysis"
@@ -81406,7 +78350,7 @@
     "Galaxy wrapper owner": "yating-l",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat",
-    "Galaxy wrapper version": "377",
+    "Galaxy wrapper version": "469",
     "Conda id": "ucsc-blat",
     "Conda version": "469",
     "EDAM operation (no superclasses)": [
@@ -81424,10 +78368,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -81450,7 +78392,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -81475,16 +78416,16 @@
     "EDAM topic": [
       "Sequence analysis"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "http://hgdownload.cse.ucsc.edu/admin/exe/",
     "ToolShed categories": [
       "Fasta Manipulation"
     ],
     "ToolShed id": "ucsc_fasplit",
     "Galaxy wrapper owner": "iuc",
-    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit",
+    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit",
-    "Galaxy wrapper version": "377",
+    "Galaxy wrapper version": "469",
     "Conda id": "ucsc-fasplit",
     "Conda version": "469",
     "EDAM operation (no superclasses)": [],
@@ -81500,10 +78441,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -81526,8 +78465,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -81558,7 +78496,7 @@
     ],
     "ToolShed id": "ucsc_fatovcf",
     "Galaxy wrapper owner": "iuc",
-    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fatovcf",
+    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf",
     "Galaxy wrapper version": "448",
     "Conda id": "ucsc-fatovcf",
@@ -81576,10 +78514,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -81602,7 +78538,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -81627,16 +78562,16 @@
     "EDAM topic": [
       "Sequence analysis"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "http://hgdownload.cse.ucsc.edu/admin/exe/",
     "ToolShed categories": [
       "Convert Formats"
     ],
     "ToolShed id": "ucsc_maftoaxt",
     "Galaxy wrapper owner": "iuc",
-    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/maftoaxt",
+    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt",
-    "Galaxy wrapper version": "377",
+    "Galaxy wrapper version": "469",
     "Conda id": "ucsc-maftoaxt",
     "Conda version": "469",
     "EDAM operation (no superclasses)": [],
@@ -81652,10 +78587,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -81678,7 +78611,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -81703,16 +78635,16 @@
     "EDAM topic": [
       "Sequence analysis"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "https://genome.ucsc.edu/goldenpath/help/twoBit.html",
     "ToolShed categories": [
       "Convert Formats"
     ],
     "ToolShed id": "ucsc_twobittofa",
     "Galaxy wrapper owner": "iuc",
-    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa",
+    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa",
-    "Galaxy wrapper version": "377",
+    "Galaxy wrapper version": "469",
     "Conda id": "ucsc-twobittofa",
     "Conda version": "469",
     "EDAM operation (no superclasses)": [],
@@ -81728,10 +78660,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -81754,8 +78684,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -81779,16 +78708,16 @@
     "EDAM topic": [
       "Sequence analysis"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "http://hgdownload.cse.ucsc.edu/admin/exe/",
     "ToolShed categories": [
       "Sequence Analysis"
     ],
     "ToolShed id": "ucsc_axtchain",
     "Galaxy wrapper owner": "iuc",
-    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain",
+    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain",
-    "Galaxy wrapper version": "455",
+    "Galaxy wrapper version": "469",
     "Conda id": "ucsc-axtchain",
     "Conda version": "469",
     "EDAM operation (no superclasses)": [],
@@ -81797,17 +78726,15 @@
     ],
     "Available on UseGalaxy.org (Main)": 1,
     "Available on UseGalaxy.org.au": 0,
-    "Available on UseGalaxy.eu": 0,
+    "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 1,
     "Tools available on UseGalaxy.org.au": 0,
-    "Tools available on UseGalaxy.eu": 0,
+    "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -81830,7 +78757,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -81855,16 +78781,16 @@
     "EDAM topic": [
       "Sequence analysis"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "http://hgdownload.cse.ucsc.edu/admin/exe/",
     "ToolShed categories": [
       "Convert Formats"
     ],
     "ToolShed id": "ucsc_axttomaf",
     "Galaxy wrapper owner": "iuc",
-    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf",
+    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf",
-    "Galaxy wrapper version": "377",
+    "Galaxy wrapper version": "469",
     "Conda id": "ucsc-axttomaf",
     "Conda version": "469",
     "EDAM operation (no superclasses)": [],
@@ -81880,10 +78806,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -81906,7 +78830,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -81938,7 +78861,7 @@
     ],
     "ToolShed id": "ucsc_chainnet",
     "Galaxy wrapper owner": "iuc",
-    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet",
+    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet",
     "Galaxy wrapper version": "469",
     "Conda id": "ucsc-chainnet",
@@ -81947,19 +78870,17 @@
     "EDAM topic (no superclasses)": [
       "Sequence analysis"
     ],
-    "Available on UseGalaxy.org (Main)": 0,
+    "Available on UseGalaxy.org (Main)": 1,
     "Available on UseGalaxy.org.au": 0,
-    "Available on UseGalaxy.eu": 0,
+    "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 0,
-    "Tools available on UseGalaxy.org (Main)": 0,
+    "Tools available on UseGalaxy.org (Main)": 1,
     "Tools available on UseGalaxy.org.au": 0,
-    "Tools available on UseGalaxy.eu": 0,
+    "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -81982,7 +78903,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -82007,16 +78927,16 @@
     "EDAM topic": [
       "Sequence analysis"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "http://hgdownload.cse.ucsc.edu/admin/exe/",
     "ToolShed categories": [
       "Sequence Analysis"
     ],
     "ToolShed id": "ucsc_chainprenet",
     "Galaxy wrapper owner": "iuc",
-    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainprenet",
+    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet",
-    "Galaxy wrapper version": "377",
+    "Galaxy wrapper version": "469",
     "Conda id": "ucsc-chainprenet",
     "Conda version": "469",
     "EDAM operation (no superclasses)": [],
@@ -82032,10 +78952,154 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
+    "Tools available on CIRM-CFBP": 0,
+    "Tools available on ChemFlow": 0,
+    "Tools available on Coloc-stats": 0,
+    "Tools available on CoralSNP": 0,
+    "Tools available on CropGalaxy": 0,
+    "Tools available on Dintor": 0,
+    "Tools available on FreeBioinfo": 0,
+    "Tools available on GASLINI": 0,
+    "Tools available on Galaxy@AuBi": 0,
+    "Tools available on Galaxy@Pasteur": 0,
+    "Tools available on GalaxyTrakr": 0,
+    "Tools available on Genomic Hyperbrowser": 0,
+    "Tools available on GigaGalaxy": 0,
+    "Tools available on HyPhy HIV NGS Tools": 0,
+    "Tools available on IPK Galaxy Blast Suite": 0,
+    "Tools available on ImmPort Galaxy": 0,
+    "Tools available on InteractoMIX": 0,
+    "Tools available on MISSISSIPPI": 0,
+    "Tools available on Mandoiu Lab": 0,
+    "Tools available on MiModD NacreousMap": 0,
+    "Tools available on Oqtans": 0,
+    "Tools available on Palfinder": 0,
+    "Tools available on PepSimili": 0,
+    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.cz": 0,
+    "Tools available on UseGalaxy.no": 0,
+    "Tools available on Viral Variant Visualizer (VVV)": 0,
+    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+    "Total tool usage (usegalaxy.eu)": 0
+  },
+  {
+    "Galaxy wrapper id": "ucsc_chainsort",
+    "Galaxy tool ids": [
+      "ucsc_chainsort"
+    ],
+    "Description": "Sort chains. By default sorts by score.",
+    "bio.tool id": "UCSC_Genome_Browser_Utilities",
+    "bio.tool ids": [
+      "UCSC_Genome_Browser_Utilities"
+    ],
+    "biii": null,
+    "bio.tool name": "UCSC Genome Browser Utilities",
+    "bio.tool description": "Utilities for handling sequences and assemblies from the UCSC Genome Browser project.",
+    "EDAM operation": [],
+    "EDAM topic": [
+      "Sequence analysis"
+    ],
+    "Status": "Up-to-date",
+    "Source": "http://hgdownload.cse.ucsc.edu/admin/exe/",
+    "ToolShed categories": [
+      "Sequence Analysis"
+    ],
+    "ToolShed id": "ucsc_chainsort",
+    "Galaxy wrapper owner": "iuc",
+    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort",
+    "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort",
+    "Galaxy wrapper version": "469",
+    "Conda id": "ucsc-chainsort",
+    "Conda version": "469",
+    "EDAM operation (no superclasses)": [],
+    "EDAM topic (no superclasses)": [
+      "Sequence analysis"
+    ],
+    "Available on UseGalaxy.org (Main)": 1,
+    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.eu": 0,
+    "Available on UseGalaxy.fr": 0,
+    "Tools available on UseGalaxy.org (Main)": 1,
+    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.eu": 0,
+    "Tools available on UseGalaxy.fr": 0,
+    "Tools available on APOSTL": 0,
+    "Tools available on ARGs-OAP": 0,
+    "Tools available on CIRM-CFBP": 0,
+    "Tools available on ChemFlow": 0,
+    "Tools available on Coloc-stats": 0,
+    "Tools available on CoralSNP": 0,
+    "Tools available on CropGalaxy": 0,
+    "Tools available on Dintor": 0,
+    "Tools available on FreeBioinfo": 0,
+    "Tools available on GASLINI": 0,
+    "Tools available on Galaxy@AuBi": 0,
+    "Tools available on Galaxy@Pasteur": 0,
+    "Tools available on GalaxyTrakr": 0,
+    "Tools available on Genomic Hyperbrowser": 0,
+    "Tools available on GigaGalaxy": 0,
+    "Tools available on HyPhy HIV NGS Tools": 0,
+    "Tools available on IPK Galaxy Blast Suite": 0,
+    "Tools available on ImmPort Galaxy": 0,
+    "Tools available on InteractoMIX": 0,
+    "Tools available on MISSISSIPPI": 0,
+    "Tools available on Mandoiu Lab": 0,
+    "Tools available on MiModD NacreousMap": 0,
+    "Tools available on Oqtans": 0,
+    "Tools available on Palfinder": 0,
+    "Tools available on PepSimili": 0,
+    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.cz": 0,
+    "Tools available on UseGalaxy.no": 0,
+    "Tools available on Viral Variant Visualizer (VVV)": 0,
+    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+    "Total tool usage (usegalaxy.eu)": 0
+  },
+  {
+    "Galaxy wrapper id": "ucsc_netfilter",
+    "Galaxy tool ids": [
+      "ucsc_netfilter"
+    ],
+    "Description": "Filter out parts of net",
+    "bio.tool id": "UCSC_Genome_Browser_Utilities",
+    "bio.tool ids": [
+      "UCSC_Genome_Browser_Utilities"
+    ],
+    "biii": null,
+    "bio.tool name": "UCSC Genome Browser Utilities",
+    "bio.tool description": "Utilities for handling sequences and assemblies from the UCSC Genome Browser project.",
+    "EDAM operation": [],
+    "EDAM topic": [
+      "Sequence analysis"
+    ],
+    "Status": "Up-to-date",
+    "Source": "http://hgdownload.cse.ucsc.edu/admin/exe/",
+    "ToolShed categories": [
+      "Sequence Analysis"
+    ],
+    "ToolShed id": "ucsc_netfilter",
+    "Galaxy wrapper owner": "iuc",
+    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter",
+    "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter",
+    "Galaxy wrapper version": "469",
+    "Conda id": "ucsc-netfilter",
+    "Conda version": "469",
+    "EDAM operation (no superclasses)": [],
+    "EDAM topic (no superclasses)": [
+      "Sequence analysis"
+    ],
+    "Available on UseGalaxy.org (Main)": 1,
+    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.eu": 1,
+    "Available on UseGalaxy.fr": 0,
+    "Tools available on UseGalaxy.org (Main)": 1,
+    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.eu": 1,
+    "Tools available on UseGalaxy.fr": 0,
+    "Tools available on APOSTL": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -82058,7 +79122,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -82067,11 +79130,11 @@
     "Total tool usage (usegalaxy.eu)": 0
   },
   {
-    "Galaxy wrapper id": "ucsc_chainsort",
+    "Galaxy wrapper id": "ucsc_netsyntenic",
     "Galaxy tool ids": [
-      "ucsc_chainsort"
+      "ucsc_netsyntenic"
     ],
-    "Description": "Sort chains. By default sorts by score.",
+    "Description": "Add synteny info to a net dataset",
     "bio.tool id": "UCSC_Genome_Browser_Utilities",
     "bio.tool ids": [
       "UCSC_Genome_Browser_Utilities"
@@ -82083,17 +79146,17 @@
     "EDAM topic": [
       "Sequence analysis"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "http://hgdownload.cse.ucsc.edu/admin/exe/",
     "ToolShed categories": [
       "Sequence Analysis"
     ],
-    "ToolShed id": "ucsc_chainsort",
+    "ToolShed id": "ucsc_netsyntenic",
     "Galaxy wrapper owner": "iuc",
-    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort",
-    "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort",
-    "Galaxy wrapper version": "455",
-    "Conda id": "ucsc-chainsort",
+    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic",
+    "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic",
+    "Galaxy wrapper version": "469",
+    "Conda id": "ucsc-netsyntenic",
     "Conda version": "469",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [
@@ -82108,10 +79171,81 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
+    "Tools available on CIRM-CFBP": 0,
+    "Tools available on ChemFlow": 0,
+    "Tools available on Coloc-stats": 0,
+    "Tools available on CoralSNP": 0,
+    "Tools available on CropGalaxy": 0,
+    "Tools available on Dintor": 0,
+    "Tools available on FreeBioinfo": 0,
+    "Tools available on GASLINI": 0,
+    "Tools available on Galaxy@AuBi": 0,
+    "Tools available on Galaxy@Pasteur": 0,
+    "Tools available on GalaxyTrakr": 0,
+    "Tools available on Genomic Hyperbrowser": 0,
+    "Tools available on GigaGalaxy": 0,
+    "Tools available on HyPhy HIV NGS Tools": 0,
+    "Tools available on IPK Galaxy Blast Suite": 0,
+    "Tools available on ImmPort Galaxy": 0,
+    "Tools available on InteractoMIX": 0,
+    "Tools available on MISSISSIPPI": 0,
+    "Tools available on Mandoiu Lab": 0,
+    "Tools available on MiModD NacreousMap": 0,
+    "Tools available on Oqtans": 0,
+    "Tools available on Palfinder": 0,
+    "Tools available on PepSimili": 0,
+    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.cz": 0,
+    "Tools available on UseGalaxy.no": 0,
+    "Tools available on Viral Variant Visualizer (VVV)": 0,
+    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+    "Total tool usage (usegalaxy.eu)": 0
+  },
+  {
+    "Galaxy wrapper id": "ucsc_nettoaxt",
+    "Galaxy tool ids": [
+      "ucsc_nettoaxt"
+    ],
+    "Description": "Convert net (and chain) to axt format.",
+    "bio.tool id": "UCSC_Genome_Browser_Utilities",
+    "bio.tool ids": [
+      "UCSC_Genome_Browser_Utilities"
+    ],
+    "biii": null,
+    "bio.tool name": "UCSC Genome Browser Utilities",
+    "bio.tool description": "Utilities for handling sequences and assemblies from the UCSC Genome Browser project.",
+    "EDAM operation": [],
+    "EDAM topic": [
+      "Sequence analysis"
+    ],
+    "Status": "Up-to-date",
+    "Source": "http://hgdownload.cse.ucsc.edu/admin/exe/",
+    "ToolShed categories": [
+      "Convert Formats"
+    ],
+    "ToolShed id": "ucsc_nettoaxt",
+    "Galaxy wrapper owner": "iuc",
+    "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt",
+    "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt",
+    "Galaxy wrapper version": "469",
+    "Conda id": "ucsc-nettoaxt",
+    "Conda version": "469",
+    "EDAM operation (no superclasses)": [],
+    "EDAM topic (no superclasses)": [
+      "Sequence analysis"
+    ],
+    "Available on UseGalaxy.org (Main)": 1,
+    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.eu": 1,
+    "Available on UseGalaxy.fr": 0,
+    "Tools available on UseGalaxy.org (Main)": 1,
+    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.eu": 1,
+    "Tools available on UseGalaxy.fr": 0,
+    "Tools available on APOSTL": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -82134,7 +79268,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -82159,7 +79292,7 @@
     "EDAM topic": [
       "Sequence analysis"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "https://genome.ucsc.edu/goldenPath/help/bigWig.html",
     "ToolShed categories": [
       "Convert Formats"
@@ -82168,7 +79301,7 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig",
-    "Galaxy wrapper version": "447",
+    "Galaxy wrapper version": "469",
     "Conda id": "ucsc-wigtobigwig",
     "Conda version": "469",
     "EDAM operation (no superclasses)": [],
@@ -82184,10 +79317,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -82210,7 +79341,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -82243,17 +79373,18 @@
       "Sequence sites, features and motifs",
       "Quality affairs"
     ],
-    "Status": "To update",
+    "Status": "Up-to-date",
     "Source": "https://github.com/CGATOxford/UMI-tools",
     "ToolShed categories": [
       "Sequence Analysis",
-      "Transcriptomics"
+      "Transcriptomics",
+      "Single Cell"
     ],
     "ToolShed id": null,
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools",
-    "Galaxy wrapper version": "1.1.2",
+    "Galaxy wrapper version": "1.1.5",
     "Conda id": "umi_tools",
     "Conda version": "1.1.5",
     "EDAM operation (no superclasses)": [
@@ -82272,10 +79403,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 5,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -82298,8 +79427,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 3,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -82360,10 +79488,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -82386,8 +79512,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -82451,10 +79576,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -82477,7 +79600,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -82535,10 +79657,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -82561,8 +79681,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -82623,10 +79742,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -82649,7 +79766,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -82693,10 +79809,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -82719,8 +79833,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 1,
@@ -82765,10 +79878,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -82791,8 +79902,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 3,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 3,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -82837,10 +79947,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -82863,8 +79971,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 3,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 3,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -82891,7 +79998,7 @@
       "Virology",
       "Probes and primers"
     ],
-    "Status": "Up-to-date",
+    "Status": "To update",
     "Source": "https://github.com/jonas-fuchs/varVAMP/",
     "ToolShed categories": [
       "Sequence Analysis"
@@ -82902,7 +80009,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp",
     "Galaxy wrapper version": "1.2.0",
     "Conda id": "varvamp",
-    "Conda version": "1.2.0",
+    "Conda version": "1.2.1",
     "EDAM operation (no superclasses)": [
       "PCR primer design"
     ],
@@ -82919,10 +80026,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -82945,7 +80050,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -82989,10 +80093,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -83015,7 +80117,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -83071,10 +80172,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -83097,8 +80196,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -83159,10 +80257,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -83185,8 +80281,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 3,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 3,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -83209,7 +80304,8 @@
     "Status": "Up-to-date",
     "Source": "http://velocyto.org/",
     "ToolShed categories": [
-      "Transcriptomics"
+      "Transcriptomics",
+      "Single Cell"
     ],
     "ToolShed id": "velocyto",
     "Galaxy wrapper owner": "iuc",
@@ -83229,10 +80325,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -83255,7 +80349,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -83312,10 +80405,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -83338,8 +80429,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -83396,10 +80486,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -83422,8 +80510,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -83454,22 +80541,20 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko",
     "Galaxy wrapper version": "1.3.1",
     "Conda id": "verkko",
-    "Conda version": "2.1",
+    "Conda version": "2.2",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
-    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.org.au": 1,
     "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
-    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.org.au": 1,
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -83492,7 +80577,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -83527,7 +80611,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg",
     "Galaxy wrapper version": "1.23.0",
     "Conda id": "vg",
-    "Conda version": "1.56.0",
+    "Conda version": "1.59.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -83539,10 +80623,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -83565,8 +80647,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 3,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 3,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -83607,7 +80688,7 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot",
-    "Galaxy wrapper version": "1.0.1+galaxy0",
+    "Galaxy wrapper version": "1.1.0+galaxy0",
     "Conda id": "biopython",
     "Conda version": "1.70",
     "EDAM operation (no superclasses)": [
@@ -83629,10 +80710,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -83655,7 +80734,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -83702,10 +80780,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -83728,7 +80804,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -83782,10 +80857,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -83808,7 +80881,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -83854,10 +80926,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -83880,8 +80950,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -83927,7 +80996,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch",
     "Galaxy wrapper version": "2.8.3",
     "Conda id": "vsearch",
-    "Conda version": "2.28.1",
+    "Conda version": "2.29.0",
     "EDAM operation (no superclasses)": [
       "DNA mapping",
       "Chimera detection"
@@ -83945,10 +81014,8 @@
     "Tools available on UseGalaxy.eu": 8,
     "Tools available on UseGalaxy.fr": 8,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -83971,8 +81038,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 8,
     "Tools available on UseGalaxy.cz": 8,
     "Tools available on UseGalaxy.no": 8,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -84019,10 +81085,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -84045,7 +81109,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -84090,10 +81153,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -84116,7 +81177,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -84176,10 +81236,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -84202,8 +81260,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -84247,10 +81304,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -84273,7 +81328,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -84317,10 +81371,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -84343,7 +81395,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -84387,10 +81438,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -84413,8 +81462,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -84434,7 +81482,7 @@
     "bio.tool description": null,
     "EDAM operation": [],
     "EDAM topic": [],
-    "Status": "Up-to-date",
+    "Status": "To update",
     "Source": "https://github.com/c-zhou/yahs",
     "ToolShed categories": [
       "Assembly"
@@ -84445,7 +81493,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs",
     "Galaxy wrapper version": "1.2a.2",
     "Conda id": "yahs",
-    "Conda version": "1.2a.2",
+    "Conda version": "1.2.2",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -84457,10 +81505,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -84483,7 +81529,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -84527,10 +81572,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -84553,8 +81596,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -84613,10 +81655,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -84639,8 +81679,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -84699,10 +81738,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -84725,8 +81762,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -84788,10 +81824,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -84814,7 +81848,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 0,
@@ -84872,10 +81905,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -84898,7 +81929,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -84942,10 +81972,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -84968,8 +81996,7 @@
     "Tools available on Oqtans": 1,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -85012,10 +82039,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -85038,8 +82063,7 @@
     "Tools available on Oqtans": 1,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -85082,10 +82106,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -85108,8 +82130,7 @@
     "Tools available on Oqtans": 1,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -85152,10 +82173,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -85178,8 +82197,7 @@
     "Tools available on Oqtans": 1,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -85222,10 +82240,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -85248,8 +82264,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -85292,10 +82307,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -85318,8 +82331,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -85357,17 +82369,15 @@
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
     "Available on UseGalaxy.org.au": 1,
-    "Available on UseGalaxy.eu": 0,
+    "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
     "Tools available on UseGalaxy.org.au": 1,
-    "Tools available on UseGalaxy.eu": 0,
+    "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -85390,7 +82400,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -85434,10 +82443,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -85460,8 +82467,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 1,
@@ -85504,10 +82510,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -85530,8 +82534,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -85576,10 +82579,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -85602,8 +82603,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -85646,10 +82646,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -85672,8 +82670,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -85716,10 +82713,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -85742,8 +82737,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -85787,10 +82781,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -85813,8 +82805,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -85858,10 +82849,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -85884,8 +82873,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -85929,10 +82917,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -85955,8 +82941,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -86000,10 +82985,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -86026,8 +83009,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -86070,10 +83052,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -86096,8 +83076,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -86141,10 +83120,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -86167,8 +83144,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -86212,10 +83188,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -86238,8 +83212,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -86283,10 +83256,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -86309,8 +83280,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -86354,10 +83324,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -86380,8 +83348,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -86425,10 +83392,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -86451,8 +83416,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -86496,10 +83460,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -86522,8 +83484,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -86566,10 +83527,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -86592,8 +83551,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -86636,10 +83594,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -86662,8 +83618,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -86706,10 +83661,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -86732,8 +83685,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -86776,10 +83728,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -86802,8 +83752,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -86846,10 +83795,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -86872,8 +83819,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -86916,10 +83862,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -86942,8 +83886,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -86986,10 +83929,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -87012,8 +83953,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -87056,10 +83996,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -87082,8 +84020,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -87126,10 +84063,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -87152,8 +84087,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -87196,10 +84130,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -87222,8 +84154,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -87266,10 +84197,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -87292,8 +84221,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -87336,10 +84264,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -87362,8 +84288,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -87406,10 +84331,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -87432,8 +84355,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -87492,10 +84414,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 5,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -87518,8 +84438,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 2,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 5,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -87574,10 +84493,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -87600,8 +84517,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 1,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -87628,9 +84544,9 @@
     "Galaxy wrapper owner": "iuc",
     "Galaxy wrapper source": "https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools",
-    "Galaxy wrapper version": "1.15.1",
+    "Galaxy wrapper version": "1.20",
     "Conda id": "samtools",
-    "Conda version": "1.20",
+    "Conda version": "1.21",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -87642,10 +84558,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -87668,7 +84582,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -87717,10 +84630,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 5,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -87743,8 +84654,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 5,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -87794,10 +84704,8 @@
     "Tools available on UseGalaxy.eu": 8,
     "Tools available on UseGalaxy.fr": 8,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -87820,8 +84728,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 8,
     "Tools available on UseGalaxy.cz": 8,
     "Tools available on UseGalaxy.no": 8,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -87864,10 +84771,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -87890,7 +84795,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -87934,10 +84838,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -87960,8 +84862,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -87993,7 +84894,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -88005,10 +84906,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -88031,8 +84930,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -88063,7 +84961,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -88075,10 +84973,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -88101,8 +84997,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -88133,7 +85028,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -88145,10 +85040,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -88171,8 +85064,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -88203,7 +85095,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -88215,10 +85107,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -88241,8 +85131,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -88273,7 +85162,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -88285,10 +85174,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -88311,8 +85198,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -88343,7 +85229,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -88355,10 +85241,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -88381,8 +85265,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -88413,7 +85296,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -88425,10 +85308,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -88451,8 +85332,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -88483,7 +85363,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -88495,10 +85375,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -88521,8 +85399,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -88553,7 +85430,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -88565,10 +85442,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -88591,8 +85466,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -88623,7 +85497,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -88635,10 +85509,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -88661,8 +85533,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -88693,7 +85564,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -88705,10 +85576,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -88731,8 +85600,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -88763,7 +85631,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -88775,10 +85643,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -88801,8 +85667,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -88833,7 +85698,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -88845,10 +85710,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -88871,8 +85734,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -88903,7 +85765,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -88915,10 +85777,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -88941,8 +85801,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -88973,7 +85832,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -88985,10 +85844,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -89011,8 +85868,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -89043,7 +85899,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -89055,10 +85911,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -89081,8 +85935,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -89113,7 +85966,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -89125,10 +85978,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -89151,8 +86002,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -89183,7 +86033,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -89195,10 +86045,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -89221,8 +86069,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -89253,7 +86100,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -89265,10 +86112,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -89291,8 +86136,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -89323,7 +86167,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -89335,10 +86179,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -89361,8 +86203,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -89393,7 +86234,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -89405,10 +86246,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -89431,8 +86270,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -89463,7 +86301,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -89475,10 +86313,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -89501,8 +86337,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -89533,7 +86368,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect",
     "Galaxy wrapper version": null,
     "Conda id": "vcflib",
-    "Conda version": "1.0.9",
+    "Conda version": "1.0.10",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -89545,10 +86380,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -89571,8 +86404,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -89615,10 +86447,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -89641,7 +86471,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -89683,10 +86512,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -89709,7 +86536,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -89753,10 +86579,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -89779,8 +86603,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -89823,10 +86646,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -89849,7 +86670,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -89897,10 +86717,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -89923,7 +86741,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
@@ -89967,10 +86784,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -89993,7 +86808,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -90048,10 +86862,8 @@
     "Tools available on UseGalaxy.eu": 11,
     "Tools available on UseGalaxy.fr": 11,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -90074,8 +86886,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 9,
     "Tools available on UseGalaxy.cz": 11,
     "Tools available on UseGalaxy.no": 9,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -90118,10 +86929,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -90144,8 +86953,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -90186,10 +86994,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -90212,7 +87018,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -90256,10 +87061,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -90282,7 +87085,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -90326,10 +87128,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -90352,7 +87152,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -90396,10 +87195,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -90422,7 +87219,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -90466,10 +87262,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -90492,8 +87286,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -90536,10 +87329,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -90562,7 +87353,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -90604,10 +87394,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -90630,7 +87418,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -90670,10 +87457,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -90696,7 +87481,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -90738,10 +87522,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -90764,7 +87546,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -90806,10 +87587,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -90832,7 +87611,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -90904,10 +87682,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -90930,8 +87706,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 3,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -90980,10 +87755,8 @@
     "Tools available on UseGalaxy.eu": 7,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -91006,7 +87779,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 7,
     "Tools available on UseGalaxy.no": 0,
@@ -91050,10 +87822,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -91076,8 +87846,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -91121,10 +87890,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -91147,7 +87914,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -91191,10 +87957,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -91217,7 +87981,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -91262,10 +88025,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -91288,7 +88049,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -91344,10 +88104,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -91370,8 +88128,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -91405,19 +88162,17 @@
     "Conda version": "20.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
-    "Available on UseGalaxy.org (Main)": 0,
+    "Available on UseGalaxy.org (Main)": 1,
     "Available on UseGalaxy.org.au": 0,
     "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 0,
-    "Tools available on UseGalaxy.org (Main)": 0,
+    "Tools available on UseGalaxy.org (Main)": 1,
     "Tools available on UseGalaxy.org.au": 0,
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -91440,7 +88195,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -91484,10 +88238,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -91510,8 +88262,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -91555,10 +88306,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -91581,7 +88330,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
@@ -91625,10 +88373,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -91651,7 +88397,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -91695,10 +88440,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -91721,7 +88464,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -91761,10 +88503,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -91787,7 +88527,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -91832,10 +88571,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -91858,8 +88595,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -91902,10 +88638,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -91928,7 +88662,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -91999,10 +88732,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -92025,8 +88756,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -92069,10 +88799,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -92095,7 +88823,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -92153,10 +88880,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -92179,7 +88904,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -92241,18 +88965,16 @@
       "Small molecules"
     ],
     "Available on UseGalaxy.org (Main)": 0,
-    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.org.au": 1,
     "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
-    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.org.au": 1,
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -92275,7 +88997,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -92358,10 +89079,8 @@
     "Tools available on UseGalaxy.eu": 6,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -92384,8 +89103,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 6,
     "Tools available on UseGalaxy.cz": 6,
     "Tools available on UseGalaxy.no": 6,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -92426,10 +89144,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -92452,7 +89168,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -92496,10 +89211,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -92522,7 +89235,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -92576,10 +89288,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -92602,7 +89312,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -92647,10 +89356,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -92673,7 +89380,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -92731,10 +89437,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -92757,8 +89461,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -92801,10 +89504,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -92827,7 +89528,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -92871,10 +89571,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -92897,7 +89595,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -92959,10 +89656,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -92985,8 +89680,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -93029,10 +89723,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -93055,7 +89747,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -93099,10 +89790,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -93125,7 +89814,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -93183,10 +89871,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -93209,8 +89895,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -93388,7 +90073,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms",
     "Galaxy wrapper version": "3.1",
     "Conda id": "openms",
-    "Conda version": "3.1.0",
+    "Conda version": "3.2.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 8,
@@ -93400,10 +90085,8 @@
     "Tools available on UseGalaxy.eu": 144,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -93426,8 +90109,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 18,
     "Tools available on UseGalaxy.cz": 141,
     "Tools available on UseGalaxy.no": 124,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -93470,10 +90152,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -93496,7 +90176,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -93541,10 +90220,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -93567,8 +90244,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -93611,10 +90287,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -93637,7 +90311,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -93675,18 +90348,16 @@
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
-    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.org.au": 1,
     "Available on UseGalaxy.eu": 3,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
-    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.org.au": 1,
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -93709,7 +90380,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 0,
@@ -93753,10 +90423,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -93779,8 +90447,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -93814,7 +90481,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker",
     "Galaxy wrapper version": null,
     "Conda id": "searchgui",
-    "Conda version": "4.3.9",
+    "Conda version": "4.3.11",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 4,
@@ -93826,10 +90493,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 4,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -93852,8 +90517,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -93894,10 +90558,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -93920,7 +90582,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -93955,7 +90616,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator",
     "Galaxy wrapper version": "3.5",
     "Conda id": "percolator",
-    "Conda version": "3.6.5",
+    "Conda version": "3.7.1",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -93967,10 +90628,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -93993,7 +90652,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 4,
@@ -94039,10 +90697,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -94065,7 +90721,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -94109,10 +90764,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -94135,7 +90788,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -94179,10 +90831,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -94205,8 +90855,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -94247,10 +90896,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -94273,7 +90920,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -94317,10 +90963,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -94343,7 +90987,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -94389,10 +91032,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -94415,7 +91056,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -94459,10 +91099,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -94485,7 +91123,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -94529,10 +91166,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -94555,8 +91190,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -94599,10 +91233,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -94625,7 +91257,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -94669,10 +91300,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -94695,7 +91324,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -94739,10 +91367,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -94765,7 +91391,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -94809,10 +91434,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -94835,7 +91458,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -94879,10 +91501,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -94905,7 +91525,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -94949,10 +91568,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -94975,7 +91592,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -95019,10 +91635,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -95045,7 +91659,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -95089,10 +91702,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -95115,7 +91726,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -95159,10 +91769,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -95185,7 +91793,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -95229,10 +91836,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -95255,7 +91860,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -95297,10 +91901,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -95323,7 +91925,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -95365,10 +91966,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -95391,7 +91990,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -95435,10 +92033,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -95461,7 +92057,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -95510,10 +92105,8 @@
     "Tools available on UseGalaxy.eu": 6,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -95536,8 +92129,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 5,
     "Tools available on UseGalaxy.cz": 6,
     "Tools available on UseGalaxy.no": 6,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -95576,7 +92168,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics",
     "Galaxy wrapper version": "4.4.1",
     "Conda id": "pyteomics",
-    "Conda version": "4.7.3",
+    "Conda version": "4.7.4",
     "EDAM operation (no superclasses)": [
       "Protein identification"
     ],
@@ -95593,10 +92185,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -95619,7 +92209,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -95663,10 +92252,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -95689,7 +92276,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -95733,10 +92319,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -95759,7 +92343,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -95789,7 +92372,7 @@
     "Galaxy wrapper owner": "galaxyp",
     "Galaxy wrapper source": "hhttps://github.com/npinter/ROIsplitter",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter",
-    "Galaxy wrapper version": "0.3.1",
+    "Galaxy wrapper version": "0.3.2",
     "Conda id": "geojson",
     "Conda version": null,
     "EDAM operation (no superclasses)": [],
@@ -95803,10 +92386,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -95829,7 +92410,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -95873,10 +92453,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -95899,7 +92477,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -95944,10 +92521,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 2,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 2,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -95970,8 +92545,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -96013,10 +92587,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -96039,7 +92611,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -96087,10 +92658,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -96113,7 +92682,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 4,
@@ -96157,10 +92725,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -96183,7 +92749,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -96227,10 +92792,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -96253,7 +92816,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -96297,10 +92859,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -96323,7 +92883,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -96385,10 +92944,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -96411,8 +92968,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -96455,10 +93011,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -96481,7 +93035,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -96517,19 +93070,17 @@
     "Conda version": "1.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
-    "Available on UseGalaxy.org (Main)": 0,
-    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.org (Main)": 1,
+    "Available on UseGalaxy.org.au": 1,
     "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 0,
-    "Tools available on UseGalaxy.org (Main)": 0,
-    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.org (Main)": 1,
+    "Tools available on UseGalaxy.org.au": 1,
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -96552,7 +93103,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -96596,10 +93146,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -96622,7 +93170,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -96670,10 +93217,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -96696,8 +93241,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 4,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -96744,10 +93288,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -96770,7 +93312,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 3,
@@ -96821,10 +93362,8 @@
     "Tools available on UseGalaxy.eu": 7,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -96847,8 +93386,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 7,
     "Tools available on UseGalaxy.no": 5,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -96892,10 +93430,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -96918,7 +93454,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -96964,10 +93499,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -96990,7 +93523,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -97033,10 +93565,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -97059,7 +93589,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -97118,10 +93647,8 @@
     "Tools available on UseGalaxy.eu": 15,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -97144,8 +93671,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 6,
     "Tools available on UseGalaxy.cz": 15,
     "Tools available on UseGalaxy.no": 9,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -97197,10 +93723,8 @@
     "Tools available on UseGalaxy.eu": 10,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -97223,8 +93747,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 10,
     "Tools available on UseGalaxy.no": 10,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -97268,10 +93791,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -97294,8 +93815,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -97339,10 +93859,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -97365,7 +93883,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -97409,10 +93926,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -97435,7 +93950,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -97480,10 +93994,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -97506,7 +94018,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -97548,10 +94059,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -97574,7 +94083,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -97607,7 +94115,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning",
     "Galaxy wrapper version": "1.10+galaxy0",
     "Conda id": "samtools",
-    "Conda version": "1.20",
+    "Conda version": "1.21",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -97619,10 +94127,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -97645,7 +94151,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -97690,10 +94195,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -97716,7 +94219,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -97760,10 +94262,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -97786,7 +94286,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -97830,10 +94329,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -97856,7 +94353,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -97902,10 +94398,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -97928,7 +94422,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -97972,10 +94465,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -97998,7 +94489,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -98043,10 +94533,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -98069,7 +94557,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -98115,10 +94602,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -98141,7 +94626,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -98185,10 +94669,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -98211,7 +94693,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -98255,10 +94736,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -98281,7 +94760,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -98325,10 +94803,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -98351,7 +94827,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -98395,10 +94870,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -98421,7 +94894,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -98468,10 +94940,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -98494,7 +94964,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -98538,10 +95007,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -98564,7 +95031,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -98609,10 +95075,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -98635,7 +95099,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -98680,10 +95143,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -98706,7 +95167,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -98751,10 +95211,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -98777,7 +95235,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -98823,10 +95280,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -98849,7 +95304,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -98894,10 +95348,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -98920,7 +95372,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -98964,10 +95415,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -98990,7 +95439,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -99034,10 +95482,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -99060,7 +95506,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -99104,10 +95549,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -99130,7 +95573,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -99174,10 +95616,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -99200,7 +95640,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -99245,10 +95684,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -99271,7 +95708,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -99315,10 +95751,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -99341,7 +95775,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -99385,10 +95818,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -99411,7 +95842,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -99455,10 +95885,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -99481,7 +95909,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -99525,10 +95952,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -99551,7 +95976,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -99595,10 +96019,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -99621,7 +96043,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -99665,10 +96086,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -99691,7 +96110,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -99735,10 +96153,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -99761,7 +96177,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -99806,10 +96221,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -99832,7 +96245,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -99876,10 +96288,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -99902,7 +96312,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -99946,10 +96355,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -99972,7 +96379,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -100017,10 +96423,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -100043,7 +96447,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -100088,10 +96491,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -100114,7 +96515,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -100158,10 +96558,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -100184,7 +96582,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -100229,10 +96626,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -100255,7 +96650,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -100300,10 +96694,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -100326,7 +96718,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -100370,10 +96761,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 1,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -100396,7 +96785,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -100443,10 +96831,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -100469,7 +96855,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -100514,10 +96899,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -100540,7 +96923,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -100585,10 +96967,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -100611,7 +96991,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -100659,10 +97038,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -100685,7 +97062,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -100729,10 +97105,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -100755,7 +97129,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -100802,10 +97175,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -100828,7 +97199,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -100873,10 +97243,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -100899,7 +97267,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -100946,10 +97313,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -100972,7 +97337,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -101019,10 +97383,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -101045,7 +97407,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -101090,10 +97451,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -101116,7 +97475,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -101161,10 +97519,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -101187,7 +97543,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -101232,10 +97587,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -101258,7 +97611,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -101302,10 +97654,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -101328,7 +97678,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -101372,10 +97721,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -101398,7 +97745,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -101442,10 +97788,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -101468,7 +97812,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -101513,10 +97856,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -101539,7 +97880,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -101584,10 +97924,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -101610,7 +97948,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -101621,9 +97958,11 @@
   {
     "Galaxy wrapper id": "EMLassemblyline",
     "Galaxy tool ids": [
+      "annotations_template",
       "eal_table_template",
       "eal_templates",
       "eml2eal",
+      "eml_validate",
       "entities_template",
       "geo_cov_template",
       "makeeml",
@@ -101648,24 +97987,22 @@
     "Galaxy wrapper owner": "ecology",
     "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline",
-    "Galaxy wrapper version": "0.1.1+galaxy0",
-    "Conda id": "r-emlassemblyline",
+    "Galaxy wrapper version": "0.1.0+galaxy0",
+    "Conda id": "r-base",
     "Conda version": null,
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
     "Available on UseGalaxy.org.au": 0,
-    "Available on UseGalaxy.eu": 9,
+    "Available on UseGalaxy.eu": 11,
     "Available on UseGalaxy.fr": 9,
     "Tools available on UseGalaxy.org (Main)": 0,
     "Tools available on UseGalaxy.org.au": 0,
-    "Tools available on UseGalaxy.eu": 9,
+    "Tools available on UseGalaxy.eu": 11,
     "Tools available on UseGalaxy.fr": 9,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -101688,7 +98025,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -101737,10 +98073,8 @@
     "Tools available on UseGalaxy.eu": 6,
     "Tools available on UseGalaxy.fr": 5,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -101763,7 +98097,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 0,
@@ -101809,10 +98142,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -101835,7 +98166,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -101883,10 +98213,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 5,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -101909,7 +98237,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 4,
@@ -101953,10 +98280,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -101979,7 +98304,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -102023,10 +98347,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -102049,7 +98371,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -102095,10 +98416,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 3,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -102121,7 +98440,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 0,
@@ -102165,10 +98483,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -102191,7 +98507,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -102240,10 +98555,8 @@
     "Tools available on UseGalaxy.eu": 6,
     "Tools available on UseGalaxy.fr": 6,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -102266,7 +98579,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 6,
     "Tools available on UseGalaxy.no": 0,
@@ -102315,10 +98627,8 @@
     "Tools available on UseGalaxy.eu": 6,
     "Tools available on UseGalaxy.fr": 5,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -102341,7 +98651,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 6,
     "Tools available on UseGalaxy.no": 2,
@@ -102392,10 +98701,8 @@
     "Tools available on UseGalaxy.eu": 8,
     "Tools available on UseGalaxy.fr": 8,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -102418,7 +98725,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 8,
     "Tools available on UseGalaxy.no": 8,
@@ -102448,7 +98754,7 @@
     "Galaxy wrapper owner": "ecology",
     "Galaxy wrapper source": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper",
     "Galaxy wrapper parsed folder": "https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes",
-    "Galaxy wrapper version": "0.1.0",
+    "Galaxy wrapper version": "0.2.0",
     "Conda id": "r-base",
     "Conda version": null,
     "EDAM operation (no superclasses)": [],
@@ -102462,10 +98768,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -102488,7 +98792,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -102532,10 +98835,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -102558,7 +98859,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -102594,18 +98894,16 @@
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
-    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.org.au": 1,
     "Available on UseGalaxy.eu": 1,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
-    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.org.au": 1,
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -102628,7 +98926,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -102673,10 +98970,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -102699,7 +98994,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -102744,10 +99038,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -102770,7 +99062,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -102815,10 +99106,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -102841,7 +99130,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -102885,10 +99173,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -102911,7 +99197,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -102955,10 +99240,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -102981,7 +99264,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -103031,10 +99313,8 @@
     "Tools available on UseGalaxy.eu": 7,
     "Tools available on UseGalaxy.fr": 7,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -103057,8 +99337,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 6,
     "Tools available on UseGalaxy.cz": 7,
     "Tools available on UseGalaxy.no": 7,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -103101,10 +99380,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -103127,7 +99404,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -103171,10 +99447,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -103197,7 +99471,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -103241,10 +99514,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -103267,8 +99538,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -103317,10 +99587,8 @@
     "Tools available on UseGalaxy.eu": 7,
     "Tools available on UseGalaxy.fr": 7,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -103343,7 +99611,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 7,
     "Tools available on UseGalaxy.no": 0,
@@ -103391,10 +99658,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 5,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -103417,7 +99682,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 5,
     "Tools available on UseGalaxy.no": 5,
@@ -103464,10 +99728,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 4,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -103490,7 +99752,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 4,
@@ -103534,10 +99795,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -103560,7 +99819,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -103604,10 +99862,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -103630,7 +99886,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -103660,7 +99915,7 @@
     "Galaxy wrapper owner": "climate",
     "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s",
     "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s",
-    "Galaxy wrapper version": "0.2.0",
+    "Galaxy wrapper version": "0.3.0",
     "Conda id": "python",
     "Conda version": null,
     "EDAM operation (no superclasses)": [],
@@ -103674,10 +99929,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -103700,7 +99953,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -103744,10 +99996,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -103770,7 +100020,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -103815,10 +100064,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -103841,7 +100088,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -103885,10 +100131,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -103911,7 +100155,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -103956,10 +100199,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -103982,7 +100223,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -104026,10 +100266,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -104052,7 +100290,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -104097,10 +100334,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -104123,7 +100358,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -104167,10 +100401,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -104193,7 +100425,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -104239,11 +100470,9 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
-    "Tools available on ChemFlow": 0,
+    "Tools available on ChemFlow": 1,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
     "Tools available on CropGalaxy": 0,
@@ -104265,7 +100494,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -104296,7 +100524,7 @@
     "Galaxy wrapper owner": "climate",
     "Galaxy wrapper source": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps",
     "Galaxy wrapper parsed folder": "https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps",
-    "Galaxy wrapper version": "1.2.1",
+    "Galaxy wrapper version": "1.3.1",
     "Conda id": "python",
     "Conda version": null,
     "EDAM operation (no superclasses)": [],
@@ -104310,10 +100538,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -104336,7 +100562,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -104380,10 +100605,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -104406,7 +100629,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -104450,10 +100672,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -104476,7 +100696,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -104520,10 +100739,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -104546,7 +100763,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -104592,10 +100808,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -104618,7 +100832,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -104662,10 +100875,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -104688,7 +100899,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -104732,10 +100942,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -104758,7 +100966,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -104802,10 +101009,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -104828,7 +101033,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -104874,10 +101078,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -104900,7 +101102,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -104944,10 +101145,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -104970,7 +101169,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -105023,10 +101221,8 @@
     "Tools available on UseGalaxy.eu": 6,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -105049,7 +101245,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -105094,10 +101289,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -105120,7 +101313,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -105165,10 +101357,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -105191,7 +101381,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -105237,10 +101426,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -105263,7 +101450,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -105311,10 +101497,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -105337,7 +101521,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -105390,10 +101573,8 @@
     "Tools available on UseGalaxy.eu": 7,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -105416,7 +101597,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -105471,10 +101651,8 @@
     "Tools available on UseGalaxy.eu": 9,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -105497,7 +101675,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -105509,6 +101686,7 @@
     "Galaxy wrapper id": "pyscenic",
     "Galaxy tool ids": [
       "pyscenic_aucell",
+      "pyscenic_binarize",
       "pyscenic_ctx",
       "pyscenic_grn"
     ],
@@ -105545,10 +101723,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -105571,7 +101747,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -105624,10 +101799,8 @@
     "Tools available on UseGalaxy.eu": 7,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -105650,7 +101823,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -105722,10 +101894,8 @@
     "Tools available on UseGalaxy.eu": 27,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -105748,7 +101918,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 14,
     "Tools available on UseGalaxy.no": 13,
@@ -105800,10 +101969,8 @@
     "Tools available on UseGalaxy.eu": 6,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -105826,8 +101993,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 2,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 2,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -105873,10 +102039,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -105899,7 +102063,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -105943,10 +102106,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -105969,7 +102130,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -106022,10 +102182,8 @@
     "Tools available on UseGalaxy.eu": 7,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -106048,7 +102206,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -106098,10 +102255,8 @@
     "Tools available on UseGalaxy.eu": 4,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -106124,7 +102279,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -106163,7 +102317,7 @@
     "bio.tool description": null,
     "EDAM operation": [],
     "EDAM topic": [],
-    "Status": "Up-to-date",
+    "Status": "To update",
     "Source": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/",
     "ToolShed categories": [
       "Transcriptomics",
@@ -106177,7 +102331,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat",
     "Galaxy wrapper version": "4.0.0",
     "Conda id": "seurat-scripts",
-    "Conda version": "4.0.0",
+    "Conda version": "4.4.0",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 14,
@@ -106189,10 +102343,8 @@
     "Tools available on UseGalaxy.eu": 14,
     "Tools available on UseGalaxy.fr": 11,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -106215,7 +102367,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -106259,10 +102410,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -106285,7 +102434,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -106351,10 +102499,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -106377,7 +102523,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -106421,10 +102566,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -106447,7 +102590,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -106491,10 +102633,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -106517,7 +102657,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -106561,10 +102700,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -106587,7 +102724,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -106658,10 +102794,8 @@
     "Tools available on UseGalaxy.eu": 14,
     "Tools available on UseGalaxy.fr": 11,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -106684,7 +102818,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 9,
     "Tools available on UseGalaxy.no": 0,
@@ -106695,6 +102828,7 @@
   {
     "Galaxy wrapper id": "mfassignr",
     "Galaxy tool ids": [
+      "mfassignr_findRecalSeries",
       "mfassignr_histnoise",
       "mfassignr_isofiltr",
       "mfassignr_kmdnoise",
@@ -106729,9 +102863,9 @@
     "Galaxy wrapper owner": "recetox",
     "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr",
     "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr",
-    "Galaxy wrapper version": "1.0.3",
+    "Galaxy wrapper version": "1.1.1",
     "Conda id": "r-mfassignr",
-    "Conda version": "1.0.3",
+    "Conda version": "1.1.1",
     "EDAM operation (no superclasses)": [
       "Visualisation"
     ],
@@ -106742,17 +102876,15 @@
     ],
     "Available on UseGalaxy.org (Main)": 0,
     "Available on UseGalaxy.org.au": 0,
-    "Available on UseGalaxy.eu": 8,
+    "Available on UseGalaxy.eu": 9,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
     "Tools available on UseGalaxy.org.au": 0,
-    "Tools available on UseGalaxy.eu": 8,
+    "Tools available on UseGalaxy.eu": 9,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -106775,7 +102907,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -106786,6 +102917,7 @@
   {
     "Galaxy wrapper id": "misc",
     "Galaxy tool ids": [
+      "target_screen",
       "use_theoretical_mz_annotations"
     ],
     "Description": null,
@@ -106806,23 +102938,112 @@
     "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/misc",
     "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/misc",
     "Galaxy wrapper version": "1.0.0",
-    "Conda id": null,
+    "Conda id": "pandas",
     "Conda version": null,
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
     "Available on UseGalaxy.org.au": 1,
-    "Available on UseGalaxy.eu": 1,
+    "Available on UseGalaxy.eu": 2,
     "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
     "Tools available on UseGalaxy.org.au": 1,
-    "Tools available on UseGalaxy.eu": 1,
+    "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
+    "Tools available on CIRM-CFBP": 0,
+    "Tools available on ChemFlow": 0,
+    "Tools available on Coloc-stats": 0,
+    "Tools available on CoralSNP": 0,
+    "Tools available on CropGalaxy": 0,
+    "Tools available on Dintor": 0,
+    "Tools available on FreeBioinfo": 0,
+    "Tools available on GASLINI": 0,
+    "Tools available on Galaxy@AuBi": 0,
+    "Tools available on Galaxy@Pasteur": 0,
+    "Tools available on GalaxyTrakr": 0,
+    "Tools available on Genomic Hyperbrowser": 0,
+    "Tools available on GigaGalaxy": 0,
+    "Tools available on HyPhy HIV NGS Tools": 0,
+    "Tools available on IPK Galaxy Blast Suite": 0,
+    "Tools available on ImmPort Galaxy": 0,
+    "Tools available on InteractoMIX": 0,
+    "Tools available on MISSISSIPPI": 0,
+    "Tools available on Mandoiu Lab": 0,
+    "Tools available on MiModD NacreousMap": 0,
+    "Tools available on Oqtans": 0,
+    "Tools available on Palfinder": 0,
+    "Tools available on PepSimili": 0,
+    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.cz": 0,
+    "Tools available on UseGalaxy.no": 0,
+    "Tools available on Viral Variant Visualizer (VVV)": 0,
+    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+    "Total tool usage (usegalaxy.eu)": 0
+  },
+  {
+    "Galaxy wrapper id": "ms2deepscore",
+    "Galaxy tool ids": [
+      "ms2deepscore_config_generator",
+      "ms2deepscore_similarity",
+      "ms2deepscore_training"
+    ],
+    "Description": "Mass spectra similarity scoring using a trained ms2deepscore model.",
+    "bio.tool id": "ms2deepscore",
+    "bio.tool ids": [
+      "ms2deepscore"
+    ],
+    "biii": null,
+    "bio.tool name": "MS2DeepScore",
+    "bio.tool description": "MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra.",
+    "EDAM operation": [
+      "Spectrum calculation",
+      "Spectral library search",
+      "Network analysis"
+    ],
+    "EDAM topic": [
+      "Proteomics experiment",
+      "Machine learning",
+      "Metabolomics",
+      "Small molecules",
+      "Compound libraries and screening"
+    ],
+    "Status": "Up-to-date",
+    "Source": "https://github.com/matchms/ms2deepscore",
+    "ToolShed categories": [
+      "Metabolomics"
+    ],
+    "ToolShed id": "ms2deepscore",
+    "Galaxy wrapper owner": "recetox",
+    "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore",
+    "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore",
+    "Galaxy wrapper version": "2.0.0",
+    "Conda id": "ms2deepscore",
+    "Conda version": "2.0.0",
+    "EDAM operation (no superclasses)": [
+      "Spectrum calculation",
+      "Spectral library search",
+      "Network analysis"
+    ],
+    "EDAM topic (no superclasses)": [
+      "Proteomics experiment",
+      "Machine learning",
+      "Metabolomics",
+      "Small molecules",
+      "Compound libraries and screening"
+    ],
+    "Available on UseGalaxy.org (Main)": 0,
+    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.eu": 3,
+    "Available on UseGalaxy.fr": 0,
+    "Tools available on UseGalaxy.org (Main)": 0,
+    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.eu": 3,
+    "Tools available on UseGalaxy.fr": 0,
+    "Tools available on APOSTL": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -106845,7 +103066,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -106905,10 +103125,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -106931,7 +103149,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -106975,10 +103192,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -107001,7 +103216,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -107046,10 +103260,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -107072,7 +103284,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -107119,10 +103330,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -107145,7 +103354,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -107189,10 +103397,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -107215,7 +103421,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -107276,10 +103481,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 2,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -107302,7 +103505,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 2,
     "Tools available on UseGalaxy.no": 0,
@@ -107346,10 +103548,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -107372,7 +103572,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -107419,9 +103618,9 @@
     "Galaxy wrapper owner": "recetox",
     "Galaxy wrapper source": "https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms",
     "Galaxy wrapper parsed folder": "https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms",
-    "Galaxy wrapper version": "0.13.2",
+    "Galaxy wrapper version": "0.13.3",
     "Conda id": "r-recetox-aplcms",
-    "Conda version": "0.13.2",
+    "Conda version": "0.13.3",
     "EDAM operation (no superclasses)": [
       "Chromatographic alignment",
       "Quantification",
@@ -107441,10 +103640,8 @@
     "Tools available on UseGalaxy.eu": 8,
     "Tools available on UseGalaxy.fr": 8,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -107467,7 +103664,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 8,
     "Tools available on UseGalaxy.no": 0,
@@ -107521,10 +103717,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -107547,7 +103741,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -107603,10 +103796,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -107629,7 +103820,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -107673,10 +103863,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -107699,7 +103887,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -107743,10 +103930,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -107769,7 +103954,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -107842,10 +104026,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -107868,7 +104050,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -107927,10 +104108,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -107953,7 +104132,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -107997,10 +104175,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -108023,7 +104199,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -108090,10 +104265,8 @@
     "Tools available on UseGalaxy.eu": 2,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -108116,7 +104289,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -108170,10 +104342,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -108196,7 +104366,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -108240,10 +104409,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 1,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -108266,7 +104433,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -108310,10 +104476,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -108336,7 +104500,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -108380,10 +104543,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -108406,7 +104567,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -108450,10 +104610,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -108476,7 +104634,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -108520,10 +104677,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -108546,7 +104701,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -108590,10 +104744,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -108616,7 +104768,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -108660,10 +104811,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -108686,7 +104835,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -108730,10 +104878,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -108756,7 +104902,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -108800,10 +104945,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -108826,7 +104969,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -108870,10 +105012,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -108896,7 +105036,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -108940,10 +105079,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -108966,7 +105103,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -109008,10 +105144,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -109034,7 +105168,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -109070,7 +105203,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler",
     "Galaxy wrapper version": "0.9.3",
     "Conda id": "htslib",
-    "Conda version": "1.20",
+    "Conda version": "1.21",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 4,
@@ -109082,10 +105215,8 @@
     "Tools available on UseGalaxy.eu": 5,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -109108,7 +105239,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 4,
     "Tools available on UseGalaxy.no": 0,
@@ -109152,10 +105282,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -109178,7 +105306,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -109222,10 +105349,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -109248,7 +105373,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -109292,10 +105416,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -109318,7 +105440,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -109350,7 +105471,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie",
     "Galaxy wrapper version": "20230328",
     "Conda id": "Fiji",
-    "Conda version": "20231211",
+    "Conda version": "20240614",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -109362,10 +105483,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -109388,7 +105507,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -109420,7 +105538,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero",
     "Galaxy wrapper version": "20231221",
     "Conda id": "Fiji",
-    "Conda version": "20231211",
+    "Conda version": "20240614",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -109432,10 +105550,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -109458,7 +105574,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -109490,7 +105605,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids",
     "Galaxy wrapper version": "20221216",
     "Conda id": "fiji",
-    "Conda version": "20231211",
+    "Conda version": "20240614",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -109502,10 +105617,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -109528,7 +105641,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -109560,7 +105672,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables",
     "Galaxy wrapper version": "20230623",
     "Conda id": "fiji",
-    "Conda version": "20231211",
+    "Conda version": "20240614",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -109572,10 +105684,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -109598,7 +105708,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -109642,10 +105751,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -109668,7 +105775,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -109700,7 +105806,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images",
     "Galaxy wrapper version": "20240521",
     "Conda id": "fiji",
-    "Conda version": "20231211",
+    "Conda version": "20240614",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -109712,10 +105818,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -109738,7 +105842,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -109770,7 +105873,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid",
     "Galaxy wrapper version": "20230809",
     "Conda id": "fiji",
-    "Conda version": "20231211",
+    "Conda version": "20240614",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -109782,10 +105885,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -109808,7 +105909,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -109840,7 +105940,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements",
     "Galaxy wrapper version": "20240214",
     "Conda id": "fiji",
-    "Conda version": "20231211",
+    "Conda version": "20240614",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 0,
@@ -109852,10 +105952,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -109878,7 +105976,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -109910,7 +106007,7 @@
     "Galaxy wrapper parsed folder": "https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam",
     "Galaxy wrapper version": "0.0.2",
     "Conda id": "samtools",
-    "Conda version": "1.20",
+    "Conda version": "1.21",
     "EDAM operation (no superclasses)": [],
     "EDAM topic (no superclasses)": [],
     "Available on UseGalaxy.org (Main)": 1,
@@ -109922,10 +106019,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -109948,7 +106043,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -109992,10 +106086,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -110018,7 +106110,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -110063,10 +106154,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 1,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -110089,7 +106178,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -110134,10 +106222,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -110160,7 +106246,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -110206,10 +106291,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -110218,7 +106301,7 @@
     "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
-    "Tools available on Galaxy@Pasteur": 0,
+    "Tools available on Galaxy@Pasteur": 1,
     "Tools available on GalaxyTrakr": 0,
     "Tools available on Genomic Hyperbrowser": 0,
     "Tools available on GigaGalaxy": 0,
@@ -110232,7 +106315,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 1,
@@ -110277,10 +106359,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -110303,7 +106383,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -110364,10 +106443,8 @@
     "Tools available on UseGalaxy.eu": 16,
     "Tools available on UseGalaxy.fr": 16,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 15,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 15,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -110390,8 +106467,7 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 16,
-    "Tools available on PhagePromotor": 0,
-    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.be": 16,
     "Tools available on UseGalaxy.cz": 16,
     "Tools available on UseGalaxy.no": 15,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
@@ -110479,10 +106555,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 28,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -110505,7 +106579,93 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
+    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.cz": 0,
+    "Tools available on UseGalaxy.no": 0,
+    "Tools available on Viral Variant Visualizer (VVV)": 0,
+    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+    "Total tool usage (usegalaxy.eu)": 0
+  },
+  {
+    "Galaxy wrapper id": "checkv",
+    "Galaxy tool ids": [
+      "checkv_end_to_end"
+    ],
+    "Description": "Assess quality of single-contig viral genomes",
+    "bio.tool id": "checkv",
+    "bio.tool ids": [
+      "checkv"
+    ],
+    "biii": null,
+    "bio.tool name": "CheckV",
+    "bio.tool description": "CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.",
+    "EDAM operation": [
+      "Sequence assembly",
+      "Validation",
+      "Read mapping"
+    ],
+    "EDAM topic": [
+      "Metagenomics",
+      "Sequence assembly",
+      "Metagenomic sequencing",
+      "Mapping"
+    ],
+    "Status": "Up-to-date",
+    "Source": "https://bitbucket.org/berkeleylab/checkv/",
+    "ToolShed categories": [
+      "Metagenomics"
+    ],
+    "ToolShed id": "checkv",
+    "Galaxy wrapper owner": "ufz",
+    "Galaxy wrapper source": "https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/",
+    "Galaxy wrapper parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv",
+    "Galaxy wrapper version": "1.0.3",
+    "Conda id": "checkv",
+    "Conda version": "1.0.3",
+    "EDAM operation (no superclasses)": [
+      "Sequence assembly",
+      "Validation",
+      "Read mapping"
+    ],
+    "EDAM topic (no superclasses)": [
+      "Metagenomics",
+      "Sequence assembly",
+      "Metagenomic sequencing",
+      "Mapping"
+    ],
+    "Available on UseGalaxy.org (Main)": 0,
+    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.eu": 0,
+    "Available on UseGalaxy.fr": 0,
+    "Tools available on UseGalaxy.org (Main)": 0,
+    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.eu": 0,
+    "Tools available on UseGalaxy.fr": 0,
+    "Tools available on APOSTL": 0,
+    "Tools available on ARGs-OAP": 0,
+    "Tools available on CIRM-CFBP": 0,
+    "Tools available on ChemFlow": 0,
+    "Tools available on Coloc-stats": 0,
+    "Tools available on CoralSNP": 0,
+    "Tools available on CropGalaxy": 0,
+    "Tools available on Dintor": 0,
+    "Tools available on FreeBioinfo": 0,
+    "Tools available on GASLINI": 0,
+    "Tools available on Galaxy@AuBi": 0,
+    "Tools available on Galaxy@Pasteur": 0,
+    "Tools available on GalaxyTrakr": 0,
+    "Tools available on Genomic Hyperbrowser": 0,
+    "Tools available on GigaGalaxy": 0,
+    "Tools available on HyPhy HIV NGS Tools": 0,
+    "Tools available on IPK Galaxy Blast Suite": 0,
+    "Tools available on ImmPort Galaxy": 0,
+    "Tools available on InteractoMIX": 0,
+    "Tools available on MISSISSIPPI": 0,
+    "Tools available on Mandoiu Lab": 0,
+    "Tools available on MiModD NacreousMap": 0,
+    "Tools available on Oqtans": 0,
+    "Tools available on Palfinder": 0,
+    "Tools available on PepSimili": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -110540,7 +106700,7 @@
     ],
     "ToolShed id": "genomad",
     "Galaxy wrapper owner": "ufz",
-    "Galaxy wrapper source": "https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/",
+    "Galaxy wrapper source": "https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/",
     "Galaxy wrapper parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad",
     "Galaxy wrapper version": "1.8.0",
     "Conda id": "genomad",
@@ -110561,10 +106721,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -110587,7 +106745,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -110631,10 +106788,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -110657,7 +106812,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -110669,9 +106823,10 @@
     "Galaxy wrapper id": "omero",
     "Galaxy tool ids": [
       "omero_import",
-      "omero_metadata_import"
+      "omero_metadata_import",
+      "omero_roi_import"
     ],
-    "Description": "Import images and metadata into an OMERO.server using omero-py",
+    "Description": "Import images, region of interest, metadata into an OMERO.server using omero-py",
     "bio.tool id": "omero",
     "bio.tool ids": [
       "omero"
@@ -110714,10 +106869,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -110740,7 +106893,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -110784,10 +106936,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -110810,7 +106960,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -110855,10 +107004,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -110881,7 +107028,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -110925,10 +107071,97 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
+    "Tools available on CIRM-CFBP": 0,
+    "Tools available on ChemFlow": 0,
+    "Tools available on Coloc-stats": 0,
+    "Tools available on CoralSNP": 0,
+    "Tools available on CropGalaxy": 0,
+    "Tools available on Dintor": 0,
+    "Tools available on FreeBioinfo": 0,
+    "Tools available on GASLINI": 0,
+    "Tools available on Galaxy@AuBi": 0,
+    "Tools available on Galaxy@Pasteur": 0,
+    "Tools available on GalaxyTrakr": 0,
+    "Tools available on Genomic Hyperbrowser": 0,
+    "Tools available on GigaGalaxy": 0,
+    "Tools available on HyPhy HIV NGS Tools": 0,
+    "Tools available on IPK Galaxy Blast Suite": 0,
+    "Tools available on ImmPort Galaxy": 0,
+    "Tools available on InteractoMIX": 0,
+    "Tools available on MISSISSIPPI": 0,
+    "Tools available on Mandoiu Lab": 0,
+    "Tools available on MiModD NacreousMap": 0,
+    "Tools available on Oqtans": 0,
+    "Tools available on Palfinder": 0,
+    "Tools available on PepSimili": 0,
+    "Tools available on UseGalaxy.be": 0,
+    "Tools available on UseGalaxy.cz": 0,
+    "Tools available on UseGalaxy.no": 0,
+    "Tools available on Viral Variant Visualizer (VVV)": 0,
+    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+    "Total tool usage (usegalaxy.eu)": 0
+  },
+  {
+    "Galaxy wrapper id": "vibrant",
+    "Galaxy tool ids": [
+      "vibrant"
+    ],
+    "Description": "Virus Identification By iteRative ANnoTation",
+    "bio.tool id": "VIBRANT",
+    "bio.tool ids": [
+      "VIBRANT"
+    ],
+    "biii": null,
+    "bio.tool name": "VIBRANT",
+    "bio.tool description": "Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions",
+    "EDAM operation": [
+      "Sequence trimming",
+      "Scaffolding",
+      "Genome annotation"
+    ],
+    "EDAM topic": [
+      "Metagenomics",
+      "Microbial ecology",
+      "Sequence assembly",
+      "Molecular interactions, pathways and networks",
+      "Endocrinology and metabolism"
+    ],
+    "Status": "Up-to-date",
+    "Source": "https://github.com/AnantharamanLab/VIBRANT",
+    "ToolShed categories": [
+      "Metagenomics"
+    ],
+    "ToolShed id": "vibrant",
+    "Galaxy wrapper owner": "ufz",
+    "Galaxy wrapper source": "https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant",
+    "Galaxy wrapper parsed folder": "https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant",
+    "Galaxy wrapper version": "1.2.1",
+    "Conda id": "vibrant",
+    "Conda version": "1.2.1",
+    "EDAM operation (no superclasses)": [
+      "Sequence trimming",
+      "Scaffolding",
+      "Genome annotation"
+    ],
+    "EDAM topic (no superclasses)": [
+      "Metagenomics",
+      "Microbial ecology",
+      "Sequence assembly",
+      "Molecular interactions, pathways and networks",
+      "Endocrinology and metabolism"
+    ],
+    "Available on UseGalaxy.org (Main)": 0,
+    "Available on UseGalaxy.org.au": 0,
+    "Available on UseGalaxy.eu": 0,
+    "Available on UseGalaxy.fr": 0,
+    "Tools available on UseGalaxy.org (Main)": 0,
+    "Tools available on UseGalaxy.org.au": 0,
+    "Tools available on UseGalaxy.eu": 0,
+    "Tools available on UseGalaxy.fr": 0,
+    "Tools available on APOSTL": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -110951,7 +107184,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -111005,10 +107237,8 @@
     "Tools available on UseGalaxy.eu": 0,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -111031,7 +107261,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -111075,10 +107304,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -111101,7 +107328,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
@@ -111147,10 +107373,8 @@
     "Tools available on UseGalaxy.eu": 3,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -111173,7 +107397,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 0,
@@ -111217,10 +107440,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -111243,7 +107464,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -111287,10 +107507,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -111313,7 +107531,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
@@ -111357,10 +107574,8 @@
     "Tools available on UseGalaxy.eu": 1,
     "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
-    "Tools available on BF2I-MAP": 0,
-    "Tools available on BioBix": 0,
+    "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
-    "Tools available on Center for Phage Technology (CPT)": 0,
     "Tools available on ChemFlow": 0,
     "Tools available on Coloc-stats": 0,
     "Tools available on CoralSNP": 0,
@@ -111383,7 +107598,6 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
-    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
diff --git a/communities/all/resources/tools.tsv b/communities/all/resources/tools.tsv
index 05b0cc48..219dbb46 100644
--- a/communities/all/resources/tools.tsv
+++ b/communities/all/resources/tools.tsv
@@ -1,1465 +1,1472 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on BF2I-MAP	Tools available on BioBix	Tools available on CIRM-CFBP	Tools available on Center for Phage Technology (CPT)	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)
-2d_auto_threshold	ip_threshold	Automatic thresholding	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_auto_threshold	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	6541
-2d_feature_extraction	ip_2d_feature_extraction	2D feature extraction	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_feature_extraction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	19	13760
-2d_filter_segmentation_by_features	ip_2d_filter_segmentation_by_features	filter segmentation by rules	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	2d_filter_segmentation_by_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features	0.0.1-4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	6834
-2d_histogram_equalization	ip_histogram_equalization	2d histogram equalization	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_histogram_equalization	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	656
-2d_simple_filter	ip_filter_standard	2d simple filter			scipy					To update	https://github.com/bmcv	Imaging	2d_simple_filter	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter	1.12.0	scipy				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	35	6156
-3d_tensor_feature_dimension_reduction	ip_3d_tensor_feature_dimension_reduction	Dimensionality reduction for features (channels) of 3D tensor data using UMAP								To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	3d_tensor_feature_dimension_reduction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction	0.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Ensembl-REST	get_feature_info, get_genetree, get_sequences	A suite of Galaxy tools designed to work with Ensembl REST API.								To update	https://rest.ensembl.org	Data Source		earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST	0.1.2	requests				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	47	2889
-GAFA	gafa	Gene Align and Family Aggregator								To update	http://aequatus.tgac.ac.uk	Visualization	gafa	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA	0.3.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	45
-TreeBest	treebest_best	TreeBeST best	treebest	treebest		TreeBeST	TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	984
-abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-anisotropic_diffusion	ip_anisotropic_diffusion	Anisotropic image diffusion								Up-to-date	https://github.com/bmcv	Imaging	anisotropic_diffusion	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion	0.4.0	medpy	0.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	40
-apoc	apoc	Large-scale structural comparison of protein pockets								To update	http://cssb.biology.gatech.edu/APoc	Computational chemistry	apoc	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc	1.0+galaxy1	apoc	1b16			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	3
-apollo	create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism	Access an Apollo instance from Galaxy								To update	https://github.com/galaxy-genome-annotation/python-apollo	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo		apollo	4.2.13			0	0	9	0	0	0	9	0	0	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	0	301	1896
-askomics	askomics_integrate	Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/								To update	https://github.com/askomics/	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics		askocli	0.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-askor	askor_de	AskoR links EdgeR and AskOmics								To update	https://github.com/askomics/askoR	Transcriptomics	askor_de	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	0.2	bioconductor-limma	3.58.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-background_removal	background_removal	Background removal filters using scikit-image								To update	https://github.com/bmcv	Imaging	background_removal	imgteam	https://github.com/BMCV/galaxy-image-analysis/tools/background_removal	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal	0.24.0	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-bamclipper	bamclipper	Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.								Up-to-date	https://github.com/tommyau/bamclipper	Sequence Analysis	bamclipper	nml	https://github.com/tommyau/bamclipper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper	1.0.0	bamclipper	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-baric_archive	baric_archive_rennes, baric_archive_toulouse	A data source tool to fetch data from a BARIC Archive server.								To update	https://www.cesgo.org/catibaric/	Data Source		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive	https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive	1.1.0					0	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-batched_lastz	batched_lastz	Galaxy wrapper for the batching Lastz runs								Up-to-date	https://github.com/galaxyproject/KegAlign	Next Gen Mappers	batched_lastz	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz	https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz	1.04.22	lastz	1.04.22			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-bfconvert	ip_convertimage	Convert image			python-bioformats					Up-to-date	https://github.com/bmcv	Imaging, Convert Formats	bfconvert	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert	6.7.0	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	38	1523
-binary2labelimage	ip_binary_to_labelimage	Binary 2 label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binary2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage	0.5	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	1273
-binaryimage2points	ip_binaryimage_to_points	Binary Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binaryimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points	0.1-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	29
-bioformats2raw	bf2raw	Convert image to OME-Zarr								To update	https://github.com/Euro-BioImaging	Imaging, Convert Formats	bioformats2raw	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	0.7.0					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9
-biohansel	biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-biohansel_bionumeric_converter	bionumeric_convert	Convert BioHansel output data to a Bionumerics friendly form								To update	https://github.com/phac-nml/galaxy_tools	Text Manipulation	biohansel_bionumeric_converter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter	0.2.0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-blast_parser	blast_parser	Convert 12- or 24-column BLAST output into 3-column hcluster_sg input								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	blast_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	0.1.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	27	296
-braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	17	109
-braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	567
-bundle_collections	bundle_collection	Tool to bundle up list collection into a single zip to be download								To update		Sequence Analysis	bundle_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections	1.3.0	perl-getopt-long	2.58			0	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-camera	abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos									To update		Metabolomics	camera	workflow4metabolomics		https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera	1.48.0	r-snow	0.4_1			1	2	2	2	1	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	30	623
-cfm	cfmid	Competitive Fragmentation Modeling (CFM)								Up-to-date	https://sourceforge.net/p/cfm-id/	Metabolomics	cfmid	computational-metabolomics	https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm	https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm	33	cfm	33			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chado	analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree	Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado								To update	https://github.com/galaxy-genome-annotation/python-chado	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado		python-chado	2.3.9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-collapse_collection	collapse_dataset	Collection tool that collapses a list of files into a single datasset in order of appears in collection								To update		Sequence Analysis	collapse_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection	5.1.0	gawk				1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1583	33934
-color-deconvolution	ip_color_deconvolution	Color-deconvolution methods	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	color_deconvolution	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution	0.8-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	16
-colorize_labels	colorize_labels	Colorize label map								To update	https://github.com/bmcv	Imaging	colorize_labels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	3.2.1	networkx				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-combineJSON	combine_json	JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.								To update		Sequence Analysis	combine_json	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-combine_tabular_collection	combine	Combine Tabular Collection into a single file								To update		Sequence Analysis	combine_tabular_collection	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-concat_channels	ip_concat_channels	Concatenate images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	concat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels	0.3-1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	78
-concat_paired	concat_fastqs	Concatenate paired datasets								To update	https://github.com/phac-nml/concat	Text Manipulation	concat_paired	nml	https://github.com/phac-nml/concat	https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired	0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-coordinates_of_roi	ip_coordinates_of_roi	Coordinates of ROI	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	coordinates_of_roi	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi	0.0.4-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	16546
-correlation_analysis	correlation_analysis	[Metabolomics][W4M] Metabolites Correlation Analysis								To update	http://workflow4metabolomics.org	Metabolomics	correlation_analysis	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis	1.0.1+galaxy0	r-batch	1.1_4			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-count_objects	ip_count_objects	Count Objects	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	count_objects	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects	0.0.5-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	25	272
-cryptogenotyper	CryptoGenotyper	CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	8518
-csvtk	csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq	Rapid data investigation and manipulation of csv/tsv files								To update	https://bioinf.shenwei.me/csvtk/	Text Manipulation	csvtk	nml	https://github.com/shenwei356/csvtk	https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk	0.20.0	csvtk	0.30.0			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	20	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-curl_post	curl_post	Send file via cURL POST								To update	https://github.com/bmcv	Data Export, Web Services	curl_post	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curl_post	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curl_post	0.0.2	curl				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	27	440
-curve_fitting	ip_curve_fitting	Polynomial curve fitting to data points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	curve_fitting	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	12
-detection_viz	ip_detection_viz	Detection Visualization	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	detection_viz	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	46
-ectyper	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	9907
-ete	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete		ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	Phylogenetic tree editing	Phylogenetics	0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	45	899
-export_to_cluster	export_to_cluster	Export datasets to cluster								To update	https://github.com/TGAC/earlham-galaxytools/	Data Export	export_to_cluster	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster	0.0.2	EXPORT_DIR_PREFIX				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fasta2bed	fasta2bed	Convert multiple fasta file into tabular bed file format								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fasta2bed	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fasta_extract	fa-extract-sequence	extract single fasta from multiple fasta file								To update	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	Sequence Analysis	fasta_extract	nml	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	10
-fastqc_stats	FastQC_Summary	Summary multiple FastQC into a single tabular line report								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fastqc_stats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats	1.2	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-feelnc2asko	feelnc2asko	Convert FeelNC GTF to GFF3								To update	https://github.com/tderrien/FEELnc	Convert Formats	feelnc2asko	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko	https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko	0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-feht	feht	Automatically identify makers predictive of groups.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	feht	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht	0.1.0	feht	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gblocks	gblocks	Gblocks								Up-to-date	http://molevol.cmima.csic.es/castresana/Gblocks.html	Sequence Analysis	gblocks	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	0.91b	gblocks	0.91b			0	1	0	1	0	1	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gcms2isocor	gcms2isocor	Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs								To update	https://github.com/p2m2/p2m2tools	Metabolomics	gcms2isocor	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor	0.2.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gcms2isocor	gcms2isocor	Conversion from GCMS PostRun Analysis to Isocor								To update		Metabolomics	gcms2isocor	genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor	0.1.0	openjdk				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-genenotebook	genenotebook_build	Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io								Up-to-date	https://genenotebook.github.io	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook	0.4.16	genoboo	0.4.16			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-genform	genform	genform: generation of molecular formulas by high-resolution MS and MS/MS data								To update	https://sourceforge.net/projects/genform/	Metabolomics	genform	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform		genform	r8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	68
-get_pairs	get_pairs	Separate paired and unpaired reads from two fastq files								To update		Fastq Manipulation	get_pairs	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	0.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-getmlst	getmlst	Download MLST datasets by species from pubmlst.org								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gnali	gnali	A tool to find nonessential, loss-of-function gene variants								Up-to-date	https://github.com/phac-nml/gnali/	Variant Analysis	gnali	nml	https://github.com/phac-nml/gnali/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali	1.1.0	gnali	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gstf_preparation	gstf_preparation	GeneSeqToFamily preparation converts data for the workflow								To update	https://github.com/TGAC/earlham-galaxytools/	Convert Formats	gstf_preparation	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation	0.4.3	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	397
-hcluster_sg	hcluster_sg	Hierarchically clustering on a sparse graph								To update	https://github.com/douglasgscofield/hcluster	Phylogenetics	hcluster_sg	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	0.5.1.1	hcluster_sg	0.5.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	238
-hcluster_sg_parser	hcluster_sg_parser	Converts hcluster_sg 3-column output into lists of ids								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	hcluster_sg_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	0.2.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	290
-helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	93
-hivtrace	hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-image_info	ip_imageinfo	Extracts image metadata			python-bioformats					To update	https://github.com/bmcv	Imaging	image_info	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info	5.7.1	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	41	621
-image_math	image_math	Process images using arithmetic expressions								To update	https://github.com/bmcv	Imaging	image_math	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	1.26.4	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-image_registration_affine	ip_image_registration	Intensity-based Image Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	image_registration_affine	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine	0.0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	12
-imagecoordinates_flipaxis	imagecoordinates_flipaxis	Flip coordinate axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	imagecoordinates_flipaxis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis	0.1-2	pandas		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	21825
-influx_data_manager	influx_data_manager	Handling influx_si data inputs in Galaxy workflows								To update	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/	Metabolomics	influx_si_data_manager	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager	1.0.2	influx-si-data-manager	1.0.3			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-influx_si	influx_si	metabolic flux estimation based on [in]stationary labeling								To update	https://github.com/sgsokol/influx	Metabolomics	influx_si	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si	7.0.1	influx_si	7.0.4			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ipo	ipo4retgroup, ipo4xcmsSet	[W4M][LC-MS] IPO								To update	https://github.com/rietho/IPO	Metabolomics	ipo	lecorguille	https://github.com/rietho/IPO	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo	1.10.0	bioconductor-ipo	1.28.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-isoplot	isoplot	Isoplot is a software for the visualisation of MS data from C13 labelling experiments								To update		Metabolomics, Visualization	isoplot	workflow4metabolomics	https://github.com/llegregam/Isoplot/tree/main	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot	1.3.0+galaxy1	isoplot	1.3.1			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	2
-jbrowse	jbrowse_to_container	A tool allowing to export a JBrowse dataset into a JBrowse docker container								To update	https://jbrowse.org	Web Services	jbrowse_to_container	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse		python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-kaptive	kaptive	Kaptive reports information about capsular (K) loci found in genome assemblies.								To update		Sequence Analysis	kaptive	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive	0.3.0	kaptive	3.0.0b5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-kat_filter	kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-kat_sect	kat_@EXECUTABLE@	SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.								To update			kat_sect	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-kegalign	kegalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.								Up-to-date	https://github.com/galaxyproject/KegAlign	Next Gen Mappers	kegalign	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign	https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign	0.1.2.7	kegalign-full	0.1.2.7			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-kmd_hmdb_data_plot	kmd_hmdb_data_plot	retrieves data from KMD HMDB API and produce plot and csv file								To update	https://github.com/workflow4metabolomics/tools-metabolomics	Metabolomics	kmd_hmdb_data_plot	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot	1.0.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-label_to_binary	label_to_binary	Convert label map to binary image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	label_to_binary	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-labelimage2points	ip_labelimage_to_points	Label Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	labelimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	36
-landmark_registration	ip_landmark_registration	Landmark Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	landmark_registration	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration	0.1.0-2	scikit-image		Image analysis	Imaging, Bioinformatics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	857
-logol	logol_wrapper	Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence								Up-to-date	http://logol.genouest.org/web/app.php/logol	Sequence Analysis		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	1.7.8	logol	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-lotus2	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2		lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	To update	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.34.1	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	114	936
-mahotas-features	ip_mahotas_features	Compute image features using mahotas.			mahotas-feature-computation					To update	https://github.com/luispedro/mahotas	Imaging	mahotas_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features	0.7-2	mahotas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	37
-mauve_contig_mover	mauve_contig_mover	Order a draft genome relative to a related reference genome								To update	https://github.com/phac-nml/mauve_contig_mover	Sequence Analysis	mauve_contig_mover	nml	https://github.com/phac-nml/mauve_contig_mover	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover	1.0.10	mauve	2.4.0.r4736			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-meneco	meneco	Meneco computes minimal completions to your draft network with reactions from a repair network								Up-to-date	http://bioasp.github.io/meneco/	Systems Biology	meneco	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/meneco	https://github.com/genouest/galaxy-tools/tree/master/tools/meneco	1.5.2	meneco	1.5.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mergeneighboursinlabelimage	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	mergeneighboursinlabelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	25
-metfrag	metfrag	[Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity)								To update	https://github.com/computational-metabolomics/metfrag-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/metfrag-galaxy	https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag	2.4.5+galaxy3	metfrag	2.4.5			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	153
-metfrag-vis	metfrag_vis	[Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag								To update	https://github.com/computational-metabolomics/metfrag-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/metfrag-galaxy	https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis	2.4.5+galaxy0	metfrag	2.4.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	12
-miranda	miranda	Finds potential target sites for miRNAs in genomic sequences								To update	http://www.microrna.org/	RNA	miranda	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	3.3a+galaxy1	miranda	3.3a			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	41	6076
-miranda2asko	miranda2asko	Converts miRanda output into AskOmics format								To update		Convert Formats	miranda2asko	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko	https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko	0.2	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mixmodel4repeated_measures	mixmodel4repeated_measures	[Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model								To update	http://workflow4metabolomics.org	Metabolomics	mixmodel4repeated_measures	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures	3.1.0	r-lme4				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mob_suite	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.9			0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	322	89021
-morphological_operations	morphological_operations	Apply morphological operations to images			scipy					To update	https://github.com/bmcv	Imaging	morphological_operations	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	1.12.0	scipy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mrbayes	mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ms2snoop	ms2snoop	[W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity.								To update	http://workflow4metabolomics.org	Metabolomics	ms2snoop	workflow4metabolomics		https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop	2.2.1	r-base				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-msPurity	mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching	[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data								Up-to-date	https://github.com/computational-metabolomics/mspurity-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/mspurity-galaxy	https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity	1.28.0	bioconductor-mspurity	1.28.0			0	0	10	11	0	0	10	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	40	709
-msp_split	msp_split	[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data								To update	https://github.com/computational-metabolomics/mspurity-galaxy	Metabolomics		tomnl	https://github.com/computational-metabolomics/mspurity-galaxy	https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split	0.0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mykrobe_parser	mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ncbi_fcs_adaptor	ncbi_fcs_adaptor	FCS-adaptor detects adaptor and vector contamination in genome sequences.								To update	https://github.com/ncbi/fcs	Sequence Analysis	ncbi_fcs_adaptor	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	0.5.0					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-nmr_annotation	NmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation								To update	http://workflow4metabolomics.org	Metabolomics	nmr_annotation	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/nmr_annotation	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation	3.0.0	r-batch	1.1_4			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	47
-nmr_annotation2d	2DNmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra								To update	http://workflow4metabolomics.org	Metabolomics	2dnmrannotation	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d	2.0.0	r-batch	1.1_4			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-nmr_preprocessing	NMR_Preprocessing, NMR_Read	[Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction								To update	http://workflow4metabolomics.org	Metabolomics	nmr_preprocessing	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/nmr_preprocessing	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing		r-batch	1.1_4			0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	4	140
-normalization	normalization	[Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data								To update	http://workflow4metabolomics.org	Metabolomics	normalization	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/normalization	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization	1.0.7	r-batch	1.1_4			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	133
-openlabcds2csv	openlabcds2csv	"Creates a summary of several ""Internal Standard Report"" OpenLabCDS results."								To update		Metabolomics	openlabcds2csv	genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv	0.1.0	openjdk				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-orientationpy	orientationpy	Compute image orientation			orientationj					Up-to-date	https://github.com/bmcv	Imaging	orientationpy	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	0.2.0.4	orientationpy	0.2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-overlay_images	ip_overlay_images	Overlay two images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	overlay_images	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images	0.0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	60
-pangolin	pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages								To update	https://github.com/hCoV-2019/pangolin	Sequence Analysis	pangolin	nml	https://github.com/hCoV-2019/pangolin	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin	1.1.14	pangolin	4.3			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	259	7276
-patrist	patrist	Extract Patristic Distance From a Tree								To update	https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02	Phylogenetics	patrist	nml	https://github.com/phac-nml/patrist	https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist	0.1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-peptimapper	peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag	Proteogenomics workflow for the expert annotation of eukaryotic genomes								To update	https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9	Proteomics		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	2.1					0	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-permutate_axis	ip_permutate_axis	Permutates axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	permutate_axis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	42
-physiofit	physiofit	PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes								Up-to-date	physiofit.readthedocs.io	Metabolomics	physiofit	workflow4metabolomics	https://github.com/MetaSys-LISBP/PhysioFit	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit	3.4.0	physiofit	3.4.0			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-physiofit_manager	physiofit_data_manager	Handling of physiofit input files								Up-to-date	physiofit.readthedocs.io	Metabolomics	physiofit_manager	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager	1.0.1	physiofit_data_manager	1.0.1			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-plantseg	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	plantseg	plantseg		PlantSeg	Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.	Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	To update	https://github.com/bmcv	Imaging	plantseg	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg	1.8.1	plant-seg		Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-plasmid_profiler	plasmid_profiler	Explores plasmid content in WGS data								To update			plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler	0.1.6	r				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-plasmid_profiler_suite		Plasmid Profiler suite defining all dependencies for Plasmid Profiler								To update		Sequence Analysis	suite_plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-plotheatmap	plotheatmap	This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output.								To update		Computational chemistry	plotheatmap	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap	1.0	bioconductor-preprocesscore	1.64.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-pneumocat	pneumocat	Pneumococcal Capsular Typing of illumina fastq reads								Up-to-date	https://github.com/phe-bioinformatics/PneumoCaT	Variant Analysis	pneumocat	nml	https://github.com/phe-bioinformatics/PneumoCaT	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat	1.2.1	pneumocat	1.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-points2binaryimage	ip_points_to_binaryimage	Points to Binary Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2binaryimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage	0.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	41
-points2labelimage	ip_points_to_label	Points to label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage	0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	31
-points_association_nn	ip_points_association_nn	Association of points in consecutive frames	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	points_association_nn	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	29
-projective_transformation	ip_projective_transformation	Projective transformation	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation	0.1.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	85
-projective_transformation_points	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation_points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points	0.1.1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	21343
-promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pseudogenome	pseudogenome	Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	pseudogenome	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-quasitools	aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality	A collection of tools for analysing Viral Quasispecies								Up-to-date	https://github.com/phac-nml/quasitools	Sequence Analysis	quasitools	nml	https://github.com/phac-nml/quasitools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools	0.7.0	quasitools	0.7.0			0	12	0	12	0	12	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rdock	rdock	Docking ligands to proteins and nucleic acids								To update	http://rdock.sourceforge.net/	Computational chemistry	rdock	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock	1.0	rDock	2013.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-refseq_masher	refseq_masher_contains, refseq_masher_matches	Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.								Up-to-date	https://github.com/phac-nml/refseq_masher	Sequence Analysis	refseq_masher	nml	https://github.com/phac-nml/refseq_masher	https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher	0.1.2	refseq_masher	0.1.2			2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-repeat_channels	repeat_channels	Convert single-channel to multi-channel image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	repeat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16
-replace_chromosome_names	replace_chromosome_names	Replace chromosome names								To update		Text Manipulation	replace_chromosome_names	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names	0.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	537
-rfove	rfove	Perform segmentation region-based fitting of overlapping ellipses	rfove	rfove		RFOVE	RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.	Image analysis	Cell biology, Biomedical science, Imaging	To update	https://sites.google.com/site/costaspanagiotakis/research/cs	Imaging	rfove	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove	2023.11.12			Image analysis	Cell biology, Biomedical science, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7
-rsat_filter_snps	rsat_filter_snps	Filter SNPs in RSAT Matrix Scan output								To update	https://github.com/TGAC/earlham-galaxytools/	ChIP-seq, Systems Biology	rsat_filter_snps	earlham	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-scale_image	ip_scale_image	Scale image	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	scale_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image	0.18.3	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	512
-segalign	segalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.								Up-to-date	https://github.com/gsneha26/SegAlign	Next Gen Mappers	segalign	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign	https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign	0.1.2.7	segalign-galaxy	0.1.2.7			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-segmetrics	ip_segmetrics	Image segmentation and object detection performance measures	segmetrics	segmetrics	segmetrics	SegMetrics	Image segmentation and object detection performance measures	Image analysis		To update	https://github.com/bmcv	Imaging	segmetrics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics	1.4	segmetrics	1.5	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	3
-seqtk_nml	seqtk_nml_sample	Tool to downsample fastq reads								To update	https://github.com/lh3/seqtk	Sequence Analysis	seqtk_nml	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml	1.0.1	seqtk	1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-sistr_cmd	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	133	2489
-skyline2isocor	skyline2isocor	Converting skyline output to IsoCor input								Up-to-date	https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor	Metabolomics	skyline2isocor	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor	1.0.0	skyline2isocor	1.0.0			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-slice_image	ip_slice_image	Slice image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image	0.3-4	scikit-image		Image analysis	Imaging, Bioinformatics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	102
-smalt	smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-smart_domains	smart_domains	SMART domains								To update	http://smart.embl.de/	Sequence Analysis	smart_domains	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	0.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-smina	smina	smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization								To update	https://sourceforge.net/projects/smina/	Computational chemistry	smina	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina	1.0	smina	2017.11.9			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	493
-spades_header_fixer	spades_header_fixer	Fixes Spades Fasta ids								To update	https://github.com/phac-nml/galaxy_tools	Fasta Manipulation	spades_fasta_header_fixer	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer	1.1.2+galaxy1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-spatyper	spatyper	Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.								Up-to-date	https://github.com/HCGB-IGTP/spaTyper	Sequence Analysis	spatyper	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	0.3.3	spatyper	0.3.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-split_labelmap	ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap	0.2-3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	42
-spolpred	spolpred	A program for predicting the spoligotype from raw sequence reads								To update		Sequence Analysis	spolpred	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred	1.0.1	spolpred				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-spot_detection_2d	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d	0.0.3-2	imageio		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	16
-srst2	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	205
-staramr	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	889	12673
-stringmlst	stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-suite_qiime2__alignment	qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	13
-suite_qiime2__composition	qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.5.0+q2galaxy.2024.5.0					4	4	4	2	4	4	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	2	5
-suite_qiime2__cutadapt	qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	5	67
-suite_qiime2__dada2	qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	31	202
-suite_qiime2__deblur	qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	9	73
-suite_qiime2__demux	qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	26	114
-suite_qiime2__diversity	qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.5.0+q2galaxy.2024.5.0					21	21	21	21	21	21	21	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	0	43	168
-suite_qiime2__diversity_lib	qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	4	4
-suite_qiime2__emperor	qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	2	6
-suite_qiime2__feature_classifier	qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.5.0+q2galaxy.2024.5.0					10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	48	263
-suite_qiime2__feature_table	qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.5.0+q2galaxy.2024.5.0					17	17	17	17	17	17	17	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	59	213
-suite_qiime2__fragment_insertion	qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	20
-suite_qiime2__longitudinal	qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.5.0+q2galaxy.2024.5.0					11	11	11	11	11	11	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	0	6	14
-suite_qiime2__metadata	qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	40	232
-suite_qiime2__phylogeny	qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	12	37
-suite_qiime2__quality_control	qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0
-suite_qiime2__quality_filter	qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.5.0+q2galaxy.2024.5.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	13
-suite_qiime2__rescript	qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.5.0+q2galaxy.2024.5.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-suite_qiime2__sample_classifier	qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.5.0+q2galaxy.2024.5.0					15	15	15	15	15	15	15	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	0	0	1	1
-suite_qiime2__taxa	qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	22	172
-suite_qiime2__vsearch	qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.5.0+q2galaxy.2024.5.0					8	8	8	7	8	8	8	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	8	16
-suite_qiime2_core										To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-suite_qiime2_core__tools	qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.5.0+dist.he540b0b0					2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	124	7087
-superdsm	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	superdsm	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm	0.2.0	superdsm	0.3.0	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	16
-t_coffee	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b			0	0	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	70	8690
-tree_relabeler	tree_relabel	Relabels the tips of a newick formatted tree.								To update		Text Manipulation	tree_relabeler	nml	https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler	https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-tripal	analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync	Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal								To update	https://github.com/galaxy-genome-annotation/python-tripal	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal		python-tripal	3.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-unzip	unzip	Unzip file								To update	https://github.com/bmcv	Convert Formats	unzip	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip	6.0	unzip				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	508	5370
-visceral-evaluatesegmentation	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool			evaluatesegmentation-tool					To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	0.5-2	visceral-evaluatesegmentation	2015.07.03			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	25
-voronoi_tessellation	voronoi_tessellation	Compute Voronoi tesselation	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	voronoi_tesselation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation	0.22.0	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-w4mclassfilter	w4mclassfilter	Filter W4M data by values or metadata								To update	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper	Metabolomics	w4mclassfilter	eschen42	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter	0.98.19	r-base				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	2834
-w4mconcatenate	W4Mconcatenate	[W4M][Utils] concatenate two Metadata tables								To update	http://workflow4metabolomics.org	Metabolomics	w4mconcatenate	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate	1.0.0+galaxy0	r-base				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-w4mcorcov	w4mcorcov	OPLS-DA Contrasts of Univariate Results								To update	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper	Metabolomics	w4mcorcov	eschen42	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov	0.98.18	r-base				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	368
-w4mjoinpn	w4mjoinpn	Join positive- and negative-mode W4M datasets								To update	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper	Metabolomics	w4mjoinpn	eschen42	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn	0.98.2	coreutils	8.25			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	171
-wade	wade	identify regions of interest								To update	https://github.com/phac-nml/wade	Sequence Analysis	wade	nml	https://github.com/phac-nml/wade	https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade	0.2.5+galaxy1	wade	0.2.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-wsi_extract_top_view	ip_wsi_extract_top_view	WSI Extract Top View								To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view	0.2-2	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	38
-xcms	abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram, xcms_plot_eic, xcms_plot_raw		XCMS	XCMS		xcms	Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data.  The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling.	Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation	Biological imaging, Data visualisation, Metabolomics	Up-to-date	https://github.com/sneumann/xcms	Metabolomics	xcms	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms	4.0.0	bioconductor-xcms	4.0.0	Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation	Data visualisation, Metabolomics	9	11	10	10	9	11	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	9	0	356	29809
-10x_bamtofastq	10x_bamtofastq	Converts 10x Genomics BAM to FASTQ								To update	https://github.com/10XGenomics/bamtofastq	Convert Formats	10x_bamtofastq	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	1.4.1	10x_bamtofastq				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	46	228
-AggregateAlignments	graphclust_aggregate_alignments	Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.								Up-to-date		RNA	graphclust_aggregate_alignments	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments	0.6.0	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	116
-AlignCluster	graphclust_align_cluster	Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.								To update		RNA	graphclust_align_cluster	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster	0.1	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	10	3060
-CMFinder	cmFinder	Determines consensus motives for sequences.								To update		RNA	graphclust_cmfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	14	45191
-CollectResults	glob_report	Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.								To update		RNA	graphclust_postprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	14	1961
-CollectResultsNoAlign	graphclust_glob_report_no_align	Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.								To update		RNA	graphclust_postprocessing_no_align	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	108
-GSPAN	gspan	Second step of GraphClust								To update		RNA	graphclust_fasta_to_gspan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	133
-LocARNAGraphClust	locarna_best_subtree	MLocARNA computes a multiple sequence-structure alignment of RNA sequences.								To update		RNA	graphclust_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	45325
-NSPDK	NSPDK_candidateClust, nspdk_sparse	Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.								To update		RNA	graphclust_nspdk	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	9.2.3.1	graphclust-wrappers	0.6.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	28	62388
-Plotting	motifFinderPlot	Plotting results for GraphClust								To update		RNA	graphclust_motif_finder_plot	rnateam	https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting	0.4	seaborn				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	68
-PrepareForMlocarna	preMloc	This tool prepares files for locarna step.								To update		RNA	graphclust_prepocessing_for_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	1932
-Preprocessing	preproc	Preprocessing input for GraphClust								To update		RNA	graphclust_preprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	1758
-Structure_GSPAN	structure_to_gspan	Convert RNA structure to GSPAN graphs								To update		RNA	structure_to_gspan	rnateam	https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	2925
-add_line_to_file	add_line_to_file	Adds a text line to the beginning or end of a file.								To update		Text Manipulation	add_line_to_file	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	0.1.0	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	193	14480
-add_value	addValue	Add a value as a new column.								To update		Text Manipulation	add_value	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value	https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value	1.0.1	perl				1	1	1	1	1	1	1	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1	591	367167
-agat	agat	GTF/GFF analysis toolkit	agat	agat		AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	Up-to-date	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.4.0	agat	1.4.0	Data handling, Genome annotation	Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	42	481
-align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	329
-annotation_profiler	Annotation_Profiler_0	Profile Annotations for a set of genomic intervals								To update		Genomic Interval Operations	annotation_profiler	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/annotation_profiler	https://github.com/galaxyproject/tools-devteam/tree/main/tools/annotation_profiler	1.0.0	bx-python	0.12.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	2
-antarna	antarna	antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .								To update		RNA	antarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna	1.1	antarna	2.0.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	52
-antismash	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash		antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	279	14596
-aresite2	AREsite2_REST	AREsite2 REST Interface								To update	http://rna.tbi.univie.ac.at/AREsite	RNA, Data Source, Sequence Analysis	aresite2	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	65
-atactk_trim_adapters	atactk_trim_adapters	Trim adapters from paired-end HTS reads.								To update	https://github.com/ParkerLab/atactk/	Fastq Manipulation	atactk_trim_adapters	rnateam	https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters	https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters	0.1.6	atactk	0.1.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	26	257
-augustus	augustus	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.								To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	3.1.0	augustus	3.5.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	516	8864
-bamhash	bamhash	Hash BAM and FASTQ files to verify data integrity								Up-to-date	https://github.com/DecodeGenetics/BamHash	Sequence Analysis	bamhash	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	1.1	bamhash	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	169
-barcode_collapse	barcode_collapse	Paired End randomer aware duplicate removal algorithm								To update	https://github.com/YeoLab/gscripts	RNA, Sequence Analysis	barcode_collapse	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	0.1.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-basecoverage	gops_basecoverage_1	Base Coverage of all intervals								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	basecoverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage	1.0.0	bx-python	0.12.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	2	308
-best_regression_subsets	BestSubsetsRegression1	Perform Best-subsets Regression								To update		Sequence Analysis, Variant Analysis	best_regression_subsets	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets	https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets	1.0.0	numpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	3
-bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2
-bigwig_to_bedgraph	bigwig_to_bedgraph	Convert from bigWig to bedGraph format								To update		Convert Formats	bigwig_to_bedgraph	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	0.1.0	ucsc_tools				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	200	5749
-bioimaging	bioimage_inference	Load model from BioImage.IO and make inferences	pytorch	pytorch	pytorch	PyTorch	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.		Machine learning, Computer science	To update	https://github.com/bgruening/galaxytools	Imaging	bioimage_inference	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging	https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging	2.3.1	python			Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-biomodelsML	biomodels_biomd0000001066, biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.								To update	https://www.ebi.ac.uk/biomodels/	Machine Learning	biomodels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML	1.1					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13
-bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	531
-bismark	bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor	A tool to map bisulfite converted sequence reads and determine cytosine methylation states								To update	https://www.bioinformatics.babraham.ac.uk/projects/bismark/	Sequence Analysis, Next Gen Mappers	bismark	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	0.22.1	bismark	0.24.2			0	4	4	4	0	4	4	4	0	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	4	4	0	332	12876
-blat_coverage_report	generate_coverage_report	Polymorphism of the Reads								To update		Next Gen Mappers, Sequence Analysis	blat_coverage_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-blat_mapping	blat2wig	Coverage of the Reads in wiggle format								To update		Next Gen Mappers, Sequence Analysis	blat_mapping	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	685
-blockbuster	blockbuster	Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.								To update	http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html	RNA, Sequence Analysis	blockbuster	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	0.1.2	blockbuster	0.0.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	34	3009
-blockclust	blockclust	BlockClust detects transcripts with similar processing patterns.								Up-to-date	https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust	RNA	blockclust	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	1.1.1	blockclust	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	15	1478
-bowtie_wrappers	bowtie_wrapper	Galaxy wrappers for the Bowtie short read mapping tools.								To update	http://bowtie-bio.sourceforge.net/	Next Gen Mappers	bowtie_wrappers	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers	https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers	1.2.0	bowtie	1.3.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	506	22988
-canonical_correlation_analysis	cca1	Canonical Correlation Analysis								To update		Statistics	canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis	1.0.0	R				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	74
-canu	canu	Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).	canu	canu		CANU	De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.	De-novo assembly	Genomics	Up-to-date	https://github.com/marbl/canu		canu	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/canu	https://github.com/bgruening/galaxytools/tree/master/tools/canu	2.2	canu	2.2	De-novo assembly	Genomics	0	1	1	1	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	533	13021
-categorize_elements_satisfying_criteria	categorize_elements_satisfying_criteria	Categorize Elements satisfying criteria.								To update		Statistics	categorize_elements_satisfying_criteria	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria	https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	40
-ccat	peakcalling_ccat	Control-based ChIP-seq Analysis Tool								To update		ChIP-seq	ccat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat	0.0.2	ccat	3.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	173
-cd_hit_dup	cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.10	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cellprofiler	cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	19	0	23	23	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	23	19	0	178	4614
-cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update	https://github.com/CellProfiler/CellProfiler	Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.7					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	43
-change_case	ChangeCase	Convert column case.								To update		Text Manipulation	change_case	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case	https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case	1.0.1	perl				1	1	1	1	1	1	1	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	1	0	1	1	1	931	10965
-chatgpt	chatgpt_openai_api	Using the OpenAI GPT models to generate text based on user input.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	Machine Learning	chatgpt_openai_api	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	2024	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	418	15690
-chromosome_diagram	chromosome_diagram	Chromosome Diagrams using Biopython								To update		Graphics, Sequence Analysis, Visualization	chromosome_diagram	peterjc		https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-circexplorer	circexplorer	A combined strategy to identify circular RNAs (circRNAs and ciRNAs)								To update	https://github.com/YangLab/CIRCexplorer	Sequence Analysis, RNA	circexplorer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	1.1.9.0	circexplorer	1.1.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	251
-clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-clinod	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cluster	gops_cluster_1	Cluster the intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	cluster	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster	1.0.0	bx-python	0.12.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1	801
-cmsearch_deoverlap	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	102
-cmv	cmcv, cmv, hmmcv, hmmv	cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.								Up-to-date	https://github.com/eggzilla/cmv	RNA	cmv	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	1.0.8	cmv	1.0.8			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	1	108
-cofold	cofold	Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.								To update	http://www.e-rna.org/cofold/	RNA	cofold	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	2.0.4.0	cofold	2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	342
-column_arrange_by_header	bg_column_arrange_by_header	Column arrange by header name								To update		Text Manipulation	column_arrange_by_header	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header	0.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	179	3781
-combine_metaphlan_humann	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	147
-compalignp	compalignp	Compute fractional identity between trusted alignment and test alignment								Up-to-date		RNA, Sequence Analysis	compalignp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp	1.0	compalignp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	220
-compare_humann2_output	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	332
-complement	gops_complement_1	Complement intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	complement	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement	1.0.0	bx-python	0.12.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1	233
-compute_motif_frequencies_for_all_motifs	compute_motif_frequencies_for_all_motifs	Compute Motif Frequencies For All Motifs, motif by motif.								To update		Sequence Analysis, Statistics	compute_motif_frequencies_for_all_motifs	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	94
-compute_motifs_frequency	compute_motifs_frequency	Compute Motif Frequencies in indel flanking regions.								To update		Sequence Analysis, Statistics	compute_motifs_frequency	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	65
-compute_q_values	compute_q_values	Compute q-values based on multiple simultaneous tests p-values								To update		Statistics	compute_q_values	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values	1.0.1	R				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	35
-concat	gops_concat_1	Concatenate two bed files								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	concat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat	1.0.1	bx-python	0.12.0			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	309	564900
-condense_characters	Condense characters1	Condense consecutive characters.								To update		Text Manipulation	condense_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters	1.0.0					1	1	0	0	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-convert_characters	Convert characters1	Convert delimiters to tab.								To update		Text Manipulation	convert_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters	1.0.1	python				1	1	1	1	1	1	1	1	1	1	1	0	1	1	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1	475	23829
-convert_solid_color2nuc	color2nuc	Convert Color Space to Nucleotides								To update		Fasta Manipulation	convert_solid_color2nuc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-coprarna	coprarna	Target prediction for prokaryotic trans-acting small RNAs								To update	https://github.com/PatrickRWright/CopraRNA	RNA, Sequence Analysis	coprarna	rnateam	https://github.com/PatrickRWright/CopraRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna	2.1.1	coprarna	2.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-correlation	cor2	Correlation for numeric columns								To update		Statistics	correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation	1.0.0	rpy				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	47	837
-count_gff_features	count_gff_features	Count GFF Features								To update		Sequence Analysis	count_gff_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features	https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features	0.2	galaxy-ops	1.1.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	49	271
-count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-coverage	gops_coverage_1	Coverage of a set of intervals on second set of intervals								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	coverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage	1.0.0	bx-python	0.12.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	17	1502
-coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cpat	cpat	Coding-potential assessment tool using an alignment-free logistic regression model.								Up-to-date	https://github.com/liguowang/cpat	Transcriptomics	cpat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	3.0.5	cpat	3.0.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	134
-crt	crispr_recognition_tool	CRISPR Recognition Tool								To update		Sequence Analysis	crispr_recognition_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/crt	https://github.com/bgruening/galaxytools/tree/master/tools/crt	1.2.0	crisper_recognition_tool	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	74	3389
-ctd_batch	ctdBatch_1	CTD analysis of chemicals, diseases, or genes								To update		Sequence Analysis	ctd_batch	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	203
-cummerbund	cummeRbund	Wrapper for the Bioconductor cummeRbund library								To update	https://bioconductor.org/packages/release/bioc/html/cummeRbund.html	RNA, Visualization	cummerbund	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund	2.16.0	fonts-conda-ecosystem				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	31	1782
-cummerbund_to_tabular	cummerbund_to_cuffdiff	Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database.								To update		Convert Formats, Next Gen Mappers	cummerbund_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular	1.0.1					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	1204
-cut_columns	Cut1	Select columns from a dataset.								To update		Text Manipulation	cut_columns	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns	1.0.2					1	1	1	1	1	1	1	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	1	0	1	1	1	5064	1957541
-delete_overlapping_indels	delete_overlapping_indels	Delete Overlapping Indels from a chromosome indels file								To update		Sequence Analysis	delete_overlapping_indels	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels	https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	39
-dewseq	dewseq	DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data								To update	https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers	Sequence Analysis, RNA, CLIP-seq	dewseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	0.1.0+galaxy0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11	72
-dgidb_annotator	dgidb_annotate	Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)								To update		Systems Biology, Variant Analysis	dgidb_annotator	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator	0.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	65
-diff	diff	GNU diff tool that calculates the differences between two files.								To update	http://www.gnu.org/software/diffutils/	Text Manipulation	diff	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diff	https://github.com/bgruening/galaxytools/tree/master/tools/diff	3.7	diffutils				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	235
-diffbind		Diffbind provides functions for  processing  ChIP-Seq  data.								To update	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-divide_pg_snp	dividePgSnp	Separate pgSnp alleles into columns								To update		Sequence Analysis	divide_pg_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	32
-dorina	dorina_search	data source for RNA interactions in post-transcriptional regulation								To update		RNA, Data Source	dorina	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1576
-dot2ct	rnastructure_dot2ct	Dot-Bracket to Connect Table (CT)								To update		Sequence Analysis, RNA	dot2ct	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	5.7.a	rnastructure	6.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dotknot	dotknot	DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence								To update	http://dotknot.csse.uwa.edu.au/	RNA, Proteomics	dotknot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot	1.3.1	vienna_rna				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	83
-draw_stacked_barplots	draw_stacked_barplots	Draw Stacked Bar Plots for different categories and different criteria								To update		Graphics, Statistics	draw_stacked_barplots	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots	https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots	1.0.0	R				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	12	173
-dwt_cor_ava_perclass	compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Feature Occurrences								To update		Statistics	dwt_cor_ava_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dwt_cor_avb_all	compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features								To update		Statistics	dwt_cor_avb_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dwt_ivc_all	compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Second Moments for Feature Occurrences								To update		Statistics	dwt_ivc_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dwt_var_perclass	compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom	Compute P-values and Max Variances for Feature Occurrences								To update		Statistics	dwt_var_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dwt_var_perfeature	dwt_var1	Wavelet variance using Discrete Wavelet Transfoms								To update		Statistics	dwt_var_perfeature	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature	1.0.2	r-bitops				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	36
-ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-edta	edta	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. 	edta	edta		The Extensive de novo TE Annotator (EDTA)	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	To update	https://github.com/oushujun/EDTA	Variant Analysis	edta	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta	https://github.com/bgruening/galaxytools/tree/master/tools/edta		edta	2.2.0	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	58	484
-effectiveT3	effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-epicseg	epicseg_segment	EpiCSeg is a tool for conducting chromatin segmentation.								To update	https://github.com/lamortenera/epicseg	Epigenetics	epicseg	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	@VERSION_STRING@	epicseg	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	245
-exparna	exparna	ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.								Up-to-date	http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp	RNA	exparna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	1.0.1	exparna	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-express	express	Quantify the abundances of a set of target sequences from sampled subsequences								To update		RNA	express	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/express	https://github.com/galaxyproject/tools-devteam/tree/main/tools/express	1.1.1	eXpress	1.5.1			0	1	1	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	12	325
-fasta_compute_length	fasta_compute_length	Compute sequence length								To update		Fasta Manipulation	fasta_compute_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length	1.0.3	python				1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	380	7758
-fasta_concatenate_by_species	fasta_concatenate0	Concatenate FASTA alignment by species								To update		Fasta Manipulation	fasta_concatenate_by_species	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.12.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	88	35793
-fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fasta_filter_by_length	fasta_filter_by_length	Filter sequences by length								To update		Fasta Manipulation	fasta_filter_by_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length	1.2	python				1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	350	48649
-fasta_to_tabular	fasta2tab	FASTA-to-Tabular converter								To update		Fasta Manipulation	fasta_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular	1.1.1	python				1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	622	105935
-fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fastq_info	fastq_info	FASTQ info allows to validate single or paired fastq files								To update	https://github.com/nunofonseca/fastq_utils	Fastq Manipulation	fastq_info	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	0.25.1	fastq_utils	0.25.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	679	5765
-fastq_pair_names	fastq_pair_names	Extract FASTQ paired read names								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	Sequence Analysis	fastq_pair_names	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	0.0.5	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fastq_paired_unpaired	fastq_paired_unpaired	Divide FASTQ file into paired and unpaired reads								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	Sequence Analysis, Text Manipulation	fastq_paired_unpaired	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	0.1.5	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fastq_trimmer_by_quality	fastq_quality_trimmer	FASTQ Quality Trimmer by sliding window								Up-to-date		Fastq Manipulation	fastq_trimmer_by_quality	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	459	5676
-fastqsolexa_to_fasta_qual	fastqsolexa_to_fasta_qual	FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data								To update		Convert Formats, Fastq Manipulation	fastqsolexa_to_fasta_qual	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-featurecounter	featureCoverage1	Feature coverage								To update		Sequence Analysis, Variant Analysis	featurecounter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter	2.0.0	bx-python	0.12.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	22385
-file_manipulation	bg_uniq	This tool returns all unique lines from a tab-separated file.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	Text Manipulation	unique	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	0.4	python				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	176	8496
-filter_transcripts_via_tracking	filter_combined_via_tracking	Filter Combined Transcripts								To update		RNA	filter_transcripts_via_tracking	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking	https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking	0.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	20
-find_diag_hits	find_diag_hits	Find diagnostic hits								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	find_diag_hits	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits	1.0.0	taxonomy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	69
-find_subsequences	bg_find_subsequences									To update			find_subsequences	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences	0.3	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	31	763
-flanking_features	flanking_features_1	Fetch closest non-overlapping feature for every interval								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	flanking_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features	4.0.1	bx-python	0.12.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	20	671
-flexynesis	flexynesis	This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.								Up-to-date	https://github.com/BIMSBbioinfo/flexynesis/tree/main	Machine Learning, Statistics, Systems Biology	flexynesis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis	https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis	0.2.10	flexynesis	0.2.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	To update	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.4	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1499	20904
-footprint	footprint	Find transcription factor footprints								To update	https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/	Epigenetics	footprint	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	1.0.0	footprint	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	57
-format_cd_hit_output	format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file								To update		Fasta Manipulation	format_cd_hit_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output	1.0.0+galaxy1					0	0	1	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	166
-format_metaphlan2_output	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	166	5588
-generate_pc_lda_matrix	generate_matrix_for_pca_and_lda1	Generate a Matrix for using PC and LDA								To update		Sequence Analysis	generate_pc_lda_matrix	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix	https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix	1.0.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	12	119
-get_flanks	get_flanks1	Get flanks returns flanking region/s for every gene								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	get_flanks	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks	1.0.0	bx-python	0.12.0			1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	555	324598
-get_orfs_or_cdss	get_orfs_or_cdss	Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	Sequence Analysis	get_orfs_or_cdss	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	0.2.3	biopython	1.70			0	1	1	1	0	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	15	186
-getindelrates_3way	indelRates_3way	Estimate Indel Rates for 3-way alignments								To update		Sequence Analysis, Variant Analysis	getindelrates_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way	1.0.0	bx-python	0.12.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-getindels_2way	getIndels_2way	Fetch Indels from pairwise alignments								To update		Sequence Analysis, Variant Analysis	getindels_2way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way	1.0.0	numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gfastats	gfastats	Tool for generating sequence statistics and simultaneous genome assembly file manipulation.	gfastats	gfastats		gfastats	gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.	Data handling	Computational biology	Up-to-date	https://github.com/vgl-hub/gfastats	Sequence Analysis	gfastats	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	1.3.6	gfastats	1.3.6	Data handling	Computational biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	418	8159
-gi2taxonomy	Fetch Taxonomic Ranks	Fetch taxonomic representation	gi2taxonomy	gi2taxonomy		gi2taxonomy	The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	27	660
-glimmer_hmm		GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gmaj	gmaj_1	GMAJ Multiple Alignment Viewer								To update		Visualization	gmaj	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj	https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj	2.0.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	11
-gotohscan	rbc_gotohscan	Find subsequences in db								To update		Sequence Analysis	gotohscan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	1.3.0	gotohscan	1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	71
-graph_converter	graph_converter	Convert between different graph formats								To update		Convert Formats	graph_converter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-graphclust	graphclust	GraphClust can be used for structural clustering of RNA sequences.								To update	http://www.bioinf.uni-freiburg.de/Software/GraphClust/	RNA	graphclust	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	0.1	GraphClust				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6
-graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.44	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	43	2605
-graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.3	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	136	6651
-graphprot	graphprot_predict_profile	GraphProt models binding preferences of RNA-binding proteins.								To update	https://github.com/dmaticzka/GraphProt	Sequence Analysis, RNA, CLIP-seq	graphprot	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	1.1.7+galaxy2	graphprot	1.1.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	474
-hclust2	hclust2	Plots heatmaps								To update	https://bitbucket.org/nsegata/hclust2/	Data Visualization	hclust2	rnateam	https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2	https://github.com/bgruening/galaxytools/tree/master/tools/hclust2	0.99	hclust2	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-hgv_fundo	hgv_funDo	FunDO human genes associated with disease terms								To update		Sequence Analysis	hgv_fundo	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0
-hgv_hilbertvis	hgv_hilbertvis	HVIS visualization of genomic data with the Hilbert curve								To update	https://www.ebi.ac.uk/huber-srv/hilbert/	Graphics, Visualization	hgv_hilbertvis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis	1.0.0	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0
-hictk	hictk	Convert cooler to juicebox_hic								Up-to-date	https://github.com/paulsengroup/hictk	Convert Formats, Epigenetics	hictk	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	1.0.0	hictk	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-hicup	hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater	The HiCUP-Pipeline from the Bioinformatics Babraham Institute.								To update	https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html	Epigenetics	hicup	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	0.9.2					7	0	7	0	7	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	6	0	76	921
-hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228
-histogram	histogram_rpy	Histogram of a numeric column								To update		Graphics, Statistics	histogram	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram	https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram	1.0.4	rpy2	2.7.8			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	242	4350
-homer		Software for motif discovery and next generation sequencing analysis.								To update	http://homer.salk.edu/homer/	Sequence Analysis	homer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/homer	https://github.com/bgruening/galaxytools/tree/master/tools/homer						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-htseq-clip	htseq_clip	htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets								To update	https://github.com/EMBL-Hentze-group/htseq-clip	Sequence Analysis, RNA, CLIP-seq	htseq_clip	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	0.1.0+galaxy0	htseq-clip	2.19.0b0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	77
-illumina_methylation_analyser	illumina_methylation_analyser	Methylation analyzer for Illumina 450k DNA emthylation microarrays								To update	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	Sequence Analysis	illumina_methylation_analyser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	0.1	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-imagej2	imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	20170530			Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	0	26	1537
-improviser	proteomics_improviser	Visualisation of PepXML files								To update	http://www.improviser.uni-freiburg.de/	Proteomics	proteomics_improviser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	1.1.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-indels_3way	indels_3way	Fetch Indels from 3-way alignments								To update		Sequence Analysis	indels_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way	1.0.3					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	22
-infernal	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	infernal		Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	67	100294
-inforna		INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.								To update	http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp	RNA	inforna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	139
-intarna	intarna	Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.								Up-to-date	https://github.com/BackofenLab/IntaRNA	RNA	intarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	3.4.0	intarna	3.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	7569
-intersect	gops_intersect_1	Intersect the intervals of two datasets								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect	1.0.0	bx-python	0.12.0			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1003	348449
-iprscan5		Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-itsx	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	38	868
-jbrowse2	jbrowse2	JBrowse2 Genome Browser integrated as a Galaxy Tool	jbrowse_2	jbrowse_2		JBrowse 2	Modular genome browser with views of synteny and structural variation.	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	To update	https://jbrowse.org	Sequence Analysis	jbrowse2	fubar	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2	https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2	2.13.1	jbrowse2	2.14.0	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-join	gops_join_1	Join the intervals of two datasets side-by-side								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	join	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join	1.0.0	bx-python	0.12.0			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	284	329556
-join_files_on_column_fuzzy	join_files_on_column_fuzzy	Join two files on a common column, allowing a certain difference.								To update		Text Manipulation	join_files_on_column_fuzzy	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy	1.0.1	python				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	117	2448
-jupyter_job	run_jupyter_job	Run jupyter notebook script in Galaxy								To update		Machine Learning	run_jupyter_job	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	0.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	30
-kernel_canonical_correlation_analysis	kcca1	Kernel Canonical Correlation Analysis								To update		Statistics	kernel_canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis	1.0.0	rpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	69
-kernel_principal_component_analysis	kpca1	Kernel Principal Component Analysis								To update		Statistics	kernel_principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis	1.0.0	rpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	156
-kinwalker		Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.								To update	http://www.bioinf.uni-leipzig.de/Software/Kinwalker/	RNA	kinwalker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-kraken2tax	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	481	14683
-labels	bg_labels	remaps and annotates alignments								To update	https://github.com/bgruening/galaxytools/tree/master/tools/labels	Sequence Analysis	labels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/labels	https://github.com/bgruening/galaxytools/tree/master/tools/labels	1.0.5.0	labels				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-lastz_paired_reads	lastz_paired_reads_wrapper	Galaxy wrapper for the Lastz alignment tool on paired reads								To update		Next Gen Mappers	lastz_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads	1.1.1	lastz	1.04.22			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	9
-lca_wrapper	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	137
-lda_analysis	lda_analy1	Perform Linear Discriminant Analysis								To update		Graphics, Statistics	lda_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis	1.0.1	R				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	148
-lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	152
-linear_regression	LinearRegression1	Perform Linear Regression								To update		Statistics	linear_regression	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression	https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression	1.0.1	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-locarna	locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile	LocARNA - A suite for multiple alignment and folding of RNAs								Up-to-date	http://www.bioinf.uni-freiburg.de/Software/LocARNA/	RNA	locarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	2.0.1	locarna	2.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	339
-logistic_regression_vif	LogisticRegression	Perform Logistic Regression with vif								To update		Sequence Analysis, Variant Analysis, Statistics	logistic_regression_vif	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif	https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif	1.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-maf_cpg_filter	cpgFilter	Mask CpG/non-CpG sites from MAF file								To update		Sequence Analysis, Variant Analysis	maf_cpg_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter	1.0.0	bx-python	0.12.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mafft	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.526	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	2	2	2	2	2	0	1	0	0	2	0	0	0	0	0	0	0	1	0	2	0	0	2	0	0	0	2	0	0	0	0	0	0	0	2	2	0	817	143045
-mapping_to_ucsc	mapToUCSC	Format mapping data as UCSC custom track								To update		Visualization, Convert Formats, Next Gen Mappers	mapping_to_ucsc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mavedb	mavedb_importer	data source for MaveDB								To update		Data Source	mavedb_importer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb	0.9					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mea	mea	Maximum expected accuracy prediction								To update	http://www.bioinf.uni-leipzig.de/Software/mea	RNA	mea	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	0.6.4.1	mea	0.6.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	85
-megablast_xml_parser	megablast_xml_parser	Parse blast XML output								To update		Next Gen Mappers, Convert Formats	megablast_xml_parser	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser	https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	338
-merge	gops_merge_1	Merge the overlapping intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge	1.0.0	bx-python	0.12.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	193	563676
-merge_cols	mergeCols1	Merge columns together.								To update		Text Manipulation	merge_cols	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols	https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols	1.0.3	python				1	1	1	1	1	1	1	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1	542	28593
-methtools	methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling	tools for methylation analysis								To update	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	Sequence Analysis	methtools	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	0.1.1	methtools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5461
-methyldackel	pileometh	A tool for processing bisulfite sequencing alignments								To update	https://github.com/dpryan79/MethylDackel	Sequence Analysis	pileometh	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	0.5.2	methyldackel	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	200	16573
-methylkit	methylkit	A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.								To update	http://bioconductor.org/packages/release/bioc/html/methylKit.html	Epigenetics	methylkit	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	0.99.2	bioconductor-methylkit	1.28.0			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-metilene	metilene	Differential DNA methylation calling								To update		RNA, Statistics	metilene	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	0.2.6.1	metilene	0.2.8			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	103	3966
-mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-miclip	mi_clip	Identification of binding sites in CLIP-Seq data.								To update	https://cran.r-project.org/src/contrib/Archive/MiClip/	Sequence Analysis	miclip	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	1.2.0	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-microsatellite_birthdeath	microsatellite_birthdeath	Identify microsatellite births and deaths								To update		Sequence Analysis	microsatellite_birthdeath	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-microsats_alignment_level	microsats_align1	Extract Orthologous Microsatellites from pair-wise alignments								To update		Sequence Analysis, Variant Analysis	microsats_alignment_level	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level	1.0.0	sputnik				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-microsats_mutability	microsats_mutability1	Estimate microsatellite mutability by specified attributes								To update		Sequence Analysis, Variant Analysis	microsats_mutability	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability	1.1.0	bx-python	0.12.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-minced	minced	MinCED - Mining CRISPRs in Environmental Datasets								To update	http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README	Sequence Analysis	minced	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minced	https://github.com/bgruening/galaxytools/tree/master/tools/minced	0.2.0	minced	0.4.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	53	895
-mine	maximal_information_based_nonparametric_exploration	Maximal Information-based Nonparametric Exploration								To update		Variant Analysis	mine	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine	0.0.1	MINE				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	11
-minipolish	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	185
-mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	56	613
-molecule2gspan	bg_mol2gspan	converter								To update	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	Convert Formats	molecule_to_gspan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	0.2	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mqc	mqc	Ribosome profiling mapping quality control tool								To update	https://github.com/Biobix/mQC	Sequence Analysis	mqc	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc	1.9	mqc	1.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	76
-multispecies_orthologous_microsats	multispecies_orthologous_microsats	Extract orthologous microsatellites								To update		Sequence Analysis, Variant Analysis	multispecies_orthologous_microsats	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats	https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats	1.0.0	bx-sputnik				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mummer	mummerplot_wrapper	Draw dotplots using mummer, mucmer, or promer with mummerplot								To update	http://mummer.sourceforge.net/	Graphics, Sequence Analysis, Visualization	mummer	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	0.0.8	ghostscript	9.18			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	83	652
-music_deconvolution	music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution	Multi-subject Single Cell deconvolution (MuSiC)								Up-to-date	https://github.com/xuranw/MuSiC	Transcriptomics	music	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/	https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution	0.1.1	music-deconvolution	0.1.1			5	5	4	0	5	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	240	1872
-mutate_snp_codon	mutate_snp_codon_1	Mutate Codons with SNPs								To update		Variant Analysis	mutate_snp_codon	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	47
-nanopolish	nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants	Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data.								Up-to-date	https://github.com/jts/nanopolish		nanopolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	0.14.0	nanopolish	0.14.0			0	4	4	4	0	4	4	4	0	0	0	0	3	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	78	8366
-nastiseq	nastiseq	A method to identify cis-NATs using ssRNA-seq								Up-to-date	https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/	RNA	nastiseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	1.0	r-nastiseq	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	40
-netboxr	netboxr	netboxr enables automated discovery of biological process modules by network analysis								To update		Systems Biology	netboxr	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/netboxr	1.6.0	bioconductor-netboxr	1.9.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	11
-nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268
-nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-nucleosome_prediction	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	861
-numeric_clustering	numeric_clustering	Clustering tool for numberic values								To update	http://scikit-learn.org/stable/index.html	Statistics	numeric_clustering	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	0.9	anaconda				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	486
-openms	AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter	OpenMS in version 2.1.								To update		Proteomics	openms	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/openms	https://github.com/bgruening/galaxytools/tree/master/tools/openms	2.1.0	openms	3.1.0			7	34	135	0	7	34	135	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	135	134	0	916	105743
-pandas_rolling_window	pandas_rolling_window	Rolling window calculations								To update	https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html	Statistics	pandas_rolling_window	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	0.1	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	269
-paralyzer	paralyzer	A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.								Up-to-date	https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/	RNA	paralyzer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	1.5	paralyzer	1.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	299
-partialr_square	partialRsq	Compute partial R square								To update		Statistics	partialr_square	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square	https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-peakachu	peakachu	PEAKachu is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	peakachu	rnateam	https://github.com/tbischler/PEAKachu	https://github.com/bgruening/galaxytools/tree/master/tools/peakachu	0.2.0+galaxy1	peakachu	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	78	3109
-pearson_correlation	Pearson_and_apos_Correlation1	Pearson and apos Correlation between any two numeric columns								To update		Statistics	pearson_correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-perf	stats_perf_tool	suitable for boolean classification problems								To update	http://osmot.cs.cornell.edu/kddcup/software.html		stats_perf_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/perf	https://github.com/bgruening/galaxytools/tree/master/tools/perf	5.11.0	perf				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pfamscan	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	19	165
-pg_tools	pg_dump, pg_import, pg_query	tool suite for dealing with Postgresql databases from Galaxy's history								To update	https://www.postgresql.org	Data Export, Data Source	pgtools	bgruening	https://github.com/bgruening/galaxytools/tools/pgtools	https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools		postgresql				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pgsnp2gd_snp	pgSnp2gd_snp	Convert from pgSnp to gd_snp								To update		Variant Analysis	pgsnp2gd_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pharmcat	pharmcat	Pharmacogenomics Clinical Annotation Tool								To update	https://pharmcat.org/	Variant Analysis	pharmcat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat						1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	82
-pileup_interval	pileup_interval	Pileup-to-Interval condenses pileup format into ranges of bases								To update		SAM	pileup_interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval	1.0.3	bx-python	0.12.0			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	15	632
-pileup_parser	pileup_parser	Filter pileup on coverage and SNPs								To update	https://github.com/galaxyproject/tools-devteam/	SAM	pileup_parser	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser	1.0.2	perl				1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	169	3158
-pipmir	pipmir	A method to identify novel plant miRNA.								To update	https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/	RNA	pipmir	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	0.1.0	pipmir	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	21	275
-piranha	piranha	Piranha is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	piranha	rnateam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha	https://github.com/bgruening/galaxytools/tree/master/tools/piranha	1.2.1.0	piranha	1.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	1809
-platypus	bg_platypus	efficient and accurate variant-detection in high-throughput sequencing data								To update	http://www.well.ox.ac.uk/platypus	Sequence Analysis	platypus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	0.0.11	platypus				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-plot_from_lda	plot_for_lda_output1	"Draw ROC plot on ""Perform LDA"" output"								To update		Graphics, Statistics	plot_from_lda	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda	https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda	1.0.1	R				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	73
-plotly_ml_performance_plots	plotly_ml_performance_plots	performance plots for machine learning problems								To update	http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics	Visualization	plotly_ml_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	0.4	galaxy-ml	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	71	1323
-plotly_parallel_coordinates_plot	plotly_parallel_coordinates_plot	parallel coordinates plot produced with plotly								To update	https://plot.ly/python/parallel-coordinates-plot/	Visualization	plotly_parallel_coordinates_plot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	37	652
-plotly_regression_performance_plots	plotly_regression_performance_plots	performance plots for regression problems								To update	http://scikit-learn.org/stable/supervised_learning.html#supervised-learning	Visualization	plotly_regression_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	0.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	79	843
-poisson2test	poisson2test	Poisson two-sample test								To update	https://bitbucket.org/natefoo/taxonomy	Statistics, Metagenomics	poisson2test	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test	1.0.0	taxonomy	0.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	116
-predictnls	predictnls	Python reimplementation of predictNLS for Galaxy								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	Sequence Analysis	predictnls	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	0.0.10					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-principal_component_analysis	pca1	Principal Component Analysis								To update		Statistics	principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis	1.0.2	rpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	88	9989
-protease_prediction	eden_protease_prediction	This tool can learn the cleavage specificity of a given class of proteases.								To update	https://github.com/fabriziocosta/eden	Sequence Analysis, Proteomics	protease_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	0.9	eden	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	154
-protein_analysis	promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort	TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	Sequence Analysis	tmhmm_and_signalp	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	0.0.13	promoter				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	451	6428
-protein_properties	bg_protein_properties	Calculation of various properties from given protein sequences								To update		Sequence Analysis	protein_properties	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	604
-quality_filter	qualityFilter	Filter nucleotides based on quality scores								To update		Sequence Analysis, Variant Analysis	quality_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter	1.0.1	bx-python	0.12.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rRNA	meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-racon	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	309	21353
-rbpbench	rbpbench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs	rbpbench	rbpbench		RBPBench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	To update	https://github.com/michauhl/RBPBench	Sequence Analysis, RNA, CLIP-seq	rbpbench	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	0.8.1	rbpbench	0.9		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	36
-rcas	rcas	RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments								To update	https://github.com/BIMSBbioinfo/RCAS	RNA	rcas	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas	1.5.4	bioconductor-rcas	1.28.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	38	1226
-rcve	rcve1	Compute RCVE								To update		Sequence Analysis, Variant Analysis	rcve	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-reago	reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-remove_beginning	Remove beginning1	Remove lines from the beginning of a file.								To update		Text Manipulation	remove_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning	1.0.0					1	1	1	1	1	1	1	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1	1409	137310
-remurna	remurna	remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation								To update	https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna	RNA	remurna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	1.0.0	remurna	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	42
-repeat_masker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.								To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	0.1.2	RepeatMasker	4.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	248	3750
-replaceColumn	replace_column_with_key_value_file	A tool to replace all column entries of a file given by values of a key-value file.								To update		Text Manipulation	replace_column_by_key_value_file	bgruening	https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn	https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn	0.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	189	576111
-rest_tool	pubchem_rest_tool	This tool fetches data from pubchem via the PubChem REST API.								To update	https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html	Data Source	pubchem_rest_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ribotaper	ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling	A method for defining traslated ORFs using Ribosome Profiling data.	ribotaper	ribotaper		RiboTaper	New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.	Gene expression profiling	Functional genomics	To update	https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/	RNA	ribotaper	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper	1.3.1a	ribotaper	1.3.1	Gene expression profiling	Functional genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	44	628
-rmap	rmap_wrapper	RMAP for Solexa Short Reads Alignment								To update		Next Gen Mappers	rmap	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rmapq	rmapq_wrapper	RMAPQ for Solexa Short Reads Alignment with Quality Scores								To update		Next Gen Mappers	rmapq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rna_shapes	RNAshapes	Compute secondary structures of RNA								To update		RNA	rnashapes	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	3.3.0	@EXECUTABLE@				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	129
-rnabob	rbc_rnabob	Fast pattern searching for RNA structural motifs								To update	http://eddylab.org/software.html	RNA	rnabob	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	2.2.1.0	rnabob	2.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	164
-rnacode	rbc_rnacode	Analyze the protein coding potential in MSA								To update		RNA	rnacode	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	0.3.2	rnacode	0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	1358
-rnacommender	rbc_rnacommender	RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.								To update	https://github.com/gianlucacorrado/RNAcommender	RNA	rnacommender	rnateam	https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender	0.1.1	sam	3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	1074
-rnaformer	infer_rnaformer	RNAformer: RNA secondary structure prediction								To update	https://github.com/automl/RNAformer	RNA	rnaformer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	1.0.0	rnaformer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rnalien	RNAlien	RNAlien unsupervized RNA family model construction								To update	http://rna.tbi.univie.ac.at/rnalien/	RNA, Sequence Analysis	rnalien	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	1.3.6	rnalien	1.8.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	33
-rnasnp	rnasnp	RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs								To update	http://rth.dk/resources/rnasnp/	RNA	rnasnp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp	1.2.0	rnasnp	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	86
-rnaz	rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window	RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.								Up-to-date	https://www.tbi.univie.ac.at/~wash/RNAz/	RNA	rnaz	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz	2.1.1	rnaz	2.1.1			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	28	43279
-sailfish	sailfish	Sailfish is a tool for transcript quantification from RNA-seq data								To update	http://www.cs.cmu.edu/~ckingsf/software/sailfish/	Sequence Analysis, RNA	sailfish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	0.10.1.1	bzip2				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	55	4024
-salmon	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	2	3	1	2	2	3	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	2	0	0	0	0	0	0	0	3	3	0	969	61937
-sam2interval	sam2interval	Convert SAM to interval.								To update		SAM	sam2interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval	1.0.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	1189
-sam_bitwise_flag_filter	sam_bw_filter	Filter SAM on bitwise flag values								To update		SAM	sam_bitwise_flag_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter	1.0.1	python				1	1	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	278
-sambamba	sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort	Sambamba: process your BAM data faster!								Up-to-date	https://github.com/biod/sambamba	SAM	sambamba	bgruening	https://github.com/biod/sambamba	https://github.com/bgruening/galaxytools/tree/master/tools/sambamba	1.0.1	sambamba	1.0.1			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	3765
-samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.20			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	296	4948
-samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.20			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1450	48426
-scatterplot	scatterplot_rpy	Scatterplot of two numeric columns								To update		Graphics, Statistics	scatterplot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot	1.0.3	numpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	61	1677
-sed	sed_stream_editor	Manipulate your data with the sed command line tool.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/sed	Text Manipulation	sed_wrapper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sed	https://github.com/bgruening/galaxytools/tree/master/tools/sed	0.0.1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2276
-segemehl	segemehl	segemehl - short read mapping with gaps								To update	http://www.bioinf.uni-leipzig.de/Software/segemehl/	Next Gen Mappers	segemehl	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	0.2.0.4	segemehl	0.3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	1276
-selectsequencesfrommsa	selectsequencesfrommsa	SelectSequences - selects representative entries from a multiple sequence alignment in clustal format								Up-to-date	https://github.com/eggzilla/SelectSequences	RNA, Sequence Analysis	selectsequencesfrommsa	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	1.0.5	selectsequencesfrommsa	1.0.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	27	457
-seq_composition	seq_composition	Sequence composition								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	Sequence Analysis	seq_composition	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	0.0.5	biopython	1.70			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	71	874
-seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	306	25302
-seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	82	3784
-seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
-seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-short_reads_figure_high_quality_length	hist_high_quality_score	Histogram of high quality score reads								To update		Sequence Analysis, Graphics	short_reads_figure_high_quality_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length	1.0.0	rpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-short_reads_figure_score	quality_score_distribution	Build base quality distribution								To update		Sequence Analysis, Graphics	short_reads_figure_score	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score	1.0.2	fontconfig				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	163
-short_reads_trim_seq	trim_reads	Select high quality segments								To update		Fastq Manipulation	short_reads_trim_seq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	21	220
-show_beginning	Show beginning1	Select lines from the beginning of a file.								To update		Text Manipulation	show_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning	1.0.0					1	1	1	1	1	1	1	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1	704	32112
-show_tail	Show tail1	Select lines from the end of a file.								To update		Text Manipulation	show_tail	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail	1.0.0					1	1	1	1	1	1	1	1	1	0	1	0	1	0	1	1	1	1	0	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1	128	2513
-sicer	peakcalling_sicer	Statistical approach for the Identification of ChIP-Enriched Regions								Up-to-date	https://home.gwu.edu/~wpeng/Software.htm	ChIP-seq	sicer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer	1.1	SICER	1.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	5	374
-sklearn	sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split	Machine Learning tool suite from Scikit-learn								To update	http://scikit-learn.org	Machine Learning, Statistics	sklearn	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	1.0.11.0					30	14	31	16	30	14	31	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	27	0	958	113932
-snpfreq	hgv_snpFreq	snpFreq significant SNPs in case-control data								To update		Variant Analysis, Statistics	snpfreq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq	1.0.1	R				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	37
-sortmerna	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	376	18183
-split_file_on_column	tp_split_on_column	Split a file on a specific column.								To update		Text Manipulation	split_file_on_column	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	0.6	gawk				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	159	5507
-split_file_to_collection	split_file_to_collection	Split tabular, MGF, FASTA, or FASTQ files to a dataset collection.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	Text Manipulation	split_file_to_collection	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	0.5.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	412	15358
-split_paired_reads	split_paired_reads	Split paired end reads								To update		Fastq Manipulation	split_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-splitfasta	rbc_splitfasta	Split a multi-sequence fasta file into files containing single sequences								To update		Text Manipulation	splitfasta	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	0.4.0	biopython	1.70			1	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	96	1295
-sshmm	sshmm	ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data								Up-to-date	https://github.molgen.mpg.de/heller/ssHMM	Sequence Analysis, RNA	sshmm	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm	1.0.7	sshmm	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	223
-statistics	bg_statistical_hypothesis_testing	Tool for computing statistical tests.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	Statistics	bg_statistical_hypothesis_testing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	0.3	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	304
-stress_ng	stress_ng	stress test a computer system in various selectable ways								To update		Web Services	stress_ng	bgruening-util	https://github.com/ColinIanKing/stress-ng	https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng	0.12.04	stress-ng				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	47
-substitution_rates	subRate1	Estimate substitution rates for non-coding regions								To update		Sequence Analysis, Variant Analysis	substitution_rates	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-substitutions	substitutions1	Fetch substitutions from pairwise alignments								To update		Sequence Analysis, Variant Analysis	substitutions	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions	1.0.1	bx-python	0.12.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-subtract	gops_subtract_1	Subtract the intervals of two datasets								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract	1.0.0	bx-python	0.12.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	182	564229
-subtract_query	subtract_query1	Subtract Whole Dataset from another dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract_query	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query	0.1	bx-python	0.12.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	55	1019
-t2ps	Draw_phylogram	Draw phylogeny	t2ps	t2ps		Draw phylogeny	"""Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper"	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	31	457
-t2t_report	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	26	947
-t_test_two_samples	t_test_two_samples	T Test for Two Samples								To update		Statistics	t_test_two_samples	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples	https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples	1.0.1	R				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	210
-table_annovar	table_annovar	Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered								To update		Variant Analysis	table_annovar	devteam	Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar	https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar	0.2	annovar				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-tables_arithmetic_operations	tables_arithmetic_operations	Arithmetic Operations on tables								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	tables_arithmetic_operations	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations	1.0.0	perl				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	14	2207
-tabular_to_fasta	tab2fasta	Tabular-to-FASTA								To update		Convert Formats	tabular_to_fasta	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta	1.1.1	python				1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	601	319334
-tapscan	tapscan_classify	Search for transcription associated proteins (TAPs)								To update	https://plantcode.cup.uni-freiburg.de/tapscan/	Proteomics	tapscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	4.76+galaxy0	hmmer	3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-targetfinder	targetfinder	Plant small RNA target prediction tool								Up-to-date	https://github.com/carringtonlab/TargetFinder.git	RNA	targetfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder	1.7	targetfinder	1.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	37	713
-text_processing	tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq	High performance text processing tools using the GNU coreutils, sed, awk and friends.								To update	https://www.gnu.org/software/	Text Manipulation	text_processing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	9.3	coreutils	8.25			20	20	20	20	20	20	20	20	0	0	0	0	0	0	0	0	0	0	0	0	19	1	19	0	0	19	0	0	0	20	0	0	0	0	0	0	0	19	19	0	15048	3864895
-tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	460
-tiara	tiara	Tool for identification of eukaryotic sequences in the metagenomic datasets.	Tiara	Tiara		TIARA	Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).	Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism, DNA structural variation	To update	https://github.com/ibe-uw/tiara	Metagenomics, Sequence Analysis	tiara	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	1.0.3	tiara		Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-tool_recommendation_model	create_tool_recommendation_model	Create model to recommend tools								To update	https://github.com/bgruening/galaxytools	Machine Learning	create_tool_recommendation_model	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model	https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model	0.0.5	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	445
-tophat	tophat	Tophat for Illumina								To update		RNA, Next Gen Mappers	tophat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat	1.5.0	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1
-tophat2	tophat2	Tophat - fast splice junction mapper for RNA-Seq reads								To update	http://ccb.jhu.edu/software/tophat/index.shtml	RNA, Next Gen Mappers	tophat2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2	2.1.1	bowtie2	2.5.4			1	1	1	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	1	0	312	24167
-tophat_fusion_post	tophat_fusion_post	Wrapper for Tophat-Fusion post step								To update		Transcriptomics	tophat_fusion_post	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post	0.1	blast+				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	216
-trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2334	238699
-trimmer	trimmer	Trim leading or trailing characters.								To update		Text Manipulation	trimmer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer	0.0.1					1	1	1	1	1	1	1	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1	188	6058
-trna_prediction	aragorn_trna, trnascan	Aragorn predicts tRNA and tmRNA in nucleotide sequences.								To update	http://mbioserv2.mbioekol.lu.se/ARAGORN/	RNA	trna_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	0.6	aragorn	1.2.41			0	2	2	0	0	2	2	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	2	2	0	236	2935
-ucsc_custom_track	build_ucsc_custom_track_1	Build custom track for UCSC genome browser								To update		Sequence Analysis	ucsc_custom_track	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	1.0.1	python				1	0	1	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	45	394
-uniprot_rest_interface	uniprot	UniProt ID mapping and sequence retrieval								To update	https://github.com/jdrudolph/uniprot	Proteomics, Sequence Analysis	uniprot_rest_interface	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	0.6	requests				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	132	2406
-varscan_version_2	varscan	VarScan wrapper								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan_version_2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2	2.4.2	varscan	2.4.6			1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	246	5191
-vcf2pgsnp	vcf2pgSnp	VCF to pgSnp								To update		Variant Analysis	vcf2pgsnp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	206
-vcf_annotate	vcf_annotate	Annotate a VCF file (dbSNP, hapmap)								To update		Variant Analysis	vcf_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
-vcf_extract	vcf_extract	Extract reads from a specified region								To update		Variant Analysis	vcf_extract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-vcf_filter	vcf_filter	Filter a VCF file								To update		Variant Analysis	vcf_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	63	388
-vcf_intersect	vcf_intersect	Generate the intersection of two VCF files								To update		Variant Analysis	vcf_intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19
-vcftools_annotate	vcftools_annotate	Annotate VCF using custom/user-defined annotations								To update	https://vcftools.github.io/	Variant Analysis	vcftools_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate	0.1	echo				1	0	1	1	1	0	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24	171
-vcftools_compare	vcftools_compare	Compare VCF files to get overlap and uniqueness statistics								To update	https://vcftools.github.io/	Variant Analysis	vcftools_compare	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	531
-vcftools_consensus	vcftools_consensus	Apply VCF variants to a fasta file to create consensus sequence								To update	https://vcftools.github.io/	Variant Analysis	vcftools_consensus	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus	0.1.11	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-vcftools_isec	vcftools_isec	Intersect multiple VCF datasets								To update	https://vcftools.github.io/	Variant Analysis	vcftools_isec	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec	0.1.1	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	35	498
-vcftools_merge	vcftools_merge	Merge multiple VCF datasets into a single dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge	0.1.11	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	68	953
-vcftools_slice	vcftools_slice	Subset VCF dataset by genomic regions								To update	https://vcftools.github.io/	Variant Analysis	vcftools_slice	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice	0.1	echo				1	0	1	1	1	0	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24	411
-vcftools_subset	vcftools_subset	Select samples from a VCF dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_subset	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	17	137
-venn_list	venn_list	Draw Venn Diagram (PDF) from lists, FASTA files, etc								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	Graphics, Sequence Analysis, Visualization	venn_list	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	0.1.2	galaxy_sequence_utils	1.1.5			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	248	5067
-vienna_rna	viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup	ViennaRNA - Prediction and comparison of RNA secondary structures								To update	http://www.tbi.univie.ac.at/RNA/	RNA	viennarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	2.2.10	viennarna	2.6.4			0	0	21	0	0	0	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	21	0	123	7864
-vt	vt_@BINARY@, vt_@BINARY@	A tool set for short variant discovery in genetic sequence data.								To update		Sequence Analysis, Variant Analysis	vt	bgruening	https://github.com/atks/vt	https://github.com/bgruening/galaxytools/tree/master/tools/vt	0.2	vt	2015.11.10			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-weightedaverage	wtavg	Assign weighted-average of the values of features overlapping an interval								To update		Sequence Analysis, Variant Analysis	weightedaverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage	https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage	1.0.1	galaxy-ops	1.1.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-whisper	whisper	Transcribe audio or video files to text using the OpenAI Whisper.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	Machine Learning	whisper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	20231117					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-windowsplitter	winSplitter	Make windows								To update		Sequence Analysis, Variant Analysis	windowsplitter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter	1.0.1	bx-python	0.12.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11
-woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660
-xy_plot	XY_Plot_1	Plotting tool for multiple series and graph types								To update		Graphics, Statistics	xy_plot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot	1.0.2	r-base				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	344	5892
-TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	42
-abricate	abricate, abricate_list, abricate_summary	Mass screening of contigs for antiobiotic resistance genes	ABRicate	ABRicate		ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.	Antimicrobial resistance prediction	Genomics, Microbiology	Up-to-date	https://github.com/tseemann/abricate	Sequence Analysis	abricate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate	1.0.1	abricate	1.0.1	Antimicrobial resistance prediction	Genomics, Microbiology	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	1764	496717
-abritamr	abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	abritamr	abritamr		abriTAMR	an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	To update	https://zenodo.org/record/7370628	Sequence Analysis	abritamr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr	1.0.14	abritamr	1.0.19	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	To update	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.7	abyss	2.3.8	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	391	4278
-adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	37	217
-add_input_name_as_column	addName	Add input name as column on an existing tabular file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column	Text Manipulation	add_input_name_as_column	mvdbeek	https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column	https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	91	83150
-aegean	aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval	AEGeAn toolkit wrappers	gaeval	gaeval		GAEVAL	Gene Annotation EVAluation.	Sequence annotation	Sequence analysis, Gene structure	Up-to-date	https://github.com/BrendelGroup/AEGeAn	Transcriptomics, Sequence Analysis	aegean	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean	0.16.0	aegean	0.16.0	Sequence annotation	Sequence analysis, Gene structure	1	4	4	4	1	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	47	168
-aldex2	aldex2	Performs analysis Of differential abundance taking sample variation into account	aldex2	aldex2		ALDEx2	A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	Statistical inference	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	13	129
-allegro	allegro	Linkage and haplotype analysis from deCODE	allegro	allegro		Allegro	It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome.	Sequence motif discovery	Sequence analysis, Transcription factors and regulatory sites, DNA	To update	http://www.decode.com/software/	Variant Analysis	allegro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro	@VER@.0	allegro	3	Sequence motif discovery	Sequence analysis, Transcription factors and regulatory sites, DNA	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-amplican	amplican	AmpliCan is an analysis tool for genome editing.	amplican	amplican		amplican	It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	53
-ampvis2	ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn	ampvis2	ampvis	ampvis		ampvis	ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.	Analysis, Visualisation	Biodiversity	To update	https://github.com/MadsAlbertsen/ampvis2/	Metagenomics	ampvis2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2	2.8.9			Analysis, Visualisation	Biodiversity	0	0	19	0	0	0	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	42	267
-amrfinderplus	amrfinderplus	"""AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms."	amrfinderplus	amrfinderplus		AMRFinderPlus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms"	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.12.8	ncbi-amrfinderplus	3.12.8	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	591
-ancombc	ancombc	Performs analysis of compositions of microbiomes with bias correction.	ancombc	ancombc		ANCOMBC	Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	7
-anndata	anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Transcriptomics, Sequence Analysis	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.3	anndata	0.6.22.post1			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	625	35620
-annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1175	25975
-argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-arriba	arriba, arriba_draw_fusions, arriba_get_filters	Arriba detects fusion genes in RNA-Seq data after running RNA-STAR								Up-to-date	https://github.com/suhrig/arriba	Sequence Analysis, Transcriptomics	arriba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba	2.4.0	arriba	2.4.0			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	38	3528
-art	art_454, art_illumina, art_solid	Simulator for Illumina, 454, and SOLiD sequencing data	art	art		ART	ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD	Conversion	Bioinformatics	To update	http://www.niehs.nih.gov/research/resources/software/biostatistics/art/	Sequence Analysis, Data Source	art	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/art	https://github.com/galaxyproject/tools-iuc/tree/main/tools/art	2014.11.03.0	art	2016.06.05	Conversion	Bioinformatics	0	0	3	0	0	0	3	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-artic	artic_guppyplex, artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	artic	artic		ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	Sequence alignment	Genomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	1	0	123	8175
-assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-astral	astral	Tool for estimating an unrooted species tree given a set of unrooted gene trees								Up-to-date	https://github.com/smirarab/ASTRAL	Phylogenetics	astral	iuc	https://github.com/usegalaxy-be/galaxytools/tree/main/astral	https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral	5.7.8	astral-tree	5.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-augustus	augustus, augustus_training	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.	augustus	augustus		AUGUSTUS	AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.	Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus	3.4.0	augustus	3.5.0	Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	685	11245
-b2btools	b2btools_single_sequence	This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.	b2btools	b2btools		b2bTools	The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA	Protein disorder prediction, Protein secondary structure prediction, Protein feature detection		To update	https://bio2byte.be	Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools	3.0.5+galaxy0	b2btools	3.0.7	Protein disorder prediction, Protein secondary structure prediction		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	345
-bakta	bakta	"""Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."""	bakta	bakta		Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	To update	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.3	bakta	1.9.4	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	151	2982
-bam_to_scidx	bam_to_scidx	Contains a tool that converts a BAM file to an ScIdx file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx	Convert Formats	bam_to_scidx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	128
-bamtools	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	208	14021
-bamtools_filter	bamFilter	Filter BAM datasets on various attributes using bamtools filter	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1195	114863
-bamtools_split	bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag	Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett.	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	197	4328
-bamutil	bamutil_clip_overlap, bamutil_diff	bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.								To update	https://github.com/statgen/bamUtil	Sequence Analysis	bamutil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil		bamutil	1.0.15			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	39
-bandage	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	bandage	bandage		Bandage	GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	Sequence assembly visualisation	Genomics, Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	2	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	2	2	0	2016	44390
-barcode_splitter	barcode_splitter	A utility to split sequence files using multiple sets of barcodes								To update	https://bitbucket.org/princeton_genomics/barcode_splitter/	Fastq Manipulation	barcode_splitter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter	0.18.4.0	barcode_splitter	0.18.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	71
-barrnap	barrnap	Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.	barrnap	barrnap		Barrnap	Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).	Gene prediction	Genomics, Model organisms, Model organisms	To update	https://github.com/tseemann/barrnap	Sequence Analysis	barrnap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap	1.2.2	barrnap	0.9	Gene prediction	Genomics, Model organisms, Model organisms	0	1	1	1	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	160	3938
-basil	basil	Breakpoint detection, including large insertions								Up-to-date	https://github.com/seqan/anise_basil	Variant Analysis	basil	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil	1.2.0	anise_basil	1.2.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	35	266
-bax2bam	bax2bam	BAX to BAM converter								Up-to-date	https://github.com/pacificbiosciences/bax2bam/	Convert Formats, Sequence Analysis	bax2bam	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam	0.0.11	bax2bam	0.0.11			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	200
-bayescan	BayeScan	Detecting natural selection from population-based genetic data	bayescan	bayescan		BayeScan	BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	64
-bbgbigwig	bbgtobigwig	Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	https://www.encodeproject.org/software/bedgraphtobigwig/	Convert Formats	bbgbigwig	iuc	https://www.encodeproject.org/software/bedgraphtobigwig/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig	0.1	ucsc-bedgraphtobigwig	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-bbtools	bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.	bbmap	bbtools, bbmap		BBMap	BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	Up-to-date	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.08	bbmap	39.08	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	6	1	5	0	6	1	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	0	4	0	0	420	6381
-bcftools	bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@	BCFtools toolkit wrappers	bcftools	bcftools		BCFtools	BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.	Data handling, Variant calling	Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment	To update	https://samtools.github.io/bcftools/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools	1.15.1	bcftools	1.20	Data handling, Variant calling	DNA polymorphism, GWAS study, Genotyping experiment	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-bctools	bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events	bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0								Up-to-date	https://github.com/dmaticzka/bctools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools	0.2.2	bctools	0.2.2			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	87	2895
-beacon2	beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff	beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI).	ga4gh_beacon	ga4gh_beacon		GA4GH Beacon	A global search engine for genetic mutations.	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	Up-to-date	https://github.com/EGA-archive/beacon2-ri-tools/tree/main	Variant Analysis	beacon2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2	2.0.0	beacon2-ri-tools	2.0.0	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	28
-beacon2-import	beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence	Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants.	ga4gh_beacon	ga4gh_beacon		GA4GH Beacon	A global search engine for genetic mutations.	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	Up-to-date	https://pypi.org/project/beacon2-import/	Variant Analysis	Beacon2_Import	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import	2.2.3	beacon2-import	2.2.3	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	0	0	12	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-beagle	beagle	Beagle is a program for phasing and imputing missing genotypes.								To update	https://faculty.washington.edu/browning/beagle/beagle.html	Variant Analysis	beagle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle	5.2_21Apr21.304	beagle	5.4_22Jul22.46e			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	54
-bedops	bedops-sort-bed	BEDOPS: high-performance genomic feature operations								Up-to-date	https://bedops.readthedocs.io/en/latest/	Genomic Interval Operations	bedops_sortbed	iuc	https://bedops.readthedocs.io/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops	2.4.41	bedops	2.4.41			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	28
-bedtools	bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed	bedtools is a powerful toolset for genome arithmetic	bedtools	bedtools		BEDTools	BEDTools is an extensive suite of utilities for comparing genomic features in BED format.	Mapping	Genomics	Up-to-date	https://github.com/arq5x/bedtools2	Genomic Interval Operations, Text Manipulation	bedtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools	2.31.1	bedtools	2.31.1	Mapping	Genomics	37	37	37	37	37	37	37	37	0	37	0	0	37	0	0	0	0	0	0	0	37	6	37	0	0	37	0	0	0	37	0	0	0	0	0	0	0	37	37	0	5844	901750
-bellerophon	bellerophon	Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.								Up-to-date	https://github.com/davebx/bellerophon	Sequence Analysis	bellerophon	iuc	https://github.com/davebx/bellerophon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon	1.0	bellerophon	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	123	1194
-berokka	berokka	Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.								Up-to-date	https://github.com/tseemann/berokka	Fasta Manipulation	berokka	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka	0.2.3	berokka	0.2.3			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-bigscape	bigscape	Construct sequence similarity networks of BGCs and groups them into GCF	BiG-SCAPE	BiG-SCAPE		BiG-SCAPE	A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-bigwig_outlier_bed	bigwig_outlier_bed	pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files	bigtools	bigtools		bigtools	Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust.			To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	Sequence Analysis	bigwig_outlier_bed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-binning_refiner	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	binning_refiner	binning_refiner		Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	81
-bioext	bioext_bam2msa, bioext_bealign	A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more!								To update	https://pypi.python.org/pypi/biopython-extensions/	Next Gen Mappers		iuc	https://github.com/davebx/bioext-gx/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext	0.21.7	python-bioext	0.21.9			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	363	15228
-bioinformatics_cafe	fasta_regex_finder	Miscellanea of scripts for bioinformatics								To update	https://github.com/dariober/bioinformatics-cafe/	Sequence Analysis	bioinformatics_cafe	mbernt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe	0.1.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	978
-biom_format	biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	biomformat	biomformat		biomformat	"This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods."	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	Formatting	Laboratory information management, Sequence analysis	2	2	6	0	2	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	98	3906
-bioperl	bp_genbank2gff3	Converts GenBank format files to GFF3	bioperl	bioperl		BioPerl	A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.  It provides software modules for many of the typical tasks of bioinformatics programming.	Data handling, Service invocation	Genomics, Software engineering, Data management	To update	https://bioperl.org/	Sequence Analysis	bp_genbank2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl	1.1	perl-bioperl	1.7.8	Data handling, Service invocation	Genomics, Software engineering	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	240	6736
-biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	3
-blast	magicblast	Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome								Up-to-date	https://ncbi.github.io/magicblast/	Next Gen Mappers	magicblast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast	1.7.0	magicblast	1.7.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	78	511
-blastxml_to_gapped_gff3	blastxml_to_gapped_gff3	BlastXML to gapped GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	Convert Formats, Sequence Analysis	blastxml_to_gapped_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3	1.1	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24	185
-bowtie2	bowtie2	Bowtie2: Fast and sensitive read alignment	bowtie2	bowtie2		Bowtie 2	Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.	Read mapping	Mapping, Genomics, Mapping	To update	http://bowtie-bio.sourceforge.net/bowtie2	Next Gen Mappers	bowtie2	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2	2.5.3	bowtie2	2.5.4	Read mapping	Mapping, Genomics, Mapping	1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	1	0	0	0	0	1	1	0	5136	380252
-bracken	est_abundance	Bayesian Reestimation of Abundance with KrakEN	bracken	bracken		Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	Statistical calculation	Metagenomics, Microbial ecology	Up-to-date	https://ccb.jhu.edu/software/bracken/	Sequence Analysis, Metagenomics	bracken	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken	3.0	bracken	3.0	Statistical calculation	Metagenomics, Microbial ecology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	326	18351
-breseq	breseq	Predicts mutations in microbial genomes	breseq	breseq		breseq	Runs Breseq software on a set of fastq files.	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	To update	https://github.com/barricklab/breseq	Variant Analysis	breseq	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq	0.35.5	breseq	0.39.0	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	50	1871
-brew3r_r	brew3r_r	Extend 3' end of a GTF using another GTF as a template	brew3r.r	brew3r.r		BREW3R.r	This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.	Genome annotation	Transcriptomics, Genomics	To update	https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html	Transcriptomics, RNA	brew3r_r	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r	https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r	1.0.2			Genome annotation	Transcriptomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-busco	busco	BUSCO assess genome and annotation completeness	busco	busco		BUSCO	Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://gitlab.com/ezlab/busco/-/releases	Sequence Analysis	busco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco	5.7.1	busco	5.7.1	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1804	86180
-bwa	bwa_mem, bwa	Wrapper for bwa mem, aln, sampe, and samse	bwa	bwa		BWA	Fast, accurate, memory-efficient aligner for short and long sequencing reads	Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment	Mapping	Up-to-date	http://bio-bwa.sourceforge.net/	Next Gen Mappers	bwa	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa	0.7.18	bwa	0.7.18	Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment	Mapping	2	2	2	2	2	2	2	2	0	1	0	0	2	0	0	0	0	0	0	0	2	1	2	0	0	2	0	0	0	2	0	0	0	0	0	0	0	2	2	2	5295	981251
-bwa_mem2	bwa_mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa.	bwa-mem2	bwa-mem2		Bwa-mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case,  dataset and the running machine.	Sequence alignment	Mapping	Up-to-date	https://github.com/bwa-mem2/bwa-mem2	Next Gen Mappers	bwa_mem2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2	2.2.1	bwa-mem2	2.2.1	Sequence alignment	Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	1220	44386
-bwameth	bwameth	Fast and accurate alignment of BS-seq reads								Up-to-date	https://github.com/brentp/bwa-meth	Sequence Analysis, Next Gen Mappers	bwameth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth	0.2.7	bwameth	0.2.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	201	10619
-cactus	cactus_cactus, cactus_export	Cactus is a reference-free whole-genome multiple alignment program	cactus	cactus		Cactus	Cactus is a reference-free whole-genome multiple alignment program.	Multiple sequence alignment, Genome alignment	Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics	To update	https://github.com/ComparativeGenomicsToolkit/cactus	Sequence Analysis	cactus	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	2.7.1			Multiple sequence alignment, Genome alignment	Genomics, Sequence assembly, Mapping, Phylogenetics	0	2	2	1	0	2	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	26	234
-calculate_contrast_threshold	calculate_contrast_threshold	Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.								To update	https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold	Visualization, Genomic Interval Operations, SAM	calculate_contrast_threshold	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold	1.0.0	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-calculate_numeric_param	calculate_numeric_param	Calculate a numeric parameter value using integer and float values.								To update		Text Manipulation	calculate_numeric_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param	0.1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	1393
-cami_amber	biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert	Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments								Up-to-date	https://github.com/CAMI-challenge/AMBER	Metagenomics	cami_amber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber	2.0.6	cami-amber	2.0.6			0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cat	cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	cat_bins		CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat	5.2.3	cat	5.3	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	5	2	5	0	5	2	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	268	2878
-cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	280	4474
-cemitool	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.26.0	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	98
-charts	charts	Enables advanced visualization options in Galaxy Charts								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	Visualization	charts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts	1.0.1	r-getopt				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	287	3589
-checkm	checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	checkm	checkm		CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	To update	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.0	checkm-genome	1.2.3	Sequence assembly validation, Sequence composition calculation, Statistical calculation	Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	0	0	10	10	0	0	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	390	5165
-cherri	cherri_eval, cherri_train	Computational Help Evaluating RNA-RNA interactions	cherri	cherri		cherri	CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.		Molecular interactions, pathways and networks, Structure analysis, Machine learning	To update	https://github.com/BackofenLab/Cherri	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri	0.7	cherri	0.8		Molecular interactions, pathways and networks, Structure analysis, Machine learning	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	207
-chewbbaca	chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema	BSR-Based Allele Calling Algorithm								To update	https://github.com/B-UMMI/chewBBACA/tree/master	Variant Analysis	chewbbaca	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca		chewbbaca	3.3.10			0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chira	chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify	Chimeric Read Annotator for RNA-RNA interactome data	chira	chira		ChiRA	ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.		RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	Up-to-date	https://github.com/pavanvidem/chira	RNA, Transcriptomics, Sequence Analysis	chira	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira	1.4.3	chira	1.4.3		Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	97	6418
-chopin2	chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing								To update	https://github.com/cumbof/chopin2	Machine Learning	chopin2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2	1.0.9.post1	chopin2				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chromeister	chromeister	ultra-fast pairwise genome comparisons								Up-to-date	https://github.com/estebanpw/chromeister	Sequence Analysis	chromeister	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister	1.5.a	chromeister	1.5.a			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	182	2130
-circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	269
-circos	circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile	Build Circos Plots in Galaxy	galactic_circos	galactic_circos		Galactic Circos	Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format.	Sequence visualisation		To update	http://circos.ca/	Graphics	circos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos	0.69.8	circos	0.69.9	Sequence visualisation		11	11	11	11	11	11	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	11	11	0	0	0	0	0	0	11	0	0	0	0	0	0	0	11	11	0	1018	21305
-cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	To update	https://github.com/Hoohm/CITE-seq-Count	Transcriptomics	cite_seq_count	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	1.4.4	cite-seq-count	1.4.5	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	18
-clair3	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	clair3	clair3		Clair3	Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	1.0.8	clair3	1.0.10	Variant calling	Molecular genetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	68	1856
-clustalw	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	clustal2	clustal2		Clustal 2 (Clustal W, Clustal X)	Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.	Multiple sequence alignment	Phylogeny, Sequence analysis	Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw	2.1	clustalw	2.1	Multiple sequence alignment	Phylogeny, Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	651	46793
-clustering_from_distmat	clustering_from_distmat	Distance matrix-based hierarchical clustering using SciPy								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/	Statistics	clustering_from_distmat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat	1.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cnv-phenopacket	cnv_phenopacket	cnv-phenopacket Converts TSV metadata file to JSON.								To update	https://pypi.org/project/cnv-phenopacket/	Variant Analysis	cnv_phenopacket	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket	1.0.2	cnv-phenopacket				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cnv-vcf2json	cnv_vcf2json	cnv-vcf2json Converts structural variants VCF file to JSON.								To update	https://pypi.org/project/cnv-phenopacket/	Variant Analysis	cnv-vcf2json	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json	1.1.0	cnv-vcf2json				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cnvkit	cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target	detecting copy number variants and alterations genome-wide from high-throughput sequencing	cnvkit	cnvkit		CNVkit	CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.	Variant calling	DNA structural variation	Up-to-date	https://github.com/etal/cnvkit	Variant Analysis	cnvkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit	0.9.11	cnvkit	0.9.11	Variant calling		0	0	17	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	45	370
-codeml	codeml	Detects positive selection	paml	paml		PAML	Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml	4.9	paml	4.10.7	Probabilistic sequence generation	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	29	60901
-cojac	cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	cojac	cojac		COJAC	CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.2	cojac	0.9.2		Genetic variation	2	0	3	0	2	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	20	2757
-colabfold	colabfold_alphafold, colabfold_msa	Protein prediction based on AlphaFold2	Colabfold	Colabfold		ColabFold	ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.	Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	To update	https://github.com/sokrypton/ColabFold	Proteomics, Graphics	colabfold	iuc	https://github.com/sokrypton/ColabFold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold	1.5.5			Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-colibread	commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak	Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome								To update	https://colibread.inria.fr/	Sequence Analysis, Variant Analysis	colibread	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread	24.7.14+galaxy0	commet	24.7.14			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	251
-collection_column_join	collection_column_join	Column Join on Collections								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join	Text Manipulation	collection_column_join	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join	https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join	0.0.3	coreutils	8.25			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1483	20857
-collection_element_identifiers	collection_element_identifiers	Extract element identifiers of a collection								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers	Text Manipulation	collection_element_identifiers	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers	https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers	0.0.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	912	5059
-column_maker	Add_a_column1	Compute an expression on every row								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker	Text Manipulation	column_maker	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker	2.1	python				1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	2379	3883271
-column_order_header_sort	column_order_header_sort	Sort Column Order by heading								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort	Text Manipulation	column_order_header_sort	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort	0.0.1	python				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	80	3258
-column_remove_by_header	column_remove_by_header	Remove columns by header								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header	Text Manipulation	column_remove_by_header	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header	1.0	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	199	8424
-compleasm	compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	compleasm	compleasm		compleasm	"""Compleasm: a faster and more accurate reimplementation of BUSCO"""	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm	0.2.6	compleasm	0.2.6	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-compose_text_param	compose_text_param	Compose a text parameter value using text, integer and float values								To update		Text Manipulation	compose_text_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param	0.1.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	375	35084
-compress_file	compress_file	Compress files.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file	Text Manipulation	compress_file	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file	0.1.0	gzip				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	164	3674
-concoct	concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	concoct	concoct		CONCOCT	A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct	1.1.0	concoct	1.1.0	Sequence clustering, Read binning	Metagenomics	0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	92	786
-cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-coverage_report	CoverageReport2	Generate Detailed Coverage Report from BAM file								To update	https://github.com/galaxyproject/tools-iuc	Sequence Analysis	coverage_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report	0.0.4	perl-number-format	1.76			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-coverm	coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm		CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	Local alignment	Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	72	529
-crispr_studio	crispr_studio	CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.	crisprstudio	crisprstudio		CRISPRStudio	CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.	Visualisation	Sequence analysis, Genomics, Data visualisation	To update	https://github.com/moineaulab/CRISPRStudio	Sequence Analysis	crispr_studio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio	1+galaxy0	crispr_studio	1	Visualisation	Sequence analysis, Genomics, Data visualisation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	636
-crosscontamination_barcode_filter	crosscontamination_barcode_filter	Barcode contamination discovery tool								To update		Transcriptomics, Visualization	crosscontamination_barcode_filter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter	0.3	r-ggplot2	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	17	347
-crossmap	crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig	CrossMap converts genome coordinates or annotation files between genome assemblies								To update	http://crossmap.sourceforge.net/	Convert Formats, Genomic Interval Operations	crossmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap	0.6.1	crossmap	0.7.0			5	0	6	0	5	0	6	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	6	5	0	116	1968
-cuffcompare	cuffcompare	Galaxy wrappers for the Cuffcompare tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffcompare	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare	2.2.1	cufflinks	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	1	1	0	65	1130
-cuffdiff	cuffdiff	Galaxy wrappers for the Cuffdiff tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffdiff	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff	2.2.1	cufflinks	2.2.1			1	0	1	0	1	0	1	0	0	1	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	1	0	228	5831
-cufflinks	cufflinks	Galaxy wrappers for the Cufflinks tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cufflinks	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks	2.2.1	cufflinks	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	1	0	0	0	0	1	1	0	319	32218
-cuffmerge	cuffmerge	Galaxy wrappers for the Cuffmerge tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffmerge	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge	2.2.1	cufflinks	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	1	1	0	122	3292
-cuffnorm	cuffnorm	The Cuffnorm tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffnorm	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	27	660
-cuffquant	cuffquant	The Cuffquant tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffquant	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	18	688
-cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	5090	232004
-cutesv	cutesv	Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools.	cuteSV	cuteSV		cuteSV	Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis	Split read mapping, Genotyping, Structural variation detection	DNA structural variation, Sequencing, Computer science	To update	https://github.com/tjiangHIT/cuteSV	Variant Analysis	cutesv	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv	1.0.8	cutesv	2.1.1	Split read mapping, Genotyping, Structural variation detection	Sequencing, Computer science	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	17	235
-cwpair2	cwpair2	Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans.								To update		ChIP-seq	cwpair2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2	1.1.1	matplotlib				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dada2	dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	dada2	dada2		dada2	This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	10	0	0	1	0	0	0	0	0	0	0	0	0	0	0	10	10	0	1263	66609
-das_tool	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	dastool		dastool	DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	Read binning	Metagenomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	24	706
-data_source_iris_tcga	data_source_iris_tcga	IRIS-TCGA Data source tool								To update		Data Source	data_source_iris_tcga	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga	https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga	1.0.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-datamash	datamash_ops, datamash_reverse, datamash_transpose	GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon.								To update	https://www.gnu.org/software/datamash/	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash	1.8	datamash	1.1.0			3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	1	3	3	0	0	1	0	0	0	1	0	0	0	0	0	0	0	3	3	0	3066	739298
-decontaminator	decontaminator	Deep Learning method for novel virus detection in sequencing data	decontaminator	decontaminator		decontaminator	Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.	Filtering	Metagenomics	To update	https://github.com/cbib/decontaminator	Machine Learning	decontaminator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator	1.0.0	numpy		Filtering	Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	99
-deepmicro	deepmicro	Representation learning and classification framework	DeepMicro	DeepMicro		DeepMicro	Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.	Essential dynamics, Splitting, Community profiling	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	Up-to-date	https://github.com/paulzierep/DeepMicro	Machine Learning	deepmicro	iuc	https://github.com/paulzierep/DeepMicro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro	1.4	deepmicro	1.4	Essential dynamics, Splitting	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	501
-deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5
-deepvariant	deepvariant	DeepVariant is a deep learning-based variant caller								To update	https://github.com/google/deepvariant	Variant Analysis	deepvariant	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant	1.5.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	182	1889
-deg_annotate	deg_annotate	Annotate DESeq2/DEXSeq output tables								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	Transcriptomics	deg_annotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate	1.1.0	bedtools	2.31.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1774	19910
-delly	delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge	Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.	delly2	delly2		Delly2	Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.	Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis	DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases	To update	https://github.com/dellytools/delly	Variant Analysis	delly	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly	https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly	0.9.1	delly	1.2.6	Indel detection, Structural variation detection, Genotyping	Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases	0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	6	0	0	124	1135
-deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	4990	95752
-dexseq	dexseq, dexseq_count, plotdexseq	Inference of differential exon usage in RNA-Seq	dexseq	dexseq		DEXSeq	The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html	Transcriptomics, RNA, Statistics	dexseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq	1.48.0	bioconductor-dexseq	1.48.0	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	218	16064
-diamond	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	diamond		Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	Sequence alignment analysis	Sequence analysis, Proteins	3	3	3	3	3	3	3	3	0	0	0	0	3	0	0	0	0	0	0	0	3	3	3	0	0	0	1	0	0	0	0	0	0	0	0	0	0	3	3	0	963	49711
-diffbind	diffbind	Diffbind provides functions for  processing  ChIP-Seq  data.	diffbind	diffbind		DiffBind	Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.	Differential binding analysis	ChIP-seq	Up-to-date	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind	3.12.0	bioconductor-diffbind	3.12.0	Differential binding analysis	ChIP-seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	250	6264
-dimet	dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@	DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data.								Up-to-date	https://github.com/cbib/DIMet	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet	0.2.4	dimet	0.2.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	42	369
-dnabot	dnabot	DNA assembly using BASIC on OpenTrons								To update	https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT	Synthetic Biology	dnabot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot	3.1.0	dnabot				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dnaweaver	dnaweaver	Given a SBOL input, calculate assembly parts for Gibson or Golden Gate.								Up-to-date	https://github.com/Edinburgh-Genome-Foundry/DnaWeaver	Synthetic Biology	dnaweaver	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver	1.0.2	dnaweaver_synbiocad	1.0.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dram	dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram		DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	Up-to-date	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.5.0	dram	1.5.0	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	39	6886
-drep	drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep		dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	Up-to-date	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.5.0	drep	3.5.0	Genome comparison	Metagenomics, Sequence analysis	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	46	646
-dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Transcriptomics, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	126	3934
-ebi_tools	ebi_search_rest_results	Tools to query and download data from several EMBL-EBI databases								To update	http://www.ebi.ac.uk/services/all	Web Services, Data Source	ebi_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools	0.1.1	six				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	52	382
-edger	edger	Perform RNA-Seq differential expression analysis using edgeR pipeline	edger	edger		edgeR	Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	To update	http://bioconductor.org/packages/release/bioc/html/edgeR.html	Transcriptomics, RNA, Statistics	edger	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger	https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger	3.36.0	bioconductor-edger	4.0.16	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	945	18117
-egsea	egsea	This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing	egsea	egsea		EGSEA	This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.	Gene set testing	Systems biology	To update	https://bioconductor.org/packages/release/bioc/html/EGSEA.html	Transcriptomics, RNA, Statistics	egsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea	1.20.0	bioconductor-egsea	1.28.0	Gene set testing	Systems biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	177	2524
-emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	107	107	107	107	107	0	0	0	0	107	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	0	0	107	107	0	1816	89530
-ena_upload	ena_upload	Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). 								Up-to-date	https://github.com/usegalaxy-eu/ena-upload-cli	Data Export	ena_upload	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload	0.7.3	ena-upload-cli	0.7.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	14	208
-enasearch	enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data	A Python library for interacting with ENA's API								To update	https://github.com/bebatut/enasearch	Data Source	enasearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch		enasearch	0.2.2			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	126	2257
-ensembl_vep	ensembl_vep	Ensembl VEP: Annotate VCFs with variant effect predictions								To update	https://github.com/Ensembl/ensembl-vep	Variant Analysis	ensembl_vep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep	110.1	ensembl-vep	112.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	119	2653
-episcanpy	episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess	EpiScanpy – Epigenomics single cell analysis in python	episcanpy	episcanpy		epiScanpy	Epigenomics Single Cell Analysis in Python.	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	To update	https://github.com/colomemaria/epiScanpy	Epigenetics	episcanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy	0.3.2	episcanpy	0.4.0	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	20	736
-exomedepth	exomedepth	ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data	exomedepth	exomedepth		ExomeDepth	Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases	To update	https://cran.r-project.org/package=ExomeDepth	Sequence Analysis, Variant Analysis	exomedepth	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth	1.1.0	r-exomedepth	1.1.16	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	29	410
-exonerate	exonerate	Exonerate is a generic tool for pairwise sequence comparison.	exonerate	exonerate		Exonerate	A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	Up-to-date	https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate	Sequence Analysis	exonerate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate	2.4.0	exonerate	2.4.0	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	59	988
-export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan		export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	Conversion	Taxonomy, Metabolomics, Biomarkers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	200	5265
-extract_genomic_dna	Extract genomic DNA 1	Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes.								To update		Genomic Interval Operations	extract_genomic_dna	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna	https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna	3.0.3+galaxy2	bx-python	0.12.0			1	0	1	0	1	0	1	0	0	1	0	0	1	0	0	1	0	0	0	0	1	1	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	285	11846
-falco	falco	A high throughput sequence QC analysis tool	falco	falco		Falco	A high-speed FastQC emulation for quality control of sequencing data.	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	To update	https://github.com/smithlabcode/falco/	Sequence Analysis	falco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco	https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco	1.2.2+galaxy1	falco	1.2.3	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fargene	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fargene		fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	52	459
-fasplit	fasplit	faSplit is a tool to split a single FASTA file into several files	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://hgdownload.cse.ucsc.edu/admin/exe/	Fasta Manipulation	ucsc_fasplit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	377	ucsc-fasplit	469		Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	242	2644
-fasta_clipping_histogram	cshl_fasta_clipping_histogram	Length Distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Graphics, Statistics	fasta_clipping_histogram	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram	0.0.14	fastx_toolkit	0.0.14			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-fasta_formatter	cshl_fasta_formatter	FASTA Width formatter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_formatter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	68	2912
-fasta_nucleotide_changer	cshl_fasta_nucleotides_changer	RNA/DNA converter.								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_nucleotide_changer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	29	774
-fasta_nucleotide_color_plot	fasta_nucleotide_color_plot	Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot	Visualization	fasta_nucleotide_color_plot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	160
-fasta_stats	fasta-stats	Display summary statistics for a fasta file.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	Sequence Analysis	fasta_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats	2.0	numpy				1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1080	35336
-fastani	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity	fastani	fastani		FastANI	FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	250	3498
-fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fastp	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp		fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	Sequence contamination filtering	Probes and primers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	1	2803	1055760
-fastq_combiner	fastq_combiner	Combine FASTA and QUAL into FASTQ								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation, Fasta Manipulation	fastq_combiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	66	8676
-fastq_filter	fastq_filter	Filter FASTQ reads by quality score and length								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	266	14222
-fastq_groomer	fastq_groomer	Convert between various FASTQ quality formats.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_groomer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1028	94802
-fastq_manipulation	fastq_manipulation	Manipulate FASTQ reads on various attributes.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_manipulation	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	69	2503
-fastq_masker_by_quality	fastq_masker_by_quality	FASTQ Masker by quality score								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_masker_by_quality	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	170
-fastq_paired_end_deinterlacer	fastq_paired_end_deinterlacer	FASTQ de-interlacer on paired end reads.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_deinterlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	122	8410
-fastq_paired_end_interlacer	fastq_paired_end_interlacer	FASTQ interlacer on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_interlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1087	17024
-fastq_paired_end_joiner	fastq_paired_end_joiner	FASTQ joiner on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_joiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	245	16635
-fastq_paired_end_splitter	fastq_paired_end_splitter	FASTQ splitter on joined paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	196	3092
-fastq_quality_boxplot	cshl_fastq_quality_boxplot	Draw quality score boxplot								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics, Statistics	fastq_quality_boxplot	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	51	1178
-fastq_quality_converter	cshl_fastq_quality_converter	Quality format converter (ASCII-Numeric)								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_converter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	11	220
-fastq_quality_filter	cshl_fastq_quality_filter	Filter by quality								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1509	15172
-fastq_stats	fastq_stats	FASTQ Summary Statistics by column								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_stats	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	221	4246
-fastq_to_fasta	cshl_fastq_to_fasta	FASTQ to FASTA converter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Convert Formats	fastq_to_fasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	419	13599
-fastq_to_tabular	fastq_to_tabular	FASTQ to Tabular converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_to_tabular	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	93	12593
-fastq_trimmer	fastq_trimmer	FASTQ Trimmer by quality								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	210	9757
-fastqc	fastqc	Read QC reports using FastQC	fastqc	fastqc		FastQC	This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	Fastq Manipulation	fastqc	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc	0.74+galaxy1	fastqc	0.12.1	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	1	1	1	1	1	1	1	1	0	1	1	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	1	1	0	0	1	1	0	17447	1556625
-fastqe	fastqe	FASTQE	fastqe	fastqe		FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	Sequencing quality control	Sequence analysis, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1266	4333
-fastqtofasta	fastq_to_fasta_python	FASTQ to FASTA converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastqtofasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	0	1	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1371	178178
-fasttree	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree		FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11		Phylogenetics	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	379	55434
-fastx_artifacts_filter	cshl_fastx_artifacts_filter	Remove sequencing artifacts								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_artifacts_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	27	1810
-fastx_barcode_splitter	cshl_fastx_barcode_splitter	Barcode Splitter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_barcode_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	128	16591
-fastx_clipper	cshl_fastx_clipper	Clip adapter sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_clipper	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	96	3333
-fastx_collapser	cshl_fastx_collapser	Collapse sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fastx_collapser	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	114	61218
-fastx_nucleotides_distribution	cshl_fastx_nucleotides_distribution	Draw nucleotides distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics	fastx_nucleotides_distribution	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	25	249
-fastx_quality_statistics	cshl_fastx_quality_statistics	Compute quality statistics								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Statistics	fastx_quality_statistics	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	63	2176
-fastx_renamer	cshl_fastx_renamer	Rename sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_renamer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	68	2280
-fastx_reverse_complement	cshl_fastx_reverse_complement	Reverse-Complement								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Fasta Manipulation	fastx_reverse_complement	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	156	10832
-fastx_trimmer	cshl_fastx_trimmer	Trim sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	205	13149
-fatovcf	fatovcf	Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_fatovcf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fatovcf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf	448	ucsc-fatovcf	448		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	285
-featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	4679	696399
-feelnc	feelnc	Galaxy wrapper for FEELnc	feelnc	feelnc		FEELnc	A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.	Annotation, Classification	RNA-seq, Functional, regulatory and non-coding RNA	To update	https://github.com/tderrien/FEELnc	Sequence Analysis	feelnc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc	0.2.1	feelnc	0.2	Annotation, Classification	Functional, regulatory and non-coding RNA	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	46	1191
-fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fgsea	fgsea	Perform gene set testing using fgsea	fgsea	fgsea		fgsea	The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.	Gene-set enrichment analysis	Genetics	To update	https://bioconductor.org/packages/release/bioc/html/fgsea.html	Visualization, Transcriptomics, Statistics	fgsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea	1.8.0+galaxy1	bioconductor-fgsea	1.28.0	Gene-set enrichment analysis	Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	307	5240
-filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	617	30483
-flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	14	331
-flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	74	13759
-fraggenescan	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan		FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	Gene prediction	Genetics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	68	1102
-freebayes	freebayes, bamleftalign	Galaxy Freebayes Bayesian genetic variant detector tool	freebayes	freebayes		FreeBayes	Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.	Variant calling, Statistical calculation	Genomics, Genetic variation, Rare diseases	To update	https://github.com/ekg/freebayes	Variant Analysis	freebayes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes	1.3.6	freebayes	1.3.7	Variant calling, Statistical calculation	Genomics, Genetic variation, Rare diseases	2	2	2	2	2	2	2	2	0	2	0	0	2	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	2	2	0	3059	155087
-freec	control_freec	Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH.	freec	freec		FREEC	A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies.	Copy number estimation, Variant calling, Genome alignment	DNA structural variation, Oncology, Human genetics, Data mining	To update	http://boevalab.inf.ethz.ch/FREEC/	Variant Analysis	control_freec	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec	11.6	gawk		Copy number estimation, Variant calling, Genome alignment	Oncology, Human genetics, Data mining	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	44	665
-freyja	freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja		Freyja	Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset	RNA-Seq quantification	Metagenomics	To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.1	RNA-Seq quantification	Metagenomics	2	0	4	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	55	20021
-fsd	fsd, fsd_beforevsafter, fsd_regions, td	Tool that plots a histogram of sizes of read families								To update		Graphics	duplex_family_size_distribution	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd	1.0.2	matplotlib				4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	900	5906
-gatk4	gatk4_mutect2	A Galaxy wrapper for Mutect2 from GATK								To update	https://software.broadinstitute.org/gatk/gatk4	Variant Analysis	gatk4_mutect2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4	4.1.7.0	gatk4	4.5.0.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	181	2483
-gdcwebapp	data_source_gdcwebapp	GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format								To update	http://bioinf.iasi.cnr.it/gdcwebapp/	Data Source, Convert Formats	gdcwebapp	iuc	https://github.com/fabio-cumbo/GDCWebApp4Galaxy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp	1.0.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gecko	gecko	Ungapped genome comparison								Up-to-date	https://github.com/otorreno/gecko	Sequence Analysis	gecko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko	1.2	gecko	1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	519
-gemini	gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@	GEMINI: a flexible framework for exploring genome variation	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://github.com/arq5x/gemini	Sequence Analysis, Next Gen Mappers	gemini	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini	0.20.1	gemini	0.30.2	Sequence analysis, Genetic variation analysis	Sequence analysis	1	2	2	2	1	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	662	4916
-genebed_maf_to_fasta	GeneBed_Maf_Fasta2	Stitch gene blocks given a set of coding exon intervals								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/	Genomic Interval Operations	genebed_maf_to_fasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta	1.0.1+galaxy0					1	1	1	1	1	1	1	1	0	1	1	0	1	0	0	1	0	0	0	1	1	1	0	1	0	0	0	0	0	1	0	0	0	0	1	0	0	1	1	0	1	4
-genehunter_modscore	genehunter_modscore	Maximised LOD score pedigree analysis utility								To update	https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1	Variant Analysis	genehunter_modscore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore	3.0.0	ghm	3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-geneiobio	gene_iobio_display_generation_iframe	Gene.iobio is an interactive tool for variant and trio analysis.								To update	https://github.com/iobio/gene.iobio	Sequence Analysis	geneiobio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio	4.7.1+galaxy1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	67
-genetrack	genetrack	"Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand."								To update		ChIP-seq	genetrack	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack		numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-genomescope	genomescope	Analyze unassembled short reads								Up-to-date	https://github.com/tbenavi1/genomescope2.0	Statistics	genomescope	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope	2.0.1	genomescope2	2.0.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	329	2118
-genomic_super_signature	genomic_super_signature	Interpretation of RNAseq experiments through robust, efficient comparison to public databases	genomicsupersignature	genomicsupersignature		GenomicSuperSignature	GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	To update	https://github.com/shbrief/GenomicSuperSignature	Sequence Analysis, RNA, Transcriptomics	genomic_super_signature	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature	1.2.0	bioconductor-genomicsupersignature	1.10.0	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11	46
-genrich	genrich	Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).								To update	https://github.com/jsh58/Genrich	ChIP-seq	genrich	iuc	https://github.com/jsh58/Genrich	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich	0.5+galaxy2	genrich	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	79	3515
-get_hrun	get_hrun	Annotate indel variants with homopolymer context								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun	Variant Analysis	get_hrun	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun	https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun	0.5.9.2	pyfaidx	0.8.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	4
-getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	18	495
-gfa_to_fa	gfa_to_fa	gfa_to_fa - Converting GFA format to Fasta format								To update	http://gfa-spec.github.io/GFA-spec/	Convert Formats	gfa_to_fa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa	0.1.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	332	8274
-gff3_rebase	gff3.rebase	Rebase a GFF against a parent GFF (e.g. an original genome)								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	Sequence Analysis	gff3_rebase	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase	1.2	bcbiogff	0.6.6			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	12	135
-gffcompare	gffcompare	Galaxy wrappers for Geo Pertea's GffCompare package.	gffcompare	gffcompare		gffcompare	Program for comparing, annotating, merging and tracking transcripts in GFF files.	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	https://github.com/gpertea/gffcompare/	Transcriptomics	gffcompare	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare	0.12.6	gffcompare	0.12.6	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	381	3477
-gffread	gffread	gffread filters and/or converts GFF3/GTF2 records	gffread	gffread		gffread	program for filtering, converting and manipulating GFF files	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/	Sequence Analysis	gffread	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread	0.12.7	gffread	0.12.7	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	680	10995
-ggplot2	ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2		ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		Visualisation	Data visualisation	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	5	0	0	0	0	0	0	3	0	0	0	0	0	0	0	5	5	0	1388	22148
-ggupset	emc-ggupset	Create Upset Plots with ggupset								To update	https://github.com/const-ae/ggupset	Graphics	ggupset	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset	1.0	r-ggupset				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-glimmer	glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based	Glimmer makes gene predictions.	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	Sequence analysis, Genetic variation analysis	Sequence analysis	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	187	3965
-goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	408	5484
-goseq	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq		GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	Gene functional annotation	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1210	19167
-gprofiler	gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense	functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more								To update	https://biit.cs.ut.ee/gprofiler	Statistics, Web Services	gprofiler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler	@TOOL_VERSION@+galaxy11	r-gprofiler2				5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	196	3443
-graphembed	graphembed	Compute a 2D embedding of a data matrix given supervised class information								Up-to-date	https://github.com/fabriziocosta/GraphEmbed	Statistics, Graphics	graphembed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed	2.4	graph_embed	2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	63
-graphlan	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	graphlan	graphlan		GraPhlAn	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	432	9277
-gtdb_to_taxdump	gtdb_to_taxdump	Convert GTDB taxonomy to NCBI taxdump format	gtdb_to_taxdump	gtdb_to_taxdump		gtdb_to_taxdump	Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI.	Data handling, Mapping, Generation	Computational biology	Up-to-date	https://github.com/nick-youngblut/gtdb_to_taxdump	Metagenomics	gtdb_to_taxdump	iuc	https://github.com/nick-youngblut/gtdb_to_taxdump	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump	0.1.9	gtdb_to_taxdump	0.1.9	Data handling, Mapping, Generation	Computational biology	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gtdbtk	gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 	GTDB-Tk	GTDB-Tk		GTDB-Tk	a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	To update	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.3.2	gtdbtk	2.4.0	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gtfToBed12	gtftobed12	Convert GTF files to BED12 format	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README	Convert Formats	gtftobed12	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12	357	ucsc-gtftogenepred	469		Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1200	8107
-gubbins	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins		Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	145	3340
-gvcftools	gvcftools_extract_variants	gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf.								To update	https://github.com/sequencing/gvcftools	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools	0.1	gvcftools	0.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gwastools	gwastools_manhattan_plot		gwastools	gwastools		GWASTools	Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.	Deposition, Analysis, Annotation	GWAS study	To update	https://bioconductor.org/packages/release/bioc/html/GWASTools.html	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools	0.1.0	bioconductor-gwastools	1.48.0	Deposition, Analysis, Annotation	GWAS study	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
-hamronization	hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization		hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	117	4459
-hansel	bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	Biohansel		BioHansel	BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	339
-hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	295
-happy	som.py	A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets.	hap.py	hap.py		hap.py	This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison.	Variant calling, Sequence analysis, Genotyping	Genomics, DNA polymorphism	To update	https://github.com/Illumina/hap.py	Variant Analysis	happy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy	0.3.14	hap.py	0.3.15	Variant calling, Sequence analysis, Genotyping	Genomics, DNA polymorphism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-heatmap2	ggplot2_heatmap2	heatmap.2 function from the R gplots package								To update	https://github.com/cran/gplots	Visualization	ggplot2_heatmap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2	3.1.3.1	r-gplots	2.17.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1953	44240
-heinz	heinz_bum, heinz, heinz_scoring, heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	heinz	bionet, heinz		Heinz	Tool for single-species active module discovery.	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	To update	https://github.com/ls-cwi/heinz	Transcriptomics, Visualization, Statistics	heinz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz	1.0	bioconductor-bionet	1.62.0	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	242	1186
-hgvsparser	hgvsparser	Parsing and building variant descriptor strings compliant with the HGVS standard								To update	https://github.com/VariantEffect/hgvsParseR/tree/master	Variant Analysis	hgvsparser	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-hicexplorer	hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations	HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.								Up-to-date	https://github.com/deeptools/HiCExplorer	Sequence Analysis, Visualization	hicexplorer	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer	3.7.5	hicexplorer	3.7.5			38	38	38	4	38	38	38	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	36	33	0	1085	66003
-hicstuff	hicstuff_pipeline	A toolkit to generate and manipulate Hi-C matrices								To update	https://github.com/koszullab/hicstuff	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff	3.1.5	hicstuff	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	1410
-hifiasm_meta	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	hifiasm-meta		Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	Sequence assembly	Sequence assembly, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	137
-hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	4183	299104
-hivclustering	hivclustering	Infers transmission networks from pairwise distances inferred by tn93								To update	https://pypi.org/project/hivclustering/	Next Gen Mappers	hivclustering	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering	1.3.1	python-hivclustering	1.6.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-hmmer3	hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	hmmer3	hmmer3		HMMER3	This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	0	12	12	12	0	12	12	12	0	0	0	0	12	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	0	439	33702
-homer	homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide	HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.	homer	homer		homer	HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein).  It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other.  It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment.  HOMER also tries its best to account for sequenced bias in the dataset.  It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.	Sequence motif discovery		Up-to-date	http://homer.ucsd.edu/homer/index.html	Sequence Analysis	data_manager_homer_preparse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer	4.11	homer	4.11	Sequence motif discovery		0	0	5	4	0	0	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	5	0	0	394	6937
-htseq_count	htseq_count	Count aligned reads (SAM/BAM) that overlap genomic features (GFF)	htseq	htseq		HTSeq	Python framework to process and analyse high-throughput sequencing (HTS) data	Nucleic acid sequence analysis	Sequence analysis	Up-to-date	https://readthedocs.org/projects/htseq/	Genomic Interval Operations, SAM, Sequence Analysis, RNA	htseq_count	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count	2.0.5	htseq	2.0.5	Nucleic acid sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1419	154533
-humann	humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	humann	humann		humann	HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	To update	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.8	humann	3.9	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	6	13	13	13	6	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	13	0	1045	19521
-hybpiper	hybpiper	Analyse targeted sequence capture data	HybPiper	HybPiper		HybPiper	Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	To update	https://github.com/mossmatters/HybPiper	Sequence Analysis, Phylogenetics	hybpiper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper	2.1.6	hybpiper	2.2.0	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-hyphy	hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy		HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.62	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	17	2	17	2	17	2	17	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	17	12	0	161	10370
-hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354
-icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	69	1127
-idr	idr	Galaxy wrappers for the IDR package from Nathan Boleu								To update	https://github.com/nboley/idr	Sequence Analysis	idr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr	2.0.3	idr	2.0.4.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	30	2873
-idr_download	idr_download_by_ids	Image Data Resource downloading tool								To update	https://idr.openmicroscopy.org	Data Source	idr_download_by_ids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download	0.44.1	omero-py	5.11.1			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	361
-iedb_api	iedb_api	Get epitope binding predictions from IEDB-API								To update	http://tools.immuneepitope.org/main/tools-api/	Data Source, Sequence Analysis	iedb_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api	2.15.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	12	1506
-infercnv	infercnv	Infer Copy Number Variation from Single-Cell RNA-Seq Data								Up-to-date	https://github.com/broadinstitute/infercnv	Transcriptomics, Variant Analysis	infercnv	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv	1.20.0	bioconductor-infercnv	1.20.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-instrain	instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	instrain	instrain		InStrain	InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	SNP detection, Genome comparison	Mapping, Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	94
-integron_finder	integron_finder	"""IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"""	integron_finder	integron_finder		Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.5	integron_finder	2.0.5	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	58	52965
-intermine_galaxy_exchange	galaxy_intermine_exchange	InterMine Exporter								To update	https://github.com/intermine	Convert Formats	intermine_galaxy_exchange	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange	https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange	0.0.1	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	44
-interproscan	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi		InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	677	35243
-interval2maf	Interval2Maf1	Extract MAF blocks given a set of intervals	bx-python	bx-python		bx-python	Tools for manipulating biological data, particularly multiple sequence alignments.		Sequence analysis	To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	interval2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf	1.0.1+galaxy1	bx-python	0.12.0		Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	105
-intervene	intervene_pairwise, intervene_upset	Create pairwise and upset plots	intervene	intervene		Intervene	Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps.	Sequence comparison, Sequence visualisation	Computational biology	Up-to-date	https://intervene.readthedocs.io	Statistics	intervene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene	0.6.5	intervene	0.6.5	Sequence comparison, Sequence visualisation	Computational biology	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	136	1497
-iqtree	iqtree	Efficient phylogenomic software by maximum likelihood	iqtree	iqtree		iqtree	A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time	Phylogenetic analysis, Sequence analysis	Phylogenetics	Up-to-date	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.3.6	iqtree	2.3.6	Phylogenetic analysis, Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	681	21598
-irissv	irissv	Refine insertion sequences								To update	https://github.com/mkirsche/Iris	Variant Analysis	irissv	iuc	https://github.com/galaxyproject/tools-iuc/tools/irissv/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv	1.0.5	samtools	1.20			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	29
-isescan	isescan	"""ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."""	ISEScan	ISEScan		ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	Structural variation detection	Genomics, Sequence analysis, Genetic variation	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	50	57581
-isoformswitchanalyzer	isoformswitchanalyzer	Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.	IsoformSwitchAnalyzeR	IsoformSwitchAnalyzeR		IsoformSwitchAnalyzeR	Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	To update	https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html	Transcriptomics, RNA, Statistics	isoformswitchanalyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer	1.20.0	bioconductor-isoformswitchanalyzer	2.2.0	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	822
-ivar	ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing								Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.3	ivar	1.4.3			5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	4	0	0	0	4	0	0	0	0	0	0	0	5	5	0	1171	1224275
-iwtomics	iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot	Interval-Wise Testing for Omics Data	iwtomics	iwtomics		IWTomics	"Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset."	Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison	Statistics and probability	To update	https://bioconductor.org/packages/release/bioc/html/IWTomics.html	Statistics	iwtomics	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics	1.0.0	bioconductor-iwtomics	1.26.0	Differential gene expression analysis, Peak calling, Genome annotation, Comparison	Statistics and probability	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	3	542
-jasminesv	jasminesv	Merge structural variants across samples								To update	https://github.com/mkirsche/Jasmine/	Variant Analysis	jasminesv	iuc	https://github.com/galaxyproject/tools-iuc/jasminesv/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv	1.0.11	jasminesv	1.1.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	30
-jbrowse	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse		JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	Genome visualisation	Genomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	2	2	0	2346	18229
-jcvi_gff_stats	jcvi_gff_stats	Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)								To update	https://github.com/tanghaibao/jcvi	Sequence Analysis	jcvi_gff_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats	0.8.4	jcvi	1.4.16			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	255	2469
-jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138
-join_files_by_id	join_files_by_id	This tool will join datasets according to a column with identifier								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id	Text Manipulation	join_files_by_id	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id	https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id	1.0	r-data.table	1.11.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-jq	jq	JQ is a lightweight and flexible command-line JSON processor								To update	https://stedolan.github.io/jq/	Text Manipulation	jq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq	1.0	jq	1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	21	2312
-jvarkit	jvarkit_wgscoverageplotter	Jvarkit : Java utilities for Bioinformatics								Up-to-date	https://lindenb.github.io/jvarkit/	SAM	jvarkit	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit	20201223	jvarkit-wgscoverageplotter	20201223			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	249	6285
-kallisto	kallisto_pseudo, kallisto_quant	kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment.	kallisto	kallisto		kallisto	A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.	Gene expression profiling	Transcriptomics, RNA-seq, Gene expression	To update	https://pachterlab.github.io/kallisto/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto	0.48.0	kallisto	0.51.0	Gene expression profiling	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	299	24155
-kc-align	kc-align	Kc-Align custom tool	kc-align	kc-align		kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	Multiple sequence alignment	Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	19	363
-khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	8	8	0	63	2022
-king	king	Kinship-based INference for Gwas								Up-to-date	http://people.virginia.edu/~wc9c/KING/	Variant Analysis	king	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/king	2.2.7	king	2.2.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	5
-kleborate	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	kleborate	kleborate		Kleborate	Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	To update	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	3.0.6	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	38	319
-kma	kma_map	Map with KMA								To update	https://bitbucket.org/genomicepidemiology/kma	Next Gen Mappers	kma	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma	1.4.14	kma	1.4.15			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0
-kofamscan	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	kofamscan	kofamscan		kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	Sequence analysis, Gene functional annotation	Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	33	594
-kraken	kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	kraken	kraken		Kraken	System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	Taxonomic classification	Taxonomy, Metagenomics	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	5	0	1209	33778
-kraken2	kraken2	Kraken2 for taxonomic designation.	kraken2	kraken2		kraken2	Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	Up-to-date	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.3	kraken2	2.1.3	Taxonomic classification	Taxonomy, Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	0	1	1	0	2367	185308
-kraken_biom	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)								Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	182	1444
-kraken_taxonomy_report	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report		Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	Visualisation, Classification	Metagenomics, Taxonomy	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	354	2527
-krakentools	krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	krakentools		KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	Visualisation, Aggregation	Taxonomy, Metagenomics	6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	1	4	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	703	16525
-krocus	krocus	Predict MLST directly from uncorrected long reads	krocus	krocus		krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	Multilocus sequence typing, k-mer counting	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-last	last_al, last_db, last_split, last_train, last_maf_convert	LAST finds similar regions between sequences.	last	last		LAST	Short read alignment program incorporating quality scores	Sequence alignment	Genomics, Comparative genomics	To update	http://last.cbrc.jp/	Sequence Analysis	last	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/last	https://github.com/galaxyproject/tools-iuc/tree/main/tools/last	1205	last	1574	Sequence alignment	Comparative genomics	0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	41	227
-lastz	lastz_wrapper_2, lastz_d_wrapper	Galaxy wrappers for the Lastz and Lastz_d	lastz	lastz		LASTZ	A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically.	Sequence alignment, Read mapping	Genomics	Up-to-date	https://github.com/lastz/lastz	Next Gen Mappers	lastz	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz	1.04.22	lastz	1.04.22	Sequence alignment, Read mapping	Genomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	188	83331
-lcrgenie	lcrgenie	Ligase Chain Reaction Genie								To update	https://github.com/neilswainston/LCRGenie	Synthetic Biology	lcrgenie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie	1.0.2	lcr_genie				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-legsta	legsta	Performs in silico Legionella pneumophila sequence based typing.	legsta	legsta		legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	Sequence analysis	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	55
-length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	322	4090
-limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1012	20344
-lineagespot	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	lineagespot	lineagespot		lineagespot	Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	37
-links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	77	405
-lofreq	lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi	LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering.								Up-to-date	https://csb5.github.io/lofreq/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq	2.1.5	lofreq	2.1.5			5	5	5	4	5	5	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	0	0	0	4	0	0	0	0	0	0	0	5	5	0	1791	4150903
-lorikeet	lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet		lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	Sequence analysis, Genotyping	Genotype and phenotype	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	647
-lumpy_sv	lumpy_prep, lumpy_sv	LUMPY - a general probabilistic framework for structural variant discovery								Up-to-date	http://layerlab.org/software/	Variant Analysis	lumpy_sv	iuc	https://github.com/arq5x/lumpy-sv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv	0.3.1	lumpy-sv	0.3.1			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	105	1164
-m6anet	m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet		m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3
-maaslin2	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	maaslin2	maaslin2		MaAsLin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	To update	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	1.16.0	bioconductor-maaslin2	1.18.0	Filtering, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	188
-macs2	macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak	MACS - Model-based Analysis of ChIP-Seq	macs	macs		MACS	Model-based Analysis of ChIP-seq data.	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	Up-to-date	https://github.com/taoliu/MACS	Sequence Analysis, Statistics	macs2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2	2.2.9.1	macs2	2.2.9.1	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	9	9	9	9	9	9	9	9	0	9	0	0	0	0	0	0	0	0	0	0	9	9	0	0	0	0	0	0	0	9	0	0	0	0	0	0	0	9	9	0	1969	84521
-maf_stats	maf_stats1	MAF Coverage statistics								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	maf_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats	1.0.2+galaxy0					1	1	1	1	1	1	1	1	0	1	1	0	1	0	0	1	0	0	0	1	1	1	0	1	0	0	0	0	0	1	0	0	0	0	1	0	0	1	1	0	3	21
-maftoaxt	maftoaxt	Convert dataset from MAF to axt format	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_maftoaxt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/maftoaxt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt	377	ucsc-maftoaxt	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mageck	mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test	Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.	mageck	mageck		MAGeCK	Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.	Genetic variation analysis	Genetics, Genetic variation, Genomics	To update	https://sourceforge.net/projects/mageck/	Genome editing		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck	0.5.9.2	mageck	0.5.9.5	Genetic variation analysis	Genetics, Genetic variation, Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	587	10503
-maker	maker, maker_map_ids	MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	maker	maker		MAKER	Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	Genome annotation	Genomics, DNA, Sequence analysis	To update	http://www.yandell-lab.org/software/maker.html	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker	2.31.11	maker	3.01.03	Genome annotation	Genomics, DNA, Sequence analysis	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	554	5591
-malt	malt_run	Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences.								To update	https://github.com/husonlab/malt	Next Gen Mappers	malt_run	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt	0.5.3	malt	0.62			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	22
-map_param_value	map_param_value	Map a parameter value to another value								To update		Text Manipulation	map_param_value	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value	https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value	0.2.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	1528
-mapseq	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	mapseq	mapseq		MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .	k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	To update	https://github.com/jfmrod/MAPseq	Metagenomics	mapseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq	2.1.1	perl		k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	167
-mash	mash_screen, mash_sketch	Fast genome and metagenome distance estimation using MinHash	mash	mash		Mash	Fast genome and metagenome distance estimation using MinHash.	Sequence distance matrix generation	Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	Up-to-date	https://github.com/marbl/Mash	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash	2.3	mash	2.3	Sequence distance matrix generation	Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	27	9763
-mashmap	mashmap	Fast local alignment boundaries								Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	Sequence Analysis	mashmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap	3.1.3	mashmap	3.1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-masigpro	masigpro	Identify significantly differential expression profiles in time-course microarray experiments	masigpro	masigpro		maSigPro	Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.	Regression analysis	Gene expression, Molecular genetics, Microarray experiment, RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html	Transcriptomics, RNA, Statistics	masigpro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro	1.49.3	coreutils	8.25	Regression analysis	Gene expression, Microarray experiment, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	576
-maxbin2	maxbin2	clusters metagenomic contigs into bins	maxbin	maxbin		MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	To update	https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html	Metagenomics	maxbin2	mbernt	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2		maxbin2	2.2.7	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	0	118	2059
-mcl	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	mcl	mcl		MCL	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.	Clustering, Network analysis, Gene regulatory network analysis	Molecular interactions, pathways and networks	Up-to-date	https://micans.org/mcl/man/mcl.html	Sequence Analysis	mcl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/mcl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl	22.282	mcl	22.282	Clustering, Gene regulatory network analysis	Molecular interactions, pathways and networks	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	29
-medaka	medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	medaka	medaka		Medaka	medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	1.11.3	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	2	0	0	0	0	0	0	0	3	3	0	768	99863
-megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	0	1	1	0	548	9530
-megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	54	475
-megan	megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma	MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data.  MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).	megan	megan		MEGAN	Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Sequence analysis, Taxonomic classification	Sequence analysis	To update	https://github.com/husonlab/megan-ce	Sequence Analysis	megan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan	6.21.7	megan	6.25.9	Sequence analysis, Taxonomic classification	Sequence analysis	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	261	3610
-meme	meme_dreme, meme_fimo, meme_meme, meme_psp_gen	The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses.	meme_meme	meme_meme, meme_fimo		meme_meme	An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.	Nucleic acid feature detection, Protein feature detection, Statistical calculation	Data mining, Sequence analysis, Genetic variation, Statistics and probability	To update	http://meme-suite.org/	ChIP-seq	meme	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme	5.5.6	meme	5.5.7	Nucleic acid feature detection, Protein feature detection, Statistical calculation	Data mining, Sequence analysis, Genetic variation, Statistics and probability	3	0	4	0	3	0	4	0	0	2	0	0	2	0	0	0	0	0	0	0	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	235	22352
-meme_chip	meme_chip	Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.								To update	http://meme-suite.org/	ChIP-seq	meme_chip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip	4.11.2	graphicsmagick	1.3.26			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	287	6584
-meningotype	meningotype	Assign sequence type to N. meningitidis genome assemblies	meningotype	meningotype		meningotype	In silico typing of Neisseria meningitidis contigs.	Genotyping, Multilocus sequence typing	Microbiology, Genotype and phenotype	Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype	0.8.5	meningotype	0.8.5	Multilocus sequence typing	Microbiology, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-merlin	merlin	Pedigree Analysis package	merlin	merlin		Merlin	Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation	Haplotype mapping, Genetic mapping	GWAS study, Mapping	Up-to-date	http://csg.sph.umich.edu/abecasis/Merlin/	Variant Analysis	merlin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin	1.1.2	merlin	1.1.2	Haplotype mapping	GWAS study, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483
-meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-metabat2	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT_2		MetaBAT 2	"an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning"	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	To update	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.17	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	2	1	2	2	2	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	192	4329
-metabuli	metabuli_classify	Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences	metabuli	metabuli		metabuli	Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid	Taxonomic classification	Taxonomy	Up-to-date	https://github.com/steineggerlab/Metabuli	Sequence Analysis, Metagenomics	metabuli	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli	1.0.5	metabuli	1.0.5	Taxonomic classification	Taxonomy	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	5.34c21f2	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	184
-metagenomeseq	metagenomeseq_normalizaton	metagenomeSeq Normalization	metagenomeseq	metagenomeseq		metagenomeSeq	Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	To update	https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html	Metagenomics	metagenomeseq_normalization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq	1.16.0-0.0.1	bioconductor-metagenomeseq	1.43.0	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	753
-metaphlan	customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	metaphlan	metaphlan		MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.	Nucleic acid sequence analysis, Phylogenetic tree analysis	Metagenomics, Phylogenomics	Up-to-date	https://github.com/biobakery/MetaPhlAn	Metagenomics	metaphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan	4.1.1	metaphlan	4.1.1	Nucleic acid sequence analysis	Metagenomics, Phylogenomics	1	2	4	4	1	2	4	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	499	11069
-metawrapmg	metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	metawrap	metawrap		MetaWRAP	MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	Up-to-date	https://github.com/bxlab/metaWRAP	Metagenomics	metawrapmg_binning	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg	1.3.0	metawrap-mg	1.3.0	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mg_toolkit	mg_toolkit_bulk_download, mg_toolkit_original_metadata	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	mg-toolkit	mg-toolkit		mg-toolkit	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	Data retrieval	Metagenomics	Up-to-date	https://github.com/EBI-Metagenomics/emg-toolkit	Metagenomics	mg_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	0.10.4	mg-toolkit	0.10.4	Data retrieval	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-microsatbed	microsatbed	Select microsatellites for a bed file								To update	https://github.com/lmdu/pytrf	Sequence Analysis	microsatbed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed	1.3.2	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-migmap	migmap	mapper for full-length T- and B-cell repertoire sequencing	MiGMAP	MiGMAP		MiGMAP	Mapper for full-length T- and B-cell repertoire sequencing.	Sequence analysis, Read mapping	Immunoproteins, genes and antigens, Sequence analysis	Up-to-date	https://github.com/mikessh/migmap	RNA, Sequence Analysis	migmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap	1.0.3	migmap	1.0.3	Sequence analysis, Read mapping	Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	1226
-minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	109	2206
-miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	178	11938
-minimap2	minimap2	A fast pairwise aligner for genomic and spliced nucleotide sequences	minimap2	minimap2		Minimap2	Pairwise aligner for genomic and spliced nucleotide sequences	Pairwise sequence alignment	Mapping	Up-to-date	https://github.com/lh3/minimap2	Next Gen Mappers	minimap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2	2.28	minimap2	2.28	Pairwise sequence alignment	Mapping	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1588	260442
-miniprot	miniprot, miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	miniprot	miniprot		miniprot	Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	Up-to-date	https://github.com/lh3/miniprot	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot	0.13	miniprot	0.13	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	30	842
-mirmachine	mirmachine	Tool to detect miRNA in genome sequences								Up-to-date	https://github.com/sinanugur/MirMachine	Sequence Analysis	mirmachine	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine	0.2.13	mirmachine	0.2.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mirnature	mirnature	Computational detection of canonical microRNAs								Up-to-date	https://github.com/Bierinformatik/miRNAture	RNA, Sequence Analysis	mirnature	iuc	https://github.com/Bierinformatik/miRNAture	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature	1.1	mirnature	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	10
-mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	66	881
-mitos	mitos, mitos2	de-novo annotation of metazoan mitochondrial genomes	mitos	mitos		MITOS	De novo metazoan mitochondrial genome annotation.	Genome annotation	Zoology, Whole genome sequencing	To update	http://mitos.bioinf.uni-leipzig.de/	Sequence Analysis	mitos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos	1.1.7	mitos	2.1.9	Genome annotation	Zoology, Whole genome sequencing	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	1	0	236	100920
-mlst	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst		MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	Multilocus sequence typing	Immunoproteins and antigens	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	635	9304
-moabs	moabs	MOABS for differential methylation analysis on Bisulfite sequencing data.								To update	https://github.com/sunnyisgalaxy/moabs	Epigenetics	moabs	iuc	https://github.com/sunnyisgalaxy/moabs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs	1.3.4.6	moabs	1.3.9.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	19	317
-mosdepth	mosdepth	fast and flexible BAM/CRAM depth calculation								Up-to-date	https://github.com/brentp/mosdepth	SAM	mosdepth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth	0.3.8	mosdepth	0.3.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	262
-mothur	mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn	Mothur wrappers	mothur	mothur		mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	129	129	129	129	129	129	129	129	0	3	0	0	0	0	0	0	0	0	0	0	128	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	129	129	0	14353	302916
-msaboot	msaboot	A multiple sequences alignment bootstrapping tool.								Up-to-date	https://github.com/phac-nml/msaboot	Fasta Manipulation	msaboot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot	0.1.2	msaboot	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	803
-multigps	multigps	Analyzes collections of multi-condition ChIP-seq data.								To update	http://mahonylab.org/software/multigps/	ChIP-seq	multigps	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps	0.74.0	fonts-conda-ecosystem				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	53
-multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.11	multiqc	1.24.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	8320	162790
-mummer4	mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords	Mummer4 Tools	mummer4	mummer4						Up-to-date	https://github.com/mummer4/mummer	Sequence Analysis	mummer4	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4	4.0.0rc1	mummer4	4.0.0rc1			6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	6	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	669	18347
-mykrobe	mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe		Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mzmine	mzmine_batch	mass-spectrometry data processing, with the main focus on LC-MS data	mzmine	mzmine		MZmine	Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML.	Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation	Proteomics, Metabolomics, Proteomics experiment, Small molecules	Up-to-date	http://mzmine.github.io/	Metabolomics	mzmine_batch	iuc	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine	3.9.0	mzmine	3.9.0	Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation	Proteomics, Metabolomics, Proteomics experiment, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3
-naltorfs	bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs	nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)								Up-to-date	https://github.com/BlankenbergLab/nAltORFs	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs	0.1.2	naltorfs	0.1.2			3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-nanocompore	nanocompore_db, nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Nanocompore	Nanocompore		Nanocompore	RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	3	836
-nanoplot	nanoplot	Plotting tool for long read sequencing data and alignments	nanoplot	nanoplot		NanoPlot	NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences	Scatter plot plotting, Box-Whisker plot plotting	Genomics	Up-to-date	https://github.com/wdecoster/NanoPlot	Visualization	nanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot	1.43.0	nanoplot	1.43.0	Scatter plot plotting, Box-Whisker plot plotting	Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	2195	63235
-nanopolishcomp	nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate	NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.	nanopolishcomp	nanopolishcomp		NanopolishComp	NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	To update	https://a-slide.github.io/NanopolishComp	Sequence Analysis	nanopolishcomp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp	0.6.11	nanopolishcomp	0.6.12	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	15	1074
-ncbi_acc_download	ncbi_acc_download	Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API								Up-to-date	https://github.com/kblin/ncbi-acc-download	Data Source	ncbi_acc_download	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download	0.2.8	ncbi-acc-download	0.2.8			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	688	5487
-ncbi_datasets	datasets_download_gene, datasets_download_genome	NCBI datasets downloads biological sequence data across all domains of life from NCBI.	ncbi_datasets	ncbi_datasets		NCBI Datasets	NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface.	Data handling, Sequence database search, Data retrieval	Biological databases	To update	https://github.com/ncbi/datasets	Data Source	ncbi_datasets	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets	16.20.0	ncbi-datasets-cli		Data handling, Sequence database search, Data retrieval	Biological databases	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	667	3177
-ncbi_entrez_direct	ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch	NCBI Entrez Direct allow fetching data from NCBI Databases								Up-to-date	http://www.ncbi.nlm.nih.gov/books/NBK179288/	Data Source	ncbi_entrez_direct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct	22.4	entrez-direct	22.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ncbi_entrez_eutils	ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_egquery, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary	NCBI Entrez E-Utilties allow fetching data from NCBI Databases								To update	https://www.ncbi.nlm.nih.gov/books/NBK25501/	Data Source	ncbi_entrez_eutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils	1.70	python				0	0	8	0	0	0	8	0	0	0	0	0	8	0	0	0	0	0	0	0	0	0	4	0	0	4	0	0	0	2	0	0	0	0	0	0	0	8	8	0	169	3193
-ncbi_fcs_gx	ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).	ncbi_fcs	ncbi_fcs		NCBI fcs	The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	Up-to-date	https://github.com/ncbi/fcs-gx	Sequence Analysis	ncbi_fcs_gx	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	0.5.4	ncbi-fcs-gx	0.5.4	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	95	667
-newick_utils	newick_display	Perform operations on Newick trees	newick_utilities	newick_utilities		Newick Utilities	The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.	Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction	Phylogeny, Genomics, Computer science	To update	http://cegg.unige.ch/newick_utils	Visualization, Metagenomics	newick_utils	iuc	https://github.com/tjunier/newick_utils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils	1.6+galaxy1	newick_utils	1.6		Phylogeny, Genomics, Computer science	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	448	25505
-nextclade	nextalign, nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	nextclade	nextclade		Nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.	Methylation analysis, Variant calling	Genomics, Sequence analysis, Cladistics	To update	https://github.com/nextstrain/nextclade	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade	2.7.0	nextalign	2.14.0	Methylation analysis, Variant calling	Genomics, Cladistics	1	1	2	2	1	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	0	0	0	1	0	0	0	0	0	0	0	2	0	0	210	4080
-ngmlr	ngmlr	CoNvex Gap-cost alignMents for Long Reads	ngmlr	ngmlr		NGMLR	An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation.	DNA mapping, Sequence alignment, Genetic variation analysis	Sequencing, Mapping, DNA structural variation	Up-to-date	https://github.com/philres/ngmlr	Next Gen Mappers	ngmlr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr	0.2.7	ngmlr	0.2.7	DNA mapping, Sequence alignment, Genetic variation analysis	Sequencing, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	1266
-ngsutils	ngsutils_bam_filter	NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed.	ngsutils	ngsutils		NGSUtils	NGSUtils is a suite of software tools for working with next-generation sequencing datasets	Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering	Genomics, Transcriptomics	To update	https://github.com/ngsutils/ngsutils	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils		ngsutils	0.5.9	Read pre-processing, Variant calling, Formatting, Sequence contamination filtering	Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	224	24740
-nonpareil	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil		nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.5.5	Operation		1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	142
-novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	162	6384
-nugen_nudup	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-obitools	obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq	OBITools is a set of programs developed to simplify the manipulation of sequence files	obitools	obitools		OBITools	Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	Up-to-date	http://metabarcoding.org/obitools	Sequence Analysis	obitools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools	1.2.13	obitools	1.2.13	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	0	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	503	26251
-ococo	ococo	Variant detection of SNVs								To update	https://github.com/karel-brinda/ococo	Variant Analysis	ococo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo	0.1.2.6	ococo	0.1.2.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	32	1877
-odgi	odgi_build, odgi_viz	Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.								To update	https://github.com/vgteam/odgi	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi	0.3	odgi	0.8.6			0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2	25
-omark	omark	Proteome quality assessment software	omark	omark		OMArk	Proteome quality assessment software	Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	To update	https://github.com/DessimozLab/OMArk	Sequence Analysis	omark	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark	0.3.0			Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	39	2654
-onto_toolkit	onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def	ONTO-Toolkit is a collection of tools for managing ontologies.								Up-to-date	http://search.cpan.org/~easr/ONTO-PERL-1.45/	Ontology Manipulation	onto_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit	1.45	perl-onto-perl	1.45			0	0	17	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	0	22	655
-optdoe	optdoe	Optimal Design Of Experiment								To update	https://github.com/pablocarb/doebase	Synthetic Biology	optdoe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe	v2.0.2	doebase				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-optitype	optitype	Precision HLA typing from NGS data								Up-to-date	https://github.com/FRED-2/OptiType	Sequence Analysis	optitype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype	1.3.5	optitype	1.3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	321
-orfipy	orfipy	Galaxy wrapper for ORFIPY	orfipy	orfipy		orfipy	A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	Up-to-date	https://github.com/urmi-21/orfipy	Sequence Analysis	orfipy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy	0.0.4	orfipy	0.0.4	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	774
-orthofinder	orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	OrthoFinder	OrthoFinder		OrthoFinder	OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.	Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis	Up-to-date	https://github.com/davidemms/OrthoFinder	Phylogenetics, Sequence Analysis	orthofinder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder	2.5.5	orthofinder	2.5.5	Genome comparison, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics	0	1	1	1	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	239	1333
-packaged_annotation_loader	packaged_annotation_loader	Tool to make cached genome annotation data available as a list of datasets collection								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader	Data Source	packaged_annotation_loader	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader	https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader	0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pacu	pacu_map, pacu_snp	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.	pacu	pacu		PACU	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads).	Clustering	Phylogenetics, Sequence analysis	Up-to-date	https://github.com/BioinformaticsPlatformWIV-ISP/PACU	Sequence Analysis, Phylogenetics	pacu	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu	0.0.5	pacu_snp	0.0.5	Clustering	Phylogenetics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pairtools	pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats	Flexible tools for Hi-C data processing								Up-to-date	https://pairtools.readthedocs.io	Sequence Analysis	pairtools	iuc	https://github.com/open2c/pairtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools	1.1.0	pairtools	1.1.0			5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pangolin	pangolin	Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.	pangolin_cov-lineages	pangolin_cov-lineages		pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages	Tree-based sequence alignment, Variant classification	Virology	Up-to-date	https://github.com/cov-lineages/pangolin	Sequence Analysis	pangolin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin	4.3	pangolin	4.3	Tree-based sequence alignment, Variant classification	Virology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	259	7276
-parse_mito_blast	parse_mito_blast	Filtering blast out from querying assembly against mitochondrial database.								Up-to-date	https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py	Sequence Analysis	parse_mito_blast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast	1.0.2	parse_mito_blast	1.0.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	31	90
-pathview	pathview	Pathview is a tool set for pathway based data integration and visualization.	pathview	pathview		pathview	Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	To update	https://bioconductor.org/packages/release/bioc/html/pathview.html	Statistics, RNA, Micro-array Analysis	pathview	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview	1.34.0	bioconductor-pathview	1.42.0	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	565	5260
-pbgcpp	pbgcpp	Compute genomic consensus and call variants using PacBio reads mapped to a reference	genomicconsensus	genomicconsensus		GenomicConsensus	The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.	Variant calling	Mapping	Up-to-date	https://github.com/PacificBiosciences/gcpp	Variant Analysis	pbgcpp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp	2.0.2	pbgcpp	2.0.2	Variant calling	Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pbmm2	pbmm2	A minimap2 SMRT wrapper for PacBio data.	pbmm2	pbmm2		pbmm2	pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.	Pairwise sequence alignment, Sorting	Mapping	Up-to-date	https://github.com/PacificBiosciences/pbmm2	Next Gen Mappers	pbmm2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2	1.14.99	pbmm2	1.14.99	Pairwise sequence alignment, Sorting	Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pbtk	bam2fastx	Convert PacBio Bam File to fasta or fastq file								Up-to-date	https://github.com/PacificBiosciences/pbtk	Convert Formats, Fasta Manipulation, Fastq Manipulation	bam2fastx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk	3.1.1	pbtk	3.1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pe_histogram	pe_histogram	Contains a tool that produces an insert size histogram for a paired-end BAM file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram	Graphics	pe_histogram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram	1.0.1	openjdk				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	312	4180
-peakzilla	peakzilla	Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments.								To update	https://github.com/steinmann/peakzilla	ChIP-seq	peakzilla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla	1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pear	iuc_pear	PEAR evaluates all possible paired-end read overlaps	pear	pear		PEAR	Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.	Sequence merging	Sequence assembly	Up-to-date	https://cme.h-its.org/exelixis/web/software/pear/	Fastq Manipulation	pear	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear	0.9.6	pear	0.9.6	Sequence merging	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	150	4305
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)
+2d_auto_threshold	ip_threshold	Automatic thresholding	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_auto_threshold	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39	6541
+2d_feature_extraction	ip_2d_feature_extraction	2D feature extraction	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_feature_extraction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19	13760
+2d_filter_segmentation_by_features	ip_2d_filter_segmentation_by_features	filter segmentation by rules	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	2d_filter_segmentation_by_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features	0.0.1-4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	6834
+2d_histogram_equalization	ip_histogram_equalization	2d histogram equalization	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_histogram_equalization	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39	656
+2d_simple_filter	ip_filter_standard	2d simple filter			scipy					To update	https://github.com/bmcv	Imaging	2d_simple_filter	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter	1.12.0	scipy				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	35	6156
+3d_tensor_feature_dimension_reduction	ip_3d_tensor_feature_dimension_reduction	Dimensionality reduction for features (channels) of 3D tensor data using UMAP								To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	3d_tensor_feature_dimension_reduction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction	0.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Ensembl-REST	get_feature_info, get_genetree, get_sequences	A suite of Galaxy tools designed to work with Ensembl REST API.								To update	https://rest.ensembl.org	Data Source		earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST	0.1.2	requests				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	47	2889
+GAFA	gafa	Gene Align and Family Aggregator								To update	http://aequatus.tgac.ac.uk	Visualization	gafa	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA	0.3.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	45
+TreeBest	treebest_best	TreeBeST best	treebest	treebest		TreeBeST	TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	984
+abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+anisotropic_diffusion	ip_anisotropic_diffusion	Anisotropic image diffusion								Up-to-date	https://github.com/bmcv	Imaging	anisotropic_diffusion	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion	0.4.0	medpy	0.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	40
+apoc	apoc	Large-scale structural comparison of protein pockets								To update	http://cssb.biology.gatech.edu/APoc	Computational chemistry	apoc	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc	1.0+galaxy1	apoc	1b16			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	3
+apollo	create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism	Access an Apollo instance from Galaxy								To update	https://github.com/galaxy-genome-annotation/python-apollo	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo		apollo	4.2.13			0	0	9	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	0	301	1896
+askomics	askomics_integrate	Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/								To update	https://github.com/askomics/	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics		askocli	0.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+askor	askor_de	AskoR links EdgeR and AskOmics								To update	https://github.com/askomics/askoR	Transcriptomics	askor_de	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	0.2	bioconductor-limma	3.58.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+background_removal	background_removal	Background removal filters using scikit-image								To update	https://github.com/bmcv	Imaging	background_removal	imgteam	https://github.com/BMCV/galaxy-image-analysis/tools/background_removal	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal	0.24.0	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+bamclipper	bamclipper	Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.								Up-to-date	https://github.com/tommyau/bamclipper	Sequence Analysis	bamclipper	nml	https://github.com/tommyau/bamclipper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper	1.0.0	bamclipper	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+baric_archive	baric_archive_rennes, baric_archive_toulouse	A data source tool to fetch data from a BARIC Archive server.								To update	https://www.cesgo.org/catibaric/	Data Source		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive	https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive	1.1.0					0	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+batched_lastz	batched_lastz	Galaxy wrapper for the batching Lastz runs								Up-to-date	https://github.com/galaxyproject/KegAlign	Next Gen Mappers	batched_lastz	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz	https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz	1.04.22	lastz	1.04.22			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+bfconvert	ip_convertimage	Convert image			python-bioformats					Up-to-date	https://github.com/bmcv	Imaging, Convert Formats	bfconvert	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert	6.7.0	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	38	1523
+binary2labelimage	ip_binary_to_labelimage	Binary 2 label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binary2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage	0.5	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34	1273
+binaryimage2points	ip_binaryimage_to_points	Binary Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binaryimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points	0.1-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	29
+bioformats2raw	bf2raw	Convert image to OME-Zarr								To update	https://github.com/Euro-BioImaging	Imaging, Convert Formats	bioformats2raw	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	0.7.0					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9
+biohansel	biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+biohansel_bionumeric_converter	bionumeric_convert	Convert BioHansel output data to a Bionumerics friendly form								To update	https://github.com/phac-nml/galaxy_tools	Text Manipulation	biohansel_bionumeric_converter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter	0.2.0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+blast_parser	blast_parser	Convert 12- or 24-column BLAST output into 3-column hcluster_sg input								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	blast_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	0.1.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	27	296
+braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	17	109
+braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	567
+bundle_collections	bundle_collection	Tool to bundle up list collection into a single zip to be download								To update		Sequence Analysis	bundle_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections	1.3.0	perl-getopt-long	2.58			0	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+camera	abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos									To update		Metabolomics	camera	workflow4metabolomics		https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera	1.48.0	r-snow	0.4_1			1	2	2	2	1	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	2	0	30	623
+cfm	cfmid	Competitive Fragmentation Modeling (CFM)								Up-to-date	https://sourceforge.net/p/cfm-id/	Metabolomics	cfmid	computational-metabolomics	https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm	https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm	33	cfm	33			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+chado	analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree	Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado								To update	https://github.com/galaxy-genome-annotation/python-chado	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado		python-chado	2.3.9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+collapse_collection	collapse_dataset	Collection tool that collapses a list of files into a single datasset in order of appears in collection								To update		Sequence Analysis	collapse_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection	5.1.0	gawk				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1583	33934
+color-deconvolution	ip_color_deconvolution	Color-deconvolution methods	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	color_deconvolution	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution	0.8-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	16
+colorize_labels	colorize_labels	Colorize label map								To update	https://github.com/bmcv	Imaging	colorize_labels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	3.2.1	networkx				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+combineJSON	combine_json	JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.								To update		Sequence Analysis	combine_json	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+combine_tabular_collection	combine	Combine Tabular Collection into a single file								To update		Sequence Analysis	combine_tabular_collection	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+concat_channels	ip_concat_channels	Concatenate images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	concat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels	0.3-1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	78
+concat_paired	concat_fastqs	Concatenate paired datasets								To update	https://github.com/phac-nml/concat	Text Manipulation	concat_paired	nml	https://github.com/phac-nml/concat	https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired	0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+coordinates_of_roi	ip_coordinates_of_roi	Coordinates of ROI	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	coordinates_of_roi	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi	0.0.4-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	16546
+correlation_analysis	correlation_analysis	[Metabolomics][W4M] Metabolites Correlation Analysis								To update	http://workflow4metabolomics.org	Metabolomics	correlation_analysis	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis	1.0.1+galaxy0	r-batch	1.1_4			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+count_objects	ip_count_objects	Count Objects	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	count_objects	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects	0.0.5-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	25	272
+cryptogenotyper	CryptoGenotyper	CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	8518
+csvtk	csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq	Rapid data investigation and manipulation of csv/tsv files								To update	https://bioinf.shenwei.me/csvtk/	Text Manipulation	csvtk	nml	https://github.com/shenwei356/csvtk	https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk	0.20.0	csvtk	0.30.0			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	20	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+curl_post	curl_post	Send file via cURL POST								To update	https://github.com/bmcv	Data Export, Web Services	curl_post	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curl_post	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curl_post	0.0.2	curl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	27	440
+curve_fitting	ip_curve_fitting	Polynomial curve fitting to data points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	curve_fitting	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	12
+detection_viz	ip_detection_viz	Detection Visualization	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	detection_viz	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	46
+ectyper	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	9907
+ete	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete		ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	Phylogenetic tree editing	Phylogenetics	0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	45	899
+export_to_cluster	export_to_cluster	Export datasets to cluster								To update	https://github.com/TGAC/earlham-galaxytools/	Data Export	export_to_cluster	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster	0.0.2	EXPORT_DIR_PREFIX				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fasta2bed	fasta2bed	Convert multiple fasta file into tabular bed file format								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fasta2bed	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fasta_extract	fa-extract-sequence	extract single fasta from multiple fasta file								To update	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	Sequence Analysis	fasta_extract	nml	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	10
+fastqc_stats	FastQC_Summary	Summary multiple FastQC into a single tabular line report								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fastqc_stats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats	1.2	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+feelnc2asko	feelnc2asko	Convert FeelNC GTF to GFF3								To update	https://github.com/tderrien/FEELnc	Convert Formats	feelnc2asko	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko	https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko	0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+feht	feht	Automatically identify makers predictive of groups.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	feht	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht	0.1.0	feht	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gblocks	gblocks	Gblocks								Up-to-date	http://molevol.cmima.csic.es/castresana/Gblocks.html	Sequence Analysis	gblocks	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	0.91b	gblocks	0.91b			0	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
+gcms2isocor	gcms2isocor	Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs								To update	https://github.com/p2m2/p2m2tools	Metabolomics	gcms2isocor	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor	0.2.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gcms2isocor	gcms2isocor	Conversion from GCMS PostRun Analysis to Isocor								To update		Metabolomics	gcms2isocor	genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor	0.1.0	openjdk				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+genenotebook	genenotebook_build	Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io								Up-to-date	https://genenotebook.github.io	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook	0.4.16	genoboo	0.4.16			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+genform	genform	genform: generation of molecular formulas by high-resolution MS and MS/MS data								To update	https://sourceforge.net/projects/genform/	Metabolomics	genform	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform		genform	r8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	68
+get_pairs	get_pairs	Separate paired and unpaired reads from two fastq files								To update		Fastq Manipulation	get_pairs	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	0.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+getmlst	getmlst	Download MLST datasets by species from pubmlst.org								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gnali	gnali	A tool to find nonessential, loss-of-function gene variants								Up-to-date	https://github.com/phac-nml/gnali/	Variant Analysis	gnali	nml	https://github.com/phac-nml/gnali/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali	1.1.0	gnali	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gstf_preparation	gstf_preparation	GeneSeqToFamily preparation converts data for the workflow								To update	https://github.com/TGAC/earlham-galaxytools/	Convert Formats	gstf_preparation	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation	0.4.3	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	397
+hcluster_sg	hcluster_sg	Hierarchically clustering on a sparse graph								To update	https://github.com/douglasgscofield/hcluster	Phylogenetics	hcluster_sg	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	0.5.1.1	hcluster_sg	0.5.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	238
+hcluster_sg_parser	hcluster_sg_parser	Converts hcluster_sg 3-column output into lists of ids								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	hcluster_sg_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	0.2.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	290
+helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	93
+hivtrace	hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+image_info	ip_imageinfo	Extracts image metadata			python-bioformats					To update	https://github.com/bmcv	Imaging	image_info	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info	5.7.1	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	41	621
+image_math	image_math	Process images using arithmetic expressions								To update	https://github.com/bmcv	Imaging	image_math	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	1.26.4	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+image_registration_affine	ip_image_registration	Intensity-based Image Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	image_registration_affine	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine	0.0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	12
+imagecoordinates_flipaxis	imagecoordinates_flipaxis	Flip coordinate axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	imagecoordinates_flipaxis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis	0.1-2	pandas		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	21825
+influx_data_manager	influx_data_manager	Handling influx_si data inputs in Galaxy workflows								To update	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/	Metabolomics	influx_si_data_manager	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager	1.0.2	influx-si-data-manager	1.0.3			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+influx_si	influx_si	metabolic flux estimation based on [in]stationary labeling								To update	https://github.com/sgsokol/influx	Metabolomics	influx_si	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si	7.0.1	influx_si	7.0.4			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ipo	ipo4retgroup, ipo4xcmsSet	[W4M][LC-MS] IPO								To update	https://github.com/rietho/IPO	Metabolomics	ipo	lecorguille	https://github.com/rietho/IPO	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo	1.10.0	bioconductor-ipo	1.28.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+isoplot	isoplot	Isoplot is a software for the visualisation of MS data from C13 labelling experiments								To update		Metabolomics, Visualization	isoplot	workflow4metabolomics	https://github.com/llegregam/Isoplot/tree/main	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot	1.3.0+galaxy1	isoplot	1.3.1			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	2
+jbrowse	jbrowse_to_container	A tool allowing to export a JBrowse dataset into a JBrowse docker container								To update	https://jbrowse.org	Web Services	jbrowse_to_container	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse		python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+kaptive	kaptive	Kaptive reports information about capsular (K) loci found in genome assemblies.								To update		Sequence Analysis	kaptive	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive	0.3.0	kaptive	3.0.0b5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+kat_filter	kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+kat_sect	kat_@EXECUTABLE@	SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.								To update			kat_sect	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+kegalign	kegalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.								Up-to-date	https://github.com/galaxyproject/KegAlign	Next Gen Mappers	kegalign	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign	https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign	0.1.2.7	kegalign-full	0.1.2.7			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+kmd_hmdb_data_plot	kmd_hmdb_data_plot	retrieves data from KMD HMDB API and produce plot and csv file								To update	https://github.com/workflow4metabolomics/tools-metabolomics	Metabolomics	kmd_hmdb_data_plot	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot	1.0.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+label_to_binary	label_to_binary	Convert label map to binary image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	label_to_binary	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+labelimage2points	ip_labelimage_to_points	Label Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	labelimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	36
+landmark_registration	ip_landmark_registration	Landmark Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	landmark_registration	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration	0.1.0-2	scikit-image		Image analysis	Imaging, Bioinformatics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	857
+logol	logol_wrapper	Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence								Up-to-date	http://logol.genouest.org/web/app.php/logol	Sequence Analysis		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	1.7.8	logol	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+lotus2	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2		lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	To update	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.34.1	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	114	936
+mahotas-features	ip_mahotas_features	Compute image features using mahotas.			mahotas-feature-computation					To update	https://github.com/luispedro/mahotas	Imaging	mahotas_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features	0.7-2	mahotas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	37
+mauve_contig_mover	mauve_contig_mover	Order a draft genome relative to a related reference genome								To update	https://github.com/phac-nml/mauve_contig_mover	Sequence Analysis	mauve_contig_mover	nml	https://github.com/phac-nml/mauve_contig_mover	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover	1.0.10	mauve	2.4.0.r4736			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+meneco	meneco	Meneco computes minimal completions to your draft network with reactions from a repair network								Up-to-date	http://bioasp.github.io/meneco/	Systems Biology	meneco	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/meneco	https://github.com/genouest/galaxy-tools/tree/master/tools/meneco	1.5.2	meneco	1.5.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mergeneighboursinlabelimage	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	mergeneighboursinlabelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	25
+metfrag	metfrag	[Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity)								To update	https://github.com/computational-metabolomics/metfrag-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/metfrag-galaxy	https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag	2.4.5+galaxy3	metfrag	2.4.5			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	153
+metfrag-vis	metfrag_vis	[Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag								To update	https://github.com/computational-metabolomics/metfrag-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/metfrag-galaxy	https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis	2.4.5+galaxy0	metfrag	2.4.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	12
+miranda	miranda	Finds potential target sites for miRNAs in genomic sequences								To update	http://www.microrna.org/	RNA	miranda	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	3.3a+galaxy1	miranda	3.3a			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	41	6076
+miranda2asko	miranda2asko	Converts miRanda output into AskOmics format								To update		Convert Formats	miranda2asko	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko	https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko	0.2	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mixmodel4repeated_measures	mixmodel4repeated_measures	[Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model								To update	http://workflow4metabolomics.org	Metabolomics	mixmodel4repeated_measures	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures	3.1.0	r-lme4				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mob_suite	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.9			0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	322	89021
+morphological_operations	morphological_operations	Apply morphological operations to images			scipy					To update	https://github.com/bmcv	Imaging	morphological_operations	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	1.12.0	scipy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mrbayes	mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
+ms2snoop	ms2snoop	[W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity.								To update	http://workflow4metabolomics.org	Metabolomics	ms2snoop	workflow4metabolomics		https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop	2.2.1	r-base				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+msPurity	mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching	[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data								Up-to-date	https://github.com/computational-metabolomics/mspurity-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/mspurity-galaxy	https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity	1.28.0	bioconductor-mspurity	1.28.0			0	0	10	11	0	0	10	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	40	709
+msp_split	msp_split	[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data								To update	https://github.com/computational-metabolomics/mspurity-galaxy	Metabolomics		tomnl	https://github.com/computational-metabolomics/mspurity-galaxy	https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split	0.0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mykrobe_parser	mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ncbi_fcs_adaptor	ncbi_fcs_adaptor	FCS-adaptor detects adaptor and vector contamination in genome sequences.								To update	https://github.com/ncbi/fcs	Sequence Analysis	ncbi_fcs_adaptor	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	0.5.0					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+nmr_annotation	NmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation								To update	http://workflow4metabolomics.org	Metabolomics	nmr_annotation	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/nmr_annotation	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation	3.0.0	r-batch	1.1_4			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	47
+nmr_annotation2d	2DNmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra								To update	http://workflow4metabolomics.org	Metabolomics	2dnmrannotation	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d	2.0.0	r-batch	1.1_4			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+nmr_preprocessing	NMR_Preprocessing, NMR_Read	[Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction								To update	http://workflow4metabolomics.org	Metabolomics	nmr_preprocessing	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/nmr_preprocessing	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing		r-batch	1.1_4			0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	4	140
+normalization	normalization	[Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data								To update	http://workflow4metabolomics.org	Metabolomics	normalization	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/normalization	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization	1.0.7	r-batch	1.1_4			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	133
+openlabcds2csv	openlabcds2csv	"Creates a summary of several ""Internal Standard Report"" OpenLabCDS results."								To update		Metabolomics	openlabcds2csv	genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv	0.1.0	openjdk				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+orientationpy	orientationpy	Compute image orientation			orientationj					Up-to-date	https://github.com/bmcv	Imaging	orientationpy	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	0.2.0.4	orientationpy	0.2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+overlay_images	ip_overlay_images	Overlay two images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	overlay_images	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images	0.0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	60
+pangolin	pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages								To update	https://github.com/hCoV-2019/pangolin	Sequence Analysis	pangolin	nml	https://github.com/hCoV-2019/pangolin	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin	1.1.14	pangolin	4.3			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	0	0	259	7276
+patrist	patrist	Extract Patristic Distance From a Tree								To update	https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02	Phylogenetics	patrist	nml	https://github.com/phac-nml/patrist	https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist	0.1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+peptimapper	peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag	Proteogenomics workflow for the expert annotation of eukaryotic genomes								To update	https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9	Proteomics		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	2.1					0	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+permutate_axis	ip_permutate_axis	Permutates axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	permutate_axis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	42
+physiofit	physiofit	PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes								Up-to-date	physiofit.readthedocs.io	Metabolomics	physiofit	workflow4metabolomics	https://github.com/MetaSys-LISBP/PhysioFit	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit	3.4.0	physiofit	3.4.0			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+physiofit_manager	physiofit_data_manager	Handling of physiofit input files								Up-to-date	physiofit.readthedocs.io	Metabolomics	physiofit_manager	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager	1.0.1	physiofit_data_manager	1.0.1			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+plantseg	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	plantseg	plantseg		PlantSeg	Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.	Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	To update	https://github.com/bmcv	Imaging	plantseg	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg	1.8.1	plant-seg		Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+plasmid_profiler	plasmid_profiler	Explores plasmid content in WGS data								To update			plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler	0.1.6	r				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+plasmid_profiler_suite		Plasmid Profiler suite defining all dependencies for Plasmid Profiler								To update		Sequence Analysis	suite_plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+plotheatmap	plotheatmap	This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output.								To update		Computational chemistry	plotheatmap	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap	1.0	bioconductor-preprocesscore	1.64.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+pneumocat	pneumocat	Pneumococcal Capsular Typing of illumina fastq reads								Up-to-date	https://github.com/phe-bioinformatics/PneumoCaT	Variant Analysis	pneumocat	nml	https://github.com/phe-bioinformatics/PneumoCaT	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat	1.2.1	pneumocat	1.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+points2binaryimage	ip_points_to_binaryimage	Points to Binary Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2binaryimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage	0.3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	41
+points2labelimage	ip_points_to_label	Points to label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage	0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	31
+points_association_nn	ip_points_association_nn	Association of points in consecutive frames	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	points_association_nn	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	29
+projective_transformation	ip_projective_transformation	Projective transformation	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation	0.1.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	85
+projective_transformation_points	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation_points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points	0.1.1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	21343
+promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pseudogenome	pseudogenome	Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	pseudogenome	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+quasitools	aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality	A collection of tools for analysing Viral Quasispecies								Up-to-date	https://github.com/phac-nml/quasitools	Sequence Analysis	quasitools	nml	https://github.com/phac-nml/quasitools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools	0.7.0	quasitools	0.7.0			0	12	0	12	0	12	0	12	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rdock	rdock	Docking ligands to proteins and nucleic acids								To update	http://rdock.sourceforge.net/	Computational chemistry	rdock	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock	1.0	rDock	2013.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+refseq_masher	refseq_masher_contains, refseq_masher_matches	Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.								Up-to-date	https://github.com/phac-nml/refseq_masher	Sequence Analysis	refseq_masher	nml	https://github.com/phac-nml/refseq_masher	https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher	0.1.2	refseq_masher	0.1.2			2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+repeat_channels	repeat_channels	Convert single-channel to multi-channel image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	repeat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16
+replace_chromosome_names	replace_chromosome_names	Replace chromosome names								To update		Text Manipulation	replace_chromosome_names	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names	0.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	537
+rfove	rfove	Perform segmentation region-based fitting of overlapping ellipses	rfove	rfove		RFOVE	RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.	Image analysis	Cell biology, Biomedical science, Imaging	To update	https://sites.google.com/site/costaspanagiotakis/research/cs	Imaging	rfove	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove	2023.11.12			Image analysis	Cell biology, Biomedical science, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7
+rsat_filter_snps	rsat_filter_snps	Filter SNPs in RSAT Matrix Scan output								To update	https://github.com/TGAC/earlham-galaxytools/	ChIP-seq, Systems Biology	rsat_filter_snps	earlham	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+scale_image	ip_scale_image	Scale image	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	scale_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image	0.18.3	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	512
+segalign	segalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.								Up-to-date	https://github.com/gsneha26/SegAlign	Next Gen Mappers	segalign	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign	https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign	0.1.2.7	segalign-galaxy	0.1.2.7			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+segmetrics	ip_segmetrics	Image segmentation and object detection performance measures	segmetrics	segmetrics	segmetrics	SegMetrics	Image segmentation and object detection performance measures	Image analysis		To update	https://github.com/bmcv	Imaging	segmetrics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics	1.4	segmetrics	1.5	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	3
+seqtk_nml	seqtk_nml_sample	Tool to downsample fastq reads								To update	https://github.com/lh3/seqtk	Sequence Analysis	seqtk_nml	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml	1.0.1	seqtk	1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+sistr_cmd	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	133	2489
+skyline2isocor	skyline2isocor	Converting skyline output to IsoCor input								Up-to-date	https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor	Metabolomics	skyline2isocor	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor	1.0.0	skyline2isocor	1.0.0			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+slice_image	ip_slice_image	Slice image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image	0.3-4	scikit-image		Image analysis	Imaging, Bioinformatics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	102
+smalt	smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+smart_domains	smart_domains	SMART domains								To update	http://smart.embl.de/	Sequence Analysis	smart_domains	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	0.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+smina	smina	smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization								To update	https://sourceforge.net/projects/smina/	Computational chemistry	smina	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina	1.0	smina	2017.11.9			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	493
+spades_header_fixer	spades_header_fixer	Fixes Spades Fasta ids								To update	https://github.com/phac-nml/galaxy_tools	Fasta Manipulation	spades_fasta_header_fixer	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer	1.1.2+galaxy1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+spatyper	spatyper	Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.								Up-to-date	https://github.com/HCGB-IGTP/spaTyper	Sequence Analysis	spatyper	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	0.3.3	spatyper	0.3.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+split_labelmap	ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap	0.2-3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	42
+spolpred	spolpred	A program for predicting the spoligotype from raw sequence reads								To update		Sequence Analysis	spolpred	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred	1.0.1	spolpred				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+spot_detection_2d	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d	0.1	giatools	0.3.1	Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	16
+srst2	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	205
+staramr	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	889	12673
+stringmlst	stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+suite_qiime2__alignment	qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	13
+suite_qiime2__composition	qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.5.0+q2galaxy.2024.5.0					4	4	4	2	4	4	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	2	5
+suite_qiime2__cutadapt	qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	5	67
+suite_qiime2__dada2	qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	31	202
+suite_qiime2__deblur	qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	9	73
+suite_qiime2__demux	qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	26	114
+suite_qiime2__diversity	qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.5.0+q2galaxy.2024.5.0					21	21	22	21	21	21	22	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	0	43	168
+suite_qiime2__diversity_lib	qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	4	4
+suite_qiime2__emperor	qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	2	6
+suite_qiime2__feature_classifier	qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.5.0+q2galaxy.2024.5.0					10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	48	263
+suite_qiime2__feature_table	qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.5.0+q2galaxy.2024.5.0					17	17	17	17	17	17	17	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	59	213
+suite_qiime2__fragment_insertion	qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	20
+suite_qiime2__longitudinal	qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.5.0+q2galaxy.2024.5.0					11	11	11	11	11	11	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	0	6	14
+suite_qiime2__metadata	qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	40	232
+suite_qiime2__phylogeny	qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	12	37
+suite_qiime2__quality_control	qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0
+suite_qiime2__quality_filter	qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.5.0+q2galaxy.2024.5.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	13
+suite_qiime2__rescript	qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.5.0+q2galaxy.2024.5.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+suite_qiime2__sample_classifier	qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.5.0+q2galaxy.2024.5.0					15	15	15	15	15	15	15	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	0	0	1	1
+suite_qiime2__taxa	qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	22	172
+suite_qiime2__vsearch	qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.5.0+q2galaxy.2024.5.0					8	8	8	7	8	8	8	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	8	16
+suite_qiime2_core										To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+suite_qiime2_core__tools	qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.5.0+dist.he540b0b0					2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	124	7087
+superdsm	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	superdsm	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm	0.2.0	superdsm	0.4.0	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	16
+t_coffee	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	70	8690
+tree_relabeler	tree_relabel	Relabels the tips of a newick formatted tree.								To update		Text Manipulation	tree_relabeler	nml	https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler	https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+tripal	analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync	Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal								To update	https://github.com/galaxy-genome-annotation/python-tripal	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal		python-tripal	3.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+unzip	unzip	Unzip file								To update	https://github.com/bmcv	Convert Formats	unzip	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip	6.0	unzip				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	508	5370
+visceral-evaluatesegmentation	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool			evaluatesegmentation-tool					To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	0.5-2	visceral-evaluatesegmentation	2015.07.03			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	25
+voronoi_tessellation	voronoi_tessellation	Compute Voronoi tesselation	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	voronoi_tesselation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation	0.22.0	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+w4mclassfilter	w4mclassfilter	Filter W4M data by values or metadata								To update	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper	Metabolomics	w4mclassfilter	eschen42	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter	0.98.19	r-base				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	2834
+w4mconcatenate	W4Mconcatenate	[W4M][Utils] concatenate two Metadata tables								To update	http://workflow4metabolomics.org	Metabolomics	w4mconcatenate	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate	1.0.0+galaxy0	r-base				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+w4mcorcov	w4mcorcov	OPLS-DA Contrasts of Univariate Results								To update	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper	Metabolomics	w4mcorcov	eschen42	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov	0.98.18	r-base				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	368
+w4mjoinpn	w4mjoinpn	Join positive- and negative-mode W4M datasets								To update	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper	Metabolomics	w4mjoinpn	eschen42	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn	0.98.2	coreutils	8.25			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	171
+wade	wade	identify regions of interest								To update	https://github.com/phac-nml/wade	Sequence Analysis	wade	nml	https://github.com/phac-nml/wade	https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade	0.2.5+galaxy1	wade	0.2.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+wsi_extract_top_view	ip_wsi_extract_top_view	WSI Extract Top View								To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view	0.2-2	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	38
+xcms	abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram, xcms_plot_eic, xcms_plot_raw		XCMS	XCMS		xcms	Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data.  The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling.	Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation	Biological imaging, Data visualisation, Metabolomics	Up-to-date	https://github.com/sneumann/xcms	Metabolomics	xcms	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms	4.0.0	bioconductor-xcms	4.0.0	Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation	Data visualisation, Metabolomics	9	11	12	12	9	11	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	10	9	0	356	29809
+10x_bamtofastq	10x_bamtofastq	Converts 10x Genomics BAM to FASTQ								Up-to-date	https://github.com/10XGenomics/bamtofastq	Convert Formats	10x_bamtofastq	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	1.4.1	10x_bamtofastq	1.4.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	46	228
+AggregateAlignments	graphclust_aggregate_alignments	Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.								Up-to-date		RNA	graphclust_aggregate_alignments	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments	0.6.0	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	116
+AlignCluster	graphclust_align_cluster	Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.								To update		RNA	graphclust_align_cluster	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster	0.1	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	10	3060
+CMFinder	cmFinder	Determines consensus motives for sequences.								To update		RNA	graphclust_cmfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	14	45191
+CollectResults	glob_report	Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.								To update		RNA	graphclust_postprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	14	1961
+CollectResultsNoAlign	graphclust_glob_report_no_align	Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.								To update		RNA	graphclust_postprocessing_no_align	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	108
+GSPAN	gspan	Second step of GraphClust								To update		RNA	graphclust_fasta_to_gspan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	133
+LocARNAGraphClust	locarna_best_subtree	MLocARNA computes a multiple sequence-structure alignment of RNA sequences.								To update		RNA	graphclust_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	45325
+NSPDK	NSPDK_candidateClust, nspdk_sparse	Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.								To update		RNA	graphclust_nspdk	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	9.2.3.1	graphclust-wrappers	0.6.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	28	62388
+Plotting	motifFinderPlot	Plotting results for GraphClust								To update		RNA	graphclust_motif_finder_plot	rnateam	https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting	0.4	seaborn				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	68
+PrepareForMlocarna	preMloc	This tool prepares files for locarna step.								To update		RNA	graphclust_prepocessing_for_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	1932
+Preprocessing	preproc	Preprocessing input for GraphClust								To update		RNA	graphclust_preprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	1758
+Structure_GSPAN	structure_to_gspan	Convert RNA structure to GSPAN graphs								To update		RNA	structure_to_gspan	rnateam	https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	2925
+add_line_to_file	add_line_to_file	Adds a text line to the beginning or end of a file.								To update		Text Manipulation	add_line_to_file	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	0.1.0	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	193	14480
+add_value	addValue	Add a value as a new column.								To update		Text Manipulation	add_value	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value	https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value	1.0.1	perl				1	1	1	1	1	1	1	1	1	1	0	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	1	1	1	591	367167
+agat	agat	GTF/GFF analysis toolkit	agat	agat		AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	To update	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.4.0	agat	1.4.1	Data handling, Genome annotation	Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	42	481
+align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	329
+antarna	antarna	antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .								To update		RNA	antarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna	1.1	antarna	2.0.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	52
+antismash	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash		antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	279	14596
+aresite2	AREsite2_REST	AREsite2 REST Interface								To update	http://rna.tbi.univie.ac.at/AREsite	RNA, Data Source, Sequence Analysis	aresite2	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	65
+atactk_trim_adapters	atactk_trim_adapters	Trim adapters from paired-end HTS reads.								To update	https://github.com/ParkerLab/atactk/	Fastq Manipulation	atactk_trim_adapters	rnateam	https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters	https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters	0.1.6	atactk	0.1.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	26	257
+augustus	augustus	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.								To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	3.1.0	augustus	3.5.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	516	8864
+bamhash	bamhash	Hash BAM and FASTQ files to verify data integrity								Up-to-date	https://github.com/DecodeGenetics/BamHash	Sequence Analysis	bamhash	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	1.1	bamhash	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	169
+barcode_collapse	barcode_collapse	Paired End randomer aware duplicate removal algorithm								To update	https://github.com/YeoLab/gscripts	RNA, Sequence Analysis	barcode_collapse	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	0.1.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+basecoverage	gops_basecoverage_1	Base Coverage of all intervals								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	basecoverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	2	308
+best_regression_subsets	BestSubsetsRegression1	Perform Best-subsets Regression								To update		Sequence Analysis, Variant Analysis	best_regression_subsets	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets	https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets	1.0.0	numpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	3
+bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2
+bigwig_to_bedgraph	bigwig_to_bedgraph	Convert from bigWig to bedGraph format								To update		Convert Formats	bigwig_to_bedgraph	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	0.1.0	ucsc_tools				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	200	5749
+bioimaging	bioimage_inference	Load model from BioImage.IO and make inferences	pytorch	pytorch	pytorch	PyTorch	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.		Machine learning, Computer science	To update	https://github.com/bgruening/galaxytools	Imaging	bioimage_inference	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging	https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging	2.4.0	python			Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+biomodelsML	biomodels_biomd0000001066, biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.								To update	https://www.ebi.ac.uk/biomodels/	Machine Learning	biomodels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML	1.1					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13
+bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	531
+bismark	bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor	A tool to map bisulfite converted sequence reads and determine cytosine methylation states								To update	https://www.bioinformatics.babraham.ac.uk/projects/bismark/	Sequence Analysis, Next Gen Mappers	bismark	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	0.22.1	bismark	0.24.2			0	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	4	0	0	0	0	0	0	0	0	0	4	4	4	0	332	12876
+blat_coverage_report	generate_coverage_report	Polymorphism of the Reads								To update		Next Gen Mappers, Sequence Analysis	blat_coverage_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+blat_mapping	blat2wig	Coverage of the Reads in wiggle format								To update		Next Gen Mappers, Sequence Analysis	blat_mapping	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	685
+blockbuster	blockbuster	Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.								To update	http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html	RNA, Sequence Analysis	blockbuster	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	0.1.2	blockbuster	0.0.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	34	3009
+blockclust	blockclust	BlockClust detects transcripts with similar processing patterns.								Up-to-date	https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust	RNA	blockclust	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	1.1.1	blockclust	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	15	1478
+bowtie_wrappers	bowtie_wrapper	Galaxy wrappers for the Bowtie short read mapping tools.								To update	http://bowtie-bio.sourceforge.net/	Next Gen Mappers	bowtie_wrappers	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers	https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers	1.2.0	bowtie	1.3.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	506	22988
+canonical_correlation_analysis	cca1	Canonical Correlation Analysis								To update		Statistics	canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis	1.0.0	R				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10	74
+canu	canu	Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).	canu	canu		CANU	De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.	De-novo assembly	Genomics	Up-to-date	https://github.com/marbl/canu		canu	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/canu	https://github.com/bgruening/galaxytools/tree/master/tools/canu	2.2	canu	2.2	De-novo assembly	Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	533	13021
+categorize_elements_satisfying_criteria	categorize_elements_satisfying_criteria	Categorize Elements satisfying criteria.								To update		Statistics	categorize_elements_satisfying_criteria	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria	https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	40
+ccat	peakcalling_ccat	Control-based ChIP-seq Analysis Tool								To update		ChIP-seq	ccat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat	0.0.2	ccat	3.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15	173
+cd_hit_dup	cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.10	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+cellprofiler	cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	19	0	23	23	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	23	19	0	178	4614
+cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update	https://github.com/CellProfiler/CellProfiler	Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.7					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	43
+change_case	ChangeCase	Convert column case.								To update		Text Manipulation	change_case	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case	https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case	1.0.1	perl				1	1	1	1	1	1	1	1	1	1	0	0	1	1	1	1	0	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	1	1	1	1	931	10965
+chatgpt	chatgpt_openai_api	Using the OpenAI GPT models to generate text based on user input.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	Machine Learning	chatgpt_openai_api	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	2024	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	418	15690
+chromosome_diagram	chromosome_diagram	Chromosome Diagrams using Biopython								To update		Graphics, Sequence Analysis, Visualization	chromosome_diagram	peterjc		https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+circexplorer	circexplorer	A combined strategy to identify circular RNAs (circRNAs and ciRNAs)								To update	https://github.com/YangLab/CIRCexplorer	Sequence Analysis, RNA	circexplorer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	1.1.9.0	circexplorer	1.1.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	251
+clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+clinod	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+cluster	gops_cluster_1	Cluster the intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	cluster	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1	801
+cmsearch_deoverlap	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	102
+cmv	cmcv, cmv, hmmcv, hmmv	cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.								Up-to-date	https://github.com/eggzilla/cmv	RNA	cmv	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	1.0.8	cmv	1.0.8			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	1	108
+cofold	cofold	Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.								To update	http://www.e-rna.org/cofold/	RNA	cofold	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	2.0.4.0	cofold	2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	342
+column_arrange_by_header	bg_column_arrange_by_header	Column arrange by header name								To update		Text Manipulation	column_arrange_by_header	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header	0.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	179	3781
+combine_metaphlan_humann	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	147
+compalignp	compalignp	Compute fractional identity between trusted alignment and test alignment								Up-to-date		RNA, Sequence Analysis	compalignp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp	1.0	compalignp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	220
+compare_humann2_output	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	332
+complement	gops_complement_1	Complement intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	complement	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1	233
+compute_motif_frequencies_for_all_motifs	compute_motif_frequencies_for_all_motifs	Compute Motif Frequencies For All Motifs, motif by motif.								To update		Sequence Analysis, Statistics	compute_motif_frequencies_for_all_motifs	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	94
+compute_motifs_frequency	compute_motifs_frequency	Compute Motif Frequencies in indel flanking regions.								To update		Sequence Analysis, Statistics	compute_motifs_frequency	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	65
+compute_q_values	compute_q_values	Compute q-values based on multiple simultaneous tests p-values								To update		Statistics	compute_q_values	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values	1.0.1	R				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	35
+concat	gops_concat_1	Concatenate two bed files								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	concat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat	1.0.1	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	309	564900
+condense_characters	Condense characters1	Condense consecutive characters.								To update		Text Manipulation	condense_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters	1.0.0					1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+convert_characters	Convert characters1	Convert delimiters to tab.								To update		Text Manipulation	convert_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters	1.0.1	python				1	1	1	1	1	1	1	1	1	1	0	1	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	1	1	1	475	23829
+convert_solid_color2nuc	color2nuc	Convert Color Space to Nucleotides								To update		Fasta Manipulation	convert_solid_color2nuc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+coprarna	coprarna	Target prediction for prokaryotic trans-acting small RNAs								To update	https://github.com/PatrickRWright/CopraRNA	RNA, Sequence Analysis	coprarna	rnateam	https://github.com/PatrickRWright/CopraRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna	2.1.1	coprarna	2.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+correlation	cor2	Correlation for numeric columns								To update		Statistics	correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation	1.0.0	rpy				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	47	837
+count_gff_features	count_gff_features	Count GFF Features								To update		Sequence Analysis	count_gff_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features	https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features	0.2	galaxy-ops	1.1.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	49	271
+count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+coverage	gops_coverage_1	Coverage of a set of intervals on second set of intervals								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	coverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	17	1502
+coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+cpat	cpat	Coding-potential assessment tool using an alignment-free logistic regression model.								Up-to-date	https://github.com/liguowang/cpat	Transcriptomics	cpat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	3.0.5	cpat	3.0.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	134
+crt	crispr_recognition_tool	CRISPR Recognition Tool								To update		Sequence Analysis	crispr_recognition_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/crt	https://github.com/bgruening/galaxytools/tree/master/tools/crt	1.2.0	crisper_recognition_tool	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	74	3389
+ctd_batch	ctdBatch_1	CTD analysis of chemicals, diseases, or genes								To update		Sequence Analysis	ctd_batch	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13	203
+cummerbund	cummeRbund	Wrapper for the Bioconductor cummeRbund library								To update	https://bioconductor.org/packages/release/bioc/html/cummeRbund.html	RNA, Visualization	cummerbund	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund	2.16.0	fonts-conda-ecosystem				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	31	1782
+cummerbund_to_tabular	cummerbund_to_cuffdiff	Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database.								To update		Convert Formats, Next Gen Mappers	cummerbund_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular	1.0.1					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13	1204
+cut_columns	Cut1	Select columns from a dataset.								To update		Text Manipulation	cut_columns	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns	1.0.2					1	1	1	1	1	1	1	1	1	1	0	0	1	1	1	1	0	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	1	1	1	1	5064	1957541
+delete_overlapping_indels	delete_overlapping_indels	Delete Overlapping Indels from a chromosome indels file								To update		Sequence Analysis	delete_overlapping_indels	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels	https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	39
+dewseq	dewseq	DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data								To update	https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers	Sequence Analysis, RNA, CLIP-seq	dewseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	0.1.0+galaxy0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11	72
+dgidb_annotator	dgidb_annotate	Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)								To update		Systems Biology, Variant Analysis	dgidb_annotator	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator	0.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	65
+diff	diff	GNU diff tool that calculates the differences between two files.								To update	http://www.gnu.org/software/diffutils/	Text Manipulation	diff	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diff	https://github.com/bgruening/galaxytools/tree/master/tools/diff	3.7	diffutils				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	30	235
+diffbind		Diffbind provides functions for  processing  ChIP-Seq  data.								To update	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+divide_pg_snp	dividePgSnp	Separate pgSnp alleles into columns								To update		Sequence Analysis	divide_pg_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	32
+dorina	dorina_search	data source for RNA interactions in post-transcriptional regulation								To update		RNA, Data Source	dorina	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1576
+dot2ct	rnastructure_dot2ct	Dot-Bracket to Connect Table (CT)								To update		Sequence Analysis, RNA	dot2ct	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	5.7.a	rnastructure	6.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dotknot	dotknot	DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence								To update	http://dotknot.csse.uwa.edu.au/	RNA, Proteomics	dotknot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot	1.3.1	vienna_rna				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	83
+draw_stacked_barplots	draw_stacked_barplots	Draw Stacked Bar Plots for different categories and different criteria								To update		Graphics, Statistics	draw_stacked_barplots	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots	https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots	1.0.0	R				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	173
+dwt_cor_ava_perclass	compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Feature Occurrences								To update		Statistics	dwt_cor_ava_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dwt_cor_avb_all	compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features								To update		Statistics	dwt_cor_avb_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dwt_ivc_all	compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Second Moments for Feature Occurrences								To update		Statistics	dwt_ivc_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dwt_var_perclass	compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom	Compute P-values and Max Variances for Feature Occurrences								To update		Statistics	dwt_var_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dwt_var_perfeature	dwt_var1	Wavelet variance using Discrete Wavelet Transfoms								To update		Statistics	dwt_var_perfeature	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature	1.0.2	r-bitops				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	36
+ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+edta	edta	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. 	edta	edta		The Extensive de novo TE Annotator (EDTA)	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	To update	https://github.com/oushujun/EDTA	Variant Analysis	edta	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta	https://github.com/bgruening/galaxytools/tree/master/tools/edta		edta	2.2.0	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	58	484
+effectiveT3	effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+epicseg	epicseg_segment	EpiCSeg is a tool for conducting chromatin segmentation.								To update	https://github.com/lamortenera/epicseg	Epigenetics	epicseg	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	@VERSION_STRING@	epicseg	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	245
+exparna	exparna	ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.								Up-to-date	http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp	RNA	exparna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	1.0.1	exparna	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+express	express	Quantify the abundances of a set of target sequences from sampled subsequences								To update		RNA	express	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/express	https://github.com/galaxyproject/tools-devteam/tree/main/tools/express	1.1.1	eXpress	1.5.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	325
+fasta_compute_length	fasta_compute_length	Compute sequence length								To update		Fasta Manipulation	fasta_compute_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length	1.0.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	380	7758
+fasta_concatenate_by_species	fasta_concatenate0	Concatenate FASTA alignment by species								To update		Fasta Manipulation	fasta_concatenate_by_species	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	88	35793
+fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fasta_filter_by_length	fasta_filter_by_length	Filter sequences by length								To update		Fasta Manipulation	fasta_filter_by_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length	1.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	350	48649
+fasta_to_tabular	fasta2tab	FASTA-to-Tabular converter								To update		Fasta Manipulation	fasta_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular	1.1.1	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	622	105935
+fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fastq_info	fastq_info	FASTQ info allows to validate single or paired fastq files								To update	https://github.com/nunofonseca/fastq_utils	Fastq Manipulation	fastq_info	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	0.25.1	fastq_utils	0.25.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	679	5765
+fastq_pair_names	fastq_pair_names	Extract FASTQ paired read names								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	Sequence Analysis	fastq_pair_names	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	0.0.5	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fastq_paired_unpaired	fastq_paired_unpaired	Divide FASTQ file into paired and unpaired reads								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	Sequence Analysis, Text Manipulation	fastq_paired_unpaired	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	0.1.5	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fastq_trimmer_by_quality	fastq_quality_trimmer	FASTQ Quality Trimmer by sliding window								Up-to-date		Fastq Manipulation	fastq_trimmer_by_quality	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	459	5676
+fastqsolexa_to_fasta_qual	fastqsolexa_to_fasta_qual	FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data								To update		Convert Formats, Fastq Manipulation	fastqsolexa_to_fasta_qual	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+featurecounter	featureCoverage1	Feature coverage								To update		Sequence Analysis, Variant Analysis	featurecounter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter	2.0.0	bx-python	0.13.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6	22385
+file_manipulation	bg_uniq	This tool returns all unique lines from a tab-separated file.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	Text Manipulation	unique	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	0.4	python				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	176	8496
+filter_transcripts_via_tracking	filter_combined_via_tracking	Filter Combined Transcripts								To update		RNA	filter_transcripts_via_tracking	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking	https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking	0.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	20
+find_diag_hits	find_diag_hits	Find diagnostic hits								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	find_diag_hits	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	69
+find_subsequences	bg_find_subsequences									To update			find_subsequences	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences	0.3	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	31	763
+flanking_features	flanking_features_1	Fetch closest non-overlapping feature for every interval								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	flanking_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features	4.0.1	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	20	671
+flexynesis	flexynesis	This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.								Up-to-date	https://github.com/BIMSBbioinfo/flexynesis/tree/main	Machine Learning, Statistics, Systems Biology	flexynesis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis	https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis	0.2.10	flexynesis	0.2.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	20904
+footprint	footprint	Find transcription factor footprints								To update	https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/	Epigenetics	footprint	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	1.0.0	footprint	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	57
+format_cd_hit_output	format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file								To update		Fasta Manipulation	format_cd_hit_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output	1.0.0+galaxy1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	166
+format_metaphlan2_output	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	166	5588
+generate_pc_lda_matrix	generate_matrix_for_pca_and_lda1	Generate a Matrix for using PC and LDA								To update		Sequence Analysis	generate_pc_lda_matrix	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix	https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix	1.0.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	119
+get_flanks	get_flanks1	Get flanks returns flanking region/s for every gene								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	get_flanks	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	555	324598
+get_orfs_or_cdss	get_orfs_or_cdss	Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	Sequence Analysis	get_orfs_or_cdss	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	0.2.3	biopython	1.70			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	0	0	15	186
+getindelrates_3way	indelRates_3way	Estimate Indel Rates for 3-way alignments								To update		Sequence Analysis, Variant Analysis	getindelrates_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+getindels_2way	getIndels_2way	Fetch Indels from pairwise alignments								To update		Sequence Analysis, Variant Analysis	getindels_2way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way	1.0.0	numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gfastats	gfastats	Tool for generating sequence statistics and simultaneous genome assembly file manipulation.	gfastats	gfastats		gfastats	gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.	Data handling	Computational biology	To update	https://github.com/vgl-hub/gfastats	Sequence Analysis	gfastats	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	1.3.6	gfastats	1.3.7	Data handling	Computational biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	418	8159
+gi2taxonomy	Fetch Taxonomic Ranks	Fetch taxonomic representation	gi2taxonomy	gi2taxonomy		gi2taxonomy	The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	27	660
+glimmer_hmm		GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gmaj	gmaj_1	GMAJ Multiple Alignment Viewer								To update		Visualization	gmaj	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj	https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj	2.0.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4	11
+gotohscan	rbc_gotohscan	Find subsequences in db								To update		Sequence Analysis	gotohscan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	1.3.0	gotohscan	1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	71
+graph_converter	graph_converter	Convert between different graph formats								To update		Convert Formats	graph_converter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+graphclust	graphclust	GraphClust can be used for structural clustering of RNA sequences.								To update	http://www.bioinf.uni-freiburg.de/Software/GraphClust/	RNA	graphclust	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	0.1	GraphClust				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6
+graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.45	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	43	2605
+graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	136	6651
+graphprot	graphprot_predict_profile	GraphProt models binding preferences of RNA-binding proteins.								To update	https://github.com/dmaticzka/GraphProt	Sequence Analysis, RNA, CLIP-seq	graphprot	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	1.1.7+galaxy2	graphprot	1.1.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	474
+hclust2	hclust2	Plots heatmaps								To update	https://bitbucket.org/nsegata/hclust2/	Data Visualization	hclust2	rnateam	https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2	https://github.com/bgruening/galaxytools/tree/master/tools/hclust2	0.99	hclust2	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+hgv_fundo	hgv_funDo	FunDO human genes associated with disease terms								To update		Sequence Analysis	hgv_fundo	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0
+hgv_hilbertvis	hgv_hilbertvis	HVIS visualization of genomic data with the Hilbert curve								To update	https://www.ebi.ac.uk/huber-srv/hilbert/	Graphics, Visualization	hgv_hilbertvis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis	1.0.0	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0
+hictk	hictk	Convert cooler to juicebox_hic								Up-to-date	https://github.com/paulsengroup/hictk	Convert Formats, Epigenetics	hictk	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	1.0.0	hictk	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+hicup	hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater	The HiCUP-Pipeline from the Bioinformatics Babraham Institute.								To update	https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html	Epigenetics	hicup	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	0.9.2					7	0	7	0	7	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	6	0	76	921
+hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228
+histogram	histogram_rpy	Histogram of a numeric column								To update		Graphics, Statistics	histogram	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram	https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram	1.0.4	rpy2	2.7.8			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	242	4350
+homer		Software for motif discovery and next generation sequencing analysis.								To update	http://homer.salk.edu/homer/	Sequence Analysis	homer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/homer	https://github.com/bgruening/galaxytools/tree/master/tools/homer						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+htseq-clip	htseq_clip	htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets								To update	https://github.com/EMBL-Hentze-group/htseq-clip	Sequence Analysis, RNA, CLIP-seq	htseq_clip	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	0.1.0+galaxy0	htseq-clip	2.19.0b0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	77
+illumina_methylation_analyser	illumina_methylation_analyser	Methylation analyzer for Illumina 450k DNA emthylation microarrays								To update	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	Sequence Analysis	illumina_methylation_analyser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	0.1	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+imagej2	imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	20240614			Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	0	26	1537
+improviser	proteomics_improviser	Visualisation of PepXML files								To update	http://www.improviser.uni-freiburg.de/	Proteomics	proteomics_improviser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	1.1.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+indels_3way	indels_3way	Fetch Indels from 3-way alignments								To update		Sequence Analysis	indels_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way	1.0.3					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	22
+infernal	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	infernal		Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	67	100294
+inforna		INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.								To update	http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp	RNA	inforna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	139
+intarna	intarna	Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.								Up-to-date	https://github.com/BackofenLab/IntaRNA	RNA	intarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	3.4.1	intarna	3.4.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	7569
+intersect	gops_intersect_1	Intersect the intervals of two datasets								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1003	348449
+iprscan5		Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+itsx	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	38	868
+jbrowse2	jbrowse2	JBrowse2 Genome Browser integrated as a Galaxy Tool	jbrowse_2	jbrowse_2		JBrowse 2	Modular genome browser with views of synteny and structural variation.	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse2	fubar	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2	https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2	2.15.4	jbrowse2	2.15.4	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+join	gops_join_1	Join the intervals of two datasets side-by-side								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	join	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	284	329556
+join_files_on_column_fuzzy	join_files_on_column_fuzzy	Join two files on a common column, allowing a certain difference.								To update		Text Manipulation	join_files_on_column_fuzzy	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy	1.0.1	python				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	117	2448
+jupyter_job	run_jupyter_job	Run jupyter notebook script in Galaxy								To update		Machine Learning	run_jupyter_job	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	0.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	30
+kernel_canonical_correlation_analysis	kcca1	Kernel Canonical Correlation Analysis								To update		Statistics	kernel_canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis	1.0.0	rpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	69
+kernel_principal_component_analysis	kpca1	Kernel Principal Component Analysis								To update		Statistics	kernel_principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis	1.0.0	rpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13	156
+kinwalker		Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.								To update	http://www.bioinf.uni-leipzig.de/Software/Kinwalker/	RNA	kinwalker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+kraken2tax	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	481	14683
+labels	bg_labels	remaps and annotates alignments								To update	https://github.com/bgruening/galaxytools/tree/master/tools/labels	Sequence Analysis	labels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/labels	https://github.com/bgruening/galaxytools/tree/master/tools/labels	1.0.5.0	labels				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+lastz_paired_reads	lastz_paired_reads_wrapper	Galaxy wrapper for the Lastz alignment tool on paired reads								To update		Next Gen Mappers	lastz_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads	1.1.1	lastz	1.04.22			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	9
+lca_wrapper	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	137
+lda_analysis	lda_analy1	Perform Linear Discriminant Analysis								To update		Graphics, Statistics	lda_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis	1.0.1	R				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	148
+lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	152
+linear_regression	LinearRegression1	Perform Linear Regression								To update		Statistics	linear_regression	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression	https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression	1.0.1	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+locarna	locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile	LocARNA - A suite for multiple alignment and folding of RNAs								Up-to-date	http://www.bioinf.uni-freiburg.de/Software/LocARNA/	RNA	locarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	2.0.1	locarna	2.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	339
+logistic_regression_vif	LogisticRegression	Perform Logistic Regression with vif								To update		Sequence Analysis, Variant Analysis, Statistics	logistic_regression_vif	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif	https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif	1.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+maf_cpg_filter	cpgFilter	Mask CpG/non-CpG sites from MAF file								To update		Sequence Analysis, Variant Analysis	maf_cpg_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mafft	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.526	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	2	0	0	0	2	0	0	0	0	0	2	2	2	0	817	143045
+mapping_to_ucsc	mapToUCSC	Format mapping data as UCSC custom track								To update		Visualization, Convert Formats, Next Gen Mappers	mapping_to_ucsc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mavedb	mavedb_importer	data source for MaveDB								To update		Data Source	mavedb_importer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb	0.9					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mea	mea	Maximum expected accuracy prediction								To update	http://www.bioinf.uni-leipzig.de/Software/mea	RNA	mea	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	0.6.4.1	mea	0.6.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	85
+megablast_xml_parser	megablast_xml_parser	Parse blast XML output								To update		Next Gen Mappers, Convert Formats	megablast_xml_parser	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser	https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	36	338
+merge	gops_merge_1	Merge the overlapping intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	193	563676
+merge_cols	mergeCols1	Merge columns together.								To update		Text Manipulation	merge_cols	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols	https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols	1.0.3	python				1	1	1	1	1	1	1	1	1	1	0	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	1	1	1	542	28593
+methtools	methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling	tools for methylation analysis								To update	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	Sequence Analysis	methtools	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	0.1.1	methtools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5461
+methyldackel	pileometh	A tool for processing bisulfite sequencing alignments								To update	https://github.com/dpryan79/MethylDackel	Sequence Analysis	pileometh	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	0.5.2	methyldackel	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	200	16573
+methylkit	methylkit	A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.								To update	http://bioconductor.org/packages/release/bioc/html/methylKit.html	Epigenetics	methylkit	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	0.99.2	bioconductor-methylkit	1.28.0			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+metilene	metilene	Differential DNA methylation calling								To update		RNA, Statistics	metilene	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	0.2.6.1	metilene	0.2.8			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	103	3966
+mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+miclip	mi_clip	Identification of binding sites in CLIP-Seq data.								To update	https://cran.r-project.org/src/contrib/Archive/MiClip/	Sequence Analysis	miclip	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	1.2.0	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+microsatellite_birthdeath	microsatellite_birthdeath	Identify microsatellite births and deaths								To update		Sequence Analysis	microsatellite_birthdeath	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+microsats_alignment_level	microsats_align1	Extract Orthologous Microsatellites from pair-wise alignments								To update		Sequence Analysis, Variant Analysis	microsats_alignment_level	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level	1.0.0	sputnik				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+microsats_mutability	microsats_mutability1	Estimate microsatellite mutability by specified attributes								To update		Sequence Analysis, Variant Analysis	microsats_mutability	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability	1.1.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+minced	minced	MinCED - Mining CRISPRs in Environmental Datasets								To update	http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README	Sequence Analysis	minced	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minced	https://github.com/bgruening/galaxytools/tree/master/tools/minced	0.2.0	minced	0.4.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	53	895
+mine	maximal_information_based_nonparametric_exploration	Maximal Information-based Nonparametric Exploration								To update		Variant Analysis	mine	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine	0.0.1	MINE				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	11
+minipolish	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	185
+mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	56	613
+molecule2gspan	bg_mol2gspan	converter								To update	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	Convert Formats	molecule_to_gspan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	0.2	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+motus	mereg_mOTUs_tables, motus_profiler	Tool for profiling the abundance of microbial taxa.	mOTUs	mOTUs		Metagenomic operational taxonomic units (mOTUs)	Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/motu-tool/mOTUs	Metagenomics	motus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs	https://github.com/bgruening/galaxytools/tree/master/tools/motus	3.1.0	motus	3.1.0	Taxonomic classification	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mqc	mqc	Ribosome profiling mapping quality control tool								To update	https://github.com/Biobix/mQC	Sequence Analysis	mqc	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc	1.9	mqc	1.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	76
+multispecies_orthologous_microsats	multispecies_orthologous_microsats	Extract orthologous microsatellites								To update		Sequence Analysis, Variant Analysis	multispecies_orthologous_microsats	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats	https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats	1.0.0	bx-sputnik				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mummer	mummerplot_wrapper	Draw dotplots using mummer, mucmer, or promer with mummerplot								To update	http://mummer.sourceforge.net/	Graphics, Sequence Analysis, Visualization	mummer	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	0.0.8	ghostscript	9.18			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	83	652
+music_deconvolution	music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution	Multi-subject Single Cell deconvolution (MuSiC)								Up-to-date	https://github.com/xuranw/MuSiC	Transcriptomics	music	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/	https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution	0.1.1	music-deconvolution	0.1.1			5	5	4	0	5	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	240	1872
+mutate_snp_codon	mutate_snp_codon_1	Mutate Codons with SNPs								To update		Variant Analysis	mutate_snp_codon	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	47
+nanopolish	nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants	Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data.								Up-to-date	https://github.com/jts/nanopolish		nanopolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	0.14.0	nanopolish	0.14.0			0	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	78	8366
+nastiseq	nastiseq	A method to identify cis-NATs using ssRNA-seq								Up-to-date	https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/	RNA	nastiseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	1.0	r-nastiseq	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	40
+netboxr	netboxr	netboxr enables automated discovery of biological process modules by network analysis								To update		Systems Biology	netboxr	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/netboxr	1.6.0	bioconductor-netboxr	1.9.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	11
+nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268
+nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+nucleosome_prediction	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	861
+numeric_clustering	numeric_clustering	Clustering tool for numberic values								To update	http://scikit-learn.org/stable/index.html	Statistics	numeric_clustering	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	0.9	anaconda				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	486
+openms	AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter	OpenMS in version 2.1.								To update		Proteomics	openms	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/openms	https://github.com/bgruening/galaxytools/tree/master/tools/openms	2.1.0	openms	3.2.0			7	34	135	0	7	34	135	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	135	134	0	916	105743
+pandas_rolling_window	pandas_rolling_window	Rolling window calculations								To update	https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html	Statistics	pandas_rolling_window	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	0.1	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	269
+paralyzer	paralyzer	A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.								Up-to-date	https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/	RNA	paralyzer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	1.5	paralyzer	1.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	299
+partialr_square	partialRsq	Compute partial R square								To update		Statistics	partialr_square	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square	https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+peakachu	peakachu	PEAKachu is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	peakachu	rnateam	https://github.com/tbischler/PEAKachu	https://github.com/bgruening/galaxytools/tree/master/tools/peakachu	0.2.0+galaxy1	peakachu	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	78	3109
+pearson_correlation	Pearson_and_apos_Correlation1	Pearson and apos Correlation between any two numeric columns								To update		Statistics	pearson_correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+perf	stats_perf_tool	suitable for boolean classification problems								To update	http://osmot.cs.cornell.edu/kddcup/software.html		stats_perf_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/perf	https://github.com/bgruening/galaxytools/tree/master/tools/perf	5.11.0	perf				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pfamscan	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	19	165
+pg_tools	pg_dump, pg_import, pg_query	tool suite for dealing with Postgresql databases from Galaxy's history								To update	https://www.postgresql.org	Data Export, Data Source	pgtools	bgruening	https://github.com/bgruening/galaxytools/tools/pgtools	https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools		postgresql				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pgsnp2gd_snp	pgSnp2gd_snp	Convert from pgSnp to gd_snp								To update		Variant Analysis	pgsnp2gd_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pharmcat	pharmcat	Pharmacogenomics Clinical Annotation Tool								To update	https://pharmcat.org/	Variant Analysis	pharmcat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat						1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	82
+pileup_interval	pileup_interval	Pileup-to-Interval condenses pileup format into ranges of bases								To update		SAM	pileup_interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval	1.0.3	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	15	632
+pileup_parser	pileup_parser	Filter pileup on coverage and SNPs								To update	https://github.com/galaxyproject/tools-devteam/	SAM	pileup_parser	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser	1.0.2	perl				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	169	3158
+pipmir	pipmir	A method to identify novel plant miRNA.								To update	https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/	RNA	pipmir	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	0.1.0	pipmir	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	21	275
+piranha	piranha	Piranha is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	piranha	rnateam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha	https://github.com/bgruening/galaxytools/tree/master/tools/piranha	1.2.1.0	piranha	1.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	1809
+platypus	bg_platypus	efficient and accurate variant-detection in high-throughput sequencing data								To update	http://www.well.ox.ac.uk/platypus	Sequence Analysis	platypus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	0.0.11	platypus				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+plot_from_lda	plot_for_lda_output1	"Draw ROC plot on ""Perform LDA"" output"								To update		Graphics, Statistics	plot_from_lda	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda	https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda	1.0.1	R				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9	73
+plotly_ml_performance_plots	plotly_ml_performance_plots	performance plots for machine learning problems								To update	http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics	Visualization	plotly_ml_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	0.4	galaxy-ml	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	71	1323
+plotly_parallel_coordinates_plot	plotly_parallel_coordinates_plot	parallel coordinates plot produced with plotly								To update	https://plot.ly/python/parallel-coordinates-plot/	Visualization	plotly_parallel_coordinates_plot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37	652
+plotly_regression_performance_plots	plotly_regression_performance_plots	performance plots for regression problems								To update	http://scikit-learn.org/stable/supervised_learning.html#supervised-learning	Visualization	plotly_regression_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	0.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	79	843
+poisson2test	poisson2test	Poisson two-sample test								To update	https://bitbucket.org/natefoo/taxonomy	Statistics, Metagenomics	poisson2test	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test	1.0.0	taxonomy	0.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6	116
+predictnls	predictnls	Python reimplementation of predictNLS for Galaxy								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	Sequence Analysis	predictnls	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	0.0.10					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+principal_component_analysis	pca1	Principal Component Analysis								To update		Statistics	principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis	1.0.2	rpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	88	9989
+protease_prediction	eden_protease_prediction	This tool can learn the cleavage specificity of a given class of proteases.								To update	https://github.com/fabriziocosta/eden	Sequence Analysis, Proteomics	protease_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	0.9	eden	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	154
+protein_analysis	promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort	TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	Sequence Analysis	tmhmm_and_signalp	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	0.0.13	promoter				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	451	6428
+protein_properties	bg_protein_properties	Calculation of various properties from given protein sequences								To update		Sequence Analysis	protein_properties	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	604
+quality_filter	qualityFilter	Filter nucleotides based on quality scores								To update		Sequence Analysis, Variant Analysis	quality_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter	1.0.1	bx-python	0.13.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rRNA	meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+racon	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	309	21353
+rbpbench	rbpbench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs	rbpbench	rbpbench		RBPBench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	To update	https://github.com/michauhl/RBPBench	Sequence Analysis, RNA, CLIP-seq	rbpbench	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	0.8.1	rbpbench	1.0		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	36
+rcas	rcas	RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments								To update	https://github.com/BIMSBbioinfo/RCAS	RNA	rcas	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas	1.5.4	bioconductor-rcas	1.28.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	38	1226
+rcve	rcve1	Compute RCVE								To update		Sequence Analysis, Variant Analysis	rcve	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+reago	reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+remove_beginning	Remove beginning1	Remove lines from the beginning of a file.								To update		Text Manipulation	remove_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning	1.0.0					1	1	1	1	1	1	1	1	1	1	0	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	1	1	1	1409	137310
+remurna	remurna	remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation								To update	https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna	RNA	remurna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	1.0.0	remurna	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	42
+repeat_masker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.								To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	0.1.2	RepeatMasker	4.0.9_p2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	248	3750
+replaceColumn	replace_column_with_key_value_file	A tool to replace all column entries of a file given by values of a key-value file.								To update		Text Manipulation	replace_column_by_key_value_file	bgruening	https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn	https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn	0.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	189	576111
+rest_tool	pubchem_rest_tool	This tool fetches data from pubchem via the PubChem REST API.								To update	https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html	Data Source	pubchem_rest_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ribotaper	ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling	A method for defining traslated ORFs using Ribosome Profiling data.	ribotaper	ribotaper		RiboTaper	New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.	Gene expression profiling	Functional genomics	To update	https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/	RNA	ribotaper	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper	1.3.1a	ribotaper	1.3.1	Gene expression profiling	Functional genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	44	628
+rmap	rmap_wrapper	RMAP for Solexa Short Reads Alignment								To update		Next Gen Mappers	rmap	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rmapq	rmapq_wrapper	RMAPQ for Solexa Short Reads Alignment with Quality Scores								To update		Next Gen Mappers	rmapq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rna_shapes	RNAshapes	Compute secondary structures of RNA								To update		RNA	rnashapes	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	3.3.0	@EXECUTABLE@				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	129
+rnabob	rbc_rnabob	Fast pattern searching for RNA structural motifs								To update	http://eddylab.org/software.html	RNA	rnabob	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	2.2.1.0	rnabob	2.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	164
+rnacode	rbc_rnacode	Analyze the protein coding potential in MSA								To update		RNA	rnacode	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	0.3.2	rnacode	0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	1358
+rnacommender	rbc_rnacommender	RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.								To update	https://github.com/gianlucacorrado/RNAcommender	RNA	rnacommender	rnateam	https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender	0.1.1	sam	3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	1074
+rnaformer	infer_rnaformer	RNAformer: RNA secondary structure prediction								To update	https://github.com/automl/RNAformer	RNA	rnaformer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	1.0.0	rnaformer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rnalien	RNAlien	RNAlien unsupervized RNA family model construction								To update	http://rna.tbi.univie.ac.at/rnalien/	RNA, Sequence Analysis	rnalien	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	1.3.6	rnalien	1.8.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	33
+rnasnp	rnasnp	RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs								To update	http://rth.dk/resources/rnasnp/	RNA	rnasnp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp	1.2.0	rnasnp	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	86
+rnaz	rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window	RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.								Up-to-date	https://www.tbi.univie.ac.at/~wash/RNAz/	RNA	rnaz	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz	2.1.1	rnaz	2.1.1			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	28	43279
+sailfish	sailfish	Sailfish is a tool for transcript quantification from RNA-seq data								To update	http://www.cs.cmu.edu/~ckingsf/software/sailfish/	Sequence Analysis, RNA	sailfish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	0.10.1.1	bzip2				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	55	4024
+salmon	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	2	3	1	2	2	3	1	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	2	0	0	0	0	0	3	3	3	0	969	61937
+sam2interval	sam2interval	Convert SAM to interval.								To update		SAM	sam2interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval	1.0.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20	1189
+sam_bitwise_flag_filter	sam_bw_filter	Filter SAM on bitwise flag values								To update		SAM	sam_bitwise_flag_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter	1.0.1	python				1	1	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	278
+sambamba	sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort	Sambamba: process your BAM data faster!								Up-to-date	https://github.com/biod/sambamba	SAM	sambamba	bgruening	https://github.com/biod/sambamba	https://github.com/bgruening/galaxytools/tree/master/tools/sambamba	1.0.1	sambamba	1.0.1			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	3765
+samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	1	296	4948
+samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1450	48426
+scatterplot	scatterplot_rpy	Scatterplot of two numeric columns								To update		Graphics, Statistics	scatterplot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot	1.0.3	numpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	61	1677
+sed	sed_stream_editor	Manipulate your data with the sed command line tool.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/sed	Text Manipulation	sed_wrapper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sed	https://github.com/bgruening/galaxytools/tree/master/tools/sed	0.0.1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2276
+segemehl	segemehl	segemehl - short read mapping with gaps								To update	http://www.bioinf.uni-leipzig.de/Software/segemehl/	Next Gen Mappers	segemehl	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	0.2.0.4	segemehl	0.3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	1276
+selectsequencesfrommsa	selectsequencesfrommsa	SelectSequences - selects representative entries from a multiple sequence alignment in clustal format								Up-to-date	https://github.com/eggzilla/SelectSequences	RNA, Sequence Analysis	selectsequencesfrommsa	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	1.0.5	selectsequencesfrommsa	1.0.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	27	457
+seq_composition	seq_composition	Sequence composition								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	Sequence Analysis	seq_composition	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	0.0.5	biopython	1.70			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	71	874
+seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	306	25302
+seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	82	3784
+seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
+seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+short_reads_figure_high_quality_length	hist_high_quality_score	Histogram of high quality score reads								To update		Sequence Analysis, Graphics	short_reads_figure_high_quality_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length	1.0.0	rpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+short_reads_figure_score	quality_score_distribution	Build base quality distribution								To update		Sequence Analysis, Graphics	short_reads_figure_score	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score	1.0.2	fontconfig				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	163
+short_reads_trim_seq	trim_reads	Select high quality segments								To update		Fastq Manipulation	short_reads_trim_seq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	21	220
+show_beginning	Show beginning1	Select lines from the beginning of a file.								To update		Text Manipulation	show_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning	1.0.0					1	1	1	1	1	1	1	1	1	1	0	0	1	1	1	1	0	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	1	1	1	1	704	32112
+show_tail	Show tail1	Select lines from the end of a file.								To update		Text Manipulation	show_tail	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail	1.0.0					1	1	1	1	1	1	1	1	1	1	0	0	1	1	1	1	0	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	1	1	1	1	128	2513
+sicer	peakcalling_sicer	Statistical approach for the Identification of ChIP-Enriched Regions								Up-to-date	https://home.gwu.edu/~wpeng/Software.htm	ChIP-seq	sicer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer	1.1	SICER	1.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	5	374
+sklearn	sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split	Machine Learning tool suite from Scikit-learn								To update	http://scikit-learn.org	Machine Learning, Statistics	sklearn	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	1.0.11.0					30	14	31	16	30	14	31	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	29	31	27	0	958	113932
+snpfreq	hgv_snpFreq	snpFreq significant SNPs in case-control data								To update		Variant Analysis, Statistics	snpfreq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq	1.0.1	R				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	37
+sortmerna	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	376	18183
+split_file_on_column	tp_split_on_column	Split a file on a specific column.								To update		Text Manipulation	split_file_on_column	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	0.6	gawk				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	159	5507
+split_file_to_collection	split_file_to_collection	Split tabular, MGF, FASTA, or FASTQ files to a dataset collection.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	Text Manipulation	split_file_to_collection	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	0.5.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	412	15358
+split_paired_reads	split_paired_reads	Split paired end reads								To update		Fastq Manipulation	split_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+splitfasta	rbc_splitfasta	Split a multi-sequence fasta file into files containing single sequences								To update		Text Manipulation	splitfasta	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	0.4.0	biopython	1.70			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	96	1295
+sshmm	sshmm	ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data								Up-to-date	https://github.molgen.mpg.de/heller/ssHMM	Sequence Analysis, RNA	sshmm	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm	1.0.7	sshmm	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	223
+statistics	bg_statistical_hypothesis_testing	Tool for computing statistical tests.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	Statistics	bg_statistical_hypothesis_testing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	0.3	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	304
+stress_ng	stress_ng	stress test a computer system in various selectable ways								To update		Web Services	stress_ng	bgruening-util	https://github.com/ColinIanKing/stress-ng	https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng	0.12.04	stress-ng				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	47
+substitution_rates	subRate1	Estimate substitution rates for non-coding regions								To update		Sequence Analysis, Variant Analysis	substitution_rates	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+substitutions	substitutions1	Fetch substitutions from pairwise alignments								To update		Sequence Analysis, Variant Analysis	substitutions	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+subtract	gops_subtract_1	Subtract the intervals of two datasets								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	182	564229
+subtract_query	subtract_query1	Subtract Whole Dataset from another dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract_query	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query	0.1	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	55	1019
+t2ps	Draw_phylogram	Draw phylogeny	t2ps	t2ps		Draw phylogeny	"""Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper"	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	31	457
+t2t_report	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	26	947
+t_test_two_samples	t_test_two_samples	T Test for Two Samples								To update		Statistics	t_test_two_samples	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples	https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples	1.0.1	R				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6	210
+table_annovar	table_annovar	Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered								To update		Variant Analysis	table_annovar	devteam	Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar	https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar	0.2	annovar				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+tables_arithmetic_operations	tables_arithmetic_operations	Arithmetic Operations on tables								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	tables_arithmetic_operations	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations	1.0.0	perl				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	14	2207
+tabular_to_fasta	tab2fasta	Tabular-to-FASTA								To update		Convert Formats	tabular_to_fasta	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta	1.1.1	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	601	319334
+tapscan	tapscan_classify	Search for transcription associated proteins (TAPs)								To update	https://plantcode.cup.uni-freiburg.de/tapscan/	Proteomics	tapscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	4.76+galaxy0	hmmer	3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+targetfinder	targetfinder	Plant small RNA target prediction tool								Up-to-date	https://github.com/carringtonlab/TargetFinder.git	RNA	targetfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder	1.7	targetfinder	1.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	37	713
+text_processing	tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq	High performance text processing tools using the GNU coreutils, sed, awk and friends.								To update	https://www.gnu.org/software/	Text Manipulation	text_processing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	9.3	coreutils	8.25			20	20	20	20	20	20	20	20	0	0	0	0	0	0	0	0	0	0	19	1	19	0	0	19	0	0	0	20	0	0	0	0	0	19	19	19	0	15048	3864895
+tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	460
+tiara	tiara	Tool for identification of eukaryotic sequences in the metagenomic datasets.	Tiara	Tiara		TIARA	Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).	Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism, DNA structural variation	To update	https://github.com/ibe-uw/tiara	Metagenomics, Sequence Analysis	tiara	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	1.0.3	tiara		Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+tool_recommendation_model	create_tool_recommendation_model	Create model to recommend tools								To update	https://github.com/bgruening/galaxytools	Machine Learning	create_tool_recommendation_model	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model	https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model	0.0.5	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15	445
+tophat	tophat	Tophat for Illumina								To update		RNA, Next Gen Mappers	tophat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat	1.5.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1
+tophat2	tophat2	Tophat - fast splice junction mapper for RNA-Seq reads								To update	http://ccb.jhu.edu/software/tophat/index.shtml	RNA, Next Gen Mappers	tophat2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2	2.1.1	bowtie2	2.5.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	1	1	1	0	312	24167
+tophat_fusion_post	tophat_fusion_post	Wrapper for Tophat-Fusion post step								To update		Transcriptomics	tophat_fusion_post	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post	0.1	blast+				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15	216
+trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	2334	238699
+trimmer	trimmer	Trim leading or trailing characters.								To update		Text Manipulation	trimmer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer	0.0.1					1	1	1	1	1	1	1	1	1	1	0	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	1	1	1	188	6058
+trna_prediction	aragorn_trna, trnascan	Aragorn predicts tRNA and tmRNA in nucleotide sequences.								To update	http://mbioserv2.mbioekol.lu.se/ARAGORN/	RNA	trna_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	0.6	aragorn	1.2.41			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	0	236	2935
+ucsc_custom_track	build_ucsc_custom_track_1	Build custom track for UCSC genome browser								To update		Sequence Analysis	ucsc_custom_track	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	45	394
+uniprot_rest_interface	uniprot	UniProt ID mapping and sequence retrieval								To update	https://github.com/jdrudolph/uniprot	Proteomics, Sequence Analysis	uniprot_rest_interface	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	0.6	requests				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	132	2406
+varscan_version_2	varscan	VarScan wrapper								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan_version_2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2	2.4.2	varscan	2.4.6			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	246	5191
+vcf2pgsnp	vcf2pgSnp	VCF to pgSnp								To update		Variant Analysis	vcf2pgsnp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15	206
+vcf_annotate	vcf_annotate	Annotate a VCF file (dbSNP, hapmap)								To update		Variant Analysis	vcf_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
+vcf_extract	vcf_extract	Extract reads from a specified region								To update		Variant Analysis	vcf_extract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+vcf_filter	vcf_filter	Filter a VCF file								To update		Variant Analysis	vcf_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	63	388
+vcf_intersect	vcf_intersect	Generate the intersection of two VCF files								To update		Variant Analysis	vcf_intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19
+vcftools_annotate	vcftools_annotate	Annotate VCF using custom/user-defined annotations								To update	https://vcftools.github.io/	Variant Analysis	vcftools_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate	0.1	echo				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	24	171
+vcftools_compare	vcftools_compare	Compare VCF files to get overlap and uniqueness statistics								To update	https://vcftools.github.io/	Variant Analysis	vcftools_compare	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34	531
+vcftools_consensus	vcftools_consensus	Apply VCF variants to a fasta file to create consensus sequence								To update	https://vcftools.github.io/	Variant Analysis	vcftools_consensus	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus	0.1.11	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+vcftools_isec	vcftools_isec	Intersect multiple VCF datasets								To update	https://vcftools.github.io/	Variant Analysis	vcftools_isec	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec	0.1.1	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	35	498
+vcftools_merge	vcftools_merge	Merge multiple VCF datasets into a single dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge	0.1.11	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	68	953
+vcftools_slice	vcftools_slice	Subset VCF dataset by genomic regions								To update	https://vcftools.github.io/	Variant Analysis	vcftools_slice	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice	0.1	echo				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	24	411
+vcftools_subset	vcftools_subset	Select samples from a VCF dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_subset	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	17	137
+venn_list	venn_list	Draw Venn Diagram (PDF) from lists, FASTA files, etc								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	Graphics, Sequence Analysis, Visualization	venn_list	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	0.1.2	galaxy_sequence_utils	1.1.5			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	248	5067
+vienna_rna	viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup	ViennaRNA - Prediction and comparison of RNA secondary structures								To update	http://www.tbi.univie.ac.at/RNA/	RNA	viennarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	2.2.10	viennarna	2.6.4			0	0	21	0	0	0	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	21	0	123	7864
+vt	vt_@BINARY@, vt_@BINARY@	A tool set for short variant discovery in genetic sequence data.								To update		Sequence Analysis, Variant Analysis	vt	bgruening	https://github.com/atks/vt	https://github.com/bgruening/galaxytools/tree/master/tools/vt	0.2	vt	2015.11.10			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+weightedaverage	wtavg	Assign weighted-average of the values of features overlapping an interval								To update		Sequence Analysis, Variant Analysis	weightedaverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage	https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage	1.0.1	galaxy-ops	1.1.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+whisper	whisper	Transcribe audio or video files to text using the OpenAI Whisper.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	Machine Learning	whisper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	20231117					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+windowsplitter	winSplitter	Make windows								To update		Sequence Analysis, Variant Analysis	windowsplitter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11
+woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660
+xy_plot	XY_Plot_1	Plotting tool for multiple series and graph types								To update		Graphics, Statistics	xy_plot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot	1.0.2	r-base				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	344	5892
+TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	42
+abricate	abricate, abricate_list, abricate_summary	Mass screening of contigs for antiobiotic resistance genes	ABRicate	ABRicate		ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.	Antimicrobial resistance prediction	Genomics, Microbiology	Up-to-date	https://github.com/tseemann/abricate	Sequence Analysis	abricate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate	1.0.1	abricate	1.0.1	Antimicrobial resistance prediction	Genomics, Microbiology	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	2	3	3	0	1764	496717
+abritamr	abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	abritamr	abritamr		abriTAMR	an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://zenodo.org/record/7370628	Sequence Analysis	abritamr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr	1.0.19	abritamr	1.0.19	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	391	4278
+adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	37	217
+add_input_name_as_column	addName	Add input name as column on an existing tabular file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column	Text Manipulation	add_input_name_as_column	mvdbeek	https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column	https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	91	83150
+aegean	aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval	AEGeAn toolkit wrappers	gaeval	gaeval		GAEVAL	Gene Annotation EVAluation.	Sequence annotation	Sequence analysis, Gene structure	Up-to-date	https://github.com/BrendelGroup/AEGeAn	Transcriptomics, Sequence Analysis	aegean	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean	0.16.0	aegean	0.16.0	Sequence annotation	Sequence analysis, Gene structure	1	4	4	4	1	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	47	168
+aldex2	aldex2	Performs analysis Of differential abundance taking sample variation into account	aldex2	aldex2		ALDEx2	A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	Statistical inference	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	13	129
+allegro	allegro	Linkage and haplotype analysis from deCODE	allegro	allegro		Allegro	It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome.	Sequence motif discovery	Sequence analysis, Transcription factors and regulatory sites, DNA	To update	http://www.decode.com/software/	Variant Analysis	allegro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro	@VER@.0	allegro	3	Sequence motif discovery	Sequence analysis, Transcription factors and regulatory sites, DNA	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+amplican	amplican	AmpliCan is an analysis tool for genome editing.	amplican	amplican		amplican	It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	53
+ampvis2	ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn	ampvis2	ampvis	ampvis		ampvis	ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.	Analysis, Visualisation	Biodiversity	To update	https://github.com/MadsAlbertsen/ampvis2/	Metagenomics	ampvis2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2	2.8.9			Analysis, Visualisation	Biodiversity	0	0	19	0	0	0	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	42	267
+amrfinderplus	amrfinderplus	"""AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms."	amrfinderplus	amrfinderplus		AMRFinderPlus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms"	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.12.8	ncbi-amrfinderplus	3.12.8	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	591
+ancombc	ancombc	Performs analysis of compositions of microbiomes with bias correction.	ancombc	ancombc		ANCOMBC	Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	7
+anndata	anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Single Cell, Spatial Omics	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.9	anndata	0.6.22.post1			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	625	35620
+annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1175	25975
+argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+arriba	arriba, arriba_draw_fusions, arriba_get_filters	Arriba detects fusion genes in RNA-Seq data after running RNA-STAR								Up-to-date	https://github.com/suhrig/arriba	Sequence Analysis, Transcriptomics	arriba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba	2.4.0	arriba	2.4.0			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	38	3528
+art	art_454, art_illumina, art_solid	Simulator for Illumina, 454, and SOLiD sequencing data	art	art		ART	ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD	Conversion	Bioinformatics	To update	http://www.niehs.nih.gov/research/resources/software/biostatistics/art/	Sequence Analysis, Data Source	art	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/art	https://github.com/galaxyproject/tools-iuc/tree/main/tools/art	2014.11.03.0	art	2016.06.05	Conversion	Bioinformatics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+artic	artic_guppyplex, artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	artic	artic		ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	Sequence alignment	Genomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	2	1	0	123	8175
+assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+astral	astral	Tool for estimating an unrooted species tree given a set of unrooted gene trees								Up-to-date	https://github.com/smirarab/ASTRAL	Phylogenetics	astral	iuc	https://github.com/usegalaxy-be/galaxytools/tree/main/astral	https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral	5.7.8	astral-tree	5.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
+augustus	augustus, augustus_training	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.	augustus	augustus		AUGUSTUS	AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.	Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus	3.4.0	augustus	3.5.0	Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	685	11245
+b2btools	b2btools_single_sequence	This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.	b2btools	b2btools		b2bTools	The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA	Protein disorder prediction, Protein secondary structure prediction, Protein feature detection		To update	https://bio2byte.be	Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools	3.0.5+galaxy0	b2btools	3.0.7	Protein disorder prediction, Protein secondary structure prediction		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	12	345
+bakta	bakta	"""Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."""	bakta	bakta		Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	Up-to-date	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.4	bakta	1.9.4	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	151	2982
+bam_to_scidx	bam_to_scidx	Contains a tool that converts a BAM file to an ScIdx file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx	Convert Formats	bam_to_scidx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4	128
+bamtools	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	208	14021
+bamtools_filter	bamFilter	Filter BAM datasets on various attributes using bamtools filter	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1195	114863
+bamtools_split	bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag	Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett.	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	197	4328
+bamutil	bamutil_clip_overlap, bamutil_diff	bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.								To update	https://github.com/statgen/bamUtil	Sequence Analysis	bamutil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil		bamutil	1.0.15			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	39
+bandage	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	bandage	bandage		Bandage	GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	Sequence assembly visualisation	Genomics, Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	2	2	2	0	2016	44390
+barcode_splitter	barcode_splitter	A utility to split sequence files using multiple sets of barcodes								To update	https://bitbucket.org/princeton_genomics/barcode_splitter/	Fastq Manipulation	barcode_splitter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter	0.18.4.0	barcode_splitter	0.18.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Single Cell, Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	71
+barrnap	barrnap	Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.	barrnap	barrnap		Barrnap	Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).	Gene prediction	Genomics, Model organisms, Model organisms	To update	https://github.com/tseemann/barrnap	Sequence Analysis	barrnap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap	1.2.2	barrnap	0.9	Gene prediction	Genomics, Model organisms, Model organisms	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	160	3938
+basil	basil	Breakpoint detection, including large insertions								Up-to-date	https://github.com/seqan/anise_basil	Variant Analysis	basil	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil	1.2.0	anise_basil	1.2.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	35	266
+bax2bam	bax2bam	BAX to BAM converter								Up-to-date	https://github.com/pacificbiosciences/bax2bam/	Convert Formats, Sequence Analysis	bax2bam	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam	0.0.11	bax2bam	0.0.11			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8	200
+bayescan	BayeScan	Detecting natural selection from population-based genetic data	bayescan	bayescan		BayeScan	BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8	64
+bbgbigwig	bbgtobigwig	Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	https://www.encodeproject.org/software/bedgraphtobigwig/	Convert Formats	bbgbigwig	iuc	https://www.encodeproject.org/software/bedgraphtobigwig/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig	0.1	ucsc-bedgraphtobigwig	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+bbtools	bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.	bbmap	bbtools, bbmap		BBMap	BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	To update	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.08	bbmap	39.09	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	6	3	5	0	6	3	5	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	4	0	0	420	6381
+bcftools	bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@	BCFtools toolkit wrappers	bcftools	bcftools		BCFtools	BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.	Data handling, Variant calling	Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment	To update	https://samtools.github.io/bcftools/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools	1.15.1	bcftools	1.21	Data handling, Variant calling	DNA polymorphism, GWAS study, Genotyping experiment	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+bctools	bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events	bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0								Up-to-date	https://github.com/dmaticzka/bctools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools	0.2.2	bctools	0.2.2			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	7	7	0	87	2895
+beacon2	beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff	beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI).	ga4gh_beacon	ga4gh_beacon		GA4GH Beacon	A global search engine for genetic mutations.	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	Up-to-date	https://github.com/EGA-archive/beacon2-ri-tools/tree/main	Variant Analysis	beacon2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2	2.0.0	beacon2-ri-tools	2.0.0	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	28
+beacon2-import	beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence	Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants.	ga4gh_beacon	ga4gh_beacon		GA4GH Beacon	A global search engine for genetic mutations.	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	Up-to-date	https://pypi.org/project/beacon2-import/	Variant Analysis	Beacon2_Import	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import	2.2.4	beacon2-import	2.2.4	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	0	0	12	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+beagle	beagle	Beagle is a program for phasing and imputing missing genotypes.								To update	https://faculty.washington.edu/browning/beagle/beagle.html	Variant Analysis	beagle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle	5.2_21Apr21.304	beagle	5.4_22Jul22.46e			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	54
+bedops	bedops-sort-bed	BEDOPS: high-performance genomic feature operations								Up-to-date	https://bedops.readthedocs.io/en/latest/	Genomic Interval Operations	bedops_sortbed	iuc	https://bedops.readthedocs.io/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops	2.4.41	bedops	2.4.41			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	28
+bedtools	bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed	bedtools is a powerful toolset for genome arithmetic	bedtools	bedtools		BEDTools	BEDTools is an extensive suite of utilities for comparing genomic features in BED format.	Mapping	Genomics	Up-to-date	https://github.com/arq5x/bedtools2	Genomic Interval Operations, Text Manipulation	bedtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools	2.31.1	bedtools	2.31.1	Mapping	Genomics	37	37	37	37	37	37	37	37	0	0	0	0	0	0	0	0	0	0	37	6	37	0	0	37	0	0	0	37	0	0	0	0	0	37	37	37	0	5844	901750
+bellerophon	bellerophon	Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.								Up-to-date	https://github.com/davebx/bellerophon	Sequence Analysis	bellerophon	iuc	https://github.com/davebx/bellerophon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon	1.0	bellerophon	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	123	1194
+berokka	berokka	Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.								Up-to-date	https://github.com/tseemann/berokka	Fasta Manipulation	berokka	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka	0.2.3	berokka	0.2.3			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+bigscape	bigscape	Construct sequence similarity networks of BGCs and groups them into GCF	BiG-SCAPE	BiG-SCAPE		BiG-SCAPE	A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+bigwig_outlier_bed	bigwig_outlier_bed	pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files	bigtools	bigtools		bigtools	Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust.			To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	Sequence Analysis	bigwig_outlier_bed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed	0.2.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+binning_refiner	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	binning_refiner	binning_refiner		Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	81
+bioext	bioext_bam2msa, bioext_bealign	A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more!								Up-to-date	https://pypi.python.org/pypi/biopython-extensions/	Next Gen Mappers		iuc	https://github.com/davebx/bioext-gx/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext	0.21.9	python-bioext	0.21.9			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	0	2	0	0	363	15228
+bioinformatics_cafe	fasta_regex_finder	Miscellanea of scripts for bioinformatics								To update	https://github.com/dariober/bioinformatics-cafe/	Sequence Analysis	bioinformatics_cafe	mbernt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe	0.1.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	978
+biom_format	biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	biomformat	biomformat		biomformat	"This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods."	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	Formatting	Laboratory information management, Sequence analysis	2	2	6	0	2	2	6	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	98	3906
+bioperl	bp_genbank2gff3	Converts GenBank format files to GFF3	bioperl	bioperl		BioPerl	A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.  It provides software modules for many of the typical tasks of bioinformatics programming.	Data handling, Service invocation	Genomics, Software engineering, Data management	To update	https://bioperl.org/	Sequence Analysis	bp_genbank2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl	1.1	perl-bioperl	1.7.8	Data handling, Service invocation	Genomics, Software engineering	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	240	6736
+biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	3
+blast	magicblast	Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome								Up-to-date	https://ncbi.github.io/magicblast/	Next Gen Mappers	magicblast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast	1.7.0	magicblast	1.7.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	78	511
+blastxml_to_gapped_gff3	blastxml_to_gapped_gff3	BlastXML to gapped GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	Convert Formats, Sequence Analysis	blastxml_to_gapped_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3	1.1	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24	185
+bowtie2	bowtie2	Bowtie2: Fast and sensitive read alignment	bowtie2	bowtie2		Bowtie 2	Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.	Read mapping	Mapping, Genomics, Mapping	To update	http://bowtie-bio.sourceforge.net/bowtie2	Next Gen Mappers	bowtie2	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2	2.5.3	bowtie2	2.5.4	Read mapping	Mapping, Genomics, Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	1	0	0	1	1	1	0	5136	380252
+bracken	est_abundance	Bayesian Reestimation of Abundance with KrakEN	bracken	bracken		Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	Statistical calculation	Metagenomics, Microbial ecology	Up-to-date	https://ccb.jhu.edu/software/bracken/	Sequence Analysis, Metagenomics	bracken	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken	3.0	bracken	3.0	Statistical calculation	Metagenomics, Microbial ecology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	326	18351
+breseq	breseq	Predicts mutations in microbial genomes	breseq	breseq		breseq	Runs Breseq software on a set of fastq files.	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	To update	https://github.com/barricklab/breseq	Variant Analysis	breseq	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq	0.35.5	breseq	0.39.0	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	50	1871
+brew3r_r	brew3r_r	Extend 3' end of a GTF using another GTF as a template	brew3r.r	brew3r.r		BREW3R.r	This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.	Genome annotation	Transcriptomics, Genomics	To update	https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html	Transcriptomics, RNA	brew3r_r	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r	https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r	1.0.2			Genome annotation	Transcriptomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+busco	busco	BUSCO assess genome and annotation completeness	busco	busco		BUSCO	Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://gitlab.com/ezlab/busco/-/releases	Sequence Analysis	busco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco	5.7.1	busco	5.7.1	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1804	86180
+bwa	bwa_mem, bwa	Wrapper for bwa mem, aln, sampe, and samse	bwa	bwa		BWA	Fast, accurate, memory-efficient aligner for short and long sequencing reads	Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment	Mapping	Up-to-date	http://bio-bwa.sourceforge.net/	Next Gen Mappers	bwa	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa	0.7.18	bwa	0.7.18	Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment	Mapping	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	2	0	0	0	2	0	0	0	0	0	2	2	2	2	5295	981251
+bwa_mem2	bwa_mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa.	bwa-mem2	bwa-mem2		Bwa-mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case,  dataset and the running machine.	Sequence alignment	Mapping	Up-to-date	https://github.com/bwa-mem2/bwa-mem2	Next Gen Mappers	bwa_mem2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2	2.2.1	bwa-mem2	2.2.1	Sequence alignment	Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	0	0	1220	44386
+bwameth	bwameth	Fast and accurate alignment of BS-seq reads								Up-to-date	https://github.com/brentp/bwa-meth	Sequence Analysis, Next Gen Mappers	bwameth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth	0.2.7	bwameth	0.2.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	201	10619
+cactus	cactus_cactus, cactus_export	Cactus is a reference-free whole-genome multiple alignment program	cactus	cactus		Cactus	Cactus is a reference-free whole-genome multiple alignment program.	Multiple sequence alignment, Genome alignment	Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics	To update	https://github.com/ComparativeGenomicsToolkit/cactus	Sequence Analysis	cactus	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	2.7.1			Multiple sequence alignment, Genome alignment	Genomics, Sequence assembly, Mapping, Phylogenetics	0	2	2	1	0	2	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	26	234
+calculate_contrast_threshold	calculate_contrast_threshold	Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.								To update	https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold	Visualization, Genomic Interval Operations, SAM	calculate_contrast_threshold	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold	1.0.0	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+calculate_numeric_param	calculate_numeric_param	Calculate a numeric parameter value using integer and float values.								To update		Text Manipulation	calculate_numeric_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param	0.1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	1393
+cami_amber	biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert	Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments								Up-to-date	https://github.com/CAMI-challenge/AMBER	Metagenomics	cami_amber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber	2.0.7	cami-amber	2.0.7			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+cat	cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	cat_bins		CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat	5.2.3	cat	5.3	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	5	2	5	0	5	2	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	268	2878
+cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	280	4474
+cemitool	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.26.0	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	98
+charts	charts	Enables advanced visualization options in Galaxy Charts								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	Visualization	charts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts	1.0.1	r-getopt				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	287	3589
+checkm	checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	checkm	checkm		CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	Up-to-date	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.3	checkm-genome	1.2.3	Sequence assembly validation, Sequence composition calculation, Statistical calculation	Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	0	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	390	5165
+cherri	cherri_eval, cherri_train	Computational Help Evaluating RNA-RNA interactions	cherri	cherri		cherri	CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.		Molecular interactions, pathways and networks, Structure analysis, Machine learning	To update	https://github.com/BackofenLab/Cherri	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri	0.7	cherri	0.8		Molecular interactions, pathways and networks, Structure analysis, Machine learning	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	207
+chewbbaca	chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema	BSR-Based Allele Calling Algorithm								To update	https://github.com/B-UMMI/chewBBACA/tree/master	Variant Analysis	chewbbaca	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca		chewbbaca	3.3.10			0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+chira	chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify	Chimeric Read Annotator for RNA-RNA interactome data	chira	chira		ChiRA	ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.		RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	Up-to-date	https://github.com/pavanvidem/chira	RNA, Transcriptomics, Sequence Analysis	chira	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira	1.4.3	chira	1.4.3		Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	97	6418
+chopin2	chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing								To update	https://github.com/cumbof/chopin2	Machine Learning	chopin2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2	1.0.9.post1	chopin2				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+chromeister	chromeister	ultra-fast pairwise genome comparisons								Up-to-date	https://github.com/estebanpw/chromeister	Sequence Analysis	chromeister	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister	1.5.a	chromeister	1.5.a			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	182	2130
+circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	269
+circos	circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile	Build Circos Plots in Galaxy	galactic_circos	galactic_circos		Galactic Circos	Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format.	Sequence visualisation		To update	http://circos.ca/	Graphics	circos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos	0.69.8	circos	0.69.9	Sequence visualisation		11	11	11	11	11	11	11	11	0	0	0	0	0	0	0	0	0	0	0	11	11	0	0	0	0	0	0	11	0	0	0	0	0	11	11	11	0	1018	21305
+cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	To update	https://github.com/Hoohm/CITE-seq-Count	Single Cell, Transcriptomics, Proteomics	cite_seq_count	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	1.4.4	cite-seq-count	1.4.5	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	18
+clair3	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	clair3	clair3		Clair3	Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	1.0.8	clair3	1.0.10	Variant calling	Molecular genetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	68	1856
+clustalw	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	clustal2	clustal2		Clustal 2 (Clustal W, Clustal X)	Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.	Multiple sequence alignment	Phylogeny, Sequence analysis	Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw	2.1	clustalw	2.1	Multiple sequence alignment	Phylogeny, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	651	46793
+clustering_from_distmat	clustering_from_distmat	Distance matrix-based hierarchical clustering using SciPy								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/	Statistics	clustering_from_distmat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat	1.1.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+cnv-phenopacket	cnv_phenopacket	cnv-phenopacket Converts TSV metadata file to JSON.								To update	https://pypi.org/project/cnv-phenopacket/	Variant Analysis	cnv_phenopacket	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket	1.0.2	cnv-phenopacket				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+cnv-vcf2json	cnv_vcf2json	cnv-vcf2json Converts structural variants VCF file to JSON.								To update	https://pypi.org/project/cnv-phenopacket/	Variant Analysis	cnv-vcf2json	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json	1.1.0	cnv-vcf2json				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+cnvkit	cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target	detecting copy number variants and alterations genome-wide from high-throughput sequencing	cnvkit	cnvkit		CNVkit	CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.	Variant calling	DNA structural variation	Up-to-date	https://github.com/etal/cnvkit	Variant Analysis	cnvkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit	0.9.11	cnvkit	0.9.11	Variant calling		0	0	17	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	45	370
+codeml	codeml	Detects positive selection	paml	paml		PAML	Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml	4.9	paml	4.10.7	Probabilistic sequence generation	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	29	60901
+cojac	cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	cojac	cojac		COJAC	CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.2	cojac	0.9.2		Genetic variation	2	0	3	0	2	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	20	2757
+colabfold	colabfold_alphafold, colabfold_msa	Protein prediction based on AlphaFold2	Colabfold	Colabfold		ColabFold	ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.	Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	To update	https://github.com/sokrypton/ColabFold	Proteomics, Graphics	colabfold	iuc	https://github.com/sokrypton/ColabFold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold	1.5.5			Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+colibread	commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak	Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome								To update	https://colibread.inria.fr/	Sequence Analysis, Variant Analysis	colibread	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread	24.7.14+galaxy0	commet	24.7.14			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	251
+collection_column_join	collection_column_join	Column Join on Collections								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join	Text Manipulation	collection_column_join	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join	https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join	0.0.3	coreutils	8.25			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1483	20857
+collection_element_identifiers	collection_element_identifiers	Extract element identifiers of a collection								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers	Text Manipulation	collection_element_identifiers	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers	https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers	0.0.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	912	5059
+column_maker	Add_a_column1	Compute an expression on every row								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker	Text Manipulation	column_maker	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker	2.1	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	2379	3883271
+column_order_header_sort	column_order_header_sort	Sort Column Order by heading								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort	Text Manipulation	column_order_header_sort	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort	0.0.1	python				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	80	3258
+column_remove_by_header	column_remove_by_header	Remove columns by header								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header	Text Manipulation	column_remove_by_header	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header	1.0	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	199	8424
+compleasm	compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	compleasm	compleasm		compleasm	"""Compleasm: a faster and more accurate reimplementation of BUSCO"""	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm	0.2.6	compleasm	0.2.6	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+compose_text_param	compose_text_param	Compose a text parameter value using text, integer and float values								To update		Text Manipulation	compose_text_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param	0.1.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	0	0	0	375	35084
+compress_file	compress_file	Compress files.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file	Text Manipulation	compress_file	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file	0.1.0	gzip				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	164	3674
+concoct	concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	concoct	concoct		CONCOCT	A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct	1.1.0	concoct	1.1.0	Sequence clustering, Read binning	Metagenomics	0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	92	786
+cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis, Single Cell	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+coverage_report	CoverageReport2	Generate Detailed Coverage Report from BAM file								To update	https://github.com/galaxyproject/tools-iuc	Sequence Analysis	coverage_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report	0.0.4	perl-number-format	1.76			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+coverm	coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm		CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	Local alignment	Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	72	529
+crispr_studio	crispr_studio	CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.	crisprstudio	crisprstudio		CRISPRStudio	CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.	Visualisation	Sequence analysis, Genomics, Data visualisation	To update	https://github.com/moineaulab/CRISPRStudio	Sequence Analysis	crispr_studio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio	1+galaxy0	crispr_studio	1	Visualisation	Sequence analysis, Genomics, Data visualisation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	30	636
+crosscontamination_barcode_filter	crosscontamination_barcode_filter	Barcode contamination discovery tool								To update		Transcriptomics, Visualization	crosscontamination_barcode_filter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter	0.3	r-ggplot2	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	17	347
+crossmap	crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig	CrossMap converts genome coordinates or annotation files between genome assemblies								Up-to-date	http://crossmap.sourceforge.net/	Convert Formats, Genomic Interval Operations	crossmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap	0.7.0	crossmap	0.7.0			5	0	6	0	5	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	5	6	5	0	116	1968
+cuffcompare	cuffcompare	Galaxy wrappers for the Cuffcompare tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffcompare	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare	2.2.1	cufflinks	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	1	0	0	1	1	1	0	65	1130
+cuffdiff	cuffdiff	Galaxy wrappers for the Cuffdiff tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffdiff	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff	2.2.1	cufflinks	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	1	0	228	5831
+cufflinks	cufflinks	Galaxy wrappers for the Cufflinks tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cufflinks	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks	2.2.1	cufflinks	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	1	0	0	1	1	1	0	319	32218
+cuffmerge	cuffmerge	Galaxy wrappers for the Cuffmerge tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffmerge	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge	2.2.1	cufflinks	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	1	1	1	0	122	3292
+cuffnorm	cuffnorm	The Cuffnorm tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffnorm	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	27	660
+cuffquant	cuffquant	The Cuffquant tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffquant	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	18	688
+cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	5090	232004
+cutesv	cutesv	Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools.	cuteSV	cuteSV		cuteSV	Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis	Split read mapping, Genotyping, Structural variation detection	DNA structural variation, Sequencing, Computer science	To update	https://github.com/tjiangHIT/cuteSV	Variant Analysis	cutesv	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv	1.0.8	cutesv	2.1.1	Split read mapping, Genotyping, Structural variation detection	Sequencing, Computer science	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	17	235
+cwpair2	cwpair2	Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans.								To update		ChIP-seq	cwpair2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2	1.1.1	matplotlib				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dada2	dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	dada2	dada2		dada2	This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	0	10	0	10	0	0	1	0	0	0	0	0	0	0	0	0	10	10	10	0	1263	66609
+das_tool	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	dastool		dastool	DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	Read binning	Metagenomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	24	706
+data_source_iris_tcga	data_source_iris_tcga	IRIS-TCGA Data source tool								To update		Data Source	data_source_iris_tcga	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga	https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga	1.0.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+datamash	datamash_ops, datamash_reverse, datamash_transpose	GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon.								To update	https://www.gnu.org/software/datamash/	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash	1.8	datamash	1.1.0			3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	1	3	3	0	0	1	0	0	0	1	0	0	0	0	0	3	3	3	0	3066	739298
+decontaminator	decontaminator	Deep Learning method for novel virus detection in sequencing data	decontaminator	decontaminator		decontaminator	Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.	Filtering	Metagenomics	To update	https://github.com/cbib/decontaminator	Machine Learning	decontaminator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator	1.0.0	numpy		Filtering	Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	99
+deepmicro	deepmicro	Representation learning and classification framework	DeepMicro	DeepMicro		DeepMicro	Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.	Essential dynamics, Splitting, Community profiling	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	Up-to-date	https://github.com/paulzierep/DeepMicro	Machine Learning	deepmicro	iuc	https://github.com/paulzierep/DeepMicro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro	1.4	deepmicro	1.4	Essential dynamics, Splitting	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	501
+deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5
+deepvariant	deepvariant	DeepVariant is a deep learning-based variant caller								To update	https://github.com/google/deepvariant	Variant Analysis	deepvariant	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant	1.5.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	182	1889
+deg_annotate	deg_annotate	Annotate DESeq2/DEXSeq output tables								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	Transcriptomics	deg_annotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate	1.1.0	bedtools	2.31.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1774	19910
+delly	delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge	Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.	delly2	delly2		Delly2	Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.	Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis	DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases	To update	https://github.com/dellytools/delly	Variant Analysis	delly	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly	https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly	0.9.1	delly	1.2.9	Indel detection, Structural variation detection, Genotyping	Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases	0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	6	0	0	0	0	0	6	6	0	0	124	1135
+deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	4990	95752
+dexseq	dexseq, dexseq_count, plotdexseq	Inference of differential exon usage in RNA-Seq	dexseq	dexseq		DEXSeq	The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html	Transcriptomics, RNA, Statistics	dexseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq	1.48.0	bioconductor-dexseq	1.48.0	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	218	16064
+diamond	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	diamond		Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	Sequence alignment analysis	Sequence analysis, Proteins	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	3	3	3	0	0	0	1	0	0	0	0	0	0	0	0	0	3	3	0	963	49711
+diffbind	diffbind	Diffbind provides functions for  processing  ChIP-Seq  data.	diffbind	diffbind		DiffBind	Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.	Differential binding analysis	ChIP-seq	Up-to-date	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind	3.12.0	bioconductor-diffbind	3.12.0	Differential binding analysis	ChIP-seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	250	6264
+dimet	dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@	DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data.								Up-to-date	https://github.com/cbib/DIMet	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet	0.2.4	dimet	0.2.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	42	369
+dnabot	dnabot	DNA assembly using BASIC on OpenTrons								To update	https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT	Synthetic Biology	dnabot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot	3.1.0	dnabot				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dnaweaver	dnaweaver	Given a SBOL input, calculate assembly parts for Gibson or Golden Gate.								Up-to-date	https://github.com/Edinburgh-Genome-Foundry/DnaWeaver	Synthetic Biology	dnaweaver	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver	1.0.2	dnaweaver_synbiocad	1.0.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dram	dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram		DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	Up-to-date	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.5.0	dram	1.5.0	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	39	6886
+drep	drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep		dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	Up-to-date	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.5.0	drep	3.5.0	Genome comparison	Metagenomics, Sequence analysis	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	46	646
+dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Single Cell, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	126	3934
+ebi_tools	ebi_search_rest_results	Tools to query and download data from several EMBL-EBI databases								To update	http://www.ebi.ac.uk/services/all	Web Services, Data Source	ebi_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools	0.1.1	six				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	52	382
+edger	edger	Perform RNA-Seq differential expression analysis using edgeR pipeline	edger	edger		edgeR	Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	To update	http://bioconductor.org/packages/release/bioc/html/edgeR.html	Transcriptomics, RNA, Statistics	edger	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger	https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger	3.36.0	bioconductor-edger	4.0.16	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	945	18117
+egsea	egsea	This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing	egsea	egsea		EGSEA	This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.	Gene set testing	Systems biology	To update	https://bioconductor.org/packages/release/bioc/html/EGSEA.html	Transcriptomics, RNA, Statistics	egsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea	1.20.0	bioconductor-egsea	1.28.0	Gene set testing	Systems biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	177	2524
+emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	107	107	107	107	107	0	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	107	107	107	0	1816	89530
+ena_upload	ena_upload	Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). 								To update	https://github.com/usegalaxy-eu/ena-upload-cli	Data Export	ena_upload	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload	0.7.3	ena-upload-cli	0.7.4			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	0	0	14	208
+enasearch	enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data	A Python library for interacting with ENA's API								To update	https://github.com/bebatut/enasearch	Data Source	enasearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch		enasearch	0.2.2			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	126	2257
+ensembl_vep	ensembl_vep	Ensembl VEP: Annotate VCFs with variant effect predictions								Up-to-date	https://github.com/Ensembl/ensembl-vep	Variant Analysis	ensembl_vep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep	112.0	ensembl-vep	112.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	119	2653
+episcanpy	episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess	EpiScanpy – Epigenomics single cell analysis in python	episcanpy	episcanpy		epiScanpy	Epigenomics Single Cell Analysis in Python.	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	To update	https://github.com/colomemaria/epiScanpy	Single Cell, Epigenetics	episcanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy	0.3.2	episcanpy	0.4.0	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	20	736
+evidencemodeler	evidencemodeler	EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.	EvidenceModeler	EvidenceModeler		EvidenceModeler	The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.	Gene prediction	Gene expression, Gene structure	Up-to-date	https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file	Genome annotation	evidencemodeler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler	2.1.0	evidencemodeler	2.1.0	Gene prediction	Gene expression, Gene structure	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+exomedepth	exomedepth	ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data	exomedepth	exomedepth		ExomeDepth	Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases	To update	https://cran.r-project.org/package=ExomeDepth	Sequence Analysis, Variant Analysis	exomedepth	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth	1.1.0	r-exomedepth	1.1.16	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	29	410
+exonerate	exonerate	Exonerate is a generic tool for pairwise sequence comparison.	exonerate	exonerate		Exonerate	A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	Up-to-date	https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate	Sequence Analysis	exonerate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate	2.4.0	exonerate	2.4.0	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	59	988
+export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan		export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	Conversion	Taxonomy, Metabolomics, Biomarkers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	200	5265
+extract_genomic_dna	Extract genomic DNA 1	Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes.								To update		Genomic Interval Operations	extract_genomic_dna	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna	https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna	3.0.3+galaxy2	bx-python	0.13.0			1	0	1	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	1	1	1	1	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	285	11846
+falco	falco	A high throughput sequence QC analysis tool	falco	falco		Falco	A high-speed FastQC emulation for quality control of sequencing data.	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	Up-to-date	https://github.com/smithlabcode/falco/	Sequence Analysis	falco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco	https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco	1.2.4	falco	1.2.4	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fargene	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fargene		fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	52	459
+fasplit	fasplit	faSplit is a tool to split a single FASTA file into several files	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Fasta Manipulation	ucsc_fasplit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	469	ucsc-fasplit	469		Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	242	2644
+fasta_clipping_histogram	cshl_fasta_clipping_histogram	Length Distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Graphics, Statistics	fasta_clipping_histogram	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram	0.0.14	fastx_toolkit	0.0.14			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+fasta_formatter	cshl_fasta_formatter	FASTA Width formatter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_formatter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	1	68	2912
+fasta_nucleotide_changer	cshl_fasta_nucleotides_changer	RNA/DNA converter.								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_nucleotide_changer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	29	774
+fasta_nucleotide_color_plot	fasta_nucleotide_color_plot	Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot	Visualization	fasta_nucleotide_color_plot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15	160
+fasta_stats	fasta-stats	Display summary statistics for a fasta file.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	Sequence Analysis	fasta_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats	2.0	numpy				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1080	35336
+fastani	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity	fastani	fastani		FastANI	FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	250	3498
+fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fastp	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp		fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	Sequence contamination filtering	Probes and primers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	2803	1055760
+fastq_combiner	fastq_combiner	Combine FASTA and QUAL into FASTQ								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation, Fasta Manipulation	fastq_combiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	66	8676
+fastq_filter	fastq_filter	Filter FASTQ reads by quality score and length								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	266	14222
+fastq_groomer	fastq_groomer	Convert between various FASTQ quality formats.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_groomer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1028	94802
+fastq_manipulation	fastq_manipulation	Manipulate FASTQ reads on various attributes.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_manipulation	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	69	2503
+fastq_masker_by_quality	fastq_masker_by_quality	FASTQ Masker by quality score								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_masker_by_quality	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	170
+fastq_paired_end_deinterlacer	fastq_paired_end_deinterlacer	FASTQ de-interlacer on paired end reads.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_deinterlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	122	8410
+fastq_paired_end_interlacer	fastq_paired_end_interlacer	FASTQ interlacer on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_interlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1087	17024
+fastq_paired_end_joiner	fastq_paired_end_joiner	FASTQ joiner on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_joiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	245	16635
+fastq_paired_end_splitter	fastq_paired_end_splitter	FASTQ splitter on joined paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	196	3092
+fastq_quality_boxplot	cshl_fastq_quality_boxplot	Draw quality score boxplot								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics, Statistics	fastq_quality_boxplot	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	51	1178
+fastq_quality_converter	cshl_fastq_quality_converter	Quality format converter (ASCII-Numeric)								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_converter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	11	220
+fastq_quality_filter	cshl_fastq_quality_filter	Filter by quality								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1509	15172
+fastq_stats	fastq_stats	FASTQ Summary Statistics by column								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_stats	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	221	4246
+fastq_to_fasta	cshl_fastq_to_fasta	FASTQ to FASTA converter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Convert Formats	fastq_to_fasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	419	13599
+fastq_to_tabular	fastq_to_tabular	FASTQ to Tabular converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_to_tabular	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	93	12593
+fastq_trimmer	fastq_trimmer	FASTQ Trimmer by quality								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	210	9757
+fastqc	fastqc	Read QC reports using FastQC	fastqc	fastqc		FastQC	This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	Fastq Manipulation	fastqc	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc	0.74+galaxy1	fastqc	0.12.1	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	1	1	1	1	1	0	17447	1556625
+fastqe	fastqe	FASTQE	fastqe	fastqe		FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	Sequencing quality control	Sequence analysis, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1266	4333
+fastqtofasta	fastq_to_fasta_python	FASTQ to FASTA converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastqtofasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1371	178178
+fasttree	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree		FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11		Phylogenetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	379	55434
+fastx_artifacts_filter	cshl_fastx_artifacts_filter	Remove sequencing artifacts								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_artifacts_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	27	1810
+fastx_barcode_splitter	cshl_fastx_barcode_splitter	Barcode Splitter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_barcode_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	128	16591
+fastx_clipper	cshl_fastx_clipper	Clip adapter sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_clipper	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	96	3333
+fastx_collapser	cshl_fastx_collapser	Collapse sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fastx_collapser	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	114	61218
+fastx_nucleotides_distribution	cshl_fastx_nucleotides_distribution	Draw nucleotides distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics	fastx_nucleotides_distribution	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	25	249
+fastx_quality_statistics	cshl_fastx_quality_statistics	Compute quality statistics								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Statistics	fastx_quality_statistics	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	63	2176
+fastx_renamer	cshl_fastx_renamer	Rename sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_renamer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	68	2280
+fastx_reverse_complement	cshl_fastx_reverse_complement	Reverse-Complement								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Fasta Manipulation	fastx_reverse_complement	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	156	10832
+fastx_trimmer	cshl_fastx_trimmer	Trim sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	205	13149
+fatovcf	fatovcf	Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_fatovcf	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf	448	ucsc-fatovcf	448		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	285
+featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	4679	696399
+feelnc	feelnc	Galaxy wrapper for FEELnc	feelnc	feelnc		FEELnc	A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.	Annotation, Classification	RNA-seq, Functional, regulatory and non-coding RNA	To update	https://github.com/tderrien/FEELnc	Sequence Analysis	feelnc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc	0.2.1	feelnc	0.2	Annotation, Classification	Functional, regulatory and non-coding RNA	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	46	1191
+fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fgsea	fgsea	Perform gene set testing using fgsea	fgsea	fgsea		fgsea	The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.	Gene-set enrichment analysis	Genetics	To update	https://bioconductor.org/packages/release/bioc/html/fgsea.html	Visualization, Transcriptomics, Statistics	fgsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea	1.8.0+galaxy1	bioconductor-fgsea	1.28.0	Gene-set enrichment analysis	Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	307	5240
+filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	617	30483
+flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	14	331
+flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	74	13759
+fraggenescan	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan		FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	Gene prediction	Genetics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	68	1102
+freebayes	freebayes, bamleftalign	Galaxy Freebayes Bayesian genetic variant detector tool	freebayes	freebayes		FreeBayes	Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.	Variant calling, Statistical calculation	Genomics, Genetic variation, Rare diseases	To update	https://github.com/ekg/freebayes	Variant Analysis	freebayes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes	1.3.6	freebayes	1.3.8	Variant calling, Statistical calculation	Genomics, Genetic variation, Rare diseases	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	2	2	2	0	3059	155087
+freec	control_freec	Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH.	freec	freec		FREEC	A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies.	Copy number estimation, Variant calling, Genome alignment	DNA structural variation, Oncology, Human genetics, Data mining	To update	http://boevalab.inf.ethz.ch/FREEC/	Variant Analysis	control_freec	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec	11.6	gawk		Copy number estimation, Variant calling, Genome alignment	Oncology, Human genetics, Data mining	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	44	665
+freyja	freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja		Freyja	Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset	RNA-Seq quantification	Metagenomics	To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.1	RNA-Seq quantification	Metagenomics	2	0	4	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	55	20021
+fsd	fsd, fsd_beforevsafter, fsd_regions, td	Tool that plots a histogram of sizes of read families								To update		Graphics	duplex_family_size_distribution	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd	1.0.2	matplotlib				4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	0	900	5906
+gatk4	gatk4_mutect2	A Galaxy wrapper for Mutect2 from GATK								To update	https://software.broadinstitute.org/gatk/gatk4	Variant Analysis	gatk4_mutect2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4	4.1.7.0	gatk4	4.5.0.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	181	2483
+gdcwebapp	data_source_gdcwebapp	GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format								To update	http://bioinf.iasi.cnr.it/gdcwebapp/	Data Source, Convert Formats	gdcwebapp	iuc	https://github.com/fabio-cumbo/GDCWebApp4Galaxy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp	1.0.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
+gecko	gecko	Ungapped genome comparison								Up-to-date	https://github.com/otorreno/gecko	Sequence Analysis	gecko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko	1.2	gecko	1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	112	519
+gemini	gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@	GEMINI: a flexible framework for exploring genome variation	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://github.com/arq5x/gemini	Sequence Analysis, Next Gen Mappers	gemini	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini	0.20.1	gemini	0.30.2	Sequence analysis, Genetic variation analysis	Sequence analysis	1	2	2	2	1	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	662	4916
+genebed_maf_to_fasta	GeneBed_Maf_Fasta2	Stitch gene blocks given a set of coding exon intervals								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/	Genomic Interval Operations	genebed_maf_to_fasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta	1.0.1+galaxy0					1	1	1	1	1	1	1	1	0	1	0	0	0	1	0	0	0	1	1	1	0	1	0	0	0	0	0	1	0	0	0	0	1	1	1	1	0	1	4
+genehunter_modscore	genehunter_modscore	Maximised LOD score pedigree analysis utility								To update	https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1	Variant Analysis	genehunter_modscore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore	3.0.0	ghm	3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+geneiobio	gene_iobio_display_generation_iframe	Gene.iobio is an interactive tool for variant and trio analysis.								To update	https://github.com/iobio/gene.iobio	Sequence Analysis	geneiobio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio	4.7.1+galaxy1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	67
+genetrack	genetrack	"Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand."								To update		ChIP-seq	genetrack	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack		numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+genomescope	genomescope	Analyze unassembled short reads								Up-to-date	https://github.com/tbenavi1/genomescope2.0	Statistics	genomescope	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope	2.0.1	genomescope2	2.0.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	329	2118
+genomic_super_signature	genomic_super_signature	Interpretation of RNAseq experiments through robust, efficient comparison to public databases	genomicsupersignature	genomicsupersignature		GenomicSuperSignature	GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	To update	https://github.com/shbrief/GenomicSuperSignature	Sequence Analysis, RNA, Transcriptomics	genomic_super_signature	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature	1.2.0	bioconductor-genomicsupersignature	1.10.0	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11	46
+genrich	genrich	Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).								To update	https://github.com/jsh58/Genrich	ChIP-seq	genrich	iuc	https://github.com/jsh58/Genrich	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich	0.5+galaxy2	genrich	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	79	3515
+get_hrun	get_hrun	Annotate indel variants with homopolymer context								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun	Variant Analysis	get_hrun	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun	https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun	0.5.9.2	pyfaidx	0.8.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	4
+getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	18	495
+gfa_to_fa	gfa_to_fa	gfa_to_fa - Converting GFA format to Fasta format								To update	http://gfa-spec.github.io/GFA-spec/	Convert Formats	gfa_to_fa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa	0.1.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	332	8274
+gff3_rebase	gff3.rebase	Rebase a GFF against a parent GFF (e.g. an original genome)								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	Sequence Analysis	gff3_rebase	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase	1.2	bcbiogff	0.6.6			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	135
+gffcompare	gffcompare	Galaxy wrappers for Geo Pertea's GffCompare package.	gffcompare	gffcompare		gffcompare	Program for comparing, annotating, merging and tracking transcripts in GFF files.	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	https://github.com/gpertea/gffcompare/	Transcriptomics	gffcompare	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare	0.12.6	gffcompare	0.12.6	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	381	3477
+gffread	gffread	gffread filters and/or converts GFF3/GTF2 records	gffread	gffread		gffread	program for filtering, converting and manipulating GFF files	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/	Sequence Analysis	gffread	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread	0.12.7	gffread	0.12.7	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	680	10995
+ggplot2	ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2		ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		Visualisation	Data visualisation	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	5	0	0	0	0	0	0	3	0	0	0	0	0	5	5	5	0	1388	22148
+ggupset	emc-ggupset	Create Upset Plots with ggupset								To update	https://github.com/const-ae/ggupset	Graphics	ggupset	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset	1.0	r-ggupset				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+glimmer	glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based	Glimmer makes gene predictions.	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	Sequence analysis, Genetic variation analysis	Sequence analysis	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	0	187	3965
+goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	408	5484
+goseq	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq		GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	Gene functional annotation	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1210	19167
+gprofiler	gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense	functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more								To update	https://biit.cs.ut.ee/gprofiler	Statistics, Web Services	gprofiler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler	@TOOL_VERSION@+galaxy11	r-gprofiler2				5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	196	3443
+graphembed	graphembed	Compute a 2D embedding of a data matrix given supervised class information								Up-to-date	https://github.com/fabriziocosta/GraphEmbed	Statistics, Graphics	graphembed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed	2.4	graph_embed	2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	63
+graphlan	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	graphlan	graphlan		GraPhlAn	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	432	9277
+gtdb_to_taxdump	gtdb_to_taxdump	Convert GTDB taxonomy to NCBI taxdump format	gtdb_to_taxdump	gtdb_to_taxdump		gtdb_to_taxdump	Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI.	Data handling, Mapping, Generation	Computational biology	Up-to-date	https://github.com/nick-youngblut/gtdb_to_taxdump	Metagenomics	gtdb_to_taxdump	iuc	https://github.com/nick-youngblut/gtdb_to_taxdump	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump	0.1.9	gtdb_to_taxdump	0.1.9	Data handling, Mapping, Generation	Computational biology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gtdbtk	gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 	GTDB-Tk	GTDB-Tk		GTDB-Tk	a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	Up-to-date	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.4.0	gtdbtk	2.4.0	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gtfToBed12	gtftobed12	Convert GTF files to BED12 format	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README	Convert Formats	gtftobed12	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12	357	ucsc-gtftogenepred	469		Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1200	8107
+gubbins	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins		Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	145	3340
+gvcftools	gvcftools_extract_variants	gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf.								To update	https://github.com/sequencing/gvcftools	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools	0.1	gvcftools	0.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gwastools	gwastools_manhattan_plot		gwastools	gwastools		GWASTools	Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.	Deposition, Analysis, Annotation	GWAS study	To update	https://bioconductor.org/packages/release/bioc/html/GWASTools.html	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools	0.1.0	bioconductor-gwastools	1.48.0	Deposition, Analysis, Annotation	GWAS study	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
+hamronization	hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization		hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	117	4459
+hansel	bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	Biohansel		BioHansel	BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	339
+hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	295
+happy	som.py	A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets.	hap.py	hap.py		hap.py	This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison.	Variant calling, Sequence analysis, Genotyping	Genomics, DNA polymorphism	To update	https://github.com/Illumina/hap.py	Variant Analysis	happy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy	0.3.14	hap.py	0.3.15	Variant calling, Sequence analysis, Genotyping	Genomics, DNA polymorphism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+heatmap2	ggplot2_heatmap2	heatmap.2 function from the R gplots package								To update	https://github.com/cran/gplots	Visualization	ggplot2_heatmap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2	3.1.3.1	r-gplots	2.17.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1953	44240
+heinz	heinz_bum, heinz, heinz_scoring, heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	heinz	heinz, bionet		Heinz	Tool for single-species active module discovery.	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	To update	https://github.com/ls-cwi/heinz	Transcriptomics, Visualization, Statistics	heinz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz	1.0	bioconductor-bionet	1.62.0	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	242	1186
+hgvsparser	hgvsparser	Parsing and building variant descriptor strings compliant with the HGVS standard								To update	https://github.com/VariantEffect/hgvsParseR/tree/master	Variant Analysis	hgvsparser	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+hicexplorer	hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations	HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.								Up-to-date	https://github.com/deeptools/HiCExplorer	Sequence Analysis, Visualization	hicexplorer	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer	3.7.5	hicexplorer	3.7.5			38	38	38	4	38	38	38	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	33	36	33	0	1085	66003
+hicstuff	hicstuff_pipeline	A toolkit to generate and manipulate Hi-C matrices								To update	https://github.com/koszullab/hicstuff	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff	3.1.5	hicstuff	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	1410
+hifiasm_meta	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	hifiasm-meta		Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	Sequence assembly	Sequence assembly, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	137
+hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	4183	299104
+hivclustering	hivclustering	Infers transmission networks from pairwise distances inferred by tn93								To update	https://pypi.org/project/hivclustering/	Next Gen Mappers	hivclustering	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering	1.3.1	python-hivclustering	1.8.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+hmmer3	hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	hmmer3	hmmer3		HMMER3	This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	0	12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	12	12	12	0	439	33702
+homer	homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide	HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.	homer	homer		homer	HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein).  It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other.  It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment.  HOMER also tries its best to account for sequenced bias in the dataset.  It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.	Sequence motif discovery		Up-to-date	http://homer.ucsd.edu/homer/index.html	Sequence Analysis	data_manager_homer_preparse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer	4.11	homer	4.11	Sequence motif discovery		0	0	5	4	0	0	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	5	0	0	394	6937
+htseq_count	htseq_count	Count aligned reads (SAM/BAM) that overlap genomic features (GFF)	htseq	htseq		HTSeq	Python framework to process and analyse high-throughput sequencing (HTS) data	Nucleic acid sequence analysis	Sequence analysis	Up-to-date	https://readthedocs.org/projects/htseq/	Genomic Interval Operations, SAM, Sequence Analysis, RNA	htseq_count	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count	2.0.5	htseq	2.0.5	Nucleic acid sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1419	154533
+humann	humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	humann	humann		humann	HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	Up-to-date	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.9	humann	3.9	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	6	10	10	10	6	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	1037	19490
+hybpiper	hybpiper	Analyse targeted sequence capture data	HybPiper	HybPiper		HybPiper	Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	To update	https://github.com/mossmatters/HybPiper	Sequence Analysis, Phylogenetics	hybpiper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper	2.1.6	hybpiper	2.3.0	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+hyphy	hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy		HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.62	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	17	2	17	2	17	2	17	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	12	17	12	0	161	10370
+hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354
+icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	69	1127
+idr	idr	Galaxy wrappers for the IDR package from Nathan Boleu								To update	https://github.com/nboley/idr	Sequence Analysis	idr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr	2.0.3	idr	2.0.4.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	30	2873
+idr_download	idr_download_by_ids	Image Data Resource downloading tool								To update	https://idr.openmicroscopy.org	Data Source	idr_download_by_ids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download	0.45	omero-py	5.11.1			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10	361
+iedb_api	iedb_api	Get epitope binding predictions from IEDB-API								To update	http://tools.immuneepitope.org/main/tools-api/	Data Source, Sequence Analysis	iedb_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api	2.15.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	1506
+infercnv	infercnv	Infer Copy Number Variation from Single-Cell RNA-Seq Data								Up-to-date	https://github.com/broadinstitute/infercnv	Transcriptomics, Variant Analysis	infercnv	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv	1.20.0	bioconductor-infercnv	1.20.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+instrain	instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	instrain	instrain		InStrain	InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	SNP detection, Genome comparison	Mapping, Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	94
+integron_finder	integron_finder	"""IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"""	integron_finder	integron_finder		Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.5	integron_finder	2.0.5	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	58	52965
+intermine_galaxy_exchange	galaxy_intermine_exchange	InterMine Exporter								To update	https://github.com/intermine	Convert Formats	intermine_galaxy_exchange	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange	https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange	0.0.1	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	44
+interproscan	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi		InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	677	35243
+interval2maf	Interval2Maf1	Extract MAF blocks given a set of intervals	bx-python	bx-python		bx-python	Tools for manipulating biological data, particularly multiple sequence alignments.		Sequence analysis	To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	interval2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf	1.0.1+galaxy1	bx-python	0.13.0		Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	105
+intervene	intervene_pairwise, intervene_upset	Create pairwise and upset plots	intervene	intervene		Intervene	Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps.	Sequence comparison, Sequence visualisation	Computational biology	Up-to-date	https://intervene.readthedocs.io	Statistics	intervene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene	0.6.5	intervene	0.6.5	Sequence comparison, Sequence visualisation	Computational biology	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	136	1497
+iqtree	iqtree	Efficient phylogenomic software by maximum likelihood	iqtree	iqtree		iqtree	A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time	Phylogenetic analysis, Sequence analysis	Phylogenetics	Up-to-date	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.3.6	iqtree	2.3.6	Phylogenetic analysis, Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	681	21598
+irissv	irissv	Refine insertion sequences								To update	https://github.com/mkirsche/Iris	Variant Analysis	irissv	iuc	https://github.com/galaxyproject/tools-iuc/tools/irissv/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv	1.0.5	samtools	1.21			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4	29
+isescan	isescan	"""ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."""	ISEScan	ISEScan		ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	Structural variation detection	Genomics, Sequence analysis, Genetic variation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	50	57581
+isoformswitchanalyzer	isoformswitchanalyzer	Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.	IsoformSwitchAnalyzeR	IsoformSwitchAnalyzeR		IsoformSwitchAnalyzeR	Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	To update	https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html	Transcriptomics, RNA, Statistics	isoformswitchanalyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer	1.20.0	bioconductor-isoformswitchanalyzer	2.2.0	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	822
+ivar	ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing								Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.3	ivar	1.4.3			5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	4	0	0	0	4	0	0	0	0	0	5	5	5	0	1171	1224275
+iwtomics	iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot	Interval-Wise Testing for Omics Data	iwtomics	iwtomics		IWTomics	"Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset."	Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison	Statistics and probability	To update	https://bioconductor.org/packages/release/bioc/html/IWTomics.html	Statistics	iwtomics	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics	1.0.0	bioconductor-iwtomics	1.26.0	Differential gene expression analysis, Peak calling, Genome annotation, Comparison	Statistics and probability	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	3	542
+jasminesv	jasminesv	Merge structural variants across samples								To update	https://github.com/mkirsche/Jasmine/	Variant Analysis	jasminesv	iuc	https://github.com/galaxyproject/tools-iuc/jasminesv/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv	1.0.11	jasminesv	1.1.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3	30
+jbrowse	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse		JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	Genome visualisation	Genomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	2	2	2	0	2346	18229
+jcvi_gff_stats	jcvi_gff_stats	Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)								To update	https://github.com/tanghaibao/jcvi	Sequence Analysis	jcvi_gff_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats	0.8.4	jcvi	1.4.16			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	2469
+jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138
+join_files_by_id	join_files_by_id	This tool will join datasets according to a column with identifier								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id	Text Manipulation	join_files_by_id	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id	https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id	1.0	r-data.table	1.11.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+jq	jq	JQ is a lightweight and flexible command-line JSON processor								To update	https://stedolan.github.io/jq/	Text Manipulation	jq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq	1.0	jq	1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	21	2312
+jvarkit	jvarkit_wgscoverageplotter	Jvarkit : Java utilities for Bioinformatics								Up-to-date	https://lindenb.github.io/jvarkit/	SAM	jvarkit	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit	20201223	jvarkit-wgscoverageplotter	20201223			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	249	6285
+kallisto	kallisto_pseudo, kallisto_quant	kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment.	kallisto	kallisto		kallisto	A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.	Gene expression profiling	Transcriptomics, RNA-seq, Gene expression	To update	https://pachterlab.github.io/kallisto/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto	0.48.0	kallisto	0.51.1	Gene expression profiling	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	299	24155
+kc-align	kc-align	Kc-Align custom tool	kc-align	kc-align		kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	Multiple sequence alignment	Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19	363
+khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	8	8	8	0	63	2022
+king	king	Kinship-based INference for Gwas								Up-to-date	http://people.virginia.edu/~wc9c/KING/	Variant Analysis	king	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/king	2.2.7	king	2.2.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	5
+kleborate	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	kleborate	kleborate		Kleborate	Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	To update	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	3.0.9	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	38	319
+kma	kma_map	Map with KMA								To update	https://bitbucket.org/genomicepidemiology/kma	Next Gen Mappers	kma	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma	1.4.14	kma	1.4.15			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0
+kofamscan	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	kofamscan	kofamscan		kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	Sequence analysis, Gene functional annotation	Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	33	594
+kraken	kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	kraken	kraken		Kraken	System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	Taxonomic classification	Taxonomy, Metagenomics	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	5	0	1209	33778
+kraken2	kraken2	Kraken2 for taxonomic designation.	kraken2	kraken2		kraken2	Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	Up-to-date	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.3	kraken2	2.1.3	Taxonomic classification	Taxonomy, Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	2367	185308
+kraken_biom	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)								Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	182	1444
+kraken_taxonomy_report	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report		Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	Visualisation, Classification	Metagenomics, Taxonomy	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	354	2527
+krakentools	krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	krakentools		KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	Visualisation, Aggregation	Taxonomy, Metagenomics	6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	1	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	703	16525
+krocus	krocus	Predict MLST directly from uncorrected long reads	krocus	krocus		krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	Multilocus sequence typing, k-mer counting	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+last	last_al, last_db, last_split, last_train, last_maf_convert	LAST finds similar regions between sequences.	last	last		LAST	Short read alignment program incorporating quality scores	Sequence alignment	Genomics, Comparative genomics	To update	http://last.cbrc.jp/	Sequence Analysis	last	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/last	https://github.com/galaxyproject/tools-iuc/tree/main/tools/last	1205	last	1584	Sequence alignment	Comparative genomics	0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	41	227
+lastz	lastz_wrapper_2, lastz_d_wrapper	Galaxy wrappers for the Lastz and Lastz_d	lastz	lastz		LASTZ	A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically.	Sequence alignment, Read mapping	Genomics	Up-to-date	https://github.com/lastz/lastz	Next Gen Mappers	lastz	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz	1.04.22	lastz	1.04.22	Sequence alignment, Read mapping	Genomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	2	0	0	0	0	0	0	0	0	0	2	2	2	0	188	83331
+lcrgenie	lcrgenie	Ligase Chain Reaction Genie								To update	https://github.com/neilswainston/LCRGenie	Synthetic Biology	lcrgenie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie	1.0.2	lcr_genie				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+legsta	legsta	Performs in silico Legionella pneumophila sequence based typing.	legsta	legsta		legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	Sequence analysis	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	55
+length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	322	4090
+limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1012	20344
+lineagespot	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	lineagespot	lineagespot		lineagespot	Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	37
+links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	77	405
+lofreq	lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi	LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering.								Up-to-date	https://csb5.github.io/lofreq/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq	2.1.5	lofreq	2.1.5			5	5	5	4	5	5	5	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	0	0	0	4	0	0	0	0	0	5	5	5	0	1791	4150903
+lorikeet	lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet		lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	Sequence analysis, Genotyping	Genotype and phenotype	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	647
+lumpy_sv	lumpy_prep, lumpy_sv	LUMPY - a general probabilistic framework for structural variant discovery								Up-to-date	http://layerlab.org/software/	Variant Analysis	lumpy_sv	iuc	https://github.com/arq5x/lumpy-sv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv	0.3.1	lumpy-sv	0.3.1			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	105	1164
+m6anet	m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet		m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3
+maaslin2	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	maaslin2	maaslin2		MaAsLin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	Up-to-date	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	1.18.0	bioconductor-maaslin2	1.18.0	Filtering, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	188
+macs2	macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak	MACS - Model-based Analysis of ChIP-Seq	macs	macs		MACS	Model-based Analysis of ChIP-seq data.	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	Up-to-date	https://github.com/taoliu/MACS	Sequence Analysis, Statistics	macs2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2	2.2.9.1	macs2	2.2.9.1	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	0	9	9	0	0	0	0	0	0	0	9	0	0	0	0	0	9	9	9	0	1969	84521
+maf_stats	maf_stats1	MAF Coverage statistics								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	maf_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats	1.0.2+galaxy0					1	1	1	1	1	1	1	1	0	1	0	0	0	1	0	0	0	1	1	1	0	1	0	0	0	0	0	1	0	0	0	0	1	1	1	1	0	3	21
+maftoaxt	maftoaxt	Convert dataset from MAF to axt format	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_maftoaxt	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt	469	ucsc-maftoaxt	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mageck	mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test	Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.	mageck	mageck		MAGeCK	Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.	Genetic variation analysis	Genetics, Genetic variation, Genomics	To update	https://sourceforge.net/projects/mageck/	Genome editing		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck	0.5.9.2	mageck	0.5.9.5	Genetic variation analysis	Genetics, Genetic variation, Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	587	10503
+maker	maker, maker_map_ids	MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	maker	maker		MAKER	Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	Genome annotation	Genomics, DNA, Sequence analysis	To update	http://www.yandell-lab.org/software/maker.html	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker	2.31.11	maker	3.01.03	Genome annotation	Genomics, DNA, Sequence analysis	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	554	5591
+malt	malt_run	Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences.								To update	https://github.com/husonlab/malt	Next Gen Mappers	malt_run	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt	0.5.3	malt	0.62			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	22
+map_param_value	map_param_value	Map a parameter value to another value								To update		Text Manipulation	map_param_value	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value	https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value	0.2.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	1528
+mapseq	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	mapseq	mapseq		MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .	k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	To update	https://github.com/jfmrod/MAPseq	Metagenomics	mapseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq	2.1.1	perl		k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	167
+mash	mash_screen, mash_sketch	Fast genome and metagenome distance estimation using MinHash	mash	mash		Mash	Fast genome and metagenome distance estimation using MinHash.	Sequence distance matrix generation	Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	Up-to-date	https://github.com/marbl/Mash	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash	2.3	mash	2.3	Sequence distance matrix generation	Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	27	9763
+mashmap	mashmap	Fast local alignment boundaries								Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	Sequence Analysis	mashmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap	3.1.3	mashmap	3.1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+masigpro	masigpro	Identify significantly differential expression profiles in time-course microarray experiments	masigpro	masigpro		maSigPro	Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.	Regression analysis	Gene expression, Molecular genetics, Microarray experiment, RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html	Transcriptomics, RNA, Statistics	masigpro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro	1.49.3	coreutils	8.25	Regression analysis	Gene expression, Microarray experiment, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13	576
+maxbin2	maxbin2	clusters metagenomic contigs into bins	maxbin	maxbin		MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	To update	https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html	Metagenomics	maxbin2	mbernt	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2		maxbin2	2.2.7	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	118	2059
+mcl	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	mcl	mcl		MCL	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.	Clustering, Network analysis, Gene regulatory network analysis	Molecular interactions, pathways and networks	Up-to-date	https://micans.org/mcl/man/mcl.html	Sequence Analysis	mcl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/mcl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl	22.282	mcl	22.282	Clustering, Gene regulatory network analysis	Molecular interactions, pathways and networks	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	29
+medaka	medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	medaka	medaka		Medaka	medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	2.0.0	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	2	0	0	0	0	0	3	3	3	0	768	99863
+megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	548	9530
+megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	54	475
+megan	megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma	MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data.  MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).	megan	megan		MEGAN	Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Sequence analysis, Taxonomic classification	Sequence analysis	To update	https://github.com/husonlab/megan-ce	Sequence Analysis	megan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan	6.21.7	megan	6.25.9	Sequence analysis, Taxonomic classification	Sequence analysis	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	261	3610
+meme	meme_dreme, meme_fimo, meme_meme, meme_psp_gen	The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses.	meme_meme	meme_meme, meme_fimo		meme_meme	An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.	Nucleic acid feature detection, Protein feature detection, Statistical calculation	Data mining, Sequence analysis, Genetic variation, Statistics and probability	To update	http://meme-suite.org/	ChIP-seq	meme	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme	5.5.6	meme	5.5.7	Nucleic acid feature detection, Protein feature detection, Statistical calculation	Data mining, Sequence analysis, Genetic variation, Statistics and probability	3	0	4	0	3	0	4	0	0	0	0	0	0	0	0	0	0	0	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0	3	4	4	0	235	22352
+meme_chip	meme_chip	Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.								To update	http://meme-suite.org/	ChIP-seq	meme_chip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip	4.11.2	graphicsmagick	1.3.26			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	287	6584
+meningotype	meningotype	Assign sequence type to N. meningitidis genome assemblies	meningotype	meningotype		meningotype	In silico typing of Neisseria meningitidis contigs.	Genotyping, Multilocus sequence typing	Microbiology, Genotype and phenotype	Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype	0.8.5	meningotype	0.8.5	Multilocus sequence typing	Microbiology, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+merlin	merlin	Pedigree Analysis package	merlin	merlin		Merlin	Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation	Haplotype mapping, Genetic mapping	GWAS study, Mapping	Up-to-date	http://csg.sph.umich.edu/abecasis/Merlin/	Variant Analysis	merlin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin	1.1.2	merlin	1.1.2	Haplotype mapping	GWAS study, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483
+meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+metabat2	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT_2		MetaBAT 2	"an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning"	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	To update	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.17	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	2	1	2	2	2	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	192	4329
+metabuli	metabuli_classify	Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences	metabuli	metabuli		metabuli	Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid	Taxonomic classification	Taxonomy	To update	https://github.com/steineggerlab/Metabuli	Sequence Analysis, Metagenomics	metabuli	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli	1.0.5	metabuli	1.0.8	Taxonomic classification	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	5.34c21f2	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	184
+metagenomeseq	metagenomeseq_normalizaton	metagenomeSeq Normalization	metagenomeseq	metagenomeseq		metagenomeSeq	Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	To update	https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html	Metagenomics	metagenomeseq_normalization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq	1.16.0-0.0.1	bioconductor-metagenomeseq	1.43.0	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6	753
+metaphlan	customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	metaphlan	metaphlan		MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.	Nucleic acid sequence analysis, Phylogenetic tree analysis	Metagenomics, Phylogenomics	Up-to-date	https://github.com/biobakery/MetaPhlAn	Metagenomics	metaphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan	4.1.1	metaphlan	4.1.1	Nucleic acid sequence analysis	Metagenomics, Phylogenomics	1	2	4	4	1	2	4	4	0	0	0	0	0	0	0	0	0	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	499	11069
+metawrapmg	metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	metawrap	metawrap		MetaWRAP	MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	Up-to-date	https://github.com/bxlab/metaWRAP	Metagenomics	metawrapmg_binning	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg	1.3.0	metawrap-mg	1.3.0	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mg_toolkit	mg_toolkit_bulk_download, mg_toolkit_original_metadata	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	mg-toolkit	mg-toolkit		mg-toolkit	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	Data retrieval	Metagenomics	Up-to-date	https://github.com/EBI-Metagenomics/emg-toolkit	Metagenomics	mg_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	0.10.4	mg-toolkit	0.10.4	Data retrieval	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+microsatbed	microsatbed	Select microsatellites for a bed file								To update	https://github.com/lmdu/pytrf	Sequence Analysis	microsatbed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed	1.3.3	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+migmap	migmap	mapper for full-length T- and B-cell repertoire sequencing	MiGMAP	MiGMAP		MiGMAP	Mapper for full-length T- and B-cell repertoire sequencing.	Sequence analysis, Read mapping	Immunoproteins, genes and antigens, Sequence analysis	Up-to-date	https://github.com/mikessh/migmap	RNA, Sequence Analysis	migmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap	1.0.3	migmap	1.0.3	Sequence analysis, Read mapping	Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	1226
+minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	109	2206
+miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	178	11938
+minimap2	minimap2	A fast pairwise aligner for genomic and spliced nucleotide sequences	minimap2	minimap2		Minimap2	Pairwise aligner for genomic and spliced nucleotide sequences	Pairwise sequence alignment	Mapping	Up-to-date	https://github.com/lh3/minimap2	Next Gen Mappers	minimap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2	2.28	minimap2	2.28	Pairwise sequence alignment	Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1588	260442
+miniprot	miniprot, miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	miniprot	miniprot		miniprot	Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	Up-to-date	https://github.com/lh3/miniprot	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot	0.13	miniprot	0.13	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	30	842
+mirmachine	mirmachine	Tool to detect miRNA in genome sequences								Up-to-date	https://github.com/sinanugur/MirMachine	Sequence Analysis	mirmachine	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine	0.2.13	mirmachine	0.2.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mirnature	mirnature	Computational detection of canonical microRNAs								Up-to-date	https://github.com/Bierinformatik/miRNAture	RNA, Sequence Analysis	mirnature	iuc	https://github.com/Bierinformatik/miRNAture	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature	1.1	mirnature	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	10
+mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	66	881
+mitos	mitos, mitos2	de-novo annotation of metazoan mitochondrial genomes	mitos	mitos		MITOS	De novo metazoan mitochondrial genome annotation.	Genome annotation	Zoology, Whole genome sequencing	To update	http://mitos.bioinf.uni-leipzig.de/	Sequence Analysis	mitos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos	1.1.7	mitos	2.1.9	Genome annotation	Zoology, Whole genome sequencing	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	0	236	100920
+mlst	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst		MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	Multilocus sequence typing	Immunoproteins and antigens	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	635	9304
+moabs	moabs	MOABS for differential methylation analysis on Bisulfite sequencing data.								To update	https://github.com/sunnyisgalaxy/moabs	Epigenetics	moabs	iuc	https://github.com/sunnyisgalaxy/moabs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs	1.3.4.6	moabs	1.3.9.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19	317
+mosdepth	mosdepth	fast and flexible BAM/CRAM depth calculation								Up-to-date	https://github.com/brentp/mosdepth	SAM	mosdepth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth	0.3.8	mosdepth	0.3.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	262
+mothur	mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn	Mothur wrappers	mothur	mothur		mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	129	129	129	129	129	129	129	129	0	0	0	0	0	0	0	0	0	0	128	0	3	0	0	0	0	0	0	0	0	0	0	0	0	126	129	129	0	14353	302916
+msaboot	msaboot	A multiple sequences alignment bootstrapping tool.								Up-to-date	https://github.com/phac-nml/msaboot	Fasta Manipulation	msaboot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot	0.1.2	msaboot	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34	803
+multigps	multigps	Analyzes collections of multi-condition ChIP-seq data.								To update	http://mahonylab.org/software/multigps/	ChIP-seq	multigps	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps	0.74.0	fonts-conda-ecosystem				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	53
+multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	8320	162790
+mummer4	mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords	Mummer4 Tools	mummer4	mummer4						Up-to-date	https://github.com/mummer4/mummer	Sequence Analysis	mummer4	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4	4.0.0rc1	mummer4	4.0.0rc1			6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	6	3	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	669	18347
+mykrobe	mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe		Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mzmine	mzmine_batch	mass-spectrometry data processing, with the main focus on LC-MS data	mzmine	mzmine		MZmine	Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML.	Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation	Proteomics, Metabolomics, Proteomics experiment, Small molecules	Up-to-date	http://mzmine.github.io/	Metabolomics	mzmine_batch	iuc	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine	3.9.0	mzmine	3.9.0	Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation	Proteomics, Metabolomics, Proteomics experiment, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3
+naltorfs	bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs	nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)								Up-to-date	https://github.com/BlankenbergLab/nAltORFs	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs	0.1.2	naltorfs	0.1.2			3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+nanocompore	nanocompore_db, nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Nanocompore	Nanocompore		Nanocompore	RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	3	836
+nanoplot	nanoplot	Plotting tool for long read sequencing data and alignments	nanoplot	nanoplot		NanoPlot	NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences	Scatter plot plotting, Box-Whisker plot plotting	Genomics	Up-to-date	https://github.com/wdecoster/NanoPlot	Visualization	nanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot	1.43.0	nanoplot	1.43.0	Scatter plot plotting, Box-Whisker plot plotting	Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	2195	63235
+nanopolishcomp	nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate	NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.	nanopolishcomp	nanopolishcomp		NanopolishComp	NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	To update	https://a-slide.github.io/NanopolishComp	Sequence Analysis	nanopolishcomp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp	0.6.11	nanopolishcomp	0.6.12	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	15	1074
+ncbi_acc_download	ncbi_acc_download	Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API								Up-to-date	https://github.com/kblin/ncbi-acc-download	Data Source	ncbi_acc_download	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download	0.2.8	ncbi-acc-download	0.2.8			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	688	5487
+ncbi_datasets	datasets_download_gene, datasets_download_genome	NCBI datasets downloads biological sequence data across all domains of life from NCBI.	ncbi_datasets	ncbi_datasets		NCBI Datasets	NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface.	Data handling, Sequence database search, Data retrieval	Biological databases	To update	https://github.com/ncbi/datasets	Data Source	ncbi_datasets	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets	16.20.0	ncbi-datasets-cli		Data handling, Sequence database search, Data retrieval	Biological databases	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	1	2	2	0	667	3177
+ncbi_entrez_direct	ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch	NCBI Entrez Direct allow fetching data from NCBI Databases								Up-to-date	http://www.ncbi.nlm.nih.gov/books/NBK179288/	Data Source	ncbi_entrez_direct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct	22.4	entrez-direct	22.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ncbi_entrez_eutils	ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_egquery, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary	NCBI Entrez E-Utilties allow fetching data from NCBI Databases								To update	https://www.ncbi.nlm.nih.gov/books/NBK25501/	Data Source	ncbi_entrez_eutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils	1.70	python				0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	4	0	0	0	2	0	0	0	0	0	0	8	8	0	169	3193
+ncbi_fcs_gx	ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).	ncbi_fcs	ncbi_fcs		NCBI fcs	The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	Up-to-date	https://github.com/ncbi/fcs-gx	Sequence Analysis	ncbi_fcs_gx	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	0.5.4	ncbi-fcs-gx	0.5.4	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	95	667
+newick_utils	newick_display	Perform operations on Newick trees	newick_utilities	newick_utilities		Newick Utilities	The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.	Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction	Phylogeny, Genomics, Computer science	To update	http://cegg.unige.ch/newick_utils	Visualization, Metagenomics	newick_utils	iuc	https://github.com/tjunier/newick_utils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils	1.6+galaxy1	newick_utils	1.6		Phylogeny, Genomics, Computer science	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	448	25505
+nextclade	nextalign, nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	nextclade	nextclade		Nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.	Methylation analysis, Variant calling	Genomics, Sequence analysis, Cladistics	To update	https://github.com/nextstrain/nextclade	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade	2.7.0	nextalign	2.14.0	Methylation analysis, Variant calling	Genomics, Cladistics	1	1	2	2	1	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	0	0	0	1	0	0	0	0	0	0	2	0	0	210	4080
+ngmlr	ngmlr	CoNvex Gap-cost alignMents for Long Reads	ngmlr	ngmlr		NGMLR	An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation.	DNA mapping, Sequence alignment, Genetic variation analysis	Sequencing, Mapping, DNA structural variation	Up-to-date	https://github.com/philres/ngmlr	Next Gen Mappers	ngmlr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr	0.2.7	ngmlr	0.2.7	DNA mapping, Sequence alignment, Genetic variation analysis	Sequencing, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	21	1266
+ngsutils	ngsutils_bam_filter	NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed.	ngsutils	ngsutils		NGSUtils	NGSUtils is a suite of software tools for working with next-generation sequencing datasets	Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering	Genomics, Transcriptomics	To update	https://github.com/ngsutils/ngsutils	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils		ngsutils	0.5.9	Read pre-processing, Variant calling, Formatting, Sequence contamination filtering	Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	224	24740
+nonpareil	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil		nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.5.5	Operation		1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	142
+novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	162	6384
+nugen_nudup	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+obitools	obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq	OBITools is a set of programs developed to simplify the manipulation of sequence files	obitools	obitools		OBITools	Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	Up-to-date	http://metabarcoding.org/obitools	Sequence Analysis	obitools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools	1.2.13	obitools	1.2.13	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	0	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	503	26251
+ococo	ococo	Variant detection of SNVs								To update	https://github.com/karel-brinda/ococo	Variant Analysis	ococo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo	0.1.2.6	ococo	0.1.2.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	32	1877
+odgi	odgi_build, odgi_viz	Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.								To update	https://github.com/vgteam/odgi	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi	0.3	odgi	0.8.6			0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	2	25
+omark	omark	Proteome quality assessment software	omark	omark		OMArk	Proteome quality assessment software	Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	To update	https://github.com/DessimozLab/OMArk	Sequence Analysis	omark	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark	0.3.0			Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	39	2654
+onto_toolkit	onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def	ONTO-Toolkit is a collection of tools for managing ontologies.								Up-to-date	http://search.cpan.org/~easr/ONTO-PERL-1.45/	Ontology Manipulation	onto_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit	1.45	perl-onto-perl	1.45			0	0	17	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	0	22	655
+optdoe	optdoe	Optimal Design Of Experiment								To update	https://github.com/pablocarb/doebase	Synthetic Biology	optdoe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe	v2.0.2	doebase				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+optitype	optitype	Precision HLA typing from NGS data								Up-to-date	https://github.com/FRED-2/OptiType	Sequence Analysis	optitype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype	1.3.5	optitype	1.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	321
+orfipy	orfipy	Galaxy wrapper for ORFIPY	orfipy	orfipy		orfipy	A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	Up-to-date	https://github.com/urmi-21/orfipy	Sequence Analysis	orfipy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy	0.0.4	orfipy	0.0.4	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	774
+orthofinder	orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	OrthoFinder	OrthoFinder		OrthoFinder	OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.	Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis	Up-to-date	https://github.com/davidemms/OrthoFinder	Phylogenetics, Sequence Analysis	orthofinder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder	2.5.5	orthofinder	2.5.5	Genome comparison, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	239	1333
+packaged_annotation_loader	packaged_annotation_loader	Tool to make cached genome annotation data available as a list of datasets collection								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader	Data Source	packaged_annotation_loader	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader	https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader	0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pacu	pacu_map, pacu_snp	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.	pacu	pacu		PACU	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads).	Clustering	Phylogenetics, Sequence analysis	Up-to-date	https://github.com/BioinformaticsPlatformWIV-ISP/PACU	Sequence Analysis, Phylogenetics	pacu	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu	0.0.5	pacu_snp	0.0.5	Clustering	Phylogenetics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pairtools	pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats	Flexible tools for Hi-C data processing								Up-to-date	https://pairtools.readthedocs.io	Sequence Analysis	pairtools	iuc	https://github.com/open2c/pairtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools	1.1.0	pairtools	1.1.0			5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pangolin	pangolin	Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.	pangolin_cov-lineages	pangolin_cov-lineages		pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages	Tree-based sequence alignment, Variant classification	Virology	Up-to-date	https://github.com/cov-lineages/pangolin	Sequence Analysis	pangolin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin	4.3	pangolin	4.3	Tree-based sequence alignment, Variant classification	Virology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	0	0	259	7276
+parse_mito_blast	parse_mito_blast	Filtering blast out from querying assembly against mitochondrial database.								Up-to-date	https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py	Sequence Analysis	parse_mito_blast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast	1.0.2	parse_mito_blast	1.0.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	31	90
+pathview	pathview	Pathview is a tool set for pathway based data integration and visualization.	pathview	pathview		pathview	Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	To update	https://bioconductor.org/packages/release/bioc/html/pathview.html	Statistics, RNA, Micro-array Analysis	pathview	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview	1.34.0	bioconductor-pathview	1.42.0	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	565	5260
+pbgcpp	pbgcpp	Compute genomic consensus and call variants using PacBio reads mapped to a reference	genomicconsensus	genomicconsensus		GenomicConsensus	The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.	Variant calling	Mapping	Up-to-date	https://github.com/PacificBiosciences/gcpp	Variant Analysis	pbgcpp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp	2.0.2	pbgcpp	2.0.2	Variant calling	Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pbmm2	pbmm2	A minimap2 SMRT wrapper for PacBio data.	pbmm2	pbmm2		pbmm2	pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.	Pairwise sequence alignment, Sorting	Mapping	Up-to-date	https://github.com/PacificBiosciences/pbmm2	Next Gen Mappers	pbmm2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2	1.14.99	pbmm2	1.14.99	Pairwise sequence alignment, Sorting	Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pbtk	bam2fastx	Convert PacBio Bam File to fasta or fastq file								Up-to-date	https://github.com/PacificBiosciences/pbtk	Convert Formats, Fasta Manipulation, Fastq Manipulation	bam2fastx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk	3.1.1	pbtk	3.1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pe_histogram	pe_histogram	Contains a tool that produces an insert size histogram for a paired-end BAM file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram	Graphics	pe_histogram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram	1.0.1	openjdk				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	0	0	312	4180
+peakzilla	peakzilla	Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments.								To update	https://github.com/steinmann/peakzilla	ChIP-seq	peakzilla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla	1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pear	iuc_pear	PEAR evaluates all possible paired-end read overlaps	pear	pear		PEAR	Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.	Sequence merging	Sequence assembly	Up-to-date	https://cme.h-its.org/exelixis/web/software/pear/	Fastq Manipulation	pear	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear	0.9.6	pear	0.9.6	Sequence merging	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	150	4305
 pharokka	pharokka	rapid standardised annotation tool for bacteriophage genomes and metagenomes	pharokka	pharokka		Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.	Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	To update	https://github.com/gbouras13/pharokka	Genome annotation	pharokka	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	1.3.2	"
                 pharokka
-            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	74	2565
-phyloseq	phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	phyloseq	phyloseq		phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq	1.46.0	bioconductor-phyloseq	1.46.0	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	0	1	4	4	0	1	4	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	82	812
-phyml	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	phyml	phyml		PhyML	Phylogenetic estimation software using Maximum Likelihood	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Bioinformatics, Phylogenetics	Up-to-date	http://www.atgc-montpellier.fr/phyml/	Phylogenetics	phyml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml	3.3.20220408	phyml	3.3.20220408		Phylogenetics, Bioinformatics, Phylogenetics	0	1	1	1	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	104	1770
-picard	picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile	Picard SAM/BAM manipulation tools.	picard_samtofastq	picard_reordersam, picard_replacesamheader, picard_fastqtosam, picard_samtofastq		picard_samtofastq	Create a FASTQ file.	Formatting	Sequencing	To update	http://broadinstitute.github.io/picard/	SAM	picard	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard	3.1.1	picard	3.2.0	Formatting	Sequencing	31	31	31	31	31	31	31	31	0	29	0	0	31	0	0	0	0	0	0	0	31	4	31	0	0	31	0	0	0	31	0	0	0	0	0	0	0	31	31	0	3735	374458
-pick_value	pick_value	Compose a text parameter value using text, integer and float values								To update		Text Manipulation	pick_value	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value	0.2.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	116
-picrust	picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes	PICRUSt wrappers	picrust	picrust		PICRUSt	PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust	1.1.1	picrust	1.1.4	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	0	6	5	6	0	6	5	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	45	1095
-picrust2	picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions	PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	picrust2	picrust2		PICRUSt2	PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	Up-to-date	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.3	picrust2	2.5.3	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	88	1000
-pilon	pilon	pilon is a tool for assembly improvement and variant analysis in bacteria	pilon	pilon		pilon	Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.	Sequence assembly, Analysis, Read alignment	Assembly	To update	https://github.com/broadinstitute/pilon/wiki	Variant Analysis	pilon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon	1.20.1	pilon	1.24	Sequence assembly, Analysis	Assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	467	7942
-pipelign	pipelign	Multipe sequence alignment								Up-to-date	https://github.com/asmmhossain/pipelign/	Next Gen Mappers	pipelign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign	0.2	pipelign	0.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	83	983
-pizzly	pizzly	Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.								To update	https://github.com/pmelsted/pizzly/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly	0.37.3.1	pizzly	0.37.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	208
-plasflow	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	plasflow	plasflow		PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.	Sequence analysis	Metagenomics	Up-to-date	https://github.com/smaegol/PlasFlow	Sequence Analysis	plasflow	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow	1.1.0	plasflow	1.1.0	Sequence analysis	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	278	22589
-plasmidfinder	plasmidfinder	"""PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"""	PlasmidFinder	PlasmidFinder		PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	Up-to-date	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	Sequence Analysis	plasmidfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder	2.1.6	plasmidfinder	2.1.6	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	22
-plink	plink	Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	plink	plink		PLINK	Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	Genetic variation analysis	GWAS study	Up-to-date	https://www.cog-genomics.org/plink	Genome-Wide Association Study	plink	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink	1.90b6.21	plink	1.90b6.21	Genetic variation analysis	GWAS study	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	46	669
-polypolish	polypolish	"""Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."""	Polypolish	Polypolish		Polypolish	Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	To update	https://github.com/rrwick/Polypolish	Sequence Analysis	polypolish	iuc	https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish	0.5.0	polypolish	0.6.0	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	239
-porechop	porechop	Porechop - Finding and removing adapters from Oxford Nanopore reads								To update	https://github.com/rrwick/Porechop	Fasta Manipulation, Fastq Manipulation	porechop	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop	https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop		porechop	0.2.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1046	185468
-poretools	poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot	A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	poretools	poretools		Poretools	Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	Nucleic acid sequence analysis	DNA, Sequencing	Up-to-date	https://poretools.readthedocs.io/en/latest/	Fasta Manipulation, Fastq Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools	0.6.1a1	poretools	0.6.1a1	Nucleic acid sequence analysis	DNA, Sequencing	13	13	13	0	13	13	13	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	13	0	409	18773
-presto	presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3	pRESTO toolkit for immune repertoire analysis.	presto	presto		pRESTO	Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	To update	https://presto.readthedocs.io/	Sequence Analysis	presto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto	0.6.2	presto	0.7.2	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pretext	pretext_graph, pretext_map, pretext_snapshot	Process genome contacts maps processing images.								Up-to-date	https://github.com/wtsi-hpag/PretextSnapshot	Sequence Analysis	suite_pretext	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext	0.0.6	pretextgraph	0.0.6			3	2	3	0	3	2	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	254	2350
-prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	70	7881
-prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-progressivemauve	progressivemauve, xmfa2gff3	Mauve/ProgressiveMauve Multiple Sequence Aligner								To update	http://darlinglab.org/mauve/user-guide/progressivemauve.html	Sequence Analysis	progressivemauve	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve	https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve		progressivemauve	snapshot_2015_02_13			2	0	2	0	2	0	2	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	286	1734
-prokka	prokka	Rapid annotation of prokaryotic genomes	prokka	prokka		Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka	1.14.6	prokka	1.14.6	Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	0	1	1	0	3233	371445
-prot-scriber	prot_scriber	Protein annotation of short human readable descriptions								Up-to-date	https://github.com/usadellab/prot-scriber	Proteomics	prot_scriber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber	0.1.6	prot-scriber	0.1.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	5
-proteinortho	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho		Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	To update	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.2	Sequence clustering, Sequence analysis	Comparative genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	200	3320
-psiclass	psiclass	PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.	psiclass	psiclass		PsiCLASS	Reference-based transcriptome assembler for single or multiple RNA-seq samples	Transcriptome assembly	Sequence assembly	Up-to-date	https://github.com/splicebox/PsiCLASS	Transcriptomics	psiclass	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass	https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass	1.0.3	psiclass	1.0.3	Transcriptome assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	15
-pureclip	pureclip	PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data								To update	https://github.com/skrakau/PureCLIP	Sequence Analysis, RNA, CLIP-seq	pureclip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip	1.0.4	pureclip	1.3.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	1423
-purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	167	16800
-pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	350	21123
-pyega3	pyega3	EGA python client uses the EGA REST API to download authorized datasets and files.								To update	https://github.com/EGA-archive/ega-download-client	Data Source	ega_download_client	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3	5.0.2	pyega3	5.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	38	2424
-pygenometracks	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	pygenometracks	pygenometracks		pyGenomeTracks	reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	Visualisation, Formatting	Model organisms, Imaging, Workflows	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	377	11332
-pysradb	pysradb_search	pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.	pysradb	pysradb		pysradb	Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	To update	https://github.com/saketkc/pysradb	Sequence Analysis	pysradb_search	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb	1.4.2	pysradb	2.2.1	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	26	144
-qfilt	qfilt	Filter sequencing data								To update	https://github.com/veg/qfilt	Fastq Manipulation	qfilt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt	1.0.0+galaxy1	qfilt	0.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-qiime_add_on	qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_add_on, qiime_core		qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	68	1909
-qiime_core	qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file	QIIME to perform microbial community analysis	qiime_core	qiime_core		qiime_core	QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	32	32	0	0	32	32	0	0	0	0	0	0	0	0	0	0	0	0	31	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	0	1155	28681
-qiime_extract_viz	qiime_extract_viz	Extract vizualization from QIIME artifacts								To update	http://www.qiime.org	Metagenomics	qiime_extract_viz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz	0.1.0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-qq_tools	qq_manhattan									To update	https://CRAN.R-project.org/package=qqman	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools	0.1.0	r-qqman	0.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-qualimap	qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq	Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.	qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	Up-to-date	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.3	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	1	4	4	4	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1	0	0	0	1	0	0	0	0	0	0	0	4	4	0	1328	664470
-quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	3567	51567
-query_impc	query_impc	Contains a tool to query the IMPC database.								To update	https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc	Convert Formats, Web Services	query_impc	iuc	https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc	0.9.0	requests				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
-query_tabular	filter_tabular, query_tabular, sqlite_to_tabular	Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular	3.3.1	python				3	3	3	1	3	3	3	1	0	0	0	0	0	0	0	0	0	0	0	0	0	3	2	0	0	0	0	0	0	1	0	0	0	0	0	0	0	3	3	0	561	124536
-quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
-raceid	raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory	RaceID3, StemID2, FateID - scRNA analysis								To update	https://github.com/dgrun/RaceID3_StemID2_package/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid	0.2.3	r-raceid	0.1.3			5	5	5	1	5	5	5	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	82	4569
-ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	237	2833
-rapidnj	rapidnj	Galaxy wrapper for the RapidNJ tool	rapidnj	rapidnj		RapidNJ	A tool for fast canonical neighbor-joining tree construction.	Phylogenetic tree generation	Phylogeny	Up-to-date	https://birc.au.dk/software/rapidnj/	Phylogenetics	rapidnj	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj	2.3.2	rapidnj	2.3.2		Phylogeny	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	176
-rasusa	rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa		rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	2.0.0	rasusa	2.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	6902
-raxml	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml		RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	Sequence analysis	Phylogenetics	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	383	6808
-rcorrector	rcorrector	Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.	rcorrector	rcorrector		Rcorrector	This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.	Sequencing error detection	RNA, RNA-Seq, Sequencing	To update	https://github.com/mourisl/Rcorrector	Fastq Manipulation	rcorrector	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector	1.0.3+galaxy1	rcorrector	1.0.7	Sequencing error detection	RNA, RNA-Seq	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	569
-read_it_and_keep	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep		read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	Filtering, Genome alignment	Pathology, Genomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	3370
-recentrifuge	recentrifuge	"""With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."""	Recentrifuge	Recentrifuge		Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.14.1	recentrifuge	1.14.1	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	48	331
-red	red	Red (REpeat Detector)	red	red		RED	This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	Up-to-date	https://github.com/BioinformaticsToolsmith/Red	Sequence Analysis	red	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/red	https://github.com/galaxyproject/tools-iuc/tree/main/tools/red	2018.09.10	red	2018.09.10	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	88	578
-repeatmasker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.	repeatmasker	repeatmasker		RepeatMasker	A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).	Genome annotation	Sequence analysis, Sequence composition, complexity and repeats	Up-to-date	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker	4.1.5	repeatmasker	4.1.5	Genome annotation	Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	248	3750
-repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	217	1177
-repmatch_gff3	repmatch_gff3	Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria.								To update		ChIP-seq	repmatch_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3		matplotlib				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-reshape2	cast, melt	Flexibly restructure and aggregate data using just the two functions melt and dcast								To update	https://cran.r-project.org/web/packages/reshape2/index.html	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2	1.4.2	r-reshape2				2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	33	3456
-resize_coordinate_window	resize_coordinate_window	Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size.								To update		Genomic Interval Operations	resize_coordinate_window	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window	https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window	1.0.2	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	85
-revoluzer	revoluzer_crex, revoluzer_distmat	revoluzer wrappers	revoluzer	revoluzer		revoluzer	Various tools for genome rearrangement analysis. CREx, TreeREx, etc	Structural variation detection	Molecular evolution, Phylogeny	Up-to-date	https://gitlab.com/Bernt/revoluzer/	Phylogenetics	revoluzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer	0.1.6	revoluzer	0.1.6	Structural variation detection	Molecular evolution, Phylogeny	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rgcca	rgcca	multi-block analysis								To update	https://github.com/rgcca-factory/RGCCA	Statistics	rgcca	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca	3.0.2	rgccacmd	3.0.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	44
-rgrnastar	rna_star, rna_starsolo	RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper	star	star		STAR	Ultrafast universal RNA-seq data aligner	Sequence alignment	RNA-Seq, Transcriptomics	To update	https://github.com/alexdobin/STAR	Next Gen Mappers, Transcriptomics	rgrnastar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar	2.7.11a	star	2.7.11b	Sequence alignment	RNA-Seq, Transcriptomics	2	2	2	2	2	2	2	2	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	2	0	0	0	2	0	0	0	0	0	0	0	2	2	0	4015	425658
-ribowaltz	ribowaltz_process, ribowaltz_plot	Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data	riboWaltz	riboWaltz		riboWaltz	riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.		Computational biology	To update	https://github.com/LabTranslationalArchitectomics/riboWaltz	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz	1.2.0	ribowaltz	2.0		Computational biology	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	14	161
-rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	109	1110
-roary	roary	Roary the pangenome pipeline	roary	roary		Roary	A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary	3.13.0	roary	3.13.0	Genome assembly	DNA, Genomics, Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	656	12225
-rp2biosensor	rp2biosensor	Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output								To update	https://github.com/brsynth/rp2biosensor	Synthetic Biology	rp2biosensor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor	3.2.1	rp2biosensor				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rp2paths	rp2paths	Enumerate and seperate the different pathways generated by RetroPath2.0								To update	https://github.com/brsynth/rp2paths	Synthetic Biology	rp2paths	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths	1.5.1	rp2paths				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rpbasicdesign	rpbasicdesign	Extracting enzyme IDs from rpSBML files								To update	https://github.com/brsynth/rpbasicdesign	Synthetic Biology	rpbasicdesign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign	1.2.2	rpbasicdesign				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rpfba	rpfba	Perform FBA for the RetroPath2.0 heterologous pathways								To update	https://github.com/brsynth/rptools/releases	Synthetic Biology	rpfba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba	5.12.3	rptools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rptools	rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz	Suite of tools that work on rpSBML format								To update	https://github.com/brsynth/rptools	Synthetic Biology	rptools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools	5.13.1	rptools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rrparser	rrparser	Reaction Rules Parser								To update	https://github.com/brsynth/RRParser	Synthetic Biology	rrparser	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser	2.5.2	rrparser				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rseqc	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	22	22	22	22	22	0	0	0	0	0	0	0	0	0	0	0	0	22	0	0	0	0	22	0	0	0	22	0	0	0	0	0	0	0	22	22	0	3206	133498
-ruvseq	ruvseq	Remove Unwanted Variation from RNA-Seq Data	ruvseq	ruvseq		RUVSeq	This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.	Differential gene expression analysis	Gene expression, RNA-seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	ruvseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq	1.26.0	bioconductor-ruvseq	1.36.0	Differential gene expression analysis	Gene expression	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	76	1236
-salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	454
-samblaster	samblaster	samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files	samblaster	samblaster		SAMBLASTER	A tool to mark duplicates and extract discordant and split reads from SAM files.	Split read mapping	DNA, Sequencing, Mapping	To update	https://github.com/GregoryFaust/samblaster	SAM, Fastq Manipulation, Variant Analysis	samblaster	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster	https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster	0.1.24	samblaster	0.1.26	Split read mapping	DNA, Sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-samtools										To update	https://github.com/samtools/samtools	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools	1.15.1	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-sansa	sansa_annotate	Sansa is a tool for structural variant annotation.								Up-to-date	https://github.com/dellytools/sansa	Variant Analysis	sansa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa	0.2.1	sansa	0.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	18	123
-sarscov2formatter	sarscov2formatter	sarscov2formatter custom script								Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	173
-sarscov2summary	sarscov2summary	sarscov2summary custom script								To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	140
-sbml2sbol	sbml2sbol	Convert SBML to SBOL format								To update	https://github.com/neilswainston/SbmlToSbol	Synthetic Biology	sbml2sbol	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol	0.1.13	sbml2sbol				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-scanpy	scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	scanpy	scanpy		SCANPY	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.9.6	scanpy	1.7.2	Differential gene expression analysis	Gene expression, Cell biology, Genetics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	766	51978
-scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Transcriptomics, RNA, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	77	1365
-sceasy	sceasy_convert	Converter between difference single-cell formats								Up-to-date	https://github.com/cellgeni/sceasy/	Transcriptomics	sceasy_convert	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy	0.0.7	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	90	721
-schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	0	23	779
-scikit-bio	scikit_bio_diversity_beta_diversity	scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics								Up-to-date	http://scikit-bio.org/	Sequence Analysis	scikit_bio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio	0.4.2	scikit-bio	0.4.2			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
-scoary	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	scoary	scoary		Scoary	Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	61	676
-scpipe	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	scpipe	scpipe		scPipe	A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, RNA, Statistics	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	628
-seacr	seacr	SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes.								Up-to-date	https://github.com/FredHutch/SEACR	Epigenetics, ChIP-seq	seacr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr	1.3	seacr	1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	50	3647
-selenzy_wrapper	selenzy_wrapper	Performs enzyme selection from a reaction query.								Up-to-date	https://github.com/brsynth/selenzy-wrapper	Synthetic Biology	selenzy_wrapper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper	0.3.0	selenzy_wrapper	0.3.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-semibin	semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	semibin	semibin		SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	0	0	6	1	0	0	6	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	39	542
-seq2hla	seq2hla	Precision HLA typing and expression from RNAseq data	seq2hla	seq2hla		Seq2HLA	seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	Up-to-date	https://github.com/TRON-Bioinformatics/seq2HLA	Sequence Analysis	seq2hla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla	2.3	seq2hla	2.3	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	288
-seqcomplexity	seqcomplexity	Sequence complexity for raw reads								Up-to-date	https://github.com/stevenweaver/seqcomplexity	Sequence Analysis		iuc	https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity	0.1.2	seqcomplexity	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	68
-seqkit	seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit		seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	Up-to-date	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.8.2	seqkit	2.8.2	DNA transcription, Sequence trimming, DNA translation	Database management, Sequence analysis	0	2	5	2	0	2	5	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	129	1964
-seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-seqsero2	seqsero2	Salmonella serotype prediction from genome sequencing data	seqsero2	seqsero2		SeqSero2	"rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)"	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12
-seqtk	seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq	Toolkit for processing sequences in FASTA/Q formats	seqtk	seqtk		seqtk	A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.	Data handling, Sequence file editing	Data management	Up-to-date	https://github.com/lh3/seqtk	Sequence Analysis	seqtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk	1.4	seqtk	1.4	Data handling, Sequence file editing		15	15	15	15	15	15	15	15	0	0	0	0	14	0	0	0	0	0	0	0	14	0	14	0	0	14	0	0	0	15	0	0	0	0	0	0	0	14	14	14	753	59668
-seqwish	seqwish	Alignment to variation graph inducer								To update	https://github.com/ekg/seqwish	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish	0.7.5	seqwish	0.7.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	271
-seurat	seurat	A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data								To update	https://github.com/satijalab/seurat	Transcriptomics, RNA, Statistics	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	4.3.0.1	r-seurat	3.0.2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	66	1543
-shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.12.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	154	763
-shorah	shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	shorah	shorah		ShoRAH	Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	To update	https://github.com/cbg-ethz/shorah/blob/master/README.md	Sequence Analysis	shorah_amplicon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah	1.1.3	shorah	1.99.2	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1008	41600
-sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	269	14982
-simtext	abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix	A text mining framework for interactive analysis and visualization of similarities among biomedical entities.								To update	https://github.com/dlal-group/simtext	Text Manipulation	simtext	iuc	https://github.com/galaxyproject/tools-iuc/tools/simtext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext	0.0.2	r-argparse	1.0.1			0	2	4	0	0	2	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	34	142
-sina	sina	SINA reference based multiple sequence alignment	sina	sina		SINA	Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	Up-to-date	https://sina.readthedocs.io/en/latest/	Sequence Analysis	sina	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina	1.7.2	sina	1.7.2	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	1	0	1	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	42	1128
-sinto	sinto_barcode, sinto_fragments	Sinto single-cell analysis tools								To update	https://github.com/timoast/sinto	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto	0.9.0	sinto	0.10.1			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	17	91
-slamdunk	alleyoop, slamdunk	Slamdunk maps and quantifies SLAMseq reads								Up-to-date	http://t-neumann.github.io/slamdunk	RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers	slamdunk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk	0.4.3	slamdunk	0.4.3			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2	361
-sleuth	sleuth	Sleuth is a program for differential analysis of RNA-Seq data.	sleuth	sleuth		sleuth	A statistical model and software application for RNA-seq differential expression analysis.	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	RNA-seq, Gene expression, Statistics and probability	Up-to-date	https://github.com/pachterlab/sleuth	Transcriptomics, RNA, Statistics	sleuth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth	0.30.1	r-sleuth	0.30.1	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	64
-smallgenomeutilities	smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe		V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.1	smallgenomeutilities	0.4.1	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	121
-smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	Up-to-date	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.2.5	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	22	203
-snap	snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap		SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	Gene prediction	DNA polymorphism, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	133	1349
-snapatac2	snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing	SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis								To update	https://kzhang.org/SnapATAC2/	Epigenetics, Sequence Analysis	snapatac2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2	2.6.4					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-sniffles	sniffles	Galaxy wrapper for sniffles	sniffles	sniffles		Sniffles	An algorithm for structural variation detection from third generation sequencing alignment.	Sequence analysis, Structural variation detection	DNA structural variation, Sequencing	To update	https://github.com/fritzsedlazeck/Sniffles	Sequence Analysis	sniffles	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles	1.0.12	sniffles	2.4	Sequence analysis, Structural variation detection	Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	58	919
-snipit	snipit	Summarise snps relative to a reference sequence	snipit	snipit		snipit	Summarise snps relative to a reference sequence	Base position variability plotting	Virology	Up-to-date	https://github.com/aineniamh/snipit	Variant Analysis, Sequence Analysis	snipit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	1.2	snipit	1.2	Base position variability plotting	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	669
-snippy	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy		snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	Phylogenetic tree visualisation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	3	3	3	3	3	3	3	3	0	0	0	0	2	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	2	0	1372	105708
-snp-dists	snp_dists	Compute pairwise SNP distance matrix from a FASTA sequence alignment								Up-to-date	https://github.com/tseemann/snp-dists	Variant Analysis	snp_dists	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists	0.8.2	snp-dists	0.8.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	367	4558
-snp-sites	snp_sites	Finds SNP sites from a multi-FASTA alignment file								Up-to-date	https://github.com/sanger-pathogens/snp-sites	Variant Analysis	snp_sites	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites	2.5.1	snp-sites	2.5.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	284	5107
-snpeff	snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names	SnpEff is a genetic variant annotation and effect prediction toolbox								To update	http://snpeff.sourceforge.net/	Genome-Wide Association Study, Variant Analysis	snpeff	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff		biopython	1.70			5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	1	0	0	0	0	5	5	0	0	5	0	0	0	5	0	0	0	0	0	0	0	5	5	0	2676	95592
-snpeff-covid19	snpeff_sars_cov_2	SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox	snpeff	snpeff		snpEff	Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes).	SNP detection	DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs	To update	http://snpeff.sourceforge.net/	Genome-Wide Association Study, Variant Analysis	snpeff_sars_cov_2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19				SNP detection	DNA polymorphism, Nucleic acid sites, features and motifs	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	533	760352
-snpfreqplot	snpfreqplot	A plotting app to visualise the SNPs across a region								To update	https://github.com/BrownfieldPlantLab/SNPFreqPlot	Variant Analysis	snpfreqplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot	1.0	r-base				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	156	3530
-snpsift	snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck	snpEff SnpSift tools from Pablo Cingolani								To update	http://snpeff.sourceforge.net/SnpSift.html	Variant Analysis	snpsift	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift		snpsift	5.2			8	8	8	8	8	8	8	8	0	0	0	0	0	0	0	0	8	0	0	0	0	0	8	0	0	8	0	0	0	8	0	0	0	0	0	0	0	8	8	0	1352	5114712
-snpsift_dbnsfp	snpSift_dbnsfp	snpEff SnpSift dbnsfp tool from Pablo Cingolani								To update	http://snpeff.sourceforge.net/SnpSift.html#dbNSFP	Variant Analysis	snpsift_dbnsfp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp		snpsift	5.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	46
-snpsift_genesets	snpSift_geneSets	Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome								To update	http://snpeff.sourceforge.net/SnpSift.html#geneSets	Variant Analysis	snpsift_genesets	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets		snpsift	5.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	31	528
-socru	socru	Order and orientation of complete bacterial genomes								To update	https://github.com/quadram-institute-bioscience/socru	Sequence Analysis	socru	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru	https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru	2.1.7	socru	2.2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	621
-sonneityping	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping		sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1
-spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	coronaspades, biosyntheticspades, metaplasmidspades, plasmidspades, metaspades, rnaspades, metaviralspades, rnaviralspades, spades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	1	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	0	0	9	3	0	3547	72953
-spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	34	446
-spapros	spapros, spapros	Select and evaluate probe sets for targeted spatial transcriptomics.								Up-to-date	https://github.com/theislab/spapros	Transcriptomics, Sequence Analysis	spapros	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros	0.1.5	spapros	0.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-spotyping	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping		SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	1278
-spyboat	spyboat	Wavelet analysis for 3d-image stacks								To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	0.1.2	spyboat				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	67
-sra-tools	fasterq_dump, fastq_dump, sam_dump	NCBI Sequence Read Archive toolkit utilities	sra-tools	sra-tools		SRA Software Toolkit	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	Data handling	DNA, Genomics, Sequencing	Up-to-date	https://github.com/ncbi/sra-tools	Data Source, Fastq Manipulation	sra_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools	3.1.1	sra-tools	3.1.1	Data handling	DNA, Genomics, Sequencing	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	2	0	3	0	0	3	0	0	0	3	0	0	0	0	0	0	0	3	3	0	6247	350032
-srst2	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2		srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.20	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	205
-stacks	stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq	stacks	stacks		Stacks	Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.	Data handling	Mapping, Population genetics	To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis	stacks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks		stacks	2.65	Data handling	Mapping, Population genetics	0	13	13	12	0	13	13	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	13	0	152	11635
-stacks2	stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq								To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2	2.55	stacks	2.65			0	12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	0	238	7292
-star_fusion	star_fusion	STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR								To update	https://github.com/STAR-Fusion/STAR-Fusion	Sequence Analysis, Transcriptomics	star_fusion	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion	https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion	0.5.4-3+galaxy1	star-fusion	1.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	35	1212
-straindesign	straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion	Toolbox to optimize biological model								To update	https://github.com/brsynth/straindesign	Systems Biology, Synthetic Biology	straindesign	iuc	https://github.com/brsynth/straindesign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign	3.2.2	straindesign	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-strelka	strelka_germline, strelka_somatic	Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision.								Up-to-date	https://github.com/Illumina/strelka/	Variant Analysis	strelka	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka	2.9.10	strelka	2.9.10			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	53	549
-stringtie	stringtie, stringtie_merge	StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.	stringtie	stringtie		StringTie	Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.	Transcriptome assembly, RNA-Seq analysis	Transcriptomics, RNA-seq	Up-to-date	http://ccb.jhu.edu/software/stringtie/	Transcriptomics	stringtie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie	2.2.3	stringtie	2.2.3	Transcriptome assembly, RNA-Seq analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2165	167659
-structure	structure	for using multi-locus genotype data to investigate population structure.	structure	structure		Structure	The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Genetic variation analysis	Population genetics	Up-to-date	https://web.stanford.edu/group/pritchardlab/structure.html	Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	Genetic variation analysis	Population genetics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	59	2623
-structureharvester	structureharvester	for parsing STRUCTURE outputs and for performing the Evanno method								Up-to-date	http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/	Phylogenetics, Variant Analysis	structureharvester	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester	0.6.94	structureharvester	0.6.94			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-swift	swiftlink	Parallel MCMC Linkage Analysis								Up-to-date	https://github.com/ajm/swiftlink	Variant Analysis	swiftlink	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift	1.0	swiftlink	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-syndiva	syndiva	SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.								To update		Proteomics	syndiva	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA	https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva	1.0	clustalo	1.2.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	30
-table_compute	table_compute	Perform general-purpose table operations								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute	Text Manipulation	table_compute	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute	https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute	1.2.4	pandas				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	741	208652
-tabular_to_fastq	tabular_to_fastq	Tabular to FASTQ converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	tabular_to_fastq	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	200	7388
-tag_pileup_frequency	tag_pileup_frequency	Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup	Statistics, SAM, Genomic Interval Operations	tag_pileup_frequency	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency	1.0.2	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	164
-tasmanian_mismatch	tasmanian_mismatch	Analysis of positional mismatches								Up-to-date	https://github.com/nebiolabs/tasmanian-mismatch	Sequence Analysis	tasmanian_mismatch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch	1.0.7	tasmanian-mismatch	1.0.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-taxonkit	name2taxid, profile2cami	TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit	taxonkit	taxonkit		TaxonKit	TaxonKit is a practical and efficient NCBI taxonomy toolkit.	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	Up-to-date	https://bioinf.shenwei.me/taxonkit/	Metagenomics	taxonkit	iuc	https://github.com/shenwei356/taxonkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit	0.17.0	taxonkit	0.17.0	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	0	1	1	0	1801	27426
-taxpasta	taxpasta	standardise taxonomic profiles	taxpasta	taxpasta		taxpasta	TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table.	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	Up-to-date	https://taxpasta.readthedocs.io/en/latest/	Sequence Analysis	taxpasta	iuc	https://github.com/taxprofiler/taxpasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta	0.7.0	taxpasta	0.7.0	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-tb-profiler	tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	6.2.1	tb-profiler	6.3.0	Antimicrobial resistance prediction		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	198	5161
-tb_variant_filter	tb_variant_filter	M. tuberculosis H37Rv VCF filter								Up-to-date	https://github.com/COMBAT-TB/tb_variant_filter	Variant Analysis	tb_variant_filter	iuc	https://github.com/COMBAT-TB/tb_variant_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter	0.4.0	tb_variant_filter	0.4.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	209	19252
-tbl2gff3	tbl2gff3	Table to GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	Convert Formats, Sequence Analysis	tbl2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3	1.2	bcbiogff	0.6.6			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	229	1584
-tbvcfreport	tbvcfreport	Generate HTML report from SnpEff M.tuberculosis VCF(s)								Up-to-date	https://github.com/COMBAT-TB/tbvcfreport	Variant Analysis	tbvcfreport	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport	1.0.1	tbvcfreport	1.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	167	2290
-te_finder	te_finder	Transposable element insertions finder	tefinder	tefinder		TEfinder	A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	To update	https://github.com/VistaSohrab/TEfinder	Sequence Analysis	te_finder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder	1.0.1	samtools	1.20	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	81
-telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-tetoolkit	tetoolkit_tetranscripts	The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.								Up-to-date	http://hammelllab.labsites.cshl.edu/software/	Sequence Analysis	tetoolkit	iuc	https://github.com/mhammell-laboratory/TEtranscripts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit	2.2.3	tetranscripts	2.2.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	33	871
-tetyper	tetyper	Type a specific transposable element (TE) of interest from paired-end sequencing data.								Up-to-date	https://github.com/aesheppard/TETyper	Sequence Analysis	tetyper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper	1.1	tetyper	1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	69
-tn93	tn93_readreduce, tn93, tn93_cluster, tn93_filter	Compute distances between sequences								To update	https://github.com/veg/tn93/	Sequence Analysis	tn93	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93	1.0.6	tn93	1.0.14			4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	4	0	0	17	1881
-tooldistillator	tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator		ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.9	tooldistillator	0.9	Parsing	Microbiology, Bioinformatics, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-tracegroomer	tracegroomer	TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool.								Up-to-date	https://github.com/cbib/TraceGroomer	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer	0.1.4	tracegroomer	0.1.4			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-tracy	tracy_align, tracy_assemble, tracy_basecall, tracy_decompose									To update				iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy	0.6.1	tracy	0.7.6			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	58	2439
-transdecoder	transdecoder	TransDecoder finds coding regions within transcripts	TransDecoder	TransDecoder		TransDecoder	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	To update	https://transdecoder.github.io/	Transcriptomics, RNA	transdecoder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder	5.5.0	transdecoder	5.7.1	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	348	5468
-transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	84	907
-transtermhp	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	transtermhp	transtermhp		TransTermHP	TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	229
-trimmomatic	trimmomatic	A flexible read trimming tool for Illumina NGS data								Up-to-date	http://www.usadellab.org/cms/?page=trimmomatic	Fastq Manipulation	trimmomatic	pjbriggs	https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic	0.39	trimmomatic	0.39			1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	0	0	1	1	0	5862	305866
-trinity	trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats	Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq	trinity	trinity		Trinity	Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.	Transcriptome assembly	Transcriptomics, Gene expression, Gene transcripts	To update	https://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity	2.15.1	trinity	2.15.2	Transcriptome assembly	Transcriptomics, Gene transcripts	9	13	13	13	9	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	1	2	1	0	0	0	0	0	0	11	0	0	1	0	0	0	0	13	12	0	1762	31951
-trinotate	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	trinotate	trinotate		Trinotate	Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.	Gene functional annotation	Gene expression, Transcriptomics	To update	https://trinotate.github.io/	Transcriptomics, RNA	trinotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate	3.2.2	trinotate	4.0.2	Gene functional annotation	Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	151	1796
-trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942
-tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	To update	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.4	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5
-tsne	tsne	T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation								To update	https://cran.r-project.org/web/packages/Rtsne/	Text Manipulation	tsne	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne	0.0.2	r-rtsne	0.13			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	368
-twobittofa	ucsc-twobittofa	twoBitToFa is a tool to convert all or part of .2bit file to FASTA	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	https://genome.ucsc.edu/goldenpath/help/twoBit.html	Convert Formats	ucsc_twobittofa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa	377	ucsc-twobittofa	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	48	502
-tximport	tximport	Wrapper for the Bioconductor package tximport	tximport	tximport		tximport	An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	To update	http://bioconductor.org/packages/tximport/	Transcriptomics	tximport	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport	1.22.0	bioconductor-tximport	1.30.0	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	88	1408
-ucsc_axtchain	ucsc_axtchain	Chain together genome alignments	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_axtchain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain	455	ucsc-axtchain	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ucsc_axttomaf	ucsc_axtomaf	Convert dataset from axt to MAF format.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_axttomaf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf	377	ucsc-axttomaf	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ucsc_blat	ucsc_blat	Standalone blat sequence search command line tool	blat	blat		BLAT	Fast, accurate spliced alignment of DNA sequences.	Sequence alignment	Sequence analysis	To update	http://genome.ucsc.edu/goldenPath/help/blatSpec.html	Sequence Analysis	ucsc_blat	yating-l	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat	377	ucsc-blat	469	Sequence alignment	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-ucsc_chainnet	ucsc_chainnet	Make alignment nets out of chains	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainnet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	469	ucsc-chainnet	469		Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ucsc_chainprenet	ucsc_chainprenet	Remove chains that don't have a chance of being netted	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainprenet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainprenet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet	377	ucsc-chainprenet	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ucsc_chainsort	ucsc_chainsort	Sort chains. By default sorts by score.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainsort	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort	455	ucsc-chainsort	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	To update	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.2	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	0	0	5	5	0	379	61618
-unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1558	65732
-usher	usher_matutils, usher	UShER toolkit wrappers	usher	usher		usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Cladistics, Genotype and phenotype, Phylogenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	1060
-valet	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	637
-vapor	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor		VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	94	3164
-vardict	vardict_java	VarDict - calls SNVs and indels for tumour-normal pairs								To update	https://github.com/AstraZeneca-NGS/VarDictJava	Variant Analysis	vardict_java	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict	1.8.3	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	16	273
-variant_analyzer	mut2read, mut2sscs, read2mut	Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data								To update		Variant Analysis	variant_analyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer	2.0.0	matplotlib				3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	3	88
-varscan	varscan_copynumber, varscan_mpileup, varscan_somatic	VarScan is a variant caller for high-throughput sequencing data								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/varscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan	2.4.3	varscan	2.4.6			3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	492	9779
-varvamp	varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp		varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology, Probes and primers	Up-to-date	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.0	PCR primer design	Virology, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-vcf2maf	vcf2maf	vcf2maf: Convert VCF into MAF								To update	https://github.com/mskcc/vcf2maf	Convert Formats	vcf2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf	1.6.21	vcf2maf	1.6.22			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	751
-vcf2tsv	vcf2tsv	Converts VCF files into tab-delimited format								To update	https://github.com/ekg/vcflib	Variant Analysis, Convert Formats	vcf2tsv	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	352	167913
-vcfaddinfo	vcfaddinfo	Adds info fields from the second dataset which are not present in the first dataset.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfaddinfo	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	357
-vcfallelicprimitives	vcfallelicprimitives	Splits alleleic primitives (gaps or mismatches) into multiple VCF lines								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfallelicprimitives	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	286	15803
-vcfanno	vcfanno	Annotate VCF files	vcfanno	vcfanno		vcfanno	Fast, flexible annotation of genetic variants.	SNP annotation	Genetic variation, Data submission, annotation and curation	Up-to-date	https://github.com/brentp/vcfanno	Variant Analysis	vcfanno	iuc	https://github.com/galaxyproject/tools-iuc/vcfanno/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno	0.3.5	vcfanno	0.3.5	SNP annotation	Genetic variation, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	87	872
-vcfannotate	vcfannotate	Intersect VCF records with BED annotations								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfannotate	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	77	2181
-vcfannotategenotypes	vcfannotategenotypes	Annotate genotypes in a VCF dataset using genotypes from another VCF dataset.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfannotategenotypes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	28	192
-vcfbedintersect	vcfbedintersect	Intersect VCF and BED datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfbedintersect	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	80	3217
-vcfbreakcreatemulti	vcfbreakcreatemulti	Break multiple alleles into multiple records, or combine overallpoing alleles into a single record								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfbreakcreatemulti	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	471
-vcfcheck	vcfcheck	Verify that the reference allele matches the reference genome								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcheck	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	675
-vcfcombine	vcfcombine	Combine multiple VCF datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcombine	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	99	1695
-vcfcommonsamples	vcfcommonsamples	Output records belonging to samples commong between two datasets.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcommonsamples	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	14	244
-vcfdistance	vcfdistance	Calculate distance to the nearest variant.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfdistance	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	40	564
-vcffilter	vcffilter2	Tool for filtering VCF files								To update	https://github.com/ekg/vcflib	Variant Analysis	vcffilter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	882	44437
-vcffixup	vcffixup	Count the allele frequencies across alleles present in each record in the VCF file.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcffixup	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	71	917
-vcfflatten	vcfflatten2	Removes multi-allelic sites by picking the most common alternate								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfflatten	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	177
-vcfgeno2haplo	vcfgeno2haplo	Convert genotype-based phased alleles into haplotype alleles								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfgeno2haplo	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	718
-vcfgenotypes	vcfgenotypes	Convert numerical representation of genotypes to allelic.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfgenotypes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	48	451
-vcfhethom	vcfhethom	Count the number of heterozygotes and alleles, compute het/hom ratio.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfhethom	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	90	1370
-vcfleftalign	vcfleftalign	Left-align indels and complex variants in VCF dataset								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfleftalign	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	279
-vcfprimers	vcfprimers	Extract flanking sequences for each VCF record								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfprimers	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	12	708
-vcfrandomsample	vcfrandomsample	Randomly sample sites from VCF dataset								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfrandomsample	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	159
-vcfselectsamples	vcfselectsamples	Select samples from a VCF file								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfselectsamples	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	29	854
-vcfsort	vcfsort	Sort VCF dataset by coordinate								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfsort	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	63	1852
-vcfvcfintersect	vcfvcfintersect	Intersect two VCF datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfvcfintersect	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect		vcflib	1.0.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	265	972774
-vegan	vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	74	2020
-velocyto	velocyto_cli	Velocyto is a library for the analysis of RNA velocity.								Up-to-date	http://velocyto.org/	Transcriptomics	velocyto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto	0.17.17	velocyto.py	0.17.17			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	2
-velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	2083	25420
-velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	255	4741
-verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	22
-vg	vg_convert, vg_deconstruct, vg_view	Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods								To update	https://github.com/vgteam/vg	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg	1.23.0	vg	1.56.0			0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	3	477
-virAnnot	virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers	virannot	virannot		virAnnot	"VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy."	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.0.1+galaxy0	biopython	1.70	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-virheat	virheat	generates a heatmap of allele frequencies from vcf files	virheat	virheat		virHEAT	VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists.  The tool provides a condensed look at variant frequencies after mapping  raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time.			Up-to-date	https://github.com/jonas-fuchs/virHEAT	Visualization, Variant Analysis	virheat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat	0.7.1	virheat	0.7.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-virhunter	virhunter	Deep Learning method for novel virus detection in sequencing data	virhunter	virhunter		VirHunter	VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).	Sequence classification	Virology	To update	https://github.com/cbib/virhunter	Machine Learning	virhunter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter	1.0.0	numpy		Sequence classification	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	234
-volcanoplot	volcanoplot	Tool to create a Volcano Plot								To update	https://ggplot2.tidyverse.org/	Visualization, Transcriptomics, Statistics	volcanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot	0.0.6	r-ggplot2	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1749	30946
-vsearch	vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	vsearch	vsearch		VSEARCH	High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.28.1	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	8	8	8	8	8	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	0	0	0	0	0	8	0	0	0	0	0	0	0	8	8	0	182	8507
-vsnp	vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics	The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.								To update	https://github.com/USDA-VS/vSNP	Sequence Analysis	vsnp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp	3.0.6	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-weather_app	simple_weather	provides simple weather in text format								To update	http://wttr.in/	Visualization, Web Services	simpleweather	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app	0.1.2	curl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-weblogo3	rgweblogo3	Sequence Logo generator for fasta	weblogo	weblogo		WebLogo	Web-based application designed to make generate sequence logos.	Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition	Nucleic acid sites, features and motifs, Sequence analysis	To update		Graphics	weblogo3	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3	3.5.0	weblogo	3.7.9	Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition	Nucleic acid sites, features and motifs, Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	74	2379
-wigtobigwig	ucsc_wigtobigwig	converts bedGraph (wig) files into binary bigwig	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	https://genome.ucsc.edu/goldenPath/help/bigWig.html	Convert Formats	ucsc_wigtobigwig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig	447	ucsc-wigtobigwig	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-windowmasker	windowmasker_mkcounts, windowmasker_ustat	Identify repetitive regions using WindowMasker								To update	https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/	Sequence Analysis	windowmasker	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker	1.0	blast	2.16.0			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	85
-winnowmap	winnowmap	A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences.								Up-to-date	https://github.com/marbl/Winnowmap	Next Gen Mappers	winnowmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap	2.03	winnowmap	2.03			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	27	248
-xpath	xpath	XPath XML querying tool								To update	http://search.cpan.org/dist/XML-XPath/	Text Manipulation	xpath	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath	https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath		perl-xml-xpath	1.47			0	0	1	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	234
-yahs	yahs	Yet Another Hi-C scaffolding tool								Up-to-date	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2a.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	64	344
-zerone	zerone	ChIP-seq discretization and quality control								Up-to-date	https://github.com/nanakiksc/zerone	ChIP-seq	zerone	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone	https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone	1.0	zerone	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	90
-EMLassemblyline	eal_table_template, eal_templates, eml2eal, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.1+galaxy0	r-emlassemblyline				0	0	9	9	0	0	9	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	102
-Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	82
-Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	73	1004
-ThermoRawFileParser	thermo_raw_file_converter	Thermo RAW file converter								To update	https://github.com/compomics/ThermoRawFileParser	Proteomics	thermo_raw_file_converter	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	1.3.4	thermorawfileparser	1.4.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	2689
-ab1_fastq	ab1_fastq_converter	Tool to convert ab1 files into FASTQ files								To update		Convert Formats	ab1fastq	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq	1.20.0	bioconductor-sangerseqr	1.38.0			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	175	40271
-ambertools	ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap	Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories.								To update	http://ambermd.org/AmberTools.php	Molecular Dynamics, Computational chemistry	ambertools	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools	21.10	ambertools				7	2	7	0	7	2	7	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	5	0	243	40666
-appendfdr	append_fdr									To update			appendfdr	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr	0.2.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-artbio_bam_cleaning	artbio_bam_cleaning	filter bam files before somatic-varscan or lumpy-smoove analysis								To update	http://artbio.fr	SAM, Variant Analysis	artbio_bam_cleaning	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning	https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning	1.10+galaxy0	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-astropytools	astropy_fits2bitmap, astropy_fits2csv, astropy_fitsinfo	AstropyTools library contains Galaxy tools for elementary Astrophysical operations								To update	https://github.com/astropy/astropy	Astronomy	astropytools	volodymyrss	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools	0.1.0+galaxy0	astropy				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3	11
-bamparse	bamparse	Generates hit count lists from bam alignments.								To update	http://artbio.fr	RNA, Transcriptomics	bamparse	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	4.1.1	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-bed_to_protein_map	bed_to_protein_map	Converts a BED file to a tabular list of exon locations								To update		Proteomics	bed_to_protein_map	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	49	385
-bigwig_to_bedgraph	bigwig_to_bedgraph	Converts a bigWig file to bedGraph format								To update	http://artbio.fr	Convert Formats	bigwig_to_bedgraph	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph	377+galaxy1	ucsc-bigwigtobedgraph	469			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	200	5749
-bigwig_to_wig	bigwig_to_wig	Converts a bigWig file to Wiggle (WIG) format								To update	https://artbio.fr	Convert Formats	bigwig_to_wig	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig	3+galaxy0	ucsc-bigwiginfo	469			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-bio3d	bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize	Bio3d is a program that can be used to analyse molecular dynamics trajectories.								To update	http://thegrantlab.org/bio3d/index.php	Computational chemistry	bio3d	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d	2.4_1	r-bio3d	2.3_3			5	4	5	0	5	4	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	510	8913
-biomoldyn	biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering	Tools for MD analysis								To update	https://github.com/moldyn/	Molecular Dynamics, Computational chemistry	biomoldyn	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn	1.5.2	scipy				4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	3	0	53	459
-biotransformer	biotransformer	BioTransformer is a tool for prediction of small molecule metabolism in mammals.	biotransformer	biotransformer		BioTransformer	BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction.	Metabolic pathway prediction, PTM site prediction, Natural product identification	Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR	Up-to-date	https://bitbucket.org/djoumbou/biotransformerjar/src/master/	Metabolomics	biotransformer	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer	https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer	3.0.20230403	biotransformer	3.0.20230403	Metabolic pathway prediction, PTM site prediction, Natural product identification	Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
-blast2go	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe				0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	101	1232
-blast_plus_remote_blastp	blast_plus_remote_blastp	NCBI BLAST+ with -remote option								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	blast_plus_remote_blastp	galaxyp	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp	2.6.0	blast	2.16.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	121	22499
-blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-blast_unmatched	blast_unmatched	Extract unmatched query sequences from blast								To update	http://artbio.fr	Fasta Manipulation	blast_unmatched	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	1.0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-blastxml_to_top_descr	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	159	264558
-bumbershoot	idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch									To update	http://proteowizard.sourceforge.net/	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot	3.0.21142	bumbershoot	3_0_21142_0e4f4a4			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	3	1348
-c3s	c3s	Copernicus Climate Change Service (C3S)								To update	https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset	Climate Analysis	c3s	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	198
-cads	cads	Copernicus Atmosphere Data Store (ADS)								To update	https://ads.atmosphere.copernicus.eu/#!/home	Climate Analysis	cads	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads	0.1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	52
-calisp	calisp	Calgary approach to isotopes in proteomics								Up-to-date	https://github.com/kinestetika/Calisp/	Proteomics	calisp	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp	3.0.13	calisp	3.0.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
-cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	101	7766
-cardinal	cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots	Statistical and computational tools for analyzing mass spectrometry imaging datasets								Up-to-date	http://cardinalmsi.org	Proteomics, Metabolomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	3.4.3	bioconductor-cardinal	3.4.3			0	9	11	11	0	9	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	11	9	0	277	48705
-cdo	cdo_info, cdo_operations	CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available.								To update	https://code.mpimet.mpg.de/projects/cdo/	Climate Analysis		climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo	2.0.0					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	16	217
-cell-types-analysis	ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals	Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis								To update		Transcriptomics, RNA, Statistics	suite_cell_types_analysis	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis	1.1.1	cell-types-analysis	0.1.11			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	6
-cesm	cesm	Community Earth System Model (CESM)								Up-to-date	https://www.cesm.ucar.edu/	Climate Analysis	cesm	climate	https://github.com/ESCOMP/CESM	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm	2.1.3	cesm	2.1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	13
-champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	19	174
-cherry_pick_fasta	cherry_pick_fasta	Pick fasta sequence with specific header content								To update	http://artbio.fr	Fasta Manipulation	cherry_pick_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	4.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-climate-stripes	climate_stripes	Create climate stripes from a tabular input file								To update	https://www.climate-lab-book.ac.uk/2018/warming-stripes/	Climate Analysis, Visualization	climate_stripes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	1.0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	237
-concat_multi_datasets	cat_multi_datasets	Concatenate multiple datasets tail-to-head, including collection datasets.								To update	http://artbio.fr	Text Manipulation	concatenate_multiple_datasets	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets	https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets	1.4.3					1	1	1	0	1	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	352	3612
-consensus_from_alignments	aligned_to_consensus	Tool to compute a consensus sequence from several aligned fasta sequences								To update		Sequence Analysis	consalign	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments	https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments	1.0.0	r-bioseq				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55	585
-consolidate_vcfs	consolidate_vcfs	Combines freebayes and mpileup files for use by vcf2snvalignment								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	consolidate_vcfs	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cooler	cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify	cooler different tools to process Hi-C from mirnylab								To update	https://github.com/open2c/cooler	Epigenetics	cooler	lldelisle	https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler	0.9.3	htslib	1.20			4	0	5	0	4	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	11	81
-cpm_tpm_rpk	cpm_tpm_rpk	Generate CPM,TPM or RPK from raw counts								To update	http://artbio.fr	Transcriptomics	cpm_tpm_rpk	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	0.6.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-cta	cta_astro_tool	Basic simulation of CTA telescope observations using gammapy package								To update		Astronomy	cta_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta	0.0.1+galaxy0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-custom_pro_db	custom_pro_db	CustomProDB								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db	1.22.0	bioconductor-rgalaxy	1.37.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	57	1652
-custom_pro_db_annotation_data_manager		CustomProDB Annotation								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db_annotation_data_manager	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-data-hca	hca_matrix_downloader	Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects								To update		Transcriptomics, Sequence Analysis	suite_human_cell_atlas_tools	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca	v0.0.4+galaxy0	hca-matrix-downloader	0.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	439
-data-scxa	retrieve_scxa	Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home								To update		Transcriptomics, Sequence Analysis	suite_ebi_expression_atlas	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa	v0.0.2+galaxy2	wget				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	99	799
-data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	146	658
-data_manager_eggnog_mapper		downloads eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-data_manager_eggnog_mapper_abspath		download eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper_abspath	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dbbuilder	dbbuilder	Protein Database Downloader								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	Proteomics	dbbuilder	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	0.3.4	wget				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	161	4758
-decoupler	score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk	decoupler - Ensemble of methods to infer biological activities								To update	https://decoupler-py.readthedocs.io/en/latest/	Transcriptomics	suite_decoupler	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler	1.4.0+galaxy3	decoupler	1.5.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6
-decoyfasta		Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.								To update		Proteomics	decoyfasta	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-deseq2_normalization	deseq2_normalization	Normalizes gene hitlists								To update	http://artbio.fr	RNA, Transcriptomics, Sequence Analysis, Statistics	deseq2_normalization	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	1.40.2+galaxy0	bioconductor-deseq2	1.42.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-dia_umpire	dia_umpire_se	DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics								To update	http://diaumpire.sourceforge.net/	Proteomics	dia_umpire	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire	2.1.3	dia_umpire	2.1.6			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	33
-dialignr	dialignr	DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.								To update	https://github.com/shubham1637/DIAlignR	Proteomics	dialignr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	1.2.0	bioconductor-dialignr	2.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	40
-diann	diann	DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.								To update	https://github.com/vdemichev/DiaNN	Proteomics	diann	galaxyp	https://github.com/vdemichev/DiaNN	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann	1.8.1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	15
-diapysef	diapysef	diapysef is a convenience package for working with DIA-PASEF data								To update	https://pypi.org/project/diapysef/	Proteomics	diapysef	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef	0.3.5.0	diapysef	1.0.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	245
-diffacto	diffacto	Diffacto comparative protein abundance estimation								To update	https://github.com/statisticalbiotechnology/diffacto	Proteomics	diffacto	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	1.0.6	diffacto	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	7
-digestdb	digestdb									To update			digestdb	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb	0.1.0	trans_proteomic_pipeline				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-directag_and_tagrecon										To update			directag_and_tagrecon	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-droplet-barcode-plot	_dropletBarcodePlot	Make a cell barcode plot for droplet single-cell RNA-seq QC								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	droplet_barcode_plot	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot	1.6.1+galaxy2	scxa-plots	0.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	95	973
-dropletutils	dropletutils_empty_drops, dropletutils_read_10x	De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_dropletutils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils	1.0.4	dropletutils-scripts	0.0.5			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	201	1599
-eggnog_mapper	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2		eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3	1	0	510	30565
-embl2fa	embl2fa	Converts EMBL flat format to fasta format								To update	http://artbio.fr	Text Manipulation	embl2fa	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa	https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa	0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-encyclopedia	encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut	Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis								To update	https://bitbucket.org/searleb/encyclopedia/wiki/Home	Proteomics	encyclopedia	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia	1.12.34	encyclopedia	2.12.30			2	4	7	0	2	4	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	48	706
-eodie	eodie	Earth Observation Data Information Extractor								To update	https://eodie.readthedocs.io/	Climate Analysis	eodie	climate	https://gitlab.com/eetun-tiimi/EODIE	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie	1.0.2	eodie				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	45
-essential_climate_variables	cds_essential_variability	Get Copernicus Essential Climate Variables for assessing climate variability								To update	https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview	Climate Analysis, Data Source	cds_essential_variability	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	331
-ez_histograms	ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-fasta_merge_files_and_filter_unique_sequences	fasta_merge_files_and_filter_unique_sequences	Concatenate FASTA database files together								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Fasta Manipulation	fasta_merge_files_and_filter_unique_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	1.2.0	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	461	29886
-fastg2protlib	fastg2protlib-peptides, fastg2protlib-validate	Generate FASTA from FASTG								To update	https://github.com/galaxyproteomics/fastg2protlib.git	Proteomics	fastg2protlib	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	1.0.2					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	28
-fastq_pair	fastq_pair	Paired-end fastq pairer								To update	https://github.com/linsalrob/fastq-pair	Fastq Manipulation	fastq_pair	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair	1.0+galaxy0	fastq-pair	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fastq_provider	fastq_provider	Retrieval and download of FASTQ files from ENA and other repositories such as HCA.								To update	https://github.com/ebi-gene-expression-group/atlas-fastq-provider	Data Source, RNA, Transcriptomics	atlas_fastq_provider	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider	0.4.4	atlas-fastq-provider	0.4.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fastq_quality_trimmer	cshl_fastq_quality_trimmer	FASTQ trimmer based on quality								To update	https://github.com/agordon/fastx_toolkit	Fastq Manipulation	fastq_quality_trimmer	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer	0.0.14+galaxy0	fastx_toolkit	0.0.14			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fastq_utils	fastq_filter_n, fastq_trim_poly_at	Set of tools for handling fastq files								To update	https://github.com/nunofonseca/fastq_utils	Transcriptomics, RNA	fastq_utils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils	0.25.1+galaxy0	fastq_utils	0.25.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fates-emerald	ctsm_fates	EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model								To update	https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api	Climate Analysis	ctsm_fates	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald	2.0	fates-emerald				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	261
-feature_alignment	feature_alignment	TRIC integrates information from all available runs via a graph-based alignment strategy								Up-to-date		Proteomics	feature_alignment	galaxyp	https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment	0.11.0	msproteomicstools	0.11.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	18
-fetch_fasta_from_ncbi	retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers								To update	http://artbio.fr	Fasta Manipulation, Data Source	fetch_fasta_from_ncbi	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	3.1.0	urllib3	1.12			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	426	26274
-filter_compounds	filter_orgmet_anorg	Tool for filtering organometallics/anorganic compounds from a list of compounds.								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	filter_compounds	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds	https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds	3.1.1	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-filter_density	filterdensity	Filter out position based on distance between SNVs								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_density	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-filter_stats	filterstat	SNVPhyl filter_stats								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_stats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-filter_vcf	filtervcf	SNVPhyl filter_vcf								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_vcf	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-find_repeats	findrepeat	Find repetitive regions on a reference genome using MUMMer								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	find_repeats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fisher_test	fishertest	Fisher's exact test on two-column hit lists.								To update	http://artbio.fr	RNA, Statistics	fishertest	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	2.32.0+galaxy0	bioconductor-qvalue	2.34.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-flashlfq	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	Label-free quantification	Proteomics experiment, Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	17	645
-fragpipe	fragpipe	Data analysis for mass spectrometry-based proteomics.								Up-to-date	https://fragpipe.nesvilab.org/	Proteomics	fragpipe	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	20.0	fragpipe	20.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-free_energy		Free energy tools of BRIDGE.								To update		Molecular Dynamics, Computational chemistry	freeenergy	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-frogs	FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis	frogs	frogs		FROGS	The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	To update	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	5.0.0	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	0	0	0	28	0	0	0	28	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fromHicupToJuicebox	fromHicupToJuicebox	Convert the output of hicup (as sam or bam) to the input of juicebox.								To update		Epigenetics	from_hicup_to_juicebox	lldelisle		https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox	0.0.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fromgtfTobed12	fromgtfTobed12	Convert GTF files to BED12 format								To update	https://pythonhosted.org/gffutils/contents.html	Convert Formats	fromgtftobed12	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12	0.11.1+galaxy1	gffutils	0.13			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-garnett	garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file	De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_garnett	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett	0.2.8	garnett-cli	0.0.5			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	27
-gatk4	filtermutectcalls, mergemutectstats, mutect2	Find somatic variations								To update	http://artbio.fr	Variant Analysis	gatk4	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	4.1.7.0	gatk4	4.5.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gc_derivatization	gc_derivatization	In silico derivatization for GC.								Up-to-date	https://github.com/RECETOX/gc-meox-tms	Metabolomics	gc_derivatization	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization	https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization	1.0.1	gc-meox-tms	1.0.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	8	0	0	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	10	1475
-genomad	genomad_end_to_end	Identify virus and plasmid genomes from nucleotide sequences	genomad	genomad		geNomad	geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.	Sequence annotation, Taxonomic classification	Sequence analysis	Up-to-date	https://github.com/apcamargo/genomad/	Metagenomics	genomad	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad	1.8.0	genomad	1.8.0	Sequence annotation, Taxonomic classification	Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-getTn5ExtendedCoverage	getTn5ExtendedCoverage	Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension								To update		Epigenetics	gettn5extendedcoverage	lldelisle		https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage	0.0.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-get_reference_fasta	get_fasta_reference	Obtain reference genome sequence.								To update	http://artbio.fr	Data Source, Fasta Manipulation	get_reference_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	0.3.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-gffcompare_to_bed	gffcompare_to_bed	Filter and convert a gffCompare GTF to BED								To update	https://github.com/gpertea/gffcompare/	Convert Formats	gffcompare_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed	0.2.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	131	2115
-gromacs	gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj	GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids.								To update	https://github.com/gromacs	Molecular Dynamics, Computational chemistry	gromacs	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs	2022	gromacs	2021.3			14	8	15	0	14	8	15	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	9	0	1442	177844
-gsc_center_scale	center_scale	Center or scale (standardize) data								To update	http://artbio.fr	Statistics	gsc_center_scale	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gsc_filter_cells	filter_cells	Filter single cell RNAseq data on libray depth and number of detected genes								To update	http://artbio.fr	Transcriptomics	gsc_filter_cells	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gsc_filter_genes	filter_genes	Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_filter_genes	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gsc_gene_expression_correlations	single_cell_gene_expression_correlations	Compute single-cell paire-wise gene expressions correlations								To update	http://artbio.fr	Transcriptomics	gsc_gene_expression_correlations	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gsc_high_dimensions_visualisation	high_dimensions_visualisation	Generates PCA, t-SNE and HCPC visualisation								To update	http://artbio.fr	Transcriptomics, Visualization	gsc_high_dimensions_visualisation	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation	4.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gsc_mannwhitney_de	mannwhitney_de	Perform a mann-whitney differential testing between two sets of gene expression data								To update	http://artbio.fr	Transcriptomics	gsc_mannwhitney_de	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	4.1.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gsc_scran_normalize	scran_normalize	Normalize raw counts using scran								To update	http://artbio.fr	Transcriptomics	gsc_scran_normalize	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	1.28.1+galaxy0	bioconductor-scran	1.30.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	78
-gsc_signature_score	signature_score	Compute signature scores from single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_signature_score	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	2.3.9+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gtf-2-gene-list	_ensembl_gtf2gene_list	Utility to extract annotations from Ensembl GTF files.								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	gtf2gene_list	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list	1.52.0+galaxy0	atlas-gene-annotation-manipulation	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	155	1678
-guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-hardklor	hardklor, kronik	Hardklör								To update		Proteomics	hardklor	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor	2.30.1+galaxy1	hardklor	2.3.2			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2	111
-hess	hess_astro_tool	Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope								To update		Astronomy	hess_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess	0.0.2+galaxy0	ipython				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-high_dim_heatmap	high_dim_heatmap	gplot heatmap.2 function adapted for plotting large heatmaps								To update	https://github.com/cran/gplots	Visualization	high_dim_heatmap	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap	https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap	3.1.3+galaxy0	r-gplots	2.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-hyperstack_to_bleach_corrected_movie	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack								To update		Imaging	hyperstack_to_bleach_corrected_movie	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	20230328	Fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-idconvert	idconvert	Convert mass spectrometry identification files on linux or MacOSX								To update		Proteomics	idconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert		proteowizard	3_0_9992			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	275
-incucyte_stack_and_upload_omero	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server								To update		Imaging	incucyte_stack_and_upload_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	20231221	Fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-isolib	isolib	Create an isotopic pattern library for given compounds and adducts.								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	isolib	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/isolib	https://github.com/RECETOX/galaxytools/tree/master/tools/isolib	1.0.1+galaxy0	bioconductor-metabocoreutils	1.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-justdiff	justdiff	Unix diff								To update	http://artbio.fr	Text Manipulation	justdiff	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff	https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff	3.10+galaxy0	diffutils				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-justgzip	justgzip	Compress fastq sequence files								To update	http://artbio.fr	Convert Formats	justgzip	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip	https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip	2.8+galaxy0	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-lfq_protein_quant	lfq_protein_quant	Enable protein summarisation and quantitation								To update	https://github.com/compomics/LFQ_galaxy_p	Proteomics	lfq_protein_quant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	1.0	bioconductor-msnbase	2.28.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	111
-longorf	longORF	obtain longest ORF in six-frame translations								To update		Sequence Analysis	longorf	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf	0.3.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ltq_iquant_cli										To update			ltq_iquant_cli	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-lumpy_smoove	lumpy_smoove, vcf2hrdetect	Galaxy wrapper of the lumpy-using smoove workflow								To update	http://artbio.fr	Variant Analysis	lumpy_smoove	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove	0.2.8+galaxy1	svtyper	0.7.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0
-lumpy_sv	lumpy	Find structural variations								To update	http://artbio.fr	Variant Analysis	lumpy_sv	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv	1.3	lumpy-sv	0.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-maldiquant	maldi_quant_peak_detection, maldi_quant_preprocessing	MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.								To update	http://strimmerlab.org/software/maldiquant/	Proteomics	MALDIquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant	1.22.0	r-base				0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	25	3797
-manta	manta	Structural variant and indel caller for mapped sequencing data								To update	http://artbio.fr	Variant Analysis	manta	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/manta	https://github.com/ARTbio/tools-artbio/tree/main/tools/manta	1.6	manta	1.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	8	93
-map_peptides_to_bed	map_peptides_to_bed	Map peptides to a reference genome for display by a genome browser								To update		Proteomics	map_peptides_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	0.2	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	41
-mapping_quality_stats	mapqstatistics	Collects and shows the distribution of MAPQ values in a BAM alignment file								To update	http://artbio.fr	Sequence Analysis, Statistics	mapping_quality_stats	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	0.22.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-matchms	matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting	Searching, filtering and converting mass spectral libraries.	matchms	matchms		Matchms	Tool to import, process, clean, and compare mass spectrometry data.	Spectral library search, Format validation, Filtering	Metabolomics	Up-to-date	https://github.com/matchms/matchms	Metabolomics	matchms	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/matchms	https://github.com/RECETOX/galaxytools/tree/master/tools/matchms	0.27.0	matchms	0.27.0	Spectral library search, Format validation, Filtering	Metabolomics	2	14	14	11	2	14	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	10	187
-maxquant	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering	Proteomics experiment, Proteomics, Statistics and probability	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	415	6078
-mdanalysis	mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf	MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations								To update	https://github.com/MDAnalysis/mdanalysis	Computational chemistry	mdanalysis	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis	1.0.0	mdanalysis				10	5	10	0	10	5	10	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	139	3115
-mdfileconverter	md_converter	A tool for interconverting between different MD structure and trajectory file formats.								To update		Molecular Dynamics, Computational chemistry	md_converter	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter	1.9.7	mdtraj				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	98	26427
-mdslicer	md_slicer	A tool for slicing trajectory files using MDTraj.								To update		Molecular Dynamics, Computational chemistry	md_converter	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer	1.9.9	mdtraj				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	158
-mdtraj	traj_selections_and_merge	MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories								To update	https://github.com/mdtraj/mdtraj	Computational chemistry	mdtraj	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj	1.9.7	mdtraj				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	36
-mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	24
-measure_gastruloids	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index								To update		Imaging	measure_gastruloids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	20221216	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-meta_proteome_analyzer	meta_proteome_analyzer	MetaProteomeAnalyzer								Up-to-date	https://github.com/compomics/meta-proteome-analyzer/	Proteomics	meta_proteome_analyzer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	2.0.0	mpa-portable	2.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	123
-metagene_annotator	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	115	636
-metanovo	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	4181
-metaquantome	metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome		metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	104	2522
-mfassignr	mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot	The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements	mfassignr	mfassignr		MFAssignR	Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements.	Visualisation	Proteomics experiment, Molecular interactions, pathways and networks, Workflows	Up-to-date	https://github.com/RECETOX/MFAssignR	Metabolomics	MFAssignR	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr	https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr	1.0.3	r-mfassignr	1.0.3	Visualisation	Proteomics experiment, Molecular interactions, pathways and networks, Workflows	0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mgf_formatter	mgf_formatter									Up-to-date			mgf_formatter	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter	1.0.0	mgf-formatter	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mircounts	mircounts	Generates miRNA count lists from read alignments to mirBase.								To update	http://artbio.fr	RNA, Transcriptomics	mircounts	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts	https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts	1.6	tar				0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-misc	use_theoretical_mz_annotations									To update	https://github.com/RECETOX/galaxytools	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/misc	https://github.com/RECETOX/galaxytools/tree/master/tools/misc	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-moFF	proteomics_moff	moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.								Up-to-date	https://github.com/compomics/moFF	Proteomics	proteomics_moff	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	2.0.3	moff	2.0.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	759
-monocle3	monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers	De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_monocle3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3	0.1.4	monocle3-cli	0.0.9			9	0	9	0	9	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	264	3266
-morpheus	morpheus	Morpheus MS Search Application	morpheus	morpheus		Morpheus	A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.	Peptide database search	Proteomics	To update	https://cwenger.github.io/Morpheus	Proteomics	morpheus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	288	morpheus	290	Peptide database search	Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	140
-mqppep	mqppep_anova, mqppep_preproc	MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Proteomics	mqppep	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	0.1.19	bioconductor-preprocesscore	1.64.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	2
-msconvert	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert		msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			Filtering, Formatting	Proteomics, Proteomics experiment	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	189	19958
-msgfplus	msgfplus	MSGF+								To update		Proteomics	msgfplus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	0.5	msgf_plus	2024.03.26			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	507
-msmetaenhancer	msmetaenhancer		msmetaenhancer	msmetaenhancer		MSMetaEnhancer	Tool for mass spectra metadata annotation.	Annotation, Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	Up-to-date	https://github.com/RECETOX/MSMetaEnhancer	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer	https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer	0.4.0	msmetaenhancer	0.4.0	Annotation, Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	103
-msms_extractor	msms_extractor	Extract MS/MS scans from the mzML file(s) based on PSM report.								To update		Proteomics	msms_extractor	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor	1.0.0	proteowizard	3_0_9992			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	110
-msp_merge	msp_merge									To update	https://github.com/RECETOX/galaxytools	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge	https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge	0.1.0	matchms	0.27.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-msstats	msstats	MSstats tool for analyzing mass spectrometry proteomic datasets	msstatstmt	msstatstmt		MSstatsTMT	Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	To update	https://github.com/MeenaChoi/MSstats	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	4.0.0	bioconductor-msstats	4.10.0	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	144	2036
-msstatstmt	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	726
-mt2mq	mt2mq	Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome								To update		Proteomics	mt2mq	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq	1.1.0	r-tidyverse				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	19	270
-mutational_patterns	mutational_patterns	Mutational patterns and signatures in base substitution catalogs								Up-to-date	http://artbio.fr	Variant Analysis	mutational_patterns	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	3.12.0	bioconductor-mutationalpatterns	3.12.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mz_to_sqlite	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	Conversion, Peptide database search	Proteomics, Biological databases	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	33	844
-mzml_validator	mzml_validator	mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.								To update	https://github.com/RECETOX/galaxytools	Metabolomics, Proteomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	0.1.0+galaxy2	lxml				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ncbi_blast_plus	blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper	NCBI BLAST+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	devteam	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	2.14.1	python				16	16	16	16	16	16	16	16	0	15	0	0	15	0	0	0	0	0	0	0	16	15	16	0	0	0	0	0	0	16	0	0	0	0	16	0	0	16	15	0	4066	365597
-oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	1	1	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	45
-ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6
-ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-omero	omero_import, omero_metadata_import	Import images and metadata into an OMERO.server using omero-py	omero	omero		OMERO	Client-server Java software for visualisation, management and analysis of biological microscope images.	Image analysis	Imaging, Data visualisation	To update	https://github.com/ome/omero-py/	Imaging	omero_upload	ufz	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	5.18.0	omero-py	5.11.1	Image analysis	Imaging, Data visualisation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-omero_clean_rois_tables	omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down								To update		Imaging	omero_clean_rois_tables	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	20230623	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-omero_get_children_ids	omero_get_children_ids	Get omero id of children of an omero object id								To update		Imaging	omero_get_children_ids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	0.2.0	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-omero_get_full_images	omero_get_full_images	Get full images from omero								To update		Imaging	omero_get_full_images	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	20240521	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-omero_hyperstack_to_fluo_measurements_on_gastruloid	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels								To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	20230809	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-omero_hyperstack_to_gastruloid_measurements	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements								To update		Imaging	omero_hyperstack_to_gastruloid_measurements	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	20240214	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-openmm	pdbfixer	OpenMM is a toolkit for molecular simulation using high performance GPU code.								To update	https://github.com/openmm	Molecular Dynamics, Computational chemistry	openmm	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm	1.8.1	pdbfixer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	25	347
-openms	AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter	OpenMS Suite for LC/MS data management and analyses								To update	https://www.openms.de/	Proteomics	openms	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	3.1	openms	3.1.0			8	34	144	0	8	34	144	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	141	124	0	886	105432
-packmol	packmol	PACKMOL is a package for creating starting structures for Molecular Dynamics simulations								To update	http://m3g.iqm.unicamp.br/packmol/home.shtml	Molecular Dynamics, Computational chemistry	packmol	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol	18.169.1	packmol				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	288
-pathifier	pathifier	pathifier								Up-to-date	https://	Transcriptomics, Statistics	pathifier	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	1.40.0	bioconductor-pathifier	1.40.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	228
-pathwaymatcher	reactome_pathwaymatcher	Reactome Pathway Matcher								To update	https://github.com/LuisFranciscoHS/PathwayMatcher	Proteomics	reactome_pathwaymatcher	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher		pathwaymatcher	1.9.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	238
-pep_pointer	pep_pointer	PepPointer categorizes peptides by their genomic coordinates.								To update		Genomic Interval Operations, Proteomics	pep_pointer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	0.1.3+galaxy1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	498
-pepquery	pepquery	A peptide-centric MS search engine for novel peptide identification and validation.								To update	https://pepquery.org	Proteomics	pepquery	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	1.6.2	pepquery	2.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	4862
-pepquery2	pepquery2, pepquery2_index, pepquery2_show_sets	PepQuery2 peptide-centric MS search for peptide identification and validation								Up-to-date	https://pepquery.org	Proteomics	pepquery2	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	2.0.2	pepquery	2.0.2			0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	13	717
-peptide_genomic_coordinate	peptide_genomic_coordinate	Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files								To update		Proteomics	peptide_genomic_coordinate	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate	1.0.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	468
-peptideshaker	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.9			4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	2	0	485	17477
-pepxml_to_xls		Convert PepXML to Tabular								To update		Proteomics	pepxml_to_xls	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-percolator	batched_set_list_creator, percolator, percolator_input_converters, pout2mzid	Percolator								To update		Proteomics	percolator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator	3.5	percolator	3.6.5			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	5	368
-pi_db_tools	calc_delta_pi, pi_db_split, pi_dbspec_align	HiRIEF tools								To update		Proteomics	hirieftools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools	1.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pindel	pindel	Pindel detects genome-wide structural variation.								Up-to-date	http://artbio.fr	Variant Analysis	pindel	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel	https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel	0.2.5b9	pindel	0.2.5b9			0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-pmd_fdr	pmd_fdr	Calculate Precursor Mass Discrepancy (PMD) for MS/MS								To update	https://github.com/slhubler/PMD-FDR-for-Galaxy-P	Proteomics	pmd_fdr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	1.4.0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-positions2snv_alignment	positions2snv_alignment	Generate alignment of SNVs from SNVPhyl variant table.								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Variant Analysis	positions2snv_alignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-positions2snv_invariant_alignment	positions2snv_invariant_alignment	Generate alignment of SNVs and non-variant positions from SNVPhyl variant table.								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Variant Analysis	positions2snv_invariant_alignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-probecoverage	probecoverage	computes and plots read coverage of genomic regions by sequencing datasets								To update	http://artbio.fr	Sequence Analysis, Genomic Interval Operations, Graphics, Statistics	probecoverage	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	0.22.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-proteinpilot	convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml									To update			proteinpilot	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-proteomiqon_joinquantpepionswithproteins	proteomiqon_joinquantpepionswithproteins	The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.								To update	https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html	Proteomics	proteomiqon_joinquantpepionswithproteins	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	0.0.1	proteomiqon-joinquantpepionswithproteins	0.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	366
-proteomiqon_labeledproteinquantification	proteomiqon_labeledproteinquantification	The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html	Proteomics	proteomiqon_labeledproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	0.0.1	proteomiqon-labeledproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	14
-proteomiqon_labelfreeproteinquantification	proteomiqon_labelfreeproteinquantification	The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html	Proteomics	proteomiqon_labelfreeproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	0.0.1	proteomiqon-labelfreeproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	6
-proteomiqon_mzmltomzlite	proteomiqon_mzmltomzlite	The tool MzMLToMzLite allows to convert mzML files to mzLite files.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html	Proteomics	proteomiqon_mzmltomzlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite	0.0.8	proteomiqon-mzmltomzlite	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	721
-proteomiqon_peptidedb	proteomiqon_peptidedb	The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html	Proteomics	proteomiqon_peptidedb	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	0.0.7	proteomiqon-peptidedb	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	96
-proteomiqon_peptidespectrummatching	proteomiqon_peptidespectrummatching	Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html	Proteomics	proteomiqon_peptidespectrummatching	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	0.0.7	proteomiqon-peptidespectrummatching	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	686
-proteomiqon_proteininference	proteomiqon_proteininference	MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html	Proteomics	proteomiqon_proteininference	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	0.0.7	proteomiqon-proteininference	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	89
-proteomiqon_psmbasedquantification	proteomiqon_psmbasedquantification	The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.								To update	https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html	Proteomics	proteomiqon_psmbasedquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	0.0.8	proteomiqon-psmbasedquantification	0.0.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	604
-proteomiqon_psmstatistics	proteomiqon_psmstatistics	The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html	Proteomics	proteomiqon_psmstatistics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	0.0.8	proteomiqon-psmstatistics	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	694
-proteore_venn_diagram	proteore_venn_diagram	ProteoRE JVenn Diagram								To update		Proteomics	proteore_venn_diagram	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram	2021.06.08	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15
-protxml_to_xls	protxml_to_xls									To update			protxml_to_xls	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls	0.1.0	trans_proteomic_pipeline				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-psm2sam	PSMtoSAM	PSM to SAM								To update	https://bioconductor.org/packages/release/bioc/html/proBAMr.html	Proteomics	psm_to_sam	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam	1.3.2.1	r-base				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-psm_eval	psm_eval									To update			psm_eval	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval	0.1.0	binaries_for_psm_eval				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-psm_validation	psmvalidator	Validate PSM from Ion Fragmentation								To update	https://github.com/galaxyproteomics/psm_fragments.git	Proteomics	psm_validation	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	1.0.3					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	20
-psy-maps	psy_maps	Visualization of regular geographical data on a map with psyplot								To update	https://github.com/Chilipp/psy-maps	Visualization, Climate Analysis	psy_maps	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	1.2.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	46	469
-pyprophet	pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample	Semi-supervised learning and scoring of OpenSWATH results.								To update	https://github.com/PyProphet/pyprophet	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	2.1.4	pyprophet	2.2.5			0	5	6	0	0	5	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	33	2509
-pyscenic	pyscenic_aucell, pyscenic_ctx, pyscenic_grn	PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/								To update		Transcriptomics, RNA, Sequence Analysis	suite_pyscenic	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic	0.12.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pyteomics	mztab2tsv	Tools using the pyteomics library	pyteomics	pyteomics		Pyteomics	Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.	Protein identification	Proteomics, Proteomics experiment	To update	https://pyteomics.readthedocs.io/en/latest/	Proteomics, Metabolomics	pyteomics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	4.4.1	pyteomics	4.7.3	Protein identification	Proteomics, Proteomics experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	81
-pyvo_integration	astronomical_archives	Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy								To update		Data Source	astronomicalarchivestool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration	0.10.0	astropy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	36
-qcxms	qcxms_getres, qcxms_neutral_run, qcxms_production_run	QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD).								To update	https://github.com/grimme-lab/QCxMS	Computational chemistry, Molecular Dynamics	QCxMS	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms	https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms	5.2.1					0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-quantp	quantp	Correlation between protein and transcript abundance								To update		Proteomics	quantp	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp	1.1.2	r-data.table	1.11.6			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	230
-quantwiz_iq	quantwiz_iq	Isobaric Quantitation using QuantWiz-IQ								Up-to-date	https://sourceforge.net/projects/quantwiz/	Proteomics	quantwiz_iq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	2.0	quantwiz-iq	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	32
-query	query	Execute an SQL statement on a set of tables								To update		Text Manipulation	query	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/query	https://github.com/RECETOX/galaxytools/tree/master/tools/query	0.2	click				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-qupath_roi_splitter	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type								To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter	0.3.1	geojson				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	59
-ramclustr	ramclustr, ramclustr_define_experiment		ramclustr	ramclustr		RAMClustR	A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.	Imputation, Standardisation and normalisation, Clustering, Correlation	Metabolomics	To update	https://rdrr.io/cran/RAMClustR/	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr	https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr	1.3.0	r-ramclustr	1.3.1	Imputation, Standardisation and normalisation, Clustering, Correlation	Metabolomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	2	16
-rawtools	rawtools	Raw Tools								To update	https://github.com/kevinkovalchik/RawTools	Proteomics	rawtools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools		rawtools	2.0.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	14	175
-rcx-tk	rcx-tk	Tools to process metadata or alkane files.								To update	https://github.com/RECETOX/rcx-tk	Metabolomics	rcx_tk	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/	https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk	0.1.0+galaxy0	rcx-tk	0.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-recetox_aplcms	recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise	Peak detection tool for HRMS profile data.	recetox-aplcms	recetox-aplcms		recetox-aplcms	recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening.	Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment	Metabolomics	Up-to-date	https://github.com/RECETOX/recetox-aplcms	Metabolomics	recetox-aplcms	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms	0.13.2	r-recetox-aplcms	0.13.2	Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment	Metabolomics	0	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	7	296
-recetox_msfinder	recetox_msfinder		recetox-msfinder	recetox-msfinder		recetox-msfinder	This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0.	Annotation	Metabolomics	To update	https://github.com/RECETOX/recetox-msfinder	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder	v3.5.2			Annotation	Metabolomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-recetox_xmsannotator	recetox_xmsannotator_advanced		recetox-xmsannotator	recetox-xmsannotator		recetox-xMSannotator	Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring.	Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation		Up-to-date	https://github.com/RECETOX/recetox-xMSannotator	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator	0.10.0	r-recetox-xmsannotator	0.10.0	Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation		0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
-regex_find_replace	regex1, regexColumn1	Use python regular expressions to find and replace text								To update		Text Manipulation	regex_find_replace	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace	1.0.3	python				2	2	2	2	2	2	2	2	0	2	0	0	2	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	2	2	0	495	60307
-regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	22	526
-rem_complex	rem_complex	Removes molecular coordination complexes.								To update	https://github.com/RECETOX/galaxytools	Metabolomics	rem_complex	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex	https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex	1.0.0	pandas				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rename_annotated_feature	rename_annotated_feature	Update column names in an abundance table using a annotation table with spectral matching results								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	rename_annotated_feature	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature	https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature	1.0.0	pandas				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-repenrich	edger-repenrich, repenrich	Repeat element profiling								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	Transcriptomics	repenrich	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	2.31.1					0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0
-repenrich2	edger-repenrich2, repenrich2	Repeat element profiling using bowtie2 aligner								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	Transcriptomics	repenrich2	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	2.31.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-retip	retip_apply, retip_descriptors, retip_filter_rt, retip_train		retip	retip		Retip	Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765.	Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition	Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry	To update	https://github.com/PaoloBnn/Retip	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/retip	https://github.com/RECETOX/galaxytools/tree/master/tools/retip	0.5.4			Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition	Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-retrieve_ensembl_bed	retrieve_ensembl_bed	Retrieve cDNA features from Ensembl REST API in BED format								To update	http://rest.ensembl.org/	Data Source	retrieve_ensembl_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-revertR2orientationInBam	revertR2orientationInBam	Revert the mapped orientation of R2 mates in a bam.								To update		SAM	revertr2orientationinbam	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam	0.0.2	samtools	1.20			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	39
-riassigner	riassigner, riassigner_from_comment		riassigner	riassigner		RIAssigner	RIAssigner is a python tool for retention index (RI) computation for GC-MS data.	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	Up-to-date	https://github.com/RECETOX/RIAssigner	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	0.4.1	riassigner	0.4.1	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	1	2	2	1	1	2	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	15
-rmassbank	rmassbank	RMassBank is an R package for processing tandem MS files and building of MassBank records.								To update	https://github.com/MassBank/RMassBank	Metabolomics	rmassbank	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank	https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank	3.0.0	python				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
-rsem	extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie	transcript quantification from RNA-Seq data								To update	https://github.com/deweylab/RSEM	Transcriptomics, RNA	rsem	artbio	https://github.com/artbio/tools-artbio/tree/master/tools/rsem	https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem		rsem	1.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	1	1	0	67	377
-salmon-kallisto-mtx-to-10x	_salmon_kallisto_mtx_to_10x	Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	salmon_kallisto_mtx_to_10x	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x	0.0.1+galaxy6	scipy				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	86	561
-sambamba	sambamba_sample_or_filter	filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM								To update	http://artbio.fr	SAM	sambamba	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba	https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba	0.7.1+galaxy1	sambamba	1.0.1			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-sashimi_plot	sashimi_plot	Generates a sashimi plot from bam files.								To update	http://artbio.fr	RNA, Transcriptomics, Graphics, Visualization	sashimi_plot	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot	https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot	0.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-sc3	sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare	De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_sc3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3	1.8.0	sc3-scripts	0.0.6			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	9
-scaffold	scaffold, scaffold_export									To update			scaffold	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold	0.1.0	scaffold				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-scanpy	anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data	scanpy-scripts, command-line wrapper scripts around Scanpy.								To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis, RNA	scanpy_scripts	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy	1.9.3	scanpy-scripts	1.9.301			27	27	27	0	27	27	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	13	0	2185	39356
-scater	scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results	De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scater	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater	1.10.0	scater-scripts	0.0.5			1	2	6	0	1	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	16	387
-sccaf	run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out	SCCAF: Single Cell Clustering Assessment Framework.								To update	https://github.com/sccaf/sccaf	Transcriptomics	SCCAF	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf	0.0.9	sccaf	0.0.10			4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	110
-sceasy	sceasy_convert	Convert scRNA data object between popular formats								To update		Transcriptomics	sceasy	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy	0.0.5	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	90	721
-scmap	scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features	De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scmap	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap	1.6.4	scmap-cli	0.1.0			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	13	83
-scpred	scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model	De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scpred	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred	1.0.2	scpred-cli	0.1.0			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	25
-scripting	singularity_scriptrunner	suite_scripting								To update	https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/	Text Manipulation	scripting tools	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-sequence_format_converter	sequence_format_converter	various fasta to tabular conversions								To update	http://artbio.fr	Convert Formats, Fasta Manipulation	sequence_format_converter	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter	https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter	2.2.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-seurat	seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features	De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1								Up-to-date	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	Transcriptomics, RNA, Statistics, Sequence Analysis	suite_seurat	ebi-gxa		https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat	4.0.0	seurat-scripts	4.0.0			14	14	14	11	14	14	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	0	0	0	0	0	0	0	0	181	1966
-sgwb	sgwb_astro_tool	SGWB								To update		Astronomy	sgwb_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb	0.0.1+galaxy0	ipython				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-shift-longitudes	shyft_longitudes	Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/	Climate Analysis	shift_longitudes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes	0.1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	63
-sixgill	sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge	Six-frame Genome-Inferred Libraries for LC-MS/MS								Up-to-date		Proteomics, MetaProteomics	sixgill	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	0.2.4	sixgill	0.2.4			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	24	293
-small_rna_clusters	small_rna_clusters	clusters small rna reads in alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_clusters	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters	1.3.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-small_rna_maps	small_rna_maps	Generates small read maps from alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_maps	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps	3.1.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-small_rna_signatures	overlapping_reads, signature	Computes the tendency of small RNAs to overlap with each other.								To update	http://artbio.fr	RNA	small_rna_signatures	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures	3.4.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0
-smithsonian-volcanoes	smithsonian_volcanoes	Retrieve data from Volcanoes of the World (VOTW) Database								To update	https://volcano.si.edu/gvp_votw.cfm	Retrieve Data	smithsonian_volcanoes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes	0.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-snv_matrix	snvmatrix	Generate matrix of SNV distances								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	snv_matrix	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-snvtocnv	sequenzaindex, snvtocnv	infer copy number variations from a vcf file with SNVs using R sequenza								To update	http://artbio.fr	Variant Analysis	snvtocnv	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv	https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv	3.0.0+galaxy1	sequenza-utils	3.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-spec2vec	spec2vec_similarity, spec2vec_training	Mass spectra similarity scoring using a trained Spec2Vec model.	spec2vec	spec2vec		Spec2Vec	Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set.	Spectrum calculation, Spectral library search, Database search, Natural product identification	Proteomics experiment, Metabolomics, Natural language processing, Proteomics	Up-to-date	https://github.com/iomega/spec2vec	Metabolomics	spec2vec	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec	https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec	0.8.0	spec2vec	0.8.0	Spectrum calculation, Spectral library search, Database search, Natural product identification	Proteomics experiment, Metabolomics, Natural language processing, Proteomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-spectrast2spectrast_irt	gp_spectrast2spectrast_irt	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2spectrast_irt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-spectrast2tsv	gp_spectrast2tsv	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2tsv	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	56	769
-sr_bowtie	bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-sr_bowtie_dataset_annotation	sr_bowtie_dataset_annotation	Maps iteratively small RNA sequencing datasets to reference sequences.								To update	http://artbio.fr	RNA	sr_bowtie_dataset_annotation	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation	2.8	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	7	4	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	21	225
-stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	10	325
-suite_snvphyl		SNVPhyl suite defining all dependencies for SNVPhyl								To update		Sequence Analysis	suite_snvphyl_1_2_3	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-topologyeditors	gromacs_modify_topology, gromacs_extract_topology	Set of python scripts and associated tool files that can be used to modify topology files.								To update	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	Molecular Dynamics, Computational chemistry	topologyeditors	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	0	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	8	50
-translate_bed	translate_bed	Translate BED transcript CDS or cDNA in 3 frames								To update	http://rest.ensembl.org/	Proteomics	translate_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	0.1.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	49	643
-translate_bed_sequences	translate_bed_sequences	Perform 3 frame translation of BED file augmented with a sequence column								To update		Proteomics	translate_bed_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	57
-ucsc-cell-browser	ucsc_cell_browser	Python pipeline and Javascript scatter plot library for single-cell datasets								To update	https://cells.ucsc.edu/	Transcriptomics	ucsc_cell_browser	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser	1.0.0+galaxy1	ucsc-cell-browser	1.2.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	78	941
-unipept	unipept	Unipept retrieves metaproteomics information	unipept	unipept		Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	115	5005
-uniprotxml_downloader	uniprotxml_downloader	Download UniProt proteome in XML or fasta format								To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	79	1360
-upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server								To update		Imaging	upload_roi_and_measures_to_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	0.0.5	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	25	86
-varscan_vaf	varscan_vaf	Compute variant allele frequency in vcf files generated by varscan.								To update	http://artbio.fr	Variant Analysis	varscan_vaf	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf	https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf	0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-vcf2snvalignment	vcf2snvalignment	Generates multiple alignment of variant calls								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	vcf2snvalignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-verify_map	verify_map	Checks the mapping quality of all BAM(s)								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	verify_map	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	351	12203
-virsorter	virsorter	VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.	virsorter	virsorter		virsorter	Identify DNA and RNA virus sequences.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/jiarong/VirSorter2/	Metagenomics	virsorter	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter	2.2.4	virsorter	2.2.4	Taxonomic classification	Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-vmd		vmd is a package for  visualizing and analyzing trajectories from molecular dynamics (MD) simulations								To update	https://www.ks.uiuc.edu/Research/vmd/	Computational chemistry	vmd	chemteam	https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-waveica	waveica	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis.	waveica	waveica		WaveICA	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform.	Standardisation and normalisation	Metabolomics	Up-to-date	https://github.com/RECETOX/WaveICA	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/waveica	https://github.com/RECETOX/galaxytools/tree/master/tools/waveica	0.2.0	r-recetox-waveica	0.2.0	Standardisation and normalisation	Metabolomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	6
-xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	5	5	2	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	175	5876
-xmlstarlet	xmlstarlet	Tool to convert a xml file from one metadata standard to another								To update		Convert Formats	xmlstarlet	ecology	https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet	https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet	1.6.1	xmlstarlet				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	14
-xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-xtb	xtb_molecular_optimization	Performs semiempirical molecular optimization.								To update	https://github.com/grimme-lab/xtb	Metabolomics	xtb_molecular_optimization	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/xtb	https://github.com/RECETOX/galaxytools/tree/master/tools/xtb	6.6.1	xtb				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-zeiss_lmd_converter	ZeissLMDconverter	Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	2.0.4	shapely				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	74	2565
+phyloseq	phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	phyloseq	phyloseq		phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq	1.46.0	bioconductor-phyloseq	1.46.0	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	0	1	4	4	0	1	4	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	82	812
+phyml	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	phyml	phyml		PhyML	Phylogenetic estimation software using Maximum Likelihood	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Bioinformatics, Phylogenetics	Up-to-date	http://www.atgc-montpellier.fr/phyml/	Phylogenetics	phyml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml	3.3.20220408	phyml	3.3.20220408		Phylogenetics, Bioinformatics, Phylogenetics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	104	1770
+picard	picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile	Picard SAM/BAM manipulation tools.	picard_samtofastq	picard_reordersam, picard_samtofastq, picard_fastqtosam, picard_replacesamheader		picard_samtofastq	Create a FASTQ file.	Formatting	Sequencing	To update	http://broadinstitute.github.io/picard/	SAM	picard	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard	3.1.1	picard	3.2.0	Formatting	Sequencing	31	31	31	31	31	31	31	31	0	0	0	0	0	0	0	0	0	0	31	4	31	0	0	31	0	0	0	31	0	0	0	0	0	31	31	31	0	3735	374458
+pick_value	pick_value	Compose a text parameter value using text, integer and float values								To update		Text Manipulation	pick_value	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value	0.2.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	116
+picrust	picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes	PICRUSt wrappers	picrust	picrust		PICRUSt	PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust	1.1.1	picrust	1.1.4	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	0	6	5	6	0	6	5	6	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	45	1095
+picrust2	picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions	PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	picrust2	picrust2		PICRUSt2	PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	Up-to-date	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.3	picrust2	2.5.3	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	88	1000
+pilon	pilon	pilon is a tool for assembly improvement and variant analysis in bacteria	pilon	pilon		pilon	Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.	Sequence assembly, Analysis, Read alignment	Assembly	To update	https://github.com/broadinstitute/pilon/wiki	Variant Analysis	pilon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon	1.20.1	pilon	1.24	Sequence assembly, Analysis	Assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	467	7942
+pipelign	pipelign	Multipe sequence alignment								Up-to-date	https://github.com/asmmhossain/pipelign/	Next Gen Mappers	pipelign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign	0.2	pipelign	0.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	83	983
+pizzly	pizzly	Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.								To update	https://github.com/pmelsted/pizzly/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly	0.37.3.1	pizzly	0.37.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	208
+plasflow	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	plasflow	plasflow		PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.	Sequence analysis	Metagenomics	Up-to-date	https://github.com/smaegol/PlasFlow	Sequence Analysis	plasflow	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow	1.1.0	plasflow	1.1.0	Sequence analysis	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	278	22589
+plasmidfinder	plasmidfinder	"""PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"""	PlasmidFinder	PlasmidFinder		PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	Up-to-date	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	Sequence Analysis	plasmidfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder	2.1.6	plasmidfinder	2.1.6	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	22
+plink	plink	Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	plink	plink		PLINK	Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	Genetic variation analysis	GWAS study	Up-to-date	https://www.cog-genomics.org/plink	Genome-Wide Association Study	plink	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink	1.90b6.21	plink	1.90b6.21	Genetic variation analysis	GWAS study	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	46	669
+polypolish	polypolish	"""Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."""	Polypolish	Polypolish		Polypolish	Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	To update	https://github.com/rrwick/Polypolish	Sequence Analysis	polypolish	iuc	https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish	0.5.0	polypolish	0.6.0	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	239
+porechop	porechop	Porechop - Finding and removing adapters from Oxford Nanopore reads								To update	https://github.com/rrwick/Porechop	Fasta Manipulation, Fastq Manipulation	porechop	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop	https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop		porechop	0.2.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1046	185468
+poretools	poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot	A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	poretools	poretools		Poretools	Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	Nucleic acid sequence analysis	DNA, Sequencing	Up-to-date	https://poretools.readthedocs.io/en/latest/	Fasta Manipulation, Fastq Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools	0.6.1a1	poretools	0.6.1a1	Nucleic acid sequence analysis	DNA, Sequencing	13	13	13	0	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	6	13	0	409	18773
+presto	presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3	pRESTO toolkit for immune repertoire analysis.	presto	presto		pRESTO	Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	To update	https://presto.readthedocs.io/	Sequence Analysis	presto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto	0.6.2	presto	0.7.2	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pretext	pretext_graph, pretext_map, pretext_snapshot	Process genome contacts maps processing images.								Up-to-date	https://github.com/wtsi-hpag/PretextSnapshot	Sequence Analysis	suite_pretext	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext	0.0.6	pretextgraph	0.0.6			3	2	3	0	3	2	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	254	2350
+prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	70	7881
+prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+progressivemauve	progressivemauve, xmfa2gff3	Mauve/ProgressiveMauve Multiple Sequence Aligner								To update	http://darlinglab.org/mauve/user-guide/progressivemauve.html	Sequence Analysis	progressivemauve	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve	https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve		progressivemauve	snapshot_2015_02_13			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	286	1734
+prokka	prokka	Rapid annotation of prokaryotic genomes	prokka	prokka		Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka	1.14.6	prokka	1.14.6	Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	3233	371445
+prot-scriber	prot_scriber	Protein annotation of short human readable descriptions								Up-to-date	https://github.com/usadellab/prot-scriber	Proteomics	prot_scriber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber	0.1.6	prot-scriber	0.1.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	5
+proteinortho	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho		Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	To update	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.2	Sequence clustering, Sequence analysis	Comparative genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	200	3320
+psiclass	psiclass	PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.	psiclass	psiclass		PsiCLASS	Reference-based transcriptome assembler for single or multiple RNA-seq samples	Transcriptome assembly	Sequence assembly	Up-to-date	https://github.com/splicebox/PsiCLASS	Transcriptomics	psiclass	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass	https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass	1.0.3	psiclass	1.0.3	Transcriptome assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	15
+pureclip	pureclip	PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data								To update	https://github.com/skrakau/PureCLIP	Sequence Analysis, RNA, CLIP-seq	pureclip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip	1.0.4	pureclip	1.3.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	1423
+purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	167	16800
+pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	350	21123
+pyega3	pyega3	EGA python client uses the EGA REST API to download authorized datasets and files.								To update	https://github.com/EGA-archive/ega-download-client	Data Source	ega_download_client	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3	5.0.2	pyega3	5.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	38	2424
+pygenometracks	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	pygenometracks	pygenometracks		pyGenomeTracks	reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	Visualisation, Formatting	Model organisms, Imaging, Workflows	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	377	11332
+pysradb	pysradb_search	pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.	pysradb	pysradb		pysradb	Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	To update	https://github.com/saketkc/pysradb	Sequence Analysis	pysradb_search	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb	1.4.2	pysradb	2.2.1	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	26	144
+qfilt	qfilt	Filter sequencing data								To update	https://github.com/veg/qfilt	Fastq Manipulation	qfilt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt	1.0.0+galaxy1	qfilt	0.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+qiime_add_on	qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_add_on, qiime_core		qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	68	1909
+qiime_core	qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file	QIIME to perform microbial community analysis	qiime_core	qiime_core		qiime_core	QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	32	32	0	0	32	32	0	0	0	0	0	0	0	0	0	0	31	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	0	1155	28681
+qiime_extract_viz	qiime_extract_viz	Extract vizualization from QIIME artifacts								To update	http://www.qiime.org	Metagenomics	qiime_extract_viz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz	0.1.0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+qq_tools	qq_manhattan									To update	https://CRAN.R-project.org/package=qqman	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools	0.1.0	r-qqman	0.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+qualimap	qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq	Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.	qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	Up-to-date	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.3	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	1	4	4	4	1	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1	0	0	0	1	0	0	0	0	0	4	4	4	0	1328	664470
+quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	3567	51567
+query_impc	query_impc	Contains a tool to query the IMPC database.								To update	https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc	Convert Formats, Web Services	query_impc	iuc	https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc	0.9.0	requests				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
+query_tabular	filter_tabular, query_tabular, sqlite_to_tabular	Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular	3.3.1	python				3	3	3	1	3	3	3	1	0	0	0	0	0	0	0	0	0	0	0	3	2	0	0	0	0	0	0	1	0	0	0	0	0	3	3	3	0	561	124536
+quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
+raceid	raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory	RaceID3, StemID2, FateID - scRNA analysis								To update	https://github.com/dgrun/RaceID3_StemID2_package/	Single Cell, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid	0.2.3	r-raceid	0.1.3			5	5	5	1	5	5	5	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	82	4569
+ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	237	2833
+rapidnj	rapidnj	Galaxy wrapper for the RapidNJ tool	rapidnj	rapidnj		RapidNJ	A tool for fast canonical neighbor-joining tree construction.	Phylogenetic tree generation	Phylogeny	Up-to-date	https://birc.au.dk/software/rapidnj/	Phylogenetics	rapidnj	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj	2.3.2	rapidnj	2.3.2		Phylogeny	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	176
+rasusa	rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa		rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	2.0.0	rasusa	2.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	6902
+raxml	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml		RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	Sequence analysis	Phylogenetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	383	6808
+rcorrector	rcorrector	Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.	rcorrector	rcorrector		Rcorrector	This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.	Sequencing error detection	RNA, RNA-Seq, Sequencing	To update	https://github.com/mourisl/Rcorrector	Fastq Manipulation	rcorrector	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector	1.0.3+galaxy1	rcorrector	1.0.7	Sequencing error detection	RNA, RNA-Seq	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	569
+read_it_and_keep	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep		read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	Filtering, Genome alignment	Pathology, Genomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	3370
+recentrifuge	recentrifuge	"""With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."""	Recentrifuge	Recentrifuge		Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.15.0	recentrifuge	1.15.0	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	48	331
+red	red	Red (REpeat Detector)	red	red		RED	This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	Up-to-date	https://github.com/BioinformaticsToolsmith/Red	Sequence Analysis	red	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/red	https://github.com/galaxyproject/tools-iuc/tree/main/tools/red	2018.09.10	red	2018.09.10	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	88	578
+repeatmasker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.	repeatmasker	repeatmasker		RepeatMasker	A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).	Genome annotation	Sequence analysis, Sequence composition, complexity and repeats	To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker	4.1.5	repeatmasker	4.0.9_p2	Genome annotation	Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	248	3750
+repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	217	1177
+repmatch_gff3	repmatch_gff3	Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria.								To update		ChIP-seq	repmatch_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3		matplotlib				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+reshape2	cast, melt	Flexibly restructure and aggregate data using just the two functions melt and dcast								To update	https://cran.r-project.org/web/packages/reshape2/index.html	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2	1.4.2	r-reshape2				2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	33	3456
+resize_coordinate_window	resize_coordinate_window	Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size.								To update		Genomic Interval Operations	resize_coordinate_window	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window	https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window	1.0.2	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	85
+revoluzer	revoluzer_crex, revoluzer_distmat	revoluzer wrappers	revoluzer	revoluzer		revoluzer	Various tools for genome rearrangement analysis. CREx, TreeREx, etc	Structural variation detection	Molecular evolution, Phylogeny	Up-to-date	https://gitlab.com/Bernt/revoluzer/	Phylogenetics	revoluzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer	0.1.6	revoluzer	0.1.6	Structural variation detection	Molecular evolution, Phylogeny	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rgcca	rgcca	multi-block analysis								To update	https://github.com/rgcca-factory/RGCCA	Statistics	rgcca	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca	3.0.2	rgccacmd	3.0.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	44
+rgrnastar	rna_star, rna_starsolo	RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper	star	star		STAR	Ultrafast universal RNA-seq data aligner	Sequence alignment	RNA-Seq, Transcriptomics	To update	https://github.com/alexdobin/STAR	Next Gen Mappers, Transcriptomics	rgrnastar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar	2.7.11a	star	2.7.11b	Sequence alignment	RNA-Seq, Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	2	0	0	0	2	0	0	0	0	0	2	2	2	0	4015	425658
+ribowaltz	ribowaltz_process, ribowaltz_plot	Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data	riboWaltz	riboWaltz		riboWaltz	riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.		Computational biology	To update	https://github.com/LabTranslationalArchitectomics/riboWaltz	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz	1.2.0	ribowaltz	2.0		Computational biology	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	14	161
+rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	109	1110
+roary	roary	Roary the pangenome pipeline	roary	roary		Roary	A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary	3.13.0	roary	3.13.0	Genome assembly	DNA, Genomics, Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	656	12225
+rp2biosensor	rp2biosensor	Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output								To update	https://github.com/brsynth/rp2biosensor	Synthetic Biology	rp2biosensor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor	3.2.1	rp2biosensor				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rp2paths	rp2paths	Enumerate and seperate the different pathways generated by RetroPath2.0								To update	https://github.com/brsynth/rp2paths	Synthetic Biology	rp2paths	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths	1.5.1	rp2paths				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rpbasicdesign	rpbasicdesign	Extracting enzyme IDs from rpSBML files								To update	https://github.com/brsynth/rpbasicdesign	Synthetic Biology	rpbasicdesign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign	1.2.2	rpbasicdesign				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rpfba	rpfba	Perform FBA for the RetroPath2.0 heterologous pathways								To update	https://github.com/brsynth/rptools/releases	Synthetic Biology	rpfba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba	5.12.3	rptools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rptools	rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz	Suite of tools that work on rpSBML format								To update	https://github.com/brsynth/rptools	Synthetic Biology	rptools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools	5.13.1	rptools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rrparser	rrparser	Reaction Rules Parser								To update	https://github.com/brsynth/RRParser	Synthetic Biology	rrparser	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser	2.5.2	rrparser				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rseqc	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	22	22	22	22	22	0	0	0	0	0	0	0	0	0	0	22	0	0	0	0	22	0	0	0	22	0	0	0	0	0	22	22	22	0	3206	133498
+ruvseq	ruvseq	Remove Unwanted Variation from RNA-Seq Data	ruvseq	ruvseq		RUVSeq	This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.	Differential gene expression analysis	Gene expression, RNA-seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	ruvseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq	1.26.0	bioconductor-ruvseq	1.36.0	Differential gene expression analysis	Gene expression	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	76	1236
+salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	84	454
+samblaster	samblaster	samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files	samblaster	samblaster		SAMBLASTER	A tool to mark duplicates and extract discordant and split reads from SAM files.	Split read mapping	DNA, Sequencing, Mapping	To update	https://github.com/GregoryFaust/samblaster	SAM, Fastq Manipulation, Variant Analysis	samblaster	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster	https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster	0.1.24	samblaster	0.1.26	Split read mapping	DNA, Sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+samtools										To update	https://github.com/samtools/samtools	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools	1.20	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+sansa	sansa_annotate	Sansa is a tool for structural variant annotation.								To update	https://github.com/dellytools/sansa	Variant Analysis	sansa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa	0.2.1	sansa	0.2.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	18	123
+sarscov2formatter	sarscov2formatter	sarscov2formatter custom script								Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	173
+sarscov2summary	sarscov2summary	sarscov2summary custom script								To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	140
+sbml2sbol	sbml2sbol	Convert SBML to SBOL format								To update	https://github.com/neilswainston/SbmlToSbol	Synthetic Biology	sbml2sbol	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol	0.1.13	sbml2sbol				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+scanpy	scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	scanpy	scanpy		SCANPY	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Single Cell, Spatial Omics, Transcriptomics	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.10.2	scanpy	1.7.2	Differential gene expression analysis	Gene expression, Cell biology, Genetics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	766	51978
+scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Single Cell, Transcriptomics, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	77	1365
+sceasy	sceasy_convert	Converter between difference single-cell formats								Up-to-date	https://github.com/cellgeni/sceasy/	Single Cell, Spatial Omics, Convert Formats	sceasy_convert	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy	0.0.7	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	90	721
+schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization, Single Cell	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	16	0	23	779
+scikit-bio	scikit_bio_diversity_beta_diversity	scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics								Up-to-date	http://scikit-bio.org/	Sequence Analysis	scikit_bio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio	0.4.2	scikit-bio	0.4.2			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
+scoary	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	scoary	scoary		Scoary	Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	61	676
+scpipe	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	scpipe	scpipe		scPipe	A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, Single Cell	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	11	628
+seacr	seacr	SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes.								Up-to-date	https://github.com/FredHutch/SEACR	Epigenetics, ChIP-seq	seacr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr	1.3	seacr	1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	50	3647
+selenzy_wrapper	selenzy_wrapper	Performs enzyme selection from a reaction query.								Up-to-date	https://github.com/brsynth/selenzy-wrapper	Synthetic Biology	selenzy_wrapper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper	0.3.0	selenzy_wrapper	0.3.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+semibin	semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	semibin	semibin		SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	0	0	6	1	0	0	6	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	39	542
+seq2hla	seq2hla	Precision HLA typing and expression from RNAseq data	seq2hla	seq2hla		Seq2HLA	seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	Up-to-date	https://github.com/TRON-Bioinformatics/seq2HLA	Sequence Analysis	seq2hla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla	2.3	seq2hla	2.3	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	288
+seqcomplexity	seqcomplexity	Sequence complexity for raw reads								Up-to-date	https://github.com/stevenweaver/seqcomplexity	Sequence Analysis		iuc	https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity	0.1.2	seqcomplexity	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	16	68
+seqkit	seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit		seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	Up-to-date	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.8.2	seqkit	2.8.2	DNA transcription, Sequence trimming, DNA translation	Database management, Sequence analysis	0	2	5	3	0	2	5	3	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	129	1964
+seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+seqsero2	seqsero2	Salmonella serotype prediction from genome sequencing data	seqsero2	seqsero2		SeqSero2	"rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)"	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12
+seqtk	seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq	Toolkit for processing sequences in FASTA/Q formats	seqtk	seqtk		seqtk	A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.	Data handling, Sequence file editing	Data management	Up-to-date	https://github.com/lh3/seqtk	Sequence Analysis	seqtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk	1.4	seqtk	1.4	Data handling, Sequence file editing		15	15	15	15	15	15	15	15	0	0	0	0	0	0	0	0	0	0	14	0	14	0	0	14	0	0	0	15	0	0	0	0	0	14	14	14	14	753	59668
+seqwish	seqwish	Alignment to variation graph inducer								To update	https://github.com/ekg/seqwish	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish	0.7.5	seqwish	0.7.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	271
+seurat	seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension	Seurat - R toolkit for single cell genomics								To update	https://satijalab.org/seurat/	Single Cell, Transcriptomics, Sequence Analysis	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	5.0	r-seurat	3.0.2			1	1	7	1	1	1	7	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0
+shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	154	763
+shorah	shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	shorah	shorah		ShoRAH	Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	To update	https://github.com/cbg-ethz/shorah/blob/master/README.md	Sequence Analysis	shorah_amplicon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah	1.1.3	shorah	1.99.2	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1008	41600
+sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	269	14982
+simtext	abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix	A text mining framework for interactive analysis and visualization of similarities among biomedical entities.								To update	https://github.com/dlal-group/simtext	Text Manipulation	simtext	iuc	https://github.com/galaxyproject/tools-iuc/tools/simtext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext	0.0.2	r-argparse	1.0.1			0	2	4	0	0	2	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	34	142
+sina	sina	SINA reference based multiple sequence alignment	sina	sina		SINA	Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	Up-to-date	https://sina.readthedocs.io/en/latest/	Sequence Analysis	sina	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina	1.7.2	sina	1.7.2	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	42	1128
+sinto	sinto_barcode, sinto_fragments	Sinto single-cell analysis tools								Up-to-date	https://github.com/timoast/sinto	Single Cell, Epigenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto	0.10.1	sinto	0.10.1			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	17	91
+slamdunk	alleyoop, slamdunk	Slamdunk maps and quantifies SLAMseq reads								Up-to-date	http://t-neumann.github.io/slamdunk	RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers	slamdunk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk	0.4.3	slamdunk	0.4.3			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	2	361
+sleuth	sleuth	Sleuth is a program for differential analysis of RNA-Seq data.	sleuth	sleuth		sleuth	A statistical model and software application for RNA-seq differential expression analysis.	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	RNA-seq, Gene expression, Statistics and probability	Up-to-date	https://github.com/pachterlab/sleuth	Transcriptomics, RNA, Statistics	sleuth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth	0.30.1	r-sleuth	0.30.1	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	64
+smallgenomeutilities	smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe		V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.1	smallgenomeutilities	0.4.1	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	121
+smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	22	203
+snap	snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap		SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	Gene prediction	DNA polymorphism, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	133	1349
+snapatac2	snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing	SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis								To update	https://kzhang.org/SnapATAC2/	Single Cell, Epigenetics	snapatac2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2	2.6.4					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+sniffles	sniffles	Galaxy wrapper for sniffles	sniffles	sniffles		Sniffles	An algorithm for structural variation detection from third generation sequencing alignment.	Sequence analysis, Structural variation detection	DNA structural variation, Sequencing	Up-to-date	https://github.com/fritzsedlazeck/Sniffles	Sequence Analysis	sniffles	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles	2.4	sniffles	2.4	Sequence analysis, Structural variation detection	Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	58	919
+snipit	snipit	Summarise snps relative to a reference sequence	snipit	snipit		snipit	Summarise snps relative to a reference sequence	Base position variability plotting	Virology	Up-to-date	https://github.com/aineniamh/snipit	Variant Analysis, Sequence Analysis	snipit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	1.2	snipit	1.2	Base position variability plotting	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	22	669
+snippy	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy		snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	Phylogenetic tree visualisation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	0	1372	105708
+snp-dists	snp_dists	Compute pairwise SNP distance matrix from a FASTA sequence alignment								Up-to-date	https://github.com/tseemann/snp-dists	Variant Analysis	snp_dists	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists	0.8.2	snp-dists	0.8.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	367	4558
+snp-sites	snp_sites	Finds SNP sites from a multi-FASTA alignment file								Up-to-date	https://github.com/sanger-pathogens/snp-sites	Variant Analysis	snp_sites	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites	2.5.1	snp-sites	2.5.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	284	5107
+snpeff	snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names	SnpEff is a genetic variant annotation and effect prediction toolbox								To update	http://snpeff.sourceforge.net/	Genome-Wide Association Study, Variant Analysis	snpeff	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff		biopython	1.70			5	5	5	5	5	5	5	5	0	0	0	0	0	0	1	0	0	0	0	5	5	0	0	5	0	0	0	5	0	0	0	0	0	5	5	5	0	2676	95592
+snpeff-covid19	snpeff_sars_cov_2	SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox	snpeff	snpeff		snpEff	Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes).	SNP detection	DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs	To update	http://snpeff.sourceforge.net/	Genome-Wide Association Study, Variant Analysis	snpeff_sars_cov_2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19				SNP detection	DNA polymorphism, Nucleic acid sites, features and motifs	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	533	760352
+snpfreqplot	snpfreqplot	A plotting app to visualise the SNPs across a region								To update	https://github.com/BrownfieldPlantLab/SNPFreqPlot	Variant Analysis	snpfreqplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot	1.0	r-base				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	0	0	156	3530
+snpsift	snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck	snpEff SnpSift tools from Pablo Cingolani								To update	http://snpeff.sourceforge.net/SnpSift.html	Variant Analysis	snpsift	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift		snpsift	5.2			8	8	8	8	8	8	8	8	0	0	0	0	0	0	8	0	0	0	0	0	8	0	0	8	0	0	0	8	0	0	0	0	0	8	8	8	0	1352	5114712
+snpsift_dbnsfp	snpSift_dbnsfp	snpEff SnpSift dbnsfp tool from Pablo Cingolani								To update	http://snpeff.sourceforge.net/SnpSift.html#dbNSFP	Variant Analysis	snpsift_dbnsfp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp		snpsift	5.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	46
+snpsift_genesets	snpSift_geneSets	Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome								To update	http://snpeff.sourceforge.net/SnpSift.html#geneSets	Variant Analysis	snpsift_genesets	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets		snpsift	5.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	31	528
+socru	socru	Order and orientation of complete bacterial genomes								To update	https://github.com/quadram-institute-bioscience/socru	Sequence Analysis	socru	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru	https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru	2.1.7	socru	2.2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13	621
+sonneityping	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping		sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1
+spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	3	9	3	0	3547	72953
+spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	34	446
+spapros	spapros_evaluation, spapros_selection	Select and evaluate probe sets for targeted spatial transcriptomics.								Up-to-date	https://github.com/theislab/spapros	Single Cell, Transcriptomics, Sequence Analysis	spapros	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros	0.1.5	spapros	0.1.5			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+spotyping	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping		SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	1278
+spyboat	spyboat	Wavelet analysis for 3d-image stacks								To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	0.1.2	spyboat				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	67
+sra-tools	fasterq_dump, fastq_dump, sam_dump	NCBI Sequence Read Archive toolkit utilities	sra-tools	sra-tools		SRA Software Toolkit	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	Data handling	DNA, Genomics, Sequencing	Up-to-date	https://github.com/ncbi/sra-tools	Data Source, Fastq Manipulation	sra_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools	3.1.1	sra-tools	3.1.1	Data handling	DNA, Genomics, Sequencing	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	2	0	3	0	0	3	0	0	0	3	0	0	0	0	0	3	3	3	0	6247	350032
+srst2	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2		srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.21	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	205
+stacks	stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq	stacks	stacks		Stacks	Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.	Data handling	Mapping, Population genetics	To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis	stacks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks		stacks	2.65	Data handling	Mapping, Population genetics	0	13	13	12	0	13	13	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	13	13	0	152	11635
+stacks2	stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq								To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2	2.55	stacks	2.65			0	12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	0	238	7292
+star_fusion	star_fusion	STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR								To update	https://github.com/STAR-Fusion/STAR-Fusion	Sequence Analysis, Transcriptomics	star_fusion	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion	https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion	0.5.4-3+galaxy1	star-fusion	1.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	35	1212
+straindesign	straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion	Toolbox to optimize biological model								To update	https://github.com/brsynth/straindesign	Systems Biology, Synthetic Biology	straindesign	iuc	https://github.com/brsynth/straindesign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign	3.2.2	straindesign	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+strelka	strelka_germline, strelka_somatic	Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision.								Up-to-date	https://github.com/Illumina/strelka/	Variant Analysis	strelka	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka	2.9.10	strelka	2.9.10			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	53	549
+stringtie	stringtie, stringtie_merge	StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.	stringtie	stringtie		StringTie	Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.	Transcriptome assembly, RNA-Seq analysis	Transcriptomics, RNA-seq	Up-to-date	http://ccb.jhu.edu/software/stringtie/	Transcriptomics	stringtie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie	2.2.3	stringtie	2.2.3	Transcriptome assembly, RNA-Seq analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	2165	167659
+structure	structure	for using multi-locus genotype data to investigate population structure.	structure	structure		Structure	The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Genetic variation analysis	Population genetics	Up-to-date	https://web.stanford.edu/group/pritchardlab/structure.html	Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	Genetic variation analysis	Population genetics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	59	2623
+structureharvester	structureharvester	for parsing STRUCTURE outputs and for performing the Evanno method								Up-to-date	http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/	Phylogenetics, Variant Analysis	structureharvester	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester	0.6.94	structureharvester	0.6.94			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+swift	swiftlink	Parallel MCMC Linkage Analysis								Up-to-date	https://github.com/ajm/swiftlink	Variant Analysis	swiftlink	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift	1.0	swiftlink	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+syndiva	syndiva	SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.								To update		Proteomics	syndiva	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA	https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva	1.0	clustalo	1.2.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	30
+table_compute	table_compute	Perform general-purpose table operations								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute	Text Manipulation	table_compute	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute	https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute	1.2.4	pandas				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	741	208652
+tabular_to_fastq	tabular_to_fastq	Tabular to FASTQ converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	tabular_to_fastq	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	200	7388
+tag_pileup_frequency	tag_pileup_frequency	Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup	Statistics, SAM, Genomic Interval Operations	tag_pileup_frequency	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency	1.0.2	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	164
+tasmanian_mismatch	tasmanian_mismatch	Analysis of positional mismatches								Up-to-date	https://github.com/nebiolabs/tasmanian-mismatch	Sequence Analysis	tasmanian_mismatch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch	1.0.7	tasmanian-mismatch	1.0.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+taxonkit	name2taxid, profile2cami	TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit	taxonkit	taxonkit		TaxonKit	TaxonKit is a practical and efficient NCBI taxonomy toolkit.	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	Up-to-date	https://bioinf.shenwei.me/taxonkit/	Metagenomics	taxonkit	iuc	https://github.com/shenwei356/taxonkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit	0.17.0	taxonkit	0.17.0	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	1801	27426
+taxpasta	taxpasta	standardise taxonomic profiles	taxpasta	taxpasta		taxpasta	TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table.	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	Up-to-date	https://taxpasta.readthedocs.io/en/latest/	Sequence Analysis	taxpasta	iuc	https://github.com/taxprofiler/taxpasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta	0.7.0	taxpasta	0.7.0	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+tb-profiler	tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	6.2.1	tb-profiler	6.3.0	Antimicrobial resistance prediction		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	198	5161
+tb_variant_filter	tb_variant_filter	M. tuberculosis H37Rv VCF filter								Up-to-date	https://github.com/COMBAT-TB/tb_variant_filter	Variant Analysis	tb_variant_filter	iuc	https://github.com/COMBAT-TB/tb_variant_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter	0.4.0	tb_variant_filter	0.4.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	209	19252
+tbl2gff3	tbl2gff3	Table to GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	Convert Formats, Sequence Analysis	tbl2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3	1.2	bcbiogff	0.6.6			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	229	1584
+tbvcfreport	tbvcfreport	Generate HTML report from SnpEff M.tuberculosis VCF(s)								Up-to-date	https://github.com/COMBAT-TB/tbvcfreport	Variant Analysis	tbvcfreport	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport	1.0.1	tbvcfreport	1.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	167	2290
+te_finder	te_finder	Transposable element insertions finder	tefinder	tefinder		TEfinder	A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	To update	https://github.com/VistaSohrab/TEfinder	Sequence Analysis	te_finder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder	1.0.1	samtools	1.21	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	81
+telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+tetoolkit	tetoolkit_tetranscripts	The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.								Up-to-date	http://hammelllab.labsites.cshl.edu/software/	Sequence Analysis	tetoolkit	iuc	https://github.com/mhammell-laboratory/TEtranscripts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit	2.2.3	tetranscripts	2.2.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33	871
+tetyper	tetyper	Type a specific transposable element (TE) of interest from paired-end sequencing data.								Up-to-date	https://github.com/aesheppard/TETyper	Sequence Analysis	tetyper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper	1.1	tetyper	1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8	69
+tn93	tn93_readreduce, tn93, tn93_cluster, tn93_filter	Compute distances between sequences								Up-to-date	https://github.com/veg/tn93/	Sequence Analysis	tn93	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93	1.0.14	tn93	1.0.14			4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	4	0	0	17	1881
+tooldistillator	tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator		ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.9.1	tooldistillator	0.9.1	Parsing	Microbiology, Bioinformatics, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+tracegroomer	tracegroomer	TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool.								Up-to-date	https://github.com/cbib/TraceGroomer	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer	0.1.4	tracegroomer	0.1.4			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+tracy	tracy_align, tracy_assemble, tracy_basecall, tracy_decompose									To update				iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy	0.6.1	tracy	0.7.8			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	58	2439
+transdecoder	transdecoder	TransDecoder finds coding regions within transcripts	TransDecoder	TransDecoder		TransDecoder	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	To update	https://transdecoder.github.io/	Transcriptomics, RNA	transdecoder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder	5.5.0	transdecoder	5.7.1	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	348	5468
+transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	0	84	907
+transtermhp	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	transtermhp	transtermhp		TransTermHP	TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	229
+trimmomatic	trimmomatic	A flexible read trimming tool for Illumina NGS data								Up-to-date	http://www.usadellab.org/cms/?page=trimmomatic	Fastq Manipulation	trimmomatic	pjbriggs	https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic	0.39	trimmomatic	0.39			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	1	1	1	0	5862	305866
+trinity	trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats	Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq	trinity	trinity		Trinity	Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.	Transcriptome assembly	Transcriptomics, Gene expression, Gene transcripts	To update	https://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity	2.15.1	trinity	2.15.2	Transcriptome assembly	Transcriptomics, Gene transcripts	9	13	13	13	9	13	13	13	0	0	0	0	0	0	0	0	0	0	1	2	1	0	0	0	0	0	0	11	0	0	1	0	0	11	13	12	0	1762	31951
+trinotate	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	trinotate	trinotate		Trinotate	Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.	Gene functional annotation	Gene expression, Transcriptomics	To update	https://trinotate.github.io/	Transcriptomics, RNA	trinotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate	3.2.2	trinotate	4.0.2	Gene functional annotation	Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	151	1796
+trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942
+tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	Up-to-date	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.5	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5
+tsne	tsne	T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation								To update	https://cran.r-project.org/web/packages/Rtsne/	Text Manipulation	tsne	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne	0.0.2	r-rtsne	0.13			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10	368
+twobittofa	ucsc-twobittofa	twoBitToFa is a tool to convert all or part of .2bit file to FASTA	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	https://genome.ucsc.edu/goldenpath/help/twoBit.html	Convert Formats	ucsc_twobittofa	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa	469	ucsc-twobittofa	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	48	502
+tximport	tximport	Wrapper for the Bioconductor package tximport	tximport	tximport		tximport	An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	Up-to-date	http://bioconductor.org/packages/tximport/	Transcriptomics	tximport	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport	1.30.0	bioconductor-tximport	1.30.0	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	88	1408
+ucsc_axtchain	ucsc_axtchain	Chain together genome alignments	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_axtchain	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain	469	ucsc-axtchain	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ucsc_axttomaf	ucsc_axtomaf	Convert dataset from axt to MAF format.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_axttomaf	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf	469	ucsc-axttomaf	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ucsc_blat	ucsc_blat	Standalone blat sequence search command line tool	blat	blat		BLAT	Fast, accurate spliced alignment of DNA sequences.	Sequence alignment	Sequence analysis	Up-to-date	http://genome.ucsc.edu/goldenPath/help/blatSpec.html	Sequence Analysis	ucsc_blat	yating-l	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat	469	ucsc-blat	469	Sequence alignment	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+ucsc_chainnet	ucsc_chainnet	Make alignment nets out of chains	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainnet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	469	ucsc-chainnet	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ucsc_chainprenet	ucsc_chainprenet	Remove chains that don't have a chance of being netted	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainprenet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet	469	ucsc-chainprenet	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ucsc_chainsort	ucsc_chainsort	Sort chains. By default sorts by score.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainsort	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort	469	ucsc-chainsort	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ucsc_netfilter	ucsc_netfilter	Filter out parts of net	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netfilter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter	469	ucsc-netfilter	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ucsc_netsyntenic	ucsc_netsyntenic	Add synteny info to a net dataset	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netsyntenic	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic	469	ucsc-netsyntenic	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ucsc_nettoaxt	ucsc_nettoaxt	Convert net (and chain) to axt format.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_nettoaxt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt	469	ucsc-nettoaxt	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	Up-to-date	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics, Single Cell		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.5	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	3	5	5	0	379	61618
+unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1558	65732
+usher	usher_matutils, usher	UShER toolkit wrappers	usher	usher		usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Cladistics, Genotype and phenotype, Phylogenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	1060
+valet	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20	637
+vapor	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor		VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	94	3164
+vardict	vardict_java	VarDict - calls SNVs and indels for tumour-normal pairs								To update	https://github.com/AstraZeneca-NGS/VarDictJava	Variant Analysis	vardict_java	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict	1.8.3	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	16	273
+variant_analyzer	mut2read, mut2sscs, read2mut	Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data								To update		Variant Analysis	variant_analyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer	2.0.0	matplotlib				3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	3	88
+varscan	varscan_copynumber, varscan_mpileup, varscan_somatic	VarScan is a variant caller for high-throughput sequencing data								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/varscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan	2.4.3	varscan	2.4.6			3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	492	9779
+varvamp	varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp		varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology, Probes and primers	To update	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.1	PCR primer design	Virology, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+vcf2maf	vcf2maf	vcf2maf: Convert VCF into MAF								To update	https://github.com/mskcc/vcf2maf	Convert Formats	vcf2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf	1.6.21	vcf2maf	1.6.22			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	751
+vcf2tsv	vcf2tsv	Converts VCF files into tab-delimited format								To update	https://github.com/ekg/vcflib	Variant Analysis, Convert Formats	vcf2tsv	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	352	167913
+vcfaddinfo	vcfaddinfo	Adds info fields from the second dataset which are not present in the first dataset.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfaddinfo	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8	357
+vcfallelicprimitives	vcfallelicprimitives	Splits alleleic primitives (gaps or mismatches) into multiple VCF lines								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfallelicprimitives	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	286	15803
+vcfanno	vcfanno	Annotate VCF files	vcfanno	vcfanno		vcfanno	Fast, flexible annotation of genetic variants.	SNP annotation	Genetic variation, Data submission, annotation and curation	Up-to-date	https://github.com/brentp/vcfanno	Variant Analysis	vcfanno	iuc	https://github.com/galaxyproject/tools-iuc/vcfanno/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno	0.3.5	vcfanno	0.3.5	SNP annotation	Genetic variation, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	87	872
+vcfannotate	vcfannotate	Intersect VCF records with BED annotations								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfannotate	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	77	2181
+vcfannotategenotypes	vcfannotategenotypes	Annotate genotypes in a VCF dataset using genotypes from another VCF dataset.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfannotategenotypes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	28	192
+vcfbedintersect	vcfbedintersect	Intersect VCF and BED datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfbedintersect	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	80	3217
+vcfbreakcreatemulti	vcfbreakcreatemulti	Break multiple alleles into multiple records, or combine overallpoing alleles into a single record								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfbreakcreatemulti	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13	471
+vcfcheck	vcfcheck	Verify that the reference allele matches the reference genome								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcheck	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39	675
+vcfcombine	vcfcombine	Combine multiple VCF datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcombine	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	99	1695
+vcfcommonsamples	vcfcommonsamples	Output records belonging to samples commong between two datasets.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcommonsamples	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	14	244
+vcfdistance	vcfdistance	Calculate distance to the nearest variant.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfdistance	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	40	564
+vcffilter	vcffilter2	Tool for filtering VCF files								To update	https://github.com/ekg/vcflib	Variant Analysis	vcffilter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	882	44437
+vcffixup	vcffixup	Count the allele frequencies across alleles present in each record in the VCF file.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcffixup	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	71	917
+vcfflatten	vcfflatten2	Removes multi-allelic sites by picking the most common alternate								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfflatten	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6	177
+vcfgeno2haplo	vcfgeno2haplo	Convert genotype-based phased alleles into haplotype alleles								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfgeno2haplo	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	36	718
+vcfgenotypes	vcfgenotypes	Convert numerical representation of genotypes to allelic.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfgenotypes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	48	451
+vcfhethom	vcfhethom	Count the number of heterozygotes and alleles, compute het/hom ratio.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfhethom	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	90	1370
+vcfleftalign	vcfleftalign	Left-align indels and complex variants in VCF dataset								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfleftalign	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10	279
+vcfprimers	vcfprimers	Extract flanking sequences for each VCF record								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfprimers	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	708
+vcfrandomsample	vcfrandomsample	Randomly sample sites from VCF dataset								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfrandomsample	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	159
+vcfselectsamples	vcfselectsamples	Select samples from a VCF file								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfselectsamples	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	29	854
+vcfsort	vcfsort	Sort VCF dataset by coordinate								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfsort	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	63	1852
+vcfvcfintersect	vcfvcfintersect	Intersect two VCF datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfvcfintersect	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	265	972774
+vegan	vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	74	2020
+velocyto	velocyto_cli	Velocyto is a library for the analysis of RNA velocity.								Up-to-date	http://velocyto.org/	Transcriptomics, Single Cell	velocyto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto	0.17.17	velocyto.py	0.17.17			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	2
+velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	2083	25420
+velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	4741
+verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	22
+vg	vg_convert, vg_deconstruct, vg_view	Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods								To update	https://github.com/vgteam/vg	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg	1.23.0	vg	1.59.0			0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	3	477
+virAnnot	virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers	virannot	virannot		virAnnot	"VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy."	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.1.0+galaxy0	biopython	1.70	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+virheat	virheat	generates a heatmap of allele frequencies from vcf files	virheat	virheat		virHEAT	VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists.  The tool provides a condensed look at variant frequencies after mapping  raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time.			Up-to-date	https://github.com/jonas-fuchs/virHEAT	Visualization, Variant Analysis	virheat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat	0.7.1	virheat	0.7.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+virhunter	virhunter	Deep Learning method for novel virus detection in sequencing data	virhunter	virhunter		VirHunter	VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).	Sequence classification	Virology	To update	https://github.com/cbib/virhunter	Machine Learning	virhunter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter	1.0.0	numpy		Sequence classification	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	234
+volcanoplot	volcanoplot	Tool to create a Volcano Plot								To update	https://ggplot2.tidyverse.org/	Visualization, Transcriptomics, Statistics	volcanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot	0.0.6	r-ggplot2	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1749	30946
+vsearch	vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	vsearch	vsearch		VSEARCH	High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.29.0	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	8	8	8	8	8	8	8	8	0	0	0	0	0	0	0	0	0	0	0	8	8	0	0	0	0	0	0	8	0	0	0	0	0	8	8	8	0	182	8507
+vsnp	vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics	The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.								To update	https://github.com/USDA-VS/vSNP	Sequence Analysis	vsnp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp	3.0.6	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+weather_app	simple_weather	provides simple weather in text format								To update	http://wttr.in/	Visualization, Web Services	simpleweather	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app	0.1.2	curl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+weblogo3	rgweblogo3	Sequence Logo generator for fasta	weblogo	weblogo		WebLogo	Web-based application designed to make generate sequence logos.	Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition	Nucleic acid sites, features and motifs, Sequence analysis	To update		Graphics	weblogo3	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3	3.5.0	weblogo	3.7.9	Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition	Nucleic acid sites, features and motifs, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	74	2379
+wigtobigwig	ucsc_wigtobigwig	converts bedGraph (wig) files into binary bigwig	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	https://genome.ucsc.edu/goldenPath/help/bigWig.html	Convert Formats	ucsc_wigtobigwig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig	469	ucsc-wigtobigwig	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+windowmasker	windowmasker_mkcounts, windowmasker_ustat	Identify repetitive regions using WindowMasker								To update	https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/	Sequence Analysis	windowmasker	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker	1.0	blast	2.16.0			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	85
+winnowmap	winnowmap	A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences.								Up-to-date	https://github.com/marbl/Winnowmap	Next Gen Mappers	winnowmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap	2.03	winnowmap	2.03			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	27	248
+xpath	xpath	XPath XML querying tool								To update	http://search.cpan.org/dist/XML-XPath/	Text Manipulation	xpath	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath	https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath		perl-xml-xpath	1.47			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3	234
+yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	64	344
+zerone	zerone	ChIP-seq discretization and quality control								Up-to-date	https://github.com/nanakiksc/zerone	ChIP-seq	zerone	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone	https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone	1.0	zerone	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	90
+EMLassemblyline	annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.0+galaxy0	r-base				0	0	11	9	0	0	11	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	102
+Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	82
+Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	73	1004
+ThermoRawFileParser	thermo_raw_file_converter	Thermo RAW file converter								To update	https://github.com/compomics/ThermoRawFileParser	Proteomics	thermo_raw_file_converter	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	1.3.4	thermorawfileparser	1.4.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	2689
+ab1_fastq	ab1_fastq_converter	Tool to convert ab1 files into FASTQ files								To update		Convert Formats	ab1fastq	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq	1.20.0	bioconductor-sangerseqr	1.38.0			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	175	40271
+ambertools	ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap	Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories.								To update	http://ambermd.org/AmberTools.php	Molecular Dynamics, Computational chemistry	ambertools	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools	21.10	ambertools				7	2	7	0	7	2	7	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	7	5	0	243	40666
+appendfdr	append_fdr									To update			appendfdr	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr	0.2.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+artbio_bam_cleaning	artbio_bam_cleaning	filter bam files before somatic-varscan or lumpy-smoove analysis								To update	http://artbio.fr	SAM, Variant Analysis	artbio_bam_cleaning	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning	https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning	1.10+galaxy0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+astropytools	astropy_fits2bitmap, astropy_fits2csv, astropy_fitsinfo	AstropyTools library contains Galaxy tools for elementary Astrophysical operations								To update	https://github.com/astropy/astropy	Astronomy	astropytools	volodymyrss	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools	0.1.0+galaxy0	astropy				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3	11
+bamparse	bamparse	Generates hit count lists from bam alignments.								To update	http://artbio.fr	RNA, Transcriptomics	bamparse	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	4.1.1	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+bed_to_protein_map	bed_to_protein_map	Converts a BED file to a tabular list of exon locations								To update		Proteomics	bed_to_protein_map	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	49	385
+bigwig_to_bedgraph	bigwig_to_bedgraph	Converts a bigWig file to bedGraph format								To update	http://artbio.fr	Convert Formats	bigwig_to_bedgraph	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph	377+galaxy1	ucsc-bigwigtobedgraph	469			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	200	5749
+bigwig_to_wig	bigwig_to_wig	Converts a bigWig file to Wiggle (WIG) format								To update	https://artbio.fr	Convert Formats	bigwig_to_wig	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig	3+galaxy0	ucsc-bigwiginfo	469			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+bio3d	bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize	Bio3d is a program that can be used to analyse molecular dynamics trajectories.								To update	http://thegrantlab.org/bio3d/index.php	Computational chemistry	bio3d	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d	2.4_1	r-bio3d	2.3_3			5	4	5	0	5	4	5	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	5	5	0	510	8913
+biomoldyn	biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering	Tools for MD analysis								To update	https://github.com/moldyn/	Molecular Dynamics, Computational chemistry	biomoldyn	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn	1.5.2	scipy				4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	3	0	53	459
+biotransformer	biotransformer	BioTransformer is a tool for prediction of small molecule metabolism in mammals.	biotransformer	biotransformer		BioTransformer	BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction.	Metabolic pathway prediction, PTM site prediction, Natural product identification	Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR	Up-to-date	https://bitbucket.org/djoumbou/biotransformerjar/src/master/	Metabolomics	biotransformer	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer	https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer	3.0.20230403	biotransformer	3.0.20230403	Metabolic pathway prediction, PTM site prediction, Natural product identification	Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
+blast2go	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	101	1232
+blast_plus_remote_blastp	blast_plus_remote_blastp	NCBI BLAST+ with -remote option								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	blast_plus_remote_blastp	galaxyp	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp	2.6.0	blast	2.16.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	121	22499
+blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+blast_unmatched	blast_unmatched	Extract unmatched query sequences from blast								To update	http://artbio.fr	Fasta Manipulation	blast_unmatched	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	1.0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+blastxml_to_top_descr	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	159	264558
+bumbershoot	idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch									To update	http://proteowizard.sourceforge.net/	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot	3.0.21142	bumbershoot	3_0_21142_0e4f4a4			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	3	1348
+c3s	c3s	Copernicus Climate Change Service (C3S)								To update	https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset	Climate Analysis	c3s	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	0.3.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	198
+cads	cads	Copernicus Atmosphere Data Store (ADS)								To update	https://ads.atmosphere.copernicus.eu/#!/home	Climate Analysis	cads	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads	0.1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	52
+calisp	calisp	Calgary approach to isotopes in proteomics								Up-to-date	https://github.com/kinestetika/Calisp/	Proteomics	calisp	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp	3.0.13	calisp	3.0.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
+cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	101	7766
+cardinal	cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots	Statistical and computational tools for analyzing mass spectrometry imaging datasets								Up-to-date	http://cardinalmsi.org	Proteomics, Metabolomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	3.4.3	bioconductor-cardinal	3.4.3			0	9	11	11	0	9	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	0	0	0	0	0	0	0	9	11	9	0	277	48705
+cdo	cdo_info, cdo_operations	CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available.								To update	https://code.mpimet.mpg.de/projects/cdo/	Climate Analysis		climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo	2.0.0					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	16	217
+cell-types-analysis	ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals	Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis								To update		Transcriptomics, RNA, Statistics	suite_cell_types_analysis	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis	1.1.1	cell-types-analysis	0.1.11			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	6
+cesm	cesm	Community Earth System Model (CESM)								Up-to-date	https://www.cesm.ucar.edu/	Climate Analysis	cesm	climate	https://github.com/ESCOMP/CESM	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm	2.1.3	cesm	2.1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	13
+champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	19	174
+checkv	checkv_end_to_end	Assess quality of single-contig viral genomes	checkv	checkv		CheckV	CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	Up-to-date	https://bitbucket.org/berkeleylab/checkv/	Metagenomics	checkv	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv	1.0.3	checkv	1.0.3	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+cherry_pick_fasta	cherry_pick_fasta	Pick fasta sequence with specific header content								To update	http://artbio.fr	Fasta Manipulation	cherry_pick_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	4.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+climate-stripes	climate_stripes	Create climate stripes from a tabular input file								To update	https://www.climate-lab-book.ac.uk/2018/warming-stripes/	Climate Analysis, Visualization	climate_stripes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	1.0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	237
+concat_multi_datasets	cat_multi_datasets	Concatenate multiple datasets tail-to-head, including collection datasets.								To update	http://artbio.fr	Text Manipulation	concatenate_multiple_datasets	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets	https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets	1.4.3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	352	3612
+consensus_from_alignments	aligned_to_consensus	Tool to compute a consensus sequence from several aligned fasta sequences								To update		Sequence Analysis	consalign	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments	https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments	1.0.0	r-bioseq				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55	585
+consolidate_vcfs	consolidate_vcfs	Combines freebayes and mpileup files for use by vcf2snvalignment								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	consolidate_vcfs	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+cooler	cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify	cooler different tools to process Hi-C from mirnylab								To update	https://github.com/open2c/cooler	Epigenetics	cooler	lldelisle	https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler	0.9.3	htslib	1.21			4	0	5	0	4	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	11	81
+cpm_tpm_rpk	cpm_tpm_rpk	Generate CPM,TPM or RPK from raw counts								To update	http://artbio.fr	Transcriptomics	cpm_tpm_rpk	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	0.6.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+cta	cta_astro_tool	Basic simulation of CTA telescope observations using gammapy package								To update		Astronomy	cta_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta	0.0.1+galaxy0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+custom_pro_db	custom_pro_db	CustomProDB								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db	1.22.0	bioconductor-rgalaxy	1.37.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	57	1652
+custom_pro_db_annotation_data_manager		CustomProDB Annotation								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db_annotation_data_manager	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+data-hca	hca_matrix_downloader	Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects								To update		Transcriptomics, Sequence Analysis	suite_human_cell_atlas_tools	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca	v0.0.4+galaxy0	hca-matrix-downloader	0.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	439
+data-scxa	retrieve_scxa	Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home								To update		Transcriptomics, Sequence Analysis	suite_ebi_expression_atlas	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa	v0.0.2+galaxy2	wget				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	99	799
+data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	146	658
+data_manager_eggnog_mapper		downloads eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+data_manager_eggnog_mapper_abspath		download eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper_abspath	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dbbuilder	dbbuilder	Protein Database Downloader								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	Proteomics	dbbuilder	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	0.3.4	wget				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	161	4758
+decoupler	score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk	decoupler - Ensemble of methods to infer biological activities								To update	https://decoupler-py.readthedocs.io/en/latest/	Transcriptomics	suite_decoupler	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler	1.4.0+galaxy3	decoupler	1.5.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6
+decoyfasta		Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.								To update		Proteomics	decoyfasta	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+deseq2_normalization	deseq2_normalization	Normalizes gene hitlists								To update	http://artbio.fr	RNA, Transcriptomics, Sequence Analysis, Statistics	deseq2_normalization	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	1.40.2+galaxy0	bioconductor-deseq2	1.42.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+dia_umpire	dia_umpire_se	DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics								To update	http://diaumpire.sourceforge.net/	Proteomics	dia_umpire	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire	2.1.3	dia_umpire	2.1.6			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	33
+dialignr	dialignr	DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.								To update	https://github.com/shubham1637/DIAlignR	Proteomics	dialignr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	1.2.0	bioconductor-dialignr	2.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	40
+diann	diann	DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.								To update	https://github.com/vdemichev/DiaNN	Proteomics	diann	galaxyp	https://github.com/vdemichev/DiaNN	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann	1.8.1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	15
+diapysef	diapysef	diapysef is a convenience package for working with DIA-PASEF data								To update	https://pypi.org/project/diapysef/	Proteomics	diapysef	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef	0.3.5.0	diapysef	1.0.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	11	245
+diffacto	diffacto	Diffacto comparative protein abundance estimation								To update	https://github.com/statisticalbiotechnology/diffacto	Proteomics	diffacto	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	1.0.6	diffacto	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	7
+digestdb	digestdb									To update			digestdb	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb	0.1.0	trans_proteomic_pipeline				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+directag_and_tagrecon										To update			directag_and_tagrecon	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+droplet-barcode-plot	_dropletBarcodePlot	Make a cell barcode plot for droplet single-cell RNA-seq QC								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	droplet_barcode_plot	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot	1.6.1+galaxy2	scxa-plots	0.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	95	973
+dropletutils	dropletutils_empty_drops, dropletutils_read_10x	De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_dropletutils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils	1.0.4	dropletutils-scripts	0.0.5			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	201	1599
+eggnog_mapper	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2		eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	1	3	1	0	510	30565
+embl2fa	embl2fa	Converts EMBL flat format to fasta format								To update	http://artbio.fr	Text Manipulation	embl2fa	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa	https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa	0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+encyclopedia	encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut	Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis								To update	https://bitbucket.org/searleb/encyclopedia/wiki/Home	Proteomics	encyclopedia	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia	1.12.34	encyclopedia	2.12.30			2	4	7	0	2	4	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	48	706
+eodie	eodie	Earth Observation Data Information Extractor								To update	https://eodie.readthedocs.io/	Climate Analysis	eodie	climate	https://gitlab.com/eetun-tiimi/EODIE	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie	1.0.2	eodie				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	45
+essential_climate_variables	cds_essential_variability	Get Copernicus Essential Climate Variables for assessing climate variability								To update	https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview	Climate Analysis, Data Source	cds_essential_variability	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	331
+ez_histograms	ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+fasta_merge_files_and_filter_unique_sequences	fasta_merge_files_and_filter_unique_sequences	Concatenate FASTA database files together								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Fasta Manipulation	fasta_merge_files_and_filter_unique_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	1.2.0	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	461	29886
+fastg2protlib	fastg2protlib-peptides, fastg2protlib-validate	Generate FASTA from FASTG								To update	https://github.com/galaxyproteomics/fastg2protlib.git	Proteomics	fastg2protlib	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	1.0.2					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	28
+fastq_pair	fastq_pair	Paired-end fastq pairer								To update	https://github.com/linsalrob/fastq-pair	Fastq Manipulation	fastq_pair	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair	1.0+galaxy0	fastq-pair	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fastq_provider	fastq_provider	Retrieval and download of FASTQ files from ENA and other repositories such as HCA.								To update	https://github.com/ebi-gene-expression-group/atlas-fastq-provider	Data Source, RNA, Transcriptomics	atlas_fastq_provider	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider	0.4.4	atlas-fastq-provider	0.4.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fastq_quality_trimmer	cshl_fastq_quality_trimmer	FASTQ trimmer based on quality								To update	https://github.com/agordon/fastx_toolkit	Fastq Manipulation	fastq_quality_trimmer	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer	0.0.14+galaxy0	fastx_toolkit	0.0.14			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fastq_utils	fastq_filter_n, fastq_trim_poly_at	Set of tools for handling fastq files								To update	https://github.com/nunofonseca/fastq_utils	Transcriptomics, RNA	fastq_utils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils	0.25.1+galaxy0	fastq_utils	0.25.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fates-emerald	ctsm_fates	EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model								To update	https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api	Climate Analysis	ctsm_fates	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald	2.0	fates-emerald				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	261
+feature_alignment	feature_alignment	TRIC integrates information from all available runs via a graph-based alignment strategy								Up-to-date		Proteomics	feature_alignment	galaxyp	https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment	0.11.0	msproteomicstools	0.11.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	18
+fetch_fasta_from_ncbi	retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers								To update	http://artbio.fr	Fasta Manipulation, Data Source	fetch_fasta_from_ncbi	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	3.1.0	urllib3	1.12			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	426	26274
+filter_compounds	filter_orgmet_anorg	Tool for filtering organometallics/anorganic compounds from a list of compounds.								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	filter_compounds	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds	https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds	3.1.1	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+filter_density	filterdensity	Filter out position based on distance between SNVs								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_density	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+filter_stats	filterstat	SNVPhyl filter_stats								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_stats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+filter_vcf	filtervcf	SNVPhyl filter_vcf								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_vcf	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+find_repeats	findrepeat	Find repetitive regions on a reference genome using MUMMer								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	find_repeats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fisher_test	fishertest	Fisher's exact test on two-column hit lists.								To update	http://artbio.fr	RNA, Statistics	fishertest	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	2.32.0+galaxy0	bioconductor-qvalue	2.34.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+flashlfq	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	Label-free quantification	Proteomics experiment, Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	17	645
+fragpipe	fragpipe	Data analysis for mass spectrometry-based proteomics.								Up-to-date	https://fragpipe.nesvilab.org/	Proteomics	fragpipe	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	20.0	fragpipe	20.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+free_energy		Free energy tools of BRIDGE.								To update		Molecular Dynamics, Computational chemistry	freeenergy	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+frogs	FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis	frogs	frogs		FROGS	The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	To update	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	5.0.0	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	0	0	0	28	0	0	0	28	0	0	0	0	0	0	0	0	0	0	0	18	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fromHicupToJuicebox	fromHicupToJuicebox	Convert the output of hicup (as sam or bam) to the input of juicebox.								To update		Epigenetics	from_hicup_to_juicebox	lldelisle		https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox	0.0.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fromgtfTobed12	fromgtfTobed12	Convert GTF files to BED12 format								To update	https://pythonhosted.org/gffutils/contents.html	Convert Formats	fromgtftobed12	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12	0.11.1+galaxy1	gffutils	0.13			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+garnett	garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file	De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_garnett	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett	0.2.8	garnett-cli	0.0.5			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	27
+gatk4	filtermutectcalls, mergemutectstats, mutect2	Find somatic variations								To update	http://artbio.fr	Variant Analysis	gatk4	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	4.1.7.0	gatk4	4.5.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gc_derivatization	gc_derivatization	In silico derivatization for GC.								Up-to-date	https://github.com/RECETOX/gc-meox-tms	Metabolomics	gc_derivatization	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization	https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization	1.0.1	gc-meox-tms	1.0.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	8	0	0	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	10	1475
+genomad	genomad_end_to_end	Identify virus and plasmid genomes from nucleotide sequences	genomad	genomad		geNomad	geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.	Sequence annotation, Taxonomic classification	Sequence analysis	Up-to-date	https://github.com/apcamargo/genomad/	Metagenomics	genomad	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad	1.8.0	genomad	1.8.0	Sequence annotation, Taxonomic classification	Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+getTn5ExtendedCoverage	getTn5ExtendedCoverage	Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension								To update		Epigenetics	gettn5extendedcoverage	lldelisle		https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage	0.0.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+get_reference_fasta	get_fasta_reference	Obtain reference genome sequence.								To update	http://artbio.fr	Data Source, Fasta Manipulation	get_reference_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	0.3.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+gffcompare_to_bed	gffcompare_to_bed	Filter and convert a gffCompare GTF to BED								To update	https://github.com/gpertea/gffcompare/	Convert Formats	gffcompare_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed	0.2.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	131	2115
+gromacs	gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj	GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids.								To update	https://github.com/gromacs	Molecular Dynamics, Computational chemistry	gromacs	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs	2022	gromacs	2021.3			14	8	15	0	14	8	15	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	15	9	0	1442	177844
+gsc_center_scale	center_scale	Center or scale (standardize) data								To update	http://artbio.fr	Statistics	gsc_center_scale	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gsc_filter_cells	filter_cells	Filter single cell RNAseq data on libray depth and number of detected genes								To update	http://artbio.fr	Transcriptomics	gsc_filter_cells	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gsc_filter_genes	filter_genes	Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_filter_genes	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gsc_gene_expression_correlations	single_cell_gene_expression_correlations	Compute single-cell paire-wise gene expressions correlations								To update	http://artbio.fr	Transcriptomics	gsc_gene_expression_correlations	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gsc_high_dimensions_visualisation	high_dimensions_visualisation	Generates PCA, t-SNE and HCPC visualisation								To update	http://artbio.fr	Transcriptomics, Visualization	gsc_high_dimensions_visualisation	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation	4.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gsc_mannwhitney_de	mannwhitney_de	Perform a mann-whitney differential testing between two sets of gene expression data								To update	http://artbio.fr	Transcriptomics	gsc_mannwhitney_de	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	4.1.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gsc_scran_normalize	scran_normalize	Normalize raw counts using scran								To update	http://artbio.fr	Transcriptomics	gsc_scran_normalize	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	1.28.1+galaxy0	bioconductor-scran	1.30.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	78
+gsc_signature_score	signature_score	Compute signature scores from single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_signature_score	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	2.3.9+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gtf-2-gene-list	_ensembl_gtf2gene_list	Utility to extract annotations from Ensembl GTF files.								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	gtf2gene_list	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list	1.52.0+galaxy0	atlas-gene-annotation-manipulation	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	155	1678
+guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+hardklor	hardklor, kronik	Hardklör								To update		Proteomics	hardklor	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor	2.30.1+galaxy1	hardklor	2.3.2			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2	111
+hess	hess_astro_tool	Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope								To update		Astronomy	hess_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess	0.0.2+galaxy0	ipython				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+high_dim_heatmap	high_dim_heatmap	gplot heatmap.2 function adapted for plotting large heatmaps								To update	https://github.com/cran/gplots	Visualization	high_dim_heatmap	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap	https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap	3.1.3+galaxy0	r-gplots	2.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.2.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+hyperstack_to_bleach_corrected_movie	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack								To update		Imaging	hyperstack_to_bleach_corrected_movie	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	20230328	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+idconvert	idconvert	Convert mass spectrometry identification files on linux or MacOSX								To update		Proteomics	idconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert		proteowizard	3_0_9992			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	275
+incucyte_stack_and_upload_omero	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server								To update		Imaging	incucyte_stack_and_upload_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	20231221	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+isolib	isolib	Create an isotopic pattern library for given compounds and adducts.								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	isolib	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/isolib	https://github.com/RECETOX/galaxytools/tree/master/tools/isolib	1.0.1+galaxy0	bioconductor-metabocoreutils	1.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+justdiff	justdiff	Unix diff								To update	http://artbio.fr	Text Manipulation	justdiff	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff	https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff	3.10+galaxy0	diffutils				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+justgzip	justgzip	Compress fastq sequence files								To update	http://artbio.fr	Convert Formats	justgzip	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip	https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip	2.8+galaxy0	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+lfq_protein_quant	lfq_protein_quant	Enable protein summarisation and quantitation								To update	https://github.com/compomics/LFQ_galaxy_p	Proteomics	lfq_protein_quant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	1.0	bioconductor-msnbase	2.28.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	111
+longorf	longORF	obtain longest ORF in six-frame translations								To update		Sequence Analysis	longorf	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf	0.3.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ltq_iquant_cli										To update			ltq_iquant_cli	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+lumpy_smoove	lumpy_smoove, vcf2hrdetect	Galaxy wrapper of the lumpy-using smoove workflow								To update	http://artbio.fr	Variant Analysis	lumpy_smoove	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove	0.2.8+galaxy1	svtyper	0.7.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0
+lumpy_sv	lumpy	Find structural variations								To update	http://artbio.fr	Variant Analysis	lumpy_sv	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv	1.3	lumpy-sv	0.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+maldiquant	maldi_quant_peak_detection, maldi_quant_preprocessing	MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.								To update	http://strimmerlab.org/software/maldiquant/	Proteomics	MALDIquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant	1.22.0	r-base				0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	2	2	0	25	3797
+manta	manta	Structural variant and indel caller for mapped sequencing data								To update	http://artbio.fr	Variant Analysis	manta	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/manta	https://github.com/ARTbio/tools-artbio/tree/main/tools/manta	1.6	manta	1.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	8	93
+map_peptides_to_bed	map_peptides_to_bed	Map peptides to a reference genome for display by a genome browser								To update		Proteomics	map_peptides_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	0.2	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	41
+mapping_quality_stats	mapqstatistics	Collects and shows the distribution of MAPQ values in a BAM alignment file								To update	http://artbio.fr	Sequence Analysis, Statistics	mapping_quality_stats	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	0.22.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+matchms	matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting	Searching, filtering and converting mass spectral libraries.	matchms	matchms		Matchms	Tool to import, process, clean, and compare mass spectrometry data.	Spectral library search, Format validation, Filtering	Metabolomics	Up-to-date	https://github.com/matchms/matchms	Metabolomics	matchms	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/matchms	https://github.com/RECETOX/galaxytools/tree/master/tools/matchms	0.27.0	matchms	0.27.0	Spectral library search, Format validation, Filtering	Metabolomics	2	14	14	11	2	14	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	10	187
+maxquant	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering	Proteomics experiment, Proteomics, Statistics and probability	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	415	6078
+mdanalysis	mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf	MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations								To update	https://github.com/MDAnalysis/mdanalysis	Computational chemistry	mdanalysis	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis	1.0.0	mdanalysis				10	5	10	0	10	5	10	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	139	3115
+mdfileconverter	md_converter	A tool for interconverting between different MD structure and trajectory file formats.								To update		Molecular Dynamics, Computational chemistry	md_converter	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter	1.9.7	mdtraj				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	98	26427
+mdslicer	md_slicer	A tool for slicing trajectory files using MDTraj.								To update		Molecular Dynamics, Computational chemistry	md_converter	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer	1.9.9	mdtraj				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	158
+mdtraj	traj_selections_and_merge	MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories								To update	https://github.com/mdtraj/mdtraj	Computational chemistry	mdtraj	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj	1.9.7	mdtraj				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	36
+mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	24
+measure_gastruloids	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index								To update		Imaging	measure_gastruloids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	20221216	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+meta_proteome_analyzer	meta_proteome_analyzer	MetaProteomeAnalyzer								Up-to-date	https://github.com/compomics/meta-proteome-analyzer/	Proteomics	meta_proteome_analyzer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	2.0.0	mpa-portable	2.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	123
+metagene_annotator	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	115	636
+metanovo	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	4181
+metaquantome	metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome		metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	104	2522
+mfassignr	mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot	The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements	mfassignr	mfassignr		MFAssignR	Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements.	Visualisation	Proteomics experiment, Molecular interactions, pathways and networks, Workflows	Up-to-date	https://github.com/RECETOX/MFAssignR	Metabolomics	MFAssignR	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr	https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr	1.1.1	r-mfassignr	1.1.1	Visualisation	Proteomics experiment, Molecular interactions, pathways and networks, Workflows	0	0	9	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mgf_formatter	mgf_formatter									Up-to-date			mgf_formatter	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter	1.0.0	mgf-formatter	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mircounts	mircounts	Generates miRNA count lists from read alignments to mirBase.								To update	http://artbio.fr	RNA, Transcriptomics	mircounts	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts	https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts	1.6	tar				0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+misc	target_screen, use_theoretical_mz_annotations									To update	https://github.com/RECETOX/galaxytools	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/misc	https://github.com/RECETOX/galaxytools/tree/master/tools/misc	1.0.0	pandas				0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+moFF	proteomics_moff	moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.								Up-to-date	https://github.com/compomics/moFF	Proteomics	proteomics_moff	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	2.0.3	moff	2.0.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	759
+monocle3	monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers	De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_monocle3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3	0.1.4	monocle3-cli	0.0.9			9	0	9	0	9	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	264	3266
+morpheus	morpheus	Morpheus MS Search Application	morpheus	morpheus		Morpheus	A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.	Peptide database search	Proteomics	To update	https://cwenger.github.io/Morpheus	Proteomics	morpheus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	288	morpheus	290	Peptide database search	Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	140
+mqppep	mqppep_anova, mqppep_preproc	MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Proteomics	mqppep	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	0.1.19	bioconductor-preprocesscore	1.64.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	2
+ms2deepscore	ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training	Mass spectra similarity scoring using a trained ms2deepscore model.	ms2deepscore	ms2deepscore		MS2DeepScore	MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra.	Spectrum calculation, Spectral library search, Network analysis	Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening	Up-to-date	https://github.com/matchms/ms2deepscore	Metabolomics	ms2deepscore	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore	https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore	2.0.0	ms2deepscore	2.0.0	Spectrum calculation, Spectral library search, Network analysis	Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+msconvert	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert		msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			Filtering, Formatting	Proteomics, Proteomics experiment	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	189	19958
+msgfplus	msgfplus	MSGF+								To update		Proteomics	msgfplus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	0.5	msgf_plus	2024.03.26			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	507
+msmetaenhancer	msmetaenhancer		msmetaenhancer	msmetaenhancer		MSMetaEnhancer	Tool for mass spectra metadata annotation.	Annotation, Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	Up-to-date	https://github.com/RECETOX/MSMetaEnhancer	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer	https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer	0.4.0	msmetaenhancer	0.4.0	Annotation, Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	103
+msms_extractor	msms_extractor	Extract MS/MS scans from the mzML file(s) based on PSM report.								To update		Proteomics	msms_extractor	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor	1.0.0	proteowizard	3_0_9992			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	110
+msp_merge	msp_merge									To update	https://github.com/RECETOX/galaxytools	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge	https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge	0.1.0	matchms	0.27.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+msstats	msstats	MSstats tool for analyzing mass spectrometry proteomic datasets	msstatstmt	msstatstmt		MSstatsTMT	Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	To update	https://github.com/MeenaChoi/MSstats	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	4.0.0	bioconductor-msstats	4.10.0	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	144	2036
+msstatstmt	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	726
+mt2mq	mt2mq	Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome								To update		Proteomics	mt2mq	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq	1.1.0	r-tidyverse				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	19	270
+mutational_patterns	mutational_patterns	Mutational patterns and signatures in base substitution catalogs								Up-to-date	http://artbio.fr	Variant Analysis	mutational_patterns	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	3.12.0	bioconductor-mutationalpatterns	3.12.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mz_to_sqlite	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	Conversion, Peptide database search	Proteomics, Biological databases	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33	844
+mzml_validator	mzml_validator	mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.								To update	https://github.com/RECETOX/galaxytools	Metabolomics, Proteomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	0.1.0+galaxy2	lxml				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ncbi_blast_plus	blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper	NCBI BLAST+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	devteam	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	2.14.1	python				16	16	16	16	16	16	16	16	0	0	0	0	0	0	0	0	0	0	16	15	16	0	0	0	0	0	0	16	0	0	0	0	16	16	16	15	0	4066	365597
+oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	1	1	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	45
+ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6
+ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+omero	omero_import, omero_metadata_import, omero_roi_import	Import images, region of interest, metadata into an OMERO.server using omero-py	omero	omero		OMERO	Client-server Java software for visualisation, management and analysis of biological microscope images.	Image analysis	Imaging, Data visualisation	To update	https://github.com/ome/omero-py/	Imaging	omero_upload	ufz	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	5.18.0	omero-py	5.11.1	Image analysis	Imaging, Data visualisation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+omero_clean_rois_tables	omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down								To update		Imaging	omero_clean_rois_tables	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	20230623	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+omero_get_children_ids	omero_get_children_ids	Get omero id of children of an omero object id								To update		Imaging	omero_get_children_ids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	0.2.0	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+omero_get_full_images	omero_get_full_images	Get full images from omero								To update		Imaging	omero_get_full_images	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	20240521	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+omero_hyperstack_to_fluo_measurements_on_gastruloid	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels								To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	20230809	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+omero_hyperstack_to_gastruloid_measurements	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements								To update		Imaging	omero_hyperstack_to_gastruloid_measurements	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	20240214	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+openmm	pdbfixer	OpenMM is a toolkit for molecular simulation using high performance GPU code.								To update	https://github.com/openmm	Molecular Dynamics, Computational chemistry	openmm	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm	1.8.1	pdbfixer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	25	347
+openms	AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter	OpenMS Suite for LC/MS data management and analyses								To update	https://www.openms.de/	Proteomics	openms	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	3.1	openms	3.2.0			8	34	144	0	8	34	144	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	141	124	0	886	105432
+packmol	packmol	PACKMOL is a package for creating starting structures for Molecular Dynamics simulations								To update	http://m3g.iqm.unicamp.br/packmol/home.shtml	Molecular Dynamics, Computational chemistry	packmol	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol	18.169.1	packmol				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	288
+pathifier	pathifier	pathifier								Up-to-date	https://	Transcriptomics, Statistics	pathifier	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	1.40.0	bioconductor-pathifier	1.40.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	228
+pathwaymatcher	reactome_pathwaymatcher	Reactome Pathway Matcher								To update	https://github.com/LuisFranciscoHS/PathwayMatcher	Proteomics	reactome_pathwaymatcher	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher		pathwaymatcher	1.9.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	238
+pep_pointer	pep_pointer	PepPointer categorizes peptides by their genomic coordinates.								To update		Genomic Interval Operations, Proteomics	pep_pointer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	0.1.3+galaxy1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9	498
+pepquery	pepquery	A peptide-centric MS search engine for novel peptide identification and validation.								To update	https://pepquery.org	Proteomics	pepquery	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	1.6.2	pepquery	2.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	4862
+pepquery2	pepquery2, pepquery2_index, pepquery2_show_sets	PepQuery2 peptide-centric MS search for peptide identification and validation								Up-to-date	https://pepquery.org	Proteomics	pepquery2	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	2.0.2	pepquery	2.0.2			0	1	3	0	0	1	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	13	717
+peptide_genomic_coordinate	peptide_genomic_coordinate	Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files								To update		Proteomics	peptide_genomic_coordinate	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate	1.0.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9	468
+peptideshaker	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.11			4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	4	2	0	485	17477
+pepxml_to_xls		Convert PepXML to Tabular								To update		Proteomics	pepxml_to_xls	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+percolator	batched_set_list_creator, percolator, percolator_input_converters, pout2mzid	Percolator								To update		Proteomics	percolator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator	3.5	percolator	3.7.1			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	5	368
+pi_db_tools	calc_delta_pi, pi_db_split, pi_dbspec_align	HiRIEF tools								To update		Proteomics	hirieftools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools	1.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pindel	pindel	Pindel detects genome-wide structural variation.								Up-to-date	http://artbio.fr	Variant Analysis	pindel	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel	https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel	0.2.5b9	pindel	0.2.5b9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+pmd_fdr	pmd_fdr	Calculate Precursor Mass Discrepancy (PMD) for MS/MS								To update	https://github.com/slhubler/PMD-FDR-for-Galaxy-P	Proteomics	pmd_fdr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	1.4.0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+positions2snv_alignment	positions2snv_alignment	Generate alignment of SNVs from SNVPhyl variant table.								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Variant Analysis	positions2snv_alignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+positions2snv_invariant_alignment	positions2snv_invariant_alignment	Generate alignment of SNVs and non-variant positions from SNVPhyl variant table.								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Variant Analysis	positions2snv_invariant_alignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+probecoverage	probecoverage	computes and plots read coverage of genomic regions by sequencing datasets								To update	http://artbio.fr	Sequence Analysis, Genomic Interval Operations, Graphics, Statistics	probecoverage	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	0.22.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+proteinpilot	convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml									To update			proteinpilot	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+proteomiqon_joinquantpepionswithproteins	proteomiqon_joinquantpepionswithproteins	The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.								To update	https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html	Proteomics	proteomiqon_joinquantpepionswithproteins	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	0.0.1	proteomiqon-joinquantpepionswithproteins	0.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	366
+proteomiqon_labeledproteinquantification	proteomiqon_labeledproteinquantification	The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html	Proteomics	proteomiqon_labeledproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	0.0.1	proteomiqon-labeledproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	14
+proteomiqon_labelfreeproteinquantification	proteomiqon_labelfreeproteinquantification	The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html	Proteomics	proteomiqon_labelfreeproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	0.0.1	proteomiqon-labelfreeproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	6
+proteomiqon_mzmltomzlite	proteomiqon_mzmltomzlite	The tool MzMLToMzLite allows to convert mzML files to mzLite files.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html	Proteomics	proteomiqon_mzmltomzlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite	0.0.8	proteomiqon-mzmltomzlite	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	721
+proteomiqon_peptidedb	proteomiqon_peptidedb	The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html	Proteomics	proteomiqon_peptidedb	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	0.0.7	proteomiqon-peptidedb	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	96
+proteomiqon_peptidespectrummatching	proteomiqon_peptidespectrummatching	Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html	Proteomics	proteomiqon_peptidespectrummatching	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	0.0.7	proteomiqon-peptidespectrummatching	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	686
+proteomiqon_proteininference	proteomiqon_proteininference	MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html	Proteomics	proteomiqon_proteininference	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	0.0.7	proteomiqon-proteininference	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	89
+proteomiqon_psmbasedquantification	proteomiqon_psmbasedquantification	The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.								To update	https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html	Proteomics	proteomiqon_psmbasedquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	0.0.8	proteomiqon-psmbasedquantification	0.0.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	604
+proteomiqon_psmstatistics	proteomiqon_psmstatistics	The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html	Proteomics	proteomiqon_psmstatistics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	0.0.8	proteomiqon-psmstatistics	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	694
+proteore_venn_diagram	proteore_venn_diagram	ProteoRE JVenn Diagram								To update		Proteomics	proteore_venn_diagram	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram	2021.06.08	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15
+protxml_to_xls	protxml_to_xls									To update			protxml_to_xls	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls	0.1.0	trans_proteomic_pipeline				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+psm2sam	PSMtoSAM	PSM to SAM								To update	https://bioconductor.org/packages/release/bioc/html/proBAMr.html	Proteomics	psm_to_sam	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam	1.3.2.1	r-base				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+psm_eval	psm_eval									To update			psm_eval	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval	0.1.0	binaries_for_psm_eval				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+psm_validation	psmvalidator	Validate PSM from Ion Fragmentation								To update	https://github.com/galaxyproteomics/psm_fragments.git	Proteomics	psm_validation	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	1.0.3					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	20
+psy-maps	psy_maps	Visualization of regular geographical data on a map with psyplot								To update	https://github.com/Chilipp/psy-maps	Visualization, Climate Analysis	psy_maps	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	1.3.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	46	469
+pyprophet	pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample	Semi-supervised learning and scoring of OpenSWATH results.								To update	https://github.com/PyProphet/pyprophet	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	2.1.4	pyprophet	2.2.5			0	5	6	0	0	5	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	6	6	0	33	2509
+pyscenic	pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn	PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/								To update		Transcriptomics, RNA, Sequence Analysis	suite_pyscenic	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic	0.12.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pyteomics	mztab2tsv	Tools using the pyteomics library	pyteomics	pyteomics		Pyteomics	Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.	Protein identification	Proteomics, Proteomics experiment	To update	https://pyteomics.readthedocs.io/en/latest/	Proteomics, Metabolomics	pyteomics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	4.4.1	pyteomics	4.7.4	Protein identification	Proteomics, Proteomics experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	81
+pyvo_integration	astronomical_archives	Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy								To update		Data Source	astronomicalarchivestool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration	0.10.0	astropy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	36
+qcxms	qcxms_getres, qcxms_neutral_run, qcxms_production_run	QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD).								To update	https://github.com/grimme-lab/QCxMS	Computational chemistry, Molecular Dynamics	QCxMS	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms	https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms	5.2.1					0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+quantp	quantp	Correlation between protein and transcript abundance								To update		Proteomics	quantp	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp	1.1.2	r-data.table	1.11.6			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	230
+quantwiz_iq	quantwiz_iq	Isobaric Quantitation using QuantWiz-IQ								Up-to-date	https://sourceforge.net/projects/quantwiz/	Proteomics	quantwiz_iq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	2.0	quantwiz-iq	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	32
+query	query	Execute an SQL statement on a set of tables								To update		Text Manipulation	query	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/query	https://github.com/RECETOX/galaxytools/tree/master/tools/query	0.2	click				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+qupath_roi_splitter	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type								To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter	0.3.2	geojson				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	59
+ramclustr	ramclustr, ramclustr_define_experiment		ramclustr	ramclustr		RAMClustR	A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.	Imputation, Standardisation and normalisation, Clustering, Correlation	Metabolomics	To update	https://rdrr.io/cran/RAMClustR/	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr	https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr	1.3.0	r-ramclustr	1.3.1	Imputation, Standardisation and normalisation, Clustering, Correlation	Metabolomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	2	16
+rawtools	rawtools	Raw Tools								To update	https://github.com/kevinkovalchik/RawTools	Proteomics	rawtools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools		rawtools	2.0.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	14	175
+rcx-tk	rcx-tk	Tools to process metadata or alkane files.								To update	https://github.com/RECETOX/rcx-tk	Metabolomics	rcx_tk	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/	https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk	0.1.0+galaxy0	rcx-tk	0.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+recetox_aplcms	recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise	Peak detection tool for HRMS profile data.	recetox-aplcms	recetox-aplcms		recetox-aplcms	recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening.	Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment	Metabolomics	Up-to-date	https://github.com/RECETOX/recetox-aplcms	Metabolomics	recetox-aplcms	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms	0.13.3	r-recetox-aplcms	0.13.3	Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment	Metabolomics	0	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	7	296
+recetox_msfinder	recetox_msfinder		recetox-msfinder	recetox-msfinder		recetox-msfinder	This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0.	Annotation	Metabolomics	To update	https://github.com/RECETOX/recetox-msfinder	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder	v3.5.2			Annotation	Metabolomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+recetox_xmsannotator	recetox_xmsannotator_advanced		recetox-xmsannotator	recetox-xmsannotator		recetox-xMSannotator	Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring.	Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation		Up-to-date	https://github.com/RECETOX/recetox-xMSannotator	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator	0.10.0	r-recetox-xmsannotator	0.10.0	Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation		0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
+regex_find_replace	regex1, regexColumn1	Use python regular expressions to find and replace text								To update		Text Manipulation	regex_find_replace	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace	1.0.3	python				2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	2	2	2	0	495	60307
+regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	7	7	0	22	526
+rem_complex	rem_complex	Removes molecular coordination complexes.								To update	https://github.com/RECETOX/galaxytools	Metabolomics	rem_complex	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex	https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex	1.0.0	pandas				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rename_annotated_feature	rename_annotated_feature	Update column names in an abundance table using a annotation table with spectral matching results								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	rename_annotated_feature	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature	https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature	1.0.0	pandas				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+repenrich	edger-repenrich, repenrich	Repeat element profiling								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	Transcriptomics	repenrich	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	2.31.1					0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0
+repenrich2	edger-repenrich2, repenrich2	Repeat element profiling using bowtie2 aligner								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	Transcriptomics	repenrich2	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	2.31.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+retip	retip_apply, retip_descriptors, retip_filter_rt, retip_train		retip	retip		Retip	Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765.	Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition	Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry	To update	https://github.com/PaoloBnn/Retip	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/retip	https://github.com/RECETOX/galaxytools/tree/master/tools/retip	0.5.4			Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition	Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+retrieve_ensembl_bed	retrieve_ensembl_bed	Retrieve cDNA features from Ensembl REST API in BED format								To update	http://rest.ensembl.org/	Data Source	retrieve_ensembl_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+revertR2orientationInBam	revertR2orientationInBam	Revert the mapped orientation of R2 mates in a bam.								To update		SAM	revertr2orientationinbam	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam	0.0.2	samtools	1.21			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	39
+riassigner	riassigner, riassigner_from_comment		riassigner	riassigner		RIAssigner	RIAssigner is a python tool for retention index (RI) computation for GC-MS data.	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	Up-to-date	https://github.com/RECETOX/RIAssigner	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	0.4.1	riassigner	0.4.1	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	1	2	2	1	1	2	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	15
+rmassbank	rmassbank	RMassBank is an R package for processing tandem MS files and building of MassBank records.								To update	https://github.com/MassBank/RMassBank	Metabolomics	rmassbank	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank	https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank	3.0.0	python				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
+rsem	extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie	transcript quantification from RNA-Seq data								To update	https://github.com/deweylab/RSEM	Transcriptomics, RNA	rsem	artbio	https://github.com/artbio/tools-artbio/tree/master/tools/rsem	https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem		rsem	1.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	1	1	0	67	377
+salmon-kallisto-mtx-to-10x	_salmon_kallisto_mtx_to_10x	Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	salmon_kallisto_mtx_to_10x	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x	0.0.1+galaxy6	scipy				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	86	561
+sambamba	sambamba_sample_or_filter	filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM								To update	http://artbio.fr	SAM	sambamba	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba	https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba	0.7.1+galaxy1	sambamba	1.0.1			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+sashimi_plot	sashimi_plot	Generates a sashimi plot from bam files.								To update	http://artbio.fr	RNA, Transcriptomics, Graphics, Visualization	sashimi_plot	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot	https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot	0.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+sc3	sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare	De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_sc3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3	1.8.0	sc3-scripts	0.0.6			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	9
+scaffold	scaffold, scaffold_export									To update			scaffold	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold	0.1.0	scaffold				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+scanpy	anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data	scanpy-scripts, command-line wrapper scripts around Scanpy.								To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis, RNA	scanpy_scripts	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy	1.9.3	scanpy-scripts	1.9.301			27	27	27	0	27	27	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	13	0	2185	39356
+scater	scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results	De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scater	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater	1.10.0	scater-scripts	0.0.5			1	2	6	0	1	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	16	387
+sccaf	run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out	SCCAF: Single Cell Clustering Assessment Framework.								To update	https://github.com/sccaf/sccaf	Transcriptomics	SCCAF	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf	0.0.9	sccaf	0.0.10			4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	110
+sceasy	sceasy_convert	Convert scRNA data object between popular formats								To update		Transcriptomics	sceasy	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy	0.0.5	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	90	721
+scmap	scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features	De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scmap	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap	1.6.4	scmap-cli	0.1.0			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	13	83
+scpred	scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model	De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scpred	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred	1.0.2	scpred-cli	0.1.0			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	25
+scripting	singularity_scriptrunner	suite_scripting								To update	https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/	Text Manipulation	scripting tools	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+sequence_format_converter	sequence_format_converter	various fasta to tabular conversions								To update	http://artbio.fr	Convert Formats, Fasta Manipulation	sequence_format_converter	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter	https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter	2.2.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+seurat	seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features	De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	Transcriptomics, RNA, Statistics, Sequence Analysis	suite_seurat	ebi-gxa		https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat	4.0.0	seurat-scripts	4.4.0			14	14	14	11	14	14	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	0	0	0	0	0	0	0	181	1966
+sgwb	sgwb_astro_tool	SGWB								To update		Astronomy	sgwb_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb	0.0.1+galaxy0	ipython				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+shift-longitudes	shyft_longitudes	Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/	Climate Analysis	shift_longitudes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes	0.1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	63
+sixgill	sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge	Six-frame Genome-Inferred Libraries for LC-MS/MS								Up-to-date		Proteomics, MetaProteomics	sixgill	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	0.2.4	sixgill	0.2.4			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	24	293
+small_rna_clusters	small_rna_clusters	clusters small rna reads in alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_clusters	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters	1.3.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+small_rna_maps	small_rna_maps	Generates small read maps from alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_maps	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps	3.1.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+small_rna_signatures	overlapping_reads, signature	Computes the tendency of small RNAs to overlap with each other.								To update	http://artbio.fr	RNA	small_rna_signatures	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures	3.4.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0
+smithsonian-volcanoes	smithsonian_volcanoes	Retrieve data from Volcanoes of the World (VOTW) Database								To update	https://volcano.si.edu/gvp_votw.cfm	Retrieve Data	smithsonian_volcanoes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes	0.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+snv_matrix	snvmatrix	Generate matrix of SNV distances								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	snv_matrix	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+snvtocnv	sequenzaindex, snvtocnv	infer copy number variations from a vcf file with SNVs using R sequenza								To update	http://artbio.fr	Variant Analysis	snvtocnv	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv	https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv	3.0.0+galaxy1	sequenza-utils	3.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+spec2vec	spec2vec_similarity, spec2vec_training	Mass spectra similarity scoring using a trained Spec2Vec model.	spec2vec	spec2vec		Spec2Vec	Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set.	Spectrum calculation, Spectral library search, Database search, Natural product identification	Proteomics experiment, Metabolomics, Natural language processing, Proteomics	Up-to-date	https://github.com/iomega/spec2vec	Metabolomics	spec2vec	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec	https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec	0.8.0	spec2vec	0.8.0	Spectrum calculation, Spectral library search, Database search, Natural product identification	Proteomics experiment, Metabolomics, Natural language processing, Proteomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+spectrast2spectrast_irt	gp_spectrast2spectrast_irt	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2spectrast_irt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+spectrast2tsv	gp_spectrast2tsv	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2tsv	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	56	769
+sr_bowtie	bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+sr_bowtie_dataset_annotation	sr_bowtie_dataset_annotation	Maps iteratively small RNA sequencing datasets to reference sequences.								To update	http://artbio.fr	RNA	sr_bowtie_dataset_annotation	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation	2.8	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	7	4	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	21	225
+stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	10	325
+suite_snvphyl		SNVPhyl suite defining all dependencies for SNVPhyl								To update		Sequence Analysis	suite_snvphyl_1_2_3	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+topologyeditors	gromacs_modify_topology, gromacs_extract_topology	Set of python scripts and associated tool files that can be used to modify topology files.								To update	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	Molecular Dynamics, Computational chemistry	topologyeditors	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	0	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	8	50
+translate_bed	translate_bed	Translate BED transcript CDS or cDNA in 3 frames								To update	http://rest.ensembl.org/	Proteomics	translate_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	0.1.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	49	643
+translate_bed_sequences	translate_bed_sequences	Perform 3 frame translation of BED file augmented with a sequence column								To update		Proteomics	translate_bed_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	57
+ucsc-cell-browser	ucsc_cell_browser	Python pipeline and Javascript scatter plot library for single-cell datasets								To update	https://cells.ucsc.edu/	Transcriptomics	ucsc_cell_browser	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser	1.0.0+galaxy1	ucsc-cell-browser	1.2.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	78	941
+unipept	unipept	Unipept retrieves metaproteomics information	unipept	unipept		Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	115	5005
+uniprotxml_downloader	uniprotxml_downloader	Download UniProt proteome in XML or fasta format								To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	79	1360
+upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server								To update		Imaging	upload_roi_and_measures_to_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	0.0.5	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	25	86
+varscan_vaf	varscan_vaf	Compute variant allele frequency in vcf files generated by varscan.								To update	http://artbio.fr	Variant Analysis	varscan_vaf	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf	https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf	0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+vcf2snvalignment	vcf2snvalignment	Generates multiple alignment of variant calls								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	vcf2snvalignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+verify_map	verify_map	Checks the mapping quality of all BAM(s)								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	verify_map	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+vibrant	vibrant	Virus Identification By iteRative ANnoTation	VIBRANT	VIBRANT		VIBRANT	Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	Up-to-date	https://github.com/AnantharamanLab/VIBRANT	Metagenomics	vibrant	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant	1.2.1	vibrant	1.2.1	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	351	12203
+virsorter	virsorter	VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.	virsorter	virsorter		virsorter	Identify DNA and RNA virus sequences.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/jiarong/VirSorter2/	Metagenomics	virsorter	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter	2.2.4	virsorter	2.2.4	Taxonomic classification	Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+vmd		vmd is a package for  visualizing and analyzing trajectories from molecular dynamics (MD) simulations								To update	https://www.ks.uiuc.edu/Research/vmd/	Computational chemistry	vmd	chemteam	https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+waveica	waveica	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis.	waveica	waveica		WaveICA	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform.	Standardisation and normalisation	Metabolomics	Up-to-date	https://github.com/RECETOX/WaveICA	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/waveica	https://github.com/RECETOX/galaxytools/tree/master/tools/waveica	0.2.0	r-recetox-waveica	0.2.0	Standardisation and normalisation	Metabolomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	6
+xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	5	5	2	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	175	5876
+xmlstarlet	xmlstarlet	Tool to convert a xml file from one metadata standard to another								To update		Convert Formats	xmlstarlet	ecology	https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet	https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet	1.6.1	xmlstarlet				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	14
+xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+xtb	xtb_molecular_optimization	Performs semiempirical molecular optimization.								To update	https://github.com/grimme-lab/xtb	Metabolomics	xtb_molecular_optimization	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/xtb	https://github.com/RECETOX/galaxytools/tree/master/tools/xtb	6.6.1	xtb				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
+zeiss_lmd_converter	ZeissLMDconverter	Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	2.0.4	shapely				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
diff --git a/communities/all/resources/tools_wordcloud.png b/communities/all/resources/tools_wordcloud.png
index 8ff1dc00f8d7a1314940bd337d823fcbbe8221eb..046e0b2c1b0e2e9076b195bae781902b9010e6ea 100644
GIT binary patch
literal 327859
zcmd?Q1y>wfv^7eA5G=S8+$FdKclU-MA%Wly!Cis|m&V-#1lQmpXrsY{2kkTtjq5AU
zIrsbSdw=1L(TrwPS65f<z1CcF&b4=>rn<sQbTV`V1caALin1UCgy#eZ2+z(?QGg?=
z2L;~1n~<BFzMHm_rJJXTiv@z3iQ6Z8CpUW=Q)&+j7grl6M_vvg4jy)DYd5z~uELz0
z4*%x_4ks5YP8xNj1>hoRpA-#T5fHFVp8lSdNqn_Ic!q$WBrB!kmA!xOU2AR-@cYt#
zLdbJO41RDl+jTC!B6f?3lKu>Z8Wj@_kyg$SuOBrL6I>vnx@7Xm^k^2bg?ft}aZp>9
zz;2Mt08UcH-Aed_h(m%GlF_rT!a2Rt<mTXH>@v}@Bs3Vf>{qk;&FAg8?Ow&9cwXFL
z_3-u%Br8LZH}Kjpv}tbRP2A@HdbuK>+Hn4Gel_@iU)k8$#F}pZ`^YQk(0j?r|9b}T
zSvH;PGr9luCE!rp=yL*!|JNZQp8ua;2%dX^`0qe^7}y=XQA0f$b$~0aj+-ob&o~HQ
z?p(C~GZ*6_&i@T&E@|EB&dT^>5P^7C<)`KcDC%2yVsp8}XvwO?PyJX<l~>>H@GP7T
zPuRWkmgBCxZ;wnSuL?)Y7xM}>IK_`W<gbM#R<0+8#!wx25u|6$h5aJKPNCMwU#Z~3
zIpn<(TQ`5=hty*F5q@D#Xu~yJ+HUr|Xnls+{+({`=I=p;|J>08rUQQSW{V~dee%mj
zH7f6{fgQIb6%xMBmE6WR`)2yE^_B+k-77O!>9<x8KiGP+%s7`J122*bKJVO;Y(*Fz
zjrL@8y!ULpULwq@R-YXuG6H8JAR<TSlGO5Bv8ANrKwn#I9qAky`;86f#6OV*&DcbY
z`X@I1F!e(T71wFJnn(1$t>Sgpp9Lx`h3a5m9qv3vF303v)W;1aWzw|9LPmosTD~wT
zYxrtix&wnH^x?L_+_F#ij!|OqCNRHvMET$6Y9;?K4xw~vkwGP=oQOmWD##TVjcINg
z(x{@iG*$7Eg`x2eIOf;SNccL>Sj%CFf3Zwj<Cya9gG_O)FK|HXBj}(ZE1qM~QIPJ9
z{|+1B?s~{`(RmakdGBF}555NF{k3^z2}L}qCCduEWf!Pu<2u<tPsa{a#NsQy`>YxE
zlyl<|c^J&XPtOQXEHxj3Eb8T5@K8$P4ki7RiNxt?AYB%YX%fmg<Jt6!{%y~T-zgoL
z@wKy(4hQv_aws#d>TqLTr@y$W_Uh^)wNCU*a6)@*(!z(<{=<6*i(h7DeCFlv6wsXi
zw9PGwpiJnqBYqYLuR8g1z8<u<f>krtW8W$bxg^~tz2~E;WG*HI@2#{Q=IpUN?1wM^
zf9}ryM)L&)@`S16t`e_+71M)ICc#7sri4c;w;MRr;}yO)C3(@a0iub<9Iu$V)NADw
zMQ<-<7iTMS7UbwzGP~Yqo%971@sOBO{P;-Gyk(Nrqh_0M+%c{~ios%e@ZW4$nW`A3
zknT5LLsr*{)jux25h+r6ykkU1_D-j(;{x3QJEE~%(n>wCj%ki$u7z`b`ZATSM6CSD
zIF*<;>~HPZXLmJx_5K~nFaJSPHd4$O%u0}PyP1Z%c8k6(TF$IW4uYd0E4#{<i<<be
z+f1ZC2usBl#k^F*7KJ3s%t1X7mr;wBI)R_oiOl<tnG$XcIn;2Ak&$1ll0WE2nuXt6
z29UPmOo5C9NGw0^1E-@CPm^9Gf^jN~FI=M$Q;%8_)wEMa0we0)^5w@93sQ|#7H{5o
z_m7cHMA3}AA&>`3)2e~rm^Ac=VN5Dl^~z<Lo-0lRJ6o2jrfp!BX~>o{I}c;YG1^-S
zW8D*r=RwOcq&s%j;DmIJUccudJ!yo^V9zh^&>vkkVG{+6+F&Y$(#)n*sje6Sw64m-
zReaNxo+Ps>DF~{DY;xx{<lak^>T?zUSwoiZZELY5R`LvSe6-Y3y1GlG<Sg1-u;g5#
zG{tXqONA{<*}`_~EK>(=OnKC>J~~Zz)0{-Z-Z`%?{ToVBmVCYJ4CAiJ$%-^XRWu`f
zA$+fmYNUBaL7<}6g(E!XFubILlP_ASlaXdIb>@q;`0==s{HP@6EUnzxHjP|!Nu&*W
zi|jbXi(I2qot1rBsk}p=8>Qh=GCXFvd;&qA5A3O$tu>VYWP#TD>g+!yLx`G}E}-o`
zZykac`-hKO$vu8AM1o$>EJm#yWzYr%DztV*Vf%na%kMsv%AT2Ab)_aSAYtxs=Wn{g
zI7yL=s!5x_LuFNPXD~h+n5Ef#QQd0D;ca$R6M2rs*6UQ{fQV{Yn3lompE=#M20&Ue
z>f!fob)QIym8*Cqx2#djXJtNv>2XFI+jGW6q`CfgB93dj3{kU_d4&$6u|3`LOUP!f
zrA2A!=*C;E1CKG9vnPF<kc|cs(6p7=9lpSzgeC6-Y2+c!o<MHQv20}dv7BYm{F}G8
z{D=k;Zrv7^icFnDz;!H{0wMxDkYsR^Uzgh`+lH46r=`E{9JfD1L%3OZxw?EEI6YF0
z3tgfweE|+$++G*Nwl|JUknp|hF2v1#Mrl0Jc`5uzcfXI)FuB*iTFWwzvPM1W;386r
zn_WPe{dD(CAnnlj^7v93Xw}7<MP<veMHrOqQ2<_|LG?YR84bXez{b;V^YS~4?8<<Y
z{!>nzvfZu&>oy2O^M+un&>drleb{nb9T>7zU|+9ujaTGG*@G6)*o^oi@Tz>GfuGW)
zbAH>;HM1NP*>4*gyB^fE9`p|9mxgvgS7&4<veV=B_NAADW8zxdG2-Lql2fg~zH8xR
zabAgiOn9I7c-^}kV=@0YiB{(nyA^@F_xk1zTz?D&YfiSoUoY#a+m%MS)ZQ34<%e$F
zJ7x{R%TS)BEiPp{sGUH<<Q^v0t{Ly?*B_6!jTugt=dqu-#x?V&qrd-DjpZIw(rxk>
zxSF3qFPK4Hhshtcsx-&QG}-A>-7U6|;q7b7B3959Dh;Fm5;gaS)uTt(HVEO(f;-uR
zO=)l1vBmS~0eu<Aa9LXvV_n=^p5_6cEUm83Ip%FS<^C@n@Eapx#c98z)+Cogd7Emq
zQU(w81IHxBnMxl}GDwsDa_HSY;u)td92{TJmz0jYStzE=W=!B$pASGXn^yV=L(ka~
z<G6g_W~wkQAQZpUchp9}qcU^l;WZWZY5m*tCB7N0HP&YENK3Rn6Fh5NLQ8y6?NlYV
z#ND}1cI5u>3{h@YV&FXtEQ$MOL@kB@T_YLG94v1eg+FUdGwYAHvZMTXi6B)*HY#6(
zSFzLOUZHe+eS&pdtIxv=<VhzjhUT0>#U0{D$XL2m^C)#E<o15ejL|P_bCy$L)v(1Q
zDa<EcMXg@PDe!?XBZq?HvP<33ba<6rdp(+&^rL-T9ophfXoWg0Vr3Wr)Pxd$I&)r!
z8=wc((074Q^TB=ZkKB9SfvRu|z2cZzy!`_r-{BlL#Pa)<q_d_#8cTO?N0W!yFWas_
z>e4sCI(7lIZK@)ayo%Za3NoTBLRxkSHfj=T3zYG-MAhyhLH(+`we8NMB8FMn4$VU`
z>%fntR`3&5Ok8}V|A%58PW(qUg>))>V@_Y%J~*>J-~nN-QNM_6*4ayKXlZffu%n!3
zIxH^1LPz*98bPN}gdMwEDX9hGFe-fw*STi^5XA+*$U#-4RS{sw$<%ACfn#oYeQsq}
z(aD|OL@Id-OUW~5)?bN9%|~KR)rdxni}zm>gs5DkOr&<$jL!swEYtV-M8uxN_lPe@
zZmcejeW_c`-x>pfrrA>^;+ry;<6tH8Brvt4$viGXF%7ymo`Z{2agyj^`6P@}=y`NH
zYQwhS`YohT!^-%8Q1u#h%IFD@$@&i>7joX=IRjGv=<6vfo97dC`VWX8=9n?yKDGpC
za8i&KVn0_Be^#(la*N-dY)SlCw9Dz-aY|V6Q0M=R0J-8pHr&NJYig_-1lRcU!opIe
zW+R%XHL_LwO0N;_J}18>7n#6ti-9`B%l%4rDOC1SpTa*)QH|I50TUQP+zQ44OW?Wm
zkN!lXcd_F#_n*8A(Jk*w8OK^A@nbnD`I(nY$K<Wf8CiZM4wBsR?(a&Af|iy7+(+>C
zgL0R~mN#ZY@;e-!53JKF8=dUZ8p_GZKzu~PUj=EUa;r|8u0^hZp!QR1+@)LIULZV{
z_)+V*a3u9Pa#R|9Dy*^>>)K26|0K1jI7j~9f5=He%&c|R>HAGifEFo3vZOT4seNco
z=^oG|79KPJQh8Qyry9noiumrA633MKss%t=R8oxpcx|(drijbcW<^@RCK|CnyQz}g
z5|?Hc)mrc0>DCZ?6UIc#{?R@dPyAcak#otTh7HpZVadWnhDh@>xyUNc5oX+vLwR@V
zS(P865-`rYhXAM+HOSp6u_-<Vu;35$pj$!2J3gvKlI~5k*H*kaA_HyQ+knqur&dw+
zTJ+LGg%WwB+(WvsV&Vn$RYu;TrD`Wq=u)503kTkJ>+n}Kei`zgd``Wj*!(DKQMW!*
zhJvnSZGDa=l&?_N3uI;gHZglQv{ap)STe149rRB@TYp`(L{;i-6?+=Ts{3T*IXpta
z&>i2I5bdkN)4n+uok$q>xZp2=g8d2S!kf3d56+?nD2Ad=>?ohN^yNMku$(Y;;%Us0
z`Ci9$CHY#6agL8VSM&Q1I-pT&qK9nv!-SCKx{8}o80d48v+dMqn3k^3e&W@PAE4yE
z9ynZ8PwcsZT+10{<`!)cPeedVvDD9qf=%UHnH^W&MKk3sZyx<KTQ3IxCq0u19#(%O
zCke*lnP^Sfzf2TVD<k6~eUq3qX;jWDS?Ni#_nJLiv&kCS3eAFofoVbMQVCO=R=VON
z&yPZR?moGXm4!Qb`BfaI_VN|&#cdd#qoElD_EB`pzs*WfQ7ww}+imx&R^G_~=*VR}
zn2?w$UgxL{T`j3ssLQf}M&ePnyv)W$NFB=hIYR5gJMgYk(B9&xtv-}##H+B6dF>;U
z_X`$+0(+b?#@sJh6kD{RlKG5*96a>>TjDBPpV#R$k|c@lQQn4VHes1lr*?X~WPM}_
z{#LhIV4EhM;J%`Pdsh7i!jnN-hu{5D7r&fEd6gY>^#bvGPuB|UTkoYqew4l3NR`zi
z#X>sx8&QZEqbnqg`ghCNFZg#oag#Dp#O;Ij!<;48Cz%K>g8ZLh;~crFmt`hzQIq2s
z*7aoCCDKlhkW)IL58xWr17JWA7j&{?6Glw=w;AbeZ(j1;A+{+RLDL@shMJ+!sB^4M
zKaA-6px$s#D1;}`ejT!e^eMO^Fk4C&b4JlU&AChKY|gi@f9W>W6+?Pf7J}+v7Blv&
zx5_9yI7(1q*06YMtXAMgoP3kYx%7gZuNMO-E41bmt(-2mmCvJ#j{ydZToEux0Hsx_
zNA=tB=wmjPSsI+~KGl+|2>Ss7@nSX*uG&6+P}d2_u=I*E+cxggYw8So{mQ?a`19(Z
zXKRtsrB*ZaU)d4ypD1!IEA-=k!^OV+DRn7AZHrNADMoTubEC(%6pa8xbWe7qPi&Of
z6sF+_mKpZU<6tqbTf<^Gcs+MWb22HAqnaP^zLVnR{XS#ozHrVKZ8;3Q8^Ap}zz9?a
z)0M8hrstHgf7tV~ub1}wB);aYnET(!03>p~{*FmCf>ZN69sp2_<S$q`c=vp0$hquP
zs6MO0HO$kgKL_6ds)6KN-cQye`h=_c@o(CJU?Y#%gDnc51%6=|gCkbA(wKz$m;~fx
zI1TMBlHA$obJu@p?e*3F2zxAs1UZQgx^41>r3cH}IchD@QCZ_UJptdV*7nDDcD3;Z
z=2s`ImK<yM9V<;sgUue%jI&}l3u=oH5w|Heb4y8p5eAvcTZV60`dwAX)|E=~r*rzZ
zdF@*aF&op(IZRbXGywz@C@NozEj3RU(3#bLhI^tlNBTd$tDF@bw^_UN3ES@?I`sKK
zqZK-uYDA~`l0BS%g>F*p=9;JcFzGMW*q>J)S$r`(S5p5qC0_LZPcXipL_R2}-i<_H
z@B^*LEnR)CaT*#rxcUV$k_oRP4JR;8WfCLGqZrufU&KZuB0KGD^5vmTaHnMa<I^td
z>D2;XYXEo1aCQ!d?HHHt<Q3y)_oP`M=!UPE`rpx2zYKV+Ucyxr)iSNS^CnWx+m^oP
z<QdZatrRf+#8KSOzG9vd0>u_Q-6U~4v=@-g9=;sMEg-Tb+S#%eriondtzd8lPJ+>7
zP=4x0D8<9AIu^=Y7aE@nh@Lq!pb88G1v~&+$&&E~xkmlI3fp|;pVIQ?a^pY0LDZwb
z7Pp+pCuvq-be_39gYJbh4=<x2_dqFlzZ&upAG630EbIB~*dkVvKQ3MFy62Yw%}Dg<
z4_bUjLA!CD@s^9>IDZ2gov}esSA~PJpg)xvKj9+@FrIH8NfI-E;?oRRntQ}FL&RDd
z+KE2vos|$o)eF8L5r$bLe;)vRliB-r2NMu2CzpT(R~b~PK^GsoWNzuT6c8cnNeU}8
zF2Q@2I4|7DcVps3D~l@UC=Xsue!<W-rth@os<FIygl@+G@=+|X4x0e)if54W49^2K
zCf;J~-{*`U{%0Pu<12mD$XD{NJ-UO&?@Lp~hnnLyoSlv?4v1E;n8dJObCDJvzX@@%
za7z81*ZVtJ-)UN<24A*G$+%}_X@SaA$ZIKsG+~LmHI`dICMw_SmHjw%yHuqof>d#)
zY=!&$t&gCFEfvz1hiYZZC8Da_S{H4IV|oqOupojIwH?5tC_0I#EDr`O-5S2>bjW4)
zTzA%QLHK_OSY$gTX0G}-dmnS-DoW4N>%6pVAWTMGh+3oO4Qa2|K%=sIIbbfQbVG9q
zRXRi9+lo0uDL+)p<rSY({=qY6h*@vJj-rvutWnBzwAek+8=UVM*tLJ*a7F?XSX@RA
zI&yR<79`!aTYfE5_xs`i8cA!${XIwk4P~tV@KLtVlhQm*6z)g?jtcaMS3q!C<6d_b
zGrpi2p)zk*5Hk`T+V<eQrnYOnZ`$&)d9oZd!2jYEl|jbjojDXm+awHr-iic0D3%e1
zeZk*mL3BTA=}lC>UKm%4(|ea)rn=(X)n5;eK}}H@i>LHnq08YJ)_x~NdenuaMLBBQ
zF}CZK71(_9LEc;1mS<d-Sjh0h#>8kK3JYcD9Z^1MwgR3e_BcRmPUJ5hH|!4tfh0}t
zG-w<Hs(hMJ$^IBGVV7(^>uvMLNyhD*@j!spjQPQ)<x+D<pOlZHd!FT|TzRj!%)sE@
zw%-P4tAFs#cw@#U1sDYBTzI7+$IS@PO_QpA{jrkO`Gqfm10Wa%*kw6gW#vggMm4>F
zmc96jt$MuD?ZFH4wFabsPyNM7fgSPBqRO42u`fAW6m2jI9;YAz%KJ0n5WleVNo<n6
zs`jc(;1g4TiW?Uc?x4NJH`a}Mi1z5){ksIrSmwGnt<%k~DpUggM}qq^vaFMd-(Lcy
zZEr#=>Mlw6f?d6^xyztkmHof7XHPtpRO9<kiI3$-)rJ8TU7FJYl&Hm}%NG&P7dEa<
zla#1`f3(*X4Ln0FAW*(qHp=C|0ZP`EfQiE$lCFH9w51Q<PgiR&pw8!C1j=%@qrZ?g
zXgO=J1310Uf;*x?!TxL2;hFy8{p%O@F#)m*Sw*{4fp@nDEM$A3vtAKSPMwgF9-a_;
z)!v#<m7={hoPMb#)+pB`A(j$L1{Ur!X65g#geyK(PQ95r$4t#JS7jzV|8qEaHDldo
zqdJDo;_W#R)cJd5!^J5&%q2%xe?#YdoJ#J{l8Lk^G~YSi{a?z|^KY7BQ`o%@5v36%
zGkcw@;{_@Vl{M^T)<7$XXikm&9^V{psmZ8AsjMi<LTZk-1WD)zfqUgu%;mwm*?n7Q
z4e96Kfgnqd<&pPBmn;)S4qmo(j9Z+!L)BmoMKF6^B-)=>sYcB;mq4aQEhfrRH<x6f
zR>A)n#H{t+k&Uu82lJ$aHks0+p3>|!!-N7_BqtTeukXUE>%$*YJbmU#Vd*;1;?loD
z^EqUobIOS{9Sz+t9e{i$Cf#D|^T|^83Dfr^*(TR_X&fW5u#?NMD#PBgzOIkL!!3vL
zj_O)R^9adtead#)96{IaA*G%D32vFQuVUb)090zWlZm}@p>J_%e3KB7nn<Ujr93k!
z!GdSKR6g0zAVJ5u1sV;}&{(=w*MRyd7K)mq*}yd;Q94lZ_Qy6LQ$0<40vV*-bN!31
zyo~(*JiN4XB5vT3kFS-(<-&^uLpa%(*R`?Lc}MlWoMRnq;Q<VZ1rfMHog;n)V{2^W
zxrs#skpn*7N<mhaMuiV@eH4>2iHl1XV8@|KjReLe35(`4hXG`inimPE`!_KD7&WF&
z+UTHnxCjAv&*W(6yDClW$C=lP!S7|G5FGHs7tk|Ee_?WH!sCz5Q}_hTvX2rnDKkj(
z)l>yLg9Xsa54nl5?3tX@E}SJ7vIf%#{S4&3n10e+FwEa@z^@?N^vlZGT2ZoeFiJKq
zI*~<V2$sn+^TA_2vYOYVrJr*U#eEh$8b@M5PQtVMumI`0{Y$c!eEH&A$9y-$_nur%
zlDq8JNQ7U#_vbdf(nGz&?t<H20}1KbvCer}Asn&!vU1Qq?*V-)61&SdC_*^|7nOFR
zcX8v&*Y#JyPQ(?+q_SUM#?*~FSP2yo#yzTC{c`aYC-G-xv)8Ts=JFb=fl&ue{W8_q
z!a7W!2W6ps!b~mUe}4!^DQz*l?ZCFS)2H-^zC_tplgI4g($E6)%MQyx2I0L4PwZkj
z`acX+cJkC+h`Nn&AJEY^VP)6GRz90fZxLn#P*dw%Mt75g9Jt#efx+R|y8(TwIu`EB
z+c&ji@bg}#(u;a-!Egs4y3gv<)p-i{!;(9KS{B(9Y2Ik%NYf~)j!PH@fWav&0VWr(
zlu=D{PAsj$V70@lI&x@`HyQ>Mo<drVlbFNwjAkOFE@t0*BZmnHYp&{V<b5;pJoT>O
zgT^I?X+u?(bcej-yt&^dfOAJ>XCoG!0_(3)oZL7YC|fR-Mb-{K(9N-M&S;!~?g_Me
ziY`;}6^B<}J@L%S_`n~FSGT~MVxb6qX*?6HD6ST^I=;`eqVt{#-w(Gdyx8Mck&ZxO
zcop3n7dW7!0v;paQbzI4uF>m^A+^{|R$_JcTHc|g`97wvfTr$|KmwbB7mhIf?X)+#
z*MQ3vkRd6SyUua`2a|V_jlQi{-|0m6wp(h6#EgG>G8$0CCw`lp_+>W~^B*YvqYtjs
zs?P$jqs4140z6`yCOt1Nru|^N*-m$cqjEJs9&qwKen^d2Gxxq?y6d=KGqn%Lp{zPa
z<bR~EQGZm^Raje(&3Qacc#DB(AeaBQM9*NNTf_Ed%QEJvU&Tey1?XckVzR(UNy>*i
zZQ3ojgZXkV_!gt3_tk6AbT49ot>%Sg2AltB-ND{HK={OO=({R5Ab4rM#!QnRT*#+U
z$A6)YpSbKv<ZrDE^QgP!jda#Da6iywooIYEJU|%mLBi`fJ&wP;m}JuqjLrD_7T}8(
zo|%{L&&VwJ)g0yR2PC#{{*V`!YUJA{cM9cxdt^vPy@HJg22clej1V*U85HELnkPGP
z%^6y2WAdQu<YWeB>mG{&_iQsYaav?X=Ll~X?1tEOs0orI;taBoJ4dALeuY%-G-yvq
zxQK+;jei&a`>CX*cT6fxWBe7JU}lO|e9O`vy)abO0i7XQdXGE=tKjs_d^*jfPzc|8
z-h1CH?Ixn`@1Mf!I0E$B=8pcT$Q6sGvbqZl$~=6!7VGNpN`;@34hR=z4OGV8W>+?s
z-8=&+R-ZL{cenJiX-9uFv6$I(@yzlN-mrHdGiE8qVaIOQ$Cwbbg2d2_^9CH<OqAa|
z>vrCFUW{XHcLlp(eJk;??mg7cKm6S>GEdNx5P=H(YoquvpTpDpti>mV2h@d4y>*bW
z=(gby7<lHMws(-2a@r&Vx`(k$a)7fJqdjXQTJURb*<JG|m&$kU<#jKMC<eRh^$Y&W
zrea2>Q&FHD035Y<Pi-w5u-7+ZtmMJhwfQRJVprz%%q+*n_4kf`Yh(}49O;+B%UR#f
zmpnx$B?=-GiJ94HWGbWb{LM+v8nj{+ukD$TKw$hVOpOYKVR6!3?t4E!g}m>}wmu69
zqg!5u!>u>QKi<U>P%=2}#2ql>{z9LCmuEb_1lTp96D2q4_xkzy5#{6<>u_RJomkj0
zVWZkF0Xg)4+8V5@h|034^q=iN6<j;v58oKcf3OT6mCgI1|592LG!1xsh;Oqn5nAP_
zGop+D$qT|(U-b;sxi{0f-)u?g7JsE7n_csWr5v6-!`G_z%Tkri3o8W04ybsv{INB=
zFMO^JGO>&cH^zXtr4(lH>8=;l;C&+jTmSk+2XOAbmS152eW)ff8hSur43QB!B?2tw
z#3I(`Q&h-yOK_54G>*733Xna`ECV~JG>KQq9X5ytObN3x^Ih!}8p%;g{Tmawdz?fe
z?##Kox$GMCgj5n3Bz*jj$lB`|GxyWhSs(4y%gB)H)gf8Zk%pvIUF;2jRT%pRbMTvS
z>%{A)t_M>mi>Jz1^t8;ZY56GzUoX74ExwsW`O2$amCX+e@a%c5fE;D^X5$prRI~lL
z`To8Ia`0t2<}$pU85ggNte{f+6i}2!gv`U0rCBeP#(GQyh(@^LNw+o!dFGfBDB&fn
z@Dj3&N%mwreT;kdT=NEUM@*5%pFFYDv~$<=n{Ty1;uaHD%{nFmtPl6Far7e5%_f+f
zuDsZsg1?dN7!A&7Y6bA(>%}{AI?%lEGs-gB7|0)?R`GW5NxXK69XkmM1I5-ur<Dc)
zvye4@Tgx-)r7@6SM90O2Th}uo2@9aG3Su7ew|`5yH${u~ug&FM{eSIvl}H_+nInh*
zoPGS@-!7r|&a$n(@ttR&$FO6qZMN0c+^1@R!S4;Dx}rbydrez=T6ft&K&{wBQ(ED4
zE)^Inc|fTf|B@U}U<%@K;F_am)DHEGbsw-?hMt$>%ML@oiU@L%;N{>B(dK{0y=>LY
zD<agfMq$X5%J9Ld%fT9oVFdLP_XiO18dnfAj5Fq8{;g$?7e<~k6R6}Fje@mT)vB^F
zPoIs<+@l(^HiHXiUgssxizzp&7xJ3stU9+fhwFc}w$tR<^4d;2Y<o$AjGhPZc;d{*
zaa<11?99MdhpOXkGWiuiH|JdOa{G8G8EoIk%bqOZyEbx!)i>l2BW~Wk{CE-7!vMPK
z5BL^v9XB!x&!BVqMw*K>UZ?r6j8xV8E}E0>-TL#=LgEW`HX|9I(??q7H~5_{e;tT>
z^)mT_r?K6ZTAUOjgDOPjXC*u)&JVGoh3t7wwHy_waevAj`e!%k+W|%;U@Mq4pDp^g
zY(l;)Ofdy%h#r$MvOS~L<hPv3xpnV;_sOf(CBFi>Lb+c;)bK`%U~t?&L@M{kNAMs-
zzgLlIOLxuL$d)H5!b^>kQ8UWst$BU?X>xh(D3`_p2~@5flg@zR9JN@1?#oaNO?n5X
z&OHJuFxX@!kv=4o6L<sO0~w11D}0veUuS|*85pYaW$C_@-Oz|YzSOV%v3JP46gKP=
zwqj-HrAW<)iV94@sf@h=*W2`;mPIsik-r^^&EP}FN$w0%^ai4rkTaiB-mM|s4Wz!J
zV%7|vG|FgvqAsE~|6-{q*kek(6*5V}Y9vdKB<;<{#+rUsw<tm5%28of>vz91@y5sz
zr2DK+sg-+iJzkd=4~)-}m!cK1*GsWVW$$cJ+izOl1A={YeUS8-3BhynNS&O++skg!
zigy%d1c@)c1Nz3YsDCZFwU({CXVy)fLRPn2S|=50YQZD(cVA+^Pk8W{m(NHV_UeCq
z^^GqBoz+V^DLvam*wlTwq}VT}Np^}!FZ}X`{1qF&4T{2-af(7*9h>L;;Vl*qp;J~g
znT5sTMj5YLN%8iu)>f`GNOrzq``t^<S%*V~^d5oUNsYwAbIQafq^YxZuT@gfqvfp`
z0<$*r1#*%GnesEk9}V0?1%DkDwyQ1z$A<rkVEg&Ah?f2&Hee1+ZD?BaL1er8G&NV7
zbHN4vVY<S(sS+<KnniW(59221*QX+{U#chg8Z6vk0_TobZ7TuCc(-@TzkzA!V+Pjg
z+W{qQk!*F@U^}J!d8U*sXY9f&?C(N<i8@^-{miy`3{MjDtxzS&RYWKn1a^x;iz!3h
zrqd<fwT3o_>yoT+r&%SGbj$)K7bQql{&l1&j_Lwjsd4Avf(*Jhon6`VSEC-!39Ie>
zzI`1o_7|NKx-`7_cdrhggqXsmeL&kMz>XDfj^W?Zg*S{_+<0?4oU6Jgw$}Fh%}5`d
z$A1Hp#^U@sR>`hZokUe8vHM$URsjx(_{uuXOvB>)?4>gD6rB#Gt5z&VlTd}xm!{P7
z@17qiTKQjbwnTA8&K26?Ie`#~m8qgFSSvM8WRerIGnWIH#Y%h8EeLT~<Ch68zmg_D
zGc?y#3l~xivv4s}R2zS<Q?#Riid>aH3ftu)tU)cTfNX7N#wAE=o?wyFx$+Gv^Pbhy
zEGfk=?^xTVqwlh(mS)7iligi!xi_Jg<?d`DdL_ZNyj^w&(OK>F*%V`$BdetN=n&P!
z4brU>7)Tcw7&TRmX)^nP0EAhHlJ3W-CbJk)1QZswAVh)zH-yj07PUmtJ&PnXqM@jD
z0?*EhlZ7R};Lz-PCg)H^CMd3JUF-lZKIPr6wAKkR>egiGS-^~e9k>3?b^6g!hqgH{
zMvuz5HeU!CZx5J-H&BO=b3^+4P3xpNBU6J=B4*hwAyFYqX|Hg+EBdXfjy$TSwC1TF
z(TIC6<P%swEj=nK$;#nnE5G8_Dp!qm6HBIvY#9N@Hrb{q5^}GoMMAj}QNcv(4IhB0
z5V!%W;80bMz6vk1*2O)<{1}hv+iOG?Zsj`t>P@yVykK4Z!kvhj5NoG|G+EH8AAK<X
zEF(x!x+Dryfd%y~cPRU8f4t?BeFm4pX})s%XZ6lR=*$)-JpJ)N<3ZaIQ;<tPzz#-y
zHF^g3bKHF%tdzQOxRjP|{&-+jD~AT}nvSZk6Cq_cJPD#Yd@u3o=EMb@My}%9;(Xhj
zZtrw?ahc~)v((}5Ah&Ln*!kVp(DJg2;<v6d`7P&Ver3~pifU)~#(_ZJ^Glc&9VqAI
zIwQ@iE+A@6{Gz1uBXlsV2_>3=x3f@T6A4e6_W0Nw&3(QrI6ke3)cb;CU_XCMIM?%8
zf;sH+qyvNb2=U#T<QMd=M?9s|myKQO<!2Hv2DYwwydOB`O1)NFl{C4jM*<L;lZC@1
z%^bo7*ig0PhJ|7l`WA72bA#0BX4$(Qd89?XxModz-tmaYW^H}0F&5SEe_D326=C?O
zCk$br<?n|q)`)`^?jp3fS421O*I6IisU9itzy+ZjPTBWl6SEq}?>3it4NjLQ<lmE5
z!6$Sdk_FrJ{+7xRsZ4h)zZpAv^(d#Fyc3n%5D!aleDpWFJc^)b_iW!AR$`0srPvJY
zXc{#<;D7j8o@RrLYq@sf_qcswH7yb8zMp%+E<XNL<`uvr|14e1Wyx{-G3*sBYqjie
zKHS5pcKg_2_^#v8&DYT8>>$knnL%90y|&xHX3Fa1VrjX%3JJQ>eBbK`uWd3pSWVkr
znZ}A4{@uQu({jSKQ^*K}s)Xp{lCK#3*Pp`fHFtIB^oO{JCeL##e~9HeUH<;Dl@~EI
z<x3!KI;qc#NFaR`L_NZp2-QO?GL{}L7pX2iC$hN-q3y*98?On;lpD4QW#*xP-{FB|
zQE>}rNQ>>Mw=tDm@a^z_9;;Y)O6MB)!gGDgf=r#MkSTF@3mQxr<UW@n)e;@miY~T6
zYs;<FiV@Y5p;rfH#v5r+BPL#<L{=UGtKfl6Rdr-636Ir)j+MY{@qL#Ts?GSfWT6%5
zXPBN3e_en3_8jctNdM@f8i=cpyHE3db@cL|D9`_o9+hIkxwDime=*)GIR7OcX!nCG
ziiv^5qf3fX)G6I>srqcNl~JYo*|biSN9C#%R#z21Gf(Ad`jMz~dcLT(u9cIV&J-VD
z42qyeaH#}ZNJY$^lpjYKm0xQn%fxeggx2Cpd-eaIZVxFiIzvr)y|uNr(Tu5_^W(2W
zB}`r2_ft#o-}u~Fn<|E6cUq@RO@ZUShDoN=kU6Cn`^ERZ4><5jKt#y+@ZAk-x84sr
zt2!dfkv4M9(owWyzvL0$TKuPr7V_sGV}G32f){q`_$VAXo_hg$1<kOiDjia-EQ0Up
zW9FaSLp4{qPxsYa5JivZg#+{68`Dj2nmGhRbF$9#k=FuotLBv&T5t+gCq1=zSaP$?
zS&5`1XnsPjCyWp_`{#`NL8{v+6Mqqsm=12NbJ%)QMBYih(a<f9>gt$S{r2-|Nn>th
zJd}y!Nq%MU4=Gf}wonPnOgf9-Y!%B2Ne>IlA^b8ucm+}?TnJST)<iWJyfl`tkSor9
z#wV@A*sDvRJWeBvW@CtoyZ_P=R~B5rHmg)h=e3KOYKjx4<LcFcEP7x5NBT>=gYHHE
z0Q+O#;WWb<ch=uK2dkfWir@Qx7jwc@e~(qbEM**H1cp=}lJ&OUOfb?A<hIBrzW$!2
z<yD)O4}wQLw0>loM@nE;uN9%RcENa+8us@E=h6KFTz$iviE7>GP5j7VohzM91Cf*2
z2gQGu0%v0f{p;aOAcqv>#V)9~+0#=r0_m51i*x*|_ahd$<;H2Hcnk>4I|am4+ClMS
zW7^Y=y%`@2{r8(1vyK9>&Ebv$9}@<PIYcI%<NlZ+1zl!pANuL<Q;KMVCzW2rz(Ysd
z%)b8fMXH$IfLsq?WV5lC^_e;*JAe9gz#G$mCC%`HI`GAn!6i?K-`zh4o_^&^ts_D9
z6NV!nbd41=u8l~>xJxsU^UR_3`l)h~a}N!6NW3@kZtUN6km`renz74j14T1o<8ODE
zxAe*T1LWuuoAI}4l(q+Y;os~B99H+c;(KUu*i%XkzLZ|+><NY9yx_nFvhvr6{PHU&
zp3y;|Jm`P@4UzbKb`n}xEIn+b*jvMeFHr8oVEI!RF_Hi~m3wY1ym4B5ZPf=}fQSJ%
ziRK&&2(Hkh1@#~q2c|WLFK^vFEMn`&wmh@Gd0QGRY@F^LS)qsck<M{i{YA%8_c*f#
z2`p6eTK0*+nU?eQn%ZPa-n_U7YYvb7J|;i4e)B2EQGmXM?3qr-mkPZN=>z1K-9Ozl
zC62H5ttuIKg(P6_H@@bmASCMy`TgG59w3cNu|oK3AtM0hNP98j)<AP_AHzxb`Aq*y
zX*$+!b`3=@F{Sb<t3>l$eU1mLSY{PwY?VG3;}(pJ2%A1;%VwV7#urGBepmLw%V=#x
zpDD)u=df2+fPg6*3@<Brbc<fNS3S44;1n%XVXWpCW(D6p`rvRwD6nW@<zlJRoDsN~
zpZ~RCALH|nzymSbA78`LG^I@|ExbD*9#fmcpTZ{Tzi}iz<FDz{(T4(r!M$6Wx)W*d
zi~F$0)b_4*PF1lA6NT!b#>uO1*V~<gU59B@-o{vPZnK<v;Z@7@!817Sy`O9aK)(wB
zMi7FB&eFGPC#>^qEdO0cbqGpTzI@r;i>~{XO$eZAchiBvn`61R@1v&To?}_D|DnEU
zWzo^!|DbkrYjlg(^KHzvF__F%3;x-$eJ4do+hFUxd*s544i18v=_W6L+q<v+HS+$m
z7xE{~QliI{Pp!8`bOwH+WnlQKX2~WmKpe0Wxn|6Kz=Je`nWI}I`>SwCz-8~;@TL|c
zlS+wV)w&!R4Sz{Xm`{0nzWtOf6J&a)`@lb<&O|De+PVWv_KY9e7J{}XiE`|JSWcO|
zUNtGk$IGGgxmO9X;CPuzb>$%ggYRMFZJ*CwN1!t!E|XNl)sKW9KV4^8+g)@OcQ1;L
ze0?`TcsW7TA2DFdQ^X`S=@2l}HKaRbB62XP5@Bsut3PZcTZ~8+kW!vMP&b7MwHwU9
z$l?oO&3)s?JkW_*kIT0C`T=s<vY;r8?I&Sek+)GYV1oz~14&Nm%h<X+e7aZg{Tzy4
zVlb{l?A_#@S|7y){@6RaP8L{ufduF#5u3a=<HDV{Uaihi^O;Z}LEcHd<Yp=3(g%T^
zT{|G{o#cK_Pzv3_r9NRP+H@@PQF*n{gly)qsk3iG?Z{TIQ%8618eJnF*KY(7tgi@-
zD)LMjZR>S1<qc(+C_a^Uk5V~3B&VDR>?vg_-T<kPw)a&?`-3@$trmPlR#(0G!+ym1
z_p$Ryl)&!~bj?W|2aWNvnkTeCGF*?&z_V*8*$#`&D4F%UJS7;Vn4%e4GJ%k0Iylk2
zWZiSl8VRug?5RZczgBelsC;kl@fZl}NYq?AM0-z8*%=5ymuxznczAWhXK!{f4IN(I
z`}G}hJfd~lqY_MfgW57(Ezd-gU}j9dC$Dz3_&%Ix{}7YYIHAwPcZcq30_IJTvo&f(
z9Yy9(UzP|lNgsSq<#612kmqVsJ32PWXnC3`s+((3z^6uyq@D_8{)WS_m53zRe(QY6
zUr|+%gJu2IA3&-Jk3}>8j$WTBAO(Q=%9!2K-NXoEnlYlT+f5PD%C!Kn<9Zjbi(TCD
z7DRJ#Fke*tEiYa_+Ebs>X;LLx!imvAcp)L>geVe%MPX`DduNWv9;gWbmT{(kims-A
zSx{jH@<SjHHWD4zgV;^sB~yHaoP~#a;=h9Z?4l701`^1}-Yr{-Il_$|Q4E#RX1%hE
z1n4J8i$vu$IQCSqjeU~e%Jy<<pDVxO9OI!7(2pujl%B$5o$27w&wZ!KEr<d%z>@o~
z7>JjjR`F9N{Z}&p<iG3ij0M=(BZ9*@eYBcct@SrZY|o)uj(@Yk?~$@)i&}f8539RI
z+vMaDI{+RAi07Jf!;~1oD|_B^dG7<64qW}ek7uo1UJndtywS?t4tzW{E-6%IKA(gs
zPmK&##(4s^KQP(77wvahv3aMCM<{d@M;1N@#hH%6=72?PdC7_~Nf5YqXZ%sz78f-h
z$h>N-xhvoK2f|LjBnI;_BQ9o2r#hmePZqVquwle**E^N>Wt3JNwiGrwk>mQLM_l9h
zATa#kK+wC$HB4glj&xI$riILbKVzI^%S;#+l;=@>T$B@iH-2Kg1+KyX^g8gftA7|D
z|LzF3iZ6alUu%m;s8a&!dNro5_0`*lVVLozoA+mUlNokX;0s|(5!mSqJBdF4e%ke(
zL%K4|HPv!`+gq@M`NnWDe}7r(nDwPHX6~Z&%PN_|?0y4B=M>av(8=^JJKt}~Is1(&
ztk158Vh8k+dX84_7=ih#Q@=#?GAsoY_a`7``+In-STXL#;DMhNQ50#elx}&B&T8Q2
zS!<@1(Uk+E%Vf)Lz-d5&Ik~SwF?cyo!eD7$Ro-#+#J~`=&K5I52M?l`UpX9aUNAII
zQ-=7d3Pa>a)lRO6Np1Rd_E-KmOOGplJ*&qBp>mu%Z779timB@nJ<XP9+&yiq663ZO
z2|FDHJYr8`Bd^-8{kuQ=BEcX5pb%#rE8u39wRdH%iFUpG4{m!0{u3d7^=teCWSA}W
zB+p{hm6)Uka*87ef<1i&HKjKow7%zFHsO!6@W6~V<I>`vUtJ!%T;amNTJ-=}9}Ah5
zteEJcUEdR>bA<j&E%AX`%FU96ohWp<&vK|@%9D>O9qaz{DW<%S$n+xY>={-%;n-%i
zAEVjJD&Krg;xT7ba5<~2xKGvr=90DY=s9^KKMAG}r<Wmellb3b8QUm?Wv+PG61S6Q
z&4ESPp%s(y6mJ#HVM0bWP*iGD7iu9*>%vZ#)%6)}SS#Jv^k(czyoj(9k4v&?sSsGL
zGxg@7V<UgRu)Egk4FLB?*m^c!Uob%zA)A6zatVov+XL1i3uO>#zJ8ynow0F3pptmL
zZ~30HQKzUXU&y-(`v7zRtST_D&#s`1Ox!}mw}SeV4kt#Bi~!cpZC?0S+f0I~?H&2s
z>+b3}l#8+go@=n0=D5_0KK^3()xNa+`qGHf>BQrRm0SrLSAVzSpOhIhdm^B$2#Do$
zbUPiLzILE18Lq!5cILqY1}E~)q0NWy@!hjd%*NqY{85beujFkr&<YOp|K8IyN!Dra
zHZgxvZ75U-&aVm!#bi8DkEEVtkvMq2?&lsk?egrg8T8Q3t&eh@KDKpyd(VzhtTDz0
zkdccxG2g+G&PT&h-ea>VN8JsegtHx-T3-4)#tD2Ec(;bZxavv1EG%GsA%@M!Y9!BF
zMwHQ@;fxBBP|_#IyjmUR8DlnW)3GdlU%G$GSClmJ?g@bYXL}p;nf}Lwc+zb&gigO9
zVCBZ+&3&M{$N_Jc%EHC{sGM4=GOtbtsz%wZ@wz}FruB1vBb#g!rd{qSv?5U&Zk7-~
zSyPt*Z)s6T<{fpvu*Kj7P(uMm_~>`uep|ndB{;+FoPBywC1~)C<D|8m`08Sg+|LfK
z7KewoqAGm1I_wGLz^1uHZc;}esi&puqCwtRaqp=YSVI5yS*KFQ@k%kH6&>uj=t2&~
zdo<0;cpI4Ohso2t{3BPYXL#V#+iz=3f|(QQ-IC1yGq@oy>2hjGJ+EHOKfXLVcbXbM
z#55BB^1B$|vo1g#-tIw%R;b*aHy9V~rcmw*q5Yaru>bmDZj&Nls&%OQ{r!VKRkymp
zj~Mo~-&fo~7u2PVX974($+lTVx3bfIzgHO}cs;exROZDX?fv)=cF;I++xzz6<3U9H
zeMEe0aj)*;=72R=qUB5upg$S;pZ$jXZ%nAe^4HUVBDDz~!-#QHwRHg|S)Zv7Ea__N
zf(I5mXIF`4;3k!@?H&|tS^dLwpc3PLs_$gRTE<J<Y<-my5g;ap<(%6fPI4^qaHm!g
z@FUVE#8}8ZyrGIkJaC^xnerTU>q#OlxBj!=4c;fm`ltVf<)J9;;lAAnsF-(^u3>B;
zgw=6#SlO55bI-?h)86QP@X6;i1t}60v1Cde6wC*t*Qo=9QHv5@H70m%1I5d6t4-?%
zYQJ1whjn;8F$hHS`7FB2AN-_G8+b@BxP}H_v5h??%nz|SkCaXvjpnPSYYlK_%rZfV
zcf0=&z;B#89vjPZHf!wJ?m2yNLD=>8C=CwaI5ode*O^y=M-l+m4JIM_#0)>4p59||
z38RnH&iiX%$U&omAbGv$qBJ_>dY9JKBw9PgyEp+*PkC+}bvbS}8ugU1{4wssK%@W<
zmRpnagZT3Cw^`--3y~uihwpK9snaRmz+rRYN;+J71~Cro)K;GNuj_9atK$VocGE|9
zz<XrsDbNh8JyBzkRzWul&z$y<2zEJ5XExX=P~xGiDwnS#`N68gg2G4enz_IqDeJ5<
z{#=`!N#gF^KQo4Dr%ggKjThPK_~umWQOp26y6{EBo-qeWDhHq$G8FLhZ6~<tJ$+tI
zz<Ss1As3N~AjN6CV?eZB5kD>AF{~V#fo`k%oWBj0pf2!7qh*b84rWvfuyiN4>RRx{
zcTxR<ym)3`T&7`H-`lrn5TE58Qvke91WxGF^T@{(nE<s1wEh={H~i;?DCV?4Jj4P@
zZpxgTh!8}nS+>bzw$X64(x1W>0Dl|tl3rH|6Odc`6(DZPziP<@b9QJ9pw73iGAT0y
zppp(GZftmmIF|1-!LNkOKzM2g&)aETJZU#_6mxtcY8s1aSmyW2^xZs<!qJm_Ol)v$
z0{SSOANIe^AHEzQ9=>lkXDx$+dd<Xb69F&U_1ooecoU0H`2%E*9H@$`iFJ2UzYhYJ
z)L%TMyjM$L2*5F>WO%eo5&&vBEft$lt7Jep=)u6C%nZs&%!~;TF9Z`I4GDlRiYvQG
zI4*#J1c@$lKR93SPdSe_mR=3Rc+ZkTb56eOb#efkYVJnZh=Cn=u7$vIFjqL=&o4eC
zZ81+fdZC*C^*6MnQT^7riJPu=#k#URrk)jvmgZa>p)ymljh#mB7>Em=Blh6d$L2QL
zCmpn;TzJ(4h5$1UPRC@RCnT)HQJX}s0C@D*!?bd523kTQ11{l`oR@&oB#2TM_$UIa
zCs6|~PI(h;NbQdZb6uzW{KD?Fph8xR+fM*>{DKUmfCj+9$`AacQseda=Oh#J>YoZl
zfyU#4s_-(21I`h~jy^lNbCwn*m|RVQ3coxEAkF|q@G1{LXCS<{mt`U+2;pOtLc;*(
z#`@1~3J_O#u5q@si@&#GI|Kn#KMe}-k=&9g0%gV2LBnE3GddU`<bAg@b0D8^!-~`5
zk4q-%PT9W>yZSlaJQppvs5cZV00{EMMSwUOPIX+1kXB|VbTMj5bp#NqyPs01n%C%Z
z&uEb~3sD_aBVO+OBmw}@8CWo;qY0p=3Fu~Z3<V%GiI^v03XZNf3uS+mB1_WZ0X?7R
z!GX(~r$=Umn*69aT{bAZ9y@Nq{tMl<Lq}o^Q1~U*Q2<oRFRw#8_kILT(zCG(3b6sy
zTxmh+mc*{y+hSZV&8yrQI1fdGwHj-FNL5{geE&JY%hXY8feis|sRPAl{j}6I=`YF8
z;Ds{_X_TMOqD&-Az~F5mq9PmHfDBl^dVUnmtJX<5BFDwA+-0>JgxhyTq6=9b4lHrx
z-%bRi<~Q|r#FbW3kFJq|ae^hi0BfM#DsXJ%-lDRpW2xPlE1ww|`fbpwIv{wS3@ZLB
zKLIDWo>=RGcBiPk-RN-mV_0;EMRO9RXjl*}!Nf#P<6!(Eu|aIhLR(eGGCsO7YlTq;
zpf*9?;ec$cFmkrPwBTMB8^<32!sbF>L)fjp$7sjQ(j_j<>Wyx$cg6NN0u$NGxcR*f
z9+AP_{E7A@LqF)w%Q+Mz4o{Cav)1+eWLhr~E!hY$`IU3yIk&a3!=F}fP7wXO7dZQc
zc^#m?P98h1+JX1!v2dL`)7>LIs5k@z=u!luD-ZeKFEJYbtn634sXDmWUsCb`q)8%r
zBGtNS15k2Xckv!q%Z<1F&Pf`y@FTO&a@j6M0Nr{wopQAQe0KnRI^?kkb+h=a!8ft0
z75=Si{k=uxBWy>|fWnE2x!^td(I<%EPV_YAGX)HJ&jwT4%QfLg!|ZDIPu2B}f}gM7
zACOe#k4xKR2DY6#w1I5~B3bIetA`&f1nf_NiuAAoHr`fsKasTD0`ZM$h@^Ra^~@RF
z@%{V*0LPWpmqyijCO6^@Wb)plkI>yCSBJ)Nu6XQhL8|5_{!o+szz@uesc8ew{zJov
z`ond9h6aKEW)jxpc1qyD@RhF9$g=H|;Z+x&gnqR#3YZdObO*inF5e8IJ+FqB?ffhb
z-Nh&0s4PTlqN?leL=XNZAdOsG2*6+t4(=7T%x0<_5b@O>dh7&uM==q)@Lb=Td&g<C
z<ZeEmj<4k<|02q;7<jizRjH+gn`a{ySnTd2eVWob@693JlhVUl!#Dn^UUaa07_m!7
zk>=9p{b84S*l%*#*q+l?7_p+;0Jg{Kw!*>XRhr$J#3ypQO$uQf?v<_$x&A(5X!*_N
zSl;Oq2fnDGA~|c=Yh836*Gao_RWZ(A*Sjc9AXaea7HTBc2rY~^og}Y+(=}K*DDs}P
z`nY_~bu={gE2ZZ0wh{!`s~Bb*J5Nls@CxgiIBjh+HrD+C((ie7<9qZghSn%IXLI6%
zSMK}{Q94IjZpQi3Is=V=H+YK{^NlI-j@?+s+cKC3G-CzLg&RpQMu{p<-rqJ0QK{EK
z^htq5&&l<~rx??mu3a86yt8tp!DI|a*7&0S1*pXloT4)d-@lSc7W<I}glVTdCzCpt
zY%Xs~#osm<5SBv4qSqi|n9dBdjsmP1z&)XL-)my1D&9%6dHxnCVdT!fHLtuY@o%pG
ze)eg+o+{#DsmXbng=`y04dNyj5Yqe5MrSw&LKd_$${^ljiiY-dDOJzCs|bjc*R&9}
z|E2EhOX{5gVfsAkd)cyYjwG<5j(fEvcr2%`>^d<YcLLdYzEi}q8}R%w0O>7#BZ4uj
zxZph^@$JYR?84Bu*VpCSf@)jGWb03r^J%{OT_kK9U~wTK;Do+0$o;x6hdh<FKW5sU
zQ_fB)tUB-!ckWYZ{ZPg!B7=MF9SHR^UXrfnSD4;{qDPAf>CR^7y>Bu<I`ZI1!^}N8
zpmjD&NP#Y)dv^!1X4go{<q0E_2N8gSfD>7dyGBOam?hQ<z5x2%#F~ClE=5Xe1G7D3
zdMIq>JAeB2qgdmf)wFPYs&4Ch|GTgfQQE!n(%tTL*V$#MsNnr>;*ECz4*RcIv&EBi
zVB7p`Pmok5b=cO=8NR{Y*o{F>LvzjUmd<`Iwd)2b2aY#(Zpo7~=g0RCjij=h6ZeBy
zWt*Sfa7zSi3Nyv2aSLjn!A4xhc74(oV60kK*2a|YZ6+Jo_(|<fuq+69@CB}-2fIh#
z&lDf(QCf?vBl$_)*M9T1u>6Vgbr>EY-lCC0{A++3_Z5+@h~bB=^POvv8*616)MO3b
zGQjKtJc`6UQw%za>5*{kvv)OR2>^gXPL~Vfq4vM2lOH~WAOU1?LcLS+pn2~w^--?_
zZ*Z8Go^b`ktE4oYCwq-4|2t(%tEj$-MaP)p+W*7USq4PewOv~QX{3?v?#=<E8M;%t
zTe?A{OJeBml5V6#x}~MNyBpq%`}ux+{|6?nz4uwiT6;)=amY3O4H&Ir^35H{;omsV
z-@C*+OOMR9sBsAg!W$JApIf|OOI-cFJ?h=ey<(kKTAwN^&YgxR(3b<+=NV-qtBxHs
zly9-xx885>nkrrq*vXY%7V}jY7<9fnf2f_6ZK^&M6ym}=KXUGS$B8;M{&LwGUX7-~
z1_}-23-nV|MYa)>_$v)Xp-3~PmE3hrUcYP%K*lsEr@%t+mS~>d*e{*ui*b}(6wWK2
z0c{0d-FE-^r{f?r@gW)&`JKF-fXf?_n3Eg+_GbWx7DCms8H_eE`@6e*EZ@=U1L5JG
zt(m=;;jp-Ws=;jI?*uSujR(P(-tEXI7vJbp=GCoa#Y{3lU@Qe>L&a+==zz*ti=ZFx
zkU(!?87R)sVTiNhJ+ij02Jt{tEk3RgC%PQ9ixxj;I64@PDfP5y_Gm8zItT1`C{lFK
zej^tLAB}QS(#p>I7Kf2T5Ww-u^dAz)vx8e;14TxF6JmZJKZ|Dn#<=#2NxhNRFPV0H
zHepS7kzR|X;^M4b%;>risS4<M%P|p*E)}bg7VoPG#?o(P20*6`cWbk~oH?8{mblJ{
z4dKz=_i2dUn7)K$;EHe;Xkm{$?=r0djWu44w00W}ogAOCgpx<IAuA73B<2JO!%Gj(
zBxxezugF3DE=m^K_9vN1X&LtX<iZ78PMz+LJa=7Vt)`IopIfc<Q-wRPB=k$Ny-I{a
zKgS8`WbHE4Rb5Kn4y~w}*`b7wdE|S4utNbx75f8_lJ`*ij<q1gZebtz@XvBX{*k`?
zBb)6iUlnO(^nU}n%>3ea_Q#ngcKOaf6<Zpz!UP<@Dkz@<r!NlMz6f`Zd(X|!C(B#c
zT-Bim7B_Rl&2A9+RbSe(!CSAQi<0uHr|uR$(D}K(s7{}9Q0^PKG<jV$!7*l}c6aup
z#t_Ukv9=hkj}XTEoV+9Hxa1c8qHAOUGA~oxu(gR0cD?~sl=RrP$T7i}!n{|3SK!2d
zD*R-ybNaN_+E$~CT;>GS`5Ag|`R`c2PLfrl8!RPQA&KB25SNOoql&ljpXj^AV=`_1
z1W{LSlWJ1R=`wVqJ(43?bEXB{ko*M3Im6s3qKRYd_ro%L1!{;TGvu({K??3sY8X@>
zGEY2MQsz&PyL5JT4-_4Cd2cD-QDMnWAn*Q^6{r6VAvuoUmQuf#QB!l-^OV>x`;$x@
zhZyE6^M^8rmU6;0?*Nd!3YLbMe$7EOv%fZdxS8mLPo`G&Ih`F>0VW7oxrp!uou8DJ
zn2woBV{6^-o*7SKNLAJYeizq-Oq+VE{&29M5u|pHe=E(~i6O0rbl&I|KV{{D8$ut@
zjd{FlPm+PSuyOG9`u9D4x7Sh;_H;y10P0sv73l+!;4|j;8e~1DXTgdEP<@XfBOZAk
za<cj!bBAK+1IyX_HUT3$rniH4KJnz+97MC{s8(jNX;DY9;6Gz<7O^ocK-Yy}r%v`=
z<OCKl{TT@!70_3l)v2Wv+YMnHjnt12UHd>ht24>ldns5Dzh(7<4aWv~Qk9kpLH2$A
zO3Dpzd}2<)(}lqe>Q|4UMjX;p?Vlq5O*MZRIWjra`zLSA9U=y!bmRM$4T1#vT}q=^
zP|dj+@RV+#&4;n^jkf&O-dZ>xzrNY*2+c}vCdg`X-z^o7)$$tbX1}hdo2K@uMlcS?
zsZ_VjbnD3CdZ^Kpbt@0`G7!jd{Y)5!3nZA437dtjVCus%_*l=aWfM-`c~={^L+SVf
z?Ym@t&x2$P<zO|AzNcgOE(_xs+^R?V1nu^p7J*^tOp8DkK^?#7UF&|&LPwna4$EZ-
z+V|3GNe*6+tQ~-#+ztaXv#%<X1TxvdmIobpIb8*}>o5J}O=%<MsGQ@!PLfkU65RU9
zNuZN5c~7jMVba0W8A1AdhgK4m)YQV7SRhKeV%Bx7N#-^-xakRr9_c{G7kWFDt7^pd
z-<s$#?hC~Y00ygf@LpmFAL{QczeGdt>JgWd2K_eljQ!g}6R|&-=nbQt>+y7;AMD3X
zoj>rq+=~iG51|9?KB~evLH|q6Pf301z{^%tA@xlYK~Y?3xv5bIZ$P3Ik_RR^Jgu51
zw2{f8Z|CunGyBuSj66SqphjhRJ}8{TV<bC`3a@zS?q1$paZIT)QLFVA7$gIhM7Z9k
zZ_r4*%m#G>e*nDNc?XjQ@4El#Xthlq|5G+}(%6`?l}3r;oK{DD2v^c&Ha~Pssq6ag
z529UQGmkS80f-gG$>Ym)qH3|Hk$F-)gZtZT_{Q-R5s1m<V7f5T?Bknnyo1v5gk&E?
z)@o{JMc_p;wp_e7!8f^7<6NY;KQI?E$pntc3I{BT1;u5+Rl?@2f~GbW10!SaD&*O)
z)o@7uMYGx3UIUWgqD37ftE9S?nf}|zssoX;^<lTV*;)=llPI$yjTdPPjv#i!Qch>7
zcf&2MO0eGDyeE=j<ZF$>1X2osZBXe+Y9R%hI|!#wC(1YWy9Kp&ywI&|x2kB~4Jy2d
zk_LLf)oHte@>2106)F-$gf<ioOBGT>49p220?ZuP(<un)5WAJvm*q$rEMNjU!=S7}
zw&}aQ1k3;x7AQFQR0b%LH9oa(eHZXDAa-k6-fwC3*;m$BUnw|fjSCZCmx<<rW9JjL
z6b&2vb!uAPerR$G(w@~Zh5%D*m&x^jjzSq}a_nj}c{ZYzcF~+w;z@_wIF%ew@C7yx
zOJ$yO^o1a7CfTOn7Z`+S5l@UvE0;>T8S;dxzuL<8vBha88rdehpGxG_=bIbDudtAc
zchOkyN6zmU)ye>yqAxbEU{M-ozvlBo<DxIr7ob1jwXe4=-sKv_c!^4rD5n3l*8h{r
z3e6@YBn-dLJPFIZiRB!P6bhxvj;;{$v}f&O#iufDDf)sKF&Ldi4tDZ-PI+O?or~Fb
zk@CpO;|aq<Huh>~%hZp%&q-K9qBYK4##{G{XT4HZ$w{CjIc&eM9*4w${%%`Yp-P%A
zu&Of=NtfJ}eE1}`4`eY#M=k8t`G|$?tKZ1wVC{}rS~26}5o54^{}S{uVUxH&g1&mW
z2qsT>@%<AnaVC4>ophQ6BB7E!yZK$*fMa*6arWg(Ybi>gCsdBf{sUK0;KNG6hSWM(
zLOrRZEDt0IbgI^VW=HQ8Kx05Q!KVZ7CBSSM8-DL42JJte&-$JflB<wy2<>Z&h6(70
z!afcNu9i1=3*s^L#t1iw20&g{95H(lN(ToV(h1vM*<;wTMm#;<#=#+;a>67;yyKYG
z4&<H;CCjb^`7dE2?m_X0!dD2Q**_hY#o<$g`NTld5l)tLXew)=LVZ}-G<h;XDj1nI
z<&9fbV>yDR*15ft_aB&F_I!t;*_Ejnsrz^FZ6bDuH$AFS=@Uys(`Nj#M<>G4pNXLW
zFom%~1wj#~e{FeDw`9fF0A$~!?|eI!vDCg~KX?zfPTT!<)CwuQ5k(m>4d!(t$wL0b
zHe_Juj{D5Wk?~p2>+Q|nP<7n|=1&G1Ml8?$Iz9$u!CO@?+vA&_5h`1O-#k?<tU5%{
zJYWL)Cq*}Zuw;0X$OON$*+<3bcy5=?5a1ZTue+31h9MJ<;`XMH1k1EzVR#@a(j63@
zeWsq15-ExJmPgRz#0e!r8iQfGh!Sx;u7njN1#gJ(5je7V4ZMQbJ=WGT&?M$7{eu{@
zy1)D1>e$5P{xi3o6c|fKJOFB4sWFA6Dm*oSpme#B&uY|Sht#Fk2T*qjLNPxgkinaI
z01IX5{*EpeKGDD6@rIZ9aS@O4@cbiyok>m_0W<y~6QDCcZ3;Bw%Q5Q#y;OdMq^@eh
zLV8AzsV&WNe>KLgBin2(p8KA8x4@VUton~c^HW`867lz0r#0<u-GAmib&ybgWTw;L
z753yO?Dyg*Q<+{5@%N>)lVG_P0o!bFXxr7kqv_AJdvZ-5MiO*^`(ZQNNq@P)vf=h5
z{ievswR=*kj_qWI9q8iu^?sH*c~RhrNBEHq%2J{*Z?|N^_G75e`5oBryaz1Q>XKoN
zw&dU(li8Sb>%FM<9NRmzTqmxYZ`E&tZzMkWXz2HiORKS;LUelq{&e|I7tkl%{QV|a
zyw|!+D9{OyC>Jwe6VNj&Q!i5ac+(Me^77FBs(Ja`85X*pDY$-P@hPNhJ#^u@vr?8W
zHM4ZWTCGIm59-yY+kScZ8+C6b<kWLP392h$r$QAKX&HKtz3^WoQZh^0@jh4^u_Fzw
zdKavy_*x50?Y=3dor`rir%p(yZF+VnH3}0uV;Cz+_mBXpnA4OR0m5CkKAd?y)XDT}
zTtiBdgA_Nd*$qhTqnM&GJAh5ta~r3`XyZ8m6_ahTpj$jKMdsh}5J1qvk@gQu%(Q-H
zYt|4r>=nGdsOHAj86^gt%`XMUE_*Y5wNN2cc%DhBRta4?A<O8hNb>dE1)EW`qJbqC
z@fLiuT0N9Gd!a&ERhDD3+CWvIhJX%_GY-h+B&DfR1=-|VG(_)->-vkq8_2>}aWVT+
zed+DYr}hpi*>cYM<+JZ(<88_tuBL)`cz8Tq{Q~GoY(KMcq>1m^_EO~BF;0L@R5DG<
zdy^3j=qSJYCA~?IN_8Nm)nBekxYKIJXiGOZLK~8naGh+z5}M||ld|EPFk*K$`}gTc
zdPdYF)oOmxL=<6(j?}=>ck~&p*pcxMl|)+ygA3YXmMjQ>v=?suztJXU!0GvrZ2y^{
zy3e^_0ioS3L*FLi&9QwU)_vQ}5JKLWpIOp)ha{D#ZuiV6w~}e{=*&+Tk{a_9Ab#Kx
z;+C&3rDI{-qdoqFr!7Ne9AJ(c2z`jxD!&9@O>@q&aw9y%miFde(LjTVvp+vTR5k^M
z!=yYfzD+@T#o(~qX+HZa)pH$D`o6gA+WFOA5}%^Z0mEv=hEMsI9@tdl2&pX`Ik@!M
zX_~)I9n0ER%>EKz3?=IuUO%HSznmd<zK}ezUzaXWQq<guY-~k_qPnFD@^xGIZC<x`
zW_v$htz-+|re`lbURJ$48u(QUxWfo*>Fq4?R9*T%4OKa{%^Fs!Ajiox?08iTp91y6
z>)mqGeFf4uhaSD~&0=S=QPQNmNhJ#Zy9@`p%gY;nf=#kbkO@6K2T>vr+w7)y4VK#m
zG;zki=CX;|GwE)U&B59!%;+Qtl9(_7x?q+_K4mKmdQ?T3SxH|&u7Fg*2lHKg_sfxe
z9R6tP1D3ilsagby9dmxrmX9w!8H`EhrT3iQSg8(DgGb0_BCOecmxUwH#RM@3>8zdr
z$1JhRxx}2xkMHf11&f_eLMMiOFUJT7+bXPd&fHh=*?>8uQ^enNiEwtuj)-_OpLx+m
zvIS(^f>Y%SMdcgC_lCBT_OKqcQNL+;pjFx>GFEelJ0hxdVy=aj4*jC1qP*zx)Svgb
zois1jzf+QEsx0yGZfa9zb-Cg*mJafk59fJ(drv1-7}S$&{rcDR8yH8)&(iQx|Aa?v
z+bYua4{OYQU;{}lXk`QF{vOx&laj1*rR*W8C-f`Aj=@ZJV@fa}E6R)%u<R^&gx<xf
zxbE&(<HWbhz0(w3aWBF6jg&1g-b|A3(|f*)!*~9KQD_bGz1?u5?qQ|+aUtucT50I|
z3cny-YL!}P@VeOZ*(Gm+p#S90=@X(uF9>q)_*kZ)3CPg%@3v}Pf9!9SmOjxI1qS*{
z2aU>D0{H?^<0cuAvME}UV0NlXaG?_sl5KxCd7akook|T+j7L*l%^Z)D=f6x-NhCm}
zq<SrO;5RYuRKNis={Un&JHuR1*XsmXfQQK??|=QDu^_Zwm)&9!L=jvMEgM#DlLWoq
zc-0%GtWq-d&*qIaTX(g=nJ^zi=cz#2y<Rl$qifhwS43GO<DqOY+1p21TcxR*zgeVf
zIsKNyZ~H_NQo(g3iPF<yOFDeQiWGo`=$YN2@_S3Ro@z>BwdC(Dbp^S5)2prDpqEmN
z$-BP((NMFP<%8Zk+lpB&=RH!?bC~b0z0+IWf68#8{c?<GS|2ax7t({5XE6go=7KBh
z-U6pzo$CkPysA%gF)$QMz`v^p#G}<dQ$o}G1+jo+=zjy`BgU7J3hD{G<N8ymh;dvy
zu7}vqHCPwY!rw--vnXWQ8#NcEb+D~f)eF*|eqS*PP23_R<Q>7m$Q&nrIK4=uR3oMu
z_oqLdk&ywF0#c|c38VnWto({~mkJ4%=>3At_TMH<fI{be+{Hga)UyIp>N2#$Hh38w
zF^;H|=(65@Y6}74yb7vp<SzUjx}W(%vfKDFp2)R9OSt91isMAZ*jU05h@^ibywFsx
z#pw0V;to-cf#>l*nt2y5K9vZgeUP;^ES}1`OBR;^vKM6J798)M5$}$u$Q@z0s{gl}
zeawM%sIo@z#iS^YMddu3;v!k;SKkQ_p$VqsyqQY7y!o$$c8C^o_)5<LR<-zxBMdQ=
zNV(<&w+Mz3!kF^;`0}k#dBdaaO{iM_H<1k1FieF}P6WZznvc<6Gh#5qN#jEme~m>^
zdw<Ick&4rnH?9@n7ltRJEv+8Ve}ZS#>f>K0I27K=uJVg%@JPRERM9ecAY_og6g|db
znN?)P<l@y&qe$?J8>L>;fd2(gi;x5Ps1@D>3{Fsq-fe)0pw4>NRr{S)VFFOIM|>l9
z89<6PF7_QMTTf(O&faEj9}U1AuABVD`0_x*x*J!FMgDF!`VgoG5B53Ko>4mz+-ZpG
z@KBp47pXbY?wzphP;xIm_E;6hTAEn(Qvk<QLIPnGclc$LW0qs>LXW0|whLR!;-Zb2
zNwxS81y6|k0s*cKuWmN5O5U+>@8WLbbu(@nuo&bXJ!bq=bS|GHjg3%Xr&b~62_@Q*
zZ9ugpjRM%*x`F@94zkEpf;{pf;?+UgU7Ab<@HLii(0I0wV~e1-45<VH6@xT-jwv41
zF#N}x%(^W~FK99!(T2~~3lbXn`)Fm_2_^9dL@*d+pnCagZn$+4&sqs8L|iJmOy#JB
zVI?f)ls(><&xqihCox%c=X_Km)^pk`Q<?K)mM3E!_qgC&WuQqB`D|t%#q&?0)sz|_
zLq1Fvmy7D#Wtz~Xt;?AOm~7)60As1@A1t6YZx{{CO!T2OcrmXG)C4r|?fs@H4M>_d
z9M<iM>W30kBg1y0{-r&)mX+g+l^ejz)DECnGc4Nb+QCJUBcoNFw;vPNG^!a@h&%mG
zpe8VnLJ8?5mSa5Zyu#n)C{h`f4Y3g7@+sxi%V<2&Qea!KD2{Sy0v>K+3UfLII*_!C
z78PtoY0-T)>_i&8<Tcq|HLX6(c&%M;;lEm>6MQo8J2G5=mUfq~fs;~6Lc^F8J1e2>
zZ(2TaP=a2_o3ZbI2pvckq%9VK5!V!ifi2nq|E-3t_w*n%5rpH9I>R_?F1|vZn?|F=
z;cmP7FG|@jQ}T|!VGXk!<psTT<-HUB`e8zwYB@^hj|O}yS&51Kv$(t<UeOkg-(T9l
zHzY;cEY_D%;cu%<2#@-nxn+cE$YG<RqHIx7Q_M<)oNvabW%Lxd+bScn;YnVtBNZ%-
z=?v4x+>g!bemSTD_z1YMs<+Mqj{o*_6)>o<0$7d~bmHC34G{l(amdBhqM0Pe5JXHD
z$w%$We*OK}C_(whhdr^AVwy<eoY$jCZ#W%-k)&at{hm@9e5G<Y^lQ=$kA@oeg%{!M
zvIbst1}~9hQ1&YCz3BO685*EiO#vf8^YI;D*)3{jZHYH%*T>`xJmHASd2!>oRe3i}
zb$A{5IHo<yz47P&<wxVcmR!K2A2*L+4Z|-?;ByCDLU}vEIYsc(jJZ59y|Mcr!&k%y
z*(K<%<ooVX`sQ7IX8t6*#`|E}bwr{Oca-Ii!Z%}+qWuA$K<bJJyaXL@07fB2g}ViB
z9tR<Z9?K?!MB45x6Nxk7?h0VLK*EKZxwEA3XiL++>{c8j!9!3TSI>5%k<AzI8xs(0
z2iATP$|CTRaf6mL$-I~vqvD2~5GCI)T_O3@x(3`=OMnIMo<}Q;3Ls*E++$M|=m2kp
zjlJxs&q7ekzT$Pn1d~P8dAStnW3<m3K8EURv4Zk<d4+~cEyDWDR-Uut`K$Z%SX1b=
ziy&jnUG>x#T!8)G{oe@Hvkx97t2|%)+^iTk%J|Im16T=JJ=L_GR$BtzpWU($9>%No
z2O6Rc7f#^k^}%JKh@{U7Mr@YpYs0W1GRn+MqA5#_4R~77XuX!OvOn5~3#JyMAyJNL
z=$?pZmL_`Nfi#EQzytWa0c~{#bEG6w<5J#J$|O_-&A4R+c#1{Dr>|_kArVUV32I^P
zJyF{hsWl;L7PeG+lKetnvoPX&Ez<y~KcT&wL+n&aSH66zRUzCh>mwNq6$_=Bkc{+I
zM~<g4JD^VM0Rm4y<^e^rp8v0T(^3tJDKCexg<}{r&y|2j=HTD{Aw~EkH_e3CHNT#n
zq?Tu;j$77%C{rTzlno20>xG;sISQ+eo=20JeCD@IH~mG>?c1)?J-Iv_FK##7@1>cX
z%3m}iR>C2x6S6CgMKT5ptzUXOSrIV)`7SOnU>H|E9U@P<|08~7YdFJ{M*kb_FGmqH
zpxb<U;Jq0%Mq9MyExj+~BQUn9bRjyXfn#-tjdk%mXkq)DI_@H}yj99)un_RDIG#{=
zysDiDxHRvk28a_X>@}jv;qz|u0!**_6eD7iJ&}DRiBT43fJYd-coI9Ej8gz)24I?Q
z;tY$x&#Xk#K$o%p34htP`Sy;6IzJtynQehGR;XXbz47CHbtDMYfG){f57tVC2i*Lu
zDNF}bHOA5$K=G#M5d2^M!%=ki;pv9)TVOzsZZR>a0v^e0N&hd!$-k^+_myLVWbA;n
zT;h%p8XNfBk`GlFUYAljou_m@ibiy`nOo>nm>(npAG;qg%(z*o9e&A4?V8AtpB472
zDVYeR88fZ)$?5CXDD0b2Xl&R4qtffp{c9cos!M(xc89@y4@{PjCe$2V?%_=jwlpA%
z0=n$dWZ`Oncu4u70HqckAPsw{eWwdoAZSojsN)5)a*|~vr@ymMTbG~Jl+k4i@r)ty
z+f6rdjUkbN>9l0R@$Y+wkBRJWynOtxsax2jw@fV;x@@;DRi_fN{}foffim6Q{}sT$
z|AA90yS_C*SR9QftE3b<3j923_3N2rVzLVxA}QR^esP3(DCL-+sYApazHzDj+5O@3
zDyoR?6~Q?t9nt?R?f9AO<l%$R44;Xw1x_#^+<{lVV#z=Nbi0a*4+J>AD;SW8aX?{W
zw}v1w%5bW;TjJ)82q+v*Zyf%PhPZz*7qYHVOM4lRvz^n(KhA8wD2NSW|BTSmWI*g<
zpu^bi(*uC_CeNnO5i0N?vQyqNUB;R*>8RmYkX&yhKm)u<ExzeOdjcHCT&oDFAkZjg
zpY*Gj(OX?!*??mheu`xH^wzmkgLOQEh~;4U-xq3TE#L!7KLZu+ji%Uz#yosavAixN
zU|<nz$1&g@E2^x4lI8G(;XI*j{zp~OJ5}nYy~6+Z=tO$k>;t}P7n^w=>iEK`B01oG
z9hc}~5wf{F%401}*3#T4vE?n^;a|W=5}dP>`0*HhPT>&%vX{O>@0y%$_gTr%uT`9I
zIr%c+0!o^vlTqRIaYmnz`;u!V)f7NraSLbjG|?BcU)Tf{(aVZ6csP3Lljn)!xmWTX
zHCs9)LCr&ol$nDMpye)N3x`r?p6Y$Wvt28{+SMzVXW542uz;-f?|<|!>1f5c1GJ2L
z%TE6yFm|gN^N+ZF;F$*o<HZDw0ELTjm;m5LSwAxY09>#)QAppx&i-ukTK#3y;DrN-
zK-1lOW9!sVI}9_$wL<^@VnM#-K6VMV|D|BBDylA-cV-rZanPadJf0@fF{<DN5l0<3
zhKzo`&%vI@h3X1S7O*lwgWADYkE-$R>UlJKkR~gA*cOA1ShgLITrw{(0hPiRct1J`
zW$B1S18iVLPK5k1rE?SQsvePpvv2(vz*5ivavS>3#JM0o9=_5+VA{L>ypDKWuh`)*
zWTzc07tB@E4I3>*TkJQB)sK;_bdPIy8{&*>Bkdx|LNKZD$QgJLx0)StpQ6vbk@?~Z
zFtlLdZ%3aEyr!SnWtLW;x@$9C=4F2MQ1^Z!&hl{!u?E>uVY8Doq<lQIrA&m@ZUKZi
ziEf@hy%Rrs;o77i5YUpv0RktW0yB4#1W*Rc`-bAQ^OU^|%5lCqYc|bNl^eZm@wcCB
zz1hJO=;RwF^*cB_U%`e%K@v4REAG>ABUmc3;Ll9&5;XTf9|_vYz)6>fRr+fi3*5<b
zjcjgBzn@Qh_8s#;?v}qd4lJV;W&sILa4$OnclPuJ(QYa?0XN;xFo3oKkiqpyLp)lj
z2tX#{VBgVoz0U9dd^87WpJ+=TNi^X+N8A>+PxT((#B(PDCAy6Am%zMPi&37$%9{jM
z6kc>+^_;vY5LUn{#!o+?9iPzz;$&4VDhQ0G_mdH(C%#Jq=gt@6^0PNj8KC-oMT`N&
zlW*hEf{!onOl#U^S`ncDkqZDGTGu`Wl<#-v6hO&XM*yD<?YDcAf5%)hmLZ^^K(&7&
z05D9CT)%kXrn?Vi`r&6`<H33WR*L7|4EiELewTQ!n3uJIS`u&pcxI2%=54i90RfbE
ztlRmN{OvbX0qn4#@n4`^{gaduZ`0P1C@;ult}-kXe-cg*_4=G{ph#+mU`d2bKX(Yx
zkpUsboF<S2(8b&rbOK@3i1-rK0r0LKz62Qv4+1zFplzf7qwoUE<jnyf7yS^+1jSi7
zvP?4%dpheW(>;Sm4qhb3$It8p0%%&&!J$S%)Y+zUu5X43_av46fh{Gy06(QF5?!Xb
zfCQ^!gSQ`4qW~~5fcB^N!V;3cDIdbW(#jNWD3rEwzku*|BB69%#2rx41d+zSXW>$~
zv_E~&|Liyi5cl(7Z!MdY7#&9ODYbU;d}4r=Egk$P$L})veooQ`$SbSy9XKWt0<HiK
z(Q7_zWDAbkSy&<9$_fS>fLOTWKk9<rPeCRq!}&}vFW16b!3%UrGE=}K5#7cddKcNN
zC2P*E0)eDP#VG*c$mMSiwi=!H1g7@w6m`&V9Y9L;$?}7GCGy;!g_tCy+<^9bttPC*
z?1|*t1T_UE9UxXk_c2S~(NT)RJ3%0LqgwsQ7XUi^FQrY$dp>pv7tj}Xf^Huu6ixiG
zEYg`IwTH3+20^@itYsFfL&e>+*)KuMW`2n{C&9E#`$d|lAL#pJQU7=Dh6Da>X>733
z4IworaVca>p2*>V5c`uRU^v4_5eqTDfi>Yul|PgCh7~bFiHkg&*8ZM0fRTjXPHhp{
zgsWxrCZtn37fl+3Cr6DxB-Jst^4t@<n4pDPJu6qqp!`P)fh1r_H@~K+xeXkFmcr$o
z>TP_=zhdg;%=Vj_2cgeeRGqK7La$};ZzJtbi0FFw+HbQro92AG#-<MA*r=Xlk($v#
zH+Sf^);TurPFErr0PZ2iP+w{i6H3s``=*?BzA{9uyr#+^0eN&kMLkoI2Fx@V%4?L;
ziXbQ-ufk;I`rMmVjhO5qDN&n++5o2*V!(8h$TTFZ3Sk4}mKSX1O}oZDQrtO~<z!rZ
zvkPFi(JkeAZ~tG{{x*@}MWI(N!xcucF?1H|6}wwox>YGIN2|9@gYSsKG2De{GHHfC
zMI;kg?CnzcEp-e;%%p(2lwc60_}6uH9RN57c%ndCJ{9p`I*?po6knEx<nM4u+f?fq
z5Kreq3E-gg<H^5z0tpo$@c~2({(B25gc3PEfQ2J)AOaG8q5-8=z7<1(V|D^AzQj@J
z?;1*g8BG6f4H$2iO*8bcyl?R>{t)D&EX=<P&q3GFVjRsmhV2GP3g=plcc^)g8*^K;
z698ey3lJYlIE*;hbpR^Gd4*4Wda1?b<YoE@V#)_ZhrntIca`BGP*FxNvZnKVZ$`|R
zlaiXTbl?l!;uZsTa|-(9x<E<-NhLHnMQ;4zDk@Acbr}Mg#cRq6X!0wde_;tuX?qp)
z0AI`xk;frw(aYD#oa^V`R#<TCSEsr(3+Y(!mpJEv`hiGTrg<dB*D|VRL0R<A9~k}u
zQ2{_-;}if=VYn(j?dV7821&h!8jvllM_+TnT8T2jhXa!`hxU#S-z9PLw(1B>>u2+#
zd($>J(&KwAq)nJ+aZWW=A_gr8EZwDGI*iM-smHG?hQl}RO{g6*X4&t_651~l<Gq`<
zJx>IIt70sY->TTl9?SI0=<C<-$6K)7ZKGPZfT?@m9ijsQDplk~c~R$p1LJcQoi~c8
zc2Rm|9kIa%oIvNWO+^*kr_4?7#aCgkeb{H8NF@!+5B+xse^$v=u%VRszqay7In<yV
z?6ki$fv>`rC^^4>NPB^*l7FV=atMi-^V&N6j6Sk&p=(P$cc*Z1yAOEpadH7}Co|(;
ziyo|WUf4j&OLKmWVByt`=&{qO@y0!~bS-2VposaPpf227It0jFJ~*Y<W&)xG0RZ23
z%3KvXCs9_G2RT-6oh_UJg5<mR?^M?jgytVE;l@_M$t`S8begcj1=$Y3MmL)&IFP@5
zn4YtIK;nD~hMt?3sdO?s^R-7_HBC8<O+oJngI5bz-JVO096R%Q9u5^c5rr>6+nO~#
zs#pn^x|Z2QcC8v&ZMllkidlr~_*Y21`P@a%BSqlt%X90+>0}e{5$CF!004vim=b)~
zQpzj@=Z`k4#px(`TPDCAA&VK}#gM4{jDM!45Zf|9DLdotSK7|5wJz-W*qL7d^&Pwu
z%|b1>QxHRg4d5t2Ql!56wi(83X&b!{QdYPVp;F)vKIR9WfQ;b&wDOsO`Np9Z-{CZq
zM6ni?XLGFJbg=_`1zD>D<`~vaKTij;bm_;xws8)x@;(A1)jlcq6nLd;@(%u6I*iO3
zK-|l;GM|iRhquk<U;O}`kRX9Z)WWmv#bcPH+y3d_+$?DvAm_e2nnrrMIcGUvHF$*u
zG)*4BYsJODouEhlepwDc5<oRGum5%05G>aR@W}VtyE5k#zqkIiv}P?2PP<*S@#<%7
z+gu>Yg}N4fe}Jyo3>7$a^sF9no1|#yb)=c4Ynkcc&oqs<G0u#Y`vFdEabCE2y*(g7
zlgX~tB#$NTxC%2>B8)6h%<%!`(hh!0Eg9S&0<p{~PQeq~ri1~$$@x|<H^H3)*|zOn
z*|r_pN8O7L27UZyTq{N#`)81`!aU*qm-7J#i6e5WNX5qWbv<-g)8qLA;_JqR1b1jR
zxbHGku$*Fi^YjJyFY~k0syf@x(VJ0;*B=)%$-wc>4|kmTjzfJK*_@+sGPSIl#X29u
z$+HO<1k@PFiWTLY?;mh%(govr^Hn~kT5Igx^ix_%W^8d<Qyny5bSsNiU|c-4cvi0b
zD_SHtKZxu<_tjJenjz5tK~k8ML5AEQ`GT^j>u=F_?7)tSuvSq4E@MD`hg}uSLa{}8
z*qs9&O|ft6GJg_+QvM<dAZX57$m$OGigyFPQ=uG~K(+8srm_aYJazS{=H(@-HR@*|
ziF5fCd2V@Lkd!?Hu4C-Qpol3X(*;j4g!9Q$rVPlOF*ph!m5#o59Q4<831_!A;h)h4
zFu43fYUdamO}N7GCgnA?ao*2(A<_AeYxf#UU&ZSG3V^3{<r8R8INx?iX#zG*of5xd
zbCqyXO`3k=pn_9i^p-EVI)z%|pljq>*TtS)pGZs@PjnA7Bk--<e*H1`iH?}d+i199
zW(lHH!%k>^tWHvnkFy?~Z=s8qgAmlQ{BwVm>rK;q6Xi2Ra{#QkChSkkpSK-^yBZ_|
zU)nxJQt>?eJxY#=nBD?n!&|jp$5uKz(TEEbn@+A(pUzhQ=<Yo5X=%wC(0}Ht(JCW%
zD2uKm0m8?GSjg+AU9Ld-IG?jz!Lj^BUz9|(0o&<~h8?~Gzf>N6%{^1VlN4TH5Hy9#
z$|{4<!c(#l`~U{j5J0}2pnexOIuM7II#JAk^tSyvIxolczY<4~&>KUXrmeT%>_L<7
zucj~Cw1j&B7LdQBZe5d(Tv3s^nUiQ1JVIE-HC_W+Fcw@Pt84m^m^wJfyU?>=qc9ll
zw?-0_GqC6F-#jF_L{`_@pF@7gl1Z2xA^fR$`{r!(o|J?G0|A<76Ct?iR0~TQRk38y
zanPc~M23D#^ty}M`c$Y&uoS2izLXFF6IdlrTN+>Pc)+!p-yGjYn&jfSCwV1TtY64-
zS4Y+7{2%xi*k`VPPBUVXL#Vu0N465hF@p`?LW>ma%-_z&p{fpLP&0+M@fhL7L_Qb7
z$U@wD&TGaimy%g&6lLUGJpMI-9A-peX25B5R)K^JCM&+al_F#_h;lf)<y{SsEKhB{
zwfI16G9Er&5AHWFFUO;u<JS|4y!u|Ly_1(2KYd?*93H_|M$J%q0ktdv@+FbJ9dJ2-
zLqx6h<e0{99how>9Av&(X#1#@wZ1(R*m)d-tVaU1b~<wP?V&Yq+n&?Qz~fa3MY9p{
z;@G?kr8)G+?<ouBOStWWr9(Dt3lFaJD_Es?=a3s=6PlL6>vcswy?d;<GICm(G%<A}
zHm@JGbB6q&aB;S2BERNKAQP~!<@c)^P(j{F{ivvPY5p&MPAi55`ui_oZyW#I{asyK
z%F|1y%ej<rg;QPKv5Pyq*}hXp=PPQ1lzaCSq;ZvVo$~%<Euzk0-DP28e%>x1M8VX;
zXleAH)`A}RY|dMKJWs0FNc3_jZK7Ob;!ffhgQS-Qp-sJ6$p@V}9)?=la~WGxK~e}{
z0M1sg>Y2mo{Jq$2Q{F2Obpc~Saui7})z*&M+EehR+0Lwg9S|dBOq$;M+`%Jw$NK7j
z^8)ItW$ZkK7T#TYK9)U_J<-;FoK&A-n76G-AEmaE#Q|oQjAFF`HB5$mfvEujsceS0
ze@Q|D@J9Z9TkF#L#;6)E7%wMNU^;1AGc&sKZ~5qCf#H_x2EgLng)Ls1S@b1MCCw$7
z)v?vDJEHfZyv|SBce7fvPVZkj48lzpN|jjKz5Oh{qY}@CsonQISy%-Ted%6rA9IBr
ztniNKMAcc1(%l}OVmZHmsLNm+A)%*w*hD6SNn-UZbxMN-d;S`XwRygl>PXsY$EUeO
zdb&30lp7q{l#bMHlA$>A%W=s=GZugO^|UjY479n^eH^?$r`^FRkb=JY#!Mt}`G?;A
z;`#S+A*TLV&vHQe{Hm+KL->3!U0?D=2#S3eB}Vh7;<@oX=afQf<TG|h>oZO_CGPSk
z5>&n^GJlvSTL0rKRiERnR5(8t{~iR10U5}q7P=%t5*=7o;wQ(}b@C6$rESN3`)z5G
zGuDN6=g;!WR3o%aICK_J`|lyINRsC#ejOY7Z9*2|rXGP$v&~-4=`E@3B3RBQ4TE2C
z&qWmA<ygC5FntKw$gpTq48K!^%jrQ_kF$2PUZ{#PHnk>u(QvqGI3H$T$i_*n9CI)A
z%5I<{PdKJCsTlW--~%`BH3!nUR!)7=_1n5b{KF+q=cRP|xa}ddA=SJ|{&Bra&eNGD
zxPSgkN$8jRWHv3XnhLZ@QnUq#tJHk@YWiOGS99$*Eb2y=_u*);G?!IQEw2=faC3cG
zVL7QzKLAHP*H=(cz4n+e>gPPM#y}ewD^#hS6sM%pBRV|=*Pg_c7}lU(pg+rcm{DXp
zYA6lSzD1U>iI8m<rci^PeU2Pyrg4lWFOBHm$|PfCv@*eC4&gi>!O;2n2)ieT?Nkpd
zwCZ<@=vWrZ&QRf<^1kfzS8`#gQRdo=bO51<j?Mv`2dJNWiZQPd)Np>~4S=@gjMnhE
ze;6q@UZ|BrVYd#nOtN#>Z<93&b-|FZXiXNJB-}^ekDt#kOxcFoF<)y~O6u98G)Wbn
zO{7qA2aQx>TPeHC$njwpWwI+`Czmcr?6mV^|NQo(rgVWv*quio@pN-xU?^bgT;m>@
z9>~<#%}pS}f#jvarejlp);#%#&Gw5`O+tFE`6s@t>`g8E5V~Tyd3wX4BO$&+H7oDb
zg>WgQC&44X3?@dE#tWay7vxiy%34e}?Q8eF9^Vjf><5i#7Y)Gk(hWJiZ9SexuPB2Z
zX$8w7G7_soQIo#@vmrQe&RX#jFhw&c5$+%Q8kt$$&E%hM56Z#2Ih%^rq6wmSgs<Q#
z;;b>fA*4?u&RS>R)d0SSd4~0koO8scQg#etqmiM|Zvw};Ut6?d&{k#DcF;6zEiDUq
z!pJpt&@KI_POKwCIdj|s9+kZZlIiy2#llf{^8!s_c|ks7xr?{^F1{~M6$DqIWWjC2
z^Ozj<twR16&zC+giI5B-q2T*ix>d}#Wt(j(2j7c8ow622?o2+Et`02CO64BhL~#Q5
zl1(>RH)HI-Q5v*5Q@DUjMm<}P;rJ~UqC^So)h6|jEU{7Qa~VlMfvLPI=b_0=)+~;z
z1>QJqp34yH{zkeleRcosxcGjM$Ru%ay*NA>*j2P7Bo%4Oa!H%DxJ2vn3vwl!v`zuP
zh;i&ekU|@{4AV&xVVrgYx5Y7=HgodF>_Dozc~7Y=N&F(QjSNG*Lb$rLu$7WJl7}RM
zD!<lb7aC4?ff&n*h)s1tAe}9;=U3ceX2QjuaAY?xXu{!wHC_{wt8P(vk%^%=4!ttB
z@QihpCfR?Jd6?H$IsoU?gtdT^+L>g*+Z-Y`%B<u*1gu8j5P348-3Lt-+J4fyD7wAp
z8~dg1R1|rSj`~sFh;?`N3^`N;1LP4v^Nwzdm+wyD$g6I&89OO&(OO3pABz!nvDrVh
zo{s%GUvx8S2>Pd+V@BDpPdYY#>Z8ef<0Ne9=(Ig?+UX+9-I#bo<VTrTu%}4}zDo^h
zxY^$3S${f5e(Z2bdw1X#-mx1qj-;D5ojD1u>i7Wx*0-#&_q(nLBBsrjuIH|h5WFZn
zGE9h(Go!HVGF@GQoQW*txH_82?$`M{VU&FuzZ+k&LA;NZMjV@Jsm?Yd-dtHsnK_1D
z%^}ayW#S@5H@a5`2_uW*YO^#Si`rgoif#UlG^-nDvdXbvIL}rnHz1+P<%|+AWB>fE
zV((?^7|Wq|Ft+~miflxRGPu71#bN(pu6huUIWgy(%|AS{pXBwk@ML|@$sB|VJG-fF
z3?TI{#(kwH6zlb~3CAD~dsiP+wx9y*Pr_&oX=Ie!%IueIx^SH7Mg-$uEhU%Bqj(V{
zgYx<kxszBO<<s+0^DR9`T3mts?OGgl3Ev2d-TJ#tw?A(7*svTG*V#V0Ox@$?@w}30
zFiO`*CRuApUb!yPHrVc>NQ&X0#;y^s;C<YWbBN_rTce~<jOSFL={9W&vFyrKN{-%D
z(GPLsMly%=UI4LvghLU$$R@mjT8Mt>=-ftR)?ev5XDmR|N)lNaUSUg6NeL-XxnPwK
zPxx-U(#1&yE~{pOo{H^pj8K{9ej@!7JI^jAOexO={d!~3+a~6ZJ86qrBNu3WZ%HN2
zkeKM09@5i{I#HS+N*8S;2W3VLL<btA+?WlB>30O`JMoQbs_{|F#PmR(`<=ek?Vry6
z=@v4bE}EW~FJ_z(35U<wm)=b;vbcqxBL%Lw@a6L;er)S+h`#{hbf9P0l^CkE!_lVo
ztnOrv_sya5Rj=~O|BuC?f3Wr~XJm^-|MB~~%bnBn%bm`x`yt?X&)QL2cO~D(ED&6=
ze`Pzi%rvhTEw96}C{+DkuUJO$@(g)(I2dDtiT`}P->3Ujm;U;p|AOT_a>^g_UAtGY
z)yMyl#2687obf{DdKJG(-bzB)>RdqcRrRUfJH~fdEy~OW(7gbf%kxV)0h;iH@zE}V
zwi&=YsGGpDf-lKCAb5#m#9NVLo3OjBpH$Umbf$vZG2Y3#QAmRq7Zpr<qDR8|F;*!*
zV6hz()mNJRJx=eXlK*0&sY;19^M2xZxl-J4h!No_U(JcOB3!+VXZ0RhDyhtx6y3cL
zbV^(&O;sY;=M2Rr6VmZ|K5#>W2Pb~SY!ii1c#9FJW3yuU<bO5=yF1hwY$Inxkm%cQ
zjg|h*7Y@B+aco&BzWtwkb%#Mq)ohwpaXvV7adAP<UNh4T&F%Z;lkIM&3EeBU^$ABp
zxrqs?wr(0~ri!;kD`#u?g_rmqp^y1dQPpaPhW#o9@wL~)SIzk2%7a6ZIhiu`oyDfz
zf5Q{(MXV>@jMIC(OP)vDB?b4aj~w=O=2+#qeFt^k*CgI2Y;c*2t@=&Yil6&eF1G?@
zz^j6Q#Aws+vBurtW>sMOj?fdgC;w|2>XePbj|H2k6E;PtR^R4D_sy)faSr&bC+EGu
z9(#`wk%8|SLQgl=h39Z&uR8`$QLitZ56O=&H<6t$<OVO-$sRA)s?DAPvR(>xzOjAB
ze@pe8nB>*nVlcmRs*|#dUeh?}TbQ&CYx=KS5iW|qTYWyq{zJRNVBlk&Vc)*IH)VO<
z^3@eGrw<xC?`165DIx5CVcpu%i40C<Pn>M0QSc6o4Ip7tA2dpXd`^7}EQ3aQN*RXV
z5q@w|Iu*$I{2kWiw$!lPS*}w%^1RSM8C-_Gj1W|u(fJ)aE5=+GMwi+8;$|^?;y2MI
z$h!j1T#Nao_|xec?uRj~&Tm+-GR4U8IEODE-2NOshR`Q{{c09a%M~eJ3#6n&d_D99
zconRtnI?ULT!=F0n@m4Kdax?2cG`;vQWG5)uJk=5<Fs!X`6wtT<gHYlllU|r*c;CH
zMHZy?Q%2VifvpG$)}+(sm_FWyHYj`a6G!Vu?uMTlP=l(h_DHxrUA`vRq#Q-PmEcwN
z$HRsCQI?*71-1LWtP>SeG;HGCjMQPQ7K&pOd!;hp^u_!OVMmiiTXNV8+FZHO@RuSC
zep7+>j7G+Se-2~Opmb9T_^I)!{^etP+N^gZ0T-*+^$l)lmhxK+q)#=6c#k7Mq^#zc
z*B^~c+!s$MvSLD-JBN1s7P*1~y1EUD!)5k+^qx2=)ySxRhA|K!nt$AUA2HP3$V8Fw
z`w8vTV6!?dW(~x9#N{zvvl!Y69?QnUH*a4xvEbdZIJAKQ%az}Rj_`(nS8DIB>vl_;
zNjmbJ+z~0kDx&_KH0FfVC7k(g?%|?j?D3jmt*f0k@fJ?wl;bY#VJ7J&GvvRYY*Q)0
zH6x1!^$FiaSGM=3oD(8f;>a)>W?_s(9nh+$j#R6*l!kKW@i1W60!jPWDMRQ6y}51D
ziMZW<fnKMfe%N8q(23weiXueEx?(ZNK4exZmSGj<31l5vx`x8P?`@N<S=->t4*Ka0
z9F-m_DQFRI`AS>}+JzGI@ghE9m+=Xo0=B-1kh}dC>UM|B)Ey{6w>bVK_S8S8Cyh&`
z5B~%fJAX>fyP|y|>gaFiQgk%UqS^)gJAAM;ll~Uie$Wh8|E=KRyZRt+wTbI#eS;w?
z%^fH^ok4{`G!dntJtWv4<^8}sV>nCmy{vt}dAo}3F!K*r1l&z_5AIJIWVwSeb}sL5
zjW$W1l`Z4jM_U+8%OIZjqiya#ezp6o{qho#7KXP%@v)s6@VnS49*Q|uI1;9j+$~#?
z<vM*nc>(;Bp2%-rUc)Tfr*bc7k-h%Z%cr=VPuUIKgo|NDphA<uMBcLqonH$ft6;Oq
zHP%hqWX5t>tOo>bAX^OkpNm<q!`zDHVK(Mdk5<bIoH#NzeV$=fW_8}Y*y$I!@sXZj
zO)K|uDytGu&&ifN(x5fH?V?%i%vLLR5oiMxx~q@(idG+lx_OCzq9@L(5hm~ZWU(-l
zJW9j&hDu1%3oWtNsY+NUf{KiyXu5EAhb#;GeRCW7I4QUDhHH8c;w}@ex>NLpO^auC
zJ+vs)(?&Cik1NL&Y`&QgH2)Y}QVSpEX=-t?i%j(j$Vg9gZ1NUTPN-&8C02aVHyEXt
zOWI{f2?<Du|JmfmT43ncIKrl?@LwWoNJ1U70fQ-b7XB?DoJmk-2P^Kvs-J-I47o3$
zsbx7?^d5frD0DVLe=;Xw?BqE?D-^~moAh`+mFi3WXBknRl{_N5v%-D<7^_{%EM-Y!
zw6a+JHn9R&IQxDq9Gb|gTI?^t{TI6l$J&hh$_<}rwVkm>@SS4(M2!s*)AO{Y5Wx&O
zW($HZN{_Hg?8Sow>cGla>~iJq{`uv=FPruFQf{9Cj#+io!i-0ghu|A<apRl<ixDvy
z_Oes}sr;U}P_lqPIf{4vA2OS6=0M84PalxuQ?v@jt@xSGxy>|oY`}pTR_plGW{dfT
z^J;`Kd{xr(H@y1gDy|^<Mt4)oU=5E{k=kH!;8_bD?D!alsU^$5Mwb`p{<547{FJsf
z0607yzHsA5TkzV3qF`jQo{oXo;!i>sUkx4xxyKXyq9fYH2lYM34>N)5?RN#zUr`Zv
zkcaQ*QXRAVxIXTt-&^&@XlUM@A0WQYfAWj_c}(r^^o;m=;>@CQ>E!b|iy~(g+r)@?
zLvx#Y{0paYMc63W`E+GfW)Qk7jso+&%!g0HVbbxOb!K4fIs0R!s-647@vI#hhh@V(
zDaJANJrq$NVPnTe(K61aS>0)RPni$NEv4i<vpP>($LR@(%tcmTO&TO{se+V63%7Ey
zmb9!?7`96jFG;Q|6@h|83LaC`@hv<0XY%D2tzOv}RQN|LsY9S>H6>Q%Pn9BzkVdHq
zilkbOtD5U(sr!U4Av|vsTMs|=KBQXGh>ifJECvl@jy4)vH$j6o(-<C8EJYd_g9yC{
zdSL?JZ=uuXwbqxjM9bMF59O&|mS&-cD>9)R50oE9RxZ$yo%l}Uh>!Dc#4Il5u`;*>
ziNfKx^u09Y59QCKfBBJe0_2X3;E_}pQfehvZP)uejj_>6;ez}v<ujHPJXZEm;31}R
z+<y32lrlDXoQ0p@TsFTkbt*DkwJa?gnf%Kqda%6{gawNWBjQoAg^$7a>Wy=$nr8*H
z2IZNgBrqknnW@(3akr6EEt=5~D!Dt!wRmRHD{kV?Z$5*s>Soi_LJRm!V{LO?`N>B)
zF)(F!97pMk26Dr~r{4Q56cFikD>kwPMbkN(xK>eJVpVKM_0Qr9+x?g;b%~m!3n%{3
z$V|J~&lZ$U7bM~KL$XXUFC?f;woJ5ul@1Ve{^`P{b9GNN3N#I*J>JAuS0O_GDTE*V
zc>~wXR=bCo&OK29>?$2wA9juQm%@JvJ|KXM@k?C@-Is!DJnD3pO<k8f8{9uV3Bb*Q
z!8OmHC-nQ`wLeRhiDD3;QI0D6OKy$e5#|TcedK=7<QLfwGOFd$p*G(_4ztmy3F5JT
zgo*hmCT*M;yN4Bk8~O`G=d#JgKY^cn5VyD2g+z#<Q_T72kXJG*j}Oj=|D?h@*Hwn0
zEnt!^_aNWpLYZfOAfF(l{`)tM2L2kEL0#_RpIk{YX0XaVvtK{+APb4Zji8eB5z);7
zRnw+@;j8iuft;!YVKH(bu5j2{U<xf5JjwWtN=7AKe0{-OqmRjK=e6{Tw}AR|zPU0n
zc!n}ns^J|n#iM=v4=AWY+z-Eero9D$o)00{|Er!c1M{?ZTP`#`J1^}tLQmN?GYYI(
zR9tbwCdmR0>P`$yhxo>#yq(I|y#JZq&_AdUIh&kO<Ch4?Vo6%}^XU3ZbLfy+sHHe6
zC^dX~A7JP4Z_-SlIe^Joj*n)qPnWY>w{7m8JFwn!tpki~zRXddr;b77H0&P=yem)+
zl-(+|ru^C2zhH54KI1-h?-UzMqm~IBX)cy_l`DsueL~`u{9)3P%vu;d2^=00pG{;!
z<GCWK2tQ9n*1GYt`x|_a77p7BW%HaXTI1g$j3oKeCc<@k-tcLRbh|kJj!!v)sk1-Z
zZh0*<o#$?)kL#BsFJdMyA-e;EL<;rQCgb(ZY*y##asT&iC3okic9vHz1uPrI`WU!D
z>dZaZ(*{2a@tqHrDqr%4qHf7)B3E-xKtQnjcjZ4eb3!utqZ0k+`w-S<t~*ua)Wk9Q
zR+h8-)K>;5aG99>b*EVQ1F-5-IN_(bN6$d`(O5X0ytnSO+Wq}K8RWU>9pegT%nX62
z6ET{OW{KltPZn4e5*O?g8k}_DH+-uvG`7gE8JNLU9MatX5LZYw#N^^kTF%UHoU%=r
zZ|UEKU+nksw9G!5;CFdjVi_$M#o8JVL-9FBO!XQRA7$hjGMy=0`WIjt6l3a*+d>C*
zRlH>X8Q?j+tb27YTHbxfcF=9}<>W=^*(2Jot<QO;6Ua+sr<a_=p!Elhxk#mT+ZLaQ
zyw2&nT?hhtu!w17f$yF{(B%7FDv(J&$@y}Lu)GG{mg98PQ1;P8S(LEs{p#X_gVve;
z&UI<0YYtUE4CYd}ngynYb1>B5Gc*2xE;mvzdFTCA-BXOibB4d`KEUI&d=fq=QuvB$
znKOZ3-LY(DmOuI=ccZYwhqJ8zJG<R8GjsM^h6P0dWrQmK^S25~624yzsYN}F9IfdY
z7ImDOeW<mcD<HD2UV-22g$?)mc^geVJ4D(1n_}+XBJqA-(0>`c5Zl)%5Yo!jomH}r
z(&odO#S(5ufFX~z26-@erMy<Q7c|7~ZG@O!*UMrI4?$W!jVlQgmjd#2Y@001drgiD
zJI;#MEy2*99K4FZvW+c#9+-S8^jQqA<V~;+b;MuVyk*H%k#|Pvf%mA-mxrxS{Xdqj
zGN{eA>6R8KP~4%ohvM$8!HR1s!QE1<Xwl;C?oM%vyE_#3;_hzW-RFD%Fqvc~li|Mh
z+Oy}J-E~%s=C*o&6NF7ubD}L0RrFKJHCD<s^tRc%iI%P-&y@K@wXTOg3(IZ-L9@@#
z@(0x<d2j@;>XU%euEDFsfEemu4)ULH-E<V{Dak57a&{;7fK`J`8P9{)>ytXr?3z(<
z`zW_2Q#IROrO?q-WNr`z7Fu1oVEe8@DnWzKJq&t%__{!=Ye32)GOrQRc$(NgHVBy^
zxtsmKrzZyPU~F2;B=YcCxKqj5KAfKVktaWTx4=w(MReBu$v8;kTfqJDZqkju0dU^p
zA|~lBc8;{15Xe~QbZIM1f~%d<Letl%XEp?vNJ_~ei{vvHIJ+D*jha8FgdmHio_AP|
zJJ>jnRQ1X<GO5dZo*(2~8Ft!5CUr;}%1M6#hm?Kw6OR<!@Bp;r3T1JU)Ap)8fHHKx
zdO-dpKH5<0GY8&$tDUP9%6^i7`ip|j1~pT?H=3J>jLIx!^0X<X!1&Htp;~&4yxX`D
z5}u@3j#&LuX0DT1XG%Zk!FzZq1$%_Oqm(aarpcEDi0Tq!0|TeIWjCSfB5^kaR0?8F
zmDQfUh^W5gum#wgBDgT$x_nI6V;dN{IH+Z&+zW)2&L+j*08nu-pKtB%qGsgJ2kZ;f
zfV5a@mv{RCb>}XT%o>AkxR>nIu%8E-<B(7*V&Qhw!6f5p8I+1D{^)U`OsWnUbc(@$
zv8Us(FPT<hOg8@E|H6;|LkANE;E%dHz=bA2c4v&IU0fdi>BHuadx(K-VoFU9nT-)b
z>Sg*Vi#-1wz;=J1mnuMzcM>3^3z60_J-rdg9jST>t=&Yaxb_yKU8I@;nYag53-%Xx
zmCjFn#G+FjLqvvD5$KU5Y9*Et(BBYcf}SOxYNh%0rI({=8=G4wKm0iY7Ie~AAr;R<
zwGl62qPnsynX~F>G++|ly`^XuvodRe-$qSTu#AO0@*rdqD#b3}WDTEq9?Jx#m4T?R
z9LAMdBsh)(8=e7PAZ}JdR!lhTtUJjp(R8qx>zRz^7V*XeTt}fE@@WO$j(hGtk$a7j
z$c@5l0=NKFZDCaLmC_Ihs6HacDu8bs3YN`^`IT}p=!mgON$P>AbU&yC7#{H@t&$bL
z5vw*~k5ZeqBmxKV_wEBFXBO7V*0=pN(?!pSoH~gTN)=+m!LGI*LlE-CEQ6a>LenKj
zX*VfbSi?!<$+tKTM*l2hM)u4{qUeK3)L)L-m*e<7ss0vta=1U$BFooN5-!?BRy+f>
zPjLdzaU--%JfjQ|QbV9fyw&(g!>xf<Y8HXJg9OvAI~=q~U%Lg?Q)<J@YMaa%4Tmx3
z+}9*l4>{${oRL=c;H|nz&#kZRK36A#QbMWtsAN9s9XvsiH~!M1SZlupih^8`cg2du
z3pgdt$%ozQWs{ftEP%3>7b+Ef;2KHoBZ3gzgHJnk@`dID+|m~*2lww}sRL|zoTzV`
z)6;}hR!gEjU*l7ubk#~H-5^e{(sfvKuPn4F^hA!)=3`;+w;h`tj%PF){@E!DPZsRA
zbxoG~G3Lb{fFc&Qm=V2J@C`lJo>^*bZKYwUEvGs58@x)=rl;SMsCsdPl#Rme?O+iz
z3WON{Pr;;lxy(12IMlxWH?V<~QDUaY{9RP%L2&&nXY!ve4`&GHSS%id4qHiZ=1lPW
zNk0Uf6cUIbT<`{Yj6rN4oO@-;)5d*6YE4bbCGpL0->_d(OkW#1OCpGtSFgRVih>Tf
z-|%4Da<l4MdCr;r$KkvGPk2H@VODSJyxjg}h;Z0JwT<jsEhyJn;*fKORH2L?zf3}M
zd7?VPSIDFJfN9B*gy9a)mhg?GlEgiET<Mupzx3IJh%#sjG#>Bm#)0q_L{(tVl3&Bj
zkbl7Nx!z2BKu~ZsqDKVjo$hx)jRHgw-K~+KAKO;RmyoVBmxMIsPRz$SZ*=F!%WoSs
zMqg!ENz9XTGp*N<$$8aX!#D2}-Rf=<Z{XyQZUTT7W!UlbBqkh|yiScm=}w0tR}#EA
z=OR3)$NfSqkMw-(o<kMu(YdXaU%U54Kd^!bD{nApN4zfS)A`~RMaKOW=`s7N+`Lru
zaJqMA{VNysBmU*8)z*kb$jyaOqE3@k0O%G7TUjKHf&+Gc_8SThJ^ZN+t&LAxqYMIr
z32=Hf;ITAG1lg$i0o@wlaXCpi*GJYfQei^#2%cDqAQMz~vVNj1inL8*y5a3XtWAkW
zG5pa7n1@2o#-4x70?@KeG6f{)clzv6K*;pY!80515s;d_QIZt3Njknsq+NdR9%t8J
zuj+7+b;+0mZfhdq^a=4+RRQs@i3nTA{M*8-O-8X9Ns9o=4_l+445n9l^+z7+!}|OH
z3JC4*9wow8AIKDyyt{;DN8QV<_U+p0TtQ+<dv9pn8Z2xT$yD&{Z{9mr{tc7GNhC0>
zIkqG;A%=4tKp!%zMVrYuZ=PyL7ta{K55jvblGIg6M>)GzJ!sk+2jB90%M^Xjqu;7~
zSj#hHR;}LIr(L>=WgK&P;f5dNdN%%;j}yoO(!ONa7V0*9VUHWVpXAISpA|Z7c#YEd
zmVUfWQFS9~Wt}TB$}2i5)Z2J5cOG`}rJqb0#?Li16Zz%+Q>`SePInAb1TduU35EWK
z)pW%S)l=Ui=KSF=1$)5TV3iTPkf$B?@eAShM=oxDn>=hHX3e_*qy7Qy%w@2z5?>y=
zfV(M4K0C7&&vNV)S(|+qxgt;(-gf^FgmCcm`NeMdqvIP>B{H_Y_i7is+P{P0UFxfn
z4~Yl|*>v>Lxa`#n4goBjapJI?ie!nkV}V2B!mWNDC{M@Ke*?zOf`%(h4EIU~rMmPC
zC>&c|gEVUU;-G0EoRR1kKiK=4^EMz4SOag(ecqqN-AeH88iIo@emWG%%%QQM1Pijk
zzvhWrglG0FA2r<9jDFn2+(pBpUNQoG?Tk^%s2ojJHBV<dZuO`7G-)TTc|J`{F_UY~
zxS28|t>2DLQ!oJe$v-o!WJ*PeK40xa-dZ)KWf&$)qQHe=Fhs=p$e_GvMC<x7pORuG
zAMaNbJ5cp(iz}b(DW}Gb{W0d;J)-k4d94qfrQn5{l7gUrsv5#B6dj#41%W_BkMT{W
zlo8i>R=_6Q%(nGPQEZW7ZxUs1`T-&;xnWDVs?3w-)~5y6_++-Cr$mz$h)<?a|0?tu
zN#ve|;oksiKGoWtzL4u9fid>&v~1=Ed>RFKfUwYp^m!8Aq@}}Inc87VKUx|N6LId|
z-SPAc(SH8I_2iQ5lu3dW0{(<aJP|&-PphlV=JeKU%8>u}Ps-4(5qdt^b0-N}eLx4N
zw(@d8V+{y5Q>!w8{6Us13;gz%Q+|#7YY`+Wy;*b$62)a9H7BDcG9wgdsF_b^AATWI
z=XQ3FQ6QKy=>!YUn;WscBdhK|#j4v0he^!3okpOv?wL~cnQkLRJEX=2UrXiU=?WQV
zj(R4AeTGnJroeubQie`(p!~g|rgqZh(YcdX(&K^XS~4BxKdt^fM2zm==^~XoYNJ{)
zuXl5CiZ!}Mnhp@?T_}$1xuuoIT=WtV%oJbUg|kNQgO%-)XZ2Q6m^;Sf5!8sL;w!+Y
zs3g(*+qaG~hTA@%a<V{a*2U~^P_O61mPT>uEFYgEcy(^getG){+m=ONzJU7h<Y5-z
z{cYcjN{NU1h9$}QQs7H+Cu_!0?iU2nPQ5$>Cg9}A&^7^g&(QU1JIy3a1Ov3<Li0qN
zPU!A?+(4P}g^x-f?Ykf3%gxgh(yy5qt^^L>0R+fY>z!!TDx70Z`Vq&TChgO!ddXNa
z+HuNsn2J>X=!fgqsA?xeqMHkcTdwKl43>otpq{&L_mwAD3AH>KUx6);>7mb7BRr~G
zqsv84x1BZ<bQ(dzX0*TMDVw@J#IG5HZs~!5V&@s(K54)&V3dcPF6pZBY=skEu3oAg
zZ*G<IVTP8k3naR)?aZ#za&!TEPdqTB@;l$gmO#_Sm0nNxBuZ;@b*;<48h5%U{~CGz
zdJ~U+8h{TPF1>MZG)>n&C6JGfr)!_Pe@D3Cw0ipVi7Lk8_NdK-{~RgZJYLh%JKd{g
zR6)Mt_7z#~_fyxAH<-Ukma?VK**;oLk|9Dsf>_&N))RiN>@zfil9ix<an<sfseF${
zxAT$VJM$(!oXA83K+$T>U#%Ify8lSD^v2QMfl**y9T+N<J#7kfnUt&FqxsmP^6ZlA
zFs|&PScRo;`iW<}`B*p$tK6~VEOegjwU`!LNz*Eg<he~wh?rRuVH#FgmW~&d`msod
z?q{&^2|BvidZTm{dIlhP2s!+ZwC=|YR<U+^T()%ny>MXfSRxfy&{9)BsFE+=S=U%Q
zLk7?eY8d&5Dl!E~yhPJI98}zdjCtttco$c>Kgkq-#$b<E)9n&{7nO)BkdOsW4q}E<
zqtk#!JEJUDDb1D;4DwetR_YjqTpW{&4N1fioFCq$yvtlrfmvdSQaQUhpy7XpY5#UZ
zl>o`AHEf-xl;vd47pU`y&=FF_lo~3;DR*qV1vEM<I_wIDGZnxZ>!29TPEWc`o@9VV
z5r0Non&?{EsF;JMiED+>>6krKn`#F73RxW8OvcTyfFK2v!zri4m`g^{NLYxKsqiU_
za3fg+igP^+K~fA5I?FWkPIg!`SU`n!eM<Gpd9G6FzPv${0N<2P{AI`T77cOw=F6}w
zgq#&oEmh)CsaAm$TZNeQXTyN@^vK{G&zA?MFy$e)PMwYzg8M2oF++qPiTC~`t>ZN7
z%H*s-*;S$3&uVFn>J2t`NjleukB-&?@-8_ML++i(l3%XBn$^qwwaf2GJBPN`wZ{u6
zd;eW&p+1G(ViGB)MV2zGY(g6o`qf{d3W1its#d)PuOy<28xk*o>qSYqdWY42uojA2
zdNdKN31G&IeAo=_POb}AQxsj(13hwB6ZdGN`#HDfYj@-r;)#bUb?v~)fn+C!<OL{?
z6hvNVtZ5vAlvua%@qJ+Pe6`4GnQE;mtN*B)V~TA{1i1}xC1=SxjWoT^y1Gf@vIK;t
z4?_^F;wCb*e=_Xq0~Pjrj_%Sts^-?8Q;5YOFyYwnft6Kxq3G~9RRTATEs2EOcC#Se
z;SslSmAXiyVW8^e092%a6K>gWBEk!K#-nEOZ!!%fEWjl=t0ZtaW-0T5(F!t%_<gJy
zCd9m=>o%nAxwF-PNN3=yMEgJ5y~=+og+&(euRn`orF5Ie$8?fwkBBs*s+r@>epcle
zLz!R@HKD?4{W(Ku`3c#_G^@Qk7_T$~@DICQ;Q2%MunLh>5pt+HBaQOVdn~|nXv#Y5
zwMIx03hwxoQwL|uT?~@katl_d9$b8auu(OPNEM@sb{*dfgGgy%fg%W5+CN7O!5(0~
z=uEdE<UndR{T*VoMc3qn3muQ*F1<xIN?z{{m`b5j;9Xlab((M^OQu7|W=!?nK2viG
z>D5b~&gZ*q#Dp6rw_DIsF$7xMRSe_*(z1%Cq$l!sMmg`*Y~0c<FnM7bAq|FU&U1@+
z#2`%J245)iiT-48?PMLAuXa^>I~wCAzmHLn9!<IqPsW-TPB|P|CNiyqQNpBCNQp^7
zHiIF$*cZ1d6Ylip+@;8=u;=^Fo{j`J0VtAcScP=@eJw%Yy9a02fSw-KAqk5}mSYzA
zdKO6yo#TNa9(+n=p<txXRQ?tp^06ppXk~PfV{HIZ0b5_=f)TdB-eHsw4*J8Z<wp;N
zFg@)IpGlPUUqT%D<RC!^ku)*bYSqf-!Wo*Lc~W-tsJmKwFGriv|A>y01h#tOkgx~<
zA!DXT?S<`4?L8*^J}qH*9K;0|svR3`g+0sz_r)xWB(79_=4a!$Gsdbsib;&Bi%D}#
z90MfU53~eJ`T`krR@{5?atb9BUA4lBnB$9v=*1hZsqW*{s*74ur~v02W-Q^q6V=tj
z8uGi^pYlT<ANkC=xhIX73^q{P!djTs+L0GjPUv71Lriz83W@kXSl7rnr9~Ih0rz`^
znJCjO&6rJcp*3?9cVVB&Qbw79ESk6$T{>pLI~DfET|Oa3b2uSC9>Zd-zBo2_VK(F~
zx{+Kg_;1}mH@Dfw-mecn@}T=fy(O<cR01hr_fR>2vHObDa{nA(g26u^GI<~ey${oD
zmDZP^A#yt6&{A>C!iG6BnF3Qena!6OT-g{*WJ+I%1kthZE)q4`5^L3$!;HfT9YBdR
zK%YEBuJOcsJIywLL*y9X-u`+_KOf5@nIA$YFQXd&Oa;=}_oR0rhZPGc`z8ObJ8Hfn
zz=9CJfXLenP%M(x$%x7edjQ6arIQ@;5uWw{XHlF~IE05+y*JWu^><xg@jfBgqP_`O
z-yo5P-F~yIx<wo+>~)LDp8uA;_pRhO1YN47p-nOeyWZj~^_M`uPV=x*#jo{#MC$Pk
z=GH5Q(_ePyCyO*-tDRxVwwogYFV}6FL@t-RaJ=#CTGP_GUDsAI&Rqwm!e9%TA>PEp
za9q^@fpO-s>ec;?B>4VAlL~9@`_=8#k$5DYg3kD38n=Ga;uL~0{^}0H6YZUr!fG`|
z2Y&qR%{-Zhyly2!!VRBO8@*f%<derQ;xZQny<dedk-nx0b`D>|S$B_A>%kdY6fC&Z
zsOU-|mM<`C7w^$c##x^gIwdeY=gFnt8h&yOHMP%Rd>vI@u#rN>9dXkydkIoIu5n>x
zKlFqjPy0K%vj%|OM3<D;H^T$$$88;@s;~XhwsK{jt2WQ5ey)CyY6a#t$r8#{%a>cq
zsob8%3%h9U-Sd%R=|#W-De|dhWbsV;XpHZ-X?RTC$gt`wVm(7xu+(@NwB<~l$;m5I
z;T2`}y|5J02f6PpT+iMGCqgJ4eP`p^1Rk0CEn-pi_*5VD4xh;Z2KjG_dO?~Qug2Yn
zxFe$^3e|6n+ifzVULgQWw=MOm+p_kOscZ~xO5+_CJAtN^KH+fm_4_Nr2JCpa$Cj@2
zNv~kPF^sRowKkLu1r<s~!ShUcktHXI=6(ywtY!6AnAGW5+*G$hdf#2k8o&?cYzvn`
z+3PFS+xJY>_!cWVHG;6KTzx@i@wt9S`u63SYOPx=8od~X`%&1Cza`EMsl-P@(tOGx
z=Q}QTy>~kb#0-|VIe22{=lU=Wv;RPbESR<k1LNbN56iJ*+hq^{tAW}u7^xpL4OtvM
z66k|5k7<Girtyv*oGH|I%js#~qeA~7Hxos?c7XIFx0^j}jI19~uE%BFeo^_t3U<Rq
zz&wszy0hqey&BVfGWLvry%=sEkrz_x9UWUx12sVg0GXhJ``4G9*ZaD!MvWdWZ^on%
zEo4R}VI46GulU4QA1@D=TUrK}gxjQk31-caV8XE?h*teo&IGY@YVO2;<r#iD2W5EO
z&%bNP<@ERJ@xJ!H3tDcfmc%SX02KjUDRZxPcB;jAEamR)L7d#pPwSCu8;{;sxSFfF
zOScW}52UYf8D85w%$_eCT|9S98sO>qqqEl6YsQyJ??;6<M00=dRBN7w>{`b(UoWg~
z?b@fx)~qL%k1ke~epS^>W>?LaK<nZ$(*3Meh&ryVTUr#VVvM{R6>SQ7K4c1y{yhin
zBpi|^HkSO0ZpyCzRiFvz6qgM#x!UR=SQW5!w?Q*ESr}HJgM0~R0lJnH*N0!V1$h2h
z<QgD{l$<&#glaMjP_$SSeE^ZCDFG%q8+E7+Ar;smcalaP(|Wik3SLJX-7G{L1e=;J
z6s$r;PuyOctP(@75Jh$68>MD3RKZRYaS%YnyR_IINy`4tt(^1YF-bRFADWR$xs0lU
z*<P*#;$PTd7MAeb?dLllK!Q%~F1zCK^l>qqIlo&TVbw1hb*R>&v|GGIIfo&+WBVmt
z5+kjQF5w^+SFmM$*aqQM-$kxxh;G0&NAuw8j_Um$p7W)U4;6U<ZHZ3VAUZbSD*-5T
zD$IX5R_Bwy?2KE8Z=Fn8;C%H}M?FE3d^593y&`(CQ1n4gU00mGl$T6U3vZ-R9E<-b
zpoPShZQ{G2qa-M=OY9$Fmq}ji00nM#X4!Obg)(%Ebz3M1M8p;;2}C)Z*aYxiZ311`
zPf8GjUhbIQi8??@f~66Vks%u=Rn!BzA4YbB#Hj@(bKX+S5MwCd7F-RaUjCNC3Ff8w
zCZ9}crpTJ<o=#?i6&|NgRvC_I^2lR2ejCa6M3qAfcl8%tI9&K(=Zyi_FXan~!mJGZ
zV3b5*(1EJpi%Z^>QM-y-m;iY|)ME=b`&w`2WcVBbjl$3@rs|lg3{@2>;xq|2yzp{E
zc>j;g+D3qVIo_jD<}+Zuz1S0oy|V~{Oc_kPPP;QON_mo_-dUsFaD3zcE%T{GQFx&*
z!7XB2IJ83~Hu{%tr(4S8wdZ5~VY6$_8Qk}C_+xYGPsd99dIz4NP0*Mo&yW=81=AF|
zbFhNdSN>jNo0s42kwTz502_taD?ryI;;?<wOrk9%X%R^71Rm+g@<a%IkFU8}Z=zhh
zJmTX^myWERwVK<+_xfSIBnS)1$RaSsgbS7k(F0gjFLCPUbke>%NAKSw)k7<Flz&?5
zCfHEqcaZv%byO=fm6KPPsnV_S?=c}8a%rZ1)A6%j5Hz=SvaoSEb+@s~-{*M$Z3)=m
zC+3p~tt|5kI+aax+?;|hKPFkSvf;Aj+^>Icy==|02ao(+s5L@~h`L9aP34Ovg>WCK
zKk|1NFJWV&e92~B1Fy!hrz*a2?~^}T>b%PI|0-}7!~ZIAS|Xjuv>+*FREpR}ax@Db
z??2=>$kxc9GltMn+srz}NHRs1ypF0ehtDC{zFz24XcQL_0aJwHNb=Ft=%+fD!0vaH
zcT2z1D?kBcc1v_9K*}_!S&Q%^hbz{&a}aaKN2diHrZXi#jEnok3<k>DH#to3dpUxH
zz*eSmaDmGHZ*V_RgHMz>#e@ZHx%jM|zjL^YcTrKxsvu?fnc&|khkfgz4f(u`7*vML
zPsQiCzV5v^dU@ENvC+FI5PC0vU&TML^2Pa7z45lj57WWLNv?UfVd{I!Q~Dvl`LkEr
z#I3mXbPuLWq3B7y&7x<r1-I^v%5U-Y2A*_bsZOZvudj!mOO+-ty0~;2UXLBmQ#zEa
z$<AN#8OMKz9qZc+`+}_#F24#@Mxs6(8J}ySwahh21r&brwyCv|q!du%Zjxnh>A0L}
zA2fXV@Kf-Y>@LvB`EX7+x=vAW*4I-+&LB`TRMo}2QWxG@#8+6%S9toE&JO|OsWuTY
zdtGNI@R#iMW9WKC+G1noNsEI_kz(Ck0%dw7=u=^3za>08lc^{#pP#0;o9$MUz_lEa
zV>=Dathx|{fmf8U+j?4V-)1OxD)E2I!KwHAkoRyVd!Af<7BMb0H$}Fv;jxPbR4-O>
zZY5Wrw!#SON2Wt6YKZmz>b$z&F8A}#J(9g|c6zn3Mezz_yc}_7cC2`E($f~p28woo
zqGfMtvm*c@6H$(<=KtEDC4LyBnR^h<BGBIipYo5mk8kcSVwX4iAxcsO3h-?`tZbP$
zHweiWA2SIRxzqxkioVC|DUXP~zBZHrWHQc(g}HDbxT&Zz{gs`?drq&@Q}09r{OF$j
zA8Sg6nWA%MR&~8Iw{vuHf=unLU3O35%%ABRwVX|r?9IN0PEtAL>t|^VPFtXg_<?cK
zr7}GxTbZ-*16Wf(Dfn)z%-OpaDjC%bKl5pUB&~p+FZU(yc@~s{ouRFe_lf+p4nyw3
ztz-EOny!~Yi5ACKKfB+rnRRo}AR9gqXZA_q`TUFI;zqX1{sVbtwW$8Xc|`~Zj5kL`
z)xSJsZt!2E6ux;~xj((oclSHa8n5z*SM3G8JQQmd^WR4{Swx1jvpeCIQX^IP&8B=6
zaCbc7ji=+J(FJFOV*CCQcDbp?i<qb8l6qx?tA|wUF{*mL5Q*%xQues=H(RphJ82Zq
z!zDoMElc|B+7oj3`0!QOH0dM2alKj#2xkki!!5r#lzO4cI#A0Ja11@VZ<>uE0Vyfx
z-&XWK#Cph?)vvV8KIc^3aIRk&Iyq@jP}7ZPygjM3HFC4w$x&3vV`STbVgyz%VP+<;
zqHW|{HYxSDAQ(-q8uV-<RUD25AH&k={-~G*@Q*Pv1N>fpVAEk$@s8jVT^}1thISgH
zb;YE7CO5?;_-|aiRN{A#bY~TN=5M+Je&l5OZF>eRaU`aSV|%CELCp-HU$3}B4b<>!
z^nKm2MsBxd=`b48a@HQNJkI5BN~Mxdhy1P)lC4R!>LEO`7FV7j72=@X^#xone5g@#
zuNv^x(19hc(I4aB+-}2iiLt>4Q@bVL-#Qf%?wl!#&ieHexpc{fv#^N8s61~Zc5;d<
z@YA_aa4o5ac<oxo+{rIpKE@Qi2@dEmNMsuXi;2Sz(s(tAj|v8XP6eaV)>r4R9$TiD
zsnn$X<Y8F?L|2L<Xx7*y6ByABCF!HOIyi^Sv0IJ(Vg$KgtV)awx3NBDss&Kai2;}x
z0C-{u8K7r)r(Ns_<+rd^7XbB2#n;5lNmETbamUd5T;mN=02h7d$gxWM<eA>PEVngU
z9Q}YBD4PnI+8Q(`#|cT&Z;|C*U7vaQ=S%4090I&joOz^nSjCUJ;yh9$s!W&G_uOaG
zT+^$(Kt$^udBy_9h_2iV*u@7J@!JVLi2*(xo0z^tmLoj$oChB`RW(Oq@(&0`CopTC
z9QYKa^FP(Za&Trd=znUNU>T_lQEDG7+Mxb+aPYHx4b7}-T{WFY`%GWTHW;b)Ey4;5
zp4B04!V2w{QTQlG@4HKY_qnh~WTy8iruXLSRVnr`ul4Q;c@;WKvs&&nVWlJIhbWa|
zLukHi+ZJ2%w^O5iG%;Jf<*c<v{wQl`on&!JGc%-AWwfuH=D6=Ti)xrlTYy)gIELRI
zaIZFAtkQEc+e|GV#L&3JmL(V&F3{Zj^4~}keS4R~LWy&mv$Ds26!et)dXp;fn7sK^
z*Zw?=zw_Km`HwhO`hT0E2a>(j#9t3HzZpmnS$I{xXbx(|=<{##)A_CRrQq<H7H$nN
z;z@>62E8%WLAqs0>l!pa!0MRv^U2DX=;8PRZiY>`@bJRykF`=)rp4yxg^F|TBL!xU
zZ*=9r;x%E^^VlR&%;>#1iDHN1JP>un2spjO8C921Ys%G-Ie6CgO~ja5ZoP%ds5`c_
zWxdkk@E%#jp1;uTursbm?|Bg~?@)d7FEn2|)6!{L#XnkK*pVsWMI}l&z@O^*-tqbQ
zkSWsr=7OYEPJcwF2344_Aya<$k}+Gy>PLjcOp)9nM3;XB2ErQ$Z(DM6Xqau;G5<c!
z|3-^ysVjvY(K3bEt7s<zs3QdMtz=YTSk8^=`B&zt1j<-_h<+?Nhwl-{&vN~LV42w%
z+kG!wovWuCylI%cM9jfo;$X>p1AOQzarFT+KEJ8qL0oSb7<|s7mYgeM0A~Im6^-iE
zr0}W5A01xDj06gn#-HkCFO({-!xCWl?$Gg2=}wg)tYh_k(156;`cXTp>ye?3R9m*D
zgT0hesfY7mU)GQlpv$rkCPN#3s{6EUzC>Xf8JG%%c8O5{<XBYwzJygCA5pB=dr>4P
z_8q0HlYEr3y)i~G?+x`bW6dm|oMD0((CZK!9lgg#$^1At`{mf3$aqfP7i2x6yy#v6
zs56Bhf34treusV<C`69Yg-@-j$?7jVRz!vlcolo4p(n;LY+oioSt2|OJ$@_`e6Ymi
z{vUFMH22|kZdv_9HHhPMqzj;Q<>*}`*9~GnDY7QM`*gr_=$O3Z=vb1$rf1cmbx9bQ
ztV#cfkj_jdyLeQqycHj-rkm&bw8A7?Qsl-9OOX7VccAMCT+go2MoL}#@tv*yqVe`3
zs+Ta?*DE>=$E^$0_~N(qRvW*$l+m#QSVxaZp2woRxI0eY7pZOBiqF~}p-Uqka(~>T
z9{sbtq8}}W5E4%mFm;SbmCw;Sb|$h-Zak-hS?KR2|0`WE62`h;qWH+}`6SBLo#*>2
zzt(wST+ZC;S0)?$7{^whSbm;-J%k^J3-|?8!K&7CUDaV2la`QXn){s4W34Tq!N;e}
zE|A=>LdmLGdR^LR#w;dpxusS#dv9uSU%6z<9!mNOPWhMN2LGqZWXcfjaNarS$D`@o
zC=0vCoE}wyEu_S~YCY3K(-pjCe@pTcPK5>bSO8eCB-V`g>xOIFSbN=*zz6-{`{h`6
z{Y<9a><`{oeQ-p>RHyR<+7CVT_O%n?V)cHVp243$ux4PV2)t64>u!L8RQgqRcCDFV
z*rp@)#!mn1?ty9S*VmD0<gTCI&pXsHY8zTK?H5x78mV8rzMa!-w**b4d`d-m5S2)y
zUu~)SK@N8rPf-pmm39%CtSiQWrX>}#sWPo=(SSjG-9Dn|Rcg$tV=G^zoIWq<Jd-!%
zZPl11ApT9VYxN8;QdOsSOH>)l=SOb*-INYe5e%xiyk^bzaLNsyN&&CtPJVQ>qLqsm
zY-Z`5)92%7+SC9~5-i*5n&F@2hBhQI;Q>JmtVU+&?x<l@9Gfk|71$Y)1e)OL`QJU!
ziGqV`<OGD!eN&*Q;`7$;?Vxp!(k+QEn+`dg2&S#$EXOS!X}1S5ojjf0hS2%l^qszF
zkc(F#^hbInXB#i5d;y_8*#+1Q&f`_&Btx!!rEf^v(zU(Xa2`fqaAqG4xT7U2ZrX=g
z76zx97f@!0p59^+S7Pbsn2-G>z*(H6w|ZInmp33&c^u$tA%qBJvO-JzF5@IFZGx9H
zw_7)&T#2%vdA1;GM+9W~{dGb~cv-;Y70-JLr^1<qXXnuR>Io1QxAIorJTg?XbU2Io
z82a5Yyp}hh@8>jtz=PKe%=X|q)v3lRpHix?@(;4Y9@JGe=kQw0CeWu<#^9}a!GMpE
zq}qrSLGyV7VIY^lAP*_}1{YsJF{+9XO+DJbar=3n-ua|qVjq?73+1Gc7&dwzD_af=
zz<>tL!dN`1`d5XayG?BoPN~T#=1w`)E|Q0jQ*L2TCA}rizDAF?HO(9(417ki=Mg)X
z$QPR?y+B+0?gzcLXmk8a_164BsNMZV@Qr>_@`@&^r<(o7XsVvaAr07qUR5&V^$65<
zcfHH|_=H&_r@lqPA5R6IUp2qnU2E)6YKLaHcsbh0!`8bz+&xDLzt9SAY%`~CB)(3W
zoh&Ax`!3|uhmVfkvFBs!mNM=nSlwD1HSlJ&PJb+=%qLIQF8g~cPN@6EnQIXnOk$B!
z?UVeDL>X+sWyiUHq)JD~ke*VYCiuH)z*)ZSDjbg$dGH@DT~-O-4?tq}-e-`bE!5^=
z9UT!Pxb%rT)OQ~k`yS+d9qHXMb36O{>IQtHm<ut>?XC+weA-i5-P~r*FuA`P5xfPQ
zVKjGF8+(GFf6@XX309DDhhPNw#Ngej^y86i(KXw3@J{#+(kDM$VXIX`r}=CG)cFf{
ze|mD6Sb2gUSvaUa)rS;WvOWSU%l_OSJn`Z}P3XrqKmB6p&Ps#2Jzrre$HdTwn+Wj2
zZ7GZAsrYiZ`E*Htc5sZdcDef607<2p5sR=&RRGSv=@48F6}g$N-jXF|A;@iR?5#~6
zQNXpaR#`kCj&*<F=H=AgywW2U4hxR)=TQLd5;060;P)l#{23AugwvMQjiHB!$Xl&b
z=4ZJE1?`I3TuLK}g6#N<Ip2#1Dodf#SbR^V!ZXfWHIHgo*q=u0Dr-^OpXB-ys5}B(
zC@f!wVqJiaO1q^TDwC$Tem1INm63$dJbG0ooj{`WuM0HsvjmV5&QIZ}{V2g!!oU61
z$<9YC6tTSnSdOEL3^M=H+Kv6ikB{~}h;?J~{ydL@YAGphd!ySUEs~AEva6_C9pc(|
ze3lMs22b*}5dRcmI|P8GVADBYYUd+I_u;%0YOri4U}GJPXyezB!Y5+($gr&)bGA<w
zo$5(&%VUYcPXl=cgsun^1T+#Mi)-;nMPmgpV*tG4gRnuj_j^^Iq$v~7EmCNs=9__J
zPC(@zBD1K(Xz4d7jLuj5AUnewVWz>mcHd3ABh0fa^ns8M@Ve%8Hoc-^2BXKQ_A=LS
zdBh&C|7|O$=A)2lUPgK$Qs7h3MB)I6F6LV^R~xta+F)nMd?Y0yEayj1?qSIkrRM(p
zjddiJj7n^4Vjq40Y3e&J$V{YPhSyI8gDiSS+n+9L>d;tm*0jKw3O=389zEwxUM}h9
zK_|5)#4fQz82WG#zgbVUCSQr%0RJE||IGB1Y=Z@l$3CYD7oDd~mnQS{75=)}wDLJ#
z%}feA;xhk7x@>9FX4<h)ho@p*ulqH(_<&7SwE`sk&0Q6ENUGX_r2gFz=zyI%hXt}}
z8e3k68|8+o?|KOzUo3Del_@sZyNu;Z0sE&wF3zgq^gY-@hhGqWWj*6~Y2j#Mv9Y|X
zj=`@`U(eL4PSU7Uj_^|#SwY=&z8)jdUT~3$B(zl8dn=m`C3ss)tsunp_A>%upz(%l
z`nbnEQGyMdcbQ^UikWG)SauqSk+Glfc5-!Bt74s{_45v%*Rf<odUAf%g2}`+;!~K<
z^&>fuk9S9)p|`>!|M?|R|KBf}v~CokX4S>9Q9et5T048UIdfU03{wGOLz7XJ!H=el
zR<VBX$@Rpf>CT@9QeZ!gA57+=UUJ{6-dee^QIL{gjEpl$hxlMOU~vgs7|Z9V<XpYL
z-@K*ML3O)4fl0AS{u4r?n=Z7p0+T?lOn6bzZAz<38z+FLDn-f0@&Tb5*)Q2KL(PiG
z?x<4Wi)o|2Y4b|qVbGnj1ZY>qo_JRG%ZTzo6cKgaX$g#KIX*1LYLT@!GlS~tOg)vl
zwp;tWO%N5n8~;xF5p-!JriHP)gAE0le1fpatAKB00XLA`-e0zEeWM>San5BzN0oV}
zIPv0fktV>PNsa8MQSGdeVa)=mVKV$IiFye3IxntliTRD^P6;)M|B8y$ToDVf_@MK>
zr*Dui&1LPe6iljDqy%yJ)jX&$P)wDBU6?(fD;BlDBWcb^bd(o3)}!m5^?sqqF^tF?
zEZb>@ytjPRRwUtKNLG3wE$glR)Q;MJ9bCiJ`s0q_0Q(cK^4;6R7k;|*Wz{aGfM7-_
z!?tiYpfdx^KE;$ctZxgi!eEL~blB&sFr@yA%w5M*T@JsG)_13nVInwah#7tRkDe`^
z)5oO0H_x&NKYDu5Q47NCylF<1`R*(JvOSK(jJe)7K?%iqS|%T8Yo}6SyP2r15@PB)
z0N(~+BKx*k_bkduhe=#TtWPGx@4x?sS4C4JeKW2cF2V7aVJJUsD{R6QOFp{_^Xkgi
zgfq5k4FM_h(Ag|_gqjErrC1ug$&!Fs=mJ+jsN!5Trm^<0*A+VX5Lt?k1YtiqTV^qa
zB#8uKysbTdWv>)MP?)^D4|cq5)*tvOEqIFBgX}t3L6K5a9qb8;{%%);j54)iHxfH*
zTl>11Eko%0{2G-#P19Xo<>HHnE{avbDSu&01acl{(*!ep-m$~4ZVwr!*i%tJ{<=5A
z)e_?D22xZ6cqZwyylU_0a4JJ)a`yDz=J#14F${9LxeM%DS6s{deXjS&?{6uvv+JgT
zIx%d?a*+mz?#Q(taZ^1Iv1Zl|hvR01-W9|KMQBH5X1u`1f*xl^0Q%kt3jD|?FCI^D
zfTBW&odC^{XLUmcvQ$-R9SiK}3EXc)dfmD8R!k`{5@S81)Tppw-y>bcH2jzEzO9=J
z{eQlr;o+#bc5!WQ9TaYTfpP^B8>X`z;wC$Oc$!)!Fm0i@)F<G8wHV1i`Ir6v0(nq0
z#=fqh+xzmReZwyEQIe?JVD=M4peyUsPfP$ip0>EeOL-5R7Z1@%P;E1N-|&_c+y*na
zqpEk2g_H24LBmHHE)?bCFXAq3amU{AB>YfG)-mR;<CPOOeY)K)Mq-bDTVawt`LyPB
znRsrE)z9X3ePy`QTEtNRV)b9Y(i4<pCk;S8{@c3=6{uqgFiHlv7-1go=ZJb7*W;@x
z9{av3WW~`L*?0;w-7VtOHP_?hW)}^=D1wco{6e$tyI%q>2Tbi!;^4TcJaBjm2D|#K
z?UM80Fcv%KpPxUg<&E?RZNg*zz#Q}v#kULxCtKn&uz>9{*K>j95y0G8BXku0r$zc5
z9J_R$p)K;Pxdda1@_S%!LK+gg;`78|G(MnSd(^*>MjhZQAR!<}yHRB@yimMJ_$Hl~
zV=%-kJ}NXe*o7y(-N$z+iOp4Df4}(Tjk<>+>vEPpjn377nP~*rLG?>sX0@mpSu4Yq
zsD3hj00=|CJhnJ36pW22w}Xzb)3RG>;&s%#M}VV<-9F&B;WR=2DLa8lzpX3hcFLTe
zhT1*am$SR&wkye)VF?)Y!E4%DsLXfy7>jR&S$jaVyS-=^%Wk!KtiZ3N+@R!GeHJkC
z3%%Di<H}Z;&}iz6izs*C7t<4Q9!q6jDESQ*Fx%yRvCCWNAV?sP$9jD%eZoAjXp0_j
zR|feg5Vn5kk_wx%dSj{)Q<jpqkEG)w^7|1%4Z>iQWQO?QjYmGjbKf4&C!NnN8(W%X
z6qhDGfTV(-_0GSHGMrxa2^Zo0@bh;K+wzpGnQTu<>+Y<R?Yl^!%Lkrw0=A1`R%E^D
zF3wTP`xaak1AdyXkDq=yT<p8+zFkI~=DO>%^Nwgxls|tNw~dO(XfU7Gu{bw-efZLL
zf%kP`7mW^9o>`-4Jf4-&k3&|u*l<(B??&;p<Jdf3yRm7sZ?vqe{qqg*Iqzc^<_ifX
zTL`AD-h77xqb2(zZ7YyJ=g}-|o%)e_0R;jo$B8U1G(popyu@Scq(^YZ!XhtQoU$qR
z)jK28^Y*W+upgvnXofMcwOQQsKa&dg|C>};I{S$#Aj%E`AqnC~xLRB`W4MLdBZ+QR
zO)@istlP#RzvvVkP^^f^E~Jd$gu?+hl17jXfSTkR;ljjInok4b-VSrneMbdbmB2-c
z{f){)8vgCFzuHd>KE&8?_D+$A!1i?M;-Ct|-UFtXBA^${;~m6$dbw*4kHmR57vb5(
zzCW=gi)tgjf-;Bu8YRysAnI)D&`{g8tK_UNYB!!`tdlLZte_%dhgrXIZfD8+vPJaR
zak{dw+G?}(oMA)w-ph_TOqn!QrR!(UQy$1rI6_8k=%G@M88s3)nNG^`Yj{EG6*|I@
z28J+-jFVKQ`PDldo95lb9|2}0N0L@h7eps1?8W)M&h42350-3@e+MQBE(!jv#$Pab
zbXRBGEvjnei3}4SzDqF-`>Ql`%>_k1tXZgr#Xo@hlxZ85#i3(<O>^^wC+pYAdk__z
z)j@_go>&w&niA?7DGdS|`6m&aY@EF}{%~Dl1N34VHO>U=A|dD`0|!MMi{b{9;hO*&
zLx)4YRKqQzxLhcU9)Kj7vHz0TAP;w|t%yMAMG{M3xpL@`Ae8fAwd~%YRRsLHVxJw*
zgoLCC0Eww&r&tjO6o+OuS?wOKQ5gEiY&foj7rxbpZlpyo=-H?4Bfm>N(Yqv#1j2OY
zCgewQ*)$d+e?ZS7qIQYbwkqG}crbdEU_Sj^vICmC+(H8MvLdxu8c=!qYTHEo7eGqR
z+Kr_GedkElq%+xIH&lbz3(J6_(O!{U9`#KL)e1v@-!I*M$j9zvp-}ikTfg{k9)~N(
z|2Oj)_(t+3IO3SLVhXReb+QEWXct}fCab2=lL-9eQ!j%SaP*eenY@I)v>WmqMOpSf
z9-~-WoQc`MJZ6Jm*mx3xZ3sPfwt((69-%M9rK8U0vK}xB(j*CJzS!DTo1y~`Ca-c$
z^OSNP^Il6|*0P@@YT)R$_4I`r?K7EI+KJtl9y{t+qOIM2-H=Ei2+^TDpIj@RDO0L}
z@D_ECVErPSKrZAnpzzAx;3qcPi_oXMd#;764!^-3L?H!q1Z9zw;iMb91?KmEHcvZ#
zR@UhER@!<8-jCdQ8S}LZ=ueG3KQ=Uwl_2DXq%UD17!!SbcGRr`g~x6R%UzBDCT{pR
zE4Kut@y}&D4tj?ZkFBZm0-Tzr_ah7qOm-Ln$>Weh-u0=aPj@bHmq_GMn9FHEeHb4e
zPt)q$mG#m1#kU)Q`IKzihE3CIUdy7YH3P0OuGDP@w^V*qgHHWYt6r9fhDv#8F+Ba9
zdcukZZdA^n<6R5Sf}Sgn?Fsrn{XZb!l4<Ier{iLoc*`e<3})d`>i)m^5klAhvs1#7
zx*+@r-dfZ5%24}sQ6RoD7}?r@`u((&*A1CmdmtX*OielR2vD^MYES89J+<ZoVF&@5
z#(jPI{N327(%SYocc&K-*Zi)->@C&YE6<_(pN^b<?N?Y*;_8^)bV^w|B-n)7d4&1}
z#8m456#0L)$<_31!}v2~Ge<?wMRErDM-zX#V_rN|KH3x1mfx4|Xx>Z~wzNFLFKz&`
z#+iNiBGg<dKUoi&=korxjXAf-SW%lIAk022#|{->=L|O^F5h*|jxlm>473pRm`Fu`
z%WYQU@jY-y!-Xgf6P41Liw`*KDS0xR&SweeZ~N<#zEn(Fp!5xO8{k*9&YHfs5>F2y
z^m3?EDT^89io4gIs4$NI5rgZF145xjj+0AMr^jLFAsimy@G6|0b>G#`EfrnW&sjSa
z^!(A=7jHyEBxjKiZc*JSVt?)DP{-e)lp*_%)u#IIg7pZi)TK|d>}3g-sijcf*CM8V
zqY6eQKS%zk3YM>WG`!klCa(g^#!<-pvmn$G#wz;CyO|&a+azg;{WYDwKzsgM)9md<
zXeNqBFBx86m-u%PrC@$VSX_pvy9eLXE9uy>JXj5!qaqd`Rb<WIoZsO)vNVd0shOfR
z)j>EaCOqP0@|Y(Z*QI1+7$0L<cbcR<H4u?(0SRH~0N$gBXOW>en!J%qa5oq{st7sM
zbGw;19!lm4jEb{~OtY8{3q+nyvLzDW$}YO1^XWvJ-$${y2};W-_BI?ccD@yd^5a~-
zAdYA19qHFJ-)0~2sZi;d%`r8L3O2m1NII9Zp(aP?vbBuNF*e^giw6ir?8+y!Wqdh2
zFY=DlpaN%47QMe2KCWI~dHl`VGzTWH%x6XI;|-a3LwRi*)mMhre6^Wtw#SSP%$mYO
z!_N~cR-6=@3~v5&#1?WD{K2tymMRxY364Eyce-7kaL;gS-t{9AymbDBrfcezdl5C>
z68Z6F)eI}%^f{j+Sdl$7IJ*BR{Tc2tesqB!Jgd}vO8|mR;OM(S2s#92gE72$@20cb
zYK>h;m+xQ=&D>3&O`%ej0ij;~p4P#N1b<P@XOGkZMX_1s&Zf|Ts~vBp$!6XFwQx&&
z%_wxbW<Kyod_kJs(b?Dy&72M+?0PayVQC$uG+k4MLSuqAmAA;7VXorQxXP8K$9O7G
zx4sB=AC+u~XMdBza2A_-hqEnOYA#Fm5+P8M5_l)jfFS6sNB6MZNBW7Mc!1c?iw-DJ
zJAg|`{o+doXewC9Ib~&Tkr!U`X#4f>n^tewnEMPlz4sm`T(#4WzoyVlsYOSOG3HCn
zjSfipuUN^L!7!}s_}F6)RNJ-Yn$V8*{3~pk{{Ntku*g%?cawPAU)ogM5bBX~SipML
z!uPXi52z<yf}a+r*olS#4{_QM{LaOs;1K`=Dy|8i_IFHXgT7SUeng%IWGOEXlVPJ-
z#*4)(Rz>Us54RiS1dltdNC~sN?S@%q$K188<5|Kb(MVe&7WuznTfo}W;}~|EgiD+R
zM|I$@5VvPc$gy%Y>Mmm5M9YfK=J)o_$ogMUtBD)}l>J^&sR(c^U`r)v7}zyaJhOJo
zfNpDtNxQn8(qc5gGrqW9doq3F)+TkffPH3Q5lcy9nAILqzw4W-Vc0Dl`7PO2=M~+c
zQ~Gog&h3`n)X_MF{Q79-73}L|hgKF8@P^(wBIdY@<?z*Yi};2|%i`Po!3}{FYrVy~
z_G}WqP{|gsux&DgMZr7>rj>_EW4|y)MZV53s;BH~$@=}fit7{(Uzm^GB)X!R5KPve
zl)fC~YKR+jC`)l{l=}gBTgG$H1?S|;5MWTnbUrBI(j?&mrz9fio>kCJBj^iZr_bfF
zjq{Tbf2U9CGgmiN4rvgq1-MM*iNhCTV*{V2AnJFZ>{#uYd}^a!aLhK#CQi~d(w{V<
zaW%8SR4%tedr$@`97iS2RU_cfF0KjBq#<>RJ@LhksaB_$36befyGSUWr`}oF$H2JW
zisvEJBK|gi=H4=+wQJhmo3Li)G|{U>`9ziK;d|7WL2MSZ?U8KJ(9w8+Jg#O60K%gA
z%#q4Z0}mh>Lnap&t&h&yAHOxuT1|z&t@ndj;ptE^e4-*zsx<X)?%_lpnUpXXJs;3T
zb)uCX9n5em1Us3wydA!0qh9L$p7lQajq*<ApNko*C5|O=efMqG9aVlYY-+vsnLPbb
zc6H|EI=vM73Lu|PUs}|?Pvhkk&ri$M7;T}BpK7^2L5eUs@2Uw6IvRZbJ#T&%TL-Mc
z823n!$Zu(G9n|?1YL)af_w`Y|4Z2DAy4Bin|96UYNP5JKRntBxg;BU#Y|L5S6!+8b
z#-&?@a&q+$TPvAD-T`pvZO8Be5wPqPuoCoTqCCQs&NXQB35q*hX*W-rJwKrSAPpam
zFP)~wjZlJwVHQTFCqu3uP@gNt`@pfzHA?tB^A(&l8M;efxNNy@K-gxur6bI98|0Y*
z5Paz21r1>8sh?XcTd`(2f&=_~Pogr|G|6o2in7k$F$^obsFADB-vQvn^Zmcfe8wu8
zM1vgrlhpR>zZe)N`~+}HfQ8fx(|0y$ifkrC@yO_x+!%J@elH9pMIeqgg9LO9@6hvc
z6o=`yzHw@4L&YrA`Dhy9!Jjfeow25KoCQ(Y-1aIJIX0;#AEby|XrFg4f(e>I5)N*h
zU->I$7MsawTSa`OO;8Vfr6?g*{=QZ|MiIVl3Q%1uvaHW$1u!Z^;2pH+HQ#=yCn+Yh
zMNQE=<-R+=LHUpBLeZJ@5yiyFV-@@9FsRFaAzN$cIltYPHE32Cp<26K#kc2$5CiD1
z=Y^?>zgO)pE_aYVdL=4uO-FW5I#>6!Id4(I3TSGt>$wG@w2M;`O@zJ+l$9FrKu4HL
zvahw3PT4|!ta@LVVWV<IL^KTab=0$hPXrC~KIc@!m=_R@B6P`^z$!)2^w3j-*)bU=
zL&ye&h7q!kZXuWs*{zbosJF$4C;noWePe`6FFqezcd%mk5lxo`oVdrWrsZJ0M(pt?
zEzl;xM%wV#`xF32MSxxsJyk{wUrU)84w1UCyY~blRG+9C3mGu=qz@G01xe74J}4De
zO=)*)S(qV+3J2Q*-t%tbrPEk;8{6w8wR9rRext_E*_Q4^pEQd38)?BM!m@c_jAD-F
zOn;#zuS{J(u46g_V3rAK(AD244Hlx<(kc~#XikbqRF&+7Kw16^2b9p5?a#Hu7X_nB
zqfR09ax*tY&D!k@+rwM(AIG28)g|}MW3uo9U@gRiQ3<Fpya=bm-}-W>YH|CKA9gcA
zQiMJ~d(_RXXX?4V8?R*9if#Y;JFxc`qp-qQEsJyrG#}^LSfoVN8iJ8WE=p*K0L`2_
zc8D&DGvzV1nJ{sh-*z+$0$!U;5PTIro}g6$MT6OJn&IWZ4^sYEaCfpj50%3j6T4uu
zAQ1QX!Uac-{tu&G`U(gMe$h<$+kf}OzKgk}OQP1|lyT$d4cF`;$LtG<n_K0qT2u6(
zT8hkTNaQsnQ4zax%5FNsV^O&yLbyZ8=)oZgbT6IPLJ0D8!TH&2=`Akv;PBHZ$vQ>w
zA|c#NOYe}APKQaoKlfw{m`?)L{}HmOTqRhdh-##E;r1xN^VG<4MVV4AG-t;(;Kr3<
zwZVg{95-QoGw7!6s?l(WC57k*kr=C~V(>F$Z3dPrfxXdV@{r2O!wfxyO$!$a^{z-J
zd>^malbfdFd=p3=tE#%yn1ZZy7;xl(F<-(Vq|G`Tem)R<t%&=9x%@cH{<>2Q9!nWu
zH68fm0)fLOcJUjcS!4+-k`dpi=njads}gT&{wRj3A-Kb1GGC9`IDa}r(xxDclRjD_
zxa&0N8=>a`lzMAV&~qMbkK>U51gf@778}g{e10-adoU@OyLN2>7!ezr6bcv2j-~wc
z-9>&KPg`6eb|)Dm1q>a<{G=bn4x?A5%a@(H66J;d*U8-RpTm|i@=FW=^SJy-UWc!_
zT?^~L{HQ)vx@d1@ru|Xc`vcdufzU4;t^uA!r+LQ<%g=a2+M~<%<vU(HK3%;-?vq6l
zk)#6u{U~RSt-h=PN`+OMUzd1^UyT<T4Hp{XLvFvr$k!F%px&SCn7rJNHUQESl@8EB
zRZcD%IkY222-)ec(|vmf#$3((3`-Gzp#hB-*73|FJ=HUd`ahPwDZ0+CYx`+zr?G8Y
zjT+l_(%4pG+t{($*hyn2jcwaT|GVG&pJnWWXsos7oR_AU_a<J0tz|W=)be#l)terp
zTT8lQ6#f1f{UI$r6ZSHzOt!#}T(>waAy}=aj`u=3|EU<^pv$s#`%VMxq=HtCA3$TU
zd$CAskjW!Qhg;A3V-EJ?4L^Ul-!4KExDS+CS~63OG%K4X$a&*DSaZxMq<F*yz3kCs
zrSj3=gSUaA7cbT*nrnx_Ecs8LFN{AE0k%4WA{1d6jDyM_F52$+tQf>l%(124b35>~
zvrtZvQ#*MxHc$GY|NGD@j4q8!shl*;-DBs#WM4umCeBIsik{CVE<8d8Wcz7zMrj?y
zh{d-?T}^0po)9f9_$BmYV>GiP9ww)H(y5(&a4Bu-*2gs`+fwK{=hn!$CC)fyHcqs=
z#}Nd7!Qj{3Fc!MyT{ik(2<1wl^vd9Ap7Zw8c=LFb2Cy>*e>?=PhuuGur#9RK`wdK-
zuqF2~2YRI^Q<J8E-N<&i7ze3s!QSHZ%wc3fKj=HNsmU^hWRj=>-4#1<2-<EmZM%r9
z<YT8N@%s}8S@P4Z#Mw@xlTW^0v_@foRb%d=&R#wl+xLW6j>YIl0ltMj@2n-yo+i&S
zXJB^DmmUuG4OIj3e?vz#zRKU7&a;{g4>~yQ4XktxccLP_BrVAJSU<30@vgbs7Mgav
zkL_ytxxTE2$x~lm6spp>^^pMM_q*X8l+bEtZ^>3EpVt--f}3c)v7Lbg2%28#3^T*&
zu2ZmULM4S}Dz#)(2WiueNU-mL4f{KLCirI0ukYo@ENV=Om0u+jldD053(`o{MjbPy
z8#wiV3f-+;vN(HhppNF22ig**xw)f}PqdFYe*<UM3i-q()ctKu0D|1OYTpJ@(B8)8
zdUhRuyqJ}(jlaeStyn_E)jl2VESB{)EPx#%*8RVH$?w}kMowvi0T-Hpe$b(7tzzg;
z900qqfjI^HxsM!5C%GVxYF6!+O{c~yZy(^7V9_qif0wnYK5-ATscoTNg2y&r+yex>
z&Xr;6T54gIQe#d02df*Ai+bn!5|$M|Y}`DarfY95w*K-|F1i1(eY)Hr**!k2JO>pC
zz)ipY({LF6ADHrtO*|9Hl~wt^S1Ggu$fW$xjNnF{Q#^AjC+<XS13FI(WrEcA=OROW
zEcVbY97cqCUMS1e2TpgO-u)fUY&Y$yZ}u+mo-Ly(5WBgZ69;uefbLm3HHty5Jz-k?
z571|fBDd7mq2B{--E~h*=Xld5lK<NY6WbZ))mz^zQrP>{0@0nha|$Rg&Ne;!dh9*q
zrBrhyrF@w%$0#P*2uMMd<brEm-Y_;>Hs?G3hw~ucqu7Lkf9@;@9Zep>T{Q!#=Y7#S
z`%UF0*^Kfmdzj@bp1TR|JA+eSEBiV9+dVVf_Ss}fKQ{+~7<t=_9@j_bC)x820rRc3
z_OYJ!2P7`2468Ye#HG?$06ChBY7*D&??X!jIsBIYbJUTQwgTt%uAt!`h;a+9LIIZH
zM2%Z7s4M~oJSY5mIfFhE!i}?;Mi`DJr2@)R(y?-C4%LMZBQGb94BZ`$F}W92%;D|=
zQWE;+ymy^4DXT~Jsh+##WaaC}uHenh?VXP+Dq>1~#qfC1yH-S=1Ak(D7NPX~I(?(E
zKEB#>EFM#3(6#|xfn|y6XI|bP-3v}lJQvT7x}lX@jNvGb&n~vy{8JAJk?LhQ-%YEU
zyN?)a-D4Za!X<NN+J{XwLO;dhVG^UvSs1A0&{3j|_TPXvlv88BHpeRh7<pcFZ+hvx
z{&Q0c^RM^H06GWYZQ0<)E=Okzu`fa^U?<SgASW9<RO(cJ>`SB^cDl2H;sXE|D>q1;
z)sf*&<UZTP^EeGgr~IzL+$#M7f)|&<^Hu>Q)<K6pWG=gFJLe>!cGn#LqXA&=fb5-<
zuj3ZQ6&1^p_axbgQN|B(CZw00L&T{Tu9w~+*LJ0JkO3KA1TyZVgCrNy^5dJ2_hf;M
z_d95*r#HelrSs)SDp(20h&N}h_XEb{;?F1zu8bNi$2+8xW1hk$AdMr!65Hpdp|s7z
zGl_1gIUPhZbAq6yWox9fV!Gahw}!7%aW|oI=kr%0jfH4N6y<k=tWE#+8dr^D^~Np;
zcpE>?RrvV?*aR(9iZ3hM|CSLKdlY?3)q`Qt{`^mbGZt<4`0{Sjk>N0IVKj}uD4Dt#
z`%!e!o-@2}4c!<Zneo!NA_^eplJ_GS543ZPIl|%teMSMf1wyR5&dIVRQmd<3*51)!
z!!!p_nVT22sf$Oj1OUZxYmPt;JvWSH0rowZ-(Mo1IJ`8@*4s_o4f9;;<-del6$hhO
zx<Dm|E5@&}*u%t^9sk{kV6z5<8dqO10zR9)*N_K^lS3*nxe4NToD!w}hMd=tRTd!p
zY@JBL+J)=i7my)SP!Ii_K-i$m-hU(zclr?x#g_UN3^&HM0f7gGGD+&(ML39-A>fQI
z&6)&mL;E8}DCNn9VkKQ$n|YXsG%JL6^07y>cldPk9wqz|qfU-RQdEyCx8BJ%ajrc<
z-+o=XYZ5do@v86~GGrBaUIqA<p#k4&`QCeg)@+f^u}X2Tc$GA&ja7}0Zcs`!GIyY{
zfCNPSn}eZ3J_krHyAg@8eA-^ospjy@ES~}%6=0|@!h@bT8p9vg09b?H8M6ot`U&lz
z>E!QH;TD>z+4ve>eC+)bwI{~zQ3VIHNWO5X&Uv?N3$!Zd2->>GcC50bvNRd4GTC&~
zw?1Y$Y1T5W-__k((C=4ZUxDu1UB|i#nJ<I%9Gu(=kSne-lL;E9kfO|k@ZsBLO^}QF
zxhcZY3b^maW%e(6(eZ)sQh5xA!lhji?<`@bmY3&YL}{8tZk#8342pX%K~S@3_p#|0
zq%i#8673m;dZ&rI3x>^Qt%Jk7$&N`^<&T~3e}Eau2yG4_ESR<!^VO%Md*sGAMWy&v
zGymO)^zPRZFy+$)A=z^-dNkAx6;E+)aKHa~rCP{jkAeM8I}Nn6h-)VOS9jLq3Q2-r
z6jVpfzq~q*giL+KT3xF`<aOC&rhD)w)p<T94*8wHnX{wJ?3`Q$=E+7!<vZ`aPy^P9
zXO{ZkzcO9hH5&5BiOkjH?oVB9DK5CdZ8&%3T%k%f6Z!HF0f_zJFiDxkPFW?w{85cV
zo&oo6RXeH^!|~74YG-{1PPKbAuslW@;fRRtZ|Z!rEFo<g$z9E1lpbFKXDJy-JmuGy
zPA&Z#sz1KSQW~2QAq-Vi=#2#di#^z=<enpXg7U!8)XbG>*r)EdRjmvc0^rTZTq-tP
zd6tUC2rMuWO0>8S3!rj_B=BRHjrZ`xTWWC7MfX=_T(?G+dP?Sk4vK%2M^2$en9I|g
z+VS9A{K2~5L@&MIqh8Mdscji(^mQtc60VxvG5G}xsvoABZF*R_`uZDM(;DuthRvP6
ztQO6VI)DUIQcJ+theK)$l<7WZ<uJ%syiLz!Qla*2<q2CS6q%`KNaQwpSVdYpyLfwy
znkA7&{A0RQ`CAMIJ|JRND<lS`gXBAIwL29%xrk<=D@5UeY%m}o6}Kd!v1yc-n&%Y3
zrY0zKeaueUy`i)GM~qR0!RB)V*_rrt(l4Kj3w3`9e*+~;i2Dsvzl!nN#>~#ZQfI}9
zM?MCt65hxD4z7H$b56Suov6mA8TFoLYhxd9U$p&M5d+VyCOSHcn!Y}0V@syD*m?x|
zE%XrHS_L8t5{*Lu2K#3@n8ikQ@NagF@x#A;IYEC~H&3U`wzvPIAc8;wXth*2HTCu@
z?-Y8wtG^)8A5{M5WBEAGO|pRUgbeyOwQoG~3axg_S1HSqyj-By{%a<gCbB0I*`Iv;
zQ%OrBU3ry&-+epF`sn5H`(enjWYU$r-cHIZ>v&=Fxwufo^W5Y(@XMRbO-swk@1MR;
zvgPjmtIgE&kG9puZ9t8_(f+{h@jtWu++O7CT<PSXgcXFzzOuQkeu#1@jLvH=?rpoJ
zuT=nHmud;oa`Fk_c9ArskSb-z7tzX;?jNTv`k)!6L#3MC782=B@h1ji`(ryc{Tj8-
z6_U%}P8=tapTQ!B?Q#Dg@N4htYguH>|9%rk#NpY<d;E*#+^KTwP$M;GSIF}+O4ar%
zpMf9;0<HS_Xld(UatQbD+Sp6S?6D9n5DY3t7g>@7$tdsz!m`hec{>Kgv1x0IAMxR%
z{0A2e<W%7h4Wx_&bmZ{H1vAS5m<5C1(X4`JOPes&t<W#OHHy@~Cn+uIw>5u|e7l*w
zvw?u10NH$x>ZKwqB2WZ+$YJ#%ul;$|%@fmmx*r;9@u-BK9mC-mkTzm8#GvRQ=1Tf4
z(JIt$AouS%FChE%46~c2l2=w&*V%VQdg%<>(*ziVIDaq9YLZ;{*0$LJWaC6JR0tMj
zI5^L+iwnjzK7sbG|CW63n|%+SX{HuSp1ba@ST(3`iF^+^VpC{;Y@3&g_PTla`kjnW
z@PikXQ%1~6s4LJGNAyFaY<6{Cq%TixTnUMoPA^G!jogc*q*$*#2gO$}EDDAgm+}}M
zoN_uQD^~4u`?<x6oHQ>Lr!_dP!-b&EU?Yg|P69wzv*d0twKUL);yeb`ahY`Q*ST2X
z4tM;$`Fwd|x?RlG+X3b3lHA+3j5;z*b-83uzxQeBf9`61Rgkl=T<})@^Yj<&lNgYF
z)Chb7VN+Bh^yS7^RE-U?TWJo_mt-4b_r!eLO&|U*fRZAzHV6gA$Os2M57O^lu!JSV
zOx9$KwfvMddUJ>+&SV5lYE@)Av4Rr7fMJ{-;bk`|snWNP|L4*{l_<c#;>)T+WJ9jb
zHexwA{8w(WH3T)~N;pd5C%h>Hg?s~bf)4Xx2Z5Gw8n5Me=!>$Xm0N7mAn&x=;Rw!R
zz}mPE^p2`gq-OEHT$T}9e&eCEeOThbW||_#Ph0GCX|zh0s#cV6a0`+rFG4HFKS%C+
zPVQMxYk1VvBUzl7e8X%hJn~;pN4)JM;@NEV%NVcyEC6H$0IBrRZtc8-k_OAcVF&dB
zUHFc{<GF0jyGWT9zXCQQZz47t9{sYLwv#>GbGywYol7MkrNr7V><)yuX;Xtz#DclD
zcd&{k^8%M+B=Bgx>QesGBm-M{RvOa?JAWo=sRtRm##)KiyKzkvp+8T#PE)r=DVJ7}
zx>fUWC&E}oT0ZS`{j>$S+V1mLUSkP5WarxIcCMah(iZn8z0Auk_4aW;&v=b1kOOyl
z9W;3cq%Fm&5-ou6qh9{aZX7unB=HxyykJGQN#83}+8vQ)GFxYd;-NyBe+?EsY}k3s
z5N+~LPvceUo^fJR&V<d{N79oYDJ<23WxU>M=1U8~o(!XohE=_HV5vg^d#rWdKOfxN
zcxeY?bAy4c%Z7{^`-89iH801#ME_C6EtIP}waTY%(go+K-YQDp$QXD<YI7)5s}mos
zYQZ*+@n?kmx5hbaT3{CQ9=>qdRH~(2mN+fYz9Bk!_X}aPHdjERw?2dE>kU1;inRHy
zr+yA-&!b#+Q_u_cmR2sJu<CUuAyp&tPuwE~^;KUZg6!L+d)~%fp5jf}WHL}yL^Deu
z`hVP`gMs;@upUEF7dNn<6w~TYb(`oVN;4?9R{VZtHeH5a*1C!xh$NS`yt;o(q3Ot(
zy!W9X`-1!}vnW`2Vscyu5FRgfCtd*R3xFr={?w^u^Dmg1AL+RfhFuW}*Tebr?SY0X
zHo=xVrX$FA38xf+gRUm)+y5%U4MQ>$o`4IOmhB2$15qfY5yM>o?j^ntP(1`1C4YgH
z+;xf4zXsPmv!vHD5upS;oiqP4Op`@#)Gt+b5j207Zs`O9VsEn<CJnblQySiG*$%!w
z%lbwD=*m;?8g3UikeYqPzJxPCQW7uQ0hxNICZAS9)EZmt6Cz0g9Da}FORvH$(?i1I
zk&bv$vP(B~JiMKs=G?@RN%S|#^i8OaEq43DwU`}muGLH1PVRWcY=QPelNjMqFJr!G
zEycYnvk1<1u+xp<s;SMs<sIT&tM>QZZ>N~$!Q)-FnLGb|!JrQV2n3bl3~wYwHz9+O
z6wkKi5kSRdYCqjU;gK)hx@hfC*DyGE`4vofVd|!>9DTz3U|8A95=0@f2uE0Bi#9~_
zK}@=^o`nBdmVmfTs1SGmYcG>(1>QI=zugQ6aAY)_8B2<HZ~t<sntB&8yWi-yU->7L
z<vnuNNf*IypYY^DR3nZzc3GFGxpKGjCHI<;te9zY#+DXNf^5^hWCx(!T3H6*B_WcL
zbJ09+zVoUbbYH5y`EHUTf4}`Ze8UfCYkWKBXv41Oc;j!(+pz=gOncUztYu`ufuQ5T
zAxQeNf7hrc0r{5E@ei|hK2DM7`SMT#XLIAP;uu@)!ie}VYo$Y2>>DcUwAS?%0GJWD
zuOE6|ZF}oZ24St><b6NN7u=4%o=XQ3NaEQTZVLyl<dZ2#{pbG_GMDIla0;!o5BBJH
ziLrI^xxO-wP=eW4N;QmI`Nzeu_I{u4fi@5TOP|E_Z03AhUYeRUju{MDTU)mtXJ%8w
z{i|PlI6QsSRlcijaj``~Hk`Y0(<LE1>In34QG>I3{#jE88B+&Do*P8$vtp=_EZPDE
zA}k9KezIOv`P9D~W$D*CkL1b}Z_DJd5|rZyGMOi56F-c;ULM84e8+}to6vB0M2TEs
znFDCaiU%+}t}LMD9J<A^OGWGjyP5n_csTapd{|LltO<H0o9skivOjnD*d6N5y0{k!
zQJH4EF1GLdX-Tx{u6$<Gg}jT-fg3y~DFP9n=Ni2DMVTAe=pet8Q1COEQLDTm0)tW5
z3$Yj+-vmcavcl^JfiWID#yS&8JT*aJJh^2MbDQ*(-<P>EA}gYQEgUkiLjuS>kL5<I
z2DpZLOw-`qQ4vr>@rkHsXo_uI>9{k7EHo_tNP<GX<#+JSiz+rrQm2whwv;w+FZ4~=
zFPgK!gGC8&BQXFSqWMVoq{nE%`@Rc=glx7B@?E(4wL2$eeNeVQRXc`{vZZ*^-&_~B
zu58OVR&Q-P+2h5SuQJ@)cz%^2y!=Z2v*3dDC<SLgi+HffFUZe{IRT{v7LW#;^o*BE
zvjMFZG6y}#>6UwTfPe-vx5&5<2dQ;+ZRal#ScZc-A6PoZ223Cm2E32EWLeW!1svB}
zwl2(a;KQu{#P$O&A*z;6Q!{iRCxoQL3n1paHH;q%sgF1UW^O;gR1-k?#Zyr}ixivf
z--=xML>D!5d>*4pBl?2xuBurGm4x<}=THKRMKYWZEcLUr4!aHyxr^WR<3)a@(<!++
zO?W|my~C7l?vK{_%_586|C^1T9mRUk!G%HZszsB?t!>rTp>j*Gk+lUY?71u5zriiT
zje8$&T)}@k$3Qp}xZRWPi?!EG_MI|+Q7DQ+<LB|?4tzomL_$nLXvO)mu$>UVWpFi>
z6RE|y;d0>Sf=hB=b~yV;=su7D{Hj{`EueV8LT1j#_k;#+F^NpGI3Cz&X529k3M0eA
z&|01enj#vh8SS);3-6)wr>~54PZJ0wL9lX5VUB5K(F9^XS7@DTJb>8qIU+m#qsbv&
zq0M&jtN4?FjJU#4nFq+!TQm8z(z0d79HYb*e9{z@BG@kKB6LXID~`7L6(D8481)re
z*-U6dYe(5VEJZl$kwo$e8GM6#JBu#udFmAtz-mA8XS1G2Ewt(PrDeTC>NJY1)AwcJ
z14aUSXVZ<cL&&NTJMO;=CPgSiZ&o6bl=Bjn%DC#+FzgDDxLz4e=LL1U|G79nmK*nN
z#g4}CwY>ddwMHGiqHi4&Av6*$*uO5P-2L=X&8cF%GcYg6w7ck*7L$cIt2$$gIF#Gr
z8HTPftwMctsXcw}6tgHFcW1wD`Um-YQJz93ZL@mTv-hexbsK$dPM5{#T^^pp&JouS
zu2=Ui=I&3doSile1wq9G4=UA)WB1VD-j7`SmZ%c@EU%#x&bn1GIIL=wZ=}UhD2$Hn
zu@ohB`v^5W<Z1#KUrMU>#&9F7@?9mZuf3NK(UiY_qvAefZGI8&+oyDFm+F1tzuw<0
z{C5$D{}(h#7Oh%IA5I=KEENVhp8uoGn{ewXl!Uy-2%xo7*<k<&Cq^->A1<40fn%mE
z+3}s-+cjVd5f-8|P{#2+DP`#ekKWen-(MNyzfdxEA;X`Afd+;UW0)Y2!#658fC@5O
zD?Z$>|42k;lu`zQr67c2hH`@Y$&KlbZ~8B+ldJkYqxDYh_NZnw<v3(X(OjX$D>=#+
z2fUur%cG+k*Bx;$f?_jhVtj|srPAl<Kopn;$2K>97C{e27P^_ABCY`zW6sI8S9Q>|
zM%jOk--@)2vY=8)B*w%XZ0|<8KIOb2bE>C|;rHs$nzn3hf3Y5~w^ZHyo!<0^mP$N$
z0&O3)xgirIB=9!WHy&GU%*|~SLNfnGfC{D*4$R{Y+~3#)B{W-DxVJ#_@vVYz+-()k
zFL7)wy(P$OrNAIy0*NIZ@}Ss$mtCG%>TRg$wX-%ThsItzd|V>OMOU0xV5sS-ZRinf
z)#Z#uyWHpozj<#xefai(X^y1QWN@NCzA0=F*s&RybE-(D*hdDIl(%;MWRA8gTy6`p
zg%4m<rBx3_A9Sp7!)-wk@!S}gb%6^Nm**P&0o9NJ2H9U=Y=+&^VCs@oZ)AcH&L*><
zeBhe6J&3B0p~P-$&Sr^w6S7E|)jfXT24aqIN2HXFhme{$kOx)S-I`?(7q!-YVJHXn
z^2&4_)<9$sQ$(1viA$GE=Ie$?Q4J?2S<H?m%pkx8-4(z>$|;4LiJ(wDOI6I<@eo%3
zF2sDy7{{=LCS2P1y72`yi*h>5Ma2G@zFrj+nPSAK<Fln-#?`N=8W}pMV$$I5^Y_(J
zjP3aDqp8w6@p4Z+b(mJ=ICAW=rqw;HDu?#bt{J2lA|gD!Lnr8$*iFWsKLev<ss^pH
zVPI*QOx~*WyVxy;?IFeXsuz?88`5dSnnlBEXThVFW4b=Y!bQ9%Cq76>{Rylg!2<%c
zenuWBHq}=>@#!AV|L{2JV3W4X-tkL*#G7j3ye>di2T>On5xiElf*KJzRZ4Nrr$fbw
ze{sYV7^$$^Mg|>C&Kus67UC^e#Fkg|qxsWN=%dZViM%R}lq?nELD{?t@Pap)^Iac{
ze*yg-Rv>i|H)2#NGB*F!^ko0><xK;1bJ58xH`jN4yX{N0*OPk4jv!FLA7VJW-S_zN
zPvF#t#JD)veUFYxlH^pf?7NYGorZHRu>Brc?)gSm$wT$&Ei`IVnE1EF2rvQB=mpFr
zOE=+t$s<vLjY6cszkj*FnOO|G4Jyf&E>N}0@w!^lOL&qBRShgNC35F)IJAHY*Mw1V
z5L~}D$4HVEMXQJx$Vw)oMcl{FimEyNlul+>OhKzqCQl&DR2EZ<q>dC%ypKqvj2y{>
zffmgYR=dSMB{zCCHxsLjW9|!sClhfDMim@@*=rO%AKq~=1T8T{hEDqFmj$X?CeO&$
zw@38ISSpFE?p%fR#t)o|f7#OR_zi#s>klj*L629V*>*PzD-z6@Dclh+cTG_)0A{Fd
z4d5E0!ir6-^rpie1+3#1L&$7NG^}P@+BJ9jz{)1N>tl%-2M6~yojs?PA)?ysj!F}>
zZ%p_0GH%a7!qHd~1FTYN$e~^KyUPD%l8#tW#+sv?JO63I>m$#{dI6Y_rO?lG$bR$n
zv0Du!!O33V3aY2TvoKxz#@6~7Aj0VDkPNj*9&KQ)pktu%(55#TGD=)psYfUOLwC#F
zR`-o<cb!M9^~P(gzE_3f^G%xxzk1H0vr5?Jli(IS3B*eF;Ic<7mqEw(L`f%4_#45u
zP2e&Lv3Lg()iBlVx`pOe!XO>cO_)XUb8z;P9Y_JUs>1CsHX@HIgYffR-Z{p(8u2rX
zt4DOw{p4J9;qi8e^y2rPJ%K-zI81VfBI^~_#h;_6+V05|dEcc2)qF!MTmz8M=w6B?
zFhp}dc=!;##TE}li7>iZ(LZT-cGismw}b1H&ZQp!rT5%Y!Q0S=;k<QJ*I}L7rR2F@
zpyT`wW0yAWy*lS~kBVc&69p(GbMUiv{@(AWQR8y9-+s;>KEdn#m{?iM1)l_ReIGqz
z&9Ty#sq&ZOL;>lPkN*Yjmabrrh4_C(=)t9t=<g|H3b*Ia{AP1)h28^kWS<@{{7lsb
zdqR5NVV81O6jHC}e?M0j_?CA+`u|<r7&QRX!Rv>e{rIMVL3zQSi=TV6a^smpn3Zq1
zo?f)ZG<%2YTs&vEV2d0v$z?@X^}uJ!9)v~tl{=mx_BaxmWi^IyT!XXO6LJ&wRUnt{
zNd2VQ{yvOh*wm*z*bI+)Y-(S}k$!x@2Iqk?#JFRp9@rmx1?944=`W{-X)|p4`Wt)I
zRyt+4B$C}~BOgpndUWW4vOQl(r$gASA~P_l0cfL@=GS_b3aCrwoM3}=sKlcd=u;xz
z37)?6F&n>(L4k%Y-5}a|LuxMP!&Xn>VYNSmhLANzG;_%#t?vVuXn2HT@~7e#<!#d>
zC5;DuayK@Taa}N7&_#zopniXLFcPDV1#S~|f-FqpMR{1J;*;JhUGO*Qh?24&-sNhh
z+EeaS1Ro#7BoAJzh+uz0`p{Fffd5lms)gn$hi75kgj1~)+wmM6Kcfq0*^9uY4ZR90
zJ|Tmga{=>cT^~2(#`liN|JYMu_3;zWtvy=&M*@^@x?qw#)_5?AmSj8hP{wWJ-I5{N
z3ktdvjK!p-(#f+eYp$u5rf=n)L)4e4Dl<A21x75W;+PNCujPDtK#eydsaUa0%sMn^
zgRt-myAI~-EJ8kqmqeze_kQO((iyMP5%V71OLq}{`@R=+7Ml2D8r*8Q5-J$9CH?Pt
zHtr-El%-k8a#?{!rDL^EJ1I29rj#ngm09oo!-C^2H3s|B8cZ|yZyljI_l5B#TSqp|
zK`%B5G!|D8p&gbwTySNc0*p=89j}yd+oqP;L|Fnu@aXWeJTD{}&we!_V49gjKFwka
zW6Ze>v#`FW`nfV7+%D?h>aOw_!}bPrFM`*8H76UF)@KGSMBD9OWMo`1#F;r$Mez`h
z(`vbx<zjp`^OqiA`ofu`N4Y6uO}5`qn{Al|^h|BLV%F|5a*0Gc$|0`xeX+P+_57~J
zaBAG}yt{2NAmY?Yxb^Xm&Y<P%;^lf|+`Zy}DyCw>Cd<P^NTYCT&)7Y5;Pz1?6LAII
z{GR;R^hHm9Lzi+@;yF@;7xf`yR1|+A#na6vrvhX)F{a3Qk^lM_TeCs@Y%?~h#A-_k
z!rx%d^URwzZix`Pm9$J;ku?(2^a-D_Y}f69o74`|of#U{erwlP9!q}Lv3C48rL=n*
zGF9tN-WfT;Igf5TYX+*u!YDBV38BaAJ+E(O6XS(foPH@X*ciH}^d1kpURSkoH)}$v
z7SrZ(TJX?!XmK?FT7-cb-Asu9dr^iGS99|zf+v~np=)78c|{E%GS+^h+e%YL^B}4A
zigT{jD+D<Ezh_fNRvpukw)}zllf;UOO<J<PU*%{Jze>Gz>O7*A+gI0LG@yRR-sz7)
z&FAieAu_hXsojcR%V@fSgbeV~;d{kfzQyhI^oIk}nS&-YaF?*7fq@&k9AhVes6d(E
z7B4vm^XxygYWW^N00WU(FdGNHPMwEy-!{K7poF-ZFTpQq%jt~E`Fj115GPYImXoDW
zm|un+8Cq`Tu146VHs#R)v9M9I0{VtJ_C~w04j1?188}T`FPE=oi%=Af4e|*|gHkz_
zgygk4-bs^hVpE)>+EDEkXjHHbDSftaBnSmYaJxUY-2jLwky`qfEYQlfuG_`ep%+C*
zn1z$x=Z{S*bI6JxDAokhVw8aRsbtWz>4B9-Y)_3<>f!fV2@7(Oz}8!LAi1>&4{D$z
zxk!SwHwL`sNjn)Kt6Ybn@)8#KgD~&Q-!5y^AxbJ((r9i^fU_~BF|v`LXhmgH&LmSJ
zH`<sng%LWP)q-c;2yJypL-nMH*w4>Yv~sRg={m!n5^YjY0q2<gt9`Yv-ldPZWX54m
z*&iYYYxfcH_2Z|{rny(UBw#<CIcDM0IDEXJcMq%1O9<UMYML~&+PthF6o)|&KLBK3
z=qZ*tctQ?Ky^0kD%t<tgoCJsU;`%GP1z1onWd73;ozNk~u|J-DH!Z7f<V}1H(4$jJ
zl$hxWYh|6=*+)xDkqWw}-3w5_FoidNjezgDogy+6o7OFnhLcH`#N7SY2m0RX?V<nE
zM)LHG0PcWZeo;ia&Dwwzu{D96lW%@;wGr>KIr&I-%Gk@uMk2S5L9<zy(!LN!`xPM)
z&4;UK>E_2`$FtqfZ}CjLrtptHVLF@iGCJkDj}e+t$r4=Fe1lPfW{<G*VSu9#eD4+U
zYKCCRq~G>;HOQSPJw%Cg=U$rq&Jcer+vb<ns(OYkZl`{AF|_jrlq5&&a$pP+LR6N4
z_bGN-OnzYV#xMiNl`<M;5O}pwL^V`p)z%)Z5R+8JJ*Y%OJht;&@PZ{rgR)=)3ykjW
z;1x;)y$476tlt;iP&M7-Q>i6`ERam4`3(dl>F$3(`gV8tMYyk>b*k$aPg>7K`S|_v
z%izKte_u?|czzi6Pwa0yWib0wfwElD%}}*dcZ-mVud^*PH#~aLfbr60ivc5jSUnL^
zUa>YyLScF8>=HIM%`GKBfAzI4xv@|1?{rJgXvc-?RLc?zMhf@}+TY>f?mnNAiC|C%
zlb~7Bpi5r!Tq;wKGwASp7?qGS{s-r$2-!LTFG$e3l0oq1-H0_Kd0@8j1KrPW-MHTy
zRPPxW-Q5*^q7f&+M!%yG@{ORVb_<yrroMeNtt8Hg+hC{1>qMww-uj|F7E2=AvP!wB
z0e^2Z_04WayL7bJ%~wN2OhYxNO!jVI8KG1LeXaBL61v%jK|W<DEQxZAAbx}hvZ{)m
z=jjqI_iX~!i3eUyO;g8u#;VxVsP@SD^Bva+J84|Y=On7M)x#2Wcck$p)biJbTkhoK
zlwN87CB$fq)8>-((vy#!Mm4?j3TcnmIr>vo=OS<!Ir_KwZtyL#&faqkK1J85TaPfI
z-GksSaQ}MV&>yWe38W+iHX^)-L_qqzjQrniWj^<%d%yb1mcc&)N?MY5MiDL<>#%=6
zME2Ov2zuY$dh6?^oGKtb#QS?F&e+-17$b`jY3S2D;B4R(EMocen?_BA*%lO$fyOFd
zX7BQY%WFWY?}09>5sy&>bpjvP!pZK4eOGpo)L=}p=J3Y?a0Nz&q@&2?mvt?7AHY@B
z%pMg}Zl5nBz5D0G4py%QXAcnJ4iHjq_(e88@TF(~pw9k1E6w95h3>vXa8$rc9Zoe^
zk)@GmQ)iRE4~ER=o&|RlIIdyXnTpI9h-yVp53o+ynf1Bv20W7Bh>7WjaerU~u(7jB
zE4r$M8^jW4qJ60Zw%YYB!#z+$@*-RqL>Ck>Atl&6s@VHmQ%o3Db~hGz&-AleaOwIT
zl9x`$#iX3z^UG)~>#Iu2xMHmxPNhSgb(9@?hFv>mo#o1coXkRgC_W#4C;9NDT(X-i
zdK=wH$+g$JySs2@bmIixKEwVq(w|ggZ1_yF%(*m5?DX?*?2>owg56lNmiNr`zT9U-
z5-fI0CMIq2EgPk6E8oGo@$$;xA}h8{8Tglmoxxc>@x)OjGo~7c9ix+)m<fVpFZ&OM
zpM^;g$T$~Q=eass1#%CpUFp}psX;E>@VC8xPN~t0cDBlM=~5;NwkLieS02)|!Xd$U
zouO1hOBg_nkX<m0Wd4(a5c%hNmluvV(->VQSM0kaV4N#}3)1u=XB9>(goRgQVM!qs
zv0)O%EP`EZ$RM4Q&+)@hUK<4GltxoupX%nvy83Dd$e`UcY^cGB`U{M<*bc7jmX&)t
z4ZMSq+1S;3nb{W?wE;;(Tef)N$t*qu$$+B>J{3$tVtHr+ZEliSfhDalc0;Rb>B1>G
z#7(?Min21Ywnv15&?6M2oAHl07Nc0BN^f9wg0fSc-kw!U-O&KSZ=dE7=e;{sdT1FL
zwaY7a4~F3XU`>L)<w%St>0ZujZ3cz+<i;!S4x(Dyg|$GDaCkpxBdG1EphJ7M^RhLn
zGP_;Jc4#asGsbeq#vv6Y>-K2(|8ntru5OS8Oq%%PiK8oPl&Xo`y=Tx>OkA36>U(1=
zn4C3SVg4FwAsM1-C5LnvV;OqjT84`HRn!<`T0mF+5QB92)5Chn`&s`diX!g#rKCJu
z!lrd*jdIoD^#@8VQPIGDUL1xvOJ;>~mFeidn?Dpz$<VS(g6x#Yg7U)t*P3iSVKq!Z
zx1TVor8!k?^+GOn%&uo;ZJWwu@9;S(u3oe74JLS5f5W+@HGkH}V@riB`r2_QToK<W
z7@37#d{C7gL0lXYE+YCQR1nll|JN-oag8hijS1<Iyb&UPMlM@8!Wm_FKzSC{$2h}~
z=4r^{O5UiPH?`u<=Hb7@MzWXPA<Rv?8i)L@04#}CrI8l(>Amk?a&!6HFFKDSMdZ0y
zpe-u`qHmJI?T!oS;1&fF3$7qu<(BAWjnT+Ke+v1Cc^})&6X)IQi8dsQH<9<{{!%L6
z?jEXjH@GFZuUST9lv}+&-%I6GO|V>GTv?;pIX8$pH}oI4*Qnr+D^(nRg8@dGra{~;
zw_I{5O`VFpwl7T!U)%GIR(bat%s4eN=hby42yrFY*n#<8?QGYZBng^Ul@g9j<c9Lu
zZ{Wqbk{wT=ogj`&zax~F*eJ*Eal0FKFc^i&4rLrgK%1mefy_*VUVwJ7u<V#UC@MHY
zCK(v`^(%N4;Y=Sa*$49vLBblW+^Z1!x@7YFr2Mi?;pG_D1-x|#;Wu>)EV50(Mu*Tj
zQfmoZ^z>?bl70wGv2GL?LF9+pEmGq>{+o_=$!L*ISlVKk#_@uD?Lt?WHfwpB4%|<d
zw5i3;4*6qa(n;!-aY-!UyV&AV(66sQQ6#%ydf7Spm=8hjHFH+B8$w()Tdwvoay`B6
z26$!mYJKF!>s8k$brz4R>2_K&ok|8fHqO4&CaAvw1zYW8Zjqtp(>)J;aGv4ng!Jf9
z2@*;1`#0D@2r0hn)<xUf{)fS?O7fr4C3jI_gnNoWO>Dk5#C`qg$Y(I~@hH66aXGxe
zDh4*5#&yi@?eXz*+ULPBR!A`J0DE0lTU<%DVeue_NOwPMOK`kxsn(WmZvi1iMS;QL
zc%MDw_LFiFQ;nHZEl*2Ebc~lF&2PH2ZiOTkO;ygwrb5z^zvax0UC+#?L=1S+>Sl_&
zH!0yv+HH|DB%`Z_mQ@pc9G|4@=Qz^^G${<m4AXf(mWc#+H(z(mPVoo`{V!qA8_W>K
zmlyvgf5WE$ZXx&Gty%X6k-;92-T5j&B)1g)#WT%vl`NXMZy5UjV>6QI{+Ndi6y%91
zep%LCP&kw1Mptd!cKZz{568iuH8}=4lIRg^_|pmw09k_-)~Ro>uj&{G;khM^e+2=?
zt(IM6%By>7cWZ7E;#|$~)f@3JdzT>?M9eUqJ)Nv|1$43c7K64oxL{mx@g?}Fyc?B|
z85KhTHW_DjQJGtN#uiB|bRA4!t(f;(PrR)+8!43xZE~N6Hw>S~7o<mgc%o*z3KQA8
zZ8t%(%P((!m`piZCEbgCqgt&5arzw!_=CVxlJizKm;JIsvG~<`UOh_^A~WBZ2TF?6
z^9~w|MHX>xR!gU*kQT1QR<X=<6vJl7LK=H<Wbf2`xw&^wfgrDWrFi9-g++}xmLltn
zpx(O-&n_g-l#r}Yu71-WB=#yvPLbgy`cNoGe&SmW10Fz3Nt{R+InO-L@3=by$B05f
zn7PXg@(hq~72|9Dp4^&l6=8X#!u|p8(nldZgo@H~6-zC0E$N9S6yaIeU2jskN1nd}
zm>)YHd{*&<vqNQ~uMJrQb4nF|-F#51v8?f;qk9%m6Vj%m)6Cu4%ZV#NKqEyfRUd`|
zEt3d8HZ~qtaSh?bgc6JNy-BX6cebT<b^|ENRF&_cd!x`6Hjy~Ov$A`vV{%e2tw}W|
zX%IFRYdB-_>s9&R<H?azD1&Ulu?PLEG_Ew5-5&~O+aKRhhJD;0-~dYb5p&>H(=0P-
z&`~~hh~{#q<6Y@{%iayh9#p*Hbn{9g^Z}onr@GlS?*@M~U2}c8f@y_EKv@#$b5Kh7
zS2H0pv&P{SJ&gPFncx3ehiT^Gp66+mWAW>msngfNI{cDi6CS95G^oV+#WfdPMo_BE
z_C|UUL#!F#a(|hf7ML8c@!YaiR1GPAfy=6-(dwz26@y9eB0+jh1R|M-O5LdjTt!VT
zuepH-F3JhCF!&l{*i`*7p++5hAumf?0f3wG{<|nrq%V(GJ<{8yS2QhWbsk1Be{YCB
z2oG-Xi>-2eMun9y6UlKPMm?$w>}PG;8m;vDn9Xh4N2Wg~r>}>iusk2Uv0z?z^dN2i
zubD^w|ING!U6twj*bKre;0SCKjq}=`g?rt1xohqv)&Y=QnJ&r??sYY_h9;&j`z}d9
zGrhC{d}7#tRd?ySa^0>vG0}})(jslY0~PVO8GGfIy0SRr@&ztbE`30?8Xu<`DxUT=
zQ3umk1O@{Z-7Uwm^moW3lpV&e9apWV_I;PA#JZk(3m$s#o|&AiH9mSF)qgnH#UGQo
zs~NagcAqr2<DD|zA;z3U;IkFmoniOGq=@8spR_@{prun8`Zl@t{OM?wZOQI2^aHJ-
zYWxgnL+&f@-aOM4X;HF7h#n%8P}I=k(jXsLBa|RXfhl%TiU^92oUnpr&E|k;6{6AK
z$Sm|RHod*0E24>p!59@4iu7i)#BfU%Rhd*Uq_|Ct#Gy|Y`ry-z+bV;Kx0+TFnqC95
z5_u?;0>-E)qn~*bTB0x%9EwC`*rFMqj1jO&gb~p*zv|}Ux*TGd9i>cvqQEuteou-L
zlk#7(NczTXXI8G+;V(gv=!bzuK~$9~B7H1@D*WE-y(B>Yi=JR^KD5|f<mX=c8dU35
zR|^}C^D$ZboRbJly|$MDPen*E_Hkq=BRjizkZ*D?l%qEAlliyYgYwG&E>E@k+!yil
z4@Qa<mBiqfA~U^J&Rh4p2QU`Nw$7K=EnZ!MPU#`;GDu6M%Pn@*X`cH5m`6*`QgQ8g
z_Ut8i=aY(tmmn_X0E%ur=54tTnF>SPkcSdDq4I*RKe-Ir2TqMa=G941ng7X8;i5!R
z24JB<pk8=grCwmCPVMW4ypZhy9a93``PS=q)SzF<z$!xXL}i$O3K~EQDev|)%CDwI
z9di(BHsa_1W}03=y)T30X8xqe1i%}#>Df$kXZM~TZ&<*{;9&<m^R0ThQT9v?jvFKz
zPSnW_q9S!_XR~J>jaCBR3d+jcoy_ycBB+pm)y?j%pG5`x1xHH+@4}EpJ9z)^WXFqY
zu;)}W#!HT_EaFZA*imh7Zmr(7i(}+oNCd%B*JAbETa<nM$%C8jVORQe^7HDsC14b4
zIC%n)#O@xy3~H(81+r<@W(B4}2p&ld`IMMdBpO$x#CYPlJm@-qL{m}<J8TprsLRZP
zyo>tJy9G$6_EGmm#@!*3fTf)+Jzo&jc*FZ{U((yUbtZMk0aH0580}_MwAJ<dGYKHC
zO|b)cZ94&A{#xacXFcn%kNHu?8Bl3H9bO39y%FT?muj}UUUBW&Q(qoWA%lN*+THZ<
zzTm_jP;qOe`xw5?){Qn6tvdUT?RiEn@Y88<!M=y5ecmHXP9iB`n5;tSPnUMjm>V|-
zrm)<s|NIRP^B&(uhE5())VwM($04h7WI{gFYQladP@}tQxMP^&$F#ls!U0!|Q0!!$
zdn6}}zR0|T^9_|Z^H<r+Rs2Xe^9f=qOEVxU+QChPkmDu~X1-Qe9eC_jd|mk*#UO!z
ze_^fsc&r&8RGy6q^rfl0`WkB<zkr~edh!@lDfv$$>Oic~X@BwDy6flr<eJZFrm=E;
zmVKr>G-G2kxw>@cRK2wWu0!Yl-<SXXlM)kF1@>yVZC{jAPoGj6Wb=&WzfTz<K7j?Q
zBDTfT-P|wJ``0-|ToP{PK7k9P-EB0D)4RDdbu0!47M}Qcoe~>l33*D8*pd18<YnPH
zOHgv(?0?DmJcq@QJ6N~YctQTV+i~wLsDwRd?R~#W7(NxtxhFrh`)Aa$`*A7fs7`^9
z(qQbIZr%(&vV^&dc__uXh4xTRhRR?<k#IVJ=|Wx^w`Ax&0d~{#V66I05wg9Ug+-%8
zb0yd7VO|9upPN(4x2qp$lWtz0m~7s>J5FZp+H`xA@%$*;c4+Lhc~=4_r~iVc9p7&}
zk%U<Lfhm`<t6`#T>Fdoa@+S`Kze$#z*~|JL*@T~2;84#zs@)@}-vYeJ8-I=zYI6&B
zI$T6@Uu0or7G^LYx!@f3emYmXZk93KxjBb0NBn`#@$)7r)xjT&aja*SN+#DmwW&Yn
zOvp+M1WYd&-0{`%GtovrW$4ih$n()(%PVHil<&M6MdFCE1gC(Y%DUikoOT;8y??z5
zMZeL+7_-rlBYRM%9pVR>Nd^ifi#~qcIj7b+heuZer64>6d<GEKgxcCwW;(_Q5Up{^
zC9Ri$K)=0np;eyh9_6=eiR8*e{1SsI35p01u9+Wg8Af>VyO6+({t-7BF>G3%kfe5P
zxrIbpPVFdR7Xxb*Z~wupJzrt+>SlOpdKbuK3xP#49q+$R)!(0k1-8S~-tE3(PBkya
z7lCgmUiwY~{aKBRHDL7}O0kQ97|m8O9irJSgYv_#TVBg85Jm;l;rOK*Q`P-8@hqRN
zk6oxbiTX<7w%9k7zN}>(UqyZMMiPKk@6;4pK?8WEEV;aZ!vRlK622EqE>E32$9f||
zA(NjyIEGDBd0WFL&S=lZqqaXA;u=Uyn$^JU;<_akoxhLWKs2ZdkZ7gGIbh_Gf8r&{
zSrP=pNZB#&=No;0*^!#;8)_AilYl{FGNZz<z78;Z3@Xk_MP##t6{pU+x&;)TbkNqd
zpirGSQ_JqUIPDN_(E(((DQ^dw9PoxO+B&qU97&f>1%vwi!WYz$;aWOU-@3ZJnW&mS
zut&pxT-U5u9=Bn7(7R@Nck4ic$t-Zk%YoNjQZ>i6n63gQ#m-hgOhSiZKdSq3Pe#`s
zA((_U9Gs19Q^#x;x}f~%Pzthj!ps_078Oz*Ng1~zBsCTW0&ykH_C|Tz>dDh4Tz#Q|
zD`+vLXks-oUY;b`Df7c^?1ggDVZyAV?Fh^Bsu0Bif-X7?@qFFM1cv372?jH#uO=#x
z>~b5<SrsM98PwbRb{nxtP1Hyt#sf%6H&-Ew5UIA;_ZD$%EE>jE-F>^ouB(V?L*KKQ
z!^5G}NFodJ@Nnf92gcH6r&7ygzXIdI!2tT*NzpITkwaS`Cx$UwEA+ElVFq~juUYz!
zCj|hQ(&>lD4$uz($AE=S=D7J-T+qMH?F$o9L?X5tH3kB_%tAS`YKXtr2YwoFmhQ>o
ztRcGi8diS#f*fmRZ}~2UFj~X1^)EqcWTeFK7ugJ~A!MbddQ(?)fa*^S_QR+@Y_fdz
zooZTYT`#X&wRf&(4k*OsLyH8cN`RI9>vKbK$VP#5RFTanr^EsfAdsw9+M!=ZvAN)W
zgb@l==<O+6Bmr2`fN}wBZ|^#`GavQeV3g=J9`frSmZ4(Or`_WKcB%emd+HZgN_R)U
zPdmX4dH*Hi<olNoYSZGa-S#!(726vt+XS)~+PE}}UupzdI-_7J3*7qYhKwo&#^%?%
z@u63@7YldPB7YFUW!3tXRFvKN&wedlT@R0208`7+>2@Ygg*5hs?_{c%oc?O-*x7>_
zt}re?v(W)hawRcJW1wKQp?{aK8cc<HY~sl}W<GVWp>YlCJs6q@F@~^NeR?V(QZ)I8
z-|v(Ly8TEb73iVX=S8&0it7n1c|@O?eFFD;q05m2dP++8&c`uKQ_^yIj6X3SVMsVu
zsVol(J6C3B+{}tB>#D~+=%Y?|PFILpj*X7^wm#n84>)#r4=Ye#0PL4(K{=2dSJtlV
zw9DOx0hg0vj*#+nvl&sje%%_NMYlz)ld8;(5zv5rNw;C>PS-->)W;%tnvUnSVyy%o
z^iQk7-pQ-hk-ukM%-K9y-FcLpOR2Fr?^b4g@2u7lH~y3!KKy_t+$8KS)S3j?w7~k4
zbIs9T29h)pee>h;3mB%PQfO_HkHSiG{}GYQZnbR6L?jO=MHkRgN3z}zBq<|RY>7)>
zhvOApEV?C;`)&<NvHEbrkf4xK#M<dwaM?6*L>gm|K-sRmt&l)35KGZV?6G6-A3hYx
z3Z*6HOAr;2&oBBtt_?wd>HYmzTZN_So?^$80q|^@-dQHz?d#(H;q*5RWE1KfSh%aC
zj?CL|u;glo(1#$U7^Fq_94d+Ae^@b*CBoj@2lB{XH8I8iO@Wwf>CIn85$9t2G*d_0
zZgVVW;x}`Ptzvb1hn!?hefljLxl@Z-wZ7r$4u5=u39$RY|F~{+7#rQ-U=vB?cScZS
zP)_n+%Ml{DCA%J35(iD(5shj+|Lp|Wodgxn%YFb}Gy6AAdo~uGp;66pal~?wyS>PJ
z@1d~M4xnZcLH)1yg88keno~1z<L_}l{9Jm}-QTvz+ck2OvPyc@sQyw-S6foStK4Kr
zj}EvvMVk9+@%>W0wt@QNWB)PR{q*wCHV60=`juU$*lX_Wya8*m96&SzZ+j?Za)4#m
zH&Q8bF;>b1G@)3SBy1AwROqWvu@cL8i#|-i?f2ZU;I0%BSVIl|DuNK|Qw}x~B^t<0
znFy;!H{PhXjfIu7Z)o?VTwi~3Z9S~N?R}Q^eECYz-Q|>HckEo!);Bms8CsB!_>|F1
zCyYh`n*am@r~Bcv;9;$t-fkipJ4|*nyC%QbMErfqu&+OFb}0OLRi(FoFlqgMc#sx$
z#FPq~AbT7t7>7~%Tp1?RyK;z&rynM>v1<F|$X4@k>f`<~%L%M9n#BB9!zNSi+{LQW
zD~2p6W3MNc`Gr`VPmvZoF<ThOaD7bEd2?T0(Vz9hub}uJ+R)Qe0}4vuqj{~}k%YpJ
z-Cn7sd4Ex35FqU7C&0dS5k7skuVi-HD>R8wib+N1S3Gqxu&sdE;m6M)cqR1EMcl6*
zvdU~w_W0~e$)`~PY%Ae|D2f$FUv;?YL}trqGRIV5NV3?{;|ZqjogQN&7fj-YR70C=
zM1LDxvw7Y{0={o8piRMNQWrv5*fMSz%@|tk=9e2+4`rIhH(4FsO7i_X_jf05MbrAO
zDc3Vn25XVq-z}wSfiki{v3&pe9!uWgd>>=3!EC<w&D^AG^5KB@@1w!TPX&JeV2d2S
z0sm)EnwFkjee>!-J)-mhea~ahC)!}v``v%LnzvIrGMyiXr1qUoDRxW!PoyO!QPB!t
zpI4^^<m!@1a<}+?m_K-(#y#T!ZQTS@^i3NRX!p+ytdn;Y9*_z<ReLjJz4Y85<P%j3
z_%QJWd3$Hj=Ky>VnDV<Hs4O%Mtm~R*f$JVjnx0APbia?0`#!HUGz_o#7)E|A`||+X
z=dv_syY2`Hy!^<J(gHa#TjfW)bj|klercQ|fDAm(P78`AB8<$5kwRJVtEnh9vA@f0
zL9eu6A*dX&8Tdxe<#M-PIB)#<gBW9MW^YYQqWrM0@bRE<(^f0gJE><Tr!s@!sz5XZ
z0@yrmoTL+Q%sysHgaVSboXfW%PbF2zx!D<LBM+{pu2@0N;q?UA?&~=PB+=@zy%%pM
zB%#RTCvbIj?dZ6pkpsfb?K0Hwtt$V23^Jjkr?A(=pNhE=1LVDIz$93FFlqE{PGP|!
z5=9dbb6HLBP{bY#dv@~ozdQ~(r26(OD`N<1<qRsS;!hgRodN!Spb=vyW-Lw)iiZlw
z{{g_i`YjHPswtZ61QU8=n6_%AKbG-FHGr1xgZg(&V8ARj1$E18LP~%|e)TDL=2WAK
zp`eN}iH;Gc$~qg4GCCY^6%%wZx!_J92($ds+OL5A4)li%a1fOEZ=aRHK&s3ztHnec
zIsA6u&aT}3F%)YRS#7P(i9Zr^qiU8DskLWSE6j8cAlryr1o~_eY)}UdX7U)69*yji
zO?CukxkZ_|Vt}M7%bC54dmyS`AP8&|US;M71f!jc_3ufL;WU~!BtVPi;N?-nwHZV8
z&%5cm2X~=9qi)2eRoG($TtR}XjeUw}x%F*owYWF0gGfIJFa6h^#(6hY+3Pb$Whtj4
z*YX9Qk+zWRFq}4Q@63H6ndBL$#(;&|zee%Co^G$Ow9g44#FMl3Du8(<L<I)sA8U?n
zO7{VL$<y0_w`}$SVp5=`fMRh)@d*Z^H8YF*-)^iHQE$V$x~1R(T8P*ZwuAkv432-9
z4TF_g+1?f*`b+)4W=B(~Wq-K8>UMPopfCf|OGQrs_0YwOZb!YaE9vyI2NL;mtZ-W*
zL0ONgs#%9IJ%WjPEtghj`)CtgR#~Prr^OC;B6mV#CgahRu7zE`$m76$>?67o#@>S{
zFa~aq75_h$&N3{^uItv1f^>%<-HmjYbax{mEz;c}(%oIsAt~L`-QC?FT{pFt@BaRX
zhawX9T-RJ<oO4X)|Bys`t7-+Xzh&V}9ecDonx)R}!lYGvK?-4P%u$Hgrcj^9&dixA
zoxas-TibbB#Qv@Q*p3nQISEUC9*SbS=|qWi39)O&MtmM-NWo9(T~n@TMPm()A>I!%
zl`TfZz{fer=_A%#hj;r?UAity3e|C|IB(pkl{m1~RaM{Z{?}Hl$aG{}0@FNErRF$p
z9&3u9k`$#XQ!dM1?Miz$8WM*q1ka2`=$#xI*<!Km-;?yMaUIoy-2)4OGc_WA^>5xW
zU6k>}DWu2#hsC#hA2BpBEvO$Zmd_NiDTP55mRfTI2&MtS|0fcY*{MPGv)p_33yr4z
z@6H~Hcna<j-vG@>fuTB?GMtd&681FmWK1xS#FK$98sd7sW%t_i=VyMU3HQIdy;rAD
zpH9apF=Iz}oxVRXwb}h=@M)#U*mI05c(+0KWa!w++*$p^EeVEMu&AnMGKW7l@b|sU
z#qKvPEN*~~5%j4F0AYHBwijc-!~)bq{H#3aAphZDY1}=bT@;dzv!t6<n$%*#phHZX
z29wpeLIbllnYNW#`#@xNuIw(HCzmrK`(RwcTmOxjM=B)C9)VxT$L{`0f8g*v&*~O2
z|K+<1m*c0-sSj%w72q0J;w}(?2A(>dR)OGvuN)T`>eLOir|;)VT3@SCJIO;)R~_83
zW_?t$iKyZNzW6VCMk`54s;bt7FJ);(YGXe6-B$H*5Y%R5x{~NE^CFasEl8c-Kc^w4
z=c(WF>`Tf1!}RVIKbQUY{eIMQC+Db$OH$>xkui`mS{T{Cbo;!?%vk>LHC;8k{dc+z
zgdSzrOQPewnM&2HK*WM-i)KsnGb%Wfmsh@J7;aAn&{I;ge4M~k0i!%|f*H=)Vbfu)
zz{~la!ETKKZ|}VC-w$-gJah9pPlsG<JCT}|mwCw_FLtO=a`3@Zj613Jv-g^ZcdS|W
zF1^qV^fr`(y>*@VIx>x><5#XkuUlRs-&;vr``sztU-RitksXijR7K$?j_-w@Uc|@1
zAYsGH?w#A;X-OUjCk*knXNvrJRP9!sZN-iYD)V*yy~<Z6!QoDFOaeZZy8Y@ot`-Ky
zx%*S!8vzs|qWyi}2Oc8tt^az3X+kP~nf#`rCQ1b!4+?Rn*esS8(~hgpl{oNhpIRCW
zj9hFYE(NISZGwn<Yav8T`uY^HaUIw9(rTnJe^l}Ub4m#amU*gd0`7t-T_X`!0S?46
zB#{L*cHKUI8qhYQBR#%4DfmqBrKF=TpF=`;@nOwF$l6osz{UIM=Hu`%a$o<|&K1j9
zdy7m{#^(8^eTDAYA7`k-Ld3F)TEH8ya2W_st8H=TOdf1Ll1{5q(j_uXv*meu|6jEP
zqey2=l(<gH6Yi6e(bbzZS;?DE4PDhOPCJQ2+Z>>VP>0fC5sdzsMA~C3$kCk6E3h!j
zB<sK2-f^N=A3We1lRpS<%oOy!#a}nwJD|wE52bEEcjQ?W!xV34bqoXddLo(!u&g0g
z`lyo}>%{NOK)7M>_`Q3#h^9;Sq*{Q81e<#<Yxm|8?kcbsX{eFnXw+$jX2KP*50NY+
zxT<Co{xIO)wh#8CzkZB|K9j+3nk@9_-Jg_<ju+DHk?q<PR2LT}B$%IbFW1o~m|eJg
z$xkqux%POPIkCv9FS2O*DA6e+s}O*DuaO2IRg=2wv|j1b|5i~2)dhMIGW#RDyc1K-
zVASCXGv02`WjYg_VG$QD?gzhXY8{<%itV-J$Pdt66PZnjW>390{DJl(!sh&;guM1`
z^i{dMhhdfc2QR(=>5)1cOr|Kemg=GGN?oI=!3!yiA5cw~BoSL<3B=?pd?{g_lP7O;
zkl^D(G!{tnPS;$e@+l&WSD4jL&TdxZp}eh#@~Jq~ZxAmfAU+o0Re7fm5HRgy*HG67
z8@MlBLo8;dQ#B5#XTHNzJU0sj!O`-p0;*lLPVDlVSD;urD(@Pd3?soaMNB!g`e?32
z0Ye-<ep)=s;}-1-5!=BXe|Rc2g#n|VrIaq{%sExcLoZuXzqx0}DOS<<g~AcG544=@
zdb`)aaqquseOTfEJ=9p1w%O)6GO@NedU2RY-kj;7PUP#8XJy=An%B#4wB6-3L$8Bb
zzxj_+Ix+jMK9BS>uVccG8J~9-aiSdV51{)M72=y{|BU=bR#O+A=fF~r87~s7DlBn?
zRP(HPJmc-J=~Kbw8ZMqbyJ3NwYiIogRv?K2yc<)*0W2wfIm(CbjSa0(*>q>l7J*h~
z5lwX~J#xHzRfuvxiG^001V=Jy1g3_Lby$@A7;DPNe$dfb`KiHL8C%k*(jc$yN--ui
zd{oZ#ktejW97pm8{b`TN=!Cdx-JpuI>5I2d%p%IrA4JXDb@MZtJk_^g{b)kJ23XHM
z^IGaherO4U#xo4|n8+u7Oo)72s`Q^QwcI-dW3yNjw4i&lWB$V2E2&L5Wem*05VHwk
zxQT$iGPdf|RN8`kV$a$xlw<wK+${3ECEY_tOeB#?1P>U|No8#3&&x)%+Bcks5+8*z
zlsPZC)8vIad`<3rHn?HxO|5=GLbg*B`nMrBFy2fQQJ7vrBI?)~5xo!{z=fnFDSR{s
zuA8}0?sx0xnNV_mU0n1qa(*?bxEZyUCO}Fqqhja4L5*YQ7~<kZ<2`0~rhlM#$@;kJ
zlgTY};3}a1IQKcgu!q`bYtY)aVTRqb&SY&lY9{G&K&_4tO8qZRen8cnWX1I$qXhrU
z478*f%HOsvLJ>H>oNozOiMeKMiyViNL^U<4#Y?B&U!S<ig#SvbS#8?24{dtg=yQ4o
zM3aEcG6qf?I!7&sCL`Vj@@w=~&c7++w1!AovSX6w3-o_+B`xB$4yC{P-Y-Tf8mCU6
zJi|I5d3LICfOSm-#fil_AHc_55Y2oq`;Y%cf@IhNZEW?+$Im2qa<~+%q_ztOVXR02
zOU-8FVHYo?ZCulqRRyimQqK;^rgv|$322o3DZ17r7qlhV1`hY2+OmwkV8?jGe5>+Y
zxD*g)Li!5xyvep%e=4fPZjInSbL{DE<0NY8(%yA1=4V6;_1*9*XtSs+w;oCBMn5)X
z2vA@Z1W-uRB(W0k^DDSBa52cP&=I$Pu+Nw{g9W|W;EEqYzoNWqg-JCmkuRGgC95{3
zy86M5S5oqk+-Q=GR|70%B|bhO=lpW(O&>@5{dN)0^F6;R8)d}uiQ_RpJSp6B2ry=F
z*7SC_9@KpfHT5?(Htm5yxjY_NQMgG|D#A*_Pr_I;hC}G2mpA<vQ=Ek>*ml+OYv~VO
z66FtQVV@}sf1M$pC5~1MCyr9Jk^Grab0|#pFr$VS5c<P{^t;fnqU7GNXVxR$2X`wF
zWxI)i>#j7H!mMCcSX2G7e$b;x7Oi)O!N2f$Q<8R<Q4GRg?EDCoPAI*4s(N-~|NNi2
zGR@Na#E7d{ax6@W=Y{@ANTWTmys~n@5B!_O>-5_0k18@w;-Z*zmOg~}J<8>NQ-UT<
z9YJ|I1Vba6ecr7UKQ|j<^5dVkHByn5`#<MIoX354Ss(|KPZ)Dgc)}QDeo{dxVbT&c
z4Ry#AH$TOxPtYkQCxo8;sjxWyImw1-nBt$`zeQ*#{@uJp7Paj+D<?B@+$>WwDLcGf
zkgqbP^3k03eWu~TC>%LI!~d^{1J}n|OTG5z<#prDYyR2ARZ(6*=L(Y|kTo+V&v!Tn
z)mh>{Jqg{@o}BbgFL(qz`g1EtVGJhwZYd*)iYh0<uGu5Ur?_lX|Gm*Vc0GU=#Mh4o
zkFoH#&4!<F`>(g{iXBk4Lb#>jV84ZEQFTug&`6(e!}&%}gu}iIR8xNHP0a%jny2mg
z*NEe`xfp^KL<}wa<uXsgwc^T+uP{8T8%?3_qW1dTT3JUoyKtLe6QG~$`_nY@2wk);
zI73Y37>tu1kL9$m_f9g0<+sIDP<0`X*J+IDDA@E@e#|`<;y-%nGGXh-6%JIdR`e3n
zMgFl;GXe<4O&`(<RWb+S2iNY2Xv6;0BRjaKTa6X!AFF(5Nz5O>u`=5m@`O>W)%h6d
zkxUXYV8Uo-Cc8Z49f)?&JhY>RKC0BzKJ(`;k5u}DBuiUGf5+47Gf!c`)eJSt#mSW<
z&%?n<#beSZTrpk#j-hCnqk*C<fgWlh=LD<2b7-jRsP>+M>rdTmx&{@FpzZP_Mi++%
zPRyxWx2t5_fOiqXIwE&aR7GJw9;(b`L+g7+JyG-@J_+r_`OwP~=x<wT)H&ZK5C%t9
z3`-RChYnV6-hN@WC!j8KZNBb~0b79)MUwCs1*@5dO$7V7##+OP#Q~?#WDLu~5h>*H
z$p2qy?w2FHAHsZV=I;hz-+&2^g>9!UqUQzkxvWpvbidZ93UlL?L87n*4X$=!Ih_x|
zcW70PDl8xYr&d$jsl{7(Mrfv+Yu_DvnVryrm!~cJI%VtVBTtd(`4$PXB}KVe=>sEG
z8G<5K^i^IT@YR!zo7_EO`K;2Dp<7qmdk(wM`y$BJ7rhdhLsRO77NoC$X*UlpYPw}C
zg0Z6N?}`-UujbNapI*+|hM1lc6;)`>A39M#{``gjAzAf4e#}3l3#zVpo(3*a0t*?I
zq#F%dAi7P<_*By|*l7FZ;R%5?Hlgnd>({%J40-p`9!MSXT%~nf54?07+5`HuWFd__
zmYoBqGVW&6n{e~wSn008{isRn+k=@F(4x7_8SNcl%`=rvt$am)hb|qL)IO4#Li%~+
zi>cg-OSVl-f8Q3Ba>|%ap#IWBst`|je8V6XK}CC;Si>SYLhk0tNf)_ek8;=2Eb>ez
zV#)fA5|*FYS24o~3w#1^2wM3lO8L$E<`QF5xgk}`7_@s*+vi@s1gdZXkCQ)y*^0E3
zzmn$<U8l6Sr%YmvIL7&yvZxWrSl_{R5XVr!2g*cQ(TZB+Hf~=mXyZ?_OkFMft?{w;
zr-+3UN4th%*E9axgQT$5=Op*B)dRkApBz&fOM)h>E2kf)ij^v<ro+#Lpx26F?ts&i
zook7v^wTtl%=SBkS^iX`QXM$|kUpL8@JhX$`4jN1d2mR&c%W;NN#c%ZIzKXv6HXO9
z2<CPVhAJ{+A;iqzIX&x0N6~QL%sM8A-Wle(G<LsCWUv`7s9W5;{5;?IG{<rDOMcAj
zjv){b8a%QVxgi&Z(wYRD<l!VC2hIYyG{V!AWU+SH+?KSItHR%>%sM2&keB!y=XJu;
z_%y#@oWNR9Vz32t3yvuYm=Da-uaN}=I@CQX7=tD;GZ{$gQ8^K=>bwF{NKnag>7ow^
z*;%?9BER}R-(Wwz`Ou7mG3DpUO(MHWvvJyohrDjuw!RBY)i?{bV=S6f6v}A{%^5y~
z!ViYNRqAZ&AxGX=Qx0>`(#q?ZJ8@F2G!!e;u~sy6g}DNDg33s@<!5LlE|sLPq~C-I
zw#7Gz@E+M?dNt0*m3G<;lJDrCOv!8?b)|>>@5W4$<NOdjf5NCIS|20b71_A6Q*lu&
z<cC&|2Jz8IzqhJrICO&C>vJn5oi&>4Fed+r9@w>R_4#C-C)z=bB-7F$bgh|$r`udL
zb|eFiTy7T!Ud9V~icF2{0!xmgy1zt{k1yzAEYHmOvv&u<q@(S@g)|f@Q%9Zw_HvF&
zL9OZ)OlYE$JEPgssdRAIq#<!`Qrzu#-@cW0nUD^96b;vT#QPhYTIuy8zvaz}F3kUC
zC$Fvy&8~;4r>=x;>Q)jot~cl}&)F;~_3W#zX20DbM#b)r0{k&d+E6)5Befh1%xNUv
z1mt(J954mr==xizzhIAqJ&Oes8hBWI000XCr%7g2a9*KF1DzU@xFYrzt1$ZVav=h?
z_0OMH`HH4kAQ=xLr&^>tXm=F*fr<)&J1W%T2*`Il&j$<z!jQ)kU7kAGDXh0bjLBT`
zks_Ua>~*p4M&VE?B>?1r`tB{0iDOCMuXV5ZD{zZAe4@h-=KuxnaP(j-N0|1LU3udP
zOna}LJ;%_5z(2=;icNln>~lYtU}}B997itJ1JbkaGme<y$Yc>JsGfLPTV2!LOWy4(
z?80a{hrP#rx5vkQyJhb!W~wlw_FGGXy+4CI4E_1-OFK(^vaR>oJ^{;zd53tXI;AN0
zko8vtHc4vxOU}xt!DC%-^A8QD7{M$ea6Ws!SL$z>Hd<a^DCPRal(99KD)Z9u7L9`R
ze<`~E9@wOQuhmpF#K)9LtvRBU`AaE_E|vnLVRe7~`Of!GUbdk9e!$jG1H0Sat1`V+
zu*sh2@r2f)0Lk}~sYAYUm(|rOXip;i4=N92NBF(MxGDkDi5tHvY(EQFxD?KjG+ufB
z{CY0B#Vj$aj%O*K(b_%lbK0N6!z*oCIAZWL7H;)%Hlz!;;WYOU&-bPS;$B*l=#3tx
zB9qI!w}Q%Kcaupu_Iys3mJ>_6z<>D!U`WRRe<+bj*XINhecK#-yt+h~U}A%fhe{!^
z;{@m2L(uo0=_TS1VrX}YLf-JnB<;(T??t>?p{x|`ga7NH;sjFUV4(dsdglN%0-r6C
zej)o5T^_bp;`RspbwlG4g^qnv%)#qTcod=bKZlCh|GJb`+w0ZuOJ>OqJf{msK@yyn
zt89r|qyA^mgN5_kAo>G!9*1XM$GilD$F)dsOPTwoD6<kG1dUb_c&BM{C2RlX0B+^V
z{n!sCBU<~s7%(Q_E>Ny!zB0yYxPO0<YRs>bx)nPG{jR&6QJbY}RTNHGc|3mlH+NcK
zxsFyCa0LX<F_%AtCS1dOTYmnd#384??H@y<vozO!CPY!vH4-km;^ul&_#eS&qxs?3
z@-k^~{P*thAR*M0BEpZr-YqRWv7n&ArC3JguDlbx40?~&VBGxOrDc3b#$VC*?>`e!
zcAam0dz`?;qdwvkHzd6bwcZwIPUEvy(pa7%(Z-Etg`IcP*wGE}5mw@eJa12rpC)}h
z2$xy7-P|&=9}3I|cdgmgHvzlSepOxr1WWgM<2D>{E*zhJv^+(5W;QCA?VM1HsapE`
z<(PLq-MW<-FX`A;k3t+F|BDoZG_AIUvy#}6bqWQBx-?VI=={nIyMmlXQ<d`e@_yy{
zN{%~{dcoqImW6ZU+R+9sq$=V`rrZzOAxRnyY$lJ`C^Wf^zBhI~W`3gBX>RZ<!Cj6^
zr^FDQgvS6)8Z%bpkF4Hss4j}!zYW4b1=c;#?~a57u;S$htzYYjP9e0g|KLm)jz{kB
zqnc8&v_4*hWO;fXYswd!um>amBY*o<<jYXGd*tARs}GbIcnNsf+fQwSqvh=G2YSx$
zin0Y8Pjw^KX34z>nE%%ad|85t52kW^x{78N6zcos>k<S-ZGOKqpGBo=$7~HHuKw>B
z7$HhmFgH8a``G4_IDyFXIOSgIh<#Gl+v7(UoUQfKrLB|r<;wPVwN_sH)DFGxF`@|q
zimmUf9(epuiN$6=EgO)9Vm6Nw?He?W%r+$7H@%+D2c5>Lu-g9|O7`7#oYBOq<y_8q
zSks=XsF<#B4(&=Agi;s0h*#XY^8($q=F2tmiVJb7)L!(sQt{qmWBp){S0Z)CHI47Z
znLfq&R9wIzdA!z#c-!Z>yMww%{)=8oZG)9BjwNH0)Tpf9CYMoTd8Kq#3^tdmzONWJ
zvs4;=TbM!@&=1uFDk6?~k-*rz=$!_qUH6o|1Lt$r`0~1^Yyb9#^pf-0j;jLe{oM`Y
zEB@CT#j5s3VavR3df!W4kv}~miT}PfigQsDvZmWH*2p?49D^2-gFv;yyIUP32x+-a
zdh+W52NkNqIoIo?fdZ5gd!pPVX?(|~UtTdnq49Z_qVEs?=+PPw2?UYxPky=j6)_&I
zocZe<@%8+8Kn&<AXYF306Nubbt2O+$O{zQeJV%!Ddr{-(JvfTS`wU2`{bL1(y&`bn
z=fN&Yjzl)r;gPD)HmvzNmOQBWdqLZ?I0-QRcR;qLNn|UlZ1Ag{+1uEJFP&@qP~~ag
zv$zL2??5acWsej%x6AvFDGF}eZGA19*clGc0Te~)BPN$#wx@JpA_%}Bi6m=`QAV!p
z&w@5s=eA58oj}Kyovd>EW)%eD8WlD6Y125PIMcqnb;PLr-m~56e<MOuEYhnY7v|wJ
zF8qaz(g)+LWkydk!MY#?73Hny<U}HD&6$`C#J=(D%BU1C$l)xQ4CJ^ipG=*tGDpc_
zq?R`F3EGV3X*ms;*)pQ9G5vN=HyZ3@XNOdbAIZdv41P!wkWGbP&CT(tmGblzAuPAz
z%I-1*M=M<JW_u+thg4f<%AQsHb~BCdc)siS)V}d$ZEukgdSpy9CGF$IY{xa0@hm~|
z$Fd90j%SQ$LHqC7_Yh1iV4Nc4(&XsNs{Zu-%LE3@B&lhU_*bSJXL6R^nGFSix>K04
zZ=UTHz%3nQNb_IE^|f(v*v}06l!5(_EjQ1QweLThguM!Ul0(#lajD^zGtTF3>a63n
z>nj``N{5P2i8p3;xG|d;!qE6znE9?R+O!|q>MF>3CZJOM=m<${y`9Qw_A;dDB+x(C
zF=PAh(?_F9FN;xq4GSy5jYy@;ms1M(QIJ+FviVTmj|O+?5!4z>iI>1#>4u+SX|P-B
znd#gixROi;?Kp-d>2L-9g+sG{32wsZRt$j`g)g@{4OxAiJehl~ozq4p4LaNiYRbPs
z5OkM*Fc7kt^S!i$n<xF!B$Os%P}3n|R71<n1m#Q0Kv6pHq7fCNJo?+BFViKi@Q^pG
z(i2Wl>Z&Q+N|aF;Yu*oUU%t2g8jH+1q?=#U1{Kd5SbKu~Q}yiPlDJJ_<K41ZA)o|4
z5B;|Di1MNw-gAf~e!e)CqNR<(K@*9gH|KHlAR521nCE@!J$w3YlP77<uUMau!><im
zfsEGColbivQOfh_RA1^d60AU<@&2zZ6!s#Xd7{R3gP;_r+%}`ejIkux=cg|XsP~o1
z%u@Neqe@Gl^*`-MrX+RVKjA*epm>6$|EAi$JqPRl?a(}Yf5bOmgCufvzHD9-D6E;?
zT;egkZdy8h7BC^JcC<LGQG#xorFyo>27SK1r*9{tAMw<gM=dAc2x0c-04A)kRW@w|
ztPGjBdKK$?Ohk2*tgL<qIj?zhV|&aF;_qlC;ZSG4#NrsaYjaZ|-{OA~qYV8dM^ZK4
z`joikM%2Bu_E63GzR6((9Hi;P&H=g1z78<dcXoj=0#Z`6@cwWnkhV1$i<3Itn4cf$
znoGc;VV?ltScFb@t)CWPGNh(@jR-GDa`OdCjgK@oPK%2DNzi$Hx4e(ecBTUOjDhr-
zeOZ1KsBHBr*^KIWCJWbjaH7g!9Kqt9H*b!j5W?AlD?RdK$YIbMgty*G@3rn8cbvmN
z6nz@31;w1ER9}#`#zes?uPrb82Jov!#dL+YlYb>#$dhemM1|i_d=~#zsx*10bR+K2
z^45l{n2X+#h*>R%zbdX%tgzteQJv;E?1u~S-*v{{WvhR;-AU6*(V)?9bdr69KE-)Z
z+Po`XK?V-u?`i1_nh0%e8|Dt?pi)50{5gGKKN8?)5>v<S>vK2=lEE16gy8*?&gGUW
zd0ZUQh}+yk>t^xjhvoAFj>L34Ix;ujo3K(9I0P*|u%_c<f);ApwpF@G#eCNz{xB6I
z$@)Kwx*#AWuu`RF1Xh%Y+5gyoXI0i<(LjWhQ(QuqR?2F-<}rpEwR+Fsnci_0P>$ir
zBc*3x;}TT5$*mA0Eh81V|2ty;cYy!hrq<lzdm&8Zu5WUxqJ#+*XY3_0Qqmp7KT8pk
znyyUrJfcLwUv%_)qcVk^cZZ}MqqI@0i+3ui7p}!SwFO3)tta%9u~sBCB+}U?#x0kI
z2IRa85M#AT3?9}l<<YGqe%!f{`{o$4qC`P2BCN@7HA_)xzL0BTtMKC^Ueo6I@-hr1
zxv%W9pbTyahU9(YX5K0$s9$dpsyLtd?Oh?S$mG|1<cth)tiD<<a8pL`pPI!V7J{Uz
z?(|<i9lt)Fo$uf%UY&q_#+pOGqtWirAXjx7Nd8Sz`orc3H%YkTc(UBpb|jzf$I%LI
zVo7aH@n_ybWAyvYFMR1c^i8DI2Rl~mdU?wSlO?V&J!+*+)AGpEoC7<ASn`2ya*EUO
zM6|eh==B;79UewFDhzaY>3y%lvHBbuGQu;_B;mn*-G15oW2;MQ$3wJFs_{61#0M8S
z=;o5`9l}z_L~EuIpZVn*x9fCXJwVeoF@uf9E(!9>f2!o4e7?_L9ddd;{q=o?t+gaP
zDHAW6q`W5YLybU}d_*)m;B01}Usl_v!|J<gNh(Q+>b%Z@&(JNUs%3p2R=9QJ-I~?E
zwCntG`g$ys`wbM-q%N3|rZZ+U-J+l@jd-K1ms#$$BWolmqt((XOwc=$ohIEjz7>%C
zdd`u{Y-ZFxbaFup?(KNL80Gp&3>IJSHuK=rW#v0s^s>1X2G;!(Jeg1|V2EB%PGnov
z4R-66SgYk=q*KWM>!w%*;L9$^Ke=CeqFpPiJRjY?YHe+j8g)E_=u+m(G@e!J?e^YS
zKHV0~1Gr*zQY6uU2ZCj+5%k;nRaNrQP-^<Bm>Wfy;3~8C7XfV|kH&|Vv&Z)A;zxOn
zHs>UWCDsjrIC*9OKAWsp?)5^{v9t-ENww{kT(8?Fy3TY`=wgwdg2nl+D&y17891bW
zRBj$sqE4FynSAc}3rkcPcq8O@{=qn-LLT9xktn+|QRMwaG+1XZE#v_t26p#bnnb(6
z?|<1odkMJ&u-GA4Q^x49P~*UZBYls3*S(1!5bXjCi`nu2GA`r&+ItAC6q4SMY<(HR
z_PO$X`Kai7i6-<Yo4qpacv?-3YIlAPjWb?Z-M+S!{T#i%WBc63WOsi+kydEL2LrNU
zwi4wTWcL>?q&c~G%gSr-K`{?PbdD>=JA>bR-pMYp@VeYMIluC#ktBmHn8**CESQB!
zD`e$TUz$_@T<Og1X&*_gII2Q-;-eT~I1;_4ldm)8;E+uBQ=@3y(w52oXn;c1mAk0}
z=i~fQhPL*8w%3{XoTtEleKp#9;qP8rvLEo?J^oE>*g`pIDb?<x%_jS`RD7n4N1r!#
z4rDZ||25CWBv^jAa9hk|O@qU9*P=;GWg9O1tUT$e<HVp91I;qFx~7}$`rS~fC4&KA
zQK_SIztZ98w{(@@L=_PZ$h==i{L0mA@l^_K^X7>im(tw&>K%I6CnU@(l}bX2gF=P&
zxNb+)xAHR5JK~MjIMXa}Pr}-PXv^@WcQ3rmZ?lD1WU(Z41!|;P<|sokPs*IbRcyFu
z!bns{nC-u0kSh|J+zjz%9bYUOxcPiejY9iexW}bqbYjncb|Zi_bjoi*ajFx%i}<Tp
zM`nT0bML%rM_ak49d@_S_=~xGb0m@e{IavQpOpNxZL{3xc?;ueiH>7q9;*1@zEocB
zu@)wSt}|QBT$^%o7ir0rW(}Yg1`|j1EWy5`r7Q<YP52YmEjuzFKs<KcBG3imXsAFu
zSGWE+d6ZEcH>u`O?h##B?uH9Q%uvpvHO8k90kpOt>iT6zPUe8i6Nql0TTUg9Z#)$g
z7TOuPTQ2}Y#l|5IYwt+?<AdRkdDO2QdMHGt7(pzN9!wmizKTr?K4`-M&HEr6Jf67h
zf8{s7daFl|!4X?Z?a&+u;w`?(ROOp$eEVkfG2zWaY-v)$8+0;1`O5xbd|B7Jv&YEt
zt5TG#a1j49y(?`czb$1LQRkCfGwRF<(c^4eYabT2l@P&G!t95i_ds5u`J@gF>u9Qw
zNW~4}Tc<|}6FIEcyOBk8vZ6~Yuo&XGrKfAT^l&8S?VSkGEL0k@VcvfgAvMP<yYtAX
zoOkmw!q8Jbgn84({1gAa_W3_OWn9OM=nPilB_is)#guP4N4o4&p&upX2k*<{T9$>^
zIKwt>m3p$0yzY><-kd!uyiLG@z7yrMNZ}2RQrNhG(ucgf+Y*~{^`6tvA>ihgaORIT
zJ$B9f+UlJBxqi%8k?7Mu$9{8{SXYcoCGm67E||#4hOEFxWv40l>$^0fiNLYT@7@nu
zAc<~|zw9t3Rm{5W7RVCt@yNGVUG2o=(k#@EQ5$e~fpOV?g$;~cs&jIMtSmzt!w7Sr
z*GshZ9}6{iL3ED%lcfgp6h|B%x_HZj9&>VibGZ%O>x6Nszz8>|aqjV<XYMhiQU8;n
z66yAXa;XILr8c6t^fS)5o(^@GQSJ88#!9zYUa<Ayh<xIKlYlN${_LTu?d{iE-6O_i
z=CG0mT`Sf8`YBI}Fbt0h#gCRbaKbg2AB*5vtkQFSIe7}|%@@Vg9Nv0)*nFxaMiRUW
zdcz!9FB?a(Q{%rMk#G%p6Gk?`OVv~s*cJ{^9=awx?PmdwLA*arbNMW26B<2kc?+$-
zn9B{tzhf6Tg=)K7yj^=_I~NfV>KW6a;c{oOEia;_LwTQ;Ypp6Qn;OO)KsNRAO1Pq{
zjJw?=SZKXcU-{mRlwOmQM(ww#VV89Srr5pyz*61ljM-uAVmdU&zv0uio^GB}yiH?7
zadq%gr-=Z1GED?pn8-$;Zbwzv8DwWjTfrAXkwc6!m13K}Y@H}!;C2JFs&sy^sY92q
zWh79OY1;a_s^)z`=-Xi&jl(+KE)viM%$ea&b57LW6+W%DXM%B0JSMx{Q*lsp2*!|1
z!P8L`g|#(_pug|H6i)QWl$NFaL%F3B{;J>9#~bdIJC}r7-G_5y#Hag8pRDy4-zQk0
z)eo>4xc`vzVOCn%bc+y(>UUQ(zo)7^wf;KKTc)eq&CJnfM$i9j9G!EB7jDjxmj0M6
z-avp!Z9Z+;1nO5A4SAU<pfT`%xg@@$Nw@#_0SE+$MSI*gUG^*WlHPUFMUzbyPz^#^
zcSJR%v=+^lXc&Q$Ramb0oe(q;8EMBhdCQvar8?w7RK++(vqs3Rk&X;;pPD%x;3~bn
zW3q_)<wl~7k$4l+hi}-0AFH7(B&TP-Ry0f{+z9X2HO=MLPsw>RoT_o0+<2`){%V_{
zD5_-9eBs>_m8H3b1>vdFYykesTQkP>c86_9P5{)KuIuu@P_PccSA@)obuRRJ@o&}w
z$bo1k?3oc}%$c<Rv)m~DCEV3Vny{-Q%hPC;W<kbi>EPpB(=3T~L@vx|M3h*qK@{MH
zNMcd{9x&^kUS`=q;>RYS^SQ~05{B1G9F*VE+XQ1b0OlE{NCvYOD*E@~mlC|7T(W}J
zUH7R=Z%)1BU*%Nd!(0D}Lky+3;J7uH^S8KZNkjf1i)u7ycHStZj^Z@V6kly!l3_3B
zeAR9={6r1+)q}{gjVP*uZEwZ5V5cnr?T5B`*o8?%MA8Qutm!wU32_0?q=}v)eW83)
z&nut3VjkBJKVv4`;T4wHZ_TjN%OdN0J|KX=CpC3LFaGg=H4m!U5N~OM4k}im)F#&N
zG0^ld!^bF#M!`-mo7ih#Z>gNU#NDi7WJWG@+~<(Ocy`6EMI_&6Hm&d{^04LfDWL$5
zIDihbpD#YlX)d?k=F!WICj|xMl0lcIQ4P>>S&uVw2tJhLQH1UU|7$C1=%IajLRHxa
zv~We0p*ybdg*Lic7~3EB_lwmW)%p>iwhTOpx+mQB%PFyLUe?K5Vn@&F@|%9E<(&lv
zD0jJ0g2MyYj}qnJ92s6QftN0YUZFG1!ejb*OxIj^ITon?gW1UCcYuIYM+JxH4l6DC
z;)$CTXS1$><<>0}uR!*wM6%8J{?rysL91v}itxNTzmSP@-sp)5d_U_~X9zfCY=pkF
z#`RVsUuuUZ-n{>XPq<eo6JQvzAAGHw?b0wVA#j?0+&nZ}fM<xs##j7B24m2yExe*c
zPR$XwxtTu4jd~vp<c&QaU;vlu(!@`fr@R7h<(3Ostsa74WT`+negi7nNmg?GvXY>+
zp@)Q`UuE?3Ej^}m!(r|>FvpFuMAmS6)wcdzex6Gc0!k69@3On+5~wnyf9~E^w6^uE
zTv#~lp49Il?n>ZyljN@7G+ytKNyk;$Il$2F+-?w6JLj*=)PEMoJQFB7>+N3gB{mFr
z-q<8ik36pyuTGPMJK*$ay&dIhy1m6H(&tui&mHJGbmvSq*gieW#HV6{)&Fi*Y=U4x
zBhfNv`g{aKpF9_mn=<~gbycRXZ+^In-TruHkjtvKRnu`!5E;oypFIDd`P#5f8aCB)
zK;2=NRw9Z?v$U2u3B0@MY@W`kUUiL+l~?1w&s^}Z6hk#a4_NKTSCEFWljD>?vJ?S9
zQ36V@E3Wo#U>O4If&kBd9lkzfV8|&{@pXk-yQR6a<Dv3ZVEpNR8^~pnE&^F{oog3v
zRPXy-b??j)sAU;4vbH6Cukmo!8;5SfEdzX{F!~Q%KSk+$2nR}~;!{sNI{*XYeecHs
zxyEN%eLg?{OPp!`w`U}4IaQF~FR}XmYW+bFKRmtl<&^FI`9D$>;sHLt!xZq@KtJ$W
zYI5EK#jgP<51pITC=U14P$sgd?#$t66w)Fc(~@w2=!VF|he8==yo|uF-QV)D&!s`@
z4{Y}1XmJblqjp@-iNNhCj$z!t(XWg)JTyUY(aEiV+agi-+@t3yix>ny(31=fI0Ko3
zJ1?_n1r~3&A0^$Gu3oExGQbrB5?Jfg7Uh;!ZYk8|6Ut*Vm}D(o-X!k0m4ELkzm(I!
zMEvOu7E(G0Cf)Q3R4srn)ku1<vX9v-MUErtRr02h@_pZ(4GSI8nDgTxP|)XTQtd{A
zAs7q+W)4oHc<Bgd6PNu9Qt2GV54Z9V@KCP03$pQN4&_;vo32|gu5>6<+C9r~doMZ7
zvZgA*i)%KC2=zP2ucWlq%R4n_zQ~Ht2`amAo>~T@F9S)){vJ-KwS7dVa`=kPQHoak
z)P-A#Ve5d`wyg5<whz21zo-FQCaQ&WOtwZR0{d#)1QwexZyG1sy55)vg}MK7t^D*8
zMXmNx_$d6LbEUgMmZaSP?fb`DSN(hfx6akzv--l4h-e(Q>rki&bw|-I>1j0wcS|%K
zhiwnd{wpj5l-JeQ>jprm$*C@L#WFx=c$owRimLlOSw_eAz=u*$);n<^e`~TZcxWB{
zhmCI0kV;b&$hh2d>CMwb@7}LJLlpDi{0zVCTyhO*D)O^-`-!UOGD~pP-(ASb?*GHp
zPIlPAygx2p7+tZ#4s8<a2r({sn9&xu@T?lUe2$V6x0gxAxc37VW_)jphSeJU3NuBB
zv4_w1@?(HBlvph5tE$N0F(!ZG=|9|_emWSn)YYrld_a#X-(G;3pI`2g7Qq$c_izXT
z?{H_()YGFCB^f==%%$FiN@hkC{`K3DXn5;pc3b_TnQ2=uq9UOYc=OAa>EdsJGrPLd
z2%pnxf{AWQc?|H;h{^t&o>0OHEV+2An3=U**N|MyrT5;9{%fg>pm}xe6batR{!PvB
z*U~OUpTFoDbDy8iZ|JccIMWIptegBQex(ErtvH41_T}n~t+9>wM()Dk%Q{zN>203p
z;i(4qS(Md**KE?qGVtJyVdRDr2X`f%Iuunzb%y0XcOoC#n+9fUhFj0;s0R~SfdfC3
zhzykf5-4LJ9H^NOE#EFKov0YtUQ7|UXTk9KJg_ULM8(e~A1!={pAz#6ePB5mL1tBv
z(Q5nMc{D4p|2((M4=FJoAxQnCj;)ifr%`FmD)^Zy6cdDFT<ds)yP8U7`A?c3KI7(p
z4=9>cf?N&SL@H7YAxhYz6L76FRHgF{hwL7@Jf4K&=-~esMHe$}3p`B00{R}KS}@TC
z7r6q4hhYd#kXUH`*UtxGKQ7SkFo=NG9zMzSB_J3fEyvK@8k8~`MEOYI>mhEvaC=+<
zucqPc0#=g>%;?M{`@2<EI|r9i8#NHrp`3{?3P%&ME0v2&`o~cK;0r*(%%t6}*M$&9
zb1Mw9^`okNNSAMWC*S{*Im!I#Q)1Vj2Ki~VGC7&A@`M?G#ukBb;FsWkO5vZdZBHhY
zUq2-!jnQxN(!*d}gRLfS3OT3n!?99b{E!r-1if0wcg?N#_e+wV^1C2YyYoqRa6(QZ
zMP59xfOmB)i892e2?LTSf73DrhGlbD>8Th0?jYHJE_1m`qiog83Wf|qTAJkX4LtV;
zZ>Vrefh_?#GoXxeyW^`5|12Ha5btnw@4npz33r)I+hE8{7)#=7VNhZ<jEoBQ8<X%4
zTim2kMj2(uZ=FPo*!4FijA4uAk|*Ue7mcSEJ|I$`#Z>M9#($dA?l)&?g~LuL2(1!M
zLl6gU6((${(@~qSc734D*9ICYY*KFJ6hIN<wGVIVg8a5isH@Iqp~g){JU3FC29S$V
z+$>R%AWnq=!X4be&@LK;R2jF3lFq>rMr-2ideRBId+GwDX&q0Wxurz0oNu!;GeC7u
zsU|9CAax*0Gc*}XFG#|H(NYV#)hK`)ZGLj<sM-Hqb2i-eem@N#L`GRap7jRBgiBS5
zQ&8Nyx4u;L1jO%yUx9)XmTE{9->+8Jaw#J_i+0(5U$$xsM>-K0R#Ci=rZ8A_vBhA6
zrNU{AMGBfjkYACuza>GsI<VfrluaSOcDogFRgT<6u~!bEgLR-ZV-2+49d|fi*C6}G
z1qX6T-K<qHz5R&A#q8zK`tSXHkr~yaZAzNzVfIR;PRUwny28muP$_!vpGD#PNb41~
zdRhA-1<0BlLp$mfw-{FSMXrBpwWX7o^1><n%^i8MArX_Q{d*^mJ(NPzbZ3nz^7D``
zFt_{K%6;6_Sx<DHgVi+!(t7j!n-FT5g=Sq0<uA0lDs7@|M@B9jmbj_Mo(9I_-t$TY
zfIENlgj?A>vRDzO$2WP4RD*m9snN&CU5)g#<KI(%nd8UVK98_vjpnXgKgFnEK(h$r
zq6e`kXJF(=$1$U|<X9lECfo~)q4fk9iedGB|HEGEBqE=0F%c^jDmE`mZM)+02~AAQ
zUIf>A)jy8HPb`02MjhR5n!=w9S{QfR<4qV^N}+_HWh_NpJMq+^M}YsOv5?$wl{yFV
z=#<*KanuX{uS)7Ha5MyJ9KH5GObf*hlN@gKKYb|HRxS9#I~V!`ZvE!ML-155`48gY
zdjiNR_-%0YAXy*D#K+KWCk#Dl#jrCJh^}5VM2DV`sm<I*pXQK_<eZFMKx7tc>E>gb
z%aUt2OiobZAX)2v*2>YZf_f2)?7p*Lkmd{ot-~86<A69wa)Tuy2nxFsq1vOfnAIw0
z!%Z$;hRj>=I3LY_ED%%w3>QmB60e2Q{piB`+Qz)|WEQD2P8mX`peV0WTlOy$w4W%?
z_75B?HkLZ+=b>}@j+gL;=SOqjO?Sb^tMN14X3Ikp*$)79Ko<Hnl29^|z;iK}*FByE
zxisd#+08^={#AorT7#`1;EN>1=jk%mHKzSE`+Bq=JnRiI&sw#|m&_Jqe|o@q8LmY2
zeL1T1en>Kn=O#rl1_p<hPXzGWSCUm65SvR>(`e3ry(Syr)w_aoW;&SK{hEzBc=-9o
z;5Be_9mGBNRP@K&IQ}^7#>{w`3EebL{UKVoanAKp>FeHjV(@rl(74SydMCohp7k_!
zsF%!heed^Ka9Hy<|I33U@TR%2Qhi@Lp7C4icjsR&Do^ruw0|DaWxoz*Z(aF5sJ1ld
z(L8ml8muIV+$&3BP{UEStwr9vzo|1Tjcb%PCB+Oqg8|oNIpcB;wUIvi2*X3MoWVNB
z`N8BGHS^&zUH$H34+cH00^ZN<y^4}ZBi+ENj&$~q?3FKdG}hunDiefA4R^#-kVa7&
zHg?zroPPc;q%Am3%-AM7>KJ-QLZ+6p@s&3_Q?N%hQM;Yj_pRh~LrI&2R1Q6D(|zio
z|9?-ciVo$=CcV~Ik-as5KEBjB<@Lc>y>M<>vIdjZ6X$w9hv%42fI6F4-?pHnG;xAr
z3IjJiieLEPoM1vq9WW{8{ZLV#b}v0*pxZK3cpOKf93YZHQR|gmr=J`FLdpXC3s`F&
z_|N7zX;a>hkB^;Bf!uMC?>VK9Sv#R|30My#AZXzQO2$|d4fpIqbs1S7Yt#4B&?vef
zuGjX7yHBlCCQjwY%kBQ?^LXm0i$l@(5Ka;FRuUuk@<2YN<XuP3=0c1BbYa|T=Fgp{
zux0bS86CgJE_E=wCxY68pM9i$Et|K^2`gjea&JO(5Qk^9bS==R;R|yvmX>83pTB77
zlv~nyGkqybC}1rn2sIL>GFGy^DdzAjE?p?(Mea@+mgR`>OWvBJC{D1m%8@DAu-o&(
zn_v@A?zs}7sA5*lSv{RTe8BZrIrRj>MdIMw<{Vb<s-c-qx_<-ZE;f{zb_}NA%D<>p
zVgGa}+M_Jeah&%R!DWn0b7Z2z8BhUoD9|v&ICIQ$gw&SRPCnS;>RQ}QnaU&BgeMV$
zGo36M0BCr^mEE7$YN;Pgei^#b?Wi4#1{o<ek}4dVk+&kwg%NTTs<6N0h;Z|GRkx1#
z=Fx#~X}X|Wv3&>SByak1&)%OcIFS9+cLy@jzBY%gqe{gE^nve2dtEk8Ad4RkNCyOg
z!r*4cjuy5+0NPDmTG{GmN4NDGjdb6aDf-r?W{G~p`*q*V>5L5AqMg>)|5`zaDvdFS
zzCKqnG^p_)PGNzxtzY!1L`GVs>v}ySJXiD^XA6j%HU}uZlTMgevZ`@$HtxSc9{#B`
z8qa8IgRIcxfBV;UF*9UfnaS%|QaY{_K6zcQ^Yq$vMX@5TdvFo!*8`u*x4$86D7Hck
zt9lvZ!G2N!*KR=3+39ysE0pQB#PHaxnt2>hg{4(Y=Dy0Tkt0s~^7kGoMD4kGR}T*c
z{fI<+bxaHJ5#}M?A%NT{D+^VErq1T$Ww^r;`J%;}{WM6;!bVjvxFvd=4YzUo7Vm}#
zj5bjskyS8psdW4lL-F==5v2y%#1;0{dd9uhXC>c;j;LUNQ?_&Z#>E%dgYb7Nc}eu4
z0o4P}##NpYEtLAgiyNqD5CN|7NI1qhr)|I7s^1cYANWY6+eKjp04GU&*&XNjad|>A
z^ZaiGzfU&~cukLkaPadDnS=?7av0JSCVvOPui2JYPF@Q@Gp7$<Z3jm&XO8BSAQTqH
z&LXo02}`gs3+5j6v;>ktN16RRV{77(ifch(_wbFmw--DA&HxpF2F2kZlNIbqP=gap
ztj*_-{uk-<(cbYXXZWZFBx5n>D;S!$KE%30=||BBZubexMM?~7Did!zH2TbeGLn#r
zE6W(o>fe51Ol=Ngv}I^-7UMD6&!1S>)eV2A0R<C2kG+Q?3gZVeQC#fihPma2F>Wus
zaly%X(}w_-#m=6c3sKAw#iB43Q#7Oxy@Tg}F10N`IpINdC<wEkkB^x%_6>dLqA5&p
zojB_%{mNyf?qc<hU*?N<wS?`2uL3Z=1TjNP=>Rwb(Fx~{7)<^Ru-oOs>6HVL0+WX+
z9S=s>(yisTy@oEDHvLZ+)a-N1Br26Rh_<@j)^~$gr^{hPSd{9WEkIP%!Qr!Xc)o<0
zBpI;#6-E|eH20n>*r(H_Ph=9>a-P$|+Qp8Ks4Yp>x=#Ak18N+3LCdD9DK6=|DBc{;
ziDkH&R?aC}M(r;CBBIF0xg#fjq35TH$`L@{>$<r~YWxfA_*A+3yS;I+DVfR0oH6UA
zx_>a)5snma?H$YJ#?|%P5SKZThU;aIKrb2=63Mh<MxFG`OdR|aE}T9PB}TB>DGVpv
zo{_{sy*)@0>FsImaJ0dl`eSsKZ5}tBmd(@Z8$Ntek3~pe?i$IjsMY+f)vlAt66=m%
zX+yEps^SYav@57kKS+8`AHXEjz0UyHMa3Kf_e68Etl~nAy-KsQdP_xblde&v$;+D{
zAKd+bV2~=HFgq4AdlrAG>Hy+Hi5X3t<I8MVZT3MB0aMg{yLTXBxjbhZ5yyG~_VvY9
zn|gS4!i;w^X!?Gqb+XNBv-<Dsml?)PI?E&p5TtZ#+z)6RHvin>?(Uq{sg$Ldeq+8^
zPrG<q6#+3D@5#MEclSN{kCw7J0$oH{7;P{G5F<wB1(`qoOtIH`7X}4M^OM}H6<xo4
zM5DOK>RD^+N)kFs!sC*$k<VQ1(im*_jZREg=p#w5`OE#qG~h8@Oa`oim^)T=T-D1y
z5c$-{S%SqjBA?u_%r$`jhR~j2&`hqc{}TL3(6BUZDzV$+YU|%a<LPd1tShb%vPKq=
z)p2XPW*(Qn8E|%!nvq3=<VysTWOv+BAJY<h;N?g)@SNqPn&4!lK0PxNSG*4pY8NWx
zhUxq;)|BGW9qS)H-}%m)*XRoFAaCrkrY-NPt&Fuq%8L>Fh;5d$c@Og7#bbIbzGT^a
zUC<7Pe8VKEQ;4(rtQn(2VtvX5C$dtZSeaShTkGtks#wW1aR#wsm<KKCGz%I+qh7Sl
zu()zPe~Z9dA>_l8y2tA!?-d1NK4avv1Qkz$)tRaN-j9iT%5fV(q?VZ<pP9SnB(a9z
z$gK>ot#J(lqM6O2<yoBVGKzekF4Q7TkBa?2D9F#J0M%zf&b0p~kW5MK#xMVI6*0uG
zAFND{B6pSU(oi$KUxy<mgL7%4QkdIICH5ttK3iekdq4CjMfd!5W$g?<ts)m6Z~Zac
z5!y$r;dt^acxPR2H`M(7fQg)yx%rfB_wgmH=DK0i{F0+VbMB=jb=Iz$MO>4W{kpz`
zD-=^GoZwG~NmzJ!8nF0bT!C=wUr_VQhH>kv);2&wIy@g3Ia~j>ztsi1L+!vEdg24-
z*D#shR^gY`zr3q|@oB%uC(^-&Q(nKZxUKSue4^M8xkJFt6I-NlsBnarpLA<=d#kr1
zh$M%NVA|cOafkC><4%v$n~M^IXd^V?lMu>5|7O<knk>lv3p=bL2<D^8lc50jr0LXW
zck(lw*J0mt>@Dt27o^(gREOK{i2D7S6&qF8$7}!9Gf6#7_r1vnc7lCQ-*t}&>?_W3
zA@>-Ov1ZezXP;4*<(JU~+b^Ra`6K4-i(Ka(qR^`}y8tCh_TwP+RB2#3Xa`wi#gsEV
zexkfxRp56F>5d*XMiN2CQ5ZvtW{ScDWWCRIk*)Re+)1o7Q2);h47@(7Q|a)|F4iV!
zQ_*hHVGj0kRocJQ(RbfqiEmyb_7{&OJjnXq$sRxv_YXb{anf!uU!>yKbAH};q^I?;
zywsjm_kql}ha_N3&!zJ5rb1d!8#qXuu~|siY<&$W?8+xiswZ>tp-~xjzJcv8bpQC=
zi1Rn(vFOTEVn0a(qUfx81fPT1^+cyRMhK<e0*)Y*_`Oxz39{pB=r}4ubwo%UoZh5z
z&)7b{j0lF2lVST=>Y-TQ^)^wnkrB=EnV<d)mE7A)5BGH+jXQi#!pdAalW>bKQ=Z9f
z%Z@kpbZw(%)>K7d*Uf^;SeSt<K_!OTOC%Rpw|By&6Eb$)-%T3=@lOR8mdOx7Ru<R_
z!Je@#m}w3VZ7=6W`~zRm3eEqwpzLgHSdWG?%HA*_+`#gHC5v;9XWmtkg*qf&DUdb)
zXBO;1GDCvzeb!Mx@~3h__D1WwWcH1Qek;ndaE;G!Hy>&ur9Ws$1H;!FzCv?4d#k>*
zj0n}7^XhkCwMx?yPGqHBU4FQO9FMITb7D86B0_#Jy(Wt6O%0H+;pnFk!3ewVm_!X&
zp|IO0A{vpH(G=0T<<Z6mS9$dT(-HQsXNBWub;#q7i)*Vk$NIv`3D)hCh1N)+4e7r=
z<tJDSRyu6EcNDBF>nL#5TIcK4Z>((TS(}dJyxz=htIp2gA0yu;GMNY8vRm-=l6;cr
z9bD}8{?^=V?0I*Un$%JvRAFlXbL%RQpHSxNS@PROj0&tEVf^1f81o6cY+E3z!=K-p
z%YV<>p;pc@O5=o8FKLb_w(8SjAFIz$!Irh`M&fxs84(ZV^bGx_8_0unHuJ^cao;27
zmrxTi0WI>%<jLOKo&M$y5$bO-vsof`^lv<i20L8C`I>^U)TL)b$yc!Zs4pWFS2CCS
zqm6ZP`oTV%@u?+yzTv?w=-?}Cs?0}Q`VDc?wf+%vc{o2hXv8K~&^Qr+CHETMiLc|S
zXAUKL-FGfR#IbU2ZS@gk(9ucMXQjwVx0~sWO~gupGQA8JZKIlQO&2f*#e$N(G&xml
zv88Z+<%bKUQF%vBaVC;mNI$XNW(1O951Z=}W7e)8Yr8!qmrh~dt>%6+b=S1|>o$Nf
zn6_-#eO%Ci`ZOWo)>t(g{Pjj)ZFQjs`A%aPfz<Bg^K{udh^i0D3MD@wHrgn;UmFkb
zz`wlZ944I#O#u?#lsx77<Kq6Gx)><x!aFTv-_wQTnrACZE~~_1gK{pdZ}oQ_AhOXb
z;(zSLmxHD^uh-e$=^Dem`1fWDNn;mz@%%0xQPV|cw+mg*{uKGA9U>Xm()rPaCg@$C
zI{(a2vCP<eY_{}BM{6}xOi2zw%MZr7gd4|EoK{(WLs8$ENI=rBg$9g3;!Fu0Rm3q(
zmxyNgflR7av(pn-b*%-1HHv6S7mBII9o{cX>-Oi&8r?RHyg4bp8$hk#;dMZU$3apv
z<kQl{&rNFY*2exqUqVu>OC5M7dw9%jsUY02!1BHGEuw0qP?L}X?v!sZ?}TZfnw7)L
zH2x^5aEOs>885c|**q~exgkS9SS^<3`ldWVUmO<o$#76Wk?WfS{~dd2+}JH=H!{YD
z*#Ae;RYyhDy<I6u0V$CjVCazU?m@b{yOeH}h5?D88-{KH>5}f2kd!XzPQUy9zO`8J
z4~x0?a_%|Lv-f`XUSP6Ye(j{D%C3c~Rcb3~Gh>`b=~0GSv3<<}M)&waXhgi-fcNcl
zcHl|@DX(3Ghva)zOzkKuX|Y3f_JQvN5iyNj*m+5?^@r8e7Jr`*+1b^mxa@K!#n^Yi
zRKm$S_4S;$qQByQ+IRKJcJX0tFTUYQM^yPXE{xj)p|(SzSVdKg^j`$rf|Q8{|I0=S
zUvEBR`cQ3RQNO+{^Gw?^Rj$U%1)vdVe7M7rZ)yfM{*py-xw*qB@>fivK2NZxk8STa
z^%_a(*c->asks#=gc_4gV+i}2o&5|^0rJ|?6%n-1JcSaErwTT10SAh@@UWuTa9SLi
z!lYkDsZH7o`wxE0ya0(Ffr1waOS{bEspcl3baw+rGNq!XGyOtQ!x>_HwyJ1(d6%1=
zm-2_O6i9Yo?+#NE6e^w-@N5=-WD#*M`ie^jWmiom3ui*#RDw6lu=s&zq(;)DS+Spl
zsW<yjkXu>cjBK@Ie+Dal66I4TfTbarO2cr4Om;hL`4Kj?85-pWVR;l_5b5*z%<E5p
zC*z3yVP^3WQ=`)vm&uolpoT38niQ(QnG#Z-AoseNZ$hC_aZK)TFsq5@7H@5gYM3mw
zMKD<WJ@VR}3uO>U)t{xmnDW*(j3>B{Cgp8@%t61?k{P)S1F&|=1h3${$KPeaNO1l>
z(#q5!;-KJnxBG)4!F^J1F+5>18dzBUU`7A-z9M`cmtVqYXLzad;qrN;4QHEdfq(J9
z6bV@8=Bc1_y9ge|If*u@x`&w^4`V;KgocLa$+7bCp8PNln58D^#q`%g(uXVfbF$^G
zd*Xp&;C_{t3DxY?f%Dxtc_;>eUn)%h05od-(Jc;!$K0iUC$aYGQH8s=z#KH{%2FH!
z81KV5<DtNXFLuq|>2l57ygNXG^W?u0!iOGDl@MN`+NYux^kKr%ocHm;9Op>YJwu0d
zgrmP_4R{psRu}*mq5O(NDG3H=#tXoU3yR;)K&^lWcs(f3Fn+B%Jx;;N;#37YlmoFb
zib^sXnpjF5PCp07BR50Yqx4R%B6r?6ph;<^vu)oR{_{L5K>Gj%wjy}YYG`#iU`E7~
zDbX=rFGfL@`>ww)WNTG$7X)pYcdVT`ar{Vjih^*oN}+S4L}u|NAQ9%I@x4k&w7M$k
zKv&_3ftt)PmmLBaEI_tD2k-74!5J|!V8-|wA6c<aWYQF<Y1PQK<ba8;4LJ@MYRKya
zRgh}3`@isFfYQn+hhr0Z-tNAy^DqW(B+??7fldLhho1uMQsNp}CBlS+iDjfVrHLY?
zRqIZ!q;_(b0anNB;~<|b*(w<x4ljpsDLG0F5_{*#x-2yY664Wvm<cyqt79i`XHd@^
z6);(1Su9RG=Y+6BW**H<YhmEwKlN#W#I-Ajs$QSkRqz?ht_`c3mbb?`=6(PJtpEgD
zz=YHEZ3vB0%>QbA1u()@0VRZf6(^h!cUhz<j4e|_M3UsN%SUtC_evZ3Tq>*?ihzc9
zFpJ3-naGyHi`3V=;X|;IhY=CuLZHNGUP?Ic_wTKkaj#~HTBvf`uY@)%1=(i4NGoaF
zM_v2ZVlFLfUD7NT+%kIyGpV+(0oc4lCjM^GK4rG(o$i5&dCQl#jI<~nJ!L)hhWqUk
z<z8X*&|DengHWE4U4r+lgW*jv(C~tt#jBdcIfbkraZ{Xp(}dYjj{erJp|A-Df*20&
z{Q8X#RJdsQdFV(~>O6(iJm%@&4~=LQ5W(mvhoDeNYKs}?@0Ps=J*q4ejG~kG6BWOL
zwUC3QW$&V*sgs20fU(#+Dq8Lk(c`K0g$p3~j#ook=cMa_Tf#LT;5@wwu~Y#AtO*-B
z9CZ%zm&}{o=~b#iTCHr)h@C>3zgR&()s?i{-%NP0aXF|YEYv^hH<?@WXVhE(VLuCh
z5*@N%r<89DPX7_`|Az{U?@T5;Zw1i`ugA1FB8bIK-E6EI+!}WJJR<_$wF=$d{7*Qv
zpUdV=%YJVr?-0%l8W9;N=?74LfbKuM#D5<le%%O2I~En+xyD#=W@V7sG{*1kFA^8?
zf)YG`%GL}v$R_@~xb2cyZp+^mRWCcMd0F~kdiX%Dp|Z#4(Cz}11*g$s=JlzfQpJ}(
z*h$bQK9heKVawpQCgHg8oKez+g~h+uy7mov$L@B`0YsTqR1lv_@X&3w;a0!HN2Cjz
zFHVnslL5h9mn&RlT}R{;sidKHq&hk+&3ZOPs~ZX(5`Z}GQPh~2s;F;@+tH|(*WDTu
zWuX2&MLOBu`2piD)Q2<tyz`))J+@`Z*45f0yGeWA+ri_T^?Jd9k5q8wCcom|B^hbW
zS&I~EI^*{HNo!TWq_512Qqv0`JoN@qTc3Qw$?@W5NsttHT@RI7CB#3V0YhAfLDl7!
zSmeu7>C8lF6MF)J+8c?N^_unXIUm7cO}Nr;_xS9emiZ>m+CFu>`6=1b_d)ap?E?$h
zpU<>}nT|Jx6QAbqPIf9-8ubm!=ML@>0Li<ZATaMiow~Cvog7kxXCmN|6k}%kw_cJi
z1qKir$(|9InI0(_tQpUuI;5<J)gM=nx5BB;m5e7kK-++-wBM}mIZ)M;Ebvk%FiK%S
zf)Yjc+ZpcvN7><q{9q?&w0<GL>S>nvz^{_!9?vNarwVmFihe4d)HI_aAcO={V_{ik
zNr!)xzW-N$n=1jc^6{j<@zZZ6%BNAUP*8(cv{l&aN2jm7|2u)jK|J<#amTzi)TIT4
zz63Lwk9m?b;0nxRhv{y?gxHZJ*n;$4Ilc->Se*^Yu``;Z)zCT|n|fQ_KMSSIiLjBj
zlD3pCtiG|(rWRR!HtIU<ygd=QeVTmFKq(=eOfMcU4>SEd7FtrK`Xm!Z`rEztwF@2|
z?Z(esJ#lGC0(G}j{;2;3z~keQ(Q)PF<7L9q(lXkl<L^r0;gQ^n8&@tgm<apG9&j)<
zl>#B-R|a{cqJju~gFZ+M)!ys%Hv%o8lzzxjd}y|~prA@a@pnomOFBdHJ_FYR=G5&&
z3ZvyAyeTuXxYBTN;VzrG+%v-OG!Pm!G|xOj1X-HXHK*gmnNmbpmVjO{#$z@wj(q@!
z8qPq6Cdslqcq!@s@7?Iu$!z!=+F|27DBgR$0G8<V2r7u_@00H*SGjk!IbMzoB;~T<
zEqQlS-;3B|XTHFQ(a)pkTu#HUL|gfI93(kaT|_$eOtbpjgGB?$Kp4~=-{V*m>_}m&
zgnT|)Hi8=73@sGkx1Pk`9lhT3)g}F)KP6ngaXh)sXiG5{V<gZDfpA5zF)x~lr~UQ+
zbPyq$s_)=mEGQ&=^a1Wk55b#%AZiHAjb?UOacC&JW+f65dB~Al_V^qU&kj9*U3MJ|
z`V;oHeB10^ly!l&pi%FyyMSKRAC$Kx^ySNV-kEWvwCK*be~@o;drv5OR6Kja&Bx#L
zY<RVrmBW`0J}x{G>CD?d?VpHbq(}{V9QaZw<4#?+=L@=V0Y?(_hEMbse~OSEU4npP
z-QKNcZdbcNX4X^p(A{p4*Jz>0O2}I+^j+~D9RzPBh(!6^zn$H@W1(cesd?6xBYE<C
z$3l)F{k4_bKV)wh*sx+w@8s(4pu;DnO+>pjK-*6w3#2$KM5TrJ+AQW6)!i^Pc8fE6
z^0L1m;^0xVm4%X@RWR1#iGNqNs@t_`blf+w*r|TLUiav>R`|=*2Qv~VQBeR}6ty!k
z+?&D}w{ERo*U=03N@Lr;>zVFN!peSP+w%Bm^4X-QnPUQYY*nAO?hur5&u*UZyfRtY
zYO36te#4KOxgANxV$k4dd@<icxV=ZvB~Kcbei)@%By)aHQBvi6!|mhMN)uyIUA54n
z_UUZn0)u?8A6-&EHblgB(39!(Ti|cz6_9uNWaC>|Z~gyu^sfqMb?nYmTF)R}aaKLe
zQp8P>cs6IP?P2Z&xblk%(j(^B67f;ym~T;xa=POV`=TO13}_()rcyalM0JbZ*_!E%
z2STDs@~?Nm@yeh+iI$;y*i&1r61{C+lps1f9(5!qv=n=?oFOuDMdu0~sZJ074W4>K
z9tdq89>oyZ*T<;F54sSPK!U_4$XKzbsP_mcNCq$VV*7!?1WBC6f2o0R!GZk<Cpfz}
zF3_j$ZQ~VZS(F7vzrW<SSYqk;{*BPHwg>z9yV3_+8cYl`yziT9{n(EoGZo0_=t`X5
z3n(}^@X3}g8H7B{gUzQ4wU0Kv5pqapnuLYL`Wi*%=UaaW@k-#v&YT*X7Vg;l2?aqJ
z%!fws=}TwSE7NEzddp}1;Df#is?&;3ip>@F=rjEfvcL1w*4%T|F`FduW@kD&K(w6j
zlGbe~EG>3jsfrOf%y~+Vs8A%C?ww}#ZxLK5fWw6%+&(yILIUBTo3iUX!kGrEue(Lj
zGY5lU*0{7B#g#LO!abk&!n{75HUBcq-}rqXOEKwONkQNO!`p~H#(t+We^+uEAir97
z@Q71uFOQeSKY*UM<y+~_cjCs}F3b}|H#$ae*@g$5#GLmHV5_RUC=j}IU+M5$J84q%
z6r-U5mOcCSi2k?J_4eMllZjdK_{_F|PsBx*gc9sefC0?>a481itfg?~hIE7Cu>9nx
z@p6}1@#FLb6D3>CMGc!V)f4h`>wV_aRQ>_~ic`b=XP@L@!<4LIb#`}6J<&5V--5r7
z&qY>i=_cE#Ub`;ArUsbboE}kZg>EO$g)pPXh%gi_>&a?ThVATBCnT2k<j&8Q4tzw{
zTLMEW9C+BOE1j0<K46{q!~=fxE5}qAi2r@=M>%XYZg;Gmz=JF0WAuWwiX$FTL*os4
zuXi^q^FJ>9PYo(?mXU$!p?8G;3&MG&rdmd9veR9)@L1mcgFp|&D!lw~C;vKWbAA#X
z9Euhh862BWMg=hkPm>kDs+b{$>dL0tn29qg^pq5A+i)Fz6FqJBi<oO*i#@s=2@|j`
zhEB3vS*eRD>SdGV)Pti?6A=;gR2eGpEukjJ;?mOMmXc!9kZf_XtTxR#APAfqopbAf
zMW85@t+;3ir9lu(kB<kY>R6>1?HtP=dymB^1p~)8)JsDI8#N(TEa?<a_o6*urT84)
zST(hhc;xgf!@eX}g24&~csR9v(l7Lx>9hwAI`mSwvZP`Xa!74+7iT(GNilz*V-|Z%
zc;9C-da23$uBUDuHY2^wz0-ACG})bp4@~ZQKKpDhuX}>ve;}tnY6L}y9-N$SGibs#
z=^PzZg|XluP!u&3Tm&BHlFSHgZ^G+lj|F!0BL2=#Vo#y@k(?1@cG{~X4#wF~eM!PO
zk?Zrq1Svw=Iw+JSvW@Aya%!ta+c_UfE$61P#^*bIcsB7Me8X0>sDjaxC;V^xT*}a{
z>RipuYVa1w%+8qIJHGZIP}^qK7@Rg{|InX#{aR<i{;B>}%)Di`z-(FSw0nH0oGF7P
zQ7!q3kz8ujCA`y#6c;7vKr*K$hhJgXn`1XL@t&+^LJ{yQYW(*n&0ycX`A1!&%rTF_
z5SI=Md&20+Z^^BdZT=Yw2$>o#J3(0Nk!zLq;LS6uCH&R4M>eofd6nE{WW@pDv3{eH
zTb}ANXekS1*|4xj`Eo|@e|@L+GO;HnHSFDt=#11vsubwz6(rW|pX^t4L&T{@fUKxx
zMwd%pz{CIx#Yc8GjJpn`6ocv>U*CUu+9sb+j&XzQcfY~beoq}m9S;A#*3_)_X)^#$
zU_^j?(JHI9z(_3E%91EvKL7Xjpp~tW5^LG{9>L3i^+n~&y;R_3k6z%`%12E_e7&WA
zZh%z>k-pQ**~nlTbmaEa+WQCQSQ}2u*Lw=M>OI~K3xgNWRNe3C(VYf&BD_vq3fBId
z{+l7q$|SQXj$c1dgMwY1U9;MYIkNrE0@Pq<TWz<tLTt`yH!alAc3}~~@}y0jr=lzk
z`Y=|G0ssz>jecKqAbSBn7!=8%?h?_p${<CwIJst9SLCm^n9}!FRpM3DJBuD~)y3G!
z@#Q0ysvj<^U(?I*!k+3M$ID9#B9~GYcylRbRMq;b=tj%)3ZMthSJu>4TW-+2H(eUy
z;)D%O>o!C0L0tZ<5ZJ~eGIFR>l5j^J3OK0&;tJ4)3vUT53AhhBUCl}?iU+4~ac@hI
zagi0>yy_3sr@<DYt+`WZlem)l1MLg($?UP83y$Zo;*d!5U%y${lr526zs-rlS-FI=
z$DYF@Qn{Gmq0|bKhUc{CcBMi5AOuf`CQ7+0#7`fa`x0dj4VXdbcu<gqydWGjbGB@0
zh3|C6vUsvq2I2J4Dk&wgBy?K9B@>Hno^?=nW6fe0Pu!-j`yR8I)|g92&nNs?cC+((
z=0!1T_Cd;D7#|c#b8@Yp1n?E##;GuRG|p`UGyy@=`fbaCBB3R)jFw`BO8ewR_R8Pm
zYp4yCGW8<}SYV^|gTqsfHp9#gwf0c&)TFb1O0$jX4oD{$V`*s^&!#aFL~bIB`JV-{
zMj<XZTqni9U)hQdpV&}ONSqtVfwT-8I-6V)LkOm=!m^6<nGXi^j2D2v-Ab*&q2!t&
z$nuR4_Y59id^}a>M6_(wnj^Pb7qQcVd5nE|jE#BBR(x?b-VBC(5BZwx92cjp4OC)w
zZ_vJT|B|+@R?V{{86&(*gF>mJ_$A~Q+<;0>+b_U3XVSij4~tx&^g);SD!L5oK_(@E
zHleZ{HV0(y6+4m;xM#Ol=Z_wEU-w3OjKa70S$?$H4L5HAdAcWgE8d-R*0rltH4a0l
z#BCA;IOsllc)(WQUhP(C&Y1{!aPTOEbASlUI@U|JT3I|=e?9O9Oag_>lCpxYam5^m
zR#=%oTNT2x_20<gpPFo$&e&x*6F$BCyPG3SDU?{~GHL|rtOP*I<VnlSC#5qpm8J$7
zMa$*=pDpwvKDO^=mkH5xbd2ZnZiHBiMAH#9+UJv^_jCidH?IOoyyy4!%m&|~peu3n
zC;PoQ|5}&*M(Zzt)#4$>t7$6we1e3LmQ~KC(|f%c{Mo-tvfk+y<^28jqQwOHM?eHm
z$v;&|z7ku@9UGOKk0H{kMzC4DzpGDIh;eNlbP@G37sA<`lk8EYeyo~m8}gp9@T^`a
zS)l5d%mwIP8dr&zrnf@yS1QIVW+mWZozB1W5{@N*{p1*sqY=g-s*!ERrXd}Gs36RI
zbw7PbUftmE<JrdR*cR58S{yr#<NxA+Fd()5Z}!@6<#6u);R<5SiNf@dc$@C8*=#n{
zpUm^}cj?W`ak7I!HAE?eVPCMzV}q<@khxuuOGb^40u3tvYWY_0;HJ6J*rsT?V9VDq
zEyJ5iA)AjqeUvkO^dddI%;}%#W9<k~HCWttt9A$&Fr3XNNco@dZ-~(EoV=s{>|5E>
z<+Tg`@^JpfU1s;=AhsK@|FlS!$F8t7_=X5S^^Q_rcF$n^yC@j#9mf@ewyfHo%js0B
z-T!sKxyHiUO7k1%6*JM@#9{l=Zj}{d!$roLdS~K)z`6@%EV~=_ly({Os#)Iz{@4Fj
zC&m6)cXWUA-AZ`eNj_k-ga8r4#TNpiLPFy<)+Omf*6Bl5O|+eG{sC;nmp_|YYsR|U
zDmAOfGcJGSICK^c_b=Y;D#&12{iFKoiTk-=4OyH>Mmbi?`{<0U>-s{#`obs1DcB?<
zWgK<1;^`9S!^K1oUdmnx*oOE5HC1d^wxinyXB>WvyG;{Ky+=>)>6rLV_UZnc!4D&^
z(iBZ_!ops$kDY&vPBH!MvydF|#%$<+N;fo|{_Yfu$&5l@3c%HCwOXpeY5J%I*(|hN
zUKppFE6z2rQ74n)Z$rml&2o4wOQ~JUwbWYYF^61RKFwc@Aeeo;&P}7YQ!{T<tH%Vv
zAV=;`7C7bIllL*(>B778(<ZsYK9xVtHT`nqggusffp5P;oz;KEY~<#m@Scd&fjFHl
zgI=n^I-_pQEBZUvhb&tvkiMMw2i^fmNyQ#@QyMhH`T;O#>Wwc!(n{>Dwi<4;Y7RKE
zzzAJNemKbC*yF`=!y@qZt|F;_tW#v$^NAd3axBH>vZE+-<wS&J<E#`HB>_S+xM3K@
z)$g+V$olv5-o+7n)WIFwzvp9|J4KK18kJm7h3#aKI)~P?)WY@MY+Q|7$2>7ix{d*+
zM%d~5#IRRF=j~(-g_*@Kco5h*@XyE|N3)FrMPn(f?_A-%7?dG%0Q359pss;erW<-s
zVtR?A|DGa891~FaUdY3Lx{J#F<{mC*f;9)2CX1I-_y>5BNU1fi+Pap^72B0CZC4+;
zR804wQ#dmMNQzh|-(-V+0KYO=BF}Wc-Nie$CYyi6kxE5dgR+?t?JEPsFfA*u^r+JF
z5$Fb6=4?e>yT~e%7)S)&!i0;<*>lF(Q^rl1MnFD(nQoj6sV`3(0@7;4NlJYCK4m7h
zvyH$a7p?QEpc^Id$X@r^L8LFYqN~&6)?2zUwBq^3wWZbRbHT6CLbl%NZB+_(#L_HY
zSU6JLbBnR!61o{w#%+9ikJ;Ph=NWhg(5~&KfPxB$rB=a$Ag<<oY}(sw4uPazJh5Wu
zc=^{o`G&rwphtdf&nqK?7wR;N#aFN;G<Lgu=fcgR68H<<12G<q>>|DFb@%&0ctMDV
zWbI@Jrh-Je-7TBmM6Dp-n^#mKw>SuqOzLCNCwF$YU-tdsB#w(bk^xZ*5dF&yRx5<t
z?4!I?hnjx?oJXC^!$i%<N{sDP^1t8%z&3T1g<v3#(G2nA80eMrc7l$pP@p!!AMbpH
z-ueXO1b!d(aZj$@N2k69zo(JEcARzLY{OFK2S1M~4I`d`U=m&bDP8!^v0>mdHwXh!
zX54gS%%x7X=tLiAXIx;W5eQ#eT%*AdeuFGiIvVPs9*y^?!ytBxULFG?&kst#_7Qt@
zKJkR-F-p-{El)icGfWy`eLqu613bxPraymP1a!br!BlGO#$+;^(V<W~pb(sh(YY0l
zRd;wFv^9r;{@L0*D`g8CT}J3k@5KGQXEgvT5!@YT4m2ek>nB(ysnQAdbiFN6E}i~=
z_hT*7*}p^i4cTCP+$Rk-2ahi_Z=s}VLq!UG_4pQkC-2m7RcWJUx3pN+_W(3Ny@U@;
z&}K}+c2yb*FB{V2qB9W<3<bvOjee)sO%bO5HV;~`DPbfL{Bm)A9poV{xqfM<%M0}U
ziZZ`bRQ-+L;t2D4fxUp8M4<bBfwymSh+*K3`D~I)%t>uV4j?=0Z){e%+8h_zM2fE0
z!&PtgEaa2>5w~zem*+mMq8?TKp!z`s6#{ThyndI-?Eg3+lVyWTS4-Z*KM;lZvQb1?
zXYO@B^NT~7aDYFj1~~8<KfryTZ2hn)c~bA!W;_C0dE>gGT{Wct)Xxb_q~^w{vlzhy
z3^IOVBWeFVi9M}oBO+hl33=dzfn1CEU;6xXh`@B$9KI5i%yo<oGClm;3b#b>FiIH8
z=8UAAkdY?{1_1UR*e6mdZ>kFqGG+^og`N_R#P;S!u(~|1dT9O)04}1iv@ib0<ZGW;
zYVCpQ&TG??--vimOyt=or3#yT{WqTI1q8_2&RE@=B&s<#vq=AU_sa&js6UQ&7g2FY
zVzFtbO|^iXAclZWPEV2-+wb;PAj)`2@Z&1Q3!VCbd|BW6zfGWICbnV8e2>B|Oz)jk
zuga^`8MsO8mBH%FXYi_7VyM+hB#GZGB))O$tb2yZ<LKqJUiZ{}RqEu$#TB@<z3JOc
zd-3^#v7k(q&H36U=MDDom|uTE>{yvUu$c%Cw0&f*yq^8Ty^K?8hTk8j9d&i_3tWT!
zt7D1caZj~OUU`<EPoR6%I=Wx^p%Q?R*1J4VrPTNZw0#OaMU*NVA9brIr=u={5S@V{
z-R?ik^^DBaJ@M%Wklg_^s#Ph^XM8}}jy8$h1KL=LCj?Z6l~e1<s_wn<yx6CFDd+I`
zROZ<sc;t@=%@q}DE!ul-kqE1b-bn|{mHl4_s1$8S?Ku>9crdWp?-SPo4XH!|?Z0fm
z2~#|d_+F+c?{Hg-TuOb4_P(|Zy@#JJl7^^?H~JY{%($)BysMu1HxmY82AC_8mEG>7
zveGX@RXXaoV#3k!QuS#xER-Lkg<l?}dY?`}X1Ts=PXZLr^al^G2TaXu%?^H}G&3|r
z2mSu2sfUZK2`Mg2Z&y$6!S>QIlSTSe1DrRnb~#b7tv+hH<7*||@OW;5^N)pokwxDJ
zMl)Aw?fS98BTB)!bc%XrGh;v|RXE{mLx-BvrA7wGJ}SjWm$Bsr6q0JCh1=47I;-)*
zyu%^5yQ#-#;=!`kDX-7)SIlR2_t+gjEjkw@6D>KRBW0WX-?{R2>shp0MSA#2UUDkS
z)yLDwYLbSJ9%4uO-sZ4TTnAPvQ16Usn=>op^)M)(>OtzZy#GFmDlK=T2eWP$&_RI1
z;Z|#j4Fge6slbv1*n3z!Tl?bjko|uJPFtndweavWkO<eq!D|gB6yXX3mc{XMM7I>?
zaCy9NIJ?2vtj8)<KJma?=2eR4pnn^);xI7xBQ}gdmEFTPHsUBk+GXj3OO~lEMjb=(
z2A4!6Y3L9vk{XhhAqfonEK$e};5$y1ShN7fFrcqxjKt-^o!?5f0sW!Ve<g5^$j!SP
z;U3IjFhm|t*U-MMZr<k(RThwf*+8@4=dM;zkEX$l+4b`PGrU<$!<YLi9Pa=}&%9r=
zxP0_Un503Pj4*Od0E_~lW}l|UA<A)+je^|~t~ap7Hy#U{)=k~x&NOdG-hxHBct;(J
zf8Jk!ZJ=9<nJ9E)ESnbQZtV<(@0$H>HUv}kEBtNFm!zVowUUOIn1Ej*8&9TGk)n8;
z0d}kA?k+-5YbM3}qw-E{SHbUFZwsEBn^nx%mJzp;QC{&{lo=l2$`xLyp?Rrzw6)ys
zWfMcH7kD}3lTwN8<=d7@GXQSaG1*jZ8aD45KPCH;Jo$|r4kvxABgO`1I96YOS|GX$
zX-n1nvDB7AD2BOT7fd(oZ*|B|JN`$u<VE$`5_b@}cChIbfM5uWs}(O>YJs{krQDgz
zmE@{^Ho%I{TP>3C!O*#?*3qkF*6A$JB8sPE61uu$Xcw%*H0$qkNE~Jq9JFgde!{&>
z8q|;W6R_k3nzpUvi&E)x4P+TuX&T*9F>X=l<F-4&;E+)KpvSUx{_Jl_VJU@y>|A2{
z5(hu$LD}~=y1c!^_F>mAy@W6oybKmKjyFk4T_RMpgar{-qrE_7?%J*{i+AfqJ`5WI
z&ZXAsK{;lJS9fZC9om_VN20u$DG^l4c+NGvQv~Ul5%hY_o_bE#pP%B{V*p2=GS{5S
zYS^6CyikBWd30qyjL+S=0%d+FU@4_{^qk;Z&UjH<1>*q&bS#!IjcF&H>_10!)c=Ww
zG|;fxsbpg|>wEDJ9~hwL?O*$g=qmmPz2*36awmQo%i7j&8#s1$TYxPg>waJ2HxnOp
zYf(+#{M^`guu1GAQ<C={r(KLHf2+kEDUP;cT(WB%fQLc`@H`gG=T6K}43ZNN*`0{k
zt->ndt~Kk$2O@s`Zb@J;q;K$;=j0~C|Cb?Eg>4zh=um<Vk3zXb{}3!$tGqReX}A;~
zLpLlR{FO;T%Ht!hoD{rZN8k!6?mjS+r)02o)@Is%_PRsFMQLv&v7I9@(nTbiPLy(1
zSSd*$p~h9%WJkWb4>q^T<2Z;83=cTH)V%xhGr=&5riHTv!-7CF8=AxR*GdAs(b-h^
zF0A*$oeu-mvNH8$;r1)Ck@j6x!3PURCaX7zkseJFY0~>}h2BqZ@wtlPjvbuMM=%C2
zwbqEm6ba~`DtZ4+iRTCIyA(AHh&|ldJZ1W&3YcVAt_*ReGQu=?xYY)d2z$U<&x>YX
z$sZ~O0*D@+?5q2)m7Tnwy{DgN41&1tHtH?hfRuXFZ#yFYQs{#g%DIv}5-X}aoIOZc
zbdN;>CZaWX_A+L-<Q%*h?C5-CY<LYo%oW6S!HfW`7)l3`cJWp6agoQB19afC4Yj>r
z8&9V$js5~Y9?i{a{F+J5Cv6?3RSPyPv*dULaM0&UL-T6g#ZL<{XNckiVW`0ZujD<~
z*pY0P*&J41h(2w$7prl<!O{}I-AK{WqI3O?l;{zM84M~UjaqgeD>x}5bk9CV(tQoI
z?v`vHT@oqn$mrdT;&P6*kP%ud9lx+q(&O3QW}7j2OrDo|v8;eB%d_^be{)o`&V3fn
zEl7;m7o?CNcJZ#17A;8R;<ki<pcbHR9O|W%QD(UkRja6vx7yQ$>BBRZYGLd>A9!=(
z(s$9irsT)1PyY$TS_Ff7ZfSZLsL|B7{_%HqRe+(0FfcWQy0sVtp{{H9(t8U0&Y^bp
z9M7(>Occ)HLWVy$Z0aTWo-QB?{*@(4-gSvrjUb_r-lCLLhGXMvGiGlZdklqbA_K-y
z9rr%-dk8Fk=P?m?<15~@W>A{w_9g?wi>6m|gfjeXC#AU_#dwO$dTR|oG%++#EFi$A
zsH4V$BwT^&ldvnb>5?3J&O7WuT{8OKFTBN)2gsZvxpi4LnZ=A!wDXDlC6jK;IW~pQ
z_*?hD*dKoAL32#v<8ul)#OD;0u0=5WPoXXn3}sMQikr#v-+Nbu<Ds`9-#8YUUQqh}
z7rDbi-B#eAtuQL1_5Nt7rJN83v?T6Cd(+}hH^lftXeC3eoi{J*<c2n|eJg*XZR>r!
zwhC4$<pW(KB*`R5wNU%W48{|ZR6iTyLgQbGi}zk(k0P0fzYXG`ky7I!=BiUn_qiw^
zNJ=1OXdu9XNWAS&dXfkFf$nI@EcU#2-oLWA(eHgr2Fh10RuA5ubmM$rHAof6Vm-IF
zqPzC;S5{!7RVyrgub3f#{l;I=i)I-PE`I0TzOHM&dQfZbRV$SX&3S)S6ho~bCCL$E
zku^0KM^nlE6FmS}sa&8q-T`Zgx%+Rudy9r68S%K_jWfMd8H&IkZo~hSfm#G+{aM%~
z|5(7#vC0%>xO$Imv6;>vRVnEJg`(a%sBuqq1`A7%s>JrrC6rR;3Mtq5Po1qt^ITQE
z{Vh;C0>O(jwCR;_7Zwvp0AnsyJ_8!!mMjqhze!GCv=m8B7=AbyC!Yeylid;e;U6I+
zqAHz`1$P7M6qg=aS|(S*^C6tAm4$8z;DK+5?FhB)ySl($)ao!ziW?ON&Dopw;7eA;
zQ04u`Dm{QUNx2CQAVN`-CdR>AOANJTzg=oB5%>KBf)F|zO)gVS``n%%g(Cz^+Fa6>
zGjbNg3lU6Eo8=tpq?H$Ls@9g@kUnq9y`5I|5kO;lu<XKm`5Q(RFuA@-B`AGiTL@<x
zwbb-jzhsxd9XcQhue+zn&5;trIPXDIO7WQ~azX!t`WDgD525kM!bensAb*5fV@FtL
zcj5c9yJEk~0~wbGp~gpz#$JX2Ovxwq9!yCxF>xJ2cdg<*@4N1LjS`?Qwf<j`!H6s&
zp3=`+<oet>2*AXKEsZ^!>WOW)B)Tbb>#h;V3Z16x9NMP#@Sip&Vq<;YK{OFLS<}u0
zgN7ZAJ%{=c4huSZ`gXJS%U8bG5@|5e)_k}f=Z<-JSrnp1B8uo^dV%Js-oRk)7`A$W
zU2WsqM)vJV9q?mf^>x5#|D}3?H6W_B2I7Xw**Q}7E^8>Q?CXB^dAEkJp<z9I`8S9i
zjJAN;?BbTKy$oO5uWy~tpY_nycb+~LboXPceup(|`f3vMe(Th~FZbo1wlE+A>&s<@
z&Hd!RwFOlzpY_~TtaY4P@?5X=u2JA>Gn?ki_#UqwDMUtrb}wC(x56xgNh49l+D2h)
zJjv&|p?AAZu>8T&Iro1r@nWn>&ECaY#I3Husq3w?$T8n&f1N+DEn(4U%E+cjD{9cB
z&JOQk6_-GhKE977uX44mmMluT5Bn>nhdW$BVv;T>t2}-8#mH|jzneh<Z}x)x#r%M7
z-J~-N92qI8fJ_1l21iQw9Y~9kIAU{vd=o9>tJ|LIXiDs34)k8S?>{7Ha94ZS0}cM}
zZK<O#Q6%JJvqNnExN|^WH7+hfXq9i%<Cj*IGVt)vdY7pWq?k<|po&tUJR)9C6YbV1
zi6tMJy?|^rj9>}KY<V^Xk$NtEbR4Q%wVFFPHx97dA8csI%V912B}?hto`XfyXf<xh
ztKn_h&KTTd<`$0P7iMMi4Pt?%1mrddobQxb0C4B$s``m+<HY;G$Nb!=L}YplZ<~Oe
zT&~44;-%MUnSm+~NT()J245bn+x4?Is-kFs{D_sqd7LW)3O**^aKNSR!+A#$spb{d
zmlpqM<L_c7^`KZgA6}<*vw}|AV<t0;f978;<u_L-QT@7dD8f7UW-m`F!ck__f5Gnk
z!4+}eMON4W0%*&+s#~FHu){N=`e^0{8O!=0Ce2?EaS9iznlu4DvRde4y!77jALKGg
z-+CxVNx5CwB|=FpKvpd@43gXdFAdM==Eag=LubE#o7A$)KEJU7i7b^TF5UnVH7|5V
z6uL<sIWHGdJd{>mcglu`5)|xg%7l}G=w~K9c{yay<QMHDz>kceXq12Y@U+vv%<W55
zO=)V+1a<$n-*|KxGTKzT`sxFk-f5u(3k=L|;!wZ1|JkMrQs7|Whj6;8FRf$g8XkUw
z$*)4bao=YPjy-dv`U;K$qc<D>Os*KMtoCU3bqY&vz&>tNDzF3Mu5u_r@#WBVP@f0V
zk`w0WIdR1<zneYGLT;c`yH0+lpn|ZM9X{8nXKYvBys|kk&ZF;?37B3g4-R<x8}fmm
zi9gyGa1yN0C*OQ$iM!U1^BgQzA9j7(=a<9QD$}luD=b`5wO@*zoQq3MH*u`{{>wZt
zU!rMm%2wAquv}XahAfBunJkw9S~ll<^}rTk%}kcTdO35z2>429S@j{YLpwS@7EJH`
zht!uGO*I*|8ogV%w(}x0<okIU>_mTRM%<f|0yEfnMAaa4RNOZFuzk`YILgeLq9eG{
zqEj&IQ99?Rn-aH&;{76C2K!1Gdc}gXfN9s@M3k!k>riB1&^3!+v|E=)j_uLbK6J0e
zX_AXqSkQ>?&p;JVine}brF(PJRNjJ{9rvTI=aN__<(dvVlnM^sY(_{qo_1b#7v!~;
zwJ<A_Xn+-HatrubXSg!<-s!&R{rgoC{_SxlA?S21PUrNy`K_*(*NsMKP^u;#j`qbt
zYzqTgvsz>%yC(gKj8)V5?{@g5f>nl2#q5|RMkzcLAH_1)lz(umN7jcAT?kebM;cKl
zv&$*dDe4B>x@W4pD@^@}DkU-Z-x=!bk&*>>@xWEABgG?T5TI20_Li38JT_EaQj0l3
zhjTlbMNa^UOtGjklG;aWFO!S@KCd>0H2jDEUjELc9Vsf)l^ii|E7+}0b*JGFE4OT7
z>VmAt2$q~nhkVlXLBV{5-L!LkSGJ_FCO7N*`CrA8uCt`KSegZy`SLSFb*7<vNTl{N
zqZLQLoHF}8BlOqdTdmwqsC;O(0hFJ_VfSj>mClQci&2{)DC9CoGfrG!HR-orqp|Dc
zFa|8qf3`<ijaxGwMr>8p8cjgk{hz|dH%D&N<?|CRJ=$51X2bsAv}yzKr_kuX7PAgD
zi=~-@3}#HxJ&hxi{1C`y$+<2OZW<}`CJGe<ajPFog1BG=Z%*>TUx3>f4x7wl!jnjA
ztjd_o8?obG_~^E!n0%>u`ThwcsbN{H;B!$N3lbM_5WS}aVtoC6{%0GUE(u~C{I-ca
zdU0Ptx&CLj>OVex>Dny^n84>}nc2J;98H4K-R|z)HJG%BvsG9SGm+AEJ@$X^6NuC`
zw!7TQUEQ=fT`{*SQu-d<zH%uk{DBM>_3AXhJI+<0mw9jRZk}%<Vcgb|b17)4ak?55
zW828mdHY;p*wr$S?I*;H)5AXCfh1^z`ZbP?)ph%GGXCH|I`JgFEJsE$S?M->)<sv>
z{(QBoS#jN0Vb~5e&A{=>KyW~KE#My;rLp0knPghS4~rh=Z<j<DMUNZDMMz$?KX!{?
zPo~_@e=zxzjOk`M_6-(8{^Vgi)hIH#xSz@ZJ-8tYyqYC7>}(wyT+oSxui8M(2&4$M
z9ydO(u(36Tf2m=@Yss2ee>%$Dx+)tsVUTn|8oVSNxMr!*EKcaxvUmQnjv4N)I^c&}
z3hxU|*uhMcyBnw3V=RA-jt=1Z8b4G@0dupQ!H>35wO+0K6QetfFH8BUIq2zkc@esj
zzU#l29Aw4;Ucle(km0?|j(!O*OMzbsT4E%mLqUdB<iaZ|IFhmA>0!eSP@nmA5INI(
zgOWBN;;-tU0|xkVcSTV&{(*mS*Y(=NNyU7lPPcxBw_drsWNqDJ1QMJ}SVRE~+y;p7
zMn;0T-$33xC`mDJzSA@A-G_<$MQl=x)0E@SO>?^@{_at2;{fPd#d=D*Rur1eC@6u8
zO@K)7=1GNb*7<@a7GDiljrQQ@W$U*<fDb)sTzZ<l6}7CLwX%zcwg-KyS$FDioeK0J
z#%5~Am4DP(+PzeRF)2}sp*(=3)&BHpdMqw17a8SdykEW+VrqE|&EJZ!bPuygw4zgJ
zK`OBUP`t$dUxwxd+czCJr{}<W+U~$PnLZX+?o=TNBOeYv$@^8i?&b5iD)c1R^+@!)
zGMt6d(d_#Co7Tx%#pUsrONy#SnWjCw@a4oP_^V(BJh|mlV^1OM)6Orcz~=q?fb+|q
z*aKpJI|oSQHuhI0`>x5qjYq?_&XGsTi7kGiN8u<qyQYiNz=%So=Q16J1qMop{~EvQ
z{dc&$rDAe=I^K=vaioUWScAS-p1dLzTKwptZAP&3-w)Z9>J!v|En_;6Ho<^L-^<-3
zo9pvDiP)D@wv?R>pN+=Q)w4D)+^EHr!KyZ%m#%-$D))B}7$wSz7ge9Kq-Jk&f7}Q+
z9s9_^eo}tfqp3DB**W$)HPu^-y^R>}gq=%ymhiD)G41><(ciddPpj)$7rFEiwXbB)
zWV|S704&*$q9||uePH<a82@_lYq*?t8A=~a%|P)Q+{K(eyLB=|RTCOClzne1-e{HN
z9lGa)5ZEIC!mH1%>;v!U;x6X<%!<dJxR~9P&(I292j>-j!EmPfsO7%%3+Xf&IjBZC
z`wviyX;0sEk2pEIANpy37j+JW$geuU!03pG&{9w|XL$4N)trjtD@DDX@u*(1k>tCZ
z>}W%$n)8W=O?<sE=eut&hxw`e24s6WdlOh836)cW=(nfn_k~oL)az*i-OR~$qI{x*
zx2d088agJjowv#u{hC5RX!1S1a~9Afn4oh!tbtV2X_C|9)`cp@d<Ep+eIWhaKey>!
z%H77X-_zZRa6@MpAA`XfC<i+=I!P(y+%W}amWT87W-e$+Go{Zxgazw<t74(0{o%9L
zwe=8y0}LDd3bljYcMlF1Fwh}nH1?v7GCvK^9r^#L8}MBxDR)AdfgSc1Atoz^LjlcJ
znk_6ep8@#B0%3s36PJ)i{Cj$i9&4gBxijy1F5G{{pa@^s;4OF519S=ZW%w>}Tee$a
zSf6r4r8z8wQ!_JZp3MJe1fcj<hT}L^sbp))QSXOP+3y!!o``(r(()L%yq$M20~V4R
z%W`j>FpCiD-Zyxf@uXE?Z4{++Wo6@g%1I4Io7=e@P|R6JypWfJVOQ-y$Ng)Gw1>dq
zy2$d8ZMWC0DUA+`yb@rv0*N}8!=OEW(Z*w76J5<2?J>t+zG-o58u+W2-jc3~Ub}#r
zxrNMaK-A=1<92i-m|ZObmX%f$pS6Vg;IFEx628|;o`J|EVLh<I7jA)q#d#8-T|5+u
zu-xjc+L4m*jxr=gKYiZ)MUZow_eBBV)SbK>dz7Nzs}TT2P!jb0z`)HOtAL0WNxYQb
zm#n2mm5%AHhbkWD6~hAUQ|w2j6d7(Ux?H{~4-^^Y$%EIt!Oo6@gLMIp%QRRPWb{8>
z1Xo%+l=0}>ea&Lk8Kp#<#1IdCoR=?SKxi&mUxmDmR+>AM3w~4HWacy50+&)#5*X!5
zqECa>liS0dUHDo;nphe+L=-C+Z4f;kj3AT1K%~gI+l?OfjvNkRPh<o%iEkF*C;C9U
z+Ufvk`)OFiMbV95!$V9m<9~K82<S1j0IFu{bvG$#JW5n>xyBq9i@~Z9k_81lFIsqF
z7?U$Wou$Wj)O<=$VqAKa5?VMYFN*WM3@uFs*>JK?8TSORs$+LY2pVkmR#U(TW-HR-
z)KqjanUTR9;7Q&O#V8Vam6?6ucK!6?gC#VyN<k4|!g7`#!EC>|N$C;c!_7f>0D+ps
zJ07g-w`ejF;&{l=3<+7a7S$X{LfWOAkAq(OC=|-g9kfG%AnJGxo(rh57N1X%aR0$3
zzeakJA@&w`<R2fJ7WGl7AZSi^{A}TJ;~w^G+hdU2hqLcUxo7AmCZyXnOpspK({II%
zd<7GkBvnxfPw!kjNte=X-ynj5%ml393_$zRzoS)My#R2@uy|)%ORZ%4fkNB;tWxdp
zQ1j_u(>ti>{S3<cj}&5^TwSM)Lm_zs<7iuvrl@awjB)893TelePvDTr2C@j8RGk*>
z3P8(CO+~w0S1zb1FKW!FF`SmfMQ1fDo@#}qC!4HJX)gl<=6*(RhfCwup+FvLFcK~l
zjQ*16{+t+(j35KcVWPTi9{OmMT(--}pu+Ig9iV?v{sUocFh+0gH&mSQur(zzirIPe
z{*0RN_or(lDyk%>kxkM->^^_2Ih{G?_y24cbSv6Ci2Cl`z9*0qC|9*su;6x|cxt>o
zmx^<KUDN)f=EmI*8#7wz<xiaGAD{<-E16N>w|D<_kE-!MCm4*4<q}OP&>yCHGvjIW
zK@q*zkB7~~Xme!F3Mia<Ttd3N+5olKzsKB{v=5ygu=QusPgpSD+xf<@e!BI4-8`bL
zKZceb=IcUZ$~gE8c6B-fQ#9!5(y|!hCrRy?43fS#uH~=oU)JZYZ(PjLigtGP^r$EH
z?+`6i*ZkEV>A)|aW0|v0;VPkP$|krElwNmj@o^v@b;dT)A&BA=^~$=mvGKmV9K7*R
z+;~;g)^z&oE)i(#g-%zCrdP_pGZAu)ji=l#rA~hSEAOj}iGr^tuXHAaRQEUod{}$)
zPq|bgpkIIoQBDArQM!q(I!lHjztE_`C$fLPejNMA)?2x3%?nZ*8E@ZYFP(Wv;PShc
zj%@T2c0Pq^D5?-K5-HZ{Iq@T40_+^7p24ZQ!&T{AtKq$OSi?2jf^#Ko*fvH-gL1_G
zWmc+(0+|{Sz?idGG<_Nbd#jv7*1N6|qMvyyluv8Pr0}G%_Y{D4WH;4D`5fpLVAd!6
z8@ZzdK4tvf$@5D{oti2b)QkzYI1^u@s!uNxul)dm!nL7cqJI}dd;e2KxHn+R7e>>9
zSEFUauSL8C96$iatEm>a3k~CMJP&s0tCf<BWY~rjrv1{;uxwMxgIZrO*Ov&G<e2xL
zTs-ov?^%~j?93k`ka<#KLvZ7p)N&xf(hyeD2yDz7j90Wp;xeqF7aV*86Q3vq;>aKV
zqd~+BJ9^{h|05N}zO%l<N|J{4?G0d`|2|~t;`D;L&_qzJ<}T5HC4Y_cM#nb=xIT*(
zPJrrpV%QGZ<<v27c(OdEpyWxh^PRxgsDTE5rB=vdis49Qy|_-t&l=MaNU3rBJ+|1m
zS}rN8Ww$gj#n)gZ<i1j3iExR$5kV!g{-s!9T25xr0}x?csI2)=3N@>&*>ERwS!e}5
zCSUq{I)_IY5~+Dl<(OUOuCN!H{kCj)#<yAGwd+qwr4yq}QoDk48{LEUO00wo^$hkX
zyPhcm-PgnOE%*PECQ)|X>rKSOaiol6_4e^vT;{Tf<?ZnAk8G9TuYjJvWq^;P#iN5_
zw>Ix^)-E;m=nBf>c*b_^Boe>`ZrhWBJ(p4cX@a<9VBovJNI(dm(Zkmjn9}QJHIb8^
zZ#WV^ZYxCy`f67y4+DH;xd<@m2IIb6(yzD3*IR91N49}tn%%9^4JZCI=wK&|?;9i;
z2{iz&j6_5k{<j~hRX<%tSenxns0|(XA7$>P=dih4eGZdc>*LlUxbKXJDjtc1|J-Q7
z_#HD)OJhMCJ~HDPZGbdG1I5!`Xj{qt^!fUMQw~RG*xHkx70Ab4_tG=8zvz~`yz;#r
zJtokTTp$d*)|qg#t?v0)Qp}LdX*u>I_Z8mTks_?{eCkoWSq+(3O7g8ov1ZwtQ#|D9
z6oTCj^DTs~*$`s_3uy^|Q}ULCAqI@)Ogb?(z}g-F2#@#{0DJ<)A#u_|v_yl+`fle_
zmX&Y$5D*OsMd3Q8fsoP37F)>e_WXWdo=j#lsd$-vYE-O!I&EKKufLAtbNcKD+)-_T
zMG|yZ3O_h^udxGd|JulTy~>I4exZST`YF>yY;?sjz2!Hjo`#Z$Br25>1cr4=zhxod
zs`qX9T$oFP_8|q>0)dC9sU$JGO+KfX+qY1n@|i`anABT{Nl;qi&)f*NmdK^<!ykyn
zs7Lls#bR-7wP|oVVcTf=s@3%2)V0xkwy1U*$&#O%I6u4Sx^5w(r2a(_1kXonFiET2
zHyoYjqZ$`~N(H-_CD6YosClYX3matQ!83vPzDWzzZkR5adJ}kZv-A!E14ZNM$!z)C
z!5FzF9g_9tvnV=#7VPS~3!^e$+4*5lh}-RjB1n*J^i!E-;nJSxX|ldAw~|($3k634
z1P>LnEnHfUZ+L`6K*nNbOilHTHK)(OH?pFj3#GS3d*&`+Gz=JjI5@oUqacdfSRH<P
zS|FXsM;R?SLYcs=As^sIK5A#mRD4|U(sT0#U~7Oxkfl<?+Zx<pXD~}+Vv7WrQ)&fE
zOB4-l4y!P@wdn{G;kf0@7?-o<^iCBKZXJlLEbeVz*(B9hHW7;c@iPH*Ti95wKZ+7e
zK!a@0x=CWTUhmM$)|VH!tu3K4M1JVZy8Pj2i2_~*g9eGWsxq-a@whPI>b9m?3_6#b
z%xE4IhpkgX=KS*QNF6!vZ2~ofY&d0@Sug^ySmO4Hi9P*p>aqWTZM0r=AkeJ#l@Phv
zMI3jqOl$|#uZK7D*uhdL>QM)RX>n^Zb_CYfL8+Jl)&Zy&^!VP-)^8JjYjI3~S%Xfg
z*bB@_fN?vb*F`xH#L-o@+52ZLV_~MgAd;Izd3m%gZe8h>lB#bzsJ|YFrrm^{DZ&Bi
zBHxixyTnh7uS}3JLd>Td=68UsLw1-f>nLJHY75+rKI?ZEm@v!DR2<cOfSYnU>tWQ+
zE=>>?@W{9nD85?P6iIOt%nxavvvqCyO?M~Vl|@o<A=dmkWh<Ez#Yk!?-0~R=2P=68
z;@!{~O%|B_PQnU#zEUQm|HYD7?e)c&6$7!j+_Zdzi_s^L%=_)KaL)&9<EP{uv=72?
z2H9E5y7%9jM8Cuo$PJ`rFgW^MYH9(6?XZ;x-M~ebFz>{F-Jj1!ylM<Q4XCIA=-Rfy
z$z92ZKOfCIkfi5g*2{VJc<t6@%!;SD<fH$6bV+&!OJ3QsSd68fc!~^`5d=x4CsMy7
z4lcjaY4DN04I<g*RA0BWyIbW!H;9QtOOOcu4`<gq{`|aqn1X?-l*mYg)p@oH!5&X$
zBpO5Y(nA@t_Ndd#uC<RnuO;KskP*GJMHqa8ot5>}P6M^reV4J)rn9#u={CAfctIDj
z%jCZUTm<nXPUHsaWLY)yeyb$aCw3u&Zcl&b6@8l6L@K*?vK+u6tIlSnYjhgVF&6>z
z1Tc7G<i*Cx3kA~2HZe~grD9d~`==wh^c*JaUtPKFL^ENjU}z~yx;Yh3yJ#SH$0uY7
z>83q^8Y!>y>b+bTwDt*bys3Te+<OxYQk~<{yv71JUEob|P>#bP9j#mvarQjq7S0U(
zGktCt%ulUI4FFyQ((Vu{nu=|LWMC2NaS3G9e6CZqS{ma>WprxGgKnkqD~E@&|E%>7
zv$)6jq(tUp+m<MSxZ`=47(o@QG4g4vo^(5vjhSp*hhKqq6*rp3H)znms~<L3bg;zo
z+o`ovZnWO+k<FQ421ocwg2@qAF2r(-ST8<a=B<TzxE)MUO=-BN_cxw}Z#aj@X!;Bw
zbTBoX6ivm%lu(T?!UJ=BpY{^$p-2hVlcA}wjUg5IJ5{pPX6RU5XMfu~T~>Q?QzkV3
z9p`w8KE{F?FA2d8ur~71>WwEDX@#iqFxb5YJQb|Qw*hLuFnxV{*oU%?L4=5Bvo|ji
zPs2I~*t=}X>sJnV^cvdyf9aZauETfrS@g)WBp3tI3J<BAOwr>Lw1D<};0mh*YLUgN
z%$W#*$hf>a9b=D;%t;X238X@&PPC4Na1DO!cll34;th~_b%KjSX{RL%I&PmQUErqT
zBt`jb&@|X(2Dku<R}Kb*aF&+e$`kU-(+PM&X8T<RzOmG&_r#~I;V2YK^m9j$Vgm-^
zYd|KDr|<g4LHw&=U=n5-7m6OLCe3pCoZeMSW&McoX8AXt*){wB5%rc~QFh<^w<6LF
zBGNIyh)9WamkcEcsI;^Q2tzkWcMOemcXvv6BOTJ+-T!@mf6s9|?|d_IaSdzl73cX`
z0)x&|RyEyv4HccHiqVj4E8b?u9iD{7ONj#>g;Lj)ttX$U)a0|wNHw}*36an4pD?10
zm+uG?1h$_NB3GI@FL_%a{^&Kd%hYhIaAyy{k8jVSUE*;h7mv7XoS~9puci{fU#UC1
z=A<xQnq+_@6l=_!4nB*q=a|F=dRB++>b|KCU3mGWfxitcjEeQ4&&vDba|Ozj|GIgJ
zeC)8i??QKAJ$o)Ru%qO0_KjwJc}L6L)FI9z%hQ-CzPrC+#iyXb;{5%I4A^9IdO!i>
z)p7;q*e{&RAt%>UVaKLRPVspGQF8Nd023e<q#yyu<e+1T+kbL&Z^KazdjI@O4Fj?{
zIj;&1nt$)#(g?fW5>Hta3x12WI@rUqXo4q-TSp5zuc;RBTJa{8xNLKR^!x<m?2D%s
zP7(i{pDx|o$JTK#ku)=)A!Vl>O_FtA|Mx?W%c4r>Fp1P4v7=WSE%zu?TIy?$56+J`
zOSq^V&*rthA6YzZJ$tw~Y?i#B(WU%f@Pc@3ImGF2prQX7^!%AxbIJEbTu`m68Zxaj
z!w}?K{BBCXqZgPz6rss`o<WXhppAEOT5uY5`bvR3ABXTA_ZXU__tW0EeBu{M60<ZR
z_}_G^2HVtsPYn$qW{mw`c<kRW7um<<u0ahhH(6^J_jK!o{Brtw8giXgl+rU_tr3Nc
z`y6u$n2MNnz~tmegQJ;v5TYiK%cc@v*Qi-uv`qA5lW!hT1pl6`uPEG~3AAD!;&;A<
zlzDp~pDeq&YR3|(Xl(>Ve)vRH!$TX0de6Jnk8R5cE0<hgz{vZM&a+j4{o+n4uL2S%
zplN?$L;VCa|BVI&UiK-!7ES2L(*eNI#mkiWE3K1%H%gM|l2Iu1^SH|R^sHvv`Aof0
zk^wbcxH<QP7H3KvDtSNgaC)hW%ueH`r_u0GS9N)~eDnX=n2{rQzcDlu{>S=rkrX9s
z!Hg43gu(U2aH@uJ6Y0LVGZ!@>wj)|Iw)+lUWvywjfbb8d7%@Ku@Dr~1hFP?$;fWAe
zhfY$5mZpTa6|M73m^(|~p&^m8yoh_V!A|6;gKRZ?T3cH#)j#7-J*C3(fjmc|=1IG;
z$Np_&MQulX8B=$`x}dub(toOIO|7NNYnXIzb&RVHCrtqDhkp9(Q(igMnJJ3$bskMk
zwTwgIhmo9yB4R2QvPM2ZpZX6gFRA@$7qv83>{cI)ni%>MUzKpg@H+VTpTX!Y5d`fI
zIe*^Sf@1i8X24CPEIr>0zXB59@=XIHC8BV{fSGuXkZhlPX>TO~$g{Wo`tZDfUBSCw
zznQv7Cw??7Z_>juRr=UI4`#`*8@dZoKA8!YD*MLqxfkE(I9$<YA>1h=%-q?*jYm=3
z{Bc1kv9xk5duDd0jIrOOwzsTZpQN6H8SX}60FxLY!WoRIfwBwBTQ+%UFX@{%$r_Ja
zs1QZ;2GA0&I_Ce~YaR%BE-FHlrar{Mo@}fq0GdNoF>fy4hFy0uG$jWe`tgUxg2@ys
z23L=;F5&hjDoxD#XpJWM)Sr>dShFVl*%OD8E1`vO34C^Zv^#$`IsZl;>~?(mGZCp{
zNeTX{vha>5ddxe{Cm+TQk!h07=F&bAb#LVdXEWi3`&Ms`?|m(tY%q|=){=es3x?!6
zCytP?QAMFq{mJt)ZuYf5lA3b6-LnLW-=7vCf%*wa6Z)K?gf{Y`cz<wFezZbbM~J|0
zscKLkBRg!x%LxkpXW*aY-Qv!nA^qLQNC*gh#fe(dz*B*0A#7<xIP`!v@D;KsJxr58
z>|mGY!cHsTS(_*&^J4jlmjt><cg^u?cwo$eQc^4mo_8%=dSUm|WVylm2Ra9?=6Am)
z8my=;N2zht>>EIO%hb0<^i1;eh~rfglRsTLMC?WMW_riH$u}=72|TvsRKY$`_K5zm
zN(vjbR%}nvaF|?sxuXR<et2jwvrm7!*B6?L@Mg)Op+!(*^{!F}e*JFGMieh&WZ|7o
zB{lzpQ|<6ld8xHq`V8jj&tyS=GEbekT8~=3;7Br-pE}4YBH&<Nl7DVsslZ>{Uv<t$
zVgKlz&d_i0K18Mq;!o$KEz?}5+w-@|w$FDc!V3P;9Ah=^+%2WvaMX6;8Gc#2e386A
z>IH^#Qw_xHUu3<ZHE<~|c9k3{l}%REj+^PC3iVMVZ|H70Qrh<GRn5&=6|2D3r1PXl
zd9Lo==`xL<!4V_2O^hdVKoTz5{@?7X?$3n8uh`+?G}Bx9r~jr$+3N-U%s%H>IJOfk
z+I4U2RH>TXE~Ctd;vKhkK97k}Z=d2+-B>$@8)XL(VRkh$dXqsuvJ_bFbU>>2$0@F;
zoU}y-F+mpSBp55>xT#eE4X$-F4T-M0IC`%{#D*0;vrVu$JhaE3D}jeR)Wmt8_tyTv
zjsjGVg@txo=Z7Deu(Z}eX$p5J_B1hTQCt8SQ+V%px!_I5^)~WDcS{TDS=$C2V1g+c
z)z8*R*PL}jdIbG{$zS=sL>MULF76RC`}J4a9b;CQT9NTdGq<6SXt!WE@FU|x!)EE^
z7W+HxKNG4y-Udl^XHV|EQytXbV)A@aR4ku!$i}TEMev-QmHt*!*q|JtpN?4Fk~8dQ
zH)H(PG}Dbq+#63i{_O8haz@RRk_dJchBuB9?DQzHlYG($|8(g@A&$^hl>csl{Ec2?
z8<qvlR=DdOwO)S0hZuTN3QS?Nfb_WdV_G%k3{5sQiwl!W@}U&z?>5XVOX{ts;t(YR
zyL29vQkG&{|8x>bd|r3Gg!tpO3Lc7Ka@Y!iH>N=)w_>JA{g8cKi_L;?{1~Rz3M4y!
z9bl#$8x$6Hk9~GbCbYQ5oznUf=9U*WDBSX#0{8T#8{EIn*?Cgj+-15Yr6;7NZ}2F`
zbxmh{$soHv6OYZ0`9LJqbvOJ>;qx1RPwCMS6MA&JZ~{zFy*yqeT>=59RadG3$w!;t
zGG7dU6;)xp^zMmiDshFEN6qF-;QH=na(1S?5C{`)vhxa?+C>iIJ(G!$uu7=U0yElr
z=1M+fR4Bb0$rxm%=n`ls^q=3-dE6v-i#4>TEY(U5&$<5#WsoJp3K?I0f&A2|s*)pX
z^V(%|Rz5!-t7K3i<ABC>8V3p3!dE_LIQ~1Lk|e0fRA7XO4WC+iHkF`q30W5`t__zg
zW!@rt`v06HtJLzVH_VVG@Bzm8{v?*EUF@Il6U0}D|0og(adY>}>AGL;VWWvisj@}i
znodArfTF;w$wayJ|C_De`9LuY-jQB=DhQR(QGR=={)EF9^g2`z<_pHZXX8o^11Z4U
z|3NiWY@Jm<<4M&1{B!dxuuSFtYtLbd9C@|8v}zQ;k8b5G7trq2Ma{$z{ntdtG~p_G
z+e(p7n*)ee)=LI@vn){JcP1XPQthWmZAYC)UuQ9aEI%k{5Y<IXMRj8$0G%n?>oy$S
zQ>1IcVS54snvh?oCB&W;7TJC+u7>Vg{!9kF3MlmDJ53($epITriY1r7CM<@}k(%#O
z581huH{O*{ZcIlo>Fe{#iIYXM2|q<cduEs#_9QpZ8-fuWZJj7A)LYcacdn3Mn4G`C
z%cZft%5Uo6_Cum&a!a>CD4#jvT@`Ax4$*TE@avJ|9q@s{Yo{L&D#q{ma(EKV#Z@B{
zD(ui++63B+0*>ooUy+?-BHTuzIW0fE#edPt`t$0A6^lFiGawO?9Z(>ub1RV|=_HSb
z!G@tS?aBhenSbH6mOn7GRBPQV1nF5&(=_vGb+`IrBxlDZ5Rm!$%8tG!KH<Aa+yHxO
zBnZsFEW0Cq3g^^E$927|S`?3y$b^)&F^FuDmWK3-@!%a6t&PbwF;(ROK?lBt%ExRP
zvOnny5+bSThHAF6oQ;&i7K^k6Bt%5dxG@xw1L$Vpq}pM=Q^sA)5fKMrMLYrE!{$rb
z8+Li$c~xKv?a$jL!b%E_dYJh1)!j@vcDc-DQRolkOZ*`IQGc1~-^xlgyAMEM-)~$e
z7g&PqfYl&=Qnu3d_jzr9;6i$?5u4!){HKf<TRu3e>XfPo^cDZP`}Z3~d={TSMyT3I
zAWtsfeBNR&e%bQ|#qjNIZVuerRfIsYFM9~&+yN;=tVh5T5}toIdF$GIKWezBqrPFv
z7|NbB4A1>45?OPZgSpB%uh(QTYDfNaA|XmHi7tzvqEq0Nt?>$QMHs-=_BwdVp}@qB
zI`%J&YQ8y0pftw8(8)^L-;8of7qGhU|MN@&i_zuJ`ShPNVHE`)oQZ2+vj&<zJ4+9|
zt!x1H&zE788xrsTS>|0$Pb3n~Fe_hc@=d*p%A7I}Y8WIIZm8)w{t;icH}v}&yWeP`
z{Hg|69G!|pr_QUfk(^0@o-Y#8Y;^|>gu-1#puX?{^_F3s#d@#x+q+xVq-+FxZ*E_V
zkTl9ptLg6hpWNzqLAb2gULH7OF?pJy(PkD`>WPrT%eOz@liuwuA{jGu*}eU%vwse5
z*z2j-Vk`3|h2c}&307QjlI}{1SogCEdq+bj1S^GLn*@tjngCQ_+nLf{!~EfFmCU8I
z(X%0doMPCBN1f$(tb;^S-+hvi3=jDia8PBhVwIGHjQ!Ax07MzfOieyTj4NQ@CH)_2
zF&j_v>9`8JjqTEoM6K}aPpScBGNI9bZ*ga!fpBuFVay}1D8+dkQIh4_r>_0&r(FA*
zI5L~ebH=v&-*7EFjQVNOGR$Q^katr-p*3INz_hvfJTJeirN!$_FKx6{OmH5>_Y-<F
zB;Vq1Buv?91iqs=fr@+QS_yA=e{qmX#>9~fM-B=|Yww{ZFudbcnyxOaUVwkE+Hbvf
zJDL|5Hg{GEXMb;$BTICGQeXV9-eksvs1qn6#WH3-a^p#tq{;9G<@Z1XE9u`qNV43z
zQBsSjOL0jPgk(&NvzX?}g}tn`vq(x_&!RM1Me0oawfg+b99J#o=q{Yvzmy!;g3Q*N
zI+OmZPhu!Pl;7??90H3gT=S2F$me|=bAAu2@0n70<(O)8<P}aW*I%S1ED~LzF}s0E
z<D1R#{`0?;km$5SZ6Zdm;jSyun;EOcjuBO-FM>pBGJ>{*;ZbLCbI<7n-d2*i#vDvI
z+&agidwnNCih-c_`iA&1TdfUn#^1FPt2T(@89><msEY791tILuJO|tk-+_Ljlu&^J
znJ^AK;|cyRXn>matcOS<<P7O0{|Sg>ZSs{5Pwmz+f|x#(>z|?ab=1i{myGf&k|rn>
z3yZNRTdDRB7?tpeL*_pNtKa1jN*$=1m~&NwK}dTe85CcoJ*5*Napl!MipWP9c-$xO
z^eE|3`WM_M+s|3v{KOQ->1E=p&mF<k`tg$+`<)n_KOL!diey8;i#q9aX@tna?&$Hp
zuE~+VqKnh?mbJ2yqpcAlT03mlYit+_E4}mRH{E5nbyktHCc%qPRW*Q#t+~yZBtnpt
zB&JTk?%Ajvo?m}+jIPuB6`aoz;e6#7{XBwhoz}d2*{MhY30Y~trC{(}JqgSa^%96|
z_J5VjvtpFpdxXXOZ$6kaDi#AdNdRC2s^2ZTQmXN9*G9R0^lY?Va%0t1CnGq05wiwn
zcItA{zHTExfBsjce71cPMn9gK&<lFU$A7Z_po{Iqbgut>Kk=&x!5kotI~PJ-LLI2K
zV;65>3&2K_lTJ-4qR>n(iCg*+h|=1`*JvL*zry?#ESWWP;eU1+Fp_RiU9EVxvTYf+
zTd)TzAC8#r+7|!a(Nx#^;PEVp>S?YKN0dAvj3@y0*Lyp>(y@JO6Wfr);$^?l7`K4P
zGjebE0Pwb5+xex;Yo+ejio3T%1E^&E!`QZ1;dpjur#_PDJVs2hbTTVvq_YxzesH;d
z_?1IZS7)>;s5h~P!>EB>pg--?uQD?u9qnL^IS8P9a7+$j4a+7%nC+eCO)6{aKZ{2|
zWU@mmdp+r9*3uGVqQw7l;zE*NfgpYLe-lwP1PRp}0giz59~_a&l0WCQmrk4zncmtN
zqg3G*xNg;>dli-Qv{)H$n`sw{+iM;N8}5D!yHFkDM=`<@GrbqM^6}@6%go%nD@%V)
zrF}lc|BwPnk;rDmTq_Tg7Ruv@Tz&3IJ&TCDP0yGq|Eg_H=&m=G10|>!r!Nniwy4i$
z<5y;=7_8OOI8<bb=T9F0Ur}e}m?S5)`bI}!(BXae<-^HNcq+E1|9Uiz`&ACrvGGzv
zaPjLzVgB~C8IGKf@>W1&;Nw}g`R6yjofLTvvfj`{ZWZ&7x0q_gHD^UojJ0=syCIZS
zMj*Fh=k$@9TiKHHagkb`ZL($F6ji>2%2?ier067kKuB1rC9P05&7C4yy-K1RH>{5d
z+P^8BbRvnw=xl^#BssATm2k!vuAya+sKr!Q%HxeW|JxXI1lrR)TQyDdvdYDc#ZQsR
z`{{Wn#L)$`IW78Ci}d>6$&-o&#*xomc-ybc0+dV0+sXt482{|>Uj4jTT0?h;GWU5R
zZBRK(gYl~IhyhXicybtAXbsJ<g1+;mdOi?usNO6&xQ|e^0aO`vi+E^2PamHSrF(#3
zPA7ke1_)%O!SFxfide!*GV$U6q}=kyzPw}RH&2H!l#m3QIEET@$BhKd5d_Xv?f)<i
zn42WkN#Ox=$h%a#=*F8=b;~wrDh%TT$13?yFdVA9oUBU6kezGv{mS+80vGEGBlJip
zJ<jup!oo;pET>;ygx3SFUKl9pwf@Z99uDj(S|o)dEP42=4<9I(N5g?t-QmoV?*c2y
z-S!w`U)1u$(kX~raCN27q0<7p9=kl2WUC?(P(lUj^CkPe^!=JFtfKq@Ht^dI7w%@I
z_t85dyXOvdb11c!;PCC+Rpe#r9yB+umY#;7{<{a%m#=sDth3rY&ZNKdvdGWrX3e!@
zKWl3hyg#*m*C@n4__(=%`+YjB+tj%_Zd1cp;lyjsUTy#UIKyUW--qUL@Z%ywLH+>o
zY1E)f7V5Ke1CmiYFm33-6nki&(pk4?d9d_32Zk{$Nh6NfEZw;?RQl3Ob&3a8;VX1M
z8A*UR42_cA3Jhj}ow=kmZ(3(8rs~cBU8gWs{J`ebE^Epf$TxsiTCAa>B$ZB$h*$7)
z=kYW3>UO|q(5s65{H5^B30(LrCB>0b??a;k4c@<ykAZuJS4SqNgzf^9f^Oo`Mw*&-
zO43G)^PzacEst<I_0i4%M3?-(n!Ow}htaRVsZ~6+bGICAs>1OKCpK`)3$h0s6Ly*h
zoEn9f%=O7ZFQpQ5V;oP9U_d{rw5!2f-4G_wGGP!Opc&(t2EYulpC_*>Ou4Uu$ZF#I
zjC;39mFw<C4&i0vX#kmZ?t~25KZJ%#60wG08jRV<^{#4D;?Vq7p6F_2v>l4*pwh1M
zrIKtnJzvP8XDKe`&;Tw>8;0_kTgrY>|CiZ9X>KGD<0=ooTaL-X*46>tVVF+Jdj)Nn
zXxmd^);hIEAzXqT`^of%a~m}Sn%#vl`d#JPbtG;p1m;>dy<QO($P+rAIZKiJN0($3
zmx%W_4H{B?^W~G@Nz{Qz2@JwkkHQwyQ2nKObI&K~mB-FhWlIqJcEy@~?j>AhD?7j5
zjnnz+m(KyhN!oI!1G&C<WSg(B(Dtj&;R@>ZIarFUO9DjRmm9lhPAum}DbASKfsT=R
zy|n9}d_VO<V*d);PW@R0`T4-o*Q}~V{f7-wMxEr<j%&3OH44cHHs7bbNYUxAtniqK
zK?S1M>+&}8luR4QqSRP)U2k}qe6W0D6vS<`4BZS(1DdmY8f|P4!FjZSCNl-l>^|&a
zTy`5Dm&w%8YRjhZV^Oh7^^E?qc#PF`@{*J!eY<pNc4JGuVi{fwoVn_VJI&W|{z&A>
zEObxQl-E1b*z>cPvpj#9<mLtjrxk#2qPLEH*3~b0U8yg=r@ZG!hAc})#IV3`AF;dy
z$tTTMrX~NJX>{?H8=jv3<)V7HLP?TJ`G@Yb!4U8fZz?>J9a)JXIKe|g#>7mOd>;k>
zDRKlf;CLncK}7!Rr4uqtBC5m0>4KWvaK>cx*qlgIi~ziqW$hNJ_TA-flWj{@OOsnr
zQP7r<Of*uukrQ-{{%aVU_y)rpk)Wq{uSR#8DK=L^P-7CjuL*kT2mFUUlfxLl$8sdc
zN?(cMeZL{TAE6IMZ7~hsW2Q|F<XHG4N*SKXj_yXTCrK%R^u9)xN7`rcYV8!c;1C~~
z=Grp=nk|#z#)=)$BkUP6aEc--J)XWP^L)|YIPdc9#vDcQ6zP?&bQHuv7di8^hX<wz
zL03ii_R%w9p=DhCs+{Hty(~O@@%$G;*RouFxd7}zI%p%no}(mS)=l*7oObgd^Ub@#
zEPY1RkGoaNf}jo`Rnh((zfl$c8mJl4dc!Q@b736x?f<G~Oh8Jo8Px9$ciMN<l}_wn
zwgoqM`>GUNj;MQDlufaP-dTa`Gb93`dsIc(4LZJk(N(tdPe*rrm#G~X=<&E+o;Oi<
zP(&5Zxp}<w1p`gXboJ$;cI&)OQSyq3?SmjiA`}{BK=iVp6zWi4qE)uA%9)|1oMt!^
z45JRklZL%lBS23lnY-MsWl>7}2IVM``*?h_$7#&i&Ca6z^y0%+KB7Z{rJGxUa&_}m
z7VzjSJ#7l5bbDk<K2Du()l&vSXwi`X{uK4;d2>=e?P^>sLsu;uZ|iTr%~F9Bh=SmA
zDpZ1hpu!rzCI@s#-I+@A*z;yd@LA{9quKAgI6p~#9(!;S`PAtpTN4t3<0j8&P<Q86
zl=_LImVWWqfB#W#Y>T>NYGN<c69089mzq;_Q;;*N)}ttKn$1Z)nFsa9?EhDPNIX4f
z#|un{?#0=Vdn?Ic9Xt_6gKIs;&#z^C7l9sl{3mDJ`jyot1?|tsFZ@q}_yV#$&R)0l
z2L;wxw<^J&#Fn3;2%$h8OI2}q9{XuuwfWx(fbL0c`LKuOhpVdiBA{le$;;f?rvA9p
zMHu$!)5D@zq%)@c6B~JklyP82%4oE43LMX2K+S7vv;1;BUOw%bSbK8X;Bxn%^>C-t
zJh*h1;ucAllaos{K30gGwZiDi^pS#+>fzD1ZzD4D22>5NSj#nckB*ayFiycv#-Zdm
z@(0J&3X|7||K2|pYOMBNMM)Ik?XoIrZ(3*A4E@Lss)wz;`_$OHvfIGALG!skb*q<Q
zsw^&J8oLjdjTd9ghdNpYx>=q5IoZcv{-*X*pz9W&yH<VphY?K_kK{KCJD1kVTEDf%
z!$DW)bJ79|G2zUGE#We*4lhMwc_BFj(NTsZ9v24xrJEqSr$?N}OVqCsA58xV*6vmI
z^zgw6=+KdL6aUfEP}#@gKYyw`8jd2d`1gRI=}%{vI7m6VYfKzmceHV}KB-k}Y-cA%
z<)?CusnUyz;VTz-Cv7~VZHuXv?1(GxqIg5mpvJ5Eckk@lW-mwIVPRj-hcdem34QFJ
zEewwx5*@R|=uZdI5cE|C#T9cxdi;I`Os!85&+*~IHv6lcKdrOvy1RCq4XpXvJQB^h
z-nOwZ#J-z`zqBQDIdMC#J?1&M1j7%U7ntD0>s)_7=|oI1)rnpG^RtHAlRZj|@=;Q_
zh}eFXZ926gr_GSOeCivF^JX7Fp`){KaN$P-953JdRN?d|-viqWSh{uGubI31=({*(
z%<p$_FjQj{ArU1hJY67}j;<oL!@~o_WKkmJnmvkpGJ4TJDt}S$a%$R9etqG>e%N@k
zsYD;Jt`O^FkON_O4WF@_H;0vm7>Cfp8sXnV0oCZbt9SK(=H1iLJ|^-%^xx~ljhRw1
z)_I6*LO=z<7V1Y|_7kssdZt;>_diO`(eIbqD`#J$w_SFMUSqT+_a}4T7-omB+UvN!
zn#27*%jHIbjXvgUI9~d#`8@USxKxXQN;E5_;J|LhxC?;t5zkSW35(!OQeKnFOQU7@
z4-YDwb}jRQo}gyQUlV>7!Qq_E>xrAWu!s=(ZqMRlfY@-~t%~LS{CYo6!i^ivGu+7|
zM)vMJcKG=A&|PBO&a&;+Gc0s>46a*Lb8kHvZfKQok!XGoQ2eX^0akz$<cWcr)7l?o
zQM~Zz{T4<vT2E?&9G?&>2_Egz{kzYUaR<V$+(bnXc8~kuqJ7@_ERaJKPw~ZegiP78
z+g5AN;4qzkx=LR4c4i;qswZ%0P`bO=pE*e5j!{s!<J?}G?Z28IUze0A<$eHPAvx~f
zRP#9pl?&%E5MlxE$JjRCYsUukWUA30b9Za|8ZHj-r|&YXz(xO`^kI3B5ZD7b=8(Pb
z()G75_%4f!5M~wrv;FtZHTFOT<-q&lfN)1hE86~Ue#801cz9^p;i(%Qd}V|L#3bT<
zav|@{aUIj@I<t0ozAKJ=G}OQy-X8~w^Sox?m-DU1th52oA!$#@_hwEy%iaN$o#^}A
zAG||rIm#=HuN?BRKM_Mj<x)md&NOAmE)5KmpaDElc?e}JP9>u@s7Tug8T0ubLQ(RS
zY7{>5FS~En84cxz>ZM8q_nkYh(jn$^wV$bbq`aQH-W=H0^v_)sEpH<KQ*lcOE<8OC
zu#PMDh4?qB3c{i~#7o$apNfA9K*Ukw;G@dG@PEZ(yc>vrfsv0686a7I`(Q-2wlyvR
zx|nadw(YcT?k9+;Bmc%Fu#{KNX3yF3SY^r(N%Dkt_sInDDDYTS_KoQUb^0(A@6rX*
z#urMZh5JsuW#JmN_4)L=eL@AlectJ9O#*RJ=wO?R*Ur~av(Jp7gl2OY3)Qd4z@ZGj
zVLc6@&{gGP10@x7H3SfIPR9&)NF<Am8kpUE>n%y~hN3lc2=)fZ#Ov^JbXTb-bt=T}
zR`G!pzR5!OR>+NL^|@&N*B6p<lA>P>WU^Z&xMXKIflz2@)G9tUhrxHf#aXnMjYpWb
z_3_43$DnF%wcCCZK!^chQf>EgynLBWEE=MsmTo}OUcNLur0`Cw$J(hdusAdSq})WY
zrt%phhJ~N9zA9j$F<A40{27Etotgzs{|_%w-aMv$=qL4R_1?I(_aSua1dQEGxWYY8
z0wL@g1E<{DyxlKD$yfaB56dUE;Te-a%lP%#i*)9|T!aMR3jP2?Tf@-kegHV(73LLU
zR!ZtI1mT5EG=N&5P2gdXD9~kWlzlxv&&<7p{qyf{FhbjQ)>cmtq<)ae9s(qb<xc^_
z!-H%Z%$81#fq7695!J5LpWC-g&L|^>@!)=Kxvd*MG6m|^FExjy6Z`O*nQYw|9#Ib}
zN$A+U8z_kUP?s63JCOk57(s<+`_4x|zW)`<KLLz%p0vXpSAac!czC(^t!!a=M?C~6
ztik(IGqbnk?kZ>2?ZJo+?k$rE*mg-SAs23Q;A&S9s_CpaRf?E;514V{ot$6!mR9||
zPVTc5Vq+p>)^BzFnPGsLlb3yg@?!iOQ;I$SwK#V$WddR{B|9y^?Bg6|UQSY-*vw_x
z&0tAJ0LgOdE=K(YgyqFApkJy>Z06UkQ$D3quE`22(|ICLwG_YSE_MzET)cje03uA2
znUf9&%3;i&O|T^{UHcGNe9qqDF5v>CCXWJIn>R31E|e)po<qCJUGk%u|IbpnX59sS
zl_2_0hG^VG-6r84Rp!lQ{=v+)D_MzYexh&U-f05@k`~9^gUmEoEIz5&oA6QSFTZ~7
zR)SoGJ{^p9z401TNE;%-?uD0=l^FO{l)xHwawz)mgqI>UHXCg1md+yRlkIrQFLRw|
zJ#RLS9_7{Mj$L~_{O7L@jm#>)wNtU1&)wUZHD;`9XcR|=v_v9D1jdk2mJ}M=-(er8
zo;j{oB^E|TpWkB8s4Xd--&W%JvJYna9Qt)A$rTs^!$+iY=b76say!^qe>88I%VJHQ
zVpI{fi!6<h#>+IkDW@I%skT**gs#$UWfqDjL$GCIR<Ff~y(2wVK5f^}fJTepNt-Lf
zr;p%~0jLIQw18FQB}|j^w+Zr?Q|C%V=xPxTnnRI5n>Au<mC)tD1?;ve?_Oc4W$W@6
zp5K0T1DC%~tH`ffQNErixkykb2AWv9{qQW4^KBDqnpA;_;Y)%68ek88brX3XsarUw
z-<Z;hIgZdaSG3dOz-F*g3yqNl^wi$3T;kfY?GJZsD{Eh$tHx~cu&mB7k6+Kz`FsSE
zp3lkv_5-d-cA{6}5$vkb#k-?ciBXEd%3?~<5;l_AeAGnTF1W(z!dB>rCvWx$=z*?M
z=~F>&dML}AfwfZ=xya&8r9lG#28&rAxqNm9m1}QA=}=Qp=2a@PYE<9&Ue}=_#Eo?d
zeT4!dVw0g8?)l{Dufpm}O9`5N<ox)`6nb{mTSJu>%Bow=l!C(_L_`Rb#mv2qTtQ<U
zSc1~iayA(QdDMzhWeBkQv&|CZ*2|swgb`3Ze_GH0$XAOD-Nl(xsW6+T{u4w?q$Ckd
zA6T!@I>M{Y0=Lskj2ClbBmVUM;wwXY+NX%qNJ0sCFcWO6Z-~sZL6?pQK;TtiE8puR
zKC6zR{5~jX5~3IXc#oc8!%PM?m*`s+elp4q-@IGnNnoZ4969?9fdrfUUACrU=nBxB
zTp-m~k4`MF5qTqtfRYjbp$eEF3Qid|PUV;-RFWHuO#Aid<##Pm6BWFQ1nB8wGrPH{
zOAwZ${|n1(X%99mD(S|B%S*_12fX1#S2Y6F=z30gb}giG=;NJj*|(D#_f2^Pa<a{y
zw5CJ<1JpL^!Jj#G{*VA@;GKsA2aMp3+KGBve@PnfLpKNAx0TYEKB;%rZ)f`I${mqJ
z7IOEQ2*-yO<@Xf_tpBG;GBC?E7ru<oaJhK*;p$w+IV3BZc(;mD_<BbEV351kPX9$W
zcJ(|X0{LLR$l9X0HO$?~tHd3+CpF_%$#i(VE?(~!+*4zTk@xGHm$lC7oz_7z>6IkL
zB(l4c7q1B<pDINq!vaoE{k{F62YR`zbU}tFoKwGAEE+xv^_e;gqGTEl(!X!te8YHg
z*VOiJ3CU7`zqM?yLrD1c8yV$Av$4F+ty|B&#%`mHUBb9=_Vq!ERtMZAP?8XaKx;=s
zaB_ZBUAH+kI+6=q^@av2RjJ_b+~U_*6s_LUD38+%uo}2E56v%QT+8RJ!O2gL|GvOd
zUhdZse3toCK2}KG;75Irh7M1!j@zStLWmGBhfF&pi?6D7by*db*j}~jXlHyH)Jq_h
zm3?a<xz;n<O=c9yq%8?*O}LRuFu*M)EOMbf-mJZ~(cd#${5mgvEeMs9Y*it0JH3;g
z7e1TRw+PqxEnCPf9wG5i({fj}yy-3aEUQ~YTQ)tM;iECm@y2qU?xR4dZq@PO$Fo7k
zvW>Up2P`M28<*S2*!8-RIw=nyc@ezraa=yM0Z>F=Num(k{n@v<)dk^6yUl+C5>5&&
zwi|2NOXUlHZ!DqD%J-z}IzUM|S1td0?)1+!zT`u{g^S@;yjLQXe9VY}SIfniiSL_V
z6kWYtj}}v`B?EHDfCSg#xSX|Ydh#@&f(PcC#z-dJ9oV~D@eX%CC*-0oLbe}lJ$&OX
zgNJ(eG4!6ofF?_DzGqeDQvYH1cT4vY{|(h?R$0x(->$@LAQFDqD0oT2x%ta&Zoc^J
zF=b(67%;p{{tvGKmTjNbd=y#4P3LK~^)hc#HINijvWtm(lkZ*p23LR@FbmH=Nsg~F
ze^|gZP!m(lGM`0BekmYAvi}mE_|OG)!cp`5;E~?*8eW~ZI`&+Sbc_ZEs}?s9N*Y{a
z-c^(>liL7Q|4%;OGaZ+i^@uOxZS~r#__hBEY$zpZIb@hZU$+eQf5sQU+o&F2>*i7L
zU-dSf`ci5hrvD*7Sk+pk&v~xyp|WkKo_VQgRsBI(8e>s7`R|%bC3HFva*UqAhlu+i
zB83-qMs;C9RjRf0zrW)yMxCX1>~&iFl%P3wT_g0`Uu>s!9$@C{>wL|DxL+j4eEi3S
z3FpnkuAq&$B!N#FN2&H9_F)6rVilNv^!^|zOCSiz7hwLihy@@g8=P&_D`TCK7|#jS
z@JBgcO<~tMS|{-+eDa|q`(2(_6`bA^)yIH<5OlNuEt@AUKY@!*OEhC?JM48&_a85h
z_6UR2KSgn_=4@1-M@lr08j~rdM0&nTXruk&qi-uo*r~%xYUYQvWm8W!oYHhkw><=e
z{e?LOtoE_)gZcO>k1+1QZ=5R%vX*6dQB*Z%`n-j3Z@QR5@5%L;vA;iF4YGL_(-|}X
z2a-FzRnsk64D7!-Pg92elWb#s(qkq+P^Th-6A7mZ%zB*Qi7BZXoVBuC#~hM7oFKPW
zV3sMaaptZ@4qx*q9L=+-J`q4#fwZ2s3&v}<NGnD^h1~^ws%DdMFG-gUlbG#<2k$$~
z5!B}=gytkM2!T^e$h^n!T=%sNdAGOH!1|khW@at`HL0pP_@jURU~6OFELt?WiD{86
z0u&ekY#F%(mFu@z;dvEqp|MXiCg5xH^eqOhCzM*I?VHm5KVBHZ`wu2+mMbj5k{JWK
z<8@h(gy%p5fJy3=S>3YtMu%Z#As37=jyr4^5{!Jj`0{IQov-QA<p>6lR9yJ4I(&Il
zRaM5z3VGgt`fkHFC>rwC{^QDowMFja;&x)dN-8dDvn%eke2Rbqa9GZgGgZK`M2S%I
zKfrkylDQ!;v40@N;E>xRMqQ17Kmz%_l`z2qmuE_BqO&qkU$3#rUxw5GQQCXyHIvT9
zKpvHg@vM!BMv!}ZbF7)Lvog#;l@!FD?Msx=BY~fq@5*WS9g;fXV*j4EAAVMGys9%O
z9mSI*o9etjE@MXl198Oou49h=-egYrknWg#h=b+6t6s#L%pWgB4W<v%p*UlIQwGoJ
z1Cio`ef4jdXXQ1yfkgGj^=1DFU}XS;#w8t*WJkHCCS&S&HM%FBS`5lBOOrWlWl5sv
z<Z~amiMqN@dl0pT$&nrC*NLJH=GM29q~qiCR*uiwRnXi0JAF1vwP1*!eN0}~CAkFA
zKX8WSy*}mtou{TY@_tF-m?fe8n%$6GOk{0!@fJ6;NZ8yPCc^z)&qqs7uWtt#jqb5g
zaGBkk^>unMZC|5${SgT%=YI%M-~V$Ykw_I5*>7tc(7A?f`V<yc!ciI)!HgaH;+;z0
z3<Yo0r_qkfAY2FqxK@%HuyF>3;;lBDs8hH}ti4c)K{;GjznEqrn4naB=r{30P~dX>
z#e`CxL449%!GH9G$TYxC2>3R^!eWk@yC}>oRi%5Vx9*Jz##W7`tJ;U4r}gn2c*PO)
z+I;UidskN*udnszYpaH;cHi8!Qn`yXST9Y?Uy3!~9u|L_>E^9_ZRo%#p%lD%<#Lok
zRyfEF{<OMoK4CT->Rl@T4TWMFSfSLXDdif(32}5y+eDmNkTd?~?j@$woc0y%IK2Pz
z=<D;_bRtHBoL8`OJ^<Zq)BQp|cwn)ys`=h|X*0>)-p4MZ`${fexn$tDXbJSt+yA15
zs%rc=t^fw4y2-S;YPBSb5!1QKAA&bYw|Rl?7q`O8AKXut6}2kG!%kc7gzs>Sg{;@&
zUpLx|6G@#l;85MKG4$K-6b?;+Pp-^ThVIkI(56EWgJdMHLR{F})087saxfBa=iwZV
z6xO&j%t}P#hdhm!U#7m+Hw}#?kyfn}CzJhac$$!wO2%Z($QUQcH<b4U7Y-)vGmNQ;
zPUKg{k2Qyu_g;>lU;dV(DrU3S^K3azarJVM6pzU9U*Xc#e1@!If}=cJA9ovM(b8}K
z*g0oI>S{$F30}{pY|8}(BTMG?M6A2p@58%?k9GF?(PF&)k2{ZdHQV;)38q>PXP53`
z`c>jBt8BKpZ5^6EI*%WlC7PpJd%n*%*7l6;+csbB+n3g}B(J`6&Fotqk91kB5&CGt
z3<{uvw>4K5kM@rV8|tVHhbL4IFI)Q3A|uK9cw3VS`k5Dsju&;bGPDjy3vG{+&KylP
zu$TxPnIfMr-mRYo%g4qEeRBPGYcDQi<ojRWlGvi;^w`;cyPA3ST&S5WGqVYjM#fa1
z$HAqQ`E?M!wTApbCqdV&UZVKB0HN6EKyKstWWYo>Tj2F*Sh0Qr6Jexe^YxpT{%zl-
z2|WL}ACZ-Sp!3b+u+J4E@6_O`;ga~I6qWgl9`UE>x9OSl<))t})M{q}nNdN3pz~P7
z6>4?WGyMmbpFW+N(h32g>3^-J1C4VzIPLab49aH`W;-O)_3nPozh~Xx4(0))5=mFo
zWg~Q;(}c$Q<o^an0B_7M6iWE7wv`(0@YrzchBx;8;<)klhZqdd<k00Ksi41SuvDYj
zv0sc&Sk6CL`e@(Y4$c0&J9gOMtrQFqa{cR1EBoDP$Jx05!7@iEP>)m|bMDyBwNyt{
zf~3nq+uzVJ>~D+3Gk#S?hzNnjCgki2a2ujz<59alk#rSKIT2OUSX?|4MpG-WrIN<;
zjY4K29;66}0aNM}BQs5^`fQKv@WGucH#ArqAa?P<w(Q1zOo_UIhRwu2QLChc&EL{I
zY~9&*=Z!f_i)+x0jNe}$l));N;?>nzA<ww{x!_>m>^Ex|4ELep)=m8p@5XcMkpvtT
zfh(wP(a^lCcgMv`Zjt&6=jA%@oXNSG*7q^Z!zXM)%CuONDqJ6Q<!a2WS2Lc^h6sHg
zPGg_Wgx?$xw|e}wEp=|NKmu*wLzLm9O}&494xz($A*wqC6yPa-&su>8`F-;Pbr}5!
zr58X~zZuxrDAPxd!_C6%G6qItjYiHEV2^CUXpP~{+@JH_R)JplT;W?THJu-$`L@SR
z;eRldY+uPMquqtO&9zp!y0B*Qseaqox>5|dY)sWUtZ1IlyZ(u-M%+s*2TWFYDh4LO
zUrYT7V|l8p&Fx!uORM8TyVIlfFRpkVvNx-ZZzsO+7Y=ckI<pL(<Gi^fod?9Tq=Gj#
zJA!*|GQ<}RINU<&-}I^n*3vMzS>IZ2_Hmp}eStIME@2)wc~JYu@wxo2ND=h?`2#ms
zHiIp_dCbT)PqIaST=P)RfHR$XWyjfG4IF;^{jxT5#0xQ!Y~M?Cf7oca&Yn{mDHv~T
zkpwbCvL<Zd!UC5Rsq6vrpoH0abw!{bKm_g`;@!H_rmB_SZ+R%HyniMCWy{{ITr$$F
zn*la<>~hjZKHRpcLnJvMM`}s<f&K3f9Qnuy!wAg-(Us3iln-Weg^ThC<aWgXZnbi>
z^l(H$0^;VzoG(`Vd<$ns7e>G)Z|)G>lpFlP!3Jzfqqwlt!+f*Hkv6O=ed(o&fMg$(
z5YXczs3RhSzNd?VrHZ;KKSv<aE<iz^D*xJx#<2GdJw*4he;TA(8A6|@>E)2JL+CV`
z8U0;J7n%NBxI-YB6$q8~F8j#%UGIadrvtS%9yM$12*j&Vla_%&Mr>yh!`8w_)t(X-
zt|XbnfB&W@9SKct+t1JSD6{LE`WP7^oEoz)v^yX&PGLksL<0YX0gbB9WjjlDRBP0w
z(JiRa?@NOiNVmo+X7G0Xh!xhxaAtu8B(dYFEQ~2XaVTkC{X#&|)!vJxe~2k5RW`8$
z0#TXZ$Tka)wQi@5&0eCF7DGT7q{Y&C+Cukq9j0ikV+s>RCCJ^nLIe|g(hlCEMTYah
z+Uw+cGjoZ1q#1MxtSa37*o)fYKGQ3JE!8OvlLD*i(Txa3y5BZllm!Q*<6V&YTtW!V
zLaHp|7WR;JeK809Gx4$bk?siO*RGQg8n?BwjlXCs;ZXFaPgPZ3=Q~<i5o^urJedGX
z;Jg0U=B5oLym5`So6DZrdMA|pf#@>F2u4t9o}yv@LqkQaK3kE+xF?P@pLYL>?XOC_
z*=KM`i;#2yd=|B;pms}LpDECJoQh#-IqpaRa7Uc4OkHB@rTFZ#=<rQH-~<F>7+>^=
zTOV_0K=T`{KIh5DtnO6U4_vv5@N%#Nw5(8QAil5?-`+J1m5xptz-T#L{gc{r?O)xg
zdcpTwMS~19*4W-@&B7Z6hs|##+Xrj{0*;Y@<G!Od?Wpwwrihb{y1I$r+06-gO4i)_
zhkq$|9=Pr{Nk&CALBrpo2+aQ6d<xR|64OI0Cv;gA%T_@e_V&k_$I-n9I2ux1HdkV%
zl*Pm$p)1R-VhDPOqdkf^9x_k{<h~sz^!jW2HOb;=_+i<;&ekO2b5YIyZThc-4(kKL
z(;605cE{Yd&1O3;L1Te9uKK6L$0mQB?j9df+*{9aH^C8NE?Zn56J~mClR!Kr6t{`$
ze)hD)?HIzyGH_h;*xC~7`?>K66O$6#==!*quup9(HiZ3AdTG1iDK{&qUJrHFjosbi
z+0gv-Ew6tjoo5j%k-%@N=o+sFt?y<IAESQ964z*Yf!GCy3iJHeRpD#aM^}c8zV?%y
z{Zi4DIl<UyXIqvg*Wc03=jKauyVGZUT(UK$nogTsejh*Lqu_4}yC=r`J$HqSn5b#G
zUgA7nxj*`WBp}gTW&H`9h~S3CZkQr;3cO7(unt9`nWKAIIkKl=x?TX=AJMZt9@(Hy
zz4wAFj1gcD>|9(nFZZuIlfu~BB0oe)F!R)Wt+aqQJw9z=zqgNnABOuVq@XAC{T_{f
zM_)#5=!H;srqBoBEz9ouHs>NLESMyIfOxzz`TLL7X;+iUy~Tr;w7(s1QK;;fGRUg0
z7U~{B<x`d+By4`iTb}z(`qg5t3!&=7mXG<O#iK{VWOwBqSTmPSZAJ5lqTGeA&C(n|
z<vgt$Mm6~mXKN8*Yk~e0Un%^m_V&T@;C!y)k=Kud(UEO&?YJ$JnLzKv%B1_!8}_Ga
zQIbe0EjJ1rHf@l#)dN5B-o&-7qvmG*yXjTCM}3BKwd`Q=uwBMIOxX(#%pn2`?xoHE
z^2VN=18$P>{JSrkkK7t)l24z)!fVYJ+5@x}O~K&%R-(ft>*jf=0nYJ{V<aRbcJ|o%
zFI&i3cRZ<tHruGgHTw<T@cP!X%h3BUo@l{e?9|GH1f<%L&KCmi%@3}Cpf7yE4)I!@
z$#5yYd!=9yI*RFhx47@##?9E=SHsX8`tnwDcVVri`FiQ3AhKnkpc50EM*oZ+xgLL9
z<6iI2EE!0pWRuxBww&WrRkDuZz6F&K!^YPQH0uql7NPqBX)l`-w`pULccJ#X%P?-~
zNfOf{sTTDa%a*{Kj|j%Q+6&--63+O){sU%VVb%4~7?RFSmU6=lg&P43spg>2dQ+QX
z4(ujjC&oZAR!~5&|J6c|swDcfc31aG0!Bg*2t%NB%{Mj;;kvsd={TJt*9k_|3M!y^
zdN2ni^6*I^AOP+PBVg{=H_RHW+ASdG|FrOh)*LuA8p`^L8mbtj7-T-}JYMx0)I$`u
zY?9Jm-$nvGeQs0*Ij@SYW0iQuDC!?u*Z*)L;Dm@BlG7*cYbF+fA->H}f?nK9R@Si}
zON{%#1pVWE|JU~oMSQE0-{)9Kxn%5Qv#@+T>+XM7>;C6a);ff5?qED#fMdjY>dO|k
zOt!2(Z#K@CcwR24;%|svvhd6f&6eG7*hK1f!{YCWj6y?{^M!6RzqL>B-0#pl1U;@U
z&9*uJjZvR(F7LP%ZWMyN6M77>z8kAyp~gjM)OdOPi5ORIKyZH~gcFVDU)J7Tm_MxO
z+$ZvXi7l(g@r1H*sT!EocceuU#_=Y}4N-^cuRzn5%C@VEbo0z@^LzHn;2iwW0MO>K
zepcM%9_D^ovb4U@De3f<O#Vw8KYQ<TWaI!Pl{oi%B6$Vb!dps^N|aZRtR0-cIMCMU
z+^JRR!c26%hvsOzas^d1(a@m9TDGgUeNTb}zzC>V8-0osrJ{{-?*{LS+b^5%ag3xk
zF<Wjhx`zidA*<_>KeaVeo5ysIC;39xm32%aS&bccV_7YiiwMuuiHp=@sUAlCzJePi
zqZ_1jS^V#f!a`~G6@96?(W&l^_|l;x#g~elKA@I@gCV8?Cc{jl=s&+&V98z}wJ#~M
zJiK8_qZ<8ca=PGt%vF~Ta})?`?w<!p2DcMqD)@anNCD64`(im<E=-MIhpa=xHkDAG
zsu%Ass|$s$m)RI6*<}o$B$0Lx4Ou=|cSl4U^G7c!u99T;WgJio^chWMpqvCB8Gzki
z$~U@vZWR1`quA<ao?L2mB4TpkSIqqO5t2TqKHNQhk|5-b2M=k{F-oGEJ!leusV2^w
znb*E{);SEWA7jNKs=c_xkjL_BfaF8n%q`lRy)o>BCnTSI<IuRv)k-ZaY3+aM&s0Fu
zW%^5wBX3faK6N`3of*o#78etX^VU3clWuvW8Slaey8u7492u?0s@cB0O1&4C;|+Sf
z&J*9nrU(^NP2t0fC+T{+pBg|oQyUQikp};r)X*sQ>{ZzZ(bu#X1W2^@g{Bg)p1k?z
zSRhR@Pue_dXSpwxZP%e=efdh6kv$VjmmF(0R(tOAL}!3mg4_M$@S;1aM$FPw)3ouX
zja4JBUGhP4d~)l+Hxw@s59tA9`N$Xvp$LK^MvY=Cwez#S<!G(XGbML^T4UCEQOUd8
zFe25=4rYI9X%FhQCtkhdyo-rLg1q~U_uWF9HcJO{@cLg}sV_194Ak-8**)A(TDVRD
z%n=wNXphkNBY~C?4I_F69{<)ju9MCE*QcZfbcRl%FNM!~@}G0|)@D)QVy<?Pn7r?-
z)$R%rnE$hUIrV6>WJsr1u0d?TA(Nn!@ZdN<lC^5jyHwv3s;o=H?nm>g2ROTTt<qfM
z3AgphWhpk++k%jlJYG7=ktye<V|eY?|LWIK1zL$|7l<?9s7VmMzY$FdR9@fZUy>jj
zSCsVej1hlgw?InKB0F`+ZZ5atOQ~_eg&8pOt8YY-P!;*<qIqIh7*c3f7@P4>sy~J(
zQK~;jJ;1h|P}lLV+*Z}(^1T;AI1_7)DN4RzJ<F@JUHsYTNB_IWQ%<yhfk^ul`J<(U
zgBVn(RsWZIQ}^F2jA223KV7Ia!eI(Wj6~{6^v|qQQph06fxMv$x~#qvlb;=KUNr*3
z!5wK_Gb>8u6XC>yCRS~)p4e2{s@%;0MqTpJzxW;f_QQ0yGdG{pc|AJ6Hjb2t2sp<2
ztA6Qg-Z?i@WcO8j#!yedE4}AZrH#;+rkSd={IkA(fulProC??>U<46{_%I?glugcH
zTJ?P)z*{Bpy)@TzXH`^vHLe2S3L`a5_$Hf<G-SWA!OvDPrI@fHm8|1dzSW(UYFgCK
z8Pl^acojQ<^DTiia#alh6J#m4$2Xf>4OO~=;jP>*Lz@UG&B93};mb|T0X29!2*{$C
z?^3O{ZA0hIy7}VuMJEpreW0|FoQyIraZ19<$oRNH5RAhIGD<y>RyLQWwjbX2bF9!l
z0umrc^XvFoa&GM___tqja9UZoUI}7(whlWTx-zfPFCynMKn^`U+5DI;_+)z@*UJ=z
zX+f!Og*sgC>fj|Z_!Z@2Bv6z};SMrHv8+-`je`yZGJj6*TKP9WmqW3{?YPM_`CED$
zmYThH9jMVV%Zc?Xo^RlWS)bMMeo_lkVG$+qMRt>J8cVNU&~wcb)31@|OMxVPod1kZ
z?1P^q6<bxn-*{gXRQW?I9h%OTtb1@o^3l~GqJ4Pa8-uNla>n@1sL4gR>MP0UnS~!C
z#rE)9%0u@{jCe6bUB>G1?Y+>Rh?}K9S_VMe|GW7uB2DDz@W2(w`S7cHZ<g}Q@Xw>O
z54e`#VHBF2NE$Y&O$i#vu)#xfnre{)dBPU_Bm*^0kh7~lg<sS>r*l#!x~9c3Lc6=`
zppG-2Vu$}NgArzpJY7he|G6o@hsUM^IS=pPnO?jyl`w}>a#FKwiMjRmy(*yfYnzNu
zn~$5%X*yX%_eptacT0^&&*jTzKv(+WZHtqZ{v6anDj4GR5UZ@rY+OmkW(;9JyS&B~
z3O>{rj+<P7@6v8^*W0aULM)>9dPRTv859j3ctR*3(6N+rm4r%-Zh!bvI1~?0`t^)b
zfCcOK@pBEx8j;)DDza<6Tcmelc5X;U0O`*y%OdCGbgtG!+qgt^G5q)Qe~c<x2CAE+
z`U|?VhV2!X_EFUorQbLbv9q{a++wRJwTCk|j&!0sRo<hNr-py&#>3yfd0T8Vd=z|w
zp;jd=N)gsOGP0g@Q?vDaf7Ff>X57W+&t#&xn?zT%Cf&=6lanm@;!ybfLCV{^@}7aB
zMRLj_1A{3rcjW`6ZA~D>MS#DeB(|zzULC(fT6du>o@!%N%Ceu(&+p*D#dv*ae?UED
z5{<3zwJV<SGf*a(3v@~nzE{`w@}I8YWJ!C@YE|YXMA70yVH4mF_PhFObYfFr%>?%M
zQ$?imWkF!CVO?h&Zd<F~IPT5&wtQ}vlRl`!u}t}yYY@h<kIT3deijo;X}f1zH(Caw
zQk2m9#*vJjiBd?Anze7aHY8XqaYQoq4F8w}`KjHORaJ#ILtdk%Lj<~haAsoW!K7os
z1Ld0qfND*uM9^kIp8krN%3gjC7xydIrVU2g(I(_RL(6aoeuIfYORHKFN*|y3mk5>M
z^sASZDWeS<YTl$05k5irgjU+lByWt6*yrBxPY9l0;&{)^rho6%tM<7CBqpqv?HLKQ
z>W4AvJTf{kTdvRIXv|@UQp6j;n?X``P`rC)9&1!FoboW!0LZbIck+1OT$l$7Sg9b^
z{OhCGimLHp%??kdFda_!>32dFq1WeqRlrZY8|T{<A+FzebCQP26pP-DHigaO`jbNZ
z3zQgP@b3R{bkzY-JX}zb?l_T@@Mxr@ySuv)DQW2j>8_)@LAs<%y1O~L5#i{LZ-3vP
zz_EL^Z|BXMH?vRrOiIDz<$Dw?K{9yIuvq=?9{Ompu(V{u!jWd;$tFeb;`S|ntr4h(
zccWdrfMxsh3)Ze6AhB+#kmy)0;3OCK5!zh6#~A4cpTtC)S;c~Xi!7Q7-lpw%AGD>k
zc$*=G@f~(_j#>jA82jdd8xPS+%1lM4GVhNcDSV)NZZA8x&E75t_^~}{M<hbe_X(g=
ziuZR8c0dtiiCS8<ay;FprioF2jOx1igq;5VJbBII<C?{w#Za&zp^~dE9j{3ED0u8o
zc9HXX($wPUiO~k5M1~9h-M#T5B{cpok99vrzOS@8kX@6&GgR`Eql0t|k=wcMBMU_Y
zWpcH~cP_6vYlFIb_~Q3ueoZIJ<&A_HL*LTr)2nLg=S?k2`gheab?{LF;>-&|j~@~T
zW`HWzb>O&Liejp>edSdyuV|K**~uYYzTtHL?02ulXtdgQ+6D~U94LFMpL?0vyuL?;
zw`^xy<G&SO9Deu_hxj?Hhjg@q6uML1^~h_np_|`0D++=indNzTd3{bH$QV{5nT)#W
z-Rul6b{zXiWU)7cADWZ3H`?_~%9-Nk@oa4&U5HT^3<iGLQqBxmeNd*i|I9n2oq>m>
ziVAmMYYF}suBQzzyhMrVa{f8_JQ6t+ArF$2AA7IU)jGN|pT%v<k9@A5qx7^&7b74P
zYy4|hmaZ5p@xENhH-RN$NvB+8!?Lzked`doR!^ItjWP$gBwoJRIS(1kPEY;)+_m0u
zPx7WX5;$sTRK*`g0or*S_EO&kRKA^+kE0(Nhf-AA&(cbi?F*(bdc%s)GAgjv`DlOu
z$)!s)?|+d>1sQ*7Wk|@A>Lrgh2aU8z6i}^N11eT?U{`oghkwxCJ^0Jbo&=J!n3<Dt
zA%%N|{1jGXxK#g(;QG(S(>F9<P-cGlTS1q&<Y&m@2zZzMIah49yzbbh&ZN3_RUr09
zAafR(N05s2Xu0t)-N?#wc`gEc@t6cWJX6C)fjtvML$2bwO4)&vfNP)j`wn;)Y}+N$
z3pHC@-)vYDIyiaY!U>_TqV2)3W#p0QUF(N@v~3W<ewbU!a;H>Ko&vw4Idtm0W|HBF
zraw~urx5W#pte9FVF4%POjl+i{RoyXNknfgRGXn0DmNQ>fQO?r{Lv9WOWA{F(sdJ*
znSa8ugkjr0WTKz5|KkGQLeGBoV*9*L_mya|^~0U^)_-_+ymC|OqaqN)KJxC~P*8R(
zRgFK1H-d4977|5m8Fg&tnnhpU;lhFt<=?egqwlejSy+*Rjf0JVqqE{A|G8_tu_F-J
z+@51c!ix+G2>U6lInHL6s3Se5=3?di%#<(yA3$DXY+q*r%a5S11{v-;Uy=Z&jq~Jl
z`;<iwfmDJzy3Rq%zuERh{$3-k&T&b<ggVXL?|)gSI;15h$jLW@6j$*}dQ{!g{Mz)1
z8{Pp^OmG<7ieW~pp2<Syc6@Dz(plcX&b7KwcPy2-3OTYU;DErjZkS&OEuM85GW*OZ
z*Gp6cKVX`8jQDSXx1w@U$Dq8np@Zv08zOFA>?E&XI&41Xb%Q^no)%t<&dlHS=h$A~
ztZ9V;{Sy#E<G?>*uoU%9_bE<PP=qZnUN&vWu_BDn_3DZI^q-fZa5Ze3Tkym+NAth4
zY3nYVd9sC?l@*@mJ*k5b>If5R9n<fZ;WD7(IL32L0#?^d)g8XU(MO1(n8`9F^73jD
z9b3(|&|X)5S2w<jszq(X$~wK1%~rt(N*s8sjoBZ+*y!;S*zL$c1+;dze?7Bc-nXcs
zSTXU#sbD<bd~nq6jS2{lIs3yV(z(lG!xHSmkUWCYWRLyJtOq7jvNrVBEZJQihn|n-
zf|d7UgPgp)X<FJuydn`nNJQDlyZ6HKZ`!hzDi_S!{=<gd^F;=(NM)jLWI(CuW2^v}
zb)@uCDmsXDf_`)pSLstM>c8D+ADB>#lwT>-21H=rwTmSw^9ssvL#ilcdZb0Tz-J_b
zgV)~a<AQDTm{7jYoSekJR~FT>Lt()C=MYKRchu&b?$fAMuHKY^Edms+CHd^--kn71
zI)a5A=_h`~u-ru#z<tGZgglLH$|blVi3mW|obh>!4M#4ds6}8A0!mc4Yh5JET*@Rf
z90e}vA`DN1P}g#$`f0!nMSqb7*$yN1uN$du15*Y=8$06UAaI7GKog*}(Fi5`(k|La
zD;ojOaY8qXHfl)8JT;S<O)!HdOAZ~*-A>%wZ@5m}n6Wpn#NuvUOKJAk?;|%-`V0)F
z937LF!#)#PTDX9qpTZynWa+Sg5OQgBQzk5Q8Gx;XfK?IGKbBupvWjwP;93TX4*;+9
zSF3Cz0kZ}ANR*ij81+*{A!}=6)sC^-S{u|`JWiT0)7>HdLftMA-RH7R7(#`*L&(1f
zbu#ce5ggaO#q=#>?IWJM2LhLtnCd9={&9)0-DNWTy>?snwe<|Z!dmGZw`!WGniY9(
zMm>%mn?-jb@YOvwT{Qs3Bu4J!wx(Cm7&LY9*Jhc)be__qfuu_+OhZE)hp^~R-tKJE
z>H!?3$-|gWIi9_Zk|y2eU(ADa`#AMF@xCn<m!_U(K{3@~a&k;j@9je%03@bP&_~XT
zeL6Qc+IXnxcHV~;d)wspQwlk%G<{n4%QeoH)d+s;cT6~*ZAX2Y-zuShdx^<WYr6`<
z*vZqyGpC9V+>Q`zJ$*B(Hj4MSeu#PP&VIn9#N<adqwu}$r(1vvF^x}D1AtuJFKir2
zOgKAUUo;$?OO>3G$DiP^p?s1L?r3n|z-&)S*uh@wP5I>c;q-On6l;0x+(hbX*eJ+-
zgM#fAK@=!-vIV=a3P?AGfv#a>$Rc^UIqfkOQzP?E5R*ca1U7={JbDEACp0#*j=sD<
zA|G5#RVc}Kza6k?G)d~pII+~SsB%lG1Th_Dj$}rK?`0T%y4+_(s5~oNy+`>-poH8{
zbC)NIz3s0K_}v)((du#yaio*znBH58M=7Ru`ej9=gNq{(-+3}^b?xywMr7aFF$RTI
zPFY>w#u-O2o?o5QVSc1d7+!@+$zj8TWxm=q{+aaNveeWpXV37-6j}aGAlZJoj(Wgs
zcd>q?0hoq;bLE}f76rOH*67r$D9RerSYVxX)@5nMPPN)i2PijY4V=>EuI@*lB1w3a
z*WJ#%zKE-UGip<_N6yEF33;mxh;SmZKTKUcJPrGKq#Tu!<UEI$a69LYY4b$$lQRGw
z;-x@QvhQl^X)DnJpbkI_V)t`j*KD|<^y(!T3DJs+eD$PPD%tsAncEkbI@jXtk)b)d
zU()ph65K-RRF9ypAsN4ONdQmLxHEmUvJ`lnJ*s;vPb&)<>eCJpLmFv6dxAUZ;^m_}
z0rE&Rq5DEF(;4zgdv|k#u{GRAh3fM0!`h#Q{hAK?ZlTLA>mK&Ox04krl`gmXToUoz
zfbPviiaK>!itxH%q4BV);Dk7ZloobcQ)%3?(19L!YW9O91P9o0?tEydr;P|Qvn1i;
zpO`aE9u8*&O5lu4;5Mzpl_%VHkVqR|&W2n{(|@0f#e{85rw$n%gu<7Gl!t#{x34lV
z$#Brzt-gC-Hfco>?Pr>p35kbmOiS;M(oi2CIh-dc5`1dvc>FjOwuHaidh@`YX>y68
z;$?Ifw_N%1r?iE5VA)T-)P_q0TbkO1y0~ul0wrRPy)B7zUN&^iziB7Bo0Thn_FrwA
ziiML$%EX^z$MZY((3~`&^IWohzB+xp>%m^UX}&uhIb2T_RNnt{PA8kt(xzzFPt|}j
zV1A*_NqpsnsmGwP?sdWj%q1)#I+wLnag=ZYHNlL<B2y@zkVK}!2?SqnH|%ucX_fY*
z3#%SAPy>FFqkw0rTfRY7T=Bk?ei76QOY+%X2Th8v^bvWZ89+-moM1<!DRf|uJv5qO
z5X6oD;J%h!b42)yI$}OnYo%cH+6^hq5xnsH`#Jwu^YZC})_IcE-li%y6XK7HUYjT%
znXD9JZ~t1`+~^g8vQi?^gd)7Rk!7fQGhKq3{`y6e-kg8RNpI?vh2b*q3yH~Ov>RK#
z6^Tpb#5!xKHHsdtBA#ux*S~n16B@wj&sgT|bATmX>JczxQQsv$TYj$kGHaUDQ$t7I
z2c8Nalk(ua{QFDbcFrh5^7Yc6f;=~j-gT<vgEQd=4t14J1^W(SDPeIHx?qZuZ$-w3
z-;e}W3=;|=ALIR+puBx~?4P?7XUk{LtP0!dIoyzhuBO30;@GGGLGF=%St(2Khf1j$
zvs}bQzy-T;2nae?rETxU;T>17c!KS)s&2nk8%;KoJnX|Xy<d_ZKdt9yG>so_APD1|
zM(Fx0ctxf|bN3fm%mN)c0N@04omF~bxL{db<G8-hU-DvEi<8`$9?=h=A9RlG&&;1~
zD?|dWDtJhn1S1B&>2Qpv6#HUchumx^`MsiKZz}$ueZqR5_IsH5<sV(LW*Lz8(Yvpi
zAX_xP*y#`h^L?dHr!TN{kcp*5t<@dJI&!vIAq`brT%WaM#)m}37Ty0ViB+Rt^J_^m
zE0b5+zYEUc>EC1Edpb|q7-$q|7g>rtey}<DedrBCweP48u=^$bts;Qv#<E95#soX0
zxhfXc-<Nvg?rwPYhk~}ZZr-zCv|kQtW5XfockD`9^;zStL+DO0Brm^|t&9=}V`axf
zF#E&I(Ez>7;<ZjDvnnl^r$%`jy3sK<Z=D1^eG~y2AZC89(7fUH^Bde4Cj*hWlNJDt
z0f%vaXP`C3fgq6_SJ?cUm4p@)x|bJ0e|doxc`F}<!77lngO(%UfBc}|-ahVCvM5P5
z4T#Wf?bViTO%7${zhgcvk!$un_zGJHW4pCYeC)AvrJlSpjmdd=ngyZV8Yw<;H`)@s
z)a#wpH5v|HKl!sQkqP+4>}(;OKl`{?rkrHqzhFFK_QqwcalZaD@&Wu{<bI_`@gx8J
zPobWytbt;nRwJJzhBPQmb&J*7OzJI^J6ro-TPUaHI>inM4&tbAB*I}-4rkt&@2k%}
z(2i~mcnv}gC;M-!6T<gYBLJ4K+V=`O*k?iyV0-2-k86=O-Z+I0^4w3q6S^v#Cwq?^
zfSnR2TPw;CKLdP{>)y}w#sq-(!Kjv-6wK$Vc;TpH#U?KNkm=_bevV<St|unfjlD~u
zN5*g;^$osbmt-cpQ<M|lt1I@w>>R&eok0z<k<mp44+2Pj!pf5*j9>h0F0yZd!1!6D
zk>A7u0Od2sQ0eYi1j7x%$-e`*HRGlJb0*42OY!bM=S&4dc)u>dSY_&o;CRykaSl6D
zc!u;SyYGQsGSmr5|E#kp7-qs)FaxkRF70*p%}r5dP<JdZ_Si2B{(;0<F%{*&81ix@
zi?t3NZ=juD8~|TBshkWk2-W(_K7uBbEzs{#3{!qV8sxsZLQg>JkLSHW@qJQuYs<8>
z0e1fB_M~0~;}G7<DXL5jST?t1T6c6y!iZd_3JMier@l>U7_i9<6VAxS_)hJu?KknH
za`UL}TnA!4=gI+)1qJon)z@`Mx@lY#TjFn-o}mNz%g4D@Ai<hC3gJrRM;KL+^svs1
zZ1!ib;QC6K6WGP7@W$H91@2ozZWudd9=td^#ZBP9hssdV^*a^e@yf5mG8ekxq+ajD
z*nm?h5+I2Gq&^x7tlKU)vOvjyqgMCb(}nY4)T>czhDK(HE?ZV8l#QG?!I4OeO(xkF
zpqQt{0}~<9C@d73ahOPKVoF2(eJW2Zr+9Sv5sb9pBzA1Cm%T(v3JN&Nh-NLS``!U7
zzd)zTND?Ko=uy9CPQD2y+pgXqR!P~G*G?Z*nV;CR5TNTyn&6Q2j1RJzzR<OS@-ez-
zxzoEO5;{fvhJ1rA=WYLk>&a!;rz|%evesd0s%A4!<bm-2q_(<?pR7{rPgGzWHf3d%
zl3`YziSRCY5U6s|+CF9?HVtCe;gIWJ-n(8Q9@D8GORZJ-N!-fbPK~lGig(Rd#sutX
zp9awcZR0&D=UD@NNOWEq8_<84WGQB<^P#_agGfOQCsOl@qyrI0H!!xM1Pr|W!_UVA
z7?$mV_{o3c??(*P^?6xnmM*lirwcsz#Ii*FAR!xUdCc8)RR&p#yRItH46$*{p@iSJ
zP{th3{=IU@Ox-0+j@n4gB*E(Y)RQ3|S4MB5Lv-mRF(6B~Z;sY}`||f4*<=<uGV3rO
zYqqf`+vtsAhHHrucHgcdAdu4QI^CfKvO{TOr27s-PPCIJ^7=1)n!4H5ofWqJhyqIl
zODk40M?6=LOxa|c7}71oQ2svOXFyC0tmlf0TG$o;*%pm2^@l-2^K5G)m^Bx(+iJp(
zJwM@26DM9kCtM)4>xa`vyk5McD)7KXdDViUE+HD<pL&=;1wbPW6Hygn_&L)V#96g_
zFKSR|;GHpm7;MF$>j&O%`nH5sK<hWpZ)@w8f2*4V1k5--ZIY_?V`A!xK+3*d=oum$
zM^XcAj0HAXg80thd$_N<MET%8l(YP>H-%p``R}(8wNWrWsUNu@?d8-3v5?~{sEKjS
ziQI{KV-XZb91p;D)mK&*oqjJi?%>Yl>1zJ8p^)j!^!&A(x#n`j?gjtilBC0C5<fw8
zI_&25%U#BNY?`-fXBLPZCe8VSg-tfae1#MkM*f#P2-VmWPhx#dtL0rtUp;uuQ=y-@
zosmjLd_Ku1rz<t_<8P)2M6)3`@&|YpJR);ZsrjU~b+TS%R-JfBJX95e^@azaZ7Rl>
zb!Z-KV_5P@`RfX37eCKhLy_};!tTNK_?n_pfbWe({?)rriEW*|lGQSj9DtdZ5PI#q
z*eY0G(a)cZVTGW;-&W)sAR=5zoaaA9FfV6sBxZC;kxyO|!Q}ZeY##GHs@wm0U)P&7
z4O`=v(c*~%xdKIG&37tc!un;Yvy6;7#3y_al=O<kT*y;YR1=PHE7=OzAwl9p0YQ`z
zyXt5_nh4U11;C%8uaLk-iQS|6_p$=WbLCJ&3ggtbyKjBF4MYgOg?=QR?8a=rYetg#
zj3rBoR~JG-M{u!j@3eL_eZ6y?%&WoasW4OKPbsZ$V+$iZ%cvVk^e~Vh6UR|JoW3S`
z@K?e{2y~(%2g2BC3*=BO=K&HR>yJf)-lx1n@Oum)^mEaiWD7j>sw~DZ?K(-#FYyRR
zjaz11pO{KDr0IB8r;Gtgiuo`%95EzOIAI&s6%<AP7u0|vE>gH{6Q}8T6@ZC7jn&HS
zAI+o_7HGYAt;e0GK!EW3`Qaylm9iTHazGeG+V^~aMt#5HP?TYSamPlexUI&Oq$p1O
zlZY$*t=(2fnWYe($_JO(dD&rMczI9co0B-ynj953IkWY&Qo4d)ZitXqgd|_pVL=6{
zXxNhKRru}aT2aN`IC*(G5xwvEVW=oP4N@3_;1^X{SCAkj`KFZDAd?EH979dkTs(+A
zAR>Slb=ses@NwYa#(d9Ev{U0xo`VlMegqMAbUO<f67VD`X|LX8r0ZGCt`DFI=o;!9
zd>sag5fK$&ssU2zPLy}F3SmKAu4y{^L}o2a+t`koUKp<mDNF(-lO!xY{~3Uca}N`~
zRb!JLLaB019x4SYKdMe5O8!rSrjUKNDJl#c6y}RKVDVL5xo_z~3?!}&2uj`~_x$|q
zMXaG756_Bu8?}v{F5^R@p>dzfNu_kQ6FJyo@c>Wehzxhw+LPDM8uKxIb2jJd-tBb@
z2vb?xx>~*#7#*OhX(EF!gzzen<!l4!W%%4Afgt2TxSLLFO#Xm?Os<|qYxkO~`r?6D
z%j5QnzGEGUm|Q0RPoFlBN+`i=OTN*)`f47Q|Ff9xX=YMr@J2Dx?-JJ4J8%77bJ6ON
z$*;|^Jgt;O3Nz+>wCf5kxwNhg>Pyb{&oEy8kVJsL`*pv`H$doVwh4$HdrvgJ-WjA#
zAQ@YHr3<<nD~UPpxx550A;8?5t$X+dD=xO|@vqt9E>FFurm6FONRYZ8D&+x+E7=g}
z)xla1JIKan&f_@C?B#A0wpw#Z9J=K--21%Q{8p>_Wc6$`n#ya@uYobzdtv*omTu%W
zmmXgN$3ScN0C(<qO>bt+UYwnlqgBPfnaotCP+R`uA~MqZ$t0A=IhSABsq1}5jDkzs
z`|>qJJW^o3He-6js<7qbO&$g}n3ER%dLN>8eO0=Ar;7o?Mh>**VtkK>*!#h_nzwq<
zsZ@(kUfvvuu70NT)~jT>pmPndgmQP3#T`zW1r4xaUElGJ3tne&Zei4OA9)AZP$>Rr
z2kbOu>WaW{wOuvGcfXGfT5U7rU(V4rar;5VHzYo{=xbkzC9=hFzj(*JjUW#&ryUxp
zgkp!hrR!T%n@wu#Iz}{9b*m5rZ6EL?wF$*CtKdqVgi~%Z*-__%FaCbWG4`yLFJIq#
zf{xl$FEo35CNWqn+yPv7q&!8ZTlQn03T9@i`FSZF>dw)#06y8<33kpqq4smK`=l1&
zh#AI<M?V@{`nj5zRonovu(+YzS^X@{eQ9Yz;uUxVgDTFK;LO)2>(<KJ+vgZA<C$7u
zqdz)8V3E9th(tE&KKdQ=rK2Uz&#v{(zSrY1tvjz!!3llJ$*S3{@xQ3{np(ejNP+&Q
zB>m~ZKlVb_G9Hrs?a=gD$mpJFbd6~63m#zHL=f!la!I05A~)$oM<_E81?uWNQz@<_
z`4Y|z&k{zdYnani#?Y>#x3#uH@6sf-c9bW_7E<BJC@@ifPbkRe5Eb<;YG{af`ka*M
zcjMj40s`<7wNDn#dfXut)q0@c@Hw<(+smuyN(VQH5l_nxmWJi}dp1r9F|eugf2r*_
zn?j$v8Z4GmBG8`vjGmHI?!Q6nTc%dFGx$<?3^sr$ILVhtAOn+KU?TpCz$jfnLUww(
zNH3}DxP!OrdZlZJW&rCl?Yuxe3sWwO{?+UmU7<Rb_zpO4bu!ik*9W7*T&kP3iL9Eh
zq+$u^optwoW2s0y$-W;AR`}9>$sy*DKAI(aeekG0C$h-c7(}rVg_Ea~ksZF6#q0W*
z;26;7H4bwua!N1OE85{YdQdPd_eD@(XDNc0QZ3<zcqX^=3aW04$m4%h5SZ-0;q$J3
z_`sj#5lrWFo(x%l2zDzeJrThcx_TXNDedPw{mJgd#S4>2sC*y}Cay|nGNKbd_%A6p
zDt(iRPCb|!H$-qv*@rg|X#5f^FaP*talKJv^I*C}1<<b0KL`Hj)n8HfH;uS}PEEo#
zGl0`|)W{b*?Do?AIu@v8h416zezmx~^e4TN*&X8Io;$usn2%f5Ss~&$?7FyDW8<)b
zvvLSu;TSqNIt}lEF=`;O=VAUp1;_ZLymxkgA3q%r=0!N=54cbS>zI7}6zD+%37$yG
zVi}Ovr^uEU`zex5p}HS>eXD(3U2i#vhe3&3_UlZ3AHIZbGAc~@t^Z`AP<M>M76a61
zNB$V@bF~6N@UMJP&GC!-TBQV4GTYoKJn!c7AZ70WG9p!(K>2|vIf}hz@$;k<%o-LW
zQ&0N;DxZ1%pj~C)!GP5-_czS>)~Lfll5CbN0!c;c(vG`R+_P#t?4OxJy{2?(wmj<?
zAu`1LF3th+E2hSs(jC(#UTqQu%LP!UBUjRPk)xxyr+CD@<TA<x`R|9VveYIJz(*m0
zcQ%2in7Y0YGT`IkhGDV60Ytpj-;L44);Z?#qm}?I+281oF~`7$B{qc|ZW(p_Xy1BZ
z{Vb1p$>rDtX!{S5OjLFEC!$>R$)e)ns93YRyFtt^LVCMBMU~vYiq?zPYR~okuviOe
z&js>Iaf?fh3Fu9Vu6$DXHkJ?pu{A~#KypbJp#$WglS`>+{d_?kG!N?Xg9K~vJUk2q
zOCx;LNsTV>YO@Q#y%E7+qz`htmnel;xw2mRP)^3A*IW?+ui=4bnIV=i<etOq$~WRF
zUmfy>nEj4ERa7rpHaw`iLY=*so;&5-lzaZQ`nIqAVBur#lkGPicA+m#kUu=<Gi8&b
z$k_xC@wuaCp(7MVihD<qz0)7w74S2Eq;};FCCyz6Juv;|Q9$zwrN9sA=J{m*8gPeo
zeeo2%^c}tT{dw@fYD^a~R7R4bC$wvgj}B_*f>1%g1Ga6kC(;pN6+?@IMmX;f4gwi=
z$T-ABM3OHE{^A7uK$VfF2tUH&{u*69z1B#<-&b2EtWVuxbbr-R=>v<?2;UYDQF<Dq
zGsldoZP48tN#jVL$83<zP^^!I1-C!0m@QPDo~^qv*Sp(5fQJUsSWGEg$3r5GL0iFZ
z7kM?{;a9Rru^J;I@7`VOExHkK&45j9V^u4U`R1}d`ZfB7_-?Xg3|)E~<I7+#yYOb(
z+c~soY`MDz5Hbu(MMlc&EzY}AoOd!eHd;0d@MZ^6(6zHIHGM$5f=hv9_du=%Zl$q<
zo%u7G${A|&l{I<d(@1RH$`|vG`Mk|`7)vg`Bu0ZGX#2C*1HwKa0*?zU#RW{jP$=yP
zHsJ+Fv*>{z&?s|=_~e(H1yO(-r|V|zOy#*018h4)&`h8|evSaA_F)>sTU`YR&@1#=
z*FaLEGF93A;Ta`YN!n@DA*snBQ%+4&ueN$eohG-t^ObB{D~2%w@SGYw`I0hJ8#nYR
z{QSJx_>XMKz|r@>D62D7WB+^8t>kB^pC1q^T!`BZfJ(LuuQD{+->*VxGw7C9R|hsD
zy?-kU{$lk}Ch=bV=)(}LN1YXp#GIYy1Og+^a1d)Kc<AbRBJ7Wv#Crwyn%%jfUi%g8
zK8Px}2o|&Bj{xo<aa=P~5vr0z70O8K43{4An?we4T<s815n{1T9bCtB#reWn1zfXW
zf!liU5Fjau3@-uZqgMf`ap7T8RPW?u`~MCSQ!AUQP}5m(r+daY_#g^hA#Q=$EUDZ!
z4s6{GO;scZ2}qzWLhX8i)<IiBs}In3C-?6vyfV&H86%>KAl^4;Z;QVi35=342=V4f
zNT?Gojsm%}v%m}hK#7Zv@G2Gg*{mhQzv%k>^Hsy(_s4Wbbi;kWCTPLDpM(6_dCQA&
z5d4+SQ0)kijsR(xroxx1*u2P<!&MULF`)8Ed{)v8-(W!a97{?6^sny&aCqr&`l{7(
zypyIe^<T$lZrW;z9Izo@>=K9R2@6Hioy3Ev(h{#I$;P{Wl3vxm3k^e-iDLl=I+(nI
z&S=~Ny!!D(&&48)Tax&c_kUerRmtx+Vhd~Runm$U4<9h1-uL|~{7kt!S6>fgS$|RE
znaG5Gb*T&?kGMko=n&@MX~Jv9qAAPDnY<Nza6p%$IySyb_LnsxKMY{Sd07Vh``M&0
zqigG-`(w)(z&udB+}70<y3{DOaU)5k2(;Bi^vQXuOeI5w3cy@+Y#c=UK0#h#|6}SQ
z4*Xl4Wa$!lL!WzWD4zmnQ+oT$J_jH%WBd#QoNtyC`P~=T)5Jwhe2ax!68DQf;1e*E
z(7oS@)xZuZ?B{;3yJ$+e4Y5&3fVD*J8RnL;^@~DceNE#_VwDm`bt>%VS{i?kF1RMx
zP3A4S?W|Y)8A4(+wgjQduvsPm)6*}rkA8gxv^{7@X3BwVBhRM@3ToW$xnuuq-VUDM
zz343h@{u1~Gn{R0wkx(7u7e*v`n8ioEPu&InWbiqv2mpB-K#kjLJ(W2h2|bl6m6lU
zzrQy=!dDvVvr+erD2>jg5={zTHHPQ^tO#q;I1-Tmp3YC}*Wu+A8Z`H0<G-B7uT^!b
zT<YBH?h(0W6{_1I*09juC;-GhZ(spE3JYp{U+STfHZQP+W~lf@QxV8m+@G7R2b%uj
zLf^$pd`!ro6nJm*`C81cYaLUFG8@|T2^|Knf*l76FHQ62r*q8cf9K~u9<p~4yPu9=
zEd3*aNHekTktvuA635kZ8xYUDvx5wz{{*AgrM4W`-I`FjR-111wkOvy3OGInY_)yT
zQoNj=%=&sd#LZ{z0<ZG*WCXJ#CK?v(oG!rB-T|uq6rSnr5dUtlgf_}-C`s-7@qh{M
zR~>DB1nz^NRV#(FjAZ<c5|hEn!r^^w*2uT~A+&xTXB|QuUp4dO!hBeZyuqXy)b6sO
z@=`uSM^L~wQEL=QnhsHJEj3sFWPv9;ZByJ8!mOCRbW2dx=vKPq!1fqE1|F=(ONGb|
zx;4*~vX~c253PJ|3M0MKw>gQ^P>}V6<mC8LGvy?kzBpd;TM!Zd2WabPFYtDx;(}6z
zArh9tFTt5Zit)3I5xNoSP_se1OHJEg043g#W)CaCC_rx?{0DWbC;W7T#?gX3FiS?g
zE1b!x=?miK?J)SxYD_UC+FjoGv1oi783Fi$jn&Svq8rY7&FnPs7^AG$p^tD%3A-vD
z3@Yrjk1;6SJ4YxHx&d|Z#e2)@Sxgqh8UJ`mpJ=}_sVt=^lYE2Po%;$@frz+fyz9J?
z6(Tlj4>I(|bXxSP?mL9B;Z<d05+NotsQ|2_Y&B)2)`>d$;<k30*fNyZ;tuVCR!L2|
z>a6RRz}#saE6h`hz?PN5)GE8e+uTMvt-{djt<CjoDv^OW+%cM%^~+k>fG8>&o=oqD
z?8O#hV7XRUGy$Fcbkga;A&62YF#%;{7(R!$=Ijr2c{0Z_5r4vvO&uFvT_mp}h4#2;
z8aAjJYTxFgf}Pe-467s!bO6F<!AW2ls^LT)k42XcxK51V{h$6Hy2v2OGp2j!PWxlo
zw*?eOnPVhf$DF+^V021#83{FZ!y)rqn}huu!EQW$+HC9yGF5jG>B;Lm*z4i3vrP&x
zYI?Ao3r#e=&y}WjezAWY%<07v&1VtS6rc0QJ(*nZ7&6N4?D>!*FlNfxza?e@uv>_-
z1z&TMQKgFPdqwgXBLNk{(=WbP;k>y2W|kQfgJpf>BpznLT!|_e8f;=YTq-2=_*7t>
zC*i$Xu1`5~af)eU6T9cn+;n{Cy(*;#HKb*@NZ$xTT1&=sLEBx=`_&yIK%h~-$m5P<
z-M6hRAbd=MlIqy|DM_rr`uOqf))16_;71KJCbFptNM&C8x`phCWjCkuRRILV)0@Yr
zvf&oaLA}1y*M)&g+wWH4vdPYtbI#5KSvn^}*0n@e!wC$fbYeP~F$|V7zz=b?M$ifM
zrj~_@^SvS`^?yult|>;m9*~4!l>OP3c;<uN?-@Wq1;5~UcR!oZZNCNCjLO=_e1h_^
zi(9>Kw8#K<Oidqh_;=Vx`^Vz2i!fyRR|3ym3yNrkJ8tmtqWXVHZ5;;(st^fw0cx89
zmY(_!0pEyNVsD|acc#ALVf~N(z?P;4UFQMp$Gs`whl@*&iB~7k!>9e7pBAJcIXf?4
zd#+D5dEHXg(9Q?A`!+laEXvQmSATwyMI)1f_x*XisyA~Hiw8&#>iWTIkyM_f8Ri|M
z_gpDU`s;gH_6CI-uo=s1p4SC7xeuHk#~B~)j*PsLEDU+1E$KtSYm#rlVNcQTN`AoQ
zWczuI;;UfSfRci|%d7QzPx2zzUP}^;$g8RTv*h<j=1wM*N=Vc@J=wEMsvlQ?hsTFV
z`1<Y>GU|xo!b2h^teOVQyM`sZWOO;~p;ZPYVye@3_A!1jh507ZsBmx;I5bXbsgPEf
z(|erqw?<5#FCxE8vY8hu_urAm#c?Q_)7%fje9}nU#^+sw`%UA6D)Qt||Lgel0TNy{
z4jxD6KmUQy2D>Z(HcfDG9^FqUJVrtFoLZanCV@sWhlH=s-xNg#L=nLap~u7R?~LEB
zd`=6>HyI|viPLlei?hpgLjcm<5o^n<{+oOPD0_TdsYUtQo40S?$cT%m{~*^9P1ub$
zGQkdR7WpGt-CeZ6X}_px+1dfkb_yFUF%#J(BYh>A)r<+skDiMURW(yrX|-oN4-H?O
ztUNoJm6Hd}3;_|{A?;2cq=T3D!CFen69D+ZvzcFUw!OvAnWS-l!imY0{R9T{`lejJ
zPy@nQRbQ69c7HO}a+g}h_s8$xtxjw>?gor9_lAJ@VEMhF54gxp9)lYwa$5A>uMML>
zzev)r8nLP%5?Dn%RpBO6jDfy$jymcQK=zrR0wh!zhBQY(e2rh(d8zHZP9<adjlUkY
zq3aWR?HSp4vWf7vwfO5{?Bu8dHav(26M2fPK*T^kjNd&YB%)eWP-g3;JRC*{q>f<m
zx07q4n0?;KqbJ89FCYX0fGF43!1~zmh5m5o4!yp%$KO9X>h34bY<U-mHhfE9(gC5N
zM3nA|38Vm%Fry5~e`<H!-_&KRM{+Nu1%&NGD*6hiYvj3*DfI^jPusrVVsD@MW3RQf
zS`!H4FhHNM_TJE8t~Ni4r{#})58+k42zsYFebjafYImqs=0NCGy|tNi*?wNd$`pZy
zXvrtSs~g<=dmOBx!Ebx9YI3hWuM@4s23}ka=E_}Yi>R0Z7Y`SQYL!HBD)<a;CRm(=
zy>9v|AP*S0U^<bE^<6Z+?=dG~Vo&b0od*Kncds8aDq0BB0fv};Ac~#N4AulSeRYGe
zv?B<ofa-MRiBS9Kh1FD9&E7Ldji%U#a=+>Sx++}|=EXpB>a0!)S6rbwg)5(?gRVmu
z?|>j6A`~{P!F9FsCz+PyR~LEdA^28C10S3AFUo?a3vXv2nE{p&kxv4mZ*Xhj)DN!;
zSL?#}fra@As?O{ZfM2IBZk19@SYU3N@$z*X`6^a#V}_%*p?wH7BIp`k4^T_PJcTEs
zZM$&FXycXHM<gTivzx1e;G>}WmxF`?g9Qtx=X0wB$$0~LKVziI4{F*q07;j)NG=z0
zj+Z(xshq@GD*b(gMeh{i2`{DvWDBWMgclEEeQ!J436I03`BBRKe#Q5L3ijch0U#bE
z<cOv?YQjFl!gDZUDco>d)~;mb%zhCL$_L8;op*Y1-#jYTk~5HmR#0~Faoz_capx;t
zZBpN<Ya+=6d?|A_-))^AW&L*(>JG*KuRF3-KDj;X`57AxBz%9tLa8Ia$dEF0{|@z9
zWyu+1%^5qdt>t-fz9-Sr<48n0V*<odm}}}X2MGm`ITm!w#kRRdy~GmxYLKV$>LD8U
zMMFCh8#U@D{>8zgmMgxAHLW}BUirhqI!&8Ooc_R8$p$f>CIt_++o`8pK-p!(+8}kZ
zQs!c*&i8KSWZiYH%*_&WAzZ-23}T7LaKHI3F*KN){h)PluY+Eo;4tK|_Sl>DeLWUh
z9c8>Sx}q;TrtRGov*6@RutHU);lajhLUm2s@}DEG_UpxiQX5Y0mu<MRn?q_|nsM~d
zS(DnyO@XQ%DGIyISlMv<5L!TZcDI_=4m5f^ag3Nxe@;mwXjyIdfUibH26AH`d7d^l
z{3?0w-tyhnn#O)UdE6{60Yp~l><p=Nx;Gi+Pjj02$b<@~s<+c4kS$$x@nsgk8T6O(
zcIj8P0s0>~;Nk1aBt)lc#js$-jT=$<*}K}F-i64|D$JpY;y4QN9_LHwMe_VAD{lN&
zCxWm4u(}kejepowiIrOy2=#;$51w1HdwJh8z#ITUxmJ}Xu(?Yc(M$f}Ao6MMK#`3z
znIh|9n%VM2q#I4(uVI$Z#tUzW-hrec@J&8no+(LfFt<Zl@mM-^F>q!0-1#_;#(%p_
zX_BzqR_#m-l9lN^yDSm>kx^`ZDL;N%jeq27%eipeeiMyG5F-16qh2J?9g77Z6{Rz6
z;pVL_rL!%uK_?!AwFtF-@O>VGx!)XLn_F+_^PO*E+z3^wKJ7pr;X4~fnB!5$dsH`N
zQ~?5bkcQ~TpuQ!6P}c%CrODVew`KkHBIv1K4L-6MTEKBv|BK*T@z_}1N5!EeRY2u@
zJ2q9Vzd{+$MyqJ*q22FQS`o~*WlZgy*%^B9V8aB1jOg+|){40q2oV)x+gJUob9D)&
z4NzYw<c^O{N{pSd+A^eIz>Of<h*jJGHbd6bhPw_BD~!sg%G`3|!ri*ZKWYK~cqEhg
zR;VS00%HxA#F<`B;gSu3Ws8!WSh0Wk^1|7QE7m{MvYQuvr-^h|83JxS$8B;XvdJu_
z!DX|1x+Nn?ioq$Umt)#ZWbRmE8qG?oav*qgnefrf+e?d%tsJQZ0u_C>mIdpYl}e|g
z4l$_H_eV~<%^i3_>keK%*T=?3AP0koVRA$0NoInBYx$7Fy}Y&O=mF7anR|5liXg!}
zL`xQF3QXvdQ+I&WU30?c8fu+|y11f|ZkUt2IEVqaI%UzZ2r##&mR@DFCL=^W!c_MK
zm?B}Y@Xj3|@~D-*fSzr+u$$TU37+p7(>jTIk<%KCex1kgYsZaGU$5+}p-XTQ*c14*
z(CXYeaoEw-s8TZPa_DN%dDntRBE%V7CW!cQ8;k9;xHIFL<T#R_+36?B5JlOTK?+Yn
zX<~LKe*Rw3JO)o<T6md(H7_<ku2K&a(Ri$4={8Iy&v?>3@9~^1*EWB!1|T2pYNwM6
zOu!aL&+>~v22DbJYUafGzFT!otA3HP?AGJk=PI$hOv<cUZg*1>6%cY@+!t82%CeQ?
z^$cf;q4rnTT4_#;X}jxEo2F)0vrxl9kwkG4Xzwjtwy#~XK7~karX)5z|Kh<_Te*!r
zr?y_z#RyF-3uin<Lj9qu&C2Htt}eIW@oQc=Ew{S~BcrePy1{8JaKO;<b~}Q2b|zIw
z8S&d=rqFAG8!&0jdH8pZb?tKxe;W(T<wHL@=ooHX{&*(O4vyYdW%b!Cr@=s^6Cv0}
zcpJlY_B%5F?wX-*R5m}1jUX;qMZ66LY*s{ow;mQ3<BOJ@B()L+WTR;#5Fe2p`2E<6
z<EU`BknIR(JOXbpQ=*}GUb#mRQH&9vV0}MoY!}-M1@R<mJ-=(S<zvKX;rCBp_$-q7
z9O4M$BB;|b*(QGs?1sj&h1`lw-Yzw?>Dy`mCdGyMDoziFok(!t_qL|&r&3$FAd9cR
zNcxAvwsPG{WM;m8#fz1B7V*sc5CX3f2FyMqBEVr@>NqN(t&q1OpqMHjY>5KXLE4C0
zQXJ#qze8L{zOh_kqBek+bI-K>*4JDb6gVJL7JY^^izN(7hJLEGEfPa1ORJg*cP}EF
z7CN|u#ot2<j@nji2>QvyFx0bdv4Qd~Y`bS^s}?@+k_iP)=DIahRXT_)WT{hX==yCM
zV*~(RJc*rNvEEe#DH<~dmJPz1fK`z-n;K7#47D8YfI?}kXmwCfGf1`5|Id-jza=+z
z<Xemw0z<SCSZ#yq^X6Z1k+55*-VOrztz4UHsX#(mQ~3)M%S4eoB?3ucN+f-Ndsh|v
zLyc!D5Ks?82ouCt3Kt#D^mG1dCS+anW`F40$mjb<gDlEFSkkyw*f<N0psYv~0rrZm
z9<hic=<~j_k#F*RT+;+%k$~H?Lr!kSmcX``pkBEK?>Ls^4?lvM4JW6z?&Y&v(}BJk
z_F~M$!^X$|$_U^gvUYfSPUZ`Wld#+sa<3jLqu!AuGJsfmaF!esYuCxDPA~uC__bu)
zn%$ckUtCdQ*G6g<7v|lCjjb$kkGYXY{D2hriWPqNP^+|^HoyzC@$3c}#ft?nuL4s`
zu2msh0VY2DA!`&t9#>>BRTiqGYM`mu<M{5yi2(#s)D7j$X_Mey#?Ae}0m9fD9~2b1
zIGd+d^Y^cQwFzYY=|%B=@OOhYZlKG6REi$k_Q^oT1lwK|5XRH{koCiGMw#s)yWIiE
zNn1Q|8KW_w6+a<o>YMOEA=DB~MF%^N4C@RIl1ZufA}O{59C!+7625)=`%v1IiFNB~
zo0}t7lE2p<Cj|w10ctFQ@|@N^!&rzLeMc|{Y^b%2$o0heZxG8!XM0m0O|(6eyzjY}
zC1Np&D*kJYtqL}I#OK(;?j{lZTiiKA>>6EL@<=#KHL|29BYUaegNR?3*7H(2e+pMZ
zrIM&dO2L=={Pls?@ZZR8@&-G09t+NMX_1$Fg^Sku=hWpjfXK`E*LH4X?tt!RE^a}U
zFrPJhe#8x|Ll;ucg})U{uo;`Hr4<`;Ag`*FlHt6g-MOg8%bwZkZVA4VY|3uA*3FCM
zH%7RRWjP<K<y{Bx7PBYkD=Wqi>n{1kj<_bESu9x2d4bgs*J2d94j{|}WzcUt0=!B|
zC)6p-Hs`0rawOdRlJq8V!@BNvtLyW7^m@b?fIB3yHHSAddHmd2N1SVUEU@LHis%$c
z)x*+LD=?95NRv^2H)jF+h<phzWC#creTOK*;S8WVSVls<^Rii^dTn<iL#9mqAF_GI
z&P!RT9UUy}Iu^D&k`y{!_fa#hIjdlU#sqa^li9o@+uAV)`!o*xIaVcuez#smR5>g>
z974lx%#}53f2W-EF{3~5u<7i65OU0{a51PO3!+GAvTpaW%@Xp0QN|n;46{j5%h_<P
zGy#^}6}C<uZ6hfgox+O_=K*gdAVXC0zWZ}Hn6V#pNFs|?1qRKER(8u_M%$|onBq9&
z+2gMDkwxVo2(^*>J_}9pAUB(eY191Pg=^A=-!poHU2N431qvKm5y>R8;(2XvJxDFK
z#BVhg)w5Hs_vBJ2`%zF!S7Tz)O;UU<MT@DA6c7HT?Lesae3gLmM`Po-SA&9Qr<9+t
zI8(#1`iXYZb?LCg%i^G6kE;4A`DWIdi(z%exujWigJNL6dbZz>ZIdx-w%w}^Ntj=U
zN7B4v;E7>qgJQzCVWdT5!goj%-krYH>CCnMOLw?ds+@V6+-VN24<GxQ;PD!Dm)o9?
z=8B8x*TqxS2CqW(=rr+=oJ`(6v?9xaN|2FJ*Vxet{>HLl3?G{~Z9v~;Kb@dz`hL<m
z4`d|Ji{I{+&*n<^N$Fq%`2QJaTX~&48}Qv;e~FItUaE|_)ac9J168I!s!7|T@!)CA
zsvR&vv^Bf)YrjK)L`2XJt3Qx3ak}2GF~C$^Je>uwRIs_@MlQd3gv7=&D{~5EPAV10
z{gM7Y_K^|q?k%*OW1`(R>Du~zj3C!!pLhIuTBwOMJ+gA<kZSes7FX9m-69EsU>kiX
zRc825(hXS{lE~1FXEgKcjdg_q^j_E&*g;fZS;5<%19DV4>U#4MW~GJT1eJo%(aWg6
zIOUG*Uof@lDXia>JJ~RvIPT6dntbs<HA%y2ClkS*LQjhIeStq%*WU)>whwyvMt^4r
z2)=xoR81dSze#^<Q>o5#`CQJJwNco*1_v;!@MMqMv#}B_UxYg|i@CG+F1*Tr6A9=K
zT9}julrezpcj8Gx9K!Fld=J_x^w(dyIqz7-xsjdmsNRaScja=H9Bf~iyb7rhfs=(o
zWaIO*`yd>?wp&!|rIqKC%-(^1PJ4X6^5tcx)09AWGplr+EY~296C7`bkK_%%Pp|Gy
ztgD?GYr6q*!zkS+2AEBGQ^uBl7w&6ntUi-;NvpQWY&mfSi~NaGH>4xo?BC|^;=knw
zM&baG>Fx2%zOm9d1^`1Pg{)1q1T2fM>sb0PYx6LNyq5m9YYt!62TMUiL4W|kQPWhB
zNQ3>;-*Pqy+|cvA%=>p~T(ErTu-~D9`H`^1d-l=YsY4MvNPZGu(j-{2G7_i?Uz)J4
z3AbB%XGyX?C&&;q$={&>`7m^BT-iGXg9pgH*!L7l>p{kS3yKNX(Y)oy*GsLYWOpLc
zZL=004I_6+w!o%CCr!@gqr{+VbDdhj`pM4STf8)I1eih&Zjs)FU&xd?r+B%^^2)Zg
zF_JN&P$4U-v|xnI`Whcap(wNN`;84qXFDwoWx+~8vkU_j1rK_uQ^rnPg13u{h&1Y9
zdh~D(lp@Ijg@VNc;HoawCsIgOF^zA~jda~GZj2+0ch89CjDZ!%vYDj8_ZRl77D>)b
zaVw8FI5?$5OQJz9Wxmq~7fN(M2XDM>CO?@Fntl!x?J1mhYi?KjWRV7TPJ$U47QsB5
zJ14cN!&$NW=h}RTI)EroHEC^rKEBQaeO(mNUUiRqywK%!`bz*zI{pnt$o6so<|^1o
zoZOX~Ihyr@UnVCLn5kuoFvRJ6U(o`AXd?u}mp<cx632fw95SbBHy<V9#&w^@yB-~Q
zKWFGRjB|DQW_wnSZk24aTWTcS_gQ39YDv%7U9;Mq5h|I<R}>D=2s%XpP!iVBGDaix
z2nvl+Bxk_Q{_yoyA8-WRF!gB|kRuZkZvd9RIwrQe*_NL|>+N6R$<TpS7c8Fqu=o*c
zwhT%O!h*PDn1Lacb($$2Vk>3A5Uz~D&Y64sxjdu5Z2-0qa!a!YMVM%IMh=)Vn`g!9
zcX)nS)sExWia+wKVr{S~CxMBole6Ih0cQzGvP8sI-#@q26)Ki4sY8X*8N98O3GD3j
zm6*}l3O{<K7L?z!6?ccHu|D}njGpiG9W+%{CQLQp<SqT>`>)=!pr?%#4bd=`oqR0T
zESPtTlZYR-i72eX3BrLf+N%Nwr7KJuDKVkaAs{<`WYA+wcKTH(KQi@kbmAcv&Qzo?
z4isZ1N1HEQw9yUGV3gRCE)L>9Gm$NS_>R9CDeBod7%YjP14>icANqypy15e~7+LB~
z(i-p+9I@*X8F&QuCSwhMUHJOL>6fm5h;Icp3Qn(vj;Zl9Ba#%~DL{DQCe+w)oy}5`
zT;Hi_!ZMUAuG-pb>qF>e$EfRp12otL&MPK_K&9SO6;}W^X-Zs%FD1By*=TU^6uye2
zfZpVt;fBtZy2FJ(a=-R_LdV9=@q5YO0Am&Qig-4yH=RxOqT=G3Us&G<v!K?#%h_|y
zO15xf(EyiZ$kVVjiwGNXO@mQXuu%%)xEPNAUGV{@1^)1^;d=$HPf2UHzw=uK$hP$(
zg_p0mjJS#!rhtGLy!yhidzDh#`c8Bg@8H}BlM|puIKT@uHFN<<Z}B=1+5o0?c2{Q|
zKkp0hQc*~)b7Bg}krPWC=NdDF<;Ru;QkuGa;#)=tA_q%qAc%F8fN_Z8M*nGBg~9TF
zo)5sfUvo@sh4kHeAmO-m2vPYXdvG4RyTxZ}6*a<0XF>n8FxV_D+y($%-)x{sn^g`{
zN{d6p*~Rt_oi3&8q+Lpat-a<LJ{!J9evv0*{K8`dR+G-Ra!7Y1kQ6r#vwm!jk?J~_
zs&K`T@NfCF13bf>Vr9VQD(-!F;9$uSr<cCB1!3F4Ooi*+%i;u^n`!3JJ2S_AP#qDH
z6^2@_8|Po3%I~hh^z$`hZxe{+zOd?jwW__+&XfupUcOMr4{GKgb@5q$T?gQ_;9z#f
zp!D}&=>g=Z?lG}zPTEE*W;?pU<MZ^-RhRy!gIMn}eJlR8pRJ<;cDl?(HLBFDrQfKX
z3q|03{-qIZ^M1@S&oOW41?V3@h5rUvn~qS^5kER-kc$?;LMT(rq~^~V`(nK(gQ*$?
zFhFXWA&I!5r2?2g#B$0{P+d3GrtlcSX!3eIBc7-Rkn@5cxvO1H;jb*@5(%br(xM-d
zxcxW-&?;@gBBqskC41{Sl?=F{wdf3pr$OZCI)BvxV2|**+naLoTisA|ykvr@xJXpj
ztlRR$Gq5-6>bA1f7zsmgkj|wvPIWkxX|gRKrXR_*S-gZJfr^0;z%qTZhk#W2IXg0G
z>O03HyOlvBCy~3|PfN?8h@diQ_Rs~?dYr}+lUw~N!*xjwvwf_@X&A09M};z^uw$N~
z_dqgvyR0zW+e&@;iUru|e(sDsxoe`rt7b-v*_l3RiLF5WgC(ZxgCqlz`HM>@R${_e
zF%P{WVLpZaZUbVbI*+#y99)zpuaOIoHIiwmK0mRT)=yK1QC=w*FPu!D@-0<O>UIQ^
z^-ao^+vDNXYOna!ag<s|6(z8HKF5pJ!TJP?+Oj^@fwa1~JINU2i)e596V0BwmoRdV
zn}0uGCM<)DLAA4|Q-67o;p9!#ntlJ+waL+?2}8vBH^@p^h=HOGX3dtFb~0#<iKLgg
z(#H})Rw?8bc`)xA@y5|em}W=NiJx*Nyi9(18}?29XUWXKXTR7KoNd7&@<fZS$0-(d
zQ;CSh*gu!v{DXtF&jQeCX9Nw>pvTpkEO$5tyXvx$z#IC48|nNoFlrbC`&Q2&N3vt^
z#ysI0k3#3!e@ZF6bN4IdoXvQOC{gkrb&c$7(w!mG@CK^{uIkG3jn`=|ZQ8w5I#Xq{
z@WLuKtuaTN)+p*x;1(s>H0fI3`w9qEGuK>WjePEpx?N2Wa*IlVTO+ggF2SBN#ItGA
z-tXAf_w})4+53f#Q9(k9CXDisPtfmaU#IxeQqb)Jdy-k+*a|hJ(N(94eW{{JvX4TT
z!tz@gYRNv$GzdjaW69=sOLN2M>mG2PbDIdQ*s-@Y(9?@OH>R^;lgoDZuOSB?ikGZ@
zd$@TdEHZsApkreuNtMKvAelTEg=I=<nfjj0tI6-q6k<fj>|A_+8SUr1_TRc&wMG@w
zf-z3wQ@mFzd(WCNK&S6pD{@CsUnBcVTBd#}J3U0D0cu6CkuJAC1q{}OFG&H@<VvlZ
zd3wk@Nc}xisGgN<T@Z$wj63;TCX8e_nH%zX3trH|TF;Gx533-o3U)Da$Dfm`y=(u{
z56hLo72<M>S~g9NIrvf47)ZtNKa$QeD$1{m;tEKKNOyNhcM4KNx1>l*4BaUy-HmjE
zfOLa&cQ+E!-TmJGdcV0?v!0n*<30D@bN2r27Nyj-icP&e&fB<chsWh*HdHei&pgha
zz+PsvgC$R|C*<k@6qcwFfP)alV^15diXJ>`EdE4=6%iZ^O8$%O9r3g49h1-IIDKf7
z)7qR!D8<h|I~70!d{jpL{C6tzD_g?O*QP%T?Oi>lfiKq{`jS|1|6=)Q@-M%wFqSds
zv~s_c!j7@W^|M>k?71?dqeCPpVZb946GwA~klXFHDCMXp^VHKLch1ciac@Z#eA40?
z?NA^zPOw@n`T{2beRplR)V@jH=WrT>>mxQlX-{FAj)Z;AMZDq$0x5t;XA{VNL0wES
z3}r<G2vgItPt6l14(3UgJKTFtR^E3fKB)jM@f?st$Lizw)0u-L9#gda;MA=Bi9jkN
zEexA5jCwfFmnv-9S^LnM`)>cFb@ZP~V8pf_r=IAPI?PLljC@&q$Fw0**CafN2s+^8
zC@q=CuoR~JXTna3f+BYYTQBt<H(xG#p%P_!TLrVKtKQy@3Htw%{(1KduA*6WQyVug
zGy0Xc(^O%!1+M#)Z}S|GChxk*hy}8=pi@Q8MZe}6Pe+lf7|!z7?y)c(dH~=rSav$|
zX`cKrqf20|tsB60K>a0sj`HaVNkX*+Bp$xA4T_MO5QAcH16aIbUV8|u)^+y*NFJxx
zIlR)Qf9J6f6y)sIZ>OPA2j#G%*&@sG2ZFm7JYHGh0%UJGUwO{$SibB%0E@Yl1{LsX
z<~aaA_=LqJ_$+t5r0qR}+tAqxjg5}5Yz+A8^ra_q$@&#D%i2MoThg}Bll%W@7r<|d
z)yE+>j63lTyKC~al^5MZn(B){d&kmR6W)Uo47j)e;1a<baUq4^97GXh-W5&S>~D`-
z-E3{VZhlA{&#Qui-7^S*;A;2{%3*HG8=J9_vdkGsI31_AX3%Fnb$RWRw0fL^@y6FL
zF)NFDzH$k8DPDeGdZn(WXTDYr{@~h4*Ztl<=4vbgPq@$<%f7MJpPBLJu>6^$bt>Nh
zzZ;lAG%Nf_ooY=|wHpI{&9p)1urG5RtX#hWB;6?d4_trgF6C<~^vN(O14w$Y#v*Xz
zS{H#^!u+bm@79^G7Bo>SH$`(zuGW8M-TlvsnKZ;`6S(KgYC<}b<B#f~3<4ikA6K#E
zR4G%~=@M049%uU}ox<`2S|0`%q&_8zD~s13tn;o4eXtP_Zq2yZMeHG?xhrrmM}~x*
z$;DP52>krAWXhf<7DvrZaMU2EiKT=Phf_{EUP%l>+4IfJG>f@!XM0iK3<V%+SjvNI
z1Zj|N>9k=icN{pz@A4jhm2>Zc^Fz~5EA|YEQ#E<sEvr^r6ml<@;xmaE=c*%s8bi93
zHUk_bVnNJHKtb&Erp;-z?Flb4ao_e{iXFIlv^lup_r2{;<}dt5!`E8ZlX3;kNKgOs
zJ|QMw1y2&(2>u~!Wn^Y<m6|bEPVL8zPYXS$iF}mkwPoi|=enWBJi#sw_bur)fW$K8
zm?Qg=_O{Kwe;vz2A%mP+-i^5~l$2gZGX&<i$7Y$-`tBI3=Wz8KXS;hM9h8CD44%ez
zp@xHEuVm=M05@*WGqrrPO1C(s7R9~1PosKd>BM?`cTqZr^;}@t+?kH1EC#m+4RZlY
z<ZPNkYv?0^>(?zzn!o^wIlH}i)NMz<$RnjANAoLatb51~4h;nV?3GhnvJpdOPO{7)
zy#%;#%^rOC(q0vc8&G-j6IbcvYH$9yzg`*3FbZYv{deE?H*>Ab-(wK;*UpMu9;~Jf
zL%d2)x}T$C#nFPM`Gx#g^H%p%EnPwe8-+LoqJYZcckN22lcz3EhC!?e`qX5<sT|Wq
zhlrp^D2R#&J&{J^$OU5@==vrm<Ad;gt&(_*9ixOKmy$$Cd`XNNC#aInho}@V&S<4@
zC%B?m8v()_{XT5h^6?UOTL^Am3&BTU((;|tIj)Xk=E8|@f0jchE_D4^uN|qHMC{8*
zU72bRctt;|Oz@_DP@VqpiaoU>AmyKCfgGL$c&TzjHm7H&Ow0_5X`Gh5_M?Z~V=wgN
zj+v`)Oq)kTuTGaxFEQo~x=3izqFyIm-oH!G?Iz0mbCi?V$qJwvA)Bteuq+@kNScZh
zNSxKq&*XWr;C#;=QAGv&D_*)-&KEx`I$Ry{JCB)|wJHE|_VEa{vAU%47P{}I$7^5G
z^-H09Jp}bA0Y8_;u`N%ezH8Sz2ik_qXNH6b_z~?NQ)|tgiwRIiRf$-`OzN?Bwt7+b
z&SA#08->sRhB%!CYWDR;+w6{fBh@F20UT{d*ba^{|KeUhBY&+HfO%dnS=u8_>Av-5
z{iJC+R-_Jw@i}?952HHCCOSd@&^i3f52u}lQ3h0;ZPyPrzZ<K<rY<y_wX>V1HVz5r
zqOn1U6N3NTw~tKs4Rwn3&^VStyy2-8oGJ!8z(0Gw7P&WnzFhN8+YU=pt55yuV;KV2
zYmZl%Ekfr=7f;{+yf@bn0H|AWR)=rldp#KKr!K+}xBXF>J=3xwP^!U~6Klork&=Wu
zdxF|LH)=BuT?!EG|2N3IcAE<ZET+T~aWTe7PFW>NoGJea+~l`;&kqmVPSPt=1pUZP
zCo%;`YcJA%>8)hX?AqO3GPGYP>U;wPpngQL!w=j1!Vxlr5(#&Y6>Z}6Glg0Q_RnSc
z@0~?`rrDB-il97uHTNwqD~xoh;ig5>v0#>&dlR$+55|MubJ<Iw>iYQuM5IrLNDAJU
zuS%Y811aBhW9l5V!cS=={<O#z{MR;JMW-?u3#8r`BOl6Z7=d3+B3g5Ab{@>oa+`)V
z+G|hl(a~{Jm!_AQ(^_dvC?&Mneq+63LD{`WT`Sf#$k#Dq(;}<Ta<NjhS0eCk)XV;R
z<<?v$rZT}s^+w<n#8~1p3Y-Tr?jkK_jNJ9&B<W!1AgU=FmaZAL&aGdqSpK>pcz^Zt
zji_8N_|9bCp&q)t)g%u!gbZb-QO?yr${7QcIg^!wu{9$%$srUWc^$LvuyY}_3^=F>
z^a)cx-E0yj@#My~Hg5*jmtv*&K%VcsIO>!NpjIu<btfFWnO+oHZEqT|$QP|P0!KNd
zPurAI1@tCyTdMDGnyC?C2J(Ef*K}@wn3x;0|0}|}Ru+vB=j1ELsd7x%)8)UOjQpA%
zpF2};er*MJ=6<rIq;9OdUY7q3G+8Y7i8AOgg2;VN|KVq(q_3x>oXvk)x%w@X={ZSd
zv|I0*Dye*!+n`oF;iL<4j?M5v1w;FbK<?1PB#LL?A$(;G+K<Vj`DgyoWu{@Z+L)iz
z!5(1iNqR&xshB{mcIOV<P(2j!l4GW|i(jdeXeh2<K3n7Yhx&cbW&rXw(=}73bUgIr
z2T_d8opFapuLr01jIKau2Y2Rg%~XDl0cT6ha&6aw^dm}Pyy%AaVU=Jh?H%Zi*Qfza
z&BLl-$9q!HMj?fj&XE>2H!MO1F2Yjef|Bn2PS(85?k$N@GY4p)LjFv?QJ=~!U8u;$
z7qo7;J~D_kqN-~0aQ=8aF9dwfY0(simM@PgSDml=Zq6QGX<^V)Rk-BE1_c!tgUoNb
z?t&UoaAVo8YSAfNJVp<i=+~`3afgGwdqS(M&+*-Sb6C@4HLas2P<gouMh)_!-<A7i
z*CI?FD=UITQa>cY#Vi=&$f_D$tdss>YTAKkVmX;SYMifo3#?~Y$ViUz&u5fa=+dS9
z`0{<RGZR@F=)$gA@nndaRiQLJ9dw~&!2JVJ&pqNR%Hc$|Zq(n6mHWc6=Zd=2%5Awq
zli>ZM?jTx)Q^n%Y7e^BP3*PVP^6EvXl7qW6tjK_E7V~9p^y_rjHJ2>XAjcM08ciH(
z_7Y(gCyUr{dPZY4f5dMMPs*pr->FM?W5vW~$Kfp$?<6nwSi6xt-P-_28J@)1wslwx
zV}t!FfZfyEI*JTYORIEpkN48u&NetlIzE(MT-5UrNuq0#E<E22G~JxJ3G80=nO?ZN
zZCL-X{R%jp-_erXkPHt!3M`OK#Xij>EZqYn#P^i&PhU}mIAkjh(BRR5MXi3NQ2ikM
zSRLHzP0+PsDplY?n;D#$&9=|ECuOdD5ojj=Y?@t<<F(=bcC?Q3p6jS=<qdKD*n$Mk
z?8>3C<|wjVwI}isXa3*Gkdu+p&(#2MPLsbKJxRo-_H_9+l?x<~$$5?#Zr)}0#ZdLZ
z8gvnSseT%WG5GkgAbRVR19@ld3k=!iC!!@Im+FC8doJc`0?#=(Hf9GEwUiC<#5+pN
zVPX=qzq{Rf0~CcPDl69ZXDirs8l`soxrA|{3TqJqMQxZ#3lifeyg-+rvSgjTZ`T-C
z(q|G<LQ;xx>?lHzC|Q@hH9iI6TmW=#{A8ZDu5YlXEXKE;myRV~9f{FA`U4H$`5{rl
z2tT20vk1m&S`>0DQRac#Yz`nEyQC{?JEH~Uz7|5sq<;+}o{VE0M=27jlSSA&02q(v
zU+8;2t!HwB@z3Eons;-y9!xGJoGZ_CAGF0k#$h=^XvzqJZ&J1%e`g0{fcjbHEok7J
zuZO>oV0B5Lc8FR<wwj0+@jdcHsZszOa;I#;bi+U3R|Je6gEJuuil$s*|4N{e9326N
zMx^D@N-~|5H4sF}Y4yB?Mb<WqkN$u}0fY)yU;K}}!}5=ry|J=F*s+^O>Q+eJ%m}KX
z_%G%0@=~IFa@TX=q$jzxYe+jl?ZOsSHa3>Xn{zmQLW5xK-RKIkTtgKLP^$ReE?wIa
zlfuWDjIOVlNOb<LQHB&!$=+;#vS=nL6?j*-4|Pt{TNJ`o$Enndx>~_8fNRXVQ>q0p
zw66pVfSN&v0r0N+JgR6PW2u<HnRi@7iFGZVEQ|u8_vtfsyeQ;XHeI|b(tXAcs!*)B
zS-PJ}Smif6SbWDK&7z*I=SXp$oxvZ9a}f1n259AEiZ$gXZv?9fM0=<A8cA||TE})>
zh0Q-nk*G!Ghu<cfD0g3PuGeROG?C^F%|Sz83nCZAi}Oxp+6*KwD2POKR!{6twi97D
z>E5K%i-Dxs>Fd5?k`I%hHxQp?{|z5tBR2J0NTlvB#)e%DsicQhqqU@`zN~A8h>S7!
z@U464;!0-oyeW0g%JI~%8(Wapu~eXS5-USE&vRLL?D#prKpd~TgQ4u-SAh}Nw1Ida
zTBVcGJ!XPnlpjo4ITjz*u*zdg#3-wUh|veqh3fJ)N3PtAzk6fyb><w9csYQeM})iK
ziW)Bt8%7xpy7c$q^V}V+{xi<Y(U@1PnQ0&XSOM4;Oe@9~uAU;MO(300H~6P0!5tp?
zCL3qhS&o#5<~PL8mt_tu-fj^uI~CrMAy%QDlQ}E(jWz1qwP8aZvzh$`w>qQ(Jtsad
zoc}dDOvAK-DO$+ZlfDQJWS_x+-)oG#&%a@F%IMMOc~+4!xPCIID<zFoe63F7<h<f#
zM1Shr^&V<)f^P4|))~F`b=a6vKLDT)IYA^n=85$;9`qXNg|t3?Y@^4%7qz9++p;0O
zLwvbkzR^751kGkiZ;6+gzdI?UuI$%dQDxp~KIhN%uI0P~K2Ot9_&k7%EIw6x_t~ty
zZ*uz{!D8s+sq31Ogn3qQ%M-iZe#W1WW!{&=&Gz5`+oAJGR-{wZm5eWI+dj`XYX%;L
z63v)N-dY8{7h|L61D~T<?b5#g=tDA9*#T=^j+74A{qIIUubOQxGRyAp%xhIlSoW1r
zKyYFJ0b!8{Ex;TnQl6ddv+-FmB)mHvmS<3vukBJNbK~~yTQKR`s1@<ZTq&bTh~QTc
z$q4w30e=^Ql3&b}`Iw>#^ijzo{2d4S0#aDwq`bAyfr=tMs$(pywVE3n0z>~nYr**M
zUI@4FB&Wn4M1d+s)6?LmjmAieknDF8#*ETRn|vt1^@)+J?Q&^%PpxGX_@%#MV3{Af
z;sEMR!{#q(Dt4TZOD8ca&$>T{f7xo9>EwZSbAb9b!RJ&992hHJwzbMLmcH&i!XL;c
zC^rNdnC~X`F2~rJqDKCAK#j~urA(JyR;4dpaVWOtYIOGYzbeHJQuOA$&uk5D6*Rh{
zke3WeMHws{jN^-45WplZ{@FA3lCF3@3<P}XIy=q!Lh>fL9skacKOUhOQojQ<WTR@g
zFVD-60$f=lLB5d%o<u}{&Em_=P{+|uxn0k_df^^0n8aPv%dVOLsWg+noKE5MM<>6>
z*G|$js>FKojZ{|<8QN!e4<w<I(a*hmA>|473ua~jUI_bqy}y|m4~ulc??B0v)7l2E
zi$eCz$NlBE-(nw?Xi!P9v}QJVP}@3r>X^?Xj=~;?!q&Rq!T#qLD;fTku<7$MZFYM-
zYVv#+*xqL1_1ZVy@HaJQ<8t|__BI1_tN^#6C?}k{lt@16Lf1R-W&80WFJ7SiW(V_4
zXf<Scd`H(P&c|y{CwCx?jdG;;5rqZo-z!$Cg!bB73>%H4yRp)f3xUt=iXyf#Z$cKt
zBLl^K+dX!Tn4C%;H*eY=PZbtVbwuQlaNq_v&A~~jPH51`9H?qaC-PUSif8!a`zDK0
zhXbn*`a?lF37a{ktTej^;<@*jfk$=6y*6O2RyDQAX2(+`L}FSWwGCaH`s)h&IwhU#
zq8-fOy!>OdIW0DOf675BB*~Z5?d)lBMB;P5sFj0=s)$Q!ffq`L96v-)L&FYSO#t<J
zNFE#nCdgvK1CP4CJ%N*yX-xgv@D(H(gm+#r;rW>HDzkJDH%&bUf$ofD|B(8Q<P*}T
zX<8|nR#gW~N>U%+`MyVw&l(6b#%xUT+dB%xgjC$sg+hP7f<Oj|Q5y}-GHzaBb;$(k
zRjpNUdPM?_+MT&CZaDBEqZfh6Uvb~~?s*0cERP$KKOZSI_WRnCTiamS*_(RC>$Yl+
zatJQ5Fe|7YT;JvLjIpQ4+ZFxXxm@Iqu+F?QbY8oNVWa}t!=|}oE^T(c^=q0Nfl0V2
z$-{QL^WAzCAv^b%?#%jkx%FCFi`)D8P=4Yxhr&5NXG4ssN!F2OMqOe+q29mHe?I-7
zk>uRy?uM{**1wHOBqTi0L5ayk!k|i5_-)#QlTfJbe*4DtC=J(bFTr0<ZYNoXiA^{~
zB2nV`Qlz!xQrDNVk9MMlcE6i;{{M$v&@j&*VVDX;G1`MGYx`8Tl)HGGGr-=HCxI5^
z>WwybT2$$h#UN|Ny{NlTzOmeq_V<fvypsfZwk2MP*xFS?mAZ*wnpgt${t8L0LZ+z*
zs!2!=;@r&{ylESfUe}}=7R0!9)v#El-Nbb4z1U*ir^RV4rtRA;)v%%}aXbkk0v09d
z)JjMlQylw7d{uBT$HCGtZuJ&IC}imhr2Zo5Em3;;U<Ky{e;LbP*q^ex+Pl(w^p#sB
zrNbtf7NJI=yiXUdV#;30?PNQJ<t{(|O67=*d4|A&B6gVZ$*54Gde-1?v3ZThZPp43
z`fK%gTiDFHo#o0njLkD5suiR!c;n8*$nG$*6StRJugOS^nF`L0Yg`Maqr^Zq?^{?Z
zQL3{2-Pmwkc-?Pm^R*($eK8CJ@t1HVbOs2*rRngZSg})bO>MFxdzF(=C03>a%oL%Z
zTNs!a+Xu^Bh@IHZsiwkQou>3ZIs*TlzMF3z%n<cYja?quYc9a$3m}3`t%S!OA`KE=
zo)xFMq<v=#x@AB)%JH`6wcSQ#r3!TlTS{_U`{lN48c9%gB$j%sZw`B0wPe9UYBohE
zg_Pn58=wBhdI&v#nQ#Usf_3o5$Hv0{ZodiR1BsJ)RWwccM-ZhppvN<~5dvnBqX_=g
zd=T1((o{ZqFz={+-OnSXZ1O8FGJ!iqfL(#z2qfiAA;|0&@FRQD$(uk{z;C21UOE9%
zdobv|@~Q~M{^KA94`l*;u$M8I-eJ~QtTeRDzBi=KrOHYp2r7<|CNw7L;`}Iz_7QGH
zZ2%FHao-OEP{7((%;}Qv$1cuR$TVnVU{cF-_K}0~Rfxu7hm&Ek*V5bHcYghoL&vVM
z_}_^ZtCs`RV);^%%=$lXH>zCKDRiV`n5pRGjVo1pg)pu6T6(ez3-9*YuaL{!PZHY^
z41$kb)k=u(>-swGD8wt-jUAdLuq23*86%~AQ~XV2FdyD02Z15f(v|e~2hgmRoKoMP
zLA5MxPEHLi=|$FEnFeTeQ`7{A8K!iVxEp^T1T|~V&hH<PxpcmZL%?*95Pr&!Iz24?
zfllp9IW`<iPh;)^<*rLDDj8l@iv%G0Sh+MJFY64)RYQwx$G5&8WGKeG579Ufh6Jx-
zdPGxQ2<{5b`^6Wx9NNz@t}FlowXgH9U9a^;Irz_Q+Dyu*J!$%A)lVUE7B*JhsIj@I
z61b^2#@cNAKt?Qz6{8OD^O8-`e+ISS$`yBe)|RaQTMsevY2Q-)N<hwNQpQeP>agLz
z4_NXAD^90^nO41?RD*5w978rFu7UWBQVY`LYp@;ck9F-jI@|Wmexz@PY3zyQlMqC$
zV7mAL85GEb8<tB>O`$1W#caLdyl<Ys7Gy)@8VFmAK`rE_kLk^Vi_7<u;8TJzDpgqh
zqmafi;o}i3OWfxVsQEH@RensNTU=pg7gNUSaV1kdQDVS>P(%v^igA)bxNk2I5#_WN
zgyKwLqUV@U^9LUfFCoC3jp^E;Y_*UZ%5EYgp}+y5zt@}b3nhz*=K8`gTpdk!3a*Hb
z-f^MA=eYsNOasL@iuttBa4}6&UGHGUMafE2w>ZPVcaveet$6R_N4Zz&Mf+G)GT>8t
z%T6sc5RlRveJn>NH?jq4r3aQ@ELPG1Kmbz|gRJ(0Qgy&bX9pT$saR@Ml9Z2$5&)Qc
z0Taaj!?9O95&Q{XY6?rm+&^w?blvTBqbE#P@EWmHq&!6^OmU5!KJ{2EXb-SA=84j$
zQDs|x^ZzO%``J$L<(SazRj}WmE!QALpAAHtmey`S-__2Q;#6wIK1Y(t#~S<j6F{$S
zq!YgSq3N72PfC7_4pNmn>;B^%4DYPk1$~#)K4GLp;0fD9_uPy;jKl7s=3T;+jq-^9
zqYU3#F}(cq9uU6Kn)O2VwFR?<xFq?~gM~=)35D=)grj)cc{aw{S?`kw$4(=LWc<G8
zGyF^@`J_sPrS%W!KLVT|&Z4N0^4Q^l3|W<|`!#fmgD=+q{4TE06hCu#Rilh<fTF3~
z_HqjglY<YHgt$+p`>EKFFR)~=s6?C{8mUt8<Eaf-Ux-u2o&>(`r>k>fN+5-z5XUEW
zlds7PfhwU^s{}Ql^E4ICFf#>wsrsHHRjb`pcs!+m8`#bh=v%hrglS#?mF&6$6IiEF
zU%#HaY5c7vs%mVXC|bK>Qa_VFQOl;5V#tr4^iKjkmX2(QB9?CBjh*{kN-eSO*vm%?
zA*1MjKgW&m?*d1V6Uz<F8J0#+XB3j0*GTfA?^;!;KoW{kZ5A$^?n<$pd9%ALeGw@f
z=;gBqDag#-9)|eC?mesvqCD%X8>_%<#nAu-`bg;kEDTr1g4GhUzzC|ng81~bl<>pa
z-Xdoj@C=)Ymn@?y^Pc`CjQ-%q8lTurdek8TV|Q=byeh!~09di6-*$zxtxx4iGi1lE
zw1n#wyeVYsfMk55YTCQc^l2Z}5|=wgmoAq8Ssd2L$NJWL?P~=elMj&-3fyZ|4O_qO
z1(us|udCK!?aaIUi(qp_&ke-o{sqE1n1~>sb=r#0KV=m`Xc3DRgk&WB0&>n&tEFP3
z9&qul>-|}|HA(LoOL9Qp+fgv-#xl+7Mxfrc49J$@_z6-K-$!yZdH>wV`cx2tVZsr@
zJOJlEX`zfJ%|P(3P%(eaBzI|pvd7#MbK&8<c9I%jExpBh;zp>gy*iYdF>fZh#@Y>Z
zg%mvHv9IdpYL^_$IUj(Szn|yQ883FfOJz_9cIUv!x1n6I!pLFokbfW^B*ZVtr(K*>
zu<@mtd9F+0zB|@8IAulbENg$=5UB`ukwoh54mcnZP%W*26ohyDG5?xT!3YX{*Qsd3
zGZSL&&fmn%CWGte-mN}m0gB%b%ri1+)hEABANx?*nl%ldcf|$qu!0K77C8pk-Kn~Q
z&lX@dtKVdJ->pNJ&;!x0ED#_#Y?uT&uVQQu_%Os@bC|GuWyxj76A*V@-TZm(yKf*@
zFiM2bv4f3MX!42dyLAy0fcBn|TYKE<=2aoZ;)i`w99zAeQ-0&OgTT4uHL5$Gw|aQq
zlgUf+nc5M$>S+_m8h-moYZNH$$@gPS=W(pd<Dz$m;`9^2k?=r(f*n&AxT^q|<n|Ro
zoDn`dy^*6x?-H6Mlv&Q0F5C>5g*M);?Ht?;b$j}r-F5EX!oj)M$rf5VJP+aw1dJ~K
z**rVtsOAx>o)Z$>JnG~i6%bs!$=L3+-BL`GPV;>JEF#lvIkmTlburL@a>~8avI@-p
z<SA;07u3OE>&V|Jo@s7zFpV(!(TmTLACkkH@76GuZJ~x{80I$+h!I%Kw6I6CP!qy;
zN>Rq+VP(yel0ImZ!hmjjy+MOpZe^4Z_l+JF?wiww%Qt=#GQ^3D@kqjfoWD+6iE9B~
z6&+}*8j0Y7Fr(w$P6>ZAl2(h|*6e`&NrNw*;X=mzwVn#Rd6ylp_R!G<3$u4z{wTA}
zA+zc@2Bp}Uw0k%x&ksvC>%3n+khW~HhtkC;%Ri5HM6I0Hhg+OmSqGUpaMbIyTjjZC
zv$mhKy><8V%UC~!t$8x-HZP@M!NEOl`bCGBrw)j6wwxT^OWQOfOo}Gf6^Vo9IPGqy
z2_6=iWQbsXdHu9>b>j3ZdEc2Rmfk<4m<TAQ$wOgST0F^UC=k-e(@r|Nq$=t!Qg;5?
zEIe0Y`u{F@c>D+8=$+%zI`An0sNK#~sT4-|`&o_xBtH;QR6RxJd7ur?TjGghp8I%S
zOFiQWzOH26re<cyM7m68cVk4f36oMJrw<0VKYtiJTD^Ur9ns~yI;3&zq~G=Y{yUuv
zu%or<=zu0rO|h!E6H;!lztNrO%tEezIfEdFfI_v|RHdFNtxWwp6F_bd4IMaD^!dBh
zHY9lQSauRlNIqo8cQ!RPvSQarNV#YjtNd?Uk%;7}fDR*+!fwAupdAEsXMvI%CvtU}
zvG&7DOa$?4*)>)qg%cQIR+4J}U_QG3MasS<m!dcMdn+u|w;8p{+tvQ9rcx-gruZT)
z(>=p%hnAjd)3H1^j#}7bgRK2w@!|2hezijhyO#qHKEuQYDU5_%?^1y;-7#YA{_^e5
zwW3qf_6K2~)2Hg)l3`tP*|jS-cW1-s9BNe=YFBRqWC+%6pU<fimFP!RW1Jy3IrZ$H
z3gIoxLBZc02(inLr(Io4EUC=LXi#Vz%)OsxRH+=XB@%BV6otoXWzuaj^fy)#<aI@^
zgQu}m^2*N+GF>Bk&Yy}?NZ^JTxyrwk9v<Y|b2w|1>Uz82HxnjF(Awh+{0dB9*J`f`
zqzl2Ksg|w^IJs-N-ma%t#N~ZHCl`lw*9s+$mBkHe<=G>pHbZs$x+;aLdayzZez#W1
zLJK8KS{1wn<=LTZZAxPGH4~cP^&r`YJIQ&M(>;6)2lzV_a(UPnz)Bv7GV4#^c!h-$
z#xhLwS21zyymyr0<a50eHIk~v?OOUR-VcuY62#*mz2?65=1Ux4Gf!RFeA4zDIZ((9
zFNm9C@;3h~{*wtRd|!3uYlLN^K3hDm*Vf!RY>TEf{sGl2^fAJJEN6&4P9t?pfz-5l
z?XS;6naH1LER4{>7`c$}5)M<U7@K7L=P|||S2GuXnf4*=ddST2nGH*uga${yB@Ii0
znQNtBS3rs+x`ZR-A1+Shg`7cbMY&#R0!DTeMKBe1M7zV*8-=aDlo}Netk4@6_1IgF
zzAqaV&AoGTEEgIk?|2Xq5hoA^Mtyer!-(W?uLJH@f<cB>60^+_{^J@d=mi!zY3Y|w
zT3;uph8?}lVa;orqClaP!PJ`6igV;vNFrYSWh&Nez>4;wv0wpSrlqq;ox&|`A`e;!
z6$igP-F|FnrW!8-9K&o<=}!-rz^E4Y;0;ZJ6{UrRqUzc&W)|FvfMr)P2e@&(b+T?0
z0%U9+yb8KinskNzxT;&B9w!|d)ry5PJA;k#D6+Y{i4_0YLJO-_s8S-M3OO^#W2U8!
zZl1n}nax5><O)pR>NeL%03`ODv#s9ywF^j|92Fl;wH}X#H&)-Iu|1LuPeSaC2WooV
z$aXa$o`#_R$}gwA8mKcjAzp!GT{JLO*y&}?SPIaEinm2?4GS<j3UHTi#tmpuO~G?q
z^pINmw2)$T(&cEMROx_pVl6X!CjabG&`vF#DqOL{W6THK1(`;;RGNs@zo`tALo}fj
z5r|Kw&5ErHW=^?5pxto}K@qyvYjcGXPL0!H$0B|#+&n$vsj#<g>;D_b-c&xmKhIP#
z*Pn+Hi<CYS!C&T_>0T|>m<-gH7FQ%0xIUJ$cT{`vquuL-Y~qDGN@XruYZmJduZ{9K
z8^a;oCcPwi{@W#2%p=a330DL`<<Uc$Y6p5&eYs{Hc&UB{bXX1$-7zzxQc+<`0|JH!
z4H0I>>rcphZ}k8&IYw3%yS(i9{0tXWsh^g9Id99U^}F?$ftLVxQD)``C7a8IGMD-C
znmtD-c!%P6-y>I##o7J&2J7#e_jwou19_255b$oRt~M!Vk@9RpDP7~(3^UwA2V8?a
zSS1XVwNr*}t-X`l2@3<RN}p}67Ur!dEtZDIuyzINGkD<l@@pk=wPO2C%3j+MRjNYc
zSh-~Guol8YuA?XC)5pyKh_AACWJV$I<=^cN@Y|-;+Jit4g5`FFb)e4#_M{R81X@?l
z!QZsEf4_3ZR1A1NPW6GA02t37_q^ehZ&Xkaq?0=Peh_F7uzB~`ql0^Q+-OpTgxPoT
z%?YZ(C=VyP{=V(X`!Jm`^l{7KhqTs>hJqK*uC`U+S$?J$YTw(9o0F`U3UfBTc)5L-
zTDnRP)YiI@g}Dkt8Ycy>^W9J8Yn!14llFWGWPb0h{@Syk;oV;7z?-W|#pEHhsr$q$
zEm+$fopYP5>gBK9xbDsP4>Mx{PpP7<)c?Kyn32?|idet^35qh1WSrbnbw#W2cT5am
z+y(fuM~C66;?SD*^0q5y8wmgnHJb@ritNSkAzWOe8dDsugrmg2#y|*;%!1Cfo&v3_
zMTt1j0ls_03GgMbY>V$Yg8`zM7BcaKP1b~fa`tpZRXHsx6l^Vwln=(XUOsu+YE&VW
zau`||Zr%o=Ay$HMD^9uuLTM|`N#Xg`yop^(8&8txmwHha&3(?*uws5KhU_V_nB>1(
zmcG`n<Xbkw83YtF<b5EPPrMav5jcooo^ij)kV(_)%T+&EzijoD`Vz2n>zL-X7-4PY
zR}q}|b|CrVp$DA5iul--o%?8T_@!>9a~UR~M4{Y0ahd|iTe_u#HF~zLRs`uq5F-y^
zDg(5QOQN6Uvh7ByOV)q+fO0oVyjMJ4oIv2iaNg@}S7P~Ce4e;rT8DXWqJ8qW8+7EZ
z!SOk4<~`niCYz&FSyYHr#@L@jBGMGMdePy)F}dJZtO^$vgdl%#+bJ#>Q3M4-&kqCB
zXHSh08bl#OWt{NS+MZSK>u}4B$_Q)dt~>L)`mypAlVQ1N6(>2ZNCXA(8oeK&Hk($A
z1f+CEV@K}vO4lCfn)mF`7F)>COxiuD5r5K<O2^ex0q<swmc&Y}mJn`{C0of7N6uJD
zpxPi@Dqvj@{U*fW3QC{=I#*e;>{=sR(skX*DdNO%72jfs>MfO49UU;%(EP~ABw5q@
zU)g?0F{xhz1Kxmu+&{R`Xns$Dnnf>$=5(QwmZc5{Pv`nH01_#n@2|r0=;quwS5U?(
zQeWI{65B5jH-KOm86E}oPL~qzHxoBO1vDDrK}<0<V(0uX?F7jHO)Lps*vwo5UMaKy
zUN066m1f~u837HKA<)r4Xg--Rzk=jBibJxLkG>vn9!;BH6`#~?Dxq+p>V7+P26#M)
z1UurWMeDRlSJS-608OX)UpJD}mFXIpz?ZV(u*n+fyU<J)8Xy{MZeElsmpi*s&t&z@
zo&=8EmlOjYJv~uAcU6KUx$iS0^wQUTaL?mR_`61H7}SF*mfu-K_=jqBAn1!Ko}!@#
zq0eal__9VUgo_p@Wq_B>fH9)+J}3Ch&?4_^Q1*u8@<oKD3vnI82W?`3a<ynGPW4FH
z6%!=&7{i|7kMdg$BnEiz#5^|EptPuRVenLmJ8z0g<VuY&;n8a)-|NM(IR<JJMv--j
zyPeowL0PP&nibI`iz1j4vnld#Q2(VK2`@Dti7wc%-j6sNruikahG)J3?!ZeTDoEbR
zEoW+LL(7EP-X#&yTw!t;BNx$}6rSt%BLrnE+t#mW85kZNv->NePCo)j12|JF{my#p
zY8NZ>Wf`(J-CtixMj0}{7N1vm6vlUt3N(0J8qbxB6{li*_L)+eaC)PRcIuDTcSRO@
zEo9SWgxHCw1+NvU+M~ykwGi5+>}S<4H1cf~A>c*C;|1Fol9=gcC^F|=i~2#;OvBWC
zVn*-7_hWcgp;z!>9bbP}%Q8V5IgjnF1`txud?h)Aqggz)DMuP~m-Hr0XKdjqoyiE^
zO{{#=($h9k-|r9aA4mVpIOl!4ej{0;l!6~qa%`56sD;iP*-UyTvi9=uN(99ghLq>>
ztn>Rv#2f;G0dLJV*{SM1IA&i&i1|M+8|!zcTN~E!I{cV@l|sf4iu6cmzLzjv>9N7Q
zYidcfVh^Rmdyzk9o<CRNKQUNm^|P1bio?@aJ$}Ss5)e%^F~&c?JK9P1B~3AR(#vE;
z>&Ae8a(q*|NhaotK856u28sQ~({xE0dnAe5XOHw~J0vYPqfYgwaz*;fCsjbuW<^2w
z{m3z$F%aRl8#(#j|G7oOJ0LAV=SD4_Mg6z9MvmJ4x8ou<Ha)Vq2%)nST3Ep^o+*p{
zNyq?Csp9zjx&3-ksC{XG&$%vs2_vobA^D`$HB6zb6uB#f>ZOPDWwdVY?%$qPo7+83
zZSxuueN~N9RQt_Fh~5wj1fzmDeZ4jpb189$w9T9QzVZ9r2!E0Wx7*FW{BxYXPei@K
zXx23s7u;i1`)%^JcHGTB95-|4a4~iTW^~G=U^{Dj*Ms}R(=Vu)vW#3f)`>S<nYh_x
zr?8xqlh6yI%>8@*^roKO7z_#&t+qM^^Ole16l1%GXp|h(L4{#VdV0X{uF?oMB9j)8
zh8=*0qKNJG#FM%6)P5J9_F3a2Vi4`ymS@7Tiy@JhXpP#gy}4t#>9<|1>;|mr8xW4B
zx&utO*DRi!Se1DLiqBUbdG?TdKJTDktOSY|eY9UfGV)!@n%8d5<k$@Bu6){uUL|rE
zKGGKIw_kZ%Kdh{nL1McJKiw3tK9TA_&d#>SX=iAiw`iv}>@=*P1xJ@guxDy$xOsT_
zzFZ8g{j>5mmbDpt5BprovYNfk_h=8zu!$u3>sru%GM3SryIh}icYV(c!B|V@9d)6N
zT)X(WBxFhYhEky;*rDVmym{s<CuQA3web3B*o{(hHTX=-;4*{#sPJ7`8BcQB+I%ec
z{JW#X5nR#_r;BrntPV^T6&G`}TFFc6WhcTvtiL_(vIx`Q%+W=dUN;cvwzo*SwGPaS
zM_Tt~YnTHG;3p%kwlhMr`pCB)Rvi&D{FIw~GL#dwTtfE0aVaMKbis2HDoBjJG4-uI
z?@4K{^oQI9&PAbx9XxI!WX2438|*9eUYvWT)NV7hpLtY#z5MC9Q}Jtao}~S{6}RDb
zf#S2U{>JWrz|>r)k`iM*tI-7CNRveCB=B!gX-V>!c#3r22m;61rdcn3+TcZQ`z@Th
zYH}+h;duDoZjdAm?w-b-_n&|6{`;n3HZP-Lzm|WU|6Tf=lFS?{ovQPik{k~7r(Gx4
zuWWv9<?8DhIaLm(;5sW{6RoeWKalI|>X{f)_3?a(y3{885cXcUc_3vo_a{I9u>RB5
zTM%l3DHU|nK=2F7d3)JOu}P`biH7sp;#Tx~d9mlo+?e4t%qx)0OM}w;qdNSZ86Ld^
zp-1__)ukfkyY;lz%N?FC$$zEVTZR`U{mIZ;Y)$>DX{GM|vM~R3eO-7w2wS1H<oS3<
zk^9NqQQpKnUx5Zc49}(Bz@T`rHc*~MvWmBSY(s`vB4oZlD4PPJ{Qcse47R*F9(}$!
zCsg+&F>x!cg6MDIiEjQxjqCF?Z$zSe^8qV=Jb60j3BHe`yy%=^e{2Auq}S)N2?K-1
zK^w0F6ulvn>PbVpd`Y@)Vv}m(D96dIh$OQ{M`*;5gXPa;;!al1Ua6|^)oW(U2<wU{
zbTAQ^w++(Hl?6{0PNiO1%2G<8E249DwFxQ*(UDRGGR7)wp?7cxY4QwLsC7q}RAMN4
zLgOF(Xc)Jy;2<+_kd2dB=IRV{3faloAoZ>=qWB7K?%TYoercu=#yfgsj|P(Wr<Y>t
zCewMM6pbSCCtcz+2Iq^#175_X{pWS(2tVF5A5__U`44InFWILE2}R~GAd)vc-(i$*
zve`K%Pr61PD)CRAA91Y_;wEZk=oC&>O~^+W(<rpj>euk=(|neR`A{&gSuPp5kSJw9
z^{Fm-qkmz*%RCSD^e|URPMNO2b+2|swFUui-5CWYbd1jVZTI12nt=H2jYHH!%gxiV
z^<kl4He#jV`?;H3;>V?$Eiv-b$L|)+vaLpThI!wMOO_Hhl@Tx`Sg_5FatHR^jePzw
zVp#F*Ux7PYs6p>Lak^-(goy==vy5WDnL2ZIf$3SoUmxPl=P0YA{=EMPGj?5M!`*m#
z%+>TEO>?rlRuD@)qGlmDnRuoaJ|Tf%JAoi=NS#W;(2d#tDY857O%;Qbk8#TLQp<|#
z_OXk1yOWtn-?7s_@A3};e~>+yXJ+pf_9MI!a#`lTR5rKX<37a%`$agfSDV+Lbw+P$
zqw8s0|5{plBkm&LEwDWH;Ff&jEn<QpRA-mJXljzbI)%GLoLUggNTa1wGEwA&PcSfk
z#7h+mKlB#cSb`#h^{h1-thGVOI0aoZhcaKLA>K$Sw^pF5u`1^Zrga4QqUE?~ig;UL
z^!!jlbYx*~vq&p)nUj$u6_6)d51rbryn4kzC_iZF#67o<_&OvHJztrptn5$Lfh&4x
z{f%Lr<w{6Agu?v%PU<a)k6Q4IkE9#IND|S{(K^9UB;Y*IBe+7{zJlM*pbxYza@6L=
z717K40^MvBPBkSP5Hhf%H&iLU*JJ*@geATo#<dFHH9h_=!4miLUL6#pn2x$-sd7Qr
z5`4dbf0*e0Mo~S9JNIg{1fI{UMEWi5?c7(tmAC>$?#J3?4O~xNT}&ZsCHCiUIzp4)
z3+rShD`Eusi4SM3)-<?6-$^JdVFlWkjhN<-NH&g0@)=&pU|6Xw&PVo1Hok!YH#!O|
zx~9%~Y51YY`JzlcU5XUeev^%@YUS}lqef0`?imu*2Hm6IU#zQ?twEL%n`*9Qqo<t-
z7sKb}KUG3l5={wj8|A$?<s-7iEJ`!+2}iT&Ft#l&Q7V&rB^$BxSIjVP!SS+a%K>RW
z0z`-`XP2q>(|iwBPgY0)3wPgrljKHCD-mFj6z1}0gHb|NkTxTqNA0{8^?pRiyj?oe
zWZ|*X1wk1pI&?+?BpIa9a(Lf_>I~bhz;aeQQb^37mKCvfA=;NesB>8`&0RM3stzpa
z*EwnNDc|`~v*>)1R`=f{TGumf{<#ZhkV>X%3t?t^_x>=q01<T?G7&}`)Q(4A6Jgmg
zQh%M#p0e3X{v<qN*Ps5JYzehCC%M@%gXwVTQ{YJHx1$k|l#C*l#)o&UI?ZEC<5bU%
zRsdv+$!|Jv9qHV@A<3hRv^4I=?T1BaE_A!a)vo33Jq+UF{PFH`Ksl%JkB1GDzcKrg
zxG+eFLrVTL<#qn1@|R+RUMGciep#p1j*VKUrVnA_G@}kSL`Fu%oxS!EDIA-JMamq1
zl8_a(J&4!${*Yzy{!xvh!^6!N7id$QvR5+37YSCuU##=rK``E+>3uDqN{VBE_vXJF
z-_?C9VBm@>W1*;?ykW>e)t|w_lJD4`$FocC{D#Uw@&<<rLU9WFt4_Y&#K4JY0|`_8
zGn=7%Jj{yIyymZ0(Zf`~)e%~8u_hefsbBqG<c>W0>+yP}?v1o#Dvs&c-E8ndE0(M|
z;|DdK+D}eJ0!)|hzG(2vdpB~oS2&<({VmO{ZV>%WGo%R;WNST`62F(9OrGniL1-+y
z#}f)qT8XgkN25jxBx+|DJ`Yxx&>LSsQfpBoED$&f(Ba7k9K)Tb#1PT>Fo!T!zJz9P
z+=F!#%CO0=Oz?Zt)p3zKBrk+%NHbBE!X$Qx7WjfnH-AqW9m`;B$rhJk+4o&ny4$}l
zKl<DFI=#-npp<Hg?N_;M{U%uU%4urbMIWRwn$X|a9CK%~84-Z@ib&ws;0Y>`9BqK1
ztKj(<D_vj&Ou0}uu#uWHYU(9v>e8Nm0<aM{?*^xGCRrV;T&1@$?&irV6+~4OE2@!g
zvsQSBVp?Pn3{yGEMAjl}?$;q|G?MEGt{^Jx4X*}ORYe+sX+?YRpsmdd0X%txOxoC5
z`likE)(S!q*UkHt>AUoo-7+)&EILRur0-juRieg0O!4>fSQ)(AFMmvHBh0@g2g%IY
z+X<46MRC6JXSFZC0{;w~^i@~SPL>_76++R=k5`;LZqlq9S~QKTG07=GUU2ke#2&tY
zZK``KZuN2P{oW$8-q3&4BEM*`y5!ZRY2}Tz#17uf)O<m%-Ff43DE+NOj4i3#ep%X|
zGgExZxGB;90D-PtuK56sgA;iHPH&0YbRV?MbXkJ^66@KHCz0Zm5Sf;!)7eA%98;l$
ztx3-n<}&fxo=cMHN3NQ6^*w`!U3Okgi9ZhR!04)Z^A*NGgJ{`Aj}xdF<Z+?s95n)i
zv$e}*WCc0>yG@}KLpnECEdp!#J3kyh{3zd!9ipil4N=L-y*X@XwOO=_raE@Bi5UpT
z%rCux3H4e?b(M=+UJ<x%OWt^>NWv(gvZLXU(TJ+F=F+N9(>1sLia<i{mz<-_iV+`<
zRe@EIqVNwt$_(M{!fO(w95qv<`g-AAZSOHU$Rc|d!9bximjqu;)zvddJNpyHPTol-
z<9|HH$Z){bR3_cUhbSi2e&fR8k;QU>0Y|Pu8|#dp+CN2CUkv5UwaT~h8`$i!Dpxa~
z;nz`^f<<Bd^Xfee<S>kY>(47int<T$gq>N&$1r`bUdifDOU_C*Msz=k7}@oP&rVve
ziJD4;6Cs@|MLbQv%DHZR9+P~A@)<2}9)&YyPdgWoyie-&Hv)HZu{xjqo}Djg*S&-i
zf@7#C(b=#}BqTZ1JXz-L{SWjHl6;=gO*_|XPlQR|kcGg!4Q0sPXUM=bH!e;MJ(2JY
z5QZJP>C#cCda8P*9d);%O;UohS1%~PEAUxBH1DE;RQfx^kf-jKzbrV+Rg=)K55grx
zP%c^NpCeJW>^d7R1&X-?gOup;-WU^myiCmMcPGzxOON}ljUL{a!2mROj?#WTGUZvl
zGfEId?yXoYhlsxSDwK|H%>_TveOMThXlqr0`|)6=b@jOISO2#rF}&amXTxzL+ksX~
z2?D=RoF_SDV^5YpPM(gRRwmJ}T3)TaXA2J=SZe>$PW0qsDVe8dti^0O#Ko;);Uai&
zIbndDFTJFZXriVb;us;`{g~h$zU6(loKcsP12%!2lR8wZ%sRS{Qwe3SEKG6-CLjM1
z{{VGHC589oWdj+k`wE|%#xie-0K*|sRb>hnjlS#L%i1sQHB3_O0#7!^m*Il<wpK}L
zKvDa*-93u*WsFo%y0+0~H>mgJN&i`uCh|Ca|Di_g67SXkZ|}QB>mR#J-&q&Ug#2&0
zeHWg7AI10nyi&o^#S#0u8#C2{NGat8iB(c}JK%34mBfElvh2Ve#rdEnvAW2+fAD@^
zNb1u20ju?^p4z`J`?(ZG3nUQ*Ju`tL0-TRBfmj@Ifo0rTCH0zKkq1)HW?VR|Y%)ZN
zJlq2D)a)gQ7-EC`iE?O0Vd1+y_t%KN<)sZmD-!ZC<~2~}k+L=Ax@^PH+$m~Z7Iu~0
z_WCk2>ZTMXsn>H$LpYa2MpqfeekVV4c691~tRA?$@+0fM@<fr3sEIMzi*%r(Z@NBO
zt68HBGC*v-nRPihv|*4|c}Xrh78k|BhcY&=ucHN!`yy7tL@5Qp2}v4W%2Sj{YsIn}
zzf(_CrglS9B3h4GpB#Dje9(T2Jw}S38xJ`>?n%qrgpcdenk|9GviZO4^5}apSq3Uh
z8Jb(C@4Lg6LUYsj%a10_wRa0p5&7lA&L}^H%VC3`!4rYQ;B?ley?b(*|H|G{)<Fwq
zdiAI1j5-X<pBotP$_>rL3hxsM;rl%aZk*D`d(xIj^eLAQORxT0lnSm*8V|52zu!56
z?OWz_au|<rg!{wNii}5MG%tUw8C6{O^fYWHrwAR>kcn4r$mZeNjFNH!bn0zA4pdqv
z%!eGVGS7_>Z(K+B@*<*BiIp=&ipOcVq0MReXxzqO;<(V`Ivao4uC;lL3o}Zec1LvF
zY_(f0BDv(~fM`O8PM(S#T(rM7#&seK#?w&*FhPC}qOxW5f2CV0T=vmgZx9A28>XR^
z8@?*0T*7nWju3BRgyUj=i}O`(d#NY&2dLy<XN_1inC!O%#DsnC=}a(`m2}mQ8=i%r
zO3m_}SqmN0YW4&3vs^}Y>1zBzmTUM~k+cyclxNP)@l{66P3cdC76PR8!~tmNl<X$4
zt+FVq;Rn)H-Q(X9T_@*}2_UgGM^{`&qxM!$x}O)ydq7@2f6{t)nCh+fZ%e-S$R!1m
z1xjPAIe${!rA|*Ho8<JVbLW`jJ#fSJ_1^aD9Bs@B1)#Nl-G<H~Y_L5=9_04l<c(N=
zj(i@I|I`Bx-5f3i^!ah7Tf9v7CJjgU#}*zpf)A*_ZkwZ;^)Qc|U5xZp$2s2w{Nb$e
z7)+E&jsb-JwF^O)gVkeaMS1nQXMKzb$-(qBnYKQsyK9FWqdbo`^J!X!o9Q1**>o6H
zOgYmId7m7P)r|4qxDDM}ey4q_e7bB_y-L0dH8zQ*DJYK#-}8v1SL6slYw-TaZ@{iC
zZS;*H#W*}AMsTK}mW4jC3rM{396~ZGbHbLF=H+&PKl{i;u3<~Y+z=ACutNjR>YANd
zyor=Ck>o3Nqsm++mXz6Ree-%r#$$h&MShANL1Es3@((LW2T%F*N|EdS?OBXfD1c=h
zuF?vUf2)OBGg%ofJQ#Hx1ugkg)V~~B8#FKZ&<xpbEl($oF8Rxm)HnAfp(~@QY<w&D
zGa+Yig4x#nn<<I#t%)}AL)%zubB4{+!|VNZ1*l{!70%E*?lj_6ehy4?+N<r=YqE<6
zgZ{v@0~C{3W6XNpbZSTrXY2yIQ)401;fk}1d(e}x$IAjRvNvv|AMdS1`p-D=-3$(E
zyt*=2Jz5#(O!ylj*oEoV_VjR*8u0Gac9&!9_-;Y;%fai4_9?rk`(%aGpF(_fT?6km
zR(}XH-}fDxEbX=YXxw?7wPt<ObmIK9_DY{wGg3AedNI0lF<-8ThCDiq%JEY+HW+)I
z+w`m&ULp~a3P07wr=Wm(c8z->hic;XG>w&HV?9}^SNB<1*b|Q}eIiAryACI2^LQ41
zAG-JP$>!p~$95>$_M82~-HvryRCQtB`%N}@yszI`@Zn$gyoPs0`Nj<`AAv68svcya
zE2er>2*Ts7znZAk1%Dj3Sn>IIrrdGush#+#+7dH>e54!}1I{;VwNg5nA2LN|TBI4-
zr;;x!j4$;W8>}qV&*qNMedt>jL^iGj?Y^AVO1x1j^p8XKXMVwDpJizKY2;*5wvOKj
zP~ip58nKC6Ex!Kmv%JoLGC?`#i)!62mQfNUlNz_#XH1h=vE(AQPR7Z-X3=6&Oeiqg
z{@4qaSE$`~G$%FG=^nGSlRDs=Aejq11tGMpcg352|L<8Y;I0pgavDqq^s?S)AV|V0
zQ74A%$>?KV{jF=7kG{*GofnMAWH_=P>m=NP<-iJe=>dY^eX3e0#mzEfE+>~3$#3Qi
z@yi1*v;fV-KGViPuUEs%U4Cm*EQ~w?(y;*tQvVcy1$>`hT6(v{@8ftC5jP>!kF|T6
zQ+KV<s5zbxN+dFgW#xR-Z{7x_q$K~Y-52WE72p3(HzvOiM@em(j_XW0XYH4lNbqp=
z&!VFTAv-s6xW7=S{xMq#mW1R{zA<4_XbFRk`R_5AsguG%WO7^gAh8V6J?9{?%Vfq4
z=PH?Lp6mPe=LcnXFd(sKT)DQpjCv9l+&}Q&O?x1JhTccji#RAYQcg-FSYKV0P~;Ns
zLz^NVj9v+cG#DMe&2d4$B^OnMRlejhv@wEQrNlj{nS!8Ple<}0Iw|O<8Lap(daf$H
zT`UKhYZY_H(6xmVq56}XgVuQh%7^0pdY>I{!e}Zmh={@7(^yK(NASii-!W<?K~n9r
z^TMd?*JVNc)IjO`(ve9_G4fX$lQZ}-`ec8TQn6=sZSq5JITfV->h%Q2kcu&T!KI^S
zeIDO2W>bO6AQfA!^a&3(4{%r3TKtcttB$JjdHRw9BCWJ^N`rKFgOsF5cXvy7cT0D7
zD|LZOcQ*neAl>lp_jleu#B)4H?tS*zot^o_%p0wQF#Lza4j%c{Z2x~OS5GqLAG=8~
z;9((GCwNB>8Px$fXf8b`(3bmGRVB<7WuX5h)lK?h>`U8;q<${vKe0#BgSnR#2#<q~
zK8;P&*0Ymkd4PdA?MUKWC_2l}ub?Y0fQB&1k>E4;-a{)s*)k-Nq!%wHA}w4TIukMJ
zel;*E7-%{ooIP3_x@!lyH=HgcGDQswuU(R%I9@gbHF?^Yoi*kIzM*CQ&t35tdFq&Q
zRKyJ$Oi|%BfVWf)Mh7c+znod%93#lULT>JUg{Jbb^NhOb^Nv4!d0$5yi@ihTD3ho*
zYV6w;frQXzoF&^Jw-CN+g3D>?&Dk?T;(bMgth%rNa?W3tCPHmcuWPZ52-AFYcC~Ms
zPHTF56w5>*hb1N1?R|Lu5nwKyncl9x;f_sX_nv{WP0=P^nkiC#238rLSD1IPqtMJ~
zaa6MS*nj=A&nOEwJMHr5>OPB<`^dn!p!v0`p<Wws|D_9jt+qhuK$`!(wwSI^m35mn
zTZK-dE-qhF+R?dLoGjPak=)N*+v7n552ZZ?x>sRUSv{|%XII;*Rx}6NGw^9D?q;2M
zK5JmmVREr3M60k$l%*NArfpxAv4ROxs)@lRoM}j#+#mFyd)s^J^mAx(Q1y{y&ao7U
zs`&v2eukBSi$KO3bqV$6#&<4aREaV1G6T|-s38#+j&0n1efY&R7lkUU2}*G>XQ?ig
z=wkjyh`R0VvTdt|E>*w&cm|q6O^q7DkHl@anw>rl<sVK_hv!us0MURY&bds2Lm+q>
zCPJE2Is3;Umct|&>WgpMbw*<N@~S(bB)U}DENQeRGE}JBAu$XBkBF*5wB4<`CPobd
zS9c13u9z~DIrkhRtM?4Gm~wD0qsCz=wM4<WD5vk=;SFyU;lwV{lunS(h>AAG$5&+M
zPa?~W+$gAMCy`I7e=O;Fpe`rC$9tZt=^4^)8d#MLuE|O#&x{hl{2e`k1y*8CJM%)H
zp+U>Gu3n==#dfAiciHAOa~SMIado~0{aKnKKc>$M1-nGV0M3pPk0KE<bv7r-L5C2E
zd(On;7>d=A!aNs&Zth0mQX}n`W$u{RqdVu0&!!m+a^OYEvuCWxEAFOeF#OwYlVLk7
zwIliVy#yif`}Qk1qF49Ds320>u4rmBlA1SJ1Es~9>wz<|^-96|0h^mqLyJ+<(-p|;
z4C;C}p4Sk@^)&@2>)%Jxg+$OP<`Pj|hv}_>5jlzrdw-f-=$p_8GvCg0Wi&3M?a97@
zp4T29tV!^Bx4<e@?-;ExtyRmF?0g$^=7cgb>1$D>Mzep?BF$A|;nSl`XJJ7zNYx5E
zAhfe>c7G`#Tx@Rn2<1qXQy!vnfBs8(c3a@F(Bzr=CRJmRp~bw#O_6clB{{9^tcfc&
zQ4us?TmcO{4ZssHTJvQvH1TqR=1-POUBO~%r(ZOVFlXpjySKf*{_HhO&V4yYiIkgr
zV1n8XnQli#8FM>Wr(H6I5X1VDLr2l}!|@5Y=F2s!aT%RIA*hFok3*}N7@>!4>5_bZ
zVZ)tQjcF5qOx0Pq6011CDSQU7fHhml(StRjh_N;)G$?>?(On5n@WDGCyimJ3l>0c7
zaBFJINVAF6iZL9NUxSi~mQ{UCN12t?b7k|(pmIHM)>~!-3;63IkZ(Ep=w34=(niXK
zzFWo2s6aw6_nR?yUmXS2dE3E8tdUgD*Hg!{a}>h8`R2pNL+2>FZWq{@*;Ce)?>akD
zRqF;OP2<sbY=BuVN+yU7kti^kGS}8Q&71i9su@qdn(&7ON>%gNvS*@r@8;km^>CpK
zIHIoYL;sXB&gxcEGXEKfAo=ej%o6HpEaYz*R85(96iGH%%vfuIe<E6d{E_r;APvL&
z=+j)Zk62nBW#XY$L7eg>|EDD{v5_?g^j0&)P;j{4T@VG8KM!+IFw@zoL88H;u2wTo
z<5al@Xnm}~WMdA3_t`Ol0P9GJJPnNxys@dCtH(jm=_rpXr*-CKn$yPBQ`OY6!iYR9
zOrUPF&T`i+NmEJ~?jJTajEXT1hj19iPFn9+kQ|Y~`@A=;Fk$ae1~6v+)IoitO2Lc+
z0D>~A%&o0kh#!AIjQ>Q3=OH<Cg}GSLp+sP@o`ZuW_C-_A4kOZ{--s8Nxhf&-Xx9<h
zaf!RE5Pb6(cX^t0jvEH6X%6zf)<ZIRJ*vzI151Jo`kR2O8+|2y=4G6;j&2#S);3+g
zOxq+1EIwDc)H1}n(qz1m^6wui;z#Xebn}3mc}3}jyFx@3+QAZmBZ1dGvKp;04PyRC
zA$S_;0}zye*#1y0%9^^l<j%0m=4|Qe-6N?Xyq7OXnP|D%Irun><O8<6%grj?m;*?S
zEs6&JSY}%-aGg8|93#r4C>y79ea$p+ZFl~$;EUny;E)auhl7Bhl@nZkonSggdJe<C
z-nL<{acoiLDwonZUfquF|Kg-}6%_nbq_KRRt*C}h1ffBtK<wT}q>YeUaGYBCY~MEH
z0?02WeZBqjxl(j)Ha_vPH1L%L|E*pbOyvTipEFrDGI)T#$ul%K^IZmGM~lJypesKw
zu~}sD;q`CMdde-2sn#{y6^@Me{}H|KN79Nzd|zo9*QF^^WAE(Y7K1si=ssOAh>OVo
z3qt&)wn|?xMK?WRVs`49*MDdqgYT=UTQ+6xs-<I9Tek$l+KoxS;nIhNeW-3OGl_fK
zL>9r`suT98JT98R4|gvDRXh{`mLCx+_}(VI0VqqGU{9M}6#*Bjeb;|5x%Sa3`=T2@
zi4>lPRc<LWxqgMW7L<fM3&f(9L8rkCHS>21FDGL3bJz2>JFeWkI@|qq1~H>4EDAPK
z`(uH^Jxm(qHolKDa=NXJqkpuGAUiX3iK1k~hlvIKM)%!;s4WW~Wcin93vV<x%q3BS
z95a)fJUMu@t8EqN8CO;=bUMENj1FewdXLt<J|U0mepQ4o88Y30h(iTr9lzVk$atF}
z$;k?@w%cQhB@cr@4l$K?+}i*49kTMCxr&bT05_Y;H-`qrg)`b>?ADxETzFIyEbguW
zIsF1zUzDadLXXD&FVDF>J`*=;IO$92<QtF6GC6!cC3(RZ81OKWP@qTE*?;Zl<vVdb
z6S{NH{U59d))jWMVInmQ;sQ3m-)YA_x2toQA=#XcuK2z{xrAiX`c_F#Yp<C;LtVXg
z&;AYe4o{8{pNJsM8n$w$0HY(gbstE^E-qSXYP;807c?=ijX8)GUjNXw*f{f2j}M2q
zbYEDRxo@pfQuL*Zy`{YlEC56$*u|kF%>OFf_Q8y`=@ae;!Ht^&&#BIj!WBpK!QKH}
zU-^26cPMb)(8;TcsTY`es=!7*3FjXaT`^UuY3Wv;C+6y#x>SvO)_gd{C4+_i`Q}yZ
zJX5AbMlql=O+3qo{yN7m=qJ<tP7LK;7m74`ditSn$44BRJjdH}JNJp{tG0njm14=!
z--o4#zdortgkT@Ltr)rJ6~)Qf8#nhaYNl`%6`;N=xUT&YM`dc+kDBa#uSj#zEiw7j
zIryym(>34o?w1r-E35wR#0#zhg#{l|O7YWw&0~cEgCQzp5@6<K|1jow&IdC~awYQW
z0?W?=OUTKlp*>HVDAl-|p<BdxGe;j;5|l2+aAWILxeg!5xPEhaoc0ku?&;@lEHoVB
zKFuzO3Z99>;|THe4E5YDoC4_3%^DtB-@j;{qW>^R2i}7Ngl9^Vq`rB5bNTA6??0}6
zEiJ1_Yi+Ofi3>P>5^KoD{nDTNDi3Qmi?|7zyK63`i`7Hc1ewINys4Mf*z%{FhYnJV
zSxaIjJ*^$Hp3dHB+32F8Kiv#Iu=)GJrP0iG>~8LwAVw9JpvWt||F2p^d-wmRm7jU@
zDb}{uzM*#jTA^k|Yz^r<J`}%l%MT!3l|4iXD2WVr#`xFyz3B>3$m@YV*RQUBTGr;{
z*x`>bEfGA&y*~tRxITK{PVrCVX6^#L$Hv{&epvc)4Br?!ETFBjna)XG&U7A^ZiKdG
zE+YBZPTr?l&Hm8?4?R3ZAx0#`>-=r6l~5F^yR~ry7dHhg-BDN4)G>fEYC1XkTDpA`
zwzfunj)Ow-Hv5!*Yw4Ds4Vy)BWazc)-Jl7uoL+m91i?R#Td&f*-8Yrw{`8r=*eXcW
zx`-TFA5>OBE1;KIBg7?!5h1<!)NH2u4!@ve3MV9<T326ebe5v-2HQvit2m~Z_VNA#
zLe6z)_6jr{Z=V05ak@GUN1?6jeSb%u>)Sk3vz}R?aXM|T4gagJsC%UuGH4q4ayKDF
zof>^HEXU<>H(>FVn=81OPDx(d8Y5`-NDn|iIp16xEIyaH+~U663urW}WZLkbelv!7
zBrRNXh<n!tQRa(-o`eBRBPGS^aR6PgNX16A!p*`h3oh{nIO@h6GkYGEsMa4g5$$@M
zqS;FZ-H*n0l01JU(ZGmc)Yocmjm){MKW*M?M7UL$*fEl$zX3fXK>Dw1;dC~QQk>`b
z_kg8H#qu<f1a@Ls(@&^XuxGfb?XB<SOr&+niq0tI1YfIJ4`I%JgBC~%R=gc7g7v%D
zrO0x>8In(sJU?5>pKjj2v3GGuY?4jXSO{-KPBurC9ducDx4rLPHv&@O^-wNuKZE~n
zD%#W)9g8Q!(6%WNuy~W!I+fL2?x#;j{qot^kPwf<0Sn(FJ~KCdrFatnb~czvrqP;)
zr!NzWNQkMTXAe9zQlKJaW-@}@yn4T&EWS<$52d@cwRayk<#vg=2HYU#993{Lk*BVD
zx+UYeJ}*Y=9)2-(Qw)BW==x^vv<j9aqpN`dHeMV$oG%x-e*I$uC{A3Q7A@If!*@fn
ztbl<)1H0brRUXp6;85J<Aac^;!Z=R?TGvU*u(;L?5z*!QyI1J3&)+?r%0~9AjyOEw
zj%Kj9d92|@k_MeGOoM|5P*Ry{9DRJ9A`P4;Ypv0t*XA7U{oA}b`|NzG5tl8phj5sV
zr*9-_uz00RW#yyxHFaWD+M3_cw^u7sAf<QI`4`iT%D)5H_e4_GgTy2|R-3O;AmN)m
zJ-sA#byIiRv03q)^h5HHy!F)Xj92u@oKWCA(A6nes;|BICFrdk$8kDcwInh~ofu|Q
z7k5v7?v_=&M)384p;1umlfk+n%3cC`vHumNC{k@UZSqvJfV18JI&6xDrEccR=5+EW
zu*)6{*N<Pv|L_tnT3(lpl%-ObF2kEqML-qvArBf0#?VZ03w1Te2x<kQ7RTt!$mFWo
z$){TGlb2^q3c6$t^hdqRbb^>8)hfwDn*}>-$K!j%<CwssdoSHB-&0(KQG&OT8c=Ff
zgnEX=2`X+M$0S`Q5jF$<d7M^LX#P@TtGz{X#ln26qfImzkiB_o*y7mwwg22nmqaUm
zYPK))K>!5!uZwKNXK<jVsNPrv^O4{EuC@cmE>@hRW8?k(&7aq9+sJT!v9Dq%CH~&B
z;0#4H7U7o;op&c>KTPOXH!d->fKLeqpVG#vKj<ZX@vY~}DG{V(s&P^+7)&5DBauJo
zCQBlLzx8*N^7)L;igeHL>x%qo!ghfwoduKJ7^K{*S8tiVe%<-4;-Zg_bQ8#e(`o?L
zD_nDwI92Y8Mx9M;B8?>ZPCi_Y{)W#BX;_YvMbkK_pLMLhGgFAu*0!T{<AP}$lJZh>
zYEfy|i~D+T{M!GiR$g^Z=ABeESWFlpFe(;y2hbmV@7H}0gWYoAeR`i^&F{!HVTLb)
zSKq#F3@+orRA-i@x6M0K*2|9#FNdk4%t`3M<2}Ui_J<<`3)OZkehs~uH6(i^&+8SR
zwO3(~+cJTURy?Q1XAci#*+O?MB!3TdiQvhEZZjvezLs4)E`{eHUHobmgI<>|ba=ni
z2(GAlv1CV_b!~7%-t1GSXAEuJbOm8l+BIuxRry)ad~Px7`Sb_M)^h$7hS}0RRj4Kp
za=1IQ7qQvb3{|se$KB1xXTx_A8ViKpx5Kb6cYfEzl2U9dmhS~E;YA8#xjCF8$xQh^
ze5`PJUeos;eIQx?u~dI5O(;M+q>?1c#hI{oV11~Z#sv%Vtn;Uy`=lGe&R>tBdp}R>
zh<laAd2KQk)_q=hU!H|L1KCR;?t24ekoL5@%SZBDea+v@zW?Z&j|DiRXS)gSm)Lhk
z<%x4VrW*L?PhDO-`?fb84@12j41%Fw7SNt@yvRTXolSo-JS)Ja@y(J}s%dF}gTt|7
z==<LwWhCG8NT@D|HWR)ccXei)v=RMaAq~mejvT&XD4%LRZeI|-GB5Xpa0_NBohkX9
zRt$|a#Pir|V!#6V*<La)I6}aJ=l4u=YVTsZqik$-B3bc{wfkko@7ifxfNT8aMCf5W
zZ?wiv3IiS#(|*r^N*)huR!JX^iP@97QIP_^4^$kfaS>E9e@Pc)m90)P{c}5%YC6s*
z90U=X`LO9v7W5MvO`&Eq`Wn)ojH+b=uNRXyLO_})O^}C#6r_X~B%KgV28oYD3L**r
z16N+SgG~6*yg&vqqA(v?_Y18r=k^?pl8+2kjA3ObapL{m?M&vXCatQSbq!1-F(oo8
z#dQC)%R9^n#^0)qggrfKKf6PqkX*(9%Cl^{Y*S-yr*HBS-<J-_i}TKYNnKRhag?d?
zt$a9b{rqpU#_twE-)9F;%2ZBg;-2MzeYbk7>f)><Qq3xx@z?(Gq#1Sh<2I^T(QIH(
zs7TZ6>zaiNlOricsF6>@@Z*?cY*&Mb5$^A7ahylxrlB>plp^WWdC;Tq1+6cn3#33n
zd7BWSuAwudzRs)P4j9{YzF?r91u*B*2qTG<9Myxo<>uvHwR*hDNb4jI9venp)ySJe
zs@$y8ISvChK>6SL>xJ}=?qQIoDwkPrygq@~igBh=R~K1$7a+Xp@thLW>-$v>PjVly
zxI7vfR{cf<ePR|7!F>v6$2+dg^Z%u{TQnECJ$2zn_px*Kbh&aYf+<uW8j5ee*m~m+
z-mlq%9Owe%K%Ty5AC9NHe$Y>`TeUAc5f+ya6Ij=s+^gW<1bQ?50(;b}-MdCzTP=f_
zv)o2ag4)y^K9AJYywly=d!kLIZTk1UXu1;6H%8x``ygPylK?#)X(jZ+<<0N43vx)d
zukIfo-p-b0^d71fM8)p83Mi_+LpkIw2<BK4N1bU+R7hU!>y%E&w>r=^CfL3UO`U%(
z>}&3n7V4NP(f~8eMwVkTa$9yZdYFyyv?r3}zO68cV9W(S<y*BeFfH6ddw3=mx*ekm
z8pK{#e_3CU*3+{)FUZy1J)irOArSJY7)OcsVI)o_GYZvArU=zAB*wN>XQ6=@456n>
z)dASNwZ^ih-c8=%+dd!+Pga{YE=@A@tpDyIJ*aL#T3X3f>-k%2Ocv<PsAJK{3TYM?
zY`zCVNPpZW^`Yxk{uple$xiQ&q@2_37f(_X7L`0iK!*#mNB%cO2^VKC){%<HNJh35
z@}9UShAFc&!Jj&l^rT1ieeY}Upnq|3B5eMzk2Ld#li<iHBMgT~hkq70eO!GDm;mbc
z4;#ZctNCN6h*}A8$$?zflWIk&>yF%Ib|M%mcFt|yCeiwjf9Urdtrot2XOODSDKEdI
z&cGTLZ+sO2aS^w31o?XW$I?BC@!q_HLu?zNe<+xBufg^7W2TPB%{0rJQ}OXt@L{Md
z{x)miVHs>UiAt4AbGGKauXNG;?<aJ-{|b?Q@#-&TA5I9x%WMSSM5+tk-Xc~tcNuj>
zP;*%nm%Jh3V+*?f-tMFGE4Q!mri<4hZt}ieT1mL)tg^3O4*<dp3>upHcD1gll;7cp
zx+IFGtscOv%?yI@R{#8wAOq=z^V)W%<{g_Nbwn=)4#t%}S8u`lOKLEm_Wol-eEK-W
zH-=+)GV#KvSvdr2j&@K~yFX-GIk%q(+^akZhfN>7P_+puI+;Bk7fpwD4TNLl;|5{t
zJjEH50!%Ic#`7o404Wkcx&aR61hzZKt#0^BUdG;ia^zXy2zKXp?1>q0_7*}>ap7%Q
z?e6>PcY0cDk1Os!2K}N@rna0V$P<x2WZZz9Bo+6J@_FROv}nMKM0dY;@7?_T&BS_&
z*LZb&Uj@8?#ara?b-$?(iW?Y_Ivaeb1wYr1H#%djsmEu<jk~XZJUzMIvc+7v3Hjln
z0GPkc-6NUsVow0}&1apMKiyH4(rKQ%?ZlCX2klrE$Jemo0N!<$DoE0uvRlbJ80NPo
zF;{yRZp}ORR~~t0^=T=SIP=OfvM3s{p3=aaKIJH0CXL_E8r34S&95g%-HI6Gprfl-
z3iGz?W34w!1xMxrJ49MBnhijFIo_}Abuq;fb(v~I<5=&u_I2eHzdJ}|7nTTqMaWA?
z_>+LvkH*(xpN}nQ6_e_t-c9!__&}o&g;n>~_Sdk0E}GmR4mwyzoJ;!G#`kh8Eg#Wq
zVxqUUgs#g9IroERGvKQvI*e4y8nv{`Y*yai`x`ZJom6DVliPkfpbu}Y+q2%VTmtaH
z&Sl`pRu18t99-q<Mvt2(LZWP9z++%EmBEGVxLaFudVm)V)X}b^vI&%)gvRvPJ6a*3
zY+&lJXjvR(GSDqWSJk!80hpNR_dZl-P(3sMolW7%*=jw}6<s;G-591Zogp2>kQWSP
z-%`m4KVt}S;NJQ`2EUdPeR@ZmA=+X?Av1*t^SWo0XcKwxzw<11$sNLm0xqASWn#FU
z<I=VYwKWsd1m^8frpUE7Q5jM)<{s~>m_4Hg;vzbt$SwGDpU~Q^uVLdJLQk_HH-h~Q
zei4;X*mBRR#ysfLaNP39Z#o{BF}Dy6TEiJ)$v^Jkoe6C^e9>1|Cm$=e?uT7O4+>kf
zl!JZ(ud9B?AtX;_lm--@DvL&r&OLa<!)$_{+;H+3l83b~r!T)xH8m@1>)N`SH;=j5
zR1KXe`;KZx+1RoSN|VUn&%~SD#WXqLMKF@>S~(q6RsyB&$``<^@~&lna?-X5tycg2
z+Rq8Bx5<B!B;LtQQU2-+rRRSNzIPQBm3EwmjoCK1pvijQz{iTm^Dkd4+=#lb=7&R{
z5s#b4l>8jh-8OP}Mw+gOgKMtV3y<A;ZpbIHKdd;4`(Q{X^q(1t#mhPSzSt}~c!L~R
z@X^=+Vx*>STAF6+%>Z3AzxIc=5=Yzt{sjT+tj~p$<drRx#%)8-V~}H8u!+~rCCqT)
za2<shIBz5U;xX7#Qeo)?_j;Z=`7PgdwIZjFgdV)ZC%hC#IuMwGFm&76L-y~8G8r9y
zUve8!EcJP=3V;r&015;EcC)~9sNdPg|EOc@<rOweNvZl>Cx;jkV$;^7Vl~-#*?~!y
zV4yx*l!tBC3v~rvgwy{jXYEt_y=C6H9DEe<)B9j2>|L~9TW5coJ_!QwNy*nYeB=Wv
zqfA60Ibhqi7pKU^bMQ;zl-M{E)=++2KRi6Uwb;ZGUSzK7#t<cJJp2RoMHdC3>?=U2
z_+1Nijk)<AbBO+oPbVKFt7E?ha6QT6l?MPl_Kw~5|8+iDQBiO6?igteLN1a}WK7LM
z!XVDu4%zPVV(RZW6n<U6@=t6KoN|6-<b>LQQu9l7)r{rJ&4Jyx{JZ~Z>wfgSi3bo}
zd={If3M|eNbM=1r7A5QD>ZBBzQ`pu21UER50Gl``HchUaHG<}YldFTys}XcjUcFS$
z0w^E@BpaYtgeD*%uB_oIo#l129xp2&4L9l=9Z$idFS=fh<KxsatW5gl_#1D8ipR}4
zDVB*@3TBkiWYY^XBtW*QZ(pC`qQvj{EXOl=Nj^)Lb6m&ngPAd9->kU5HFZpNh0ca#
zLSYrDLC^7n?@!Y<g$9$)WzAZxT6roKPA;~A8V~E9ESvy1tH(%pDs<)AM-mlTalG68
zgOWQ|wT{itP`L9r)uO-5YV%d~U5=k^fGUmTZP$h`@<uFYJFnjBh496>?CQY%JLf8C
zrPh~*%t-Zdzix23d{|EUEA#W*GP>vK40ra=n)Lcsbu+2VXO^?J86$ZG96;*8gZMBN
z|2GA@jiK(H{o8<{H6NFz@qOG>EzMGpLA~+%Gvn5Qw(xuY?jR9?68Wp2$+fW7k^!yz
zLl+N|uI|>Ls0YN328soM`!5^ZgW%5yNc#E>!31Dy8(W#D=A{)>oV?9F+!Fh>S5U{h
z6%zf;KdZbw-uufjds7_2Q}L+#IhkRD)4B=nx-^;LQa68W7HR9F@<&1kmDSXO4-+XW
znbcYVu%35DWU4ErvMa)JCKn<id`1^aZc$nvLw|%POQb4uNlkOpY^=Z;{t=(|>sy+?
zh6oCx@F*xYJ(AL4^kqT4QYkpSD=PV?uj{kKQ>0$O^om_pUy%All9FETi>N5i8c93C
zXffG7c*hb%FtD;^k$vDAGTV9JrNIeMwA=S+`JP`+Z_MTZ0BKj3KVBGxGpzMXxBhJJ
z??KfCxR2kzRgyjXmL2k|%23*Lv(D;>XkueobY-3X9$?&A2Uv5)6x-P0Y_|)RC56KS
zs^bw*32h_ive`}1gUx)NqDbEQwY8ce>L#2cjMH?9;*Za;dn+Od!U=$M;!ec&08r-s
zMI@Ai;HKCO1@pLYUAH{{h@M$MNP^c!a8j5#=x2S`2f1&-O;>}}OrCeT0RX<iCmc%{
z>u(u(CXJ&E-%=r%nZ1^;Sf*$GEIh~2qz4xf!H_uIpO(X5f4_SW_|E<{CFt?!jV0#C
zru!||WHCmmXnNgnNjSHN!l|)kQvl!sWy7#Vh7nU!sO|6TG)_V=@*&1-aj*1L!69jN
zcCm>ZYar%l{_*wnd|=>RNGN+!M436wi$j`AP=M_M;PQvB2niV&)#<)y>--Xz2{7)Z
zOblmLlV@kwBTZFcVNIdRREQhv4}-i_Q~34QMihz6-kJpJO1GQ1+kmWXlj$ueQZ*04
zl?qb}-iL8;UZ_6swR)1kV@Cc3i_gr&G-IvZA<I~(N)7fR*n{#)@6s|D{^K>XBd$29
z3OmA5r@X>f{Uv5yon+#^8G$-RG`QM@xdA)>n@E8LYY#?Ieo6!oVMF_Fua9HI3M{~|
zV_r}pERL^-h}CKK_h;ix#6t(ui6&GTiiZk~qGH4|eTwr8@cz7q8$c&V{K9l(xbh*`
zJ0U)ANTdUl-IhzU1jK*3f_*x6SU8eELH49fD9yJ8<(%J$QG^&+v^6)$)MD4C<E1-i
zrG8B_^yYy6m5;BRA{q`7sW*#j)Jw(@(8xI!KP64(0QWpVeG=#R0k0VCn5YPe&WiD3
zLw|a97LqsCQ^yFA<TW5CtJAXDc`ec(wr=7}91<|s#7mf|0GQ!#p{KS7^mpDIr+6e#
zhx=LDJKcmll?>zF#SA~&n@7wy?ENep?Q7h3x>?R6fat*|kevaXrT?Jq0w_WLyJRiN
zH!74mg#3DEc|Lu@Vf@^zwNr@wyZVAcCV>U@U7xZHb<|f<hE>O_>&{n@vwx4^hl3u;
z1bXc;Ev@U`AMJiie(#MOvCy4cP++cW`t8FNB~Yh3N2MRaLSiK^CV;<??GW$Id;3FQ
zqi>fIk6?Q-sW^w*ThU+ll7U5g+WkK_iit$U5oIc@Tx>^a0H|;X=QYTJde-^<=;E_q
zOX5}ngACZf%st#=>8b_tO1N~p*yhW=qKpIv@^SJ6|7Eh}BLM#Z)cgwKu>{@~dPubj
zeIXw47*;HxI1%d^NZdmv6fs0MJ4BRJ6u>A<?YEK1goKpr4p@hH8O7@;`Dp(}4Kb9x
zBgka1im@O`*m$x5g&8ze63f;rMexQ=K#>=2b$oMp`*w9wG#-azsqipW<a-(A)E;*T
z5e*KR=;{kvM*asWjpDPlSkJ?8pG!B=(|t=pe?Nq|TNKl6KPO1TX%XWLNvSKJZOzf&
z=2xH9gLkAt-5C4Ukow{*tH4a9#{(K%H~#TS^$<C_uO1E=xH-A)HD3H^mm6D<TqgUi
zZ4@Y9p@1-lf7F2Ue<8!|<vH@dyN|x@A;yuU{ewlIF}p($hWAypQRmCl+jVeN3q5wc
z>1Zd^Z);ZUGB_Kwk^<Qk`3LsqkqeeMs&Mhu&D}Z!)F%^A%&Z{dJhZxd1SdD~ZrtC~
zkw$)2^V(a~7r8%e*S2B@z!u1p@F7d-m=rJ#stC_r8y@MyXZ&@c@^FbJ;Y;b$KG_sO
z0A<Ef!h7uKxpjx^fDEZMX?t}Ex%&>JTJ-y0_u2^239Y%KtWI2VX+*9K_*$#|VhgJB
zhx!c({9b_1ba5&yyEXS*E<yZ%niz-20~Tg}p<zJDzAX4Xxq)hyqceL&yJ>k#N~mq9
zuApyJ5%;s<pwX~9dT*R5bbC8l9k>ivb<3wat7;NV((9&B%_hXJo`>Y)cLneJchL&_
zK$qjC`u}jAwBo_Dg1(0nBQOgOb^;xUbk3H*yz@)k)ElB12*eRgMLZ*Up2{p#trNg^
zdh#^Dqi3IyFfEP@68$$Kr>fi4Jf8cwg087ueO$Ug6SN7!_o{C7`C}WhVX^BbLl>}!
z0oaqX<=1PHjc*N|Ld0F7Ov9II{u>Y3sX*Mz%9*g_rZaBR@^X+}E!H))2M{1F9Xop?
z-^79js$w*Ev2!T@{LSYw*W2BOOdbEuY!(6a&Hg&f=i7}J`tYD`yPGB7A5<S^fWsjq
zBL4k>9J6@OX(nbBa9jc)2>@rJ;FlITsgABfZc?bi^K=tHO_l58m<`64=Ej_s3+>;*
z0NQA@*U$v=ja-=C<b3*#>f^lI`1$JL*~4^0R9dF2arHEGlE>@!{ONz48ni=i1Y5_)
zis*B_+lPjYD6$0DyK6S@l$nN4yIfpXHm;6to(_OyYN)>cIArm^P3;B<nl%U4HF#g`
z+BHq|DKC8DVQ?MM`rSU%#6zjC=T7bB9?tl&cRT>!HGB4X{ce-@<zzyrx4BF2Xl?b8
zI_BsC-S<Ia6mDAaIuHYT1|ALJz3quLcX26Ok!ZxrCW&7#fCQU7di00tgP1Bh&z3O<
zA@#sVwsNYwbI%DQA%wKFYQEhLbJnUzmdnlYe%lr!??>}e?+I_3L$+&|96({Ttk}Ig
zqtX+N3hNzkJiggqRvLjgAc=`z*;v~CQBwp?eV*=M$GDL!>!&D2!VH9Emph`6%@DNP
z<1qJf!I2S30LnOjdSdT#`2+nvrwtJ#!ha&Sw98JV%UYB?=(j-z$v-=UHzzRRKW_Sl
zt=+xkmnKR(BCC7BZ1~`A_@HayM^+Qg$0uV_wuKe<z#dF(L+*GCY9lZ{VNCrjN#Br6
zkt4<Zx2lif{sjh?5>87ND@2`=E*$d(B0c>h{VxLa9B>}qkB15XAYXGxs5(LciU+^*
zP&*cObz|3dX=`+@-ZfGv7D!o?87Liyb3vKJq`RDcw{)`jcpS_8?^vI&Z@2#!Q=`fu
zo>VOA*?onSbjgnQ<#2DaNHJ-cX1U+}Q>@2ck%jNYika8n^rtnc%jvx56SMe^{FNE}
zWweaq{{W57%U+xYb_v7RLn@vbm`I@!PH;5l+ad20!xvbRLgkR(20^c`C&KCQ&+i$E
z6C`<pp0VLICWYfKLzylL0vO~vZyzaZx;gqHCzMX`aF)>P)44;c&re^r2>*LH-`gE#
z`?cd0VT=%G##DfK<PEX)Tt_E{<~+9(>vC=0N3;Dge5VzEpnWobYFZKrxSrdGo;!Y!
z(ipNfm53dEWf`MYzpk(&64RiZKGam=y4jlK^0(w*e12pW+B=_X(hCd+S5|zyJdS(@
zqW}*3S8|l%Y(bvEmvf;<0>6hH=G(_!whF6g8wlaTl?5lG@BIZdOOSO04D_re#1R$0
zx!vw%6M7t$(5_lj6{5-~g@QU^e>WTxh{;TiDIX>`+R^(ahxQXX@25GMcV>=xLk(rw
z@s0|<&x5iQpgzq#0JU)*+5K2Uym$4*l+|e2-}YHrrGGU77FlN9{R$}uS6qJg0V(Ta
z{phZ83OLe6*b;vjKTe;o2It}3l70C-ueBz@#hMxJ@OKE~W%IPBe@OZM=aLG*ql)P|
zuja5dQ=m0|I~<@WP@}(APUjLuVq&V?K_J^Vl_J519%+gFPh@u<>-(Z!OpUU8fqdyx
zcX<+=KLoNZFp{fW`td53>2LYclDQ^r1X1)GvF+|a&lOPTGysL-Qlslyr{8m1IAeN3
z=<&kE9p%RJZwrkD0&DB$1Lth7L2VeIpW6k3htVPX-)HbR!9VNt&inAk0Xgzzf_d8u
zrbHh&f5YRY2d=x~*?!JMixlqSe<v?XlSPqepGyxS??>+%axOA!#fo^PrGgX`8ze8w
zm_I_DK$$od8pn^%Rr}fGtzJxlEN{JYoap+i_Xe#poBAhIB5yD_6SAn|E=nEkU>S79
zH7QWJUcDyM4%(tui4&(rMC$#9Kk@WR-47W#nWZwYkW7v@9?$WWd(bZhSU(tlxLz38
zq;HrQw2ldrJ>VC<8W!&rmPQWPM6Ay;`DWH31Xgv~Gcb9M_MIsWkW&Gq`m4Kd0?;Y&
zzVq7jx^@e>XoEjY8V=v-gEtsTuCQu>uRjeqx*uIz+`Vg1uwLn7nT5+dAoSe5b#rbG
z+D8C7BOb@QRnuR49x$mj)ha_Y<{TZMBysleTdUhaY}9`5<U}~Cx3TycD)HGEh)A&^
z1sr{WX_^8bktBq<N~h1Di@u3xw~^>R3L;^93vqGC!8gK=m|p8*LGZmLgleq2yQ-MV
zNqb?x_&&w&13Ul~y@-Uq)Qo^2qx>JxFlaMI#tJH`R5!Pn$RJ_jlUG&F%TOtFKR4|h
z#Qr*Kv->*5rR1+e4GZKdirIKuKqb^~xa=?A4FG)gWVi*gU>*N<z{=5maWmbes~4xn
z-aoJo2UTra1}%Tm5s)XRg@mlXnFnmgjJakK^w{RAsaJWkU2x$yCqPE@FJkTR;fUbD
z#FeE+O|1%cHy=1R^tFCtFbz=N;d+!C1Ty=}p-KOw0`#U-0%CUd*Pd$~tawKhZwJQ4
z=3_Q=)lKTV)UMMHxBWX5<Pw4`EYpgcKUHtk&{dMa!{-UdQyGFmELM#jUL9kh2GXDq
ziYKF&iIW|mO;!QdK5@kC_hJd_pDU_MH=fTw%ybKf9F4ad$2w(RRU}i#;M%*o2GNLU
zA6f)b%IrEifRrGMhext3NmMoYbv0Z)kxf{1>~EmWxDm`MQL#B4I&s#^Ra^n34M<d9
zvz^+s5YKbw`x<ktK|vh}0_L{EQ{LN2!{WhNWB)uA%HXM{X1mN}%gi=HLd|A5yulM0
z3L)pq#Zk~!nT|4?Mgdmnn{oa3N;KV^9(f?L&V?~<#H!i%yNTJ%C4)>|;nm<i!%XT3
zBZtSml2Do4!<h-+SEhW6oK9vGk|3ynhn{a#G(>j)ZEL&j6dUm)X%UN2Pi%e^M#z!-
zICCA}3(5B33wAw!K&5;hWN@mN-v5E8{F%27^x3YDj(83-h-6t5p8G2C*(^R8tHruV
zO<a=<)mGA4j7Nh1tcM22MqGLD<oPA85Kr>&DOoRKLK0=l;{;~D+~$VxBH_;&=CsGs
z|7g-&-xniJPMr?Lzujj|iJi}X7_bZO;9Lw;anetpmz{v1n&)MJtx0<y?Y%NdH%Wc>
z)aLRkVy;j3P+J2wAdK$jGa>2eOpYKat~h#2zrxT?L7b0B;^&I3pn7|};pq?5mfh8U
zAfF<6xx~V)sjSzsICftJGR)y{{+_2y<~T*6Tf>v35a(|m_T|QooDW`I-52(Mk2@!O
z(FjJHd}V)ei^_Hg4F^N~L7IGIm%TZcY6gU?yTY)%^$ei0y_mk38H(ubxo<fI;cxBi
zw(W=zoXwY8^sf+(M#%Q9cT2cDC-#2PKF!^_oxnsJJNAQYsu!01-3S2yx#~a%9f!{V
zTe<U2SkO=3ihUVg2!k}jz1fvX2&%4l{M|BfK7FD3sQ+yD5+hsHP_<)<ha$-1hb@G3
zJHMdxnSt^qS+<)5P?!JZ_`02qvK3uU_ckOwS8EMfJOck=HLkQ7A+acdbswxDE1yb%
zrk>x=HNji(tiOJBzQTq+8tqNRr%qB*B(W6EKa_^NG$nF;<1b=l%^VlaU~dC3x)Thy
zQJHMk)z%B$(#4uU*Q#h<jA5}iFbHHpy^CH@<i8gc+>6_z)w`>zA=)8%d`cZM-FdC?
z`uvV^$vSIaF%|%59~WFrAz%nRQ0Il@u?n{LcwE^6eQ~R^$2+r31?bAz;}Y^$Z{I&Z
zmpd8cvbZ^cUgU9aBWojtxa~h#Vg%>B3bK=uSbktg{t&R*0m|xjMaTn}y*iPOatrzR
z29cZpe?&f|jAZg|hc9UTy0_wMi@;d<Lq?KhFb-SiSO0+~g8u<AvrSd7o19OpACfp;
z5i!*9gG@{yj#NVAlwBV^Qcp_(84R1~Gz>oFJDK)|f+*Nrl=>`*gof`95L;<lqTbp7
zq<PH6))Qv0QHWyyN>b8?iq9em>|IAt0V&J3?)O&;XoLn6)<Bx);8a(CoR3CM5p2yl
z4&<(&O8P_gR~J7-mWgnG_Y9LsS9{4d9%f4M+O%x|XcWLYJ8r^AsH+35bm!gRXTf`8
zf619;jeaep{}iQw0)Mk#%z_#%s#NO92QM-N{@0^udSvPs^Oj>98npx*<gHx(4;Cl`
zJNK$x-+frbnTrkeOO8`1oM<pHP;wJIIw6LL%zr1ZIW<pwqv#25^Tfu}$jaVN?ZGEd
zQUraQ<Bi2`W=-bs|A!<No0c)4tWr3Osl86H_Cs<_k23E)9RXxA8Ggh@tP+Dv!R{TO
z`P3Pgr%#QjC?lpS8|5rH;WgFYAO572I4}WmWEVK)){?wQCvP)O=w006m2b@*vw~E9
zDko6R<>gRY4;4GTW&XPv%qa>logg~Q@6QC8+?9f;MRUw@0O&I-erwd9k?B6FNS=BS
zSSxYPhZ+5!kAeO0Sh2q{;k&4y2kD->GQc1E#14m!U1^<u*d~QW1C1<Dq@0Y*g2@mK
zW`k+zOjxlNuSZn==+n#_nPm%p8jQYE_-$)#>*bAsM4*uQ2KS5m^XjhHYn+Ecn3O$7
zi&zEXu+bkVckqxHR91F%an)oR&Y?y^L?fTe<G!3-=?xZhzM=Z4CH7elHPq~fE(P*p
z3Je_)EQxp^Wxr>#u4lo4&-;1tNW9WR>7Qq%LszXda*;|%{C?ibIFb4aa14UovTU}7
z>vK2NNrZUqo*PjUF!_J|!Iw?Pn@E(;5V*Mxd{ZrxFnX&QBRRAEXZ1ejm>GwhEqDbY
zIpI5b$eZ-hCcq}@2PwfR7`6#`ZuyFqmvy#uJh7r|6S#XVJW!o^Go1~=fze+01Z{a7
z!_KH1=qx*f)x4E({F&~argd=q9F?^aYdQtr<iCxCSA8=iX@T_!g~!AS`6Miw5GgJG
zOH^ir^gD~Sy<ep;0`gm#aZ>1t1;Ua*$~K#U=CK8*<OD6WkCX~CA0{D&62Ge+PudX;
z+&?#PpjD70m*e`XMCBsKCu*8=FsUOQ&+nGFuLF~3NY<E*6{zrjEqnTW$xd#HM%-s+
zI3wKfJ?WNcy`h&%IyXAc*5^~`*s;G`CRnp=wfW=JG!I~@^ZV$xfF<x|>UPOqAqyf!
z5(T76D{o78g_ygsZ{9_3o6NfB#jSs_r+|%S3v<1tk0LF<_ts{x-ni_`2RcT_JhuQ&
z1-sz8W(n!Ace6b4&uET+c{q5w=LpyTcFL{kk=u=KhY+v+5S!wc)yO3+icxmMU8=2N
zS$IaKsB55{<u9)+kZvLJKnRHN3T*Ef(gw4d3V#ey7t}TEMr&bN`X`^zsI7U3ZtVoW
zhY<`(pe)|S464-5Rc)?OaZ9azB+yVc>*p8KCZs4!!GINo)u@^<_c+q@jTUaDt&b@y
zlqoNgB2tdhMc4Om`2AB}#8!%$7`$10`XWu8no~UG%O`2Mv)_jA^wdebgjti>(zAvx
zu4=N~Ed#<olfJFi+W_*hCOuUO7lpmKR8t;T<AXeoG1tIiI?6<Vld&L({>4*<H|PA1
zuJS)SBLW1>=GOfKX;^?&uD<SieAyiMyd4mZ6hDv{n6}^kyzySei@L(>Wg&>{BF_3s
z#>O}G>D?YO8j)Ed>$C%$s`^yZP?dXS8Z{Eaxgv}N8B!p|0=nyxa-6dIUbrC*to7`&
zZkqmna6v)Rk<IgVb|mmm4wu+Qhr((yaSfGh!_^hM7G@|u`}2_<R1;|Ogx9v<?^>H&
z61mhxnFM-NQO*$?g0Vnk+Gakqqs%d{der;LPs#GUl57@4+#+PDGA#UAOX?^RNdI{P
z1XH<_1l?L5U`sPZc~gs65)7Q$6!Ai&#Y0N;=bL~{RS6>R`W;S0n-S{^8*PH;kL9q3
z5K0QDQCO`!-l{kfAu<W328Ce0%Jy@`?zo7uj4bKLouNMrY^r$SLXykv-6228Q8mak
zrGnm)3L}NG=)P{&PeZe(0YF885-t#JUKpZz!uD<OjvYu}D?<Td>wdMTCHUwLBcr|M
zklLnww0#Eyx>_Lh!sR}eN5~7NZbpAG17OYbSgwzBS9c->-Q&MgCVQjq(M$2&UT?R!
zUtsi26WYt44WFTDN1Fw&*cjuxwbQPlwtZ@VM(h89@!`DtG`PbI7tq`zGp6_B=u2H7
zVsU~<ytAQfN<-U*STbtHI>B4J@V4I@XQI#O@kO-it7rtby#{R0DD7Fo$qF1xt89As
zG1+8QvD5!jq|0v*-@<Nf1rw+6lKdE<wo7@Q`M|C#nYdG04<ns5<c%xj3?tH~lXqC9
z?3VIREi$~nLVgg~s-qib@8UXH`{d89%pEJua;OXtKJoe@(3mHx$z?&GKe$f*M9cUu
zfg0xjg?!8x`}avHYCkQTDM2>lb;h+jpRv~VYPtiC)^?5G<v<KIW;gD?VKc7J@6xd$
zB>Ls8`9t2v(MDN3pCSy1bm{*Y^wm?a#|-SzS6E#UKg=8Vek;YX*nj63T5(opg<{v~
z8C1P@e(mK1%uL5Oc1<>dK+k<tL%bEVBhcvn1e|3+gfw%~+QHjonb8|w(Dzud;gy^>
z{fn@WUlw)n9tpTNFQ0?>4!D+MAV5MbHIqVv;7hBiSpzuN1WHzc1d5h7eKPS>z&WZ;
zo^tGJqksfJ>z(k5Q!_KEG~%&DnY6|khwiKG&tG|XeqH{{hDkep`2*{VfyTypid{|*
zNEnZuIf~u-&=w0G&V-^B7dMl_5K-j{mxI4`OAY$mpeMcwcF4+W90k<^P5C^5A7`Vs
zz#MYEbQ>e$8#a%TY-tAhG-!}F(`Yfz`*_YQB*MiJVWdTn%vl#CW5E!5UIdN0cLb2t
zBbG?AiyB&=3x{Z<&K8CE8_apkeB@p-)Gu+AFe<QGbXXBg<bN>`<&X@>df8q@utic5
zZ&s%mOUg_0L}Dn;9?8OxUY$^oK|Np#rTJJjg^^NOG^LQ-HcvXy;SG%4m8*{V<7BY<
zjWDgq9E1;F@rkIu1Ga|nApg9IMLzC&j~u0zk3g2Q7~>Y&dLsg6<Z&pNlqUV|cgR&C
z3qD2QtJmV>%s9yC-BwACj~^8{$pS@A(H=o0bWV@v?SIhA76(lXdLnc%mq4#MFa#rB
zM%FlrJdP4yOC>JOp;u#KKroQp!rU<`i8G3cCXOn(+$%7p#~-7GIyMg}?t75-Pc^m!
zxAZ(bS**Cpq+8<Onl0lu|AL|kU8i>O@O=#BQpo9R!bU#YCVwHnHwsm7ju%cwm8Xg(
zSw4^rNK2q7h+T6aVQ#Do@VtzY4*Rg9Luw!J{;N6huGKnroAvH>Y592`_mc$OdVmVu
zfHdRGn;bh5EhN!jKz1&9G1VQoLMAiSYh?*KDoS7f93w!(jye8Z23jF!=`|GsTY#vb
z2=zM(*PqtW9e`s1`LQmi2orY6-<B4}%+uGv$rEjwY6_KHP)`bVKTWm_jUIb1QtKm(
zOrD}mO<bTU%_f-Q#c;CyI{cTWU*yuFl0ze7>bFc3FqmY|F;in@uwGAo=bK&*Ittd5
z*Cjwp9hNGafH-J4ezke!GJ%o|idCGKUpCSVc5vxj!6@(!PP*((YL46l0!Vo7;To7>
z`;Egvzk!_r9coEYBvYw3i`8yF9hD{ov5*5n9A?Vo=5Qq!&lnvp3@3-)@)<WGV<Nz~
z8DXBjekvx0C#yaJy+HTqBjiW<v&KXeR9R4MCX#$1XV<gt{0x^HiSP#@A-3g#^A}Y8
zq=sxiVaSEUcylh8axT!iALy`9s?EWunD{vh=ZlUh(oLVRwI|%~Z+a!zyJIk4&^@)o
zUc<?Z{3x|B-gAO|A<%f}A=S1XF~0}0PfU)TquY~`pe>WiYd>VXAxCmH%g-pUHB!vp
zb(5SA1i#am|HJp8z=9sU3T%iZnjTash03s4QZV(0nrvOC%7y_hu{Sd?e*xpMlXJ5(
z?H<6Xl^Li#F0Kl6+v`WXNY)pxTNM{fEZPQp9$QW?j_tC4>*x!)Ku$M2>|)%6S`~{{
z*Buflp;$FtY*42X2)CQ*_K!}<99bk$Zv*y)dwh^1J5%|S@U|NCud*j`kWTL6Iedx@
z3LrnEoW;sRs(rlIU_ld3QCBlan3NqtXR&TKNUheVs@@I%c<1&0BblJ@fqmKC0>_#O
z2bDjr>scR@j7?C`qQ3ra2(k7$uew)`aO>=9<}2wTonMnu;Y){DkQg+QdqYpt^03p;
zj`_Q8<DbKjA;npaVB_9Rz{wO-U&K}sp$AxY_1(SkD!Elu_|4;F`8WQsd88h&FS`KK
z>AcyBCJrP5_Ju~Zo%7^Rjy1$0QzV_<T%M>Bb#R35^EqnwClu{>0TOd)DWC{~sZLlr
zFNK(ehQ^WRin&ZPA1BB(eit370(c21e*`f_nmY36+4f^%RBT+e)~)|NwJ?*yKaxBT
zx5T;8)-XVmWa)I7zcqN*_?BV>02kgQ$A1d{0*Z7vhh+h2oM{K&ou<SUM1ggFzCeua
zGJ_Z)I&L;S;3V6U=DWn$&|||#V0tS?fh6{5<NOvV=bIzFgkd-rt`4=Cw$M7H%IUG$
zuf#lT6~5%ZI<`$DB&)SShb(<vxUP+p&IEKojrR@1S(1zcM`)$A&a@JocN+^5Et>uJ
zxcEZKa#uvH@w`K3386&xAxAVBML2>8wqRRdX2Z8wurT#({*^deOlCYX5eAgcxI-fc
z0&c2TUntm<i38#=y%5xn5pYbX4duySA#34_B(QxCD({H`Vk!&j5aBSZmw!LkM;cI8
z&dgi>>zbZDeqAPz054XAQzVL|9`9CkOag!J9|=s2aZ2^=^NXwqDx{06)}M!{&>2Br
zF069$i$73yV3J;_u9-REZawJ|5rJF*Zv*gJ=EQHIHq1zXRed&1{|MTbwrY_rlI@Xy
zSQsue>bxF71+EBvPZ4A0#?rPoLAU*L{5xl<wE?`J%yL$!us}KuUzLL#5lYMv_n9SW
zmKY+_BJ+`d$V=S>PE2Myh;df=RPW+_)(?d~9Z6C0vbU`7z5I(?WM_2RDu~z;D6vs;
z?Fpm50NDl|50*BJLIi7~x6_flLQK3ei4Dfb#PIkDYBV3mbkMS*-XQ@wP|@vyLye4l
ztwV8Ppnf&1=sL`$8_?nf6u?0)=F`hDcr9A81I+MiPE#uM#X#G@pWx=@<>v>aoOf@a
z%13|Qy+JERkD_KHp>}=17FL4sCa4F;m__rkKv3ZE=V2R!P8#q*hr_UQ+GZ=?^D!_&
z42(zSYj30Na`QB$Khq0pS^N~C)zqz-X(j^Q{uU<WK{GHtIEn~zR@M|qbC(TV1ct!F
zy=0=$!!u3i^M4B%nua$az}g<seAJ+2*U+j}vfTJD@LQzG9s<l^>o2=b*YiBhQGHIZ
zxq(`%>)Z5JXUnsTiHs<h8qvZE=MSXM81{VZ{SRV7kiC?zo6S<ln8PIeyKBv2`VB5$
zQc1%Z@k6A-eK(c4C=i=%cxE{>Uda;?e}LcXF$UFFk2pp?3Coe+bsX)}&5tZD6Vj0U
z4<esqFHi8vk>Zq_Pbld6hDM$>$rFqX`@36?Pt}e&%3VEUFR0Xx`>P?P%XE{9S0h%K
zA&itadKj_HpH3{kAKf~)GgYMoclD90isr}3B|ryBEIjqeZ9xk-w=R95Py4m1q*OB7
zv%~SUpBmD7Z~DNhbdwY%jWH+T6ArVmW#z57v^jeugTqUh$=4BHj741laQ-X;Bj??z
z+R31>gb0(I&PD}&?#51+ASBi#O0nO_%j?vNlY__^IuL}sP(tT_VuZ-y)%p@CIN*lv
zUw<<6OTgd8M#3cnhA>iR<e*UUM#k#`YMOt+k+|Boy@+I2tG`WFYZX>jghhMRrcnnJ
z^M(kz?P~*dLf}5rH_A#2ldhJocB$DS<Eyg)63S3ErZvNi;n`3KwLMw#i8fv~y^x(1
zZRW3B0wtD1!G5jzrsuDicGqT5I5DLhUq`{ARcWq(MwEC=MN^;llvRGBW9xl%9A1yS
zil3kYdPe@~0daC$7S^0T7T4VAc|twlNajP#xfb2n0@Z+WS+kqo4qf@^sM=Qe8*%|8
zM58CY8+knWsJ&Ku50?e6uifo~fJFcu2w;UM(>V&hRWJx(I=%+ZHw_y@z7Jn99IuCv
z+GbDMp%D!1oEdolS$2=Y03NK{yOl5Gsc!1jsgXu_%kvjP<7O>-xdYL>`*xLey0)9G
z&%~K<6n7jO9((Xg(vKHq!h*R!G^Ib3*O-wc;2iFs;0R-rC-5%PExJ!)1mrvp{0hZs
zfsN=OpXT(@bplO1ksiO>LQQ?@P=4OV=SiFVMb;riwRivD-m`!7u=ev$0z=?m?D8v&
zN>#2WPYy#r@t#QaH|<Z()paT1ZI+3&fyTLYqO~jA@&S2yICoNi%Pk4wt+q}gQAHX|
zrcQ{W{*R@zj*9yGzP<tyN;62OL&}Hll%c!3q(SL!M7mQ_Kw3ahx<RR-k(Tc6Zunik
z&$AZGKL*w;Vcz%NbI;lPwejZcfD;JVtRA=h?>^r3``-#v_z1SG9&7_=tfO;rg!K-m
z-fRC8dy#L`Gk#Pc>1LPMzS%Em@$Nzg5Xk!8q^r9iX5fDeG_HE5>)l-5;4YSe2Z>%)
z|GI0#uLZ8+xZsRcF(WIptfj`js`t^o<w3=HkK$U0YtI_*fv>S3prC@i6#SY;fI``=
zywc7nmzibsNRvJdE^VC$?mS{&T+C=X)bF@-ABaWt9{qEr8B1)GIb(3NUO}Qwe`sfq
zUT|A^lb|BOf`mGfQQ2q+w%;NDm)uC9;<!N=Eu<t%V*F1~LVwVdUWR*5&gK54z5RpM
zGx~(SIM0Y5!o6{xCk}=;-1M(i(Njiaq4yFK5MbFs60Ogh<q(%|0(w87%k)|!&I7`)
zH&q2i-P6}@F8r80DJ23QCjR&Ik$@npE(L($=8In(vnkNGGbY{<er+||;hOhbH*ch1
zV#aeW&Kyll3mDc_dnn4;2J?Qu|IvnL`bMYqJX+1?Y8wG8RFv-q@FG>~)5QmO5y0AD
z=h9jF2$YUaf^eXeh!y%zIT>2nOGpB^j}3pWKT=)0eAQA^IJgpaHCP8f2R{{i@;$~3
z15$rxdB4&9k+a{$1wI%Mt#8Fs8G0F~zu|~inObf4D(h;y*|uzUbxY<MmN(sU|1eH8
zlV|x;WS<^i^=T3nevuEA@irqw6%_HYqUAqxdCmnitwkR_XOS_40K&eK!b5)=BY7VL
zgEZM0igF^8*V^s7q29%1XiaXp+33TirZiNid5y6pGv)(5R#K3a7Js;X@)biBrJo6E
zr-2xJeUHyVj~B*FdDO0;9)Cz?iSsh@or`ilFQwE5gOFw(bX)p+Pl71D4bt<7q<7eq
zL6MZ~0^vi^*kPD{+Fh^uf_9csY%!5vCYXIIDZ*}FkGH84D%jFxj!v#AjY)#afU~&b
zUmkwGmIjf+tT(H(kiS;SP~ba%6T5U`Q&Sy_!dFS9|Je<s)Mb7GqE;>&=Z8p|#$>sc
z5t@I-MH*8YK+kJpQTe;afmlO>+)9cS`?=j#h4qxx4cXV<qVW(Hojj|xuu@vIb;S)B
z{Lm?fFEnRMN&g+22~lCs_L#JE=QycTEKQj#a*0ixa%7PBa{;2@xKG-tZwg`)lwZ03
zx{l~(YbK98R+N?&kLph1ZnxSaEy*`!BwCSuE~Y5iJDL#1M41<x*GG$rrlYC?jZRJI
zQXeIhjri<n7HLc`!_NLv_UDiL&CxYNnp0@bQ5+41noM4QMcHDYqGoodasm)dVD}`*
z%J+VgiM7C?lZl^9&M75~r3Y|!+}@xD%U?tLN)Hq`-pg*Og_5*n-e#hYfuFDu7O@;j
z{ref*pD<7hcyT=F=OFG=U4e>-=Wli9yd{-WiCwKtJF5xtg1yo9_4EDO=uMQSN)>sr
z$N?DodHDEHlM$#w1#(Cj8w{744G$}ubr&yqMUyn=fJazV8aoI~XGusD(iI|I_$3*w
z6NYJOcMkH*&QNn*+!VeLv6wqFKbt+RQx&Xx8wr&GTB;B^>q6RBpp5ucCv#iq9{p68
z2yNJFg6SS>6sgB;hyl>@Q5%1wKY8PQp$wi^N_-x|p(565f!ntd$tWC;x8l_0mk779
zOBSk}@PGT7x!I+6taaN$QRSsjJlfh-Jfus*@pEbdtKp_DRl)C#Had1|tS$W>Z)5<P
zBlJT^)#;$<1ip)itoNh>hEO3^YPb>XY1+Z7?~l*IWO{pwWSpVQdu5D4br+WNUH)6|
zbHiT&BtJ}UoeBFm6Y`g@c+fhS5l}RksrzL(8-fUa;Dlka?bGM{%Ken{D_)s(oB@nY
zP;mgp8?7BVz=IzlA|W4<*lQ2V>rrG2;ttER1~%kF;lDV1SRy;~RvH?)68q$EzS_s0
zuOsLN;C8<ftz`j9$-B$9_NF?Q%tL{cot3bMJr<Ga({vz1X?x7r<aP830=?<q=M%4d
z8SMhIZCZ!BHb{5ff>TYDSu1_2&WP2HRbpuA4pG0`@@hP|T*D#fOlrs8T#6KQ5Sb2j
z_OH_ZmQ$-C|8&@M9+^SiA-~~%aHT_W|7=nG&Yaf6Gj_KJJ;O4Wg0`)7zhc<j&;9ZQ
zmB>Kx$m9Uay*ZYNL7v8N@t8jr0iX+a8QB1JI0dtfLIVP<r@b>?rc<i`#G`M$N`4~Q
z?iL0|kGLLJ>+-`vXiOFZ2!p=6arHEp87TSK-x`$Je;&$P=@H2)U`m}{xU}~>*QUl6
z$XQPjKP!J@ywsAMJpsf8+qXK70zmF4R=}BlW5db`PWnt%7kmRXAZxT<VT+!i@M*Lp
z2CC7&2fPD|KL9Ys^bOI|HaSqtw&1aknkH|f6tXW0t}&XW3X-p^!EL9*o8Yy>+$ZHQ
zGA>qg9qLSWK6bse3?qR*Mvq&sCimuV=U5@YJp_FCCquVWMC7s@>axd!KQq^^0Az!l
zh??BnMe$!cb)sAs{W>oCX6+(6*}(lF7ErVMfHT(AKJ=-rmXy1&XV;Wt;cB4Sf*iAo
z6N2(_ORdyZ$KWU4L0@gu=euI{z265-Kxrj!%v*JC*sct+ew~zN0O}6w$;M5p_)8wU
zR+_}9>!kes?UYIZClxpB>a5NIW{ikilJw^lH})0kU6yc4`0qEU8A!&FscuLTLw_Ab
z-k>)HwbNQRe`ZS4UU&h+dG<NzK`_8-ta8zFZN>mA@Q=8OKi~{%I=fH8utV<7Hnpy{
z5;N}3vD!S$%-?G1a;8s~iy~4{clRkq4tIQl$_xx7NkbKcuRO8<lA`oulTx>P`^X!b
zn1Q4x&QaRHL8Fv+&ffUdpPk`&X!vTe^#W6K7z@IW-y35$=EC;+>+5qwg?Oe)`bQ3Q
zq-FvO`?{CT*`fc9`3?Ke`KIPdr-s}}6Y)ea#mi)P?`*vg4YO_Xmj8=|Qo?AO$~daV
zIr19z_rvULy3!n`hFXs~-quYX8l`=x`Y6yUS8Ut-<avt}6!2}nHavs>Lpx|KWMWt7
z{dXs%Iy<^eSO7bz_}E1T0Z+}v6WHV0=QGf20TqovdeR)mA{H=HS7b_*52rlgEY>Q~
zfcyZ=TNv=wfZ$0PE3Jl3j$LdTVlcZ(kZlNe@?8n3Ey{_3%7A(L^@bkZ^gkO%bGyu4
z9_|bI{yo5-0+MF`^NwLpp!WxlENB|2Fy`~J>*YRqNz#Sf9{-56Q4*v0c|IT$5KQ(K
z;nJV{XE|dwuyj7Ari7n(=O~&$eJ`w_mW9TB;nuT`J1_uAYtxyo#X=Jc*nGh>_ajab
zUK@pjg#aiuPx3SsEY;+^fltR3OkjW)*s$$Ojs9X#H+07fPbNXy!bF~e!Z>dEa=jfG
zmZIL6(CB`beNH2d9e!F$356|F2Q_`c{qHCano0SCIw%rKBt+$pfr`^k2fb-vv_xyy
zjQz8f#~=Y=5bgIwp%Q!tiyxDQ1r*Vz^8S8Ut{0xfOsDomef}!)i<EZBEg+MlEFro3
z_n5DOmSlVyZY#w?oy<FtOcy7?VGugd(UBJF7PWu%Iz{jFs|<xPJNLlI8mH!aHOCK3
zE}B-i1{*Vxgq4b#a^Nm|uekM03Cqmd-#QEhO(vQ8(#-X;_HXtbMaZWcLuE(<e8GFI
z&hI@cXgJspyQoMchr`d|mEZT;lsc5z2E)o~$EKpQ;P7*VgA^sa3b;_a5JE(q%l*MA
zvJ(B%b3jNgn^(dPkHx%9ZH^DTGhA)J{#?F3TB8rH7y~RefZJ3&AplfyZt!ikX0Ed=
zo1k22l!I??W#YoNd9#!XMrbCTvlo>pS<*NGiYA7fVfp%bMn-%?zu}(2la%`@2^$tq
z!>N!nQVq1J)M2d}RM}C4@RHAkZ+lR#_9`LPUz175O3IkucoJwN*Ufxn#`oWHnPzzf
zWpJwYCuQ!4eF;?gJq{M|1_`JwHbAC)1O6cnjVRShirm%^<FMTqN&RI8WP4m(qwWJ{
zE6~KtI#D-lAjfVHc7qqpZz13&Fi~|5Ric4m<&&nxk=`kS^_R7_NH^AQP<z+8)^P`a
ztviMokpyaNx%>0DI2uH3%3kq+cWDpIfzWL$RovN(j^hpGd}w7ZPLP2e7I9xfIFzXR
z>m_!(<Px>VnN8etOoHTfNiTJ!{m!?<s91Vpjsj1*<1>_>r;$bm=H@kuEhF>pd?sv}
z`rLmm{Z>hflwxv7pUw8-32W5-saWH*e{B?2eH8?vq>uDBct5(OiRj$Do!n>79%nhZ
z#apC-1ab@gz5pX=ZF&FvS5ea64aDX<8u?HWm}cka-><}hjlLqaf(~&@<}>zRI{|^6
z{Bx>HgvLJKLL3Sxr-8&2ms=!#h)`h6Q>&F^@!=a8kVHjWxGRO^8h_}#WPRzG&Pupj
z7YY@n%3c$>j&1#O{Ynln3F9g5_C0r8cU#e^1V!>yZBGwSraT|>Jk>P{)uq|E(l+<f
z91VRvlL0Mo=My4w0)(xpNXn_%%`2fR+Ka`ZqRs1VKW^LUrQuo`kAS?w8W7n^4Ea}7
zTi(`_iPEEzW-AR#Z9afu6|isgn63Eizl8%4`3iVfTr|Y}Puy>viU}7z9(u|)>*eBD
zjCY0yEPfk{X_(2Yc^8i90Vy?DUq%lTmH_lfW;zJ0L5v@FF%112OX?b~m(FV@DjQr}
zqk)_OkT;y+pH_MtLVyBVRc19O`~}u$R#csaig0XJ&Mf!=f9HyqQs>EZ86M(XB(Mk(
zh33TM^$|VeWD}>?SEq?(>XObd>Qc5;{zA&;_*K}O4Z=)GO>0`Mh4v|E&Xgxayvh|#
z^c}rEgfAdSQeOZgA!@u-7suO?P+^E-$62==Zjm=ATO(6uJ5o*BeQKSRK}<z7HgchD
zhUxH#`uSJg>f?AhJMXjk4V2GNnRt$EkE|)9%=P)ppK8Umm-0jj=Hc-<=)j`TrOe>_
z9^s0ez3~SQ_DT@Bql5&ArJ|B9aSVwP{JEBuw=-$&VJlo}RJbyUCUFJvzkiPTDuGGp
zm*`)_MYRZoH1Gdxp7d~k%C|E@gToB&Tofu_#5438VkY0)Gt0%s7UVLXEJQNm6nqs9
zL$q2PFlKQpE$LA?THU@G7cgO+T#TH(<sKU+q!^?I&LN@6Ns=dUA=vD7now5i`ld=#
zuva|KHW1_WZ1b$u=%J~ZjG&)Jzm|xC+leM7S~D#HW;Yr+6Rx#8b=cl=zCZ)02`GnI
z0vs{cTj*a@^+9$NfasLDUKk|zRMR>QltqShc|4rbOipHiG6YPj0cr%a=f3SSre7>M
z-=vna34NVCzHBUH4WmE6QfYhKLU$!c0ZN7p1<;rS=uhsqvvMSy>D&Ocx#0Q84_cN$
zN6;c4ecwhxg#@$>U`zzUGcwN&^w((6Btyo4_B_T~kRM}IppUZOERq4#B33Uo;o;p8
zmUaB-zYw455yAv0&RC4|M@HATyr|e?vG(_~%5?662Zm>KE0^Rc?2B9XyBFKDhEv`i
zE;cE0{TX*F?Sd&OJoObS>${dQ%6-t0ngO5@sndHWh=I7J_$s^X=N<MiHWF19h2Y>v
zbg$++DL=g@hfFkRU9_ENRsl_BzV7Z`gR%xBZM#?S3HU`wEK8y7l|$VN9p_bC8gbC;
zG(nDEZ3xQQf~=D+lH4L6Y6`En?0EX=JftQsb`d;ZDJ}=hNaUMF*;vkXqT<b@M(=kF
zTQ4B)9I3p5(mf|?wVLxUfA2rEt{Ez?I3mjf&E@=?zt}IN5!-F&_%GZ2#@017!mFX#
z@fs8Fe=HK+*9r<JKY;_!%mP3m(fT;G+2Cc1F?(@vTML_GcWh`-Uk{A6i&O0KIE~J0
zcCbs>%+7c>VaB<wY2Y8%pilU6vgAKA9Z6LBDS?0G1ZkCfc?TEvM6tWgCoAYcE(0pW
zD<1y~901q?vD1_X{vq!L$ZJ=RAEZuuTB0MgjIx${<ilMU!8NbR(x)MNGd6=?3LbfR
zcjwsiUT{Con_*X}!)r@)Bn1I*@Pal&1&|?nwj{$?SCMTGNk)&|)-Qu0GCDKvg&~xq
zR|Yz^4#y{q{-=2?4qr2Qpb!a*50$@3ev(nW9-~+rA%6)&HIp!LX$;%-0Ab^v1tFU^
z4!=*(5e2WG`c<6&>^l~Q9Z@{X0!3-<PHv866r)rAS-D)bJ(N=5h`fUfKL4SS;X<0?
z1-EeHRbsne6G-P0%D`wE^bibWF69)A>~j0^#V+t?Ea{s9q53zb*e^f7|E=szNZ;ZT
zFI@G3WuHbOS*50D;)Igm!1GOiUFhPwWN5j2GDDgtWP2#M;qySl09xUS>0RX=+i50E
zc@4o)R~|<V(fdziR1*8vBIsT4f}E>rYScg>1)JQYQ#gsTI)q4JyT5wRgc3Ih%dGDW
zP{MR(J<s(6+g~^xX7|nQJK+>c93F6NS61trn&$nPJsbptKQrs%n|Ft-sIc_^BI_0#
zy03>*q>D^_*3a_*?#N?*ok(57ld|}^Mm(R8ka&yjsn(%BOa*$f-H9m24qZVG$vKho
zKO#Q&O1aK37jFC24$w_n<>gYM+qdH5Mp8Ci0OoUjwCWi{M)U;oYrXkm`ec-Gbv{JN
zHZbZsMKlx^7Df%*L&R<QJ;Lz-xXT*?Kr5ll&;|6*yyb2GeOz?)DK|7I(%d}(bi0$j
z$T86Sl2^b7<yfbw7bo}G-x^Y;ep5i98+D2X)Bo&Dqg=4GO5o|T=|1<RaL*@itI1Bq
zmX;m!l+{F2Po+4MHM^kBdn-W{C1cudfQ<qtgj_%%<}-4$zsK*t6~ENslH|sDgU`Xr
zb^e}gCg|Jf!RX!$XCr3bHGH+O29W2geM8>`1;M`czKnq8^}RG$EHH5=WKZ038lRhO
z?GKsn#>%T^p##B%VHKwIj5*j>)N{HHyAcu0Z>>%Y2CypH$P5%T;_RINdaF{(jfxcw
z3DVy%NEq~++qML(-rSn7p;B$R8BB7ggS|9rp>xfcu9dCpJ-@Kz?4eyh@1BuJ8I8<$
zwr*1~j~uvqGYr-sLRR^_RnWr(5nD;y=!|p8+QU55K$7Yo!5aaSM+zrnavD$_wt}HO
zxYrgZ$p{vzF+ss11aA*w1SV=7K~^f93cbTO<`ze;{)v>P{e2e$*ebwW8ie=aC*-Sc
z_zL`xs}yG@gC8T14x7>gWG*MgzdH#HkX>N`h%Le-FEl&eVaIM?`2kA^(4o0B+I8YC
z6zu^{|7|H?5>N79`Grvgp<|hYosNw?Npvj9Adu0|9uJ5E0Lp&0aYHgnVd@kI-hFs`
z-8SISo_-e~mhj$#chF2|7|f@DAZ)PEb=WZn8_XOIK4g9<69d0SSuMzfX|VY$t{=Ox
zud4pD$pEGQ0$6c@&UPKRL3d9xaH>2*E1@g=!LS4%EC&b_n=(XlE|7OOW3jgP^#mb`
zT<%1NYm?~z^U8l=1;HGQ9Wy1T{wQnMT=p892crs?Gmkj@XR~O@n+z?5Go;B({&>wZ
zV{W19IhrnG7>lQMUe;^E<Ipg|SY=VObwgfNELeM};>iCmAeOpczOyQ-izBL=!+p+O
zgxMkiDHw*^p?vu7i#IMv+sVt*ahisAaJmX*zamJvrg-cU0O+-gar(d>+f%^LA|7OZ
zoP9k1>Ado<Cm@v)nnYMMCbb><$xUt|G5%Wjm}Y@qaQHClp4jpHk4`zLiNjL$m-C|O
zUmmr*A9l;{iSO7PGmAQ@&!P7&N_a)(K<2N6veprFh$8fQoLt^sL(=b)L@c!8rx(a$
zY`sh>LR}2`qy6}v{&fQ6l?+(3xwEdtT>N)C^L!fweSopE3plaP+0MPnsQN5RDTn&&
z9kH9&y~E7MO>OtoKbv_6$IWmw=Kb4f<!}pZfS_Kv2TGs6+M<3R3KFY;iYqmJU=@W5
zpyB}i<9h85T)nNboEm_rZ|>4Hka7(;!U3D)>MAh<Xk7>Vk7C=}L6zsiU%To_Hd`=V
zL)2SvboXh3Y*dqFagGwTBOs~&*(Gqr@;UmXK3>Hx{y%Qi-8M|=^32e~@YCjtyS<c@
zx|^Yg#Y!kued6{49ntRv^sCLGDCd(aRG@%%jt#~hk!qPUIiBHvr8Oy?Z;Bo*(U`xj
z|JnX7FomL2boN;+xzgl!k>3GSsA7U5Yf{+;1tT?lY?@|O)5duV-RFoaAwvVoF{^nJ
zA(b-EKI}91f1yp$;s#LS&#XY&qOP+%cZS;K^10UpSp;>PmwEAV2^USxv@+G)uSK%o
z%|R$TM?PU$KZ3wQGMwaw%)F$wkx45<-*6#+w;t><Z(pj3@fFJHbe|AGblT4m7h0SW
zyPN_|^IqsCcgS+#7DW>gv&hG?Cn*Rk&s1Q4{!rR4S=C{ATKca%lpu((q}_qJ>v)9v
zO#`H{<gcsX#w4S@UfI#m7m3E0$U^!gJ+ha@VQH>D)jb(>MVDOL!sw{aZHGl+EBbax
zT%}zl6YtsM#ZvHnaQ@q?dz(Ra#pFtyWFphO${(3YthqFLE)-J~%8LJ`z%H}e&;GA;
zGL5>qdjXkFvd4BXgJcK?Iu;pbY1L1zaT^_a5X4~(xUuD%tJlvP%M+rudm`kqQ5kEv
z+0^LB$5bHU+OW;`35|r~9*JMmwa1`qhsCCVp`a#BgU&SD;plVHfK-?hAGV8i*J1#u
zmsoa3z+VnHvAzvTZvUl#C_kY258Ax}()E>`-Aw4YSeUz^6lwrjV||X?AP7UV-#Ft;
z&&Sak^j6J7srLurUi;T`KPGTsM{`?8F#(avs53E<wEd~+vh$VO^~@Rj%nkK2!sKsq
zc2WBOwkn+=M#Qq0X@}8&@no6oPu>`#q_OnhN}J#7;z#Z1dAD+Gr6w76vp;{UiiW14
zqD;PY+plUrFq_wQ4)l+&veM!@6WJ$4=%JKpoV}amw(ly8lpr)t?}la2fa<k(Ks`QB
zDg?;g!B=XVPR{?};kT`|*dv0ulUpZ4-c!Kzc{1B}F4&;|*~Y?O2l4*Il_|9AoVYhN
z#`B%3XdQ}*I+Q()7x+YQ9W&F4sm~?Bk&MsHljr`cVY+jcinj`6Pda^U6E@mVYI{Vp
zZ*@!pu44MvwMvirKWpn-b*VDKRBT<ZAAT~&$)tBi&DLxpMUuG68~Bor&L9f@*_zr+
zEoKwaSpv>Dz-K+W@Sgg`WDn<St`D3iyT7M2JWW6X9y*{XF?!r_EG&E(J9l+p7c~e8
zr$JBH<~^>KDJD?n9Dti*bNpWIdg|LyqrNCVJaymP)MlExE=y5z@-1usGVzjZmMSIe
zcr@OT9WBv>HUNpU3Dfx_zMqp{%!KYMmZNwmk%0#AjINp%(0?Ngsb&fl@jZMcyNzW3
zHFa(NZKMsSfD2RTn>Q~Mqwx8Jbvwsv%4DoSar)uE*7}C-*x})kE$you%JPrRJ}zHb
z(HZh_L74sOb+hv|?V*vung9#AW!3a@Wbl*WfsALw>+`_1`d#aQL=bim?AL;ovunY?
zqMuW6A^r=PX~<CVF>VAjK8A$8QfA7vp;mWelfcfw(Hg|SkEo{=$dZXgr^osp(A#Hy
z6;3*=7eVE3m4l7&r88H2;F_+UC5(t*>{t0vg^DJ@sq-qB5<*3VKzH=-mmaAC0a2vo
zReqy5+#OB4M_W(~HgR2DJ5Zn9uvs2Ko%j8uya6)->bx;dNEd?vPKTo$bas%uGs&G{
zlbk^x(XPxU(PBJOLk({S5bc!cJO;qKbug`fG2^|-h*2wZ2ixd%*UJWZQne}VSsO4n
zj#-UY>;g?6Nm=V1g-FomNq%zThhGJTQ-&IcnR@%2Z6iDpS8S#)U0YYLcojR<(L3S*
z)>K(z`!|=|&3XR1tJO7G@(->cfWndg=j=bUn`YVVv1B}Qs7LALjvHUDY&58F=I^$P
zj-(RT4pQC9;WdLVMd^7t*u{JHn<nd2>BXqNyZ>j>7?Q)tX&d^Xu74u>CEhe=2^4RP
zliV^@>x^rPd^uMhyWqt^K{Q=Idt)IwVZ?1v=fi-e`0#VjHtVR+=OU=?W>Gex2>YT$
z5qbyf-YIX`**v*(ah3YCA34RwAe;)z<KZen*v)sNoM12tI*;E<oB;rS+r{SY9rne|
za0|G%?Z<Q!WwWpY_t7+mO1fPke0=thXN#Zw<HTgGBn`@Qon#=q1oDuIc&5!E#lPG2
zPo!C`pJjmJg4pi_R79e~&pwD`s2KEj85UPmOhYqc;=`Vrux8f_N&C99CVn;DyG4cH
zYZ~wF?pzB)oY&OqKL14c_oJ@2VCAVT@(krw$6ufoIC`pg@zwMjY9(tXb0*wSu|zF3
zlc7+Zc2;!|#MXRs!ug~mQ{FzdpFvl8O&?<cd|xXJi7QqYjs(`9;9*bQ52+SY6>E1#
z!R*6kkI#>Lhxo<rOw3H>r;B%k-cbbXkOW6?a)E(u5nU)B7aNFl>crT89A5B8(Mevv
z^j+H2_s@3U=6GAh*zfMD<<0S$1Chr8i5`JU6<0zf?wfX+`HyPduI_RZ9&QtS^x*23
z+u8Hq2q6r*(v+y!gy<Hm<Qzg{V`HtQ{TXKmp3e6|w{TyUeshb4A3Hncm(g40C70#?
zmkZ8Amp=ZBEdRmtW)6-o+pdwdK>WsqIP7azg<0u@gqB7#>x#(Dx)wveZMs3q&o<u}
z`)21Xty`!bUj}s;uItL<Rgs8UbKH8J$SFDsTvj_ovSxnumcnrP(DxL>i6OFB6;o}>
z>O!Ae&wxGoPch=^-NA6%fMnj_ie}*Bb%x0Llp((iO-fE`#mIrGE}0~okjRq%!v@K-
zJCdJ5gYpIMgl#J(4vsI@%^%wQAMhSljXb0A#`2OX8T_^zOno-4NFR@8?MKgjx=(Zr
z1=$Dpq}fRl+0SF=IeMZI(px*~w1$_(pA!w54O&<HEpslY>RKOqtqA#s796Y?U7AU(
zC7{8Xqs*?VZ>^=XH7>o2oSwTB^n8a*v9HpF-Fg=@Q!~vYi1*<k>j>lfM3cV3_miDh
zD2^?kcothEA#lRRZURH0_HNCLOA+1nQ|cgu0$94@l$^BGRFP`mQI}Ti$?`RRdD-|o
z*`R0r>|rJ{OH!yv#@Nfe!s&&=%4vVTl<I-Utjnm?FW#cmeR1}BTTe?H+@kOPLDler
zeYJvZJYAXHldmG9r>0MKd{0=nU8e46^DM$yVq5xryh3nF>wn%pK&c~Wv`SowV>&d8
zLUW1<OJw;H3%7YW$p{Sg@pKUGSkaKv7}w|vY`QCTTr_B65^?K4)WIc-IzCiI7k-!D
zsCwpM++*~$rBj^>-d{DAq{{upCE{2=q(CyVE=B7)*Y_wO5y;$(A!E*Ww*WG1)T6!P
z^?aEOc_qE@y-xRE&O2tRAZc37gE(p;I9vJdB0kQ^uO$=}RahhZyCTkKo5}Xt1B38_
zkBrk%u2MCHhf=&l2jtq>oPx}@_eE&wB~M;>6VBmnwXri&fL-FI@T+dG3I1>4YFdL7
z-d4I3%o=6Q?S0qbe<CJ)+6N4RT1M1~6@P1*J|gyAa~5GK#ml4t5vuzO4V4}<c|#w&
zn6V;@qx-m;Xj%{rvf$?)5Ia-`)Onq*?n?D!l*zb@Sl5&8!$%|2_z$O#t1K$ag);L_
z%)_MVOaBH?r;}u+6;8hp#2k$tBMw9_{&kN(k`lRlCK5%+jU~1h9Da=O#VO=**Z;Uw
zzqzt^c%ii~!`>**@bF+(7$V_dWfufsJw`X}j@?qH@(Qmj_U~Vj`YO|xw0G*8|H~#e
zk*4>X!Rf-4K<$p?qm9r3Urx2X7Nv58a1bsw^{Uo<x+3a!eF%4UYzwrQ%R4li<hacj
zIG4%0*phSDbOzW|22=+At*O1%nUzOQ0ysN5G6Xo56(9L|d50MTe9kI<+lgFlN;(ah
zZx$MnsJd2d&8pdh-6eB9ZY5mhyO&&!BhDrY8F5YAUst7_F(|=kX3d?Do9x%6b<UHZ
zmE)_d4Y%FVH~5LupXvqAnRF!VwX79098C^Ds;upmW*%HKg$(4rd?BXNYelOw55s?1
zn5)8RgK7SD&E=JvhDxw(S08J3S==N#XAXOOAD&#ecmjvbXWsTmn7oFVmU^Mu3nzhm
z(cQ)n^Z7LS^ZTtVS+7I<1o7SV`sY~`lm$?9Q!~=P`_~?ZCq(xNE)3?m^~(69Q&Jk@
zs;yC!sMOVdsy6H%3BF`HFm}d>Z<|-CA(FyPO-93tVJoS>W9w_R*Y~b9bZt=<7q1&p
zsQ`8dM}iF~XuR)v72lODfa_DT3chG@>dX{wnC9PQ6Zhw0BSc*N@-z5I;g^xL>Mjzi
zCYAvzRXwO;Ft+4`kkwHqp|6yblDOv+L1e>un<&~|ZBc^gy}Gou<y8~=Ii-w=o{ov1
zD|WAKT)k3tSFCFm4wPl5w@P5+S|lVT5jobM^7m;GuYZ`&IkGPqzllf?HS`G_T{C{0
zY{K9;zZ66BbCzb9;*#kv9a8UFM2sJbQ8RtQ*;fI)Ml3{`NAqtB3mH9l2ux~HQ->|L
zr5|1<7c7n_{yv3y#XJ_v;QH&&+$g<5J|q{LVs()&K(7>)X8aPAvc~?}@vD5YoyII6
z)C;oAsoj%wv61N6CTo%C>wRbUw}J>&3FQ29_WjHX(}3hBLD(k^F7qgmX3dvi&_sya
zDD6(8EWbJK6;5&i2it;)XMtkV{;1W(g`hhcryeE@wfsNzcvYvR*RT<8*F8Tz_ZfCx
zZjL@PKB;TuSttVy3SFOvD6b7g$Ui(8)VOczeR0!PIG6WW?(N@(ae~1JK)n*3sZw1-
zbo((4iN82sl@?qy`gI4$={eYvH~;RTUN<Xn-+Fi^zoI($$3wW%`}>I510jwZqt(GF
zCd!sNh|-n_GWz;W1E&g;^*L!i)6&)R-E;0mk4=Qq^T~@F)pp4|upFeA>@T{ASuCzs
z)Ixuu3#DDxDMS!u$Z{(TpKf2EG}O4oe$mAfQzPoN<mKk7Y>AfT?h23%=vbwBU6(HX
z{>S0&_tKZc0}9H$g*Y(ffq(K4XZbIu;*J9~(Zq>eOdAH6nCS+g1!c%3%Jk-Hq}k;2
z59MEF*bIi8ZJdGzEl|YN`1p0Mkvh3vj+Th_jeEMTEh!ZEBo+$-HuYTfSy1Ncsp;vI
zNROdCvOE7+Hi<~(s-aq~D05xi2T@rEeTu23Q~A^Tc22HQhCt_($xofU4Z4S;+n&v*
z%P@A5tXdFzC<E*K5=kT*%;|@nGw*Z=#Soh17)J=p7avo%nSF0w7O)u{wU|fEicY-~
zP5!gZF`VMziaM*Vil_-&W^?s4n-5mEdu+LQ^<K-UQnCt8aW^s?mY0e+M&rciy%-gz
zHLuWGcdho2Ic>BlZ4u*GiVnT(Yi#OjxX^g$ZO?X~7wXCx7--!)O^ni(<(?t?%nO@R
zw=oc-)V6n57FXp?XXl)w%wKT!@N$aUhGmI(Y$B>t@p5}PH|UgYI+ST{@+fA0TfOzU
zA9x|mBhv3e1$Utu2LFm1)%<hN_w#X$Up2)yOigQV#HutC!3n{cx05H7l)kny%u#`i
zSzR1_|DdArVs<iACdeHv2i2)T;4LJOGFNwh@5ay@VpV65J~;m$6iKGno7U8LJ`^_c
zSHp?#EyLsdDKBZs#1LHfp(WenX$f(-C={qmt9c1WBl$h_D><(3(Au~9emV4cWcs)}
zD3o0WWt#+vFbb{LnH-Qv>&mqG-q2{TP_I&{KK33<n{L^(PzOzS6e?VjG@qf3C7TzE
zv0E-et=Icle9m^kJPXa0LZUS!f-GRvb39M+b+v1Alb6+C!FAeXa$_?qbMd$-C5Gai
zEMIje;Yv&#u8&Cm$QB3=>T<RB7Y=^b@t1x>Z5APvG7Q&9*PyHRtaDSyR`np1caVbA
z+y)A-$XhkzcwNYs{~^TVj;&cP`xz<~YxHi_j!cpA-^W00*f17vRsEmC$MvRWuf1p4
z0&G%jrk7tnJ%7BX@b`z?mPRB%Ef$t^*pDy~9cO)_<p(+stS{`pWi|Qj&04xGKG@2%
zPv)r%3EI%Z9CBGh%JnZ_G;KOJ2K;KAb*<8gbYiHg8#j=xt(_Ss&y~5gqLG{7u9e}T
zLZZktDgcDbohwL4IjwsH^*b20q;_G}cXa31lG#3K*`*-1L=Hi=)742s1)^FTV1#)b
zXeB^%VMk@Y5?<Z7u%^`ZK%T;EzsJX#Dx_@ju!NfJdycvfq9T_amPh$X^y=Q?7bLkf
zkstd03c~(u^!UZH4r7|)toAjky84M%^5^({d$mtVkSHcTq3D}u!%IaNuulaauk6HI
zHkB2pQyXIlLR@?(;I9b#Ex^bdnTmkB^nTPTT3dE<hD=lMzps>L4I}MXZ$?9UrFJud
zROA=fZ$C(g!cU7YNx5eXUXv(%Xd$<qGA$i5Ets|_SHIF0)A{Caf8o<;5G%j2oH8n*
zB44)9<#<8M$s}i)|Mgyb3`ax;`;)a*zAAFVSB1LWeeFroi~Bh*kXnYET6objqq&H+
zb#~|1dwcM*!KFK2TRv|-m~KsxRUy-f!5OYPYSC|OS|vl;D<%0|ME-v@6cLZmTU8Tc
z;xRP|RffQ{V%+{xjMnQiEGtg3nap{aQxJLNO~G_>YQ*1rWd+<R3(LqhZU)J9>FOi~
zmDZ8RPNUsL@`09^O2Q|&-6XLpV-R-h#3{q9&7M0#7C`~Hdz*jq`j?xS`)|+NSyu+8
z%_SL$KpfWJnoLC99oyE+1DemQw2fWKZ=y_I5@jsj?G+o#?qfHBNGg?5_p3mW8=^=#
z*U8EBD;{XAUZEtvEp0)csV8msD{*6S2;FKx08C{JH#oPj7$hZGe=r+;om`waNL%|N
z`;2V|TM0QNXa(=tbE^oav1g~<;#%RISg=VF+lAK3_MdG&31cX9AQI48fLw3iuI<Nx
z8$E1qWx|ys?K>kvnUO9|mm{uSF73vK3KLpx7^Qrlf<04H94@IyCstmkk-Tg>FKyV0
zt@F9J=QLyA`98d&^YBm&hkDu#vKmTNk~_z3MF?H)=0Tzn#Kiucn%U&fek?pCGmYHv
zqowXcfSJQY1AHmoTa?=t)Sx`YOjDB?NTQurR>D-xw{Tw6213pa#8anFPHbYHv3>KR
z*Bgo<i|(-DW1#gp9rAu<W9RC2PBg|Dd^|!*rzG#>Pzx*CbzHeZ(yPIo@Vcx$&zDaU
zm3!+N^l8}tg1)xk(vp+n2VO1%W9^4rv@fEqMSF?2FJGoBSE%D@pnow$M2$}hl5#|c
zK^e8E;u7{1q0qy)+TDPlDC=*fj4>2vi~l7UVt-?N$=9E|?)3~}LsGTaFg`AByNmpM
z!Y<ZpSX4_RUtZXoRQA6Dq$vys{l|Fh2uG%Em-$XHdn^$CC~PT`aMG%Tm>{ae9-c6m
z>S6b5^;YhpWk8?j_xWex_+zUWHq<x#WGR&Y^t#OSBo`4?=28%3rZg(2#rInYK(55R
z+btE>F`XgCZGH8*(o5uFeX4Bg>?(#7cKI@HUUxtI@1y&kO$(bsaJb$p>zd5{O$Rz?
z@g9!eAae|b4PID7(nR*}$1CZm0Gh$Q0Cv+nKFon69o=%AF18v;_o?4Md6R$GSAU=6
z4_~Y)sT@1XpFj0@Jeeua{aj(<rq{{ZiOmDMxV3r;@9H83@o`@y`x|7S-{`?D#lnUY
z{%UxTjl%%Ypjn~Fp;zjr()5_|=y!LlGBlw06)is$adNEb%OFVEx<IM9j2!XF9YD)V
z1#jkF{=>n?D=8_bYGlX3x~wlWlH_hij*gF2^`GHzEVZGCcXW|Ox5vR>XvQF>oE}EG
z?YQT`67&=gKdOl{3z^>B2K_%O?z$O+h1TZwJCATx?k=yYjxW)~hX#79n~H;=o>=oj
zr2IYV+E_j;SrtekXlO1pO(uv*!Oi#uBp4nP2PLRh*6Zh~_6nb^HdGX6Ws?|tm4HB>
zI@id<It7ZjxXTFo2ypEYUKwb>XEvIj;riar$+=<i7Bn;j+s?ief&E3jZ;i+Q-m}pF
zYwDG@e#t&>9FR<cL-uOYU1a5I#8LQmXW3hLNRQ1V*`wf&vww)crDu8jP6Y|OFU+0T
z()!BQkTEmY1oIw`DveO*2TzYK?eMU?lV6@}|2b-2*tSVl#~YfVa@&;<D!$pZvvFRO
zeu*II9t;W8hy9c+30YQ7*Ni)IdV72-<u7Ipi=GGD4`wm#;=*!FiQ!ZdsOnV0ZmuiO
z^d`7>N&aJ8-xH%t0fJ-OG8s#(bIf=Aw(J~g?ai?XQ*=bYT`AOCL13*1B$9^KaeOAZ
z^s$mJX7+EGm?s<$mF*0eEmN}?7cNhY^^gnWk&*~Q+!CqRC9g!q>o%(zC&kY$Z$ZO-
za#F;)$AW23EblJ!@rvMThG$`Oxb<3CPj8<LZ?Hffru+K!$F(YkEIzIp)3){T9LE?k
z!sVS0(NVVSn#Af<N7`R*(=ArsUh?>DYP?P^xpRM9%?5!*+b(Y8iQ@73num@Tcl=5K
zXr8S!UmI1(Xl9#85Ie}qV+ge+;&}_zSg)`a3-xHm4q=-w@6YzT7xFvnrm6ivmb>MZ
zt*?Q9!k1xmH7etG{8ougIGI9I4E<RAJ$PaRu)~cVX;Liwng`OlFiQ5x8N`aFPs3IS
zXIXzm-%@<CE|KkK_guGHskvB~&`2&(0D6+m7aqo)W6pR{7h=kv_C?)>PaEoMyL9su
z@^=63HGbu1?GA`X(3uriK>}A&sYsG~QEBiUC;jA71wWSyV$)zK+RfECeMq4R2|vq#
z(wLjzLR)QLyC#|3)V8Pagj?*GbE15b)0*leHxUgsDIo(Tl23L0kkZh94z^VRIVGU1
z7Ib~TC+Z(^+x?F3`g?pO?gWg{eCfhh)Gj#b?}10PE@oy-q&X2*fn!TehfVs8+q>TA
zMWG(_<@+DA`(EHqV#)Hu>3n9gyiZ(1AwkN>%P(d+jom_oPhaCjZGrRJ5n(w2Xv=py
z+G~B2VL<yFR<)_6f&_+MGW@m+YStHJ4%8`Jb$umO!8toW`1B|#6WCtOYs~%I4GnDW
zZ@8G)KSw%J-L~$tSZ=+%mkBCF#nh19y8o7x2E$~D3Nw?R<gDO~Ml3)u{(ANIwJNuy
zh=aL<{d66=iQRoBN)9a9&$k8cxin_O$4T7s;3@dEE-5L&aJXo~tu7GREzo@XUu}%}
z&i4-Wc5hf8cPb%^!^6r=R{sR>Dov7*W>NT>kqy`lo0=EIxT8F_`V3iAC$t<oDN-Rt
zAb_h<MVyImUd?W$F$9cZ0kcd=Fz1T5=3I#w`85;q%Z9ImXJ+xMQr*|q{Z#1gO5+D^
zLNjFUQy++@u(leWHx`;~%^;rRlhY#Gn$p^;GMn@IxqN;_Fy&4Ip*pVl$nD*PEZ$Yo
zi2(y8!<BKEEiq4xqV?=I4-|<5Y$aMy={)sUnrFU^?9GeQ!c=#BcGe)yRrr1D@*>Ua
z$NPC0Y@L3~$2OuN|9IwPzt7znz>*kXaY{PiF*sUTwr+h~HYYYfk(=TZ7V5k6NP~4R
z(B9b1TrkgSbPjgF|3od>w>m}CF|!<7iU>&6jJ=7Xw&_^<l817&z8S-&#_-;X(O_6g
z1EMam^n&Wpz+knd^sRVBerm;a=CE)___oSPv3OeD$ktJ)$n~cWO;S~xsvj>wb7eQ0
zyCJCy^h_3SPUL3SR<yE3x*OIN9=fm=3r1WW?&FfIkH!ZGjeM7RL%aJR98>+q_!3XA
zP+o5|ZSu7>N)UE~CHwQM@LdIN1O>sUb)pGj{O~j{2omNMV4kvT8YdAdsbT(7=>ZLl
zifwWhr2M=yNIvztr1}1!Ju6VjK#c)^>~3^88-xtcb1rFU{MjzDBqZrQPWfpBMa?CX
zN#soiKgy*)wfQAw10>kKKl^!p?-G^amr+&LKYmB+=X3kcfbuW?m+Z-fHU>_~XNebE
zcvAE`C4Hcg=OUP`JG?x;MwnbkBQqQ$H+$~k=Y>o4Z5JgUV>L!LF4M0r_9McwAMmMN
zo;A;~aHb2@mXLV~`Abb;p7qDEzfP<6GzuV9;%6s{1S=`I;j(5HNR-cKUjJ-yy2`ml
z!Ca^+OYZ3E-*rD5W&#QkrPnG4&YyUAQ{rWlD@FuKGWHGjUx0#fE||+kZ*yz8;^8Jc
ziSE)uaLD#P5uxC4UXVwx8w>OJPnvmS%RE|_+icFn&i;*W&2--6PCPqC{U0@-Pw;I+
zGNcK7C+?rEE~xP11}EE(Q|pPJk`KzmSB*)>90eDenh`$vMHY;CF!Wc2(h-fm6GLb9
z5GEcZ7r8r@NY>mDsO8zN?%fn|4tjHH>K#H2p2i{!G1#%%O9c(kC3{@A_l>8Iu|MS#
z<TPA)yqGo0NtKDOKv&mTUeXR<yx!yRIlndyQi-BQVo-x~y9hh`yl$e{GuioE0SkFt
zUVOxOxjk!?YUBe-RWd?L&g?&p0smC+|ETjx3HzpkZ4XH$;aLg&=dZT$a%tKjwFaX^
z-Mwsg?Nw40F3~Z&ROShHf(gTMjmGae40=z!+s+t8A)sSrhfOP42SmQ~pv&w*6`4ar
z^9!$l^tyWRPX(?q1n;utc(hQI$~LiqW<>QFun@AOamZ`E>~vgN&Sm^;vT>0RF;DfE
zYdywdxFQKjWnh&Yx7eDIE>;NyDqHFbV6juOu|6yV!01eWXs_V&Xd6;FFQHhT#m2t6
z)=Qk|jRP|8Pb@wM^zc|kWd=*PGr>M{TZqK6mfx}U&{u=yB71{*M*$V6j;`HN+e6jV
z^`Mb|jAeFOgT2$a#{qU5&!a$)qjYm*b{uSl$YZyzYP)zgd4h92rqvbqsN)JRBc`O3
zk*~jV(pCOHG#S-TxweTMgZr1U9~hK^F4x*k@W<p~mgKZG4z@Xc>u)o>y=F@y+V|ws
z;!l1-PyLjE4*q-`V)Ph!sRF6k<!G$emrBT=IYl)*S0Pm^bG<&w!*86Q*N}^#1{`vy
zwVo@)TgxGG`Y~r8Vcx3hT_FNwoWth2cfyv(4O21SO8V&dzncG>6d|X7JxVI5-0((c
z_j)Aj^|N!g*x(xek2T!WNeyIu3AGr8!j4N7)DRTbn_AZ3_60CyjM(P;Q+`OVHbux{
z&c|z*tJ)LC9-Wb;F#A^}>(hm2n70_I99Z)r-kZeH-TS^?R7kb94m)dS3J-hWxQ2q`
z+D|qIH6Zt8j8g2um2WpYA0LO?tR>M$%hS8?(epK74ODfp<>|mg0cL@OVb+AUmQE>D
z(LPS_;N}VVh`b}EtBR=1MixpQR_;5P4*)NpuC5EEG~m?6V;8Io*j#p-^0;ECO&xeJ
zxx*4zJyA?(6lJw3+)X4jkP`7;)RuUc#(CWnttZ0i>N?!X;h4LDCam@79bsQ4XhG~w
zx#8@LYoY!agh_65X%F=jMGAz%!o9_&G(blxFBER=t}iUu^m+GS&iLR$klA42y>$Z!
zo(bp;Z}$aJbZ6*N>{UEj^UQJ!t+skC_d>bn(UX_3l}E^Ya`TnU?{|FPzwapE@gm#^
z|C|!>Rt;esw20Mhi9Dpi6TCIJ;W$d0oBL4JIx@!*C8_cv?~RUAN6droA672eE|--}
zi(Qu{fzmv1-2lp@($!oN;tMhLKv@Rs8hx<(&n4}roZK}uq^FUuzba5YE)_(5QMG7t
z@v7tIPfh?S)S5M7V890i;d_18D1UyH`3nL~tXp5b>GZ?Wd_4)LhQyS{XV!Ks*qt9m
z*I)Mx;kzp;h-hD{Gee6RHf3GEThO~HbtW}BTjGC(eri13qcyP{i56jSh$!JQ@AI0Q
zp&c!W?YGva#eS?S*kXcwgbT;uBS)nYUs-i63XmX_1SO5%ue#nlIL7>6kM#mEF#Txr
zxnC*o2kB9MXNmm)xYxTT9xqE1c*8($HohbDFy(*orku%UWZ})ZQ+~qw)d-rQ-!UbM
zrPPJ`udT+uk3UIaWB8hyBwzWOWJ`UURH3NU+@-dyw}G+RhQ-HC{=2X8)h@FtOVRKZ
zniN~1e&KauIG>vs+G}pM$6&v9-_gaG=+;3uFphh>ZY)UV|AJu@t7`9pijLFIIChmh
zK%KxnY;CLGM2ade7WBS(=3Mo~S15$;MPp&ExjN=>>~iDt!{)Z?HvzNz*S{u~2kXk6
zK;5N8w&=OyD6({mBXZMA1GbNx%{{}1G?|R2U$9d<OaA5$9z2$eNQy@tUF=Pad)B{r
zTz-RCXM)MA)t@aLKOaUp<Q4p!5PyW&-meDm#-MdrDOF;Z-*z2@6k%S7=@jmo*#uU!
z!j2`C7U3AGeSS_i3v@rNUv5`7lq%Ul;4Yb;+*!)0wOjUY<6-Ik?t3&zx2a)dD`RLf
zxvh4bO-&a{7zQBSPF=$%cVbHn-BE-PHv)WAVL9~Ss&IC$I|KDFQ9>Z8b~MPQk5EaP
zZ($Wtq=zXp<pX7><NL<W8;g(dZcW+nLlh9}${v9YNI+lPE6?C3U&+xE`n9;hp%wWt
zQX_pZQ?4WE*(`TzCd29VFe!i<EUGxN9*Jd=vK$2uljS{uss5B_X4IU&R&Bq2wF_)R
zL=^ptV`<eL<a&nD&ikdDf!v~`3!JMz(eU-SJX<{yrq42E5J$AWrxhwLg^CNzT^d84
zZWwMY@SD~}tm+wNKkNjVjBu_Fq5O%%;5D5{khlI?YgayofPO>OY6hMM+2IqmZ)^HJ
zrlfEP1_B@We*ED2SK@ZT<URo+$@<=VRZ179E=-wvs8Zf=JP*Z+#zn#by*Bac{(50l
z7#OZS*T5moq>#{<xW$A`V~App?0YufK2U=y$D280Q1`2!SGp=&3(N2)V=K_21aDAT
znLg*=l%u<Qa&Q|d=<D>d<L~z*j_e-ynWr@fCO<YB0!_%x81K_=vUc7};Lul4CMW2Y
z!ZoYp7*eRscOcHUw^<7;;>OMUUz!M9{wv=4r+{NLkbl*_E!H$-Q}{#RmIUkAjEZXJ
zl6E$bHFxS%N55Q+!MtZPbmD*O5PZ0Tep_unF%-JSYm_GBhrh8ACpCtQ4EZ^VVyoG^
zY@hplrtEAE#Cd?fkic21lyTaavkBImoi~qrZcONWaYsB~4&M~<22`k#>imw&UnnFz
zjMm5nXSXfG`JK`rH;$GfQ%QBnEklL?7B@T%h8m}Rk)a0+P!ktU_(!5d3eblCP*(Le
zhj+^(yX{v9HY<NZlWFLdWOX2B3V)=J`zl6qCPt$%78UMcn{+o}grdqYn{o79yfW#Y
zng+y14Xo2#kD~W!sa|<fb(_n#%WgC0t1&IIwsk4nkM<72`{i;)yEz{jQ)jqy>J3V`
z{^i#@pHIBM479x!m2R0{4Xk<#re?I}xz>GdM018yXOo8%XMB$HpWKDD^Yw=S!S`Ql
zTxZ~^6{q*twqJ^6lYboDvDR2`k^Ww3XSM%Ie0;~t%L9XSeNUGq4HAgy4WtCIZ7KBl
zV}O{&XinYv(7cN>oWA=4+{!4j3<@=O4;q`XKkH8dEJd*|RW-_UoV4n$Wie9^!+N?L
z5Yl8-Lt4(P-fQ;5Z!5X-5NWrg`&U_8LzKs_UMYzr%%RfRbI^!5Bo^lSWV@YjV|wT=
zbl<ycky7&^G7yhO_L?);=4D)6=4{zMJWu$NH3D?k4*5KhWFGkw+1=?NRovM^Ty=|~
ze4Rz4uxW2qZgkT|q1ca8waQ5OW8D|Go0AhEcuZnGGptZZsK?$n1{vxz|BKS>4m1R(
zVx{Z~cWzThhuZewei9e{I`^1-c|pjqkv?5YmFIewm_UfDAaiO)*^!q2swaTvR?i-k
zlY0anK5qJ7`DXcgg|L9@Lu0vcLN`|gO%}ngU&;llz3i&fiw+@faC6hD!MaxO5U|y`
z(c#HN4L^1tHuo)y<^8*8Dds^pkm#Se+hGyv0I%HT`CsH2pb(T39I-r}>-lVa@$8m#
zPKrotx^UBRn!N6wiM<-#>env$Gd1PcQx$9~sK(npdmejaLLtURSRw1~yH{Jr!K1Z2
z1N)+T?}q!XPu$bRHK#9jv3a0>m;%~@MH7KVGM}Y{4Q2Rl3|X!h#g(Q(iphXtVfBr3
zDo~|V9NlA!ppJ09I7eO_2#_5+6>DduHqX!otR_pmAek+7QaMhIKdhXf+5tJ=_0PL}
zB4EN2ecZJzg)7=Cw^Yf+WBZ=!y9S`iZ~c9(l3N9WCyCQav3x@{nA~B-C&z8N|0->l
z_c_>%-t|qYK>o<FkoqiDj`1ej*wuJ$w!H9r#9GX6M9D#PF!PHtm4e^WTz16V1->_7
z!csk%t3uJ%{tkxx&9+1gG@y#eZt=y3pI-yoaQrmldd9)&ZP&NG<BY|JIPjh54>f^@
zhl0h_NZ@9@-gzt&GZ4G~amRt%^kl+_R{|oT-&)yF>i-7n7x4&)>)lFzUTOZfi$2lY
z#VbN@yD10+du@G5<&w2_&~m<3{Q3`3!Q169ku{3X-#D}F>LS#osY$OG^*QLrW0KMz
zdbZ^8T3F|aVoRE-(vn1D3W=;OiCastGpFUB(L-=W{(7gO`YMBl(8$&?0r(Gg70hJy
zZ#Z*@V#UTc(&#&eQIR8E|4<PA2&Cl3gonKG`lasI-jDs4d~PmZ!5@Op(Ix>lR5*vF
zKR&LsU^a>^HitoO6k-xa_ZkM8W`zIkk<XpTgqm+B^%IpZ<fwl%FZ&Z5xhv>u5`ivQ
zn{V>eZW!j^(#fB20x9Zy_4<U}pcIkQ;;xX-jE`qZTz$cA9Vy>ESNBJfl<vbH!{Lr|
z7`QBWRY}$D0z1PB(%vkkn5+z`+=m)wicAAz-#m$rSc{!7;jS&|m<B|A#`OU*L@&Ew
zYy=5V7$Rg*uyd#9jqL3cCSb!8bX)pIoieL7r+9ro6pDOrIz=z0_&<)WDj>>j3m*X`
zq`PxSQMyaIyG1}s8l)SPX6T`$rMsm|ltw}th7RfOzT5kv5Bf0i&)#c&i43ke3occo
zQPYwa^m#w*Y+w$vdAmIN?!4g}hlo1{CflS*8lm+UaQSeun)<1~3pYGKI4wJ&g}(j=
zUFwMF;$y5zAALFpIM6EIg=vU}U<W2$Fi1e?gDPUu<NT7vi?;sQ2_T8%zNan#V7$}9
z=V%+U+ugLR^#qmFd<_{1%9dx%<;ujpO-B7X6+wH?nIz(Nd@NX?vpNWvzAtS3dR)p5
z#;h)?(J|nh$N#jZv*qp$^6|%*o32*~%=9tqb#3D-KxmMf#-vta&U`s#dUf0C?RR<(
zlnDTPRYEB+l!y(Mlc;83KqD9A4=fa2y85#oWAA3vyLKJ#^q%p9SzWu?jRn3U7-Rwa
z1+XANC)U(dmc@LXR-y&H!OriX3bFvB^0f|XVCKUHlKgRZPBU5^*QOt10*~^)6NV$%
z(z~>OT)}VV`1R*^Vg%>ySSf&ze9!m69MUS%zYuFi_CD`lF{~kAp0-~69@eR5^)sIA
zQgt?<lIGYWQx;}}L_vVk#dYwTnw&}M?WIUV_SM|C05Idt5SG0+C<n3M^KQ86Gx)4<
z>h$^sc+es>HgSsrv9zcEEEdW9!{V~lB{;U7+;S8KRYrue>k>XCe7{j+Ran!*mF57f
zM&)a}nwF*fx=0Cilz++vlF0Yd^H<o_G+B05X@M4dT7x8{(MvJfI3{0<t&}zQRR78V
zSwn~fnxSrjN4qmo<+`7CUM>@p#5Zt_8P7Jr2G-t>bd**9q6ziH_Y|Ispb5QBq)V^i
z=jQvFT30rChZvoCyo9XC`g#WRt4o4-pOQo>RoGOmE7)$hs(x$!F1k*6x~(uI@K(on
zSzQyfwZ&L^_z-V=w>k0eoY+a2xYJo8?c?a6a=w`-9D3yjYS^|aJct0##;UpA7_cX;
za;T~IIZ<AJYwoP<e&XqX5p*tzDF0F=&t56P(<B$=c3$SXmp~~jg3dN{SptUbfomv3
zq_bhYRvg>u@+awqOss-{B(Lq_)Mq1F)QJ8a5;Pf1)NQDYjN*y&4vDA@P!i8{j825m
zdH5|fRJd%fpnxx<yjG~h6TIG6Wf&@AB0;%KQPKNVX|A14tAj5hhj{*CCYJDcgVrHV
z#+WEN?ECFuMSN#ws8>4HXocFFk6($0>T0LW?ehkHo8!>H1_G0&UKm_p>ZX(?qFDoB
z!AnJL@YUG$uI-2L0PtD#Y)v@pUt_D@`wBc6j=Bl@T&AU(Jkn4ODkHr)%3ve?Ss($B
zc_kny5(@+cdyYoE>{?j@9E)rO3(K~ymkTT@Z|px1lLBPncy0!BIYm{wea_6SzDw+J
ztE#SfstYci`2sa3aab=ylxKL$NGQ-`KU?BJUgnMM$)2%aGJ80PuL?36WnB6)Wm|9f
z&OSx#e!Y>OUw75<@nSS?w5Z?esz}YAyA`B!k91zAIR2wWYGmOhr4beVqX9b*<Sm&)
z+W;SNb)=BCVNJ%O2-AV5$Eu};y4SI}Ux#hN0`5nR|1qEcUf`aw$Z)@0@_YBEQuf_{
zJv%8LONJoa7X#>M?zf(H*gy~uB+2_z&ve4VbePE+g*TWE0kqJs$q4$vSx!?^wg7C$
z$)PUCuzzXcI0Jq>Wwsb#k9!mZ19G|jcXvbHgc<-+XfRt2EUk8EXm{;<#skn{W_mi6
zbij;+)RgG?RDB2wSgU?`bb7={(DdBrs2c%ryJUd2FIM>+H36tQ*`q#@XN%qS`eX<+
zf@(W6-AEj5^{=Tc92`d9;sS*IsKc%|B*6R47_J*7Uunl81gr=+=kfc1q|q4+0apQ@
zj~!P9)+~i3;B1{MmlsV5#{t9|af!Lt<M}gAYg^-`J+Kjd1B;O=)6dxgBAuFg+Ll_M
zUu3;+O!iHS_3=5#qYj9mJ={fEX@Bp;T7KNh*y;uyP={ObQh<wl>4QVVPff-`etrX*
zl=@3<L8|k{Tqar+T5lB%*xZiiY=a7mMcmN*9dBI{Qx1eNMj0k=kRg!5bW!T#X&~V6
z<F8J-qyHVcn9m)Hn22YH2D4=IzlP6P`<+>4F6NVi(Vsmvkf_}JU~VXAJM2T<77(pS
zmK;4Pnemz2rI@!*@vciLu6+ks)f6Tu$5pBp&<8pO9MLV^eTtCDYb<mA!OlGhUVV1f
zYRJ}K%BFio6mbUo)1FZ(Iv8xY0yFxfW1r7}8^Sc7LEFh+0?=y;+>@PVr-gxUiAcrC
z*ZM>eKGDT`kNwn9x@Y<ki@0Vup6wyQkl>lxe$|Cr+S0t|M<o+MG)(m{0ROF&;<?(a
zU&yGK2xYc|H?8}L5u3Ld#TBOsz6s3%!4>A5(;dm8Kiz&E9;}C3n5xl3IFq#$NHD3$
zbCz7IUuUvMvEPc*@MX!@|0!5J@!Z{pG?z;=*u#eP_$x=lwsiHDZE%oqnBhO1{HA#g
zl%k3H^Oa==Ni-S;RAM5X$m=@hUf?>uhL6__?@?BQ(})2LRQI`XZThF)1Yw{f9|a%S
zN}RTKJoeH9L}z7f69dqMQ8DHM?1n$N&nbpZ3KA#D3`v#4Ug<VoZ!fTb9@%L=c$3dH
z145#LwdmD64mjV4@9xvZ2GsCFlzKN(H7A1AyJtFYo()frJk$CQs4~F--uV>k{{vup
zsXLr5br#P0>CVg;3;P^AO^)}}re<|L(>niRR*(FvyFsL1&n9WR&~-6I7S;OXfII^u
z+8u1)_tlG|ZzUxNp(Uq}sTPFb94zO(e9sm`UuLW99iv*Y1Qu*A5pDB)7<lGLN+6}u
zenK4F)_HkM3{Z&CGE2^c(~i3cIp2q}`J6?kV(_GpwVT81-yFn59);bN^83T!x6e$O
z0mEw>$pfHq9UW40&WKZIQ(@INwp^lVbSZT}3DC2)n1X_AGHwZ<w{d)hFlwl030{1U
zB3Wzc*$bdPJPR46EEv=6KSG_;&3pO9V%v|$=M+>~IE+_@IGGONWEfkN%`;?jGAE7W
zpE5&3@bMmaOX5`Hhu_Wmy^Ik`^6qs~!tUn2g+7H8u<Y$c(4H>zm}|JQb(;QC^E%k{
z0vR$s#R})3EeT3*@^l5w%^$@HbvnJG-hUzidMWj<zV4UzEbUpHw#$~)2QEZ2)%J*a
zPnbYDCaH)Ue9=*=uT6k1DXmT5YN)ucsb#T@KPvgYZ^fH1(%S#frO&F7;@xXdZ`*3N
zcKbkmxNN|gd~GzIV$Vy#%L@lhYY`SC_Zvkipz)GJG;3>f3kx<nC!g(n4aYj+0O+Qu
zi5#h!Jj5@f7+RS>7Oc#Q2xIy$VjC|E;R}_=NgiREDS~$Z83)YMr@71W?Xsug(&RSQ
z?^)y_RH=aT*SA9q*%-+QL8HNeACC2-5^*Go2X0aFqZ|Y=y%1|S^sXG_#`u%vAcK-9
zyR#Ue#|O|{zSF&+V^ec)O>f-Acgc4TZR#Bn4Gfo{Dv>6=PTj$b^R_crNiLdNNpS5T
zCTRTy_pZob0eX@`sH?Zf#O@u~C)z$2mVl{Dfw+g;V5AbsfVkIHkkWFr3e<iozQO>%
z79|z@?F(T*i@cxitvxsYmQx}Hz9Yz{z(4fE`}-}%9XPIZ;1>23J-gmPG7~gyJu^0)
ziij`d^Ns?Vx`FK5=Y^zR^2mnNm*zP%WXo4~Yk8(=q_SACE;oaORMC}xc3OnowSw4b
ztz<Jgn_eJfiHWo>sxM-c=EiHhHihIwu@fNjUFv(3nb+fIR!72wn?3y6l1sqDuAtD(
znrY;?H8T56Ya{cDP;c4F)Zj(!a@XMIK3uWPq3!6Oz!nHG;Afu}%vVx_oj0oO{FYIB
z#3O3<UNjlK#g^&T$VK~t1Qb9g@eph&b*WBn4L~VSN8S1huiVlAAnbRMT#>Tf(2p@5
z-cozfmg>;0=i3jpL=8hZ(dIXab6D>2a0}Cc4~*SslH`0|eJFs3xG3zZz?NtBe`9u_
zh+A2>nDJMniP4O?+1V`;fL-ZRn1D#yw|g!*BUco4Fmn9iNP_`XN%QC%JDvcLsO_$c
zc4+8A2nI<jRO>JDye(lKEco3~V1*UGa0K2qmnOn9$2PC$Rbtz7s1*&0t?RYg2h|;a
zc3<6q3AVv;mAVqnexAL_6mzl=2Xr4VA2dcm^NjNvys^)b4e4v)$d^>yQBfDrVZkix
zr$;R86ZV%S*hJ#9O#DK^wN*U@IPRzF8Rp7+y5=~M3x}e#YR}23%2cn5G+vaZEi{@u
ziTrW#d*4^2qbhd^wtA;#nfiGXx7W<b?I*Xyp$gx_OdlVQH|j6=#Er7Ii}_kW8)hSc
zbl6|qR|!FNbWvKI8!o(AR4@e+bBza$BXJ_n<HFXQhf|Pf0CX5iiQ&3c_9xRqFXjJ(
zQ`*?c-6GN@v4SfyuH)qt$c{cBpy@A!!8X5)dtzJFt$WwxZ!vBhdK<qk*<%6!F)vRb
zhMcrOPmV)0t?2zo+_2up*$n((W75&O^KPSX@421bcVKSt9b?=P6KsTTh56|CZ>It7
z-TAzqAI~gADC@4BcK@mXIpGsn*@Gjls<)maiJ!JpLF_BxPruJ#mwf2Bj+@|Ptt8v`
zdIPSP?^?2&+IEVv6WZv8zc?=r-pU&4{<(O(N`qSLZp)nRe+_N$i=JRcRBjbYPp3JI
z0<~(h@lH$rRo$mHc~3sFK95;fk^ITs563{ZC|_t-S++tT&Ca90@k1$Mpawx5KW`7U
zOPDo?a!nlwbVR=#=Q6YxD=fA`3kW$9xnGT>2iGV<{Kn^*(yG;iRi=a#hg-Y5ey4Cu
zqQkzrR|itL4UlM};6pf6^dxBqw)2pju*42=dnilU<!tlhARIL9A6_cgfcb_x+~O^x
zUXR90JsX_QYAxqKl{x463)5t&w?hoL18p}hNYLqn3iVtAd0JK(1kBJ-o76LzR9*~|
z_ys1uqqSXVo-9~&ISCAR7Il-In)dHv*WzCMdt-_9A&oTP<~Brx4AO@o;9(Lyq|0~n
zOU(bJp)NDN2B_b%wxXs^mM`i%``N+r2d=||jvH=)Uezu<YH5^O1R&Y%yC*cJl=1t+
z<$Lnwhanf=Bjl}{?S<V+#NlUw)TST_d-omUreTf9ua?Z1>7!tVoyHl>PX&qH4=!Y$
z%suLyF1~yNtyoZiIyHG(2W7W;S*UITc$PekZ1w8#l8A(C=%|djuClD{eoefv5PE<0
zG{L85;AmHd?$Bd!#9CcDz0qBR`q6R__!~SH4--WOb$gBI3f>h<Y;MUI|Fx{gx=Bbn
zqQ&00U>zk=)!=;T;a8qk2#`>K_Cl#qZXU5l*Y8^IVw#O4nC>5`9`Tixh0UQo8y$^G
z6jEaS^ie4HC}Jp$mQQ)$<CNvx`I;#x(8K1t1DPw2wm)!;kZb;0xOMG&0H+$W5z?|X
z#2k%Y$dB5Mr8{{DkFMa=O|dDr=XPq33*sWk5)c?(P)Y?TL$==*qK11e?c>5wm^wj-
z%!G+Acb}X<P$?5wbFxGQdRnR8j30U?Lak#)V_i1Jn9>dG36pJs#{&ceBt}}tkdqfo
zIqAc#Ot(p)uzNx$@`;_xSjX(cApmh0`R!m6y{V|vKlrq{`&YTUX8jt->}%UJR3{1E
z<yM24O>16CQyUU-mAj4vKvLqKVDZGbdXMe4R}!CgyYW@Uc!mLcBSYq1Nrl!c;|yMs
z|6Nr_cWT|M`<<EPMePb2dQYSN<}>hm+Pe5UU0!IbgWNhHiw~rzCBk2k6a!-<e8p&?
z3GS@3^xC&F8_vAO4<SWft8@BbBdj}0Ko;s6)ArwLG+JBe;Q=6kb+bxdv(L@he<s9#
ztj;~F4vtr4UolBQ5W5~%#H?>&mKqLtB7EO{oFuxXoEE5jd$FWn*O6uAH$18k2OAqU
zeeWuGmELx9S#OV^tc{eGhW!?iv!BxQ9k?ju7y`htKjY;u=ljyht;i$G#LD-up04e9
zpA{@D3)=r_;P;i=@sKc^dv2EK`@6ey(EQGCvlN1YI!gn`+M2nwyt-Ep@(tZj%IZjk
zC0E*w13Ys0?ks@yzIfn$pw5S1++I27swp${9+p>&IQhZ=5$Uyiy&;L}Y@k<q!uEKT
z?QHK9X;T5ea!3+dDjJaG^PSdp$IO}%e+yS3E|v<oyyRK(ay)6d%&l6Z#126e6~wU`
zBeH;Gmp}ujb@`vD9)sAN*0zyu+S-q1Hh|cN8GN9f7ki^;bGos|s!xqnb>H82nyHQb
z`aun`v2Py$UkrIh#c_J)rLZh!ET<sMXQPj+J0Y4T=Nd@@=LMQguEKs9#$s^@i|hD2
zvB^Gm#ODmrXa-iToV-`^W|L@ysI<uP;ds;P!BA|pQg*fAn39d#(q3L`d-P|nzlI;3
zSz2H})h52$B)eD3;QQp)tJCgGVDME>BGjNC=e?;Rq=|P8bc5jN`ynX4{)Un%=PgHz
zv?9f0O0wQ(uVF)CD8DL$!R?gE9iIEOVV!<c!bGZ4jEt-YW^3#A&M>72GX}5))K=~k
zYkIJnVNnv~m~14f*}|Ao7L;#GhxB#fg)!?lNG3|eJ$|Q>U6b6Vsfo;~GHW66ss{3w
zFZo?R1p}qZ(<&|)Gq=#sKSP{Q)$qR@g+*9K7sfI1-q90_OA+^6`;Q%YF1Jz4D1Owx
z^4Z|n4q$;&gY7q)tj7&OSj^m|Z1}H^&*+6?S~Pry4jzCm_>@v*cM9Yo<d#>sgfvKi
zJaRVoPgJ09wJf=9H?7W;@=F1mI#XKVC;OD@Z0ab$BP@A)Jd;*uN`Y-OXQGUhC;$E6
zoz|8mt*OOup#E+S6IUK$=IkB1J{N?4-g?DHj!tS>sOah6e@6vM%msXsD`jdRy8&!c
z&X}mrl7!1(k99Z<SM6INLYU<gd^81=y(@KEa)Z3!_L>>u6!@#jQV2j&vokZWo&|r7
z0GAVaf^z!r(P%a10%iivL`7?E9{B*B;1%F#39U4}7;a2h*4OyWSc)Z$0~nZ+xW7NN
zybMadLbzVCD*iJK{vNPK6G(TR&;P2b*?$M{;+9GVsEl@3171j;#qM45Jah2dDSQ?3
zbo0`Ke?27vUCP#NL05DCm9lJavwZB6)=rcXSr5DR3mISh+296%8_TS$)$LV|DA`2T
zJBWlfLGWiu7lQmmpoIJ<@zhTvmN~g}LHouM=r9VW{7+WhIQ8#yDL>OyhkwlGq<K6*
zNQkLM#bDTV;;5g1$Wp*)r9NfL>*_%oppSD4Hp?g1c+&N4uf{i=x)LU*mtVoINE_Sh
zq_SCgZ_#qa$G*}^Nt9j;nfZw=XntwMQ|RH|)CjfA&N8`tTd*A4P6i3K9KFz=w;J1T
z0!!jl5@|@3@|(=rpoQ1XP0C1zpV(|m!%CUA-$|60LTeY1sq_+qO?+hu{#H~gMaL_|
zB=j+WC<=t3aVn_bD|9;2VWZC99X_L-f7)qL@<bBWuOytS=%2kC@HtO7bMRWg35}o_
z{a8N?R!WDN))M2hVh+y~-gL~NR~Sp4duXMF-<Z$}On0*+sltfY{5c@_*>ATM(3ET9
zA@sj+BZzngNVuZlqs|p)B0u{r7W`wr>-0pY<)7oU7560H;V`=)Ny>xYrCLa6<t%8T
zVy%Dsj_em|*|mBY;?5{eKc(*ca+ew>u|gWmjaYNQq(r*((Cg={ncxFU`Uvu5TO_eN
z18Pv5yh7z$wJWxGu8&_EjGs}%C^4Q`0)xNpBkf6zGcuS?dP6frhkK^8^CI@@62<ZB
zTBdTRcmM1Ql4n%{owoz_=|~9uw2i%j02!QHEqG;N?S&CGr;v_<;Jx~9nfB<ylBg8t
z+0Yp5<E|v_@#HQ&=Am7k$jZG5C*Sd8@p)b*3;Ul;AIs(nV54gN^X8hUIWIrm?jULn
z>iZw(odJ3Ev5m(JdrwVUUdl+{a~jxqb^;@VfU_t143>b8KUk`wWS#A>njSyIkt5+4
zOkp~<`$W$KI9tyo>dS@00B*7cw8YSm)?=O)to#Xv!h*A1#jyU5<%X!zpWXX5N1xUZ
z?G(3;bJWq&V0uUk&hMX#_~7a5jh`v$5r}H~6S7_Y!H>@M52*VF?h|&fbs~!?pqCwO
zgz$Y%9P>jzx*Iq_z%%p8<wxaeR;S<;O<R7v8_2_h2V|$0EHqF|OfvnQ_^p&&Sq6PZ
z(^6de^V%vV2$>~ft-$y%x5l8ua!OEbq4>9<cu6xp`v7(U7;A<w)<6EGwG&uTp-zi&
zRlX<u8URv$1=@2<4g^eSBXY54{HjO1XtGT|wsh<IA0pwI-3V2&cO#0c<Ht~Ce$yBM
zx~qW8=qu~S#a2pm*&3yC+J(<|_B2QlEEmla$oyWQXwoPvAfMhi=zI?tNIM@4*kCH@
zddVv7OFgkivG~`Jm5GJvBR<?U{+0@EAF)s1*ZGHT-FGLF@sRnO_<x~=>h>2+Z5lln
zl1O7NeweDU>|%yARqv{?#9uY4K=z4h_0uO*M~~-5$yZD860i<DV$D)LIgzhau0?GY
z_~ij+u(l)I?Y9oZX<+Nnw?77p7ofogP8Ixghe~B5sH61sZI7!uFEI;qF3P@q#5VQV
z3#191RYgbbVZ>I^%EK%FbDA=+oA6mmT)KJFT`gEb>N64FPDr{ONy1doTLn{+c)r32
z3ps2L^^h;~x=6iJNHxD&?kN8Yg~<?*B7A{H(BcwARpv)n^xGW0zHhQ7s<`~`*?<4Z
zONnbmmKagp?<kNmmaq0v*wxEnyEV<<yaBfz_GJ4IpC?D)TWM+O>bu|N*n!m0ZLeo(
zrE&79iP7AebkDV<O>#3Bp{At=Z%R70#y68}a`8D`3uVy2;hGnM4m4gMhe25%+yMof
zyY3`07FH<FjIhVITV_K??zKXkMWuUr9n(0*wL*ZbG2qJ4H#z%$pVRSiAGBT#-({ux
zW_)8Bpxz_uyvHw69sYE`&F|Rm5^ehuSWvg(lRsj7+hGA_Ze)e2sNAmr#p--Qc69zH
z?KNN9wgMn70-K0f--Z+r6?^fi5p+e4Qa}<K_<c;0z+QaN-~)FC{)-D=kk-ya&bYFC
zZ_B31Qm{%mny)fzHc{qM&?@(8o8cL2cQ+?<1g^xlmq{r@qo3GC{9^mkiccPU9XkiX
z&Gyf5X5p6?(mEOxEsNnsr8pNNH~0t~oPhaC$<8$U4g=*%SL4RM_<lpxRHQjOEO|++
zK-&07`_CcKxYXRcS!RG`A+ucTszRB*60-Ht>+qa4FKK^_?*xZ7rOp$KnYAPdAt{)r
z^<n|pK$OtxawlZfNsY8|#tcx))q*W7=i5{gpxN(ur?3D&K>?8vTvZS}Ie>kD7N4$G
zD%Jy%?qm7BqWX$X42f@KETxwxW&TQ%X6BHg$kEZ0pF8>hgOtDcC1NKDaO@~)pz5K>
zPNbJJV5k!10cJBfeLm!p;xwp3F_n-(nKfEr&Pl2+mdhuH;L$c=)q;$hCM?@<Rc3O&
zZxbiimmZ_l-!-<@Hix@YmQbxcE-%mhCd17JVwan`2W>LJJbx;17eDKd&e0vG=8HgM
z5&ZT;afv;al;*J6`9zi*eKali+i$3dk^}#JLrF^HmB9D;+^sVtHLe&g;grd=FBFbF
z&@K6A8v5`VUxYdOFu}hNCXI`ufTg`{WrL%vCr4Y};gS3HL&<ZAoi*v#v?O*Z`mZEf
zJ5-tP`b_>q&>VJ1v0nCngi$LgP)#I%nPQWk<_V!j-w_lIdUPz>viDg8f+ycWS~D^&
z14Hl1WwyC+>nmX;LuvIy`_4-K<ZF{)i|q|A!ns80+ZRU-;x|S1JLDpqD(%K902c=0
zkgBcaa;Dp06E$}Zxw%A*@tr0V8t{{cJR@{?OMGz1c=m1VmYz2>#{~XjE@}XXUnKmm
z%+G{!mbPnJrZ@IOv`KvuFH1_nvG(bDj0x!SPMgCHOz4<WxBxT;=(fO#mkkf$4$}BN
z;I_bq0)Q1@a&VX$+$6=e-9jf*xg}l^8%yq6dgGS#m8eiU`dc2L9s{j>fE6@F1?)YT
zMQXI3)&mn^)X<2ve2B7kcf+PQD@|0c{S&QyoC+z{&!S34MAWoGPU38gw$iAMVTAsJ
z(O~SaY0&AbuNvAR3e2%;`12x;J|qQH)wKWdq5Qe+OHOoWywjfQ?qh*g1r&n1t<IUZ
z0-Up$)$Qfes!?rsxGi0`xSftT@d_m5VuIpD>wgZL;LH_4$Kl8~nIUq*vz+<~rlLJH
zbnE0I!b@xqRLO#33cwaskRd*(4%`@Eq1Iov0tvgh@H1HcgkhWE(Q^bft><tRg>%b7
zDEJCSxKu|$+<`aKqqT>hogdqeKk?)tzEF2K&>8|J3xpqt^er<GQiVo5{Rf53Qi2&#
zFf*U=C`D{n<@$TWMWX~xpefC;9R1L&RZP~pBeJ6~8kMXz0dY&Hi4B-R3mGFb1UY){
z@0k+TL+;>KV%t@-x+Rtx3}&1AF_clM-{lJuP3*W;i`Lg##Kl-QSA9HK9vX%l&JW^J
z@cI}4Jp;xvuj@)G(`Alh>BV^);D*@%93=p(Jj(yWm9RtJ{`&Ak(rs)su$6Ijllm(+
zsu*;=TZnhNDCEws>bQMA_F|Y2XwWL$8h-7B60e#3AEA-6rpy11MsNqo&7OG2j_FWT
zuacjI{Pvq#jfzG?jC~o=Sugp+%pxxbQ#^cN=)W{}_9<b!%a>nmV#t>BgC;+IhPt(N
z7I^yjeUTH5$APLj=;>ZwC6GJL3A_KYoVgOYzO(xq*_c17V48}aHj&&_UoU9bXPF<@
zb%IDr5jJHLDbu$)eoEMoiXAXBVV<CpvXq@_RMybcqC;mviewTs&c>tlqIc~*mWdj{
zmjc_?(iD7YwSKtoW+dbFg01XzZ=>i6pxcd}2Bd*LUiJBc-|FqAw|W1^*D7LMzarN0
z&b>wdsm=fK!2oofo3%OcAwh@CxB+W!x967|$-K7fd-C->0U+7AGQ=d3<_LHsqH+ef
z{LrflL!m#VX-GyOvy;aEp{$7NS*j<6W`gu%d%&H`eNe!?BxwcZ;^Bz=;M6-<?cMNE
z#_C3me8+vyI-g%aNnO8K^JUTfLcb#U2sw2Tqv)5$T+>6!{aT{n4|k*@0p7_+_baSK
zZ|slTsWS3r&M0HvoroUYU3jOzYwau8Wa%kaW=;Va4lz{K?`%PqK}#X0PXCybA8$GZ
zx-$GS3+?tXMw702!{s^et|2+w2lw*uToiLw{gV3Qdu+*>ui30FR=M5rL3sl?FFm)`
z&|apy3C6^h*aBZfY7GJu+t<}TQ-fEUImNVWuIHu1dogoJHjVv`7F^_>`sYgt1_c3)
z<d~e2@);pJp4Q({grHTFKc>Wkyp7tlHX{$F$R*<JSn$gP`_GPduzK6#pU3^OFt3}C
zp!<#Cq4!PSM~r>9(1#1_EIDs8<7zP!3b+C6@sDR81VrcTVK>&v2{@!QSS+r^o-&O;
zn$&>8IM$N~sw_*3dhv=Szm)^q76lr|v!8V?<O0IIqkfOXC5fq!bWs_x*2*&Br+rq{
z?6ki#o!)7D{_aU-GY!{Wds}#$e=&DY{N}0(<5bdx&nCHL|Mu|<i}jwHpX4wYE{Cfs
z8g$|*X|9)bUZb;#1jLQDy9dvJt7TjxI(DRrVO1PUy@Y#P6Hp94{|US9Q&cqG6bx7#
z+%ZG~p-}z2d0XOUohp@*DE|I#>h*nHU522*a19;aziCY92pEIL1uK&4ESu*2sS|hs
zWY~6oFP`OZ11(Zf0`3z(tP?Pm1zh|0hYaoc?g>$y931%pUmM=himbq~jNfG{382q_
z^j5wmu28L7zDQ}Zqv$b{of_+xsMmJOv&>2$DFiMeGXQH$*%|=6sitT%X)9!M&#>bv
z$mQWf%MEf1CQ!-p{Ud{kD@WH*C&~KT$y%}aQZQb@A>Tg4bucz}5IDh!7d0aBhl8x3
zA=tZ@&O+oE=kh<(lXn<@qjq1OFx(}=eHM239hOdqp`^;%#T#7tuY(jsqf1dV{OVV_
zA~?Yw$ehApL8=$Jq)USKlYKtxW~6|%ykp>QQZ6ge;v9J;qE=2jF<7syMoJ1tFH~ia
z(_NXAA|tPm870T*^cs>!Cs4=;8bTU@j1i!OfD#19-i4(0Pil4L0X<q!2BWHt?@C9*
z2e=IOgpEn1-fm7ev=FHtFg74P;1EwQd&ZPv%l{XS4Q_)jaOQT+q1lqXp3ju(0yNLL
zH|1hwER_uKz-E46MlLPy2w3>`dyw0;yyNExdxFdGmL1?wz|8o5x=>4jOGF=%!0U+8
z+!TAJhE$}Y0yI$TV_orvDVq3SEOx=yAuebk3Y$CYdIQ9E>Gl7P9gq+3^Geb^eMk$x
z3*0$TIu2MmHChSkWl}P#@zZt+GL#|kBNNT$&hCva9un-gfIrfFV?oSpIlHh6Og#Y9
z2S{Vxrd@givbYp^pH$5P!#xj=JP&!kC25Nc;M)~Qz<$AzZR+0eGbf1dD(SebZOXiC
zP8ugLiwJvK=&Ls_HH}=BkTwptAf`X@g_z<<)shqOYjfg(qB$#96guS3rqdt4$C>2)
zd4XH7`uTIKy13_h1zxXH00JFq;PFq$b6rgWCBwX}=S@?DA~SuwZZRscYW8mW74=SS
zpMB>|-OKxB+LhZE>0t8EVp^nncdUx4>IRHV@K4;?4ED>dYp<YqE`B7&Y<ar)UrbOi
zM|AovUONk<*Vi*d%f!}46Sil`7VZ6Ux$l_KYkT-@`|c_8<DPjPA)o@mR%gmFe69Dz
zOtu%G<yhx-VkpoXd=MYN9=0WGeISmXDGW+JZ39Z9$3x`axq?h?iUB9!T-*6BU$F%G
zBxUM0$84H`D@s@_f94G3m#5H_PB`RdnjKd9MQad}$q866mQD2L@?lVBu`@smv{Fj*
zQWH~sF;bMpm$<4^kgsL$6*S*i0>X!z6nLvLrE1_RgIm60-A)hPs@zcxn!Ap6%i6EK
zWL_)wak>HRdpd`Ffl{r0q$!Ou13+4`0AB-+1`hOtcoCxP<OcsnmkBL#URw?!O_~3q
z*As;Aem|S10M!BoMn|h&&%h__CK*V*AJ%}O5t-n6DD^z+`)_%&V!N;#>of&kGZTG5
z@ZM;$vGIWOL!kijxj<tit~Q#Cq5Wvx7uyOdk+*)j)RQFj%xd?ys;>Kf4P(hZyNEU<
ziIXX1LfFM7)L{ll)FB(PGkJU0NdDpLFFcK^GfhRT8rR7tPlLFDMho^>R%r@<0sQ+z
zbNRO>X6t4GU@ih5j+vQPEs5>jk|#b>3g`bVZ*%)1W02Xr;Qug3w5yN0bkB4EJ3#tK
zdhP!`56xq2i*zmr>!uoLLhgI3gd^9lg;a!J#xwoJq9SdtI#6WZ5fB9ceaFROEWeL`
z^b%%QB$T!|u@0EffE+Rd(5g4S&_4=<aNg>>h(m>^2fwX{T8c`NzKAD_H<s(jIAH1u
zsv`ihK}&E8zp_;Z8`hLz64V6W#jR%WdQ8?kTo#FjDnun9oDmJ+wF+301G(XSL#;H2
z$P`R#-i)l2NTi=cYED8I0u6<1`QCUmGJAUXWjJw;b$WUQ0SOfmo1<EVyPl!rm<?k-
zK>gu}j@pVF7loDaDr9;M;w5nm2^_%w7Ztt9ykYkdE0LLS0{^r`Wb{B?Tmf|7BzWib
z$y(}yQG%X1KHa|MVZ8rYJburKd)Nebeeef45+I>%F7E+P`9J46>*$vqT<`!&h+fQM
zaEmctS9`@D*>!Z){3f@^`{8QCT|?GnQ5^qA<LmB&hn}O9DFfxdBi^K>w_u12h;j*2
zN?lthE6G;)A9-tvOVOZd*USZW6hanizl-FHFo1Z3C5iRMU$#6>RsHaeb#cg#tzg6W
z;TVyZl%kO3MrxBNG#?$Yep#JdiI`jPO<bEXXM;SD7a3KYF02BBH21&^7)3tzi6c~H
zeYMEVSXcG;eZfp)Pya;?tm?|C;O75I!o1+h>X>1;vg_?<fb%-|Lup3eBoC=!m`q>J
zoLjsGr~b%E(pKzo9#)mJH9hkm0b%Xcdb~Q{vx>8FyZUW!(Vi$}4zmfThkU8I$yAcp
zY9mD?Y=`e}FR>m^j89`9cVgYOw+UY|7cxZN7d`#a<##vt?XzY10&aCZW5?6OFh#90
z3XqboWxKfH;a-(8USx*|SC|aPTYoMy_>V>zp0&zK-N8M!YNH8j;_G&Tp<qSWtgRKe
zB`5E(R&j&mse&ozVjZC-htJEp7EI8$dqr_@cTP2m5_2G=5^!=2RG=SPu-h!;y?4Or
zi75E-Ve!GC@rbbAI|cAlVOu&Nwt)4`Ovy|u&>H~t61Ei5gF6<aw9p|zxv<16jTAhy
z5+mTTNhM}edt(7qW9(dpv{R~|o|@oSWGC{rdkG$sA8_w3dCk~eVUU6dfW3j=2oRhC
zWpBx}P(%m_rqekBTI{TB?5H5At!G{~Y2M33YJCmdAe_Xs?JdBsz`_kQIT{?pKxQ_H
zOpWarLKNKg_(-s8pCSX7SIBnZ?L0p{Y1MF7NKG{NHtMhMVF7M@AbhvefxEVfUU++?
zvwFPmq{79;LHfgMoqM5~{hEu$SffFuIgvi4E;aQH@E3n2ALZgRph>8qjP&2b&UTPv
z2E3Zn&ESit;eaaubj+&zmG7~DdFEuz#l`m`C5s`whO)&tClQ7v_HOmQ$L%p7;HmYx
zYecFl7ea{tFKzAdvhz&f!}S9C$tMmiCd`^6xqJNR^ucs0qWwvdIb|WQMz{|#Hm!OZ
zMMfFez&7SAKLRd<Ix3v5c`-gAPRTZ6FVjd`9-p!__giT$TcfTz!I!10OV5n7Bn1J*
znz)ZPxp7QvcbOx4g9k3{2f}w9kf6B(arrN~Oxy1`vDJCp<T!=@)5<YL%k0#9;!xRO
zh!|aS=Q(y%@eA34GG5wurWLaDXqy8E2v<?zT~Jjwm&~Q2ME*v@oe>kNIJ=s#jUUWU
zE#{Q^>cNU55*uL@i`m@n)H=Ok{m+?i!#hLFg4YUjz*{zP*gV-H!g9k6Y}-5Y%Dd(j
zj;){E+DFE95)v&SgILN1^SilBfrxp}?ba`Gd%ozJnIb=v)0?-U4*oHw704ukGj=8k
z(BY1!LksUL)n49`25(k7Zj@WZ7Srj%3{|{74p3<M;d^)@Or}p<H(|YFd5@q^K6l6H
zEC~U(e!wawPqw#l*-@R?QT6`3?~F-8e#zSA)Ylf!`#Y_r9bulr$J3{10oRWtMwyu=
zg4w|N%Yiu@4GGqdOAMD$_dVkp9zOWWYt^asd}vaQ=b|IxhnVjZI#s3PY0r(o$5XGr
zuL}Hx;jOYlm-^`QzD0H2E%2O=g87!NXgX<6$8);OMH={aK6l>l14a!4W=f#WzgpkW
zkY98t+&N`R-9hRvIAGcKtR|(Tqlt{}?+Xuwx-~R7HGwn@Tty(*DwqFo8Sd=ktarI=
zjcB}oaJF%~5x1?|#N?-ax$@pk<i_uc>-;5d&+3;NT1~nLjZaSP@k-Q-zZ`HoRbKCu
zsifdmO+E?<N8JvZrG8%=pc6forEFV9wojYwz#KSAzh-5eLPqOF{4NV-<f`jP$L!Uh
z*kliSyvPuIvpfO+D@VU9u=O`*v>%ObIq>^hB`VEtY!YEPZ_X1c4qd>LBg_VFy*aHX
z99r`=dfD?G!o#36IsDxnlHq-k)h#$e!($6F>`NA-=O!bU=neL%f?oww4LVc>mpHTo
zBGWpPSj+N>8yUv%DK2oBB-{IYB1L%H-SBfhFfkCAA!)YXX-U&`UsCtiQbzYpV0(m7
zV_Jua)Ox2yCDT^u?{kl{CqCRQzPM_)w)z_Sg39d2&uAt~&0=Wa9y0zoZ}WHQyglqb
z`D#u49#?Xz8C8WG5Dd7iYD2}g*+0)9@s>V?!7M#rDX%Ij888fF!LH<3d1B%FO`<Y0
z?e=kY+bnrEzm@6h<Z0Wwxw$!WBB+8{9qSt+v@})Yqv_HNiIkPYhn(MFAaHBbqe%W_
zD$G!%vCzm$ZHR`j{(ZLO<TE9T?r-^P4D@=q?w(v{hRqtg`ehe<j0|1ZP${ZWqL_NT
zmRm_%uO7Gi<1Vsr-j~93)Pn<-o9udZjHGytWNIk87QrY&ot5*a^3xiM<zGMYZ1xHg
zubrf@WnB@d4AnXCpNpx456LN@YfBTL0V{Tbl7{{+MpmO!Fp+e*5XE@Q7rf{ECUV5G
zvuRn_#y>QQ<RR;Odp0YBD9`jtV+wY*2iJweRT0q4nAP)V8BTXnjFw7bg|3ZIzF4rZ
z`$l7(pvn@<0JIqZjhjh=CvQ56lbn<15DCCiCV%rlm$raUi@GrQ@in-nfOy<61><M2
zV;&BApRS~^D}dU8rX5Lw7S;SmY(vLTcGZ*Zf0zZar!$t1B2bx##AN^NzUocK+P`nk
z*ixRD3r#t!mCvRkmQ4q<yteNs*H-gLz6;EB{0wlucKpQZfvqf@iuQ~KsqZ6h=kG6l
z2CQaFE!9XrG+oTzzbkR}s#m~Q?1hr3jKnzooqth^eLru@*l1a4Ea3FPrxme2lon}=
zkgvJ=`#?z$DC!#YNzoaYebIbAym7BtXO<zz-;pO_8+T9M$6@@mBcM^(RmN!9n3R-0
zOsSbf&PI{mZ2dsiUVix!W>EJdjMy~%S&RSMUrsk=qZ#=y6^{6!lf_8g>reJUVxCWu
zqC$K_12uPNPoxN?4k>9f>+QRw1h1rf6zUFLKjmTbp^?;a<+}wb7e!Kqcsg}!392eg
z;QUC2TTJX|T#+jj4%;;L^ynnDY_Vs*%6k=|aG9=1bexB6t0Jk3w|2a^%TkK{`(q?|
zKR%NIRwtW#XE^P^Pnk>ywp4UQ_=}KoWr!KlF5cV{@D=94&j84GSb9&kay~K9b~{eP
zY3*Vhlzj+Nt3bj%63};laGTlm70aD-2I(<T4^9lErr{KTN(77|9(r?MCnay1c&3{N
z0iW{;ZLFM(=bvBlmE^fcx)8H>CP5gEnHU~P4wD6V4dLd&i5!KdW+lAzdA}3=KEu>|
zb?k$it}s>K)uq<--Bi296L<s#W=Vc(J(_**z1xwHCB{tbS%xXc_dH}Gi~%JVMO&R;
zSlh(ER%sH;avVRT=wl!I?Piz|i-?2T=O_ZMHt)6nT9SiN{{0<VX|k}^r}=vxK4ZKf
zg*JFFN|5u(yfn~X(z>{ig*=;tCZ)k$&v+@H+iNn8lNQPsu}*68Jtl`rQXLIt-{-O=
zm>B!Yt@8-kbcd!O=%_O+H}TJf7gF!#iIh_Uze5g-bnw_Sv%4klI5SmN_R{WJWo#p9
zO~yZy%)xRrClR^I`0?T>WHd_DQVLjN{E?7uZWX$*XY~Q(|HY;tFBhS5g$R@U`j%MR
zSn<5qg`}lpw2{rIaPu&0MW8zqr<=osJmHVBx5<ww_e_<Q1TG~b($tS7aP#JgT#BZs
zd6KLF)lUV6MZ4}11?Im;*!kYAU0m1>1S{d2Fp)MC)=gToCl5O3v;UN0NyknsVO<<6
z+HB3|MifJ9o-bAB)QsiHDP{_EHs%4|7%;HbVodfm4Q?B)hSCt(YFAF~y|?Es78GIN
z)c1dwbwW#)R-j^OJS0@CAPn$7K{zYG#Y<%cf6f=NekfmbZ}xSwomt83j#01xkyBrG
zI0ySSw9EcQQ1x<Obp-rkQjo}Tmn)()4SxXq1G#B9&EZRjjWJZX6elf=Mm_FcpxaII
zN=~MmQ$q9nAb8_$$G4l4AsJ_}dMLSZVCs<mjmPN3@!n+M>!1A8FdS<hNtsa&d#blM
zXi)6!L1LD9x8?TM;DR)*-?U|i47P`abRSW*7Y>beI3lTD<$T4icqUPd#e=l_cUhT}
z&#3!Cvf-V`;2b`)B4Z4_$V}0aTPmx0b=0DECZ7XaN`sui3xf(uCsq<RdW&I?Jpzxt
z8s$V6KAf=9Ty`FqtgfS~$OFGT9kUrV1Uik9#}jzWQYsjO%^X}E&q+(ugnx_K^bjya
z_W1htDJEk5kXJn=&TJ;41<AwzMS@w26NSSZR--SG;gb?Dg%D>+YFdtcM?}e?v8Zi}
zYVCF+ke-DEFMbGs>AB++KbUo%_%_Dc-7Po52B;&}Sk%9Np?d%JTTUq*3Tys(c<$@q
zQtIFr#B!#PXX2jEBf@g1j(nz3P3QJ}+|uMq9Pl#uj8hD%`aV>19@oMjZZQMZGpMC-
zKJ0j}Wxwz=2{vEhNJ-2!qC!FCe4vKN;g06%tx2!Csq!L0|I?gkh<IqHzN4>JCtrU-
z(^AUNfXIi`aHB3YcJ+nqhZ>%$X<n5=!rQ*HyJcpi2Qx*4G}t;jkDJg+F-%2WzQ{o^
zx!hVqX%2KGP%Rk?2_92K=YDnQ>-p}=dN+_z;He%?C9PK~v*==VjcG!z&i?wZi-k_h
z>s=!(KD4g`_+Lkpn#UG$|6Zb4{8nNZbrp;)v5{kT%Kf&STw2ag0o8%#n#A+5{$_&Y
zk@1^+CJT}GazjdYAYyB|TIR4Gg}h#-Te5)Z{a09;!;BW{{3JgufpSU`$pk|I65G&1
zhK{6c*g!CQjNXx}Kx=&u+_o%ZZec~Q`R5kqZ`k++O^zp4v4BX2%LSTI;&(6P$mgEu
z?Wa^oB7K%_6<-=9y}3W<G7*P1P@G;lJ@-MC{*dZ%86RWTZ2M^lTXLTfB>Z86X~~$F
zqYq{6b0e8pkB)ueKFRoeg+r_=gQ=;YNm$upB<p$QvFQoVsrNGj<wdVe3bnH`tp|*b
zhTAGDB)56-1hvq9|J>@g;sm4z)yhJ4b*q(54G+(}+WU>u9~+s-=<uUYMGhu3lv#9~
z;4f7dL*m+a@;BA#qI}AQ#ON%^sV#qt)IQjhD$HxtDCapcVU;2@e^+L(pdajRT}Y-y
zf&yq<E-M@Pwb+Q>U*(J#?6|s$uoPOi?6_K4{F&|ZM{I419&Yf2%Bo9|qM+ts<XYir
zzs_T_##i4jBQZcR`4-L!)u2tL$n{KcIEo#s589qLaeYAP|4iKm%{9mQDT8w(TGHS%
zBRhDAvG-MuBsZKJssTx+pq9a5eoJkkgl&ZIRy&f3HjLI8MF}_X&vO$PdW$gRO^xfb
ziU9HlTk3RI?||^aM2_<!wM1d4Tn-Zf^;_J}QMY?@jpS8fi4@)=d=cgp@LSw8!64e&
zftGP;7*k&eyIhtYBF!xvhQsMD9^BpSnkn`|i*?<L+wFz6a-gE=9BtIJniOyIr2-nW
zByhmD#b6V*2=*OFZ4b|GyXxC;--J1KNOm<`r?ZI;dGZETmiiv#ow*8Av7ycFURnvh
z+2U;sFObsJdNekEK&$IPU^d(es>gWapna3TwY7aCDvqC1!cw3GUH07N?~{E+Ub%3S
z=~3`*OQB*!%=?U@gI%mI1&hkOFiuuscGvx;u8znvz%9Do-SW=w&gBeQK!f?L;8z&R
z`q!APv#0AbN4$Zrqf}{|2b(;EyBOf2P@);#89?<v*x)EUZ8nTGYhPS_*WM-dMv>Vs
z-~j3K#F-wDGX|Um+*;lz1#EHMPjz10+$~Kr66nI+cr$n#3h}ye&=54II1<ydeH4Lx
zUJVD$Yw<(#glYRs&f#U;kFX0KCHmAv#dii@SnvhE$o}%s-{%FhwB9y%wRW`J;GF}J
zkI4`3s$WNbTUgfKBQZn8603ZenJYV|{GEax_Z^pr5ypr6o=!eS)B|!iO$O%=(h7Xn
z`(F^-gn6X-j&FnlE_rJIj_o^zXZ|^80sh6~woC$OVGf6Y5p^c7*wXPUR44MI9c>Id
z<aZ$6=vObeHr8rnSn1oxEQV}rHtd}Fxk7S^-|tqg$qf7eA>3%*p=Qn2uF_^|<$ut;
z?V8+5{mIxaQP+s;s|blXPB+fE@!WSBQuUbW_Z%|ax2yk7<4Qk=eYb&4X(|=5=#@4v
z3Q!dPA#5Sz4tk^A8BHxekXbt<2jS^dp8Fj?p^-Seplnma9%B_IQfic*wp>Ui=*J^9
zj@qCdwBAgjBrWR`h2FvSE?M0+V+)PVgoVMvB{=c+I{8XiL5eefRaf6FMSt6HwPaxj
znbrVqlA!FES=t#v<wFb|$QOvNDD2;D?zmMSLp5;y$@^*qS7ifx=xb!AOK?eCU_3UW
zhtT_eE8e=2fiDa;Gn?b{4_N+Jfr%XLpMvCW{WN4{aY$QWG%!)|1!-LksqtU2a3rT#
zc6Zc*2{uL@)OE^u^syw@r#AW=r9o7l9vM8~Q91IX7FzL+U|)Dg-Y{Y5(JG?tcO0`!
z{rX%bTZA%PJhXdUnnp#z`EC)G?>noEAJC<bPaj=5j3-mp-xQsTj|2bmRz0^na<AAK
zJsjm1JvAf-E_K2{&3>-Ql;1eeMn+?ygkOO@G;%4Z5&Bt5vxq&>^oa{gIW^dRGb=37
z@TV1yrdUWWz9ULqb8{nAA4RSeMG56w1qvEh2uJ^C{z|-;c;Vr>Zl)&RBDtO3D~>2q
z9N?ukQV3|s$O-48s|8Q#S~GNKC5oDS4=u%4Hz%ZV4OWZOkdLXWI!rj9%5}<974CgF
ziww`zrk!Jm*^_d9t^U?#qT4B<sq_Bg+qcZ1(KY^$c@vv!I!R~g+6>P6y|vckp<fD_
z<WN<xYnOJa7wkAR`?)el<2f(_nPgDp$a*ikLrY3FloIgr=#cz+qKKsBRw@bzoC}*@
z<uC>Rz>u7VQ;d{5R!<*(GSB}l#Ve_x%79X;5=&)l012lnJoD;xnL9W?iB?HrPtM57
zc&n>z%B*kO7-1?8KTG{>!92(Ndb9_NPE^luD+zG|-~Oe+jN`6Lw+5~h&dlz=vqeCQ
znIm=R&~w29k(u5ETODq<?)q@IG{Q(?R)U^fXu<+qdpNxu5-8A*r<GLoTyWLD#hKrS
z5_ZU~hks~Qb&|1aOTw5mqB|UO$qGmm>G%Ha24T;vm5WRZ8k2$$Eo?`c?mo9X%U9BB
zGw{Re%lw8G(r~o8Py}=Pj|M62_WGQe>IFVcH8+Oh1Xwu@+n*AzX+$5wX(QH=x=%)w
zGILQ_xzv9IWUwshDZJ;~4m&--l-6cPcavkmJQ@49EqIoL1b*eJ0kWyO`#-09_sD0R
z5=N>gu~q(&Zj3Z9&%B|UHv*3dbO9kz4rVNZxO(oT_aD|p{B=5i6wc)1wak`^zvJ<$
zcZQkGSu^a9E8mgz{~YBeY8uo3E3|jCA|>ii?o7?|b9Eom$#Frt?vC1SY(zpAu@*j4
zM&;B{|3kHGOFbm8fb@QFV@Qhg@4>CK5evn-l|x!veAg^xlmY@t?bzbV@ci?oQe*R+
z))=ZVCW#z#bCO2I`%JS=>4APxonX^HOq$$-<VsYJO<0>XlGw<s0y9ku0;A2BVZN28
z7N_2;9gU5f_SIvp3PM)#<Ks$tnr-iISrabtH7{AAYPV9?EHmCI*S)vdW5;{0zc8zG
zJ7cNt$cM9(<my}Zb+w{s=|!@OIo-GUMfP#gBJy`LyCO-0ov;iCa$i}W_KLR^tGsHG
zk;#_%hTClz*c3!nza45TXUc8z2Q&G2omXJ}KZNJZX26^VVaQX4P4_v_;fEE_@U5@9
zrzJQW({LjRDj16+b7(Z&?Fv%$Jzz@A&K9cTSK$r4Y2l5<CS>`n6fV!4`N*s7`$PfZ
zfWm&AEz`&B6%R5M=P~U|{RYLW@b2+BBSvWQGsGd^=aK<X>Lw{xIFmPNFd7Qv8TdV}
z`w>YGn6b1bJ(WqR6NvGLRZ{G}LehM2QH~K|KAA@SSx0TAWq~i&^cFjd(ZY|Ugjfjs
zS5U1(K>$Ux{|@)(z(h>(PlVd|>QaPmGxFJ8PE8NG!I%=_xaU=h5-QKT^dTI{H>Bd8
zA?z)I_Wm7J;R`oL>cQ0Ew4(2pR~TO^w$;@RK5Z%*e`wJAmZ;Fi>GKeL9_^koQ}yOF
zgl+g_;T*}OfYylkUu5gV!W%Nm;rs#O7i<(?d&jx$49yCr{@(v3e45Jk4+4!L;MRTa
z&>5ypV<qrLxo_2g=nanIK)_AGsHW1KIXc~r7`MTFUUvJh&XeDozB|X_F^NM`8sje!
z9`~vOBJ1|j+jxb3$uUG%>~I^#>h&U-bhA;3{rsblnznviA3JjPbn_T{eUo>lHO^dk
zii#@gIf{-SbHrM8+PjAPw3#A0+BIGTPq;LZK<U~!H4n&bR4rRRy`y4_ac=W;*&g0G
z-MCyv-aO!|^x3o2P%t7%UwpI^PJ%CORqSEb@KMU7`*hAcPMgiie>$#qs_OF>>*Jp7
zTP$yFl<p5QjP((SX%)yq2APliDr1f1O%zaCkcDQ<5I}|Ggg;@|+?xCm3p82oOkTLV
zfW!{Me=}`1%C!>^=$-x=#`;=4bU%I_Nem5T(c1M-uZ^cGDpDgzQj^KBe*LM?EBY#3
z_hxO|TBbrcH1|q7TGV>D&~(Yj|NACS^SI&G@Vr+`{7@&)l?Ch6TRhSf!B^b(m;q0x
zGdHg^vsatfgd1#X|4#BxykGg%tL+`%cQg_}V8F!@+&ec-`${D#WQjp_)6#K1B@w1G
zYu4P@Bi3}f1upr%TFv{@?npgoJi2!vC9b^s=m%!WsuWeUK>iOUjc>WE_J=NG%vIPw
zDyxk}Zk!8GT(UlI4=;H)(@uhu7{v)yyB^%GI`+Qsd4Fj1jbyUq#=y>-3_qGSw5ioO
zo2x?6*K!@h-(`15si@cS&VN9E%eHKJYfHxHubzX0@yMAD1SwLAfPp$9UzN!a8$ohl
zH8{Q7k3j!dtI|a0p!sc`RLxM@nI^YME?TrhH58k)bWGlwZd)NVkvFvASN-+MZ_a<t
zxCFkc6=c;y#%++E$<M9(&%n)o9yX(lO&gut4aVhCt+7c&zayzw>LvxqUbj=UUc;Y6
z)=+;0w*Qgzl~HZBU9(Rq#fubo4=%x-;%>p+t++ds;uhSkcq#4<MT1kIxNC5CJ$b+L
zJGUfj<(j=`%ZzhW5gv>PQgXSY7t!nD=$<%PqbX(g-fn!w;wim^10hIGqnN40E6L$F
zQHHj4DSsEksoAJi%t=W9O2QktJ=FYePICWbIU<<H@Uwv4R-?rE<CY9)y-JdvDjxRM
zCf(55$Q?lSJAzuH6tf^wqL`YaHb1H<U~gWY49m`DIk;P<NM4*HOKv!BaYccR0eR|Y
zw2=6SJ$Xcmh*;}?vY|<0^tvg5-Z7<GswrIIZ#cg}7QEsv1?wg-)swYU&Aj})UD4-N
zI}%2Gxl>F*-C7pq*f@4=R`$FJDp?$}WtO}`C5UC)+&<j`9`X)>6cWtp<%|!Onv2Fp
zIw3I;QAC@w+H02IlCWypy(~u+jcbp_TFk7-b$x~$rdzc<>|jh@J<WZZ2`B`@u5_5I
zb&tDMj!3CCx072jkS}?-N|aEvXh5PI&crK8nXm!G;fKSH?#Rn+1&+c<lU{Dn<sIUG
z{%@NkbkZ{Pi}%%8WZRyr=Ltb&w`98wlxJw7(K@G%k7Hq<@UlK1fh7p&D6LC>U-9ON
zOca=5Da_jVvd$UBi*|SiR~f~pL17hrLJ257I;j;^wk06H2Wp-G+Lppnr~(AtvjzRB
zAr&4n<`3L1wR}5R)tz*7xQw~J4s}tSldB}u>xS(4=GM7~Un(N7Mceq0X&-S1I-XI`
zNlRx8TliQz#EFXBV@;_jn*Anns;b_UqD+kSar94W6HlBX<#Sdk)}1@N+#ls&nJU_O
zG^kt{&c;K$@_FGa#D_QdrR5W7mV{4N#-~GX@=dNIuv^cvU}={Pzj`~=)O8|Ee4XQQ
zdzHlPaXW9J{?Mn=W7&UahW3Shw<ga&x*jHcsq_upZ`Lr<Qf*Lp=+i0&8?Y*^=g%V|
z-CMdumVfnH8`O)7xn(pW*b1ZkykJ>1TYBgt%iv?`n$+X^LepGYAS@}arUu_$U7!6E
zw)|d=k10idKF|OS%Motr+t;#NunfgqY!)j?5nCW92aaOqEB~*IEP@qj8H@i3mcL6;
zkNI2u=*$C@=vE4F!;*7tE|~G2i{zYL-ConLM;H<3fVgt*x@UWC{zWG3<fExtHv-R~
zkg|Gc*@OwZ7r1ipDrl*gG78ki@{_Z<c)BHOk9i0b#FP*<{vg8_9CI()-I&5bPn?Hs
zJJtSO`AT&Nk1po_Y|?P(rR#NUa9DY%xP{4CuBLpypdH%Rt`CV5Qq+_Qi2WBOaT4n=
z7ll@i$i3<fO)Bw|TBlE#=ipO|uS~O^$?FcF{80KWv257DH}5{%>BA;OMEPG4ans1i
znsBG16t#_8sYjGCfu959T+lQgBOBkR+4-GJ*-P407`GtN22Y}|J4peH$mkzMk_cR?
zZ2N%AUpD)+2Q^eFmO`Xlop2;VYMiLjV)lO|;Yn+CvqlwOZOy8CFy+&>os;u2+`|+(
z0m~D;y9Q&~QKz_W^1`@6nvy)14Sism(spaeNyQEh?I#;qLTbw@@;)lrnWTy1l5SVb
zRq<_aPsELZ57jbVH*<mF=T4kdV7uYgm=spIOqUuJ&*p@B)KJ-%-JV4$ln6dYYRPsL
z3u)P;giM_~%o#CCz@-$|^D`(>R-@?$CQ<dfbWqUfXNc=DH_VPl%;Y=Lv+bnbyCKf)
zd$R1|moZkx={v6xYxKI4pYqrRixlqgj7bD85(m*V@P|g)VkjSqRl{;q)R{Wc51S3*
zWrqwZc)cCJC6)VwQylFhvR0AQ)nRi0^`&y7vXk1l3k-{5HiK3z5ZKYa^(+%b!W(!E
z2)mr1WaOoSN%T#bR?ThcRf!F8We!`_H5R{PDn#K+!<53O?rr_Z!b@j5DSh~z^l==B
zPt)po6=pLSc7e|;99+2Sv$Y<%zl@jtsegBojZN^t3I=@Kz|jKN^8A;V&EyDiB!9M_
za|hdZ{@Z-W9d+sm;U(r}UpTafl8&Tdi^8$Wc#Z<(Q=e_-1r`~w`)7cPaeQf#Vv=R2
zm=9|2q=^Q0vmES-aqjc&EPS%^axJG=50u@+6moDDp;YXOx#A3Q2l3k>6n$PFeMy~G
z=oDdFhgIgfBbOWHq32>6ih@;syrx?DT2f}rv@SSwVx|}c?jSgBh$$@jIhh9#udzC?
z`B>A7i)rKJu*)(d%I0OqG!bbZd3*y)upv!rhNV=yb+?B}a^#KtT$iX_`cI8y)?GNT
z);X>WGUWLD_N{1A(5^yA6c|h{RoSRt=^@Z46yKyAVU>@hK#0IHwFi4iLl~UTSfPCx
z3@#tGw&8U9X`FN`-Iw{qzT=14M9b6A)+nlM@C4W6ud-Xz&6zc<lpMBKdJ5Rv3d1;6
zO7)Hu7POg%K?e_eiFvk-B&7VG5vHmaY1)c|Z?A`?(a<!ZT$$YQkVEM9=C2%z;^kwP
zHY4kTrLT7iuSIWyz9nnhdJVm16;dnL7k!waf8wb^F~@OHEMf;BjfZW_Fau0aKX{iJ
z>8iULYXZnPZgfZY>^*ig)!&=75OAT+cIyYzpuQtDro@sINwwG=1lVT(f%~dqI=9m2
zv43^UuLufBFv%u9*gT<xKNY5e90heA6DiDCfaE%Jq+5)~qCT0Ig((r1N-fe|xJyAm
zpY7-Rv{<AWRuj^FIMaNy{mpN!{cTUUt}~IXX3bZgVTlyy?k!hP^OJg-uRbiny2!jj
zo?jCXU42T>9;3^cQsl@cJAM|D>lV1=*qN6KZ1k{#bawOFLEHZ6TJi`_R-|ITY(K>O
zdTmtt-kB%vdY)%5;qM<Ab!iq6whmK=vfgN}K#rr%+*y_T2&-P~%+nCE#IU-<5yCKN
z;%9Fp5aD@1L58CgpFgzYcl{mAulW5-en+VnG9?$6>0Q9a7Zjj12~}0R`u!xfLVix*
zcUj*74jSumEIE9(-$f{-r|93RC`GJ>+0_t6HxZ<MCKrDh<H5w1Cbs!@J(QXd`mn`c
z*cx3ri8)3#arQ2bQ$=C<-LktLqKu37%4gc>8Iao=W12%1+hXJS{z0uVnu=p_ANnN5
zejK1_cI6pg$SCHF%f=V-r4-h70o`e<rlP2IN?{repo&nWp|^Wt&M{Jk&WS!HP;|<l
z_{XK(x*?fj4|2n3h+($)YDxXW&@t9+a>MJU#CB^iQ5+pvJgoho<p0jB*7=F!50|p}
z0bSCUGw<B$Yi|2%O)d|VG5<_<Jt`zNI3DpjOe)mYfO@ZUFVNVvYS`w(FcQ-Q-uubv
z{ll8Jkp+#L-(%Bn`o;EcJ0uMPh`WD&&~2~G%kDB&(EUPSVz~j>6`-_o%h%I3c)Wn;
zDV(Mwe<X}(sL3ayw<V*EuVc^k2z!jAx)W=UI&N6ddn*3JTr#9NIUf-diA$3*l4`lS
zr^|no-LZp6@NqueWn9$fSa^QLLAt@Vn=dE<zm)DgLot9C6HY^EYi3FF?c_daG+UHU
zrfd)9!cY_NNCScGP;EowDRF|K4=)(+_d#-HhZh@fI~)D%H5jPXdB!{EuWO=voIMvf
zki5*T#aT}G71rZ1?zi3i_t3$yZ1-$*H4^IYuvLEOusSUJcIt7Ty_7VKJ^$nnHSU>6
zb+hxonH1-sh&QWD>AkeJdRTcM)CQgo7`r|m;aRV@4`IB$1Y|X_ni3?+XXgZ3=2;u(
zLI>OsYt{Qr;$*@oB7e2`?sD=pH@&BFsF7SFk_QaScPK&bACJrOww9uh6*UKu;q>w#
z-hhyT->op?M}zM1^PmTj_pKN<mtu{5Ny|`J`+V8)+BgWR4+EtU9f5uwK*%c+C<nHn
zGSB{46Zm-jQslL<mEZkN76hGJpx5JJi&d##b-XMZ`~=o!ToI{TqcG{#*baI+s@V>u
z^nh%Mz7H)dop?U>osdwM{}YaY-2C_t`K71l3f2Go2={G;{FS!nzAuJ^8OO)hA|=i!
zo!p>fbhfC-;_2w(&;b0y^0Mt?Lq?Xg{45Lr+f=JA-(S{S)G&oaU9Jff4plnQKn*<s
zdno^VMh*#~rBJdMQZRn_OIOSKfU4%({-Jf|xYbA|9_hx8zBcRi{knhhrD7I4nBPFY
z(~+9t@vTo2(4hM^$&_y@luT(y&?tnVFgtwu(`Lg7rrsf9U1TfR6CuoI0-G7H*!l86
z8Gd<Sn*vji?gOQIt?LiCc%jFuX@)Ij!t7|;3ItptWq$l`V1o|DM_6fkxNv>**wfD1
z5SOu`TrDdwy)$n=?nsx_ODjVu9{3HH0C>H7d!rOB%0LVJ!h2Qz?67WUV7gT9+ScGX
zdouf5eJ}>Dy+DD^IWoc9<tx)c;*8>zuYjCAE*t}8#frt#x53=3GOfQw*aERSKJ|J>
zr31aWlc&m<;(y}=+>6l1CgGG}YLmiLne<ierY02(GkRGJet7y#K-^<6r+vjFhus+m
zY;Ht#y?S{j3|y|4Gb*gm+v@dR7JRKrXXAvJfCd&$p{$FY4vl8y;*z2+DFx!j6siG=
zEamJ7aXfkD(m*qD0<DStX)R)GM_bautBaILz`9tquxKhA(6_9VG(ZhLAvYxHIAqaf
z#b|eXkW68cdv&-s&cIhK!dLa2+z%df<@x%V)nhVwCdqwKA84wSxPVF`OWMg$YyCa=
zzMxfsNA;#j>hkMW#8>QP(jaKoMlrDfU*cGFLohia^Np4hQs#dNd<773CtSm6a-t;`
z%w5=c+f2tHf28GiOcb~{9fZGhxSzS>r`aHiDJF&QT?3%80eG0KhdRs8Xg}UD^6jm!
zNFT?%ku|GUFEYc*MQ7hhskt2BC^>$OBH6%cl1eS?|NVC?Zzxq<H!(%Uj@2iw<|=zw
z#Q5ojLWzV|jDEo7Gn-z=9zo?myc*$gx)R2Gd4XMoEKUN7%c=wxAo}Xv`n)HEw&UtW
z`NVCqO(a0XX;e_7m;3Km-sO9DmH2xJ^bxGVIU95HHY|ha!bX%qMx5mY(*q0!9(uKZ
z@*3l3Nd`#@=xYR%HxITEWbVA*!&!c+zWF4x1sM5(-&!B**DLOg_;F4;*<d{)t97?2
zVczR?w;t&8b0Curi9|FNLLBg;{V@(W0G$?s)LBCn8kaO@THhFglPc7!o1#{qhwaB_
zUx6VE<^M_{#m@XpMuADM3jxuI=~%QYWf^U728zQk-r2%`X~hLoSs*Kr(q43jr|b#g
z>OWAR5k#E_A~^W!e1j{o3WshJ#zrL;M&ek0H7$SKdWipw8;dTl^pRnx_?eN;%dFX;
zknABAAFkSgyKTw-^5}|D<{PeZ{OM=u4(vwYfUR`SzA3TgLeW8ctNf*BNB^zWF?b|h
zULL$)mm-}08+v&)!x2-(!^Xl2G_GPdWCXdBj^-&0x-FgDwslT#_Wgrz2DNF*;S|Ib
z6yJ$lY{ZyZ7R>DrX(h)wVl31@yhOnU%=XkqZu`H_BT)WvVG+5WL#1(%ZV~=Ddvv|s
z!sc>!`H01UFEi3zUaCjDO;4-jQSChN*WTUddXE_XQ@VQmI6J@o;DJG+Mm{|!zy8|n
z<i1|^m=kMV_o_JKNP6JYNN2I?Zl0xjgQh*Cj{xZzYwCULI5Z@qA%1cT-=H{&MoxY)
z-e+ryl>?}5X<r{}?0k0E(J;H>Oeb<A5@DM*eH7N%{;`n01avjMoM1(W-9!bF*Wwk_
zkuNO%IXl(UB9D@iqLXIkTRA`>zxeIm<y0uNbR`~1DB@3p9H&wR=VleLT}~FcbtmX2
zIRL&}qH4Ec{RE4SA<rCZh(Rp}#Prw-R@z*;_Y7n=aN<FpO)0as&SXiY7eG(L)B%}c
z^lNaK>zv;n3_el~`Iq<Em&aP`Y6!<`*a1-Z3p~2!ino2vQ44h34MwXKrd=*rh_!VU
z;ltGU&&|sEDdd1{^!Oi1YP9%ydB9F9i}IA;lXgs)<aoiqeC|bM7#4Xxt&BXIuJFkN
z@o+Mjai;(5n|u|OTh#Stm;J(n7*OrV{UM|Z=ak;8ZMJ|^YG8?lcAclW@54g2QZ;wW
zg+n&EXh0Tr6OrcBSQTA;tTIX6^66*f%`puFjH&v_`V@ui>;YYArf8e6793AFg8Pr9
z5tcia3#2fgml{l*g}Pr0C_3|R3ufkMa!GZKtGlC39+Np)0v8P!#I{*jbcAeg7YI(q
zdX&-Xjq}fe^Pr?18At}fM$Z>0W`y@59}N!1Wuo{X%CBWF<uA>lyOJ(hS~KS3EY~kX
z#KnM}s3T;uDiY}QC=hOsDnkBGZs|&*vJGv3(Q5m^#ah5U)=`F7T6Qf&VB({3vBJ`w
zj6M=2y$)IT-ah<+h=a%MhY+r93){3Gx6ZO)&zZt>5AT9YQld+QIPVbpF{kBVMvi^u
zUCGR=a>1R}nSKH{NcQB+CO~xYiPgztgJS%OV?9^h-T0Hnses#CA|e$IFd?xnl}m?Y
zb@O(9%%1i$Pa!uIX<{at3?Cl{og`#cj?pu9cF=A7>Drr-_in=}wq*`*S}aGsz8iPP
zWRDIh$+S;82>oZV*f*4hz5`oqKjVV@NPb}aQ}0k205bhRMLHv&)j8vzSXC^>Y5O;F
z9@#^-S)%Q}Z@vXX$US&7xe3Zgma{GE{PG5IB;TdA;#WhV2<uBkf1X`#sU>XE`OLc*
znazx*73ndax(=7y7*yeartgyNIWw4k=7)zv6I#4~M*d(fJ$uy!U2Pfi^mp{D_qcF+
z#3W}9b-w7DI`>r?{ckG3%KPmqA@%gSY@E-Bu%_cUi`Ei|!3tb*CT60W<cq*$wQZ05
znskUD=lj_FI;UC>wiAs?Sg&@lKjs2yMUVxf0BK%Qf1C61pTtm<onF7;RINpWU#`jI
z<ASemM2dbQb+Vbo0@&hsY-T^&r)2%9Q~8jP`MGd6qT`uWo}OFe23UDUpdI{0Go^BS
z(Jx3Q=}X#ss&LKonYHxmqKMI0R=*j-Vl(ez6-hTSSc55tq~iMK1+C{1)>Y9p+CoHC
za4(8XzFjt~mhUi?F6l?0r2(hX>6Ge0k!S3PpOa)(YKwPoymNPMiL8f?4GfH-Pg=?6
z>pGjWe>Cc3r#;G_$gl_DVor1HR|!*Q4sPX|hFVUa8T&c=-;AB?FHh}w7f<f_`L&=G
z*2>@?b`+vsk1xBuNNnb=vw>qE90ig5$7xi01sH_w=D+rf?r$^kK1B7rFpHxY+`l2E
z?@Ooi8g=(x&Z;YtmtQ}U`=R|;#eG`!){U`nJf`&aqQaImz;GM&Mf83_G~{@Ro_1;Z
zU{|iVT8gCXMu2hymfG_LdS;Qo?^*M|9x&&f*VZj>ANO1abl=`Cc;Cf9FZ_vnoV^BT
zcrppB4_T?CB83t&JH`V<#$`E`8aOwXK_OONf9ej2GUsplLqVIS`q9T@pGhEn4Y)DK
z4)u!WD<~_Vhw2H*CfPD_7msqWl7kQ+b9GBbC2r;~+^Fr8y*QqYpdCQkXia~GJ}JPC
z_8V<}>I6@2pk&p-><OC9EdmTK%k*xL&(tP<eO|S1p<hJL&&#&{tusKz=s{W{J&*KC
zV^y+Zno#PUHt63r?hd?9W#L251d>!~IHzoXYZzIoyZm_XQ?p1|?}o`(tuS|8XW{6g
z>P!Ma`Sd$aMN~=bYh{DsLP>+Uc}{)?fzJRQX~b`+shk{L^j(u|J8?8vkcds20dB=q
z2#J6V=Kuf%?e7h(;KBcQ%4b%$wtt+?hE>Xc$S~Yrh9JkmD7yYgyhMU_Kno0V-(!SL
zWd3;HJ+!9pII|I>A$b~fym_v47qk!as|rfNxk=7YCW(Kd3MELh(1ro7^s~RH?3P1o
z9&9@b3;LgCKJbxhxKBJJrU?!b4=(!WC*!#<kqk56a*^-AzJhM_^uZht<&r{rs7I4>
zgn%RecDq(cNVhT15h6mjDMdgDpmlY<RB9Ho3Nok-`^fDZW42oMg8ste*--Y&`qlm8
z^37}x^W=s7>xm69XQ$1_m%ddfpJvvUx9K-yszM9Ihta{rd7I-G^XG>n3Qq<`uRgT*
zwtJa|km)I3gR|~I;!|xMBIdti?Xom!jqEeDoP=wY6DEJHxed1WH;G_y^zv{srB*-c
zePlxY0QCCNP=eYzYM$^pvOd9a*(%|7NuKDu9{N{q#oulxzHPc^v~Lq3q*63%pmj!y
zDoSbmE5?DPaMlQ(yiVs@K*&`5D-yRKiN_yCQ_<t;*p`Rf)S!Ox_b1iVjPwCi$^`mo
zt*<$QlDfk)Cc#b4VG6mtZOa`4IYB8kO0Qhs$URId&7XARwPt8W#YwhcXpME8km_uE
z)8=CRMMmJ)tI*%?K<gh#hJo}c+LhEqmw?ww(Hk)sqMG#O_H`@Ns!XFq=5R1=Njnmo
za1f~_kDnNQ(i8_Ct6Y_gSo4#e(5kGHua4OSaFOF+)P3$<Ckn93U+^?*k!RChoS>5W
zKnqcIg@Xum_+gt;s`g*)thAI<hEDa)mPE+?f<7zHwES(C*nCAw%OX8pNm9q@%<pu-
z4*NrNcWHXJbGH-V<;6hxM=P2wU!b=w$|dkMjJ$UK6y!|Gs;C5NlaT_O>nh^K2>H2_
zF?@P26Maxm!E8+%9H|rNcHrdJAY4ZVA(4#1oYZ`i?DX|tTG%>eQ%Y}kLao8$F0Pf6
z@B1>{f9@SwuV%J6Hrjnjg*CQQh0`D9!`@Ha^4n{|P#n;@`1bcoEZ<HmoJ{0K=A@H(
zwH7>^t_MzVL<7&zAm21m&I`w#_74d1A5LtAHpCcvZ~Wtyiadyp9q?+L3Y$#t4i?vl
zmxH6081vt*sD<7mYOas&t82YIavzhE$MZ8x?rcb{$$z-oHH;Cn89}XsZuylBGbV()
zG~S3=v{8#{G|j8}ui}*K7tGAs``YOCT>=mp;CIw<!8tjbyN`r;)sEjWV^ubUz0KPe
zwxnA|-k;~r>qQRYjB5DE-WR6c;CBMgu<z9*OSwbndp(#@^7>OtCZ<VvltH22o2t;8
zOPn19>C{M3H=1m3#h*-Ld3=Tkz7<Jq^3&7G)c92^b&;4bj3gcsU8`%B4#{`=1mFf8
zIJM86&7Ot*lmFn7HcdRBlh%IDF=o)^)zWss^5M^0)~r{2?(>EdhD+LW#hJhQ>9s*&
zD9IAd3C%_G{gxhHUekRZhbv9M_x=^Fyt7c8ZLP?twx&OMwo0OM5BK<NSFa^fZ~L56
z9BTBc*Z#gP<Ed2$?}Oz20UNJ3+Zi<KIn@gX5a9dC9QhS$yuspDQwDh$&JPHn>_OE3
zk;#vR8eT&fW24^7N2*;AX%_=-=ax!E)F&3E%gu{vPwGu%<iCf&i{FxwSII7_y)*3p
zDtxS-WW#Etw?7dx=Knmku{9K@)ZP`+g&p$8)W33oQ-$2z?8U@sM}lPAbUQ&+Xg~(#
zapG+f`@x|^Z~BUX9z%ign{uM^4BhCL=51E(4ko^tWhr_T__PGRnL;x}#a2yaeCQpw
z^m@6yhPWAO%s-2PCoTS3VEDKV2d4qnDs<jL0abw!L09sMwd<ge*}~L0#HwDZk{Yne
zAasbO^9hukbQJ2jT$<f{SV}ryh$Pcq89t`d9UvoKXM&sQeqFpFD>EQqCaecbkEZ3b
zF;=b3(aPlxEDfvgYihr+*5UFJc+p*^s`N6Np(4`aB%;fCoFRHEe6YccOk8#sweKOf
z_USP^+>*tY5rCy}Nj%l=QS}KrGF%aRqZ7rw+nWG50t;b-!*j~rlv?K!NT{Hc*;NwI
zfy37}ea_j3Pb^JBrJt%A<?fJN(RWtkgb^d;zZj2k-$wb2J=)}86eNugDo?|LrK>;6
zNJh1Sfi0s}s{`s}++}?k`fIoRGRyyRIAng<qRc<%%lg(}Tw)Z;-w0>B!j__bi{rcx
zqFI(}enbg=4z3WmUkM6a>*}Y5iY(YM$Wv6A+BUeU1cr9BEcLjbo5sfz=vgA+fLiJK
z!K=7rySt2#dxGZ*ma}&qraZ_}6c7;eY1GIFSM@qz)zllA9fd~?#IDN>V*@bSfG&%l
z-d~$+-o$8{bk$#C*$9MD0=01miM+gQ%hJw!v2X1f+cyscw-gl4_VBSHyvF6Kx1FZ8
zr0~rXhnK+lcHu%U^SU{}Bq&J{J3Drmra#F&xQZrTNd>63>K9P+B!XWGxcdGP0+=SG
zUD)&Pk~Ue<=@>?mDCAa4tK&J~P-k_4`o;?OdpJZ}VwA&!<Vm!*y?L6=u_BO1@{Y5Y
zs-%g+T~25ueiV+KOalSdc3ks<Xiq@miYm1zk2azc%BLBcqK(hU(PXK5AKHrir<cWq
zO6258XptyuNn(C_$5=FzqAs*teoUuVj6}E;juR7%(m84NwzJDkePdDCX+OrcI(+_e
zb74d|#+7R%o3!r+VIP%~RA5-{LK2iGkVGEZttrWrUWS`$I=rDS<SJS^oIMH;brCPU
zRdx6zmzJEG`XgdTM>f;=G!{tUKrnzD=b3LrfK7YI!l8=PM^D*~u~+e5G&lq%59^p7
z4OMeBgy%=jC*-`ri}>SNn?f@iu1qo=V-B|hn9E{Uvc(t+8>{wH*$!E$W6>MN?ay+=
z!CK@AUoEP|r$d{uxVJZ2-ACzPOE)fFRCtTK_+vcMb-kI(2+f`N=IZKRv|-(}Vp*zT
zRt;OadR(<>I<x87)Wx%0n3%1cO*x(bDCF|wSpv!6bwKF-znI}xN>AGV`8!Fjmg!+z
z6M{j0c{R-}MI!WkV5ue|)hdJ(1(B-Bx8CSn<;eN)7$+7^By%)X1|PoaIH=z4?)~ej
zpMD&{AcI^IkYM2E3D{*cK<vZ{)5&ErXltJ|!A!P%P8X0+jwZ{kQLn&5dWqjR8=(~O
z{XYU%2MN_T?W=OGb`NFhvSjs0d!W;P|L(X9#fOUWKIPET1n&X2G-0%Dz8{dL;dL8%
zT`V!dFfE5*KTu`JduoI?qa-1on{dkMQpGRTyp4|f>Y?Z2H1&KRQdQjB!t<7a9X2au
z6p%%p`@#^dWh;p@Bw*#@9CGd?JQbrKq|A0&k5zS<J0ZF=hHYH5Ptw`PbEe2~rs$dn
zk*P5}GTN1XXXJfeSl8^y9>HS@ky^L!iRK}aY4>-yvgZ3jVkyGcZ1*E2Bb1%kxymck
zbGb0zlV4Xz;wO6G$(82!8o0?6vV#48nO9bsm-`u)`}8ZRSR<uzfPa)5cK+E4YcZXx
zFJw$xR8e5v17qvHY^(9i#W~NpYPBXi5>(}SVZ#`uJ{YO2X$<`O4V04L@A)z|{wxDy
zoQN}d7^u08g9;P)HUq@;1+ed8J(}IS5i#CLs@Wkq$Ld0pQEHE`i_H5_cR1x*SgZ2;
z27=ST$xQ-*>ExdC**^2Z;6FF2?u&eYP|}Bz$_;JZ(-6n&S`&S1k)Oh%215LT6W9&2
z9o3G_Ng63*??+=kna`8=-JU#bry}%R4s;@JCrDGIf^b4j#~vSEQp?CTyq@#BoWc2R
z&W;Oy)g^pJHCI7z<>YI#`6Fh*#@;6{2YKr%U-VptubCFyKBYSpg#Kw@esdDN$9}wP
z5tb6+6dj|3T4Q}J<hBc86@7p3d3&18Uvx`YwwZ^OBAQyfE!{FXcg+8J^P=+XcMnIc
zl+o)E_lf;bb}~d{YJyAE3s#3(A9{!zJ-=zL`#&NCz0u*9gK_x-Ow)`XRk|C?OgVq^
zcF$&#a&TfK?&zO-`8c@6u|Gespx^d~dTH@q82ZWn05Vzz9zPM;W=&&Y`!5W+F{kk?
z<3y}Sn5O*f$Rh7-`zjiXT*TG0v7~xo*!~*ng~vlsgZFp&?^#$Sub)oZfE%-3Zo+xD
zZ*H6xh61v?RV|CuCjY8|14rbS(xdxQaFV!lpxKX9$Mg;VW2(Gc0&}tN)VOMC(_kuj
za0o3e-EU2Ka6g5Tx0^Ys!{+6PoSwu+&%%P%<L)@KilS2751BK>YS2S-oYP8UUqTBn
zZyP&MEXC4bRR`*87jtXmWkGkX76#jDO52xP2C2FT!!gkX2i0~Cj4_QNCY_cYdrZcw
zT#PK~<{7t+)b!j?1-aj%EM)1wT!lf9>=9{c)Wg1*W?kt!8SXOCDZ4rfv5B1zVU4Y^
zHVn?#sO|N`txV1};ge+!+VsObFf2D*U_bpZ^d&jyQpl}=ds396ALi~F{<uU00fVo9
zMig^bRyFBvoLt?Nz=U}N60=c1r)g!~3z5ULPq6);GO=-D&LCFkUXd80=*WW-{wE1X
zv0=Re1hvJ5_K1spM7}*9x~MG|DH65)4bIP$CNmWm<#jSTgj@$S0h1}va(*fKG?hy1
zC))wNe-`uPMP~T5lGTC!jjpjJy?_wr?YdDH|2?X(UB7InYpZ90XF>YD%xw~sk%|es
z&ZTa#2?p1CzL1Km+8C=<>Um^!BZp!uA*AM723^a^baJTTr4VgJEK9E1a0H9P(3%_=
zv5deXz{sIXvY1+{pB7>1t-`q_e#$RcM@CX$z@#=btj52z)Anf6`|Od<ks+9w*&mnv
zoSb$ZST0AuGADS)ru|AVnVwHEj?iW{#RyXUw96i8NnGvDuiyUlH@4$V^<U)`3xFlH
zQJG09q1#<^*N#(LyLrAFi|5;Qo=+74&o(z6B5&J#ha%gtnL-5W9$m(L{Q7L5SD@7p
zF*F8yO4W@KqiSlX*oN~bX_stL6(`;cntWg@9O(Dle^U(%>0P84z2~3NvNT!}`=p}~
z7pMs9O$Eu0C{w!eVp#K_6nl^&ix;u(9`cl$Wtq7t2T>%K+VE@E#u>kvyH|TyXn--`
zrj3I1Aw@)5|FO~|-$f9XH6h$0(lb||2xN>KRMocRu+2bB3m<3m-D&BcVZJ2vG{DIt
zI5}0IjM1Yw0c|EU)hHr5o5}k(SjJ?f=uJ|0RJ=t>R1T>jH2PS*k<{u(NA{^xWwXz7
z)2B({KzK_zfvOML6%JY1hC^jc|ArL!s>6g884Y!9RP*W8m>(-ycy)Dc{(ifO^r9#1
z4^%9hE7L%B4#<W<!6gc7a)V~~<L!cu;p*~iyx9`;;E=)5NLRwHf7kxg7zl}h;AUIR
zTd{nbQ$!Om##JR9e|%oa!L8r#$=rVW!A?Obt=j2gWGdIxtkf4`z9CJ0;?|ZL@zsA-
zmDO8_)6ZgeE3Jf|--03Y*@g%<GF9p1v1D_XLB>QGwt3ZuFuP+3R@9sZV0g(T#V*%&
zwrSm57dz9sIK=2JL1R>M%{ujdZu0Y`g^{IQO1ng-{HT);=0gq-O834mP)!lP2rGiL
zu7A7if-!=NQOj<Rou}%|e^YsWq11aEV2}{Ea12j)3lERCoq5PckAIYgT_e!{aM6V<
zH^+jCev@8`6YVi%?EG(xTTgfPDPFV2%h-Z((b@CAfP6MmQRTr~dJG5r(dsdkTz-Wl
z%m007E`;RF5@x;RJ-V+EfJVE^ntu{c#9aQ%hYSjV91a5CA0pUxbn)_1D-cLaem#nG
zH*NTgL+hF~a!84x+T?ye@YC=fwvHIfj?BkXM`IB`h`Qa8z%mWq6_&uAi3OKbB81M}
z(X)KPdnB1ruND?>(Yn{pi`^X=dU*7j?z&-$Sh?BP5g`Y(xGFLy0|S^&RhhvJ0Xdr*
z63LH01v<`k%wd)zTmJG1mOjIpX|~%mv`QT9U6EoLnBmA1TKT;c@9$Pc3N6H>1l{%6
zbMk-8@vVGd1rEQnQ}0NLRWQtG8k1bm2CZTXuY6ud{EMHafo&1cUfO}Dh=+Ei%>G={
zelF)rye1f?<v4EjZ{OD`l|Dvpl_P|?H20=;*^p9|Oll1Bh2PYtop0<q+v%_J6Z2;x
z92RmJz0O(PU8|tiKS`^PCO;(0&}JfG_~X><q*^P4k`|9sD`3MhZ1!6ji-BgI^rfBI
zR^8(W7T#S;Q?jAwt7TuJqYW)bvrE!%TNeZ4=uwxVi3bFhEn{B-sW_Kx%m871X*}I1
z7b)rK(*!`@Wp(j_P_yyeR*4ut%FxXNLpYV<1X;?=>-bv2Dz)Z{n+B205gR%ds(@PS
z5yZI8P7!lzJ#$(EGZwwxFL<;aeV2W5L%Ac*jtyrT-i5Ad+Y-#SJT{HUhl4fKD(eMg
zF9a7`R5&r8(#?7;{VN~x&gfdiWTR$8<l*_|U-OGzc<tB$fN|f&`p8$2lmW7BOy}e0
zmSpgAtI!`Bfg-Fs-Ge3@Daz_b)ozPbRL{rYrox2mH9WUL4$~~xqS@l@heeP}SA*2V
zb!`dFD2S(Dq=r|kuEea5jRLcAJ3(RMb15qAQ0MpZpOH+sD^khj^UR(r_EG_QE&~Py
z;})tG06v}9CMATX>;PB+fZfdk%~Fm>OV54zV-ih~fL5`_Wu3j0s`DWiBJ+lQtOl$)
zsl>CeENNP=K!}ZQ2D|dV)^3S%B6d{oJeUR0zQT=w-+6La($vccGLaqWjK-|v-8F|E
zZG;$W(vde-&!%cQuCqamGiHOg!^ee&OSp(3y@-9Qcq74L9-~5@K<M$cCxHSJy6#bv
z?D<ykOHueAH$FEDGi~Q#9?JUbCYlKy13RD=Lqaj(Idi4k(=fbDnO)J8LwY8W`LFbl
zRb$`QpB4-w=4DpWr`pkPHspdZ@4iVnX@+yBE%z0>noYj{#rE7Gz;PE@CITc0M!4|7
zq~_HcqY|k@M>vKN?{9nQIwy^`H;6uj)zB+#@_-!m+o$1VZbfV(JzcAYjWWXU0o^?G
z_nA=+DM-QDvycdPSOs%)dDRbx>!n9(p&sXCd_4Tx;^HIU9OC?++ddiru;v`Q?OE6_
zjyO)mZ=Mk!nB@0MI?__S)3|R?#y4uv`n5f&T6Bk78qPSUbx?u@naMpPUTaeecXtbX
z#Mw_GsA^BudZNK&QF^&n1edwlysmRiCEjPlYVy@%igl8<5u@tJa=p!$%-r?gGMG{c
zuRjLDQWV#k{t3_QnOc&k+3V}h*~Q(eiO;OOM2&?B8pN=q$Xj)@g3d7&tPcYJgZ+$@
zEPuKjArWv1&8^<oBIGs4R+-+eI3v-*g?JsERdIQ-x=ppJCk>_#=1p*5^R4#zzekks
z!lmT^B~FBpP<DA6F5gB$$~7Zdk}|}zV+ua-;G#~jijYeRHe@I>hY!u1f8aUh|3e0W
z`2m0u<_6o@>5*xKmqZx%B`FD4)dS^a<^`IGahC*2c1&INP8_$XzSVkY;q6fpMMZ8P
zP~pd6&bRHEtn0&(k?ej=H2DE+QT%1Te#m?o)bl{BBfiCu4IP@~gvMWkyCS>d+nvW*
zcI2~rJno=vi`^sl#OV)DR~Ub#sl$r*aWb8ma#$y}e+#BNrBrg{{}Pc{YjdkN9AN~W
zPMF9M#{p)xR8P~%GOS*V3eRG(tUi()emTyl@=g}jeHI48LwxF=&^}dscf-iD#=x$=
z`qi;xKXgohmWVzw9?@d)E#daC*dZ|JwnY~?ot=P;L3C)OkI<@%+WY8DPEcE55gf3P
z^e!Pp(0G`51jz1s|L&A;I{tKt_>GR!Fv&eGZrurVnOC$ObVqrAgBh_%9!_9R1wYSD
zvcI#l@Glm@-|vwqKTDtwY7I6Y>k2gfZ;i&RWPx%ni(WzZ$kTZg4_pK*pG&Rus`Km^
z1xN3=)PtZFB|~+f)QVG<#_3p}562;7b|GZYZyiwDs7akeFP$@wMS}3?)pF2>KlLnD
z;D47w*;++oq7OB1q+O1(NyP@<M+7}L<N<kyZA8`iej#teQzC;+E!q#{Z@uJHsRN$O
z;JiFZ>u^Y(u(AVWd-MpD>;!8K8w8q1ISNYZy0*q`yBYh%?pT-J-9QK0Y~N;f@gI{n
ze510p=O24sPTwi%^4Yz+`wvkYUYg!dm|&n%Vzj&PcBXPMNgVTX*5e->$V)ZG1vYoN
zf;E?}@&hxIq1N<i=be932_*#4bq_sS*Bz7m2NX2ULt)ztdBOrCiRFx^j-j9*ZZdQ-
zD1EQZYbu$6Y}LQTg&uzVa9a6akaY@r;w%=Ro?Ss*ee8Rf#Mx?xs=Elkjj{Ph+5b|+
zp`x3ITOp*C{HO^3=`Cg|kj&xgYl+73G)(KkRf>*ndQH05<>BfQ+kbx;tB{L0U_I$u
z<Hgy^oinAEY$1Brd*EB*wg2fq+uwQV5y-eGLL&SyDv`8v<pw3&Qh=zi@1MWDErTwN
z1Gi%SyEjA-(xtyrfRbDKxj>qjyPa<c@-y;EPxeuXxTm0(BMhJ_hK`o~Sz`guoT+j0
zEz!WI!!0HW5D4jQ*<3}n)+wwshmd&ZJmA)@HLWk{8`oso&V`rgwJwLlg@fPClO(3<
ztq`lCB6w0gQ2CQQl6<w`(@9vAobm$1m3#_A47m}?Pa+J0p1)MpT+#)3CW=1Kuei6j
zIc?|uY$}-je0WQprmaWqDooy|zuvggE4UIYyb^5eW%uqW%iv5BWBia=#^>f64b2md
zIwk=LMtHxwJX8q|L=cH1p`<~gwz-TmpWw|MeHP+^L}e*6Zhq4U&`uM+=7tuMsy3mL
zAOn8!`)NP0l&ea+GG`1Vw*~u(enxJ9*It4jwd|_^d7$|4pE+k2UhwN@75x;FZ;qEV
zQ;1O?B-HBfqW!u8DaG_2-I6pV3h7PciECB*#`Q&P5dD{cl+fPKGw~ChnNqU_=VCWV
z?SHg5;7;6D6VI1xu|J8dQWXProB!AkN_t&eW$j&OZ-1+o{Y23?A<DaA_+?P#BZ|Fn
zs+#k!xG@=!hz_e{%E}xRh=Yn`^7UbTn^;(1TnyRHdp4*>db2lC#YTO;5ZCdpW;&8r
z)?IOp(0o#Kbb1pW?0!ZxR8QXAlfUvD{90Az$%u0&ky4FmU17q3MmRK3+%D`ZI+8W8
z#IY>df6qz64Xy&HQhh}WIyZF<k#zci;2;iK>rLZk)*Wh@iWTu<zjEV~WlhdRAF`q7
z|9N>jE6dy%CF>rdcpo7jkLF+|bc_UgGT|zBOg!QdmyMma!QRrF)u|7sttc{yWABnL
z?I4)(H-_^+rV-~e;pn>&P-`Ei=*oJ(D`H^Qg-Ji_gP~ex(z7b-(%G2iT;Vvu11&1l
zp>VL_$MndVPklE;S|F)WxaQwQk{=Z2BO5G1Ypc`YLk(cFkuM;4a$>0^%Jrb)B@`E5
zY<(q4OG1V9p3%F06rjds<4$B#V0!d%fn+tiEd(os>s~#!KF1jbK!<cd)3gM_I7;oc
zV(A9l&-BaaY2ylSW>v@yDbjpD(<Ln=3MGgoc%y9Tuul1kNh55EV7F9*6cMD7n5h+$
zKR!F?M!Rxvsv8G}K1oJBS!D9bBO?O!h$n>vAgh-y_H^3g1m+pSJmHpd%lg7-6sab6
z2LvGbeU(_Z-G3HjrBpP7Nsz?kWF+_yqfpf^mU}e2<<||0lP4^u?glYOI>Fe`QsijX
zl4wy-Lt8iJY7ddHzY2MIG7UqQvTP0Z{+oaG;3cOziJ)*8RM6`dL7~a2YNLcyhTM(=
z>ux>B>Ak~_iFvQUBM;u-BKM<aD8_S>UvD#Ruv<KGk315N>ixNqa6xggCr17XGQ+^I
z%w?dOdye6H+zQH|0}hGx#;zw2t#TP4ys^A$Qsw2;eMAe{lB`nhZFY%xZtr^kMv&qv
zc;=oX7$q}2HKkJ<RBJM~A~^JoK&Zhu>-MyD!R<ZJB>O*il9;wkqWGNbl7$$bohn*^
zwFF1r_MN*Sg8K0bqjqL`+Hx&_z>tEXk`~|lFtZz{Cfo*p&MfKn$6lBaLgYQ^K9AMD
zGQKD+O|ns{T+L{DSzc#Zy@9@-kdbij&K&m3fbfmE_V2CQ(}q2t$u#I=-|kMwlb`BL
z8O}vp6y$DgN+HfmHclj=)-82nWCo2+fz#{Ybj=hsJ4-m6`n+;KS==;ct+<Gij%eKp
ziPAY#VS;eydPlTxY~uV<zG3k84Y&H1?RtAYpL1`5eP8iHXAfJ^uYu%NWt$$+cDLFS
zz3=XEOi^C+*rog#V7J9cJWWJ=Nu-AN<>*5lIAU*sVcF)!St$DV%?GtAuW%rO5*f|4
z7SyA=;nJEb=`+gj;gP<jg7kgr^WU$zfBWJ8u22rX5e=PA-EC{z-n?TvAo%!JF((`W
z#CMYy>AQNZ-tT2^1Tx8fD#;E$lW4wQd(W$}qyMy(nwmxL!LTWG4-@l^O1j4R1Ql{i
zeJ62I!6FJD+Qc}3q<;@pya&>ZYrX;GQ(%ucz3>Y?{0z^td?V+P9M#9Rqjya})joZE
zlN^I&9~&im1GwFU&<o`MJP<)1f<w~}5w%R{l(1?iNQV27c~xUNMzlO&|M@M}=!Gcc
zf9LsY%G%EZp*U;OlI^(<QIwWN_xh5D90^HBtRS6n?KeEogH7_x!MjMv4T@<NcJ=En
z%jj9zMWuPls>)29Q7LhccuLhzrC1;^d9X*^B!2{QPyO?2*K2!Fi`~_0<D=usV@#C)
zN#6svK*&bfW&jyP0DSx3JPNs1D+oxM(mL;Wq2-nf87jR<31h)k=;8_CGOb$yjDHcb
zynfneG|j@adK3o`z^zbDa<I1WWZt;N|AW=*k)A7W1P$zXBO7A>G>^n0z*oGoj&-5K
z?vGjHp@qPX(>N~EIPTbsvw7J1htNVyxCO5aeu1Hy*ERiye72W|o#((nzie#lGJY4&
zES2}+#}4q=OBC|H%4+^zWIfI(Na#Kl_5S8@B$F|jQ&Z%zt>L~YKR422bY((`r~mC^
z%cV<j$`=OH&L>BXevHdNirFlqqzfmu?h)Q<<Bl>1Sg?F(qRZcwtZHVn^^Qagv19<y
zjrwnKT6>@Lk-Xm+`$tqP@U;FjeE!)H4%N#M79K3i7anO)$v1H=jCBa&Lt2t}864P3
zg<_rywjT;)PviP)_G?Np-kk^wj}w|ly7RInCwlSH^bm6~sLc;1ewZhf|E7+ebbzFi
zis^O1{_>MDY#<T+=)*r7axRiX*Lvshdc!U8N96UhZaL~@6I16n<(blSPg}ree_Yl2
z(H!PHQ&^2I@yeXuwBXFy2thYrYi8F^f5Vj9z>HdtdIl>Be5v`J+HlnK6K!Qdd|_d_
z=VI*qq1D>G3(gtoN?ufzMU1H7`>Wc~Z7b)9zjG{k<_mCWt*gZPe;t7d@t{<4`>sjp
zMyX;i(Sc=gwMMvZfm@RJ6qU16Y9Q=?nB+hiI%u)QMja}V!#W#fOf}Mslzc3?gfb)<
z`zRV!@|$J}L9KaQ`n)BB_4PBeE?|~)rt&jEX>?E=yWvmV0K^S}DC>z0wZsnMA9b5_
zzkH1;=m7YU^|XDv(quMNZgcfGWa@)GKY$E%Ms$i!m@*YOIj4wbBNmtG34PR~X;Cwl
zdedGEeE7qPG3;HzK!$2=8Q4)>Mw9i3nBVjv;qKMhDr4}=?^9DBKInkIWBC1+UT0xR
z@S7^4t0|NIg=#tUyJ>;}<#hJVc8vF(8p@=(#>>=Jsf=yJM$w6g(vly7!u)?ovrIJY
zA7o2of&vKEXDkv7sN|hE)Srlp0s?eQV@q*+q6P|fb0%?r7IPKxI$NX`x}AJj<|=Ma
z&rg1!l6vNof)4ooeU9fuvu&16F`#kIfBh+V{a4M^Ade)Ua+HIkC;~+)Sn>juj+~Y=
zD^olwvr@9MLG97JkW;=nrU*w}B42_Qo|Z1({N-f?6~`exX$Nzh|G>0u*OT95?v~&h
zPFeFv@skvDLB>Uh8pVLS>eF9(ACYmS*%aQEc^z_pzVodJzJWkhj(dieF?_N;8Suu6
zaQOir35zxo8O7WaOik~6MMo>K=LU7Ewt0PPTYn7ZZZS0aEoQK!>f=X!GQ805X4B@C
zS}-@{p`}^%*!Xn5K=)YRs;^B%B&Gc1+aDqS7e79?6*AI}>)A{3{+Vb3F3bOwHdhSC
z!CO(I5?GKd2=5LYB0$i^Hs@+Sjgt)>-<6CQAS%84y>geiR}xh$`|p<qJMd%sA%c{h
zzYc4g;daK^kxYgMQUgz#v+7KE0f&8u6Wrrh+7b+6xZp2GBEzW|7%8e6xkTM48O~+0
zO7dd3Q693q$6qWdiKmx`;SGuo{e%Hsgz{RMU-y{K1?Bb~K7mA!>quB#%dY`r|7#<;
zltferje2^>g3@YBLTFi-O&bWSIESCmZgOX9M3G`sf^;J$ymMilr^Y0}vJI@uZuLq{
zf()kKpnY6ZdNMd>acye(qqk_n>9{SAsKOtr8%v9$SvJsc`#Q%qWI?k8$iieWfO{qZ
zwIb2LQ1}av+zr6CS<323=XZ3G6()V(&3;0P!mvWltihf&7dWdgVY^tpbsnubYu8A_
z)5=EAd`uvX`6E9tHS>c@GZ^PAK{Z8o3yTl>AuhLSI-V`*2=CJ*b*Ll?;)X~J?U;^k
z9K9ipGCt74qFq!22ZdR;<UmN;3V~(`PybbPD1(4Dn(rG?Y-zqhU(-H=K>YgrhR{Wy
z*3Nf?-Cv;slk>H=@bWk=bIkvJ^dOuPkv3ga&f-R%%`R?_<G})F!J~m%-3!k-W8EJA
z)Zn#Ed`+YKo=jDDMcBB6ekn&#%tXJX&MpH4P;*j-xDzseJOSV|$^8XLA>*@K0Hl$k
zzU~J}Q-t;<BxHW*+691r@7<$d2V=^Tpdk-gP~gO#k<Zt%JU4%;df_d<{m+4_@h~}`
zGX#?r4wcd%Hi{k42g0Tfb4=r&w)&1kCf+LB)={i@jA<_3hzye;8hN7k{s4-Nf_(_Q
zRJF`wT7&;W30Lfl`JB=W<w5_52GqO1w~wh!DEyAYY7%#sd06$r7b#b73F?y0sw%Qb
zrRf0L8&XJNF?0$;uGNBzm;oVXc~%O_9ZvCEw$}G>yQh={E9RPwhVZdMy|KWY-?4Eb
z>Wymw{Vbzkh~icnt%8FLziB}JOrOMw)NgKBP|Mw&+>3&py9neJ<S}c=5WinW&0WFQ
zyqQWqKi{nK5tMGbBIc-bL5oa4G$@INmb8?&tb7Pf7)!=e&dMonxf%NFztC}sgknrt
z+6dcIloFaWTEYr^*ffgs_5*yr_cl`U4lRIgEFu**;^FV+|He(85hSFUj4YVi#i+Zb
z=Q3qbVm#ZW>2wRStJRyJs(oT8a%>I>N0IG*aO}l^eZ6}h4s5s5n^ej}MB-^$_@sJa
ziKV>W7Eiwi_axlDN-0635|enf+95d)SvuW4z4Hzd<h+72G6^IpQHQ_L`1C8Bi!(AP
zgL)5m#9Nk=DLp?bqHU5-j<U<-;k8ab5=_5dOn0~O&GaUsPtEmw2T;#4z)l_Ur9cgr
zu?35sDXg))ki~Z0?3>&oi2pdgi2r!A2$ji86HLqq9b0R8tSSkTqMHaf2P6EiBEzhr
zAtE=z`WZJ@&{n5+C71UABScxm{&q6lAos!gIA}O^ofZ#)mtL24|AqSH-#8n`p>h#f
zUrB&zZQp`+_k?lQJCPLA<_60vF#oscWWz1w;cOp+&;qNuHsj_9@rHAv3p<f-o>^Q+
z_HbLzO%}^UQ96YctCaU(s3y62MHcHnB3jhec_HydBoY{hOZh;ErEnS)%7ayYsCwJ|
z)g*r_4@n9Xi>!P4=GJ!ukjEKOj8MFHt|YY2B#)>XQmg0Fpk_*;-?c~|Ay;J49c%*c
z2VkSnMt=to|3>1Rr5nX_`=J5;07n~*WSN`=5Z}mVOQr<O2BfX@C>LhaW1)3nQXAOe
z_2)|bXpDjpwWkqSkQ69irz(>|ORL<4?n*d!vD+XVqL{YJ^R_AX=E;owXU^p^Pcg|8
zRnNk#JCGz*=$@+65?PNRfAX35h%V+P`P0#xx&@$+u=|Id5=EE-lkZ0byo*YP=sTdj
z=H9%&!EEftSLBH3Yx=caBGdNZilYJD<iPf?CKFq~1T3xJ&kfj~ctQ?nmqXsa&kIxZ
zdgTo@?_cK75lV_uC>ohNp1eny?@8JeJ;NkWoYXEvV$Ox6M&6IAc@QthZi>!lV)7tO
zQyhk`qTr`&3#QP^3U|aH#S|l&vF2e#R7w<j-Gbd$`n+p;+V`?M(r2R^hrV5^+_&?j
zLzc!viqQBkwD!;RmhaHZ+%o4%YIcL4izhD<2$wMfBixOLg-ZExckdrVNf;i&kbdC>
zhW!ahOL}j5ev$TXrD$#GI10>Hd)6ynU1^T+_9C!A7Bw&yVfGOjpoFQ|sIvO_Z;uoS
zy)6pqmfAKW!mJqDJk4Q4D}d9x?<N0_q^kgGt8Kb14#nNw-J!U<Q>?hVyH;>_hvKEU
z2X_tb?(XjT-}n26Nd_h}H@QQ0pWU<PoK4mw9-WSaD@fuT3j>};Ci#>_wbb&H`flv(
zbXDQ>BA`>nrp((63ia;O|5UPbXyh4uNy{iVLJF5EI-d}K2iW++PBOH_+x|g)$y5Rw
z1L|0QWf5f&5_~+wnzTOFkh(rlrBXH~=p4AzHD9&8nrdY%OawH@IpD*INrTBb=(5eQ
zHcGc$Tj`oa2^39WtP;soc}v5}UYcsd$|87cMGE<UN+Cpw&Qo%sxgYRWGHwk)RMH#E
z$FfFx-kmwD+XKy=VcG}dft+;O-QYQX<uwl83XiP3Hf}+6lHyu=mj*E@z>*mCxzRiB
zkYzck#jC0#uBgUm=Gam)j?^`amYR_RSy3ta=%mgTCVfknX2{u;af+(dABbnZ{>d6E
zG3dQ~A6iK1=Iiguu)e#$=|kLuZoes?Q_wA|gfpSqa6*AH=E=V`6h%GHM%5}Z$D9|`
zr_QX=+DB1@Q65C_T7Ad;#wm~s9i9X|smQ(t_UBWSvheY43X9XO4FWa@)k;nIqf76t
z>#2FkpydV$Q~J4(E0EH)D3eyRnl;(L(48yRBpxxVwuFhAf)OMS!i}4+x0x9N+x|Hh
zx48NeI$Fo|#hjk34C)}j%4>!cT6#8_D_Ho*2<*l|VZfoHhlp}EQjC4?TS9=Vp2LMc
zfG~Cm=3OC-mhSklcfVtOHJ@eSBHW+{9jo38MPrUv$4WBlY>AF!lkf`<R=rNw!NOp9
z|4}U2Rjpc!v`oc=xwa~-4zFVx`i{#9VpOYFjyn`u?n9h5C)DXy)j(fcPetW2Gn0_e
zq0nMTKm;3wcahJa1)8OIW$by-(}0()(sOdYJ%rUMqOXae2(p^4EkD53pJQ0^;PtVf
zQCDp*7o+tM(7#^a`)u*Z)>74<*ST&+g|q#QWn(+dq|8AQ=IBaWvndncmi?vTbzfk_
z@$JvPLAvoZ%yN*|xGC+|kc58YAHHTSvck{AvL28V-buQ%I+f*|R!NNe#uEIS{K|P|
z*|P?gs6TQ<U)eieI8z7*)tW=|QIR`tFhLnBo^3*MO{ph`uxMt^VQ<DE-P~ieg+$U4
zOW8OE$j)H^7t(+%NTeidmSaGL3Pr}5C^8+)Zk#r0g95jc#49H|ZTIi{sFdh8lQcNy
zqORImE8oEeC!$EP?*1FQVe=e0Fby!#G>)4FBGb74|LaUO8H9UW<N3c<(dyL$R~o^h
z^MrrNU+NRN?2a)0@huku<px491*9FCO7(z@qJq)fQ8AL(Ob<HqvRVBMmd*2_kncE4
zPf7TY{5vBMfN4=(rRvqkkD9@vNyTjZ?75i^affkFn*h%c*S}0ubS|!ke3-BG*#niV
zA-dTp>*EQ`-``7UBD`Dl>36Amfn4<058Ac7Mq@xoa`6B(XPO1(0QKPCS9d!Hw1@#K
zKn4T!SuzJG+Z_mxW_MpBJm8hjsPa8vnu3-{X)rG`h}#@5NDk93;1UxHZKn`eI6KDf
z-Zgscx(fNnmbShB5WGNiAP`q~zMPH6<-s%N<m(Tq%Ln&p5g&{ci@?3#ZIfK5*U&ty
z8IabP1rIUCS?J;>=Bff!-*VqBRku4K)|U3nY#YnYO0kr#<HrZ~Ljsw~w{{kj5(E>s
z$_x8)^)-t)18OaWag{F}Vk`lWza;Z{9&X=_!uaW53NNeYcmp5NOJt?ZCrj4Fz!39s
zvrEjqT$JK>W&=us-|`7=6B%T-w*KKAziU~CL$Eh1<nwr(J8yVEaf9#&RlUhiv@a8B
zYZNcTR{;NeulqzA;DIvYI=QO$BLc!0#HZ%_ysrLjZSas%E8IO%v_%FiENV0{6~VH1
zkM&Y-IRsZXXI$DKnhB+%%}zRH4+H2a0x+orN396N^Z9YFMWVkwgxA8<I2ezRS7wlo
zfA76o8!NPE86)*c54eR;z2?T)>kPCf>aB@E8>m91x|k$<9hfY>F)mqx7UPA(%LVeO
zH-fz4u9+c7BFn(C{mn4Z!WOe_VtZ+vNo>k3eCFh~z%lWdT0QxLC?!J*%(q-WREyNJ
z8*S_>>482W`BByzmlqU$FH9O`ShVYpG~tao;cWveYVl+9PcOfG{Fo4xrBm7LV=naX
zx8>E4@ssO^l-e^ZTT5FKDDS4a&J}Lh6{3#JM+3x<I)BUuJ}DARP;3Jp(jxBdAthP(
zyBCeXMd-@J*R(1BThWQHeqIwVWcPz--KHof4=5yS7d`j>U596e0~I^V)Tifni$SQ5
z9f2483NfkY9o<0KunqhdHYk`S;Y)B;i2fD3m(JgJ>B+ZpgQY22q`-enMg>L7UnE-O
zX>^LR%O{mmRC~lS?Yw4Ilxq@{X^C`5NBQieQq!+U26N%-kk{NG$uJ3~u%f19@>r!P
z3MCL^ZA@TV6lwGaQ;0L{lsEL;y*RvuH_LunJErJ-z~vz~FLg?#1p_VAl07{OBqiU{
zT?=MH7yWkF+gKS=h{v=Ug@NVQ@8t7nDJ`8Nh3GEItV(G}VYi}k9lqk_6dmnPmU<`c
zy+FxVT{ITIi7PC4GosL>?lt`5A5}SeIE9@_HmU_0#GxhR{0<YsFwL+@J|pqp#PhoL
zOWMU))MAF)gaw_W*9SPg!dsa-CQ9UA{`ho+Fkp>&-w%iS3R_@O=smn%2e%b>guL8m
z_IE<<U;&L55k^{Z^B>*7@0_2laX6rI^u^f8a0BufE!jFIPWS<duV0_yLdG?BlJ;oe
z6HkJUAb2u=keIsERvr7pFAQtwrV#dO$644fZ+XHe+9s_6C5jHhy|*2gl2J|`RzPIH
zE4L~r?d2$*wCV26eU@^$uke3OT0TL$*pe@{v?BWA0o)8U`<i*p-9{7${<MyF9?|?k
zN9gdkyeT{16;{1$2sidqek?k1pj$AnZQ>#KClKR|V&#-Pj*R<{e}t<@8yVdR(3PNf
zX*-==nWF>iLB}a&Y}6jS_$5^kJl^e2CU0#71%r%n{LyFIH{i9@Aq4?7b_;6qYD*`x
z=#@dnIRZDB&PYt?h;<ygXG2LaJp|6)oO5~N?aoEw(fw!oKG<I(KpS&IS?P{W_oeru
zCb(z-c)9+i6UnUaNQ3Z%mX!nF)wCxs^lxwi7b90Z1L7Fe0AI|BKm<A!)VjT|JE}Nz
zGp-U@@Q@(6XIbz?gZ5*4;J{_zoTP(W=Btr?{GDj55_(=kcO9c#%t-n$FF=ei%-|OV
zd%&Nz!V;7tx0K)czAp7(rTExu!sxd+2Vp{N)Rr_0VJ+-oVAK(^%<&rL^revK*^5!&
zSL5A#0}SROgG{MKO8~vkp>|75qaB%)Iv7Ef+oF|RyQBNc%n{5k9f3vtMjjijxJCcv
zL|l#<*TwwJHd@1ANgEG(&5w}`%99UCHDy}S#9&R&xOu_2Xajf#SYGu7aoUz<1Gzz6
zDF_p_aEt^SwdpLHY1i@qG&8<HL%YoU%iU3vDD=^(`;&2sOVQk>MI%_OxF2A2@q{lT
z!b<4Km2%<XQ&EDFFzs<RYVjT*0A>eURTo$;nvG@Csw4!H1g0(tw)fZ~v}g{y^W%(X
z$?pCT#Y7G|w#MdH=Tn(s?jZ@x3gI>?%J2VX@fZAzN9fw_N!2&-r;}x@Kf>y3ib9zL
z1vH4C=!WwqvWtfcgb#A=YJzzvN%f<^xP`4F(|sy$xZ3Veh=Dp#a=cKQMDn|zSwNSf
zKNA2DrrP`u=y>R7S1CpC@Cy3N-5Kyc0#?P!Ht6gHHAT@(M0U;$w<4rc3>C{}l+<{^
z+jgCuIrPeLsY+!;7uE$wmimQpkB$28CPWxVas8JTf1t91DcGL_NaMu&D+0%_13(E(
z^s>p;j@Y9PABihk@ejI0XMc&7Wg}1882}xF1fSV(run#VPdQJlFeL_(g|ct!3-!78
z-JCkIsRPzmyG9GG!y+<A&q`GlA%-nJ=#fF}mkp_)I9k;%&7G!sw5S+B03VKi9#^PZ
z8&)xJSzge$v@BDS!V-D#HcL%DtckkF%iqJuil^GbDksuG5Cq&ZlC<Jy{2&Qcks)@u
zM_Qd>`DBeCHh6DVXc^<3@2<4^_$lxNh1H>E5xDoZ_@*w<=I;hyQDWKP)6ajg!r2Mf
z60Z!;G!{8st6-fBRVTUgFMSO~7Xp=T{j+ADfuxj63F(OboKlV)JJO#(C2&GZDor)%
zZ3scgC28RvK9fweaey+j^HW5Y#9A-ODb#$)BF%$|^=H8`9OXEzg7i)aTar_FZH0aX
z-Imb^0*KLMggmCy2uv>Lq1rPTX99*$Tm0GGKwWM2IjAeS!FVXOJB2Fg_Hq^qM$v*?
zk1K>}#5blZEsRpPt47JBBwc^6A05RMM%%{Zuzx8a%#<ed17X_EUq+8c9P;r@*tY&0
zStGa?4ToC|Q?(X(0JT`_#tCOlx&%S(QJWowe;M$s{>Ul|Y3#IYe2(AH-}tg8m(Q`y
zxMSlR`3OSS)Y6$1$XOB#FaTlEj**4m5AU;Ut?0J3b@cfx786LD4Q!TVshm==odhy-
zEtqy_n^&s*HR3NIP0q$GgkR&`9vi^t;b$^f);0mc4q#Sh_Q8?CB`MC`{Nrs_l;$6=
zvX++DKmY|&%=uQHgQG0ssNJ^10G;)ueN9K8$|?eEIa14QVwOsjJ0Il+RLr+UIn@V0
zInan)=g2_rV4>mYOeIll>500lzh04x%a%VmE=R%CK$J`z?MPT%(yUbvCos}BPPu;G
z$Jf%0=3mEBEAXzX8F<cpPyyGr;HXp+4Yaq5%AjC0Gy6XXh!KbjD_ZrF*}gGHS5GkT
z!}TWzga#yZlAJ^-pvY1dUCuIzIr~pq4qvchVTRWxwH$B|CH-q6?l3nE4}Ia^P?EXm
zL(^J`h7`7x1*hStc(ke7Jo|=^RV!1R&d6{3gRSYH<Ybh-*<hZ9uH*zeL{?adB%B%0
zri%UdLE3({csgxrBo*Dx1VxL+T41_3+X~WPwlZP2GPO7>Pz=NOOITW&s)(6H!%0Ru
z3+J9=;krV8zXB4D2nPb*!<QtY)Y=^~;lju-u*R-sgGDE{b`E!kp-)@{99f~A6JJnQ
zelf{r)YQxseY>Q^d3Y8h*+wOSCPa@2_1cIJEmo*|V|8h{?bnA7U-=jlTo{dG95&=P
zctu<>u<<5XsZZ#}9rJnQ{_;k0x|nIi?FE2O@@t32@M`b5D)j=yW$&XhOWHM-p-gAz
zgN2?c@E3^u?dT6DD`dooT0V|5VLV5cg4Anxf7{Xp1H$4`U$_&Q0Q9G6y|ri92tF|H
zKebbFwF3nxC~h{}Ibxm(!YB^OtLTZmIKuL)0dK>}P39Dz?G*cm@zchX9LQ^uGbM|%
zv4r20bB75~L2Bu;%uM(Itix>?%Ot&yn?*zz_n*V(Y6ptzNA3M6x*H@!H>uPCNju#~
zsy%mS2xD(f!gQN6>rjRnUf3JgDq`2oSH+L_1M;t#!NMY+OdX<?=ZTB<PpPy$@=pV7
z{spa|Kuqxc(h?AQeK}|N43~ck0|2yrbusELIfaKpU%%1XRNB7@K7-BAsVcM)P)Y>$
zhd=0Azvz2B9NY_OPn);g@|<4=WCOFrv!e%~yyjnCTeqN*jZY0Csd#5`T<OHU=jl@I
zj(KprxVYDl1B&yQx%Woj=TD8XAC-*DD=6=fzc7(!x??{*xw|*goOwW0Hk~E=U2iC-
zF5<pERo=^u12B-RlGcytvz_v0Wi{8F#RfPwe3FAzCwb9szH!ix&9jIHUH=tnXh*RG
zJNStJ#6iB{KWc`?rezdXYvL!N(zN*G`L|3!SBfXWl3-CrxrC31k;$>vuURJ^JFL3^
zOEq}8hTp#{kC>06v-G@SS|V%5B~SN=U+Esw^|l(<_OXdG`dxL%rD|*g*a+@iFhkg0
z8MLciGOSGUBdGIc_CUJIQtD=`$o6%7E>fV=CC~x=tT}^*uOLx^@nKnp><JKKUa1dG
zTmz3QFxVTxrAp1bW@Y~=nc#IMlEtNHjdadOxm7i#77OLm<JJH>)`BS??Ukp{)mLJY
zOk%X03#xp^9TU^+1Fg!NwdBmU+8PC6MXAD}ZcpxB(iz0sAdf7DW5X4_&kksKmZdua
zJnl(3eD845a#(T?xrct*z@XD0!Kq><7Y(^-YRRNzArI}odDW&G>rRK@_WH&}B>aVY
z*|~4yZT{jD%7xs&pj}Jltb-%)*MPgzcTG|hNC=m0t@UU7eYyG|9{jS`tufEXo!}A1
z2fiTd7SohAoOE!QyA(_K68C%4>?-cL^d^13LS7%vfzst1MRBuAX8!&Y%G>#ryvZNK
z=I$TwmLKn36SM6<JN=%WJ6L@Iq7k9*kl<pZBcs9IhCx7f>O9U-G5F7e|H$8Muh%!0
zH^vEtap772kDW-CYyJi1+WCufat_FmEes5f*XxqO$6)nX;-<If+(FySvez>Cs%s_N
z#9)V;N}x6YnvxoW3r^2bYN(VXfQQMF?U!`$H}<;dDY5B6r~5{9r=c<Rk>|%HyYOAn
zAg{mO?}I-AO1M;o>3=snA1Lq6!V;4j#*jZ=Jv$~2{_ueha=yNGJZu5r8SbN%K0NYO
zO&4g`c#z?=tv{NWI9eiXYo`!Ze0p;pWb)4d?GyEf0{G8>Mk~!}4B{el$$Ci>tGLPa
zyinsqO)CjMi51H6${<#_l6I`-QBk(QqC~M3XNi&yJkC<o0$3q}JHcRiFLaEgnzJb!
z9b1kzNkzNouT^pyN{lglgY*=h1(~jMpl1tCbNTvTBP=>?Nju|M2r0x2+Q>so|7F=k
zskUF3zrSA4y1uLaZU0)n0w)umYn2R0E5G6s0_tzFS;&CJS0VYp%(kfjENMO~PF3t_
zInd!>eJIu~CFgRd2!=KJ2QGt^4QMUzEC#`Wy>nf?3qxZH1FAF1KE45Up_J+=sRBhQ
z8}t}x8X##AGGr}F{;?{Mb?fQb<V)pqOgQ$-$6?<L9%%F~d-D;Jdbq^GgcA~e$D(ex
z#`M$zf6GQckfZsx2wkYs)C+q`(al)`rv3hz2EkRK$@4yF<;8cS(-T&77~+?I2(2zP
zVii)Lh6{8G(+RIlg2C&v0lMXEeP7BBEuIm08uEVc{$wt@5p6qn;w-ckjr&3FaP`QQ
zWZiaF<}L&;yH|H%y?tRP-a4DLsZ^@p+f2(BREk)2*N74SqBj`&V<r66_2o|dtnRGB
z-XVV0cVps0I06>Fo6QW@#Nh`bCv~CVBhmIPy{Ze^f{^rPfK6Hw^XD<m3q#WT8c$R)
zqbN!z;XqR&07{NOqE2_1i8UaPVqp*aA=CZBUg?iax31eT*WUFheLPuVWs=&|f3g5C
zl#)*zUX~~Pai*UEpj-0cG|t1<?Z)&?d!(O|MtWPzv_*SE??;%^$AqH(mauGFTit}U
z1$c@LjoL(R4^$Wrwyimo0GZ)+{jRZj%KEzO;7^Y__Ph|nkY}KREqeA<&oRUTzwYbP
zup+jveTpv;jCG6c>N)I+uK56~42FYS2Bpq`)FM#gY%xeHvF+jDJzP-zJQ8}aM`Wou
zpr4elKx&ayU<n6URK^*TvgE)YY1H*0Ra8126Y{@MIw^gcI3I;*vk8l;HQtGAq#!~0
zpF92U$QPCY3wir$p+hutI?s=k^Zp@EOz}bvZW#Y}zddSQ<Dr^q2;m>s5bi9w`)j(S
z%kAf`x+Pwy?AZ+8Hdu(3K(THfBArqT1rNF6%ed^>7rqA%oKtvXRw7Nxi*bOV#E0Dx
zeQHMLe-+!x7*fX6rvAsfYwT830ECSUV?Yu@P9qL(4=+F`#H#`fEO6r0Hu<nYY;ZL{
zf+u~$@1#<T8n7#rWN=AfWQev4{+}<5aO!E=k{!1Az_C(=M6&ti9v6B5d38h|u%xJ3
z!;rn6lD0vgFTk45Pi{lhmM)~GnqoUEloURT$BPyLCbeyA-hsgY!nI{0PawYtxF<|!
zn=EHa%7M>B%}ZqQ%={g0tK!o!A$zC4WQxFuUk^=AJX4@6AxP#z?7tNN<f5o%4Buzw
zAj)cl*(|o0$HAi_{qM4gBkhek2soF8%0^g|W^Oac&M9Tuz!(b8lREt>77$9a%e*`Y
zI>fkr)!|iSSTeD$7NN18k>z7VcGxcaq`PcJO)*DT6Z3ScJzCR47lWmAZbPF?6RQ)c
zse`+U+fICv#<N_t>e&hCrYu*p7k93jNC0yN(WindlqBgT=4+WJC{=7z*~rqjb>C3>
zt(_$rfSh+kbAf7Ui>p=-PuDtO0tRS6PMh~)+HfQI?-m=G?+&Szs}n(-8v}9X)GXPx
z=dnht1Gx>N!)uZF-kHt#FZU1U%Rhed6ZQrY9<*<FR1WsWESE-AoGV_rSD^?$EXTHA
zpd>b;Tw=D*%zL(_rXiY=JN$^^?z`=AOt2U+^NCFO*a6^U-g#gH5?kSIzGFeC?2fMw
zBUHx??m$+rD=|&f1~Bz0=6K}$-gqd@VpL*n#})aFm;|P1`;1kDANhz1t!BJhvQpq>
zU|R#|owuYKy(jFczTYUh2KGAu?npk^8@2y<i3e~K^0qIE?x=u6%lTozgLEFxIqB;4
z+8t0o2>WhBOrxPhtE>j7#MCBv5CV~=_}{fMBNvFn6k0IQD|AS1wMlN9rX5(d%30NE
zMUmuUBAMpIS$?%OHH<S5FuWdZn=d=pSE-${5JD}=<p)U+hyzlkin@MB1OLE=fLP7f
z^VbYdpnB&Iw{ongo3!WH!tt`RLkP?}ZMv`pzmVakgdB7fuPjnm7cc_3#Lx8#-;q<(
z+uQUh?|dcBaDuRicJZ7DSig+8NSw+G9(iftzJ+0XW9@cjvXcjtl1Z4Y=t+$Sn#;RK
zqhBrCm`FcUL8qv-is?BlvEwCB5`0JPx)&?J+zlV^{i>5<oxo{oUNAQOJyMCMa3S^x
z$>dYv&`bdnReZ0nWP(MXbA<gtvXrck?UjV=uLN{k-dKTGMdIzZ|6zUr_%71Nx9{>`
zUwKzmJ=w`!nDS{fZgpe?5-C@46gVqP4h!7nzfkh(2=wmE6}$9r+oxu$_tyb7OzGgo
z2p(%{UAJlMa9OM3Gh>G4<Eq?<Z&~=o2$tzi#k__Ah|25U$*)#US@50-7!@<+LGo==
z-pQi#6Ccqp6wrH1+tAc&)_+QbVMT;buHGsx1W@x1<zl5rl-1miv*?6+7%FhA2avdT
zki-Om>fEU)kV3!IBih+BB18Y6S4OQWB-3r0I8!z9$tdCL4+Jf~Ua<LZDyH?3rq6VK
zelL_9MIUq-W`*?JR)tQX!!`VZypdVo{7~TI9cU<H)NSs11eJGv*1{Zkc0*YVEG<C8
z7|Lsg@LI)!M*a<Bqkhq(O&X;I4O<N)>wV5l<HCHN6K4$|9~mlIE#!OiVRps3DGJ&q
zsNjcAfx}(|GCe!4P;SBP)91=-lTW553AfbW8}FCqMd48FpRMu*FD!i`dD}zSuI%lp
zZ+B9w=O~Ld4=%GUYbv~59F?Ql;H^O^zESH_<l{XFJD95zs7*PA=&y{x^mP9Fk66|K
zEHcL7?uoVgmnCWy*SStMeAf+$<KAB|fRblU6R^-~TDQK2<yp_m8Sq@Y_t>RxOZ#zu
zKO(^I9`w<lm;-R<{yUBe77UG=7rZwE9D@8MTmygjKXLuZ6uO?2qvQ$!ptOTj$4g-Y
zpJ0Xx#bxK)NpRl^P#RX&b3gfRd|(I(x(EGNpt;hpsJN2+u|YDbS=j$x+%2_8^YSHa
z(GOM6JQ1&V@1FW&jezC4V$T*RLobeS-4nxD<sYjI9w|CFJ%1avUdrx&N%lox=j-bg
z{mVsQ?6`0@_Niq4HFKou28iK~2EXWl>&tLYDyTo^uI1l$^xO$;NiMEY2<q8hJwNta
z+x+dLl~~N&3&ayFUVnV_H#!l08BxpnDg>@s;_C$Hc~|YP7T$aNFg#iruicI7g-dvo
zN5R^1YRperU%9(u1w2!vl@#)3E7%T0;ccUlKb{{9Ow8NIo;70`XLv#R26UGNIf8@1
zGc$lpzpA~xZ=v()ziZXEl4Uy#0a5njL%LbTDBobWnI`rIJQ(BR214%QG4Klg*f;b`
zG<;o7OhO>;e2E5p^f4>AVzaaNMr+^$wj*(>XMK0f{Q&J8{D1aB$X94$l~O}P3KGIP
z7NhW9`PY~b;3S?v1}2j=5gH^vu4Gv7>R+k4V8vVr;20?8K&%E%m-rV{=9KER>ua;g
zd=0<N0A*j-#a`6R6|{d4%TrmjS-EygNv46=bykq!G2!kQ_T;7Gst_9aW?F!tO{K;*
zseCxDP2h3g`U~txZQ9krRT8XNlv=7QiGov**?{nH8i(u{F$G00I`@Gb&Y_n*z?4WT
z_tk2YC38-eULzKVLOqHD2!_erV1@GwGkF4OzQ<`mD4%Di^*|_1Ol;=N$SVuDc^fl$
zV0p)yr@nC(X1jT{x<*?}|Hbo!XN>j!ks(p+HUoffFw%i|#}0e?4`-yiM;FLy?K~(<
z1Gvv`X`EoVUZ{=68v8GSWHD+mZ@4T@abm2veNV#;^NXNhb6LFw6L0582c8}fmfC)4
zyj7eL>tpY%h$$&y9~>Rvw^eY1bto!K9WgDCYZVtqO}9nb?aZXNFmQJ&Sau+rHFY9s
z$K|7-kPK#5tinN)rc+I-Ze9XLi6DGIy@lZi4w>sYcX{++IwLp;98;J4%Yi#2!0oV>
zF=*&v<|v4k%2|-$bD!#P1H(y_a!Ps{y{TJe2w`-l>6Z6BEMNK=5;-7bXZVtd@=fg9
zEm4fZ!avNnsowrI(%@Lr?7lQ1XP<0J{jPs}YEWi>#j}{=%tl^Hp^Ip9&C)q_$;MJ-
z>!RBfmaNp)NWs`Lbx1~4(l!n+d2H098$90LZW$GcX7Xk)r5K_oLh07Oz@LB-xC?ZC
z|9w3x4J#Kci^~uh-f`lwyBd&a1f!NJ@m1hvD^QCbP>nNczaG}jUO2V417NZgRlqOv
z13J(!`8-|t{B6RcNQ)vt@0demdaeXR4A6>hfA@_9@_~cP37G+c=#)owkr=#e+TI>0
z&|eOXjE2EiwkI>1ODV<HOp0Qo$XqVV9C14BqJsJIdH`K(1t|mg54Lv4BghZ8xp}0C
zR45v}XCJRhtJ=DfvRMydMMgVy?P)@4>10(XITe00u2c!ITKM_R7QF&|p4a!vf&k(g
zJLBD*&~k7oY3R1;ly~X!*6O`Pov5u2>PvVcU*$%_veXIaxKP7x^&ek&)~~F`_xs`g
zt0yb6tX#Zk`vocxAQl6{fGNC`IJccJ`3l8#tMY3P*F+`4HTCd1{68F@3!hW;Hc5Ha
z*p6^$m(HaJ_*F^M@L2#W$#zkNEHePfO8fIqg}KG6a%}Zm@YQ$Y1p#?Dz=LH@PGpn6
zP=}61e1dZUn}D&R0k;f0jgTQPWaFh_jQdL&Q^winUl&fLhlxjR-+{GF6Lq2VlCmY6
z&SrlHNEPD5;{Ilo)S$c0XneBS`{~p0({uy>AON?netvu3B@tXhE^T2$DJzv=Vb}1?
zSkBp8Q{TU<eZ;!D2Y~fL_*y~0d5ub8#z#5KtwZ3K>DqteXK~8VdpjNV?LnL5^`|Ik
zIKC(L;OK87TEw60tE34-!E51_nfo)0p5Gd~b*6>^R{ovsZvt3#Kdby~Kogp~QxV1;
zmj#QpLDZ%@pq+Sr!R|i6BnpJjfC`6qyk-+uSwpz}<Zbr$kb1#cgGe`}ItUWZk7g6c
z;^X+2e<u#0l)-8pxY}HgN^#r>MMqHf@pHeXd7>Bg?$Ue!R?DP}c|~evINnr5<LICe
zSRn%3$DQOl&O~G_-!HH0!;O!7PgU*3LEFAarof@AShi$o-_Sp57cIx6b!1=Z+2rk?
zxb%ddQlb5QksJYIo44ru7g|g~YHGQ*$2VKR4FMj3IfW{GCuwevnvY|YhzRm}dVen%
zCZ!@Ry^Kvzx9Hn-h&kBXkei3EKEpo+rxEu*XHyLemzLkF)*Zr>&-j`8DJdXc55QS$
zOuMN@*0f+mvp~L#tLuS?QJ$SmX8?r|+mXAPF_?t6yrQ0U!0B}tQzrvW5`N;x3A$)^
z{{vBBf?4{0#R3jI!g)2yZwKG5oHuZ0)(^Ls8;cl9Fz)TnRMXsGgu>W2mE%C)YQ42n
zr=tPBkE$Q<Nb~qF7&e|gB~Q-p&l3V87=TsjP3c2@bb`Cwd#craKp<^Ey1^|G;R$Yx
zdlaj8BCmfat2ZQ_K+@vbSDO+#J1%9*OLvj2rGt1EL{pRJDbJ%|765Utp53+gO{V2S
zrY4g!pcxYi#e_zLY?*324Bj9g!KZD0z*TGSCJlf#g@H5P(k_ngfn?m?CCa~LU%o{p
z?@HKNJ%4LD>!vkFlaB`2BM@|d{EfZr<Kg@YZ&fcK^A_bzfbP`K^a-DbudxRfidCOh
z)mec04I;W)nE@F9uLvKz?0*tuQ@itQ`uIjVGVAX(jLmI{KQrB>QeX|ranZ*}cYA1`
zHdslKeOYU#pH&r}Npoa2*c0<l_;!L858z_OY$NU5AD43nI_K_IQV*KP^k@LqoUo(z
z00H#dRC{rDWB%|stxN#g-U91#eYQUk_RY`7CC2dU+hZ$lsrV`ZA`hS9``zAxHS&xP
z%I^Y3gp{#S*6ua|1<HBc@2WBsgw>0-XecuQ7a_A&29D*m+=ni0dd2(CkMmnQyDz`a
zYInL>`<t!!8Sj=~69H%|utCycee1anLk>>Qd~bo2?2v{neae%P{0nF#c$t!G;zI^?
z$om6P_+ySns_O0Iea^F~r5arIx;v94#61o~Flgd{7E5ndAvvc)a9q2gOPecq4$1qj
zg6jQU_+5Ryss1<SZ=a%{F4r$RWsWS)_BFqf5?K6?ISu`|a~?cj&=znA6qJ)nlKcb)
zx5HiQ1e_gG9Q`hcDw*uAw+X(y_TjKxVi@vvPO$9``AcmL_rQRto^(GFSs+-$)ZR}%
z?qj_U2Kd$=>^d$_kN$u3hkWrV)Jr)}Q7oTdyY?r#ul%l>U@lf?u%jZHHb;TI+FC*8
zD(Rg5z^kRo3+~8|I2kt-dvrn_V(3q8FWfJMEwS8WYP?=Hgc1fy+%j5dV#eX0sO*vu
zLu9){Mk!^s$N(yah%9V89lIJOd=G7p8<JuKlRWKKL6E%7vsGfgViazvETN7VTsT{Z
z4A1pLb+!3V^v}j1K$Jt(?q}%9%kn~`93Z~xEWqA{{$A1X1%(bX12J&vz^iu3CYKvN
z(2R)AE(w^wp(#owG=LR|O*VDaaXG(B+l8<sW_-pvV5}@P9${amG~=V5VWVYZ#KA25
ztDMAD9SZfA3W6PQiiNXJ*pjOpNHJ&hzKnh`R%jCXC%Yn5-;V+^IH=pn`2_h9aHV|x
z{>i<#=X<>@g#)_zgW>nbyuhJk*)38jxN3XJDgv^gT<!bC)x-P-KnPuk$y+IzVx5!#
z1bcc$32C8`OQ`}d8R?0Jp;1=MX9O2DYPwLBCuM!*Q6#j~Yj2aP+1-l4a=egwU-^=#
z*MIy^P)JfN%x@(`F~yoSu8)qV%8~u6#{MI)<MXlyOJD=|P1fLbU1MJJyWid*$p{Id
z51Mn92_kPy4>KPe8Y`DR7~EUJK4y{QgsM*KLn%8PZA+l%WfzmX$<C#3>{8m(XO@1~
zz}-%?vwu3X(FvzgE4LYt!fBhki<{jIP#OxIT*+0mG22<<|CX6GCJVldCu-OJVZe0{
z9UB*hU<|6RF(X<Kim}bfCF!iU<)`y24K^f`TQ@=N9I`n02t-v<`aVow>CV>(i~6E?
zLkR(p7}%{r5o~k?)f~o1BUwLw{eJKkIGEaUcjj?H87O8A=2T9PF{GAbrU;5mkc?Pg
za4O&V*IL*mjL7Jw`??<8*gU_UpV;@9GDbsl;AP?R=jKi}0u)%rxV<I*=$TS=BV~FP
z6A(sV9J|qe#SKt2|0`T(tpv<fJp=;w`zW$#7kE`GO;M5q00mOR#@<u%i67vfa>76T
zuMx1(&Y>>9Yt^&o;#DmXj+>Sy5Vzp`;dVo0psf#dNqMP+eni+Jb9c=uIlBt(S%B_h
zrwG5YRtiCq&L!BSl&b`M*axT)w{2RxPcm&+PeD!16m%YrIh-3h9ZDSdPKDZAZst+o
z&F(UM&{cRio=xRo^YNo#s<WXr*COF<^RxqDQ*arkVY;xQ(aItUctQ=nJ8`FukU@h)
z&KH(!E~Lt^Q^JN**Z7B_`S#N?B}Xv2vf?QF77p$W!lNcJjF}??reY;;RBe(0zH3P{
zSgmS|2d8Q}hQi0Q8VS&L09wn7DyBHRF-yys_TqV((8Xw0MXMlxgEj4~=mC6|a^`9*
zq<cRHV2FASomHmDdW3`f@a3DnV-mWM8Z9!Uev9nrb1vY<(7e132+WP`CxI?9i7<3<
zptz*@J@k*l>OlLgYv;r_Iidb8su>tdZErOMy#X6&rO^d6h>WxD%1?juFSc8`Bg+&k
zR~L<J%KNUK*!&juAN7bP8fuuhmJb596d$HHq=D5Fi%U9s3qVvcf)fu8biUhOJ@bzU
z1UTGR+W$vaAo#CiTF2NeYNjhW$M}2Vg$>ty)|g~0gQjg}AtJ0JVY0VNsQIVN0=>sA
zns%k|T#)PbXv7d!>W@_;4a|YPZGHIXa7>%sCrbrxzpjK{SlZr-!h^HOrq81>u(TY@
zsl-0o@MJQz)FpTT4Od{Z(x2a}{5DSF4Aq>eKD@^4XYs%!A2o;fQk6(N7}Zd5w`i1t
zrP*##Ik*ciB^~U?7-E`zh+KjfcZ{kWotGq@)i6cf6Bm=9Xpe{ZR;{*OE@>f_ba`Eq
zfNHK71y)%W)y9xX$8c&DCp+KqQV9EoLAym(9Xd$LwkwAk-hSfc;>a4v%~pbkYOX7j
z7uO?2I#n2?11SyxCqT_g&4PA84G4^34Hb>Sp9n%WlFelN_BX;uZ)M#=d2RC*voNYt
zq-~!2S_JVIqTuKllbr9Px(7eEGn#$XJ2?1VrJ^F#*>GFjrJ`Zu%{y%occyvfw`d#!
z4qpjbQ42fE5kQ1gtDo;>Ur*y40kT}{5={(;o)%eQA3A!)SlB896!Wi(O&{)o-9Hfq
zo1455O8lc>XL(gxpCM6&RxVNmjA>39x*3VYzxW)d^4yGN^FEKu_A2xjp6KS3vLWAo
zJ6Lwz+9lhx$ED8w(~DlTx!3u=*yHT5cHY44-CR2l1qwXihZ3z+a$C##7u5rJ7WGU{
z+T7RJeVM2OTC#~c=QZQWv2kbq+|CP{!l5xR(MnH^hQmK0#IC8{o7d`A+M-a3*zM&5
zHtHgbcQh$LXDOp25zeM}0wp!*3nwYBND&-snM0veg;sR&Q`Xfzmp{BB#-z-8+K!0I
zv4kMF8sLj};coA;%YpzVhg{0lDFVnJk<9=4CB2T}Ovi}K{3jdycTbtRyDfhS(-L@K
zD7oo}zQETU%YKb*$0fZfmeeMjz>I318s8%gMp$+O&y;NV0&XmgAa1MvC&)XyywTui
zOv5bxZi)tYzmpU>_F*-|kZ-mDO*IN>MK1|vYn0m!V_20S0w6u%UT?;m7ST^Ak^m)=
zi?a2FTosU}0Gb0pX-e>aJyk2P?k6h?WR{lGScR?jP;{4KK=v-E8F*O0MrL%z-0ci4
zJ>k%$z1dwv%t=ez@+uk!yS#N7;hG|b&vO=hcC=4c72BqdG(ew{$AEc(D!>I;N5NE7
zRX|#B^*=UXr7!bSA!O2|(?*^NMt^W|UK$rw5p!v1cQ?W-rovK=QdV~td=359K^J7y
zp<VPI=TGSv+U-=*5YA?ywOl2#sS}ZK=2FQ$UNVep_=msyn~I5v%=x(|^{q-eH%3wu
zkXmY1Eb>+;&n)|33oVMNJ1zCCxoG)`bJB%UCW?hEZgNo=dKin)kiAT8qyLku9XCi{
z>~(5M8ZBj&&!*EQc>~A7lSz8BNxEz&Z@tap+sY{o{28y7j$?@baE$ca)g@ErTtKR9
z=g^c|bdTYuiBWsUK3>_wBD}SLb4S8Kx?cym4P;RX`l*F#Qv~#oNV;c23#s^ze-r`F
zlS`tcgx29w5=`|SDhnEh-Y#rlaJK|TXb<R%tZKvy3hmbT&*|Vlw!Yx+yi~?Xd53Dg
zM{10B*QC=#xV*4h#g;2~gnI!a+(P-j7Fn8RF{81aQhdo5T)7rRZz}XP<G9Lc#mam|
zv2LN?j*2_F>aF+qC)m#Og=ifSOp#Fcgi!*psZJV1(sPGYJhF;8j3=fg({YpNR%-Pz
zS7&%hPBLz(zx{)Lb4haq5ZSBQ=~!^Q0))Thr)_1j;6S!#Ad|tRhg(TGvJcINO)Dad
zvlUi<?$*48X?Oc9tqBM}e2x_N5e$1%f_;5x#}yPT#Mm(~ijXv6JICBECI9}OsGa_x
zUhcy@_2vU}v9BFSJZTLn$O!A?=P;X2VxD>XfFVkVe-2GZ(sT^lU7FLMf3?#wJK($%
zjVU%7GY0nvM&pQ3_yx1t{`@K0B9`W$aziZsDbS5*BV$0_w0ZkWAothi>|-YhA+dA!
zv~=R=!%%UTZ!>U)l5oLHU+jW}MU0&5A7|_&9jmcAm8ST_Y+TIG^tPl+T5ziSx<#=`
zG}7`A29lBgEDQe>hrf&W{i(flIC&Pz$xrsn62lAGIx7m;$P&$*nW_I>*FPzNHzs&K
z3O%vNsIUiv{D(g(HD{*3W~y#bV2~Ww=5)V+agE-UbjeUvy9<VC?staC6G=uUhZ?6k
z(Z5LQ99Y|wS{axK%-J48{Ek&>^stNfO!K0)z0Wq8Mg2?;>x-KJRy3Ua(*$g3U(^pc
z8+rKtoQw5-dRa*0SF?PV$!=WN>v<rOGbfpF4ciIwTsPQy1k}kfO>V7Zfvgth&HZ-_
zCw2~QSN@rlb24<QYDS3ly8b}#T3!j&=L`%8Th_w9w>ORadwmPJ;E!5}5D2hHiLPL7
zXSG13mXMWeBmwXX<J<E$nFleI+YVs9Nq9H?W7I<>P6U{IR=jrx`(vjEIjP$GzPjEB
z+3H#H@P&XDBag#;tEz3i)!zDE>|DN+6qsY~R!3;x$X_mVDq~SIOPPXC;q(WOdHs~K
zqfch3DTm#e=GtT6%I1gT;`seLlvq>2$*FHNt9+;g*(em%`#6oz#M3inF@q_E<O?@p
z$>a2?te*8094x@V$c}b$ywqescsjq1p86eL#wf(^pVWD`YYD_L{5{=O7GlJI5>~*Y
z3ZPy#g63r(bewdKJiXmrg8?-;$>Ek?$-<VQVL<YMmV*<JgK}*q>+Ar1-N*CMge!=z
zd&xNNH|BPw^(ZJQ>IK^7&jg414REE6j%RA1+`05!*x++|cdnb+Ch54=w<`hmg4Bt6
zPke165m3t%F}>HgIfaEpoX+A5FuvRW<*i@&&CmHB3dnm!p;B>S#&n0`Hs{Dq*|S(8
zVCTovQMUKxB^vKSZZ<~qPTy;gh!K1@#tw(xKjrJ-rJdJMTgNMsO2gf`F)Wy)?u8NH
zBTq(&y$`3;#2>2^JO%)Y`0e1i%-4}dLt}fVk!5j&Zo9lbpw4|<!Z-kG&cbakTJIB2
z78G9j4)ZM?$$>YBW!w&4&);@wE+5DH2r1vPN@7%Nh2MYKMKUO2FJ!#FH!@Ej1>eE~
z%fEYQ&Hc+p)DI4DtFRWme|aCj3KYjEsW3mcxtk|%Jk2aT6?Z-f4wOO*ecaLs-Sx4>
zOvJXIoB(d!m=Fh={NyZC9z>ZQJe0B*4(fnJL%{BTyscQ$YBS?QSsbHq@)X9nL#0Yg
zOl(yUm!B6pZ>^ls82U-YtEMH1C5>$IA@bTTeF^+$@iYgck@li*sx7i<73$TlzlY<o
ze2(1NF;uG$Wbb|kv?!GNS|yMzC3VHQ)tZO@_UELb9>ZRy^qQA&kji%dB-))Z5i9Lh
zV;(Nyc|^r?zT6mSq#&1OPg+B}C=EA@38IJm{p~@f78&aRQH|DQO)N7^!f~YZJZe;;
zP$!gjg?yR`eT|5YsR4}P3Td0cYm06?H2UdRpN2ck5`8)`>R*Ddc$P5Q)6$u|G^(Mc
z6QQmGYcJ%O6l(y&rZPQ<8x7pxd>8s>XkTJwfbGrh?evq2G5dbftf@2tKZWkgtcqer
z8DcaztPZ=f6hoUM$lCPZrCnkM@%MubSbOs4BXZK~D@-AhfuMa)NZs$4Ny=%Gtuc%o
z8Nu%ewyJ@(8UXpYVrA$gHC0F3x_0W6-GG5zP;-0AbOsX=Wug;{R;>&xUJcNEazwFd
z&$D*>@sbATDUY4%VF3n|$?e9x;XR0o<I;Je<TQ|EH01JBB<AqMAAPFy|79U@Tk#Z|
z)4U9op;aws+nagFKvakg&$RT4>u_aaO8^7ASb<|hrly$$Iu1Ij{)ABTy|P8w1mhL#
z^+{beMJ}~{vs~2QiN(cnYAUoX3KR3RT7GsbVz%NL7LTIm6<+5(j5|A22$DF1c=Xtz
zJ1L>le$}0UU9M^Wu)NR1cidpV{=%ifvj&#&0V=q##3*^5d4Q0tt!FO;)xYi0T%C>K
zY0`-Fo7-1@N=i3Ez(h2RzbvEA{vQ3w!$yX9eFM_KVTNqO-DtSNL+H`==jY*=k#8#h
zwPNs9)m0EIJS$oXP?E$XIs3_Dd;ai}kQD5b=m~Xm&Pv~o6`mypitdqc6U7Z{kATK)
z5C5W`d+}n)A&%NkNW`XwEyMx6ZuR1F`k9>|aQ&BAKGltou#nK$(lJzBF#4a`^D-z_
zEnfO^<I7PXq^(S?q#yyHXgcOWmWs#wa0~#yODhMJiTFc(x)Qbpk`zuca6DO~*u<xA
z&tK{b`{EG}D9~A*Q43L_QpU9Qm4Wt8M=9y#8zIU>OXJ4F{Szo8NWC8`t4eu#0v)^6
ze%}3}D>ui1a4HO@9HnJeFDK#ViY8MCQTq_&ZG1-^{ZCk}B!wt8<K)Uzdg4;X{<nHE
zpT@#Q(PRe(Xe7rGZIWK=o*@#rOEti3$u+n3Y3FBKME~V=<`>3t?h-A8QALfb(7pc5
zF=An_xBbcpl%c`#T1@DTt=V{IzXc1I^1f@SNLo4XlVf_o;B7czR9Qn>Xy$44@_k>y
zIRojSuvZaD!ddDsSEZ@o<=s6%vf_EP+K@!K$_oKHBkF;=znA6kdKxt2pijS;B7&Ci
zOYlflfZ~PgLDj({!1fzoTOw;@9d*Scc?VY{I<qn8chy6R$=wVV5Fpa>!lC#=xm*Pc
zLkdHMA74Q|TGsuJdl3?3u2_`b@b>w>kMo%B7x37=ofD+`q9*Z2sFQsy!Bh|eT;Z0A
zCX-DzS-iGu>Kn+vsm<dm)jX6`J;t|7hh^{*Qt2M(7NtXX_kND{74p%rG|E5y^w+xN
zSS!w{L_JpAE|)FsHMVvX>X3T`s<pnBKpCu(^PM3C$rrfnU4$CzY5CL;`a!tZ8nP{I
zNrW%$%GZa1gv$9Vj|%I2Cl()l&1VbS<zUj4p%)5FP&ulluFS~aeIcN1>s33;;!K(z
zK!=Wln8;YnYl|0;?Snx75;*>1qNrA@jBXBOC9>g+W-$!fC7Maf+Zpr1>LG=`_PACO
zF5aHMHmOHN{xCYclp9<nO5Sy@!E;W5@Qo2P!uWeE7TU+p2UU7IMUh_^s~W$$n`Hsx
z%&Sw=K_Kd;S~AK|LkrW`Lh?wuh)DXBbJ9aN8ijb;+ld+tI9}RdSh*DLR+c78(gk(_
zhgO!iP5ig@3Rus<8n1nInv%IMS>9$Ax6h+?NF0=m7qf<@h!}~@XiuQyY203#KSJEg
zAWfFj<ElkA;tBuz(aQU1Hs67>KnXf0I%sCs#1~lTy*IAcvZ~I$vJ1wV`uP^iyP4L(
z!3(}C<DMWxK%g+Zbj%ym!hyuKh4VN&D*!N(##%wP4E-~St^od^;(X!YA#7NFDdV3Y
ztkX0aaJ1S^X<<6KqSfw2gKNZb?AqSm@2TZLC?g{W^{4h}cUR!Y)9nt>1*~h(mwh5E
zdfeS5#2W0?z_xum?+DuFMtj+QM$e|)F1smqzK9<Z=nL#liHJD4(i#`)u2G9#>Ir;F
zaY)<-dKlMoy}ek64!~e4eCG|m-yowJ>%Mu(Ixk3o5_5w_&zc9Ii=6t{PqR3cvJd=l
zdrt&NlAFZgef-9mvw$k{<#&K~9L-ltza8I;>Zavg$JcFF0T-8qMCpOgUI)*7wwXi-
z@8{kZ_k=w)Se7x$PWz8g16@7G*j4)9_ZNQbc+>B#{x<Vz17yD9b}Z8S<ng{&8iYXr
zC1kl_BLEkTitbkqEF@qKdcpIbv2$DKQ2QnD?M<qn2$tmU2ognUN9TeNl~Um85CgE#
z;+}|r78w?u!W`yFdB?c)ur59^19S`8uf@(9{u9Ld8dNian$H_u@#X@y^r=s{;OEWO
zLZ6=nrD<r^-Xr{MGl6XqD`r+0rX%POU{ZZD@OOzNY%v|UyrI#byes6RnyiHnvyFkd
zLDFmfQ2{MIW9Ju}rEGp&{Y@X39b8BQ)vIq9z}I^gX<${EG^miskPPf2p%W<kF(b1T
zcgUUnh@ZWC9LLFFMosuke(wJm<`&q$PBN{G16CL<{2=_)?)Gc650|~iE)eKyjK(Gv
z9dg6b7PZ-NOFua(Q+IUkq%-(oE#MdDFwaC+&BU;f)m)Z4N8CFvUtzU?-J!6lUT`%Y
zAgB&7L5x$14y1tjMP|ke??B<|;VW`X>E;lEdbeeWv51Kbwukn)e`2j`LcV_#>&r*o
zLyl-l`I9%zz3;~DU}mX$NBf2CenvX~`e%;IT(nOK@?n^ga;y5`vms&|^<@14DnZ;H
zT4)3bDYFi7WXx2R9?hTN&_AVi8EwLFq^0vO+;g3^mW^bp4<5+A9E<<q)1L!=*7WDN
zf1vrdUVKgWULQ@Q8B3h__$Z%3I<R`u3QLMCNe1Jp2MwEp-ddZcTxx}yQ?Is>TDn*N
zbS_wC_b$l>cpnqA>34QzwJP*F-Uu`K$C4}nUawL76t6wI3u)s~!bf@M@WNq-_x_s4
zMDyG&{7Q8Nq@dK7&FsHRC$<l`p{V!=<H|_c(O_GM-r0Ner-y9M*eXFJF<?`4k;sg>
zi>k0!PtNtJYbob&^YEg-ya1Uq2QiBV-4ZhBuj7fNC(Ym4$Ja+hng|MC{K0>Tdomqi
zph)>jg2(cfHCPW?Df)f>x>RpRceW#~mJv6qk$o-Ywox1!WY;DY{2-@O6!m6^4I#IL
z$Y>4r5ODBa5z!#qhV`~28P0qvuO2N&_KMD?vbWnhe&!ZO0Y(;MjLIU7=)^Q<#NV-n
z;uuvBVTbF<aOI4TYTw>IzW0n7z2_yF0^JH*p%l3GscdlKCK+51wWt$Cv*@v_Lmh)9
zin@ccOdX|JYet9x&B(~p>|-0PT*-8ET>>vPvLasWz~rzAjYd(#2(mZI<m=B8|C&RV
zS~FR==)nXVH<q>t>XvI4FWB3@hqRN2B?~JkTpP_Uu6q#r(|ZO>m`w~UWW5M|y?o28
zZ}m6e=T|Ihda$WVN_r#5!c<2N8l$0C!`1$7uA+wEqLM)soLu-+8YkmzHBHR>E@#CK
zNsE}?pJXnQD+?=4LZRjlg`c7cO&L(%-rbIg{a3R)av@YO8&O9D1AOgnU9f|wZ=Nam
z#{_FD9ElYEn04>33N@%rvu_gJGM3pT?K>S_<{}?Ak$f5Qys@K9p6N-!qcZ{d=VK3L
z26b#z9~quB65cD9L-s&aba@7vkM-$d8xFjsS-Bz6v~Wy5h;U~1-Kg|ma7`LGVX)u{
z?v`rUO7UN0H-VE0aMD%rQ#2t(+iJLn)1stTJJh-tL#9~y;L&Qw?Y9M*NM<{7AFJts
zB=f?_rM8)k7NN`nPy+&lEGodi6~};y;g%}&aqBxZl9yN+Ft?_{l(mY*zeki8^GtXf
z7e#=SCZJMdHkcK`QDPTL?@pj1Y)^?&{6#l%Xfom>WNGFedNhhl(pYI?i=C*1M3zh9
z8<k;RY7tLo85QMGjdb|%MHtQ+l=uad?K671o4Zt2wm*J!Z>u9F(oy|z_EH@l^76Jk
zGy0dpwXVv1_(r_n1J}9Mmk<9$je>zvXRU84S|3_cR1Kg14_JLUkROed<50h8<$P}t
zZLMpgLC>4UqzEpb63P_R?wj60Mg={yUv$i?-rUpClmyy7gaQ3^&DSp4^Yzm+TxUc5
zOA^f4F2u7;V1~qjg^BV>l$@GqJe60gB%Y_jpJ5|K%tVG)jkc~sT>fW;1ii)B+4Kro
zInCZC_z-3=QbQ?4ir1jr$a=!S@uV19)MZU$^y}@a(dDJi<hf6|qgx4&Pw(sjzjeL-
z_iQ18F=9}WDIQ+{s+yw**qrfNCsWVk#hWarhIZf1O;OG9zRArLdXT$XAzN>NJhi5}
z;%v}~1<u-2uyXDHSo+GasJicM0|Duh?jE|ELApT(K^kF5$)OwR?x9Os9tj7eOS+U!
zDd}eDj{ouZzFdA|K(4d*S?jK~w@PrP1b0*YwBX?QE?bk@9)X7UeQ~h)P|%tUloE8W
zGO_(yS~s5zUin|KXAh6i%X$ny+JTKyB^0{X-5^w%#9$BSIBaByLw<VWY&>>4UE)Su
z<r&Ux=8|;rElMsknSV0=wyR-ZAI^Fh{&ww8;3oAekh6<OJ=*^D%NM!7em)l&A&IEG
zf0djAi_GDb?e!rO@<m|xy{k9*bFe7r_d8Lv=4P<ib0O`5@=}b5fY*6n8j=Riz02&}
zejb9zu2GuFkO2vz^C~ZM8kCXFe0~8tKrG%Zzx|?~_!3rak!!_wcOhA!d78_z@G*Jt
zK+}P&h1Q9Z+HdV})}_zPrH_v7Qq`~?T9XrfF_AVjv9Qu>ahV;`o<L`g7yr?&XzmaC
zoBdSI1%l*>5HFrS##gQ89WuQE-XhC`2g3DgPxofZgu?<i`w;>0v^e@#+4e#X<yrDr
z<qS01J6!=|HZ6XB?om~~o|z^pDnqrS@9TfA`oTsy%TajJ26;1oPaZE)$%|=E0(Up_
z-?WuoZDGg!m%B6#n#X)Ob9WRkv*_rhr8J2=yBw1EkbPlXMo|aMs_I^E{d#>s6%4(M
zar&KOA@*V8%9?u|x0|XVmn7`IB|H7~TE=Ls2KAht$$Jj<vMmd5JHK!zjr^Z;+sn2P
z^yRPWt4rN&n12=VKV-X)=v)%ZWz=*~4y9kCRr@8Sl<ei*F_j*~mMZhb4+1(#Z^=IU
zz3|gRJ|TM;^Q(T`1PGhO^=10V(GHiXo~_I7Ek@vd(Xf}vThhLaQjHS$YDr2;tA}H_
zD@)&aL!)8>6**HnLd3hcPn>3H&GT{RMQH&qzt);{hhO}MQ4M~6t>sHm#nS(XT!o%)
zq;7DGXS=T$z^)$Awf+4!mmfwxQvZcXF<A;vv~g{I#5bR-cKr5P#LqY8v+I?eA$MQz
zTgFM$Le#lG13w2nD71+q%*SU&DMwlyZW@wEiGC51)(GT0EkjclOjJ>-#icx*76X!5
z8<gA)(<(`0mF+#b58HbjkW7x0hnK!DBQ*LlWPsY^h;Yvf3PF>Eog|`Y*)N5MykZDb
z9v7?S%#o+%MGcZbcNpETotz`|(7<VR&0bk%_H3`W41|2bqy2tSi+ucLksZ}i+TvO<
z%Ab7~Md9t0lt6JAA#;%h3CXsU9vny+zuH>#PImL5u8pBMe+W^!R#%><0@YYla+~k5
zM6ID_>9#+qfpFD2e}J-td_{$vOrk8@pou?PT@QW7e~{Mk+nAS~O^?hqYbXeNNMt|n
zfvMpsieJ87j?-xvp0>(0A;nuMx>`Gdr1Ec)hfB=$OUeU;WJ4r}yLNH^`|1*v1kryP
z`;}stxmsdD2}LDA&+n8+ctlO9ip;HX7+GbV?}Sswv0GWmOY@wVba``sb|*}_?yp--
z4FUrIF2(PdtuwA96?#>8x2wKj#=UO2eXG%DGG~qG82PGG_))@3-=Tu2?P~&;fW3oL
zTZ3@5bhdPaPIV{ZfKe2ReDl%swCO{9;;<fN-hT%>8w;&RlJ3QQN}|KpHfCN@@3^d-
zIYNLkrHf%qNP2sC7iW=2Il0c%#R~NBEM{kp6a&G2xk~5R6HN?hI^^-Bsfc>*;l!Sg
zP1cvhI#D5h8Q#Dv*$M-}QN%7=-KRX-*hur<Yo)wTpqTRg?z~wLC?VzjJ2laF9?f5t
z_w8CV_(h%@_`Hf~yI^ZwIekU0zdj%&yc`mHC5_VK8)x31X1P}X@}wZGx%(bK*7=la
z`^$A;nFHFHC0<lIJQ;|9ro^cib-1s?+0yd7nnD}0=E^p9ln)Ud^<ItNW)jmlt23=V
zMB4XSQ=43~?n|TXi@j#>*)Vo1@JD$6Qri8iSAAwLfac{fNY3m%8SsUnp@_o5&6PwH
z|Fl$odQf6abQw+_UxgG?EG9CeJb8vHKXWHpB`|aB0ek7_^5fmAMfvU97ds*Jp|o}x
zaEFNQ8@>nDMXh(SspjpI7W0Q=Cz4o(g_5#Wmu0yXW-j$cMfRe;dla`{(CG%qm_@t0
z#<A(&5FRG}CSaH6K7Z}u!@v0x5B*anWy<`El==I-03=3lVM{oZdf(xv2~+?5mQQE5
zfoG`;xO2W*`PoZMl)vfAtiy5TP_Pz+?Xm4B;$6SDD)s&d=Bl?cS9yrvTxl;|xy@7o
z-6r*C&Hgp_O@p<_=z7k@I=l~wSjawGcA{wYv5NjMs<!0Yg3-BJjuBDD29%Gj_60ZB
zJSaZ{Wp<FTso0Ng@6gXieQPn*G%Zh9FaPVs>bFw3UfU1*@k4U6oDRTPkY{)qe4{Z8
z^si61fKz{DwDS}lFVegkPF^FYq)Okov1T-Ja;-1ir<UiN_pnJO@q*DQDyeCV4b@ch
zv>|!g(WQ0U;E3$G<|O#*qe50<te7NUI5!eFC%||}Zfd~{kraJWgyzc1<!0F0()^iX
zsYP??W{5POEZ2`iI7@$NBZe@-x%)FkWgJymRFF<Xx2EnEP<K&>m7T;dV`?^!O9mOH
zauy$00#MY{p;LndefY~bg=VpZ6euXTq<rvG8ylJ9%_s&xE4Q`hTM#z}5^fwDREI2S
z65&%k^xGsw@dGWvn7OR5qRa|!^_hF-b&prTCnAguq)Aly_4b8P+l1VS7X@YB@H*<i
zpa~{Z{RuDBY<bL?p6f_co;+OOk~Vy6HIj&@iMU3Ls&q(q4nPE4dgRU-@&&8qr`g_(
z)y9gy;p;p^lMlkscb>I*Wh_=O>{hCv;mJyI6EgQplPW6lwpcMKxhD7gS6*`0a<1Jd
zrVP5krLIfjsrdv>ixKiy(zruSvurQh5i6_JdD((z3A}Ls_D2i#p<_O)ijxlnlE;Gb
z<#iNY9U9leR9Ne_L}}@|O<&#}UsoxEB5fFDvweM`k{oFX5dt!(bpfUsyOadn%`Rg(
z3Uzd#lUd9YRie4tf;qzBYTMCQ>cmH{o?|Y}#GAh#>ZZe=3!#oin`b8^2wI$R-{30W
zRAKTb@??w95ETjid}1H3wcR<C04;G|2RAIfvCnLLMG+A3PToeQJ5j88?0Ef|6b^df
z=kOKgclf-~?j6csWcae;NN%Pch;zr76cG47oEZ`VHnjO%ZDb%<3-I3(%~RnT3bK2^
z2Ob7kiWWlI%zry!<wof*mD1dV!g@lrmu9LBLFjAfp0uA8*nB=K@`FGiG-)>0(qiCi
zvA22lZ(Cp4eFV#+m^DT}>kis}un23Rh?QeW=c!MO#%SO~x3aSGytM!w!i`FHatw`r
z*<^gP?UlTuFl)w)Y|{;4dLg5(cq4F!;QLse*!q}vwW${Y3Bz%M_r`LfioyW4jTO^Z
zDSgnRj83a^t%t1pVhSIL8h7uX?e?*m<}dr|n+~<{3dZHw@}{y=H+ogPmR1n<e8}xl
zSq(3jJ%KUcQ4XeOju2COwPSa5r;bQS>G-B}XYy|O+F7_~XZ|A9;n!cbcY3X^RMXrI
z>Cg}m(KY@wTKKsGd^Wkb$LU(&9mm@e48kV9wL{U0lsO68Q$2^~Bdh(DezR%U4#zI&
z^i^O8e*4vX$zeit{2L*BUF;r`U^ttk)OUbkO6?s+Gb^=K+A@^cwc0Wxje)KsCv{4I
z|GrfuJP{5rO9Be0va&aA7f<0VZicDt_vM|M?-RxAz<%?;1<*+EwHf?e5dY(jSUBCF
z81YSP7?dLR119_whhdX)GdRRn;!go<{F~XWnZ~Af+nUSmz$GB)19QyPd3kHw?S4m9
z-f)P30T)mt(w!=643J}cm$voBKpToR=aB6mV~Tf3c2{#Di^)78DDev)G{EoYs~5Bk
zAcaF3A3mF`Z1>6JDlC-Dd+0m4?cUL~wdV_%#G4lrDS^h(l-=sfwK*-ziEH1h>c?y7
zAUI#DgMFSjK)~(412#BhoFE22^1HfFGr6{DRm#XVFfb8UwO`9S7r&I(KjD+Td2wlc
z##P+_yL<k0^K^%c_=TpaC;>L!bh^LK-f8yR`2M_vX!-A5JGf)yk3u@|(>~uKXhP51
zKC^20P+Ho*9G)7SW7e*tFOdm{PU^VC%lC<TZ6j#puB8VqZrp_oB)8JDe>D3qwkIs$
zMy_SB>WZWV+1hOI2~9)7lOXX$lRBqlF)~Ldk<_CEgIAO;P_x{)wBfZ+DH@|i>ptgq
zg9yRMwN8Z2M{@Ggg4H?Z-W>HlA<}PK<wP~`7=1Q*G-KaKryl|!n813$Eh<i7gNOgh
zgaGA|NTR=>)pmQF;p_E`H01cD<RUBMvLz0%mq#~v1P>7pRRVM%Lmbh`t|@_F8|$)n
z!snU$0?2IQoEl*iWm3i75k}vm=YcCPcv)9g9$bZ}8bAqX#!5BegORx<js530>Tt-$
z1y%$<v@xl__flQv4b$c@y=cHS?5B~F`@)IU*@9FK8SpY29sZhpZTv}>Ow`MBh`NN#
z%?7Q_p`T9F=4lMm*uX5^y(5ZC;069E?2NqfyP}Dv&$I&DTG5u^q6m!J@tRY&4VC=?
zb@%~W<_#f0PCOBMN3$n@6#sZ^#yR@JDJOeX>L#M&=MCXHJVw*g^4(C3;{VFRB1s7W
zUH8R{#r9EyqT$qe9b(-qqdeoHd6>SF$L^&>Fl`}CXw)?mN?K+l4e(H#5(^URMEG<{
zbO%>`o|_RR)u~f1$W0O;4ubk4RQlZPQdgcj%ig-g<&OT*D;*gP*gdG<eW2~alp)s5
z=BN_#ep-`gNE6a?a?`K$MDIeEigo5793C6kwvQIghAbB>9rE)+ej>0fc<+7&uWiXU
z(8z^qh0@5`|L_r5;L0~Kv?^J)axd!c`jk?&Ke=~#a-YZ(J0=iSs;p*Qlvq0`!mM2+
z&#VxmHmxF(Ce6E@IBG!J9Da$n;6f<7XW@=U*YkJq$BT>e$ms4vQiVl>Pw$*O=4~$Y
z^lT^g&h`Im(5v*c@w^idf1vUm0pN0OUVqo8vx2_wut&U(Oa5x9bB|@C2%hMZkVv0e
z)uO}G-3v=#=K^_oeIuvUOaErce4cnM3=A^Nej(6?y#_V8Wkpv17$Z;sQbm;M;SlDy
zk*n3aKa|!LME=~xlV>*WcSg-kU8e>y!@{$AP98Q_5`T;nY-k6zDKQr&KqP!>@x+<`
z0Y)4TWQe}_r;xjw`a%N?9K+bJD_>1B<}N8@z?JS;@x66<Yp=2{h-bNI@(jI;)XCX?
zy10kWjZ$1Wml9+RvT(rB)Xg9T@g3dvz+$0fb7?_f5f6z3B|4sBzn#3FS6Qm*eE7T6
zE=^ZCn%F*OOVC0+kXU;J1!_y0_)9%Vk-gZ?>B;K>2s-7`&v7?<bsEb2Bk-7ymQvda
zL!{F%A@^3b|I<LWkSK$<m)qY3$RbYST<UvOzlt4*xviK!bnNBj^X~#L4f#dkRM5JW
zFK^s<OX5N90Byx*ePu%V1rytNZ!Rkp&hS#OMNN8?Z@UUWhrMiT^5Cq*_mw?MU*R(J
zW1&4WYUe@k%9T02y~xq#vZ7?hvBW-;GAgndTMGvZktgRI{q3g<ihj$p(?ZHv<@THL
z8)dLaPlu+{{B}_J34!){35#Sb98RVDsuvE2-w`PA=Fyxk1fJ8SJ5?Qb<2wGuHFDLW
zBxHXFOKz$6mcs8JlmcFWNy4dYV@Iwje3|2it11Rm;ofzISIml-_Y<?GTLTthnJ1_1
zvHGALH_63-x0LL~YE|JydMA&)-ph|RX~@T8`ndWS8igL%#3-A7LTJ_g_`Yn>Iv)!P
z<YxlcqD4jWc1$((x}m8=chmYht_WAywqmO<EdE=qUF+2@<?Pn%&bdSv4|O~Pb)=$U
zgDsIFp4_?o+m>y*&vp$nXfHy(WViw^<R(c+K%T2&e<mp>`26ylz7AOGlr8;_u>M~4
z$;}YEURD$x_2QuCyB>r&tYk0{m|vr6rIm9Ch)`L21gHMdQu8xF@6NDu-M_ys%Dx|5
z_@GCLKBz_Mq#tou9<^VIH@=7X&ekZ=5)6+T@LL;0FH49$NpC;l19tYjzZ<)PmKyLj
zpasH`aJfd##;2K@s}xCl<+LOgM}Ys}K|oAWPVqYg>Fn+C2K1`qCIZQCFmlp&BkOk&
zx1J*gVaP||{;@clA_(QBnq6;bKLe*bRviP6@Sax1D6hqSRzx?n=Q=>CWgF2vPDX7g
z2ufZLV$P)Ggt`6K)zIM;P8gw3u9G)fdhzFb|H30uE-P`zmsJ_e+9hIMuuw>~D6Yn4
zXYh+iW$w><M+JA5&}0++hwOdvOXUL;aKKbCO({<A!&`J-H`dbD43TE(UXRNuE;Dw5
zLBr{EJVqT>sIFzq0C#xQp#IWocAfA$!}UBgn~-_}!jXaFI<GM)Z4&YbzIE0To?;Eu
zY^RxJxpZ=Z&QVRj=OD(cv9J1@o#xZWXDLq$d(mn>;~HWNttQ|wt{<x~FeF-!Dc(P`
zw7;xaLJK0z%d`oi*Nsj!NsntEj@#<{GG5m;?%r1`8lTE$5x3+!e;}*^>SD#0s9H4G
z3{gD;3XiSFZTHsDm9at%E!<oWjJVKW8}gwrPU+6xegF<5*+$C<*I2>*S9fWQvbMWY
z<!7=bjgZTlLQXNF(UEe`BBAo-e?OAr9-;0wJ*PONmb(9o>Z*zj?DukEU$4hyr}}yf
zH7&n8RIX@()pInYv0`r&ri)L7o2m6gRzqjPK1qF>?o~DbzX;3GRmt6gshg+9j&^j;
zR8EMrGZB&r{vA=~g3eBohS*QttX*d^%QqJBcCL1QUfw~y)68+wgAZ+UL|IzV78B^B
zm;kII=#O^kTs@Wxn;jWpw7kJZ<U7`Y?2Q{+2NqpIJf$+B9<Y!&U1a;h{Sl0Baa5|U
zJ+#~oFeGofz9|lhG1mjdeHu-jlD$x5E5%NAQ4cs}{)yAz&dc67jq_CBPLJ)Wl^#_i
zBgDChnf@@PML#aJkm9!GQe&|PFS)|8Q1ZFu@|ZwPvnYpeD`5$dH063PT>z1}%Hhvp
zw|q}E^=_}=JIkRI%gKW4pPba8KZy(-A3X6HUw!=4XS}woE7Yr2LS)~>wdjLIfL_sg
zQ6^(%yLIfYK0uY;F=>~TNb0FXOb|v8#s45*>8zyeZJ_k87L}ow5Y3XigH22~O-&yG
zB(kcAU#Av7syTAZUN#Edpq3asHH$*?Us`_HAnrITqv37Q>&NxzK+NyL13K>JbQ?75
z9hgV5{M%XIG2(o$+Ghy0D4Je3^}l*qHCoNzu;{h3DHcD7$izR@zYE%S@VNWMDSX`~
zbr<PzwOo~=UhkOd>!8Vvo@r{!*D=9}1qJYco?t?&re?2U8`Godho=Z}F#io$D21Y<
z;c_JY?6Etg<5BLFJRRxf{^A>V<l*J_mZk1r4ImUWX*r-0RJY$fuZ?kcT(S;qT>*bl
z@{s}1V^iJK-x5N?U$GxZD=o&|MM;s%Xc9yfMWhWh#}QJkJz>L`Mp?#9Wg>Oy{&h=d
z*T<*y!X!dpbxtX>zVZODfbRm0db@UL3vuC#G+7^AX&d?-CZ^ST7vAO?b0AM+|HJst
z(&Lx1JqGNnas?c@ju1V0b*!GDmwJ~bk?_L9yXzBx%NVP;gx~y(FM0SmB~TNN*uODM
zLK!>n{v1I1F>5r?bTmZnS?LrHHPqX8Xflkhj?w?|bAp<${-eq0tT?A#b@kz86I$CN
zK&*Tj{)qs2^hEEFEktTDPk-wgSoMerI<K}ICoo?=?nWSwJxv2b);EWsWSZY5w>=*>
zUP#?s6Q2#oIm9!nt8i#<A0T*#!mx@qDQ_wyca~U^Kc?`ME*(y~rnJYX?sJkmr2Etg
z69M9S3?MFLLf1F=XWFYnXhH?V`~!|VfmhVtd3ET8r0~g!O%^RQTP>ED3}iWIZBHp~
z`?DHe2>hnQJK1f$Z%c}kjA0eOcNqjRaOqg%;WbKhBE0-V!0R*}H*zcq>gD-p>GDH~
z3#tXO3UAvYib5ZEPkEMpA<aFUOR4S@C@>7btq&TSypW+}caN3&ei#0Gn$d>`hw7-#
zz-j;Dn4<Y|H2nvEd6mu{o1~{<srz1IV`DQSSJ(Ct#SbJm%Pq6@ZNj{ee>wb7zg>>r
z#gM@C5<sb#ir75&l?FwwX9Qk7Xx<F=H(X!;A&|T}I^Ru#q>ZcO5%M!^)Di<v$4$lE
zI6+~-(!1?908#-5;xTQ-s&@T!HTBh_)6;#+{iaiUmz{MffS7PO*yOc-MWhp7w;}z1
z-H~hqNES&z$R9uWOD_}PPO0YMkY(u<WhM0n<mCR{FRmGVJqN^(KV7(8oSd)xh;=FM
zKLFzM>3llQ*|2F~ruoroPRA(u@IGhzSx8Ll-7Y5pWfywnj8iP^Q}`9_-bd@R^#T{z
zO74WPqIYHR#M-#ux)~)X3|l&uNViOuE$?BcYyVmRR!79wFQ>x)*i2G0Ii$IgNJ5|A
zIJU3>Euv7!nS)Ah{_0^YEW9n^Z&m;)uz@hPLTK!?>!G&fGnjad@EZPRxL)(6krb;6
zz(GC!f7N&{(i~qzk;D4o>mM=!P~-F`7Z@}y=0eA3b!n|TfFH|j7tPPdKeKmwrhek1
zy2__i%2e~TTE+gaX*E;-y~5C^m{jU|3ouM{dIPF|gs*wL;Jx!#VPBw}?%dJkkwCb_
zVs%`JT!gk5n3<8G`(YI`;zrGgfA3wK2hHRd;P$YUaP;PM7ew*Zxy1X8XgIc_1)G1H
zEZg@Xs`W^2TsXk*<E>N4lNky48fp!&KufjKPfQY0#Y=}N?i^~`4BL8BY@(l1CA6VT
zfQgg@Azl#Raf^C!8}PPlI|ZSxyXOE<>!K8qr21&d3tetdL3INH>me`LT*K3=+<A?z
zo{RK!5MJ)M+$vVz`K_$XBUQ4Sr)z9OXw`#of$uAEZL6Dk@F&pSPw1GSx9Qb(E(*YL
z$2a#5$n%X1OXpz`4+<rCq~Qv6aLZ<0^G_85L{%|2>e5<cyG&hLB^mM{Jv%obH?|r<
zXO@9d_>Y4a8Ln-nq{ODV64eN;Js*;RmH=!f(|Gakzuqb&c8<0=B=Z@boCKlw$Q3hM
zKeotBf+YW`vWxmM2lEGDkz-=wQ3h&^o%*dwBuS_oEOsHG$qgFjLf3t;hRTA=G`Kgo
zEfMIcnoY-XSk=!mn+9-_9p8n9{T`*HPoUv>=z1*N^?i(fw6`^B1wkmjH0k)K7C`da
zucV%jm9IUlX<hC*lfCC5kDdstc#sP%?H`n`S|VI>!3Y*<b|Pz)`#8{_e%$&-9SeL1
zHe`DbBUqFnA3FWI0|Da;e;S(Xw8HH<_k<@Wp9&;mM1w$@_z?8=fE}AtWM_%YS96o9
zxZ1tT#%UkFxZigHZ`-EVBWM<TE*xVr!nuI-@#CM-w$600Yb@du7rt1}NC`$ZPD3$v
z0e$qF;R_)ESb&?F<#?R{F@lC|$(#FEwZQcQGH_^tW{Fa)0w5_Op7uE%_i;dn*dXxC
zB8`2F&-(ovY`N5~S+?!!;24(!H7COjy#Aq<n}2%`Vy+@igdF#dQUZ?|zzb?nL$OkD
zBQH@yZm^*iYy0KaYoL*_%%<OX20p%Cx#{e6II0%WNQQP?rF?7ku*y0~>Z)2#QnGh=
zS}I6*2|{V|6)_BvHn`GQtA@WYPPd>sd%K7b2LeTF|61wtqgPtfW}E|3G`{nF<v`%^
zH&ZjK)?e330mA{`{rf5Jb8PC30RnwLxpIr?$TbrYHLX>#(+mzg4$%abIP>Wm`NR>H
z)3!}*=g<Axtl8NzDI4>`0ht-D0k%8ocueJn`B{YmHSdbbdi289{q{a(<@Wgpr%KrF
z*3d_cor{;tcW!xgaa>R1)q%N_iv45MKQC@7R(<GzM=Ry^gxX2GooTzX!ABg3{Lnt2
z%EC<gZNp=}>h&k*&wnHoZp?c26e0j#v6x|6_TCwwgWxOkHNpmbYFZ3=(*CPAM1mj~
z4r|6%04aodGyUpjhc+7hNV_?=h6JVge+361O=ThfY=o-DnXk2f_9reS4cZl#+%pF@
z5$?G>@$)+^fCFus3GRwaF%w9!tXcx5w>G=}@C6VN^kS%^^OX*=7p=!yyT)1(TtO-T
zdjW=M9{~=UHENL;amFPDc&7OM0U|{&D;&Jzv>rxx(LUU7$NtOH;Jlkh*-@T1mm4x{
zadXgf{slMZZOeKeZ~U8YZCnAAylWOb)Y_S<E&Jm(ES;DqX)di5P}t?1h<2U%n!-fg
z-C~b@peCDqNuqRmR3bD}EIt*kN)_5tIPdXqVdD3phN#s!IUE0+M4(<62x`voj{mq5
zZ{Vwss<Nfb{ST+NJc6p4nJI#q4XFAjNiX=<nW9A_Dxf&VN>|J`Mhko*0w!DcC$F;{
z(mlaV^3{P0%H;CAXYA@Yn#(P6kNO_LOMwTz$bQ#E*3{5`V0z!{X+q+{%5&ikc)N~=
zv^1#7VKy}~yw*j?z0YsDEw}iH*Na{STn<~`tVReEpjmuV6i|`|+;=zi)4@7Rt3Fj<
z6)j{F_`)h3x0+*d+U`9@XJ!$!)yF3~B|?D=w0(4P*YuDDrBDK0-&$+(@j|}Ld)Rs`
z7VIO0Z8)8Gw=kNkV5eg{uI2ck<m7YRGEF=Osrs~292VR-K5(+8N<Y%q=+9$bVz3Hb
zh={<D5-7%UR~GT0{}{KDu<iMqI+i81B}FbxvcFsk1mY%zEq3FAX`_jw)&(i=43+fd
zBNzF-x#p1<QR`fIv~tgrFz!I0@-G>ue!L5xjt6hq&JKlu8`gxgDRL;vlNvYxw5|XR
zxzUKhXX)M@VlB$#0B&B(uc|&ZOa~XPqlLmknVEFN`B~XXX)vObqIX|Cr>W#TTOOiE
za&oWA)0t7O?}#ZzTeb_iqNppO>iC`)C5CClNaeP4`VPnZc$shWSH#QJFPcA9Yne3v
zj}~0}rQ!;tA&w+`s-}sN?u2)2_rlimRu0yBs7tq=ks~3XQkmRQ#&0hyL}l3&+iOwT
z82EBI%wx1@=?w3Mf{N&}&n9|xUe?-uR1}&)e1RQlv%-w`xrs#<Ga%Oh|GY2GyRT>k
z+~R<}QkF1v9GnP5e;f#j*7XpLGv-B`;L{9kYV2163;t;{27WFMwuau#@E5YPUi+Kf
ztu8*%QR7{CISMl99NN}B1E;@7bGt5HY^72BXnrX8GPmp91N&7rn?5Gkd9G(Gf^>8<
z&Iif@iBrYc-nmmCb(HMQc@p``;~JS&->|R89(i+km2&&_p4QN-2v2aEJf4EA^!S;q
zgw)3A0b5$RtGN|QNuDg7nsm!T+2o-UA>nfj(d?86yI7)HT=$%Di#6&|YX=<lMN<(C
zZy~&3$*-k*QBgk8EG$-~#gs&!uJcK7ON{)UB=7%H1^=ZF4?ykyj!%D89C7*XVD{Gj
zGT_61vXob27nJ|&C;v9VB7Tt#8g+Go`f=d(LHdnm;B}di-PDaZcSmQ_r?@mEth`-A
zDpo`a0u?i5wAO1C5(=Udv^TacS+J~M`r8rk)PH~5H0m6{sEo*UYPgPzp+Ov7zJ2{z
zZF(o9KPg9&oVKD!n4Iju&>(>@*mb}8txBU^;}EdhL)I?liejwNCDNBbujb$xkxzkI
zaoK#IK*G(F!hJeB()vs9@+4=hn{}DE>$JjkZH$!#C+?KrR6<qg%<mNuWnRU*f%*Fx
zns&{$X^LnaM6|w%)8s*M@LCFUy!qpO+c%@e8m|xE2Z8p$UItuC>lPc8v?eQB<z{?(
zJ5R<IhV|4NcxRk8yU=|lA+^>b)f@{s-n!|&a)0#qvJAT79$CLzSYQV#xM{!xX?1Sq
z)|l5#fluUKvjxy-Rvt?lu1Pwsgf0@S8rq)LF>3)lB6Tsd+kbhyaZ-rh73oZSU0S?|
z8T1n_cI$7%qg8=AjhhhIfw4|1jCEv~=3ryX2OFxDrR+z6oy#;km2f2gz9+9SefEZ-
zr*@veI_1GI|FekW<W<01BF@C&M{Yd&R0sqzVJbc38u9j{t@6!DlKE>8idMx}OBaAM
z#hQJevz^3FZvU(TGJi99DJej=8{q@tJM`vo7yIF#pa()3!+yavGYfoNZOercls1sb
zoR!$U`$Ie!w-|4(Ii5ydz&`=#H{Utf>SeKZ#07M9*_uL|03h4e6vVvo(SK;}cKv1^
z*uYI8cLTV|VB@7cKmgmhT@InnW7MuA=r8@R+c{+WH6WI5*;5Yx922~!#Scz>!Hu3$
zbI}RD=kWV5%AnG@sN$ME1{@}24eWJ+*UUbVq3geqKj00S)ZALX<^>iShNGZwYTL&P
zmJi1FE(b-oB!|k)9Et!))>pq__H1%W6wE(l!_=^jFsoj7;|R%&;scO$ti#0q%F*~A
zn=8GAoeALQtU2uW2SXnzDPL&MdJ;kJOa?x+sgGg;LbpF|B`GA&DfDk1E|qYUR>*N$
zzrc4+IkshOCpqIGX)jfkp-Ih&HP-h1=YJ<vh$@TTlY|Blk%h88!zeKdKBmtSif8VR
zD%6MX6}?Ac#Un7zmPW^<OO7~{*|9Nr1v*7HbNxW$^aj6wzvsW0Xv5Da1q|}fL6}OJ
zq%>=ds-(Y}^NWb0pMhd*T(H6-AYfQ)yJZttX3pl12*l!998c?Ol#r7?bhAR+$q>X|
z&woMDzC9<XSk$eon+%rE)#K?x{Z}sLe-!q?QdkWX@PneChr!<zbG+n*Ez)CE<A<k5
z6<P)#YZr4c$m4)wx)0NnPYaU(^f*cdLGP>eX7fPRo&?t3a$(gOAvft-kS&0ARk&f*
zvU}0Ay!cm`%RiI?r5mNogcN`j_pIdTVZrst6QH^WBBzCKZhvXHl!giIJfsVI2CV4-
zK}<3K(3Qq>d=lOCOeaB6{qobkYoaoC1|p9P%_O7Zr^h(<`;P%>vwh6o4)($PsYxLV
z&Ytgv#Nn8kEsJWu>xUD-t%K|=ETVvs0r$*{GO>2blj^Z6E6X4L`~qO+lV2deYL*WW
z^-SX;==8xn%<($OO7|%JH}r(;y}kRxMs0N-v%UbW;coQ_l^O9a9v!fDupj<t)vC6F
znQ5#dV+s$Bs~-lA?AmwT&k+%jd87_r1JFH<u|6YUo1%~{{H^>D&tniEkp9DRPi;E-
zS8RGl)te@<1`Q&Xk^ekqp@7A4(c}(PZ?#ykX>cJP5K>_UZtbr6u<sCXy{Zl%TV(~+
zd8#sHZv=3%&$RllyK{~BHB#>Aa3=4Bl#SZ%J24`M-#^Fmt5;ly&Q!mmc9dK96zrfO
zfu+JLj4q(*7Fc;EQ)rW?a3)2UeIr<tX<D*yr(S47UDC|@hBj0de04?GsYS6gX$^XD
zyNvs~TlKoL<#Q0+n`6B;W6PT7clxu)LVdB^z)%RCN*J(VY}=*#Zoc)L@M--}>v%%@
z{FW}N=#79wwA$7Oo;Ypv)v?0|%r&o<B|gBf-$cJzT#=ttz%P7@XGDutz3Lr^!x(Hr
zRQ)llI_3Ahj(}(!UZ!N_2Rx&~?MG(VqICJQV?<@OnZD_BiLPT*$*TtR?%vKz*YOL6
zj6QF*Ggq5G>n)0^%HCQ3VCpu`a~l~)!uZgStoPFNb73$wVf5>D!&z@n?<6NGutsOi
zU^ejs&tKh^L6&{?1(K@wE}d15QY(Lqwj4E*D{P&c#fDZy?l9ORTBh!}97fl#s!TT8
zHszUJyaOKR${lvUsV)hvw0Xx(o1`P`<DIC%eHL6#dP{8j{e?!qcy!ni%LfxjK5q%m
zfl_i4(s2!EZ_owQ$^Hydl$Zmi#SK`I9l-+MKX+2cbu{$)<_lwx5MW$x;m9OGqJdc+
z?3=~X0`PC3sVfYZOr9Or!|^ebB0s0fq$NQd`;kY|b67%R5?TfOx3bc(6pzvME%V%6
z1i{V0(%GG~Qtf2f^x?Wsr;xS62rp=xKNenNaiB=}N+<yzIxV4C_H9wGqPFhE94>=Z
zx)AGzJ+p$RCQG0$P`iMT%Oq5O@AvX|q%EET;A#ilC4m1fX>MQNvnys)ydkUJ${&K-
z4Rsd1R_?4p{O~ocLW9W-BMHGl$=2K$ws((JfM+L|Swu1SugS;a^<qdx=aEGeR?$d*
zS@&6yN5@VPM(?Hw9j6S3;XISNM#tN^<yAX#f4@ktYkd2FG$-A5&T(40as{f~8fxAX
ziH!@~?=tX}jO<5X&p?)Oo=^Qy2DU1iIUM6S1QXqi0ELEDF75Ynb?FIP=?%G-SBzfW
z$pg)o_h{-A(&#U{MH0+%7~&~dr#syPNrrD<l-|sDvb=uVU(+60MMH<>^aUQX{|F}A
z=4SX8b10DsKIYSEjm0CQ+-6tOqSd94)1qp4YO%;MRhZQ@H(dFdPD9v_4g3M}Lu`<=
z@Ty;MILW_MfHzmtnj=eE<9eMQ=vHf><W`KPg5!jy{Zh2_OkN=e%g!+&*6gSeOLj7H
z4d}!v6C1yo+p;I^Gl_pDlI!#rm}>%huath)cFKj0qYwqacht6H?hnROY#6&VrLgn?
z1amSW5nsihH0)Z>r!wQ`r+fSRd&KX*@C^lFd?IMc@qJ=KH5YHg;+I7C9pC3<{XY?E
zSjOh0<PfD|zf<9#x3o$n8LC|vdDd9!3y2(FS1Es8uGoBG3GOfRu#<adL!<;9ifBK1
zIME@R%ugFp#S*WpS8gkqdgY$S-OdrBbXd?V2a*Pw#c8Q&gu07<Ob*mcLQelu0|+<N
zeR`}~mm`t~q#-xsz;w}k<50Z0G-<FMzdrl;Rae0m(%$F+TyNys;@`PXgbMhjT(E;;
zwWYC?)7i4sxh$7sEUM_MT}jd&-ld-`KC!?K+U-ez`m7!W7XneJPZ^Mw>PbGPO<Ot$
z?<4<|tX4|Vmn23qJMFh>q?`ou-**1szr~YxMK36@734TOd)a9p7Vvb1?-EfKE1n1k
zc}8{VyV<>1c*GdYO_<|TCzxiGBkmT#jO_GtSZmZE9Vyt4Ks&S9xuxSc<CGEAAT=r6
ze?SMFea6k$`SYG{*(;7GtJggcS6!;>u!a7)O#fH{G|P$BGK}{6S;Lc1{KKTL-nR_a
zESC6e^wp2#+y%BNawiy7cWBp-cNRHMWLdg>JQ{@kob*X#e!6UoKoSRtI%BF96FHLN
zm6NJt4AsldC~0U)={5G=4aayI(~@vxkH%}d*69Nm!9bheefel$BQtS+E2o0}Xo^J@
z(e~52e%gW~yXd2VU%;pE$!UDBFmG?*WfAgZb&oGwbSMdO|BXH0xu{9H2ziRRZL(Q8
zNJhCnC^5~w&3}K(9T2~ASDOH=Ykd?}Tfo~D%$t9JvfeUrIHMJIgcs2_+<I|p28eo_
zUCTpQILUr9Ydh~RL=SrFU-BI$T?^EVdo(ra^>@e?PZnEzs*rO>J3*S^%kY2=J~jn-
zR`=;PjMg;?E^;dWHH5W&roeO;lSEcs0RkT(L$74<@1tB5(D3`pQ09i1zX5nKhk&@0
zh%4QI3l2UV_LGLd8_vgGWV`x$mwFfHokGL*<i6AK=;H-0;Ohe<%#fRA>wmtG2H+k_
zUg0W22(Zd|Q@Gy=ARqiaU*u;WqCOZ?6H_v(cZ?d9DU%{OtgPHp5NbH$ZwR&X=zPrH
zwym^$OFy2B#uF_jPKxyOUu%p<K4s|D4Ol%gYq_QHw1zV)j$052faG6Ws1a4;_g6~#
zYfuVDuImW+V}KOr4hv~_m%PFpksY$=XhA~G&%|tMUi5qps-n{93wk?rK+Dt16s`L_
zs>&e%CyL@-T{1Xg&%=&}u0py)4lU8<4~m&rl!$>s`JGh8dp7#$EoqS3;lP*CLIB%6
zk6g3-dqQIfSPE|dBXBcJJ|#HTktcPyHe>kAy1_9~n3Lll0ish#60E=CVlxoR&(7FV
zunPfzQZB`Z2<*uRR(iV(Kkr+f`qEm_58UXDKM;MrJ`>{V=>*(ZyC`7jJf(iO96b=P
z2_SVbbI+XD4N>SAy<=BB@A~++QBC8I^|zw;xmZlYVCNI1Stde;S0hvuW%C|4JA3rG
zdBRu^k*NR)y{GNDc)_(~1R&)JcYlQ;{r`G706!e434nNOoT7B&^-{}CeQgf)kM_|{
z)Oyd&{Qlh_&1^p|!@rCalO$dU4}HAOsr6s6#d~pd20$)zTWsn5q6jp)>+uNTlVIoU
zV+2jC?kQ!qh7Sy^Hr8MJ7Eht^;hB4XToj(Nsm$c!%EibW>Lt!FR#Aq@3d`~)DkvH-
ztU91C5DvQ{^@wUo5l&ea=*l5V0#x1!Eq&uG6aZPV#9lX3j4B{5BmEw#Pz3AS-cQ$0
zjw{=17jI@LjDZ9aFp>_?V}P!QRj4=p{bFmdXW)mEM32A07aml!f8On^*a0UAv-dix
zDqNPv!=)Z-Hv3Ex)*{vf<OI#dcMQk}l56;Vv15HH9Xq|=fu?Y~i#Kk_V5}H)_$rFC
zR?kvsTeHro8D&x|0T@JA!@5}j7ta`01diXqH&4J_3VYo}&H-)MSC=Q^B<v5lqjq>f
zr}~xlW6Lv8GJL}<`k{1E3tPrKM;a;T^!>dP-s0M`hW>BwLm^zziN9&dOA0&Pe7zFs
z<Z2vt3f{B4wj|?VA)B^JjCr>4F<<Fb9~`cpH`>wwC!yxO$9+ksVIP>VF&NnE0dVXh
z5|sNC+yI#hqO_{B)J%rCtdYnRy4sR$P0p0fbj`fg6{8z?L;BWDVEb7&<BwPJ%RHh6
z9A{hCMB!86WzD6?ll5M2t_rT&G1~%FY*`f!<L&AkiT<V}U?w<Nq>$qJzPF3h$`Jds
zw6~+x%gmQs>2Kg&ABk6;kj8io?)}>0m>{zPrr$2Vq9~vKD$Ua{@?RrcK5)q9ihh$s
za(pt)^z8AR<wH3UKcKn;i2*`DkONq=ERbSBR5omOu9)m(F+#Hwj0ajt#05tZ)-rTw
zEzL@Lfp}QcCTgW)eyR^e1I^zX{9KcK+SuceNZRN~b9qvQP%Sm0UU3ZRyH1~?VX0f1
z$5@}*2BhWJ{J>50zz6G<zXu4!w!yoD3nbTTA{ih*E*>3-8}l}?j+654i1@V`(YX7A
z*|VWsdkpV!oVz3_g)*|o|NghwOY5`T{vbV&Pu0^RW^_uCe866%b`IF+-(lH+0&C@a
zCl(R1a&ecw6;U0ha|+1$e(SX?B0`c~sw^x6b1&!|Y1ScSr)NP#$rWbF!kp2i>Ub9(
z2Pr$@&w<OEO(=0jxzXBi<zT<Uw<oauf_>35$+|z%8~#il-9C}r98U@Xk6kh7iknIu
zvLr>@-ugEOC6GuN7HUm69qRylZ}g5=%ZR3!D}8(e9bu1$l8-~_h4&2ywn)lI#KJVX
z(12WeN~4cSeznF56J(x@X(`3-{suI)EJ|e`ickGJz_I+_Cl<x_jAu$d!*zoH5^j9F
z-8d5qvDmCEuzU_{1>;e#OS`yzF4e)8S*g+RtWJPn1j!9)71{)`=Dpf{Nr(84WuJqc
zvC9HtfIa^6=4-t}^?7UdX<>5Sl6D@uNx8anp%IgA^x_x4o0Y&rR}?L|`T9W$<=x+E
z?U5xcEl=AlxUhPI^>ob~`GQ1xP$03)v9@A7f6{MUc}aC3q4bv`BK`zmgbt$&)H(0m
zG6kr(4K9U*7vFP@u6W<Li?t_^grO&6vVc(Pe*G*E+4-$k<M23H{e<<vBbR=P10uo;
z&h$%a^=|mKO$&O%CsIH7wB_WN8kWi|bz_sJS;bx3_=ocHsX4`?K@(`8|7`SF=>Kv=
zW${xPWZY*rz_fuY2j58NRTvy%PWDGT{is4Iw0XW)3>hHSf9jKMsERGY{S#B>)?~to
z8(p@L6-KY1CE>>CcqvEu_z){0ABg|j)0H*3@%&s73))0DImP3-<4PLNYdpK4^DY(@
zr!P0uR(lq4see4}jy*huY|aOA9HSTL!P_6+En57@0RlDGD^Hb9F0KV5VZ$-4fwp-U
z3M8`&H*?M7N8>O_0NESWkj0oUZvkEw5SH^h+U&M)IP0}JIex+W$y!vq>IC{kZ02=^
ztfdL7Xpz+Qp#r7={=4jKpg1W^Oqfa6hlyY1R9VdDaLx{Z3uZV$no?<{OAVSfYHN{g
z>0WI#D6n6CWy<V3G&|drSg2_?<o?Lf9p8=w+xDP>d=!){p(wa0uy=xw2@Wp<l`D+i
zCc*;n)ukjF^9~65-Hnh5=)kpzUBl;#fpMkkW~A0U=Y&f7z4aYxl%6*APueKV5R0*k
z^_{-gZind20Yq<r5NJmNM6#HYE<WXp2;EWOZ|F`0Z*2PU1McyICwho#&wmkk%=5ph
z3n*B^C)wT*^kN%bt*qTh(Z{Ea{ZOU^IDlL@YjfTHZAKqiafMk{HQseF?RBUl()0yE
ziO<d-f%yYdn#d~RtQ=H8=eF^D#Lp56G0W*1)1>b?BcV@Et|9r?x0?#h#oyaoFW3Qk
zM0cPexdm^zNCS7hBEP-@zql|1*nnf@B8v-!ut|b&<4T}3*36~Qs14~x{z5&aRTNxT
zwh7kY(C!xy7@?+u7Q=hbWD51nvc<kpP)SHp!nb?7%iN_&2}6}{s_?$pkynub1785a
z1M1=wn|Doo6Eb*67bWWJ^^YloUKl-Am5><Vur+%5hXK+eu2Ix)-w}4p<TZ9Q+xEc@
z<srdm+~`^`HcqfZj|zV8N&HF-bMIsH68-#&rw@c0ccR^s-;0$%3&w&L3BRL3Ne+!s
zI*J{Gd^O8_I*WH80|K5mgoH#j%KADD$dplo3g7^t`)8xLuY-3y&=nFJ;Vo79C?-3}
zdb|?#@qlNELFPh+=@5}v3b#%Ow&l;{{Gy88XlS#HmHF+;crQ=2cZBj9#2v}7C8ln$
z+!mG|>&Tb%8@kL=?z7_c`Ay(s0?#OFR-%mzeb}7fqGGw6h}2HaBTqbVOwTUrs5xtf
z+@!*o1sNTsn**wGKHaY7&KGzP^EWw|Tm^YZ%|}dQDe!@|h{(&LH6e5=b&BWaq-iRc
z#m-|FgrTeIz&?C|Y4Ntg=Sy(sc4}fxFrGIYLkosR$A@l48yW|H^;U6+O~!sX#TGqD
zda^Xp02}lT@M|ivLQcZb&CE#4>PwWJ(lpp_zcz+Jp37K_Ul5|35q`U@+E1~68N@s!
zR}&4NE|x07co(Xq-!}$?EX6-5Wy%hz@EI>k503mK%cNF^m>B(wfH7H)GBS<H2b}D4
zpB!@M7VP`@J+)B)n$r*vW@xJWfhdA%l@}kJbq~k*xw%J4J&s$BP*Sb4SJQ0U<x39g
zxjU^LoB_xl@bT}Z9$Ta=JrE-Y6R5BX4<eY*yxR{ee&V!(bv@M5f&#lJLiJg}V&+B{
zS3yt$PF^Kn?sk5Q_O|f+mFm0Rs^C?V+xJWR4-eGef`eKv<9Y4l*FoOs$09uLanMNy
z%FO>xE4lMZ0f@MYCVai|hmXXG!xdTpJ}_=c)dStruCb6<d0(v?-aqCC4()GST_4=Y
z-k+0bX#Wxw_cIu(?R#JKGrJDdF76q&CFvHQus5ui)psIeX}UmoAjge$9aEz3=zjD-
zYd<w|tl*H`ijY#iypqM~DZfMPUTS)u0`XN;9q<FsB5$QcEL3-iYw7r77+4s~%hx;p
z=4e?)B@fJDe`h#%DNLHSTXW+(HfZ%EiE6#lX=gs{rra1)WjVP0_?WialeWqDRA1>7
zT%y#a(+JICeA~;n(#5y3c>1V|3ayz+^B&6B+Rxbf7Q(CS()6_X@iw=Q0(WcJY=?VY
zWTj7F#6drR&qVnGyr1%sbeku3($g=m6)Ki%zco8x6<|5+B~%84HhBME>{Jo~5<q|Z
zX>jr_=#_OsoYuDu5i#IOdq{{vOFy6y?#FRmSm8=FF3FjI<cXNfUN)pr_&q)B?=<%%
zm1E?KN<J7xU;rLsd21jnPqUia)juFN&I4I>Iw3Ps3ir$)<xF-}Q+b8f&&P|6y)ZQ{
zfGwMDV{j^9I?0%&mbcd+4j4{<?zmX9!u!U{@&A+eoF%x5umqUg3~#<2OKO!ehjxc*
zg*Kziog>o#t}3a#cp9f2#60`9s)HZ&Dy<xOZ5*oA3N7C(!jnIt-Pk@_PEIQ?lIp+f
z(GBm{eJ&H^KprWPBM$Dg5$&IcLKltZJ{B!O1DXbbwx`>W(6Q-B%`Q&~^6}3HLVzgJ
zp->7S-R1mv?e%A2m#oa(8W=)O=I6kgU#L4cGpN;=;d!kS`+n_hyJrbe?oaEsm36BY
zX;+enLZV<^7DdjKqK|)e63P=0pv`)ow%m7&jt#T{j|*%PhxSKBS#S%t5T1C?gLR7k
zB2!JW9sfF|q+Mc`B=5xskUBRZ`g}S(SG@Ct9G{j2Jun!QmzRetpLFqEgfAibKh8v`
z?emrlne6?kfrA{rF!X3t!Y^yU*$YnG{pIh$z?_WAZHyAItgHf{akatnZb6Y8qgc)=
zA^mdC>od=4SHNNoz#BhWGHxeT;8nHb1bn{F9|2t#u;qC|FBg}u`&95z@R5E#F;WkM
zI*y!9_6y9)`i&OF@Xdc=hS3oo-9cBc|74mH>7dy*E>{$CQs_664b@`@jRMG}iM=3R
z_1u&Q#ocCbUPFiZ=4zA*B<qGKZ0kU{nHj<1uh{(#PwtLu>Xn%s>5_j@g)Kckk>`BG
z#@m4f5WXZ<kw32T>va+REh=U@x@1^8Yw((GDBe!iTThOE#pKsG@0uQOLu+T(rx=<*
zuN1&zCg5f_SjzAkGj&hli3aj6A03;53hY{4hBg71++%u@Lv3h^!j=|Nxl6=}*-}Q>
zBi{0(s$mcC@@asXr$U-B&*k&GigU4F?&Rm)xudVM@Boo3*7}r4?e1+Kg0PSJ_5_s7
zXe#xFD4$$_Zjfw-R`CAls$0YgxSWp4t4D>YW)zHEF{7Nsepw|jYr9wmm)acs4!Y;t
zp`vD&uGsjiNkCk8Vbs7`{3#+}J$v$q$SM`3{=0*ewh9wx#8HM66CmOKi|j!z<A7+H
z3*GR!7a0%%bN3H8J>d}E+6Stvotw|2@lg{l*Kb7qIAG_);?;CAso5nnJ85|AD2xM+
zAKk&Ntv|Z}Hz~u0oE&ffI&Na}H^;m(|2K{^CKzRFBP+c2@Xqj?-er>c$ZGZD`M0ln
zhksUf%y_YLV;#P%^lP1R00D%s3fFWS^8RRGVrOBcgMcfnaQ<lW$j7tIdWXCzr|sLj
zvVHR2oDhWU7gfNNorZZ<mj$3VOD4pn`ObowN@&yTc&~ULZuJ$=Nohd9Z~)BQD%8}&
zUraKA2FUAe&c9iHu!z@f=uppyhxR5&H7nPyyVy4mon+!GuybqJMQvk)P|`|IrU#3N
z)FY51#!IkfAZ&3lgZgy2C2vv{4@_@~C!YM9?e?;Er<RKLklfVE8fn1IT}$1&4vIAs
z=4+Oo;X#XI_MkQ<Vz*kr21Z^igs>rA<O4gXEUG%Kti`pmPhCnNgMj?(O4NTxY#5Vw
z&RhxaY)1^&`Zd<ewISCOZTB<E@TFoK^_{+tyV^GUW9fHI#cWhe{?Nq=-VuX_`JFza
z*8AihnQH#u`!B1Pw&zAZ0iT&)y&5jm9atqrP1l`qRtquUih+`&X#FZv{r0{VXWD3D
z9YGUX@uNkJ=nT$}Q|Cv_`M*{F7p|5*E=&wx=}i<1pBmUBHX$0rGP3{umV{h?i7}GF
z?@iJ;)?2(j{M_%Fc#5%e-U4)5D)|4Qm;6i|ZRgiS2X;F!O9G{kL&%accRmNy{{7oU
zy|1<P;{{9mxb9IVQXhfL?Vm-l-qy24jA%ex*sBy2GB`5Us5W34O&Y`~!=3#n`lor|
zyly5@0S?t1e~zNRlT~cscg$PDs8^~1wqDWsQ~@uXJljDgZ{59P-D#$7qmomRon^H+
zG#(yySBDJDlin_+qXN?1?8TK%^^xy$s@WFRqN!p=sU4E6WJ*JI*?s}q^$a*BuL<77
zuD4!keDoV&ykWwo<%e%W*ai^tTi$VTcZ@R-%*Tix<xzf?zTt&XnLHZ{V}y93Ny@X8
zQhEJbp23>T!8b50sHWtrD;aKdn_Dg*FmL4KaB%y15Kivhy=GIO_S?I4JHEm(ncsuW
zw^hBuoY<F>xn|dC&9-w&Kp~f7MzYJ7zC_Pm+-O;EU8!9n=TfUWzx$u{4vZ5w&FL{j
zdXfxj=W!%K1bqArsucUr5ZEE_Y+2ocJ73}$W3=)VPHP&KLeO=^je+mBAXibJXTf_A
z^mdt_zigwSgbd;MI%8X4AKAKrU?GWlG{7DLS=*amc=>dd7E53jf7l0saNjN=kNby7
z$Z9d)|DxPhP2p(74)_s}3o28a9&)J{84O>soZfe)H<hKeL6HQ{HOepT9}n|aui6au
zI!+=9zh!9M-L!m74axpHJF0QEw+m{22;;w>@s#@8PvUr*lHlY(I4xE+n&0jk=EB=O
z%)*lY_bYC^RoUo2kI`WL$Y+DQ%_BBlL&N!2=`iV5>9UOxUubi;@V&E0#Sp1yab`cl
z-1h%SI_r46-?xo#raNxk&9s@0>E_EYZJJGYo9^zZ=`k_gOm|P-x~IG2x%?h~@p`#$
zd|Y`R$MHVPB=ZiBpyrGarc3Tisq6A<5c3n?Ftu_t{}f_ONRq{zFtq6Xu5D&lwcPb;
z>W54oaQV&9wB?a!<a`C%A>%fgLE2_@U?NN(=gs0!i2LIrYWqWN%B}hHc8D%;&NpX|
zTBCgbS?}?13jOqQ+?c!Q7fSwqR+ER+@rgdh@C$#t`ymWqj#Q=?P3@l(e`2G6jpTDz
zN|7GFc*KJ2G%Nc2<{dI%URu}w)wb`XPTv(Lmd5ktV<MSx<GT+m3C6kE$|Vq2K7Ba*
zVd&5~L@~WWiPXDvLw-K3JBPP3=yJ<b>Dt~KjtBL2@dnj>Y9U29yp{cP?d+OBefi1q
z!g|{$qx=JMLrCS{FK@ySGda-KHC2wAhSkC&x2wQB*3~OJPndW1*<O^j65pv`xrb$h
z3obPL7Z%nPLAA)<J<f$3Eje`AP}3q+3fYS6GVr-1`3_-#o1NM3mYX<#0}J$cgZ#yY
z#6-_{ph~j|Mzq2&jc>@<1S;)TZgMlE5klB!e<jS4A_qr7{Aoe+bK8LMw2s*LX`cwm
z`VR1wY*8pH&EX%@k^SGB+`RE+>$`OBOTC!&J%ReW6DNAhE2*@h)WSRt5I+jl@GT!4
zMp)B#5vl_T7aF@pa+w)6@4oC*);_YF^CH#>bIh2iF5LAtzW71@-?I~92r(q6Y*@&h
z@_zD|VMt0u@)VV6onKNp5#UnUzPUhLClkUx2ELsJeO067>uVmaE&JF8XU{<UltSOA
z3=YZB)cN`?6!%rXqU&yMG?1k;TFzPCn{dRr{#*(vEANx~)i)@Wt~%P`CGjaM+|Z@C
zqjPTwDM_o($fGo{R-Uo4To%~bj7BN5Yj-bfnh`w9mBAPTcHl(Ue*SBhSBF7cm)x^E
z`>u^&(DVQ&G8b5R1gakA-c~ByoPF*4ndIo@;Egnf5yFBiC}Lt?5Y{|qD95M_uQQuA
zihCPGZGQ8#u2^2ree_)_PVHk$tDrK_WQmLPP2Ya{ESTW?^E?8^pJDy6R&rTSZxz5r
zs`r*3{}|!CZc#~JFRLW9QuIAQSP4I5-`fP+%Mv@qqNo#^`Y_-yB{T|>m$3oDQ(MI^
zj;+rFgm^nl#t#Dz@AEO6!##+z<QKJfFl_bKbPIZSdd-3xTQTJF<2QFPW|MD5%b37=
zwt6^;bD@<xdv3w4_kD!SkbvGh!}`tCUrTOJ3sqHSz7J=gtLG04p>zeR!R(PIkD;~G
zcxjQ6bm_dO{uKGsP7}^(Q-66KoFIC>4`p8hF*SpgijF5R#J=1zBk#Hi-z9&b6HnM=
zi6Gub<6`Wer&B4dyZE5s@wVL6gUfTERT@(g@yF(zW>c?$ZgxS2Jp(Vd4*_K$g)xy;
zgSVPc+ELH`MMk^>&x@eiS-p1s)04E2({w>J`*s;VM~?Nwjt6n1CMDuHW=()_8HGKL
z)^{bgvyci)F(V5iACgHVA?^pVI8_U=_=yo~q!1sH31nRxr`eN@SjPg{PToRtxW(Pl
z93<IQnwdwLp3-~LswPPj#zC{I4)Lihb}>XJJv*x=IZE?{N;Gg{?^mvKgfJ16k(J{g
z%@N#cN%w?PM7l5^Lx5!1r%C%ft}O6Kp#byo;Ty$V*+2^w-8WwQN+eiBzYj3T1xA<-
zbFOkZ9~c8;t@KNn*7NH;Qg2v7Drk{Bu_^10Gvs;(Ce<9`+Ah5da@Poqws5*hzdzwR
z{fnJ0N-)LAQ;Wo0_-u9NcZJsR*<isEFA32OL2(lPPkw4Ou<QKyAMEb^Yf$P1HaIP)
z7mX-zhJw|kYT4`%JtP-1765)q+=od$XkaY9)8wT=s_=R;G81_*Tr}Ab|22_;Zfu1)
zLh(O-s;PcAu)WgM{%Y&Ufc!eR{Nu09ett{YiN{z~ioi`^ste9BOovw?!04juWH-v2
z?n22LGv1E~#Dw`cMNs+9%f~BtzYJ}gzl<~?oVuW4p`?1<<z{#nmLt5y(ohCXu|NNK
zHu<w(nbi?}xG19q$po4gYbo35(H@M5RvNUHL=6W<ev0oS(bmWUS8!s?Y!5Z8R#&dY
z{H9_AxX3_&)T?>q+%W&;<X<nc<d7787y*Z%`GH><G~BQBvL^67LqX_<grIxkU`St3
z**?i=3WFAUVc{Xs)fCE`7KTmwU*{5X_Jyil@%&8+SNltK_cO<DH8?~`HY6#l58=s6
zS<W(bK3Uv7u3bJ?NA3ibR=8^FS+2QL78WNAeCLgp^=^$Ql<#C0`yzW^aC?gu-jna^
zPyrH+x5K05ADQ_e5rly<$@6o&lm&mPoX|;q9HOrkJNQDWYdSc3|8jx!)cEGAX7NWS
zEA7Yp9@UOIq+C#pj}=3&Kzd~FL=mql^kb#1GyKniBp<T4V6iSeVYi?d#~Der;BBk(
z{)60LgaU{yx14mp?TvU-UiZn4I$MTO*oJl0f^LOKB!=>RzKoJ)vY8zhPiNdBqIA{3
z09Pb+^1Wj8rW8Sa1R`bX@%#9v&}Lni9W-K{cf6B?9T9KLIMtVbt!yscF&iuS5%f%t
zB1fAU?ZeZb8AH%QN|K=U`ZCJEnAxuhUn@r@5~_J=oAL~<Zhf*u7u9yB_Y`iTGMIq^
z$q~qLiER8a6yw7z?{9AQCWSl~8R5PjdER`9qBzPKLJb~{pXd!uR2FCm%bR64Aybq1
z;c;XCM*3F{3URF4DZI~L3FJ3=W_C3yO=~bdi*)A0s}|HIQHQkqqKh3d=~fpaQixF*
z_K1=SrD7f(FipejyLl#2vI<%xi_x^XW;_i+<UICWxSV&e$r_Y-F{dBGn`Ar)mbGk9
z2ZBuMkF8Pq`53q;-Od+LqfKAZRyBvMJxO%F7hUoX1-5NxGE@s-j{q15;`4pxiWL_i
zTQTgA(tV{>A}0kU=f%yxaYU_cW9_#IF?D=jn!$nR;fB+|?UEsHYf(IA>JS0oUK=Za
zkCqigS)=!O%@k@3*x&UNL_b~#RA%ETh|_=7iBvyhe&h2C!D?BMzO(b(&B`0An4i$c
zW1EJll{NYA&3R9{Kq0QDiVUXYgZc3TBTky2!FRz<P#}uNeM`a?wfOEezbXe>#aI#X
zuZP=pMd7lFv*iVtR`v#S+s0FctZV^?U^YdvHHqT8?($C#O#^`12WA!(`Lrurj<>C~
zAJd5Q)8OfOiyGlZk(tuxul&7l0t0(Ku$}x15>8IOm>oTE)a>uVgvE+*bPnHQE;yT7
zc{86#1Wr3c)AoChWGe<4ODfDE670{T2e`{RdaJF|aBUpk8IDOr^vBf(Oh1TkhFyqS
zsyWBDq}H9RZoQjC|IC!<H^uI%u1l`Hn^mryJ=fB<`u1vSa==Vs;ZT@qh^6hOAmL)^
z8~M}j+jmpA4(`OWmjh-j%tNcK*EW+@7X+juQ-^L`+}J4_{W4h<K8L8sZH@uc(^tlg
zHVa`C;i+Xj1Z<mp!rE(-XZ!_`BeTlnk_p(>cJ18y!zv@D!AhSPyH`bTueORwpJ);K
z$|%Ao3JBomd*raBI8+hyF)^GnKnOAGr80$|<^ONBhcX2^Wa1q0UGGnX_=n2Bw(-*}
zBqKDobGu^VDGMjI6t}*`IT4%1sl<0qox&_D1-K1}@i@xsCJKv@?n@n$PLMCF3JQTg
zMrOHa+`FXW1l4N`{0ayO&Q3F0jvOWqr-Up7?dUEa?Q}3CDdY2v^%9h8xGsN;=SvKl
zJkR|LD+EXgpN6lDdp6ybofu+xGvB*Z`#iB2W7u87)Ia3kVTylZ`JpCJD)!JIS^D7j
z70W5ECzda8{9nkgK>HX?IK&*RULpQd7XJo$g;4xygw74peZ2bJ;D}UhEJaNMPI)$6
z%1{AKZ9>UFV%Ck_T0dfkp*t)rMsks(&%a_r7{6ePeb#~BM)x;bL9wXO?PMV1<wGA;
zrwUv>F-bBjib*tr_PA9~?Ev5OFXGJZp43V*3lce6Q$bMR0m^dz{v9;ALbf9(Y;Zi&
zt-br?^ot)Tl%_TXw@V^kKg14Ie|@QTm2AX2mg>FHcOj<-&<o)PE&yK;u=4yp&@JPa
zcFLJtEHYk|jf;LTN5quNP<V_GIB{tF3j)&>E4#ks_%d%M0=p+@i-rJZu{&v-pE#@8
znA0XQcgquTwet@9k$v+^^=QF1e_f%mCI9xxVqzjph`j{#IzeLT3Z8uSQ|dk!f>5?A
z9@YyJ&b~!+D{2Aqp8kHW{L>K$0;r&+lo&HRK><{7{&KAxUlO)*NP2&$#w*4LqRP%v
z6&zOZPX@bBr}XcM2aCqQiYN(IN%z(ahPXfP`qmyVwNkP|`OS?6QD|ps&@I2clc$ik
zh>4F&W>??WvA`b;fgi-}cnw~@^SG25v)FCcyPP}-`0P@MzRop`iq-dQ^%6zftnT*y
zAx*Er4hN{2!ysW$`KyF(%Q<ES*+i(<H?ssv;`rxov41gVfTDv=Lu<if8bhIqDP_kY
zGKz)*bXoY5#|SmrtZn$Y1JESmCc3cBP_sPXU?$*K$%o$>;m?egCXo8OPwFA`OqRrs
z5R+p`Ql8ik#fvs%*BVZ6WoFh}Sw=UZxa%l%b-UgdDEO;4#ZZ9VS2g$aor70j*b>13
z*mWiTw-qVy(vmD~KD%zPxfOGbeCksISH|}hBN!SL>_?C^r$Lgj*`sP2Q3(AxOEU`|
z!Xut%A=syq??yIbpc3=p9A%-z@HH?g>J{MP!O{GI?QDW;AV(p|xjg_sDD`{v(_Hq2
zt-Foutl~*PrVNi{4MQYgUPNi693@vNGXl?6C#Q41*OLV7)L#xXZw4CcrL0qmfAve3
zWHSG$y^%Km1>ISX!hJf({N>~-bG0O_49mb}NQb{rnI1lB^6J&|iL8XEnlyceByvEc
zuqbBj$xq`@k~)1_TLt5<dEJBNUH4p!yvguQzme8i6`wilxWg$OFFI+R))p_*Y#QXc
zn)~A(*bE0Z>3$uqbfcy4WjssrcQ6kfVKAi9k8frAn^66cD#1X^mr<P}hoz**uKew4
z*IWxPBp}2_6TR^U_jf*|#mfO(1Z3}{C?bP%SG4oQL8gq!mZT^aK$|3Mi&o~hZJ8pC
zgj*|zpD%W@$LHfOP(Bk70jA0JoD;4!Mteox6txK{Aa2;Teq)!D5Sc}}8R)B4h{5Ia
zuIa5TjuRa?T<#;3<QV$O;&VMFY-ZDFKkEc4@8^?YNKT5&pKiRk=Y80hDvZAp&>0!E
zPD5wdRHkTdBclujv-@W7)5fC4?5emr1(;BDt;?s7TrgxU@5n^7vo@rM91&r0p*f$m
z)ef2AraEKeWf+@8sTzizzc(1lh%BVXf_1~oG?J&U@HS1HKKo|GWrqEB;V(xy*Z#x5
zPUlX~hGL_Fn~q6l-%73_TfNplnsj5DbkaQz@!0l^wkWE8$|A@h=~DJ1hB%l@Fh!Hm
ziSaf@_?%Y1Sc&~S6|RQ@(fvAP_N2w`Cb9Ec3~zgeLm@M-@7VS6?&4&y9~M`j%U1sp
zkqtc|eoAjQ=rx#Px?f6ZTaTGTst(!X1`^&Wa8aIagz96CqrAauQuHwVop;j~R{W2I
zNzKjK#D8i_1zg#(_(WB{U=PXN(aJFn>{#c%q(#g1wO&(XyN)B!jzt@<-(%I=lx^_R
zB^ONX-$IblljNd<g3$aa);mKSt*o37W-FC@b5d&++8oXhNA$B@RyL}o3thcFqt=fV
zT?-I}kuHeP<gO`I2*u3O0$QHb|K=5dUU88;9feiIy^ALk?>jdhHu(j(h6RLx`$75s
ztwyqKWM+YtS@5|sZ^7Evro_JoR0buPn@MM=c`oRBG?qr-K&UK&{&OCVIql)1jn~8f
zgQQv+3AIKRbt6_MFVTfwO=_row;bAHT+F%If2Z`e28IR8bm6!kYu8tmEj3whf1tk=
ziM)Ago^1p{J&jrDc5bCYz&q(aLia$<!6HJ@_#d7YEyH_KJFFc$naVb62$UkvN#_;|
z%iU=pl~quS*M1p7Zg;zle7H;|=Nj~i7Be8;@HMXo8f>?lrU#tj+>Hv3Uob>tl2~QH
zFLaJB(t}q6O>quZ3Lle!%Apsv&c{`mRNTzI21{cp`^ONfmUnzAqT)j7^$N9`w}KW;
zX!^|r{F2>kCI;gnhxKF#wz%2pI=?;UXUm?P00%Z1N``IH!CTaV7V)ATG`K2?PzzU~
zmxZ9zCh~NKDdf6kF@(~X7?h80dnz(_4pFKXbroQ66a9IkZ!<+2{{%5bJS@~3<Y^3i
zWLbi$=OzO47jQ~F9bOA>cMYL{+;n}TFA85esBP{T2n}{y7%FenC}zrWbO9hoGO(kb
zjnX@IU9W4Nf}l$2U+BYLy@9z$X}4OL+scL?xx~et@bi@?`HN1%gTHst3gxkkPJ*3n
z@p1WnPEVHwom^zl@Y-P$E|~v^(-)riQ61di3cpI$_z|y*h9W#_J+HE{f+!sAqR;P<
z%QR<&Q8MD9#CDwnW%s&?pnQw@hsPA*J}8sp!%<X(?$?=r!PoA;19P{o{{_9?_jaAz
z`R_GAy%eW{XyTy?J0Mlsmuha=W_o9K-JX4n^D04-?HN3|Jr%!E>27bk;y`;|&aq7w
zqMlu3WoZ|&a7_s0q4E9(z&zb=>4+L2Jfu#_O*9%jT%)c00g2f32{p<{53xPBXoY4a
z%5F{=QWG_?ja0tp7v?tugCr}N&2>e$ka2Xu76y~NWAuB*-Zvpe5T+IenkMO(?s!v2
z27~n#-+wG;g+UOQb0l7Ca@^TVEqxmfZVic9T6{KE&iCru@3Q&0oV<`J*-_CL;cB%V
ztSL;f)pFI&Vkfz9Le?!<vJpd(g>Oy#qN0v)aAsgX%gAyVCsZpaJU*%8zkuQ7|2NNo
zh8i@Qw%&bGoBI!y`9#*OXFKfU6wSx9v%1^rCP|I<rEBKAbQ7lp`y#hlCmj_z4(?Q`
zS7P{GV+#5>p`>y$<oGC{%ic)Y#J^iEs10^5b`Nh|nCV_vfXtw1TGa=-T9`kF*u$G<
zJiQoV3$4Q0`Ucw@Un6dwu6+CpbL=g06*#URmM(0L1d@y23C9;rogZOCY*_#j8=i@n
zloMdUc6Xadgx^OYK;I!6gMOYEQ~;c9=U6!k)NsH@%Vp^0y6A8c5Sf@Q2*AGequ>eU
z#exq{m2uas3S_Njz|E0IP$a0gEtFyHOmH_29JjAgq1t+btn-VG%D6=c72LYynWkc9
zD1#Bn_4vP0sSTiI6{yPu4iM<g$;zO-2Kky!vMUX>>s@(|ibGpMeyzTI)#35$E?{hC
z3L*~%v@FRf8epsM^46KMSuwHIm+1@Ww!x+M-ERU0{A(w}OjsOC$T>P2Y4&G;F4^)h
zXDDHW1GTh^yVrnnGkFc{KT5jI-wC+M5JXAnd89=NK!BjCVPU;B;(VBmr;g7z=-U^L
zp<%bM0c}4q7u$9=#e})!j`=)eCr>gENAE?kp+~6r3$5`atH{!)M5IR5Bd%kfTeLys
z*oES6AYdJ4NdsX5%-KcVpSJgCh!iQ6z@-H2*}|&6z4w(`3;Ds%jT?_0LtV$2k1PS7
z<m|s%1{Bm@u_v`I9pdzHBwK=XLhmZP<@wy(Bi=fjCUJlE+~XhsIRLZV;dcA2A;emz
zEYjM+BDaODc#%;VUlozL*uITF7(WP9*v3)3fi!Qu(!3ML8Jh4Pa!QD!K2p2}ndH>A
zMNTKUT8(P-g4#*fbv6xno!-uW<^B742@iIb$pGtlyrvMa>ADglb~jO-biq{c*`(&1
z;TIFf0q4A9+F7l}hlJ*6F9HQcdfU!l)Hng`KX8e%n#-8odAP;hJTP_{62(5tME%o^
zOX$JUCnE&lg*O;_U%I~fnZq%{Hf8bRIO|olEqBzRy`4VXnHk|0Op6S{MAbV;Ka}Mj
z@^<9&bQ5M~p_3g~R``zuu_rmPI6N-?EHU;8$cRTBqlBUNjSqd#X`Ve8Q~<;!a(6<v
z;(7g66_K+}mgCsY$|JB+E=zUU&@2C&>E7JT;VOzq<Zh$zQr1{hkaO}3^o4<AGX|wo
zc(vOE2GvQm0l#$FofkjkHNb)xxNpD$0KlG<In?u5FJou0?7apLe+D0a@4q}_fCc*<
znIEIOf&uLQ)e&d_NdX4p3livWx{#pAhXiaW7ccia|D6!sG`-gS^B~N~1>4^`(|J@%
zs^8-vBO6^3rr%P(*|1A%WanFu7ae)~7bK+)`WRE3Fa}~@bV??Bip<q5wzvmk?Vxct
z&&hBl#tkPRUd0|<$}Tuf@V_TPNdH(o5-|&{5McoJ-?qD6q^G59-_CVBb6paqr<=YM
zx8rq^V}tJ-2bJ~!`B2g`d{SJG9|&uxP_zR`X&(AOz)CB}1$$5H#fJ?5r108DF}HBK
zlVNn<+0gQ5$Kp*mZW#4F9eau$n4p?6rq$;Yl4Z=!Q5{Al3P1q_5MY$3Pv&t0U?cEZ
znGJdEmMd-0A1<yJea7qd(il=b`X<RKJ-ByP*fT!TxN2edY;6nf`ytKRG6vPdpRM*=
z@^)noTgN@SC_s+_*%lC*9(P95lUopqQJUR2J3t1cMo`jFYKD>{H+7A1I_vYjAE<a<
zH|OJ0S?2g)-u~ZPd&3~ZjL3~q_`^4GeBtY5e%trqJJNuj;eMUK_w=yzRVIx@M_NwH
zjBXJ8#{h<{_t!w>G}n6tJ@Gga9jIQ6&Dch7C%@y6;)|miOg30(kA(OvkaSPZ4fvGH
z&K`iM4sdHbjvFDMj0kD>J~S5AHQ3}S*QW?QV*4Y=Tv+%ndEm5uv}N>bUP6m5DKRpe
zG7i0*I{KD8xUpSp;NKkXlZ)U+cRorXidJUKUws$DlAI_PLd-TpEj|r86<07r$zX^+
zQ5JdPNJ;<dcFo}H0|6Zm6xzB)+_q3MDxx{|Xr^DoO;OougS=+5{NBY>|6ixH3GJ+?
zC^9)lpS_~7y#40vXV((Mxx+=*1GlJuX>WVIJC{IkRG;L<&t!^^e)kWmG~~PB;mDB0
zb+^(&5w!u`$^}|iv}x=Zjq(ScCE3^uSzs=<0Mw$qrAt6i2~??3R7g}k8603#A|or%
z9$nW|7A8FX(a%q39{sn$&fPD`BfU22DEY9&?*4_5FmdD#mbZ`n^I_t$$erv|h{i<L
zDH?sIwG#ys4yO;8j5K|P(!9d&#2Al%tJ)qjFo;p@43Nt0;27FY)iNAmA37O+tQ*ad
zM`2V5-#(=&4H6A2RHgVcj=UKu4&AObA!Ouc69fTSs`}6{sHD^3D6Dzyy!^?8$1DKA
zyo?M_{2lC^uMy&`;R(XYz)k?5oJ`ffOb(%=UF_ju>jWzpr(L1!k^hBS!z}B^iBUL5
zo%i)sqGoCojqOQQiJ)rWi^yaEA!q}R5<Hg5kq*iBAIAt6y4e7GW1S~nL2h-gmloU$
zD(&ez81~z91k_uL>=26zM9Tlgz{6~Pj%ZXM@0x2m9+KNaIzB8mH3AcXhwjMSCJ7EB
zttzshNcXw;43Xa6h>fZZ+4AVbUuW4~?%PT8=+nVsSrE}E%n|u}z340iC=+D96i>k_
z5)dZvB*Se4_&0cEEnDnN{a!$z(X+s*gt6Q{8WqG}kP%QW&!zZ7mgTk{viqIejm6$U
z1DSA?l-zff8&id(y11-2;5ULuB!HOwW(n}>6`Qpo*TDso03b>za+miet*!y+0@lz8
zsv^72>AmrQx)Y=PAEOx=?+N49{Ab7Psn?3L?xrS@;fJ4P21Z;0bPnmxm*}2^LnE4E
z6PeS)tg@<;I0_x%^vN?#ICcK~%^H1_M-D5dwW;?{Qw!7mQeOFY|M$@q+1%+<4R#R6
zY&kPd(CLY6?QziXN{Qpy@QvPRO%W+2>~~DH1Js?8_dZYkmgTil?!MMx&h<mVJHlr?
z<}zVrgc)U#07SlBFvts<CCC*DInB#c{?tZiDvTm_IjZk3f@h=!Me;EyL(lIT_lj%M
zYmX5wXQ#&wsN(@{ff&_vA4W=8qWp}Y&~A3?R86?dCHz{-=tozKB#@LnangSc2)%;#
zE^;ksd2W62OCh3DG==4-z~tWI<lryY;a)EOrYd?MEpG#O-@(}c5CpJo85PkxL(>6e
zi}h$(^I0h$GFLbXELUFVWgp#q`aw<=L$FR_9Qr7xfWu8aYJQSOC%RZ@l_`m{edx|J
z)KrU|tl{x(Y_ZE}ec2ewG;I{DYZm^GJozV&$AzwMx?|V5I3NxPzy}>juo}k=X<ldB
z;g4pgu8vCt0qd4-6C(h`{k*w4v~Es^y*zLhOqZeT=cNmwXL>0pcWzpo#@+2GPRm8c
zKs1+jf9%I^UCxZRA`G~s{|_?e^<xWJl&Tl^-NVDDG1~I+`-{jH{LHK|S6{a<mod=d
z<U-K*KWq}3;<Es<XcfrHR_x-S)X)~d=5jvxLgj3-028+o6;*FtlddqWMT6CZ*WE4A
zv9FKZV(D104&G3q`Vd|3M~r`=EXmL+AS`ZO#Bs<0L0n3nV!WVxZjB^I-a57A_J<55
z;7TSgM7K_J-JYy{NZ(kHt&!_(_ATg0KjhFai3Z(hI*V14$eBmZ0(!K7n}wUqkOX7!
z_L?pajcntaOv_p{Na-*Ee`2_SphGgCq2u2FTdB{FZQ<wd04n)_mETIUdz|Yh{N0=7
z-;pjKBUkoaWS^AkMhb`Y@dw^COD~WG7zb1iwV{Xo{uOq3Z%QDg`(WXt!yvyJG(0xV
zm{gr1crGI@hVO8_k{!Ey_W5oui8+1!4=wMkB{ow-L!}tc36lE5hn1z@L`El>rcMb}
zhbPm;c`d4$s{j$6fZ(GuBMt*-a<x7&mp-=8GgL+43;P`(ivVmZ@j+73LeL5El}mGU
zyedV3RL<{b>%d`eFWw|C*L2@ku$9PR>*!0XoIW*5y}Z$4=Jz};jmsQ{i()?vzsUY7
zDSC8Ej6V~6(bO3k1vvS%^XHGwkLVrUL{(uL$SqXah4i<9mFxv@qR-Ev)R^i{$qEzr
z&DMJjwIbvD=JS2C?YriNj;Nqklu(^w2q#GC+$P!j27}vPVV_)0Q<#qBGnR}Kb6F%K
z3Pw`hL;eI;7z-L;47H8wRFJG0JS;=OW(&sQb@uHm5QHAme2KUv6Q4UTH}m#ow>l;j
z)XvlihhlVIXvT?e;QCxKnFBu;phn*HZ*_@%E0^_I`^9!TGbGLH{IfUY6W-0{9`=%e
z#C)sjFf>D$vlm}qsI!>*y%H%|mrr+kVjKR+QIVt5l7!6Sfk4yzxx>vd0?AP!@%SM^
z4gX{Q*xw%^35ot*y*@t>D8&##d>e3?@LAcg11TrOdG%a7xwr~@<yu@kzK><3ZBI{q
z+^oi6^AKSH>sYDbSxo!wCl>{;>A*kZTy)i*D5ML6V`RcTpNgW->c`sJ@+efQtX|l4
z=q>SECkDRf6__QdnQi)vs}?!_KCdt)oQeTe`^+&!`K1vNXk=R2q$ga?=J;#MWaO}F
z?&}m948I?co4bD+z6xS||JEhA#gZd#;9UY>>TJ3d@GEuHAW+3T{%yi`r8ZA}+4wWr
zKpLObrWCx`vAVWn#3i9{#eC#&U7AuKveqLT_6ulrg~oDd(mcPpG9wMyw>KG5xj!~i
zsSo8CnY)?N%u8WJ<n04+`a}K7-TO{GbPX5=9rS2>Xssy$QAL|Qtm14xs?WI}c@=Mc
z$DGN(oW3`9pc?&r(U{#CA?AN`wEsc0Dyqa~`zY-?OhrI`peD`ZaHzCVZ{|)2pb`yh
zSGLT)2GsgY^3)LD+}KNqAgjEcFR~t?Fi!<~=|5e+lFTi)%E5t2#EmqPJS9A7o^h83
z`00XP5wFXLfbR1{+A)XKT)|L@<95d@#izZ~l=zTW0xh;*h>{E6tqVSgHx&8FI9p!%
z%H-d55B9}MqL#^x3Wh9BiVH_VZzhm^5^2-~?hGMe36)1rNZ<Savv2dyQJ?6k-s)A9
zbtiMHD~AV%ATr{-B$8I2KfoFkpQYzbUVn@uCEG7X&?Cz$kspi{nm*gEiWms#61D-p
zO$E|E?twY@K65EP=Z4<2y!Rzri;jAGEdzz0wOLFn6*56-q@Q0_*0_0R?UvG;jUZ99
z#1IK+1By5@jFpO{Q-23EWwlQLG8fSP0G3XxPl8dB+t`qZ$dKSz=Q!VRfCIa`+I<0&
zig7cGfF;*5K1Eqcm6Z!1&L)noPP-6oF$1wN#6EFnnk@WKlbPlEUy67OB+u8o42Er4
zT}!oP1~a<yg+3I-8a6JI@$Y+yU}fZ5$QPe{_67DwV|q&A+sK}^Fl6b%w;B8y2RL=N
zc3WMp(I1Ox7JImzN6E;=89`T<p?zyzHpccVgo2)QZzSBe_O7xVh}IL}5A>SJ)gE?u
zy5TjCj<h!^k#o@;eLRt{U(Y&1i&nW0Qmxm62sj^Oi>-QiV!Xnn`nU5BJ-Q4C|84l=
z`v@S>#m-P1vyo5ZvC9B;uu@#42huHv6R>5PkVaVbZUQUKPIQdpolKNNM+aBd$jZJ3
zHcxbK@#GTYS&TnHqMF9Hf8Ka-PK<o&WJ|NAN4PI8NuZ*b4&|84M_xOos&cNIXdPdJ
zUf}it-;`Eyy2D<vnXZR(7D&xI^b_M5r;z}(EYLuJCJ0{mMY-JdyJ~o9s{WjDPJ4fY
zkkZ6ldTgnztj2c}w1n|6j{JNuX>`!l1>}dWHLsg)0P9-PZNge~f(S9ZF3V~bBtZ8}
z0ImS^#sI&96(8X1M@q}U%>+tJ(VD-lUAyBBz<X>^Hvi9o3A4coNh~vznNKK$QBiJ-
zxyfGVzl+vb{n@TM^258q3AAX);C1%NH%zh5Ux*3|<K8RCC3m^48p;fOhvt0|03jc+
zJn*2#AG0dKSmwWypBez&I;d~U!9rmige;9>TH-=ye|PARl_<vU{K|jrkzj0_aBQ3W
zen;3QF&uFnEw>>?^))7SP}B$WDe6p2>|es7i?0fPUk(_0nL@5HRhK!uK}({I&H468
z1zA}>OnssEJwx<#x5f2J9PN{zZHha3h?%TvJOLaFNN-K$%0(%>B;5B2NCe>svQ_qe
zs=@#>hz*7X$9s+S8(?4qj_5I9pG<VU$$p;P`N`7+c-|*nC_JeKHV)1%NdVTgPX|Md
zh^iMqM%(%iT~RHSh{^uWE((C+J~Eos!C3>&PC<rvL2AK-O9)aYV?DsfN*9$p9Q!;H
zFKRD*2DynB6CW_Hr$@-%ofM|lYb9qB(xj)L5SA1$Ppc+xOi?RDC0&^+Y*4%RN}qXM
z6^PgHdoMrT;PGtFHUh~1jB5Pi;?Y$Ij6LPo1ZM?6RRZ;60A4$}yA=nq9l#@j(z@Rt
z+>P+dws(!SIT4JZxZQ8)ykvIl+~blixksYqtEcG0u|>I4I4W5J0RPXatQ%B<c;GiO
z2pGvUF$#+a8DX=9d_!N{i6{m_FX`(Sq7<M$0zkfYUYAE+1QcTzburlxf+ZaW?Pccz
zl$<IjI;n8Aa6*u~Z1MOKUiqR@PD|sNf6QV#3zl5|&6~(3q_)ynWNo`AO_p85c4nY=
z+xO6F>>I)s<Mq!kB?qZvLM$jR2-%k7eEjjo1<HNze&AhkDm>df>+ZQhN`tLOS8rol
z-96Nk;+FS7^llXOcKzy1BZvx_dYx1^XpB>9iQ*SMx{BM$#a5BEuTP~)_gfkNo4_bl
z%F2a*P491KjHVF^Vmrlf_yXDOBgHMKLdwPjmvf5p^HKjlM$tUiLXeCN@K~kV6#JTy
zQJX*((---3-X*Fjvu+cLU>X$5TaiyUVLCZxJteCC)})`0?t5Lkw|PD$I6}vcX+|d2
zr3h?RbJxm6%dM>r+LHy2T;kEdtPZ;&O$jQ2?D;_hY=AY9<eQLOk_JKNsD~f628_qC
zW6P|yi%l#=eew^F29J~D)(CcPRsK0c`1%%ei%RLEL0>o`EG+;V5?FMLK<qiUo0h2O
z4So)&+p5yB>Od7d{^2@sYwb)7%G&x`!xTV($*6zfg*w-TBdcXqv_pF@VJD#0@i*Zc
zrsH@Qn{j%ihQnO44~2JWT{I51imoO+;EAP{BmsnLI27X~0Fx~=*v8ZtbH+pm9snRm
zIf~WK=91ft$vdPC^Ak77A3P0cL)Sx)huk$$_3|{9niDp!D&Nm%gQ5(mGHp;xwov>y
zrd8TftY6=@ciyj5Cl0JJvBnvi1hZk<C_2*kV8Kmft7mi6d+m1a9k=IpF~X+=ctLq+
zPmDJ><?8!HVO7gbm%REc8&RTFV3inV+ymOu>(Ay*JB1ks?Z6E$>Fyj1O{qy`k=H{v
z9**Kqn0v}<;oI-8idtN(;=5`&akc~(92d_$6VjQ87j>6b_tyFIdPv$&w$tA5wp(3M
zDe4Bx!QGth{pfZlWYZ>6NI?t>f5p=hRHkUSmnTsffz2Tbg8OF{>uWmbFV`p%V3v!I
zuVNCT*$M~h2jek&t8#Sdqf}_VlT)eoDnPc;3uOoa<X@dByXta#78@Y&id=6w-q*G4
z#EtB)dCgE|*QSzqKhP?=R;87ceg&7Bx5^&8*AfZXigJZt07X8LGALt&&HHf+0Of_M
z)2{SDbB%aYvxk8s$Wah`G}5}oxb5-UJgN&jIzu<*7I!7k2@1)Vju@NfpQmOnnqe4J
zvy@-}XlGOHh#=%$2ybE|Gz>Qw>o9q!*CQoqi_V@46JkD_CVb(Pt(@hu&TG~<vF+;f
zfRvn*;K<x7$CstM_Pk+SJH3@RZ`yV};jE+(eS%^uEY>s@jhO#CzNn>t?W^G;ohobP
z9!~F};fjqSZ?}y9Pe00EUG5M{!$rw2_vB&;@$nA6|BIZ_{_n%|6YI>U+tISGUanVf
zhgwI)*>=jpEZf-aLxHy@JU5A77Ck;mKLk+ve4kF60j8w1Q3y0{+L#ygJ>KFW7}_j0
z%{u%q1phUU!zopazy6<Of#&u1iVnNG40*<qbcI8kDBN-#lb!I>JN=nAG&1q|3BF%d
zQ74l=UcJ%VCLDPfCapjY9ItdR24#EMknWI@{-4GSe}715OaI_VzBk1-oFr=?0SOMW
z7e6E*l&a+<<{pRqg$fC`Gy+4@sYBMs1ZvH~C$Yrzd=kMIR61xq>S$^h)kcop%h6Lh
zVnI2SGjZ0IvI7j_UvKOchW4u`_kYh>i(EMDmCN(EH8`ClwpKQp?(nnt)Nu9nL^*3L
zp(~E%;oO00nyUsLpFtG5+J9<tYdyk;zem2;OJO2(zlDFzC#0-Drt+Ri;%)BHEYkY7
z|AK0|(1W@9zYrP~z*p23r<x9$!F8BHF*~HjS2b*-(R>3^LDQkU83rvO@c{;F0h<u}
zK>Ta1^BIc}Qh#28Kxf%6R}6$K;`(D4{y!l$o0CyZ%-5enf%C-(f-J9Xa>;CbMG&1F
zy6$tZAxVbvDB03atvd1H1``rR1()|HRNedMVQPcI{o=v0N!JSak?8W({T7712OP|n
zx$>l4<92Xv`ri&{%CH8LNR)cLF4)fDq>x2xW4FGtk#5Xs1{w7#RUlj;QPO;$Ya~@!
zmurbqMdm<-TeLdN8JA3k1|9#q2G5`7e^^j_g4(S@n<A9_`_}d;r|a~qHe(nfy_EWj
z;ZxtI=ZB}d>$b}U*{3x&-?RxMyb(b+QG3VMBi-y)o0I^OsV<+Z%#~>$<{ho}h9mda
zDLb<_((Tu8@b+0e^#2S=_uih}<~`I_;7v&E$-LyPqzFjTSM;=2vwa^}fpIKH4te^M
zhu)rd%1VQmpN(BO&zFQhPvl*=vP6zd7WT#7X~z}M-=aQKW1Yrk^po$X9noZ$wS*Bj
zw#?pq(-_Ysb!nJvlpA2+Oh}^(ebb~8GjurAqT-Xu!(_{D7DI_?@$7r`^sc{3Q1Q6S
zr!Re9Z}}o^OYi=ua>>}mb;gM0H^nP#&iv3=h7d$XG1TB2by2Agcdy_mB|lL5e=ZIE
z2Fn_{)MGbtFdE%4e4*f~+`M;2$K<_zx$TyRv9nz^JUGmn0=n~h`(VABc0U%n%JLjO
z_g%imqB%l6UX>&hv2BkaZj_MlD!YS^NOMOHg6WQg6B9X`b0L2Cd1_paVKaUz5b7UD
zXX%x9_a1MUud4BYx1jA`t!5Q)IBy#mB5><(VqvLFmyirGpOu9fbhFdFCV&+uvI(%Q
zcxF_r55v`#un(k>5&YEfXZ~Sc8V_Pjbtf9rzWfC09H3{IdTnP5Utj%RyM!bYbyR#o
zS<cX%TsmmFf|i7@pC)~aO4I7AeNgkrC#1I}a{p*>Q}b!ZQPCl~=~^&}P5`tuK+FG>
zmY6uk;YZGSpqc7Us=gu;eyB}0yV9&^T_@(<=CSML#q)=ZfAP*PjW^u=bbkl4z#J+{
z(8uvf8|{H%UCh}?xq?vuagN}sIE~O@Zv)OzkQrLnb7+%Zz4i81nt?EKJvD2mYVx>}
z<KR5$A753>Z#1E?ExBJEm11EF?{vBGdpJ^(d2Uy)`0IIecwag->1xdvCXd+}mksEa
z$!vdHk(L|Wf%7x>U0ppFgY;c^$JA|%J6LtP+0G8Jhc`^^PyP<3Q4vvw=W)0N&ooDt
zsNz$*oYW`<5|z)Uqp@9r>%uX6fie~HK&wB#`>ThigX2momh<W>Xp4qNl9pp~iMA*<
zP5EVoikiHvzdZ?61Tt+w|4Q03)Gcm|g5X5-`prxx8s4y^!oUYyb${N^BU(Ev<=*Lx
z#^JNS3<^rr5v7mXBU)oL>ok5^sB=2NOa6EB^BPO2eeCvuuP}-cS<a6g9SbWCHm=m6
zKGAJSe<yF5)-2LeX-BE@^C(s{NmLcZM^*Ax>An5wS@+@_Y@bbfN=k`EqD3Q2)Z2th
z+w%yVl}&{wu2(&(!PR3Uzd_L)T6gpOR4=mL^9kSmbh=0SnF_4C;6ph0r480?Vptx*
z3QA~aC_^M>x5|1N#gCtyxistZ!ici#w(N2$Nl7LW{Lz#|1-EilTynfoDriaUp@=Q7
zBtONvAbHu7;M`DN{mH4EDU?Gp{EJVAN)00-p+R$y)3vSoMlxvt_npj!X|LzZ$hDW4
zNPguE9cnyiA5S)>I2cZ&1rvWU%Z`X8$sy~nQDCoqN*{zDe51nqHU~2{sJVE`hJXTD
zHakP{>o*+O;T;r)+(0h5N9WFO!PapfYu~{2@J7G5j-wHCEg&Ca6D@94WC;3x<_1#G
z^yn;G=s{$~uq8G<uR_S_reIZMhUzqrT+;@&RcO<IQ5p8N3MAf`G8$=v!G0Pk^7|=$
zG>R4^%=jcPHrcrH@8QY9CaMZaOfnW$&yUb`q5b3*_^<%3P^yLK5r+!-C9jhYX}r-1
zmnhV^yh_opML#@2dUkk&%~o<Js&}=HZZ5C>6u$rc57oMG@K)LSQCQXmo8^%LY31Z$
zvmqjP^L{~v+{K?1A}gnwp-!lUJ;e>1ZKx)jn@_A@dLHT@3+od(x}!ouA6+xiNEb<c
zmv#U1bxSr8c-W4vp0B!9ESIWje)iJL^75eCb*}!ozR!yA{^Kbv36XY->l;~9-1Epx
znBP#VeOvNlRf2UEfoIOCe)nd{-rx^GtVGyU<408Sh`L!i>U0H*_f9HBYws;QSUP!0
zyoIH3)X(IysvF<ksC;1CJ)4>tBY?;2vJ0ge{Q1)@PI>Iu(a|lUXP7D?4GwSkHa}y5
z{6yp48onboYegK(6e4SeiE1wvlB=CxKArY=UnW<90KqLMgl?JC#DO}*XFM-InUMi*
zd&HfFvawenC*ZB{`nSYa?|LuFMc_JlX+phhFj8*Zcl7ibTNMaGWMulQWa#p8N;vIF
zs$1ucdF{w<J-sx-Hd3$t(1lWQewV|Pf;9{!UTi&{f)J`F_wT-ifw_Ka@k|z9agh#Q
z+4PEi&*da3^>I^t3}Iv6g20H6%!dF=3d=qNwlmECTMi>bd|)x7F@iNg4|t!gyMaed
zNDPyxgvy6c5VhMQuI3bcK;~X(@cHmQn-Z1UYOD_pCYK>C<n54!Tve;U>>jUDA$b#-
zKISTDI}*ce*t|U9!vX52*|IN3v8|82j)FG6HDaE>r0XZ7$1M8819KTkd~Kq|-uFq{
z>WjzIa!Mv_4Sl`Q|1%smP-!=-YfH_9J)OpR^@lRrILr4D^{|YLN2H;vku59#_b(1t
zlD^WF1*5||I@_mz%`Ip0V;sINL|Vxf)-IZ@bsd|PNTJ5u$6UL$@QZCVy?-l-av45f
zW(w_Vlx}J9iUj1!Nf<g*i|nHR<G$1Nz2^33;B3^SM#iqJs+{TU-%H$wGgDSh81Stc
zu&QsiF0W0W6aB_Ips?d$0>M?mbTfC1YANAJVfy{|ko`oEKU#d6y_kUR{X6kl=Y|;@
zRnkXqHXleO_ip9lewFZUwI*|%iW+BlXRS*@vax-kZda@+m+W>|FP#m6U5T10Cx9oB
z#o1Von?s2lnr97H8!vQIzIr6oipB`Evf_5-8xf#-lMh|b*M+E|;(XNDZ5rKO<20d5
z&od#&U{vQYHT8NUbRlTt0<}U%&}<tsstjcvu!!$2*ygq&a43!C1srOSH#S^tuCYpY
zOj>wzd`%I#3uPrf6!wM|WV~Zc<;UsClW!E3gN>KiFqe>avudHp7jU|<a8D4>v0iR&
zR5G`i+JjzLr?5xH(!@oU$4;m#DXFIw<K3(m^KH}1shuHQi^;iP@qH|D$kp6F&T=Q?
zLELp`by+n=c<nvbgZAbwtB?J}LV)}EU|nF&@7c2AO1u*Eb#-F)XCTZUDkf^8G43Dq
zF7#<?SmBe01lqH8();1k_^%dL50td_PCwPgu`@+31-&Az2;h@58yVs=QIWz`cT%CI
zHZ8Wq`FqJvF@C1Q8z<i~WY1?lYA@_drWG4UOQ<)QI!SNYpr}!b3;Xd;qC#B;%Yr_!
z;@>pRLd{`js_4N&bw$&T40EWpoueC$=(mit4X-DX`Vjet%d6{#_bnrV8e2i@D2daY
zINH`@PwA6IVaOc5ZMXPd1O}Vit90~L^r@5k!)cEFofASfVWBN*URdgCx920r<CmUJ
ztz@*dGQT)hw=WgFL?oslPaV%sIu>`;&Ie?;&zmbxq0?q5D{hC(Uk`;{>jYX{9dY|G
zCLn2_lt=Ac3VV;ex7<;kpM~$peH`LMZuYZ{8;{(6Zyx&`O13$;_@%^*{pd&75$yY;
z;rgd+1n>E(Y-n-WYGN17zV(%JBKG6RPPDy8(_lr51H3F|sGpQ=|KSLp@6{--jjgN2
zMev0+zM@j$?Ovn1lA`)8u>o&L%{~H|6i408dCc=}$iu+`=kpEu12-5YA~(BuBJGV*
z=AYl#8Mci^^cCK;RtQQndR}WEy1jnh9*NM^pI^@;{@TzMQ~tK4fmd?$FNc~ti5$3!
z#XDfW+-lAk!QQCD#1a|Vd+?8O#>VRNr8q>r!!co^NB`@G)etToem56Rqd73`2dHwH
z<5<2E5N1wFyk0^1ea}5|i5@VDxq@<a%_~9ik$oVU)8q_(K3BHx^Q0|CSSNv25}3w;
zqM;PXkgx80=jsbOdR{yfCtX7Og=u?jPjrTuYt6#(G*~y3&>=+{TKo6gOng;v2}Wh#
za>=|tUeQzre2d-yMS7`M+#zpFIPBrcm=gQnzLnIIPN4D9+LkCD9zWM4zDOJ1{*M+(
z1Qi1fFBGt+5kp^VVb9kE*T531$M-Y5HC_7gCG|omB|VcHx2rog>9qZN(#5K-loI8Z
z3e8hy#nF-vPc$DG@{D#pOD{Y@kBqJRQnb5nj!m_s=>7lxb5_DbsUb}-G!=EPfcB!j
znL!Xb`>xc(K2L%U-W|6~0$YMYVVjSrAbWJ1@P?JN&z)g*bo{iTs%a#oo@ed|omc4N
zMz`A5M_dTpYcnP|ZSM$e%C0}Bh+Uz@4q3NhRF_70m$3*TV=$rwp!3J92C<bhg08{W
z-!p&?ty9X?JXapGb;k=R*^;5Tp@+BBejH{1yE;$mVAM3IKszSiS0o+XLtj7ENnvDM
z5EQ4vI7_xHMAXMoo|%ZTx8XSZSaeE4-gi2$Yxyy)U!@qI>`P-=8QEd)H!FQ<9`&;V
z)UG!1Rk+O|!d&*=bC|kWe!zQw7`W?qC)v;>^Jn<+Z?I@RF+l>01FxTn$glKsKe7*G
zT^dUXlg1C<kk`eQDL3>ntYT|p!hxB)?DdL4qvDG4;vm~}A#XC9eXgdckCYT1>}yml
z%DkT@xVS^tVJ^3llA=Gd22}rM={86x2)cO9)FSD>ZEdJ_@tiTHto}fNfXafRf+_v@
zCBYL(6f+jqe)FPPU_}TT&d!>K2TS=cjrY6w+5FAX9VR_GN8p6BbxReZ*m|<E?wxF^
zocb>cib(m&*EXm&zbS32a%}9V95WVw9`G@lr*hJ{mtDMdN#%t}*H4IE$=Pr%wp8C9
zZVXwDK?rYyk?{{?2$its!jpO}AuFM73h#|DhBmi+pi*u&Q8SkPa~J+~ncs+V`C`Xk
z^|yQp6<IpnXkx*2(&iTDM`iD`3^H;-5~h7ecyrh)YUOFt-D(z8O*Wd3S7dbWCt9V~
z^Z?NC)T`~fLs8?q-d%E+Zf*a-0CE*g6q5{HxK>r~(jJ~)cMyXtRXmMDi~hD-YsT=q
z$P@o>0#H);x;`+$8BNj7wwIH6fQy=x|DjpF{<U9Z`Ptq8p+7|@npoiwU&-xomYhG3
zD56}lU2V(P;3#*@==*oWa8%Vz7T%;6u%Pg`IoNE2<{IYN|9`eddiXX{U_I)6N>gOO
z*PA)?3w1%<M6%aaFqb`dg=pLsqw)^@GU#nd`M9oa4$<4DV#k9{=39s4GqpG$^ZwuF
zm6d=0xO$_voMZja99f$u+Zv$S@`w|omG-QTc$LZ*(5p?{=YT~Ux1byJv4UiS?YWtJ
zQsnbem84@$Mm{rVH06c3V4w86_nlcIy{Z8U9o@r(F9#4WK6(4~DMs4bH`!VH4u!fM
z=w8B2wLt*y5kI^l>}klnM;H#{|0kkW)~Bs;bXp^UO?fPLh;!{H>cx-M<WK^7)Hqnb
z$lR)h<Fz14juVvgK3=_Ys#huBp}N-ZZ;0tf*%OAy_wX&FV0&zb*{c4kH%wbj{bn&*
zB|h)Fx!vZ+_tZ(P^2fcgLcRN$D}x#2L=qzVZfNL|@#$jweN*{6R>v^Hf-fPjnF7cR
z*pkx*wr)Rt;_fdd(vp-+pnc#qDOjNmH>MHY9GY@O^^W;fwk__idsjE)$uoQN>)Pgb
z&Gb6)SoVix34LLXbHtVP2?}JGKDwc~tTC(FKT^#x8*mxv>8lqCQS;iT@8-`ucN#AJ
zzxi#PZph2OEb1%XPU)Z3;(ag;A?pZ~;t1N05}Y3AgPi7OIQDLp`nfcz8zIT`l$wEt
z{bfx1YWr~ENsIbCGfJjc(XX(MJ&bowb-%6sp$w<u5;tY$j}&h9^sygyBkH@_<wEc}
zsZP)Ew9GmyKc7|NgQ8z2=fAcpcW$`qKz<jYK3Gd~s~YU%+5h`EmL(O|Cv@7i;c5+8
z1;XKKWb~jzdSOK)D>0RH`fya=c3s}LQT1`VoPu<34ka&?#j~Npx~uw6^83xlL$s&#
zm}SEuBAAooZ0|S=Ix`Lf53@R1hy-W2oahw8KD>=v{Q=eoJV`tU$uGgT-DB3d6jiZl
zJ3K``#=0=5p5m=U`U$3AX=Qcsu8xdfp9=Tc3A!*xS6EUr+DoSfPS~2HFf_7dSZ#iQ
z3NdS||5E#lOz%jqNwjRZG`~te!t<J)HlRd%iI%}^U{DKOMzTOp<5fC*PyBg1?w1or
z&_km%Hsrd@JU1~KPBjz@4ofTXH6^3_=ohPU;4aFB^3-8U`WZ34TfoTf`8B_WN*Z&l
z*D~;Fl+^+3#f|ew5A5sPQVAkH=hVV2tsU}xg-F}E-u~+;N@M3e9~~Qf{=`%)u7RbY
z;rL8f<j1?3+k|Xy3C~q_1E#addCSq^8HODN__`q%*AFw}{e%ly$Kr7kPLg!Cdl^~f
zoLYk)hly$s@WA=x;k?}={p(l7HlH<K`og#OusxYu&$nY0_Fh%P=Mf3ie*YDiHzJC0
zve$Tib1InFnjFNl)iYSTa7r?`>y(Y29SY6u50T$5<!X9(*e06R)%K1Brvu*qKOIoZ
zQO)NLT*)Q)c*<1pedFyd-Cb;K8r_Rhgx5on{Fs{6PcMYMk=k=!t@#F_@9aNkI7xY*
z(RcKFo8ffNci9hojzvW`gSM@5g}<N8J|uQaU|L~F+enA$kh9`Qa>P?%Ne(cy9^Wz>
z=$nocQG~+G=Y}zadCrv0lKif$8Ce)%$;cT3KaA*?V%-r}-21d~j6NPE|5x90D14De
zyGbD`5-9~jJdUPIA5u))9Pi;J^~~QU<n1(pDc9cSh{AL-U`d1q&HbmjxL2EYi1#0D
zSfj3?GEz8kpswY6DcWjTWd(5+FxWonpxHQmCt*t_yd!(pD0pmDZeQ6r07^O~aXCf@
zk8KKCqA9dKElmo2&fxl;TTYEcC8DX{iS9MnBs!#|8{7WdE~9MiTlxMES?od9`c!hs
z(u=0Wf6k3lhjz_SQEWK5?;RsH>03T2k+}fBouUI}$W7(thJ7s_{~v8yJ<p6C3^^Mr
zI&K!a(W;xS?n3@Mucj7xLdC7dAlaw$_WQDKccLB>w5ZZ@AG#h1nZfi=>3UB~()G8e
z1++HSb%gw^KA1;@0kO0kjE$TLZSwlD7eQ5vty`t?I@Ux>lq!((o+-zN?UYf<2yEs5
zqv<QdqHMdam5>mmyL$+wyQBp{98#pEyQM)u8U`4;Q(6#Ey1S8*?(XjJJH4OxI}U#M
z2N}5bwPUTd*IvEhMK?-G)vX_TI`sWjd?-SF(I;b`kJ_Ri=R_Iv-%3LjJsX1e=tV87
zkP*2{Vpx+J?{fFR1eoZvb6;CvZIl~M|5k19Ca*vpyP|2ai$gtZl04o6rqgCDcN$_e
ztz*HtKl78!o8<!G1}<NhAQydT>$V(h{oUn5)32`n?>3w7Ca@X&Y^{2`EmM8wK0T^Y
zs3$V_lHkj<JK@FTO;L{7Vz}*jCXOmaYAy=!>Mc!bV>+vT`_Ko|2fKvEj?ZTN+s-AC
zFPyd&J=FMuycg}PeN5*C^pjJV3e4}rS&u5j$bUPs<#W5|SGhl~ZRs1)=zDz{;4_K+
zq?4DEK=Mq=XWlDz>p2mmxQ{D%CEAc9uaGeG5G~T3IN?A&>|sDe-wj6nV&_hjFa2fE
zO0<PhN?MxK>#Y1qb5DxKUZakg_3B@pje@~c$QS`M1DEIzStC=H`V=UI)(vwZ{%@en
zTsDf(Nf!J#ghbE88|WF+bT+SEln;jiHb!BgNu^_u(+#)U1Xt=Iq3_Sj9<|91se{9w
z{014~V8xwSR8(o{#-)d76RTuq@30(|)@WxWc-+?H2H%!`l2n59D}5cZ1@6;2jE+fy
z<TEFiW;aWiosIx3n*oulDqdtLBe1CC{<@z6Nn$x(>KPwi_FY?ot5sE(XU!jyda>tt
zGLNn;7ti9;<TW&77-D`z8#Zew&WGeSZwRkrq~ob_{gNcqjqec+v%0}}{tH*U{%5CU
z$w0bns=}giv&MXlmlm!dx9Uch(YV(`JEyZc2<`T<;a1nNw+_Kk3H<J$292;Qp6-Tf
zfqX=q0uLFF?P8O_AOA(}@n@?X%M6h60kQuST$x;OHfS;%kWQN8<L30m?aEN2=`bq+
zm!x<d!2m1wH<fRS^j>rGl==mj7WP`6IwjzvX{jIUQc2+V5^&chgip4xuA;uqH^?zZ
z-|)a0dXFRhR5Ul>NpXHwF}fesa-EomELox$9coB!2D|WHHQk5J0YPU~GUR>;u@=RU
zTBy-)3{27795Ws@T?&*&FH&QIcn`*Kwy;9@;MZiD0t+yySDQp$K`rRH(EVR)K>JEa
zD<L`ZTzIC0x(T7HNwB?rW~E95ELDx@uFlb11>8!A${$RjvT*TTZi`;@3&o&((OcWq
zPSKglD|FiwHdSseRR1r`1B#}VY7rR4^f=uoh2ptkkPza^L9ga7Pt4&FGz0iQ^M2+R
z?)Bzoe9=-jX&<BxrwyYA!YOPSPMr7L+}DO76xV&1QGX-|7~-Hw5iETZ+%qV<FRRCS
z=1;t;>k-M1c6Poqq9VZQ=@D{H`WQd^rXU%1$~KIAk0eY?sM*$fvC`WWH>vKdo*g~P
z$s1T&7Q?GXFAuc3w+T`sjx&dt_Knocp_jmUd;PSZaI&#a!weuxBE%HDoS|-v5$%Q^
z6s*i>gsr3k81;N%EO>!92i*n}88oyQQrOg*92GB#MwGtNd2VxU&q^CglXv~B_Hfm0
zbcooy2LFn)oPpL(ESNcsoK!q}bs$T-ZsG{mUXM?9Xu3Jnd30s4TU`;!=jdP(_%cW`
z(_6G*Ys6N|FtZ6OERsv>`hyko+4Xvy10*k*QFHf9DdZKL>6_-;=APRh!BnF4trt8$
z&c07YU~IACHL9hWvWypOOe>n4Dw<TLK{Oy1cNFjB0_oqF=X6JK#{ML5;A4ik3;6^S
z|Bxc%cjnv}Z06cTk$4R-@%i3wYpwwPKBmp|`7MP@f9jYKkwy}nZJs0hZWubXClJ$7
z{7V5}PQK2?fQ~jgwhFxIDTO$A<EOJo4zH(<XlZc~eb#BvX|)6cAoESZ740;0hkP9d
zA@m_3{vrQSAk4|;W4Zd;AN9fwIXW@H%c|&MFt<0IJ>+EyOM{aoiZFGq1>BzbPy$>>
zVK@)Y&3xoIlboXPJvtlCePe#Jh9VfK``1_8qk7<DLoiz?e$}&{T?RGzS-dbe;??cN
zkJwq<KTiCy#UrNCxSbz5Ev)Ore6T4+u%KD+k@qi+3)io%u9_2ve;YRNFW>8=f264@
zsL3f}R+GCMb{w-$0P{h|f6@nK61tMJS@sqV$Ih?ka~-2rBiy!6>D%8uRp#-S#&NZM
ze@Nm^`7_u#)%#szZR-RuV8JPCX^<`$CG(YqOY1!bZWX>uypH_a#gEguPV?Ckzq8Ua
z85rh`S_!vnHSRefgg!r-`rBdmB=ilpt0kBF`)PL#?9cMHnWqm2JC5<Hxs_|BIj5jq
zk63!XMjW%gc_>|kz_DA@DR6+d{4JC@N1z)G!RKfFSE9wHwt-^O7RP=1)i=b`H=4vl
zRMT^6o@&K1<W5Zs>kC5{qI-8<Ht;R0ixZK{IL#h;{lW$R{3pOv`0^g}cw?vTWQ8k{
z{d6FlspqIm4U285dC3avR=r;0^^{|6-6DNR&WN*qyV=vZGxxh$bpAi7KjoC>TyF)^
z^$VRm^1Ioa-QXUa1IElXX0sU^W4qe-ZTd|^7Z;3F^NUa5o5wZ$b4e)*oL0wV<>@B%
zr}o~@sF0pMm5EPIDL>wwdUqCJ*D_+-Bgv09%B{_zrEQ5TgHv2gJwWSEz2f;aC7+||
zgNaAB|JF0bq4>JfN3H?>n(IxwrU+5{>$XhqFA&u2{C@U_;gZq?i{oLea;~Ni65~hm
zRs_gki;c9N`b!S;d@c$tE3WDp0jT>LONJiV3S~(mwepp3h`%;iRb551rfic$?gXOC
z${Jag4PJz^&et~%pL<nef*-|MMVeeXyt>1Dx`9#G&P3*Xp=HoPdTi+Q{0c3f$``JN
z8Cz_~*rwHhRSu<UV~TvWb3Z(2=V)V}o>{%Pnm*hhkS&ETXB>|q^X-jp<}%b4RSo(r
zUp)rf!kyyLaxW9`%24tXj|*0|q_eoV)$4l5b1v>pjK7QXM`vr@%GZZ~uC||rzAp?x
zFW1yJTTIL4L)S)Ii)MXbWz%NWp_+fAV;NGYg1daW7uzDM{yk#KtYdL~Vc1jWP`?{Z
zSDGfdoH^Mm_tIr^a7J!1it6H(10d2|JiXTwVv{EJ22;=O4+oE;V~-McN%Q;Honzio
zl`RX2)iwHY6vMAYa^BF6Z-~?(K6^eO7~AIvqw;bN&)A^sJFS-rj+adYPhC+ks!ZhC
zsG1C^l+W{i@@}fOvU2ESNzZ4yq;u;CIQ?c?QRJNf<yZPJ@{+{lUhxn5yJZ`{_vaMj
z&peT)C{FXc0g~fU;@Ua^uz6;*|7*Tc+dtIcnS=&9aYItPt}b*l!`B3GaMwKZ7Xl$+
z+d=&^>}k~6gVYMN<4n71`EOmf7|_jw;HaT%lu~`Y+lO1T=~?j$-d^49W6dKA<C$hZ
zm9A_%##@^tr$4BL8|9693TMu^+nCjR7L3w|j&JN{jOoiLl81UGaHeQ{s_ABl*rH-$
ze?MY8y53Z<3Af$Hp?1B>7BXM>T)xz7BfkESUT$^8^*K%X%JaadvsJcaM8hn4p1dH`
zFH;D#t`}!Ls5wb~2b}gI#qP1?Y1+%z#(^Hp13JIH6cu@<)Jm=DU<YEfoc5D!YF3+H
z*vukY={#H5#&qAhWwA>W?^YYre0=jZ(+J*{_&IlE5=#Ts9~FuVV63O1y~B_XPyJ55
z$X8MVwqsf7>7Ul@aZ=nMocioaFQf2QtUlw|ALv>!wJs*<hD&XOyC1xXN{)WdACAuN
zj?V7ly2;ze+ZLWT@a0U?>hsJr4Rp7F)3y)n%mI|=)}RX}P1PkO)8*loPqDMPvbT=f
zG)+_-em!XnYE#%Jp`oY6#qUekQ9Dr8RUvWQwblH%JSOxzKHgg@pYfz=l;-jeK46F*
zWzPzT49z!fdY$^iU(>dlY_RnV$~cd<qQ7j1P}2gKoJXFaeEq2(=mw=v7JR-u-z0Al
zeMnU#iA{p{#fizta%pjFF|!~$%Wv5!K0HHah+<^y8y4;x<?hB8WQc0jt0`xJfIhN3
z4j@IB0=Db4(MUfBiMiKKw<%7J>)HYRg`B~v^QQWZ!M;za1+Vi?S%=eXk}M9vJL4$4
zZW>`j&dNd#v%y202g(E@^pPrqVQ!3|+zag9HzcPDu+lUM!Yd85PGN6wG=1*0+xBpT
zjx*vmnDR7LY&G-to&GMxm59i+s0wkH*WV89`5D`@(e#(5EbhZYN)cr(eT~fze@t#K
zAJY9RA+%!Vk(a1`0m?YSZEuvhaKsoGHfEUqJ86y!N6}3Z(vT9N|Gj(|u(NW8V*;AF
z!Vygz1{?|eq@)sZv9_msCxzvr{brOYOm6y4(QAim)e`tf((<1w-V2>`Uukz==R2Ld
z&Tuf3Vf}e>S9o=l-7{yz=2YP9Tq2w`L*`>j`6tuGS$*>x-Z+nk)Spz*6z}jZkI<#t
zF?W_a3@s^9=Z{J;P?J#h^kgP8^ZV;l3LSCc=V1%k9r5utK`?$?v}K5IErKMRPxSml
z)54RdJi6Ia74LaTWa4AwhOuR0aHI|QaTAOk*dkCQdhI9B+Xr`e_&u?u`0OI0&W0vG
zkDXH6ExU_lkS%|p1ZZoE6<!x-C7YosuSie99O>$vCxxwlv_QX%{A(yY;i(}pC%M1}
zL?X}a(Y+7bdSB?}r=^H`E_Ynn)YN6U<MPsGu!t`ycvQ3120mfwg3*XiE30Bg>7x<^
z7ak{eFNy)o$ZW8->t79<b*5kQM4vD4a$p278|@m2r^a6;n7t#7RV0mFYr&K+C|+oa
z>Wj$*hv473vACW#@6m;GxpRu+a*9(zu?1s99hOE8II^dbep>}Mw~ULmMLnP#k}$(?
z%al!&#g1M0Vbtif##+(|^z9svUiwaJ>sJ&M%iG~=ZqDAgFzeR0#Fz#$4VQOKU@Z%$
zi_>oDgP}!<QkC5aKrHnHIXfys9Ub2h$-H`L=U`Rkt?!`hfhxg?(|kn8NO2wtdXTug
ze|P<ul}VBtZ$3;NTer~<lexal5toYSsvX%ezpGNf@ACTjv+v^9W<e7Ra|8C5@-*FL
zFf-=}$g0wZX(7tH{csAVe%%ze;o9Qm=X=p{WpNHS)|tXWZI6x|{&H|=pzpD{ma~h#
zbemev@Jd?3puot7ysJUsIu^6>%8O>8ue#}RU<A<r^+jBQ+CVz6YJPsBn@SbcUW6@?
zzyP#zhu279EZGsaQnJvoaU9&Om983FoNHGZMDARNm0vQjba2%D8mYbr0U?&#r1`?L
z9OoHLeGyFeWy{5tJ`*g~1@GJX$}y4eR(xJ!QMO7d3n=`fy~)h1xK&JyPu{EDIPJ-L
zsO?iPFMN053wluYR96wpMRNE;<bIzzDQ?=O=bdE%Ga+>Ue$Nu?K_TVwgYa3xMrHHt
zW?kYYa|Ap+UYYaB(ReqOl!msb$K@k@Q+DLj_nBPKQj$j}-9zvd(`OX?_{-;M?9AOH
zLfAq*SrlK;!i>N(0pM}VZNG({sNg_f5qf2uj?+DL9`6r}%iyR9r}N(zL)&VOBpTYf
z`K)!`M^|jY@fxo4SHeKtw?X|Mxy&qy{Z(`)E2`ZL`et6@ivyP)vCM}u<q=0fa*7VL
zVddm$T@)5%vAo?bR+QB&TIVJ%j>u+_yKJTC;e_Iklg4{q+7Jz#9Cw6JWAx-UhtcQs
z;szB*bMq=HeS>rNd}E{H_x&=!s%`!APX4r-nmQDLojf%^?%_H(B0V}HdySKvfAXDz
z7||XBArr3IhT$G|4`&UZwsY`{1HbgR`EZ1hmx}O7-t!nY9Ke=PExSFHn(FxcK#w_n
zaUwhXYaln{weVNyps88ww~d#M-M>&~m*5aC^<mY1Qbm!hHv~PL|F-83oorn0{PJfE
zE917#t$9gKeEn%7slEziC|emAMZtE!UF-G`jxczo2vk}f-gzh~%T&VTjZPr%v3<%|
zdzYS?;-BA}YpJu++_T;^ZWT7DCK&9XoMKPhC7_4<$8q9mZVrTgg-KYP!_bcGi>H1=
zq5zDOD>vgKLa+Z%v-<P{VQalBMy4Kz2odyT^nhsVMQV&g^stod2>;@B(ebbxo(x<5
z8P8j)ZU;rilBg*qjl7CA`PZ+pk;mA!<a(kc|2z}*SR6fvzLl>_Ovl|W)}UE!BM&3^
z?$2l$GXFQ@6*}F=?=<Ouu&uVoY_ZUCQK9&KTbL6}*su#W?5{Z53p9JcTrBdHyDA;b
zaNDDlufh5=%Agv$nqx3Z(taH0(%ljYbdY#(D(rs!lp+N&{K~Fem3<SEL|RD?-YY#~
z5btn^O8=ru2h+=7xMvYqV5PN}%mlMZ?m~gp4ARQzGg);fM$mz!ri+yfQCfYcB+-?5
zon^-~uyFVSE#oAs7-R~jfvq!iKy02W(xM|&#^vFo7<PWF8t4*E^>Q|g#Y*JcenC+$
zh4QAe!10ekW!hG!T41@ZKsP|!6@S?quga1K5PkLf@v|-cJ6~dAO<mJuzOb`wQ5_Is
zL?93;rq_M+b8>PaWK?MM@xjrJKN5DN=;Hi)dUtekkf}=<^%*=j@kjl~7v<@<*Rn@|
ztR4A#YGYf*Uso4%o{0BECgB>T<&xnsSO2EnJFrsR_m1UgQD?0{GZ8H7swZ5t{{_NH
zKpO2h`ZU7Q{W?4vdLl0v!C&<tduYrwRo3oJ6@TYRfM^qN9awEjwF0Dcr0>nc)nQAO
ze802r73;{!Y@b&1#c2^r3L~t|QPk(SP3duz%I63~<_dp{8|?47-Cu;DVrsEAt}$?z
zdvW(<oOPg-M+p4R5=)LG0+b1RbZ7|q`S1J8Ag0cGB4R^DJ1pfHX$+a8&@MUGtdN`^
za?xHNDs(lCO-qm!ZCdh78h};K!qnS~LTn_zB*gwcF<HfV(S>1O@m{Md?WpvO&>R-0
z&8{0M@hb><wJoz;09lZZCBOM}$NzFzZ%zdM+k3|cZ7k7)fcrlI0C7NJb)J>F^$vFR
z{rnt?59LihV;^)ZJKoOb7~#^x{?YuWAcdP#EpUsF5v@HsmF(qWb45E4(*Ir7Z0Q89
z_;Uz>4m_{)VXH|}r|+L6l@s)Bv;4j7A*!odSZTQ#sJZTT>JjAD&NU#O&QSI=0QoJb
z_&89tYVD{diF5izFkn_T_Xm;i0x_zIjz`nMme#|bGClFex-$Vg#*Oda8)dYPq&^kc
zS}cJvbbYL!@d&8jZardGaRdc`U`;F)+}i^H7k2<PqyMV#l%|%2^UdKMzd4q5eS(zT
z_HwY{>U;V+w53BCpxOAP5yi?nr-;w(wRVFCFnz~+BU|dD;DcL0|2DdByqKCI)zP-%
z_#p~dqu(d8dpMD*Werj&11H-rY!a%402rL9r@IMY{Hb>%oa(bj$Fra(QqYP8pAXC=
z9AWkkUl!kp45iNcVUY_DH%`hXnl9Df356z2k<6C<@=zpnf>6cQ&TngjpJ(Kn!}4|l
zokStI;Z-qpgxlXsA*zL$^&wW*A39Xxs3i528C0vthNPX2SU%XF>L{1ouY>@yTvlc~
zzOOZ1raa{c>M3;uX!oPnCAyzWk~YyqW^|2|y*eWjZ|Mh|$PW(aYJ6-})P|ZD?!K+!
zU;4xo2Ve1RXRNc?fZ-#EV3<!nvuEfUu`q^t10R3G%a5=Ji*l8Ivm~Y)&v=tiAQSw3
zH1kti3SWj6gRYv-BU9Uz7EBRoso#yv(Wm}Y-}J>ZfR*zT#LD_^{tWS9BIOb2(2@(}
z(k78g_v7lOY3#S}m)G^rk2|7lo!m`Q|E@4m!6(&E^M{XG9udxd(MDr<Xq=HeKJx1W
z@%u*ZhElWd3E|S+F=I~j&+=%7m@Oj4<Z^<Z4s|%>bgw*P15i7edfJ;<zV}a;eD-it
za)9;*HaXA>2ZoYz9^@3|iG3ubfXjCddf|IN4k}zkey<`v*F?CM&))Mbx2w(Bn3vq3
zQdaeBU9tR2TZ1@3IMqb<How|7CSNW#I-2bx#C3JnK|)u}@ddjbz1jGg8FYd9xCsVm
zYjk6Z2&$4&D%smE*FxlS-u(wqtRL*Ldf9shL~8ho_`i(k|IXkLm&!!%?bS$au<T~-
z5**^+YTBT@<Otaqq~~>||3eX%mBtG{{R1MATJdXpc4{2wmeRqpH-QYW88zFE=-~Pc
zPKXYiSX|jy-e92LA$O$*Z6MBlv#XQesfOefagiv=Xda<wfm*%$uL!f*{JI*H!-iJ^
zpWD!!Cd^d^s5I$<fjDY?aaKR>SV!DN)VyUqi|TN4uF5Dh)(d`t*5TIJlEEW9aP;xT
z+yXu3O}9tD0ITOf#W!el2yJMmgCcPkhHlif-({;Te(aUAdfO!eOj(_Sm*4@<$1TE-
zLqwoX8@Fq{!TZY=mGCi%8>J6EEDA?AVbla!RipdeEJqmXT9V%pjx>z~ek5izoSN|f
zS=wTR=Su8LmqP>@P;vr5^=qz?t^w1e%IkPzeCR)g$R5^D@z2Aee#%oWmrd-b2=3}q
z1OQwUf(Lgj%#EMTBfdQiOMzuWLPXqSt}LjZg{+;pl6B)q#0f-p|Lw*R9Wkt1`eva$
z?bl)_Cbg8iF<tt?Gin2=jF>TnUVNhBr(NnQ;HQt<qaTgp%%1xL3EOt1qO72Z*G}xG
zE&jDgpAlQ)i1HPv*AyKa44yy$mBd9>gUZI|RSfuE`C#UTWFM^r(Hx3O2qP=?L=)sO
z@hn%I-929gZN^D%H0U*2<i4ZBZP7g+Mi3&v*kTL<=M`LTt|VkEyC(_~s>XC`?%}AL
zK!CRNeCH=y-YD-^sr(1F+<x3Myl=)&M$WXXF6<wk$iM~ov{on7;%5{LM;;Va7)6&a
zO;g_vXkQz?A@5O)ca*nV{v36%_@%T=Wys`*>w-SB3U1cv=?Mu)LqqQ}H)InpTWL{g
zd1M%^%%vSf>g5yxW$ILg*9-6c7XLD(i6&t$mYWBroRD0!&dGx;jyj4@a*&}x0%jp{
zrniF5>ay;wo_U}CyjC@NH8@pQ{bxDg8)nLbJ$*#VVBDD^ekDj<_}oQr!5O0sga1}b
zHj)hi#i_hh-%izXgTos6LV}pVKaP!)w?0P2Bst^2ppG)K>=%<ox#*AUBj4+%Z&N`o
zoxQ(IWS_6WTCvR$*jycBJX-p=mHBr=TRy6ldj9N53*GL->5K!3aju!6r<nHu#fTX&
z<t!Kf;da(f@mR3r5ebrm`^Ea8AOAgGAlq|1hO$!Yid=V_&$p#Do{9;MD5euUccCGc
zf{W9?>aM)Q_x6+s_W*4<E{p{Ix`)i;DV6eI?A)BhoAjNqTlDHPz<j$r1m!P8S}lN+
zAW<TpIo5uKwhBH{zJef-i4g973vj&_Ev)Rkxj|!mi$!@#6Mc?$e_DrZ*~Nx9*MW%;
zR2{r_Cy+5>Sv3Nn{}DTp4^{U)G!e8xu#uMAw!8c7F<i~5>MPV_ge+J)G>imMDFHPn
z#P48iUmGKReT5<H(>!E-WU;wjx%^etBn4O?lxcR}Ty~rT;^(i{SI-0<AD!n_h5?i;
z^8VM^2%pBa8PU>;LIdZa$<;-&OtWB3Z~3dV{4546Zl#`2<D{qTWsN=Qdcmm+e0s#R
zp$IN?1Idn&RU4!&?)MlbL$Ae*TbI+n^Mdu&`<XG`>hCm4J+e45T$Pfdu^Ry6eMiW8
zzuRtsq2;q2c0j!C_QKckjO*|AcdA2AeH@v`l>z+?FB5<E2{TIjva7A81I$-^{5LIs
z?|YC?@_HZ5^sj|leD--{hOXz=KX<n#h-U2xlwx?4V%_~D51(s#0Y0LU0P*wCKTki=
zw$=dq_L0Og8u6ec$dkX5?2m-{X=yTvln>RyVMdEO`YYgbKF)O2Pzk0;#L_P&=`BYl
zBR^j5Y*D#;!_e8$cLZKg@$qZzx?In6vrtUs9|$>%lKD>XzsiLe6GY;5ag8UFvnwk)
zHFLG8G1ip3yqR;kPSjl78j3XbJ=pwv+`o6<zbc<U_%Kd^%-QGaQZQvQPI?S=ip8{Q
zP1j3IFft78TMos0R%;mYbDT~yuGfk*KSzb1JB}xyPcZ>65S^E<qfP-+9sd4nM^u;3
z$mZt7OY*t59$loCxXbumQR@c2e{hhVs^i>@B@60(NK$x~MS}TSUf$05A_F~AQg&;}
za}D|Nk7g#_e32dOD8@(5PhU77e&0KB#}Nj=J60xBT#%Q}{i9K%a;WDi&Ji{(kpbw_
z?D5%<XIT(8Sq4W7R~9il0%h1WTG}rn{}jvj4%44QQgZ|4@P_S4e(|xVzPx1ri&=4h
z>f?*&JsIXyJD`0xOZ}%tl6N;XKgX5RoT`KpBoo0V3pcsdPD%Q;5M>gg8F1#F+lyp^
z-UdjUK<@`|na|nZdFl&KN%cjzqv(NmPQXBr>l&<G#^<w5GDuVZgt1}NK_EMU`;XJc
z%yP1teMc!<t?~-lH9~!buDSeq+&@q5^GYuk$gBj)Mk@NaNOZeu<(3CXN#oP%%qZ@v
z-@0zwUsXG?HyN&ed7cY#sPCh#q<_jO)nm5pX6^bcnD6HDzH?z4d8O9uy{u}{Cife7
zt(h)>5sK4L>rv2tg0r3bT3?}Fn(y(ES=?jsR0*2xJr0eo9$vs99I7ux;!qo_eB4#d
z9CE&{1p|Ti7Rt5ZS0bdiN*f-TTWO@O;omC<R;)T&3#LsA9Ty$a(s2y$hSZAIxdt_!
z8@t3ul+nJW1uj0fq2ty3&b5t|N}dLw7GE1mk2qc*Up|}k3Igq5k)zL&)L3l$1>zs=
z2TvVR+Ms+e_C}yMD?X!>gDyGs9F|lYRoQ46O{w&_T%XKRysD|W`B5Q1UST2Bcb7v=
zPs8V+IQI+65VID@_3w39Jv^xw+;{rEuzpuk17f{)!DjqQC#V@b1Pp03v-RkYWal_I
zf>1VxY!%<vu3D$ZZb{*aI5P7bjdxid(qA2T^fo2@bI1az=I-{Yx*c0ORLTcXA~EaB
zq~<Di>R$x3=2~cDctw@%ah!X%BVJCu@WBVFi68nLzQq19v5yXDIh_ty0#CUz=nav@
z7I9ESL@+|{I95Fhy1MOKgNKwfZgok)(vBY4fU>k6Ywg{`2S2$HCr}$B4Kss`9IEC%
z38ijLhFYAa$m%IQqilzK8Xz5WEcI@YvOB*M+dV+b4H15j=4qU<so;BqwExR6vuy9T
zvvrWqYWwGoC*le^Rq_VmU)aJhys^|1w(I%wOC1ZARy1m)^d{Y0J=4*+2aFj9oZ^M@
zD}9gOB`|Ply<~QR8L27Bs&62oP>3t{!rjcZlRa^epDM|hX#?k?x&<k?wB^P=B1!_9
z|Ccwk<YK78!*25Ht%N)d<lH|+$fpYCYWhrh97!m=)fN!;8|=J(Zy>B4h(;*y`p|;%
zH$(s5-JuK;K4C=g#Ut}6Cuu`dPjKkwMySBd5>olo3~3Tes;r#%W+xuNvNAx4cnL>|
z-8guWn*Oxqa+U;Wi_FM%_!`OPE-ajb?>8EzKFsb$1PaLGL$;K_JP5qgJc6p6@Ya>Q
zGp~Qw=-S%+yrx>J9|XdJ?YTop7yo8YqHWdK_UW%J7*lB7)jTmFw-8?7V8+27hV@6p
z@D6L1?|xk#C2#S2df_2O3<&D@O#Yun9Az0MP{h@Q^v0MRYdl|B6@r3!rx0f%Z)}*;
z+1}aqPKq5BY*WeN{^kT-(C#;KBEsGKe%1o4#Sl7!txYjAa}=KuD8A~Dc<tH=bjAS!
zUd#JFWp)P>m(&B>)q6GLP@s_PzA;MEFFf1eK10dpcYPVGF|vx)eD^|AlkBJLYUvts
zqmxm*%AYKa-uJ`FYw!Xl_0{Ss(ds=XtK6>E=DUU6V#!|yFuWnEc*Et<A7Brq9StGD
zgW~aEh}FyYg700e{<6haLd>4kPfoELKEdpY!>6BY(3KEKVu)*JY|fVSTY9lH6Q`S*
zzS5z_et|U~Rd8)*htRSDoA(s)wq%u;7A42M+Oendj^8GiLHRi=s436i83J(mRwM*w
z-x1Bvui@tFnJ!-M?yeK&L)@1YAb#j_v)TPG-K#Om9ZpVZ4HES+_X&!H(2-ULZcy!u
zh=MTAStq|(1hX7(4X{os`AL4)%5{slDM`$2+xF!-Sw~xjGAjMI#SzWDMgh*QPt9&w
zS%o`X8~tyt!;EquvixeD!R802T68eMbFrP~aaqoqL!MFIWJ|$;+z9mj=4ZY-lIIWG
z&M#+m!^z&x4Jr~Or-C|%yJ}Qh@Na($=KsH(zIi>wp0U*~na)2<MVDIwf&V;`&?m%;
zVKp;POD{Q5{@cS}2k5d^2e~$Snx&f?b)Z-Z$9nI0_jusa{I^Z1S_rX`8i(64NcLCs
z3f1E!*`V4fh!WxykF0HjVss#SyI-(t?Bv%MX#2aS?9=JdF!HCDp>~1dc%<cwu;p?$
z*&D4Jq{6z77Rt#$P}ghP;A@V4pkW5|`Fw`>G2A?xmNKXLL3_caHMc*X5%Tk=1Ycs3
z3s4SdQ;;8(*#oH^n_`?8Unl4?R|PgZz9}s>{OSgA-whK}PjI_fXKT5Of1Z|}nw7)}
zU%UAd0Ld*fH%b0`Q=_*AW-{~2&iF~2TRP68)pR8=%sV}gmDe9;vVMz}n*`MVSK^I*
zvIXKkO?rc;@lMa9(lKUSC^Vkw0$sy_Uhv<!Iq`MVf<Pi4ukr!n54$edIM+mpOKW6R
zJxL=3Hv_`_*L~ewOWJi8uW41WWppfUvIn@3m9~gBVcf~?r>jo=Yq95Y59j1=%IFf<
z85U4sMw0!z#eSPdj}1ogg%8;q)AE`1a!LAgN;<xOH<Vj?N-jtqyDPXwG?QDSBsEZ)
zm|iiWKs)n!mr+V;ZXS34ZQY!UBvu<yZR7i>eZp;n#?UJi!|2J`uuUt4oSye*Fq<$m
z>4~#&{@%p^CfR-)DlAD!^<hL`r(q)o+wTWciR&d_<&IioS-1pESh+iD1@wKi9l5V2
z^)6dl>?YCu>qL^Sqd{k6UTXalN5=0XgItZ7(F`SQ4MbK@cBO!(p<$V1g~6CLR;{y5
zI(zfaq{XOjd3j#D{~vszM=uN;3@t)8GmUlJ>bOM!3AKp1_ft@5HkbCx-}_i3Fr+RB
z3}8ap8ojH*IF-P5zZ?QP35Xv0oLN#bH?7A(nOC;1NN6cDJU9W_h(PqjflcY+_Pt?A
zp#`z>?wuxhaNmc&5Zm8>v9iMaml|6gIMq$|SvYv(C1sb!J3W`(&e^VhKRs(c7~9p7
zhK>RDlegE*nQcmr+ToW=&<h`I*g%eJR9=J6Yfl5beOx<5_3SiWN|s(m2AVKDv;EW0
z!Hb27`4Ch!M@9fnfRv|pHWP)Z9`lWU-MCC6Z?Z-}P}ihxl;l5>ii<)>DplnVb*}hK
zYoO`Urz&o61+(V_jzSM|w=o7xS%b2+bDtxPBkMrOT3hN*uy<KC87N&(R5dQW4)x4p
zDUht^2&s7Z1T{0Va#D4yZ5?yR$%WH8p#p)gPnX?}ygnH$dzNB)c>SJUe;&&%?XX$l
z&#NLv!XwXEzN45#f^l=aX3v!O?SL}v*t(aim_An?H;QEgE%(BGpYSunx_V@vB5aGr
z1vp_N57V1mt`tTHgvH{z4O|gF6O%aKd0rws%*KxKualUVU0pc9JUkb!4aUGm{UWr>
z%Y+u%Apl!*uvZnhJp^}~J{E-1unw9&pBQ4ZCH{Sp=IzHOS10-z`}dX3E4~`H@`|>G
zxjk#G4uIARZ(-vY(&sVGomC7VaaAe|4U&6cCYYcJ5+uQ30*t6YTd^ZGLsdIn9Yqy{
z5%lT+1`f3wa|>0{bN$e%_x8M}m}i9u>AkKJ?WE9Uf1vKXKnSXrYp|jT1FZAd!Q6Cp
z@WFLqSj5gV^33v_qCR)y0!2V=GHh5-|6er*024r%pZDYo@N4>J^$5!(KzecQbUx%I
z@m>cU)S%_ko1EN!jP)-X-^XM&jX*?>rbgAWa;a-xT<-W5DeB$Z?Dg4iYJ^>-FBMBf
zfi0BQU3Kfod(Gr=bxZTc-U9KBEn8ystd6e5@#q-i$jf(zmVHuE%vRVkIQ7NU!g_GY
zX_EK-q`~z<d~!{69S~Y8bGC`M_}tGHvID4F?RhdYHUR6fDLN<SEOKaFbM@6GuJT#<
z1=nsz9$Uc^@V|)Hx`negjHRi|tfsQ3txu|Q17shIx24M?x#ebZ>)PHTVCbC+rI}}_
z+dsf`l^E<mh>Y1xD-p}wPc}?lFJE@ovgcF3)=*Yq_C4u}H9qgb!}ly3aGc*@PbeFA
zu=xm!q(|MZ986XrkjF<`OWHel_7L;CHZ|Yq1k^ysY8@FunaAT>nG`xsD4~p^){0sM
z9D}~ozUWsZ!S!8dA5hfhJ0&j(d=9(OdCKsT({nd@h~Rp6LIh9t8NYyznj^TuD7ubS
zt}F8Xx1d((k7!nh#`hlUPp~AglZG~_Sf`QUaci1;+(0n4YL{N$`uob>Us}M)|BK-=
z_wjs8(&p)(O%^+F((vc^yD;@kB+efunAdW44_~a(pS^7w&Ymhy&+zA-5fN0+&DwFx
z?cB7n>ivCXexv}6T1~nlBm0+-6>#0vO}wXt)k;OsZJkqfEN##9@AvO=rFT&9*pcC9
zQUBHg6{STEX&QtlZ}p^?r7H&c&7xujv*rai(5O+tim6!Y#-6@VpYmee(8b&wagb#B
z(U0aC<WC~v^hS)LQD<5KlNT?__MCR7J2Pgwpo+w@kjk&rsMkKdjtyO{j>%<2A+#Sp
zS}?TdP-hi!`BN`P9(IuTY%v|pZ(d8rYw9P-`3_oHD**5s3XZJ-3CakDpz7MS+D3N2
zAhHBC%m`FSFmO2%9-KRbRfuFxnu5mn1wMWg_4=kqxaksQc&M;aLjkKhZ1U}$q{3m1
zSk9BlM){^BlghZ<$(rtOJ&}viB_){eMkcyxGpXrc^e8Nn3!|XqzE7aWh>^>kePT$w
za{W|v;G3DC{8(=Bdv;T1Qzc`0azPth&9`7sOXKGJ)#RUWaGQI2XxxM^PoHZALREzY
zB8Fc^1weAXxrd7DXQ6Ay=hpE%j*r<Cb^vI6Y1~UfTF(;oc6<$D+B8`JA0Xf1+t26z
zX>l3U=xr3Ax;J#PSIl-cc^00QS#DIwwMt{+jul1}crFs0X;X&X#fc{iuKWx+6ssA&
z(teGP>pJr758=SWE8k{k?=%%OI#&n$lh_M_gga4>j9?Z8HRo8nVM-%DO#{YMIea95
zCOKNArY;aJ)j1hO6%u#id|s}yz?>$2ku*e*u~Rudf=I9+&4M-&G1wDSh9SFg{`dA)
z4&_oVwSQeev*={D^BfU{ja*uupK=b$^U9S_217!EP?}3YT0<R8cI6*+)`_D>{QKw2
zvY*u!!k4Nv5IrmY+F4tBn|0h~*GOrJ*RjTW-<7%J`zoSYRX7J@ju~-aI-v<ioadr^
zr8HAQn14{bZ9i*&&0V^4O|;9B=kmEe5hbA_;Kv}orCic&?z@Xr3ThTcKb(nTLuFfk
ztA-J~qX<Le4rgXH#z)qQi<aH`0f9MmeDOPq9O2cS$~M#nWdg}zP>m7IxX)@fn_(o=
ztP!&OaLIyc)>=Qg5m*)Lb#pGlJ&B<D?LK#i2L=e0$KNZvkuR-#q*NKKdwPBo45t;Y
zp*($P9_r4QR#YVK3a-w13jeyD9u`fEp(_KWUxhF$mrpr@d|gIFzZEg+zP6eEtdrxX
zj)!-uhFNbOO927hzYS-he<~^ftVd7s5?V5x%Mqt%vTTriIBX6UntJ}h?xK*WO6^6`
z@N-F9yI(sPhY6kX@HeuW$q>`zGJHxQ2`D~tm{vePB;M7a!Dyw7_ebro(b@62_t;4E
z&^-9S?<yUzPnEsLX|HonEgAFa^C5Ep<kK?H)BQ}Xt;SH#*XUIlB$eNpG52;w>iS4C
zVEv232NRCFFKZV<^)<x*OYs|H=Rhx6<*vBk&gYW1)o*j{Myn3%EdjIip{Y~)WTi{|
zKT%3)OrC!fvJ9N-R%51qgq$)%;9XkNLGut$^a5yb+MKBgPe!8ky-Bm12W*_1cj7Kj
z77ULY5mbD9eZ{2VH@N>s3^MNLaW33A_-jer-&lxJwY_{d_&$^G<3xiPT{v)g^{cu9
zF*D4TBa!tuwP(b!nM*=`97ooFwazh;pFiQ|vEQZ<s<kmJGS6W=Kw4>nnLH$#mddjc
zTTr-z&r2aDD;KhsRJN7nqbTS!*=yhUesv?%g6C$Z)`Sq4B(y#eeDQ+7)6Nr7%ICC6
z?MP0<aY6Tp$GxSZ&9TKPtF`DYmyGUKiRxKex#ICh?`KjP-E(!R*+&&Z+h+?KWQ|MH
z2Hw*>FTC0XHise!zR(>QqPjYXenx7c`o6I8a1e>88!b%3lF#N;ueRZqJ$N=LWHz9#
zkRoB|yf{N6-vqOml@coJi2ocgDG{}ozA3QrC|%K>mrR!{GNVB_!XklxVrUjwvY@nR
zSAOj4e&gz1A#&%&O@M^-)SAh_;urE4i^A#QXzO7E+x)@EIc<!WiJzw=RT=PQBom~i
z<>@i#4x1$6Hl*Jy-aNYKO2DN-C`0KPi``di<?y>aJKH0_zXFy(fZo{~KM+<_qk=+|
z<bfxhWCpAu_n*iGg}S6<a1xzr&g}5F1?Imw6wbYaL9q|TBAYv_YnoYIcfM%d(Gg#s
zwKR&V8l1p?r=-c8bSo7e+Q4k;44TvrRu{wqq1RK}FX}4mMPK;L098KW9zzgp05p;U
z&qlDcY(6KmZGeTMCu~z|yZw9%y6x(Jet#g37h#11p5-fa%*qM~a~3DA;(EF{F{~3e
zWQnG*-W!K@g>ro>jR^~ldYvo0zWdQgry40#7^+E--;W$dau&0d&h3nz|IW-H$|HiI
z33DzWz_VTSh46~RzbWpY{)<%9%6eCbpTBJ<nY27pKQG$7kt4wq)cHUizrW*F`fJ7&
zit=-w<QWh^*(B?y3Af38e+h74&-^3LSBN5De{S*?<8R+{{q+yoil3(f>Yk9Z$NfOe
z<ToX(ou2>XJ-x)8Df|GI@z=kF7AfoI0R&OwI0t*+>ZYcq43zF&F-}hArwP}>W*J)-
zJIHz&N$qj!&RSyU9!9<B;WxCtTZ3o!v#S>Gh)No(es$}Y&wH$j(k(44F1I`$zkF3g
z_5meNz)EG+|1q`T)p6i0M!{QkXF+B=4Vj%*r{E`V{9kwVz8}Lht#tPnXvd<vZ4Rem
z3}EFw>k}MNy`&38Xt}=C0$L>O!}_ls9FlR;_*$#eI?0eQJU{#MNm;`|gYDySSG%KR
z{i385GJV0okRMx%P;4Y{^pF^HaacJ~_N?(PS>Rpg4J0ha1V<}j?DaoscESG*)~3;N
z!>@N}8s-3pL=V~oX<5w*9bYy`5OlEh<nn9OK4X~CZ9;g%TMQNY7)e<<^}HT*v-c*U
zpZF{`n*!EQoL>fW%-;QG2t)WbxR@2m5e768VI)TPDgRLZAfuiX2>N!I;^G7+FM+N)
zhYK$n9V*={qFI#HD@GhG8}`<Vfb~sv9LUxneVY)03MFaJ)eh!?=#m9_kDElRwq{}<
z=`0=EFU}t`J8Rc%83?RBSYp+7^HS_gFfc(iADk`@xs;Xj&sYOB7PdTo-?qH}4H%Bs
zl`s!b=R+I%deKc5j5+n`%Pl>1$l41PxeCn5S>rxXU0y0tbvcZgw)S$w_W`?yPyPMP
zH-&J;caup&gte14N2w#NPCMc&6Vt#7h&17-N@%;n1k+sj4n;^&#zahWU9G6U=u;s4
zGq~yk#Rj|M>RcSgfkc)rx6K2=kxKO$PUdK*YuH^lFMCXFey^F<L~h*Op=<NXe`+5*
z?dsFYDE}j<UizND>S`e)9rO>VUqV<Iwtfr1m@S12$&FCNZdF&|4~^8Q2s06UpJyoX
zd%qo!E-&8955Ljwet$(yN21DLWqG$*wf3l-fVNAAkpi3s^SnOhnU(%S!k?+fFq>km
z%k7&mgwk%L^|hXKzi6gbl&)J~=x#vk2)S%+cQ_Kl!Pf#MCQCfuKBoj7&`!H$P*Z^1
zand(#`MtrH&S!PEwOb$%x~B$5rhu8mbkRYTZl*Sw&9my@C*Yy}`CYiqg(_J&2=L)Z
z;#ow`efxQuuus*Vi1kvb)Dg0Ctel#xDjZRN+%MhR9KBN>nwBhxyMEsC{oVR|sT}33
z#mQN{7m2))+kWY#L8|+>li4f}Br2q6r}<^}r5Rs;cwOAn_TyYl;eScC_6ziiN#0-C
z&<!d*?(f8}@pw5s|F@YfOhhw%S*=1+i~rKsKw4HqP`m8J$H-{OQ+Fi$V47-)ij{%E
z1S|E=7pn3l!#T=TnY;2T7w(QFA(sq5_I&6iqVjkwhMWw|tiAE?9eNk;TKxx0>A;5^
z42b~;m|~WUqS{9?Px@2(27XyQp0Rt!M&#s(nPNwAu-GKZclO6AN1;%h<2^z0^Ln=x
zc!s6n*wj$tDrBAtnugN<bcdh|hEr$tkI^NPJeQ<ZIQ;zlD-`#WV>z9DFa%a1N+sUN
z`b^&cOBp0;0mHLk-^CS8jmI&--6w?TD<rp-NFG0_Y@ONUC=8I#m7|nDI2`y_{#+s?
zRDZ;vAcEp2v2DOrHb%Md<&CR9wmNzNQ7T|I4i4=_gebc>QxBe|uaxQe!aJS6y&e{+
z)zs|oSwo>oAd9$D6|=~Jh*fg<gA>6W(RP3LafyzsD;FptVq2b*q^pjrKQ8j?t)44h
zwCb5fg;S#{n#FPiq_<#6#z>o1A)oHH<<zi+fIOPaQAKsvny-L63B~Sg!VrmS-ip}`
z1!v5Mt3}sArS(9m^;FU_1W>sZclgB7*_=p3y2Yj=vd_abNy6;{6D`EUu=h&S?hI<R
z*Lr0lvF@szu@*Q>Pa-2jNF`Ewu=WNyA7xAapePt^!E<Z?_^HXe&;DoP7H1ZeZV#7h
zI>CJ-d)KAQFwPnJ_JpH?iO~T;wqf4HKRU!O$`cWS+U|D-taPYJUplQ{&!Rc@k+KLI
z%@`7olL*Q8?U_G_iW@Yf#)*VWsuZV9PFA3@zNMYi2_ksu@Zp>-vH1X376{95WjKMJ
z>USNhN<aJ!gW0EIEUKVbcrDHY^*j+RD{83IVFjtfVt{}GQX-{OMni`?=<2R)%g$ED
zy02@arDK4&AMiru>1kcRCq-LIawVzddtaJU9f9*vF*&vd<kU!#Dzt)z#z*2*Q2G*c
zl(1Y|;?=Kmd-uS%s<cw|amGp4)<t_7<(zD=m{eV~<3#eN0)<|oz75a=?&@SrHB<yp
z^0h!3%~|>4^QJdI3^35h!`U_Ch^g+?_!*K3uKBIX(AXv+eUx#)rH7xpfSp$~DHUvF
z2a)TYuVRQxGKuh~P;rH^t`3MKHarYnN%2<p(5oClK14%WkytJlJ3WL02Di$6LW>Xv
ziA=03U~}VvuLbwr3T0>JvGj0OLL&Wt(!L-&0rDGmbhI37rqfValWyUsa$%6{a90#J
zS9aluSOao)bhu{~w02=w42~2NQ3^wd9h=wy`D%pde|`4;N$&`ngQIHwo`lr$n%u8g
zJ^p<h?@t0bl|9#fTXg85b3foCStVR$RI9->tdYaDD4(!p&nfKEaKE$QG8M2)xW@C8
zfPA#W0+yPe0QuxdrIyWQ;b!dm{D!QVGHN8tTk=d6)qYVAx8AMfblKg877H1|QG#Tk
z#>%5(!z08=Dqc@66Y;strTW_F?H%}c32SL<b?jNXpA-ghie%fw&C>m*rl6QQ%@tB?
z3o;Vp5F78>T9l|fHpEgWC?^8>s_7^kczCHDaZ_nw_gRtdKHUfeRu_R1mVlacfAR^=
z_Y@=}?S;!`4nlcsw<5l-z<#8DoZ8g0;&=IZT<Jqq^GB67SX7=F!eIY6-^k(DLYB#q
ztN5_-SsEk`fNKVqMjyFFBH6I!8Ydfvu=vWWY+Wq`5RIXd1Pq&1Chs<wuC>p~-;Y)r
z$LA@m$Z7Lm`|94&ETss^NsQk7sOtVM5wKxMrUXysL2uL(Zku9Kc3=^&FmqROZ4Fvj
zi#lxV37a%rI2^m8pqI$YB5l;kSabIAUrO=B(VZ0!xsfo7uOV~2E*Tnd79nHD5J=86
zP#IAj8<diAr~R~O`^w>aO`m?Le*VS_2g%H^1Vc{kjc=!HEgbGa^)YgdTVd4)=Qk^x
zE{m409ISpD%#qN0i^zm(Rdwp*clz4jzm5BaA;a6GtROFc<Msd3r?3QV6w4-qZHN6x
zKqNIP<g~3XJQ|fWtg%K>2-b#`+w=J~FkGS9ca=L7U_N?Tlpu{G70+ynnIam_5eB@;
z(xBoE%?DgRVx@ZpU^vKrA8FqDXdX#v;T92adA93{i06$`M02b0$bg}~;<MnWnoPdI
zZWP#$JyWQ}x=Pq(g-ieWeLd^c!wLKGw1FCRT`Apz`L6dYWHoR7@w?T)KON<_AwH=d
zCYTYvAWqT9&}4E60kcU2BH1JriR2j7Nfz$9Cyr}-qO^lPBme+e&?DhYim7dhx!76@
z6+vL3B@wcklwdS|wSef$kAR?>yf099?Jz=<LrqN$_CZ;K<U1%SldqRt@C+xgq;e29
zKXP)Vy;8pl6crtkc90(URXe)0Sr9pAj2}6!kgi%6dXiN{{e`)x5Z>5xaVSUQy|mJC
z$$~uD8mA81vQ#8N4)T+e?rivO!Wb!%0^znw=r;7oiB8iu%E~umwqoQIe)apy%YqSV
zd-pmKW%UslvXD52)-Pe5UE5<H&%m&R?6R#`X?uAI>1A2p)QqG3xj)Uo6v-Mq)KTYW
zgDEnmL#yVm1+@~d=2#~#L^PHiL^R(%%Ll)rnS<Hy)uC=1V~J&BTYtQ|kMMfMh$qC3
zl~L;x>Hh|8L3(eY|0w*B9Ab7<_lYMx^jiG%^OIOmd?X$jAs)ex*vJ^_i?N;LU7Te^
z`^*78`0X6;;BiMd0$njrzU`x1;m9()$u9=x2IDoNfbpEE`k|945Tvn`!~LUYh3bFW
z>%~b|D5zsB?xzj6G(tYDA4}w#;-q32fSSl#c*pfyKQ7R)_7fKtWnI7NJ$=+mE@p%F
zlioj)ji_>56y%85%1y&^lCsxMdhC2UBQG|mhgiaZ>=oSpA@SK7AWHg<pK;Ae^CT!I
zYk*4Mw&m<D8VN@W8|~12p9s5`nY7zmMFklNAG)5^(@q_R<<bHyfH6))x9;U`<_&Fx
zGJ>4Y==~?Ve<;t*uphssT^!j8S2S}%Y5rTN7%?_qUQH(Vr>5Fao9(JT_yt7K%&}2~
z^Fi?&N3g@->5s0v1NG)ApX9$6$#(YH0$piZ-7mbK`3(f8tA`cKzxxw?gq8%#VJ5Gg
z>U)ewrk<8To$Ag!=(43<Y<N2Fqd32>g8B$8I&G{hrG>MGIue?$N^gmflWAy|bzn|P
z8@f)}Rn1L@u=v*ZO<es{K<xGyNsOX_{rT^wRoyl|v$aFMUbmRAjpDSy$=W}2tCv}Q
zncsD#UuR_<VlG<NN!ec3+=Tyn3v?_kzV~kjlVncAhEpb2K=9tDZd`GgL{^(sBz*_+
zYferpjo_&IJukBdT;HQ<qHBc%fiqJQ@fRdWuM+F`Li}IrjrQ!!1CWL}lWB}w|3A&_
z9?H*KLhh&!!z5pEA{Vi(G(T1Sx7XTFgN0C;Byj6dEoC(!)OYre-rny~9Q!4jIrNTd
zq$SnM!V-O>)V*+k2B6!DaUT{BIezMXL`-cySiKh8JD{9fXv?tCE=?>XtZdMW1zi_F
z7J-uR!kc`=%%WtdD49i2%BU(fPXrODGxG=BzcT%%Iy&<&Vu`EjrW~Dh^sbj85=RYP
zy{_=2q$F^_Sh`z&cC_$uYl~l_r@b=&%|y81qZv?vaaZvID@D0?+P)tYwcM9cE+{1Q
zPy<EZnL@vm7Uzh5k#d-juv+qjdN~{NGiTZXCUGp@MNNHk{UlUM=5^0WotH~`pNC&j
z-)hFyEJe7_lBvmeDVlO_QFYqHNoZUF9i~8pk;bj)N0`g<9RdQLX+m*^;Mj%+W-J<=
zQ=SbmFkj+tuxY<uei|5N=vetd@P~T)xB_`kE%Y^ZFzRdBKagUQVh@<x#FqUm8})PC
zpu9t2S!4+V8dbwrs;hgk1--qb#So~PQdn_c<RhQ<yG$x;-8HL=So7S|jfhe%I>H-J
zod8H!p9j7hO3rD4e_dE5yX5-emrxuJULhg}s?MXw8gPd??V6>vQ%o}$gBbL(Aa^ah
zRrd=IF{B(~3(wD$pE=qE9F^*>N;;$%&7kX-QA))cgL0K)65<CltKu=|I@a}Zef(xj
z^;8dkS*}lv%OpO>682Taj{}y(g>J-THY@&5?|1eFT$BVaAJ~b1v-Fv2mH|Hs9{a%Y
zY1`v^Mfa(4g0y3O5G|D#9V8SXu+*<?-sR1Wp|qL#+5x(hJHBR!FnS~E=kHNvz4%<W
z*)Vyf7|0d|z7~0+eS=TP!84%ReSj8KvY{1*Ne}<#_#9XSR`<(Tl2RmPHID<Hh=-V8
ze(!W4>A|peO<Pap{?#ebvt|-3Lg6@55KzXrR8;$x{zW_L2o}g+5tN@SGZzDTVX~XI
zG~b)MCMRuPy|VdDI*nxb6@m(42d0$Z?&AReNYk*D<WWfvYYS#(5H5B1qgBAdzo(v8
zC%B5~4`q%5n@(<eud!vXeO~8|_Hd|q{X4Lg!yyU%=746p9E=h4LVHeBQT3b3@M^sn
zbruBI2OIY*PTBvX>8!(|3b!sU3X;;&-QAti49(Cf-QA6Jcek{3N_P!i(%qnRr|=!`
zz29FxKF{dD%sKDbd+oJ;`<T5^yiE^LOd}Uhgf-UqW0$)}{LGI}0c8ZItpiHQ<awq0
z-Zui~Uu&@_)R0Rmm1bRw%%zpkp`n1YV;B!+@cZFv<*J^X)?hrQ3n;(b6te0vEvO*E
z`QtaQl^3$<o&kqR3cMgBS=qpH+GPFe4ru_0xRX&;F|4r|;CK`oq?*7D$B~OeS5Eh@
zyPiBK50}s97no+SMa|t1m@=XjegcVLQI>llGb7x?M-ndnJ9Fx6QdnY_++e*GE`2uv
zPkScN5jkK&K)el9BkANbvj_qUr%brOPo#>Zm0xKZ4}Ce(^!lIXBJ#hqe)G_P)B48s
zoe*Oc6hT{nvq{;D>{lz>qw*Q+k7<3I+m=fvnX_5R5MTiK`Satu)MH2ADv?E}aLG;t
z;*jcn2UpXqZ6=5bW#0Cj+~-?VDfP)Y9(Cq(G?%BQelGxqQH89NGmx)2j01S+_vAjE
zeuEu%S^z}bJ_&QevFp~>nF3>8xlq!HE>5=+`IM`1Rm3>gLWYx<&BGi0_S7k|aRiI@
z(V#+}p-=AtKTdc-x^dFJqT?qFbv(k?t@iVa$r!cNX8r+3vKAm!;(vk2e7$pNsUW9D
z^yuM_3H`<I3+aX5wX*o{46iN4N1JU=C~kZEUsj(i+(TX3xCR494%FlL$K=}tvmRU7
z3jQ@f_*sM>Kcv}B^|7eB=<Scre-c+V@G2kPGYJTJMEGeHdmF<<tglU;_KOwi_Lcq`
z9`zp_5*`@~6XtsXKIVB+$7?MnW=??_2?5U3jRn$&yz0XfXPT&gR184!`22SnVK*Ko
z;V_aNT3NjR^g7Jl4<Lf@Ce%1~u?)8MVcO3rf|a7hU|p=dQbB^kD~s+klp!H<A^3l7
zn{s+-e0h7L-fN%5+t>IE$MkYF!^-2GeIt=sd+P5ILx;{LS=xpBv=jcRRCay1A)Yo4
zW*n$)4OSQo!iaPxHz>}k&ucks9Dg>0kY0XO2rpgxjZ2GD9EjTmvLHlAp#6*2(yEFa
z49#J^*&Tm;v-)kTuzyT2wcybz07<ig{P?Yfx&0gU>Yral$nt+4;(YVgHBEa%@7KS=
zJ}5v4M^@+5S1<)h&8#UAGKcKO@gs5o@D~70cPz0YuoBkEcR@!Gun~_h$_&p2MKR3K
z$eFhDn{=*2uFr)W)SRfOspx-P^>UYn0&^|X`;K!DD7~@bW&Bv#lqlRFFV?i^>~r*Q
zZm;bB%un^YS_v0{@sjS+<_5or`GS=N+>DZ)KBfQx$TM+i8OXkOpsmf~rpno0EeU*H
z%nHw>jp=-Tnf<$<a3EMkF1u4oM<eMtu)3(x+R-sMSS-Kd%a4X3kzjnwR+F2#e{urE
zTZ+byliUoY11}!PN_tA`&wzDW&?3V_W@)<WhjS4ip%)7n>0n6^x-w?OL={ndHZir8
zXL(9Gim*0d4fbLFqDJ{%*u=O&tj;2F!eXs0=LSKbNl9Wc51AG1oAPidF`-W^Hc=nv
z3ybu<u668tVI;@EzwqZ|@7ov(!)Mt&?Eo^{vRuN~Oo6dz<)VEp7s0Gp^XtMYeBh+P
zVl(Yx^~94;MmZ`R4j|?9rpLSMdQ&%!SPi1WZnsWWO<J@DcD)xtYQuZFSKE3=Yh!3m
z(t>tp#!*%m6G_fM78{O&9|6j8n1Dtma9(9h5%_ghS>c)}<3$w}kSNVJyzK00VKt~V
zWeX8b^~JsS>+lUytC(oi+S4eRDwJi5Oc&Ay<T#%$=_xOuKAA%DUERNvL>#+>D?AE-
z4$Q$HO_2;Mp6CoLpg_RM?7M-$MMg5zX)-I1WDF-J7YPi3(nq~2rcNig*i+soJ{TBD
z5I}%BztFsH9=CR#Fm@B;o73dhlF6fz2%w`|g`DK}U@fBjMkWMWo(&d9EG)U42qUb^
z_}Sl;`O3^@2^46Xmln5-fGUx@e+Hig008NDuj?j4>M2M;?J$ElW48`L5PE!ntZ7VK
zsB{_=OTa7s9VeI++uj~LVhRYWzvErDVfRIXh}<wFXLx2FcXB4`5H(PHrZIsd<pJ1F
z<K$B>x4^SB_*{e*C#odS_Xs>y5rAal`jJYN39nz}&}~-M0BcKb90mN3^6>+8Zun18
z+b_$OF7gLg^R5Ln@b7=AW{|)wubefo9Bv<q+A-UzR2+D|_A#{G-K;G@zF~*%#@Bj-
z)*w4V34a_Di0dW#g0`e)ez<to3{b*-m%U0rOwWVnUknEoe$kt9?&6XEMR*Z3VeK=m
zk6%hF{55lXepH~q=;XOtbVpffV&iXp(n^OnFMr3cw*J9Myezl4kP&vDD!<4<8yGRL
zl6VBr(cI^Js4?Ux`|1;Zt-5rZ(RrMNl$gt`;K(IBf{#Isvd&yja)uE;rX9-tr_`g1
zLk!aJxG|(weZ%G1{Id`CRLzW?vP+jgG(6)!)9^h0*#`Z8Rcb!~_5{LYKyJ_R@3%#T
zi46^&%fNV`n+QU&zuc&D?Xx(f!UiTXJnVXf$((mL&8smCk${QE+|0^ne@(z%PX{-w
z4e;OFrsC`U$H*%uclvq;L^h7Jnfx!-n_JsfTG|OfCI#{P0Q)a3R<V$Hws3L|6L9`J
zmBf||1K7Cf+oeCqnszQj@Apl3A(v&N`JFiQynwY>O;rmIvB<rN??<9|Ej^5PdA9ML
zqiik=jfsoX(E4l>OC;cVGHej+x%{B2<z*EJ%7q5POjT)$$`j@-oy#8+^|OgLmcJxI
z*N2YcAI7mNk8hYOgzY|&>Z8Wb%)@S^5wERm<>1r5{MOM}I{O4U&gABN)#$$b4E!Rz
zf+~WlTdx$-Aw9`cfH@|9?2nDz?Qa(wFW)ep*j7JZM2Q4caVRJ#HMMEg4EjYbbkdnm
zOLjN7NCc{CK&l#`RRP6t^~O@sJb=|p*q_HjbpE`jc-h>Rh2zkNdj3vC866rE<VDtP
zt(G`#l0jbSF$DjCVRLg)3>cRnX?aq?40_Yje8kn-y+3e%8NGqw>l*aG?9Hp+zj=H;
zaP3mkGhx+PW|!~(t)g_}+rEq}V26@995@`DyNRLhRM<UHKEJ(KGIed`n!q0N)Z()o
zC&rg6-%of#&zvS@Ib(?FXuh;^=o7P(&RHQlhJWU%_YNqNbxY*NaA)UjM^_*rcLc8r
z>NBh+DVw?eX#5vPkH~KivtR2^ksf*vT=i)t9J+XXk8b|c^GN*fIYSz0+(ELpqWu9-
ziWv?8-m{k2`k{KXBy!8?Sv(+1R7^0P_O3UAlu?2DgI$B(uaaF3HJAdoHGB8PCufX)
z)uYhtAtyhG#?A9>fzNrK%=ssomYziF9XBgV9~|Ub%l=-={uW@@6x5C7{GewuKcq^h
zI}}z=2S~IMsl(BtYP!NbZvSWq`McX^!DTpr?cMX}Ll(dRx;}Uiq4~J-A?h|(1``4&
zN>*a#5;IQvmy(zuz-WlXej`Vb0HUct7Obyl3xxY9Dy)f*Z+tLeH+}_@z>TX#0h0p2
zaS60wPf)SgwKHeeuT`$2T1mP4N)zVOs<`s0NpstJtC`S95}+Sr(hTl@zvb>zoh{QG
z0O9@U=irV9k>P_M%tv9eSsc$;O~>T#*i!@==8X~$bVmv4>`Da$#T|VNejASd3Sy9*
zqrMU^6sdX=Co)pPgjY*JqlEf37f*raI(N?%ZB$Yk2?8}T<XZxW_N1}jBc7z8Wh3t&
zvjeJW!}w-}Ke>(SpEpZNbq*;O=$*HqTtE>Vq<XJJ?1aafV+^4Ifc@E22_z6H)li&R
z0Z$(_Rd~PesnNT(+=<j*=IdvPDV#1KL!1^HK0);=WMHxO?A=D#NpNm(;a@6}tq>^n
zbm-j14$=)M)2m1tR_jzC*gS6-Cf^<w{*AO^DPL;r=aSpgjjy}F#N^M00#lycs@Y41
zg%jjs^|Z=@e9(xo1FD3FGMJGx0^OAJcNi{&m2iqGT&#~rK_(LhUS9Q!0zoDyUQU{2
zCGJ0$7We-ytzG8L&LIFc`Yr%FR^HJtUx<l*9Y_GBHn+dr0I8)3MIocA`N2!{I(ZV>
z-oHbL)I97u-rr4g^D5X?XfKk+##(@#*-kioL`}!nim!W89Zp7}U;R%R4iBkmOrm|K
zh++?&&D;C)UT)BVAoKno8RKkqMuhjkxT^atCM~_{^LaZ{0SSxpFq_u+4AByY7uKRi
z^KUJt4H^ftf_TIH-0))9y4}$=J-*Jhqgi(WAR&T9DJP$w%t>QLRAbpi)3aj|VfI%2
z4ex{4;y)GF|3c&Z;@<z#6tFW6Z<NAna>(fW+(AnKKerer43Mgby|=HbTakMzX0&w$
zoa+wOg%fpN5nsJek$$DTPbwyeY`lMt0(mLAF@{wskPX>2J_8~#j9Th&2H)H7bAOE8
zc=T67z@D4e=^H})Rez_-8pO;UFd%Uo#hkkrgBYcoUK2NXnOvGhf`D?WmUiW0aD-6P
z(fCD<O!Wjy%jg@=2EPZ(lly%JQ*07;Zc0NQ9pTy(OQi7&4WCkxmu}+wwZfbl054b2
zICYByaRe_A66-Gf<=B-%J8#ygeUCzopgEj8GQt;HRC{`-)zI!DkX2yCl7Be8-?^9!
zoT2PCGnWiq&5kL6nq%28JiqY~oBz0DUU#SYP=8N$e$ZqyhUUk|&?1M{_TFUWJ&&eH
z!Y77LSuZnJ-nzf-sLH19EA1s0JdAfJHrHGF6r1d?z@DkQt#pujwbW4gGbA0KIX&t~
zW2ey#@6=z9AZX~<8tk{gPwi3?6At+t6UoXXAHB#8IiktyBPSP+OXE?)!&~R{3Xgf0
z5~doJzZYeuC(1yY0WE+d8_Ew8{HwtvS+SH+`k$w)6!hO-{T42e<!ql@ZSuPJ)U_?O
zKkw~@?p*h4el~a60o#wrU^38BZrte;z`V9`hqZD2=$)8@O+EH68*NiBM|p2B5*^8q
zz|HCREPL4EVV-2)?TR~v0#^v^S~ytGvbJ##0|XqlHW|`FYLw`}FPm-<yAB{Oq`rwK
z{0;6sFpzw2Zbq&7BW?K43gqK=xWF$25Y=m3AT*bz(PRn4q^2N<?*Y%0nn|Qqk_=Oj
zL%6X-!Wlwnm2&wtK*2M&z>q|PQ891JRt#Q&V4kD9>j#)k88vBt2mEcOyQcvYVY2uy
zi~g_dGFm}aLP2D*|H8nr*&cr1PAOOKQk<{H)uXc0%h$}yBEpZKpeDLPh{XY*A8{~{
z0z8j<{Ui!BeY#)m&$9e}F7NXTcS|lPDVxBnDZGa^p?$Om$&B71;1Y_duyEcgNgYiJ
zWz(2FuGi>(QK4weI%cqKhL}FMH?0C18h(xt5M!ECMN-3U=L%wR99q#wH`{#>TF;L<
zedKr+vwA%7eI^)k9G|`fTu=aw*uHk=&$@5ip2%Amw!NdPE8r#ev4N<t7G77><mLlJ
zYkCtRYkk_VU8#}FoG0U4{h`Ady}s?U#id(q0X&{%L0bW**z>GSmB@D%JH7io`~~I2
z62LFz5*z^1$Jq(lPDtSw154Ttk9NKKI3l^BZiP+deuo2vk2L){44T9fj;{H@QeN{8
zN}pk>KEBMMi$y|&^-hi+?mc$ouf5MX{QX!OUig{;ai3eh^(_7=eE_>AV9T(3dolZU
z`bAn6_9)^tKb#GjZdk2JCQxuFn+d5%Vo`*4ML8)F%ZY(KirL}_y}pdEPEh)7Xb;6>
zUX{l((Z0;iX*Hb)al^(40z1+efI0GWR86hveap(~o|Qd@bSyte`h8$7^Q02^egh*i
zP<pEQQOntKEy?>{h%cc+dA>oHMovZP{_H;%o~aN29fHjPb1oKE9r~-a7Yg9%4fKux
zOac`KAkt^h?a!#;$|oExGXbj{k3QWee+NupCBwk8vcthAQk(R;M+Bpuf(!wHIWJu#
zmBP=>HRG;l$VqCaIIA+Lj22*|FbX4xqd{x`B?XK`4QHu46n%NY)uXza>3gjqeEZp+
zKMF7OuW)m~L+?m`GxE9!yu$<ysD1`+h&yAM6iSdBfo*7LSs9Ru>pB%hM~^8PRYk}U
zL>`i&L<^SxGsplK&HYe!9(s8gSDk#D+JOuaa8f5fm)A#QLqCWByGM|0P(YY~KaNFp
zKLDT%`}$cIhU~($kfTkah!Jr2ASUJp0fY{noZhbAS-w#KeLRtqLshF!=`%1{srn=@
z0`QB~%u2xD6S)C~L!4SrKu7-N?4_lhedCdi9oXvR5r~}w`8A>?25vs`=I?+RFJ2r?
z8Py@^8%el>TXEodPV?)RP7FO^$0dEe<&}F90*Hfer|0*cCmJ9QBH(Wm8C_ixxPvhe
zM+U5Nl2!wtAbkOb8224_Bzc~HaBo2Z3?!6PR7+@>#f8VuIO5v@lnrq~WHJ_s9aFe?
zXuF|MBA9~CXPzSO<P!mlQVD<2ze$*|<L?nXnE5UIq*C6DEQ48|mbj~EEnvI`w5^;K
zWA*cr7^Z)`au>@Hv&R)#l4zj{zwjANV*bHN?DIbTyikQq?DZisazw6Vpv>o!1Zu4)
zGkp8<PdSO?^r__K@p+3@->zoQm|S}daaME0q;b>H4$VwcknPM}rJ!gNEj>-aFm`#=
z+L7&LX$A4DOBm976vG=oWloQ3o*25bzqy>OxT?0TVk@~JgdRY!4xLS2KaXcJLN|uC
z;hW2V;g^3^!PNWzzdB{ffH0WP_6<Sz>k4jtXy0J*040tjh`Dv&%-n~a7y>HTBm&qw
zH0GcDuA>eg`hI)r^YSKf*!jajLmgNRDx*6`2tWR&^z$=L!9Sj;8yk1>wV5jAcUhv9
zlU*>csnwdy>Ts}${Ob3}!AzW2lFd$3F7nrfSIXNUh5*C;(AJ8s)Qk>u{5g#_DzHbi
za{y>&PHyfy(zsm|<kVT>YW+8iItSh^?fruMFFV~mudmQ6CN>`U5&FVeZd!I9DXIgM
zJvV7`03}mSZ+#K-ZMOvog#)yP*Y@*Qg0WjjHI9KmUV1uBB+7|z<LpuW@)<cCe;1}<
zC3fsrj4h3?y!}9c^<iPG^o$-3Fip|PzAU6MU&LT5Tu2GG4g;{5my<tivDndz<W#h)
z=Q?NWAN4P{Lww$YE+$-lI($XriQaJ}Zcd*1=sQ(>+;;zFATvrG47aEHc{l#p1_{U$
z$6Bj!6AMQF(P!9%T)mJpdUKhE1eTxSGe_>E0~x|w0<UUW1>cJ=m5TTh@&7a^=Rw@p
zg+6*99=~D!9)y}oM#Kas21XDv#e9fU=tBO2BQ;{ML__Q8Ue<u`c@sqHDma#`zZEje
z!2MBnjetRg+lr<j`itDJYlpt@Hhm-TrnfHKm-T6nF0cWsKaqrL`ZS%~A7En=7O*;M
zC;Z>w#$><!L;3L?mh~i7X+7k}F(2;ywzykBy|zjJa>4GsMGNEPKJ||ugLN2c;#;k=
zNQaRsFMn=e$j&y#;0vFj)RGgR(JnJA#Q{usqEq94Q#UGcG~ob01W4+NsqwI@^ecU4
zm;&Z^7AOoWzTPK1LE>LHFkw{GhBNSfr3l;_r2?HTyAC6TU40k@yagHyM+&eC1K6(u
z9><ZxYybdFIRWxhZkI0(b7L&6m#Qg6;#`Flm~uhc`HoI)eV1hjfL{QxiQSS8PWVWc
zrnBA&ZULH{IB8V%=so*bz&l_ZWDq9~aE$jMQXzD*s)+w+V=-lv1r7jw3duIKa3jVK
zCzcW{kr+QPpl0<0AtYMiXFREMo>0`kO#WfmjV;RRHL;g(A<dBQyV9uL$A{it`Qvj_
z$iCqZwnU4IwH*pimC|HRP3t=VW(DA+pqm~d#MmPf!*G-_f!u^%f|3cYSjtEiz=&nc
z+g>vH=TdOle}#Zo_+LS!(E|tl{yvx0u=j;VTi!Q<)VI_n0-QiaqCC%<A~w0m3M8!Z
z&k27!g#~m|r|;4Xm(x-H-HLC(0c_cy%)|4Cr3LVrI7LvEpmF!>)Va}!*y}?XB0;h-
zJ$+F?4maw{PW2*XO!cPu`i2oJyR0M^Doi+h_yw@PBh=)3B%6W>#-NaEXE1G<OQ(?A
z-WQ~jN@FQ5!xMJXWHgur7Ps&VxXU9iF$xjUG>(skUoZ!j0wz*d3y$wEjq}n`LD9ex
zmd}hqG|3~hc(_`W6b7isKa_CbL*GY|<dfvfTJmW9EBZwKcV&zyfQ^x)6MJlaO7rH4
zphD~OvG%t<@*N)h@$oPZijvLpX=!A|x`ifn+*G^5rIO|SCrbgK9$<}8df6UvI|V3(
zvi$KMC(^QmWD7_`1KV_*FDI!00PF5;c!bEej<O_f*MstZX|41;nyaA@W1RA<;e2es
z3KU`Fw%LSJ-uEK@J3yQpDqsZ6<hWhetjShbCZ}=rLyCrGG*P@a`C&gz@%kym_~rJQ
z8&E<HX0Na+Vvs+q8gI40^&OE)EV6K9fB|Y$vT;GYsbhioBh<70*$J>PJzAi}#925%
zIfe4y>Yqi0Nh41od;Qk_E4Q>LS$x1l39ucWQu)!f$vLz{l_`J(cwm_dy$P_s5MUA?
zreLt|$)5(uK7_<YF$#*hf%SzIH$FM0CEb$r@$l87hUFMno@#Os&{ugVcv_*t1i-V)
ziU=+-5@Y;oWL$~;5K^dP2l;8qdzbKvIoj6i!WHHbu2Zwi2Mm|x%$zKw+(&#4!Xqp_
z2)+FBY@0(Eq-hF7<>?!&?5_;Z5$b7F)MUj6Y}y%{*0F%lh5m@rVtHc+liLxCx!iUz
z6aFNZj$IN>Yz7yVg{K~{KCR(#w<RCqy)FwEzLek3XbmGaTUJg94gJDnu)Z;b{Ev*j
zrSp&w_n8k``5Osb@=r2eN?8fUOXYJsy>3Vc@3rOmC}0-?tY804g_ffNLg?O@IrfA9
ztNj}lD@bcXx2i>oLWLqCLnap>5eyouAlcYs?j-Px1}nc&skPz@0aH}xW5WcA2<K~8
ztYcH4>qB0>y>zdFrJ!6*q$r?Az||AcNOoKrDg?au0^K|#{<nEAXSq&#|A0C5$@Ta4
z$V?IMzX}LKT3g|}9(N)H&p*rM02au#4+yF#K@<@t93lTerTe?TUarPU0fZ6&km>iR
z6ap25Qy|bJh66id>%}SaJPi`A*K`3WSORd6VF;B_GDj15ZMd$Sg*C3nT@*r*0W$L8
z{4%x{!@qTOp>_P32SGC&V&W94tW!R(&BIaHEl<4&z-EOTqZHuS`&TV~ZLgI!ZkMWH
z{m!QL1x&HS^P93wg^f`bB-&h7W)UgAF-P3;R)Q`fzwpowQDpHh7y@?m7@uavi6xn0
zQAMV&1hvZKxkC5ErwA7NwS(5=gziXvS%^beVzqE@T7I3^3*&R{`}yP!oGGG%P&1}J
z|G<Mqc_+cTcGNU%%~!Kf8fVjr-!D`Vw2?q1t!R3+BvM;ix@njCOz79)7j{_gS|7&C
zCJa091#--WWD8i9FaUmOVTl^tPP}amNUuU^Cb26L_@Y@F)8{HMlh?W)KZ!+s_6|x~
zhA|P@aeAW)>gkKnO|5c$$ClWex@yqBJe2J6LSwMLOcgEWqP)95>zNu_QMrVVnap6f
zSBP*$<k+(B+OpBzpR7z-YBGEE&uf+(_P<~qU9hsls5tAG_~k{H46sA)4_!$$Tkp*6
zS1(O*Wgv!2V<yz<(w*a5M9cP-kNr*ax(tg=6%o{WLLEW_7Y+tz{-pq1MnJw}+3K?H
za6d$EAvDdR9ZHXzYUm3lrYb<D6iv;{*w?ot!-J0$Jg53#ACVsZ=I{OXnL^90)IG4<
zx!UEFNV{mE80MSRJ3R~44<}T;R9Rxn4gL8s2?SY$vu17+ZsS7-hBmevZZXeaoNNyb
zNAz}=m=;5|T~M-O?7rjI<J0^omr*X0FtOOy*7cke(siGTj+RzV(Mr)$JA{oAErNVL
z%=Ok=o9cdhOX?H(ovs>EMANjWL*Y0&pc)Zqt3uZ{t{$13B0-su&C?Zr%v%JKA)qXZ
z=)1MSxpRmvpg68dr!mSwx30~R8<*Ls)WyrW4NnFeEo;GRZ`AQ>(>a<Mh8`*qk2dAd
zCGre5F&3qy)Rd_ff<yLAj^RnA6O%cVm#R~EO*o6nM6F{^H8oQQ9EID7nQdt6!bJGI
zy_~I%sL_J<g3`9mr3x^EIPyQkxD;$f*jzURk0aop(-Z&Lc7_Z$5);ruf1WBmYT=nB
zQ@$^Wx8{1%Yl7`Oxon@U5k`_RCuN>s`HqWBWPfq5<f2RUS0LBaIKpBITlLnUC&n#E
zA6;2Zs3|@#-654)z7hjH<-3w58OCSl)Hr+3mf7A^uGreTV2Q~qh;Z&tjc|EanIEDI
zhK90PB6#R!>Efj>i9}7csG{h_P<1lHI(~P4;xg%y(iB}TjwW}0d(yBWl94AFHJmrU
zgsNKl-R2Bfg=H0lI^G(44Ono_E|&ie*t6guee5SkFOje2c%$V!=S5C?#W+Ch4y1IZ
zXp1A4IXQIpTH<qjw|dM7d^wey)$9#Qg_?I|@@W98xVEjae_O@*-HA<8tE*>_TjyB9
zuj{4Qka&mZKU9v%^&TdX6bcc$$szqo6rj-|ry!be&`$7oVilTaxp7q<51&jYN@1e9
zh0K(!)y6-9TpD<CQyR3X&f<o0-T2ex_vyJcJBNA%i$>N}gOg@igXAhau`%FG^-fuw
zfpNn0?_4TIuUq{pEy7irqFdTnFsu1_1MLH_A!cRkK1QUNz$ZL^fQ;YClyfw4SMbcR
zrG59IzqNn^cvZUg6-w;8^4uwxuATsJ#!vk)lGfdE`JV>>0q3eotQ<4dN8qbw`~XKE
z6u0)L)RhTpuc7kXxY^7>Fm8yM_w?rN{b~*tzerwI6;;<hOV*nW)e2%y64M8?X}DF@
z9JbH=h_WCxQR=fgLaunYlFqPhDW2JU6YSQR_83W(`fHjTbP6bCJdCJd=|RlX_th?N
zv+)Hv=A&5#^pzMTXx$dsrAap+m-<q7+e#z9j%%izA}Qw623)(s#sY&w;w9Kc;0r`@
zX9+9-zR5MQcI?{alX@04(sSPn$+a@@O%Tpv-H_>ma`yDe$K)%bR+KvV{$GYJ9|}O>
zvsB;~%xoB&3<x^Wdqmo7J#ON-He?g-#bT>m^3nrKo1d2RDhDWvq>P|UnrYM<a=WkV
zMVfaRnT#q~OfySo4$q@hphPlM8~er|3aRPYjMp1+HQOy*)cTqxk3(2NegpX!4Z$Mg
z2QoRWL7aQF0^0E~jdR?q6cIZ|8J^m=M8{*U1dDz33{;17a+9euc-6UIsUlR0k~!Sl
zG@C+fbsjv^z?@S9HW{Lq4aXNaVP{Lo?2lv>om@ff;+R#OvN>3YgKTv&4fU_EML#y;
zlz9)my8BTy>}QZ-_%HhnWFy#Jl83wrT(m5P@4k22BXn%{M&}}8_{CyVnOlTyGl`&m
z$Ct3V@y=dd-cl+X-SZtSBo3(($#dt@und7xED`%nIB+2wxL9&n7raJJLstc#lzd*b
z_Wd)=%QAUsZ79>eA~{6%*UNdVU%-b)yd*zIpKLsN?%xSNf_eQTl_YF}SH~Zc=GG9H
z)fCuI<>Q+hB4a_#p)?4(o`>u+*~0Q8v<C1|1v!UGeo%rhd0$YANb@6ywU(dd%GC~h
zFtHLMFN<V*CwFy-B1T0w$Ow~uU@EpP^&N;`vg~gQ#bRQ?tH~9hTiJyK=CB+6`~H32
zMSr&dE{FT+Kd}GyF@rBI3Fx04cwc;Y+Y*RVy!r^CEE{zb=`uT^_B+Cib>K*%F&6L%
z33PVa?`j94F2nX_n9i7zX0;1%1y{}Ad=YRqZ(@hs%rj>E&wYf2{p8lzW7}K2ZPo<!
z9nD9)$J)+rs%9-_^^6H)G)QnIT;YJBLvx1r7o$)1gmXg2!<RzDU9lb3!tTULc(F$t
zrh^{O?ppWLMHZN4$PsF=q&5Q9P94IuCzUQ%KCA*yeD6dN=rAM{x>|-&y0uF22Od1J
z$5M+d)$0jv#8PYQuUc!e52i=7f>D91h(T}Nz^pFxn3toeU2al6J-f=`?(|sI3a0Dj
zn7JNEq_Twb`dG#O)Zy3VZI;8N@ZhCxZ{n~hF0*$X-q(v2Z0?!r@{gF9{|Iab`dP--
z5QPC;gTLM1r&im7%lFFUFfF*B;AnxDVj(LkXECt~ejR*@7ZJ;&a%$?=%?B<h$hUTA
zi7mJ0!2r7uKlG$#y-F0E9TqRHL7BQ0+v}itoyO?z4*_VR28aRVj0Cdiw4eevS>-Ag
zgN9AYd9B$e^PkbTjz1nf^)s{gPwqbQ_u7$G=MC80wZ9lSrv&bTubsU&V2MMCQj6?w
z+FvYuGt_TPFmi#@W9N1mrp<9ckz3s@4k}!2)IHUHI?i~5&mlS6b{EOJOz6zD;j8d)
zsV8GD&6GodK*RZ_m!-O$(4k_3fMy|Xv$8h(wpzwTc~8z1n~Hu+nW69?8e%K|D&y#T
z81Lp`AK^OYcI0}`L{T=7>y&vM8nvtxq??$T$Zx9-59wpjb}x>|%)h5bKJh^1Jpaql
zUrHIzv{r4;?3K2SBO{$epk8EAfZI*ZaU<TWE5r2hnJU2+_j&8Y&lck8&k$qZ69{v&
z?}@qPn=eqLJ#VQ0RWNhbFmuGFL$6HxM37r``t)OsFj)6%&95_<V8>CH;%}7fXw@@>
z-#Gz~QA=!$t(LCNx+FsHns|hQunFoQw6bWgb2`nT<!zwNxUy*LmJ02|Qqv$wwAQi}
zs}`-&jb1YNrZCt|*q~gu$K95J*5Y22FDPD&T}{UGyvuT|jEF^=t99me5h>9%&;`F(
zg<*R~3xff(TVcXGx1;kLN&B{!`SaT-iPoX!W3xr@p=Gdngc`A|2j&S37J`3d=Dk3*
znqkpHXTz<3eqN<x<&_RcKjK_aLlND;&r#KmU*p(aGRuMy1CoVGd}hVZ&yBnIzzZy@
zP~oWlYS6Sov>5z81x!eruH(HVXPx?sRq~5l!b*&5pYwC{UrTRqYjIj_T#xT}i!SqD
z1}t6<7z#}FI-b$UfU@gbXANvE!}jrY7`|=}xG|VvS+BJ;4o!?569}-1v4m?1u*qlA
zO=psqn!&@OVf*<dEp7^g#0TE{`NT}5P_5s6%kw=)w=Abgy>9%YH>+CbWt|1)l&VYY
zpK7J3+o9fUm7b2HS*#a#9ZU4+3QB&z`t#p^iB2tUIKHz@+qlq(CujrdyUwQ0{_%Ij
zv~TKic8-91bwcpHR62#O{lcTv`QKz=?;A{JKn+sL_Cvq!*7u16Lgx-;UGgp(aLL<2
z+ge!E^hs-HO-o1jZhudmjKdVNTaSjtMtrYG)$-i15GlL-9(Xppd~<%<g-M@wscW>^
zzK%TRnSaHH?@e$z?b@b(MxzHbtqLFaN2+f3YqrxkX(boNC~oZ7=?Jo}W}hgp=}lJ#
zyq0x4)^KBO<sN^h7f<~>Ed#c+?l|bXBbut;;-qz83K`avsoijMW(94sN6}MCvd<Vr
zXy!814(ERiAC!%=Lp}!eUR)YOO9b^Aw7^zzT9!N5L|`VKs&hN<!v|18TTG}oNM)CZ
zgGN^rvI5V)H<~TblA#7W2IAd?B$8Rb5{k2yjb^^sbMQ5KL#>O1@0uXD_p|@h3vJ_3
z<KX+yqyzYQ1mpyoYKurf4YoR|<GMDM<0R2D+70vQF0g2hiQrLB3Yoh3lUZDGnkw3T
zfj%C?ie)kB@SWr{l7V^(!)%h_(WV(K^hV4;7KPs*Nhi*}Jw|}B?i`5&O|twtMoE^x
zB<zeLAaJ_jM&|Qh+C5#;<s9*y9^pm&F^qaIx?%x-8o}!{!Cfrh(j44&`<_-g9bq>e
zW1sK?DwcsXB<LgGrM%3gBY_r`{S-z8@?Vo2{d&>#v#nvHgQmGmzxn`7<W3Km&CH>u
z`d1Aw505%-eq}zRoB;?MLT3z5tdUx0N<@3sk>VHcT7)S#p+=*|ZrH@9HE>PHpaU*H
z$k5B~xh2${GIMGYZC)o1E7_CfHNzrBFe;)<Pp4x&lDhFG-M1pD;#5vI;9ut4@!;yR
zRc1K6aALAdWb<|i1poYIt20+3GvFAgjyL5#G&v9E3_D)V$Qr9l*Z+YY#tN$ZA)hv_
zP0lFNb%YY6IsS?8%giN@c6CBS&Wvj8j7f3hp&J*EcG<QT7vdm#Y@@?{9ewN?s1AIS
z6rR)jtx6=$y?L>9*$TZ#k%{%GA)Jx%0D%(Eu;(M-PqOKH&R*U4{<X}p65QWRcoIfY
z9_PEF9rygfPkZbuaj5yK+#?J!CcVu~yY~}*sO6|v%~;42mc(K|R$~33iko2N_VZaM
zO;yCNWJ#XyxF279oMY%GY%_b`ee%wAR(ubYtQR*Znt@$v_BePzcl*8DS~y{J=;n2j
zDoj=lT*a%O@qLR2lOU~Q*C2`?N`qW-Ra#Z1oWn2^wU{=Dql6fO6sj-@JX4$mt-6HW
zgoUhuQnOCx8<9l&H}h7M2q7<)xV8<y#RxQ<Prw0R2)Mm~tK9(wjGznINijxzsGfMc
zD@3&T6wCNHgg-TdNY-_GP46LQzFZaaaX%1N)ZtGLrpo824}kZyl#W3z^;>1w4h=jv
z2)xnR6lx4Ap@(V868va5J_b2x)rpVTNj_DNOF6{?ZUgR<kt0nksYB`?SkB`MGB(`a
zHeBtP&P?kf1M?|_?|c>yj%#xE?$ncnh5RwTY12-nedXy}KDO>~whhro-EHT(#-Pkx
zhtjEHD$a(O@J?+nudrC^I9PWoWYatuM%#|*RkwLB6TKuW_<SIxfJO8VeSFb*H&8B1
z-6pc3)zeUJY=~M<wx{W;b?%$@p;&mL?9b*vqR{CP0yh2|^PgU=r%OD_`=i=7gC_NY
zrxPT<UZYFJOWjldII<En{VmbI{$>?##(^eDh5Oxd)NPaCdv|HoZ|3q>S9|_pUlRX(
zYvA|KlY9`03=ZjA{GnM2)m!vNm-JfkuCcJfrt0Nz{9tp>W50QL^;-H&zW8P9xZ|>7
z%G4U67cs9}C6u#4X&3RUV1u<*)s0e5Qadree#3J@2?8xXuyh`B>3qi2d481fczJ#u
zMh#iT5Iw0t)NUFZvnLpn8JjzE#Bpm-Vz^xBHGWyGz;2<%qwsR4wIwIG0B{2w{ZPXC
z-4mN$+pcC;5+zR0VZ24!zhd8S)YxA>bJtvK+<gRYhat)~r=`%XjT^20{t+#%n#u8B
zNFS<y{%L>3qL&anx<>K86!Y`kX7NA0ktLvCq!B7mVU<yN0?Ca42Drwizbb+BjJi`h
z8Yo1?2hT6ehyGp1eDfA$DOcy!`de{!Uw7>V?)d=p$kosbl+W14Viis?EznDyGi`32
z-0^k$o|65gkc3Jd?$bN-ofL#GLhaxX9DAF2Lx1~~_d<F~L(v6s<dsIZYs`8nY!Ifj
z=YM%hz#stl3Vm}7rPeB{x_N89f#19w#i=7T&l;DG+*_CJoD9vAZvDa#`LjA&J%XE&
z33iprBJG8<I@1{wZZ~cjcMmvmkV2>4ODb^ye|k@AV^Gs-Xf$2w;%~afiyG)8T37H7
zSjw;-n#T64UiKwu?NAi|LcztoZxa!3;5I1Dxs6`2a@DeT(X4T=EjFo7rdErj0c9{8
zmSNp<y;n>r;D^h|quE|k;|rp};Bv-lqI3-Vi>veZ+kVyfEgB`f=$GuGoA(osS;sg1
z;T?z5gyO&h!@Q<O`TU0Vfyi@H0!}2kNEJb-+I9wotO(U3HU{&3F=yGrQtH6H4Hur?
zj=1v3IdPYvjzr~LDRK2ogdMoH2JC`tJVroye=(ikd~Y_K>S=b>Exs%mN*)DgxIK#S
z`JN-lB#C4_z}pVpHp7_i-V<Sxl;Jn&PqE2NL*Q?HMGEvC(X(hGZ4(L?Ot6ug-*<BR
z(1k>$gPVSMGEYaPSwdr{Uw!R%CUVO`cAPqY<~J9b<13^jIxt8iX~bc!_$fL3eBS__
zF3clRmN>Q+wA1^HV|%VVboFD*SKYBlV)@p?)r=_Qfclu;8(orAHq17RG>4|>U_X6y
zpSF#usWBeTC<VQk_SWDFH}dkId(E?^W%#Ee8Pgo$kUe}U#T^~4w}U?+)L0}1xLsJ~
z$*QzQ#o?jdQkHxS-EtA3rs<BE=;gsVB6*sp%m*fAbFLfuUrTm8d1i^i3R+TALW;sG
zOY<2is~c-g?;ifHS;fgtI(itNz2jb$_iJjEi63a6OrFiG@{1GJ(lKh-G_BLj-}6!x
zAf{!TaxM5=HY-j?Dh)PDnT=|gvn7T0zkXcgRnK{tHkL~vn}5oER0M?{QsCz1@yJWN
z95}SEtmWf}c~`?0Hze;=Oc46jIw3BO1_lUN^DL6_V=p+o64EwoG9t<jhqbYvo8D;O
z0##L)EkFs$vO)3k4h%*wJ`zXsuXPE@v#-9G&`Haf{5-s@kP2PJSqAhl)Mz??iL5)3
zfzK+QYWW!Z;%5-#!Zz#8VRshe(=S{-Z<y8nFLmQJ#Js&eb;I2D`lQNMQw=(n67fSX
zHpVIRF@P4@B{zS4$$+@&G_=?PUVgStFM+m{%Pw)*4HrTG6+xD{{ml>E{CPUloYzs;
zdSV~Zx(JZ?_R8e390jvv4>f9Sql{<~v9A9@FvL=3*V?)wY;_2D1S~hg{xuM^M*pj#
zXrW_mXO55^Y@@)F{q+=JnLjylBn;R-$zbuGgk`)ceE?l}(30PQs-@*5JZwi7#6qe7
zelnC3j?SPtgf9#xi7iXHQbiPU%p^Nw<EJPSg-b8{T(;-S#9&Jn(({v1mmlLZsk5+K
zP<Y3=0SGkdDvd6YU1Y<-rwIm6KHmiLAcmDSqlqd_dM`DFfHOsKlt-R1orv(uV~&@2
znh0P!q-ig7fnpB0(R}V-xuIhjc81Z*5a4DR`7S3;SSx}VqqJy7g#P9+Y%AX?Bs7@U
znH<>Fn&bvHe2KR~FPkJ%mPClF_kO>bIVvs#RjrnPLS#<9K_cfa?JAet^m|B_r(S$A
zlWOKKgNY=)ZiQsL-LI%LkgESwOYY}0S7f14c~#eP@w!AY?W=9FZSsxe^{HNqmVW7X
z{CZhr(&!tj+SK6RL;;0FNIzgd*frt<6#z&W5}XIYkK`7~M5SP*??e_s$JqEqKa+w5
z1KE#h{Q$gVv&$_(S~$Zm@=}SzCe*ipgHpO4eO$8`X~%}aFq2KX9ui1l7;o}-7yaiO
z&Wdu+sX|o4>T$9z%4YqgEv%HxRcsJFqrlh@@ki}F8`!B)qO1#NW7cC30$i@Ca{=E-
zfKdiKGo(bu9lk&dF(h1}VRGIq=eKS^;xTI$v%#k^jood&Ac_)vDQJ)!J5p^ig?anS
zqp>;95G*$4?ZsHOKEX^B`BQ%@5yi4A8touSY{YCbi+t#z)Jz<CDj(yMV@J*RB_vn|
z*G!;Ob`@9**?wtHm7ko1t^xXAt^R9c{yoC5#9iMX=x1WZ2w=Ea4XSBv;G&&v?;-(P
z1afQx-L}(`zRACPxFuQ8o+0xL>B(i+La`@`oU-fmVr5*wb9GyIqvIu^$l1Fo##+nA
z&MY9?_ImfHX`5rJfv>%FkS48N6Mp*ww#j0)x#{_?WjSO~!Aqld*iV2STmZ%^R$X{9
z(KKcX{z5-7J7KF@E{&oPKW1M2khR!!;f&mH{aGf3AeEAxyMw?_Uo?94!?0oA(ac>v
zWUocIMm>{4xw495WS;;TY5f)`#0)(6{?~GEAH6^$s-$egYWC(>f$Qk^wLTd;*{+Jx
zPhd~d_;7n`{k695OyorkHMMibpv>hLh%z=8M2(x2|L(G&IFlGCf^%JXZ-3ebRleu@
zI;){Sgd3SriZc0ac*t01;UV;FF2FK&Lh-B(?QwbEbOB$l>t#pThuXQ+_pS37+ObbV
zUnrFG^;@oMmW<lLmt;`~A44|8Z5+SaW=0+%VGv(OKs=a)cnh3yB`mcp7(hPOSTMHs
z=fxXPl!YJeFdH7ZGe$Z^Mg;ph%aeQh8cJ#<UaKMESjl8KrIP3RQaht;sVyq{lp!(H
z))wG`Mo=;r$OWZJg^BZ(HTA*`K2t{OXgj8A=hu83Q=0P(FGlKB<HIj0g{!qaB<>a0
zYEFCxcb$8^CSlBi1usI$^=`>4(YCk`qgaWH=2#C=)VYWBQDK%+q<{jbj>#fT^v37s
zZXJVoEC0G_?k~w4;YK+bm*^_RG}KP4qK&a;{zkvfb==7$ys0~ZM-;9srPfQB^E7#0
znC!V({|M>6!{$}b=<)6=?hj;0dA5d)WB*EXdGGh+yWo}c9H|V{F<#T=tqsq*v6J)b
z*B32<Yh)?)b9PtE%z3+;x}EW-#vVlV+c9?lL^xV}(mRfPK2ztE3V2Up?e?4)rD!~*
z=mWpKFGQUm&AYpSQl<NHts=WpUitMK6ek!C3xV>rl-W1N-~ZIt@A*lhn$!I*e6Q!B
z^U|#}0`+|a4k4jTT<qU!+YkThD}2c01%L~TakxnEKfD~h5rEKP5HP4ebY^KhEX=B9
z8eU8{eZYg84Q7!?ty^*>5~g)o`M|ZPV`JMG-Ukh-qt$TULnM-2<i2!bf+$YSSlunJ
z*f<|QQ8gf{Arohrxwa}06wfucCyxph%P=8^9ZNAVpR#c36{t=s(>!tD3#z9ck29)X
zIwRA_H!PPfAN^W7V-wWzTTw9t^vXQX|LK+nC}W)lFZ<6eHr6-xOUH@0>-v^ev=3(<
zg6|k2j!*nX=AS0z^Jg<7z<!G{VAjL4m00U@fAUkL^+@+P+j6kD3~0l7=y+mIMjRA*
z&f7i;E47O%me%XHAqHux{W(55N~GkK4zuXNlT6zVX^2PHD#)wMca@><5TDHLMQ8H#
zCOUJYLr8%4y|;Ou?7C~;pQRz=aOaI|l>BXxj`xQwgk8a&sTFcjMQh`z*xD2?ePSb*
zM^>L`QAj1k2q=Rt)jb+mao}60J;JPFg(#Z!WA!-}hGSs;(3TDtaH@oqY3XO>9=48H
zj^--<0Mq3v##1SZD@Cix2*)lH-5gO~8r!2tLekDaPrf+0rk}j$1wEG~kR&EXbYqj|
zL0ugF;m1{c*vC5JmTjfjn@1hRaa+*7Ycp1Y3^1``O&>eMYA(Wyw3CntONfKba8To9
z?TK?{tXn84ll*c4*&C=Ex=b6E&+BK`kA;Y1oa4Mau+OFkpI-JjYUBX*W{<%Wl27E<
zsNhTrU2UrDBp9nk_0YFQCfYOj#C7|9O1mZrrdDvk_Tk4h4eFi^zq2)Rzf~?U;+eL)
zgAWR(kgsEiFqL)kOw-*UPjjc$aC)~Sa_5nMq+GqXq-l+YMCQaB=F>}_cdw~u$8r<~
zjPgn`;wccunxqo}MZZci&W`$dXTgz?s#K;iYs!u@;Ge3U`rqlsN&nGD>9y;nLZ9fj
zFJqtd0zIepiwlYM$J^ZVU`y%8<uM%@tQkUyvZiDv&Q2xV%n9PyHo}<GPx}iGI;AJP
z(WYH?SLgcgTb3TAc-Z1*(YiQeTor#`!^#KE(HPB3{Jw})i44|sMeXZrlHsWjW^Blf
zkdpCFpnY?7x;r61?>Bg0i4LI?hHQFWI=@{0K^NBT9PIA&%JpI)dHQBF86J7qphR=|
zwe!XkInA1YNdw9P`UB8hc{w(g3g>KZ%k3k`J$SwzAl6(@F5taQ-TU=TepgHskNc@d
zez+-u5MaLQWBH0&GsVF2`|uxNJ?3?P9O?~<a;fsBV;Jbvt_dm@c=R*2v@2f4p>L&n
ze=@|XT8)2>^f}#f1df2`?9Jsp6g$0QVhFJ&Pd9NBrreXK*|o$0Vlm1Z<O+oGk@Yr*
z2@GVVhsJnS%VEq8%g4txM)vj04(Q-W;Xb0VU(cV|JAYPB{UdJJm$1vOTJGrtlScfu
z1u&J_`M>6`5>4CP(xx^r|BaN$1EODs@wZ&QmnlKneufDXw<Yi&*@1@1{2e(BAQShO
zqHelgG<M3;jC)T8jT0#X#c8KWhN{%V0(9!IAw0?=-R>w|6U{rUC(x~@ir|9Rrr5rU
zfHiuRiq|Ec_22W|QJ`=^)SRU>pJGjVCX2ZsP+r+mdYl5JqzL&U?IJp|d0!uEJP4go
zLLDv=ImJca9ui^*dR~^6LE+~9%OsWcIx=v<dUeb4Fa#06$22t#uL5`A{+F_G6Q-$=
zKNQpzN#od~z(+c~o^ta?6ASpqtBTVjcUofa!p79B{9=t$;Hx>BwNBkyR5we|keBdo
zjwDHESQw-b0x$!!Pfh-!GiCweje{<56jQwjIESD|NvLFca;GLg^ldN3W$#@(M|HSv
z(JX4aE_f3%Ei@kupsmvsVMC0=eh8nOwkR>M|32hZ%i43XjT|(}0N(CO;Z7GW%vVZy
z65U8jJ6U(6hLEq9d4dq=a1<Qde;HX%?@CrEki#tz+#C&}&FJ|`VHDREhfqStnkv^4
z`mCDGPN`h_lsLg4r_#wG)j)uvt4x<@%B!u}K9%v(CrjP<TO;&!)I17iBUy0It<7Go
z;`N+dgdH^r5=J=&jKGxPty^jfQ?a;ptqtN-!}7)-)R!Bob%k%of?1%&e*&mh-+!c`
z3)+FM!>s2@?46`jK{w&PMv+QB3QJhogW3?qaxwJz{?w3d#a!y`^%*`&IeetVPhOX7
zGEz5*rhP79ft}JbywMcLWty&2CfoEQZ0iqPO&6$3;+EEHc{2&71VXrh1q+!RY7`L#
zi-=*}rCNnAq@v-K#3i=d&&VNx+)TFqsl&V(N-Waoe2zSRKA3zv!&2>T6}eLhPB9|r
z=T7|c9<5Rc38-*3v>6lFyxL{!w>-dCJ$?{H{7_CfaT}ahc<?yBhiG%>{g65VX2KvG
zC1ghA1Ys0#h#ZgqRdvvfj2)YiiCOkZz@|3mRn9Tt`?|Ca4q!;$QEC<CM}VJQN3M!I
zHiif8nI_Zi7A)oT?<qs|l$MEl{ISlZ``?g1+cBiyM<Sg-LluFzDq_74eZ)nOM7MYr
zJOq?+$cuXF8C1(dZQ)$74h%sAi+I!_!U(yImkiJ3%$wMvN=|~n`|IWp1m_tSuMRcX
zG{I_>JMbff6{xWxp(J1uz(VSWSCKh^8taxvwVdtuVLE*(P3u`0fub8BaLBY*LrMpA
zyTa|4iFxAp^(945dch$XJ^`&h5hJ>}z_c0+r>!hak8~tCQ#&VUO|0agi=0-m>}+V2
z%Knq~0HL_<Sl?Q{fMZ1J@5Hj8CfEoHR^~If3Xnz}E7na4H;Z>XZBU*n-S}NX7ZsRe
z!;{I>X=59QXjdf`0R;y5l;>UufSUnAk0G~zMZmNeAE){ELb=ctE0)cRS-EVI4jOt7
zk;(6D@|LOSyXMVhXkcO5*z2YvBLh8u?jLce)jGKTbSF+lro&mgTS#Bwf{?cLOLi10
z3y%1n6I1J2n72OezczBj@IP%Ni-0n4byZyegW>b<F5zU72*gw6%GbH(eD|JK8&O(x
z*TzPmJos};yk1_rrZ-N<mEJlT)lT3;^D%89j*E0p4D^m)&Dks_)ZaJ9e=`RQlFXx3
zS1LImJAHq!-aE;lX8Ax&ysD$e#ii|YtaGUO)xNHExn!Lvy5G4ziz(~_ES1OUExFGw
zehpGcUa8>KdIzibx5X0d(7(UWus+o5o5s-@yeyQZJ;+k)<Gflo*ZvU>tbjByU?G^k
zLcV%Msh*zYP=}HY@228o5vGX_?klw>uBRXKcP^aGiwtd3^i#|wIMi?20H^tDMcM|=
zN9_}$c4Mt0O~<>OtU0PE0zpp5&wCBr8&NZC>Lp#<+MgRnmlv2#Nw-WY{DR0ZT>j?+
zI>10ZIkD;|m9{l<Ub=*I060_D+};>85>WW7Kg)k2#hHE&fk?&qbLJ{xAPE`405C``
zPm+ku&g{Py9+pxHu-75B7FL4KE|+%#T0Ee}LGnJ@fEQWj<YUD%z57b~W#hBMl_3m|
zhBiT!+{I?slf>)fn7z+Kkf*4osF8no@FDEBOw@0mfDv6l!}s4eS)kh8@FY5A%hF)Q
zqC6*zn6;X6zTXv3>|BVh&S9P)Uin<|;kh}a;~5W6aPwSOYAQ6Ir(hFNOV7^fs@0PK
zva{yh?D<;!K~5p<VJEB9%~u21P-5?QI{q*g%FfL2p5**VbbC+(#k3}f?s-;3n#ap1
z)bT25Ym)2S>qP6>XdD<}3Pt_5uR>BxuJ=ZgN_D8h(}q}JiY_e`eA&o=pwTKjq3I|X
zM38~iGj0{ps5mJ;1jmMnunJNrxhWb&5R?%aM6Aa`(-I(@K?zhy4)TM_MHzl4H6PM0
zMeW|02ZS&>&2=1(Xt85v2Wh28#fsQ&YpEo!@AA}hY&5C+HrkP!e3~kEEPwi{<f^zO
zurslq<EpSjqICIekpQVz6u65~!Wp{pLi2xtq_w(QXN{#T{&xB3(oU+J%)3^EIpCPt
z%6rB1*DoEQtoC}d$c{Rq&hBn$Voe(JI7)G!<(l?O860)Cb5~$0@>F@?U^)tuae$I%
z&qGga+<>#oF&jNZ3s^R#IoHf5Eo;EPz@kYyb>fpkp^oH5s-77^DzRBSfAp*Tp2y20
zRCl8oOpl607APXldtR7Q(!NZ26s(!LH=ZH!v>q?w`;D5y^KjV}d!1J?5XGSAMS6(z
z-D16?Fj3GWWbz0{ifn(^Z{nu$S7Kg@^<iNVc*6PV5hjw7`2VVV>$j@DFIrfUMmj{K
zyIbiLq)|e;yOC}X0STo`x<R_Tq`M^#AqX5gB@b~I`uX1HzJJ2&!w<p(=bXLvTyu^&
z##nPxAkd8sbMd_&6rbN~&9XYz^><9DbyH?$a!Qo-pd(fsG_)8IT3hvv{JZD3|F`D}
zJogxf>^2w=WEc+^Hc#xUAVyIWXnvwtt&!$rueH${syb8ei3^i^CLd!x4pXg-(okKR
zQeEPLEelGog1sGeYJOC*^W+VK=oe<{-excPFy0#sWU@XX6yzGUuKUAS+F}jG$79LA
z8W;S+XIN^is9Z@d?%dUE8x%21wYn!X14|6%>CQFX+;Oi%c%;R!s#}*<n^#)<^W?0%
z9h!<;G-Wvm@TRz#LL+jVXTz7wgB)V6EAYJW#Q)4UKOY&yfh|Ra$0I65W!BP$83ocD
zow90MvpfQ{09r6@p#pwVdikU+CgGpgYrJy0wahXF^X40y1p2Vka;35jY~&gBoo=PD
z47aViC$6sqs2yY*6QJv8NDbb0NgF8;>VYYzsOJY`1#6AjWI{soN2}iz2pH5)!F{GL
z<?}Q`y!xh(y#EY??hV0yu%H>}z&;lQW8(qsr{hS&g7UfpQ>iI<@^Jz)l_Ykbuyl-F
zRBj6I`QyMN?76^W{Ix%?+D?g+qv#tIzv+l=leWPGWnGY`O`AIEqq9XP{LqGyJ8|-Y
zF*hl`|9PeLQppOPq6k@2EN{pnE&DwhLjhLRr#Rg2&S~7OVWw=KKFCbbOkN6FdOzp6
zD8SARoT1RN&2jlygAs)<%c$D)m_D~QBo0^FI%bcBrx{n-it2?_Qy3Oa?#sxU{73iE
z5yl>kqxJ1R{^8*SvX+eTg8G-89K!cOIn1m-t4Liaaq(iQX(DiF3rPL$gbV+`u<uXw
zZ@w8#K>H^w71NS)bVh~t4Sh=HB6^b4F&wsAY1*#J{W>%5nDjIGm45BLwKIdOp%L4y
zWH%5XC_5yVpyg)B16`~`9AH!VWwIY!Pp2Yn;;e@peikv)c_hHr6k&}UEHm?Dy!L}G
zB;-*BR*b}P`TZH>yQ<U9A7ZHpd9JhPzWeNZlCu6-1hG>z+y+TCrhw$R9R5d(vI~-G
zMHe9!9+<(sKuHLxJTsx?EW(g!3ZjwIn0YELElO#MP2u=;@e|w&23ZrkPQpAGGBegm
z=$YbFk-su}RqnR17J>yy)O7uV#S#L(e~GCWOH)R?%@eq!_z%0xlIpvJX?7S-bm3)f
zpAcoeeEM21Zb2f1_!Chx9zF@?MSHAel>Dh!*qLW*)W!xV2EA3(TwJCYB<brv3;8yo
z#hML>NxV_{47YlLyFRa0PJZ)d&7w7Wx&&yIiZ;ejMP$eiUecjZzz4;=txPRY9Z_L~
z(kD3K$qFaXRHiXYzLyp&`xVXR-cW{sY@;1B)T~Mu)~yu7Vk{GgSL5obQ70kme<+Yk
zLpJ6nGZp7OA%#pI=M5jl<_;2lg$<Rc;1_Bc*>*CA+XVtyCeS7hkBQu}6LwYi^efOW
zjcs~`{dF`NETaI3&~Y?pfy1f9j>IpC9aSW3KxG=l+ZbB6+23f7r7eX$*D#|L*iY<{
z?t@qQL<fdUKHlAM96h{kLE>rjTXoyEhV<9w9i_}4r<luvN7B}hXYXIG9YspVSkH|@
zKO32g)Bb6c-o;ALMOu>73LY<#i_z&kZwoUeAt$^+8>fH^{e6!pei<0x7lb7|sWs=f
z>`W$R+E6aVCUsEr#7<|$h&_Zp-qHIi@$JdU5E7rWg=35SOtY*J1ZT|a=27Zf#_%_h
z@$rbzQI_h8cgBX5Z(<%!0zZNz2;MJHq<fu>H?$m$==)JHxlCWTZ3Ke#&RVZ_H?h(=
z5fslu{k(CG6shn;6K>B}XcQyu+v<4eTeYJJ^H5i>AH8qBpgmKIO87Nb`MlFGQUOHY
zLk{rb`0FAhOn;=wNJEKB#LeMQ#eD;zhbZr9k#crW?7Gn$2(nUJgibyg50kJp3_a2C
zCU$5!$%y_g%x8_LEogLA)bEcWvvx7w6dlh}OrZ5rdMzWz<(Yr5vP;|owZd%0<a>Am
zaYfTn@oBLFND`M)+`DZpf@Mm_k7&}Wo=+;UvXS}43en@Vq_*H>OS4?a#>r1CNTO+Z
zDu~G_NLjv9%5c$5(2q1K5B!FWl0JswPQ&)7jLZv$P8`#?-+$G~%;+JocGE}mVnYMZ
zhW4G6CrBnA_q=dYm*w-ljv&Q72{?m)DfpsB%g1hInIZyL@M``Rr}N?B5xa8!S6XP{
z{8KFbzrssO7A+vJQU>ze40Ll+?Adr65bzR@Z@XL1uW%>B=QT+)^)1~Z1Yt4bEnokl
z!bhkf%$(e?d0Q1W6HwCaN&gX5lQ@CuVw_*J_?4_{C1F$f_-nCulqSzh1-5F^LW3y<
zK9!VcQJElMSxh64WJX&|!=;%~=Fyu}=j~`*uPSCL&50&6cCwQe@I6C4Xc(T4;=n=I
z9uZFI(u@6k>w&jwpQ^`n;9=7~4&Ox=HsO>9LDA5+j;2N(^J+4_ZkW)DrAB24+D3UW
z1Oj94|B?%VxO<#q`)I4sqnDl~FHK0h<&OqEGU%ZB$PUnm+Fw4V4L`TujONGO%Y76@
z&A?Q~xFNT>sLlG2M8jt;l5?W&0F~m^I2R*6{Nff*g=TZ%!VL8Y?0;e~-`5yx;&Y+!
zy{%fo@G(yNrT&w(vbJcVAwCQ(6NsOxn^Cs3iV(r$K&-ihvpI&847G&BU7ePO^CT9h
zSA?YT;UljO+uOwnd+|^+SR^Y&LfoN?wivAPAGUsUPmxCajnE9_e>~ymK1%EH^!71*
zDI<t<$rJzfq3O8N_GS}J<O+#s0W{&ZT?Qvb5AyQ}%XWuP)#f_vj#?3cQf?V8Qbub+
zeJqR@HgZqS$4_dtpZ?U!soflmM@PI3;Z+Qcb>5S2akjK=vBBz26=@$ncMY~y=Q$^?
z-`7axs}`j=jPZkyCRf0BNUdsH&RvPza($A`PC>$dL)_Qtz-(0u7xby`k24BG^}7h9
ztXkTqxSj0z6I&CzLGWVo>>)Do;(3~dC2??L)dN?ojV(iqHVCuT4#c}{2RwP)4yofd
ze=O^+{{(~OkkDzY>Ns~r%H!U5{ZVV3vhE!$yWu;_oGQ#Uwy0z3Zo52hUjE{!I%9=e
z0bkriXj7IZ!|LVzJM-lQt=O|Og8lPHeU;ym894>C^OPI?8t*pEQc6o-2?*#q@+BJg
znb8vn5%=Xo(6?OScFtH^^`ujCsY5$saE5RI%iHs*Z%+q*#f@~wU|K6SKdgh?$h!D-
z0WKE&@f-@;FOOGc)+)vL-&GyshCG<%yvfx;x9%%qG#)v(yv?~49H=BtOhcb`yHv-*
zEcdJFRb#3gE0pu)`)(H!or}BKju3iT<gP$at^>p*>R-fAGcdlFW~d|yh4QOfd!Qmj
z78XvjH=f@?bhWJ=w<n3TtOdtb=PE4$<z#f+F|em)U8W1ko!*-|cnY$oDkC45Dbxv}
zqqnRfqsV-B<i1}^Wl;*O=C#wbt-jLrxL9<kc~z&j0t9XLTrV{#^^d^0Nx=$dp)ef&
zw2x_NtR3XEVYt_~As`{nE!xBa&FRDKHEjY-ql*))t<UYU9}kr5eUGxm<}qIpN@Sx~
zJP`PR5c02~IowXVXrG}vYfZ1(4&Twct1@{AuJoRs*EzW}b3gs`jaPQ-TpU~vyZm<^
zSVLJjpheqagYY$D^h78Xl~MT;oiDX=RA-#H-PDUi#Xc0E2SEV}AKym=S|oG<4~?|W
z2kP;?mKGT|n?7sldDKv2gW@YprMU4I66@a2ATh{~CysnFzg<KrXU64=gn)Al-lJWo
zHYbfzFr&f0`JB%GKTL=1STB0vP;y~dfBPNg73V_s9-f3B_waR0?#;nrTi2jtfUB2i
z0ha-L$hK>MuFxaM{^R@2m770p5C#IDJJ|gl53jSuiT|gy@2UJ@I893*$?lFg<>Ul(
zTARdt3V1Ng=@Xq)89ns8_SvN(6;3x(3aXud8Qu@y+TBP&4xABfY-+B0*z6omdkM6)
zZPnCYyw2k2sN)hdbS&!c^bUW5WaWMPwzdDKYN#wt;u#cT4wGeA*#GDRP4GBug)p<t
zTGn2dl-Gx3o6L!D;9AejB;QPs=`|b*KDx=cYqmeKZa-fm#kR99?z-PUyhZv%{zkTA
z<ql%+007tYPFFy{vX_16%KfG$tDa7d>gaJETiUN#zgtPh_#Rl9)A1VP%I$%q@5#9f
z0YTACY5Upx2$Ga6t)c3=nf1X97vGcE-NmL_g=V45*)N<Nub>|;kMN`-6;BI%_a)8D
znRrKUgN7!qz%yRJ&Re;^qbbwTH1}!kIaf1h&Qw$+D4a%Zxw|&hb3Y~@6KM}Q6!>um
z-B{i?Z|^#HP1)E$6uFyt3CdBH-r=OhAAotdr}0op+YZ?|luUfv2G@+j+3rtdXlcXb
z<?%?HGW6I?%nSMe;!OwGV7AP5a{noE7yN83L%cUFom|WLg5d*H8{v6t42g*zaBDaA
zxJc8!xoyAq$}KdqD(VL7qQB8S&=`yw_GsmL#$z<Cb)@G@aVo#i7#bV#FOl1~?IBS7
zi={D<OQaPEWL`&;WWOU!Oq@Q3{qv6^*Ewj+Ec+ie1`(I+L<wo#(-j(HjLq_g6Wg3)
zsDcZ=Pe&|X@Yc*Y^HZpo*&O{Q(>1j%l_`E{V4A0hM?)=hu2VSc1@2wj7}@PA3{$Y~
z{>J`>6A8ons_oO+R;rD?8(>$CmkwLTKpq<zc~z>G!9CIz1)>n-t$_hbE-w5C(zMOI
zL=5(q?~TmP2hN>TWhX4o=N1kejV)8Ukm#btE2g$4!7~o+>omR<$6V;1cqD2MxoGV_
z4#oh_<whA%%V3wSU>;c0aoNMr*R_wKM(vB1SHL?K3@+w*#jvhpmOn%+#4UMjCx&fN
z3$vMR)@f?$==6@)qIo;&HfQ-qL#wQsSDz-sDO!2l2Gha~kyt=5+*rHYVerH%K#}d&
zuQm87T*<#2c)+T0&tJOKfL$=a0=?Bvx}6Np<N$v*|J~8n1=Yg-<EXQD%!y8263|wj
zvmo(Joyt9=M2TR-&QZnSL%&0uXKbaF&ekcuB7g|(yG5$~tVov$s?Nph(KPMNJ+Gmg
zL12jgxy?7YaU<+cHectp^znWp!#gs5ns&r2!&iiwh@XH$j+~Tl{ne|58m%XG%Zr;c
zr6ds<-!^#sPG8FAEx!A)0M60)ikNscckM&Ke7ry`5O<l=J6wbkxrMzB%-$;<WKEF=
zQo@G^Uc_%>sg-IVPe1||wZ2SSx#ELBbV2>N_1#pKRguIp!6+(L=W!r@0jVS1A>DU|
zBMK*NKZS^xyVQ0J$_Ci6Q9s31O-}R5<396@1R1Az8hUf}e)Cz;O;Gz0|I`#snB;vH
zYZa6Fs|Ih6G_w1xop%y@9E9BxprRBQo7<H?<0LehT?Vymcb3OvHAr%B11Xpd9WhD!
zVs9P-3U=p=nO6%*|6)1Fk~ZhtXX09=!W)he7c2T3wX+zfgG|Anp?BNqH^VH+BV8Lq
zyE@)}@fXX@BjC!rpn8GIs1%&Rjxmg$OHpdoV}G1O-{ka###R#x)bS{3TN6GN-#I%t
zYQ)Kj%T{ADDVwzuO*WHRzH0dborkrReWl00MG{u8t8ZRxX^anT9&!Qy^-3+5wQO37
z0(Wo<g|qTzkbmDbBd0I_YT*x>#!RdLolH@Kqf4wTM_;0_-&gO^yjjdjRv8TDpS-RX
zVRGs`TduD+&6ye^B$wSZ^lY*E7?k3UCQrXyrg!BPzv!CP3w@-+;}xz6vA_=GNQYwe
zFfdu86PPjK9bPL-F^x>WNI|B!oP<W2mdhzu=^j#kc4}^&>ZzkadPXZ98%G{e$s&W*
zo7&zGwyQB$XW~;GWNiAI2cX4()!+YkegpR+P)uFEzWE)t#B-`;jfWcQy~A@A`Dqe0
z+*kZJKHeAM=^Z_(nN2e<X8MJ?9<XLQ%QVnKmx6Ui&F!NAVhJiSJ4?%8Cuky{n`;ui
z><8j6-W^>RoR95PS)cbXKp;uvHPut54wY~6k_+A)VH+J*GR4O$={MI649Y&CfR8W^
zM^J_&@RlhMc2mo!%`6=TaqkF$xH9~9)Wb$fhW6>At8PPsy`}oFM2A~}%T23R&A_oL
z1iE}r^==!xyD~B*I&+RF!C4=aD&m5<I?2Y=7ZE%HiI&NsVTH;KWj^|14$cQD;iUC;
zwx^>4ayE8#06gf7=4l)aY^0Vj>sx;!$GxAK;Z$<BEgje`CjsqnPxk#Iq{4jgcrCr<
z)tf8RWgq)cF%f_O1;;2vS`gvkD9GOvmEt+1>Y~ZSWPg4vaUl@Fs|c7oowk<It1Oji
zmulrJfY?HJ5+q|xOmiIKDr%?AyqaIPlPNP^zvfwoFN6J2DXMmy`}TsT&i#Ik(R_^6
z7=kkt14=+I%>tD}*-B)C3lo!ZdP=b}D-;xGoS}vL+Wso)bm%V+w{)i6-I1&x--IrT
zrv<0AR{hKBVev5YHFoZl+haaWefw2dlC);&rh^cY*!eY(U-P(?QUSWtSWn+h$msW8
z4xdbR<;jdXrBAG41Cx|S+EN*=hvgGJ4m)Mf5u~sJ5G`ezS`7q8t!UmZj|EEi)g1|<
zp*M8)I@x{#PzB}Naq96|;X!EPtZ2at0FO3eB5gIlubwi?;771n*5(*mdA`b+Kh?&5
zg908#s+ITgw?<O4^H%q(|8MB+EN(54t8t7aW{~9zns@W(<GRt$A$aeu<^{b?k(T@u
zLuy*^m5LPT)-Eh}qbs-9WsVcr;Nb_FcZc^!7moozz1e8LK?IfB;ny!;L%22nTcpQe
zGlF#R+wacrM!59+Be-zV1T)_abww@#?cR$ehsK?2&se{^G2h`Gs{jC*?^i`yx&#iF
z*ZeNYd}AHwSANqDZs^!R*5cJMoi6*iuTqCViWnYK2mL$F?1;`gCA=v+%**Y!_DAQC
z*{iEDJ1lr?IXTEpvmcD>?#8~YuKdRiF98y!VnxNf4W7Hj;^w>aw|4^<SF4z;)s+)Q
zhFODb?H*y}zGqLlxGtVC+CY4>Bfis#6>$AZb4$?B8XQc?@LPS<7ddtW^4YhvQUI}K
zVkWK5xv-&w{3<Fmn@}dqJ)wE<Ar9QwPMX_c7$Do~jBZ>(pIyb5r>_ntc@R9amQD&C
zs84j&Xlm^exi=R9Z3<{<*6(3&{rZR4$kq;T(#kP=id$ip^+<m)BAc(nm+HeMS{Xc$
zP*n;xf#lIeEW|(35fJ-Z*i$pq???EqHg}4U=WUd6Uw+cJIc-Y8wd*s5GQFi=8Mozr
zoUX0Dt7v_^4vq;Am)4UV3FUiTV49ehN8$^0^X(|rh5%r3gyi?(Z@O;36}jPea*7Af
z^c2C^5fHjN2GFCVq;c;w@qX|bueW>H?>_S=@$4Ei<JO+}YB2C!q~!;A4QKwx?H68$
z=w5b;TpXH<8|-n)6%883c4dRw_G$CA?JIZt`bProw`i|;w83V&T$t7W70wgku-^aE
zr;nH49ESawBayB2nC<Q=lJF@dfbaFoo)L+9{QXX2Z0}g1QOYKEdwQbfi6|T3Ige%f
zkO!pYv~`4cf`ZnZ5I3xtxP30(c9nKY%*PvQE2Go5?81C2)*b)ig?m{z4Oa)Gjs<>?
zDArcad(70hSW@`V;qn*tKn2tYt2gcopIN@#`r%cl)T60bn&f@qm77rn0%$R41=Q_r
z;NZq;m56L8q~C8=u&(PSsO?ywBR#W{P?Alhk04Gq+Ic*N`IpBLM*XizE>INNo|5xo
z#!NWQ4QA4%j?r5%E^O~MvWqTKk<1EtFaKRUObuI3i@uaF_lY>Zas_I?AzQmB0ySd?
z4uOZj+v&oC1@l}=O8kkh$;cG+3q8Z{1M)NeROW@-Uv)FSL6sRPoOlZZ+mJ!i!>mX}
zaHtC#Ls>dmDYn)ioGOSaZV$&}ch!&t#-RnZyBJ^Mbwhy{N7k9`JR`pGAr8ZQ%`h@u
z{6eR>POMqz2bi(K(wFFW_0Vi_aH-_04u(sHhK5qsv0UY`kwQU--gYYW44^IE6oPvD
zLv|5;Lr>3o4Z6S|Rn+CJuHQPydtF%a3x?u`02m?$hTf)zvLIV?3eHk9zpd1vK~8nG
zoj<S%AE+F%e;f`pouRr^z^EuLiTqa+nO#{rE#U84bjCc<6bY^-6BXHc)D1yNs@yV$
z5XdqJvh8ATU5z$)U--@%V0G&>R15;T$yMOTg)Z1gH-qY9A9j8c1CI2>!+y^<HHpP|
zK8B~=G0bhHv8T~#=%*W}p@XHRxqIm%_MMcNAV6lPP_+lDCO-^lhrAy$djY^_z#vUE
zF{+ZTO(xSviZE7U_5@Ym4+~oo<*KE*yq{+hQm&&1?SvHv8p>C0f!JO@8zWgA&yoSG
zLpsy|;@IH*nBvzLeZkQ^`6Q9cfNJOF#~?xz>};t%UIp#M3I~yWi>A7~Jl526H;j&@
zg93Iyncf5{!SF4a)nRR&Sqv+3sn{WP(&|i8*H)Pk>WUHu3dx=Wi@^C-V+;$|j^(vs
zI#bT%nVyIV;4)McSfM8;Ou?>cu@iZgnm8+NO0ryhnkI&AgZ=@ys)LPm%Zlo<9cw!A
z?DB+9jcCE#KV@<(`I#{3$5I#yW~TEWZDn%fBpl%QQ@U=B<YHp`%q;4zYXlzGT0Mru
zl-SnMKl7orlFX*>xFD95jPxw-bIobCX2z|B+lYBvPNr14ekAn5#e{#i!dkOiCJgwS
za1p|;n7_Xn+_UB>1vcSvc1@<JF~2IkslP<<z`rvs2JSoH2z>Z=v20vf*U%W<PHc?u
zhK{RqkKF!6icrNZ8X+Qw00h6sD<`3<5<*2&UsHy!t9d)c$Su0j5w{<`^&EER@`CSS
zN8hF<u{*b;3^Jjp7cEjzPOHMVi>`M3nM$-&^M#7INHN}Z(M(8#ZW6mtG4#EBPvN@?
z)VWDB+lpRT+QopjM=sld_QhKqUjoATmUNN&VbFoikDQrA&(CwVpIfuND_p;5hy)P9
zXyUiJ-<gNiwBQQt00xdgX<3%(E{V!kO1%q|XTMx~_EzwNU>!IJr6qWOL%F0VT7X;8
zww%2ZsiA3U0(;IVJ*FjdBBg-U4I0>yXKf$8LNoN&t@XXq7lre_H>RTDR=698)LZph
zU?2sAWZdr|*4yo4edfT$MR@45UaYu#5Gp%fG(H2lk|Ev^?+fXzUjNl86X+#g&1ma1
zwnQ8XfK#v^0sR9=Sb;-k5U=9MimCnZRrWXY>gPg{5ynp%eadruA`tU_EneX-d%1;j
zPs=OD^SW3?u=!n4tElAZ%ArLg;Nzo`_GFK(cByzDdOdsoG~0o(A?_pz3ood@>~zX}
z^QyZ27?q1FUY9b{)Rd+Vw8uQ^t8^l*qkzk%p5RV-Aaqyfj-NYX+6i4nXR2;`lm5wZ
zppVILa=$(6T0dPrBIY8%lPX0eouNCGG0=?Z>0wkhIq07dWE)-C7IEL~UQ9E7-nv<F
z;R4-&Vjdk_K^FCFkJi>G9a0^yuKD$E7C9nFlf`$HuIe{i(U`a)x5rJ&vceaG6sV0Q
z<!ctir`6M|iQ3H<g{pOF&A7lkVJo%!a9+0K$l-t7s|)<6mU!s&V6jc$ixQ;W77br)
zDgI&4Y7kWNp0PGT+PS%bmfsq2m2~!Wx}!1D|IDGdz0=C7S(9Ex#xLk>E_HjJ8z2N*
z40YAmVRLA5PHu_si)U4DR=4a`NM{m};<9qgaeD%fw^uUknu*B0h8P|8ofluPxUIMJ
zj^$OCf?gRo#1ZDHYTlcXwdu>5{JWrVZL!g`On(KQFn^qN4F(hFeDl-F131Ho`S?dR
z-=wh1^ZFSE=`3&bJi`<`Z=eNk0}+lPOy3V4#PGO146@ti*~DkR&DJG+03K+$+GJQn
z`t#8nujaEa+nTvZvrNv!NO$-c$wnjeS#{MYOuo`q4zLu=%rm^+CSe;87r?<?jIsiJ
z2LI(tb2*GDakkOfGTdY?XY`b~?feXSf&TQ09SGjq+9WfxDL;3G9z~F)tUd&A=M&`-
z3fw+(b0)xfVB0PBUwgH|4sf)rmoM{--<o(w20-~zJ?#8*qzaPKS&didGzMI%eS-l&
z0#u3(MwbOqxbP0c*>o&U(KK;Tc5oc!?$iR>)!hZF!)7Cb;v&tQkOHY>fY%&lAI4iQ
zE=|f1oLoF&{v+Z%BfFN{=-tylq4T;v7zj}phh&dj4!dBXpWnO&Cx#Harn>(%{q8%`
z6qR}4kbfnKEp8#Q6o114Ni%MbP`!F(n2h8mPEBB~b&^v5kVT^eo!2>^BVoiRRc=j`
zQwz-?${7wEnQR<>nPA^ZI#mi;Q!x&j=0H)bT|y~--pS{QI(|6PI4@b__gtSm0=WSI
zC1&d1!fwTy-^0QW1ppOCbjDm-uXh+xf7)P@*W6g?{ymQL-kSiShuLM;*eDxNZQGSl
z@`%{1t++G+3Iosl;dPT^f4c(txtal}E@M2gb#aV4;Uq5Nar(w?I4J}|QZv&~rck*B
zinE!Kkv-cm=4--UZX#X80Ol6S5au&)-?r-?&TA#PJZM)*X)M)^^KYz20Dtb;%EKJK
zEMl_xyR(i4wD^NG_x^BIaq~_ud7Q6MqJ5MACu3!gHWP_J!Fk-E@h2&jdD7+_r7IA4
z9s0yLHXJd=hCU_b#*x8Jua(C3yAp<=I)bzL6FbJ5F$>?BuhP#@uaM9dF(J?#;Rhib
zv8ylWKi2bSWl%Uya~iieGG3Toay+lVB*g>@j?Cy_C5atXpus{4tr|yVSkl-?PK}Yk
zL$)?|sTd?DiP~`<6FyZ-FVfx+hry-)(dcK(eCIy-+Xzbeh^CpFfOf2QbVANE&@#mS
zYR>UO`#T;d(}1EEcQ#@|#W%-8GP5IQK;i<*bL&iejW;D{pb!V3eZk3**4+hpg?Lc-
zCu|<v(^Gc)E&;xTI<xt_ctmf$$|8w;x#SBD2&M&%OXR*H{P)>r8@pPRPbJjT4$Od<
z93B<cDzeM^#qsieZ`G>@3jK^ApktXd@x==TwOJwy^ja<d*TJ+5iRr@}qOR!XKCg1J
zLQGXk3BIKi3&(g3xv)eKr){1)5;#}Z%@`PFCHq*CUtlI(HGI%b0o2_&I^{y7&N4|e
z=aeeC*PT!+^vj_Dv9Mr|cKfy9%Izo&bjDYa_s6<-myzY~it#;8ndtZc4xiN%5Enia
zuC!kJ{YKV5j)3bTZuZ6Bv}Xy8y&AQB5EkF!Bb_42xP(b?ZYZwGK2vW3*sxqxFKctA
zUy~2DNpzl7#mQQFy@6JqL9$3iR+08mLYh3Dj4JIBg5{6W<x*W(P2PzA;^X{924+Jg
z$ExM<P{ninQto648ftzt&jC$M89@I?O&1!We35aBQD-b?-%#-3R4&X3^c5kxScL=q
zSXp(`WTwt21t}$C9iXsu^a`eTa$W`+#stCdy{1Jp^MTFGChz@h1|7uy%tw0JkZc>>
zJZ{UPEtf9Cg~M2EdXa4n<*!p!8G%d;$T7Nb2FZ+fzb?j(&m+rKn1yZ@bisu1rb+TJ
zPAPlB-drnt4_mD6r-&Sx$AT$F15#QSm|<6$)S*Bnd1tw)GqRyW481#8@QPM8Gn%R3
z$x;SqJ^~FtLFc7C{1Sglg=2L&9SH6a9`J1zd~c21^mDBnPHgwaDaCtW-5V-6ooie#
z2Otm0GR<v8)5xx@v)d$kssPH6==9TyY_!8OQ?<9=_Q76ey$Cz9Yh(BNn4IX9Ju3Vg
z=WmWO$N!I^ETjxHn8_fyZ{ATWY<mBQc>6<@GpDwld$pjf5y2uh&AHE0g}671J1dkE
zDB2S<WgrkvLAf$UTC>pgnbo~?&wvTOG8%0DEzT^kQTffoyoDk2k=JavIjvUye9YQ*
z2!TvCa)5i{$Ll*-am)SP4$^W$+$U<8zQ<49xKRC2K79iu+u3f)VoUAFj9SWBEs%wV
z4X|)NqsV0ULS%4i56^|aNHc)bm%AwOL2s1A@s=$SGUGP;MB2`?>Na=@jw{+XTDz6_
zmm_~`{9fOt3zEe*B+Q9>6H=nO>?w-b?}bh2G#NgaQ`@G(>TQpD5)AEP@X{QUfwi^b
zlGXK1j7{aLF)5c406!GiK!CwdQxq+K=D0D~dsz$Jny@4wuyRiy=@hr6f2wU<@Fz!y
zOB@-Py1`d^hBv1W|AT1;Ox_{;Z#{AQTC<mLNvrclPB);HK|-#05fz^)mwk7IlqR+3
zBTo@Snss@wCF}!I;h>F?u1_zFw}@I&<bSw3i<t#teezz0)Z0`}p@7YQbAPu@R$Vn|
zV4NdKTwqap>=O(;SXxX^N!)SzDnmK}f7b|TQuaki%3<thwW$0^^(vNJcO!<URDD}Z
zT>~47hKKc-bu5t4z|LDwf&*3+GFSdv<P1kLGuPTXiy$7Mz1u58!m}4Q)Ku^-H-o@Z
z;2W)fwd1td*4i~W`AXz|UIB<*062p0FqoLoN7GwJ7IlJf>CCQ10ACA|ny{GR-|<6;
zU9tbGd1mwKyxu>}&XB2NKE3~eLr}Kid+8Ig__-*2#&#TqT#T1o@CV%VV?zoFHP#}f
z%<HJKfCVrPq1e4471QFK0+z5AQf9y&ht7Dwo)iIALlV{%b_nWZOxMY{KqLvsMte4<
z#0N+H$iO2)EW|0~Ye7wITT<WPZW*p!UpGI$4Fbo>3BRaTP$iZI978ag=sM*r_+~5D
zl=jig`o~C$b_S{#$9phMRCqty<m;w~b3`7V;Kd?bUQFcfJejmvqVk%@E0x$DA-`%H
zJ^~`C(RMmMq{$ed-^Ia|a!Hva7aa?ex}saBA^iNBS|M)Ybet<Y<X^daUM>A9Xx=&i
zI=}9CFeg)_JTeNnfNf6T;ZUSAur3zTdHVraR^U3KbEarV=Kkt)=2-s)jmj6SwSjX^
z`9$)zM@?vR<i+IXqU+?1$l1s<Hy>89Vze`x<`1`Nqr^{yHPDizziVfnW@=^5i1v}w
zQs^Sq!kt$RcUX{kIre>cR%Q*nHO-zhzGubempkfX>|EL&Muo-ZW6PT>x6K)ql@pzH
zEM{hdH%TI=oaHT^Apjp$mbB8OSz9Y4B-C9UN0v=)3nr~^70BQeJVl(~!e!)g{2T!k
z6aCv_`wx3_+_7YwIz}RoM=x|7`H-+cJK9VlIKk=KS4p4X%`BH42egWioYumFi`RuE
z`cMlJ280OX=pnvlIDgV$_OB?PE|aihGYG_ynb9^k8HY#SyKlt51`L1B1lhTY&hN;(
zEjXb1m{q^6)dG><lhqabwl*>EpF!pJKZA<!wBWp>7y>nLjf`XG@>F@Mt@>k3Y_n7?
zhX^<52d*<x&wfP4A|C<<6MJ)roEo|AkZg7->UVx*GzpYR{F;ak{_|)&vuCKnTwKYi
z8SzAPq1h9A)osg0R!uGC;}>GmI6VNn009ap=98)%BKjL+w~gu^t36M^2M(5L@`_}A
z&_R!0Cx%5dcughuJ#EELa#9$S_a*`k$zL4@GNms;FTHJMx-usFw%@Au$GQp1tjjw_
zacdwls}!z(OJx+QgpRDMMuQj;7X=ELhet4wqGcxOlt;Dc-H8Qx{h<P{>kVa#r-7C@
z0PtGYMipp9V6JIu)*rFhg>=mvs~YH5HJ|E!vC?Q;+?DJ;4hR}jA{#ez60M&1EBSrX
zaQPje>vVfa-FLN9?}Jk*UVdjvz4pqUo(uIx4<|H8LWT#$%)dyCr#qc4{^zkk_;V!E
z2}kibKAydpU$e7lP&V<sxki<sM}dweQqm(nR!cjKlzMdXrT&>`tXsZyB&$#Br>^=j
z`dn;L5i-Olx-PitwZNx#Di&gX;nO1Ek%yOd{!x#OSfB>bX`q!$N-KTGc;%%NmDA=c
zh6UKtcQ9%sKdd)2CG0!Km#dL-$e+cqllmw8;Kev_GsHbxKfKL8pQ2850<MLyo|417
zH`TRES<74KV;!;2&1+-Kjj}&teIgIBd<6r>9?#aJP@9!gVu125+qj&;le?BmoL?y%
z>YJ6gB+!xup`@hjue!tI;sW(oP<)S|J$KmC3zeeEX#q1d8!3^4PDZx;+4x~_SMIKP
z%7l|-$R6J}>K&?Qr_6F|Fbp)bmx`&WtCyjgX8F|y#cy)PMit!_52yZFh^qgCo(7kq
z(m#xD2&@zWe6T`9*E@t`<He{bZWK4){iL8)CvQxTm)mu2XhYn6bh+~J&#S<d;7h?=
zrc5ul{lgqX>ZsO}6N=H)0omHIHn$XeKbT;vo@k6<`nQ5OT0&Z$$fyMBjEf8OqlT0R
z_Vf>(`u0UmA5p;Xg)ZNyq|DmtC5i|U9T5Qtcvd_?KUBA7X0fHR=Vbr-$t;k>?$+Oy
zRXJNjlN{*8X^HW_km|etCj9c{rE1Y-2PW$=Agx2P*F#Y<3dV*{*S;Y2GW=@Q>wl1&
zMXq9t-<rUBviq`L#}e~%cPx4%!0WVDbsXN`@ii?WeMv|g{aAZOD*~HG2NJ(DgZswx
zYr*@@wRBUTF*B>8klz}ChQskg)_Z$`8ha~q7N=cgdO-9Ru4BJ*0OsS%Mw~tr0SHNF
zF!JVG90r;x6`H|~5(P<Oy0<OR{C^36E||gNpGu%qng3D6#I8HbOGab<kiQ>ZQu9TE
z2xbsF-xK(c0y;AYOr&99CN$%YL=~UQdY@ytp4&e+^}7$j5+~35wO+`#M!f+#-|K)7
zfTBfiI!rg8SuwND07nVn4NWz33n>*;I@u|n;_|0G4u6xutLT1rCF#ibY{ji=yNWsw
zu-8jh4HJh_zyXndW<MOM9E6|+lp>%BHM-iy$|cUs%~^=leb;1m|7nE)WLMy|X#fW9
zvs&7q7CGDOhT?7&1_eACFvZaJ5Z}?Z&&ao}*8mH1$VwY9n5_DG=4ScwmUBb)>%Ndh
z8<3dR()1UNd~*0)eT8h_j0&u{0r~R@kYd%;h-#939&}wV;5}aRCjxO@G%c7w6RjLW
zt@%p^*vDbmx4!)|YQf&4K=$YJUYS=h(qZ<LSH$P@bWR>A#V9q)0467C+#ZS2AH(uV
zjx<u0TT~L85nr<90}sx`f!hPHJAe&kg~p6EH>U>7zkEvfb{JcVVb@xLXhfK&%>HEA
zOOBYAy~F=WY}YQ2Kmpj)+wiGEUO=X;Cw!W1xFV5AC6%9)QGSqA?Y(SlnDwT0IR{Ww
zdUhXvUlW|3zQiE@zS@M55a0OhH!m;@48$|-ww!*^cJ^B3aylTB0QMmcrS<cDegF+i
zwFOGbUVTev;NVbN+@K{TDKH)I85*2Yt!!GzUBTRTg##SL`Y9`D93geRyI+-m2&8>f
zv;F~W*(IeffhcqWZU}C_(ce~)E9_sZXy7gpSQ~{<v?msOrjGZKm^CL@#4R)uCj6>9
zxoww>3fnegBb{9tRnPZ|TpaoC2=a_`R*h$U<sO#dbp1!L{Z9`rF(0R7VO-Zmn!}Io
z@6Km4rM9g4S_KevK(lfP=`PdI&(NZ-f9?c8U(xHwn4fR#z`$fha7GZ8ri^j3kO8=8
zznjRzs+yXv-Z#6IQw~hif?U<6%yQ#aXWJLA0YlS$K{6P>$m?$WbGHJ54gwX18dhfQ
zwBFARAO@s<7r11Uv`%9)7Jr@1V*ch;S$D*ci3zn!WGi>tU!WDaSv8&H#?>cPC-;c~
zr)VBr(tuFW;cXYMo`>$lqu;&1ux<OZ5u3{YvM&_3+C4pBci|6g^>WePuI{tZHcoZ5
zX?{M}#I~J-46;~Z+=J&sj*V;`?4jgv(r0XDM#lzN#|yhsyq?Yvtab%68b#*RfJFD%
z87<Qg`pm3$S7s*X)y<vdK3ltEi1+eu*h;%Z&T`)T*75D3?i#Qb4{iu<Q~_1!WB%0h
z54$rMD|hD}z$Hr=h67Uh@Tl4YV;B^)lfIug$Op*D)rDFGE$}Q@I~%1^{3Gu~<$(fa
z?8`Q=ss4CU0MD$`c`J?YW!KP0-_6lm-#A&}YA5`?(-=Lr^~t>V>0WmJKwSW!@An*X
zbZ97O^PJ&MJlyofIAoN;_A~Y=?E$8MmZP=D04sretC01}NOOKSS(zxFv96B4q~zz-
zL}YnY^%8;sScw~N7oE=!oi0$$=l@gA*#)uBnG}`}Sud3izKSe2L&ZCO|Jn9<5Gwio
zF89%Z^>GkzmuA&tL1;|w>0Hi*rrDX3$=ou*otm8nSm8l6&0dG$gH~@d(xJurLR}Dh
zebBL<g8ba*Ya8pxCzTgNr+^<o4l)ZkE@elzzLAJ|lHzyga@W&-$sr(+hRM?V57>^q
z^>a)EfC`W1=G^{1)!t|KrXe^d?i0Q21iy9o)$ILsqQ~!WV5pq}tv<0*Dj<*_*xYlq
z;QOQY+fRqyP`EbeFDS8UQAl>6A`d(|o#HSCOqKs;eSeqiT2RQ6S?(Px43K}81kdO$
z)$dPi>*^LtO1LjK4_o^#+PpZJ{Nv#m;0u*4@?>y8D<k0`Uj8C`;FIhD^aoR-)6J&6
zZ$x7wW1e!vDb#Li`|0I_RqSezAH1pOE4as$PW6SV*gXv3kX`L&ygG(*>BgZK^Xch(
z@0C^Ht7kj?qQAHX{2wiV{YzvmJ#IbJ?K~y6(KhqJ%?a!vCq+US8CAPH0WND``!caA
zYOp7q0Dd0*+l5n|_BI*fg1tTGMsLgT>3IGJngis2DBpwQgbs)i>DEr0!*KCd5%jX4
z-R4RESqK9MiJXa6oOof&IN<!uXO4$3UG{}7%=s|oQAeo6O(LVLT=p_O;Omog+i*C?
znVFQ9+jE!EH2nuV4VzQtLfy*)kLQvchTr0O>}_45l;4%&10ga4+Q@bKmf05a4@<=U
zU+d7TNJe7eqIZ|aC}Bq5baWW6z#bg~<(&P>HJChPe)#~WZ-95nRW;j26IcWQOUDXT
zPNDzh(JU7v1xZh0aJn9bD=t<5Mx8XfA3)UxTe2rx1P@=Co2ai2WKt(!X9Lw9pi<yx
zjalysa#tPXn`~qR!uf+BZ4L~6UXOakEtAbytGt(6?N{DFz@M=?Z2h7JkwBRTEJ+rx
zyud2HL-iJcS>)ByW?TS6V5%Tr@a_V6Rn@k6kN}iU?zOOoRfPBQgCUF^&z&plY_u_v
zQ{W<}YFd^CH%NDuw0ZOZOlJm7!9y-Bo-UXo{TiT2bVe$Z{rQ%LOHz4oFLln<)o0_B
zG{JU>$3^F%2Lz_e(NxV$2s&_A{CokxUr3rKCPO#-J4y5|sVb+mF({v_O)_X%`8;ii
z#+=R-($Ad~H!B4A)6UMGbdu-m9ah#(iy`~(Y9-OLRKcGW4&W3hj({Py`{%!s+~)DW
z++7OFFw8I7Ozj8NXlaU{Z7mj9y0QR+-jZU)VO=2B`l%-D2_ykbONfy`C+Rct#;BR0
zmf<HLJoSilqycW=P*D25rIZVwp8lgJ|Hr&^82mW30b2ddbo;s7%^Q(*B$0+;kaK{j
z($V|IDfQ=G)2npoyTVPdl*Gc^0|P3j%&dwZw#MNjsxNYSlDN>o0{3MF!~(lf59a+P
zXSipi9Z&AWR`^u@TL4jib;z_GhpPiJ(Y>q-$SS~~7XCt;Y^UJ_0aFBevU0=I-kT@4
zdovJO_F;bq5vY=`0{y9K;_pf~0f_|4xmc;%oSU}z$3p=ialSom93$IESrHrp%)ql1
z{k&<SJ=v<VX;kk6Cn-L_<<~FscZI)z0N?WG(<t`j0<p?173S-krFNJL$d@;N3TD9`
zORKG=WnwyWXdm`o?m4po0Gx}9#>||t<$A&Jp&1-axWHd~qml4yS{?IrQV!`MEj^^#
zfwy)QP09s&hZA-eePZlEpCS(h<Q1OreK7bGfJFCjhpo=;FeLjW+Gq7dI*)O=Zmu(Y
zLqVb=9vVUiZp;D*%3qHpJ%JA`-Itb=K?-0RULPq>?RB|0Oz|+kiP2F!(QZGJ13`SX
z$us7-JM(I&e%H8w>PNSPKj_|oz3~$+9Tb?0yKeT(c^Vu&Zv9VBnSa4B(xFHCcZv3u
zpm5i>`S|B)Lx73#bLcL)=_W4=fe;2+x{;adJ!yFamB)5o04PJiT@4J~+(beTMq)8}
z!d@`2Fz%DisHr38?(7w~Xg*(~1a*BOc|fWjr9PAtF#n|qxisU9VB#;;M0l_XN*{2m
zz9h#T*7G?#(!lc4nN*FY4%^t^2OiBgIa1{>u;>^D*aJJNSOnQ{35GU^fuJW#<43$$
zk?|or&I~Y0ph5F!RK)7;R+5cbL~;GDfcFq*0<XB7TV#B%V|TfUe3DB^A7DZRaZ=l%
z@IkP0atC>~-eFbMWaj)9b|8w<H*$&1{1d?!vrhE!-ioQ;OwBg$40$b!dMVADh59Ey
zbOln&U@M#CrL_$K+DKWGU8r8H8NHNN$5%v5HZdrO2qYK|KFy{>UptmkfP4lwJwKTW
z3=hZgIv5@J8^g%yNn&%gHL3#fB;zK3F9)5akpk0cfdDxPKe8<y+9qID#g}RHKNKn+
zyrakamgb4^D+?-VtpLE~6gUcDKe-JLA3&cXGEFY4#;_UjyNSlJk-0lZ^#sHX+^h;Y
zkw(>LnnN~LM6pD%ano%z(fSuk<rkpFalhA4UTe~PG&C&FhZ~KlNN)0#milWsRZ!$%
z>bw(kQi>urJoaq4Ikatw6r6~RYop?YwRNo-(aMhv$IZ`KD3!bM`Pn5|mHq&ZW@x%L
zc_IXYc>>HZzSmPPEb<06bRK{tU>gTtcdM4ZJZ!7(o^cJnR!m&z4!AhY+<%IQ4elf0
zvn*>7pI&1d#yuhr`r%?rJe#dN;B;g_dwEcw#x8GBj|3=r%U7PjYwjyTETCLF+U*UA
zxdcs0by7M*By^;%R9B4sU(BSl{4<4s?~Vcog!L?OrZea7No@E+jmKh~^h8m~!UsJO
z4;by+1uCRsiwFv>R_9KUQ=1bSt5dO>Ng}nFs@`QZ*S}nlYTD(<dxCf@sbh`Nm)vgM
z+G;3H<TK{}GC5H3$S1d7<xg9S+{dAa`-6R%H#8$KBwU70lThD3q%`*msm<bHZ^+)O
zEYXIP|C*Po*jPVue*<axZ2}RpKhQNE-#c*O*HX`Pj#PEAKyM3RVNyM9cbHvq8-pBR
z<u^xojPbR)Wt=3rG5nQPfvJ`;e|`RMwG3FLB3D!ojloAeHa!_db0?-y<WXvp!qV@l
zG^;du?k`!?OuhXo-HDLlgdTr9aumBe@%v`Gf1G3uM)leIXAGweGn9N6jk>U>u_=KA
zE^(+>oqe^NQIkmUx0gQ5(S6`mOz}&pKCLq<H}K97i+Lxh)`m=x5L@Fgd_mU1nI>0M
z`>-dO+fRi>U8I=3)4hHD?(3pL(L(n&qM;*hDU}WkOZMVj(-&n5ad+OC#dql{65F=Q
z)08qV=v(XA^oxkPtzyaB!dU1kO+xK1sp5z-odb<W3<m_^%x7CPtG>>J(d*K_w-to3
zC;do_$rZ4`D|;Dft6;1hi)_e+1CKjR{(eOF)GSmm?3<V~hPL9W2G>XGY2EBg+B%^x
zG=rjHlR_~yNh9^|JE|kAwI#rS!-ufAT>np)1`<u=BmV#_Qt<|9%^xwQaTrScqT5jt
zrfW$o*7VbKN(wrykHo10zhJ>BB!}u~Vbi@JhgT+$`H7KGvNvBa=@U~EVXFWa!>ik8
z21g-SgCXOBO2k|bFP`o4aRwz*#wA$w0=sjxH~e*6Sxk}Lc|#GEBxVg91-M#XT{@@T
zC4mUi)pyij3QKK}vQW)|v9`)bh3vXV=tQ~nnGzwiOMa|DJ^k-d7%U`XW*&#qFwrkb
z7Guq7ExxqZq6^&Sv|J!Ut%4vMQeY+RD)UOOQU!f!fEriMV9O%8jik`V^NAXSawag7
z2g=2jEG9MA_$N@n@sS4Lk-{BTmeD-$_h1Fg(Wkcm^0ENLqr{$lPU)z|T%8X--s@^O
z7vnruSk-tLQ=>?zFO@S+O}~W1oJ+s9fb?NMU_R325yL6`fT@nPfA&R>{JKi35R3#R
z7UANhHxypXF-T%R(<Ovu$inE;Iwu^OT-^Az;{1o0I?;m5Q3h`)by=&lh-V_brg#{!
zOp_#*KAm)#!2qY}eX&MWlT^r)kSPVvRR}!^d6dKeOSVZ6@6z)~7I{0YZuQVfNL&kB
zj9dB(RIg@TZ*k;YdMe4s(!mIGVbn{#I0%Dx>Pr0NiaZYcJ-Vl~fv?%TQ&j7*Iw@rB
zacP*Siz2MYqMa01`RFQ4Y{xh(*1R_NQE#_&!ESXtU^zM1bw3wFJchv^$J<1x2Cz5A
zqa@C)FHT*KqUgZL#lJ-^{YxyuLWIE&qvs!#SE(P%z8;<$3lIvJB9GIxDP>L&9>SV4
zNh#Hdomxz4Jh^>VXmqypw`E#2ND?H{eN6ZziY)q;<l!SChA?VN<CeFj#-cIb5yxp|
z)hafq>rzE=sRD!XNXfC0b*xDx18Ip9FM6$Fd6#lu+y$!EMklnJ6Dt#ZDD7E2_BSV^
zka3fK|E0NoEa5ehInOnMOjE!lNAl8sYwZlRRWPq6ooqsA3?ylb-X`#aD+^PU*Cxx0
z;2_$bYRoK`uamb~0o-WJN=<Uv$=%zGh4fejLxIN%IJK?T%Ql*CkRx4>bZz+jX_)3_
z;AJt#1LtO_mECiT&@}+X{B1e(zqRoBZ=3*#Agb4tl7{r&mT?i|{9=PTGmv*&tj#0W
zw>0!Z<h!+rC}vtx<Ui_)EJ$L$3nx=+tD(E@E9?>~$Y$?IuNrAjJA~H8A;6O+sJ=Eg
zQrjtUkuQQt>*O8<n=WY1eKA&u-O*D^wpF04n2->aEvc(MvDh=*{*&f_Y(wltkatbK
zmqmy&|5z@tE{akF506Coz0|fCfkrj7!CB2yo?EcD1aBS(q^p>bJi^fAlXMT<E(iFJ
zy_NY&R-z?88%n$c?LFD?xbO>ia{d^MwP?=3!^x!DJ;nSvAUorNk%u%_6-FaB&qo@T
zmrvgR@7@<+$DY{y?SMOuu(N8#anXl9m1fbqy2Wt5j%H=@BG5275EXDD-x+?1{1k>}
z6-PS0b&CNeEnLLy&=!SH3Rzu=e4!~`l%X*j6Mh_r5uBYFL`wV2+!(9trI9E)?$><>
z`yUe=7HJ?p0=5>*9C*(K`Jlt@DLCer%|vu;=8!f4Y(89m*aV;QbW1gdq0*ma(J*2y
zI^@--eH_W<t2$ZO4Y1)9qDajM`0mx?#gxSo=Ri@DPt+H*W?l59{E&;K(|j=T={Fw{
zjj*|sCGo=uWN>Z5w*OCn2V&uLq{aMVPW^2sb{vuEDkV=G>WdK~kgZPp(R3}-oJ<TE
zjp0l4xp|@0W)W_W;Wp<Y_VB?HoyOXzRL3oKxqRkS$ZFGCnS)6dEzuXeKE1ixbQZcQ
zgQVs<>cgwKBoemYm8M?fyfaUgH{D7Zf`ai_krTZnCnk6gZ+s71IPh*8b_vf(8Tx%T
zjSpK)PgnOAW|sLl|4Zl2#{c`!Pcz7C)N+eLu~=t>J{c8VTL6b;JTu9{-+T3t`H}yP
z)Oy&pbRl~=+Hn02<y``Pasz|Twkl@U|8AtgW&i*EwSP(SVM*Lg<o8nl?fC!qhyNE}
z{O>*32}z&-)3^TLU;ZrB``?k6e;@kqJFQ0lC+z$!OaHyOyUG7QUh?jqle8I63vIaY
Q5%?z~sVGq<Zt&^<0B?`;F8}}l

literal 315464
zcmdqJg<F(g)CEdONtYlcol19iNT*15cee<FbPNqc=YXJqbVzp$2uPR2(A{xg_4j?x
zckiEYpJ#|+-idS0K6|ab_BuqWsmNiXzeI<FgTqvim)3xTdqw~U2Y-%=4E#muAm11G
zA>bkN&O_7L%EQ~#%@R)8)WgNW*~7us?3I_Lo4c*E6W1I5H(ac*Y&<+%+y&X#9RK%%
zH_mR>Z2epBG=UdEbCK6`hl9g5{qqH1CRS<-2M-6QAT6QglfD1oolvxpvEm&xE>NwU
zyQ!>u*IrWH{|Ut^oEUK=p&K_sh*mB+6+QC3ZE=buRc~gnm$?+_H;pg?sv$KNTc%pG
z&n-pr(2*E^WGNFX_8*^`8XFrQ>l-$eZvzel?)tM*45tm38V(NZ#~2Xc^J-25RogRC
zrf({?h2z=#h*^hg{_pMZW5D9`umATita}^X$Wf`5djIFP#6!yX{{P(9OZA*}$g}ys
zm*~wH)`k@Pzn-P%J^KHb7jmb#LijgHq6+K6mgx*(L*0q!k>aQ)jcNZgX6)E6YIT1v
z^85T~vElf*NqJv-KiIcWDf6YjjqJa9_uFy!^lzGGqzJar^cB+hRR?2(7KfWYaUjQ1
z4dK7Jm`%Uj8$pWgZ>zk++hz(C-nuo3HX?!!hs#sBhFMT$=WV3|SJX@X{JWBSRR1&Y
z-WD+=Pe=VEBa2St{vAOR2QyzZz~53lZor$AC!6J^V)Y?rV)2clzt+7|gL`_HU%t4r
z_nFN9eSLqrXzf$bJaFzoZXOe;{O<2ci%9eS8_r&R42O*&l9z_)vUte=CN@@h-HiCj
zMSt5^eCXyH?<{iGKCMWBurDwKXRyVOxkFC5VXo}5k#9IEczek~L?>Uq=hnPDaA_3o
zE;24&M~e4v`WH&M#Q*aS;_pf8X3kr1`-mamab!)6aCZq!3psu;`Xp=Qk?~Z$Os*l8
zH;bVf=bk5y;pLB$mXCxYQ%MXJe5vIKXC37z;jh|b#*s-+muB*<LX*U%y220y9+>Jq
zaaVrF?8Il~-GorcBZ(Te*zzdHLh?+1xck5?gV><_xajRPTB0Pi+#Y+M$p<4|S}2KY
zPFy@bBetsGhPZ?GLB^PZr>t1Kf~Shp>ADwEyIbG(-1nBzrZgFYLuZ%3Mg<1)uO!~U
zlp=|v$qb&LB}dQ@gtAi0fk>5;tZgvxLaGgfVG{}{#6MD^AozHUM>(_gcRqe|2?vdG
zqpztx<)z6K?wR$?u5R6>LxZ<I(t9?Ha9wntpQVEvhsByM17kS$i$ow!aKFT%|5n@d
z+kd+ZMR7gZ$bW!k#V>+;?0UYs{j-`(0)DFS>Bz($)?iXL>oCc=8T0o9*o~m87LwVt
zA1)jTVwSyQfkc-}0y~#+sm61Xb9~{Ie1q3rIjp04E$vcd#TE)<T~MZEn#jUrmhG9H
zeGH%VCMl%+h!>6W>PWe5hY1%cybF8eId}UUtv~4EG=x_q6cjpMtleOxy!SZ{4Mci#
zIr~ec`A^hi)TT>YlQE4STO8m7-yG{+J#(42!2_S%u~fTOHH?scdHY+I1}DI4omTZH
z(M?KInro3{3^PXqh~kBR#eL_lYNOyUi`Pz6xcnNY4hN{J(^w~a5$!QFbgy=-amAJe
z`kjrRsAiG%&uc$3#y3qGZ&MmQP{7qngjTDFb-$p`wGeeU1;={-Qfzi$FkC(|C``jd
zOBt`dpb^&7|9xcih*dtwZ<MpiMs|zG#v8wKHt$6_?me@z=A3=QaKE*do4=KM{l#AF
z)g)RIwDqU(80fpy{e0I8mm<m7L-!)#(fmn*kJJ{)sKPKc9nt4&Nb|(0DEdmi+Vriv
z5toble?vTQa_--{RU*O`6G})VR;i0ECgN=!uWTGI(sP{il35{W@G(@%ZUv^2r97*<
zpFH7=?z<w@QEiFO&DTvOQ|)G|8r~V(7Jkp4Vaz9s+!m0Lv0!74tH691OW;>*@^cLh
zYPh}~N_lNC-g!dSl@zhTEWE-5p><cTCQWp{`g4Ju2rZ*8QvOwbc;pYCuCsAvv1oWV
zu=}?TSs~b2-<XWbEH)RV3fxy*Z~mz^BP3_Z)3@$yrb@WnRkA_`2hOKfcYijt(k%}h
z855I$D6m=?&$Hx_1TvMj4R*e`S$^#-ethX}3WDITD?}8#WQuW}kvTV1eZ_5P5?x%6
z+(jsbJcrW)Czz)Q>^h-+82Rln1+R-jDy%Ptfg0569(U0gJL`Qt`4dz(1%FguT?6)j
zS>n=du1w9_`H%68M8UHN{=Dy6d~PAg0414?&^I7;IQ7~_ms9K|vNF-yY<g<mmIY;I
z8xgIc%1l+PDqKND=l)ADod26(`Un<24}ZsD8zecWuF5gq?z*eU7H$()J9Q!Zv?stQ
zM;-R+CH+@NpQqRgIN_(84S6_3C_B|lT2!ic#!k>9nd^|@5y{Z^g<%_vb-WmN94+oT
zf(P(Iq=rGa4`*7tRHlO)^To<VNsM&ms>w{ch(uVbF%8&P^N8~cfqyPh8l46n5C||s
z7IP8%*-5sio&~`_osE0EZ^S$45WH)to1zd~79Dq(uy|vG@b%@vaVhChLS~FYb)WJ3
zTV@T^b>U6toCoqM?E34IO96-qKNf)qOzmn22+cUWsP1B0Gcb^6?jw%w1FJCW`DgWk
zy#8|$FXWV854<gH85gd<rV)%8yT&qAdb4?x=B)SR<lGxX<R18S)L7)+{bw7en4_Tu
z11t%a{q!(sZ0g(C+c3LqB6J8<jtDC}7`&>fH$?7MtW%!GyxHsT5H;!#_S<S`6kXi9
z0G}1wyWH7zD_KkHDKU_%c}6jfht&L+re?Y=5M};iAJ*^2D7Ri9?Z7<44TNhIOL=~r
zk(XHQ*?ej8uu9obWt+%`xWV@A)b-L|Oh*;hjPtkSf84T2so!xwm_)WsqAE7w|EvHa
z+my%2BkTR`03My@)!!rM)p-xBN7d0Qxj@`PiI@!mr2PKVO=Ys#PESJn;nzCVj#Edn
zw65WMLOwz2y^S6LnXk@8f9_p14Qc`*sI<gV7$!|R3cIDM!s7Mq@Q;<CK+I!;;26*O
z#dmm}ZwnY2Q)^L3q8h9nH$^fu{xsg`7uxoza`gzfSGyT`hBZ%&gdithbgC}t*2+2l
zD*D&wd1?P!j^+3$e3v3_<z7st*m}G)@CUSN$zC)@0a1J-!q}2D%naV|DDM}nGa3HA
z6s9ojxOb4DiSym|cko$u73JDb@|nA-8M>gl!0;QFkKLQLSSj?b#SaYCf7u2wsZXB&
zehVo|_Gy3nU0sqnat4{|*`}R%V1ZJO?d~XN%6s`HJhk#q77DUCwk6wp*CB7KNn=aj
zu+W`IHT?1uez~4RFA%iKzTf{l0~x+*8z(jD6_={J!MFs(>~&lP4lyu=*al>Bgbltj
zlzn{`pT7RaP39g-<Yr*``O@;^ME8a0V(=w*8#*ZH3+j|Kheydi()AGCn5J7Hyu9Za
zyQ&RCpjQ$F5b2A=NO`fQ46sS%h&m8_WIOH;TXWzFl}Q>XNyZ!GTnkyQktkEf$gzpS
zvqd&J<}PRg5fg2Q8(NC0-ZMt3M0v7uc7laeN)JcR2BoQrMdJ4~(e_Ow4YqWFNef6t
z<zv5MS_~+iz6mc{m2;0KPGYp*yRc}!{u_0onEw&gnGiDFwZ^Ez!VsnwP?ocjZaAp)
zMbs0UiCz7#sJBqg#I;vzZG2TkpzKd3PUQ;bHC>7LTpQ-U-`9R$UOR0n*e=);7$LWF
z+xbPHD%>*Q6uGhN9yd$%Om^jZr9UTA%m*B=FpVa+;Okr|6={a5pu*Ai&U~jt3Ry3v
z@7TLK0EMon{qBPVdL)}6XCTdoy%NMKOx_!7d$G-Vm*|5cq2@FbmP7V6?RUf%HUT(z
zA*E4jRqrx-aM8Wbd5|^~mRn{YC1!{OMd>z=S`Y{set_P9J>&(^8JuU7Bkspev72~*
z6@kxhR>0SNQoi^965!02{~i1#vRhyJ$<xY%bLiZah}n?`27Jzu%k{Mf6kA=qe0`&N
zto;b2q46b+KftWy`bkj@g49?wAKVJ{J@Ob^QnOz<i09C16(AD6_D7=Y@7H~U*Ezdw
zWKj-;INGHc7LuZTPUUNWqw!^)wP^=g-$aaDV;b3znNzXe%5TY@jZV+PpP^DNbw)Aw
zqUh@<Ghm#BL5Gn)NDzT`V`?@w<i9^<_Z<ga2?BKT52_Rick7m_Or1j*^PL3R|55CV
z)&E9A(=<3iFPDW88lqlAmDpI5j&t8wv3!`q5iX65`x#24;obUhX+(D3D7N#yF{k@H
zU;{Dkd2x+u`Tok4;Nj*awk|HyvaJllamw3QhQgbt0UM0tJaONMRbq~8WvgXlBw})e
zL|z)5F2#D^jM9j84-N?%r~BcByn-@0e`lLgj%X06CIjn}#x85>U9;O1Qrb9%vKHiG
zM)x~L9Za>cQqPbOGW0CrGj7Sgn5y-+H`uS9R6rR)#%$-lAfW5-sGe>9Z$zE{Ga}tP
z=Nby|w!slfk8iFPHkwun+7nI(_m%Vd0Ne$~-82b|qQn2e8K;c1c1=M=yF+Od4AcxY
zmum7vT?#=~w<Ja@O#>I5M8U9QU9^;V7D6F~ct%wKNdE$J(r%2FHLYObT586rJt~rr
zLfUj$uh2n-jd`DDk#oI}iKU3$H_-WxH3wZkVidFF1)PL|9fgBqwNq{(2ur{yLyr2h
z#}G@_5yybJQ4W7+k+*r**{Ml1-$L5WVV}^e)s?{AT=U5ab+?b$l~~{ZRZ52|{d<~;
ze+DXo(4-J~CQ5oDqf=OW4T)hJMx}BIlk3e8&lAm?*)JR<9)0DUKPZ0=XO49!W_^&h
z7q-_uJKzz+O9H3CpPa40JcdE&y_KJB-B94xRsCnZ((d-oYd%vtfh7hDR?M=k8#UCu
zhm~%%k!0BV!u7WR!24d-OZp|cQdX$<!wayQ`&;jTHr_V$DG4w{-^{bIJJ+ez@cfNO
zfYk#sDCnYHsu#sDi@~stqqR9Ob<t*Bm<Gzk!}mLKcfE|w(v$^udOP+kHDZC0$+t8x
zMclWs@XJ`7R&w$<^b`XWbkI&QE~gHm;S{l85mmJ^t5Z4AB2m>z$55eG->}p9n};gp
zI{y~KGo?lln))PrgWZR)&9#>MjJXb#rL4j&CHy^6JQUsAOT^n!`GULFn#ZStT*ri6
zc(@$aTCGO}28gkLp7==~qhmRDuffFXl}^wIP-;CLd=fKB=<N|KUen<>$k|G>G6pI{
zaa4&s;kZ=mo8qPyH<!1hl`^lz*-5$6v0n;n8}=kd?epU2V5gKE7j-9|VjOu@osNFb
zT~$mgo+Rktd?GP&ps=2=UU3h5^Fdtn*E~_T0<+VPCzmyBm^E(X*!4&cnu^xe&CpL+
zpa?-V7Vphc3T0uKIBI9`<)ib#!ljW8e8gML`{@4m%Sd#BjaFp_!!^0AC-Mge5Wn-(
zc{~@4ayxptBa#IXDfjTI0%fW132K*X0>p_PrN}?RCVHVkUQ2E)g(@)(wxSBiteNUb
zq@bHJ@vi@3xfDCDlD#hG^H}X#!>Jmm$^({mX%0#++|&a;_qL0z--=_E$930l5P<Go
zxf#AWi@$9!s$5W0`aRTEbisTtcyH!1tOX3kl(I|3q4ChPH~AYh@R&*mbJVR@0m{`~
zfB06YF#V8uQ3BGC`HZvLm15)MS}lI*XHUffE~|S%MfsqIi5IR#p={)mo9>O=qaB{R
zx)~?Y7YbBBCWtOp$SHesEV)741hpx&_1ScN>S>#f&CTNP4L<HNmWt_Ue%k(-n51^Y
zno@FjVS6vX@OkVjZ$PwDvt+@Y4G5}IWu`QCd+fNojK|}==E`>VEy^>E(fJ#>G3}7P
z$E2l(2<;R{IR$l?H2NooxBS#ayJPC^FUtJRerEe7A5&aO{gHDj<GKGyHo1OHgTz~4
zGx2a%bys>+u&N3V=wdDNdDh6MhD#IzN%qaz9}(S~FnuRY)UEEw7E#qXG)5u#h(iw6
zg)gn>$^D@3y+T1p67d@rp22FHLwIaF@nXr};kB|q%;j|&Ox*uq{<dJar`l}VF2!I-
z4;69KM5>QG<QVZL{;i)p!oVWlM%qWr-D~ni`U+OMcV6o`Q|Jw|Cf)BzllO?%lA~>o
z7cU44t%ms2C@l#o6$us5ORle0pyyP+N~nMTx9G((`O6^pG*z==7?0r1>b~EAuGZ9J
z>>EXW<413Q`=)D_iZx+9>JfF_{B-g@q-F7#+-qHUbetdL@q;nH#OyPfDD;K#8R<7g
zDxBvLza%hTcRNzW<sbPp&Q2~odWPQ-!lL;9eKT9G_7SUqPo^^^X^!7G19BzmLuJqA
zFP%5!DL-TiN$K(Ev4UmM^|U(EV^o^Q=9aGn4E%DMg@*kCLQH4!a}VHF<>S$uBb)jB
zhqX41ntR!gzET*{^5AB~xmtW+K+If5Ahb@35<>gx>|e?&aA1*QRIkipNH;AN!_ml@
zx6jQaq)h+N%|F?)+1_X4267L)#;Sno`OOg(ltJ@hY(!TVSeh2)y$^2Sq|CBL72gPn
z8EQV6X9+YS0eU5eW0S{QOah*HzeIC(;L~o!sAie^S#rB|=?qBrTaaBvUyb=^?>&5g
z2=z){6NEtW!k+(lWzRM6-k~q;^F@Ldwrf}fO<<<cw`Jh-uWl@=RB;T<@6)pM{y+!O
zeCoob$YJIn&3>ij8K8G79o|nF9M7i|b4KyyH@fSxOjdGcgM6M{a`s?<b5$GUP*}5*
z30QOmk9ej2WUvAd*Pd56A-5h{@3Nrwmgxr*Dpj?dK433Duueb*qcbSu`b|8iVA5bn
zjF%r~=$gYewjQc+(IL4k+HAY=A8~4i;=eSJGE?B*y7Wjy3bjlM5VxcD3XM5(x+l*=
zg<z!_o4gV3m4q=7Yd`#^x1?$Bq5SgD5a76F+*{r{GB?Hoj8rdr3^80y+ZS@_PWC0h
zij474$ME|U4{yQS*1226+Z(LVO65UYHLuL<%AgRbVrwQLOe8ylFbja?knBO9=@f7o
z?6fJeEl83o&)IU4W}Ao#%S?kM4|Et0ZuTpn7J_SLM?A>B(VLw@s8I<AS_f}OK9#1Q
zW0}TSTyeQu;UVi~MYrkB#jw><7`}o^ae{FmFL}Jf3sc5jH2lH};b^8fmOMbS^^a)X
zt^LWtVK2EFkfPL=EgAH-RA--f-)?S~HEZ&B$qlXN(ziK8e_!)mwtJ#l@(2Y&sSFYZ
z;eCIE|8ucizba9-R#14@&m-}98ztw6P?2C?qG&!u-Lv#Y>1>>foUAvEt}-4gL_E^0
zh9{n*G4c#+_O5zTu{vp2RBp()7)JRZ|13)Rh&}GOaq<p6)BqQnzea94DK=OXd_SeB
zZv7(<R$^}ed-~uGcAgy8!M>L51k*<!RU2@7OlgPDVJ&$)Q%z+Om}1;CVQKxt%lDA~
z%T9`NifkO4<a9i^U=Q$F8|9?R%mn?$@Ki9NGXd{2$VY~^@;^iReLL<9dDq`^w>_hO
zpfj?2WR4_3P}A^)_)C6%cQqGReX6sE4J@X6&FwQqmCz&z$B6%VE%}&7`&+)HJW!=u
z!L1B}Hhf-6)r6vskLMkwx?85O{?jw&LnJ(4U)BI~({dn&Y%(M^1U<FB{89_9gevL?
z7(I}2b-LzM1cObNOL86EtL_lr4>HqfThsHacoKY2%y+RAFSAqfc?*OGJY7Jtiw#3X
zT@vB)uN#pfwcqsS^!#zvLrMcuO1BYn3RUjySBP=R#s%w#N0^Pc#uk>xqL$Vl!yA5t
zHH6U^aDu+#8vZu8B7Adhv?+aYmJCK?Rsr!-vX2O5!-CSl78w#V>+fzhU3sj<R`Nkr
zXR>?P3Gzmn*JnsIQ8XfWBCm%0&ubj*4hce<J&8YG_yk(s+Q#WVDid{~DXJWIdizL+
z-(bD)UolNTGMP}iEoE$>{E`!v&lOV2e80c=gzKn*ArOb^YRQg{FGk*(#>+I^J*!7?
zAI1e1do{Gc7Z?G|j!ZB3O^%%POXKNd3lb@n67%<igv~JKG`|(9=}=c~b1S^tIppn@
zU}*sHdm~qR2ruJt{uCnLhySBK8iVEdW$4JE3~wuCwm+YVHmPJ_s>Fs0H|cYDlFFz}
zmu`)zd6t&9)YAHW2E;+1-9D5FtrrUsD8Bv#T4W`=DgcBLTfBa+psqJHT(1|;=2quM
zL$F`0@6bOh?;$M}u7uKG*2KlQHZfigD<a+Dw`OUNq6uI;GA^ZJ;3FZl{s^#Y&@x_V
zt1{ct?|>t1vn6wycJ3fDID|+VVaOPFdnNk@Wp@gE+&QWRiKAP%Z(2~jl-NQiacmOB
z8+dJRKY~0X^LepwUcVL3{o;kX$rQ7Sdb`zFW@3C16P6|*7tr&OC_5*H^Qn%4t<pVV
z)(hDO?Op8lzz#Rz5Ec=&Dgmk6G%CEZ=U()M9CEiagLXtiD?jC?qG=IY*L|PA-Ldf_
z%rx5k2JW!2PDt7jZF2x?VdF5mf%23uf6aK}&>1AVWE>Au-jC+GAgI@QOrQ~CqLQs`
zR4|7?IPgW4doxU#`DF$(`qH$8wfoYuM`!_HEz1OOcYe^bd5(F$=mQlW6Zp3vo=gGC
z0MxVLFIoR@eY7~%YJYX@qrPC$`o^RpZvb0c+)VAv6dDe=Mk<9EccrY6cQm9qp6J|V
zakt4>g@VXfI)s<e4LnQAo2MM;bl;KZY#3ajv`$>tCd+k{S7WYhxjlKtr5c;%pP#p*
z_cRO1S!v+7wBONif=<oO#t($N%XX8&^Z+zj&WrIjudp@+$E56F2%UJ2d35yG1t-Ju
z8V%826dUA}1^Na|dufAh$zW$j+p6-O(kyzN$;QMhL1pKxRT$T6TPxPg{IXVN25X22
zp;kb?KRpi2vAsvo?1Y{?6twm)90beG*`7)tu#i=>Dk<>vZ7W>}GeB~!MVf)01&grW
zot~FH<@Z6L?BK`?lPa@I2KU(rUDAS<O;gze-a{HH{VjL4_0Oj;3tFFjpgFwfauhMr
zXk<+_LPlEhNZDN5EAkUx66#4DN)ym{<WzpLIgv}v3O;=1BVNuOLT_Gv@4M{ygmu*L
zq>DU9lu7o%%P-}fw+(|XM^(xCSimprsXqe0XwtumFp&AcxhmNHheyNc)mw<lG?)ot
z5W7*eM6(%2?`ouVcv0(E<Z`)4QHyI_l>0r3Sq@|>OUS3bTnwrtyi%@mbv(XoH}{^x
z6oerI$RH~kEfLzp0h>;wu=HL}?L<IOn6sT6e~(d6E5j~e#)v%OApHWiDO8ta$w>~%
zKnl&za+(~j@3&v7fW1!0Kw=_Cp2OPfem)Y;z%DzbI4g^2q+xZx@pEbJ<e_d5Rt$*n
z<nIU3Lo0bG5;PZ$&J)RgI~G7EVwUU)1U=~mMgn}IOqVzNg`U!Z2mqiGpR90SNzL6l
zA>i2EGVqodW69!^QT=0Mn%PqE5|xJM5l*RHM_4t)f*uGQPE6-Wh)@I`h2)~|?ssl<
zRqb?i72HkZO@r+$Afnn0vtq!%ITd~Wae_+Rf5<X}c&wdK1C$IV!xCN$iFP2)k!Xbp
z<ZghTEocuD5+?QTtB1TAj5x0)T5^c~a*eKw?7VEMjck72KB0t`rlx)MEM3jv1%?Ho
z?saeKkw{1ZFVi=Q8X~Z@P*b0sM=JjjXom_}xkR&|^=*kc_sz8{g4U9)2Kidl2h(Ls
zfIC{a_?&m%3#uChymP*d*2<0~o&B6`x=cUKf!uB7aZ`^dh}6rg9V(lLs`X44c?5~!
zUG$i1`xOmjjKH!~!3hr_e}78lxAK|>5&qajjyN}imOGZD7&Qm|Z8&>XgktfQ)|p=y
zr8TvfC@UVx?6iD?bmegIbdk7QyNN;WO;@FS&!PkX;HWu+?iSnrDX-!|m;`^(7oIWS
zCCpt{%9bZntDmeQAUtCgNp3i|$x-Z0NZ#Qn;Z$bGq6I3_I8Xana&Y?G>QBe<jp5VR
zom2!<YIFFv2W^|LDxd<(PETB3>wEl@8@2esAvIhQgXL7N@8ZYKz_A^%)lTGEuM&|U
zL*=_^J68JH2SM@XDQODl3GPdjc}4vJ*R+JwJqxwki|J-BFC1KwdM9lGbR@$b5Ew`f
zZcINHE^zV5zhR;E8?c^Io+&unryXuxy5*Hb6(%{|gawDpt@5|G&ISdpmps*rDqw^k
zT$6qIeY#;3<ryDEL`3m+lMT+QuJ>kH8%!ds*99U((ocuhZ<{5ZqsKbHsH*1wZnowB
z<QHt|#rltjRvL@}dM`1xTx=T88c#1N15#Z2=Tc}ygbArX^`sHfxAqEUZ_n%sIdUci
z@Xu2OgmxzUMsx$M4w)F^kZc<A77qU*?n)EqM2rHM2--5Qc8c~29p~;42bazSCjr>d
z(PAt~BmV8U-m1!?2cTJO#1JY~KVg)lyfDeSJT?=7r?=Nn#1oUa^DA8v^uCm+s^bCW
zI0h*VL#4B2g{moqS;lg~cH=Fh?oJ`hoo}M;F;E*2$3T7G1OAuz_@yhjD|mk+#kKVz
z9J;_{m%$OIJR5oCy6TS$e+PT;-(cg@#Z6?jxjday4NA|a90RnQ%`cV?BP>Gmi*~iL
z6>ecz882|lcERJmngbcTpPlNPs^zE)3%zS!7qrSvgL{^^VgO_VqV+`bOg9}n*J4sk
zxGMdpg#~?n?)L#Dx7C-zByM%5c!1n94`W_9;R*N6n%-fp?L;GbTk0H^TWDVt_I4Bu
zOixKxBWL4=dD~K|B^?=p_J$gaWR(QS^q;N-SJqVd9(nE6zfA{B8aH40s4WJ5a0m>r
z0fAuYUT(2Y&9{wd<|4cZAzdI#13l{D!u8?4gxz&)wm*EslJLKwQX+%^m6UJIB^N+W
zlkG!+4%ZC@rgK~~9}2M>i12|hRsuC0Q)PV!F2qDM0D--A_6F+}YW7QjBIGc~LNM-n
zZs0=c)d)-O3-7w>8IL$dTK>Ec<I&_f5%HGc?HuncinBR88B>RJZwA>)f1)T|sRYB)
z4-l35axYwyLgTMH4twa0z8}Nk_m+dEwb$$il-p)U+SE&O=n>(3<4P_8#_?PsKhi97
zDgyxs0aWbPZUBswe4>@E-+quF6={|gkR>j8Fh_#?YF<?4+bNN;*+osO;o`tz6@tAy
zu=pg6ePU^=b>VaLfM4u#sm(-x^8pYNSem+CEfi&aNrZj=Dc$?ig*Jy3AA+1eWdU%5
zyiBd^3^`6>`dPG$$hoL-juEe&qTwFjh@a9$e*8gI2Dk*{)tPy}mDIgTGBAM2!HGNz
zvF8FN>~wc4SXInWE{lx4v8Lw?KloD;mqgyKcdHojvf~3*MK@n`o|OTNxvY^Z!0Xgl
zB9>X(`N>C<6aS>|@=16Z!W!0<D4Gkt*JW&(5?9Z!P*xObQYp9t-ddtw8G?dw`lW!+
z27s_PM-`I8$|J?gxix|Tp<D+mcdHC0@i&uig|(mDH<%Y&EMwLJt`_Q&SoUetR!bo3
zLQDdht^6mtC$iej@tGtS_KtLE#1=wzpgoMU*XylvcHxD4IfX?LcyHP(@gVecrGrIJ
zNFfm1vRgST`6L_!4C2!huWdtgZ)5*wf7H6$y8k>Cf${-*W^ed==a0#RtTJM+5h5v)
zvSOCRzoj`*%Y_Wo1v><+{3SI2w4*&ZM0{V<i-96RqB?Q5MG9IYXhhDHDZ@h40}5?R
z?d9{?2|5k<mP``783jB6_`HL_i;!rzTSpyq&Cv@DqMHmT4ao*Xsx*hQd|W^l?af2X
zjhZTgz5WU|pn)O=kZ8EQOa@1~_HMk9^BX~Cu%%<Mpf}}eRw^-<rFl1D(+smxm!n+@
z)bH2`5a(O6NN7mtqMHf)S+-sSuH+n8Xrz9n#UrWR7SI0;RpA+eBljPb#_LxU+gFk{
zIR-;3h9*e}3T?A-Po(5p#Y;kKKLTn+<}uc|<LECbg%?ZCc{QXsL~RTaJ<W2-4RbML
z6Uwu{;@H>+8i2x{_9(uiqwEKId2{X0MH#z8>MB-TK_CZ8t&#tVa9?Rs9vfQqtOvcd
z@I(E;W}jX5fKY{TM9gT0A;7c;Z86w+<Y<b#GK7_QhrP(`h{QRK3n`$d8N36wL*M&z
zA~;1KA4u18{0@bap%*rwq~C${8`080dG3&9R4<$Cy;D*F#L&B|#-`jdi7CaZ#S_8B
zI2y#9$|p`_&++Q-;A?6iHuWglgN8E?iw@tMD4or^juc|z$8y+!;y&)eFPz9U!(Qs2
z2sFdc)t9M<{B1yqSp>Ssj4<3GH0DDLZEqr`#ghckx^?HX9&^kW(U+Jd*P);0&P17e
zL@<4Q7riLuoHV$Z;!yjKzDs^yzo8+0f^N7Pd;ckQHwOQ?pf0EYRloT3%!k>6rM<7^
zz}db0N$|k|B~n@;EsAT<3}%b<sdP?Xf^UtoU~BZ%Co@N%IF^UpQ<b~;0i_rm89Eb%
zX@0|}m%AT~kK8*IRJ6p#hmJAQ{Hjleww{0zfh<m2Y}mjhNpqTw`Z7$uwo{>9@S$V#
z0vtSado29)_3j9eu8hO8Awe0Rj=6cfiF6kQTGLPCC6!MPzCR&5y2WW5y}4ze_^P6d
zM8+)kcIPL*R#58Id~ny$u}IL@3+yNyb$+cyCaaI;WUo8w*b)dNLlUx&9?DROYG-^D
zy#{Ro<n!@epXJwkKmcTnyK*(HuKqj)kBHfZCyIp=0Ucy#0z&1&$f=fTZ?${f0+jPf
zPoyK4Z&#(s*=Sqc+XC8mf?R7{S0du;$Wqzf{0leqf0iwJnSKz3n6r)v`D9-opM3<s
zARxl2c__*UKl1m%j9AIqYgfpn=T?_>x$kpt;R<PW&lmC@!DP)OZh|n*99B)wZ72T~
zEo@lPu(aM@3HvvGMJqF}q_;m?rL;Ep9pmx0MZ6}5E$CkczgF`EB3JQxU$lS8BUZ;P
zgVN!CmbRI%s*<HDddo|@ex{QXACRS2?VeB!4xSPK92)77!SOyDhfCO@u#u3C)^S6l
zLON;)j!)tml!W=J%mgLER$(ZIA=h~r0vQUQPv1mR#B{t#NM2;R$F|`)Q8%3^YVP+6
z2={VJEIu7ytLVGNCJxV5aYLg+Kq%!vCp+ku{1ZaUzgEcp=w78pc|)vWs+!*0?DQQ6
zzc&qA^u5HU?s))UE$0U{Xw8#Lf2RIXAvh(!mb6O+Evr$Bsh>iINKWYktgi4f%wL0%
zOqjk^ioXj`0+ID17K;ic=;3o%Ibf9e>q;?4+w$=Y_QrHtJOJYGPnsuq+T2EOpf>~T
z(9;{4X)*BNPr~xH7SQp{uzh0eZVe^CiaSro&Jjn8c!!<9XaJ)m#*u`MPk`W&Ls>$h
zyqmirgd8oiW&28SA2+6{x+}Zcj|ir@CGjB4+TNKZ4PV(}SgMwUf%1=LsHMk`eOY#|
z;?(D>QXb?=+m=>ZeRN8tD)F}nZ{ZcJgypWQQe<T`R=hW+UX4iKIl>oU?ZU;K_C3x0
z8aHQ!Q9u0kHE}=N0!pJT!|XeXRu!Q(#boaZN`7H8K1mklZ`?SWujkAEEZ%Q=Km}pv
z@yl_>GVZk@Rxf*bT~ohZmdWUxxbsLpo|6@3RIlQ<`kkdplWpOZN2a&1iWPPE+-1At
zP!+4X8+~Hg$)!gK>$*D$*}G1Ct>O&zUyZ@h-)I7gToNdc+g-SHQ;%SGR}jCmqLQ7t
zv@8NCBdx3qGDl8M{KUPmpBP7XWLMq9fUc02<_Ls8gM-XAkiux2gNKRMJ`z7{%YJp7
zD5Q){Hf<lZ3c#w?EzWgxYrLm3z%BUQX1EtY2So%b$oZl>BNRM^xs3U%_rU})&>mmX
zFljUtCSjzHi?s4<)UFfs`DKiYfgS8UzAfn<uSJqkWrG7wa0b?Sq{68XTTkp6`D{;e
z;t`Pk$jbyPLO|hB2Hk7)S;i7nbxML#YH>>vh*>LM*RKOA{GR5Ie;R?@%;;3;+G9ib
zvcjOP3*@%A<<^J_DegEOE$%G(?5QshTn)%Ho~7x}RhFk7iqw>D-vT$F<POliI<Xko
zrhi($ey@Vke|Y=SkGV&aYTUQOLv^n;gDjAr2sJ<(==MZSlGF1cCWDbJOFNZZ_TyH(
zj|1bxCj5@1(L1d?!j0<3fbS#wPW^8_tAC*W#7u8;ghuFH?DxYeAXOUsSJXHcY4)3X
zlok8D&-8puY5ptbj@P^_-F%l|Yj2sBJ-iK<2oY@yzM0gF&j3^6GX!E`LLs*VMlPY~
znKc^&5FcE@J-!(W?gxj8GWnL!ksgmE%SjP!6MtI}R9UyI>C9U+E^eoo^e)`;x<+z3
zW2wQi1+@ziz=`s9o-h{3Tle=0bw}?ILKs*YIeSPic3buHA@P0;%Xj`WVcr<VI;h$p
zE$l%h>7=UxC7|bnQ3G%ksnp&Eq`df{L;nF4w~Wyp4CkZ!4e0lI|HrIgqTkon`DIAt
zl$gX1tkTvyrKFV@+v%sdMf*xrqhCO~Vi>N=`5@L6&Hx!ynNhvGb9nfxP{w+yZ9w%Y
zQfsUUE8Rt<bzSZR5f*v$1^-YBD-_eWIG-d;b~({XQ4^4dZG0{$?mE1frAJY(W1gUw
z$wHF)K>X}TX45l1fIx?o8xRI9P;KfIoCUBY6L%>52m)Bv3c}(w9?M>Q#UunuO3}gp
zWQ(HBJ_1VhX9IWFCQb*%Yj2pDDC>1<hEg6?PqZ__g~p45k>va+1N!6BX^-5?ua-_G
z2!STVxEYM@<udNj7&o0YLP#jVM_NiCqmrKJ@fKYDiWy7T?c|5swI;O?TyMJ+v*ZQL
zcc<Hjwjv8B&)!_L52rj{$$=uBdwBBg)LgCfSb^raA*}~Js>QP~;;TiaQ;LPbXS{{A
zz%KjjY28{MyCVXCJ)pgoucB>rZ955ch^x78lUV3)RNHa`LPWmzd7QoKMZ&>v1lQ$f
zNcnbVN-B2Lbqa&ZT`B>QXisBnE(LdWQx%1xS)YE`s$HdBYQIba^cn397OtnU$7LTH
z0j6?_<9?PW+@<}#WNRkj)FERNX8zuQ>wEH9H!kC8HG)9+Bkd_M$x(e1K_3We@TgNt
zMIZ6#?lETl`dRDB<C1#W!%lCr6r17p(v0&r5-^FQ_R1HyDs@+@cdUWoKzpSu6A2PR
zfEPl`1+)Sum306n2GB$kmUi~#LyB!ffUD2XJPqWZTKg7U#`bf<6{i?%Dn8xaNm@rn
zGYl)CsH%BcQ_MAauh(MK@QCAW3Z2*Nv8Hx>WRcWC7PDgJAGJ8<&VmY|(s~~8Ysh2B
zJTv2Kl4WS>iJY(2xWHO^l$JD$F%=S(+ELnwWNwFmGDTmsbQo({zl^Qk^{E+RU!m4g
zPCj=Qh%bczP|1-~xjx8z@S8d$bJb;YTXs7BvakfeGlq=7v_AqQMa2^2MJUx2GE)>Y
zyCcTDxD$8e*g$Ol`t`=^Cbx63I*yHb7Lnbw(jJED&U+_k&PMec_l>8c$0IUX#8*+v
zAu^s?(6?+dd&F|uKNf#=-F~gs#0^M4@#6wbD)9YMsnXQI1k~0X46)R4Rdta%fy1`h
z<J2<$h;%f-V-imkQjkgJXh>AJ#@Yte(Tn9JSvc|4Adjv8O5f8wtP_y>!<N0&JlRFe
zh59Q;rZhH?tR19}psIZRDM1>I{9T1G@=}iX`b$F6gBd?4pG6UW_DthHS{pLqwn66I
za4%~9WtFuf+BEp<^KyR*73gu$_4|}j2xRT(%OaPISbr!4?rKOGDA<_&KE#!T*n?>5
zXvbP?KwJY2a{Wyl4>vO#Js4**We8QPQ6DC359jdSE3tYXJ1-!zO}U;JEY(fxyg~yb
zYkS8H`d2cx8v|xF^{!`5Y2_C+o`7yg*++@$g%Tj`oAu?7MuNWNfXOaTmVBIk97ibj
ze9d<EkUF1B05YLv616SFg-bWxlPId_*W;UJy3EYHI3RzK06dS-JDkz^2+e|0#GE@L
z64)%j2Dq!A@P{bvaGz+C>xwp0#JetAB{*t$zL-0R&fG(#qEl~|;hkU3*<H3_aaR<b
zAIr}8{H_63+@Pbo?9iYgz{SxNC%2G~IsaSw#_PoW^ABxHH@x*$L#=BH7Yawt@HwJM
zS2T-IC2aXma)7M+^T7i4hXeJ0{wrct_P?3R)Utm+_(8l0X^3iw%dK!Qc1_Yc+6(Vw
z{U<^dtEg$j&@=c4?#>i+UHNd|a2h(yBd7|0AekGNcs#@xsW-LWK<<M?BzhCzd8DXv
zfXj<iE6`998k<!(RW8^U<aweK=HZy%(m^uD*2GP=l=hA1r<_nsYx?!X@xo7R{jFxl
z;C=+bknl^Z#o-YUol(whTE=<2ru&O4M}}pfQ4UarDkUyszYx>*Zp!L=IiOtaX+|WF
z7%pDEO6aouc8+Ihy@eRD2y}`(ujyxz#kLfmQ1-tlu~z(Pks4>-h^cvQ%ZkuD2gU{J
zb*J&z9STPb<uX7;+8Z8?zmgjhW4{|z20EFPNxSgMPsEs4>^aTQ7hlWN4Dzz7VmnF(
zVKMbeD+;(2V1}_4`FtBcIp}X`UvGkDtX~Rm0#{v=T2+Obnu8gmff|$i=7&+)%+j!e
z9%cJ*Mb=aIjsTO9dx)Ky`-|(-kq+fiePT@Qri+V`FhGZ$l1M3EWvWx~9R`~QUcY(a
zAB@00?-umQ<kxD=RUlSc2YU{}!vJNjf-PN|Ui`A9@3H2k(?$-u3I~36pJuV#dmfTK
zUiJ3wZ}YQgQ%r84n0nHq@DD$1(kBj$XTooYT$jz#9oa{C<wsX}+gP1(<da>{EHHIb
z`;61d)Z+&V<krKUEL`Ip%(VoVu!Q3|GHbZHJ+1?wyW-->&NL~KCnpusf3nJ9&VP||
z_`XA#FLuyFW$uDW;LVXkwYr;#QRe#}iBU@SW8WJFJjPxryQXv{CMCHkc&HS(2f!wd
zr4%t=$jK+)A2(cyGP~BxW>+V|-Y6!!Oe4A0f23znJNs=V?u3j=&{t&999>GU4s_vI
zY=9<B7kish$%59Rrf}40qE`Q(Hl&v^(69sTz-PqiF^lvY_(b)gocG-EmkGKnUH3;R
zvQD!i2Q7YE*H|5bvvDiC*9*|zP<-;=(8m-23fzkwL#&jc!lO13M-82D=ZPq`+6F&W
zw6yY7g*dHtEeCZ1ir(Y!tQq>tC(2LJ3@kt+J0&SI4^(9$`#^~)(B=WQf6zs<j|~i=
z2Iy6<E@ASqtOyNH1_{x0hA*WY@*U)5bSFdLdh6SyD=57bT3Qm<Gh#B5NtLRk35F?|
zl^>=veI2$5Dp2P)bUfWqoJ<VH+bqAD7&iNO%i(>7M0#@;K~<phCEPwE!_GsPZBc$N
zqd4~42Xcwhwj8yyWGNZ|AM*QlwcnypQQ(6_eJ>ycScO_s_~tdXqzDf!{HgtgPGo**
z-h2t`FY^9)bNmT90g=;ndr?MT&SesKtr<Q?zjV&*`9ut8So|RAIbN1f%1MRl)xnq7
z2{8D`!#w5o>g}(*B(BS*362wQb!~dL8C%@B+ZYCvr3+flYk16-df_xXr#9}6M5VuN
zN4~vq(Sqfy%rCq{y`2*zg=Tq7?Oj8{+4kg3yQKl=jH=+j4nq9WeBQ7Qx45Fj>v2Y*
zH_lGg?BrV4r;E7BIKSV!7cUf~^*P8P7UB2|nSL`U1WS7)eTL<A1vK@2v%`l4)U1cm
zu2>`(QIF}kSj7I&%S+2)s&8uw#6W9`8&D48#kFmhS{+#*Qh+>8r9+E;F?Ogp`DraO
zPz(xkfj9?*3=W^dMz1;1BbtuUuu^g?hr|>I%f*t;g3_4}S!>s70S#}#DZecPXp1m!
zb-#e?OnGG4|H2w`3YZ~CtUgX9r?(!sMk!P>kwO7)`QAqLbEGO(4wCFu`OV>8xQG_A
zQ|eEWuLQJiSvB~x5ANa1ISR|a0%FcPlKbTDO*RczFDaA|oL(<ARUH>;aX>(m;6N*n
zlfTF-!&_{KGfQ%-Y}t67EqNU_CXKtgW1^*J)2Clu*c!|5wt)<Y8{>8lZuR%CTxF-m
z9{kDj%$9O^1pvAx2s_OwpG06X$b968(`h$wP$jxL{U!;xa1=^_gBc{M6v)I|uV*5T
zi0~UmV`mo%lVItl^`j}vEaz9}h$)h5<>)}Fo9YA&$la6Dxn%yPw_*_OW?unTKF{-G
zf~TTglxe#%LmL35;*Gs|w2m5_hIN<;T_m5H-MCGPr79PCe6yUIG2~w^y8=F{u@>O2
z61Lm}aeU1CmyM`M8vKRg%Q27gJY)?Fzx*i}m;DO@fD1mKz6M&XgS+kd@_!(R0TfvJ
zm$tOPzQ%MO_suZ3Yg`X8-7=Up&e*$upIyJr>&|y0Hx{@aGG(AhAO(_-Yq1$`C8s`Q
z;#{gg7&tn11=7s>oMdS*U4;4``8<h>n6u~@rwiya6Fc@2GBO_yntcxC=((ZqD<Uv=
zL?V`OT3>I+zR5+%hpazixK8;L?EEuAX%+Q_oSzKiIoiZ=D!;+ay2zC#zPwde>7bHQ
zo?T(kCz<Mc>N<b0=CpC^1_$yDV8h4&UvsK2Qv@%8EP?6oDhkF^)scPRI*P5f`?(~=
zs@>i*fBd=`rsz865W#;0RrsUSBDn=K?hhpZ+MJGG3ZpZ8@7H7<zgQ-c{e?>#_PX_9
zkEAx!GQgfAiIzrt<Z7w<X^VZqN~m2Ns7$@dVoSgV)(MXB9VKCMQ$mt?FR$)@eOVY*
z?)nq1v}ygu?$SS$d@@VCW0JUhji>VvWb$4DwybYNZ6ZN!#eU+mv>21h)D0H{x#P89
z=NeJ;ovX|B%BJVS3-_2-p`~(1hVk`OCewxm`y*U1F=f8CKAm%{9LVYr-r44OJU!2g
zJy2I?ie-Q{+wF9m-;5o1JA}%$yfHe=E(#D_s6Po|AxQPpsbS{iUhl~~ndZA#d=_^p
zxU7IHRQq=AYk$oU<v8Q-w{e)mFxX;(q5MQUwdPI?SfIFeN$r6~!~Y!c@!N+Oi92CD
z-+URD+^Dg}6p^{N!PKjzCX3n`@Q#KrlX2YUmZ}MwOjf;<&q${%M)nkZ!$EfI$`Dt%
zQ9&T5GjQ=iiD=5z`>GU8997T3orp>?nS-`4589oukuKOf^XnK9C3umIi9iDoS;Uey
z#Eg3D%~W+zwaiy0;#*pU;*Npx3J~MjM*Bm|s_?^oqeprQ^HEWp3sp`j02EoIz4I$p
zSkrKSfu{9P#e#qJTKTitSuLx&H+F1&5D_3wG1Y&P^^FjpF;N|tXEKnq{%BM$+OFz^
zS5W!svL<WHf_O_v+ShvA5@_kg(FA0xr~JG=*`*3~ux};5>@(#Cf(pBkX(k_ax`&25
z`@~jL3#;V3b`&ao_>my0hU*g>%awLy{oTAy7nRlp^zz;i*--;;i2?c`N5n|)n`^pk
zCe-vp#m)A-_MMh=YBrPIGBxPYH9$Mq;wa6Z2~aa!l2sun$=M`ixCLR+G>WfAe16Rw
zUVyqtut(u9zi6%%BtPG;o*|US!5NCwpINP#cbxT}@C{Q#f)KykC}+OoQw**NLiuwn
ztKr|#l#6$0ROwhlN+^~pKN<Qd<t~E=GM+nkeDUzEIb(Pze7gfE*l+#Y&EO<TS{yK+
zZ0;p$*F_>(NafY%HH%B;Na6IZ<fzdsz-rTS`SWeKs2Hn5oS;Vq4RS&$j1MC{7ITLl
zo5XTtWKkEjnD0*r>*mCKIuk{w)-;pBFn^<2Bfx4xnq%d8-S@h|bBa)Lkk-@Nb%kXx
z1s*dv60im=EwW7`HqW7F`1-AIV1#?sC^-uc6#p{P^V~YNhy)CJml(y7r$h%9Pd^PA
znF(6vn7h?wXk#R`k0!{aaQBvNG?k1Gi|y~2&7$ol=su!2n0_Ud6+$^*V5xs_0{o&r
z1V@H|ZK2|U((TI=GuR`zcV7}F1E{DOXgR(++YcrPs@ml@a;O%FJXOEirktCx_u2xV
ze93UxafOu!Gn!z$cP)K@E;RL@E@aLS_JcTd@d1b036l`J=1Mfarhlf5y)Vyww9hU2
z3FdtNMh}90-|oh<YJ4m9Brx<Hr&zS{*79kCrAr!)PHOkjnz2ATl!ZYq@aylK=RSqA
zDV|SZYRTD=X8x;z?aN3Abi#^ucE&FCEMr0#XS~|mtKu9(Lg%&07<b0Hco9)tp$x+)
z%STR3FrZ4tt~@2R09*;N`t66PxtT3rk3|2J$+H8>HBVWw`B`6LDo8~1N`7;@7R9qj
zC7&N_Khq5_Y9?-UJJb2O&ffbq{edb?Y82d`<~=(*d26D+T#!~3U-cB5lN)*HT6O1G
zg>A&3c16i-RXD2<tm?TJyFjf$e&E~S&tEqP)Z*WSeZXf+!F?{{^*7=?j6#}Z)%PTs
z%ebrE4@))vZ{)(0(<RWn4bTExJOkeC3GE2WSf1m>VTc}IMRSB}*{Av&KAr)l$|+5*
zR(6s8TFu(9swHYiz0?cWzo)4xRhi5&e5?9%af|T=`uPcOf<y@dwIqA8Y|VGPBkr%`
zmuVtv&60L@{7PMMW4P&A?zcJ~-X=4PF3RLJuEh4g{`3}5aXwcxILW<owY25t{{5&B
zWs2Q^^^M&^ka`NSQ8@<CkG~z(@GXXzJ%?07_^}(O4bZK*O*Urw(|3ZPTnDM{Ey+KT
z;u>8K7ki{{#@b(fO)sk;u@dSjd_7);(T_-$e4fy^IyA|zrZoCNqTNs_VVNth+vM}<
zO#AC`goq^b24OL!a*Cv#H(Mp!!hC28CpU6_hl>_AAeXbf1Bt(lUclA?6yiVyy|M9}
zHs5aYIF5ZYw_txvxbAG3h0d#iCAdx@A2qwrFgVx=<BQM0QFd^yQ6@V{n6Lnc%z)g}
zw?Ajr|84h~(qxXWUY=RpgE$EE)}&gym!a3)c|{gxC4J8Kq#ZxLzQD)E_XAVy4GXni
z_8*BHZt7hrpz3KsMQrjIf0kV>e(48LwPa&qnU4!M^6==n4-z_)fdMWx<#DbTUWB+d
zwt+s-J@ZFsHLSw0z3o4_)ItXGnodBhlH5l1COy>{V9&z@Fc{9#Ix4)O&iSL$C>Q|7
zxbRMoK~Kd>e+znwh}7_Gzy#ZwQ{EZ}_}JwR)KViDr*K`DTZ*YKyYmzVM@L2YDV5j^
zOF>54{aH^BHhHQi?zFCqEt=V7L9q<G9ZG{4UkQP3IuI!Ee+9V<Cd<05w%Iov`~Arf
z;K0wk_z4xRBu*HGYO6~+w~7KN+f;1*UTD@a@A?~kf}}_oJSHAfHX`D4N4L`~l!Sd#
zSt(9-e*_t-XbH^EDAn_XF>%E>1A!769G1Lo#YRei1AVyg>ofzOD@QV&GboF|ksCpx
z;7=zP%Dc1P*bX7m{CH(BB|aUU&xeZfQc5NH`)BPJ{U;o<g~}?~4GI@HjDEKQkaIO=
z`7fm0H?JR9yq9*Mw>BRe3LLw;1umV~1}=8U0TmE{ABz&ymSPt)Eila{8wX)FGcswu
zXbs`<-_fd@{;`Nxs^%{pG^{*zH|#iEWe5omE>6;($(2xCO^RNI;q)SnD*kXc=7*2*
zlPe}Mo!h3o*In@&VW~UR<xtQ+$%9vf%0cJw2Nv@NonS8-kGw!jc*pWT1C{67rqGKS
zC3~|Fdqca5&9VS9t2U5>O>+`5(uGwAm13ymR&ln;1qUyvamdlMLLoveNAJVz+*Vvj
z%(>ef0vA`t@&NIWeSr!Zn77lrGt8XByZ|i3kg_292j{rNUPgjopZt|kpnHIFAF~*}
z<apYoKw`0A0PE-im~Wxt!aA=mveuHG3STf__WqI5aLN1kjLn|TU(eGm!O&#3DVy2F
zE^nw)&*Iu(e;e)a?EqK0I$H<I!lUhk1-%4l#Vrf(kQ|YNuB|||z$E*GASD#r-M&mB
zi!4yHxG0Gt?%0{MG<6!u(>c-Smkh|19itX7een`n1G>+Y;+3ky8=)!gR+^1Yd^kX8
zl5gnO{MI?4oCYk1ZH@&$1wm3gn`AFIe``#v$KIrK=Ymnh2@8s-z3s6vTh<a$CR(s(
z<W=Hg3H!17U_|>zRLjYAdJ?GzHntxsF%lk~a8A|JORml-t!xrfSuwNvEx-=92kQOX
zbjX!dNS?IECb^_e+F3ntNVQy2%-RpR8zjMKQg9~mfTuKYWc(x<`2Zi!6bJZ5V}riF
zp6iS0`ax>C6#HGk+aQZ&xL3!LO4gf)){h-R&0S<Qz-|wma4tfpZHM5L-L@aBv_tS9
ze(E<?QBpF#S<>Diq@lK#qS%02pe*yi|0)439}8nH*`>VcObMAG<6KoZJSC9boI5jH
zrFq0FAaQgj&}@mct^Qd~rJ7f1#;Ga?EcXX)r}@g3LyT#9F-C2S6CTJemKT{_o=RO(
z?IIvxQ|+QPaPNSgL%$n7f1{wNhgd4v5~G$NRsu~Sk8C$ce9%+fEI1m;9HWT?V=`GH
zm0gL8vvBacY+O5^2bpAl@zxC^QzD8%wURxuts-9}i51h_&SRBUvTz!I#|1VMpK&Pd
zIEh6s2XK;U7MThuN8?(N12@@4ZoA_~fU6H@8~8^DQ&H5MU{GvTzWA#A|HIN%Kvmgw
zO+_RWX#{DI?(Pr}knS$&?rxEiM!Hctq@}w%CFIiGT$)S&$M^ePx@55sFL2J@vuDrD
zBemNAFYm~R>V*RC)9liJAp^686Wh`e=TKd0VhS`zzXDU=>UX(Pm!DUXmhSlFC33tG
zi6xOqBp3aL^WVb>Xf5Mrq$*`M%c6ak&N(^uwuP8{Y;s<mHPb+7sCHSnOUk6(KgOK%
zz@a%79;gF5435^^k6P(&PQgHGMiGrf!>gjYbmOaL0gjg{8W`C$$m-$`5>zMS41q;J
zPW|d-IF5UCN%Oa|0Ivo@jMbqtMzybffYI8Cei1}mznDkS)E~qB#092IgqtfES6H_$
zjA5MXiCgw%;fd)HYxxCetjqI@tCyEJkMmpSx<_?;=CpklR{9^_Bf)OEsXeTm((DNZ
z8=-B&+KppRcTps#>mvehgh^-8xVhCmot>jZ(iG3(va&L^nT1YKvQzaw(=i;~Sq?`1
z#FD(Xxa1SoZSAuz9k!7atIH+NLm^5wFEqP3TqO6uf?;t4K2un_RjS63Y^iG+f$9r%
z6A+aCLi1A9&2DrGUh%p0+_aFsJMvR@Hg15}o<ksPPZwS9#*S?!WiS)42}`+oXEHVo
zJdaJc>DB0tJE5+)+Wfi}w&(6E-hs6u*=1|bY*E^jWfO;d+}yrXQy0Q6RSJ=bbP}yV
zR7?B+TEVkOu8-Y8nNg_2$z1cgwycM}DBi4nc#+SU9Zr0boj6U5$|Zbrx+bZ292W_6
z?yETpTW2;N=9rzYMoU$#$ebk$U}xM}&9=Qgb|gLAZSG0j?f%4Hf{j(~*X@1$R(wNR
zzg@{^4?`=a=J)>0AJ_Q#hF%^lTr`WT+&bIqi|?e7_#R~HjA11R$P3l?bXC!AqY1YW
zN1z>OL-`9>H&YAdh#hVY>C)*Lo64R)$irjfV9ZE_IWcbTs+`Np&RNK+p$W|9&f21Z
z;(imq@`&7rC!P4E;(q8{mYKuen<Ud3;o;lL&B6*LF$L-Bf&b0xJ1<i+%Q4{x{+0JK
z&ZyaGrdH(vxD72=nb+TLSuHcFT&$7?=lK-cT!N0rzRa2>*ZX+{__=>d+8$w&W8u}=
zNgXHZzs&IMU-s3@_CCO;&KB&M_6amrV0O4%#3!I<RA;iqlth+F$oZEcAUiUhBFxsi
zxF)raWt!l8a$Y~Yn<Ke3Yvt`TVkk_7PqEpEV0<Em#_WJ3BlPFBT*)YAM8BDXK=AqV
zev<4^@{dw-7o96Uh`_F8#-F?F;*Bhz)|rfBhZ`9cnnH+vf{hjP@~87tfYGG2-9g8X
z0S#BtnTBqNRf0R>ugFJbu$EI=MnEY({xe?3VnVZ~;%I*Q(L+W&AFSw6kY?a97?lN0
zVr|(+bUv`!@(nHA)n$d2hzzDS96^5FZIrT6&a`Y@0?xRQAkXiKwe0XJl2#kbMgm&H
z=L7C&;wSgMdVcbM<k3jTxbijX+P9M`4Jx=EEeZN)SlKyrGVDE7SFCXqvM%l5Z>kyI
zM%Dy9TuI_-|Cw0JQU3G;_~>qz;t`w1A)kC{VYxj@*5OvBl~%vhD3O>IkF$AS!?b4!
z2^604%we8ZPEEVlbT6f{u*~1#F7VSRsop$Hea9M6v%44K=&Qtf!`s|CC@gf1`aoe=
zuDey^9KlmvRPJN$oT*M2<*l=96I<{*hwN$fq5d!4+ln$~CWbXy@p8^1o^|Q^QK$jm
zFxDt-o1aQi+BUCa*69&FF3$?2;5d{))ha<ZS=O4ZOzJGd3~yc9bcONXYAW_W68SiO
z79rERsZ2;?yyE;eJ8SJQUBlAWZGL_?$N5E{V#&({y5}m+Z{&sAd#1wPCCQH+zHU4d
zFgMTbj%m9@ZGXCM8z1?JtPeY*ZM%;Gf)qdF@Q&RmX!Zv5VN@7?m0kFbq8&z%y>ji_
zEz;F@Nu+-lf8F5c7<hooy;qBP!QXu<ywBX$Jd%H{j%rhGkWF(g0}eP(mX}SydUwlg
zvzyp}MQmjwWIGC)xdC3AW@~lttTtlq8)a#;WU3T>i&%5s+Y9n7?FOg^$t>cepZUOk
zBID!Q$}N{R0hO7Rz|GWme#CHXkd<(s`*alp?wCl&YXhNLX2p^7jFqS63iLOaZLmvo
z-kU?rEvo^N`*GnPwUee3QLuYvq3%I*G{^OMu|pe|2H4}PmHRv4&(8V1l_cjQJJHVT
zsp9g2^+8S)P8Wvm(1Y7_|EJLVE_<J7m2o07H_NZi_Iev53Kb`P^gFxYYvmIY7$;-6
zBlNWj*lG8{+(VMaY3IpmxYUk8WU?6jf$MzK#b>VH-gU6TFXLS*Y2GZEwrycsG%GeV
z6AMxbs15kKK!#1hHo>R8Zasu>h(%6|T)~D?imSa!qI*5h4i&JREn-5D;j<Xliid1t
z)&>PtzF+%L%~9oM+pZ0<kwrD@{~2|A(Yv^aPlHe*@x#vlkic*!${KS=59rg8utQO5
zY<~})s)dE~2fpw2U11LTplEZz#EZ2_MK$vR*ld)RfBuzNqMkbP)#-boM)J~NwtI8X
zsfyB9AhM`o8)9-%?Hbo2{K)IG_;c}?FPu0Z18}xu?(O2-Iz*w@$~+z=Ba=fKU;-#^
za*lBx1OmxEd5+C%<}6b-hSU6D%C_H?Js&m62c2gT1-U|Blw>J5d@v=&o?AT}qY_0D
zVsGwv&3-Px&f85Y!&_g|>%BnG(&Uv%pZT`kYn|3-E3*Fn6`4a`*RxbEA2YY4!O9-l
z;*nX04#<!G($cxTLgXcmwXMeBhXC?QPC|$B+Fq!E!0>QQga9k+;9N`=Id_^m;c3iR
zOLy?>m2JAj#Z*wDU(8C|iO^3cj~w1!4cr(Om2z}bT7R!2wiTVWuKIG_&(z_t-uKk8
ziylX&+J9uQ9xrZ9$Lif+HT~JE7n>Y~Y4PChb4xW$St>c{Nk?1jPynBwAnAWZ{8C|U
z>B2Al`OT-h?5F1-eW;1Q7m>bSje#%~gkHpcy)sJ%r+M4y^_;tdpc?#V63pB;S_P*v
z#8Jg`iC$q>>M^tG$p^Sx=*klr<!s&-U#)U|h98D!zT_&5C}lVJ4xAPVhFcR!(mou=
zwx4I;6Kjl>J09KRBg9HO?ZQxy2G~chw9{*?7c#uh>8P^=d*Yc1w>2JnD<)EWeC9Tk
zzJ<~b<8n8`#@H<5p2PLKe)^LEIvo*HTeGZl(~ypELkB@cM)zyIE~}0oB<Eu>%#NUY
zP-p2G?QJqhf^#j_#1%3#tm9I5*Ydc;uFKyp;oU50Ts;I5PEvcRbp9na4J`;abp*Rt
zoFDmL7(doNEf}m$guSEM*+(qr4`ZJ#w>w>V2yGt)b)#;M{}b7XXmaCwl@uksCCf`t
zq_jXS$Y(EQ$jn&V%JzOmwCKxep!D-ESk_JsbJ6g|7kNJxCXh`E&gNcABznKp2!fZ#
zGEjF6@?Y?tTl7T1AACgT;KTq@Jcm5V(dH+zcYqjRgV6@s+$AmSFO#J`eqTTx1RMum
zJlWMRTcD;<n0vPk#NvX-zPm%1Dvwe=t|#g$lt6f9Y{F+0Yx{lwx#K@W-JjuE;0WFT
zbb!=MX6`nl!xK*UI@dKL!nD9HX;uuqBs{D{VoC1<DPDBln?gP#AmjPdsRERGt!5<t
zJjN3jHE;Z?FWvt}j#tL(LTY>s9DbcSkA#lbXnNg5FI<y^suNa0pcq^4&bR1Rc-+D_
zE~!k%yYU91mjA?@T=^;o$BqP<J}!;><?kl%Hdq+*%%^+?7py(QGyS@b%hTLCGq;v1
zVrJc3@!8LfliKcn*!{iHWP}n@Lc%6wLdLk<1(Gp8zgafQc{}*{>Oj}J&2<aT-oA_-
zBMDZkqHr1^DX(~We|nUq+EUxtw{p8zidg<2Nk8Y|ddY_gTU;c6>XR|}ag5lYY#0eT
z*;;U_=VM>#%2rvFn*NIBnnl^5iKakuAcJY`TyAy&y!5Gzq=HkCwsC<f(<72K3iCK4
zX)sNBZd0=`)jxL!;(wauS-~mo_<Y{Eu?k0k+jIr%L&i7_=gp5#C;*t+3#J<Sjznf*
ze~EWN4vxwQquf+R3HfH|b?5LUQArf047HhMblpL@-a=>lewCXm0qsk0i~6(lKVMDs
zFkWAa#iWX1C6um()@|#>oM}UUxi`2OX39XzK<g2u>%IRjmB!9#h9*ZU5wN~L!wAt4
zWXjeu1%s(5l73V5O9XtC><mTLFcmHh9eB!^ADfOBdoTGGe20?Z$_@U0wk{iO7H;bq
zGfP(HT!rn4S2OI~2D>IP+fFU-)p)r^Kzho4ay&!OPS*oWjc3+ID6tH+xfUO5#121C
zR`;w``j}fbXeOo;5g_`kJWHqh_2L3T_|XyZ!JK=8lUcAw3VG0Kk8@}d=P*a1b#E+2
z+1?=v_)dUVP|cCcs@3U8l-E?BEiR^%|5r`}N%f6uC>bT9ULcJ<`-r=QAhtb_#G8ET
zO_h*(iWXA?wgcdQR-?bAimo%Tj-Qe)XIslAougIexmFkC#qW#T)YINm!xY3@p$gW4
z&#I2DuxsBkKt|I@axhW6NTYa9@J4ZdiLQ+Rj&4oaslbjPOZq1bFIEE^p&p-{oidPw
zWw=L(F!zxv(X4F@okX`%3x7k0BijtXk!cJ=JEXm_Bn5)M<Pv@Zl$m!g!x7|iya5{u
zJn#6+Yy1dnG5V*Wx$;f2{Ec1eKGA+ntmU#UA3x1x8V~)m?P4k<3OiwC>J=jqhE6zs
zJByUbeEV~QtyqjI5HpL<qx5`KwEyS!-AFP$Y)B;PIF~iUN*<FBwVT1zn#Y8$1*7Ec
zOeZ+pjz|s3*ep79&SeV)$vq|#&{BEMj{P5!)X|cOQ8;GOiR2}?aK<R1C7jwy@J0p!
zmw)?yjMv(wm+Y|X(Xktp9}_%+rC6+WAZv(zTBXn~yGGM#R$dT=10h_Y$5Zp7CE2sE
z&*Uhli8+T&F|BE{|2ToJ|2Tnb8X0FWC-|SWw~f)aUsDAx$L7a7w_MCn!)^_3$Rqj-
zPQE^nsD`wrBo3#;C;{v~Z9#(`)kA2MY!i4+N7iB1&{nswdViOIYk#MATc4r@So_Bx
z_hkeg&L+`p_1rg<^bgz(ntSRW*GhGL>{BZb&lhnO&Z64SUS{1aItr{1;V%5H_ttH%
z?DRi}KE3Bk()suHWZ_$nv)*o>)8s7Q>Eu;0_FZw%H}KnG$wK`R27X^F9vgB0YTBKS
zmEztYK3&!~c-cigUHab=XWv0A{cf_K$PFH9nB($!?Vonx+8>^7P@w=OzqU7ErqgQo
zI5>@B)#a@Z*`Nc-e(kUd->7lFBg-WDk(`Y67xsktpiQo~-}ygcm1i25Kir}U!)Ey}
zyeDl9(sv|v3c1VcQvfUWoq8Ll@l^3d_$NXx0rIrwJrVVHez)4om7qBMG36TT*nR3i
z7uqh}&CiC~avUO3gV8>&?h^g+`fBMdpPX5@`N^g&+&qRtQfI2slyCqxYS|{6qO4Hc
ztbZa{5(ZC2<PHvAtNUW@=mB%^aNyj)Mbv)ohgl0)XmJC(JE6W3e7LD}$=?#fE!&(H
zpn}bd*QFk_zo>E+|MZ97ZQ+YDa!iPON*SyRW}O-atSJ{$wMxu=Ia5`Kvg<=^XV2lt
z!@4jYchi>sLaZlHs%P82T>g<jPVPN3fA*JHm?UJR2h1(b`tSnWr^ybR8z|TjoO-){
z=`(9OK()2R@!LGa9KU@GNDlXxr;K$sj^vVuK9Qx+Ycwv-uL(b{xx==M3q7oi!n1{a
zzNSGp2KY5pUz4RUCTjgsb<BrwcQ&jy0cDW*652qNVdH`!U&|ex94)+xVOZP-rs+Ga
z^1&#Ps4+v9Ul&ame}W3rR5<QelRO?3YXQKqYo76FT-g%!4lSfE)GC^`LsldZ`BsRX
zrTkH=Z_6!W<C4H1smzNQICXyNn%1st*|*&4>8GXc)HuJszhA?W4L03>-0;f;#I~=~
zf0>X6#IA0)_nZ9C8aLAjj!_;LqokcSkFOOEx5Hp8c3505bA=jow04+oD`FL6ONXJ=
zik_~v_mH%-LUXS)?j#+{YB-F&Tf1w|4|Ki!Uv7PR8zXoA?~sFenf~^DH~|h$zI4ao
zPvo}Kbc4;i6`u%_r&I5i)7F|@h8<@E{wP(<8#1Bn7)aN5OL@U|kdJ2-#nzv#Ps#xG
zd&WLOXytTU(|;m{3-B6oc7f^}7Rbc>9{b^n=e{*SN6BrEgoRlKMqX`7HX0;))^n~F
zvg-e6hMh!Vk9dH&e(5b49e){`*PCQ9{2RlHy>@dyNp7-yw9#-~yB5kcnyP*30gvQq
zFNp5$8h2n3U#0kn0x?O*EJhOm{&dWx4JW8K5PsS<sVOSQkAyO>uKe_0Ki>G>1^l=#
z^BlmoRH+je%($;<3A0L`v_uQTKKQOeeh&`Fbv2HWR1>#KmdERKr2xt~#%pisQL`6<
zt>&IIjS_ao6?V)HoKvRO;%a2QZ%rjbrdxs+5UQnlrWbpC1B~r}7oM-%C!GiS8JML$
z&ggYuEC;swBL}d=eNa0!HJ!f3_&qo;#WZz-3h<CL?9=HUgo-w}Tla)PX?7d38cN|w
zB8U2czZFQ&!7>!<krjwKa@AX|HE*mr8V4=%H5`IMnGbU5x|;8bfLf>KZR_aSDm4(9
z-PLt7CkYS#eu9t4PnLL)6i$QADI=9+jkiB`?KJ#dURx@2WvX{?_zT&-8=liFnc-Eo
zKB<wBw1hnm;A?m_PolQl`FJfH&;f*VbcD3Kg~*P6xzbH|W-79pZBv%cZszfJaT9Vz
zfLR=JDtFWQb?IH7QN#0rRh4qkSvt3qmAhhG<(0vbAD(oaxy$;u?DC50#e=ilnS(n8
z!|+aa>p<c+!g*Nzd7f=hd_Lu~<Sd`0@llfXP<o9$O5~L`r|)xf8mTBU0)o7wGVHGj
z%V#2l!bv9Q0{@Bs0{%CRPgdeOKOP<YuJgjPP0>kP9l&xHxLN<cu-xxB6Yzjs#_x?i
z$2ZKeaG+PGzF<>UXDP3dnn6#6&0h}TR?<WY*lC`o8WOk;j@R|Fe@P3kF<v&AQ6AT`
zN7Hgk0gocyFq=}sQo|FV8u#OnwRNKBk_cVgfAIEW>dkwVhVnpk-qAfe{Z*iV{Tm~-
z&Ts#wY+6R(ywP}sBr8vOrF}`B_iN>$^I4-<%hMlvycb7h#7nbB)PwtrKU|gMwmn`6
zUra#2JRYrcu>^VO*lj?KK2R)Qewx+%VyG`mye!2O6DmNnK^oLl-2S6eQ8pv$jO)QC
z9+1qC!AG>g=o4CAIsE1C&5%0!;BHliIQ_cl_o7Z%#uFB7kUg~#QuC?{Hee~$68RC^
zy9*aYgTQyBr&9uaTirt^Z`{@+HY$<Ar8}$HdtFW_juBNAlrsVpIZwB!6jgDkn)*o>
zsAjrPZ}r}xmmr*R1$;*jpGd{KY^0|{h%n>=@)>s*hQRl}K;rd6jrzE}Ii*^!S8dDj
zhvvoRLSD8l%Rn6<o20#RiIa>3`mLaxORd=-{K&f`19G+*70<V6`TuNEiN|CO)7WF|
z=mD<=%jWcwc%B1>C|NMR!5o3a+yEX*lgCn8%ip#NWAI|Z2++-_|K8`r4+~i(S}oPt
zwlR61RFO7L?fQ?%F|<z<AY7&-cR2^G%~y{UN?z2ip^PNjzqXSUU8Pt|9=ysw$5b_S
zaCSAzCzFXV9ED1qj`ay%WN+0vH;B;QS!kC~85??8JZo~>*Jo@yVqqbb&dmkLUgIb?
z!pZRWAzB#NsMSFp3Sa6qSVt(Sxtofj1xUFTj|M&X8@YNs<*CEw@lhKlnrf2|j*WkL
zEHgT92GJ}B2!k1X(kosh?PPWvU!%zu5V=a10&Y3aU73HZd%~NV>l*%ZWH0gmZ^F&h
z_wLXU<{2N8!2K76%AK_VV-F?1t`_=E+*=!si2M%=fX(D5TAs^$%zg#t<ArS>_Bm%w
z0j^#^b(o>bRW?o;S+{ogx+iN1aLF0(U-@ncF%e3xC;4_&$B?{Ti#*^PNb7OLj?M-3
zl~xUIagxg^pTclZk~WMrghG07>hOvhLouD^d|e}(f`O>zXylX-@J7Yc5ks|p+(r(e
zCH*(=<1hGM1bqQe#N4>?U;d`C!sz*Cge0*SXJt=sY<$``4em!ot7Ae*Is-F4kMOkm
z551}Mx47heB1`*~MH$-f+T@w_R&Xt7)|^|efM+TD=la;9+v?yWCk@p@{3aFUq#%>q
zQ;=WX^A6Glqm+7Bd@TqJsPC!TAD_C2R(2~uQX`V+kNKyqt`zb~o>@!(C2s#mKIvM{
zUA=2V^KwU%p>;&o<2Ffz1rbAZ@+5|3!2Ov-XZB}7FZbUPAWE!oeJslBFVX$|C&HmI
zY)a063M&dvAX)<PPJw=P!37?fH`PNy{)bt0Su1`=U*A2^vV`b2@!gh?&AceTG{{db
zKmYiUY<Vkb(GaRMMS!-&x@kg1HF%dtMLyOXR3fsZ)AE2UECG*N)9LJEdAqV6n(hxw
zN{bD`Kgo7Lj8WsFcW}*-JsVb5!7(H28c8n>rLGo!uziRsu1d4YQekpA>xj<pxYFN$
ztO3Q8)6xxW4jyec1n?yYi=N(AW=3Ofeldxi1iFX5<}2gs^Qk%eOe|~J9m$+rAy8qM
zD>`Oa&N1U!u_XI6r3<0F!k9w|Z?A#hnU=O=5B;#l&Epx4UxQOrrp16v&Fg#q?3<~8
z>zK1hL$`yw%Fb9TxwsvZ#sUoZge3xzdpC|vf1d;Dmd2{S#@V+|_kYHn^JZ5+8h@?U
zv8jE`1?aVNh|}-7t87mB8O}KMAZIHF)l5A?Odv;oHpLy)Z|D|3>L}^v$K1g`@$5dP
zr&s<07l}sX3`Ykq8tEMfw})^Zga0tcZSpE*oef=<wluen*=Kvl)cR$=zeIStW`4R4
zcpwMPl3&fn|E+eLe=qn5$T@542u|_zUg}Yq?W-P;Ja)t>R7-l6o$G>y0|pu<I^cG6
zgEZE!blM{JdBqjain(NL%4(%HA^{7u7rgzVY$sRrQ@{c3W|plLLLi~-YbHB)#b}6o
zGrCa*@;lpxKP<Y;4#-_byTf)XJvy^wG_$Px{+fj6S1Oa#1=b@(Sw?$344IiiOPSB@
z{hkO9=IXWD+r*rkQf!2pIsT<H*KYYbi4WMoY*-t47APitz2^C>Cl^r8-x>;t6yb}D
z|A@`=`cx7Me#nOuxM0Vd+mY)b0EDeY2sNGTK!WG4H>!@J-~g6kfXD#uH?rWI^zyfA
z1_ebW>=xzM2EfNb7RxE1MaNVbFpVO0`NhpCQ{BlF+of-#EC=Ydov45#zi^MJ?cn)a
zI4PjbpN_KXTg(GaOUxxnQkr6_fRY*=9PhjSA_vp3I4d9>PnFsQ&KfhG$F`+cy`ik1
z#Yn*c4|65qg<<q<<{lV+a>)iu&dbgiOKJ`9vS`-Gg4vt4bLpBVpW)iF72H!F^C`Bl
zVi%6HtT0i@#FSjSWvj@k-`5Y$N3P^1>UUNO{~jEP-Re{T^Rz}%EKhC;qdA9*L^K>U
z$E$jM%<nT^^BtjQ$;VN>&rCkVk_f-vtca%Dv@8kDrpY%&qB~7<pW{p4<}N3|v6rxo
z%E_7;<@}N>xdWpvSWj0S<J9k2D3tAFTE+vLOm3z=31S9!xwvdXy(Ur1=>!!Y{o4A#
zmkywu{or`5-7LK}VASyq%9D|mVMdK#P4s3S@4~+M=r5iab+o0p(&WlSiX%xc#rQnl
z)jPA^ladgU$UxCAJmWlb5b`0Ff^Ifyf_MN(QkgZ72}4z_omB33R%^wUUhh&OTL%ht
zGc0ibe))q)^024-1r$y3+86wb;#t_x+NUz5dpn_3Z+FB>nAMZ_?QvrQdV<7U<uARg
zl$5T|9`#is{9%m{%lHF@oeMW`>O=px`M#!!Vt3<evM2*|rpo!7=FA%mPk?O3Ir-D|
zLIN9L&p4ERYPUBVhu~yyyF`_m&wYxIEUV=Lv<QiXAPG)$z|TeY0TaTvuVR%~Z^j-;
zPYRYIAt|6IBhn?l=u!&aII4gBcJ0W{K-zc&Cbq}8LJRL4O6@2Z`frA~)^8q}=dL)D
zeA?s$Iq^bTYhWR^vm1Zzv!$W`gG;IJbegfhL8q<c6fF5QN!kFsD75L_dAAK>!=Fx)
z`blFqSoYmSIYs{PkAPGh$r;V-0+3bcXtrx+-N2Ry1XV9OKVE-|1F>;KZLUiWI}HWf
zOe{DVn;u&`Cqh3eHuOb5(TyF_urOEv8&5@)`j4UpX8`S+`SgESsV=?r+T$yJHzAdL
zy>vW?$>~l^c`Wd2y?i#>gv$pts_!V_)8#YvR|;%clf&d=ZjYbuA25SI;E0ff5X`Br
z4znptw|7?UYe3HqLl%2nYD|GUId0G5_ZttMS8JHcD)&$h5@3t!X^LpGyt7Mi_o%<r
z;bH3m(NIX?=(6xMd%1ZL)S?L|id{RJm*&u>ray_4gxs5|N4P29VydwW$R{5h)k?W&
z1AQVo9S)dC&IA8Y5vi5gEjsD2Vi%3dJMI0<9LEt);W6;aD&fDLh<;576QceSw{ZrR
z&Ik_qoA&Jwd<TIG7p(AHp}xAbQm*<Jtc1S4u>~0m^9AWWG+-jtC_?1cX6W%8<JTb|
zESdFibPE|D8DrOLI&Ef^!BW3#HIhCLfd7*ZR8+Cob=<oYtX|j_$3k^rVVtOcUDr-!
zCW8|_eb7>0D^=jUJ(TDhXeu;tRQ~flC74c&?}Yd#WBt8OQRcje&iL=!{tFRF`5*ok
zN!v8BjGn}o#gKrBux505H4x9#ay9);OE(u+T)o{dk10;*IVTFjwkVUz!Orw&qa%dR
zLBg`Xn=dO;Zh^k($@$B7Ec7)y(W<5=`zhHkB-w9U3UC%X{r>mFfbyQLfS&w;W^Vmk
z3+<D%4j)cY0N8WVm@Pbd;qyYcB^h0M6)9WliHFlYKx`}7v+z=9W54@hgs8j6DE$~Y
zTEjmnb=A^GtF`o~2eCrhsRa<j2!#NA0tTQ4C!63Juf<c(eH|&gntxPukMgYyGy57*
zzuHzaB&1a)2Ut9Tw#~bcaz(S^$1&rwD;}uNa!{m$$%Q=bqaWBb0$M-!$Ao_)cej<W
z90_*<Q!5{E!HfW3s^+zwC*iX+!hp76?IwP9y!DoT36~Ieop#QBW(yXH81FZ4pB5rZ
z$k<1C23kN6*U<&v*Cnf-oVi?V%-G)X8<=%?>WL-Y@rYnq?Kb0jDW5^=jk{*VvXL*0
zEB*AwcVP<}`T;<pVxB*+>Z`C_VNYfzS8X69(6y^C@*sBJqBETX$to1A6$}Pzh{JQ>
zkZ6{0*?DIy{iJ-_vR>IK9<-F_pq8rsNBBK$9yYtg2dRuo$#YR(+v2+AnUw1qrWCZ)
z)Q-((GJ08leNU;uXIt*NaPP21SK1obElUY+Am|d*;R;*69KL_-t@(A;?Bn-{4#B&%
z>=JHu2&v)M`NDhRJ_rED^uw3zUu7rVi3j)Q6|G$|?B}w<lyLpDb+U!X=5BRB5H0M#
z$rIq@pmwVL4@6H}I<_u={OI?!2tPO0>BXtT8YduYG3ELnNqJ^cT1>-#16`Y|{eNNx
zS7wPBW$&jV-}ZPTk}jhO$YL?+;l>e$zO^x)KRRyxf`aR_DtDdV^MYfN$*hZx%_kzq
zF0|p+uKsfd&(1L9c&>et^W$rPA`;Nspr6msQv!8FV33`4N8cH$jx|w^$jHb#JRdhh
zX3BF<ceQY7o?dlHwZctVWlnbBp3Di7ED1HC5=~DSq1Zq#YA`Zt8C6Bb)d)$D0J(Vg
z)Tt*5KYAYI@Rxj#)R%Y#v<#UTgo>>HW%Yy~)$>Wj$JCE4H&lE?3hNSig-fX?ZS}RJ
zzQg9^P|$X+)l;pUVQnbqm3(^oZ9XzmpH7x=3cZ-9Ih^B%)e;cPDJG!RR5)>7M~@2^
ztYagFmYtveR*<rJk1kbyK#pyBz1f@bjhV|a`R{n1PisKkBxqkVL-l@)|F`5!#&zND
zjYmD3uRYlhbU1|s$Dnat7-4fo{YYMqXUqu7B(VPajMqX8S{tuxse?q3>x)tnh~Kz}
z?OWVli;Uk;&$GzQhlOO!FH^Ya)#Z|z7UBs^$zhhe^Si{S7)Mcsmef~Rpb{cJ*R_F?
z=2Oh18KyavEo@uWj~eCot!Zb5kf8H%YrphRc5F~LZ=5rw4hN0307nwMqioL5cY?m)
zW9dR|DLN=-nj{w~NYdb70|d&4DjupO!5=;NyH9PuV~v45pREsXdq~YG*VEoQ@B^=G
z2qoMW%ZM_9Wmn@YSHui{>MWk?#slRfFIf7ETBnO7O)02|_IGNOG=#LG9`P8pDQ_s|
zhhYAvp7TQg@2@7rv7#>N$hwn5l8>jWI>*PstdVp_s96m#$Lpf<+Ssq87Y-Tg8lU4#
zOa_<qx*2AAy5V!>SYO_twmuVnRn0*iRukj4e}gVJGHWS6$8)(z1|GCBtDRo&=MWG9
zWjtS6d7xbYg{|Dy@pK6%TClaF{W|;p92O9&OhUMwnE9?`Ss)rEmWLEhKLsY2(*m6T
z(Y0&;GHz`8cK`<CfyR_{hC3942I{(_N#`F>!rvd{?;}79GdwX#%}vZ+Q@lCP^BSmq
zi~*FX4ay2wW~1++N-YzFdba^TL~L5~rzO3-W5z1g$3+?>`txVCMKo(`rF5L`(RNJ|
zW_C8;v4JZFQ_cOcJQ{~jj_TgH{^HYOrhu+8*0<36aV?Dy+1vgixkq59+K`5NgBiu9
z7k4)wBy_PrQ1vd*T}{5d_wmvCxhaoPgb=@sT<}!|%~g+t5)OnBu7VcHt9|q8$R*XU
zZVXsVv<KC0=Rsy^rmQ5$96G)%Iyo^x)<^`FI50+a3+tkwI+<Gn^-9Mh?Q5*(bmfvW
zmyHw4hGi=R*Ze^_+-qyvf#!wgH@Ncc9X>a!BA-Q(vQjgCuHVRpQZ6rP@A&hcb9FQ1
z@81F;aBoF6-{^47>x7I4VHGUHfqyL6&Ft2>&%w~k$8GBs>Pg;cbig%rgL(aF7}qaE
zxXml9{RVPvFUajsq}{KA`cydXpJ=bo*RL?Aabup$ta$1J8t3Ew-p*-axBn@GUUgB&
zKW0uK8#M1H*go?~Umu;n$DY7H35rE8hGUkBn;u>HxbvSH59Kv_&XP7p;0q#0(mJ~4
zS%9q9kG0BV?11%mH(CmcOh#7P8bQDO>Ebj4<#nfb#Xq7q?Z1b}91tTtk1j3Zk_Jz^
zkRSk?wV~Qr=?4+~-!XL1ppIvr1(P?KDx{g#w@cqR+PYPjVyYxv%M#<Jsp;V<(PUYr
znpRqU<6*7fp)%%$F=L$IQ^~2Gw4m+02tzkolo`TPv6+ATayIRe!m=w-e<T8vdLQ(G
zhV_;AODuNIET2=BKd;~5tEe%x){msG2rE>ms50pD*7S`S#fPQpl=>3BJCWUBj`Zru
zhcA&BOeIv)z!?wh0Eq+m$5S5s7e25>3m!=}D^^+%e#~47E0JE}527yJFnou0S(WQ>
z@?9AydUN*2CLNMNc8hMAMR@QA5*nqhk6O0|C!89!q8#BK)I0LJ2K7sUd%~Zn_76GU
zo7;Wf2_Wrd$DwD*R_V$#F|B#Pd2|KOR**OoQK|@^;~^KVRkVdCi>CbFrnm4kMO^ar
zND!;?)~CihNu+=TR7^xkkA{*+dN@&Yqu)n&Oygl48k`^!;AUjA{X&ss{Ahg8_xgFu
zDf<tWPts%X(HBZx#$Cc9Id>qmn#=O^KE_MwElybOT-LAEfmp?v2oa%bWfX_T(2}Zj
ze|Zv4N<u;mMaN^?bl6f6;&UX}IdxV}GSx*~iVFt^1)iL67Lur$Od>ymAp#OnGBYFb
zwuy5b^9b|zZQeZm!a_?_94-EksmJA_=vdG=h4||SK57~{Pf)WXAde)_%fgd|mbkW6
zd*IQ+hXQ-&!<&d}(jqV7LTYn|{PnGQanQXBvDL<R=8LrmX>Y8@TLygchm`Z%?2E$D
z;V3Cp^4Y+Lo+PXT{S?Z1g6x6Pw_O&EViui}RcX%S$)Z{^XrYO<m_F0^$;V=;b$ln|
zf!}?};U8$y<U7`sqr!It^MrQ}8?SO#Y8?}*TbD&>!#3#BRMdj-YNg*jq%+cZ;;G#0
z*g5CF{LuIoGeJOi+z*&?4>mg6bp8=v`AcYu(K~=~0=sH$0yi$cY3kuhkEcI=FCz;M
z;0o{v<6^wdkJLLCWv%5Z1WBWhH^inl{{HkuBi^c2kIv)Oqh#;|v5}cVt@0Q&%g5U3
zlgrx{u@m$A@jLi)&Vb}P`HHrqv3HzjN>j(WlPZx;K=K(?+nqyp*F7XV?So?lc_fpH
zZNjAX`KEdFS+{-L=uFMQFTE8r@3PS?c6wNV_vatGL$T)R{-=TC?|rS7;XoF<l0c+4
zRj}x*-aP;Hs`A`D5|E7SySf1@`C36IAbgrk;-mDw58E}3<bsPvkw=tuOE^F}wCC0X
zV;e?H`E>jk>u@dX4QHUPMbkPUy4Ty>GA<d2{`JEQl4=x0Pd!VB!Trwp)=}~L#lD|X
z7>x8cD^Shh;wCxd<A>S;kg~JV6f%eV(d=6)=OH7!n(`EisD75t=2qiEJ%0+L8tne?
z=R#ctO*65Atn6t|&k-WCpl9g9rUjg9HyRMP-UgDe<kIdnQXLeUl)li{&nVDlW^MgT
z2z45m%HSB>twWra-a2)&H%5_2_l?;RdHnRV77*N8Z4E#)3AXjOA77G1_%FP<W&JD>
zkV7`^q+V_V$5J!#u^7Um==0aQhGE$2uTaz7zh~eH<$&r`XdoovTOyifa=*I(bpmuf
znu}~PMWWX?T<oWgquN^+9p80Br-h#+r=)9{8qC#IEzaXRD$>zZM{oU!NUn^lV^(MP
zz=A4pVgn4G=4Mr4vmrJ1`Wx%b!#zq~3ndc_gN=TcfndM;iy69l!vsiq$?P=$j-hF9
z9rwn!;E_&YDi9sLkX8%bBZpX^0P=Xc95&%rsDUM5h$<F`jF4omH!^4bP)3WeTp`d4
zc|atfF!a5@$PFqzU`(p#v-y43@s!;v{HB^hW}LlhCu8Ga2^!@)=vzDjDQ)r+v44jD
zjDX_P*Ht(rj_+yja%l*nrSJ!BdPt_2rTl+K%@0VhrN2|6B2a#hij2we-2&4Di}Z_~
ziw3iro}P}G`tiHesukbUOTvc}g75F%VKhppo0{FIB&j9NRgeh#m9IEIv^@H*ycS8A
zIF8Y@zSgq5Y^a?##Wq8;&Y_@;#OmS^c~zw+#uSMK3B)KZBc?ASPG2H3%=nDr68b!S
z>G|;JA>NT+(v={JF<0{oW!s59mT=4v!x5H9q4drH&tsND6n$>U$>1F~&-F2<ovt>e
zoN~D7)A!)w(L_|J-xJ)@?CMYJ3n8h5I2u|EWrxdqwrrouptf9p#{_f~F|V?<=#l6^
zfo$)nT6s=KJoepaJeL=dgFPzw6v|QvtzXdmd{Sp6pkWt`)YQ~FQn8XW+nbx40u=h4
zYbV9;z_4fL+&Fqx`^HY+veL&l@K*KZT&>8VPxvp_D{Q`K%t$V<wfCIEGXE#*LhP^o
zggIJ?>u^4V@aJ`{?WEO#ls8M{E(apmxr>@R+xPc+8_vI~*afKbm2uPP^G;F<R4fKb
zK~9B^>>f>e8KrDGmFyBwZ!l2A(n|Hp4KxkCszmbD|8n`yhZEynNa)_4P#p~0#_^aQ
z55ULQaNe&MYKTp`F$k=5p4vzR#`4I|YueSg)%12%F+hy13F9az@q&IW{@v`$pV{dP
zyS0mCy?}^KQS`dm63#)Q4;$|AXSJaXOz3b6b!_Gb8G7GcV)zkl-q9idMSXeyYX`>`
z<w5C_IeO(Jk>ZKXtMb6-Ub(TCZY22>j%iaQ;;E(0nc^P7j?&E}=v<gS{e5-VONIjy
zg)y<1Wt@fyP8LlP`J|ebSD&IpUWwpQ{!Pl+<iC(08(l^puVO{uYI+f#6=l7EhRvCp
zmO@H25yg!>6`FmQuQ;8lMYy+7yq=3<JjVW!kTOVQWav^3lJ0xEgrO80OGPUc$9DKn
zgXvQ8U0OMtCf6n`AucMBODc{W9ea5B>c#kIEtAGLvkJpqkP1d{b*QNhjZAeTM5GYk
z)btud+VtIX@6j5sj4;P*A<<V1GKRdb`fIC*g5^0!Yl-zIJDD4P&wBSbewF9kvU*;z
zy568gLO54|v;20ej+`UiT2CU-;qH0KWXNaiBTpfzxVWA)>DDjR*vhYf)<Y?Ug;j6<
z+~=5cw$DT<BAwngBoJvq>BAL2MP7#+LmqY{g5lMp_r<6iLqfhqxoZt#XP+X?T|-vX
zktTfZH$U@l;0akB%ncqd5i3qUn^HM}U&JB0iX(%AgPx!E<4xPH%ni1tLS?|2>bl9+
zdmoJ%gza-szib4=PfXuw<&<wT$<j;pa!9u?tV3hZuCN&rf9NtRrZXsImsD0w89u0|
z`=7_GY$yAl%jtVO3`8exgKsXAze~LE&Dc0GZC8ovWvYHru1&8)ZhtRYl4j#%-U7a2
zHr;#Tj=c3ht5T7*)fDm0oYC#SJLnCBIu)LF1?HF-&J~^xgf|!bALv^yW~+{Zu{wSb
zfQ!KQblCnVHfs-H;7PB6(D3UDlFn-3)@-GUT}4Z5OIeL?xj}Z$9WhTQ#(bmC{crrw
zWHhgi7HgG+Hz7Bsez%f49@pMGVL3ZBV^kf~(3Kx^_$<5{#$G?irtgnkJaXCB9B&{9
zBoCXf0++u@=k|>J<jW6#dUtWV_pvY)js~qGj9*5iB{P~i`ztS{6en)dtmT!2jSC`!
zta=I!Zf8egB9-usN!a^8oDzm3l5=yg%X<AEo4nwtvLnHEZ|SfS;gXbL<)i;T?!hE%
z!x<~GE5(_67FNrx;OJ7&neF58a-}NOS``Mn#jm5(O8MnvTs9h<egKP>L#Molb-mFS
z<m&%fjE|N>6Fns~7fN!vF$#6CJ$V$1380SfvEH_4JIMZAb<*`d%6P0stU}PlIe+xd
z-oWVZYnmiMNV?!F%4DP7oxXg|<(v3(lsmHC>S1pGjW<KJaOKbw#Hag0mvrAC^cGmK
z@d#0B4_<epd&L=b`!z8EJ(1a4{0tAv0EkH#_zWu#HQ6lth^hpX36y}SUAdJp=(uzz
zsQjqZRY`IPF)tNz^sNTpKjeKCoUbASBu~rZJZ@%Lxy&PgTRqd$CJ>Z(h~;kcOEWIq
zNfG7>+n84+5a-h1U+ABNpi3e{eV_tsG-gh9ebYXf95W0CD}T>@_(p}6W@GF9_D~YF
zG3M%dK?zs4vpG9@>eM*7;>mvKYtlRgvTsmX<4K;@BxT2DtJw%Ppv|#yPPHu2X(Md%
z$20YPF2PQ%9oKE=#F=K<98$b@!Nv@P={Z7LW_xG&(1%s>HJTn^Susf28F*boD0E|S
zsq73c&9OMs|JU-QGBA+%tfiZuL=gL5Jb8zX&M*nz9*6!~wotZBuozLT%XJKC{qh-a
zYI#?s9H&SwiPz1|FBGr#a#@Vp95z(Z+Cy@GtN<kL_lI}5yR`_iqy8WAl|E3Xv3zRq
zG>sB*@2SGwwk&tIEOYI5^(2mTD(kqPl-fpBi0w(`xolmzd#54P*1Px}nL&mOKFILv
zhIWRJ>GydtELmoOhQSVz6N>)Zzw@36lv)PI6WUOxwbp|k!;yuRhcAPT5V!Cth;sb4
zSIi7SIySw~xg@pcgEe!dgO8P@w+^0h!|5Ph>sah(ytp1(sSM0$awdNt>pNeil#{>}
z|7@q$2BP4f3}Hu*5eBXltwr8hQ6!tW^@w(#q?nb)zGi=?tOyc@N!^19Yc!e!ftIgg
zpkKL5EH+ikWA_mXH+M|sbADC&h%My#=c__G0j@@)n_uviM4bb@+H3G)>WtUCxIm)~
zMJ|<*Q!lrl(mr5gRWV(IarBRksbv0LV7xpJVGW@tVI<4@ygdOgErtH|GrCdp+u-W{
zO57i{1&U{N71j%N)!+0}eGTf!gK8iKl~s#fc-?C%&Uu#7X%;qfUArT-OQ$w@aUXM$
ziYbzeF<!EMrb)Qh!x)GOjQbiqh>z6iRX8qT{vpn4j5v#UPKuK-JCjrv6Y}s(MyiXa
z)0sh+KY~T|?CM1%<MmCq3g<dSzTkjWm7C;qODmc?roy*WdvC<nIr6z*6({=W3$P7G
zU2-iMc94FnOvu~i6<D+s(!R}|UuIUwz86qr@J3SF0kY;C(i|bR?SVaBs+|(-AtCmN
zH~Kec$m+>yJ%(K~&h;sRY@M6BQ4ZJ}IJ){?2Y5B1)J4-Z-)1j$Y^lsjL4|bOj*(YR
zr<nwx?_eJR2mvdJB5qxRouT^1M`q5Fkkd>XhWbWNQ{OoudhRsRo~wJ?-(+$s+SYog
znJERDS3Ku^7!U$M^<-@nzW3$&nr7Q4%h%M(CKxf23geTOs1{}JQaSL&AE}teX52Fs
ze(tV&p>i{oujA+zY+Lmx#VrvCUTDr$5{lba_Y`ZO{Q*C?-IpnjD_12oUKMS%v(1Yw
z)zPYP5EJC~%__H=K}gwKgS)HJ$PkROOD21tjh6*xr3qFqhq9F|lQJ?g#z`7~q{PR^
zpU2Y3DACZ$w>crrxqCc?Chv0HEjBa^on6Z5t{7e^8WV2C=MP3AkY$bv^&9A}?!K<E
zXmx+Je<7M#V^6e^Da<>5TgJuBTrsH+UBe}!+Of)$QioR7E_a{Ww4GTq=h}#~d_$5z
z(+?b`Z=jK3bvKEdB+XkPJ_7);!O1Q)ctb_gEoq${UjloWI18#s<C)#`17_0SB+{t9
zc?9+QHk)>^qv27(30m=Xj4VLkaw_U}9LOPL%F=JChBG`ozZ;wHTyvcLU7xLeGn<s=
zlJ+8pg$fl5fUC=@`1c<$seND@!`MT_<vXjlTuH`jxOxmaN0``TSegbN8%W)L9XIY3
zliCMU`p~MX#R6SM#gbc;rsuhaZc#1w`B;R!f+F6n$;dq8KY#qSexupgHYh3F_*E5d
zxC)dV2f<L$K}!5yEqqAS=+XMspNKa=;AZIcv+8~IxhEMr(InnT-K65x_~Y@Y1Od2j
z<oQ1|uN+^aDoX*=kA7!w^>p12q^}m(7|}-IIKmM^*s*=7pHq5hl>t1qVXBvkPbj|e
zN|L~%Y-kId3}N~9DGocI;^7K?xauSvb&W>!Re-@6I^r%VW$+L6GmGocXD$ex4XcZ@
z{P66TY>sit%y%@jVOSvEb3{E{)q0)6^zaWn65Y#~kJdwN$x(6{$R*LXO3XJ2uZeS6
z$Rn|a+GKKdS7ZGA!qojgrdcH<c%U8bH(g56B~<nq1+9(w@AwEg=H;w6B-kc@wSE6=
z&b`v6x5p-tLOwOEl&w~=kV}a?OeNejrtv-2uIe9KRL$m@9L>vO1+`e|Rb1We7&)b4
z+|$=gLvgD6;zKiV5&eZgT8K~#PtVQO=xQ6N!px|gO2f*kvUTr0x5tHe_bPm8_Vc(e
zXiGC;n1<-_k?k^;R(LLwJ%(Rn<BD(a%XeaXXu;9UHEghdV?y>4b8y<nY@*u7HjrZS
zQ)=e0{>}?6qM-;9CQwodg+IIahCU=bfi5PLD)^f&$rn_7P`)t{CI#C|uJ;%Aqo}wm
zei>`Ms$ZQ<DR+1@pWEfQTW~(KK(BVN34dRBR@4Ko4z<kx_bDI;E=<+3Ve$6(YQ2-}
z`4o!V=yd!xbNh=muKE{->OSTsY-wUi{gkaO=1g#LoEKb|kIf$cVym3H+AOR?f^n7~
zj}dLk-S%oFFCgzhDbLs6#C=*PAmroi=6<>-xF2l4fA=KxZ7*u{B{B9w9gN^9Lby9B
z0zAiB_=$Fo`4>QkYml3*BYcTOiSNq2g{t(cUd<{#LX25GnhVig)jp5i?bkb6ja7r7
zHN`3{w|9cCaE`hB>wGw7(Nv1oYMFu8cPwT`hl@jj;5hg3=^p4)={4-6KY7mvwJta1
zSoV1^gXn4K$^#3Qcb}4`=oi)Sl}81?VBB^Gn;0RTmdBYtBMkBm>-pk-C-y=Ekw!^r
zDBfh&+&a^RbR&dms~V5{xSksa%o8ak6S@agE|!V<?l2FM9+d%t6@l&xqZbvc;QgSB
zg9{i(fiLK`QD@t`erjnJBkORsCEf;;VP@kr@Mr4nK@p?ZCX)?~ym+R7<6s&P!XEk=
z>df__V&42O+O9hSA%F8H*Xof`8S5UyNO{gbq14a2(Vk|!FCeKNPgBVX<oUokR>QdL
z-PV2hT}r;q4bN2SHuJeKOauD!m#hgPD%^ce|N7uNJAK{!Mu?$vZJ@zf_3k9rpJ}S$
zY4Z|9KDuJA#l_u;L(}g;M~~kqW}4?N*T;N0=tr66)O9j+w2iU*M!1IVr>u#kN+$bG
z`bl)D!d2|-+<3Tj%$w9jX$Pmg(xLY-LT+w8Y~4@;pG%(d%&;#Hq#p^o2ZN>P(3BQN
zFu6=iJ2U*@p2K^6%6V^ug;^kmiG{WIMOX9w{&cHRTt78!&<gie0Os9XXjE>Hd%Jr8
za41#cDrVBG!GPcHK4<vCC)41r)WFEKc+lN{M-mjT{t=@<l?p;QHo2p*><$j8u&;Ov
zwI@CV<25xFLbTTp#f$bNyj<!5ha#c!oP3jcmP1i8rFd-pR{7ZA#x2c0%ghrP<MhA2
znWmBkr`i6gGxUQ0{j6P`$Bj(CmVi*y1MQRD;!-`2Jdy;)W!O}MUC#PUMMh6`O<H`k
zxk@^n|NaA*gl>G|UWfDY@@DfwK7Jfz3$y#aj~ap}!$req@3Sp_4-Gb@&%=~up02mQ
zDtNn(;`O|HndeL#35?0~JkwM%|8B&lE~5<fVyT=A8Ko?V+{A3`l|{T=jTp;R!Xfj9
zr}!(=m<{GJcHZRFT0&m-ex0QnpbR!zgI&D1)JuO}OsrVaI6_>024T)H0dp5m7c<_R
zKzzcG5V$$1VsFAtp`Q_sF+4Dh8H1js=KEXQ@|<rg(Or^{UNW_AqX&u%G2|C1GdqDp
zS%6Ehz<GV_YMbSCiLT#i`1iGEgSdPWUz39kbX*B3V8fPIb{q@keRM`ve(myT&Igo)
zgO?>(l+l@)=3Z^`RqN-sa|({Tn;c-|y)4fBo~SI{1}jV6wYfT#IX=b@f?I~&S{C$w
ze|s)j=w_3kd@`leuOtmn+SYFB4UuiKwfI<zX9A6M5l8rSR0{eAzTdyTtkZt^@(Ype
z^5~`wPCmsN4X`~=K%?<4#ils0uo-m>=fiJJQUNe;%#D{FnW0f{Ib!u)X2G+I7W#>6
z&-Mv2o$+qSEig?m3fr5R?d9j@xAHcITH!p>cvliG=?^0;B2r&Z7eD_V)LqXf4Z~v5
z>ais>qe9jhJ6&S|gAbld&42`L^#Nrx<~?RY$;)3=s|GZlf6Kvuu0NU2;wB+DFfNHi
z(}aq(1qZ>i5+@n2!hoYH71!6y=&Hp@!X(Tp2VDqTH=SZec21_n$t6jm@k80J@gReh
z6jDmb+wY=^v?i0GI!qI7*6bS08~j{t#v75NM9P_?ugYz!ShVs_(9x_DDrvMiw;xon
z%jl|5rQ}47jEsnK<fMOzHJu_XnZ(<*$XjKt;Fs{$J2JkW^XkaY9Q@b|z)0)7WOQc8
z^EjHN=nE(pBAD3LXojX@qB`9e!OTW4BNz9PomE9dD?BWf4xnZ}U?U&<CSw1a5#?C?
z=OMH)Mm0{l>{D7Ea7B$&l3)h2ib_Ya_85v*aDJ2ytEQ03_!<EIm$`RUU}ypySW=lq
zxtoJ8Vm<}<WL!xLfVtq9;{&6a6;{6Bct5>KDqL{2Bwh~yA=0M)?Q^_Gywk>kiC1RX
zTh;^|8bGcIZ1(oownt_Wqcf=B5P{!Y+E@H-8Y?#aMqWSV-D|R=BEC44ecLcqDi%e`
zOSqFz{>PCKQv3(`&Qo(QWA$NNfxEsTlc9M9GJ~G+MjKJ%P1e`q(o(fbIS?90r~A!E
zM~tosp5I@Ey%WPU#{P-P-|}+a;8soBb%$xR`FsU`)_+E06cPmOy%E^q`4cKVLUc2w
z!u(4hwdyU64CtRHTLzwc9gzEor%rCPyt0SC(!qQ;XX`IopO_yc+Z&)<3so?*$GP?@
zs2dr4`-8i`>$t7*tGwT^sP-F9zYTjo+wnScR8H8H!PBdi#{&b;A8oJ5Ds3X{A8)u}
z+u7~cgrq^hKn7nEO2u=xJ&9=b<k^oG$VE%y_LwrWO1I<@*xU8ataXEsxh=ZaZ$0q`
zXpbITTiV|#q%7?({_0w8G;q}pvUMLLkyT%Fw$RmC+ZOWhm&;-Ir0zaLX?hPin15`&
z`m+Bqm1FXwRJckdt=g**qRgB|2qmF7c!OL{C5P0|s!e3$OD@*)goF_})s*sNo+PeH
zwQaN44o-e?@#pai(1)qlq3(zLYV@aIM(C<jPF=m}3ww#b^-CfZ{i|V0Vs=V#@(o0$
zzs>-WMZ#E?sys;`nLR><f1hm`O{WPkYx`r%UH9s*E`pb18Yk{pN!;7AUxzmj5T6|?
zHQC`R+(Fj^$&O*ywmYtX<x2p~)Vx-%9}PJq@Jp=@qmbVY-O~0KjzMzAdaH*U@#MW;
zgq`Ka@M`P||08Vu&aEDq*Y}V9Ph5uR?3^08wUfhr3Wsjr5mPdX$@Bl###G~gNl3G;
zsgoZ}o_oQ!4SkiOQ6x-mI$|zqAf*7wK_GorA|{bQPU!v=2apR5S)+;P|3}nY2F2Ai
zZQEA}4nYTZcXxMpcY-?sf_rcVclQ~By99SnfH1gQf`ni}gMK^r^HzOT{Gupe_U^U1
z`{=W~zv_}0sf~D^o7x6<P6N5{<SMf?s`+0SSZo&H?NZiVQ`bRc*3HJf+F)0ntlk;>
zyIA|z#j)?Jzdf&D#1f&8)XpkuF5`PJg)d{NDeQ+KK8e$rs+umU23Xn`R&9;;+scb@
z_S>RU{V(S)8FQRg-_df6R9iweAs`iXb@iEaN&*l-6vREDtlBqyVQ$5=fBHt8&ikKh
zyRQMD?(ep{&cG<h@trgzhOyWCb(1`tvQt&yp1fL9iV;mN1UE1JN;D-WR%;DH;>N8i
ze79|xpc~HPMlRzVL975HvIYnUC3IpWn$5$)H2zP!qMah{^kT9b%=K3A`GE@+FIjr>
zkOfbI$IU}GtFQ9iRGQ#^We<)00gz;-q6ChWsNwTH(N6xNI(x72M=G~I%kOvsy~z3$
z8L>I@$G1{PdX`Z$DQS{TD(6#id(3IgTeFNc3A*b!Y{k-MhlN9FtUzwU`5~yl8zd^x
z$h={wGhuIZ3J)bJB~Xs5WX#+t|B__uEoMg2uv5Z1nJbX|@%o$S@Oxx;Qxd*<vLifG
zz^lIMWeX}R>Zn!iCEw|&PA}fWIQkVi(WQ_9UI|S@eiM2ddXMMj1iW2}kh`}Z%#9A8
zzi?P~cV`zYUPd&zz20Vrse*zYyD6HR7i@M{K%NTpf-f*Q^TA2#K-|O=Tc%zB?;xei
z>BTqcd~DN#iW^y8uJC$*Xv(4DW`pf`+Dd(Y3AQLvt;@6u79&~x8CA~w#p~_eM79j7
z#W{Mt6P##jPW%9@LaWqu5=8&GhW9f|LGTr$bfegkHtH`O+n(^@rzWK#t%6?uv;1aI
z|5LsjP85nqhD|U_*JDy!bF%~N{o^S|I=!&xJbTybWl#(d=W_DB@3t>I1Y-Dt2<rct
z$XPr;)mkJWE_I_;b6$Bb(OU;?9!e#X6(?e*W?pHTa4zhsGpmUYJ@BYhtgJ>zv{t6u
z3aBLGc`~S&bSjEXp%2STT<^G))`-5;y@`;dl6%91w(jbHTXuuxDo@z{O{h8THp_{!
zak7Z2f>1lHHMduWu~lizH3CNt%1Yh%g@9l+XJp@VVLyv4va!j=b)$ZTJYLqf`N3A&
zLRB=Re<Y1B(tXT2jSWV|mxyl*^*Tn}?yo4RR14Z}+7eetPszcs{1~AX1ZFfMPPPvR
zk!uSoYHhr@+!DWjYZCn2yDGB6ZMH8Q{?piUU5y*4m+Z!RE2dn7uVY6<J5Z9b!q*ng
z5FE<2;68{DTXz)xv0vF8+Hl4MlDglilcx?9LuBPR?YI4&#UJYwtBhBQRLJ=YFSG<J
zb$>OVbDMBjn*c~l8`aK<ZmO^QL{KSD4iKp*=eF=5ksy3o%=+&~nDLsZgw66UGQ{M_
zi-^jJk`FF|>uti;e<10lur>Sj)whz!O%)xw#jKEVKGe)Kk-oq&LeuTBoH~$kQ|~56
zmmflmS3!3JYiF>A-_eMwk81977K;kkQPOR#feGuQVEuF{uC>(19u4Q-{M<o2Q~EKj
zg!Sc{d%-p^4rPkdp>L<=pGu9)J5r?n4&ORh?+hTQX+7svYBGzT>?Ag);z=j=QZTal
zL4F9)>1BJ^1fPg>^vSq>?C(=My?WTPe&>EP@@=J&o+l@De|G%x_Y*lY@Dz1u{?B++
zu-;n{hK^7^U>UG+>%1h7nV<vGQQ{ZzubZzV3M8-g%4hk=E@eOHrGj!32PLSN@(HzF
zgrXn^IW<q?*4Wdb&==Y+nT#!)w#Pg0JU#gMKa}=@&wIfU)vxb@9v6JJMIaI-1TT@Y
z0#b~$x$d2s&+m7Q;}x~2=Un%^GV=>x;jmVkrE=I)^Qcm^?_SaQUT1fVW3W2*+Z%A`
z4Gd3SL%-X_O6^Y=nVukfX7;zRNsb*e4<FGiJ-q&>vXnYRr&v#|$!KKN{>S&?lt6QD
zu83Y@#W0XIAf405s_qq&aFhUL&zbg^UONEU6!<Lnw@kmHBqA)%1HfYgKq^Vm6AXU+
z6?)f=nZbQqqR8ZK8sC3Q@roMyGxVV@!dZ~v&{I}m%f{a;RaT<o<T0Wduhj1`s&GBI
z&}@LP#Vp?ST%P>TO+^maDHW`2nN3*<{qf^zq-ZXzC6SxwM*Cp#3BBm*N=lXZ8B{00
z8GvWoAB9CH`3BV*UO0rJ^mEg~V8*haF?P7w-ZK8(6Zvq_4fq^HM>4O6QJf(3ytXSg
zJ=Z?MZCiDE9%|hsP0Elvz;r7<7IA&5)p2F`b(tR+g_4>0lRxp8*?w!H45N*|AjscC
z<M3DARjS5L=|srBd%r7?v<PYB{jZ$U$&ppNYaHW%*&i=y5j$u|s2zTfT6Jt$BLuy8
z6UP4rau2t8fdncrNF9<w&Zl)PRg;x?La7f<D7*SYb7POytCC|np7zf4gi%>P3`7^-
zv6Onb&682Px5`msLuM_FmBwgBufB|ue)8Y_Ezy95s%p;0fL4p&ty0h-LMsZ&Uc3V?
zC-U~Fz78^LD+-bPIZuK_+1?AB^a`>i5Qu#$A$h^t7EiP%LxRlN$r8RFzDnL-uV517
zNIhCIMDK~@;<CMCX-s~5VonH|qYo-+Vqf6^t}K&j&6^M+O<KqJ<~ur8AuwG{#}ai`
zp6tech17pQg5%UTlfNx`#YnOJ;)({uU#r8oNNXR|XAZ%DgT$*N_1o-00+)4fQ-}8R
z7cFLJ=dQM#2Rxf&r#zmfUmaU`VM5lAevr!Famf<SkLS!8{_w_bj-6}FEG<bVA)J?~
zhES49mZocbLUt@1fwCNV2?h2uQZ7<UXJPNP@NfrelHZ7QF5h;)&leGus`{l<MQ{h|
zWi_#F*v4)W^|i4QX}+8<;5hrxV#@K4(g10W^y)f3O8GZx?7Qkxzr(+xlYL@G?GYn{
zJp3U%goJ2)e?_wZ^7+4f6!TLZeJYG*i6kYC^~MO96GbZMO<m0Wtz*WwGIks>3&LUu
z&%+&Q@qPcE5rby4w7?TN<VbY$LW3#yq7*@nX9j$N;D$@T%ox}&Ip-gd_GsL`2_-D^
zAoi3$z<*{|&Pt_LaXUlYt{{2(#My~@)Kr3us8+zfZ+w-pv3&7+-hy{}&NnuV?qOG>
z(r;UmxmXwTNI}9HtM}_A_!UlJno<sYdvu4AR^uff8VORTXM|gWmpx`9<<l5_6s~WZ
z;CzX_J=*4ulb}-1&)DRU_`v{CqOhvXWQ5odEgRD=nuXuvI&FQq_`Sd4bT;?_0|BT3
zpp94DFS+&Jq&)YAt}CPBk2C22!)Xu1l7CN5uBzRV5tWPa@0)aDE2z(q6K={?)IcwV
zBx!6=R4J^ZZKkr&%4GGKX=N&w=O)!61;8cnLo{mQaAJ~`2(TYGj@P)9auZ7KtkA|H
z6sb!k;EkN~ZUu6MUhm%d;{a-$g*!zJd@FmRm|3(jo2pCUMI+)K8Z6jvMY-AkpAukx
ziUJ{^-l}~1Owgk?=#R}5?-edFsx`mR<7PP-fIpXQ`X72<Fr127nT>u#jYaVwj&0uX
z_Hb7Eo#@_H4l6Tvr*c}o&Q++lDUCatkh(%&uyy*;JH$C8bVzaf5xaJW>?CuOdBu;O
zXgas;9=jX#6G12JZSi;zdES4s!qNrxxF`70pgJV@Nq^|YMeV*}a~LQW47}iXbnz}2
zFMlxxbx{da)b<Tq1eZuDn|^}m?o?bbLVQhMzl$zJoHB?kJ?;na<F@E20~>Zv#%w-B
zn`r!LoB6;`A^OOGi+abr)mP4Na91lNboZISty#27)&)cSrx3%TkwPUCl(nQ_`3*@G
zed=vIvX*`SckWWVRAktNYl<E;4=EjvOX(uULLONNtchEKL<<QGKYhg)yb)XfI_ZBq
zF=fWO?Ew3S)PC#K5#)+&SXh0IJ2`*<C<?f(zx4kv=E1_T1|{(o%eB)PxYzo#vf}iD
z>pr{Jjy6%LWNo2QMkSBPBYQudHz)ARw4zY-(O7FK<^QJ^Sx&r8&uJvVg9{=gLB_(V
zAW7KsbV!$DM>UOf$66tTgcYg>OLtg%=6Fas)1(YdYxj;LA_0O^X-4S9*zpW=4H-S)
zykt+_1dNB9C(z&*xDFFixnwX#D1C>1(YT;O{82K#mN0MB$`3V$*ktvkgCmT(iue&T
zN;EI$jDe@=KnSSbscy=WGs4x~WIK1XuQyqz-Bi<@TDc6BtyF!!vC3WeJbI+1<*8b<
zWm;j$18G}1EumuK)(0MS9n^Z6!KU&3yqYATVqo{nh%n{%x8YEMqV0dRM_L|9m6km4
zklX~ZbOtteAY;dJLn9Vl3YFs%*AP1Qd#YV)EW%zPerwP1^S6ziJVTfMG%##S;W9h{
zB{k*IYVF3j`(HbotBJr|MR7~w?_d*9Ej5B(nM0=L-k{3J4^j49CIij{K+BRQNQG{N
z_?)t4^I`(jU;O{?rH~_sL4Sv&Y6XQYU5E%eA<jnY`lbx6@=MLx4TNa?eRr|KPQKo~
zt-%YEJtlrWGUI=Ejf5n=($L+hK`)M@+~(0j;5UALVjkNoZM<{g61mq$x;0{T5h^|F
zY_Plg_|wBo4I`vBT^DzR>zT6bXibrdXq2m6+fW;41VtHDxoDU(0h|VUYihc>6GKpc
zHQh4q?iwF@Hz?QV9+b*aWH{2sHqxQ8sU?ZUun>=+U5By<zdW<no=L5$9nNTnCBLGq
z&4Jg^+BIohp;5kr&A=4FIn>75%H?v4*yHCAO+a8@B=<h1px`YP9~a3kPN74gB&PVu
z8KB$|Ko&~GLQs9s;G!RdE;sc^AT>*JKZs$KH%%5qq+A)kC`Gni82LVe=fEbWM5aIP
z3|<f-pySK*p}9Oivjz3UA7zt#t3tz0hFP9=ANmhm{_2@m_07~Qa%eVwWZ2h0gS=D9
z0LrXsg1aN}XtW;64PvxvAEme$4zE=I2l7QJah8Q;(>~x-<f8*?b?66tXKZH1O}up*
zJ?do8A(&v8EzYLYF|+o)?Bu)fd+vJU5&dLs1_jE<5v_U2Dat3JdT)5&p#2XCV>yIW
ztj!fwZwM2ywgl6@52oN$oFwd_tv`xgD<We8e?{P4T&qjEx_kdfG8@P_b4*9ul1~-K
z`RS>Y)@hFsJ-VXl7?iwYw1P00R2a2(ELr@~E|09)Wbw61)jshL-kyM$fLBDR&R4aB
z9v-Xf%v!G4M!$%tpoDH@V<8c%*tR=5>Ife`sf?|nlmSxBitosxj<xC<{-jm#{Ws<%
z83`SoKt9Wn2dIo6k&e!Gw){xwK51IsO|szghKu*=(L0p=NE#jQXv-1Ggzq+584;Xz
zpwUQ=W;RoD-Zckmu`*zA9D|zhC1NT$mvSJjFg2f&ev3LXFh-j-LsPK%6O9<@u~s|%
zg>Gt`7`P&C1r}T@PGs#M|J7^Hd&W03Rw`X6qg%BrzQ_D=(QGbnj4-@aqXelI!GMU?
zOx`hDYmI>qWevLDXCeq2&LXd8)@-W)7H)U(#M6<ob`~FnglebboP7GwGst-iQ{hLM
z$Cg@S;C@r3#2vFoX6?9(j5*7^I|b)$pH-$;Zly*&`ZD@h%z#72qZ|nDSge^$Nb5>n
zn7B@PjB|`#=vR2N^H3jbGKXp@{A0WJDLBLL-lQMl6~VkZ<SiXYTGaeUCRg-`Ed22&
z{T^wK58TRu=;`cWu%ee}U)Eq2d%Js6xyp2IX$doLfsm=5-|zF;h?Jw)5m}c=0iw@j
z0Upjzg_vNqSbkz_^meZ%Xd+E8fLOz;Igi=*Cg8SkW7h)o{fQ6f*b<b+?AWpu_cb_=
zZ6k|hYxWiS&<qvZKFz5moP{-FHz$2GS6~oOOlLtBlAZW?`*PS3T}31zxcPS$SB%;M
z3mJ+vF)L+L#-H~AwmWvgOyRS&Pf!t(>F9<rIh<SS60CmOA;+@z<KPH!*lU3DxO5H~
zUQVyfX*u`OF82!m4&>CvA1Re!;0`28fW8MylC+}Z1+tC#PgeK%BisrADsQP|?Pkh!
z-?_qt-wUtN`Ymyh^7%dn8|LCRyUzv4mgO^=4W;P~*?>8FldRb+YSz7<xxegDs?09R
zpfg1a#{2ND!s+i&0<+w~b#`NCV~5y=hRxg`#w`>zLE}slOq8iZvrZIw*kiOKz#{st
zXoydKsOXBJAdrWLN#|oLb%7<RZNZ$K>KXMrMhcC(r?*1DC6C<%oLOh&T`T}XPV!~2
zT7P94Av<0(*-!mN6%B8#t<59rKoCY+;VSWDxcyQ<n!%WsCl3B#oi9GL0$podJH}=p
zrh;cVCHKhFzBL2nM4WL|59C#IUh;1uv?8&>t>?WnKnwBW?b?h?Rd~TJD%cfyXN*uD
z)Q<KoyL$7_N5ZBiZkC)Y%z??EaHm1*di}8$Hsc8F2u^BsKCOZ>DD;QWk%w_Rt%_lC
zT87{pv<mSnsbT48o#On$2rd0*0)bUzw?=ICCSp^|6rbZU64?MnQGD{|rpy)CAPxpX
zjj~kcrCt=%9hPl(7=5`FaI8@1nvuUNm{H!O(bo*(g{(a-@3;D2=z{l0m;HKgYedRy
z-{mdPUZ>Ib`lZ)IU^>XLc<u28c%-k$(h3iyvS)c+=n-jTG8%c?^;+wmGMVZP7}&Cs
zyS!=g4vHAd`F-C6Cj4x+G<?zu;aiGuMu%bac1&`frsl*dCR1LSPCw8zzhs=E#OWtS
z4LK6uvbMVelkU^-(++hEH;9KvB3t+Q0<5Wgc#Q2bypHJ9jOUn3$$?`N*v_T6hMvZM
zviqUwQYzMo%D(3PG=5962Sy&q73i;t3EB9ubcDMULE^RlZtape6(bggU8RJjD5^K2
zgCMGBwIv}pohy$j7v-X^Gej<OMgH4&%R*6&8-M$;7CzfSt_C=AM<W1=PN6)7sKpH?
zM6o4@>)B43LG3gkk!q9GR8b>1{8prkFQVp<yS?KA1q5XKg2a;Meh7~zes7qPTPZM<
zj5Wc09B}{oSRdi6sY}vP;>sdh)yuqb)4j0A-qM6cvc((~j4Pm^nFxb)Q8XS_hC<Hz
z6%f@p&OX|@r%G(yvp48&TfhpX#CP5nu6x$gtG?wQ=KGLPf8}v^=(Wdx>e1EpU$sx6
zkz0{u@n;vkrt-pRBj1E3u4sTqkfFifBM_`>F`oP-@CDfAncDyPCQz0Okez`;uGt~?
zqT}>08XZe}WalZ2TBW~&aTTT;w_aaAkR&l0Nlp^;l=nx~eg1M6JI|NZ{fddRNxdj0
zKPN}+k?uVG`Yx$0w&oz0@#Uw7GPWxIE3xIrLI6p87J1n6Nt9Gk)AZ?ATzy0kJrOJl
z4i_{VZb@!jdvt5wLcwHG25lOoiW=KQ3`m1fZ-(4<);Zj39^YH33W|^8B;{FlJxOd)
z{jf!3k0F$!NQa(89@lv&H(Pyv61Y5_w?QM}q^-SvVHx^?2>yUQlC9{SO;Y#zHYsnk
z4Zn)ug|$5|@Th64Y^MjAkRR!_Ko=9pvR0p|+l2>JPgz;&Qh>c-x@hD#Wg2xy9yO~F
zAwtVZ<Z*3P17$y4{61?QGd3<{>LI~WQ}-q)RR5w9ki^eQRsF7dU|TGwkcHPmhl7n^
zjZw9<p=PDkdOrXqrtrhYjbGSwOpD<P8MOONozq@*3I73FXT0t59U&y*!W<NLu5(|Y
zgfNH4ejU<7CRMH$P9ATAIGu%_np!p=nSwpsnk}bC*|`zw+jG=bX^5L~irBCmk_haf
zZ1ue#cp&>MBP}MK?-dy4`n@)x{zB<|JP7v4Rp@6;YMGfNhuuqNjq~f1B2q$Hi2gdx
zWai5(lcB9Sa^KM89|A%1fYZ{kCL;D0qRk&c=L%kBd`rW0t>8I&IzAM{7PgrjvT_7U
zMO=#s%H!_|S=iDaOYb18R$6%ey)P`^{Kf^fgKSMQLbo^_vJ|rKH_Kmx9<P+ux`Llw
z6F27*=ywk;a6e#hTxi_|UZ?YylG|<5LGGTO(rK+yTCt^@iB08Dqv%}l(d=`4k}u?+
zmoM~C6#m|c-^<+al;hT2DV;Nz67`G+_*t`((?i#{vkRX|X;H%2H~k9Rc9?NSHS%8L
zqIt%pcX>JV`js|whtrGu9Y!lW$-SF4+!86onVNs5NLI?R3MKvw!IjAa4-C=NfC=B?
zR2>Y6M`P&?NKZJr+$}e5yq6_>D;?%O_V|MozTzv#$1<<H2HrldBzT|3TQ;?;pp?9f
zli{x}k<Q5*@-9|+yNIt=Kszg@fulT02MkgY*P|JN{YjR=l*D{D{Y7ZzPTWeUV{~_j
zt55hcp7BF`)RZ>ptGG(`vQhV{)w5mxs?0m}zMhWl-G4O$hJPM!##1$eJ^_ZTV8lq(
zL_x#%o$!d^jmNK@l?F{5_A&Iv#q0KAt_^<q$&uC!#!fk>0772nj7FPxCTeco*!GWt
zez#oOViEih)(4H14krv1HCxxsOWh^?cLSPU=5&h@9#i#FlgvqZa$q=Vo8#pqK84k1
z9KbWF7Id<GC01U-iaqt(sas~*TE09bI6KN8N&|QxNP0z4YeifEpaNKt$J0$El}$Ey
zD(Y4>Owf+riRm&_S5m$hX9~GV=9Jtn!6i85r8B>Vfi?_V_W6KMkOMCIkv9A$8!{C&
zJM6e*&LtDW>M;9a=uwZnQ?%l)-CRPmRGsF4L%wc>ZV={jJ7Wh1gt3$$l9iYFJ}L2h
zMKEiqjV-P|0w-KIo2ips8})MyKz-xOLF7Pv0-soqHCGOVXBxx1NNdca#a;p(X#(Mv
z!^tfJdu0-77l8rtmKkz&AX1Vy-xjA9P|3BClT;V0@Se%WIFci{5Y?0gwk+5>reGJO
z`MYWXlk{uQJGcMZN2A%S6L<qX@^!~Y)*aI^mk!?Eg|c$e(U0L6!C%zP$pKd0A=D))
zVs6`^LAyS)Rk0qdt{RzXyaEfXl)gutW;|`dH$Pn4iD0E>a-7%Trzm^Z^6ci?EIukZ
z5-WMv$t9|ggVAy%r#Jd#3Ulc!*ePMlxt@2uO?%Ww@^^Ytj*_aXgrnG;H7T#jcDZ7*
zA-NggsHne06FADTz#n5x_s&ayk)uyf%UkDj6Br_)6)v;V;NE5DJRuv-I<qd9{s2Dt
zB46A{w7EBSLBl`98t`Yvdb_*WhN)Xpu-=*}5?bPPy`h!_dOw77W}S)dr|*|{s6_=I
z+dE>0Hb(d6?1|rbbLa?TECH)ITsH=Lh$Qq7FBWd-p7PpH!^0x=PqA+#mf+Bv0tTyx
zKdohnpYiyJXzw2C`UFgl=c<(4%T<PRZ3ZP|SF5>?)!(ePhwIt!8SXw@aDRo+fzlfB
z?S|?|RS?EXfQ}qA2e(_IcQVS05rHWH9lQGdKf%T<R|M~mrAoPBCap$Nm#_Wj)BzIc
z(TgP!gP(VwnEyG0i9(%;LRXWIa3*Sd>l|mRTZQp%CVV+euQ8Ylm{jn}x|+>Hwa>n1
zk0IOQVo5LE0w%8POD`>C4Jx~Ps{m2o@4oe@6(V&`D(enyT~e>mQ(Ao_z8PxRY~heL
z1RT{=@MBL@9evXxEy7_r($=^ZkDya@+T%mLD;~vxQ*=xG{3`4yX_k30x}ncKC+*OV
zp2Z{>u^J&ccg>Zn!n`NA<=8N;?1WQ?t#rKoyUBFk<%=&GH_zg_>+xk9-6#2~fuP>z
zQz0G`7K)CX^qko8UH=!a=i<4zY_OO6Yaw~KBqpV0H~oSXL<t4hE0U5ITg=-(Z0w%c
zcCkkD#Zf87=#`MJCgfEh8BiREnD1M?Ry@_-xKaFF2~0)NW1{eV%^+D460I329WoNl
zL^<-Ua6XM%ZD#C0v6`7;`7L4K<U00990^kF1O^e`E%ZFEsCzGR0r~NH-K$RC9QUT*
zbJO}3a`p<k8*o4W)cuPFVqnqz&Gb8_mZKd~Ob>{no}hmljNa8ZzYuO`vOOrphrq08
zItC-V6{mAQyYOjJv&>)iyeFA`5bcUmuP;qMA)J?vb<F6E`8(m$x__9B)Z5>)J)DR1
zQ>*_3^Q-x|&_w&K69-@3&mH=@%D)5SeJ!q3@L7%S<qCi?Et!;5DhE04IcL=VX<w;K
zv`e`L#w76946@a~Yv5FTxK3xc?GES5LT%-jwN&k1wSU$p8E<h^)oXwJ(=%%e!1Txe
zk=I!+2(6Xv!WcfPj9rK&N))leqa!+4y=6kCF88hmnTl(y5#I}}ro8&+A~OQQ%0Kj5
zsj7i=U`G*6!EP=Yb<%EyhMTGH<3(m7iz}j%qLucZhfOM0c(hK?2OZq==^5Rbio$M*
z(!T+@PJ_b~3MgkcMMzF}^@Zfn#NMqd=-GQ~+&>|Y$sJrzIX*qgwGfd9Dy<=_F%e}c
zy{eUT!Kq;!3}wda4t0ylm=WO;iZ4eDt`AE2T5D3tCr(1J3L7AKO44d4K?=dBQX(u5
z&Wb(+Vr|xUvplNZ>xUL7F<m@~ZhDNB-0j!x{pps%w6HgYequaNiXw`jr0ZOtWX;xU
z%neLBR^l1b^fPMQGwM?ZTaj=ycx6W5JAKSLtxljiC%d6iQO?zf1j<ufXfR+4bq=<V
zqGz;<k3Gu|zJ%75t2}<yu^rAH#Uo6PX=$=d?atUSC<YRJN}c9VQ<moTR<NzfH`3ez
zmJY*qY7Fa0EJZqCZbluSW7(WBL}&WXqBrTX-Q_juN79_gFj^(>aHRC=a5KfLz6vGq
z@h-FRU$Y<k80N629db`1k`0Lq*PH5gziG8q_%}UxyBv#NU-Ix2t$Y7RfgT}$_2IF5
zgE)A|*xl8X#FGIpFs%#-z{SE@f=!JkLSi^&k7K3QJ{PwdzN^PMv3PvoA_VgNnut3h
zTCzUTzXZS|*{O*M9Vk)igoP%@KNmOiiheodJE+md$3AA=tHCK^PCUs~q86i7jRCR@
z;9*2Sdugh<zQ5%kB6%A8CGkV`@7IFrAaFSId6#@KLs5*s7n&`ZOtn!03YL}c$m<~)
z7@F<XA>K1I-ivuOO4j9p6ah3jO@HA0Ipf~po<QV=aZXN$8laS|zOmO`vrV-j^GRG=
zaAs}~C5b>|m-#&G(IKG}&kYurXG(5bg6m6IE)(t*3Boa1xv&0I5oFiv|G8J_^Cr=T
zNC?R}Ek75;YXWv5T-Y(H>>jU~jO?vgYYk0V*9z0?o>5s`z9{dvFK(OLAT)#Exqb}x
zi!z7Vrd)S&cPOUVc^>#?g=R~bzn;~1*16~j83_+x!k9j9Z2okO(@$+sd*S~0RLD|E
z{U^!al=32THd17?X-}yhojoll^2Py=>4%SQWd_`Mn~+x!@p#j!;qgw#Y$((l$m5?U
z5k?CN4s%wZ=<~5!#HEq6b4+qy%Pl%bgy~=?&w>^?^83Vgc<|8+4i8ELjETr;u}TdI
z5LS7|1g>Z;;?yH}6=q^}ltiipltMqn6nb=B#bG9^)i`xgS{M_tT814$2}^r&@TaJ2
zPmH2o@%*$y?LXw(T31@)cingX+RI768nW>XVlx{WQ(}d`iOJv*13FawD57&g+it1h
z+^^_Fk=?ym>Z%80B)_nMJMcqK5`o)ywGG$#uyAIbb`sDj@foh-zOwfarDF@RsV!TF
zGKZs8!dR+!5%caO_57BlvVLKj*?6WnoDlv6BK+}x27l4hFnoSnC6wAM@(gN--&3oj
zMl~pB)FA?p$Pz|1r**I;^1^dUR_?G^xq_=(ivl#Vxg>%CjEgZ0O$R4@O2CVN4rk$V
z+N5ea4|)SB?K41fdJB&m5cfFg2_vt&X#nY=pz2D;Ds>VLOt;0OCd$Cw@tZy%w}8+N
zo2SUht;Yd7vC=Xu1qLozSrq`Gyj3@U;wteJptI1*!9w5y+F?G@rz+dh5t3i#ZLT#q
z=n3hCIB(y{2@g<&NV6D+b$f|uWL2)t7qIq+(NKu1vGMf!30|^raY?NmE*-(C45OjX
z&)l|u8(bdKk)tm_aGC*Ky`TYi1BZ%YRXf>a_a$PXO`%~7fUlmReD&SA!OOyz!o$$7
zU|7B%H||3_xw#l}UWQg$F1#68kR-?I233FxZJ*v}Aei~d&V5o?Vxh-W{cFY26o)og
z-VsxRIa$q+^kLFYpCQGI_2RBW{5~a5Y&ydie)+1{1d>%@OWw<qcH%K+IKd2zONNpz
zcofN@M~~39Lhz-C-Tg063M=IpKDd!YE&c{hNFq*Lnw~rgnu=jylAaZg{BbP6a?$7C
zAj;HQ!#s#EBTB6dgiHl*2lN_s($kJ|+T1f2Epjy;4v)uN<&RUe(oo{ES}!t^8&DHq
zR9UT#g1CZ@qVP#xiVRLoyj@fB9b>Q~VM}7HU!M%^G0R*Wd5*t*cc;(wv9A)r6|^?^
z(>>c;?BytbvO#EGPWGi80zdDO^|j8zarPq(?hNfa`*68nhuM%dnC0Mh;JUs9tK~jZ
zakb7kv5^CWs9YvZL`5u?6{jB%8t}$>t-l2}mQ~~c>@4WR{|?*in`wsuyOqPG%2Ad!
znI2OU8^@I&2aTf|{2W)(wn;KkC|Kc!4A*I&G#Pk@#kb%04+wmoy|_89t+%Me)mL!k
zA0h`U{q;lxK+)}er6(>ryyM8|3$xo&@*k&X<j@|Uq7mq~M{oAKWkPzY(BWrhy!COt
zzw^@t74ajo2{7{P$8$j5x!!<Ai=cPV_Rw(QbedhYqO*@MX9x%dk^<HZ2V9H<2wUf_
z(*Uk3yo^M#TLly@2JtZ|*lsBSk|g2wN+l3;2n4(i+Qc)WF{t+b<+t&?1^%e|bTy~`
z22Z1|#U^S{nIW%%fR0Ek9EAW(qVg=R6S7%&ChJD%G+<-j0>&!^b&O=!^d-jPYYX=s
z$1u+F65YYTS7^(hJEFuy?)LA{T112Uj;r9Uy!#eIU)jBK<Cc(?(VMHULHD<E2TAIC
z4;Z_g(B8RCbI_vwhj>Jff{PbS@j-{geW8qM@m<D)iqH!xx0gThJulNOhV5lQkI7bX
z0mSeYOZnsOW(|5E(7pR(`E^OaP?Rgt#4m`-yzJt(GA7{A$Hbqp>2XON6`aOj&$<_)
zJVxm}$S3|Qq!@5|zU4w9)dRJ@1r6#i_<*OTt0|J3Ms7N{mrxY`_Ycn<^jnDaG?{5|
z^PyBJ-78&*uqMu2l3a!Qx~yDS)NE+M_D`onCvSFRT%uJ(zPY*_YqvT*O?}(888WgM
zG9z3b-rSt6JAY(6o!2max?Gd6;^~=`Z*6@p(!~6y_5*4q{amlURYLR0*TDg6{>BGd
z*3BP@l*Nrk_veLY<`rvc>M<L>$K|!|)3<Dq+IA1k?QuOQ6$3Ye@+%I@AlsJnYsR+e
zy({3vJSyG2W+(d7n63T!`#Uez;g4fAk${ql70<@bpPeC^n<g?oBQ%4*h2^1&EFa2J
zz6GGE{^hx!qTxpYoS9SOP(Tlmpb_^myH|VJZ5!E$nf|P(qxf@mt8vUAMql9Qq#gl4
zU>tsk*T~1l5!ey20b;Scw;x!*>HUvo`%qlEg?i6BsK%m`dygNmkO`JT@g-z{lML(l
z)3Vchi=o^#zW1Oy>Z=zjW&NM2V|Hk{tM8IRW5#a?&W|AKd=M$c3cixwxxm^O8z79F
zCHSXiy(+Ly*ga?j4|4w0XEb6@S$u4U+6=L9o$BTOnPQ|OJc^ud)L{8NpA?OrmSVWg
z?jx=$ou%OVOFc~KOM)~Gl<P!_Ktsp@;$hn^2~<*+P}+4#nR$=KWb%;rJWyL7JKd!~
zj7DQE$vj$5HGWH}vt2Smca*SPh(j5KOzws4m=o|EXWz8ii3KsO{__~`^}*jYAgM@1
zW!-gAm=gnEzXC}kT0OU-$R~?AiQxp_1nY7GM?p_eEo!^_c{gRs&=Afo*-r$DK6x_9
z!D`M?su}(MIGlf$h8GA-)7Sh>R@EGFdC)BOW}tK^9<ZU>m}TD{*Nj`oQQyyc_D8xc
zO&ewFzpY#4E24Sl0F0jjM@1*Bq*S*4h(dJ{&khNZ>=&cNurA}2cUBXO1LjnC<-ZM=
zirp7!<qtU0rHKOikr?&RfaYaeGF9V~=kZ{bA8Y%;zQ}DF0oV=+^b0a;bIdBkSMd9c
z5H_f00c-Cha2QbR!@{erz6K)KQ$M}{p9T1L0i-MAvpoi%X9?T<&|TaL+!w(4s9c-B
zQw!r8!#c)(hK^3pAqZcNC541r3`$Jbh88g0amv;BY=^-4*;IY!(CzyMr2k>$oXUag
z%Qh*uj^j182+N#=#4{UWkAGSJ7|lYAox?dTdsppS#CAq@l}yKn{>z#=XyjCGh9RtB
zF)(Q(Ptjr4y{lU4XpbUAi*(HE#g_-Fo22X1i^4Uh&MU#BZ`<n{7p@rax7Dn)`G<i$
z3p<9Fv>X}lp*ERJ#&ptTI8YkW-Dd3iCY-Ikr6a_8FC*69!5q-Yp-lFcEm5#~tlBq9
zqLiaR62Z-QAWj_X;4k42o6$G7UCOVpGVq9$QC5c11bAdiCLb}FVc;btME&YL{94BB
zF)=GUr>LOX$>Rqb*30!Ug3=_7j0<f)reyBm_jai8tXYVe+79Jzq&~1>E&LX)zh*RA
zm4Rpp?>(P&%L-G%9rVZnzm8H%B)~=`CeCa$IQCmuZ>*QBz;Q|*NM$9XZpw$3&Zb|Y
z-PN*{3apc%T{$~=Q<$Fa8T!9cr{}=pAR^o#$qhvJbm(?Ewt+MW#2{qq!g**fj|OC7
z-V3EfH;xK#;R;hWELmY1(&E21e&o+{H0}s!?zNW~dd3OD%Jx9+P-;1APGIt+jeoR{
zs4O+uTe=K$Y4z4o4mqs+mtpmb=4U3M;&)QQHaTA3={Je0XiWh<K5xNaBp>WPTq@Zt
zr&{HOg4~GTe~M%SMwH!&CVnLpvWA954WSh<_P%JIGFp~q+^jgR%GD^(Rdb(;6_uDb
zJ9WSgZI0D48gH>c-Mo;WVhE!*`D%!TR7v*MtEfx}N*NYH`0Z@5;Tg2*<5F6POtgz&
zU}?_3*4Ez$v>tK$h9g?i_7H`@UIiS61+(}WyJ8DMt$Knl^FzvudtnQjL0O!Hh)TZe
zOn=qefBE+5J_pdVuC`#(y4$HYkiWA}%Hx^lJO->10JaD680hmD+-Vzx1u~$Y?f&0;
z*D(L3c7-Iv$>$$G;wzR40_)5Prrz7Z%z}0@+)RWGhYm8=IQFWjPj<ccD0_yV{S`^0
zHi&KK^xxTISby`xJH7g6*d!0bDJsj$LcX?%@@<Oc1>mS6XG<le1`5EeJ<_;QsWZ|#
z>g7l)WIf{aQjt?LSrlPF4~T=Wf?$$d)qj?x>7R|@PnSG?wZSb~`4ni+Z6+B86^XBR
zD~;dWnpgLXu`CMQOFy%K>ef>iQZYQrzjgxc)RA90xVoaT(m43~`YQA*pwgu|dT5gT
z1OmhF<c}{>Df;*zYCu|nbNoptG}TQtBp$^#4o0@Tv*ew36sf-ft&Hn%dPPF!s~9x8
zK^>2;NRfuQ)B6&IIr5GXN|SxGCLQe*H7>Ks^hJ%6=G;|3b?7g?zE}>5R-*VM_sUtJ
zY=5VQ7pmJ1yOAM-CGabGNoyJDo<1ZQXKSOn2;lyl*R>WxwN)88<YX3LV6bN>Zs^_s
zI#;QrkwZKl&=H5b>zoVNXUm|}y~BKWGu>U1<FzqnIE9m8zWK4=9`MX7gTR?3(;{^>
zx&?3uKQH9>8C4?ahiON&@Qa$O*2L39sIC7<vj}MjtwCw&{iAC=&(wx<?T3tZMt?0c
z8MV!Ji6DjJ;E$^`@F;f&t^CD3D}W4nDGC@f@QF|u0@Bm${%2y~s?|w6T|s{1kwIzO
z&ZxYX;STb+`a=vfZ~`TUIMPDHAJ-%bT-K#rYP{xygEwR$e;YzjtXJxrDs>W@@wAmQ
z((Y}~Jq_M7&tV^SO8|5+-E94H&+s>Y27tk9H_?-qdWXq+G(X`38TI!2m(a7ySpw)=
zAUeU+z{|bU_}D+#FYH&G4?z<tJEFv`PsV?5J1C*HnHvmkwE>U*3tUuR@IzZ4woly+
z1sueWUo$2m3+jW8J0D$vc_CWXlySJIeZx;)QI=Rut7lg)QMLya%(`FAv)b7al<nlb
zj7dWNyzuQAraKMSaD3BY_Xh>r|Bgmesd0^l#9CtQ3*#3#b4loodb8Ovd@bm11q3(k
z<$_(DgEqa2r8}bb#b@fks&=!VewUzz#jQ2l4l9)WmP~^qIx&afVxI*lK$F%Gy$>)P
zAI*IsS(*!{V=L~Cp{$l#x}&c1X}u|m_|G!3!oYJuEX8mb%@=XT4H<Lb1$fhkqz{dx
z8#Y6^Hd`XHqxHKJ>qfGU)kL>%s}rf~?Ri3N;QH_H%S8ckPf_sy?m(fjOnmQ(iJtc|
zB!-xQE8OwT7kcd__@8Lp6wHC!?H8yS)Uxo?fvfDmMnDyB9VzJGnK(7cQDGH#Kl~^6
z$s+Q+jfp0!5qZ0=sy`m8zW#QlP3OWUbyDk>!q1-M6g>4@i-~WcDH(N-70m~~6G6GS
zdz+97B>->$)Pheb%jX(B!DF<@VoF4I)oEvI*yzegnv%&_PgHL#4WlZlJv**SDONR>
zD?sFrm5LzHUHs)0V}Bw+1a*qU6=-?A7Kw1x!32hz5SXF<EIhU`aqW0HU32yQ^5y1r
zcE}q}B$2L}pm{kmsDsxr(T=A}N#euVntrpBYM{b}u7^V6S0uWVm=Y_E61DIeR9gD2
zB=!aRa@+<U#kI&|WT46eIuX7ku5-xk9(||q@Xb$w$>=7qLTJ0Cc&7?S=Zp$fAA#kg
zqUwQ{3+MHoTEHc}mheaxyRxVRon%q8zb<mvi6KZdW|t8<kGA51S(#-jx=bC5Bf9)q
z`w#L^2BZ4XE!>b`;1L!blX3E4rY<f6(`Lwk1&9mPT6s)PIcy2>t2QV&dyw-RteQ=Z
zaCDt%ZnmW?XVX)caUGBO_QO7LSc#3^h2EPe>Lu({3<*7<xl{}}78W_I&u@Szmy+ib
zQzee_#5(qbw1vdLa}@|Da$~t7_@wK$jvB8!PO>DC9)|spR9ifY<I3BV)G1_a#bZpf
zg#FGw4j?}!TkEkZu^Wb5z)Ye4X}gQ8?RuE!&AlJZZ~Ytt9$%erw>0z!o`kPLf*+$5
zkekSC@9mzC$Xu73Pxt$01N780?N{OgGpJ3*o^v}5zT64v<Q^gvodllDMt(!!`pH1D
z%xK8p&*{C_at7mx2l&J3L%Y%dKH%SBJ7i8Xyl7GLAYFu}bM3w3UCmuN;OZh$5tpz+
z_(Vr4st2tlzW#R5t_e~4a?(z8{Y>-qEGHon1a$My1nu5Kd{uv6z0M*#mbHXGDW{DX
zB?^rP3hr|7p$H&S%qI%?y5_s%3!1&`(Fmz+D`_pJBw4|XWGRnFoF#An-lgLMaIfux
zxaGxzv?<iJDRU0*1BOIrjgM7US!mZ&`Qwsh4@Euej<7iH3^f2k0{kM_E<fh@9FLsT
zMjPb1<1<b^Sd*PN?zI#tl!HKM?B$epAX?TsFG6$~QWfn6{G3WW|3e6!9nh;UC^{L%
z;(U!rrH!0MYYQ4#x1t_kjCJshsde#cVw3CL)2X??uTOMk0+f2j+_E0@su&7$uIX9!
z?&N-iF2{|Uf~uqSr;p^|kyMN#W~}^JKhgK0#;P6j1<Zv%_s<?{qrX1QOovXyXa2(l
zW6ppAOj9oCWHLvu^IugEd1NK`<#_T_tePsv@dc9eYn=YZNE*J|Lf-@!cKnU@1S2C2
zXmJHraW;OmPQNi>1Lh5UJV@+e_XD)fh5r=b{z=%<qSp`l$Zy6<A~!-B`<8Vky5Fx>
z3;8tcOE^$`Bv1N4+DLTkAGnXIW6neXqIhc(a9^#uIP;4r5k{UOXNGY6i6!C=`6k7B
z)BwQDsvT&#Bzrpe9xN#<uyU8hs<rfPe56@!ldDu&OBG*@InDI4#I2;rEl&)Qoujxz
zD&t`XwSEz+pHs~8_Ej6>@5P=5yeT8RQsj_+&9zUUt==3}!vV69!D?}Lv7u)y>KYHh
zU3RQv3lq%^tBhNKP^$*U+-*oKQ2|8y`&%pAvz3D>xW4LyX$kV#C^O_RE=|wR$8`CC
zn!+a*r3u3^`fEllB3%)M)FtqGqd>q|9o=5VIp3TjMnK_bnZaqqvKPqz-tR9K!gi_g
zt&oRJoS=G&bmP|VmO1jqRdP;JIS`r=o9uR*|4HVsq4r)Ef4#LO6ZphXSD8HBW9qj}
zE-xQYFWh9@73_xa77M_`X#^O#_KVHj&iHGgHrZ}GS82C7#}09s*Yu7$r7U{%aP`RZ
zto>MW09Tt?!*cgDcNuMKq(|#FeZ{w@&{vU{fv|gNSTCHH^81^n$ucaR^zVrx*L&=j
zNxX-%`q~@69!Ix?>fdq9C*^0<a@&99;5wPs*&60DMh^SQh@Y$h4D_<6lVYA#Sdsy7
z>3-_}MB?2mU8w;%B)f-}T+g+zWSJ}lGx6UWd+twu*nGvlF2_J{r)QsM7_*LM$vGmt
zvvh&WKWxHi$#qIr>Y&#Y8G*CZK7TY%$*x@LUam1%tr?{5#ITi!MXgdp%AtKe^1Cu8
z(^H}yR+!Fc`TflE6har7;fIh7;b0qji`XF_Fv56>laDoh+7$_`U(p+)cojm1Y6AVb
zU6*6^u2RBKT({rV<(+a?)X|PHhDg4-O`mE|@2g`gl#y<`_1j6TJ=EL}NAr$i)qB)y
zBi;(l%n#X%B~N*DwE(Z-{7(qB_3}kPUCuKZV}c3+@_@H1Gz~r4QlG;E#HGcd&D7N+
z$P=G&cV<Ap^!t_b)?WrWjHYGw%&{EEm@47yr#Q4U<(7u|ggxSK+%s7s;ulU4uU@F7
z740^Jf@)%=OK<%yn)nPp)6*?s*X(kW>@sIR5F9axAx?ghOjcBruC>NVPf2<WT5@@&
zcWPcZsTuwnwD2qhAcTT11HeJf^{QYr95s7HWom?41?>Lyzeoj=8cxyPmQbM64^XBx
zasRrwI>3>7Slw<E$6OiOS4r$2VCbco-!i44vs8hPRg+B{dGfmw5rman=;hq0bM3Ob
z_go{&)jX^?rXhvVh|zD#bU57&?f6p(1PBWza6vt${!+XzTmEH@j%@9-tk;A2+#$zf
zI<}!l^9=_d7bwpJ_}K&V6cn9iSo3$M&DIee^Aj%~*qhwrDao3#Sx<5Pz=!9FsjY^9
zhI5{oOmKC7S9z@MyHb-ilA9koJWPd=pF8e27AxF+-2zS$j~2^^3Q@Gw^1!K>N}{{J
zd6^^a$WOd9DFsaZLtq$MP}QX#V6iPYtXGzYVh>8mp1qhIK%HQ<`j7rIO96B7Pub(^
zBG+<g5bQNaV)N+^z?d`(Z|L+ahYD@BBve<KtyM@&x&S@|)FL$UC7v>7{X&<9@m_46
z0mAeetKT|la?{}6>=kWL^L`*?W(x98_~-vGWMVi>?N~6e=lRXEo5jc&Q+C?O>o6BD
zgQ(PD7U;3YqT>OCNWYTuFBKW!mA*||=7*%6rW2>*arL9AD61RTF`BUBF{m^V(qo^0
zanshtpj(Ihx`%iCHZ7H}MT~s{VuA;14+kJa#)bB2OMQ8>rEqp_MboNEVT7e{@?M7#
z#>7-<8}-l+VQD{`4J*$LRSB&X6HAHS9gV)3c9(?Wmhp~SaPuJ9>Uah@{R29!uF;+h
zP3kDH9Ft-G2wG_9IN^%6rHb6-#}=;EU{Tvdog?&RB(<)~SRdX!$SwC_cg=O#r=MCe
z=j@^13RUu&Pq~k?a{8^&Te+a}EyBOJ6{XkaVig%^jjboNx6Et-s?>hB?aX!4u{<~*
z3rYj>!UW%p;n8eE%m!@ea}$p>{$KoGZ&Jyze^H^vYpso2FdFeO-_pv}M6;k})DlZq
zJ_^f|-wRQCWF`m1orr!Grl*@8(;ug$r(T*9G!v2{0rpm(bP}Tnh&+s!bPDxImOOTo
z24IE*-ORm$HPe16$NtjDc0JYr*=LB?SoW2&vC2-tS@s2{!a%0myKf?{`M7}K$VV;)
zl{V?R31h)ec1Jl>!!uiVJo4D#{ncAn9BQ(X&cN=0RPy$X{<A%Zg$kxUrVg!|at=mu
z+);VNfn%=1U6;$bH=BvFMU_HvLvi)_b;Ur-$98FC)1Ou(BnAN^!ecrJt#hsW`1!lU
z&b!RL(BZ{hTR_)F<eL<(x1v=h1#y&9TN={)keC(g70Y6#o}oVPPG7nD4pkppWhJ+g
zk##^6FBgq)*a^^k93cwG8_db;w49K#71@mC59=X`oc{#qx%kAtQdNP%-d)z#p~f=D
zRpN0vDf1Gr*kzBx>@OGa?o7|>?5zs5pML!|GOyyeFp1e-X?mr^=oE6f5?S8bP2VEU
z4m^Q(RE7G+zqS4PQzG#1dO_99ADE%0DQ3XaAw@_wq#VV(^4o=zb!w(oc4*KI!v<-q
z!#E9Tm7saik2)~qDU-(S<H{5@`If8s;hkG>WP=O+CQgF@{@=4dLgFr)dk2+?Y<RZo
z`zq-QLS{v~Uy}QxARwopliEZo7>a}&n@4@i5atrcJUWsKVz4%(32HUd@aJH}a;re_
z8^=t+mX0PVJvIvjqd)N3J_u&ApMJ(Hm4|hbQGE*7w0cIx{q2)Vk7=>}ScA*mE~dfE
zmDD5sxyx1w0TTK=u#~Y*E5F#qeBGmfC(|gz<CeGI``#OMpG(n8IfXtb^clw>;G}21
zXHfoo1qBkVyiT(zeGkrdQD`bbbxV-v!NP45<{x1{;#6s^mWrmY?B4cC=dMpc%^~}k
zPQ=XlU7jM+1}ghUmX3+eElfaTS}is@2_wky!t|(qLLfb+qG-WiAEu5RN=5jgQxJ`R
z{E70^)7dLk3icV-?Yjy;&}1r!37-FC7_%Rs%aj+XYcFlB+`}d)j<V(a{D#7(PeEc;
z^!tJ%9cxJN**PaLQ*TSe-{Mr9T^czfE#pLv)g*O<>GX!(F%KMv`Ae51KUOo@Cova<
z^FEV&a`mry@U0$-J?13`7gs6y+2d+CJ=OPNF$4tzJP%AmO|Q&k2DJU4_4NklbR6j0
zYfmOd@y9ENnX4EOP8dKRzlDe97%;ni2d~${f4TqS{F;_OeDc(DrGr{M0Tr1Bv|^^-
zk1uR|DA^B(o!s}4fEFSKO+iRkaO%DJJ;|f|ogDodzrYi#QsP1Htwx7%2T+p{QqP?E
z2z5{R^6S0Og%AgDdtMFCcf%%tF_6E2pHp^=Ac>%tFzgq_-%Yv%tT_ReLzyUKoCn?A
zs?RM?w9Juxs%;yQ=)T2RBRqI!4*jrei&F<&W}#n#lBOLbB{1$2M-A?WMl8*1D9T*U
z`*v5+kqXWMeWBYs6K3-&whOy`EI26va;^5@15`cJPS39SG54x3Gnre61l`W6esq2O
zo^S?h*Xb$KC9_d8%qkK1JR!OBnM6t1EpS)TpXg|7AnXPKB%~Z_f2_Qd!hc$f9o|Vj
z;#0J_c{F_)D|r7?v1xEbaB4OI@>arO`v=AQXC})$O-+o@zZdyNyis8xINYjM#&iGC
z!S{Xifr5IM3~l-}_ov6O#m`u;JnW+uOTH!;?9Q_F^z555Y*5F<y>pszC6Hl)S4OVC
z<#&jFJELpI#7|0UTbgJmcH~(OppEyP1Aot$$CYt;Hvk~+n=uVBMbZ$FMiw=)fSK*o
z;D&;IdS-sU%&s73J4Anpojzk^osezzX&vi4!*pMq?ff2?kK$Vd;A)!D>`Of&g$E7M
zI63OZ$ScCsRK)K#%&>h0eM0mx2cV4%=ur58F$*M2fSg0#v3LYfOiwwT=U(4Z@QxjM
zh^B9;5Aq#pl*;cNRv<#K;Aqg>?QxT+qw|B~@F<pjkz=TkFHp~d*Ok0gYlp>53C5Q9
z!{ooAW;EV`rgeZZK6CX8Cv2@sVDCm1P0%MC{$G+bOfCFuj^}Bh)_*d>h~(yAV!x%s
zxq`#=?uL9oskQa~N9GiXZk@1%Q%JJZnzfjz<)8%oM$uy{7vRhzpqK*%Una^zz23iV
z41obEf-;KTJK7qiyteKell#i9AAgSMzl4(nefQ6{6y5>wi`!EFH}D>l%khux@_#q$
z|7$!Va^<a&@_l?csF`QT<<QN&WWL`2WR9cVYzDj?>?sRES}MR&B({3S2#8~HuWEw4
ze+eQImUCqXl1zkIWXKoP&0Mw}r|Y^%cp~@2hmc~GqaY5q8UVFM>UR~f4K9E$S5`*N
zifCbx{thHZN{N;k@}wLZ9$mu2875_T?>d&;KK6A_$*&v+`DR9&bg?l~w?CFe{!na^
z8fN1@&E`TBo=X8t=jRLJ*Iqt-c{0G)gGJ!mMxeC`T~7}Cs1+<cs(#*EIf9XFAZ_F&
zc`^Q>Hw0b8+aKK*X6^@~q!Xice#knax}r}zC~{!rT(bPT`;vIPGu7rkUM!r-HG{s)
z4jNzpMyC3R$J`!6rDA(F_6E4U=fE+wNI=|h4qP5n-WRMEN=W|`$L1;$#Hz*O;IBc^
z(|qW|6CsD~@rC)3-)SS~{`<7JgF1hSjc6XTCz#maq>;EDk|r@|_4{{_M8y<q;r+}r
zH*XF$^8d%vSFlCZcHs)rAl)59NvCwz(A`LPcZ1U1ol??BcgWB!Lw8AufONyz?|061
z{=lA@Yxc9&v+i|AtRR7gpyWd9ZR%b#WMgF2Ej7+ltRfQFcPt}01B_vMfCvvO+<wR(
zb&>sZndh@Z5B2PDT)e1=C}b;jxRIqaC9DK#q)D~aj2kIgUL@&T#jL-~T6C>|Jz~2J
zo`sr=zw|5NHDA2Xx&462?FMVIzd)oYx?Zk7p-|k@Lw(D~LfV2;U+zO+N*=~ln;OBo
zbiqSvS%GDU6(qm7&;miCA%UoDKzN**keVzx?y#d+tJonOOXAFCj!?;t`=wNt-tP3t
z#at8)*4{xKF6k(2d2m_CFwN=q7quD9IGPP_u_x(q{SgHKW+0)44`3{O{_nEB@w*QK
ztnLyOi+K(am;%fnaf6@cml}x!$Hf!uT^$!TI=LEIXLH>1@#=0r9gk4;ae8O8(Iv1O
zS5QgepWYr~^gslsP6AwZ=yG?yOqqy{0cN?lIs@b-pxxlNN8{fXmO1c!ydqY&Afn`r
ztjaFx7PM@^%ObP<x8LE$yPB2}wm<Tu|Cq?Nm|D*7?@e<8t#n(?)jBzd78HClN^oC0
z;B2u=+Gfu@EU;hp2>bRAy7oNXQs~yul>jVEGU;G`5$f+mX=g=$VOu!xt!)_9p-Z%G
zAsz{w!SB%%mOiO_Rq3>h%Vp_hy#WAZ)`VtYB`K?rD)>jn(bwyoS)y>k_qnj}1s_4x
zyus?k=*K+4{qQ8?Yuov&dqyOgh}{-M1HUQgMyxK>8kv?Ept5|j>l<fUaK=7Pn&|Of
ziOOhS56)EXo@O{b?{Ky=)0WB9L#=b|eWD>gBmJS-HwHvf0@|v=%k00>Nyw4!7%*A0
zkj!O37f*8h(Ty|j5X{xtB{5lH5zQaJgeURb;;??mp(Oj~dZ+Tx{`4MrTGVyaeCZun
z2Y(qlgsrTNs;(<&XyUlTE+^1jyihZ}gCigKDnx~OPn#(2E$7`d@(4vB<hyuO`;MWa
z?zAon(RH~~yeeH$iNf)IUO6W#^b)=MbJE05FM=|2CzNx=Jr}<Q=pfuTCGg|hX6~H0
z46RuVhu+nBFzW4Jgm$bU!O?0Br>?w*0_BXv+e>;iLI5BN9U7j$7x~*Q+np#rA7p``
z=7|7Kq$8;bXG%N$Z|6X6cZLGRI``h(>6sP`m=8>p3@;&ND%f4J4#GKnr=a>D6C>z<
zObq&;+M3h(3K@qS`C>>6`mCPiKjVyxY&!fGQP!iW<jl?TrSUq)AsV->-{7|yNo4i+
zXqOjt&w5-u%EB$d-@7?+oUjZ;d~oBiQ&RR_o4LVL7q0WCjI&6RLl?l~diW@zZ6!{v
ztKJKn8Wp%9$mMdgUTPB9adSa!ce2|CyjmmH<4o>>zXnYzRz*^sqB{+~*%8$L-c;i>
z2svIf({wVjHe<3pe|1VTSPQg2Cm9cM`#Dui5{`*Bm*tcAn4xEo=td?)vQ9qYI{sZv
z7h*arDl=Q9rius9HbP64nDkAvZjb0|$!1mba8u~yo&fDY-E}ZJQUo|N9CAFv4H-V-
z73c})cn`-bp={!TWA69ui4bJ#Mx^+K152h2t1%4IGK_&zD*A;Q2T<@AUTsjgn%{Fw
z9WAyyZIErzf&di~eJpM*KmagRAdr1zuysa_R+qzFT+R~zR<Dc93UD8fxTyk1j}o8M
z0NlA9U?6#XGb_W!FZgIG8sD-F2N;4m8W5so)T*{ho7c%y-kLb=V58DHp7qkTQp4VH
zfqik&tOR+2yhTA7&36kYji+66&uH19C*mY84mVe4#vF`rtpRyZxEX|*C!rj7m+Mq=
zQ(_CXa2xehV1aZ*yWxsIk!00822k!o#?drNRT+vZR$7?V|JAX*%GXbZZ^|0Bu<bAc
z+8_x2t=F}24NZv0U|ByrFN7yxU&EbPu>+u<q)#LRAq!LW_;r+OHSkRD6mP6tN@Hnp
z#fg8Z_^p#}n4~3C@PAkg*^eYfq{VfAg$-?<iJ#>G7G<3Bkx~M&|I+2uQ%%6RRYoNa
zTK~@2gE)uT<({}pK8TzJ{?xBmG)r-$x;{8s6{fgGf%CKu>2$A8xciUMK=JUyS$P`9
z#k(_w7s2t`E2co|Z!Ywj88u#A4wySqKikR*ocFL>U<Hi%m@>jS)Rwgl%dICT`1j2+
z>Z2DlXSpc&f8X1TWw}Z(DT@{sjchzsYZV4MX7TkctosxAI^peafQV7EQGlg67+jG`
zX2m5Tws4VsJ3-2#^iTYRj-u5W3&g>;c)+KTKg1>|XDSLX%uKv)-V!t<z+kXXJ5&Ni
zJZW&y&zWOe4JcCSwL=qtVPOE@kU@5~-1_f;yU3dGrKm_fzw?dh+MKk{(BFpVk#SIw
zS{s1l$8bp{^)FPW`~);BOBjesB~&Vqpv-3KL1LQ^OI9@J8Ruj^`L09<%MG^jyXvA|
zQp`(lWe#)M1^v`H;51KIn%}jVyzn#E1A}8{lIyV0WL#Krwo1K~u5tI_4pU#`?3ocD
zFIls8kk(WJYBAGIQE(DEdb4&3Zc3xpNV1CcW8Vq?@@FsmBRpXg%fg{l_vOvd1zb(&
zF#eer%Q6eVPaE_v#SkHnP5|FwzNIz0l(sqlal_yLbJij3P9eH{!pH+Ya0*x|110f|
zukBDj`EL8>%DST`09!0PXY5j#=;&yV!CI4Ot7c?E0H;acrYpDvHWsp-%aDF8a?9$t
z@bw#a4|AXJbH~?yKCS`l;rx;cc|Pb++?s<7Nlj#RDII{>n62hpHn_k&)%jJ)GvGf<
z)*wtQL#=E*;^S>TgceoA_>7kmIRb<qfQ9;7_W~F7)sz>~^53h-oPe(ajTc0Mqwox#
zUg)P?b;U6NIy$x7`xtFNAgDpgNWMkI0PC@f-zKBbJ?ED@U&>JQFHNOXGHBEHP-H|W
zud+Mue}Ly5?SDoA=uxKF$#Dd{eh!_kEq&4D4xcNg*%i%;xp6Yg^0AMzh9vSsJl{Gs
zRhVGK7jBzuS`i1aQwZ$cnLn)YL3f|3Gi|~pg905u*k#DU?EwiBFCVO4P_BZ~`TH83
z;Udc&s#+8MM#ICzR9l;n27%>#lAgw2+K+iBH7@4MyN6S>0<L0$!~jJndKM&L={rva
zJ$4EX;rOvY@ZirDm`mXVgdHy*NLYts2u^?m_HArK28NJ<DfrqeemIm)`f7UE(<xp6
zc-*fTfcz7shMk;n@@7byyRjZC+ksv{A5#@WADc$pGFilT+QcoS!li#8aV`r;2$#bI
zZ}pHl+vWy_2(mr!v#-$u=>lh@2K}^Sf5DX=)0;?OqJL`?m9S8Y#{DTE^*u(e)YBpF
ztoxJB(|HrAVKEVlwG5fTh!n8sB&asFZg7c!f8(yZbS;gfHJsOVXctwfJ6oUKWtw~{
zM;B86kZi<;=m_Mq03OR5@gftM+Im95k;XxMhbpq2K2@W2NYbf*2N_6!ufCVq98hOc
z3$M0JVWZbEpULa2OCXaNr>puKS_3+0#dEE-s~u!0j5zf0%w8KMoGI4VgKXyZze3qP
z7nFOqDoU0)#7=0AbRA`px6nxB^eeUt&`61+@Ykt)WYDujCwo(2)L*Qt=z@P^H?9dz
zCmE;)7?l(KO4rMOC-8aY8JKOa)Ngo*r{UPNK3fB96*YHP)UV&nw0s*bKlXn77j#IL
zGfSuQSZHAo4#))3PCsrHJfM=Y<wG>!S?}0PgrzJxv15SMKZ^A1N8sK<1t5}TuMels
z^ePXEU0kGW1*=W*K=UW?Zf*LGo$69|2NUBTd#;yF8Czv^sQ9oSxRnWLQ{Ml_{Bk$(
zNX04vDWH0$httw-_()|9dlX}paMMANqZiG^IjDSxQ5#Tyrnu<@Lj0-1zn$S{-As@&
z^6H}cMe&ld@?s+GHt2zidH$Oo{Ah(**2vsZX)Q7io{?HAn5n!M=+<-d3pLW{nv1Cl
zuNT|b4Gs_Lm6C?{X84$1YvZYAkG=jJ<~!W9m_4O^WbFZ!I{15(VA+c&PL<Bwh{v)k
zWx2%qa4MkQjU104ii@Hj57Gcra1-aBMj;35;=B9R^_WJb_+idF@{<3(jm);@rh6Yn
zpZ<>Fi}Zd3rchu%=dl+*>FE`~66O~LMgxd|b<FHz*3Fps;mo_3B<2y{K5@aQF_h-L
zYry-Om9#&f`IYe3Ui0A#e7SZvKzfxb4JET3$Z)Ax)c}Nnx(s<%<A4i6$awqs5ss@r
zt1cdjCVKaVHH<l$ZJsca@AAViK5N~_vz){hjxfN0mZC0US@<b>Op1=|Z1sCsC_U=a
zZ7|bKK$}bc4VQq}4i4wit_#MF21<A)YRpeAkwlSjz+h*Q)99CQBmX+A9*mxJlx$*3
zYnjsQM~-tAcEw15)>P1WHxOC;u|bzlB29)nZ!GY9C9S@d2C<F7<qfea!Q-|zN5AES
zl$CT%`TZF!8E_+0T!RcJvjUXE3YRow>lDdwnq{+dbvOwm=HxOW3KsHmk~V<2#XE4*
zfYVfTFkiWr3gCz)(*{42StC(L7<8opU{d=N2-h(!EiEuJrSGY~6%*DNFUy6V-%2?_
zqld|3@AjTgwK-<~F9N*%IsYI&y7Yfqo!Q6)bRFIH%N=qC;g73?&Af(2_OKz*ZeNS-
z_m&^J0p=ldQn1E<Me-_N%L(0}2EhnGy!rGBWXzA~U_@8CV`%Z@M^ACpscuz5g9^q_
zlnCyjzd5Q}XWm|(DK1LltDiTgFkD6;E0uq^t*f}6_XnKW_tOh?11p(nUv};c$UPr6
z?9VTIT4L9UTOOEXH-7^aZf>8bDj~6&+0gRp?eX{1bLfQV`rExl$Pocu!ao3447&Pd
zUjr|kAxrjp+~VC1UHkoZxzo4fT=*!^C-el%rfJ=P!N7C&vZ&PC=M}wW@W@ZQw!cL1
z`5=58%{?f+)8J<Yeyiqlx#;702Xu=s$vlW06A70$5|yn{mv3O@kIqO0D0uv)KT<F(
zMoKpCyf<FVrRI9o8fsjLpKNFP+{SY8<ki!Zzuxh(8A0&wQzSvV$g_>k2S^py7y(Ie
zhWXG^mJga__<U)YUm8gxDP?%0Y?)dyhmIr)(qq5mLj)i$SBDx&7})_h5=u$4w@DyR
zY4e^|M3?$8uuIEwA-Ii)yU~mWpJUz{p<0EmDEA1<`GHfN8haI<y-G()yP}v-5&gQY
z^Q|4p13z-WfGEr$!5BLf;+-&dC_6!@-OiyeP?}FhO(dG90@h4F-WjZr-W4za489%3
zeaqG$$=g`+*QTbvu^%(9L$XH;ua2zuky&>H4`zGSdpc*mcbm3Gca#_vs8w>}c-gr|
z>m}27r(UhAk82}u)@ufDxxp_qb#;MaJ-@GR2of(^nq=>Um4~X-7y(MZfV+-q&e}-w
z(=#~*Q^9YW3pnF~`^Uf;Yc}-N(;!i(<{Sp~>*m{&AOqtA#S4_A+cn^;q(+O%{{4S5
zv+RF*a8k^=Mqt#yTchWRu;Me}A~iuC>ozv$`h)Ww87O1`*v&-jR4x}>upC2pEJZWz
zty8&5{$r8g{$P@kG+WwBxm}uWy@tH7q^7)%70MocU)mOd8v-<PHWhO7;UB+TP};|b
zlk$x#_WWap&1CaOC)LXS-0MnQ+F!9<0$Vm<j{}X1U``astD5|~qO84aoNU))lzSP(
zJphyGccMvJNHc`oE8rP|+$J~Xc9Eu3f#c^YW_I1nxW?brF&7|~Gg;{~E%+5TCf+1k
zYDCYEBYRBj(<Yy4^8V~&*TUfjYI^><^V7Z2u*omr+E`+7*TE09UKC7lPNz8Ta*U(m
zz-j=z0cO7v2MYaI=WXl!)Xy$qFKON?gFB1{qzgT6<9uN;0+ys2(%58<<rPjw7z51;
zqE2e{9}|r}sgfvhbxO0@o~|BLQuA2*ZH<a5tlp;qB4?dP!D7S#k5L;36kwU#8t~i*
z%J+%a2A~;<2wGCRX|x1C0eib3Z6W)sBaP^KaTe-4=MaH7<X09-b~<SxE6uwCD{{J_
zETm$J(0~0w_9M@)-!LKyrG#hwvlE4sbN_8SUBvwDj^ohN0|g!qbUl$B?)djL1*>@9
zj%JYNmJ&<iH{63bG5#Yfq5ZGBiQzH>*Y~1$8LFcZs!+aCi>~=R*b~!4Q|$OHb3$6I
zNB5d}k6lGo<`r`HpzuD=U4r_uRbF%78~`vb6ORqqXFpE&>EKmaxy7RH(nEu0#n;cU
zN8he*5rz&sl;bHh+yv-t%abg%099$Wp#kH1_sf(^{rQa<IGP5pa;0h}+e&$6&ob1+
zA!xwy?oe51cd=e+<wBQv(Wj-izGsSXfD%~`!%ynCKL;nE0Mq=_F5@{So_`31<Fmpe
z*uRU_SR1WZDGA-15IZnJIB4?JfG}<r@VBUl>}nN&P81KEC9?(=E=GGKy>KAr<~)|J
zT)~7cKhBUlt#~t6kz0T}&Kp-8-cHE#Lm5WlhQ_6`rwmv^)Y5Jq`WJh%zcHZVYKF@t
zMy0Zd&jQ@yfl>ug+nuUib7aI}U>5upqfH1pHChwa0_3=-{%Ew!rJDEV7gx&S9Dqw-
zvx=x~QP_)a$Zke^LD}E41l8s;g@tU$Lz+5jp>#oy@Aa`563M(!g>T#gEOigEU)z0<
zDj_zzWYi{t9^z9iy;qGjnE|8W1f-=Y@(4Ja{4<>Y_dm<4oJ`5!spK%<LBOs}me`h$
z9Wu+Gw~5IZs4?ExwM_}RdEjn%XCq59-J;{u(JQvWvZ-eO@7NgWK4U7`E!6&n4gl((
zO<p)tKS#%$HVFJ_6!>$ov7e|%?#ZBkR!4soJsYsxJGAghci!gY*2$@~!J_INW7D`A
zd(P|Z($E$`85<&`k-c#@><(dZZ4?@ysLMMvbB=$zg<|mO=X~42kA`w{)wv2CJb!$>
z&#C5zM^FEgcV6SB%+TBB6<xKrBNq#-P6_-^o-Ou>b9X4$4v*h-3-m$wt=9}|A0lis
zl>^pJXHABOc5ccuK3|stwgkL8y~&~2s5<!M4*?pfE}s8H>~~s5jt{Kmtgf0<Uj})&
zg5F++K2bHwv3AI6el{z1Wts4gih-4Hp$2CqNg<<_A22MUEGOKkZUxgiD5q_j*m@L9
zycC`;w~}ve1LI@B?5q3o<!ta9Q0IXYDdQ8mL#9@b9qp`T!{-htOU~^>>UH_vBW*gr
z%_hu0h(izd&hGdP9*E(qpGRNNpdvjMsqz01YHd76T0^P;L!qoIWfS3H-GI;c-BTqq
zq{kmibtsJvY!joNY98#3gVR9^42&0f0gMHJ3fduc#*CjI@e3xb&c<5HT!x(iYZDwF
z^wH3sJ3$jDcTPgPetlzwHGv_tAi!!HlYz>$w1s7UAs>QMU3Ooe#+*q|?G7x*|5S`b
zo*JY%CISajkvfFi3c_NAz*7I?{SAAx?uSkrZuouG=8Z|MRl+)q94TAKM2jyv0g0l|
zkZXS4hNffTz>q-f5CVX6N_eMx2^Bl|6PjnaDUdQLaUQ3y$k*gv$^)xS;BCP^PP@zb
z#ITCqS`Xm%Js^{DrrCJefZq8*M1_;UW!?`F^Pn!n(DeEOxtJyE7)&IZyLfC)8*ChN
zWRi<_5-a(obW~6p?NBC<;+xQ;Q<{dGcY|>ne&O{aA!)-|9#4Jp_)T(DKeOP>&5Ez_
zDFIdXY8-p1t{XPy9&aOqWT;Fo)oNV*Z@3i}11qUe4y2tkLi4YK<Xsk9N~N+uMPId$
zQF{vH%_#d9!y4ZqQ0A8`u_9aXB0ABNB*A%1UQFVgP*Um~T#f+FZP_LsD2-(i{@XRZ
z6XX!@FQ{*6>5(lLxmNijDLNaVWfyCWWK0K^2-x2;)08LTrd*@L2z3p=zWsgCNut#&
z*o=NjaPhtADWXxYt{SiU16^>_kAtB3v8yWBV1~3Jtk(5A*vg2^#<6h|KZu!fhbAkm
z8DT46hU5*wh7y@H|FJdF+9+#kRFD0&`{(5GU%&Hu+-TfnOw=Uv!W~KMaSf6vB$2{f
z^ziEK?WwM5TU4ASe<*pg=y65GfEk^YLr&1*K)Jb1OtpcoQa4o>`aqguQux<>-ohwq
z>)py|Fm$cMUl?4Fz+|XOj|G|52pv0DX~fTB8O`ZH*txAz!WF;&rb7A4A(oBed%mG0
zXxM@z$x&i4Vka=M=C@;|Z<uOH!^E2JOPv=r<y3s56wGyl=@z*eD_N;C0_9K^3@DST
zCjtCJyc4Z7>ZmL0)Wd-1ePdiw{J`C*J1iC40z`M$gkD5H**A`3_@3Kbks*O&cm&C{
zF!+tx48n40w#U%dbx$4)#1;p8UzL~i=}GL^=i2_5oS6~nZ))-F<#WY02o&HonsdtT
z^SXw2sPuK*6L@<)$d%HQutOU`@l3!Yc@EVu-Yqw1yFWfqa%g!{V;aq`6L!QZ<=8Un
zQKUydqQz>}<db(F{Ndin-M_{6%6a$^01@vJQveOPqCah&$5O|y&j(NTI!D7)Y5+Ny
z)wp8He8xTj|HNd!(({nXo%x<8XXlGTzSiqP3q>Neok}{LPmya}pZ}%S>)xriE^5~u
zE!W7s&F{)1te(;_O2@>Y!t(Z~<w7nA@#6Z@SX|<--6PzzJRCjk(&CvIHDm;3?*%S^
z^4hCHzv7d&AwtO+2aalLSw|7mWCwhrKY)KGO`^HfHXTtVCuPIfE|&7&tH|xBdG&$Q
z)<IK#Y281PPI9G@YM!^ykWvi>kFli>wbGd1MR1>(D#nz3Unc5c2p^oIy(VYu+-Q%M
zO3opa%)!C%7DxIzpK>V`UEcRNSR^Zh8k;(FcvQ}^>14~98Yee2Ws~gHIQ=lblq8|n
zb_k^EP|@tm-zl+r1xclxW~A4rj{tUPihNg3o#pt?P0LVm=Vc39-kj=}=BfQNl1blk
z#uH?^jgpG@tl3=Z+My)ftrvwygI$MJVs16}XjhvnGYdU$e6HUPZ91b?9?Q3b-sd@s
zy&3<;^7x*6f>KqY`fU6q=bhTvM3#$<*=1l<(7R)5eh!<jB9Xt!i~bphFmtSmkbNhE
zKA-Pku<sN~JmX`2`DN1crM>{}-1!i+bL;OtKfM%r`W#GYG&ONtj`fI!`#M(djKNii
zzWj;n%QeFHr{FOfoF-4oFe%ew3JkU+)Xg6>HHSYR9wo0Gfj5-UJWhpXIBb{DJV5cj
z+xGGKa^3fH1;vnd4r5#Uxtlogm0;V}j=Xg~##(iN?<ENSblcuvN{?1gh7Gx6WotJ+
z9@vEHA1K=9<m~OC(})B6=eO%IXKLv>3f-1F6~%y})}O#SvQSEsT=mR=>(HmcHO-3@
z5UL$cbf%;<o?gUfy9*f@d?Wf0ajdQSix>XXrTN!42VWtL{E<0)+CW(v1(g0Ujo)R%
zu0V5r;iKj~j{2n`v2CAQ?3Hy>mF95Qe<k}x;&S154tUJA0hdZrR@x+Cv+BG<BGC_t
zvCcU}Sz9~E;SbWl1Sf20LTK`<=B!(#ph(l_aA!6lg)G|paWhEAodAUwd4Rra&mAkt
zEcLJju19)=u<T0C&y+LP592Q;28XAM+wYxjH_LOm!QN7faz%iOK&^pJ)OZFF1|kMt
z0_bR6>Nqfd;8+X+(chXEzH|%8fm%e?|H-q4rW5r@4NG$!HYDi+^P-^AfO9o?5iZr_
z%e)6WUH<|-ro;gIv<t~_sRf<P1aca)X(c$tBVW@44CUGN$ftb8q*XvNr3shLxfxR|
z47x^FUq&j5#EQVzSNa?CFYQ0_q7JR07D(}l26$tzLYoJGPt0;v;XE%~yXq#N62e`E
znnU@=xzY>w)bBoYO77u?QcYn8H9q)H`q2BfJ}Sv;zgH2yUonlNnug7}_(-rOx~qTA
zk~8~p1-)@qhxX4R8a?U^@N;iHSu<Q1^*&5z_KlzRN7lgU$Oca+4g(*z5|iQE@mif$
zgFL<{E2}%CCzo~WQ+`8+k4UfrSblg<YW+vqo#c44rOOX^4X!&27I`>48vXF817>#w
z>HNnbR_MD~lB8O(YkI;LT*!m^tACLgFXnCRx5VGc!SCpPN{Rji5nx@Ya6A%96t1rf
zyl*jYq`Q9O$>NpB_;xQk1O9}q_)JdM8<i9sHd~IlI48I|MrkB5cpm!Z{f-2QV^)RZ
z_=D87HDTam9Vg<z*T?TO7&PnznBl=8V39AssX-K9@??DaL~69Y>W_NjiJAjKpsoAO
zH7VEe*|Cq=9AT~ygQX1Q;w-+YEax;JT;TqIi~fR?WU15Jegl>IwJ`V}vB8GO24ygQ
zd+WjEI>?xhV}fhMihLP^i`(`1S~BQ*M=7IqwZ_5o2muQLh}7Hd(u^e!-U)Y43q;%+
zv&4lmn_~_e8g1;Zj?*n^w;qLKZBRngvDcu0RS;=m-9`9b(|tm?_MJ?JvHt3|@$(o-
zz;U#BURK@gapd}@jr-2x#~#Y1RhCC|wt}3)aE+@pVS*MKBucObD~pqhqi3wQ6Z0Hd
z7~!|im;8dC`jewSf-{OlX}`WV2kO8p2OaJRPz)q@3@vlq(|e2}&m$ddbT1!=KP-l_
zhH~#lkE5Xm#mDT&-)@;^lw%|6K}bkG9nn&4fIhXa(BY!4?l5VTV=Ub9_l@Tn2X1pn
zASq{--#+JJW0!&GV{!5r6q79JJ_%zzAQPsty;CR{2r-akjK=)Shi+)fajvENue!sf
z4~B85q9*NOm|^0wj}|N-AhXf3y}J1=pF#PrKU%Y<O{GsK@7vG4s@AukeH2#Y0XYqL
zEbd*w$qXc_4c{+u)zIobehZJs#EzCi;^+R^z9-{1qOg>doi<qtXPcS6{c-8(9MkH>
zXx0x~da9u8TXo@Jr3kM>E)1SWcyZlq%+fNrCS0#@Xj>8xWJ?=KEBF)c)35L(NJ_>I
z4u;t#PT52oyxeun1{d1c6c>e&r=U{&=-0|=K~7z>_%0YHj|Of+Pcp5x1)+a4$xN^)
zK&ZAL0^$sI4#Y(OBhuW#F>LVwtlB?vJ4F^m=A4wY%G#I`G?52n5_~Q?zsoVP4chst
zzWf*;)MJ<5<FSy^`?<R<nf7b`uU=YxM1<-ZvbB}eAR$_o;FTV7kFz^A6`a0qS}k(I
zy-Fjlp;eNXTqI*35n~$y1*Rno*V))k%d{$lxU*q1I&#yO%`=tGen+X!BN%`%<&r$T
zTjkZ3Dpt9;^Ev`=w2;1H6YJpd?}~y&9h<N=sW~nxZf>^edP;}X-h?W_zaSFG!rgD)
zcXL^BX=&onqD%+Z+9!OH*<InYfr5|fP35wnwUXi6NUDJ&`Az@H+w>qsI=aG~!;0hm
z%C1FsBpy`Autjc`&HEG#EI~QeuW)Jz`@i9`L^AH^PfSu!lMErHZEnT!sff-aXg8`#
z1UN64Mc>89;18>j)DR>TJ7JHN6rY_6=z3yFxqXRSkH6edODMm?qU#Z6zJigs_fB7-
zN8k8_O7(F&-~v54$MLHG`ZQb6LG&dvSGTWcv=b)u4<cX+k$3r6W^g?aMX8+StjWiz
zwm(Lrp{Nz(j~xTfaRrXggaKKr-}_GSD0^E!@j;K4doc;uCvwNT_u4r|o86tGQ#W+6
zxsIKZbIb}%cG8KJ^2t96MWfIECYf*oa>5A%$IXt0$sq%K4+N@H@u)Jq)<tICRkY%)
z4*lp3KT8z}*OIxtyWmGE%NcQnewp%_g?*MFw|(B)Ah8T0`Q8BwfRt4-M|eJ+N<YOJ
z!nY5-L^$8j-9ZGbIxwiiFcp_#vL-39K(;9Uaa+Jqy*M7euOkBvuL$pT3c%zU@YWXn
zZQ+{I7xY*9b3UJIqR2NG-U0I7){c#>U9;*L?fG&G{;uM`BDPX$61cR@YcQ>~jJTx5
z3{+rsgwQAk`KY}#8d+jF#-lq)!zBqu@DGw=mhi(Bk1m*DvC7{Gf0)ySpxk9Ee^Wt3
zwmBSxQkow{nwl0=9_K~d0LFRJZ9DV@(CVv7m?}`nJ}UatGyM4o57@=3m>?r6bTU+8
zApx;#)>HuFic7zg#M!Oqja+<{b`qhBd%jeauj=PqdSQu`D4)PiQw+_k21Ah^vEgc&
z`;tOV_tqnMtxY_@Hft)=0Uk<Q9YHFy9lrAAGZbj5u1#+u2D6-Pj|5RoE<Q%w@J8S5
zRGK*3Ws+`04w`U~G+$|i(rUJkO5}ESb?L!S7RYbnx(*y<hOp2S%jO!`5cUq~taVCx
zr(_EQi|>h;==zJ1BMWkkbhfSGm?(@w%>2?xhICUI9Lk;LUc;sCVeVx*_qJCU-pP8=
z(LP-d<%Z`yBa!(_e18hdZ59|SP}cB<=s-LiYP^(+PlI%zNm#3mR3Ww3-LEngRx_%t
zbjxuWK++z`%bkprcG?GB(tuHCmRByid>YMK#su7gK`mM#EeYiCe#}xM{r{9>@%BA!
z$K`+<leLaTu~>2VRP2rMe$*SN_4;-{s^^0aKA-V}zKD$8VEij^Gh-)C1OcSlj5iYb
z&VJzA>b-GG8<kYp$rU95x_qNY+uW9a_zIyD+<SPB;3w8v(XaTt<qB*U;eXmHmQyQ)
z(LBiE-Cm}+>DQ(<g1JC+<k;PbBS@zjSEMZkuy;CcZRTo|Gg^gH(XU4{94o^KO%$Ef
z7_zn?dP>JIk?^tAB*)(Zv5}7S_WPCnV+JN~!VJ%3m<y%`<dBDtGSgz`Z(p(SAus70
zr$_GFK_tJW>W-r#>pw%HVBvzJl4;@kJlbP#>jR%i&0ALXAX8ci%8OaGnGdpk_nhiT
zAq+dB&-a0wy}grf4_kqeeb;|90-pBi&l!y`$zHvK-*lpO!-8-xjNhg)+Iv^mKkejL
zMg(8bJO8_Fv8=0cxV&y43c4wy=NHkE27@t&fUb!{%ZQT>VU+*^<{WK{`N|eh?+=>F
zD{&2pX$!5KfBJRJ^gT@HGJje#1bVLM+rAE;u>Ttdne%4@GuLWKTzY0j&HG5vH|&Jk
z=+v}{36eZffhnnus1)yM$DWPDTbbD4TZ63ucV^`o9-o^@wJP|`+RZO*KiIB}-_9^r
z{vf2SzXY}u|96Om32|cn>%=1n!rc1F0Qx=}zj?r(zP!y4J4vXXItzx?MsVC*?;N6x
zXIvw<oFJ2?57IYL?EPiW`(&ZV8&~)B^exkpNYAQ0C@>$SZ0ij>PD`-V<N`RLa_0u_
zGEhySRaZMAyhMp(a&V|Y8gb>vsKD7+Bm8>&!+S&dAG{UKD96mG`NiN;TJ;B#;k)aj
zG8P%eQ3qY#7dl6Dfm10@p-QcCO+ExgbeM_)ve_;Ps;$KBRsY8F|C&o}6i|)90?aD$
zRWfP3gJBeoTA%bmDWsoj@P=B1cHf9nnCT`T;cOG*k9c27m6E(*zGmQ$pv-JnQWtz|
z#A6AD4KoX(18f_H7O&)XXu?A?T8hxAExya9t&@}gaHF^4ftO2T-aW!$(33{_^vQAd
zeOe7ocx(#1rZx?ihTINySUk4n&!lXZEbTxxdF@dCH?+*o9~fi(Cf99)gV!neK=0#B
z-KnBZ=*9`p%L$7M1I5ZIaz8tV{y;zTU=Ej{j06=busMFXIlml*#HBHi{EAtMYW$K0
zr_jC(l}3q%*=06K@&eq-1jZ09$my81{B!i~KpJOi^4h0A8C!g%%BD)))8@)D2}^}n
zFNpIka7GX9)8I>*PY0zQ0@B0P!i@6ZrS!z;SH2O|LRADyOXNm`QWn+V6A0Wk24i@#
z6K7x^v$Nxd`Xi-QzF6EVj?I15Kx51v8<iW4qvArY?)O|A$Q7h!Z94(CF9a7VclX=5
zyyxjwUi)1kw%><?9W9}Ns=zn-V2v*ICFo;831p(=eR#`2%^<94>IwW=+@%tgy;-By
zsCMM+7lg2%g9MZY?|FtclKT<ut>1kY4e(e-;+Pl09bhn36C33m_Mkcm1+SDvGZ-fA
z3kmyc4$sUrDLLDK+;vGCoeM7*248*>N)ncn=2l%yHV`RK&nHV@(i6>)7w-HSr=wWc
zH}|a`km-^w+dh@wz(bNRko=>Ii;X(ddYiwxhGEVt80b{PyYlz;0TQiOAi_HU^gYE4
zR5?bV1?kVyD{DB^CJFwCey6|)oPVDihjEBhc!<5mB`IA9EKV8BNV%OyNEC^^0i2rK
z+w{8)adM-FA$Qqqps90c4M1bKxd1=fY<=4_)28^cT3!m)I-GJwSthOC>p_m`N#$)p
z-c)fpOxo*^sC28tBDW8U8NrR6sT_d1-aLTx{~tqHTa?xBHvG+dUnuH~%XV;W2<+w^
z3i&3Y8pG^+KGb<GKJ=8`xt3XtvvBNZFa*aG<4_sb6TUw=aa=w9;${Ekd=2mrDEnio
z2Y4wEi0T$^pf9if0ghg=_7%UUUku<fz=LSR0#1n=8e$R1|MHp5%(O_R=kxY`G#F^d
zeB&j_jeqx)PM`G#Hzt0ig>ftBqW%yK>4aBjNWhzRZ@ee9w8v%<HIjNLft0$#u{Zz*
zRlJZj8VOgDQ=fc*z75@m_MT`;?2S{;Xa$qAkfkv1>fbr820SCMnBDJ)jZ@d%z{x+#
znZAduC0_RXD*lYFmLtn;yCOD$kRZbA7SuWqLi8N;tO-XXH)yhAs6cVn3s&R?b$U@x
z`h}S$-uzn(n#R_7oIhO&B<=d7ocY;eTzJ^38KUlDE5+bclIt+5)T)c>Oj_}oW8N<B
zO8LreZ^>r)itkT9_6H0|oOcZP?#M;?GdWhw8d8&p>AW>fXJ8@m8HPe9&<H;}J`-!%
z1O8Q_E@Z={hBj|stePc~ysm7Z%ygVE;0zp>24ujfTApnSH9Fe2@8xAS*ty)*03xkG
z!UC89B?KM*ft5Bg9~X{Lf7;>=ATB78Xh+gB{lrLrMUmRo*pyH0WG3e<c5SYBtzQ69
zOrgki+#fNxn<L+l6=Vnf^^+`~rCJhS*Gooh%*xHr`jR|wSwUt`nBAVr?sm16-T&+1
zA&JjpD+nQqBza=0+r_TH*zc7&BW2*GkZOt(NbY*Q&SzTJcXqQck?wEt#)%oAg31?L
z)TuG-zakB3vu%eCdDhh(tVZ_Tj;H43*t&SQ1?QxxBRMEsOkNNb@CP~LI*Z2n9ACpa
z8yg?UQfz{vQW52;JVK*F?5|FK6qM_`c;}B)uJrI&{a|+fH&-1COr7fxP~YpHhkygL
zlRJl4`TqT>Y6V1U+_tBV_(?)VD^>l?tF{+2Kx{mEDR=_hAPe#0kcR*aXwN)UOtsPQ
zHP(G=+s!(@Ew}9<wCoNXA!SCc2V2nSns$&LjU!|%3aQ)$q-Ff7#A_p8`zebT{xo&2
zioZ*bk?r`q!-pS4rDEyCBN?#Oe@A9@ScUYnl?N5|1B7z8RdBt%S47^rZV{zKPL>Kj
zH&=Mv5@V~a!_^#Trb)C|$6N>vXdMw;i5vcr>^v4i_x3NZR2BMw!3lo>LvXa-Ik%QQ
z3hmj#$H!+e)n>bZz(3CJWluQ&4KvVf&IV)*!&Gd1c%vP|W37XiCen*SSTxhckraxz
zNCa7m0rgZuPB?*2>f)}}?)l|XU60&Wgj%$}B&jb<e>{X1hRQRL?qBVX^^IR{qlm6N
z2CiN_(&G+gmxBmA;{lTgybOd)y}!Yui1`#yg|)$z9qKB&Jev8xwgq(o`JKWF0|i@c
z!+S4JjH-~`p+~kRyju3Xf^EMyBj7Lsw=Y#se9wH~>PkOuTng~(j!C6s2ZRScM3nW@
zE)EzB>P1nJ*nT=-oVL2|3Z<l{)W9~A;+?N2wIz{v*jHPOH<DqX2v=Eh_Yggaz-^>e
zJbXiXB!oPm=t|CE!NI*DryBn5U;7@|OfydTv7@A!=-vCDJsOK1RQ3n9bI?em8C-Tc
zF$)$|!RACI(Iu_4AwhwN$bQLNN8PcVwKv>>7H(Pk>a@Vaf>8(!4jzJ9+&lf3B!d$c
z<!NpoP3JPJ;GaWl)unneE!!8@vqbWnB?_n+62BM@ZK2}0siiBw?(NU*`L`-u{93=(
z-cbM+LPYhA3p@87`Pp{I1$ydi4|#cGCqfMW%WZArG4XVb75}t-kK@i)7rt+^%id2|
z&n%r%T521i<06-urreZxB50$470HoNa)IJqmp6tM8YK5C@n38QzZog5Zh{Qp+`=Vh
zfU?wv{K%he%pf`_%r{I}sP@0t_@1;R(_<xuw{ivG$fM6?iFCjhV!|pg6jV){fu-ru
z+gH|#&0*EelVEXSRaWLn3+Kwf1yz%7-OFOZkiacev-^eBJBQ|sv~lvG;#fyUQk~Q?
zB5<A>!!iSH16eGea<aNA!*5FnL;say*cbVskw)%S^)S<d?^d?qhx&YV!=B7FlFaSH
z%c22VMOHKH`=pjhUPw(aVEp9d@*T^PDgWV(48*kqe149iWQpQ1VMU_mY>xzvV{+5}
z;E+b1i{$CnLQ99OYJA?gGr()iKkJq>ZkT5(#Wd!C7dfRI^Ke#n09TQ_)x%ZmD_{%Q
z9h~8N&J1rv$Hk})Fvw`sx}a1PpVFAWwFg)Ek#{qwnu%6I5CiLk?|rC1P^9m9=18E4
zemv%5;2IazC{hW&(mW{2jwgy2q@e~ECrOlq4KG<5`nESepZb0a9|~(qB2g}~8Lsw7
z`OpbY1;s|#HjG7)u4&({@t$Cf8d|H^FduWC761lg*8QT9<?<MK+3ig~LJXf~u~|)5
z>BkWmifl(nKy<{np8nI{OS(iq5n>JCnv&3Rw_aE1&jHY5*4?yvOSx-l@X=jXKRclv
z&v)-K4pFq$^PaT7%JqNIl>zg&3>UArOPYTx{t4gtIe>sFp7(b6*Ek(x$XHgTwD(Dv
zPRhf`1W0ZrI6RT;#Oz6qrqGskEWI?ZQWXqSzX6ZGbHA~|5EPk~yl~U0X77-1l;q-m
znP9_lJY+eMI66{X`7FAqrTr%UdI|&1NueW>KuJq$uM0n4x!?SCeT*6SOMX{>vFCX3
z%lR^{5eXx_TFNhEiAIOS=6gwMdG(y0b<E+GOF0n(3Nb$uLR*4CWO3X%40k9ynfxVy
z7+RI9utmu=IdU~W^;x3SDYa}<?Z1w=VGdnGvX1qUXBy5K5A|~z&(~8w_E21}zAt8{
zI*M#w6!gdmv`eM!E{-*Jv2nbWOT}GszjRmT+GWqguygisea5WCdvOx0`~xKIN}x1y
zm#h&3c9&|nCC$|F8v40LD3%y&v%up3#kn6<k2XaS=ySigd^F!+2QXh)<C#mi0`ta*
zPt$|I+vV_EY@h#M3inQ*gb2WSgBAmY5e@+Q02psZsc@wsxWiu(#;qd!#x{^8bHZ0@
zciphSuQ4Ci7tv}dbMq7}#xanf7B3t~4GnPo{kQunYyBd72lC<j_whmj^_!~*-*dF4
zO<SOfCwq1G>-(g(YzqMUqDA%vcDXJ%y~24ANKeRvl*eZ0Tj?-1I-WhON~R4TDllGT
zx!`BHC76P(D{$_cV87y{14F7CaOnZwVBQkiI<GA=CjH_};Etg$DZvPsT(U5ubSjE3
z0TCPtcm>~`X58k3?c_KQNc?F*y--|DJmXARVsG=`qZ_e+AX0Qd-X(s@C7WrZ5URXr
zD_sq^lDgt2W5zdMk{+8PBLYz#2C29n;kOi&2k&6sy#q^$Yck#urcTewLd%g4kv>=#
zXp|jBMhFt<k{cEg)z%ZSU|YeMu2RSZ$*&i+elL%i^tG;Bnd^!w9r0wt^GJ8!XLGB%
z7c%ADwmVni9iY_?srDUrT{KVfk`2qMM$v_qReV(Jl&#d&$YT&v0MrMKbP?apMFnTh
zX4c*3LB5^!(U%OOJntdn;NfdxI$wem@5t#H3>Y;8{@D7$NDsWnH{$2M%v2A!tfME)
z7q~nf%*CDq@<9Uk&pL(hj9=hzdeCR>P5R<g>CaiNTyH*LNa0N)&|P8bdCR%zi%Arq
zzxs$ovDP)W_p}ea-BScZR%J48rdSK?)tEblu6~oUi3aBp6beTi>PPBJf*CK!P<v!^
z8nv+%n3&7J&^TpLP+*kDN*7>X0f5#`EaSZcrUf+F90Bd^(}GKx4;MqZ4jzv+-hS5u
zSq$LlU5_nLg|&T5LEyKzBH+Z3h559G+iwUWGP7KeJ&`xwmL!!CIR~CgHcqk!o258a
z&m7pr-hGZ`TtWc?Yr7wMFpeE=09#PLg7DLWFsqFHK{L|fK{d#MT`t!Q`M&*D5cx>c
zkvD+3N1m(aGOHI>Vcyd4X5@C?(i3Efa)3P>!z^t(PhoPISXviXamUGnA1H#~FL~GJ
zaSU+|&!7)C1^#zJM%h6FHZh@61VYLVYzMfz<}1dYySyi}#5$dsM`cF8jdGK~)-jnU
z#sc+8qJQ}aTD&_9X9CM#XV2UoIIQlqwEqemoCUvsT3ml9O|l3qZl1Eb7eN@1*g1)s
z(Uo^5->|GNlLarSNoYV@iuk3R3Cq$_jfX9KHP>CPC?jPMfSbv2Nm=NR@%zrWALBN*
zG!$k+Ar_&7XfB#~j1C}t9)A=T=3b7MHgDTkzVULW8MRiCN16~0q8AHz%;l;$Y~D+(
zjv1#JPmbrl7@lyNKwwEECjd;LdGHpJI;*D~&1Hhm7ZtjxfbboAQTVQs!=?9;2mhH~
zhB#iGLB8`<)jSY0%yv*_zVw?gsqNmVKMlKx(_aVUB1VJMW$1t!IZ)?E{d@<r02M<d
zmKQb)x4I2r<H|sx(2nZ?Z=6ZdDmxGaLzl?Qd_?TNNi@C)XSzBOuh<wiKS-!ZUPQ;z
zT;K3tjLcpYwPp2JnjXZ@Td1eihJQA<_aEodJYjVBpStP19~m)$-yUYMC@j5@W40>X
zy2p<hFA^5-fn+K2IpHG!{YU7BC0dco7x{KvRQtEfiVB43NhL*ex8AV!Uf!$kq53wL
zU81L{zcLh-d^;**EXWzuS}6KDLDSn7o{wWat@9I&J#-6hh4PcO8YRlN!kwa4rL`-S
zjGr&4Nt=+;3HJLBajIXwde9`IG=GNgL5yabAml;qKi}t?L8CN+;fb&RyskBDL59?a
z`aNGzbHw=oj*%5p@><4;vm}AC<_cr$la{OtHVwhgu&meMNGx;-9}{6zH{zm1(xB&C
zu@nm+bL`V*XaCwckY{kJ^!UQCl&`EF!oIVCs=&Yq-i_1w%qQO9^3TIGm8clBk;*U`
zN2TP>B27zMU{01r=#QC}wk&^ec!d?g=wC!2(;ak-4*<vep=<VvI<dfrzQfPokz+-a
znaSJUvH2TP+Y-3Ih~6I5mJVrfqdx-mWVS0p<6I)W_P$aMG6d?$ix>S?WA-n#9frnx
z?y}3+M(cR|3qV|JI`&4e$QDPcH$<Iis29$C)Fg7ORP!jp#DquAuO$x+lJakg#f1H_
zt;*nAv#|*RtFMO)lp2+2UNktwch3}<0B7pQ{~NCli8o3IZZ@@gyDsQ!!mIhbk9G1{
zgvS(G*hKJQO+-C|po0S?QYrA)sap8{Tm2?kYyplHOm{0Gn6T0Xe~wQ$ai$@%1doK6
zr6h322<o~v$nvY2HH;q@0pZ4`70gp;Q6@9`oB~UjW@4P`Ix-a;ZMDo;700niPJ9_=
z2yht>0C|$(i{m%&=~|9Esx|<TYLB?bJqIrUzASC@qB*&L`eeUW=AW~d*d4F1aq_%*
zdB=A)vvZGMCy;lbdlpcW<w2nob}%4@JapA!98lxvu}f~?noHsM;h#r5U}|d}86+!Q
zb$CRH?DHd#$RMM^0?XCA>a-wf0I*8*&&EJLDtd?_#}33F{RnwQp$j4l5ru`5$-sKV
zm6!?<KnVNG`I%o%P!dTE?$99X-wf8VqvF3Vu_OxfK$xPLkQZu+zf@e5)krO0kb^NA
zJx2vhgu_*>FB{!tAKQ+_ugMfUk&cP8ri!?@l4?yXu&y<bo)!$*E~%dAEbwRo!bBpX
zMZdf{f2n6LhJ!~eqWu?zJj7kLf$Vd#VGwW_Nr63boX}?pCl06w0GtPtPUvd>xd>@!
z@^@wb3Og;~S<OZYH;uAJ3bP~=cn34t3nL^2c4=|YRt9s#LQlr(ckkK}BF9$nn*hc7
z=e=S5RD$3gT4lv0exA8+NBo4_iCdk67^3YB&Jq{j>RTW!Jf?Y=w8z5cgylq`3<p08
zLM48$M!7=1k$iJhs;pvIiuGvqtEp`kLo(bd(q!DmBO~3SI|>(zA(h9{YaM3epD&+a
zpuKV?8UDs1onvv`MKyJU9{M?IZw0qnq^xSD1vS=2L9GhUB{0`)XvB@%tq^?^*q`|J
zXQ`3`Q!tE!J@yMTH7`d`>BJbswt!i9N{6num#MQqnb*yjBn{y4STtaDPiWu6lz;RD
z2@vcA!?9a1-}EJ7^Cnc4gi8Xh6~jTl;#Qv@9#wogUb($4kfa0odiwtxtv_EwVYb%p
z8CBAhcRyx^T;7kqqYT8Iz1QhjEUZbw36j)Rp}uBx>6Jgr5(;Aoy|YKUBZy=jPQr;;
z8{A`8cP@XrFkKZt7^a(^`TBwlfpa(+q0ZY;fw`4G&fwxNIt*YDEnpTUC$aGLCgO(~
z3XY*9!j5M2=G2Nf9)WaBjP6rCW*AI=eG`?&JUC#Dde+q=zrC6*p8IfrEci)p?dUHx
z&iU}JTk0m|?m65K(yDxMLU;QfaMLGBaFfw6^OAO3dw26!jtBrv7zJW+ggY@R7eYo-
zQRkkIc3E0G-*5IbKmc^^_)pNa@0G{ir#fbJ#`b`RvAuwsN*tj4=t>HY0*`d>8In14
z8P<3bFEKP})!x0lq?0YLy0hVS@_ID<yh<sL{a0AM_#BZDekS08ThFRhBjj?6iGQAb
z=7S!liJm~B5ce-<jH6Z{+8$q7iG$yGfT`WXAaFBy?@vWS>LI~DR92^c^5ii(E<g;a
zo^nj{A?zK`Ja49a!q^~35Z(W_+j}@)I3nWWYHd;}$$lyLJFu<BbVij6RcVub{b^z|
zG-c|i3Za~mz9~!kU-H0WiB=p(`*@j?it4Yf=!l?IbEZ`jE`5ql2?_B-%M&ki9b!`}
zx1#GQn@~y;Afn?zA6p!p>6$LPu)2u0Ze&HHPa}tj2JLrQv8ykQrxym~JsFd85OjkB
z_EANdv~WOh=Af13Wi5I*-ARF=j)PN97UB`gcS03LJq5d4BPpMU^I4M6Tu!kNbTX@=
zeZ?(qjwxX}!C6o+Ij0x7L_3B6(km42l(E7_i{M6OFI{eoE3v!xBSz2q?i5EQw-nVR
zqPE&;{!EFR!K_|?5cwDoG9M<T7c1Tvfy)~r1dDSiZ9gUugUu?>XEA6&SB$d(Cx#L`
z50~W_$g@F+?Rmz~NjL2`5H(#k>#ELY0~l-{$R_k>M@K0Yig(Kk_R4(f1#@+eiq-Cb
zv`Dq2Q88o}uq4ptGIhX;1wkV6y!a@xTK{gY8SJ=uuuNA$a!bcDpOPTOL_t5rw18?T
zyHIZdV~`%Xmx*m12&u_VEF2R<0%5DDn2uq~|NYc*-4qW}04qZ5+Q(WpsTD$boUSw9
zEyt|hkC%ND9v_I39xdq;04FN1)6kOS6v{PgGW*QgR3-r$QEUsWPkyoUe^ETULTFib
znXS0&K5TfwH*EqbAaNYmb6+Sw=%KdB*tWMe|4W}J)u15G6-yiPNFgUtLp89$^c}yw
z?O{Ju+L04XY{U(jwD3rU=_yrVI*a>j;9#rPBClCPtu9xrw#5mkV^!Xh+G;eS0L4EV
z*nFxrP0ZJD*0w98Ndq5)TrQ(_7^Yx_mOa+KX$<0FERT_uiJ-@bjjsobPR;G2u9jOJ
zUI|QNYlnPjR@GIXOXvatd1OSr0K;E$pt2||pvF8uC+@~2Rh$^A5|SKLPa1D<{A<`Q
zdrVGo+-kl!^E$fGq8*<d_(BD4m22r_v}mE++kU~xd=p0BKB&%%;3(r6tXAwaIf!2Q
zJ>`>FUi1zVqq$}@VmUS7)--VImV6TyIt2<>`*@K99)n%*%#j9_!!Q36WR#r`;O23o
zKAjGPZ5Wp<FE^+pl@#(a1*1oKMfy_pL4?#{Xu`s`?--hI1J{n%BHHoqGX#ZFKqU)A
zm_bq>T?lD`t?|XL{X5DC>UWi6NX22fCoCemhUTr>GAN^shPnU7$LXY(zH9%pNeh@a
zDuuSrMgw_$TpcuBV{f0PICnwP;Er<Ug!AP|p7FH6$Q!T1wmKH9LFDYQ8#H%eu>r~$
z@Lb%OJWTC8E0l|*HP>pT0)tNZ7#_=@2Sy>+F{kItNcfoB*KnC|Z|Azk?uGq<A<sY3
z7z#|gp#1~C)CmQWL9pMqUx-w2pJ&Oi0?kG|H?l=~+=ZIBOGJ$NnfM0P<UNa}8d7o_
zN?l`456<mt@yhJTeUI7~SyR&kYAx%@PSCkJX*w^hO+Ns81Hu1SV8mo(@`ixiAakeN
zAFd5oFhoSy{i*xbd<TWwOgP4}$kHi8-AjJ4+Uv#n+#Rc35~8Poaob#Y6Dd>PZ|}_D
z*g+7pkL>;MZ#K8O=lQx@{7?h#J(i%x8*^$L(>MU%1Sb$EU%2ClCT94h6=!CJQGU4J
zIq>dS=^Jj@OkWq1vMHz(no)b>`?1(36!&Lh;{T9zj^T0jUl(rE*tTt(jWe;0#<tzY
z=EQ2;G`5q*jcqly?e{$Y_e(w`nQJncIs5$fUTfd0sE>Vf^O2+Kq1w4V(7)w~Ypw!X
z`fca+_15U81CNy1f$<0-GzfcE$ydDsABroE&__LD7MWm6Z|(G*Om7RuO6AYIJG@US
z@7cd!D{+NLosZn(m*Q1!??Tqt#(!%het<6c;?h3It1`c$@Z`Lig=)HGoaAhh$!FoJ
zwp}r8R}2+BK)AlA@fkeX!g9jIb{HIeq+56;ru4*L$95)Y7s!nB4J9`QMo=NZ=EKe+
zX+l>!H@=Zv-cmw<Xu2ZFBn!OTu9Rr?hAzVo1Y|V5eQ!SEKIt2j60B2m`;(gHUov4w
zZ5CKD{S2FC>hwzV@XJBT`Vc{%{lf0YB|gmGn|v4eJyjSznsmL0$Y5XgWpg%)8KWpG
z<VdqBpO%y39fxj}Mu*mqNZGr=_(GteV6*~C<g=M#dKCHW`)GF6D;J~ApM>P{(N2<@
zwU5sPTLQR<Igiljv8lp0p?QVJ+2%98#D77%ihenJ?<m?w9})eK;tvLSJH?J1M?&Gv
z!8NafrU}rTJILLgkELs;EY6jIz?(m~NSrz~=Bp;CB0L=3c*B`Z|7p>u*}L66ktd6U
zRYtrhfp@0FCgm}l=A9j@Jfxfu+WJpr5B$gJO!u~JGRt*rnO1sDxt%1_yWJTVKZt~m
zGVtVY^*<yE3I`O;mSv-T5vC75>r}@onjC%_1Oz|da{^xa_<n~$`wbg|T@<Z=uYFbI
zA>XWPq%7FM39o0Sn-&{c79(X}o}`{_F0gS{w4S#1^~|XI0Aoz)1VgMPVD00~by<qh
zeH~tj$D{lVRGGeWAnTMaw=#RLav!E)hq=n->3MF{&wSgP*`unKu)?*~GuSBi9bQR8
z5oJ{lZZ;y&e@A3S;rX>X@0q4$L`o=#?@sfC97kaB6R#G3&tj<|#7}~Ur}aIN(u!zs
zCAo-om$bn7w9=Oe%y{RyyuCDwt{~NW0EtQ){j~9{)H-dnt@;3+q%S?ChHRAM_oG@~
zP)YQq_5Jd5VmerHW~cqc(J9|Qw9zTr>`~=nV8uHQXa8|<F6WRb*qCeS9}mt)`khm>
z!wd}vo|4wYWi*G8#fbGkq{xo9v6D0Jw$0iJd0CG0%NK^t9oY+REgv2oBp$%fNR~PU
zyj@1WvUiS-b@n^U`V=DAgl_<^;6wtgA8Oqg>HwT*I_ePJ#AhUqm>-m*k2}rG&d$!U
zj@`GEx}aX(EuO$fX23)gr!ddUr*`nDZa>LiH@3?k;VciP^!|OTj8ls<_}CPhv`t*P
zBQ*@jJbYZMKXD{pZ$$iJ(<TVFQtG97xi!S)K&UkOddmgCPmbjdeqjpA8U_T~P-RqL
zT6w_uIr+vijAq^T;jYg3IoYP1l<RdkKXF$M$<PXWn?(g#-dqG+GCLX?P;!J-3%h6g
zOq<qo{JWED_IjIP@-dbu^y4kPeruygp!3=e-SK^|WLGI-zxww!$Xw?H^SNVI+a-oA
zV1e~N$KVdeAKjMTfr<Z65Bf(}CpUpae|gk!fWa8y+V<Ik5>WYyif*d=-x`Lt|6#K%
z7)c_GqwsW%0=xWTm*ZtdMMTYB{wLC$I|^+em_Qisg_x!qgYa(N7cDlke(HU(7XxgV
zX0OsW>Y-N*&g``gV?OQO%6+9nDkAD^P;PZswsb^B$Y`hB+M!XO8nLt|csZ)6W#uIy
zfd8k(ytn%n11uyS9>CQZ24arrwXY{|?)t!di0tgWjJv82<lkCm+C#9hQyc#KGq>cO
z)<pQ;3tE(Rjpi|YhS9ZFyCnyN`@j$AalbJrPk`#+NtBnE8L`?aLd5}R$q<M^hB;{F
zR&ZiQsc-v16PFg4QjiVv6EEOz<pv3d-XnYyV_`_&`1!?bTowCHr`UinSJXcN+TRnv
zCVEb?Szq;-Z7`2=ud$F<bfzn^k`e@}r2+qyLP-Y>?eY*Wz1;1#q|X((UJulEL%2~k
z6e&e94p8fejA#6F`95rms4Y1B;>Rc%AG#*5u8kyQKqi1gq`DT%@SnsJOF?lsI``Qj
zzBRT>{fqQmPU$Z`rGLNRu?`R|=>vlqayE<b40pYr7M(Qgao72NP|4Yq{)D4+e-Na4
z!3D~qC@ech{YoGaYX!<i(Uwp&1q1Kz3GfHIr0ox<@=#1{>FDl=N_y?O@71NX=H9pl
ziD)GXRh|JbMw3oW&pc>i$!7jOSN1-`_Ce>+r3`^Ytqh^(H*i{fbD_IgYSk{SzQM7-
zh7lTXvS}yO8b>f2r03~l$uB;YtV0L6W-}8LWW?zotry|Bx2^%X7(4@!y@FLP={2@~
z_Scfzj9Vz0U6VK`lQS^_eoLJ_2#qv+D%yXNGAZRE>e3gvH_bV0uFE-$`c%Acm+m&m
zKLvKZLr<ztvhM8PwB<oEA}@HgxrBK;M)ihF%GONCw)E_sD?D5O0jtrBkgqt$UsQBT
ziN3rRw>oaiME4izU$E4naXp<sD?MKKyB4}O6iJPe8|C?BRJM%UW?fv$zTq{@y}pk;
z9MOC!VBG&DB4>vV)a9XuBw`h8(?~&+GmF5CC?FR+t+ptDmdA(;QV+lja*KSUTKbd7
z%`!j9v9;EIWQ5YJjnE7{!;KexybqlY6#PhE(s6AZ*LNyRrBo%C4%W%?SW7fmXzRc2
zm2!~Qe__tb1r7LuOV_`|_em}7DlHmPaM97gOF!<<m3zA}gpD}mIs~eZi7?(yiCw8b
zVdlD^!3rPhOCk)MWL;d%N8(6@YzOS$4R1TV^~dAeno??%k7>~Wp9$mKMyFucVhlkI
zVaa*=En7#-M!vyG<_1+v1mx6!OBk3+$|}>X75tM=bd9UDZQM#k85X})fBsu}U9iQ8
zNDg70P>=%T!^h%-NhgPZ<J`vG@aU5@eaGt@&ua93IP27__i+vW;Di*5a6krs!Ko@N
z`qrkqJ*q^!)9;oO>CzR3L(XIIl!BA{uZ&{$b-7&&I6aE^(|jzkgnR}4D8@8r@%*t-
zR;_(a*!6au+~MvX`QT7>c>&bbR86a5T3+m2`zxNVd#L|9(~Gy=?H@xHB0zzRgMS<~
z^2r4JAUuniulp#QebZ4vwm_!prERtFfMd7Ek0j5_gH^+mhnLDDl6l>abDu%q2)2OK
z|93`{EGa4gG$-|U_RWuIGXcnMES{$tUoxf7^)`Z9{-1vU$#hz6Br~8D{S$){W2HFQ
zfh7sIS>&O&WK8$OMV>&3bf|`H>do|5fa<I9?sgV`Sn40-Ruio(FCT**#iE`E1DP24
zSab6^r>HOXoeQXL$0a{{YJd>C{5NLT4MB{1OqMxAY7RV6Y^O%gP>;23n+tSzUlR#h
z<Qd`79&}^;e<u)=>bXPs_!x{Z(K2MtDa{P?kF4g%Uw!}?-N6mgB4_nzmH8n+kWd*Y
zvM#~<0v7+SwzW4vw^q%`k6_i+?`88-MkL%UbyiRNn3s{+;0t+f?l+E(uRL9F0-SUl
zs;U@uc!qycsT9G1NL2cN5;7A!++r&){rBsu<41r&T~iQ3cI7+M$bvJY4shHeoA3dj
z?RfbdPn}O!IeaT;*KPR@)G#6gDmMSND+SpF2v$D9$p~8e?IY0ddmZ|Fx~5)~gkBSd
z*MH2epTxmUiA^PTc|~?4BuQnT*B`kn582Bir>LohpWO-x8VYR%HD08>d?1+ozD~tD
z)S-36mgCQ@(@ghD%aIrX2GB>gH?s`52RuKa;L-;dCu}bt^t8x)>;h7@&%hCu9b-1q
zQN?|N4BU?n#n}E;baJcVgGtv%zGZUf2xJHBK)rEC5?T^11UK`lX8+vJ76--C+9zhD
z$Nn?eu8^}pJ{Nn^38CUjodXVWpK%5ETpCzMpRVyr)(2^c+-TreOh@eh(b}eCGaOR-
z0~f7L%a3ZI5LE5n0xK-9I=`sqa25BP4bEWBpJ}(&OB#w;@jpYz2}_VRk6EVWU<CDq
z<Wyd?RS(KKwxBOOtDNTYh!XXkv1cRO=g#11;1LM#4q9e9f1KM?xjDvinin$Wr`@*B
zbPlMcr~#kGpo05r@EYeguC;H@H6ziD0%%vdyE`sbZrKkjT8{xA3hyhuEGo58uS3Nm
z6l3H`jQI{)+6X*HR9^smv?zW-V?i2n3sHq?ouA)ce*gP8%)J<xN<t?bg<tCi)9wt=
z3f(3-mjm!oEznA%htge+56QMHSY;^lz5Ps)NJGtf%VJeWLQxyGnYDbI;bs!{zU8>?
zVGxE?Z3g6eCJSG1itOq?@k+ny82%QCWva|4lyr$N(Mca%N*zZF48!w8*II$p0fMo5
z8UaA;?>rKs_B?O@sakB+pT+xbN3>99D$2yJ8<+<Sr5P^x+Sk+eMgUzJ6veiSTpb^Q
z+hR1b_v3^$!90kSF`o%$)GknvU$BmoViXaSO`5XizG0n2wwnM(_k0FGs5&+^214X@
z#Pi<7*s>s5$p;FM*eWnYescCKrMQ5JE6!lVNw2`HWf~CR(L4-iQ%Q31a0tSf<uVj@
zHN(Ve!O&a(%(JNX`Y)K^_L&Tnw6FL_HK7QPXQ8R3t4)%S3Rv85bt#z`L-z0YlSfh_
z$+9TXG$~%*16*>z?^xXj2{QCHrI)49`rNa+>&8??Tj~jVn#2X5)~_79SUcy?f@&MK
zfo&43&AsS@IP%c{PHE?I6S}f0Ec=P^Rh1~5AAUn(ay<-|@s|^K=BeDPfa&Nns}_s1
zO;gVe&4KsZHWOi`Q-jn<yiv51?^qpYU&3T{eCDi<#oxMh>swP7=a@XM|M@4DXt=rC
z`<=Ocwq(d?(+n8pc9vecQ`p%73i*c3dq{WJWizjiU@(OcBm_eAO^Ri!P|L91c%IX5
zuQ(k~<WEXi>COkVhY(fQ=`N)%244+&w1lf%==99llc$wl<~(Zhl)$<BZdZ&|E@(1#
zrZ;wbe5pZt9h(8+YM~rJ*K0jwuh|Cx3R!L{kBqkEui)%5SQ6~aZ(QD@^)HO}1Z)HQ
zuX^d?uoQO#lew|VM^ZMZxC`BxJvK}Sa{y$$#X^oWqWgl!Hc;_`O+zt&$#tLG@fuw{
zM)Oh>&(m3P;LyxJ>^L`GLtao{hTq}6@TiqLG$OPLvy+fS+2OZU{KaMLES}q0tb&Tz
zLVPbD7a2Q{{`|LI-(1l)HhPj`CZA#UPOr$yQ;5!a$tF*_jL1YWl;O@Cnc;{;0U1L!
zH@)?RWx-p%u(U%79&MtIFjV*-1q7ReNl?e<YG!L>{Y6er>i#mQxt}28ek<2uYa;}R
zWxIRMG1h3L1aV1^^M!v+1n8h~tTGF*_0)q!lqE_Wuc%Z8Blphw8U#s^Q%<>qNs`RX
zA52^ak>WXdWTp%qUuoKUd@iY7e$~&%I&PK0(N9<-q5%CCLa<wkqF?koE4zEyhtTy&
zdUC8RZ_Dq1U&0?1-<W_~#{;%wBQv@MT2sSP1h5x9mb|AHqQl9*kixB$qQoZiMOP*5
zV{74pZAbC)A?^*(?l2dWwVJYSTNm_-IAadWwIy#a9f7{-=SmbnJ7KO~$RnD!m&^LC
z0i1tE(E_1AgDc4EHz+R}fokUB{0?+l13mb_H#p8A&C9=k{YRIEV|(xvoO0ou@1MdN
zEj4W~d8S5aBdvL+TGd?22v&a_5eJZHl3pYEHfi4Z_n0|FL#yM_9W!2Gu{Fa4Sr^v>
zgE-okmc%1W0$g|^OOJG_GTepO-JCaA6KP6YYc$7zg<NihWS9jJONQh{TRb<_uhunI
zFBps2^S@)=oEam`$yi%5<Kygu-{mq2JL0<8pS=yFF5x@&YVKU3aguLt$g6)}w7<=i
zIoCNsQc;!-r@PY}4*IV+hf}uSAoBg~*tpORTx+@Buur1hio{V8WM?NGWtX>*3PTDX
z_=z*MLVLAB^2);J{Ek_gm(#DA8Gf`6sMz~H;n5<k6aD(Ju9GCC${rxKzOzvVK!Pro
zHMWvUWIGJ&cv!*W*3$KR((3xI<>va<LN-GwDI57H)0{0G?J~U=Y8iL^oVD1>JGZln
zFci=2bzcSr|GpJt%x)Sn8>2NryoEqx@uVm6K*+afJEdAs)ZciQOCpjh!Z$Q4UHY_u
zLDS;ypM&7IzFS<KZEn&Qv!fegEI$?hIPJ--%Gl<&cgprE^n9e9xeTl*U*539-J;gp
zH=A9nTT?;in*JD$G%f~OS-|2LaF#;z^xrY>?HV8Ums0AbKg`eqZ|eS%8PM*&Qc_JW
z-w5XNarXs&7`-V}80W;fv%>exM5Rp<ZapQtzQ$Jj|2UJ*07E33Q5yHMa9UjXg|p=F
z1$D#ly|g5j;5mcq01GNdSRqZR@U`$s6HEnDBaq(X<c~1v+fwlxP-PfR{<mE%O$y>D
zpxuJ0HYi@li!uDyRP23z1a;g<u7>fV)E-%9b?e$0m_mxsGTog@P?H{`7o24`(5f@a
z4F~Og8$@+FU7!aSijA+gB7Wt;My_9%KitQyzqd^vZ$E7p`A17QwdSbw%{U~8Yz$(X
z5dtx8jhQ1xl_M#L-b60kaD`&RggqId<^@QzZ2yzlEXH%>R2~=%hztbJ_-f~fk_INd
z8wv|VC1b`vLpQK0%OsdltBXo(=0OU*x-BDP2`xgfO`%P$rtxpmWyB3*J5s6U{h+~i
z90%94!NE9T_z4lVQM1DSSAF~Nd$%w)Jh8u9lSDI0aF&ZDtnqvxmEK+rB%o#VY-FmP
zni&9qFBke;pn2gwsYm4XUG64Ej1q;0%PaLSC#dIx8Ihp6?-pK>0d?~8d_3$y!*ETn
z@1~XwQ0R1wl=yrrZU@jbxE!2ncyAtF6``05_rvjngNPS<ei%t{=UP2ERzYV?>=>pk
zY7YTGA53{tj}`DW`|g*35_xDa83hNMu8(&qvgqIagUtL8@o9ds^>qa=`Yn^unH*P=
z6b_0s$w#;Gmw1GXVc403;vW38HlB260_~aJRBn&W0xVB7lLw7q3alGGoU9Pm*vNWF
zs@u!lb_^nLhJN6~`BPD-7#zrC#=uo0O7PkCMF%z}hO>!h*t@&=BvmF~YT6B=#*CRS
z!K|G^wfL|52PFj8+^4kw;x(e_U52!sQ17M!?q=vw!Q|ZHJm`jGVk(254qC*S-(<rr
zD07OW6T<p+lB7S*RH^~t0(rC6cWioyZ^0OUTHzTmB>chcJK9zuw8k)Js|7iwaQLMX
zBZv7Bf)gl`Nn18MX{Y+`LWwi~m{E@wqJ)wX2#X_gR6htTknrf95CsKDR1^Jl3&@SL
zjIFx(Nq`zo*JPQ`6l!jpL`$Whmc&bxQ>5kg6*h_2{B8mI?f(1l6Td@G56eEu#0+Ke
zBJt0LkrS7SM28LFq0(?owuOxnI`G9<vU>fX3`%DilNwLIU<4mB=WJ4QV(UY}?^Azg
zVt8e>+q!y=$C2!YdhhHTivP09?0{(_uHcbZ*_Xv&8;V(VqzI||WCrXo8*y*N9SjWf
zwXXns4JN~Tgapy8SQ4%1D!%>RL00ioJBPx>Tv{5Qun{sV31E+uWj;_;n7xqJZ)+PN
zje+ZftaP2RwW%9RwzTB?=wJKMh~e3b8(fUlWx6Af&`)QKn=FNw!78(gPqcUj`R$Jf
z5Nt{qJ#3TsZjo1Ds^(!&pBoIgKlQVwYU$dMtBO@j9%kv_F@i)xh^4fACUU&-5XomK
zN#rJ*YZ(;?OB*tU7E*ONOJpCR!cCU@7T`mFe$$bm`jz(D5!h#&LPbZ<MyV2{0zaxr
z=`5R6RCtQD3TyW^ZN1}rKfa(XE0&2SjTcv_vU)~Imyha|8Y*yFio1XT?W`E1>m3;L
zxp*&*cGaz6!buRJlFFI$)HT&uUQxHL%YU;qMVihsL{z>TC&?VTHJEVoBvY0yOmT)z
z1s5e2I$ZbGGnN3_ZjoQT?G0EX!2bW~7zOGO+?m6l?xzQl{r$7b=?jFe*af4#wWADw
zjHp($-tV*sY-X=cJMHbNxlLrD{Ym!;xP<S>Y@ABV8*}SqST|aZiu4YpNN0#<HAOiX
z@rCA5e^i)tbs?9(&rv=V@SP=_v89f2L3>Iu!$MYF*MvwWAOkr}Qek2$wdLSSc-THw
zr>sTpfUh)1s70Syc)I%8K6u^BYfto1)b?2u#5UBVMRA;qMr(WFnhF#ExgncA_vvrj
zc^vX^Sbx?^qTw~^E<t^8iuc@-t!PR~n4!on%KNGR`=J2I>GSI5b9wdUEr#pZxaRV^
zI>XXCeXi+?U|7R_T=%DRvd=07-^QK0?(<MyY7Oo;gf&kwibAVh8gEvMsQVYyv<o82
zPr#>z+SmW~`6J=rW)w7GsuR;c8|6N2nt}qCY@=D%J7`>#U_+Dct1!=V4%~Ub4X&2s
zoi($cop82%EMLdORiF`bY8Q3RKRy{LIR{(^h9x0qM1}=k5Jml3JGVX`F)*&W#8OQ8
z&<$WlX^C6?yGMTg1q=?)eDEz^Br18O`7vh(%;teI1k50X-nEooDfT<9?X0f~$D09l
zM$*J%vh(aFrY_xZMjA;C1Y`X*vlxXiTp)1uCH?iSAn}FtL`pi{cMtXcw}?_`#|>hF
zr+wTFxp!;9y?2RE>ZZXv^P+FGpL>Bc&k-Q*sh<LYZ+(&-@GcK~w9$Z+SrM955tc=$
z<_bF|<SGWA(XE7XNZ7s8f8G-?)RqTr7ouRe>X&9&e(-p|wpd#%NppVCHniL)19$4a
z?%|kv5tfS2MAGpjG}f^(Xgugs&Ec)Sr0p<meZQn@4@7vH(=oQks3&oPmi4V?t?$be
z(&)hYjCvTi;=Q60-2^cO&z5oA3978Xk>g`U1G~E7x|b){%%v(!#I10hnqWOh4)6gr
zVOl)KS=)OYH9gN!kMO}+)7dTd-Vrru;(l=kBf^0@#ue+Oo4NkfafQ}Bd=+C;;CNpD
zF6X%ZZxBY#?~SGVZ@(SZVl!wv+b*U6*A#JN#G0s#%8-plI3*RhKr?qQ5}i<MTW7X?
zKdux2W#9ERk}po=h&0@K;B1_^bK$$m{18JMCIc}jdlzzsv|#mk))9tKfF~M!-xbT%
zl;2pOdi{9KP|DXf^^fPh@1&yAQ+xAN<<j0pBafxqFX|wVZ>0VJM;WFfkVeY$*=enh
zwWM|0d@5d9cN-^La0R(<P?q3}`fuUTr06p%!pUA|rUuQTGO{=h!9R7^f2BqzhF^GP
zYjXq^d2l5vn7M%ep#I{Z2av&W!ubLjoZdrf;!`DCR`FjAHPqQ@ya@Qq!9r~5QzezZ
zy9eozjXng2&n0`X?ohfpx>~00ufI81=U)H>QXxe4dZn+}{!#)@p^ye%EH+1_2&`Ys
z$1T7gov}e@<gX$-=_^cM!v>`@a(Q)0Vp2;Oi&YcE{2drn$LqG5y?}mdl^T{A`EzF<
z)B4cb?eAPjo4*LRq<`@bi;!?}LL>t5qOr5;$b$fIH|wVMc?SY_TGN<G_Wx&nKyq{Y
z>bJLwVhVL|FL`k0QQXY!<mJ6%VRukq-Z_Y|$Mb^6TIx~OslTQ}Lt3+<%TLZ~zDVdu
zh+<9s$0`;*K#TB(G?%d>uP`1d>Y0*jm(Yo*hF`iiJQ#<%piQ3O9C}j&kmQv`!&&1z
zht&3hd-eZ_@@*DL+Qtfl*eqI(8XhY1((%Q!OK!I#1{A{`Fr7=L|7hS#+Xhh@oeJn~
zlC4NoNt=O&i^q|;p}#0D5_swE*eHm^v3>2SJEUO?<{ebQ{{jh;@2RUzA(z1bqiU<7
z71KcnQ(+lrqEgeD(<q@u&R}XC7_~L`e$u0hT2R)rjCVaoAs6nblWp%LNfY@|PF=HS
zALN!yx=bmb#rs<<oqHL6lV-w)VrDXxY6@ChEZt!`ih0k1gg);EkIfqUXK_4kS5iU6
zD5;L=U?7&(yj9C2xiYOW(j5*8vMKsZMLZ@pzOuM~&zuBjVRXNBT0!Hb%Df<F!!4~I
zjrRFRgo9ret37#$7(yDLfGYY4@x-ab`i{sN7lw#u-+{(E7wI|Rtogsf!%zv%DOZsW
zLp1e1pwYrF5Km(Eu-2)gSsD<kbsnH<@kG=km%$y<ls6Ot!Lt;<j3rELAlOwa^09Zh
zRZXp6KA)@$12VW}2>~tLku+M|!l95`QV8mjE^w#@rK&jD%{hH0E^XzgOr=*6A9Ydj
z6U{|WEy8ooM9$0a>(ax%7cU_ahE<iZvraaHdoxSed=PNpG({B6Om3?JmVshZqxy>&
zkv0FD%?I&xmQRo(c~|>q0OvVf+V_!O7Ss~7?#|m%@8c@|*iu6Hl>-^$FcG7`U{d%)
zN&{e^RJ?EUz(3l<54a&{bzo?=2o#~j2Yng_e82*4J|k3P<QoqDGTBtwjLhFaC%G~M
zZ@_3jQ)5tz83L%%20@&=86(RE7Tn>Xs7W__YM2c}Pb1bqS9h%!9oV}m_zc|kw*RV|
zb$ex-5?O+BnJWOQXZ$VF%hC7foD)D;#1L=33>G85N*N8}>GNqB2HMK(>g*nLpR}+7
z_wIPIhaThoJL3df*?ki2m*MYY!l%-SFch(B3l5Gm`WI6xhu5xwM^LXx(wKu1#$!Km
zt`|NY@rUx#cjk?J!t&mqU@A6NC?nO@f?|!F0GBc?SO}0drb)>UrLA(L@$gMsE(bOE
z_52%(Tim@<9BltEbUy+Hf~xNBh&gmbeXlosjv;EV>*C~=+(yg5m-X)h47PTRJa}&6
z)CaaQRLiTTyy0wNj9lJ66%!OpDI<BYs_@&iTi2^Rk$sShp0qqsD3qzQ#vu#eWRC4@
z**r4eRD@J;>wRp4TQSrGZ;ClM7X=!4+W)KgHfrY72fqtt{`Q&p)JYVdvMtl1570Sh
z7nl+2=rFy2qt1oShr=Z^E!H~P6kY2_pIxF?BobW)U_LijSJ!*FViZ#uquwmUSG&AF
z6^;?v|9gUw3su+#BRFnS681|t_dYAFYB%kdcRS?<u>4%dcY0aj7yDYNLMeCicgqbo
zl>acCZ<vd+c2^nY<#|toQBTbllP=Yu2;A}Z+^7<DJ0Cr2C3iJ4nX@xktWjm4o6n{}
zjcDSqseLfOlDD;VL`P_O;oaIeZEjlWs<gSyyOqOJb+H_`qwAa0sRF)yeh@bE=^Df_
z6z;i0(Sn6W8=6#feVd_QWUfr=htp+<GLMgJM6Pmly&1u8Dx}l$cQDi&s>9lRooD&S
z>m70>g!=TFCQDlM?>dyKAyr;JO{cAO7yusmRv#tu%QCD~eooskDpK}9L#J<qXs)Wd
z+VYKt!EgSrFa3Y&m-Np?6di+$1j={|wDRIX6=o=)<KO`tUl}+1H@9>yX{M%ig3n4;
zGvQJ4f2ZYq+>$10HU#T_CO5#<e=lG*hC@JYnHkVTPOZ6Nch1UO|2z9xURJ<??JqPC
zOHMnF@8Wq(8SPvYTrOy%nd2~%4=55>`wyUPAVS(~q_w`4S3aYUbQpb`u{Y^nhE<q?
ziW@E1?W+ko{BN)LxVg8fSn^)Vd;;l;d!L5h?_n2PHVD#my>7JU!ju;wpY*Klifin$
zEO2Y)&XgYn1#>Wn&R8M8xK9@1NW1Msz*T>>U~dZg&I+1RMYH5nDF~&+dv8DXaVt!B
zz(g;lgN>+1G_nPQD;{3JcHscee83Kus-mh94-)VoeMLZFLeQ?0Pj5WzUyQ7W4mOLW
zJvoiKP3{GzWou-j3z1dHnXohr7c!w(GRE;UQ5*m`;)}k4<meihQi%k+Uk8UO+xYqX
zJ+XAb8tlY|`#j7J!6l0^G4?+3W=s}3sDfpuBLSCXSSMrhY;`mp?TA*Q2WSzz#~b$f
zRMAUyW28FkisS=H!m3MFTPU-?F054Vlg(p>BkGtz++LsX7@XAI4>vj^P?P2mYs{R1
z`nqK@OkR~s%7J$F=o273GXZpYUw=-mw9}A};~q+*5p)U<CDE(mH$8ujBQA-wSgyf|
zDe#ob?IV?iO%9>Z6i)jL?JSQ=v!t6`L>Ej+HX5c<qnl`fH>|AezbapDcuAX(d>v20
z{uM!CoF1(Rh;)R`b#Y1wE<as+6=#*@atDuV&WR?S%(y2Dt6*P51%MP}MSzH(ZiRG7
zz>i=VH567g;#h;mt%K5>{!m&|R8oZSxI#5yk_vO;wK9;DS=_@P%()vOB5sUg8WSJH
zKor&Xy;MJm(b&2ss#>U*(S%Q18g3v+B$$d54kl0uMCJ@uP<ioM*|P|Y47%63EOGXf
zoFhSo_@&(%w-chaBjp%rv1Y-iJu33ta{ogYD7H+JxfZ9g;goVZ2u(7>OR!lX*7CoR
zt9;=-W$?9H39l?+>(hbx+p(g%1gV3x%0k6;@b8tv>$l01@E@2-zct9m0fHKm{?R{c
z93?*9nSdf_CNbC`LmAgfg{k-iUA99g$hU}}Bz0cyv9c6tYgWKP&&bY%6+8=}%dnzn
zfU2BDkCGR;do(JJZfaYsU|T=>I!sr<n%_8WJcR^Y6ng|G@?-PP{#o}HX=2M1hv7>P
zpjoaAGI*2cobL|h@mg-QU=qQHCOGP1tkhyBL6}kE%nF%L;@udi$mH9+-cE;nq{U<7
z9APTo;?k-S3Pt-zVv&kc)5mIR*NU|7Km}%)^UL}d$`#K`aVgT&!u@CGt=ze`YUP5j
z;Supc!-#q(L~UoHiu&}CO;`|zZV;)Cj%<MyKiH;Lj%Nts4&EZRUdTof%jKAoctz<3
z_I+ShYa<Fn90b0(HY(uuFU1YIxaAfwNK~2g&EePBg`VyDWLa1hao|c&f{4q~OLr|Q
zn7L~Wq9c#kI~~4%MZKla)e~CK(p4vb0#bo(3kBp&m1^y6mHc}Gc-HD2bu7+T<5bZb
zhXi>tj7=LAjA?PE&JYjX#kXnmXYp&A)*wus!l(1rC%%6}t!-K>&>vU3Y|r_uD!WZf
zL;OIAIebtz1HZa(%im)qI%AJ=-%%ops>VnM0Ad!A0J;7e`{yDOvY-QCv(_2>pUpb{
z&#_N90tqvka1bou-Grh(h0CoJoGd<v0g@PAXU2^BHJEj^8+Nc&u-Ro^<ayPWwzr@H
zSll)W^X_?7c;R3R7`Jm4vif!UmuJ+#mHOqsf62-70U5=)TP6qo+=WP8e0R}(>Sy11
zngS#epak{&e`Na81pQ8K(1A+@QW6FCRMe>m_f!jls^QIcvvzZivcu_IaRKK^)kBqY
zgHv_^^Oj7w#~R?<JrFw}65PAl9%E3iIF?>W!RyOnkh|T%Wuh8gXU?G|*VZMB@+if$
zBS5r6eCCzivWX6L$tV;1L4%*{Rv6J35YLmE23+<YxKoG_MX1@o7eV1iSet?YNtB~4
z9gRH;q~8)K!Gu|?pu-R{jmg4&pAPosKR(?<<BHMq4k+IXOi}JEN#!vV=a0v*q8|*Z
zAAHCz{A(oY*Sjat+Q~u{mW2V=MBtyZ4bPU1HzGTg!Npmix)nC~{dI?Jy!0-(f3OZq
zd#t%5Fq25%YOGwMNxwF<82ljD-H#sBzhT+7c!+ngG}}T%(r1iI4amrJJtt-wj1Qt3
zRX>HGdZ8V^Bp1<r+bpP2W?zI<f8Ig+ghSiFSf~7ojrD?w)AY^<S{VA~<Q^N8yQ6=1
zVO;LZ^MG+)zf{*BUKtq7hNtU2_GDCOm-lS}z@q#%9)2ZkzhVlgdF>V*&PHThkxqQ@
z-jkyQ{Bx!ZuiqcIKLi?XYcwJ$28@21<Q1G}OaHvOL!9J(m(zR}+3nl^NCTtFhxM?Y
zb&8GiMQd68iL)}Ig1QSD@@W={nnT)2FSpHt1S#S&H@mtLFi|;YZdnbK4MUHfA(!V6
ze;hKfu<MMy1en_=>y2Y~+0VwCaQpg4H6cM{27lVDyJS=lK!n>4@j$&^>t!4w;EGe4
zn~FE4GHM?6bA86@YJR5<Y`e#YI&<mI+dI0(%dN~Uwn+hWhx7{;=fdv(?v8go+&>!F
z7#^|7p`iwKh^;06-~;QPO}p6c*t@y!6lB}J4%1&&9%;31=xv)E@P9n+8VzVM>w5dy
z9&0$<X+2(4e^}&N*!;9e<J+ISI$L%mjM}X$mK<lkIk^F-O$YcNXY+x8g;-YRw?{^r
z&4G9AJ0{hrWx_d4o3|t2lmYBi-5pnYf@*xDlS+YC$|?a5!G(4u73@ZtUU8xCh#!69
zn+HcDc<<M}lkte6_g|RiObJff40=?!>(429UPfQ@nBQ;E$o%VgKc;3#0DUI#=CJxQ
zr*ZKKbOQmrcwOc)lYh%Ad~wh9uWP$<Fu!NfpTFKb*U;L;S1WanDP`e2^6&)07<tRL
zx*JyH97JBjS*&%goufdTA~xCH?2gjVfejd?XD^^`+dpTCqu12W7j6=x!aV6tF|>gR
zpa>T&o@Ii|p76_?dDt@YS7?Df4cd8xv7GFFhTV&_1&cJ`h`lRE1I#A9pu#6KbN4&C
z=5_(S#pU*taf?*UdSImzY3-$m^+hsm)`(ZETi|Eo^wwbbC~YP0)!eK9q?%roY+;M#
zCKz)mPO??S@7v0)A}~*I##O5TNC4$yND7QW0sZ50qu}4dRTs)Rj5}!^`WMWj!>=4h
zyo1vmvxIyCHyN^@6=q{r7Z=Nvz}|bd2ecX;WOP}!QVx}#Psc3Tlk<hMYrN+EjS6Kx
ztaTg;9N3O_-`Ox3ga?wMjof5r!IgK&&5m}LGij5`WjMftr*SoHgi~~Xm@J!GbWM!u
zzdNhS{xGK-F?R$fA@f-`w{C3xjRZ}I1TxZ0^M3)Vc&h_x5KS(h7-1=}-I7{~cPsuX
zmb>T7qpQ~`^n!g`_|ilH$vd&JvLv=<O+9-34#8U`*}84qj=lGLGIDm7lc(KHH&}4M
ztFGU*I+suq2j#gHxp?PX;Z(P&K>zB>FDv?Dof`h;r6VxUwykz$BL2aSo+}VMfw(I8
z+A|1{LWM{Fx4CtNcIfs6J1y(MJzfB|$>@=*y=OM%pk<?5ECJfj@lDA%{5`*1za-n5
zUK2@=C|4N_+b|{1uZHQCc;V;=91bGnLq6e8P?knp(j8s@a>SURoYXP`&Jkt|E4xaX
zfh6MRicFzqGa38(M|AXU{5CZ5;y~tI)g3d2C7jPHVHhG6rhEAa+6QhIv#@$b-?s#0
zZKO0EIGh_cJgEmNYU2$7v2_R5Bl&nlD`9x5Rcb{w&6m#Uz%={t9###$2-n~&QqZ+J
zlliYU=3*lH;|w;$BwWPD)X;J!Fe+^Zf`VfjN>X}k52=Wv?MRcjkxT(+vDLDd?kw^b
z?%>Z^!JkvX+OjHjK(35DxY#bMT+phASc0uNt@#k;+<m8mVD(OWrqm=)3Km4+jZZ~r
zr_rn74!_{%;Kk0)^hrsHJRyCiIw29lo3gb07_-v5;Z{aLg2j+rhKJ3JknSBqmRE*s
zSYF<Syr~z#YKu5sd92Y1GkN0%fE`Kb;6#eShL#`0=A(Ttr*YAc)G0U@95@1op4FvN
zciMF_qLX#XkJzar2PLV*xw*S$M~ig2p4_ggR(?X`MGt~dLg7@=0_0)%GSaRUx1&YW
z(1^Ovz|KhJ$S)ybO28dM$4N612xrP(G}UJ{$iEsU2N8|;q0xH_w_U;GHqzwe=8p+w
zKiWPlD>|)<8`l_$3A{kSw4*<dd#7WfG6lrFu>30nv2SNz@+dc8U)%cOh$iES3&1Yp
zBQBjj93e(_#lC-<oM}ldIb15zAy%-W3&jjd@kmod-MFFJtmlFnD#4JD03~67t=Zv=
zB4=Ou?925(7)B9QBLv~E+2CqgN46q(MsWzj>WfXaRn=-`<pq%RQ<8Jgd!~B{#bkVj
zKZ!f+s>}sAD3Srn&gaX<(T3H3X_j5R!@X#JXXK$pKLr(W;#Hc<`*nh-?qt5$_Es5#
zq8&4}WWrb4yIjha&Hc^_%!P@e{&Tp1jdI@j@C8(@5LQfADsPG-S(KHZ2DM;+h_Rh0
z{tPWBLcm2tk1RF7?x6GABTK++oSfa8<sIos#HJcO08Dg_m+%_xF-%NdY)|Yr8<<dM
zXXKd;>V+}`bs9fyQjjHX&q6r{O#k8ygY|}pO4JWb!KF`%?MS<q0Zu7>H}f>WoTYlr
zpoB``s%2;e@Ch#FmE-}VxQJAExm{OKME0X6N-Ob{s!CH7FukxCu}3Z1I^4*)qW+~@
zyj9;*V1o5DxI6kN5TQaxiPS!_OpXbbo@XZUGW_yFe3DaB1RV8a(Oq_(45x?z8&ar$
zSF;GbDkzC}YetVpyS24vP&S&zP*5}#pI=X?K$O#uXOnFP&E#c0Gnvbz)UWR{+7P`|
z-}i$Xqh5ph;AD<^v_T^c!BOAbv~^&?ChI9#Z7FWxRxEgY9y{3K&vB&!K8MC{40B-a
zT)J#&Ulut7PxkM&URp(W+WtPG@AYZX{toVW>&v9;iw<+x5r)a5sXTGU(#m07*Aiqh
zL5mj@&ML^2-KurqxRR;LNZZUNzo+-;C_5ehc+4JHT7N!gip$RExw79^Qb4<P$pMv7
z=^pTVteS(-Ww>ITUcq9Z;pSW+1(BFbyXa+IJUXgbS1v#@ertA6u6o9lBOX#z+QK2C
zwiwax?vTZ#s$k+NTks#jidVG#0|@qwd)Pcx73hd!9ld_J>>DULM%G`Hs~!pY*nSwf
zWElLKK7)h|=2aR_L0_ydQ^bVpOFz+CsBy4Yt$H3~o-3Psef3E)N**8}pahL1VkAo#
zJMh+Zt@N0+s*Kdm&SJ_jW6WaJG48zaI6A!yLVx28@ZpdDMA<E3mU+ft-=Th$o?E^#
z%d=RYp1#~p^nG9RVuOvgP2C16NVGpoq-~_q*7i@%ADvoLWXBUn2L=^KTYTBp&iBp_
zh;I$T*kSg`qxP7x=l)e?O3fHGjnk&~#R^x){GuWS>i3}8(?2`h07Aw5e-@w?l%~6j
zm7LGfqm|OB*NDo^Ct&vs!<9YF4`{$+;Tpt9IbkBJnMh|DX3{BPljJwe?2@KHHD`rZ
z9<p-Q0R#>oPE&(mmBn`G)A$^bjj*03o=MnbVET2&mS-^J1?scuvn4NN@NAZnG0UmC
z>feXfPK^$77L>x=^#nBn!gM_2>IZ0~;!-}TV9&&4cFaE0=}kkcU>Af8CUINJDX|~P
zyY>q-*<yI7vxkeOhuTS<=${!BWVy-62bKCowe^?ZRkI#2P1Vpm+=c4HiVj@i_QUA~
ze|DcN-Q}IrPtzo|3MVTYmf@(+fr>&8$~;l=$WFw3=kD2}m0Z53)!|l!eFg=w!GWMf
zlcu6gbVa}R-O!<|0u$y5_TN>}jyi4y2_ESmW7tucc3GJxNoIJ)ne9HZ&Vh@n-$^4{
zJLlGL@>`IY{OKn^^b^DWv03HEEx#4#Tf3hWvfZtR7GY<Q5b=iOx`RqxOE2amAcvth
zb)Ku8H2e=Ga_U4<We|rIhQSZLT@#a<=J>~gNDr?D-7LoC=%GaY`PkmN_hlnS%kCAJ
z*j>3jiyTgiU5oSX`p4iijF)4S@1-=CxBXv+l;H<rJ_h_3;aV5;dol~Zjk9g}Z+&*R
z6%>jrrFjsFvre5Rglu^Jq8psxfQv){^99}`vS25{9F>YrH0hsC<`{13ssSRjbh)1^
z0JOcd&x$&z+c-+b3%0fHHD0N&#0=Bdsy*H-TZ{w5R3xM-VwA!|`f%^SOz)4LYeeZc
zow#R`%4oeQVW=~X1BJ8a&T0d|+vpTU(H_7O^7CB%mjIR`<~d0YWGmXp@{IFDYTV|0
z2@e1jllG+}%Wxr(Z$+BWQrv9bNYeP1alG6fptUP;6~}zkTw=6dZ}%>otbT@$RW7kS
z68U^~pf>0refJ`YD6T^p1Q-mn87{h-&ts+?D%FkJJG3|b^F)5d4sk6sHFy<YjrpGt
z#D))h;57;TY^ET0$=da8yZ&~=X89}B>!C48jD2e^-O1)5<|N>Ni_os3*%&n5!886!
zF=g7}NRUcBikP<1A?jN$UCr@_iMPmEwwvHv9U_?vMuPng6q$Lha0R8<K3$*cy7M<2
zahxUF3znqfFhIwT&4B-eW7s|NExk>r;?YWO+8*V<^4d7goHI_m=acyC7CN4ST^Y-)
z$8e^PPByO1D-_&>Ss9D$oK0RtdKm7Bs8{FfD$ukT*J_wem@~xvy#Bdz9QbXf8D6SL
z^thZX3c32%2U{ZUw5+w3mKf!v3{wnk_U?laOuNb^whZHEt1s36oK8;(7g?Cu4jY~9
zVw<=edPI->6zYT=@+@eno(2v)HaV=5*nNv8Vj0Ri9%i%DZG>aX*b!)`X;XwO_HBWh
z2uM#ewkTfL%M@T+s0A&725w)wD$f@G|45U(0sNk&4m>Y*m7bs^%%N%ZV`0N-<M$=X
zaybPDeS>j#=#>6Dd;DaoB22%Jcox)9xOrV-9j)J9v?-epVzAhb4ya*l2tzcm!Cp&>
z;k2?Yo#RsH5JEym=C+-qz9OBX%|bu5?|*ScJxY2W`s7X?Wb;l|>!fD*%5Q{xR~@jt
zmwC(W8fTo#$f&Ms^>7q;3y`rr*<b^fy@6>p@Sg>&-6`XD6Rf?CdN<1Z{kJtnCNgaf
z7?DrTeJ{zcJNMkn&GnP3lOy(#sjobIvMHU_*2VkvwHx`Z^X9IV$yp5&bTpF_aoN9`
ztNX0hgvAqEOk<o;VQ)Z7F+j9~<tOLtx~}ED|HQ}F)y?-|A(s3g$D8;M#q;aev1F7D
z?X}p~rqNiHZGeCol>g$Gt5^~`s3zPrR#*>hecqp)2`*p;a`Z4f696VuubOaVq_vcS
zUrt(m$N=ftY*bbsdy?S{kpqyG<Wf_tV2o?tI4e1y0E~+PIWAk0B1b^04RFwCg&LR_
zFanvBy>4G^RN3oP)U!DlT|EW<8*zkK%ZQ9mQW5Yg!jl18N@u2U2zvZ4Hhs9_;1Wt5
zZdqSV)q)UGt}x2c!t<tXWXDDC`g!sZ)gsguU1J8x@w+Ki<l$}otSjm0X1Jt~IWs?R
zpk4|n8EBFl5n7WC1L;wC3(7Roq!F`VUb$)Z_;XdU%Y|e1<`w%O&Mm9fURREKOh(@{
zxG=V`JK*i;@DKjz`?&LzsXrwiF0xNMVCi<TDKdR%K`kZ%SP#W%jOaxKfVn%|i+|JY
zVVkOL*nVUAv77Cv^AE;+_hj*c<5Z-hV2vUjC)Nuk)(hh7dyne#pqH1~U_ud{aS}Qe
zT^9#uR>Zanr%7tYv?~a?5Lo)8`NV-(e#U&IY*~BC57<5&SO0Fg(s6k2CJ;)k;GSEh
zTR=0WY?j6a2;xVX3KG6M?Y-!q>RYbZI~COYxoM>Nk<E)Rld#ylu|uPG5ojg^I3m>?
za;oJ!zWYFyHRW*w>5p|0S#MMUmPeB!*N<&##=T`%DT6ohoT0BbKr7sN|DAGV+#0ao
z;)=T$fKR$TzQ|_^G*UYUoveawLObNM_b)6MJi`>XIRh6Sx!)$fJE2k({c&dMD3HVK
z2b6N&zlAfONA4g<BLISqyiBqm(Uuo>z%Ye^Y7%ep>S<wvgdTkNE}4YG8rp54$|eyH
z%gqD|^YqH$8Xt(vN<NK_CyFsUvt$zvm?^q+eh0JD(1)M7WxnapDweNViAAgtwPB!!
z!!?!H5+W=%O9$FI-lO7%V1j=`p*}r@1gCR?5>-vwu??rm;*!=<c*bi^JE|tpW7t~T
z9n)EHC1_KU3kT|yGIzsRjZslR2IBeY0uVHyR9nOQ>su{*I(SK%z>i|QoP|#ub3$%H
z1f!}FDoK-RtWvU(nn@-D6mqVW|Lnt^>7W97h>q-~jL)?@Dl>F`dztA3#0s2!rXHQ$
z6cSl{SX=m5r7lWI0+$Q-kOE@R2o{Mcz=(@za_MVm4)9B%Y)ft}W|Z`=lkhK)XjEw_
zbxf^<4enfR-NXgBa){(fL~-M)pb@MKVo&qY=^~JD^)~N-2WLQ!@l^ERI=`y*wx)?Q
z+mrSx%hr80T5m=|$K3}VntwTq)xi4gLEzbwiodVHEaxz6U%DuZQt1L<A}|1uy5CS$
zh)Y_-gK4|>b&(<mulUVkCUFMQ0G_Wi34l@A*Niu0=?Iti)3%dV#k|j$(3^U2fc|~&
zFbl26E8p7Q{qLpidw1b!zzT-AYv{~p$Q65QQ#k@+@r=15O6y)=agOdqPC!ehp&|VS
z`x>+3OPluwiWn?mWo>LveMSD!NKR-EcgAPWE{BrAnvDyJ+5E299n}VV`nc#dYUknM
z1h`Frsmg9jtBoCMta~HPEL`D>v+F)dGr<lhK*t-_wlpz6EPTI~3z2&FyS}obif#Xb
z7j09t0MY`@p+ULZ>@tgRv%toNil0!9Er+a#XJWv&9C)VAM1m_^5|$!BS~fjdA4S^i
z3OwHDF0=nT`%^C%HA#Q+ZzCgolfr<fCt8HlLGEfCBr(g1NDk}Zl%fx$^;eGb8hi)9
zgbZ9u?(KCa+GN+9Yj20>K7H|Kc?adpe;WxOc!+_t_XofGcxM<f*eLPdelv@-of_02
z*-l>0YF2?6n*5gV&k^-~55JY~ujKet>T*(#yttceoe(ByU91UKRC(V!&t&vWmwk%d
zTQF>_*b{*ef-GDqSG~BwjeIPckgpd`Ze6P#lCVFTI9Fy`-Z##c9?0Gs09N{lnNHa7
z7_F?@6LOsG=2Htl;o{5ujm{5Lh}8w{)Ls_;!oS93xM-oP(2T2#M1Pv70Gj#+*S#u)
z?sR&ar@sE=U<-8j;i+t&hAvr3f7NE>{>F0Zj_#5ov3vVlkUD+*nyviCYTUuWqIK4%
zwW=W&-ol8le+yCS$518VnoQ3!yH{PO>s(EfJD)weJ%~A>Lkk4h<MHq&65{WKJpU2P
zy`9;D&7nsZmd?)`Wde+3pgSW-{}xIjP~nV@#Cn{2D#Q*Sw4E$3RdM-D41%KSu%Jc@
zXAx9nm6`4Hz7)C+$A~g;DTWj8xc*?v2PldUqPSH09d*6Wnit9EBa@s3oJDw!S07#P
zn^Q^;o=iZFcjNKvPV&b<uGwkfA49qCYdVge5qaoAuCar}(ihBXHFjNfPHq?7BoLM-
zND~Veo6Nfio#i|Wt&I)tzqpCH8ZOgsb7@90?I0a*&i4bO$%v>KZ5efT_1`X3r#P&R
zTuZJ+o{HK92Tdi2a~OC9?xr6m*Y^e=Z^`@q+vF|p)bsOvL&EonwQla=Na1)C;Jku_
z(Bkh<4Ghydeo%sX*9oGqSH#5TbvD^5L?Pb!(_#c)g&H1+Bj@heaQY?_($_$dBH_R=
z1)CsyxhwaOHshsFq8ow=>#ntq!sd{Nb?P1<0CzMrKN#@rG*y%YfH1|r?^qeWUcXVX
z3jcP5p_;ya+1@IcD8>Xjzn(;lhfH27(BK|IbVKvAoxPj){T{{~O;md>3{WCSM<|#J
zc?X)*&mq?Fz9AK(3Afb69IObsI>fQc$|NB!P8V5AVU~jBnC~gv%1D3|9{3#{!T;U`
z!czV2Mv!gZM6;<NvGz=fiN@3Yni1LX{Xs)z(O{x?!^qB`U~JEDov*@iP!9peV=>0g
zt-~WW2NdydUI0NGm<q)f9v4v)CP_Zw7}GJzKEvuh=e;P5OtPQrue=%TT<JgBiIVfG
zq+9lu0dwu16y#i&n}fSJIliu{b~fVpp=jwh!)~M2$=>HJR^G$bfCcAnSKqmVSJpGa
zB9<4Sd*jKA<n$d94MVz~F~8VniOA(bcR&JPX%kO8)eu%x-FW)PJv`;McW6gciN$bY
zUxH6XEhh;EyZMqi8nqzpjxL{*j+vt|jvrwpt49(0WJ3!LS`z+`N_gJu@hp~IR8i4%
z<Uw+p$uqbU3V7VOfXz4HlX2Y|#O7@?50L4`_e&|@J;4r+B>83}Plpiyanmi4ft%Q2
zD0FGmgOqtZfZq8ZOdX1jYX141@>f%0Nmy329;J2IjurI@RrXlT{IMF-i?*f%`XUNB
zcUEUMC!{7%J8x5o>UDZvrRt?!!~3iCd)!rh=>M(`U(!*;VAAd2(NVXy9-8$Wwn495
zR_GbZo#Q($2PTJrnRUGXp6`E83VfOTgb2#qD;u+xZN@>R9oRmen%4(8u<*bYh7?=?
z*LTJbpW^Qq%j%=8wW^q<EqTrc)4+rO1HjjQS)Gooy#GE90JTIVl1?XKcW)qpdz`2|
z?f|FW7idul)Ir3cbk1>^B(NJTD`V(anIB2w`8L2F9>Hegm0*_cfVgd=+;{I7CFE7t
zjzyGZoBJaq@&c>CvRzZZfEp&%jkEAuAF^@HJXTp;NH*u}Bt!$=X0Dnht{;MnBY}ch
zQkCEBZ3%rz21WDGfDb9|K!d>NH&Kap3}Cn2IQ@jgTt_MsFXV5YzwF*bR#T-jA;PLE
zIO;!C;3bir9vMl!z_TIiAmSud{yg#2NjRjjSm2{#^bVMF{I83gPY7n~kGRSy-7S7>
zsLerlrsH{t)QQl0k!axch@#G(g+dy?cROdJ546fzrDkktpL&%>3ff50{Q$FXlG;St
zTLXXOI2Jr|oU7&g|FLw{K~a8R->)Kqf~0hpq;yDk=hEHXNT-5;v`DvfNq0*(OCv0>
z(%s$f^*8T~e>uwR^4xRIr_Ox>Ca-=&SAF<o*e9vXYf^+d0?BeZ4)XY0>$MYO3!3;C
z*5}m27xP4A!}6)4O^vOC_jDSg!8NV25+0r-g|;Y>gJF?Yo{ngN$+WWD7nDC-x7zI8
z@n6%^NzLim25Vr>jY45nob8Tle^Mb6qy1KPI48y3m$zj?-?pzPQx61Jj+;n&Z}{l(
zo8wJ|ckX#@@+%oRy@l+dj?kLQGH`3JAD>Ub)Enf$WJPW=JYE|q5O_3iO8b-ub<U@f
zm1SfIaQs+bpu)WBgVURRGqLvL-Kkz$;E{5vr`oU}<h3FrNAfS+6M;0!8qOaa-5v)M
zZdJeTGgOXGx5{RBa|uD7PwAtezEUhWj3X=_VOQ|8s}<IU#QH|}PeEkz(o?UJI(=Q+
z(1K!2$<sUnu0GlU)@JAKb=PH|s0sV^YeNW}um)UA39yvgF~U^lL=@pYQ>f;om0ZEj
zt!nO2FjS*7x<$yWdqhwu<z;}z{utxqD|Fa?P}nwt$5rpG*VYd1n27V^;TP)jdbD2n
z1(svJ+d5q}9x~d>mt(cmF0L+&x-B<V4s2S)^d`(Y#ihn!K-SZsqU476V~U!|8Rab8
z`WwAl(U1xpr`_IucgLewcldFyF03tYcogRscTYMu-Z?OF-W;F42Im!!hc^Fq>o>V(
z>&ZJlIKW%4z)7~kE>83tOHT(8rje>(-kI<i^CgD;M;@mu9t7hqfV{3gd~jZyMYJW<
zcVM!gI0&v?coE3*KDBz}XM(t`MA@n;BaggdJWsQ-rA76~Cn!-i<h1hF5@D9onqSMD
z9#ZbtjTxLdM~CX><;~qFH=T^nWfn0SKEil?C|!DbLUO1&TXXKUB6S=Wl3#L;l*_J1
z6xE9~d=*Ku%yLxn3@*+TR!HoHmiJJzHm)v>ovtpTa=t!3WwkxM{=qO>!(RpWxNtil
z(RuZpAZ)sXt+ceHv~=ct-xWIIaJ4`3>%zrDMwc?l)|O-K&5dMD{=DGv7mmqDqM8{#
zb^*Se!os?u4-*OM3EBymVP7T5YTcPC?ysGeUI<h0V^cgA?ouMaOu?9Y*i}kDx`$df
z`Z|9K_Ra2FkW5Lqcs-*NAzBr^ciWh$RJtJ%*6?|PCX`9FpN(?T_$RXrg)tldcaxvY
zgTeuUHH9IS_Ak1XN#~E^9M;kkmD<&|Zp+kXXXUVEQE@bLJX#=8%l2?ItGfGxc>SqX
zrSSKwG^{WqPZkAw>)7F*6ujXd!+jrpY>@Qf9}(85U=?d!alRpFQ<{D^?8dZ%xVwzy
z*p1$l-iJw=a@cZiHmFG!Q%j1}M~wbGCWys(3cS|N?iSy^JW^RIp|Y{1O9p%%_lC@E
z4x3^LA!+L~*VL=5jJ2WGpK@x<%Er?x=rA!;D8s(c)|Z(Q@D}Iw{uK__;~IliWSY2A
zbr%l`a;R?%AFQwa%|^J69~J)4*~{Mj?Gj2O^$7-hi<Vda#J8XK<!l``LE_D0gX9Ha
z@<bEhe|h}y42m{SKV8I4^tzWf-z7+A$(Y@6Dbp%p2(`p5G&uiW@e{%`H3=5ML`o8N
z>Ao^bfid<%#G57f4S}~VSHR+Tw$sQ~H;<^`{O5CyWmVM%IR+j@v${NrdFxJkPmjAs
zx})SI%AfFV{ocjR8*D%=R?p4X^mzD2@;^~VzP0?;KSHVhkO-Ny@mkdVvwHQk9(Ry1
z;=selJ}^He)_Sqaagyw1)<1FZhkgd9<}B_0G0Qh{D;TX9u|0AaSE|X^I8ts)s<JF7
zbO^!t+ZJN{LP_4JZ-UNfwx0EO=GkIyqWafvHWxTEI_Hr`?q!l8lT=tZDX#m{Q=hP$
z<DOQ9?%d;DuHwtS3ypq<tnvtw`g1`$?rM}sZ`yK@K4cOadsk;Uwtc$H{$l$_gWBKU
zJ}iHRg4CZ)s(3OFVy{wGcij3p5i8-y^;?1Bu2tT1^kn;&pUrpkRB`5A)29j%y*7fK
zY5G5zu~%WKuglQg<aV@nwcRi!YRaK0$WPb193MUOmA2lRcqol|FJ(h)PnKVKXz4RM
zZ!Jsej&7<t@~DL8`WRlEjk~E}W2+l&(>MDY?wAu0u<Bac@eE&EB?delwT2Xw^q1V8
zJbXiG<Lek)YEp1mHYkMHLdxr{>h$!u|IlEx)pv>2<G$t%=WJ6bz?aPHVMmQpn=D`^
zv~=a^-m8#j<^OKs%JZP67~Z8k>B66=5zhDl_xk>pt(S{@(XJ`>b;FK5Llf^@Hv4}8
zMM_xDCBTbvnrCVBk4ooF>c5y<|4HmT7bo>=LYTtxlaJmSFkiFJUpv7Jhq`q5;eCZv
zSE(4=*L1zt#L+TfkXUP!{iG|iUmJ!9Ma#J(kPVa$e^cpanBxOe!7DAY$(v@6l#WV^
zOzT;r>3(5N(^rjh`M$}?or)r5H142=pV`QdokH_)%$|)8mkBY^mPxO_`|L$3Q-E$5
zK}hwI#uBM5ZTRW;Q;j8!WyxJm*z^Qyg4rTPS{SI=kKkMh8~&J@dSNemdOfYC8%#iI
zsQovBaQN4+gqZV|eyJLHh4t%v!$x6x>!XJ+rd_W{;cJFZD^fA{dMXI)st@U@1b;Q#
z-A=OI#fGGHebz4N8Enl3udhjZA-Mt`*7gm1?eJnot5RokzW-Wt^X76Say>_Wk8`fF
z22HG>1ig@Hzr00x;U@!5;(Jfd!|tmWMBIPlptxGv49*9$^udq}@1=PfG~En|tXJ<g
zvLnY-FjQc_Y`2>wY3xl?d0FLzesF0`VLwj51JYtwIQ-^$M3K6{OLeVHw&}wz`As_B
zBq^D~=f%)sf|eP}Ln}D);yF@3Wa5g)A-~^^pXJVdw;xsZ`bIQEwyt;AJ507tB76Gx
zS&)DxW{@&lN3u}j+F?AAP4-t)wQdht6C1Zsoza!ceMAon?(6kkiZosIbiep6cN$}3
zJiDY&p>4imTlywDA}AUQN)$^xDCo+OBJpEdX#Rw&w$@Nhvq6F0!J(hFEe}HW`eYLZ
ziauZcS5CTIk%vBw;Q1RS|H~7i@`jpSPWr6zK?{@gOp-qus{5~^*CeRP%eJ*0IRswk
z^CsBD&0Mf0*r;`Nv}@<<*jBY`cV3AFIysuJ?s})pT;vijzA&3))nSSezxPC5dfQGP
z^pP&Nda*9*HL0)fQ7oJxoD79}_eGvTVQZ6WmyeHo(EN>pU~_e){%R}iF$em}Q@o_X
zo>7e6TBVGy$L<C4fy;cZU&B?`y-8*%cVd&9$3yl@GIb2C#4+YpzfE$?${-dLYYqXf
zhLT_Q@i(AM<QOCl7h!)sWuY11`Z^Jjdh-01L!!k_t0f}!lDEGJ!a=+U83sR%uwkyz
z-8R9NTf>TDi7Ta=Pn3?l(U3yhu@Rf}+K&s%)U;HV&3MAbE4cs%!=~VIz)ir~HQswP
zF?7w-Zqs%#1NL{UO+m1|TDWTQr=B&*-@64r0?dVqJ~8OSi|zQB#39rWM98(jFby$f
zTG$bH-u>@u`U}{dNT{-P9X|nTQd2Mgo8gy&4<@m_8x*||KSQYJt1otO5&zl2|Mum=
z=)%by2qRG}X*JU(Zgdfw<Rc&35kktdN!9`#w_0uMtWF%={p0o;X2G`zhSd<p?w&qN
z{eJf*<?8N1=V4-8L>*(j+WGbqGQW_KS<#mQI+Sy285&0UGf&13ME#~-bpu;-Nll*|
z&!jtA)U3(!7u`<IsVbY)m#W}6qRORwNE^l!tai+anzl@!z+D{4p;B3+Qf~~H9H9>{
zMWlsmkH>d1WjF57?j+lXKq2eVhzy@pF=mL5EWSnlc<3&GLY+yfT+Bh2NVwS8)(3v$
zO64CMVl1yj(Z3>ya5&m<<=R%KRFLdA?=}xrJWZOr%wJzZu_dyZvEUo3XlvRe9+%_Y
z2HP0n0=^q3H8DrdSIaa)k2m^5Gc<MH5iG4oQ{*rbh_Mgkl;7H2f38ru<jgX_F9BNq
z!TD^Apd8nZK{NV!CTV4r`pVtWjOWu<O&)}+<1DS>)8#ojvjGubYQ{5G*x&sT^rsg1
z1I^Pa{4pI(C}Yq2ZHCBjZ%sF-03%-xAG7`wvOEMR>UC1UH3q0Xt3$SDk@JX-9fG4R
zj+vXbj_HyDpE1{G_Yt!Ubyxd^TIAZbz-J-vzI!owX~M}CsZpL)XxSQM^_os4+BWei
zURZYU)H^J@b6QM@K|R&?e4anxdMk^qL+z)Ahr9aFA#Q?A1hidiz3)IBB9j(ye$>%B
zpCa<Xkf+(>t`bR9rfp@?1*kvW93(WNyQoQ7_xm4&9-I=h0$i9+Q~92;R^gKPLV0(8
z=7z+_(%*y%wT+JQ+4^3E&gDWX>$}d2lo=)R7DxH^@_yhPwR@#D7-p?RX%^JW^u9-?
zTbY95Hu*UQ2|boFOvA7a|03O0XP|%m@%y3))Jn^zG$0)ejSGjXsy_7BLn|O1ZKTo^
z)ql6LMoy;CEN}kiYM0b$tjpjGQ8HTi;u+)JG|pI1s{f=w=(xHQTDwSke=}+r5d6k6
zRE9Knp-im)e$b=BWo?%JD1f7-teJnv<8By9bWo#RvR!%Wa$hoUd`9i@5bmGAZJ4sz
z8(|vrhxGi|^E;%vRm0@^zu=$o$`viXr#H_7&XY771zHsA7ATOqD1A1$8%pdpY!{nb
z#)=31mwnAs;nxYc_=IEW(rJg@f}hTG?~e-`ZYEwe%>Vhd>h&0V*)4EB-hGlQMSFRi
z0PutvrJ-r5a_-FOWu5nvdZ?Yxc3FASzi(H*tQ9snK=dTcuzUwMtPTHT*Yp)~+Sz~g
zhkn|MOMfg2fBA#R$NgsoHK&#-1Z$Mq;BN{hoEp6>i346uQXz@zL_<Tf##9{}QP2wN
zQ5Rw`_tM_sXubv`egM~2zae72&wYMy-ShCb`C(K@cb`T=nJCk#q^*Duv@sr23Gpi%
z{g;V%?~oDLdfo(G!UYxoPNC@CmQf|<<TB6)7M+j2@q12p()CPkX5wog;jK#X_iy(e
zRAlG}SsA_qeg5RsYB1^%fAoYo?$i(Py9rc>WqnigHlpI$=+E-|WGK08`>z$2pR5ug
zO<&Lhi%;6IRDT{K_J=)xgCYQ#m8MJ49jR&60f)S!dr>q~lCN>Kh;<y-(u&1voxVMK
z!NR<(CkkeJe;@Y|pel}qNA3PE-v*G1W{DjZwJGC&h*tH@Ehm#_RKt2!2U#N^l3#}x
zyn}UX_I!QKza-3HZpeP(OJ2=G55epnPfq=od9&8|+OW>w=jcJsR|sIdf4}JK)lK?_
z!*bQK21PY%oR>s{(TNxe>O0V0($h@7-G?TF-={XQw%nRG`@0mwrPMmn9wrfAh=opA
zzJFu!#xZfv8}pqsKQdJ3Nc#{aiA_ZP^|za!|M8mcVq*=sr8t|o`BSa^LXhkoK&}jP
ziQ7kVPBzt9njd0Fb$veM=V{r1cCx|j?-T_(E-bUKe<JZ>Tnw#0f+YJ-w<bw~O^yEJ
zJTL3iRv~`IX@A|tYr{pY75L*$A&2gVNB_W&B%iIG_Q;YrtdjH}&%3n~HFGh~zO++?
zdG@F6oFFn66tlC%Zw8-H4zQTH`<L!L8@YP%?{QcRucaMj_OiJ}hb!&J(=%1z+-y&I
zC2GpXmoCX2LS!N)vN;R`_E75Gj$NuHrzj17sg`qDb1e1qoLZuhW4=E=?s_JK^3B>p
zjRd#3))$xiy!h^|dWFP98F>#azCd)@Zjq>jIzrj+Ze%}#cCm$T#&o>u6~P6x$tCR%
zkqn|nw7aSbw4&3SZu}T&OfkOX5O#Yz^`d=~m*btr%LmGm)P+J1H;ln1FBCKZcIdHN
z3rp&$U-)W5^A6_l<gl#0b$g)xxLMc`qkh27k!({c5S<8arSj7UllpJW)9LG)Gu>&z
zm_+8o;O<4+xr-)&mQHZ?(;DWI@rJYMRR$#9KU-~dej@M$V|QJt!zUrlW0r&-CScuT
zN`pK0R?5Fd$``eL=;6}A>LUrEF6ZNVg`lNd+lWT?U6&sBw}XJHvRNTUHFa_fZhR7X
zQxetPrucC?@5Pj*^_a)i*JpA!Vi$X8nOAEle!<`FcdB>rf?f>zVT2pLi-?UAuh~#>
zY~)BK5f!f6Jl=wL3<0d;o85kNgb^qvu+<9*GAaIIY-P7us@KjF?vEl^nPCag!_dLJ
z+v7EJ#b58oOlT1Wg0D5>gy75=ZbR5{?wjkKRx#Nl{KM=}{Rv8JpY4^8V(nU%el=ZB
z$38+9*7?$HEBij8OEP|u{iF2(-+x~O4zM(Bs1$QuCE=m`Lpm!;X;#fcH&bHwyUYfn
z>M;dV{yURAxs>>z)GWbpUywBKKLCi0`{>sR^V46k_M0*7u`v|l!AE^&Bjcvu|G;#M
zP^)5D)ftthHQMykSVddU8{EE1rnQ0c&a=SgqvPDDJtTzG95x%v;yb4DM4Xh!t2p*t
zgjI{b%C5GHv=v4r1kb;KSG$#TYB7dld5_FB6ea1_K96B44A0-qJI5<1F{UR7vPdQ8
z8~u4<7CC(NhAw*|^8S4J$um*cV^-UMq2BM&U6S9z1dkvr`HQjmvJq2%?uK}~`6#&D
z@4pcyhuEhzg2Zg+m3<`UbW*<@>Z*%ovEoG|GuqKj$pl@GxtpmY|FOlc*)Id)&ff-a
zMy8)xT82csLN>kr14#AhFzYF~DVQH{)jN%4hVX9-$H_8`7C&uOl;!)+1#P;6{4mt(
zbRrVhPT-F<SB<U?UjweMmZ@SZD;0m6R&0324=Fr`!tapZ$a!tzoYkhc3G`leiD6B@
z@c)n$eR7y)iMK5$c<Jnm4;AZZ!+P8e1&ETJ{=Em<apYdJEI9jbwI?_elx6vadffc@
znE^`td(#q{CxE1{>9ui+P^g4zq<vczi!z!x+;Q8D*5qXw<?|-3@$hjvxr8A0cCazb
ze$T2Tynqhy=_4t1{OCQ^vijp7BREuv-ui5{mlZIV{#%FA5>YneSjG7~)yw)Hk36`(
znOwCxByS?T%9nJ^{pp~KqW+qtL?Y*UG+11T`PqB)A>|kd<mFqc^qkHMGFx}O7rLcD
z6dB7RF|qLe47xrgPtBcGJ^#=K&C_O#&?Zn~^qBwDDb+D$tYmZiQ%F8$QYKUaYu!~}
zLiJs``>|RRrq_z&rme5HTQ>2g3lH@tMx2`$mQ$>l&g`<E4&~5mlxBtMLrF5<og?*<
zWYW6pNbv5?REjTBB!#iEB`-9@FJI&!3@lB*6%~gQyZx2Yy>$^HKizIumBpui>7dr=
zY#9~2@mx1pXRb4~gnqkOmWvps$T?DAnp_~c$TflbPF-bTjy^RRdl(gP51sC8pnPz*
zq|vt+eBR?s$$*Kgi^n$-amSebPW_gKM9$;kjZQ}?^fSZP5)2l-DBsSp3=$J3G6^;Z
z;^sU{UCt?&CO?mi`~-?%NZXzf9S%Eq(rf|~&}(T#b%8~jN^@&7c2)rIIj)M$jvr`I
zt0A@ryhbtoD6ab5ysK)%u9Jd4Ski?<u$Oql(YM1x%66xHLvwU3sS+i~tb$3}Q7}Zw
zzyIgZ@^v_gT=6ffRlbv0R<&l~P76<V4B;)9?n&hJC0KLvh@*vR(!S_`v5dCtfo^5w
zV9Y=tVF$M)&*6aE(Rep7$-R$@HmwWdLJ<>FkEh-5k3#B&<jd6HKP=fa>5I{m(X+az
z6L@TKv7%<26^4%2<~CseVb+5d&PPg5T$ItzIh0icW_X_eGx{w??6(w^9~C4ofhieJ
zQC#nb&PNv~LQCn=6$9bYWpYd_+F``WQ=M4fqFp#u3~16Ws;b7xS8=pc_sDRf5C6@<
z`NR1QY*L1rkr76Q!5%g*>1wF<vO$4M%|_*$eBDCMgsW9uPS(M6$jfXhCtsYTH_0J=
z2lJ>F1+Q3cr`^MkPZ0EFkoVHm0U%n;Trw(EUP=m-Q^~2F5+CVdQIi*g(?I!(8^Y1Q
zx;~eqprAqOI=I_!6dcvyQ@QvL^8*RHOupUir!Y!t{merDyX=SBinB!%aU5=4hdF;W
zj6k)?uIh99oJ9@}wqm@HY~yW=DjHbv9|Ip>&2kQBe$xIErv>EdD2sRmlBJ{2FiCY4
zJkrt0EIEE`?>a&fS5NFaWf!ir5BV-}d{<mr+RR4_W4o!c6vmh_DOv@R;B}AMh=a*t
z<~y+Bb`kW|S1az%-Row%oO9|+HpH{_nEE3op)i?Fw61#Bg1$RxnqPhmD-c=VxfsmQ
z{GRX>w3pHQ2vg&D`${gC(`2l}f9kW3?>|>&>=GheO_g>FJH+L0*nBc1r&i)4P)OqY
zM7Y@0(7EbDetO~e*B|M>5RA6rlVpsgPpa=TqK#89vWps!C7@??iD|W|BndikI!oEh
zPF5U?`dgw=1#;P1TboO6fL(-5EXHc!PunnUCY}Ness;Pys*bgg7;TR)uXM@Eo4ztq
zEJ7n$1Iw!^kU&0AY=M@k>6%S)1qBmiZq=w4Rn;4WiQ;)^b4XJ&nbgZrI5-4Y7Ag$q
znf90>4t`Z&v(6=rqi+Ir?{>Z%Ns`H9MoSu7MM@2d4QN2DoXZW&_^k-D-1K(uY+9dI
z?B=31r_>Buc_af216RIGN5hD4x`XIk^#vdm1VTu3@w=^8HL&{$L%nPbxc<ub$h7k-
z>YD^d{q<=xp}4h=fa})k`v%e1(QL@ZDG3>_*DxnGy7+-nU2kjoxHBW6F(;?T&)t=x
z`a)ibC@RHoWcKD&#|4eh{UDRY7FY312Jvv#aKgZqy%|qb4$`u(8-dtI->L0J!9Buv
zkMkWjpG}IZ_J;NVr|>_3F*~j7vph8QWM6#*zo${n0zAU8eTH{vIe8tv#hrJgV~0BQ
zUYpZoVlU_l`aVhBM(bE`+`x`{elg_rB>l&Rz>K2xYwN`9bGen-InPJ-PTYJ6QT!k5
zn0Y9K3Psn(!ZWsz^WAB`q-MBDop!jODOGahmC8x#FV10U2`OBHwG%<R8J^TPP9s_d
zOeaE*%SuI@=~D3m1=&A_dv0b7TYE;%p8*Ll5+#4)!U5{H{;{#yVDnC>y%)fe!%@cr
zFO+}Zdo$_O_n~YmR(8mj?W;-K$`58PEiL-vmBLT=6;Fp^UBsAU_QOU$nL8Ph-X{|r
znL3dTPJ5Ep6D!!stBPSfhsXHR?V*Nl)KLH#3y4TSDX6a3Hg+rfYHXDk$JHIQL#h5t
z=5HIC!`Y+MRdNO_e3H-Oi~Wv#<c8<k2HjXD!TJX7`%0#V*w3kN16fXgweU3z&e#tB
z6QB!8M-NNRi_~=gaZaI|tj7@e0~#FcU|U2h3{t`9YmOea5ruAU^fz%DF3VVIm@>o{
zR}+TUz&B0-pVW>=j>5QJ-Iq5cTktROwhBEr(83uj68{WoYU?n$>>VQZx&-;Q+-o3p
zo~sD~IdQ$Zic$c+RR%x&schrq<DLPnVEW`y?z39)3`K0?BB_u^K;ZX=oT+@w6-La_
zQo~osq!kZ<2soPI>k*vga6NPDx`82`Fwx?Zan5nKga*Sj3ll~UwZa=D@J~j@99=dR
zPRk#vpRrk|aT}y;=7S%laPI8w{j-c``JgrTSr?>Oq;A&4ffc%7k#ZBv&wW&`$~Z$8
zPZHfamS_6!F`--@br7E|eRgS=EL$Wy7As(m&ZcW&Znd0bZ9l22x$lBm9t9|&$97zV
z1g+h|cKQIG((th25(v-d6}sQC|0j%Hod}d^!D!Ez9}l3#vpRe~22%^z_>=$9>sD9i
zNL=QqSa~g~)!Aq`Ziot>yN5#@v|RG&Y9@`r=SM|?PK3}+DO9FM;X{L%XSB^ZcSHOZ
z+T%G^qGm)(N%Z?Zml1i?<E)1@L$Zv>$=<83H(OHQA*V+VyK=sly_f-ybDB5j5&5A%
z$~q#G43qy(-e4H`ShMLolka6Y4~6Hx3T<!0d?fMq#1;^(3dIsLJ0>d5;qUKf;q+xT
z@^TLn=ar<uqC6G@`ujXhJ1$v%4-2f+-r+Mbw=(R-+5^{aZnw2d3f>y!o&0Hn)7>)S
znVgs4wN<_CLtF{HeAHHQ>h{`5ap!~Il^{k9s@lcLjIL7$e}#_y$rk)B5Qu43^{wS`
zKkRt>{z!*Zv<Y@^JB1X72?B;?wrEot=`Kh^N6k7ctd4EqO`clWcDqU?bUmmr%QXa=
zXA6lbpa)B&2HjUs_Hn>}&if(kZsofC7EZU*&jR-Nl5UoLxV7NF+#g18f$GSmub4$Z
z6<1sJcEud&_$1*a;7NsQHm*#as_Mb2aejKdLS1r6eKI{|{mpYt@<d{q`1nKnE&Nu1
z*G$UB##D@`9tqBx05H6>BVyohd@qgcpsr34xXId~iZR6H%wtrb984CE$$gGrJK4h-
zhda48a9JOclY?ITeUarinxBgWCbPUz32#A3?wfZCDo)*>*^yuAPq3&*CENTAv!q;N
zLjnTRtEd0E2J79x%!J=BXw&q$q-Wq$WmE$xu~r|4CGYE_-j8JBg#R*x1bX)GX^#Ay
zLU%vB*6cr_!zKjnnop0H+r=#L`74P!oCMLO)|R0~(Z_5KJqe^fpzlX+d7gCPHQA-d
zc47~H4Yntw!lFqn$+3~0rg@QCfF6ObLYH68#+D4~sK1n15vY>D$7>K1sg~L<)GVuO
z1WFZ<akaHZj%>y&N&@E$GfjLshKHHuS^i{E#Z`yF5L4^V+7cl-^si5n2Z1dz*x1{9
zMj07n-o)L}n_xQ(Xt~Jo_Je!d=TXrpFfyo6sNvTO^QI@s42cB3_cs)PJ^_t;J{Hd(
zJp`lp0?0X==hM%`g6IJF1J>bSqXdORj_rh>+VtH+8v1KiT`BdoydSX?1v9%_5Wn~a
zLq3VN6@aiT*bVcwY{1AkcCY?a0r&R>fV<qlus{P|CM$ltAQzYZk#k^=SqU`no#DRR
z6IES>#RCIrI+ftx)vhk#zgg7!B-!L6EsAG|fe`?-641PQ6Q0*K2U%N1qL@n;US{nx
zQcpkNIOtwvvgi005CY=}G|o%qmIrgI)Gp?BpUlA%B4&MpLT23eDU~eeMM6slH*uJ1
z|AmR0IUC~<tmOi+ie$5FPEo~He5(y)ol`0x#r4TV!)$Evef3uz$puBv87!)~8f2Vv
z17WU%sQLJrB-^(sW6naJ*97$8=(OQvIMSHTwz|$cJ|ZpCb)5-&!*_!9h4}vH4tJyh
z_({x>Y+OJ7iH-Q%a+B~RvbgAhii}J*x(#>y`)ey4*knoyiBYA{V3%xcX^UP>wA9g%
zP6~LyJOSR@<EE=`1Iefii>hiN|Fn_P>SYd&+dItGyG?6@W)4MqW67_Z|1GFbjVGt<
zZgKl>ND$3gy8B05jAoR@%yKjI*abNTJn--2MNMcpUw!K)@%|&^{nZ5R{VQa}sc!2g
z4qGM@8A9lZRtAiUJ6`g6`&zaQy|K<Jmp~vHS!O-*Ly=y0Wv#uavk<!Ic#=T!shli+
z!VTxr-C-Y}usXtv2bq7R!S`TBGju2Rp027FD%jM&>)liut}v(OGS9OGMLCP|7-M5i
zUE;2y`}&9ECk+-(oaslsIZH}Iz@jwfh7i!?*GYlca5^|6QSkoG>*f?8BwN5;I2`@?
z)HFWv*zv4w;r0FkW-ugouL;V$0lGI(Ik!`*+X$NBA`*rChkXZiRut1tE%E14b2k7K
z6&4~UXZrdEq?&b6r2O#;ZYGqcq}cUPEq`Xl?kpKPl`bG~eQnca`k5YkQZn*HD|*LM
zeBZ+%g-rH5%66h|e)!C0JUqTHLpkHYchfpJ{*>HMfE*#Lu@|_V6&-#dz`TRaKJyW&
zm3yr!6S30C5%eGv0^XU?Q5U}TQh!*1FD@4-*%WEftn32g^)5W~wmPMJzZ^9h{e2Q#
zHvDhOOOQ<JJJ+?MH9sgFmw7;AW#;ih>i1YnY}9yRCltQu{^-@UdU+a-D&<@<R3t(h
z&1d`?wr}Sg%c~mIjM(7<>7sMkjKhDy>`Lbo=+UjnSeSFewNFDGp01M5=zPR(C;dJO
zF1!3^^4i%2a|B7f4-~mGfM-Uji8{9NMitOW&04sM%E%_rWcjxLUX_h?$@dw5Cr&+9
zoHsh4oH}Qax}Jbb19-rpt;<4FzhoNrsQDV&!?K%S;+*Va8r;OWX&@!#Kg74-dU`^r
zWyjLIQvSl~;UdlG=2%`(4ibv~+Uh*UviAWt5HLi9K3~XhE#NhWWZS}CSL}op3B45?
z?1E(0MX_b+v(sVcuHWi$Jr3}7?A?%Aza+W%oxRIdss2KO)@pU-ZtCMvRGCd)^MPo*
zt<AYZ$D?c>k02kr=g-U98v89`C2CR<Zl37=d&n1`vowI8O#DiR{zxa<Z5q9y6jd2V
zjq=VPoR!6B*q}f_A^z^FiTx#~NWY&hb4yjBUz+G|CjTgs*v&UKR_|GLfX`RE=8fAQ
zF3$9EgGt1<2!Nas@IfTtLuZO=5YQG9^FN(k68NJZ@+c;-=};}uPbUMwHf;ts#R|`k
z2WZ~TPNU_A&$EJJR<87w(_R%Y<WGNZ%&L6*{?9!Cif5L-e$KMf{GXCT&+;1+0Z8E<
zK|ywQvC>h_Nm5LQl=tOv?N6Y_JDE7?kO<ueq0!l^7vt=qD4ZKF@RqNs&~a(Cwk=;u
zAfM=G*%W`-x<*mDio=&?<w>MYiSE=iU3AK6bg>Tu5>XR-%lu6GJPSwr$tAu)6Mttz
zz{-8S>}ln<))v>tPRF*fvX(uba_FK-rs&B;EiWA<`z~lX-}=kXJp3=H*>-a2h=&VI
zsn&2h&fnnTk;tC~k-`^MHZY2dckiK3r-i-;7x<5dj;$^~F=H-9UvoQDoIFa^fU~iy
zV~{1gfP$KL9UAadMw$6pFzcH&&Cz+5#JeRqm$&TexAdq}*b*!p-&X;qy*_~Z27#xq
zwObXN%>nHDvP38@x8`+2z^%-jJ;2zc0ZyThdV!$iP%aDKa-0ag{uj0(^q4(vC9D2J
zMjt>-Ab--*@$eQfAuuZr@~-+@&Ppi2*{$_!Uyr@no3&v&WU@QC3phodSvVA500Z^(
za<A}ulMh4WmM5>Vgg!l!;3qTI)@d;7V@trJsRPu(RXutMxG2CO_JH$t_gE!X#g1fO
zJ&@%^PV3Hrmm;*0>Vx|N?SwGcfg1GK@HD}lOax`+jhE!+sO{gLBKcZg3WgRwzWiDT
z4hfytLg(3{BknM2dt;q!>9C0e7cuaJ3OyeZWIkjNN=`*zF1-0~EjO0!DEN&j%rxZB
ze`?;(UI%`)P;s(dEGe&E2)E;0-cFmJP<8ey>j8=gg1)Fr0nIH>fJL$<vl5Zqb&Ro9
zdg{KV3FB~!W5)bk&YB|9!)HlO3amNY`fb9opM>7Ef=}wZdP>hM6;V&4Dl%5mj?!WE
zV!Vvl631^0`TpTONYh}QE`z?<oBt9u!|(5>KDJ->p%kw_CN%MNUOgAQGYPxty)TDF
zq2%9y2g_9O{+0yhqoslXzu9~V5)$CnyTFd1=60=;wY&dF1KNL&s6EAMrW14W3U*0p
zvrdCJ!2jF=WD0sO4YijH4iw$!&=Y53Qgu{hwU_uq_SAtER<tFU2_g)Ep7bH!2;^^}
zSiHp0E(p1-%=ta>AjeeXeftMPyp3tKCsQ<{zwHau7!7y?(kDY3&cJ<xX*zAan<x{F
z0xE?Shd!qB-Z(imny7tJRYoQWFyFHb^z#fn+~p-M?mq*8>y4P#Chi$<qbkdm-lIcg
zb)x$hB!hwVL5scDs2@)yiUcw<0P^K9C-EGw=Y>jTBYmlhs8})1%&O2K%q@PsrHJMX
zERuG;=VC_&&zmZaZ0}qZlrAT%ctKXASS^juTTli+pBE>bGf_j<jQs@bJvJXX3Yv+9
z&1c{url;-}9(^v!T^d)BBBIWV2Lw&afDTg3)siS?liDS07`QViI5vtBtGJLHvtv#x
zj;$6aFIkTQ#wmIJKZ5UW*DoOSbJ+<b1Bew=qrWT1gWebZoHx~Aj>>{OXX}#-fBy};
z7+_kg<4M2kqbU6<_^xh>jyU;`9^A1-r(}K}ZW`OC@=|u=Ly&!RCA{N3j~@lc_^84H
zyLG<EO_XIb5VYguFUYQ6x`nrj1RZ=%c7S@Y8QUk3l1lL{c)>~UT7rdD-f`$lOsV?{
zks-ZJYP@R|MH2adWop6!d}K-xvhs<Rx;o3KHy=-mIO_^l0XjqrW;hV_EZRek;F@eC
zmrHL&2X8GlVp(cm8SC=ysM+1&2c&c9ek&5CP6}h^`A$W`ZM~1q^RB*oCNVK0PnFA3
zk=Q%QM|6mGTp?tFUvmaq7#*S0{W|UFB@($ZC-s7ctgAjHil`p*PYrttF&SP$cqZJn
z)!>~3di~afkGc-9J5_T2*I?1Z$zsDWl;-j36>Ap4Wq(Gv$-{)FIF%P<(hB;77saR4
zQc*+Y1Aa`XF12Z9a`JPq;7;&f1PSq#C<+e^m_31KaJ?VVTmC4Q5<hw^op|JXwn|CO
zBK4*7k*ecjucERM0w^uK&ehhuOuh-+WaRKevG?1&l;!@@(8hq&exXpu@TpE%RGHKR
zcDHhMErg1M9oTNi!|>K`=DRJoEWz1%Y7Q=IV*~-WOQn363F9f-^sNsIbp9&`HL;FM
z7{%t^+s52@A$=b0&Y3%5kCbwI8rYppQ({Qujh+r)K{K~Hfb`WilVBWLDxsO^F2RfA
zJ_ASk`r=cor*pb$+=J4EY(Qbu&H66L&6T^Wm;CpqU~D+)z2`-*j6plUb6&r33U5L7
zNyJg6sVnX1%-%3xi2&K_g4>C^2K46!0oItFt%3?ew4)b6Af>Q(D5+WfGRG(FTbl1d
z6u$r7oFPp@Eva1971c5S6>Q@9SGnO6chul2rVK#xq)h0XTEEF=G8n|67J|fRpK`7H
z?b(9|1(Im00`A;}hrp2?P2ag0JeDpi=1q8xQJ*|!3eTWjx<+pBo~I9uz?BneYJro5
z#dkp5&t`3<hFvzQo&9$RaY05mIL%|OrJfa#b}|%a0a7~B%LabhKr%C+Fj)9oGJhh^
zStHn00`Ok&2dij*!Osa-d?M-UCiQ$Z|M>Cqhwrux8q$UK%Yv)659m~l2jX6HsFkLO
z;piM`hg`9S6(3_Qt-A7N&W|6yyGmvQyF?Ck^UwhufgG1P##kG%IeWrRJn?yR`D*ij
zAcML2Hjx`xr7=POtkN)%IZgx5I~3_KWdvh%OhnANlRtVNDw`lZpL|#8(stxbwOFy1
zl#ySAy?ffFYZA>_G3(D)5p}hXt~_B*BxEeZ)`tI5E_UPQ?r`;w2TH<kju=Y`Id%0_
z=eU$Xe=aTtFdSb7g#O4RLjsPV$D#dCTBntf<5*$<%BoX%Iv#W#kHH{cmpXzMY<Ti{
zi<SLKxIRRyVE>3iO^9~+-lO#cL^OBj^i{wm9rxj{m1aH$nP-T%KmO4T(0fg-$ifx~
zwXU3=4_KIh<_V-BX?T+F-{|Kc1qQ$AdpVS_S>7&fOK4uMhjrgq(JD<d8r$G@*L!Rf
z{>Cz-37pHYs(sTWHDc~Amea2L`-P!$>xR^VAEP}$&@?bJIlqQj@gX;W=2}&+Jzs?l
z^nHL~85wc4v_7y*XL&O|l}S$Jt2waob@UGDSkKw3(xr9WH5hDc;P!>}j~1pf9)@f+
z!4su{bK@+;XSc}7ab*2P7<~!_(k!77gC!e=<sB2x7itfM8C59PS^iD`4;@3qtX~0h
z2d}wY;8V|I+*foA>&H@fb1m_uYy7wx2=1BLQ4Is}a}%fD-S;w(?6<S;X)wV~yuu|b
zBPuUR_{<0URP?}=&hx7H)4k@QYiXSR6AvovAQm&{{DCIo+nU_3TQ7ZYCy4yfbLvY^
z(Vy$bl$>-av$4c?U5Rnc4ylzY@N*k^a)?nF$I8N{OWuwabdT<p3Ui>by1o-avYsYJ
zQSGirHSna{C5#r6fQz9SO2#Pfuk`#Zdi_9|A{}=1cl8$nzHF-7tA>r(fxd0RK_eaB
z=JL8%G|<^RGQeJXvnLfZgSYkWS$a<VP}C(bUWY$pMmi2ehmG%`wD7{6|BwZFcY}2o
z;kx!uHbmm$y7B9Lp9_c?W$ZhYvA<+noo``+U>%?@QQshbco50bWJ29{w=Pmr{`^+r
z{wIq_S2*>J{<aA-QK!*ZNkDX;KL-!&yX-vpkF-O%P~(~n2qX8u(oDE;nH&6UZ3Qw~
z9}J01Jz3oTo(?G@r=wqu!WyzFxG0(O#Z?d>l2F5~lvw-KP3?58tK(~F8phkZA0T08
z(r={a2;*g+dN7;fYA*ll#fSA@hEcr5aPQTN^Y<JBqqSH8ukPYry=C*pJiezrw=gXg
z&7StFHcjK*i5~?I5wqXbKosc*azwjcAg~~#3Scw36&fD2iMxQG4HTHhD9~<3aLR6g
zwA_>%pS~(^bqpF=hK`L0!~(cN8=*cO#BTO2H5SA<eiiXYg)f`OrFU7;{|-A@l6Lx`
z2m7PH#CAWk@}Jx$(!~49qrgp{&E*#F7lLqsE;6TPQa?E2DirikO!?$55!RK=wqxbn
zQmICUL~3u#YqR6soj>o2ra&txdsqLuK`spuNc}ygQp{v3*dn~<9%bX-AwZe1;y4PW
zBk4aQ2qE9wd-q(ZheiGV(i2Ek{LJ4($8RwK8CuW@^R5d%dZ|L^YWUfF@7n+K7NXj)
zg5F&J*>e-t7tlAfID0)<ID>f#e?tdy8BTYB9e-jMUGMFANlx;3biytcIffz%Q<e1U
z(`3`lRGNyIL{^s|x7g;;!(~PaBSf^FA!w+t=Sdj-&Y^&!V4AOIT&J^kaiU_<tVq^P
z`vrC2&uq5uFK#Y|`}6Mka_i*Og75NLAXv5@e3o0Zd-C=gfUCw#C|ZC^L`K;xCENb;
zJx*97vSX&;<U?r*Sz6f1MZ?%XhLClyB(%uNq&{Tz_faaqIT$2dK0X+t8tL9rGWh+=
z&F)^91H3+Nci<}-PT{%IMGK^!EtsKDK#{sP^bOL&W3DltSEZ}0GKcy+i5e9qjR<Y=
zOlr>>PDuF*k6=Nu#9U42*4sjwJFlI|>naS-#A0^AALc-J101q9zbm@OyXIX2%W@iA
zRP|j!AF0sN{ZF8A7oQ0FU%-;23rXOPhg6jyCV$w5I+S2_I*z&pee3)<!m^{bKk$OS
zJyLveJ;{Hi%N<#l`<K1i^@NfmJO6iY#()kGekAqhg>x#j2JIC41E_a;nqOtbdWzo*
zxPpi5?A0mLuNhsvwyKdHEkHl^v#&fBkIe^s{jlDje~cr_UZ2f5?!3$~e3e@AT{_vP
zehO41;1^xCKuqKD?!1X5L!nCWjoKq!?6dYhc&X(63vtKT5>zn{=R8!{a969}0jL%L
z#RC*0(cEl3u<cjM?d}-hA-0aTyH?*{%_o8+P4$cNjNKo-B<H*0pX9!=gYftXQN_}Y
z)w@{lW1eeAncC~sW|jF*Qu+oJEmqBe#O!!kBP+GOTyqR4XqL*HFAFy?Ldb7M=@adZ
zdQm2=(@e4ztCR~Tj*lM((q`Ozby8u9(nqn^0_iB3OBkAHP)2v13yc!so7ctF5u-E=
z3G}FQ5<|2%H5*bJl`q10IQ#QwU5aXnblRa7Wnb3ru8jvws^mw;Wl|A`H(sMc*D{J_
zB440CCx(}SB?7OyKQnVsHaE#ocB<9Qu=rfpX{Hu87f2V#*;W1FIemzzH#7%S3<yRb
zJ^|9h8#9y9FwK&Gy0)*2`4<4wVH^JCd#WWI|AIMnX{C+j9cxC~bLv36v1L|pIXp*S
zAQuY;Cc})*n_)Jq`r#)I{Z0-J#8;5`Aym*qz?uSb;CJ6_#g#96NuxcL@?`?jyQnOg
z@6D!ILqaF}xhk>ksqH?12s~}~sjRhB{tNLuv464J9fLkEJ>_?ufR+I`8J6s|9@g3)
zESo<#X=AOa{_6L!QEF8zWBBQ{h=vd7D}9pHpf|eeAC%;j&Jp7zM%1R?9jqC@Ez`5E
zZiH+%XT7D7td>_g&$ZcQ{}{V_0mI->=&W}IT~KmrDfTm<OTZy91DcNT2bq9?)nebm
zmp|#~ZSa1Q4G=gp&IsR3VmiM^p~hjC?orr9wd`k=08T16@nAH^Zt2lHPG9VZV&Ekz
zy7P2T9&m=Iy>k_#<WBdW480ry9@@WL-?(YtLszxys`IBgzr_Y}9^azqqfnK*Hilxx
zakUN41&;qp>OJuE@nn64tQ<Yg=k$?8_#J)>_H6Gd*_93lk%_CnOf5G_;Y}@J6JQ^I
z`y0zM<0lU1Ya0xTW{+am$S>L0&qZ<%E35U)j94VNaHY7_dZy;6E|1?yfJvDhYAW2m
z{CBpG2J|gO^uI6v^G64->E%t5uusZK)M4sUKJDzn^gF=|3ghuO^}-D4G~?>VwI#Hh
zC2VD74e9K}(}be|Lk@`WEw>ojiDN)f4{P+IFfiH4>;0XHg*AAq5nN_sfA<vQEu1jg
zBTXX@q}h;iI(_6`@9royt|Pdl3W8~_Ho`bqY|xDOXY3`|%IWt@*XPF#_jzqarSzY2
z!bax6+C`k=0(Q6?PU342w3yt%OL2|#tr|OZ`7(GScu!{ZsZ{o#x9)2P`+Zdd^pJ%Y
zKMHM6C%R84lA_qT(m%S-cm#YH?9qw_E{TUauQa~GH@SpdL&iUEN=iVW&yi2yR9mEK
z(a1kZIPxv13s`1FKdQbaJ}KBEqN$Y6AVcyvk1m@f2C*NGRD%}c&>;Cq-h4~2loOoK
zzf6L)@Q;<I6a2+r$80!hy@H7XrH|5r5PVjC$F1)_yt_9*diPKdFQ1w4eOwqhN0pyI
zCgP8>vwH&3ZdG41^hryaFxy#5F0PEzQ=rYp)sxb<`J$)Y5Nz1Q%{M7<sC(rhT*zd3
zyr*6aPXjZEHNZ6ZUI)2*8ZUi-*!JU&CNeO_EedX9{5pTLq5g2Th2E_+cV<TDv~)VY
z#~v2gy;V1NoIGMd|K`V36q?<GCVFoAV~Sq%9}>BE&lBK$PQF+1>Yz>j?|tvYfGI2Q
z7pt23i;1AEi7E_+bz3kx=g+!PV$3pSS}I90_5Y=Iym=6{z~%#v*mDJF?xG8xbdL-k
zq6n?E7l|9xG+T=%9#da^{M}2=T{<gI5>3syV&1o#<U@0SZh*8|pN6?EVh5I;s-+9R
z)GD4Viu+=g{SVoBA9`f4Oq5{rX6|Bw<3dZCMP2=RjGGy(U>Q49{np5?&lS=HC>(gl
zmG(iNBWB*!F*o_opSq78z6R&}&aK3j(6^qPV#9B5Zw8>lJgo@aAa#z*0()ydkY^9v
zf$ip@Ekj01guE$M8`MzmC1d;C)8E29y=Tv{FRl~h1o-vQDNa#{c7-0%e`bH7s`G}I
zW0BEO+Y%<2vg*U%loU95dw<XF%)QFxRm7Hc1NQb|>fx`F*Fd-j6GM^FOcF@{e#qb`
ztb>%4PW06P7Z6m-g6%dL?A}3MwI4wwBe-uM83}bRn!%AJ^mxrfKtY8Ku0bihA1?jQ
zH!xc-C#n9KW{GD-OvvKU{wsLPU;?1jW85Fu*n!_1k((THsm7Qt^E>Ik;Zc4?yc?1a
z+z~x$L7lNlDjsBWg*3OGC#yV!x^?9^uQG9uJ04rm@CgTxFSwz{tNE;bQtVnj@nKn1
z*b+v4C>93kWC>9<o<67#biD0_#K5&E=<_&Iig{j;Z34SJe2{D*ULJKZW!_E=G`5QQ
ziXqTSDl_cdLSIArDjO`X9F|8w!YNo>-@(|T%O1vE6Os%vBKPCk%^vC~+t1I+uVjRI
zvDWIim5k^6oWC*nY#VF-|Iz6|33~KIkyEw45tNxSX2E#xkjkMKQ?O;+#4F2Z);*~<
znJBRkJ#zlQl6UBhLbFOsoOALFDIYL@h+|{R?W|R*EU$I$-g{NY@{*zYuTPynQ<*7|
zx&}P|ped_ud|nuN$YoA4vg7FnQF&jXpYtxHDhpq;^YrYiYjxK9GB~L!8}*F*S>c>y
z!c*8Gx2p2dSHO9HHZ`qGl1s#3K?o!jW4xT=*Y)P#M<w$WGjWYldF%5{t>`nefhkc-
z6hrnsZ^}L1onGAW`w3AtJ5RklYE1;jjS2;b9Tn~i45r(ZNt7)MXstE=L<-iUQDl2O
ze^vGS;dIVoDp$`Q)BPj^GGmp46NBHQDD5@h)bFk<F>8NHZLYSfQTkEM_U%K{`WGZ9
z*k!5he&(KLW|Jz)Z$Xll{Unn;=LnZ#GiKwQ=m$$%w6rEtFByf~wQ^^j01bK959%hk
zU5|g4J&tSFIYIgGMRi#}<ZEE@wv}l1D!0ds)x{PjNL!3^zJtQ%WhG=mYhCjaoOfMM
z(Q)Jf3LWfC7GmlxcKm}}SV3trYmnzqU!@Otb1#`V$EF-jnW?5OL-?P$JB*N(W#si1
z;C#C(%xfSY=CvmXPn|d|O5qlg;AXU&ap!lG7as(FU$bS#miW&9IpEA6r=J&Q)hxTq
z3TXuSR_F2m#a!`N5@p#EWd%8$d@HBLWW9v8b@p2=u8hzxMf$Og$v`IbAocZYuv{1P
zFxW5qm!B5<zk=f2o!xSVOc8WQDPK{Ei`^H@5(;2To@71dR-D0~&aP<VcR6(V&@2Qy
z>PIr>Q56*~rfj^hhnI%ARAtiO_ZOO;JHf0plB95!$MfR<K->%oW*!uHm#<%~N`LbE
z@}GkFu=)DNB!k;9t&gMDQloCFdj)(3up4G_iG1^mI+tTdV3-2rlu(a;@$f1Zl^B6G
z7VyD&^-d5aFTR#2OSY`Z^oPr<#Nvr0IgsfLE3N+F92eU;O=+xd*a!Awz(OpT7;h)j
zy!;0yZNg;TJfNfEBW5oAq4tDOSH8Kuh9f`$M}bQlo%Oi?flzk_1V!S<ZM^RPzUTHj
zvh)Bm$zwU$7>K5heh)-Dc@N?*2Gz)UGVuD;I53+>ZEB>+y31wDfVMDbz6K&vz9C1i
z^ut`~sKHDLxahXMAH8dk>5*^0xcHQwhQB(4`yS-9ll$V*R>3Y$&8D&zQ=B0KD=)h=
z{CJ8m^Q=}F=}S2s*q3SAKe;odmko7-`w6kd$0RV8HzWj9C5z<l92Qw6vC;29NrM8K
zk3xU_N-COlKa|5Jm!>JR9D17%LSHohU;D0z|Dm~0xP-zRo-F(A(d1}ErFO>uuqW7q
zj5O)}d|}=Xu1jPEMV)A=rpd*rzaNouk=-bGNSNbZX<o4H;8o~limPCQj6RT(dp-R>
z+sP)npVU9c!<S|Mn79T4KPYeWqRoWy{6ZHsN(8Sn`25<?S@`1}LTRjEo%jO$Ldw`L
zVO-Hm(`_$?r)7F_;vxAFInuI4+{CFqc^4$FdfdJDYgqS@pUX5&{+wB8yC3FoyRCLU
zuW!1Op|Bu4H^=h9oSo58d)*T1H%o~W$kL3+Cof3))qV%%;yr6*TnD05m_dghX>$Q)
zgMvYTd3dt@G4~Ptumtk;&gM_Sd84yW6j+)AyIzQQaiHQ-Qg&nZNfA|Ju5n3l5uSeu
zWPY*h5RqW<Wkv&8p(wJ~WuK#&9rg|p1QE1BBxLQM$h{OA|F=m{o$lXO!<&eg<$Ag%
zF0C<oG<_p#LLfdN&+AUH1q1_Gt68E%hYH9-$#@ALaJ2dReG1^vxX%T2puZKA3&uZx
z{3V9;CFga>D~P9ou<fT%E`3?9`VtUb=P8fzN3ap0qip#J6cD$z#SCS&m$_p2)hU0%
z=0kv7tceWm8)y!-e4QN++t7KY(;~(*BD~u9uFBGn%;o!9z#@AB1X5OKRp*}dFNXUs
z?N9p2vHu0WEYaM1q?R}jss9wz0d58n3ehPw!Ru`j|M7*Y^Lf-4TxUx&>Z0ObS3zRU
z(h~7X?T`rJmEYr?qI4Lw`I|hnu4pw}sPHen>GEsgXKV<@<e6XA1d*`S#Y^h2=zZ8-
zQDKu4ZXf}S)IufDpwq89S&RD>J(lS=mf8Ukf-xSX?4!@E41TjDuX!$Um+h6au{O{^
z+P2tdt$3z)UnyNimy6gc9etRZ9yG`5FEA6LJHI`+Q=XwsUjZzAJ9P*ul##o!Pc&ZL
z=7>*S`+*VH2p>c@EWoNa2rbN=foY2wBNaiC!J$pwQ<Z?oAWDXTz?Qemt?ifq{#2>2
zt*EcP`ng9RmOKa&9w2)CPf+ygEH|@3mwn#91-1x{uq2SiGD%Ead5AIS{lAsl;x#wx
zuX?Ai=b%tK44c~4iRUhKeG>SeuyrA-efhb7o(gmJQuJ688902~N|53@kSpRp^+5))
z5<tVELgenhLH5C_hRrCsVbR2Hj;jWCaCRql%8Pi)E1<$&o!CYG^6@NCF6W|CBUo&0
zP#j_N-00$AmFpizyK1}<`8Fw6D1hF@0%_RKclAug_)0!n0Q|O9T4$S*EMP<0HjFug
z<;}eY4YYHw;Ydt^fU`M+&B>eC_nR=+$?r2y?;DROC!aWJDSuuH?1(K8R=+*GlRl!q
z_P{89Vkn|ix-E*vF3CY}h@zyfy9!iBV1@m(;ng37>PE+`kq9!KD)&?83`Sb-LQ!_G
zzsBm=GrMIPi~D=0dY^8Y6X>j;)rAV#)om&l*T2<c!$r7jL9EXQK8d){I^LSK2ng6<
z1BZy6<2wZkwb0!<2~bG>)QSETkv6i=1+=#hB;Jz?6nU*b9iEec;LAUQzDfRG%N`xU
zsF=4~BT<D<YOw4`n-x5@igup=<LNAes$AbLE{L!}knY}ehX_b_gEUgoNS7cD(%s!H
zB`KXsmo(BKAl)Gy@4e4|=AAj?`GQ-8C$4*4YyFleH>nA*rQ~>BeF7)FyN<7Ui6bEM
z+?lwY!1S`mm^Q3w5ZEKZruA&-<p%Ji%8(@Fe9K3PPb1hi;P35I%|6pi`c(v<_GqdF
ztq*|!6+fd-%jv$vnz5==K$bwxZdrfTk$4sj1dq@AeO-d8I$dDaikSA*E8%ooq>vkZ
zZweR1HJD*ATKM_KEbzynoZ7^6c(|2eR0Ja0B<(SO!-I$uR=_uEff}U36=zJ8ow9`w
zEKz)lv*(WOxr!uGVNs$4Qe<-bGz#KWS=C{Sx0gMGjt??;RZR5Z{=kQU8Kp&}h(AF~
ziKgiNO(gOoX1v9EhnD-K8k&2j*A}(m4$*1TAOHopefR+!3+BU%8ieD1&z#a=#ug4v
zk|ZKw9!Lbnw=d3q36#F%<dg%nfiw^vs-R6RRN#Q8d(S;Hct64AqSdQIAlF5~>86#G
zpi<_1o0P!lB7h>p;Mlf|tL^Y4Bpf!icm4OU-hS-LRk8F4k%6jy@dHA9J|mcd|BBO-
zVYmC-89^x7VVU{$gAs~fnmC%T8>@lIYH}{b<-cfY=*BHQEGsRlf-qzC(l3_{1k@<x
zC}Mh1IZI3ap3*NMGthLPYTM$e1d8d^LkcBU#nIRTe{i~h^Fk*7>mIO-(xV-152|SB
z@;r7Ov<}$-j)(eS`Q}M#b7G)pfbcBfPJn=LwXmdsxy_w|(2={VP?Z(qX<bwYS$oQ$
z9?3o-a*szmhQEc<dE|u}l3zX}(3=Q$#!S-qD))~GPSnf!K_(WDA>0J<x%Z$r<~MM|
zmQMZwz7e1ww?uC$s!^p?1GitS>=jP9;DrML>`fYt3M9KXdUn5TPbTVLbevzhO92lW
z^K%B8%I)vfIuf%Qld=&ujKTA?w*VJmT;x|-3ienctbQA}iRCPhw*eU!MH_mVgytSx
z(oj6i@J*eB3gay2$u3Ukcn)kuHAs=Ece#HVBXCM7O!m30KqMI~58@(k>cqRk;=)LQ
zSD(%I9GYDE>0Ie=_w+B+M^XClKVY8n**@+V?6IiC_n+*>4#}5DaNI;ldL>q^uQZ3I
zI%H8ZaE{sX89MYyLv4}9w7;XAN}ND0Gr5tj8HeSEAR(usEw;O7y-W1|1~1ZagcyS*
z_j0Ax?BRwo4zrr?C35eF&UPxB;Xg^k*uav0ex&>Hy7+0&8yw7m#e#4A3Jm%4PGI?)
z1&aesAh`|{nnXsKUjOFb=6y3Ww$G+Wmd3{{F^Qt*)8g_{e}bTHvXCnxk<3I`wH-Xh
zI&3m))=(puBp-J>AHQtQK#4PEo|A?gBVGIaDAvM<yB;RjGXW2Ju(mO{>%~va-r2ZM
zTcffi*U+boi<T}d!)O2G?tfs&hZ5_VOtg+2oKH^>9DIiRZD3M8DB`2^`^A#j;hs6h
z->!Av>63`>uRpqm_M+;rq!>JI^@_JAWZW>qj7RT$K8FNt8qXdAm*oZ(A$UbX({|!k
z{{JVBqZ+K@o>rD?Ids`myLnru7ej%nZBTXcbKA^kGwb}Xsw3WPIL?rZ+zj6HW`udu
zIx(DJEMZ7K?j41M_1!X;4(sf3<yr`(D8<eFC`xHlFL4SjgC@~*`m3m9`Svx{N^bYN
zO-sb@vdrgiq3)*Yj6O?`0S1!5H#jXp-g!FA2KHdL4D#j6NYJc9HUol<^=3@q-yEC$
zbcvDO|H-E%kA4U_!2-TpS>=kJ>6Lic#&yXeaspk*$K9EW0EaP7BS}nxcNTEsYDwOQ
z{3qgG!U7hw^6LLE0zJ!mG&Bs;$2!DnX6;==F#O#{L}pd*NA25T0YI?3g>6%k>alch
z7NV_++m-Ekfz$Rn;@DRdB%l&<md(sta;DUtX9~Rm%i_Za^7~X=gs=JMI-e24demL8
z%7Q8g_0_Un#b|N6*|{DQo=)`fl3&6;;$+GlrHHS0at+JzW$!@o5df>wfn5wxBilUO
z{ecAs7(^O|YtjGBJPY)ZDOfNyDgAM_>;jgrnj?`o-v+jwBkOnqL;Dg9B!i$54>Qwl
z(I8};ay@nY!N{zlZR4|Q*GDaUZ5;-%(FX5z*vcgsQ4QQ%skQ<as9@+GJ{`cf0)rA5
zC5$YK1}f%V8c>$K$225Q_9C#`oZO*0B>ZQuK|pZ(Im`=96@&q=p)#(Ht2Wz^K&L-e
zJmKspm?PHwbGcX1XKjYCtFZ95GySX%4ig%)TK8V+R-+bYw=xt#C9Lk*Ec$yrHq1t}
z^#+(gXFgoC>0yIsjWdL%uAyAUt-bv1M68=KBhpBaYByUth&^#YaEnF^auJ>Oq{jVa
zmmoCfLdAuawL8EP)x_R_QxY=CkfA<FYv=o>-Tv~$yx0&50^H)>OCu>ix;icI#j(^x
zvOnVQk^C>o;pizMvxKqnL>oj3^T&p0uS`t-eXb5)evH0UqY|fv8?b8q_BPaqjhI64
zGvkENNR8wj^5WgD7p)C>4#M<KOuSU?1f@a2*z`jGZ<Q_~x8;$Lt4|mLVOQD`*um{?
zqzqTm$%13Ccg&=?hfYUy9HOf$S7eJply|k!bEn_$s5R>8Vx7E6cK$84dN%^sU7LeX
z;%OXhSgI^Ru!@-+y(0;F|M_X#LnBKz{vTLo@TH;#NcI4h4CJ{iqh*59JP5Lc=aYn2
zYX*wx#9%^I0)J?tDVRMCE{RF3=_CWyvIlrs+2>L~G8jWQrb{2H`{mi}qHn2J`6fU|
zfVYK>JY73R_qaL;?bz@I+Y-P3`Wf_xe_HNVUVlsW3j}kTl?oPmmZj_a&tFkm=zbE|
zrF!e(oLyi;JG%L@;Qk=N6MP8KudE#4WM$M1;_D#ie3RXM4iARvv^p7@Z=n~oL`FA0
zBLBIJjlqcu#LL0T7>NGU|J<AvX_D&Rf<4F0>u!TIp+aydL&#<eE($RTDuZwi66_W#
zG8%CRB~qqD-&-`ux%_Tmw868o!6^fr5>a{%m#CL&;seUH8f7)rIz8vlSu=^CMi~%<
z(!gF3?w`{ZuOuNvEHU+7L0W8)=R-G+jP<`SMeNJpn^?9>uwuK<p_yWrg!?~{R9+7&
zAH6M!?neb@Z{?)oF<l!cX6ZKlKA-s5AHaAgd>`@7Re%2A$N6)iTjy+We!7)cyVzb&
z-Fl=$H9%{UITp9D{c^=2LkI1-;Q4t^n|ch-x5y~<M8=sKveoHth}|UsL6d;b>qOmZ
z{CSUv{#m8=_6c!2B=(-|M-I}qC&q6P3y2Hiw_}MMwc0CTy8Q{)*(YBaUrc{V<y(=#
zFFu5S3uFUA-Zl)x)Ik3E`lE7-Y!!^j(m`31NJ_dx|2`2;4{|f?iM|i&d-A{d__OoH
zfQ4}1;>4TRD^>=L;vx;JPYHhyOhX`xo@$cg*!4$<KRYxORQP?*{(htO=(}7xH#&CN
z)?SEEmz40Hqx^hY2UMM7^ufYjV8VmRbR_-Tdr@XbD~o@p%3m&}FXyTXx|KDN2Ld1E
zjp!P{Ud)q%@Ge-iu=^g{cZ#uM(~-SKzwpkA-@f9u2P=vP^Y}!&gh^XYsRI$l-d7+O
z3VerdH$jfT*$UF~ryyNmzTF7+&M)k9{NAAF&!1Vm#r1i5C)C$~20r-gD5Lmhf%rA*
zzvA(K0Z2l!49G=2)u_gf5oek%t$&+Cwuze+G8Kllv^rhFPUBF0AKTelSb1NF4rF-}
zgJjDYIPXenBp$xNRn(eL$89`(b8x3Z<Uvo<(b-z7{|wti+h@CR<!^690hoiby@Naf
z?@IK4Gffs&n38{1e&`{4;@1t8ipCTFlAp&4Sm5MAFU3^uuk*d$wvHvxV)&6}rltGd
z$uG_iC%tSuM`_%mWvQugRHs91iTjxhoh`{&@yz8WM);3$jS+Fw&}<ipS>LNyoLRN*
z`!kj{^1cUL@57cpeOcOFxtg*C$y82D;%?q%b4G|5jBWx_E@0`^;ni6fDR&DPVIYmB
z-|={<jd(XBm_X908cT_=Pl09lsG1@3DRzyot208qHaACloVyJVQH(lv;f3<Y1%q|z
z9ArGqpMr(La0`FEld^66nf+Y_RZr4ZLleChbF{@gw0^h|Q|3=A?XJFfvMaPvmlpMf
z3nVLrJiLf4k{;W{=%)>M0oj6MlZ((ah=%kUzJ?0Tz_EXLPD6S~9{VT=!J}Z7pf0%~
zg=!SccG$VbLSNkm-OV26HcHA}ie8a0+<PaMNSWy~4w0=PjJ-xsVL1L^>t>3EmEE*@
zaM|$?4Q=Mfp()ejWnT!NZBL(IPjvfmlBC?0?cC`-&0FfDiwQ5OHo=9fua-tK418#%
ziM`Vj!eHqEUckLhR47o#2k&+&5Ly(5Qftl*%OI~lths=^ULRPrJa+VS<e0%(gm;;?
zk$*`wkDq2<PaiZ&tCwLQtj~df$w?Xlb9#qOF!#zORCq;2{TlMS=cURy|Dw#tT$Olz
zu?PM471%aMVu$+%&DQV8#$*Ufv0v_+6(*)O`0cx0hd|8t*2+Ul6t#FiSv}K-rMN);
z5CkihPf5|l=Z~zrLOR4X0Gf-^VvOmk!2dYV=K~)PXz>sQ@;pUWZO-aYKG<SF|GVx;
z{FQJ=AAU-MXn!gH;$%{E;VQZ~cmk$JhkT)LKK82(jsEGHr?-8+$OI^5j>Cpdyu(A9
zX~duQzu6=b9=(HOpH2bC0loHiBKO|}M9HNl8GT_{PgC%UYL^O)N5iz&AeRWustubD
z>6FS#4CItp4xoT6h9|c-+;P6*QxQOon<Z5C1@IR@jajHyUmres_|n|V@_13D50n6q
zizc<wc$$}#phr1Jg<dXF=$lpte!HKQc|wFIuam{V<e-%xNu&(?$3(%2iHxrq`^a2-
z<|}&Jh$$yrB97@k=Xder4t2ynzvq$C5Zdih@+b_gefL|$7c*3P(KCl~86BfbY^RFS
z*te=Z$8%ul2`vySE*Jfea{tz<NK1~CmF$CA;6GQ&5vm7WnJdA-N9dd{dE%PPA>@y~
zXbU-&1?9yoW=$vhq%`92z@BfwMQ7;fw%`6|3>gMwrBsV}iJsBy!5-3$n`~$<Q{Xej
zW&Wa8(E8gaeB=nrp5q_fM3$D-R!#1(iI20Eu57$T?xOF#sy3T>hpkk*`dB8SfeZ2!
zu$Uk);h_{E-iSq!KOMXRahy-vD}24G8$WvP%mF6m{r2wzKA6oA*v{siQ6*Pbjq{*5
zsFK^gBRC&+He_>Bt&ADtv@#N7wrMPM5!C<_P4NQ!4FGNI90cU`47Rp&mP|~(w<y*f
zU)6aFo4OQ?nCA`k=dc0K2~bMG590XAjfPh-<zEm>7e$ZUdzh>?yZR1K5q%6U5JQiT
zoZ<QK46X2!X|z~r$1#Vz1O;NXwBc;ZglyE)Ca`jWNd5QM0b^rbzUYD^RItd2baVtT
zq(+;{_8w!yv1O8NT}TKU5v(Iog3Z-*PS?0Pt#mEwR(xg#5q08OM+np~jmUQ!pDn<~
zbA|>mEY{X{Da~nbE%?aDeQLgxO6L&n$#V!5vcJug#Huhh!@AU(j4|bb0Nwmp)(Q-o
z6-OjZiQB{UEoRB-<qCa$q1Kw}P88n21EpGk97E^Lt>d098Zi|ntDYytG@lnDk<Y~E
zhk9xz!elXVl3~;0ej7#N`0FcfOOJX)UG~CbByC+oOt=UxO8&!`QFVtl7<Weu9{&*O
z-n7eSbw<McQ$+)=Pg{KQ<upEr_-t7+{)cLCMqmEfj<dpRO4Koks}R--hdBF2S3iwD
z944XC56Upmb3uK7nil?@Vv|77X@c{TouE*t_Cd?*9A_og6e$$-CG~eVt&W_#grdeh
z>Z!|RUJLtuCSuR`w%#!GW>RGcz6rT<3^hskiHA^b*ztTw=FW36_ab02CJ_$$9%*9r
zarD{l>a$~PnR~56lh+0NC8!c+Gmk8Vcdr8<T+v<RVXVD-!NGQ_AcWNjvAUMLjn?9Q
z&jhov*Pz#$!{nG-AaZ0U2O$j)!ASR}{;mUXEE`^ZXkkm-`JUe5D*W3<FwNQ_k$2bU
zt~^|Q5^BDG-v_Gc8#{fn!7ljnfX|v3m{OX%)}7*vOFP)&Sx{*ziBBG`>>M6`qco7-
zFagWqmA611>WSGGd_-pc7hIB?#zTB3U3+%QIHKIxROZsu8;vV(r7M1~gA4vV;sprq
z0v<r_rrRB#{VKX8m)_$)a-W`{@7;imHZEdiz|bUyN&Ouem@JuHg$)d?o4?pu^k8Ym
zC>*R&Qm@m(Jc_KDgj>KNG<N0dl~DhWGlHo#gpv$Ij^ZLSfH5`_P@3KXV|{5@$BMB6
zxOOT3ckKdxA7LZejW(2a5snEx<pL-WYO^vuk%t&5uhb=tn%HJOM4_lm(?2j1Hij<7
z!GB~=k-&sk)TmZKTbvGC%wi9SHa@!{>IEW>i!HxdE3p`Zqkhf_haheHc)@{2>8%F*
zE_R*%CV#|42P*xYhTI22x|0&OH#n4#u2}Oq7;85@?)ViJTvML>V7W0vT#7l9GX{it
zrszNu0+F>u79+%h%I?c@Ir3KJP(ZYGs~omh5J7@_@38hRE7zJaK4h5fnZF1Y0vQln
z#<`MQS5tpBpp9TN&-*wjV-6{+w=6azb&1h;%PbUTc{$L$jqG~Y1yy<LNFYf6Q*$wp
zjgiBrE>Tsoq#zF6xYd~;Pnz1W+F7_na_I8vH&u?L3qjsrXfXWqz$oS5Sh+P7u~X%K
zyoRR|k?kyO+tSb5?>s#Tlipx!F3c9aT0@+)$Ih!IOR@-=DIw7zvw7ij7h2eJ{!Xd+
zx5`g9pC+cT(z3YKtTO>^coO*V(D;ZM!M2?)cEA()i%p3`lik`VHZeZq{X);1P)q{(
zw`Wqp3%^L5@G-Z+bJ?p!14)TTD;2^zTf)Of{rr7^2h3zoeE)THOEU>TB8E>b8kY2P
zj2LKc#7O&3n?3EZB{6|faS>10Qxp>=4;2Op>I^C+c}Nw3)R5{Vgk}JSoaI}xmP)`p
z=sDQYQ7>aDtH=BIHKJAetuuj~=I>$f;aSa!;LtOHhvLkCJUWJ}@iRPQ=WB3TX`o-{
z{<epkP@W}NtPSq8&uI8u4(iRmz}<u!n`4I@>(bXVt>8$8_2J1)yIQ4(=aqw{MVfkK
z#I_VH;PI(ABy|2ZTkeDm*u9_J$jn;=1tfPg*YR!;U2+^CKdBPJN5^P`zeC`{Qo~j*
zu{~D$ne(#*+GbJoFap)BSP;?QbDs=cVXOxUxmulzs1IdxsG3IMprzw1bLJ#=82%WE
z8(;TQX$~Uxn0}z8sS=|QpVWbuuMf56t}<oKgS;pz9Y@XN=3pqfQ-mixb3A2K`g3A@
z3lF|>rs_26k!Pa*+An7LN_-D3r1NpYW##VAs5s3Px>#uFpQB^>KX-5$`s$Hd9q*03
z3%Vlk`%*#H(MrJekBP@61r#^O&4E%hDpW{9BK!2mYrJog2!`hdRNZ11o|Mp9)}_$4
zS2I6JFAF5#=nNRuR#>T$e?B)ge&GOReJ2|b>b*NR`Qw#Ugg8ltGN;TN{GeX?!#fsh
zjAROCXds?DFG^IXf(@PKFiP#M@AlesxDraxiqKeh93oh$R`FjW$vk?I$UvRSKe#$%
z9$998&C4la+xw29p)v5)c+L|+pxI6YZ00m@J@kN=8pwu*=*CQ7?cG=LJOLSIiCcKT
zbu<>S4|>j`#9yciD8e3t?tWz`up<i~Ai&5}V2Cs>{b}%ULe%(?=lUX|S5TfsoT2m$
z$$wl0gWJ9rAbe^^M{(R?|3XwQM#X7=skG9#6wy-f^FdEKhM_KB%4m$!?mfhaejfOP
zKCqktIx7r=88I9rjVIL^$)3pk4d>?gY2NdGyYo&F@lNdyWeKFi);-e3(I=dfer-a%
zsnV$UTFE-BVmYxg6PeH$>!qJ3acTSnXc4MCbZeIo_Q)0Osp)Z-3Pm?vaPTkwdJ8+;
z1G)piWrFj<)Oh1yKe+nVEGCF&t{jZ#Y@gN7{;?`vjreRRPisaM+QyMs%>M60Rs>UJ
zKBm3D2i&C%C~tsJ7E|9DjZ#<8jRn76rl>SlJ^nuLuZD7<zsUTG5-#IcV|K$!xZHfh
za@u4oj@9>F=m7&rY8=%X3I4iLh>C%9C*tH7ym{g>1PsseM<$+A7fAVTN4WUhf9D@z
z*(!aLS-I(HLZwaH4~u4-mMd?tb^2Bu4qlvGs)~U`dO*%n&((8~imyp^Y*P0Bh=^tS
z{BOX}D7)$+rDzzOoNg9AbonZ7<zsF%WnF}AZ=Ognjm3kcdfyW69fP&jLPvl{MvgT+
zI$1^}M39W4gKT@Q?i_+scn)lzcsG1<JPRQ=isP(MKAHsx#;J@pgR$Wg_c~@5wuo(t
z2zhkuEB{!liXd09Lh<rVm5R42^uw&L&)t@;<r0Zx34<bLGL#CLUvv3iHd}{_&1nir
zuf0Y`N<NgHFDyaXO^h;=Ovtr6jNiBgB<MD5Xf!M!t7>!i;V@WYi8^hmRsC!jydfDa
zjgCaixJhFwyl{^R(Y^n>0)GS?Yxghmlkup$336S@TmxD)YZm$DcQ!nbI|P~Rqg#C=
zdJv-hR*}*S0;y@GK3J#iIo6U8R7t8z?YI<Uw>GQxtWj-<EZ7{<``ddRGJ|a0Z*E2y
z;4XX<G03=m{|ZPiMGMBj;&kXq4Cck9*QhcoxCeo~e<a9DI}mErBY)Ox8#&g81pN5t
z1%9hub3+fX_kc~0S{46drxwmnL*Mwp8j=*YXiWQ<qGcqpCiORGSu<~5h|dCltuvoa
zDu}O6G7xu<$2j|38@euKI9-m5!))(_KrNjXLUbM@4upcGyP$WufG~wY$zd7&0y<7!
zuIrE+b%_|ptPQ7BJn;<euiT&_0)n!R_AID|dLEXVt$N;{z*ot}#wCamQ5xW#IcuXZ
z^Fxzm$>Al>1;q3V6bF3O0LF_KY8?5~4h$++%dOI8!(eQNnU#u?jAzw9N@4<~-R)sh
z78a`nJV5ex-w=S+j;prh(g!qIK@gG86y^szJbEaRpVu2?`!G~%Nd3(ZnPKT*T&Ng_
zsKi%En(oOvoJ?}D`%Z)hsF?5DTm5P*nl};4iC^!Ue8gTHa9b9Oy_aNEl-Qm#{eo(3
z02LwMn48`mSgkn~4#<r0B32O@gdTLhSV)uki7YZli^GE982HaRSBWCgFC@n7?zkIs
z!Uu!F-up>t*E@6U!|-XzY?gkK5GhTwE&0;BV@q*5{pJ;ihOn;Weavghua#ianN4m;
z1PqqBCGd)tAqfW?LM7o8Y1P#Vq#C%_kE8fAE})nIv4cEwz}p9-B3Zh5i5m4Y+nebA
zU!iVq{}`158kgmvCGi?BnQqX6NkZ8j@>BfTBf{D66I$y#)+;?;!8P!B3^LmT?@F*X
zv}_On?@&<!r~OeP@EgQ!w^Al-++l=SfIxC%Zx<HB^!r*eSLTPm(ir$w7D5?1KVb|;
zyzuYEA;7*4)WI#hvqYv}l`o$g(Sz@NvZg#Z_c?i#`H~0b|EPBP_Fmn}wjYGs?|K$X
z$g-83@&1Bjyid&!=^U059^v+X%EYV^rW{-#sJl6geP3bFqQGcoBJjd5<SHN<iYY#Z
z-V(A+3X`D8I{cM!gTf|AhM9`=8?CwY&9`~nZ-P$y7YsV%Xp$5g5?;blx8&#Lo>*O~
z{{1wk<ccRYuf!Y3R`Ip*DJ|?B{GnfyGNxGG*g(UZPzp21p(x+sF{egCz~9i|JXjKE
zYvC7|l4~Lt%{Z-yh(NaCzW~)u27Zkq=_2Q~wC|H*$JL4=SeN?#eXT0>{3PemEBRj(
z%G2G`uSNnA86Ov<iOH~O&sz9PH+3?SZ({pnR6#k9pLIFt;i@WDUSjMiw=$=fjLdbS
ztrX{G?W>-7VbB9zu+;X;c?w1c%I_*^t6ql}ndHx2UA6w~=WTF!?%#Xa+(AI24<5M^
znIZ9IRNky&zHkf~<M+?U4G{Ndj|>Xf$w`ZyMfhKk2zUV&G7#MAgT;qWt1p$^1z8!B
zXftm1D)%HP5rAP6@$Qn`;-t>luIR^-Q})CoPH?4)eT$c)XHtCy<E|;!E(h8hl-vpR
zTHtprRHU^`h}6A9v6-xsDdGhT4BLX*jdjWL&6-Uu%Q}E?6r{bC2GHo<Gabu!xCh`d
z5|?-3_x!uFqL~+$ycN2O35+FU6rqXV8vXzRHeSLaQ~5vGXVDtGQ53~tu<QQ*XhH~F
zeOUldr5lt=-y>1VP>&oIe$t<XfJo{;S?WW<ZcU|@)g#K5Di7{a;p+;Xxw*14wx<&+
zyH)+|l`hTMF_86!5p01+XHJVZ0w0mr?;Vu`;EfbI-;J+1N(V`d{NQ$ZJb${@g{75`
zJ6!`}s+g6T-?aFc+Znyoz`S2?-R8L3iO>8xymtWR5iB>jn<Ol8K;sFXY&T3Mdj_zm
zBW!rrbWc<049Vmg^XTYbVJHOO>vtWJAd=2#>01Ab&vKe1<?Ftx9dDsc!rI7p;jg=S
zA^oDThvfT{&6(vY=D4#&F%^Vn1+PVsR$_oHXEG?5KZE$6jMKoS=jR=cXUb4Fc=&Q&
zZ;ICal^>J6yQ1x*TC_AcoAb(qYu<1Ja(JWpY;$95@r-0z38RYpG~n8#5&Vi*cn<-O
z27r?b1whLA5iN!!;+T@!!a&vLpZBVX)%1RAKd19zZc2lcq4pw}F^OM}#;Bmo%+Dz4
zA0UT%8R`)OT#1y*{S>J$v?URTDatWyqy`6K5}(MfbMrgvWCNMStKlE@3(v_gjkMrt
za9`xu6u%K3t+|oet$VJ?{j+oUv-_t-c~wS2Wkk#@c0w1FyvBUn0JFk7IF*zoR&xB$
z>Wr)b;wjUxEva+q42gm`|L@ODza8k4iCbw8Q7F>t!j30c1z!U3$$YqA*RAQpmu)04
zEbl3Xq!tx0PPE%M2&79KmRFWhZ~X31)#SfoBzwI(Ofxs4HD8*~lNdMIqH3*D+ORWB
zwj_O-yHg?$_8eX{o`aw0Civ5;WoSp93-^aZL;DqMhJi9Gz&3ZfASu+unxs>n<zqv#
z2e9HKWl4C!d6EsKBF#%bEZqwiHuFLA7@b^$UA+K^K<aCqK0K3D0q^)4<$?)^M){O(
z<@`n#?a%ur@4%&*ceok_I3iwXY&qmbn%3Bx*_{OoEt`PQUEXxZT%#38@s$uYRhH8u
zv&me@QHjMvGY^pVK`?jor3nzORm%DGlR9Q}A^^^_^Q7Q2clx%QTXc+(rN#f$#)!=s
zEP#)M`J?y|5TZcz%k6V&o*&L>YV$|lS=s!<Cds_txts0~ii~QGI<kt%?(?vfgw<}2
z{MUnS9(;b=FT%^%Ig*Py+5GZDD--U`b$6Ams$Qjgrmm9Xz}F}e9Z5Vp`ggY>2AIR{
z6$2m#WUVzu4QL-A&b`=qgSgwEMJFMo1#BX{>rR-n=Qs0opZH&O0l^6%u#cav@!0eT
zHdpVG@MCr(v#A%>DEk%%{*b9ZWqgheL%v;vY`kIb#I+51W<)j87}q8B`|0g?xKCwP
z)R0e<{kig&;f)_|NOj+p?|dn<I{o^Dqhv(Q=v5JJXBYpHJA2`yyV}4*e&#$sCaV4S
z@v0M>c!USDZ_)4pF;wAhZUz1j%H@l`yX^m)ybf83@P?MiUOH!j>{tgFr8R%cn{skQ
zPxXEJ#H31muvJVK2*56m(85_qaZDBDPt8O(>dEDb>Cq9T)~2c)>kUdH+yFkOY~S?F
zUZVyzYt1i!h4C+^BiI)KXxKr^2_}GMTLE8&66>dXKXeRtXFFUgU;sFf`(}~uZ%YV_
z)ZjmUyYIxneX68WIK>TOiFwm=r#EN!&#LgM>vRg)h_??$#`9#Ze?_5ucjc+JCG8%U
zrDm!0uIcIX2&y?HnYYROnTHePMLKpq!S$m56sQuVr9KL3#q$m~7gO$<$r0e6q@V^K
znsXe_H8g6z9eE#2P1*}r0r=hHC5U(yY&wCi2(8*S5U;P7x#2{WG?^P>w=rw*z2w6D
zp$4!F!LPymCs8y>z1sV(M!Bq@3}sCSJ{Ks~$<+?&tVZ;N!u$%HDLbXuo^yTggflmX
z>H)y`3gXCy&~~%O)p>pNcAewARE74lp%sxIS#7n3gj_0*eA}nb@sH|NEJtfM632tb
zYpE0rygZon)E6o^c~r^;4$lcO<WdIcbwn{eE?&bYHi*$B3W-@j5b`dR1EarYW@_c<
z)7u8gy2>DPCJyN1ynTm~6`KwaSRmcOw7*F@{Ig4Wy$SAI{zc{LhmEtK3BlpoS3b<1
z*HVWjf$r+2Ce9sXT9quP1y{$)Wn8Wr>g}+MY$j>6LYB+FIN2Y=DRcv-#;}`>5x~=(
zql#cVt~!zwpf3^by^EJykaiM^c}|HC-r^e9glbmEd$bkt@d@ehPuw{LoBt`JOpHw0
zEYcnZJUGQ3&?B)y6EVlxYT8dI;wcmYL%+9wN1Du(JRpbZi{@mS$l(M#_7rtfn3TmA
zf)3H#s)T`a$52z!E-49Tl$X<(;|7tFsf$0Ekc7DB{i`wJk{;0{);n!dcwGURyE^cq
ziYmi5lHG?=RSJq>AwvVVRRxW7h0gr_EE9=InlL%mJvfgf9kRpkYkvKH*l3oA3H-y3
zvagxI<?TZ6v}@Vzp!+5dB1#Wp2!D`3?m28RE?sO2M+)inwP>NC0-X&OQYOj2tKPRf
zuLoA||NgFA{Kc{rHs2SP__O6d3dt`ow0^V}5A(0_cxoHoJ+>RlEN;c^hoCS+P*CJB
zf+oE+may^I4hUJmq2NTY1;u+ku(^(d;<D$GqEjEVf4%dcbfU^#V4|(Ak*8``+mtFj
ztL`jbpku32T4%vclKC|R(D^1gY;@`HB5*7_j=wKf-&yW8=4b(9GeG@;go65h1PFOk
zEducD#_a_EF;eSozK~*%5s!0X4|c&@K!y!cHIYV_U5y!Cyef!)T*fg8FEd==>)22k
z)B>QE$ZR6&shqvI@UgdmH9B+l9)!E=RJ{tHfN`rsFVj!Y--ho}ov|9A8;+X3rR?`8
zX6ZqLF(%wPu~k7~#uzqCYwU*)D?F;A!q}0+(%?`YR|fq<`uEj@r!VPu<T6G05GF-&
z@nmG_+e4LcP>go+7`V&WLuCdw>`QRXd`;ysh8~i9GuZ<%Ky(0V$03kPYw+!umm^L>
zE+Og{3PAd@W|K-yUE&j+FoUptc+o)M{rUc|zF?y|=yoB3dBQ=QH@Wm!20jw)V|9g0
zF9E_@bYOmBb**M!gEPoLhidbMH8qp|Jt?HXsiCucg)tOs*vP55QN;G}w`=826N!pk
z>|rT;ab<OkiT_D&CpYRjKL&$XjE{X=$I}DJpE=X_5urZ}@$R){?#VHS{%~V5T1pCE
z9oGfu92Mh3aS*orDt{V*TMAe^F&e_w3VgP@l(7OS0r~5fR|S(O8-hg{@U>8-xm^a-
z#XCkwjNGddgv_ZB&T=>ik4OLq8L&v(r+jmL88Nq1R+}EShGbOt-XSvl)fl?=2Nspe
zgKq=}6y_P=5Xb(jpQ-U3EsInLC%~7;B^(KbG40dDBQvQ+L<}UHP_QdzsWVCyE%l&z
z35@k~aU~{F;PHgfF{?6Un0M2hh?~-@ym_(sJ5Ivvq#`-QuB1>ku6D8k4Mc1;)LO8r
zNP(f2E<!0MGc*mjBgb1X%vGgkJEy)1?T0SB1VNqJv`~Wi-MTJiJG%K}mz8kn_+m%F
zFP#XfUzEvpj_ItyMO2q-l#AV3*d64m_ATJZ1LE~mowHm)Kx!xBxl(BJRfU-GCsu6c
zqtqN8uYe1P>AwpIA&fZr)Su5z*^&wK4Rbv@&$r2w-=|%C;mWdvQ(X6Gdyk08=~B3~
z>D8yESt1^(a_NCWN;xi=8mV!Ur>REiM8C<*Bvj@0(6&pJbV$e)P608-%)P$Jq<{G*
zXwLvdQm==@*B0ruAN^OqhZ{GKK3%i<bO9?5O0UPP=;?rRa0+YG=~np^Ko7Pgj}ZpT
z8E}vK-t!-yB;>4a8a$m!>(fO=Fws0N`reXt-tiw}d`Fusoy%)KjfQXeYP{H&-6Q@T
z_eSxu8e0GoVJrDnY`W<4O4hS3KDQicvPe1dMYC19(D`PTbe5Ra$6vEG3J(K0&6>j|
z0K~uU<TvwARZEP+JmW7X2cYB-5Gs%#iVBDxTzQaP)?S%m_n6>yi(3-0G+JA9{Rcsk
z?s!j^RTtJDZ4cEfZ@dPy!nCYoGCeqUf!M$M_F1$E9s-h=Jr>a?E`u??J}Gh)GcK*b
zqE#|Odc>k<Y(XJ=^rh(Eyk4d=AXbcsOh*IyTW8#pkpw&1tFJrcGEP?J6wo{z$Ij)a
z$&b+Z@X!3MoyEDc_QKjF>65f4u8-c%!no>+?qy!f08?LSbP!*{8VC|6>Kc;s8*M;H
zj?8F^epgRWubmO$E_A<NuIIDOoc3Ht_~K+nv|z2aO?A(TFqaX9W6`5*@wNP{%mVG#
z%1H<Pqsr}OE}?1c)ytEm|ClE>%0Xf3@anzP5K@78ibT=Y%(qYin)u+(Fk;QvNpXw^
zJq?BX+@K%QxQOA(kfK#h1~Oq(#oqCH{r;!CL~zzFPPdWmfsub?ifx$H_V<2jSo6Y8
z?4aiathfhHmypSKPsQX00Vf{B)vmT0=|3~<VnU%pebSt5m+RDN&Nj26ipA;{z!-L6
zN)DquH0dp!rhzdWoE(0&TKCvw0pL<p9=W}8pWV2+nSm%N7*gfx=XJf8G0pjV%mkq5
zS>(_l(xB-93<t{h(E}3a87gltkkQ`~v!nom5g3*zP<MyPY?~b`)*L{aQSaoDA2T4d
z^t`XExO}iu=(@T)0+^dhdX$z*K(+>@Hu^ANaH%>tsF?(PFGdV~cS-J%vrO?{=|O{v
zk!8J1{mbTAOX*MZ2nF5RsGw7-4;wiFK;OWqRsVZ$Vfz*)h5hXw+j6^^<Sk8%^7!J^
ztfc%x;M@4^S$_~ChN=|G0Fn>g=8@dYLq6=s-c<Rn{>a&OOkMIPSN(HA-7)xd#T1Y3
z-CIw6HTH!yvAY^M<hEzUYvWeD7g44Is9y;PhK*8VX2~v2Y{c!JzP}a_&V65L-}tYg
zNZ93Adt8&AQH(+zS9~h}$!93~dkC2l3QV^!@&BQWRkA~16&}1q4I$z(BU7AvZ-uCl
ziZGdXR0Wp{c`h!S&*X^uCMc1zW4dM<HN864jgFR)2i5jn!8v;(nEutvDr}whEcX>A
z86w=gVgbO6$-1Z#J3*>7aGwrTzU<S)gw-%RIBkD_-R#PBcjR>iZYaIZ_CDZ`(U*6_
zrQ8|r14U{*jU7H@`imLY${Im&YpB~+EU*fyq@j9Jx;7x*Gzh@zggTTr>Qjox>yH>i
zH-f)1%zcfn?S}(KK~M@eu)&b#olJ>CoH+HzKx_!F_H+ztAPLV0$7NBB+1CmIj3M9k
z!Tgys`lNkOXc3$UT6t7$1;L=&rUexEocsG%#JWlPjpRG;oK6oMTJQhWe16aq4W+kz
z1W^YWhGq{F&>G;c4Co4O#{r8VtvD@VaCa`f7+v`-r3s*U?~Q$CowxP4`+y-9fZ|CT
z-$Ev3i5I5{58kO%e5S)G3Y07AHSjuq$*i_<uq%oqj`V89?y$ZYV?D0kufU@+XWQqF
zw;%p)*%gKwo^BCZ1(?r9v^xDZZ1mP+B*)2ZeUL~<cKu)zRN_Quw|@s!0>kH9p(v{a
zsrtdR6k5V8!oL?034-Xo+az(5^>_IZ8`s~y!JxhjT12T*W!AY%2}CisK412c;*7Oa
zWOTOtSh#^?Umgg<&eVwHj@!3~CSpmJ6h=+S>|(D|DXU0u4WtBuOW}|;=r^mSW}uv*
zn@m@On2I<q7|QscgC!JzuTG7}<u#g&i~I>$YHJ+@adfGvZq7H;#UuDq5WlaCFrf;#
zB89KNziX{*Y5nlyop76c>0!jbzH&9`O7lHLhM$h!0AC3a!*V<ys5EO|1C4k$kDffu
zjvp)d(@G#%$PvCLS1W%<E+|^Ql3Dok3Z-w(`tH6+){KBif{|mvu@%7ODw6wMechtK
zDhy;kPebSr0)bt22qD=l*OIZL^HciCy)l`FO392qc=Hx~e0-vh<iWg^tbXLanmWu&
zAc=~Hr%_Zt^8)5CA>YecEe4!@U=z!a&C{1#ybO5N{7>@kUBUeFttf;5BuH<E)#fzc
zWjQGWn>R>VfnV)?JTickzab>Y`9_x&7?(vxxW~DI0K5?+CQaH2m8HKJl(gXgkE9E6
zMPB7Vi#qn&fCBI**<c4HW8VF5{*M4}dhP1_s6BfKa@?Ts;%cQ8_OyEXbKEB7%X%{>
z6ipWf$TdeLhG^n6WQ|IRo@W8EVtJ$Y#vQhl)vx1-W6~mHHrZp8Ew|lORJ{OqJ^eN;
z+Z7mjD!IT4GoU%hOKUM%k9KrN#@yiXTiI7E`FUziN330fUo8QPXC9`;=ySjpZ%}I;
zt4>c-iGT86X;jDi^?mysqiVK6fPGZwBx)rHzU?8Wp`@^srnGLz%M+q{kOw<(r2oyO
zln7tb-FH65wXoNI?KEIN{WGw+YZ-~A4;ot5IjD%3`D2u_`Dn%f6C3Q+sk(O$2hXNB
z9d}9k0YOi5m<p4}l3TEibbtzMUX8PQlc1okky9WMWL0((moI<4O`qXm*lZ|m-oN3}
zC5zqw+y!=LwBgCndBi=FGtJtHl5%xjaQHO_K8rr{`u)qnz~2A#U_>Arkn&Dbm;;yT
zD8O{jq<7z%n@I-+Y+NUrB>;u0h9%(jQ~*Kn=k*T?Wo5=`pu4c2^Np20q*rITNZAVT
zJIt$vWx26w2!vV2t`j7k(E=BcF5uKeE)IewX=2Hglxb0Q0)0sR{285{-}tc_mkbTQ
z=M6L(0G&HGML1xe4nRmEoR;;n=K-tIvr#LHU^Y2o`OBcydba=y&C;rOhG{`w=`$MN
zj*%-sH6S9zN5+_HzaKr8`3y8Fb#Pcw1;tmeotX?nqiio|gJGZnwHNfiwe_Nzsgh^O
z6t@n5kOYVgU|j?9bkbiJ)DS?;A!tbh8@uR@jpOl-&oY(3u+~8i!|L+d{V?>!8lG-s
zVJ5q3;@dt(Qkk^>zAO2%q)cpto1HwM+Bf^|kRlO4Z}K?`i?AEfP{pb2hyk0$4R7f4
zjd8&mXJabpWf22!IJxzO<WcZx-MlTmZ~Fg%UQm$d2*!MI?p#?8Y9Fy`sf&87b!$f0
zwg&O{TayKf<GDeq_c2;hVywn!5181tudi1|O(My%*_?4YvOYT%cPPjW0>rITy(BAf
zF*`<*$j8Z=yTJUp)(f)yA*vp4ay<>qotEIQj0C~qmKNw2FYi3Z7T#E<wjfH_7X0;j
zuVU}D)O{Wdd$b{M%v+cSVF33Bhy;SOI`HT5+iknUfvnlt*yAsx`;Aqf3>fQdlkfvC
zzZfm)1`JkaZv+%B)mhtZ{BvN6Pc;~Q4KnAece+*aO7qg`BYPe~-~t7dK#-p@1a$L{
zIc#Sz2raORnoiYJmZu<r&No=;-qY~Yt=jMN8PcS$q;01|TvZ>k4XyHh$3(J$f92=u
z<0d|6jZDpG)B+0%0beB5iGMdo=%B>uE%1Xv{kH=X?1Mr_w(0smfuuEPRsw%>urAlt
z@HxKn?Q86G%(n0NbX4lqm&2|8fLnG1Z5--+w`@?nyFHP_3o3HLde}IzJQM0TT%i3>
zGxff!wU6f@pmmn>xKZ_K?EqrZohI(R3WhO2sDIof_Zhg|Iw~3kL};Fsx5Gu}R3Maz
zUf)RuwFb)#=BEk!&R?C^0Xb^d&K>&=uu`|JL!ey#fe}#wWIcqI8ir7Fj6fGo+m3lW
z1G!<+#t5gEhX28_gkYponME#21dxjYOT&~8seeWf5HoI$UP^$XAgAWRC$OFtn!<j#
zzjgia2f$&2V|X!2-iNDB3wLnFY`*|*L;Lp6;cC)<jBW%j7nO7s+uL-E&Dwj2s}x?p
z&E7cF`Z!>2qdM3RDujZ?I8<pLeV_Wt<Jp|wl_LRc-dP{h6g9TAD>JdK#^awcAu}_O
z9o#)T(k+JBz>7W=pkB~b18XBYDh+Xl2COXe>GGYBk#~9RzI#sk!S?3x#?BpN7}EB|
zquI}Bm-@RSQ9WKo@YDp(#R&<BP&n(Gn3v_~EU#^4)sy0vfXwdj>Geiu8<rsFy5UNl
zEx#_acnq@-bAa0tHDM!wfldG*hv0mFS{fxHdehwe+oeLYaR)uQf3zPkF3FC`vUOp0
zOeIwQDjGp=Mf;CtgIrv|HUQIQktM%??FQ%vfkl5uSpGJ9`6NnoExDGaCDyj@kpsVe
z^nRW-BdkGIvzd<}0Xzj8R|G>WEr2U!FY4&)h7mo8UjTf-^@jm4t^m~*RDP~=eDYk+
zEoE$3QF$x5jTy*!hJOmLH(RXf>Ohj?(G99<RqeqjUp~F}sz?rWT{@X|EIFOFQRuAk
z!<Q?}qFwKXd<V7E3VBOAEqr!qL?9v#Y*gzY59563&><rRDNF?JDzNKW@jmAQ0Do6S
zv47pM;0}VdtzkK0i)(RQV#YhEV~FK~-T?{nsNlsU<v^J@7-#?eNbZD#`&t)0u;ufa
z9q+ppB_bGIc!Bg;_BNGYhs`|`_V}q8IJWAD`b9bh3+-c-u|o<2@PBJtw#8IzjVJLo
zq>G0pG$R634>Qj-Y`So94FD(5sT}$7l&FMXJ<2m#GrF}EeU-m;fNbRm{!CEm2aePC
zq>%GhsDf7gu&%t*I2-$!$JiY`p5bXwtn9eE1c}~oeE6-Sm6W|50xEvuz$5}53#Svz
z56uWv0hZ4C%W>DcB}^p!p!e`QFa!b%!c=(#c%aa0rR!H<0`x>0A1GV|Y&zQf+Fw*{
zt64tGDN*MYuA}SjLQ!AE3)Vg#vVxJz8<Z6pJpFR9TV2lWWP?F}02?KvA*^4)SrEl2
z0*6_}_>*+~R*O(JzOpqhcvMJr7rnO|w`c<W3jiYmT0dr@I636E4|XZrsFaNbs~)%|
zyd{TE>60>mtkDIgjG$h4a9UwBdp(^)jmZO|@}NH~xfB?i7E2dADN(_aj2d*Om2m;V
z1b`fg%J<EHfkUSv>yVi53NZhAVJz1L9^i2m2Q`e!^lxCU<xel&L53%<lT8$A#|aXr
zN!2pc%#*S&r>4W^5ycKFLifBnfqg;V1q7{e<N^D(x$9mvTddSmx3UxkgepPP02rmc
zOC@k6a|w0+7VX>yiptb0Z>-?UM`jZJSP9yB)fLO0c>O_SyhF<ez!JfN+Ad|z)91^E
zlqTw?)fJcX7jw}0R`O~8hz|tHS^z*F1!PQj;^5UaaGe!Fv0Hkj9TNzzdV9_Z^Bs;x
z;P+3sMBVfXRN_1TV{TtvA+7X_%L~beknjKmWI>HWdywt!Qb*%Y0LTX#{AgBmXzyvw
zLAFp{OPQes3d?N&zW|xI;VIsN!@Q6L*qSXbgq0mN2~eIucgR7De#H?W^|xI;lH%dL
z1b8~}=cOTNtp$&th!>w2X!0Vl`1a9Kq`LEdJAl0q=k8ow_PY^ox9upx@FG6YR0Kjf
zJO@Ij0PtAbp}l#z>;f2Ru%e99C3+BU0}kHBO_Z9{8t?4N{S73zic1NAvjq|v$ezPw
zt~O0mCWDQYF1$*70ZtASGgqf|3P^V>==g$Fh`QPZ=(Kwh#{AcB1FQT7*4&tS14@Jj
z+wmOvlX@O=(0c{4h5B?~0K3uW!Y6{qAd5C7%7kFyxoloPIwb<oWD}Vb19Pnj3$~E}
zkI_Le2jIIw7r7TT=xyOMqvLNPkO}S5%T-Li17DcVg3n-<!G#_dXp;dQaJVZE43&vd
zzJ=gmz`wA~Xj>kAnfUX0GRk4^%e>rNJMy`J0C5JYCrw!hrx*Q!ETrCcC|9UDXU9hD
z{_@7z2QSO>f{^C+>Cz`NH<0-E;KS4W-7&@6T7gdN`=-z6ENb%9ShZ!!EiGj&<vOlo
z7Y-LAqspjBajgyOm%pR?+lAev(w7&q<_Tvnqlb0LdMA^mS)(!uqwxf%mZw@;>VoA$
zr}^rf53fR`5jg!u0u`QVgjNxvibynt+@0ee9eb}{T|Mme%alz~CnD>t(CQwdH|gC`
zIV~_44?$WI_iQ}vDIs}fzpmi#N8dJ8#_TWLU;kpFHU^~i-h+#0uhnioV9fk8lUTNH
z(*O1yB;!M>4Av)SKnu+!?T~91JJ@_%>}-Bq$~ilF_nJ%5$c=q4Y@U*2c6&$+ZmjO=
ze)-ntM{~2wR?188op;|Fp_VR2Vs}oGk?4ikU0A;4Tbv=L9k!+!{qWwzr*z=mN{7EK
zxk5ZctpuZy!|gR>OjyuGp7ATcC?nxo@3wi9KqoF@a_VSDN7J*42E}q)@a&>V_&}Ex
z>9BP{ApRT>{a^om&4DUTgEtXthOCWu%8#I%^4>aw8|1KNJTi=%2iKj#fMAmpWUDZ|
zTmQ>Y2t2bqR>MxS{-}7^9S82;)GctQY&XKWZ3jpit3*jG{kb?bI&0>gN_dM{>lp7?
zp!I55WBup~g7&QOoLNVkDd_T93Xl6$fModQmfx%r&Wp)X`hcwJyl(o=1{)xa{9Wq(
zw_=^<oT%RQXSxP6I3ykwjhf&vc3mIqKKE?wNN~wfzzQv)Xa)<P)fSL<*Z;Xz8mEu?
z4M|AG4VdSHY8(P$rPcTaZGdM~lzQgHCW7-q$0Z?YnAkKp9%v=<uY#|tPX-rgFn%>e
zEmNYg4F3dly5uMm&-Pl+DW{T|1$ApA>~Qei%A5YPzKMpF6-%d)6o(rYTA5F8T->84
z8b{--FQw6SwW*ZeDw2w@>fLZD+t=D%YSInVgvL%^;D<hle0ltE)s&6?VTWgN&pDx@
z>y1lm9#fAopTXl2vJ%<LW0o?;sR#FCmn<_Ci8yM7{@%-b<>k3!bZ>#K9qe%LiyCxP
z{mps0;`iF+4o3jYm4V8gqS-yU^Xb#R1Qp|iOp|{lBUU){N;A}!PF-M*6l=n<ZS)H(
zi8{?XUrZLsX6NIgK~wQIRXF@aXde?BnTa{$Sm(W~u(54{+#xMfD`*X_{b2N|brk8N
zRxCB9Mlwc^@*1rRqAuLp4QAj_><{!X)Y-#t+@2rob9Z=;@=!@ynj9<xhR+w<{;hQR
zZR1B+jf|q6@c15@A)Z}TlDsx95qP?A{`h16?B~4Mf@cYtO@EQ<`AxU*-IwO!jQc*{
zOXIQOO&{>nAQOHg_YBqRNnl2YcxpjduRz%bKn}nlQ?QRR*dz+gGue?NFq}TEsLLAH
z8ma3F`(oLgnjElwbKUWdD?bh#u92RWc|=&0*@eGu;?}e=(pbO3MAn`ri0KI5)Jm&*
zddp!Jm@3d^lC~;>DOTHVY>;>Kt#<tSRkBv^>0YRRAS11;_3Oxfp?6aJpT$!XHhAVO
zIu!?7WCq&;H&c+|$yH(rxw4@}q-M}t#(0df$mLwc;br5>+t#eJO?c5il*o+fiRPS_
zl1{g>`9m_ttx{BM*nglDRLCg#xfn?yVN8<iL-ZdEC!J?yOQm0#X?wb{_s$CWhPw*s
znHrVKv|C>KeCi-qwodgr?#FjOtYESTR}iQyum%k-E2rt$H8x07&KBIZjQ=#HYfMe}
z?^4=6Q$kLXwB9-1UbEMf{Jv6Z3vt^!MFyo?;B8yUiU)4<&XzeYQecd-!QU^D+xhg7
z0Ohnqi7TIy2^!A)*{6WDepE1bzLve>MBC+cZ&u|XNfy~3wx{)T@P7)t8FX7a8hL0~
z>L^dg83OF`$$82E&DIT<ZJi%ttm-A(jcPSYsD|^1WRK`4TOW1uDK4^mmp?YFsxSph
z6vRxaOwH+=tx&FmXTmCKMRJrS;5}7j52+rNj5sU4@~$c%YQgi!w=7%IrT?@%epfSJ
zSHi=hF!i%mpJaC5y^D;i13U19@BWrepnpW2OuNJP>ihD8=H5SjSu7QewD(-<mV4=u
zP<cUnX<^8q8u;$$zDlwxZ>;|4I@-Sf&`d6&0$xtt26r=K4);5MSaKTa!*(#E`h{Kn
z6WB=59wa4e&Ts2`i)L3^x?(<bj@)YE4x@O#6<j^O=(X-}UiQ87ab4p$C|}+Sd5B+a
zrFUI$aA}Wh5_h2=r!j3U`;+zb>gi~Oj!R>!=YU;pL%ZXCZ%~{;+&3{+NfM|-olmP?
zQ9LUhLm9^`)h!?9r<g9;jdWf$Y@GJ5K8DV&rfuu43XfGiE`3*cw-qXVRmt^TFQwry
zmYoYccQ!q;g7!M(YGS0Zy~S!`gf2y0DTD<Q|6Y$^9DCPEl-nLwt?wzc>DUrWA|rh-
zl6%d}mQaNm9=*TbvQ}7VyTBXWY3*+}Kao+{u!4*rDiV*NItYoUKAQ`}%n$Ah8YW)b
zJBAC`&D#Fl?ZfXY{KH)eJ$u_^o)zq5SoKzNSJ-Q=(oiG(fBbbzrb=)RM#Q?}s!_p_
z%#W*<*qJ^x0)^%wv-d52s<VH6T-yEf2Y`$qTMWILc{edGjyn(DU92BgOh2_Y93yo9
z;~Rn-7R7oYw@F*`o;OVe2if0R>KOcK+IIG5#>c6Vv>SP~U02WjfApPMO=p>rbcV4O
zvA1)g6-)fmrlz2Pegrpjw*A^Ii-f4C#1UyRvjqjMGQx9+w+-W^#^fjmDucYlD4eRy
z=i4_rc7FLTWW(i@5q$Zv1&aY@qQ~^aRe6VYQx3l^T3;X_K%KHFPB1VqU*M|58iouh
zV<4zox=vbQAPCYJV>Chh=VV)jNlL;c0Oi618d5go<>lj&(lT%rpxnHua-3YIs4huM
zG%?OcDcXRobh2O@(qKtmg0L9&UY#l>%*m9ozvn%k>_Pe4BN}LMFnwsIkWeIb*z}(5
z5NYin4+OYY8BtLTv7q!kLjuNHYRX}wx2a~WTtr*hS7q%K;cKRMJ8^K)fGhGQj*4s+
z{f%MS9m%knF~t9e37s_Xet&NwL7X8etOMSTvDF-kLo5i=;fBwKiksak<2}U>*XMdy
zedlr1a2jaxUuIrSlrTC~@lmUP^c3tZvu$nkI`XFgNL|n(+dJ)6IeT@4|7x#sG8%(I
z@nrz*-^wge3=az3<OoZCE+Wkm#J1k!BniK;Q|8xG?zH{2Swa4~{Pv<47}S0PihZ0j
zIvJbwSWNq73g2HVodkHUu(iq!JjA!6`!A_<GL}uB(#$}}@;!U#(Dc_UCQ!;-6{dEX
z#f~fSntl7RFJp8By)LyIhHvEe-Ll6v=%ig4a#}Gys~0#Q2Ha9*3Xz#zAomL0@;>u_
z_AZ+Y1ZfOm#lFGcKMwT$+j;dDow43qncew?xYl)f=NTcm)c&mAhvZbZs5F~kof{Ep
zx+Gv3c<!TAwYzMJm_<=X++U=SZOn~OOn7Tj9^=t{3;`B4@It}`D|&UiqnqZ<=;N6y
zU(Wu7n5gsX!3puV+3ge%;D2AQx}SV`-@59NrP^G>hTMw%q5pU{SAAenboqlQ7VZbK
zd+Cwc$H?-3!bXb%@|ygk^3R`QT~VH16Cb)-G%rGAEL2ex<tR`%`{O%9Da|+vQIic!
zS|2d&@gEI({>FUya=ODLlXbTHe<WR1R9s!N43-ciXmA~z;1Dc0gS!QXU_l3WcXxM!
zTX6T_?hxFA%iu2eeE(f*9(b5p9ND{fb#--D{8x#k*1q{=uCz!mzx=}-@=|#UGD8n1
z*j4#99S=V1#*JbNW->$&)-*F4i5J4VK^w)I{V=-TCe_vx1f1xFUx(Hp<oB#@|IVMW
z5YVao)b$0T-#rVy9p(VsFl$8zjcW3)p{7C0+M1yuLvM;c&oIzv69@fJLxkk0yJy<<
zO39A<cS<#lw8Je;q{eRc)Sv7iZB4~|ZH?6oX*h7A>aFKWR^cBWvHaTntM!MlW_gCP
zi>9}ceb=isH}CzJbrYj<=U+XKKM%?<NyR<Wb5`zPvvH@aSL$u@RNHhB{e2lCJkQwc
z_}=C?Bx3%dRb;-&Z@LNG1P{MnfL-28VNP?T<-C;^r}DD_5oeFYM-*|?zGQBhBmJ+R
zcRL#9T9E3fb14^N`iJ|*TRR7M;e!Mo7n6j-Buv1JDQW%&378wFtyj;-;D}4~I!oF)
zI;I+Z7)CTLnaa_H70!@b&epiU^#LXw6ta7ccF_EEup^wWKzlnqC~#0I&~HePZy28Q
zII}aRyY{bvt7?<`49@3#jjpxR7C=d3s@Yw)<vCjcbzjDqKi{99jL4~xgdm6|vp6;w
zReF0+%1qHsYps-=d-yyGT*(B%ji!i)sK`czbcU_XP4+4R#sZ-Rw4R3!G~8TG6FHtw
z`CcoHOSSji3QXiuAOO+&Sv_Y{>XHU#!GL=Mqy(PQG;5deHXgbWv>+ZE?}B@MnM`95
z;H0J$3*j-`d_(z!RPjYH)v#Ip>Ba2=IQ7uuQ_~Z{82R_EL;k^JlC*{>x)ZUAG#KzO
zqvdB>H%!_oCCkW>;B1=W9O|M-&_{Z*U(y%RITUR}!eWu22wqf&D2oswS^9*bJbC3T
zFb)Nm8sU3a1}<-*c|Edx5}I6D^th{#?Ht4{__q1lFan^LDpLRHVV~Q_Jd5ia=es-i
zOX@Jd?BH?<H`@OB;76)IL07|6wtzL-8k@WlHXf<mRReP-brJ_K5B_rC+tmkx)eYp5
z@V<Mq;MqY5ZYR&w{8>24ZTJ1fGozA3#L~cSU>7Dt61HEQsU@qAX69&jF;e}dfyo)z
zzg<U<y;FqeM>L*M3jPoeAWL9aNenA%`qF8X7aGtemwWo;JVoq7l!O1T?*v^TlYlBC
z`ZoGPZ)f(J@O0-#bM}T(0`C36vjy{kW!vJf`9=>tV1BF?{$uwB7X0c>N41tsU9H}h
zgpJNN@cTN6_bweaZA^_jteMikzObdG3inKr+(VmU1W2$S0}V+#61V=K$=Fj#p?Epp
zN{z9va8@2;9TpsUE$3Pym4WQ`YFIhs_JC}`!iinBykk<2^bTpQwn>Lmo|;$`ySFy2
z;YQjl+KQ(+>vE`<;5^LVm)7aUynrQ?8so6=>pD|9V?<O10o1cvvSnu3MTlGqHsArC
z=4S|CRuL<U_u=f0tbb(uJz6|1h!(b3A#(FUVB_gROm=iBVXVd~MMj<L8w@L4K|)-%
z{<Hy_vM~?CE{~mKXlQQm@Zv6YgZ#tJi{dG*AvUlKkl1QV@})mI@&r&*W5mXSQKhEN
zVZWhBz<`B6@*~3`Guxi~SMpLF#06At{M@fEJhYl}Mn;jyJ`T!rBuDbVYA(YQ{cPmw
zC%W=QxeiyUA1@qF6o*36e+D^r30ZG*^RYrc%_%66Gm3m)sjycC`p_9;!c$TvOZ|EG
zp|}`Gqmmlfgwf-pZu!r_Sb^1VVALd4ww_r9SzBYa!8zC4^-M`pk30_r$>O|%cnqsS
zDh#gX)@r#9gCLWvyQv)o^qwcpg}T!r<81cgLD#cVy6u`?Mu+vcRCrJ@;Kz`@)lCVR
z9hmye$yv^?&oFpl&8yVWW^{1>n+~(J^4IZ5ZbN_ZMT-|dJdB}I$Nt5VZacrMzb6f)
z6gU}-EoKO$<I|-udhXuAxqk4&_uWQ8ZGH@4eMY<&sqz);1C1Se%NGWs=pq?7VsR{v
zK{dJ9!0R}FR+){ADwv*oRjr9>3pi~~E$Rh~*3c%aE?-FX3zRK46vgV<A#H@*b2p8j
z#bAWn-OTOYxn?iaY_@ziJayS??j+T6cYN!@m7N9XS^L{<0w7wXmHO$LZ)B5hJ_;zw
zQDIEu$%hDMdZRn~KMK4!><BzAhP|rfq47<cx^)UwEa&N%v2dhQ$Fbp&jGr7bJ&kYp
zq<q2Uyk~x0UkF>5sA~G~Q5c<DfPDyfMl|wK7ri-ScGlKeXcHAbRzhsXyfx4flf))7
z(>B9Y^4l-B8G!oA`kPtWoq$%JqQ&~$$)h~kDCp2Qa4Q!Z*lk9R-2JmLQCLwH#QIe$
z8L=(dlcb(ka1;7kKq09WN+zsC353S>>s1u}w;3ZaMN=~0@q_R|94PP&C(zc==?gkM
zFiVaM30Cm!hQ{sm^ox$}>NoO*JGgaEm+byRSf9792VSFIbB@#3wW2|ZSrk-iJVGfu
zZ|f}54(~LFl)t5amqP?<;uPZ$t3rJ7;zLV9vu1Xpz1*4a5qj7TTiXUiUbGjzi5G0h
z$u=J$>1Q}_1NbO(ZI<?shp$#$e&qY^TTEQNKmM7|EGwz9iY=w@NT0@VYrneS*(XmQ
zi~<XuqEx;nhu9_e1ta6srF0p&FNrmK=ox~|>Rv48By*75!xJ4s8%**;|8dn$&(%E~
z+Qm7z`vCF2e<Ui}T~E?tO=IC^{nodym%4jDEexn)LMnfs?uhd_8zvgD2k_m^agge3
z?CxBZx4+)<H4H>0G=39i!!R&r87^lgHnQg%1;CQhJPZ7`@MIQPN$4|G=XDEK`}4C>
z=WYKWw_wx6LksG<w~wEDZ#xCFUR#(0lNwFX<7fQv1w)RTd%EnNt<OqM^8T$Jz#ery
zM@#|}b9T3P<<>oI05d-NtB4iXPM-y2vJbiC?O9nQKb(KYretT3<1b7*?UIx--whtv
zh66(fm>sq*-^+ZV^1dE0;Y9ul7+Http<=}xq5Q+*d-_M2V5F(%c_wK?{vynPeSLA*
z8)B;7Z0nY=@sRIQ$|XniG!T?s`7&|-Bfgk4$Jm%wiuW^BPFN6(Y`EhnRX;!M^pyvU
zQIbW3VN17jP4_n_b1gucHEOQ8kVX}ayZAW9d2&u1?oea})tw_IPW1GO<e~`wS#|eI
zFoG+{f6sdQcki>;^@X`ej-qFu(qfqs-B;KBn=h#l!ogb&O?u2Qi!mZnLtAb!Z`u}_
z3Jp3=O?}24j~rRdQ+f2q14%GSlAmX$3XQmAA1d1+Z9}V6A>iO%Uu_lgbMy>fsBOIg
z#<nT4I76CN%8)s!Dnqu!5($XQ0LS;_toN=AL?MIuVAW2uCrybml7zDo#5*3%rIc^J
z#m!W7y4^~Wjazx^L>`vgs)pHn8&8GNt0>xq!OtPP;1uM@CIYHVkQ+?Jn~aqb8!j*!
zs&$osTV(k`6;L)piG^|dr6A5EOqPCR`Vb~BIGh&Iz@m78(E)XmoJ{r;ivPP&J57e~
zk`gG&N?A$DpQX_8B?m+dWqcD2PRb_`Wzyi|KL!lSN9UDb0%yoAKd!DyD43VZc;+Rm
zR3<CF+><k!|1)*_o`c=UJWh~dK(cvAX%}O;sXg>mWB0U@33_rI4$7y`jTch`k{fYO
zVyYa}4`FS^9Sel|8~0kFzVC7%S4Kw@NM+c)v2_OA$goA~JrM0I<-Ikan@%bA!jmv3
z1B(%G70t~HWmR6rpi~k|QRY~6dj3;rJdP1}CFw7%O0r(4dhHpJUMJF@U3~UCemXiq
zl}4%X9(8#3j=&(VJp}sH@gsz#LvtH|^I^??Ws<;%zyC@g7OC5-79qn|)--W#EAPV@
z$cI4~x>SaNKK4s^X{vz~DsIv8Xe_a4y-{aP_Ahfa2AHf_0Pyf&Ivc75^A&Au23(s9
ztCQ16!2<Xut(32f0b^Q?zJYV)zoDXHEA{4_6)a1QDmZJ9D(jh=qTr7$twrcjW_Yb4
zfNCHs63DCmgB%Z5nHtwybkHMBF2~2a9|9QPmGJ0?1LYfjDwlDXarTCp<l|$Wepl~4
zc)Hh{QmJ(u{HDC`jU!OryIIQ8EGaf?jA<7D)}g`YN=+L9W^74PN3o#%6Uc<pytH)O
zwFpz@#ZL~nm-Q(Z4xhyFjekF|`KwD?(@L+p(A%ifzL^e7$KbJQ7p+`kA5U46lDLZc
zYsM+ac$JJ`9*^|Xd?kP{*-8;xD^D!0di^QG!1?s~y>yOp-B&N4U}gZfQ6uMP2r&&q
zL;de_t!4QVW0dD}&lh53YgiFxMG<TSRk2TMp~2y~U(Cv6dGX29Sn!7W)6xjYQljD_
z37@{xu2}+d&--VY!IHl#cXC1QT&Z}YY<#iJJFfx)>3hXp&x@T<iAa_)=8Wjmr!<c+
zS6NeI+F|uBTO>=;H%%$*G@y%j^V4%I<7lpiwf)v5HEE81p_V07b17+Z0B?xO^?8mq
z;DLJ<%MG}T=@N0!Pe<>jriDFS1VhTaZEh0aG^WQV&xyz{H9*|<AZ1pe<-EOyMSBSr
z1$w*{2U+IUo$h$)C00-?sN2bY<m(LD>->CQ=f&JFK*Hn6D*+f&uq9VoJ6xR5cfFBr
z2qlZLwQy?_s)3dMg_%;jU0l&fn&g+1!NMc@3l+{7d*ruTR^OHgB~!)Q1x)fez`xPu
zD7W+jCW0;H+6)Yzff^t~RSN4k3vq+VGJmbu!e><~*#*`4SiUh6LjXHq<(mWjZcDO>
zKs^y-=e5c<EN|*dOIr5W#X}0LR?&FB3?X0`qq$KANJH}UY=Fw9c>}|kyuXbL8xT#5
zIb<=^!oaG4>ug^>?}JWeTrOpcY^0IId&O^93m#4<Rqd`;8+T{~cpljbz4h)n>~pp(
zHcrwNBjcPKulH;;5|>1T!&ki#$R)LX4iW?IBmMWG&Z2DRH<DBo?bpvJ%>055rZjFj
zQ>Pz*aKYp47-~@=2Y9@$p`|P>R@OG?8o5;vrK>ktF|3@TqJO5M1flR}dP-0bgr&-Z
ztXWvosgojE*b)s{NR!i#)BU|Z;3L5ZcyHD&-g7#cCJnOrWc_ybPb6rBEOkciswwpm
ze%K8+Ba7fo*6&9i)225^^M5BbHDo~pe0+V=>twt6MnekUKC4Ayz%#{}k?;l@qQi3o
zHphRD6MyqqOt8_+cFF7DiwX%`52r&zwg|t?Gv?9eg@b?$;p$#0M_n(|#Gv%gvvOP=
z?gDLc#%~+d(yz<)E1b#1j-j990RG0X1jUJZg+f#++rz$0lpc)s;(6ODpIaRNCq<9P
ztz^RsZxQNw_CAjm^Q)>n5%Ko@7+F<2H!!|*dv%o;Sq7mI$q6ueoFk;3cPE^6bk_?A
zCraikN>Iwfi1K8bSd>in)5$C*C8bGYku3hC?&iWwCY2k`1k_vr`c~h47w}-nC`Vpl
zs7PL9;sn|Tlx<Rh{?#K?td&o2Vg8@U3mp?R%RnK05!CEc<Vq^Tv_=$kY^Ah79gh<0
zeb@($Qaiz%mAbY4TN2}uiC0gqm*%Goc>pe}D9Mu$e!`WoN*O;TAk_Z4mx46MyRTB(
z0C348Nz{!yP9v+jfVkcHAdxf}*{K$kTPh9J;}nRe&O-Vayu%*wpIYha;)6({%cKWD
z9Stdl4=O|jn;%Dy0uR%$Wtzt(L90V97yEHSt^8D8q%!2R*}ymSm;(J4Rkuq#kY?xo
zMe2WNJ#eT3N7o@11#rD-AFfw`AsABGUiO!Mo_7I%(q?xudH7#{q2-4Fj|upw42qu}
zdbiyLh>vbRukzZoJ0zh^RGvI&3i|?tq`=h)M(6X06eh8yU)u}5bC{#%CsACLVaff)
z%@&$sO&vN=ILOAQy4t4s2ReKry&Q1YC}`9kyKl)m)3ro8lW4f}aLu)vl=CdyY_Tm*
z0UP@om4hAa>T6LQDx_Wj`y@exJ6U<T^$qzssq2b9O()YzK)%jenX$?Bi6+H$pC*Op
zZHrCtuADh`cu)yy^sw9eNf=#{(vgF4a8pQwX`7d%=ycO#tFLcGxb;>QZRV>Wy4c70
zcR;o=q#P6LhBqP$Rs!@~(c>s=JjwmFy30T*BlwGho<uixwxN11wez#92&PE9$Yh1B
zJ$0_rh}l^~I33~-FYk<py3yy0w_7+ep?Jz*>blI=F$VqnUEJHX#=o3yE_PAwD?Jx{
z)U|X+kcb<LEE*c|DeSOmNB`zra(I?hM5(f$reD?F5G&^mKm@32M9f_*0g#X*#94dZ
zg|~D9_{!4ERv$_waJ*=LUS*J%&g{R5g6jzxssOS-gWbqPu&^NIPhu!ZrKm0eWnUGh
z+l3~$<pNhLA$7}Al)@&37`Iqz(wIpfFwpJ1kQZ#WcQE2UpvM9PP;i|;?&5*+drg!8
zBMv%0YAU6ES`enUEh9V#5w>wWresOxchfqkIOiwz1*+jCOS~<2*tSRa-5n_<l1PaL
zKIu4c^6@x%a;v^98hotZxPl_dytGL(swGYH`o!B2KL{jorG%rd`&bH4da9-YTlO`~
zn`ABKN-0q>?&Y7+P9`@m-m9}*u_&)&`)#EP?MUrho4(5^$&MYd=A&_PjZB^pUzvl|
z&)BeOl*XOuGxXBR6}9d6ZNITw|H-R2EU39Ssj;njXj0nSjCew+J{`9(O2Rnofe4d8
z>KWy#neUVLHxUHFY4gL8jN<sP;)M0a1)UUVe)*%{?gC36NN4}KQd6$zROL5c+htlF
zwV!u>KH(lz%w<FrQ7EL9g4NpRbxyiM%TN<_9b>~X!Ut-cW3s!Vu)Q}mS&I0(&3eVq
zT2sNZ=x<`IC|+>|6YLrv2Qz9yohNaepAL*@fRxWGe+2qE`~+CZ-agB6<Xx_+sI;G7
zb4&{Gi2cKXgq|S)wb$1f^_*X-*3~U){k3<M8l|d0#7P7)=F)XbR#7o@va<5#>=??>
zdMm;^bhSod^i2<#(;_K!AwDO|Wd0_&$s3@_$%^T-6dEOqA@A_Xi_+-r#qa=)3&;8(
zzi{DdL9?#u?LWkTUOMG8+Qw65dJc`|*8W@Zq}>YGFEV0)^3{yPtAvCzhtiSeUl|DN
zEzwQNnFg+wGO#=-B!$?{1|7bh5Ym_|(|*_C@J_O}@48gUp5hRW%gHOpVzgk@%7~XK
zoKnd$<F}ecCK3K0#n0Qp!IeXjc|xk{AN{8!rcV=5ytRC=)|A!7K8+TTaF!UNXj}bo
z`<gyMt@mTrzR}F1KYD*VDwJNdSvVu=@3;C@NZBoH<%YOW-xVXQCs>#oq+dtO(t*^d
z-+O6kfZ0&8^?=i;4h<TnH8ft}`g<ZK{g(*UG^^ejTXV|1MVl-TJ}}UqmKOYP)z6Q~
zCEPcoid!aLh@lK4!s1_T(;Wr$)??6_F8R0*Q@o1roMqEP;PiXR{kmq^6Io3i>QTcj
zq@mj&M<E4!mZN5;_wl?O8Tz$#l2t5D5j(%w^PzsbI(sGAbk-4Yhx)5wRq2r12=0Y!
z!IP&^MPQbdY$A}fx<YfX);yBPOYwNQP?g(K5d8sfM+imhWa3kr@p^{@Kmpxl3mxnv
z#C%wiKohAmxtsHXI6#%Lbyc{5V}1C7DBz*bi>K0h_Mo+=PoqSc6Xo-YIg}^4$tpz4
zs41oyB!yQd!fUbV?roNXeLoa(&_Hl+uo$`2xD|^ihFC2ZVo~EqhSVG_0mAaw6d3m6
zdj^WtG2B*PWY<Uj?ey^maHu8W6Ubi>zCGZ&LdVP7@AlNZuQr}TYf6cHcDkN1&-htf
zq4_Z(2;r1*(Rf37lB3QVw5sP`q;kn&7W8(yRQS_Uc)YB-6!_B^2!4Lx$cIx*r&)nH
z>}dh(K-wW%k;LIeTslpMcJ*gd-xy!8R)%nbvMf!fe07M#w(l$aM-$jd7dp*-x32R^
z;MJlhe~l5>1C{51O6Bih4UQ)0sg6OT<D{DiINqCNxw)g}fUx6zRPpd(F-DN3@r=mM
zidFr(82YB+jZ3rY6P)v-@W8IY_6RpK%JYk;oQHtyV)E!r52w#%8}xiW$1Pq(fk=-|
z-I}a>!RL&Q?D~D%#%tcwmi)@50e_CbV>8LsxKkyk`omp>kNhaI3|w)3FJ&SvE06yv
z&tj*jPS`J*I|V;4!A*E3wc;?QGTOXIYLfLlDN?W1k0b*EM^7;Odw&7?6>#iay<!h%
zh?f_8c*G?=j@!G#@<(6RKt-iYBbv0k?K#SZaZ27*uF`I^>g<c=pOG1?OghfdUGKYi
z_DZgWl63Cxq%w_L5F!qJDm>$vrjZ8aQGz64k%3wOYEm2p+zBrCq6De#|4zf{W^s^7
zbqyx98Y)U*4;Or_SlIM11L9V}FdA&<O$fBERdrQuePOU8WdDJ?sCQ7XrSEZ@6Y%TZ
zD&?z-iCq|b@z13v!XNt4!W6yFnj~|F9SRpl8(hW`Cx@Z*8B{i6#_Q)Rq^goOR8*}4
zRaB=U1=Oa0YIMr_-`fBjQhlg2hr#*3FEpX66b&&<g}|!`E#Hy!_xF_)$@+mZRX~}Z
z2>)ZsHNAvS7C?asJxM3P4waM69Zjn~BPK^N#X#j?74{7w8(N6ZLwJWF78%b)LQ(c_
z_=v{t+18gDl%PlxIt14Nd8fRLlAcHj+P{F~T4iPnHv>xdp>(}%0%$D6Z}e_2tU@Ox
z2+n9j9IVmQRCg%R50qqxzp8bOJnF<7W<K#ReZpA#@jK+B%j|o!ormk`K|KvFWSz3A
z9}k~+7>5DVK^jbzf;qhO5`e$c+r&sfojIa$u>0p82*VGP@iR<t!!;oxjBX$jMx27D
zK=jkxQGSeeckil10AT&rCJ!`r-?5h(C+ctp=YB!!<25Yy*Hz#33KOa_WvqU>A$vE9
z+F=Iw$G#(aT#XxN%|X9%aJh#woE}R?d@7%y^3?w31Sy<8-;C|FHOQzfl`-SQHr|z2
z`X`yNTid|QD(^dSSvcPBAN2kdqT#S=<8<Q24uPjZ^gm}o$&s<d^5kDI8xL)7c0Suv
znAeJy5;lfWqr4wrqb-x=uvT2Fyi-lfKHlNoveU{M34b<AccteG(P|mqQ^r`hh^6#1
z28LGPLQ`Y}MgA8ZFozM-tRfqBLE-ee6xiSJ@JCs=6AJ*o(#I_U`h4+(jqH@DV6L^-
z3%hY+{#ADU{tC?v`m~?MCondv&%H*2jRq6<DHrjCfaOHzA>w%9y8?yQ<?^xk{bRA)
z>4e3K6);-$#pi)IK8+i0M>CrLs}mGaj3<f-$|R#urb0Pis#}FBmfd2olE^74onb)P
z+9k1P?I;Z^mX+y^#O-v&2=5okiM-5^KaFd1stxa#*2iUikxIhQTG*&Z6ZiUPiy(}s
zLgM0Vzkz0}8xz%llwtXqzzJ*A(Y7^k`4jVaRyU^~>GfQ@KN<S{LcCMZOXJ6$qz64%
zo8m<E#9Mjt8$Qy>D-VJCP8Z09<-UvKn~xV^U_!tzE~&*OoSA57`wnOG_|+ka_9Q7p
zVkwC%INP?zX@7PwpuYk>QAdB<yJ_K!1@(z*S*()d`#Ee3IsfSXrNSln=%6^5Zxu~%
zv(6y-{$-wY`;jD^jNQukFe2>9RpY$+cKY2S(;Qt=`ja<xLNoxXJjgZBkZLJ&>1R6O
z+%~T4h;0`5IT3pb_V=QZsAlbQuXHxhvXATdn&c_1S-9iGrj5sv$CtP&(ZdeG3B3JL
z^ryjM9dpKeVRpgAmy|O~^g#r;8`@;wQbGKwh=a7kzWc5^t}fXl&cu^9_}_Si*a-9M
zHH~cfWEk*;LoHI}BI<1Pw))s-3u-S28}ac*V+o}wzOcomMmJNatvK;7%SBw-05pKr
zW}CoZPPU;duYxmo|6l1aG#|bYqi?ijJ^#Wmz)JtEDfGwRQxws~*@8XiX6aE4Y*AVs
zlarzGLlHTG-El^uecQZ(uV)A&{k&db+grJsmUb6wZr`h{lmQPYNeOeP3g^^dKyN-v
zl}5Jq{$+>^u!3xf(Z&@oRy$9-ixC=6XRMc=FQDzCj}~F`yO^E(0c5e`{XE|8fhqd@
z!qzN)d6M;7I5u6*K~3KFX@w6E0@MVH!tt(G{a62u$EGS67Pjo&IV>Z-yKSY~hge4q
zeY(0<o$cqP&y-Sz_Pm2nHj{N6`oGp{@$n~ZkHYNq+;_Pjx)uGj=$dG)7ajsO+#`Cv
zN4a;5$1RZ$(9}JTF$)BAhE(n6Jg>JsKah3~PQG4VX*7;nZnXKD2Y)%r-_ev85EvQF
z5tL%6yc5BzZ0P=G1^HfzoxyQLU4)<hTOyzLP&QKkzF{9fV+<q(vU&S=yRs=iF?i)^
zHM+avb4hMFN>!=1PKnr~Trq1pkjBqCHp@&T9N*VDIV~FS>uUdJf^m-grwjgviC=YH
zwl;Ux{(3GeiN6WF(PNbjGbLp)lLT}-rxz&5ezY|7TX+zzxSaE}R|f%SAQs=47Y8Ej
z$UOD@<NB4fFF<-Fv5?$zFV_<hFk0%98fhj^IpNz4!Zn(#%&p)+C#t4vi5Uh>Snw$b
zV~8{^Po4zk4dEuQ03iDD`5oY*u0@9_BW|0;9k9c*U5Xg6qq+Xn?Y925h47PvltwUp
z>rh>x*3}?Os}$qA<nN><9VW~u2|T=U+wC-SY`Nff-<fQtemA&1F;B3uWqp8Gl`E>(
z-0f+*;<BO`o#|A=`jW!c?Cy*pl??nQc4$DOv%Y)v2@n?8ct-!M7zdVP)$48wUfM*y
zg|sV?7a!Y!{;34fp%sc0rk!rgfj~HgFnTBr3g3c}yK|_0sZ`-&v&~_449IHKz@rdc
z_jkZfhi?Iy=D~}I-r7avm6q0@J_y)bNYSU;%OvY0g`{4d_R}S4RyKbZ*MHBLX;8+C
zOP~&Zo!2SOKn@J&RZ9u$zhSA+PL4H+lT@XcX8jn`|CPhbCBAK^nS+p8<_f`BlagTe
zou5XJP&}2R=xNDAC2<BVl4PwUL#0Z2quK8?RcWAY9g-saD6c9lw^wCVXX`{Lmc)`r
zUklo973c@JgL0+sDKfIe!*_`N?hWI6;z`@iS<bW6*(|)~H3AX1TtjHo0Llw`6)`M9
zY){~9PPi&nTLvWci#k<`<qcs2POySP=<tBwIoODRVh8^c?xW*Qw}<HsOy$NOWGhuV
z1V5oEiYFoP(aXlo5u$$}Xh777<sC_uKEWo|CKmkG2E0JL**lRzXJN3=;tl>J8qIlG
z;)%xWeJCwr&nZ^q+Q-IYk45j2_9TR`k^+kL?pFaRMBiH7d<(9g<9VOGn~T^j189EZ
z&K6PiJyB7GVDpn?li@E24<Iw>Jf#^0rB`0l!#L+bzST1luH1xL&`XJS9X`hH2TPrH
zLPOLDI%6QM+`$q1k9bN^z_Hn=!n*joft-v%?97<h)mlRfqWx)Hi%<-CLk5i!9Uf-#
zMsjbvo)9OffvuK4{}AcWk1~()tYuuddYQ998B0!m3MENWRwBm2K<&eIS^G{Y;^7l^
z<?LW@kU;KzC`Cq0!uViXHgWr*X~H2bbEkVIu0FqatQeT|?p;Oe@Ge?PNy;5F?m>Rc
zlixhRI8IhT=^IXVW&`>kAnP7i^vS2TCw(kk&+7UjWDIsK?rsShvJ@G}qw(-cWSH}=
zhe<o_=a&o{Z-04`agj5hY}52#ESWFHOn-iQuKa_hk<CmN4%_1C&+L85S`_mM6CS3K
zxCnQ^g))sg{(V?M_r`;uXWDKMtk3l~s1D(uvpZrS(m%Gp-SW|plJ0apdI$!Ujif>{
zd|uyPagHrbUbizyFOj=$VQXAVYFpWwx-$ejBcUHMU9IjRX_W6^-o29o3#%sPyiMx;
z(zC2<(c2<@&3T0zRQPnI{x<Q&*uidYqU<TFzB?;(GN=xykM;5_GiHPx5_R1l=a3`9
z9yM^jjS9X}n+oa_eTQ7l=kWBNA9RP^daaUjWQxh!WMp12z+QgJV-~_Og7=HS)lmKI
zAekqx<>5btHadvBj3{Xk@A+f<!>7uPqd?)MzC?3);U45=N&jfyK*D-5M5+FChcL49
zVZzCs_dqI{C!-noO_kw2ysKXbp{tNDZ7A)wb;Cq4hA?{dl#Xd($IUOaLO{3IC%Ps9
zXG;YAgFbl%yBi?VWYq#R`_-ted~U793eJs}5)(ZJ<_BvIOu?#(iJ+@u<_(?LChPFI
zUooF$+HWGb>iI$u?z3^DYY;*y9YJ<*nn^<FyvW}?V!Ct}df6b3qN41Tn(SfmL+7g5
zGe4smf?(&B6UKh{Ge6H<Sux=*X)vr-j|<yooqHI5gi}k2Qwvj>9RFpJ3(YSZrL1E$
zE>!r!Uv{AXAVJiWU%h;@q;RKk>DOze#h|NGtO?;i5Ix+%82oD=cN5g(rT=p4nS(Z2
z`Jdl8Ajp=OFd)zSPrfX8r=k$QE?m22X_hX_V9nxUK&*tG+Ew5EM={<^$JCf3>bE3q
zS^Fq5I&V-C@r7ZD;pz(9x%<7a5dG)f-N~FEW|To?((r*MVrA46(DT!!8?UBjAH*cz
z;>k#d=Q)7u4_;IfmYqbY?oi9G)*Y;=l5<Q){qHnf!s`9^9upB34<iZ8Cc=j=oCv1h
z#TizGm+LBmZC~ST&bs>eIUWXJ@tLx<cgqE@C{@_ufQuA5D0Kyn*hbDWo!06J(=OZX
z<mEjB@SRS1|NE#`sfNWr7At^`f2TRbqU!SgN<wnYD2Ij=cfm%fhUpzTyg*r^5H?5q
zpQ7E$8T;=T@E_@>N;OO`Jh7Oot6$haNVRyv*c@PCkyVUU)rQHSaSS2f6(zE=5@k$X
zq|xQ)KSdV$1;=}Z;lsKguRXdibQ>#>kjI^HGLGx{k!ftrJvdFv)oVO6-f^pE?C0pc
zDiA~dHN1Wa1L@;?X2USbX+>>JH35tqDqni`@WT-wLb>#C<+SYzJiMg8q;goCA}CXu
zh`exMsO0I3Zu_6XORMiID~TrrUn&^2vZZ>z+67ck(&mA|oT0<-2e+||=eT>_ttX9E
zIAjvDcpYx22&^-LXZJ+B{Ni;#Y`%;Tm7g+tYq*lyq1oRCotWzlWg}@9*1h?w<(jEI
zL{zv;fs<hP$4zUChs{g9CM`Q_23j>YJ1&XLzjn)7C1Qoq#gBZ=186=A`GnnDoQ-wQ
zh^0lmeDUnrVT!pmobn3BN{)pR9=RiVcG);+J=8aQTh<~ul}I?nx?bZv;2oE(Cd8(0
zdHH9{Y$f9)SOknoWv>+v!`Q3p7}}n^?jY!qd)QdIhzj6fx^GTM-w{?^Y@b;c<#8w-
zm8c2_r07}YX=2dhoIoCwAs>W=W+5uhM>@ZmmFmmpvTz`iM{(<JjAGJZ7aEs{N=sy*
z4UHlw0*U1*tU6(NyLwAsNt~&W!qw6$eu0;2b2RkQ?uNen6vD*yojWP@r^ci`FHaP0
z=)LeC_qIP49vKVaq;|Y^ffqyX;M~*w)wb-tf*8yF4>cD%Bj`uW;(MA|CG`~S*jR%o
zCEGgRsvi&J7qdl2*<0o`a*gK~IU+Q?Q#Y9qVP~R`u~I0q3hwYUAu$`J?^=s~5i8zm
z*`$6*29t6E!XRM0Mvx)#to<$V&VUhbZ@{pwQ361aEwf1-5I|N6Pq|k|(%WdmP@+xg
zZ023Bv`JZ6vitA6z?w%<D!#f7Cx6gNlGEo#<tjbf$7cGSC^ZeYo(b|O*#y4zJqb4d
zIhvOnSy96TX6F`k1C`de=7}leXsuE|2rr<ZewHK<OR`y{#$1pp$hWFWZh79qJVr*q
zR{MF;LjYJuKM&I}c~wiAfBB`!HH<<TN|oQo?v>Lg@SkSt8~R9>XkjSyAq(^OkIC+K
zG9)l)IUDm_;EZT3ENQ8BNsrN>@#KS-q!(Y_`OCYFt5T~4TFCdin-m@fcyFM7<L7|8
z@NfmqYOC6KVIjlk8Zt5R+?`Jdk)b`J4^xF-xF}IuVPM8~htsCW0}W%&@H@N43~)qe
z5iH3mkJwgSRw5|<0KoPl7)LDu5Xo&^;p0iqSZOf)ZFHf7gNzm~)ra=g%hNg2JSeG8
zUE6xpL7>{no*L)vzS1qj%hG9%)Y5Fkxl8puMvb~`OL+aKyp~_6td4C}8qwhVNFDh=
z!~mu<Dg>LiP3%dh{bZCKZ<Gz`)gDJr6%g>8{Mb)+eqm?UW|^gIjHZ+-j)Tztr{M6n
zVjVMvN)aNMbP}@T>a_YRYWFiBQPzyi3zssU7D}2yl=Kx^Swp-F2`A*Zfcv0^642vF
zhvpYUx>&y^Co-Z9QnWd9J4O)r+%~a0fCNoqR(42F?UVy{y5|RGL?7nkQ_#xy-Qd&D
zN_%1dl=5oj)7K0b*Ep7gSMto%ADZ2h3jb0AEB<qFG%5U$KUhy8ZZ;lF88A(zpvtBQ
zHlMt-;5sj9gWzZrGH`Nn>udiy;wW8o$|OUPPy`1RU{Y03qx)VAk?}AF1v<iMs@f6!
zZV&}knJttoI*rH^FQBbhw-CF}pQ<16|0;G9@UU3W@>nyk`O9=(5ycfohw*b~CsSUY
zRFc+O(`3(L^!Z^RBU0l1yVOXOQ)+C#WYgN2<$nqbJ|g^g@X1h?&&0Vu)KbftudGd?
zA$79TWq_pMBgl=h9|$)2HLTailC9Q~iG;2ICm%76I-$1DqptmHkF%6Vj#3zmVLSkG
zD>9-8_4g$=C-<X~{O}%qsZ+Gyyn1yV7!FPKcN{cYAt$>ra6x3O^y%Y|;U9}bY`;uW
zBR}PaV(Pg3_TJn<@Rp=(YI1Gz^h^57Y0@U&3n51WrI)af;2TR$#!q9SnBik9iFclH
zzmWYhQ{&Os-UP0_$7q;hY+%rh=c%u==OgnuK;>Q;+#m@ud4}$LaDPlu87^J_OuzCK
z2x9lMH#wV+B;NaXbyGU~r!#KJS{ZX|oJFR&(n!Gt7aE4?hl{j8_yi(kYjg>Jq`-2A
zfB=l#r11)aLnZGd5QH8E=ou$_t|4GyA)KCL_Ftw$=29H2It7anirDB=U-55z-%b7;
z&0A-=Xn&`K;=B|<MD0(85@N~0SUF~+R9SEPNl{sxg1$u-MYHwi)qE}SQBhDXJ-qL!
z8{%ras{*zdTYwZm%vmC@a5qN$mIm*<2h#PTFOs!$mdI)<Qy_Zhl_EWBWsRz--%U!Y
zX_w!l{4P+IbmG6S70k0-=)^p0;4H|qu<`qreJQxI)4JgV9u%7$Pk7!4msP^pfFgF9
zdyAA^zDV6)k@?SMLA=8{nW_RP_BC2KWtBjdckYEI{7y4&nu2~iKpyUB$1nFkF>ioL
z3&%0F;A4ctZ^o2Gt*R3;92bgYmiwyLC!1^OfyZVpMA$_w`s$iyIk)m)=!2wJ)rbJe
zJFNyzAkP9YdV}(gFsVFgNMI?2oA|&CIFJ5IgjnZGG3iW+HX^L&nM^UayJ0F#PFgFM
zA1Q1f*87@f?~;TMFp>rNeena8xNY53*-hVSSP5o_c6Y2Q)uz57^?e^L0*22qHvOPK
zD4~OH#13D1S|m~bTp4I2dhHi{zzMg9<YByvKE;I3UB38PIEzN1B^NOt1o6Hek7>T&
zVjER&vV-7GBD*7JhS1C5Y&r<Oz#B<i-nljz#=OIZ$AI+<WeX1+aX)@q)WesWLXY#v
zNhqXMMkl9M2&9?`1m{v74CVQqs#mwOWtl1H5M)6Ctpatle)n~wxqJD&pPcwN(NWF(
z-HLeB?AAk8m*HFkewi-<OHxdzVZkx<>KYK69eAevI6j4fXpkNkBpE&qgF-^K)9#}8
zR#!_e!>8?Bj_Gd-@U?sydJHL3P60o}dYuS=HG>MZO&zDWgfJ;RV%PBE*}*$i`s50N
zjScUdg$Pn$U5nxv=hb!|<4HRwmCgR>z$sEy5DPH}It_LbP>#|FqxEss#H08E+;N!C
z|BE-<b95SN)D)s9X6E)<_6j|FW>zPDpU>*~BOrA>(5e^T-M`eN-z!-POoz-q0zX8p
zlFJvhrcR`_qY4JCx-wg~LjI1yz8xKrRzs3Yxlu8t6H5x%@ripJA+nQu7DiEDqP})E
zJ&*{pKe7$(VDaVfG}zz;?SAvL+>x7Dz;Uf}{50qi2OkH+-y54rMNg>FDL49csdhxC
zgs~Q6bAfDBb>fz3(l$|~xvf9>hH?DUuXPqwPAye#_tTJqyHjG6UDM2(MO}ZdV#ZBx
zgnweRg@!vWwQo`M!ZlUH+{WO6v#ah=*J`r=qmFna5rz1tQ5RY*wQ%PsQe1)U{3A7{
zIh^~Y=}9~4uWgosA@dSmu#IDEHi;9L-$pm`4;wMy{R}81zRMU45kP>A&k+7Ss^t-s
za%{+)YR=1Pzax(@RFGGI`NSN|RFw>TdHj_AP&Lu@<aLY&?nk-e{tj~aGxY5c)#9cD
zju`<)RqZEG=?5fsZF9-3Ab_7|7^EWpnmSS(Mz|~og^6cibMs7%JLH@6zTmJQln$P7
z(7_HmZ<xqC8{KdXpY%Na$RTRt$~!r1S`3U3;Nz70=#@p~r~k;@6}jPNJyI4)8L{Qf
z`^4w`GhTxp(6LFDMgErbu%?g#!5QJpcd&?V22m}RRRSF`i-)+cXSg0DE8+CyQkd}!
z@sfk7ZdODU(4FU@y#IE+Xv^Y{vsL=zFH}eKIB_MdRV-wfvuNW_J$F59#YfIrKP!l(
z8yIm{>g|ZD_IIg=LGcXaU+m2~Nf*MXKnFl;D(By}Y2BDVXaL9npoT_s_4`07`?PM#
zr7dhDi4f~!*YRYry5;RliBS%EgRokX>CiqWc|H$#3iqAOem2OmQ-XU-kjZjA0k!kW
z06;r4;Arr5{Y5tT`0T4y`d^lQKVj49Ei+hPfi&s0TeBXp`F-<AVB8|Zxwk;iJQxXM
zw%ba}HGAV5i7<Ao@kcpzC8snnuQ&%jc~VSBVVsLW?P?Y{nX`<;5;CH#HdYj6^sO1t
zm<BEIrL#;?&_7J0#7%Ss$!qkiZF)Bem#-Hom()2LWc@6@Hu7{1ty#*|+b%b1OXMu)
zpl2Le`ARg}Uqei$bE@hTWVT9{&VrXYlt*A;LuSVgbcyB9^jK-mePR5a90cL1KcbGZ
zPuLbu8gcHp%V5{WDXgHcdb#kRbhyYk;s38NORW&SuE@4B*bAfiQ3f(V<8aU_viSi!
z0u=~iyYj=Mn~L!|0-fcnxMyPzBC8kQ_{Uz!!h50$OcvS>TKBa$N%s#f448Cv2HWa~
zj|DT2OK}Ei93mr4LI>*kQU9SGqX3N_x`ayDJZ#@2`3zPSMX05LzQs7{4S$zeQGYVT
zk|b@b%4FAL58USK3na@3G5Y=iuR9C=$ZB@Ek*PFtOm~X+v?AETv0+0LX37MUO;i6+
zK=y+)UpSUh;Nbuq78it=_sj9MB<t>=goL<~isy;ekVq^ND~Sft_S@jQ_!206+BzBt
zWJlE#8Yh9_a#z!E%SreXgT}WWbKeofaEe{IB2e1rURIb@!tKN~pQ332QMNlmF*_v5
zjaN!Qgw@FIb#I$eVX4dz6DZR$U}KX7&rE|&7GCnSXL#}P!5Aj*Z#a~O$tuC_fl2@(
znprn&Xc$-aNbuL)RrX3V;CF$`#Y>_16@t_;#WiEPLcep*givNY53e#!PMzQDk=*m?
z;PAt(XF0c=YF#KpxbGjV()>sQp1fK=rn1y*xl#5d4w*<iH%FzVD<S~B=|Fzht}~G#
zV~V;b1F<<?Ix>-<_f|)CgL*@<#sEjttkR*SQw06b;Xe#VrH))EkRX|~4LmHv%2dcL
zXZOb~(rSL~HU@eK3XCKP8li>{|KXoCh|`=cZ>=jtxTCy4+Y<M_#63u^E)e$~z&mN7
zDDi3ueMyLVfZq!z0LQ|elUg3xfIkdtyF=rS=@_94HvsHu|I>>Gd+DBDBd^&&UDoU;
zF<hox4WwV$Kydr-p;pt+Wm2>9%w$*+e<!_xjhVm2IX;D@Y8$AIqsXV`&dMB!<={~2
zz9nYZ$o;DV;{n`r{L%U(u`v3O$&PWO<x^wC@dKdEg8H<N)uahW%LWUZhuG=1PCmQ$
z0>a0u^+B02-K9J&_B+&QCF8K^T<j%BY|#y`w>WqVP0U`N023n~rZf$BuaJ;m`%j*4
zmwe%r7yk}eT0!}eTbXL{l&Tf%HiyCMr*`Y^#`_)GBJ;P@C!h=Y*i2k{egFqn>*Xq!
z7-cZ^s@N$%fF~`)&;tn@52HsZHAUuaPCZ&zLgN<|oV@#{yB@u+tJ|x`bDoQv0I{!`
z&OV?$jH|kHIuM#SHr`z?bU0OwaIKU8Leh2{GQ)U<!$p=G0FesEk;c=*jspvI#Z^UP
zEc#TG3`=P#BravMh)m2tgEgi_ta$|S?M)J6^D!w8_ct=ngKvilFp3;$#d`e1SNd+x
zjUW5nTZVfc)LzHm&f9ceToHWzE*SD9K0FA%D)>MYL~7J5>)cHuMoF2JR!af}a0t~#
zGQJ`ae%5)?dPs*p{ARYQ>#QC}^M;;k^A@QJOb9+i_z3+Zvm?uGt^*8yO)Xo7mOWi{
zWN;Tsv5$Z_S*?{TElx&BRv#+v%q>QbyT7QS0$lFywP|$x(17BZFGKSyH<M3u-{tCi
z=-Vcr_NbUeA$5f~p_m#Fg9l7QfY^1p&6REVe1I;h(y}hScDgOxDC|}@u*Ai5rTuo5
zQ^VKv>CfcLzW(+;aEc7a{1oY_THZc6PHDNkU?Y9G2Q?_y72_qUrJekUugMpcB_iFs
z>bfQZqJNEQA{nCf<BK0@b&cw;YOTEyiBYQxY~aFw>#Y|knJY2=b@A%d`{bnq;JEv7
zZR?G$=ey4C#S`>A&|QZ*sYu`pJiwZ=cscsw3V1|TjMEcZetungyEg^s__)xKI_8O0
zAzIkB4)0qHKX=81lVkq%Pd)#}-j!NKlD=(%Oa(ReUYc;x#bEgJE_bW`t6v3Bs(e6q
z4w(WJi0Bc7!1V7t>F4b#ui(RcIAi-9tFAmUM8s#`hC*1=4ZTgl*DL5&>pI*=FW%pk
z_$oAEtSy7zVBq3#TQ@of+ZM*|s?d}Ui@^FTOwDH-TbxQJznkR1_-l7<l_3n$|LRqX
ziCo+lJV@26>}xs$H+z3&Z#g`$5B01U4z)$MTxn}qLoUW|7JzsGm}4@dWbUP1+f5Xh
zev`l@*${6V(rWwT>5vuW9CzdF$6l(bY=I&tced;z5_T!O#~t9FUbM1zF{d=gA6i>C
zU+$^e(gUsZ&MBMSjN0arr!Gp1in$Y@K!g<)PbRPJSRmdo>8uf7Y0!WdkAfjlAlV(h
zK0z&53J_0043{LBG?BlI0Jyn|KBYp-yJO%`;6()s_r=!h-W8lVx!1Wy1OEd1H+>9M
zF;7DJuBo^lbzyKs2rO(Rv}SI3v!O>K%YG-qDxIp6`yR#otGDQil@=8a!SQp!J!>QM
zmkfbEiDxuWl8+t`ce%-}+~03h>%O)E?nr7;m=-hM+|=^wd3rgfloyp6B>KEM^o2-4
z_5>6L)a!wY*Zdy++x3i%Lut*Jh(i{Df<?El1cD{3QmFud#(t=oJ)XHq*vowS_`;Ei
zV^X|+QL$=R+Au6_nQ<W*N1;Sqqf+Fh;Wc-|FHosxQq$mv)y$VAFfiPQoii%fLc`i(
zl5F05`pK>9&M=7f&owyN;`B#MpGC#^e=4x&xfFSJj#x^j!;{R~)#19UWeV=*ts6iD
zid$uMPU^kS*ck4_;Neq_t_%2zx<^iLVJ|y@vnj)9;{$gd5(yYN%TdMI!gT4y2Cwdc
zj&%$v(S4u$G-h`6m|Vw^A_OI&)<HD_AoU*J65yZR9SIp#l|fB!;CzVVfZJJuYidb=
z9_Gg|kyI8NlA>XcxAq??hv~nqRIxaChRSj_R&C2*i}Kv?i=tzO*?2t}B{NrCZN)Gt
z({Y&1uK-v_XQjVJhwo0SRBQIioQv^jmpUF)<8G1=<6|ENrXHAlu29Dp<m?&S+2MNF
z{tysV2oikkb!j=jRRd0wvBoGPo-H1d&0V`Hg9b?W@#po2h&mnqww{qf)MeBJAP-&R
zu(LvIgY39@+w|<a2}JK0WaLinEI;GafCHh=gE{9%%>0x8E)1gi1iV)Q^Ne^s&v$qP
zp0~s%I^0?$GM9=1j+<SxWA-1p8v`KA4EoEPK!lLZA~1QJ!=uUh=I{A|Dhy4A&~dt~
zVM&i^x}<SYhyD_`>%qP1q*>2;`%H4efgwe1rSQ82i;r_!i_3l*w?GfB_bx&(wF9NK
zVKPwPgnHi*A@8fV+)wZ|9&Ro&{TywrdZ~{25Mo~=)iOtx6_tC46c;K@nHMK37COLz
zt@cSxXW@z;7N~RAf@%P!T+h-d?NfRsIz0OQt8Qr$l;&ujld#+*Pbtceedl>@l0S;}
z<50XLCn-(sU>>^d0R*V{<nQ2T1AR*_>+K`A-=oyKJdxCrFu;E9U$5~w<U;(q!3y)w
zEP#oM)$G<v*V8BUiHab#4<RR$^wO~Dm24cz)JYMn9LZF1(XsfFEWBPeqrf2LCw}%y
zA6@Rvj*Jd(A9VC<&$B&(QQEw**zDa1xXBaEfz0naq5eY&rJ6Vy07R)|UC<E05!0K<
z5?;oKomHxq0|%eOqN%A`)Aj~Wak0`9K0oYbaEx&xl>6^`wYHZsZiwShc5*(#*45Z4
zOIxMXRz;Lpoh(tvZWQftv@GkG6n2P-M>znrEHet9m*~ef%21R;&7X$(d`SWm0JxEB
z8u!@!FY<%}Q%1cjJI6eBBe*+9HH>{t*=e}5P()>Kwa)<>dArs}v^w-~DYJ^PdUd&A
ztC1U%cnfS;i`8mx)MBNl00YCkN3stvzDc*#(3E|%7HVc=1=7W$J51Ogk_3WZpFvo0
zep7>XgDuDL;^OGs_&FjN#!Pd#bSqAr%Tz^qy?<V6_>a~@#DrJ5V&C^1V<n&(D=o7>
zBZ$nHTXBfCEQ4|)RLYxbZqFZ_baDV&bf4EXhs>On&BFbkcqGzn>`4-8|Jp8Xtec1}
zZa7CRO#rVh(ky)w%eDz;)@KLyjlNtzN`3ELO3{E}!gVfHDwOm~FHDRqKjX}1@2mLz
zCj`wn?u#+i)Ov_VlaA7y1gT57K<=UhApe-QUP6g3NEP5+WUmvHy&mdz&j7%}>J##q
zPkYY?!S-gE1~O-9+1&{+QV*cNM@W@J7DOybNq+}Uct5VyrjGN-($k<rFi&0KPFN11
zKu@MCPshX*Z<J{>>O>>{*h-xb<*MoUG;BpAg>6IMecth|9K!BnorLD?>Nj2p+v!qK
zpo1-DtR}uj4gop?CNFB1IV)PFDi(zj!9ccpKlBcf#oLPe`d{;~ajVCR?x2xnL*IW$
z=X?-Xle;S%61<@Bof1G>F=mdsF_6)It0nBeBY^ni`<k&WNT#i(33sG-_5DKrJPVz*
z>iGiffAMHKX5ZEdcjHcp*9*+9%E!gf-MGRD@Mi4@h2sP_(h<Wd6lNHo`3W#Zo-ztW
z%dKxm+R2|Q#0+^mNdxZ!gTwY8JMO?zl<6$iX|&VOIa~>VdkZpCrErMlJy8jF)d5-o
zte0vx<)^KJKMn%(QObt<@(3DFm8u%P!RH5KOj|3yA;E%oc;iBGmL;(XelvV#1rdbP
z=Q>rctugR5Xmg$dajp%hu$ytp>MRU8d2w=;f%6UU?Lp?hR)e~7cbe<dziXtIjTF==
zftA46J^gUAjzaHx72|d-_Z`|Gwr%?qhz2~jaZAETD^7paM}Jo&DkfS6=0QWc#>e<S
z;qWkUJ0Hxqb2kkGPH(triya|H7@yS=Ja*T&yaaz(R?KM2PDh^W;YA&1J!xwM?>@oE
z(~R{u67eknB~_ES6UBHy;VB^>9Xs4V98(ZR6WM`wt!R6Gbx$UCT2TgpI%jx%?8*->
zUvw&y4*-}attfWGe~Mze!8@~*NgA8%1*X8(fbIDc$ynEO^MxRfj11{gE=dDWN`i(u
zlusH>gQ)Veyzk7bw+`O#jrED+v)Y?^lnlTNFV4oGAHWv{E|eUmM~YwmyWyY^@65l#
zaXzI19T)sp?n?d=^_gMApqJrV#CUUgvC>RU!yK};lb~uy6rm8SmH^%*^l@2(E|pu6
z{6W>>90REp`|Y&-tH%y-|2e5@m%H;ZUDZ%lJb009v{^3aYu%!X&N}mue;|3OtXRl!
zSr}nr2l+#J{Cqq%ub)J+&FuB^9TkcKI=rKl*lE4TEac9+X>GwJc*!gtc6Id&GtNBF
z+8p_*_*}<EL4*|%Rtu6*IM3E^pP))Fl5dhbgoz<4re<O+1x7~zZ;7vDTBj<iKb$>m
zvHx-6Cy<K(2A|LO!)B~}U4Qryr?pm4V`SZ+?_tc&3iR7X#{3LDsZpf)2pdmpxXc8M
zLvVVIB29h@qYW##^eC{on;s<pe**RQNFS!Vq_PInk=Lc@d53RP=MAgieMi&%K?9GL
zlS5Ng+`DPxz*Wg`W6tQjFQNWIb?Zf%keUvyZcd2RtnhbAkX-<cK97_$t&{%$k#v?(
zaW%~r4us$Y5AK5#EV#?y?(VL^9fG^NyA#|!c<|uv?(TNa``xwp3BwGW?yj!A_fydy
zvWzTQ2RGf1kY;?IkV74!UeJPn1{LGxXfrzQhb|!U+DO^s4fn6$vfs8VE6dA+C3nC1
zBV(vgWXTyeT8CRD5ynBsj!*&$Q{?1VGzn~MCIZ1v^%nJ=s-{=3Gy_qRF^kMAY`>mA
zUPy>K*@kY173%u7?%Jp!sVdbT)jlqpHL_Rqy$w9oo>u-DXRnGM+E5RZ0^)q5cD`b%
z<5Pf$YPD@`mwK*-jZs>2HIEzBvOdiGL9^QlH<9Cc)adN!cc3rb8pkrM9Z41wRe(d2
zo~QVIwhR+56CjJIt_;=+nQSG+BtNEnY&Jh8ecYe$e9Td%a`1ITKrO*Zpt--(#yGwn
zQS;q2Qo3|5lr~b^C_hdSbxIjDA_}k=#EuO;T~~L3Ngb^~8&f|LNXk4icIXsPfN<~_
zKvRnwUOlsUrS>iV3$#?WW1~h!2cT2vf8Q)WFep|w)qHPGvGaN!<DeuY+8a=d&MR$y
zi6w@`=jM#e7taLp**`z7U|#3DJ&{xr(s=pC%=la*&2%}0_UTmz`MrL|vH$W4qs3we
zgfit38880ZbIyk?=3(W)SABoImy;ZmYkGgyHYQ4-{mtj)8prO#vH-^oA*{yfU>$3w
zo4GYGNl3<SXA|oK>>!i}j?ZEC(PLk)$NAl2ik=`pVm?kT44Z6t7AWIbQaRcB9T^Br
zoVEuYibGJfDom<$)y=Fbr8^xe@nuoI#HUgHpcHdEpW7J&SPe;0sB%GtZAR^{dOkaP
zH4e^r8^|1Yvlv5!L^~DTw{+$7J1-D-mg-Y>d%au-8(O>DFH#uImU;30cbpDhsU`fL
zkvnFC+=Ztl0rDQ|ThN3lC$!e7BA-ObK1+*+xFpr;A_JM&`5&D&P2=zq<lmB+)_aQ3
zU@_Gcmj1-D9NQvv?+i4j<X<JgHlmCFK*u91TYc{p8nCsiZ354*PJw~|ajDMoT0n@4
z<_PGquqfnhHEGz|*z@>Qj`9B|#se+c(aOqy{PI#)($5@iZf1E@O&4}RLuI&}1eWwi
ztpY_pj24DP{76|pOT@S{a0g*i6=vvt32jI>2E|j7i2WOQQ`v<hmz0K!8Nb(&p5&XA
zE~m#3{7()qwz@Vw!rxf)N^zCK(y+F5;9=^qw$3yli=bK6-3<N|iB$5K(fyA0@!q_#
zJMMb$z)LjaP(v58@saS*cl=4ikTHk&e=${J!%}boZaG~@KS3T$!NJpFRftVHOZqo}
z=p#B~SRr3v!_^=Y@(0=5ns;M^9V-_><3Bo!-s_;!e<5}7&mK#5x`m?krc^CJBjZul
zFl9s~GdShdJ>fTder)(3Rz;W%YX|6BXtdOcbT02d8Wj+H6ytSHf(40_8PB=OW~?=|
zz0CYtANDocTB4WgJdC&hxFwGX_!pQ_h#MOM{l#d8d?<fkBTn_=H8P!WD@>k+zEHqy
zI!KVzz0Lp}h(KS%7&^g?8`1AGzrYmc?|W85X%wj2P*GdZ_^FaobHlIJiv5mZVd+Hh
zZR+6SlwdSJchtp~ekIg8GHQoD3t*p8rjIVyJAtV>n=WnA@N|ejOG5kkx&#B*wE)YV
z`qw*$1cZw*U;&qDk<QHTH>-El436x{loKfVD4>ZWgWO+>jDU6l1vfx8iEy3%*Gn7+
z*Z{}ScgAvb41hr^8B$*|KflTo?z1h10rJ<M5YZwLP}R-j=uj#TlaMV)#)T^EcOab2
zS#i)3Bj@!ZhZ>)*>H8`3UZrMfsilUt$1hZoB%JIq5|IJk7ogR-JH!mCW4bPAmpQH&
z;1ZSIP!XlB08Fwyw?_)h&Ekt@&<U;>$z-qqdJF(iEPkhP<d*>eej3TP#MkGn*8y;{
zyiBs7a)TxU?FEE4Ka8-rD}eW1<}K_4k|529xVb)%Q>2@<VEqo#0Hw$=x`VnaE<lQ?
z6eTxaS0^zE(re3swr-#SrAe6|Oi6vr1azZk?g7Wa{<fun{U?mTVj_m06XMSy7`xEn
zOkD){G2jvs00b15u(MB;svBD!ED~bYwRV5xWQfFrZe<k>P@q!314C1{vvRbzW{r%D
z9qggDmZ7#>mI42%m?{`iaBp_U2r;HOjVFG{o(B?us;ks}wx^(Q>@@OO1Qa!O9V-0`
z`3kCXFsS$@sQVVQ1N6Fbuu0fc1!By%+~KyMlvF`rh5m<5**Sl4I*VK!gRs`(3g9y-
z>yTtcF?m~uE_6FaPrGDE*7gj<sM=}AtlGsJb4i|dm7^2!LP4?cqK_hA$pHRp?TtP5
zl<xYUr8y^_bSw)RR#?8V;5zS;gKAe^8kel#71KVt>3cfO?4UDlH@}zz&qpZW_5kz=
z?upjRliK|#%D|w{5-1l`bW=#$xVCr<m$lw01N+b@HH(@Xt{LHL`h9eYj#^NHzI&W4
z?~S#;iJ(%mqtIJ`*P@^?&kv_4XTMutMfO4Yce}jkb7(>kcb7rI7U3@-%_L7A<m;Pk
zHg*41wG=R4#S4L_@0AzN0vCrvLN1%@^>VrwP`<=<ByX#GWvboC*|*jLRusVdqIe92
z6NU2`NFtDlW@jdo(&Od1IOp6PmEo`k#r0ss<lqh<L-IYk;dtgK?)b)n`acg{Q77ZF
zXnkw+z!Qm6P=S-^m>+s0RwnZxFq}GG{IwV@)oHNpk@x(eN{pgP4D3cgR_{Nu&n|PV
zuJ5p}mU#Z(I6p+^nS6_7SpR=ybgs73F8KQqChK|{B_`Z0U2@V&!$bKzY|P>#|2)0>
z?!0^s0_x4{`VUNt0V8HQ{)7pwO+u7rR*~Wt35=)LQ<iw_a60SBf<^1Asbz{J)r_W{
zO_*G9G*p%Su|vjI^T5K|3}PEiw$VMB(IlE8(+E}eOTd#hY&JYZI`(xJ<xAcT_X8FC
zO6JO9;ViSo%Gdl)62fMTs0WV%Rcg;`lnO-Oc{(Dch#m;iyfS}G%H9kjA8?p?mZl5w
zSfE5XBWAj;;(;U(DXlyo8&=`lnBQI2cGoVl_j*^<G&<{+JoPZX44Oi7dYJm>JfBp@
z{_PJvXL>~Tuc52gwPpV0l4M#b@(FA>*m>vHF%;U5M0$lcIrIPwnJVaLB*T$`?SpXW
zqc+W19X))T08j?OznSLT7ZLpb{Js4|nVm)PBNfd3C!wN6!N9TX@2V%lqwbd>7eH|W
z-UQIy1U%8H?q1u)Lp5&pS*;J>7S$KeljcXt#{dsc^?OoE8V^%l$?|LyK3fXB*F*Dq
zZikAIXVENe$V*{kk8EPICGbU6-v2iag6|_@(tf*@3{h^q^bh>!$YrmOhxK0TV2N>E
zT4jduPHwq^>0PPrXB-w`k;T3UQIs!09)!K)tGqfx2ze+soQMbo+DsY`=g2>j3g|C_
zzzHOP7W{BobF{Or@5V9?*z`+s_#L!Xf<B+sfF9<mSG75_Ci=zA4DmT#PV&^y0rZ^h
z%+7h)LCobW;Q{F=nwTjJpav~^jyK^;4nR8|%mZ;;wMYJsf*dnL8ZkP;azr2pX;RxC
z)8!d`@p=UFdRooXOnZ9h@}I9=3`0a&W%sJ&{H*gsFi+F6&dV8ZsLQ2#-YH3%Z(`xs
zlRI+&T>cfF3Zd=LJvdRst}k)MHmt2U<e`+_J%dP=$<qUIrlAZ2Pn)k<)SzHw2r%q>
znM6?P@r3*Sd&z$9Kd=LAzuy=7k5Sxd&%UcJYkA4HdP%Jyz_$2>)CZIv$I%I<2I<t$
z{LT<r|E^bPy+FOFf@_N~<XX#v*DOrO<>#4mnD&A!qZ~H!OaRQC=@P3KqvF!Gq;qVo
z9jlZSVpV_(6RwJ5Cp4I@+X?Abkx`ri?NveAczLB~hoL+9<B*>T3=jn#?I>tmc>i3f
zXS}EnDW;*po*u8ByxZG*sOSs#7nhZ?CuItvw^+3LiZG4@_}E&M^`LwIq@a=w-7G0(
z%1ReRz=xOqk?H+lQ88uA*(@8P3>9&v*IDcTsZL_=_Q{_(SCzeNPNu2p1jgsymIQVy
zlkNYhHhRy;=#kNd4|LAw6FLFJ0%%{NV|JISST(3sxv5Xs^G&$5m+7zXx8V^0;dH@-
zitwOcKiZ2<Qdz~LFz>|kb%lMMtja1AA79|xz`Ez2YDWD@hL`I(O*-Ap$W&Q&yD1P0
zq*r?ih?%HYE|<4#viHs@Esu}F#SZspNu)G5B!G##l+|RF;ZxT+phOteUZ+<yZ|L2W
zP}n^wiLtjd_bqs`jv=vG`YN>t|I5K8`bj8Fs6L1ePP$NucbYk$=A}u5C`b1{^q@zJ
zgF)8Eo1RyW=vqHA<hN?;JD$j@U%H@p=#R@^udLg{+zbSzYMQ^lTi?8GxJPKVPI-Fk
z)AdDcxWylI-Et_Eh)I|l=F!*_i34;If}Q^Qna6CoPsoj2R|fs)IlL2BX2rreS<xX$
zPUu2xX;FEW@Eea>)z?7B;c@Gt`?Igfvi6f*oYLgv>a=V3N2jCLYl75*7Xo=4!|OEy
z{x8dP^hxQ0^CUVcaa*M5gU8cJzR|~8)b~67XPc&lk!Jh(_ABC*O%EXaf}r;+erHnp
z<}`&6;f?I!Nt?yuGOaqx0O(VG>~_C2|7Nh=QK#Rl#O*rx@vsgFXx`YI%rysm&xbn-
zK?g9iRyO!UB8gyQjZ^mkV7!n`t9ECDVCyU>EjqvaTBqWg$a%Kn`+Q1x`?p`R{67YU
zODO&#_A`;bphJa|l8mCU<+11QxV=oYibx2sEBl<Y^Nl_|d|T4|K2zFMrl$G2|MAe?
zaXFCi`nvH*7Y`!PTy`YdypY%2Ys6sU6w;MiV}43nP(;LA!W&6YTUqgP+;QGN9<@#*
ze<dc)1LORg85<lFV$Cdc=_QBkYJB>J*&cni;e*-t7Dxou9@?tqw|M2)j^~6vh$(0&
zKN%};*sP8FJCqqPXLh77xAy74bNj(yp<-ww$aS;7kafs5AOFOD_U3zKPisIUi%&J3
z{j1=Zo>|RMH@m7|);jFqncz@42=w&>Jc0#zN2{ZLg*BuTSFLvB;Ac(z;E4q<U;+^C
z9e^SzU(sy83WN2Ig%*ZJ8H2>cn!Pt#ok<F?QYHuGk+EMqeg3rHRM1(c3{&R+jqlf|
z>AGN(S=paf^~>=&<@nKx*mUyW$+ppD7u22FKB7q7rzT4%($>ef{RFYm&NAuH8cr(t
zdWMy=w<r+p>)U3bWX{6L%OgO6d-MkVM!ea%=REP#`l_8M`(Um>>2<cuD3Subr7Px$
z1FW1BT7C;_wD9oM{Ig@or9eVj=}C)$w+~DawAZ4&xVjIMg7wchtjs#SIxDkt=jLc9
zA&l>2S`4`@FP=y`mY}6I&I-`u@5+4uaroXc?b-!t2wts*RhXPNcJpy&CX$c<#Gc7#
zN3>=XiwUQ3l)|t^Z8!{Dy8;R^5fP2~vwMX)Uv2xK`@ox{+1grR?a9y*9bv<T!A^t0
zUO}*jEFRv!8>TQAgXGME@F0bYCGQ-xY6maq3uY7TobI<?TROf8Fb{YGy45@N!jVJ-
zq{-p<>Z*X*b66W+BxyLh&|+3Ik*ypEB)41C)+!TcN8kU46K(mLPpl7CHUtPe)A}~8
zflDs`SX!~pYa2C?Mt?;kp@x-vv##j$)@o}a)nie7j>QT6!JH&~1XX+b#m^3+2=D8z
zr%$Q*hM6J*EMz|H(-tU6D0nN34)AD|e#`hxkFlsuuk@V_XjnXqGdwE<2w+1^%S4{V
zhf$&{HA_<gUL-(XstjiI4PG%ErTL+zXIQC|yVb;ri$_^qgw1*l6k~0L`BJ!bD9KRo
zb}s=igo=)|g~?ct2IgZnjQak>t8=Ykuz&p{eSN9KK}j3{WuWi5QiTMtd`m{fDOW$S
z!$Y=9)^z?ELhyS1!(XF(4+w&#{;RZUE}ya3IZ|WcxyUbkC|g9o74o9j{KS&oyz8~I
z{gM+{5==KD4!FVR#Vg=C0N$=8nEbOyVkwslyi3xZOB_(&0@9P5om60cUIkTM|7jeA
z*G7q|6+lWXUS}+uUum&bZ}K`kSgdsn6LCfqCP|94b6^8u#7OTmBHjrw*CHq&N_a_N
zFkz&XR^^}8bC5@n+RGU6B<(H=d>y(eYx=(3HfUPuM<c<0=fZ;x@qMM(K%>DrB($6{
zH57G$<v3Yn`kw?YSGv<#hySPK5zKijXRx3?6{-<ijtNgz|Bd%@bim1%g;yGHq8a;E
zZ7PFS`boKHri4*DP)d)JPI{A!;(|uyJeTpyTBaOP4)|6~!Ta`db+n%6WqL~MwZU$o
z;`v~`r8mg6YMV=U=#!ql9qA}=jqG@in0!bg&iV8=yuY@j7`Ot?dyYGLTMi7$3^#~2
zjt_3LY0;9G2h|h`DjMIGP9)@T_dI@279ISd0NgrvhZVGkR-EY`J_A|c7a*6A?X?G`
zR5ECLbQ4a2E+ygy+#t={dQUc9Kf%t_^S=+1v*_&YI=U7opBBW((JIUA1Lhb&uu)yv
z;(yH`nz2@Qs{)=%TC{{2cUc~`5q6&~9B45`<mXuatN#K;4vuP<%bV)KX$fR7s-(n$
z56kCf_(LmueJw=BBBcE3+X%moB)aZ$0E3XZJT;qoSK9zgwcb`)irMh)#n0oD0!V;g
zLZv{esIJMETf+G*XH#vkJJd^naa8aUu0>sMf9DvJuT-0&tRFi9@p6Ok1(Vq_UrDnK
zuj%6Q0;}6O#muqf5G{|OXkUh6x%lUl)5=35k5&?fq9me5qC7b5>X4YhglOk!tc-iT
zgigHQxIoQv^;R0VHKDgq5nNxpOp((&|M<OF%59Tg<-W=0v#Io-hdJs~{~oNuk%v@}
z)$=g%qH9!sNbb&_`SU}w)3c8dmWnKSG2p`|CC;^8&;Ts8LnqZtYI>$cjRP0e@3B~p
zF-({QT}9rK@qeevc*H0iy!Mh3UJs*2wKZ1vff)?Nz}TA#BCqckUjXiwHpQT$oD4H(
z_FijAai}Ou!%C@T0@#m|BAAmawa-BZL!w_E^Va)5E<*I_cvyqthlP`dXo>+v&ekZU
z>EnISsPcFX&1EzRY#}MM)f|@^JUO4{8W@#4I|rA{;?S7XbJ6Mx-%tAA|6K5Wo^P45
z35iU&@ZjBCk~Lg`Y-9NNH!SvM9NGS-xe}rwd1GS*a1uxsaUb<d+^@TxW_22sr*;N@
znA_28BJ%&0D2p3j_jWa%nubPs|7h`0z<xmcB#n!6nG&6!8byd%Y7SFb=g1w_0}v@a
z+^RyT&In+qZBwo3zty-FYEw=tKvOyxv|jN^CgFX}oB0_+;W!%}^&(5PE`xXaWn4bY
zEWck-AyNyG3^2(HVgSiTrKPU@?jujW6<Tu3qCp5Ppl@6dZf9U^$Q6RBkjBdzY2=w@
z7Vk?14_IT5tP`#Id=4QvV;}*vP}8bTg3FqG*x+3Tz2ZoCAf4;1M0AMBGK}nd`@^a@
z*a#pX)e;!61Ck1m<j(Z6gap#OArL^bj@5y#k<HgCY}`lem#dgbuAsnDm4b8nC%^_;
zTtL>p3!7fLS|c}84|u!jHr6q59i)aB!o>+#Gh$*~Ge!h~2ag;F#SStic%`kZywZ?e
zojrnAWbI8rnHf6<F*kySynE2nD#9{<NvgL?i8YUO1eAo$`CVeFO2H9VyR4cShk%r3
z!$%~J^lv22=iki{K+FTMR~Mr3+5u5k4Qm_uT0B@-L>!#!=kpOtl|;|s9h=F*y+-7Y
z2_SzBl%KW83o93@cFo?m9=D<ESt&fesn&o`eAlWk2XGP4$Yvqciw|_&)tWRDg&7`N
zcmYlpfYBB$y-%&C2~2YW2IsJ7u>lh|OlNvo2sDeM4uXs<7w$X^==}dtQ>F+N<(7+=
zmIF;+Fd1$e1;E`bM1w{ZCeMjT2t5L(!hL??0FY=b`FVdmLna8Ez6R42h?8bl2Pc1y
zUsN*GLzch@wSXUqcK0O>?`Oqaxw(98*WyF@;x`lw1Effz52hMyeC*t_*|F5HrTaP3
zCmlT8h!KsCtkFL?kM`btW=8#dMq#7hPVYP;ga&5O5K0l=bHDHcQNQ|Z3_0lV@c%*f
zmjjpmB6@)Sk6};P)}MV6$j&i&=Miux4i-WA;>B>7);e-snE+z<l0ylWOJt+z+!Fwp
z!Q5Pn2%d*2$-J+yDm=_}qy?o8rEKKHm!G{DUdh5wH7*PQh2SJfXLxKXP|%0PTmNXq
zXDALwI^N@xWJ0?|KxghTe62AQS^3!sQR{}iafnjk^#UD&7e8>*Ezq#hBRhZTu8?Ev
zedJLVAthYNv5OXAMbv3EF??45Ka|7*qf>~a9m20*JOyGt@l0MQlWS*ysmt-9#nyJ$
zL8Eygq`pS&i^ZN&e5U19j4a9PjRG^4>Ax8;Ysciwt}psNDWLqdpawQRiCDmm0<Rj>
zWJV&M>r_n4UG2$m>-&lS67@^1m;->3`_!PF(1cZ<2H251l7&)~cM1H6*4`R;66$pN
zuCrFIDKHKbhg?Rjyf2#GuuKGnFfpMZv^R>5nz-R+2}unPysCnDTDrsrEaV$3T}#y4
zWU%8$e6xFESs)>SNEskm9cdiK2QNxhbzX4+q*bkTawQjNRS9v>E@0%77_L%q)dV_P
zKy1sd`z1EXXXw`Mz&Ru~mw>qru<ZGN(lSl!NbW`A0rl$~O$myjT0XG>Q81uW4%q6f
zESQfQnc{tYX=tbj6en(NG^@g}9>ufXVHRGAc{hfxZNgQ9+E&_Dio0o7BlzI6>_-1k
zj;&+-6h8z$gpA^FII{%nU<}tigi49TXuG#c9x<$V{GUZ}Tye+aM_2&==}<JV3dE4+
zz5xUA!iy;GibX2td(YkWmz(hD=U;rpDZ+&=TJ;a%6@&q{9xyNFDpiyQ)5Mrqg2n>C
z2Fvx!|GNta@Us0<PUl#WFDi&4PwtM@N)ZlO4hnL#aiMoQ{Xj(I0w3Rb)l$Jqn=1Az
zf0?m&GxA9r9bi70<1#t|A&r`H;85n%lyZ+`%M6L2Kq2n!lh9OQCG&*%RHD^2tjwvR
zi8zT2-guvWJ;Dnt3Td7OdwaqEqr`YQ%&RE(IBP%9NZ;7sc}VH)Y5Mf>_HmX1gav?f
zLTOS4z`akHBogfGyG$U4UDTznt5rUXO9lY_KGvyQM_mgmlt@BmNp=sLj2w1F4Reed
zdW)6vkwrp5+h-I`2$1Zt77uu?)6kwI>5PA)3V-6l)(=6%5)H>L#f6>%d$g5Fc@eZ9
z5%FzOca9sZZyv4J(_BKw<=AakP68NJCF$SKfW-5H7#Kghs{v$6$(OZ!C<wChJZB*-
zfVbdL<PH>jzr_KVgJBqKT&iq^#q{sA-(x?G8eamp4FthJ&cy-5Hj*|A;N?}*epX$r
zjQ;9LC^O=TOFwdZI13Ju8!oR~T{a|T7MBjYo%Z?y5pUUmg{|m}Ypqd)hv5wYQG9S|
z`$Sre$(O&sS|zDRTtFc~vqicm>6sDw`^I`7s@%=$VYUGmC}ouu^7dK&6FkbgB57#w
z!=lc)E^I1#@doNMD|Jo!=r%V@8AsQMNl(n<M}~J<AOMs7_V~8Oa`x~-h#si2|0k6K
zGAvNROsfMq%VI;a(tLlK(`<B}<V?{7W55zS#=h`$mUNLXMFS)uBXK<`*B3IOi_OrL
zNU8iIDT2;y#Bt?{O*JfRnAEhk9S+)KC@FxFoxJ)?mC!bo{9F3T>%cyDgEqR(tQ(1A
zc-f-(#gBYqW@BTZm^KzPT=`8*>X6s;H#E*@lZ$mHWNvf}a0y%6{A-hFz1!M3f1&cl
za|1reK&&%#Ba6b40IF@~N+WLu;4{Vq1ZPhmni=e5rNY84Oj?B=VF?hAFS#8Rx(ggm
z;>{trJD&V=Z+@e+{kkhpf+E5HfQ1ar4+Vu0Y%6#XhjT96P&cm_7c6v8d|xP7Wt&Q>
z3V*@{G4aSQJY2bs5z#FaEL!e7@_9CT&=_7WrBP>R-~&X=Z&H}+8oGOOlM{KvXhSeJ
z9bU%ySjq9>hX5eYr6BBxP#P@8lB7-Nf8yCdkWp+?Fv=_$lG}ivVptGFAwks^O2?bp
zbiUK`KS^1*a@o|VaqL>iuU9q8T)RYpy(}@krD_9nu%=eESk>a{aYo4w27%X)Xp@T&
z5MIvZOGpBZC3io~$q)ff+xmRtW&%wlU<7iI4OglRt#V}>Vb#voiw_6HEw`o0ByuO?
znU+$7(^e~?>FDxa5qSlghq7?XTE7qw^PFpETj<`fslft?w2?PX+@V1IL)?Q_DFCV=
zS+~_XkCP&T7<m6bCD!9xk1`#9fXP1Oq#JAbq5y%c)5f}5c1DM?DiU37aO>;nkV`(d
zel#`>Dp?0ayH7?PYY5gNl-uqtrF{Pi0ybn#2R!)+Pu0(Dm^IIOUt)2@L%IA>m=NPT
z`v-u07w=3sL%Z|5fWhcboF@g83Tbk;Kh=Sbib${Ho0STxEeGL0vg59GOUS$fljhS^
zW`cC2gj`2tzET;$k{{a(SM)nDoP82WxZ?E%1?sX?2nEVmkhG-8jnp|YT&Lui1?b<2
z3gqsk0fllMF$ugOcHNdI3vWWWj@b+ysv4<zeDFFB8Z4~w90-TikMu9gDqx)^B~qnF
zSIa-l4@Ym|=#rW$cPOfr9Jg@s!Vl6?RfhBb<C|@|LPLgthS@%7=os)o<JfQfSw;Sm
zdtfE|;)l60_H=#wJqZGHTOpI>E-EV3GLTS7Vf4;uTM_!!dtg8MgIXPPVt)S$GUj)B
zp}xxb*#O5U9n3>%YYc`<Ak7QZaN57W$IU4gCUGz=9eUBzku`b4%rt9Q*pfyt_lerd
z>5ctP?!P7&jDi@E&8pKmC^*KXkqsFBixN&nhM>sMFmP`p=|V8%>Q3S4--3UH8V)H`
z%}XRjxOH~@1u&C5j5y9_nwBbKs(1-C9w=G`G`je;t&kQ_U{C)5OdMAPd-IUF;eZM}
z0=T@QT*87^w%4vj*v8R>MWH27t{`)o%<Q|G{z_U!6ru@ZfGxA8Uts(^r^HA=7}YGQ
zS8$=?xYVrC^yLK3Hl-R3-XU!(rmc+<J->k<qSDkBp7<(v5LI}m;-MU#W^~`2P?$E0
zBuzdrwGU`&Rs;dli^vI>T;QHaEjixxD(1vRoY2~$k2n(3zb8v#N)M42>tuKVN#!Df
z^#w!`imEc8Ivcua>8RX!=Cc_ZaH{&A9p?YXj#)5oYWLbDE=@aFn@&i2Mrfd%NZ*s5
z80Cx#uOMBL0#^`Cgx=cvN18-jnCK;-^Q*1Wpe#7&Ynt<3Nf4IY+P?s0HsChzQr!0Z
zb&pyxN)FQ4-DAkytt8Sjv?7z<OajHJOPjq<Q>f9~UPkHpeBJqqEi!pmtLYMw+A7)w
z)Gs`kB<Y7GtQ$XXN7S@)ENdsOi;$|ab@DnijJypZR4ZjF45oiK+2JD(!4K<C-q_Po
zg63^!U<xyYI({t4%wdq)zcul)d=a`3yrY-IAp`?g4}klEbQkRfZY&Kp)ox}c2rSIE
z;WCi4?1pr~^5UtQ|A<ZR1h3HAQQYXEgspW-wwY%aSWni<e^As9>+P#wr=W7;H|FlC
zw8%dpr|P1zGd`XE`*@3n9Z0Y5e;N2dmNEOhg8Y^T1zfNWlD2-mhLK`aQ{MAS1gwlU
zZUDns2wBb2Y`qicz}VqDaz2M+0lY2kfpigv!TvU!PM?9kW!_v(C^_<Zy(n1tBK9z<
zElkt=Hgq_k>Sr^9cz9s`2(j<Ua|7<Yx5PK^StddpP<7FwIo5wEP#|3jnEk@UagE|2
zoD_u7F@cypkZql(*MDMbx^Q4&6BU(#+-i{*(5K;&Ub8_>at2(&{wjO?^xh$nxImN0
z!p-K`HX@=?#IR0KJB+#1%wxEr84}fRX^{g6hf2Von8vZz3rtnTE9Vy`xltZ16r5>z
znOwR9ghVn7k+9IhE9GMVJtkjM;pKWlfGA<a#urRcF7Ds2>6sC{QhYkgnU%V)Y?w}j
z#ow`zvQ_*jeb2HJ2LWWy7Fnd|n%GjU=ui{L5KlB%m~JCzSCA}i6Y>E!G=b<X9m7Gk
zK!Pp)uPAJHMaj$qW=c*yy<K2My&Jz#n&*!Ik&!?&5(=CK-i#(Qg}MrWMG#L6{Bgi+
zg}UK(>Z0H6xZD8*TA!j-!rVPuclYyW=sQFU@(G}pJxWZOWM8oGuz`XyH8S#|{}pUN
z);`*;08DNYG*F+s)_w+UxNaDY(%fW>ZW#Ri%Uo#oPXu$OeyKrH`4pOukHM74Xq3)z
zKCS!b!hy$smFVUpeRawNkb{x0DMviEFmwQc&bR}AmhEV@tu8|mlOA=XdS({XPQ7?9
z=Wrxy{dWiQi!=7m10xPSXway+ogJf1M#k8&<g6KBep)IO?5lJC>7Lc&770ihwM(X5
z>id-gDu(Go^e$%_M=%f(Ma-Xs!`xC2=|(|FS%G<|bIMSDI&AR%#FvkMiOm++06~ME
zF<Ul18h310`SlMVhXTL!Q*oVzlZYq=qUnu>WF_0L+ba>D{o0*=r>LegyCV5*ZmeoM
zFXAC5`kOG^pLg~@|G((ewzj(uAn&@bm-}H4n!Hp`FREDSd@vCqO$*z8fr#>WiB3|_
z#!4@Hc|Z5-Acp;Gc_^|l^fu7jsseZ%+)lKJ6u!?=V;whG+5kB*YYjJBY{u=jbygEy
zwXA~|cA0?{1b}G<Dcy!b4%ibe4h=vR(`PAg7k_|uY$tJOFF^{$Xk8#^Z4uf4#eaqt
z>vYE_7Y~a%5H80LxmS=i3z-nk#Q(?A2kuIRp}UHz7JuQ{H}h64<mZ332zkGfW6tJE
z7gHq4XRsa41&QXr@0f2N;6(X+ouO4~qE~F9S8z=xyfs)u$3~4(W&>!vTb_CFO{%ta
zox0@giK`1YN+?i@t=Pj(*u9&s-y{G{0ysZSH}_qzR9A}UYJ?bQCXsXaAEqkK6@utO
zvEv8XMRm7Z$0XLN^^8Yplp1KP)ArWEYTw8~f`)+jsc49Js4-X&0Nz_G>j*Bi2MXSe
z)OTngWm+@6o`1|%+J^K^E29*EGnQvcj04Me(8)RwnHH$-Y*(4{U{R8sO%07+$IE_R
zDgeX?g6-<P^xw@00L+n;rf}}DYtK8q@N(o&0$@)xZUCj=(avU3jE;~0i;#{D9YqZW
z*j*IGT)WgA8eFa+mEH&c`eW5!@Raz+=k{^`LxrT{HSi|vsXijYs+2I7Q~f~2F=S!>
zQyNEB*8lIGx_%B6#DK`xSNjMBbf1Bevvd*3QZ}G`jhI*f0}O^TRxo7alU0?8pF;!h
z;?X7pc`-Wi*S)gp+U4c#w-NFYm#p-e!c{m)0JmvCCI!GTj4hLo7GV?ONLcJInEr*v
z9gGT30$UD{3j^}MHM}7M`&{9<xxk%{b7bad2e4NM-_j8&)7v-QZ^DYSuzM?`n&|$`
zG%aiFNdm&@3#W}m#DVGd60!17X**YNfEPOw*F9U7h>V^HKm5jASRly++E76^J$v)4
zNTtj13La^65E+tUT0)nLxhGD$*wqH4uv<dJJpr7p%_*vB49VQb0$)_(pRTWP_M70_
zyU0JOj<6<=sL<Q!)uSc|DM?dIQv)5hr8i#xKM6*Cg=Em*hxR1%`dg!Hcs4Eq*FrOK
z2n<OR44D%k1p(pGXKRcasDyR()c4sp-a<FCkUcL5hE3d@UDAi8%k|D*Ve=<fZ>It*
zxG<Vd5Tl9#G+HF;T<9qy6P5^sN|Mlx`9gOO_Py#9!PrG(CslZkcusSyy2n2;`xiT#
z6w}UefVQZ{r@ftZky)f`W55RZZoq((Sq5%&mTU0IDSqxSQI`}J@F$BFxog>=pxG~!
zg|;}7#}UK2-lBNM+SE{<8@^1CoONn-OWEDo^Ap2Cm!}fbAm@kH!gzBuL#aqJ>hlDh
zG}m_0sJsBv^JcaaM5rJi{i60%%G6UB3r{J-<)tmeB%lBUEII`0XvMVCxueG$iQpWj
zA)HYPWcwUrSrQ&hf+vtB5M@v&hwZft=`~F<7vhhVNA&+^I?$wJJ$m+N@9hB0`obHI
z?ycU_ESz2GPH~p9i~)<`{F?^w6CF6k%s<n}tv3dShGLzZBuwO`e*6!m5U09b%H6Bl
z7N{y2=19RBamG!R-|t|BKI&TI4I`r{@fS6^Uz9U0b=TZFGJNgN9WU@O4HAOpfEpe`
zBvzs#>jLim<Mhoe)_5sv4etHCQ?A_wnIKNn>_`ZL3d2dtiCrsh{G23%%q4hmt7_^m
zLp%3tlWDu@4^!?R_&?Gs&z8qd=~W)0?ZsUleAmWR1%wL}N+IQGDilZmp;oQsbiHix
zK7{^_9E-$INuuiaGa;E-+h~6{a-HP;a5R**Fg_jzfy9OJO?Idvf>l~8QZg~(zc46u
zyhw=Wqt6F?!xN-L;6MqdE}8J>9=@4NSRCn<gEU=(MrxOwvKylA+Ubf5vTqqNm>>30
zYaWSV2_*_D#Yh}gN-A&*jwrdl9;+GkSj2r%{)QBjzol3&nMp-xJXmH#dvZ?Q+`3$o
ztKFeZ(6as0!Ldd%RupW}^z*xgBD3~>Cv|bwvrgwLorOO9fYKfr%WviY(5A<)w5S>x
zcHG>+{&)(Q|Go#BVOCb5dE|k|HKJIm$BsjX58PviLjjRhD#uUge{T<xR;QqhsK=)#
z>{nqs5zNpi5gee~rp`D^2ufz5#-*>94S=f<8lYRBn;=>F*u-JOtoRc-lWUqxg+0Lw
zAnq49%LBK?4ZbPSC}ss+BW{y)wg_k5OEkn(N{5TaeW~tQx`qsahe@qF!M-j~%YSVl
zh8k0m#8z~0s+*{E3Bjvm)8W@ISKi$<4iJu_ah$t;<d7oa;AHjt<m2QR)@YkU9Gymw
z#i?EG;NlW5h;6t*(J^IALffoK;LkxKp@iS3-=w(RKMQp;$E-Ba8$BVDRClsfwnXh?
zXB4N^`8DH>L=l!w*xsv7uukUj$8m-U)kNiQdy~##(_g-MAjdi8A<7DTi`mr5L=?M?
z5kGIQh8j7lb0fsK1d!yg4!TPM$b<uyNm?Y&oc}gTh&pI5)fFW~(`uV>qGO#<(BfW@
zOh!?N--B+iiijn-s`5tc<J9W)^5nwdruRDfc6?AeX<0d_K8Hipxm?=04qT+$?;xG&
zA7z0<MaG@H@!m&t&HeGfU}j?Nxr&UVV0OxZ9M3`?O(e@2UwlMRzR<bZw+hovB2nje
z(RUg^6&aSl8$DSRuU_@Ext{pqW<KV|z;xF6_iCh?B+&1*)@>CY<C~<WI3k?}IE+Y4
zPD_TeV?y-uE7tNyv_Gd5AdDKgT298MiW?YG!HB8U7(>{n^gPGljj+Z%k)dnzcJs)p
z>$WcKUbm9--7hJf9<#}@xn=8?);3M!{`wZoRPA%7lTWqvFD$LS=?IxD`KR@?4U+iw
z>AN{LTC@H|N$v$ixAUdhW7KE<pm|*3avh26P60TH0lMp;VJvaV`afUBRX2MNvm6rN
zX>WGd*Vb8VESPs@p9YrH#P3wyddyL1QN&3Uo;<o3?;vw>ys|$YFH>p?htI7#(W3!C
zRB@^^rHhT(tX^ZpuT7V+_JlDGq%Mv-!+pyX{*3{1Ek_51*tpLhZ#N$(egbf<CvA8x
zNpf;LqeCZVgM6;YX#MsK*h2QdIVR(J>GU!^?D2z{;8XF=^m@K&c(F6vbC;`zg{y2j
zJ?T@>E&7}e&no-VS*Y*7XFLcEUs7S{e8n;yI*6awI>F5n3zmNX-H4*V>Xv42KOIZ>
z*xx7dSn!yZJ-mP=(8bfJXQ==$kiJV*&*Y>Rq;UDEHbIdh8HegfVl6-K+m*C;TEZ{a
z0Pyuu*ump$|Bu(o0R9j(OSzX%gm3t)LBK1*WmghXW)1UT?Kp{3dWGEeEG%LBL@;U$
zsiI4}W12>ojNHFwSLfv@t4m&Od^|Jweo~_0^RYAV%9gAPv{X7rbinu%=aCf92%p36
zW9)Snb%CmQSzjXeDKa4~3B~K^6wc>-%>Mn|j6a*;tpnS%f}pWtQNK=ovzpgCT#v&u
zUb&=SL1;e%DcK@-S2i!$EG;uTdv_6R<b@OyNGu5(2pwm-HzySS7JHCG{K^q&cYg)Z
zL%TReKileIkpz<9ba#m+4xPdc4v3vA`i3>}J)d=q!2DE_>-@_KrXF{04-r&gA4=cr
z)s?~+&+RtBJBA#WQ~8p%O}(2%(1UJ!@4jRP74qM-)C&8<Tl}FMZgKCnk+D3uj`#pA
zCp%uxQ{f`SH1g6kwCdf}k^$~K(SsfrAtp)K;3?ra3;Wbv<i5@=iA7-TggN>@liUj)
zih;Lm%8DQp<C5a}BN=x12=SMEX@7P2<hE;{T5LKk6g77*M)P<Rw#pIlu%rui^fKy_
zk$Y?w-XWuNQy%v>@e?5>j?mBCG!i5PkKfTtv9pQCx4)3UL!ke_JVrMu#Lz%9&$PRH
zg`W#UYp(h|m0A|b`;7!oo>D^6vtS5sqZ8~{$^AajfHcC2Y{KInXqX6svhVe%o+OSm
zNA?aj=qC<`%})heZG*@qW~_bFFMd!%1;<lS+arD+m0t`N9ImyO4v4o=vbWKm>1Vzt
z{CCF@T7G7O;|T&a&a?DcAtrpwG7p1$;YgSWyLuKa+|p$vb^Hx;TkHML<y_qd%p3-z
zHPkunC}vWsSUOaNf=5sy^FfN&V<NfFQdO>4|CP6HnTm{J)_Zv2Mern0dC1A1J#ISB
zn)mK+k_;J|19&rP0<98>BC{Uk;X6-V#l%D*R}`CiJ>lrSdsljX{Z@4rGc0`fXJLgb
zr+_o9^R2W{kyzsoMoyve{1Ud;XA(rjJO#s_P}g!?fhaBW^R+DZjHZO-DpJ^#R2$JN
zcWgqT?eF(hXVx$6Bp?Zlcu_bsSZIjOd*4B8%smYwle&3hpDPK;_{hIvGG(fP$_XF|
zTk`mSnkVw*m{bc0J2an2{(7%IOlHN90u~VONCmofd_KPMCs*5AH=_j2g1<FHzVl9+
zpEWahyRNV<<SVg&B*Al@+5L~k#2`ft_Z#u?qAA2SzCIt{2P2HJcnWGiqWoWxV{47`
zzqR!aj$5@lZaSrQCWA1>2+{zB{SDpgv}8gtr)=GoH#Vu3mkNRcDeUYFktnPesvGMR
z_GAfxWhuZ`%<}Oq*&Xt}$2PPeP#=Y-WkkV@&|u4sGLNcgOu6Sit9+9Zf~>oJ<)|VO
z3is@D?b%Bu#B%gq<T3VCI~{+oOYhkPM%$FDX32_p>GuucxaRJaKQ!F;MmB$JPLhan
zd#y+7uXJB7?NjotvtC?RKDZx9P8|@Nb@<brUYofWAc$RmlWDmWDux}2HXja+x;uE*
zeQ)$=DE?k|Zhsar#ka9OnsqQ$y4QXYAZGRJg_DEp;@q`r{i*$I=z8KkritX`17<DS
zq4Lk`Rv1Cx_Om2jk@3D<g=@17iV!2Ko{>Y7zao4kdOXM8Hg_{sB7tmX*3h`h4rz+J
z1u>%Ge9DT~1MNjk(=1{2qzj!T`W{{39-M#+(b)S&jG^Y|97idu-!7ioYvy(HC-v)i
z|8O4z?Z+6yVYdURB*dMI6`2zIS!Jw+6=+)$2{P(->~eMU_FM5wRXA2lnH1>ssls-L
zk!dw=7-|T$cRfC;-P)cjjD)W24VumF6T0O1VCj%IwzKZL&3ZiJ;9j6uPyU6h6)`Ci
zBpgDV^i>;-;F_G2Jyd=t!B9B}da!wuqbaPp91C#U7sNd`6QAZYn0~EkZ;Tm2%2Fe8
z@qQHyHK0zfAh6ZZ>~Z+96%)_wi7w6xJfa+tZ~?HtQ1TlGUFwYw{~(i$2MVgKcMZSR
zQfK<J5{?=ZKJEK3?uuc^4Q9;pWy9igaSd0$?hidZ=X4E3S>e4Re=P9pI~GWF6J7GZ
zBmWXA+GlE)KX{5E+FC5rpabR!<X9&Q$>)?YGpQM!&70m|=U4)7Vt}@l#k3;Eb;q`k
zpdQ2}_24Z}ilD!Upx#<5hz)-DxI*`5nag}xH=%zwA3fZtLCp4e;$ZOEqRV+~HKS6#
z7d@s>ki<7F8$uQ;ZT*r_7JwveW(8fnfm7q*7_bYG82sr_+GcV2aQ&m1Gds|`1`j%m
z<RoGoMo~+MjZst2dRlu8mqm&?HMK&)79&TT8CCxW$I#uontbnI;+NxlYPL7mCBz9P
zX*LMPAh9_<(JAds{i_njz|X6kWEB$Xgk6#hZNqIJ-vp;AWJ6#D;9!(6Q|+>gjOiH<
zye)^g>Uud6T%3@g{qZ`hQ9uN}4H1<zE#*C4TaJn2!im3wxPfKj+syuf(`g>((=l^#
zuKu*Zq5Cv9)Vksl1kO|V4fC`9_#?Kc#}zh#KJ2S~B(BK~W5UD@OXiQo@@w^#`TqW+
z*nu9`Be4jle5*%^1Tc(wmi`E7GTjd~x1jh|fi=GR6OZ6w+&;G`;4Lsq&tL7x7!nW%
z_M*^#F~VI)-Ic#Gt5Ly}O7f*UdRBZGy)6)VzGBY0#I@%lmV9|NzxfzwuiRLhn)v-d
zO*60X6{9<JaZlR=Tl?beOGZz7YMpNZF2=a~H<*n=qVG)7>8aBL@#Np&b4twV<(uXB
zlU>9v6J#cuKUjUHNvDLff4+X^*_r6SHoYWdf6*(!TI*Ld(an4m3$+=k1j8UEu&P2=
zPkm*WiL#A7j0KCOPWPb@nmGCe-(WZ&&_$QqP&-@%3`&2QVWvvNPe0L#=P24hT2w!?
zJIc};Bg!^5&Fea;i#AfsptHX>3Tg4NPulmuV$pWHq4@Bs9T+zI`Y)B{hhwfR#^9q*
z|J+0JqWY2DUT2Yg7^^^|!saak%vE@dn8tf)%hGYp>iPBD1AYDCxr29s1b^h9<p7mL
z=*)K&!(!=GQc@*iS*2bM!B9F4Wr?tO|AlHiY)M1vARAm|{EY6mumesmg`L^4-H^^B
zA{s@sc$W5VSdb)7cHNeD$1m6fR_H6|SK}{Np_W75r#qB5XHoPAx}D%6g?#y|(n)35
zU=ktNsxEJY88#|q9^i=$$d1`rq7pVth0ih_dAu8-s9<MreH>)v`>-M^QNN2-1Zs8o
zg-Hgoq(AoGEtN1$W26-=68TQY*N0wwy@l+Fj9RkC$1;0Xd!Q9EYigGb9NL7u^8+nt
z!pT#f0+3Ai%cZ502;00ISY9%Q^CEt4SVnu3&VOUyaAignz=3bAoRvr*{~Gg}L<rTx
zSlGIZlQPQ3+;0<(lNF~IQ(vfQC1X`7RkB3%i=s&1vTLGWJ8GnV-S$z_3Ys@ZADfRc
z&XkiPNz`7fym<rJywchA5&K-^doHU}hWGQ?R`$v-wExbQ-cZ2>N^DWEL8QTXC5w!e
zjAwzE>&iVWHT4358}gPr*R{)XSK|D0o)^tU5Y^cf($7!0<OKiHZJp5hmq0*gU6GW_
zoJDZjq}K<2sMM(9IQlM70*@aUTbENn#4sK6EzDV<e5V8dFXgnie_>c<`HEA>Q&U|0
zai~v2AVrT{I@ltI>I}W)b8lfp0j_wST_jEL<#|4rw1fm~yy`dGc$ZWuzBl!UrM1|2
z;OUfgOG->7wm>i9MI%5H@m9<tX1a_V9xIS*iBZUcDU&@ET{sdOMch`|b`mHzQbfyd
zn2bfjFOUR=wav$^(*FCKGKmqKb;z}L$(40U6Gw<r!WZ@xLXa-l91V>i_Sifl991CU
zn31x}{}fr_-959~Xr*hKDIKPJV*|mbF0O=$R(p<EHUx3U*}p+J(Isq#u*<v-wL>`n
zv*bPmq6HZddRW|XsI60iL5FA|jH~qxY}`4puBN{-Y?VH%2XSygD=eG*;1J{P0JFCV
zrn=mCV<#NPiX-|a`g7(KrSN~UUMW<!FPlYRVfS!idpTr5@HlA-)==rEM-d`U%$0ZI
z@Nx(qZ?qMqf(+38lZ!>1Wb9ogVpSl9K@R2fw-JH%mYXkNecq!e9)p(fCWNwP4LL*r
zmzVaH%Cvxgb8U~c%9iD6s?tPtnb)>)8CkiMUy(g}9X+1_6P^3PVyPB881>4iE9HZO
zRQmaL8`D~&H}>nf&190d*CRG{xe@_mBo+>M0UN9am%s`YFZ;+AD+8}t9*p)yT4f?d
zCUk~A>|UZV2JMR?X?`K6kB@p?G)YA26DVVzI_y4d`kVbU1-Yoc{$JAMa-+Y!(Om-;
zA<8gMH<ZM4g6E$tjLK;g>Ll_*sJ0ABnVUQweQT^CNl0W@z!KcQzEYSI#LQhOF1m9k
zJQ=4^$iDPj#HhPUINxhS`JsK4<X9X;^zU3DUTyzLkl!F2Z#oHwLZu-9$G+jxT3NSg
z5FInoY;n>m`A(<SD=dLUyK(Q`c-4t22A4I?S8QXrNFkA_A@;>b^@=>HpC}M)AdL?O
z`vmT#D^p1J8%U#>C6iV*ejQH&=5=giSVQs~r^ZA`uYk&0lqqRrFt}P{DDeQ>1K(h*
zqW%)J-s^O|d%R<>9m+Pc@Q4a>pFH;9Ik_@&z>|@Z6I;8s`wKMJun_C|>%BY5WtyJ*
zRc%8p9+bZ4x2F1WE9$uh_BO<}_s`YUol`rnCu&5Nz_TB;eOkzsPwZhgx89k{dS;rU
zYZc+87`(k%ra`f9>8UG&R<g>`{r7n~AVmoH&%?-0Y`JL-85p&SFd|;P@L6P@6MJ8L
zsbpnmsH*X@vAG~{`>(Qu4Mw$CHnOo#P#j-z)N?9ty}p;R)mF#(Rg4IfAQs0nb1>&2
zv7|RxD=wXs_VGaz9mqa;XP58_%SI-bxCs-EW1cw$`qHRJ5E(t5bjaO9$Cu9dDh9po
z!L7Zt+{t<b@3DBD-NyEp-w}@(cYOTIy)o2GcGGei4#lJ}#yG82_V3%(^M#>@X`})!
z^ebq@B)b!X;>9D1di18Es%~6va_m9xUlMCdSIijull|vV2;~+&5YPxvioB~_K0c3c
z@&M<V=jqF_ZRj*#fLqW>XLqhSy<N-W4V6WKL@OX7tX)z>y!|w!iII5Iu0r$Td2l4D
zt4kf<<V~yrDuz7s2_tx9U)B$#`8W2K#rMya_i(@$kCADHA~X3M(}C7U`uL`f<e;B6
zgex?)G#UY8sH#OsN@!yYNhg6HQ!$-G&E-sCKZtA7@a5qUsFOt(I5nP-OjlD}ZWmNB
z6P-|b)}J$!hZ_7{QH2afAYmf-2Qr`FB^Ox&Zmgj%?8|OofRY4b3}<A2i;~7qGvOaR
z!_D$Ce~*$<%OHr72ADUk1A-24!vr?e^X@PdNGVLhzs*WCerM^K-dBvlWo~a7Sd5ip
z@p%h`+sH1If@0><DNjq?S7@}&>8l-eO?|lA`+Kamb%QI_dgIMO+|Z0d#t9_|Viayq
z5oT10{5(O1nZ>K-O^*xJodd4)dIuvOH=nNzlZ71I^4VmcUL^)i-GUs?_zfq#lfzj<
zPWUFphU;$&{6WA@@YBxVCTEjU3ToIxc9ohfcmrAhE@f%ETD~^Nr1!<TDU-0~=vR)9
zTehH6Qr#P!LEVJn$0+FNlb>PJV})`SRvOJK%cruhIN%hGvk%USfNo;xc_x*pwwvMC
z=E;jgt(gzLzDMZ3M^#xD-Jw{*Dtq6f?aBJtH|DiVf|2_fmeomz+*cyr-fVG+X?m-G
zZeyEEl~=bgjx$uyNiI4R<N{BB-~;DZ)%UN(zk&0{<q|sM-PPi`dV46soPaD)aF|D=
zhifG6_ya=t+rw{`4J0yVd+$f2c^JJC^o}F~vb@q|2E_(h``lZiyuzVFT+h^<1ep(L
zmbZ&~zDJ76O<)Hil93$nNzQlo4@mmhjcY!jgb;#9RAM@O?l<r^p;ooE1{Pb?vJ(zD
zIXgooqjT=WtajGu&y7NPd(QhY!KxfRL&sJTjDAE<h-90o^}{V>q2%i7g#83fa$$pZ
z7hTA=9qjAom`?o<$(5n6g=L~6(rL!&@LNmj$$lm{;?$^+`BXo28?(eRmiWC)v#CO#
z1~0lr(?N&I^&Un6Cl~Zr=MM}&JdMMT2~`Y{p-4(u!V@jm9}8HftgBqit6UDP?=L0K
zy%UNPIB+)H7E;o|Jx20W;hCqargS;Q>9X~cxhDzzaEiQN71eSRmvJHsoY~MDho)^R
zSrt%j2Ad}w-_{0R80_#?^ZS4n3r!T7?UcddXwxJSl(yFnv}WH{{mp|;3_t8q<MV1;
zL+|qVILu*BNH_9%Fw30wV-IT}iYF;X0i)^S-T$^89ZkYtRfq#|CErrHYCPe#I&%?&
zwCr5milF;qCq#2NA|(=7<m^3p0;<6;u!vuieZte7!_&R-h209lz<%OiD3UJflz)N|
zSqWZH7DL=YTHZ2Y3vex4qNGZL;gEl&wpJNeaf=5bm1+(#nm`D**}=pmqLuJDu9u|Q
zWt;YTe<QapluxY#&Sp{WjuB#A6ZcDAU}<{sYQ^?~VZ$(>i|NjZ@%drR2@;M&KL;_$
zH%0%eks}KfDyTJ%OWLwR+{R=Jxbe+3&GE1fOc&6Xj4|5N6V0trhLcJjJen`2k!Lw@
zD|uoForcJ|1YRr#Za{emY!O36ggu+7v_$j*f|MvXk{pC6zX$G`MrG6LYp`hxNmeZX
z3f(PiA;|dukEOGWYO8I!aE0RTPH~6e4#i1u*WxY(3KW;3#ogTt#hv0_ytunVA-Dzk
z&hxJCFDvV;B;?GQ+56ga`!$ts5(%jX$b#o%Nr)AT5H!YjSa3y^`vf8@%Yp7G8eD#h
z1b=}Xj;?#`Pf)MpQ-C<YK(;$%5^$oR+N`WzuT)SJ{YedE`NQqgoS@RM!6)QMq3Yr`
zNyP6-35k<zo5`f8eVg62;F5hipu%9z4R(OpMtRfHs?M*6V&h6OD11(YRa;!@PQPSj
z#pxc+S#@5cD*OIJRO<0NbZV8AF6Y^3aY}aAp7*#pR-FI+j1jEhs+d@QFwNkB>u~ad
z;v>bOwg+z$tL2dmKG^N_*hdOY;%(v>_j%wu3L`j@2HFel8jT=EsMTA{-aKRSKCR}|
z3%lM1u-NZFhcVL;<S=G`g39_k;RT&;j^=fq5Rg+85ncP_RtADD0O_m0Ti1-P1iO6_
z`z_HUJW_P`K?~+Dll9F8!BNdEr}Vh}&++Eu#g24uQ8;BJMzKQdjOa<9BS#bghk5+N
zwByIP;9)wuplYDFfz+QqK<0Im7%Z7Y)D$%H?Xw4x@RFSBL~*8(*7GSomymP@*^zd0
zVF)|rHa*T;l-*hMnv+R-kutpEOXyf<|96QWZ1r3I2$TF$!=kNbuOfdgfPN8B54e6*
zC18WJpHAdV^1;C8z1Yd*4%-;u!cg}bYofvk)F^FVXbqQ9=ZVy)q{?xo&&Q|3;tL}Q
zwvkGpBV``n`iZf>{x8`;N!Xu|@q-!|8ING4o^cMDKL<@>^UkNeE>hc-VIDaxMZDE;
zcXL>`WdEcH3?a2jQJz5{VUWC-Ru)M{!GKF~*v3C?H}Kjh*es0r-?-B63?Y=_j}f4&
zWLY8fracx`boz^e*!KhJSCk5dGTj(?dM`9AEhRnqnvSuuk!@6af&Vq=7ypM$iDB{d
z^x?;jACamX(;AZHSe~!$%%k}4A~a(qmL!?L8J5Ed+2iDuH*Di`=p_y@GZgN2eDZY>
zy6ts?BR6h>BpqSv7($Ps-OdgyLlTG_>s5YMfAWNA2tyaEZVve@-iGFXtB|!5`LbiU
zH&_VW23h_k`}%Uj%<|dyjfFA#O5<hS0ro(|P|ZOiUB=(oR<ASsCcCejvn*;OpJNLr
zM2bS!C^MNI=D&P7le=hV&k68#;ycuE*~`vsk<KI#b%(e3Q;V=owuK}J94AK7K~_|b
z`EG`j-^p}8-yRNCeGB)LjPYka#grY!Il^02Of!+euRT(-guNCM-XRH|aRmZGFIBx*
zT4B{dtIzpE>%4OQzD<K3b%)2RmDpj>I~?i2#&T6z7;`CIy03rsU*Z^nXrz@w%y3JA
zKrDfhv*ELTV8g)gS6<msp;5&8%X5}uRZ~+$1V*vNw{3LNiJYe$Qgebag~v<2aEeQU
zauvQ`Zo9<!+H-KiV;vD$gZnYjQ9>q9A3Gdo8PZ&`9AB%`mqCX43FKt{xe1tdxf-%W
z&K46YAj|XF-NlW6hHshF7%JMwScOtai$Iui3cCFqw^f3E+}7A+`#G7pJzOOq^O8X3
z3>2EO$>NDrqCw`02S?65zklzK7uMqr18Bx8-m&PG7>{iesWTjzZ?U=~d3j<YQu4c+
zhMF!(gNM0t`Fo$Xzy_1Qs~3Km5NjO659MYcph2Gx1)r;wu}kkXl;jy}NE5$~?+i?4
zZEjwa$>!kt>d@FgFo)W`PVpVttIpR)9uel7tkN|^=;gheMD4q}E7f4}JiR}&uqZF>
z{BRfDRuUedYT0>UIdC&gS>dcct^~ubgQz!{I3XeK7+37eRJ0aiBDwQ1PRa8HO(d=i
zuXr$rAI0c6$6vu=XtSVIO?}elzh+KH{ixATjY?oJ){oU~`laK{iQZT>pg$PvAgv^G
zi0Rx|qWdVb(mFS}62I@OcvZJ}I%@f<&R|k=@~oMtJPr3Cq%HXJS!>=d>TUt1X_(On
zoFNWB6Ovn4SppOljWFD?zOhult4@a@n^coJsf61L;19U|CZvY=Cv3JWyScdVDH+{r
zI7z2gh>3229%$oh^cm`8IQ`5DExBeT_wqo)fkk77TJVc|#6L37GizWSic^x=Z?nEG
zi5U@2K8@@bFpm_<!m;;^8p?uGtoS%(5on(M8^&m0MlNYtfFvGBIf`4c<FRidd<A+Z
zUeSiSBmKA~{WyhJ<U}5!vdScWRww#IoKmqx=%PT-8O+EG^s|-+{`q8|3r}A$Nxx9z
z-hK0txx16XSS0mB$WAR#_7sb@P{;$fOg)h4y|^v+kbK+?Q(&-VyTJ#$j%@X!#?*bI
z#ih=!;a<(dK|4<jcpoy15vAga!i%6hZmA_BnCbe98!|>dA@?vvXy%HOlLag_56ph)
zYmS~enTcH}^rlc2{ht``{F1Hja}&F<sqJ@?$U<tndJ%yB^y6j@-Tw(z?fiU6{Ce=Z
zvXOU<Xft+G#yMO@WcW~g0EjehReQ+Q#lP&HCj4R0*7L%XEUybt?sIbNR<c2bcl(p9
zi9++z!Qca}V5SIqR$B2Y!*q+hgkx=1`Xsra$k6h*qSvXo<=IQ$ucye@eT@5Y|9e{W
z?DUm<+|`(55)zirpLdL&`25cU%3ENc%u8-?xHQ}A<UxplR_{dk_2D%0X{zg9Fc&tL
znx<zhtj8q*@-|PnwM=#I@+Sh$f$}_Mb~J0l|4&j)u`8Hm>mewkL#FP0*jw;CsAjv^
zcV`3rJ3aGmO!aHOAE@`B4HJ7jFrrsfOW@y{d`)$9xmjf`SGT~AnN-PS*{HS0E(OL)
zpOaCsP5svwxA{~(v+!r&$+n1QlW@7Ly>9uemH4&ek9w}~;J<jGKD=oSu79Wx6BN&J
zj;~u7mri*KjQY95sBy|29_EvNaVuN+_9X<wNw(6f1>-fT*^xo(an;Z3zp@?|u|%&%
zV`EWOdwaDkh;NsKlKkH^m2VRzy7vC+_xhzEG9^mVvjV6u!Es|Axp}rC9@szoyH$A%
z%&4@Z9JJYxP`5Zu#H5AVA@sjxya@b%W8j3kI%%Lyrv2_S!-k8g;4%>#mvM?QbhXnD
zgu*b?JrHSCdnu<VO_r(Gct3Fk2XU4Fty_5Gq)_H-LWXa`Z<kP_J6Z#?gaVGc?>BcQ
zl$bho!DieH87}S&pF%)C_33S>7OyvGArzD5vpa!>$AD^jd`kpOd%9QtQq1iN0{}%S
z+EEzwY(fdAFs_-N#^iE+&646^i6ey3Et}<c_Ax9*S-lK6l2~@Z^TrN3WdMzV`md-m
z2ms3GW}=u|XreN^(|(9#tQ+U9xU-EzqRXhA&t8W-OEZNr_CJnIr@|3+ml?t~;RR8a
z>upUo_paf~bJpc4s&Mr4D0t12k14L;!5l|@IoCfQ*LMduVfJvTi->GE#gYZHL#ni-
zntOS7*fVFkC9By*y+WsAyZf7Nf>Ts}(>=<9?Nd+9t=0Co6ZFB`9!HT1g7o})V{~9{
z#%GW0=uJ*Ogz72ODlD4My$!LHpILM_jkjoz=dsZ7#6FlKKMrhVHWcdH!x5<J^e<a^
z-t%&usVlT8W0k&L^9Zr)fC9#zS|h$k?Zt}DgB!0x#&v-ko9k<!VS@y_;b^#WNM(eA
zkkwE9Fag6CMpS2dlUgDJ%W<*Exfge$LB&uo39Uj>!_PDq1pzC5HJ^|`4(FjuB&^IH
z%}$c1NqczhqoGU&%BvlhfSF{YJkts2@>wEWB^RfA$@Kz5+EAR%PMlZBc+k%Z_aI#S
z4_6FL8B$0Hvg2kyIGZ@4S?ecRbY)Gkidk81HZ`f^Qq97&8FYpibgklhWsp(i6^(y^
zSv0ACEP$lm%3JKfeGeD%`*!S1R71;xyw6ckB$;H7S$f*m;N>r6Ln3Bau+uf{^U$or
z@XE@<^S%2Ma#$$L#@;OAB-=j(^S?^IR{OLbs|?9<)uDKyoe5#*(0{_SH^XM+{QApO
zEEXI6*Rxn(94*6nJ|*p*(8&R&#NQg`elPbGrtjTablQ5O?MuIV>FFm_c*PcDP$<t{
zp76ZyVWNK9wf_+#QJ^0-4!8gBeY?8;vd^0#uBn~hJEd65TexvX!63h^A(KE%%0Gv&
zS&2HM`eW9$u9j>N?b6kXRCTq<VbklxNS7U}{`5#oi7%TA{-~%nP18dm0~Zu<D-%0M
zasn3=2PsS%ZiG%ZsRT+a?H$gb+&_P$#{F*S{b&4Y^yyF^TH88ZzyTa(wU|IdiH;NM
zn>!%?i^a&u>ShpLaBhq=!`P)*@lecb+NH^ebU#L^&c`A9%#xxqzj1zR4QiCnt7~Fw
z5+t!C{YN1rohH4PD;#^8TbgOO)(U;S(Ow@hO?1)Nw=5)yO8rMk#;sTE36%BXzq0f-
zKSsZX!+|Tac%IlF6Z8+kzN+EB`saL;t*`4pimry}mA#eIK`vVlb&)M4ynR2?_%0|%
z`B2tX|9whz<yBvGwwX(-qFGaf_A+uD;xnc{W{r<qw!2Z=*z_C^Q#4hK)r{WBzuIRE
ze~N$bEA>tWk$&{*hMhOrC{iY4mp5p@^`=!AXu|{3x-oRyYKL33*`2SpFFio4MaE}`
zxI?)jKlEMC^gFvwUWPj~=??4^*tlCR)=lx-u}Tg6PUyf1YE^j7m(PVspGwmSY_oF1
zY_d38RW>r_+7XgKTtQAYPzDRKJ9=$N>uIuLS-nyz8+Q78xD*z%VT3z)94hq?Ig>M%
z;_;1)qCZJrB;>YT`L(iF<$3PJC5_Ej0%|3b>l@MNQdkPy5}1`Z8%KAJy6EN@`#iGc
z?vN5E__qXTCo}=<WqC5DP|4j1P6F|7#BUd3N>tvbX0V$SeS5@5>feAaZD5A2uUTWU
z$Cl4e!3zgjd}uXay;b~1gL+gDEL{<{0yz?Wx?&(vXCT!y8-(#!o@0x*gT?e{rX+!h
zdRRE1(l%*K;jP&S0zE+pCSmA1$u*aPbHf@koMM_V<q30(QHh$)RdSL)vA8%fcK?+|
za(k!CqYwMB3fs8<$h6QYaAlA)=f1?cr)XJY_ymf;^$<bS>Kq_V(!;eJ$-Nx)?v&x5
z5CPNHhqU-pEOu@me?CQMuygOnh%^>FfUr_g?iP`^BkU(>=*_HnJowQN%Nog`JCu}8
zRYp*WRovI6<Vzz+Gf!DnZaS*=&1j-a|6<alj7r*tST=d+PD*=@A=5?9<S!Dz(a=eY
z44Qt5GqBBFF9|mq$=>t8+`w`Y)UPFtYO`~^?D5r-x<#QJr(|_Tr|u1+DWLc90o7Q&
z9-TU#aM}{nv5r$XtTLkC=F?PKzp|h`oHk+t8@9l0_*^S(7%pATRQD8~OvuWbbqK>v
z`c2M&rY4K#A6PmjjY!58n${EWF3eZTAogp~b&b%Jl!__WLQRDu<KcHrO!>jd%wToi
zpkLfUzYyWvPC&6EAlFb)0xdqo#9$f>RL-PcUfdyilBBFKde&l4T^z3NgrsJZ<7?pt
ziWIq1!rGO^3%QAfXvfZEltO+v4tbN{N0d>ntAjFSe6ND<G-7v&t6mncdU{$gEZ8QI
z!DbH%(S`LL(m5}W=1O9`u4mZhN@0M*ReJ{$+@z}JKY+}M)aSz!(ZkPTb3Lj5?cJNN
zkj7i*@}F`=5gfrmH;0(b5?nDqTN1Kc=7YSTl+jRxhEOHp?gaR%Iu&<Mqj-r;rbwM3
z?mo8R_wd;w=&Pq|JAHoiOGB|3|Lg2Hn228HwI?}5^!LPGyp0HD`;6M!2V40Z&mCU|
znjcmtMF&Q6MM7*u9#P$E^)?UuU^9r6iv~8%50xZveTdvyuRWR*ubWIpuN~TD+z<sa
zYn3X38hf1JkJplc;(tb>(cnMlPFR*)GiY!s|4=(!=Mru#L(YXY#@5%)5~u#UU3vd_
z`W842^g$BRNHytm3>Oj+reAY`@V3J;H<LhHr~NlCn~SK2ZHkqcO9b?33S&vfR%H5x
zFqK{j*Yl_}cfZa5N%D7QI<ei}BRum0U(4eJ-~w8p=YH<4Lqk=^LZy}vE7%~%M6FM%
z^grKt<{cP03ld?ZEj1E^9Lf@wh?5Qwr8iCOHCDHedslzn8eq?{_?oZe`#XUdK|Q6a
zqRz`DvHA6w3gAkVcw}=$1NO|HTdw!fyefO%J6x5;lI0t)UpD&RiKJ9j)z;2Zg=2p)
z)Y*4`T@f?i>gUFB;X%*Nn4FO128{P8W8WKO)g<8G_fmX7gf7wfdf<3kwnlG5VK3`Y
zH+KCUK6U+f&%SM>*n{@QuDAaq;2XxPQwRm>H`IQP1S<BeOlotdi-|!Xs=m}FO0HPn
zsFBxM71Ih#9Pur-Qm026w_>ZO2~l=YQQ7`Yb!T7OMpy63M(dx|DMqG5TG9ooVF#SY
z%D4FxTNv;Bj`@uCBfBn!VNF&)VDUJG8r|8y1r;Gl=yI+}!1gH&*{>h3>L%LO7HCSY
zG2`g5Esr9U6ONiOkr}he#06I<L%vgraC3y;P6<woR*}c*G0su`dcm*`(_TF1nzK&2
z4R;e`wwXnWQ(M%uNxONFJ4#KvT3$W&k9K=i<b85)S%S$Iffxu~NSU5daVEGFeoq#X
zyX1}ReD5AZ>TC1O#fsQ(x?+$y?_u1(d<Qurokjkn&Q0J^^5U*b)~UqR(tWd@TYJ_u
z4ALz$9#iEc;MaZ5)Tp4waH|wyBP`ioToQ=M&fbaadJ;Yvb$I-oJ1@gdy@EPCYme4!
ztiFohd1->4poRwA+4om2sfQo#v<2iT833BLgg7fBeRFIK*KN|`w?RJ#nnH1$1STzG
zAA>2TOt7;8AL7y>+TtNbOM53kp>{Wp^UBg4XJzF`4P(46PZd?%9{^;;_})4nzwV2`
z{;HJ?{}9lM0VO5N?v=8``oqGa03+>JwTXle$b)e7@?z1&5jq9kfWAMz$+WR?pZXCl
zN7Z7`mpGmI1)acX%XllXNUD9|MSXsL!lmNcvn0EItaXx;>TZu$g2qlgFF1tpGpXjj
z%9e$2VGK1h(A+Lhv37R7u-k<2rMoIk*Tin^lGpl8|JM~}!ASA!a_V?SD|;|n7oSnk
z@eNBX$+o3-N<Dn9+;xaLC580h;H0Th@VJVCDj^E3r9br$oXkTQ$m)m;_Y6*ATLkXk
zx~$jFo>FsbSklHH##wqqXFfw+YGJ89wwF-VMs!uqQluGClVvNndo~LfbnRql+M6js
z3!8KJ4~0Eb(+2`-Pu$Wj5#sH`<2@(9H-e=N+bE`RRH;W_&mZ(tG1#!bdc7Zo)-6$R
z{-_&%NHF8lWIB)aJH}I*Ts@0!ahKaN9)`TMuPbSZupt&TH2u(}tUKVCpBEa?`S8ur
zJJh?03e}$HJDn-v8ljljc7uFU6L?w_nC#>9HATwMk7Tv2AFHRYji@2Ke`x|fD(D52
z7?XPjJ52hZ?KGsql!WAJ)m;mU!YJkYy*?$NU%Ho8-o<o~=So@G%;}ZdqjrK_?zP)a
zX^Wh$xKA($f)-`d$<@EzR9TEc<jS?M!t+Ql<iy|r>Hy}UAuK?h@9T5O?_(bU9H+p3
zbz0pi@6s{qfB(F|m_%wnv`gZDfo?s%aW7Qu^qB6skAIxryNN~lm7?uH%spfHLD1;I
zsB5%Ro*7W_ANe~t6xDuLzEvfx_v#}=5C^ox1R9{J<nKI%&ywGReyHAcdTI^wxje`%
z*15P}&+P=Kg*gK+pgB7SECRE%bSf6G+BO49*Es@ZiNpCAGrhpog<1O(%H)5Io@?f_
ztQI3O<xj<whcWgpxoVz|irjo`EU}}Wd?|XaeBKr8yhAU6-~`K&8jv_q!m-rR`d$|m
zwF^dW_JQ{6XzqSvmq(->lr_E|tR=dBd^O0o(f5s2VQ8#FfxFM|69|>)*5`NzkGNjb
z@3iZQ=rNlTU^c#<Tpqtqv{6F_D)!61*c0}~Yh<&>^Dk)4SF>#Xv8SYY0^ptbYE?N#
zSv>TBXpl_{K$iRGa41714@(;_+;)7KS>89CJs(?sal9tBU^Er#+@y(c4ulh+1CN*8
z75{t5P!Tb^dWt;MbVl4her4?|@THl903BBt{rwobf7F4fcShO!Xj$|N&;8^?4f+uS
zuN`>1W?q{rOXR=CgmoSkJa?o#oXIMpj96hDdRB}x)CI4dn1zwIJ&#OrguT+pTqyl=
zFsUO<by1z+KXPvqI;^3gQ7yBeFVM5yov`<nW(l)hzdU`)&9+_Rn2EA$zivAlkNYQT
zIfdJGi1lES<DG!G*6BeZnFwAC+(?f0Ps(?sV@Nb9ESx*Off>FLK?A(mhyNi=(VL`z
zJquL45JnV_!C4$U>jZHeJ2Cc|_R+htuJMB@uZp5;kBwsoLz`ww#T|pWww2Z#??$RJ
zy`hUJ8{1p(lX)V5#fHA3i!bjRT)C&Q`=o^QS}~^8-+ffsFp4^J(6a+v^6JB=pwGd$
z=?NVE+7C5z_~N84&JIB*nXJ69pjzaUFZ?RMKt`-rC+t}k1v+_Wtx04gGb;Qg;n>vd
zZDZATMG6Wt@e&+#i&ZM9)cfVMwmD%J!I%;9ea(kb@?$N^Tu_mr3K&ZY%VrrdtxLwu
z<~udQ{^gC@3S4A){Pe3FD<+YU!g2<ak1B-IgDKJ@``p%w^m-=K0wN{<xOkFirlP>y
z;Uk)t^J!AJ?!vJ^6aN>eaC;Fll6rCqESh=73Tm~T?>^D%mDo>2BT2^}VW-!`avf!v
zr*Q)XQO>P5$~)z^Z&JBiKp@BW$_O}cn4Cptb%`q@v3eH6D|d-&JrW9wnki}F$jCWa
zV1qonVc&{O`|;`|5A6p^z^sx@K93@fVT(V8Q=Y3WN_Dt9y+uWg*r!2*5e|(S^{ZN-
zZf%wmn+WFN8BV@yDkzraocyadgCa5SC9<xsOCN=^{j`j@11CRx(IqS5jmxvU11tgJ
zC#>sNxFA>}^-C>z_1)H@VEnhLUi-&&E43!t237YDcr^H<?jGdCzn7P;On_aLJJtdx
zwp;J@*LC4&8<Pe_gHb3$!eM|0tY}%*G`6~!1|WIJP`C1fQ@e!Lr19KicM5}3i}_H%
zeV!pmP?xkiFa1|8BbA}FjuS6YhP3HVZ`M3M4X>_IvCL)o{lhuIrM}}_8xr*c7WVu%
z8ryb!D%-wTUuh;pmt<>i`=MP^OO}|duSjRbBz!k*Vu>+Zwl4eJtQ|EHYlW^jomK|i
z*2pOi(|RY^_ms|Q@iI0U(~cN*xc#hRHkj{<>$;Jft<BP8a+EAg((Xh%SXYWT)PZ>z
zK`t@rKUa2PB1zLZDV_)5yau}{;@v~boFdUf>PCkN&|NM=`bhn6KPJmyjq*^)FV*Wi
z@w?i_^jYm6*<T+vJ;DV=Nuh-4wmJ%F%f-C2lggRi!_RJG!jZ+KBC(z;Wfq2|tGCAP
z#u>ILlhV>S_a2XrR~jc|^^?W_GF-CQ|4Rc98|T-hN;S2sri*u6H;3<yxw~CZc$NK+
z;nv2<Ng@>`#7zH^U_VZ^w6`|SlR1`}FceV&jMf-M_V#XMn83x83F+h@vtYlf0_l32
z&klGAp}DU?Ap$QJ2$2jfn<mOTuI8;A?_fyqrepw4a;#BRz1f!~y3n$pN+|*!wlN1{
z{u!;*iFYCxw}D6R(Tb8t1=<2MIIpg+si$d*H;7`MWo2nYCCq&}QNj7!A~n@}?<EmY
zkMh3;U4c%qi=PqbaosYyP-W8vUjAtKlaj_^7yJGdWHuX#KF_5o+ASV4x9wI97_=r)
zBg5IJ9SU`-dlN7uRd-zgXi$y^e%`W-87Q-->Wk$Ow4;bLj93R5T`t;t-9OnOI=Fkn
z(k|qc>Jd}IKt=MKHXnb*I<1iuGwg|DV{^xjFn!vnR0+aBfB0w^_TWh~bPzrfE0u*V
zcZFG?dfvD5oe-m<?jw8$wSg`3AF8pL2I%%tQX(uybtqqHNl+@zm9QUBFXgye{+Pb%
z0|FuO1d*`Wu_VQNB+8o4k@QQ$tPr&?je_>q2&jcZ9pufD$UPF3z3J&-QTJ`c91Bwt
zic0Nol{{<KNMc7Sjra`d^+{t#7k5=vYMdp6gNlL|(+=_|NgyZ9WDR^dSE(%c)=OS>
zJ7$x_1WcMWvP2d&xdwc>_!y|bQilrFKnL^$LbzBL#~ekCO@?z~+-@kTLnBBhCn!XR
z2ltK<Rk%=TI7<eMqV8p_7O~H5;Q}w4%uyVcz*~zh_chlr{5vD9v{{4(eUTvDlrN`P
z`&hXoQX=RGr}%};fyu-KIaLSN%IO?H$%1O5u8Fcb_eDH_ni+ST@pyjAp=($ppVo!$
zDqf*Yctk|&eaFW<p7W(cXjW7s>Hw&keCas#4doRmN8zUG=G3r}LQxHn+a`sjM*Xuv
zx}_8V1N}+P_EsLZ5+|)Lt(g2o*p}^d>auGRz%Ycb-tgS*FsOdQnL*j;Q%>=mC27G$
zhj_`M0ys~JqCL;sWn<h$>|#Y!O$o5$39)zg3~+5)QdHe;9s-7yNfl5mRY<m@B)Oi{
z$W8`}FD^eP^)X)%8``h-(JMmJ?7zq`DVxB`G5Wj(*y2#oPT|eBx>#9>eLI@_;{R|M
zc?Z8c{}*|-T%-KfsU3<Z?XLcw!o;yLO)O~NSd+%PmHPYQ*MC>2Fwv9dj4arT#TP?^
z{q5MQDI0X_>N~<)-vs`*l^hN@qa0<*nhbNuV`SO8=Sv?f(G@ROOO;JeYiF;@Qk9*6
zGLiM%?_8DBHjuf|+I{2hIJNX|X8q6t0)AVp_Z?8-d(`WNZ-#eBg?Wa;4=_v)_RnsP
zkQ3{99%J*ANF)O|@x)-whFdfKr_zSc^?WUUe&JVQErXYhJV4{pmy;Wx1=&tESS?WW
z{oM;77bO@<#(H;M?edLO>^?8tC_|+>M)ntt8{Wx#b|<U9TNJztQ<JBF12LB_>;b#r
zKLkaco#J3NQZ`M1`}>}`ADiq1+a^Bw7k>JpZe{_WvjwpUdf<4w>X!%o)%KP#{SDE{
zN43N+cHK1u#(MByrnb7niAwN~+n<UL(!@l^|80R4R?O$tjBo$IIpfYO{oCl;qPM1q
z!u){M*ExA{fPS%RrF^x0FnL+%*g2Zq?09)=^toW+c*f3Rg_jEJAXd?3vmZ70p)u8Z
zOruOOg==8bEI=cnEJV=%wd;kIt;;2G)Ny?i!N@!8rWl`jVgBN3^J5<f<nVr_{-?4w
z;Chn+c1_RBRctYZdk{9d8w_>){GA?s1*##nk}o>G|Ks=hL~I-yR)C2JvL>3$S}XZ9
zE9Lda>l`1VlQbT*B>#jHN^^shfd6bwq>k$xeM)OeEVgDW;(?>D#hB(2t64UMR9y?e
ztfu6q6VEjCBV9R(`nnI(a$70K=WmBF0}}+4d$LSMJX5q6UWD*r8wF$ry}0Cfc6Vx(
z6;ERyDO-M-UOflM;LtdP4hwczbI5z*>+dz`(R24*0Y(XA-efH79M(<}9Jg2piKPu}
zNXOdk|8wyxhi>|P=rDZt`DKjx46G-CR^ivDsV4`$9@-R`e+Y%+G%A}~V~pAP`CA7u
z#`D6oW_)ek({<RAISIV<%67BZ1t~jeTH&@J1+NiIRD33uPtH|gPB5TjlqSwfNkt*U
zb$f3mMFH&k2bhKc%Rz^@T{`X?AZFR*SPMt#^OsARI(QC>Fqx7~qgH*jyMM103guMb
zCF&m+h6z{@HZu?>(ny(o#gTbw3|Spg-8F1p+F;e~9;=pS#Ko3QC^eMS`Yo)WXK?Hn
z4UisM9*HK?G{fq-K}GWWbBBq?tOd)M=z!sH4-V6iZEw1$#*|Ru!2q3#N{@^7Q$lwL
zr<XKoSur&#K0x-z$Tk>FjFDoK()fKFJ_%OxKv}C@JbfMChCy0%%4O2*^MYk7U<_MS
zpuhbAKHKF8<OFJD(-_rp$CwLg2j<TdJA^KX`Ilg&#vL77vV+7TN{H8@E&g|K0m60R
zuZE!JLpaARVwBifcJ&nJDBbdjNVp3oKEbZhp34pLQej8bE@`2AO1A^`q|;LJeA@8*
z5rq~b8pz7(;S*aJ)2l!XM-aB*es&tbxAK-$Y-d2BumcfqCb+Oju8K$2&h~rlr{!K|
zjf!_otJq}yf+k%5E{EiS5=f<ldr&(YMnKpU>nqFxXkxi4*KMMFRh7`kY$cwKvp7g&
z_n=-Zx1#RnFVx9JE992usg(akk7|=d`sVEm_R@3@M}$dZ(N!}Ucg9Ghf(S)04-xBX
z^JR#T`!sMNY)U;Pg1QA9`XtOBpjN+gj+3N@RuQXa&{xJ-Nu|<}OO0Kwk3NJx2bfG!
zbcG3iAZd<^{|4ynWy;!v`)7J~InQG@bOgX5oQ>y9=pmt_d)Mzy&*14J=%IpU#HAeB
zEzyiD_BJLE7h!L!W%v(AUw4n*YtW4XLfqf=Lo9U3-j5@*#%iVlmbWW)vaPB`2F$D4
z`AE90wMp=MGDv;g9$Qyd){fWKRZSP(Z=JIO-pp`=91@o`1n3=0>rN+w90928x(7b@
z^#s^2o?0Kg1_)BW$GI#Whk!sza000)m#kZXoLhlZwa7<8^OawyAr>UFB}_?QzczEK
z62su;OGbS5Q^f}NAte5oQFuR_%?`s*g9s-%IFh7@Y=?ja;P#xprtsTv`90itB{!R}
z&1-qttL^|8Gze=NNQp5*z@(D}qM!Hg>jAJlC0&$X9E5m|(E3#z+@2umP_E!x-a9Kn
zR=rygHB=}}QY~qD@Cqnt5HQO^(FXbS`k^KAHjOkSeB@3&|KGL;?@c=L3<5c8{FC1w
z4T>4uXaVFwmdbO$2XxjzlTYT5!rxCk{6RxjFvVb_&Jp`>JJtfY$Mb^6i(v0UYp{Cr
zC|IY$0XNUVcHWtILS0CW)h%T)F)X&on#?Mwjax_wOpHmFy_)2EJ<Sd+3-%<8g2!X-
zTOg#%<o;JLXYvjp_7l-wNlm5!JU1i5H?Wp{j~8#BL5dav^K3OxC;<^-(ygtYi;&br
z<Ho&#ED}yrD|p|7xwJ6_13p5$U3={s`bLWcWxxk9ow7#(Ae))U6uEFGO*7Jj#4?sp
zpq2#|g<xXK&Yk5;;PC@pTqKRnCjg>*JXa(w{QfBqT>s{yiRs9+nRdM#Dm-w9!HleW
zJ(2b2;(BT1GEleYSmH^CgRi(Jnz+yY37h(mThJZ@Z2nN_waN1MBz1b~TI7W%O$fLr
zs}SciHTeB}sMtq2z1C^236VLrY1E1OOfN~h=-dh%y3dan*eT`4$c{ek|K%|y=-UHj
z%;X4U=g6(kJAGUd=LYbLBO*_Aa7WQ&tV}Wnb@rZArL#&{n%l0QyuImD$TABP-RL4d
zM8qW9IEWR%EOz%8p=$3KRnu+Hn<k%&`Tzr0>-p|*=-2GOu|7vvW#j~MZSM_naO6<2
zs*-E}_GVZ^F9}dohioOq@sW$%M&{O=hrV+*Q@1HKU(f7JHh=EZU)1v(7t1Y`GLk@w
z1RqF!8{gYIlMmuM8aP?4eU<vgUap5Ahk})Ii8v$bOgt5xLPV$7TO>Ot*q!7e*tIc2
z#{6fb8+yyuig$d;@RvA6NMzp2J2Q&U;==-eKxK(s<D}``-B+k+YJnT6Jdab95cqEg
zl@fw$Q1g#zHr3^PoOa2qrYS)a-+Q;v3p7;SK^{xSG<x#i*<pQhZu}qR=5<JXKB#M5
zxlpPz<5%M7lz*=*!Rqafqh*@7qOs|IJhyZ01FGs@L2;za0=IuL2?zYAGw6QYw=(}i
zq47n&MXtIeEx?edQyx=j33#(_zEeg5z%Dk8os>;t@=NYMWH=bK)UCn8bnDVG*b}yV
zS?P`z`y0mDcPQxB-amLw(kc;Od%VtrFM16&`o5`Q^H!a>z0>nM)Uk7@e51%DIo=cR
zlhAQ3);C>Jd#60mK<ze5lg}mHue;h<m`Se66Owcr&*q%t=f#_1+5O^d9CZuc`QH_6
zjr{&!;*0ea+a<mgx`;%+52GU|$!{SGwNSB1`pFIHKYDkQ6I4igY?&RX+8-Bt&@d-R
zt01{<-_;Yn#q;7G_DVkEl9=VQb^g9u9<j&D|Hf>`KMdRrBD$=0d|}(uO2!#TbpOmd
z&msRpWl^XwP*G6CL7sy|31SV}nG{`p?;&(%@$M9lti7PG-@sw=WQA?%4uWntyyf`P
zmrLQFTa>}A=t5H6(cx4g$c!xP^X)C=W(a#0kOf-<J^Fp^oM3-lV_(04VR=0V+*szO
zhjYf5<s}uVd>w-2Es@u>Ok36&_Pek~xT}(Vq1eS6VFTt@$CpC(QyYC~Bdbk9vIB!8
z;1y^29UW3vUa4|iR%NCA;^5GR{e{(&LDG^cJelUP%I7(>o)?Z}7N&{-VY{XLJLZ3}
z6~gNG#QK_ynPHA3vy7-mwfkM-LhTYIq>LtVsX!VIVBe7vd2=`hD(;X_TNUGZ*jPu@
zymw~lA>RF-BgPd7Kxjr`k1`~r=TFeZ1$Km58iS2X$DJl*|6x^o_`TYf>n<6-cBQo2
zpDU$lt~qPAMpo~=D*^Qi;N5_*O%a0Ul3~g3tHkm4_SK2ee=IUV5cy<hjp#2P*<W0P
z#y3f;Y~KVL`b6GrWdajr;vu4Z67<kJ>6=ZMw$4BQNQToHr<_5x;wao%4!^pd<8#^T
zZCV<5V6Z%B$_r&h6gG?K)T5dgB@s^{6gd)pFOhJJDXVB)_O%Mr$H!bzMq%Z;K$`8F
zACOj3=RN>%Um!#Pu*FA1%mBeZhG)25Ml}xg2Ol3;3`_PlWWt7Miv-OHt7Fv*(2gu<
zqaU0#dJ9a+{>%OpNPf9~P5A1OtP8ck&dyHMZu5u4HMkg!u1t0%8M;O)c|;HNG?(ef
z0_vFobtW#L9hJXI{@y~XJNYRwZ14ws(y_H1g4g+abI0#w9|0tkpSF;Q)h)~gGD&Bs
zu9RCy{BL&@Dx|@^<Cd8*(2Xni=)j>Xl=@keGuf)K2l04C!&T2*(teWmg$H$bXG{63
z>3)BR0DF2$nrk8L{Ih&44>!XUC4sj;m|f2Vlh3p2mM`5&2~f)Og2CnLf>U2Dqn%;j
zRwXg~#ES2ud+u~^HVR2tU0UvuWh1Ip8qrN52;swb^RGmF@YQF>-w^?!Or;qe5a5*g
z^tJ{!dA^|e$qBU&N59+&82E&gdt%BmwnQ&#^e&b-`T6Hft=c#0esRCM_Lk=XnIlaK
zE3o^-j#j?XW8+As@T<J6B>m%Z$Bdw2Ph3aYZWx8UDiifD5DqpYCXOpS{Nw>50}y=1
zG+CRL>fPY&pXNTJE6%%J0&HbrPxr#B&vpkw6?95MsN29Hvael3xeybxKiF5rUE%|N
zbkw*UwHn!s&`5x|bNK~x42Vi%)f;l2Wy$dbu~%;#>t}t_Irb$IGo+EzLfR4jBQ5th
zC5@^J<fn`GeK_fHxstc-k5T~)ISAOg&^q<-S?!cM7(Cz?Q{b5p3PZL{4ev$}5KY(K
zovaafB6nUkE4xFG0!PZ-fh>^J=XDvLEoB<~e#A*!N}Lix<X(J^cwS8R!hppSi<yIQ
zOAOF`<7hx6I|@FqmGx|OhM)8RNnA`^OdW0%9vsF(xm+m3MDK_F)E|&!2nQ>wUB4B3
z%G~8fjj54}a7bnpUH_JZf39fAS7~qu4z^JK;X0;&O2J{Gtj0j#<mtm6rp7?JcbOhO
ziBs}6=C?Y}RSl>JEY9HPdA8t^xYlNthWem-g+R(kI>7kbqx`&c?KP36c#dfL43#mJ
zloUv<)et>mnIvJ#IG^oRmuU*4(jK9`+vcYQ*O?2BYG}APc5=_LR5fuV6>aKyRE1y$
z_JDSK=QOK;i2PW%u5I!=uEgRoZc!y2gD+;lVJ%jwO#E`5cNQ|IEY)stYEdwjkUTL&
z#KK?(h+N}f9V+qMyJwU61IRF0vw)yca#FB~0`33<?KcM984VY^)`3UM*nwo;lKeO|
zHI_wJZ_%~RST*Do&Yvk8)!1Fa3R^)9zA!}NW#8~Rx3rTEu~G`w8D#dFt*-23ALL{V
ze$tXv0uGC#m^}wgv-PYY9y*m?Q|I$a;mzXMPe6{x%I=j>eZocKH1Vec^1wHbbS2m5
zt5bjZEc8px1}*Z-gs(thn-6u|CI3uUa?Stw*}<{{R%#@MII=H(JkN-{kE$xTsRvbd
zDK-hfj0hAMmDsu(YsoD#o~SEUQP3rR!UH-(K5wJ(kvrF3kS;y=J@zROhk6a7<b+bI
z;{#Rifd1v}2kI-~OgAy{;k3zFM4ME1V9yh8FsD<LpymmoRr_mj=5zHaF@8aC;)e=E
zLOK#)7$d6WD$Ysxb_P4FQ@KZ#1~eJi>}R})^hc;Ji|&X#cB(G1PbN@&>RiNiNLgOE
z@lFUWu9QAp6^d^Y;owFI&}Ee_Ax_pFzXpJgb|ExDJ9|dOrewvI*&~`+L|zxzBrig%
zhtD6LJw7N(BwZuU06%goYW^X2trvE)ke_x6pdH_Y#N@8G0hIQ{w>Am0L-9Pkfz7&C
z8^&|5SfQ?<V97quh_Ojd6Sw<EGVcj39)(u%g7+z58^AZ9R-o`qrHHy^I*dKZ`yz^V
zz+!Q7zS!l;-r{VN?D%}7zZer9&pbgk+51faK;Dz=$Zv+R)$27Q@KTRL1Vid1^Y8C-
zCMoc@xh*RB@+ekUtXhu+va+*_jD2U5ncgYSAx@K@9^!KyWf#W<c_jL^`wi`Y<h(1;
zCpk_;CHn*hi+tb7<E!jOSd#r!o_C%Wg5IpGP{a$DDRG7Hy8Ayv+{TvAg=3gp8t#co
z*0_?!m!5R<t~gJ|YfHCxB)D2q;=@CfISxc+*F+=YmG_Hi;B3Og+gl6!z4#W(qbNTE
zrfe88J3zlaoGrh~@#*akZfc_A8Ww!q*oX*Ri?baMNk#+Gn|Ce2KxX58ahG&K7|oG!
z#b02Lo9&8uE;c#O!A?@e49)M@$`WYpI%-O}bIoOL!tuxE!yiL0^;FfIe{dg``gO)1
z2rZtu%g{j<AHJJ*UXxg7$ACpCQI+OjIn)+)fGj6a)=?5P;iq`2nqLL*V7fWEkENaz
zxOqT+6UcDgOh7S9MQkVN--J`jD-ig74~6NPu1((MNksSV1%Ia-z|`MimgnKudxo_V
zIHie1%6f}c2ZPM<<LW+yV}Bq%V+Q7Ez!}Zp&NXMwD~e1AA&a;T6A)c;vs0}F(uCw@
zP4}ZkG}hU>!^;2|z35EtLx}lljqOU}l>c>ZX=7XB4uAB8uCgX|?=50a`iS_5<@bYM
zLuq$(X>KQXWL#&VG;1_qZ>b|r=en4A4m{`q=F`0x-`&N|cVCGMdfbxYpUU`9dA-@=
zHUMXyl=yQOb~6Hr$AJguew#HNFru46!nwuuJKm8)&~DY49@JXO6NO0rRwbZCg9|j_
z`~w;M%RkbCi!WWsuhoW@NEwe#L??-z{ZCM`qLFT%BgniPM4ngl4o&q-18Yc;?K~)$
zLrc*z=$ulV7_)@ZnYeH^n`vT-_ja4ju7`=ahcibt&pZWb`i=fF|HyzUI)ou~I8H}a
z%0_Cb!gw#?UZd1nP3u_`)#Pst{iXQHmzBiyUYNL)BPIw@0`kEMK^H!d0fN|zxWG}X
z5OfnwP91OJPpERvGD1rrhIkS5<IAM%4}}{(A<dpTT-B_<XQ;XcHZI0hN|fv<N(o5}
zkV6c~Y3|}RGN=1)xEP0Zw{#%j3d1@*!>r^{L&n!YlLTwcx4{9$l~#_?=`+d-r?q=n
zuu0T`9#C+b4|e$JLe=EdF@rhQ{5~bo=-7Pw2j3S5Bqfd>8`>m!SDx+HoF)7*r_UZ6
z1m7DBjTo_sWu+#=%7AUKA12R=4KOxJC{dEeKA;{M|2igH*#0R3G?>I!Mc<;D`$*!R
zV8|&fYR!|z!`O^i;?tD#elm7Q2>QuRb8t=N(JNR$&jzoa;-vXrb`DDd7>=z@6HR|H
zRb?0h6K+9kfLkUsn>?{w_aW!g=1;xboXLrzo{A)%EoaU_wKPEIS2!{$<NUxAoy&bR
z(EKKP7Cxq2y*384B^+(1@ULKX_)&~F36ei(zD3qWJ^s|u<N)x)awaPE${asZkEG?T
zv5P=8=IMa~vg3l{Vuo~zlBAj&;w2VRc36{X!y55eJ8`76fEl(;jH6MBqfybPQ_ihq
z-9aW{9%MC{mTw{!f=l<lR+uh~E2Q}9lhmSN{0GW3ewl1wHW#mxDW`6T0TqSOj?SKP
z0bh`UZu{x-a8lJ0#~*mp6eg3hH90KB@|k!9xz06Y`DBK4lp?{8v!9<l5<i~q9@PwF
zy%`(%R9KW*su2755fmI&X$ySd&<nx*L#$HC;6J?-24<XH_&Ei}6CyS5>=!Ytt4=kj
z7$r^hBE}op_Vm6#YJ~6WrK$}SuKiOl_rM+flC#*3Ct;CBL|OKAC4!zz&+Z9C1%Z+g
z?x(>=2ZlYQ`8efjAW{NIvrX1?<N_g0<~<mJ8bcjC9cMBPkaDYjU9*DJXd!Wgt)_a2
z-~u!FVY)SI9_l`KMb62U$&TA3Q1~>Z-}LzVWOLD4wr@$Qv1*AtjG+x2QoK{~A)jvu
z`!l7yess!aVg%7(AafN(Q`S2uUSZaXXPxG%28@0y5~PG6coHTJ{_!RGtU3M|GlDlI
ze%m&*3hnr)g#E-&!gGDJK7?!>98c`T{^GGDQXA1YuD9*?Cs6rTbjrM(saXt6YIYX0
zfmgXBU<0JL2*A@@IrF&=)l_qDRhLZ(Hww=D66&5&ODaHAxM9w>6WDZ_{YUd6TFCEL
z(t0gzCs(+U{XH?w!>{0haC=#sCdO*#SP(_-)CHgB2X)N=j7j<nLre){q@eQuHif-;
zCqCt*d&>vDJowgErP3Uc#YT~5%+G(kMHgT9rYV3Qc<Adtz<#b1(4XzR?-R|x$BAeK
zRPh7onlAC<$2cfXKH<p^t=a9yaj0{vf4F=H$||A3!B;4DC^rM~ha5Jsp{-t3bo@Gm
zb+4L<g@sPYc)1xkvU%Cjyx(x!rOq`&z&%G<(FZ<6BJpdjd(OZX>-t$cnD5LOlIZWc
z{VFxJNQI1@{Wl`xDer;UvB_U<+!nKx<D`dJke<ok;f3#~KANqT7Sliaw~oyl+sB*8
z3kcda(uy&-F&DWMFWy2;9CGh}JBK+|`9_oUofw>cwj4Lw%f8i5o6fVH=U4ZOz$sRr
ztq_EMTQ?Cgu&`<QGdcN0Re$!>5(|{juJ+s4V%z!qN%YsxQCS)tWPp)-`fx8UML6IC
z6G~0DPvYk`I#`PwHTc~**wZSQdHPn{(f*uS?2ct1aD1WDI|s5<tas}H>%~sIp_)mw
zSnp^V8}UlDT`F8UbJ@{K%zgQ1Q$i2v2SYFiQNt)9$WcDVy9ij%;&NFu25qgw`cT%(
zm9ASPe9K?%pZ6~t-SD;b0Q}JYrnPZ(o1pU?x615-qVty5IZGss-c}kSof&Nz8$C{L
zlC;^1Z$~1s-dfW?lq2v*s^dozyj`Zq#AgG`I#sEUHLO8b+FHOx3U-$&9IjjZ>=L<#
zERlNCTnJKa8WCK*M6c>KH!q5^#84Y1EUz8IFn2pypkfKGNg8}!;XWSR|F~vPXQB!U
z+?gHad4Tx6)jEt+;;=30hsAMqNbkW{<?dAiOvME2BFyycK96T=303FckIn8r??6WP
zV{EMd4C^!+W7HdCYE_<kbDCk!DMCW!JucC&zMbopujGuc+hmn7klHWM(X2a0%Z^k5
zb(oO%7x%X5kLt`G!k=H+7o%CoPTT6-JoGV|Z@*I-p!SW&4y+B&uf%S2Y!c06{d`)!
zS6FP#$)>f9MadXD`K#(?*{;la>T8<X<SuqAZI)x|93zQ=$<VOUsM3V4-h_VYCHlot
z$j<73=YSZeMJ5P**DCbbQ9n1-3{Bvt4Og%FtV5J)9sR|EdIe*YL%_*C!PbyYM8v3&
zS9N>y!UkyXAg6t8^iaIA`Rl$P46V%xV?2r_qtX?z9<BACfIgRSw6EE-?WRjr#jRl0
zs#i2Lx4}l5PZw}J`1E?UgdDJw8i2YLWS-c#DU6Vq%Apo16$Wr`z>-dRnqV{k#kNLA
z#@IlPVHu}z1~LF^ixD9~Gbt>J&SqW?iSv+&))=a|hjN~ZMq}gG-nR1GzioyWGsbjW
zom!9$F-zhwO9ig`!7LCUKlpC|6hvU-L47_5rPY0P!Xa8cS3ihv(1exe<V}eyN0B6-
zUI`BCRw)_8G&GPSU0=ti#v0>&%JOGk*!#z=b;JP*t0F-fr8a}bC+HEJ<Eaf1BbkD(
zY1RD+qRHN!9S~Po645CH6H4(Ng%E%&7`4&;8t7^K42%(_2UyN81{oLkVv-1k#Pmq&
z6f)4|rtw2F2IJiNVIY&=vA(Nl6sOI}zN>gZ+Q5smlr0Iw@RN#O-s-0wkJdBZ@jP7V
zs1*aTH0crNk%B7EFQF89ur9{Dio}J)jhP%J7+jX_79nGkNd@NI8QW&Wm^{BXIdRid
zja-9QCRP+XswJ;*E_V%0(A~1RVENU9{M<4$_d;91O^Opy!mWFbzDZ1;cuTXP^Qu=u
z)rw}>8Lh0DlmCTB=OR^LmuyRJi$S{ZM=3J*Kcom5ELz<9Gt#w|KHHjvGQ1f=THNfP
z<9aoafeMv+TZa6zN8^aZq?>W_(=S?=s}!Lc1uR&gDI&0ob^iB*CD*IzTToQ^Op@)=
z&YvEnd0uZ^VY`a+6O4B`f&!5T8TaA}goD@cZyW2v4)pk|q&xKTvQmG!dA}v86eY>@
zU0$P<6r%#G7vbWHcrRE8c2L@p=(g!ePSp=V)Q32y@EK^+vYE_u;Y|p+mKaP36YTi-
zY?=^ILn%x0ow8XfhMG`?hsHD!h#rFi3^xwOYKauor;gEUSwd{&EK5iFoh9nIjD73F
zu-}o}U*3Mt=lKtWN3BJBFA3?TVLnxAwCq@+2lJ@!QGFK6J3t_{)!;~?`eA0@_X#Y{
zjtHJk;+~TNM_}rLKPMGQffJJF!WBAf|3oqTNPv@M%o1LdwNp&6-R7nok>7Y`u&i9M
zYEmoMU50yT<yJEQQ-YF-+0Dun(6HzkRTC157{#+Tb?F)<N^TVz>7sCYX^8H|W6kh0
z$!v2Xt@IJ!LJ(1lhfcy1g89MW>WXut6C`3097Qx>9>)#6d_5<APE~3MRd7Io15PQ2
zYJw>VyrAO>H!cJ@)Fi45x617`wQefvVdqwAm08O0%x&nv``@J2D@7%SZswg<#M&vW
zgRN_5efI>eh3oIu^Pu&gxMVsgS?r1M@`=~kxdDl?obbdGG&?P;^6TS6Py-+AzAx^J
zUEGpQQK9k2HyxEshJ`^tXu!I^0eG@<^ieHSf)T}qaREq5OV{oKxVV!@rfs2I{;mpx
zfCh;)%TWIW^o{~v=5CS!%$2(d`#DyOyBK=$T@lk)2NRL_R`pXokwHF%qf_ynVoIpk
zNZ%)Wx-7G#F&o}K;BL6lh~6n?pGK{oj^*<xd~j6lm5QNb8`CvCRR__1a}?TWws1)S
zUQvT(kdMO}vtWi8DFD@t7{qPL#)=57;Wv2VK0U{;JQqAz@eif#aQ^Btm1a6E@UWOX
zd3AQhUk-?XY=EFvi)Anzln(d7EJA81*hY*#?aPW%9zo?_WXC#TAC%xvfF%}1XEN^@
z%6Ne51_SN0ndn0K^!g|lc=e@*5vpUJKye{OxM_?pJjZ9F-umz%xV+LQaAoKWdZmPe
ze68~@1m;`T)Hn7(Y8VKEN-cRE4=p?176zY+W<XQTL33|25LIYwNG?yjo3C$yJzCG*
zFX>IO95U>!HW?k~$KIYa$lov063iXLup<IhH+3%fXC_cL^j_(>&R8Zjjq)t#hb$)A
z@^KomB+iSMj0*BNIoZbL?+1emFck!5W-A5NC%6|77QRY2yWfW^(;tH@lwG=o{zP#N
zd9S&!pgTI7IiY#4$fq$X?yq_tYXu2d#c1=r+Ag>ePxr^sl|rn3rn_}EUZCN(zZcf`
z%|WtzC;6o#&bBiBYe_3di;|G7)!wqr4>dNRden7E%~hy2)5UF{4bgzrcr$!|i{vUz
z4q=!U7_5cCQ+~MO(o~SF{hgC6FQpndufo<!n)S=&;ZYER+zT4KqYeaF7HIXWL|A%%
zA}xgzk2=xeZxXl_y1vBS|FU6aR<B$yQnWDogwY7kXdy#)RyXEEICX@^C0!9<+9NLa
z9e-1YP7R4=)Yz6v{X@kUSKTyLHKs+M9q-gbw08ykJ=|PS$;uuT<WcUwHuwSWfFa8d
zlVge@;W)`_t`CF@VYJ0djRs;^Jmd3kR=m0tM<^lcK%>ib&A7;0qK4YXK+g=vmr1rw
zlmBnI!VL!aTig-kDfx$wl(a(=FQV5jmmmv58HWGk=qiBX=(^>Xgy3$$b%BN8E&+nG
z_+r6bg1bwCySuwB7TklodvJog6CB?BuWAaaV2fF{=HA<<PoHl3OU49W%o&UVhviIi
ziBuV?pspArozcFDQN)H|ifF=MsN@_yWDujdcKv^vbg^kdGf+JxO}ZS`fflVVE{-@`
zwrT$G0`MIgKZQa?^wAEO1g=C%2+Ssrd|Dud*U?-7!PH9eYx~SpASAOxiwW$J`Ij3u
z9LG-O!hPKG@t|EP9)Q@bX4Pe$!4M6^BvAe<h2=}4QftGRZb<Og5=Ts?)%T}W8ekPd
zenfCw;mo^08KeCA1=(#WySY84!*C}e2|MBFK5sFBhMD+IRqT|yw@)r;c9PWKav46$
zEcuA&5z8Ub<eXG%|LmRT^Eu~yq2bt`C7u50K(tGGanB{=9=g1e1+E4!dw-vE+JJM=
z2Pqt6niS=6vG6f;@ttlbQN+UKHL4v4YKY2~H~XHilBf~kfNp?=5IZJtt^<xX3vCly
zn`jFmpCHcC)0z2(=IfzaCC=MPr1%I`FvsS5`W}TC+xni}v&C3~)S2z?hjqA-kjPap
zwOxyYw!H6h4yE_>kC#Ll-TWyp)dht?G=j*IAB-~=v#@CqkjV!zxyLUUcn~(|rm-3s
z*-nMH6l5lpcbb;R;$Z+IcA}(VPJeCd`-Z>Gjd~cFu==iet?mzO4A?M;yCrP<Nv+lL
zttT7{?+N7&v5zT(?HwJRtlk(5u|aEWm+480bj>jTat0E5pJd2BoSK#4pzrV(tJBCr
zyf#JkDCrF;D0gG95KqSG6U<eZA-3l~Lss4UB?KMzHaoasc!?+6jtkxN*YcH-IhrcA
z5aTg+?R&gT-BX!=mm;E8@~Hzcr+}Apm`94zOk5?h^h|vSzStB}s8>tRnK5|`#{b)9
z4b7Nx?XS0Y?|H_I-`f5Y?Hsiu9o#YZJ@l~NAC6a@Y<0qo!j2wmNAU9=c>HT9n-Q;R
zHlb@UGeI_ES|=I{-@YgqlCv&QbLsFk4=79~5_620G-&4O0SIBprSVtij#RJIH`3y1
zoduIR$cPgiywqXs+GMV%zTA3UzI2G3ZGQP_!#BoPxNw&AiX%sGd`$HtW$iV6IJVx)
zG?!Tk!<V-?(PAa*f1yrA1E+s%(!@~E7)Li}8o2(G6NB2HM$Wa3I?dF`e_1S^B{oWj
zm%>ok<fnDWtZiJ{UamxA*3qO1H`+6Uc|W)G$|)vdcI7<pu5b#7sV}yXq}wSm@ULpw
zP9K_*C5-?3Z_?+-<P+z-_xX$q>;<_l2|GnS1DFIW&P!$Z1RSVRNPbG;p4|mp7t>nT
zNlqyQfmj(Gl(R`xxBjDXVMJjIsQ#Gpdy_PQxqKHbHA`Dr+T{<vN%inTBDg9pr1(d8
z6BCMt#PGVpo5JlL*$Z8R7{<OYMJ2z`KD=x9wQ;CWzhO*}oG#!%4c$uRo$s?KrmFBn
zkG4>%wfVBr!;M$0Y|KJ9gkC~&S2_N$dmHI~BbF?%)UtxY-fuQs1Lo(BHdJ!7L8WI^
z<<=HPrDm??N-ImWXG(a`N*i{3H^|x2-Utk@NL#TMa-bd{P+m8%b4{A&>E+c;_rw?_
zVvecG%%Q}vAX*Ca)XNL&?Ru5JaT&HYIghSTVrIf#@m-!c(Vpo4>64J7rl%UVckiBc
z?#tZ8kb4T^9V60x{(&RB-uxExqvsOPa`3*+dE+N06#{nDC49LXx0<arB29b-01`Md
zO0e}B8X1>|fBEl+{hi|w&{Sv@O4-mBg$xT+>xvO#7w!BpuhF;!kcCp&r&M81ks>`n
zE4+7b$QORD-L-&^T?x6Gig_}6ZhskW&X(Q7omBl1#j&eD20w7XhQ+J=L`v@iZ>5cx
zK(A}LV5nE|2FNq7klw`wNh0x-D@{Yr0>G|}ZKTl*#*i3A`PUTV>Yiy&Yt27#2Fyxx
zV;>SnR7jY8`7vNq0^TH2ug#*N?c}t;{EHl437__hgpS&%Or@!xxz&$^|BX)@$VIMr
z6#rY~Q+X&NwMiKx1gK=3e>GpcsYn%#QfJ1!zqzEVk=an+$^B(L7VIr_iZ8jXwz*E2
z+cuz6X(ea_GsL9)9_sF)8(47>uv`!cZ=hEw63z*V65O$OELz)+(jL8^?g$9~7uOxn
zg`W7z&5t3w6wSywFeGM>?X9>J!%vlUp*Z<Q_W4z>H~1_{kyGJ113|d+*iD%i(J;?t
zZ<PMmCYEwP(3(f+7s_jnVQW35{2al=oT;7PutW_}4i3QlL7)ugD=agcx-OeT{$I~H
z-Qq3RPzFVcZ)tSKIDI`u)JO(LC4Kt>k7iEerCA$tz1{a+09n!xpfP+`spsjTL~M~E
zH(Sg=(|x$T$u1@jln{k&q4%0@Ic_3&9cev>QmADvBQj{@Su4keA;HJ1U!v?N(j_j4
zf@N==;5k2v`-7f0S)|4Q%J@g4MYKZeA8)-<iH@`ViFId^EV>GgX}toyJNHLB*)aEN
zQ{~FbYZJNNSof+h3oyPJ3^A?DRElQCB7N(RnS!OiRR*xiYsTa*0sQY-*_9Urk8@j5
zuZ1j9v}3mWyCr?vslq|HkU}<6fvd6T`<!dAV>>y4B%3P%8zMElp|mg}n-QeD5s>wX
z5X4!^W15b1`^J_bY=in^<9WY<&>hwCEx?Z=yv#*s2$Yq6it&XMU7<9+tRt$NJ9z;5
zFOo#=mlG*0976h=C{m??x*howN7STf8X}5GhgyIrCWBfeJyUU_SjVODuQ!!-oxw$B
z7&lULBUl>FAsxGK=^PL)4O{zDEEoTad%vZMLjx@?jHJ>Epp43wf@--Zhn3+1XZ`Jm
zWifK$k$7S>`mn7)&^)engdqXjT>1iQ?#a3?+RMQZE?HH27bXVeJ0h#Zy9Y{leIHH=
zb`^Kc9u+U1icZpKSYBX<aOlbhlF6RS+G`i*mt-qIkoI5o_u2Eu`V61qeXAQUA>z+C
zsGje7eY@-dbrG8%Io3UvL+U1m*cO-))i|Gm_I)$c@mE4@^8&?cjzU$3Lv94X0C7Hy
zN~Nv=BT#7$qg3SqqC{->ZI@o{ubwT!KbvlG!Z35gA*r@I)3S49vGq4SVX70{1=5$6
zPjY{aWImNzSE2-2sRD_-@SA6~<hXkp<M$K<apf4TBtI*|{~Vp2^U0V!{WT<IkTeRi
z#r!pMh*cs?h}<7CSlS~asPuDKNazco!!t^xWyIidKqZzXYMvq5*y!a%IXvnY3lEl^
zwm<hg@4QPD7+y{=t&hf{s$*YX1Zcj1p8sDQRl0iHim#h4fL56{8Yem@&HQozUX~|4
z)6+7VHMHe^9h;@Y(f@GiC}eF-H!rZSS@vqbw_3$;9q`u<V00+gbOG4E(HzD%N)gY9
z{c@I>2(O!bW;8GVU@nJAI-scaek>~3j<1E5Mq~P$E7}zm%5#UyaX0FL_RV41odR{Y
zZCW%cwpslAg6R7MB8c6?1uB_e_$4x*{=Lim!rnhjtx{O_+nCT`(UkUB0=S~d(@D<H
z<C^9^>G63Cx{~EbFQmUxh|7p{Xl;&#5hjj2k4YYTJp=*C6&ZjPweW|M=(QHX|2Ps%
z<5i7`EEmtoc_d$d9IpvMGbw@$FeRNsgfcqbeLf|F#{c?r^lR>@cIJ#-jb53>9hVVD
zc;cA_Nas+SG;CEi=@6iZ{GcV46Xi|HH7S8i(1#UmXut=bQ1m|A6l(w}IxQ{~I9_0?
zU2Ld5yv2eynwBnQcsfTPW5l9}{KpWcRk4L5|B#@j0b}Nj_ypou!K$h{#DgQxIaO6W
z^!(Z%S~%zHL%N&o5{e=Z$b#9bER<YNF3m+Ul^i(c3#<sOZ{V%}g~*|MxB7NDwhiWm
z5mi|zyV@k;)`tj{X9=C=O**%PYEO)`B0$9}Hyul%{p`4AO_N3QXfhK|QgdmwKe4%4
z<eqy&6c=&dOQ}O=4Br|qyD61;VFTS;lYnF97Jz9#@~AFdZ1_fYJPmgbo!c7~*B;*)
zV*bStv(?ip=~yy<*rP3vU|J>?wAIxvnLVj%Sr{KFcB`?3Y$f`dOLr!)MeX~>7UfZ~
z_wS7Pb<o5EsO!nyTY4t3K`$r5idcXaAJ~^;-WSGtw>yOU|FzHaiU?OT>8bj)$;B$Z
z7uR;gV-YNv{6dSe4l@57!YZz(=C)FBlIzw4QIwB&eHUe%4N~BCyyXn_k#Qg=$Nc}{
z?r95*W^cow$>$r*J@mP>?DEUg>g-<fz~>Vd^WE`9=IZIy10Wk@V$^IyA8}~t3tF$c
zbpP|gxDhg3@~<iWensyybzD<OM6KpPGWSdKq(D|vs7v2;j{~E{+Fe==@jGsAlyz!8
z*QfLP1%c4vl^+@O%R8hwf@ADWDL>cBCqG;1YOTF9R~%!9vgDgc(yrSHoX_*nn<le9
zzl#l1Mg%YrG>e%U7*r`!2%E)S;RG+^OVFW|rGY&XNivLQT}Wodk^JHvtzTJ!y4Y*&
z<4Qi^TENQO(W`*i;M(9KcCiOl^CMw;xM&MjRBBr;0ieD@+#E7No2&&Ud8=&LH5rty
zbr^fQl(5BYKYEEnMDw`}NsI~M8x3RkXf%_Rw|!Q@p5l<6Hd(9fQ&*;h1P&aMG{Asq
z;7{kY5;hG@W8MH{F*z@mN)|4M;S<t!VE8^J9lhG3VZLftot%Q4B1KV`GJKAZLns(x
zFZY4I_Eg>lf9ySQQy}D_P7ZjyN|Z>FDq19s6U8r;VtYLG6CJ4E_%XM)Z(r-#kQJ9?
z{&lR_NpT|;SUu=*JQV19cDk7FhDe}ZUJPo5j#1lGU057V5CR=~4l=#V`vm`vbt$yj
zu7vm?Y8<)oML>6i{euAOBU|rpMO<1qU-4=Vz^u(V-3R_9)=)Tig>35hzG8J15G`Y(
zHYKV1{&(#MNndNy{*bfK^=3fi(}O9__QGmXv{JAiQgK@g$%-bQx)#gVnI@xUgQUmr
z;6y7+GZwKX_Kltor&UV&#oMsyG6R>Aqc!To_BN$JYl_Vc0<ioT-8^sne~!P#Mw7Fm
zauoSwKG{lIyeCQ=%k~RS)ClfT4)?c#I-W4DjyciuaRY<ZFr7ZGs2aP21phd82LeeQ
z4PEoHH5!@toUU>sl!EKOk7gNr23@z~+!-(LIw%VH2%-glacR2e+kkaOflr=RRsvSl
z>!+2}Vi^WI{^BtB>|o%`1SpmcQGEarCV%hGD)Onz4?UprWx|fnbQb^41dtI_*?(Yg
zbLgLhXLNk{rkfI$FSX<VfO*y{s}qN>R^yf3M219{L1p{yt)8hKZto|5VLb?h<pkCj
zyh9;Ak2^?InA?w-omAmIt6!!kbW<ThNn`~0G(%^hZ(yQ_m3yh<FMkFTBL3gP56-u5
zKr4lsu9)v>RfIt;X7rqCyA_{qVhmb_mzv6OU0I!NY+7^cm-qz*F8k^~5jsmKD>8_G
z02e=4wKPPD+OqO;meP=jJrtOxk%r+sItY*U<1$bmki9Qc0Q%hieI?{~5NFW}V^0SR
z8j!NI_2FvqUV=O9E1(O5M#MvbmQyh+bcVo7gds0>rW;D8T;D9z99*trmPr`tl^VSf
zZB6m2l+kqDN>*QaXPmb37Xj-xIUA2|p2n{`xzN>eQhMR$kUGr&aRH^t5Eu0s6m2mm
zJ)D}|@oxT!E#Y8{-XAGJ`P<N+h9s<11_+w2PwYe*$N!M{1^szt1+puX!OQB&^>U5X
zv@$`YqcM+-q$`UZK5v$lWzFco3A4zp^<SzC)YZl^TXwqUOyl*RkA1Z(QGey9+S6`^
zej8Zt+T)%UEl}@Vu5a{>LfPwZ+q}GdlnBV%GQW^K<P?|DMq&f>*`B(mcY4BHftBSA
z$sdJHi;jfMN!;NT1iq!10`OAt<9v&o&O*G|u`s{>kMv>?MADhRG3`#*u99a19xf2N
z7i30+P3d-5KwL!m*|4CQC$F@Db{N4Inr<K+MsF&_I<%l$gRb)TBKz)X!na*`w6MiZ
zKhx}YL-fcORdQO9`+w%I2wdOQ7_P-C=G>AEY%$_xw*rCc+1G98sFL<{@29I%*P|oK
z=-Kr83EP2S=Eh}cuEO+o_uF@6<C}BN&S+<t+cUF*au2Uz(TZ`=?Aq+AA9+6zsL^bO
zk9o^$zyMjQiF+uVehN}OcKA;|vp5i9Ry}=!(bBkN;>5aRRyXcx*X3#VwN991#rWO<
ze<7*RLhm=7!`N6={)tJS=2A^sxq7J=a|j(fm0|t?^jAfu35U|vFtw`WzO<QaJS(cP
zZG*t7WkXBtdLiG1rls4`$=xA5WdP7s#_r*LDwx(x%~VchN1>^c4@f^&VlhbwpWVd<
zYFxP%>CECp5|kCzYotzVc3bBkKArz24?NgqxD}nvY7%ztazNu}IfBBQ9Z6^lZ6D&j
zLUAM)r+`H*Q*!s`>GP0x5tG>8RPso==YQsAn1gT*k>ve4dK(61YujtPYCx|gJ%IA_
znvh7M=I_Ytj%bU>>Yxv|3@SyUwtflN{YVmnJ!6x2&DR|$6mr<hAKt3O&q^6~dnxFo
z?uK~B*D;>KD^f44J6lKa#~ts!@uY9V5~E&!8sbjhe#rMu1Ifod>^y!~?%|RTkCq>9
ztP68rF@mX@{MIUlUJT%jHpYEKV@Q+#DSUH{J+3uHD@~=4f^i|Yi->@n;PzZajCLp`
z^zCt!@rihh-=#S7=tBcdV9?k2!Vd5FC6L##N9|d_)BS-_j?(HNfdwqAfMBtXKDoBL
ze&QtioxNa0?_lx$EX!N$=TG0Hx9;?rzRN_!ED8@Ny_)`Rzj@*vDY8~||NZzLWnE-%
z_2H>{ha1HIck<h7;H^QF!kp=nz6s{tgTCGKTWPAArFvEhakUbc6-N7+!rWd=N~avp
z5u5a5#p7sw4{fIt(3Y<w0_fbFjOVTBLQ6%D_Eq<w>khYv4g4P%ig*A^lMVaQ8`lG+
zJ;}nzO(;@n4(|P-@hGNe>z!W0Fu7HFm-2k?(CgPigi<%}1xxkS`IUvTcARYewx*Zz
zsp-Y1RwGyM4;9nA&%a&0#ST(sL|WO8M=L{}Ys)Pib{MlE2)cWNPZdi7TOi^<IFUf*
z`278;vqxtHp-<J-D)cQR>E)(n2U@d-4~Y@zNk*==g<3fM^oF<z#p(IxIB-~5*@_J(
zR7D1Lg1HAvxK8n|^<zcER-7vzqQ?{s(vgecqD?7^#^CcH_y-)waWh>}yZ9X<T_`1W
zsxuVfPLrx4nBu9yqB6tUpYWkF_9nk;@V0J3HHe%w?hx8*YKDf7;7UHLBr+k~Dg~fP
zJEv!zdwl^$e9{a_9LhKLM7^?H53c)Lj1!qM{2%PY$DpC{*fAjoo~q(d(P}OOpQ7H%
z^5c3QFTmql!Ky>nsbFxVlJ=Ft<j=Jm+WQq0&Z&Ps@P^`Eo3mFyLX@}@YvHFrW8r1s
zDI_yXMhRdwa$=>3<hWf+{k{_LZS~tm+nB!YZ}hE8G=!YAoWJBh4zJ~skk8AnmSd>!
zwRI<$svUg*Yx+go8X#+D<}j{sX~iVI*jSXCG~u%w(NLd-WHF^do$wICKZ^eG)k#+B
z1?0xzl4!D>lM`GPa=syFvaVZ@VQLP>57#rQlm%{&+ao4;!y(p4X<NEt7vH8?f!hiQ
z(LN51HfTD^`@O5UXXGnyu}F6<FPmU@oMco14wsO}&VP7|-F535J{+iGp1wmyZKIBK
z)B{y^jekxsG|z4{&YTYsuzJDN^5;R><bXQrHRf$EhMc(NH)*5AMNx^u#Z0${@4u6<
z!QZcKhCAdB;}MJQx6AT+oxg`HOQce9j?y-qeSKD4$;2V}3Qenrjt({)bQ5rRi$HGB
zbA!2pgR5(J47uK)Bt%)R=gk4^xBHD3gdWgR!}5uJ!GQ2f%qx-U;OkUXQ8_V_E%(av
zlE9~yX=`9oErC@*+PQU`tTwA}-Jv5lEIyH<(@d*J%DJ`0-sHFy`oIMMLmY{ifLn%1
zrZHCi%8Qx+CtOmLNl*JY2#jlgdGQi8L|^}&Q_bpb*jSq|6Flkk+be*ao8>Q^8wN$2
zm9_=3e54IoKRdosZSdxBE5g}!LDc`lfz;xBC1=FvP~XWCol91^Ae)Q|<|dJ!+Zq65
z!#-!LyuhLiG8svmcw=S_3@g_m`Uh9FOeOH8cia6E^ii#gtKAFTH4u}r839=E&wcwp
z-F||jfR(GW3!sKSGm?mYpLNkaq+&}+Pg_QcY`NT9pBYsq#_pX|v`Cmq02JTDX)=)}
zg(NW#gR+L>s$zL)Z^&7&ZjZ&rE3t;B_7r}{wa`Gb_Mn4)hoETl18O@JGSfQmLH-{z
zd2=y?uV7Uje1)-#2mLqR@p<n5qLvs`P+T(oUzAJ^wzVV?W4)YpI_aj}Q_dSxRyK~m
z3tIEN7BJSW>^r3Y!a{AHx2yYe&MHSmVp^+IYG0~RaMmttF?G(vz2c+J-D+aW@m_%L
zCLUBIZ~>XYomG`vlr?so;+#uWl8aBY6*lnb5Cc?pnx7+IWKtFczUqzG+I7S}iHvPo
zW<;sytW#_b$l#2s{z+ydTLse)-eZXg7bb@A$S;H!meC^ORI%`2iN+Sw)3Bh}YU$W)
zx8PUV%p9Qs&(ybQ!R1*7g}T~a*(@~f=XW%-100N~MN`jjOHY#&qqTx<7*C{jRXm4v
z?4zzOE)74{IP9{s(s<Ufy9^MeDKNjnNyFzMDkTy;i_+twhUN5O3WISGkr1i=3;hqS
zXB^cWemncFdc#V4-Aw)Qc>HqT+K2aUeWXH0J4tPR-shXRo7$S!q~KGt&z+vv%ObYB
zgEZX*o5@Fc^<SzsCi7Df{&8A8N~+G9l+s50euJmB0Z1IOdOTo4?kj@~g##Qqq~QGG
zJjq(QM9`D%ESir|oB=}_Og_oPA5{ETz<WvqfufqYZ1*RqWLM2kiV-e3KX3RBkI4{w
z79{|SFAjREN}t%bdc=*m71|=_7YS&kh~BgD7KcoBJ5XGRy%)}3alBajX*<||_z-Yq
zhEQ@oYs1HREV%kxv3vpe8Lv-{?;s5_c{Zn2tG~rD_^7)RPXzb+Wo6X*_R-q)5t!0b
zS`VUjiNgtmb0CV{MfZn2`lcoyk+RuSMH(+7U@}QbOx__RTx=7!pwV5BE*9*1QqLSH
zbo5)ciFNGTH%${I(Fn~5!N18Oad!up_eacZ*2r3A)FZ5SRgcMYBuzS+<v+`f3MYtT
z4zMk9TU9i+tu9+$bdT^KXOU@l%n?77-VIzFMa{K%=_vA`9wJcIGEO@PE-aIBxA`z=
zW&}C<&CavWpKO<H2VveI?EH<Y<X4D|4?KO>vhMt4xk_pSqZC8NeZ}^1Io3pY>~cVK
z>N-ZDmIU4`ak&j{@VWgo2&@2ncrofcnieki>y@Uq^F$SHtvBtPQ~Tnmp#$zKIBcrd
zFBfOX4cTJ74jwMH>5jAw4unDoKEk=D?sHG*(?3(aFi9sjl6HQ?18$YhU(%yTZ^!wY
ztk4#gb*rqcrw;@;N$=wDgIvFG7(IO!phTcF%!I)Lc=z<`0xHWhVab|cVWWAX!*dHd
zXYgTL2uZ)_6w;GB<o;k^duHa9%>rwH0kV}}PUpTeSI9QNOEnO<ML>N}ELoObv~m4?
z&U5FAJGjcw9PJD!5@%gY<#rshe&+e^H^Z0o4lf48#-*{Dr*WIRw_F_goL9X2$hKOX
zi|5hyJR7o{LPg&W^*mO}8MpAzWBNT&-oNP9p1p{?)6gS^JRF(+*PKD0cg_tXZ<ycd
zAJX0lPRQf)FHl=49{qQTtK~Dvf5zU=(99u~%%STU#Vo=O*C~!$uxZRBwUF%~A&AYb
zP5#yUmS11HW4L(5v}f!psm1B}u_q|zW8OWOrmS3>biJ)rbbuS)H{KsdMWVJ*WD@D1
zjZ%<@!uW`wbwsj2c7R**3ArFpvTag|XHjF#+R3pBF!C~NO*i-GfZ)<)W>#X-A@%xs
zZ``&xTV+v%hi(Uso3Y4;H=(AJrhp+s8vM8FIc9^qb2>pw!|$CEKH}2Q2(YYaDMI+=
zixQiV3R1~^>&5x(RG9z383wBIW?Ny?uysuBuPrm2cI__WGb?e`X~@VF-}e42(o68S
zjZ<?$Rg)mo2@l@i9H4BiP-3@s*6ogZul{KBdb94L$24ir{*9_SqhO<fsVU@B2(C*;
zWU+BMkwWtuH&=DcCn?o2R82K0HPcM6!T8}t<?V{M?GXrN30rggYn;gz$guZts~>Cr
zok$rP?pI%unltAqU^9XK!n1Kk|J_+5PIq(vd;{5I{|H#J;<x2|*!?v!y7t&^10!iV
zpS9&(ZE2J=E+4%bmtROe=4@=OSTDm03IUB2`gQm*8k(UpBzV+|fxo?gx9-+Ednzm8
z-Hyh^NM}nvLgIg|A3E3+43PV}C+(VLWN1f~G`{g-HA99FJ`;O4w|3{~whUKyKEG#~
zRH##8Mwh|Q(Q^9vbmzo~{U|b|uhY^0zt^2F%t#kK6k^f6=Rs`IwQ_7rUay0BXO(#;
z=kWRXcU}#Q#>j);b3T!cj^n>=g^&X`t(`wsIp^D++e5JLoa4>ketfPb*ZCWegvMNH
zL$>n5%9!(dG_U>qhy7uqlIC@N(l<GxPNi(b{wpRoX-MNS*1+T|k<ED%4yA^bTXTKm
zaOeFr!m3rHMO%!S$|YDjFn8O-`Af`711-%;-_*=TSCHdn+;5cxJR_{St%b7mk1}n~
z3PF&*bnOyykJ9)@X_&Jnd)UXoO9sRCFh<j<Ig3KJJl+A7o>V0g<G>aiJl{*6bpy}F
zK*R6S*qQu15>(i)Cm8Dmv#xQVRPE9W4q-1c-EW~1;<1IFC*wf{!~9Te>@ZAS1-dN1
zi)qsjgoJcwdAYg6v^CP>(@eXsxsnv2;(^4sQ+PNM%18<S`F#xy^!(-b-(ICk9~DSW
z)S4^eivEbx?$-7fp7oXEU#{ZDGU~y5lU)4z(kB}QQ!}>2kZ%&RTa$1e`nnr*A9~AD
z7_$Y-zJnQ9@afWOou03rJzgK8ayI*?Ic#PFLdE^brJi5cWOtkc^o1S%c3qnh67BlS
z3mIeeBaK&yO<qc6%Tqz@bwnm_FMC68wag1~6HSo@QJPzHdT-x5Gu<*E7o>W&2~%L@
zt)Cfd6BYRj5-^sKMH;4VhERrAVA8!GM7ikwuCzx3-eYtmOem8<SNW#7^u4ZiDSzR}
zn3x~Q-*;#GkrJAjTZRl{pdMw{!~Bad=;Q-;*ikC2Oca_6E@0o+BbdVYkPrI%MC^7L
z^6qW;VRBOfYxITt^9wf=n<Hb`n1M)Q4TN2mUrqjq2$!CzY-gnq^0`tT1nG&OdTn<J
zh}flPPA-lESuEP9XQ8KLWPF!_89jIJVSkcQ(E%%9(Hz1lCxJLMB@<@<E2ao@==o1L
z%;KK;e>;_V3I0Rb@W-kqD^Bl_dEX3JTHbe!v1Jc9Oe8<z5O-)O?dJlSpB)o^m1GL@
zSV2G&rM7WZ4kv?0z`Ba_uu*p*g_zfeeDd;g)c~^#8`B-jkf3OIqHSzQO<shDvv^;2
zC!9OMiH1SN<EkH(1I3h4dvJtcEXVWDtYu_x-eL1|Mvix%lvRd~ZZ&XpxKGy|;{-|L
z&2F^T^fiq0+Y($YY<;m~9ut~(MeP7^bAeSmVD))t%QAcUTmlGVg7QS?mFA66mMvSD
zKUXrJuWOTnU*e&i!UH}aQKfUf_PY9!^Ufb><;2>YcbBZ*IycWhizFl7?s$H50Ryma
zho5}IWfo|y4k{X375ieYpmB)ZMGf*oI!l|vI;}z%8K-}Rw|CAXtFDXcN;DYB*Itol
zMk0A4%v+AFuc}izhm$6-uU(TMb(}DUaxa@Bk&yGnYUKqd@5U>tWKUIDWDyb`h&TpP
zghsuzI608Le0fH=on|Ztj%E|BGH|#$0X^hL85TE5=9zH(s13I`ylEvf#AM^s-JDyZ
z$CaSP1;Wi`8Mip&G#3yPV!=qi60KohK$Q4c*w|~o1eN}Hz=fp*CxY>7r3JpRxFRNC
z3SWkaM>0ahA)$=)rM2P2B_edTt900uP;4W5?k|3cvoR<@6mE@d?7e%K6o>WZAenjH
z{&3lY`C7XeWi*aIMgEGz<!UUif|44c?l<~mj)M<LLv^%KLg)ul%v_zrk!ljjJ9Ck`
zGGc7l*zLTz<SizuC~C^nrY?mSXcDNQb5nZCk^#w_iIk$rGnhyc@l7^3lzmfeN|I#C
zLS8x%oS9T)A2CX=US0|zbC+O2O-Ztc|Img*0!<QyQbJW5lH&^x|41bzPII6B3IX|5
zYJ7OVy(G9F4oX;*ziJ(>$l9MgJ?8YeOKULafpd_fyJ?=URAECe5vq~Tl3^2@0BGq{
zagauFaQ+bPHNH`7Gpr0boGPJ4IllD#Be<56;uNkWGR)=>w^m(-5r(X}@-^0$m<}nL
zm;!<gB{9bMJs7F#EZ=edfwtsMj?$P4?LBD3gIHJg97Xrrum=A_WEiFe-_?|zLv1Ea
z3fnLmZldPsS2c9>JjC8qaHIvdr+7dvf$q0ymmo(j9{21W5zGj71}yl4kar#6t|)5m
zRWkXFC9L%sl-bSDNLWl&7}c6x0`uoo%k-f?<ls-{93M>}`F{nR#d0XZYE*3|ZO(4B
z8TVws@#3HD58;JuaSOwKDKDF;Kx^i1zJvhIo;MEpv9<?JO^ZAIM(Hx7H1zaq=<Qe*
z;6Q?`0K=rOp6DiUn<ozFt^wyk_j=NsB@6U`l`8sBPm%za)~!&(E%)&#8vnRZxtkSG
z*fkULG5QskmBJ!n<p-_d`6CCx!4}6Fjoo8LL88NEkK#c`a(+g9y{kreYjfyD3M9sM
zePOwOn=9)1S7CyJYFoaTUpvk>rLfM|v<uS5?Q4}mc4>-z0d|AG5$*t|8b&TH9j%p}
zjwBcLl`NkCscd|>Tn6^t$f!KB$qw>9BwK<R$MzZq2aG-l(U^1j!p_Je{&{tUutShR
zCWu$02f(|wn2s*S5q0_gdHCO3n04Q#84;sVdL55gqn8eDnty9<cO-EEhpAAlV2?wO
z5?*a_w>8__P<CA{s0Of;l%}e3Ij`B{zS#Py{)Zg#JzP|-ERVB;agINCf7&WztGDyH
zn8<rD*byrZu5b@?`(chi5o3FLj(|FGgfP5lEcz-|nMSrIbGP%M^A&H4mloBSQC4bE
z4WyZWXy;hxmgYJKlJnjIQPD~wiu9*amF%Ul?;iv*tv1IHw^5rKvK$$d6aLl!rm~j4
zCY#vaFjGpG63te4x*bZaiFnur5njV#vm0(Xmb(!`;-NH2?dqa0a2b=qR6CA$)Mqz#
zm(YDN2CXD|r}S^g)%ilABe!)wkMCDII{I^-yS=<`UfEBJ#ahyLchVrfcXr;<{VF&i
zSGA9vxrELwYx<@m6|qnzY&aUGn4*Ils+5%%Jm1ykp8g&}+9>vjv@|HgS@H&jjFGBl
zUg2)d{9HgCd5iUfJbQRh-T`jI+^7VFhEtPtAVvAopYSkdt5O6^x2W8J9JuD1$wW=c
z>LPIni{sK2(M|(naejgdM{`XK@e^)?jushF8$o<9BRy}86o{$^M1)zwkRTaGfpj>?
z{G;YU3>WgZ=-I+-j3G$y%l854n!m0s(`5h{lnPuF;bqe`@r88_4fu27{>LV5P1ep0
z3RIj_(^#=|dQd+aH9sP%&dH(6;i`cj`RCUao7Z4Pg0f&~Bh=c$y}Z{`X5mQqVO9x2
z=;xuYqyx1;PhjC+ecm=!ha4X=&^h|X#&2D!nZ+bAutWMSnbl|c*9YNO{9`MoR-2Rr
zb2?34&0V`Ub73i3D`jqLnc$!*aOOw~lqO9aG1*K0=(pJTvC7?(J2VjRax#pYN8`?9
zUhCTS^osB|bY%aQUs|&9ZAyL*o-Fe}1>D-@^NXOvSzPCY*2NMdlh~j6wlgcH#5~AL
z&TY>pCxkM=QJ<s^!h6zJcD)UOKPOl}u72QDr(!&MJbOX<X!td?Fv8y)1<zW3TfJnW
zbvEx%z}w7-Oa(fPcl+1rr-4O`(=Xy=I~&LA0<|+8{gRe>(}xAxsBz|(Dk=7xYa%!m
z*7i?sejo@qy=P1`=*lEI?SY+cLQWaBr{QgwF3KlXWl)4d-FtJ<jmECm#7|~|8kHmH
z7VbIu_r>dYvXxI@>iWZP&s%O^+}T@i-{S_9MC;>CG$6I~XNES~Yl!d@ev>8Ik>GwB
z44Yh>&-fbU(*$eQq~LL}x8-IqWyYG&+nw+WZTTsB)a$HvsB=K5z%BmU3%O6!hR-qH
zYr&%4mTgDBXWP@<@~=<%yoQzYyFZ>I&h35b22QoE;{xiUiBWc`_Df)6c-P-!4u+Yj
zuXoG7xtBF}c^8kgjc2T$+FkSxG;|yBt44mo>*&(gy~k$RQ?Tde3Gp;h^hT1HD3B&}
zHq8cGP$R-aCXFL6oiDt9VHtnHTP3#_M)b2SMa;`RelL*}hd^o#<L3Njg7T3N<CE+J
zs;HP8>Qa7g(xnjs&l!d)Izw%K{xE-IyhsvfAryfDD*}%02#2ohibmS|xvw|s=_Vgt
zWJ_g%&VE}ct67RFyOL24Rql<(HT}m152wQ0+vZb95EcDcYTci3`T0~(fyoeT>0KHa
zjdp_E&PBg%_u|D)e}AG<p6HhB_a`dLGT6btad}R8L*E+y>;tq|M3K)2Gw5D(FWfA9
zitIM(p%S90;_e?Z{PK*-aQ+<z`Yd!1{r8bcR-qv*J{8aH1KmFds+gqjIJyh&mG03B
zJ5%Uh%{3w92s-CXPW&8$fl#WFrMBWBSFsS=Ir6yJWXovPFxd$rk@)xkuFfD@tM)|U
z@!)Uf<K@?qmtSf^HIJ&HY%-~}6XWab@gU=2{)XHjhBDlGRA@Xc>7zp^L&@$M#`=aR
z;=(F3SJNOyW3op9|6s;E=Y!ilga`RBknC;mA429>(*4X0p&Sj(uO84}+v;wBD@yXs
zpoqros?RF1G`p8`Av3;MD%i4Ukf*wJwf@Mwq0`o{+}YoumqDCG#8o{h-2ALdaeL`e
z#@Qd4wXIrJTTqEXmv_Er?)B!Q7DvCsnCQ1GrM3$VzhXr_q-2qj$WN`4M5a_z8`3DF
z+m`04k3w5*V)4q2Ns_WjkhDXgbk%7JcpUJOby<JtmS0fMsMl7|^7X0)Qq5O?w+!Ft
zgbkNH8?eljvXH}<I`^LXeLAf1asW<cBndf2xXP~Hh<s8T$j@D06p3W_JXR6O`Ls#=
zmZdVBh`_crTE6lBWD2&u>@zB0969ukB`ce@O~b(dQWu1*#u30UTF{7&mmB-&&gGLr
zp^(thG`LXzA;mWKQJoJO`l*EGVCE;i0$ek+FC@yv?DPvBN8LW(A2eAW?uUOl-e1et
zdtGLf@D?xK)F?)31GBh(Inkz7K=LxXM+k6b2puJeKN~AmnAEVtx3o+Awl-dd?{|dn
zor#h614FPs&gN#;90=yunwJ&}M$)C`F_@seX#ALsaD99x-FLGL?+J7CYca|m)(Q69
zSZi8UOEPs<Go;F(G(Ipv%Zj%#EM-V8&SyY|G3E_jQNV$_(L~$9`2g8J?^1gEc=OyF
z^bI8XYwr8ynzpR><q3pQzE>%Uj$0i&U}hXcokzp6{@|h8&m^A_BDY_+BNs5NlU$L9
z5nt|tt4YMPgQ)z`6PHfhL2mH+vL`lrAH!c!^vK72<C;BflvR6(EpFVva`4*vdw66~
z(P6U`6pS1Pn{5ZnB(&fCgd3`ro0x*;eEpMMR%U{>{RcN=g{>X;d_#L5D7d*>1s{Fg
zOKq6s`)4>6)MR($1M+PQ4=py6sYU_Ebb>)3EPNZm+WE=a<;nRAInQcK3@_y1@f|Sz
z|1|-x%5Gul<X_B_Jq8+^2J7Q`B~6v>TytZMM8}VtE<E|TX|<#>Z+uy`8fP?Jh|M==
zHHb<sLbtRbAbor0<OL&I@H77vqEst^(M-szld;S}WFY<Rme)pSa1u;npHF6E+NW!l
z!~H6W7)@x)4j!Z^a8wZgQj3RTVmZu+Vxp^tk5m~y0PL7;BvL<{q%^ijJZR|Z1>Ko<
zNi|U<<fe<XK!%~%h*EkAo78BiOybHij^eT=5!ItXT&#+cvIHiItE$<X$izq!KvkmB
zQ_rYOiBIXfRSYA*6^%<)@(K(2B+y6Iqh8xw6F__malbOf7nq&si$>?i@|Omc)_!5%
zBB#P1mbS<{xq3xMrM1R5GbfPaFrILv{NXT1CQS#9lV-&=UF2I`ukW%?QQQwHo^|xt
ze`?aux0yaJ#)17hov~<RT&s#3*BoO}b+!0g@(J*_lzm_2mXgLfnt0ojyUI%`oiB3e
zcvP?uqr?3IpP~0bLRpE1hGusskj6aA{^Fr+f<L{`QK)k$d1EKLPDF2XD(X?ka)Y)&
z%S0`rqR}f=g2hqe&a$GFi&N87avH0UW~#}n92_sFF#2n!f?Afngu}_&9nJP%a!abP
zJecaNB?BBUqtMW@)D}`iAV)-Fd#4UH4f=*`PN+<h7aAMHc@g1tzYbV}=-Aj?DOPs|
zfFSL9Y4S+L-9D${l*G0vKOA4AybT|5?GzacA&u`>d3QY92AUS^u5Eoj(jjAt+UIeO
zr+Ei`ibyChS(oab{jQx(Kmxsce7@}XT)|Juy$0a>S_U@_hvok?!bj|w^>!MrPQ(JY
zY<Wxd!6uc^k!!=ol)``}4_p$OA}`^JD$a*X3|p0rBW%>r%4PLWgGd^!Dq=jUv?W&-
zOV=Mh__D~%`j|o_lak`t*`=w{e{)drbnt?f8}E~ZI<b!x0M3v%t2%xj6~C6Is;Q~e
z!{_XF1*kTjY!e8rok|u9aop>@Q#c+HmE<bXzLIK?qGHh?Dd0v|pgT)Q5GJxTeTdP+
zEgYVq@&J?a(X<;^H8f6{28E|BU6Y&yC#`5dUmSmPYcZpDU{%EhHYON-B8(4U0vKjL
zDrBbTYK*h}s2!Q}4)Y$C<cVgH_hcDThMhR}&Xr$7V?*J1A`hAoo{BYF2b_iE)r6~t
z4Y;hxVb5>iDcqnm(d;zQXy9w~v9LIpA)b>+YPnT%VTz9fYDSe}NR_gyS|q)|3D%-b
zF3u}Q4u%2UcVFCTdma9&!G>|7Medo8b@s7|Ua9O`N$MfV+t6da4_8;if6PMt#=E7;
zGyX>bKE5M!iSHYVammv$DURLl8G}n`Vf;8+nBFj*#EB_N6li)IFlW4gMy;+*x?DAA
zS>7vCE>^j}8Dt@2!x%sJroO7^mki&xD@Q3c+!%eDHjNh)na80$Mt-;i@N~xy^*VO?
zqENE?PW3uM>z8}HZ^6aN_3{;T7i;fDG7;B1n<f^k){2+hFhIIAU*k-#k|6-7TG%3~
z>;Dq5OZ9Q3Pe~0Gm{tX3yyL&cD$ngbY!XI~wTDib9a!X($@RS6xf}NF-ZEJV(xIVv
zik2;fh)}_aWL~@oj6R!qM6KNJWy{<kuz~JzHK_`YcjU4@(U#-dB-Gj%9}^YBV%c1P
z#8AdIkx*jE3O7&ANAxI>)&>E0J!OBDNNax3rb$uXQrL)b7)h{CQ)PPQ@VFx_&r@Iz
z{6|qZP!Ej)$yT8sCYC>(h3W*`0D&UDv8Y2NR<fPl<r#+E<rQ&+Dy<`~41$;aZUa@a
zBbLZAJzc=B(7C55sJ%G<ADP&nnd&ABI$u-Ju(6XLn+TNkO?}?$F4QEQNUzahmWAXO
zD$moYkTWeA^kh=vPe&`I(0zPYAwasy+Y==UM3C~0cSTS)u9CU6qD|n_f)8jLVd%bK
zkf)!bz(w<{l|8e*Y0t=3Ka@W#0WT8_hZNq*#h|_RJBR+Wlmd@^&wskmA<ME9paI3S
zv0JbQzo@1CeAR=p!-eD5rKE}rDJFFnhsec(nxUaokjx=`DUgXChh+DAMIsRb=*H33
zc`g6SA#Z)gON^T4R9zs&ZG{)xk9Z~VdxxLQ<@b=UBBRlBA+u&d^mV9THCYTk)4Fs@
z2>)x|u7EC}XoL@k*M0md$u(Sx-)MwMgS7Tban0^h^3Yq$h~&{E=>;jr^^bA?(w68e
zh>uB3WHf)6K?Hjmk$+4>jTv8o`klfF6eXRv#_fl4yN&+`ixx}B<h9n}7c4eCl1-X-
zjYi6IjyrSps9qE4;!8z=cR@XUxjNhc5pUnp(!C^#rvjlvSX|D~v9)o`;~j2!hLczm
zjRPI|=KOGd8RYzeARK*fxA80y-U?xa`%&+mR({I#I(~}LtdYKTJzGL{$S)Mt=mU`a
zjW8!#{oT%|vFZy$rz{L2tM+gDra~$^=X&>y|FL89oer0>3L)7)3Pow9fY<qI@WOI6
z&!g}~d>{HAx_iEP3V)98n;g#~mER0WkkFp}`d#B=6k*#}&im6*YZUslQQUh0mRD6+
z7vVFRs(eN!_n>Uiu;0-QcU{`E-^xw{A9Hd^C;|?(_WU$L9#fsGU#H6}6Z^6cd1;VN
z7}951_WN=4gun_jig!Rag2OeN<KgJLaI)u*+Lv+^mgtcJCbg9}5)$mCb_loK_3~t9
z-j_6Eqt+o{vyx->(VfS|Rg;`m#;bspkY!!rC^4SGYtP=V<ai~36(;8ky3oXI?YMwS
z@>uxGl)!0aKOey4zoI4=M<;g0popn~mlmWiT{D|m1&8f^6V)vrZQka0zp7g6ZUZmf
z3-_3iQ|0A=78?-$X-$6g8evb*r;sgUVB3v9|2Be1nfiGzENF8)NVA<)&BW(=z=pZn
z?n;VWkD4fX_}mX@Vi*qP=y!ChS5H=VJonU)3$tDYJRQwv=#XOOc!_+&Q%IKe{(C}|
zBV0G+O&`OjqzH2)VkjD#iFSGyi|A!QN9pe1=?{X071-x$S@V%K_~z_NX2dLTYg)NI
z7`Oyb$mA^M@O2E8Uk?)RxWTlHs#5poTMntC{*nl94gv{=KzQ?ShnI=$oI12D05rZ`
zea_i_zPUsI5C5z@CRo128Nbc$#W-KzMsPcKF!ee9$_`DY*+cgDeYHg><OOJ3=tfL#
zRMX1nN20w%QRlWC;)6H6A6DrzDGIkeo~J_={}*Btb5@1fe;4qRC|Ydr+7)wr@;wjt
zvG?_WE^uq~(eZzILw%}c43_|T4D6Nq{BH4<3uN?}yMDEr$%Sz+7w{B8{0lT5lg=N&
zbWevZttxho<qIa2Yr9!Rcz`_#zW=xVVvp0lu^Q$sR4fedz9eJnM-Xn2e`wQ1?;Sio
zIjvar72AM25y2$$072f`iPLR?nnEY5yy=#`A$fRV{+Ha%rK%d@$|*1*vR0V1_)f$7
z#`I+VK`P0VTjzO68R3#)_+X==6`{?7qTxF_6U81LwrHFlRx*O0knid2%5paam~_Y&
z+lX{B-|m2RTl#O=aVPMB;4^QZvP!S7n!0j}4|WNCD)cAeW5vzN_gYcO`MAP41M(N4
zxH=zUuIilhM>;IN@vq-h=R}l3a)7;u^Sh!nBOKafUT#JzEEosAkBSoiJxjC_O`0#k
z6uQoG-ek}gXaR?to?J8@gzIwW_*o6Al+$H!<`GgxP%0|&jWgJ^)FM?3#(gx%+%ZJx
zfrFmZ>VUo7N0t{l^A%^lFGkECM52LScvnnml^QO>bFxkI&UXtZ;sv2Sz0iPxU*ROm
zU-in;409$H8^1C)gt#P6CcV&TgumG6*DlXxLag2aChgrQF&?B_S<YFLyaGmd_`;5u
z6eb}ma1u9bjcZ!M*H~7%!x;c9;6xDP9YBnZqz0^5%$_<_Zx}JFn9Phshf?r_H_z#m
znEU}YX1+8gD7!T_WoqM91)r|18?oxRlzxRfkxfFOvl0x<UYGVhLocS*(72rc<Jyi%
z<BePe=D#DUn9rIw&6J~ue2J2y{2!z(w0`9m`h3&lakJ*}X3~|D9j%ty*M6@l4SviW
z(_UVBI}8_98;(>x!Ole&Rbu2~`j}JWwBv%Kraogp;&E;>)@^?#Vuhv)E&cNAzzodL
zS`q16-ehMCW=OBd9X*PUAN_lY4?jp8VN!?>ASV)Ri&BNieYksD-e$KMNS<x!L2!6+
zIYF{eYe@E<4-*EiattyhoC3kj^#^p0?mCyO79%q4*=*^weTRa?8er!zW6zODGOaCE
z;L6DRuHDYhGwv)jD%#Q&rtBA)C#*%7mzNN#dO3ffm_NcU8^tXfwcwZS>=2(UBs{_O
z1<`^vOty0WM0=s?GqS|!7O>IirDg1`nglrx2wl1O+8-(+iqKf8I9Oj5hgHGGl01Pj
zurVW9DklxhktHldZUl*!3~wob|K=>1Q)EVb{4)qaGakTfKw*bd)U(ZbS7s<};PNE~
z;~V#%lN$^<;S`#%IvhNOZ?f&&!sAQB$WHw??if#{eGq@*W#G+66%REV_KjD<3r<RP
z{gm@^#fOGr-n{&rcTK@iUnsjHZMT2Brh1p=$JJxaHkpA^mkGxE-xlU?Dx_=>j_D6p
zIQaN3xhjqW%?z2(S&dMWQEpe|$#1Y*De8cZ65xO7ob8RtS<uUfJn%UZN|j*;c0n)G
z@AdQ=+;qQg;9yICmyQpECB7qsu+In&0%8P3r2j`V3yWIb$K@&aE&3iGXFc1aZ$#wM
zoPZ0Xqe_~=X<^uSZE?HnT6CEygf|*$l4e97P+UF)6Q{edFTjMve}7~~oBSJ-Tuns{
zWo4|Y=LS?nnzYq~06!RHZIO7uxB3eF(ujd!)-^k!1zT;_tl5kaQ{bOdQ456ShD|ML
zN$#D>{E&r(zePF;j4fk$TbvT;7wYSG^q1+R!IDH$X6DZfhl{C3t($d)tSg)vI{Lkf
ze~Ecqf$}VncV%1?FIq_Z<K<i8`EGI#XZ<_WKZVF_mS?pAypphrPm=GB(zUiY6)i4S
z<uBRTKyZ9d%j$b#y#P~lQr(5vxFHz6$_K>(xAYW?Ai>6V+PVcerL{VFyaK>8!Mo(2
zkO;Q&oKrjW%VfQpDJ6$|uibT2CHZXB<Bn>^q`Dp@t$fZabQ`;4C=bh-*H96<aL%H2
z(h!{<8mK<Eo3&@EN1tgrk=@=o-bF=Ge&p@y_>L$1zI%^7r!1S`exkclAq#`p>iM?L
z&XHT6)Vm~?_|e;Zo4M2Lk;~WVk_KjGhHK<l!x_ae`aGI(&VCshxHZ^fqxiw=Ux5@M
zNLWH6S)nYxXx25Xscg_hGoL?>Iz_lyReOCGJsE_Q^b+>|p*x5J^8Q_Mz5~BLWjUb<
zmvM-)QMFC9|4U=sf2TkDi`Nou+p+?By8uy<V9xpLgVat0A+1^X7_&M!nIn@|5aPk0
zXv#i$Bl@vdRpoY=fSh;?*HM+7+m2}rs}HMsOyTnA8TGoTrzV-81g^Djg>IjZM{QTN
zq3`V`i~Kq(!|kr)1&8w9-X$T^;_SL?uvfil5|G)T4fd~vfasTLS>)93pM>A|*n@+M
zNj4s8>irm6W4FhH>f2{fsBP!dfkw;oO__(|LV^H-@v0O-KhWQNe!63s6`*L)pt}9=
zd~DY_(w_#=OY`EyD`SM1I7jLKc8})4H*<g5`SP}%^J8D>XsE=G7t*Y2b(K)0_Ih&_
zB~}K)(=^M|*||2ye^{Gr9}{PGVobt^QK<lFG0DUIY0f%nh$531-)~5ZQCf^4L7xzh
zd_$^je-A3A^E3ll+kf32TFMq5CMRFuKQaZ7hqSM>$ElM_GuS0g#_?TgKtz*1n~bvv
zyJid$Y(rUTaR&)Rpty{(<fUw6FJ7+NSRUAx{@XepSfZH0Y$@yddoe%W=s-0T`oHc+
zs@q3ytmBSUvuD0aG%ue|!BNFgP)EtcKl5^JG|@x_r@-*#C3+*M7qXab3G#>8*~{oM
zDL>0;Yr@pc#7m{61^(gCvc-e`N@5vem-veR7av%8WWpIBNAPRmd<y*wCnV1xH4!ah
zC5zUy*N8j8ylA8QR_sVGM`5!7GDz1bj5?CUDEt(`avgB4v;Qwjo&<=~7-1FA-+J!n
z!&gx7t`IZLro}%6&;YzP8${Z@!9Kde(wKoC8=FHtiABC0Xr~a=3Q-`Q`sI{~@Jh>P
zvjI%SSR|habd=3bK3BSI3mRu4<B2XdT}JScNF)SUsU~U}U&R5!1GK~~p#n;4PX~@o
zV8q~mt5*Yb5HHgY&K+i;JD~@9J1Cc^HKEfcctFq*r;Leef`?Z;I1DKvl)f&qQtMf6
z7mwZYXwjWtKrykefZb9v-o5-8J1%tEG%Ekqo}q{nJor4;hxGgZNV>|Xs+zX_s7OeP
zDBXwdZjkN{K}uS>kw)q6?(R-$>F$z{BYEiV{KofN>-_KsEP*|H=DM$%I{R;%T-+%9
z=5S~VSPo!_>Q`twmMr<q{nq!`X0>4ZdZ_p=xVppxEn`yl6$g<K$MeQYBUOOk-PF)-
zR8jZl?4oqX12WTTk<X3bm^=CcYBHa)sY}ObGjg3;>3x~|)qX45-hzvVek?>y%XC<V
ziX*lBfMow_X}j1}4SjfE(WfTW=yV0EA%gP<_93ECNH=IOAw?nk+`!n9<FHF5i&GeA
zU~YW&A+bWW+?Yn)(fItsJ2r6#@h}yNuoM=htZ2zq91kO@;D`P)Sjao!Ax;{T17+Sl
z`$upYDv|brt3m0o*$2~*^<-kEsv~WgRcEi%NZAql8q~+%hr}(J6YfRdvZMa?rO@bQ
zrgcxx38!42W~CiYswdp4Wae7Oa-htfa_@(bzx4%hxw)+aOkU{q+~7do?%PEIhp1^I
zH{!GV=o7zfYI<7vnJiO=QAaXN5l#B9fb@-WZ<bEW_&wczkj01`>3|jKguchV`Ug7k
zVO)<*nmg{_*7rFJH3gP(QYl7@ioSn)=B;fm=WmrC@wCR)MZA9;&sFj(4J9@1W&+8`
z_T13mM|cbVsZcp`tb~VD6Y(g?z{C~K1jhf4E+<`5{c7o0|6ft?L*whJ!WW1yI<RYN
zSN<;Rw~E9fQc|9`o%NI5itO1YPdPn6E*GRiVv@^Evj<rdb5Vz-DdfcS(r(Nb9WdWQ
z>@EHy2=Wh+(_kAk=f#yT`l`9f?kI+asG?8Hr68Le6e`IiBg$b&iWp~{O`=?_9#L*u
zy;ey1==LYSSR2bJOmjAdBBjl=R^rY(TC5~rk1HnYd(yPt;HDg72k*qTJDvQM6`$M~
zmfKo4ecidq@LbSPt|A?+#E($>EZ3B#B9}J($=c01lp)UH2_+{dtsadrWv%m*W`;ej
zH)MV!m)Zm!Hf0|Y4OOPkH|tR<s)Gvf5VMKuzrjg;RpFK9dhb_m8aH>K%rj7}Q(KO$
zLVklVOyuYgSZ<-pp#n`lJT|F2&-0SQDF_<x8yY<rgjq9P0=YhYT>WNko^@XV+w2Rj
z()ry_WjHB0EuPR<xq_HT!kFY3<vfJ$IYMWDa79GAHP}ZbQH<S)maZUnN<w$`eZ6Ww
zlJt1Gw$L>uofGsHOipJZR1<Q{9ICy%rhQKa*-~es6!TedSai4_Cge%!SQRFEc5fl}
zcuye2Y#%>q%~Ow$UKC9m8lEtflFq>5l`H2)HqqToL;H?LL<pikoQqpBkz1ZG=oDH?
zGBnLblkk+ko`dy`1{Ik%yw(EN*kkE%!HH8kY|J<U;Fk5m#$&>zR|q~+sNKW&NLU`K
zuYTk^J)9|rE5&B`WTq`1EgCfb)64@LIq+VJ=YG}3I*hV?zL)mHuq#?ME}80wQrW?)
zsIRSL$A9Zc7HZr#-o+~{JiGJ!{PfVU--MKVlM)lEoc<S%6iE4XvtJ2s+{9y(X*Riq
z)VCbXJ`8I2*Oa;u_nv$c{uIwnaEwFZ|JTLGPy5li@qyFPB_T9(BPhZW{eVDCItTaS
z=aeo*uouQ#lvu>+XE<L(#217}xWR8B`MtR;t_;#bLVId`*_Z~unT8JZ$C)AYP1cIF
z*7znTtA6*m8#9qn&~W2$v%q&nlsA{1XCD@-%4<57){}hhBNWFhd<gnhem3?m$!z4P
zjgXdV1lF3@CDTRe$s#Q{#R@&-Xh1^zXGO)6)IXl6#+{?^?X1Zp(-%CcDPWxldkLU!
zd^GGIXEQM6NvH~MxzvQr3IvTrjKw6)muHww4+BA1L7)L1T7ecGqPR6otx_6To{Wpx
z>lMUI%ABRr%=X<HKV3kmr+Ww~7qAFF=<|wM15YoOPNjX@WN8X$4<Fl(3U(4=2B|+3
zvDR%ipd?x`>$*9^8dWUdJ9-qYxhT#A@0HQ0A6Huc+}oB7y`f?i-#&O5XPUTw$dK3~
zZ{xflj}kVanANM&5HrkFgp1V>uk<_?kaY8ht%}XuL^6N(YbT~3?0V|-V%f#Bq&mvC
z=OT|-QjJzCv;gHf==rKiDi$sV5sL%$CCixovs3!bZdU6r{4736g1(;$AFV6K?%Lra
z#?Zc1+D`sHsP?WBb}W<qdrVIlvElE%uyJ&W3e;)R5zJb$s3&@j+Rd{M$YxX}<5=LM
z$<HUA6K`Nq$$lnEv~kMf*+JZg?L25sFrae*<_}6oE$`<?I#<7%K0Q$U@rlc#tz0gK
zBl4)dkvN?>f9+>p{_l3?m<d+h!HD)T!LDHOZZ4aZwc)$@jx1G^6q)&Lwy^Vu`7-QG
zsp$)R<hpn^P9KL|c)AMCv_C=E7Mbui3-~L)%N?!rBw*h$?POI`Xg6;FzUfYy$RM-D
zRfG_1Nt2VVNk)_*lHM#A`Ghz&^Ehd3L90B!4Zzr?O~y-4^v*v3a7+!-+W7v+!&rkn
z7(~7J7=K<~_FZs%cSVhrpM<_d!4QZ(BSFO`M=0&jN9!fQ7WV(;=iPxvQgko&dJ*S=
z&)*oi_xq-r;>%&i|1H*kR!l@?oSA+1@>R?HcN(JN3v;@!*qn5?BC>cR3Vm2@av*Q5
ztetl1zj0j?1riSi|8Nt^o2u@8RKGqnyqMyRg5=aW%74A*EQP4D92$7P(2^feQ<D?_
zbEWH>Zll66gOo@+^4sE$M_zeSiRjKoyuE6d6>H0TIlo9KKEVV@OGA(Y?lP`lSr!eQ
z)>_RZz&Ei^&52!FJgLDifxorwv6v$M{%9LxD=8GB%)*vFoUrKRAx5_5($wWyI4DOc
z^rjaFemS|czeGodd1b#Lc?4_F9KIB?LB*nsxiK&mSsO2DeLrKBMmdsP8j2rqk@uY>
zWac$|eiy8OikDfanE3Ihh=#E-#icvp#*heC{nSq&X%?pf^S)XUay+HO#S&wMdz5K=
z5bVZDo3V0ZgXhJcM8D%8Zrv<y@83m?Xh!b97#+H}^fj(C&fwA|LT)@?ZOi~BCnrn(
zY4poyJePT}UuNTHh1-wLh_z3VhhoZ5;JZ}^<HEg-r8n52wNEdcaMu&Vk#O}EYe*N?
zFvg1zOe`?a;%zAuoIe(oSfE*?6kqO+GP?7whMCPcE&L6+8A2kR?hAf}C{Eg&qhdYa
zD!3N(Ru`(+<Cfmu<3=K{CnTh9(iq({-C*==oe2MflV|2Hzy}Z1?xz0hpIb+O$LWbw
zEf!qGRR=D0RAP)}i;zUNzr*>6xD&`2n9E{-HH3QLMZ_O#p#C;Lhew1Pk@OWQB0?-&
z?lQ^JuFnv!h-<c7+&H~guuYLsTR!R@veYzIHklX`1>DRB;aT6DQf2>-C}jUhld3aW
ze18)nNP_$tf-1rGd&gy|65)zXgEo?dNIZf?q-wv`$s-K^)BH{&VaN4l*>Buebmu2B
zHXUE=*Am`k;fMgn>gZ1eke`n3dCbvS6_z9zBlSE^*gUL^O7WPmsIH()m=ry^#srlF
zhD|P!t@kWfzKoV?5$km}{YD1k<LB<qk@$!I#QZ}&zoZeiHjPYiLL43Rtg!OZ^OQaQ
zcIv-EE3L!3A|~-|tH@sNF^VJKXz)1~g@cE$LUJ(-2j2W}{riZ3(5cvBEsEoiO8*B<
zH?`x(yMW(*v$vYT%AtSbx()89SOovzBqZVD&6T{IE6G?*6+yfsjM7`!x=P^S{FG)@
zUjNg}B*L^}BvczeLE1KG=Gy*Fa17x{NGoyDDIq1`&DIcs8RMvO#yDG@(%M5A6$m7d
z{~cE$96)v5eLzVq%q?X-Z1gLo#R}u>_}75l;2z~NP@r*qy1kE_T-ZN{zb_}hnUYDH
zy%j{^6a_E40CN6p0rcKjgpo@8zh;h<N#F=1;tBg%gt4MNxc1)|=MckzG>Vmrd;OL4
zeIR@LO_-UYL#>Ku?$&W*<!Lh;GCM&Kh?OW>3AGw<GqyC${T+}k6GLzn8u3$sb>3}{
z0E^6o`0%6mj`->?OzNPVuQ&ELCqa#i#QnWANWpL-G9i4ae|=s-a5qI{_J$~wu!X0m
z$EjQq#JJSSWIzk$#~=CdYf-|2DY1c5CMtW9ucxHnhvbUNu+oxD_~oNrslTYd@Su3d
zO!Dxb*#6pM_<gOSK!08_iv+d0L)*h0S&@D+W#n|id=B=MA2S20{PSipPcHS^e1tsb
z!tz85jZrvDKlv9yRk67D9WCw|&P8ExfW*I*d$IKbv*L^9Lj#-bKh+>Ab^pOn7D^#!
z_`oee40`qLx7qg^F^>a}PdZn;vsz%2C-<JeH3y=|*|pZ(i~93Z){HAh1J<$h(|I1%
zmN|RFGkP>Q^yn38cCT)#I<Gx;LS-~&Zif$$fyUXUneO?ub))+yG2zC~FQ!iHqJ5sC
zuu<7MIB);uYXl#6_C|LnZM3v9d9a1J<SBaPiFWQ!{oaf2HDphb#{{;Ja;T*e^q|_I
zHL$QOIkErwsPlegQ<fOodl5x<7pa)H2%DbcFfDu|r{-v7<#O^6%`I)MizQyDGDIeg
z`PeZrx4&OpDpIr$T7w4WKZqx4(PQu4zM!iB)OpxDP{^4nm7P#hx+(u^>pSMjews7A
z{6>+&`0;%+OQs^w<bX!`gZMDx0+r^`a39Z>VVoraDs-`LZ(u<S!bYbX1@GC#1(_k+
z+;5S85KF9-aLv^3dR;L{V`7^Xxq@I%pTk>Gj}DqQNYuMpSkk78i``1~y4E3W+?ze~
zgz4O0`b%?Z;=ZE{VU{2m#$$Ts$*^Plr_!QtI7`icZ2Un_eV#4%@-F+e-=UaUH6kOF
z$t|&#hK71Ho&<|=Qt>$gY05!Hv($`a*RR+w{l$Uq6<dE1;l%X}Z+{J09192!5bV{J
z7H0EH-0lgRke*zO&TMd#zA;LTAZlNIS|$3oL<Zhz$s;(#qo#374}Rr+PcACq!L1~k
z^j-l*2mG<7f2-GAcHxK~sUc;BS)U+oL1xBea2Z`N{0_caf{(E$xzR1hN}N`0x*FM8
zPRoJSYJ}<<+-X%L<n|5iA+&Ti_Wt-miutp)!S+JD{r12?p~lfL$V_xnEr%&gFfhx-
z>y(OSDa*mj5Y(>`Wk^AR?I<2L8HLz`14Rw#Mw~!JYO_=074TmshL%MEmht2<*tAYj
z&`c%NidP`Y8%l*}q$V!0pe|E@B25;&?yoQ)o@nAJ1QC=_5sihMC5Cu?N6;k`!;?FO
zd(d@O$Bj2Tsw!Rr9#*ra-8;d?N<t6rQJjen0uyExe*~iIXVe42E7?*;VyCjKc9O_O
z;;qAcO$_&Wbtil**68iiCtU<SS4u8lUU9_4NQ;I68HqLUNhgu#_&Y>->fF`-S8ScM
zUfobJJd$~}8J83AhUslO6m<&I8=8*3DUC(Y`e>NHnFaY+8JqY4ogbM38RHd4&T9u;
z=8ugZr{8u{T}p=w59jxiU`oA?Cc|JEG|zS2i^BO2Nviqc9zw^^kT~mvk1Hh-ZKXny
z$3p@U;_1$1Awu8KuVs-amfNOQM{iQ0d@)U)Y;QYof*_xm&n{^Zk9Ti8az^C80mq)^
z#W}z1v^3s@51u;?F&_{#hN^Flp-&A{+3J7t!llS4js)3QCh+HYp5~h~h>A;!BHD~T
zYICqXBr*B0T>ipqqipmd&VQV@F`os;0lE#i3e`2Op7#FfL^o!WYN;v`90Zy05F|Bq
z1B=GqO{*9-rm;wRL=_)iVXVITJ+IH&x{RIQk{Sx&i62kUwDGO)GGHUn^NnyZL;|kt
zh3nlbe$GZ-IAJkHBTWCd23Ru|m-Z|FX(dYN)l|O22plNFjHeh(qnu|%W?z0wWj=in
zr>R+DY(1`^Hi@qJ)#rJY7nJ5SeSo>ymky^4^)ReQoqB#LTY&BLf9QJgrf<<Ovri@@
z-8@@htyT{S(B&mMiRY^CJgaL1@sFS#8zKYeZpW*<mzj>)6yND(J&!J4GL7*!(}orS
zkNxfRCY{a^{izW27I~FE%cPrreSj2SFYegJt2Ypuzx~a%$UcKfzGJv*v`t<i3qc%V
zYqQaIS<q!U@n<=`gO3xplyRhuu*0`%tq-$d<~U)-R`)B+!tN*SYaV`fNlYk$Tyo(=
z2WIgXZ2}ZuboTiBz5e-*Tt3Fa>*?Lg@%NCBN%zKh1^G+GMfE^PgN^nSh+mAt&c&pC
zi3euyy`02NIJ2n2$qY#+-@hh>tHCIKg*g*th@~YF1IdL5Cl;{xZX&+hUVEvVH*aFn
ztUy5MgFA}z&!WkEW}=FAloXhy9<7A7Xd)GRp|o^1Q1I{h79V<Ih5vh~l>QiE2ENPJ
zC+*RC%YD}(Anw_@530V}D`kszC(SRk^v(ax%y<GKKG@HtEJR2}*ky7Wj)*V%e8mOL
z>`(i&*15YTIo2V<FCBQon8Q=j2XoLxqQF!CJY<j(g!s&h1#wd6iHCkZ^A}M*D;(0H
zQIuE!b`Fx&c49eykc)g6D%dY?<SqZ^p_87{JMYYHavhLM^+Ruf0+H;XJfw7Z<5!!J
z$OQWDohvj*1ywC>;rZfJ`o6T`&7)S&7uGCcT@UvTe{U@Ns>MR$1L(CysN6hrGTn#d
zQGrFwlcLv1ApxV1Scvj9pBR~Gk9DpT>sa<cRNBG|B=N-ChhA|#hD<|JwjY$}uv&CX
z7g1I_zDE6#cnFq*Nm}gG$5>VxY3f6X{|cW!49k^j#-l*YxfT9A{XxG%Urzctfb%bn
zQiCd;jv>L)QW$v`b138_`u;ntuxunXljjWGAQ|GSEX9TRbH;|$Kigv2U)uLw;EDyu
z&{y6$xj=6W3`!(7Q7RcYJuCxr^E3Mi^l2v}@vbltcJVGXHGhme&O;RC--*5aDs1_F
ztq~2JBi}606aFH?DaU8Vk#H|rWI_teOKZ=*?i!mLe!0u~UAPht-yya<mxCTC9t^R*
z-{Ed*vRr;{j2l=^b7fcIBuu9o>Vdxv3dkKC^xJS-`7w8*)4Pmv|BcUf*9|XSf7%Eq
zGi{A$u|mFQgHVsSv1ATHL-<kZ?9s7h;neE-YRMaldW`Fqt%px*6L{TqqJsXu+oQp8
zpz-w4XvJF)ZDu^r@ZO#@uymvSSd``w8oBZNP&2ajm^$>Bc>nJW7>{DlY!;ZT74NjP
z5+x^k)~X)uw9TEK`56NzY+2nS5f+q!g978LpX(mE58YPpr`Fg`iYfF;OZgL|p?W`k
zI%b|Dj(VoT&=pxE7zp*A4}Fqcj+rt!i0XwGb9nuypc~X(j<5F82wTPk_pejIAv9LO
zm}bdvr<=6oo~AdD2Xzj)Qt6gPnHJ5u$?;kT!4)$F`N+z#6Rv``u`q}G^F}r@8yM%n
zG||UTSoN=b8Hi9OcojAoUa7|nYQq;69!XQbbb9<Q)a;aT>5}xhYQmVaM~soe(>O%e
z#|LC7HjZ6%?sS<N7+E>uMN2pRzd+5lyRL<79!KN4Pui{?zK_{Fe-yE2O)_YS_9}%@
z8SThz)dqFU54>Os*EDywLnFb8_<^tsd`}$rLnrkK6d~`f;N0dUlGHj>TYFnP&{gN{
z45QGOzopa+k7~a6_TF>;z@|F7y!?vyTPxR9tG<e_q6+2rM?XR0C6yGOY1n|+Iu5$w
zzsywkB`_FlC<<*ZJPm7)W>O1Xh{EnkFDn>*?(UCkJ&XFEpPnzYjU9tz3E>grl8GxS
zF(^PziEx4()7O@X$-Yp{G)HN(rM!Cg;<o7%<J6hXy4XoTz-x=ho~@-1Y>Nc1dyF}=
z%<>kD@}NB`9F%OFwh9xuWwd)&F36htmQ#m6t;(Csn+TRF1k)_7TXdtAOoJ4b`<y*J
zZDGbuTF2*#PeS_Q3mg~Z@RR9o2C0rr<7dd7cW-VbnTe|w+}qCmv>$d_xqf=k$(zu9
za->f$Khy3!=R8Mu*L}0&q+_EC{d*OG$~mtM2LAQt7nScw;08m*C@sHe@g`QVb!ryq
z4Ar_?_?D!Q-TFp2h)JsvQ0R0v_TLM2jAT7e-Af88KteiCzjgE?W1A+Y(hzywBSb@9
zLXmHupA?~+LC|Kj1MgLhV~*w~H5ecCr%c{_!Qzh5B5z}b<53^3LRQB59G9Y@7H?=v
zoLY;QW1NR9s`p98KD&j$odCL4;@~!YX&le$(}9-hwoE!dTl4X+W#?BN_Ysy4BR*#g
z|H;Y10+8z-E?^U<R}<;4vu9kIy-gyneH@auTAlZ_3Dwm5Yf%+4GK@_dd$E0<DCAT<
zq*&S-r;Ux;$GD!>L2XTxM0*fKdM9xBz%#`WX2$K|ovLa^Nqk1*p$0gnvMsxfJ-mi7
zv?g1t>0>wU$fy}vFAordtVNYm1^%3m&SV1*A_3TX>7@GgEW|Yo1~?lRUQa>K%f~e}
zOE15y9k4N%{rBR(|D?r))i&WAkxibKpbz|s8I)xDowfaYGJeP28?=XsvYoJ)krb>@
zPC(0^-Dwwb*J$=NUJ@EnLZg0qIr^0)X*9dIB}B}9Fu)?0#he@B-?E6D@Y&^$n|TfX
zFi{?~yUzSe)<OH97QS-aS(P_@<-EJ_AbQMH#OebVAe9bNhlU$`HFl(2Oz)eO`*9`~
z>BuC<#-j_-=k^q8r^}r2u3tF+>0ucr^w@L#^P#Jq+%{_{^})>NIVm|^rs}v(gaFw_
zSHDR4*xt5eeETn+(=wwl&YFh-UOxQSR9~B7oIr^h<G7(zIl1kWbVij@V{S*AH-D6-
z1S12l$qq$Ztb-~VKD0-U%v*%H)F~D%ni&-Y%$$Gay6aVz!$j_8CJT9OkM$1q;WU?-
zh<;Fjza$A#T}RoRD{n#@mBEqK^~2ktdO>kTcxH7Y@FBd9H56h{iYIj6O*7os2a?mx
z$FSFS&UO7Nbz|4IOl+!y=c+~9ZeHGj0S+;-)&g&9wIROD;Ybg`B*Cge7caVIty>`>
z*-Et`dB!IM6jHVRg(X(jE_UvM0kIM0yT-Nf1{m)KkPI-Uj@?{sejS9crh3<h=D-Mj
z)gl%yJ@Fo$K-DHKZrYI5Rmp0t+sK#7WXZU!OuRW@!&*qYczA5L7{N_rduI}^n61KD
zrq!mVxoPb3MhFc_oWJz<jLCa>jX`tH)CZOac`$Z}8hTzwviR=9TU9nSe`^YaNRN&t
z;aU*i2>_mHU@l7I>%2!)zQntihB1Ew-|7(ntQYGfglN|jO%e%|eX4)e#KHvR-vjqm
zzUiiBN@{R1W4(9$Vtg1#no9qU0!cYG+vd{@%B+5qja7BcyrE^CXw%{J?$24yR<K4Q
z+-=!O-7xIam6i_#r<?29;O9d4?JvIS2>>3@oCj<RcCh&m(F&38#rv<1sxDBa0~$O~
zEz)#B^QXzKLIl{4E-yJdu>Ur{5>Za9VdE_<G5E~;=>4%KK4<xKl089gUQ9Xi%81eb
zm!l|N!%=aDq<GUlCj99SI%tr!Vk}}K=ThF46CV-DNn12^s5$4|N^`@|+(_BV&lZWg
zsiHpzMq0du1w|&e!r=zH>0Sn@I^$xo6gphl(DUZAsW;$o2VbdBHq~SQ5`t8#6{k_B
zNNF@_&bJxHnG*iPMCf22BIfSnvOHd#QCMJ*ipQjvE{Z5zH)ZD4&?kA!<al^STXvnw
zzNf1Ot{r3VX3m{)081DMsiy9Y!Su4b?KAexZeD(^O-(=TO(HaAa^?=mrL%Ww!OKO^
z2j?wCX{khSGPpe|nfhPvtINfCi8P7!fjf(^WpI_oY%4vqa_z!v<wZ>f<fU{Xvpivs
znt21kp0+Npb<(e>Vzs)_@uZ<mxq}xkTz^v{#RwkL$)X-H%t^v<;q2+{K(z=J#n<E2
z#r6I<=N4V`qT{$BoK55p9mIx<ydA`+>wQ}6^5U^79Fk>=u)OP}W_#xh?FFviOFJ0i
zEU|EhUG{(?YR?QZu-H7?&XLBC$@d!pWhKt9K1X=FkKqZ}Kv(krI22pEeC5c9Pd~ih
z^=ArIR>KufoI-uiXB0h@TL0Ng1|OH7>dTQ>mJG+ps1B0+r>S~!!Ho%fp;VO0`#X#M
zn7bmK)o#aExsof-8ziBIz<vTC!;H&Md+Q9aewSq8Dk>QNG=d!t6RzaU(KS*{U6>2Y
zNtax|zS`PPqC&ELzCdYo^4LvI;XSu~ZD=ViUwoJ1s~^Oeu5UY%G8cX!Bl!kXhoAoW
zuPF;N^l}VMVIi+^DreaNkc1Zd);d(&lL*SVaK2w#d<}L1Q)^(311t(<o3fmXZQ>=V
z<Z(W7wU4-8id7=k<GIz<U&FtfJ+$~plkfuVjs{6RMl#e)I#x<dro|%F*Wr7ME!V-d
zN6oc|;+}V0W{If;Fs5m(kBS9kVt?6}y-}8Hi&7awCU0ZzMtaGc8C6o!8}bEo_=uH!
z?4KOchSw4$b~_?Uy7Q7+k@OR%i8klD7c-Efw4B^8d;_%_7n#B$>Ax09&s411SE<|{
zG>(|H`Gs0+>x?nf_$ELR*B`^xK+NtJ2Qe9lx`b2V_n(oVsFPamC^k$)#rh}iV-kD`
z0L)85ctmZ5$Y$J2@z@&mSK1sBRRYCFU?YJM{!eQSG#*`e>Isq?$GTN~n#mHM!xAI=
z>E-1&atz(@xh;Zjhv_#D{yPlWAHOz5k;%%L)zbG_C#G4KYQQ^I<IP=p9W{O~cj5&_
zpmU8WV_QllDRX*Bna4&b!>M&GUAu-M|1&sIj6iI0T<zJJdlfp_LNN&jVEWJJ$ERzp
zvIAZ%nY_Lv8DDI&R(QR#B-$s0ZiDpAc3rH+@(&`7C5P5Bw6*gbW}eqO@7_}uoqt`5
z(|Yfd2v$1)>pzIsE<8KVBj`MzwHI!uu3cymyO}AZIk}cRFIHKhkMrtJt3H=y=|1LY
zJ!)F*3!6*8DzYea2Y*=+goHVPT4L=CAV5OM5PvP%d3P9FIxnAdv5SOq_qIfu_XK&!
zYoVtu21c*yQR0W?Z!WX!@ZSD2*Ch+?U+-9x1a-C-p7SP7=sIuV152iCS|4r@nr`x-
z_bkNiO>LHZt=36t3-d}G0o0*9-wYBLgdESLV9tmOs9(A6A6k8GU)ii`!p?%|@*Miw
zF>c=08(8MCxiiGE06OAk4(c5jR+awuLDn&9HuG?&p0JUV4<apMUC|TeV;2T}UJx=g
zX|CCDtRTsqJE(Ii>IZw^=xE}N?Guwv$UiR^oen4>Xc#GbsPnnF)Ez2F*n+1ULH+lu
zl-XwXI*P8k-eYYIueE(&hmf9-uRagy9<45|r}@~YnC3~gI@|q}#_aX)b=8w9%D`mc
zs;Y=u&H8^g1oW;|XrvbySxA@Jd#Ngjz4ZR_zBu+graXSWVI*$zNLtdkRucYTpZ@or
z^sjQ&;Xx4uiCun6R^Kh8^D*n09~_$Az0lJE@w$1VbG<l^Z%ryuJzJF8mJFXGh%84g
zm3hxQ?6dDbCQ_7#3!AVin$S*!)Wu=ZX>BWLq-4@51Lp+#9SrtfB;QM-Xn*bYZ9toN
zECkMgpL#>Vr}sTiL+saYy2j##(HuzKu74ei*Ad=&aeXOG6=lhUo}b$PpqKXCU6DR3
z>;f8`LBm|m24Onckt9pmAtU%auT6tWnYD^Ow{b;vxBX25V1-hxXNU|yi2bNx%&C!9
zzEZ*Fm>VtzuluPPZ1CRDBBgOVSU>zX8=JE$*f{9@@#KPBkn0S<`1D)5!<Z%jD$Y?p
zu4$fMM}W5Vhs3FWn8@GAP{fzUq(A~}$rtlujDm1+4ojiAb7M>JvId-CUGGY=SRSta
zAZ4Z)F|JV&6Ur@KbL%hKN5b8Ri~OJHMx~%}JJ)%E>wWPD9}ou}cLT)HLwGxZ{Y{<j
zDa_%w4V@1knA%-@Z~KO0<kL;0O=;7}^Y-P;>cAzaWJ4rBN{VqxyRoqqVo9pioTH83
z6y*goOCxS1msf(ys#-_^G^Ye7G_-Kg*on}Yi{_cixQ6|W5kMH+3JKDOg*}SiPHEqK
zoYKJIAz|FD{AGt0089~51_PcwZqZl@2cEdyW=w3o6si-^T;`0)Kyb%q?~U;1$ZzQ-
zk&?oHCF`}(B0ggy-OTIjm^v3UA9H3V#rhpT-k>Q!{{i&>y}A!!vKK9@9m{WC{HYvR
zcs?M<5;wKU@hzl5KqH9b&iUg2aE_IA<Ly&Zl_P9>yW`rHfMV8C0N{)QwQ+~1Zu&Ah
zRL}(jHM(4V8lV<ydA#m)%<!Iot<zDdG%S-+EeS_wE)aX(^Db1D+wVS_EHRknt8mi>
zCce>su8Y#twXnP2rp&sZcB|!a+?01!1La&UZ0hK%Z5>@)&+Dueran;X7D99_oAaLI
z)i2&T-64In(B~_TO3(VUXraG;7%#ybbF-J_JqQrL&Z>wyI_J{yHUIo4ZO`ZBg=Q}!
zza<T`k8cD7QzHb0F;0)4e4wy(OJvVA7-RGhPBGB61*0B|ONTelKZF%g+5PzsiVXZj
z%)zIR_4;Ri(bO_TTCd&Gajp)9?pEa!k7r$B_gr8%GZ(0iz9^1{gn$}=l62bGtiq&u
zjHK1(o`t8sy5I@gRS$0P2zC&!wXO~NI5SDb`WMoH3KW<5eAX25xVph4tIz~`js9%4
zA%oulNX3k4gK8^EOG6VB6jgEW&^2tumtF&~D~E{8cNjo}gsdTudQoLZHz~d6K^3Gi
zD~YdV|LoQM!(ArE#7TZ@Hsp=hfEk$L;+vQwHfq|r5qt8tGC?7-*XPI}VsUQaWZJfM
z93dGx&2DZ|1<ZA^d>^zA?Hdr%x4vIb%rN>^Dmefrl{w6EfFPcj!u0+I`gF1Xuv@V2
zS>GbuV~<V<7l$Z}F`xr2uUR~_H!%tWLC{$1^KP{O@Q+22$XIJ)TK{cfl!Vg40wc4C
zS#8&o)eu#6fTq$u%>&hS<LVWPtZ1T%#wWabJTG1bgoRV2rnh3Ll@9C13BZJrETqL#
z`}=R)cgWj|hcEiaqlbe#yjthGv{)SKUGrIyBFZS46C|Ohz9%2&3axkKHd&+c<H4O4
zh{Aja<fI0ryrud1j(Q}REW()fO`Sim5jNS=LNkl3`1vdofIXkU^UnQ|<x0$iOtL0@
zZM(twPB#i2s!Nu}R%4Zc|7ii#8lPOjCRm!3ax?{7%q!`ovE<`?4VcqLj%hC$wXeNu
z0}EHlMQ;&0s*JVb%e{sZ;P+bP=ChSnmVM|@jMl09ufJ7h10$7rf$5xNhO3DqWnsY~
zqN1CQm~!|&T(3PZ>8hrs{cVqj=XKhr-D}TSF_Mw%9!X;@yZ}8E)W@I>m7ZVN@}E+Y
zN8`qDqw>{aAV_?ctUT&}SHjr93o#kBbM58HBqwW3Af&E{O4+B_N<bNEnC>m&RTg#}
zq|;m<Dg_77cqX`NK@0<aDwsL6J6R9M@%#>6nvD8W?Fz{B1RXPwq7Tb*sN-fVlLSjO
zzV33>8!SLS0%(<opNn8c6agbN<k#+fo(gRLlg8rG&KETJi`e)?I|;vip_M}D<<BNH
zswDkFrFt!0o0G0qS<tL!qSlBU{ty{BkOJ`q`f!c)s|D0*tH)m+UN}x`%`Ys=<X0b0
z30FN}XorP$JtumJ6lx3%C2hn`WG}9J<a2+Zf0oIIhzVrT5m!zgyVs|Bjd!w#l@9;L
zHLBV^2qOvJx#Z{M;-!a{*l*>%SCj9mbvD)_Dz1I!DTMbnrvrQ1=IY<9VSr(<$oq+@
z!eL{Nx3qNS7(M^uq2PM#@g(20o$F_$fM->Bs=&`fVT>6YzLk!euCaZ5KB+~6?~%No
zl|e5!{hq8f=QAL_5QX54i#9Yc7l1<r0owipBHMPchvcLyz@KwNaGeL*V}?>kvx+e!
zkskF@Uml>zSo)FRB}DUiWif}N3!Dlmpd4p_pV>u6(DPeJS<<K5o%StVQOKt7vmgpS
z9(*NAr{&iY45}e&Pm7<r&9MMpA6WFAu-hG9eGs}?N_Zud6zhF0+6v)m_rX%{uScac
zeS<ZEyRE3GRKA&<&cN)LD^mGYHFH#G!GBHo#5Xu0g7YX_X9b;{pDBO&I=OUHSv|#c
zfHd@-ntINni`~k1jfFl=4%Wo36}1-ws9)>v{gpk19uAXVwRCs6k`w)&2Jz;ZQ()4?
z^9pKEi0UAobkKFz`;IMPPNJU<x?2p=6Qkjk<=AgBFB;-q!`A&Z^Q#2H%)asEcX2nQ
z*W8>ntI~6QX1`-R`aUW^U2GK0{T9fP;G^@W7`W_Z8pUULy257O^}b><R8^hAdaa%q
z6NS+T`7%jNC+6pkpUs;hIit4v*mXFoL9Q_A{GK#h{dmf})rs#YvIg^e?ywr=8OR5!
zQ3_`GOOe6Z;9wHPDzU4-mz~Khm61<)FDLI|vHf2U?2#E#R#LLb@NSDn+m2rv5pIk`
zcau7{PXl$ctND5(T4Hib!Ztx~M}^}}a5za`>epIc_e|g{cI*1rZU!eEtE3(Py~$|$
zt!aJA^nBX%)6vLJqizEFc;DIEy^CZD8=>CYs3IXOEc0ABQk%h=Z5#4=^m#h;nzI*r
zTC=Xy*V~HnKBnS(KpIIvc|L_cyet}*W9`&jbiDtQUHT@q@XP0crafZ#w;3)Ly`4_q
z!k!nNH=-7o4kq{A5nlwBC}#}X8`j7aq~`Iah%Tr*iT2?~duXQ-0*xH7jEg$9aU<Go
zcl~4qXH&x@LD425CA%*ZED{%1`J2g+zIn*N{_t@;J$Bx`SYWEEX`T{nbac>!g#1N+
zI*gihdas_)e6xh4=jIgyYTVYTO~HKK)ae}n5c9VcIsl+Yrw<u`d&BYCWv|QSbk1!X
zo3`!ripE%+@`U{9Axh|rb%7hSmFexz$ceK*yvNU*jJ9oFp`)ZyETn%Wp{+w1X=&hw
zm485KQNInOtzIm1f}H}kSMa{$daR6ZFlvjhA;!nRhxsk{c{i3L6|LtLGK_gNKK@~T
zfw9iBX#A3{EYDh(DZ6oTt^M1P-BZD$Xuw8&8d{QI+knu6&l7HiDRB|;0g0fMHkE$0
z8_>Sl1a!X`(kgP=77#@#i!^Oa@4M^VehrxOK(*1+h6=M+ty&fq42zshmr>nhbUrP<
zTCQKXb-ELLz99BST|i=%OUSw}_yov2gCns3KulQIjSxSze*4PlPX1mKqxaziFtdPL
zh+5SLf2{z6;<mH9mu3?ac6$eq(9-JW)onig&hF_9yfKMV&+uITpTu^DXLzZFC;iJs
zXz7~?bXpE>Vei7!0n(AAam_JSr7tkRd#C#Pjd<E#@83mE^<3r#Rxn-yR%!f9C1Qkl
zwa4-J+C(H@Fgi)_=RoJ38FWqPDJ{$FbaqYUzbu&dEHj6xsqDjgRcB&gqLrfbYGUr=
zzito@0CZcASNffOC6^X9$fV)^Jx=0>G-CV9Y1+fabBq*j$Zyl_5w%hth0M%fwWwCw
z!~v|$Hd0j^)4SZ|^c-KC?f{cSCf4%(Vn*Nfha(da$JFVru(C0`u7N|PSVz3Uk#Pc`
zCC|h%n^o0oUx%HE5&bJhf#j7-<#iIn$W{m5WA47Jpq0(0F}5OXAj>PGjirx)(7c6=
zV1kC*hB3}qxUF1yMk7O9ya<=93W=z>2+l}s6#{xGB5X|3lf2;TqYB5WMQ~?A#C{qF
zo>$W63F$}tzV8=A{6XfikBwO82DJiyRyzp2WqEKHMwXYSK+B-T4ePvI<hs2~nmAYN
ze0~Qi7jC|oY{Ya_!EU*|e;v0kY@iFZ1%i^Ew9;x##<N?tFrDN~5Z>m)!ri#vwe8DD
z)29Ek)O{`b0r0wK_{heN9}F<+YSoHZQ;h5lSTA*s+;@-d(-{>G5^0$P4BvNAy#`Su
z&*zU-zequHNRwSaV5d~1e=-wKYtH%cRgY%i<okf~N}t@|dQHef*WR_=#&^{en$^m5
zv#CrnOqOGI+Y_cE@Aq6+NO6clNN(*;fn2h%oAut2&HB8c$q1JIy53}^hxqQ@`|@Mu
zD;j^mm=A8tsi}jB5n!l0jc;ln3X56Kk>@1Iu+jN;Tvxh6*iSHdsR`MW6xEZ_kK_|g
zYW*%2hS}t92t<O}56|!BI6yAR%EsxW9YgmMkF!gt3dKlB-y6Up-ujAne95zTlUj-a
z^lJ<jKK<Oeof#|M@+!`uErt&Y>O%w~;tlv<2v*Kl9zM|f%6Si{8_!;>-3_t2DXKV*
z=9@hvJ@+j*CY|Jh&tq??kZyg)`rX60Lz|tA9P96nnqPokP0uC?tUfsfY}d;O@$C<^
z^qHw2V@-0Iw=bI%3~^{J>BgoSMLt&T*ECEK(fo(zr#B&r*tP4ZYJPVbpcUFDhu31T
z53%pwb`LAyb58f>)kOA1oI2IivLTUXW=VkcC2gym?T=!mW+v)%p52i(r}rJErHL8v
zlc{?O83GldyJWA!`khF0uP-==n_bKk+$;DHXQhj90!sj+-*z%hAE){npbgoQc-(vu
zypmy7Y1B1cu3xoIrZ5>bsx#pKl_=W!dtY)#dWxBNJYT~G4=BxeDhFd?Qs6j!t&L9z
z+^|(`HG^T;u;dgb<%(^9v*PJ^D)m|hhHLxJ{um^OWeagP*%KIj#+w@=uzi>{-&TlE
z$)q8pGv_&Ewk!POAd&wSuXH9)Z=X<x15`q`FtT(ib?x5owD9hEP!=I?B6H5viNEPX
zNhuc=w9T=2Q(72}GMiE05NJr#Gb{H(UiG)mv7K2oMph#Y#rxycRhgL|k6)ei4}xIL
z#0d~2@r3Hx$2r%<@(>&TR<&tv1)y2PX>)OEc4+4<oCgz;*isdqVZGr5@&{#67?v!j
z>P(+<?zxhEDlM~@&OdT70GQG(^F)ib{==jKFr-p&>E*Qj$5;wu3U$K$z|ag1=EIBQ
zl=J{|^WR#2h8#f|9K~|)2j9~>1h6M8)}uQ3&7LW;{dke@?ONL_MiFFQY`%E*J)Le#
zR83t%-K74<p$Ma;As${!X|`3JVYU2Y%_qA6jNXu6NH0N&FeqjL`+;Q|hlOs?oJ$bs
zXUK%jTxOw~Ki31PGZYfjgrX+CeHeER;#6)kn>Ovz1Lx>l72N*+8Ir0Hw=j#mJeq%>
zP9i2^m^Wj@n`Km^lK(YLjr9tRY3wlC1ZieAS-%`OKesFr4SD?dNw(#+VFzJsfS}y6
zKvP#|mWyZ(ka3U5gX@u#O@G0v^-3#-IsBsek)1rWuef%Pgu0gh&63;aXbPn)m7Ne0
zb!sBxcWnM-BRipIA!l~jh!);K)FCx*C`<FBqpOcN7B5oS{fMy7sH(C2<U6J5F>S8q
zZ+3^nCR%ol!tITLjY5&;bA%xDX>Utlqy!>uXi+FtwrXaXH&$?+q}8F_LliHq)i^$@
z&yY*Ntc<_mO6va?-^UwCUHvP%REy3k@UCw-D`cgu_k}qIr5aO&eDSIXkitY!B~NSB
z=k3_Y#7UeYxR2rYa#~_ctT@N_+5Pvbr(`fit@63y0e&6edcD$jt)c~=;}geR1QgQC
z9j+cwI?uFinOW3vtm!bjF09^;O#dryIeD}bqi@jm0`G+c#c<G%eK>!EQRvOEIB=|O
zgNY^2lDAWd^pljI<I@TB(N&CELRkdsH9fRKncl>8ch0TjAq?B?k*(;cN%ddGWTm~K
zFYEaf;it3+R>7gupYH{H+HDuZ4^I*A%#m(CJ#W6U(OdqV<NIn5oBp3PS@mQqI8ag-
zN7Ge5@p!X`ALi7$YuG3BgrL8*x266d{5Jxl8W>g~3O8%tY)|IRCL+}`B}p*@Ll({S
zlDC_DU`4KL-J@s@^r41$4FG2R<RZiRp*-ZBx4N-zN#(lMhwHunZFO~xkdN=v_9*g9
z`5((#r=q|n`IM&S)k4kjgQWq%;I*~3hb5%pIeGxP?5`f!!DeW3dePfq{OAYTm{rZF
zZco}xj#d|!lm-6)NV~+?@HwfuLs6Ny%2&t|krWi_+xk4dNfOdov`0q+Zg}whTmLlE
z>8f@KPBX*gpjN6}>V8L2fG!Ib4;)V$-f7O)-Tz56!3ASt`agCqS%{|#^bkyoMF!NV
zf_f*~xLf6tN1Rrp-&J2ryHomTaYuf!H;@+v>hbqC-q`nkE*kjPX8g@&b*o>)FLK}O
z0LxzyIW<?Q8q52>AqkW;tyDDKBprMHnu}m)*?%I>!hTWS&<Z|nKDHUY=1Rkw4+RTM
zXVV7|Tc+_t#HQcgLOU&~iIhIK50%i25$%U*+s>K|j-FZ9`*WBSyv6ikX8+vK136J2
z6|(5WuO7_MQu@5Z?b|0fQdyPM+=qCH3xjkF!s&G>bz_vnMTR{AB*YiaoqnX2>Gef}
z#UGS09SiDu1<b;vdLQ~%%y<$~*8Q#sSIu=`f41eH&K_V{&NBeU58}KF%~J9A!)$IR
zk-i?Az@Ctc?L~U54C10jsAKC_z3#>*@0&M85Ra*`@|*Bpdo6h1ht2&wP2apC=pBpx
zF?O0&*8k&b-!i>{Qolo+yieia76WC`n{+RGcZ46jz3U~wE4BuGE+c-4j$oM1FVKbU
zbJX4A?XAN5mocG^J~Q*nu7b7LMYF=kym`J0T84aMubeNAcPjww4x_j0S8Tg(9L{)d
zFfsNp(r&0w^dxmU#O&(IBys3c#Ib4db960PIL;#Y3ybB=FDsX};B#{E{ZHT9o{yY%
z)=Df^*mgTVRDIa9?Hqat8P1Vr9+?JG*vUV`KvSjdiQ?1R0^-Bh+0I!@-Twi0!<JvO
za%+=f!x+FSM7;>4ES~Fil*ab+yP?|AfF#(dU%M)zzQ;L)soi}&$00q3)ySdc*Mnie
z^73p&Mx$u!qL7NfYKr5`D1+M1n_;AbaA8WzY(f@(@kEO83`Oak5#r3vqY4JR%M63p
z`(+HJ@0{O=@4w^t?nAW3`vRCSgzk<|ITwf<{eavY>WFQ63sRZgy~de3UA!tdeq<xS
zB)f}U7}AZi%!zj4=oNc&R@K?x{AnA=l&OV=n!JGpIp(w)5{e0l8`=)~n{|{~ZYDp(
z5FwB^T67H8-V%q4J6D?4&Nq+ORd!W#1|_SxyFa;wZ%QcM5sR&|^YCe{9eW<Jfvy_j
zaw|J$a)wu(+O~weqefg8en6bPZ93Ll$6v5L_vj<g7yOpmCldp@wFg}ErIy=15Bx@Y
z;dl1f!$3lNHYE^1j9tsFBraHBnG8=uXme0D%vx9~$WeQ4PAWy_q(xDt1^kK0y$|_r
zaU^KBR$Jn<?r5?c$#t}COwio-PUv3a{Wu#N{wz5+Gy%E8#<l%Fwp<Gf>eBWTG8XmS
zoG{R?^X`Z440sq_ZGsDFMn@C4on2x->FH-H)nCi~`LNyr8*|xkR{tbn5xBNjN-ym%
z9gaPK6Y5J=(8Xx@*CZY>CeUkec&GJ>w&M0@*Er7R8_s~-h(dvt%PnN!L65*pX@cf~
zML=u9V_$ox<hxdVuw2g$fJ@mmUf#7Y3Ba3@WKdL5@=w)ZZ)I(bze#nG`Bh-RFdccE
z2mv}Es0~H8=Cdj)q`?|VAv7NVV#7rnp#f2=LGe$krgXwRF|EXuOom!J2VdaQh}<;c
zMB(M}vU#JfP94wc2N`lY?Y<UCOxgpYHrN8yb;WsKlEzZT6u}&ul-^4FI&esqq>C$W
z#=O~hswuEITx^~ey}qr^=Zxc^!D8EGL08Cu1^iU7+d*o8NCV~A?R$wR@oFVhmD(gZ
zdDPJ`r+eNMMk-RXaJf^Dp2g4GA17M1uUzH4sA)NK_%m;T0?A3#$h5K-EP8G)mr$Lj
zlQ4<A;}{Axtwk;+n7N^8PWMH~897x`R7~k8CGEs&AcX>^yZ5hl)3h>t4sTZ&(f%JI
zf#V&Du@ZL~k;KietldXabSe6j`|FX%|6=bqu(?o>a&ev!ugDbNiB7cnnykZ<78U~M
zbtrudqVNK;o!@^<p&{!xQesx@h;7ZPwzcy|;ChH$<3%7Ta#+T3pjhd89Mmk`xcwo%
zZWlrigb1WL#}&Du_Hm-m`jK?0N@sa<N=4Dh7?QoM+n%Sf&{8ldteLCFT2euQ0Lp6J
zAZePV|K<i*_q=6TJaW6CcT62;gUhmZH}R7K(I~v~ZXY#KpBYF`59XJ$(7`G3v<JN*
zfQ?V&%k;d$pfvB!#tta14X35!Rt^sLFDbpT7fVNEP3=#e*|2a7o4IA>`SVK&tBtxl
zjNIMedqFY%W*GPqGC1)bcgD*3QLC8ScUuAoYJk9=D9Tr5mMRT&`p<N+BxtpJXfM-`
zXl8mQzSr76?>OL<ZF^4@cj7QEm_&cGIrE_oRa0YG0iUJIGH$zBGG0I~!0aIcs7vbV
zIlM7OMim_H4565x8G`JH6Nr8t?x%SkDhlCcq>;+WZg4%HX@h~nb#t;%WXjY#XY`Zz
z?fZW$BXN5tO8(Yu2e!j)kBOT4c9Qpo^JpG*JyuA7s(R^tz9O0z60&&ODhU$KNA)fC
z-$s?aqdIOAxE~p9RVq!tQRCbTfI!HGmN+~}rB!vf#qu>xE9D&SIP35(AEmKm5;A(Z
zMxn3j;@vc?c78%p-2k$o=T#W&_Ez8fwxmoe6Dtrhi8CR@n>q3CMgd#B&Yo|!3~%`j
zr)$Y%f2a0~G0JwamY7=0$@k53)CR@`O7HNdlA*_1sH<s-EMT#VgXZlH=X1sduKl*w
zHkStk_fck!goW)QHxnC+k8q8kB=P31VHuc#$J;d!xPEtj{=x**?@7m-ET0=9kRRG#
zfZYTjo88=ED}d7Z;hRMdvS_K}4bd@O_^|U33_xDSB9O|S<wP-k@FfWqQZ`P7!@5KX
zg@CoS8;Isj;84`mWj5?4_{l58H<9%1OC~gFF<&x)_Sg&1F{toAkZP>86j#lS;*W7N
z^yu(G9uKFR>TOLh=w?aoEv^+&XaF^&zTi>^%$VW7``$@n5V_<MVqG%KJz;ctl@wOw
z-l0cpe~ezTE+uxX-8hySceUhK(>t>%(lQC7Ih1DY%-M$?I+pX3?@iP`Gt<u~<*VUl
z53y$aD#E|1e}xWOa_w3`9KXEq9fSpQ@=Q0eg~8q67q+RQAvN)HW$!qiv4cmDJ5XC7
zvdM{=vA(aS<&+_3ZXVf)EBC9aSZ>jUp3m;R_99q)K`NVQ2FZB9KL@UakJhvOVPIi?
zd)!DnWHl})KW(zx!2<PL9x+cjauF|+f>XviF3HCVAwe+$ey*{Gc{GYVoBS7KY>pJ6
zTRnfGT8UNN4**33#@?$*GYf59U>1>%R1!ohNu@|?Vm|!iwGntvw1fz3OG^5AyR_hc
zEu^`x%(Mi?h_8GKZUhAjPg)UC@6{=jxV|x@pmopUJB6D?NmLB%Ib_`YFq>d^X6$hH
z-A!4~+&hQ8&0=R&4)(twB_>MpClQGzId@GUApV3%Iz7ED5oY`6=Ll%ZogDtCtDMZZ
zNv#EfX@;~}V8uBU3eQina3qB1<PE(^r8O$vqplW?nP#^I#OxOP*5??L2kP~_2KjPb
zT6DokoWMrv{DMr?X8OQV5?M?pIrS3f`;}4-^9#axK3zPoYblDUo{!;~#CAq?kp(4A
zx>@=^?GizEW-&sLeT2Oj$|DlGy<X795w$|5#q@bK=B{~!G?o^x+8K8~Y@_RS2t-<X
zfg~J^V)E*CkI`a?a=P*YczO3QCBz@4`Cg(p6z0S^gFn4_KQ&x9c{0B6#)*1h3=-y0
zjzx)&WmQhU+AqzGh9KFKO>(@3gHujFl8i;n#SvF{BsPFmYsW&sPFZrV+tG3RA~4<C
zbiR_=QXSa4{)G<TMr4c9W3rZBhES#q+-$Dj-dqxH7$N-l74ix*X77zPMMn8GSrSPI
zVjK?D8OwV@)p<}#B-Oi9D?^Xz3)!^siIeKp42^^gA;QT%GRTP+m77T}<J5BgrW8py
zQali<ctu8M6s~54o(Me(Q21Lne|+}mk^<aaQnm{&px}PX?v><g^Q9DT>enmEx4wzT
zF~R=F6%3B0O6zhtzP-P`{&u{r?vNfkJfE3C#+m5y<ceb%G#&Fg#s@D+;PQ}*c+5<^
zp(=DiNJ_&PMf8s_FIq@TUNL8&FdssK4`^yPD1anlm@hlt*2{ffN>h}RrIB|Iid90i
z7rJ!AhKK;az@bLgSj2ebH9ecUi^3Qdy4*`a#FiZUqX%|iE*KX*p5x?8E|efBy57l|
zSvLvM8RusX1_4ZZa652^58Hl=OpP)6@ZalIjX5kQ(LeUnAhHvgnSmXdJ7`?HT`6<M
zETsw+5;pt}L+dfCP~HcX0<OW-TnrJPpgP7DjW;NtuMe2_{CXQ>d15-4Z;Yt&t$n1X
zABBjMe+$%H#gd5eD<$Mp6oi~$kclL6T*Y$;72)V*EjPdeKz9<c|1B6j=a=Gp9adaX
z80aGcS0NRZndoI?6&k0-A4pz1I{SY2HUDBEdA{(-{V^6Yj2q_AzwXo^hXI7p!6sXJ
zd+WM>#l%midC9-eRqyfaT~R;b46IagnR7EH%{TsJW(%pL#VK{phfcDf1;UZ%-ZKZU
z*URa`c2P5pNQ2imOCAr(YCXTckcx-gtc^QBsilM0lOy+wXiboKBa;|Aq$w+j*Y8Mi
zRV78p6fos<Mb&|B_fhq|oNmE}D?}u_>`iQZY=;5{#=y%TIGX5#+}_EUNulAyVu(^9
zBh-|k?`m-%B9o3@^x!+O+<~8|j9kS2|2VqJpeVaG{E8qcxpd<KODG-E-L*7GNSA<g
zhcrufgLEm<4N7-+Bi&1Pe2?EB2AJ6$W_b2K_qmea6l~Bx;>6H2^wNC&`acYv%?Lb}
z8X(HPypVv-;YjU<A1JyQXYbE(oB-@X|ICR*F+r^19=}~emG;Kp>f^=%S(?J(sq7I7
zX_D$X)S{Jtxtf-n`ij<y3d|-<ku+3GkV?ha6pRUuP|bg^SA+5BCZcW6)1y8x?7@1O
zf+giV3G{)spJsXjCg2j(^h@_dborQ5=cInZG`Q7Hh07KeBAMFl|J~TEQax(MAcHFW
zY%{DSiw+e*5egw8m~u_F`AK4zn9O(6`JW;*J7YiIYJWa0a8gk%rsMcPL?><l|LAp>
zh$#cDLw(Fdf<!^VB#zYA=G@qkG-ON#4UN@Oy?Ai-$HTwlsmN5+xe$JNAa7j)T3sy0
zhC*YvHV@<m3SX{vJAX^Cpo3CYO?&XGYZU2?Kr2iclE3hgr+_K2S*|DmCY?{Tj7G3v
zI{;ir5sDn#-CunfiwosZ4bF4)hl#A3(F#Q;ybC@f;{nT(+)fKVW@E?R`^FIWSOoLR
zea-au{3&l+{-Dz2lxyj99c;zy^|E`H@P>L)$O&lC2299x+i#A|bL?tjrfvWo!5?(w
zg4`e@Ys+Ssl?~uk1~&8>bo??7Nk+9hdIQF6Fs9LD5uqLpj!=970%~=ET77$DH~r!L
z9aLfL=I#crzq7JkCmt7`6geW+)c;FQps&<AyvGq$O^r<*Nq$Ntnl<^Z0C-BOi-rkD
z-=EJ8e0-ifWO4X4W1c^?+tP62=v3Zu?CB)ZPKGHs))zzbJkj9SO-gTm$Di{utc~O{
z97`J>nVU;l{Tp>Nl`6W@!xQZOFY@^79{8Z|8{)iY8LtpV9&g9neDa7z_?p4?wN#+)
z61B~~0=|>Gku}oi3_ek!%}^Ym*rp#hxuURx*T1kFB`!W*lqiAAg)Tw|Jc)FU1^+R%
z$5(q#q1MA(pX+4uGo*+Sup!v8?l=Wv>nr}m2cB_431_kxYa#It?z9|;>c9f%DD)}H
zOm^pZ&|}opf;S<H8pH+zU+A7;cpN`(w18!`VWUGm39Z`NRK*l4OdgSJ*<3<xKZc27
z-U?$n<oo+>6>g6it7Jz4^$G!C8o9~yUCr@);>%b>%W7Crft(~NiljoU1fpyhWhfZT
ziJW7PBnXnF)0~{lRp|z->r}dX36VyB5T#G^s@0?NjHvzdj8r)l9GgWsA#NW?2tx93
z>Dit?e+S}&Q4v1Pq}A2{qrKHGj{)fTVYS_ztZm*k{ajWym@9`&slc8HM%CB4W)@v-
zIv(}In#q<v3y#D00AV;4xU!#W34~cDxGLK$|6=A3$K$iLm;+e?GEWxmzWDzbWEn~=
zbV+~|?_awK7;<f$RJ|8s0z6b0d0lw0g57P_)o842C!OR8=PMCMEfPpVy`LOPbOGJM
zTQQUXDjGBsZx%3yNgf1nRK|m8{S&|%KQUg&?m0XRV&5z{x9Yd2zFSE!ArsyJ1HkjG
zucuE#SG6<yg1Uy+bRv8gM>aklJ~Hw_X{~t4QM)+~7e>nT7VtryP?a#Cy+aTt5pepB
zg(BHCU1IOtPrwZHh$N8O0uMKA8<4ih91~^BU@P1&_sOPc^ZG}E2Y{>#1TQ<yWz6t)
z%CEl`j0$IrY93Azrd(xk6Td|CIL6HZO^t)gpo>BTyanl+-g&H?#8m|f#0d~{LO{~<
z8&k!s@Gk`PDE;YgJcdl$RthN*ImvmBA8zhOwNc_(H_U&Eu5!-rT>?$)_0NwCe8Ls6
zU@P@(KO%tWK23Zb1ZX3ArEAtb$bgt|A;`9HSU1KdA`iwwd(klx4p6@qM$;-%ba;;l
zwVsJbLCH`3ECMN$vko4=>AGAd(bd(ZDBd324}gDnrpG}viX;uX6rlXcG<AVMqK~Yo
z5w>9}5p*p;DK3v67EK70lN%+j-%^*+<d>oyycP?f2Fub2Lu{fY6jHnU<GX7$fK}n8
zf+=1>cC5(kB0k`nfnYfD?9teJF8WL+HnzXqiYW90ld~AIY`pfc0?;G`a?U8v^5TtC
zh8Sn^iX?!H<EY}p!h$lbjT!i81?44%VV^8UY_REYM!tvQJrGq($qpHpzagF>!j8r9
zhB5T0(u%v#xD~v*TT;8o{|)~=gAwqmsWys=`1zxe*`yzq8UfZyfCU!d4tRU@hg)7?
zFEBp2y$qQa9iH^vy}K%-jFG6wl{L4&3$dt(DU^naqSdp@rd>-dA7W%v^Pob6E|UA1
zgH3~XHmLo}tg&^oOxx^=Xni+StZlZZw)S;W>N^=#IX<$TRsj{p3W%z1ukUzGJyX-m
zZDJO-%F^EWm&+zEuLwZ5?z&XiKGSo7Ai(p-1)&oHP+%Jnx@eP5RyrUU^Q*n#FkAL}
z1Yu*F{HR@_%rJhoBn!`?+foMENI>$^x2^m<64U5ml_U>e2A=3{>DmY)vG_lg&PP8w
zc76ZSSQw;l4*fnOX|A9s;TB>9El4G+n-0+6P|Kj=l2n`e(u`cCq`!Y&4=e|8&miR6
z`+e9T;VAPtM={~;$lQklhA!pOtQ;^vIRF#6sdTUed><p+Ji1+{_}sNk+9)dG?oVRy
zpWESkQ`rq=mbG;tAq~KzJou1L8T@Hv0S~vh;4&~8ke%E7!<VN>rGe%iVU!$_T+2g}
z`ifizG$S&&Jma-@&WN4;x_&B+$$|O>F#)|?x3LQDdsR{ljbs^9R1Ijq&Kn>kx<B;?
zR|}$&#F{cw$t1hQHyWn=XK9((nzzPrKtfYgh5YXsQV*eCS#~r@xi{J24mABsbRk9Y
zTrQ8SQpvPRO39d)9krl9j)eumH6F7pEm(1kt0MrYnuPq*KE4x;GgC4v2HaCBz?2L^
zG}S;?n_x3dx@hvC!AS@Uq6$Zik1h0#$~0#)Ng6kMs}auzdh7B1v<eg$gs7nk?9SA<
z)#<^E43^aaKhyL7OI2p#R1~arqp1ue3KGXKsP{Vj@(!~nFx+`;VM~O9sF@PK3)g6$
z2(`xNhR1R@|10V_j(~SG0`+9UwtEV`i=r^uD^E~Kdh4MZ8Z}@_VC7vLY^RZziCLF_
zC#zbf;DeT8fbvZSv4Yg`;+_wvZ~+v6faT^ZS&l(pm&<De;ZCPO(e*K^OL`ou(y>3?
z0<x2El7w(dLvT2eejl=tE=lrFxYrsgwakY4Pm)`sGTkVoZ<NNn3P(TE;?Go@WpLi$
z$TE*Ba<v&!%>M#BhcJcpV43PjuF6pN_<|yMFlPf_>%&UMa(nY=k{f)|?h@#u<dvfc
zR|rZB!+HwyrMX>4ZqRA^WZ_aedYB{F)w#ehh}R^}FpAaiD^|M^1s5zUo>W6L$eFH6
zk|^xg8jB%D99=d`rnGe^7<vQ$IdMTr*V*vS;y}HI*!QecM@czRItfF0!xtA}nbq?E
z_N(~Y@vb}q03zhex3=;ATNDV3${$Uwl0MbZ&GFb^1@jArC2yV|XSjXjKdnlPR@rCo
zT?OPMt!5O>-3^=ng2*khr|?23C4q9ZTdPC?tP=)cbz2~KKi7kPgBft>`O4<_1Jv<_
zIQtg?gV}o^!eGKhd(ryUzN#%N3Qi)eb}A&U&e<`!!<3Ex09n^3<;pw-EGwV?YjsIX
zZEKovg`2@tL0z&JJ&&_nGN695YU04bu?*nMmi5Xxp#7{m!<e8Ft8w|vf{R@BEcdTm
z6PvBVy+mWLg?#g~*s{@qAiP?Q#j{0~znn)Twp@zSNpD`zH^Y3l)Yu$bV>3u0KU`f4
zG~WFdpS$peYAPd_(NXHnHouh?4D@<x6od<V#xo0&EYOkroL})0d9DefZP8DU8tot3
zZH4ARtnOFXPBfvW&L%h2aH=rZ0tHG$)L7Fr>FWLX`Ki!TUN+7pw@iQ6nz5u9%|=hF
z;6trhz@ia$jp7#fCaat?wmdrhW1|JWER8HhRx0u40JSV`0M#N_o!*=p*Oe$rK-izR
zfR*X*ch1%0;=gaxD<<L1GBT<4LfY6eu?2~i&MTj%$HFAO?*laNMhkUW5t)po5M~JN
zz1^C{m0gxwyGs<7pL>RDzTcOFwA|4B6;je4AD)21UpN(i{bM`cV}aXT#(6NKyTJOZ
zv5XVnUl}8I_48m!78s4BLjhFA#FfTXJe_MXD>XGdD=R7rwa40x3pQRM0h?6Gvka-<
zUnCWZvH1H9L1k6ne$wKE(gQAuuX0KO_sutaUDBN9!EV1Z;MBhR@ZihDJp41C6fHeB
zel!h&;8y#`nafx#Z~h$}A|kj$ETL~=YobLsJcGPt&R)d+2YB3THbJrjJiarCV5Gp}
z%@nD^8LZt{t)2Rq{fvq2mI^_JN_4q4HtKYpRn+~Sht*baBr9G#R-ih%;WRojg~|5g
z3VWWT^psPF)5Jrn{c5{UShxCbQOXkCTi?%+I6tk2v?l}UW!-~(Gtr9Jl8~DPlglXt
zD7K81bza!!PB4S*T>f!mH&!h4G9WhkP>3~{#-BOd^lend?n<o6kvj$H@hG=gYi1q9
zY}f$l?GN>gZlEAef|h}JGjd1GRDoPg&GX5?QG<|&bb9IfGewi8eQrN)Ix`z|`13x=
zM|q3GE5i!z(|}k(6C{vq-fVr^huwKWT_W$Ym#CE=$`PB5T2N#fnmj7ZHu+F@V>U1-
zw6VA`4p#}s%m8vE?m3)j8$%+&rej2E(6tmePY;3zsd@Vc{s;XJ+FW*hP2li*`i(<k
zfdE|Mi>#yA*R`Qy-FOLgjn#?Wi7Fp~7jC*}1euL2{gif|jVFpz{(9w_iEZKMmfstX
z`}hQejP3?uaO6Oh^zsS7Q1zZ%BZ*DH1$#QbL^W^nT#R6cr&P=S$c4K*P#V-5j%!aZ
z22HRhq1p0!MZelEvMwE_dX908+G+kXV(QHOW~msZD-7t2+OUjPpZyLjg-xvk`!_6V
z+5OZ5xOG=_d0?t?cAx=1mo=VROKv6QBE;0O(c3CvigNTK<K>Z*(<Yqp%p7mU6bd=x
zqK)=MC;$70{}Koo@IUZO5PmjXT_3T}+@gHW@r$1r5GbrV($9(TkA&<Y8f8K1zY)F5
zZa;ilMLVhw+@<Tz&g(B}mTR!3Z}%cjP?{=Qa+EQ9iwLDc5hED=F<w@;@N&dlmP^CL
zo+Xv?2P-U}XiRpxq6Jg&JF(Uevrfp4W8J7+zGUB(om{E_kKpJ~jaq7%=NkQl1KE_T
zy@Iwtc&tQRV$m6%G}hT-yUt{D??94E^cahw8>w()iOUy)GM5jUWk>Jv?d^8iyA|Vt
zs!M?M)E~K1&da39w|4aabGnE%{ZM1X&pb`SQ^(kt!U_srP|Z$0oN%tF8{W@f+;=o;
z<2#jEMthYCF@;$CAdfOtzthb*%&N!nGWjSflbw|{do1l_g=SSFje+icU798l>^{?O
zk7Pu4b~SSo9=?!~{&^V^tMTL0vS%1I1q%jh5A_ML9iI`QNQ#{uf?xruedOOOkMpyB
zpRRydj6beK->&3s;AZ{Oh8?wd68i%>+sE{a6+dS`-c8Ur?apfJR7@=57SO;D(u-nQ
ziexOD0WqSS)juyOWUqPgVkI%ob6X&udE<e4#4|-Ip92h{l*H(N$;vJz4F%I?paa0`
z)K%4?zTD<VQ^~xQO28f_3fj9CQ1)Swm@&mrGjS?Zs+lED{3IWr3SnrCr9zod#D5Y>
z=BK~$?q5(Q_;@owGjnC0mwqS+4<GRtX;18}<g7+Q*HFX7($g1>$DI_Q#xZ%M0-PV-
zEL8}ndO1>c;w?r~cKWj6F`cQJU3AfZx6b4deMOAGE9eQ$7Z(cmZQz-Yz4Wk^Y~8At
zr<LFBWjeM~^I!g6PZz~AZ#t79ihgHJ?g9uzeL@KKEp^6_hPBOGy(JTqQaL{RIEEst
z89w*ul*HZ#YABJu(~BganRUg*s{ds9>7!Xyd8|0Dy#cO!!(PKkd${$vthg}B$fP<L
zy0x(HuuQdndGIEhQZHp3wvk%2scPl6pwBF@t|^?h7g|jW6C0i0cVBfOd`-<D_{;SO
zIi1e*L8z|6XR7+v3sobYNVa%<d+@EWg_rCS5I;J1!3Og9w8kti>v8sTU8#OwJh|I;
ziO3B{4}|Ab)dqv0C}g~oIE(U83MJZb=#5n&+o-Q{`F_`!(t*j=jm;BE1ukQ-3hmG#
zl5Efj@MZ!W0%Vs5cd=ApYK8{2^B2gw=ne-TC7<f<-%na=xjOI-!@~AN({OLL9`s*F
zMlZPzz4RBuM<4P@8Jm5dI_%2LoILCT?}jpl4VPQjirKqu#jt}8>B5jj-A8=Bj$Fr!
zv}f+eiF482B(gC_6*eh)kHL}ByHSaY2SHNoThi>_=hsLiN!&0-lOktlHCkB0xyc$j
zM0sZbAD+X<1~c|%Szq$Ie3df#W20#apCK>twwS`xl`x@(HoBEnJ~tCWSA&G^5%J2`
zkJ;EwQ1|MCO$1jNsiIP=TR1v>N~60c(j4lW9CT0cL(a=}3t){7HB6O^FKDUe+)EJ{
zQhh}e4mrW?^AS6Hj*ih}sc^cRW+#onM-T>|CRDpgCM~#F#zPdmdl8}E_2H+hbHcrY
z=|st+NN{!&4zuA}QJ1=82(goS9>Q_l@F$!eHqxJ%@4Z5&Z^>EXhQ5BT4f4hs9JCMO
zRq{5O`(#VfFkerPlg@mWABrV{VL$r5a`j;S<ooqO{^Uuuy8ZcM1&TZSYH<ugb;zjc
zhc3@@r>^grNm3E5R@e#i1j}0T{;M_1u7b1awgIGx-D@_0tLVfy8;elW?zSm<cQe#h
z(+hP=iu=i5*Zl>%hmCS(cbqn9ED=+fP4-e8qY5u1Xal<;s(oxUR)NeoOc_}M+Fe^q
z-sKP6vFe|^4yJY=aH5Z~)a89p5QwD2Vg*o7Tm31$4>>7;%3RH^RZUg9RL1=u9fmJy
zglVaR98Kk6Ns|*UNK@+e6pT3bclKe@nDJoaRK|Gk<C{HRp=-?jv88%KNh!JuAcZ%<
zOR7IfH4Jb^?7y}bTtml}#2HbM*<}W4>@>|`f*ICD!;JQ2;$_z9pG%-1lftV9m%;yj
zyr0o-tQ=i5PBMRjIcmmB6x~Es!u!E2?Y^;b0|J_I^jRD#Tu72hu@&M<R_T%IGPxOy
zK*+E8b&TrT7d0LG^Qbl9(M8p$q&o>}JV~6St2ZfQzs?5u2^ZW<<DF+)H!pCI(zIE_
zOmcWJabj^0!;y12=H5p+chF#nWmZH00?e50aSVK&q_Y+OKj_+RjnPvsaT;mrqcll1
z{UByjjiUNlQ>Rj?b!3GT@<OOB)X*MR-^?Bd&*VYq<b9$%EYH6bQowoD{xHVpD>CJ(
zZB?5P8==f50sWp??{4Rr`8z$M&(<(UrS^4B^5Gc}ABGr@JN@Y_H)6x<(<=wzIG(rH
ziD=%{t(ba-Y%SB4##W5=yC#?Mv2c3hc=p4ZL;PiAA_G$^#?U_L+v|m<3}0@T32;2&
zN#Wor|Cft0(3uOCDKI6!Q=@?Jbtgp8n`m-(zYbo?@ZPhgktIYjQqiSG>HLg9DmC#3
zs8QFNQ0~R;VOqLG#(x?^@R@b|+`DuWvScknk#I{#`#Qeyrl|lC4BHTu)oI=4g|d{Y
zc=}V5iesELiem>ESRL2ld9I;<wT<x_fV>e6Gx3^B{DK<bU&I7a_7|%%ykAguzHU8E
z`0XrZVaz^OwQG@@ItbV)8dfZ>@bp97FR5S%p1*=_tQ(_aOdfb1PY|Jh6b^|PqP#x}
zuK!YyKlJ&2)0gZ8zyMN3XmgK`qIo)pmCjZPu2U2xc#;g%f)>|Nj(chP0x$R9vg!At
zaxR`f0{H=8c}uCh`S(#~4i?@(*ul{5EVjhAs3cF8k9@uRp3^*^m`80{+bn`E$+a0U
z0~9vGh;nQe9*{*L2c~EY63{>U?#_xC6Z^QZ4^ux}Q3AiNXF*U9np8u+Fo^Tn$B%xJ
zsg?j;3GgBjbC|3<>+{9?*j|{Rcotkljnl(SWhDTF2b6z!H{F71JLg5CmTiy!6#q$0
zgJ`4(YA>dOWOOOgc3B~6Pw}<pu_<-c>xfNMSBrS0z`ktQmY>39DR<jbCePgvwa3>I
zI^|H}+{}Y<+%z{14v$lSB^Kq%Y`oRTfM(v-5-`6@V}c1>UvsCIe1|#OGxL*0zCGJA
zmVsb8Eb%r}cIdW^#4WHXD0Ym4zRc0XOfWQve?Tf`blpY6C?yhW2$Cx%_vQgXGq>4z
zmA)}m4*Q#j>&IA#lB(=Opq4O(3IJXL3|#?+ss{LxsvArEa+OV=<<B?>h|FJciKE5Q
z*VyCz;DBKz-gEYvjOBYOTO9lXwvH_>z@P$(n+PW>C7+hR(hZ$Sx);3Kw&MDdOlX7n
zX;27>8p@V5s57av`R0=_T^OFr?gM<ds%o`$XKt*$GUL}{cg^q#u_%w-S|2^eI{?97
zH&P-AZTtYzC{mGw6SY^@>-Nc6HDvdC&_|zPp_Zd-2zefgiKSixs|!)ahf}wgGpzx9
z)sp)aEJY1PDX7}xq~9H_Qk$@{OIy#5b(Rtnv`S+(-TSoHBiq;NMn9-VV!lH_{{;cS
zP0{Qc#XyF_-s=X&a~-Hf*D+IuD#yRtT}ky<pL+YS>3w!4#>m0?GDZcL-&httXMaFB
z^5sK~i!+Uj+sAbPQ8Q`zAP06okgk0Wp!zO1r<Jg3lWDNB-qkY`DjzK<ra~M3qhc*_
z92e<ZDDg2p8bWf}YN8B!XIRCqu*%x+mJWCBE~l1t;ns`4Z-oha*lhc@k0a2@(ulVI
zSnjvi4P3oe`ej?KZ8Nziq>cZJQ9ja4b(p|unBZdAR`b_`zLdjohSSBZQGbk}Pi$uH
zT2koWt`G<c+34tc5JhqN1rQ2vPBh5gjR&L7<?XiZx<()&4=o(wgE`acR4XF@qYI2S
zy~vG#keuz#32Z!t3$!p30v=LMKFl)av(9g&2C(Em+jWf5gj6U9`g89vOnT86)OC6<
z#6SF+``YTCm^)#3yg$}-ztIn5M>vx?OVZiw6Qu_L@4Cb-nivaoWv|n1gi?nP<sr)^
zLt+Z5R6Wl#ZHckCNx74vX8-iR*d;0(5gEA&@{uFA9NMXM5fuTdNV@H)2CLd92q4@C
zV)d7<PFsI=TW#Q_F=<Ce?W(BnM^{*32XT^K*ZW|d?TI8yOcIlG6y}l+atDmKcmq0m
z-8ykTlh3IKE;mm6H@*4a2OIc502YP61Y8TZ3UN=;bXAjlFjtG4hnYRC50=ehxtTks
zPA#{4#{dxA91T1*!G2m}(vjfQ5>;YZ)-Yp2C~IsGvRVbb9L+|ugF=q~?E5JFP&(A7
zZgDm>h1`sAvmT{6R~tV@6t?aSuI^fYf4U(E&%T$5aR4g~ig+hP4A%{lqWKe0Ye^)j
z_hb6j)FWyA&0w)IUH~L-(=&)iCsM@>RXmB3q!5A<4&NLJ8>2$ocNen5UJs={e~oh2
zM5>)WC^JZ7v!~9-UGMi)ZLx&q?q`(NYF24q5ccP3KR=6VeQS{9@aMJQ+Rezg)~M1J
zI~fs!Lz6CjWX0NUv*;gPAe&`We`9-r!5ntC>Pw*#2&a}1-BR&P=PK^iv%uF^wYt}L
zEDHvQq3C(R(Gfs17}dO)-!aeJjs8DhzCHmqv%izpQ6(wWmIr7K7)j=YK<y<6RXB{5
zGkD+8^}Ft}rL(0o*@10_T#fwVG%q`UNG?MdLZ;60_Zf#+aGdTE9m+eQn@c-qT84!?
zOS@ptrJ}?-6?{~UWJ_0l2~jGulG-mR6`N`{O9jqJae6R8JV|E_^R`)~$WycMw28-L
zj^>VxgEMUqxpCM7nocqi`B2;_QTXm6f!|N5pF`=hEcC4{-wZ)goCoB(iWzopEungR
zCMu9ZDA!$4VQkE60hT}Yf_i;xMcp9DS5uSygsPFtRgR3Z*FQBE-A@ALgvhV+8vy-x
zzp3J+)$6IrhTu>jgs5e^vVBn`F^Ciw7DIYeA?=bc*%<s^`U2136w9&H45-_y<O?3+
zD^Xm48OeTH79wD=t8`{Sg*e*g40__NwX}~d{}dsp3Cn}g5X65aU<;)&^T1{p)5=$t
zvMlO-wy=PEQ}T1_V8<gaWh71Zvbh_D5lY=c!@#RcR#G|i5qU&?SiBAG17~;J%57p*
zYi{nMGF=XKB(1qa?8!w!oQ_HoA}QM$MW^>h5<qu>AmtoZY@Kuqi-Hv+46ItIz`eKv
z{OS5*n^6(yN2ClmQf%iV2fyv{0>>H0c5ffqnWAO|S6+@kYf(!NIow?@d=#j7`EhU5
zEtlUjC-kvPn|s8WIus&8h8{y+3ZePR+k!3&x|_WZZOrXcbxRN|bx?;c#BqXf`ulhO
zT}G<9{(X(ceyu+zjSH09cV3AFuy$W~F@=>4uZGjGRZi>~TQb^VSL-SoST-e!ezb^V
zb8*&?B0$O`(qs8^C9WU~wmB$)4WCpYBuRxPq|BWLV(Z|db_TVc28OXlq9A>X-ppr0
zW6(Eg&LpjMDa(9USS}OL?^ri5X&z{CqlDqhA}_Wv;5swJ7)i5eyGvqULmhHkD~c@w
zrIqS)BI6Yp2<BjF6nv?%<AJJX3AS}kSJ2?8-DMmd-|x8!uKH{u$fMWU`0{+zUmuSf
zpbt<8k`Uc%nxoT+$n#H{g!8!<%~ap*-O`pNA?M2xUFW-noRtbZU`07R{%o=x7(K4<
zYIr`!Gw?b7uh4Oay8aZ1XYuBX`T%v`?qyNlN?j4IHxU_W^N*XHcd`snKasnI!I5f7
zuepscuBmZ)xa}IFhxnjJ>qv)T0Wjtw_pQS*``39?u?^15PqQdlGg1-ghZ>ksNhc9)
z!(u->;AAgBSOl7uO($PR0)kBSZR$L3CTSEOdd+Th#4W&Pf}AmYI=IBL#WGfmd4Jw^
z8Ex?HJW2u8loyYe-S3o{!vp@5dlj*11Pcp$oHXYEXH%V2#tmUIL!pAf8jrm0+=<mE
zg2T6?6}IQIJxIEvfmO!ysG(Bw0Ias=3pbes$}mr^#QPSbhv<iF9tZl0b;@||_ARo-
zv?zX0S_os_`ei-&e5ls~j1kOB_#mhl-prwpTUp8J8s!te!r;xd5E1Zkj{5%r_0GgP
zv4#OLUX@rQ8KpCp3O25eB(CU<FRv59DhG-zqoJ0kSuiLwT^t|R@L2!72SWhv5eJO%
zka%t`2~iO>GiJryr3-7af#TCgY+)2OP9%Mek_KA|D3#5@UU~qdd}{OLg<+)3K4Vb@
zU3*kT=q_>~yX}9n@v-=*f6F?6J^<$syuZM4b!)eMPB+CNxx-?IfzktkIgsZJ5%P>X
zr&Wb7Q%US=;`FhJVgu=Ldaad8ZOvJTc!-eXNgzQ7yHMJj+aW?`FvIm(pR6aaz@YKT
zX2I^`G$Z-!TzcbmAQXc6Fu^Zgm1^u*_6Hem5b!=I500eQ-q>-pigQpmDnkC)_%3=g
zJE;Tz4Up3VG>5H)A;=QQnnl_gDFs%B@?#_%2q(xse~|(4OT-~#&7_??i;7U?0|ji=
z?~hJA=Z~DVf6M^F?pBLyb_W)9`?i^#N%JV>WKAz>JggX{NFW^m!|LM)+qri(dzRHf
z6YoSQ5)oKoCYtH*HA&xdFRhR=a?^@Z720emZWiT2ZqR|fhKW5S?=u8Vf9>~4KGAFW
zE4sqO9u74Vl(T&OYi2ZrnjW$lCBjmkhK2oUV_Yt{V_Q$3ybT#Kr6{f>hM9#;z>+AD
z<gHQnvUyaEO~!Qd=<By8O(e-hs?`dv_>PEBZ*eiU$b_{qTg^C$I19QyNa1_5<ZsUC
z1M6;qjX<RkqHGUvpf)5*wR3o)j=@Cbnz+{NC1WWcsM4v0vWReD;>+CG3;Z2bf_M_$
zug7A3?hgez%f=J#JeR6YQg?B0e+Kn9>&GOd%!YZc+9;1j$FZxQ?=#6E0C1c+5tAvl
zfBo@!Z|Tqx1rsZO^6rS*#U8Bl;(<P)V`BCiMXRV`YMWWD5CdnxzYI%XtMZ2pJx4ob
zb+w+!*mISa>v70G80Mty9R$|>0M{#6X*NDNZhYl;Ee)Tt;upBO1XX)KynZ&%ADR?P
zg8N>8qkYUO8Bh?anH^705m|g(DF<haUd1q|>vwS0+1zKbMwZMh&g--6i`YATA(mvz
z@vi(sPdQRE&II?y{{OTI45gQ~z<55lq1@op>No7W28NNDYN=`N5l4=2qX}ek^NlPn
zl#6(+MRnt+HCjmNN<(-a7)DeCs|{X=mw2V2hJ8}qtqTH~c67&(nND=ax>3t}WP@F3
zz;iZQ)P0t8!F2NOqVw_}R){HCD*oQT%30!xaE-Y?3i3z2eZo>YKRai%H`Mjs8|<cv
z)V8m`D{t~xZL00YqFn3(n&<wW#UaaK%mW6^R=)rMyC`uzKJ-;0kW|nxDvC9Ek=g$i
zysP*2)i{2d@t`SV&bD!(Yggh4W#(^%!j)~N&>Lz9+W9+$=CFW2Of^#|D37COc+P_G
zko{gt!256Kli;(Bpd6LtVeP$DvGmzXDC1wsOjgY8SBLG~`0#P`zZ0CkI}7i;;g7UC
z<yRSY7iW_s7ITc8<e^$_@D2JL4>UDsEc_zRk*rIs?i*pq(T5$V*?zQYBfjVcCHeiw
zyrsQD#6R&l{^K3gLN4y?=H}u8DwiXph3{YQ{KWfan-IWD5$pD8pp7>=PU4k*QX26H
z9^SjyTPntC=ctbkWE|SEGaA9-Q}0ZFfCud0?l`izUOQ_`OO^Sr?lfMMb}{7g(`;HZ
z^mx{fO7YEIQ%W`IfG8^ZqGiW0>J!AY9|K#?V$86-KL?KF{=Bdfjm1o%s_vZUzYjo4
zfdOor^T0*yzxqyK(IroT`&@u`$9`-y3;j)Y?04>6U;m5ROXo;bbl;!CzrqNT6ypK0
z>)?%{BZI9$J%A{6(K@T9SSxi!O=`;i=W=oNg0acZj+@^;useCuo0_}1&+{>>#Hv<V
z=awN)p}jh~CDrwl^Vbg%gtKQ){;8=0`!o-j(bPkew&nOsKf6<$O@7L9Td>!ayR#^7
zCg)nSYwGr$xJw8+J^#US(5KW%f)8D+XhEevwHlgf^bYR1{kT`?A5Ueq-V8nrs*)!|
zYV1I>`nzB-aFKu{3mPEd1G<hcX882s_XoRmni;97JUcrJYK)ckTchv>s>qThOp7^g
z-nQlrtPgtTg$tg0rpA;;WHqy2E(Xp?6#J+xNPtdx1=A_ek092eJrc<w5m1kp6z9E>
z%+eWeQ}bxy2#NjZNX=qnRZnnXDH#Pz0#8(^6kTUhl}88Xg4%~lb^Fy=l^;u(giKt3
zHb9Lmi)?dTn^@A*ISH0d!x1lg*3`z~-PqWv+UBt`CglKVLmv0TYcfCm8h6&aPDD>s
zowY@(>vq63b~4Hz431)ikFfyX$?d+e{)3DpiXBTECvIZKnDqf!TK*qda3oIE)Hn9S
zZqh-Jz~*hVVl-Q_VwGP(5S@I<dDaw>5$NyjtC<SLAqSlbo>JE@ni;m5B#Hn*vF3M7
zD<RtWP7FsRWqRqPI9nm=0b7~xANuDO^vS0~AMW&&Q(isnezx<h^2sfqaY<Z*PQHOc
zuTsqm`0sjC2N#4b;ePR9`TX~sZYY9lR*STxEV8HvC6AR#x}hDi!5hMRSMx#)ZT)@z
zNFCxH%lZ?{;B4+jJcp|N$qHj|97vgycRG}S4sWSbXe7v5M0Rjg`h27E(Cmcd%{b04
zTb`eMa>^90sebRG0YYNe3GC`CVu&&wuk9O?-t`2ez#3|R@41=WErW6DMx1*#U5~d#
z&Vw@$5-u}Y=Oar-Z<gVJVT4`XzPR4GpdlpS8$M``4h6kg8++=lq-^6LDv|?zI$Ge7
zTbKUviz~b#@oNS1jJ9EU!ay33h4e082ME`J7OY;qst2Xh<A0J3*Z=J-1T$vLusx{5
zBpj`%vZ=qsMwLWjvQ=5J6#a#^dLypa*C)5XjAdphEGRUu`lbwmTN>$*(jLWTbhIw5
zh$zuH-}^S1b;ieSZBH5_fQkwg!Ajo*m}hMZ?bO67hl{+vxNm^9AfXAPIx*I2<1K;r
z=5yN;`Z;<&5f2Ig3i1m59(Ehm-#XGo;+eP0rHY_&AY0>Hxm|r{W%1L-sZ@1SwJ?NH
zcI$m$*XBFmF&5zG8r9~GVh*>gP6W52A>@r40)0KaaRQ^C2)7feJ!S5v8{JwVuqvON
zI`fR14=iVYH_+&l=j=*?0>PYH>y~MmrS>(?9@_nBd>p}K_A5b^RxK3J{GNtUJ&9y6
zoud^qSCtH|q>;sj?P1;0IsDn>=n1Py`h2zgkopp(B+u-0V;FHLiVnCRyv1)b0-g0P
zBLHVVvA(z#zJi7*P9YOqq<)$5$;s%UX5;pi#ccfdyx#&Y*+o9I-z^Tg4h%z)QFTCR
z3_IGk^}MXQd5emwmG;xokZ7F}E^XV|TT`p3qGJF-ml)-gu^~w&xMEz7KWKc;sPtpf
zTewMr3r7Fa#^)rDxwFm!W&xgj`LGsgromEy(Gn0p{CKRD-K7ryvJ9N0FxCQ{kXz@^
z?!{PVrP6%1*fBjv3;dnHaeGzA#1w9XeYOH{ja{25?oR+N%bsjzTqeR;m~X{y1j3re
z&#I5uz2_w54pvQ{lu6gGDWr!X5*wrF5Zn#q_=P7>vQ$^A7ee71mvUT(GnmK8T`#+S
zWeF@r?$3pSk<k_mG3K(xE&v;eh8OeOb?NU>DQ)sjd8S~SLXDmM#R4AUd|k_MoJG-H
zc#hAjF8A6gayTN4@odB5+VMPJvdlhn?Ybpq_4n}d9hat-^-=nJhub~Q{U6^d%DWvh
z3nbk1k_pOybP(R>Q6%7fnOQXVYk{atb5jBNw#D2fhXy3yWh@L}r3}qwdOTY5Olt7^
z8m(K`b+2pk>CTC$`*EgW>~uB5$@>^<)xugUPW9smaNB9l{k(VJPvisyT+S6PIRG}Q
zNlRxPgOW+RkGBRQj6W|H33E1jv~GkFo!-an@?I`~m`%2E7o?mWv<~cPdRy&*ekOD)
zu}Gd0QLJUjQ;`_3BWH#An>E5k%WR7+oihMT0x`~pxH>#as#{&2kUoVO*Qf4U<nVVE
z${mLk*8LYvdCK1>{5Pt}qus+idhTYdx;)mzuL)>Z=TH97>mVj&SI^HpO9D*VLF2Z8
z2XuL70m?q~iZkSC({M_@%242ek4e_FBRV~!S`Vhq_=#yhf6@95_ITD;45dXC*O*Tl
zi{rTZ=E-JH99f_yC@e~>5fAlT-GYKPrKzJSH;`T>DW&Mn<<9OqTH6LjX@)jMF_MpU
zopoizhXbGLHJLa=&pTpRvPajL5Cp(c;y9e2H?}^KL_3KKD=b}j+?>-8ax(#oNsNcj
z8Z%xKhSwlcb#rn-?9k+AoStKkmZj_%JVf4qbby0*PSNIMt$rTw4u_W;Ted8Rexr*+
z=g;q%a{n0TszsUp8+6hn(riN_NoIA@$9vMgyBa(ThC*h86~Pfpx*l~Q@!s(XQ)0zr
zhlkzGMgU}X%D^ABR|iH)Q=?ALHNuy*H7VmAg}?waV5aDgS>(<(+I>2q&(0<?V^5)e
zyvMq=v`Q+}-7I1h5{97&#0c|yMB8VkZO*OnDs`|!bm_dLVFjE~wME7yXz9%PL#i8p
zDMK1X!wBDSen}}h9<L+^=qTNaKJylN?BKw$H%38(tMj8qVbmdw1ma>2VakHI%Jji)
z$i1jtsZm!u_4qYPeH|Cxqge(<CT#<Ya<6NOvBUFHsUlC?{_DF2_6VgVGuJVcYG!sW
zeRp?y*Bl_rreMYSt9}kd?#)*tBAlD&<@=htBob1as8?sT_`tXZCaXNUhJ>sL$jh1;
z+E{(R{E$|}q|K1^WwiAWv`l?Mw$S>oWzWJea~oKyG_?-q_3c$ETAC*EmaZyQ`A82H
z9q$;6O6h`(K_+g3M-_dKg@AK41Bm?f6nzUsKXoWrk$vPI`6iB6Fx88vcF>An4Q6Yx
z2+}PKw6fx@=V`>0^}}^MxkQWdOmQ9RP}sLD%LFe!ysFr&shTY?IQ)9{$Tu^>JrWXS
z2T7Eg6u9VQ-c@>E)2vr)aJb4T^VjYaa+MDS0l(;S@D^a9LIbkIXaKz~FQDA*+><kO
z*_p=8I8^NX{17C7A|`bA_1nxgUsFIZnD!|Sq7SVN`{bJ}XSEk1*Zx^w?cV1dO5Qk=
z_=mIMf7yP|w2Y*-e8)^eh4sgO8--RX<N*ZCnmqk2sYb$tI<YKn_<s450NGNp<{^;F
z`{f7MndejOf3IoaMpSC7Y3c864}X`FDkihopHJ7coD8vLRrGCN*f^)7zM?~k9VAkK
zGvu$$hy{zNey78cu+1xx$L0#(^r8#`^{}x`e9p@#c?^30I|gNg75bZ+3hn8Eg)Xe~
zTlM?M1h3`TdN0l1?jQimlIh>LnlVl;Vow@lO;)U#I8iy)%TbS%O*AVX0r2OLvPu=3
zN|m2jVK}lN&sQI1m+rSmqAI#{%SZ06&`6Il%SW!G<%(KM)oPiu*SI?FqR>(pxfUyU
zRLlgK0oCu`O*RM5T{{^12TNQvU8-)1_NNUX(r7iylf%^=D_6vo1j!zij?%PJQKOSa
ziw`*fSKt&zmxKBd>lzn%#4<1%8PR)(&jk__>=P6?OTY*LI-92MnCo*O&|jfMUp>36
z=PqvDJ>H|{S=Cp0O2khdB5zU<lU{-<3}R!e$>)@xFTMG)Lm?;vTn2O&%U*uEvI?E{
z*D=Y!&RQNtpg;EeZyT`$jv_rZUq*C>UQTm|cU^QLZL&%k_-$Bq^x>3ig5ye$XQ13t
z(PGsv>TXl0DPPX^x_0=TT-JKU<S`txnFb5NRYLUpHt)QFzgr*`wG06%u12kLm(qQ*
z=Um5IvB>N^jwWRA^y&p(5RNa=hBOX2AcyjF){C*Ghe~r(8lPVQRE;drXn!aX!Z>Fd
zi|@9Ty5i1OA37@AtQVy;pmcuI`mhuHX?1NVXC>6Al#GwvBS-h~)Zt*0b~Ibp+@$T>
zA>CHU<}IRcn5~z)U2I87GleMjwZiSMm9aVB7v4OuF%h6@`(DQ0ockSun_l$Y3Ju0+
zM8x=RQ|J1Ga&!KIqa>JqEdRj4p9-a<tovw{{r5eVU+UV^2#@=2)CKbgb>M~`noYXi
z^veEaeVLs6ouLAopxQ?9OYcymlBqpE*S*8HJh|4>a{~dM_595gZT-^COVzYZUg&Y#
z&Fr%6u^RSw6}gM)35MtEwFd#e(<S)n$tOZfZrjfF=Za=w#wSaVWb0L+(~qB=C7QYb
z3keT)w#5P%%@qT~ZCalsI5OgM9UgPbArK%r;}+j8qc!e=q$7JzuaVSnqtV>i{@O%A
zfzbVI#;4@K78@1-RI`u?2y{#<#Jy}AcJ1TI|66*0jzxL}J#Bag_uQdXe*HAJ4TU(6
zWiV0=;rcyh*wbh(0*iBDjZOETUB4sZ+6N$BtHi~9cd2+mPaXvHW~q`4ogZ0T#|^G7
zyh>o@i%X4Vt=_+PLWI8M(GyLQw_N^|WDE*LbO^({NAaf_4C}<l`pEBWh0I-4k{iYj
zgWUW;HeU246vjN;{Ez=MEIf^UP$rKPB8-_I>-yPb;7zsrlTG{t9_{!PUcS3%|0hC1
zyRsdtOLfuWIb1_6sDEOSkriW69(ICzzl#7C3yS?gc|HEapk%Z{^tscR@Cfh%-nQxv
z0M7a2b=&UnPZR+qs?nBDTq>qquaXoMNuu@L*rUdbiTPYM`0hez#uRm6+QaPTgR^84
zb?&^h7-on!e7Uei$X8D7?(tbiYVyWcfZ?)L*kDa~=sAuCKEhHp`(=&wZ)1#W%%iUD
z>O9_sCKVcL+RNaHmGAvR@h#z+M@IA0X&7gzmhtn{7{$&)slx{i>mQuD>U=9pi^?w~
z@7Fp7Il8gMmks}Er9!CEK1V8Uxj%0UiVOqS-Sn%ZEPNMnu(oc=*NuE6?pacx=LbZG
z_MP{H351tqOeDc`=@5~Z%Bv($p+_&0h-;Qdh4xxf<pr)*M+2jAT0iX$6kMRL&&_Gg
z9Nl{yj}aK@02)S5c$BMJwf{~o_j1?${VApi2JTuWV<TVp`oYNA>EAiyeT`MKej!UH
z@t#g2{=Re*9-Di)6yIUd($+6qnP`{W=FH#x=)2XIW8_&BWM!2o%>e}ZH@VwI#XgkF
zxvSq#0MScd&69w;x;i(I;Sd(?*j%g`X`E+Z=pqONP{KoljDiktU)R;nt0~L3eg02Y
z4rIc1`Y7MvmxTnV%)TX#8a{+uc<co0tUj*l?6BBYx;MdWz1)7X;v>FdvRy7@gr9sa
zavt17VDb5jO{nzY?2MmK$FO44>y<qKT-6}=&b!^75N^c7`L~YYnSYO@(E)|1iJKmv
z@Ccs6`nnaYgZ7R%u|=hsUdWw2-ZED82Co-Wmp7bd)yr?tZg29EKl6(Lg0WPsKyv{#
zDvidkU`pg$s6T^MNuHQ4w}TiVzatdUY+aw|>T!0ofe<P|tf+2<tRKKDfn(Ymx$(X*
z()VuM000e{XELVw^mQ9>9<i?yr3{EBLAdyK^J<$b)}=<H;~&}C2DLEZoAX;l&CCg0
z&Y00jI<|HD0>(ibT>&)V0>5qI2`%DZ1{n^Gc&tbfsfpn}fB!H`4t=((8MLlZJVb>?
z1Db|H#z?ct$F{Ndey<Dp$L)a&XCHXT_Sg*?49p&{bQZxvzL{3)080)h1#gdIkrtIz
zmd9@XzU^dc^|6X`1IkD2eDH4G{1p(#VC&8gr}rx2?#6CFfr4Z#Fo4jfaMaUnv~HDh
zSCoKQ*0A^iOEP<oVdYLb&p;Xm>JC6uz%y;oc`Pna`Vgr(We%V;y`C4*C<Q;m0Q*+h
zU%H@BqY@xAzmt4gLR>&QEHA7m{AiWGvtK*p>WZ$64oFvgU0Ajo+C7nU?)Le#6(ztQ
z93c}Q#!PQ&oSV9FTE&p<=?QxsN|(LIiuqYYB1vizXf7;laxq5KTk5(%04zl)VjJ)0
zu;vMz-!b9FgMpd;uk7L``gGWd12kj>lB7xC>L+|3g#2B}>)(?ZVqMsCubW`KeS%N%
z^uU8+w+vTjvK@>XCVybLB2>91Co?f+mM^z@H-u}14J~&)eTw}qZFf!hWh2#AVzYj?
z-0%JN7O|Q}8lWRcJL<YnR#X4@v9Aj+NVGp#ZKyH2Z$~$<hVnfXl?udS+!;xhpdn~%
znYaHnQEX2;;YN#)Yv1N@=!G6{lS0j`B-BimIPghXnXQhWdKnISGU;^?0ky~k1Vi>v
z`olWgQgoW*l)LO}OmEbE!}j7~;IJ=^E}gtIbiHw$>d@XO@67QYRQ*ee0m}iPEexlZ
z`seouW*LA@AA;ldQa2aGsZBLZXA5p4lrh(|q)LMjmsz{9IzK6KzRlZ<9*jqduRfem
zfaNFT3kb3ec2qf@J82lvWQevzY|Sl&vQpXn!c6r9>=rnZ$&l1H|FBG#8&0(*j9&6L
z3d_nU;MGik9s`J7N;<PuEo8Vrg$g*l_QNR<$YVg{=xCO;?RinOJ?8fMn*^$MHM1*z
zb!)R%`q>u}agEc?ZnaaRJW9O;E>440!6?FzHeB<J=Hv0JM^TX}Y(U1dX9Cc<Y~2J~
z=nT~#6VevgudGAeRt5Ti+j3GN36nfmW`%Ua;ada8klgQ=gR4N9-F{>TkWLQl_wy}&
z7+0v6xJ1S%G9Xu-o{i$?UU@)oSEn0_N6B2-th#v_Zk9gs;kZb#WgAeZRc9vtA`R)B
zH_eW#V&<qZ!xZLFtV*Rz;E1K&kAsYPtEgxY)3RJd{JtjvuGQf&z^L=h0$`<K!^MIn
zSF47sSEv?+fHJkCmh<|Ev``>@d)}#qh<HeqVgL-*gWo4fvjaNCcPpWl5r;+qa7m6R
zN|nHM7f0z8!s300620kk-sSNRTWW3`1?=@wKjq8!*RKW}@*z^#A~UAW`aP@~0G|2}
zaaI4O-y#pp+oKiXkRsvbLk2mTUw&6aEm%?SP!QlRGam_dxNmD-ZZYls4msEEyEX-0
z7GL#Rz>fF@!qX<%)OhG#Hh7DmR#QJ*cpuJac7=4dmcwa*7k%|YJwT38tb(6{g|B%G
zI|i50$7*Afz2ZY2Fhg3=WjW)zLDi|R*l#|+XsNi6>RGbj;N_#R<FJ)0A@Q8c4!nt{
z!px@UxzuqWfRuievyL8G(O_QqJWFDd+afw*Lyd-T{HJK<xN?Y0oWNzLr5sfE$)<r(
z7Ql}ld4!)O+kNj5425030WN5V#|LS389=Jl|2RSz<6vqW#6qzgNF)22ejvc?{OFR%
z&*Nb92lokLK&*RbS{V#*`U}3qp*YX$GgcO7?rIr$M2CM#cjODcMER{IDf-#4>Cel)
zv|rfT%Q_gYr@J*0fj)<LDo}xq^ld;d<QK)l7<voct(LHR3f|D6-h9b2;pFh7x*S7<
z-|f9Tpl~sBV~7F604^I4W)Equ`{w;xfBYNh<zWlQSQB&$$74Et{3~5-x$t3BoGyuS
zh29(xKEMC}VLl%qarZ7>4v-S|=e|<|Bq3JQ{6Hp>w=hs~a(_4uqoHR+)1XOWAAbwv
zgcqof0>)xDfpEZ;?t|P5jL$CV;`*nP()@p~be})(1AbQFOtV{BDT+nSPc1r}bS7KO
z?sMjj0K>xBT!}CT1)Oy{C)L&WVKGyhh(;1i7jKrd%R2XDl6}0Seq{_Zpdr9$&Nj-u
zWG&uW*GDnK_NqI-b>SsSvCsSZgXw4^<XCvAL%LB`j~#EfiOsR1*J~4GONy9)c|ABU
z;rnTcY;JeMI5^5W!hFfdsjcVHI(VXumhL(+jb!L;>x`;aofdXH?wa6(^j+!iv&s6k
zV}9PzTT_Z{x}tsQoFz#I@W_OPMc5{hDE54ted5`Go}=5fuPYa)qWOy&-oI+4RY%7a
z2^@{2)b#cz)wcF#g{j1E2VY-u*`#`FA|uVK$XU+jjyzria-ck*sz~C4Js_(9$umev
z)o3Trsuip}x4oC8X|6aeq!g5En<akKn*q5Ve@GZwYn)~>to(<nL4UbbwhXxC41J1J
z#+O+Gqq=^f!D2%+%A*Pl0y8I1$uwY(P6)3(b7d~*_f|Xi(mRp4TO<71g)aJyatfXu
zt8oQS%7iE=<EJj>X4a`F;7GFx1B)G&YV8d<5pZz0t*J*~wNT>IejD?Cruw%`O?iAR
zbW&@9MMj#%!D&v{VYn<!K$Db&hMBo*%%$ot4&Zb=s)#UoKokvvhX#6yYf6A5m8RVp
zfC`v_ZADli=YC|gm6e;~hlUL9zTbY=^-22xsvFj(Y6LCNIRtJX0g&${xb1}FKissN
z5vysO?jA{;=u-e4`-lpZtBG*YC0GDGFsyQSV##iCo;;<lhXg1Ooz*&M)Q^F{V)4VB
zM`^T_fYs?6B@NSLy^Ze!wn`yFQ8lv8Fbx`Cb*dETMDNaB&~ygGF-!E$lL8tmGxWwa
zwI@n|#2}Ov6E&QngqRbWTVf{5L}xW1flJE?rKZh@Jn&Gh{sut-wkGmsP#rTaO&LT@
z#a;<={VRnTwxt+YOfQ9l^sTm{dhrW~Vd>_Z4nZ};()eyb#R2Gz0dfwVBSB%Ceee9*
zEqH<HJ(oJbyHLo;mO@Zc%Lc1T*~r#*jSHpPmXzaM9G=$O%YWQk*E%lJSR6zasr@_5
z)P;uBh2-Vb;waYxCXY7;pTKc5T-j+P@{7zczz4xRmvO^oDJ{|n?~bEF0j5nUV`Ra5
zgC(9J(+@*u9tkt%5m%bXOE<r4-a0eI_JGN~l^MoNKV$@*MkYgw-<zJn*2?D8@PyI!
z8f24bO=V5jWN>P39!IrEztr>VRRB8rn;gU${IuF4s6rY*^bCV83OMn%aeQ3?78d#q
zdu?pK51{Wis(PcEL#gCiakk&1z50&_rAfQop;XtTbYe^X;U;eYmy2H(a+Fd9Qb-v1
z65?#X?#|WRKBk&4JLPcJ89U(&`%wYq{AE}%N155}0K`dT8ms|vw6G#kU3of>jI0lG
zEYJycTm+!ua@1b4)U`#yoC81`I^RZbHVP%_h6>-$_O<$1#|_EjZx8_mHsyxAow<Vf
zkK;@a_TdW6b730=M?f`L$IUr7<t>(ji5|m<LcE?4x>e8VYGca0Zr&BxaA|ue<8kf9
z?In9%bH=hwGPHfSU|t?EWy`d~Y=7g;OcY&Ka?NItZhTJ=_ApU@S!CG&Hobv&_TlCt
z#Y(;Sx-@@#jfAYk6u!`lNgwa!(T8iYbSkY{NVF+7?O8>8G1V8GZri+hNf9vuHJN~L
zhygYJCU4Q<L#F=H7X0}hzREdr32>z_zw;T&PW8lBIJI@Rzm)yDyBl-ImS*tgb0a8`
z$c9exznim~Jw=Zly6z{H+_XPMB<%9mRd*O>3P{%h*<5#ws{`QtH3V6Z>><golkA-u
zFSoOU6RX~8E6~2~q|iYU^u^xyFveqdlIBF?X4jp2Bn9hun?9O+V{dDoy!PN8NY?7Z
zx*ctj*IWK^K3XWbQ|?lxpTYV+j?OYF3a*R7uZW6>fJirpFoblcAk6?$A}u8h-5p9Z
zbTgy^Lw8C`mw<re&_joml+<_qexj^#E#cmK&e?lE2mX*`#ZdWMz2BQ^hMWQJQDs%2
zB=kq{B#4TLNiMeFJ(k160#oM98fTxD+TL?^eG@RJ+x5g>THqrr|0}0EanUDnEF9W9
zNSWT$aNd22-^Znv5k%yR{^PmWR@?8Lk}_lI{@Ba6Yd^#EE`v?^rS;bJTGboMOmcKx
zYfZmc#nP?g0_`%%ZTsEl6EMDI$J%Emx~Ma{(cun>{wn%j#{2)4hpQ(;KpZ^WWEuhI
zv1Z)TfNXR=5RIjGOOH+eU<g>Q`o;#-3{fKBP<53{*~xWuff}uf>fcxuj91y`X+N}0
z(K4zvCutB@)8hAX9lT<%8Mivw>n43UVa8xScH}dKqVhXPcn&oi-y2-_@UkJ4#4mIa
zZfURWR4nP4FwKq3V`Ho#W7B#WNuNwUoaZ912E>-3VPb!$9kwf_2Tma)-Vv<eMraY_
zQ&3SQG#wgdEN1&UgiU5ZfuCSq#y?p;TomPs9Wu~nat|2wgxURlc5u8S9^fWM{Mb0@
zcKjh*@TTts*2r!@%;8k2zbc2j*ZkX6N5AZ-?jXa=7#Xtv_qrR8N>al-NAP1_ETj2$
zWYRcZ@LNHD&%mXNz=q51e|^-O1l1P26?}nS^|B7D)}8|z358blPd9zTd9fa_?7&Fq
zuY>#n6VZ~OW0tdZI-v%m_n?g7jPLmheGEN&wjP@1ZoK{bxm^XN^6O8psAGKN$6TNH
zd>}NG`&>I|q=Anw^R=KeL@@f{im(9rFg)iqqrLHa@}{pjWY`}SHxF*6jm!@;+^LU=
z`sldm94SvnRHa@^<9ENxRtR`&Be8t#wVwa73jDlSvSkR$|13<uAOvTH$mO|_x(S<t
z9Pvx(ZjtioW&^1z)x7CuT!YcvxvIwZMOAZ_j>a!^3iYhrEQM4EuvT8~^l-vsUxE?m
z7!d+YS&Ff95rm!-AJ`IBzsrXQm~$s9zkEE=6ylUw9O5Uk!Cz8Kb&$4OI!GY&hRL4%
z{aou)#+}dwUfV}~c$Ur7%6&+*mwx#aY=$3LAb_AzzN=AVODXaF=%(ZJFo5%@b1!&C
zAt#J2yf8k)V~~Y_S?eXz8uYZ_s*0=aaiLQhtA-RPL$wqLYPBACJ{muDlqBrq^)mEQ
zMy*`SCMgzl&CA+4P_gdYNv%B;H^hHR+$f{ArIp`bSS{U@0<nW(uP4eByD!L2Fdrum
ztQ>K_t1!Ef{35ZBn-dnY4;1mV`k|u9r&D^i8~nwk4RgFyDT>VzBtTmbER-HICsWd>
z<V`xVNy{;>E=aU+FZymN+ylHP$f7(~TU6&eQW+PqY@_SDn@8+6n)Wljp$d?*gS+TW
z<16t~JEy4POm-3hYt3f<h`NWvi*+R^Ts!>L3vo%0mor8FG?4fpHh5}r0J1obHz~k8
zcARgJIU-y?tp&zFod6FgVmtx1(=jucpdYnKnBMowHP3$s?jeW-9)UToT$iImz<(0h
z13SV2Y%8I3;L2BudI*jSx7eu>pbLE-m2K{lXOWTJ#k=izOV}w0_K~^B$R?PZsX+$=
z0zQT8j-QEYDo7=nWzc@8nJ{L{lu9z^7pCHFk|pe`6-%Lo7tXp7K<VI?PFb%Bx4pzc
z2;jG1IJsIPmiPTcPI$uj<E6f%KwB$f<>bdXVTuh(6RnPjJoH1h@+qv&FsS0@&nzw%
zWjZ)Lp^j8Mji|ze>a<<0jY@{W#uE;MY<#NKiNJ3KYuKG;$JK9(c(R6K$LpF|D#%xL
zHRlZ2?Wc|cVpm@z=X-Gg!Mc2ZiT|s|=A*rmk%JZ}2i#;QiT~74K87Kput}<5eO_w<
zQ&Q@66P@QYhdZ#8j;h2g%{saXetIn>_%Z1h)&7a0<ko|DLbkvb@DB~gPSxG3QrmaY
zQEq^pG2R+1G2v9aB%DYKDJqIIFAb9ZktZamOK(B?UQ8rR57yUq+^Ra;M)tRZ?ZK|1
zc_8``AS*0#7rNW>qp0{%2EtjYWu~U*y>xCdSPFXvUP1luz?MU`hj}H6irQocTI!%G
z5tAD0ew)N3tNaoh!*hbxo*a|~sjXKKB<%6mndW3)^FoTCX#zMrl0_lUH7YR~Kjg(W
zA<TdZ-(IJS)?x?mPt)mvsZ2Zs8SgC?X`-oP(mF|pEGiX1{jv>JEI>UeoRxyGa3>eX
zj)NT)KocBTbovaIcdHLdHAe3UlRfEnzg~<%o2}%l?S63A*GJLB`d7yX`4P!-_rrNB
z6Si_ujz>0Nm81xk#dA!M!gm?zuH=n0lz&GkD_AerV2qv<kEi)?aZiUSpOPh&dyUaW
zH(F`JvB=eS=M-2K%1k~!B{Wd^dkK*uq-WFU<t5BlddZ!v()*J+A4gh(u}~07=+aw?
zqsSD}-xXyrmml*HQi$aJ6LO+5-378Q{CbIf&Uw|n%U63b?P7fvmrlX@WAxgJc*Gr`
zPEzOtW?hpoI=61Qk`i#1(%5*ki>lw+S2n!werpy0={*C><YL(1_mebo@WQ-H0>ZN+
zXg{$GMItp4*&?D3YFJZVmh7g&J5f&}G@JMzbbTnAH7i@#*vt}_nmz%jp`laZl6`(P
z%G@FD2X8hrgI}^Nuw!Ac4ii&k;`;B-=5}+nw6_El6?S*)mrlj?n0-hXOVGL+9U1vz
zdn7nvhA6VBm(%ph<Gaacj?1E{RI{z|F7E&JKFenA^)$7g``q3)%^j+D0%<cNxyDUm
z-CaFq;$70>UCunuTfAX$Oa2E8WavfjmZx0Z=pfE82jSnRT5)gYxuoxXj1c+=7cxv!
z&}=$NzC(qNlBRNEX@8p)m%R8UmGIm;2^7+w_ldc+%lner^<y@l)nDID?cR^M<7?8|
z8?-=-SO`tAYPJ9UyKtDbb3<oybNRw$0rNHS1K`XR;(fPq>dW(=*y_QYGs?@*w|wW_
z??6cO<J=2j?cEKmz%V=1ik`niM$A$cx-<Nx58(W~P&CzH{HS=n>VIjjh}Jnq?!%5i
zyYbD#D%k#}!;yTFf7pxUA3ICK2bgO&`<1*sb{f}OP|E4fG#rP$Mp?_(OiHD%raqZH
zv%ITf25sg^$=xhoZXtI7!)u&_yJgC|8;L8vw&N!pH5MNOB(6u!VUx|EZz&Rcu{W2p
znc{!xoaa16yS#ftlYwr(viFNxwr_);7b)Cs3ACv;!$2n^XE-zb`wbfS4DK+B^J%dh
zj{aa<h-Yk``|mej7u@w_FW1qC)ena@EmSsod<?!r`5#eSUsU)cXa7|-e38Hx_q$UA
z+_TgqqSs`H|AtZW^ts>${=V)NNDGJPeB=fUCrquaq}am9_fxOGTK0ouXI#wU2{Mw^
zZ>6`3KaZRd%qQ=HTfUiz=^=9v)oAX%r+m)$MU&5Cn(*`F<T&Zir+^^umY!ytpss~^
zPrX=?GVnPj_|1H7N(RsGK<e7QrS@H)na1tE$F5ln8Wu{jS3HQ;snpwqnxPEA2C3%V
z>ZVyU&(_cT7i^`!W=k7D?CIWT4&ROcp1;sx)5u+Lg}G6Jd-m&CHLTVqXOYEO+>}#1
ze*OCoEJST|F~fr6JjEYhCpW~fZfMUWxgS1(3|O)rJ46bq9?Cf$Sw<wt?G=nvI30JA
zQzQ{bSi71m>)B_mA3K>x7-fA|^*Ms&_d5O8;_nm}GXf$waRx!g-Ite7bqz>H@%r;|
z7-efH=fo7*O>yS<r2_<`k6Jz<k>o~qf5U;rQh*Sbn$*Ip>3etb+w4c-x6*GCF&QNH
zn7OEvihkk8ypUF4NDz43BG)x@7d`f*k9>8}c(=J#b>2s}YO<vMJTP=BxsME0j(+a(
zlqTgWZ*t4&xK-(w0E#rfSM_GcIxJrBZD~4lCbUCpqC8RF9fix9!s>H9^<ZPP;$+X_
z{Ob;Oarv@0c$K(X-Gla$e~RiP%bP3Xiq=FNd*I4wgms2}#}m35!%%Xj&=+p)+%n5r
zeNQY;u#AS7oE|f#u^g>ud(x@l%5rV0vaN`SXScY<`Kqc`7g#vb{rArd_P$Gz;<|sd
zJ@KN_iw@+4t9=?f`|L-#>I!~bxWs||CBu`#7#MX?#6u@Uy#*2SPRG8ljONT-+d8*g
zKKn378Czk!Q9{s(za$+Y2nDWlsyKBmUHFhyO)!#$5PDxL{%xMLuO$n1e!NE%DSV!_
zNB&w4M}{$XLGU#auMh9AE3C=|n+a>nLwoR(wB!fwbYuIk-}RC3Pp^^I8oP76looG4
z{=(CL+!<EC8?Ua#$W1nwEVIL6lu@E>k)VYNi<o4P-v~YXoo|_TpHI@iQlR1O3Wa@!
zaqD=eo3F4zj8|?11fG$lM^*aiAp2FqQ0n`9+3BO1(t6L6Kqa;cf%k?L&t<p*Ae@GS
z4u8H2&L&2ev)&(PhntE@ETe0N0LJ@bZI8Qt_jw2%Ov%EEt#8HG6dJQWkmr&E+34(K
zT=GFfW7eRNhcVgu%eg#CdL&z(>j)i2IcF@448iu!gWJnTARdSxa=m;(NioS!)t8&0
z>bUolVK(ve*OI{QZR71;BCt*DS}N)8P|x1roM*OlAjbEUw3y{U9&$E-hD3V}-t(%)
z{F)-oZlh$e=N)uuEXe5=%F3J_55ZAv_`T8Wbn}Tb`q8cAYBKs<={QGFcAwd^3qlTH
zQhZ)1J>7l7c)3Bp2r&sS;dhALM?qrgpSt6}kQCElg-P9Ibc^5$ZcCut$Lk?*Z{z32
z)i=qvuL*-XPJiFoFxl|ME~OP0^=orfGwg2}X>a)#3^<nGs$6Xng6L}m=cVB%LD@Z9
z=hpFt=3usn#NO%{v9Ay;h1Kia5KhIvfqsuSGjsf76azd)h2WJ1dz8t4Udk&fm|j<I
zewG)7C>%(H##jkC-L;P6JsHotLQ_n)r(E@^9ZWddA*pVH7s{+==<FixhF0d~B6xQV
zc;BojNnFvt)0M-2K+Iu-|CbJt(O9NhC&KPr06^_W^wtqtZO11ZTx})&{hC>BUA+gF
zo4N?rds6ZAaU;5W{$B9Z)NQdB;lkDHobFEHQS0O<n^Qk=%wI#KxLxM-ZNH?mNF1?d
zgC&Dt*yMjV+CI`5?5aZDE?xiODVB^$SZ=B;QaN{gmFaF|6O2N?<6R2eO=MR!y<Pcr
zq_h>%c~MS}tYYhlV*`kqLf7|*3Qn-6YiClrf=%<iQ85>nUd~&UTnfD21ZQw%KM?hL
zQS@)J68CzBg0exML@PN~CY%%g7)`2x@8uUHz9i}&w-78k3Z2)HTFf%}9OV{zcbbsE
zOPNxB;JCIm5nf<SdUSS8Pg7Cq=vUME*(uJV%rT3MCf5p;u`n-9Kyb1jS)MS?8yywp
zWaS&!ut9<-(Gq&k;#jHQ^!tc4lii+!&B@C&a9Abfz<_YZh~>ER7eff!i_?c`64!|P
zEyq7_BuO2AA3wa?IA1iGmd*-~V>7zlldN5&Wy!94=&x-aUR!iDzrvg)!9D!T16P3%
zT%8hkiwf_+Ch*-Q--Nq85+l>QJ*@wpu<~te2zXxQ4w+2|--Y@gzW9Hl(Pm0mS}caP
zM&P}gSvZIP27ZNTO?t$Wbnt3)R@^M6U$<s^Cyln((x^3YTe7cfpcs=SNspM8E`tyQ
z80~+ijk>utb4c5cddc`%Ufo`{U*X=NjBe;3ok!xvV}yQl2Ur=JjOHJWlgf+jEznjp
zi2lJDoXo5e3krHK#^YMeBBjl(ukHa;jK9zBi{#>`8zoN})M(4BTdLhjMu#JvUA*?n
znac03ckK^H=IQU&3flTT_}?&Rvf%&=NCP{YgO_KZQaa!5n6{A|;e$nC300)6MuV*i
zTlxL)r0<(}FPRhCZ_fG>$B7dzaqhP9TBU_D3!mL?+P4g(Z*E>rP8)qFnp>_IF~~>%
z1&=P2d2|!^$06c|XAMeqi8}(TnQTPY8x;R~U&?=hK37$<Mg0<XGubO=rpzK=ueowN
zI$qqSdcM;@4>z4kr}DdL23i_dF~d<wMf+=JTY7A%YOK|7*S|%WQY(HTP=y3NT*>*z
z*FP{h_OjL*5#f?^9N&ZMSRy7L_Hl3|aPhhkIs2fyJ(I1Kh0FUi5?+Xk@%6??c*oBB
z%6m~E`cG7EXE`L!s53BPS;h44Ix-#XT07lG4cELk*{c?J=8yagQxVHO2xh~~tZwy$
z^I$fm`vja=QlcEBvEzEcv!X^gvEKxUC=B5)&FpY`@F(`IVxgN4d~Qzz<;M>fDra{p
z$1RWa4*Wn;PNvROLs2g>|JChT$tYL6ikjkr&*xL)FKBN~n{@w^6~`9Nwf389yo1yn
z--g57Ziy2ke+Np``Q?)T+3A&2M*7$7ri>yxZYyNJl`xqyh1Hq;JvfU7sREC`U(%pg
zg6d+HsgpZm+xG?Zw@U9!HNE|=l2y8`-=Re|CwCmWXwzcm>JLMH62nhDvin}tk$Qb8
z#rd4VNi-KcEX6^k-H_rRKRO&W4UpA~AF2)7@}uMo=Z9;uQL0}vBqz=AG0&(FU~(?*
zc}~ACd!A;CD<;qtVI(NcV)~_UV0FW}Vt@0vk(cIn(zDl{Na*jN;eW^LyxCV(rnOd7
zi&tkb0O}B-eLL#IIXY(&HSK>*s^Km7dmTw*5++Ce|5+9_hH$xDt7*;R7A;&#3S%C_
z_<0{!(z}%U-D+KX9<6?Etsjdn%_5QuZkFEEV7j!HwTj%mvUG~)6-=vk2>cXT{?-17
zQuAfFSP#Y}6=OBnehoL}RiM6LPli5MkRN1p(P0e3VbhW!Brq9$O9b3g?sTIb!cj;F
zn1A8ObUemjkd#h%=^_(C%2-V%t+vM;iydh(P704?2&0uHRDQ0N_|uF`O<p`@j4!`N
z$0<Z|wp!kLjxP^7_)8uUPEb8oJ*J6BEQ(X6fJSa`)><bV63TRP^MP6oQr+EcNvuHV
z*!pRpO4RvDx_;_X_h~@K+WZNIE)~eL#wmc27f&9}QyJnaXcR5hQ5RNS0rmrV9rFCI
z<J(Q3rN7s2p$tAr0P0EnpH`fLp74aJr+U6D+xO42&s4IER@N@HilcDLqTlfQ9)yRh
z@{k*Z>P~O0jSHVfE6b{uV*K4nE{*f>v~!i!E#-e-$Y1Ezgca~zb49UnR0^rGI6jaj
zoN)Q$wU`G}VSO|3)qe9MAowXq*!RyGRxqTS3s_q6ShbWf>$(Yw1xiA;W3^Nu3kK!{
z3fnBtFL9`*(Vbqw$@}qKyqXG%QcxDxkqRvk&l|HL=a45HO5eu?hcbn~m=ZxL^Ul8A
z1rnJfVn^Y4?32g)^m9<{e!-5Reg(HdKeyfph)@{tF#q;9b;L>GCoriV|E(^MNF1Ny
zCvd78Bfln*e)jwlnv-=8q#*#!S!&R%DV55j*-P>@$`PSg@wO6*BSUA(kid&NVa|u*
zXtmjcwjqwxQ~u?3_Cqi_D6_87w67kwTsZQ}KhXi>r;l~YdWlCZ|7j&9oW~=<s?z=F
zH>78i4Pu{N><MUOxa#-g{*OI^V9RHPp)Y3Y8<dZ(U@~{Dt>ZRF9i7+~+5$TEu9kwh
zPf=eN>x8OWR5;1Ss)38N4}|Vz8zM*^x^GpwJ7Y1xcjFO}R5Zyfm0*Nk@h<)gg$`r%
zq+I=v3$=ickjT-*_XdShI1$biE@}Kpbq|qMl<#B<c$3Xbkc!I>0H6Z;n>~&L7#mza
z@Hn;xhe0AMMc7XjBkYEH&dcW$z_j0O`sHC4)s4LdS)h+lR9;x1lg;qkF_#BRPaY2L
zlyPd1&jPn-c$i7GGK=*G<Wt?J6w^nK&Wr6}Kd4F3fixMW&UK$RF9675IkeV0n<|?<
zendQN^e=Eo{huZk;(_(Ptj=TiTGZ%j87GbHgyZ&h^b5S9Uj1t98oMBQ>N3z>^|-;v
zKdb%Za`QlmV${}d{7BUAXx20XRq9}u+bPSW){oRoO37#Pgn7k((RQ1blbyII>I!w6
z2l%ov+dE>+&j_DrgeWBiO>1%O*fL4BSQFaMNvvmTW$gHa#7$XrWVC}v9u#L9T1X@v
z9c^d-X5^=*t=q;1$r|p59T3@6XSdPrAZ_Z5kaHh%6>YohC7XW*D>5cTpAy_itG(7>
za8Z`kSpUp&WGG4aAex$V^XDShN5&_w)w3>>rnA7ibGv#~fH3-Zip|t}9e()YIXdPJ
zB9fHb&Q{2>5Y*@tiF3;4Ax{?>@WX!W^|JDB^6}S$%*KAbO_EeLvx~i3vNk6diD;Ti
zP3uF|yFXVmZKGDX!yGL>iBdZqZHp<p%EeUa{(qGuMjoZ4Tuv|f#_$YLKuMgh8zfF%
z`khpWFH5wYa_tWD!wi%(V_J`I1xAfF>h9NEPfMH$Hx*Y-S)PE8_11r1p>B%;+7{_f
zUC_;qjh^mwYQM!Lf+QxE$F<iPmKHrU@0D~nba4H^lSk*`;%mX#7gFtKa48c)8rf$?
zSBE$xQ><I?A4=Z&7b{)f4N08sJPrLvL*Zo|C(TTk+a$Q42_33qyo-^zWH)Z<_A2S(
zXmi4`9daj^ezrNy5^1K74T^zNghlFJTwFBG^4|^vgBrRl9BIcNjZbzl7d~0l1(vgd
zpTzHlmmr2VS@$qAS`J^fzgnKK2kbY(XNY(#iLb_j9I#M6+oz(#qSv*3BuOZ*GxsyP
zE))&^YZ~m^MrBLh{L~B5v92$wZN5Hhra5{MdhTemGg2%_&GvhVge8KWS#4cAT0DVr
zo9-#3SS7{Yuqo^-WX<({h&8ey2)el1!$HZA!1K+=F3SG4!*Pe=75OA?h3_fEI|h1$
z%=Wye(-!YVb3qqnMIn>aPo&<!km1lo{e)!7bC-e%A<`&aHqICwPt+!hjQUsz-JjLD
zXPL*#Eo6<FF(Q0`slc!kRa74G5kksri@KPq<aN<NPACpmKboesIG*1;J6UvBb-vug
zE|Vo0eX><c3BXj2gjIlCG>D542r^Ug|L}jLt6V)d>;m3iHi=DW2Ok)jL}Y*Z!vw^i
z?-g(HF;@ktAy2QqjnO(5ES;WDFg>t$jcs&I&pf+>c%UyN!_W^YB^qBNr;N>WCGn*(
zjpb|hD{GTISY*|pluX@wmdt?=Y#$e|aM_`ayG#4Fp7JA%TqMq@IG+N)ZS3fL?xd=u
ze7}^^!3|Gbp=EJo5p&+FsObGMOA)byft9@@Lu0$vL8ge3mRbvVL4oY7)(_)C?0DK(
zuG-J`*$iP9|59`B3whrc^IalG#fG3<F)T{*IsNjCJtWz4LydLHi*1$Pjr`p#r0)E3
zK9Fs}Bg^~qo<>yxmq@P}cQ#}f$Y!Qn_x*o~YwE1lTv>Q{StTZx1Gpoz!TRAE1lXdj
zhxsL4+zov}Ls$FNxG>yAH;DlttHw34|BYFnDaRGLG~GY`g7<avMzBH6yiL7e(Uo*4
z|1z%NoGWhBZa1bAVq%xuTeR-#cUd!9ZC@M4IMm$@B2+2oDpl`oj|VzgMovO2geoA>
zh<=NUG1Et+!+CGL4HK&&CdGq%z9(ofLebfJ_jol-r^ID6F<Gl2it6v0=5v|Ew>=^>
z7*}fF(-yj8wV(<z35niQBW>r4t+OPcD`#U3@5`oH^|}`k!6&UiYrYMsmd0mXGtL=*
zX4ybxrbC~?6UXpOS%Z{fXv|K;rHOjd>XDYKgAI*V!XxqKY<_7+>Aq9gO!%s3OR)qN
zIu+@qj<KLkEm6p&Fywk!(&L$|_v#($m9&~P0Vc1`>gl%583{afkZAQqv}tkuu)W{$
zGXsgoy*xz0MbKo9gT+9`f%|-CJ-SKf?^2k_7}anJ1Oyy9KheSkHCcENBZt>Bf&sLk
zqhR8n(y`(bGAbE&p*n8r@IUJu648})@y*WPJx+1ngnd&$LP`5btAA9*ah+{E*&AWP
z-X69Kbx%$~*#9b=JNqImlfZC0w|E21=OL|z3LJt+*-}<}|Lh>+CQJG?g7$D_heb!(
zv|F)CBzsdH7G%TGU$HTxX`6na-zGodnlOm3(5<fJ=W^gz-K3&BN&Q{m((;S{QuJtI
zKcRXgbOSckq&Y>Nap{nSw<J2crI{6uAjs7iz^Kb(xX1dLWW3bfuFxtPoyr;czNvP=
z{wBhn6ZFqjqkHCFOOR@|XZM#byUt;nsOgHP*^aiAj}Erkc0;rL1=S+#U>*+LhRh|M
z2SLKO@(0&!5FhKhf}an)CJ^TVoo|Dt^!B3n6!6C7M*o8m;J?`m3x|?xXkD0@KULBK
zQjm^8-wgMEt!Y1-HRcEW>}rQ|O)3}a#K7iw3-<Dw`dKsA*AUqYNhucDR)T3m;s-FL
zH);%wveklFqf8dsmi3hU)>KZgz$2%J$_j)L@h<K`pa0t`4rr2jzy#vp4F4SSENB2|
zqi|T-`SQ(Vs?C&wChp+a&@^|_xN&jS`N|@d-E2Tl+l=6^Rs!3os$$fxL1;1>I0fZ}
zOi!gqXhEcvl-1F=wG-rA4LNEbP|u(8XcFnf1IbZYC9Ju{Jif*SI7|0u2`-F-XbkDF
zUaFbdH-7hEZ>*p@5~Li?FRX2@r8+NHVm-*SRUpL;G6VtF8NVF$!vK6G)$#S_EdSwF
ziav#b9odpD#a0D6b2UW^Az`t$R}3%VfOV4tAb0QV!9D;0N1am;%@QtGo%-2G`s;mB
z1C|?Pk^mD#5g+vpg>@z!c$F-fNH~0@kxPmt@BB_dOdFPaZ;bBDYqD^f>6GTWti5@R
z|EAr(m8H|QzHzLzal8I7=Myte3?b7!VZDaOXlc+eVql;G0|Nwi>c04A4K(Lac<}l@
zQkr_mPvLmbWFw}nfd6Q7;)({}USygUZh67~Um67O?_p;B_JMst{ppg4UPUl{IFN))
z1}Py)S62uA*^V55e1={VZ&?f`{LZZ<{p#`Mwu?T1lAOQ6(V@$n;({h|MmkW@=)}dE
zb9u7!B96w`vS@%I98sIaCJ5uk3QrTqdXXsNA$~Qg%==B^YKdc7KSqx1W^>^v;ja9~
z7a%3Kyl!#zmW(dc`b|m(f~|s;PQ3^mUNVfLZTLsuv(ycjGe(*=we>abFe*<YSA_d>
zq$gZG{cJLFjB&AgicL?B{*s%%BM%d*Ym^i?Jj%t=P^;e;fSVRa4@=c_gh%mhSn<ie
zits<Yj`&_@ni{fOIR^spe_34nzM`*!9HkW}A!Lj%rjn#TFk!v7<QLSKHLF`txt3HI
zIYPv7Ri}l}4PmMUQC;X4Pd92-XgJ#tr$23Ki=i8G@rg++UL`7T5!sFITKCGFNKyu7
zH<A$f0C`0%A^!M6WeH_a7t3J!1tF#s%yD}2pMX*~-C9}PbCVv_uYlUc?HS=m70ae%
zcFdSX^0N@EEdEa?4oLGB6|roEfUQD{Eo}_Vo!jUV7~v7t`T+XfO(T&{rSd_N-Qn)+
ztBoB|n@<{M-GSqDSXV%eQ&GWHvS9nCtw<jC!yV$fuMq68VknGlXiM{R(j_)Pdb{g8
zAqj)yx}CNix7)$!%J3h_2p}>=fc|LanmGW?FGyX^zlZt8rZ1gFf0d)nA6t!JmM?2l
z+i%BwJU@gXT>t&d+M@%5<%Tvl9~6Hzg9#bS-N0y@R0*29T^)_)8PeA+JyiAIr}&{l
zd^!Kb`{HZLIgjq(yw;V8*LLMtoteztIi6zTx96}w439c$GrQ&LQn?i<1hNt@B;}C{
zFQZLy_!QK&8!pZia^&gEX|XY)$^)lawOgjK>jXn~9UsBj;we=~8Pcq(gBVXk$p%JO
z1?SETA_891na7P+=--#zN-$|n+-SBr&#bjYE}9`1S7R0>WXen@T=b<0>W0<J1~i_(
zAk>)Rvvm&qRN?PKjZz)oY4_Tr&DGgW^Pa_fV`V_mr}|6zZsEY!R4>OFDk}eFifBDe
z{goO%s8pB@(6TWKgni%CKG8e?zq27I`rNHZ3L#9)7RZOMdNM>rI0|$XY0}-bK989G
z9OZtBO|31}7*`LpWq0T2VtA@F)em`SOsRg-WJYw~K;1zq8xkEB&c%?#8C@<E&8BZO
zS^u+a{EuyK6eS!)vj`pxliSp+)LK5mh4p+-)ErmLVR6d+)HvlOHT#$|fAg&jnF65$
zJq-tTtPJe+aov3q4jhLrTDtoWNGEu@Uk|w-<^pI;SXiZ5RDjir%ssm`bdWeq1~@b@
zF|P&Z9n*7?o9s|H3X&=HDSi7i%v^duPHIM}I-X+aMx!)FAG%PI2w(wg1=T1hG%n8V
z{W)n{DgaPT)YUSe^edixzu(T~<UrR=kn6p2omhO#dpg9-glyG13Au8N_uiIc8-LRR
zVKn>@z&Lq5X#rzt%7BE^Fky8@3E?<CalEFDd&l?h=}WvH8o%}tbA!V5_HYlDtgD<6
z{HeX|Zh85HVgXkL|L`O<E8i^beevKyhOp%D_HlZ)Pj}3L#P_i{R&$gi<w?gJwx_{n
zcFV0Nufq1Ftr6Wi-O;3<tyjoqZ||kG_xX{8&z%TLb4MFJ%8{|zn)EU{QC9FR+tI3Y
z{2+>Hydgg6<-}^=+5V;l9+e8Q4ZdJw)rbJcuwzq`!h-8XmG2|@5^`pl^>(jqqD3PE
z<D$v6%`D+g)`SW0>O;iLbLn3y3QAymIy-)r5O)vp|Fg51`ooOVEI5H;SKsQ_<*=&w
zT2DChty_i9)x;;2p_Oq2(J_*@s8%xH^6NHBuu~dzq<j0Dv}9r;(|Igw{>2ZFpYdK2
z>q6jdfa47xD-vBlqEwmgam7fR<exQx+jP+XxsSo|-TgkW^^d>DRU-s&!6}lGe`P|{
zy0B?8{CuxPg{D0cbvkqMOEB##!9%(}e~09xA)@HE>d>m~PCgW+j~xlZ1TOJ6>R_VS
z9q@dNE=K)RedY4Awj6iy-{|ATOzU|A4~PdXY2h8_O4X}$@6;_;xt&+($kT@$R0}=j
z;iAZv;BscYUoWTaQ0-?S<>2DiP*Z;xKbj_(1?+r2E+4~5vKM={_)vz3nLm?k0%n+|
zTf)@Q-sTQ8ec?OZrx=vea#{>fgGT%A99wT*J$@!twh2o^h2;e4xKW>v5{Ss?9C_7w
zcm-QHq&kQK^P*!U$c`ol^5GBTZ%NXX&}YV!c=0jlEPF#}B#Y7j<{5jrwo&+`w!<m#
zanx_3556St+BV7<^InW8<4)<FwimbF_%Dc9hw54DLF3K*O<<V`L%Z+O6c@QGd5Q2X
z&-<y~B)KyP%Se7n<>%5$G8xR<_sTFTsZ_U)=ZU)K$p-k)Y%e0hrH<EIC-Qh*zl`s_
z+3~ew8rLBVvK{Qs#P6ni+CG%FkVhn#s;-{%q;i9I8<U-{B9J6F$g#U>p3socDZep*
z<Ux>QBs;SiVIVCw*w{mh4SNK>Nr|wJaztfWjxI$w{YR<{cX0>ujIk;2?N7F;3`UhL
zBWFsbskq?GNlLYhLYZAd5~e?nU7swDC%}W#V>^Lk)AYGdy+Kw-wMKwXYI67IQ_;E4
zN)rv+LF_VoQS1X)ue)lBzP-vX6^*B*eL^3x!18LTBUV$l?Tvto!VtMJrDJ(x2+Kei
zmd&?UvZrihGE9tWdgVe-H5KSltY3dWq~1&`nYKxI=TdB!K7wnz>rbKw*i-STE#6%a
z`ZDW(M9mOEzt}&clAnOS3<zr+e;(5g(8HaATNa9oTgO^!CN?o8x8hFRwO8l2=4@(3
zT3j9DqId5(c=!ZuOGP70en+b>&^*Mv=c3d5mWWO3>+T~|c{&6OjNi%LcrWLf;LB+?
z8O*iGO`pWc#GTru*Qt2_{9Sfa!Z-jfhA{KEiG;V6+t3h5^o56S)Cexa2g7M*Jz|~V
z*9r0Nqmwr|AYmCVO*-@*-lR;`O5}UG|FNOVsia4hTCf|+uOvJ1sQo<G5_RTBS`BlD
zHB#G=g7kRGuIrSrE%-kuEAD3KFvr5kFU%PV7yHZ(K1NCxG)K;Xkh~Q^8#j^CdcBs0
z>L2T}R9f-xt@vj5++g0+hTnL?@A5j`@AGSuvt<}D9ZC_3J(i06C;Ku-eoUR$V9adK
zq2*(XS_ti()h~LXK%d>h(--{QN@_m%Sv7+i<<OTxCxXZvc>oiBl)WJ1ThrscBs7fV
zVST;YmpX#zKlcy?Ejq8p`o4W8#&>6*y?Ukk501-Qygg&qfgBS$&+Qp#vFUR-)!ygx
zFm7iExjZCa)d>Gr%|HKq``XM}!f*J?Msd3Vo#Co&HVxFQqUL6jqq?MFX)YFZdV~_j
zUnnx$b8Bc_bUT{7`_^@aTg77ntQq8G?AGbZxWB2_zyFStRIJ^7@Qa*3v)p^XUaw6~
zD~|LPlI#`o=sMP?cR4eL<D_6oXkhfFZnJ#$-Ha5&>7*IKboT4sZeA1^;fe^lQ8Mk<
zP-VOI_530lXTE7u4$-v@RZ8K%9QMC^NWxxfB;>ATGF?tkth>lh=BEz0Tgmx=AJCNL
z-c@a{LpYEYjxqKGgL0`4Pl^F)bc;xw>~V}&ER`QOc!kL@__C_NFzS)*6Lji3RXSIW
zBgm<MBM`=p18Y()ej}8wH;uf43m9bu`7<HT?{*dFPu|I_zw6KGZ>u7B)T`Li<eqkS
zgx5ZNS*M(pjWAoXj7!YImyb_PtShb#LKa=`Y-X9}#D4v-fO3(qC{VmEZ2R6cu{L>Z
z*ttltY~meQJT3eBLr;0lc6}=Mu?t2DjZKD<BK#RCAGaA%Lb8R%i3oTf)#~2Y@0JQF
z_eQbVkvinG1+g=(SJF(9kWTWL5oR`?2`ewPZ3tG=(hW^(Z$5OC?}61=PQS0){gJPT
z^}X*@2B0FtUa0UT&ty}Z>W^|w>lSQ_Smyj#R|)R1OCmY0kq`Jxi)GXF3X~wT*<^2s
z8C=v>pw3B83wlbm%&PQEd&-?@c|xB5ZP9D(PR;5`)DkZoafXPD{MLLdlZfSoS<E;<
zSQkWU^Y_fP0by<b^Kj34&P{AdMiL)TI%CTz$^m8?MAEBWyl>ED;`Zk!jr!KE7aopD
z{--zYvzD&^T~KgPuR8<UL(-@y|0I46tqF`=$AHO#+@p-&&jZPkA`@p2%!W+7{O&XP
z_oj{_D5K2I$;mXZCP^7+6;IzxiP)N{F%;~gh$GdD;cW24S5LI!!Ro=*OAI&s%AcZ2
zeJAx)a`>1ZtA%<eV70FfGMa^k1*2!T7^D|#a!m=NSZ|E8Q|G;+sg}?-<_YK8+V5@n
zxd?-!H`S_|^E8v<J+E$H_&ufW!Zt3=rLJ?=XGJk;^+AmAfY%+I;;t=myBDQwniq#r
zPuL9K_iZ<Y#fKHMP<p}yKpyJk*9i|qkIkhta%6?%;}IndtLfo_#O0^|^Z9dku)*tI
zaeWPHeB$R)fbs)TUAvf%p<Z9G&t56B&%nIrgyaQecOWByAjN3&ptcTJ9N<<fwR6RS
zJ*|dKBFB^1TjR4Yu=HiJvI@oiPp0}^(ChiT?mkK}>#BdP%*;P0?4LCe%4i=y@N^<G
z^upyI0QpFIdEP46=xVB2l!vGHJ^OIuB(`-F|C4lALLGWj%a(8M@UDaxlo>NwxEl}X
z>Y|754%___UTEZAM`_0#1@fe%E|of4!Ne3$M3{!N?Ga)x9*BE8d_=wWE}B|f>m={v
zV6Pe5`&nrV)uJo2_Ssm*X;u`9R*6|SUY>s<1>WJy)&>bl0%<mb^%Nuj=*03xhghl}
z1>wVNe~;vZ2y1Y};<mZkd|YVY49|L>P1X+=Azf8C%A7rOWv5Sp12jJ$cvKDNc?K58
z==(nQ9_&SsV#q)IRn1_$#gbf9RjJ;^t9b@ZDHO2fx3+D&+#uUX0S{F3J6M$=>}wHr
z6Qf4I4t}3t^e7U^QWmYmWp7{_z=0JzlxjBdFdo9$uD_l;p(I)-FvjKOCqFn|Z%ZP>
zMU$bMx9dSUFUC!a3#4Bm6{Ghrvbko(v`pNpJ(d{X42KNQ)|9w3FAhswV;bMRe<px+
zaf?vmwM{wFPph&a*GjHz{SS2l5GUXZnfQLahX5r49HzH_a%(8FNLP}4CoUxWb#sTa
zeLNnTc<e8;Z5S}(091+8;Bw$4Q2@k*EhT@kPN$InqN8!>Lh@n;dSOrE8(dBj5~L>I
zSip_}CI{at4cEKJg}r65flkDSdIEyE%xlohF&lWc|0TqkLdy?*)prR5a-YlXn@BS@
zGcL8SRFoVOPWrch&^17lT7MFH_JuY4Z`GoLVoockSyQY`(t%GuzwsKxiW%3uw`xuL
zRo!o1ojM9Lt@}EO5UcGDAv41JI{0JKi2I1DZlhO+g-r&U3ai`mlHA3gnM=T!K`YS%
zSsU6kZQkgGNJD+iLk<)(5;Y8`EwpS18vFQ~+ffEGvWRA8cWc&u#;AP$?T0%{9^q51
zMCL+fHk}t?Z;o}bCGjuv+AzDJ=?`#p_T%nJRfwYI`HLdaq{{K0<(zL6xxCDbc_Fh|
z3PcF*6JF8uQj_tgzD_xjEG%Y3&y`zpI3vR=YNF&+lo`{s8<dH&TYBR4I=pIz!Sa&%
z-9#%1I}b-U0)x2AR&;jdl#NCWl`IdemxtMJJ!vzQd7awQ8;lG<AHO8x8b1nEK8Z2B
zp=`>jT!fvJDUpo1V~uS$I@{gp{CG;zOsF8$DtCT(mV2IoZ@*SEx9?=-9JnOp8bGt;
z9&6;W1H+LqE;mH)BV{5**fUj$$DlICqL~{s{u{2nrN5GrAJaw<G#Yvg6+8%z!!i1c
zAn{la#X}2=tC2n>t}2U+wzGm1x1jYcmd2RD5(&?<nk%qGiBsN3$6SWqNW~Ocp+Dp!
zG`#75t&?>%e=no_5k@~eD4(@3EdcVk`&k~hwok!1P3Efqb(H^i(EI~?+WhJZpXC|e
z=Cc^5y-8of!ENg~eqpWU?UXZzy`<LeRyZx|Kl@B^xqd^C&=Es4B+7jD{0{@-x(@yM
zA1n65|8JBp``>)3E8%R9e~I9NNi~qG6-y@4Q^A^4sNyu~sJT4Z4iWm)uyOfON-_Z4
zq@1bLXxaijTMg!ll`Gw;y*pF8z?uhiR)95Lw@OHe*!^KY1#_Wl%92z1hddr(vtNEh
zH_=0xoUhMAH~%*c?zPbkWEm0xs|<t1yi|TNB6Shmt@1=n#^UPo-5PysC*!)#;7M%s
zC5~MMPJGtaW|AOHlmRjSZYkfKpkb^B?<|39PsiJJ1_tBWu*It@{DzoYxFw@Gr`m|R
z{Txu58#&u0YxdRc-5z_J=W64%+4L2tAFN*8gR`mGx;&HD44jmG1Y(4IYOklu_uE{x
z7;RyZgcG20+1wO(o0x~g97%uno5kRbbch<XdDjtE1UE12=K802yNTs99k10eCOg{d
zEVc&NdfSu=9JMf+ns}Cw4&<dWd$x!*$d^s5cj^Kq`DKtvMJ<%@ONL6nsa7J8)@CMH
zDs}CRS+IL*!)bzS>V<y^^G^h`fkSVp_ZQ*Smyf>mko*otjzezYxp};Q$7P9><J8Q<
z|IO|)6=4bCJ|UA{5sCTgih8v`kCOFHH#t%W{`6XR0_>2iEAMhDlOgQ^A6v?&E1%==
zW~sA{B!zKkk4m}!LgH?VjrEim$X<D_PnDDge={DFow+KpO{cMGQ2-?lXFM&vKEY!;
zoc?)Z^NA84!vp2`f&PcZ4A1+Hz8pAuBfZlgFCK@-<kBk^1_ZGe<q_Ry`UAUEsh~7u
zh<ve1+HF`Ez%ockl*w1n(KI2Ak4Y#g{fwb|vH5HVJ?|2yycL}Bz5X?+8a`G|m>}+3
z>BlnA=(s)YoNZK|+0z<rL$ZWKt`J9Q{NP%QN6PUEtl?5hQnUrSW`tB4;}6XbxIPS!
z3r%*$KUe38d~q#EAND2y(*0O$t}Ves)zBiH7XDTm)>rR4r>SyNp1c07lwWr`FHgd5
zYpE01;N=)iR4O8YtPUboM>ZiKi*b`HbDZyprdlu+1c7m99azIpGsGJtcQM1uy8-R2
zfikQdGrFFq0a*txTzv63pcp=Gy3z!VQ{}5FV@pco?uxu(ByZH@iv})o?TKFe$%2U-
z!oIPymJtgXY`!guWK^1w{4~ef-nQrnsyO)USgtm072<7Pp8agn0C)OOu7dh;aG%26
zA<Wy2&%oHF`uo;enf=58dO|0`Wy;Kq-haYYQ~9fCR<3AP^Ex`OhEdLFwi$gi(U?bg
z>2)>nG|6Vs#HGn$;Y(LZpJ+LH0ycMH7-kHE9#F~f{I;WW2Ua$Ve<9*5$o29M5Z72s
zG4hU{#vQ3HNi+p&SkEa-`|bWYNFDp(A6^!m?QJQznm9)JpA|?fBU=+%DlOuTF0Y*h
z{ld@>`r}_uwN%45F7GV~bM+lXDEXWuoLqNWL_2<H>CPI%poqf#r?H+j_j#Uo(i@T<
z4K6Z&lq=^u-^Wt~vvRb@^-x9ouvbk~5%cw0M5rfhiLfbWPtarg?#I!66%PADiMvY*
z5Vc`8Ju>n=tyzQSYV#+>J`Z65=BGiO2pZ3i5;_yKrk3DR(U~bd;b=eNXRRadsU3(b
zQgfOLq{5VddE6cnUY2&)-wZe|igAtFU*GB_9y7~g!~Bl=jF!75BG}4kmiVjAu0MSo
z+E8ux4v4Z!|A>;@x!fOCAr|y<2;gY*iXEWxF~Bh}KG%#hx-3e$>^Ktg+qFIztMi2#
z&}DO7_W9opQ7*doXc`baF!cPGEC|0WtDv&T9nVL5L?&^IdV9pT-)L~~@Fh1_Aazfh
zhKnXxUECpee(^`Yy0LhWqR|J=z?pV;Zqz1OX8K(ESxC;|^&Te2?<|vg&DRG>qJEeC
z;#t|5Yt!vl)Jx)GeHFe32B18)wFKQt$mm}722xA|Ma+J?n&8~xYy26Y+>}ws#k%L6
z^6?jEMM8|nu>2=Nw;d!#IT;F?q(*|Z=?m)^cgK46M;pPOw?L);l2HY&sEe`OE1~A5
zfu5+jH;s1Z6!8!fE9?rIjF;Br*CqDtJgFZJsF>f%Bd)i`KrQ;fK4?}wx~1r(LHq>g
zz(9XB`*!>MqW$(-JN4D30*s}CCUqUL?dW&4A0t>(-Eq+F9$$|pxbHc%9K4_b1lRcc
zXk@c+MJBuz*Q~dnnKAoUO03MYH|p}Ne_gZPCGk`16oVZ5X*hi43rH-F^^HTSlck=S
z&$SJ~4L0A~k(i4)ccJs_-u`BbAW$JaBpG5V^rixTyZho1^Dd0uWJ7mXbDlpW?+ctj
zsOQUy>*JhH?>^)zJcf~VKg;}%T&+h~S2%yI`~3WJPc<e!*|jrk)MgZGy=l5UMlc%8
zO;}XYoy)ZN=ZS~hGHY|tG9A&V*BsA0L+c+n2DRL8Jjnyt%a!iqgxt4mNGO~+;f?9K
zq}4ZChV##V@TJHzXm!~5iOgf0_T=b@nukP&l=e6X<*iX9*t^kh7U~=43wg2>6UO+&
zb&X8RCN|y{LEkms!9^ADQ=tWj5wpwNYx69YBu`H#>@ClWhxgzNbP@FRG(f&gF2)@h
zi;x1!=%S(F>Q+CN`HAjiDg!(f4kroWH8>})mXBk|=h1=ceBJlVD0zpEFZdQ3@S6V1
zc2i+IFRe(ZhmT_!`}xK<mybzG7Viqn`DU(uVUD(EF{t5jbr%r*^Qtjn3u!P}Z&M<u
zkr`F}X~JOYUyOa_^)iIUz;J!tcS3{!o?pzFrF8OZ4GX;8FUTTj6&05;@72EAVV8*X
zu(ylL-#^^j!&Fs`sczP%O;N<TK4A{b<uL_SgneeZ#i;x(xs)1#4A8lsNR5=+91e7n
z+u?J@jUMjY8thRse;Ew_+CqzkiYGBw*a>F9^tnMhgCjmhh}itdG$Znk*4DCroQNn4
z!m!!kUMt`GlWYh%MntBp@Xlnyi-4XMtMZ+FjsM<n#!6N0!C+pAQ)KQMHzNoqIAv-L
z>-U<)&>l|vUqJSw1JMstL%{p}14{hU`!*;cx3S|~bFe_Lmc&da&)WN&A%Jv&ZB6W^
zoVrkr#i})-S#k4i%2^4Ox$z=i;S0YoHYL(DXk+YZaa4c43${+gP0b4z8<HhFU|=&{
z$1z3nrd2yX9$KLPo#fbn;!jefSi-Y!8+(o^iT{%@Ja@u0a+8~qlEd^$VJn&~9DD&?
zn?Okk^Xf3#llvSUQtwcO>J~)&e6l~I^@9sBnj=5X&w}p%1@WBtGF5jJz=`<&WT0DF
zn{Yftw)ZDz1C;$F`7;CjdR|FxyNSA<<^wEz6P@MsdD|q~Ynsv265yn(3{3aPm_gJR
z&H(HKhsYP+16#r{0~vfw(8+xrAh?oMTJw6sW8~*0@u+tQy1{ebzT?)DIt`*x3C)`2
z6Nd=38RWU{N2BV!^Ij`XL-KI~APRaT1<-#PN@wqlnhj$AX5ge?E_kKhq$rd?E-DaG
z?BL=RDK)q@i*S^!De91lVG9S_Ewn+c=wI6Xq`3e{t6^hA!QnnmG=+Lu=W#aJGRYU|
z72;hkD|5lYWp8B=YGO)~3Is(B#Un#tx2eXvXU}3~9=}oib;UvKb{?R_FzA&=8{J<*
z3{UkaS=Wr9#SULhjWnS>9Z$hC?_-8-e?C|}jm}lVwp}uA(^%j~OfZnWc{iKM!ehP>
zhgp@vPsJEM7|@@H=u6aW`W#9RC-g#&u)1Z!r&mtn0t0DNLM*@-^tgDyIatT7U=Yl4
z0<6Bmx#gTSFdc&+VUaszW|Dbd^5qAFvzhlzrIq~LAR^*e1&`5KT8WqAGtXQUI^y}%
ztD{*4rx!M)tTUUITJvq`F+5KvG+0PvpVgHsFVuteczoOIF|2<VZC7po>MU}sxdy7S
z%FIF?+jQ5Le6Q)^AwM1T!NF!**QK}lr6`GWP{zij_0+Mu(JDAG=XkaVHaL~JP+*6D
z*m|k-%OJD~T{&a5^6*}}_YQ-Q0aGqaRD@sLa-wRC%SGp7)nuLtlld?gFdy?I3{<nG
zo3bQ)wM=Vut`%&n{-IkC1;GNNk-fo>4M<6Q8QBRBm`VJkTZDvd!-a=w)HBwea%eKb
z23JE3V0pR#d%$K%azvBA@qNY7#<*0DC9%xe26iNJ{EgI+Mu1>Q(xozg@@|I5Il(`t
z(2?h5D4z2n0%mqO@B|k`?@%58)@6iC(V27W^gCEqi*gQ+>O9QPuk>%}21)2}B;WjQ
zEC~Q78vJl_$ob*I<-UOK7HjW}+0X`@d~xp&A#a|)fD#hO$S!h&g;Rn}))^WRyFQz1
zltx1JcWFs)6`+Gdz#$zT%y)a;RTH^B{v+|kXMN_Ddc|X3iREbP`Qx0ty}u}?%|dq@
z*=pu2l-NI$SX}qMLPbC<)W$u@2})EGsJ@+Q7EsJg5UfdX4V=%*q1o&Kn{IE}^DcHs
zqUZlOBN9~@kvw8;&WOHW@1segq4rlgTo!6SbSUS2T|-XFI=D5@Mx!hJ-PZE6i9RJ3
zaq;LZgVZ;k%WFa)UF?rpiTv7KNVh)>lEf!?*{$(h;4bU$TeHV9$sRY$zx5V3`qv<G
zw|9Ft7O@7fti|w~Mf7OnZGMBiN8-MdZE>?j{;-1^rQ91QzC3wH@jZF{^4eeAQq6Q~
zf4^{GZwH#ZWJkvK&tR!n&8x{*t#N)7>{|IzIb3_N^LvN;KWu7wGsbZv|AV8=$xvr|
zjBs9g27>%gClQ4h4#SS;Gn>A*cNRM<XUH5|wc1ztG_>!YdboP|pxT)RA21H0yop*x
z`38qHP}8TZ9GNq&UisyYAAN#&&@bHY8^@bvyKHBM-MSbe$Wir1G%m9rLkEB0CV5_6
zbnG@8W|5=U4eINPtTQr6SN6L5qt7+zDxU^7#HiAEi0Af*=Js5dPoTK$wM?N4I_$54
zKJ@?4;B$hC1fFO}7#s3<)Ogv9!W5Yi16t3T6GgIKsW_aq&F=Hlgy)ep>BB1Qu546z
z$he&|n4>j*{tl6~LE^lq<O}55T}0#!wQe+Q%ZeLOd55QGy4tx+ZA-)a`<~T&r)d83
z&8vvF@$~#z$@ef<_a)MXgWq=+aMbw`H|}#c&%Qq)Kbiyi0}texXK{qR*-;S;5ZN1A
zME>rI7}M`=3tYOw8Gb)XaKqNjSUDQ|63Gcb(ioXoCjU^YtC9X;A(Z0OfyB#$LW_^z
zASDfzYnj@@D>}HzSm5}lIgkmahl%vZYi{r24>R?v^hlqyO9?qpb2l(S9BvAfb7c+j
zs6ia;EX|bO`gk(965rOG`*+G#$aS5^s;l!Vw{d%CWEgWAupk3W#78~KzcZ!pUb|f4
z3K>}RI|>?>&(}nwm=TNzQ0VbNxxq^3Uvkf`Wlh&G4yX!G{7@VZ4lkVt%p)}(cFZB}
zlRatoh(qyt%PZy0hLMcj24YW#$M(H7;W^k)J-NxmNAFhTnRS{cmXAj_FB|TTuht^?
zlj1P^H)*bkdM!#&Ui=@;TEff%OnRMV`0RPqn16fpk7*^%u5j;`v9q4yj#1;~%k-`O
z>gF7|FH6-*o3ro5+f4m@9fPT_SR|e_7@v}YrDk?#e5>(S6MIya(sq`ia4~(MyZ80d
z?OJo`FBJIhyTj@B?xQglz<Y$mVZ$X_xJQ%LUCS$MoSbaJ?yj}lXWU8lTZ9!6(S%02
zx|<0|Eq1o@u{}>-Z*~QVSr@<7k?<<I0LX?A7p|FTuC!X`WC?&w3uK?=n2Dlm^|K?C
zO0H|{+uWBA2&w)@(p5%9*>>GWNs(^pX6Wvc?oO2u5CQ3Kkd~J2hM}apC5P_r?ixA<
z_-@~i<uBKoxZ%1^?6c3_@yWm@ifZR$Go<O;I8x~0P7%qL(A}6U1tITy*k$jq5V#Bl
zL2~xipkdX}uSigq`UDzyQ)Ur9RFw+UtSK3{*9KDKmo*~tz%s;kAD+(V%%XPCxJXZQ
zj~EO_5N0N^qH3*+TaA~OhwNWi_^efK64v=TXZ|i8zW!V#5+^JVSxLLlB5fJ*`xsgb
zy8$S-3?;3`tyAJZ+4+a@wHM)7r78bh8u^~z+-S<`6S!ty1Y9QB9k?@Jk5<`m=pC8b
z<gri$4A$`*ICUAXj5?lZsZy;Ar^*zT;CNlOn2PUMz6{pguk3KMp~Y-LEQQ`nYCCX~
zK9Nn<{Sd-cj(<H(_KoG2Z&;}d$J{~VIxR_omh7&iL+<JQ?lBlJcB`HCvNoCi3#a10
z>u07PQ@+?W@**wFKGQGVtI^nxMCBCc*cOn)8WPE`aKn=LYQZQ`(7kB*T**z#6632j
zo?d*O6c!Kf|967Nb(n3E2Txi17fzUxhU`XrEqWdxA%Ey@`N<d;at*V$+VN$Bq$F%0
zP#TE+ozV&a(fu;<^!+%=>GqsOF0F5{wlQ=mIIqJOt8p7>G8JJ=2w~=10)-RyHl4Jh
zadMIc)5QL<tFx?M0e<}-#`(jks!%hlHD0>N&*B?V6>cLEyFCcew-rQ7&krP|b<yXG
z?p_Y%85lmGm#SGHvNrtKu%K%w&1X`5)w%m**g!9jOV7-=?A%6BW_}j`jcG+n{lhT%
zMg{{sBOrlLTYk8()FlDZlJ+RJEc4mlcK0=>I)6?{bFFe|vwIZip}6~R`|rn-i~)0F
z;&JK*Q%<j=ud~Dw$kvcvS0#nJM)aY9fdTlw$o&YZAz#KT6%Ol-rseZba_WfP+b<YO
zmJbGP<*Da}m&+S2%G&H&F6nchj;}4Qg*((3fQA7O#_)qqYU>c$`0lUH-(~pWLjG_s
zYh9to&r)3xqXC8rFB=eo`>4h-=+eo3^f`A6>+7Y^dF|ZM)UEdmU<L~T?iM6u*rHSc
za`nLWx|@As{}~WpN8jS#+>3IV)A^$6rOuh<a0%`ruElBN5Q0vuk3JH$6CzWBEbtLV
zm+EmJEH9bamgD;)s6;;*nzvtV)i(oA1pK&@4gPzs@P^~s#lusJYtp`VOi{e@R3&?v
zHc^Kdfi?%YHW6)Rn6w-b>B=h6Xf{ug2~|_p(+8djB<~^IQ$Hh~z@|q;owxm;bka%j
zdDFdLr&!w9O>7Igfjcb|E+p%Um;1X>$uRT7{`{KoFf^92k&hU*v-CE<kHnbdYH8%Y
zVFO((yt$>O%U#TQZ{{A8y05OeGr@8|sXaYO%v|`@8#;=k6rIE`Af&``x09*wkYVp-
z93M6M=bFXTj#Hd{J4bl<X{ff%TJ<dhts&v0v(KKDOIrI#YF6yOAE@x}ci|t#@eIUr
z)?6F{kqwlGqw@K4_mQmYTICo%F!EzCTl!*#fHzZQmN3-2Gd&}s_cdLawY0_QEG>pV
z*Gev5mF$s{Xs*YOlvy!?!O)=*elAHe%~|YqLBFV7&xrRCRtY2#j$$Q`FF)}#r&Ipm
z1N#CQd1fYuM6WM_!z+4a#_57ZkkBW~i4u1r$UEXwvS~>(aG7+ehdI-ySu}~yA~Def
zU(L|_2m<13donV71m)M{<1j-w($h%=NzY4|C1v^}6fmWq@reg@tbmBnSRoteYZ2IC
zY)DwxJ`&g39*QTObEAl(d}@nPzp4<6bSe%5Q5}Z*7iOP^3KbvCIlHF!8=?mE!9aP$
z@U6ad=7bhMKDW5z=4B<sfmD9QeOvcHN5n9Kr{s7R*`2c^9uA_3{enjwmO#UqyZi8`
zVaeLnv&p#0RM3}j@^VVtSW?K_s3y-WugvYP@TunlvGTlAC5}D%-S)S6GZD~R{|ZLJ
zwD3Z)XD=p(>2+#_DY7ti61!*HJM`Z7v8=77$hgvncM4jrB4hDVTfvmZ8JKj-Jus4<
z1wk?4Xj5aRIz@#z8iUG$^;f9v#m1^wV@qXtozd|I35^sHd*MwWCXz8LTQ~HnAa?n-
z_POEw8FJcH`Tovtm)$3Ti<1*wg%0#xSeMzF_mgeiLoG%nyO92O;6Rq&5b@3Z@IIdc
zDpp`Xm?hGX_}?=~uchC}=ZR#WK<A++TmLVI^O#CBJD-Me{;Fx=<eutUXHelWY}8Gx
z2O4|SF<rJtiqbF$=uwSdLc393Vd-LB?<HZNz1_pfa^jsQtiL1nABHDBBELK%B|n_M
zT>8)rN$<%pjYJhNIH#4e>kLi1`iQo*k1W#z%?Y7c<ii*}AAe_+LJ^xUaHCa-qR5z-
z(2j0c+YRRwnW(qrFQ>mK!d|?{9c^r!%92-G>CGReN=&_<SLDN=*W&9dhCPdVI$stM
z@Q+z+XODu^BTJEGE<IGDbOc0rM=CoU(`ro5(~40py1GeiZD;QL3y-axJ!e|UT1vkX
z3+4xtR4PX~nG|%-k7agG)gjT@qW{KDs~GO=v`>76@cA`u`zUMQKXqPvj77&>?2Ys!
z51;qRDl+MR{<NR%voEq`@OJHGlg%&8$oGMUcG=gM%(O7*MkP7v*r{mJq;NKO(y7_N
zO5^xe&&H+L#bAZ~^ttT|WpB1YQ#T)*fvoOqj~(Be*W}mxd3P(<ABs7M7cgYXzwC8z
z%0jVmceX5-lUpdAuiF^6XO>t0p(^iQ0n#DeVIO>-Mw7{5!4QBY&TWvbnl#^JV0C#F
zEW~XP^L;#j*8^BrS>$jA!eMnT%68$~O4S%ATkjO8iLvZ|iajn5fp=^dwGXtSpY<1S
z*Iof(v<<6$752{q=g6`GfIt!84D!j&t+}qI|8wiGNx6Lc{$?=cD#hOzDi}xxujJzo
z3lxOuUJg_l6oH}WJ_}07ihbf{ThHR8v9t2(Rfo{F`tOgZ#V2go=xGXJNZz)5i0>}*
z#IhqJBO&ttJD8{hBqY;vnf?{y^@(V_OCrGiPtC=qhlKEph{ELZ*MCQ^{V45jE>X{;
zG0vYgYhKISM$k7{{EJ5A>HF7$V_Z*QytxERVeG}MFq~>aJ(ak8BLoW~!^k|p47)$F
zp<_ZoNeU}D7yhP6keBl{JtLKH?=sT`#=cd=hwsqyJGTvp>I)%bLiFH83pYz=k&dfD
zG?M9$6bmQU_NbXaW!Mu;PY+UHcw*(ro}C3~vRhAB8Vb1DUx|o<1ES)&Qqves35ohy
zmp6O?TJn`dQqs|N%Nt<%2Dfl9prs;@m@y=mLs*L<neW2~)&lC8m;-$gR1JjyitfAo
zj=%UDEpIA_0YwUN!q{s`pP$?YDtLt8kP53EC%|!egP$%@0o_0~lYe|`!1IXk_skE2
zq-5gf^&LyL*=b1yz?J9P^G$h@V%aY6t=h9x3HyW8m9Q0Q9EWZGfKXbp&N>^)H9>lM
zN#ccDIi-wgw-%=)oLRzfvcc!F&aI+1K>Le!=<L%?@z41Hq+-CUk#}vt-4fe^f+k6w
z%*CM`Wir{{fM&fcXCTv>ffT?G-u0aEVm<B1X_`E&o;<{&eJ74Ped)c{+1@)_uMDJ9
zQvgM3pQcs7#-+UINdbjfHj4^Kn!6T{5KrTP!fSRB7Z049>p$&>&f9SrS=n3Viw|EN
zKE5f9YiR&>3aMzVPSHcaPJcdcT_0Rz4g0PqQB%68&ABq<&T1p@p@wa_C!dpLfmANK
ze|gT+D!8JA8{)>TJTb#EYFDhQXDl2nJu<<^>c@rcfEepvnO0dqm#c-9RBUC>v7KBj
z9GWltS{`svam5>H(#^iNRPKVwt}&{~xUiseguh}({ys0o5L4rrtV4KtLTjlbhFlus
z<-$}#L7tiRDjjWZ*?_gO!tR|tAK%e+z)wTWEksInG4;h6Zf5147?ZgrgR}}rrc6Yb
zhQBU7WFWnN?yom4{h#_)Aj$|uOR}Lp`HaRy&pf1sJaK!Hy}v<pBeMCCNv1f8uRL#B
zyFGOS*UjJmo;r`lB^`a`R~n<mp=bzr@}QX?+?5Ad4%?~MF<1PtX3uaVWZmHx;)N+S
zDQ2T^iVq<(NMgSAkEVH>N)hBwBcVV}i3*RRAwz-No20k!s*3!ZqEI$tCTvUSV2LE$
z{<jn|chJPsIsr2GRzXMtSt(}_reF@-yWbRMzc3kdD9w&=2_&S4UY>g84r2#+OF6@-
zlnNrB*41OD5a1<J?*7EwD6R3CfAc2#UlAA{zbzS={GNIK3-jz}{f^q`5=*U1-cHyf
zgQ(k&ka3dq6=?f)+?_qxT~gCyzn6P9BdX96)+al!w~%3;ze;PDo<N#z<afnvPA}_m
ze7|%1epZAR=4GUV+f@R+-ZLv-+!V@Q*#U0r1FYl&U0ETExWh%eS2CYnY8xk4KVX5f
z#(B?oo>??^=wRy@1a<V!vjJAX+eR8$_4nD>);3<BPqQg$ajoOoveUQkEfAI`&ar0E
zJ9u1~7+SKs9@k$Nzg!WIjN4tdpBsMn$yY9)qm`!#$<<&L%HZc1x^_-9dPvk|NX{s)
zfv&Q`0xcWAkR21-yuilCo%U5SA0Cuj46<orcdqCP<0P9;F6O>Cjf|lePS4JIDL~22
zmHVETbEct|+@9XolQv1o>3=F3^bBmKjvu(cu!>`1NgqaaRFvr@sT9WLtFfo1l9@Qx
zjLc{S&l{#wCUZR<J5JQZK^hHP+sPsC+>(y<TRR%+Ri3;9{dsmMo)&s8r5c8P0*~)1
zLK8}U)itbb9nET27#I}l03Pi{;ziq&hwcC@oKW)HdRY)$5<9+}FwC2uFRhY6Xy#n-
zm#I=|n;)^%^R8>Zc>bKdvnzg~AEQ=Zwpkb{6YxbOQ366t(RNLh+BPg$=uc&1O7?oe
ztfOV4foJ<qeigYmc!T)~mqd+0%4{x%WKytssaBbQN;Z+Hw=k*qBsT)XuK!#!G5nv#
z*52pKzK2mkzw1p}Uwa=iwiSkuKW;6+zYL?#yL;cG8e^29m-nC$I<-XS^^R)weT+4+
zag2)bS_dO!*%>x}TQAXw8~m11d#l<m-SMoAUVA)kZ9{mLv*wMdA;I+~=ge1oC{ejN
zbGrbr*+?2g4m%P2k1acEV<b$SS<&z8uCl9{Ha3nT{2m&GFveDXLBG$2(>EAxxP6D+
z_r^f%Yi&ANqgabWI*_{DOa6-8AGHFVemvK7l7M<#)#TySaz4Ue^-9$YntS6Bq{d_*
zAC6@kw52r&3VyVF{F>QAxI!UPS<bz@EK2>KfwqU4W5PTblFE!{q$jS99X~+G@P$Gf
zSN-D<YaDVgXV?iAJ&#sl<VV_ATSitC(h1BjTX_mg__@-UhTwg_<hJK@iz9xGTTH6Z
zydBM4RYv4ZOqnYwC}I*+FkIs!mZ#BQ)ZaBxzj-C}XgHsrgX(_Y%YC2>q6pW0mq)DE
zZ!RvMtlcGph3}vto09{YEx%C@_D_(VCZeX^mZrwR<;r5>md>?Eg<Z0B1Sd>f1=g{J
zmvU-VO=pGP8Cx*s7Ye`LoWCG?41dehpfD$c?HRY}?=V$n?9?y5Yh$O1oQ`8R(Eh-<
z<C-}q)%;i2NM!K176*CPHoNCdPajF=WB&(HKhF?~Z~+e9I$F984!*&|Fk|4qlEM^>
zA$3OSnO|+|h6u(+G#r`xhl5#U_o`z#J8#B@Vcm)l=o3a*X`b5Hr-cxe2{$B=1p6hX
ziu631C9f9@<MoK1d1Y<I(*U^`eOJK6F|rfNx3<`#Mlau8Z)F9$ke$Cj0IVbU{sEUW
ziFja@41N{l9^TC8aR5TmZ>bw;cEa&~P%KJK{Xmtx{HbBh`nJg(iZ14RE;wIVS>3VL
ze+7t5&_rwU>9?Lv9wS&=*L^auQD<C)Z6N7B^cnFFr*ds;F^-vb=KeAroYII|Zscpe
zA0*w|=X>n-4?UNK7k@M&p_fu$iupnD2LTv;n0SkQ^D)>Q%R~g1n5GKO=92XE03%tC
zaHoB`loXKZC)G0<{%~w>u{<5C>BGlAm2MV|`k!r*qoUAPD^&B>3U$t>4&8%Vk@4WV
z**9NrR6E0Lh=rnKB&j#*b%Ez7xs2#^N7wdg>#W5r`On)9Su0Min|-T0nAUc6X(te4
z&$8a&GYdxJxzaW4x{(}N?)Mp&d>l}7oHjJl@@I;523h_{7)Gz<k|Yu09WfX43eXtr
zZ@8f*n9%3j`Lg~P)Cn6_^zyX@Vv-`8^5x=q)>jLV-?yuEtJIg(Y~O+MbmEcqwH3$9
zwTM$fts!*3^K&1U`Kx~8u)H8YC|gI*r2^L}g6H_32-@`OYV1zvaklY~(wcp4pi27l
zhx_5>uCl6n(b%V4y66}Oo+B%{B?0NFTSt{WwFN(rB2PzC&(P9-drz>XVv8TKIYU18
z>(xzVdoK_lap+~po5-Dovv<Eo0NdYcZVyF%52h6rHns*hw-ORYm|72k*+v@?^f4UT
zte2~0jrW7)(!TD`yvlc7J{tM_n?py4(YczV0^ScZ95N_EaD$v#A_Yq0R^xe#D-%4I
z(ei}{m_ZJ&h9Ak~l(c$_TCdV*L@NHhfmoC1xK|_o;>j)Y_Ptu-8|C?)_tY=v>yMP#
zsaYGkhN6AVP%NNWEnEbjiW!P?;IVqa4*G3;olX7A%7{ydtCyD<XGKwHFzMc<m1@+L
z7ilzK{sHcHFVx1_1(m@kz`~!#lEUm~#ps)NVb_FBh}#7r6)O2<@lu0`r5atlogW#e
z6|fJfgTlaLIUt0Om{N^$1<P)NX~?)Af794ZjU~JJePO%*MFWr!O?w9s)!S4^D&bH{
zKZ}3O1)(QF@g-884`<}!h(umxixm)*NhP#peos+f`2DWHh>N=dNJYY5g%3wFVxcAU
z{|grImJ@@6)s!c2ArZyl0X87-+ntfzy~7m2=n^i&HHNd(XHqx_cM6EW&1Zdz2V6=E
zE-fTI*S<oZZR;6P^O!%^x#Uf38$G!gySqw~U*mN1Iadd?(dW^coDb2HSy}A7?40Ws
z>>|;B^Ny{poH#z+(vkbM4FFfV7162J;pqF-^Dmiv+44DQy142|s=}Ju-M=5W4cu0L
z0@nn1{na47Ta$-VCjXkpyf7w<2wTDG?ZS%nw8eEw1_;P+55SHHxzEE@&PwAn^w8C(
z!oX;||At5O(ZV0Nzz41vu3W50qmZYw4wd~1>TeG6rWVEjapKkFfs9S4T$ob#wgpz*
zT1B(Sw{8P`n*qmG&j`RT&8%KJe=>jZq`GA(ZyH)WD|pzm4@YKEkf7gOQ}Y^%?r%!G
zyiy#4Gf6(8mf%c|)^pAO>5G-a?hvDHW%=c1Xd@JM@zHh^M8xcjy5eGr{3Z=NW!>W3
zB1%n-(BB`fq@trCe)S9f6N4s}jYD<+_*!TE{yx#Dx&kfIx|nxLS5H-)*8bG48LOfG
z(v92bJ`3<7sZi#k1WuN6<@Eaqn@XeRmZ2zOD{i7?Quo;((Tj_e9gm4lLSTeLkK$R!
zW*4hKK*dh<-rip(U$ORK<8r9$zn<F{AGgk;W5x!Xi^t>XgkdC{-6?p(n9q$6g|gA$
zT^>*0pHe2P)8DCnZIO<F4KZux&Mu)-j75-;5`Nxn=1K=2pZFUU0=d3auP;&e>TRp#
z@9Wy@Ue_K9wMDr^#_T(@?e+*g8aTKUGc46ytgn5>cr?IyYF-!w`HSbD%!`k575fn0
zO16G+6>BowBf*))n5M{s%Yr$9yVTY;cjW5HnW>-VSv~I7v9VK={<g;Cw%xI#&as7?
zCK1^H#rf6CX<f{rA?@zlDXT=eKt04j0(G$zhQm;%V28he8+vhgw^s9j9AykZP7v|4
z`u*teCx*Pw**lx5jM%%ase61c8R*VkZ3L=_Elap87g<h@$4Ew|d7VQXz3xJu>nP!i
z!#DKmBN=avic%FA4D1%ERd^>7unK_I1TU^&*6j_t5|a2j4<R-^8t!Heawy2KRjA9$
zNh8QV5BF)T?-zebEDb64VIJclS4@Iv9HB#YQ!)+ORzX-rbUckgo_jEV2^^IR1)~7&
zCwQuY$XHGa6(YG0*fQ_sW)VzqW2s}?%WvM)0}E?NXPfD<u@1>fY9sCyO~>0q?m7z#
z7PZZbfVKnRqj4qi0xaz&FagRA2itvc>nl&b1CV`!CT}x@o*DO>L`ypQ;g63$pEpC_
zXNYwUyk1nUEjv<^S+`&Tkju*{`D;e@%QfBW0r@lCuH)H2rjI-owC%T@-xJQidqe(w
zFW5nDBa%ac&_Q0^rf+Um*mdV;pQzBcc@8^e<K*KTDbX~Q<&1fHSbS=1a(4(Le?AaA
zZBQ)QwhMy<X4%>E#okCusKY0f=UbNiY_6HwiC1*He_ns3jFMSm;}Qr!Qe)8cKYF~;
zwq4WT-xtf?A4zq18C&;F9vtK>)WEO121#*tMNnI7%L;8w_vg_6Xc~s|CZT6$w!RGY
zyBGZzK&CV@`2|{h^Nb1M-ZW=~#S5h@=j}eMRPa3X)6ZKpkwsOcpLMp39ZpheN&lv?
z_c4u+ZgjdZt(^vT^bD27nBZUc0wZP~cjMCXz7iAB%Z8{u1}Y}&@?CV>Ljs>A$_KyS
zadyHk<-tsS%($DHf3*q+TIs(Nvh3WR`X9(*5oeOU-u9@v;yJ5Cp>t?5I9M0gjLtr*
zA*V3oHA>}pmO&n6(xH=7S>)<=w^LfCxAV++lmPMraDQX2=GWZKm=^MPAKZ<l#xV}>
zMSXFnZ@qmx>_ai|lS*8?#zTscfyNSM^t#om|D}w>sO;Rs_rtGWn!8j08RJ{J<yRxz
z+O@-}D@mferpRq6M_-5FVWwk{gjyA9QaTIl!on+YZ8+*inYGgP!szwkZfcz>65Y8n
z8>J8h3^xApS!`1fd>ncxGDx<r37<hyaiLhGx<N9Laq)+%c;nITWzSCZ;xjcoVQDz|
zXZYB_+-wSYPxwjf7T&;*k_s5|ALD313h0#1s18XpVT9I+qD9Z>JRfryJqoVX6BX7I
z7ic2!)e_#O2?ms+Qks3lWuq!YqS{$25~NhpD*Tn3EgpwSPl|fVALjhD4vno*#;wHe
zWAX_#BmGaB5E&JoNWJY{Z}AX2@Nra^AcZ$wSI{r!--IoJi4IWYR>#p;9>}$432F<H
z#xUvX07Zl-;P4`dFUhK}M-@i9y<N!Sw)1qpzI9YT3&-E?N@aF*y}V%I1l=Ot+Y1qJ
zFuBexs(q@XZSP<@EfQ-Ve25`vZm$a450<5(JIz?n;pX|MFzD9dm0Bp|0(5^sEy93%
zi-F{+w`7xib2GDh*dlH;GC-Jf%;<|*UA?%+_IimuZ}&&D(hd5Y52$CCzXiS+kb53#
z#hy~wd=I&cRHM`x1=ySq=K_CgOhvu@ku_Y{FW8dzwUlUoh?*NNrq4EhzH~cbG}DI5
zl{(x+kkl_-Q4rWu-t;;**zb>WVKp!W>zreg8aI;_NZe95mpXn7HNh-G&&g(Ej+c|?
z*}s@Op>gWL12akE(w;)x&0GQtJtNNb+v{1rQoFGCwfQ}v1JH}jxU43w0z!nF>IkPg
zE4y~bu})`O&6qdfNM1Q=hm)K~({+01q<?;$!c4mIkPUS%=I1pjP@px(IdxJweth#D
zkoCKqEHpsqo0Q1X%<lolFAf%zpZ+t0tSM0G;2|jMs&^9(PoxmCZ0YsGq5YOXp7H$|
zYKr2lOdF1K36@Ww0YF>wqH+cp=zHz*Hc+EQWl{JdhSb~H&NMeP4Bp%j)!W*I{^Yht
z?d0Vd1K>vB(y5JgO}PNVCP{H1`GW^bg-ZabERPZ_D@O;uPIUr}`p8}7xakif<2pap
z{vK>8tageWq<K51moY}tb^6G7gT|^-WH1vgWAvy6Wi}%A5m9t(gYx9#epS=DX3cSE
zlkvd!B3WSYaib4Rr}CsYbw)Tok7!nnBDFk-vY=+Hfn6_T{gg@NpD0j>r6;Q*bu}E+
z=<X-Y<faafmT<#Cw~8Te7-HRjO5n2nr$97E1w@Ol77+CWk~m}tOyctqGc#^%2e^b<
zPJ)6`K27eBs+TT2PF4+3i`xZv7!x@+o<=#YAh1F?k5OC81(%W}$X-oKusDf^HGJ#Z
zNcSn?165E5E%$fZ`^d<iSYW*K;X_O&#jk~x6Kr_O8_yW4d7VSo^CXeN`3qkWloJ6@
zK};p!BJ|!#cD&pq15sTjA2Pm{ZSGLraC+r-jy7d^?$&wiL3tw+^PT{Ik~?@CBKtVa
z4@2wE0kjYun}JeG>}4ARc>jrG(zf}DRhwF#*_XPz*R`CwC$II^?jgrOeg#6JA)xjO
zcXVc$SdCU~U(21p!l2y~9WUTpVyqyp0wVsG^^V?4N7D86PHyWbU!jc+^l|a-hoc|y
z3OurfCu$(QXQaTB5Dz|@2^4Qzw<B0+U)e&Mih3g<C#lXVI=S_VafO-(NW6OaCM>^|
zHpwC5_Ajgpqr&0zk#WAFT;wZbsN}SklBTIUziP8LyW0<3dMSr)*$5`Uk|p&=Dge^s
z8VL(1&N?&<-LjSc`R7+J*3$fwe8`4MB17&Uq8Thyb{+6L-1J`up(}QU&88Zu;W~vo
zN)xMZu)IOvm~;;v4YqlMCEwZR&^~KiK5Lw(H=r<)<-i!N+*d8oF>YRvP$wLdk$e8&
zg-+m@K~#P@R$UT`EpjWViKk?c&jiP<Y}ORl(}2GAMF;DxwDvg`zuS4&<KU2Bw6XQO
zRMm*C=Do)yI&!vh`_{RISq{r$M(N?5)%e;rVUD3Mwebrr9af!NhM4w6lY7g_b{Eho
z6yVhR;>OAiVpOgpcKIvDV04fjW*eroeD3t~$%?_(y><TkBmD0a50H}_yqku~;!QI?
z5QDe$5>8GJ+XLfnqEuo4l>;-gK%r6m`FX1nF0M#^4$fXZ4%Id9>Ze1?BT(8Bxjq41
zDU>m=BTU>GPX0d&izD1L!4N9PUo3BQupusO7s7{lI+F9>)f1^oIqP{a3|2oREWYw;
zJi5P(KW*iG)GSg<FnK*UeKw1if(jb91>|P;Onm?E%@IG?_p+k|J&OzRsjS-oX~*ZC
zCvcdN=zul^7?KNR5!6&w4bGM^F|*nbXvxT+>^K7Wc(fr~&hpKtPnKuP=hhA!r>UG`
zorC3Hj`cg*B--Z|Z%MWBl$5pYN#ga#3UrRAP9Oi2*WUtmZc_gM0}ka(w{?-=($bh~
z_G3@V(}v;B`~CIZz4DtEPtueAR<)`s=1c$sKf8O5$P1$QWxx9KGmA?zX)l($S8jj*
z9#WIx-^1x`?`JDO+45stWP+4}@8ud=h5jdFvqEvq6BfFq27fb4Ek?`1cFQ9Q&1#4X
z8~{)}v!^4y?rDHGMb=+#=~tRM`o->%{DOfGVy_u~v6Z8-vPF_c_O&{rl{tM2E`>ht
zrvJGWTsf@2$P2tfjxY^NIIKSMpiC;f0vd^jK~>w!+B>_`gXSiJe-5vVY2e>9HS2W7
zua^h0v2UH6dKMa>6BRR33f~!NUm_~~Vl}C?hZ@>XN!-1g!b>c@cSlH)b$Oer)z@#I
z8we)wC`<D$`bTJ92b0(KdgT(^Ty%e7z1<681R^0&;rs)?ew5YP2)@6;mwX@r21@ZF
zJ7y&K2J=-mfr?_S;`3-#%9(5(P66={nXKD95&Uj`V1@Dpwxzw+>0=(6!heu>KfmS~
zJWigyIhy*8Wcu%1y-1&$;&f_B(*3br`@aF)&dvZPIZMUG^YN7|E6v)tEWmnsi4ofX
zQo<Rl2oaic;SoP<@7UbK)HQB8Uvi-(y0D0L?1*e%Od7dVAic(hLwy9N|DAY7Qe~)v
zQifcAcnqJ~$#lfWubX<E$TSqR5)POa1#eeZ#~BpfExSLR-36(n-Fsu=!s91F5x?YR
zPdv2~G_u8%Y7Kre634<vYBjVr8Uw~wveaHR1MaMV8F3|f`bMu_BGmDvBnI2u8geCJ
z%Vu3urDtkZ7>23FDujwbkdj)V0s5SvfSyG>af-0eAYQw;tO<MHlVaQX=W1^h4JdAV
zFsOns2}6bk<USwqd08Vvc<o67WvG>jdC{U|YGqs7xsd7Pzlllp7Ovg`$`-i0n~If)
zW4%#Pu8f{zc2zA)OS;G!+QE*CT@I)ukZ<n%F*YAcsus?B2p}an2S60}Bxod<u(&;N
z_7)_?m`8JCp(ZboG3x9H!3^LN<x&*2+vJZCeKZ8=MMmSMrn+J<C*7|6w~le>`s@=N
zJ30CGQ4~WEBkJeo=G(r!XDNMEW5Vh>Epy}Q{w)n4%QTc%Vg@)4_Me5m(H=r?Fa@4F
z1)LS`=c8M3Tu9|uw5?uQwB?>ZNsYQKqF7WIwDg@ZuDrY+Q$qN5W>=Nzt$*PU5Hh#4
zaqpOMDG_Z?9x<X`Y4qc7q0yXG$;xCpr}d6Z^wPS|XS~LrknKrurf2L);FftOT@V21
z`Nj)D8X5MBBJx)rx84tX(F51%pbL<~z`ioj3tOZ;PDE>cnJ?b4j>gahEza>m;xJ3z
z7h9y0l<DX-tHKAh8YA@xq(e3QO(pRh!PP7aACdh_tZ<p*OB`dD>-(b*onb#4_Ql}(
z@;_vM*Wz&rTTW8Jlxgy9Du-NNxt1M-P?nYRmX(j`U`%^eJ7)r~0uCY&O}~TAg{zDT
z0d5p6-hm^y3y876JG~z+b8g$H{uQpFKvV%ys2#njA1wzESCe8!Nr6zl?{w~Fj*(8L
zJ(0;M82Z^=0_wWjYF#IxD)I~;#)NvqdeORVjJ0IjZTY^q1n_^S(*3JZPa3^ac7t}5
z1xOPiCxHvarN>e8*0I0dsSVm>;}S`boMlN;d_)dfsI&<^7?+jBYrPR$IsMOX4E-@O
z(){PY#*vkuN3{19YWFfUZ5SCT0;KedC_8-sKS2%vIN1*)$6T;EyY|7sc+=&_$3BN{
z3_tg%D}tnZ-Pfab5riU@`Tg|umVb>_UmuY?)svYog6~t~`etV1eo6+jonn&>uR+Jd
zXawv4GJk)lYIiDVF#f(|RuGuB*dNUhw)hf?b13&bFOJ(ni~Jt38tv@Pj+Fwn)b3aI
zRqW4B;LXP(olX`mItE9KQ<Ag{+uTEA#0)oJ!O|5*M$3&Ew}BY8wM}~F-@pG#9#bZf
zSNn(00++3_L(pd<>nDJ-)BqR>?4eIYT25R0zRyS)a$!$4EZicqh=YU2h_@e>@Y1kM
z<_Ck2W5Q2XnA8{-w?X@vi&UbZspBJ@TwGGD=4TJTh2%tDH+npPl4<K{y>n>kv(@@~
z+bT3{D~P<)EmPMpbqu~w1oLmn6ni`9>+ER`ihubJ*kiSmzTNEo;L_XZmy5UFMcdUi
zQyW8x+P<(g7t#BR+vxG)((Y>0o)INoey8slnnjQjEyu{{9d&Jl-7KVUz`Rod3F}`x
zX<6EtD@S8BY?CaX%QZab5Y*Tybc)BwJYoG=q7b&2%c;5BPL6M5uwT9?kAI}>J9Zg;
z$0NNtTf(6dgRVY$YCx66g*q0E;pE_9e&{ysQgX9`bmuxSuz;kkU1gKWXOx;dcjDk=
z47bhkPI~;URXMs?lWY2otK0nLMzu*+Cv=X<+toI$IrmahbzM!n!}AP2q@qU6>Y{6l
zGiq(DYf+X~$wbspe{(C72mff4^!$BJTCE4r#=fpr`Xy%M+9}40p-L14%BRKAMT@Dt
z>;`AoPMu!38TrPW_Hk+kpYAXF-EMk$U)`d;EE_#ojo=PP3L+f`1K>t1l-u36vh)KR
zE}Mi=mF>YavL`MYvE(E>ZvFa(Va=hNMKGCSJ0j##5;a}GdR9&-Sgv_iA7+UKd3V|%
zODIDa(m&t%!nr@D%q}DpWMg-3UI0QVQjMYZk07A`r2l8yx<v>qV87zhDk@I})VU=k
zD4jRD>pO+XbR{}YprP9=hiFq^pa&_QZDnSe{bXc!&S>G%a@g~D?R=v~N!Ok=uIlF+
zp_sj5Y*Suu{?Gts06sFg!#xea+6;YM(j5D8^&KZ}+E=ADz{kh@bim2dDA{x0O|<mA
zj3;Jhp1Zdvm^86k6(n1KoRj_*cdNyWe`=F=+{4MKL6hB>l2t**|BW8iG=SplJ#Fjz
zaDd6^@+0!F1f_Z9%%==Ja65%C<W?$!!7}XV_99XIYyTHJ((Rovbwe+k5QV<n&!eWR
z)5}(kyPDbv(=+@Yj**T6kd+nWby&YNK0fa!!^MXQ9tu>Pv23FPwJMMO(`{s^Nd^}=
zzBDqkw)w)4`kld<^A~srC9Vth*&YEiU7a*|<B_`#w^X6wsPcIp<y^I@e-HEBJcQrN
zHN#{QtX0E+PpYK3>`1uw^aX7tvcyZ>%rS4IB;K^`d5+{X8glxe49p&P@1e1wtabzv
z>^dV{apN}6UVPlz#%)>@c4xl&rQzMy^&|Gaew&86+NA>Kx|BJ@LC!D=CxFI;y_%(3
zyF29smj{y3)DEKhJ>cJX$iTJ<Xh9!B0nSUEh#$nOA(zW==&E^}3qzRq&g3F<&@r|$
zOK8x$9O@3=2ilY6vvYE>F`d8D*51@L6d1MA+}??-yW3XRpU#?bf%2(l<r9QtFzXHy
z3n7)#Eb1x9$n+P50?~57T`JBua9`XtWU5m<ali&c(#?pxEj_N`4gQy{uK`M8&f|6e
z!D#aK+&FO2qzMR%zl6CE8-}`c_T1bGO0R;8zodlI#Jw{lxgEYqD57IV55l8_2THhp
z;@S~X;_ns~<^e@{$o&vSci#c%c0PCdSw(;eF72{H9*d&6bzN`kc~+iURrR0D3f`WH
zlyqWa&(iJzx!BL;tz|g}EtFPPECB|dw<nOCndbTT{C>W%%kOzUmuC)({^fRIOeC>u
z=YcHNZUe(<^5Xr)kKfppgMpDuem?CMKczf231s7F7SCHuIj4<$Tv4-TKN{`oa#)i;
z`av$hq}oE0nT)yE<Sz`ir*rsZi2TMhpB7vc3c?*xE&tE;^`-Eb5h%px4Kp{(8>1ay
z_sC0cRxu@zf%eAxPw$0V77j#KPrn#Tn#1b2+$OC14jc0B>MA`$SRhGM%PMA$_}W7X
zIrf%76W1}V%cN*fp;9@eAhmps5}|Ll9>2T+LZ6)U?r9%K8z|!gfiGRzDcS?ft{om{
z7X0tvdM4OWZ4@oYksq=M9B+;ocWWf;(<G<K&YJM4T%Hq7o{`kGa@9r!7QB#?!sAfl
zF*2g_)YwN2aD1NGyWjT&vU$t&v)+qKm2G3e1D1nd36GpoUD?b$RTmvaDk|sg-2_|#
zPd>FV0Dg9vzeo(tO>=Vh@yy6e6g-O2fGHHv{4!-N|5H1&uy`wj^;T2U!^<_icAJ_o
z)Z+Al8%yHic3~z^EahJ~W1#%k$&kgW>{Rc$Oaup%{D}M{y~1BW0BGB$1ttGh<GJKd
z6X&vj7x#-IYyuZgQoV$zgj(t?5aiV3a+pxGsYCNW+{*_Mgu2Tw(W~Jc!le*|)=|fZ
zeR+Y`Mi%80hBO)Us-rE%Lh9#;#MYVy%^A5OmuXdSL$Z(DVFPmhgM%oQ?Shgeb)CrC
z<vaIFx<=p43Kubq7m1~@ykD;9J$4frN@rnk<b+@_W83pB$-k8Rnf0heba+@f0I2|a
z*1z{XIlYnhzMqeE>iE?89V*Zt@vRH@+r7rDZS{s>U3whHN|9;fd2ha_PfaHVYdPNE
z8u|X?u($g1qMEL~J_tvBkLi5P_KljHM7rx9baz(L+`b0(GVk0vM^2OyfAF|jaOi5|
zX=!gZ`W`DAdijJrET=mQu2nqMCd7HRLoOWykNM_OPLp-aPkN&y&zzS>8jr0#MGVWL
zb8nuCKM(b+bNbx1CSyr#cpSoYVA^}zrU2vC`^@zRn9jje{;x+kX2pFV#$!qx(l?8(
z+#v*1OJwE3UIr&hsX&YP4Hb4~-)+5&07$41Nkvu@FTA0?EQhe4V^g$CALvHACbR%m
zq*=>c<gTzq<8Y5-fh$@t<SWpE9{*!Dtz-4)A$J{5Z?|!CgjbZrw7p0V)0iJ9C4@82
zez888s)SYn+#z6~QeUt9V>J`52B+{XB$O$Gl-#)V61LtdZ1?m7h&WfW06Xp*Nt_hj
z42&!)2U0o@&iS%a7zY2tH(9715nPHx$8nPbX^#7d6_B1;7bK~xC72spVS&qt?~8r&
z<W~Rtqc|VKftxfRANr@OCE%PfYeUquur)&S$Ylw`!wU~Ao;la~<?XkBx18S^@TzwD
z=4sV@AZ9Z8^a!`g4{+85Khq>Dk~+6GpCW=3(hh`04Ufd+&i&r+@zeE4K8TQS^|0qo
zLvJ(p4VhO<xWqceEBDVobmv*3(5r&Y!UAcI0$bu;C9hAb;UL>U+|lpsP$-`Rh$&~E
z!&j_Zm|5o*S5Cezdm2rQ*cy-%NFaYV59N2DdLDg`aE#@5H8ZIX(nH1A6>zmq0qm53
z<Ad};p21=D_h=M4&i1b4_+7Isc>mTAcM3)Ls3QVgfU%M5eSg)}{<ad#kOCgFs#JE`
z8-bUU^l&!tvY_95Uh!Hvidi5Z1E9jwu4y$~|2$+Z=|!v|iXaMeBB21pGkWC=ZC4lH
z{xBNfk#{v8#>Gn08t}rlgD7ITmsuru_bbT_rZ6}T-Mi2^upXmdO+;B-_9hj*@F+3E
zB^Ike`_{az?bNM3)?T6j@-L2S7c9K0$g^*6QV?!>u-u)MrG1p8D0I<0`3I|Ce%=2=
zZW&|IkR<9NI-b@3e_qTuI$oro{bR^wdo}Xj1!F;sg>}D<$isn<I(NT{TD7x+OEuV)
zY#WK4dw#O36fdFoB=tZw%#K$`=s3hloC+Jn=}|3^MBn=7mPYPhM)C`UoRYj<u=i?f
zZ2LRhldrTFK^Q*d*f<L8-t0JM1{hyXO@P|j3veEp>(cqt#)c*Hr8t!*U%okIst`_~
z!C^C~V=lDxf2$af>iB5L*C63yl8V{?PM0{n4iF|jr;I%aA1aPFWllEl9kW?Ryo=L8
zU9}<Sx_=VCdp^Az^=ix;1nBetmp)PwhxQ%c(y{fU0WS=Fx)}wovR|Tc%!`;$AWJnJ
zW@Nz{KaYwkz1<#_zEIkgpt)ya`axNpUz^0Z=eX*mLGNgG5-*XVXrw9?5d@N$Ko_ZK
zm`kZsOevL7;rh+leo#_SA#I@kWHwbYK}g48n;~eb1--Uw>+e^{;1_kI;ET3AQc_A_
zz_(V?%%6XM3;Tm<+1YLi3Bjl%u|)Y{sVYv7OqDhoScKoRnjZ6hpP<>^*mC`x2&m#Z
zy+fSL=?RIMNZrYha`oywj>`oAqQ~Lw+cm$}xr*-ZwTt=lSHKh%&Omo?pS(l&TYr~2
zZkLc9`Tk1tyM9Qx?A*B}1r;FTLn2Rghl~5h(;&OBP_Rf<%#(2ZDv}C*mHlhav17jW
zvgcO;Z8ETlsJ_Q*yPnSDm*=C(j<FFXyy=;21}r0FdsLfojlI@v#o-=pX>m=wEt<u(
zHA&>~q%fNkaxgct_=3&*UU`WWnos1_k+KrgTFhK{xXYw5vp4uXv%-?IFsEIZ0`{O|
zt#o^%R|K9k^7k?`y1RE@1W~v9gyVOq_~xvT&T?TCbIT%oR?1r<V7^bRz_bAOwunaG
zJa=^mu>SG$fWm$DSH*<P7$nD8LcIWy1R+z+R+Mn{IC}@DD4|SVvCoEoBP2+a_g70k
z`Fh;aNY>I%^cgfBp6Ub=M-i<Xq!pPgX0T#Fk>*+L%RUv6!ncX=4(|6CJqWRNR?~tW
z)ul#{p|7nl4!(4r3Z5Sp61mo&y=`vcjnV{VTmWei6y4)=*m>t20Zcdh8Nv7F-jXq?
zNA{Qrww?X_bI~L$ewWd_w8y%|z?S<M);0THi9n%Em^+-j4@eBYukjd7v)1-y+Vqj8
z+|p)@MjK*jLZg)<nOp89EwmsRc?qVAhkUDS`}&S9;DXS|p|lLLDUog`e~-S}J#4-v
zY8mdJGV>%=pS>o+p_doLyv6J^h#T;Y$n{FsGW+&zWxQzH8sJNy<}skqqfi6uRW0kr
z&GWrc5{3+_x2rz`l83h8<(23!C-Knu(B%sXO!(V$QWb_%wtvZNY*`={MNt3ovT2DO
zA04AJ)rmFcilM``)-EboE*>(#8qshG`k7}OJFWEH5pTq|vp3FI^XN`9!(JhBxv$8V
z;g61!l2Q_RX{dV1H!eYqjavzud0b<lw`0kSjipK)>dHWBuu)^(SDRf;rpCkd@(L+A
zk-;r|*9Nr5j=M)gS$y-s0euH@{*CKtrr&m;iN|fXOWY3ueSHy%QtEBTfgU9EZLcpZ
zFp8a>!AVF1Gn*j5DP~^!R~<m2(MTVzSrqqg=FRo=7FO<@Rx8H4O>EY+4hTr=*Co|;
zwcy{1g*B1@S;UMiMAtBD>-~9_$+v=w0hMk@u+0I6Gd{YS9BKF+pE}M@(*q181-zd%
zp{Cz9SO*8(aS<!Niv79>0O28Hsy-VY6o;90JJu?jVu-6#5HjqP?A_W)UQ}s0^7hCI
zj{+ux%jqt0A|yj_p?NPU@hLIk+l46kD$&gv!613k@Ym-)jAE~|jwfSg9NYS%e`irw
zHH%t~>PN+JwtnY`s!r0yc1q<)Mvl8GzYYyf#mxMN>Z=5$_;sHLWycorl-`B3==`Er
zwEMkNV(+?+04n%ScAt#S*VJ(!6Qhmq5;xjW1bv-8hR&wqETr{Uo1{`ie>$pT*N$SB
zSA+lKDzs1<oiK4Bg1@ZXpCP>6JcA2`_M;?Q5z}Z~7M6T^*<3b~ifd@lb87{9j}L>p
zjlEJo$=90yMeLb2vdWmqtJcakc`90$@!fGd!`=2o=`?@Hytyin7Pe?|j}Za=a4KA#
zA1oDXhWoQPI0tD%p}NWZq5{3p63Q)pJOUd{2*$MUc2Y?^O&lnCk|&BHvZ<p<yl_K}
zMPSDo?&bs0e?W(m<j#9;!Nn<xhiuKlA|j)(6dOv_J16=3KSr5o_ArJ6{BX=(&co$1
zgfz7YyhJ%V8XAl6=#qlNT4U^K6cHGW&qd7BCeu4?Hk8I7d2M7=X-QpfC28uSRkTWW
zZ8XW*1_g<%;5hSTUJ(8%T(cu0d9_WZKI^LQAnP$OElsl7SU^l_?xg<y6I`;;&{0(N
z0WuivyoQ7o!U3?{+t&&w7h1E`DD60e^}l{Aa4&{G3<O$b3V9lU8@3^P-(}l=^VOlG
ze?l#bKM8~~Zr1Zy6lFsUuu^4YF<3ptP}2Yhrq2}FjcT~n`@Y0MSmjAiY7!3-A>n^D
zc)~;E`|2F(t|=w3OqP4bdMKnkvxvyq9L`R9V{eqaNe;q2Fa9EOAmg=G#^lN2WRN$t
z-!h2B-@(MFx2t}=R1?#ed@Mgc@?XmHUiyu_WcagD^|$^S_khS>9#|EBNVMsZEaQZ0
z;BWA8^|F}~)?3I#3IA>GI7Brqz!>-=0wyBJxe0N0YaOu-;qDtDIFbAwqGBA%2{g>E
zX|Shs-34ba{R*3lzQIo$6*(z#@;z4|BK#!q)zJmvcC&C;!o7pi@7{y(C5(8bro}&3
z(0)d{7-h#&{oRQ8T6c%uOqB>bwv}(?^OOqM9sC}s0EM%GG><0t%)|NQC%=3ZccvlX
zR8)7lE2Yaiu+o_jc}>>1=><$3;2oqE>)cJ9-<Gk-ty#|%e@2f6-(}}ck^6ScZglrE
zN>7`B)wbT_aM5Tu7ESMojTo7?CpTO@T+WcVW`u{0Mn@1x@h7R&ZdbQWZY{VYNY3l6
zS*Q=Beqq7Dr37TfDhM$9-bogc0E+|;K8{J^fC}QQU~#DgrTKR_px%D^x3KmhlqU9F
z#42LCFTqcl3F@SGccSoUWDRH1SOI;unPTt8oQmctDpO%YJHy;?$;-BxAbI5Y6qm}V
zc>?rgFJ)U7-sTnkTml58C0a&J^oG)Np}8zMd1f5n7LIYC9GRyZyF55;!cZ*%&c41o
zXmZFwX~>K?7kNP%i6PM%3@$x*?2;{0*34I{QoC)URK}Lal)~7RTUxOAH-G`i-A^d7
zMdOiIkH=go;9I??YSf_RTJ!#9p3W{9Oyw>uA<k-kZeUmGGfT4mSTA?&aJM>_i1ua_
zUv%uSNLJksZEZp#Ml}YZoh$sz=*DAFLU;!wwGq$h(_k=2ODP@5f?fOl-^1bv6=w&C
zzYDrMBRd<I+S;bX7xnY|c%FQ~=YmfwwGN&j@nw8#pe=^?Jj$76*A2*XBU=8aw)U+!
zj{aQO&tFSJL9nCKs)cJMe&dYfl;V3=4QP1|J^3<!;{DsSipKmQ$-}$vEQ|P(%{`4-
zfaY2$QKz6=+H|6^H49z<y`!}6Y40ady)S#A!;KH=`-aQVc0C1^gfiIKuw7mmN+1}!
z0eojwMDfe?hhYrU4Vo?Y4_I~wj0vbn0iH;1DJU5Gb-T9ma=)<xYTj6JDdutL0+b9|
zW`ts4z>%elZE_e;oW-h`;llz-Jvf~f(!F%F4t9YaEz0t4z(WIXdMiDuu5el@x0l#7
zUW+9?IaH=`$>QT9e4^Z7a1@VkO---Z%aWb_AHB6D#QbLAPENP9>_5zx&q9q4%WR$g
z$TVW@O&`ZGeq$R7@%Y<Vj6{M>^1zHrF-ewgKE9q%-r8-vHj1sIQ<tOD>#S#jHQ_<e
z{2qEf-4r4Q(+@;h<QhI7e}0pZk@;V5MnnmZH!ZG-OEUVE*Qifp8mob!2({;{6=H~z
zdkObgRiZ2w3Nq-Jw<tV+gda~y8)(rkTi(4@8CG8bZG1BhQZM_784zIWkjIWHrw}5k
z-pG!JhJZl1aWjP5&-$()U&o&fl^imublLJS^WFzlv&SJa)H7#}8)0?gR^PE_VqkwX
z6q_L!)6ytWq$7@o6VHHb3(=!2V`lj|#P{!jz5inB55Jd~^E*t597_}~F3CEfmx=(Y
z0$Zg<0$@8}>{^Q!2bUafS0TE&*%(#Qi@Eb*<GVf|x1&J3;rP0?no?ZQ-<aq>^RriS
z%(R9ij^)jREz5m6JkHvETG}efAq)p4gi!X*e9Iphf;>YPYQE#*k>&{6CuDJ#RVT9`
zAS}w~flB1gkg&uFjS1JBQps5TDZ<_0X;ve^#WBKqRZeLrORNm1F%pEd_v&@|r82<$
zrEq_nU~`2EXvzrnmR6q-wL!ROIB%Q-zCv;uKNgscrbXwL3cYnl^o#f=A#@RD7EoHS
z&T*a^0|q6Ga2HpS-UrDClpg{oj@u{Z#t=hu7C9~@Oy6H;!?cv>c$L+v9i7-VrpD6l
zh9rwM0aK!C!j`IV$Gps~Y3+|XH}jabY|01$;W!><!S^Uz!Yv3^=ET0Lojy>F?x4Z_
z#}?hRSX{ecxhYd}D522sg8NoUk~$oR<O_sz`hpC?dlC2x6kUQ#qA%7v!&BNfQ>|xr
zbKv}3zIN?E1?~9-8aqn{=GaoVJ1Maaa$33UKk$l)1i%@bEqS&G*(Adl4$OXyx=Y8i
zmjAWH#!$ga>SQ&Bd~Y;3c^@uq$W=n5a&)0~w#Kck6dHbLU%}mRT+_zG-Fkc+xE5Be
z)F4BbO$W|3UhbC^xZ+msW3Ln0o{jAIb;%yEMUl&G)6k~Lm%xdKi{rs(y(`XFm01Dl
zmOwjy^L!X0i!w5Tdb-#N1*vNXn>tDUu{$B1d9&e3`Tji*FeRx@*y%XXViefhlOY?D
z_98@;>~Xji#gA(`Z}a)3@j?)#2aeico6~JxTKKjyScH!8Cf~I~jQz?!1>C<_i-U?r
zKsL-tju-IK3<bgWQKzZM^ylY*4*#Z|hhDF+vpB63G2d%OB)~)00`f3{@D;tn^M_$5
zt4kr2HqsPk5U_*$rlF#pea!sL0${ZBp%U4D+U@A((PXLN9C_fl1i5+rflmc{$@plG
zD`6(l-Olf$H1eg-W(`3|uY5oSNNESfy5-*=UZP;EC(N4>q(C#g%3HPy9E9X>GtJY`
z(GmRNNCA%)@xKqF+8v$F>9dANU#9P)w#^?_dQquW$dr-uq;BI&Og)VUI-5O>(*qrT
zR+R3b;rvE+xa%;)dOJKJk3F!67+q4-9?JqJjod9~+?3ICBZ(sLet1F+w@aorJv=fb
z1Pm_6%Hu!0GZ+P?FERfQC{Mk7_7XZclO|xSOfD);^SEt6n09j@5@l2s+We#r9}<fa
z=tawP9$d=sgu($XQD<HXJ$f#(WGpQ`o77Z^>wPC5M>3#2^TPvxS3-`@vSe%s84Kfj
z0LWE=_D)J>fk%1wy2K#~|M<zbV)>@o(JZyOnKH%mB;ux<{UB49RS4*g$vxNo^qiIZ
z9Bx(6qqhKF_N}#RHiul&HDUcF$jqNW8XiC#rF%8Vethj`=T^xgEPQ0ZJVr>ZW#4|F
z49A91P$kz^DP`s=pf7W0-I|aJU~BNrvYs+)Nf+4GL+tgA)50Bk=j(IWXja80m@reG
zFJ}qfFywx?zs_sbW~){z{y&<|I-c(L|NmpAd%D|U)6Fp5&D8XC$FyV9ZMwS|V~pu(
zreiuLk2c->F7NN>cW&no++NO&bFS-pJ>&7XKd)JFAsN$ox3aqcqn;&!1J4(+Ek%9Z
z{Y!Ha77LLBfsZT-{bZ-A7HY^q*>7yh%5T+E){`iHhQuW6?>{1-fURyDt(4qszX&P(
zpogbqyYNPok7Ia`cKvR8AVp`NTi1^7T3eeH+*6wJMq!K=H9XM~=4RF;=7VdG{|;w}
z2RE7076#8>z-u8hoJxU$y1gOdOm$v-mlb_zRnbB4NleYAX&nps;MmoK<wT;DoL(hu
zLY-0T@;55f0;0jG8YK*#J+|z)8pgET)VSlYeO{M(!U*grJt>!)!`3MZ3q7PwT~B_+
zK}Rh-EibE8m9S>z&Lvf?&9S0F@qKIGMP?sQ)sLl#@$6B@tzR5w7-KvLZ8fz(d!_pI
zeT~o`M8GZ}IAEEXHyo*Bk1CsKM$o-EilYhoRgdvnLB*gRD;zl2qr$sVf1x4YZvIX>
zKB?+}kD$3=DN2d2bP9-C0(6UVlH_8O3c;)~8L=-jO5Df)l*y!Uwwt8OHjH&;NW=c=
zV5_VQJbX<+B>8|eUh-KCKkOM%;%fUZp)0i&%w;2WAG|kL{oWigtvU=}-R9ACF`eV7
z;yl$zQUNz6EKA63x0)Fb<Vnly)jZKf?k}~FdtG1Pru~)1L90ZpQ3OXSsAn6fF%c8s
zZcD*^$wqpWJY1bc8y6p$Vf#~U)^XEq24^pX+9clCh9t&;eQjex-2owsDtE_cN;p=B
z0TBMjn9~Tl-eD?C5`QNHL5F_TAbZSYt~}E?{tE+*GCcB52&leGXmEVQIL*GTA}{-k
znt0;woiqBk&goKjeR(D)7*-1U-f91Byns^iol9}w8c+wc-VK%K#jkeU3CXkFAX~2~
zd|48(_Q3Z|js}>Hxb+XS4<(;<je*Lj$(+gvIkhB-9&psA7Ka=i86NK5QY%D$Y+7nf
z5nW%EOYj@SI|;Q5V#{lsD>m4x_Vr6T?@`L9+M4k{veglA?F+0?ooz@o{O#uN$3fAD
z8Cq#GgwG7JJKOJF#W2pp4X+|j>D4crBiAhh{j#g!7<3=r7<TegN3HMk-{9ri?0hPK
zg?d86@+yLw6DOhbIA;leJR1Atapi~@V^u<hOq~t1@uCcFIOXZY@Nn9xScC%jw@6QC
zP!dvI|KN1eSrpAYh3D%!HJw818v0`NSdmo_5Jqt&neZ-A_`BWXf{fvWlyPKLntCvc
zz~A%WrF7OCqqH>IlD+MS&guiIPYy(XrKxKY!I>&4_x%s)xH^wT1pS#0w5vxsL8+ln
zF;8)s9YVrDKba2*Es8Id)Nb;UnaZ(SG|7tyL+*~x6<T;i2CP_BlxN~_r<Yil*ndUR
zjJykF+GJ__w_79OxYt^>mlg$XkL*uU-gRWT8$UaMP*pT_@n)t7mQy5Rl;pJMJ=hjB
zpX`m)=!+{W50Vp4qyyn)BKB`02{koIJ@*o3)R25!1`c)k*Gi0Gv;lO~C8Pk|@DfqS
zX5Ne;YBEmn$D>CORmp(?<~2W#c<$b=*-jb#P1V<uk2@*q6IM-U-Vbd#lOI7VqQSoV
z%$e(|5=8!b!?iWzy(>MzL?IkM^aw@6>a#Jv!_CRasNu=elTJ=xH3+|$6-da1y$t4%
zc!`g`@b=H2edS9I8ac`l*QO55s<6tPx~@+;3|M{-b+64T9PPGTJVnCd`CE%E;@7xT
z;tN@i97anP(8AUbMps1n4>ZEDQ_~~b6i~hv8p*}cNjj5sI%~r6sbWyp3h=EyD)mhK
zAfHiW>Hvme;qtfHjNEyDw*|k&#!LdK)lR5rF(D$z`braENqK4_d>qjQl*+1PcMo9B
zs71f~)y{9+qi@Tr3B%`gcYJcG{e)g0J)>r1di!@gy6`4pglI*S&z`H+*vS`5b-AW7
zC8iGHHylJ}IK)<*D?OM#kT}ycWWS(EW8c~k&?jGw9v`rW<IW+@%C%YW^|#Kxwg`NL
zjrvQz*|t_DIpfrSjYE&CAawW8GE?)#;2YQfF)2QfQ3D%1UGd}*QoL;V+rND{P@}uO
z5V)S%ZdLC2`%ye}+Exw)+#ww)n&WjMg~_oXaW>RRoHtrM(duHd@P>G+z0~EhGMDq8
zW2ZV)wdOyEGEc-Avc*h9wigE`s@#b)Az0lOGK<dFy@)vREcU}L404$1I=x^coaP2f
zJ88b`76myzZqyf%-mT4hx6YYkhn_)V%uXc>oXu(8ns`#cecwyVKgn$%^+)pq%>WiY
zMAH?*CW}>8@|o^{k_Wk$q~4XPLnU7#sgWdPT19y@rUVuYQC9EM?&TWI9hM+tw2tj?
z7bof+UHX+qg}-)D4j(6*&re?WE|z`A%jq>)QC-z5`E-8Y6#=d|msbOVtql)nks>}k
z0>4QaXq98Q{+KxM?D={e6C6O}Phbqi0$RjtMR{sqyA6Kcq577gv)e&&G^!aw{L$t8
zqRzTS?Z~-wWzIi4P)`yV(G2yn|3G$-EwV4w^<ip&8XNCsU{FB#BYAm5?gu@^EwqJB
z*F{MFR^#2j5qPi<V`&tX3aoT|9Zb_3P16!Kck6KvUxEsndyMV55-7=n*&_0cvK3ap
zi=|%En<+zONIXHCD&ff@#u<Z6J#n(w1mj#Ouid%)@~ME>`Xs&Fq?CDvguKneG8>~I
z62am`3e>$M++$vyf9#~|)jWra;shrYF=w$G7cD4f*wV_%W<?k0k4I`(Yew(*;;_Xa
zucbP&zL!CUY%|1IsPeM3z43Z|VE<h~U|@ZT6<$f3QbG5Gs^{1`jxPS)WY0p$BJsqh
zMAHr^vw3Vt_K45713GhN<|c=?4SR8ex}(E^)02`o@C)8oRQYh~@`vw@y6l@b1~Dt6
z35KHyCQBG5koxxd1YKJAH<TNOeVdg*L0bOf*P}XYB&cjN;ow9~C5#PWO{(|+sZLmw
z3j#$Q(|pl4?RENxn0L>>fn^%=kN2jo403;lb<>f9EXsMd!r(a(6PW?OCL8k3jkRcN
zK_{<UL~`Rg1zlWxF>KsLcs^TYnHzIS;-58_RY}1iPQW?VvUf`R<&7m15rbO%zlM?4
zHgi>WEqslI><9ERe$RZ(RdDECEMgt@O>j&9dGmO!e}qeqqK4}j3}#bBl-VqRqG3Dq
z1_1cG1rUrcV6>miiZ~xvR_^q-@29qXmJ*JXM?gOs&wp=mPj*6NBoIa~@uynTzR$6Y
z2^C0-k6P|Pry0BZIN385%I5dLf%UWMNlqTS4;kv`7so|`;*F#D*|aGTF#;<fGeUZP
zF0vRK>hW3_za0B*ry<=-H+m(t(=~2qmaxgK?&5N_F^mBI&Pee9x<fwA>ErycD)fnQ
zccz^nI8ZQ*6mK&5lvhsYt!D^cCKZ$tH{@iV+a=u!$HZH5AUg=0$WeabPBgzP+-`>4
zcdzuRUEEXQNr~}IA;oOTsEK2DZ@7dGd>@|u{I@^IEf4u?W^g_e@@5YvfoG;{8gJK;
z6!q}00%A`qd6Hh-fl!a4vhsi%Jft_-j*^e79+w_SMcG)pfwxcn*ci$W-fJbFB#RHb
zA@U3Oi3%5a@ZYmP24Ul|yj+;QJ*-;4b_@K3LlKzk8H6M;!VVFbuDX1sUVQr1!@$k}
zraK)nsTx~1^<F+a&qh)%fKsOJW@q?C*P=J(&y?@hpMhVk$LFyIDMS$a1XJV_k0&oA
z1L^2AlMnr5KQok7v)47)pxw+`Fd0$mv}2D02oWQ4jmhqWz<aL}YI&sznhQI$aVV9)
z%)0h!w%n_EvdYc5Okt1=0)eI6)#e~M#h&j12E<#6=BX{&$$Vt55>-`^*Ae(I)q;MF
zV_2Y?gLYtq>|jX&-SYPvHjjmV==^-~!n%9&K;=7fDF}a4$CpiZJE26S465)39ucU^
z8<BHb79TIW1b-^^0GL$J>cfH-1iovwnQq59AAB)J0kI2K3pxtbMg50E9rTO+Oa?m<
zq1ZlGA5oSlyPVU<9aqc0nm^Oo6OVd31dh}&Wp7xiikJ82{9+-Yu<sF%fwsD~i>1EL
z*0X1$!E%yfnisC*!hWHH*?pb4i|1j=R?khoPk#ik5H7J}jkkC`KcW5Jm4SP~im@pJ
z_UGJw^9mkrrBC`Hjd~Bl5W4tihgk1X;fZTrZ`L1GK81ba^e}cc=EEHkyPvELw$V_^
zNlQYMZuJQa`1EX**Dn_#AAT&Dlx2k^Ms1#KaCN)}wjqs?Q$EF%xMRF=yd*Wo*vg&E
ziYU7mh1<UkEayF0u}%*Asm6{9tl$I6%{6}5kGu<+oPd*((#B_Sc>%S)k<>$6qWqCD
zlHyc=tuU!7wVRIu@Of-lWBBw3U8SY^O4(Y+ZoN3&u6E@S>#1~eMyhX0OE39VpQKq7
z5b>Tkx`^+~#xgy*9@{1cW$@K548zg9IV~O-uPo!)U{}A7S|V={COeJjG^MCZh_~hE
z^*UA7>|r}mmPl|<J^-5iCm>1i?PY@>5y191)a#Zv#4KK4-O(Q2o*oyJqc#;!9Nt`s
zA<HsIE2!8#sGv%zr81|KZtWYasL%nNG1CHp<A@@~obSv$`MdN=+5<DbcSEa)_)`Y(
z7SED*S)hXL-Gd1Q8$*_tf<*MzMyLL+=kSzYSzfM8UOLklZ4B4QjcA4p5RV=TegF@$
zpr=5aUmTCRf2a3d)9Jk|6Vtf@8iGfKBqATNbG&N3oubydXH8S(j+-){6Sv=j$M52v
z)}FEf;mH7)_Aj6MFG$Q4FAJ@wR2a=Oo)7EG%f)}d8juNn>y;>}1eczdR|@}aZ~dd+
zo#9(t#`}Mn`^cg;coV!Y>AMO|1vif58luegsw^OB5@)(%8cB6@2Gtd{^B58>|E$#g
z)+N`Za9CyvHg9A&hY3+W&-yz_fgWjG@+h--?u9-<x3f4fq)QD<pWk>1#NZ>)FVI+~
zTYob8E)0>9AJA(av}kBJKa$bCl#~a}mmP2J_eZk+wE^awi5~2AZd4BspEJEj*Qce)
z`NAf?q}{*&t%47#&A`<q-Ymz4K8}yCKXV<tBcQAuQmS*2-DwR<ioGSl|79kfVZslX
zJHtn?-eL{4f6rFhA6Mq=2PWS-eYq)vW(<~u3<Y(n&=*&7333gkJkDF{Hq}SWoM(@R
zmcX7HsFkMjf>DzD?_S>F4gA?+NFm*8(IX#4w9UrBqaNc)$~5_lxLSX*B`Hr}Gfaz?
zSNhRsaj~>^es}Bw>@yP%ZhVQ!i#P58kY2PdT9zEGn@VZr;pl3^Jttd}=b};d7~LXR
z$Z+O;rgdM;n%)DZRd3{>pzBMfYbO(8{mHPK)>g_*&b441rJ40<i!30bj(e~$U!aML
zFLOa*n!^=CdObyI=k7B!vrClzdmATYh>X4|pVJO@#kPDy^Ek-YUVYFirgB~~t|3GV
zc4X-jjxUO_KQQPSHNw0|&OlI*<x4F!3Z37t&GnS;xXC`r#gE*I<pVsWCeK1&HZfhD
zt-)f93>m$3{<VfIivP4+e1YpUYMgvn#B5uZx#$^lSOL__$UXCoJ>ran!X(j%(APS_
z?#o0z1v(EB7KTBoPJS^Bgx}PQZ=drmc$W+UqrY|2^7z+ZXd%VOZdzhm2sCp7zosvq
z+ZbHR>Z8$x(?#J1umeEQ2*)_jW}}cdQlI!hJwF$(<lt#NO2jjO76B7BPIeI|lW5E>
zFHg1uRrfA_I$0(q!(68txbt)V-kxkgsx?#<al<L4?yh>_4MhL$!IbkLZ(P?F|LU3A
z%)`-Wae{|P>xYnH;6I3xk<`LsfP|QwO(FD9g;8AP7MK3kK#3lhC1;|K{y_kqP`;0n
z)=kNR3Y=X#1kRZZjUo>7_fs&t1yOzekP*+a>VlN~MBpegu37FzlUS3;^g${a;+N|g
zI5KQaOZK#Qg9oI0T2k6t0O9o`#kCezGr#+VZh-c(gshG_d<_AZ0~)EFGgX;qiM;1k
zuDr-{E4S<nGbk7x5A2#JF~r~LlS84mm>F5idAMUmiqD^EgCDq=t=5F^HI<)S?Bg*?
zmkXu9As3{A`SHN9wbUD#U)OybhP#9`*?8Ih^iM{$4v;+=*@$C5VZ--vut(jilmG{E
z;P&TLme@dk<(t#x$KF|PZo36vR?0e&BxH712IqL}8)~yY>1s5B@+x!0Mjzy^Fe?70
zztK@Dgywx)o5yNfe57?P2Sxpcc&@euBmS3NIj4hcSsRPp+d$ilLG$nzMtF67AOsAx
zt1@$K?m7UncI6Z-bWX6BbudzEyO#kX1>kNEqIwMbOzKS2=<OOEshz^K!J=qDn={Fg
zZI*Hg=rL^BY3uqaj@65HFPHhozE9YlK6)KVB(~{$)a%W2DS7eb)2*%-X#o&Uw&VLI
z>4Hm71Stuv>$`B``Ru;SZ%g^hr}agG3dUvQ-LW)_{<lid`yX5_ygbr9&J+TzfCU#r
ziQUWL9M7KUI(C5qeWG!Cj{mn)z~Xp|%&v%W4~NC{JjM79521%n4mn`^Gwnfou_@79
z^l7bx-rCo4RJly-P#iVvINgo<gg4ZoroFXt%iO7z$u%GS`h3*o^|D8SVLt{V$yqTl
z&KFZjYs>=&1rgQ{kptW<=}|La&0H_Scd(y!j)nZ)l#<fG>y7YA7xoX$ojrffD=1v`
z)nQGBqxKJOaj`IaovD*9=}*|yZTSlXV`9PjqJ+^jtNBx(=vuevIPq)%%Sw8eAryU4
zf7uFIQ!eO9`hy`~ADmYPY<ex$x%;d0iiLC$W_sBwgXaS6b)DzudMle(p3@S@rLzPt
zH)$+;Lj?RSlPuVl-8WAQQh~7UTIiLccEqzG46SMma{ZZVH*zf;q3OM<J$~wBfGc})
z1>v1bWYSCvfzYjs16{s;SnZG#<f81-47dg=&)X33S)DWghT^1`7Y{x_@*JMlp-R}(
z=?va!gdpt12;P|1_6(W`+;pWB_OQ$Q#dRuVvw8bi$h?6Y4m_SzN1dD9g69U#LsWs-
zv!=2F8|KfH-`(tkAyH|90x{_tTq&kG>=7tkS7jj-=5K@<<X^P8T=4t5Ja9JHV&vZ<
z+V2Xd0B<gU?VYS=pxvpo|6`yHCX*1boZ0CKFWkI&Z)gC^NU3s#S|>#g+Uh&7Ny+&X
zkQWEtNcBzdET?9JOBUz9I{L85<Jz=RJZ_MR{spkW|EyJuPMg1!d#GXn`VPFiOxE9e
zfk}&qlnECBr@Z`2Z8VZ$h3GISr<hdup6{cCoM1i?2kQ??)QcB(utb0MH?Xe!b@V^{
zXqZm4eqg4d(^PMZb(G7t==V7PhVby~2_vOZFNQeoz`KBp`@TiBTu8u7aqpFp-+km=
z&f}7i%d*kZmO6q{S6BuZwYzZifY8T&HQ)G>jI!$ANjIcKIus}{liO|!9Qv@f5#bch
z8Eh*-{D$!)u$@12@-oi?*5nhk5?CrT;bms8iLQYoP7sG#*9%37g>on7`!B&lAIs@O
zeMfw&F8_dI1ooeB`{`rDlTu|C;2(M5gPIUM8L@MWt+(D9AK!<0w<_Qruv*xp%hy<$
zk=XE(JiMm<HIjBEoCAp}Q`Q_)!uSTG#;bOjo;2*VgdfFlUg|p{6Vjq!P>$ax^6DMa
zN(wMP`Mp5|_^qpJCz#FxEOB<@81Q!x;HuPg#cXW5Dnu5;>qBrBZ-o`Z5gf1rS29ot
zs>Ppmc_SDJ`@m~VUQM2A$Gm<k`I}pkA;N4;5|@79-2lMMO3G!n5foLGv&Y<u$0{W5
zLk%5&QZ(?A`u?m|9OoU^!heD)(;t|XLbm01r!?_v&fDe**D3m-4ts)*LyAtWwIfJq
zgZklv&*LS5LjI(7K>_$tfgV1<TD>}|?aQmMBE^Nb-5gM`DL5Rk9i-^*M})q)+LfXg
z+P}e*!tUE~uCU#Gev8m2Cr(2zhF7v6NODKuvd4##(ERPi{r8(H%Kcf&cuDo6i=RK#
zV2lj}w|U&CA?Xf}l`G<q?ec*71Ha?99$WXw)L+z3Cb}Wu_|JOP0HO{dJ-8re@rBdt
z!B-9Z{+7{42F*QA%N;<RX`m2TbyL*dN@ZL-X;wCFT07Z=HVGYqznU1(Ra9ChO{t=^
zP8~5`aYYXtP>(Yb<myvh-dfOh!0j8rjD=>>{WSRnn4BP<y|!`={+<vKo?PX4a9N`m
zcpShF=%fH)xL&k3d*N$ikYf0yjY44#>#rag6dN!Y*rV$lOU;WhZI~u+J0LN@iIZ2@
zt_yfhCW8DS#<rr-`9z{&$X#y!3F@Z$i1kIZl7f}e3q506pxagxjf6M_*ozH>*cY+w
zHUbTs`}TG3^Z9#gqAIPWotu{O`8z%a*5S3puiPlt9^gu$6qlK7lWaZLdj<q#Z;U?3
z_&&vev{XU4s@3(Gem+YYGHQyobF{wst;=+B@SiEiZ5n+9@qp(-r*0gB#g$RSEVcf#
z$qurVDltpkD*;boN+~TvPcdiJwe4%_Y!B{${KOsF4~d0XiI<#duZlNaWjITs3TW_6
z+(u$BRzs-?kG|qC2$5H0EKz_bu=;`tel{a{>9v#J_458oQ5#|doZ_k!PKV!fcECs7
z5zG-4kr?5=I*pu>T`O?T1WO{3uI{~~0>riJ3wzAY3mh>#d!J!6+7|Zw9dAjW#M_29
zu|3`irylQ^QW2A@Om+pE%Gb8_m|f0Z5E`geqmyfBad1cHn{xtxxVjEEPc)ZVmts<6
zqFur;|J;^C!k6S}ZxQWxd_*HKNGf7M&tmdF(r!6syCA@8>yD;L7betFtH#LsmL=3k
z57}+H`Q=Whe|ngsvdG?v(OGGKfQSS2_a_Qd1%*Py@#NG-RmTZ5z>5U-JK@-1?*uFd
zHZx*9|JywP=gljh4at5WNDnEqCQ1)5BT7vVG21N-MgAhdt0}F4zZLRZzw>YFV6tpD
zp|o#xH4tx>(|`kLK%W6<yXA57`7Hpw@i>rNZm^t&T{D``lF=DG%h90CxiDbunZgV^
zPf`P{xIYb1G|Q+HLp;FB=em{-U(WICOue7cvtp6iDrU7z)KdrSqJUNCpl|;<aabVm
zI_n-8>k204<&`r>Y&W!{(B|`tA=e)^0=q`UTAi>GO@kp;XR7;*LSS%y5JD*)(&oh9
zYw91;go9HY7#M?7IKL13Did8Q?v)GX_OP53eoG;VHQ5c<XVk-(=r+iKnF6INl|90_
z^@}^BFibN76Fyi{KHVNmG|UNDo|or$HPSKK%s;dc0bKt7txW^~IqZp7DvDpw_<4H&
zrKkw8)$m_;GD}>%UaLawpRUVG0#0C6u_%^5gkv3yVvH@X(Ciy*IeqmFq@T`-PUkQ_
zCM-fG48okN6SBgR$-kd>ol~f8p^_!*lY7?)9plImVz`t44BGr)h$*{!XZhH2yS>*r
z?RNso1fek>M2KZZXN&}U(rR#kP!&WUjgwXf*K>f&6m0)4BkLis`R#-XqO$v8b9(;2
zv>g=a`nl^9-3yf2{?u4|Qy5-t2TDG9>AgM%K0e5ZmXHQf(OVboE{PVkyz(4u^I?|T
z$UbeKw5na+JsIzGnJ-cL^!Af1<=KnoM{66B$1BGN2G_1l@`1V72y6fhHWF~n1kM5f
zlVQs0iQRps{i!Bl65$kJoWC!!{7b6v((@KZ%Ea+Q<|P|&Y?dvrJ>5Us@3$wWIqCf_
zA@MBZit!P#XDg=#Qykvyr34BC;;jQN6~ij9l<gy%`_JKSUijmWO4w(Q5!eB2nW?KD
z%U)Rtv|6ai*Q$HKW8hiyOZ4W)w|^xtw$l>ADi_y+dI>s}8I}0%_#W?y_8jzjPJQK`
zgUJv8BfSFrzAdiFb#8;l8Z5~+UV)KC)!<{(&yI#|BModTg`3_&h<=AM@X()rPH!(_
zi~6MEWuYhI_HWn#{oWzlD0dR=Di*q94%i?qW-hkQ300)*?}s(|^?`IyN^QFd4)$$P
z3<3{yOywIt{YrX0puW*`a;o^j@&kG5?hrzIZwJ|Uy6*4~=9NG?b=Ny%Sn#Ex`s<SS
z@6PiD(kT*y<m5ecZ8S}J>%GuTFmLf2>-sE%Gudfi&eGo^jrB|+o)PKFu6c`$SXNeN
zU-z)%I9%k8dFhN-d^55i0*+)B^%ggNxN5XO9Z>stRsZ~#N#pz{K!1vf&z7Foo2yoC
zIV~A$i*dxfY%<6(Wczh4{#wIlzo3CLZps#*#r;=Ccba<tsZzM6kd8%_^cg>@^58eG
z;ES9|tg%Cxsp;~KLg*8bkR!tBBI1!ko(VIX5KTHXOUlfOawMZ<vA?CN=3&9dYmg+X
z|IN&mE$kA~0r(`aSQU+GbaXBA#yOfWk3-6MD5UFov9%3za+RxvT`FMxJkglr?Qwcg
zUJQ0e=F{Tf-9x}^MZoVri;*RZO$g$b`$xf<G(V-;X;43>#*WPz>VgU4Bu`iOczx1y
z&HddJ?58n*7>6cR?XfcNjZsX<CY^+nGY*jaA3jO?UG8)pGG>tTeOwdXz~cDnU{&4;
zsL74tYP(gT#mKxu!tWNA3`(wZMZ%iOO|6-qUfJF|Q=370fEaOj`QeffEOvMel?q1X
zn0IC8-T<NT<6J3SIQEBoiq4_%Cm!q^tT&?SmW8e=I>TL5pQS5873s{nqz=FCy7|D#
z`F~--FvgKhqbLY8Cq<vekUS~$Uy@s!QiBA&)snkqmIq7chc_Wp2fJnfJ43|e_l?%h
z$HGMJbm8}Wxti5Xgmw{LXu#x6l|Q|GKA3|6ieC}9-VSexdg;O?CpBGS<Z8Y^`%WdM
zZS55$6krRFj%+h-PxhH7xb#yM3J!>ykJo9ZY?cge8;kN@3)`Hto_nX%jIWtdwnnc9
z={NA|8Z9i8JvUwu1fT@G6E=4g``!m+YIY@zgU`bK6Pz1;YVaOx09jH$O~c=rTLA1A
z*Q~YIoG+C>lOB+mJm!r~apTh2FffU@hP74LK#u<T7(KieZEO4$TeY$Uto1>94Gs9E
zC)Hqf0Ek%HFC%lz>h(;E)y0v;CeMjpZGlj{c#r(xcgr*MP4aSq(3RT>A>X>XPSM9@
z6+jt`QB)k3HHauKKIsAA4`HF6cIe|9SjxMr+Q^w3*2PdE(UKyV7xZW_$K2s(XZR{A
zAMeD*DI-ppxfO}41U^VEpx28`4;y#p0MERhk>W6h79c^nep$eT3XJFA01H>gIWRG3
z@*8J8N^NoTCYwR4evKieb(5bv@eMIfpY;#-j=;gS?vVcWWw*R-x;(X|2~k<9$H^=*
zm}=a*^Sx;tk%=h<z+!2SO7&^(sv;4;I@GaqCwYjtM){6(kMX?4KJyWYiNymK>5*d@
zXwQB1_^jFghKDa6ksO2Ynb;_rj-kCelfZV9d{JW8c4VaP2Q2{km-zo5VNv`rFm}Ih
z@kH7_yl&hS!l*LTHSvTz{@VH%E00J2zOkwEMBZ#=R3PTbsg8%LBCU#t3b7HCZ>Llj
zfu=0fMkV4ltk-yzj9ecXN&nGA*M}92W-(~b3+G)p7eL^ZG{(;BzD+nFh)LEqdW?<~
z<j=V@`kJR@`?z6(vR3M=#2qPWhbO0zpvhaIGqvEi1Kr)0$zoK&G=KMJ*(C%rQW#`(
zY(M^N`QBmEEKzV|g}PRU?((;L^5*{1&cHHXGdI3gK;->uw^I^GcPGsx_(PyG_eF(=
z-_A#tVK-5&#K^xufyisnxFr?V>zxG>;yv380B|36hy`K!i!q3JE(Bgd0g30eQh{+A
zzx2FW&Hii@;b|29sfy2eHgS+_puuZ{e+rf{r@&W#G^E7UK4<)6Y4zrY!9cWd59utx
zX>iVB7f3)j-VHgDqm{^n0A8a27q4PfP7Apt&I1m=8>NMxn-;wz3iSAlEGLZuMyNdO
zTry_?c;0!_x#KGy-cV*vZxh*Bj{^+&&@<?fyuu`)KfM?%Os`FQO~@p~>ndU1dvhC~
zC!CoJ2{QK17au*p?!9E?XxA)&A-1^L<R5KE>b`dXEDCIKCtr(HGYw_~K4bHOo`WJ1
zXEF_2H!s+^nNP?L3LK+F=y70Jv>qdd?u5qpIJf&ZUNwXvC9H9)MqgOp3}lN1)hlww
zD4iySOF%?uC@I6X+qrW>K9GyC7o@TvaKe@52yCwJ@Tz|ARxh7#AS$V?1xhqWsaOa5
zAc?;^i~o<3L@e`ZJr#f!t8WH;e0Gd8eqbsnoI_&;u4jK|uk!<r9$>9=le7wp0w7|H
z89S%?FYX-00oNPj()|?=x#HHaLf;w%%Y63Y85dB6h5w{ceZBat?ejezyl%aGwH82B
zT)ei$>`GPcqm4OC&LiJ+5J|QCwg<4$W-AZ5SdqmLJoE$|&;#!skE+{84`)b(tx*q5
z@PwQSfO1Di%L1R)jHaD|kkfa&4#3yM-+r-Le-D<D8dh}{f;EvOk0qBbvz-qcK4)g=
zvLoWH)$S*S7Xjz)DJ|wMpt{$(L~luQubS|MDnj;|f!aXE6VlhAv{Q$p?-juQkW_N2
z_dEK8h16xbeSe?3?7Fj<lAFO5<#tbLI;W&W@0g~Ti274yuE^5L+Ns}c?oWd^w)9)c
zjtPj)i{jt(y$UZ5r!r>shNMgS<P{1wi%hr;iSo`gVqLvSOxLyrlio8U4r>mgZ`y$q
zC<1HF(FqL>@J{P1$#2(bzp|^}>_A9R;gdRIsKeh%Q`NO;*f%@zBsOqxpT`~H;Jt+e
zm`O-6{1yPjny1`f)iIwbpm=Z6O;`{*=8-H%Cc$V)H1uvTiomr+P@s427^gQfxDw%?
zSo=6qk~}4kjcEAYtZFd796y)fkS`0qY=uBZv~tR(MMnMJx(rSh6<ySX=B8LgeVO$J
z%geqo;#V7BF@y04pfriTNfv{lH6fA`I(sJm%ZaDY0)yai%DUd56S{Llg)MdQ+{D}A
z3t}#MfL=a=WIFbe>+>}o2LTcciLQD#H>Hj-9=pL@o$BpIxP!Kgu^J3T+ND_U!wcwA
zpkbCo5}6tZgtzqkn+s7!lFPVw-y3`VkSl>DbmK~BfGO&N208r7)rx)#=N&Z|41K?W
z+-EzyQk94c?P{>!Gw**P4Q;O8aNOu9CnxxAucLoSue6h`8-$?;GlqTab$#zH7Ht{<
zUKhyy%vHqHkUJJ@Okzf(K>(DkLz82&JA3f}$BygNiaiqvNy_dw6;4P^9@*Z<HhMT1
zb%EX3r2qR0QTY*<W4(hHNdTt5NeR8^QSLK?LZ8q0_`*rb(Et*{>BH@5-GYp^3kf~S
z!7rGpeY94?ux3^Fv1yWX$=h-MLe=A_<B=LB!weD?AGal11XSv3w}ZE)RKHd{Z?ztF
zEe+)r77jC%M|_=rC6tvZ;ziy$LeEpKj2@HNR!)`m9!gMO9DG{aGTcyl-Zz$3g?C%@
z>E1XR>d*OefshMh2wT6b$;Rl{yuB@`u{_qY`MX!BthVYjg%pdtH@O3z{+2faza3lL
zFUp#~2V?VxJP`GqViOMo0(KB@Ahr~qdC(-SxiV&&FVq5VfE`jG%K_iHINj{Fr^12E
zf#Y{9V@FRwi726!M#_Ae<F|Qwx16#f5O5wP=1tczDprHDOC(MVr--;f6;7yjvjCF#
zg$5oTrOzV!H;eRg!3uMdgd|<Ts7G6NB5d^j2g4~1!S{=i*ty6rq|T&T3?_;bBt_VX
zHl6d&ZeL}SkgoyC(&+H8-Ja;r1!s}J%TzQ)l$wR8MeWO>Mhw&lmNBt$WD1^pKXgZo
z+CUUcs-)p;m*q0PCHfHEaN}U}Ils6{ZefDBY|Cr&3_)D((q0LyC8d~Abo&>Vkcin`
zGy!aP(bEYx=D*=?s&>vr9oK^%^(@*Pj%v*Fnc1Y~Zl%8zN_rcLt%;bE%QRSEo;y=l
z)89e6yqtMR`Q3y)#N7LFykzRA!*h2QIXn@WKFgnh0gO`9`Co2`lM6u&fz!~y2ho-G
zx2pYJ_5E{rFt~-!v5JdF%fxQ~xYRr{k_TY1I!-6>el20c#|&d|2^-9zrg-660Rzk%
z{>0)xE<5hRe+Np4MPJHpb9?_J$4cuz>yQwgpZe2fykPxIt#x_n$5(-fcsJ2+Mfc*b
z@IwnU->&nUK%ogjgBVSIux>TbiB{FJQ|i;?Np4b_UcyAnLd+r0GU@jgEZUL@FD}Pg
zA+#e@RO*_-^d}X-4kD94idiOa-7Gyw@uQ%ZH}Vx`=GGFE@G3mG-Z61v4U0P_SA7%2
z8Bh+qr&8niUns)N@%)hU-Vjq8o%L+gNnRme$fPAtGL~a<KC21H$D$2FDW!`GkK)13
zK$fDZ+mSE|EK+PJ!sZpPbcvOWp@X9-bQ9Y~p7@kh@b{r3h;g{yjLZ{}HTGU4yzE~|
zIqGJ7U?T3|)EE!Glp1?<7L1nqt(s=tt-@EW8b=>8CUbA--jN_@+y;5V+`w-AsBUqH
zJ?VCOM0xQe#>9FaB`U3$6*F!<S$g349EKE*ejfYxZ?nrsTO*+U`QU|f`2MMnL?L7?
zp3^yyP;e#I{lm7RSy1UcAK;?7Jap2?(GZg>^?WaAf+HO|1+1Fo+W{qb(fL!Tkrv)a
zR@UF{@NwF-OR@2f_7&W|Y=wzadj{!Bmjf)bTp@|^H#RRD)^W~nHFuultTXjuz+4%?
zpaFm(pFO|lR|ed)q$CD_HvVmn#GifwWujNZ1Gr6^28XKkCYike&ESB_-9)8G2fTk>
zNnXHf%6BGUSPErE=qcH8BIUQBxDaB4_h=Zr_wQ_lA8TD$XJ7GhIU7vbTxu@~BhQ(8
zXhIbiqoGPi`Vl&2xN|9`3ipDE6x)&J$4e>&tkh-bH_<x}_m$)mxV^>&ANcN(a~%0_
z;f9Xnf<u!TMoH-u^^|qv8-2>yiSM>^a1-x{g)S=shb>|Cb31lJvc%{U@8o%l^Wt66
z&-w~Imv3w7)Iqq4uH|y;yKX4s^@#7~F-rRLO_IUa^vk2?f&T4OCC8xnZ1De2>y2nW
z3nl{lw$m(yGw;<Zj30iY8*C42@X_9}0IOwY)`OJ%j4}~m7_Uzw@AmIAd`|{&)mnTc
zj>J1mtstX=-xN8x43^HhVk2#OOiWwq_J(&q(ZzwQ$N?pxk}p=cqsS)&+jvV6)P~L^
zdSfumU@Y7cKIQbIfXZQ3+vWSO<3L#97Ve2U!>uo@oI|m&)5K3#ncUYaozZ?3i3V;K
zu^-YeftIN97wla{uWxh5PYq)Rqt4yPs2oI4DjjyfqE;tdRUMgQHo{l~v+t~ZL_qT;
zCL8tkJX@ygBa<#eaTS==xX2EAR^DQ=6Ks)WBQSOzd?xxI*$S;N^?G|dVT}GyXP@0`
z7r?BPJBVq%=C5fDOU=ns>qZJd*xj+F>Wl=TP^_)p&!gJaRu#6Uz(kISF{1jFVyjGx
z?uXaRy|jKXxo=76qX|K<&)AZfc_Y+Q&e#m$ml(g05F#E3#K~Wn69omTGWUC)XIr1Y
zkSYrJA`(CRu!qu*Dd$E^Y=}7b+#I>*>NRJX*n}9v$6TcEfnzJur3J`Ein!1ybhg6D
zcjb^9TjU~iNcS?IIwKv5xIcMb6xGy#-}E1P_eVcLf72jAB>5LoLejW~@-Kv+nImiY
zzf9yrHcL6*`L<WJK!q^3WH#3uw;G(apy&Kny8EzQ0)j8;h9Q;lyeLA|QZ|2(ZdD4e
z2w_*J+<A>UVI*b+i9V-EI)PW+oyz)Cyv(?fbm=4&GgfP8%XT6fW^iV3aan9p^ruAZ
z9xx+l{RPep;q-tILjo=RS=&PO!s)FaX$P7(x`A0;IwP{#8eIpc+Zr7;@}yxb6q}>{
zy_xCH{%)u6n7smK)ZoR_@r$Rny4C-hg|vn5M>qs`xkL;t0Kdrgu@g)oto)&)^VRu$
z9<?|PRWiAZ^0zgolXBexMMVV*tAU=y$0E6sT8|t1#(jWPk}S&Xa?ajY%C{%QL*2o+
zFofd;Z6YgsK=WTW)4eexUGjIwv1*DaXQGo6$7Sq}6%e?l0?fvOf*0KOkDL>L?NV=6
z-L?!MA@vuvU2imcoPk>M^*8RHem)7CNeq?K<IURi@v;n_&OxN1nmoXjF|gMgmoiMj
z;~YPB0Z&pTGkL!K0?uo)aBVioSuv3gOlAYPA|l49UX-}>v131Q#o+mIXIP81v9;ij
zDg|&kB6UC=g0i+2nFN@)#bWZEFbIz&A;27n7NB@f6ODQ}Y7(QiT<OZYBgH{APj80a
za$A-T-;hj<BaXWDA7++Qw!2ec(A3ATvPt~MavLM;$z8rMIcjs}GdW!uh72mZAlXj{
zY1|rqsuxeAc0PPZq(e4Oof0c?HPRNEh;a~fY3O@NTx{MfM=lni_>Q`aHUU$XkL4A^
z{wO1&32lN>ycI<rI<2J0$7c)&%{d8hxo=w#IK@j}?(^y;j5H)wG2*~;Wrd>09g}cc
z7v_k`^gGOxsu58Q8BD_{O1AtK-u~w0EIasaCnE0bzBIj~`%3ILfh^Y&FQ=F+itHDT
z{%1@=$Y~+N{e{7byzUPo-#<sqXmDtFf5K9yS`XGFdNPF(7-)}s`ChV`;7wXxBIhHB
zBI{Os{1<?{zzx}C!5-T$oROzS$fnG<#c3+WmINl0Tw6Ff8Xyf=m_jK?wdkX@B;K$~
zsM<5z*84As-<SViE>B%t#v%A_qrv~yzU_8t@a|vejQjn2qF&#-V;Vk(ucsc5hlE}`
zi*$g}McHIW7eg<4KgaS!UW<L$z8Ah_!1O%$L;MuymS}pPV4W3#8)g~%W>ZHMQ>*$D
zWJVT+66%@3W!c;CyUPd<AvZ&?ycpM$T4Cm0SU~E)OS4je)3QdqzCHyY;9pOL$fwZF
zwQe6gjxPK6>3rY3_WKLVe0gzmR>eH1Eqrv_$~!r^WG0YFJd7^qEL$ZRflH-2VMDzg
z`{LcKe-M6kKsB0)b^rmId|@3fiaZ%=SK8|AmZFN!X$#xY_X$fw|E`=`|L)<hL%)Yk
z&JA0k$JQUT+kDnj`EiIZd-<U4E0?{|46TOUM-PV?EjPO;hS2M6zgS`^6g~p|yThZl
zj=gV2#dBnDzE3T;#N-EC&J{{?$-czR@>_E#zLXbLzIrICSdc~)ZTtSqt@5`9SHjmz
z#INVxcRh21ikiRQ@Cb#&Av$*&Wwr)cE?mV7BSpT7N>aG{W2t;vFgSB<WsXsq2g(SE
zZ>DejNZLl@#u3HhaZ8B(oe$wBf1vjD$uy4dRxj?jn0yS3*yCI%&Bu_m{_Vr}Zgv~X
z3PU_5iua_jc{FZSJzwbk-h)V-19k8qSHUAn8_#E6CV76@RVv48J*cR?2#4Y)<z>W4
z3BAxShkS1};lv0Yh#8urT-rZ>p`{`%ynjR)^3l1_xa9wWpe8XtN;PGocmmg3$9}Bx
z3@s?IdW33&PJB2X^MSC=3ris;@Gvm^#H&>IOTqS4bL!a|d#596H$?D;Ra{3FcJ14u
z@4?fWJ_FG#ko|~Y(vFNgMp_v7h;N-E?%f`s`ZD#5dFQV`;-e$gW-E%5;5BlB;Vc)Q
zVi1Rs4EBMp?K2Z^<UQmGZ}`ne2K}=2XA^=EU+~@TXveaAGq1=M-K|HDIp*NShp9K|
zI@4uzRE)oq7Iuh=4KS&O9v;u)zp>F<f?M%A#f_=NMo#9Nx2wP9UU;4@#1pxv^IqR(
z3v)=BB5rv%#Mj9grLX>r_}C%hY`s*`#=og!VlsW|7q2Tlbe6Y`nR={Rho)w`TtwL*
zkSptaY&<knR8$IF{qf*zTY$CUe)Y=!owgtt1|=51uOzHI83h$xYhDrVD^jp+`6nJ(
zHbC<7rIxhx?*;4phKMMO?U8gk;#aT8lauvdv($U;RaU(IR_AD|zUsxRA|fzYHmRYg
zGSg6iASxGxt&_ZQbu5<{|Gv52`ENZb=@Y>55}<kj)r*c%SrK!o=7?3#PQgt+K8jzt
z!2r!(U-;q20)nS`iWPPo12L@z2HA}CTu#+s?K-4fEB3mppwPN^&2;aVeIV7=lE=4~
zJxmq0_SxPpG2Tlh;}G(n5Bhy}>|xvIG^|F3mLDs-`Y7344i`D^p>+z1LukE`p{66I
zC~`e6{JNB8Q|BnPc-p#}_Ms8?)<sFn<nqYU@&Jz`LfZPNd=JnSUMHbNsUvTZ@D$tN
zZ^`U>)=P=TSYyJ+#NLuoQs&K3{?#GKxPNA!`(XjXM9g$OH0|o_gx&Ym&D*W>%NA8G
zVXtJ--OV(nIIs6}W#uTf^Y^{X^ewAOd+!URGcD}S5Wl+nG_ZL6n+)TaQzdePEUf=5
z|IA`b#0?*g9k2gbeN-~c7)mT%gMuxRi*5P}_Z2Bg+|O$)X8&k}!^U01AUU?pxZvUx
ze<~6rGj(hULI;zTJL=~JINw9+MxL<>HV2K_BJUAxGo%txS9}V@=AD4r@Q*$h(N>Ia
zz=5(FV_tHpVD@vt1^w%HtdMLIzH}CzCxJ~jrqMm(+*a}s)oQ6|pc}P&8K#o|;B~C>
z^Zs=#cWNJmkq_TF=+Bq#BMNM$cma1pF%*IYR`$pRK~(axKP+m6ja|OV7j0Be@4u8r
zfftMaAi;(Ic{-g+aT|l?wZiu~3e|5n+{_}c_6)u@-;HRgssdWd|CS_YjG6QPHbNv{
z`fHXSI{JHGioI1Nlcq!XmAy`fD>8)|hK#YF7Hr9+HCbQhN0uNweGcUP*8w@j#DQW%
ze=7C>S_Gcb*E2AZQ2R3aVnJM9ta1P3?(~#Ql(%D6XEUy{;{Y4}wSx2hEP@#J$~#rN
zABet3w=j;45Z?85e0h40ZCs3NjH!{joh)g%uC=u;wwYE#S+CiP+IW!zZ{Fle+4aP@
zGQl4;%<6tkrlt1!iShy0*Bk*<ZI!u1eN3<sw#gmD*Q~t9!l8|gad}L!vmzk^e6d;6
z>BGY!dwT}Up6i?-qdncy*S?gLkY{pQdb69q;_nnlz=Y6d&ZS+&v2_Dl()5EC-KWP%
zt$qsk{PHI9@+572>dk{T4Sk-Cl1m;ng_6jh@#1&9gVVgD=cFkP79vj)&1dRUtF+Qe
zljXRS_&|@vccHg|rFW3tf|MtD-k_7;T<LNr1m}Q?P7ycWq;eVzfWV;57UFKrLTpW9
z7SXM&p5HNvGAZDjouQvIcFBrBH{%XLcdztzfYR55n37l}<SRwtHFAC9m>XlJX>TMz
z4ytxXcJf)Us^uAZM=Ic}vd<yM@d3DfvRo6qD)i?!);DPM@{uHUGvaxIOQZ*+D7ow`
zsY9&eE+@A%y0+g};}SF`IEh0u-6O0U2mejaZ#`Npi1u!;www0VTer0_Jb!6Cf##K7
zMNIWof{KnWc4ox+<Wv>;MSi@@!2pTwKOdr#)85nvC;f0DRL4%ixDrXqs}%cZ!iok2
zsg-UUtDaqx1U0Qjrp?2Zw+T6XrYk)C{ud({=pPiWNe*=P?lK9wTxoMMdX&_hA$aL_
z+gB|-y<&Z#?<Et9R&{PG&(}YXBUXm4RHBz6d8+<AH~75T?sE0-c+zz5Hh((g^)UOq
zU3*ocB&L55Hh;ZTyhW-aOnHKa5I^BHAu*Ck6kdS*fVp+0M7#w!lG81$DxE`FhxJH-
zAha+5ip{0Rrt!+>y@4IBWR9U%a6mvnUxv8qYX}75Df#B{?u|@L)Jt^Js`m!4oAcr4
z4F{KI(0_qw04Hls)(3z$ie(#PR*A=cq<!`Mbqo>e0aO-d1v1#(Zq3wci9ov2ruIe1
z>m*!PIWu)*273NNzDR{{{<rgMK<H=ug1hVuxFX}`z37vTM(sn*M}{z?`_+Z1J^J3h
z3QcC#`bt&#ydMmM=xT}IB#62Z#1x5&&b+C0i^u2xRkYv0m#C<mo+!vrJR(a`?aOd$
z3uXH6aaJ9vS|_Fn2}GYWq2<fVwH-&75K(?RS(S<Gc9u^j_w8z|pDvo)cfCF#$+py}
zxQ>c`SE~8uF20o|9!X4`h~fHLxIfkeyVvWihsD&i^^i+=>2D7qi~|u01I^zBfklj(
z5i2QbQJuEme+&~OHW6FtOzF1)UQ?tmZg>5?#OrU5M0B8SYT6Pn^O+${I-`=GzD9xb
z_;sYEMTyQ4=GDr|&8I&Ov1NL}+A%{li-+H*4~~fG|D+Eqzb!szr`ckV>689Po+0}1
z_f7q8Fw`%HUwr9Q$Lfc5C=POmwEx?IrALwvV~gAOwt~k}(_J%iN}r}tV!r;>U61l+
zW7oRD<$)nQ8w@;huD_1uSHIV?(>1sLXW!`-4Y6G<6~w<~uieZkS<MDju@L*VuD;>N
zY}!97ztngLeEgMD?XmZG+jyjgMMlPV9slYk@Y{Hl1t)c2Z8LzbsDH{3f>nZQJ*L{n
z80ViS+U`Ge(F|egw>dZ#q;yRRUsxw&M5IwdZI?u62@q6b?}UrxjXE^UF8_q6Na)~+
zbb1lLe0)akhm~O1uOv1_U6_t2AVzS<ntQ4j-~vyrywRz1f+KkUEP<73ieE1VYblmq
z_pGudCdW{sqReC%NQ-hB=t-)?SW}5#nsv5+%ByDD;4U>wwS!AA?ER1;)*v?hEU+#c
z0m1qTsd4PJbVoW;8CK%U;E(7ZqV4{Hn2W_fpc<1_^2O#onP6+!;iHPzSuTV+D`&u#
zu~_@^FxF54@KH`ymw8k*kOgWi9mHd(GE>-(V=t<Hd_?_#Z$jR+O<?^<Nqqnd`AA!_
zeek0#sK0mI<>c==ZOJdPyH7{X1q-{b$5|EJ+Vk7o>lOa@Jc~%|Kby}EdD368OcV0*
zpHFZox4PX?k6bJda1IxFRGqAgdPko3Fqnwa#F#3#`(`p43Us7tt8nVEoknY`<b|fa
z(kJ>=%Mye=G#X{BkGh~9#rvBmK{RpJhBkQC-NW4u4KDM|o0uZJWcswMuc8+`K_H|O
z5k?iO$<59Ei?e!*DKD4pZG+kOW7}Qg=HAL^b(AO}l2IZj94gxR(Vmy@)-yZWd^2A+
z{zH(7cr!V+6qB5bljIsf<EM4!ts!(q6=k)G>zv&LkAB)gX=!;y6+V7<y8u$YbcBu$
z91F28*a%*UCe7qy2O)q^olGC6p8sPm=1OrgieDb33pDwO(bw!b%4g8R^FJ8TruN~O
zp(oRqsZ7ZhB)*<pU^>bvrea2jiq=ZavUghRrb9y;_QMFP@8?uX-VFGu9^fvNJBb2G
zB6~ARf!Zf1YT+zj!9x{O>t`@wqEq4a9T*aaoX@tq$Lwz`@Q&_Hqo~K3NCNTVab{@$
z5R0YTt@wslzVI9Z!9Z(<%tKZxQO}Rpbpr*6_Dp5htm>%Dhr^vW$?8K>6`t;&gul$n
za~d+O&+#VwK~3Y}mmi0CX$q&%4MK!4>1T+g&o;#GHCbZat2{B&m^gG<XoGY2`DfL)
z;tK0~WCsQfq*x-uZM;TBJ_u4x+cyp1Bko|l=ZWBo`im?3y0Jm2{1$zJl)E6-=?}8H
z&QBWzdIhVOID43+s|(;8?P!{6+4E0g-huAE1lrLi1Gp5%aydiYL31Ret3pw?Y-WQk
z4muX_YhRW48Wlx#f2n;$PdaeghS+|mXzTd-h?;zcqoea(av-}Wp5AncVMGtIy7^6?
zOE%6Qqrn`5BMRD_!<&PNOI?915UeWWa`{0GP7P6akXHPUCWSfVb&y~X_K&<%XTR;z
z{Y~-w*BBUzbmGdik|+f-CpXZ1_=(>|POH=(F#7j;h?f{V{Hk1Qv)8DDO0oLNXomQ8
zMEW^PIj}!sb9#tNQ%T}?Ba8pcO$lY{Y@i~;7EvF@dTb8B#t$l`nSyklxpZjEQk5fr
z<X@4Q%Dx|%EIxQXor`&r+&G{XR7&15t#j>NN=r4LyMU}lQOvb)U8Bl%&HJ5~tfcAa
zSd2e+kcu(HZ?Gl1;G9mJo8tJ|?MRmXc#u`DAZUbp4Q>$fvrVaNSA)Fr@0(BT*VWj_
zh4K8^!~L3p+{(y^IDyK)8u`9C?a$F(na9cxkV~r^#at3@&|AD`Y`54Lj~=N$T3T3|
z?{z&m;H^KO>)!^q!7DciLJznt2FL^@!jINoN3VFsof5tSy9v~d%>7zD`szW%XN)~*
zcNmS`q}|*1>do!G$x|wC42AC3jEM(*()$AoXSBHDdx$2yhCSZ(HAMeiq#1PK+jHQ%
zL$J68BM);$4A+y4d}D%L6%bngeRfQzm~Yt?0ekOQzx^Eb@x-XjOJB^HQP*PolJ@34
z(4gN@hE+Pn>#(uwu5#spMlBQYfqNxzba=j44J(%Y4%<7O-!NhI$f!%e)-N~UGm0e@
zi$A&Or1>^9di+WyXNzsrfcj5*k9%li?=Uwk>u2&>_)hpihFYT;h7tdpF0`Tj`G>I>
z5eIwlr>**cqBx%cM{cwj#^}s-oM7!aa~dyy@_d`~l3Z$4El%5@^c91#C-m+yip3VP
z$|;*Hs}#mdUBB4M)=QLpv(l;k@{Pa+7DV6mr%h&2M}w6#rAy7d3Pe{U@j!xKXrA@5
zU12VLbEoE!wu(e*05@f!U4pN1Xl`1xGg*uI!sIP(VZ~P@#~Q&aYGY5EGtr@7h1J^G
zM_0XZT@kwne^0%;oPSgN^<O!6MFvZ6Uq1^xLv;N50888_F27KVnTDdt@LrH5+*+UR
zP(8!iX$f&NT(>Ac8V=R^E!sIewUUt^<W~Hd?Qo&u1dEb=Il1C^Sf7ymk)EM7!p%^k
zU+qglb1#kyVm-R%#n8c#6W2Y-7`fYB%D(oks*WYL4dVaf>8qonY@fd$6_Jug>0Vg6
zyCkGTmTu|pZj|nB>5}d)C6)&1?(WVd-rMK<{N8i;gL9~x-MQwPPt1(ULt{{-QMY}M
zov+ESdn7)kwbMGGMm_%w$3>pe-<Av+OuLR;`&CI>s_9Z|({G^jFLy@^t{lNC&#t%L
zr;~-+mpqq&SZD=IWN^V_!-5GN#2+AtRH%{X6JtVsM*}q4t2wj8XTdK(Q-|rxkn0_w
z{)u=$7Ag*wXYMzWyG#XRh%9-1azV2Opfr+A!G8b-LrZVYYH{N%hs6hG+W}3t)mh)@
zRRIbvTKgY@HIh6-ac-F-mX*Lhl2EBk&lBcNtZ8eO^T}u3rt4lOtGcdmCPIDp=8?cl
zy0-J3?RWB8Pv)O2Mbq-zp32ce;V}x*qHC}t2k<Xgqy#WUzA$?7UvJSr>GrI5=Xo7!
zkzfU#Q}6{viicKLBXvF>GC3UWxn;6um@h>BGggc6+EH(ZegT)Ufol!{rhUSRIGHeP
zrm6UgR4$~ZO?PFp`U0lpV%6bfl{t*N($)}Cj?FQ){YR2$6=<cvYg?Q>378|Jwb7Xj
zU~cUZ??2?1*1y5QB2#dk>9Oh^lq5{BYs|a3SO~*wSkie>K@gti`8+Ks-R=HbM)gaV
zao5Xh(&m{bZ-ZrWS+(knbnC+tyn|6h+8d07D|E2Qpk6m3K^eSIZq`aRfnLrAp?(Zw
zE&m;-$}TR*GN{HI0i+EVCiTLRV5f298!ucV#@F#H<#x#>63SP;_*8aXG;-pO>q3xr
z6!Bq&#!KMW(g^CCv}3dy+I|*X{9LQ){-qV0PR_>B-{4<g1EQ<sYgdD7VzB(stfsw}
zG4F4BT#l`rN%-998l!4CX38zwuagL81h8Gt$zEcj$KKRbPi-CBdVfl?nBX?PUf@lP
zWmS@(YVvWxpm|&QJQyA!&-F7>^=_~4qq^4I+8}HeFC7p;OGZEX+`lCp8$GOJ<TS5n
za6jcEc^@f3dK4%LqM4R%yNfJpeA^S*OQj~Hxi;ZB3k+OIHH;_pb;-<AAnDj`R*@Kd
zT)SP(ZeA#Cou`oFfFSM2%dxo{q$x2G86HEaMiMzmyk6*IgeVW|;hQqMr^XRS+Z=ur
zQ(*m*P(rLE0kv=AulZt%PXnqjJ@sgEYn%mCgk^>Fzgbm_=D+M3g8sVT!mMI9D~no+
zm9TH);abk4J%&^=NZu1o!Y>xG#{D5NOr~9Tqj?wAe&dc(LGa#9z<o7W+l3~PFq50j
zKkj>YvMS<tx0II0wTkvEjfmf7-8&BP;1ESsA1vjP`)0*4!;818&J2Zx2mI$-C_V!_
z-DtLdEZ*<kZU(#PBFD~JIsNb|Yi`ES_1OnUiX)n)3~s|XGcDsO=e-fb;6<rJ&BVz@
zz;iy{)vLmYp|%=eGLm%XRWvP{sL1H5KUTGKC#<TBO1C-|nVx;_$YduP(%e5sMsjXC
zn0k)`QOO+Gu)hTgV;$Z!NahCwqthx-EEl1zrsW%qZED0z>gzKnY?D0<y#EJ66t~C7
zH@V?$8CT<tD-lT=*o7-P!Xunw{Z&@vM?FHV^B^JBxHa$jTiQ`Y!fDb;49zX^x6&S9
z05?<3Fno97;979=Qb-OSF3<hQ?_@7`L?jx5)Q|CNyYO58@#0Zx-dtK%#w_|$rPX&Z
zS%72hi1qEYzP%%%A<9BN9|SUeqX)Dd7+qlRta~n6H^^FCY|Rsy2x|eKhHrhdZZN$J
zsr2@@`PJ*{uvyM7-~9N@Ax?D&w;Xe6t0S%v2gFR*HBkwLv8E+a5@Y$rZ?sVsN3Xd3
zy!f`O%dywZA*-iwWvg?4<2Xdi;f#*>X@*n*Ru4G7hFLugkc?@%gnJ$g!jWxt3Rj7l
z_uwOBXByx3dZua>C>m@Z@Y2oB%xT-i_uO;j&K~6@Y)#4Z?KQ%eF<G6RGzxXmwE_`W
zo`~9DIli*T%p){<w*-brS<OQ6eMUj{(v{N^2tOkdVgoN7goS?_egei1VPj)^i6FdU
z>TnAv%F5iFW+L2Ox;OT@$_ob;+mj!=RP{M+=-LzZ&Z#GU)aC9f)#HYqZ(_;HPF0ol
zy~ylZRub)|nxdX>0UpNt8I=_u7(TG14Xdw_EA8I=v*fp9O|Sh~T`E+p3CixuChqQ*
zAJGJTQS!`OTwO~`;N7vxvrQ5mV57C|9~(4cZlp$Sm(*1Av&70D8@(T+9gKW{)fScS
zngTb~2{TDH0am@VG{civl-$k63SYqDkI9S3W0XhRp`-?cRgs2Glkt3bi5<c(*mb$Q
zQEFZ&!vO?|=D5V;*L$G?gE1w?C^lf<H$UqiUZ+osQeKt^AMlh&zkt^bWTh>-a^5&a
z6^Wlu%~gDmcAKmDP9f1RD;ZOs<18C@jhjEDZSlfp)ADImEInZgC8UN*v4O>Dioq=b
z;Slco=8_Y;4|*B@g8fS@an<QN3J#XiacA5#^QjC(t91jJWceDYd{~0=dkK%G61Yz$
zm}%!oB9ho)X#!FBGpk31a$RN7m9*Rw-Adc*+=z$cuN#~i_0+mVe7+Y7)%H;ra}LUm
zD8xV!&C|~7eJ{ho1>7*Gaa-8fQ7Db>)AlaU^AUgK0PV>1Xa}zyX3<hp)iBf3a@Mxm
z^D|dW($)r_+I`lG?aTLROM)_O9n*(BIJQ2jRBm>0@3yXkdgmFNBR!vOo823_my_A?
z1=9RqW}=?$LoZLK&yCz2BV&&<rG8{`tN?zy3w-GYUO-=%DGStYy`1h*;pJXv_bip?
zU{i$(Ejq_#ipi?d`7Yz-L661V?MLUuZKr&Fbz`BGFc59ja{opfKXZdMfT+B#OHF~L
zCmv(4sPdn)-i3vSw@bIc4il(f%~l77WnZ+M-Bv$$gSTxmTLGmWY@XU}XP<aq5JT>D
zidV>fffm<IGhOvphnj}t3NE(g>}g`a##^u&jf-ON@C4@i7&>X)jX?$nK}v{gstB~E
zqs57a3>0X)q@<OxutIj`&ZVLV@l2iSz8`8vxBnysCT=kd8gqNOCD606AAlJ3H1ZbT
z2V>Y`C?*ipTH$$Z!Gp3BK1qi{UJpSeX{xOQPv^O9h|Bj|I6F>(jYrr@@z?Kku@+T_
zfkv8ZJ>T<R*3um#@d~4?g1S6*>Hc$RdIgG9a%?q}-7X9X)<o)}=YMh(JMMbp33*tn
zE6<~?X|%@-oUYba1Hd5rz}~5-OAmt@0P1~p%p3cP&VtY|YMF65`Nw?`*FWK&<%-`E
z*2b8uLyMC<KaT-$ML&4hMy`~-wPcsvQHDUlm0sJ}BRhWb)N>qMWA#609*@nSPv|0F
z!#!KglOSgWOqp9##l<-^!@7lq7P4|PF4I(A${{&^cXtCLuF=>?;h2Ui$W0a~YTK_B
zO5Ui#uXZ;U;$G_JTa9e|d|<FH*CAgmKaVx(dpR|+MOqvE$?zxT_{DfCgF4ueKwl`Q
zcs(=6YRpz542PdLpy_h=x!eTDv+_yH{Qmy5wPAHI={W)Jvmwf|lRq;7y78N?GKsP`
zv@-~jW}hv4cu6@}mW|@W1iDgEC?>pf>9aG+^kvZ09?aNNQTM3`;54GugX=bMN^Zbd
zC;aVoQe|(*my6PE;!*?fUMMr^H>F>&7ESvc&q@V-K%}AAQa`?w+>w$ZVmYO4&sxqx
z&#ef@glR)pc45FwUWazE0^LGwrfn)l9FoO)$M{w=Tz#uz>r1RffhO7C89PZ(8uK{&
z>pX%0e+0veON&3Kd-d>Q!Zrw|{f86}DkPl;N+mmoS|#^)IMM9#`;8ANqFirJEJ>EX
zZZGf-LV#){MTjl<_(S9Q+qZAC1bY*I0-VIRbAAE<M=knVzP#Q<>q=!~1Kz&wv6n|B
zw0gZE$YVz5WkK-5?lO6Skx~9|zho+#smY#;<L-v*N;4EFQe<Qpl9Dv9U@XTsU-=>(
zWtbgx!ee7ur%U>BMDvD+BbfOX*XB)86^om=N4qgFT#HIi9=%<4>VgBUwT4F`fgR3+
z$sJB{L&>uMuWxsA#LD#{-OA=hL+2R%GooSwdJqj1mr!Dz`$H69<mGW6be%W$%9YMj
z+&EiT1f(Zf`Kgq&l6CjdH`6iL<Xnq9-X3X_MYl+MXvk!61q;io{Q}opgbD&YxBWY{
zfp{wz$4cfA;(21gF9>C0v*Lu+X}%GBT!RPx4OP{JC3P!cIg7ur819PfZDZLZZd8;_
z#;hUmoOXME5XJ;NQyk_$7yBzk9bRMl9yjW`PqlU+1258b=kq|6d#BYC!|6u`kJ^fZ
zqL(#cgh0%&`3tU~jXoUC?%O$()lJRYTYDpac7iQuR9g(}w=+bRA6BFpF;}q3ZFDbD
zS}li{jS3%~p>4b7O$w*zM6RQTbShW1^vA@*qho=vNWm5N5`nVI6PInAIu?Xj3G&sJ
z<(a!hUkco-vz!oS16Y0V$nwdphm*h00u+;zV4Qr!E%kn4GGC*s{&%oj$#={!g5T~`
zOQOo<EI`WluM=g{$g$%1sZN2*uE_aS-wySgSbPnxw$Y%F^m67`P@721^_g<&wb{23
zv(PY(?{(YM^x%a%9JIyS#?OL7^?y>SWZ13*rgrPCdV6wMXeqXjC54O!a{Q=6@~$!m
z9hS^(G~zIV5rytIUDfp#D5EgxWnw{iPcB*P@+_MEugq!iu{a*X8ofj9`O~XYF`Sad
zmyh)8ptzwdXV14|HD2zKfTrSDRLJwZ^w>^s`8RD-{3i(s8aIelF?sJ(0wK~zqxd72
zO*GBq9_x7heJnb;LU8?*OMdR=TvG)HwhnOv_$w|Ya$D=U-dEW$Y|gQ$7t^~L!jvb=
zQ~{I#zxjE1K*fwA&L9oLoKW7yNbi35uDR>rM_3Vx{koVEvZeT=p}dMd^l(AFp{v?)
zTv`yGaUjch#pj9D_UVrG<5)TRdkX%4262*oPlX=b#rtRzN{Q=B6b4*>&U$TdgQ6}&
z7G*83qV~i@eRO5Ws;mO*oq=ubV~1Jt_B-(g>j&`R$mx&Ir)~1MEBq#jC4I@AE<y38
zCfq(22TDKIb@T0h&RsTHB-p=z4o=KH25>5FpJUP-zqfcEeCrEooQ$^}3`z}^yz=9=
z%*hWgf_~}xon-9AAyu}BGNB^gzKi~@@cXlqp5co7Ca|!!>~dM?<*Y;6`EjFCaE$43
zdYAa1o|`RA%(RC$dbDDW(Vx9AOI-WddPA}|b`ZB=_z>-80$pLA{RjW&xqpgB)lnA8
z;D}HY37Q6>AL76=q0Ztdpah0s#YT}brGNO1F-&L_lOXjv>_Mb*l1}0^(@+;Y*P*LP
zT*K`3rS?y14ftlPHYlTSm=EMP!O>uXKXRO@c4%xHvhjQ95)V#s&K5Vg9VHXes{2I@
zU1ei+o&jPKR?zUKk^oFj<I-<*GDcJd$qoHZ!^ML#b6q2Ofv1YuzGnPolOoJzJdZIC
z1UK&J=|c>R?VgFFCduQ)@T+%PdSsE9K=r$Fe-qr=Gej@1(cU3kIo*fC_N7aBcp_0H
z)9V<UV)A`{9KDX_b{>h|*C%nT&W(%f)o0fFanCUifOZ1ADPw;(_#1#lA?WT?ImR^n
zr%DeOK3XWnh;t|_VptS`G9~Z)f+W<{q!7NH^4$qeosdbNUWze73(VqU_81p>%;LY!
zNxOcK)TgMnR~C5jUQ}OuHn+ZM_OegBU2PVxqL^+}y~Vqtu(+OJj?~#M-hK9u);Rl$
z@_><kD6rzY%j@q`_vB$%Hyo-oIXoQc6;|6C%88g76%_0HnuZYIHYpAh%FJ`EGMII!
z+15qzm<Bc7eLehQQC~}?lw%pE<Dw*i*MGu`fax^~jmFSTb-p{LDx-brBEbJ;RyWWu
z8v=UN&)-t0{5c0?Urn=%6Rp`lxBB0&mH<iT;RkufM8pH7I0d?>Jqu_MbEb>2L3xTW
zy5v|N`7<9XGbejcGPN~(xzR6^DMN+>h$H_Gda~*J=WP-FAL&o(jOq4S!)6Eaq2Qsu
zP-kfi_GL=KLMehSdf`0#{M;-tNwQO^FLeQtJ>>mBNgBXJCuv0dj*b#V={zuIv3MR6
z8Fb-J%}dVt$^$o)F2;!JC88=n5K~nb3tN~9&Ld^x#k|0M70-VrZAUu&8rU8)+j^De
z?Nq3tHJ8n)TA+O0*vn^6ZAkn^m?^(?KCgMAuy)+|52{&30}u-G)^#Ec3W%{!{WbiN
zyhw(RQ{CrBOW-kAJMDKv9rqanxRSX6qvFYlmWO-Fwart*GQJ5q(kfY$((~$84mZ>v
zrQ#D7%-&|0x1<ZSj0i@C;x`!P97){THU6di<^LBpK;W1rfVHS4lQoW>SlYMn{kM3l
zZFXYQn-Y%QrElmj6IXj0cfpG=0!?gee$;?{_~Sdmq%*~dBCC;a{ee(<uT)Z<zFI0p
zG@7@LY+k|4I>y7khzbBT%{trCsle3{Q7T@{+gHq2gaHP)lPG21c)E<24Am<#6&Qjs
z3>^@WN?>9d@v2@)inkhrH~I;7B!h&=CsBt_RI3_13iB@20b&H*b$W&qr4#b64KgOA
zUT2n#F`uY3Evy<XRI(@yD(%9|hi}!GFio1lO&?tLK^V4Nm6u}PY37|#Vt?ewStob+
z=yvxD$V?B|)X6_?eSnv1G4Bzd+LW~pGw%$dwr-K?={<pOh*7qVo`*bDyyf$!Vx!TY
z>5D@Z0kg7N?Xw<c88K+CEv$(?m<Qv%!1ev$Ss1|gFN=I-K!j=RT{m#15}3DbsvcP}
zDWk<b(Tm9mQZbz16QQ188yOJ-vI2rrv}gfa^jXL<i8w(V^ZM;`tI#$y&{(yy66-As
z?i}!T?QCzhJ<u^>o`&>v5NQ<h+(JRmN50RfrL(hmPH(>J_IEXdR-VJr?zVk*4=G*e
z)eLi?>(o0T4=f~l9sSp};R%+YgmT=BlF5{x*0yx{*~-`MFECR8bUUXFSwEKaDe3X|
zK4R4ZwU#<JprNkbhX_5AJpV9MAjzEoJ3fyLeaaktnthJ%Y_SF_eE~cU=86bmKsole
zB4g=tO4M~oja+kv-zQ(bd!35-hmzaD$PEi0!-S5qWrQPpoxfLXf9P(8eui2d>+mv)
z#YDYkt#-HNQ7TVL(mBiILa>;aw7LQL<n2DMG&f<%Bdf9HO-_Vbb@WCti|V`8u|t})
z1fP}=OwM3B-@qDgw?*w<mG|OHMSJ&Z2opG}-$_VC-+_+Wx-tiDvrSG<F`p;J>QC5M
zbT)g6X*TqE!obo4LB=!_>=ZJ!-jP$pI1OJC7?Ml2$pW)8;NUbw_z(vosMvx?We{ot
zeDG`Wu8Y+fQ)d<nrQjvy#8V2&f^>i*PY$LD4%@E5bov%!LLcHB2Euk;EJ_bx-xO?6
zW+%)F+h*RLHk$*@<Pj(J>*>Ac%@<!)`V2MsQN)l{(IH|$4#_|-6ad0yXH>D_fRdMz
z0};m(8^kcE`d*6{0lPSKoT@ig5CRteVQ#gLbx69Z%7HHOrMAyr1y4_9E+W|sWVu-J
z=N*eurGZqh@1vuh$f;8J**1mal-F%Vh39oOt=?V1E?#QIrkYnt<b{hyghP7(3;ber
ziXd-j4Gz=u659{2bMTY=r=%T>fa`O7L$>!8hB%KU3e7v0fAR2eR<nCMZidC#b>}_E
zBwArSrNnSP44~h<wz+h3R`FtbXf)#1)%c}3vIayAjZ$|K^*l1i`G&1G&gO1XgqgY=
zu%j#~3i4sof&ki%h3s7OC*~_(@|-VW$hX-AWPj9e{g5~L9%>>HBR!E)cD^(w82T^!
zJBr$kTMRb|taO`|arLCd0k{-?%>PM`Kqg`nPq41SX!{+xLc%Kf5krz*r8kMg%M#y^
zHP^}?yhu7lcNI@3_6(oN5lTS-UVjxGjL}Cu(2l*<+4|hzy9mNP;jCcJFJ5sm>%0|q
z!Cy=9<Tc6KIbSwksU2du<#c2<V@E9Cqj(s2tvCZm2?3Yf*aP*-4y{md5mn<N0=9Hh
zKQKGJd_Pj8pXl_Iaq^3E)JFebJq=LR6ld~{#>VYNnbqz;OV13uP^RV`%+)}fURX2s
z_-8$RrOUMPTY^D@+$HiOg7PN0Z*CN`1N?i4Td-C~s++Soqcc77dZwH*;uT~8dqgg2
z!73ndCI}0WBN%Leb7tS4mO?k4)_!W&mCg&oiwZ^dN0`Kji>4C_o1j#WhSUV;Vq)a8
z6c2pq*AMf|<SdIU#Cc~VzDbi_a;#V@P;tW<>LgOa2KPPAnC&284@8zhX|z<jMuV)!
zBkQ5!Wn9Z_rdW-WCm$N<6E9}U_Y6Lf<(em*c%?9<Ybc=km7zucCk(95vLS1DB=u{{
zlbiokTJ`;^GFa>V)}KAI@D?`V=?=VcDlr=h<=Q@GDD%#+)vS75fcIC*0`%|2nu)-N
z=?-z*vxRlpV7Soj@W{uVzFR9c*NsBN1>{w?hl&SaIK?8jwNc5an(yJXPNf`4#@C0v
z9&6bA^)u1VP2%cZ*SDvXoa@?z=KY29-RLv6&ijLoMNTRUb}9>g7@NY9i_O0oh$=8!
z9Y{(*TEe4XV+lRUHVQ3qjJrS3%j1{*jjg`rTn_=VND-0uugK>tK#|(;x>?<fR4^!A
zuxlLylI}wJE8a<E3qkWZz@ryssUJZW1+kLIp${~stK&2ZrHaC0UP~m51BzluE;E%J
zYc8|CgG+#BUY+R=AL^}zUKOgsL)qb}b7@rQCqnAEhCoQ1Fq4P|=4@@qCjUaAvJ2t^
zhQE(k+7^bMVhXdMN|CZXq6fwVq$%?=a|jFc3$165q6lH(l(>xgOkSy@2Xz-|&LZNU
zRB>9V`V&L6*(=h)8G0M@1jJKhGt7wjFuS3{Z?x-QOYt3onYneIktj~$=Sp~G*;W|*
zBAOH~r{`aYwN$I~qqj^FqD!G>+@{=`Fa{Lh$n@9|O3cK<#LOZ+nOHUiyREiA{x%X#
zHsf*n*-&llJd3M!H$%xJ|EPyS?wZ$Nd>v)!1~^m^QAzMjO>6?FGcy;h<BV;d7mwi{
z8(*eLs#_)smkIeVc;sNt`0|LLt%l!&NipS-10y5MO@ktc19f^u@d0hKnqvP*OJ-UO
zZ_p4ZXmXLDemzU{2Z1Q$-51X_2x=K<iD{$H!UV$@Y{EPmlqKQvY~F$>8<b`5-3LqC
z-sQYVZsUEg>kd58lFR{XQAF_6E{+a0uQhi1dB+qF9#53NjSJ&=O`M=iB;nyIF#A^z
z_&!FGHP#yX@2B6#m>bHzG(>01g<*%az$iO7{B5m2hi!4SJG){rm!WjXnTULM3gxzp
zJrHat^R>8qsY7_jvV7x5Ij}t0Ei9X4UL$K56srtPS+ZV$0Ln0?DcqCUqF*5=Wbo}P
zGK6;+=4r7glLEH{)F=iE=>iF$*re<gaC{*ifu)YL@yEWANe^q8oO%=Q0?{NBc5ynh
z@&Sk(Hr3*$Rhf$!7tZp`Ka161wf3C&Vp1ff32u-aE3Na3(tT1Rh_<}a<?gKgZQYDp
zW_N0lN%4$#$<6Qm8^|2@AXL$n>BoG{_hZ5%4-2WR5=W<(^Dp3i#Tt`fappz|gl`~e
z^#nVW&5B)w`;Nq;REd=xMT&r5_6&rxxyph~@<y#3zpl#^hI5vakhD%dl-9F!d(?0#
zr8VZW_YJ&odzjlmjL=3PUfXLlp03Ia2C$ZY7B%j;^3)3IOHVU8wIJ3nHmefFp>ZX-
zU*I${ca8=z8?L@w+)&v7<BSFO+S3hwN(_|f4=o)xudQ#W@#DukM+vZv^-t}dIyM1$
zy(s*D1~EVzk5H_RR%(bwUAB3j1U_wD4uSE5V9aWKouV;}@q4KLPOq3U@=vDRv>{+2
zni(}duQMnPDiM(c?LcpI(wC&38thUTz&pt<ep#OYfmkN&)xRratlwvck;2tp=E)AT
z<7QRt#(rBMEttcQYxE=x$ezSUhhrfqwKm!9+pmAKa(@nj7FkY73=NZH^|;XIW4ApY
z*E%h}3XY0m6Vx$v%H@r?8tUVLt-KzoXCx>klE#TXFUG&5F0$hfk4!|BmbQ{$VOi|&
z9aQ+nE$t4wrh9aK850t>9Jw=!?0g}4B%~gbRbtRyL>45wm=mZz>~wt=+(^K+x6$)I
z$-aR_I=8L{qVri&F5!qE@M}QhjSp^)l^jT@GU?X`(ho1(=_1d;7$VFZLZefU+zK5Y
z7n7Ote?i?FrT-OSS)#01vHLOCYkdLpwEjk~tPN1`wN%fi;6SFCL6__?vyaWK(iivQ
z#i)Bdy8x$vGVwXr>Wv{L3cieLl~HP%V_F=C#5B*hPs=PK{kZ;|Ecy-7OdYaJ&9b?C
zlr7<Sg~Xa&64I{fGIsE4k&3QaxHDfIPq<HYy&{>la&Ww3ZZn*j&EPO4rq9dFy)1(;
zZr$lM@JC@cTv`h~_nN^%RI+OO)U%DV3yRMC98&XwBHi9d{_EnW(Fl_&n9Dm(o2vju
zSf8<nL!bzz$-G~39TQzzLJcexmvW9~Ka4%_Qx<x_?&-szx!?_Y(hWc-rEGQ=i&Ly<
znv42u$j;PMS)U_R_DYR}L5YNc0#3c5x8E&rUo@|d3wG7|%2I}5LzLoOlu|Lwt;7Ft
zv5cX9&sCIOOMmf0#V#`spGYIe+CzZ~psdtj55@tBxQHVgav7SJaJ~Hjf^<M(ToQ>1
zL8O;q5md=jwihPgoNXy%y6ulUQqtI@pImBc`2C>yuH3mI$BWhY3JJ;OoH?)x7JApZ
zdQ4n5;(zfI$__=}PY^RjnFy)bhExmr(o6?_(gN<PNwNQgqbTO?R+#c_$i#cjZmxZh
z+P)Y`-oR%@wJ60JG{spteh%S6fA100n=1jQul>USVKN>iSV-h6%O%)Hsw0w)D;rdP
zz+EF>0?U{8%M-u!Fy8vU>Z8{X$%4zeVHNM=5NUG7II>67WtBl`nIjj*vj3&*%6=MG
z1%_=5W5$6Yh-mhE7j~+k4W&fLqU}+u?Nfc!!1GGyUL-`y!4m;%1G5!*<fjEgZRIvu
zzfo9jam?IivEgDaQ;c%Xqpap8Yv&O8)V0rKre#}=0p~T7<J<454_;ZiUa8Dln`Xz2
z_IRs?RAdeXXHm}Ry?>%UA=+wv;V{CTSZsiqf7ZaP-1^1LFngJy?=2!%e6;bvSs%-)
zQR29}!2H|gvd&<(G1$BpF;O%0K{Awn+Q?iyX`dg&Gder{)lS<Jw;ueHL%KP8ZytEF
z^UcKz4irn85(XLTV=>oB4VXjhwF&y_fqNMuUBlkZ#3M=5&l<VQ_fxuqM59n@BSAAy
ztayWEF9<m6<_@;<HE38Fcr&VeP7A-=;f=fv!0T%ziV5_`TBlV&#u`V@XYr>uVLM@?
z>Dh(+>u&x3-3NjaxU87V`Z+Kd{nfLda7_r=XC#8LG-whIE74A_&K<CnK{VekrVE<F
zC&7;gm`poG**v1_*WP_~=zhJLCW1r|Ksh+GUxa+ct7bn1Ms8o-9Pam(9O0=w7WAT9
z=;@iKIxTzI1<YRo`?L`5?g!K00T7|w59_!+)F-2FE>|oS98jbEQgw%ygtc;w+qfZZ
zn-`_D^;Woja?&azywx;O1b}wYZxQ2G*N-HrB7Tg)IDI=B@%Sd+?iS|;g;(!zg{11w
z(;N8x*U%&FL)uiteQ5F=!b&!gcSIcM;hY0=xw&-H-E}M1#Nzco^cqkP*<m6<b1D=3
z2zlj3q7V!N*lioC{_|-Pe&hBRIykPpBe+H9b#ds>l!Wx~aCD86cRbok3(^*pp(ryo
zZw9QtXweEKdo3^IX}0)QQ#v%}H6Z*D5*vH9MB$|gNP>dKz1@#F4d>)@I-CWQG9;=-
ziHJ-e{(v<K?Vl7Rz%r8&mn00;UU~P$5x&4+YM&(gm&BYu&v#AKAF&_nE`b?;$o^E}
z!r@E`Ka2)Ty%&^d|K-E}`OnknC}tv}xejyMlmT8)=@xE_AjMlALXIeqjOckqv-KLr
z0ml`y&i#yJa|WeGI;l<}R#rilb}yzNFge@Ul6Wjl42j?y=^$sQbNI-aT!hpf^{kl$
z30VyLlIh&(j^H3CZvHId#Ak@WuOw&j_K#;}h}t|2+pVcZ*J-a58{|#M69AS(h&yg9
zg<phCP=cB_oD-wLg887sFYkcc0xkv@v&$(^*C7!&y`);d<r&8#R`M*ee%0R0G!Dv2
z(s^Xrc*Qbn2_t^&<8>=nTBaVJk#wSt-tj^(q9UJu($B(pjjXkUk((uv5Z9mc)r^^o
zLME6I>0LptHKJdm4RydL1b=1D>6WbUSijx*gi^r@(>!{fB^$G&s&04pT{no-QqGs=
zV`fW-zNPXPRp}FZpSk(q8f=KvQAP!N7PBS+&|y=j6>Y289>*Bw|Nise4xIOv`pE^^
zpHo0anybyg{RG@lhX0c*vAyJ(sT7=b4_@%f_e2er3)cllLT<@T@n8M{weyFehtyK}
z8^xk=y;y#CinYRBZpg}R0yV(xBbEA}*5Gx>C0Mg=2=-ZRC#TZ9@Hdo^2ie3Hp8({b
zSJnATcCvP1mbN~}9dWe{a5ufCxIy51y5cS0^ZxFHBQf){xrk@{&h;lx(d`tAtn;UY
za?Jc8BdRV%il5#G)H~)=X(MOv)5crtHg1a-sEc{}c-S6D)=L!2^z}WgSs}~Yz%`|D
z^n!T2_l9?z2e3DHtplFsl5;O_7X;zr6V%y<HydTnYL?64OtEQ#|3LVg)?)WxRoh?~
z6BzM+lKQA1hjPg3BbZmyK>pS>jbX{0reUnoyI~O%nYxfbR(91`$n}0jbrm*x=~vNk
zb2|A8S2W4|Lq&OQ^$N_1O7Y8Civ9`3t?#bsfKTOW@u~m9>d>4k+i1qZsg<c8fj`wO
zEIpzbXPD@L!Q%a28v_6He~j<0-_jpS^3gP_09$lZIk*qOw4L(H-VV6Eu9MikaX5pc
z7=_Y8{(1QH*PV!jgmT$Z`_yW{KT1=5vQ~^J&;Cqo?CFzY<5g=*!>`RT=ylzwPUMyB
z;}Ga_^$JR9L?wo3t01Od_y)541|_KkQmycH;G*Mo5hiM8T2In@6nytz5*fnrsUg$9
zZ}*@d(dT3nJN_o9CJU=%1ezH2n&FgN)~J&6b?EDAo9Yjbe)caa_$Nvs`V0*c?K8I`
zKz1~_V@yS~pXTPcWv{^Zc5>bfBltDOAsq9^=DoVs{-0yGtQ#jF>X11%1ZN)zyj-sd
zhlJDRF~8LF<I9KYWqK#+;$KjQpI$EY>qjN^x$9psH&ii0&-iA2y1KGMD+xQ8T_TeE
zqD~I@#_>j)#(b}Tldx*xubWaSoQqi}wZyj;_wj-xv3#n0zHMiZY(Mipv6GKN_>GlZ
zy$aiS_0oB}BUZBwj$cSEdCY3@UG8QEHPY;}RQZ2>1zOjtWC$6f?ekfomWF+<)1Ogl
z0$z>}qBRf~$^wW+os$5*v7yebv;LP*`=h_k=Hv3F-ntAHwTsXh&A(~N>OVtMpI?T;
z{wel1yH15;HY|XUS8Rv^+6SAIGYk{TyFGIsFRqNjYXlU^77==^Wr<NzQ2|p0Pyq(~
zQsuB1HMi1Oj_PThZxmTmbd;ZnWcr6(p?q{^;OZY52J}{;%zzlK&rLbPGKE0>m>rN+
zR9TZ4RC1wg`nXsT%z_A<uzVS@d3foEgd<VqjCk<+i9^N*5z?wgrSwF*U}qdPDW~8m
zxH&$HYGW$Oae-VXBI~%|rWw~@7QEC@T*}#f=<X~3@&o0J$!2uVcM`|2-O2DMx~BKh
zcPUmnx!--nS~*Bj3?>u?j9aqT?0@5m=CaLnGm_NXo+)~U)>ny^DU~EiP$M=?X&JJe
zoX1BFDbq)nZ0ERo?da{7J65#HPG9io&R5n2Q4M42t~PZI82!S!#=~@+bdn(uHDIl{
z=4uk0+j{sKFN`0*hoS}c8q(+4v&-iX!i;k;HkjQ83{fWRz!ed`titG|wnzEuiCrXJ
z`^!?@0|MC@L;BQ_4{l*(4&JRsxJOw)a|*r@V$?7*6y0c`;@F>lN2zS?U(UfU`o9Bb
zD0+h6d8lUYZ&La-ZEp9e)i`DeNKT*Av1O9%r{OX={PV=otdyLi&<^j3_zTJMlC>!%
zKT66)hdF<*5s1z^SXA`%j0ITI3VhM8hLZhGpO~7Z=LI8}Tz8{9EW*OP3CXaZws;k9
z(d>-;gKpUkS3cTkEuNDC+6iz`s5gE>D7j(bx5R{T27wyN$gEBI2LHrh7M7xH98N8<
zE#~fy)XNheXs$AZo=ijunHZnx%=nY!1Sl+f$5GUGe)CM{;RkkMZml?7fA4#B9x4{C
z+gdZ)9Q{FRGM7_RSlEOe*<Y@s-6P4@?U~8l-YN5=#P0pV6c(JhEFa?CQ(&VyzW7UE
zV~8c%8xUoba$WpCdOVNNoR4_UbZ&ztpuIDjOMKskE1<vCv4wNQ_hE~PqIYC$vd73N
zE@rj;8GcnqU~IN9b1kvjkbgP_G>)f_?+83rk=5Yf=M{&HbB6R)!3)~r86)V~YUUG_
z8tjm;G~)8$4pA3RpurMmU-_MWtLI<rkMch{$c|u`8GkedTQsR?1F4$Acsg4y;uCp5
zB&U5Qd_W-jK~f!&lm)yQQBJ60S8tq3gw%knSPY~7&_V-xGBVq1YjRdBtb#-Jn(wA^
zD7%I+U0o?Ca$%rHqF7VU&X}S?g_2f3VMH{E>EKKLyP?*&#2kt<Yq-yOp*3=t8MCtC
z&ha*0nU^EJ2pcXUSvgqVC`MMz?50#=ry&({T}qp{d<7@`QZbAeCYEJyh4O(S8Y=@p
zL1$BNI51r4q>H+JJ_N9PdGGrOsc|auVb!K_n5gFXyGCnM*|bK2LXc&AOsbjd>Z0X{
zsLml@?5xevq(VjQ983x57zn6Jp?^Yof2(1o!8ez^^9o}NN)8FjNkyQv9~^{)?*Ig-
zNtO*YX{b^z_%lKbWX%J$<Md1Uz3kXbv9dRmx-?olg&i7GnC4>nsdV1dx<C|YL3I`Z
z2(S@$jY36;!93DfqrFc0_&E|qo-qKC4z4i=J(R~YyRY1>)mz5%7ZKI9PX3$*0?i=U
zI~)EnuV?G+0e{8cZ^seu8;pohX?XuN9~*rAbr%PoH{+Fl%%6QYIR6wo^hxt~V)`PD
z1P+@E@TEi6ac-_o2Aw45?Y7>-eW$D0ESfDv)znmnvZGV(8~Z$u6DyiOZ$$|U;Dm<{
z9MW~UzIxZo5EcLnDzFQ1;}0tv4D}boET)Sf*SL6eY&<%Bw;9%^#}ZOW<{ry2F0~4P
zH^{qQ6q_nQSR^jrs90R`8w9CO5fH*VPMLXhidZ0p9o@!lq(!su5#cdpxHJJ(v)x9r
zlLVj%rQ&kyf1A}>uO+-3^KnOg29O71t1^LLo*|C*7}OrMqoPRsQr|PSR~T7MqmADq
zf%>qPkRdugB|;b<U|u0Ls_Li<Det1>R>Ltd)#kn2Hz*fysoL>DL%%WO6pLhYl>jAb
zLF$*op9QvHWlLWBPePFc5j#%SVR?y&sLA4hVlj>PA5+$Jk#zJLj-xezj4Q<<v0k7k
z?U-dJ$<_L_c+pq>Z&85Fulrw;vL1NbJse<0L{SjTj6_5K$?#9U1_>EG{eJwxEBHuI
zn>KdO>tUBcn-Wh-jo_)PDq|uVepWWpfflEY%Y-rwIM!%CHY76aR75G~EL{h@v9w=`
z?^)S?;YNZ0i5tM81xq^h_coyEH;@bhAMpORe5b3VcfA;*j4Ha_T6vT(mTCEM$EH<0
z_hLR)R%fvD3Z{Y~il-7t#}b7`N4(7xBbHJ!c^*MeB3E5aD0e3_=Y;=ToFL<-q_Kaj
zRj4CuIopVebTkc@wJsEK!r12O`HXny$Czj7(<qL#vv2FpX1Dg?Vr&tV0CO1trY6NN
zrrl`?pu#~RnQ5Lth9TFZUEwd%R^cC|;>Hg@Yx8z?6(G}TH&;P7BIV$pQsh1TAeaSk
z_2Q}H)kw9$;%+y+6o6>`g@k6=$!KT&!|tks{3t7M8Z>mR9Ih{TNjf|;My`p6!hs(S
z0n3JNVlS%Rfr7>JWb02H4?^*xex$7RS0nO|L3_nZg89Z6ggJ-UrGP$*3H<O`uKTn0
z!!pKQ)WHmwlU(|OY+WYB;(J0Nf!_0YB|;&N&&5aNUf&W7z~I4mNDy{tRr5+-^ZYIp
z7%)m8z{%x7ue+MRj9=9@M;-;Kv9fjA_zDKEpeYErhM4Mcca3jip;3Zu5~KQAN4}z0
zSI=zc-F{TpwX#3y{@jw`r^^N4lRtn>F<blmOa_(BF;8}EipRqN)0hUZf+&{|8zgVu
zdMjA3x?5O><RwG`ldG62?T;_;O@-9+*|2}TdkWzmbx>TXr%}-^EF=I<wA(|oC?O9^
zs4-v@bX_zj?0J**M$1c8EUTP{!0=CM&hk+$@DSy*Otl>g#_rVv3l>}-`-6)gGzzPU
zkcX1)Iz$cgWeW~i1SY?F)j*dX!9Ow!XTW5ZtkJ_OyPAmy5w}`g>WGU#^ORa&^yOo}
z*Rwe_T<SRc<|}E0j#iJ8*rU!k%)l+6d^?5tl&~drbG~@&ivo&2t_#nQDOFxNT#rWB
zC%ZP@f%OS6mW{JI65P&^;k!&U2m-B(Zt^&;KLZZH<e9J21*bW}CMaRmv;Eua8M9oS
zY)ihr|LP3X|A9x&{K7GhGYVEBfK9<h0tsky$O|>g|FDkPJ7F$&{t?F!jLoUv5Y;0t
z6`kgY1d>K@$f21TX|r7hNxmmoKkU)KqS0o>!Yrgi$cgFdReVp#!CEE?mUR9U!&rmS
zAs^>VGhfT?04EW-)*rhF-)J6}bC%f3LASnAeb$V9lZhYV$<n+gP0V6EfS*MFzIVL!
zMfKz-i<QRWY%HF`?_>4jRr3BMpz78j@(T8G$k6o)9a(#?IS!-0d4W@qW8G=*5!<Jm
z`VkLSH0TT*pg{J2+(9JJQUM6VhO(vWAFrfm2$M>V@HfZHuYa3ivI?weUy@9Oj>YaV
zZmxX%*{Z;D(jLZOdAoe8Lk3trH^2qU_-7KGFe)|13Wx0te8q$qF&e3~oO)r?G(ZN%
z4Wa><@Ct41?GX~aLWr~bMXG4q-2scP+dX*NWB*(3;mzh#W2NKq1+VYD>FJ~m+MbI@
zF7v?KHp*@@e@^#&NRkEcH)auIrR}yiXd4XIJvhhseNzmni|(5Be1ahJzwJq)=H=py
z=vU1ycA}XsXA~HLQ1xJR3joZ%Ic#!C?`^-o?NLmQj3k!fN_*UbeLUk2-qjNv44qVZ
zT+(y@K;x*t<&&p3NlAf#`MfXm%xEgq1a$fv6%$veg^kK~*xaszVNw_<2EfU&eO_<X
zZf}F$*A4~vYkvys3XnZqZ%#$NB$eC{%$V_utY;+YthDR!P6GUdhVd#sHy<-MdiKqu
zGEzK#UdnDn{3hMt^L@quUaX570=1Cu0o>A|xsQa?8iKQ4?QiXWOq@!vb9sOZ+-^tc
z66hG~TgGO6*3EaK70w=IBuLaLS++RNr%Yw7%>lzpQ_F9?#{p06_BtrkBl&C03&XY$
z?@RhDRrDV=bO}T$dW3g~87_Va-;qs|tLX!e!Te)|+UMNYJt%s27l^tZ*KiHxE>EGx
z;*Q=`!X+FEQ>I|869)0)?|F&#GhL(99aLIwN!|Hs-T&w(#o$E-E@T!}5=N;|r_e<^
z6gNVBFVC~=+gN|g<Vm>sIAz*5N>5+daP?5=A3`qA0v>}G_5P9oyMh0s`kUTE%^=GZ
z)2~v2ii?Vk3~C0n&y2V8Z_iQYd-$P$fHZw2r63)G_e2p5_>%8Yl|f5jDi>GgUoPH%
z^$*2FP80Uuru`2|;P_PZI;uhXjWV8y@1>jl&?xLxK5qga?A0XKTXQr^_^1}9B^Fv+
z*H+pn3)0?aE@}};eoI0c`g}Xdn$bUz^VHKikVy(zHA!a@khYadU(AGE)@OWETe#k+
z>$tA2*!Lx)fUkW=*CjJffD8N3W_ea&XVi#}l|_2i;TuP@WJ3972}a2%A^=#MztG*f
zo_e`qePbVTus@ri{V1sW*Bn<$_imYfSJ6$=bTL=Hl3>DI3+S6~-q?VlD)2joK<0ZF
zqH0>Ai{GDq@LY}=i6k}^(%w2KP+`>52BBbXxY?#XjW%eQG*Fy&eNC~Ths(5$r^K7A
zb>4}VW9HQDy*z%GW{OJ%(3T_}jlY_sZS3|Rkq9i8{SPtI_y<GS6}Ah~$I2ns{WTHI
z_bgUgWF({_EJE^WKx__$m%|RXlz`4b;k$>#_enPFJh$WI;mC3}+KWx1;IkR~v9~J>
z9?O36roVcW-{%P<4Ge3)>8lPZpas@h*p@jr`xs}`k}x_v4f1kTSfhLf)+Cy<{?XuM
z?~>ZP72z#^1^B)SO>EGE5F^D?&qHaqwaDpgxk%nz#f5-}(3#6plUa2tHngJqX`adA
zDDi;X@OcyTH#<D`4bd}k?$@0jeX<!Iu{<34xtPv@8i)>DsF3;X(9tEI?PwOD3Q`mS
zAU=IH44=v`&f#pzzkJ(z3^hJHKmFW~IdZ>{EOfL#f@(5tyJ|$FQ!1u6fx%Tl4<hNc
zZP&&s%ywW;VOE22efP6H03N!G<XC`#FP|E8oY(WDS9BUw{!So67{PCM%aR&yE@{Dj
z$%Z`O6H<R2-bs8v>{SAGkCeDj2#q^x1E_jx<S6K0eR1(W5vK9;KMvsMYYgRnS=kr{
z!%)l${B9*IT=uk(IF57zSA=i?q><_nY8G!fe{<+Y8zF5LHX)CY`a|^@CGUbA5t=Wl
zIApoLe~61xVZn@hV{F{)ScT09X=<9`Hiq>R-HJJ|y&jE;O%31!&Em%!+!UKP71^$n
z29wZqaELCurvbx-#wm(tO^0|J%9Kj8#M1)+){@Bg6TlU2KXZlFP?i36-S622&j-7^
zUvvWem*)=o7s*)UNa;J}qs?J8-*A>wWHf$YuF(vvt|zAE!(&X~$?0V1nEn9m=1Ou3
z%?o+nip=f!uJ>>kZc9cC+G;yg2u9K=0qppZ^KHknPeA_XZ+6}D+`U(LX6l5lQ*2I2
zoRr_Jl$%*MIr#(%!PHLA9?+O-npZrtpCeeb`CEtUhb-GJp*YVAK>ul_*Ew8pbd>ch
zV;hNTvZgkFXP3~UZHE+dlTf3PA<C|x=GMcs^QdoI57Wy6G9fRk%c|o8J=SN$p>PJD
zQ@zIkE+4nh856YfQ=vFkBqh~kzQ^C4ZvMBc9njFp$;V~imqS_E8RDOrCQ0V1$&3F!
z=(6vP;X?Uyre?yeNSqO+6twd>?-sxcj_aGC=L6f0VK$~=!+F=tT~+pt`x$uTc1{Sw
zf@1$ccHb)ZHT~r@)O+kWK6mxKhTien3+%-woM4s<_i8hE##Ps!1L%H`Qp%8^Uir=$
zq>Bk@&>n06Ea|V(i>$P-v$NvgWsSj$=5h#WcJ^<t@Y-5y>$9Cq%80Z`Nm{Vu;aj6n
zm&AK6ApgRQTjhQv7vg%N>})*yK+>3ew{sEvICN;cuED97$=$0)t#G*=8n0|^E8(@-
zO+CbJpLYIx+c*H7Fw@GaRW5pV$i3Ll>2@{Jn#Kx*C)P}Q#PdNhF4+`(&q$Z9Gs;wE
zfAEK!0w>F3du6if?<6I`%KyU(Rr!5@7OUSNn^FNZmx*FXqkg8a#8pgA51XqA6OP{_
zPND~NTlD;)fU-B)`TjjQ>w>k*;)l5Y#7JMX6#gt*$74#&1j94d>mP%V%P$EiWK`^o
zHY><q(`(=%rG1wTc7OWh2qT!8+H(GA>k4CtakH>81HZPPAs^+uxFr_O?-~^ZeW>7&
z7UdTmNGmWPDf+0lCH@jUAS;^!jEN8`G#~+bBu)?d;z0ZyQJ-Q{0cu^^BsZ9KSE7EV
zb)Zq!DY)R7O9RbEOsGA|R8Fa0!LI4S_DjRAP_?G1V!{P==j{goWOgwRAfI`1N<=9z
z^Qz{sXcj`wFBU?i0f|^YrpnGZBU1mkE8`nTKLwbVaasAYCy?pp5vBKV{jvWrb_Mp_
zV?TJ?>6{cTq`v0wS}}PVw0J5-Q$;^8juk(J527kM0A$BwZ~}IIcfu}^fRAtdWOmg;
zx{UZN7-SqbBS?Ht`7P<JpLbTDkfzguJ)`%>%;PZnXjbnpqwntgfv$-ZD+%RX^sn<_
zqL+pda>}Wx1izgb2>TX3L@$iIvMeQ<2^O+XsOeZ(rxt1gE`#I?1Sss224?5hneFqU
z-o{6t?dCU)txo!Z1q5;{4+GmeB4z~#=ZTd<zqgz+s?Ys(rfv<5=qsx=XjioY%2|SZ
zm^Kc!Ii9Cqp5cK*m%sYnH8eEJQjwO2kdNoHVZK<oV%H^6z&{zO>pb|5n-5g!1m3D2
zv|4ksX4G1NBgFM`rX&9&b4Ny~)i<Ms4+G_*CHLjR7lsH_JQK%otx@g9G=#Goa|2Qb
zk(itD9NM#8HOh=tJv930wQX~`%lLNJ7Yh|Xp}=Dt1&1qJ3J%FI_?#qX{k}dqc_h3Y
z;+9sd*WtDAAIz5M_2J&(j!wHYO};z7Wvr^6S#~}_CNqoJ*_~D$QJt+n<M-s-<>1<v
z3Rawa^Uxl$-AlDjN``PTrZ?v5b`$6hG)%#ClLP$XwzC5$hYhX-)o#HuAvKFnI!MeL
zzs3S3i%=%+K8YqHFRKWi(4QyM0WDi+U3>gEL)}W8NeNcs-W8~vck2tiPZA_2$qYCu
zi<^JxV<+#VO8LwUFW1D#pMAjDehuK3$DQ?LTzg`j@|9_mXo5rQwB>(%-6E}TMRF-W
zBm6cg8cQsYJHR0Uz0L3mfMCi<4|e!-1_3iI=RPD29_pcX1?ZwL(^Dw^r5x>M|L=gt
zbOF7^!c-q#hsOy7gJjfmYx3sgpFvJT=l}wbkg7I91c`^%-ZZ3ah1y%~uWKlY<|UO2
z_EZ(6U$@%aWb|=+%uu#cV4TRQR~y+pyoyPU5p(@R)r*@ET|M?*vE*I;&P}Ygh$P`O
zF1}C5lAAd2Md550ZUrH)fS9@5?+kPaWughkhV11u0F{VkG}NP!F6=<0rFx4L)-^`)
zF)(nPMsbF6Qka-!(4VJCu%vz^lqFkE?1yy?AVA7{eWSDlcxgbi`8w>2_xnj=a2f0M
z1pDSlmNwAp_*byq=2!wE$>ih=41jSwJO;x>B;$c4xI8QfEsu6*jeKP~-#goan?m4P
z9s$bbQe4Bk1t!4^0+9Nxi#A~Q-0N$*+`(bY)Y^ewj~w47#N8FNeONf3oRl2_z^*}<
z#Yp$16+I|)GvX_{{qZ0?a1MDh`~YI8ktn9nouL&h%kAqDx?>WpcUL;5uW^z2wwGIe
zzYgB(Y}8rM!&hG|tsGdus4{f`iXzT3dY<Dh%1SFxb^rjiVhUyuB3(E`g|05}C%Q=W
z|3m|*hVh3E&^$G9^-R9v@P=q0xx-_pVe#p#b@y(s{q2h9;Q^!Y`0Zs{6yO(eyy{s2
z{|p{UDwb=VH(ej(6?z=y=^~w9@g;MJPXl~|d+LGISv);gR{jI~_=#y*1Sa`uHq_aR
zh+q|d8|`J%JqeTtMP0|S6zkx%MjwY%%2Bud`px_M@{^Oa#*DC4WDOmg%lK2h?D~1?
zFq^^|&7^#YbMdsy4<Co5;(cC;sAwhHR={A9X3?eZ-47fw4GoL&g(ECD`xA8mc2|G_
zIse^?eC2^r`7}(E9|sekUY2$r!kD|HnRn;y%oEHx9Q2MOs4@fU%B|xp?ZQRGhDth!
z6rltQ$K=|dN3dyTnz2QpaPbC&rgbsvP#7JsKyuD{mX$Y{+w2q?F1rBKBefhGtxEJ}
zQ4ucQV&_T4r!~6ZVO)68<gIc;#(=pBEjK=4#gNBKk#zpBGu2#rJftvKEw|YP6pAz2
zkeqU5@uNbHO^?`cxcp0_cf}2to8u+zDc47v)<Ws6SwFV=)Z^y1={9KK3DRl(2kuoJ
zeSw2>8Md*d#B8&Z$;p;UG!1oY3=oYpQp7i1^l>6FU`phKcyM%OIV+c9A0({aB)NQS
zX}_9QlYn!<8#ugU)fX)tqIrzgCjz-0e{J-a^8d4VEWOR-h_sX=RXk!ys?%Eg(p9uB
zz=w_e7P^9A+>;dI)=Dty5A#7EoFQW+A`O%)@k9w4g(j74l#F{XUTuUs<<|cCtylLp
zti&-*-U~w}A+(kXkT^5$=sP%qZ3R4D>4$5p{{XD@iS=tRxP4Z|2C3Xu&j#mm#QZBj
zE8w=o$Pahg3<o^>C8GoHq-TAUExqZ&pM>&o+Q$ahTIXt{M+Ca}V|_o(3tmW0jG*;w
z#d-iXCweW#^83eQ-`mn3?hZ*5eN<l>mev=3yu7tq?rA>@Gz3s8z4qc-*7N46-F?@A
z3wta}l~Z2mvAWlx!s>2wauhR{uWfN_GE<qub{DPC-B7I)AD3kjPgHNty<*2jB=z0J
zZ01+1+^|h`unc)H*Lg^K{Zyvg4m!}GTk3mk>~nTp`?$8a%MBCO%|ZnNx~wp5^`2U2
zYkM~8a;WpUOJL-3uvg{zQDJ3wA#usin3}@Sc=Z4A^cGN2es9;X7=(1FG$JiIbR*p$
zAW9<)-QA(2ba%HPA>AQ0(w#$hcjtTj|DNw#%e5R`#@y#V=Zbypy$?T6-{SS9S3E%Q
z)`LR~>HLUa;&$)|UiTB5=1XVC9(wLV2fgb4W<30XJMbdtZ|U5*lFKW5ZD!nk15NVw
zWxMuB831v^iHSD39w*I-c?5+^4lpT<*K6!c5c-F&)+WkQv&RN=gdV3JkKI9)DrZme
zCNY%L<L(bSKmiMrc!yd&&K5@d(C^kWJlhmooYM!w4ocaLhiY9{3VB+tDhpiC=?i{N
z$*PG8drk2NI<D)u?Q<(7+O6Io{x9ht=z56R=d^0OEzPcTa85Peb&<8g3Tcd85AygD
zdeye7)%JjCUM7inF@{?x@nvnAJDFrOx8d>)H4sXb+gL)sZ2Mp5toD<oEFC@~EoN$*
z{<frdE_lP0mb{!#+idtP=bWXh9v7s`^$zFPSWk8CPkNrs!{Q=|nZoQmfA<9Li@QlX
z^sS0?#69qG`D}c@Rj$^O>D8my!7*@Gsd?l3db6R=07<NE5m}?D*)<Fx+x)5->*gwo
znPOgHF~~mb8#2~uEV4iUHsS`qcuMtrD1vyy#xz!#@c5?tUn0fcg-Z(ajkdpjZ5tmw
zANUQ>5#CD=%YIZIJwPhvY%H$5t#T(9##^0zT^${`IW0xL^#c2zg&G-`L6%ie*(g`J
zy^_(YxHc#zlv_Ro`G3ATx0(N0mK;2#!<#d#O2B&Bb)V-qKlAGP;e`a9HiP<~+Wepj
zbY+1|5^v;htF34oM(kNYhlBw<$+o%^4zOh3er)ejg^tgS0i-*(0l25}qBD2nfD)Gi
z7^3&x_Bn`|-E^2p1pT7E2wMoLkO$Nb96=d3wTdc%3x%2ul3nUqvFor1hOEwo6x|?y
zDv$Srkg6cSr2_whO*=2>2BTjwxSBKOX?>jzZX2iMt|*5JM!1#O<IGdZOqs&SM#F|E
z{Id1Q3_IO17Lym8iXL)D(`tujhw<s`SI+PxBNSN#xJ2?c=AB4O%{QsBm2GZ%)cvqh
z@0Yr3p2Qj^>(DIS!DImh+q0+LU~7f)6hO>8x63O|1_WzLx&TI!1ug^QxRr7WQ*?3j
zaLIU{dY82ZP8tPy5P9QYb6WF?rZid2pVRO5laOY?(T_Yg!_R>|3rTcJiYHT=E=XZc
zLAt;Q%wq$~I6b|OqOe!N>WLkZgS7qK8JG(JI2*z_>4tVQvj1kU;D;A8@bEIW&FZ-^
zGfwa|FWj>;@rq4ob@BOE#fE>eA>O^%{AmnT$AOo-T;x%JE}zU}lUO~O?2^65gzMJh
z>cA0$gaGPRQ_grZAI_~{YIz3qT@_W+vvC`H3B(dG`lhoTTZQy=BaiHWRSi+4hi|U>
zt8N6dp*9<Z>OR8#m;i#a;_4^qW0Pn3aSbYIzzb6pbT<hcZWU?)Q+xq_Lp@n>BeV-B
zX;z|PfCBw=ZTN1dK^O(B8<ZNW2^WyvhG*%<tFD~tMG(Y0Wh?w@viL~iGKFD9ib1D%
zZn!#NIEU)euq8_sr0z4=m$ce0(cJz}$zP7G8`jp-8(#A;_76~biss9(3_hLCzhbRa
zDQW`pOe!kj*JFwlKI{@0ITT#kqzSjX3}~D|6|ud7!V^mI!=XrLV?V@<$4SU!X)Wl0
zR*~(X^7Z+!gi0m<8VM`T`*_J2J2iB^;^&s}z86mDJ)g{rYMeD=k~L;lkHmZ>W;z@h
zb__G>gAl7L0*&FhNz|dZ)ROO~YxHw>aK%vcqF4AhWuz@+l`pg`sLC0D*(0T?L`f=Y
z|38rXg|njV#6Rc8E8@tIRMK#>VVjIB5>K%&x(0=hW#9-A9<bG;{_e4sQYOL52bM}g
zSs;s8QsDW2_^MKa2~oY_)oYN5WU{S3WtNiv_Dg~;#C0wGr<`bZ<5~1C$_8H?Cfo=7
zTa?=7tCzkG*o(>CmDIE$9luF3>?>P8T_RV$njJyvR7dseRKcCDXc=mHg_B?loN|t~
zsNYN@gHEnqW`IYuCtY-Zm%D@@7Zq3rrdAW!X3SI33iehn$RzaDK0*L(2!}ERsAX~U
z%2;&o<r&oH6<S*-_U#S{`91y|A4NgD&TDlx#*+xl!W!9>>42)mFd^f*J4Q}^isx};
zl!-iZp7bb&Ol!%XnRs;r(t0{qJ?U}w@O1I<0@m3x_?J1ba0bzP|Ii~!W@5;^VE%>3
zOVH930#li@PD<;CD;&MVNMJi(DQAB?$2w+@KKYrqzdsxl7Th3<F;rh2&F?m5Bm4jD
z8qx(?Rvs_AV7HFeUr_42wL)V|r9!v4x|SXyp@y@196YYc29RX>&wsgk4l?G(0tmwu
z9GAPvMK^R;B#0$V`r(orXX~9gv&~Hq!NOgSVSAfJ$T#56x_BKD;d0~es*s-4{pEl}
z{7{&AWez3_u<II_fV)9ee>twoUAJ{>@UF(+M!B3ChOR5IurIB4!77S_b{8GuKEiU@
zr>8>UDqd&Jr`L<{A%P%WyU5xgxs)^d&^oGaj|?kfZ)!7Iqa-8y97z_bizer*Eqp~G
zZ+v)tYsG8uy{<8ERosPCth(ZZ!OUh%;pv0Rw!nkOH3ie<<W={X3ZM?qpj`FEMX0~j
zfMXZb+Wq7g;UhS5M`c{F)BzoqBG(2Bemo*$ORZD7eVU<i+CID`mslc=H3SS*HMDlE
zzsjOovRhl|Eawa=lL{nBgqCwTHYP}TOzW&^c>7x692t1V2d@L<MWg3iUgp3qQNnRt
z$4D=Cc-{TE)#$GZoSN%{9Uh}QUKOt}2p5@iWOr(@!ouf|sU&3(w$JnDbT$TV22-Mm
z_ZYkJ=GUK7N}%3mFn2y(U_4DrTgUhRaS8nx&527NsAb#$TjqX^&~{Qka;~kC`nQ3<
zoMdN%cp?*ppZEliv`{@SI~tGL-g|ZX{#fsH7R@{oPdUDuZ(R!+zX@8zXVPIfR1E6x
zCJ<&jDI0+Bv9m#Rf=9SZ5D1E9Te!rV*I0@E5TT8}h_xwKwcN_z*Y8m#Wi)vQ2L9O=
zF>kg10QNwMI+&r_PF%Ivzow<WV_qpzYPX03^B-Zmw14b6Ah)%a&+&`+5S<JpcWCHZ
zoOZ@0o6o6sv8db+$V<*qc#nCic%<$|z=I4NS(Z9I@aTcNL*C|z)4N58)dpI@Yg_5;
zCTLHqTaQ1EW#{36K+faAUUs;-m=lE9cC4bJ7O!uXuked!`t_fhcUP~=tnI*9CvXGy
z(fMcI^lpGw%kSP5kr*fQZ!_fM0+*xM3PL=xc{_`$B=wp~@$ILU>7L8TrRJwMn9f9m
z>{ISdkCPlls*i0Be;G%`PXF*t0rc5ZQRV~y7XaAaz=&XFbvl$l0`*$UgREj@-S3|E
z3CDv>=ErfH{eLafMZG|2OSt(ls`t6Nf)EFvoOR1(3q41~c0G2>Ni|#Qqf1cVo6q0*
zdAY)snLL`rsyB{jzbLHM)jr;uaol<wYLZnpj4qrm{L<y=QW+xc^)GA06L5}3_4i@+
z*rp7NVzqAda=mTlmQimQS)*AT62BSoG<)*$WUFS}q(S=c`XF@)?N`U)98T}x6DZUB
zjg{erDPLicTHGV)*uEGM)>SSS%RBC%!K>fRe;Ws02%0e~RS@^a!vGQHE1k*lQ0bk?
z;`ABKPUZMM&eTl`5F0M43-n!14sKG@#lvu`33LefdLP}^VX-C6Q**{dfna}=&AFtU
z*TEid_cHWQ{Hdr^bkeRzX?6MSQy-5<FE8eiG--Eg6alYlSbKSX!?8lI{-x%|JuzLx
zshnrHF=1f9NDR{HY$r<oJtC29L|10lqun-=n(~TNNb>$E*M_cM`>%Oh%R|YFM(q?4
ziGQi0PU!zX33v)j3tcp{@J;(D+1hDjU6@M!-#mE{qo+9YhI8Jps64>X#zTPr_u-sh
zcfmpGAAI@9g}*BHIr7;K0*b1ysg!ZE<;9|_SxnFn7nAEtP%9vGNd&{POi;N1te2XT
zA3Gd&`0u%a=^Df&_KZ$F@Fy<~u<eVV(+$Ob>S6xUQXixz171otNb}XZ?^?MTT0>*i
z*trdgW{3v7ZJB^gXn2cE9GUGQWX|X>%3SZq>27W)tYc5l;R)#RR(9AdQhHE1nMfua
zW2C8-S?Qi+XnL#H7x)6B$V&-{zR=LmCZTf?eFd4HnIXJ7dJe@hczJN2mH2YNWdk-d
zeS6E;<CeRTB6!pcOzhiLzS@r4PmDGsxIG;9($UzR-sOEzj|Q0|g~)x^9^(dE7FB-5
z#M*DX#6Y96B9X{+PNw95&DkYZW}?yj%R-t<%RtsO1fXQ$=Ggw1n<sbbf6)BHKUWT&
z|JrQ~)yu`JD;+3TQIQ*9Kj3Axr4d0UhV>3`E6A6(%&xQkf*+b&s%h^3wsG|R(&BI{
z1%;vkkI8d-^Rq@SvbV@l1@&Zttlf9VD7j7cJ7->M@lP=~BErUY{TrW)m!PLPwN1#H
z^B?yw1d?msHW<DFRJa5&FvJl~=D*l@C9<|suIxTlGKD^^wTmr|q8!90fhB~jjNBXF
zS1i;H27=Q++;ThE^{6NfQ58PX*kA->y<%C3#cHbz6HVP^Vv~ZpnbtA3kuXKr{bX+^
znxOB$Lhp?anT>MdUsnB{yVgAU6!6Ue2PPM*Zgj=OHC4U!Pe_jB)xoSQ5aTY`mD14_
z&XT_B>-vIG;_@LiPmDK5zy4DmY~%#Lz)U5zP;vDqd{INe-7yy{wNwExZYpr9MhgF^
zaF$l|9AvM-gu`bqXE&@C=>HeW1^%Oq9r1`{+N>c1s%)>pHoeyF9mf0>YsuC#ABPtm
zIO&81E5x8UPft2w)@KnTBEpZsGC)EN)}-iH^@=MTok~1v{m0A(1ljpD9O>D290)Ql
zQp+o9t5=hFuWq?<AKo07%<O-f*CaUBX)BkAYNzV|4CKo=^Y2(8vj$Rn<o*EV?x;1w
zKi4&ya|b%-vu{=F^8jK?HM?_{yU_&%bZGsfypIJC)dS`rf-hActx|Wbu?e@LO3fz0
zr7rlp2hfrPhzUOjq}VgD%+c)T-^kw*CwH3p>EFnmZ~bBxC`q%Fpb(pr4HaK;up+W_
z6H<#`=`r3&Oj%rX*s%I%gXg_YyW!Z;J!@5NWmwo1hx&{Ex}SWHZ_9jMp^eX4C%?XY
zis$w$hK>JxFY6X3t|n61W^I~#e^Q71Hvn%hI*9(w)HlNK4GK3#{Z&85^SLjiBoVCx
zr|OmKOD1X&COK7eK>+CS*jYq}Y{p-X$KIN@Z)xRfYFpU@9HI2bklh5-qoTKmjcxpp
z_0{8B8LGf3uMKuEq+GZ=&eJ~BZmkH11nA!GmbH~osX1dIqLk>(_otmY2&8DtZ*B$A
zg%hXLmC^Px#>O@s^(sAi*m7Q+J73svOK@JOYyZ-63^b-kvEm)aKf@HTcSGOG6WCf;
zLL(4rpb&3|R5$3MZ&)p`5(lS@Sb(EvZw^_7Elg4{L%OWHPIDa<3agQKs1Ymf-`aOL
z^97P`FY|}>xxZ#=us3$({W$eYce*WSTv0!oj8-s&A!X`Y$7C7T{&&aoPQpqb*DT{A
z@7^%4VJ2$T-%kF{C06)M!}FOyGUX0?X>d*tQk5Jdl6|mZa2_|{VQR5>jr{yVo3P^_
zg$s|L^#5Sr%^xKx__BbcN^sdKHo!CR^YUr(b2+BedNaJm^scC!Z+bO%vSJH}g$K(;
zkj@rFj(1#BZ6ZB5fLIuRMh8Cy$sPE50Pl~mw)W^e%c)hsK4ttxOd0Gt$*ny7agwq@
zGP}_PS6?oGTr@L4DFod@HOGRaT}6ejUk#&S1RK8l&gKNqI4R`^rMj_6OSB}a%<`Jh
zXxEo9?xODn)EIaShfR|}S{6_^QORxQ#}ERMu>Uv?wbEkiPP}}{ejwz1z65o7l%fMb
zJx1qc$7J)*3Ow8x)!y4&xyuIf6e58$?X?35rQTkB_XKD~EKr8T_PP#qBZ)30q<Zc$
zciYO;;zlm`yA)LG+2_cX5$(B_Y1t+v7A-pCO-%Br6}pCo#ziSd&g(Q@$;IR+pHE=i
zTh-BcHUXoOjAFfcfA!w9$oE|5g`WiOqDAp3;q6kjF_LY-*)M+Elj3XGcQB7H84yh3
zY<!sWT-38`2;Wtgay=ZWY{dFl=mrK7c@?4{>~oNHywwBrLHy2K(*Wh$vJl2sNvsSP
zjcCz{Iyh|033T%r-S<J6vAL795J7c-b^hrFY=B5QG@N82&xgB+MJUkJUPEz-lgaWv
zpAr!K;*U1rptH*wYFPiC1PPF$K}s&SY-KtbUxnL#%su~{yPft93A0EuvG$EKyJkI6
z&E$pE#y>NLk4H0^b;)nQ7P-T-`E}i$W))o1S>7|6a9H#xI-%QGa4lugd%<t$o}O|k
zR+}+4DToifr~(SGQo@`a;?@G!y&e0%`;*<3-N*O^8>vkNwpOtDVn;zC(MU%7MiFNb
zT98>6lN&-F4*KV<5+XcrS84nJ6*FI}-d=2LAB?&>KUwPP*~xxnzgcp%-d7=}0zD40
zPl`{rGSEQVYNPhm)QAV%{=xS({N<@F97CA{M{%ydARP|`7fGCxHXkf(E!uTK?TP|;
z+r%%d00$Lt&@NR&4lBiyjfxp+FSPpr;JxNxNt-G#&8-=g5mzKxzk(x4ryif-+-&v3
z(7Cp&(bJz4I<2-lJh!*+>a>(VoNr77KiI_d!Sb=|%26Khc6dF9hX=gG6;Kc%rqLv{
zQkFb?WoQjm*^vswwnhdkf2c2hD9K<%IHz?;c5hW7<(hhtNJWP_nYU%!J-|VZ<#sg+
zV1C>)#TbYHJUv=E;otOb*Gl=FUOGF;|07x6IVk_9#}uM6Vb{NEg?(pK1eTLS_f_?{
zZi%z>OKq_`uxIukzpmV$iA5WVsY{r#AAH37;V3avfh{tusLw!Go<}LehGyhG?~fI0
zk;2`FPYFREf+^KTL`HQG2450o)%hFJbr<Z!USLz-Hvjl+|C{D!@AC?`;cx_?133q|
znI@0y`roxa^m+Sl3e^>gB^#h2x}!UcQsw|VfkYh(G=rq9=8kWOCnoZ6rGM-qiS3ph
z{)1eNQ+$##!H>b0#^2co{>dvAVIvI-v=AOu@1N#?8VtJEwUy%|HKLe;a_eFz8(?MG
zspE?R{c7K=2&(<lbX~iobdvg<tiEQ@j<QweP#zQNxm1=GKmsO>GQdk_v!}R4v@4Ln
zHKrrd`-bNu8pnHJOxdtE17Ko7)lITT=f~tO|BVCQJZk4>hmInk8t2BdljL?V2nFxM
z_2#-`oQTTo9LCq&2#|Gvt&go$9*6z+@k3S5Fd+DWD}$8F3E}OrA27_B)_tP>WCH(H
zRI1`RWO3xR@Utn#96V^hQ*z9V61#MY#nuzEbvUqje{XHdt}InG;-^j~JF7M-tcQNf
zvbE1?cl)a6k0lzRKx!+_q!SVJOz<`*usU(=VvaqzKR1`RTg4F1Op_m1iZzBvl{U+%
zUmktx1BL%=RMGhimca^xp(V@P5%qLsl#Xgvhg^|o`?Q^^FNZ4rR&}=xdr<366|H86
zk&h6(f;H!4)*1R8Wl|%FyaYtiS(^9E(rhbRgWd0d9RcMGlM2RPf8rPdE3HM3Or8al
z5_E8Lg`0D8r6#01lTAL^s8L)wDn(qa#*H=~yT)?4VbXZxu30yf(@(f!v+fypcwER|
zOvr41%`2Ur8K{At94Ug!FM{EVTl{R=nM<u2hM+?}Oon%dVukzyy7P8S1ThJSU^sns
z+4{y3t#Hz$L|BT|{`3@q)LJw|V?a`-XS=}Y*dy@Qn=jkv@3OOgCS#Og-|PHPj<%vP
z05dLU3cqhrBdoY%j_+S#4%HTZI<>=(I2HUCoPb4Y^#5fr<5V?CKlO-9_+ob)ReF)9
ztBWzMO`f8e{yTxU6DUd2L1*8BIYh)cemH!?!%_TP)78-_X246uff9a(C53}aemc7Q
zT>T9lCDkv5V$pvNJ4yWpoxGh<q=n)2yjMRO1Qa@wGIPzoeTcy}L`agh%?+fcU_+@n
zl5(sn2>TPc^@C+MCdn^)qAjxrnBn^8Qj?E9E1INzW$wqaOMz9_OEY@S{ZyFQv;v#i
zuI}u4OHp(pvSyuHdsadXmWZ<QD}9paBs9hNzj87bA~Hn*RHUmudbhs`p5Jv%$a2e&
ze~a_NlvE$rN-)A7R>a}-MKFYA>GOr&P~~EEs!Q;_1V~@Qu9C9=wTxl+9Znu!eJ1kv
z-D$N8UzD%P$oz{lU!-JLVp-%45{pQlLzL=TRW4}6nP@k%SA>;prBm1S2N`cE{M(r8
zF`ME6t*lo&+q>5hs{|bw09IsVZp~g%ZR+g=snzt}#@4<J4iFZiZV0;q|I&yc(^7mM
zZQOhyp)_4yCo|t|@R?rX-g{IVdd;Z8(uyrA$W#M@Vwi%y)?>L)8lbVCTRbeZKBB)a
zwLBW|KF0vfuK(_rsY@{)<0K<!Nnf`{g7aciFNlvRz&!&7jON?vVcbq;!3ixkXz+5<
z9iC7B($mKy_5A<PdBIiu7|Er$Pw29<ehouLO=6Kw1hxg($W<fo5$PmpQyTNC7!Dkg
z<z5_>1#AmqwBIb;ft+-23pFV4(fXEOQP1&o&+#;v#(aXYufEb!6?xeu<Ki!c1h!HU
zM=(}2%dS$5RsQV@^#r0nJU+#eMYtZSGvN$)Qmmr_mNhtWzQvM4mX)OQACQB@vJDmn
z@jE1%{+c<&d5ub-gapsG#k?Y3SE-gLH%!;SH}cdc0j7d&Dz9XUf`54^$5i0x0GlrZ
z-Ym0-Wf?L>)uT@YR~9J2ks->O*ugU_qbyQ5{C(|}7Txza`X;YgcCPW!=DE9<qRmn&
z_A|ru>KCb6P-!p`q-6Q)u-=^zn%th}u%$_6%u6V;Q@`1{z>Op2s<3!;eHkTLR2WG4
zo{p;A;#`H<5C3f#+nHeDhH|jyi)ticy6=|z+Fzh2Rk!Q{SHyBL7K@kucs~Qb65E?+
z)RbJ5WYxbK=tF=6*C=z#VCT}=#%F~Q=){qMTYd1MHrgRzI;DHtRlwurmR!BgN!DE3
zHmebsN5nWv38&aGNB{G7<7NUKVCRyDj7KAlQ%M5+|ElnQQbJecZUxt{-mz-ahe~6w
zu+=!}{5!%)5;V1ce(^ws_vZf)05*kmoZ{n81mw@NNPlC`1LIK&Fo1Jfk|HC=GfLDT
zHu6-)Rr%~Fk!Bj(s}eeu^P;Nfw_o39!c%1%Y{fWyM`MCql6Uho94P3<FTdOrOH3hG
zk_yjKINVH+il^|ax`wDB75ja`&(&6r`B+iJ-QJ;M$QqMftCDEl+{5WN^G#<qH-R&%
zy*-Y!MHN_W;e=Q<NOR3+CRF|Qlh1_V+i#qlnd(^=umrjR1L4=cA+aUA9PY6Y=Ww+^
zxP70T%ul58JqW|L&-Gp|uQj=UTP4E^0|o9(jY<L5M_VnezHFn$PF{+U<bcg}(;-BD
z!z@T$uYM$DRrXP-Rvh^oOVUrs*tOe|yK|ju3Y9&|o|)vqu}@*;k(iJ?2O&T1X;;UP
zlKYtg4rM`pC21K*YM=2ge~WP_`Iy_{sjAHPNX**qVyvfy7rTc>y|)jibG#Ssi*Gao
z-eMkqoIkLB-*;wd?)jd)Jonv*tH9@a)xt}*Yz0){&Ioupa?srVyK)r32@-h;_>@%m
zonRF6acN#V|7}p^{!ekb7hn==b5p3E8x0b_OwYbX!eu3?2r@%fB7N8qTvFHl=dJdC
z=T-XS{~1fzGHfrY8{QSmB%Z5bFyU-J(QFvsNAW4{({M?nST88ggUPsnyUN}LIew#X
zPSG`qiAqlFH?ZiIP1Fl(|3q^(##v$z*Pjbk8Qt9ngmgBYtm2)!M|fiyb<f~g+u`FW
zY03hqQ!fxdbf9%d;fLoC1>?~n((Ti7ex6ljambRDPI&40Oq*Wh3l0S*9@+s@wHDhS
z^>9s$z|=ozEKd+k*tJqlRMq3+9<FjiVv@kaHa0X8CU)}+J=Zc!kFjo{scbkYgl*Lb
zCqDNJ5_+k&K({@{5tFKvZ^HSJw!ITJZebxHNi$6?7x28?c?hC}Gm6RQ;A1%}9Mh!K
zt&9<#4pYWJfw(`sj*R4bA3Lz!WBbZHIeI3O=wSGSYx;bWKrC%U0}X9JOmqYjPAM&?
zz^uf+Ln}`s^Yo=e9GyG%Jzf86Qv>_Eh5C?AX`eR%cO5&dVHV-WJLnFU{OcEkNK3Yu
zb==Yi1fjSzC`vdnY-Idxl;mldH<`kenEZ;-@tkB%q#fhsq%8NJDM(E8NtKyW2WCDM
z@jP6m=zi5JyinWa53hV<bdXYRivMzqw{FnS@96o3on6b?GPRpf$>>9hWNcp`b_?13
z1m?xDzh3C3KN9u1S#m%O1hctjo20D<ondz=Vp%D6>2}$ZCP}E6Tfv=^G``++MnVI_
z`#IN3g6D$qr7>)b@0|idkIxJ(BGyqkXHvV!yiZZDbpF~b+3vrgFD|Ka*{2~ZuO7*-
zpAfLoBBo)lZLIP>L$Gdf3V9>s9$^2b;Cj{C3wvyI1QVSBmD~?2!wTmkp2&}a)KLey
zf$XoJezPN~RQ7DWz`;3@AW%{7lop$$)i--h^$YTzK>o))zBb#o<i65dX5le*)}jv!
zKXZLmqWy}MvJEE7V?`&Dsi@zvy+`7VlkZAa2+aSAMeUXR{pXwVSYM*^pcs51Cpvsp
zhB)CVv~0=`Q)qJQxd?ro6hH3W!wIHpHU{1YR8SB7`GgT*6dLfelcl$fjU83$M>Lk?
zP>wlufKd#a%=rEbxj4k`3O8&`L)$Y38MbeJ#X706N|Mqa7HFYA3r>A2OYwLN^VYo@
z{uJs5RqRLB?n&d@YAw06_9s&UqwGnWqd`-nB|YJgz$nU|sPEF+UvfSy-%|wV7n03-
z+uV5&jdjtGejI;716^?TcJyR-SdYvi{qrEq7(q@L7wkRj8=M?(ltCI#K<E$oPL@7R
z=_qx{anvDtIl+D?l=-(RRMdCDmU#7cq`cB6f<ij_EH%)eBRSt|%iZj5;n0N%-XZ9P
zm)C0WmS-e$4<=9NuN=v|)j5+WGV;gqS#X|1vYY)cQTxUe1=Pd(J$84oWs|lqskx#S
zO_6Y}nxNIh%SCOdQK<;@W{Ld}hD~$)Q&oI6aO^WR_OXeSf|%S*UwWvOzKL71K#}QI
z^1IM6AwKjx#X%_DYTMCU@VZxQr9UVklc(DS80l|Oho?7g`YzN}F_Y_Y+FPBRXR9i<
zrc-Wd%-Y++HM_?xV)H-Ze=1QQT+3+PwC&!cPda~Q&K=k6aTwT7$=J1U&NYq7iNL~<
z65tses+4FTzM$=u==Dv&MXtxf=Dqv&2kP~!`iXsi(Mv;*10VIQub&fpQUz?>E0`$`
z4~E7SHIq*D*yTG$9d%OE1zg~e2%!TeO3JH+Wn3pRiB!ruD;txZ3ez1m7=G|qV+M=c
zuPofbP@lKCYJ;PR@4Z$GQvwR1@Qv>R3M<d8tB`0Q@?6Lwb5J>$*KA&gMX~5J$M0k-
z=w$rEn|gl2e(ryHIOHi}Am!osMLAIlthE^KVF8eXHkxn+t28CNRg9<YM@u}G@HQR;
z5|nLs+mgj)qgwH)OXN^wl`lCL$UQU<53X7=Uud;$4_44NnFf!pzc3B&Vr*9h-W|Cg
z+O7J^>)ekZp&>nd*D2r<n$4fti>BvpI+^GjFL>G3Bj1b>gU^Mw^<4CAmeHG|6)fhL
zTY;or#4Fthl?q8dNm*|&AaTN<Yr$_qP+oNW347Yaoolu}%ssP^DuPVz_Z-h3YvoI9
zfW*AcTWU&$ckH9fPto0vhnMC%GIW*Li*mB4GlwB@{-q@M;J6T<UhUo)UVqE`OK9K3
zfA9SSLKs|J|Lr37PARPu#l7)ak>g?cAg({8ae&G9&!1C+O3pmHi|=H?;Q4zr4D316
zooToUuCVu;5jt8T4g+(R)@YpXIT+E+)<Q7SiIy5n>%F6MlRo->mux+Z8c;KdP*UE;
zcy^Pv927tDz&eVacJnF9;$i7`sDitceWSg;dd8Fcbl9X(ppEX4=G3b=jdZQ$ABQ=F
zpUhlk*7v@r1c+vo3~;u1+aY{i#GIM6SUpJDD2|mVkInluK!QAKo{KO$qlGOyRemmT
z^L^;zcf=dX9LmcAp`Ue&F70>py3PHl%o!VTWjY&aTnY8(Bb;TAXBz^oEVf93WshqV
zMjO3ab?mZ*(aqMMcRGfpkc>E*ndXPrH@?#BLkS9SYtiLlpLof@bskbb)m?A0U^P>Q
zLx;Fj5GuAlmXqVv$i?(#nVEk5_xCE!1AbT{9(L*Bige(;gs=ZznvOzXL$8on?%}`K
z5@Hna72j}yMF_6(k3%rA(fA##y`%-z!lv|gUKrWwUi*DHHHoIongS!~r9aLs5!~V1
zRY-y9u)#!w(+khClzdZsiR7NdKKS-<kWw2>u)aRC9?Ow!;GZmkJwb(4I`~Yg{1k!0
z)8I&js*9#b;l&PHIZ|W4(9IWUhz|uVYwA-RGV5rA<N^pto)J#&kw#QPMsFFUN3-Zl
zcgJ=y4(U$0(EJT|4Jsz1%9!PSMMlUIYR3-aoV8ysqRyC~AJQp#k5^Mmix78R=}6VG
zHPPVbOT=WP6+3Qug;mC&ekM$vw?zUMnKL6RR9W05gz4p4B5x?F24yGau{p-(>&+kn
zF^qKC=1N3`X9tUsc}~ZmQvy&hXC?BKD}F{nQHmZ$58S)Cm%g^ghmG&^$EVlqOrIh>
zw-xK^AHnpT3}Bpn_(m(e<xgsbhed_$MSQYk`xz{BXGhexY%K7BR1=S?nCWmd(XB~G
zzvYeHX@}*7#{IL}iJcd(Uz@`SzeV=JwHjDq?o*R9cJP=o8r$}LA~;?!26I!>SrAfO
zTxt1lHHsq&UiS`nD>!`LemBSR<%`X7)(oc<fyvKKL4xZ9!SR+h7kBK{Zlu~%KMvj#
zEofQiM8(sQwL-R*+gXf^e{~!<MO-W_r9aWki#N8)lAtyxn}y+yew{DO;~f}a3Ml=N
z?ZP^pH%5B&r;!NlW&v7;J8IrqIgvNNv&hCzo#1TJA4`kJ79-si*h4`5GK?j>ke7fd
zb~n~?Gl9D7R$5u6!%0r?F%OmhcIBNgmi_&{>Vn7qq`)P7*5q_hvya^<_;S84a9NzZ
zBy;HIw>%&I$I6o{+rKPlJi3Wb*(U=T9pt0f7zWpf4A4X37mdkPUZ5jpMdYEeHb{^3
zf2F&grUALYpeKXjUu<!)u*Iuv8P(sGgW}Y=B&yAG6ZKt+ezxK;Jwz=<z>_7|341Cd
zz^yyvB=<VrteD}jeWSUSanUTg56=HMiW3oc<NP$X^e5NLJqxl_2Kd5mrJZ@8>`*@m
zoAITNbgI$le)Wxor2_^@uWfX!jQi;R8yZu^zxR3I9*r?}xxP%bL5P4R*eU|9azm(F
zPTDn`yx$}W?S9W))jbtj+X&RGa&kwiIDcQwUwLZipxtQwdzQtq!Zl@khP5P()K^#|
zoEQ=NK3&$nu}`5=w&ZwAea$xYcSRFujd$B9ceECa^vZ+x=e%tqN7*g3Hyz4-vhZBT
z+DE-PdW~R1BP<TYFoR=<`{7H|B}s6Kg5t+CWeQBVwHW%BBoKHyj9`Z&C%1S5XaV^#
zBVb`Wlo9hs>5|k3-{eD73IAfOU}>u)%D_H%mx*Dift?DIeH#4VvMS+Kdi?6SmSqE4
zc*0Znx`^MadX!v()B4u6&Px||9I!Jj0>@CaF1g8-vwAwO<L;C1aI2=)Amwcvl(;#e
zqto1N8K_ZB|HjS2cR1LdfbAT!2n1u2;I?MTF;C~3MvLNV1&3jno<pAAR`4@i-&Mcm
zVeh@~0+`vRgaL&rg&S&WMPsx3xB;e_gO?(1+6i%RKK%S_wL!UXp3-9uoB40Mhs7iO
zly&2Y@9lQL8c2^_7LN`0tdl6DSuMFQr+w4M$Gza^{H!@n_@e0iPPELvX_8W*?)ZVa
zuht1;E}fY-Rgh1d+Wt}cqCt5}#<p<O<tOa1YQ(W?yAmC2A<Vhg0obLx872|Rnq1|M
zF-2(^9+rl``)<BQRK!vIg0G<y<;`C|sFvHumh4e>3wU*f;%a-p@@WGrD5#Thbhz#h
zPW`bd77V3iUJ&Hf4dcfvg!zj<XdOuPUY228I*nZ*t#~~SetbPPTFCX1fnh?Of2_{>
zw^6ZL@6qVy&~Jx);k@|P&5pBKvk>sKC->m~m=rQAfiqskXuTc&#}m`|K?Rb(TUxr7
z$Fqup`s)`MCG);iOPHgx+sDp}o`DnV+CI3%C$@Mr(C9usq;yFvF;Ho5Igvha9McYJ
zC2ss`y+^B`Ywl3j;#$&tyx{P<h>1Y%*!nQJVCyg|`Z>Y*`j7L%@}wjPN9G#IJx<$6
zJc5tCuKm!n&Em;Zk9(pa2%D~;4Sdo2QM=`~gzLEJD2jD4;916g3C815$E6EYH>gyP
zcH?zX(@Aw-Y;S#_;AL4hxAaz3AlfB*4Z^5b2@g_Ux<#8+FOyv!yX3%N4ABc*%p6;5
zDc$xTU?tP>dO($rOzsub1wuQ`nFpp&aG?RQLtgkDi)$^V^g)jTfw7vnbbA{nOKd<X
zUVbUrt_LO#A~vWG4z)F*X8C@m1l&ot37^6vPVXZ%xsvCuY*2^L4^XnFYk)K{Nts8M
z8cJf$7?7pHV3?H72;tJrf|Fte<W!h31AV;B{XU0W-`fOd+Anta`7(h@{Bp0q65}F5
zI<gd(0-p<uQJX835;K3yiOp8-Q!3n`jjKFsI7nli9}%3pGa>32?s-FuCMxiIjZYc}
z(KBMh$&GQ=-B<Eux&Q;b{4WVBI}I8|4cBbdC1RZwFWROwqOMFH8fplKOdRoj3(O|=
z{*5HWoW7A^ac=n{jC#!8kd**6kJMuzhn5=c9oVJy$A75#;M)9$gIFYEtUo7DK+X2a
z+#lK;Knz<OSB}%j`Ova7d{`f|TU9;t$4Sm=(L~uA4?N6Iq*x_U!f8w&hoaNo5|SFu
zS%+EQo_!h9PrEO6!rq-rAdK-Q6?V4D`Me$IRh1E)dUfsNYenmzEub8)!%k>XS>6KE
zF}GQA>f@xtV+)MG&7hR!lITzir&j;>-UNY@(tqzw+*WSr)b;%0CDA-->tjFFNsYfH
z|5e113H!)o9sQG6G$_v&fwzpjOt?Hpie6Eq<TeeiTHW>X>)l_BCocl&zr3llaXt9n
zjMtdPzPk&5JlOQG@x1>a@i{MfwXgM@fvqwxP$NW{Fys18y?26`OK|QT+M$7f6QAhA
zed{$H`1RTblBUOMgbsK^dhknTg!!RM3J{YP8f&_{%|bSu66l8pPE%Sh@5;j!X&#I~
z;5l9~9y&VBm^ZMF4NIgnZEf*BWqyn@PS;)1mGe$pf%p{JrXD>s?l#?bvwEK%dOdW?
zhQZ9jp0<#Y{(Vb=;rZ_vC2Ie)c^GA|FL<x$(C(BMPovv^G#3&w9p1xdoo{#u;(YbU
z@&uXZ2m8tnuE(wfZg;QXy%xFd4m2b|z5%Ak9o+{Cu!B>c)4__W`E_sSf29g?#VJ?|
z27sWu=TDGc?-uMew0i!<TCP;pydaS8?7H=F=<s-b(Jg@4bDwo4^}g-9m>xdpsW)yH
zy;2Sz1~l2Z_+scbBaOy9x6QxQ-Hg7w_OS<(I!j*nXAe8fUUJk>Wd@_`y|T0%tsW&>
z0T~))d^G-KP3?yZp%zyYb00H-p&8V%jNYYU5ZY{o{(Hsg-`)mK@0?3VKbIc^*VN{h
zLU)2EhYgo*O}<$Yt}&+2h6ly?y$v3Y4H#uViT596XU*s7d54z$gC)HD&@DCX;fcyr
zIl6DLY2*_ttdoZe3_f3k&0UV*aCx59;bVTpbj3+_^<9Vhn)-o5ot6)Dr(0wJj@nsg
zRm@uaJHA&Phs}LRQ(P_=*D7G^_Er;LH~E&*J7{+}KI7;5>gbwqKJl7NXAwBHh%YS?
z-4#uqf<Wtf(4_*d<AY+l5g6})nuJz+HE$@*==yVV5@$T+@0!u}OA6jJ@;I~br0bVm
z`e4ard_y$cN?AgGwBtK(u@NKIiDpbHM0hRcRFCCU!;QI*=<rBhD^5i;JFhw_48^;y
z|4LBTUdUUtr@4)!1ox`BJl-IBA8&dOCD{Y{5MEL;BUBwR-V)0nqK7}Si#9XAT|TyV
z95Q8HSzaTFFSbpo+m|`Bmu`|#d*7XuG*(H)&d7+VkRg`5ettpJ=c3aln;{@tpA1Hm
zP(JE_LMi<p*+1U?IBJe$`GJq&Y3CX!0wL+PA0J=4XJ;IcyKPTk`uN^hy?)+c`VvLr
zPlJy0-x4DD9jx^R=)w&Lb(6C`4Jy+b{xx7=m!}BFozwfac~e|gGd;U!bKA`cGC%*v
zhIx=_H}2RoZqHB0iMpW1L1Bl^>pM>sy4Nnk_Sr-16O9CKy#DT|!0(P4r>O6xW!D+1
z-4OaXsSj)4BHIQcz=<q18a+!}D|-hpYq$5%50V_TiwsQVUb$YQ8Yl6o-j5qqiYv*P
z7r^YMx`=>EY60=uN3>ZfS8E`Oc{;Y2#{xzf1A)kq<l!Zcg3ETA*|%KL5CuV`r>}LM
znVW{%dq#L24l+}rsTjNEckXE=-F#Xur!N187AaDo(7pse)6h!eWK;e@7p-yg%;pYw
z&Y(>rnjBTb<zR{)*l8=*WBc2|H;W9b6Wa?v%al;Y)Bp`v<;!$HcvgYopdK+U%ydH!
zkH$q$s#2&8f>se9WVrTL8XpmXjNQ3@#!TtAB|CaAL7*PiQUJMnpMkUcUpP^U$NC)s
zDbwYlPCy|Gqp!ywJ?<mZ+NYo@eodyOYiwORR5<4NI(}!I(3OE6-S4bHv>}b$y4fpb
zJw<-O)BXH|dTA;Bj*2+wRe0RJ2=}pj4d^HM!=cA}s0B~L&f_Kp?oUB913#=5r}IDc
z*gdQ;s8mwPtTTXv!1+G#99&?D3|cjZivW;i7#7V&cN?lC4I=}x>Rb#lrqIK6hOvvz
z`GM*r`Ox$BjfG{6DUxr`^X26><MRs)c#37ZyKPh+8#<F9n<S@k%)soG*N?*&7S>L6
zo|QeIL20@TQPtx5Ko=&%A(@q!RSl=`@IerVLBM&)H<op=vZ2Y8;!Rx7!Q=$zfjkH|
zf3uf?VUiY)bvj%c5BA*4Z}aBNowSr_c!7uo6w^+n{O_fOyxJt_!i+P7{FMoX?iTng
zVA}1&RMMj#viK}ca}IS20FVOyIG?VbTfSIUtT0^|t-@AK;2AH|)PjZ)D1$)YY^3>6
zV46w93vy=sAZOjl+#N-nU4|e$^V8r-#zO~@>4yc>F_d||{tF`-#vyOxu=zC7e@6lM
zu=MenvhV~GV0bi;Bw#LRL!p+;0}gXj6w2F#6B@IDXD9ZjYbUTF1>#znAFF;Wp>GMA
z*(G%q4{jvwrp!5mqeW%+ec$R2Uw&*LtcHHGEohYvRT-l$A#@OxZ=oTTB!-<ef-UPb
ztp;B$$yn^}Nt7FkRaYxgGG9y5{0Xp^SQ!EfSaKB(vQK22q9)f~HR9ZjNy;VoCicx?
z&QrG<V{J8P8*j|z24chKS3ZD7=!*TnCeyZkL2W*h13#NROtVB_l8@w}aj01g3)bXm
zkD4cp)z#F}(7nEmh#H6U=;EF<`Sq`IUcXyGpHtaTM$-|)xfaIlkN$*=Ih`yHd}SL8
z&PIXcW`x$qJ*t;A;`jx^U0Gybx6G6;_~V8OJPBg_CY%B_Cr1YEBg~CT+wb(ltnZdX
zfMSx>`#zy;r2(Pi`w)>(V-MV#DTj#nrtV8xJYwPs_n*r#i>mwYfm#dsT0JL<kAaI{
zkL6aQe1f1g(33EsJG4#a0aiBMjl&lAu#&I~%CAVKt?e5|3C;7u$+m?DFTaM~Du&;v
zhd*L;Y<03ebbp@|df0dak{OQogSRKyzdI1Bv>a2fuP4oG>n<i=E?!Tj#C)acp^YTz
z+Kydfd3PjQ!IR?OMd*D*!(8c*|L5_c^{&-nwu5F?al}^c;Yd+vDB|%!U=sMw>+!ob
z(S{O82nt=norfL$^|o>z{GEN2drTr=j}QHuLnkxL>CkP9XPXGPL6?;zF(F?zt}-5L
zg;s>_CWc&23%JyE&E;iww5MQ;FRvFCoBT_6V|K&iOR1U%O*7fha@>7_o`h}VRHD9m
zn91<;uUCnaJU}&_L9BL5f86%IM=X21LR`G5Evu|{rTMmgOD>Fm47R@{7hZl=4juKB
zAgR0qhEF7IC{0o#^xCImbOy2YQj*#BJddh^=XN@&1*(L93hI=*Eu_Ph`fax+y$@J^
zSHgaqh<-WV1qcU``vVGu-{v-j9=ywrI}Wu$?=GhTs~I>ux88{<Q;+|?pWBS0`>>);
zI7YP-)=sg{%+edMpa=D29*E`~)gAuX*g|8P3mNqTCN$LdO1?{jw>HJf1C_r&t!CUu
z=w?AwJ=Ppi{)Jz*{|mozW22bYCCgY`$RCqA339VR2p4=Ng#LOfIUtK}?rkT!h)j6L
z!mzk#2f9cT3qNb-w3Bv2I;>D8sB|-nKJ5D;bep#(3mPU<j9Me#Ef<)BpB(Tepm@*m
zqfGfHMyR0CW2Xp26k7E6PUO`Py36wV*xc3E5C!+P%)?bzSO!b6Lzq6KuU$W`iwzxg
zC7+7wM_L3m+9bx<LCOSe`ImIf%<3^{b+WOi;hQORkWURh#WxDs*k}c0{U(Vq6L^$r
z-X29Ot~%oh)-P?T>g?7C*&o0-V39)Fqg--bF2AVM7-HklUb!A(C<pypiPGDcY66VW
zZ$mNJ4qc$%7~9ORvvd3oC*#;YpOYqQrCk2-_~+I(Q1A~e{efO?hvR6^7@NIeDL-EX
z;+8cnue)zgW-@Is!C6ErX&%5FzMAECCfTc`*0Xf=dn75-@wv_g#u+Vd%gKWZQZISP
z;{olkrLxzmQqrD}QAKg(`DG+Z$E83)DTG5M8=|tZ6B5FZZu+rgGlIj<sFhn`+Wg%0
zaF+Kw8BRE2T<Eju7NM6$;fT0leMgvMyA5bJr16HCyQWT+ruhikeWacP>@19FG90k_
zkTJXv*rE5&*mt`9U*SfC#R}eUSTuHXnp<J4>LDU@9eMQj4C#enDc*rnJCpVwgg++n
zKYXDR<(CoLm0suWuU!Mim}}*zP}8rpT^8kS=Je*pHH~uX_TzTy{Yu*zmiYW^eEz0e
zozm?r$lI=h;+se0m?Tq%_|N&-*u*E<A+g!J*Z2+k4IlHirtwGuua&=ty3#cM+61!G
zbIiKopU3O=1wHDR3D?!SCFz^v%3<AdL3WHVa7?_fH-%R2ou}#@p|@GU=e%!iuFF*C
zddINkYF###env8Vke3tVeSg1dViG-@cTx9A3AOiqnT{dUF=FHMX4H_th5-Y}v2QYx
zjGbCee(a7XrZa;6@9(;W*HyFg^$2Du@GIkubaWDuG1YRl`u?xSK=M9OXMkrep8ouF
zYKk~>5Q9p))1YtE5~`P;r!jQ;=5c7ze$|)JP5UxPVB;P?Kp|`EsM?wzw&``x|1YN6
z-OmzQ-<@^S;+`xI8fzc|FuLqvu(IhWi7MSw&o(;gin~lHj~#SPn?jYHdB&Sp7p>mD
zm!%~D3~&uxibPvLf}r`wlwY-5Ypt!s@wA+14&{12t(Md@#_O`MbaJ_$Aj0(A^O8=j
zF~<+U#E6{Sc~R<R6f`SpK$Dz5cvtwIPjfqW^FAprLQWP5Q{c9p&g(HkcVk@HGIsxZ
zdrzDWAk6$f{vrM%KX6~upy&~gT#i}@Ytv<OBj99nccY6SwnX$6BsuF5$2{>|+&mO)
z>X9gbIkgTMzuvHs^9@sofR}J`IXU&fU(3d^CKM3$#|2j*iniP?1n!|B?xAZBPW&3T
zukYcVd%H$c`$e7h4bPWfCxhLu>Gv^q)0m{Ahc7+7_Rrpl!@5V$C2wrBO5P;$sfvFg
zY=Dj=zCY1@*xod;0^Gq#R^Xukdfq)NXWQl~JdLprri1{WZb{727_z^y@O8`i8}|!!
zya3$!F-VJiaz!=`E0DtZ_lg;K!0?olYqYv#&SKOGApRz7#4e`POT!tlTtorkR<x`H
z^!wV0l@jLtpqwE+SLy@FEb9ns<`dFXp<W`dJ*sNUMdQ%F>dj?y;8il5B;K0S^bj5Y
ztXVofW0a#pornesVf$j_)Y87^;omnjpi;6~Zt*N{RC&QnK(UN3mm~SzeXdC|7%{Bh
zbrG~&54Cn)7zLVJm;4^v%NL+`cDvG<y@W_V36t*mWx5k95mWptj330crT%)lepuqm
z64ULrOplS}U#+*qL*7O~%%110TtajD&b33mC22kB4Wb#8(jObz!C<#9Q+Y^*X)`gI
z&i3XGZ$cv-)PXW_dqK}}4|NJg$K<AlTJ6#SUV1!-8e&m;SYAJ3v_6S(pDtO(*LnK1
zoh3as99|<_pG=Y9%w7Enh%x)mw352m9A)zMpf7MUIP04_zIg4bmuhKe*1N{7Ys&NH
zTsoEQu3$WCm?zi6lCPkHdA@_K4=Z%H+sc8{HsSVNnWqo5pr3YK!DIxS&fjUUTk+6;
zKwDMJ|6q38_9m82R0`Jkpk`~{)3?aOs=W0x9|@(Odf~|j6tmwxLlpjoXdwTrZ+N?I
z;pbtB#Ly`LB7$x7$37#3FnA*)VoupQW5^!u>M&$Xn9;q1JWfs{0DjKTTN+qM-_D)C
zd*f#-=FyKwOB17TVk!5AX3S)FOdJ%@$uiHlKuvwsPh5Z~SOc}Y-Qes}4meNk`nm)H
zsi}1SC~a&->@Rijz4=e)=<<zZQyaNY|K4wrij9rR{r32i1<}?wZUk7cY+<S)_`qpC
z0s?TLpl^#LURS4*kKs0czA%%u3at@sENegGr@~1)hBQ+afiL-Ly`%(HD65eyD96wY
zKlX1?92IIiUoQ$v>0jod)%$d`E2H<ZPOB}-(r{QiZ#xBm9)o=pXH|q;l*!tD$0Dqr
z&2U2@AyHGtH^?_vF@T+gkL^qM<zcK`La(~ri`#M^N6B&$+&<2_WM@!i;|J(_a-_wk
z49sj-?R^(2G;m@yB@=*i7EYk9y~F@OH)w+aoVgX?R(zg2*7eGGP#(hfvg%czIyi8N
z0fIAQUW*jcI1bu0V5XT?WzZm~3XrNa*`Yy|(v81HC8A}gb&ollh%t5xfhcQv&3uj<
ziWAh|cQm<b{>{g_P15#1XDqX%X_V}4-wsrSu{TynD=xara)651pyG9dS5vd>!42te
z@8;zEr~wVR0b<q`I_ZPte7lPG6T~ycVb@sCTp8eBw=H}@!Us6s{`}L%0aDOIPQ&-d
z4qf-EZ(?*J!0x*-BMfL~aRh~d#bEvdEeo42aFnz=?^4M*B#C%HefGbUCMFvl$oRkc
zPNz~d<+5(;F{i-dCT2!+f7twME+>st^YJZLQlaMNUh7nW0sXwr2&)BZYxVxPkh`^w
zmnbOSH!BkkE-0obRo&dH5Nd_!Dzep|G^;LkGFW*rSsd&PqQ-Y4f}zmt5!(i3wFbfK
zM_TD&soVafn=~jX-W9Ts!v}HVd4d`}bqU_Juj48E2V{)h2=y+kX>NFR_~^n??(?Q5
zGL6Rgy|6fGj-*7At{7p+s+YgBVhIVe@mz{^lMzSndm?X7kBs|xq}qCcx*q0P>k-sO
zm#99n{`)Wdx?abBtHUlK!K2L~IgJ;QYw6~%u}4B0n?@c8tZQ_UNYDn}8n0dNj9c45
zyitZwX*ThNXvXBq=52iyFriHkl;3GXsb|u+9~LyN_|wn$W;88{wNz-eQ<@YM%(S;T
z6y0&d-Hp4ILJ9Xf1a=8@H%H7rH7b5yu>r@X{%#d>(b%n~)1H|@KjP-8;4E)e{Y2Kx
zo^nZ^us)oXpp}yYeb)UMCl`Et_eF(ziU^&(aa%w3E`R@3H6*>r<C6EA!&Yz0Lz-=B
zOY0?>y>gY(MbRkP0|)OyD|axBuldTcO`ad0O3|e!P6OYQ;_<Z0>nomz_Xe*2zycUK
z!M}M(CrS$AtF1axkYKFvqbnJD!$rGUxHW&_bYrK?lZNX>I$OL?LSyTCih>eunz?wM
zrRppF#8yaq?4vYm{o?~>1AxRrpGK@Mr5z_eQ|nh!-?^V_#^@L(xFH2o{Fus-uqv@r
zVY1#pUnDX%417Pm&IJWb``G0T1Nm|CTgOE9t!#m)Z?p4u65*!C0XoyrKKR=Gfn)aC
zgC{m@Xo_2(c4)roZywt;l`?`leV@J)isaB&`jlvOkumnvh<Y*m6T-<4X*RD7h-qS4
zLS;<32~f4Cq*nZvS=t;uiD8{A4h-<OXz$u-)8+6KrT!XOqNzktqBQb(IwcF_8}}Jh
zzOHZb%{K+3pjtM$!17SUz|f2-o2}J)g!nXtEzW@|h6VO>2azKamLS9VdaqKVrFsOJ
zLZuAR)0RVjmowBS-{iWJ4eavGLjdKV&I**`G2^4nq?hnd$>Bmb)}m9x5{E(exB0OW
zOM&dQe3yH|Elarw^&_jad3gx(eA@PIa*u70RZsXMcQ@21NwApj`!?)09Sj0Resuhg
z72?OOmyo}+hY@h+VVKrrsnW|W_r{J^UdhH{0d7_?XU3+=0OETR-P-m9y`OC=A`02N
zXB)x<Y_qgE$1yB}7CVkwPBpyjMl#&$s2#)queK}yhwA_SN!hZc-nKDBvSf)d7$eEP
zH1-x{-%XUpzAI#3$`)fwn5l>mijX~I$;gsrXk;CfFt+%-@cukL-+$mcKitQ?uY2!n
z9`~MeUgw<WdEVD+#Oj=MFf)q>V?iTx@A~cfuYy*dB54)r-qCh#XO!h`6lt~=8<)Kv
zn+y89Grp)bL0O*7AVb`WF`JcZcDbpIFcmh#YDnOR-?A}|^Pm0_JQBG%mKFEMDdV|l
z{{}B|gLh=MO!v#n8RQZ{9T`g>AAdoeJGk%ZgI~SEL}CC`1L!l?@1oJ=4iH~U#6>$w
zH0j;+So+s8@$9L-*?g92U&_)A%k8n-I9yD=^&M>8`?~Q)xaaCg+Cs4}Ml)6ovt_je
z$a)}Lx|<RA3g6gm#EM|D7D}$;T2lf59Exx*Sr!A+qV-EY(R5De*ZJehSbNt5%DEV}
zDtSe~yK*gFGI}#3#rT*{ecD~l|EAt{Dz5R{TIUK;p761kw}n2Buk6D_8=OETuX!U6
zLLpW+m-Mzn5Apt%<O@_92LoexDo<pVgHgAAU#jY@ixO6Y@P!ZJTaOh&MVbb@ij5|1
z^2}|o)9=1Iy?J`EsMfW#dSrZg(w-3gvdXT!_M1Z=MI@yH!If-2;WuXo@^$^9-UpM(
zmypF{&gEs_e^B-_dyPtFl&75b=R${_9Nss*+0z>19uweiG!)Xv|NO20&ld;wx2byR
z;l5>EMYYO~%@%fk4>Hd&M@4g$FpFe3%)tI+by+>PF`#-YXFiqPGn(>-fnHkPpKq$2
z*N6>+^hpzS!iqh1qKb+hS*<dKN_y0J#7oihQ(e1lE@D0%xF>M3B1(Uodtyy)_;;0`
z7e%<G#kA9QFr&H8b8t*HM@*^rTmPxVI%SAU0C{=C)ao8s&Hd-y1YL<p^xT@iWC;iB
z34Z0x9>sx$lfknMzB$#zJ2P#Oqv1B;_aM{mppbV3fS;9V?SE8hsFk7OaE8Dj0En7p
zLS07-hP=@CeKvPXvxPG&{8q-jJe8P!Sp)>68jE&0HTbfRUb%dAE`VR&%@tHo322sd
ztfY~?`@o7!9b)O}E1(=Ckokz-DhH7)Ln|X+eM85FBW<Az5Pk93#1wf;G)5<MMa#AL
z9=H@x0St>cHrFp%*?QFJ6?r`%GOC@9_?;IpS#t&WPEL*DH_Psej>&Gjjj<>_j>O9|
zFBhp{E$aUllnMo0sR1vP1z3!D_t-rMO%>)>BC&aS=bdg+xXPt$?5GP~O%Q12ab-aU
zLOEfo4?hHj%>|^m_yH8-X~Ls-1+dHt`sS!{$7dpO%2QBZxK7d&R#F>pQL}@07`qBN
z40l>fIzT5D8WI_o<ItIr!*fPh`s<vVcE$00K>^)<8$}-{?wYb|1Y%pP1sooVIL9;Y
z6S)7|FJI7>VBs`Gyr6yj1p+9~DJAc}7F8ehVE#xI1iwwYOF7Kkk(0>~t2zW$b>hXa
zRmhn;hz884Z;0|bFf(rlBj<;&tJ|Oeq^DJym$z6^Ig(+oz7a6tT;rvh<@4EIVmpXM
z4-Ln~yfk7l9@W1VLxo)82j!h>c*wlMHgDJ?gQQP`j+wf$28Bt@P@43JNJY8?aRUSG
zu6IF~K&Ck77&+WS9n8qL{xt3d=MWQ})|qHRCDSn48$gA&W8Xrr0wRK1KGEa0**!35
zZ>b7(BYyr0B4}RNk6d~*`}hc21$m0;Xfvg0hu33Z{q%uL!^a+GX>^z$V1;zKfZ8Bn
zV@vUJMb$pOdp~8ujZmee9|8Pf^}Wi0E8NdYC8cT&{R-?Zt{)d<6_#EUtF<rRIFrfx
z7xTdG8LqmuTE4!O!=?0>RqnQ12bbSQD7&&-UE7;Iru*w|zi2%|!r$<$YCbB}`^!H5
zwky#mIGiJ(Md!;cZY#Vsdq0e%)|unB;r2wHVR!zOo2}?63qo|VuRBpBnln78zIqGV
zGu^u?d}{xM)`)Le@A|Uh*fQ~lVkU7WSA5R|b%S5~_{4BP_TsqD)+~NMF6Ks|HT!1c
zpwDe+36DrdFb_fILQE@TwHvu_={<<;vXlU%umHFq{Y#9%AFTyQ)<2`}pPz0uc7$sn
zdz)<ILG9Xx)###=XlnV{7%mX6Uw=I>T~~6gT4uWGCl^@lQ+Mds$A_STa=)VMhjF}9
zNe^j<N`<qc@>`qKKl*LRw~k#fgpUnYDsFgUp}b~HfWb~uStf)y`+6}3C1+9Fzhd65
z-|pb%_Gu_&Rsj_E9`Pl06uhAVApb;&TUcc(`=yXQagS5~z?bHN#L{3XVv#G2%le7&
z>vD>tQ17Z*Mp|^o`~J%Fi3$rCKthW)4*?^t>aP2fBchSMIS?LmkffExxft8y%IflG
zA93_gER|J{;_Ku;K{u26*;oR;WKVJO4iWG0>r7^FaFk_-QDx&bgy;I0YR`7FovgU3
z+55r;d0VO7b{Sq;8QfVyM1_SUH!5-8T^m9?MD(y;j>Dk`$jA#7;f3Oi-H1M7UwnjT
zs9g5j?(RLN;Njg~PON^4I@wom+bB2Pv)?B@+%t^%Si-WQ)G7OTaR!a<lBrf+vx%AL
zC8LIwuV@yXq;OEC@Um$7S}^0O-SOT);B5niWMNX!j=8C4mr}=pAvH_**9qX+T~fqu
zM^GoaG?*3+d5w%Y1BmH`X{VIptvuo%-#_c4K(t9+BUuU{rXfr`GK1WUpk`?{%xXZW
z$+>{p!5>7bZ1ea_h6T^m_sT%&NaYpd4q#-fpOlhaO72oT8_NYG;#T+JpboYDofqFL
z_v`Ny2;cp@#d(r<t(teHP<<{9DL{$xsb0_Dnzx*``H=yLi}25hsq_8~b_q3CfPIB;
zdj8A$($8AlJ`t>Lhg0{t-c-C8^ND3-WV!zy3rM6kEw7%{O!Pz{cljks>o;a#u}*k|
z2Zn}FBlGE}V8p|~tZkb_m0`Ryd&h!;tCGZGRcg1nW5O*THSb-hE$^kPCemWpi@76k
z`S0FQ#>X?_?vwi=ZyY$89+0M#+DAKuoTmHWQ9qsp535nbI{EXR%2G6v1XI2++@I!E
zK+PDvZ+;j&q`~Jv-U`-c!xxU{K){^eH6?Gw?Tnd=7w6X;nze;x#R~gUBe?Y_H+9wK
zxfk<cQznPxgnB-AKtH3Q&TahE+>w6$^+7rg!j|IF`+f7w(u^8~*!((ql#HMvb)a$!
z+-rv8bvjPJT1JrWg;8%)l=WH-k*_#x%?ol!f2t<+qgjSc-SPp)>Ovaqgi4FnirYbx
z3lm*)lvEsWo;IUGvy!Mk%Zf#wweuwA?TNe{IqzZK69CIT>8zWH`cl86<TWg<Wx;n~
z3V}7+2V`MT?pq$1M=F|G)UTI@boO{7d4BBvR5*q;gT4?EN?4Hy4@$8M{{3BV@R`qT
zv-{FKn`Bq7&B{^>oN15Ehyf{4;SLr?37_x$WJp7SP#5GG!LEUzVY1q(9y2M&q|qoo
zsl`kG#F=)e1pXK)V6tlTZNaZIRh&@q(^G<bdX-rh9k^7TtGA=sMsM}E+ew(Jb=K<6
zbjIw=*LUzJXYQDhtyMw0-x)=CFkH}B!{U8|^P1LB(Xr2F`yb}ge8`G7juGpXD4_ai
z<o(8GAsweunFcEJtHk}0TYc}~bh8K{U9@;kiHwX{8>RW{y%>c4`@Novkj15d9J|Ui
zyrCyRU1qz$x9A*}3W+ua$w}F99Y5xgfAFsX(NGa9z%-H-U*dx59rLqv>NUtq0dzp{
zqSs$FJqm&-y0YYasQL7`tD*(7JrSFqZY%9U{GWRJafkG?A9#{WAKWDpjnP7B_vccI
z6x<)fU-qR-0#{_i`Lu<e@F!L4N?V8NSuusQ9@)<`t{~oscoo7U{Xw|tE7aA2q$z1h
zKHWkU;m9gTCDHJ>|Ez-2{xDYvt)kdOSKk-7qA{UQ7HT$v=u~+HzseyjjbXz-9>g}?
zloO;6CZB1!V&j_cf^2sFd~PAvnWeS1f-zM$GA!=rDSd8FeYTVuleX**)3>Efo6FML
z33j%lG`}q}JaK4iPWq~B8q1aC?pKR32s!4<J-#8uYPdMF8r7kHs_gVb-7s0!ib7jW
zbyU?TA*N&4hy(|&>5c53^0PYbo8OmnR_qmh_OwK`lbR_@FO@h$B)XpuFs}(Kk<)kn
z)j<FMYM?Fw4uFX-mj>T^df6mN$a*iJf|72?G8<lAkmkr$@_*S%xVg+|Sb2BzsTP5V
zgTCWb4+73oWq7u3xt0^#80a|FQn9zu1p!OE2*gn%RWd85F8;|l3A+d_KHYL9n4B!L
zn%-G(_f~ZD{7EQMg;q`GGnZf0nBHKdi-CPS>G@djj+J72A*g1LZ>`ie1RE#j57enB
z6vBIQa%ad}^XG@wp35p1=WpB#tdATC+ktvCv>(O@1cM_wAOZt`6u}PrV{JB6(Z8Pw
zHEZzxPRBP!*0F59+^5QZ-ks2(CQn|yvv>pi>uc|L(Ew~KnJvu`<VYWlcVPF)tMU*c
zx1M#vFWW@Ihzv@BkdED&qzz)!H36=`3LTiO-#7DZobQjv`u0nrt?Kw|!dtvTrgGvN
zSH|vX<0%HN)TtFLv3&pq^N%=3udNx9T|j&Cz5c>S;lBvsE&m|n#C@rNUx@Yti~lh%
zbeMpsUOt_SuF)FvHg3PnRAUplK6MA_d4c=M*9y-j=AvbQyeKF|;=rc{Dw@6SS3(|9
z{D(fszSl`=0q@fK?5ppx>@Ykt>cLH{oT!n05~o*-W#KHysv#y&B_=a8gUN04&sNiI
zlQdn;qbD#@SaR0Y<9_*9Rgo7=wVc{AG}K5dnfn>(oMs9GOUN2r?wld}!N5fKyMvJQ
z*Y4-RE`Lij1L>g@J;A*0gl+#`7+OjaYM#Wb!=G)LtsbtUo>HKu43}66aCV*%O!xJ9
zD67L3Dww|8@QTa%dt(woB$|%oDH5ex*jRr)G*Kss^-SU*n>)oIZrgb{CT~1r8*<?^
zhV4wtJQ8j_O0*pv{XuI+B*j+V+Faj$#v63zfSm}em+6RK7w+4{=wJ)xxc`a4z1U+_
z#-Xthh0tsa0_TDRh}vE(>5G~LL0VzvgDljfuvbQh4b`nWG~KRu@KjL-koh$6!)MBg
zvR|t{==pyh@UR^SW?1mK$k8=)CWUI&+#6>V&Qo+QX&p#SHH($2Q{eEd{@AA07yGqm
z5fMmx!vka&(0sT5HKv0D(1LMYb+J9%JKD6A9iae+7ayKKVkRB-2R1yJN5SrYZ)yKm
iMUHyo|Np*ybf0B?+UfC{W!S<o@YB)IS1(bu4*d`P%rG7R

diff --git a/communities/all/resources/tutorials.json b/communities/all/resources/tutorials.json
index 4a9ab568..02264a97 100644
--- a/communities/all/resources/tutorials.json
+++ b/communities/all/resources/tutorials.json
@@ -1,8 +1,5 @@
 [
     {
-        "abbreviations": {
-            "TSDB": "Time Series Database"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -10,8 +7,32 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/monitoring/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/celery/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "mira-miracoli"
+            ],
+            "editing": [
+                "hexylena"
+            ]
+        },
         "contributors": [
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe",
+                    "deNBI"
+                ],
+                "elixir_node": "de",
+                "email": "kuntzm@informatik.uni-freiburg.de",
+                "id": "mira-miracoli",
+                "joined": "2022-07",
+                "matrix": "mira-miracoli:matrix.org",
+                "name": "Mira Kuntz",
+                "orcid": "0000-0003-4302-5091",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mira-miracoli/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mira-miracoli.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
@@ -42,92 +63,56 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/admin/tutorials/monitoring",
+        "dir": "topics/admin/tutorials/celery",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "admin/monitoring",
+        "id": "admin/celery",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": [
-            "Telegraf provides an easy solution to monitor servers",
-            "Galaxy can send metrics to Telegraf",
-            "Telegraf can run arbitrary commands like `gxadmin`, which provides influx formatted output",
-            "InfluxDB can collect metrics from Telegraf",
-            "Use Grafana to visualise these metrics, and monitor their values"
-        ],
+        "key_points": null,
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-08",
+        "mod_date": "2024-02-20",
         "objectives": [
-            "Setup InfluxDB",
-            "Setup Telegraf",
-            "Setup Grafana",
-            "Create several charts"
-        ],
-        "pageviews": 5731953,
-        "pub_date": "2019-01-31",
-        "questions": [
-            "How to monitor Galaxy with Telegraf",
-            "How do I set up InfluxDB",
-            "How can I make graphs in Grafana?",
-            "How can I best alert on important metrics?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "shiltemann",
-                    "hexylena"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "73M",
-                "speakers": [],
-                "youtube_id": "drUaYQtMBLY"
-            }
+            "Have an understanding of what Celery is and how it works",
+            "Install Redis",
+            "Configure and start Celery workers",
+            "Install Flower to the Galaxy venv and configure it",
+            "Use an Ansible playbook for all of the above.",
+            "Monitor a Celery task using the Flower dashboard"
         ],
+        "pageviews": 3076381,
+        "pub_date": "2022-07-16",
+        "questions": null,
         "requirements": [
             {
                 "topic_name": "admin",
                 "tutorials": [
                     "ansible",
                     "ansible-galaxy",
-                    "gxadmin"
+                    "pulsar"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00015",
+        "short_id": "T00326",
         "short_tools": [],
         "slides": true,
-        "slides_recordings": [
-            {
-                "captioners": [
-                    "hexylena"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "2M",
-                "speakers": [
-                    "awspolly"
-                ],
-                "youtube_id": "qcp9lEUxCGI"
-            }
-        ],
-        "subtopic": "monitoring",
+        "slides_recordings": false,
+        "subtopic": "data",
         "supported_servers": [],
         "symlink": null,
         "tags": [
             "ansible",
-            "monitoring",
             "git-gat"
         ],
-        "time_estimation": "2h",
-        "title": "Galaxy Monitoring with Telegraf and Grafana",
+        "time_estimation": "1h",
+        "title": "Setting up Celery Workers for Galaxy",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -135,21 +120,22 @@
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": true
+            "video": false
         },
-        "tutorial_name": "monitoring",
+        "tutorial_name": "celery",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/monitoring/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/celery/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/monitoring/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/monitoring/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/celery/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/celery/tutorial.json"
         },
-        "version": 45,
-        "video": true,
-        "video_versions": 1,
+        "version": 10,
+        "video": false,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 203,
-        "visitors": 2066415
+        "visit_duration": 228,
+        "visitors": 1277589,
+        "zenodo_link": ""
     },
     {
         "admin_install": {
@@ -159,8 +145,37 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/gxadmin/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/external-auth/tutorial.json",
         "contributors": [
+            {
+                "email": "nate@bx.psu.edu",
+                "id": "natefoo",
+                "joined": "2017-12",
+                "matrix": "natefoo:matrix.org",
+                "name": "Nate Coraor",
+                "orcid": "0000-0001-8083-2963",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
+                "twitter": "natefoo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
+            },
+            {
+                "affiliations": [
+                    "earlham",
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "fediverse": "https://mstdn.science/@nsoranzo",
+                "fediverse_flavor": "mastodon",
+                "id": "nsoranzo",
+                "joined": "2017-09",
+                "linkedin": "nicola-soranzo-7884125",
+                "matrix": "nsoranzo:matrix.org",
+                "name": "Nicola Soranzo",
+                "orcid": "0000-0003-3627-5340",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
+                "twitter": "NicolaSoranzo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
@@ -191,62 +206,59 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/admin/tutorials/gxadmin",
+        "dir": "topics/admin/tutorials/external-auth",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "admin/gxadmin",
+        "id": "admin/external-auth",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "gxadmin is a tool to run common database queries useful for Galaxy admins",
-            "new queries are welcome and easy to contribute"
+            "Remote auth is not complex to set up and can help you meet institutional requirements"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-08",
+        "mod_date": "2022-10-18",
         "objectives": [
-            "Learn gxadmin basics",
-            "See some queries and learn how they help debug production issues"
+            "be familiar with configuring Galaxy to use an upstream (proxy) authentication provider",
+            "be able to log in to your Galaxy server with a file-configured user."
         ],
-        "pageviews": 5728058,
+        "pageviews": 5898193,
         "pub_date": "2019-01-28",
         "questions": [
-            "What is gxadmin",
-            "What can it do?",
-            "How to write a query?"
+            "How can I connect Galaxy with CAS, SAML, etc."
         ],
-        "short_id": "T00009",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": [
+        "redirect_from": [
+            "/topics/admin/tutorials/upstream-auth/tutorial",
+            "/short/admin/external-auth",
+            "/short/T00007"
+        ],
+        "requirements": [
             {
-                "captioners": [
-                    "hexylena"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "2M",
-                "speakers": [
-                    "awspolly"
+                "topic_name": "admin",
+                "tutorials": [
+                    "ansible",
+                    "ansible-galaxy"
                 ],
-                "youtube_id": "QFwOgDyFSSA"
+                "type": "internal"
             }
         ],
-        "subtopic": "monitoring",
+        "short_id": "T00007",
+        "short_tools": [],
+        "slides": true,
+        "slides_recordings": false,
+        "subtopic": "features",
         "supported_servers": [],
         "symlink": null,
         "tags": [
-            "monitoring",
-            "ansible",
-            "git-gat"
+            "authentication"
         ],
         "time_estimation": "30m",
-        "title": "Galaxy Monitoring with gxadmin",
+        "title": "External Authentication",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -254,22 +266,21 @@
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": true
+            "video": false
         },
-        "tutorial_name": "gxadmin",
+        "tutorial_name": "external-auth",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/gxadmin/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/external-auth/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/gxadmin/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/gxadmin/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/external-auth/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/external-auth/tutorial.json"
         },
-        "version": 27,
-        "video": true,
-        "video_versions": 1,
+        "version": 14,
+        "video": false,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 321,
-        "visitors": 2064469,
-        "zenodo_link": ""
+        "visit_duration": 199,
+        "visitors": 2134233
     },
     {
         "admin_install": {
@@ -279,41 +290,8 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/interactive-tools/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "natefoo",
-                "slugger70",
-                "hexylena",
-                "abretaud"
-            ],
-            "editing": [
-                "kysrpex"
-            ]
-        },
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/data-library/tutorial.json",
         "contributors": [
-            {
-                "email": "nate@bx.psu.edu",
-                "id": "natefoo",
-                "joined": "2017-12",
-                "matrix": "natefoo:matrix.org",
-                "name": "Nate Coraor",
-                "orcid": "0000-0001-8083-2963",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
-                "twitter": "natefoo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
-            },
-            {
-                "elixir_node": "au",
-                "email": "simon.gladman@unimelb.edu.au",
-                "id": "slugger70",
-                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
-                "joined": "2017-09",
-                "name": "Simon Gladman",
-                "orcid": "0000-0002-6100-4385",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
@@ -345,89 +323,78 @@
             },
             {
                 "affiliations": [
+                    "CINECA-Project",
                     "gallantries",
-                    "eurosciencegateway",
-                    "elixir-europe"
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
                 ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
                 "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
                 "fediverse_flavor": "mastodon",
-                "id": "abretaud",
+                "id": "shiltemann",
                 "joined": "2017-09",
+                "linkedin": "shiltemann",
                 "location": {
-                    "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
                 },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "id": "kysrpex",
-                "joined": "2023-10",
-                "name": "Jos\u00e9 Manuel Dom\u00ednguez",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kysrpex/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/kysrpex.json"
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             }
         ],
-        "dir": "topics/admin/tutorials/interactive-tools",
+        "dir": "topics/admin/tutorials/data-library",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "admin/interactive-tools",
+        "id": "admin/data-library",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Galaxy Interactive Tools run as jobs in largely the same manner as any other Galaxy job",
-            "nginx routes GxIT requests to the GxIT(/GIE) Proxy, which routes them to the node/port on which the GxIT is running",
-            "GxITs require wildcard SSL certificates",
-            "GxITs expose your Galaxy server's user datasets unless configured to use Pulsar"
+            "Data libraries are a great way to share data with groups of users"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-26",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Understand what Galaxy Interactive Tools are and how they work",
-            "Be aware of the security implications of Interactive Tools",
-            "Have a basic understanding of the Interactive Tools (GxIT/GIE) Proxy, its purpose, and configuration",
-            "Be familiar with wildcard SSL certificates and how to get them from Let's Encrypt",
-            "Configure your Galaxy to serve Interactive Tools using an Ansible Playbook",
-            "Start, run, and use an Interactive Tool"
+            "Setup a data library",
+            "Manage permissions",
+            "Import data from disk"
         ],
-        "pageviews": 5729755,
-        "pub_date": "2020-02-27",
+        "pageviews": 5831294,
+        "pub_date": "2021-01-14",
         "questions": [
-            "What are Galaxy Interactive Tools?",
-            "How can I enable Interactive Tools on my Galaxy instance?"
+            "How do data libraries work?",
+            "What are they good for?",
+            "How can I use them?",
+            "How can I setup permissions for them?"
         ],
         "recordings": [
             {
                 "captioners": [
-                    "abretaud",
-                    "hexylena"
+                    "hexylena",
+                    "shiltemann"
                 ],
                 "date": "2021-02-15",
                 "galaxy_version": "21.01",
-                "length": "44M",
+                "length": "22M",
                 "speakers": [
-                    "abretaud"
+                    "shiltemann"
                 ],
-                "youtube_id": "lACsIhnbTbE"
+                "youtube_id": "6BWu29Oiihw"
             }
         ],
         "requirements": [
@@ -436,25 +403,25 @@
                 "tutorials": [
                     "ansible",
                     "ansible-galaxy",
-                    "connect-to-compute-cluster",
-                    "job-destinations"
+                    "tool-management"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00010",
+        "short_id": "T00005",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
-        "subtopic": "features",
+        "subtopic": "data",
         "supported_servers": [],
         "symlink": null,
         "tags": [
             "ansible",
-            "interactive-tools"
+            "storage",
+            "git-gat"
         ],
-        "time_estimation": "2h",
-        "title": "Galaxy Interactive Tools",
+        "time_estimation": "30m",
+        "title": "Data Libraries",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -464,63 +431,41 @@
             "tutorial": [],
             "video": true
         },
-        "tutorial_name": "interactive-tools",
+        "tutorial_name": "data-library",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/interactive-tools/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/data-library/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/interactive-tools/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/interactive-tools/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/data-library/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/data-library/tutorial.json"
         },
-        "version": 24,
+        "version": 32,
         "video": true,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 316,
-        "visitors": 2065601,
-        "zenodo_link": ""
+        "visit_duration": 275,
+        "visitors": 2114956
     },
     {
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "bwa",
-                    "owner": "devteam",
-                    "revisions": "e188dc7a68e6",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "data_manager_bwa_mem_index_builder",
-                    "owner": "devteam",
-                    "revisions": "9e993022c762",
-                    "tool_panel_section_label": "Data Managers",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "data_manager_fetch_genome_dbkeys_all_fasta",
-                    "owner": "devteam",
-                    "revisions": "4d3eff1bc421",
-                    "tool_panel_section_label": "Data Managers",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: data_manager_bwa_mem_index_builder\n  owner: devteam\n  revisions: 9e993022c762\n  tool_panel_section_label: Data Managers\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: data_manager_fetch_genome_dbkeys_all_fasta\n  owner: devteam\n  revisions: 4d3eff1bc421\n  tool_panel_section_label: Data Managers\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/reference-genomes/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "slugger70",
-                "afgane"
-            ],
-            "editing": [
-                "hexylena",
-                "natefoo"
-            ]
+            "tools": []
         },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/uwsgi/tutorial.json",
         "contributors": [
+            {
+                "email": "nate@bx.psu.edu",
+                "id": "natefoo",
+                "joined": "2017-12",
+                "matrix": "natefoo:matrix.org",
+                "name": "Nate Coraor",
+                "orcid": "0000-0001-8083-2963",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
+                "twitter": "natefoo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
+            },
             {
                 "elixir_node": "au",
                 "email": "simon.gladman@unimelb.edu.au",
@@ -531,13 +476,116 @@
                 "orcid": "0000-0002-6100-4385",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
+            }
+        ],
+        "dir": "topics/admin/tutorials/uwsgi",
+        "edam_operation": [],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": false,
+        "id": "admin/uwsgi",
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "layout": "tutorial_slides",
+        "license": "CC-BY-4.0",
+        "logo": "assets/images/gat.png",
+        "mod_date": "2022-03-01",
+        "pageviews": 5897141,
+        "pub_date": "2019-01-28",
+        "short_id": "S00028",
+        "short_tools": [],
+        "slides": true,
+        "slides_recordings": false,
+        "subtopic": "deprecated",
+        "supported_servers": [],
+        "symlink": null,
+        "title": "uWSGI",
+        "tools": [],
+        "topic_name": "admin",
+        "topic_name_human": "Galaxy Server administration",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "uwsgi",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/uwsgi/slides.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/uwsgi/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/uwsgi/slides.json"
+        },
+        "version": 9,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 152,
+        "visitors": 2133582
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/database/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "cz",
+                "email": "marten@bx.psu.edu",
+                "fediverse": "https://mastodon.world/@martenson",
+                "fediverse_flavor": "mastodon",
+                "id": "martenson",
+                "joined": "2017-09",
+                "location": {
+                    "country": "USA",
+                    "lat": 37.0,
+                    "lon": -122.0
+                },
+                "matrix": "martenson:matrix.org",
+                "name": "Martin \u010cech",
+                "orcid": "0000-0002-9318-1781",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/martenson/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/martenson.json"
             },
             {
-                "id": "afgane",
-                "joined": "2018-06",
-                "name": "Enis Afgan",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/afgane/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/afgane.json"
+                "affiliations": [
+                    "earlham",
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "fediverse": "https://mstdn.science/@nsoranzo",
+                "fediverse_flavor": "mastodon",
+                "id": "nsoranzo",
+                "joined": "2017-09",
+                "linkedin": "nicola-soranzo-7884125",
+                "matrix": "nsoranzo:matrix.org",
+                "name": "Nicola Soranzo",
+                "orcid": "0000-0003-3627-5340",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
+                "twitter": "NicolaSoranzo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
+            },
+            {
+                "email": "nate@bx.psu.edu",
+                "id": "natefoo",
+                "joined": "2017-12",
+                "matrix": "natefoo:matrix.org",
+                "name": "Nate Coraor",
+                "orcid": "0000-0001-8083-2963",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
+                "twitter": "natefoo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
             },
             {
                 "affiliations": [
@@ -567,101 +615,54 @@
                 "orcid": "0000-0001-9760-8992",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "email": "nate@bx.psu.edu",
-                "id": "natefoo",
-                "joined": "2017-12",
-                "matrix": "natefoo:matrix.org",
-                "name": "Nate Coraor",
-                "orcid": "0000-0001-8083-2963",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
-                "twitter": "natefoo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
             }
         ],
-        "dir": "topics/admin/tutorials/reference-genomes",
-        "edam_operation": [
-            "Sequence alignment",
-            "Read mapping",
-            "Genome indexing",
-            "Generation"
-        ],
+        "dir": "topics/admin/tutorials/database",
+        "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": true,
-        "id": "admin/reference-genomes",
+        "hands_on": false,
+        "id": "admin/database",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": [
-            "Understand how Galaxy stores and uses its reference data",
-            "Understand how to manually add a reference genome and tool indices if required",
-            "Understand and how to use data managers to make all of this much much easier"
-        ],
-        "layout": "tutorial_hands_on",
+        "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-04-21",
-        "objectives": [
-            "Have an understanding of the way in which Galaxy stores and uses reference data",
-            "Be able to download and use data managers to add a reference genome and its pre-calculated indices into the Galaxy reference data system",
-            "Use an Ansible playbook for all of the above"
-        ],
-        "pageviews": 5727367,
+        "logo": "assets/images/gat.png",
+        "mod_date": "2022-06-16",
+        "pageviews": 5897142,
         "pub_date": "2019-01-28",
-        "questions": null,
-        "requirements": [
-            {
-                "topic_name": "admin",
-                "tutorials": [
-                    "ansible",
-                    "ansible-galaxy"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00329",
-        "short_tools": [
-            "bwa",
-            "bwa_mem_index_builder_data_manager",
-            "data_manager_fetch_genome_all_fasta_dbkey"
-        ],
+        "short_id": "S00008",
+        "short_tools": [],
         "slides": true,
         "slides_recordings": false,
-        "subtopic": "data",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "1h",
-        "title": "Reference Data with Data Managers",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5",
-            "toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/bwa_mem_index_builder_data_manager/0.0.5",
-            "toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.4"
-        ],
+        "title": "Galactic Database",
+        "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": false
+            "video": true
         },
-        "tutorial_name": "reference-genomes",
+        "tutorial_name": "database",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/reference-genomes/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/database/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/reference-genomes/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/reference-genomes/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/database/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/database/slides.json"
         },
-        "version": 7,
-        "video": false,
+        "version": 5,
+        "video": true,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 453,
-        "visitors": 2064122,
-        "zenodo_link": ""
+        "visit_duration": 152,
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -671,107 +672,150 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/galaxy-docker/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/poll-ssa/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "vladvisan"
+            ],
+            "data": [
+                "bernt-matthias",
+                "lldelisle",
+                "hrhotz"
+            ],
+            "editing": [
+                "hexylena"
+            ]
+        },
         "contributors": [
             {
                 "affiliations": [
-                    "gallantries",
-                    "ifb",
+                    "uga"
+                ],
+                "email": "vlad.visan@gmail.com",
+                "id": "vladvisan",
+                "joined": "2023-02",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.19,
+                    "lon": 5.76
+                },
+                "matrix": "vlad.visan:matrix.org",
+                "name": "Vlad Visan",
+                "orcid": "0009-0007-0529-1002",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/vladvisan/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/vladvisan.json"
+            },
+            {
+                "elixir_node": "de",
+                "id": "bernt-matthias",
+                "joined": "2017-09",
+                "name": "Matthias Bernt",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bernt-matthias/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bernt-matthias.json"
+            },
+            {
+                "affiliations": [
                     "elixir-europe"
                 ],
                 "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
+                "elixir_node": "ch",
+                "email": "lucille.delisle@epfl.ch",
+                "id": "lldelisle",
+                "joined": "2019-08",
+                "location": {
+                    "country": "CH",
+                    "lat": 46.52,
+                    "lon": 6.56
+                },
+                "name": "Lucille Delisle",
+                "orcid": "0000-0002-1964-4960",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/lldelisle.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "ch",
+                "email": "hrhotz@googlemail.com",
+                "fediverse": "https://genomic.social/@hrhotz",
                 "fediverse_flavor": "mastodon",
-                "id": "bebatut",
+                "id": "hrhotz",
                 "joined": "2017-09",
-                "linkedin": "berenicebatut",
+                "linkedin": "hans-rudolf-hotz-542b31",
                 "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
+                    "country": "CH",
+                    "lat": 47.57,
+                    "lon": 7.6
                 },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+                "matrix": "hrhotz:matrix.org",
+                "name": "Hans-Rudolf Hotz",
+                "orcid": "0000-0002-2799-424X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hrhotz/",
+                "twitter": "hrhotz",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hrhotz.json"
             },
             {
                 "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
+                    "gallantries",
                     "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
                     "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
-                    "elixir-europe"
+                    "avans-atgm",
+                    "uni-freiburg"
                 ],
-                "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
-                "fediverse_flavor": "mastodon",
-                "id": "bgruening",
+                "id": "hexylena",
                 "joined": "2017-09",
-                "linkedin": "bgruening",
                 "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
                 },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/admin/tutorials/galaxy-docker",
+        "dir": "topics/admin/tutorials/poll-ssa",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": false,
-        "id": "admin/galaxy-docker",
+        "id": "admin/poll-ssa",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": [
-            "Use Docker",
-            "Integrate your tools into Galaxy",
-            "Use Galaxy inside Docker to have a flavoured Galaxy instance"
-        ],
         "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
         "logo": "assets/images/gat.png",
-        "mod_date": "2022-10-18",
-        "objectives": [
-            "Docker basics",
-            "Galaxy Docker image (usage)",
-            "Galaxy Docker (internals)",
-            "Galaxy flavours"
-        ],
-        "pageviews": 5726877,
-        "pub_date": "2016-09-29",
-        "questions": [
-            "Why Docker? What is it?",
-            "How to use Docker?",
-            "How to integrate Galaxy in Docker to facilitate its deployment?"
-        ],
-        "short_id": "S00011",
+        "mod_date": "2024-07-10",
+        "pageviews": 301227,
+        "pub_date": "2024-07-10",
+        "short_id": "S00122",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
+        "subtopic": "maintenance",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "1h",
-        "title": "Docker and Galaxy",
+        "tags": [
+            "deploying",
+            "maintenance",
+            "survey"
+        ],
+        "title": "Galaxy Administrator Time Burden and Technology Usage",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -781,20 +825,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "galaxy-docker",
+        "tutorial_name": "poll-ssa",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/galaxy-docker/slides.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/poll-ssa/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/galaxy-docker/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/galaxy-docker/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/poll-ssa/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/poll-ssa/slides.json"
         },
-        "version": 16,
+        "version": 1,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758,
-        "zenodo_link": ""
+        "visit_duration": 149,
+        "visitors": 124234
     },
     {
         "admin_install": {
@@ -900,7 +943,7 @@
             "Extract a list of tools from a workflow",
             "Install these tools on a given Galaxy"
         ],
-        "pageviews": 5728903,
+        "pageviews": 5899224,
         "pub_date": "2019-01-27",
         "questions": [
             "How to install, update, and maintain Galaxy tools?",
@@ -978,8 +1021,8 @@
         "video": false,
         "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 386,
-        "visitors": 2065110
+        "visit_duration": 384,
+        "visitors": 2134981
     },
     {
         "admin_install": {
@@ -989,7 +1032,7 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/pulsar/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/stuff/tutorial.json",
         "contributors": [
             {
                 "email": "nate@bx.psu.edu",
@@ -1002,6 +1045,37 @@
                 "twitter": "natefoo",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
             },
+            {
+                "affiliations": [
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
+                "fediverse_flavor": "mastodon",
+                "id": "bgruening",
+                "joined": "2017-09",
+                "linkedin": "bgruening",
+                "location": {
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
+                },
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+            },
             {
                 "elixir_node": "au",
                 "email": "simon.gladman@unimelb.edu.au",
@@ -1013,13 +1087,6 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
             },
-            {
-                "id": "mvdbeek",
-                "joined": "2018-06",
-                "name": "Marius van den Beek",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
@@ -1048,143 +1115,48 @@
                 "orcid": "0000-0001-9760-8992",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "gmauro",
-                "joined": "2019-03",
-                "name": "Gianmauro Cuccuru",
-                "orcid": "0000-0002-5335-545X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gmauro/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/gmauro.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe",
-                    "deNBI"
-                ],
-                "elixir_node": "de",
-                "email": "kuntzm@informatik.uni-freiburg.de",
-                "id": "mira-miracoli",
-                "joined": "2022-07",
-                "matrix": "mira-miracoli:matrix.org",
-                "name": "Mira Kuntz",
-                "orcid": "0000-0003-4302-5091",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mira-miracoli/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mira-miracoli.json"
             }
         ],
-        "dir": "topics/admin/tutorials/pulsar",
+        "dir": "topics/admin/tutorials/stuff",
+        "draft": true,
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": true,
-        "id": "admin/pulsar",
+        "hands_on": false,
+        "id": "admin/stuff",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Pulsar allows you to easily add geographically distributed compute resources into your Galaxy instance",
-            "It also works well in situations where the compute resources cannot share storage pools."
+            "Galaxy supports pluggable monitoring extensions.",
+            "Use grafana or the reports webapp to monitor your service."
         ],
-        "layout": "tutorial_hands_on",
+        "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "logo": "assets/images/gat.png",
+        "mod_date": "2023-02-17",
         "objectives": [
-            "Have an understanding of what Pulsar is and how it works",
-            "Install and configure a RabbitMQ message queueing server",
-            "Install and configure a Pulsar server on a remote linux machine",
-            "Be able to get Galaxy to send jobs to a remote Pulsar server"
+            "Learn about different monitoring strategies.",
+            "Setup and start the Galaxy reports app."
         ],
-        "pageviews": 5730429,
-        "pub_date": "2019-01-28",
+        "pageviews": 5897142,
+        "pub_date": "2018-01-07",
         "questions": [
-            "How does pulsar work?",
-            "How can I deploy it?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "hexylena"
-                ],
-                "date": "2021-06-28",
-                "galaxy_version": "21.05",
-                "length": "1H28M",
-                "speakers": [
-                    "slugger70"
-                ],
-                "youtube_id": "f0QdF8NDhsM"
-            },
-            {
-                "captioners": [
-                    "simonbray",
-                    "slugger70"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "57M",
-                "speakers": [
-                    "slugger70"
-                ],
-                "youtube_id": "a7fKJT4Fs9k"
-            }
-        ],
-        "redirect_from": [
-            "/topics/admin/tutorials/heterogeneous-compute/tutorial",
-            "/short/admin/pulsar",
-            "/short/T00017"
-        ],
-        "requirements": [
-            {
-                "topic_name": "admin",
-                "tutorials": [
-                    "ansible",
-                    "ansible-galaxy",
-                    "connect-to-compute-cluster",
-                    "job-destinations",
-                    "cvmfs"
-                ],
-                "type": "internal"
-            },
-            {
-                "title": "A server/VM on which to deploy Pulsar",
-                "type": "none"
-            }
+            "How to monitor a Galaxy service?"
         ],
-        "short_id": "T00017",
+        "short_id": "S00022",
         "short_tools": [],
         "slides": true,
-        "slides_recordings": [
-            {
-                "captioners": [
-                    "shiltemann"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "14M",
-                "speakers": [
-                    "slugger70"
-                ],
-                "youtube_id": "M1-Z_2tuQPI"
-            }
-        ],
-        "subtopic": "jobs",
+        "slides_recordings": false,
         "supported_servers": [],
         "symlink": null,
         "tags": [
-            "ansible",
-            "jobs",
-            "git-gat"
+            "work-in-progress"
         ],
-        "time_estimation": "60m",
-        "title": "Running Jobs on Remote Resources with Pulsar",
+        "time_estimation": "1h",
+        "title": "Server: Other",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -1194,19 +1166,20 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "pulsar",
+        "tutorial_name": "stuff",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/pulsar/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/stuff/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/pulsar/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/pulsar/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/stuff/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/stuff/slides.json"
         },
-        "version": 48,
+        "version": 6,
         "video": false,
-        "video_versions": 2,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 333,
-        "visitors": 2065824
+        "visit_duration": 152,
+        "visitors": 2133582,
+        "zenodo_link": ""
     },
     {
         "admin_install": {
@@ -1216,8 +1189,41 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/empathy/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/interactive-tools/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "natefoo",
+                "slugger70",
+                "hexylena",
+                "abretaud"
+            ],
+            "editing": [
+                "kysrpex"
+            ]
+        },
         "contributors": [
+            {
+                "email": "nate@bx.psu.edu",
+                "id": "natefoo",
+                "joined": "2017-12",
+                "matrix": "natefoo:matrix.org",
+                "name": "Nate Coraor",
+                "orcid": "0000-0001-8083-2963",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
+                "twitter": "natefoo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
+            },
+            {
+                "elixir_node": "au",
+                "email": "simon.gladman@unimelb.edu.au",
+                "id": "slugger70",
+                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
+                "joined": "2017-09",
+                "name": "Simon Gladman",
+                "orcid": "0000-0002-6100-4385",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
@@ -1249,59 +1255,116 @@
             },
             {
                 "affiliations": [
-                    "CINECA-Project",
                     "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
+                    "eurosciencegateway",
+                    "elixir-europe"
                 ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
                 "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
+                "elixir_node": "fr",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
                 "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
+                "id": "abretaud",
                 "joined": "2017-09",
-                "linkedin": "shiltemann",
                 "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
+                    "country": "FR",
+                    "lat": 48.11,
+                    "lon": -1.64
                 },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "elixir_node": "de",
+                "id": "kysrpex",
+                "joined": "2023-10",
+                "name": "Jos\u00e9 Manuel Dom\u00ednguez",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kysrpex/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/kysrpex.json"
             }
         ],
-        "dir": "topics/admin/tutorials/empathy",
+        "dir": "topics/admin/tutorials/interactive-tools",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": false,
-        "id": "admin/empathy",
+        "hands_on": true,
+        "id": "admin/interactive-tools",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "layout": "tutorial_slides",
+        "key_points": [
+            "Galaxy Interactive Tools run as jobs in largely the same manner as any other Galaxy job",
+            "nginx routes GxIT requests to the GxIT(/GIE) Proxy, which routes them to the node/port on which the GxIT is running",
+            "GxITs require wildcard SSL certificates",
+            "GxITs expose your Galaxy server's user datasets unless configured to use Pulsar"
+        ],
+        "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "logo": "assets/images/gat.png",
-        "mod_date": "2021-04-06",
-        "pageviews": 5726878,
-        "pub_date": "2019-01-31",
-        "short_id": "S00009",
+        "mod_date": "2024-09-25",
+        "objectives": [
+            "Understand what Galaxy Interactive Tools are and how they work",
+            "Be aware of the security implications of Interactive Tools",
+            "Have a basic understanding of the Interactive Tools (GxIT/GIE) Proxy, its purpose, and configuration",
+            "Be familiar with wildcard SSL certificates and how to get them from Let's Encrypt",
+            "Configure your Galaxy to serve Interactive Tools using an Ansible Playbook",
+            "Start, run, and use an Interactive Tool"
+        ],
+        "pageviews": 5900082,
+        "pub_date": "2020-02-27",
+        "questions": [
+            "What are Galaxy Interactive Tools?",
+            "How can I enable Interactive Tools on my Galaxy instance?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "abretaud",
+                    "hexylena"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "44M",
+                "speakers": [
+                    "abretaud"
+                ],
+                "youtube_id": "lACsIhnbTbE"
+            }
+        ],
+        "requirements": [
+            {
+                "topic_name": "admin",
+                "tutorials": [
+                    "ansible",
+                    "ansible-galaxy",
+                    "connect-to-compute-cluster",
+                    "job-destinations"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00010",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
+        "subtopic": "features",
         "supported_servers": [],
         "symlink": null,
-        "title": "Empathy",
+        "tags": [
+            "ansible",
+            "interactive-tools"
+        ],
+        "time_estimation": "2h",
+        "title": "Galaxy Interactive Tools",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -1309,23 +1372,27 @@
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": false
+            "video": true
         },
-        "tutorial_name": "empathy",
+        "tutorial_name": "interactive-tools",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/empathy/slides.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/interactive-tools/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/empathy/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/empathy/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/interactive-tools/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/interactive-tools/tutorial.json"
         },
-        "version": 4,
-        "video": false,
-        "video_versions": 0,
+        "version": 25,
+        "video": true,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758
+        "visit_duration": 317,
+        "visitors": 2135477,
+        "zenodo_link": ""
     },
     {
+        "abbreviations": {
+            "WORM": "Write Once Read Many"
+        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -1333,14 +1400,12 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/ansible/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/backup-cleanup/tutorial.json",
         "contributions": {
             "authorship": [
                 "hexylena",
-                "shiltemann"
-            ],
-            "testing": [
-                "vladvisan"
+                "lldelisle",
+                "natefoo"
             ]
         },
         "contributors": [
@@ -1375,123 +1440,105 @@
             },
             {
                 "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
+                    "elixir-europe"
                 ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
                 "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
+                "elixir_node": "ch",
+                "email": "lucille.delisle@epfl.ch",
+                "id": "lldelisle",
+                "joined": "2019-08",
                 "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
+                    "country": "CH",
+                    "lat": 46.52,
+                    "lon": 6.56
                 },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+                "name": "Lucille Delisle",
+                "orcid": "0000-0002-1964-4960",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/lldelisle.json"
             },
             {
-                "affiliations": [
-                    "uga"
-                ],
-                "email": "vlad.visan@gmail.com",
-                "id": "vladvisan",
-                "joined": "2023-02",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.19,
-                    "lon": 5.76
-                },
-                "matrix": "vlad.visan:matrix.org",
-                "name": "Vlad Visan",
-                "orcid": "0009-0007-0529-1002",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/vladvisan/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/vladvisan.json"
+                "email": "nate@bx.psu.edu",
+                "id": "natefoo",
+                "joined": "2017-12",
+                "matrix": "natefoo:matrix.org",
+                "name": "Nate Coraor",
+                "orcid": "0000-0001-8083-2963",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
+                "twitter": "natefoo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
             }
         ],
-        "dir": "topics/admin/tutorials/ansible",
+        "dir": "topics/admin/tutorials/backup-cleanup",
+        "edam_ontology": [
+            "topic_3489",
+            "topic_0605",
+            "topic_3071"
+        ],
         "edam_operation": [],
-        "edam_topic": [],
+        "edam_topic": [
+            "Database management",
+            "Informatics",
+            "Data management"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "admin/ansible",
+        "id": "admin/backup-cleanup",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Ansible lets you do system administration at scale",
-            "Many system administration, software installation, and software management tasks are already available as Ansible tasks or roles"
+            "Use configuration management (e.g. Ansible)",
+            "Store configuration management in git",
+            "Back up the parts of Galaxy that can't be recreated"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-08",
+        "mod_date": "2024-08-09",
         "objectives": [
-            "Learn Ansible basics",
-            "Write a simple role",
-            "Install a role from Ansible Galaxy (repository unrelated to the Galaxy Project)"
+            "Learn about different maintenance steps",
+            "Setup postgres backups",
+            "Setup cleanups",
+            "Learn what to back up and how to recover"
         ],
-        "pageviews": 5737371,
-        "pub_date": "2018-07-11",
+        "pageviews": 5897653,
+        "pub_date": "2019-01-31",
         "questions": [
-            "Why Ansible?",
-            "How and when to use Ansible?",
-            "How to write a role?",
-            "How to leverage community build roles?"
+            "How can I back up my Galaxy?",
+            "What data should be included?",
+            "How can I ensure jobs get cleaned up appropriately?",
+            "How do I maintain a Galaxy server?",
+            "What happens if I lose everything?"
         ],
-        "recordings": [
+        "requirements": [
             {
-                "captioners": [
-                    "martenson"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "61M",
-                "speakers": [
-                    "martenson"
+                "topic_name": "admin",
+                "tutorials": [
+                    "ansible-galaxy"
                 ],
-                "youtube_id": "2KdT0sYKUeE"
+                "type": "internal"
+            },
+            {
+                "title": "A VM with at least 2 vCPUs and 4 GB RAM, preferably running Ubuntu 18.04 - 20.04.",
+                "type": "none"
             }
         ],
-        "short_id": "T00000",
+        "short_id": "T00324",
         "short_tools": [],
         "slides": true,
-        "slides_recordings": [
-            {
-                "captioners": [
-                    "martenson"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "5M",
-                "speakers": [
-                    "jdavcs"
-                ],
-                "youtube_id": "KFpbfmN0OTE"
-            }
-        ],
-        "subtopic": "core",
+        "slides_recordings": false,
+        "subtopic": "maintenance",
         "supported_servers": [],
         "symlink": null,
         "tags": [
-            "ansible"
+            "ansible",
+            "deploying",
+            "git-gat"
         ],
-        "time_estimation": "60m",
-        "title": "Ansible",
+        "time_estimation": "30m",
+        "title": "Server Maintenance: Cleanup, Backup, and Restoration",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -1501,20 +1548,19 @@
             "tutorial": [],
             "video": true
         },
-        "tutorial_name": "ansible",
+        "tutorial_name": "backup-cleanup",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/ansible/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/backup-cleanup/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/ansible/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/ansible/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/backup-cleanup/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/backup-cleanup/tutorial.json"
         },
-        "version": 48,
+        "version": 5,
         "video": true,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 251,
-        "visitors": 2069384,
-        "zenodo_link": ""
+        "visit_duration": 755,
+        "visitors": 2133958
     },
     {
         "admin_install": {
@@ -1524,18 +1570,18 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/cvmfs/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/object-store/tutorial.json",
         "contributors": [
             {
-                "elixir_node": "au",
-                "email": "simon.gladman@unimelb.edu.au",
-                "id": "slugger70",
-                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
-                "joined": "2017-09",
-                "name": "Simon Gladman",
-                "orcid": "0000-0002-6100-4385",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
+                "email": "nate@bx.psu.edu",
+                "id": "natefoo",
+                "joined": "2017-12",
+                "matrix": "natefoo:matrix.org",
+                "name": "Nate Coraor",
+                "orcid": "0000-0001-8083-2963",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
+                "twitter": "natefoo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
             },
             {
                 "affiliations": [
@@ -1565,45 +1611,47 @@
                 "orcid": "0000-0001-9760-8992",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "gmauro",
+                "joined": "2019-03",
+                "name": "Gianmauro Cuccuru",
+                "orcid": "0000-0002-5335-545X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gmauro/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/gmauro.json"
             }
         ],
-        "dir": "topics/admin/tutorials/cvmfs",
+        "dir": "topics/admin/tutorials/object-store",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "admin/cvmfs",
+        "id": "admin/object-store",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": null,
+        "key_points": [
+            "The distributed object store configuration allows you to easily expand that storage that is attached to your Galaxy.",
+            "You can move data around without affecting users."
+        ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-08",
+        "mod_date": "2024-06-25",
         "objectives": [
-            "Have an understanding of what CVMFS is and how it works",
-            "Install and configure the CVMFS client on a linux machine and mount the Galaxy reference data repository",
-            "Configure your Galaxy to use these reference genomes and indices",
-            "Use an Ansible playbook for all of the above."
+            "Setup Galaxy with both the Hierarachical and Distributed Object Storages"
         ],
-        "pageviews": 5729458,
-        "pub_date": "2019-01-27",
-        "questions": null,
-        "recordings": [
-            {
-                "captioners": [
-                    "slugger70"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "23M",
-                "speakers": [
-                    "slugger70"
-                ],
-                "youtube_id": "X3iFMZP_fQ8"
-            }
+        "pageviews": 5899105,
+        "pub_date": "2019-01-28",
+        "questions": [
+            "How does Galaxy locate data?",
+            "How can I have Galaxy use multiple storage locations?"
         ],
         "requirements": [
             {
@@ -1615,21 +1663,21 @@
                 "type": "internal"
             }
         ],
-        "short_id": "T00003",
+        "short_id": "T00016",
         "short_tools": [],
         "slides": true,
         "slides_recordings": [
             {
                 "captioners": [
-                    "hexylena"
+                    "cat-bro"
                 ],
                 "date": "2021-02-15",
                 "galaxy_version": "21.01",
-                "length": "3M",
+                "length": "18M",
                 "speakers": [
-                    "awspolly"
+                    "gmauro"
                 ],
-                "youtube_id": "g_cavAO-fBM"
+                "youtube_id": "Hv2bvjk5sjE"
             }
         ],
         "subtopic": "data",
@@ -1637,10 +1685,10 @@
         "symlink": null,
         "tags": [
             "ansible",
-            "git-gat"
+            "storage"
         ],
-        "time_estimation": "1h",
-        "title": "Reference Data with CVMFS",
+        "time_estimation": "30m",
+        "title": "Distributed Object Storage",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -1648,27 +1696,21 @@
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": true
+            "video": false
         },
-        "tutorial_name": "cvmfs",
+        "tutorial_name": "object-store",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/cvmfs/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/object-store/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/cvmfs/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/cvmfs/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/object-store/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/object-store/tutorial.json"
         },
-        "version": 49,
-        "video": true,
+        "version": 27,
+        "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 347,
-        "visitors": 2065420,
-        "voice": {
-            "id": "Olivia",
-            "lang": "en-AU",
-            "neural": true
-        },
-        "zenodo_link": ""
+        "visit_duration": 245,
+        "visitors": 2134797
     },
     {
         "admin_install": {
@@ -1678,90 +1720,8 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/poll-ssa/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "vladvisan"
-            ],
-            "data": [
-                "bernt-matthias",
-                "lldelisle",
-                "hrhotz"
-            ],
-            "editing": [
-                "hexylena"
-            ]
-        },
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/empathy/tutorial.json",
         "contributors": [
-            {
-                "affiliations": [
-                    "uga"
-                ],
-                "email": "vlad.visan@gmail.com",
-                "id": "vladvisan",
-                "joined": "2023-02",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.19,
-                    "lon": 5.76
-                },
-                "matrix": "vlad.visan:matrix.org",
-                "name": "Vlad Visan",
-                "orcid": "0009-0007-0529-1002",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/vladvisan/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/vladvisan.json"
-            },
-            {
-                "elixir_node": "de",
-                "id": "bernt-matthias",
-                "joined": "2017-09",
-                "name": "Matthias Bernt",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bernt-matthias/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bernt-matthias.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "ch",
-                "email": "lucille.delisle@epfl.ch",
-                "id": "lldelisle",
-                "joined": "2019-08",
-                "location": {
-                    "country": "CH",
-                    "lat": 46.52,
-                    "lon": 6.56
-                },
-                "name": "Lucille Delisle",
-                "orcid": "0000-0002-1964-4960",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/lldelisle.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "ch",
-                "email": "hrhotz@googlemail.com",
-                "fediverse": "https://genomic.social/@hrhotz",
-                "fediverse_flavor": "mastodon",
-                "id": "hrhotz",
-                "joined": "2017-09",
-                "linkedin": "hans-rudolf-hotz-542b31",
-                "location": {
-                    "country": "CH",
-                    "lat": 47.57,
-                    "lon": 7.6
-                },
-                "matrix": "hrhotz:matrix.org",
-                "name": "Hans-Rudolf Hotz",
-                "orcid": "0000-0002-2799-424X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hrhotz/",
-                "twitter": "hrhotz",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hrhotz.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
@@ -1790,15 +1750,45 @@
                 "orcid": "0000-0001-9760-8992",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             }
         ],
-        "dir": "topics/admin/tutorials/poll-ssa",
+        "dir": "topics/admin/tutorials/empathy",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": false,
-        "id": "admin/poll-ssa",
+        "id": "admin/empathy",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
@@ -1806,22 +1796,16 @@
         "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
         "logo": "assets/images/gat.png",
-        "mod_date": "2024-07-10",
-        "pageviews": 130963,
-        "pub_date": "2024-07-10",
-        "short_id": "S00122",
+        "mod_date": "2021-04-06",
+        "pageviews": 5897143,
+        "pub_date": "2019-01-31",
+        "short_id": "S00009",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
-        "subtopic": "maintenance",
         "supported_servers": [],
         "symlink": null,
-        "tags": [
-            "deploying",
-            "maintenance",
-            "survey"
-        ],
-        "title": "Galaxy Administrator Time Burden and Technology Usage",
+        "title": "Empathy",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -1831,19 +1815,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "poll-ssa",
+        "tutorial_name": "empathy",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/poll-ssa/slides.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/empathy/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/poll-ssa/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/poll-ssa/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/empathy/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/empathy/slides.json"
         },
-        "version": 1,
+        "version": 4,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 144,
-        "visitors": 54203
+        "visit_duration": 152,
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -1853,56 +1837,127 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/users-groups-quotas/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/cloudbursting/tutorial.json",
+        "contributors": [
+            {
+                "elixir_node": "au",
+                "email": "simon.gladman@unimelb.edu.au",
+                "id": "slugger70",
+                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
+                "joined": "2017-09",
+                "name": "Simon Gladman",
+                "orcid": "0000-0002-6100-4385",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
+            }
+        ],
+        "dir": "topics/admin/tutorials/cloudbursting",
+        "edam_operation": [],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": false,
+        "id": "admin/cloudbursting",
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "layout": "tutorial_slides",
+        "license": "CC-BY-4.0",
+        "logo": "assets/images/gat.png",
+        "mod_date": "2022-03-01",
+        "pageviews": 5897143,
+        "pub_date": "2019-01-31",
+        "short_id": "S00004",
+        "short_tools": [],
+        "slides": true,
+        "slides_recordings": false,
+        "subtopic": "cloud",
+        "supported_servers": [],
+        "symlink": null,
+        "title": "Galaxy on the Cloud",
+        "tools": [],
+        "topic_name": "admin",
+        "topic_name_human": "Galaxy Server administration",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "cloudbursting",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/cloudbursting/slides.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/cloudbursting/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/cloudbursting/slides.json"
+        },
+        "version": 6,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 152,
+        "visitors": 2133582
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "bwa",
+                    "owner": "devteam",
+                    "revisions": "e188dc7a68e6",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "data_manager_bwa_mem_index_builder",
+                    "owner": "devteam",
+                    "revisions": "9e993022c762",
+                    "tool_panel_section_label": "Data Managers",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "data_manager_fetch_genome_dbkeys_all_fasta",
+                    "owner": "devteam",
+                    "revisions": "4d3eff1bc421",
+                    "tool_panel_section_label": "Data Managers",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: data_manager_bwa_mem_index_builder\n  owner: devteam\n  revisions: 9e993022c762\n  tool_panel_section_label: Data Managers\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: data_manager_fetch_genome_dbkeys_all_fasta\n  owner: devteam\n  revisions: 4d3eff1bc421\n  tool_panel_section_label: Data Managers\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/reference-genomes/tutorial.json",
         "contributions": {
             "authorship": [
-                "natefoo",
-                "bgruening",
-                "hexylena"
+                "slugger70",
+                "afgane"
+            ],
+            "editing": [
+                "hexylena",
+                "natefoo"
             ]
         },
         "contributors": [
             {
-                "email": "nate@bx.psu.edu",
-                "id": "natefoo",
-                "joined": "2017-12",
-                "matrix": "natefoo:matrix.org",
-                "name": "Nate Coraor",
-                "orcid": "0000-0001-8083-2963",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
-                "twitter": "natefoo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
+                "elixir_node": "au",
+                "email": "simon.gladman@unimelb.edu.au",
+                "id": "slugger70",
+                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
+                "joined": "2017-09",
+                "name": "Simon Gladman",
+                "orcid": "0000-0002-6100-4385",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
             },
             {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
-                "fediverse_flavor": "mastodon",
-                "id": "bgruening",
-                "joined": "2017-09",
-                "linkedin": "bgruening",
-                "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
-                },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+                "id": "afgane",
+                "joined": "2018-06",
+                "name": "Enis Afgan",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/afgane/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/afgane.json"
             },
             {
                 "affiliations": [
@@ -1932,101 +1987,106 @@
                 "orcid": "0000-0001-9760-8992",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "email": "nate@bx.psu.edu",
+                "id": "natefoo",
+                "joined": "2017-12",
+                "matrix": "natefoo:matrix.org",
+                "name": "Nate Coraor",
+                "orcid": "0000-0001-8083-2963",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
+                "twitter": "natefoo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
             }
         ],
-        "dir": "topics/admin/tutorials/users-groups-quotas",
-        "edam_operation": [],
+        "dir": "topics/admin/tutorials/reference-genomes",
+        "edam_operation": [
+            "Generation",
+            "Sequence alignment",
+            "Genome indexing",
+            "Read mapping"
+        ],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": false,
-        "id": "admin/users-groups-quotas",
+        "hands_on": true,
+        "id": "admin/reference-genomes",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Galaxy has a powerful user and group managment system that can be utilized for Quota management."
+            "Understand how Galaxy stores and uses its reference data",
+            "Understand how to manually add a reference genome and tool indices if required",
+            "Understand and how to use data managers to make all of this much much easier"
         ],
-        "layout": "tutorial_slides",
+        "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "logo": "assets/images/gat.png",
-        "mod_date": "2024-08-08",
+        "mod_date": "2023-04-21",
         "objectives": [
-            "Learn the Galaxy user/group management and assign Quotas.",
-            "Understand the Role Based Access Control (RBAC) of Galaxy."
-        ],
-        "pageviews": 5726878,
-        "pub_date": "2018-01-07",
-        "questions": [
-            "How does Galaxy manage users and groups?",
-            "How can I assign Quotas to specific users/groups?",
-            "How should I manage groups vs roles",
-            "What authentication methods are available?",
-            "How is dataset privacy managed?",
-            "Authentication Systems, what is available and how can I enable it?"
+            "Have an understanding of the way in which Galaxy stores and uses reference data",
+            "Be able to download and use data managers to add a reference genome and its pre-calculated indices into the Galaxy reference data system",
+            "Use an Ansible playbook for all of the above"
         ],
-        "recordings": [
+        "pageviews": 5897655,
+        "pub_date": "2019-01-28",
+        "questions": null,
+        "requirements": [
             {
-                "captioners": [
-                    "hexylena"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "4M",
-                "speakers": [
-                    "awspolly"
+                "topic_name": "admin",
+                "tutorials": [
+                    "ansible",
+                    "ansible-galaxy"
                 ],
-                "youtube_id": "crywu31L8qg"
+                "type": "internal"
             }
         ],
-        "short_id": "S00027",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": [
-            {
-                "captioners": [
-                    "hexylena"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "4M",
-                "speakers": [
-                    "awspolly"
-                ],
-                "youtube_id": "crywu31L8qg"
-            }
+        "short_id": "T00329",
+        "short_tools": [
+            "bwa",
+            "data_manager_fetch_genome_all_fasta_dbkey",
+            "bwa_mem_index_builder_data_manager"
         ],
-        "subtopic": "maintenance",
+        "slides": true,
+        "slides_recordings": false,
+        "subtopic": "data",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "15m",
-        "title": "User, Role, Group, Quota, and Authentication managment",
-        "tools": [],
+        "time_estimation": "1h",
+        "title": "Reference Data with Data Managers",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.5",
+            "toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/bwa_mem_index_builder_data_manager/0.0.5",
+            "toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.4"
+        ],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": true
+            "video": false
         },
-        "tutorial_name": "users-groups-quotas",
+        "tutorial_name": "reference-genomes",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/users-groups-quotas/slides.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/reference-genomes/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/users-groups-quotas/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/users-groups-quotas/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/reference-genomes/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/reference-genomes/tutorial.json"
         },
-        "version": 19,
-        "video": true,
-        "video_versions": 1,
+        "version": 7,
+        "video": false,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758,
+        "visit_duration": 447,
+        "visitors": 2133965,
         "zenodo_link": ""
     },
     {
+        "abbreviations": {
+            "TSDB": "Time Series Database"
+        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -2034,7 +2094,7 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/data-library/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/monitoring/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
@@ -2064,81 +2124,54 @@
                 "orcid": "0000-0001-9760-8992",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             }
         ],
-        "dir": "topics/admin/tutorials/data-library",
+        "dir": "topics/admin/tutorials/monitoring",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "admin/data-library",
+        "id": "admin/monitoring",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Data libraries are a great way to share data with groups of users"
+            "Telegraf provides an easy solution to monitor servers",
+            "Galaxy can send metrics to Telegraf",
+            "Telegraf can run arbitrary commands like `gxadmin`, which provides influx formatted output",
+            "InfluxDB can collect metrics from Telegraf",
+            "Use Grafana to visualise these metrics, and monitor their values"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-08-08",
         "objectives": [
-            "Setup a data library",
-            "Manage permissions",
-            "Import data from disk"
+            "Setup InfluxDB",
+            "Setup Telegraf",
+            "Setup Grafana",
+            "Create several charts"
         ],
-        "pageviews": 5660754,
-        "pub_date": "2021-01-14",
+        "pageviews": 5902242,
+        "pub_date": "2019-01-31",
         "questions": [
-            "How do data libraries work?",
-            "What are they good for?",
-            "How can I use them?",
-            "How can I setup permissions for them?"
+            "How to monitor Galaxy with Telegraf",
+            "How do I set up InfluxDB",
+            "How can I make graphs in Grafana?",
+            "How can I best alert on important metrics?"
         ],
         "recordings": [
             {
                 "captioners": [
-                    "hexylena",
-                    "shiltemann"
+                    "shiltemann",
+                    "hexylena"
                 ],
                 "date": "2021-02-15",
                 "galaxy_version": "21.01",
-                "length": "22M",
-                "speakers": [
-                    "shiltemann"
-                ],
-                "youtube_id": "6BWu29Oiihw"
+                "length": "73M",
+                "speakers": [],
+                "youtube_id": "drUaYQtMBLY"
             }
         ],
         "requirements": [
@@ -2147,25 +2180,38 @@
                 "tutorials": [
                     "ansible",
                     "ansible-galaxy",
-                    "tool-management"
+                    "gxadmin"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00005",
+        "short_id": "T00015",
         "short_tools": [],
         "slides": true,
-        "slides_recordings": false,
-        "subtopic": "data",
+        "slides_recordings": [
+            {
+                "captioners": [
+                    "hexylena"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "2M",
+                "speakers": [
+                    "awspolly"
+                ],
+                "youtube_id": "qcp9lEUxCGI"
+            }
+        ],
+        "subtopic": "monitoring",
         "supported_servers": [],
         "symlink": null,
         "tags": [
             "ansible",
-            "storage",
+            "monitoring",
             "git-gat"
         ],
-        "time_estimation": "30m",
-        "title": "Data Libraries",
+        "time_estimation": "2h",
+        "title": "Galaxy Monitoring with Telegraf and Grafana",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -2175,19 +2221,19 @@
             "tutorial": [],
             "video": true
         },
-        "tutorial_name": "data-library",
+        "tutorial_name": "monitoring",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/data-library/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/monitoring/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/data-library/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/data-library/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/monitoring/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/monitoring/tutorial.json"
         },
-        "version": 32,
+        "version": 45,
         "video": true,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 278,
-        "visitors": 2044055
+        "visit_duration": 203,
+        "visitors": 2136259
     },
     {
         "admin_install": {
@@ -2197,7 +2243,7 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/systemd-supervisor/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/production/tutorial.json",
         "contributors": [
             {
                 "email": "nate@bx.psu.edu",
@@ -2210,43 +2256,52 @@
                 "twitter": "natefoo",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
             },
+            {
+                "id": "blankenberg",
+                "joined": "2018-07",
+                "name": "Daniel Blankenberg",
+                "orcid": "0000-0002-6833-9049",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankenberg/",
+                "twitter": "dblankenberg",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankenberg.json"
+            },
+            {
+                "id": "abdulrahmanazab",
+                "joined": "2019-01",
+                "name": "Abdulrahman Azab",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abdulrahmanazab/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abdulrahmanazab.json"
+            },
             {
                 "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
+                    "elixir-europe"
                 ],
-                "id": "hexylena",
+                "contact_for_training": true,
+                "elixir_node": "cz",
+                "email": "marten@bx.psu.edu",
+                "fediverse": "https://mastodon.world/@martenson",
+                "fediverse_flavor": "mastodon",
+                "id": "martenson",
                 "joined": "2017-09",
                 "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
+                    "country": "USA",
+                    "lat": 37.0,
+                    "lon": -122.0
                 },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+                "matrix": "martenson:matrix.org",
+                "name": "Martin \u010cech",
+                "orcid": "0000-0002-9318-1781",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/martenson/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/martenson.json"
             }
         ],
-        "dir": "topics/admin/tutorials/systemd-supervisor",
+        "dir": "topics/admin/tutorials/production",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": false,
-        "id": "admin/systemd-supervisor",
+        "id": "admin/production",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
@@ -2255,16 +2310,16 @@
         "license": "CC-BY-4.0",
         "logo": "assets/images/gat.png",
         "mod_date": "2023-04-16",
-        "pageviews": 5726878,
+        "pageviews": 5897146,
         "pub_date": "2019-01-28",
-        "short_id": "S00023",
+        "short_id": "S00019",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
-        "subtopic": "deprecated",
+        "subtopic": "maintenance",
         "supported_servers": [],
         "symlink": null,
-        "title": "Controlling Galaxy with systemd or Supervisor",
+        "title": "Gearing towards production",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -2274,19 +2329,19 @@
             "tutorial": [],
             "video": true
         },
-        "tutorial_name": "systemd-supervisor",
+        "tutorial_name": "production",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/systemd-supervisor/slides.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/production/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/systemd-supervisor/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/systemd-supervisor/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/production/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/production/slides.json"
         },
-        "version": 5,
+        "version": 9,
         "video": true,
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2063758
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -2296,281 +2351,35 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/database/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/users-groups-quotas/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "natefoo",
+                "bgruening",
+                "hexylena"
+            ]
+        },
         "contributors": [
+            {
+                "email": "nate@bx.psu.edu",
+                "id": "natefoo",
+                "joined": "2017-12",
+                "matrix": "natefoo:matrix.org",
+                "name": "Nate Coraor",
+                "orcid": "0000-0001-8083-2963",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
+                "twitter": "natefoo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
+            },
             {
                 "affiliations": [
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "cz",
-                "email": "marten@bx.psu.edu",
-                "fediverse": "https://mastodon.world/@martenson",
-                "fediverse_flavor": "mastodon",
-                "id": "martenson",
-                "joined": "2017-09",
-                "location": {
-                    "country": "USA",
-                    "lat": 37.0,
-                    "lon": -122.0
-                },
-                "matrix": "martenson:matrix.org",
-                "name": "Martin \u010cech",
-                "orcid": "0000-0002-9318-1781",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/martenson/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/martenson.json"
-            },
-            {
-                "affiliations": [
-                    "earlham",
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "fediverse": "https://mstdn.science/@nsoranzo",
-                "fediverse_flavor": "mastodon",
-                "id": "nsoranzo",
-                "joined": "2017-09",
-                "linkedin": "nicola-soranzo-7884125",
-                "matrix": "nsoranzo:matrix.org",
-                "name": "Nicola Soranzo",
-                "orcid": "0000-0003-3627-5340",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
-                "twitter": "NicolaSoranzo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
-            },
-            {
-                "email": "nate@bx.psu.edu",
-                "id": "natefoo",
-                "joined": "2017-12",
-                "matrix": "natefoo:matrix.org",
-                "name": "Nate Coraor",
-                "orcid": "0000-0001-8083-2963",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
-                "twitter": "natefoo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            }
-        ],
-        "dir": "topics/admin/tutorials/database",
-        "edam_operation": [],
-        "edam_topic": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": false,
-        "id": "admin/database",
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "layout": "tutorial_slides",
-        "license": "CC-BY-4.0",
-        "logo": "assets/images/gat.png",
-        "mod_date": "2022-06-16",
-        "pageviews": 5726878,
-        "pub_date": "2019-01-28",
-        "short_id": "S00008",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
-        "supported_servers": [],
-        "symlink": null,
-        "title": "Galactic Database",
-        "tools": [],
-        "topic_name": "admin",
-        "topic_name_human": "Galaxy Server administration",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": true
-        },
-        "tutorial_name": "database",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/database/slides.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/database/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/database/slides.json"
-        },
-        "version": 5,
-        "video": true,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/production/tutorial.json",
-        "contributors": [
-            {
-                "email": "nate@bx.psu.edu",
-                "id": "natefoo",
-                "joined": "2017-12",
-                "matrix": "natefoo:matrix.org",
-                "name": "Nate Coraor",
-                "orcid": "0000-0001-8083-2963",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
-                "twitter": "natefoo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
-            },
-            {
-                "id": "blankenberg",
-                "joined": "2018-07",
-                "name": "Daniel Blankenberg",
-                "orcid": "0000-0002-6833-9049",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankenberg/",
-                "twitter": "dblankenberg",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankenberg.json"
-            },
-            {
-                "id": "abdulrahmanazab",
-                "joined": "2019-01",
-                "name": "Abdulrahman Azab",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abdulrahmanazab/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abdulrahmanazab.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "cz",
-                "email": "marten@bx.psu.edu",
-                "fediverse": "https://mastodon.world/@martenson",
-                "fediverse_flavor": "mastodon",
-                "id": "martenson",
-                "joined": "2017-09",
-                "location": {
-                    "country": "USA",
-                    "lat": 37.0,
-                    "lon": -122.0
-                },
-                "matrix": "martenson:matrix.org",
-                "name": "Martin \u010cech",
-                "orcid": "0000-0002-9318-1781",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/martenson/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/martenson.json"
-            }
-        ],
-        "dir": "topics/admin/tutorials/production",
-        "edam_operation": [],
-        "edam_topic": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": false,
-        "id": "admin/production",
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "layout": "tutorial_slides",
-        "license": "CC-BY-4.0",
-        "logo": "assets/images/gat.png",
-        "mod_date": "2023-04-16",
-        "pageviews": 5726878,
-        "pub_date": "2019-01-28",
-        "short_id": "S00019",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
-        "subtopic": "maintenance",
-        "supported_servers": [],
-        "symlink": null,
-        "title": "Gearing towards production",
-        "tools": [],
-        "topic_name": "admin",
-        "topic_name_human": "Galaxy Server administration",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": true
-        },
-        "tutorial_name": "production",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/production/slides.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/production/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/production/slides.json"
-        },
-        "version": 9,
-        "video": true,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/introduction/tutorial.json",
-        "contributors": [
-            {
-                "id": "valentinmarcon",
-                "joined": "2017-09",
-                "name": "Valentin Marcon",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/valentinmarcon/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/valentinmarcon.json"
-            },
-            {
-                "email": "nate@bx.psu.edu",
-                "id": "natefoo",
-                "joined": "2017-12",
-                "matrix": "natefoo:matrix.org",
-                "name": "Nate Coraor",
-                "orcid": "0000-0001-8083-2963",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
-                "twitter": "natefoo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
-            },
-            {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
                     "elixir-europe"
                 ],
                 "contact_for_training": true,
@@ -2623,225 +2432,74 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/admin/tutorials/introduction",
+        "dir": "topics/admin/tutorials/users-groups-quotas",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": false,
-        "id": "admin/introduction",
+        "id": "admin/users-groups-quotas",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Galaxy is scalable from personal computers to huge HPC and cloud-instances.",
-            "Amount of expected users, types of common tasks, and storage capabilities have a big impact on the deployment."
+            "Galaxy has a powerful user and group managment system that can be utilized for Quota management."
         ],
-        "layout": "introduction_slides",
+        "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
         "logo": "assets/images/gat.png",
-        "mod_date": "2024-06-25",
+        "mod_date": "2024-08-08",
         "objectives": [
-            "Learn about different options about Galaxy deployment.",
-            "Make an educated decision about your preferred deployment model."
+            "Learn the Galaxy user/group management and assign Quotas.",
+            "Understand the Role Based Access Control (RBAC) of Galaxy."
         ],
-        "pageviews": 5726878,
-        "priority": 1,
-        "pub_date": "2017-06-12",
+        "pageviews": 5897146,
+        "pub_date": "2018-01-07",
         "questions": [
-            "What options to deploy Galaxy do I have?",
-            "Which platforms are supported by Galaxy?",
-            "What requirements does Galaxy have?"
-        ],
-        "redirect_from": [
-            "/topics/admin/slides/introduction",
-            "/short/admin/introduction/slides",
-            "/short/S00015"
+            "How does Galaxy manage users and groups?",
+            "How can I assign Quotas to specific users/groups?",
+            "How should I manage groups vs roles",
+            "What authentication methods are available?",
+            "How is dataset privacy managed?",
+            "Authentication Systems, what is available and how can I enable it?"
         ],
-        "short_id": "S00015",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
-        "subtopic": "core",
-        "supported_servers": [],
-        "symlink": null,
-        "time_estimation": "20m",
-        "title": "Galaxy from an administrator's point of view",
-        "tools": [],
-        "topic_name": "admin",
-        "topic_name_human": "Galaxy Server administration",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "introduction",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/introduction/slides.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/introduction/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/introduction/slides.json"
-        },
-        "version": 6,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758,
-        "zenodo_link": ""
-    },
-    {
-        "abbreviations": {
-            "WORM": "Write Once Read Many"
-        },
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/backup-cleanup/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "hexylena",
-                "lldelisle",
-                "natefoo"
-            ]
-        },
-        "contributors": [
+        "recordings": [
             {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
+                "captioners": [
+                    "hexylena"
                 ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "4M",
+                "speakers": [
+                    "awspolly"
                 ],
-                "contact_for_training": true,
-                "elixir_node": "ch",
-                "email": "lucille.delisle@epfl.ch",
-                "id": "lldelisle",
-                "joined": "2019-08",
-                "location": {
-                    "country": "CH",
-                    "lat": 46.52,
-                    "lon": 6.56
-                },
-                "name": "Lucille Delisle",
-                "orcid": "0000-0002-1964-4960",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/lldelisle.json"
-            },
-            {
-                "email": "nate@bx.psu.edu",
-                "id": "natefoo",
-                "joined": "2017-12",
-                "matrix": "natefoo:matrix.org",
-                "name": "Nate Coraor",
-                "orcid": "0000-0001-8083-2963",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
-                "twitter": "natefoo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
+                "youtube_id": "crywu31L8qg"
             }
         ],
-        "dir": "topics/admin/tutorials/backup-cleanup",
-        "edam_ontology": [
-            "topic_3489",
-            "topic_0605",
-            "topic_3071"
-        ],
-        "edam_operation": [],
-        "edam_topic": [
-            "Database management",
-            "Informatics",
-            "Data management"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "admin/backup-cleanup",
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Use configuration management (e.g. Ansible)",
-            "Store configuration management in git",
-            "Back up the parts of Galaxy that can't be recreated"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-08-09",
-        "objectives": [
-            "Learn about different maintenance steps",
-            "Setup postgres backups",
-            "Setup cleanups",
-            "Learn what to back up and how to recover"
-        ],
-        "pageviews": 5727341,
-        "pub_date": "2019-01-31",
-        "questions": [
-            "How can I back up my Galaxy?",
-            "What data should be included?",
-            "How can I ensure jobs get cleaned up appropriately?",
-            "How do I maintain a Galaxy server?",
-            "What happens if I lose everything?"
-        ],
-        "requirements": [
+        "short_id": "S00027",
+        "short_tools": [],
+        "slides": true,
+        "slides_recordings": [
             {
-                "topic_name": "admin",
-                "tutorials": [
-                    "ansible-galaxy"
+                "captioners": [
+                    "hexylena"
                 ],
-                "type": "internal"
-            },
-            {
-                "title": "A VM with at least 2 vCPUs and 4 GB RAM, preferably running Ubuntu 18.04 - 20.04.",
-                "type": "none"
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "4M",
+                "speakers": [
+                    "awspolly"
+                ],
+                "youtube_id": "crywu31L8qg"
             }
         ],
-        "short_id": "T00324",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
         "subtopic": "maintenance",
         "supported_servers": [],
         "symlink": null,
-        "tags": [
-            "ansible",
-            "deploying",
-            "git-gat"
-        ],
-        "time_estimation": "30m",
-        "title": "Server Maintenance: Cleanup, Backup, and Restoration",
+        "time_estimation": "15m",
+        "title": "User, Role, Group, Quota, and Authentication managment",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -2851,100 +2509,20 @@
             "tutorial": [],
             "video": true
         },
-        "tutorial_name": "backup-cleanup",
+        "tutorial_name": "users-groups-quotas",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/backup-cleanup/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/users-groups-quotas/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/backup-cleanup/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/backup-cleanup/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/users-groups-quotas/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/users-groups-quotas/slides.json"
         },
-        "version": 5,
+        "version": 19,
         "video": true,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 840,
-        "visitors": 2064092
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/uwsgi/tutorial.json",
-        "contributors": [
-            {
-                "email": "nate@bx.psu.edu",
-                "id": "natefoo",
-                "joined": "2017-12",
-                "matrix": "natefoo:matrix.org",
-                "name": "Nate Coraor",
-                "orcid": "0000-0001-8083-2963",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
-                "twitter": "natefoo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
-            },
-            {
-                "elixir_node": "au",
-                "email": "simon.gladman@unimelb.edu.au",
-                "id": "slugger70",
-                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
-                "joined": "2017-09",
-                "name": "Simon Gladman",
-                "orcid": "0000-0002-6100-4385",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
-            }
-        ],
-        "dir": "topics/admin/tutorials/uwsgi",
-        "edam_operation": [],
-        "edam_topic": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": false,
-        "id": "admin/uwsgi",
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "layout": "tutorial_slides",
-        "license": "CC-BY-4.0",
-        "logo": "assets/images/gat.png",
-        "mod_date": "2022-03-01",
-        "pageviews": 5726879,
-        "pub_date": "2019-01-28",
-        "short_id": "S00028",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
-        "subtopic": "deprecated",
-        "supported_servers": [],
-        "symlink": null,
-        "title": "uWSGI",
-        "tools": [],
-        "topic_name": "admin",
-        "topic_name_human": "Galaxy Server administration",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "uwsgi",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/uwsgi/slides.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/uwsgi/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/uwsgi/slides.json"
-        },
-        "version": 9,
-        "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2063758
+        "visitors": 2133582,
+        "zenodo_link": ""
     },
     {
         "admin_install": {
@@ -2954,19 +2532,8 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/connect-to-compute-cluster/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/advanced-galaxy-customisation/tutorial.json",
         "contributors": [
-            {
-                "email": "nate@bx.psu.edu",
-                "id": "natefoo",
-                "joined": "2017-12",
-                "matrix": "natefoo:matrix.org",
-                "name": "Nate Coraor",
-                "orcid": "0000-0001-8083-2963",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
-                "twitter": "natefoo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
-            },
             {
                 "affiliations": [
                     "eurosciencegateway",
@@ -3026,256 +2593,55 @@
                 "orcid": "0000-0001-9760-8992",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            }
-        ],
-        "dir": "topics/admin/tutorials/connect-to-compute-cluster",
-        "edam_operation": [],
-        "edam_topic": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "admin",
-                "tutorials": [
-                    "job-destinations"
-                ],
-                "type": "internal"
-            }
-        ],
-        "hands_on": true,
-        "id": "admin/connect-to-compute-cluster",
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Galaxy supports a variety of different DRMs.",
-            "You should absolutely set one up, it prevents jobs from being killed during server restarts."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
-        "objectives": [
-            "Be familiar with the basics of installing, configuring, and using Slurm",
-            "Understand all components of the Galaxy job running stack",
-            "Understand how the job conf controls Galaxy's jobs subsystem",
-            "Have a strong understanding of Galaxy job destinations",
-            "Understand the purpose and function of Galaxy job metrics"
-        ],
-        "pageviews": 5732896,
-        "pub_date": "2018-01-07",
-        "questions": [
-            "How to connect Galaxy to a compute cluster?",
-            "What are job metrics?",
-            "What sort of information can I collect?",
-            "Where can I find this information?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "cat-bro",
-                    "shiltemann"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "31M",
-                "speakers": [
-                    "hexylena"
-                ],
-                "youtube_id": "R0NbHscL3jA"
-            },
-            {
-                "captioners": [
-                    "beatrizserrano"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "6M",
-                "speakers": [
-                    "hexylena"
-                ],
-                "youtube_id": "7CYI5yw9MN8"
-            }
-        ],
-        "redirect_from": [
-            "/topics/admin/tutorials/job-metrics/tutorial",
-            "/short/admin/connect-to-compute-cluster",
-            "/short/T00002"
-        ],
-        "requirements": [
-            {
-                "topic_name": "admin",
-                "tutorials": [
-                    "ansible",
-                    "ansible-galaxy"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00002",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
-        "subtopic": "jobs",
-        "supported_servers": [],
-        "symlink": null,
-        "tags": [
-            "jobs",
-            "ansible",
-            "git-gat"
-        ],
-        "time_estimation": "1h",
-        "title": "Connecting Galaxy to a compute cluster",
-        "tools": [],
-        "topic_name": "admin",
-        "topic_name_human": "Galaxy Server administration",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": true
-        },
-        "tutorial_name": "connect-to-compute-cluster",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/connect-to-compute-cluster/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/connect-to-compute-cluster/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/connect-to-compute-cluster/tutorial.json"
-        },
-        "version": 56,
-        "video": true,
-        "video_versions": 2,
-        "video_view": 0,
-        "visit_duration": 354,
-        "visitors": 2067055
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/object-store/tutorial.json",
-        "contributors": [
-            {
-                "email": "nate@bx.psu.edu",
-                "id": "natefoo",
-                "joined": "2017-12",
-                "matrix": "natefoo:matrix.org",
-                "name": "Nate Coraor",
-                "orcid": "0000-0001-8083-2963",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
-                "twitter": "natefoo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
             },
             {
                 "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
+                    "elixir-europe"
                 ],
-                "id": "hexylena",
+                "contact_for_training": true,
+                "elixir_node": "cz",
+                "email": "marten@bx.psu.edu",
+                "fediverse": "https://mastodon.world/@martenson",
+                "fediverse_flavor": "mastodon",
+                "id": "martenson",
                 "joined": "2017-09",
                 "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
+                    "country": "USA",
+                    "lat": 37.0,
+                    "lon": -122.0
                 },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "gmauro",
-                "joined": "2019-03",
-                "name": "Gianmauro Cuccuru",
-                "orcid": "0000-0002-5335-545X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gmauro/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/gmauro.json"
+                "matrix": "martenson:matrix.org",
+                "name": "Martin \u010cech",
+                "orcid": "0000-0002-9318-1781",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/martenson/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/martenson.json"
             }
         ],
-        "dir": "topics/admin/tutorials/object-store",
+        "dir": "topics/admin/tutorials/advanced-galaxy-customisation",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": true,
-        "id": "admin/object-store",
+        "hands_on": false,
+        "id": "admin/advanced-galaxy-customisation",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": [
-            "The distributed object store configuration allows you to easily expand that storage that is attached to your Galaxy.",
-            "You can move data around without affecting users."
-        ],
-        "layout": "tutorial_hands_on",
+        "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-25",
-        "objectives": [
-            "Setup Galaxy with both the Hierarachical and Distributed Object Storages"
-        ],
-        "pageviews": 5728838,
-        "pub_date": "2019-01-28",
-        "questions": [
-            "How does Galaxy locate data?",
-            "How can I have Galaxy use multiple storage locations?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "admin",
-                "tutorials": [
-                    "ansible",
-                    "ansible-galaxy"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00016",
+        "logo": "assets/images/gat.png",
+        "mod_date": "2023-04-17",
+        "pageviews": 5897146,
+        "pub_date": "2017-06-27",
+        "short_id": "S00000",
         "short_tools": [],
         "slides": true,
-        "slides_recordings": [
-            {
-                "captioners": [
-                    "cat-bro"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "18M",
-                "speakers": [
-                    "gmauro"
-                ],
-                "youtube_id": "Hv2bvjk5sjE"
-            }
-        ],
-        "subtopic": "data",
+        "slides_recordings": false,
+        "subtopic": "deprecated",
         "supported_servers": [],
         "symlink": null,
-        "tags": [
-            "ansible",
-            "storage"
-        ],
-        "time_estimation": "30m",
-        "title": "Distributed Object Storage",
+        "title": "Advanced customisation of a Galaxy instance",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -3285,19 +2651,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "object-store",
+        "tutorial_name": "advanced-galaxy-customisation",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/object-store/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/advanced-galaxy-customisation/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/object-store/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/object-store/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/advanced-galaxy-customisation/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/advanced-galaxy-customisation/slides.json"
         },
-        "version": 27,
+        "version": 18,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 244,
-        "visitors": 2064970
+        "visit_duration": 152,
+        "visitors": 2133582
     },
     {
         "abbreviations": {
@@ -3605,7 +2971,7 @@
             "Have an understanding of how Galaxy's Ansible roles are structured and interact with one another",
             "Be able to use an Ansible playbook to install different flavors of Galaxy for different purposes"
         ],
-        "pageviews": 5770977,
+        "pageviews": 5941658,
         "pub_date": "2019-01-28",
         "questions": [
             "How does the Galaxy Ansible module work internally?",
@@ -3700,8 +3066,8 @@
         "video": true,
         "video_versions": 3,
         "video_view": 0,
-        "visit_duration": 254,
-        "visitors": 2086723
+        "visit_duration": 255,
+        "visitors": 2156852
     },
     {
         "admin_install": {
@@ -3711,45 +3077,94 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/cloudbursting/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/gxadmin/tutorial.json",
         "contributors": [
             {
-                "elixir_node": "au",
-                "email": "simon.gladman@unimelb.edu.au",
-                "id": "slugger70",
-                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
                 "joined": "2017-09",
-                "name": "Simon Gladman",
-                "orcid": "0000-0002-6100-4385",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/admin/tutorials/cloudbursting",
+        "dir": "topics/admin/tutorials/gxadmin",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": false,
-        "id": "admin/cloudbursting",
+        "hands_on": true,
+        "id": "admin/gxadmin",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "layout": "tutorial_slides",
+        "key_points": [
+            "gxadmin is a tool to run common database queries useful for Galaxy admins",
+            "new queries are welcome and easy to contribute"
+        ],
+        "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "logo": "assets/images/gat.png",
-        "mod_date": "2022-03-01",
-        "pageviews": 5726879,
-        "pub_date": "2019-01-31",
-        "short_id": "S00004",
+        "mod_date": "2024-08-08",
+        "objectives": [
+            "Learn gxadmin basics",
+            "See some queries and learn how they help debug production issues"
+        ],
+        "pageviews": 5898339,
+        "pub_date": "2019-01-28",
+        "questions": [
+            "What is gxadmin",
+            "What can it do?",
+            "How to write a query?"
+        ],
+        "short_id": "T00009",
         "short_tools": [],
         "slides": true,
-        "slides_recordings": false,
-        "subtopic": "cloud",
+        "slides_recordings": [
+            {
+                "captioners": [
+                    "hexylena"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "2M",
+                "speakers": [
+                    "awspolly"
+                ],
+                "youtube_id": "QFwOgDyFSSA"
+            }
+        ],
+        "subtopic": "monitoring",
         "supported_servers": [],
         "symlink": null,
-        "title": "Galaxy on the Cloud",
+        "tags": [
+            "monitoring",
+            "ansible",
+            "git-gat"
+        ],
+        "time_estimation": "30m",
+        "title": "Galaxy Monitoring with gxadmin",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -3757,21 +3172,22 @@
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": false
+            "video": true
         },
-        "tutorial_name": "cloudbursting",
+        "tutorial_name": "gxadmin",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/cloudbursting/slides.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/gxadmin/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/cloudbursting/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/cloudbursting/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/gxadmin/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/gxadmin/tutorial.json"
         },
-        "version": 6,
-        "video": false,
-        "video_versions": 0,
+        "version": 27,
+        "video": true,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758
+        "visit_duration": 319,
+        "visitors": 2134305,
+        "zenodo_link": ""
     },
     {
         "admin_install": {
@@ -3781,8 +3197,15 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/stuff/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/introduction/tutorial.json",
         "contributors": [
+            {
+                "id": "valentinmarcon",
+                "joined": "2017-09",
+                "name": "Valentin Marcon",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/valentinmarcon/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/valentinmarcon.json"
+            },
             {
                 "email": "nate@bx.psu.edu",
                 "id": "natefoo",
@@ -3825,17 +3248,6 @@
                 "twitter": "bjoerngruening",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
             },
-            {
-                "elixir_node": "au",
-                "email": "simon.gladman@unimelb.edu.au",
-                "id": "slugger70",
-                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
-                "joined": "2017-09",
-                "name": "Simon Gladman",
-                "orcid": "0000-0002-6100-4385",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
@@ -3866,46 +3278,51 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/admin/tutorials/stuff",
-        "draft": true,
+        "dir": "topics/admin/tutorials/introduction",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": false,
-        "id": "admin/stuff",
+        "id": "admin/introduction",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Galaxy supports pluggable monitoring extensions.",
-            "Use grafana or the reports webapp to monitor your service."
+            "Galaxy is scalable from personal computers to huge HPC and cloud-instances.",
+            "Amount of expected users, types of common tasks, and storage capabilities have a big impact on the deployment."
         ],
-        "layout": "tutorial_slides",
+        "layout": "introduction_slides",
         "license": "CC-BY-4.0",
         "logo": "assets/images/gat.png",
-        "mod_date": "2023-02-17",
+        "mod_date": "2024-06-25",
         "objectives": [
-            "Learn about different monitoring strategies.",
-            "Setup and start the Galaxy reports app."
+            "Learn about different options about Galaxy deployment.",
+            "Make an educated decision about your preferred deployment model."
         ],
-        "pageviews": 5726879,
-        "pub_date": "2018-01-07",
+        "pageviews": 5897146,
+        "priority": 1,
+        "pub_date": "2017-06-12",
         "questions": [
-            "How to monitor a Galaxy service?"
+            "What options to deploy Galaxy do I have?",
+            "Which platforms are supported by Galaxy?",
+            "What requirements does Galaxy have?"
         ],
-        "short_id": "S00022",
+        "redirect_from": [
+            "/topics/admin/slides/introduction",
+            "/short/admin/introduction/slides",
+            "/short/S00015"
+        ],
+        "short_id": "S00015",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
+        "subtopic": "core",
         "supported_servers": [],
         "symlink": null,
-        "tags": [
-            "work-in-progress"
-        ],
-        "time_estimation": "1h",
-        "title": "Server: Other",
+        "time_estimation": "20m",
+        "title": "Galaxy from an administrator's point of view",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -3915,19 +3332,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "stuff",
+        "tutorial_name": "introduction",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/stuff/slides.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/introduction/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/stuff/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/stuff/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/introduction/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/introduction/slides.json"
         },
         "version": 6,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2063758,
+        "visitors": 2133582,
         "zenodo_link": ""
     },
     {
@@ -3938,31 +3355,18 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/celery/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "mira-miracoli"
-            ],
-            "editing": [
-                "hexylena"
-            ]
-        },
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/systemd-supervisor/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe",
-                    "deNBI"
-                ],
-                "elixir_node": "de",
-                "email": "kuntzm@informatik.uni-freiburg.de",
-                "id": "mira-miracoli",
-                "joined": "2022-07",
-                "matrix": "mira-miracoli:matrix.org",
-                "name": "Mira Kuntz",
-                "orcid": "0000-0003-4302-5091",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mira-miracoli/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mira-miracoli.json"
+                "email": "nate@bx.psu.edu",
+                "id": "natefoo",
+                "joined": "2017-12",
+                "matrix": "natefoo:matrix.org",
+                "name": "Nate Coraor",
+                "orcid": "0000-0001-8083-2963",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
+                "twitter": "natefoo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
             },
             {
                 "affiliations": [
@@ -3994,56 +3398,31 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/admin/tutorials/celery",
+        "dir": "topics/admin/tutorials/systemd-supervisor",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": true,
-        "id": "admin/celery",
+        "hands_on": false,
+        "id": "admin/systemd-supervisor",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": null,
-        "layout": "tutorial_hands_on",
+        "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-02-20",
-        "objectives": [
-            "Have an understanding of what Celery is and how it works",
-            "Install Redis",
-            "Configure and start Celery workers",
-            "Install Flower to the Galaxy venv and configure it",
-            "Use an Ansible playbook for all of the above.",
-            "Monitor a Celery task using the Flower dashboard"
-        ],
-        "pageviews": 2906091,
-        "pub_date": "2022-07-16",
-        "questions": null,
-        "requirements": [
-            {
-                "topic_name": "admin",
-                "tutorials": [
-                    "ansible",
-                    "ansible-galaxy",
-                    "pulsar"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00326",
+        "logo": "assets/images/gat.png",
+        "mod_date": "2023-04-16",
+        "pageviews": 5897146,
+        "pub_date": "2019-01-28",
+        "short_id": "S00023",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
-        "subtopic": "data",
+        "subtopic": "deprecated",
         "supported_servers": [],
         "symlink": null,
-        "tags": [
-            "ansible",
-            "git-gat"
-        ],
-        "time_estimation": "1h",
-        "title": "Setting up Celery Workers for Galaxy",
+        "title": "Controlling Galaxy with systemd or Supervisor",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -4051,22 +3430,21 @@
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": false
+            "video": true
         },
-        "tutorial_name": "celery",
+        "tutorial_name": "systemd-supervisor",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/celery/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/systemd-supervisor/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/celery/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/celery/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/systemd-supervisor/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/systemd-supervisor/slides.json"
         },
-        "version": 10,
-        "video": false,
+        "version": 5,
+        "video": true,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 232,
-        "visitors": 1208298,
-        "zenodo_link": ""
+        "visit_duration": 152,
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -4076,36 +3454,18 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/external-auth/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/cvmfs/tutorial.json",
         "contributors": [
             {
-                "email": "nate@bx.psu.edu",
-                "id": "natefoo",
-                "joined": "2017-12",
-                "matrix": "natefoo:matrix.org",
-                "name": "Nate Coraor",
-                "orcid": "0000-0001-8083-2963",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
-                "twitter": "natefoo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
-            },
-            {
-                "affiliations": [
-                    "earlham",
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "fediverse": "https://mstdn.science/@nsoranzo",
-                "fediverse_flavor": "mastodon",
-                "id": "nsoranzo",
+                "elixir_node": "au",
+                "email": "simon.gladman@unimelb.edu.au",
+                "id": "slugger70",
+                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
                 "joined": "2017-09",
-                "linkedin": "nicola-soranzo-7884125",
-                "matrix": "nsoranzo:matrix.org",
-                "name": "Nicola Soranzo",
-                "orcid": "0000-0003-3627-5340",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
-                "twitter": "NicolaSoranzo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
+                "name": "Simon Gladman",
+                "orcid": "0000-0002-6100-4385",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
             },
             {
                 "affiliations": [
@@ -4137,36 +3497,43 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/admin/tutorials/external-auth",
+        "dir": "topics/admin/tutorials/cvmfs",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "admin/external-auth",
+        "id": "admin/cvmfs",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": [
-            "Remote auth is not complex to set up and can help you meet institutional requirements"
-        ],
+        "key_points": null,
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2022-10-18",
+        "mod_date": "2024-08-08",
         "objectives": [
-            "be familiar with configuring Galaxy to use an upstream (proxy) authentication provider",
-            "be able to log in to your Galaxy server with a file-configured user."
-        ],
-        "pageviews": 5727928,
-        "pub_date": "2019-01-28",
-        "questions": [
-            "How can I connect Galaxy with CAS, SAML, etc."
+            "Have an understanding of what CVMFS is and how it works",
+            "Install and configure the CVMFS client on a linux machine and mount the Galaxy reference data repository",
+            "Configure your Galaxy to use these reference genomes and indices",
+            "Use an Ansible playbook for all of the above."
         ],
-        "redirect_from": [
-            "/topics/admin/tutorials/upstream-auth/tutorial",
-            "/short/admin/external-auth",
-            "/short/T00007"
+        "pageviews": 5899798,
+        "pub_date": "2019-01-27",
+        "questions": null,
+        "recordings": [
+            {
+                "captioners": [
+                    "slugger70"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "23M",
+                "speakers": [
+                    "slugger70"
+                ],
+                "youtube_id": "X3iFMZP_fQ8"
+            }
         ],
         "requirements": [
             {
@@ -4178,18 +3545,32 @@
                 "type": "internal"
             }
         ],
-        "short_id": "T00007",
+        "short_id": "T00003",
         "short_tools": [],
         "slides": true,
-        "slides_recordings": false,
-        "subtopic": "features",
+        "slides_recordings": [
+            {
+                "captioners": [
+                    "hexylena"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "3M",
+                "speakers": [
+                    "awspolly"
+                ],
+                "youtube_id": "g_cavAO-fBM"
+            }
+        ],
+        "subtopic": "data",
         "supported_servers": [],
         "symlink": null,
         "tags": [
-            "authentication"
+            "ansible",
+            "git-gat"
         ],
-        "time_estimation": "30m",
-        "title": "External Authentication",
+        "time_estimation": "1h",
+        "title": "Reference Data with CVMFS",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -4197,21 +3578,27 @@
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": false
+            "video": true
         },
-        "tutorial_name": "external-auth",
+        "tutorial_name": "cvmfs",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/external-auth/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/cvmfs/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/external-auth/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/external-auth/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/cvmfs/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/cvmfs/tutorial.json"
         },
-        "version": 14,
-        "video": false,
-        "video_versions": 0,
+        "version": 49,
+        "video": true,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 199,
-        "visitors": 2064406
+        "visit_duration": 350,
+        "visitors": 2135296,
+        "voice": {
+            "id": "Olivia",
+            "lang": "en-AU",
+            "neural": true
+        },
+        "zenodo_link": ""
     },
     {
         "admin_install": {
@@ -4221,149 +3608,34 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/general-monitoring/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/galaxy-docker/tutorial.json",
         "contributors": [
-            {
-                "email": "nate@bx.psu.edu",
-                "id": "natefoo",
-                "joined": "2017-12",
-                "matrix": "natefoo:matrix.org",
-                "name": "Nate Coraor",
-                "orcid": "0000-0001-8083-2963",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
-                "twitter": "natefoo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
-            },
             {
                 "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
+                    "gallantries",
+                    "ifb",
                     "elixir-europe"
                 ],
                 "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
                 "fediverse_flavor": "mastodon",
-                "id": "bgruening",
+                "id": "bebatut",
                 "joined": "2017-09",
-                "linkedin": "bgruening",
+                "linkedin": "berenicebatut",
                 "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
                 },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
-            },
-            {
-                "elixir_node": "au",
-                "email": "simon.gladman@unimelb.edu.au",
-                "id": "slugger70",
-                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
-                "joined": "2017-09",
-                "name": "Simon Gladman",
-                "orcid": "0000-0002-6100-4385",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            }
-        ],
-        "dir": "topics/admin/tutorials/general-monitoring",
-        "edam_operation": [],
-        "edam_topic": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": false,
-        "id": "admin/general-monitoring",
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "layout": "tutorial_slides",
-        "license": "CC-BY-4.0",
-        "logo": "assets/images/gat.png",
-        "mod_date": "2022-03-01",
-        "pageviews": 5726879,
-        "pub_date": "2019-04-26",
-        "short_id": "S00012",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
-        "subtopic": "monitoring",
-        "supported_servers": [],
-        "symlink": null,
-        "title": "Galaxy Monitoring",
-        "tools": [],
-        "topic_name": "admin",
-        "topic_name_human": "Galaxy Server administration",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "general-monitoring",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/general-monitoring/slides.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/general-monitoring/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/general-monitoring/slides.json"
-        },
-        "version": 5,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/advanced-galaxy-customisation/tutorial.json",
-        "contributors": [
             {
                 "affiliations": [
                     "eurosciencegateway",
@@ -4394,84 +3666,49 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
                 "twitter": "bjoerngruening",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "cz",
-                "email": "marten@bx.psu.edu",
-                "fediverse": "https://mastodon.world/@martenson",
-                "fediverse_flavor": "mastodon",
-                "id": "martenson",
-                "joined": "2017-09",
-                "location": {
-                    "country": "USA",
-                    "lat": 37.0,
-                    "lon": -122.0
-                },
-                "matrix": "martenson:matrix.org",
-                "name": "Martin \u010cech",
-                "orcid": "0000-0002-9318-1781",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/martenson/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/martenson.json"
             }
         ],
-        "dir": "topics/admin/tutorials/advanced-galaxy-customisation",
+        "dir": "topics/admin/tutorials/galaxy-docker",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": false,
-        "id": "admin/advanced-galaxy-customisation",
+        "id": "admin/galaxy-docker",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
+        "key_points": [
+            "Use Docker",
+            "Integrate your tools into Galaxy",
+            "Use Galaxy inside Docker to have a flavoured Galaxy instance"
+        ],
         "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
         "logo": "assets/images/gat.png",
-        "mod_date": "2023-04-17",
-        "pageviews": 5726879,
-        "pub_date": "2017-06-27",
-        "short_id": "S00000",
+        "mod_date": "2022-10-18",
+        "objectives": [
+            "Docker basics",
+            "Galaxy Docker image (usage)",
+            "Galaxy Docker (internals)",
+            "Galaxy flavours"
+        ],
+        "pageviews": 5897146,
+        "pub_date": "2016-09-29",
+        "questions": [
+            "Why Docker? What is it?",
+            "How to use Docker?",
+            "How to integrate Galaxy in Docker to facilitate its deployment?"
+        ],
+        "short_id": "S00011",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
-        "subtopic": "deprecated",
         "supported_servers": [],
         "symlink": null,
-        "title": "Advanced customisation of a Galaxy instance",
+        "time_estimation": "1h",
+        "title": "Docker and Galaxy",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -4481,19 +3718,20 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "advanced-galaxy-customisation",
+        "tutorial_name": "galaxy-docker",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/advanced-galaxy-customisation/slides.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/galaxy-docker/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/advanced-galaxy-customisation/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/advanced-galaxy-customisation/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/galaxy-docker/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/galaxy-docker/slides.json"
         },
-        "version": 18,
+        "version": 16,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2063758
+        "visitors": 2133582,
+        "zenodo_link": ""
     },
     {
         "admin_install": {
@@ -4554,7 +3792,7 @@
         "license": "CC-BY-4.0",
         "logo": "assets/images/gat.png",
         "mod_date": "2024-06-25",
-        "pageviews": 5726879,
+        "pageviews": 5897146,
         "pub_date": "2019-01-28",
         "short_id": "S00026",
         "short_tools": [],
@@ -4585,7 +3823,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2063758
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -4595,16 +3833,14 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/beacon/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/ansible/tutorial.json",
         "contributions": {
             "authorship": [
-                "hexylena"
-            ],
-            "editing": [
+                "hexylena",
                 "shiltemann"
             ],
-            "funding": [
-                "CINECA-Project"
+            "testing": [
+                "vladvisan"
             ]
         },
         "contributors": [
@@ -4668,73 +3904,94 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             },
             {
-                "funder": true,
-                "funder_name": "Horizon 2020",
-                "funding_id": "825775",
-                "funding_system": "cordis",
-                "id": "CINECA-Project",
-                "joined": "2023-03",
-                "members": [
-                    "shiltemann"
+                "affiliations": [
+                    "uga"
                 ],
-                "name": "Common Infrastructure for National Cohorts in Europe, Canada, and Africa",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/CINECA-Project/",
-                "short_name": "CINECA",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/CINECA-Project.json"
+                "email": "vlad.visan@gmail.com",
+                "id": "vladvisan",
+                "joined": "2023-02",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.19,
+                    "lon": 5.76
+                },
+                "matrix": "vlad.visan:matrix.org",
+                "name": "Vlad Visan",
+                "orcid": "0009-0007-0529-1002",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/vladvisan/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/vladvisan.json"
             }
         ],
-        "dir": "topics/admin/tutorials/beacon",
+        "dir": "topics/admin/tutorials/ansible",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "admin/beacon",
+        "id": "admin/ansible",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "While deprecated, Beacon v1 is easy to deploy",
-            "It can also tick some boxes for grants!"
+            "Ansible lets you do system administration at scale",
+            "Many system administration, software installation, and software management tasks are already available as Ansible tasks or roles"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-04-21",
+        "mod_date": "2024-08-08",
         "objectives": [
-            "Deploy a Beacon"
+            "Learn Ansible basics",
+            "Write a simple role",
+            "Install a role from Ansible Galaxy (repository unrelated to the Galaxy Project)"
         ],
-        "pageviews": 103,
-        "pub_date": "2023-04-16",
+        "pageviews": 5907762,
+        "pub_date": "2018-07-11",
         "questions": [
-            "What is a Beacon?",
-            "How do I deploy it?",
-            "Is v1 the same as v2?"
+            "Why Ansible?",
+            "How and when to use Ansible?",
+            "How to write a role?",
+            "How to leverage community build roles?"
         ],
-        "requirements": [
+        "recordings": [
             {
-                "topic_name": "admin",
-                "tutorials": [
-                    "ansible",
-                    "ansible-galaxy"
+                "captioners": [
+                    "martenson"
                 ],
-                "type": "internal"
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "61M",
+                "speakers": [
+                    "martenson"
+                ],
+                "youtube_id": "2KdT0sYKUeE"
             }
         ],
-        "short_id": "T00325",
+        "short_id": "T00000",
         "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "features",
+        "slides": true,
+        "slides_recordings": [
+            {
+                "captioners": [
+                    "martenson"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "5M",
+                "speakers": [
+                    "jdavcs"
+                ],
+                "youtube_id": "KFpbfmN0OTE"
+            }
+        ],
+        "subtopic": "core",
         "supported_servers": [],
         "symlink": null,
         "tags": [
-            "ga4gh",
-            "beacon",
-            "git-gat"
+            "ansible"
         ],
-        "time_estimation": "30m",
-        "title": "Deploying a Beacon v1 in Galaxy",
+        "time_estimation": "60m",
+        "title": "Ansible",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -4742,21 +3999,21 @@
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": false
+            "video": true
         },
-        "tutorial_name": "beacon",
+        "tutorial_name": "ansible",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/beacon/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/ansible/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/beacon/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/beacon/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/ansible/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/ansible/tutorial.json"
         },
-        "version": 3,
-        "video": false,
-        "video_versions": 0,
+        "version": 48,
+        "video": true,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 194,
-        "visitors": 90,
+        "visit_duration": 250,
+        "visitors": 2139319,
         "zenodo_link": ""
     },
     {
@@ -4767,36 +4024,60 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/apptainer/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/general-monitoring/tutorial.json",
         "contributors": [
+            {
+                "email": "nate@bx.psu.edu",
+                "id": "natefoo",
+                "joined": "2017-12",
+                "matrix": "natefoo:matrix.org",
+                "name": "Nate Coraor",
+                "orcid": "0000-0001-8083-2963",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
+                "twitter": "natefoo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
+            },
             {
                 "affiliations": [
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
                     "elixir-europe"
                 ],
-                "elixir_node": "no",
-                "email": "torfinn.nome@gmail.com",
-                "id": "torfinnnome",
-                "joined": "2021-01",
-                "name": "Torfinn Nome",
-                "orcid": "0000-0003-1659-132X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/torfinnnome/",
-                "twitter": "torfinnnome",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/torfinnnome.json"
-            },
-            {
-                "id": "mvdbeek",
-                "joined": "2018-06",
-                "name": "Marius van den Beek",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
+                "contact_for_training": true,
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
+                "fediverse_flavor": "mastodon",
+                "id": "bgruening",
+                "joined": "2017-09",
+                "linkedin": "bgruening",
+                "location": {
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
+                },
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
             },
             {
-                "elixir_node": "de",
-                "id": "bernt-matthias",
+                "elixir_node": "au",
+                "email": "simon.gladman@unimelb.edu.au",
+                "id": "slugger70",
+                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
                 "joined": "2017-09",
-                "name": "Matthias Bernt",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bernt-matthias/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bernt-matthias.json"
+                "name": "Simon Gladman",
+                "orcid": "0000-0002-6100-4385",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
             },
             {
                 "affiliations": [
@@ -4826,102 +4107,33 @@
                 "orcid": "0000-0001-9760-8992",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe",
-                    "deNBI"
-                ],
-                "elixir_node": "de",
-                "email": "kuntzm@informatik.uni-freiburg.de",
-                "id": "mira-miracoli",
-                "joined": "2022-07",
-                "matrix": "mira-miracoli:matrix.org",
-                "name": "Mira Kuntz",
-                "orcid": "0000-0003-4302-5091",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mira-miracoli/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mira-miracoli.json"
             }
         ],
-        "dir": "topics/admin/tutorials/apptainer",
+        "dir": "topics/admin/tutorials/general-monitoring",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": true,
-        "id": "admin/apptainer",
+        "hands_on": false,
+        "id": "admin/general-monitoring",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": null,
-        "layout": "tutorial_hands_on",
+        "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
-        "objectives": [
-            "Configure your Galaxy to use Apptainer and BioContainers for running jobs"
-        ],
-        "pageviews": 880,
-        "pub_date": "2021-01-08",
-        "questions": null,
-        "recordings": [
-            {
-                "captioners": [
-                    "gallardoalba",
-                    "slugger70"
-                ],
-                "date": "2021-06-28",
-                "galaxy_version": "21.05",
-                "length": "43M",
-                "speakers": [
-                    "slugger70"
-                ],
-                "youtube_id": "q6Dt7j713tI"
-            },
-            {
-                "captioners": [
-                    "hexylena",
-                    "cat-bro"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "16M",
-                "speakers": [
-                    "hexylena"
-                ],
-                "youtube_id": "airzg4-ETEs"
-            }
-        ],
-        "redirect_from": [
-            "/topics/admin/tutorials/singularity/tutorial",
-            "/short/admin/apptainer",
-            "/short/T00323"
-        ],
-        "requirements": [
-            {
-                "topic_name": "admin",
-                "tutorials": [
-                    "ansible",
-                    "ansible-galaxy"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00323",
+        "logo": "assets/images/gat.png",
+        "mod_date": "2022-03-01",
+        "pageviews": 5897146,
+        "pub_date": "2019-04-26",
+        "short_id": "S00012",
         "short_tools": [],
-        "slides": false,
+        "slides": true,
         "slides_recordings": false,
-        "subtopic": "jobs",
+        "subtopic": "monitoring",
         "supported_servers": [],
         "symlink": null,
-        "tags": [
-            "jobs",
-            "ansible",
-            "git-gat"
-        ],
-        "time_estimation": "1h",
-        "title": "Use Apptainer containers for running Galaxy jobs",
+        "title": "Galaxy Monitoring",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -4931,20 +4143,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "apptainer",
+        "tutorial_name": "general-monitoring",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/apptainer/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/general-monitoring/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/apptainer/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/apptainer/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/general-monitoring/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/general-monitoring/slides.json"
         },
-        "version": 11,
+        "version": 5,
         "video": false,
-        "video_versions": 2,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 151,
-        "visitors": 679,
-        "zenodo_link": ""
+        "visit_duration": 152,
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -4954,100 +4165,178 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/k8s-managing-galaxy/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/connect-to-compute-cluster/tutorial.json",
         "contributors": [
             {
-                "id": "nuwang",
-                "joined": "2019-06",
-                "name": "Nuwan Goonasekera",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nuwang/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nuwang.json"
-            },
-            {
-                "id": "afgane",
-                "joined": "2018-06",
-                "name": "Enis Afgan",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/afgane/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/afgane.json"
-            },
-            {
-                "id": "almahmoud",
-                "joined": "2019-06",
-                "name": "Alex Mahmoud",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/almahmoud/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/almahmoud.json"
+                "email": "nate@bx.psu.edu",
+                "id": "natefoo",
+                "joined": "2017-12",
+                "matrix": "natefoo:matrix.org",
+                "name": "Nate Coraor",
+                "orcid": "0000-0001-8083-2963",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
+                "twitter": "natefoo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
             },
             {
-                "id": "pcm32",
-                "joined": "2019-06",
-                "name": "Pablo Moreno",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pcm32/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pcm32.json"
+                "affiliations": [
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
+                "fediverse_flavor": "mastodon",
+                "id": "bgruening",
+                "joined": "2017-09",
+                "linkedin": "bgruening",
+                "location": {
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
+                },
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
             },
             {
-                "email": "jdavcs@gmail.com",
-                "id": "jdavcs",
-                "joined": "2019-06",
-                "name": "John Davis",
-                "orcid": "0000-0002-1363-1245",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jdavcs/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jdavcs.json"
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/admin/tutorials/k8s-managing-galaxy",
+        "dir": "topics/admin/tutorials/connect-to-compute-cluster",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "admin",
+                "tutorials": [
+                    "job-destinations"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "admin/k8s-managing-galaxy",
+        "id": "admin/connect-to-compute-cluster",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Modifying configuration is a matter of having some local config files that are mapped in their entirety into the Galaxy container.",
-            "Scaling is a simple matter of changing the number of replicas.",
-            "K8S enables zero downtime upgrades and sets the stage for continuous delivery"
+            "Galaxy supports a variety of different DRMs.",
+            "You should absolutely set one up, it prevents jobs from being killed during server restarts."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2022-10-18",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Have an understanding of how to modify Galaxy configuration",
-            "Be able to upgrade and scale galaxy"
+            "Be familiar with the basics of installing, configuring, and using Slurm",
+            "Understand all components of the Galaxy job running stack",
+            "Understand how the job conf controls Galaxy's jobs subsystem",
+            "Have a strong understanding of Galaxy job destinations",
+            "Understand the purpose and function of Galaxy job metrics"
         ],
-        "pageviews": 837,
-        "priority": 1,
-        "pub_date": "2019-07-02",
+        "pageviews": 5903245,
+        "pub_date": "2018-01-07",
         "questions": [
-            "How do I change Galaxy configs?",
-            "How can I upgrade to a new version?",
-            "How do I rollback my changes?",
-            "How do I scale Galaxy?"
+            "How to connect Galaxy to a compute cluster?",
+            "What are job metrics?",
+            "What sort of information can I collect?",
+            "Where can I find this information?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "cat-bro",
+                    "shiltemann"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "31M",
+                "speakers": [
+                    "hexylena"
+                ],
+                "youtube_id": "R0NbHscL3jA"
+            },
+            {
+                "captioners": [
+                    "beatrizserrano"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "6M",
+                "speakers": [
+                    "hexylena"
+                ],
+                "youtube_id": "7CYI5yw9MN8"
+            }
+        ],
+        "redirect_from": [
+            "/topics/admin/tutorials/job-metrics/tutorial",
+            "/short/admin/connect-to-compute-cluster",
+            "/short/T00002"
         ],
         "requirements": [
             {
                 "topic_name": "admin",
                 "tutorials": [
-                    "k8s-deploying-galaxy"
+                    "ansible",
+                    "ansible-galaxy"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00014",
+        "short_id": "T00002",
         "short_tools": [],
-        "slides": false,
+        "slides": true,
         "slides_recordings": false,
-        "subtopic": "cloud",
+        "subtopic": "jobs",
         "supported_servers": [],
         "symlink": null,
         "tags": [
-            "kubernetes"
+            "jobs",
+            "ansible",
+            "git-gat"
         ],
-        "time_estimation": "30m",
-        "title": "Managing Galaxy on Kubernetes",
+        "time_estimation": "1h",
+        "title": "Connecting Galaxy to a compute cluster",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -5055,21 +4344,21 @@
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": false
+            "video": true
         },
-        "tutorial_name": "k8s-managing-galaxy",
+        "tutorial_name": "connect-to-compute-cluster",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/k8s-managing-galaxy/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/connect-to-compute-cluster/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/k8s-managing-galaxy/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/k8s-managing-galaxy/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/connect-to-compute-cluster/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/connect-to-compute-cluster/tutorial.json"
         },
-        "version": 6,
-        "video": false,
-        "video_versions": 0,
+        "version": 56,
+        "video": true,
+        "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 140,
-        "visitors": 549
+        "visit_duration": 351,
+        "visitors": 2136949
     },
     {
         "admin_install": {
@@ -5079,16 +4368,30 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/sentry/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "mvdbeek"
-            ],
-            "editing": [
-                "hexylena"
-            ]
-        },
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/pulsar/tutorial.json",
         "contributors": [
+            {
+                "email": "nate@bx.psu.edu",
+                "id": "natefoo",
+                "joined": "2017-12",
+                "matrix": "natefoo:matrix.org",
+                "name": "Nate Coraor",
+                "orcid": "0000-0001-8083-2963",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
+                "twitter": "natefoo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
+            },
+            {
+                "elixir_node": "au",
+                "email": "simon.gladman@unimelb.edu.au",
+                "id": "slugger70",
+                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
+                "joined": "2017-09",
+                "name": "Simon Gladman",
+                "orcid": "0000-0002-6100-4385",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
+            },
             {
                 "id": "mvdbeek",
                 "joined": "2018-06",
@@ -5124,56 +4427,143 @@
                 "orcid": "0000-0001-9760-8992",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "gmauro",
+                "joined": "2019-03",
+                "name": "Gianmauro Cuccuru",
+                "orcid": "0000-0002-5335-545X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gmauro/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/gmauro.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe",
+                    "deNBI"
+                ],
+                "elixir_node": "de",
+                "email": "kuntzm@informatik.uni-freiburg.de",
+                "id": "mira-miracoli",
+                "joined": "2022-07",
+                "matrix": "mira-miracoli:matrix.org",
+                "name": "Mira Kuntz",
+                "orcid": "0000-0003-4302-5091",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mira-miracoli/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mira-miracoli.json"
             }
         ],
-        "dir": "topics/admin/tutorials/sentry",
+        "dir": "topics/admin/tutorials/pulsar",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "admin/sentry",
+        "id": "admin/pulsar",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": null,
+        "key_points": [
+            "Pulsar allows you to easily add geographically distributed compute resources into your Galaxy instance",
+            "It also works well in situations where the compute resources cannot share storage pools."
+        ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-18",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Have an understanding of Sentry",
-            "Install Sentry",
-            "Configure Galaxy and Pulsar to send errors to Sentry",
-            "Monitor performance with Sentry"
+            "Have an understanding of what Pulsar is and how it works",
+            "Install and configure a RabbitMQ message queueing server",
+            "Install and configure a Pulsar server on a remote linux machine",
+            "Be able to get Galaxy to send jobs to a remote Pulsar server"
+        ],
+        "pageviews": 5900760,
+        "pub_date": "2019-01-28",
+        "questions": [
+            "How does pulsar work?",
+            "How can I deploy it?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "hexylena"
+                ],
+                "date": "2021-06-28",
+                "galaxy_version": "21.05",
+                "length": "1H28M",
+                "speakers": [
+                    "slugger70"
+                ],
+                "youtube_id": "f0QdF8NDhsM"
+            },
+            {
+                "captioners": [
+                    "simonbray",
+                    "slugger70"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "57M",
+                "speakers": [
+                    "slugger70"
+                ],
+                "youtube_id": "a7fKJT4Fs9k"
+            }
+        ],
+        "redirect_from": [
+            "/topics/admin/tutorials/heterogeneous-compute/tutorial",
+            "/short/admin/pulsar",
+            "/short/T00017"
         ],
-        "pageviews": 173,
-        "pub_date": "2023-04-19",
-        "questions": null,
         "requirements": [
             {
                 "topic_name": "admin",
                 "tutorials": [
                     "ansible",
                     "ansible-galaxy",
-                    "pulsar"
+                    "connect-to-compute-cluster",
+                    "job-destinations",
+                    "cvmfs"
                 ],
                 "type": "internal"
+            },
+            {
+                "title": "A server/VM on which to deploy Pulsar",
+                "type": "none"
             }
         ],
-        "short_id": "T00330",
+        "short_id": "T00017",
         "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "monitoring",
+        "slides": true,
+        "slides_recordings": [
+            {
+                "captioners": [
+                    "shiltemann"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "14M",
+                "speakers": [
+                    "slugger70"
+                ],
+                "youtube_id": "M1-Z_2tuQPI"
+            }
+        ],
+        "subtopic": "jobs",
         "supported_servers": [],
         "symlink": null,
         "tags": [
             "ansible",
+            "jobs",
             "git-gat"
         ],
-        "time_estimation": "1h",
-        "title": "Monitoring Galaxy and Pulsar with Sentry",
+        "time_estimation": "60m",
+        "title": "Running Jobs on Remote Resources with Pulsar",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -5183,20 +4573,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "sentry",
+        "tutorial_name": "pulsar",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/sentry/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/pulsar/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/sentry/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/sentry/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/pulsar/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/pulsar/tutorial.json"
         },
-        "version": 6,
+        "version": 48,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 97,
-        "visitors": 137,
-        "zenodo_link": ""
+        "visit_duration": 331,
+        "visitors": 2135697
     },
     {
         "admin_install": {
@@ -5206,121 +4595,100 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/tus/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/k8s-managing-galaxy/tutorial.json",
         "contributors": [
             {
-                "id": "mvdbeek",
+                "id": "nuwang",
+                "joined": "2019-06",
+                "name": "Nuwan Goonasekera",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nuwang/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nuwang.json"
+            },
+            {
+                "id": "afgane",
                 "joined": "2018-06",
-                "name": "Marius van den Beek",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
+                "name": "Enis Afgan",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/afgane/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/afgane.json"
             },
             {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+                "id": "almahmoud",
+                "joined": "2019-06",
+                "name": "Alex Mahmoud",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/almahmoud/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/almahmoud.json"
             },
             {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "ch",
-                "email": "lucille.delisle@epfl.ch",
-                "id": "lldelisle",
-                "joined": "2019-08",
-                "location": {
-                    "country": "CH",
-                    "lat": 46.52,
-                    "lon": 6.56
-                },
-                "name": "Lucille Delisle",
-                "orcid": "0000-0002-1964-4960",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/lldelisle.json"
+                "id": "pcm32",
+                "joined": "2019-06",
+                "name": "Pablo Moreno",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pcm32/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pcm32.json"
+            },
+            {
+                "email": "jdavcs@gmail.com",
+                "id": "jdavcs",
+                "joined": "2019-06",
+                "name": "John Davis",
+                "orcid": "0000-0002-1363-1245",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jdavcs/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jdavcs.json"
             }
         ],
-        "dir": "topics/admin/tutorials/tus",
+        "dir": "topics/admin/tutorials/k8s-managing-galaxy",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "admin/tus",
+        "id": "admin/k8s-managing-galaxy",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Use TUS to make uploads more efficient, especially for large uploads over unstable connections."
+            "Modifying configuration is a matter of having some local config files that are mapped in their entirety into the Galaxy container.",
+            "Scaling is a simple matter of changing the number of replicas.",
+            "K8S enables zero downtime upgrades and sets the stage for continuous delivery"
         ],
         "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2022-10-18",
         "objectives": [
-            "Setup TUSd",
-            "Configure Galaxy to use it to process uploads"
+            "Have an understanding of how to modify Galaxy configuration",
+            "Be able to upgrade and scale galaxy"
         ],
-        "pageviews": 1022,
-        "pub_date": "2022-03-01",
-        "questions": null,
-        "recordings": [
-            {
-                "captioners": [
-                    "hexylena"
-                ],
-                "date": "2022-03-11",
-                "galaxy_version": "22.01",
-                "length": "7M",
-                "speakers": [
-                    "hexylena"
-                ],
-                "youtube_id": "v5sbIqF_0qo"
-            }
+        "pageviews": 849,
+        "priority": 1,
+        "pub_date": "2019-07-02",
+        "questions": [
+            "How do I change Galaxy configs?",
+            "How can I upgrade to a new version?",
+            "How do I rollback my changes?",
+            "How do I scale Galaxy?"
         ],
         "requirements": [
             {
                 "topic_name": "admin",
                 "tutorials": [
-                    "ansible",
-                    "ansible-galaxy"
+                    "k8s-deploying-galaxy"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00024",
+        "short_id": "T00014",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "features",
+        "subtopic": "cloud",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "30M",
-        "title": "Performant Uploads with TUS",
+        "tags": [
+            "kubernetes"
+        ],
+        "time_estimation": "30m",
+        "title": "Managing Galaxy on Kubernetes",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -5330,20 +4698,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "tus",
+        "tutorial_name": "k8s-managing-galaxy",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/tus/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/k8s-managing-galaxy/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/tus/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/tus/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/k8s-managing-galaxy/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/k8s-managing-galaxy/tutorial.json"
         },
-        "version": 17,
+        "version": 6,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 331,
-        "visitors": 679,
-        "zenodo_link": ""
+        "visit_duration": 136,
+        "visitors": 561
     },
     {
         "admin_install": {
@@ -5416,7 +4783,7 @@
             "Install and configure the CVMFS client on a linux machine and mount the Galaxy reference data repository",
             "Configure your Galaxy to use these reference genomes and indices"
         ],
-        "pageviews": 424,
+        "pageviews": 435,
         "pub_date": "2020-06-17",
         "questions": null,
         "short_id": "T00004",
@@ -5448,15 +4815,11 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 134,
-        "visitors": 299,
+        "visit_duration": 149,
+        "visitors": 306,
         "zenodo_link": ""
     },
     {
-        "abbreviations": {
-            "FTP": "File Transfer Protocol",
-            "NAT": "Network Address Translation"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -5464,7 +4827,7 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/ftp/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/database-schema/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
@@ -5472,359 +4835,94 @@
                 ],
                 "contact_for_training": true,
                 "elixir_node": "ch",
-                "email": "lucille.delisle@epfl.ch",
-                "id": "lldelisle",
-                "joined": "2019-08",
-                "location": {
-                    "country": "CH",
-                    "lat": 46.52,
-                    "lon": 6.56
-                },
-                "name": "Lucille Delisle",
-                "orcid": "0000-0002-1964-4960",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/lldelisle.json"
-            }
-        ],
-        "dir": "topics/admin/tutorials/ftp",
-        "edam_operation": [],
-        "edam_topic": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "admin/ftp",
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "FTP is easy to deploy thanks to the role",
-            "Users can be authenticated with their Galaxy credentials simplifying the user management process significantly"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-02-20",
-        "objectives": [
-            "Configure galaxy and install a FTP server.",
-            "Use an Ansible playbook for this."
-        ],
-        "pageviews": 1451,
-        "pub_date": "2021-06-18",
-        "questions": [
-            "How can I setup FTP to be easy for my users?",
-            "Can I authenticate ftp users with Galaxy credentials?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "admin",
-                "tutorials": [
-                    "ansible",
-                    "ansible-galaxy"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00008",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "features",
-        "supported_servers": [],
-        "symlink": null,
-        "tags": [
-            "data",
-            "git-gat"
-        ],
-        "time_estimation": "1h",
-        "title": "Enable upload via FTP",
-        "tools": [],
-        "topic_name": "admin",
-        "topic_name_human": "Galaxy Server administration",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "ftp",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/ftp/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/ftp/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/ftp/tutorial.json"
-        },
-        "version": 23,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 100,
-        "visitors": 1020,
-        "zenodo_link": ""
-    },
-    {
-        "abbreviations": {
-            "CI": "Continuous Integration"
-        },
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/jenkins/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
+                "email": "hrhotz@googlemail.com",
+                "fediverse": "https://genomic.social/@hrhotz",
+                "fediverse_flavor": "mastodon",
+                "id": "hrhotz",
                 "joined": "2017-09",
+                "linkedin": "hans-rudolf-hotz-542b31",
                 "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
+                    "country": "CH",
+                    "lat": 47.57,
+                    "lon": 7.6
                 },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            }
-        ],
-        "dir": "topics/admin/tutorials/jenkins",
-        "edam_operation": [],
-        "edam_topic": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "admin/jenkins",
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Automate all the things!",
-            "Especially regular tasks you might forget to do",
-            "Automatically run Ansible to ensure machines are in compliance"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2022-10-18",
-        "objectives": [
-            "Setup Jenkins",
-            "Setup a simple job",
-            "Automate running of the Galaxy playbook",
-            "Secure Jenkins"
-        ],
-        "pageviews": 16177,
-        "pub_date": "2019-08-06",
-        "questions": [
-            "What sort of tasks should be automated?",
-            "What are my options for automation?",
-            "How can I automate repetitive tasks?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "admin",
-                "tutorials": [
-                    "ansible",
-                    "ansible-galaxy"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00011",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "features",
-        "supported_servers": [],
-        "symlink": null,
-        "tags": [
-            "ansible",
-            "automation"
-        ],
-        "time_estimation": "1h",
-        "title": "Automation with Jenkins",
-        "tools": [],
-        "topic_name": "admin",
-        "topic_name_human": "Galaxy Server administration",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "jenkins",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/jenkins/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/jenkins/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/jenkins/tutorial.json"
-        },
-        "version": 10,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 39,
-        "visitors": 8129
-    },
-    {
-        "abbreviations": {
-            "TIaaS": "Training Infrastructure as a Service"
-        },
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/tiaas/tutorial.json",
-        "contributors": [
+                "matrix": "hrhotz:matrix.org",
+                "name": "Hans-Rudolf Hotz",
+                "orcid": "0000-0002-2799-424X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hrhotz/",
+                "twitter": "hrhotz",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hrhotz.json"
+            },
             {
                 "affiliations": [
-                    "gallantries",
+                    "eurosciencegateway",
+                    "eosc-life",
                     "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
                     "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
+                    "elixir-europe"
                 ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
                 "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
                 "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
+                "id": "bgruening",
                 "joined": "2017-09",
-                "linkedin": "shiltemann",
+                "linkedin": "bgruening",
                 "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
                 },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
             }
         ],
-        "dir": "topics/admin/tutorials/tiaas",
+        "dir": "topics/admin/tutorials/database-schema",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "admin/tiaas",
+        "id": "admin/database-schema",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "TIaaS is an additional service you can deploy which can help you provide a better service to your users"
+            "Be careful, when you interact with the Galaxy database. And make sure you always have a backup!"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Setup TIaaS",
-            "Request and manage trainings",
-            "Join a training"
+            "Learn some of the design concepts of the Galaxy database",
+            "Extract information from the Galaxy database",
+            "Get to know SchemaSpy"
         ],
-        "pageviews": 600,
-        "pub_date": "2020-02-12",
+        "pageviews": 4660,
+        "pub_date": "2016-07-20",
         "questions": [
-            "How to deploy EU's TIaaS"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "hexylena",
-                    "shiltemann"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "24M",
-                "speakers": [
-                    "hexylena"
-                ],
-                "youtube_id": "tz0ZbK_8Vcc"
-            }
-        ],
-        "requirements": [
-            {
-                "topic_name": "admin",
-                "tutorials": [
-                    "ansible",
-                    "ansible-galaxy",
-                    "connect-to-compute-cluster",
-                    "job-destinations",
-                    "pulsar"
-                ],
-                "type": "internal"
-            }
+            "Running a production Galaxy server, you some times end up in with a situation, where you manually need to interact with the Galaxy database: how do you do that",
+            "How to extract usage information, which can not be gathered using the given report tools",
+            "How to move from MySQL to PostgreSQL",
+            "Is there ever a need to manually change the contents of a table"
         ],
-        "short_id": "T00022",
+        "short_id": "T00006",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "features",
         "supported_servers": [],
         "symlink": null,
-        "tags": [
-            "ansible",
-            "training",
-            "jobs",
-            "git-gat"
-        ],
-        "time_estimation": "30m",
-        "title": "Training Infrastructure as a Service (TIaaS)",
+        "time_estimation": "2h",
+        "title": "Galaxy Database schema",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -5834,19 +4932,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "tiaas",
+        "tutorial_name": "database-schema",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/tiaas/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/database-schema/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/tiaas/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/tiaas/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/database-schema/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/database-schema/tutorial.json"
         },
-        "version": 37,
+        "version": 22,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 210,
-        "visitors": 437,
+        "visit_duration": 65,
+        "visitors": 2763,
         "zenodo_link": ""
     },
     {
@@ -5934,7 +5032,7 @@
             "Add a custom welcome page to Galaxy",
             "Activate and customize themes"
         ],
-        "pageviews": 421,
+        "pageviews": 446,
         "pub_date": "2023-04-16",
         "questions": [
             "How do I change Galaxy's front page?",
@@ -5974,8 +5072,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 341,
-        "visitors": 334
+        "visit_duration": 359,
+        "visitors": 355
     },
     {
         "abbreviations": {
@@ -6156,7 +5254,7 @@
             "How to write a dynamic python function destination",
             "How to use the job resource parameter selection feature"
         ],
-        "pageviews": 2197,
+        "pageviews": 2232,
         "pub_date": "2021-01-17",
         "questions": [
             "How can I configure job dependent resources, like cores, memory for my DRM?",
@@ -6218,8 +5316,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 187,
-        "visitors": 1329
+        "visit_duration": 188,
+        "visitors": 1355
     },
     {
         "admin_install": {
@@ -6335,7 +5433,7 @@
         "objectives": [
             "Setup and start the Galaxy reports app."
         ],
-        "pageviews": 564,
+        "pageviews": 571,
         "pub_date": "2019-01-31",
         "questions": [
             "How to monitor a Galaxy service with the Reports application?"
@@ -6385,8 +5483,147 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 187,
-        "visitors": 420,
+        "visit_duration": 186,
+        "visitors": 427,
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/wireguard-headscale/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "hexylena"
+            ],
+            "editing": [
+                "natefoo"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "email": "nate@bx.psu.edu",
+                "id": "natefoo",
+                "joined": "2017-12",
+                "matrix": "natefoo:matrix.org",
+                "name": "Nate Coraor",
+                "orcid": "0000-0001-8083-2963",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
+                "twitter": "natefoo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
+            }
+        ],
+        "dir": "topics/admin/tutorials/wireguard-headscale",
+        "edam_operation": [],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "admin/wireguard-headscale",
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Tailscale is a fantastic bit of software that Just Works\u2122",
+            "We use headscale, an open source reimplementation of Tailscale's control server because it's easy to use in training",
+            "But if you can afford Tailscale, just use that.",
+            "There is a FOSS plan, go check it out!"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-03-17",
+        "objectives": [
+            "Setup a tailnet across a few nodes"
+        ],
+        "pageviews": 2708,
+        "pub_date": "2022-09-21",
+        "questions": [
+            "What is Tailscale?",
+            "When is it useful?",
+            "Is it right for me?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "admin",
+                "tutorials": [
+                    "ansible"
+                ],
+                "type": "internal"
+            },
+            {
+                "title": "Three or more VMs (they can be tiny, 1 CPU, <1GB RAM)",
+                "type": "none"
+            }
+        ],
+        "short_id": "T00027",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "cloud",
+        "supported_servers": [],
+        "symlink": null,
+        "tags": [
+            "wireguard",
+            "networking"
+        ],
+        "time_estimation": "60m",
+        "title": "Deploying Tailscale/Headscale for private mesh networking",
+        "tools": [],
+        "topic_name": "admin",
+        "topic_name_human": "Galaxy Server administration",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "wireguard-headscale",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/wireguard-headscale/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/wireguard-headscale/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/wireguard-headscale/tutorial.json"
+        },
+        "version": 3,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 29,
+        "visitors": 2033,
         "zenodo_link": ""
     },
     {
@@ -6487,7 +5724,7 @@
             "Have an objective understanding of systemd allowing the user to obtain the benefits of this new system",
             "Realise the joys of journald, and how it makes logging easier and simpler"
         ],
-        "pageviews": 698,
+        "pageviews": 711,
         "pub_date": "2022-07-06",
         "questions": [
             "Unix is supposed to be about FILES\u2122",
@@ -6537,8 +5774,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 35,
-        "visitors": 610
+        "visit_duration": 34,
+        "visitors": 620
     },
     {
         "admin_install": {
@@ -6625,7 +5862,7 @@
             "Add a custom welcome page to Galaxy",
             "Activate and customize themes"
         ],
-        "pageviews": 95,
+        "pageviews": 104,
         "pub_date": "2023-04-16",
         "questions": [
             "How do I change Galaxy's front page?",
@@ -6662,10 +5899,13 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 221,
-        "visitors": 79
+        "visit_duration": 207,
+        "visitors": 88
     },
     {
+        "abbreviations": {
+            "TIaaS": "Training Infrastructure as a Service"
+        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -6673,12 +5913,7 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/wireguard/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "hexylena"
-            ]
-        },
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/tiaas/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
@@ -6708,61 +5943,108 @@
                 "orcid": "0000-0001-9760-8992",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             }
         ],
-        "dir": "topics/admin/tutorials/wireguard",
+        "dir": "topics/admin/tutorials/tiaas",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "admin/wireguard",
+        "id": "admin/tiaas",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Wireguard is incredibly easy to deploy, and very secure."
+            "TIaaS is an additional service you can deploy which can help you provide a better service to your users"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-04-16",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Setup a wireguard mesh across a few nodes"
+            "Setup TIaaS",
+            "Request and manage trainings",
+            "Join a training"
         ],
-        "pageviews": 1103,
-        "pub_date": "2022-09-21",
+        "pageviews": 614,
+        "pub_date": "2020-02-12",
         "questions": [
-            "What is wireguard?",
-            "When is it useful?",
-            "Is it right for me?"
+            "How to deploy EU's TIaaS"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "hexylena",
+                    "shiltemann"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "24M",
+                "speakers": [
+                    "hexylena"
+                ],
+                "youtube_id": "tz0ZbK_8Vcc"
+            }
         ],
         "requirements": [
             {
                 "topic_name": "admin",
                 "tutorials": [
-                    "ansible"
+                    "ansible",
+                    "ansible-galaxy",
+                    "connect-to-compute-cluster",
+                    "job-destinations",
+                    "pulsar"
                 ],
                 "type": "internal"
-            },
-            {
-                "title": "Three or more VMs (they can be tiny, 1 CPU, <1GB RAM)",
-                "type": "none"
             }
         ],
-        "short_id": "T00026",
+        "short_id": "T00022",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "cloud",
+        "subtopic": "features",
         "supported_servers": [],
         "symlink": null,
         "tags": [
-            "wireguard",
-            "networking"
+            "ansible",
+            "training",
+            "jobs",
+            "git-gat"
         ],
-        "time_estimation": "60m",
-        "title": "Deploying Wireguard for private mesh networking",
+        "time_estimation": "30m",
+        "title": "Training Infrastructure as a Service (TIaaS)",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -6772,19 +6054,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "wireguard",
+        "tutorial_name": "tiaas",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/wireguard/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/tiaas/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/wireguard/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/wireguard/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/tiaas/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/tiaas/tutorial.json"
         },
-        "version": 3,
+        "version": 37,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 22,
-        "visitors": 951,
+        "visit_duration": 207,
+        "visitors": 447,
         "zenodo_link": ""
     },
     {
@@ -6795,103 +6077,162 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/database-schema/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/apptainer/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
                     "elixir-europe"
                 ],
-                "contact_for_training": true,
-                "elixir_node": "ch",
-                "email": "hrhotz@googlemail.com",
-                "fediverse": "https://genomic.social/@hrhotz",
-                "fediverse_flavor": "mastodon",
-                "id": "hrhotz",
+                "elixir_node": "no",
+                "email": "torfinn.nome@gmail.com",
+                "id": "torfinnnome",
+                "joined": "2021-01",
+                "name": "Torfinn Nome",
+                "orcid": "0000-0003-1659-132X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/torfinnnome/",
+                "twitter": "torfinnnome",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/torfinnnome.json"
+            },
+            {
+                "id": "mvdbeek",
+                "joined": "2018-06",
+                "name": "Marius van den Beek",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
+            },
+            {
+                "elixir_node": "de",
+                "id": "bernt-matthias",
                 "joined": "2017-09",
-                "linkedin": "hans-rudolf-hotz-542b31",
-                "location": {
-                    "country": "CH",
-                    "lat": 47.57,
-                    "lon": 7.6
-                },
-                "matrix": "hrhotz:matrix.org",
-                "name": "Hans-Rudolf Hotz",
-                "orcid": "0000-0002-2799-424X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hrhotz/",
-                "twitter": "hrhotz",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hrhotz.json"
+                "name": "Matthias Bernt",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bernt-matthias/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bernt-matthias.json"
             },
             {
                 "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
+                    "gallantries",
                     "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
                     "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
-                    "elixir-europe"
+                    "avans-atgm",
+                    "uni-freiburg"
                 ],
-                "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
-                "fediverse_flavor": "mastodon",
-                "id": "bgruening",
+                "id": "hexylena",
                 "joined": "2017-09",
-                "linkedin": "bgruening",
                 "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
                 },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe",
+                    "deNBI"
+                ],
+                "elixir_node": "de",
+                "email": "kuntzm@informatik.uni-freiburg.de",
+                "id": "mira-miracoli",
+                "joined": "2022-07",
+                "matrix": "mira-miracoli:matrix.org",
+                "name": "Mira Kuntz",
+                "orcid": "0000-0003-4302-5091",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mira-miracoli/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mira-miracoli.json"
             }
         ],
-        "dir": "topics/admin/tutorials/database-schema",
+        "dir": "topics/admin/tutorials/apptainer",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "admin/database-schema",
+        "id": "admin/apptainer",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": [
-            "Be careful, when you interact with the Galaxy database. And make sure you always have a backup!"
-        ],
+        "key_points": null,
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Learn some of the design concepts of the Galaxy database",
-            "Extract information from the Galaxy database",
-            "Get to know SchemaSpy"
-        ],
-        "pageviews": 4622,
-        "pub_date": "2016-07-20",
-        "questions": [
-            "Running a production Galaxy server, you some times end up in with a situation, where you manually need to interact with the Galaxy database: how do you do that",
-            "How to extract usage information, which can not be gathered using the given report tools",
-            "How to move from MySQL to PostgreSQL",
-            "Is there ever a need to manually change the contents of a table"
+            "Configure your Galaxy to use Apptainer and BioContainers for running jobs"
         ],
-        "short_id": "T00006",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": [],
-        "symlink": null,
-        "time_estimation": "2h",
-        "title": "Galaxy Database schema",
-        "tools": [],
+        "pageviews": 947,
+        "pub_date": "2021-01-08",
+        "questions": null,
+        "recordings": [
+            {
+                "captioners": [
+                    "gallardoalba",
+                    "slugger70"
+                ],
+                "date": "2021-06-28",
+                "galaxy_version": "21.05",
+                "length": "43M",
+                "speakers": [
+                    "slugger70"
+                ],
+                "youtube_id": "q6Dt7j713tI"
+            },
+            {
+                "captioners": [
+                    "hexylena",
+                    "cat-bro"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "16M",
+                "speakers": [
+                    "hexylena"
+                ],
+                "youtube_id": "airzg4-ETEs"
+            }
+        ],
+        "redirect_from": [
+            "/topics/admin/tutorials/singularity/tutorial",
+            "/short/admin/apptainer",
+            "/short/T00323"
+        ],
+        "requirements": [
+            {
+                "topic_name": "admin",
+                "tutorials": [
+                    "ansible",
+                    "ansible-galaxy"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00323",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "jobs",
+        "supported_servers": [],
+        "symlink": null,
+        "tags": [
+            "jobs",
+            "ansible",
+            "git-gat"
+        ],
+        "time_estimation": "1h",
+        "title": "Use Apptainer containers for running Galaxy jobs",
+        "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
         "tours": false,
@@ -6900,19 +6241,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "database-schema",
+        "tutorial_name": "apptainer",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/database-schema/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/apptainer/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/database-schema/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/database-schema/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/apptainer/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/apptainer/tutorial.json"
         },
-        "version": 22,
+        "version": 11,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 65,
-        "visitors": 2728,
+        "visit_duration": 153,
+        "visitors": 737,
         "zenodo_link": ""
     },
     {
@@ -6923,13 +6264,16 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/wireguard-headscale/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/beacon/tutorial.json",
         "contributions": {
             "authorship": [
                 "hexylena"
             ],
             "editing": [
-                "natefoo"
+                "shiltemann"
+            ],
+            "funding": [
+                "CINECA-Project"
             ]
         },
         "contributors": [
@@ -6963,73 +6307,103 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
             {
-                "email": "nate@bx.psu.edu",
-                "id": "natefoo",
-                "joined": "2017-12",
-                "matrix": "natefoo:matrix.org",
-                "name": "Nate Coraor",
-                "orcid": "0000-0001-8083-2963",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/natefoo/",
-                "twitter": "natefoo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/natefoo.json"
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
+            {
+                "funder": true,
+                "funder_name": "Horizon 2020",
+                "funding_id": "825775",
+                "funding_system": "cordis",
+                "id": "CINECA-Project",
+                "joined": "2023-03",
+                "members": [
+                    "shiltemann"
+                ],
+                "name": "Common Infrastructure for National Cohorts in Europe, Canada, and Africa",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/CINECA-Project/",
+                "short_name": "CINECA",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/CINECA-Project.json"
             }
         ],
-        "dir": "topics/admin/tutorials/wireguard-headscale",
+        "dir": "topics/admin/tutorials/beacon",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "admin/wireguard-headscale",
+        "id": "admin/beacon",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Tailscale is a fantastic bit of software that Just Works\u2122",
-            "We use headscale, an open source reimplementation of Tailscale's control server because it's easy to use in training",
-            "But if you can afford Tailscale, just use that.",
-            "There is a FOSS plan, go check it out!"
+            "While deprecated, Beacon v1 is easy to deploy",
+            "It can also tick some boxes for grants!"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-03-17",
+        "mod_date": "2023-04-21",
         "objectives": [
-            "Setup a tailnet across a few nodes"
+            "Deploy a Beacon"
         ],
-        "pageviews": 2645,
-        "pub_date": "2022-09-21",
+        "pageviews": 113,
+        "pub_date": "2023-04-16",
         "questions": [
-            "What is Tailscale?",
-            "When is it useful?",
-            "Is it right for me?"
+            "What is a Beacon?",
+            "How do I deploy it?",
+            "Is v1 the same as v2?"
         ],
         "requirements": [
             {
                 "topic_name": "admin",
                 "tutorials": [
-                    "ansible"
+                    "ansible",
+                    "ansible-galaxy"
                 ],
                 "type": "internal"
-            },
-            {
-                "title": "Three or more VMs (they can be tiny, 1 CPU, <1GB RAM)",
-                "type": "none"
             }
         ],
-        "short_id": "T00027",
+        "short_id": "T00325",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "cloud",
+        "subtopic": "features",
         "supported_servers": [],
         "symlink": null,
         "tags": [
-            "wireguard",
-            "networking"
+            "ga4gh",
+            "beacon",
+            "git-gat"
         ],
-        "time_estimation": "60m",
-        "title": "Deploying Tailscale/Headscale for private mesh networking",
+        "time_estimation": "30m",
+        "title": "Deploying a Beacon v1 in Galaxy",
         "tools": [],
         "topic_name": "admin",
         "topic_name_human": "Galaxy Server administration",
@@ -7039,19 +6413,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "wireguard-headscale",
+        "tutorial_name": "beacon",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/admin/tutorials/wireguard-headscale/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/beacon/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/wireguard-headscale/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/wireguard-headscale/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/beacon/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/beacon/tutorial.json"
         },
         "version": 3,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 29,
-        "visitors": 1972,
+        "visit_duration": 169,
+        "visitors": 100,
         "zenodo_link": ""
     },
     {
@@ -7101,7 +6475,7 @@
             "How to backup the Galaxy server database and why it's a good idea",
             "How to upgrade the Galaxy server to a new version"
         ],
-        "pageviews": 885,
+        "pageviews": 898,
         "pub_date": "2021-06-08",
         "questions": [
             "How can I find which version of Galaxy I'm running?",
@@ -7169,8 +6543,634 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 174,
-        "visitors": 539,
+        "visit_duration": 171,
+        "visitors": 551,
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/wireguard/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "hexylena"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            }
+        ],
+        "dir": "topics/admin/tutorials/wireguard",
+        "edam_operation": [],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "admin/wireguard",
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Wireguard is incredibly easy to deploy, and very secure."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-04-16",
+        "objectives": [
+            "Setup a wireguard mesh across a few nodes"
+        ],
+        "pageviews": 1141,
+        "pub_date": "2022-09-21",
+        "questions": [
+            "What is wireguard?",
+            "When is it useful?",
+            "Is it right for me?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "admin",
+                "tutorials": [
+                    "ansible"
+                ],
+                "type": "internal"
+            },
+            {
+                "title": "Three or more VMs (they can be tiny, 1 CPU, <1GB RAM)",
+                "type": "none"
+            }
+        ],
+        "short_id": "T00026",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "cloud",
+        "supported_servers": [],
+        "symlink": null,
+        "tags": [
+            "wireguard",
+            "networking"
+        ],
+        "time_estimation": "60m",
+        "title": "Deploying Wireguard for private mesh networking",
+        "tools": [],
+        "topic_name": "admin",
+        "topic_name_human": "Galaxy Server administration",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "wireguard",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/wireguard/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/wireguard/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/wireguard/tutorial.json"
+        },
+        "version": 3,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 21,
+        "visitors": 988,
+        "zenodo_link": ""
+    },
+    {
+        "abbreviations": {
+            "CI": "Continuous Integration"
+        },
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/jenkins/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            }
+        ],
+        "dir": "topics/admin/tutorials/jenkins",
+        "edam_operation": [],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "admin/jenkins",
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Automate all the things!",
+            "Especially regular tasks you might forget to do",
+            "Automatically run Ansible to ensure machines are in compliance"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2022-10-18",
+        "objectives": [
+            "Setup Jenkins",
+            "Setup a simple job",
+            "Automate running of the Galaxy playbook",
+            "Secure Jenkins"
+        ],
+        "pageviews": 16192,
+        "pub_date": "2019-08-06",
+        "questions": [
+            "What sort of tasks should be automated?",
+            "What are my options for automation?",
+            "How can I automate repetitive tasks?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "admin",
+                "tutorials": [
+                    "ansible",
+                    "ansible-galaxy"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00011",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "features",
+        "supported_servers": [],
+        "symlink": null,
+        "tags": [
+            "ansible",
+            "automation"
+        ],
+        "time_estimation": "1h",
+        "title": "Automation with Jenkins",
+        "tools": [],
+        "topic_name": "admin",
+        "topic_name_human": "Galaxy Server administration",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "jenkins",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/jenkins/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/jenkins/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/jenkins/tutorial.json"
+        },
+        "version": 10,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 39,
+        "visitors": 8144
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/tus/tutorial.json",
+        "contributors": [
+            {
+                "id": "mvdbeek",
+                "joined": "2018-06",
+                "name": "Marius van den Beek",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "ch",
+                "email": "lucille.delisle@epfl.ch",
+                "id": "lldelisle",
+                "joined": "2019-08",
+                "location": {
+                    "country": "CH",
+                    "lat": 46.52,
+                    "lon": 6.56
+                },
+                "name": "Lucille Delisle",
+                "orcid": "0000-0002-1964-4960",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/lldelisle.json"
+            }
+        ],
+        "dir": "topics/admin/tutorials/tus",
+        "edam_operation": [],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "admin/tus",
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Use TUS to make uploads more efficient, especially for large uploads over unstable connections."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-14",
+        "objectives": [
+            "Setup TUSd",
+            "Configure Galaxy to use it to process uploads"
+        ],
+        "pageviews": 1065,
+        "pub_date": "2022-03-01",
+        "questions": null,
+        "recordings": [
+            {
+                "captioners": [
+                    "hexylena"
+                ],
+                "date": "2022-03-11",
+                "galaxy_version": "22.01",
+                "length": "7M",
+                "speakers": [
+                    "hexylena"
+                ],
+                "youtube_id": "v5sbIqF_0qo"
+            }
+        ],
+        "requirements": [
+            {
+                "topic_name": "admin",
+                "tutorials": [
+                    "ansible",
+                    "ansible-galaxy"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00024",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "features",
+        "supported_servers": [],
+        "symlink": null,
+        "time_estimation": "30M",
+        "title": "Performant Uploads with TUS",
+        "tools": [],
+        "topic_name": "admin",
+        "topic_name_human": "Galaxy Server administration",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "tus",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/tus/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/tus/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/tus/tutorial.json"
+        },
+        "version": 17,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 325,
+        "visitors": 707,
+        "zenodo_link": ""
+    },
+    {
+        "abbreviations": {
+            "FTP": "File Transfer Protocol",
+            "NAT": "Network Address Translation"
+        },
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/ftp/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "ch",
+                "email": "lucille.delisle@epfl.ch",
+                "id": "lldelisle",
+                "joined": "2019-08",
+                "location": {
+                    "country": "CH",
+                    "lat": 46.52,
+                    "lon": 6.56
+                },
+                "name": "Lucille Delisle",
+                "orcid": "0000-0002-1964-4960",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/lldelisle.json"
+            }
+        ],
+        "dir": "topics/admin/tutorials/ftp",
+        "edam_operation": [],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "admin/ftp",
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "FTP is easy to deploy thanks to the role",
+            "Users can be authenticated with their Galaxy credentials simplifying the user management process significantly"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-02-20",
+        "objectives": [
+            "Configure galaxy and install a FTP server.",
+            "Use an Ansible playbook for this."
+        ],
+        "pageviews": 1469,
+        "pub_date": "2021-06-18",
+        "questions": [
+            "How can I setup FTP to be easy for my users?",
+            "Can I authenticate ftp users with Galaxy credentials?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "admin",
+                "tutorials": [
+                    "ansible",
+                    "ansible-galaxy"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00008",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "features",
+        "supported_servers": [],
+        "symlink": null,
+        "tags": [
+            "data",
+            "git-gat"
+        ],
+        "time_estimation": "1h",
+        "title": "Enable upload via FTP",
+        "tools": [],
+        "topic_name": "admin",
+        "topic_name_human": "Galaxy Server administration",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "ftp",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/ftp/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/ftp/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/ftp/tutorial.json"
+        },
+        "version": 23,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 98,
+        "visitors": 1037,
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/sentry/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "mvdbeek"
+            ],
+            "editing": [
+                "hexylena"
+            ]
+        },
+        "contributors": [
+            {
+                "id": "mvdbeek",
+                "joined": "2018-06",
+                "name": "Marius van den Beek",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            }
+        ],
+        "dir": "topics/admin/tutorials/sentry",
+        "edam_operation": [],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "admin/sentry",
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": null,
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-03-18",
+        "objectives": [
+            "Have an understanding of Sentry",
+            "Install Sentry",
+            "Configure Galaxy and Pulsar to send errors to Sentry",
+            "Monitor performance with Sentry"
+        ],
+        "pageviews": 180,
+        "pub_date": "2023-04-19",
+        "questions": null,
+        "requirements": [
+            {
+                "topic_name": "admin",
+                "tutorials": [
+                    "ansible",
+                    "ansible-galaxy",
+                    "pulsar"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00330",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "monitoring",
+        "supported_servers": [],
+        "symlink": null,
+        "tags": [
+            "ansible",
+            "git-gat"
+        ],
+        "time_estimation": "1h",
+        "title": "Monitoring Galaxy and Pulsar with Sentry",
+        "tools": [],
+        "topic_name": "admin",
+        "topic_name_human": "Galaxy Server administration",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "sentry",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/admin/tutorials/sentry/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/sentry/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/admin/tutorials/sentry/tutorial.json"
+        },
+        "version": 6,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 95,
+        "visitors": 144,
         "zenodo_link": ""
     },
     {
@@ -7253,7 +7253,7 @@
             "Have an understanding of how to use Galaxy's Helm chart",
             "Be able to use Helm to install different flavors of Galaxy for different purposes"
         ],
-        "pageviews": 2304,
+        "pageviews": 2345,
         "priority": 2,
         "pub_date": "2019-07-02",
         "questions": [
@@ -7292,8 +7292,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 146,
-        "visitors": 1311
+        "visit_duration": 143,
+        "visitors": 1349
     },
     {
         "admin_install": {
@@ -7358,7 +7358,7 @@
             "Launch a VM with Terraform",
             "Launch and tear down a cluster with Terraform"
         ],
-        "pageviews": 5755673,
+        "pageviews": 5926026,
         "priority": 3,
         "pub_date": "2018-10-27",
         "questions": [
@@ -7401,7 +7401,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 205,
-        "visitors": 2078824,
+        "visitors": 2148720,
         "zenodo_link": ""
     },
     {
@@ -7412,7 +7412,7 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/ai4life/tutorials/welcome-bioimageio/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ai4life/tutorials/contribute-materials/tutorial.json",
         "contributors": [
             {
                 "bio": "Post-doctoral researcher at UC3M",
@@ -7427,14 +7427,14 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/cfusterbarcelo.json"
             }
         ],
-        "dir": "topics/ai4life/tutorials/welcome-bioimageio",
+        "dir": "topics/ai4life/tutorials/contribute-materials",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": false,
-        "id": "ai4life/welcome-bioimageio",
+        "id": "ai4life/contribute-materials",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -7448,20 +7448,18 @@
         "layout": "tutorial_slides_ai4life",
         "license": "CC-BY-4.0",
         "logo": "topics/ai4life/images/AI4Life-logo_giraffe-nodes.png",
-        "mod_date": "2023-05-18",
+        "mod_date": "2023-05-24",
         "objectives": [
-            "Overview",
-            "Content",
-            "Models"
+            "Get to know how to contribute with models to the BioImage.IO"
         ],
-        "pageviews": 1651106,
-        "pub_date": "2023-05-11",
+        "pageviews": 1789000,
+        "pub_date": "2023-05-18",
         "questions": [
-            "What can be found in the BioImage Model Zoo?",
-            "Why is it worth trying?",
-            "How does it work?"
+            "What is contained in a BioImage.IO model?",
+            "Which are the requirements to contribute?",
+            "How to contribute?"
         ],
-        "short_id": "S00106",
+        "short_id": "S00107",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
@@ -7503,8 +7501,8 @@
             "bioimageio",
             "image analysis"
         ],
-        "time_estimation": "5m",
-        "title": "Welcome to the BioImage Model Zoo",
+        "time_estimation": "10m",
+        "title": "Contribute to the BioImage.IO models",
         "tools": [],
         "topic_name": "ai4life",
         "topic_name_human": "Image analysis using Deep Learning",
@@ -7514,19 +7512,19 @@
             "tutorial": [],
             "video": true
         },
-        "tutorial_name": "welcome-bioimageio",
+        "tutorial_name": "contribute-materials",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/ai4life/tutorials/welcome-bioimageio/slides.html",
+        "url": "https://training.galaxyproject.org//topics/ai4life/tutorials/contribute-materials/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ai4life/tutorials/welcome-bioimageio/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/ai4life/tutorials/welcome-bioimageio/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ai4life/tutorials/contribute-materials/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ai4life/tutorials/contribute-materials/slides.json"
         },
         "version": 3,
         "video": true,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 143,
-        "visitors": 712068
+        "visit_duration": 144,
+        "visitors": 766489
     },
     {
         "admin_install": {
@@ -7536,7 +7534,7 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/ai4life/tutorials/getting-started/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ai4life/tutorials/welcome-bioimageio/tutorial.json",
         "contributors": [
             {
                 "bio": "Post-doctoral researcher at UC3M",
@@ -7551,14 +7549,14 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/cfusterbarcelo.json"
             }
         ],
-        "dir": "topics/ai4life/tutorials/getting-started",
+        "dir": "topics/ai4life/tutorials/welcome-bioimageio",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": false,
-        "id": "ai4life/getting-started",
+        "id": "ai4life/welcome-bioimageio",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -7572,20 +7570,20 @@
         "layout": "tutorial_slides_ai4life",
         "license": "CC-BY-4.0",
         "logo": "topics/ai4life/images/AI4Life-logo_giraffe-nodes.png",
-        "mod_date": "2023-05-24",
+        "mod_date": "2023-05-18",
         "objectives": [
-            "Share what BioImage Model Zoo is.",
-            "Provide a general view of what can be done with BioImage Model Zoo.",
-            "Explain who can and should contribute to the BioImage Model Zoo."
+            "Overview",
+            "Content",
+            "Models"
         ],
-        "pageviews": 1754502,
-        "pub_date": "2023-04-18",
+        "pageviews": 1821376,
+        "pub_date": "2023-05-11",
         "questions": [
-            "What is BioImage Model Zoo?",
-            "Who participates in the BioImage Model Zoo?",
-            "Who can participate in the BioImage Model Zoo?"
+            "What can be found in the BioImage Model Zoo?",
+            "Why is it worth trying?",
+            "How does it work?"
         ],
-        "short_id": "S00105",
+        "short_id": "S00106",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
@@ -7628,7 +7626,7 @@
             "image analysis"
         ],
         "time_estimation": "5m",
-        "title": "BioImage Model Zoo: Advanced models in one-click",
+        "title": "Welcome to the BioImage Model Zoo",
         "tools": [],
         "topic_name": "ai4life",
         "topic_name_human": "Image analysis using Deep Learning",
@@ -7638,19 +7636,19 @@
             "tutorial": [],
             "video": true
         },
-        "tutorial_name": "getting-started",
+        "tutorial_name": "welcome-bioimageio",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/ai4life/tutorials/getting-started/slides.html",
+        "url": "https://training.galaxyproject.org//topics/ai4life/tutorials/welcome-bioimageio/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ai4life/tutorials/getting-started/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/ai4life/tutorials/getting-started/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ai4life/tutorials/welcome-bioimageio/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ai4life/tutorials/welcome-bioimageio/slides.json"
         },
-        "version": 4,
+        "version": 3,
         "video": true,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 143,
-        "visitors": 759114
+        "visit_duration": 144,
+        "visitors": 780840
     },
     {
         "admin_install": {
@@ -7660,7 +7658,7 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/ai4life/tutorials/contribute-materials/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ai4life/tutorials/getting-started/tutorial.json",
         "contributors": [
             {
                 "bio": "Post-doctoral researcher at UC3M",
@@ -7675,14 +7673,14 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/cfusterbarcelo.json"
             }
         ],
-        "dir": "topics/ai4life/tutorials/contribute-materials",
+        "dir": "topics/ai4life/tutorials/getting-started",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": false,
-        "id": "ai4life/contribute-materials",
+        "id": "ai4life/getting-started",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -7698,16 +7696,18 @@
         "logo": "topics/ai4life/images/AI4Life-logo_giraffe-nodes.png",
         "mod_date": "2023-05-24",
         "objectives": [
-            "Get to know how to contribute with models to the BioImage.IO"
+            "Share what BioImage Model Zoo is.",
+            "Provide a general view of what can be done with BioImage Model Zoo.",
+            "Explain who can and should contribute to the BioImage Model Zoo."
         ],
-        "pageviews": 1618730,
-        "pub_date": "2023-05-18",
+        "pageviews": 1924772,
+        "pub_date": "2023-04-18",
         "questions": [
-            "What is contained in a BioImage.IO model?",
-            "Which are the requirements to contribute?",
-            "How to contribute?"
+            "What is BioImage Model Zoo?",
+            "Who participates in the BioImage Model Zoo?",
+            "Who can participate in the BioImage Model Zoo?"
         ],
-        "short_id": "S00107",
+        "short_id": "S00105",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
@@ -7749,8 +7749,8 @@
             "bioimageio",
             "image analysis"
         ],
-        "time_estimation": "10m",
-        "title": "Contribute to the BioImage.IO models",
+        "time_estimation": "5m",
+        "title": "BioImage Model Zoo: Advanced models in one-click",
         "tools": [],
         "topic_name": "ai4life",
         "topic_name_human": "Image analysis using Deep Learning",
@@ -7760,19 +7760,19 @@
             "tutorial": [],
             "video": true
         },
-        "tutorial_name": "contribute-materials",
+        "tutorial_name": "getting-started",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/ai4life/tutorials/contribute-materials/slides.html",
+        "url": "https://training.galaxyproject.org//topics/ai4life/tutorials/getting-started/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ai4life/tutorials/contribute-materials/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/ai4life/tutorials/contribute-materials/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ai4life/tutorials/getting-started/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ai4life/tutorials/getting-started/slides.json"
         },
-        "version": 3,
+        "version": 4,
         "video": true,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 143,
-        "visitors": 697705
+        "visit_duration": 144,
+        "visitors": 827896
     },
     {
         "admin_install": {
@@ -7879,11 +7879,11 @@
             "Visualisation",
             "Sequencing quality control",
             "De-novo assembly",
-            "Formatting",
             "Sequence assembly validation",
-            "Sequence composition calculation",
+            "Statistical calculation",
             "Validation",
-            "Statistical calculation"
+            "Sequence composition calculation",
+            "Formatting"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -7896,6 +7896,7 @@
         "hands_on": true,
         "id": "assembly/general-introduction",
         "inexact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.eu",
             "UseGalaxy.fr"
@@ -7912,24 +7913,24 @@
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-09-12",
         "objectives": [
             "assemble some paired end reads using Velvet",
             "examine the output of the assembly."
         ],
-        "pageviews": 5773889,
+        "pageviews": 5945572,
         "pub_date": "2017-05-23",
         "questions": [
             "How do we perform a very basic genome assembly from short read data?"
         ],
         "short_id": "T00034",
         "short_tools": [
-            "velvetg",
-            "multiqc",
+            "fastq_paired_end_interlacer",
+            "velveth",
             "quast",
+            "multiqc",
             "fastqc",
-            "velveth",
-            "fastq_paired_end_interlacer"
+            "velvetg"
         ],
         "slides": true,
         "slides_recordings": [
@@ -7966,6 +7967,11 @@
                 }
             ],
             "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -8014,12 +8020,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/general-introduction/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/general-introduction/tutorial.json"
         },
-        "version": 28,
+        "version": 29,
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 317,
-        "visitors": 2091066,
+        "visit_duration": 319,
+        "visitors": 2161888,
         "workflows": [
             {
                 "creators": [],
@@ -8175,7 +8181,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nmutant_R1.fastq\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nmutant_R2.fastq\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nwildtype.fna\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"FastQC\"];\n  0 -->|output| 3;\n  22a51e6e-2e5f-4415-a127-e0b1c179a1b1[\"Output\\nfastqc_html\"];\n  3 --> 22a51e6e-2e5f-4415-a127-e0b1c179a1b1;\n  style 22a51e6e-2e5f-4415-a127-e0b1c179a1b1 stroke:#2c3143,stroke-width:4px;\n  51ec8c05-eb47-4359-9120-0eca1a6d5c2f[\"Output\\nfastqc_txt\"];\n  3 --> 51ec8c05-eb47-4359-9120-0eca1a6d5c2f;\n  style 51ec8c05-eb47-4359-9120-0eca1a6d5c2f stroke:#2c3143,stroke-width:4px;\n  4[\"FastQC\"];\n  1 -->|output| 4;\n  5[\"FASTQ interlacer\"];\n  0 -->|output| 5;\n  1 -->|output| 5;\n  225edf5f-3b90-4f84-a38a-5c786000a3fc[\"Output\\noutput_pairs\"];\n  5 --> 225edf5f-3b90-4f84-a38a-5c786000a3fc;\n  style 225edf5f-3b90-4f84-a38a-5c786000a3fc stroke:#2c3143,stroke-width:4px;\n  dae90093-ae96-4bb2-824d-c92b61585096[\"Output\\noutput_singles\"];\n  5 --> dae90093-ae96-4bb2-824d-c92b61585096;\n  style dae90093-ae96-4bb2-824d-c92b61585096 stroke:#2c3143,stroke-width:4px;\n  6[\"MultiQC\"];\n  3 -->|text_file| 6;\n  4 -->|text_file| 6;\n  85e3704a-859d-4657-b3d7-9b67e4981d21[\"Output\\nmultiqc_stats\"];\n  6 --> 85e3704a-859d-4657-b3d7-9b67e4981d21;\n  style 85e3704a-859d-4657-b3d7-9b67e4981d21 stroke:#2c3143,stroke-width:4px;\n  fab7e06a-604e-4432-b0ed-b63157a8643b[\"Output\\nmultiqc_report\"];\n  6 --> fab7e06a-604e-4432-b0ed-b63157a8643b;\n  style fab7e06a-604e-4432-b0ed-b63157a8643b stroke:#2c3143,stroke-width:4px;\n  7[\"velveth\"];\n  5 -->|outfile_pairs| 7;\n  607a214d-9137-4e73-9b73-954c79678937[\"Output\\nvelveth_out\"];\n  7 --> 607a214d-9137-4e73-9b73-954c79678937;\n  style 607a214d-9137-4e73-9b73-954c79678937 stroke:#2c3143,stroke-width:4px;\n  8[\"velvetg\"];\n  7 -->|out_file1| 8;\n  b0cf3779-6199-42c9-963f-a733559f90bb[\"Output\\nvelvet_contigs\"];\n  8 --> b0cf3779-6199-42c9-963f-a733559f90bb;\n  style b0cf3779-6199-42c9-963f-a733559f90bb stroke:#2c3143,stroke-width:4px;\n  54926701-ccae-4143-b649-b7e08e1c6a8e[\"Output\\nvelvet_stats\"];\n  8 --> 54926701-ccae-4143-b649-b7e08e1c6a8e;\n  style 54926701-ccae-4143-b649-b7e08e1c6a8e stroke:#2c3143,stroke-width:4px;\n  9[\"Quast\"];\n  2 -->|output| 9;\n  8 -->|contigs| 9;\n  0babe959-4d63-4838-9e18-4526b3dd0db5[\"Output\\nquast_report_html\"];\n  9 --> 0babe959-4d63-4838-9e18-4526b3dd0db5;\n  style 0babe959-4d63-4838-9e18-4526b3dd0db5 stroke:#2c3143,stroke-width:4px;\n  f41c43c4-763c-42bc-b36e-9ea76e7752c2[\"Output\\nquast_report_pdf\"];\n  9 --> f41c43c4-763c-42bc-b36e-9ea76e7752c2;\n  style f41c43c4-763c-42bc-b36e-9ea76e7752c2 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
+                "modified": "2024-10-02 12:08:06 +0000",
                 "name": "Intro to Genome Assembly",
                 "outputs": [
                     {
@@ -8685,105 +8691,91 @@
                 {
                     "name": "flye",
                     "owner": "bgruening",
-                    "revisions": "291923e6f276",
+                    "revisions": "3ee0ef312022",
                     "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "racon",
-                    "owner": "bgruening",
-                    "revisions": "78c533842eeb",
-                    "tool_panel_section_label": "Assembly",
+                    "name": "prokka",
+                    "owner": "crs4",
+                    "revisions": "bf68eb663bc3",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fastqc",
+                    "name": "prokka",
+                    "owner": "crs4",
+                    "revisions": "111884f0d912",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bwa",
                     "owner": "devteam",
-                    "revisions": "5ec9f6bceaee",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "3fe632431b68",
+                    "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "bandage",
                     "owner": "iuc",
-                    "revisions": "ddddce450736",
+                    "revisions": "b2860df42e16",
                     "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "busco",
+                    "name": "bandage",
                     "owner": "iuc",
-                    "revisions": "ea8146ee148f",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "94fe43e75ddc",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "fasta_stats",
                     "owner": "iuc",
-                    "revisions": "0dbb995c7d35",
+                    "revisions": "9c620a950d3a",
                     "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fastp",
+                    "name": "fasta_stats",
                     "owner": "iuc",
-                    "revisions": "c59d48774d03",
+                    "revisions": "0dbb995c7d35",
                     "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "genomescope",
-                    "owner": "iuc",
-                    "revisions": "01210c4e9144",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "medaka_consensus_pipeline",
-                    "owner": "iuc",
-                    "revisions": "fc8804320156",
-                    "tool_panel_section_label": "Nanopore",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "meryl",
-                    "owner": "iuc",
-                    "revisions": "29dabd8db6f2",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "minimap2",
+                    "name": "jbrowse",
                     "owner": "iuc",
-                    "revisions": "be1d967337e4",
-                    "tool_panel_section_label": "Mapping",
+                    "revisions": "2bb2e07a7a21",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "multiqc",
+                    "name": "jbrowse",
                     "owner": "iuc",
-                    "revisions": "abfd8a6544d7",
-                    "tool_panel_section_label": "Quality Control",
+                    "revisions": "17359b808b01",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "nanoplot",
                     "owner": "iuc",
-                    "revisions": "a02b8b3f5a0c",
+                    "revisions": "edbb6c5028f5",
                     "tool_panel_section_label": "Nanopore",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "quast",
+                    "name": "pilon",
                     "owner": "iuc",
-                    "revisions": "72472698a2df",
+                    "revisions": "11e5408fd238",
                     "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: flye\n  owner: bgruening\n  revisions: 291923e6f276\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: racon\n  owner: bgruening\n  revisions: 78c533842eeb\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: ea8146ee148f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n  owner: iuc\n  revisions: 0dbb995c7d35\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: c59d48774d03\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: genomescope\n  owner: iuc\n  revisions: 01210c4e9144\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: medaka_consensus_pipeline\n  owner: iuc\n  revisions: fc8804320156\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n  owner: iuc\n  revisions: 29dabd8db6f2\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: be1d967337e4\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: abfd8a6544d7\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: a02b8b3f5a0c\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 72472698a2df\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/largegenome/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: flye\n  owner: bgruening\n  revisions: 3ee0ef312022\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: prokka\n  owner: crs4\n  revisions: bf68eb663bc3\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: prokka\n  owner: crs4\n  revisions: 111884f0d912\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: 3fe632431b68\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: b2860df42e16\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: 94fe43e75ddc\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n  owner: iuc\n  revisions: 9c620a950d3a\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n  owner: iuc\n  revisions: 0dbb995c7d35\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 2bb2e07a7a21\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 17359b808b01\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: edbb6c5028f5\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pilon\n  owner: iuc\n  revisions: 11e5408fd238\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/chloroplast-assembly/tutorial.json",
         "contributors": [
             {
                 "id": "annasyme",
@@ -8794,94 +8786,106 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
             }
         ],
-        "dir": "topics/assembly/tutorials/largegenome",
+        "dir": "topics/assembly/tutorials/chloroplast-assembly",
         "edam_operation": [
-            "Visualisation",
-            "Sequencing quality control",
-            "Sequence assembly validation",
-            "Sequence composition calculation",
-            "Pairwise sequence alignment",
-            "Sequence assembly visualisation",
-            "Transcriptome assembly",
+            "Scatter plot plotting",
+            "Genome annotation",
+            "Sequence alignment",
             "Cross-assembly",
-            "Validation",
+            "Read mapping",
+            "Genome visualisation",
             "Genome assembly",
-            "Base-calling",
-            "Sequence assembly",
-            "Statistical calculation",
-            "Scaffolding",
-            "Sequence contamination filtering",
             "De-novo assembly",
             "Box-Whisker plot plotting",
-            "Scatter plot plotting",
+            "Analysis",
+            "Sequence assembly",
+            "Generation",
+            "Gene prediction",
             "Mapping assembly",
-            "Variant calling"
+            "Sequence assembly visualisation",
+            "Read alignment",
+            "Genome indexing",
+            "Coding region prediction"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org.au"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "assembly/largegenome",
+        "id": "assembly/chloroplast-assembly",
         "inexact_supported_servers": [
-            "UseGalaxy.cz"
+            "GalaxyTrakr",
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "We can assemble long reads from plant or animal species into large contigs",
-            "These contigs can be polished with both long and short reads",
-            "We can assess the quality of this assembly with various tools"
+            "A chloroplast genome can be assembled with long reads and polished with short reads",
+            "The assembly graph is useful to look at and think about genomic structure",
+            "We can map raw reads back to the assembly and investigate areas of high or low read coverage",
+            "We can view an assembly, its mapped reads, and its annotations in JBrowse"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-31",
+        "mod_date": "2024-09-18",
         "objectives": [
-            "Assemble a large genome from long reads",
-            "Polish the assembly",
-            "Assess the quality of the assembly"
+            "Assemble a chloroplast genome from long reads",
+            "Polish the assembly with short reads",
+            "Annotate the assembly and view",
+            "Map reads to the assembly and view"
         ],
-        "pageviews": 4728,
-        "pub_date": "2023-03-06",
+        "pageviews": 9814,
+        "pub_date": "2020-12-04",
         "questions": [
-            "How can we assemble a large plant or animal genome?"
+            "How can we assemble a chloroplast genome?"
         ],
         "recordings": [
             {
                 "captioners": [
                     "annasyme"
                 ],
-                "date": "2023-05-16",
-                "galaxy_version": "23.01",
-                "length": "25M",
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "35M",
                 "speakers": [
                     "annasyme"
                 ],
-                "youtube_id": "BM70nvwWjOY"
+                "youtube_id": "eyfCyINTD_E"
+            },
+            {
+                "bot-timestamp": 1726113532,
+                "captioners": [
+                    "hannahkimincompbio"
+                ],
+                "date": "2024-09-12",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "16M",
+                "speakers": [
+                    "hannahkimincompbio"
+                ],
+                "youtube_id": "gIcbY9kXdTo"
             }
         ],
-        "short_id": "T00331",
+        "short_id": "T00030",
         "short_tools": [
-            "barchart_gnuplot",
-            "nanoplot",
-            "fastp",
-            "multiqc",
-            "busco",
-            "racon",
-            "flye",
-            "quast",
-            "fasta-stats",
-            "fastqc",
-            "genomescope",
-            "meryl",
-            "minimap2",
+            "bwa_mem",
+            "prokka",
+            "jbrowse",
             "bandage_image",
-            "medaka_consensus_pipeline"
+            "upload1",
+            "bandage_info",
+            "fasta-stats",
+            "flye",
+            "nanoplot",
+            "pilon"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -8891,46 +8895,64 @@
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
                 }
             ],
             "inexact": [
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
         "tags": [
-            "assembly",
-            "polishing",
+            "plants",
             "nanopore",
-            "plants"
+            "jbrowse1"
         ],
         "time_estimation": "2h",
-        "title": "Large genome assembly and polishing",
+        "title": "Chloroplast genome assembly",
         "tools": [
-            "barchart_gnuplot",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
+            "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
             "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
-            "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1",
+            "upload1"
         ],
         "topic_name": "assembly",
         "topic_name_human": "Assembly",
@@ -8940,73 +8962,51 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "largegenome",
+        "tutorial_name": "chloroplast-assembly",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/largegenome/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/chloroplast-assembly/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/largegenome/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/largegenome/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/chloroplast-assembly/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/chloroplast-assembly/tutorial.json"
         },
-        "version": 11,
+        "version": 19,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 131,
-        "visitors": 3651,
+        "visit_duration": 172,
+        "visitors": 6133,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
-                    }
-                ],
-                "description": "",
+                "creators": [],
+                "description": "Assembly",
                 "features": {
                     "comments": false,
-                    "parameters": true,
-                    "report": {
-                        "markdown": "\n# Workflow Report for Assembly Polishing\n\n## Workflow steps\n\n```galaxy\nworkflow_display()\n```\n\n## Fasta statistics after Racon long-read polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Racon long read polish\")\n```\n\n\n## Fasta statistics after Medaka polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Medaka polish\")\n```\n\n## Fasta statistics after Racon short-read polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Racon short read polish\")\n```\n\n\n\n\n"
-                    },
-                    "subworkflows": true
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"]\n  4[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with long reads, x4 - upgraded\"]\n  0 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Medaka polish\"]\n  4 -> 5 [label=\"Assembly polished by long reads using Racon\"]\n  1 -> 5 [label=\"output\"]\n  ke3136060bce74af387c49dcbb0d1f531[color=lightseagreen,label=\"Output\\nAssembly polished by long reads using Medaka\"]\n  5 -> ke3136060bce74af387c49dcbb0d1f531\n  6[label=\"Fasta statistics after Racon long read polish\"]\n  4 -> 6 [label=\"Assembly polished by long reads using Racon\"]\n  7[label=\"Fasta statistics after Medaka polish\"]\n  5 -> 7 [label=\"out_consensus\"]\n  8[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with Illumina reads R1 only, x2 - upgraded\"]\n  5 -> 8 [label=\"out_consensus\"]\n  3 -> 8 [label=\"output\"]\n  9[label=\"Fasta statistics after Racon short read polish\"]\n  8 -> 9 [label=\"Assembly polished by short reads using Racon\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina_reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nNanopore_reads\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTiny_set_illumina_read\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTiny_set_nanopore_reads\"]\n  4[label=\"Flye assembly\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"NanoPlot\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"Map with BWA-MEM\"]\n  0 -> 6 [label=\"output\"]\n  4 -> 6 [label=\"consensus\"]\n  7[label=\"Fasta Statistics\"]\n  4 -> 7 [label=\"consensus\"]\n  8[label=\"Bandage Info\"]\n  4 -> 8 [label=\"assembly_gfa\"]\n  9[label=\"Bandage Image\"]\n  4 -> 9 [label=\"assembly_gfa\"]\n  10[label=\"pilon\"]\n  6 -> 10 [label=\"bam_output\"]\n  4 -> 10 [label=\"consensus\"]\n  11[label=\"Fasta Statistics\"]\n  10 -> 11 [label=\"output_fasta\"]\n  12[label=\"Map with BWA-MEM\"]\n  2 -> 12 [label=\"output\"]\n  10 -> 12 [label=\"output_fasta\"]\n  13[label=\"Map with BWA-MEM\"]\n  3 -> 13 [label=\"output\"]\n  10 -> 13 [label=\"output_fasta\"]\n  14[label=\"Prokka\"]\n  10 -> 14 [label=\"output_fasta\"]\n  15[label=\"JBrowse\"]\n  10 -> 15 [label=\"output_fasta\"]\n  12 -> 15 [label=\"bam_output\"]\n  13 -> 15 [label=\"bam_output\"]\n  16[label=\"JBrowse\"]\n  10 -> 16 [label=\"output_fasta\"]\n  14 -> 16 [label=\"out_gff\"]\n}",
                 "history": [
                     {
-                        "hash": "091a0834c77e69841f4d07570420c632c6c5043c",
-                        "message": "Update Galaxy-Workflow-Assembly_polishing.ga",
-                        "num": 5,
-                        "short_hash": "091a0834c",
-                        "unix": "1715074278"
-                    },
-                    {
-                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
-                        "message": "new versions of workflows",
-                        "num": 4,
-                        "short_hash": "e8ddbcdd5",
-                        "unix": "1714537936"
-                    },
-                    {
-                        "hash": "f294a05b57afbe9ec436008d1d2571f6d42fb977",
-                        "message": "Rename Galaxy-Workflow-Assembly_polishing.ga to Galaxy-Workflow-Assembly_polishing_old.ga",
+                        "hash": "ed613d5a1151b9f28f238d38166228cd186f2462",
+                        "message": "Updated workflow with new version of Fasta Stats",
                         "num": 3,
-                        "short_hash": "f294a05b5",
-                        "unix": "1714537220"
+                        "short_hash": "ed613d5a1",
+                        "unix": "1683677548"
                     },
                     {
-                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
-                        "message": "add/complete creator info on workflows",
+                        "hash": "2b2bcd3917fafb9b8bc912598edf3ab28cee70d5",
+                        "message": "swap version of tool for one on every server",
                         "num": 2,
-                        "short_hash": "62e77944b",
-                        "unix": "1676627603"
+                        "short_hash": "2b2bcd391",
+                        "unix": "1613141279"
                     },
                     {
-                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
-                        "message": "large genome tutorial",
+                        "hash": "ebcd3d5282b03ce89bd65e0d39748970c7738481",
+                        "message": "updated workflow added",
                         "num": 1,
-                        "short_hash": "9fcb3aeec",
-                        "unix": "1665123856"
+                        "short_hash": "ebcd3d528",
+                        "unix": "1611556716"
                     }
                 ],
                 "inputs": [
@@ -9019,22 +9019,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Assembly to be polished"
+                                "name": "Illumina_reads"
                             }
                         ],
-                        "label": "Assembly to be polished",
+                        "label": "Illumina_reads",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 19.464939294568495,
-                            "top": 0.0
+                            "left": 294.1953125,
+                            "top": 123.90625
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "52bc9ac4-ac3c-48eb-aead-94a0a14417fc",
-                        "when": null,
+                        "uuid": "35434963-8a88-47e2-99f0-ef3eb0484f7e",
                         "workflow_outputs": []
                     },
                     {
@@ -9046,22 +9045,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "long reads"
+                                "name": "Nanopore_reads"
                             }
                         ],
-                        "label": "long reads",
+                        "label": "Nanopore_reads",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
                             "left": 0.0,
-                            "top": 142.48340578478533
+                            "top": 354.859375
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "688866c4-de9b-4b78-8df3-b169d28b1617",
-                        "when": null,
+                        "uuid": "59b157b8-f5c4-498c-b66c-0d206ba06ee9",
                         "workflow_outputs": []
                     },
                     {
@@ -9073,29 +9071,22 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "minimap setting (for long reads)"
+                                "name": "Tiny_set_illumina_read"
                             }
                         ],
-                        "label": "minimap setting (for long reads)",
-                        "name": "Input parameter",
+                        "label": "Tiny_set_illumina_read",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 13.133522093825794,
-                            "top": 247.1519749531627
+                            "left": 908.265625,
+                            "top": 919.359375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "c1f18b5c-e8db-4046-b876-9b28a77cf66e",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "ce393bcf-42e3-43ee-9056-a99e8c077a29"
-                            }
-                        ]
+                        "type": "data_input",
+                        "uuid": "39c47516-8e9c-4d44-b6bc-326c4be142ee",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
@@ -9106,2990 +9097,1213 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Illumina reads R1"
+                                "name": "Tiny_set_nanopore_reads"
                             }
                         ],
-                        "label": "Illumina reads R1",
+                        "label": "Tiny_set_nanopore_reads",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 617.719019724734,
-                            "top": 600.0866464299372
+                            "left": 908.2734375,
+                            "top": 1040.5703125
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ea859a58-c81a-4ef6-9bd2-4ef2f17bb5a9",
-                        "when": null,
+                        "uuid": "1257e34e-ad76-4f76-88dc-f22c5cc60b8b",
                         "workflow_outputs": []
                     }
                 ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with long reads, x4 - upgraded\"];\n  style 4 fill:#edd,stroke:#900,stroke-width:4px;\n  0 -->|output| 4;\n  1 -->|output| 4;\n  2 -->|output| 4;\n  5[\"Medaka polish\"];\n  4 -->|Assembly polished by long reads using Racon| 5;\n  1 -->|output| 5;\n  e3136060-bce7-4af3-87c4-9dcbb0d1f531[\"Output\\nAssembly polished by long reads using Medaka\"];\n  5 --> e3136060-bce7-4af3-87c4-9dcbb0d1f531;\n  style e3136060-bce7-4af3-87c4-9dcbb0d1f531 stroke:#2c3143,stroke-width:4px;\n  6[\"Fasta statistics after Racon long read polish\"];\n  4 -->|Assembly polished by long reads using Racon| 6;\n  7[\"Fasta statistics after Medaka polish\"];\n  5 -->|out_consensus| 7;\n  8[\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with Illumina reads R1 only, x2 - upgraded\"];\n  style 8 fill:#edd,stroke:#900,stroke-width:4px;\n  5 -->|out_consensus| 8;\n  3 -->|output| 8;\n  9[\"Fasta statistics after Racon short read polish\"];\n  8 -->|Assembly polished by short reads using Racon| 9;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Assembly polishing - upgraded",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIllumina_reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nNanopore_reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nTiny_set_illumina_read\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nTiny_set_nanopore_reads\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Flye assembly\"];\n  1 -->|output| 4;\n  5[\"NanoPlot\"];\n  1 -->|output| 5;\n  6[\"Map with BWA-MEM\"];\n  0 -->|output| 6;\n  4 -->|consensus| 6;\n  7[\"Fasta Statistics\"];\n  4 -->|consensus| 7;\n  8[\"Bandage Info\"];\n  4 -->|assembly_gfa| 8;\n  9[\"Bandage Image\"];\n  4 -->|assembly_gfa| 9;\n  10[\"pilon\"];\n  6 -->|bam_output| 10;\n  4 -->|consensus| 10;\n  11[\"Fasta Statistics\"];\n  10 -->|output_fasta| 11;\n  12[\"Map with BWA-MEM\"];\n  2 -->|output| 12;\n  10 -->|output_fasta| 12;\n  13[\"Map with BWA-MEM\"];\n  3 -->|output| 13;\n  10 -->|output_fasta| 13;\n  14[\"Prokka\"];\n  10 -->|output_fasta| 14;\n  15[\"JBrowse\"];\n  10 -->|output_fasta| 15;\n  12 -->|bam_output| 15;\n  13 -->|bam_output| 15;\n  16[\"JBrowse\"];\n  10 -->|output_fasta| 16;\n  14 -->|out_gff| 16;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Chloroplast-genome-assembly-and-annotation",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "minimap setting (for long reads)"
-                            }
-                        ],
-                        "label": "minimap setting (for long reads)",
-                        "name": "Input parameter",
-                        "outputs": [],
-                        "position": {
-                            "left": 13.133522093825794,
-                            "top": 247.1519749531627
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "c1f18b5c-e8db-4046-b876-9b28a77cf66e",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "ce393bcf-42e3-43ee-9056-a99e8c077a29"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
                         "id": 4,
                         "input_connections": {
-                            "Assembly to be polished": {
-                                "id": 0,
-                                "input_subworkflow_step_id": 0,
-                                "output_name": "output"
-                            },
-                            "long reads": {
+                            "inputs": {
                                 "id": 1,
-                                "input_subworkflow_step_id": 1,
-                                "output_name": "output"
-                            },
-                            "minimap setting (for long reads) ": {
-                                "id": 2,
-                                "input_subworkflow_step_id": 2,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Racon polish with long reads, x4 - upgraded",
-                        "outputs": [],
+                        "name": "Flye assembly",
+                        "outputs": [
+                            {
+                                "name": "consensus",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "assembly_graph",
+                                "type": "graph_dot"
+                            },
+                            {
+                                "name": "assembly_gfa",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "assembly_info",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "flye_log",
+                                "type": "txt"
+                            }
+                        ],
                         "position": {
-                            "left": 299.6429464825318,
-                            "top": 72.0364210406818
+                            "left": 301.03125,
+                            "top": 244.03125
                         },
-                        "subworkflow": {
-                            "a_galaxy_workflow": "true",
-                            "annotation": "",
-                            "comments": [],
-                            "creator": [
-                                {
-                                    "class": "Person",
-                                    "identifier": "0000-0002-9906-0673",
-                                    "name": "Anna Syme"
-                                }
-                            ],
-                            "format-version": "0.1",
-                            "name": "Racon polish with long reads, x4 - upgraded",
-                            "report": {
-                                "markdown": "\n# Workflow Execution Report\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
-                            },
-                            "steps": {
-                                "0": {
-                                    "annotation": "",
-                                    "content_id": null,
-                                    "errors": null,
-                                    "id": 0,
-                                    "input_connections": {},
-                                    "inputs": [
-                                        {
-                                            "description": "",
-                                            "name": "Assembly to be polished"
-                                        }
-                                    ],
-                                    "label": "Assembly to be polished",
-                                    "name": "Input dataset",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 0,
-                                        "top": 216.625
-                                    },
-                                    "tool_id": null,
-                                    "tool_state": "{\"optional\": false, \"tag\": null}",
-                                    "tool_version": null,
-                                    "type": "data_input",
-                                    "uuid": "c7796c36-adf8-49e4-a8e4-66e606d70311",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "1": {
-                                    "annotation": "",
-                                    "content_id": null,
-                                    "errors": null,
-                                    "id": 1,
-                                    "input_connections": {},
-                                    "inputs": [
-                                        {
-                                            "description": "",
-                                            "name": "long reads"
-                                        }
-                                    ],
-                                    "label": "long reads",
-                                    "name": "Input dataset",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 4.5,
-                                        "top": 360.234375
-                                    },
-                                    "tool_id": null,
-                                    "tool_state": "{\"optional\": false, \"tag\": null}",
-                                    "tool_version": null,
-                                    "type": "data_input",
-                                    "uuid": "e2e4a70b-6e36-4b8b-bdf6-12b97189a6bd",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "10": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                    "errors": null,
-                                    "id": 10,
-                                    "input_connections": {
-                                        "corrected_reads": {
-                                            "id": 8,
-                                            "output_name": "consensus"
-                                        },
-                                        "overlaps": {
-                                            "id": 9,
-                                            "output_name": "alignment_output"
-                                        },
-                                        "reads": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Racon: polish 4",
-                                    "name": "Racon",
-                                    "outputs": [
-                                        {
-                                            "name": "consensus",
-                                            "type": "fasta"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 1496.078125,
-                                        "top": 431.1875
-                                    },
-                                    "post_job_actions": {
-                                        "RenameDatasetActionconsensus": {
-                                            "action_arguments": {
-                                                "newname": "Racon_long_reads_polished_assembly.fasta"
-                                            },
-                                            "action_type": "RenameDatasetAction",
-                                            "output_name": "consensus"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "78c533842eeb",
-                                        "name": "racon",
-                                        "owner": "bgruening",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "1.5.0+galaxy1",
-                                    "type": "tool",
-                                    "uuid": "53f4572e-3a4a-4585-89ab-9459f8a61720",
-                                    "when": null,
-                                    "workflow_outputs": [
-                                        {
-                                            "label": "Assembly polished by long reads using Racon",
-                                            "output_name": "consensus",
-                                            "uuid": "bcf0f03c-5951-46a7-aa38-545aed9bc183"
-                                        }
-                                    ]
-                                },
-                                "2": {
-                                    "annotation": "",
-                                    "content_id": null,
-                                    "errors": null,
-                                    "id": 2,
-                                    "input_connections": {},
-                                    "inputs": [
-                                        {
-                                            "description": "",
-                                            "name": "minimap setting (for long reads) "
-                                        }
-                                    ],
-                                    "label": "minimap setting (for long reads) ",
-                                    "name": "Input parameter",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 0.578125,
-                                        "top": 495.859375
-                                    },
-                                    "tool_id": null,
-                                    "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
-                                    "tool_version": null,
-                                    "type": "parameter_input",
-                                    "uuid": "fb80c05c-08d4-4ac2-b4bf-81ed906e4d72",
-                                    "when": null,
-                                    "workflow_outputs": [
-                                        {
-                                            "label": null,
-                                            "output_name": "output",
-                                            "uuid": "3983ef22-5f05-4384-8f34-6ac8c4b2cc83"
-                                        }
-                                    ]
-                                },
-                                "3": {
-                                    "annotation": "Map raw reads to assembly; output paf",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                    "errors": null,
-                                    "id": 3,
-                                    "input_connections": {
-                                        "fastq_input|analysis_type_selector": {
-                                            "id": 2,
-                                            "output_name": "output"
-                                        },
-                                        "fastq_input|fastq_input1": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        },
-                                        "reference_source|ref_file": {
-                                            "id": 0,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "fastq_input"
-                                        },
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "fastq_input"
-                                        },
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "reference_source"
-                                        }
-                                    ],
-                                    "label": "Minimap2: map long reads to assembly",
-                                    "name": "Map with minimap2",
-                                    "outputs": [
-                                        {
-                                            "name": "alignment_output",
-                                            "type": "bam"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 377.640625,
-                                        "top": 0
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionalignment_output": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "alignment_output"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "be1d967337e4",
-                                        "name": "minimap2",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "2.26+galaxy0",
-                                    "type": "tool",
-                                    "uuid": "0c06144f-d1ac-4b45-9669-1ddf11fcb06b",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "4": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                    "errors": null,
-                                    "id": 4,
-                                    "input_connections": {
-                                        "corrected_reads": {
-                                            "id": 0,
-                                            "output_name": "output"
-                                        },
-                                        "overlaps": {
-                                            "id": 3,
-                                            "output_name": "alignment_output"
-                                        },
-                                        "reads": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Racon: polish 1",
-                                    "name": "Racon",
-                                    "outputs": [
-                                        {
-                                            "name": "consensus",
-                                            "type": "fasta"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 458.640625,
-                                        "top": 518.875
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionconsensus": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "consensus"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "78c533842eeb",
-                                        "name": "racon",
-                                        "owner": "bgruening",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "1.5.0+galaxy1",
-                                    "type": "tool",
-                                    "uuid": "6c144354-91f2-49dd-a1f5-7c4119859730",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "5": {
-                                    "annotation": "Map raw reads to assembly; output paf",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                    "errors": null,
-                                    "id": 5,
-                                    "input_connections": {
-                                        "fastq_input|analysis_type_selector": {
-                                            "id": 2,
-                                            "output_name": "output"
-                                        },
-                                        "fastq_input|fastq_input1": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        },
-                                        "reference_source|ref_file": {
-                                            "id": 4,
-                                            "output_name": "consensus"
-                                        }
-                                    },
-                                    "inputs": [
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "fastq_input"
-                                        },
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "fastq_input"
-                                        },
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "reference_source"
-                                        }
-                                    ],
-                                    "label": "Minimap2: map long reads to polished assembly 1",
-                                    "name": "Map with minimap2",
-                                    "outputs": [
-                                        {
-                                            "name": "alignment_output",
-                                            "type": "bam"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 698.859375,
-                                        "top": 13.390625
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionalignment_output": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "alignment_output"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "be1d967337e4",
-                                        "name": "minimap2",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "2.26+galaxy0",
-                                    "type": "tool",
-                                    "uuid": "c1b83dad-a8ed-42cb-951f-73f59f2dfa92",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "6": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                    "errors": null,
-                                    "id": 6,
-                                    "input_connections": {
-                                        "corrected_reads": {
-                                            "id": 4,
-                                            "output_name": "consensus"
-                                        },
-                                        "overlaps": {
-                                            "id": 5,
-                                            "output_name": "alignment_output"
-                                        },
-                                        "reads": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Racon: polish 2",
-                                    "name": "Racon",
-                                    "outputs": [
-                                        {
-                                            "name": "consensus",
-                                            "type": "fasta"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 759.9375,
-                                        "top": 485.71875
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionconsensus": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "consensus"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "78c533842eeb",
-                                        "name": "racon",
-                                        "owner": "bgruening",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "1.5.0+galaxy1",
-                                    "type": "tool",
-                                    "uuid": "3208491e-b831-4238-957e-5b7388d7ff8d",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "7": {
-                                    "annotation": "Map raw reads to assembly; output paf",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                    "errors": null,
-                                    "id": 7,
-                                    "input_connections": {
-                                        "fastq_input|analysis_type_selector": {
-                                            "id": 2,
-                                            "output_name": "output"
-                                        },
-                                        "fastq_input|fastq_input1": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        },
-                                        "reference_source|ref_file": {
-                                            "id": 6,
-                                            "output_name": "consensus"
-                                        }
-                                    },
-                                    "inputs": [
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "fastq_input"
-                                        },
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "fastq_input"
-                                        },
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "reference_source"
-                                        }
-                                    ],
-                                    "label": "Minimap2: map long reads to polished assembly 2",
-                                    "name": "Map with minimap2",
-                                    "outputs": [
-                                        {
-                                            "name": "alignment_output",
-                                            "type": "bam"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 998.75,
-                                        "top": 27.9375
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionalignment_output": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "alignment_output"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "be1d967337e4",
-                                        "name": "minimap2",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "2.26+galaxy0",
-                                    "type": "tool",
-                                    "uuid": "42af524b-7f74-4c75-8d78-f6888078dd2e",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "8": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                    "errors": null,
-                                    "id": 8,
-                                    "input_connections": {
-                                        "corrected_reads": {
-                                            "id": 6,
-                                            "output_name": "consensus"
-                                        },
-                                        "overlaps": {
-                                            "id": 7,
-                                            "output_name": "alignment_output"
-                                        },
-                                        "reads": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Racon: polish 3",
-                                    "name": "Racon",
-                                    "outputs": [
-                                        {
-                                            "name": "consensus",
-                                            "type": "fasta"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 1089.71875,
-                                        "top": 455.53125
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionconsensus": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "consensus"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "78c533842eeb",
-                                        "name": "racon",
-                                        "owner": "bgruening",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "1.5.0+galaxy1",
-                                    "type": "tool",
-                                    "uuid": "21f339bd-ebc1-4c73-a976-5d0b9ab2127a",
-                                    "when": null,
-                                    "workflow_outputs": []
+                        "post_job_actions": {
+                            "RenameDatasetActionconsensus": {
+                                "action_arguments": {
+                                    "newname": "flye-assembly.fasta"
                                 },
-                                "9": {
-                                    "annotation": "Map raw reads to assembly; output paf",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                    "errors": null,
-                                    "id": 9,
-                                    "input_connections": {
-                                        "fastq_input|analysis_type_selector": {
-                                            "id": 2,
-                                            "output_name": "output"
-                                        },
-                                        "fastq_input|fastq_input1": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        },
-                                        "reference_source|ref_file": {
-                                            "id": 8,
-                                            "output_name": "consensus"
-                                        }
-                                    },
-                                    "inputs": [
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "fastq_input"
-                                        },
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "fastq_input"
-                                        },
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "reference_source"
-                                        }
-                                    ],
-                                    "label": "Minimap2: map long reads to polished assembly 3",
-                                    "name": "Map with minimap2",
-                                    "outputs": [
-                                        {
-                                            "name": "alignment_output",
-                                            "type": "bam"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 1316.53125,
-                                        "top": 38.046875
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionalignment_output": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "alignment_output"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "be1d967337e4",
-                                        "name": "minimap2",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "2.26+galaxy0",
-                                    "type": "tool",
-                                    "uuid": "7d36291e-aa76-4312-9943-b5e56d0e90c5",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                }
-                            },
-                            "tags": "",
-                            "uuid": "c57efd37-4cf6-4cc7-abf4-2bab22a2e9a0"
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "consensus"
+                            }
                         },
-                        "tool_id": null,
-                        "type": "subworkflow",
-                        "uuid": "58c99e4b-fd6a-401d-b9c7-cdf7e6d1757d",
-                        "when": null,
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3ee0ef312022",
+                            "name": "flye",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"asm\": null, \"g\": \"160000\", \"i\": \"1\", \"inputs\": {\"__class__\": \"ConnectedValue\"}, \"m\": null, \"meta\": \"false\", \"mode\": \"--nano-raw\", \"no_trestle\": \"false\", \"plasmids\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6",
+                        "type": "tool",
+                        "uuid": "efcc01cf-bb71-4c46-9eec-83488a79859e",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "2:output",
-                                "uuid": "50fa1032-8037-454e-8192-b95405bcd5d4"
+                                "output_name": "assembly_info",
+                                "uuid": "f14c4d31-93bc-4e19-9d81-f3061ed8898e"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "flye_log",
+                                "uuid": "33126b99-3149-4da0-bcaa-031156d82f09"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "consensus",
+                                "uuid": "1e33ae8a-4d67-44bf-933e-ade1a94b7f85"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "assembly_graph",
+                                "uuid": "89d53ead-feef-4079-8988-627850312bd9"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "assembly_gfa",
+                                "uuid": "de2f80a8-f73f-419c-81e2-208b63c84c1f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1",
                         "errors": null,
                         "id": 5,
                         "input_connections": {
-                            "d": {
-                                "id": 4,
-                                "output_name": "Assembly polished by long reads using Racon"
-                            },
-                            "i": {
+                            "mode|reads|files": {
                                 "id": 1,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "Medaka polish",
-                        "name": "medaka consensus pipeline",
+                        "label": null,
+                        "name": "NanoPlot",
                         "outputs": [
                             {
-                                "name": "out_consensus",
-                                "type": "fasta"
+                                "name": "output_html",
+                                "type": "html"
+                            },
+                            {
+                                "name": "nanostats",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "nanostats_post_filtering",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "read_length",
+                                "type": "png"
+                            },
+                            {
+                                "name": "log_read_length",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 515.5164024294684,
-                            "top": 305.08460859328346
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_consensus": {
-                                "action_arguments": {
-                                    "newname": "Medaka_long_reads_polished_assembly.fasta"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_consensus"
-                            }
+                            "left": 315.015625,
+                            "top": 701.8125
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "fc8804320156",
-                            "name": "medaka_consensus_pipeline",
+                            "changeset_revision": "edbb6c5028f5",
+                            "name": "nanoplot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"b\": \"100\", \"d\": {\"__class__\": \"ConnectedValue\"}, \"g\": false, \"i\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"r941_min_high_g360\", \"out\": [\"consensus\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.2+galaxy1",
+                        "tool_state": "{\"customization\": {\"color\": null, \"format\": \"png\", \"plots\": null, \"N50\": \"false\"}, \"filter\": {\"maxlength\": null, \"minlength\": null, \"drop_outliers\": \"false\", \"downsample\": null, \"loglength\": \"false\", \"percentqual\": \"false\", \"alength\": \"false\", \"minqual\": null, \"readtype\": null, \"barcoded\": \"false\"}, \"mode\": {\"choice\": \"batch\", \"__current_case__\": 0, \"reads\": {\"type\": \"fastq\", \"__current_case__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.28.2+galaxy1",
                         "type": "tool",
-                        "uuid": "14c5ce9c-df92-4e20-85da-7a161eaa759d",
-                        "when": null,
+                        "uuid": "655afaaf-7a0f-4103-b68c-32ad0c03a32b",
                         "workflow_outputs": [
                             {
-                                "label": "Assembly polished by long reads using Medaka",
-                                "output_name": "out_consensus",
-                                "uuid": "e3136060-bce7-4af3-87c4-9dcbb0d1f531"
+                                "label": null,
+                                "output_name": "log_read_length",
+                                "uuid": "a87ac909-55de-42d8-b637-981e0b37c062"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "nanostats_post_filtering",
+                                "uuid": "46189275-9aef-4c23-8410-d6a6eb14299d"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "nanostats",
+                                "uuid": "1f5ce9f1-eec9-48c9-b175-8d530b9d9024"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "read_length",
+                                "uuid": "18ebb4bc-a4a3-48a5-b2e2-c8f9fb801dd6"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_html",
+                                "uuid": "5192b242-50f9-4205-aac7-d1deca088724"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "assembly/largegenome",
-                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_polishing.ga",
-                "tags": [
-                    "LG-WF",
-                    "GTN"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Assembly polishing - upgraded",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-assembly-polishing",
-                "tutorial_id": "largegenome",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_polishing.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_polishing.html",
-                "version": 2,
-                "wfid": "assembly-largegenome",
-                "wfname": "galaxy-workflow-assembly-polishing",
-                "workflow": "Galaxy-Workflow-Assembly_polishing.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0"
-                ],
-                "workflowhub_id": "1174"
-            },
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
-                    }
-                ],
-                "description": "",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": {
-                        "markdown": "# Workflow Report for Assembly with Flye\n\n\n## Workflow steps\n\n```galaxy\nworkflow_display()\n```\n\n## Dataset - fasta stats. \n\n```galaxy\nhistory_dataset_display(output=\"Fasta Statistics on input dataset(s): Fasta summary stats\")\n```\n\n## Contig sizes\n\n```galaxy\nhistory_dataset_as_image(output=\"Bar chart showing contig sizes\")\n```\n\n\n## Bandage image\n\n```galaxy\nhistory_dataset_as_image(output=\"Bandage Image on input dataset(s): Assembly Graph Image\")\n```\n\n## Quast report\n\n\r\n```galaxy\nhistory_dataset_display(output=\"Quast on input dataset(s):  PDF report\")\n```\r\n\n\n\n"
-                    },
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  1[label=\"Flye: assembly\"]\n  0 -> 1 [label=\"output\"]\n  k3960e31d7a9e400cbb21f6e47b75e649[color=lightseagreen,label=\"Output\\nFlye assembly on input dataset(s) (consensus)\"]\n  1 -> k3960e31d7a9e400cbb21f6e47b75e649\n  ke524f295a9574c91838cf8e98e809b6c[color=lightseagreen,label=\"Output\\nFlye assembly on input dataset(s) (assembly_graph)\"]\n  1 -> ke524f295a9574c91838cf8e98e809b6c\n  k48b854e2dd6e43458d0509abca6659da[color=lightseagreen,label=\"Output\\nFlye assembly on input dataset(s) (Graphical Fragment Assembly)\"]\n  1 -> k48b854e2dd6e43458d0509abca6659da\n  k8672c17271a7432c9679a8e37f36cf53[color=lightseagreen,label=\"Output\\nFlye assembly on input dataset(s) (assembly_info)\"]\n  1 -> k8672c17271a7432c9679a8e37f36cf53\n  2[label=\"Fasta statistics\"]\n  1 -> 2 [label=\"consensus\"]\n  3[label=\"Quast genome report\"]\n  1 -> 3 [label=\"consensus\"]\n  k17cdf8e08ad44570afae1861934fc678[color=lightseagreen,label=\"Output\\nQuast on input dataset(s):  HTML report\"]\n  3 -> k17cdf8e08ad44570afae1861934fc678\n  4[label=\"Bandage image: Flye assembly\"]\n  1 -> 4 [label=\"assembly_gfa\"]\n  ke66bd129146f48dc95b839a2a1ffb68d[color=lightseagreen,label=\"Output\\nBandage Image on input dataset(s): Assembly Graph Image\"]\n  4 -> ke66bd129146f48dc95b839a2a1ffb68d\n  5[label=\"Bar chart: show contig sizes\"]\n  1 -> 5 [label=\"assembly_info\"]\n  k6d0a4e23d6314e3789303d22fc91369b[color=lightseagreen,label=\"Output\\nBar chart showing contig sizes\"]\n  5 -> k6d0a4e23d6314e3789303d22fc91369b\n}",
-                "history": [
-                    {
-                        "hash": "f3dd8377556ae73d56d73612a37a5a7e20c98093",
-                        "message": "Update Galaxy-Workflow-Assembly_with_Flye.ga",
-                        "num": 5,
-                        "short_hash": "f3dd83775",
-                        "unix": "1715074300"
-                    },
-                    {
-                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
-                        "message": "new versions of workflows",
-                        "num": 4,
-                        "short_hash": "e8ddbcdd5",
-                        "unix": "1714537936"
                     },
-                    {
-                        "hash": "43baea079b7b412f3f272ac1ac887cd67aef6c49",
-                        "message": "Rename Galaxy-Workflow-Assembly_with_Flye.ga to Galaxy-Workflow-Assembly_with_Flye_old.ga",
-                        "num": 3,
-                        "short_hash": "43baea079",
-                        "unix": "1714537239"
-                    },
-                    {
-                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
-                        "message": "add/complete creator info on workflows",
-                        "num": 2,
-                        "short_hash": "62e77944b",
-                        "unix": "1676627603"
-                    },
-                    {
-                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
-                        "message": "large genome tutorial",
-                        "num": 1,
-                        "short_hash": "9fcb3aeec",
-                        "unix": "1665123856"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "long reads"
-                            }
-                        ],
-                        "label": "long reads",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 398.40625
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "501d7387-3bed-4510-891f-a4571a48d9ab",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Flye: assembly\"];\n  0 -->|output| 1;\n  3960e31d-7a9e-400c-bb21-f6e47b75e649[\"Output\\nFlye assembly on input dataset(s) (consensus)\"];\n  1 --> 3960e31d-7a9e-400c-bb21-f6e47b75e649;\n  style 3960e31d-7a9e-400c-bb21-f6e47b75e649 stroke:#2c3143,stroke-width:4px;\n  e524f295-a957-4c91-838c-f8e98e809b6c[\"Output\\nFlye assembly on input dataset(s) (assembly_graph)\"];\n  1 --> e524f295-a957-4c91-838c-f8e98e809b6c;\n  style e524f295-a957-4c91-838c-f8e98e809b6c stroke:#2c3143,stroke-width:4px;\n  48b854e2-dd6e-4345-8d05-09abca6659da[\"Output\\nFlye assembly on input dataset(s) (Graphical Fragment Assembly)\"];\n  1 --> 48b854e2-dd6e-4345-8d05-09abca6659da;\n  style 48b854e2-dd6e-4345-8d05-09abca6659da stroke:#2c3143,stroke-width:4px;\n  8672c172-71a7-432c-9679-a8e37f36cf53[\"Output\\nFlye assembly on input dataset(s) (assembly_info)\"];\n  1 --> 8672c172-71a7-432c-9679-a8e37f36cf53;\n  style 8672c172-71a7-432c-9679-a8e37f36cf53 stroke:#2c3143,stroke-width:4px;\n  2[\"Fasta statistics\"];\n  1 -->|consensus| 2;\n  3[\"Quast genome report\"];\n  1 -->|consensus| 3;\n  17cdf8e0-8ad4-4570-afae-1861934fc678[\"Output\\nQuast on input dataset(s):  HTML report\"];\n  3 --> 17cdf8e0-8ad4-4570-afae-1861934fc678;\n  style 17cdf8e0-8ad4-4570-afae-1861934fc678 stroke:#2c3143,stroke-width:4px;\n  4[\"Bandage image: Flye assembly\"];\n  1 -->|assembly_gfa| 4;\n  e66bd129-146f-48dc-95b8-39a2a1ffb68d[\"Output\\nBandage Image on input dataset(s): Assembly Graph Image\"];\n  4 --> e66bd129-146f-48dc-95b8-39a2a1ffb68d;\n  style e66bd129-146f-48dc-95b8-39a2a1ffb68d stroke:#2c3143,stroke-width:4px;\n  5[\"Bar chart: show contig sizes\"];\n  1 -->|assembly_info| 5;\n  6d0a4e23-d631-4e37-8930-3d22fc91369b[\"Output\\nBar chart showing contig sizes\"];\n  5 --> 6d0a4e23-d631-4e37-8930-3d22fc91369b;\n  style 6d0a4e23-d631-4e37-8930-3d22fc91369b stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Assembly with Flye - upgraded",
-                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
                         "errors": null,
-                        "id": 1,
+                        "id": 6,
                         "input_connections": {
-                            "inputs": {
+                            "fastq_input|fastq_input1": {
                                 "id": 0,
                                 "output_name": "output"
+                            },
+                            "reference_source|ref_file": {
+                                "id": 4,
+                                "output_name": "consensus"
                             }
                         },
                         "inputs": [],
-                        "label": "Flye: assembly",
-                        "name": "Flye",
+                        "label": null,
+                        "name": "Map with BWA-MEM",
                         "outputs": [
                             {
-                                "name": "consensus",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "assembly_graph",
-                                "type": "graph_dot"
-                            },
-                            {
-                                "name": "assembly_gfa",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "assembly_info",
-                                "type": "tabular"
+                                "name": "bam_output",
+                                "type": "bam"
                             }
                         ],
                         "position": {
-                            "left": 260.57143695759436,
-                            "top": 248.74363091133793
+                            "left": 637.8359375,
+                            "top": 0.0
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActionbam_output": {
+                                "action_arguments": {
+                                    "newname": "illumina.bam"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "bam_output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "291923e6f276",
-                            "name": "flye",
-                            "owner": "bgruening",
+                            "changeset_revision": "dfd8b7f78c37",
+                            "name": "bwa",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"asm\": {\"asm_select\": \"false\", \"__current_case__\": 1}, \"generate_log\": false, \"i\": \"1\", \"inputs\": {\"__class__\": \"ConnectedValue\"}, \"iterations\": \"1\", \"keep_haplotypes\": false, \"m\": null, \"meta\": false, \"min_overlap\": null, \"mode\": \"--nano-raw\", \"mode_conditional\": {\"mode\": \"--nano-raw\", \"__current_case__\": 0}, \"no_alt_contigs\": false, \"no_trestle\": \"false\", \"plasmids\": \"false\", \"scaffold\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.9.3+galaxy0",
+                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"illumina\", \"__current_case__\": 0}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 1, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}, \"index_a\": \"auto\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.17.1",
                         "type": "tool",
-                        "uuid": "8bed3591-266a-41f1-91d3-11b3456e8609",
-                        "when": null,
+                        "uuid": "95ed65e8-2534-4cef-888f-6de9f83a3770",
                         "workflow_outputs": [
                             {
-                                "label": "Flye assembly on input dataset(s) (consensus)",
-                                "output_name": "consensus",
-                                "uuid": "3960e31d-7a9e-400c-bb21-f6e47b75e649"
-                            },
-                            {
-                                "label": "Flye assembly on input dataset(s) (assembly_graph)",
-                                "output_name": "assembly_graph",
-                                "uuid": "e524f295-a957-4c91-838c-f8e98e809b6c"
-                            },
-                            {
-                                "label": "Flye assembly on input dataset(s) (Graphical Fragment Assembly)",
-                                "output_name": "assembly_gfa",
-                                "uuid": "48b854e2-dd6e-4345-8d05-09abca6659da"
-                            },
-                            {
-                                "label": "Flye assembly on input dataset(s) (assembly_info)",
-                                "output_name": "assembly_info",
-                                "uuid": "8672c172-71a7-432c-9679-a8e37f36cf53"
+                                "label": null,
+                                "output_name": "bam_output",
+                                "uuid": "2a0f0b99-d8b1-4585-8272-159d9f3a6a6d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
                         "errors": null,
-                        "id": 3,
+                        "id": 7,
                         "input_connections": {
-                            "mode|in|inputs": {
-                                "id": 1,
+                            "fasta": {
+                                "id": 4,
                                 "output_name": "consensus"
                             }
                         },
                         "inputs": [],
-                        "label": "Quast genome report",
-                        "name": "Quast",
+                        "label": null,
+                        "name": "Fasta Statistics",
                         "outputs": [
                             {
-                                "name": "report_html",
-                                "type": "html"
+                                "name": "stats_output",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 697.3759752425051,
-                            "top": 194.46891558901518
+                            "left": 640.78125,
+                            "top": 365.859375
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                        "post_job_actions": {
+                            "RenameDatasetActionstats": {
+                                "action_arguments": {
+                                    "newname": "Fasta stats of flye assembly"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "RenameDatasetActionstats_output": {
+                                "action_arguments": {
+                                    "newname": "Flye assembly fasta stats"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "stats_output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "72472698a2df",
-                            "name": "quast",
+                            "changeset_revision": "0dbb995c7d35",
+                            "name": "fasta_stats",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"al\": {\"ambiguity_score\": \"0.99\", \"ambiguity_usage\": \"one\", \"fragmented\": false, \"fragmented_max_indent\": \"50\", \"min_alignment\": \"65\", \"min_identity\": \"95.0\", \"upper_bound_assembly\": false, \"upper_bound_min_con\": \"2\", \"use_all_alignments\": false}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"false\", \"__current_case__\": 1, \"est_ref_size\": null}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"circos\": \"false\", \"contig_thresholds\": \"0,1000\", \"extensive_mis_size\": \"1000\", \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": false}, \"in\": {\"__current_case__\": 1, \"custom\": \"false\", \"inputs\": {\"__class__\": \"RuntimeValue\"}}, \"k_mer\": {\"__current_case__\": 1, \"k_mer_stats\": \"\"}, \"large\": true, \"min_contig\": \"500\", \"mode\": {\"mode\": \"co\", \"__current_case__\": 1, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": \"html\", \"scaffold_gap_max_size\": \"1000\", \"skip_unaligned_mis_contigs\": \"false\", \"split_scaffolds\": false, \"strict_NA\": \"false\", \"unaligned_part_size\": \"500\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.2.0+galaxy1",
+                        "tool_state": "{\"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gaps_option\": \"false\", \"genome_size\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0",
                         "type": "tool",
-                        "uuid": "5bc29646-ec4c-4eb3-af01-73d82fc690a2",
-                        "when": null,
+                        "uuid": "e4b5dd88-a21b-4b20-93b6-5de72b3883e1",
                         "workflow_outputs": [
                             {
-                                "label": "Quast on input dataset(s):  HTML report",
-                                "output_name": "report_html",
-                                "uuid": "17cdf8e0-8ad4-4570-afae-1861934fc678"
+                                "label": null,
+                                "output_name": "stats_output",
+                                "uuid": "083a96d6-2e0f-408e-a343-9df5cccbcbae"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
                         "errors": null,
-                        "id": 4,
+                        "id": 8,
                         "input_connections": {
                             "input_file": {
-                                "id": 1,
+                                "id": 4,
                                 "output_name": "assembly_gfa"
                             }
                         },
                         "inputs": [],
-                        "label": "Bandage image: Flye assembly",
-                        "name": "Bandage Image",
+                        "label": null,
+                        "name": "Bandage Info",
                         "outputs": [
                             {
                                 "name": "outfile",
-                                "type": "jpg"
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 583.546875,
-                            "top": 446.40625
+                            "left": 608.78125,
+                            "top": 588.5859375
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "ddddce450736",
+                            "changeset_revision": "b2860df42e16",
                             "name": "bandage",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"fontsize\": null, \"height\": \"1000\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"lengths\": false, \"names\": false, \"nodewidth\": null, \"output_format\": \"jpg\", \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2022.09+galaxy4",
+                        "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"tsv\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.8.1+galaxy1",
                         "type": "tool",
-                        "uuid": "395f2dfe-3fa5-4684-bf97-7dd12e970f78",
-                        "when": null,
+                        "uuid": "11a0fc24-13ed-4199-8524-1ebc317e449e",
                         "workflow_outputs": [
                             {
-                                "label": "Bandage Image on input dataset(s): Assembly Graph Image",
+                                "label": null,
                                 "output_name": "outfile",
-                                "uuid": "e66bd129-146f-48dc-95b8-39a2a1ffb68d"
+                                "uuid": "5bfce93b-c6bd-42c2-8910-d99b2f472b70"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "barchart_gnuplot",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
                         "errors": null,
-                        "id": 5,
+                        "id": 9,
                         "input_connections": {
-                            "input": {
-                                "id": 1,
-                                "output_name": "assembly_info"
+                            "input_file": {
+                                "id": 4,
+                                "output_name": "assembly_gfa"
                             }
                         },
                         "inputs": [],
-                        "label": "Bar chart: show contig sizes",
-                        "name": "Bar chart",
+                        "label": null,
+                        "name": "Bandage Image",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "png"
+                                "name": "outfile",
+                                "type": "jpg"
                             }
                         ],
                         "position": {
-                            "left": 595.421875,
-                            "top": 688.984375
+                            "left": 605.78125,
+                            "top": 764.40625
                         },
                         "post_job_actions": {},
-                        "tool_id": "barchart_gnuplot",
-                        "tool_state": "{\"colList\": \"2\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"pdf_size\": \"800,600\", \"title\": \"Assembly contig sizes\", \"xtic\": {\"userSpecified\": \"No\", \"__current_case__\": 1}, \"ylabel\": \"lengths\", \"ymax\": \"0\", \"ymin\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "b2860df42e16",
+                            "name": "bandage",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"height\": \"1000\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"lengths\": \"true\", \"names\": \"false\", \"output_format\": \"jpg\", \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.8.1+galaxy2",
                         "type": "tool",
-                        "uuid": "cb9d5059-bf42-4a0e-8150-f5089e0d5b1b",
-                        "when": null,
+                        "uuid": "528ebaa8-2c95-472b-b719-4752804e2d00",
                         "workflow_outputs": [
                             {
-                                "label": "Bar chart showing contig sizes",
-                                "output_name": "out_file1",
-                                "uuid": "6d0a4e23-d631-4e37-8930-3d22fc91369b"
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "64a6e260-f828-42a7-9ff6-415e3fa5c496"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "assembly/largegenome",
-                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_with_Flye.ga",
-                "tags": [
-                    "LG-WF",
-                    "GTN"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Assembly with Flye - upgraded",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-assembly-with-flye",
-                "tutorial_id": "largegenome",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_with_Flye.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_with_Flye.html",
-                "version": 2,
-                "wfid": "assembly-largegenome",
-                "wfname": "galaxy-workflow-assembly-with-flye",
-                "workflow": "Galaxy-Workflow-Assembly_with_Flye.ga",
-                "workflow_tools": [
-                    "barchart_gnuplot",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
-                ],
-                "workflowhub_id": "1170"
-            },
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
-                    }
-                ],
-                "description": "",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": {
-                        "markdown": "\n# Workflow Execution Report\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n\n## Busco results\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco short summary\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco summary image\")\n```\n\n## Quast results\n\n\n```galaxy\nhistory_dataset_display(output=\"Quast on input dataset(s): tabular report\")\n```\n\n\n"
-                    },
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPolished assembly\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genome\"]\n  2[label=\"Busco: assess assembly\"]\n  0 -> 2 [label=\"output\"]\n  k219e495236e04b01a407e774b5b02dca[color=lightseagreen,label=\"Output\\nBusco short summary\"]\n  2 -> k219e495236e04b01a407e774b5b02dca\n  3[label=\"Quast: assess assembly\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  k77ab01864cfd460fb71e39a923414ef4[color=lightseagreen,label=\"Output\\nQuast on input dataset(s):  HTML report\"]\n  3 -> k77ab01864cfd460fb71e39a923414ef4\n}",
-                "history": [
-                    {
-                        "hash": "1b47a1ad8d46b114394c0579436c448e6bb7efcf",
-                        "message": "Update Galaxy-Workflow-Assess_genome_quality.ga",
-                        "num": 5,
-                        "short_hash": "1b47a1ad8",
-                        "unix": "1715074319"
-                    },
-                    {
-                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
-                        "message": "new versions of workflows",
-                        "num": 4,
-                        "short_hash": "e8ddbcdd5",
-                        "unix": "1714537936"
-                    },
-                    {
-                        "hash": "fc05e79f01c6b59c4dfc6aa59ebf592ae615641f",
-                        "message": "Rename Galaxy-Workflow-Assess_genome_quality.ga to Galaxy-Workflow-Assess_genome_quality_old.ga",
-                        "num": 3,
-                        "short_hash": "fc05e79f0",
-                        "unix": "1714537255"
-                    },
-                    {
-                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
-                        "message": "add/complete creator info on workflows",
-                        "num": 2,
-                        "short_hash": "62e77944b",
-                        "unix": "1676627603"
-                    },
-                    {
-                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
-                        "message": "large genome tutorial",
-                        "num": 1,
-                        "short_hash": "9fcb3aeec",
-                        "unix": "1665123856"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Polished assembly"
-                            }
-                        ],
-                        "label": "Polished assembly",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 101.09375
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "2ed19084-9eaf-4efb-acdc-b81536e7c024",
-                        "when": null,
-                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Reference genome"
-                            }
-                        ],
-                        "label": "Reference genome",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 246.765625,
-                            "top": 0.0
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "5b12a6af-13c3-4520-a549-280de6a3df17",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPolished assembly\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Busco: assess assembly\"];\n  0 -->|output| 2;\n  219e4952-36e0-4b01-a407-e774b5b02dca[\"Output\\nBusco short summary\"];\n  2 --> 219e4952-36e0-4b01-a407-e774b5b02dca;\n  style 219e4952-36e0-4b01-a407-e774b5b02dca stroke:#2c3143,stroke-width:4px;\n  3[\"Quast: assess assembly\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  77ab0186-4cfd-460f-b71e-39a923414ef4[\"Output\\nQuast on input dataset(s):  HTML report\"];\n  3 --> 77ab0186-4cfd-460f-b71e-39a923414ef4;\n  style 77ab0186-4cfd-460f-b71e-39a923414ef4 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Assess genome quality - upgraded",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1",
                         "errors": null,
-                        "id": 2,
+                        "id": 10,
                         "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
+                            "auto_selection|bam": {
+                                "id": 6,
+                                "output_name": "bam_output"
+                            },
+                            "reference_genome|history_item": {
+                                "id": 4,
+                                "output_name": "consensus"
                             }
                         },
                         "inputs": [],
-                        "label": "Busco: assess assembly",
-                        "name": "Busco",
+                        "label": null,
+                        "name": "pilon",
                         "outputs": [
                             {
-                                "name": "busco_sum",
+                                "name": "output_changes",
                                 "type": "txt"
                             },
                             {
-                                "name": "busco_table",
-                                "type": "tabular"
+                                "name": "output_fasta",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 294.42303466796875,
-                            "top": 200.68505859375
+                            "left": 886.65625,
+                            "top": 262.0625
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_fasta": {
+                                "action_arguments": {
+                                    "newname": "polished-assembly.fasta"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_fasta"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "ea8146ee148f",
-                            "name": "busco",
+                            "changeset_revision": "11e5408fd238",
+                            "name": "pilon",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"auto_detect\", \"__current_case__\": 0, \"auto_lineage\": \"--auto-lineage\"}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"lineage_dataset\": \"eukaryota_odb10\", \"outputs\": \"short_summary\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.5.0+galaxy0",
+                        "tool_state": "{\"auto_selection\": {\"auto_enabled\": \"true\", \"__current_case__\": 0, \"bam\": {\"__class__\": \"ConnectedValue\"}}, \"changes\": \"true\", \"options\": {\"selection_mode\": \"default\", \"__current_case__\": 0}, \"reference_genome\": {\"reference_genome_source\": \"history\", \"__current_case__\": 0, \"history_item\": {\"__class__\": \"ConnectedValue\"}}, \"variant\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.20.1",
                         "type": "tool",
-                        "uuid": "8f5f17de-a21e-49f4-b55c-6eff5f4fa213",
-                        "when": null,
+                        "uuid": "a445d29c-7b0c-48a0-984b-945f2acb64ac",
                         "workflow_outputs": [
                             {
-                                "label": "Busco short summary",
-                                "output_name": "busco_sum",
-                                "uuid": "219e4952-36e0-4b01-a407-e774b5b02dca"
+                                "label": null,
+                                "output_name": "output_changes",
+                                "uuid": "d48e11c7-ea49-457b-8a96-38b6dc0f1bc2"
                             },
                             {
                                 "label": null,
-                                "output_name": "busco_table",
-                                "uuid": "fc06df63-3453-4303-80d1-c76823ba384a"
+                                "output_name": "output_fasta",
+                                "uuid": "e898b32c-b4ae-4f5a-b3be-f7a2681e4fa0"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
                         "errors": null,
-                        "id": 3,
+                        "id": 11,
                         "input_connections": {
-                            "assembly|ref|r": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "mode|in|inputs": {
-                                "id": 0,
-                                "output_name": "output"
+                            "fasta": {
+                                "id": 10,
+                                "output_name": "output_fasta"
                             }
                         },
                         "inputs": [],
-                        "label": "Quast: assess assembly",
-                        "name": "Quast",
+                        "label": null,
+                        "name": "Fasta Statistics",
                         "outputs": [
                             {
-                                "name": "report_html",
-                                "type": "html"
+                                "name": "stats_output",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 564.8660278320312,
-                            "top": 56.71406029052495
+                            "left": 1170.40625,
+                            "top": 139.0625
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                        "post_job_actions": {
+                            "RenameDatasetActionstats": {
+                                "action_arguments": {
+                                    "newname": "Fasta stats of polished flye assembly"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "RenameDatasetActionstats_output": {
+                                "action_arguments": {
+                                    "newname": "Pilon polished assembly fasta stats"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "stats_output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "72472698a2df",
-                            "name": "quast",
+                            "changeset_revision": "0dbb995c7d35",
+                            "name": "fasta_stats",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"true\", \"__current_case__\": 0, \"r\": {\"__class__\": \"RuntimeValue\"}, \"features\": {\"__class__\": \"RuntimeValue\"}, \"operons\": {\"__class__\": \"RuntimeValue\"}, \"k_mer\": {\"k_mer_stats\": \"\", \"__current_case__\": 1}, \"circos\": false}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": false}, \"large\": true, \"min_contig\": \"0\", \"mode\": {\"mode\": \"individual\", \"__current_case__\": 0, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"RuntimeValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": \"html\", \"split_scaffolds\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.2.0+galaxy1",
+                        "tool_state": "{\"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gaps_option\": \"false\", \"genome_size\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0",
                         "type": "tool",
-                        "uuid": "6caef18b-b257-472d-b8d0-fac523a72d37",
-                        "when": null,
+                        "uuid": "465a0ecf-4f47-4679-ad02-c06eb48449fc",
                         "workflow_outputs": [
                             {
-                                "label": "Quast on input dataset(s):  HTML report",
-                                "output_name": "report_html",
-                                "uuid": "77ab0186-4cfd-460f-b71e-39a923414ef4"
+                                "label": null,
+                                "output_name": "stats_output",
+                                "uuid": "ae93f473-d571-439c-8fa6-3927026fdb49"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "assembly/largegenome",
-                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assess_genome_quality.ga",
-                "tags": [
-                    "LG-WF",
-                    "GTN"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Assess genome quality - upgraded",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-assess-genome-quality",
-                "tutorial_id": "largegenome",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assess_genome_quality.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assess_genome_quality.html",
-                "version": 2,
-                "wfid": "assembly-largegenome",
-                "wfname": "galaxy-workflow-assess-genome-quality",
-                "workflow": "Galaxy-Workflow-Assess_genome_quality.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
-                ],
-                "workflowhub_id": "1158"
-            },
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
-                    }
-                ],
-                "description": "",
-                "features": {
-                    "comments": false,
-                    "parameters": true,
-                    "report": {
-                        "markdown": "\n# Workflow Execution Report\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
-                    },
-                    "subworkflows": true
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR1\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR2\"]\n  3[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nminimap settings for long reads\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genome for Quast\"]\n  5[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nkmer counting - meryl - upgraded\"]\n  1 -> 5 [label=\"output\"]\n  6[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nData QC - upgraded\"]\n  1 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  0 -> 6 [label=\"output\"]\n  7[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nTrim and filter reads - fastp - upgraded \"]\n  1 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  0 -> 7 [label=\"output\"]\n  8[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly with Flye - upgraded\"]\n  7 -> 8 [label=\"fastp filtered long reads\"]\n  9[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly polishing - upgraded\"]\n  8 -> 9 [label=\"Flye assembly on input datasets consensus\"]\n  7 -> 9 [label=\"fastp filtered R1 reads\"]\n  7 -> 9 [label=\"fastp filtered long reads\"]\n  3 -> 9 [label=\"output\"]\n  10[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nAssess genome quality - upgraded\"]\n  9 -> 10 [label=\"Assembly polished by long reads using Medaka\"]\n  4 -> 10 [label=\"output\"]\n}",
-                "history": [
-                    {
-                        "hash": "01cffeed0413d12d37753e72aa81c95fb47e2179",
-                        "message": "Update Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga",
-                        "num": 5,
-                        "short_hash": "01cffeed0",
-                        "unix": "1715074366"
-                    },
-                    {
-                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
-                        "message": "new versions of workflows",
-                        "num": 4,
-                        "short_hash": "e8ddbcdd5",
-                        "unix": "1714537936"
-                    },
-                    {
-                        "hash": "bd0db2c9632aca4fc5faba5e811b23e9f98817f0",
-                        "message": "Rename Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga to Galaxy-Workflow-Combined_workflows_for_large_genome_assembly_old.ga",
-                        "num": 3,
-                        "short_hash": "bd0db2c96",
-                        "unix": "1714537274"
-                    },
-                    {
-                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
-                        "message": "add/complete creator info on workflows",
-                        "num": 2,
-                        "short_hash": "62e77944b",
-                        "unix": "1676627603"
                     },
-                    {
-                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
-                        "message": "large genome tutorial",
-                        "num": 1,
-                        "short_hash": "9fcb3aeec",
-                        "unix": "1665123856"
-                    }
-                ],
-                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "long reads"
+                        "id": 12,
+                        "input_connections": {
+                            "fastq_input|fastq_input1": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "reference_source|ref_file": {
+                                "id": 10,
+                                "output_name": "output_fasta"
                             }
-                        ],
-                        "label": "long reads",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 37.09056155334109,
-                            "top": 117.80110422489305
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f9154ba8-6c56-4b8c-b3a6-79bf72638963",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Map with BWA-MEM",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "R1"
+                                "name": "bam_output",
+                                "type": "bam"
                             }
                         ],
-                        "label": "R1",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 296.6915657131622
+                            "left": 1195.359375,
+                            "top": 628.0546875
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "2152a89a-64b2-4e77-897e-97c2e951f0d4",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "R2"
+                        "post_job_actions": {
+                            "RenameDatasetActionbam_output": {
+                                "action_arguments": {
+                                    "newname": "illumina-tiny.bam"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "bam_output"
                             }
-                        ],
-                        "label": "R2",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 18.331891780359495,
-                            "top": 404.60599487314124
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "04ed4838-38d0-47c6-9692-af43b305750c",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "minimap settings (for long reads)"
-                            }
-                        ],
-                        "label": "minimap settings (for long reads)",
-                        "name": "Input parameter",
-                        "outputs": [],
-                        "position": {
-                            "left": 953.979654343896,
-                            "top": 53.88085686443145
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "dfd8b7f78c37",
+                            "name": "bwa",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "925fcb63-babc-42b5-9510-c82277158288",
-                        "when": null,
+                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"illumina\", \"__current_case__\": 0}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 1, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}, \"index_a\": \"auto\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.17.1",
+                        "type": "tool",
+                        "uuid": "79954680-1c4f-4831-889c-53c4e502aa3c",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "3643a598-963e-42d9-b625-41f5256dee4a"
+                                "output_name": "bam_output",
+                                "uuid": "d2513973-0987-4260-9db6-3ac95c45c770"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
                         "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Reference genome for Quast"
+                        "id": 13,
+                        "input_connections": {
+                            "fastq_input|fastq_input1": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "reference_source|ref_file": {
+                                "id": 10,
+                                "output_name": "output_fasta"
                             }
-                        ],
-                        "label": "Reference genome for Quast",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 1271.7306972391564,
-                            "top": 75.04279962197629
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "5bd59f90-9351-4b1e-bc0d-11fee8b4a435",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nR1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nR2\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nminimap settings for long reads\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nReference genome for Quast\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\ud83d\udee0\ufe0f Subworkflow\\nkmer counting - meryl - upgraded\"];\n  style 5 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 5;\n  6[\"\ud83d\udee0\ufe0f Subworkflow\\nData QC - upgraded\"];\n  style 6 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 6;\n  2 -->|output| 6;\n  0 -->|output| 6;\n  7[\"\ud83d\udee0\ufe0f Subworkflow\\nTrim and filter reads - fastp - upgraded \"];\n  style 7 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 7;\n  2 -->|output| 7;\n  0 -->|output| 7;\n  8[\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly with Flye - upgraded\"];\n  style 8 fill:#edd,stroke:#900,stroke-width:4px;\n  7 -->|fastp filtered long reads| 8;\n  9[\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly polishing - upgraded\"];\n  style 9 fill:#edd,stroke:#900,stroke-width:4px;\n  8 -->|Flye assembly on input datasets consensus| 9;\n  7 -->|fastp filtered R1 reads| 9;\n  7 -->|fastp filtered long reads| 9;\n  3 -->|output| 9;\n  10[\"\ud83d\udee0\ufe0f Subworkflow\\nAssess genome quality - upgraded\"];\n  style 10 fill:#edd,stroke:#900,stroke-width:4px;\n  9 -->|Assembly polished by long reads using Medaka| 10;\n  4 -->|output| 10;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Combined workflows for large genome assembly - upgraded ",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Map with BWA-MEM",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "minimap settings (for long reads)"
+                                "name": "bam_output",
+                                "type": "bam"
                             }
                         ],
-                        "label": "minimap settings (for long reads)",
-                        "name": "Input parameter",
-                        "outputs": [],
                         "position": {
-                            "left": 953.979654343896,
-                            "top": 53.88085686443145
+                            "left": 1192.3828125,
+                            "top": 904.5859375
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "925fcb63-babc-42b5-9510-c82277158288",
-                        "when": null,
+                        "post_job_actions": {
+                            "RenameDatasetActionbam_output": {
+                                "action_arguments": {
+                                    "newname": "nanopore-tiny.bam"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "bam_output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "dfd8b7f78c37",
+                            "name": "bwa",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"ont2d\", \"__current_case__\": 2}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 1, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}, \"index_a\": \"auto\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.17.1",
+                        "type": "tool",
+                        "uuid": "c91315b3-c7f8-458c-a182-2b561d825837",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "3643a598-963e-42d9-b625-41f5256dee4a"
+                                "output_name": "bam_output",
+                                "uuid": "bebb5b25-00c2-456a-92a0-cd133a169e0e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "id": 9,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
+                        "errors": null,
+                        "id": 14,
                         "input_connections": {
-                            "Assembly to be polished": {
-                                "id": 8,
-                                "input_subworkflow_step_id": 0,
-                                "output_name": "Flye assembly on input dataset(s) (consensus)"
-                            },
-                            "Illumina reads R1": {
-                                "id": 7,
-                                "input_subworkflow_step_id": 3,
-                                "output_name": "fastp filtered R1 reads"
-                            },
-                            "long reads": {
-                                "id": 7,
-                                "input_subworkflow_step_id": 1,
-                                "output_name": "fastp filtered long reads"
-                            },
-                            "minimap setting (for long reads)": {
-                                "id": 3,
-                                "input_subworkflow_step_id": 2,
-                                "output_name": "output"
+                            "input": {
+                                "id": 10,
+                                "output_name": "output_fasta"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Prokka",
+                                "name": "proteins"
+                            }
+                        ],
                         "label": null,
-                        "name": "Assembly polishing - upgraded",
-                        "outputs": [],
-                        "position": {
-                            "left": 1260.7587450660599,
-                            "top": 269.3075732043599
-                        },
-                        "subworkflow": {
-                            "a_galaxy_workflow": "true",
-                            "annotation": "",
-                            "comments": [],
-                            "creator": [
-                                {
-                                    "class": "Person",
-                                    "identifier": "0000-0002-9906-0673",
-                                    "name": "Anna Syme"
-                                }
-                            ],
-                            "format-version": "0.1",
-                            "name": "Assembly polishing - upgraded",
-                            "report": {
-                                "markdown": "\n# Workflow Report for Assembly Polishing\n\n## Workflow steps\n\n```galaxy\nworkflow_display()\n```\n\n## Fasta statistics after Racon long-read polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Racon long read polish\")\n```\n\n\n## Fasta statistics after Medaka polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Medaka polish\")\n```\n\n## Fasta statistics after Racon short-read polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Racon short read polish\")\n```\n\n\n\n\n"
+                        "name": "Prokka",
+                        "outputs": [
+                            {
+                                "name": "out_gff",
+                                "type": "gff"
                             },
-                            "steps": {
-                                "0": {
-                                    "annotation": "",
-                                    "content_id": null,
-                                    "errors": null,
-                                    "id": 0,
-                                    "input_connections": {},
-                                    "inputs": [
-                                        {
-                                            "description": "",
-                                            "name": "Assembly to be polished"
-                                        }
-                                    ],
-                                    "label": "Assembly to be polished",
-                                    "name": "Input dataset",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 19.464939294568495,
-                                        "top": 0.0
-                                    },
-                                    "tool_id": null,
-                                    "tool_state": "{\"optional\": false, \"tag\": null}",
-                                    "tool_version": null,
-                                    "type": "data_input",
-                                    "uuid": "52bc9ac4-ac3c-48eb-aead-94a0a14417fc",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "1": {
-                                    "annotation": "",
-                                    "content_id": null,
-                                    "errors": null,
-                                    "id": 1,
-                                    "input_connections": {},
-                                    "inputs": [
-                                        {
-                                            "description": "",
-                                            "name": "long reads"
-                                        }
-                                    ],
-                                    "label": "long reads",
-                                    "name": "Input dataset",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 0.0,
-                                        "top": 142.48340578478533
-                                    },
-                                    "tool_id": null,
-                                    "tool_state": "{\"optional\": false, \"tag\": null}",
-                                    "tool_version": null,
-                                    "type": "data_input",
-                                    "uuid": "688866c4-de9b-4b78-8df3-b169d28b1617",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "2": {
-                                    "annotation": "",
-                                    "content_id": null,
-                                    "errors": null,
-                                    "id": 2,
-                                    "input_connections": {},
-                                    "inputs": [
-                                        {
-                                            "description": "",
-                                            "name": "minimap setting (for long reads)"
-                                        }
-                                    ],
-                                    "label": "minimap setting (for long reads)",
-                                    "name": "Input parameter",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 13.133522093825794,
-                                        "top": 247.1519749531627
-                                    },
-                                    "tool_id": null,
-                                    "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
-                                    "tool_version": null,
-                                    "type": "parameter_input",
-                                    "uuid": "c1f18b5c-e8db-4046-b876-9b28a77cf66e",
-                                    "when": null,
-                                    "workflow_outputs": [
-                                        {
-                                            "label": null,
-                                            "output_name": "output",
-                                            "uuid": "ce393bcf-42e3-43ee-9056-a99e8c077a29"
-                                        }
-                                    ]
-                                },
-                                "3": {
-                                    "annotation": "",
-                                    "content_id": null,
-                                    "errors": null,
-                                    "id": 3,
-                                    "input_connections": {},
-                                    "inputs": [
-                                        {
-                                            "description": "",
-                                            "name": "Illumina reads R1"
-                                        }
-                                    ],
-                                    "label": "Illumina reads R1",
-                                    "name": "Input dataset",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 617.719019724734,
-                                        "top": 600.0866464299372
-                                    },
-                                    "tool_id": null,
-                                    "tool_state": "{\"optional\": false, \"tag\": null}",
-                                    "tool_version": null,
-                                    "type": "data_input",
-                                    "uuid": "ea859a58-c81a-4ef6-9bd2-4ef2f17bb5a9",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "4": {
-                                    "annotation": "",
-                                    "id": 4,
-                                    "input_connections": {
-                                        "Assembly to be polished": {
-                                            "id": 0,
-                                            "input_subworkflow_step_id": 0,
-                                            "output_name": "output"
-                                        },
-                                        "long reads": {
-                                            "id": 1,
-                                            "input_subworkflow_step_id": 1,
-                                            "output_name": "output"
-                                        },
-                                        "minimap setting (for long reads) ": {
-                                            "id": 2,
-                                            "input_subworkflow_step_id": 2,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": null,
-                                    "name": "Racon polish with long reads, x4 - upgraded",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 299.6429464825318,
-                                        "top": 72.0364210406818
-                                    },
-                                    "subworkflow": {
-                                        "a_galaxy_workflow": "true",
-                                        "annotation": "",
-                                        "comments": [],
-                                        "creator": [
-                                            {
-                                                "class": "Person",
-                                                "identifier": "0000-0002-9906-0673",
-                                                "name": "Anna Syme"
-                                            }
-                                        ],
-                                        "format-version": "0.1",
-                                        "name": "Racon polish with long reads, x4 - upgraded",
-                                        "report": {
-                                            "markdown": "\n# Workflow Execution Report\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
-                                        },
-                                        "steps": {
-                                            "0": {
-                                                "annotation": "",
-                                                "content_id": null,
-                                                "errors": null,
-                                                "id": 0,
-                                                "input_connections": {},
-                                                "inputs": [
-                                                    {
-                                                        "description": "",
-                                                        "name": "Assembly to be polished"
-                                                    }
-                                                ],
-                                                "label": "Assembly to be polished",
-                                                "name": "Input dataset",
-                                                "outputs": [],
-                                                "position": {
-                                                    "left": 0,
-                                                    "top": 216.625
-                                                },
-                                                "tool_id": null,
-                                                "tool_state": "{\"optional\": false, \"tag\": null}",
-                                                "tool_version": null,
-                                                "type": "data_input",
-                                                "uuid": "c7796c36-adf8-49e4-a8e4-66e606d70311",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "1": {
-                                                "annotation": "",
-                                                "content_id": null,
-                                                "errors": null,
-                                                "id": 1,
-                                                "input_connections": {},
-                                                "inputs": [
-                                                    {
-                                                        "description": "",
-                                                        "name": "long reads"
-                                                    }
-                                                ],
-                                                "label": "long reads",
-                                                "name": "Input dataset",
-                                                "outputs": [],
-                                                "position": {
-                                                    "left": 4.5,
-                                                    "top": 360.234375
-                                                },
-                                                "tool_id": null,
-                                                "tool_state": "{\"optional\": false, \"tag\": null}",
-                                                "tool_version": null,
-                                                "type": "data_input",
-                                                "uuid": "e2e4a70b-6e36-4b8b-bdf6-12b97189a6bd",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "10": {
-                                                "annotation": "",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "errors": null,
-                                                "id": 10,
-                                                "input_connections": {
-                                                    "corrected_reads": {
-                                                        "id": 8,
-                                                        "output_name": "consensus"
-                                                    },
-                                                    "overlaps": {
-                                                        "id": 9,
-                                                        "output_name": "alignment_output"
-                                                    },
-                                                    "reads": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    }
-                                                },
-                                                "inputs": [],
-                                                "label": "Racon: polish 4",
-                                                "name": "Racon",
-                                                "outputs": [
-                                                    {
-                                                        "name": "consensus",
-                                                        "type": "fasta"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 1496.078125,
-                                                    "top": 431.1875
-                                                },
-                                                "post_job_actions": {
-                                                    "RenameDatasetActionconsensus": {
-                                                        "action_arguments": {
-                                                            "newname": "Racon_long_reads_polished_assembly.fasta"
-                                                        },
-                                                        "action_type": "RenameDatasetAction",
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "78c533842eeb",
-                                                    "name": "racon",
-                                                    "owner": "bgruening",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "1.5.0+galaxy1",
-                                                "type": "tool",
-                                                "uuid": "53f4572e-3a4a-4585-89ab-9459f8a61720",
-                                                "when": null,
-                                                "workflow_outputs": [
-                                                    {
-                                                        "label": "Assembly polished by long reads using Racon",
-                                                        "output_name": "consensus",
-                                                        "uuid": "bcf0f03c-5951-46a7-aa38-545aed9bc183"
-                                                    }
-                                                ]
-                                            },
-                                            "2": {
-                                                "annotation": "",
-                                                "content_id": null,
-                                                "errors": null,
-                                                "id": 2,
-                                                "input_connections": {},
-                                                "inputs": [
-                                                    {
-                                                        "description": "",
-                                                        "name": "minimap setting (for long reads) "
-                                                    }
-                                                ],
-                                                "label": "minimap setting (for long reads) ",
-                                                "name": "Input parameter",
-                                                "outputs": [],
-                                                "position": {
-                                                    "left": 0.578125,
-                                                    "top": 495.859375
-                                                },
-                                                "tool_id": null,
-                                                "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
-                                                "tool_version": null,
-                                                "type": "parameter_input",
-                                                "uuid": "fb80c05c-08d4-4ac2-b4bf-81ed906e4d72",
-                                                "when": null,
-                                                "workflow_outputs": [
-                                                    {
-                                                        "label": null,
-                                                        "output_name": "output",
-                                                        "uuid": "3983ef22-5f05-4384-8f34-6ac8c4b2cc83"
-                                                    }
-                                                ]
-                                            },
-                                            "3": {
-                                                "annotation": "Map raw reads to assembly; output paf",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "errors": null,
-                                                "id": 3,
-                                                "input_connections": {
-                                                    "fastq_input|analysis_type_selector": {
-                                                        "id": 2,
-                                                        "output_name": "output"
-                                                    },
-                                                    "fastq_input|fastq_input1": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    },
-                                                    "reference_source|ref_file": {
-                                                        "id": 0,
-                                                        "output_name": "output"
-                                                    }
-                                                },
-                                                "inputs": [
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "reference_source"
-                                                    }
-                                                ],
-                                                "label": "Minimap2: map long reads to assembly",
-                                                "name": "Map with minimap2",
-                                                "outputs": [
-                                                    {
-                                                        "name": "alignment_output",
-                                                        "type": "bam"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 377.640625,
-                                                    "top": 0
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionalignment_output": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "alignment_output"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "be1d967337e4",
-                                                    "name": "minimap2",
-                                                    "owner": "iuc",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "2.26+galaxy0",
-                                                "type": "tool",
-                                                "uuid": "0c06144f-d1ac-4b45-9669-1ddf11fcb06b",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "4": {
-                                                "annotation": "",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "errors": null,
-                                                "id": 4,
-                                                "input_connections": {
-                                                    "corrected_reads": {
-                                                        "id": 0,
-                                                        "output_name": "output"
-                                                    },
-                                                    "overlaps": {
-                                                        "id": 3,
-                                                        "output_name": "alignment_output"
-                                                    },
-                                                    "reads": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    }
-                                                },
-                                                "inputs": [],
-                                                "label": "Racon: polish 1",
-                                                "name": "Racon",
-                                                "outputs": [
-                                                    {
-                                                        "name": "consensus",
-                                                        "type": "fasta"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 458.640625,
-                                                    "top": 518.875
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionconsensus": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "78c533842eeb",
-                                                    "name": "racon",
-                                                    "owner": "bgruening",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "1.5.0+galaxy1",
-                                                "type": "tool",
-                                                "uuid": "6c144354-91f2-49dd-a1f5-7c4119859730",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "5": {
-                                                "annotation": "Map raw reads to assembly; output paf",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "errors": null,
-                                                "id": 5,
-                                                "input_connections": {
-                                                    "fastq_input|analysis_type_selector": {
-                                                        "id": 2,
-                                                        "output_name": "output"
-                                                    },
-                                                    "fastq_input|fastq_input1": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    },
-                                                    "reference_source|ref_file": {
-                                                        "id": 4,
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "inputs": [
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "reference_source"
-                                                    }
-                                                ],
-                                                "label": "Minimap2: map long reads to polished assembly 1",
-                                                "name": "Map with minimap2",
-                                                "outputs": [
-                                                    {
-                                                        "name": "alignment_output",
-                                                        "type": "bam"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 698.859375,
-                                                    "top": 13.390625
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionalignment_output": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "alignment_output"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "be1d967337e4",
-                                                    "name": "minimap2",
-                                                    "owner": "iuc",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "2.26+galaxy0",
-                                                "type": "tool",
-                                                "uuid": "c1b83dad-a8ed-42cb-951f-73f59f2dfa92",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "6": {
-                                                "annotation": "",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "errors": null,
-                                                "id": 6,
-                                                "input_connections": {
-                                                    "corrected_reads": {
-                                                        "id": 4,
-                                                        "output_name": "consensus"
-                                                    },
-                                                    "overlaps": {
-                                                        "id": 5,
-                                                        "output_name": "alignment_output"
-                                                    },
-                                                    "reads": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    }
-                                                },
-                                                "inputs": [],
-                                                "label": "Racon: polish 2",
-                                                "name": "Racon",
-                                                "outputs": [
-                                                    {
-                                                        "name": "consensus",
-                                                        "type": "fasta"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 759.9375,
-                                                    "top": 485.71875
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionconsensus": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "78c533842eeb",
-                                                    "name": "racon",
-                                                    "owner": "bgruening",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "1.5.0+galaxy1",
-                                                "type": "tool",
-                                                "uuid": "3208491e-b831-4238-957e-5b7388d7ff8d",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "7": {
-                                                "annotation": "Map raw reads to assembly; output paf",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "errors": null,
-                                                "id": 7,
-                                                "input_connections": {
-                                                    "fastq_input|analysis_type_selector": {
-                                                        "id": 2,
-                                                        "output_name": "output"
-                                                    },
-                                                    "fastq_input|fastq_input1": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    },
-                                                    "reference_source|ref_file": {
-                                                        "id": 6,
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "inputs": [
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "reference_source"
-                                                    }
-                                                ],
-                                                "label": "Minimap2: map long reads to polished assembly 2",
-                                                "name": "Map with minimap2",
-                                                "outputs": [
-                                                    {
-                                                        "name": "alignment_output",
-                                                        "type": "bam"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 998.75,
-                                                    "top": 27.9375
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionalignment_output": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "alignment_output"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "be1d967337e4",
-                                                    "name": "minimap2",
-                                                    "owner": "iuc",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "2.26+galaxy0",
-                                                "type": "tool",
-                                                "uuid": "42af524b-7f74-4c75-8d78-f6888078dd2e",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "8": {
-                                                "annotation": "",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "errors": null,
-                                                "id": 8,
-                                                "input_connections": {
-                                                    "corrected_reads": {
-                                                        "id": 6,
-                                                        "output_name": "consensus"
-                                                    },
-                                                    "overlaps": {
-                                                        "id": 7,
-                                                        "output_name": "alignment_output"
-                                                    },
-                                                    "reads": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    }
-                                                },
-                                                "inputs": [],
-                                                "label": "Racon: polish 3",
-                                                "name": "Racon",
-                                                "outputs": [
-                                                    {
-                                                        "name": "consensus",
-                                                        "type": "fasta"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 1089.71875,
-                                                    "top": 455.53125
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionconsensus": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "78c533842eeb",
-                                                    "name": "racon",
-                                                    "owner": "bgruening",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "1.5.0+galaxy1",
-                                                "type": "tool",
-                                                "uuid": "21f339bd-ebc1-4c73-a976-5d0b9ab2127a",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "9": {
-                                                "annotation": "Map raw reads to assembly; output paf",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "errors": null,
-                                                "id": 9,
-                                                "input_connections": {
-                                                    "fastq_input|analysis_type_selector": {
-                                                        "id": 2,
-                                                        "output_name": "output"
-                                                    },
-                                                    "fastq_input|fastq_input1": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    },
-                                                    "reference_source|ref_file": {
-                                                        "id": 8,
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "inputs": [
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "reference_source"
-                                                    }
-                                                ],
-                                                "label": "Minimap2: map long reads to polished assembly 3",
-                                                "name": "Map with minimap2",
-                                                "outputs": [
-                                                    {
-                                                        "name": "alignment_output",
-                                                        "type": "bam"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 1316.53125,
-                                                    "top": 38.046875
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionalignment_output": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "alignment_output"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "be1d967337e4",
-                                                    "name": "minimap2",
-                                                    "owner": "iuc",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "2.26+galaxy0",
-                                                "type": "tool",
-                                                "uuid": "7d36291e-aa76-4312-9943-b5e56d0e90c5",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            }
-                                        },
-                                        "tags": "",
-                                        "uuid": "c57efd37-4cf6-4cc7-abf4-2bab22a2e9a0"
-                                    },
-                                    "tool_id": null,
-                                    "type": "subworkflow",
-                                    "uuid": "58c99e4b-fd6a-401d-b9c7-cdf7e6d1757d",
-                                    "when": null,
-                                    "workflow_outputs": [
-                                        {
-                                            "label": null,
-                                            "output_name": "2:output",
-                                            "uuid": "50fa1032-8037-454e-8192-b95405bcd5d4"
-                                        }
-                                    ]
+                            {
+                                "name": "out_gbk",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "out_fna",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "out_faa",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "out_ffn",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "out_sqn",
+                                "type": "asn1"
+                            },
+                            {
+                                "name": "out_fsa",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "out_tbl",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "out_tsv",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "out_err",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "out_txt",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "out_log",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 1704.984375,
+                            "top": 350.234375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
+                        "tool_shed_repository": {
+                            "changeset_revision": "bf68eb663bc3",
+                            "name": "prokka",
+                            "owner": "crs4",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"centre\": \"\", \"compliant\": {\"compliant_select\": \"no\", \"__current_case__\": 0, \"addgenes\": \"false\", \"mincontig\": \"200\"}, \"evalue\": \"1e-06\", \"fast\": \"false\", \"genus\": \"\", \"gffver\": \"3\", \"increment\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"kingdom\": {\"kingdom_select\": \"Bacteria\", \"__current_case__\": 1, \"gcode\": \"11\"}, \"locustag\": \"\", \"metagenome\": \"false\", \"norrna\": \"false\", \"notrna\": \"false\", \"outputs\": [\"gff\", \"gbk\", \"fna\", \"faa\", \"ffn\", \"sqn\", \"fsa\", \"tbl\", \"tsv\", \"err\", \"txt\"], \"plasmid\": \"\", \"proteins\": {\"__class__\": \"RuntimeValue\"}, \"rfam\": \"false\", \"species\": \"\", \"strain\": \"\", \"usegenus\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.14.5",
+                        "type": "tool",
+                        "uuid": "489e19de-1324-472c-8c8e-77e95572b6c3",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_err",
+                                "uuid": "a5f8d2e3-b2ca-46c3-83c5-36bc15507046"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_fna",
+                                "uuid": "1d83fde1-6207-46cc-b65e-a71815c578d8"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_faa",
+                                "uuid": "8e49b1a0-fd5b-4a80-8714-5fe51e7e6096"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_tbl",
+                                "uuid": "638f81aa-0004-4497-aeb9-6c1964cb27a7"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_fsa",
+                                "uuid": "773f3ba6-43ff-41aa-b498-ee509d71a58a"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_ffn",
+                                "uuid": "fd75d3c5-5cff-448e-9fd6-92b8af36e5cf"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_tsv",
+                                "uuid": "0efb82cf-84b6-49dd-bab4-d64d7356e0c7"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_txt",
+                                "uuid": "da1cc1bc-e00c-4f65-afbc-1a118b23274a"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_sqn",
+                                "uuid": "a5a04271-fc67-4ce3-95dc-9f01ee77775c"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_log",
+                                "uuid": "ca98afab-a3d2-4beb-b3f0-de7f38bf5c6b"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_gff",
+                                "uuid": "bae78be6-7c70-42bf-95c1-cae45c51871d"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_gbk",
+                                "uuid": "9a2a7aab-fde6-4a9c-b098-17b958ff2f20"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
+                        "errors": null,
+                        "id": 15,
+                        "input_connections": {
+                            "reference_genome|genome": {
+                                "id": 10,
+                                "output_name": "output_fasta"
+                            },
+                            "track_groups_0|data_tracks_0|data_format|annotation": {
+                                "id": 12,
+                                "output_name": "bam_output"
+                            },
+                            "track_groups_0|data_tracks_1|data_format|annotation": {
+                                "id": 13,
+                                "output_name": "bam_output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "JBrowse",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "html"
+                            }
+                        ],
+                        "position": {
+                            "left": 1469.125,
+                            "top": 558.828125
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "JBrowse-view-assembly-and-reads"
                                 },
-                                "5": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
-                                    "errors": null,
-                                    "id": 5,
-                                    "input_connections": {
-                                        "d": {
-                                            "id": 4,
-                                            "output_name": "Assembly polished by long reads using Racon"
-                                        },
-                                        "i": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Medaka polish",
-                                    "name": "medaka consensus pipeline",
-                                    "outputs": [
-                                        {
-                                            "name": "out_consensus",
-                                            "type": "fasta"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 515.5164024294684,
-                                        "top": 305.08460859328346
-                                    },
-                                    "post_job_actions": {
-                                        "RenameDatasetActionout_consensus": {
-                                            "action_arguments": {
-                                                "newname": "Medaka_long_reads_polished_assembly.fasta"
-                                            },
-                                            "action_type": "RenameDatasetAction",
-                                            "output_name": "out_consensus"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "fc8804320156",
-                                        "name": "medaka_consensus_pipeline",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"b\": \"100\", \"d\": {\"__class__\": \"ConnectedValue\"}, \"g\": false, \"i\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"r941_min_high_g360\", \"out\": [\"consensus\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "1.7.2+galaxy1",
-                                    "type": "tool",
-                                    "uuid": "14c5ce9c-df92-4e20-85da-7a161eaa759d",
-                                    "when": null,
-                                    "workflow_outputs": [
-                                        {
-                                            "label": "Assembly polished by long reads using Medaka",
-                                            "output_name": "out_consensus",
-                                            "uuid": "e3136060-bce7-4af3-87c4-9dcbb0d1f531"
-                                        }
-                                    ]
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "17359b808b01",
+                            "name": "jbrowse",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"11\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Default\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"auto_snp\": \"false\", \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"force\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"auto_snp\": \"false\", \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"force\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.9+galaxy0",
+                        "type": "tool",
+                        "uuid": "9ae0aa01-72e9-4481-b992-248f3ec20a07",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "b5c7a4ed-bb41-4486-b01f-270071e23e52"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
+                        "errors": null,
+                        "id": 16,
+                        "input_connections": {
+                            "reference_genome|genome": {
+                                "id": 10,
+                                "output_name": "output_fasta"
+                            },
+                            "track_groups_0|data_tracks_0|data_format|annotation": {
+                                "id": 14,
+                                "output_name": "out_gff"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "JBrowse",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "html"
+                            }
+                        ],
+                        "position": {
+                            "left": 1981.40625,
+                            "top": 224.328125
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "JBrowse-view-annotations"
                                 },
-                                "6": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                                    "errors": null,
-                                    "id": 6,
-                                    "input_connections": {
-                                        "fasta": {
-                                            "id": 4,
-                                            "output_name": "Assembly polished by long reads using Racon"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Fasta statistics after Racon long read polish",
-                                    "name": "Fasta Statistics",
-                                    "outputs": [
-                                        {
-                                            "name": "stats_output",
-                                            "type": "tabular"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 611.8186129984722,
-                                        "top": 131.47863560473016
-                                    },
-                                    "post_job_actions": {},
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "0dbb995c7d35",
-                                        "name": "fasta_stats",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gaps_option\": false, \"genome_size\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "2.0",
-                                    "type": "tool",
-                                    "uuid": "e78db141-a6d2-42b1-b2b6-aee5e900d3f4",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "7": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                                    "errors": null,
-                                    "id": 7,
-                                    "input_connections": {
-                                        "fasta": {
-                                            "id": 5,
-                                            "output_name": "out_consensus"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Fasta statistics after Medaka polish",
-                                    "name": "Fasta Statistics",
-                                    "outputs": [
-                                        {
-                                            "name": "stats_output",
-                                            "type": "tabular"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 816.9504695700908,
-                                        "top": 343.05724959525315
-                                    },
-                                    "post_job_actions": {},
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "0dbb995c7d35",
-                                        "name": "fasta_stats",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gaps_option\": false, \"genome_size\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "2.0",
-                                    "type": "tool",
-                                    "uuid": "96f313ee-4a6a-4ba9-86f8-3dedc1d5d30d",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "8": {
-                                    "annotation": "",
-                                    "id": 8,
-                                    "input_connections": {
-                                        "Assembly to be polished": {
-                                            "id": 5,
-                                            "input_subworkflow_step_id": 0,
-                                            "output_name": "out_consensus"
-                                        },
-                                        "Illumina reads, R1, in fastq.gz format": {
-                                            "id": 3,
-                                            "input_subworkflow_step_id": 1,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": null,
-                                    "name": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 915.3758175639219,
-                                        "top": 512.306732089216
-                                    },
-                                    "subworkflow": {
-                                        "a_galaxy_workflow": "true",
-                                        "annotation": "",
-                                        "comments": [],
-                                        "creator": [
-                                            {
-                                                "class": "Person",
-                                                "identifier": "0000-0002-9906-0673",
-                                                "name": "Anna Syme"
-                                            }
-                                        ],
-                                        "format-version": "0.1",
-                                        "name": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
-                                        "steps": {
-                                            "0": {
-                                                "annotation": "",
-                                                "content_id": null,
-                                                "errors": null,
-                                                "id": 0,
-                                                "input_connections": {},
-                                                "inputs": [
-                                                    {
-                                                        "description": "",
-                                                        "name": "Assembly to be polished"
-                                                    }
-                                                ],
-                                                "label": "Assembly to be polished",
-                                                "name": "Input dataset",
-                                                "outputs": [],
-                                                "position": {
-                                                    "left": 0,
-                                                    "top": 72.5176329833982
-                                                },
-                                                "tool_id": null,
-                                                "tool_state": "{\"optional\": false, \"tag\": null}",
-                                                "tool_version": null,
-                                                "type": "data_input",
-                                                "uuid": "28669894-74e2-4ba1-9d49-6e3209b5a1de",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "1": {
-                                                "annotation": "",
-                                                "content_id": null,
-                                                "errors": null,
-                                                "id": 1,
-                                                "input_connections": {},
-                                                "inputs": [
-                                                    {
-                                                        "description": "",
-                                                        "name": "Illumina reads, R1, in fastq.gz format"
-                                                    }
-                                                ],
-                                                "label": "Illumina reads, R1, in fastq.gz format",
-                                                "name": "Input dataset",
-                                                "outputs": [],
-                                                "position": {
-                                                    "left": 8.5,
-                                                    "top": 341.2832579833982
-                                                },
-                                                "tool_id": null,
-                                                "tool_state": "{\"optional\": false, \"tag\": null}",
-                                                "tool_version": null,
-                                                "type": "data_input",
-                                                "uuid": "bc936fdc-22a9-4507-aa47-4a70a3f93923",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "2": {
-                                                "annotation": "",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "errors": null,
-                                                "id": 2,
-                                                "input_connections": {
-                                                    "fastq_input|fastq_input1": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    },
-                                                    "reference_source|ref_file": {
-                                                        "id": 0,
-                                                        "output_name": "output"
-                                                    }
-                                                },
-                                                "inputs": [
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "reference_source"
-                                                    }
-                                                ],
-                                                "label": "Minimap2 round 1: map reads to assembly",
-                                                "name": "Map with minimap2",
-                                                "outputs": [
-                                                    {
-                                                        "name": "alignment_output",
-                                                        "type": "bam"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 399.936279296875,
-                                                    "top": 0
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionalignment_output": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "alignment_output"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "be1d967337e4",
-                                                    "name": "minimap2",
-                                                    "owner": "iuc",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": \"sr\"}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "2.26+galaxy0",
-                                                "type": "tool",
-                                                "uuid": "b01b8c3d-c33b-47b2-9a83-297c19d63ab7",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "3": {
-                                                "annotation": "",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "errors": null,
-                                                "id": 3,
-                                                "input_connections": {
-                                                    "corrected_reads": {
-                                                        "id": 0,
-                                                        "output_name": "output"
-                                                    },
-                                                    "overlaps": {
-                                                        "id": 2,
-                                                        "output_name": "alignment_output"
-                                                    },
-                                                    "reads": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    }
-                                                },
-                                                "inputs": [],
-                                                "label": "Racon round 1: polish assembly",
-                                                "name": "Racon",
-                                                "outputs": [
-                                                    {
-                                                        "name": "consensus",
-                                                        "type": "fasta"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 635.5625200274146,
-                                                    "top": 432.13610641498093
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionconsensus": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "78c533842eeb",
-                                                    "name": "racon",
-                                                    "owner": "bgruening",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"error_threshold\": \"0.3\", \"fragment_correction\": false, \"gap\": \"-4\", \"include_unpolished\": false, \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"window_length\": \"500\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "1.5.0+galaxy1",
-                                                "type": "tool",
-                                                "uuid": "fe32d046-4ff2-485e-84e8-191b04803afc",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "4": {
-                                                "annotation": "",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "errors": null,
-                                                "id": 4,
-                                                "input_connections": {
-                                                    "fastq_input|fastq_input1": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    },
-                                                    "reference_source|ref_file": {
-                                                        "id": 3,
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "inputs": [
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "reference_source"
-                                                    }
-                                                ],
-                                                "label": "Minimap2 round 2: map reads to assembly",
-                                                "name": "Map with minimap2",
-                                                "outputs": [
-                                                    {
-                                                        "name": "alignment_output",
-                                                        "type": "bam"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 859.5,
-                                                    "top": 23.955132983398205
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionalignment_output": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "alignment_output"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "be1d967337e4",
-                                                    "name": "minimap2",
-                                                    "owner": "iuc",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": \"sr\"}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "2.26+galaxy0",
-                                                "type": "tool",
-                                                "uuid": "ee834cad-027a-4a84-963b-141b22eaa70a",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "5": {
-                                                "annotation": "",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "errors": null,
-                                                "id": 5,
-                                                "input_connections": {
-                                                    "corrected_reads": {
-                                                        "id": 3,
-                                                        "output_name": "consensus"
-                                                    },
-                                                    "overlaps": {
-                                                        "id": 4,
-                                                        "output_name": "alignment_output"
-                                                    },
-                                                    "reads": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    }
-                                                },
-                                                "inputs": [],
-                                                "label": "Racon round 2: polish assembly",
-                                                "name": "Racon",
-                                                "outputs": [
-                                                    {
-                                                        "name": "consensus",
-                                                        "type": "fasta"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 1198.765625,
-                                                    "top": 332.4707579833982
-                                                },
-                                                "post_job_actions": {
-                                                    "RenameDatasetActionconsensus": {
-                                                        "action_arguments": {
-                                                            "newname": "Racon_short_reads_polished_assembly.fasta"
-                                                        },
-                                                        "action_type": "RenameDatasetAction",
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "78c533842eeb",
-                                                    "name": "racon",
-                                                    "owner": "bgruening",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "1.5.0+galaxy1",
-                                                "type": "tool",
-                                                "uuid": "b3c89c40-3ad0-454c-a4d4-dfa34fb09f24",
-                                                "when": null,
-                                                "workflow_outputs": [
-                                                    {
-                                                        "label": "Assembly polished by short reads using Racon",
-                                                        "output_name": "consensus",
-                                                        "uuid": "594819c3-668e-4575-b9a6-4459ffacf952"
-                                                    }
-                                                ]
-                                            }
-                                        },
-                                        "tags": "",
-                                        "uuid": "1b96b1cf-dbd4-46b1-8a59-aebfe80135c2"
-                                    },
-                                    "tool_id": null,
-                                    "type": "subworkflow",
-                                    "uuid": "46288abb-a2bc-43d5-822a-a93af0d346cf",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "9": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                                    "errors": null,
-                                    "id": 9,
-                                    "input_connections": {
-                                        "fasta": {
-                                            "id": 8,
-                                            "output_name": "Assembly polished by short reads using Racon"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Fasta statistics after Racon short read polish",
-                                    "name": "Fasta Statistics",
-                                    "outputs": [
-                                        {
-                                            "name": "stats_output",
-                                            "type": "tabular"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 1179.1223817823236,
-                                        "top": 547.060000097866
-                                    },
-                                    "post_job_actions": {},
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "0dbb995c7d35",
-                                        "name": "fasta_stats",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gaps_option\": false, \"genome_size\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "2.0",
-                                    "type": "tool",
-                                    "uuid": "3c06b177-02b5-4068-8056-56b653d95379",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                }
-                            },
-                            "tags": "",
-                            "uuid": "af8b99cb-cfc5-4f96-ba6c-6a178826ca98"
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
                         },
-                        "tool_id": null,
-                        "type": "subworkflow",
-                        "uuid": "6b6668c9-25b7-4135-ac9b-140a6d1593b0",
-                        "when": null,
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "17359b808b01",
+                            "name": "jbrowse",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"11\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Default\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"force\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.9+galaxy0",
+                        "type": "tool",
+                        "uuid": "7e5c8b63-2538-4898-9644-71453e17c0ba",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "2:output",
-                                "uuid": "f740de36-9921-4f0c-924e-3902bc2083b7"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "4:2:output",
-                                "uuid": "2b5d309e-c47e-4a79-a69c-4d4fd6a93d8b"
+                                "output_name": "output",
+                                "uuid": "5ad68433-82c3-47aa-b3e4-ef1b07ed790e"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/largegenome",
-                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga",
+                "parent_id": "assembly/chloroplast-assembly",
+                "path": "topics/assembly/tutorials/chloroplast-assembly/workflows/Galaxy-Workflow-Chloroplast-genome-assembly-and-annotation.ga",
                 "tags": [
-                    "LG-WF",
-                    "GTN"
+                    "assembly"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Combined workflows for large genome assembly - upgraded ",
+                "title": "Chloroplast-genome-assembly-and-annotation",
                 "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-combined-workflows-for-large-genome-assembly",
-                "tutorial_id": "largegenome",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.html",
-                "version": 2,
-                "wfid": "assembly-largegenome",
-                "wfname": "galaxy-workflow-combined-workflows-for-large-genome-assembly",
-                "workflow": "Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-chloroplast-assembly/versions/galaxy-workflow-chloroplast-genome-assembly-and-annotation",
+                "tutorial_id": "chloroplast-assembly",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/chloroplast-assembly/workflows/Galaxy-Workflow-Chloroplast-genome-assembly-and-annotation.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/chloroplast-assembly/workflows/Galaxy-Workflow-Chloroplast-genome-assembly-and-annotation.html",
+                "version": 3,
+                "wfid": "assembly-chloroplast-assembly",
+                "wfname": "galaxy-workflow-chloroplast-genome-assembly-and-annotation",
+                "workflow": "Galaxy-Workflow-Chloroplast-genome-assembly-and-annotation.ga",
                 "workflow_tools": [
-                    "barchart_gnuplot",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6",
+                    "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
                     "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1"
                 ],
-                "workflowhub_id": "1176"
+                "workflowhub_id": "1139"
+            }
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.3567224"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "busco",
+                    "owner": "iuc",
+                    "revisions": "41030a6c03b7",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "chromeister",
+                    "owner": "iuc",
+                    "revisions": "b768cc4cca40",
+                    "tool_panel_section_label": "Multiple Alignments",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "merqury",
+                    "owner": "iuc",
+                    "revisions": "f8113c25bc6b",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "meryl",
+                    "owner": "iuc",
+                    "revisions": "29dabd8db6f2",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "quast",
+                    "owner": "iuc",
+                    "revisions": "3061c8b029e5",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: busco\n  owner: iuc\n  revisions: 41030a6c03b7\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chromeister\n  owner: iuc\n  revisions: b768cc4cca40\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merqury\n  owner: iuc\n  revisions: f8113c25bc6b\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n  owner: iuc\n  revisions: 29dabd8db6f2\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 3061c8b029e5\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-quality-control/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "eurosciencegateway",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
+                "fediverse_flavor": "mastodon",
+                "id": "abretaud",
+                "joined": "2017-09",
+                "location": {
+                    "country": "FR",
+                    "lat": 48.11,
+                    "lon": -1.64
+                },
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+            },
+            {
+                "email": "alexandre.cormier@ifremer.fr",
+                "id": "alexcorm",
+                "joined": "2021-11",
+                "name": "Alexandre Cormier",
+                "orcid": "0000-0002-7775-8413",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/",
+                "twitter": "allanssx",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/alexcorm.json"
+            },
+            {
+                "email": "erwan.corre@sb-roscoff.fr",
+                "id": "r1corre",
+                "joined": "2019-04",
+                "name": "Erwan Corre",
+                "orcid": "0000-0001-6354-2278",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/r1corre/",
+                "twitter": "r1corre",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/r1corre.json"
+            },
+            {
+                "email": "laura.leroi@ifremer.fr",
+                "id": "lleroi",
+                "joined": "2021-11",
+                "name": "Laura Leroi",
+                "orcid": "0000-0003-3748-4179",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lleroi/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/lleroi.json"
             },
+            {
+                "email": "stephanie.robin@inrae.fr",
+                "id": "stephanierobin",
+                "joined": "2021-11",
+                "name": "St\u00e9phanie Robin",
+                "orcid": "0000-0001-7379-9173",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/",
+                "twitter": "robinstphanie1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/stephanierobin.json"
+            }
+        ],
+        "dir": "topics/assembly/tutorials/assembly-quality-control",
+        "edam_operation": [
+            "Visualisation",
+            "Genome assembly",
+            "De-novo assembly",
+            "Phasing",
+            "Sequence assembly validation",
+            "Scaffolding",
+            "k-mer counting",
+            "Transcriptome assembly"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "genome-annotation",
+                "tutorials": [
+                    "repeatmasker"
+                ],
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "assembly/assembly-quality-control",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Quast, BUSCO and Merqury make it easy to assess the quality of an assembly",
+            "Post-processing can be necessary (purging, scaffolding) before annotation"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": [
+            "Assess assembly quality"
+        ],
+        "pageviews": 2940854,
+        "pub_date": "2022-08-26",
+        "questions": [
+            "Is my genome assembly ready for annotation and/or scaffolding?"
+        ],
+        "short_id": "T00028",
+        "short_tools": [
+            "merqury",
+            "busco",
+            "quast",
+            "chromeister",
+            "meryl"
+        ],
+        "slides": true,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "assembly",
+            "quality control"
+        ],
+        "time_estimation": "2h",
+        "title": "Genome Assembly Quality Control",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0"
+        ],
+        "topic_name": "assembly",
+        "topic_name_human": "Assembly",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "assembly-quality-control",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/assembly-quality-control/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-quality-control/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-quality-control/tutorial.json"
+        },
+        "version": 4,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 271,
+        "visitors": 1228609,
+        "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
-                    }
-                ],
-                "description": "",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": {
-                        "markdown": "\n# Workflow Report for Data QC\n\n## Workflow steps\n\n```galaxy\nworkflow_display()\n```\n\n"
+                        "identifier": "",
+                        "name": "Erwan Corre"
                     },
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput file: long reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R1\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R2\"]\n  3[label=\"Nanoplot: long reads\"]\n  0 -> 3 [label=\"output\"]\n  k73d0e4cf366e41c1810ab269638826b3[color=lightseagreen,label=\"Output\\nNanoPlot on input dataset(s): HTML report\"]\n  3 -> k73d0e4cf366e41c1810ab269638826b3\n  4[label=\"FastQC on R1\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"FastQC on R2\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"MultiQC: combine fastQC reports\"]\n  4 -> 6 [label=\"text_file\"]\n  5 -> 6 [label=\"text_file\"]\n  k8baf8700876e4a74ad996e656f3ba618[color=lightseagreen,label=\"Output\\nMultiQC on input dataset(s): Webpage\"]\n  6 -> k8baf8700876e4a74ad996e656f3ba618\n}",
-                "history": [
                     {
-                        "hash": "d35221f6506e7b95e8b3ff679a2ad01edf1a560a",
-                        "message": "Update Galaxy-Workflow-Data_QC.ga",
-                        "num": 5,
-                        "short_hash": "d35221f65",
-                        "unix": "1715074384"
+                        "class": "Person",
+                        "identifier": "",
+                        "name": "St\u00e9phanie Robin"
                     },
                     {
-                        "hash": "a737e5f1b936379382f4d568b0caeb664d81c392",
-                        "message": "Rename Galaxy-Workflow-Data_QC_-_upgraded.ga to Galaxy-Workflow-Data_QC.ga",
-                        "num": 4,
-                        "short_hash": "a737e5f1b",
-                        "unix": "1714537191"
+                        "class": "Person",
+                        "identifier": "",
+                        "name": "Anthony Bretaudeau"
                     },
                     {
-                        "hash": "9ca497557dddc43b116a61592a953f455046bc86",
-                        "message": "Rename Galaxy-Workflow-Data_QC.ga to Galaxy-Workflow-Data_QC_old.ga",
-                        "num": 3,
-                        "short_hash": "9ca497557",
-                        "unix": "1714537118"
+                        "class": "Person",
+                        "identifier": "",
+                        "name": "Alexandre Cormier"
                     },
                     {
-                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
-                        "message": "add/complete creator info on workflows",
-                        "num": 2,
-                        "short_hash": "62e77944b",
-                        "unix": "1676627603"
-                    },
+                        "class": "Person",
+                        "identifier": "",
+                        "name": "Laura Leroi"
+                    }
+                ],
+                "description": "Genome assembly quality control using PacBio data and with reference genome",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGCA_000146045.2_genomic.fna\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nScerevisiae-INSC1019.flye.30x.fa\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nScerevisiae-INSC1019.hifiasm.30x.fa\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSRR13577847_subreads.30x.fastq.gz\"]\n  4[label=\"Busco\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Busco\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"Quast\"]\n  0 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"Busco\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"Chromeister\"]\n  0 -> 8 [label=\"output\"]\n  2 -> 8 [label=\"output\"]\n  9[label=\"Meryl\"]\n  3 -> 9 [label=\"output\"]\n  10[label=\"Merqury\"]\n  0 -> 10 [label=\"output\"]\n  9 -> 10 [label=\"read_db\"]\n  11[label=\"Merqury\"]\n  1 -> 11 [label=\"output\"]\n  9 -> 11 [label=\"read_db\"]\n  12[label=\"Merqury\"]\n  2 -> 12 [label=\"output\"]\n  9 -> 12 [label=\"read_db\"]\n}",
+                "history": [
                     {
-                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
-                        "message": "large genome tutorial",
+                        "hash": "9e51f44fe902a2db9db2b2895df49c788990df15",
+                        "message": "Genome assembly quality control (#3120)",
                         "num": 1,
-                        "short_hash": "9fcb3aeec",
-                        "unix": "1665123856"
+                        "short_hash": "9e51f44fe",
+                        "unix": "1661523060"
                     }
                 ],
                 "inputs": [
@@ -12102,22 +10316,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Input file: long reads"
+                                "name": "GCA_000146045.2_genomic.fna"
                             }
                         ],
-                        "label": "Input file: long reads",
+                        "label": "GCA_000146045.2_genomic.fna",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 0.0
+                            "left": 10,
+                            "top": 10
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "e2e4a70b-6e36-4b8b-bdf6-12b97189a6bd",
-                        "when": null,
+                        "uuid": "67e22573-10a9-4a09-bc6b-ad54147f931a",
                         "workflow_outputs": []
                     },
                     {
@@ -12129,22 +10342,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Input file: Illumina reads R1"
+                                "name": "Scerevisiae-INSC1019.flye.30x.fa"
                             }
                         ],
-                        "label": "Input file: Illumina reads R1",
+                        "label": "Scerevisiae-INSC1019.flye.30x.fa",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 535.703125,
-                            "top": 21.0
+                            "left": 10,
+                            "top": 130
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ea859a58-c81a-4ef6-9bd2-4ef2f17bb5a9",
-                        "when": null,
+                        "uuid": "056f45e5-b3d7-4d43-8c87-497977c8b9f6",
                         "workflow_outputs": []
                     },
                     {
@@ -12156,240 +10368,367 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Input file: Illumina reads R2"
+                                "name": "Scerevisiae-INSC1019.hifiasm.30x.fa"
                             }
                         ],
-                        "label": "Input file: Illumina reads R2",
+                        "label": "Scerevisiae-INSC1019.hifiasm.30x.fa",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 530.703125,
-                            "top": 379.984375
+                            "left": 10,
+                            "top": 250
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "472adc05-88a5-4955-9e43-e82e9550ad08",
-                        "when": null,
+                        "uuid": "e812ab39-31c2-4595-8f11-f1e939e68704",
                         "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput file: long reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R2\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Nanoplot: long reads\"];\n  0 -->|output| 3;\n  73d0e4cf-366e-41c1-810a-b269638826b3[\"Output\\nNanoPlot on input dataset(s): HTML report\"];\n  3 --> 73d0e4cf-366e-41c1-810a-b269638826b3;\n  style 73d0e4cf-366e-41c1-810a-b269638826b3 stroke:#2c3143,stroke-width:4px;\n  4[\"FastQC on R1\"];\n  1 -->|output| 4;\n  5[\"FastQC on R2\"];\n  2 -->|output| 5;\n  6[\"MultiQC: combine fastQC reports\"];\n  4 -->|text_file| 6;\n  5 -->|text_file| 6;\n  8baf8700-876e-4a74-ad99-6e656f3ba618[\"Output\\nMultiQC on input dataset(s): Webpage\"];\n  6 --> 8baf8700-876e-4a74-ad99-6e656f3ba618;\n  style 8baf8700-876e-4a74-ad99-6e656f3ba618 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Data QC - upgraded",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "mode|reads|files": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Nanoplot: long reads",
-                        "name": "NanoPlot",
-                        "outputs": [
-                            {
-                                "name": "output_html",
-                                "type": "html"
-                            },
-                            {
-                                "name": "nanostats",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "nanostats_post_filtering",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 240.84375,
-                            "top": 104.359375
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionlog_read_length": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "log_read_length"
-                            },
-                            "HideDatasetActionnanostats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "nanostats"
-                            },
-                            "HideDatasetActionnanostats_post_filtering": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "nanostats_post_filtering"
-                            },
-                            "HideDatasetActionread_length": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "read_length"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "a02b8b3f5a0c",
-                            "name": "nanoplot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"customization\": {\"color\": null, \"plots\": null, \"N50\": false}, \"filter\": {\"maxlength\": null, \"minlength\": null, \"drop_outliers\": false, \"downsample\": null, \"loglength\": false, \"percentqual\": false, \"alength\": false, \"minqual\": null, \"runtime_until\": null, \"readtype\": null, \"barcoded\": false, \"no_supplementary\": false}, \"mode\": {\"choice\": \"batch\", \"__current_case__\": 0, \"reads\": {\"type\": \"fastq\", \"__current_case__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.42.0+galaxy1",
-                        "type": "tool",
-                        "uuid": "3b8a87fe-1506-48d2-a4d9-f4dca8b6065d",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "NanoPlot on input dataset(s): HTML report",
-                                "output_name": "output_html",
-                                "uuid": "73d0e4cf-366e-41c1-810a-b269638826b3"
-                            }
-                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "results_0|software_cond|output_0|input": {
-                                "id": 4,
-                                "output_name": "text_file"
-                            },
-                            "results_0|software_cond|output_1|input": {
-                                "id": 5,
-                                "output_name": "text_file"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "MultiQC: combine fastQC reports",
-                        "name": "MultiQC",
-                        "outputs": [
-                            {
-                                "name": "stats",
-                                "type": "input"
-                            },
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "html_report",
-                                "type": "html"
+                                "description": "",
+                                "name": "SRR13577847_subreads.30x.fastq.gz"
                             }
                         ],
+                        "label": "SRR13577847_subreads.30x.fastq.gz",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1233.5,
-                            "top": 230.844970703125
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionstats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "stats"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "abfd8a6544d7",
-                            "name": "multiqc",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 10,
+                            "top": 370
                         },
-                        "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.11+galaxy1",
-                        "type": "tool",
-                        "uuid": "3e29a59b-dca0-4993-b20d-495a3f17e291",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "MultiQC on input dataset(s): Webpage",
-                                "output_name": "html_report",
-                                "uuid": "8baf8700-876e-4a74-ad99-6e656f3ba618"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "f0a31b4f-fdf0-4417-9300-a4e52dc60580",
+                        "workflow_outputs": []
                     }
                 ],
-                "parent_id": "assembly/largegenome",
-                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Data_QC.ga",
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGCA_000146045.2_genomic.fna\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nScerevisiae-INSC1019.flye.30x.fa\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nScerevisiae-INSC1019.hifiasm.30x.fa\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nSRR13577847_subreads.30x.fastq.gz\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Busco\"];\n  0 -->|output| 4;\n  5[\"Busco\"];\n  1 -->|output| 5;\n  6[\"Quast\"];\n  0 -->|output| 6;\n  1 -->|output| 6;\n  2 -->|output| 6;\n  7[\"Busco\"];\n  2 -->|output| 7;\n  8[\"Chromeister\"];\n  0 -->|output| 8;\n  2 -->|output| 8;\n  9[\"Meryl\"];\n  3 -->|output| 9;\n  10[\"Merqury\"];\n  0 -->|output| 10;\n  9 -->|read_db| 10;\n  11[\"Merqury\"];\n  1 -->|output| 11;\n  9 -->|read_db| 11;\n  12[\"Merqury\"];\n  2 -->|output| 12;\n  9 -->|read_db| 12;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Genome Assembly Quality Control",
+                "outputs": [],
+                "parent_id": "assembly/assembly-quality-control",
+                "path": "topics/assembly/tutorials/assembly-quality-control/workflows/main_workflow.ga",
                 "tags": [
-                    "LG-WF",
-                    "GTN"
+                    "assembly"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Data QC - upgraded",
+                "title": "Genome Assembly Quality Control",
                 "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-data-qc",
-                "tutorial_id": "largegenome",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Data_QC.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Data_QC.html",
-                "version": 2,
-                "wfid": "assembly-largegenome",
-                "wfname": "galaxy-workflow-data-qc",
-                "workflow": "Galaxy-Workflow-Data_QC.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-assembly-quality-control/versions/main-workflow",
+                "tutorial_id": "assembly-quality-control",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-quality-control/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-quality-control/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "assembly-assembly-quality-control",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0"
                 ],
-                "workflowhub_id": "1162"
-            },
+                "workflowhub_id": "1128"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/6947782"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "gfastats",
+                    "owner": "bgruening",
+                    "revisions": "3ef480892a9f",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "86755160afbf",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "86755160afbf",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ncbi_blast_plus",
+                    "owner": "devteam",
+                    "revisions": "d999e774072a",
+                    "tool_panel_section_label": "NCBI Blast",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ncbi_blast_plus",
+                    "owner": "devteam",
+                    "revisions": "cbf3f518b668",
+                    "tool_panel_section_label": "NCBI Blast",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ncbi_blast_plus",
+                    "owner": "devteam",
+                    "revisions": "d999e774072a",
+                    "tool_panel_section_label": "NCBI Blast",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ncbi_blast_plus",
+                    "owner": "devteam",
+                    "revisions": "cbf3f518b668",
+                    "tool_panel_section_label": "NCBI Blast",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "kraken2",
+                    "owner": "iuc",
+                    "revisions": "20e2f64aa1fe",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "kraken2",
+                    "owner": "iuc",
+                    "revisions": "cdee7158adf3",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "parse_mito_blast",
+                    "owner": "iuc",
+                    "revisions": "3c9ad4adf8d2",
+                    "tool_panel_section_label": "Extract Features",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: gfastats\n  owner: bgruening\n  revisions: 3ef480892a9f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: d999e774072a\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: cbf3f518b668\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: d999e774072a\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: cbf3f518b668\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: 20e2f64aa1fe\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: cdee7158adf3\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: parse_mito_blast\n  owner: iuc\n  revisions: 3c9ad4adf8d2\n  tool_panel_section_label: Extract Features\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-decontamination/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "delphine-l"
+            ]
+        },
+        "contributors": [
+            {
+                "email": "delphine.lariviere@galaxy.org",
+                "id": "delphine-l",
+                "joined": "2017-09",
+                "name": "Delphine Lariviere",
+                "orcid": "0000-0001-6421-3484",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
+            }
+        ],
+        "dir": "topics/assembly/tutorials/assembly-decontamination",
+        "edam_operation": [
+            "Taxonomic classification",
+            "Data handling"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "assembly/assembly-decontamination",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Assembly decontamination is important to avoid false identification of genes, blast hits..."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-26",
+        "objectives": [
+            "Remove contaminant sequences from an assembly",
+            "Identify contaminant species",
+            "Remove Mitochondrial DNA from an assembly"
+        ],
+        "pageviews": 71,
+        "pub_date": "2024-09-04",
+        "questions": [
+            "How to remove contaminant sequences from your assembly?"
+        ],
+        "recordings": [
+            {
+                "bot-timestamp": 1726801100,
+                "captioners": [
+                    "delphine-l"
+                ],
+                "date": "2024-09-20",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "29M",
+                "speakers": [
+                    "delphine-l"
+                ],
+                "youtube_id": "-5oxfNnNwoA"
+            }
+        ],
+        "short_id": "T00452",
+        "short_tools": [
+            "tp_sed_tool",
+            "tp_cat",
+            "Filter1",
+            "ncbi_dustmasker_wrapper",
+            "kraken2",
+            "Cut1",
+            "gfastats",
+            "parse_mito_blast",
+            "ncbi_blastn_wrapper"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "time_estimation": "1H30M",
+        "title": "Decontamination of a genome assembly",
+        "tools": [
+            "Cut1",
+            "Filter1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/parse_mito_blast/parse_mito_blast/1.0.2+galaxy0"
+        ],
+        "topic_name": "assembly",
+        "topic_name_human": "Assembly",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "assembly-decontamination",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/assembly-decontamination/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-decontamination/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-decontamination/tutorial.json"
+        },
+        "version": 2,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 278,
+        "visitors": 59,
+        "workflows": [
             {
                 "creators": [
                     {
-                        "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
+                        "class": "Organization",
+                        "name": "Nadolina Brajuka",
+                        "url": "https://github.com/Nadolina"
                     }
                 ],
                 "description": "",
                 "features": {
                     "comments": false,
-                    "parameters": false,
-                    "report": null,
+                    "parameters": true,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n### Worflow ran on: \n\n```galaxy\ninvocation_time()\n```\n\n# List of contaminants\n\n\r\n```galaxy\nhistory_dataset_as_table(output=\"contaminants_table\")\n```\r\n\n\n# List of Mitochondrial scaffolds\n\r\n```galaxy\nhistory_dataset_as_table(output=\"mito_scaff_names\")\n```\r\n\n\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                    },
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads, R1, in fastq.gz format\"]\n  2[label=\"Minimap2 round 1: map reads to assembly\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Racon round 1: polish assembly\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"alignment_output\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Minimap2 round 2: map reads to assembly\"]\n  1 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"consensus\"]\n  5[label=\"Racon round 2: polish assembly\"]\n  3 -> 5 [label=\"consensus\"]\n  4 -> 5 [label=\"alignment_output\"]\n  1 -> 5 [label=\"output\"]\n  k594819c3668e4575b9a64459ffacf952[color=lightseagreen,label=\"Output\\nAssembly polished by short reads using Racon\"]\n  5 -> k594819c3668e4575b9a64459ffacf952\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nScaffolded assembly fasta\"]\n  1[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nDatabase for Kraken2\"]\n  2[label=\"soft-masking \"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"hard-masking\"]\n  2 -> 3 [label=\"outfile\"]\n  4[label=\"ID non-target contaminants\"]\n  1 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  kc380857b51804e82a14f8b575f10abaa[color=lightseagreen,label=\"Output\\nKraken2 classification scores\"]\n  4 -> kc380857b51804e82a14f8b575f10abaa\n  5[label=\"blast mitochondria DB\"]\n  3 -> 5 [label=\"output\"]\n  6[label=\"Cut\"]\n  4 -> 6 [label=\"output\"]\n  7[label=\"parsing blast output\"]\n  5 -> 7 [label=\"output1\"]\n  k1478af1e52f448feb9660a61e2014a58[color=lightseagreen,label=\"Output\\nmito_scaff_names\"]\n  7 -> k1478af1e52f448feb9660a61e2014a58\n  8[label=\"Filter\"]\n  6 -> 8 [label=\"out_file1\"]\n  k64156e28aaf045789a7ed6d21774c2c8[color=lightseagreen,label=\"Output\\ncontaminants_table\"]\n  8 -> k64156e28aaf045789a7ed6d21774c2c8\n  9[label=\"Cut\"]\n  8 -> 9 [label=\"out_file1\"]\n  10[label=\"concatenate scaffold lists\"]\n  7 -> 10 [label=\"mito_scaff_names\"]\n  9 -> 10 [label=\"out_file1\"]\n  k77084ec5a14540c19cfc476d091105ae[color=lightseagreen,label=\"Output\\nfull contaminant + mito scaffold list\"]\n  10 -> k77084ec5a14540c19cfc476d091105ae\n  11[label=\"removing scaffolds \"]\n  0 -> 11 [label=\"output\"]\n  10 -> 11 [label=\"out_file1\"]\n  k88a8e9edd92c4340aaadc6d450a336aa[color=lightseagreen,label=\"Output\\nfinal decontaminated assembly\"]\n  11 -> k88a8e9edd92c4340aaadc6d450a336aa\n}",
                 "history": [
                     {
-                        "hash": "3be0312ca5a2e27bc1f8573e28943833be988894",
-                        "message": "Update Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga",
-                        "num": 5,
-                        "short_hash": "3be0312ca",
-                        "unix": "1715074403"
-                    },
-                    {
-                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
-                        "message": "new versions of workflows",
-                        "num": 4,
-                        "short_hash": "e8ddbcdd5",
-                        "unix": "1714537936"
-                    },
-                    {
-                        "hash": "7d222309ffbec070126e3e749ba6f3d4e510cc6e",
-                        "message": "Rename Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga to Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2_old.ga",
+                        "hash": "8508dbeac22779c511121fb4d756fc77c6812d8e",
+                        "message": "format workflow and update test to the latest version of the workflow",
                         "num": 3,
-                        "short_hash": "7d222309f",
-                        "unix": "1714537293"
+                        "short_hash": "8508dbeac",
+                        "unix": "1725390032"
                     },
                     {
-                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
-                        "message": "add/complete creator info on workflows",
+                        "hash": "eb3c5175f70749e069a63fc91280cef0ba9b6811",
+                        "message": "Simplify the workflow",
                         "num": 2,
-                        "short_hash": "62e77944b",
-                        "unix": "1676627603"
+                        "short_hash": "eb3c5175f",
+                        "unix": "1724446543"
                     },
                     {
-                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
-                        "message": "large genome tutorial",
+                        "hash": "72a8cb1ed14633e460c6f1ccda17cfdc53ee5923",
+                        "message": "creation of a tutorial for Asssembly decontamination'",
                         "num": 1,
-                        "short_hash": "9fcb3aeec",
-                        "unix": "1665123856"
+                        "short_hash": "72a8cb1ed",
+                        "unix": "1723825233"
                     }
                 ],
                 "inputs": [
@@ -12402,196 +10741,799 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Assembly to be polished"
+                                "name": "Scaffolded assembly (fasta)"
                             }
                         ],
-                        "label": "Assembly to be polished",
+                        "label": "Scaffolded assembly (fasta)",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 72.5176329833982
+                            "left": 0.0,
+                            "top": 573.2100224386197
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "28669894-74e2-4ba1-9d49-6e3209b5a1de",
+                        "uuid": "f3335a9f-1793-4ba2-98d8-253eb5380a3f",
                         "when": null,
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Select the database to query to identify non-target contaminants.",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Illumina reads, R1, in fastq.gz format"
+                                "description": "Select the database to query to identify non-target contaminants.",
+                                "name": "Database for Kraken2"
                             }
                         ],
-                        "label": "Illumina reads, R1, in fastq.gz format",
-                        "name": "Input dataset",
+                        "label": "Database for Kraken2",
+                        "name": "Input parameter",
                         "outputs": [],
                         "position": {
-                            "left": 8.5,
-                            "top": 341.2832579833982
+                            "left": 0.5475811709443406,
+                            "top": 692.7734375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "bc936fdc-22a9-4507-aa47-4a70a3f93923",
+                        "type": "parameter_input",
+                        "uuid": "4bd1b150-bdb0-4458-9ddc-62bc29356aa2",
                         "when": null,
-                        "workflow_outputs": []
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "34f0edb5-742e-4de2-923f-1fb93e511ca9"
+                            }
+                        ]
                     }
                 ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nIllumina reads, R1, in fastq.gz format\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Minimap2 round 1: map reads to assembly\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Racon round 1: polish assembly\"];\n  0 -->|output| 3;\n  2 -->|alignment_output| 3;\n  1 -->|output| 3;\n  4[\"Minimap2 round 2: map reads to assembly\"];\n  1 -->|output| 4;\n  3 -->|consensus| 4;\n  5[\"Racon round 2: polish assembly\"];\n  3 -->|consensus| 5;\n  4 -->|alignment_output| 5;\n  1 -->|output| 5;\n  594819c3-668e-4575-b9a6-4459ffacf952[\"Output\\nAssembly polished by short reads using Racon\"];\n  5 --> 594819c3-668e-4575-b9a6-4459ffacf952;\n  style 594819c3-668e-4575-b9a6-4459ffacf952 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
+                "license": "BSD-3-Clause",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nScaffolded assembly fasta\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nDatabase for Kraken2\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"soft-masking \"];\n  0 -->|output| 2;\n  3[\"hard-masking\"];\n  2 -->|outfile| 3;\n  4[\"ID non-target contaminants\"];\n  1 -->|output| 4;\n  3 -->|output| 4;\n  c380857b-5180-4e82-a14f-8b575f10abaa[\"Output\\nKraken2 classification scores\"];\n  4 --> c380857b-5180-4e82-a14f-8b575f10abaa;\n  style c380857b-5180-4e82-a14f-8b575f10abaa stroke:#2c3143,stroke-width:4px;\n  5[\"blast mitochondria DB\"];\n  3 -->|output| 5;\n  6[\"Cut\"];\n  4 -->|output| 6;\n  7[\"parsing blast output\"];\n  5 -->|output1| 7;\n  1478af1e-52f4-48fe-b966-0a61e2014a58[\"Output\\nmito_scaff_names\"];\n  7 --> 1478af1e-52f4-48fe-b966-0a61e2014a58;\n  style 1478af1e-52f4-48fe-b966-0a61e2014a58 stroke:#2c3143,stroke-width:4px;\n  8[\"Filter\"];\n  6 -->|out_file1| 8;\n  64156e28-aaf0-4578-9a7e-d6d21774c2c8[\"Output\\ncontaminants_table\"];\n  8 --> 64156e28-aaf0-4578-9a7e-d6d21774c2c8;\n  style 64156e28-aaf0-4578-9a7e-d6d21774c2c8 stroke:#2c3143,stroke-width:4px;\n  9[\"Cut\"];\n  8 -->|out_file1| 9;\n  10[\"concatenate scaffold lists\"];\n  7 -->|mito_scaff_names| 10;\n  9 -->|out_file1| 10;\n  77084ec5-a145-40c1-9cfc-476d091105ae[\"Output\\nfull contaminant + mito scaffold list\"];\n  10 --> 77084ec5-a145-40c1-9cfc-476d091105ae;\n  style 77084ec5-a145-40c1-9cfc-476d091105ae stroke:#2c3143,stroke-width:4px;\n  11[\"removing scaffolds \"];\n  0 -->|output| 11;\n  10 -->|out_file1| 11;\n  88a8e9ed-d92c-4340-aaad-c6d450a336aa[\"Output\\nfinal decontaminated assembly\"];\n  11 --> 88a8e9ed-d92c-4340-aaad-c6d450a336aa;\n  style 88a8e9ed-d92c-4340-aaad-c6d450a336aa stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Assembly-decontamination-VGP9",
                 "outputs": [
+                    {
+                        "annotation": "Select the database to query to identify non-target contaminants.",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Select the database to query to identify non-target contaminants.",
+                                "name": "Database for Kraken2"
+                            }
+                        ],
+                        "label": "Database for Kraken2",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 0.5475811709443406,
+                            "top": 692.7734375
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "4bd1b150-bdb0-4458-9ddc-62bc29356aa2",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "34f0edb5-742e-4de2-923f-1fb93e511ca9"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1",
                         "errors": null,
-                        "id": 5,
+                        "id": 4,
                         "input_connections": {
-                            "corrected_reads": {
+                            "kraken2_database": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "single_paired|input_sequences": {
                                 "id": 3,
-                                "output_name": "consensus"
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Kraken2",
+                                "name": "single_paired"
+                            }
+                        ],
+                        "label": "ID non-target contaminants",
+                        "name": "Kraken2",
+                        "outputs": [
+                            {
+                                "name": "classified_out_s",
+                                "type": "input"
                             },
-                            "overlaps": {
-                                "id": 4,
-                                "output_name": "alignment_output"
+                            {
+                                "name": "unclassified_out_s",
+                                "type": "input"
                             },
-                            "reads": {
-                                "id": 1,
-                                "output_name": "output"
+                            {
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 1300.1257061709443,
+                            "top": 147.58203125
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionunclassified_out_s": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "unclassified_out_s"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "cdee7158adf3",
+                            "name": "kraken2",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"confidence\": \"0.3\", \"kraken2_database\": {\"__class__\": \"ConnectedValue\"}, \"min_base_quality\": \"0\", \"minimum_hit_groups\": \"2\", \"quick\": false, \"report\": {\"create_report\": false, \"use_mpa_style\": false, \"report_zero_counts\": false, \"report_minimizer_data\": false}, \"single_paired\": {\"single_paired_selector\": \"no\", \"__current_case__\": 2, \"input_sequences\": {\"__class__\": \"ConnectedValue\"}}, \"split_reads\": true, \"use_names\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.3+galaxy1",
+                        "type": "tool",
+                        "uuid": "17141f21-ae3c-44ac-b0a5-d3bb9b8726a4",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Kraken2 classification scores",
+                                "output_name": "output",
+                                "uuid": "c380857b-5180-4e82-a14f-8b575f10abaa"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/parse_mito_blast/parse_mito_blast/1.0.2+galaxy0",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "blastout": {
+                                "id": 5,
+                                "output_name": "output1"
                             }
                         },
                         "inputs": [],
-                        "label": "Racon round 2: polish assembly",
-                        "name": "Racon",
+                        "label": "parsing blast output",
+                        "name": "Parse mitochondrial blast",
                         "outputs": [
                             {
-                                "name": "consensus",
-                                "type": "fasta"
+                                "name": "cov_report",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "mito_scaff_names",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 1198.765625,
-                            "top": 332.4707579833982
+                            "left": 1821.3783868183484,
+                            "top": 482.19337215633186
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/parse_mito_blast/parse_mito_blast/1.0.2+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3c9ad4adf8d2",
+                            "name": "parse_mito_blast",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"blastout\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2+galaxy0",
+                        "type": "tool",
+                        "uuid": "4350e47a-2394-4381-a274-e238985195df",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "mito_scaff_names",
+                                "output_name": "mito_scaff_names",
+                                "uuid": "1478af1e-52f4-48fe-b966-0a61e2014a58"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "Filter1",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "input": {
+                                "id": 6,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Filter",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 2001.9694561709443,
+                            "top": 0
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionconsensus": {
+                            "HideDatasetActionout_file1": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "out_file1"
+                            },
+                            "RenameDatasetActionout_file1": {
                                 "action_arguments": {
-                                    "newname": "Racon_short_reads_polished_assembly.fasta"
+                                    "newname": "List of contaminants"
                                 },
                                 "action_type": "RenameDatasetAction",
-                                "output_name": "consensus"
+                                "output_name": "out_file1"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"cond\": \"c1!='U'\", \"header_lines\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
+                        "type": "tool",
+                        "uuid": "f5d80335-9b98-40ca-b706-4bb54d9801e6",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "contaminants_table",
+                                "output_name": "out_file1",
+                                "uuid": "64156e28-aaf0-4578-9a7e-d6d21774c2c8"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1",
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {
+                            "inputs": [
+                                {
+                                    "id": 7,
+                                    "output_name": "mito_scaff_names"
+                                },
+                                {
+                                    "id": 9,
+                                    "output_name": "out_file1"
+                                }
+                            ]
+                        },
+                        "inputs": [],
+                        "label": "concatenate scaffold lists",
+                        "name": "Concatenate datasets",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 2538.6178936709443,
+                            "top": 423.9453125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "78c533842eeb",
-                            "name": "racon",
+                            "changeset_revision": "86755160afbf",
+                            "name": "text_processing",
                             "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.5.0+galaxy1",
+                        "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "9.3+galaxy1",
                         "type": "tool",
-                        "uuid": "b3c89c40-3ad0-454c-a4d4-dfa34fb09f24",
+                        "uuid": "5b7e33a0-0ec4-4539-bb91-0c862597df69",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Assembly polished by short reads using Racon",
-                                "output_name": "consensus",
-                                "uuid": "594819c3-668e-4575-b9a6-4459ffacf952"
+                                "label": "full contaminant + mito scaffold list",
+                                "output_name": "out_file1",
+                                "uuid": "77084ec5-a145-40c1-9cfc-476d091105ae"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
+                        "errors": null,
+                        "id": 11,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "target_condition|exclude_bed": {
+                                "id": 10,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool gfastats",
+                                "name": "mode_condition"
+                            },
+                            {
+                                "description": "runtime parameter for tool gfastats",
+                                "name": "target_condition"
+                            },
+                            {
+                                "description": "runtime parameter for tool gfastats",
+                                "name": "target_condition"
+                            }
+                        ],
+                        "label": "removing scaffolds ",
+                        "name": "gfastats",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "fastq"
+                            }
+                        ],
+                        "position": {
+                            "left": 2977.7819561709443,
+                            "top": 798.078125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3ef480892a9f",
+                            "name": "gfastats",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta.gz\", \"__current_case__\": 1, \"line_length\": null}, \"discover_paths\": false, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"true\", \"__current_case__\": 1, \"target_sequence\": \"\", \"include_bed\": {\"__class__\": \"ConnectedValue\"}, \"exclude_bed\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "5113c945-c811-4cbc-81ac-20d1d80e97ed",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "final decontaminated assembly",
+                                "output_name": "output",
+                                "uuid": "88a8e9ed-d92c-4340-aaad-c6d450a336aa"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/largegenome",
-                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga",
+                "parent_id": "assembly/assembly-decontamination",
+                "path": "topics/assembly/tutorials/assembly-decontamination/workflows/main_workflow.ga",
                 "tags": [
-                    "LG-WF",
-                    "GTN"
+                    "VGP_curated"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
+                "tests": true,
+                "title": "Assembly-decontamination-VGP9",
                 "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-racon-polish-with-illumina-reads-x2",
-                "tutorial_id": "largegenome",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.html",
-                "version": 2,
-                "wfid": "assembly-largegenome",
-                "wfname": "galaxy-workflow-racon-polish-with-illumina-reads-x2",
-                "workflow": "Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-assembly-decontamination/versions/main-workflow",
+                "tutorial_id": "assembly-decontamination",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-decontamination/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-decontamination/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "assembly-assembly-decontamination",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0"
+                    "Cut1",
+                    "Filter1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/parse_mito_blast/parse_mito_blast/1.0.2+galaxy0"
                 ],
-                "workflowhub_id": "1148"
+                "workflowhub_id": "1359"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/records/13367433"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "blobtoolkit",
+                    "owner": "bgruening",
+                    "revisions": "7d9ee8cd14b8",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "blobtoolkit",
+                    "owner": "bgruening",
+                    "revisions": "8c2167481e72",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "diamond",
+                    "owner": "bgruening",
+                    "revisions": "e8ac2b53f262",
+                    "tool_panel_section_label": "NCBI Blast",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gfastats",
+                    "owner": "bgruening",
+                    "revisions": "5799092ffdff",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gfastats",
+                    "owner": "bgruening",
+                    "revisions": "3ef480892a9f",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "samtools_stats",
+                    "owner": "devteam",
+                    "revisions": "3a0efe14891f",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "smudgeplot",
+                    "owner": "galaxy-australia",
+                    "revisions": "5e0825476fb7",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bandage",
+                    "owner": "iuc",
+                    "revisions": "ddddce450736",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bellerophon",
+                    "owner": "iuc",
+                    "revisions": "25ca5d73aedf",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "busco",
+                    "owner": "iuc",
+                    "revisions": "bb935709506a",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bwa_mem2",
+                    "owner": "iuc",
+                    "revisions": "b4a22d90cce9",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "genomescope",
+                    "owner": "iuc",
+                    "revisions": "01210c4e9144",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "merqury",
+                    "owner": "iuc",
+                    "revisions": "f8113c25bc6b",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "meryl",
+                    "owner": "iuc",
+                    "revisions": "29dabd8db6f2",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "minimap2",
+                    "owner": "iuc",
+                    "revisions": "5cc34c3f440d",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pretext_map",
+                    "owner": "iuc",
+                    "revisions": "dfb8a4497339",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pretext_snapshot",
+                    "owner": "iuc",
+                    "revisions": "44c66e8d21e6",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "90981f86000f",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: blobtoolkit\n  owner: bgruening\n  revisions: 7d9ee8cd14b8\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: blobtoolkit\n  owner: bgruening\n  revisions: 8c2167481e72\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: diamond\n  owner: bgruening\n  revisions: e8ac2b53f262\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n  owner: bgruening\n  revisions: 5799092ffdff\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n  owner: bgruening\n  revisions: 3ef480892a9f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 3a0efe14891f\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: smudgeplot\n  owner: galaxy-australia\n  revisions: 5e0825476fb7\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bellerophon\n  owner: iuc\n  revisions: 25ca5d73aedf\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: bb935709506a\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_mem2\n  owner: iuc\n  revisions: b4a22d90cce9\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: genomescope\n  owner: iuc\n  revisions: 01210c4e9144\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merqury\n  owner: iuc\n  revisions: f8113c25bc6b\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n  owner: iuc\n  revisions: 29dabd8db6f2\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: 5cc34c3f440d\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_map\n  owner: iuc\n  revisions: dfb8a4497339\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_snapshot\n  owner: iuc\n  revisions: 44c66e8d21e6\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json",
+        "contributors": [
+            {
+                "id": "GitFab93",
+                "joined": "2023-03",
+                "name": "Fabian Recktenwald",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/GitFab93/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/GitFab93.json"
+            },
+            {
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "gallardoalba",
+                "joined": "2020-11",
+                "name": "Crist\u00f3bal Gallardo",
+                "orcid": "0000-0002-5752-2155",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
             },
+            {
+                "email": "brown@izw-berlin.de",
+                "id": "tbrown91",
+                "joined": "2024-08",
+                "name": "Tom Brown",
+                "orcid": "0000-0001-8293-4816",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tbrown91/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tbrown91.json"
+            }
+        ],
+        "dir": "topics/assembly/tutorials/ERGA-post-assembly-QC",
+        "edam_operation": [
+            "Data handling",
+            "Sequence alignment",
+            "Sequence trimming",
+            "Genome assembly",
+            "De-novo assembly",
+            "Sequence alignment analysis",
+            "Phasing",
+            "Sequence assembly validation",
+            "Scaffolding",
+            "Sequence assembly visualisation",
+            "Pairwise sequence alignment",
+            "k-mer counting",
+            "Transcriptome assembly",
+            "Genotyping"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "assembly/ERGA-post-assembly-QC",
+        "inexact_supported_servers": [
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "The ERGA post-assembly pipeline allows users to assess and improve the quality of genome assemblies",
+            "The ERGA post-assembly pipeline consists of three main steps: Genome assembly decontamination and overview with BlobToolKit, providing analysis information and statistics, and Hi-C scaffolding."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-06",
+        "objectives": [
+            "Apply the post-assembly-QC-workflow using the necessary tools",
+            "Analyse and evaluate the results of the workflow"
+        ],
+        "pageviews": 1211,
+        "pub_date": "2023-06-23",
+        "questions": [
+            "What combination of tools can assess the quality of a genome assembly?",
+            "What metrics can help to analyse the quality of an asembly?",
+            "How do we evaluate the outputs?"
+        ],
+        "short_id": "T00355",
+        "short_tools": [
+            "merqury",
+            "minimap2",
+            "busco",
+            "tp_find_and_replace",
+            "pretext_snapshot",
+            "bwa_mem2",
+            "gfastats",
+            "bg_diamond",
+            "pretext_map",
+            "__EXTRACT_DATASET__",
+            "samtools_stats",
+            "genomescope",
+            "bandage_image",
+            "blobtoolkit",
+            "interactive_tool_blobtoolkit",
+            "bellerophon",
+            "collapse_dataset",
+            "meryl",
+            "smudgeplot",
+            "CONVERTER_gz_to_uncompressed"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "plants",
+            "animals",
+            "genome",
+            "assembly",
+            "QC"
+        ],
+        "time_estimation": "3H",
+        "title": "ERGA post-assembly QC",
+        "tools": [
+            "CONVERTER_gz_to_uncompressed",
+            "__EXTRACT_DATASET__",
+            "interactive_tool_blobtoolkit",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/3.4.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.0.7+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.2.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4",
+            "toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy+2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+            "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
+        ],
+        "topic_name": "assembly",
+        "topic_name_human": "Assembly",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "ERGA-post-assembly-QC",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json"
+        },
+        "version": 4,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 97,
+        "visitors": 918,
+        "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
+                        "identifier": "0000-0002-5752-2155",
+                        "name": "Crist\u00f3bal Gallardo Alba"
                     }
                 ],
-                "description": "",
+                "description": "ERGA post-assembly QC",
                 "features": {
                     "comments": false,
                     "parameters": true,
                     "report": {
-                        "markdown": "\n# Workflow Execution Report\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
                     },
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads \"]\n  3[label=\"Minimap2: map long reads to assembly\"]\n  2 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Racon: polish 1\"]\n  0 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"alignment_output\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Minimap2: map long reads to polished assembly 1\"]\n  2 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  4 -> 5 [label=\"consensus\"]\n  6[label=\"Racon: polish 2\"]\n  4 -> 6 [label=\"consensus\"]\n  5 -> 6 [label=\"alignment_output\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"Minimap2: map long reads to polished assembly 2\"]\n  2 -> 7 [label=\"output\"]\n  1 -> 7 [label=\"output\"]\n  6 -> 7 [label=\"consensus\"]\n  8[label=\"Racon: polish 3\"]\n  6 -> 8 [label=\"consensus\"]\n  7 -> 8 [label=\"alignment_output\"]\n  1 -> 8 [label=\"output\"]\n  9[label=\"Minimap2: map long reads to polished assembly 3\"]\n  2 -> 9 [label=\"output\"]\n  1 -> 9 [label=\"output\"]\n  8 -> 9 [label=\"consensus\"]\n  10[label=\"Racon: polish 4\"]\n  8 -> 10 [label=\"consensus\"]\n  9 -> 10 [label=\"alignment_output\"]\n  1 -> 10 [label=\"output\"]\n  kbcf0f03c595146a7aa38545aed9bc183[color=lightseagreen,label=\"Output\\nAssembly polished by long reads using Racon\"]\n  10 -> kbcf0f03c595146a7aa38545aed9bc183\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMetadata file\"]\n  1[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nNCBI taxonomic ID\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nNCBI taxdump directory\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nLong-read FASTQ files\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPrimary genome assembly file fasta\"]\n  5[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nPloidy for model to use\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDIAMOND database\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nHi-C reverse\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nHi-C forward\"]\n  9[label=\"Meryl\"]\n  3 -> 9 [label=\"output\"]\n  10[label=\"Collapse Collection\"]\n  3 -> 10 [label=\"output\"]\n  11[label=\"Create BlobtoolKit\"]\n  4 -> 11 [label=\"output\"]\n  0 -> 11 [label=\"output\"]\n  2 -> 11 [label=\"output\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"gfastats\"]\n  4 -> 12 [label=\"output\"]\n  13[label=\"Convert compressed file to uncompressed.\"]\n  4 -> 13 [label=\"output\"]\n  14[label=\"gfastats\"]\n  4 -> 14 [label=\"output\"]\n  15[label=\"Diamond\"]\n  4 -> 15 [label=\"output\"]\n  6 -> 15 [label=\"output\"]\n  16[label=\"Collapse Collection\"]\n  7 -> 16 [label=\"output\"]\n  17[label=\"Collapse Collection\"]\n  8 -> 17 [label=\"output\"]\n  18[label=\"Meryl\"]\n  9 -> 18 [label=\"read_db\"]\n  19[label=\"Map with minimap2\"]\n  10 -> 19 [label=\"output\"]\n  4 -> 19 [label=\"output\"]\n  20[label=\"Smudgeplot\"]\n  10 -> 20 [label=\"output\"]\n  21[label=\"Replace\"]\n  13 -> 21 [label=\"output1\"]\n  22[label=\"Bandage Image\"]\n  14 -> 22 [label=\"output\"]\n  23[label=\"BWA-MEM2\"]\n  16 -> 23 [label=\"output\"]\n  4 -> 23 [label=\"output\"]\n  24[label=\"BWA-MEM2\"]\n  17 -> 24 [label=\"output\"]\n  4 -> 24 [label=\"output\"]\n  25[label=\"Merqury\"]\n  4 -> 25 [label=\"output\"]\n  18 -> 25 [label=\"read_db\"]\n  kd2dbf498515543b2bf2affed5c45100d[color=lightseagreen,label=\"Output\\nMerqury on input dataset(s): stats\"]\n  25 -> kd2dbf498515543b2bf2affed5c45100d\n  k0b43d206253f4c0ba1f4971402851c6d[color=lightseagreen,label=\"Output\\nMerqury on input dataset(s): plots\"]\n  25 -> k0b43d206253f4c0ba1f4971402851c6d\n  k811a77e8eb994dc79295f0000fcb9fe5[color=lightseagreen,label=\"Output\\nMerqury on input dataset(s): QV stats\"]\n  25 -> k811a77e8eb994dc79295f0000fcb9fe5\n  26[label=\"Meryl\"]\n  18 -> 26 [label=\"read_db\"]\n  27[label=\"Samtools stats\"]\n  19 -> 27 [label=\"alignment_output\"]\n  28[label=\"Busco\"]\n  21 -> 28 [label=\"outfile\"]\n  kaf98aae6f1a3493c9cef08e0926210d3[color=lightseagreen,label=\"Output\\nBusco on input dataset(s): full table\"]\n  28 -> kaf98aae6f1a3493c9cef08e0926210d3\n  k929439b7c68845ea848a97c13d3e0028[color=lightseagreen,label=\"Output\\nBusco on input dataset(s): short summary\"]\n  28 -> k929439b7c68845ea848a97c13d3e0028\n  29[label=\"Filter and merge\"]\n  24 -> 29 [label=\"bam_output\"]\n  23 -> 29 [label=\"bam_output\"]\n  30[label=\"Merqury plot 2\"]\n  25 -> 30 [label=\"png_files\"]\n  31[label=\"Merqury plot 1\"]\n  25 -> 31 [label=\"png_files\"]\n  32[label=\"Merqury plot 3\"]\n  25 -> 32 [label=\"png_files\"]\n  33[label=\"Merqury plot 5\"]\n  25 -> 33 [label=\"png_files\"]\n  34[label=\"Merqury plot 4\"]\n  25 -> 34 [label=\"png_files\"]\n  35[label=\"GenomeScope\"]\n  26 -> 35 [label=\"read_db_hist\"]\n  5 -> 35 [label=\"output\"]\n  36[label=\"BlobToolKit\"]\n  15 -> 36 [label=\"blast_tabular\"]\n  11 -> 36 [label=\"blobdir\"]\n  28 -> 36 [label=\"busco_table\"]\n  19 -> 36 [label=\"alignment_output\"]\n  37[label=\"PretextMap\"]\n  29 -> 37 [label=\"outfile\"]\n  38[label=\"BlobToolKit\"]\n  36 -> 38 [label=\"blobdir\"]\n  39[label=\"BlobToolKit\"]\n  36 -> 39 [label=\"blobdir\"]\n  40[label=\"BlobToolKit\"]\n  36 -> 40 [label=\"blobdir\"]\n  41[label=\"Pretext Snapshot\"]\n  37 -> 41 [label=\"pretext_map_out\"]\n}",
                 "history": [
                     {
-                        "hash": "ea8cb9df4cc68241e9b406bde825b4c16647280b",
-                        "message": "Update Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga",
+                        "hash": "49cec9ea83fb11ba5bbf653257a0723f4ce541fc",
+                        "message": "Rename post-assembly-workflow.ga to main_workflow.ga",
+                        "num": 6,
+                        "short_hash": "49cec9ea8",
+                        "unix": "1725444408"
+                    },
+                    {
+                        "hash": "cf8e17d6d77d0ae7c26ffe5f83eecab712ed5a94",
+                        "message": "Add workflow test",
                         "num": 5,
-                        "short_hash": "ea8cb9df4",
-                        "unix": "1715074423"
+                        "short_hash": "cf8e17d6d",
+                        "unix": "1724836602"
                     },
                     {
-                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
-                        "message": "new versions of workflows",
+                        "hash": "93e0f85071edf315b8b1e58830a40fdd0e32b858",
+                        "message": "Change mapping tool to minimap and add more details about the downloaded databases",
                         "num": 4,
-                        "short_hash": "e8ddbcdd5",
-                        "unix": "1714537936"
+                        "short_hash": "93e0f8507",
+                        "unix": "1719568805"
                     },
                     {
-                        "hash": "7bd7c55df24dd71009cbde6408fb87d49901a84a",
-                        "message": "Rename Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga to Galaxy-Workflow-Racon_polish_with_long_reads_x4_old.ga",
+                        "hash": "807026b8414e9d8e35cb6805104338150b1131f0",
+                        "message": "Update topics/assembly/tutorials/ERGA-post-assembly-QC/workflows/main_workflow.ga",
                         "num": 3,
-                        "short_hash": "7bd7c55df",
-                        "unix": "1714537311"
+                        "short_hash": "807026b84",
+                        "unix": "1687524556"
                     },
                     {
-                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
-                        "message": "add/complete creator info on workflows",
+                        "hash": "c5bb8031a5b03030e4fdc5c0a478a87e7c1e3c13",
+                        "message": "Fix testes",
                         "num": 2,
-                        "short_hash": "62e77944b",
-                        "unix": "1676627603"
+                        "short_hash": "c5bb8031a",
+                        "unix": "1687511093"
                     },
                     {
-                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
-                        "message": "large genome tutorial",
+                        "hash": "893cd527b9bd282e7f98475f5c3cd3e2f3ea89b0",
+                        "message": "Add images and rename tutorial",
                         "num": 1,
-                        "short_hash": "9fcb3aeec",
-                        "unix": "1665123856"
+                        "short_hash": "893cd527b",
+                        "unix": "1682673537"
                     }
                 ],
                 "inputs": [
@@ -12604,21 +11546,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Assembly to be polished"
+                                "name": "Metadata file"
                             }
                         ],
-                        "label": "Assembly to be polished",
+                        "label": "Metadata file",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 216.625
+                            "left": 707.9000006004667,
+                            "top": 0
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": true, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "c7796c36-adf8-49e4-a8e4-66e606d70311",
+                        "uuid": "7ffa45d8-0b67-457d-bb1c-25c83c87ad8c",
                         "when": null,
                         "workflow_outputs": []
                     },
@@ -12631,21 +11573,54 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "long reads"
+                                "name": "NCBI taxonomic ID"
                             }
                         ],
-                        "label": "long reads",
+                        "label": "NCBI taxonomic ID",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 707.9000006004667,
+                            "top": 123
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "2ecb111b-eba8-497c-960c-4ba9c3717606",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "55a176c7-cffb-4f80-9ac4-e396051e30d7"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "NCBI taxdump directory"
+                            }
+                        ],
+                        "label": "NCBI taxdump directory",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 4.5,
-                            "top": 360.234375
+                            "left": 707.9000006004667,
+                            "top": 246
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "e2e4a70b-6e36-4b8b-bdf6-12b97189a6bd",
+                        "uuid": "f5be1515-252f-4f5d-87ec-d0a8c3c29802",
                         "when": null,
                         "workflow_outputs": []
                     },
@@ -12653,243 +11628,176 @@
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 3,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "minimap setting (for long reads) "
+                                "name": "Long-read FASTQ files"
                             }
                         ],
-                        "label": "minimap setting (for long reads) ",
-                        "name": "Input parameter",
+                        "label": "Long-read FASTQ files",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 0.578125,
-                            "top": 495.859375
+                            "left": 0,
+                            "top": 1252.495997073411
                         },
                         "tool_id": null,
-                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_state": "{\"optional\": false, \"format\": [\"fastq.gz\"], \"tag\": \"\", \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "fb80c05c-08d4-4ac2-b4bf-81ed906e4d72",
+                        "type": "data_collection_input",
+                        "uuid": "ecf4c98a-b500-4c53-a953-6588d99a669a",
                         "when": null,
-                        "workflow_outputs": [
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "3983ef22-5f05-4384-8f34-6ac8c4b2cc83"
+                                "description": "",
+                                "name": "Primary genome assembly file (fasta)"
                             }
-                        ]
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads \"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"Minimap2: map long reads to assembly\"];\n  2 -->|output| 3;\n  1 -->|output| 3;\n  0 -->|output| 3;\n  4[\"Racon: polish 1\"];\n  0 -->|output| 4;\n  3 -->|alignment_output| 4;\n  1 -->|output| 4;\n  5[\"Minimap2: map long reads to polished assembly 1\"];\n  2 -->|output| 5;\n  1 -->|output| 5;\n  4 -->|consensus| 5;\n  6[\"Racon: polish 2\"];\n  4 -->|consensus| 6;\n  5 -->|alignment_output| 6;\n  1 -->|output| 6;\n  7[\"Minimap2: map long reads to polished assembly 2\"];\n  2 -->|output| 7;\n  1 -->|output| 7;\n  6 -->|consensus| 7;\n  8[\"Racon: polish 3\"];\n  6 -->|consensus| 8;\n  7 -->|alignment_output| 8;\n  1 -->|output| 8;\n  9[\"Minimap2: map long reads to polished assembly 3\"];\n  2 -->|output| 9;\n  1 -->|output| 9;\n  8 -->|consensus| 9;\n  10[\"Racon: polish 4\"];\n  8 -->|consensus| 10;\n  9 -->|alignment_output| 10;\n  1 -->|output| 10;\n  bcf0f03c-5951-46a7-aa38-545aed9bc183[\"Output\\nAssembly polished by long reads using Racon\"];\n  10 --> bcf0f03c-5951-46a7-aa38-545aed9bc183;\n  style bcf0f03c-5951-46a7-aa38-545aed9bc183 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Racon polish with long reads, x4 - upgraded",
-                "outputs": [
+                        ],
+                        "label": "Primary genome assembly file (fasta)",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 707.9000006004667,
+                            "top": 1310
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "6baf378a-2cb5-4e3d-8d52-f129b3f86ff8",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 5,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "minimap setting (for long reads) "
+                                "name": "Ploidy for model to use"
                             }
                         ],
-                        "label": "minimap setting (for long reads) ",
+                        "label": "Ploidy for model to use",
                         "name": "Input parameter",
                         "outputs": [],
                         "position": {
-                            "left": 0.578125,
-                            "top": 495.859375
+                            "left": 1287.9000006004667,
+                            "top": 1011
                         },
                         "tool_id": null,
-                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_state": "{\"default\": 2, \"parameter_type\": \"integer\", \"optional\": true}",
                         "tool_version": null,
                         "type": "parameter_input",
-                        "uuid": "fb80c05c-08d4-4ac2-b4bf-81ed906e4d72",
+                        "uuid": "bed1e2ca-2039-4f88-bd25-2646c6b5887d",
                         "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "3983ef22-5f05-4384-8f34-6ac8c4b2cc83"
+                                "uuid": "8c56cbc1-c86f-4aef-b0b9-8ef1cde9c5b7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "corrected_reads": {
-                                "id": 8,
-                                "output_name": "consensus"
-                            },
-                            "overlaps": {
-                                "id": 9,
-                                "output_name": "alignment_output"
-                            },
-                            "reads": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Racon: polish 4",
-                        "name": "Racon",
-                        "outputs": [
+                        "id": 6,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "consensus",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "DIAMOND database"
                             }
                         ],
+                        "label": "DIAMOND database",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1496.078125,
-                            "top": 431.1875
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionconsensus": {
-                                "action_arguments": {
-                                    "newname": "Racon_long_reads_polished_assembly.fasta"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "consensus"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "78c533842eeb",
-                            "name": "racon",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 707.9000006004667,
+                            "top": 1735
                         },
-                        "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.5.0+galaxy1",
-                        "type": "tool",
-                        "uuid": "53f4572e-3a4a-4585-89ab-9459f8a61720",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "7d4e2fa7-0b60-47ce-bbc3-a4bcb4443ccc",
                         "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Assembly polished by long reads using Racon",
-                                "output_name": "consensus",
-                                "uuid": "bcf0f03c-5951-46a7-aa38-545aed9bc183"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "assembly/largegenome",
-                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga",
-                "tags": [
-                    "LG-WF",
-                    "GTN"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Racon polish with long reads, x4 - upgraded",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-racon-polish-with-long-reads-x4",
-                "tutorial_id": "largegenome",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_long_reads_x4.html",
-                "version": 2,
-                "wfid": "assembly-largegenome",
-                "wfname": "galaxy-workflow-racon-polish-with-long-reads-x4",
-                "workflow": "Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0"
-                ],
-                "workflowhub_id": "1154"
-            },
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
-                    }
-                ],
-                "description": "",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": {
-                        "markdown": "\n# Workflow for Trim and Filter Reads\n\n## Workflow steps\n```galaxy\nworkflow_display()\n```\n\n\n\n\n"
-                    },
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads R2\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  3[label=\"fastp on short reads\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  k656e413841ab4561898933de9ac9a2f3[color=lightseagreen,label=\"Output\\nfastp report on short reads html\"]\n  3 -> k656e413841ab4561898933de9ac9a2f3\n  k0d53f347036847cb953a2e4dac57e013[color=lightseagreen,label=\"Output\\nfastp filtered R1 reads\"]\n  3 -> k0d53f347036847cb953a2e4dac57e013\n  k10fbe1e5400c4ffe87949b776b0d7322[color=lightseagreen,label=\"Output\\nfastp report on short reads json\"]\n  3 -> k10fbe1e5400c4ffe87949b776b0d7322\n  k639ed3f70e514e5db6f8081378962109[color=lightseagreen,label=\"Output\\nfastp filtered R2 reads\"]\n  3 -> k639ed3f70e514e5db6f8081378962109\n  4[label=\"fastp on long reads\"]\n  2 -> 4 [label=\"output\"]\n  k5e0d2c3d41a44823ae9cb1e4d2826541[color=lightseagreen,label=\"Output\\nfastp report on long reads html\"]\n  4 -> k5e0d2c3d41a44823ae9cb1e4d2826541\n  ke6018ad686f44e788cf2ccc8b97022fe[color=lightseagreen,label=\"Output\\nfastp filtered long reads\"]\n  4 -> ke6018ad686f44e788cf2ccc8b97022fe\n  k69f8383ba1be4a7495f43dba35e01426[color=lightseagreen,label=\"Output\\nfastp report on long reads json\"]\n  4 -> k69f8383ba1be4a7495f43dba35e01426\n}",
-                "history": [
-                    {
-                        "hash": "1fe24b92fd7cf3bf693a850751a6215f7b9273bd",
-                        "message": "Update Galaxy-Workflow-Trim_and_filter_reads.ga",
-                        "num": 5,
-                        "short_hash": "1fe24b92f",
-                        "unix": "1715074442"
-                    },
-                    {
-                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
-                        "message": "new versions of workflows",
-                        "num": 4,
-                        "short_hash": "e8ddbcdd5",
-                        "unix": "1714537936"
-                    },
-                    {
-                        "hash": "12f721099e26ef4bd152c1c2b56ccb51e6bd31ab",
-                        "message": "Rename Galaxy-Workflow-Trim_and_filter_reads.ga to Galaxy-Workflow-Trim_and_filter_reads_old.ga",
-                        "num": 3,
-                        "short_hash": "12f721099",
-                        "unix": "1714537350"
+                        "workflow_outputs": []
                     },
                     {
-                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
-                        "message": "add/complete creator info on workflows",
-                        "num": 2,
-                        "short_hash": "62e77944b",
-                        "unix": "1676627603"
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Hi-C reverse"
+                            }
+                        ],
+                        "label": "Hi-C reverse",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 427.9000006004666,
+                            "top": 2172
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fastq.gz\"], \"tag\": null, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "26e380fd-6706-4c6a-8915-e6a11fd442fc",
+                        "when": null,
+                        "workflow_outputs": []
                     },
-                    {
-                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
-                        "message": "large genome tutorial",
-                        "num": 1,
-                        "short_hash": "9fcb3aeec",
-                        "unix": "1665123856"
-                    }
-                ],
-                "inputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 8,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Illumina reads R1"
+                                "name": "Hi-C forward"
                             }
                         ],
-                        "label": "Illumina reads R1",
-                        "name": "Input dataset",
+                        "label": "Hi-C forward",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 29.045160466974437
+                            "left": 430,
+                            "top": 2600
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false, \"format\": [\"fastq.gz\"], \"tag\": null, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "00a54054-e3f7-4e4f-9195-563e54df899a",
+                        "type": "data_collection_input",
+                        "uuid": "2a65547b-b40d-4d99-9bd1-388460eb3faa",
                         "when": null,
                         "workflow_outputs": []
-                    },
+                    }
+                ],
+                "license": "AGPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nMetadata file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nNCBI taxonomic ID\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nNCBI taxdump directory\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Collection\\nLong-read FASTQ files\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nPrimary genome assembly file fasta\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Parameter\\nPloidy for model to use\"];\n  style 5 fill:#ded,stroke:#393,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nDIAMOND database\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Collection\\nHi-C reverse\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Collection\\nHi-C forward\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"Meryl\"];\n  3 -->|output| 9;\n  10[\"Collapse Collection\"];\n  3 -->|output| 10;\n  11[\"Create BlobtoolKit\"];\n  4 -->|output| 11;\n  0 -->|output| 11;\n  2 -->|output| 11;\n  1 -->|output| 11;\n  12[\"gfastats\"];\n  4 -->|output| 12;\n  13[\"Convert compressed file to uncompressed.\"];\n  4 -->|output| 13;\n  14[\"gfastats\"];\n  4 -->|output| 14;\n  15[\"Diamond\"];\n  4 -->|output| 15;\n  6 -->|output| 15;\n  16[\"Collapse Collection\"];\n  7 -->|output| 16;\n  17[\"Collapse Collection\"];\n  8 -->|output| 17;\n  18[\"Meryl\"];\n  9 -->|read_db| 18;\n  19[\"Map with minimap2\"];\n  10 -->|output| 19;\n  4 -->|output| 19;\n  20[\"Smudgeplot\"];\n  10 -->|output| 20;\n  21[\"Replace\"];\n  13 -->|output1| 21;\n  22[\"Bandage Image\"];\n  14 -->|output| 22;\n  23[\"BWA-MEM2\"];\n  16 -->|output| 23;\n  4 -->|output| 23;\n  24[\"BWA-MEM2\"];\n  17 -->|output| 24;\n  4 -->|output| 24;\n  25[\"Merqury\"];\n  4 -->|output| 25;\n  18 -->|read_db| 25;\n  d2dbf498-5155-43b2-bf2a-ffed5c45100d[\"Output\\nMerqury on input dataset(s): stats\"];\n  25 --> d2dbf498-5155-43b2-bf2a-ffed5c45100d;\n  style d2dbf498-5155-43b2-bf2a-ffed5c45100d stroke:#2c3143,stroke-width:4px;\n  0b43d206-253f-4c0b-a1f4-971402851c6d[\"Output\\nMerqury on input dataset(s): plots\"];\n  25 --> 0b43d206-253f-4c0b-a1f4-971402851c6d;\n  style 0b43d206-253f-4c0b-a1f4-971402851c6d stroke:#2c3143,stroke-width:4px;\n  811a77e8-eb99-4dc7-9295-f0000fcb9fe5[\"Output\\nMerqury on input dataset(s): QV stats\"];\n  25 --> 811a77e8-eb99-4dc7-9295-f0000fcb9fe5;\n  style 811a77e8-eb99-4dc7-9295-f0000fcb9fe5 stroke:#2c3143,stroke-width:4px;\n  26[\"Meryl\"];\n  18 -->|read_db| 26;\n  27[\"Samtools stats\"];\n  19 -->|alignment_output| 27;\n  28[\"Busco\"];\n  21 -->|outfile| 28;\n  af98aae6-f1a3-493c-9cef-08e0926210d3[\"Output\\nBusco on input dataset(s): full table\"];\n  28 --> af98aae6-f1a3-493c-9cef-08e0926210d3;\n  style af98aae6-f1a3-493c-9cef-08e0926210d3 stroke:#2c3143,stroke-width:4px;\n  929439b7-c688-45ea-848a-97c13d3e0028[\"Output\\nBusco on input dataset(s): short summary\"];\n  28 --> 929439b7-c688-45ea-848a-97c13d3e0028;\n  style 929439b7-c688-45ea-848a-97c13d3e0028 stroke:#2c3143,stroke-width:4px;\n  29[\"Filter and merge\"];\n  24 -->|bam_output| 29;\n  23 -->|bam_output| 29;\n  30[\"Merqury plot 2\"];\n  25 -->|png_files| 30;\n  31[\"Merqury plot 1\"];\n  25 -->|png_files| 31;\n  32[\"Merqury plot 3\"];\n  25 -->|png_files| 32;\n  33[\"Merqury plot 5\"];\n  25 -->|png_files| 33;\n  34[\"Merqury plot 4\"];\n  25 -->|png_files| 34;\n  35[\"GenomeScope\"];\n  26 -->|read_db_hist| 35;\n  5 -->|output| 35;\n  36[\"BlobToolKit\"];\n  15 -->|blast_tabular| 36;\n  11 -->|blobdir| 36;\n  28 -->|busco_table| 36;\n  19 -->|alignment_output| 36;\n  37[\"PretextMap\"];\n  29 -->|outfile| 37;\n  38[\"BlobToolKit\"];\n  36 -->|blobdir| 38;\n  39[\"BlobToolKit\"];\n  36 -->|blobdir| 39;\n  40[\"BlobToolKit\"];\n  36 -->|blobdir| 40;\n  41[\"Pretext Snapshot\"];\n  37 -->|pretext_map_out| 41;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Post-assembly workflow",
+                "outputs": [
                     {
                         "annotation": "",
                         "content_id": null,
@@ -12899,481 +11807,375 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Illumina reads R2"
+                                "name": "NCBI taxonomic ID"
                             }
                         ],
-                        "label": "Illumina reads R2",
-                        "name": "Input dataset",
+                        "label": "NCBI taxonomic ID",
+                        "name": "Input parameter",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 145.03474842418325
+                            "left": 707.9000006004667,
+                            "top": 123
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "14062fd8-1aa9-4a18-94d8-bbbb0e1a9262",
+                        "type": "parameter_input",
+                        "uuid": "2ecb111b-eba8-497c-960c-4ba9c3717606",
                         "when": null,
-                        "workflow_outputs": []
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "55a176c7-cffb-4f80-9ac4-e396051e30d7"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 5,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "long reads"
+                                "name": "Ploidy for model to use"
                             }
                         ],
-                        "label": "long reads",
-                        "name": "Input dataset",
+                        "label": "Ploidy for model to use",
+                        "name": "Input parameter",
                         "outputs": [],
                         "position": {
-                            "left": 576.5103981711648,
-                            "top": 35.50348455255681
+                            "left": 1287.9000006004667,
+                            "top": 1011
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"default\": 2, \"parameter_type\": \"integer\", \"optional\": true}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "08eeb0d3-6ad6-4e7f-ac6a-d00c8e87fd08",
+                        "type": "parameter_input",
+                        "uuid": "bed1e2ca-2039-4f88-bd25-2646c6b5887d",
                         "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nIllumina reads R2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"fastp on short reads\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  656e4138-41ab-4561-8989-33de9ac9a2f3[\"Output\\nfastp report on short reads html\"];\n  3 --> 656e4138-41ab-4561-8989-33de9ac9a2f3;\n  style 656e4138-41ab-4561-8989-33de9ac9a2f3 stroke:#2c3143,stroke-width:4px;\n  0d53f347-0368-47cb-953a-2e4dac57e013[\"Output\\nfastp filtered R1 reads\"];\n  3 --> 0d53f347-0368-47cb-953a-2e4dac57e013;\n  style 0d53f347-0368-47cb-953a-2e4dac57e013 stroke:#2c3143,stroke-width:4px;\n  10fbe1e5-400c-4ffe-8794-9b776b0d7322[\"Output\\nfastp report on short reads json\"];\n  3 --> 10fbe1e5-400c-4ffe-8794-9b776b0d7322;\n  style 10fbe1e5-400c-4ffe-8794-9b776b0d7322 stroke:#2c3143,stroke-width:4px;\n  639ed3f7-0e51-4e5d-b6f8-081378962109[\"Output\\nfastp filtered R2 reads\"];\n  3 --> 639ed3f7-0e51-4e5d-b6f8-081378962109;\n  style 639ed3f7-0e51-4e5d-b6f8-081378962109 stroke:#2c3143,stroke-width:4px;\n  4[\"fastp on long reads\"];\n  2 -->|output| 4;\n  5e0d2c3d-41a4-4823-ae9c-b1e4d2826541[\"Output\\nfastp report on long reads html\"];\n  4 --> 5e0d2c3d-41a4-4823-ae9c-b1e4d2826541;\n  style 5e0d2c3d-41a4-4823-ae9c-b1e4d2826541 stroke:#2c3143,stroke-width:4px;\n  e6018ad6-86f4-4e78-8cf2-ccc8b97022fe[\"Output\\nfastp filtered long reads\"];\n  4 --> e6018ad6-86f4-4e78-8cf2-ccc8b97022fe;\n  style e6018ad6-86f4-4e78-8cf2-ccc8b97022fe stroke:#2c3143,stroke-width:4px;\n  69f8383b-a1be-4a74-95f4-3dba35e01426[\"Output\\nfastp report on long reads json\"];\n  4 --> 69f8383b-a1be-4a74-95f4-3dba35e01426;\n  style 69f8383b-a1be-4a74-95f4-3dba35e01426 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Trim and filter reads - fastp - upgraded ",
-                "outputs": [
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "8c56cbc1-c86f-4aef-b0b9-8ef1cde9c5b7"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.2.0+galaxy0",
                         "errors": null,
-                        "id": 3,
+                        "id": 12,
                         "input_connections": {
-                            "single_paired|in1": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "single_paired|in2": {
-                                "id": 1,
+                            "input_file": {
+                                "id": 4,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool fastp",
-                                "name": "single_paired"
-                            },
+                        "inputs": [],
+                        "label": null,
+                        "name": "gfastats",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool fastp",
-                                "name": "single_paired"
+                                "name": "stats",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "fastp on short reads",
-                        "name": "fastp",
-                        "outputs": [
-                            {
-                                "name": "out1",
-                                "type": "input"
-                            },
+                        "position": {
+                            "left": 997.9000006004667,
+                            "top": 1150
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.2.0+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "5799092ffdff",
+                            "name": "gfastats",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"assembly\", \"__current_case__\": 2, \"expected_genomesize\": null}, \"tabular\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.0+galaxy0",
+                        "type": "tool",
+                        "uuid": "94888424-570c-4bd8-8fd0-32691fec5ceb",
+                        "when": null,
+                        "workflow_outputs": [
                             {
-                                "name": "out2",
-                                "type": "input"
-                            },
+                                "label": null,
+                                "output_name": "stats",
+                                "uuid": "e0521266-b734-41e6-98a4-bb89b12f6220"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy+2",
+                        "errors": null,
+                        "id": 20,
+                        "input_connections": {
+                            "file|input|reads": {
+                                "id": 10,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Smudgeplot",
+                        "outputs": [
                             {
-                                "name": "report_html",
-                                "type": "html"
+                                "name": "smudgeplot",
+                                "type": "png"
                             },
                             {
-                                "name": "report_json",
-                                "type": "json"
+                                "name": "smudgeplot_log",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 290.5382191051136,
-                            "top": 0
-                        },
-                        "post_job_actions": {
-                            "DeleteIntermediatesActionout1": {
-                                "action_arguments": {},
-                                "action_type": "DeleteIntermediatesAction",
-                                "output_name": "out1"
-                            },
-                            "RenameDatasetActionout1": {
-                                "action_arguments": {
-                                    "newname": "fastp_filtered_R1.fastq.gz"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out1"
-                            },
-                            "RenameDatasetActionout2": {
-                                "action_arguments": {
-                                    "newname": "fastp_filtered_R2.fastq.gz"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out2"
-                            },
-                            "RenameDatasetActionreport_html": {
-                                "action_arguments": {
-                                    "newname": "fastp_illumina.html"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "report_html"
-                            },
-                            "RenameDatasetActionreport_json": {
-                                "action_arguments": {
-                                    "newname": "fastp_illumina.json"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "report_json"
-                            }
+                            "left": 997.9000006004667,
+                            "top": 2319
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy+2",
                         "tool_shed_repository": {
-                            "changeset_revision": "c59d48774d03",
-                            "name": "fastp",
-                            "owner": "iuc",
+                            "changeset_revision": "5e0825476fb7",
+                            "name": "smudgeplot",
+                            "owner": "galaxy-australia",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired\", \"__current_case__\": 1, \"in1\": {\"__class__\": \"ConnectedValue\"}, \"in2\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": \"\", \"adapter_sequence2\": \"\"}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.23.4+galaxy0",
+                        "tool_state": "{\"file\": {\"input\": {\"input_select\": \"reads\", \"__current_case__\": 0, \"reads\": {\"__class__\": \"ConnectedValue\"}, \"mer_len\": \"21\", \"lower_cutoff\": null, \"upper_cutoff\": null}}, \"homozygous\": false, \"table_output\": false, \"verbose_output\": false, \"warnings_output\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.2.5+galaxy+2",
                         "type": "tool",
-                        "uuid": "c38e84b3-771c-428e-9d2d-ce84d5e1153c",
+                        "uuid": "2de39e7c-bdfd-4918-8d52-baf5f67f5522",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "fastp report on short reads html",
-                                "output_name": "report_html",
-                                "uuid": "656e4138-41ab-4561-8989-33de9ac9a2f3"
+                                "label": null,
+                                "output_name": "smudgeplot_log",
+                                "uuid": "a6e4bae9-63de-4258-b429-6a6b9a46d7cf"
                             },
                             {
-                                "label": "fastp filtered R1 reads",
-                                "output_name": "out1",
-                                "uuid": "0d53f347-0368-47cb-953a-2e4dac57e013"
-                            },
+                                "label": null,
+                                "output_name": "smudgeplot",
+                                "uuid": "150d5e72-b06c-4556-915a-d23d410f5aa0"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                        "errors": null,
+                        "id": 22,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 14,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Bandage Image",
+                        "outputs": [
                             {
-                                "label": "fastp report on short reads json",
-                                "output_name": "report_json",
-                                "uuid": "10fbe1e5-400c-4ffe-8794-9b776b0d7322"
-                            },
+                                "name": "outfile",
+                                "type": "jpg"
+                            }
+                        ],
+                        "position": {
+                            "left": 1287.9000006004667,
+                            "top": 1499
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ddddce450736",
+                            "name": "bandage",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"fontsize\": null, \"height\": \"1000\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"lengths\": false, \"names\": false, \"nodewidth\": null, \"output_format\": \"jpg\", \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2022.09+galaxy4",
+                        "type": "tool",
+                        "uuid": "255d0a7d-e006-4392-99db-c313b0154572",
+                        "when": null,
+                        "workflow_outputs": [
                             {
-                                "label": "fastp filtered R2 reads",
-                                "output_name": "out2",
-                                "uuid": "639ed3f7-0e51-4e5d-b6f8-081378962109"
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "1483321a-d6af-498f-9873-6280c6057cb3"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
                         "errors": null,
-                        "id": 4,
+                        "id": 25,
                         "input_connections": {
-                            "single_paired|in1": {
-                                "id": 2,
+                            "mode|assembly_options|assembly_01": {
+                                "id": 4,
                                 "output_name": "output"
+                            },
+                            "mode|meryldb_F1": {
+                                "id": 18,
+                                "output_name": "read_db"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool fastp",
-                                "name": "single_paired"
+                                "description": "runtime parameter for tool Merqury",
+                                "name": "mode"
                             }
                         ],
-                        "label": "fastp on long reads",
-                        "name": "fastp",
+                        "label": null,
+                        "name": "Merqury",
                         "outputs": [
                             {
-                                "name": "out1",
+                                "name": "qv_files",
                                 "type": "input"
                             },
                             {
-                                "name": "report_html",
-                                "type": "html"
+                                "name": "png_files",
+                                "type": "input"
                             },
                             {
-                                "name": "report_json",
-                                "type": "json"
+                                "name": "stats_files",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 804.010509144176,
-                            "top": 22.482646595348
-                        },
-                        "post_job_actions": {
-                            "DeleteIntermediatesActionout1": {
-                                "action_arguments": {},
-                                "action_type": "DeleteIntermediatesAction",
-                                "output_name": "out1"
-                            },
-                            "RenameDatasetActionout1": {
-                                "action_arguments": {
-                                    "newname": "fastp_filtered_long_reads.fastq.gz"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out1"
-                            },
-                            "RenameDatasetActionreport_html": {
-                                "action_arguments": {
-                                    "newname": "fastp_longreads.html"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "report_html"
-                            },
-                            "RenameDatasetActionreport_json": {
-                                "action_arguments": {
-                                    "newname": "fastp_longreads.json"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "report_json"
-                            }
+                            "left": 1287.9000006004667,
+                            "top": 581
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "c59d48774d03",
-                            "name": "fastp",
+                            "changeset_revision": "f8113c25bc6b",
+                            "name": "merqury",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": true, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": true, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"-G\", \"__current_case__\": 2}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"single\", \"__current_case__\": 0, \"in1\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": true, \"adapter_sequence1\": \"\"}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.23.4+galaxy0",
+                        "tool_state": "{\"label\": \"output_merqury\", \"mode\": {\"options\": \"default\", \"__current_case__\": 0, \"meryldb_F1\": {\"__class__\": \"ConnectedValue\"}, \"assembly_options\": {\"number_assemblies\": \"one\", \"__current_case__\": 0, \"assembly_01\": {\"__class__\": \"ConnectedValue\"}}}, \"output_add_headers\": false, \"output_selector\": [\"qv\", \"plots\", \"stats\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3+galaxy2",
                         "type": "tool",
-                        "uuid": "93602736-2d22-43e4-a53a-803326ccab9e",
+                        "uuid": "72f5cbe8-5d1c-4d0b-942e-ed18718ca39a",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "fastp report on long reads html",
-                                "output_name": "report_html",
-                                "uuid": "5e0d2c3d-41a4-4823-ae9c-b1e4d2826541"
+                                "label": "Merqury on input dataset(s): stats",
+                                "output_name": "stats_files",
+                                "uuid": "d2dbf498-5155-43b2-bf2a-ffed5c45100d"
                             },
                             {
-                                "label": "fastp filtered long reads",
-                                "output_name": "out1",
-                                "uuid": "e6018ad6-86f4-4e78-8cf2-ccc8b97022fe"
+                                "label": "Merqury on input dataset(s): plots",
+                                "output_name": "png_files",
+                                "uuid": "0b43d206-253f-4c0b-a1f4-971402851c6d"
                             },
                             {
-                                "label": "fastp report on long reads json",
-                                "output_name": "report_json",
-                                "uuid": "69f8383b-a1be-4a74-95f4-3dba35e01426"
+                                "label": "Merqury on input dataset(s): QV stats",
+                                "output_name": "qv_files",
+                                "uuid": "811a77e8-eb99-4dc7-9295-f0000fcb9fe5"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "assembly/largegenome",
-                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Trim_and_filter_reads.ga",
-                "tags": [
-                    "LG-WF",
-                    "GTN"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Trim and filter reads - fastp - upgraded ",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-trim-and-filter-reads",
-                "tutorial_id": "largegenome",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Trim_and_filter_reads.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Trim_and_filter_reads.html",
-                "version": 2,
-                "wfid": "assembly-largegenome",
-                "wfname": "galaxy-workflow-trim-and-filter-reads",
-                "workflow": "Galaxy-Workflow-Trim_and_filter_reads.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0"
-                ],
-                "workflowhub_id": "1144"
-            },
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
-                    }
-                ],
-                "description": "",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": {
-                        "markdown": "\n# Workflow Execution Report\n\n\r\n```galaxy\nworkflow_display()\n```\r\n"
-                    },
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"]\n  1[label=\"Meryl - count kmers\"]\n  0 -> 1 [label=\"output\"]\n  k899ddd934c0f4f81a9738120494ed983[color=lightseagreen,label=\"Output\\nMeryl on input dataset(s): read-db.meryldb\"]\n  1 -> k899ddd934c0f4f81a9738120494ed983\n  2[label=\"Meryl - generate histogram\"]\n  1 -> 2 [label=\"read_db\"]\n  3[label=\"Genomescope\"]\n  2 -> 3 [label=\"read_db_hist\"]\n  kefc727b61ef44c4c8cce35c7d3cc8aac[color=lightseagreen,label=\"Output\\nGenomeScope on input dataset(s) Transformed log plot\"]\n  3 -> kefc727b61ef44c4c8cce35c7d3cc8aac\n  k701df341576744bcade26af498ab7467[color=lightseagreen,label=\"Output\\nGenomeScope on input dataset(s) Transformed linear plot\"]\n  3 -> k701df341576744bcade26af498ab7467\n  k85fa4004b35147b384aa6788d338037a[color=lightseagreen,label=\"Output\\nGenomeScope on input dataset(s) Log plot\"]\n  3 -> k85fa4004b35147b384aa6788d338037a\n  kc71ce05598f0435493972f8833b90cc4[color=lightseagreen,label=\"Output\\nGenomeScope on input dataset(s) Linear plot\"]\n  3 -> kc71ce05598f0435493972f8833b90cc4\n}",
-                "history": [
-                    {
-                        "hash": "b74cf5a09d0d563d658d374ed6d287db85df3a8a",
-                        "message": "Update Galaxy-Workflow-kmer_counting.ga",
-                        "num": 5,
-                        "short_hash": "b74cf5a09",
-                        "unix": "1715074461"
-                    },
-                    {
-                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
-                        "message": "new versions of workflows",
-                        "num": 4,
-                        "short_hash": "e8ddbcdd5",
-                        "unix": "1714537936"
-                    },
-                    {
-                        "hash": "0be0483e2cbaa0ab18026da1f19f4b124d78e1c4",
-                        "message": "Rename Galaxy-Workflow-kmer_counting.ga to Galaxy-Workflow-kmer_counting_old.ga",
-                        "num": 3,
-                        "short_hash": "0be0483e2",
-                        "unix": "1714537366"
-                    },
-                    {
-                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
-                        "message": "add/complete creator info on workflows",
-                        "num": 2,
-                        "short_hash": "62e77944b",
-                        "unix": "1676627603"
                     },
-                    {
-                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
-                        "message": "large genome tutorial",
-                        "num": 1,
-                        "short_hash": "9fcb3aeec",
-                        "unix": "1665123856"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Illumina reads R1"
-                            }
-                        ],
-                        "label": "Illumina reads R1",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 31.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "3daa3f25-6fff-4766-9d45-b991fd6751a5",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Meryl - count kmers\"];\n  0 -->|output| 1;\n  899ddd93-4c0f-4f81-a973-8120494ed983[\"Output\\nMeryl on input dataset(s): read-db.meryldb\"];\n  1 --> 899ddd93-4c0f-4f81-a973-8120494ed983;\n  style 899ddd93-4c0f-4f81-a973-8120494ed983 stroke:#2c3143,stroke-width:4px;\n  2[\"Meryl - generate histogram\"];\n  1 -->|read_db| 2;\n  3[\"Genomescope\"];\n  2 -->|read_db_hist| 3;\n  efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac[\"Output\\nGenomeScope on input dataset(s) Transformed log plot\"];\n  3 --> efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac;\n  style efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac stroke:#2c3143,stroke-width:4px;\n  701df341-5767-44bc-ade2-6af498ab7467[\"Output\\nGenomeScope on input dataset(s) Transformed linear plot\"];\n  3 --> 701df341-5767-44bc-ade2-6af498ab7467;\n  style 701df341-5767-44bc-ade2-6af498ab7467 stroke:#2c3143,stroke-width:4px;\n  85fa4004-b351-47b3-84aa-6788d338037a[\"Output\\nGenomeScope on input dataset(s) Log plot\"];\n  3 --> 85fa4004-b351-47b3-84aa-6788d338037a;\n  style 85fa4004-b351-47b3-84aa-6788d338037a stroke:#2c3143,stroke-width:4px;\n  c71ce055-98f0-4354-9397-2f8833b90cc4[\"Output\\nGenomeScope on input dataset(s) Linear plot\"];\n  3 --> c71ce055-98f0-4354-9397-2f8833b90cc4;\n  style c71ce055-98f0-4354-9397-2f8833b90cc4 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "kmer counting - meryl - upgraded",
-                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4",
                         "errors": null,
-                        "id": 1,
+                        "id": 27,
                         "input_connections": {
-                            "operation_type|input_reads": {
-                                "id": 0,
-                                "output_name": "output"
+                            "input": {
+                                "id": 19,
+                                "output_name": "alignment_output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Meryl",
-                                "name": "operation_type"
-                            }
-                        ],
-                        "label": "Meryl - count kmers",
-                        "name": "Meryl",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Samtools stats",
                         "outputs": [
                             {
-                                "name": "read_db",
-                                "type": "meryldb"
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 228,
-                            "top": 103.5
+                            "left": 1507.0317775869937,
+                            "top": 1886.4967353214358
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4",
                         "tool_shed_repository": {
-                            "changeset_revision": "29dabd8db6f2",
-                            "name": "meryl",
-                            "owner": "iuc",
+                            "changeset_revision": "3a0efe14891f",
+                            "name": "samtools_stats",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"operation_type\": {\"command_type\": \"count-kmers\", \"__current_case__\": 0, \"count_operations\": \"count\", \"input_reads\": {\"__class__\": \"RuntimeValue\"}, \"options_kmer_size\": {\"kmer_size\": \"provide\", \"__current_case__\": 0, \"input_kmer_size\": \"21\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3+galaxy6",
+                        "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cov_threshold\": null, \"coverage_cond\": {\"coverage_select\": \"no\", \"__current_case__\": 0}, \"filter_by_flags\": {\"filter_flags\": \"nofilter\", \"__current_case__\": 1}, \"gc_depth\": null, \"input\": {\"__class__\": \"ConnectedValue\"}, \"insert_size\": null, \"most_inserts\": null, \"read_group\": null, \"read_length\": null, \"remove_dups\": false, \"remove_overlaps\": false, \"sparse\": false, \"split_output_cond\": {\"split_output_selector\": \"no\", \"__current_case__\": 0}, \"trim_quality\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.4",
                         "type": "tool",
-                        "uuid": "0a85d93b-8f53-4bc8-b89b-4be6f306f2c6",
+                        "uuid": "c5d1a111-ba0d-4299-8d29-643377acfe3e",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Meryl on input dataset(s): read-db.meryldb",
-                                "output_name": "read_db",
-                                "uuid": "899ddd93-4c0f-4f81-a973-8120494ed983"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "fbad75d5-c42f-4368-a8dd-45eafcc2f42e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.4+galaxy0",
                         "errors": null,
-                        "id": 2,
+                        "id": 28,
                         "input_connections": {
-                            "operation_type|input_meryldb_02": {
-                                "id": 1,
-                                "output_name": "read_db"
+                            "input": {
+                                "id": 21,
+                                "output_name": "outfile"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Meryl",
-                                "name": "operation_type"
-                            }
-                        ],
-                        "label": "Meryl - generate histogram",
-                        "name": "Meryl",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Busco",
                         "outputs": [
                             {
-                                "name": "read_db_hist",
+                                "name": "busco_sum",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "busco_table",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 465.5,
-                            "top": 110
+                            "left": 1567.9000006004667,
+                            "top": 1293
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.4+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "29dabd8db6f2",
-                            "name": "meryl",
+                            "changeset_revision": "bb935709506a",
+                            "name": "busco",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"operation_type\": {\"command_type\": \"histogram-kmers\", \"__current_case__\": 4, \"input_meryldb_02\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3+galaxy6",
+                        "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"auto_detect\", \"__current_case__\": 0, \"auto_lineage\": \"--auto-lineage\"}, \"outputs\": [\"short_summary\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.4.4+galaxy0",
                         "type": "tool",
-                        "uuid": "80dbb867-84f7-4349-ae1d-1c7b87d0dce7",
+                        "uuid": "8f354503-9332-4dc2-8e7e-2ec42adab839",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "read_db_hist",
-                                "uuid": "bf11e7cb-61a2-4c27-9aa1-4c7a42028330"
+                                "label": "Busco on input dataset(s): full table",
+                                "output_name": "busco_table",
+                                "uuid": "af98aae6-f1a3-493c-9cef-08e0926210d3"
+                            },
+                            {
+                                "label": "Busco on input dataset(s): short summary",
+                                "output_name": "busco_sum",
+                                "uuid": "929439b7-c688-45ea-848a-97c13d3e0028"
                             }
                         ]
                     },
@@ -13381,20 +12183,19 @@
                         "annotation": "",
                         "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
                         "errors": null,
-                        "id": 3,
+                        "id": 35,
                         "input_connections": {
                             "input": {
-                                "id": 2,
+                                "id": 26,
                                 "output_name": "read_db_hist"
+                            },
+                            "ploidy": {
+                                "id": 5,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool GenomeScope",
-                                "name": "input"
-                            }
-                        ],
-                        "label": "Genomescope",
+                        "inputs": [],
+                        "label": null,
                         "name": "GenomeScope",
                         "outputs": [
                             {
@@ -13412,23 +12213,11 @@
                             {
                                 "name": "transformed_log_plot",
                                 "type": "png"
-                            },
-                            {
-                                "name": "model",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "summary",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "progress",
-                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 699.204345703125,
-                            "top": 0
+                            "left": 1567.9000006004667,
+                            "top": 977
                         },
                         "post_job_actions": {},
                         "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
@@ -13438,76 +12227,123 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_options\": {\"topology\": null, \"initial_repetitiveness\": null, \"initial_heterozygosities\": \"\", \"transform_exp\": null, \"testing\": false, \"true_params\": \"\", \"trace_flag\": false, \"num_rounds\": null}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"kmer_length\": \"21\", \"lambda\": null, \"max_kmercov\": null, \"output_options\": {\"output_files\": [\"model_output\", \"summary_output\", \"progress_output\"], \"no_unique_sequence\": false}, \"ploidy\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"advanced_options\": {\"topology\": null, \"initial_repetitiveness\": null, \"initial_heterozygosities\": \"\", \"transform_exp\": null, \"testing\": false, \"true_params\": \"\", \"trace_flag\": false, \"num_rounds\": null}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"kmer_length\": \"21\", \"lambda\": null, \"max_kmercov\": null, \"output_options\": {\"output_files\": null, \"no_unique_sequence\": false}, \"ploidy\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "2.0+galaxy2",
                         "type": "tool",
-                        "uuid": "fa7a5012-8bd0-4b35-b337-249245e0932b",
+                        "uuid": "fc99955a-fa06-415a-9073-973432021b09",
                         "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "progress",
-                                "uuid": "fedca588-8be6-4e13-9ff5-62387a5a90af"
-                            },
-                            {
-                                "label": "GenomeScope on input dataset(s) Transformed log plot",
-                                "output_name": "transformed_log_plot",
-                                "uuid": "efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac"
+                                "output_name": "transformed_linear_plot",
+                                "uuid": "e90780ce-d82c-4cd5-8d10-c8702c7fa312"
                             },
                             {
                                 "label": null,
-                                "output_name": "summary",
-                                "uuid": "fd17af72-7c2a-4167-9880-7fbda525ccbb"
+                                "output_name": "log_plot",
+                                "uuid": "deebd887-e5f3-434b-80c8-b3978c7e5c47"
                             },
                             {
                                 "label": null,
-                                "output_name": "model",
-                                "uuid": "ede2b1a5-4017-4aef-a6d2-bac5d17bc7b5"
+                                "output_name": "linear_plot",
+                                "uuid": "0f6ee759-0f6e-4d66-9426-dc0b6349d16d"
                             },
                             {
-                                "label": "GenomeScope on input dataset(s) Transformed linear plot",
-                                "output_name": "transformed_linear_plot",
-                                "uuid": "701df341-5767-44bc-ade2-6af498ab7467"
-                            },
+                                "label": null,
+                                "output_name": "transformed_log_plot",
+                                "uuid": "b6ba52b5-bbd0-4764-abf9-e8c11b3ce327"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
+                        "errors": null,
+                        "id": 41,
+                        "input_connections": {
+                            "input": {
+                                "id": 37,
+                                "output_name": "pretext_map_out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Pretext Snapshot",
+                        "outputs": [
                             {
-                                "label": "GenomeScope on input dataset(s) Log plot",
-                                "output_name": "log_plot",
-                                "uuid": "85fa4004-b351-47b3-84aa-6788d338037a"
-                            },
+                                "name": "pretext_snap_out",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1857.9000006004667,
+                            "top": 2162
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "44c66e8d21e6",
+                            "name": "pretext_snapshot",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"colormap\": \"5\", \"formats\": {\"outformat\": \"png\", \"__current_case__\": 0}, \"grid\": {\"showGrid\": true, \"__current_case__\": 0, \"gridsize\": \"1\", \"gridcolor\": \"black\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mintexels\": \"64\", \"resolution\": \"1000\", \"sequencenames\": false, \"sequences\": \"=full, =all\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.0.3+galaxy1",
+                        "type": "tool",
+                        "uuid": "414d726e-7a86-4c9e-a8b0-3d6afc9ec374",
+                        "when": null,
+                        "workflow_outputs": [
                             {
-                                "label": "GenomeScope on input dataset(s) Linear plot",
-                                "output_name": "linear_plot",
-                                "uuid": "c71ce055-98f0-4354-9397-2f8833b90cc4"
+                                "label": null,
+                                "output_name": "pretext_snap_out",
+                                "uuid": "16969c99-f550-4bff-8df6-98b1fecd3b00"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/largegenome",
-                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-kmer_counting.ga",
+                "parent_id": "assembly/ERGA-post-assembly-QC",
+                "path": "topics/assembly/tutorials/ERGA-post-assembly-QC/workflows/main_workflow.ga",
                 "tags": [
-                    "GTN",
-                    "LG-WF"
+                    "ReferenceGenome",
+                    "name:ERGA"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "kmer counting - meryl - upgraded",
+                "tests": true,
+                "title": "Post-assembly workflow",
                 "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-kmer-counting",
-                "tutorial_id": "largegenome",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-kmer_counting.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-kmer_counting.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-ERGA-post-assembly-QC/versions/main-workflow",
+                "tutorial_id": "ERGA-post-assembly-QC",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/ERGA-post-assembly-QC/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/ERGA-post-assembly-QC/workflows/main_workflow.html",
                 "version": 2,
-                "wfid": "assembly-largegenome",
-                "wfname": "galaxy-workflow-kmer-counting",
-                "workflow": "Galaxy-Workflow-kmer_counting.ga",
+                "wfid": "assembly-ERGA-post-assembly-QC",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
+                    "CONVERTER_gz_to_uncompressed",
+                    "__EXTRACT_DATASET__",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.0.7+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.2.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4",
+                    "toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy+2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0",
                     "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
                 ],
-                "workflowhub_id": "1166"
+                "workflowhub_id": "1127"
             }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.7055935"
+        ]
     },
     {
         "admin_install": {
@@ -13516,184 +12352,105 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "busco",
-                    "owner": "iuc",
-                    "revisions": "41030a6c03b7",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "chromeister",
-                    "owner": "iuc",
-                    "revisions": "b768cc4cca40",
-                    "tool_panel_section_label": "Multiple Alignments",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "merqury",
-                    "owner": "iuc",
-                    "revisions": "f8113c25bc6b",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "meryl",
-                    "owner": "iuc",
-                    "revisions": "29dabd8db6f2",
+                    "name": "mitohifi",
+                    "owner": "bgruening",
+                    "revisions": "99ddbf037d98",
                     "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "quast",
+                    "name": "compress_file",
                     "owner": "iuc",
-                    "revisions": "3061c8b029e5",
-                    "tool_panel_section_label": "Assembly",
+                    "revisions": "09ea79f9f260",
+                    "tool_panel_section_label": "Convert Formats",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: busco\n  owner: iuc\n  revisions: 41030a6c03b7\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chromeister\n  owner: iuc\n  revisions: b768cc4cca40\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merqury\n  owner: iuc\n  revisions: f8113c25bc6b\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n  owner: iuc\n  revisions: 29dabd8db6f2\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 3061c8b029e5\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-quality-control/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: mitohifi\n  owner: bgruening\n  revisions: 99ddbf037d98\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: compress_file\n  owner: iuc\n  revisions: '09ea79f9f260'\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mitochondrion-assembly/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "gallantries",
-                    "eurosciencegateway",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
-                "fediverse_flavor": "mastodon",
-                "id": "abretaud",
+                "email": "delphine.lariviere@galaxy.org",
+                "id": "delphine-l",
                 "joined": "2017-09",
-                "location": {
-                    "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
-                },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
-            },
-            {
-                "email": "alexandre.cormier@ifremer.fr",
-                "id": "alexcorm",
-                "joined": "2021-11",
-                "name": "Alexandre Cormier",
-                "orcid": "0000-0002-7775-8413",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/",
-                "twitter": "allanssx",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/alexcorm.json"
-            },
-            {
-                "email": "erwan.corre@sb-roscoff.fr",
-                "id": "r1corre",
-                "joined": "2019-04",
-                "name": "Erwan Corre",
-                "orcid": "0000-0001-6354-2278",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/r1corre/",
-                "twitter": "r1corre",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/r1corre.json"
-            },
-            {
-                "email": "laura.leroi@ifremer.fr",
-                "id": "lleroi",
-                "joined": "2021-11",
-                "name": "Laura Leroi",
-                "orcid": "0000-0003-3748-4179",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lleroi/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/lleroi.json"
-            },
-            {
-                "email": "stephanie.robin@inrae.fr",
-                "id": "stephanierobin",
-                "joined": "2021-11",
-                "name": "St\u00e9phanie Robin",
-                "orcid": "0000-0001-7379-9173",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/",
-                "twitter": "robinstphanie1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/stephanierobin.json"
+                "name": "Delphine Lariviere",
+                "orcid": "0000-0001-6421-3484",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
             }
         ],
-        "dir": "topics/assembly/tutorials/assembly-quality-control",
-        "edam_operation": [
-            "Visualisation",
-            "Phasing",
-            "De-novo assembly",
-            "Sequence assembly validation",
-            "Transcriptome assembly",
-            "Genome assembly",
-            "k-mer counting",
-            "Scaffolding"
-        ],
+        "dir": "topics/assembly/tutorials/mitochondrion-assembly",
+        "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "genome-annotation",
-                "tutorials": [
-                    "repeatmasker"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "assembly/assembly-quality-control",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz"
-        ],
+        "id": "assembly/mitochondrion-assembly",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Quast, BUSCO and Merqury make it easy to assess the quality of an assembly",
-            "Post-processing can be necessary (purging, scaffolding) before annotation"
+            "MitoHifi generates the assembly and annotation of the Mitochondrial Genome using a reference sequence."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-09-26",
         "objectives": [
-            "Assess assembly quality"
+            "Generate Mitochondrial assembly",
+            "Understand the outputs of MitoHifi"
         ],
-        "pageviews": 2770269,
-        "pub_date": "2022-08-26",
+        "pageviews": 78,
+        "pub_date": "2024-09-03",
         "questions": [
-            "Is my genome assembly ready for annotation and/or scaffolding?"
+            "How to assemble the mitochondrial genome from PacBio Hifi Reads"
         ],
-        "short_id": "T00028",
+        "recordings": [
+            {
+                "bot-timestamp": 1726861719,
+                "captioners": [
+                    "delphine-l"
+                ],
+                "date": "2024-09-20",
+                "galaxy_version": " 24.1.2.dev0",
+                "length": "11M",
+                "speakers": [
+                    "delphine-l"
+                ],
+                "youtube_id": "0ehAZ0DZsFU"
+            }
+        ],
+        "short_id": "T00453",
         "short_tools": [
-            "busco",
-            "merqury",
-            "quast",
-            "meryl",
-            "chromeister"
+            "compress_file",
+            "mitohifi"
         ],
-        "slides": true,
+        "slides": false,
         "slides_recordings": false,
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 },
                 {
                     "name": "UseGalaxy.org.au",
@@ -13701,27 +12458,14 @@
                     "usegalaxy": true
                 }
             ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                }
-            ]
+            "inexact": []
         },
         "symlink": null,
-        "tags": [
-            "assembly",
-            "quality control"
-        ],
-        "time_estimation": "2h",
-        "title": "Genome Assembly Quality Control",
+        "time_estimation": "1H",
+        "title": "Assembly of the mitochondrial genome from PacBio HiFi reads",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
-            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/compress_file/compress_file/0.1.0"
         ],
         "topic_name": "assembly",
         "topic_name_human": "Assembly",
@@ -13731,63 +12475,54 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "assembly-quality-control",
+        "tutorial_name": "mitochondrion-assembly",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/assembly-quality-control/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/mitochondrion-assembly/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-quality-control/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-quality-control/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mitochondrion-assembly/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mitochondrion-assembly/tutorial.json"
         },
-        "version": 4,
+        "version": 2,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 265,
-        "visitors": 1159110,
+        "visit_duration": 189,
+        "visitors": 64,
         "workflows": [
             {
                 "creators": [
                     {
-                        "class": "Person",
-                        "identifier": "",
-                        "name": "Erwan Corre"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "",
-                        "name": "St\u00e9phanie Robin"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "",
-                        "name": "Anthony Bretaudeau"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "",
-                        "name": "Alexandre Cormier"
+                        "class": "Organization",
+                        "name": "VGP",
+                        "url": "https://vertebrategenomeproject.org"
                     },
                     {
-                        "class": "Person",
-                        "identifier": "",
-                        "name": "Laura Leroi"
+                        "class": "Organization",
+                        "name": "Galaxy"
                     }
                 ],
-                "description": "Genome assembly quality control using PacBio data and with reference genome",
+                "description": "",
                 "features": {
                     "comments": false,
-                    "parameters": false,
+                    "parameters": true,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGCA_000146045.2_genomic.fna\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nScerevisiae-INSC1019.flye.30x.fa\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nScerevisiae-INSC1019.hifiasm.30x.fa\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSRR13577847_subreads.30x.fastq.gz\"]\n  4[label=\"Busco\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Busco\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"Quast\"]\n  0 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"Busco\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"Chromeister\"]\n  0 -> 8 [label=\"output\"]\n  2 -> 8 [label=\"output\"]\n  9[label=\"Meryl\"]\n  3 -> 9 [label=\"output\"]\n  10[label=\"Merqury\"]\n  0 -> 10 [label=\"output\"]\n  9 -> 10 [label=\"read_db\"]\n  11[label=\"Merqury\"]\n  1 -> 11 [label=\"output\"]\n  9 -> 11 [label=\"read_db\"]\n  12[label=\"Merqury\"]\n  2 -> 12 [label=\"output\"]\n  9 -> 12 [label=\"read_db\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nCollection of Pacbio Data\"]\n  1[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nSpecies name latin name\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nEmail adress\"]\n  3[label=\"MitoHiFi\"]\n  2 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"MitoHiFi\"]\n  0 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"fasta_reference\"]\n  3 -> 4 [label=\"genbank_reference\"]\n  k31807e4be616474292e0934e6c3c09ae[color=lightseagreen,label=\"Output\\ncontigs_stats\"]\n  4 -> k31807e4be616474292e0934e6c3c09ae\n  k8393c665a328469893e5198c6fea52dd[color=lightseagreen,label=\"Output\\nmitogenome_coverage\"]\n  4 -> k8393c665a328469893e5198c6fea52dd\n  k85061673df5e480d920aa11c72bf8f56[color=lightseagreen,label=\"Output\\nmitogenome_annotation\"]\n  4 -> k85061673df5e480d920aa11c72bf8f56\n  kfe4d1d3d9caa45f6944ec4b101105dd1[color=lightseagreen,label=\"Output\\nmitogenome_genbank\"]\n  4 -> kfe4d1d3d9caa45f6944ec4b101105dd1\n  5[label=\"Compress files\"]\n  4 -> 5 [label=\"mitogenome_fasta\"]\n  k6f918a081ca14d6ea4d87e65e13a65ed[color=lightseagreen,label=\"Output\\noutput_file\"]\n  5 -> k6f918a081ca14d6ea4d87e65e13a65ed\n}",
                 "history": [
                     {
-                        "hash": "9e51f44fe902a2db9db2b2895df49c788990df15",
-                        "message": "Genome assembly quality control (#3120)",
+                        "hash": "d6520a5b9509ae003760f036f90e6dfabb10cc4b",
+                        "message": "workflow reformating",
+                        "num": 2,
+                        "short_hash": "d6520a5b9",
+                        "unix": "1725310848"
+                    },
+                    {
+                        "hash": "7e2bcd1f09125f7773f63c1601b1e48c6d3d4aa8",
+                        "message": "Creation of the tutorial skeleton",
                         "num": 1,
-                        "short_hash": "9e51f44fe",
-                        "unix": "1661523060"
+                        "short_hash": "7e2bcd1f0",
+                        "unix": "1724079096"
                     }
                 ],
                 "inputs": [
@@ -13800,135 +12535,355 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "GCA_000146045.2_genomic.fna"
+                                "name": "Collection of Pacbio Data"
                             }
                         ],
-                        "label": "GCA_000146045.2_genomic.fna",
-                        "name": "Input dataset",
+                        "label": "Collection of Pacbio Data",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 10
+                            "left": 0.0,
+                            "top": 0.0
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "67e22573-10a9-4a09-bc6b-ad54147f931a",
+                        "type": "data_collection_input",
+                        "uuid": "861c3a49-1055-4030-9a91-e53cbf1ac436",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Latin name of species",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Scerevisiae-INSC1019.flye.30x.fa"
+                                "description": "Latin name of species",
+                                "name": "Species name (latin name)"
                             }
                         ],
-                        "label": "Scerevisiae-INSC1019.flye.30x.fa",
-                        "name": "Input dataset",
+                        "label": "Species name (latin name)",
+                        "name": "Input parameter",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 130
+                            "left": 131.640625,
+                            "top": 108.3515625
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "056f45e5-b3d7-4d43-8c87-497977c8b9f6",
-                        "workflow_outputs": []
+                        "type": "parameter_input",
+                        "uuid": "27257feb-04b0-48f9-8bd3-a3a74536eab2",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "65196658-7776-4165-944b-c7876483edf4"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Required for NCBI database query",
                         "content_id": null,
                         "errors": null,
                         "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Scerevisiae-INSC1019.hifiasm.30x.fa"
+                                "description": "Required for NCBI database query",
+                                "name": "Email adress"
                             }
                         ],
-                        "label": "Scerevisiae-INSC1019.hifiasm.30x.fa",
-                        "name": "Input dataset",
+                        "label": "Email adress",
+                        "name": "Input parameter",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 250
+                            "left": 200.78125,
+                            "top": 290.66015625
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "e812ab39-31c2-4595-8f11-f1e939e68704",
-                        "workflow_outputs": []
+                        "type": "parameter_input",
+                        "uuid": "4ddb385f-ecd7-4d48-bc7b-e9c7971a1e62",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "28bbbdb1-62b7-4d3a-9076-09cc835464cc"
+                            }
+                        ]
+                    }
+                ],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nCollection of Pacbio Data\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nSpecies name latin name\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nEmail adress\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"MitoHiFi\"];\n  2 -->|output| 3;\n  1 -->|output| 3;\n  4[\"MitoHiFi\"];\n  0 -->|output| 4;\n  3 -->|fasta_reference| 4;\n  3 -->|genbank_reference| 4;\n  31807e4b-e616-4742-92e0-934e6c3c09ae[\"Output\\ncontigs_stats\"];\n  4 --> 31807e4b-e616-4742-92e0-934e6c3c09ae;\n  style 31807e4b-e616-4742-92e0-934e6c3c09ae stroke:#2c3143,stroke-width:4px;\n  8393c665-a328-4698-93e5-198c6fea52dd[\"Output\\nmitogenome_coverage\"];\n  4 --> 8393c665-a328-4698-93e5-198c6fea52dd;\n  style 8393c665-a328-4698-93e5-198c6fea52dd stroke:#2c3143,stroke-width:4px;\n  85061673-df5e-480d-920a-a11c72bf8f56[\"Output\\nmitogenome_annotation\"];\n  4 --> 85061673-df5e-480d-920a-a11c72bf8f56;\n  style 85061673-df5e-480d-920a-a11c72bf8f56 stroke:#2c3143,stroke-width:4px;\n  fe4d1d3d-9caa-45f6-944e-c4b101105dd1[\"Output\\nmitogenome_genbank\"];\n  4 --> fe4d1d3d-9caa-45f6-944e-c4b101105dd1;\n  style fe4d1d3d-9caa-45f6-944e-c4b101105dd1 stroke:#2c3143,stroke-width:4px;\n  5[\"Compress files\"];\n  4 -->|mitogenome_fasta| 5;\n  6f918a08-1ca1-4d6e-a4d8-7e65e13a65ed[\"Output\\noutput_file\"];\n  5 --> 6f918a08-1ca1-4d6e-a4d8-7e65e13a65ed;\n  style 6f918a08-1ca1-4d6e-a4d8-7e65e13a65ed stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Mitogenome-Assembly-VGP0",
+                "outputs": [
+                    {
+                        "annotation": "Latin name of species",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Latin name of species",
+                                "name": "Species name (latin name)"
+                            }
+                        ],
+                        "label": "Species name (latin name)",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 131.640625,
+                            "top": 108.3515625
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "27257feb-04b0-48f9-8bd3-a3a74536eab2",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "65196658-7776-4165-944b-c7876483edf4"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Required for NCBI database query",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "SRR13577847_subreads.30x.fastq.gz"
+                                "description": "Required for NCBI database query",
+                                "name": "Email adress"
                             }
                         ],
-                        "label": "SRR13577847_subreads.30x.fastq.gz",
-                        "name": "Input dataset",
+                        "label": "Email adress",
+                        "name": "Input parameter",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 370
+                            "left": 200.78125,
+                            "top": 290.66015625
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f0a31b4f-fdf0-4417-9300-a4e52dc60580",
-                        "workflow_outputs": []
+                        "type": "parameter_input",
+                        "uuid": "4ddb385f-ecd7-4d48-bc7b-e9c7971a1e62",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "28bbbdb1-62b7-4d3a-9076-09cc835464cc"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3+galaxy0",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "operation_mode|input_option|input_reads": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "operation_mode|reference_fasta": {
+                                "id": 3,
+                                "output_name": "fasta_reference"
+                            },
+                            "operation_mode|reference_genbank": {
+                                "id": 3,
+                                "output_name": "genbank_reference"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool MitoHiFi",
+                                "name": "operation_mode"
+                            },
+                            {
+                                "description": "runtime parameter for tool MitoHiFi",
+                                "name": "operation_mode"
+                            }
+                        ],
+                        "label": null,
+                        "name": "MitoHiFi",
+                        "outputs": [
+                            {
+                                "name": "mitogenome_fasta",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "mitogenome_genbank",
+                                "type": "genbank"
+                            },
+                            {
+                                "name": "mitogenome_annotation",
+                                "type": "png"
+                            },
+                            {
+                                "name": "mitogenome_coverage",
+                                "type": "png"
+                            },
+                            {
+                                "name": "contigs_stats",
+                                "type": "tsv"
+                            },
+                            {
+                                "name": "hifiasm",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "hifiasm_filtered",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "hifiasm_contigs",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "left": 767.6689707083681,
+                            "top": 134.09873055610626
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionhifiasm": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "hifiasm"
+                            },
+                            "HideDatasetActionhifiasm_contigs": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "hifiasm_contigs"
+                            },
+                            "HideDatasetActionhifiasm_filtered": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "hifiasm_filtered"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "99ddbf037d98",
+                            "name": "mitohifi",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"operation_mode\": {\"command\": \"mitohifi\", \"__current_case__\": 1, \"input_option\": {\"input\": \"pacbio\", \"__current_case__\": 0, \"input_reads\": {\"__class__\": \"ConnectedValue\"}, \"bloom_filter\": \"0\"}, \"reference_fasta\": {\"__class__\": \"ConnectedValue\"}, \"reference_genbank\": {\"__class__\": \"ConnectedValue\"}, \"genetic_code\": \"2\", \"advanced_options\": {\"query_blast\": \"70\", \"circular_size\": null, \"circular_offset\": null, \"outputs\": null}, \"output_zip\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3+galaxy0",
+                        "type": "tool",
+                        "uuid": "ccd83410-608a-4b9d-a43a-11cecd6c2d42",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "contigs_stats",
+                                "output_name": "contigs_stats",
+                                "uuid": "31807e4b-e616-4742-92e0-934e6c3c09ae"
+                            },
+                            {
+                                "label": "mitogenome_coverage",
+                                "output_name": "mitogenome_coverage",
+                                "uuid": "8393c665-a328-4698-93e5-198c6fea52dd"
+                            },
+                            {
+                                "label": "mitogenome_annotation",
+                                "output_name": "mitogenome_annotation",
+                                "uuid": "85061673-df5e-480d-920a-a11c72bf8f56"
+                            },
+                            {
+                                "label": "mitogenome_genbank",
+                                "output_name": "mitogenome_genbank",
+                                "uuid": "fe4d1d3d-9caa-45f6-944e-c4b101105dd1"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compress_file/compress_file/0.1.0",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "input": {
+                                "id": 4,
+                                "output_name": "mitogenome_fasta"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Compress file(s)",
+                        "outputs": [
+                            {
+                                "name": "output_file",
+                                "type": "gz"
+                            }
+                        ],
+                        "position": {
+                            "left": 1065.5131364872464,
+                            "top": 265.5261773629027
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compress_file/compress_file/0.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "09ea79f9f260",
+                            "name": "compress_file",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0",
+                        "type": "tool",
+                        "uuid": "5207adc9-f36a-42e9-8631-e01da77ac446",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "output_file",
+                                "output_name": "output_file",
+                                "uuid": "6f918a08-1ca1-4d6e-a4d8-7e65e13a65ed"
+                            }
+                        ]
                     }
                 ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGCA_000146045.2_genomic.fna\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nScerevisiae-INSC1019.flye.30x.fa\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nScerevisiae-INSC1019.hifiasm.30x.fa\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nSRR13577847_subreads.30x.fastq.gz\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Busco\"];\n  0 -->|output| 4;\n  5[\"Busco\"];\n  1 -->|output| 5;\n  6[\"Quast\"];\n  0 -->|output| 6;\n  1 -->|output| 6;\n  2 -->|output| 6;\n  7[\"Busco\"];\n  2 -->|output| 7;\n  8[\"Chromeister\"];\n  0 -->|output| 8;\n  2 -->|output| 8;\n  9[\"Meryl\"];\n  3 -->|output| 9;\n  10[\"Merqury\"];\n  0 -->|output| 10;\n  9 -->|read_db| 10;\n  11[\"Merqury\"];\n  1 -->|output| 11;\n  9 -->|read_db| 11;\n  12[\"Merqury\"];\n  2 -->|output| 12;\n  9 -->|read_db| 12;",
-                "modified": "2024-08-18 00:06:20 +0000",
-                "name": "Genome Assembly Quality Control",
-                "outputs": [],
-                "parent_id": "assembly/assembly-quality-control",
-                "path": "topics/assembly/tutorials/assembly-quality-control/workflows/main_workflow.ga",
+                "parent_id": "assembly/mitochondrion-assembly",
+                "path": "topics/assembly/tutorials/mitochondrion-assembly/workflows/main_workflow.ga",
                 "tags": [
-                    "assembly"
+                    "Reviewed",
+                    "VGP"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "Genome Assembly Quality Control",
+                "tests": true,
+                "title": "Mitogenome-Assembly-VGP0",
                 "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-assembly-quality-control/versions/main-workflow",
-                "tutorial_id": "assembly-quality-control",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-quality-control/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-quality-control/workflows/main_workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-mitochondrion-assembly/versions/main-workflow",
+                "tutorial_id": "mitochondrion-assembly",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/mitochondrion-assembly/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/mitochondrion-assembly/workflows/main_workflow.html",
                 "version": 1,
-                "wfid": "assembly-assembly-quality-control",
+                "wfid": "assembly-mitochondrion-assembly",
                 "wfname": "main-workflow",
                 "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.3.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/compress_file/compress_file/0.1.0"
                 ],
-                "workflowhub_id": "1128"
+                "workflowhub_id": "1360"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/6947782"
+        "zenodo_link": "https://zenodo.org/records/13345315"
     },
     {
         "admin_install": {
@@ -13937,154 +12892,246 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "flye",
-                    "owner": "bgruening",
-                    "revisions": "276f5d8712d5",
-                    "tool_panel_section_label": "Assembly",
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "5ec9f6bceaee",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "busco",
+                    "name": "bandage",
                     "owner": "iuc",
-                    "revisions": "0d243f458b53",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "ddddce450736",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "busco",
+                    "name": "bandage",
                     "owner": "iuc",
-                    "revisions": "46ae58b1d792",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "ddddce450736",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fasta_stats",
+                    "name": "fastp",
                     "owner": "iuc",
-                    "revisions": "0dbb995c7d35",
+                    "revisions": "65b93b623c77",
                     "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "quast",
                     "owner": "iuc",
-                    "revisions": "7594365c546b",
+                    "revisions": "72472698a2df",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "shovill",
+                    "owner": "iuc",
+                    "revisions": "ad80238462c1",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "shovill",
+                    "owner": "iuc",
+                    "revisions": "ee17a294d3a3",
                     "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: flye\n  owner: bgruening\n  revisions: 276f5d8712d5\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 0d243f458b53\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 46ae58b1d792\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n  owner: iuc\n  revisions: 0dbb995c7d35\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 7594365c546b\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/flye-assembly/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 72472698a2df\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: shovill\n  owner: iuc\n  revisions: ad80238462c1\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: shovill\n  owner: iuc\n  revisions: ee17a294d3a3\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-illumina/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "bazante1",
+                "bebatut"
+            ],
+            "editing": [
+                "hexylena",
+                "bazante1",
+                "shiltemann",
+                "miaomiaozhou88"
+            ],
+            "funding": [
+                "avans-atgm",
+                "abromics"
+            ]
+        },
         "contributors": [
+            {
+                "affiliations": [
+                    "avans-atgm"
+                ],
+                "id": "bazante1",
+                "joined": "2020-12",
+                "name": "Bazante Sanders",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
-                    "eurosciencegateway",
+                    "ifb",
                     "elixir-europe"
                 ],
                 "contact_for_training": true,
                 "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
                 "fediverse_flavor": "mastodon",
-                "id": "abretaud",
+                "id": "bebatut",
                 "joined": "2017-09",
+                "linkedin": "berenicebatut",
                 "location": {
                     "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
+                    "lat": 45.77,
+                    "lon": 3.08
                 },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             },
             {
-                "email": "alexandre.cormier@ifremer.fr",
-                "id": "alexcorm",
-                "joined": "2021-11",
-                "name": "Alexandre Cormier",
-                "orcid": "0000-0002-7775-8413",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/",
-                "twitter": "allanssx",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/alexcorm.json"
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
             {
-                "email": "erwan.corre@sb-roscoff.fr",
-                "id": "r1corre",
-                "joined": "2019-04",
-                "name": "Erwan Corre",
-                "orcid": "0000-0001-6354-2278",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/r1corre/",
-                "twitter": "r1corre",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/r1corre.json"
+                "affiliations": [
+                    "avans-atgm"
+                ],
+                "id": "bazante1",
+                "joined": "2020-12",
+                "name": "Bazante Sanders",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
             },
             {
-                "email": "laura.leroi@ifremer.fr",
-                "id": "lleroi",
-                "joined": "2021-11",
-                "name": "Laura Leroi",
-                "orcid": "0000-0003-3748-4179",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lleroi/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/lleroi.json"
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             },
             {
-                "email": "stephanie.robin@inrae.fr",
-                "id": "stephanierobin",
-                "joined": "2021-11",
-                "name": "St\u00e9phanie Robin",
-                "orcid": "0000-0001-7379-9173",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/",
-                "twitter": "robinstphanie1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/stephanierobin.json"
+                "email": "m.zhou1@avans.nl",
+                "id": "miaomiaozhou88",
+                "joined": "2020-12",
+                "name": "Miaomiao Zhou",
+                "orcid": "0000-0003-4426-1758",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/miaomiaozhou88/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/miaomiaozhou88.json"
             },
             {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
+                "avatar": "/training-material/shared/images/logo-avans.png",
+                "former_members": [
+                    "dirowa",
+                    "hexylena"
+                ],
+                "id": "avans-atgm",
+                "joined": "2020-11",
                 "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
+                    "bazante1"
                 ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+                "name": "Avans Hogeschool",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/",
+                "ror": "015d5s513",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/abromics.png",
+                "funder": true,
+                "github": false,
+                "id": "abromics",
+                "joined": "2024-01",
+                "name": "ABRomics",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abromics/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/abromics.json"
             }
         ],
-        "dir": "topics/assembly/tutorials/flye-assembly",
+        "dir": "topics/assembly/tutorials/mrsa-illumina",
+        "edam_ontology": [
+            "topic_0196",
+            "topic_3673",
+            "topic_3305",
+            "topic_0622",
+            "topic_3301"
+        ],
         "edam_operation": [
-            "Visualisation",
-            "De-novo assembly",
             "Sequence assembly validation",
-            "Mapping assembly",
-            "Transcriptome assembly",
-            "Cross-assembly",
+            "Statistical calculation",
+            "Sequence assembly visualisation",
+            "Visualisation",
             "Genome assembly",
-            "Scaffolding"
+            "Sequencing quality control",
+            "Sequence composition calculation",
+            "Sequence contamination filtering"
+        ],
+        "edam_topic": [
+            "Sequence assembly",
+            "Whole genome sequencing",
+            "Public health and epidemiology",
+            "Genomics",
+            "Microbiology"
         ],
-        "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.cz",
             "UseGalaxy.eu",
             "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
+            "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
@@ -14092,50 +13139,86 @@
             {
                 "topic_name": "genome-annotation",
                 "tutorials": [
-                    "repeatmasker"
+                    "amr-gene-detection"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "history-to-workflow"
                 ],
                 "type": "internal"
             }
         ],
         "hands_on": true,
-        "id": "assembly/flye-assembly",
+        "id": "assembly/mrsa-illumina",
         "inexact_supported_servers": [
+            "Galaxy@AuBi",
             "GalaxyTrakr",
-            "UseGalaxy.cz"
+            "UseGalaxy.be",
+            "UseGalaxy.no"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "PacBio data allows to perform good quality genome assembly",
-            "Quast and BUSCO make it easy to compare the quality of assemblies"
+            "Illumina assemblies can be done with Shovill",
+            "It is hard to get the genome in one contig"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-09-18",
         "objectives": [
-            "Assemble a Genome with PacBio data",
-            "Assess assembly quality"
+            "Run tools to evaluate sequencing data on quality and quantity",
+            "Process the output of quality control tools",
+            "Improve the quality of sequencing data",
+            "Run a tool to assemble a bacterial genome using short reads",
+            "Run tools to assess the quality of an assembly",
+            "Understand the outputs of tools to assess the quality of an assembly"
         ],
-        "pageviews": 4471,
-        "pub_date": "2021-11-29",
+        "pageviews": 10837,
+        "pub_date": "2021-03-24",
         "questions": [
-            "How to perform a genome assembly with PacBio data ?",
-            "How to check assembly quality ?"
+            "How to check the quality of the MiSeq data?",
+            "How to perform an assembly of a bacterial genome with MiSeq data?",
+            "How to check the quality of an assembly?"
         ],
-        "short_id": "T00033",
+        "recordings": [
+            {
+                "bot-timestamp": 1725486412,
+                "captioners": [
+                    "meltemktn"
+                ],
+                "date": "2024-09-04",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "39M",
+                "speakers": [
+                    "meltemktn"
+                ],
+                "youtube_id": "rRHH77qtZHg"
+            }
+        ],
+        "short_id": "T00036",
         "short_tools": [
-            "fasta-stats",
-            "flye",
+            "fastp",
+            "bandage_image",
+            "upload1",
+            "bandage_info",
             "quast",
-            "busco"
+            "fastqc",
+            "shovill"
         ],
         "slides": false,
         "slides_recordings": false,
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
@@ -14146,48 +13229,52 @@
                     "url": "https://usegalaxy.fr/",
                     "usegalaxy": false
                 },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
                 }
             ],
             "inexact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
                 {
                     "name": "GalaxyTrakr",
                     "url": "https://galaxytrakr.org/",
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 }
             ]
         },
         "symlink": null,
         "tags": [
+            "illumina",
             "assembly",
-            "pacbio"
+            "microgalaxy"
         ],
-        "time_estimation": "6h",
-        "title": "Genome assembly using PacBio data",
+        "time_estimation": "2h",
+        "title": "Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy3"
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/2022.09+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2",
+            "upload1"
         ],
         "topic_name": "assembly",
         "topic_name_human": "Assembly",
@@ -14197,300 +13284,283 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "flye-assembly",
+        "tutorial_name": "mrsa-illumina",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/flye-assembly/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/flye-assembly/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/flye-assembly/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-illumina/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-illumina/tutorial.json"
         },
-        "version": 8,
+        "version": 15,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 118,
-        "visitors": 3238,
+        "visit_duration": 227,
+        "visitors": 6735,
         "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "",
-                        "name": "Erwan Corre"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "",
-                        "name": "St\u00e9phanie Robin"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "",
-                        "name": "Anthony Bretaudeau"
+                        "identifier": "https://orcid.org/0000-0003-2255-1631",
+                        "name": "Bazante Sanders"
                     },
                     {
                         "class": "Person",
-                        "identifier": "",
-                        "name": "Alexandre Cormier"
+                        "identifier": "https://orcid.org/0000-0001-9852-1987",
+                        "name": "B\u00e9r\u00e9nice Batut"
                     }
                 ],
-                "description": "Genome Assembly using PacBio data and Flye assembler",
+                "description": "Genome Assembly of MRSA using Illumina MiSeq Data",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPacBio reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genome\"]\n  2[label=\"Flye\"]\n  0 -> 2 [label=\"output\"]\n  kd7badcb24d384ddab89bb4bd3ffbc64a[color=lightseagreen,label=\"Output\\nFlye on input dataset(s): assembly info\"]\n  2 -> kd7badcb24d384ddab89bb4bd3ffbc64a\n  kc8f96c22e06e4fecbbfad993b7b103eb[color=lightseagreen,label=\"Output\\nFlye on input dataset(s): consensus\"]\n  2 -> kc8f96c22e06e4fecbbfad993b7b103eb\n  ka288fb935aa5423189e4958c57106978[color=lightseagreen,label=\"Output\\nFlye on input dataset(s): graphical fragment assembly\"]\n  2 -> ka288fb935aa5423189e4958c57106978\n  k0e0641815cd442c898f9fe417303956c[color=lightseagreen,label=\"Output\\nFlye on input dataset(s): assembly graph\"]\n  2 -> k0e0641815cd442c898f9fe417303956c\n  3[label=\"Fasta Statistics\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Busco\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Fasta Statistics\"]\n  2 -> 5 [label=\"consensus\"]\n  6[label=\"Quast\"]\n  1 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"consensus\"]\n  kbea191cbf88d4103b8fab3683d77cc93[color=lightseagreen,label=\"Output\\nQuast on input dataset(s):  HTML report\"]\n  6 -> kbea191cbf88d4103b8fab3683d77cc93\n  7[label=\"Busco\"]\n  2 -> 7 [label=\"consensus\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDRR187559_2\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDRR187559_1\"]\n  2[label=\"FastQC\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"fastp\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  k45c8ff4e7e474c698e46863dc3a688d3[color=lightseagreen,label=\"Output\\nfastp_json\"]\n  3 -> k45c8ff4e7e474c698e46863dc3a688d3\n  4[label=\"FastQC\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Shovill\"]\n  3 -> 5 [label=\"out1\"]\n  3 -> 5 [label=\"out2\"]\n  kcec0f15e2836442abfef55106e8a5d18[color=lightseagreen,label=\"Output\\nshovill_log\"]\n  5 -> kcec0f15e2836442abfef55106e8a5d18\n  6[label=\"Quast\"]\n  5 -> 6 [label=\"contigs\"]\n  k14ee7f86cd6747ad825ecbbb5737fbda[color=lightseagreen,label=\"Output\\nquast_output\"]\n  6 -> k14ee7f86cd6747ad825ecbbb5737fbda\n  7[label=\"Bandage Image\"]\n  5 -> 7 [label=\"contigs_graph\"]\n  8[label=\"Bandage Info\"]\n  5 -> 8 [label=\"contigs_graph\"]\n  ka1b831a624a34643b0d2fafac0deba79[color=lightseagreen,label=\"Output\\nbandage_info_output\"]\n  8 -> ka1b831a624a34643b0d2fafac0deba79\n}",
                 "history": [
                     {
-                        "hash": "6e12dcba4982df8a8c154f51242a45ae66e32aa9",
-                        "message": "update quast",
+                        "hash": "597f8ce954083c7cd4e43765b6c4709619637e6a",
+                        "message": "Add Bazante's ORCID",
+                        "num": 7,
+                        "short_hash": "597f8ce95",
+                        "unix": "1706018263"
+                    },
+                    {
+                        "hash": "03e4290900ade23b2dffb3f61ea2875a64f2c396",
+                        "message": "Fix workflows",
+                        "num": 6,
+                        "short_hash": "03e429090",
+                        "unix": "1706004257"
+                    },
+                    {
+                        "hash": "c88bcbb6f04ad1847e0747f7fb9256ee0ec858de",
+                        "message": "Add license and creator to workflows",
+                        "num": 5,
+                        "short_hash": "c88bcbb6f",
+                        "unix": "1705678137"
+                    },
+                    {
+                        "hash": "5fbcc03b0d2408af8c03f0c7867791b47b4cceff",
+                        "message": "Update the MRSA short-read assembly tutorial",
                         "num": 4,
-                        "short_hash": "6e12dcba4",
-                        "unix": "1638177109"
+                        "short_hash": "5fbcc03b0",
+                        "unix": "1705072112"
                     },
                     {
-                        "hash": "a086911d08bd6aaaee479fc075bb8d64ff1265a6",
-                        "message": "update workflow + minor changes",
+                        "hash": "31848c0ae9109d020ddee510ad5a1c374c3df96e",
+                        "message": "fix linting issues",
                         "num": 3,
-                        "short_hash": "a086911d0",
-                        "unix": "1637938578"
+                        "short_hash": "31848c0ae",
+                        "unix": "1610039782"
                     },
                     {
-                        "hash": "b8606bace2788251cf703b48a07c34c5897bfc23",
-                        "message": "flye-assembly workflow modified with new tools versions",
+                        "hash": "9c83730d5b61b1ed51890ee8c00dbf73834d7b54",
+                        "message": "Finish illumina version",
                         "num": 2,
-                        "short_hash": "b8606bace",
-                        "unix": "1637931503"
+                        "short_hash": "9c83730d5",
+                        "unix": "1610038238"
                     },
                     {
-                        "hash": "e817e8cfdf08abdb2d4dee03fd7461c008807ee2",
-                        "message": "added flye assembly tutorial",
+                        "hash": "c1175777fc34b261481e16516de8fde7c890c4ae",
+                        "message": "Add Illumina version of tutorial",
                         "num": 1,
-                        "short_hash": "e817e8cfd",
-                        "unix": "1635261060"
+                        "short_hash": "c1175777f",
+                        "unix": "1608293515"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "PacBio reads in fastq format",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "PacBio reads in fastq format",
-                                "name": "PacBio reads"
+                                "description": "",
+                                "name": "DRR187559_2"
                             }
                         ],
-                        "label": "PacBio reads",
-                        "name": "Input dataset",
+                        "label": "DRR187559_2",
+                        "name": "DRR187559_2",
                         "outputs": [],
                         "position": {
-                            "bottom": 242.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 253.5,
-                            "right": 453.5,
-                            "top": 160,
-                            "width": 200,
-                            "x": 253.5,
-                            "y": 160
+                            "left": 0,
+                            "top": 216
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fastqsanger.gz\"]}",
+                        "tool_state": "{\"name\": \"DRR187559_2\", \"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "022ec16e-3c15-45db-99c0-167a7d3121fe",
+                        "uuid": "8e9c45ae-139a-4a69-af24-f0d9f58041cc",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "Reference genome from JGI",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Reference genome from JGI",
-                                "name": "Reference genome"
+                                "description": "",
+                                "name": "DRR187559_1"
                             }
                         ],
-                        "label": "Reference genome",
-                        "name": "Input dataset",
+                        "label": "DRR187559_1",
+                        "name": "DRR187559_1",
                         "outputs": [],
                         "position": {
-                            "bottom": 418.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 255,
-                            "right": 455,
-                            "top": 336,
-                            "width": 200,
-                            "x": 255,
-                            "y": 336
+                            "left": 0,
+                            "top": 339
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"name\": \"DRR187559_1\", \"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "abf0462d-3f02-4be7-8079-a97f496b4683",
+                        "uuid": "1290afbe-52b9-447f-ac30-6f8c92f93ff5",
+                        "when": null,
                         "workflow_outputs": []
                     }
                 ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPacBio reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Flye\"];\n  0 -->|output| 2;\n  d7badcb2-4d38-4dda-b89b-b4bd3ffbc64a[\"Output\\nFlye on input dataset(s): assembly info\"];\n  2 --> d7badcb2-4d38-4dda-b89b-b4bd3ffbc64a;\n  style d7badcb2-4d38-4dda-b89b-b4bd3ffbc64a stroke:#2c3143,stroke-width:4px;\n  c8f96c22-e06e-4fec-bbfa-d993b7b103eb[\"Output\\nFlye on input dataset(s): consensus\"];\n  2 --> c8f96c22-e06e-4fec-bbfa-d993b7b103eb;\n  style c8f96c22-e06e-4fec-bbfa-d993b7b103eb stroke:#2c3143,stroke-width:4px;\n  a288fb93-5aa5-4231-89e4-958c57106978[\"Output\\nFlye on input dataset(s): graphical fragment assembly\"];\n  2 --> a288fb93-5aa5-4231-89e4-958c57106978;\n  style a288fb93-5aa5-4231-89e4-958c57106978 stroke:#2c3143,stroke-width:4px;\n  0e064181-5cd4-42c8-98f9-fe417303956c[\"Output\\nFlye on input dataset(s): assembly graph\"];\n  2 --> 0e064181-5cd4-42c8-98f9-fe417303956c;\n  style 0e064181-5cd4-42c8-98f9-fe417303956c stroke:#2c3143,stroke-width:4px;\n  3[\"Fasta Statistics\"];\n  1 -->|output| 3;\n  4[\"Busco\"];\n  1 -->|output| 4;\n  5[\"Fasta Statistics\"];\n  2 -->|consensus| 5;\n  6[\"Quast\"];\n  1 -->|output| 6;\n  2 -->|consensus| 6;\n  bea191cb-f88d-4103-b8fa-b3683d77cc93[\"Output\\nQuast on input dataset(s):  HTML report\"];\n  6 --> bea191cb-f88d-4103-b8fa-b3683d77cc93;\n  style bea191cb-f88d-4103-b8fa-b3683d77cc93 stroke:#2c3143,stroke-width:4px;\n  7[\"Busco\"];\n  2 -->|consensus| 7;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Genome Assembly using PacBio data",
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nDRR187559_2\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nDRR187559_1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"FastQC\"];\n  0 -->|output| 2;\n  3[\"fastp\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  45c8ff4e-7e47-4c69-8e46-863dc3a688d3[\"Output\\nfastp_json\"];\n  3 --> 45c8ff4e-7e47-4c69-8e46-863dc3a688d3;\n  style 45c8ff4e-7e47-4c69-8e46-863dc3a688d3 stroke:#2c3143,stroke-width:4px;\n  4[\"FastQC\"];\n  1 -->|output| 4;\n  5[\"Shovill\"];\n  3 -->|out1| 5;\n  3 -->|out2| 5;\n  cec0f15e-2836-442a-bfef-55106e8a5d18[\"Output\\nshovill_log\"];\n  5 --> cec0f15e-2836-442a-bfef-55106e8a5d18;\n  style cec0f15e-2836-442a-bfef-55106e8a5d18 stroke:#2c3143,stroke-width:4px;\n  6[\"Quast\"];\n  5 -->|contigs| 6;\n  14ee7f86-cd67-47ad-825e-cbbb5737fbda[\"Output\\nquast_output\"];\n  6 --> 14ee7f86-cd67-47ad-825e-cbbb5737fbda;\n  style 14ee7f86-cd67-47ad-825e-cbbb5737fbda stroke:#2c3143,stroke-width:4px;\n  7[\"Bandage Image\"];\n  5 -->|contigs_graph| 7;\n  8[\"Bandage Info\"];\n  5 -->|contigs_graph| 8;\n  a1b831a6-24a3-4643-b0d2-fafac0deba79[\"Output\\nbandage_info_output\"];\n  8 --> a1b831a6-24a3-4643-b0d2-fafac0deba79;\n  style a1b831a6-24a3-4643-b0d2-fafac0deba79 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Genome Assembly of MRSA using Illumina MiSeq Data",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
                         "errors": null,
-                        "id": 2,
+                        "id": 3,
                         "input_connections": {
-                            "inputs": {
+                            "single_paired|in1": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "single_paired|in2": {
                                 "id": 0,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Flye",
+                        "name": "fastp",
                         "outputs": [
                             {
-                                "name": "consensus",
-                                "type": "fasta"
+                                "name": "out1",
+                                "type": "input"
                             },
                             {
-                                "name": "assembly_graph",
-                                "type": "graph_dot"
+                                "name": "out2",
+                                "type": "input"
                             },
                             {
-                                "name": "assembly_gfa",
-                                "type": "txt"
+                                "name": "report_html",
+                                "type": "html"
                             },
                             {
-                                "name": "assembly_info",
-                                "type": "tabular"
+                                "name": "report_json",
+                                "type": "json"
                             }
                         ],
                         "position": {
-                            "bottom": 441.8999938964844,
-                            "height": 286.3999938964844,
-                            "left": 547.5,
-                            "right": 747.5,
-                            "top": 155.5,
-                            "width": 200,
-                            "x": 547.5,
-                            "y": 155.5
+                            "left": 280,
+                            "top": 296
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "276f5d8712d5",
-                            "name": "flye",
-                            "owner": "bgruening",
+                            "changeset_revision": "65b93b623c77",
+                            "name": "fastp",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"asm\": {\"asm_select\": \"false\", \"__current_case__\": 1}, \"generate_log\": \"false\", \"inputs\": {\"__class__\": \"ConnectedValue\"}, \"iterations\": \"1\", \"keep_haplotypes\": \"false\", \"meta\": \"false\", \"min_overlap\": null, \"mode_conditional\": {\"mode\": \"--pacbio-raw\", \"__current_case__\": 3}, \"scaffold\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.9+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": \"30\", \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": null, \"umi_len\": null, \"umi_prefix\": null}, \"cutting_by_quality_options\": {\"cut_by_quality5\": true, \"cut_by_quality3\": true, \"cut_window_size\": \"4\", \"cut_mean_quality\": \"20\"}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired\", \"__current_case__\": 1, \"in1\": {\"__class__\": \"ConnectedValue\"}, \"in2\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": null, \"adapter_sequence2\": null}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.23.2+galaxy0",
                         "type": "tool",
-                        "uuid": "b46b2319-5fa8-4055-817f-15eea86c4049",
+                        "uuid": "a3f526cd-bd95-4a6f-9fc3-8624dfc49323",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Flye on input dataset(s): assembly info",
-                                "output_name": "assembly_info",
-                                "uuid": "d7badcb2-4d38-4dda-b89b-b4bd3ffbc64a"
-                            },
-                            {
-                                "label": "Flye on input dataset(s): consensus",
-                                "output_name": "consensus",
-                                "uuid": "c8f96c22-e06e-4fec-bbfa-d993b7b103eb"
-                            },
-                            {
-                                "label": "Flye on input dataset(s): graphical fragment assembly",
-                                "output_name": "assembly_gfa",
-                                "uuid": "a288fb93-5aa5-4231-89e4-958c57106978"
-                            },
-                            {
-                                "label": "Flye on input dataset(s): assembly graph",
-                                "output_name": "assembly_graph",
-                                "uuid": "0e064181-5cd4-42c8-98f9-fe417303956c"
+                                "label": "fastp_json",
+                                "output_name": "report_json",
+                                "uuid": "45c8ff4e-7e47-4c69-8e46-863dc3a688d3"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2",
                         "errors": null,
                         "id": 5,
                         "input_connections": {
-                            "fasta": {
-                                "id": 2,
-                                "output_name": "consensus"
+                            "library|R1": {
+                                "id": 3,
+                                "output_name": "out1"
+                            },
+                            "library|R2": {
+                                "id": 3,
+                                "output_name": "out2"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Fasta Statistics",
+                        "name": "Shovill",
                         "outputs": [
                             {
-                                "name": "stats_output",
-                                "type": "tabular"
+                                "name": "shovill_std_log",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "contigs",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "contigs_graph",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 278.3999938964844,
-                            "height": 154.39999389648438,
-                            "left": 905,
-                            "right": 1105,
-                            "top": 124,
-                            "width": 200,
-                            "x": 905,
-                            "y": 124
+                            "left": 560,
+                            "top": 351
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "0dbb995c7d35",
-                            "name": "fasta_stats",
+                            "changeset_revision": "ee17a294d3a3",
+                            "name": "shovill",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gaps_option\": \"false\", \"genome_size\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0",
+                        "tool_state": "{\"__input_ext\": \"fastq.gz\", \"adv\": {\"namefmt\": \"contig%05d\", \"depth\": \"100\", \"gsize\": \"2914567\", \"kmers\": \"\", \"opts\": \"\", \"keep_files\": {\"nocorr\": \"no_correction\", \"__current_case__\": 0}, \"minlen\": \"0\", \"mincov\": \"2\"}, \"assembler\": \"spades\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"library\": {\"lib_type\": \"paired\", \"__current_case__\": 0, \"R1\": {\"__class__\": \"ConnectedValue\"}, \"R2\": {\"__class__\": \"ConnectedValue\"}}, \"log\": true, \"trim\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.0+galaxy2",
                         "type": "tool",
-                        "uuid": "6ec5c36e-0b3d-41b9-9cc8-899350540545",
+                        "uuid": "2676d037-3faf-4974-8357-1113ff27de62",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "stats_output",
-                                "uuid": "400afe45-b895-41aa-a2b9-3c222c344f7b"
+                                "label": "shovill_log",
+                                "output_name": "shovill_std_log",
+                                "uuid": "cec0f15e-2836-442a-bfef-55106e8a5d18"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
                         "errors": null,
                         "id": 6,
                         "input_connections": {
-                            "assembly|ref|r": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "in|inputs": {
-                                "id": 2,
-                                "output_name": "consensus"
+                            "mode|in|inputs": {
+                                "id": 5,
+                                "output_name": "contigs"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Quast",
-                                "name": "in"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
                         "name": "Quast",
                         "outputs": [
@@ -14500,233 +13570,437 @@
                             }
                         ],
                         "position": {
-                            "bottom": 593,
-                            "height": 266,
-                            "left": 902.5,
-                            "right": 1102.5,
-                            "top": 327,
-                            "width": 200,
-                            "x": 902.5,
-                            "y": 327
+                            "left": 840,
+                            "top": 302
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy3",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "7594365c546b",
+                            "changeset_revision": "72472698a2df",
                             "name": "quast",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": \"false\", \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": \"true\", \"fragmented_max_indent\": null}, \"alignments\": {\"use_all_alignments\": \"false\", \"min_alignment\": \"65\", \"min_identity\": \"95.0\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": \"false\", \"upper_bound_assembly\": \"false\", \"upper_bound_min_con\": null}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"true\", \"__current_case__\": 0, \"r\": {\"__class__\": \"RuntimeValue\"}, \"features\": {\"__class__\": \"RuntimeValue\"}, \"operons\": {\"__class__\": \"RuntimeValue\"}, \"k_mer\": {\"k_mer_stats\": \"\", \"__current_case__\": 1}, \"circos\": \"false\"}, \"orga_type\": \"--fungus\"}, \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": \"false\", \"conserved_genes_finding\": \"false\"}, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"RuntimeValue\"}}, \"large\": \"false\", \"min_contig\": \"500\", \"output_files\": [\"html\"], \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}, \"split_scaffolds\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.0.2+galaxy3",
+                        "tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"false\", \"__current_case__\": 1, \"est_ref_size\": null}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": false}, \"large\": false, \"min_contig\": \"500\", \"mode\": {\"mode\": \"individual\", \"__current_case__\": 0, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": \"html\", \"split_scaffolds\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.2.0+galaxy1",
                         "type": "tool",
-                        "uuid": "f734c70b-03c8-4fc3-8350-27a7230cbd58",
+                        "uuid": "0fa4aa47-d6f1-4b9a-9db9-91131f80a410",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Quast on input dataset(s):  HTML report",
+                                "label": "quast_output",
                                 "output_name": "report_html",
-                                "uuid": "bea191cb-f88d-4103-b8fa-b3683d77cc93"
+                                "uuid": "14ee7f86-cd67-47ad-825e-cbbb5737fbda"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/2022.09+galaxy2",
                         "errors": null,
-                        "id": 7,
+                        "id": 8,
                         "input_connections": {
-                            "input": {
-                                "id": 2,
-                                "output_name": "consensus"
+                            "input_file": {
+                                "id": 5,
+                                "output_name": "contigs_graph"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Busco",
+                        "name": "Bandage Info",
                         "outputs": [
                             {
-                                "name": "busco_sum",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "busco_table",
+                                "name": "outfile",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 847.1999969482422,
-                            "height": 205.1999969482422,
-                            "left": 906.5,
-                            "right": 1106.5,
-                            "top": 642,
-                            "width": 200,
-                            "x": 906.5,
-                            "y": 642
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionbusco_table": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "busco_table"
-                            }
+                            "left": 840,
+                            "top": 610
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/2022.09+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "46ae58b1d792",
-                            "name": "busco",
+                            "changeset_revision": "ddddce450736",
+                            "name": "bandage",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": \"mucorales_odb10\"}, \"outputs\": [\"short_summary\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.2.2+galaxy2",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"tsv\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2022.09+galaxy2",
                         "type": "tool",
-                        "uuid": "fb896bc9-5ebd-41a1-82a7-1dae23e23dac",
+                        "uuid": "f191da8d-81fe-499e-beee-abb31d05ba71",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "busco_sum",
-                                "uuid": "5a62f2bb-17ec-4091-985f-bd9c69f9fe61"
+                                "label": "bandage_info_output",
+                                "output_name": "outfile",
+                                "uuid": "a1b831a6-24a3-4643-b0d2-fafac0deba79"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/flye-assembly",
-                "path": "topics/assembly/tutorials/flye-assembly/workflows/main_workflow.ga",
+                "parent_id": "assembly/mrsa-illumina",
+                "path": "topics/assembly/tutorials/mrsa-illumina/workflows/main_workflow.ga",
                 "tags": [
-                    "assembly"
+                    "assembly",
+                    "microgalaxy"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "Genome Assembly using PacBio data",
+                "tests": true,
+                "title": "Genome Assembly of MRSA using Illumina MiSeq Data",
                 "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-flye-assembly/versions/main-workflow",
-                "tutorial_id": "flye-assembly",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/flye-assembly/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/flye-assembly/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "assembly-flye-assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-mrsa-illumina/versions/main-workflow",
+                "tutorial_id": "mrsa-illumina",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/mrsa-illumina/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/mrsa-illumina/workflows/main_workflow.html",
+                "version": 2,
+                "wfid": "assembly-mrsa-illumina",
                 "wfname": "main-workflow",
                 "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy3"
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/2022.09+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2"
                 ],
-                "workflowhub_id": "1131"
+                "workflowhub_id": "1135"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/5702408"
+        "zenodo_link": "https://zenodo.org/record/10669812"
     },
     {
+        "abbreviations": {
+            "G10K": "Genome 10K",
+            "GWS": "Galaxy Workflow System",
+            "Hi-C": "all-versus-all chromatin conformation capture",
+            "HiFi": "high fidelity reads",
+            "QV": "assembly consensus quality",
+            "VGP": "Vertebrate Genome Project",
+            "alternate assembly": "alternate loci not represented in the primary assembly",
+            "collection": "Galaxy's way to represent multiple datasets as a single interface entity",
+            "collections": "Galaxy's way to represent multiple datasets as a single interface entity",
+            "contigs": "contiguous sequences in an assembly",
+            "primary assembly": "homozygous regions of the genome plus one set of alleles for the heterozygous loci",
+            "scaffold": "one or more contigs joined by gap sequence",
+            "scaffolds": "one or more contigs joined by gap sequence",
+            "unitig": "A uniquely assembleable subset of overlapping fragments. A unitig is an assembly of fragments for which there are no competing internal overlaps. A unitig is either a correctly assembled portion of a contig or a collapsed assembly of several high-fidelity copies of a repeat."
+        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "quast",
+                    "owner": "iuc",
+                    "revisions": "72472698a2df",
+                    "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: quast\n  owner: iuc\n  revisions: 72472698a2df\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/vgp_workflow_training/tutorial.json",
+        "contributors": [
+            {
+                "email": "delphine.lariviere@galaxy.org",
+                "id": "delphine-l",
+                "joined": "2017-09",
+                "name": "Delphine Lariviere",
+                "orcid": "0000-0001-6421-3484",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
+            },
+            {
+                "email": "a.ostrovsky@mac.com",
+                "id": "astrovsky01",
+                "joined": "2019-06",
+                "name": "Alex Ostrovsky",
+                "orcid": "0000-0002-7901-7109",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/astrovsky01/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/astrovsky01.json"
+            },
+            {
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "gallardoalba",
+                "joined": "2020-11",
+                "name": "Crist\u00f3bal Gallardo",
+                "orcid": "0000-0002-5752-2155",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
+            },
+            {
+                "id": "pickettbd",
+                "joined": "2022-01",
+                "name": "Brandon Pickett",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pickettbd/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pickettbd.json"
+            },
+            {
+                "id": "abueg",
+                "joined": "2022-01",
+                "name": "Linelle Abueg",
+                "orcid": "0000-0002-6879-3954",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abueg/",
+                "twitter": "llabueg",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abueg.json"
+            },
+            {
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
+                "joined": "2017-09",
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+            }
+        ],
+        "dir": "topics/assembly/tutorials/vgp_workflow_training",
+        "edam_operation": [
+            "Sequence assembly validation",
+            "Visualisation"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "Galaxy@AuBi",
+            "GalaxyTrakr",
+            "MISSISSIPPI",
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "assembly/vgp_workflow_training",
+        "inexact_supported_servers": [
+            "HyPhy HIV NGS Tools",
+            "UseGalaxy.be"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "The VGP pipeline allows to generate error-free, near gapless reference-quality genome assemblies",
+            "The assembly can be divided in four main stages: genome profile analysis, HiFi long read phased assembly with hifiasm, Bionano hybrid scaffolding and Hi-C hybrid scaffolding"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-19",
+        "objectives": [
+            "Learn the tools necessary to perform a de novo assembly of a vertebrate genome",
+            "Evaluate the quality of the assembly"
+        ],
+        "pageviews": 3049,
+        "pub_date": "2022-04-06",
+        "questions": [
+            "What combination of tools can produce the highest quality assembly of vertebrate genomes?",
+            "How can we evaluate how good it is?"
+        ],
+        "recordings": [
+            {
+                "bot-timestamp": 1726177737,
+                "captioners": [
+                    "abueg"
+                ],
+                "date": "2024-09-12",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "1H56M",
+                "speakers": [
+                    "abueg"
+                ],
+                "youtube_id": "LO-migvwcM"
+            }
+        ],
+        "short_id": "T00040",
+        "short_tools": [
+            "quast"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "unique",
-                    "owner": "bgruening",
-                    "revisions": "7ce75adb93be",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "bamtools",
-                    "owner": "devteam",
-                    "revisions": "befc9dad4ca8",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "bowtie2",
-                    "owner": "devteam",
-                    "revisions": "f6877ad76b00",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "bowtie2",
-                    "owner": "devteam",
-                    "revisions": "03e9b2fbc005",
-                    "tool_panel_section_label": "Mapping",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "pacbio",
+            "eukaryote",
+            "VGP"
+        ],
+        "time_estimation": "2h",
+        "title": "Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
+        ],
+        "topic_name": "assembly",
+        "topic_name_human": "Assembly",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "vgp_workflow_training",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/vgp_workflow_training/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/vgp_workflow_training/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/vgp_workflow_training/tutorial.json"
+        },
+        "version": 22,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 164,
+        "visitors": 2135,
+        "zenodo_link": "https://zenodo.org/record/5887339"
+    },
+    {
+        "abbreviations": {
+            "SVs": "Structural Variations"
+        },
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "flye",
+                    "owner": "bgruening",
+                    "revisions": "cb8dfd28c16f",
+                    "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "fastqc",
                     "owner": "devteam",
-                    "revisions": "3d0c7bdf12f5",
+                    "revisions": "5ec9f6bceaee",
                     "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "bandage",
                     "owner": "iuc",
-                    "revisions": "21e491ad532a",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bandage",
-                    "owner": "iuc",
-                    "revisions": "21e491ad532a",
+                    "revisions": "ddddce450736",
                     "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "collection_column_join",
+                    "name": "bwa_mem2",
                     "owner": "iuc",
-                    "revisions": "3ddd99c7efee",
-                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "revisions": "bfaa0d22c2e4",
+                    "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "coverm_contig",
+                    "name": "fastp",
                     "owner": "iuc",
-                    "revisions": "6941d0d453ba",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "revisions": "65b93b623c77",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "filter_tabular",
+                    "name": "filtlong",
                     "owner": "iuc",
-                    "revisions": "34d29339abab",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "revisions": "8880fb74ef56",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "megahit",
+                    "name": "filtlong",
                     "owner": "iuc",
-                    "revisions": "14ddfc8ffb93",
-                    "tool_panel_section_label": "Assembly",
+                    "revisions": "1f296803dfa3",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "megahit_contig2fastg",
+                    "name": "nanoplot",
                     "owner": "iuc",
-                    "revisions": "4ec5b3777508",
-                    "tool_panel_section_label": "Proteomics",
+                    "revisions": "0f1c34698076",
+                    "tool_panel_section_label": "Nanopore",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ngsutils_bam_filter",
+                    "name": "polypolish",
                     "owner": "iuc",
-                    "revisions": "2e957d4c4b95",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "revisions": "f355085dd2aa",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "quast",
+                    "name": "porechop",
                     "owner": "iuc",
-                    "revisions": "3061c8b029e5",
-                    "tool_panel_section_label": "Assembly",
+                    "revisions": "93d623d9979c",
+                    "tool_panel_section_label": "Nanopore",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
@@ -14735,52 +14009,37 @@
                     "revisions": "72472698a2df",
                     "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "seqtk",
-                    "owner": "iuc",
-                    "revisions": "3da72230c066",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cutadapt",
-                    "owner": "lparsons",
-                    "revisions": "5915ea1ec9b1",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "metaspades",
-                    "owner": "nml",
-                    "revisions": "fd128c111ab0",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unique\n  owner: bgruening\n  revisions: 7ce75adb93be\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools\n  owner: devteam\n  revisions: befc9dad4ca8\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie2\n  owner: devteam\n  revisions: f6877ad76b00\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie2\n  owner: devteam\n  revisions: 03e9b2fbc005\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: 21e491ad532a\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: 21e491ad532a\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_column_join\n  owner: iuc\n  revisions: 3ddd99c7efee\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: coverm_contig\n  owner: iuc\n  revisions: 6941d0d453ba\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filter_tabular\n  owner: iuc\n  revisions: 34d29339abab\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: megahit\n  owner: iuc\n  revisions: 14ddfc8ffb93\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: megahit_contig2fastg\n  owner: iuc\n  revisions: 4ec5b3777508\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ngsutils_bam_filter\n  owner: iuc\n  revisions: 2e957d4c4b95\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 3061c8b029e5\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 72472698a2df\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 5915ea1ec9b1\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaspades\n  owner: nml\n  revisions: fd128c111ab0\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/metagenomics-assembly/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: flye\n  owner: bgruening\n  revisions: cb8dfd28c16f\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_mem2\n  owner: iuc\n  revisions: bfaa0d22c2e4\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filtlong\n  owner: iuc\n  revisions: 8880fb74ef56\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filtlong\n  owner: iuc\n  revisions: 1f296803dfa3\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: 0f1c34698076\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: polypolish\n  owner: iuc\n  revisions: f355085dd2aa\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: porechop\n  owner: iuc\n  revisions: 93d623d9979c\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 72472698a2df\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-nanopore/tutorial.json",
         "contributions": {
             "authorship": [
-                "plushz",
+                "bazante1",
                 "bebatut"
             ],
+            "editing": [
+                "hexylena",
+                "bazante1",
+                "shiltemann",
+                "miaomiaozhou88"
+            ],
             "funding": [
-                "gallantries"
+                "avans-atgm",
+                "abromics"
             ]
         },
         "contributors": [
             {
                 "affiliations": [
-                    "uni-freiburg"
+                    "avans-atgm"
                 ],
-                "id": "plushz",
-                "joined": "2022-03",
-                "name": "Polina Polunina",
-                "orcid": "0000-0002-0507-4602",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/plushz/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/plushz.json"
+                "id": "bazante1",
+                "joined": "2020-12",
+                "name": "Bazante Sanders",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
             },
             {
                 "affiliations": [
@@ -14809,193 +14068,257 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             },
             {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "affiliations": [
+                    "avans-atgm"
+                ],
+                "id": "bazante1",
+                "joined": "2020-12",
+                "name": "Bazante Sanders",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
+            },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
+            {
+                "email": "m.zhou1@avans.nl",
+                "id": "miaomiaozhou88",
+                "joined": "2020-12",
+                "name": "Miaomiao Zhou",
+                "orcid": "0000-0003-4426-1758",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/miaomiaozhou88/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/miaomiaozhou88.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/logo-avans.png",
+                "former_members": [
+                    "dirowa",
+                    "hexylena"
+                ],
+                "id": "avans-atgm",
+                "joined": "2020-11",
                 "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
+                    "bazante1"
                 ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+                "name": "Avans Hogeschool",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/",
+                "ror": "015d5s513",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/abromics.png",
+                "funder": true,
+                "github": false,
+                "id": "abromics",
+                "joined": "2024-01",
+                "name": "ABRomics",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abromics/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/abromics.json"
             }
         ],
-        "dir": "topics/assembly/tutorials/metagenomics-assembly",
+        "dir": "topics/assembly/tutorials/mrsa-nanopore",
         "edam_ontology": [
-            "topic_3174",
-            "topic_0196"
+            "topic_0196",
+            "topic_3673",
+            "topic_3305",
+            "topic_0622",
+            "topic_3301",
+            "topic_4013"
         ],
         "edam_operation": [
+            "Scatter plot plotting",
+            "Sequencing error detection",
+            "Sequence alignment",
             "Visualisation",
-            "Sequencing quality control",
-            "Primer removal",
-            "Sequence file editing",
-            "Formatting",
+            "Cross-assembly",
             "Read mapping",
-            "Sequence assembly validation",
-            "Sequence composition calculation",
-            "Sequence assembly visualisation",
-            "Local alignment",
+            "Sequencing quality control",
             "Genome assembly",
-            "Sequence trimming",
-            "Statistical calculation",
+            "De-novo assembly",
+            "Box-Whisker plot plotting",
             "Sequence contamination filtering",
-            "Sequence alignment analysis",
-            "Read pre-processing",
-            "Data handling",
-            "Variant calling"
+            "Sequence assembly validation",
+            "Mapping assembly",
+            "Statistical calculation",
+            "Sequence assembly visualisation",
+            "Filtering",
+            "Sequence composition calculation"
         ],
         "edam_topic": [
-            "Metagenomics",
-            "Sequence assembly"
+            "Sequence assembly",
+            "Whole genome sequencing",
+            "Public health and epidemiology",
+            "Genomics",
+            "Microbiology",
+            "Antimicrobial Resistance"
+        ],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
         ],
-        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "genome-annotation",
+                "tutorials": [
+                    "amr-gene-detection"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "history-to-workflow"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "assembly/metagenomics-assembly",
+        "id": "assembly/mrsa-nanopore",
         "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu"
+            "UseGalaxy.cz"
         ],
         "js_requirements": {
-            "mathjax": 25185,
+            "mathjax": 11271,
             "mermaid": false
         },
         "key_points": [
-            "Assembly groups reads into contigs and scafolds.",
-            "De Brujin Graphs use k-mers to assembly reads",
-            "MetaSPAdes and MEGAHIT are assemblers",
-            "Quast is the tool to assess the assembly quality"
+            "Nanopore produces fantastic assemblies but with low quality data",
+            "Annotation with Prokka is very easy"
         ],
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-18",
+        "mod_date": "2024-03-13",
         "objectives": [
-            "Describe what an assembly is",
-            "Describe what de-replication is",
-            "Explain the difference between co-assembly and individual assembly",
-            "Explain the difference between reads, contigs and scaffolds",
-            "Explain how tools based on De Bruijn graph work",
-            "Apply appropriate tools for analyzing the quality of metagenomic data",
-            "Construct and apply simple assembly pipelines on short read data",
-            "Apply appropriate tools for analyzing the quality of metagenomic assembly",
-            "Evaluate the Quality of the Assembly with Quast, Bowtie2, and CoverM-Genome"
+            "Run tools to evaluate sequencing data on quality and quantity",
+            "Process the output of quality control tools",
+            "Improve the quality of sequencing data",
+            "Run a tool to assemble a bacterial genome using short reads",
+            "Run tools to assess the quality of an assembly",
+            "Understand the outputs of tools to assess the quality of an assembly"
         ],
-        "pageviews": 2,
-        "pub_date": "2024-08-18",
+        "pageviews": 10976,
+        "pub_date": "2021-03-24",
         "questions": [
-            "Why metagenomic data should be assembled?",
-            "What is the difference between co-assembly and individual assembly?",
-            "What is the difference between reads, contigs and scaffolds?",
-            "How tools based on De Bruijn graph work?",
-            "How to assess the quality of metagenomic data assembly?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "bebatut",
-                    "sophia120199"
-                ],
-                "date": "2023-05-02",
-                "galaxy_version": "23.01",
-                "length": "1H",
-                "speakers": [
-                    "bebatut"
-                ],
-                "youtube_id": "1ZYGy85Im7w"
-            }
-        ],
-        "redirect_from": [
-            "/topics/metagenomics/tutorials/metagenomics-assembly/tutorial",
-            "/short/assembly/metagenomics-assembly",
-            "/short/T00035"
+            "How to check the quality of the MinION data (together with Illumina data)?",
+            "How to perform an assembly of a bacterial genome with MinION data?",
+            "How to check the quality of an assembly?"
         ],
-        "short_id": "T00035",
+        "short_id": "T00037",
         "short_tools": [
-            "bg_uniq",
-            "megahit_contig2fastg",
-            "ngsutils_bam_filter",
-            "megahit",
-            "bowtie2",
-            "tp_cat",
-            "quast",
-            "random_lines1",
-            "collection_column_join",
-            "filter_tabular",
-            "seqtk_subseq",
-            "fastqc",
-            "bandage_info",
-            "coverm_contig",
+            "CONVERTER_bz2_to_uncompressed",
+            "fastp",
+            "filtlong",
             "bandage_image",
-            "bamtools",
-            "cutadapt",
-            "metaspades"
+            "porechop",
+            "upload1",
+            "quast",
+            "flye",
+            "nanoplot",
+            "bwa_mem2",
+            "polypolish",
+            "fastqc"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "metagenomics",
         "supported_servers": {
-            "exact": [],
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
             "inexact": [
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
                 }
             ]
         },
-        "symlink": true,
+        "symlink": null,
         "tags": [
+            "nanopore",
             "assembly",
-            "metagenomics",
+            "amr",
+            "gmod",
+            "jbrowse1",
             "microgalaxy"
         ],
-        "time_estimation": "2H",
-        "title": "Assembly of metagenomic sequencing data",
+        "time_estimation": "2h",
+        "title": "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)",
         "tools": [
-            "random_lines1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.2.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy10",
-            "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
-            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0",
+            "CONVERTER_bz2_to_uncompressed",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/polypolish/polypolish/0.5.0+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3",
             "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.15.4+galaxy2"
+            "upload1"
         ],
         "topic_name": "assembly",
         "topic_name_human": "Assembly",
@@ -15005,595 +14328,1053 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "metagenomics-assembly",
+        "tutorial_name": "mrsa-nanopore",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/metagenomics-assembly/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/metagenomics-assembly/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-nanopore/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-nanopore/tutorial.json"
         },
-        "version": 0,
+        "version": 14,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 6,
-        "visitors": 2,
+        "visit_duration": 204,
+        "visitors": 7147,
         "workflows": [
             {
-                "creators": [],
-                "description": "",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0003-2255-1631",
+                        "name": "Bazante Sanders"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0001-9852-1987",
+                        "name": "B\u00e9r\u00e9nice Batut"
+                    }
+                ],
+                "description": "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  1[label=\"metaSPAdes\"]\n  0 -> 1 [label=\"output\"]\n  k833d79ffe16f414c9c41db8dbfa8ed6b[color=lightseagreen,label=\"Output\\nmetaSPAdes on input dataset(s): Scaffolds\"]\n  1 -> k833d79ffe16f414c9c41db8dbfa8ed6b\n  k10319152d2f947d8be41f956a57e86d3[color=lightseagreen,label=\"Output\\nmetaSPAdes on input dataset(s): Assembly graph\"]\n  1 -> k10319152d2f947d8be41f956a57e86d3\n  kb1ffc3a48e394255ac57fd7cfb9c1633[color=lightseagreen,label=\"Output\\nmetaSPAdes on input dataset(s): Assembly graph with scaffolds\"]\n  1 -> kb1ffc3a48e394255ac57fd7cfb9c1633\n  kb6b74c9d5a164725a1d111c1f05ee909[color=lightseagreen,label=\"Output\\nmetaSPAdes on input dataset(s): Contigs\"]\n  1 -> kb6b74c9d5a164725a1d111c1f05ee909\n  2[label=\"MEGAHIT\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Bowtie2\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"megahit contig2fastg\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Quast\"]\n  2 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Bandage Image\"]\n  4 -> 6 [label=\"fastg\"]\n  7[label=\"Bandage Info\"]\n  4 -> 7 [label=\"fastg\"]\n  8[label=\"Column join\"]\n  7 -> 8 [label=\"outfile\"]\n}",
-                "history": [],
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nNanopore raw reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina forward raw reads\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reverse raw reads\"]\n  3[label=\"Convert compressed file to uncompressed.\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"FastQC\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"fastp\"]\n  1 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"NanoPlot\"]\n  3 -> 6 [label=\"output1\"]\n  ka97e6f3381824a3386dd6cfbb83a842d[color=lightseagreen,label=\"Output\\nnanoplot_before_filtering\"]\n  6 -> ka97e6f3381824a3386dd6cfbb83a842d\n  7[label=\"filtlong\"]\n  5 -> 7 [label=\"out1\"]\n  5 -> 7 [label=\"out2\"]\n  0 -> 7 [label=\"output\"]\n  8[label=\"Flye\"]\n  7 -> 8 [label=\"outfile\"]\n  kf12e718f1bd5490dbd41f0747aaa41a6[color=lightseagreen,label=\"Output\\nflye_assembly_info\"]\n  8 -> kf12e718f1bd5490dbd41f0747aaa41a6\n  9[label=\"NanoPlot\"]\n  7 -> 9 [label=\"outfile\"]\n  k89524090f590434d89e266f0b1a23c7c[color=lightseagreen,label=\"Output\\nnanoplot_after_filtering\"]\n  9 -> k89524090f590434d89e266f0b1a23c7c\n  10[label=\"Bandage Image\"]\n  8 -> 10 [label=\"assembly_gfa\"]\n  11[label=\"BWA-MEM2\"]\n  5 -> 11 [label=\"out2\"]\n  8 -> 11 [label=\"consensus\"]\n  12[label=\"Quast\"]\n  8 -> 12 [label=\"consensus\"]\n  kdabfb8fd87914959a9dc9b3c1e57a69c[color=lightseagreen,label=\"Output\\nquast_report_before_polishing\"]\n  12 -> kdabfb8fd87914959a9dc9b3c1e57a69c\n  13[label=\"BWA-MEM2\"]\n  5 -> 13 [label=\"out1\"]\n  8 -> 13 [label=\"consensus\"]\n  14[label=\"Polypolish\"]\n  8 -> 14 [label=\"consensus\"]\n  13 -> 14 [label=\"bam_output\"]\n  11 -> 14 [label=\"bam_output\"]\n  15[label=\"Quast\"]\n  14 -> 15 [label=\"polished_fasta\"]\n  8 -> 15 [label=\"consensus\"]\n  k4e465b5168bf42039a7c897f46c70277[color=lightseagreen,label=\"Output\\nquast_report_after_polishing\"]\n  15 -> k4e465b5168bf42039a7c897f46c70277\n}",
+                "history": [
+                    {
+                        "hash": "96393a7fcb4d6dc37d86866cf8a61c931293502f",
+                        "message": "Add MRSA Nanopore assembly tutorial to AMR learning pathway",
+                        "num": 1,
+                        "short_hash": "96393a7fc",
+                        "unix": "1709135526"
+                    }
+                ],
                 "inputs": [
                     {
-                        "annotation": "",
+                        "annotation": "Nanopore raw reads",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Input Dataset Collection"
+                                "description": "Nanopore raw reads",
+                                "name": "Nanopore raw reads"
                             }
                         ],
-                        "label": "Input Dataset Collection",
-                        "name": "Input dataset collection",
+                        "label": "Nanopore raw reads",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0.0,
-                            "top": 480
+                            "left": 65.66800632871802,
+                            "top": 217.27323322511424
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "cdb65097-d956-4715-9cd4-fadc9b0c07c5",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "c8ca2f5f-b0f4-4d90-8259-9e4796c4a35f"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"metaSPAdes\"];\n  0 -->|output| 1;\n  833d79ff-e16f-414c-9c41-db8dbfa8ed6b[\"Output\\nmetaSPAdes on input dataset(s): Scaffolds\"];\n  1 --> 833d79ff-e16f-414c-9c41-db8dbfa8ed6b;\n  style 833d79ff-e16f-414c-9c41-db8dbfa8ed6b stroke:#2c3143,stroke-width:4px;\n  10319152-d2f9-47d8-be41-f956a57e86d3[\"Output\\nmetaSPAdes on input dataset(s): Assembly graph\"];\n  1 --> 10319152-d2f9-47d8-be41-f956a57e86d3;\n  style 10319152-d2f9-47d8-be41-f956a57e86d3 stroke:#2c3143,stroke-width:4px;\n  b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633[\"Output\\nmetaSPAdes on input dataset(s): Assembly graph with scaffolds\"];\n  1 --> b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633;\n  style b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633 stroke:#2c3143,stroke-width:4px;\n  b6b74c9d-5a16-4725-a1d1-11c1f05ee909[\"Output\\nmetaSPAdes on input dataset(s): Contigs\"];\n  1 --> b6b74c9d-5a16-4725-a1d1-11c1f05ee909;\n  style b6b74c9d-5a16-4725-a1d1-11c1f05ee909 stroke:#2c3143,stroke-width:4px;\n  2[\"MEGAHIT\"];\n  0 -->|output| 2;\n  3[\"Bowtie2\"];\n  0 -->|output| 3;\n  2 -->|output| 3;\n  4[\"megahit contig2fastg\"];\n  2 -->|output| 4;\n  5[\"Quast\"];\n  2 -->|output| 5;\n  0 -->|output| 5;\n  6[\"Bandage Image\"];\n  4 -->|fastg| 6;\n  7[\"Bandage Info\"];\n  4 -->|fastg| 7;\n  8[\"Column join\"];\n  7 -->|outfile| 8;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Metagenomics assembly tutorial workflow",
-                "outputs": [
+                        "type": "data_input",
+                        "uuid": "cd4fd302-af94-4771-9b80-7c7acb6619d4",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
                     {
-                        "annotation": "",
+                        "annotation": "Illumina forward raw reads",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Input Dataset Collection"
+                                "description": "Illumina forward raw reads",
+                                "name": "Illumina forward raw reads"
                             }
                         ],
-                        "label": "Input Dataset Collection",
-                        "name": "Input dataset collection",
+                        "label": "Illumina forward raw reads",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0.0,
-                            "top": 480
+                            "left": 0,
+                            "top": 479
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "cdb65097-d956-4715-9cd4-fadc9b0c07c5",
-                        "workflow_outputs": [
+                        "type": "data_input",
+                        "uuid": "b3fe89da-544c-4066-abcb-b33d4f005796",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "Illumina reverse raw reads",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "c8ca2f5f-b0f4-4d90-8259-9e4796c4a35f"
+                                "description": "Illumina reverse raw reads",
+                                "name": "Illumina reverse raw reads"
                             }
-                        ]
-                    },
+                        ],
+                        "label": "Illumina reverse raw reads",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 602
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "16545abc-0513-4a32-9ea5-4a168875a854",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nNanopore raw reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nIllumina forward raw reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nIllumina reverse raw reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Convert compressed file to uncompressed.\"];\n  0 -->|output| 3;\n  4[\"FastQC\"];\n  0 -->|output| 4;\n  5[\"fastp\"];\n  1 -->|output| 5;\n  2 -->|output| 5;\n  6[\"NanoPlot\"];\n  3 -->|output1| 6;\n  a97e6f33-8182-4a33-86dd-6cfbb83a842d[\"Output\\nnanoplot_before_filtering\"];\n  6 --> a97e6f33-8182-4a33-86dd-6cfbb83a842d;\n  style a97e6f33-8182-4a33-86dd-6cfbb83a842d stroke:#2c3143,stroke-width:4px;\n  7[\"filtlong\"];\n  5 -->|out1| 7;\n  5 -->|out2| 7;\n  0 -->|output| 7;\n  8[\"Flye\"];\n  7 -->|outfile| 8;\n  f12e718f-1bd5-490d-bd41-f0747aaa41a6[\"Output\\nflye_assembly_info\"];\n  8 --> f12e718f-1bd5-490d-bd41-f0747aaa41a6;\n  style f12e718f-1bd5-490d-bd41-f0747aaa41a6 stroke:#2c3143,stroke-width:4px;\n  9[\"NanoPlot\"];\n  7 -->|outfile| 9;\n  89524090-f590-434d-89e2-66f0b1a23c7c[\"Output\\nnanoplot_after_filtering\"];\n  9 --> 89524090-f590-434d-89e2-66f0b1a23c7c;\n  style 89524090-f590-434d-89e2-66f0b1a23c7c stroke:#2c3143,stroke-width:4px;\n  10[\"Bandage Image\"];\n  8 -->|assembly_gfa| 10;\n  11[\"BWA-MEM2\"];\n  5 -->|out2| 11;\n  8 -->|consensus| 11;\n  12[\"Quast\"];\n  8 -->|consensus| 12;\n  dabfb8fd-8791-4959-a9dc-9b3c1e57a69c[\"Output\\nquast_report_before_polishing\"];\n  12 --> dabfb8fd-8791-4959-a9dc-9b3c1e57a69c;\n  style dabfb8fd-8791-4959-a9dc-9b3c1e57a69c stroke:#2c3143,stroke-width:4px;\n  13[\"BWA-MEM2\"];\n  5 -->|out1| 13;\n  8 -->|consensus| 13;\n  14[\"Polypolish\"];\n  8 -->|consensus| 14;\n  13 -->|bam_output| 14;\n  11 -->|bam_output| 14;\n  15[\"Quast\"];\n  14 -->|polished_fasta| 15;\n  8 -->|consensus| 15;\n  4e465b51-68bf-4203-9a7c-897f46c70277[\"Output\\nquast_report_after_polishing\"];\n  15 --> 4e465b51-68bf-4203-9a7c-897f46c70277;\n  style 4e465b51-68bf-4203-9a7c-897f46c70277 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available)",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.15.4+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
                         "errors": null,
-                        "id": 1,
+                        "id": 6,
                         "input_connections": {
-                            "singlePaired|input": {
-                                "id": 0,
-                                "output_name": "output"
+                            "mode|reads|files": {
+                                "id": 3,
+                                "output_name": "output1"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool metaSPAdes",
-                                "name": "arf"
-                            },
-                            {
-                                "description": "runtime parameter for tool metaSPAdes",
-                                "name": "arf"
-                            },
-                            {
-                                "description": "runtime parameter for tool metaSPAdes",
-                                "name": "singlePaired"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "metaSPAdes",
+                        "name": "NanoPlot",
                         "outputs": [
                             {
-                                "name": "out_ag",
-                                "type": "fastg"
+                                "name": "output_html",
+                                "type": "html"
                             },
                             {
-                                "name": "out_ags",
-                                "type": "txt"
+                                "name": "nanostats",
+                                "type": "tabular"
                             },
                             {
-                                "name": "out_cn",
-                                "type": "fasta"
+                                "name": "nanostats_post_filtering",
+                                "type": "tabular"
                             },
                             {
-                                "name": "out_sc",
-                                "type": "fasta"
+                                "name": "read_length",
+                                "type": "png"
+                            },
+                            {
+                                "name": "log_read_length",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 247.0,
-                            "top": 0
+                            "left": 598.8807084399002,
+                            "top": 268.83097889129806
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.15.4+galaxy2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "fd128c111ab0",
-                            "name": "metaspades",
-                            "owner": "nml",
+                            "changeset_revision": "0f1c34698076",
+                            "name": "nanoplot",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"additional_reads\": {\"selector\": \"false\", \"__current_case__\": 1}, \"arf\": {\"nanopore\": {\"__class__\": \"RuntimeValue\"}, \"pacbio\": {\"__class__\": \"RuntimeValue\"}}, \"kmer_cond\": {\"kmer_sel\": \"manual\", \"__current_case__\": 1, \"manual\": \"21,33,55,77\"}, \"library_number\": \"true\", \"mode_sel\": null, \"optional_output\": [\"ag\", \"ags\", \"cn\", \"sc\"], \"phred_offset\": \"auto\", \"singlePaired\": {\"sPaired\": \"paired_collection\", \"__current_case__\": 2, \"input\": {\"__class__\": \"RuntimeValue\"}, \"type_paired\": \"pe\", \"orientation\": \"fr\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.15.4+galaxy2",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"customization\": {\"color\": null, \"plots\": null, \"N50\": true}, \"filter\": {\"maxlength\": null, \"minlength\": null, \"drop_outliers\": false, \"downsample\": null, \"loglength\": false, \"percentqual\": false, \"alength\": false, \"minqual\": null, \"runtime_until\": null, \"readtype\": null, \"barcoded\": false, \"no_supplementary\": false}, \"mode\": {\"choice\": \"batch\", \"__current_case__\": 0, \"reads\": {\"type\": \"fastq\", \"__current_case__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.41.0+galaxy0",
                         "type": "tool",
-                        "uuid": "7dc08460-f398-4f1d-9f30-1736cf636a13",
+                        "uuid": "ad46f297-04f2-4959-aa09-db88cd91cc27",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "metaSPAdes on input dataset(s): Scaffolds",
-                                "output_name": "out_sc",
-                                "uuid": "833d79ff-e16f-414c-9c41-db8dbfa8ed6b"
-                            },
-                            {
-                                "label": "metaSPAdes on input dataset(s): Assembly graph",
-                                "output_name": "out_ag",
-                                "uuid": "10319152-d2f9-47d8-be41-f956a57e86d3"
-                            },
-                            {
-                                "label": "metaSPAdes on input dataset(s): Assembly graph with scaffolds",
-                                "output_name": "out_ags",
-                                "uuid": "b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633"
-                            },
-                            {
-                                "label": "metaSPAdes on input dataset(s): Contigs",
-                                "output_name": "out_cn",
-                                "uuid": "b6b74c9d-5a16-4725-a1d1-11c1f05ee909"
+                                "label": "nanoplot_before_filtering",
+                                "output_name": "nanostats",
+                                "uuid": "a97e6f33-8182-4a33-86dd-6cfbb83a842d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0",
                         "errors": null,
-                        "id": 2,
+                        "id": 8,
                         "input_connections": {
-                            "input_option|batchmode|pair_input": {
-                                "id": 0,
-                                "output_name": "output"
+                            "inputs": {
+                                "id": 7,
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "MEGAHIT",
+                        "name": "Flye",
                         "outputs": [
                             {
-                                "name": "output",
+                                "name": "consensus",
                                 "type": "fasta"
+                            },
+                            {
+                                "name": "assembly_graph",
+                                "type": "graph_dot"
+                            },
+                            {
+                                "name": "assembly_gfa",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "assembly_info",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 278.0,
-                            "top": 464
+                            "left": 850.0098909589506,
+                            "top": 593
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "14ddfc8ffb93",
-                            "name": "megahit",
-                            "owner": "iuc",
+                            "changeset_revision": "cb8dfd28c16f",
+                            "name": "flye",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"advanced_section\": {\"nomercy\": \"false\", \"bubble_level\": \"2\", \"merge_level\": \"20,0.95\", \"prune_level\": \"2\", \"prune_depth\": \"2\", \"disconnect_ratio\": \"0.1\", \"low_local_ratio\": \"0.2\", \"cleaning_rounds\": \"5\", \"nolocal\": \"false\", \"kmin1pass\": \"false\"}, \"basic_section\": {\"min_count\": \"2\", \"k_mer\": {\"k_mer_method\": \"klim_method\", \"__current_case__\": 1, \"k_min\": \"21\", \"k_max\": \"91\", \"k_step\": \"12\"}}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_option\": {\"choice\": \"paired_collection\", \"__current_case__\": 3, \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"pair_input\": {\"__class__\": \"ConnectedValue\"}}}, \"output_section\": {\"min_contig_len\": \"200\", \"show_intermediate_contigs\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.9+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"asm\": {\"asm_select\": \"false\", \"__current_case__\": 1}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"generate_log\": false, \"inputs\": {\"__class__\": \"ConnectedValue\"}, \"iterations\": \"1\", \"keep_haplotypes\": false, \"meta\": false, \"min_overlap\": null, \"mode_conditional\": {\"mode\": \"--nano-corr\", \"__current_case__\": 1}, \"no_alt_contigs\": false, \"scaffold\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.9.1+galaxy0",
                         "type": "tool",
-                        "uuid": "ffbb16f2-580a-4832-8b6d-e67932e24b27",
+                        "uuid": "8cf7ff30-4007-49cb-a959-e25c337f05be",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "061ac8dd-de43-467d-9c15-a4f46a125103"
+                                "label": "flye_assembly_info",
+                                "output_name": "assembly_info",
+                                "uuid": "f12e718f-1bd5-490d-bd41-f0747aaa41a6"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
                         "errors": null,
-                        "id": 3,
+                        "id": 9,
                         "input_connections": {
-                            "library|input_1": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "reference_genome|own_file": {
-                                "id": 2,
-                                "output_name": "output"
+                            "mode|reads|files": {
+                                "id": 7,
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Bowtie2",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "bam"
-                            },
-                            {
-                                "name": "mapping_stats",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 556.0,
-                            "top": 130
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "03e9b2fbc005",
-                            "name": "bowtie2",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"no_presets\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": \"false\", \"aligned_file\": \"false\", \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"own_file|__identifier__\": \"ERR2231567\", \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 1, \"own_file\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.5.0+galaxy0",
-                        "type": "tool",
-                        "uuid": "9f445c6b-31c9-4ff0-b559-6be00fb0fc17",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "mapping_stats",
-                                "uuid": "ff350260-91cd-4f01-a82f-f64e8eddd4ed"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "2fa389b6-088a-4686-94e9-de884f86e1b7"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "contigs": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "megahit contig2fastg",
-                        "outputs": [
-                            {
-                                "name": "fastg",
-                                "type": "fastg"
-                            }
-                        ],
-                        "position": {
-                            "left": 556.0,
-                            "top": 444
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "4ec5b3777508",
-                            "name": "megahit_contig2fastg",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"contigs\": {\"__class__\": \"ConnectedValue\"}, \"contigs|__identifier__\": \"ERR2231567\", \"kmer\": \"91\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.3+galaxy1",
-                        "type": "tool",
-                        "uuid": "c839a8b8-c719-474d-957e-d94614491f13",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "fastg",
-                                "uuid": "91718981-2ae5-4cdd-8007-0ce9cc3c68f6"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "in|inputs": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "reads|input_1": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Quast",
+                        "name": "NanoPlot",
                         "outputs": [
                             {
-                                "name": "metrics_tabular",
-                                "type": "input"
-                            },
-                            {
-                                "name": "metrics_pdf",
-                                "type": "input"
-                            },
-                            {
-                                "name": "report_tabular_meta",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "report_html_meta",
-                                "type": "html"
-                            },
-                            {
-                                "name": "log_meta",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "krona",
+                                "name": "output_html",
                                 "type": "html"
-                            }
-                        ],
-                        "position": {
-                            "left": 556.0,
-                            "top": 636
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3061c8b029e5",
-                            "name": "quast",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": \"false\", \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": \"true\", \"fragmented_max_indent\": null, \"report_all_metrics\": \"false\", \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": \"false\", \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": \"false\", \"upper_bound_assembly\": \"false\", \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"metagenome\", \"__current_case__\": 1, \"ref\": {\"origin\": \"none\", \"__current_case__\": 3}, \"reuse_combined_alignments\": \"false\", \"min_identity\": \"90.0\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": \"false\", \"conserved_genes_finding\": \"false\"}, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"large\": \"false\", \"min_contig\": \"500\", \"output_files\": [\"html\", \"pdf\", \"tabular\", \"log\", \"summary\", \"krona\"], \"reads\": {\"reads_option\": \"paired_collection\", \"__current_case__\": 3, \"input_1\": {\"__class__\": \"ConnectedValue\"}}, \"split_scaffolds\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.2.0+galaxy0",
-                        "type": "tool",
-                        "uuid": "12072d4c-8ad5-4de1-bbe2-3b081b8373be",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "log_meta",
-                                "uuid": "33c6424f-fceb-45d1-9462-ea3e7cda79ea"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "krona",
-                                "uuid": "44457a4b-760c-4080-b552-dc4724906b2c"
                             },
                             {
-                                "label": null,
-                                "output_name": "metrics_tabular",
-                                "uuid": "9b2b72ac-a297-46a2-883f-8f1704664cf3"
+                                "name": "nanostats",
+                                "type": "tabular"
                             },
                             {
-                                "label": null,
-                                "output_name": "report_tabular_meta",
-                                "uuid": "1259f3a1-4952-48f1-be69-0fde3b6be9de"
+                                "name": "nanostats_post_filtering",
+                                "type": "tabular"
                             },
                             {
-                                "label": null,
-                                "output_name": "report_html_meta",
-                                "uuid": "b8f1b46c-1421-4952-9e87-1790bdd076df"
+                                "name": "read_length",
+                                "type": "png"
                             },
                             {
-                                "label": null,
-                                "output_name": "metrics_pdf",
-                                "uuid": "ac4aa63b-5dc1-4b4c-bbb0-6afce689f0d2"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 4,
-                                "output_name": "fastg"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Bandage Image",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "jpg"
+                                "name": "log_read_length",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 834.0,
-                            "top": 466
+                            "left": 850.0098909589506,
+                            "top": 859
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "21e491ad532a",
-                            "name": "bandage",
+                            "changeset_revision": "0f1c34698076",
+                            "name": "nanoplot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fontsize\": null, \"height\": \"1000\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"input_file|__identifier__\": \"ERR2231567\", \"lengths\": \"false\", \"names\": \"false\", \"nodewidth\": null, \"output_format\": \"jpg\", \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.8.1+galaxy4",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"customization\": {\"color\": null, \"plots\": null, \"N50\": true}, \"filter\": {\"maxlength\": null, \"minlength\": null, \"drop_outliers\": false, \"downsample\": null, \"loglength\": false, \"percentqual\": false, \"alength\": false, \"minqual\": null, \"runtime_until\": null, \"readtype\": null, \"barcoded\": false, \"no_supplementary\": false}, \"mode\": {\"choice\": \"batch\", \"__current_case__\": 0, \"reads\": {\"type\": \"fastq\", \"__current_case__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.41.0+galaxy0",
                         "type": "tool",
-                        "uuid": "31b35530-ae7f-4e9c-8021-6983cf3f3401",
+                        "uuid": "467fca53-715f-4717-ab4c-c4410d321086",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "e02c022d-3067-40ce-8bb6-4cc258d8523a"
+                                "label": "nanoplot_after_filtering",
+                                "output_name": "nanostats",
+                                "uuid": "89524090-f590-434d-89e2-66f0b1a23c7c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
                         "errors": null,
-                        "id": 7,
+                        "id": 12,
                         "input_connections": {
-                            "input_file": {
-                                "id": 4,
-                                "output_name": "fastg"
+                            "mode|in|inputs": {
+                                "id": 8,
+                                "output_name": "consensus"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Bandage Info",
+                        "name": "Quast",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "tabular"
+                                "name": "report_html",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 834.0,
-                            "top": 679
+                            "left": 1140.0069535390257,
+                            "top": 767
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "b9e31c5c01c7",
-                            "name": "bandage",
+                            "changeset_revision": "72472698a2df",
+                            "name": "quast",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"input_file|__identifier__\": \"ERR2231567\", \"tsv\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.8.1+galaxy2",
+                        "tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"false\", \"__current_case__\": 1, \"est_ref_size\": null}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": false}, \"large\": false, \"min_contig\": \"500\", \"mode\": {\"mode\": \"co\", \"__current_case__\": 1, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": \"html\", \"split_scaffolds\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.2.0+galaxy1",
                         "type": "tool",
-                        "uuid": "b63e03dc-b9be-4a72-ac81-64b63ddf99f2",
+                        "uuid": "6949cf20-419e-4cee-86fa-3b08ab60cb9f",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "6bd3194a-9e8c-4677-b42c-2fb3bd1116f3"
+                                "label": "quast_report_before_polishing",
+                                "output_name": "report_html",
+                                "uuid": "dabfb8fd-8791-4959-a9dc-9b3c1e57a69c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
                         "errors": null,
-                        "id": 8,
+                        "id": 15,
                         "input_connections": {
-                            "input_tabular": {
-                                "id": 7,
-                                "output_name": "outfile"
-                            }
+                            "mode|in|inputs": [
+                                {
+                                    "id": 14,
+                                    "output_name": "polished_fasta"
+                                },
+                                {
+                                    "id": 8,
+                                    "output_name": "consensus"
+                                }
+                            ]
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Column join",
+                        "name": "Quast",
                         "outputs": [
                             {
-                                "name": "tabular_output",
-                                "type": "tabular"
+                                "name": "report_html",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 1112.0,
-                            "top": 732
+                            "left": 1700.001078699176,
+                            "top": 853
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "3ddd99c7efee",
-                            "name": "collection_column_join",
+                            "changeset_revision": "72472698a2df",
+                            "name": "quast",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fill_char\": \".\", \"has_header\": \"0\", \"identifier_column\": \"1\", \"include_outputs\": null, \"input_tabular\": {\"__class__\": \"ConnectedValue\"}, \"old_col_in_header\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.0.3",
+                        "tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"false\", \"__current_case__\": 1, \"est_ref_size\": null}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": false}, \"large\": false, \"min_contig\": \"500\", \"mode\": {\"mode\": \"co\", \"__current_case__\": 1, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": \"html\", \"split_scaffolds\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.2.0+galaxy1",
                         "type": "tool",
-                        "uuid": "e9dc42b2-c638-4b9c-af5f-ce84f6b0d654",
+                        "uuid": "866187e0-dd7c-40d5-b121-a8ef4a281c80",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "tabular_output",
-                                "uuid": "fe5b4460-6fa0-48a8-84e7-b3b8270e9b8f"
+                                "label": "quast_report_after_polishing",
+                                "output_name": "report_html",
+                                "uuid": "4e465b51-68bf-4203-9a7c-897f46c70277"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/metagenomics-assembly",
-                "path": "topics/assembly/tutorials/metagenomics-assembly/workflows/metagenomics_assembly_tutorial_workflow.ga",
-                "tags": [],
+                "parent_id": "assembly/mrsa-nanopore",
+                "path": "topics/assembly/tutorials/mrsa-nanopore/workflows/main-workflow.ga",
+                "tags": [
+                    "Assembly"
+                ],
                 "test_results": null,
-                "tests": false,
-                "title": "Metagenomics assembly tutorial workflow",
+                "tests": true,
+                "title": "Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available)",
                 "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-metagenomics-assembly/versions/metagenomics-assembly-tutorial-workflow",
-                "tutorial_id": "metagenomics-assembly",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/metagenomics-assembly/workflows/metagenomics_assembly_tutorial_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/metagenomics-assembly/workflows/metagenomics_assembly_tutorial_workflow.html",
-                "version": 0,
-                "wfid": "assembly-metagenomics-assembly",
-                "wfname": "metagenomics-assembly-tutorial-workflow",
-                "workflow": "metagenomics_assembly_tutorial_workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-mrsa-nanopore/versions/main-workflow",
+                "tutorial_id": "mrsa-nanopore",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/mrsa-nanopore/workflows/main-workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/mrsa-nanopore/workflows/main-workflow.html",
+                "version": 1,
+                "wfid": "assembly-mrsa-nanopore",
+                "wfname": "main-workflow",
+                "workflow": "main-workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.15.4+galaxy2"
+                    "CONVERTER_bz2_to_uncompressed",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/polypolish/polypolish/0.5.0+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
                 ],
-                "workflowhub_id": "1120"
+                "workflowhub_id": "1178"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/10669812"
+    },
+    {
+        "abbreviations": {
+            "ASM": "assembly",
+            "BUSCO": "Benchmarking Universal Single-Copy Orthologs",
+            "CN": "copy number",
+            "G10K": "Genome 10K consortium",
+            "GFA": "Graphical Fragment Assembly",
+            "Hi-C": "all-versus-all chromatin conformation capture",
+            "HiFi": "high fidelity",
+            "NGS": "next generation sequencing",
+            "QC": "Quality Control",
+            "QV": "consensus accuracy quality value",
+            "SMRT": "single-molecule real-time",
+            "TE": "transposable elements",
+            "TGS": "third-generation sequencing",
+            "TR": "tandem repeats",
+            "VGP": "Vertebrate Genomes Project"
+        },
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "bionano_scaffold",
+                    "owner": "bgruening",
+                    "revisions": "5258e18bbe23",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bionano_scaffold",
+                    "owner": "bgruening",
+                    "revisions": "3371c5bdc17a",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gfastats",
+                    "owner": "bgruening",
+                    "revisions": "3ef480892a9f",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "hifiasm",
+                    "owner": "bgruening",
+                    "revisions": "0ee0c3089254",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "f46f0e4f75c4",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "column_maker",
+                    "owner": "devteam",
+                    "revisions": "02026300aa45",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "column_maker",
+                    "owner": "devteam",
+                    "revisions": "6595517c2dd8",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bedtools",
+                    "owner": "iuc",
+                    "revisions": "a1a923cd89e8",
+                    "tool_panel_section_label": "BED",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bellerophon",
+                    "owner": "iuc",
+                    "revisions": "25ca5d73aedf",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bellerophon",
+                    "owner": "iuc",
+                    "revisions": "321347bd0494",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "busco",
+                    "owner": "iuc",
+                    "revisions": "46ae58b1d792",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "busco",
+                    "owner": "iuc",
+                    "revisions": "ea8146ee148f",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bwa_mem2",
+                    "owner": "iuc",
+                    "revisions": "b4a22d90cce9",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bwa_mem2",
+                    "owner": "iuc",
+                    "revisions": "bfaa0d22c2e4",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collection_column_join",
+                    "owner": "iuc",
+                    "revisions": "3ddd99c7efee",
+                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "genomescope",
+                    "owner": "iuc",
+                    "revisions": "3169a38c2656",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "genomescope",
+                    "owner": "iuc",
+                    "revisions": "01210c4e9144",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gfa_to_fa",
+                    "owner": "iuc",
+                    "revisions": "e33c82b63727",
+                    "tool_panel_section_label": "Convert Formats",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "merqury",
+                    "owner": "iuc",
+                    "revisions": "39edec572bae",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "merqury",
+                    "owner": "iuc",
+                    "revisions": "d7edbc9c3a07",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "meryl",
+                    "owner": "iuc",
+                    "revisions": "eadfd71dde37",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "meryl",
+                    "owner": "iuc",
+                    "revisions": "29dabd8db6f2",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "minimap2",
+                    "owner": "iuc",
+                    "revisions": "f54f5baedfdd",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "minimap2",
+                    "owner": "iuc",
+                    "revisions": "11a0d50a54e6",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pretext_map",
+                    "owner": "iuc",
+                    "revisions": "dfb8a4497339",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pretext_snapshot",
+                    "owner": "iuc",
+                    "revisions": "44c66e8d21e6",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "purge_dups",
+                    "owner": "iuc",
+                    "revisions": "a315c25dc813",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "purge_dups",
+                    "owner": "iuc",
+                    "revisions": "e9bd16ba5ebd",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "quast",
+                    "owner": "iuc",
+                    "revisions": "875d0f36d66f",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "salsa",
+                    "owner": "iuc",
+                    "revisions": "f77f7a7f3b83",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "yahs",
+                    "owner": "iuc",
+                    "revisions": "425e63adcc5d",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "cutadapt",
+                    "owner": "lparsons",
+                    "revisions": "48f587c13075",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "cutadapt",
+                    "owner": "lparsons",
+                    "revisions": "8c0175e03cee",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "830961c48e42",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "90981f86000f",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bionano_scaffold\n  owner: bgruening\n  revisions: 5258e18bbe23\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bionano_scaffold\n  owner: bgruening\n  revisions: 3371c5bdc17a\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n  owner: bgruening\n  revisions: 3ef480892a9f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: hifiasm\n  owner: bgruening\n  revisions: 0ee0c3089254\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: f46f0e4f75c4\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 02026300aa45\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 6595517c2dd8\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: a1a923cd89e8\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bellerophon\n  owner: iuc\n  revisions: 25ca5d73aedf\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bellerophon\n  owner: iuc\n  revisions: 321347bd0494\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 46ae58b1d792\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: ea8146ee148f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_mem2\n  owner: iuc\n  revisions: b4a22d90cce9\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_mem2\n  owner: iuc\n  revisions: bfaa0d22c2e4\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_column_join\n  owner: iuc\n  revisions: 3ddd99c7efee\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: genomescope\n  owner: iuc\n  revisions: 3169a38c2656\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: genomescope\n  owner: iuc\n  revisions: 01210c4e9144\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfa_to_fa\n  owner: iuc\n  revisions: e33c82b63727\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merqury\n  owner: iuc\n  revisions: 39edec572bae\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merqury\n  owner: iuc\n  revisions: d7edbc9c3a07\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n  owner: iuc\n  revisions: eadfd71dde37\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n  owner: iuc\n  revisions: 29dabd8db6f2\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: f54f5baedfdd\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: 11a0d50a54e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_map\n  owner: iuc\n  revisions: dfb8a4497339\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_snapshot\n  owner: iuc\n  revisions: 44c66e8d21e6\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: purge_dups\n  owner: iuc\n  revisions: a315c25dc813\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: purge_dups\n  owner: iuc\n  revisions: e9bd16ba5ebd\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 875d0f36d66f\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: salsa\n  owner: iuc\n  revisions: f77f7a7f3b83\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: yahs\n  owner: iuc\n  revisions: 425e63adcc5d\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 48f587c13075\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 8c0175e03cee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/vgp_genome_assembly/tutorial.json",
+        "contributors": [
+            {
+                "email": "delphine.lariviere@galaxy.org",
+                "id": "delphine-l",
+                "joined": "2017-09",
+                "name": "Delphine Lariviere",
+                "orcid": "0000-0001-6421-3484",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
+            },
+            {
+                "email": "a.ostrovsky@mac.com",
+                "id": "astrovsky01",
+                "joined": "2019-06",
+                "name": "Alex Ostrovsky",
+                "orcid": "0000-0002-7901-7109",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/astrovsky01/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/astrovsky01.json"
+            },
+            {
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "gallardoalba",
+                "joined": "2020-11",
+                "name": "Crist\u00f3bal Gallardo",
+                "orcid": "0000-0002-5752-2155",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
+            },
+            {
+                "id": "annasyme",
+                "joined": "2017-09",
+                "name": "Anna Syme",
+                "orcid": "0000-0002-9906-0673",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
+            },
+            {
+                "id": "abueg",
+                "joined": "2022-01",
+                "name": "Linelle Abueg",
+                "orcid": "0000-0002-6879-3954",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abueg/",
+                "twitter": "llabueg",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abueg.json"
+            },
+            {
+                "id": "pickettbd",
+                "joined": "2022-01",
+                "name": "Brandon Pickett",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pickettbd/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pickettbd.json"
+            },
+            {
+                "id": "gf777",
+                "joined": "2022-01",
+                "name": "Giulio Formenti",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gf777/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/gf777.json"
+            },
+            {
+                "id": "msozzoni",
+                "joined": "2022-03",
+                "name": "Marcella Sozzoni",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/msozzoni/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/msozzoni.json"
             },
+            {
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
+                "joined": "2017-09",
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+            }
+        ],
+        "dir": "topics/assembly/tutorials/vgp_genome_assembly",
+        "edam_operation": [
+            "Data handling",
+            "Sequence alignment",
+            "Visualisation",
+            "Sequence trimming",
+            "Genome assembly",
+            "De-novo assembly",
+            "Phasing",
+            "Sequence assembly validation",
+            "Scaffolding",
+            "Read binning",
+            "Pairwise sequence alignment",
+            "k-mer counting",
+            "Transcriptome assembly",
+            "Mapping",
+            "Read pre-processing",
+            "Primer removal"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "assembly/vgp_genome_assembly",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": 29087,
+            "mermaid": false
+        },
+        "key_points": [
+            "The VGP pipeline allows users to generate error-free, near gapless reference-quality genome assemblies",
+            "The assembly can be divided into four main stages: genome profile analysis, HiFi long read phased assembly with hifiasm, Bionano hybrid scaffolding and Hi-C scaffolding"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-27",
+        "objectives": [
+            "Learn the tools necessary to perform a de novo assembly of a vertebrate genome",
+            "Evaluate the quality of the assembly"
+        ],
+        "pageviews": 17734,
+        "pub_date": "2021-06-04",
+        "questions": [
+            "What combination of tools can produce the highest quality assembly of vertebrate genomes?",
+            "How can we evaluate the quality of the assembly in a reference-free way?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "delphine-l"
+                ],
+                "date": "2022-03-13",
+                "galaxy_version": "21.09",
+                "length": "10M",
+                "speakers": [
+                    "delphine-l"
+                ],
+                "youtube_id": "0EoBDiyd-84"
+            }
+        ],
+        "short_id": "T00039",
+        "short_tools": [
+            "merqury",
+            "bionano_scaffold",
+            "minimap2",
+            "busco",
+            "quast",
+            "tp_find_and_replace",
+            "pretext_snapshot",
+            "yahs",
+            "collection_column_join",
+            "bwa_mem2",
+            "purge_dups",
+            "salsa",
+            "gfastats",
+            "tp_cut_tool",
+            "pretext_map",
+            "hifiasm",
+            "genomescope",
+            "cutadapt",
+            "bellerophon",
+            "collapse_dataset",
+            "meryl",
+            "cat1",
+            "sort1",
+            "Convert characters1",
+            "tp_grep_tool",
+            "Add_a_column1",
+            "bedtools_bamtobed",
+            "gfa_to_fa"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "pacbio",
+            "eukaryote",
+            "VGP"
+        ],
+        "time_estimation": "5h",
+        "title": "Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step",
+        "tools": [
+            "Convert characters1",
+            "cat1",
+            "sort1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
+            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+            "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/salsa/salsa/2.3+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
+            "ttoolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1"
+        ],
+        "topic_name": "assembly",
+        "topic_name_human": "Assembly",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "vgp_genome_assembly",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/vgp_genome_assembly/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/vgp_genome_assembly/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/vgp_genome_assembly/tutorial.json"
+        },
+        "version": 54,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 119,
+        "visitors": 11232,
+        "workflows": [
             {
                 "creators": [],
-                "description": "",
+                "description": "VGP assembly tutorial",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nERR2231567_1.fastq.gz\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nERR2231567_2.fastq.gz\"]\n  2[label=\"Cutadapt\"]\n  0 -> 2 [label=\"output\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"MEGAHIT\"]\n  2 -> 3 [label=\"out1\"]\n  2 -> 3 [label=\"out2\"]\n  4[label=\"Bowtie2\"]\n  2 -> 4 [label=\"out1\"]\n  2 -> 4 [label=\"out2\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"BAM filter\"]\n  4 -> 5 [label=\"output\"]\n  6[label=\"BAM filter\"]\n  4 -> 6 [label=\"output\"]\n  7[label=\"Convert, Merge, Randomize\"]\n  5 -> 7 [label=\"outfile\"]\n  8[label=\"Convert, Merge, Randomize\"]\n  6 -> 8 [label=\"outfile\"]\n  9[label=\"Select random lines\"]\n  7 -> 9 [label=\"out_file1\"]\n  10[label=\"Select random lines\"]\n  8 -> 10 [label=\"out_file1\"]\n  11[label=\"Filter Tabular\"]\n  9 -> 11 [label=\"out_file1\"]\n  12[label=\"Filter Tabular\"]\n  10 -> 12 [label=\"out_file1\"]\n  13[label=\"Unique\"]\n  11 -> 13 [label=\"output\"]\n  14[label=\"Unique\"]\n  12 -> 14 [label=\"output\"]\n  15[label=\"Concatenate datasets\"]\n  13 -> 15 [label=\"outfile\"]\n  14 -> 15 [label=\"outfile\"]\n  16[label=\"seqtk_subseq\"]\n  2 -> 16 [label=\"out1\"]\n  15 -> 16 [label=\"out_file1\"]\n  17[label=\"seqtk_subseq\"]\n  2 -> 17 [label=\"out2\"]\n  15 -> 17 [label=\"out_file1\"]\n  18[label=\"FastQC\"]\n  16 -> 18 [label=\"default\"]\n  19[label=\"FastQC\"]\n  17 -> 19 [label=\"default\"]\n}",
-                "history": [],
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBionano_dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHi-C_dataset_R\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHi-C_dataset_F\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  4[label=\"GFA to FASTA\"]\n  5[label=\"GFA to FASTA\"]\n  6[label=\"Cutadapt\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"Busco\"]\n  4 -> 7 [label=\"out_fa\"]\n  8[label=\"Busco\"]\n  5 -> 8 [label=\"out_fa\"]\n  9[label=\"Purge overlaps\"]\n  5 -> 9 [label=\"out_fa\"]\n  10[label=\"Collapse Collection\"]\n  6 -> 10 [label=\"out1\"]\n  11[label=\"Meryl\"]\n  6 -> 11 [label=\"out1\"]\n  12[label=\"Map with minimap2\"]\n  6 -> 12 [label=\"out1\"]\n  5 -> 12 [label=\"out_fa\"]\n  13[label=\"Quast\"]\n  5 -> 13 [label=\"out_fa\"]\n  4 -> 13 [label=\"out_fa\"]\n  6 -> 13 [label=\"out1\"]\n  14[label=\"Map with minimap2\"]\n  9 -> 14 [label=\"split_fasta\"]\n  9 -> 14 [label=\"split_fasta\"]\n  15[label=\"Meryl\"]\n  11 -> 15 [label=\"read_db\"]\n  16[label=\"Purge overlaps\"]\n  12 -> 16 [label=\"alignment_output\"]\n  17[label=\"Meryl\"]\n  15 -> 17 [label=\"read_db\"]\n  18[label=\"Merqury\"]\n  5 -> 18 [label=\"out_fa\"]\n  4 -> 18 [label=\"out_fa\"]\n  15 -> 18 [label=\"read_db\"]\n  19[label=\"Purge overlaps\"]\n  16 -> 19 [label=\"pbcstat_cov\"]\n  16 -> 19 [label=\"calcuts_cutoff\"]\n  14 -> 19 [label=\"alignment_output\"]\n  20[label=\"GenomeScope\"]\n  17 -> 20 [label=\"read_db_hist\"]\n  21[label=\"Purge overlaps\"]\n  19 -> 21 [label=\"purge_dups_bed\"]\n  5 -> 21 [label=\"out_fa\"]\n  22[label=\"Replace\"]\n  20 -> 22 [label=\"summary\"]\n  23[label=\"Compute\"]\n  20 -> 23 [label=\"model_params\"]\n  24[label=\"Bionano Hybrid Scaffold\"]\n  0 -> 24 [label=\"output\"]\n  21 -> 24 [label=\"get_seqs_purged\"]\n  25[label=\"Concatenate datasets\"]\n  21 -> 25 [label=\"get_seqs_hap\"]\n  4 -> 25 [label=\"out_fa\"]\n  26[label=\"Busco\"]\n  21 -> 26 [label=\"get_seqs_purged\"]\n  27[label=\"Replace\"]\n  22 -> 27 [label=\"outfile\"]\n  28[label=\"Compute\"]\n  23 -> 28 [label=\"out_file1\"]\n  29[label=\"Concatenate datasets\"]\n  24 -> 29 [label=\"ngs_contigs_scaffold_trimmed\"]\n  24 -> 29 [label=\"ngs_contigs_not_scaffolded_trimmed\"]\n  30[label=\"Purge overlaps\"]\n  25 -> 30 [label=\"out_file1\"]\n  31[label=\"Map with minimap2\"]\n  10 -> 31 [label=\"output\"]\n  25 -> 31 [label=\"out_file1\"]\n  32[label=\"Search in textfiles\"]\n  27 -> 32 [label=\"outfile\"]\n  33[label=\"Advanced Cut\"]\n  28 -> 33 [label=\"out_file1\"]\n  34[label=\"Advanced Cut\"]\n  28 -> 34 [label=\"out_file1\"]\n  35[label=\"BWA-MEM2\"]\n  1 -> 35 [label=\"output\"]\n  29 -> 35 [label=\"out_file1\"]\n  36[label=\"BWA-MEM2\"]\n  2 -> 36 [label=\"output\"]\n  29 -> 36 [label=\"out_file1\"]\n  37[label=\"Replace\"]\n  29 -> 37 [label=\"out_file1\"]\n  38[label=\"Quast\"]\n  29 -> 38 [label=\"out_file1\"]\n  10 -> 38 [label=\"output\"]\n  39[label=\"Busco\"]\n  29 -> 39 [label=\"out_file1\"]\n  40[label=\"Map with minimap2\"]\n  30 -> 40 [label=\"split_fasta\"]\n  30 -> 40 [label=\"split_fasta\"]\n  41[label=\"Purge overlaps\"]\n  31 -> 41 [label=\"alignment_output\"]\n  42[label=\"Convert\"]\n  32 -> 42 [label=\"output\"]\n  43[label=\"Filter and merge\"]\n  36 -> 43 [label=\"bam_output\"]\n  35 -> 43 [label=\"bam_output\"]\n  44[label=\"Purge overlaps\"]\n  41 -> 44 [label=\"pbcstat_cov\"]\n  41 -> 44 [label=\"calcuts_cutoff\"]\n  40 -> 44 [label=\"alignment_output\"]\n  45[label=\"Advanced Cut\"]\n  42 -> 45 [label=\"out_file1\"]\n  46[label=\"bedtools BAM to BED\"]\n  43 -> 46 [label=\"outfile\"]\n  47[label=\"PretextMap\"]\n  43 -> 47 [label=\"outfile\"]\n  48[label=\"Purge overlaps\"]\n  44 -> 48 [label=\"purge_dups_bed\"]\n  25 -> 48 [label=\"out_file1\"]\n  49[label=\"Sort\"]\n  46 -> 49 [label=\"output\"]\n  50[label=\"Pretext Snapshot\"]\n  47 -> 50 [label=\"pretext_map_out\"]\n  51[label=\"Busco\"]\n  48 -> 51 [label=\"get_seqs_purged\"]\n  52[label=\"Quast\"]\n  21 -> 52 [label=\"get_seqs_purged\"]\n  48 -> 52 [label=\"get_seqs_purged\"]\n  10 -> 52 [label=\"output\"]\n  53[label=\"SALSA\"]\n  49 -> 53 [label=\"out_file1\"]\n  37 -> 53 [label=\"outfile\"]\n  54[label=\"BWA-MEM2\"]\n  1 -> 54 [label=\"output\"]\n  53 -> 54 [label=\"scaffolds_fasta\"]\n  55[label=\"BWA-MEM2\"]\n  2 -> 55 [label=\"output\"]\n  53 -> 55 [label=\"scaffolds_fasta\"]\n  56[label=\"Busco\"]\n  53 -> 56 [label=\"scaffolds_fasta\"]\n  57[label=\"Quast\"]\n  53 -> 57 [label=\"scaffolds_fasta\"]\n  10 -> 57 [label=\"output\"]\n  58[label=\"Filter and merge\"]\n  55 -> 58 [label=\"bam_output\"]\n  54 -> 58 [label=\"bam_output\"]\n  59[label=\"PretextMap\"]\n  58 -> 59 [label=\"outfile\"]\n  60[label=\"Pretext Snapshot\"]\n  59 -> 60 [label=\"pretext_map_out\"]\n}",
+                "history": [
+                    {
+                        "hash": "b57efed6057cbfaeb5e79c2ed6a0182d59c619d0",
+                        "message": "VGP training: fix duplication problem (#3271)",
+                        "num": 8,
+                        "short_hash": "b57efed60",
+                        "unix": "1648533596"
+                    },
+                    {
+                        "hash": "f764939f89074b68169419b828862b8c4333e671",
+                        "message": "Update VGP training 06.02: synthetic reads (#3157)",
+                        "num": 7,
+                        "short_hash": "f764939f8",
+                        "unix": "1645040160"
+                    },
+                    {
+                        "hash": "5552083ddc045639e0dbed4422cbf97c71052110",
+                        "message": "Fix bug",
+                        "num": 6,
+                        "short_hash": "5552083dd",
+                        "unix": "1643108875"
+                    },
+                    {
+                        "hash": "f7354f457234a89e026e4960e48fdc211f3aeef8",
+                        "message": "Fix workflow lint",
+                        "num": 5,
+                        "short_hash": "f7354f457",
+                        "unix": "1643108431"
+                    },
+                    {
+                        "hash": "e87377be94fcab2333895380c4167a4fd0ab435c",
+                        "message": "Include Linelle and update workflow",
+                        "num": 4,
+                        "short_hash": "e87377be9",
+                        "unix": "1643108189"
+                    },
+                    {
+                        "hash": "a45e1874032e2d30c3d3801599900467134ba5b7",
+                        "message": "workflow tag and annotation",
+                        "num": 3,
+                        "short_hash": "a45e18740",
+                        "unix": "1622754288"
+                    },
+                    {
+                        "hash": "54179df03c881344d118a06596d7a8ee75477e16",
+                        "message": "update tools",
+                        "num": 2,
+                        "short_hash": "54179df03",
+                        "unix": "1622753242"
+                    },
+                    {
+                        "hash": "3309edda7618f96ec58d14e47350ea4d5897b9e0",
+                        "message": "add vgp training skeleton from workflow",
+                        "num": 1,
+                        "short_hash": "3309edda7",
+                        "unix": "1622750872"
+                    }
+                ],
                 "inputs": [
                     {
                         "annotation": "",
@@ -15604,21 +15385,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "ERR2231567_1.fastq.gz"
+                                "name": "Bionano_dataset"
                             }
                         ],
-                        "label": "ERR2231567_1.fastq.gz",
+                        "label": "Bionano_dataset",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 174.98046875
+                            "left": 10,
+                            "top": 10
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ac2a7e31-6a0c-43f0-b39f-6764ae421dea",
+                        "uuid": "80e89ff1-902e-42f4-be59-f33bf55a692c",
                         "workflow_outputs": []
                     },
                     {
@@ -15630,1325 +15411,1071 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "ERR2231567_2.fastq.gz"
+                                "name": "Hi-C_dataset_R"
                             }
                         ],
-                        "label": "ERR2231567_2.fastq.gz",
+                        "label": "Hi-C_dataset_R",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 1.03515625,
-                            "top": 365.0
+                            "left": 10,
+                            "top": 130
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "2e1fd5bf-3b01-49dd-a091-75c7215eb3f9",
+                        "uuid": "07cb8e4c-afd1-4007-ad83-e7fe9ab14ae6",
                         "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nERR2231567_1.fastq.gz\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nERR2231567_2.fastq.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Cutadapt\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"MEGAHIT\"];\n  2 -->|out1| 3;\n  2 -->|out2| 3;\n  4[\"Bowtie2\"];\n  2 -->|out1| 4;\n  2 -->|out2| 4;\n  3 -->|output| 4;\n  5[\"BAM filter\"];\n  4 -->|output| 5;\n  6[\"BAM filter\"];\n  4 -->|output| 6;\n  7[\"Convert, Merge, Randomize\"];\n  5 -->|outfile| 7;\n  8[\"Convert, Merge, Randomize\"];\n  6 -->|outfile| 8;\n  9[\"Select random lines\"];\n  7 -->|out_file1| 9;\n  10[\"Select random lines\"];\n  8 -->|out_file1| 10;\n  11[\"Filter Tabular\"];\n  9 -->|out_file1| 11;\n  12[\"Filter Tabular\"];\n  10 -->|out_file1| 12;\n  13[\"Unique\"];\n  11 -->|output| 13;\n  14[\"Unique\"];\n  12 -->|output| 14;\n  15[\"Concatenate datasets\"];\n  13 -->|outfile| 15;\n  14 -->|outfile| 15;\n  16[\"seqtk_subseq\"];\n  2 -->|out1| 16;\n  15 -->|out_file1| 16;\n  17[\"seqtk_subseq\"];\n  2 -->|out2| 17;\n  15 -->|out_file1| 17;\n  18[\"FastQC\"];\n  16 -->|default| 18;\n  19[\"FastQC\"];\n  17 -->|default| 19;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "workflow-generate-dataset-for-assembly-tutorial",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0",
+                        "content_id": null,
                         "errors": null,
                         "id": 2,
-                        "input_connections": {
-                            "library|input_1": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "library|input_2": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cutadapt",
-                        "outputs": [
-                            {
-                                "name": "out1",
-                                "type": "fastqsanger"
-                            },
-                            {
-                                "name": "out2",
-                                "type": "fastqsanger"
-                            },
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "report",
-                                "type": "txt"
+                                "description": "",
+                                "name": "Hi-C_dataset_F"
                             }
                         ],
+                        "label": "Hi-C_dataset_F",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 248.0078125,
-                            "top": 260.0
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "5915ea1ec9b1",
-                            "name": "cutadapt",
-                            "owner": "lparsons",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 10,
+                            "top": 250
                         },
-                        "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"internal\": \"\", \"error_rate\": \"0.1\", \"no_indels\": \"false\", \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"revcomp\": \"false\"}, \"filter_options\": {\"discard_trimmed\": \"false\", \"discard_untrimmed\": \"false\", \"minimum_length\": \"200\", \"maximum_length\": null, \"length_R2_options\": {\"length_R2_status\": \"False\", \"__current_case__\": 1}, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"discard_cassava\": \"false\"}, \"library\": {\"type\": \"paired\", \"__current_case__\": 1, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"input_2\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}, \"r2\": {\"adapters2\": [], \"front_adapters2\": [], \"anywhere_adapters2\": [], \"cut2\": \"0\", \"quality_cutoff2\": \"\"}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"quality_cutoff\": \"20\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"strip_suffix\": \"\", \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.0+galaxy0",
-                        "type": "tool",
-                        "uuid": "67ddef5c-cde3-462d-a189-77028682a357",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out1",
-                                "uuid": "7b3621e4-5077-4ac8-95d3-61a94a6ee664"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out2",
-                                "uuid": "f7db5a96-f4e7-4caf-8e78-093d4e6b007c"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "report",
-                                "uuid": "ff6985ad-6afe-4cf7-9def-223fdd5e5f62"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "8395a577-e9a2-41ef-b2bf-ce303b637892",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
+                        "content_id": null,
                         "errors": null,
                         "id": 3,
-                        "input_connections": {
-                            "input_option|fastq_input1": {
-                                "id": 2,
-                                "output_name": "out1"
-                            },
-                            "input_option|fastq_input2": {
-                                "id": 2,
-                                "output_name": "out2"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "MEGAHIT",
-                        "outputs": [
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "Input Dataset Collection"
                             }
                         ],
+                        "label": "Input Dataset Collection",
+                        "name": "Input dataset collection",
+                        "outputs": [],
                         "position": {
-                            "left": 735.9765625,
-                            "top": 301.97265625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "14ddfc8ffb93",
-                            "name": "megahit",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 10,
+                            "top": 370
                         },
-                        "tool_state": "{\"advanced_section\": {\"nomercy\": \"false\", \"bubble_level\": \"2\", \"merge_level\": \"20,0.95\", \"prune_level\": \"2\", \"prune_depth\": \"2\", \"disconnect_ratio\": \"0.1\", \"low_local_ratio\": \"0.2\", \"cleaning_rounds\": \"5\", \"nolocal\": \"false\", \"kmin1pass\": \"false\"}, \"basic_section\": {\"min_count\": \"2\", \"k_mer\": {\"k_mer_method\": \"klist_method\", \"__current_case__\": 0, \"k_list\": \"21,29,39,59,79,99,119,141\"}}, \"input_option\": {\"choice\": \"paired\", \"__current_case__\": 2, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"fastq_input2\": {\"__class__\": \"ConnectedValue\"}}, \"output_section\": {\"min_contig_len\": \"200\", \"show_intermediate_contigs\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.9+galaxy0",
-                        "type": "tool",
-                        "uuid": "0e1e0ffb-4536-4802-b886-5f5f391255d1",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "7a0e5487-3923-46e0-9976-d3fdc3fe7e09"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "d99feaa3-653d-4a95-bd1c-6975baf1e946",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nBionano_dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nHi-C_dataset_R\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nHi-C_dataset_F\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"GFA to FASTA\"];\n  5[\"GFA to FASTA\"];\n  6[\"Cutadapt\"];\n  3 -->|output| 6;\n  7[\"Busco\"];\n  4 -->|out_fa| 7;\n  8[\"Busco\"];\n  5 -->|out_fa| 8;\n  9[\"Purge overlaps\"];\n  5 -->|out_fa| 9;\n  10[\"Collapse Collection\"];\n  6 -->|out1| 10;\n  11[\"Meryl\"];\n  6 -->|out1| 11;\n  12[\"Map with minimap2\"];\n  6 -->|out1| 12;\n  5 -->|out_fa| 12;\n  13[\"Quast\"];\n  5 -->|out_fa| 13;\n  4 -->|out_fa| 13;\n  6 -->|out1| 13;\n  14[\"Map with minimap2\"];\n  9 -->|split_fasta| 14;\n  9 -->|split_fasta| 14;\n  15[\"Meryl\"];\n  11 -->|read_db| 15;\n  16[\"Purge overlaps\"];\n  12 -->|alignment_output| 16;\n  17[\"Meryl\"];\n  15 -->|read_db| 17;\n  18[\"Merqury\"];\n  5 -->|out_fa| 18;\n  4 -->|out_fa| 18;\n  15 -->|read_db| 18;\n  19[\"Purge overlaps\"];\n  16 -->|pbcstat_cov| 19;\n  16 -->|calcuts_cutoff| 19;\n  14 -->|alignment_output| 19;\n  20[\"GenomeScope\"];\n  17 -->|read_db_hist| 20;\n  21[\"Purge overlaps\"];\n  19 -->|purge_dups_bed| 21;\n  5 -->|out_fa| 21;\n  22[\"Replace\"];\n  20 -->|summary| 22;\n  23[\"Compute\"];\n  20 -->|model_params| 23;\n  24[\"Bionano Hybrid Scaffold\"];\n  0 -->|output| 24;\n  21 -->|get_seqs_purged| 24;\n  25[\"Concatenate datasets\"];\n  21 -->|get_seqs_hap| 25;\n  4 -->|out_fa| 25;\n  26[\"Busco\"];\n  21 -->|get_seqs_purged| 26;\n  27[\"Replace\"];\n  22 -->|outfile| 27;\n  28[\"Compute\"];\n  23 -->|out_file1| 28;\n  29[\"Concatenate datasets\"];\n  24 -->|ngs_contigs_scaffold_trimmed| 29;\n  24 -->|ngs_contigs_not_scaffolded_trimmed| 29;\n  30[\"Purge overlaps\"];\n  25 -->|out_file1| 30;\n  31[\"Map with minimap2\"];\n  10 -->|output| 31;\n  25 -->|out_file1| 31;\n  32[\"Search in textfiles\"];\n  27 -->|outfile| 32;\n  33[\"Advanced Cut\"];\n  28 -->|out_file1| 33;\n  34[\"Advanced Cut\"];\n  28 -->|out_file1| 34;\n  35[\"BWA-MEM2\"];\n  1 -->|output| 35;\n  29 -->|out_file1| 35;\n  36[\"BWA-MEM2\"];\n  2 -->|output| 36;\n  29 -->|out_file1| 36;\n  37[\"Replace\"];\n  29 -->|out_file1| 37;\n  38[\"Quast\"];\n  29 -->|out_file1| 38;\n  10 -->|output| 38;\n  39[\"Busco\"];\n  29 -->|out_file1| 39;\n  40[\"Map with minimap2\"];\n  30 -->|split_fasta| 40;\n  30 -->|split_fasta| 40;\n  41[\"Purge overlaps\"];\n  31 -->|alignment_output| 41;\n  42[\"Convert\"];\n  32 -->|output| 42;\n  43[\"Filter and merge\"];\n  36 -->|bam_output| 43;\n  35 -->|bam_output| 43;\n  44[\"Purge overlaps\"];\n  41 -->|pbcstat_cov| 44;\n  41 -->|calcuts_cutoff| 44;\n  40 -->|alignment_output| 44;\n  45[\"Advanced Cut\"];\n  42 -->|out_file1| 45;\n  46[\"bedtools BAM to BED\"];\n  43 -->|outfile| 46;\n  47[\"PretextMap\"];\n  43 -->|outfile| 47;\n  48[\"Purge overlaps\"];\n  44 -->|purge_dups_bed| 48;\n  25 -->|out_file1| 48;\n  49[\"Sort\"];\n  46 -->|output| 49;\n  50[\"Pretext Snapshot\"];\n  47 -->|pretext_map_out| 50;\n  51[\"Busco\"];\n  48 -->|get_seqs_purged| 51;\n  52[\"Quast\"];\n  21 -->|get_seqs_purged| 52;\n  48 -->|get_seqs_purged| 52;\n  10 -->|output| 52;\n  53[\"SALSA\"];\n  49 -->|out_file1| 53;\n  37 -->|outfile| 53;\n  54[\"BWA-MEM2\"];\n  1 -->|output| 54;\n  53 -->|scaffolds_fasta| 54;\n  55[\"BWA-MEM2\"];\n  2 -->|output| 55;\n  53 -->|scaffolds_fasta| 55;\n  56[\"Busco\"];\n  53 -->|scaffolds_fasta| 56;\n  57[\"Quast\"];\n  53 -->|scaffolds_fasta| 57;\n  10 -->|output| 57;\n  58[\"Filter and merge\"];\n  55 -->|bam_output| 58;\n  54 -->|bam_output| 58;\n  59[\"PretextMap\"];\n  58 -->|outfile| 59;\n  60[\"Pretext Snapshot\"];\n  59 -->|pretext_map_out| 60;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "VGP assembly: training workflow",
+                "outputs": [],
+                "parent_id": "assembly/vgp_genome_assembly",
+                "path": "topics/assembly/tutorials/vgp_genome_assembly/workflows/main_workflow.ga",
+                "tags": [
+                    "assembly"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "VGP assembly: training workflow",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-vgp_genome_assembly/versions/main-workflow",
+                "tutorial_id": "vgp_genome_assembly",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/vgp_genome_assembly/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/vgp_genome_assembly/workflows/main_workflow.html",
+                "version": 4,
+                "wfid": "assembly-vgp_genome_assembly",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "Convert characters1",
+                    "cat1",
+                    "sort1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/salsa/salsa/2.3+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
+                ],
+                "workflowhub_id": "1187"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/5887339"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "flye",
+                    "owner": "bgruening",
+                    "revisions": "276f5d8712d5",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "busco",
+                    "owner": "iuc",
+                    "revisions": "0d243f458b53",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "busco",
+                    "owner": "iuc",
+                    "revisions": "46ae58b1d792",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_stats",
+                    "owner": "iuc",
+                    "revisions": "0dbb995c7d35",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "quast",
+                    "owner": "iuc",
+                    "revisions": "7594365c546b",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: flye\n  owner: bgruening\n  revisions: 276f5d8712d5\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 0d243f458b53\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 46ae58b1d792\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n  owner: iuc\n  revisions: 0dbb995c7d35\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 7594365c546b\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/flye-assembly/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "eurosciencegateway",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
+                "fediverse_flavor": "mastodon",
+                "id": "abretaud",
+                "joined": "2017-09",
+                "location": {
+                    "country": "FR",
+                    "lat": 48.11,
+                    "lon": -1.64
+                },
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+            },
+            {
+                "email": "alexandre.cormier@ifremer.fr",
+                "id": "alexcorm",
+                "joined": "2021-11",
+                "name": "Alexandre Cormier",
+                "orcid": "0000-0002-7775-8413",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/",
+                "twitter": "allanssx",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/alexcorm.json"
+            },
+            {
+                "email": "erwan.corre@sb-roscoff.fr",
+                "id": "r1corre",
+                "joined": "2019-04",
+                "name": "Erwan Corre",
+                "orcid": "0000-0001-6354-2278",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/r1corre/",
+                "twitter": "r1corre",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/r1corre.json"
+            },
+            {
+                "email": "laura.leroi@ifremer.fr",
+                "id": "lleroi",
+                "joined": "2021-11",
+                "name": "Laura Leroi",
+                "orcid": "0000-0003-3748-4179",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lleroi/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/lleroi.json"
+            },
+            {
+                "email": "stephanie.robin@inrae.fr",
+                "id": "stephanierobin",
+                "joined": "2021-11",
+                "name": "St\u00e9phanie Robin",
+                "orcid": "0000-0001-7379-9173",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/",
+                "twitter": "robinstphanie1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/stephanierobin.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            }
+        ],
+        "dir": "topics/assembly/tutorials/flye-assembly",
+        "edam_operation": [
+            "Cross-assembly",
+            "Visualisation",
+            "Genome assembly",
+            "De-novo assembly",
+            "Sequence assembly validation",
+            "Mapping assembly",
+            "Scaffolding",
+            "Transcriptome assembly"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "genome-annotation",
+                "tutorials": [
+                    "repeatmasker"
+                ],
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "assembly/flye-assembly",
+        "inexact_supported_servers": [
+            "GalaxyTrakr",
+            "UseGalaxy.be",
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "PacBio data allows to perform good quality genome assembly",
+            "Quast and BUSCO make it easy to compare the quality of assemblies"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": [
+            "Assemble a Genome with PacBio data",
+            "Assess assembly quality"
+        ],
+        "pageviews": 4626,
+        "pub_date": "2021-11-29",
+        "questions": [
+            "How to perform a genome assembly with PacBio data ?",
+            "How to check assembly quality ?"
+        ],
+        "short_id": "T00033",
+        "short_tools": [
+            "flye",
+            "busco",
+            "fasta-stats",
+            "quast"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "assembly",
+            "pacbio"
+        ],
+        "time_estimation": "6h",
+        "title": "Genome assembly using PacBio data",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy3"
+        ],
+        "topic_name": "assembly",
+        "topic_name_human": "Assembly",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "flye-assembly",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/flye-assembly/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/flye-assembly/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/flye-assembly/tutorial.json"
+        },
+        "version": 8,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 120,
+        "visitors": 3363,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "",
+                        "name": "Erwan Corre"
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "library|input_1": {
-                                "id": 2,
-                                "output_name": "out1"
-                            },
-                            "library|input_2": {
-                                "id": 2,
-                                "output_name": "out2"
-                            },
-                            "reference_genome|own_file": {
-                                "id": 3,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Bowtie2",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "bam"
-                            },
-                            {
-                                "name": "mapping_stats",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 979.00390625,
-                            "top": 40.9765625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f6877ad76b00",
-                            "name": "bowtie2",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"no_presets\"}, \"library\": {\"type\": \"paired\", \"__current_case__\": 1, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"input_2\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": \"false\", \"aligned_file\": \"false\", \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 1, \"own_file\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.4.5+galaxy1",
-                        "type": "tool",
-                        "uuid": "cd8574f0-da3e-4dc1-848e-6f21c57831e6",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "mapping_stats",
-                                "uuid": "cf119c49-eee7-448a-bfff-0f1053f87821"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "44b0908f-2158-4ea2-be6f-65c0dd803bcb"
-                            }
-                        ]
+                        "class": "Person",
+                        "identifier": "",
+                        "name": "St\u00e9phanie Robin"
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
+                        "class": "Person",
+                        "identifier": "",
+                        "name": "Anthony Bretaudeau"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "",
+                        "name": "Alexandre Cormier"
+                    }
+                ],
+                "description": "Genome Assembly using PacBio data and Flye assembler",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPacBio reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genome\"]\n  2[label=\"Flye\"]\n  0 -> 2 [label=\"output\"]\n  kd7badcb24d384ddab89bb4bd3ffbc64a[color=lightseagreen,label=\"Output\\nFlye on input dataset(s): assembly info\"]\n  2 -> kd7badcb24d384ddab89bb4bd3ffbc64a\n  kc8f96c22e06e4fecbbfad993b7b103eb[color=lightseagreen,label=\"Output\\nFlye on input dataset(s): consensus\"]\n  2 -> kc8f96c22e06e4fecbbfad993b7b103eb\n  ka288fb935aa5423189e4958c57106978[color=lightseagreen,label=\"Output\\nFlye on input dataset(s): graphical fragment assembly\"]\n  2 -> ka288fb935aa5423189e4958c57106978\n  k0e0641815cd442c898f9fe417303956c[color=lightseagreen,label=\"Output\\nFlye on input dataset(s): assembly graph\"]\n  2 -> k0e0641815cd442c898f9fe417303956c\n  3[label=\"Fasta Statistics\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Busco\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Fasta Statistics\"]\n  2 -> 5 [label=\"consensus\"]\n  6[label=\"Quast\"]\n  1 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"consensus\"]\n  kbea191cbf88d4103b8fab3683d77cc93[color=lightseagreen,label=\"Output\\nQuast on input dataset(s):  HTML report\"]\n  6 -> kbea191cbf88d4103b8fab3683d77cc93\n  7[label=\"Busco\"]\n  2 -> 7 [label=\"consensus\"]\n}",
+                "history": [
+                    {
+                        "hash": "6e12dcba4982df8a8c154f51242a45ae66e32aa9",
+                        "message": "update quast",
+                        "num": 4,
+                        "short_hash": "6e12dcba4",
+                        "unix": "1638177109"
+                    },
+                    {
+                        "hash": "a086911d08bd6aaaee479fc075bb8d64ff1265a6",
+                        "message": "update workflow + minor changes",
+                        "num": 3,
+                        "short_hash": "a086911d0",
+                        "unix": "1637938578"
+                    },
+                    {
+                        "hash": "b8606bace2788251cf703b48a07c34c5897bfc23",
+                        "message": "flye-assembly workflow modified with new tools versions",
+                        "num": 2,
+                        "short_hash": "b8606bace",
+                        "unix": "1637931503"
+                    },
+                    {
+                        "hash": "e817e8cfdf08abdb2d4dee03fd7461c008807ee2",
+                        "message": "added flye assembly tutorial",
+                        "num": 1,
+                        "short_hash": "e817e8cfd",
+                        "unix": "1635261060"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "PacBio reads in fastq format",
+                        "content_id": null,
                         "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "infile": {
-                                "id": 4,
-                                "output_name": "output"
-                            }
-                        },
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool BAM filter",
-                                "name": "excludebed"
-                            },
-                            {
-                                "description": "runtime parameter for tool BAM filter",
-                                "name": "includebed"
-                            }
-                        ],
-                        "label": null,
-                        "name": "BAM filter",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "bam"
+                                "description": "PacBio reads in fastq format",
+                                "name": "PacBio reads"
                             }
                         ],
+                        "label": "PacBio reads",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1265.01953125,
-                            "top": 0.0
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2e957d4c4b95",
-                            "name": "ngsutils_bam_filter",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 242.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 253.5,
+                            "right": 453.5,
+                            "top": 160,
+                            "width": 200,
+                            "x": 253.5,
+                            "y": 160
                         },
-                        "tool_state": "{\"excludebed\": {\"__class__\": \"RuntimeValue\"}, \"excluderef\": \"\", \"ignore_strand\": \"false\", \"includebed\": {\"__class__\": \"RuntimeValue\"}, \"includeref\": \"\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mapped\": \"false\", \"mask\": \"\", \"maximum_mismatch_ratio\": null, \"maxlen\": null, \"minlen\": null, \"mismatch\": null, \"nopcrdup\": \"false\", \"noproperpair\": \"false\", \"noqcfail\": \"false\", \"nosecondary\": \"false\", \"properpair\": \"false\", \"uniq\": \"-1\", \"uniq_start\": \"false\", \"unmapped\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.5.9",
-                        "type": "tool",
-                        "uuid": "e2b45ca6-2a67-4b95-a454-5c67fa87bccb",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "c1c6c99c-c810-41f4-84f3-5998c50b1422"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fastqsanger.gz\"]}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "022ec16e-3c15-45db-99c0-167a7d3121fe",
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
+                        "annotation": "Reference genome from JGI",
+                        "content_id": null,
                         "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "infile": {
-                                "id": 4,
-                                "output_name": "output"
-                            }
-                        },
+                        "id": 1,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool BAM filter",
-                                "name": "excludebed"
-                            },
-                            {
-                                "description": "runtime parameter for tool BAM filter",
-                                "name": "includebed"
-                            }
-                        ],
-                        "label": null,
-                        "name": "BAM filter",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "bam"
+                                "description": "Reference genome from JGI",
+                                "name": "Reference genome"
                             }
                         ],
+                        "label": "Reference genome",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1268.0078125,
-                            "top": 354.00390625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2e957d4c4b95",
-                            "name": "ngsutils_bam_filter",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 418.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 255,
+                            "right": 455,
+                            "top": 336,
+                            "width": 200,
+                            "x": 255,
+                            "y": 336
                         },
-                        "tool_state": "{\"excludebed\": {\"__class__\": \"RuntimeValue\"}, \"excluderef\": \"\", \"ignore_strand\": \"false\", \"includebed\": {\"__class__\": \"RuntimeValue\"}, \"includeref\": \"\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mapped\": \"true\", \"mask\": \"\", \"maximum_mismatch_ratio\": null, \"maxlen\": null, \"minlen\": null, \"mismatch\": null, \"nopcrdup\": \"false\", \"noproperpair\": \"false\", \"noqcfail\": \"false\", \"nosecondary\": \"false\", \"properpair\": \"false\", \"uniq\": \"-1\", \"uniq_start\": \"false\", \"unmapped\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.5.9",
-                        "type": "tool",
-                        "uuid": "eb538482-dcf6-4509-b4b0-3da71ac6c600",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "b7c08a3a-296d-4352-90a6-423897d8cc74"
-                            }
-                        ]
-                    },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "abf0462d-3f02-4be7-8079-a97f496b4683",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPacBio reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Flye\"];\n  0 -->|output| 2;\n  d7badcb2-4d38-4dda-b89b-b4bd3ffbc64a[\"Output\\nFlye on input dataset(s): assembly info\"];\n  2 --> d7badcb2-4d38-4dda-b89b-b4bd3ffbc64a;\n  style d7badcb2-4d38-4dda-b89b-b4bd3ffbc64a stroke:#2c3143,stroke-width:4px;\n  c8f96c22-e06e-4fec-bbfa-d993b7b103eb[\"Output\\nFlye on input dataset(s): consensus\"];\n  2 --> c8f96c22-e06e-4fec-bbfa-d993b7b103eb;\n  style c8f96c22-e06e-4fec-bbfa-d993b7b103eb stroke:#2c3143,stroke-width:4px;\n  a288fb93-5aa5-4231-89e4-958c57106978[\"Output\\nFlye on input dataset(s): graphical fragment assembly\"];\n  2 --> a288fb93-5aa5-4231-89e4-958c57106978;\n  style a288fb93-5aa5-4231-89e4-958c57106978 stroke:#2c3143,stroke-width:4px;\n  0e064181-5cd4-42c8-98f9-fe417303956c[\"Output\\nFlye on input dataset(s): assembly graph\"];\n  2 --> 0e064181-5cd4-42c8-98f9-fe417303956c;\n  style 0e064181-5cd4-42c8-98f9-fe417303956c stroke:#2c3143,stroke-width:4px;\n  3[\"Fasta Statistics\"];\n  1 -->|output| 3;\n  4[\"Busco\"];\n  1 -->|output| 4;\n  5[\"Fasta Statistics\"];\n  2 -->|consensus| 5;\n  6[\"Quast\"];\n  1 -->|output| 6;\n  2 -->|consensus| 6;\n  bea191cb-f88d-4103-b8fa-b3683d77cc93[\"Output\\nQuast on input dataset(s):  HTML report\"];\n  6 --> bea191cb-f88d-4103-b8fa-b3683d77cc93;\n  style bea191cb-f88d-4103-b8fa-b3683d77cc93 stroke:#2c3143,stroke-width:4px;\n  7[\"Busco\"];\n  2 -->|consensus| 7;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Genome Assembly using PacBio data",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9+galaxy0",
                         "errors": null,
-                        "id": 7,
+                        "id": 2,
                         "input_connections": {
-                            "input_bams": {
-                                "id": 5,
-                                "output_name": "outfile"
+                            "inputs": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Convert, Merge, Randomize",
+                        "name": "Flye",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 1559.00390625,
-                            "top": 110.9765625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "befc9dad4ca8",
-                            "name": "bamtools",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"convert\", \"__current_case__\": 0, \"format_type\": {\"format_type_selector\": \"sam\", \"__current_case__\": 6, \"noheader\": \"false\"}}, \"input_bams\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.5.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "8dc250e9-c89b-40be-8432-08a7330d6e27",
-                        "workflow_outputs": [
+                                "name": "consensus",
+                                "type": "fasta"
+                            },
                             {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "8ad07a76-7793-43b2-add3-7e236a696172"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "input_bams": {
-                                "id": 6,
-                                "output_name": "outfile"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Convert, Merge, Randomize",
-                        "outputs": [
+                                "name": "assembly_graph",
+                                "type": "graph_dot"
+                            },
                             {
-                                "name": "out_file1",
+                                "name": "assembly_gfa",
                                 "type": "txt"
+                            },
+                            {
+                                "name": "assembly_info",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1548.0078125,
-                            "top": 462.98828125
+                            "bottom": 441.8999938964844,
+                            "height": 286.3999938964844,
+                            "left": 547.5,
+                            "right": 747.5,
+                            "top": 155.5,
+                            "width": 200,
+                            "x": 547.5,
+                            "y": 155.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "befc9dad4ca8",
-                            "name": "bamtools",
-                            "owner": "devteam",
+                            "changeset_revision": "276f5d8712d5",
+                            "name": "flye",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"convert\", \"__current_case__\": 0, \"format_type\": {\"format_type_selector\": \"sam\", \"__current_case__\": 6, \"noheader\": \"false\"}}, \"input_bams\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.5.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "b5c1bcac-9624-477c-998f-a0988b110a26",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "9801f8ee-e700-4e9b-bbfc-7ccf7aa99372"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "random_lines1",
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "input": {
-                                "id": 7,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Select random lines",
-                                "name": "input"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Select random lines",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 1823.0078125,
-                            "top": 182.98828125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "random_lines1",
-                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"num_lines\": \"210000\", \"seed_source\": {\"seed_source_selector\": \"no_seed\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2",
+                        "tool_state": "{\"asm\": {\"asm_select\": \"false\", \"__current_case__\": 1}, \"generate_log\": \"false\", \"inputs\": {\"__class__\": \"ConnectedValue\"}, \"iterations\": \"1\", \"keep_haplotypes\": \"false\", \"meta\": \"false\", \"min_overlap\": null, \"mode_conditional\": {\"mode\": \"--pacbio-raw\", \"__current_case__\": 3}, \"scaffold\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.9+galaxy0",
                         "type": "tool",
-                        "uuid": "88f4ed97-5899-48f1-a5de-256be6e58862",
+                        "uuid": "b46b2319-5fa8-4055-817f-15eea86c4049",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "69da2900-e66d-4d95-9bdb-1d9f801097e3"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "random_lines1",
-                        "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "input": {
-                                "id": 8,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [
+                                "label": "Flye on input dataset(s): assembly info",
+                                "output_name": "assembly_info",
+                                "uuid": "d7badcb2-4d38-4dda-b89b-b4bd3ffbc64a"
+                            },
                             {
-                                "description": "runtime parameter for tool Select random lines",
-                                "name": "input"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Select random lines",
-                        "outputs": [
+                                "label": "Flye on input dataset(s): consensus",
+                                "output_name": "consensus",
+                                "uuid": "c8f96c22-e06e-4fec-bbfa-d993b7b103eb"
+                            },
                             {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 1826.9921875,
-                            "top": 535.99609375
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "random_lines1",
-                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"num_lines\": \"1000000\", \"seed_source\": {\"seed_source_selector\": \"no_seed\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2",
-                        "type": "tool",
-                        "uuid": "9064c0e8-fdc9-4347-99c2-bd6d97104fc9",
-                        "workflow_outputs": [
+                                "label": "Flye on input dataset(s): graphical fragment assembly",
+                                "output_name": "assembly_gfa",
+                                "uuid": "a288fb93-5aa5-4231-89e4-958c57106978"
+                            },
                             {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "fd4f3605-1f48-4583-b11a-91a9869e7946"
+                                "label": "Flye on input dataset(s): assembly graph",
+                                "output_name": "assembly_graph",
+                                "uuid": "0e064181-5cd4-42c8-98f9-fe417303956c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
                         "errors": null,
-                        "id": 11,
+                        "id": 5,
                         "input_connections": {
-                            "input": {
-                                "id": 9,
-                                "output_name": "out_file1"
+                            "fasta": {
+                                "id": 2,
+                                "output_name": "consensus"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Filter Tabular",
+                        "name": "Fasta Statistics",
                         "outputs": [
                             {
-                                "name": "output",
+                                "name": "stats_output",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 2081.015625,
-                            "top": 212.98828125
+                            "bottom": 278.3999938964844,
+                            "height": 154.39999389648438,
+                            "left": 905,
+                            "right": 1105,
+                            "top": 124,
+                            "width": 200,
+                            "x": 905,
+                            "y": 124
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "34d29339abab",
-                            "name": "filter_tabular",
+                            "changeset_revision": "0dbb995c7d35",
+                            "name": "fasta_stats",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"select_columns\", \"__current_case__\": 7, \"columns\": \"1\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.0",
+                        "tool_state": "{\"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gaps_option\": \"false\", \"genome_size\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0",
                         "type": "tool",
-                        "uuid": "302a62bb-98f7-4998-b290-281bb52e3c70",
+                        "uuid": "6ec5c36e-0b3d-41b9-9cc8-899350540545",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "e83fbb91-742e-448f-8592-bdf37ce3cbdf"
+                                "output_name": "stats_output",
+                                "uuid": "400afe45-b895-41aa-a2b9-3c222c344f7b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy3",
                         "errors": null,
-                        "id": 12,
+                        "id": 6,
                         "input_connections": {
-                            "input": {
-                                "id": 10,
-                                "output_name": "out_file1"
+                            "assembly|ref|r": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "in|inputs": {
+                                "id": 2,
+                                "output_name": "consensus"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Quast",
+                                "name": "in"
+                            }
+                        ],
                         "label": null,
-                        "name": "Filter Tabular",
+                        "name": "Quast",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "name": "report_html",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 2085,
-                            "top": 566.97265625
+                            "bottom": 593,
+                            "height": 266,
+                            "left": 902.5,
+                            "right": 1102.5,
+                            "top": 327,
+                            "width": 200,
+                            "x": 902.5,
+                            "y": 327
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy3",
                         "tool_shed_repository": {
-                            "changeset_revision": "34d29339abab",
-                            "name": "filter_tabular",
+                            "changeset_revision": "7594365c546b",
+                            "name": "quast",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"select_columns\", \"__current_case__\": 7, \"columns\": \"1\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.0",
+                        "tool_state": "{\"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": \"false\", \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": \"true\", \"fragmented_max_indent\": null}, \"alignments\": {\"use_all_alignments\": \"false\", \"min_alignment\": \"65\", \"min_identity\": \"95.0\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": \"false\", \"upper_bound_assembly\": \"false\", \"upper_bound_min_con\": null}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"true\", \"__current_case__\": 0, \"r\": {\"__class__\": \"RuntimeValue\"}, \"features\": {\"__class__\": \"RuntimeValue\"}, \"operons\": {\"__class__\": \"RuntimeValue\"}, \"k_mer\": {\"k_mer_stats\": \"\", \"__current_case__\": 1}, \"circos\": \"false\"}, \"orga_type\": \"--fungus\"}, \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": \"false\", \"conserved_genes_finding\": \"false\"}, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"RuntimeValue\"}}, \"large\": \"false\", \"min_contig\": \"500\", \"output_files\": [\"html\"], \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}, \"split_scaffolds\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.0.2+galaxy3",
                         "type": "tool",
-                        "uuid": "ab1a4102-7bb2-4ba7-80d1-2a532b410201",
+                        "uuid": "f734c70b-03c8-4fc3-8350-27a7230cbd58",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "2701a2bd-2ec9-433a-9f26-7f35410ec018"
+                                "label": "Quast on input dataset(s):  HTML report",
+                                "output_name": "report_html",
+                                "uuid": "bea191cb-f88d-4103-b8fa-b3683d77cc93"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2",
                         "errors": null,
-                        "id": 13,
+                        "id": 7,
                         "input_connections": {
                             "input": {
-                                "id": 11,
-                                "output_name": "output"
+                                "id": 2,
+                                "output_name": "consensus"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Unique",
+                        "name": "Busco",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "input"
+                                "name": "busco_sum",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "busco_table",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 2330,
-                            "top": 265.99609375
+                            "bottom": 847.1999969482422,
+                            "height": 205.1999969482422,
+                            "left": 906.5,
+                            "right": 1106.5,
+                            "top": 642,
+                            "width": 200,
+                            "x": 906.5,
+                            "y": 642
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
+                        "post_job_actions": {
+                            "HideDatasetActionbusco_table": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "busco_table"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "7ce75adb93be",
-                            "name": "unique",
-                            "owner": "bgruening",
+                            "changeset_revision": "46ae58b1d792",
+                            "name": "busco",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"ignore_case\": \"false\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"is_numeric\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3",
+                        "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": \"mucorales_odb10\"}, \"outputs\": [\"short_summary\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.2.2+galaxy2",
                         "type": "tool",
-                        "uuid": "2a68a6a4-4d3d-4de3-bc64-35edc63287f9",
+                        "uuid": "fb896bc9-5ebd-41a1-82a7-1dae23e23dac",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "b2bb66d7-fe76-4ce3-bb5b-72c979a755d1"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
-                        "errors": null,
-                        "id": 14,
-                        "input_connections": {
-                            "input": {
-                                "id": 12,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Unique",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 2331.97265625,
-                            "top": 617.94921875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "7ce75adb93be",
-                            "name": "unique",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"ignore_case\": \"false\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"is_numeric\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3",
-                        "type": "tool",
-                        "uuid": "c2d1dc5c-4d14-45e5-9bb9-bdab787ea5f3",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "df0bbae1-b735-4cf4-a5a3-ef4f8b525a4e"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-                        "errors": null,
-                        "id": 15,
-                        "input_connections": {
-                            "inputs": [
-                                {
-                                    "id": 13,
-                                    "output_name": "outfile"
-                                },
-                                {
-                                    "id": 14,
-                                    "output_name": "outfile"
-                                }
-                            ]
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Concatenate datasets",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 2575,
-                            "top": 417.98828125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f46f0e4f75c4",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.1",
-                        "type": "tool",
-                        "uuid": "bf2ba224-25ae-4ec3-9a1f-7cb1afd0aef2",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "53ae320a-b570-4985-ae2a-8344e15e43f9"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-                        "errors": null,
-                        "id": 16,
-                        "input_connections": {
-                            "in_file": {
-                                "id": 2,
-                                "output_name": "out1"
-                            },
-                            "source|name_list": {
-                                "id": 15,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "seqtk_subseq",
-                        "outputs": [
-                            {
-                                "name": "default",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 2847.98828125,
-                            "top": 819.98046875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3da72230c066",
-                            "name": "seqtk",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"in_file\": {\"__class__\": \"ConnectedValue\"}, \"l\": \"0\", \"source\": {\"type\": \"name\", \"__current_case__\": 1, \"name_list\": {\"__class__\": \"ConnectedValue\"}}, \"t\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3.1",
-                        "type": "tool",
-                        "uuid": "478adb2b-4910-4aed-af4e-2a66e9a1922c",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "default",
-                                "uuid": "b47e4af0-c185-4b6f-a529-6f0ef96a14ab"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-                        "errors": null,
-                        "id": 17,
-                        "input_connections": {
-                            "in_file": {
-                                "id": 2,
-                                "output_name": "out2"
-                            },
-                            "source|name_list": {
-                                "id": 15,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "seqtk_subseq",
-                        "outputs": [
-                            {
-                                "name": "default",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 2836.97265625,
-                            "top": 1019.98046875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3da72230c066",
-                            "name": "seqtk",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"in_file\": {\"__class__\": \"ConnectedValue\"}, \"l\": \"0\", \"source\": {\"type\": \"name\", \"__current_case__\": 1, \"name_list\": {\"__class__\": \"ConnectedValue\"}}, \"t\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3.1",
-                        "type": "tool",
-                        "uuid": "81ae5423-c7d0-4ceb-a6e4-168ab1f3fd35",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "default",
-                                "uuid": "c7de5bbe-f941-4772-bb32-15aeff98678a"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-                        "errors": null,
-                        "id": 18,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 16,
-                                "output_name": "default"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "adapters"
-                            },
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "contaminants"
-                            },
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "limits"
-                            }
-                        ],
-                        "label": null,
-                        "name": "FastQC",
-                        "outputs": [
-                            {
-                                "name": "html_file",
-                                "type": "html"
-                            },
-                            {
-                                "name": "text_file",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 3135.9765625,
-                            "top": 775.99609375
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3d0c7bdf12f5",
-                            "name": "fastqc",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adapters\": {\"__class__\": \"RuntimeValue\"}, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"min_length\": null, \"nogroup\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.73+galaxy0",
-                        "type": "tool",
-                        "uuid": "6d6cee2a-b879-463b-81d1-7ab4f72ca04b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "text_file",
-                                "uuid": "ca3ea14a-b1cc-481d-b1a3-2b46b8d24809"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "html_file",
-                                "uuid": "6849e3f4-33bc-47a9-8ef5-b7cbbdfe0d93"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-                        "errors": null,
-                        "id": 19,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 17,
-                                "output_name": "default"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "adapters"
-                            },
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "contaminants"
-                            },
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "limits"
-                            }
-                        ],
-                        "label": null,
-                        "name": "FastQC",
-                        "outputs": [
-                            {
-                                "name": "html_file",
-                                "type": "html"
-                            },
-                            {
-                                "name": "text_file",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 3133.984375,
-                            "top": 1104.98046875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3d0c7bdf12f5",
-                            "name": "fastqc",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adapters\": {\"__class__\": \"RuntimeValue\"}, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"min_length\": null, \"nogroup\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.73+galaxy0",
-                        "type": "tool",
-                        "uuid": "54fc20b8-5520-4b93-a7d8-ed447df19b3c",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "html_file",
-                                "uuid": "a85a4180-b2ab-4cac-9c71-76aee3df673f"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "text_file",
-                                "uuid": "65e24721-ec93-4648-9310-c3c2609b7818"
+                                "output_name": "busco_sum",
+                                "uuid": "5a62f2bb-17ec-4091-985f-bd9c69f9fe61"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/metagenomics-assembly",
-                "path": "topics/assembly/tutorials/metagenomics-assembly/workflows/workflow-generate-dataset-for-assembly-tutorial.ga",
-                "tags": [],
+                "parent_id": "assembly/flye-assembly",
+                "path": "topics/assembly/tutorials/flye-assembly/workflows/main_workflow.ga",
+                "tags": [
+                    "assembly"
+                ],
                 "test_results": null,
                 "tests": false,
-                "title": "workflow-generate-dataset-for-assembly-tutorial",
+                "title": "Genome Assembly using PacBio data",
                 "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-metagenomics-assembly/versions/workflow-generate-dataset-for-assembly-tutorial",
-                "tutorial_id": "metagenomics-assembly",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/metagenomics-assembly/workflows/workflow-generate-dataset-for-assembly-tutorial.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/metagenomics-assembly/workflows/workflow-generate-dataset-for-assembly-tutorial.html",
-                "version": 0,
-                "wfid": "assembly-metagenomics-assembly",
-                "wfname": "workflow-generate-dataset-for-assembly-tutorial",
-                "workflow": "workflow-generate-dataset-for-assembly-tutorial.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-flye-assembly/versions/main-workflow",
+                "tutorial_id": "flye-assembly",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/flye-assembly/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/flye-assembly/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "assembly-flye-assembly",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "random_lines1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-                    "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy3"
                 ],
-                "workflowhub_id": "1116"
+                "workflowhub_id": "1131"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/7818827"
+        "zenodo_link": "https://zenodo.org/record/5702408"
     },
     {
-        "abbreviations": {
-            "SVs": "Structural Variations"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "flye",
-                    "owner": "bgruening",
-                    "revisions": "cb8dfd28c16f",
-                    "tool_panel_section_label": "Assembly",
+                    "name": "bowtie2",
+                    "owner": "devteam",
+                    "revisions": "749c918495f7",
+                    "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fastqc",
+                    "name": "fasta_filter_by_length",
                     "owner": "devteam",
-                    "revisions": "5ec9f6bceaee",
+                    "revisions": "8cacfcf96a52",
                     "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "samtools_stats",
+                    "owner": "devteam",
+                    "revisions": "145f6d74ff5e",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "bandage",
                     "owner": "iuc",
-                    "revisions": "ddddce450736",
+                    "revisions": "b2860df42e16",
                     "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bwa_mem2",
+                    "name": "bandage",
                     "owner": "iuc",
-                    "revisions": "bfaa0d22c2e4",
-                    "tool_panel_section_label": "Mapping",
+                    "revisions": "94fe43e75ddc",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "fastp",
                     "owner": "iuc",
-                    "revisions": "65b93b623c77",
+                    "revisions": "1d8fe9bc4cb0",
                     "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "filtlong",
+                    "name": "minimap2",
                     "owner": "iuc",
-                    "revisions": "8880fb74ef56",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "53c0b7a1a0c3",
+                    "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "filtlong",
+                    "name": "multiqc",
                     "owner": "iuc",
-                    "revisions": "1f296803dfa3",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "b2f1f75d49c4",
+                    "tool_panel_section_label": "Quality Control",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "nanoplot",
                     "owner": "iuc",
-                    "revisions": "0f1c34698076",
+                    "revisions": "645159bcee2d",
                     "tool_panel_section_label": "Nanopore",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "polypolish",
+                    "name": "samtools_fastx",
                     "owner": "iuc",
-                    "revisions": "f355085dd2aa",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "revisions": "a8d69aee190e",
+                    "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "porechop",
+                    "name": "samtools_view",
                     "owner": "iuc",
-                    "revisions": "93d623d9979c",
-                    "tool_panel_section_label": "Nanopore",
+                    "revisions": "b01db2684fa5",
+                    "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "quast",
+                    "name": "seqtk",
                     "owner": "iuc",
-                    "revisions": "72472698a2df",
+                    "revisions": "3da72230c066",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sra_tools",
+                    "owner": "iuc",
+                    "revisions": "aad3885b3216",
+                    "tool_panel_section_label": "Get Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "unicycler",
+                    "owner": "iuc",
+                    "revisions": "9e3e80cc4ad4",
                     "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "830961c48e42",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: flye\n  owner: bgruening\n  revisions: cb8dfd28c16f\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_mem2\n  owner: iuc\n  revisions: bfaa0d22c2e4\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filtlong\n  owner: iuc\n  revisions: 8880fb74ef56\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filtlong\n  owner: iuc\n  revisions: 1f296803dfa3\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: 0f1c34698076\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: polypolish\n  owner: iuc\n  revisions: f355085dd2aa\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: porechop\n  owner: iuc\n  revisions: 93d623d9979c\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 72472698a2df\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-nanopore/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "bazante1",
-                "bebatut"
-            ],
-            "editing": [
-                "hexylena",
-                "bazante1",
-                "shiltemann",
-                "miaomiaozhou88"
-            ],
-            "funding": [
-                "avans-atgm",
-                "abromics"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bowtie2\n  owner: devteam\n  revisions: 749c918495f7\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_filter_by_length\n  owner: devteam\n  revisions: 8cacfcf96a52\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 145f6d74ff5e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: b2860df42e16\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: 94fe43e75ddc\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 1d8fe9bc4cb0\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: 53c0b7a1a0c3\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: b2f1f75d49c4\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: 645159bcee2d\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_fastx\n  owner: iuc\n  revisions: a8d69aee190e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: b01db2684fa5\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: aad3885b3216\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unicycler\n  owner: iuc\n  revisions: 9e3e80cc4ad4\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
-                    "avans-atgm"
-                ],
-                "id": "bazante1",
-                "joined": "2020-12",
-                "name": "Bazante Sanders",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
                     "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "affiliations": [
-                    "avans-atgm"
-                ],
-                "id": "bazante1",
-                "joined": "2020-12",
-                "name": "Bazante Sanders",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
+                    "uni-freiburg",
+                    "elixir-europe"
                 ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
+                "elixir_node": "de",
+                "fediverse": "https://scholar.social/@zerodivision",
                 "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
+                "id": "wm75",
                 "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
-            {
-                "email": "m.zhou1@avans.nl",
-                "id": "miaomiaozhou88",
-                "joined": "2020-12",
-                "name": "Miaomiao Zhou",
-                "orcid": "0000-0003-4426-1758",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/miaomiaozhou88/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/miaomiaozhou88.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/logo-avans.png",
-                "former_members": [
-                    "dirowa",
-                    "hexylena"
-                ],
-                "id": "avans-atgm",
-                "joined": "2020-11",
-                "members": [
-                    "bazante1"
-                ],
-                "name": "Avans Hogeschool",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/",
-                "ror": "015d5s513",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
-            },
-            {
-                "avatar": "/training-material/assets/images/abromics.png",
-                "funder": true,
-                "github": false,
-                "id": "abromics",
-                "joined": "2024-01",
-                "name": "ABRomics",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abromics/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/abromics.json"
+                "matrix": "wm75:matrix.org",
+                "name": "Wolfgang Maier",
+                "orcid": "0000-0002-9464-6640",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
             }
         ],
-        "dir": "topics/assembly/tutorials/mrsa-nanopore",
-        "edam_ontology": [
-            "topic_0196",
-            "topic_3673",
-            "topic_3305",
-            "topic_0622",
-            "topic_3301",
-            "topic_4013"
-        ],
+        "dir": "topics/assembly/tutorials/assembly-with-preprocessing",
         "edam_operation": [
-            "Visualisation",
+            "Scatter plot plotting",
+            "Data handling",
+            "Read mapping",
             "Sequencing quality control",
-            "Sequence contamination filtering",
             "Genome assembly",
-            "De-novo assembly",
-            "Sequence alignment",
             "Box-Whisker plot plotting",
-            "Sequence assembly validation",
-            "Sequence composition calculation",
-            "Read mapping",
-            "Scatter plot plotting",
-            "Mapping assembly",
-            "Sequencing error detection",
+            "Sequence contamination filtering",
+            "Aggregation",
             "Sequence assembly visualisation",
-            "Cross-assembly",
-            "Filtering",
-            "Statistical calculation"
-        ],
-        "edam_topic": [
-            "Sequence assembly",
-            "Whole genome sequencing",
-            "Public health and epidemiology",
-            "Genomics",
-            "Microbiology",
-            "Antimicrobial Resistance"
+            "Pairwise sequence alignment",
+            "Validation",
+            "Sequence file editing"
         ],
+        "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.eu",
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "genome-annotation",
-                "tutorials": [
-                    "amr-gene-detection"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "history-to-workflow"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "assembly/mrsa-nanopore",
+        "id": "assembly/assembly-with-preprocessing",
         "inexact_supported_servers": [
-            "UseGalaxy.cz"
+            "MISSISSIPPI",
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)"
         ],
         "js_requirements": {
-            "mathjax": 11271,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Nanopore produces fantastic assemblies but with low quality data",
-            "Annotation with Prokka is very easy"
+            "Certain types of NGS samples can be heavily contaminated with sequences from other genomes",
+            "Reads from known/expected contaminating sources can be identified by mapping to the respective genomes",
+            "After mapping, use filtering tools to remove identified contaminating reads, and use conversion tools to convert remaining mapped reads back into raw sequenced reads expected by most downstream tools"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-13",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Run tools to evaluate sequencing data on quality and quantity",
-            "Process the output of quality control tools",
-            "Improve the quality of sequencing data",
-            "Run a tool to assemble a bacterial genome using short reads",
-            "Run tools to assess the quality of an assembly",
-            "Understand the outputs of tools to assess the quality of an assembly"
+            "Obtain viral (SARS-CoV-2) sequencing data with contaminating human reads from public sources",
+            "Organize the data into collections and check its quality",
+            "Detect and remove human reads",
+            "Assemble retained reads and explore the results"
         ],
-        "pageviews": 10571,
-        "pub_date": "2021-03-24",
+        "pageviews": 5905025,
+        "pub_date": "2020-04-21",
         "questions": [
-            "How to check the quality of the MinION data (together with Illumina data)?",
-            "How to perform an assembly of a bacterial genome with MinION data?",
-            "How to check the quality of an assembly?"
+            "How can a genome of interest be assembled against a background of contaminating reads from other genomes?",
+            "How can sequencing data from public sources be turned into assembly-ready polished datasets?"
         ],
-        "short_id": "T00037",
+        "recordings": [
+            {
+                "captioners": [
+                    "mtekman"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "25M",
+                "speakers": [
+                    "gallardoalba"
+                ],
+                "youtube_id": "jNFLYhjgJPs"
+            }
+        ],
+        "requirements": [
+            {
+                "topic_name": "assembly",
+                "tutorials": [
+                    "unicycler-assembly"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "sequence-analysis",
+                "tutorials": [
+                    "mapping"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "collections"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00029",
         "short_tools": [
-            "nanoplot",
+            "samtools_stats",
+            "unicycler",
             "fastp",
-            "CONVERTER_bz2_to_uncompressed",
-            "filtlong",
-            "flye",
-            "bwa_mem2",
-            "quast",
-            "fastqc",
-            "polypolish",
+            "minimap2",
             "bandage_image",
-            "upload1",
-            "porechop"
+            "samtools_view",
+            "fasta_filter_by_length",
+            "bandage_info",
+            "samtools_fastx",
+            "multiqc",
+            "seqtk_sample",
+            "fasterq_dump",
+            "nanoplot",
+            "collapse_dataset",
+            "__ZIP_COLLECTION__",
+            "bowtie2"
         ],
-        "slides": false,
+        "slides": true,
         "slides_recordings": false,
         "supported_servers": {
             "exact": [
@@ -16956,41 +16483,69 @@
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ],
             "inexact": [
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
         "tags": [
-            "nanopore",
-            "assembly",
-            "amr",
-            "gmod",
-            "jbrowse1",
-            "microgalaxy"
+            "covid19"
         ],
-        "time_estimation": "2h",
-        "title": "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)",
+        "time_estimation": "4h",
+        "title": "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads",
         "tools": [
-            "CONVERTER_bz2_to_uncompressed",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/polypolish/polypolish/0.5.0+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
-            "upload1"
+            "__ZIP_COLLECTION__",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
         ],
         "topic_name": "assembly",
         "topic_name_human": "Assembly",
@@ -17000,998 +16555,488 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "mrsa-nanopore",
+        "tutorial_name": "assembly-with-preprocessing",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-nanopore/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-nanopore/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.json"
         },
-        "version": 14,
+        "version": 13,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 206,
-        "visitors": 6851,
+        "visit_duration": 364,
+        "visitors": 2138036,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0003-2255-1631",
-                        "name": "Bazante Sanders"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0001-9852-1987",
-                        "name": "B\u00e9r\u00e9nice Batut"
-                    }
-                ],
-                "description": "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)",
+                "creators": [],
+                "description": "Assembly with preprocessing",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nNanopore raw reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina forward raw reads\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reverse raw reads\"]\n  3[label=\"Convert compressed file to uncompressed.\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"FastQC\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"fastp\"]\n  1 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"NanoPlot\"]\n  3 -> 6 [label=\"output1\"]\n  ka97e6f3381824a3386dd6cfbb83a842d[color=lightseagreen,label=\"Output\\nnanoplot_before_filtering\"]\n  6 -> ka97e6f3381824a3386dd6cfbb83a842d\n  7[label=\"filtlong\"]\n  5 -> 7 [label=\"out1\"]\n  5 -> 7 [label=\"out2\"]\n  0 -> 7 [label=\"output\"]\n  8[label=\"Flye\"]\n  7 -> 8 [label=\"outfile\"]\n  kf12e718f1bd5490dbd41f0747aaa41a6[color=lightseagreen,label=\"Output\\nflye_assembly_info\"]\n  8 -> kf12e718f1bd5490dbd41f0747aaa41a6\n  9[label=\"NanoPlot\"]\n  7 -> 9 [label=\"outfile\"]\n  k89524090f590434d89e266f0b1a23c7c[color=lightseagreen,label=\"Output\\nnanoplot_after_filtering\"]\n  9 -> k89524090f590434d89e266f0b1a23c7c\n  10[label=\"Bandage Image\"]\n  8 -> 10 [label=\"assembly_gfa\"]\n  11[label=\"BWA-MEM2\"]\n  5 -> 11 [label=\"out2\"]\n  8 -> 11 [label=\"consensus\"]\n  12[label=\"Quast\"]\n  8 -> 12 [label=\"consensus\"]\n  kdabfb8fd87914959a9dc9b3c1e57a69c[color=lightseagreen,label=\"Output\\nquast_report_before_polishing\"]\n  12 -> kdabfb8fd87914959a9dc9b3c1e57a69c\n  13[label=\"BWA-MEM2\"]\n  5 -> 13 [label=\"out1\"]\n  8 -> 13 [label=\"consensus\"]\n  14[label=\"Polypolish\"]\n  8 -> 14 [label=\"consensus\"]\n  13 -> 14 [label=\"bam_output\"]\n  11 -> 14 [label=\"bam_output\"]\n  15[label=\"Quast\"]\n  14 -> 15 [label=\"polished_fasta\"]\n  8 -> 15 [label=\"consensus\"]\n  k4e465b5168bf42039a7c897f46c70277[color=lightseagreen,label=\"Output\\nquast_report_after_polishing\"]\n  15 -> k4e465b5168bf42039a7c897f46c70277\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nCollection of paired short-reads data\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nCollection of long-reads data\"]\n  10[label=\"Samtools fastx\"]\n  7 -> 10 [label=\"outputsam\"]\n  11[label=\"Samtools fastx\"]\n  9 -> 11 [label=\"outputsam\"]\n  12[label=\"Collapse Collection\"]\n  10 -> 12 [label=\"nonspecific\"]\n  13[label=\"Zip Collection\"]\n  11 -> 13 [label=\"forward\"]\n  11 -> 13 [label=\"reverse\"]\n  14[label=\"Collapse Collection\"]\n  11 -> 14 [label=\"forward\"]\n  15[label=\"Collapse Collection\"]\n  11 -> 15 [label=\"reverse\"]\n  16[label=\"seqtk_sample\"]\n  14 -> 16 [label=\"output\"]\n  17[label=\"seqtk_sample\"]\n  15 -> 17 [label=\"output\"]\n  18[label=\"Create assemblies with Unicycler\"]\n  12 -> 18 [label=\"output\"]\n  16 -> 18 [label=\"default\"]\n  17 -> 18 [label=\"default\"]\n  19[label=\"Bandage Info\"]\n  18 -> 19 [label=\"assembly_graph\"]\n  2[label=\"fastp: Trimmed Illumina Reads\"]\n  0 -> 2 [label=\"output\"]\n  20[label=\"Filter sequences by length\"]\n  18 -> 20 [label=\"assembly\"]\n  21[label=\"Bandage Image\"]\n  18 -> 21 [label=\"assembly_graph\"]\n  3[label=\"NanoPlot\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Map with minimap2\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"MultiQC\"]\n  2 -> 5 [label=\"report_json\"]\n  6[label=\"Bowtie2\"]\n  2 -> 6 [label=\"output_paired_coll\"]\n  7[label=\"Samtools view\"]\n  4 -> 7 [label=\"alignment_output\"]\n  8[label=\"Samtools stats\"]\n  4 -> 8 [label=\"alignment_output\"]\n  9[label=\"Samtools view\"]\n  6 -> 9 [label=\"output\"]\n}",
                 "history": [
                     {
-                        "hash": "96393a7fcb4d6dc37d86866cf8a61c931293502f",
-                        "message": "Add MRSA Nanopore assembly tutorial to AMR learning pathway",
+                        "hash": "fc35e6581a2e34e4420f19af4619c92283609e91",
+                        "message": "add annotations",
+                        "num": 2,
+                        "short_hash": "fc35e6581",
+                        "unix": "1587558793"
+                    },
+                    {
+                        "hash": "7ed054469d1ef84a60abec55758ee2932f9a9655",
+                        "message": "readd workflows",
                         "num": 1,
-                        "short_hash": "96393a7fc",
-                        "unix": "1709135526"
+                        "short_hash": "7ed054469",
+                        "unix": "1587555276"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "Nanopore raw reads",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Nanopore raw reads",
-                                "name": "Nanopore raw reads"
-                            }
-                        ],
-                        "label": "Nanopore raw reads",
-                        "name": "Input dataset",
+                        "inputs": [],
+                        "label": "Collection of paired short-reads data",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 65.66800632871802,
-                            "top": 217.27323322511424
+                            "left": 268.13330078125,
+                            "top": 341.41668701171875
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"collection_type\": \"list:paired\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "cd4fd302-af94-4771-9b80-7c7acb6619d4",
-                        "when": null,
-                        "workflow_outputs": []
+                        "type": "data_collection_input",
+                        "uuid": "3e7dab04-77db-4780-b1dd-c724b80a8b7b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "daba9931-3837-42b5-a93f-e2e51f5f667a"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "Illumina forward raw reads",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": "Collection of long-reads data",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 267.13330078125,
+                            "top": 756.4166717529297
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"collection_type\": \"lis\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "bd1f5561-95a1-4fb5-af1e-f3d4cbb40639",
+                        "workflow_outputs": [
                             {
-                                "description": "Illumina forward raw reads",
-                                "name": "Illumina forward raw reads"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "7146e49b-ab4b-44a8-ac54-e98539fecb97"
                             }
-                        ],
-                        "label": "Illumina forward raw reads",
-                        "name": "Input dataset",
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nCollection of paired short-reads data\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nCollection of long-reads data\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Samtools fastx\"];\n  7 -->|outputsam| 10;\n  11[\"Samtools fastx\"];\n  9 -->|outputsam| 11;\n  12[\"Collapse Collection\"];\n  10 -->|nonspecific| 12;\n  13[\"Zip Collection\"];\n  11 -->|forward| 13;\n  11 -->|reverse| 13;\n  14[\"Collapse Collection\"];\n  11 -->|forward| 14;\n  15[\"Collapse Collection\"];\n  11 -->|reverse| 15;\n  16[\"seqtk_sample\"];\n  14 -->|output| 16;\n  17[\"seqtk_sample\"];\n  15 -->|output| 17;\n  18[\"Create assemblies with Unicycler\"];\n  12 -->|output| 18;\n  16 -->|default| 18;\n  17 -->|default| 18;\n  19[\"Bandage Info\"];\n  18 -->|assembly_graph| 19;\n  2[\"fastp: Trimmed Illumina Reads\"];\n  0 -->|output| 2;\n  20[\"Filter sequences by length\"];\n  18 -->|assembly| 20;\n  21[\"Bandage Image\"];\n  18 -->|assembly_graph| 21;\n  3[\"NanoPlot\"];\n  1 -->|output| 3;\n  4[\"Map with minimap2\"];\n  1 -->|output| 4;\n  5[\"MultiQC\"];\n  2 -->|report_json| 5;\n  6[\"Bowtie2\"];\n  2 -->|output_paired_coll| 6;\n  7[\"Samtools view\"];\n  4 -->|alignment_output| 7;\n  8[\"Samtools stats\"];\n  4 -->|alignment_output| 8;\n  9[\"Samtools view\"];\n  6 -->|output| 9;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "assembly_with_preprocessing",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "Collection of paired short-reads data",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 479
+                            "left": 268.13330078125,
+                            "top": 341.41668701171875
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"collection_type\": \"list:paired\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "b3fe89da-544c-4066-abcb-b33d4f005796",
-                        "when": null,
-                        "workflow_outputs": []
+                        "type": "data_collection_input",
+                        "uuid": "3e7dab04-77db-4780-b1dd-c724b80a8b7b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "daba9931-3837-42b5-a93f-e2e51f5f667a"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "Illumina reverse raw reads",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 1,
                         "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Illumina reverse raw reads",
-                                "name": "Illumina reverse raw reads"
-                            }
-                        ],
-                        "label": "Illumina reverse raw reads",
-                        "name": "Input dataset",
+                        "inputs": [],
+                        "label": "Collection of long-reads data",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 602
+                            "left": 267.13330078125,
+                            "top": 756.4166717529297
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"collection_type\": \"lis\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "16545abc-0513-4a32-9ea5-4a168875a854",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nNanopore raw reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nIllumina forward raw reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nIllumina reverse raw reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Convert compressed file to uncompressed.\"];\n  0 -->|output| 3;\n  4[\"FastQC\"];\n  0 -->|output| 4;\n  5[\"fastp\"];\n  1 -->|output| 5;\n  2 -->|output| 5;\n  6[\"NanoPlot\"];\n  3 -->|output1| 6;\n  a97e6f33-8182-4a33-86dd-6cfbb83a842d[\"Output\\nnanoplot_before_filtering\"];\n  6 --> a97e6f33-8182-4a33-86dd-6cfbb83a842d;\n  style a97e6f33-8182-4a33-86dd-6cfbb83a842d stroke:#2c3143,stroke-width:4px;\n  7[\"filtlong\"];\n  5 -->|out1| 7;\n  5 -->|out2| 7;\n  0 -->|output| 7;\n  8[\"Flye\"];\n  7 -->|outfile| 8;\n  f12e718f-1bd5-490d-bd41-f0747aaa41a6[\"Output\\nflye_assembly_info\"];\n  8 --> f12e718f-1bd5-490d-bd41-f0747aaa41a6;\n  style f12e718f-1bd5-490d-bd41-f0747aaa41a6 stroke:#2c3143,stroke-width:4px;\n  9[\"NanoPlot\"];\n  7 -->|outfile| 9;\n  89524090-f590-434d-89e2-66f0b1a23c7c[\"Output\\nnanoplot_after_filtering\"];\n  9 --> 89524090-f590-434d-89e2-66f0b1a23c7c;\n  style 89524090-f590-434d-89e2-66f0b1a23c7c stroke:#2c3143,stroke-width:4px;\n  10[\"Bandage Image\"];\n  8 -->|assembly_gfa| 10;\n  11[\"BWA-MEM2\"];\n  5 -->|out2| 11;\n  8 -->|consensus| 11;\n  12[\"Quast\"];\n  8 -->|consensus| 12;\n  dabfb8fd-8791-4959-a9dc-9b3c1e57a69c[\"Output\\nquast_report_before_polishing\"];\n  12 --> dabfb8fd-8791-4959-a9dc-9b3c1e57a69c;\n  style dabfb8fd-8791-4959-a9dc-9b3c1e57a69c stroke:#2c3143,stroke-width:4px;\n  13[\"BWA-MEM2\"];\n  5 -->|out1| 13;\n  8 -->|consensus| 13;\n  14[\"Polypolish\"];\n  8 -->|consensus| 14;\n  13 -->|bam_output| 14;\n  11 -->|bam_output| 14;\n  15[\"Quast\"];\n  14 -->|polished_fasta| 15;\n  8 -->|consensus| 15;\n  4e465b51-68bf-4203-9a7c-897f46c70277[\"Output\\nquast_report_after_polishing\"];\n  15 --> 4e465b51-68bf-4203-9a7c-897f46c70277;\n  style 4e465b51-68bf-4203-9a7c-897f46c70277 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available)",
-                "outputs": [
+                        "type": "data_collection_input",
+                        "uuid": "bd1f5561-95a1-4fb5-af1e-f3d4cbb40639",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "7146e49b-ab4b-44a8-ac54-e98539fecb97"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
                         "errors": null,
-                        "id": 6,
+                        "id": 10,
                         "input_connections": {
-                            "mode|reads|files": {
-                                "id": 3,
-                                "output_name": "output1"
+                            "input": {
+                                "id": 7,
+                                "output_name": "outputsam"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "NanoPlot",
+                        "name": "Samtools fastx",
                         "outputs": [
                             {
-                                "name": "output_html",
-                                "type": "html"
-                            },
-                            {
-                                "name": "nanostats",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "nanostats_post_filtering",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "read_length",
-                                "type": "png"
-                            },
-                            {
-                                "name": "log_read_length",
-                                "type": "png"
+                                "name": "nonspecific",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 598.8807084399002,
-                            "top": 268.83097889129806
+                            "left": 1333.63330078125,
+                            "top": 852.4166717529297
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "0f1c34698076",
-                            "name": "nanoplot",
+                            "changeset_revision": "a8d69aee190e",
+                            "name": "samtools_fastx",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"customization\": {\"color\": null, \"plots\": null, \"N50\": true}, \"filter\": {\"maxlength\": null, \"minlength\": null, \"drop_outliers\": false, \"downsample\": null, \"loglength\": false, \"percentqual\": false, \"alength\": false, \"minqual\": null, \"runtime_until\": null, \"readtype\": null, \"barcoded\": false, \"no_supplementary\": false}, \"mode\": {\"choice\": \"batch\", \"__current_case__\": 0, \"reads\": {\"type\": \"fastq\", \"__current_case__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.41.0+galaxy0",
+                        "tool_state": "{\"copy_arb_tags\": \"\\\"\\\"\", \"__page__\": null, \"output_fmt_cond\": \"{\\\"__current_case__\\\": 2, \\\"default_quality\\\": \\\"\\\", \\\"ilumina_casava\\\": \\\"false\\\", \\\"output_fmt_select\\\": \\\"fastqsanger.gz\\\", \\\"output_quality\\\": \\\"false\\\"}\", \"idxout_cond\": \"{\\\"__current_case__\\\": 0, \\\"idxout_select\\\": \\\"no\\\"}\", \"read_numbering\": \"\\\"\\\"\", \"exclusive_filter\": \"null\", \"exclusive_filter_all\": \"null\", \"inclusive_filter\": \"null\", \"outputs\": \"[\\\"r0\\\"]\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"copy_tags\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9+galaxy1",
                         "type": "tool",
-                        "uuid": "ad46f297-04f2-4959-aa09-db88cd91cc27",
-                        "when": null,
+                        "uuid": "31e2b4e8-7631-46c0-8382-b805cee2b739",
                         "workflow_outputs": [
                             {
-                                "label": "nanoplot_before_filtering",
-                                "output_name": "nanostats",
-                                "uuid": "a97e6f33-8182-4a33-86dd-6cfbb83a842d"
+                                "label": null,
+                                "output_name": "nonspecific",
+                                "uuid": "cfbf839f-53f0-4a82-8966-2bdb6919de5e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0",
+                        "content_id": "__ZIP_COLLECTION__",
                         "errors": null,
-                        "id": 8,
+                        "id": 13,
                         "input_connections": {
-                            "inputs": {
-                                "id": 7,
-                                "output_name": "outfile"
+                            "input_forward": {
+                                "id": 11,
+                                "output_name": "forward"
+                            },
+                            "input_reverse": {
+                                "id": 11,
+                                "output_name": "reverse"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Flye",
+                        "name": "Zip Collection",
                         "outputs": [
                             {
-                                "name": "consensus",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "assembly_graph",
-                                "type": "graph_dot"
-                            },
-                            {
-                                "name": "assembly_gfa",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "assembly_info",
-                                "type": "tabular"
+                                "name": "output",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 850.0098909589506,
-                            "top": 593
+                            "left": 1754.63330078125,
+                            "top": 477.41668701171875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "cb8dfd28c16f",
-                            "name": "flye",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"asm\": {\"asm_select\": \"false\", \"__current_case__\": 1}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"generate_log\": false, \"inputs\": {\"__class__\": \"ConnectedValue\"}, \"iterations\": \"1\", \"keep_haplotypes\": false, \"meta\": false, \"min_overlap\": null, \"mode_conditional\": {\"mode\": \"--nano-corr\", \"__current_case__\": 1}, \"no_alt_contigs\": false, \"scaffold\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.9.1+galaxy0",
+                        "tool_id": "__ZIP_COLLECTION__",
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_reverse\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"input_forward\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+                        "tool_version": "1.0.0",
                         "type": "tool",
-                        "uuid": "8cf7ff30-4007-49cb-a959-e25c337f05be",
-                        "when": null,
+                        "uuid": "9ba89e81-9c53-4f5b-9d61-42319b7d574c",
                         "workflow_outputs": [
                             {
-                                "label": "flye_assembly_info",
-                                "output_name": "assembly_info",
-                                "uuid": "f12e718f-1bd5-490d-bd41-f0747aaa41a6"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "ebc8f563-c45e-4e17-a541-b1275e7f61ad"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
                         "errors": null,
-                        "id": 9,
+                        "id": 16,
                         "input_connections": {
-                            "mode|reads|files": {
-                                "id": 7,
-                                "output_name": "outfile"
+                            "in_file": {
+                                "id": 14,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool seqtk_sample",
+                                "name": "in_file"
+                            }
+                        ],
                         "label": null,
-                        "name": "NanoPlot",
+                        "name": "seqtk_sample",
                         "outputs": [
                             {
-                                "name": "output_html",
-                                "type": "html"
-                            },
-                            {
-                                "name": "nanostats",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "nanostats_post_filtering",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "read_length",
-                                "type": "png"
-                            },
-                            {
-                                "name": "log_read_length",
-                                "type": "png"
+                                "name": "default",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 850.0098909589506,
-                            "top": 859
+                            "left": 2129.4166717529297,
+                            "top": 711.4166717529297
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "0f1c34698076",
-                            "name": "nanoplot",
+                            "changeset_revision": "58c8ece95b53",
+                            "name": "seqtk",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"customization\": {\"color\": null, \"plots\": null, \"N50\": true}, \"filter\": {\"maxlength\": null, \"minlength\": null, \"drop_outliers\": false, \"downsample\": null, \"loglength\": false, \"percentqual\": false, \"alength\": false, \"minqual\": null, \"runtime_until\": null, \"readtype\": null, \"barcoded\": false, \"no_supplementary\": false}, \"mode\": {\"choice\": \"batch\", \"__current_case__\": 0, \"reads\": {\"type\": \"fastq\", \"__current_case__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.41.0+galaxy0",
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"s\": \"\\\"4\\\"\", \"in_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"subsample_size\": \"\\\"0.1\\\"\", \"advanced\": \"{\\\"single_pass_mode\\\": \\\"false\\\"}\"}",
+                        "tool_version": "1.3.2",
                         "type": "tool",
-                        "uuid": "467fca53-715f-4717-ab4c-c4410d321086",
-                        "when": null,
+                        "uuid": "4f7c9133-a664-46dc-9583-c9980d5d1011",
                         "workflow_outputs": [
                             {
-                                "label": "nanoplot_after_filtering",
-                                "output_name": "nanostats",
-                                "uuid": "89524090-f590-434d-89e2-66f0b1a23c7c"
+                                "label": null,
+                                "output_name": "default",
+                                "uuid": "be52344e-6874-431c-8d86-9d0e9371aed9"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
                         "errors": null,
-                        "id": 12,
+                        "id": 17,
                         "input_connections": {
-                            "mode|in|inputs": {
-                                "id": 8,
-                                "output_name": "consensus"
+                            "in_file": {
+                                "id": 15,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool seqtk_sample",
+                                "name": "in_file"
+                            }
+                        ],
                         "label": null,
-                        "name": "Quast",
+                        "name": "seqtk_sample",
                         "outputs": [
                             {
-                                "name": "report_html",
-                                "type": "html"
+                                "name": "default",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 1140.0069535390257,
-                            "top": 767
+                            "left": 2116.4166717529297,
+                            "top": 859.4166717529297
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "72472698a2df",
-                            "name": "quast",
+                            "changeset_revision": "58c8ece95b53",
+                            "name": "seqtk",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"false\", \"__current_case__\": 1, \"est_ref_size\": null}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": false}, \"large\": false, \"min_contig\": \"500\", \"mode\": {\"mode\": \"co\", \"__current_case__\": 1, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": \"html\", \"split_scaffolds\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.2.0+galaxy1",
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"s\": \"\\\"4\\\"\", \"in_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"subsample_size\": \"\\\"0.1\\\"\", \"advanced\": \"{\\\"single_pass_mode\\\": \\\"false\\\"}\"}",
+                        "tool_version": "1.3.2",
                         "type": "tool",
-                        "uuid": "6949cf20-419e-4cee-86fa-3b08ab60cb9f",
-                        "when": null,
+                        "uuid": "79064891-aa79-42e3-b848-7a6240022acc",
                         "workflow_outputs": [
                             {
-                                "label": "quast_report_before_polishing",
-                                "output_name": "report_html",
-                                "uuid": "dabfb8fd-8791-4959-a9dc-9b3c1e57a69c"
+                                "label": null,
+                                "output_name": "default",
+                                "uuid": "3e196eb1-8ba1-4be5-90d0-c5b8d3df4ff0"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
                         "errors": null,
-                        "id": 15,
+                        "id": 18,
                         "input_connections": {
-                            "mode|in|inputs": [
-                                {
-                                    "id": 14,
-                                    "output_name": "polished_fasta"
-                                },
-                                {
-                                    "id": 8,
-                                    "output_name": "consensus"
-                                }
-                            ]
+                            "long": {
+                                "id": 12,
+                                "output_name": "output"
+                            },
+                            "paired_unpaired|fastq_input1": {
+                                "id": 16,
+                                "output_name": "default"
+                            },
+                            "paired_unpaired|fastq_input2": {
+                                "id": 17,
+                                "output_name": "default"
+                            }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "lr_align"
+                            },
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "long"
+                            },
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "paired_unpaired"
+                            },
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "paired_unpaired"
+                            },
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "rotation"
+                            }
+                        ],
                         "label": null,
-                        "name": "Quast",
+                        "name": "Create assemblies with Unicycler",
                         "outputs": [
                             {
-                                "name": "report_html",
-                                "type": "html"
+                                "name": "assembly_graph",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "assembly",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 1700.001078699176,
-                            "top": 853
+                            "left": 2365.633331298828,
+                            "top": 706.4166717529297
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "72472698a2df",
-                            "name": "quast",
+                            "changeset_revision": "88c240872a65",
+                            "name": "unicycler",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"false\", \"__current_case__\": 1, \"est_ref_size\": null}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": false}, \"large\": false, \"min_contig\": \"500\", \"mode\": {\"mode\": \"co\", \"__current_case__\": 1, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": \"html\", \"split_scaffolds\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.2.0+galaxy1",
+                        "tool_state": "{\"linear_seqs\": \"\\\"1\\\"\", \"spades\": \"{\\\"depth_filter\\\": \\\"0.25\\\", \\\"kmer_count\\\": \\\"10\\\", \\\"kmers\\\": \\\"\\\", \\\"largest_component\\\": \\\"false\\\", \\\"max_kmer_frac\\\": \\\"0.95\\\", \\\"min_kmer_frac\\\": \\\"0.2\\\", \\\"no_correct\\\": \\\"false\\\"}\", \"graph_clean\": \"{\\\"min_component_size\\\": \\\"1000\\\", \\\"min_dead_end_size\\\": \\\"1000\\\"}\", \"__page__\": null, \"min_anchor_seg_len\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"lr_align\": \"{\\\"contamination\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"low_score\\\": \\\"\\\", \\\"scores\\\": \\\"3,-6,-5,-2\\\"}\", \"long\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"paired_unpaired\": \"{\\\"__current_case__\\\": 0, \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"fastq_input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired\\\"}\", \"min_fasta_length\": \"\\\"100\\\"\", \"mode\": \"\\\"normal\\\"\", \"rotation\": \"{\\\"no_rotate\\\": \\\"false\\\", \\\"start_gene_cov\\\": \\\"95.0\\\", \\\"start_gene_id\\\": \\\"90.0\\\", \\\"start_genes\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"pilon\": \"{\\\"min_polish_size\\\": \\\"1000\\\", \\\"no_pilon\\\": \\\"false\\\"}\"}",
+                        "tool_version": "0.4.8.0",
                         "type": "tool",
-                        "uuid": "866187e0-dd7c-40d5-b121-a8ef4a281c80",
-                        "when": null,
+                        "uuid": "851c6be6-c202-450a-9cd3-19e205dcc496",
                         "workflow_outputs": [
                             {
-                                "label": "quast_report_after_polishing",
-                                "output_name": "report_html",
-                                "uuid": "4e465b51-68bf-4203-9a7c-897f46c70277"
+                                "label": null,
+                                "output_name": "assembly",
+                                "uuid": "702dd61e-6072-49d9-a502-44e0a23f5a98"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "assembly_graph",
+                                "uuid": "3285cc00-6b39-4f3d-87a5-87abd483ede6"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "assembly/mrsa-nanopore",
-                "path": "topics/assembly/tutorials/mrsa-nanopore/workflows/main-workflow.ga",
-                "tags": [
-                    "Assembly"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available)",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-mrsa-nanopore/versions/main-workflow",
-                "tutorial_id": "mrsa-nanopore",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/mrsa-nanopore/workflows/main-workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/mrsa-nanopore/workflows/main-workflow.html",
-                "version": 1,
-                "wfid": "assembly-mrsa-nanopore",
-                "wfname": "main-workflow",
-                "workflow": "main-workflow.ga",
-                "workflow_tools": [
-                    "CONVERTER_bz2_to_uncompressed",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/polypolish/polypolish/0.5.0+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
-                ],
-                "workflowhub_id": "1178"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/10669812"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "5ec9f6bceaee",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bandage",
-                    "owner": "iuc",
-                    "revisions": "ddddce450736",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bandage",
-                    "owner": "iuc",
-                    "revisions": "ddddce450736",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastp",
-                    "owner": "iuc",
-                    "revisions": "65b93b623c77",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "quast",
-                    "owner": "iuc",
-                    "revisions": "72472698a2df",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "shovill",
-                    "owner": "iuc",
-                    "revisions": "ad80238462c1",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "shovill",
-                    "owner": "iuc",
-                    "revisions": "ee17a294d3a3",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 72472698a2df\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: shovill\n  owner: iuc\n  revisions: ad80238462c1\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: shovill\n  owner: iuc\n  revisions: ee17a294d3a3\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-illumina/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "bazante1",
-                "bebatut"
-            ],
-            "editing": [
-                "hexylena",
-                "bazante1",
-                "shiltemann",
-                "miaomiaozhou88"
-            ],
-            "funding": [
-                "avans-atgm",
-                "abromics"
-            ]
-        },
-        "contributors": [
-            {
-                "affiliations": [
-                    "avans-atgm"
-                ],
-                "id": "bazante1",
-                "joined": "2020-12",
-                "name": "Bazante Sanders",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "affiliations": [
-                    "avans-atgm"
-                ],
-                "id": "bazante1",
-                "joined": "2020-12",
-                "name": "Bazante Sanders",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
-            {
-                "email": "m.zhou1@avans.nl",
-                "id": "miaomiaozhou88",
-                "joined": "2020-12",
-                "name": "Miaomiao Zhou",
-                "orcid": "0000-0003-4426-1758",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/miaomiaozhou88/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/miaomiaozhou88.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/logo-avans.png",
-                "former_members": [
-                    "dirowa",
-                    "hexylena"
-                ],
-                "id": "avans-atgm",
-                "joined": "2020-11",
-                "members": [
-                    "bazante1"
-                ],
-                "name": "Avans Hogeschool",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/",
-                "ror": "015d5s513",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
-            },
-            {
-                "avatar": "/training-material/assets/images/abromics.png",
-                "funder": true,
-                "github": false,
-                "id": "abromics",
-                "joined": "2024-01",
-                "name": "ABRomics",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abromics/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/abromics.json"
-            }
-        ],
-        "dir": "topics/assembly/tutorials/mrsa-illumina",
-        "edam_ontology": [
-            "topic_0196",
-            "topic_3673",
-            "topic_3305",
-            "topic_0622",
-            "topic_3301"
-        ],
-        "edam_operation": [
-            "Visualisation",
-            "Sequencing quality control",
-            "Sequence contamination filtering",
-            "Sequence assembly validation",
-            "Sequence composition calculation",
-            "Sequence assembly visualisation",
-            "Genome assembly",
-            "Statistical calculation"
-        ],
-        "edam_topic": [
-            "Sequence assembly",
-            "Whole genome sequencing",
-            "Public health and epidemiology",
-            "Genomics",
-            "Microbiology"
-        ],
-        "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "genome-annotation",
-                "tutorials": [
-                    "amr-gene-detection"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "history-to-workflow"
-                ],
-                "type": "internal"
-            }
-        ],
-        "hands_on": true,
-        "id": "assembly/mrsa-illumina",
-        "inexact_supported_servers": [
-            "Galaxy@AuBi",
-            "GalaxyTrakr",
-            "UseGalaxy.no"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Illumina assemblies can be done with Shovill",
-            "It is hard to get the genome in one contig"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-03-13",
-        "objectives": [
-            "Run tools to evaluate sequencing data on quality and quantity",
-            "Process the output of quality control tools",
-            "Improve the quality of sequencing data",
-            "Run a tool to assemble a bacterial genome using short reads",
-            "Run tools to assess the quality of an assembly",
-            "Understand the outputs of tools to assess the quality of an assembly"
-        ],
-        "pageviews": 10369,
-        "pub_date": "2021-03-24",
-        "questions": [
-            "How to check the quality of the MiSeq data?",
-            "How to perform an assembly of a bacterial genome with MiSeq data?",
-            "How to check the quality of an assembly?"
-        ],
-        "short_id": "T00036",
-        "short_tools": [
-            "fastp",
-            "shovill",
-            "quast",
-            "fastqc",
-            "bandage_info",
-            "bandage_image",
-            "upload1"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "illumina",
-            "assembly",
-            "microgalaxy"
-        ],
-        "time_estimation": "2h",
-        "title": "Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/2022.09+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2",
-            "upload1"
-        ],
-        "topic_name": "assembly",
-        "topic_name_human": "Assembly",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "mrsa-illumina",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-illumina/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-illumina/tutorial.json"
-        },
-        "version": 14,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 225,
-        "visitors": 6432,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0003-2255-1631",
-                        "name": "Bazante Sanders"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0001-9852-1987",
-                        "name": "B\u00e9r\u00e9nice Batut"
-                    }
-                ],
-                "description": "Genome Assembly of MRSA using Illumina MiSeq Data",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDRR187559_2\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDRR187559_1\"]\n  2[label=\"FastQC\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"fastp\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  kfaabc87368844cfdb66dffafda580c82[color=lightseagreen,label=\"Output\\nfastp_json\"]\n  3 -> kfaabc87368844cfdb66dffafda580c82\n  4[label=\"FastQC\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Shovill\"]\n  3 -> 5 [label=\"out1\"]\n  3 -> 5 [label=\"out2\"]\n  k25b137fd331a48608718be6737321bce[color=lightseagreen,label=\"Output\\nshovill_log\"]\n  5 -> k25b137fd331a48608718be6737321bce\n  6[label=\"Quast\"]\n  5 -> 6 [label=\"contigs\"]\n  k3a915c59ad7645d9b4d60ab3ffe2beb0[color=lightseagreen,label=\"Output\\nquast_output\"]\n  6 -> k3a915c59ad7645d9b4d60ab3ffe2beb0\n  7[label=\"Bandage Image\"]\n  5 -> 7 [label=\"contigs_graph\"]\n  8[label=\"Bandage Info\"]\n  5 -> 8 [label=\"contigs_graph\"]\n  k5a1a539618ca48fa932e0f00eb153387[color=lightseagreen,label=\"Output\\nbandage_info_output\"]\n  8 -> k5a1a539618ca48fa932e0f00eb153387\n}",
-                "history": [
-                    {
-                        "hash": "597f8ce954083c7cd4e43765b6c4709619637e6a",
-                        "message": "Add Bazante's ORCID",
-                        "num": 7,
-                        "short_hash": "597f8ce95",
-                        "unix": "1706018263"
-                    },
-                    {
-                        "hash": "03e4290900ade23b2dffb3f61ea2875a64f2c396",
-                        "message": "Fix workflows",
-                        "num": 6,
-                        "short_hash": "03e429090",
-                        "unix": "1706004257"
-                    },
-                    {
-                        "hash": "c88bcbb6f04ad1847e0747f7fb9256ee0ec858de",
-                        "message": "Add license and creator to workflows",
-                        "num": 5,
-                        "short_hash": "c88bcbb6f",
-                        "unix": "1705678137"
-                    },
-                    {
-                        "hash": "5fbcc03b0d2408af8c03f0c7867791b47b4cceff",
-                        "message": "Update the MRSA short-read assembly tutorial",
-                        "num": 4,
-                        "short_hash": "5fbcc03b0",
-                        "unix": "1705072112"
-                    },
-                    {
-                        "hash": "31848c0ae9109d020ddee510ad5a1c374c3df96e",
-                        "message": "fix linting issues",
-                        "num": 3,
-                        "short_hash": "31848c0ae",
-                        "unix": "1610039782"
-                    },
-                    {
-                        "hash": "9c83730d5b61b1ed51890ee8c00dbf73834d7b54",
-                        "message": "Finish illumina version",
-                        "num": 2,
-                        "short_hash": "9c83730d5",
-                        "unix": "1610038238"
                     },
-                    {
-                        "hash": "c1175777fc34b261481e16516de8fde7c890c4ae",
-                        "message": "Add Illumina version of tutorial",
-                        "num": 1,
-                        "short_hash": "c1175777f",
-                        "unix": "1608293515"
-                    }
-                ],
-                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "DRR187559_2"
+                        "id": 19,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 18,
+                                "output_name": "assembly_graph"
                             }
-                        ],
-                        "label": "DRR187559_2",
-                        "name": "DRR187559_2",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 216
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"DRR187559_2\", \"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "8e9c45ae-139a-4a69-af24-f0d9f58041cc",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Bandage Info",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "DRR187559_1"
+                                "name": "outfile",
+                                "type": "txt"
                             }
                         ],
-                        "label": "DRR187559_1",
-                        "name": "DRR187559_1",
-                        "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 339
+                            "left": 2665.633331298828,
+                            "top": 811.4166717529297
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"DRR187559_1\", \"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "1290afbe-52b9-447f-ac30-6f8c92f93ff5",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nDRR187559_2\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nDRR187559_1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"FastQC\"];\n  0 -->|output| 2;\n  3[\"fastp\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  faabc873-6884-4cfd-b66d-ffafda580c82[\"Output\\nfastp_json\"];\n  3 --> faabc873-6884-4cfd-b66d-ffafda580c82;\n  style faabc873-6884-4cfd-b66d-ffafda580c82 stroke:#2c3143,stroke-width:4px;\n  4[\"FastQC\"];\n  1 -->|output| 4;\n  5[\"Shovill\"];\n  3 -->|out1| 5;\n  3 -->|out2| 5;\n  25b137fd-331a-4860-8718-be6737321bce[\"Output\\nshovill_log\"];\n  5 --> 25b137fd-331a-4860-8718-be6737321bce;\n  style 25b137fd-331a-4860-8718-be6737321bce stroke:#2c3143,stroke-width:4px;\n  6[\"Quast\"];\n  5 -->|contigs| 6;\n  3a915c59-ad76-45d9-b4d6-0ab3ffe2beb0[\"Output\\nquast_output\"];\n  6 --> 3a915c59-ad76-45d9-b4d6-0ab3ffe2beb0;\n  style 3a915c59-ad76-45d9-b4d6-0ab3ffe2beb0 stroke:#2c3143,stroke-width:4px;\n  7[\"Bandage Image\"];\n  5 -->|contigs_graph| 7;\n  8[\"Bandage Info\"];\n  5 -->|contigs_graph| 8;\n  5a1a5396-18ca-48fa-932e-0f00eb153387[\"Output\\nbandage_info_output\"];\n  8 --> 5a1a5396-18ca-48fa-932e-0f00eb153387;\n  style 5a1a5396-18ca-48fa-932e-0f00eb153387 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Genome Assembly of MRSA using Illumina MiSeq Data",
-                "outputs": [
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "b2860df42e16",
+                            "name": "bandage",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"tsv\": \"\\\"false\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+                        "tool_version": "0.8.1+galaxy1",
+                        "type": "tool",
+                        "uuid": "4aa230bd-3269-41c3-81f5-9085fcc4001d",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "cf5eab6a-97ae-430e-a27a-6ecc33d4b8c0"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
                         "errors": null,
-                        "id": 3,
+                        "id": 2,
                         "input_connections": {
-                            "single_paired|in1": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "single_paired|in2": {
+                            "single_paired|paired_input": {
                                 "id": 0,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": null,
+                        "label": "fastp: Trimmed Illumina Reads",
                         "name": "fastp",
                         "outputs": [
                             {
-                                "name": "out1",
-                                "type": "input"
-                            },
-                            {
-                                "name": "out2",
+                                "name": "output_paired_coll",
                                 "type": "input"
                             },
                             {
@@ -18004,1619 +17049,1554 @@
                             }
                         ],
                         "position": {
-                            "left": 280,
-                            "top": 296
+                            "left": 585,
+                            "top": 365.04998779296875
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
+                        "post_job_actions": {
+                            "HideDatasetActionreport_html": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "report_html"
+                            },
+                            "HideDatasetActionreport_json": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "report_json"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "65b93b623c77",
+                            "changeset_revision": "1d8fe9bc4cb0",
                             "name": "fastp",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": \"30\", \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": null, \"umi_len\": null, \"umi_prefix\": null}, \"cutting_by_quality_options\": {\"cut_by_quality5\": true, \"cut_by_quality3\": true, \"cut_window_size\": \"4\", \"cut_mean_quality\": \"20\"}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired\", \"__current_case__\": 1, \"in1\": {\"__class__\": \"ConnectedValue\"}, \"in2\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": null, \"adapter_sequence2\": null}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.23.2+galaxy0",
+                        "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"report_html\\\": \\\"true\\\", \\\"report_json\\\": \\\"true\\\"}\", \"single_paired\": \"{\\\"__current_case__\\\": 2, \\\"adapter_trimming_options\\\": {\\\"adapter_sequence1\\\": \\\"\\\", \\\"adapter_sequence2\\\": \\\"\\\", \\\"disable_adapter_trimming\\\": \\\"false\\\"}, \\\"global_trimming_options\\\": {\\\"trim_front1\\\": \\\"\\\", \\\"trim_front2\\\": \\\"\\\", \\\"trim_tail1\\\": \\\"\\\", \\\"trim_tail2\\\": \\\"\\\"}, \\\"paired_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"single_paired_selector\\\": \\\"paired_collection\\\"}\", \"read_mod_options\": \"{\\\"base_correction_options\\\": {\\\"correction\\\": \\\"false\\\"}, \\\"cutting_by_quality_options\\\": {\\\"cut_by_quality3\\\": \\\"false\\\", \\\"cut_by_quality5\\\": \\\"false\\\", \\\"cut_mean_quality\\\": \\\"\\\", \\\"cut_window_size\\\": \\\"\\\"}, \\\"polyg_tail_trimming\\\": {\\\"__current_case__\\\": 1, \\\"poly_g_min_len\\\": \\\"\\\", \\\"trimming_select\\\": \\\"\\\"}, \\\"polyx_tail_trimming\\\": {\\\"__current_case__\\\": 1, \\\"polyx_trimming_select\\\": \\\"\\\"}, \\\"umi_processing\\\": {\\\"umi\\\": \\\"false\\\", \\\"umi_len\\\": \\\"\\\", \\\"umi_loc\\\": \\\"\\\", \\\"umi_prefix\\\": \\\"\\\"}}\", \"overrepresented_sequence_analysis\": \"{\\\"overrepresentation_analysis\\\": \\\"false\\\", \\\"overrepresentation_sampling\\\": \\\"\\\"}\", \"filter_options\": \"{\\\"length_filtering_options\\\": {\\\"disable_length_filtering\\\": \\\"false\\\", \\\"length_required\\\": \\\"50\\\"}, \\\"low_complexity_filter\\\": {\\\"complexity_threshold\\\": \\\"\\\", \\\"enable_low_complexity_filter\\\": \\\"false\\\"}, \\\"quality_filtering_options\\\": {\\\"disable_quality_filtering\\\": \\\"false\\\", \\\"n_base_limit\\\": \\\"\\\", \\\"qualified_quality_phred\\\": \\\"20\\\", \\\"unqualified_percent_limit\\\": \\\"20\\\"}}\", \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.19.5+galaxy1",
                         "type": "tool",
-                        "uuid": "a3f526cd-bd95-4a6f-9fc3-8624dfc49323",
-                        "when": null,
+                        "uuid": "7508c22b-dc6a-4071-8dd0-d5616718e62b",
                         "workflow_outputs": [
                             {
-                                "label": "fastp_json",
-                                "output_name": "report_json",
-                                "uuid": "faabc873-6884-4cfd-b66d-ffafda580c82"
+                                "label": null,
+                                "output_name": "output_paired_coll",
+                                "uuid": "a7be7eab-3e80-4be6-b1a4-ab303c314096"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
                         "errors": null,
-                        "id": 5,
+                        "id": 20,
                         "input_connections": {
-                            "library|R1": {
-                                "id": 3,
-                                "output_name": "out1"
-                            },
-                            "library|R2": {
-                                "id": 3,
-                                "output_name": "out2"
+                            "input": {
+                                "id": 18,
+                                "output_name": "assembly"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Filter sequences by length",
+                                "name": "input"
+                            }
+                        ],
                         "label": null,
-                        "name": "Shovill",
+                        "name": "Filter sequences by length",
                         "outputs": [
                             {
-                                "name": "shovill_std_log",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "contigs",
+                                "name": "output",
                                 "type": "fasta"
-                            },
-                            {
-                                "name": "contigs_graph",
-                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 560,
-                            "top": 351
+                            "left": 2574.4166870117188,
+                            "top": 1254.4166870117188
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "ee17a294d3a3",
-                            "name": "shovill",
-                            "owner": "iuc",
+                            "changeset_revision": "8cacfcf96a52",
+                            "name": "fasta_filter_by_length",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"fastq.gz\", \"adv\": {\"namefmt\": \"contig%05d\", \"depth\": \"100\", \"gsize\": \"2914567\", \"kmers\": \"\", \"opts\": \"\", \"keep_files\": {\"nocorr\": \"no_correction\", \"__current_case__\": 0}, \"minlen\": \"0\", \"mincov\": \"2\"}, \"assembler\": \"spades\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"library\": {\"lib_type\": \"paired\", \"__current_case__\": 0, \"R1\": {\"__class__\": \"ConnectedValue\"}, \"R2\": {\"__class__\": \"ConnectedValue\"}}, \"log\": true, \"trim\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.0+galaxy2",
+                        "tool_state": "{\"__page__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"max_length\": \"\\\"0\\\"\", \"min_length\": \"\\\"1000\\\"\"}",
+                        "tool_version": "1.2",
                         "type": "tool",
-                        "uuid": "2676d037-3faf-4974-8357-1113ff27de62",
-                        "when": null,
+                        "uuid": "3cbd67e0-3e55-4726-8dbe-0c61aec4d293",
                         "workflow_outputs": [
                             {
-                                "label": "shovill_log",
-                                "output_name": "shovill_std_log",
-                                "uuid": "25b137fd-331a-4860-8718-be6737321bce"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "e4143f49-239f-4266-ba8d-e6299a331403"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
                         "errors": null,
-                        "id": 6,
+                        "id": 21,
                         "input_connections": {
-                            "mode|in|inputs": {
-                                "id": 5,
-                                "output_name": "contigs"
+                            "input_file": {
+                                "id": 18,
+                                "output_name": "assembly_graph"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Bandage Image",
+                                "name": "input_file"
+                            }
+                        ],
                         "label": null,
-                        "name": "Quast",
+                        "name": "Bandage Image",
                         "outputs": [
                             {
-                                "name": "report_html",
-                                "type": "html"
+                                "name": "outfile",
+                                "type": "jpg"
                             }
                         ],
                         "position": {
-                            "left": 840,
-                            "top": 302
+                            "left": 2667.4166870117188,
+                            "top": 1052.4166870117188
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "72472698a2df",
-                            "name": "quast",
+                            "changeset_revision": "b2860df42e16",
+                            "name": "bandage",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"false\", \"__current_case__\": 1, \"est_ref_size\": null}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": false}, \"large\": false, \"min_contig\": \"500\", \"mode\": {\"mode\": \"individual\", \"__current_case__\": 0, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": \"html\", \"split_scaffolds\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.2.0+galaxy1",
+                        "tool_state": "{\"__page__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"lengths\": \"\\\"true\\\"\", \"output_format\": \"\\\"jpg\\\"\", \"height\": \"\\\"1000\\\"\", \"width\": \"\\\"\\\"\", \"names\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.8.1+galaxy2",
                         "type": "tool",
-                        "uuid": "0fa4aa47-d6f1-4b9a-9db9-91131f80a410",
-                        "when": null,
+                        "uuid": "ef2c6a46-8421-499e-a840-8dd03483c5c9",
                         "workflow_outputs": [
                             {
-                                "label": "quast_output",
-                                "output_name": "report_html",
-                                "uuid": "3a915c59-ad76-45d9-b4d6-0ab3ffe2beb0"
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "5e535f98-b740-44ec-aba1-9d9090acb89a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/2022.09+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
                         "errors": null,
-                        "id": 8,
+                        "id": 3,
                         "input_connections": {
-                            "input_file": {
-                                "id": 5,
-                                "output_name": "contigs_graph"
+                            "mode|reads|files": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Bandage Info",
+                        "name": "NanoPlot",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 840,
-                            "top": 610
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/2022.09+galaxy2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ddddce450736",
-                            "name": "bandage",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"tsv\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2022.09+galaxy2",
-                        "type": "tool",
-                        "uuid": "f191da8d-81fe-499e-beee-abb31d05ba71",
-                        "when": null,
-                        "workflow_outputs": [
+                                "name": "output_html",
+                                "type": "html"
+                            },
                             {
-                                "label": "bandage_info_output",
-                                "output_name": "outfile",
-                                "uuid": "5a1a5396-18ca-48fa-932e-0f00eb153387"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "assembly/mrsa-illumina",
-                "path": "topics/assembly/tutorials/mrsa-illumina/workflows/main_workflow.ga",
-                "tags": [
-                    "assembly",
-                    "microgalaxy"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "Genome Assembly of MRSA using Illumina MiSeq Data",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-mrsa-illumina/versions/main-workflow",
-                "tutorial_id": "mrsa-illumina",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/mrsa-illumina/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/mrsa-illumina/workflows/main_workflow.html",
-                "version": 2,
-                "wfid": "assembly-mrsa-illumina",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/2022.09+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2"
-                ],
-                "workflowhub_id": "1135"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/10669812"
-    },
-    {
-        "abbreviations": {
-            "G10K": "Genome 10K",
-            "GWS": "Galaxy Workflow System",
-            "Hi-C": "all-versus-all chromatin conformation capture",
-            "HiFi": "high fidelity reads",
-            "QV": "assembly consensus quality",
-            "VGP": "Vertebrate Genome Project",
-            "alternate assembly": "alternate loci not represented in the primary assembly",
-            "collection": "Galaxy's way to represent multiple datasets as a single interface entity",
-            "collections": "Galaxy's way to represent multiple datasets as a single interface entity",
-            "contigs": "contiguous sequences in an assembly",
-            "primary assembly": "homozygous regions of the genome plus one set of alleles for the heterozygous loci",
-            "scaffold": "one or more contigs joined by gap sequence",
-            "scaffolds": "one or more contigs joined by gap sequence",
-            "unitig": "A uniquely assembleable subset of overlapping fragments. A unitig is an assembly of fragments for which there are no competing internal overlaps. A unitig is either a correctly assembled portion of a contig or a collapsed assembly of several high-fidelity copies of a repeat."
-        },
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "quast",
-                    "owner": "iuc",
-                    "revisions": "72472698a2df",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: quast\n  owner: iuc\n  revisions: 72472698a2df\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/vgp_workflow_training/tutorial.json",
-        "contributors": [
-            {
-                "email": "delphine.lariviere@galaxy.org",
-                "id": "delphine-l",
-                "joined": "2017-09",
-                "name": "Delphine Lariviere",
-                "orcid": "0000-0001-6421-3484",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
-            },
-            {
-                "email": "a.ostrovsky@mac.com",
-                "id": "astrovsky01",
-                "joined": "2019-06",
-                "name": "Alex Ostrovsky",
-                "orcid": "0000-0002-7901-7109",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/astrovsky01/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/astrovsky01.json"
-            },
-            {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "gallardoalba",
-                "joined": "2020-11",
-                "name": "Crist\u00f3bal Gallardo",
-                "orcid": "0000-0002-5752-2155",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
-            },
-            {
-                "id": "pickettbd",
-                "joined": "2022-01",
-                "name": "Brandon Pickett",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pickettbd/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pickettbd.json"
-            },
-            {
-                "id": "abueg",
-                "joined": "2022-01",
-                "name": "Linelle Abueg",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abueg/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abueg.json"
-            },
-            {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
-                "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
-            }
-        ],
-        "dir": "topics/assembly/tutorials/vgp_workflow_training",
-        "edam_operation": [
-            "Visualisation",
-            "Sequence assembly validation"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "Galaxy@AuBi",
-            "GalaxyTrakr",
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "assembly/vgp_workflow_training",
-        "inexact_supported_servers": [
-            "Center for Phage Technology (CPT)",
-            "HyPhy HIV NGS Tools"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "The VGP pipeline allows to generate error-free, near gapless reference-quality genome assemblies",
-            "The assembly can be divided in four main stages: genome profile analysis, HiFi long read phased assembly with hifiasm, Bionano hybrid scaffolding and Hi-C hybrid scaffolding"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-07-26",
-        "objectives": [
-            "Learn the tools necessary to perform a de novo assembly of a vertebrate genome",
-            "Evaluate the quality of the assembly"
-        ],
-        "pageviews": 2930,
-        "pub_date": "2022-04-06",
-        "questions": [
-            "What combination of tools can produce the highest quality assembly of vertebrate genomes?",
-            "How can we evaluate how good it is?"
-        ],
-        "short_id": "T00040",
-        "short_tools": [
-            "quast"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "Center for Phage Technology (CPT)",
-                    "url": "https://cpt.tamu.edu/galaxy-public/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "HyPhy HIV NGS Tools",
-                    "url": "https://galaxy.hyphy.org/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "pacbio",
-            "eukaryote",
-            "VGP"
-        ],
-        "time_estimation": "1h",
-        "title": "VGP assembly pipeline - short version",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
-        ],
-        "topic_name": "assembly",
-        "topic_name_human": "Assembly",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "vgp_workflow_training",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/vgp_workflow_training/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/vgp_workflow_training/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/vgp_workflow_training/tutorial.json"
-        },
-        "version": 20,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 165,
-        "visitors": 2043,
-        "zenodo_link": "https://zenodo.org/record/5887339"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "blobtoolkit",
-                    "owner": "bgruening",
-                    "revisions": "7d9ee8cd14b8",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "blobtoolkit",
-                    "owner": "bgruening",
-                    "revisions": "53dd00a4ab68",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "diamond",
-                    "owner": "bgruening",
-                    "revisions": "e8ac2b53f262",
-                    "tool_panel_section_label": "NCBI Blast",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gfastats",
-                    "owner": "bgruening",
-                    "revisions": "5799092ffdff",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gfastats",
-                    "owner": "bgruening",
-                    "revisions": "3ef480892a9f",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_stats",
-                    "owner": "devteam",
-                    "revisions": "3a0efe14891f",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "smudgeplot",
-                    "owner": "galaxy-australia",
-                    "revisions": "5e0825476fb7",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bandage",
-                    "owner": "iuc",
-                    "revisions": "ddddce450736",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bellerophon",
-                    "owner": "iuc",
-                    "revisions": "25ca5d73aedf",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "busco",
-                    "owner": "iuc",
-                    "revisions": "bb935709506a",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bwa_mem2",
-                    "owner": "iuc",
-                    "revisions": "b4a22d90cce9",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "genomescope",
-                    "owner": "iuc",
-                    "revisions": "01210c4e9144",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "hisat2",
-                    "owner": "iuc",
-                    "revisions": "f4af63aaf57a",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "merqury",
-                    "owner": "iuc",
-                    "revisions": "f8113c25bc6b",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "meryl",
-                    "owner": "iuc",
-                    "revisions": "29dabd8db6f2",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pretext_map",
-                    "owner": "iuc",
-                    "revisions": "dfb8a4497339",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pretext_snapshot",
-                    "owner": "iuc",
-                    "revisions": "44c66e8d21e6",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "90981f86000f",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: blobtoolkit\n  owner: bgruening\n  revisions: 7d9ee8cd14b8\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: blobtoolkit\n  owner: bgruening\n  revisions: 53dd00a4ab68\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: diamond\n  owner: bgruening\n  revisions: e8ac2b53f262\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n  owner: bgruening\n  revisions: 5799092ffdff\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n  owner: bgruening\n  revisions: 3ef480892a9f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 3a0efe14891f\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: smudgeplot\n  owner: galaxy-australia\n  revisions: 5e0825476fb7\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bellerophon\n  owner: iuc\n  revisions: 25ca5d73aedf\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: bb935709506a\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_mem2\n  owner: iuc\n  revisions: b4a22d90cce9\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: genomescope\n  owner: iuc\n  revisions: 01210c4e9144\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: hisat2\n  owner: iuc\n  revisions: f4af63aaf57a\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merqury\n  owner: iuc\n  revisions: f8113c25bc6b\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n  owner: iuc\n  revisions: 29dabd8db6f2\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_map\n  owner: iuc\n  revisions: dfb8a4497339\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_snapshot\n  owner: iuc\n  revisions: 44c66e8d21e6\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json",
-        "contributors": [
-            {
-                "id": "GitFab93",
-                "joined": "2023-03",
-                "name": "Fabian Recktenwald",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/GitFab93/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/GitFab93.json"
-            },
-            {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "gallardoalba",
-                "joined": "2020-11",
-                "name": "Crist\u00f3bal Gallardo",
-                "orcid": "0000-0002-5752-2155",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
-            }
-        ],
-        "dir": "topics/assembly/tutorials/ERGA-post-assembly-QC",
-        "edam_operation": [
-            "Phasing",
-            "De-novo assembly",
-            "Sequence alignment",
-            "Genotyping",
-            "Sequence assembly validation",
-            "Sequence alignment analysis",
-            "Sequence assembly visualisation",
-            "Transcriptome assembly",
-            "Data handling",
-            "Genome assembly",
-            "Sequence trimming",
-            "k-mer counting",
-            "Scaffolding"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "assembly/ERGA-post-assembly-QC",
-        "inexact_supported_servers": [
-            "UseGalaxy.org (Main)"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "The ERGA post-assembly pipeline allows to assess and improve the quality of genome assemblies",
-            "The ERGA post-assembly pipeline contains of three main steps: Genome assembly decontamination and overview with BlobToolKit, providing analysis information and statistics and Hi-C scaffolding."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-07-31",
-        "objectives": [
-            "apply the post-assembly-QC-workflow using the necessary tools",
-            "analyse and evaluate the results of the workflow"
-        ],
-        "pageviews": 1088,
-        "pub_date": "2023-06-23",
-        "questions": [
-            "what combination of tools can assess the quality of an post-assembly?",
-            "what metrics can help to analyse the quality?",
-            "how to evaluate the outputs?"
-        ],
-        "short_id": "T00355",
-        "short_tools": [
-            "bellerophon",
-            "meryl",
-            "collapse_dataset",
-            "__EXTRACT_DATASET__",
-            "hisat2",
-            "busco",
-            "genomescope",
-            "blobtoolkit",
-            "pretext_map",
-            "CONVERTER_gz_to_uncompressed",
-            "samtools_stats",
-            "interactive_tool_blobtoolkit",
-            "tp_find_and_replace",
-            "smudgeplot",
-            "gfastats",
-            "bg_diamond",
-            "bandage_image",
-            "merqury",
-            "pretext_snapshot",
-            "bwa_mem2"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "plants"
-        ],
-        "time_estimation": "3H",
-        "title": "ERGA post-assembly QC",
-        "tools": [
-            "CONVERTER_gz_to_uncompressed",
-            "__EXTRACT_DATASET__",
-            "interactive_tool_blobtoolkit",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/3.4.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.0.7+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.2.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4",
-            "toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy+2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
-            "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
-        ],
-        "topic_name": "assembly",
-        "topic_name_human": "Assembly",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "ERGA-post-assembly-QC",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json"
-        },
-        "version": 3,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 98,
-        "visitors": 820,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-5752-2155",
-                        "name": "Crist\u00f3bal Gallardo Alba"
-                    }
-                ],
-                "description": "ERGA post-assembly QC",
-                "features": {
-                    "comments": false,
-                    "parameters": true,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMetadata file\"]\n  1[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nNCBI taxonomic ID\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nNCBI taxdump directory\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nFASTQ files\"]\n  4[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nPloidy for model to use\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPrimary genome assembly file fasta\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDIAMOND database\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nHi-C reverse\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nHi-C forward\"]\n  9[label=\"Meryl\"]\n  3 -> 9 [label=\"output\"]\n  10[label=\"Collapse Collection\"]\n  3 -> 10 [label=\"output\"]\n  11[label=\"Create BlobtoolKit\"]\n  5 -> 11 [label=\"output\"]\n  0 -> 11 [label=\"output\"]\n  2 -> 11 [label=\"output\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"gfastats\"]\n  5 -> 12 [label=\"output\"]\n  13[label=\"Convert compressed file to uncompressed.\"]\n  5 -> 13 [label=\"output\"]\n  14[label=\"gfastats\"]\n  5 -> 14 [label=\"output\"]\n  15[label=\"Diamond\"]\n  5 -> 15 [label=\"output\"]\n  6 -> 15 [label=\"output\"]\n  16[label=\"Collapse Collection\"]\n  7 -> 16 [label=\"output\"]\n  17[label=\"Collapse Collection\"]\n  8 -> 17 [label=\"output\"]\n  18[label=\"Meryl\"]\n  9 -> 18 [label=\"read_db\"]\n  19[label=\"HISAT2\"]\n  10 -> 19 [label=\"output\"]\n  5 -> 19 [label=\"output\"]\n  20[label=\"Smudgeplot\"]\n  10 -> 20 [label=\"output\"]\n  21[label=\"Replace\"]\n  13 -> 21 [label=\"output1\"]\n  22[label=\"Bandage Image\"]\n  14 -> 22 [label=\"output\"]\n  23[label=\"BWA-MEM2\"]\n  16 -> 23 [label=\"output\"]\n  5 -> 23 [label=\"output\"]\n  24[label=\"BWA-MEM2\"]\n  17 -> 24 [label=\"output\"]\n  5 -> 24 [label=\"output\"]\n  25[label=\"Merqury\"]\n  5 -> 25 [label=\"output\"]\n  18 -> 25 [label=\"read_db\"]\n  kc2fe83a3754a4544bb87df16f3537ab4[color=lightseagreen,label=\"Output\\nMerqury on input dataset(s): stats\"]\n  25 -> kc2fe83a3754a4544bb87df16f3537ab4\n  k8f08d8f67615420c8a15201a61b5d3bb[color=lightseagreen,label=\"Output\\nMerqury on input dataset(s): plots\"]\n  25 -> k8f08d8f67615420c8a15201a61b5d3bb\n  k7a8d951a6a314b02aeba0eb3061f85ce[color=lightseagreen,label=\"Output\\nMerqury on input dataset(s): QV stats\"]\n  25 -> k7a8d951a6a314b02aeba0eb3061f85ce\n  26[label=\"Meryl\"]\n  18 -> 26 [label=\"read_db\"]\n  27[label=\"Samtools stats\"]\n  19 -> 27 [label=\"output_alignments\"]\n  28[label=\"Busco\"]\n  21 -> 28 [label=\"outfile\"]\n  k1d4e45428bf14e32890b2e18df95a0de[color=lightseagreen,label=\"Output\\nBusco on input dataset(s): full table\"]\n  28 -> k1d4e45428bf14e32890b2e18df95a0de\n  k680b817736534630ab99c1d2304dc485[color=lightseagreen,label=\"Output\\nBusco on input dataset(s): short summary\"]\n  28 -> k680b817736534630ab99c1d2304dc485\n  29[label=\"Filter and merge\"]\n  24 -> 29 [label=\"bam_output\"]\n  23 -> 29 [label=\"bam_output\"]\n  30[label=\"Merqury plot 2\"]\n  25 -> 30 [label=\"png_files\"]\n  31[label=\"Merqury plot 1\"]\n  25 -> 31 [label=\"png_files\"]\n  32[label=\"Merqury plot 3\"]\n  25 -> 32 [label=\"png_files\"]\n  33[label=\"Merqury plot 5\"]\n  25 -> 33 [label=\"png_files\"]\n  34[label=\"Merqury plot 4\"]\n  25 -> 34 [label=\"png_files\"]\n  35[label=\"GenomeScope\"]\n  26 -> 35 [label=\"read_db_hist\"]\n  4 -> 35 [label=\"output\"]\n  36[label=\"BlobToolKit\"]\n  15 -> 36 [label=\"blast_tabular\"]\n  11 -> 36 [label=\"blobdir\"]\n  28 -> 36 [label=\"busco_table\"]\n  19 -> 36 [label=\"output_alignments\"]\n  37[label=\"PretextMap\"]\n  29 -> 37 [label=\"outfile\"]\n  38[label=\"Interactive BlobToolKit\"]\n  36 -> 38 [label=\"blobdir\"]\n  39[label=\"Pretext Snapshot\"]\n  37 -> 39 [label=\"pretext_map_out\"]\n}",
-                "history": [
-                    {
-                        "hash": "807026b8414e9d8e35cb6805104338150b1131f0",
-                        "message": "Update topics/assembly/tutorials/ERGA-post-assembly-QC/workflows/main_workflow.ga",
-                        "num": 3,
-                        "short_hash": "807026b84",
-                        "unix": "1687524556"
-                    },
-                    {
-                        "hash": "c5bb8031a5b03030e4fdc5c0a478a87e7c1e3c13",
-                        "message": "Fix testes",
-                        "num": 2,
-                        "short_hash": "c5bb8031a",
-                        "unix": "1687511093"
-                    },
-                    {
-                        "hash": "893cd527b9bd282e7f98475f5c3cd3e2f3ea89b0",
-                        "message": "Add images and rename tutorial",
-                        "num": 1,
-                        "short_hash": "893cd527b",
-                        "unix": "1682673537"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                                "name": "nanostats",
+                                "type": "txt"
+                            },
                             {
-                                "description": "",
-                                "name": "Metadata file"
-                            }
-                        ],
-                        "label": "Metadata file",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 280,
-                            "top": 0
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": true, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "4e2925a6-af6c-4a48-95e1-334ee4cebee4",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                                "name": "nanostats_post_filtering",
+                                "type": "txt"
+                            },
                             {
-                                "description": "",
-                                "name": "NCBI taxonomic ID"
+                                "name": "read_length",
+                                "type": "png"
+                            },
+                            {
+                                "name": "log_read_length",
+                                "type": "png"
                             }
                         ],
-                        "label": "NCBI taxonomic ID",
-                        "name": "Input parameter",
-                        "outputs": [],
                         "position": {
-                            "left": 280,
-                            "top": 123
+                            "left": 630,
+                            "top": 650.4666595458984
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "ffe0dbe7-597d-45ed-a356-f036d807b80a",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "NCBI taxdump directory"
+                        "post_job_actions": {
+                            "HideDatasetActionlog_read_length": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "log_read_length"
+                            },
+                            "HideDatasetActionnanostats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "nanostats"
+                            },
+                            "HideDatasetActionnanostats_post_filtering": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "nanostats_post_filtering"
+                            },
+                            "HideDatasetActionread_length": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "read_length"
                             }
-                        ],
-                        "label": "NCBI taxdump directory",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 280,
-                            "top": 246
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "a04c5335-88b6-4d11-9924-5752df4204e1",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "645159bcee2d",
+                            "name": "nanoplot",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"filter\": \"{\\\"alength\\\": \\\"false\\\", \\\"barcoded\\\": \\\"false\\\", \\\"downsample\\\": \\\"\\\", \\\"drop_outliers\\\": \\\"false\\\", \\\"loglength\\\": \\\"true\\\", \\\"maxlength\\\": \\\"\\\", \\\"minlength\\\": \\\"\\\", \\\"minqual\\\": \\\"\\\", \\\"percentqual\\\": \\\"false\\\", \\\"readtype\\\": null}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"__current_case__\\\": 0, \\\"choice\\\": \\\"batch\\\", \\\"reads\\\": {\\\"__current_case__\\\": 0, \\\"files\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"type\\\": \\\"fastq\\\"}}\", \"customization\": \"{\\\"N50\\\": \\\"false\\\", \\\"color\\\": null, \\\"format\\\": \\\"png\\\", \\\"noN50\\\": \\\"false\\\", \\\"plots\\\": null}\"}",
+                        "tool_version": "1.25.0+galaxy1",
+                        "type": "tool",
+                        "uuid": "9b1d43ac-82e3-463f-9c88-08c8826a62c9",
+                        "workflow_outputs": [
                             {
-                                "description": "",
-                                "name": "FASTQ files"
+                                "label": null,
+                                "output_name": "output_html",
+                                "uuid": "cd8570c7-02db-479b-81a9-cd0d26643f71"
                             }
-                        ],
-                        "label": "FASTQ files",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 1182
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "7cb038c5-3dd4-4313-b178-dd05cdc96721",
-                        "when": null,
-                        "workflow_outputs": []
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
                         "errors": null,
                         "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Ploidy for model to use"
+                        "input_connections": {
+                            "fastq_input|fastq_input1": {
+                                "id": 1,
+                                "output_name": "output"
                             }
-                        ],
-                        "label": "Ploidy for model to use",
-                        "name": "Input parameter",
-                        "outputs": [],
-                        "position": {
-                            "left": 860,
-                            "top": 1011
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": 2, \"parameter_type\": \"integer\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "e586fc91-192f-45c1-bccb-b3a017ff5b26",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Map with minimap2",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Primary genome assembly file (fasta)"
+                                "name": "alignment_output",
+                                "type": "bam"
                             }
                         ],
-                        "label": "Primary genome assembly file (fasta)",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 280,
-                            "top": 1310
+                            "left": 709.199951171875,
+                            "top": 1131.9666748046875
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "1b4475cb-0cc2-4371-ac68-c1bd2f868e50",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "DIAMOND database"
-                            }
-                        ],
-                        "label": "DIAMOND database",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 280,
-                            "top": 1735
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "53c0b7a1a0c3",
+                            "name": "minimap2",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "68be0d0c-35a9-4c73-a61e-56c1486e3548",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {},
-                        "inputs": [
+                        "tool_state": "{\"alignment_options\": \"{\\\"-O2\\\": \\\"\\\", \\\"A\\\": \\\"\\\", \\\"B\\\": \\\"\\\", \\\"E\\\": \\\"\\\", \\\"E2\\\": \\\"\\\", \\\"O\\\": \\\"\\\", \\\"s\\\": \\\"\\\", \\\"u\\\": null, \\\"z\\\": \\\"\\\"}\", \"analysis_type_selector\": \"\\\"splice\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"io_options\": \"{\\\"K\\\": \\\"\\\", \\\"L\\\": \\\"false\\\", \\\"Q\\\": \\\"false\\\", \\\"Y\\\": \\\"false\\\", \\\"c\\\": \\\"false\\\", \\\"cs\\\": null, \\\"eqx\\\": \\\"false\\\", \\\"output_format\\\": \\\"BAM\\\"}\", \"mapping_options\": \"{\\\"F\\\": \\\"\\\", \\\"G\\\": \\\"\\\", \\\"N\\\": \\\"\\\", \\\"X\\\": \\\"false\\\", \\\"f\\\": \\\"\\\", \\\"g\\\": \\\"\\\", \\\"m\\\": \\\"\\\", \\\"min_occ_floor\\\": \\\"\\\", \\\"n\\\": \\\"\\\", \\\"p\\\": \\\"\\\", \\\"r\\\": \\\"\\\"}\", \"fastq_input\": \"{\\\"__current_case__\\\": 1, \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"single\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 0, \\\"ref_file\\\": \\\"hg38\\\", \\\"reference_source_selector\\\": \\\"cached\\\"}\", \"indexing_options\": \"{\\\"H\\\": \\\"false\\\", \\\"I\\\": \\\"\\\", \\\"k\\\": \\\"\\\", \\\"w\\\": \\\"\\\"}\"}",
+                        "tool_version": "2.17+galaxy1",
+                        "type": "tool",
+                        "uuid": "098d2283-1218-489b-9882-8822e79d9444",
+                        "workflow_outputs": [
                             {
-                                "description": "",
-                                "name": "Hi-C reverse"
+                                "label": null,
+                                "output_name": "alignment_output",
+                                "uuid": "9972015d-4bdc-440f-b8b6-84e92a64ef8f"
                             }
-                        ],
-                        "label": "Hi-C reverse",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 2172
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "8e598f70-ebee-4264-84a4-5d40642004a4",
-                        "when": null,
-                        "workflow_outputs": []
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Hi-C forward"
-                            }
-                        ],
-                        "label": "Hi-C forward",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 2602
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "b1a0825d-054b-4d34-a735-4f8b2f57df4c",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "AGPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nMetadata file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nNCBI taxonomic ID\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nNCBI taxdump directory\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Collection\\nFASTQ files\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nPloidy for model to use\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nPrimary genome assembly file fasta\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nDIAMOND database\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Collection\\nHi-C reverse\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Collection\\nHi-C forward\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"Meryl\"];\n  3 -->|output| 9;\n  10[\"Collapse Collection\"];\n  3 -->|output| 10;\n  11[\"Create BlobtoolKit\"];\n  5 -->|output| 11;\n  0 -->|output| 11;\n  2 -->|output| 11;\n  1 -->|output| 11;\n  12[\"gfastats\"];\n  5 -->|output| 12;\n  13[\"Convert compressed file to uncompressed.\"];\n  5 -->|output| 13;\n  14[\"gfastats\"];\n  5 -->|output| 14;\n  15[\"Diamond\"];\n  5 -->|output| 15;\n  6 -->|output| 15;\n  16[\"Collapse Collection\"];\n  7 -->|output| 16;\n  17[\"Collapse Collection\"];\n  8 -->|output| 17;\n  18[\"Meryl\"];\n  9 -->|read_db| 18;\n  19[\"HISAT2\"];\n  10 -->|output| 19;\n  5 -->|output| 19;\n  20[\"Smudgeplot\"];\n  10 -->|output| 20;\n  21[\"Replace\"];\n  13 -->|output1| 21;\n  22[\"Bandage Image\"];\n  14 -->|output| 22;\n  23[\"BWA-MEM2\"];\n  16 -->|output| 23;\n  5 -->|output| 23;\n  24[\"BWA-MEM2\"];\n  17 -->|output| 24;\n  5 -->|output| 24;\n  25[\"Merqury\"];\n  5 -->|output| 25;\n  18 -->|read_db| 25;\n  c2fe83a3-754a-4544-bb87-df16f3537ab4[\"Output\\nMerqury on input dataset(s): stats\"];\n  25 --> c2fe83a3-754a-4544-bb87-df16f3537ab4;\n  style c2fe83a3-754a-4544-bb87-df16f3537ab4 stroke:#2c3143,stroke-width:4px;\n  8f08d8f6-7615-420c-8a15-201a61b5d3bb[\"Output\\nMerqury on input dataset(s): plots\"];\n  25 --> 8f08d8f6-7615-420c-8a15-201a61b5d3bb;\n  style 8f08d8f6-7615-420c-8a15-201a61b5d3bb stroke:#2c3143,stroke-width:4px;\n  7a8d951a-6a31-4b02-aeba-0eb3061f85ce[\"Output\\nMerqury on input dataset(s): QV stats\"];\n  25 --> 7a8d951a-6a31-4b02-aeba-0eb3061f85ce;\n  style 7a8d951a-6a31-4b02-aeba-0eb3061f85ce stroke:#2c3143,stroke-width:4px;\n  26[\"Meryl\"];\n  18 -->|read_db| 26;\n  27[\"Samtools stats\"];\n  19 -->|output_alignments| 27;\n  28[\"Busco\"];\n  21 -->|outfile| 28;\n  1d4e4542-8bf1-4e32-890b-2e18df95a0de[\"Output\\nBusco on input dataset(s): full table\"];\n  28 --> 1d4e4542-8bf1-4e32-890b-2e18df95a0de;\n  style 1d4e4542-8bf1-4e32-890b-2e18df95a0de stroke:#2c3143,stroke-width:4px;\n  680b8177-3653-4630-ab99-c1d2304dc485[\"Output\\nBusco on input dataset(s): short summary\"];\n  28 --> 680b8177-3653-4630-ab99-c1d2304dc485;\n  style 680b8177-3653-4630-ab99-c1d2304dc485 stroke:#2c3143,stroke-width:4px;\n  29[\"Filter and merge\"];\n  24 -->|bam_output| 29;\n  23 -->|bam_output| 29;\n  30[\"Merqury plot 2\"];\n  25 -->|png_files| 30;\n  31[\"Merqury plot 1\"];\n  25 -->|png_files| 31;\n  32[\"Merqury plot 3\"];\n  25 -->|png_files| 32;\n  33[\"Merqury plot 5\"];\n  25 -->|png_files| 33;\n  34[\"Merqury plot 4\"];\n  25 -->|png_files| 34;\n  35[\"GenomeScope\"];\n  26 -->|read_db_hist| 35;\n  4 -->|output| 35;\n  36[\"BlobToolKit\"];\n  15 -->|blast_tabular| 36;\n  11 -->|blobdir| 36;\n  28 -->|busco_table| 36;\n  19 -->|output_alignments| 36;\n  37[\"PretextMap\"];\n  29 -->|outfile| 37;\n  38[\"Interactive BlobToolKit\"];\n  36 -->|blobdir| 38;\n  39[\"Pretext Snapshot\"];\n  37 -->|pretext_map_out| 39;",
-                "modified": "2024-08-18 00:06:20 +0000",
-                "name": "Post-assembly workflow",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.2.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
                         "errors": null,
-                        "id": 12,
+                        "id": 5,
                         "input_connections": {
-                            "input_file": {
-                                "id": 5,
-                                "output_name": "output"
+                            "results_0|software_cond|input": {
+                                "id": 2,
+                                "output_name": "report_json"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "gfastats",
+                        "name": "MultiQC",
                         "outputs": [
                             {
                                 "name": "stats",
-                                "type": "tabular"
+                                "type": "input"
+                            },
+                            {
+                                "name": "html_report",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 570,
-                            "top": 1150
+                            "left": 938.699951171875,
+                            "top": 250
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.2.0+galaxy0",
+                        "post_job_actions": {
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
                         "tool_shed_repository": {
-                            "changeset_revision": "5799092ffdff",
-                            "name": "gfastats",
-                            "owner": "bgruening",
+                            "changeset_revision": "b2f1f75d49c4",
+                            "name": "multiqc",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"assembly\", \"__current_case__\": 2, \"expected_genomesize\": null}, \"tabular\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.0+galaxy0",
+                        "tool_state": "{\"comment\": \"\\\"\\\"\", \"__page__\": null, \"title\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"results\": \"[{\\\"__index__\\\": 0, \\\"software_cond\\\": {\\\"__current_case__\\\": 7, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"software\\\": \\\"fastp\\\"}}]\", \"saveLog\": \"\\\"false\\\"\"}",
+                        "tool_version": "1.7",
                         "type": "tool",
-                        "uuid": "7b6264cf-7b3e-4df7-8091-4fe9db70ba0b",
-                        "when": null,
+                        "uuid": "73566697-4a46-4d35-b8e2-61770acc62c0",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "stats",
-                                "uuid": "6c86bd99-c6d3-49a5-9ffe-5d86d045128d"
+                                "output_name": "html_report",
+                                "uuid": "15f42a94-2c97-4932-8e3f-f26a72b58be4"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy+2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
                         "errors": null,
-                        "id": 20,
+                        "id": 6,
                         "input_connections": {
-                            "file|input|reads": {
-                                "id": 10,
-                                "output_name": "output"
+                            "library|input_1": {
+                                "id": 2,
+                                "output_name": "output_paired_coll"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Smudgeplot",
+                        "name": "Bowtie2",
                         "outputs": [
                             {
-                                "name": "smudgeplot",
-                                "type": "png"
+                                "name": "output",
+                                "type": "bam"
                             },
                             {
-                                "name": "smudgeplot_log",
-                                "type": "png"
+                                "name": "mapping_stats",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 570,
-                            "top": 2319
+                            "left": 913.9166259765625,
+                            "top": 564.6333312988281
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy+2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "5e0825476fb7",
-                            "name": "smudgeplot",
-                            "owner": "galaxy-australia",
+                            "changeset_revision": "749c918495f7",
+                            "name": "bowtie2",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"file\": {\"input\": {\"input_select\": \"reads\", \"__current_case__\": 0, \"reads\": {\"__class__\": \"ConnectedValue\"}, \"mer_len\": \"21\", \"lower_cutoff\": null, \"upper_cutoff\": null}}, \"homozygous\": false, \"table_output\": false, \"verbose_output\": false, \"warnings_output\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.2.5+galaxy+2",
+                        "tool_state": "{\"sam_options\": \"{\\\"__current_case__\\\": 1, \\\"sam_options_selector\\\": \\\"no\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"__current_case__\\\": 2, \\\"aligned_file\\\": \\\"false\\\", \\\"input_1\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"paired_options\\\": {\\\"__current_case__\\\": 1, \\\"paired_options_selector\\\": \\\"no\\\"}, \\\"type\\\": \\\"paired_collection\\\", \\\"unaligned_file\\\": \\\"false\\\"}\", \"reference_genome\": \"{\\\"__current_case__\\\": 0, \\\"index\\\": \\\"hg38full\\\", \\\"source\\\": \\\"indexed\\\"}\", \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"save_mapping_stats\": \"\\\"true\\\"\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"simple\\\", \\\"presets\\\": \\\"no_presets\\\"}\"}",
+                        "tool_version": "2.3.4.3+galaxy0",
                         "type": "tool",
-                        "uuid": "2b550197-cc54-44e7-be71-8d15a093fda6",
-                        "when": null,
+                        "uuid": "43331d2c-7116-410e-a6bd-7e7520d93a52",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "smudgeplot_log",
-                                "uuid": "7573ecef-1ef1-4879-b602-f4dcc92e0bfb"
+                                "output_name": "output",
+                                "uuid": "eeae40f6-f1b2-4c56-9860-ac7b8eb1dec0"
                             },
                             {
                                 "label": null,
-                                "output_name": "smudgeplot",
-                                "uuid": "ab18b562-de82-40f4-8c30-3f730479d97c"
+                                "output_name": "mapping_stats",
+                                "uuid": "c567226e-efaf-4188-bdec-3ba20d0733b0"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
                         "errors": null,
-                        "id": 22,
+                        "id": 8,
                         "input_connections": {
-                            "input_file": {
-                                "id": 14,
-                                "output_name": "output"
+                            "input": {
+                                "id": 4,
+                                "output_name": "alignment_output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Bandage Image",
+                        "name": "Samtools stats",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "jpg"
+                                "name": "output_collection",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 860,
-                            "top": 1499
+                            "left": 1022.4166259765625,
+                            "top": 1254.4166870117188
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "ddddce450736",
-                            "name": "bandage",
-                            "owner": "iuc",
+                            "changeset_revision": "145f6d74ff5e",
+                            "name": "samtools_stats",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"fontsize\": null, \"height\": \"1000\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"lengths\": false, \"names\": false, \"nodewidth\": null, \"output_format\": \"jpg\", \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2022.09+galaxy4",
+                        "tool_state": "{\"__page__\": null, \"coverage_cond\": \"{\\\"__current_case__\\\": 0, \\\"coverage_select\\\": \\\"no\\\"}\", \"gc_depth\": \"\\\"\\\"\", \"cov_threshold\": \"\\\"\\\"\", \"most_inserts\": \"\\\"\\\"\", \"cond_region\": \"{\\\"__current_case__\\\": 0, \\\"select_region\\\": \\\"no\\\"}\", \"split_output_cond\": \"{\\\"__current_case__\\\": 1, \\\"generate_tables\\\": [\\\"SN\\\"], \\\"split_output_selector\\\": \\\"yes\\\"}\", \"read_length\": \"\\\"\\\"\", \"trim_quality\": \"\\\"\\\"\", \"remove_overlaps\": \"\\\"false\\\"\", \"filter_by_flags\": \"{\\\"__current_case__\\\": 1, \\\"filter_flags\\\": \\\"nofilter\\\"}\", \"sparse\": \"\\\"false\\\"\", \"addref_cond\": \"{\\\"__current_case__\\\": 0, \\\"addref_select\\\": \\\"no\\\"}\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"insert_size\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"remove_dups\": \"\\\"false\\\"\"}",
+                        "tool_version": "2.0.2+galaxy2",
                         "type": "tool",
-                        "uuid": "17e86ff6-8432-4125-aee6-63630ea662cc",
-                        "when": null,
+                        "uuid": "15f6252f-79d4-4319-855d-09665deac6a3",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "25323480-dacf-41b4-a7e9-c02f557737de"
-                            }
+                                "output_name": "output_collection",
+                                "uuid": "faed6306-eed6-40bd-ac9f-9fb3a4e980ea"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "assembly/assembly-with-preprocessing",
+                "path": "topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing.ga",
+                "tags": [
+                    "GTN",
+                    "assembly"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "assembly_with_preprocessing",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-assembly-with-preprocessing/versions/assembly-with-preprocessing",
+                "tutorial_id": "assembly-with-preprocessing",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing.html",
+                "version": 1,
+                "wfid": "assembly-assembly-with-preprocessing",
+                "wfname": "assembly-with-preprocessing",
+                "workflow": "assembly_with_preprocessing.ga",
+                "workflow_tools": [
+                    "__ZIP_COLLECTION__",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
+                ],
+                "workflowhub_id": "1132"
+            },
+            {
+                "creators": [],
+                "description": "Assembly with preprocessing and SRA download",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nList of Illumina accessions\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nList of ONT accessions\"]\n  10[label=\"Samtools stats\"]\n  6 -> 10 [label=\"alignment_output\"]\n  11[label=\"Samtools view\"]\n  8 -> 11 [label=\"output\"]\n  12[label=\"Samtools fastx\"]\n  9 -> 12 [label=\"outputsam\"]\n  13[label=\"Samtools fastx\"]\n  11 -> 13 [label=\"outputsam\"]\n  14[label=\"Collapse Collection\"]\n  12 -> 14 [label=\"nonspecific\"]\n  15[label=\"Zip Collection\"]\n  13 -> 15 [label=\"forward\"]\n  13 -> 15 [label=\"reverse\"]\n  16[label=\"Collapse Collection\"]\n  13 -> 16 [label=\"forward\"]\n  17[label=\"Collapse Collection\"]\n  13 -> 17 [label=\"reverse\"]\n  18[label=\"seqtk_sample\"]\n  16 -> 18 [label=\"output\"]\n  19[label=\"seqtk_sample\"]\n  17 -> 19 [label=\"output\"]\n  2[label=\"Illumina data\"]\n  0 -> 2 [label=\"output\"]\n  20[label=\"Create assemblies with Unicycler\"]\n  14 -> 20 [label=\"output\"]\n  18 -> 20 [label=\"default\"]\n  19 -> 20 [label=\"default\"]\n  21[label=\"Bandage Info\"]\n  20 -> 21 [label=\"assembly_graph\"]\n  22[label=\"Bandage Image\"]\n  20 -> 22 [label=\"assembly_graph\"]\n  23[label=\"Filter sequences by length\"]\n  20 -> 23 [label=\"assembly\"]\n  3[label=\"ONT data\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"fastp: Trimmed Illumina Reads\"]\n  2 -> 4 [label=\"list_paired\"]\n  5[label=\"NanoPlot\"]\n  3 -> 5 [label=\"output_collection\"]\n  6[label=\"Map with minimap2\"]\n  3 -> 6 [label=\"output_collection\"]\n  7[label=\"MultiQC\"]\n  4 -> 7 [label=\"report_json\"]\n  8[label=\"Bowtie2\"]\n  4 -> 8 [label=\"output_paired_coll\"]\n  9[label=\"Samtools view\"]\n  6 -> 9 [label=\"alignment_output\"]\n}",
+                "history": [
+                    {
+                        "hash": "fc35e6581a2e34e4420f19af4619c92283609e91",
+                        "message": "add annotations",
+                        "num": 2,
+                        "short_hash": "fc35e6581",
+                        "unix": "1587558793"
+                    },
+                    {
+                        "hash": "7ed054469d1ef84a60abec55758ee2932f9a9655",
+                        "message": "readd workflows",
+                        "num": 1,
+                        "short_hash": "7ed054469",
+                        "unix": "1587555276"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "List of Illumina accessions",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 257.683349609375,
+                            "top": 215.9166259765625
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "1a61a3b3-4515-47a1-8ee5-fb79f05a8dfa",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "ea340c2d-d9e8-4ea5-bbc0-7ee7d92a57bf"
+                            }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
+                        "content_id": null,
                         "errors": null,
-                        "id": 25,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "List of ONT accessions",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 264.9833984375,
+                            "top": 522.7166442871094
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0988bf07-dc80-4d7b-a62f-8e5e852b0982",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "fb053f14-71fc-45ac-83ea-a308a5c22918"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nList of Illumina accessions\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nList of ONT accessions\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Samtools stats\"];\n  6 -->|alignment_output| 10;\n  11[\"Samtools view\"];\n  8 -->|output| 11;\n  12[\"Samtools fastx\"];\n  9 -->|outputsam| 12;\n  13[\"Samtools fastx\"];\n  11 -->|outputsam| 13;\n  14[\"Collapse Collection\"];\n  12 -->|nonspecific| 14;\n  15[\"Zip Collection\"];\n  13 -->|forward| 15;\n  13 -->|reverse| 15;\n  16[\"Collapse Collection\"];\n  13 -->|forward| 16;\n  17[\"Collapse Collection\"];\n  13 -->|reverse| 17;\n  18[\"seqtk_sample\"];\n  16 -->|output| 18;\n  19[\"seqtk_sample\"];\n  17 -->|output| 19;\n  2[\"Illumina data\"];\n  0 -->|output| 2;\n  20[\"Create assemblies with Unicycler\"];\n  14 -->|output| 20;\n  18 -->|default| 20;\n  19 -->|default| 20;\n  21[\"Bandage Info\"];\n  20 -->|assembly_graph| 21;\n  22[\"Bandage Image\"];\n  20 -->|assembly_graph| 22;\n  23[\"Filter sequences by length\"];\n  20 -->|assembly| 23;\n  3[\"ONT data\"];\n  1 -->|output| 3;\n  4[\"fastp: Trimmed Illumina Reads\"];\n  2 -->|list_paired| 4;\n  5[\"NanoPlot\"];\n  3 -->|output_collection| 5;\n  6[\"Map with minimap2\"];\n  3 -->|output_collection| 6;\n  7[\"MultiQC\"];\n  4 -->|report_json| 7;\n  8[\"Bowtie2\"];\n  4 -->|output_paired_coll| 8;\n  9[\"Samtools view\"];\n  6 -->|alignment_output| 9;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "assembly_with_preprocessing_and_sra_download",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "List of Illumina accessions",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 257.683349609375,
+                            "top": 215.9166259765625
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "1a61a3b3-4515-47a1-8ee5-fb79f05a8dfa",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "ea340c2d-d9e8-4ea5-bbc0-7ee7d92a57bf"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "List of ONT accessions",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 264.9833984375,
+                            "top": 522.7166442871094
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0988bf07-dc80-4d7b-a62f-8e5e852b0982",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "fb053f14-71fc-45ac-83ea-a308a5c22918"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                        "errors": null,
+                        "id": 10,
                         "input_connections": {
-                            "mode|assembly_options|assembly_01": {
-                                "id": 5,
-                                "output_name": "output"
-                            },
-                            "mode|meryldb_F1": {
-                                "id": 18,
-                                "output_name": "read_db"
+                            "input": {
+                                "id": 6,
+                                "output_name": "alignment_output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Merqury",
+                        "name": "Samtools stats",
                         "outputs": [
                             {
-                                "name": "qv_files",
+                                "name": "output_collection",
                                 "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1328.4166259765625,
+                            "top": 1239.4166259765625
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "145f6d74ff5e",
+                            "name": "samtools_stats",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"coverage_cond\": \"{\\\"__current_case__\\\": 0, \\\"coverage_select\\\": \\\"no\\\"}\", \"gc_depth\": \"\\\"\\\"\", \"cov_threshold\": \"\\\"\\\"\", \"most_inserts\": \"\\\"\\\"\", \"cond_region\": \"{\\\"__current_case__\\\": 0, \\\"select_region\\\": \\\"no\\\"}\", \"split_output_cond\": \"{\\\"__current_case__\\\": 1, \\\"generate_tables\\\": [\\\"SN\\\"], \\\"split_output_selector\\\": \\\"yes\\\"}\", \"read_length\": \"\\\"\\\"\", \"trim_quality\": \"\\\"\\\"\", \"remove_overlaps\": \"\\\"false\\\"\", \"filter_by_flags\": \"{\\\"__current_case__\\\": 1, \\\"filter_flags\\\": \\\"nofilter\\\"}\", \"sparse\": \"\\\"false\\\"\", \"addref_cond\": \"{\\\"__current_case__\\\": 0, \\\"addref_select\\\": \\\"no\\\"}\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"insert_size\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"remove_dups\": \"\\\"false\\\"\"}",
+                        "tool_version": "2.0.2+galaxy2",
+                        "type": "tool",
+                        "uuid": "ae176340-d7da-4c2e-851b-e6129a0c222d",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_collection",
+                                "uuid": "8652ea8a-35f5-4531-8b89-88bca189ab9f"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {
+                            "input": {
+                                "id": 9,
+                                "output_name": "outputsam"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Samtools fastx",
+                        "outputs": [
+                            {
+                                "name": "nonspecific",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "left": 1628.4166259765625,
+                            "top": 852.4166412353516
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "a8d69aee190e",
+                            "name": "samtools_fastx",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"copy_arb_tags\": \"\\\"\\\"\", \"__page__\": null, \"output_fmt_cond\": \"{\\\"__current_case__\\\": 2, \\\"default_quality\\\": \\\"\\\", \\\"ilumina_casava\\\": \\\"false\\\", \\\"output_fmt_select\\\": \\\"fastqsanger.gz\\\", \\\"output_quality\\\": \\\"false\\\"}\", \"idxout_cond\": \"{\\\"__current_case__\\\": 0, \\\"idxout_select\\\": \\\"no\\\"}\", \"read_numbering\": \"\\\"\\\"\", \"exclusive_filter\": \"null\", \"exclusive_filter_all\": \"null\", \"inclusive_filter\": \"null\", \"outputs\": \"[\\\"r0\\\"]\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"copy_tags\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9+galaxy1",
+                        "type": "tool",
+                        "uuid": "31e2b4e8-7631-46c0-8382-b805cee2b739",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "nonspecific",
+                                "uuid": "cfbf839f-53f0-4a82-8966-2bdb6919de5e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "__ZIP_COLLECTION__",
+                        "errors": null,
+                        "id": 15,
+                        "input_connections": {
+                            "input_forward": {
+                                "id": 13,
+                                "output_name": "forward"
                             },
+                            "input_reverse": {
+                                "id": 13,
+                                "output_name": "reverse"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Zip Collection",
+                        "outputs": [
                             {
-                                "name": "png_files",
+                                "name": "output",
                                 "type": "input"
-                            },
+                            }
+                        ],
+                        "position": {
+                            "left": 2049.4166870117188,
+                            "top": 477.4166259765625
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "__ZIP_COLLECTION__",
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_reverse\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"input_forward\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "9ba89e81-9c53-4f5b-9d61-42319b7d574c",
+                        "workflow_outputs": [
                             {
-                                "name": "stats_files",
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "ebc8f563-c45e-4e17-a541-b1275e7f61ad"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
+                        "errors": null,
+                        "id": 18,
+                        "input_connections": {
+                            "in_file": {
+                                "id": 16,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool seqtk_sample",
+                                "name": "in_file"
+                            }
+                        ],
+                        "label": null,
+                        "name": "seqtk_sample",
+                        "outputs": [
+                            {
+                                "name": "default",
                                 "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 860,
-                            "top": 581
+                            "left": 2438.0833282470703,
+                            "top": 688.6833190917969
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "f8113c25bc6b",
-                            "name": "merqury",
+                            "changeset_revision": "58c8ece95b53",
+                            "name": "seqtk",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"label\": \"output_merqury\", \"mode\": {\"options\": \"default\", \"__current_case__\": 0, \"meryldb_F1\": {\"__class__\": \"ConnectedValue\"}, \"assembly_options\": {\"number_assemblies\": \"one\", \"__current_case__\": 0, \"assembly_01\": {\"__class__\": \"ConnectedValue\"}}}, \"output_add_headers\": false, \"output_selector\": [\"qv\", \"plots\", \"stats\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3+galaxy2",
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"s\": \"\\\"4\\\"\", \"in_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"subsample_size\": \"\\\"0.1\\\"\", \"advanced\": \"{\\\"single_pass_mode\\\": \\\"false\\\"}\"}",
+                        "tool_version": "1.3.2",
                         "type": "tool",
-                        "uuid": "60379717-8086-422d-8300-9d1b459a473a",
-                        "when": null,
+                        "uuid": "b4e40092-e076-4eb0-af30-c8c47885fefa",
                         "workflow_outputs": [
                             {
-                                "label": "Merqury on input dataset(s): stats",
-                                "output_name": "stats_files",
-                                "uuid": "c2fe83a3-754a-4544-bb87-df16f3537ab4"
+                                "label": null,
+                                "output_name": "default",
+                                "uuid": "cf3eb8ef-fce5-42af-a14d-60ff915fbff3"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
+                        "errors": null,
+                        "id": 19,
+                        "input_connections": {
+                            "in_file": {
+                                "id": 17,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool seqtk_sample",
+                                "name": "in_file"
+                            }
+                        ],
+                        "label": null,
+                        "name": "seqtk_sample",
+                        "outputs": [
+                            {
+                                "name": "default",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 2413.0833129882812,
+                            "top": 864.6833190917969
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "58c8ece95b53",
+                            "name": "seqtk",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"s\": \"\\\"4\\\"\", \"in_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"subsample_size\": \"\\\"0.1\\\"\", \"advanced\": \"{\\\"single_pass_mode\\\": \\\"false\\\"}\"}",
+                        "tool_version": "1.3.2",
+                        "type": "tool",
+                        "uuid": "1ef9ca9e-e447-4933-8871-c0e8e9a953c4",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "default",
+                                "uuid": "bf722cb7-0b06-42ed-8fbc-9dc3896e9340"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "input|file_list": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Illumina data",
+                        "name": "Faster Download and Extract Reads in FASTQ",
+                        "outputs": [
+                            {
+                                "name": "list_paired",
+                                "type": "input"
                             },
                             {
-                                "label": "Merqury on input dataset(s): plots",
-                                "output_name": "png_files",
-                                "uuid": "8f08d8f6-7615-420c-8a15-201a61b5d3bb"
+                                "name": "output_collection",
+                                "type": "input"
                             },
                             {
-                                "label": "Merqury on input dataset(s): QV stats",
-                                "output_name": "qv_files",
-                                "uuid": "7a8d951a-6a31-4b02-aeba-0eb3061f85ce"
+                                "name": "output_collection_other",
+                                "type": "input"
+                            },
+                            {
+                                "name": "log",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 511.783447265625,
+                            "top": 273.1666259765625
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionlog": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "log"
+                            },
+                            "HideDatasetActionoutput_collection": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_collection"
+                            },
+                            "HideDatasetActionoutput_collection_other": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_collection_other"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "aad3885b3216",
+                            "name": "sra_tools",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv\": \"{\\\"minlen\\\": \\\"\\\", \\\"skip_technical\\\": \\\"true\\\", \\\"split\\\": \\\"--split-3\\\"}\", \"input\": \"{\\\"__current_case__\\\": 2, \\\"file_list\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"input_select\\\": \\\"file_list\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+                        "tool_version": "2.10.4+galaxy1",
+                        "type": "tool",
+                        "uuid": "b097b5cb-44a8-4881-9ba0-a089ef1b4ad6",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "list_paired",
+                                "uuid": "c6b4e7f2-5cf4-4051-afd1-a110381c4679"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
                         "errors": null,
-                        "id": 27,
+                        "id": 20,
                         "input_connections": {
-                            "input": {
+                            "long": {
+                                "id": 14,
+                                "output_name": "output"
+                            },
+                            "paired_unpaired|fastq_input1": {
+                                "id": 18,
+                                "output_name": "default"
+                            },
+                            "paired_unpaired|fastq_input2": {
                                 "id": 19,
-                                "output_name": "output_alignments"
+                                "output_name": "default"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "lr_align"
+                            },
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "long"
+                            },
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "paired_unpaired"
+                            },
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "paired_unpaired"
+                            },
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "rotation"
+                            }
+                        ],
                         "label": null,
-                        "name": "Samtools stats",
+                        "name": "Create assemblies with Unicycler",
                         "outputs": [
                             {
-                                "name": "output",
+                                "name": "assembly_graph",
                                 "type": "tabular"
+                            },
+                            {
+                                "name": "assembly",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 860,
-                            "top": 1816
+                            "left": 2673.4166717529297,
+                            "top": 699.4166412353516
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "3a0efe14891f",
-                            "name": "samtools_stats",
-                            "owner": "devteam",
+                            "changeset_revision": "88c240872a65",
+                            "name": "unicycler",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cov_threshold\": null, \"coverage_cond\": {\"coverage_select\": \"no\", \"__current_case__\": 0}, \"filter_by_flags\": {\"filter_flags\": \"nofilter\", \"__current_case__\": 1}, \"gc_depth\": null, \"input\": {\"__class__\": \"ConnectedValue\"}, \"insert_size\": null, \"most_inserts\": null, \"read_group\": null, \"read_length\": null, \"remove_dups\": false, \"remove_overlaps\": false, \"sparse\": false, \"split_output_cond\": {\"split_output_selector\": \"no\", \"__current_case__\": 0}, \"trim_quality\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.4",
+                        "tool_state": "{\"linear_seqs\": \"\\\"1\\\"\", \"spades\": \"{\\\"depth_filter\\\": \\\"0.25\\\", \\\"kmer_count\\\": \\\"10\\\", \\\"kmers\\\": \\\"\\\", \\\"largest_component\\\": \\\"false\\\", \\\"max_kmer_frac\\\": \\\"0.95\\\", \\\"min_kmer_frac\\\": \\\"0.2\\\", \\\"no_correct\\\": \\\"false\\\"}\", \"graph_clean\": \"{\\\"min_component_size\\\": \\\"1000\\\", \\\"min_dead_end_size\\\": \\\"1000\\\"}\", \"__page__\": null, \"min_anchor_seg_len\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"lr_align\": \"{\\\"contamination\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"low_score\\\": \\\"\\\", \\\"scores\\\": \\\"3,-6,-5,-2\\\"}\", \"long\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"paired_unpaired\": \"{\\\"__current_case__\\\": 0, \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"fastq_input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired\\\"}\", \"min_fasta_length\": \"\\\"100\\\"\", \"mode\": \"\\\"normal\\\"\", \"rotation\": \"{\\\"no_rotate\\\": \\\"false\\\", \\\"start_gene_cov\\\": \\\"95.0\\\", \\\"start_gene_id\\\": \\\"90.0\\\", \\\"start_genes\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"pilon\": \"{\\\"min_polish_size\\\": \\\"1000\\\", \\\"no_pilon\\\": \\\"false\\\"}\"}",
+                        "tool_version": "0.4.8.0",
                         "type": "tool",
-                        "uuid": "d6f1f5fe-736a-4e1f-87d5-0ae8bba7ad11",
-                        "when": null,
+                        "uuid": "851c6be6-c202-450a-9cd3-19e205dcc496",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "c26fc7dd-b185-42fc-b831-e3e9a5e6d741"
+                                "output_name": "assembly",
+                                "uuid": "17700863-7cc5-4a67-ac0f-aa5f7b258d62"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "assembly_graph",
+                                "uuid": "3285cc00-6b39-4f3d-87a5-87abd483ede6"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.4+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
                         "errors": null,
-                        "id": 28,
+                        "id": 21,
                         "input_connections": {
-                            "input": {
-                                "id": 21,
-                                "output_name": "outfile"
+                            "input_file": {
+                                "id": 20,
+                                "output_name": "assembly_graph"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Busco",
+                        "name": "Bandage Info",
                         "outputs": [
                             {
-                                "name": "busco_sum",
+                                "name": "outfile",
                                 "type": "txt"
-                            },
-                            {
-                                "name": "busco_table",
-                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1140,
-                            "top": 1293
+                            "left": 2977.4166870117188,
+                            "top": 803.4166412353516
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.4+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "bb935709506a",
-                            "name": "busco",
+                            "changeset_revision": "b2860df42e16",
+                            "name": "bandage",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"auto_detect\", \"__current_case__\": 0, \"auto_lineage\": \"--auto-lineage\"}, \"outputs\": [\"short_summary\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.4.4+galaxy0",
+                        "tool_state": "{\"tsv\": \"\\\"false\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+                        "tool_version": "0.8.1+galaxy1",
                         "type": "tool",
-                        "uuid": "3a41b74c-9ed5-4a4c-a92d-f48cf6d5f35d",
-                        "when": null,
+                        "uuid": "4aa230bd-3269-41c3-81f5-9085fcc4001d",
                         "workflow_outputs": [
                             {
-                                "label": "Busco on input dataset(s): full table",
-                                "output_name": "busco_table",
-                                "uuid": "1d4e4542-8bf1-4e32-890b-2e18df95a0de"
-                            },
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "cf5eab6a-97ae-430e-a27a-6ecc33d4b8c0"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+                        "errors": null,
+                        "id": 22,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 20,
+                                "output_name": "assembly_graph"
+                            }
+                        },
+                        "inputs": [
                             {
-                                "label": "Busco on input dataset(s): short summary",
-                                "output_name": "busco_sum",
-                                "uuid": "680b8177-3653-4630-ab99-c1d2304dc485"
+                                "description": "runtime parameter for tool Bandage Image",
+                                "name": "input_file"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Bandage Image",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "jpg"
+                            }
+                        ],
+                        "position": {
+                            "left": 2975.4166870117188,
+                            "top": 1017.4166412353516
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "b2860df42e16",
+                            "name": "bandage",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"lengths\": \"\\\"true\\\"\", \"output_format\": \"\\\"jpg\\\"\", \"height\": \"\\\"1000\\\"\", \"width\": \"\\\"\\\"\", \"names\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.8.1+galaxy2",
+                        "type": "tool",
+                        "uuid": "7683e21a-0fe1-4871-b044-7e74321fe44b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "12e0cc76-0374-4ce8-b882-f5f21a942ad1"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
                         "errors": null,
-                        "id": 35,
+                        "id": 23,
                         "input_connections": {
                             "input": {
-                                "id": 26,
-                                "output_name": "read_db_hist"
-                            },
-                            "ploidy": {
-                                "id": 4,
+                                "id": 20,
+                                "output_name": "assembly"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Filter sequences by length",
+                                "name": "input"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Filter sequences by length",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "left": 2978.4166870117188,
+                            "top": 1220.4166259765625
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "8cacfcf96a52",
+                            "name": "fasta_filter_by_length",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"max_length\": \"\\\"0\\\"\", \"min_length\": \"\\\"1000\\\"\"}",
+                        "tool_version": "1.2",
+                        "type": "tool",
+                        "uuid": "ef08963b-e96b-4841-b1fd-02056f6ab1f2",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "637c866b-dc17-4c32-aa1e-5207ae2c79a0"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "input|file_list": {
+                                "id": 1,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "GenomeScope",
+                        "label": "ONT data",
+                        "name": "Faster Download and Extract Reads in FASTQ",
                         "outputs": [
                             {
-                                "name": "linear_plot",
-                                "type": "png"
+                                "name": "list_paired",
+                                "type": "input"
                             },
                             {
-                                "name": "log_plot",
-                                "type": "png"
+                                "name": "output_collection",
+                                "type": "input"
                             },
                             {
-                                "name": "transformed_linear_plot",
-                                "type": "png"
+                                "name": "output_collection_other",
+                                "type": "input"
                             },
                             {
-                                "name": "transformed_log_plot",
-                                "type": "png"
+                                "name": "log",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 1140,
-                            "top": 977
+                            "left": 516.13330078125,
+                            "top": 540.7166442871094
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
+                        "post_job_actions": {
+                            "HideDatasetActionlist_paired": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "list_paired"
+                            },
+                            "HideDatasetActionlog": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "log"
+                            },
+                            "HideDatasetActionoutput_collection_other": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_collection_other"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "01210c4e9144",
-                            "name": "genomescope",
+                            "changeset_revision": "aad3885b3216",
+                            "name": "sra_tools",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_options\": {\"topology\": null, \"initial_repetitiveness\": null, \"initial_heterozygosities\": \"\", \"transform_exp\": null, \"testing\": false, \"true_params\": \"\", \"trace_flag\": false, \"num_rounds\": null}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"kmer_length\": \"21\", \"lambda\": null, \"max_kmercov\": null, \"output_options\": {\"output_files\": null, \"no_unique_sequence\": false}, \"ploidy\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0+galaxy2",
+                        "tool_state": "{\"adv\": \"{\\\"minlen\\\": \\\"\\\", \\\"skip_technical\\\": \\\"true\\\", \\\"split\\\": \\\"--split-3\\\"}\", \"input\": \"{\\\"__current_case__\\\": 2, \\\"file_list\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"input_select\\\": \\\"file_list\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+                        "tool_version": "2.10.4+galaxy1",
                         "type": "tool",
-                        "uuid": "123fa27b-c25d-422f-ab18-5996179a50a0",
-                        "when": null,
+                        "uuid": "2ea0a236-4ecc-43b4-a815-40f37bf1bd59",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "transformed_linear_plot",
-                                "uuid": "a7482d1b-bc8b-4d99-9095-14008f64ca7e"
+                                "output_name": "output_collection",
+                                "uuid": "9cd44dd5-4375-4c34-9edc-804544192c34"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "single_paired|paired_input": {
+                                "id": 2,
+                                "output_name": "list_paired"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool fastp",
+                                "name": "single_paired"
+                            }
+                        ],
+                        "label": "fastp: Trimmed Illumina Reads",
+                        "name": "fastp",
+                        "outputs": [
+                            {
+                                "name": "output_paired_coll",
+                                "type": "input"
                             },
+                            {
+                                "name": "report_json",
+                                "type": "json"
+                            }
+                        ],
+                        "position": {
+                            "left": 879.7833251953125,
+                            "top": 365.04998779296875
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionreport_json": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "report_json"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "1d8fe9bc4cb0",
+                            "name": "fastp",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"report_html\\\": \\\"false\\\", \\\"report_json\\\": \\\"true\\\"}\", \"single_paired\": \"{\\\"__current_case__\\\": 2, \\\"adapter_trimming_options\\\": {\\\"adapter_sequence1\\\": \\\"\\\", \\\"adapter_sequence2\\\": \\\"\\\", \\\"disable_adapter_trimming\\\": \\\"false\\\"}, \\\"global_trimming_options\\\": {\\\"trim_front1\\\": \\\"\\\", \\\"trim_front2\\\": \\\"\\\", \\\"trim_tail1\\\": \\\"\\\", \\\"trim_tail2\\\": \\\"\\\"}, \\\"paired_input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"single_paired_selector\\\": \\\"paired_collection\\\"}\", \"read_mod_options\": \"{\\\"base_correction_options\\\": {\\\"correction\\\": \\\"false\\\"}, \\\"cutting_by_quality_options\\\": {\\\"cut_by_quality3\\\": \\\"false\\\", \\\"cut_by_quality5\\\": \\\"false\\\", \\\"cut_mean_quality\\\": \\\"\\\", \\\"cut_window_size\\\": \\\"\\\"}, \\\"polyg_tail_trimming\\\": {\\\"__current_case__\\\": 1, \\\"poly_g_min_len\\\": \\\"\\\", \\\"trimming_select\\\": \\\"\\\"}, \\\"polyx_tail_trimming\\\": {\\\"__current_case__\\\": 1, \\\"polyx_trimming_select\\\": \\\"\\\"}, \\\"umi_processing\\\": {\\\"umi\\\": \\\"false\\\", \\\"umi_len\\\": \\\"\\\", \\\"umi_loc\\\": \\\"\\\", \\\"umi_prefix\\\": \\\"\\\"}}\", \"overrepresented_sequence_analysis\": \"{\\\"overrepresentation_analysis\\\": \\\"false\\\", \\\"overrepresentation_sampling\\\": \\\"\\\"}\", \"filter_options\": \"{\\\"length_filtering_options\\\": {\\\"disable_length_filtering\\\": \\\"false\\\", \\\"length_required\\\": \\\"50\\\"}, \\\"low_complexity_filter\\\": {\\\"complexity_threshold\\\": \\\"\\\", \\\"enable_low_complexity_filter\\\": \\\"false\\\"}, \\\"quality_filtering_options\\\": {\\\"disable_quality_filtering\\\": \\\"false\\\", \\\"n_base_limit\\\": \\\"\\\", \\\"qualified_quality_phred\\\": \\\"20\\\", \\\"unqualified_percent_limit\\\": \\\"20\\\"}}\", \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.19.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "7508c22b-dc6a-4071-8dd0-d5616718e62b",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "log_plot",
-                                "uuid": "2fd6f906-f4ec-4d9a-8043-2185ffde267d"
+                                "output_name": "output_paired_coll",
+                                "uuid": "a7be7eab-3e80-4be6-b1a4-ab303c314096"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "mode|reads|files": {
+                                "id": 3,
+                                "output_name": "output_collection"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "NanoPlot",
+                        "outputs": [
+                            {
+                                "name": "output_html",
+                                "type": "html"
                             },
                             {
-                                "label": null,
-                                "output_name": "linear_plot",
-                                "uuid": "ed2a9a05-d98f-4edd-b033-2312990b215b"
+                                "name": "nanostats",
+                                "type": "txt"
                             },
+                            {
+                                "name": "nanostats_post_filtering",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "read_length",
+                                "type": "png"
+                            },
+                            {
+                                "name": "log_read_length",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 924.7833251953125,
+                            "top": 650.4666442871094
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionlog_read_length": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "log_read_length"
+                            },
+                            "HideDatasetActionnanostats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "nanostats"
+                            },
+                            "HideDatasetActionnanostats_post_filtering": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "nanostats_post_filtering"
+                            },
+                            "HideDatasetActionread_length": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "read_length"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "645159bcee2d",
+                            "name": "nanoplot",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"filter\": \"{\\\"alength\\\": \\\"false\\\", \\\"barcoded\\\": \\\"false\\\", \\\"downsample\\\": \\\"\\\", \\\"drop_outliers\\\": \\\"false\\\", \\\"loglength\\\": \\\"true\\\", \\\"maxlength\\\": \\\"\\\", \\\"minlength\\\": \\\"\\\", \\\"minqual\\\": \\\"\\\", \\\"percentqual\\\": \\\"false\\\", \\\"readtype\\\": null}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"__current_case__\\\": 0, \\\"choice\\\": \\\"batch\\\", \\\"reads\\\": {\\\"__current_case__\\\": 0, \\\"files\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"type\\\": \\\"fastq\\\"}}\", \"customization\": \"{\\\"N50\\\": \\\"false\\\", \\\"color\\\": null, \\\"format\\\": \\\"png\\\", \\\"noN50\\\": \\\"false\\\", \\\"plots\\\": null}\"}",
+                        "tool_version": "1.25.0+galaxy1",
+                        "type": "tool",
+                        "uuid": "9b1d43ac-82e3-463f-9c88-08c8826a62c9",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "transformed_log_plot",
-                                "uuid": "3e5db883-c25e-470e-bb18-be0da5dcd4f0"
+                                "output_name": "output_html",
+                                "uuid": "cd8570c7-02db-479b-81a9-cd0d26643f71"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
                         "errors": null,
-                        "id": 39,
+                        "id": 6,
                         "input_connections": {
-                            "input": {
-                                "id": 37,
-                                "output_name": "pretext_map_out"
+                            "fastq_input|fastq_input1": {
+                                "id": 3,
+                                "output_name": "output_collection"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Pretext Snapshot",
+                        "name": "Map with minimap2",
                         "outputs": [
                             {
-                                "name": "pretext_snap_out",
-                                "type": "input"
+                                "name": "alignment_output",
+                                "type": "bam"
                             }
                         ],
                         "position": {
-                            "left": 1430,
-                            "top": 2162
+                            "left": 1003.9833984375,
+                            "top": 1131.9666442871094
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "44c66e8d21e6",
-                            "name": "pretext_snapshot",
+                            "changeset_revision": "53c0b7a1a0c3",
+                            "name": "minimap2",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"colormap\": \"5\", \"formats\": {\"outformat\": \"png\", \"__current_case__\": 0}, \"grid\": {\"showGrid\": true, \"__current_case__\": 0, \"gridsize\": \"1\", \"gridcolor\": \"black\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mintexels\": \"64\", \"resolution\": \"1000\", \"sequencenames\": false, \"sequences\": \"=full, =all\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.0.3+galaxy1",
+                        "tool_state": "{\"alignment_options\": \"{\\\"-O2\\\": \\\"\\\", \\\"A\\\": \\\"\\\", \\\"B\\\": \\\"\\\", \\\"E\\\": \\\"\\\", \\\"E2\\\": \\\"\\\", \\\"O\\\": \\\"\\\", \\\"s\\\": \\\"\\\", \\\"u\\\": null, \\\"z\\\": \\\"\\\"}\", \"analysis_type_selector\": \"\\\"splice\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"io_options\": \"{\\\"K\\\": \\\"\\\", \\\"L\\\": \\\"false\\\", \\\"Q\\\": \\\"false\\\", \\\"Y\\\": \\\"false\\\", \\\"c\\\": \\\"false\\\", \\\"cs\\\": null, \\\"eqx\\\": \\\"false\\\", \\\"output_format\\\": \\\"BAM\\\"}\", \"mapping_options\": \"{\\\"F\\\": \\\"\\\", \\\"G\\\": \\\"\\\", \\\"N\\\": \\\"\\\", \\\"X\\\": \\\"false\\\", \\\"f\\\": \\\"\\\", \\\"g\\\": \\\"\\\", \\\"m\\\": \\\"\\\", \\\"min_occ_floor\\\": \\\"\\\", \\\"n\\\": \\\"\\\", \\\"p\\\": \\\"\\\", \\\"r\\\": \\\"\\\"}\", \"fastq_input\": \"{\\\"__current_case__\\\": 1, \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"single\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 0, \\\"ref_file\\\": \\\"hg38\\\", \\\"reference_source_selector\\\": \\\"cached\\\"}\", \"indexing_options\": \"{\\\"H\\\": \\\"false\\\", \\\"I\\\": \\\"\\\", \\\"k\\\": \\\"\\\", \\\"w\\\": \\\"\\\"}\"}",
+                        "tool_version": "2.17+galaxy1",
                         "type": "tool",
-                        "uuid": "576bcaf5-7b61-494c-b6cd-e10084628f08",
-                        "when": null,
+                        "uuid": "098d2283-1218-489b-9882-8822e79d9444",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "pretext_snap_out",
-                                "uuid": "ac2cda6a-0fdd-476b-b6ba-7e5312d9f409"
+                                "output_name": "alignment_output",
+                                "uuid": "9972015d-4bdc-440f-b8b6-84e92a64ef8f"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "assembly/ERGA-post-assembly-QC",
-                "path": "topics/assembly/tutorials/ERGA-post-assembly-QC/workflows/main_workflow.ga",
-                "tags": [],
-                "test_results": null,
-                "tests": true,
-                "title": "Post-assembly workflow",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-ERGA-post-assembly-QC/versions/main-workflow",
-                "tutorial_id": "ERGA-post-assembly-QC",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/ERGA-post-assembly-QC/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/ERGA-post-assembly-QC/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "assembly-ERGA-post-assembly-QC",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "CONVERTER_gz_to_uncompressed",
-                    "__EXTRACT_DATASET__",
-                    "interactive_tool_blobtoolkit",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.0.7+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.2.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4",
-                    "toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy+2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.4+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
-                ],
-                "workflowhub_id": "1127"
-            }
-        ]
-    },
-    {
-        "abbreviations": {
-            "ASM": "assembly",
-            "BUSCO": "Benchmarking Universal Single-Copy Orthologs",
-            "CN": "copy number",
-            "G10K": "Genome 10K consortium",
-            "GFA": "Graphical Fragment Assembly",
-            "Hi-C": "all-versus-all chromatin conformation capture",
-            "HiFi": "high fidelity",
-            "NGS": "next generation sequencing",
-            "QC": "Quality Control",
-            "QV": "consensus accuracy quality value",
-            "SMRT": "single-molecule real-time",
-            "TGS": "third-generation sequencing",
-            "VGP": "Vertebrate Genomes Project"
-        },
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "bionano_scaffold",
-                    "owner": "bgruening",
-                    "revisions": "5258e18bbe23",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bionano_scaffold",
-                    "owner": "bgruening",
-                    "revisions": "3371c5bdc17a",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gfastats",
-                    "owner": "bgruening",
-                    "revisions": "3ef480892a9f",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "hifiasm",
-                    "owner": "bgruening",
-                    "revisions": "0ee0c3089254",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "f46f0e4f75c4",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "results_0|software_cond|input": {
+                                "id": 4,
+                                "output_name": "report_json"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "MultiQC",
+                        "outputs": [
+                            {
+                                "name": "stats",
+                                "type": "input"
+                            },
+                            {
+                                "name": "html_report",
+                                "type": "html"
+                            }
+                        ],
+                        "position": {
+                            "left": 1152.4833984375,
+                            "top": 200
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "tool_shed_repository": {
+                            "changeset_revision": "b2f1f75d49c4",
+                            "name": "multiqc",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"comment\": \"\\\"\\\"\", \"__page__\": null, \"title\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"results\": \"[{\\\"__index__\\\": 0, \\\"software_cond\\\": {\\\"__current_case__\\\": 7, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"software\\\": \\\"fastp\\\"}}]\", \"saveLog\": \"\\\"false\\\"\"}",
+                        "tool_version": "1.7",
+                        "type": "tool",
+                        "uuid": "73566697-4a46-4d35-b8e2-61770acc62c0",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "html_report",
+                                "uuid": "15f42a94-2c97-4932-8e3f-f26a72b58be4"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "library|input_1": {
+                                "id": 4,
+                                "output_name": "output_paired_coll"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Bowtie2",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "bam"
+                            },
+                            {
+                                "name": "mapping_stats",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 1208.699951171875,
+                            "top": 564.6333160400391
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "749c918495f7",
+                            "name": "bowtie2",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"sam_options\": \"{\\\"__current_case__\\\": 1, \\\"sam_options_selector\\\": \\\"no\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"__current_case__\\\": 2, \\\"aligned_file\\\": \\\"false\\\", \\\"input_1\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"paired_options\\\": {\\\"__current_case__\\\": 1, \\\"paired_options_selector\\\": \\\"no\\\"}, \\\"type\\\": \\\"paired_collection\\\", \\\"unaligned_file\\\": \\\"false\\\"}\", \"reference_genome\": \"{\\\"__current_case__\\\": 0, \\\"index\\\": \\\"hg38full\\\", \\\"source\\\": \\\"indexed\\\"}\", \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"save_mapping_stats\": \"\\\"true\\\"\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"simple\\\", \\\"presets\\\": \\\"no_presets\\\"}\"}",
+                        "tool_version": "2.3.4.3+galaxy0",
+                        "type": "tool",
+                        "uuid": "43331d2c-7116-410e-a6bd-7e7520d93a52",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "eeae40f6-f1b2-4c56-9860-ac7b8eb1dec0"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "mapping_stats",
+                                "uuid": "c567226e-efaf-4188-bdec-3ba20d0733b0"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "assembly/assembly-with-preprocessing",
+                "path": "topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing_and_sra_download.ga",
+                "tags": [
+                    "GTN",
+                    "assembly"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "assembly_with_preprocessing_and_sra_download",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-assembly-with-preprocessing/versions/assembly-with-preprocessing-and-sra-download",
+                "tutorial_id": "assembly-with-preprocessing",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing_and_sra_download.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing_and_sra_download.html",
+                "version": 1,
+                "wfid": "assembly-assembly-with-preprocessing",
+                "wfname": "assembly-with-preprocessing-and-sra-download",
+                "workflow": "assembly_with_preprocessing_and_sra_download.ga",
+                "workflow_tools": [
+                    "__ZIP_COLLECTION__",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
+                ],
+                "workflowhub_id": "1197"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/3732359"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
                 {
-                    "name": "text_processing",
+                    "name": "flye",
                     "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "column_maker",
-                    "owner": "devteam",
-                    "revisions": "02026300aa45",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "column_maker",
-                    "owner": "devteam",
-                    "revisions": "6595517c2dd8",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bedtools",
-                    "owner": "iuc",
-                    "revisions": "a1a923cd89e8",
-                    "tool_panel_section_label": "BED",
+                    "revisions": "291923e6f276",
+                    "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bellerophon",
-                    "owner": "iuc",
-                    "revisions": "25ca5d73aedf",
+                    "name": "racon",
+                    "owner": "bgruening",
+                    "revisions": "78c533842eeb",
                     "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bellerophon",
-                    "owner": "iuc",
-                    "revisions": "321347bd0494",
-                    "tool_panel_section_label": "Assembly",
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "5ec9f6bceaee",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "busco",
+                    "name": "bandage",
                     "owner": "iuc",
-                    "revisions": "46ae58b1d792",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "ddddce450736",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
@@ -19627,31 +18607,17 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bwa_mem2",
-                    "owner": "iuc",
-                    "revisions": "b4a22d90cce9",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bwa_mem2",
-                    "owner": "iuc",
-                    "revisions": "bfaa0d22c2e4",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collection_column_join",
+                    "name": "fasta_stats",
                     "owner": "iuc",
-                    "revisions": "3ddd99c7efee",
-                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "revisions": "0dbb995c7d35",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "genomescope",
+                    "name": "fastp",
                     "owner": "iuc",
-                    "revisions": "3169a38c2656",
-                    "tool_panel_section_label": "Assembly",
+                    "revisions": "c59d48774d03",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
@@ -19662,31 +18628,10 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "gfa_to_fa",
-                    "owner": "iuc",
-                    "revisions": "e33c82b63727",
-                    "tool_panel_section_label": "Convert Formats",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "merqury",
-                    "owner": "iuc",
-                    "revisions": "39edec572bae",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "merqury",
-                    "owner": "iuc",
-                    "revisions": "d7edbc9c3a07",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "meryl",
+                    "name": "medaka_consensus_pipeline",
                     "owner": "iuc",
-                    "revisions": "eadfd71dde37",
-                    "tool_panel_section_label": "Assembly",
+                    "revisions": "fc8804320156",
+                    "tool_panel_section_label": "Nanopore",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
@@ -19699,413 +18644,3341 @@
                 {
                     "name": "minimap2",
                     "owner": "iuc",
-                    "revisions": "f54f5baedfdd",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "minimap2",
-                    "owner": "iuc",
-                    "revisions": "11a0d50a54e6",
+                    "revisions": "be1d967337e4",
                     "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pretext_map",
-                    "owner": "iuc",
-                    "revisions": "dfb8a4497339",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pretext_snapshot",
-                    "owner": "iuc",
-                    "revisions": "44c66e8d21e6",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "purge_dups",
+                    "name": "multiqc",
                     "owner": "iuc",
-                    "revisions": "a315c25dc813",
-                    "tool_panel_section_label": "Assembly",
+                    "revisions": "abfd8a6544d7",
+                    "tool_panel_section_label": "Quality Control",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "purge_dups",
+                    "name": "nanoplot",
                     "owner": "iuc",
-                    "revisions": "e9bd16ba5ebd",
-                    "tool_panel_section_label": "Assembly",
+                    "revisions": "a02b8b3f5a0c",
+                    "tool_panel_section_label": "Nanopore",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "quast",
                     "owner": "iuc",
-                    "revisions": "875d0f36d66f",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "salsa",
-                    "owner": "iuc",
-                    "revisions": "f77f7a7f3b83",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "yahs",
-                    "owner": "iuc",
-                    "revisions": "425e63adcc5d",
+                    "revisions": "72472698a2df",
                     "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cutadapt",
-                    "owner": "lparsons",
-                    "revisions": "48f587c13075",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cutadapt",
-                    "owner": "lparsons",
-                    "revisions": "8c0175e03cee",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "830961c48e42",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "90981f86000f",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bionano_scaffold\n  owner: bgruening\n  revisions: 5258e18bbe23\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bionano_scaffold\n  owner: bgruening\n  revisions: 3371c5bdc17a\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n  owner: bgruening\n  revisions: 3ef480892a9f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: hifiasm\n  owner: bgruening\n  revisions: 0ee0c3089254\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: f46f0e4f75c4\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 02026300aa45\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 6595517c2dd8\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: a1a923cd89e8\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bellerophon\n  owner: iuc\n  revisions: 25ca5d73aedf\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bellerophon\n  owner: iuc\n  revisions: 321347bd0494\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 46ae58b1d792\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: ea8146ee148f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_mem2\n  owner: iuc\n  revisions: b4a22d90cce9\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_mem2\n  owner: iuc\n  revisions: bfaa0d22c2e4\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_column_join\n  owner: iuc\n  revisions: 3ddd99c7efee\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: genomescope\n  owner: iuc\n  revisions: 3169a38c2656\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: genomescope\n  owner: iuc\n  revisions: 01210c4e9144\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfa_to_fa\n  owner: iuc\n  revisions: e33c82b63727\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merqury\n  owner: iuc\n  revisions: 39edec572bae\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merqury\n  owner: iuc\n  revisions: d7edbc9c3a07\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n  owner: iuc\n  revisions: eadfd71dde37\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n  owner: iuc\n  revisions: 29dabd8db6f2\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: f54f5baedfdd\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: 11a0d50a54e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_map\n  owner: iuc\n  revisions: dfb8a4497339\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_snapshot\n  owner: iuc\n  revisions: 44c66e8d21e6\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: purge_dups\n  owner: iuc\n  revisions: a315c25dc813\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: purge_dups\n  owner: iuc\n  revisions: e9bd16ba5ebd\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 875d0f36d66f\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: salsa\n  owner: iuc\n  revisions: f77f7a7f3b83\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: yahs\n  owner: iuc\n  revisions: 425e63adcc5d\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 48f587c13075\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 8c0175e03cee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/vgp_genome_assembly/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: flye\n  owner: bgruening\n  revisions: 291923e6f276\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: racon\n  owner: bgruening\n  revisions: 78c533842eeb\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: ea8146ee148f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n  owner: iuc\n  revisions: 0dbb995c7d35\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: c59d48774d03\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: genomescope\n  owner: iuc\n  revisions: 01210c4e9144\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: medaka_consensus_pipeline\n  owner: iuc\n  revisions: fc8804320156\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n  owner: iuc\n  revisions: 29dabd8db6f2\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: be1d967337e4\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: abfd8a6544d7\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: a02b8b3f5a0c\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 72472698a2df\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/largegenome/tutorial.json",
         "contributors": [
             {
-                "email": "delphine.lariviere@galaxy.org",
-                "id": "delphine-l",
+                "id": "annasyme",
                 "joined": "2017-09",
-                "name": "Delphine Lariviere",
-                "orcid": "0000-0001-6421-3484",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
-            },
+                "name": "Anna Syme",
+                "orcid": "0000-0002-9906-0673",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
+            }
+        ],
+        "dir": "topics/assembly/tutorials/largegenome",
+        "edam_operation": [
+            "Scatter plot plotting",
+            "Visualisation",
+            "Cross-assembly",
+            "Sequencing quality control",
+            "Genome assembly",
+            "Box-Whisker plot plotting",
+            "Sequence assembly validation",
+            "Mapping assembly",
+            "Base-calling",
+            "Statistical calculation",
+            "Pairwise sequence alignment",
+            "Validation",
+            "Sequence composition calculation",
+            "De-novo assembly",
+            "Sequence contamination filtering",
+            "Sequence assembly",
+            "Variant calling",
+            "Scaffolding",
+            "Sequence assembly visualisation",
+            "Transcriptome assembly"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "assembly/largegenome",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "We can assemble long reads from plant or animal species into large contigs",
+            "These contigs can be polished with both long and short reads",
+            "We can assess the quality of this assembly with various tools"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-07-31",
+        "objectives": [
+            "Assemble a large genome from long reads",
+            "Polish the assembly",
+            "Assess the quality of the assembly"
+        ],
+        "pageviews": 5225,
+        "pub_date": "2023-03-06",
+        "questions": [
+            "How can we assemble a large plant or animal genome?"
+        ],
+        "recordings": [
             {
-                "email": "a.ostrovsky@mac.com",
-                "id": "astrovsky01",
-                "joined": "2019-06",
-                "name": "Alex Ostrovsky",
-                "orcid": "0000-0002-7901-7109",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/astrovsky01/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/astrovsky01.json"
-            },
+                "captioners": [
+                    "annasyme"
+                ],
+                "date": "2023-05-16",
+                "galaxy_version": "23.01",
+                "length": "25M",
+                "speakers": [
+                    "annasyme"
+                ],
+                "youtube_id": "BM70nvwWjOY"
+            }
+        ],
+        "short_id": "T00331",
+        "short_tools": [
+            "genomescope",
+            "fastp",
+            "minimap2",
+            "bandage_image",
+            "barchart_gnuplot",
+            "busco",
+            "racon",
+            "fasta-stats",
+            "quast",
+            "multiqc",
+            "flye",
+            "nanoplot",
+            "medaka_consensus_pipeline",
+            "fastqc",
+            "meryl"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "assembly",
+            "polishing",
+            "nanopore",
+            "plants"
+        ],
+        "time_estimation": "2h",
+        "title": "Large genome assembly and polishing",
+        "tools": [
+            "barchart_gnuplot",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+            "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
+        ],
+        "topic_name": "assembly",
+        "topic_name_human": "Assembly",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "largegenome",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/largegenome/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/largegenome/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/largegenome/tutorial.json"
+        },
+        "version": 11,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 127,
+        "visitors": 4015,
+        "workflows": [
             {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": true,
+                    "report": {
+                        "markdown": "\n# Workflow Report for Assembly Polishing\n\n## Workflow steps\n\n```galaxy\nworkflow_display()\n```\n\n## Fasta statistics after Racon long-read polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Racon long read polish\")\n```\n\n\n## Fasta statistics after Medaka polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Medaka polish\")\n```\n\n## Fasta statistics after Racon short-read polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Racon short read polish\")\n```\n\n\n\n\n"
+                    },
+                    "subworkflows": true
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"]\n  4[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with long reads, x4 - upgraded\"]\n  0 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Medaka polish\"]\n  4 -> 5 [label=\"Assembly polished by long reads using Racon\"]\n  1 -> 5 [label=\"output\"]\n  ke3136060bce74af387c49dcbb0d1f531[color=lightseagreen,label=\"Output\\nAssembly polished by long reads using Medaka\"]\n  5 -> ke3136060bce74af387c49dcbb0d1f531\n  6[label=\"Fasta statistics after Racon long read polish\"]\n  4 -> 6 [label=\"Assembly polished by long reads using Racon\"]\n  7[label=\"Fasta statistics after Medaka polish\"]\n  5 -> 7 [label=\"out_consensus\"]\n  8[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with Illumina reads R1 only, x2 - upgraded\"]\n  5 -> 8 [label=\"out_consensus\"]\n  3 -> 8 [label=\"output\"]\n  9[label=\"Fasta statistics after Racon short read polish\"]\n  8 -> 9 [label=\"Assembly polished by short reads using Racon\"]\n}",
+                "history": [
+                    {
+                        "hash": "091a0834c77e69841f4d07570420c632c6c5043c",
+                        "message": "Update Galaxy-Workflow-Assembly_polishing.ga",
+                        "num": 5,
+                        "short_hash": "091a0834c",
+                        "unix": "1715074278"
+                    },
+                    {
+                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
+                        "message": "new versions of workflows",
+                        "num": 4,
+                        "short_hash": "e8ddbcdd5",
+                        "unix": "1714537936"
+                    },
+                    {
+                        "hash": "f294a05b57afbe9ec436008d1d2571f6d42fb977",
+                        "message": "Rename Galaxy-Workflow-Assembly_polishing.ga to Galaxy-Workflow-Assembly_polishing_old.ga",
+                        "num": 3,
+                        "short_hash": "f294a05b5",
+                        "unix": "1714537220"
+                    },
+                    {
+                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
+                        "message": "add/complete creator info on workflows",
+                        "num": 2,
+                        "short_hash": "62e77944b",
+                        "unix": "1676627603"
+                    },
+                    {
+                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
+                        "message": "large genome tutorial",
+                        "num": 1,
+                        "short_hash": "9fcb3aeec",
+                        "unix": "1665123856"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Assembly to be polished"
+                            }
+                        ],
+                        "label": "Assembly to be polished",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 19.464939294568495,
+                            "top": 0.0
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "52bc9ac4-ac3c-48eb-aead-94a0a14417fc",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "long reads"
+                            }
+                        ],
+                        "label": "long reads",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0.0,
+                            "top": 142.48340578478533
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "688866c4-de9b-4b78-8df3-b169d28b1617",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "minimap setting (for long reads)"
+                            }
+                        ],
+                        "label": "minimap setting (for long reads)",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 13.133522093825794,
+                            "top": 247.1519749531627
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "c1f18b5c-e8db-4046-b876-9b28a77cf66e",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "ce393bcf-42e3-43ee-9056-a99e8c077a29"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Illumina reads R1"
+                            }
+                        ],
+                        "label": "Illumina reads R1",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 617.719019724734,
+                            "top": 600.0866464299372
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ea859a58-c81a-4ef6-9bd2-4ef2f17bb5a9",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with long reads, x4 - upgraded\"];\n  style 4 fill:#edd,stroke:#900,stroke-width:4px;\n  0 -->|output| 4;\n  1 -->|output| 4;\n  2 -->|output| 4;\n  5[\"Medaka polish\"];\n  4 -->|Assembly polished by long reads using Racon| 5;\n  1 -->|output| 5;\n  e3136060-bce7-4af3-87c4-9dcbb0d1f531[\"Output\\nAssembly polished by long reads using Medaka\"];\n  5 --> e3136060-bce7-4af3-87c4-9dcbb0d1f531;\n  style e3136060-bce7-4af3-87c4-9dcbb0d1f531 stroke:#2c3143,stroke-width:4px;\n  6[\"Fasta statistics after Racon long read polish\"];\n  4 -->|Assembly polished by long reads using Racon| 6;\n  7[\"Fasta statistics after Medaka polish\"];\n  5 -->|out_consensus| 7;\n  8[\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with Illumina reads R1 only, x2 - upgraded\"];\n  style 8 fill:#edd,stroke:#900,stroke-width:4px;\n  5 -->|out_consensus| 8;\n  3 -->|output| 8;\n  9[\"Fasta statistics after Racon short read polish\"];\n  8 -->|Assembly polished by short reads using Racon| 9;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Assembly polishing - upgraded",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "minimap setting (for long reads)"
+                            }
+                        ],
+                        "label": "minimap setting (for long reads)",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 13.133522093825794,
+                            "top": 247.1519749531627
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "c1f18b5c-e8db-4046-b876-9b28a77cf66e",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "ce393bcf-42e3-43ee-9056-a99e8c077a29"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "id": 4,
+                        "input_connections": {
+                            "Assembly to be polished": {
+                                "id": 0,
+                                "input_subworkflow_step_id": 0,
+                                "output_name": "output"
+                            },
+                            "long reads": {
+                                "id": 1,
+                                "input_subworkflow_step_id": 1,
+                                "output_name": "output"
+                            },
+                            "minimap setting (for long reads) ": {
+                                "id": 2,
+                                "input_subworkflow_step_id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Racon polish with long reads, x4 - upgraded",
+                        "outputs": [],
+                        "position": {
+                            "left": 299.6429464825318,
+                            "top": 72.0364210406818
+                        },
+                        "subworkflow": {
+                            "a_galaxy_workflow": "true",
+                            "annotation": "",
+                            "comments": [],
+                            "creator": [
+                                {
+                                    "class": "Person",
+                                    "identifier": "0000-0002-9906-0673",
+                                    "name": "Anna Syme"
+                                }
+                            ],
+                            "format-version": "0.1",
+                            "name": "Racon polish with long reads, x4 - upgraded",
+                            "report": {
+                                "markdown": "\n# Workflow Execution Report\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                            },
+                            "steps": {
+                                "0": {
+                                    "annotation": "",
+                                    "content_id": null,
+                                    "errors": null,
+                                    "id": 0,
+                                    "input_connections": {},
+                                    "inputs": [
+                                        {
+                                            "description": "",
+                                            "name": "Assembly to be polished"
+                                        }
+                                    ],
+                                    "label": "Assembly to be polished",
+                                    "name": "Input dataset",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 0,
+                                        "top": 216.625
+                                    },
+                                    "tool_id": null,
+                                    "tool_state": "{\"optional\": false, \"tag\": null}",
+                                    "tool_version": null,
+                                    "type": "data_input",
+                                    "uuid": "c7796c36-adf8-49e4-a8e4-66e606d70311",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "1": {
+                                    "annotation": "",
+                                    "content_id": null,
+                                    "errors": null,
+                                    "id": 1,
+                                    "input_connections": {},
+                                    "inputs": [
+                                        {
+                                            "description": "",
+                                            "name": "long reads"
+                                        }
+                                    ],
+                                    "label": "long reads",
+                                    "name": "Input dataset",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 4.5,
+                                        "top": 360.234375
+                                    },
+                                    "tool_id": null,
+                                    "tool_state": "{\"optional\": false, \"tag\": null}",
+                                    "tool_version": null,
+                                    "type": "data_input",
+                                    "uuid": "e2e4a70b-6e36-4b8b-bdf6-12b97189a6bd",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "10": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                    "errors": null,
+                                    "id": 10,
+                                    "input_connections": {
+                                        "corrected_reads": {
+                                            "id": 8,
+                                            "output_name": "consensus"
+                                        },
+                                        "overlaps": {
+                                            "id": 9,
+                                            "output_name": "alignment_output"
+                                        },
+                                        "reads": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Racon: polish 4",
+                                    "name": "Racon",
+                                    "outputs": [
+                                        {
+                                            "name": "consensus",
+                                            "type": "fasta"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 1496.078125,
+                                        "top": 431.1875
+                                    },
+                                    "post_job_actions": {
+                                        "RenameDatasetActionconsensus": {
+                                            "action_arguments": {
+                                                "newname": "Racon_long_reads_polished_assembly.fasta"
+                                            },
+                                            "action_type": "RenameDatasetAction",
+                                            "output_name": "consensus"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "78c533842eeb",
+                                        "name": "racon",
+                                        "owner": "bgruening",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "1.5.0+galaxy1",
+                                    "type": "tool",
+                                    "uuid": "53f4572e-3a4a-4585-89ab-9459f8a61720",
+                                    "when": null,
+                                    "workflow_outputs": [
+                                        {
+                                            "label": "Assembly polished by long reads using Racon",
+                                            "output_name": "consensus",
+                                            "uuid": "bcf0f03c-5951-46a7-aa38-545aed9bc183"
+                                        }
+                                    ]
+                                },
+                                "2": {
+                                    "annotation": "",
+                                    "content_id": null,
+                                    "errors": null,
+                                    "id": 2,
+                                    "input_connections": {},
+                                    "inputs": [
+                                        {
+                                            "description": "",
+                                            "name": "minimap setting (for long reads) "
+                                        }
+                                    ],
+                                    "label": "minimap setting (for long reads) ",
+                                    "name": "Input parameter",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 0.578125,
+                                        "top": 495.859375
+                                    },
+                                    "tool_id": null,
+                                    "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                                    "tool_version": null,
+                                    "type": "parameter_input",
+                                    "uuid": "fb80c05c-08d4-4ac2-b4bf-81ed906e4d72",
+                                    "when": null,
+                                    "workflow_outputs": [
+                                        {
+                                            "label": null,
+                                            "output_name": "output",
+                                            "uuid": "3983ef22-5f05-4384-8f34-6ac8c4b2cc83"
+                                        }
+                                    ]
+                                },
+                                "3": {
+                                    "annotation": "Map raw reads to assembly; output paf",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                    "errors": null,
+                                    "id": 3,
+                                    "input_connections": {
+                                        "fastq_input|analysis_type_selector": {
+                                            "id": 2,
+                                            "output_name": "output"
+                                        },
+                                        "fastq_input|fastq_input1": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        },
+                                        "reference_source|ref_file": {
+                                            "id": 0,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "fastq_input"
+                                        },
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "fastq_input"
+                                        },
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "reference_source"
+                                        }
+                                    ],
+                                    "label": "Minimap2: map long reads to assembly",
+                                    "name": "Map with minimap2",
+                                    "outputs": [
+                                        {
+                                            "name": "alignment_output",
+                                            "type": "bam"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 377.640625,
+                                        "top": 0
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionalignment_output": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "alignment_output"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "be1d967337e4",
+                                        "name": "minimap2",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "2.26+galaxy0",
+                                    "type": "tool",
+                                    "uuid": "0c06144f-d1ac-4b45-9669-1ddf11fcb06b",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "4": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                    "errors": null,
+                                    "id": 4,
+                                    "input_connections": {
+                                        "corrected_reads": {
+                                            "id": 0,
+                                            "output_name": "output"
+                                        },
+                                        "overlaps": {
+                                            "id": 3,
+                                            "output_name": "alignment_output"
+                                        },
+                                        "reads": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Racon: polish 1",
+                                    "name": "Racon",
+                                    "outputs": [
+                                        {
+                                            "name": "consensus",
+                                            "type": "fasta"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 458.640625,
+                                        "top": 518.875
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionconsensus": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "consensus"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "78c533842eeb",
+                                        "name": "racon",
+                                        "owner": "bgruening",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "1.5.0+galaxy1",
+                                    "type": "tool",
+                                    "uuid": "6c144354-91f2-49dd-a1f5-7c4119859730",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "5": {
+                                    "annotation": "Map raw reads to assembly; output paf",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                    "errors": null,
+                                    "id": 5,
+                                    "input_connections": {
+                                        "fastq_input|analysis_type_selector": {
+                                            "id": 2,
+                                            "output_name": "output"
+                                        },
+                                        "fastq_input|fastq_input1": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        },
+                                        "reference_source|ref_file": {
+                                            "id": 4,
+                                            "output_name": "consensus"
+                                        }
+                                    },
+                                    "inputs": [
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "fastq_input"
+                                        },
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "fastq_input"
+                                        },
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "reference_source"
+                                        }
+                                    ],
+                                    "label": "Minimap2: map long reads to polished assembly 1",
+                                    "name": "Map with minimap2",
+                                    "outputs": [
+                                        {
+                                            "name": "alignment_output",
+                                            "type": "bam"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 698.859375,
+                                        "top": 13.390625
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionalignment_output": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "alignment_output"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "be1d967337e4",
+                                        "name": "minimap2",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "2.26+galaxy0",
+                                    "type": "tool",
+                                    "uuid": "c1b83dad-a8ed-42cb-951f-73f59f2dfa92",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "6": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                    "errors": null,
+                                    "id": 6,
+                                    "input_connections": {
+                                        "corrected_reads": {
+                                            "id": 4,
+                                            "output_name": "consensus"
+                                        },
+                                        "overlaps": {
+                                            "id": 5,
+                                            "output_name": "alignment_output"
+                                        },
+                                        "reads": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Racon: polish 2",
+                                    "name": "Racon",
+                                    "outputs": [
+                                        {
+                                            "name": "consensus",
+                                            "type": "fasta"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 759.9375,
+                                        "top": 485.71875
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionconsensus": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "consensus"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "78c533842eeb",
+                                        "name": "racon",
+                                        "owner": "bgruening",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "1.5.0+galaxy1",
+                                    "type": "tool",
+                                    "uuid": "3208491e-b831-4238-957e-5b7388d7ff8d",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "7": {
+                                    "annotation": "Map raw reads to assembly; output paf",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                    "errors": null,
+                                    "id": 7,
+                                    "input_connections": {
+                                        "fastq_input|analysis_type_selector": {
+                                            "id": 2,
+                                            "output_name": "output"
+                                        },
+                                        "fastq_input|fastq_input1": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        },
+                                        "reference_source|ref_file": {
+                                            "id": 6,
+                                            "output_name": "consensus"
+                                        }
+                                    },
+                                    "inputs": [
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "fastq_input"
+                                        },
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "fastq_input"
+                                        },
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "reference_source"
+                                        }
+                                    ],
+                                    "label": "Minimap2: map long reads to polished assembly 2",
+                                    "name": "Map with minimap2",
+                                    "outputs": [
+                                        {
+                                            "name": "alignment_output",
+                                            "type": "bam"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 998.75,
+                                        "top": 27.9375
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionalignment_output": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "alignment_output"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "be1d967337e4",
+                                        "name": "minimap2",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "2.26+galaxy0",
+                                    "type": "tool",
+                                    "uuid": "42af524b-7f74-4c75-8d78-f6888078dd2e",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "8": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                    "errors": null,
+                                    "id": 8,
+                                    "input_connections": {
+                                        "corrected_reads": {
+                                            "id": 6,
+                                            "output_name": "consensus"
+                                        },
+                                        "overlaps": {
+                                            "id": 7,
+                                            "output_name": "alignment_output"
+                                        },
+                                        "reads": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Racon: polish 3",
+                                    "name": "Racon",
+                                    "outputs": [
+                                        {
+                                            "name": "consensus",
+                                            "type": "fasta"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 1089.71875,
+                                        "top": 455.53125
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionconsensus": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "consensus"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "78c533842eeb",
+                                        "name": "racon",
+                                        "owner": "bgruening",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "1.5.0+galaxy1",
+                                    "type": "tool",
+                                    "uuid": "21f339bd-ebc1-4c73-a976-5d0b9ab2127a",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "9": {
+                                    "annotation": "Map raw reads to assembly; output paf",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                    "errors": null,
+                                    "id": 9,
+                                    "input_connections": {
+                                        "fastq_input|analysis_type_selector": {
+                                            "id": 2,
+                                            "output_name": "output"
+                                        },
+                                        "fastq_input|fastq_input1": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        },
+                                        "reference_source|ref_file": {
+                                            "id": 8,
+                                            "output_name": "consensus"
+                                        }
+                                    },
+                                    "inputs": [
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "fastq_input"
+                                        },
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "fastq_input"
+                                        },
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "reference_source"
+                                        }
+                                    ],
+                                    "label": "Minimap2: map long reads to polished assembly 3",
+                                    "name": "Map with minimap2",
+                                    "outputs": [
+                                        {
+                                            "name": "alignment_output",
+                                            "type": "bam"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 1316.53125,
+                                        "top": 38.046875
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionalignment_output": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "alignment_output"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "be1d967337e4",
+                                        "name": "minimap2",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "2.26+galaxy0",
+                                    "type": "tool",
+                                    "uuid": "7d36291e-aa76-4312-9943-b5e56d0e90c5",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                }
+                            },
+                            "tags": "",
+                            "uuid": "c57efd37-4cf6-4cc7-abf4-2bab22a2e9a0"
+                        },
+                        "tool_id": null,
+                        "type": "subworkflow",
+                        "uuid": "58c99e4b-fd6a-401d-b9c7-cdf7e6d1757d",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "2:output",
+                                "uuid": "50fa1032-8037-454e-8192-b95405bcd5d4"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "d": {
+                                "id": 4,
+                                "output_name": "Assembly polished by long reads using Racon"
+                            },
+                            "i": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Medaka polish",
+                        "name": "medaka consensus pipeline",
+                        "outputs": [
+                            {
+                                "name": "out_consensus",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "left": 515.5164024294684,
+                            "top": 305.08460859328346
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionout_consensus": {
+                                "action_arguments": {
+                                    "newname": "Medaka_long_reads_polished_assembly.fasta"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_consensus"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "fc8804320156",
+                            "name": "medaka_consensus_pipeline",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"b\": \"100\", \"d\": {\"__class__\": \"ConnectedValue\"}, \"g\": false, \"i\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"r941_min_high_g360\", \"out\": [\"consensus\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.2+galaxy1",
+                        "type": "tool",
+                        "uuid": "14c5ce9c-df92-4e20-85da-7a161eaa759d",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Assembly polished by long reads using Medaka",
+                                "output_name": "out_consensus",
+                                "uuid": "e3136060-bce7-4af3-87c4-9dcbb0d1f531"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "assembly/largegenome",
+                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_polishing.ga",
+                "tags": [
+                    "LG-WF",
+                    "GTN"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Assembly polishing - upgraded",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-assembly-polishing",
+                "tutorial_id": "largegenome",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_polishing.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_polishing.html",
+                "version": 2,
+                "wfid": "assembly-largegenome",
+                "wfname": "galaxy-workflow-assembly-polishing",
+                "workflow": "Galaxy-Workflow-Assembly_polishing.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0"
+                ],
+                "workflowhub_id": "1174"
+            },
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": {
+                        "markdown": "# Workflow Report for Assembly with Flye\n\n\n## Workflow steps\n\n```galaxy\nworkflow_display()\n```\n\n## Dataset - fasta stats. \n\n```galaxy\nhistory_dataset_display(output=\"Fasta Statistics on input dataset(s): Fasta summary stats\")\n```\n\n## Contig sizes\n\n```galaxy\nhistory_dataset_as_image(output=\"Bar chart showing contig sizes\")\n```\n\n\n## Bandage image\n\n```galaxy\nhistory_dataset_as_image(output=\"Bandage Image on input dataset(s): Assembly Graph Image\")\n```\n\n## Quast report\n\n\r\n```galaxy\nhistory_dataset_display(output=\"Quast on input dataset(s):  PDF report\")\n```\r\n\n\n\n"
+                    },
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  1[label=\"Flye: assembly\"]\n  0 -> 1 [label=\"output\"]\n  k3960e31d7a9e400cbb21f6e47b75e649[color=lightseagreen,label=\"Output\\nFlye assembly on input dataset(s) (consensus)\"]\n  1 -> k3960e31d7a9e400cbb21f6e47b75e649\n  ke524f295a9574c91838cf8e98e809b6c[color=lightseagreen,label=\"Output\\nFlye assembly on input dataset(s) (assembly_graph)\"]\n  1 -> ke524f295a9574c91838cf8e98e809b6c\n  k48b854e2dd6e43458d0509abca6659da[color=lightseagreen,label=\"Output\\nFlye assembly on input dataset(s) (Graphical Fragment Assembly)\"]\n  1 -> k48b854e2dd6e43458d0509abca6659da\n  k8672c17271a7432c9679a8e37f36cf53[color=lightseagreen,label=\"Output\\nFlye assembly on input dataset(s) (assembly_info)\"]\n  1 -> k8672c17271a7432c9679a8e37f36cf53\n  2[label=\"Fasta statistics\"]\n  1 -> 2 [label=\"consensus\"]\n  3[label=\"Quast genome report\"]\n  1 -> 3 [label=\"consensus\"]\n  k17cdf8e08ad44570afae1861934fc678[color=lightseagreen,label=\"Output\\nQuast on input dataset(s):  HTML report\"]\n  3 -> k17cdf8e08ad44570afae1861934fc678\n  4[label=\"Bandage image: Flye assembly\"]\n  1 -> 4 [label=\"assembly_gfa\"]\n  ke66bd129146f48dc95b839a2a1ffb68d[color=lightseagreen,label=\"Output\\nBandage Image on input dataset(s): Assembly Graph Image\"]\n  4 -> ke66bd129146f48dc95b839a2a1ffb68d\n  5[label=\"Bar chart: show contig sizes\"]\n  1 -> 5 [label=\"assembly_info\"]\n  k6d0a4e23d6314e3789303d22fc91369b[color=lightseagreen,label=\"Output\\nBar chart showing contig sizes\"]\n  5 -> k6d0a4e23d6314e3789303d22fc91369b\n}",
+                "history": [
+                    {
+                        "hash": "f3dd8377556ae73d56d73612a37a5a7e20c98093",
+                        "message": "Update Galaxy-Workflow-Assembly_with_Flye.ga",
+                        "num": 5,
+                        "short_hash": "f3dd83775",
+                        "unix": "1715074300"
+                    },
+                    {
+                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
+                        "message": "new versions of workflows",
+                        "num": 4,
+                        "short_hash": "e8ddbcdd5",
+                        "unix": "1714537936"
+                    },
+                    {
+                        "hash": "43baea079b7b412f3f272ac1ac887cd67aef6c49",
+                        "message": "Rename Galaxy-Workflow-Assembly_with_Flye.ga to Galaxy-Workflow-Assembly_with_Flye_old.ga",
+                        "num": 3,
+                        "short_hash": "43baea079",
+                        "unix": "1714537239"
+                    },
+                    {
+                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
+                        "message": "add/complete creator info on workflows",
+                        "num": 2,
+                        "short_hash": "62e77944b",
+                        "unix": "1676627603"
+                    },
+                    {
+                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
+                        "message": "large genome tutorial",
+                        "num": 1,
+                        "short_hash": "9fcb3aeec",
+                        "unix": "1665123856"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "long reads"
+                            }
+                        ],
+                        "label": "long reads",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 398.40625
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "501d7387-3bed-4510-891f-a4571a48d9ab",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Flye: assembly\"];\n  0 -->|output| 1;\n  3960e31d-7a9e-400c-bb21-f6e47b75e649[\"Output\\nFlye assembly on input dataset(s) (consensus)\"];\n  1 --> 3960e31d-7a9e-400c-bb21-f6e47b75e649;\n  style 3960e31d-7a9e-400c-bb21-f6e47b75e649 stroke:#2c3143,stroke-width:4px;\n  e524f295-a957-4c91-838c-f8e98e809b6c[\"Output\\nFlye assembly on input dataset(s) (assembly_graph)\"];\n  1 --> e524f295-a957-4c91-838c-f8e98e809b6c;\n  style e524f295-a957-4c91-838c-f8e98e809b6c stroke:#2c3143,stroke-width:4px;\n  48b854e2-dd6e-4345-8d05-09abca6659da[\"Output\\nFlye assembly on input dataset(s) (Graphical Fragment Assembly)\"];\n  1 --> 48b854e2-dd6e-4345-8d05-09abca6659da;\n  style 48b854e2-dd6e-4345-8d05-09abca6659da stroke:#2c3143,stroke-width:4px;\n  8672c172-71a7-432c-9679-a8e37f36cf53[\"Output\\nFlye assembly on input dataset(s) (assembly_info)\"];\n  1 --> 8672c172-71a7-432c-9679-a8e37f36cf53;\n  style 8672c172-71a7-432c-9679-a8e37f36cf53 stroke:#2c3143,stroke-width:4px;\n  2[\"Fasta statistics\"];\n  1 -->|consensus| 2;\n  3[\"Quast genome report\"];\n  1 -->|consensus| 3;\n  17cdf8e0-8ad4-4570-afae-1861934fc678[\"Output\\nQuast on input dataset(s):  HTML report\"];\n  3 --> 17cdf8e0-8ad4-4570-afae-1861934fc678;\n  style 17cdf8e0-8ad4-4570-afae-1861934fc678 stroke:#2c3143,stroke-width:4px;\n  4[\"Bandage image: Flye assembly\"];\n  1 -->|assembly_gfa| 4;\n  e66bd129-146f-48dc-95b8-39a2a1ffb68d[\"Output\\nBandage Image on input dataset(s): Assembly Graph Image\"];\n  4 --> e66bd129-146f-48dc-95b8-39a2a1ffb68d;\n  style e66bd129-146f-48dc-95b8-39a2a1ffb68d stroke:#2c3143,stroke-width:4px;\n  5[\"Bar chart: show contig sizes\"];\n  1 -->|assembly_info| 5;\n  6d0a4e23-d631-4e37-8930-3d22fc91369b[\"Output\\nBar chart showing contig sizes\"];\n  5 --> 6d0a4e23-d631-4e37-8930-3d22fc91369b;\n  style 6d0a4e23-d631-4e37-8930-3d22fc91369b stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Assembly with Flye - upgraded",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {
+                            "inputs": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Flye: assembly",
+                        "name": "Flye",
+                        "outputs": [
+                            {
+                                "name": "consensus",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "assembly_graph",
+                                "type": "graph_dot"
+                            },
+                            {
+                                "name": "assembly_gfa",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "assembly_info",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 260.57143695759436,
+                            "top": 248.74363091133793
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "291923e6f276",
+                            "name": "flye",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"asm\": {\"asm_select\": \"false\", \"__current_case__\": 1}, \"generate_log\": false, \"i\": \"1\", \"inputs\": {\"__class__\": \"ConnectedValue\"}, \"iterations\": \"1\", \"keep_haplotypes\": false, \"m\": null, \"meta\": false, \"min_overlap\": null, \"mode\": \"--nano-raw\", \"mode_conditional\": {\"mode\": \"--nano-raw\", \"__current_case__\": 0}, \"no_alt_contigs\": false, \"no_trestle\": \"false\", \"plasmids\": \"false\", \"scaffold\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.9.3+galaxy0",
+                        "type": "tool",
+                        "uuid": "8bed3591-266a-41f1-91d3-11b3456e8609",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Flye assembly on input dataset(s) (consensus)",
+                                "output_name": "consensus",
+                                "uuid": "3960e31d-7a9e-400c-bb21-f6e47b75e649"
+                            },
+                            {
+                                "label": "Flye assembly on input dataset(s) (assembly_graph)",
+                                "output_name": "assembly_graph",
+                                "uuid": "e524f295-a957-4c91-838c-f8e98e809b6c"
+                            },
+                            {
+                                "label": "Flye assembly on input dataset(s) (Graphical Fragment Assembly)",
+                                "output_name": "assembly_gfa",
+                                "uuid": "48b854e2-dd6e-4345-8d05-09abca6659da"
+                            },
+                            {
+                                "label": "Flye assembly on input dataset(s) (assembly_info)",
+                                "output_name": "assembly_info",
+                                "uuid": "8672c172-71a7-432c-9679-a8e37f36cf53"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "mode|in|inputs": {
+                                "id": 1,
+                                "output_name": "consensus"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Quast genome report",
+                        "name": "Quast",
+                        "outputs": [
+                            {
+                                "name": "report_html",
+                                "type": "html"
+                            }
+                        ],
+                        "position": {
+                            "left": 697.3759752425051,
+                            "top": 194.46891558901518
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "72472698a2df",
+                            "name": "quast",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"al\": {\"ambiguity_score\": \"0.99\", \"ambiguity_usage\": \"one\", \"fragmented\": false, \"fragmented_max_indent\": \"50\", \"min_alignment\": \"65\", \"min_identity\": \"95.0\", \"upper_bound_assembly\": false, \"upper_bound_min_con\": \"2\", \"use_all_alignments\": false}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"false\", \"__current_case__\": 1, \"est_ref_size\": null}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"circos\": \"false\", \"contig_thresholds\": \"0,1000\", \"extensive_mis_size\": \"1000\", \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": false}, \"in\": {\"__current_case__\": 1, \"custom\": \"false\", \"inputs\": {\"__class__\": \"RuntimeValue\"}}, \"k_mer\": {\"__current_case__\": 1, \"k_mer_stats\": \"\"}, \"large\": true, \"min_contig\": \"500\", \"mode\": {\"mode\": \"co\", \"__current_case__\": 1, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": \"html\", \"scaffold_gap_max_size\": \"1000\", \"skip_unaligned_mis_contigs\": \"false\", \"split_scaffolds\": false, \"strict_NA\": \"false\", \"unaligned_part_size\": \"500\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.2.0+galaxy1",
+                        "type": "tool",
+                        "uuid": "5bc29646-ec4c-4eb3-af01-73d82fc690a2",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Quast on input dataset(s):  HTML report",
+                                "output_name": "report_html",
+                                "uuid": "17cdf8e0-8ad4-4570-afae-1861934fc678"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 1,
+                                "output_name": "assembly_gfa"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Bandage image: Flye assembly",
+                        "name": "Bandage Image",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "jpg"
+                            }
+                        ],
+                        "position": {
+                            "left": 583.546875,
+                            "top": 446.40625
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ddddce450736",
+                            "name": "bandage",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"fontsize\": null, \"height\": \"1000\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"lengths\": false, \"names\": false, \"nodewidth\": null, \"output_format\": \"jpg\", \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2022.09+galaxy4",
+                        "type": "tool",
+                        "uuid": "395f2dfe-3fa5-4684-bf97-7dd12e970f78",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Bandage Image on input dataset(s): Assembly Graph Image",
+                                "output_name": "outfile",
+                                "uuid": "e66bd129-146f-48dc-95b8-39a2a1ffb68d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "barchart_gnuplot",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "input": {
+                                "id": 1,
+                                "output_name": "assembly_info"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Bar chart: show contig sizes",
+                        "name": "Bar chart",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 595.421875,
+                            "top": 688.984375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "barchart_gnuplot",
+                        "tool_state": "{\"colList\": \"2\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"pdf_size\": \"800,600\", \"title\": \"Assembly contig sizes\", \"xtic\": {\"userSpecified\": \"No\", \"__current_case__\": 1}, \"ylabel\": \"lengths\", \"ymax\": \"0\", \"ymin\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "cb9d5059-bf42-4a0e-8150-f5089e0d5b1b",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Bar chart showing contig sizes",
+                                "output_name": "out_file1",
+                                "uuid": "6d0a4e23-d631-4e37-8930-3d22fc91369b"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "assembly/largegenome",
+                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_with_Flye.ga",
+                "tags": [
+                    "LG-WF",
+                    "GTN"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Assembly with Flye - upgraded",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-assembly-with-flye",
+                "tutorial_id": "largegenome",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_with_Flye.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_with_Flye.html",
+                "version": 2,
+                "wfid": "assembly-largegenome",
+                "wfname": "galaxy-workflow-assembly-with-flye",
+                "workflow": "Galaxy-Workflow-Assembly_with_Flye.ga",
+                "workflow_tools": [
+                    "barchart_gnuplot",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
+                ],
+                "workflowhub_id": "1170"
+            },
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n\n## Busco results\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco short summary\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco summary image\")\n```\n\n## Quast results\n\n\n```galaxy\nhistory_dataset_display(output=\"Quast on input dataset(s): tabular report\")\n```\n\n\n"
+                    },
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPolished assembly\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genome\"]\n  2[label=\"Busco: assess assembly\"]\n  0 -> 2 [label=\"output\"]\n  k219e495236e04b01a407e774b5b02dca[color=lightseagreen,label=\"Output\\nBusco short summary\"]\n  2 -> k219e495236e04b01a407e774b5b02dca\n  3[label=\"Quast: assess assembly\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  k77ab01864cfd460fb71e39a923414ef4[color=lightseagreen,label=\"Output\\nQuast on input dataset(s):  HTML report\"]\n  3 -> k77ab01864cfd460fb71e39a923414ef4\n}",
+                "history": [
+                    {
+                        "hash": "1b47a1ad8d46b114394c0579436c448e6bb7efcf",
+                        "message": "Update Galaxy-Workflow-Assess_genome_quality.ga",
+                        "num": 5,
+                        "short_hash": "1b47a1ad8",
+                        "unix": "1715074319"
+                    },
+                    {
+                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
+                        "message": "new versions of workflows",
+                        "num": 4,
+                        "short_hash": "e8ddbcdd5",
+                        "unix": "1714537936"
+                    },
+                    {
+                        "hash": "fc05e79f01c6b59c4dfc6aa59ebf592ae615641f",
+                        "message": "Rename Galaxy-Workflow-Assess_genome_quality.ga to Galaxy-Workflow-Assess_genome_quality_old.ga",
+                        "num": 3,
+                        "short_hash": "fc05e79f0",
+                        "unix": "1714537255"
+                    },
+                    {
+                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
+                        "message": "add/complete creator info on workflows",
+                        "num": 2,
+                        "short_hash": "62e77944b",
+                        "unix": "1676627603"
+                    },
+                    {
+                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
+                        "message": "large genome tutorial",
+                        "num": 1,
+                        "short_hash": "9fcb3aeec",
+                        "unix": "1665123856"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Polished assembly"
+                            }
+                        ],
+                        "label": "Polished assembly",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 101.09375
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "2ed19084-9eaf-4efb-acdc-b81536e7c024",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Reference genome"
+                            }
+                        ],
+                        "label": "Reference genome",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 246.765625,
+                            "top": 0.0
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "5b12a6af-13c3-4520-a549-280de6a3df17",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPolished assembly\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Busco: assess assembly\"];\n  0 -->|output| 2;\n  219e4952-36e0-4b01-a407-e774b5b02dca[\"Output\\nBusco short summary\"];\n  2 --> 219e4952-36e0-4b01-a407-e774b5b02dca;\n  style 219e4952-36e0-4b01-a407-e774b5b02dca stroke:#2c3143,stroke-width:4px;\n  3[\"Quast: assess assembly\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  77ab0186-4cfd-460f-b71e-39a923414ef4[\"Output\\nQuast on input dataset(s):  HTML report\"];\n  3 --> 77ab0186-4cfd-460f-b71e-39a923414ef4;\n  style 77ab0186-4cfd-460f-b71e-39a923414ef4 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Assess genome quality - upgraded",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Busco: assess assembly",
+                        "name": "Busco",
+                        "outputs": [
+                            {
+                                "name": "busco_sum",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "busco_table",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 294.42303466796875,
+                            "top": 200.68505859375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ea8146ee148f",
+                            "name": "busco",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"auto_detect\", \"__current_case__\": 0, \"auto_lineage\": \"--auto-lineage\"}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"lineage_dataset\": \"eukaryota_odb10\", \"outputs\": \"short_summary\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.5.0+galaxy0",
+                        "type": "tool",
+                        "uuid": "8f5f17de-a21e-49f4-b55c-6eff5f4fa213",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Busco short summary",
+                                "output_name": "busco_sum",
+                                "uuid": "219e4952-36e0-4b01-a407-e774b5b02dca"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "busco_table",
+                                "uuid": "fc06df63-3453-4303-80d1-c76823ba384a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "assembly|ref|r": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "mode|in|inputs": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Quast: assess assembly",
+                        "name": "Quast",
+                        "outputs": [
+                            {
+                                "name": "report_html",
+                                "type": "html"
+                            }
+                        ],
+                        "position": {
+                            "left": 564.8660278320312,
+                            "top": 56.71406029052495
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "72472698a2df",
+                            "name": "quast",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"true\", \"__current_case__\": 0, \"r\": {\"__class__\": \"RuntimeValue\"}, \"features\": {\"__class__\": \"RuntimeValue\"}, \"operons\": {\"__class__\": \"RuntimeValue\"}, \"k_mer\": {\"k_mer_stats\": \"\", \"__current_case__\": 1}, \"circos\": false}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": false}, \"large\": true, \"min_contig\": \"0\", \"mode\": {\"mode\": \"individual\", \"__current_case__\": 0, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"RuntimeValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": \"html\", \"split_scaffolds\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.2.0+galaxy1",
+                        "type": "tool",
+                        "uuid": "6caef18b-b257-472d-b8d0-fac523a72d37",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Quast on input dataset(s):  HTML report",
+                                "output_name": "report_html",
+                                "uuid": "77ab0186-4cfd-460f-b71e-39a923414ef4"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "assembly/largegenome",
+                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assess_genome_quality.ga",
+                "tags": [
+                    "LG-WF",
+                    "GTN"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Assess genome quality - upgraded",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-assess-genome-quality",
+                "tutorial_id": "largegenome",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assess_genome_quality.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assess_genome_quality.html",
+                "version": 2,
+                "wfid": "assembly-largegenome",
+                "wfname": "galaxy-workflow-assess-genome-quality",
+                "workflow": "Galaxy-Workflow-Assess_genome_quality.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
+                ],
+                "workflowhub_id": "1158"
+            },
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": true,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                    },
+                    "subworkflows": true
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR1\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR2\"]\n  3[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nminimap settings for long reads\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genome for Quast\"]\n  5[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nkmer counting - meryl - upgraded\"]\n  1 -> 5 [label=\"output\"]\n  6[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nData QC - upgraded\"]\n  1 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  0 -> 6 [label=\"output\"]\n  7[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nTrim and filter reads - fastp - upgraded \"]\n  1 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  0 -> 7 [label=\"output\"]\n  8[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly with Flye - upgraded\"]\n  7 -> 8 [label=\"fastp filtered long reads\"]\n  9[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly polishing - upgraded\"]\n  8 -> 9 [label=\"Flye assembly on input datasets consensus\"]\n  7 -> 9 [label=\"fastp filtered R1 reads\"]\n  7 -> 9 [label=\"fastp filtered long reads\"]\n  3 -> 9 [label=\"output\"]\n  10[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nAssess genome quality - upgraded\"]\n  9 -> 10 [label=\"Assembly polished by long reads using Medaka\"]\n  4 -> 10 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "01cffeed0413d12d37753e72aa81c95fb47e2179",
+                        "message": "Update Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga",
+                        "num": 5,
+                        "short_hash": "01cffeed0",
+                        "unix": "1715074366"
+                    },
+                    {
+                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
+                        "message": "new versions of workflows",
+                        "num": 4,
+                        "short_hash": "e8ddbcdd5",
+                        "unix": "1714537936"
+                    },
+                    {
+                        "hash": "bd0db2c9632aca4fc5faba5e811b23e9f98817f0",
+                        "message": "Rename Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga to Galaxy-Workflow-Combined_workflows_for_large_genome_assembly_old.ga",
+                        "num": 3,
+                        "short_hash": "bd0db2c96",
+                        "unix": "1714537274"
+                    },
+                    {
+                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
+                        "message": "add/complete creator info on workflows",
+                        "num": 2,
+                        "short_hash": "62e77944b",
+                        "unix": "1676627603"
+                    },
+                    {
+                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
+                        "message": "large genome tutorial",
+                        "num": 1,
+                        "short_hash": "9fcb3aeec",
+                        "unix": "1665123856"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "long reads"
+                            }
+                        ],
+                        "label": "long reads",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 37.09056155334109,
+                            "top": 117.80110422489305
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "f9154ba8-6c56-4b8c-b3a6-79bf72638963",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "R1"
+                            }
+                        ],
+                        "label": "R1",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 296.6915657131622
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "2152a89a-64b2-4e77-897e-97c2e951f0d4",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "R2"
+                            }
+                        ],
+                        "label": "R2",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 18.331891780359495,
+                            "top": 404.60599487314124
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "04ed4838-38d0-47c6-9692-af43b305750c",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "minimap settings (for long reads)"
+                            }
+                        ],
+                        "label": "minimap settings (for long reads)",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 953.979654343896,
+                            "top": 53.88085686443145
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "925fcb63-babc-42b5-9510-c82277158288",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "3643a598-963e-42d9-b625-41f5256dee4a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Reference genome for Quast"
+                            }
+                        ],
+                        "label": "Reference genome for Quast",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 1271.7306972391564,
+                            "top": 75.04279962197629
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "5bd59f90-9351-4b1e-bc0d-11fee8b4a435",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nR1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nR2\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nminimap settings for long reads\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nReference genome for Quast\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\ud83d\udee0\ufe0f Subworkflow\\nkmer counting - meryl - upgraded\"];\n  style 5 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 5;\n  6[\"\ud83d\udee0\ufe0f Subworkflow\\nData QC - upgraded\"];\n  style 6 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 6;\n  2 -->|output| 6;\n  0 -->|output| 6;\n  7[\"\ud83d\udee0\ufe0f Subworkflow\\nTrim and filter reads - fastp - upgraded \"];\n  style 7 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 7;\n  2 -->|output| 7;\n  0 -->|output| 7;\n  8[\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly with Flye - upgraded\"];\n  style 8 fill:#edd,stroke:#900,stroke-width:4px;\n  7 -->|fastp filtered long reads| 8;\n  9[\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly polishing - upgraded\"];\n  style 9 fill:#edd,stroke:#900,stroke-width:4px;\n  8 -->|Flye assembly on input datasets consensus| 9;\n  7 -->|fastp filtered R1 reads| 9;\n  7 -->|fastp filtered long reads| 9;\n  3 -->|output| 9;\n  10[\"\ud83d\udee0\ufe0f Subworkflow\\nAssess genome quality - upgraded\"];\n  style 10 fill:#edd,stroke:#900,stroke-width:4px;\n  9 -->|Assembly polished by long reads using Medaka| 10;\n  4 -->|output| 10;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Combined workflows for large genome assembly - upgraded ",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "minimap settings (for long reads)"
+                            }
+                        ],
+                        "label": "minimap settings (for long reads)",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 953.979654343896,
+                            "top": 53.88085686443145
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "925fcb63-babc-42b5-9510-c82277158288",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "3643a598-963e-42d9-b625-41f5256dee4a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "id": 9,
+                        "input_connections": {
+                            "Assembly to be polished": {
+                                "id": 8,
+                                "input_subworkflow_step_id": 0,
+                                "output_name": "Flye assembly on input dataset(s) (consensus)"
+                            },
+                            "Illumina reads R1": {
+                                "id": 7,
+                                "input_subworkflow_step_id": 3,
+                                "output_name": "fastp filtered R1 reads"
+                            },
+                            "long reads": {
+                                "id": 7,
+                                "input_subworkflow_step_id": 1,
+                                "output_name": "fastp filtered long reads"
+                            },
+                            "minimap setting (for long reads)": {
+                                "id": 3,
+                                "input_subworkflow_step_id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Assembly polishing - upgraded",
+                        "outputs": [],
+                        "position": {
+                            "left": 1260.7587450660599,
+                            "top": 269.3075732043599
+                        },
+                        "subworkflow": {
+                            "a_galaxy_workflow": "true",
+                            "annotation": "",
+                            "comments": [],
+                            "creator": [
+                                {
+                                    "class": "Person",
+                                    "identifier": "0000-0002-9906-0673",
+                                    "name": "Anna Syme"
+                                }
+                            ],
+                            "format-version": "0.1",
+                            "name": "Assembly polishing - upgraded",
+                            "report": {
+                                "markdown": "\n# Workflow Report for Assembly Polishing\n\n## Workflow steps\n\n```galaxy\nworkflow_display()\n```\n\n## Fasta statistics after Racon long-read polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Racon long read polish\")\n```\n\n\n## Fasta statistics after Medaka polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Medaka polish\")\n```\n\n## Fasta statistics after Racon short-read polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Racon short read polish\")\n```\n\n\n\n\n"
+                            },
+                            "steps": {
+                                "0": {
+                                    "annotation": "",
+                                    "content_id": null,
+                                    "errors": null,
+                                    "id": 0,
+                                    "input_connections": {},
+                                    "inputs": [
+                                        {
+                                            "description": "",
+                                            "name": "Assembly to be polished"
+                                        }
+                                    ],
+                                    "label": "Assembly to be polished",
+                                    "name": "Input dataset",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 19.464939294568495,
+                                        "top": 0.0
+                                    },
+                                    "tool_id": null,
+                                    "tool_state": "{\"optional\": false, \"tag\": null}",
+                                    "tool_version": null,
+                                    "type": "data_input",
+                                    "uuid": "52bc9ac4-ac3c-48eb-aead-94a0a14417fc",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "1": {
+                                    "annotation": "",
+                                    "content_id": null,
+                                    "errors": null,
+                                    "id": 1,
+                                    "input_connections": {},
+                                    "inputs": [
+                                        {
+                                            "description": "",
+                                            "name": "long reads"
+                                        }
+                                    ],
+                                    "label": "long reads",
+                                    "name": "Input dataset",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 0.0,
+                                        "top": 142.48340578478533
+                                    },
+                                    "tool_id": null,
+                                    "tool_state": "{\"optional\": false, \"tag\": null}",
+                                    "tool_version": null,
+                                    "type": "data_input",
+                                    "uuid": "688866c4-de9b-4b78-8df3-b169d28b1617",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "2": {
+                                    "annotation": "",
+                                    "content_id": null,
+                                    "errors": null,
+                                    "id": 2,
+                                    "input_connections": {},
+                                    "inputs": [
+                                        {
+                                            "description": "",
+                                            "name": "minimap setting (for long reads)"
+                                        }
+                                    ],
+                                    "label": "minimap setting (for long reads)",
+                                    "name": "Input parameter",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 13.133522093825794,
+                                        "top": 247.1519749531627
+                                    },
+                                    "tool_id": null,
+                                    "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                                    "tool_version": null,
+                                    "type": "parameter_input",
+                                    "uuid": "c1f18b5c-e8db-4046-b876-9b28a77cf66e",
+                                    "when": null,
+                                    "workflow_outputs": [
+                                        {
+                                            "label": null,
+                                            "output_name": "output",
+                                            "uuid": "ce393bcf-42e3-43ee-9056-a99e8c077a29"
+                                        }
+                                    ]
+                                },
+                                "3": {
+                                    "annotation": "",
+                                    "content_id": null,
+                                    "errors": null,
+                                    "id": 3,
+                                    "input_connections": {},
+                                    "inputs": [
+                                        {
+                                            "description": "",
+                                            "name": "Illumina reads R1"
+                                        }
+                                    ],
+                                    "label": "Illumina reads R1",
+                                    "name": "Input dataset",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 617.719019724734,
+                                        "top": 600.0866464299372
+                                    },
+                                    "tool_id": null,
+                                    "tool_state": "{\"optional\": false, \"tag\": null}",
+                                    "tool_version": null,
+                                    "type": "data_input",
+                                    "uuid": "ea859a58-c81a-4ef6-9bd2-4ef2f17bb5a9",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "4": {
+                                    "annotation": "",
+                                    "id": 4,
+                                    "input_connections": {
+                                        "Assembly to be polished": {
+                                            "id": 0,
+                                            "input_subworkflow_step_id": 0,
+                                            "output_name": "output"
+                                        },
+                                        "long reads": {
+                                            "id": 1,
+                                            "input_subworkflow_step_id": 1,
+                                            "output_name": "output"
+                                        },
+                                        "minimap setting (for long reads) ": {
+                                            "id": 2,
+                                            "input_subworkflow_step_id": 2,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": null,
+                                    "name": "Racon polish with long reads, x4 - upgraded",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 299.6429464825318,
+                                        "top": 72.0364210406818
+                                    },
+                                    "subworkflow": {
+                                        "a_galaxy_workflow": "true",
+                                        "annotation": "",
+                                        "comments": [],
+                                        "creator": [
+                                            {
+                                                "class": "Person",
+                                                "identifier": "0000-0002-9906-0673",
+                                                "name": "Anna Syme"
+                                            }
+                                        ],
+                                        "format-version": "0.1",
+                                        "name": "Racon polish with long reads, x4 - upgraded",
+                                        "report": {
+                                            "markdown": "\n# Workflow Execution Report\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                                        },
+                                        "steps": {
+                                            "0": {
+                                                "annotation": "",
+                                                "content_id": null,
+                                                "errors": null,
+                                                "id": 0,
+                                                "input_connections": {},
+                                                "inputs": [
+                                                    {
+                                                        "description": "",
+                                                        "name": "Assembly to be polished"
+                                                    }
+                                                ],
+                                                "label": "Assembly to be polished",
+                                                "name": "Input dataset",
+                                                "outputs": [],
+                                                "position": {
+                                                    "left": 0,
+                                                    "top": 216.625
+                                                },
+                                                "tool_id": null,
+                                                "tool_state": "{\"optional\": false, \"tag\": null}",
+                                                "tool_version": null,
+                                                "type": "data_input",
+                                                "uuid": "c7796c36-adf8-49e4-a8e4-66e606d70311",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "1": {
+                                                "annotation": "",
+                                                "content_id": null,
+                                                "errors": null,
+                                                "id": 1,
+                                                "input_connections": {},
+                                                "inputs": [
+                                                    {
+                                                        "description": "",
+                                                        "name": "long reads"
+                                                    }
+                                                ],
+                                                "label": "long reads",
+                                                "name": "Input dataset",
+                                                "outputs": [],
+                                                "position": {
+                                                    "left": 4.5,
+                                                    "top": 360.234375
+                                                },
+                                                "tool_id": null,
+                                                "tool_state": "{\"optional\": false, \"tag\": null}",
+                                                "tool_version": null,
+                                                "type": "data_input",
+                                                "uuid": "e2e4a70b-6e36-4b8b-bdf6-12b97189a6bd",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "10": {
+                                                "annotation": "",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "errors": null,
+                                                "id": 10,
+                                                "input_connections": {
+                                                    "corrected_reads": {
+                                                        "id": 8,
+                                                        "output_name": "consensus"
+                                                    },
+                                                    "overlaps": {
+                                                        "id": 9,
+                                                        "output_name": "alignment_output"
+                                                    },
+                                                    "reads": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    }
+                                                },
+                                                "inputs": [],
+                                                "label": "Racon: polish 4",
+                                                "name": "Racon",
+                                                "outputs": [
+                                                    {
+                                                        "name": "consensus",
+                                                        "type": "fasta"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 1496.078125,
+                                                    "top": 431.1875
+                                                },
+                                                "post_job_actions": {
+                                                    "RenameDatasetActionconsensus": {
+                                                        "action_arguments": {
+                                                            "newname": "Racon_long_reads_polished_assembly.fasta"
+                                                        },
+                                                        "action_type": "RenameDatasetAction",
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "78c533842eeb",
+                                                    "name": "racon",
+                                                    "owner": "bgruening",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "1.5.0+galaxy1",
+                                                "type": "tool",
+                                                "uuid": "53f4572e-3a4a-4585-89ab-9459f8a61720",
+                                                "when": null,
+                                                "workflow_outputs": [
+                                                    {
+                                                        "label": "Assembly polished by long reads using Racon",
+                                                        "output_name": "consensus",
+                                                        "uuid": "bcf0f03c-5951-46a7-aa38-545aed9bc183"
+                                                    }
+                                                ]
+                                            },
+                                            "2": {
+                                                "annotation": "",
+                                                "content_id": null,
+                                                "errors": null,
+                                                "id": 2,
+                                                "input_connections": {},
+                                                "inputs": [
+                                                    {
+                                                        "description": "",
+                                                        "name": "minimap setting (for long reads) "
+                                                    }
+                                                ],
+                                                "label": "minimap setting (for long reads) ",
+                                                "name": "Input parameter",
+                                                "outputs": [],
+                                                "position": {
+                                                    "left": 0.578125,
+                                                    "top": 495.859375
+                                                },
+                                                "tool_id": null,
+                                                "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                                                "tool_version": null,
+                                                "type": "parameter_input",
+                                                "uuid": "fb80c05c-08d4-4ac2-b4bf-81ed906e4d72",
+                                                "when": null,
+                                                "workflow_outputs": [
+                                                    {
+                                                        "label": null,
+                                                        "output_name": "output",
+                                                        "uuid": "3983ef22-5f05-4384-8f34-6ac8c4b2cc83"
+                                                    }
+                                                ]
+                                            },
+                                            "3": {
+                                                "annotation": "Map raw reads to assembly; output paf",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "errors": null,
+                                                "id": 3,
+                                                "input_connections": {
+                                                    "fastq_input|analysis_type_selector": {
+                                                        "id": 2,
+                                                        "output_name": "output"
+                                                    },
+                                                    "fastq_input|fastq_input1": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    },
+                                                    "reference_source|ref_file": {
+                                                        "id": 0,
+                                                        "output_name": "output"
+                                                    }
+                                                },
+                                                "inputs": [
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "reference_source"
+                                                    }
+                                                ],
+                                                "label": "Minimap2: map long reads to assembly",
+                                                "name": "Map with minimap2",
+                                                "outputs": [
+                                                    {
+                                                        "name": "alignment_output",
+                                                        "type": "bam"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 377.640625,
+                                                    "top": 0
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionalignment_output": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "alignment_output"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "be1d967337e4",
+                                                    "name": "minimap2",
+                                                    "owner": "iuc",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "2.26+galaxy0",
+                                                "type": "tool",
+                                                "uuid": "0c06144f-d1ac-4b45-9669-1ddf11fcb06b",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "4": {
+                                                "annotation": "",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "errors": null,
+                                                "id": 4,
+                                                "input_connections": {
+                                                    "corrected_reads": {
+                                                        "id": 0,
+                                                        "output_name": "output"
+                                                    },
+                                                    "overlaps": {
+                                                        "id": 3,
+                                                        "output_name": "alignment_output"
+                                                    },
+                                                    "reads": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    }
+                                                },
+                                                "inputs": [],
+                                                "label": "Racon: polish 1",
+                                                "name": "Racon",
+                                                "outputs": [
+                                                    {
+                                                        "name": "consensus",
+                                                        "type": "fasta"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 458.640625,
+                                                    "top": 518.875
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionconsensus": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "78c533842eeb",
+                                                    "name": "racon",
+                                                    "owner": "bgruening",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "1.5.0+galaxy1",
+                                                "type": "tool",
+                                                "uuid": "6c144354-91f2-49dd-a1f5-7c4119859730",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "5": {
+                                                "annotation": "Map raw reads to assembly; output paf",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "errors": null,
+                                                "id": 5,
+                                                "input_connections": {
+                                                    "fastq_input|analysis_type_selector": {
+                                                        "id": 2,
+                                                        "output_name": "output"
+                                                    },
+                                                    "fastq_input|fastq_input1": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    },
+                                                    "reference_source|ref_file": {
+                                                        "id": 4,
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "inputs": [
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "reference_source"
+                                                    }
+                                                ],
+                                                "label": "Minimap2: map long reads to polished assembly 1",
+                                                "name": "Map with minimap2",
+                                                "outputs": [
+                                                    {
+                                                        "name": "alignment_output",
+                                                        "type": "bam"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 698.859375,
+                                                    "top": 13.390625
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionalignment_output": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "alignment_output"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "be1d967337e4",
+                                                    "name": "minimap2",
+                                                    "owner": "iuc",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "2.26+galaxy0",
+                                                "type": "tool",
+                                                "uuid": "c1b83dad-a8ed-42cb-951f-73f59f2dfa92",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "6": {
+                                                "annotation": "",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "errors": null,
+                                                "id": 6,
+                                                "input_connections": {
+                                                    "corrected_reads": {
+                                                        "id": 4,
+                                                        "output_name": "consensus"
+                                                    },
+                                                    "overlaps": {
+                                                        "id": 5,
+                                                        "output_name": "alignment_output"
+                                                    },
+                                                    "reads": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    }
+                                                },
+                                                "inputs": [],
+                                                "label": "Racon: polish 2",
+                                                "name": "Racon",
+                                                "outputs": [
+                                                    {
+                                                        "name": "consensus",
+                                                        "type": "fasta"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 759.9375,
+                                                    "top": 485.71875
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionconsensus": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "78c533842eeb",
+                                                    "name": "racon",
+                                                    "owner": "bgruening",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "1.5.0+galaxy1",
+                                                "type": "tool",
+                                                "uuid": "3208491e-b831-4238-957e-5b7388d7ff8d",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "7": {
+                                                "annotation": "Map raw reads to assembly; output paf",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "errors": null,
+                                                "id": 7,
+                                                "input_connections": {
+                                                    "fastq_input|analysis_type_selector": {
+                                                        "id": 2,
+                                                        "output_name": "output"
+                                                    },
+                                                    "fastq_input|fastq_input1": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    },
+                                                    "reference_source|ref_file": {
+                                                        "id": 6,
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "inputs": [
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "reference_source"
+                                                    }
+                                                ],
+                                                "label": "Minimap2: map long reads to polished assembly 2",
+                                                "name": "Map with minimap2",
+                                                "outputs": [
+                                                    {
+                                                        "name": "alignment_output",
+                                                        "type": "bam"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 998.75,
+                                                    "top": 27.9375
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionalignment_output": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "alignment_output"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "be1d967337e4",
+                                                    "name": "minimap2",
+                                                    "owner": "iuc",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "2.26+galaxy0",
+                                                "type": "tool",
+                                                "uuid": "42af524b-7f74-4c75-8d78-f6888078dd2e",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "8": {
+                                                "annotation": "",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "errors": null,
+                                                "id": 8,
+                                                "input_connections": {
+                                                    "corrected_reads": {
+                                                        "id": 6,
+                                                        "output_name": "consensus"
+                                                    },
+                                                    "overlaps": {
+                                                        "id": 7,
+                                                        "output_name": "alignment_output"
+                                                    },
+                                                    "reads": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    }
+                                                },
+                                                "inputs": [],
+                                                "label": "Racon: polish 3",
+                                                "name": "Racon",
+                                                "outputs": [
+                                                    {
+                                                        "name": "consensus",
+                                                        "type": "fasta"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 1089.71875,
+                                                    "top": 455.53125
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionconsensus": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "78c533842eeb",
+                                                    "name": "racon",
+                                                    "owner": "bgruening",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "1.5.0+galaxy1",
+                                                "type": "tool",
+                                                "uuid": "21f339bd-ebc1-4c73-a976-5d0b9ab2127a",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "9": {
+                                                "annotation": "Map raw reads to assembly; output paf",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "errors": null,
+                                                "id": 9,
+                                                "input_connections": {
+                                                    "fastq_input|analysis_type_selector": {
+                                                        "id": 2,
+                                                        "output_name": "output"
+                                                    },
+                                                    "fastq_input|fastq_input1": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    },
+                                                    "reference_source|ref_file": {
+                                                        "id": 8,
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "inputs": [
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "reference_source"
+                                                    }
+                                                ],
+                                                "label": "Minimap2: map long reads to polished assembly 3",
+                                                "name": "Map with minimap2",
+                                                "outputs": [
+                                                    {
+                                                        "name": "alignment_output",
+                                                        "type": "bam"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 1316.53125,
+                                                    "top": 38.046875
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionalignment_output": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "alignment_output"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "be1d967337e4",
+                                                    "name": "minimap2",
+                                                    "owner": "iuc",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "2.26+galaxy0",
+                                                "type": "tool",
+                                                "uuid": "7d36291e-aa76-4312-9943-b5e56d0e90c5",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            }
+                                        },
+                                        "tags": "",
+                                        "uuid": "c57efd37-4cf6-4cc7-abf4-2bab22a2e9a0"
+                                    },
+                                    "tool_id": null,
+                                    "type": "subworkflow",
+                                    "uuid": "58c99e4b-fd6a-401d-b9c7-cdf7e6d1757d",
+                                    "when": null,
+                                    "workflow_outputs": [
+                                        {
+                                            "label": null,
+                                            "output_name": "2:output",
+                                            "uuid": "50fa1032-8037-454e-8192-b95405bcd5d4"
+                                        }
+                                    ]
+                                },
+                                "5": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
+                                    "errors": null,
+                                    "id": 5,
+                                    "input_connections": {
+                                        "d": {
+                                            "id": 4,
+                                            "output_name": "Assembly polished by long reads using Racon"
+                                        },
+                                        "i": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Medaka polish",
+                                    "name": "medaka consensus pipeline",
+                                    "outputs": [
+                                        {
+                                            "name": "out_consensus",
+                                            "type": "fasta"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 515.5164024294684,
+                                        "top": 305.08460859328346
+                                    },
+                                    "post_job_actions": {
+                                        "RenameDatasetActionout_consensus": {
+                                            "action_arguments": {
+                                                "newname": "Medaka_long_reads_polished_assembly.fasta"
+                                            },
+                                            "action_type": "RenameDatasetAction",
+                                            "output_name": "out_consensus"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "fc8804320156",
+                                        "name": "medaka_consensus_pipeline",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"b\": \"100\", \"d\": {\"__class__\": \"ConnectedValue\"}, \"g\": false, \"i\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"r941_min_high_g360\", \"out\": [\"consensus\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "1.7.2+galaxy1",
+                                    "type": "tool",
+                                    "uuid": "14c5ce9c-df92-4e20-85da-7a161eaa759d",
+                                    "when": null,
+                                    "workflow_outputs": [
+                                        {
+                                            "label": "Assembly polished by long reads using Medaka",
+                                            "output_name": "out_consensus",
+                                            "uuid": "e3136060-bce7-4af3-87c4-9dcbb0d1f531"
+                                        }
+                                    ]
+                                },
+                                "6": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                                    "errors": null,
+                                    "id": 6,
+                                    "input_connections": {
+                                        "fasta": {
+                                            "id": 4,
+                                            "output_name": "Assembly polished by long reads using Racon"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Fasta statistics after Racon long read polish",
+                                    "name": "Fasta Statistics",
+                                    "outputs": [
+                                        {
+                                            "name": "stats_output",
+                                            "type": "tabular"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 611.8186129984722,
+                                        "top": 131.47863560473016
+                                    },
+                                    "post_job_actions": {},
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "0dbb995c7d35",
+                                        "name": "fasta_stats",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gaps_option\": false, \"genome_size\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "2.0",
+                                    "type": "tool",
+                                    "uuid": "e78db141-a6d2-42b1-b2b6-aee5e900d3f4",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "7": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                                    "errors": null,
+                                    "id": 7,
+                                    "input_connections": {
+                                        "fasta": {
+                                            "id": 5,
+                                            "output_name": "out_consensus"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Fasta statistics after Medaka polish",
+                                    "name": "Fasta Statistics",
+                                    "outputs": [
+                                        {
+                                            "name": "stats_output",
+                                            "type": "tabular"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 816.9504695700908,
+                                        "top": 343.05724959525315
+                                    },
+                                    "post_job_actions": {},
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "0dbb995c7d35",
+                                        "name": "fasta_stats",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gaps_option\": false, \"genome_size\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "2.0",
+                                    "type": "tool",
+                                    "uuid": "96f313ee-4a6a-4ba9-86f8-3dedc1d5d30d",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "8": {
+                                    "annotation": "",
+                                    "id": 8,
+                                    "input_connections": {
+                                        "Assembly to be polished": {
+                                            "id": 5,
+                                            "input_subworkflow_step_id": 0,
+                                            "output_name": "out_consensus"
+                                        },
+                                        "Illumina reads, R1, in fastq.gz format": {
+                                            "id": 3,
+                                            "input_subworkflow_step_id": 1,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": null,
+                                    "name": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 915.3758175639219,
+                                        "top": 512.306732089216
+                                    },
+                                    "subworkflow": {
+                                        "a_galaxy_workflow": "true",
+                                        "annotation": "",
+                                        "comments": [],
+                                        "creator": [
+                                            {
+                                                "class": "Person",
+                                                "identifier": "0000-0002-9906-0673",
+                                                "name": "Anna Syme"
+                                            }
+                                        ],
+                                        "format-version": "0.1",
+                                        "name": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
+                                        "steps": {
+                                            "0": {
+                                                "annotation": "",
+                                                "content_id": null,
+                                                "errors": null,
+                                                "id": 0,
+                                                "input_connections": {},
+                                                "inputs": [
+                                                    {
+                                                        "description": "",
+                                                        "name": "Assembly to be polished"
+                                                    }
+                                                ],
+                                                "label": "Assembly to be polished",
+                                                "name": "Input dataset",
+                                                "outputs": [],
+                                                "position": {
+                                                    "left": 0,
+                                                    "top": 72.5176329833982
+                                                },
+                                                "tool_id": null,
+                                                "tool_state": "{\"optional\": false, \"tag\": null}",
+                                                "tool_version": null,
+                                                "type": "data_input",
+                                                "uuid": "28669894-74e2-4ba1-9d49-6e3209b5a1de",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "1": {
+                                                "annotation": "",
+                                                "content_id": null,
+                                                "errors": null,
+                                                "id": 1,
+                                                "input_connections": {},
+                                                "inputs": [
+                                                    {
+                                                        "description": "",
+                                                        "name": "Illumina reads, R1, in fastq.gz format"
+                                                    }
+                                                ],
+                                                "label": "Illumina reads, R1, in fastq.gz format",
+                                                "name": "Input dataset",
+                                                "outputs": [],
+                                                "position": {
+                                                    "left": 8.5,
+                                                    "top": 341.2832579833982
+                                                },
+                                                "tool_id": null,
+                                                "tool_state": "{\"optional\": false, \"tag\": null}",
+                                                "tool_version": null,
+                                                "type": "data_input",
+                                                "uuid": "bc936fdc-22a9-4507-aa47-4a70a3f93923",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "2": {
+                                                "annotation": "",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "errors": null,
+                                                "id": 2,
+                                                "input_connections": {
+                                                    "fastq_input|fastq_input1": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    },
+                                                    "reference_source|ref_file": {
+                                                        "id": 0,
+                                                        "output_name": "output"
+                                                    }
+                                                },
+                                                "inputs": [
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "reference_source"
+                                                    }
+                                                ],
+                                                "label": "Minimap2 round 1: map reads to assembly",
+                                                "name": "Map with minimap2",
+                                                "outputs": [
+                                                    {
+                                                        "name": "alignment_output",
+                                                        "type": "bam"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 399.936279296875,
+                                                    "top": 0
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionalignment_output": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "alignment_output"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "be1d967337e4",
+                                                    "name": "minimap2",
+                                                    "owner": "iuc",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": \"sr\"}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "2.26+galaxy0",
+                                                "type": "tool",
+                                                "uuid": "b01b8c3d-c33b-47b2-9a83-297c19d63ab7",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "3": {
+                                                "annotation": "",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "errors": null,
+                                                "id": 3,
+                                                "input_connections": {
+                                                    "corrected_reads": {
+                                                        "id": 0,
+                                                        "output_name": "output"
+                                                    },
+                                                    "overlaps": {
+                                                        "id": 2,
+                                                        "output_name": "alignment_output"
+                                                    },
+                                                    "reads": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    }
+                                                },
+                                                "inputs": [],
+                                                "label": "Racon round 1: polish assembly",
+                                                "name": "Racon",
+                                                "outputs": [
+                                                    {
+                                                        "name": "consensus",
+                                                        "type": "fasta"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 635.5625200274146,
+                                                    "top": 432.13610641498093
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionconsensus": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "78c533842eeb",
+                                                    "name": "racon",
+                                                    "owner": "bgruening",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"error_threshold\": \"0.3\", \"fragment_correction\": false, \"gap\": \"-4\", \"include_unpolished\": false, \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"window_length\": \"500\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "1.5.0+galaxy1",
+                                                "type": "tool",
+                                                "uuid": "fe32d046-4ff2-485e-84e8-191b04803afc",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "4": {
+                                                "annotation": "",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "errors": null,
+                                                "id": 4,
+                                                "input_connections": {
+                                                    "fastq_input|fastq_input1": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    },
+                                                    "reference_source|ref_file": {
+                                                        "id": 3,
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "inputs": [
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "reference_source"
+                                                    }
+                                                ],
+                                                "label": "Minimap2 round 2: map reads to assembly",
+                                                "name": "Map with minimap2",
+                                                "outputs": [
+                                                    {
+                                                        "name": "alignment_output",
+                                                        "type": "bam"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 859.5,
+                                                    "top": 23.955132983398205
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionalignment_output": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "alignment_output"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "be1d967337e4",
+                                                    "name": "minimap2",
+                                                    "owner": "iuc",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": \"sr\"}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "2.26+galaxy0",
+                                                "type": "tool",
+                                                "uuid": "ee834cad-027a-4a84-963b-141b22eaa70a",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "5": {
+                                                "annotation": "",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "errors": null,
+                                                "id": 5,
+                                                "input_connections": {
+                                                    "corrected_reads": {
+                                                        "id": 3,
+                                                        "output_name": "consensus"
+                                                    },
+                                                    "overlaps": {
+                                                        "id": 4,
+                                                        "output_name": "alignment_output"
+                                                    },
+                                                    "reads": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    }
+                                                },
+                                                "inputs": [],
+                                                "label": "Racon round 2: polish assembly",
+                                                "name": "Racon",
+                                                "outputs": [
+                                                    {
+                                                        "name": "consensus",
+                                                        "type": "fasta"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 1198.765625,
+                                                    "top": 332.4707579833982
+                                                },
+                                                "post_job_actions": {
+                                                    "RenameDatasetActionconsensus": {
+                                                        "action_arguments": {
+                                                            "newname": "Racon_short_reads_polished_assembly.fasta"
+                                                        },
+                                                        "action_type": "RenameDatasetAction",
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "78c533842eeb",
+                                                    "name": "racon",
+                                                    "owner": "bgruening",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "1.5.0+galaxy1",
+                                                "type": "tool",
+                                                "uuid": "b3c89c40-3ad0-454c-a4d4-dfa34fb09f24",
+                                                "when": null,
+                                                "workflow_outputs": [
+                                                    {
+                                                        "label": "Assembly polished by short reads using Racon",
+                                                        "output_name": "consensus",
+                                                        "uuid": "594819c3-668e-4575-b9a6-4459ffacf952"
+                                                    }
+                                                ]
+                                            }
+                                        },
+                                        "tags": "",
+                                        "uuid": "1b96b1cf-dbd4-46b1-8a59-aebfe80135c2"
+                                    },
+                                    "tool_id": null,
+                                    "type": "subworkflow",
+                                    "uuid": "46288abb-a2bc-43d5-822a-a93af0d346cf",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "9": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                                    "errors": null,
+                                    "id": 9,
+                                    "input_connections": {
+                                        "fasta": {
+                                            "id": 8,
+                                            "output_name": "Assembly polished by short reads using Racon"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Fasta statistics after Racon short read polish",
+                                    "name": "Fasta Statistics",
+                                    "outputs": [
+                                        {
+                                            "name": "stats_output",
+                                            "type": "tabular"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 1179.1223817823236,
+                                        "top": 547.060000097866
+                                    },
+                                    "post_job_actions": {},
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "0dbb995c7d35",
+                                        "name": "fasta_stats",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gaps_option\": false, \"genome_size\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "2.0",
+                                    "type": "tool",
+                                    "uuid": "3c06b177-02b5-4068-8056-56b653d95379",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                }
+                            },
+                            "tags": "",
+                            "uuid": "af8b99cb-cfc5-4f96-ba6c-6a178826ca98"
+                        },
+                        "tool_id": null,
+                        "type": "subworkflow",
+                        "uuid": "6b6668c9-25b7-4135-ac9b-140a6d1593b0",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "2:output",
+                                "uuid": "f740de36-9921-4f0c-924e-3902bc2083b7"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "4:2:output",
+                                "uuid": "2b5d309e-c47e-4a79-a69c-4d4fd6a93d8b"
+                            }
+                        ]
+                    }
                 ],
-                "id": "gallardoalba",
-                "joined": "2020-11",
-                "name": "Crist\u00f3bal Gallardo",
-                "orcid": "0000-0002-5752-2155",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
-            },
-            {
-                "id": "annasyme",
-                "joined": "2017-09",
-                "name": "Anna Syme",
-                "orcid": "0000-0002-9906-0673",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
-            },
-            {
-                "id": "abueg",
-                "joined": "2022-01",
-                "name": "Linelle Abueg",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abueg/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abueg.json"
-            },
-            {
-                "id": "pickettbd",
-                "joined": "2022-01",
-                "name": "Brandon Pickett",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pickettbd/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pickettbd.json"
-            },
-            {
-                "id": "gf777",
-                "joined": "2022-01",
-                "name": "Giulio Formenti",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gf777/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/gf777.json"
-            },
-            {
-                "id": "msozzoni",
-                "joined": "2022-03",
-                "name": "Marcella Sozzoni",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/msozzoni/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/msozzoni.json"
-            },
-            {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
-                "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
-            }
-        ],
-        "dir": "topics/assembly/tutorials/vgp_genome_assembly",
-        "edam_operation": [
-            "Visualisation",
-            "Primer removal",
-            "Phasing",
-            "De-novo assembly",
-            "Sequence alignment",
-            "Mapping",
-            "Sequence assembly validation",
-            "Read pre-processing",
-            "Pairwise sequence alignment",
-            "Transcriptome assembly",
-            "Data handling",
-            "Genome assembly",
-            "Sequence trimming",
-            "Read binning",
-            "k-mer counting",
-            "Scaffolding"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "assembly/vgp_genome_assembly",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": 28717,
-            "mermaid": false
-        },
-        "key_points": [
-            "The VGP pipeline allows users to generate error-free, near gapless reference-quality genome assemblies",
-            "The assembly can be divided into four main stages: genome profile analysis, HiFi long read phased assembly with hifiasm, Bionano hybrid scaffolding and Hi-C scaffolding"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-07-31",
-        "objectives": [
-            "Learn the tools necessary to perform a de novo assembly of a vertebrate genome",
-            "Evaluate the quality of the assembly"
-        ],
-        "pageviews": 17115,
-        "pub_date": "2021-06-04",
-        "questions": [
-            "What combination of tools can produce the highest quality assembly of vertebrate genomes?",
-            "How can we evaluate the quality of the assembly in a reference-free way?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "delphine-l"
+                "parent_id": "assembly/largegenome",
+                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga",
+                "tags": [
+                    "LG-WF",
+                    "GTN"
                 ],
-                "date": "2022-03-13",
-                "galaxy_version": "21.09",
-                "length": "10M",
-                "speakers": [
-                    "delphine-l"
+                "test_results": null,
+                "tests": false,
+                "title": "Combined workflows for large genome assembly - upgraded ",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-combined-workflows-for-large-genome-assembly",
+                "tutorial_id": "largegenome",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.html",
+                "version": 2,
+                "wfid": "assembly-largegenome",
+                "wfname": "galaxy-workflow-combined-workflows-for-large-genome-assembly",
+                "workflow": "Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga",
+                "workflow_tools": [
+                    "barchart_gnuplot",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
                 ],
-                "youtube_id": "0EoBDiyd-84"
-            }
-        ],
-        "short_id": "T00039",
-        "short_tools": [
-            "bellerophon",
-            "meryl",
-            "collapse_dataset",
-            "busco",
-            "quast",
-            "collection_column_join",
-            "yahs",
-            "genomescope",
-            "pretext_map",
-            "gfa_to_fa",
-            "cat1",
-            "tp_find_and_replace",
-            "sort1",
-            "hifiasm",
-            "tp_cut_tool",
-            "gfastats",
-            "cutadapt",
-            "salsa",
-            "tp_grep_tool",
-            "merqury",
-            "pretext_snapshot",
-            "Convert characters1",
-            "bedtools_bamtobed",
-            "bionano_scaffold",
-            "purge_dups",
-            "minimap2",
-            "Add_a_column1",
-            "bwa_mem2"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "pacbio",
-            "eukaryote",
-            "VGP"
-        ],
-        "time_estimation": "5h",
-        "title": "VGP assembly pipeline: Step by Step",
-        "tools": [
-            "Convert characters1",
-            "cat1",
-            "sort1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.19.8+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
-            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
-            "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/salsa/salsa/2.3+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
-            "ttoolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1"
-        ],
-        "topic_name": "assembly",
-        "topic_name_human": "Assembly",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "vgp_genome_assembly",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/vgp_genome_assembly/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/vgp_genome_assembly/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/vgp_genome_assembly/tutorial.json"
-        },
-        "version": 52,
-        "video": false,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 119,
-        "visitors": 10751,
-        "workflows": [
+                "workflowhub_id": "1176"
+            },
             {
-                "creators": [],
-                "description": "VGP assembly tutorial",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
+                    }
+                ],
+                "description": "",
                 "features": {
                     "comments": false,
                     "parameters": false,
-                    "report": null,
+                    "report": {
+                        "markdown": "\n# Workflow Report for Data QC\n\n## Workflow steps\n\n```galaxy\nworkflow_display()\n```\n\n"
+                    },
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBionano_dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHi-C_dataset_R\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHi-C_dataset_F\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  4[label=\"GFA to FASTA\"]\n  5[label=\"GFA to FASTA\"]\n  6[label=\"Cutadapt\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"Busco\"]\n  4 -> 7 [label=\"out_fa\"]\n  8[label=\"Busco\"]\n  5 -> 8 [label=\"out_fa\"]\n  9[label=\"Purge overlaps\"]\n  5 -> 9 [label=\"out_fa\"]\n  10[label=\"Collapse Collection\"]\n  6 -> 10 [label=\"out1\"]\n  11[label=\"Meryl\"]\n  6 -> 11 [label=\"out1\"]\n  12[label=\"Map with minimap2\"]\n  6 -> 12 [label=\"out1\"]\n  5 -> 12 [label=\"out_fa\"]\n  13[label=\"Quast\"]\n  5 -> 13 [label=\"out_fa\"]\n  4 -> 13 [label=\"out_fa\"]\n  6 -> 13 [label=\"out1\"]\n  14[label=\"Map with minimap2\"]\n  9 -> 14 [label=\"split_fasta\"]\n  9 -> 14 [label=\"split_fasta\"]\n  15[label=\"Meryl\"]\n  11 -> 15 [label=\"read_db\"]\n  16[label=\"Purge overlaps\"]\n  12 -> 16 [label=\"alignment_output\"]\n  17[label=\"Meryl\"]\n  15 -> 17 [label=\"read_db\"]\n  18[label=\"Merqury\"]\n  5 -> 18 [label=\"out_fa\"]\n  4 -> 18 [label=\"out_fa\"]\n  15 -> 18 [label=\"read_db\"]\n  19[label=\"Purge overlaps\"]\n  16 -> 19 [label=\"pbcstat_cov\"]\n  16 -> 19 [label=\"calcuts_cutoff\"]\n  14 -> 19 [label=\"alignment_output\"]\n  20[label=\"GenomeScope\"]\n  17 -> 20 [label=\"read_db_hist\"]\n  21[label=\"Purge overlaps\"]\n  19 -> 21 [label=\"purge_dups_bed\"]\n  5 -> 21 [label=\"out_fa\"]\n  22[label=\"Replace\"]\n  20 -> 22 [label=\"summary\"]\n  23[label=\"Compute\"]\n  20 -> 23 [label=\"model_params\"]\n  24[label=\"Bionano Hybrid Scaffold\"]\n  0 -> 24 [label=\"output\"]\n  21 -> 24 [label=\"get_seqs_purged\"]\n  25[label=\"Concatenate datasets\"]\n  21 -> 25 [label=\"get_seqs_hap\"]\n  4 -> 25 [label=\"out_fa\"]\n  26[label=\"Busco\"]\n  21 -> 26 [label=\"get_seqs_purged\"]\n  27[label=\"Replace\"]\n  22 -> 27 [label=\"outfile\"]\n  28[label=\"Compute\"]\n  23 -> 28 [label=\"out_file1\"]\n  29[label=\"Concatenate datasets\"]\n  24 -> 29 [label=\"ngs_contigs_scaffold_trimmed\"]\n  24 -> 29 [label=\"ngs_contigs_not_scaffolded_trimmed\"]\n  30[label=\"Purge overlaps\"]\n  25 -> 30 [label=\"out_file1\"]\n  31[label=\"Map with minimap2\"]\n  10 -> 31 [label=\"output\"]\n  25 -> 31 [label=\"out_file1\"]\n  32[label=\"Search in textfiles\"]\n  27 -> 32 [label=\"outfile\"]\n  33[label=\"Advanced Cut\"]\n  28 -> 33 [label=\"out_file1\"]\n  34[label=\"Advanced Cut\"]\n  28 -> 34 [label=\"out_file1\"]\n  35[label=\"BWA-MEM2\"]\n  1 -> 35 [label=\"output\"]\n  29 -> 35 [label=\"out_file1\"]\n  36[label=\"BWA-MEM2\"]\n  2 -> 36 [label=\"output\"]\n  29 -> 36 [label=\"out_file1\"]\n  37[label=\"Replace\"]\n  29 -> 37 [label=\"out_file1\"]\n  38[label=\"Quast\"]\n  29 -> 38 [label=\"out_file1\"]\n  10 -> 38 [label=\"output\"]\n  39[label=\"Busco\"]\n  29 -> 39 [label=\"out_file1\"]\n  40[label=\"Map with minimap2\"]\n  30 -> 40 [label=\"split_fasta\"]\n  30 -> 40 [label=\"split_fasta\"]\n  41[label=\"Purge overlaps\"]\n  31 -> 41 [label=\"alignment_output\"]\n  42[label=\"Convert\"]\n  32 -> 42 [label=\"output\"]\n  43[label=\"Filter and merge\"]\n  36 -> 43 [label=\"bam_output\"]\n  35 -> 43 [label=\"bam_output\"]\n  44[label=\"Purge overlaps\"]\n  41 -> 44 [label=\"pbcstat_cov\"]\n  41 -> 44 [label=\"calcuts_cutoff\"]\n  40 -> 44 [label=\"alignment_output\"]\n  45[label=\"Advanced Cut\"]\n  42 -> 45 [label=\"out_file1\"]\n  46[label=\"bedtools BAM to BED\"]\n  43 -> 46 [label=\"outfile\"]\n  47[label=\"PretextMap\"]\n  43 -> 47 [label=\"outfile\"]\n  48[label=\"Purge overlaps\"]\n  44 -> 48 [label=\"purge_dups_bed\"]\n  25 -> 48 [label=\"out_file1\"]\n  49[label=\"Sort\"]\n  46 -> 49 [label=\"output\"]\n  50[label=\"Pretext Snapshot\"]\n  47 -> 50 [label=\"pretext_map_out\"]\n  51[label=\"Busco\"]\n  48 -> 51 [label=\"get_seqs_purged\"]\n  52[label=\"Quast\"]\n  21 -> 52 [label=\"get_seqs_purged\"]\n  48 -> 52 [label=\"get_seqs_purged\"]\n  10 -> 52 [label=\"output\"]\n  53[label=\"SALSA\"]\n  49 -> 53 [label=\"out_file1\"]\n  37 -> 53 [label=\"outfile\"]\n  54[label=\"BWA-MEM2\"]\n  1 -> 54 [label=\"output\"]\n  53 -> 54 [label=\"scaffolds_fasta\"]\n  55[label=\"BWA-MEM2\"]\n  2 -> 55 [label=\"output\"]\n  53 -> 55 [label=\"scaffolds_fasta\"]\n  56[label=\"Busco\"]\n  53 -> 56 [label=\"scaffolds_fasta\"]\n  57[label=\"Quast\"]\n  53 -> 57 [label=\"scaffolds_fasta\"]\n  10 -> 57 [label=\"output\"]\n  58[label=\"Filter and merge\"]\n  55 -> 58 [label=\"bam_output\"]\n  54 -> 58 [label=\"bam_output\"]\n  59[label=\"PretextMap\"]\n  58 -> 59 [label=\"outfile\"]\n  60[label=\"Pretext Snapshot\"]\n  59 -> 60 [label=\"pretext_map_out\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput file: long reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R1\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R2\"]\n  3[label=\"Nanoplot: long reads\"]\n  0 -> 3 [label=\"output\"]\n  k73d0e4cf366e41c1810ab269638826b3[color=lightseagreen,label=\"Output\\nNanoPlot on input dataset(s): HTML report\"]\n  3 -> k73d0e4cf366e41c1810ab269638826b3\n  4[label=\"FastQC on R1\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"FastQC on R2\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"MultiQC: combine fastQC reports\"]\n  4 -> 6 [label=\"text_file\"]\n  5 -> 6 [label=\"text_file\"]\n  k8baf8700876e4a74ad996e656f3ba618[color=lightseagreen,label=\"Output\\nMultiQC on input dataset(s): Webpage\"]\n  6 -> k8baf8700876e4a74ad996e656f3ba618\n}",
                 "history": [
                     {
-                        "hash": "b57efed6057cbfaeb5e79c2ed6a0182d59c619d0",
-                        "message": "VGP training: fix duplication problem (#3271)",
-                        "num": 8,
-                        "short_hash": "b57efed60",
-                        "unix": "1648533596"
-                    },
-                    {
-                        "hash": "f764939f89074b68169419b828862b8c4333e671",
-                        "message": "Update VGP training 06.02: synthetic reads (#3157)",
-                        "num": 7,
-                        "short_hash": "f764939f8",
-                        "unix": "1645040160"
-                    },
-                    {
-                        "hash": "5552083ddc045639e0dbed4422cbf97c71052110",
-                        "message": "Fix bug",
-                        "num": 6,
-                        "short_hash": "5552083dd",
-                        "unix": "1643108875"
-                    },
-                    {
-                        "hash": "f7354f457234a89e026e4960e48fdc211f3aeef8",
-                        "message": "Fix workflow lint",
+                        "hash": "d35221f6506e7b95e8b3ff679a2ad01edf1a560a",
+                        "message": "Update Galaxy-Workflow-Data_QC.ga",
                         "num": 5,
-                        "short_hash": "f7354f457",
-                        "unix": "1643108431"
+                        "short_hash": "d35221f65",
+                        "unix": "1715074384"
                     },
                     {
-                        "hash": "e87377be94fcab2333895380c4167a4fd0ab435c",
-                        "message": "Include Linelle and update workflow",
+                        "hash": "a737e5f1b936379382f4d568b0caeb664d81c392",
+                        "message": "Rename Galaxy-Workflow-Data_QC_-_upgraded.ga to Galaxy-Workflow-Data_QC.ga",
                         "num": 4,
-                        "short_hash": "e87377be9",
-                        "unix": "1643108189"
+                        "short_hash": "a737e5f1b",
+                        "unix": "1714537191"
                     },
                     {
-                        "hash": "a45e1874032e2d30c3d3801599900467134ba5b7",
-                        "message": "workflow tag and annotation",
+                        "hash": "9ca497557dddc43b116a61592a953f455046bc86",
+                        "message": "Rename Galaxy-Workflow-Data_QC.ga to Galaxy-Workflow-Data_QC_old.ga",
                         "num": 3,
-                        "short_hash": "a45e18740",
-                        "unix": "1622754288"
+                        "short_hash": "9ca497557",
+                        "unix": "1714537118"
                     },
                     {
-                        "hash": "54179df03c881344d118a06596d7a8ee75477e16",
-                        "message": "update tools",
+                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
+                        "message": "add/complete creator info on workflows",
                         "num": 2,
-                        "short_hash": "54179df03",
-                        "unix": "1622753242"
+                        "short_hash": "62e77944b",
+                        "unix": "1676627603"
                     },
                     {
-                        "hash": "3309edda7618f96ec58d14e47350ea4d5897b9e0",
-                        "message": "add vgp training skeleton from workflow",
+                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
+                        "message": "large genome tutorial",
                         "num": 1,
-                        "short_hash": "3309edda7",
-                        "unix": "1622750872"
+                        "short_hash": "9fcb3aeec",
+                        "unix": "1665123856"
                     }
                 ],
                 "inputs": [
@@ -20118,21 +21991,22 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Bionano_dataset"
+                                "name": "Input file: long reads"
                             }
                         ],
-                        "label": "Bionano_dataset",
+                        "label": "Input file: long reads",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 10
+                            "left": 0,
+                            "top": 0.0
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "80e89ff1-902e-42f4-be59-f33bf55a692c",
+                        "uuid": "e2e4a70b-6e36-4b8b-bdf6-12b97189a6bd",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
@@ -20144,21 +22018,22 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Hi-C_dataset_R"
+                                "name": "Input file: Illumina reads R1"
                             }
                         ],
-                        "label": "Hi-C_dataset_R",
+                        "label": "Input file: Illumina reads R1",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 130
+                            "left": 535.703125,
+                            "top": 21.0
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "07cb8e4c-afd1-4007-ad83-e7fe9ab14ae6",
+                        "uuid": "ea859a58-c81a-4ef6-9bd2-4ef2f17bb5a9",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
@@ -20170,515 +22045,240 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Hi-C_dataset_F"
+                                "name": "Input file: Illumina reads R2"
                             }
                         ],
-                        "label": "Hi-C_dataset_F",
+                        "label": "Input file: Illumina reads R2",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 250
+                            "left": 530.703125,
+                            "top": 379.984375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "8395a577-e9a2-41ef-b2bf-ce303b637892",
+                        "uuid": "472adc05-88a5-4955-9e43-e82e9550ad08",
+                        "when": null,
                         "workflow_outputs": []
-                    },
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput file: long reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R2\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Nanoplot: long reads\"];\n  0 -->|output| 3;\n  73d0e4cf-366e-41c1-810a-b269638826b3[\"Output\\nNanoPlot on input dataset(s): HTML report\"];\n  3 --> 73d0e4cf-366e-41c1-810a-b269638826b3;\n  style 73d0e4cf-366e-41c1-810a-b269638826b3 stroke:#2c3143,stroke-width:4px;\n  4[\"FastQC on R1\"];\n  1 -->|output| 4;\n  5[\"FastQC on R2\"];\n  2 -->|output| 5;\n  6[\"MultiQC: combine fastQC reports\"];\n  4 -->|text_file| 6;\n  5 -->|text_file| 6;\n  8baf8700-876e-4a74-ad99-6e656f3ba618[\"Output\\nMultiQC on input dataset(s): Webpage\"];\n  6 --> 8baf8700-876e-4a74-ad99-6e656f3ba618;\n  style 8baf8700-876e-4a74-ad99-6e656f3ba618 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Data QC - upgraded",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1",
                         "errors": null,
                         "id": 3,
-                        "input_connections": {},
-                        "inputs": [
+                        "input_connections": {
+                            "mode|reads|files": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Nanoplot: long reads",
+                        "name": "NanoPlot",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Input Dataset Collection"
+                                "name": "output_html",
+                                "type": "html"
+                            },
+                            {
+                                "name": "nanostats",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "nanostats_post_filtering",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "Input Dataset Collection",
-                        "name": "Input dataset collection",
-                        "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 370
+                            "left": 240.84375,
+                            "top": 104.359375
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "d99feaa3-653d-4a95-bd1c-6975baf1e946",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nBionano_dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nHi-C_dataset_R\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nHi-C_dataset_F\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"GFA to FASTA\"];\n  5[\"GFA to FASTA\"];\n  6[\"Cutadapt\"];\n  3 -->|output| 6;\n  7[\"Busco\"];\n  4 -->|out_fa| 7;\n  8[\"Busco\"];\n  5 -->|out_fa| 8;\n  9[\"Purge overlaps\"];\n  5 -->|out_fa| 9;\n  10[\"Collapse Collection\"];\n  6 -->|out1| 10;\n  11[\"Meryl\"];\n  6 -->|out1| 11;\n  12[\"Map with minimap2\"];\n  6 -->|out1| 12;\n  5 -->|out_fa| 12;\n  13[\"Quast\"];\n  5 -->|out_fa| 13;\n  4 -->|out_fa| 13;\n  6 -->|out1| 13;\n  14[\"Map with minimap2\"];\n  9 -->|split_fasta| 14;\n  9 -->|split_fasta| 14;\n  15[\"Meryl\"];\n  11 -->|read_db| 15;\n  16[\"Purge overlaps\"];\n  12 -->|alignment_output| 16;\n  17[\"Meryl\"];\n  15 -->|read_db| 17;\n  18[\"Merqury\"];\n  5 -->|out_fa| 18;\n  4 -->|out_fa| 18;\n  15 -->|read_db| 18;\n  19[\"Purge overlaps\"];\n  16 -->|pbcstat_cov| 19;\n  16 -->|calcuts_cutoff| 19;\n  14 -->|alignment_output| 19;\n  20[\"GenomeScope\"];\n  17 -->|read_db_hist| 20;\n  21[\"Purge overlaps\"];\n  19 -->|purge_dups_bed| 21;\n  5 -->|out_fa| 21;\n  22[\"Replace\"];\n  20 -->|summary| 22;\n  23[\"Compute\"];\n  20 -->|model_params| 23;\n  24[\"Bionano Hybrid Scaffold\"];\n  0 -->|output| 24;\n  21 -->|get_seqs_purged| 24;\n  25[\"Concatenate datasets\"];\n  21 -->|get_seqs_hap| 25;\n  4 -->|out_fa| 25;\n  26[\"Busco\"];\n  21 -->|get_seqs_purged| 26;\n  27[\"Replace\"];\n  22 -->|outfile| 27;\n  28[\"Compute\"];\n  23 -->|out_file1| 28;\n  29[\"Concatenate datasets\"];\n  24 -->|ngs_contigs_scaffold_trimmed| 29;\n  24 -->|ngs_contigs_not_scaffolded_trimmed| 29;\n  30[\"Purge overlaps\"];\n  25 -->|out_file1| 30;\n  31[\"Map with minimap2\"];\n  10 -->|output| 31;\n  25 -->|out_file1| 31;\n  32[\"Search in textfiles\"];\n  27 -->|outfile| 32;\n  33[\"Advanced Cut\"];\n  28 -->|out_file1| 33;\n  34[\"Advanced Cut\"];\n  28 -->|out_file1| 34;\n  35[\"BWA-MEM2\"];\n  1 -->|output| 35;\n  29 -->|out_file1| 35;\n  36[\"BWA-MEM2\"];\n  2 -->|output| 36;\n  29 -->|out_file1| 36;\n  37[\"Replace\"];\n  29 -->|out_file1| 37;\n  38[\"Quast\"];\n  29 -->|out_file1| 38;\n  10 -->|output| 38;\n  39[\"Busco\"];\n  29 -->|out_file1| 39;\n  40[\"Map with minimap2\"];\n  30 -->|split_fasta| 40;\n  30 -->|split_fasta| 40;\n  41[\"Purge overlaps\"];\n  31 -->|alignment_output| 41;\n  42[\"Convert\"];\n  32 -->|output| 42;\n  43[\"Filter and merge\"];\n  36 -->|bam_output| 43;\n  35 -->|bam_output| 43;\n  44[\"Purge overlaps\"];\n  41 -->|pbcstat_cov| 44;\n  41 -->|calcuts_cutoff| 44;\n  40 -->|alignment_output| 44;\n  45[\"Advanced Cut\"];\n  42 -->|out_file1| 45;\n  46[\"bedtools BAM to BED\"];\n  43 -->|outfile| 46;\n  47[\"PretextMap\"];\n  43 -->|outfile| 47;\n  48[\"Purge overlaps\"];\n  44 -->|purge_dups_bed| 48;\n  25 -->|out_file1| 48;\n  49[\"Sort\"];\n  46 -->|output| 49;\n  50[\"Pretext Snapshot\"];\n  47 -->|pretext_map_out| 50;\n  51[\"Busco\"];\n  48 -->|get_seqs_purged| 51;\n  52[\"Quast\"];\n  21 -->|get_seqs_purged| 52;\n  48 -->|get_seqs_purged| 52;\n  10 -->|output| 52;\n  53[\"SALSA\"];\n  49 -->|out_file1| 53;\n  37 -->|outfile| 53;\n  54[\"BWA-MEM2\"];\n  1 -->|output| 54;\n  53 -->|scaffolds_fasta| 54;\n  55[\"BWA-MEM2\"];\n  2 -->|output| 55;\n  53 -->|scaffolds_fasta| 55;\n  56[\"Busco\"];\n  53 -->|scaffolds_fasta| 56;\n  57[\"Quast\"];\n  53 -->|scaffolds_fasta| 57;\n  10 -->|output| 57;\n  58[\"Filter and merge\"];\n  55 -->|bam_output| 58;\n  54 -->|bam_output| 58;\n  59[\"PretextMap\"];\n  58 -->|outfile| 59;\n  60[\"Pretext Snapshot\"];\n  59 -->|pretext_map_out| 60;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "VGP assembly: training workflow",
-                "outputs": [],
-                "parent_id": "assembly/vgp_genome_assembly",
-                "path": "topics/assembly/tutorials/vgp_genome_assembly/workflows/main_workflow.ga",
-                "tags": [
-                    "assembly"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "VGP assembly: training workflow",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-vgp_genome_assembly/versions/main-workflow",
-                "tutorial_id": "vgp_genome_assembly",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/vgp_genome_assembly/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/vgp_genome_assembly/workflows/main_workflow.html",
-                "version": 4,
-                "wfid": "assembly-vgp_genome_assembly",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "Convert characters1",
-                    "cat1",
-                    "sort1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/bionano_scaffold/bionano_scaffold/3.7.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.2.2+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/salsa/salsa/2.3+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
-                ],
-                "workflowhub_id": "1187"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/5887339"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "ddf54b12c295",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "add_value",
-                    "owner": "devteam",
-                    "revisions": "745871c0b055",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_compute_length",
-                    "owner": "devteam",
-                    "revisions": "de2db1bdfbf8",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_filter_by_length",
-                    "owner": "devteam",
-                    "revisions": "e626b3ff9922",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_filter_by_length",
-                    "owner": "devteam",
-                    "revisions": "8cacfcf96a52",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "lastz",
-                    "owner": "devteam",
-                    "revisions": "e7f19d6a9af8",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "merge_cols",
-                    "owner": "devteam",
-                    "revisions": "f2aac0c5c60d",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bedtools",
-                    "owner": "iuc",
-                    "revisions": "e19bebe96cd2",
-                    "tool_panel_section_label": "BED",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bedtools",
-                    "owner": "iuc",
-                    "revisions": "e19bebe96cd2",
-                    "tool_panel_section_label": "BED",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bedtools",
-                    "owner": "iuc",
-                    "revisions": "e19bebe96cd2",
-                    "tool_panel_section_label": "BED",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "circos",
-                    "owner": "iuc",
-                    "revisions": "df7356989ac1",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "circos",
-                    "owner": "iuc",
-                    "revisions": "df7356989ac1",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "datamash_ops",
-                    "owner": "iuc",
-                    "revisions": "562f3c677828",
-                    "tool_panel_section_label": "Join, Subtract and Group",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "jbrowse",
-                    "owner": "iuc",
-                    "revisions": "fd5dbf0f732e",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "25136a2b0cfe",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "830961c48e42",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: ddf54b12c295\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: add_value\n  owner: devteam\n  revisions: 745871c0b055\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_compute_length\n  owner: devteam\n  revisions: de2db1bdfbf8\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_filter_by_length\n  owner: devteam\n  revisions: e626b3ff9922\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_filter_by_length\n  owner: devteam\n  revisions: 8cacfcf96a52\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lastz\n  owner: devteam\n  revisions: e7f19d6a9af8\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merge_cols\n  owner: devteam\n  revisions: f2aac0c5c60d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: e19bebe96cd2\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: e19bebe96cd2\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: e19bebe96cd2\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: circos\n  owner: iuc\n  revisions: df7356989ac1\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: circos\n  owner: iuc\n  revisions: df7356989ac1\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 562f3c677828\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: fd5dbf0f732e\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 25136a2b0cfe\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ecoli_comparison/tutorial.json",
-        "contributors": [
-            {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
-                "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
-            },
-            {
-                "email": "delphine.lariviere@galaxy.org",
-                "id": "delphine-l",
-                "joined": "2017-09",
-                "name": "Delphine Lariviere",
-                "orcid": "0000-0001-6421-3484",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            }
-        ],
-        "dir": "topics/assembly/tutorials/ecoli_comparison",
-        "edam_ontology": [
-            "topic_0196",
-            "topic_0622",
-            "topic_3301"
-        ],
-        "edam_operation": [
-            "Genome visualisation",
-            "Sequence alignment",
-            "Mapping",
-            "Read mapping",
-            "Sequence visualisation"
-        ],
-        "edam_topic": [
-            "Sequence assembly",
-            "Genomics",
-            "Microbiology"
-        ],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "assembly/ecoli_comparison",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "We learned how to download large sets of completed genomes from NCBI",
-            "We learned how to use Galaxy's rule-based collection builder",
-            "We learned how to use a combination of Galaxy tools to create complex views of genome comparisons",
-            "We learned about idiosyncrasies of data formats and how to deal with them using Galaxy tools"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-24",
-        "objectives": [
-            "Identification of the most closely related genome to my new assembly",
-            "Perform sequence comparison to locate rearrangements",
-            "Identify genes located in deletions"
-        ],
-        "pageviews": 12067,
-        "pub_date": "2018-06-14",
-        "questions": [
-            "I just assembled a genome. How does it compare with already sequenced genomes?",
-            "How do I find rearranged, inserted, or deleted regions?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "assembly",
-                "tutorials": [
-                    "unicycler-assembly"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00032",
-        "short_tools": [
-            "circos",
-            "lastz_wrapper_2",
-            "random_lines1",
-            "Cut1",
-            "circos_interval_to_tiles",
-            "addValue",
-            "collapse_dataset",
-            "Grep1",
-            "datamash_ops",
-            "bedtools_sortbed",
-            "tp_sort_header_tool",
-            "bedtools_complementbed",
-            "tp_replace_in_column",
-            "circos_aln_to_links",
-            "cat1",
-            "tp_cat",
-            "fasta_filter_by_length",
-            "Filter1",
-            "tp_sed_tool",
-            "fasta_compute_length",
-            "tp_replace_in_line",
-            "join1",
-            "upload1",
-            "jbrowse",
-            "bedtools_intersectbed",
-            "tp_grep_tool",
-            "mergeCols1"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "gmod",
-            "prokaryote",
-            "microgalaxy",
-            "jbrowse1"
-        ],
-        "time_estimation": "4h",
-        "title": "Making sense of a newly assembled genome",
-        "tools": [
-            "Cut1",
-            "Filter1",
-            "Grep1",
-            "cat1",
-            "join1",
-            "random_lines1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.27.0.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.0.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7",
-            "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7",
-            "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tiles/0.69.8+galaxy7",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.8+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
-            "upload1"
-        ],
-        "topic_name": "assembly",
-        "topic_name_human": "Assembly",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "ecoli_comparison",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ecoli_comparison/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ecoli_comparison/tutorial.json"
-        },
-        "version": 29,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 182,
-        "visitors": 5938,
-        "workflows": [
+                        "post_job_actions": {
+                            "HideDatasetActionlog_read_length": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "log_read_length"
+                            },
+                            "HideDatasetActionnanostats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "nanostats"
+                            },
+                            "HideDatasetActionnanostats_post_filtering": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "nanostats_post_filtering"
+                            },
+                            "HideDatasetActionread_length": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "read_length"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "a02b8b3f5a0c",
+                            "name": "nanoplot",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"customization\": {\"color\": null, \"plots\": null, \"N50\": false}, \"filter\": {\"maxlength\": null, \"minlength\": null, \"drop_outliers\": false, \"downsample\": null, \"loglength\": false, \"percentqual\": false, \"alength\": false, \"minqual\": null, \"runtime_until\": null, \"readtype\": null, \"barcoded\": false, \"no_supplementary\": false}, \"mode\": {\"choice\": \"batch\", \"__current_case__\": 0, \"reads\": {\"type\": \"fastq\", \"__current_case__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.42.0+galaxy1",
+                        "type": "tool",
+                        "uuid": "3b8a87fe-1506-48d2-a4d9-f4dca8b6065d",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "NanoPlot on input dataset(s): HTML report",
+                                "output_name": "output_html",
+                                "uuid": "73d0e4cf-366e-41c1-810a-b269638826b3"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "results_0|software_cond|output_0|input": {
+                                "id": 4,
+                                "output_name": "text_file"
+                            },
+                            "results_0|software_cond|output_1|input": {
+                                "id": 5,
+                                "output_name": "text_file"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "MultiQC: combine fastQC reports",
+                        "name": "MultiQC",
+                        "outputs": [
+                            {
+                                "name": "stats",
+                                "type": "input"
+                            },
+                            {
+                                "name": "html_report",
+                                "type": "html"
+                            }
+                        ],
+                        "position": {
+                            "left": 1233.5,
+                            "top": 230.844970703125
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "abfd8a6544d7",
+                            "name": "multiqc",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.11+galaxy1",
+                        "type": "tool",
+                        "uuid": "3e29a59b-dca0-4993-b20d-495a3f17e291",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "MultiQC on input dataset(s): Webpage",
+                                "output_name": "html_report",
+                                "uuid": "8baf8700-876e-4a74-ad99-6e656f3ba618"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "assembly/largegenome",
+                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Data_QC.ga",
+                "tags": [
+                    "LG-WF",
+                    "GTN"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Data QC - upgraded",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-data-qc",
+                "tutorial_id": "largegenome",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Data_QC.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Data_QC.html",
+                "version": 2,
+                "wfid": "assembly-largegenome",
+                "wfname": "galaxy-workflow-data-qc",
+                "workflow": "Galaxy-Workflow-Data_QC.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1"
+                ],
+                "workflowhub_id": "1162"
+            },
             {
-                "creators": [],
-                "description": "Making sense of a newly assembled genome",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
+                    }
+                ],
+                "description": "",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  10[label=\"Collapse Collection\"]\n  6 -> 10 [label=\"output\"]\n  11[label=\"Text transformation\"]\n  7 -> 11 [label=\"output\"]\n  12[label=\"Add column\"]\n  8 -> 12 [label=\"out_file1\"]\n  13[label=\"LASTZ\"]\n  9 -> 13 [label=\"output\"]\n  3 -> 13 [label=\"output\"]\n  14[label=\"random_lines1\"]\n  10 -> 14 [label=\"output\"]\n  15[label=\"Filter\"]\n  10 -> 15 [label=\"output\"]\n  16[label=\"Search in textfiles\"]\n  11 -> 16 [label=\"output\"]\n  17[label=\"Concatenate datasets\"]\n  11 -> 17 [label=\"output\"]\n  9 -> 17 [label=\"output\"]\n  18[label=\"Cut\"]\n  12 -> 18 [label=\"out_file1\"]\n  19[label=\"Text transformation\"]\n  13 -> 19 [label=\"output\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  20[label=\"Datamash\"]\n  15 -> 20 [label=\"out_file1\"]\n  21[label=\"Compute sequence length\"]\n  17 -> 21 [label=\"out_file1\"]\n  22[label=\"Collapse Collection\"]\n  18 -> 22 [label=\"out_file1\"]\n  23[label=\"Merge Columns\"]\n  19 -> 23 [label=\"output\"]\n  24[label=\"Select\"]\n  20 -> 24 [label=\"out_file\"]\n  25[label=\"Sort\"]\n  21 -> 25 [label=\"output\"]\n  26[label=\"Collapse Collection\"]\n  23 -> 26 [label=\"out_file1\"]\n  27[label=\"Cut\"]\n  26 -> 27 [label=\"output\"]\n  28[label=\"Cut\"]\n  26 -> 28 [label=\"output\"]\n  29[label=\"Concatenate datasets\"]\n  27 -> 29 [label=\"out_file1\"]\n  28 -> 29 [label=\"out_file1\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  30[label=\"SortBED\"]\n  29 -> 30 [label=\"out_file1\"]\n  31[label=\"ComplementBed\"]\n  25 -> 31 [label=\"outfile\"]\n  30 -> 31 [label=\"output\"]\n  32[label=\"Filter\"]\n  31 -> 32 [label=\"output\"]\n  33[label=\"Filter\"]\n  32 -> 33 [label=\"out_file1\"]\n  34[label=\"Intersect intervals\"]\n  33 -> 34 [label=\"out_file1\"]\n  22 -> 34 [label=\"output\"]\n  35[label=\"Join two Datasets\"]\n  34 -> 35 [label=\"output\"]\n  1 -> 35 [label=\"output\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  5[label=\"Filter sequences by length\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"LASTZ\"]\n  2 -> 6 [label=\"output\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Collapse Collection\"]\n  3 -> 7 [label=\"output\"]\n  8[label=\"Select\"]\n  4 -> 8 [label=\"output\"]\n  9[label=\"Text transformation\"]\n  5 -> 9 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads, R1, in fastq.gz format\"]\n  2[label=\"Minimap2 round 1: map reads to assembly\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Racon round 1: polish assembly\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"alignment_output\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Minimap2 round 2: map reads to assembly\"]\n  1 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"consensus\"]\n  5[label=\"Racon round 2: polish assembly\"]\n  3 -> 5 [label=\"consensus\"]\n  4 -> 5 [label=\"alignment_output\"]\n  1 -> 5 [label=\"output\"]\n  k594819c3668e4575b9a64459ffacf952[color=lightseagreen,label=\"Output\\nAssembly polished by short reads using Racon\"]\n  5 -> k594819c3668e4575b9a64459ffacf952\n}",
                 "history": [
                     {
-                        "hash": "48cf52ea88fe32cfc059494bc1b464c4b202bf99",
-                        "message": "on purpose mistake fixed",
-                        "num": 6,
-                        "short_hash": "48cf52ea8",
-                        "unix": "1579772724"
-                    },
-                    {
-                        "hash": "b3f79801438efc81c5f2a3f0af17a26f82e6913e",
-                        "message": "test",
+                        "hash": "3be0312ca5a2e27bc1f8573e28943833be988894",
+                        "message": "Update Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga",
                         "num": 5,
-                        "short_hash": "b3f798014",
-                        "unix": "1579714684"
+                        "short_hash": "3be0312ca",
+                        "unix": "1715074403"
                     },
                     {
-                        "hash": "230f6e12fc9de41c8cb554a353e0b816eb656724",
-                        "message": "linting fix",
+                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
+                        "message": "new versions of workflows",
                         "num": 4,
-                        "short_hash": "230f6e12f",
-                        "unix": "1579705852"
+                        "short_hash": "e8ddbcdd5",
+                        "unix": "1714537936"
                     },
                     {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
+                        "hash": "7d222309ffbec070126e3e749ba6f3d4e510cc6e",
+                        "message": "Rename Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga to Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2_old.ga",
                         "num": 3,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
+                        "short_hash": "7d222309f",
+                        "unix": "1714537293"
                     },
                     {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
+                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
+                        "message": "add/complete creator info on workflows",
                         "num": 2,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
+                        "short_hash": "62e77944b",
+                        "unix": "1676627603"
                     },
                     {
-                        "hash": "485411d09f88e53fb83bc584da92afa171aed32a",
-                        "message": "workflow for ecoli_comparison",
+                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
+                        "message": "large genome tutorial",
                         "num": 1,
-                        "short_hash": "485411d09",
-                        "unix": "1546963139"
+                        "short_hash": "9fcb3aeec",
+                        "unix": "1665123856"
                     }
                 ],
                 "inputs": [
@@ -20691,21 +22291,22 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Ecoli_C_assembly.fna"
+                                "name": "Assembly to be polished"
                             }
                         ],
-                        "label": null,
+                        "label": "Assembly to be polished",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 10
+                            "left": 0,
+                            "top": 72.5176329833982
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"Ecoli_C_assembly.fna\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "2eb3a31a-f5ec-4ce0-a4db-f421ab573412",
+                        "uuid": "28669894-74e2-4ba1-9d49-6e3209b5a1de",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
@@ -20717,504 +22318,169 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "inline-supplementary-material-7 - Table_S4_Essential genes identi.tsv"
+                                "name": "Illumina reads, R1, in fastq.gz format"
                             }
                         ],
-                        "label": null,
+                        "label": "Illumina reads, R1, in fastq.gz format",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 130
+                            "left": 8.5,
+                            "top": 341.2832579833982
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"inline-supplementary-material-7 - Table_S4_Essential genes identi.tsv\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ac567420-400d-4a74-adb5-cdaed90cebd6",
+                        "uuid": "bc936fdc-22a9-4507-aa47-4a70a3f93923",
+                        "when": null,
                         "workflow_outputs": []
-                    },
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nIllumina reads, R1, in fastq.gz format\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Minimap2 round 1: map reads to assembly\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Racon round 1: polish assembly\"];\n  0 -->|output| 3;\n  2 -->|alignment_output| 3;\n  1 -->|output| 3;\n  4[\"Minimap2 round 2: map reads to assembly\"];\n  1 -->|output| 4;\n  3 -->|consensus| 4;\n  5[\"Racon round 2: polish assembly\"];\n  3 -->|consensus| 5;\n  4 -->|alignment_output| 5;\n  1 -->|output| 5;\n  594819c3-668e-4575-b9a6-4459ffacf952[\"Output\\nAssembly polished by short reads using Racon\"];\n  5 --> 594819c3-668e-4575-b9a6-4459ffacf952;\n  style 594819c3-668e-4575-b9a6-4459ffacf952 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Input Dataset Collection"
+                        "id": 5,
+                        "input_connections": {
+                            "corrected_reads": {
+                                "id": 3,
+                                "output_name": "consensus"
+                            },
+                            "overlaps": {
+                                "id": 4,
+                                "output_name": "alignment_output"
+                            },
+                            "reads": {
+                                "id": 1,
+                                "output_name": "output"
                             }
-                        ],
-                        "label": null,
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 250
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "8cc3e0ac-13bd-4e29-83dc-8411490fc85d",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": "Racon round 2: polish assembly",
+                        "name": "Racon",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Input Dataset Collection"
+                                "name": "consensus",
+                                "type": "fasta"
                             }
                         ],
-                        "label": null,
-                        "name": "Input dataset collection",
-                        "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 370
+                            "left": 1198.765625,
+                            "top": 332.4707579833982
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "6bc17455-70a4-48bb-a511-e484016e9ad8",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Input Dataset Collection"
+                        "post_job_actions": {
+                            "RenameDatasetActionconsensus": {
+                                "action_arguments": {
+                                    "newname": "Racon_short_reads_polished_assembly.fasta"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "consensus"
                             }
-                        ],
-                        "label": null,
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 490
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "04145efc-b9a4-4bd4-9a72-7cdf0e98e752",
-                        "workflow_outputs": []
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "78c533842eeb",
+                            "name": "racon",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.5.0+galaxy1",
+                        "type": "tool",
+                        "uuid": "b3c89c40-3ad0-454c-a4d4-dfa34fb09f24",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Assembly polished by short reads using Racon",
+                                "output_name": "consensus",
+                                "uuid": "594819c3-668e-4575-b9a6-4459ffacf952"
+                            }
+                        ]
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Collapse Collection\"];\n  6 -->|output| 10;\n  11[\"Text transformation\"];\n  7 -->|output| 11;\n  12[\"Add column\"];\n  8 -->|out_file1| 12;\n  13[\"LASTZ\"];\n  9 -->|output| 13;\n  3 -->|output| 13;\n  14[\"random_lines1\"];\n  10 -->|output| 14;\n  15[\"Filter\"];\n  10 -->|output| 15;\n  16[\"Search in textfiles\"];\n  11 -->|output| 16;\n  17[\"Concatenate datasets\"];\n  11 -->|output| 17;\n  9 -->|output| 17;\n  18[\"Cut\"];\n  12 -->|out_file1| 18;\n  19[\"Text transformation\"];\n  13 -->|output| 19;\n  2[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  20[\"Datamash\"];\n  15 -->|out_file1| 20;\n  21[\"Compute sequence length\"];\n  17 -->|out_file1| 21;\n  22[\"Collapse Collection\"];\n  18 -->|out_file1| 22;\n  23[\"Merge Columns\"];\n  19 -->|output| 23;\n  24[\"Select\"];\n  20 -->|out_file| 24;\n  25[\"Sort\"];\n  21 -->|output| 25;\n  26[\"Collapse Collection\"];\n  23 -->|out_file1| 26;\n  27[\"Cut\"];\n  26 -->|output| 27;\n  28[\"Cut\"];\n  26 -->|output| 28;\n  29[\"Concatenate datasets\"];\n  27 -->|out_file1| 29;\n  28 -->|out_file1| 29;\n  3[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  30[\"SortBED\"];\n  29 -->|out_file1| 30;\n  31[\"ComplementBed\"];\n  25 -->|outfile| 31;\n  30 -->|output| 31;\n  32[\"Filter\"];\n  31 -->|output| 32;\n  33[\"Filter\"];\n  32 -->|out_file1| 33;\n  34[\"Intersect intervals\"];\n  33 -->|out_file1| 34;\n  22 -->|output| 34;\n  35[\"Join two Datasets\"];\n  34 -->|output| 35;\n  1 -->|output| 35;\n  4[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Filter sequences by length\"];\n  0 -->|output| 5;\n  6[\"LASTZ\"];\n  2 -->|output| 6;\n  0 -->|output| 6;\n  7[\"Collapse Collection\"];\n  3 -->|output| 7;\n  8[\"Select\"];\n  4 -->|output| 8;\n  9[\"Text transformation\"];\n  5 -->|output| 9;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Ecoli Comparison",
-                "outputs": [],
-                "parent_id": "assembly/ecoli_comparison",
-                "path": "topics/assembly/tutorials/ecoli_comparison/workflows/ecoli-comparison.ga",
+                "parent_id": "assembly/largegenome",
+                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga",
                 "tags": [
-                    "assembly"
+                    "LG-WF",
+                    "GTN"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Ecoli Comparison",
+                "title": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
                 "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-ecoli_comparison/versions/ecoli-comparison",
-                "tutorial_id": "ecoli_comparison",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/ecoli_comparison/workflows/ecoli-comparison.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/ecoli_comparison/workflows/ecoli-comparison.html",
-                "version": 3,
-                "wfid": "assembly-ecoli_comparison",
-                "wfname": "ecoli-comparison",
-                "workflow": "ecoli-comparison.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-racon-polish-with-illumina-reads-x2",
+                "tutorial_id": "largegenome",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.html",
+                "version": 2,
+                "wfid": "assembly-largegenome",
+                "wfname": "galaxy-workflow-racon-polish-with-illumina-reads-x2",
+                "workflow": "Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "Filter1",
-                    "Grep1",
-                    "cat1",
-                    "join1",
-                    "random_lines1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.27.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0"
-                ],
-                "workflowhub_id": "1113"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/3382053"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "bowtie2",
-                    "owner": "devteam",
-                    "revisions": "749c918495f7",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_filter_by_length",
-                    "owner": "devteam",
-                    "revisions": "8cacfcf96a52",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_stats",
-                    "owner": "devteam",
-                    "revisions": "145f6d74ff5e",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bandage",
-                    "owner": "iuc",
-                    "revisions": "b2860df42e16",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bandage",
-                    "owner": "iuc",
-                    "revisions": "94fe43e75ddc",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastp",
-                    "owner": "iuc",
-                    "revisions": "1d8fe9bc4cb0",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "minimap2",
-                    "owner": "iuc",
-                    "revisions": "53c0b7a1a0c3",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "b2f1f75d49c4",
-                    "tool_panel_section_label": "Quality Control",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "nanoplot",
-                    "owner": "iuc",
-                    "revisions": "645159bcee2d",
-                    "tool_panel_section_label": "Nanopore",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_fastx",
-                    "owner": "iuc",
-                    "revisions": "a8d69aee190e",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_view",
-                    "owner": "iuc",
-                    "revisions": "b01db2684fa5",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "seqtk",
-                    "owner": "iuc",
-                    "revisions": "3da72230c066",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "sra_tools",
-                    "owner": "iuc",
-                    "revisions": "aad3885b3216",
-                    "tool_panel_section_label": "Get Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "unicycler",
-                    "owner": "iuc",
-                    "revisions": "9e3e80cc4ad4",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "830961c48e42",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bowtie2\n  owner: devteam\n  revisions: 749c918495f7\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_filter_by_length\n  owner: devteam\n  revisions: 8cacfcf96a52\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 145f6d74ff5e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: b2860df42e16\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: 94fe43e75ddc\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 1d8fe9bc4cb0\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: 53c0b7a1a0c3\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: b2f1f75d49c4\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: 645159bcee2d\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_fastx\n  owner: iuc\n  revisions: a8d69aee190e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: b01db2684fa5\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: aad3885b3216\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unicycler\n  owner: iuc\n  revisions: 9e3e80cc4ad4\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "by-covid",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "fediverse": "https://scholar.social/@zerodivision",
-                "fediverse_flavor": "mastodon",
-                "id": "wm75",
-                "joined": "2017-09",
-                "matrix": "wm75:matrix.org",
-                "name": "Wolfgang Maier",
-                "orcid": "0000-0002-9464-6640",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
-            }
-        ],
-        "dir": "topics/assembly/tutorials/assembly-with-preprocessing",
-        "edam_operation": [
-            "Sequencing quality control",
-            "Sequence contamination filtering",
-            "Sequence file editing",
-            "Box-Whisker plot plotting",
-            "Read mapping",
-            "Pairwise sequence alignment",
-            "Scatter plot plotting",
-            "Sequence assembly visualisation",
-            "Data handling",
-            "Validation",
-            "Genome assembly",
-            "Aggregation"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "assembly/assembly-with-preprocessing",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Certain types of NGS samples can be heavily contaminated with sequences from other genomes",
-            "Reads from known/expected contaminating sources can be identified by mapping to the respective genomes",
-            "After mapping, use filtering tools to remove identified contaminating reads, and use conversion tools to convert remaining mapped reads back into raw sequenced reads expected by most downstream tools"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
-        "objectives": [
-            "Obtain viral (SARS-CoV-2) sequencing data with contaminating human reads from public sources",
-            "Organize the data into collections and check its quality",
-            "Detect and remove human reads",
-            "Assemble retained reads and explore the results"
-        ],
-        "pageviews": 5734441,
-        "pub_date": "2020-04-21",
-        "questions": [
-            "How can a genome of interest be assembled against a background of contaminating reads from other genomes?",
-            "How can sequencing data from public sources be turned into assembly-ready polished datasets?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "mtekman"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "25M",
-                "speakers": [
-                    "gallardoalba"
-                ],
-                "youtube_id": "jNFLYhjgJPs"
-            }
-        ],
-        "requirements": [
-            {
-                "topic_name": "assembly",
-                "tutorials": [
-                    "unicycler-assembly"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "sequence-analysis",
-                "tutorials": [
-                    "mapping"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0"
                 ],
-                "type": "internal"
+                "workflowhub_id": "1148"
             },
             {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "collections"
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
+                    }
                 ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00029",
-        "short_tools": [
-            "samtools_stats",
-            "nanoplot",
-            "fastp",
-            "samtools_view",
-            "multiqc",
-            "samtools_fastx",
-            "__ZIP_COLLECTION__",
-            "bowtie2",
-            "fasterq_dump",
-            "fasta_filter_by_length",
-            "seqtk_sample",
-            "bandage_info",
-            "minimap2",
-            "bandage_image",
-            "unicycler",
-            "collapse_dataset"
-        ],
-        "slides": true,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "covid19"
-        ],
-        "time_estimation": "4h",
-        "title": "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads",
-        "tools": [
-            "__ZIP_COLLECTION__",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
-        ],
-        "topic_name": "assembly",
-        "topic_name_human": "Assembly",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "assembly-with-preprocessing",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.json"
-        },
-        "version": 13,
-        "video": false,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 363,
-        "visitors": 2068028,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Assembly with preprocessing",
+                "description": "",
                 "features": {
                     "comments": false,
-                    "parameters": false,
-                    "report": null,
+                    "parameters": true,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                    },
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nCollection of paired short-reads data\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nCollection of long-reads data\"]\n  10[label=\"Samtools fastx\"]\n  7 -> 10 [label=\"outputsam\"]\n  11[label=\"Samtools fastx\"]\n  9 -> 11 [label=\"outputsam\"]\n  12[label=\"Collapse Collection\"]\n  10 -> 12 [label=\"nonspecific\"]\n  13[label=\"Zip Collection\"]\n  11 -> 13 [label=\"forward\"]\n  11 -> 13 [label=\"reverse\"]\n  14[label=\"Collapse Collection\"]\n  11 -> 14 [label=\"forward\"]\n  15[label=\"Collapse Collection\"]\n  11 -> 15 [label=\"reverse\"]\n  16[label=\"seqtk_sample\"]\n  14 -> 16 [label=\"output\"]\n  17[label=\"seqtk_sample\"]\n  15 -> 17 [label=\"output\"]\n  18[label=\"Create assemblies with Unicycler\"]\n  12 -> 18 [label=\"output\"]\n  16 -> 18 [label=\"default\"]\n  17 -> 18 [label=\"default\"]\n  19[label=\"Bandage Info\"]\n  18 -> 19 [label=\"assembly_graph\"]\n  2[label=\"fastp: Trimmed Illumina Reads\"]\n  0 -> 2 [label=\"output\"]\n  20[label=\"Filter sequences by length\"]\n  18 -> 20 [label=\"assembly\"]\n  21[label=\"Bandage Image\"]\n  18 -> 21 [label=\"assembly_graph\"]\n  3[label=\"NanoPlot\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Map with minimap2\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"MultiQC\"]\n  2 -> 5 [label=\"report_json\"]\n  6[label=\"Bowtie2\"]\n  2 -> 6 [label=\"output_paired_coll\"]\n  7[label=\"Samtools view\"]\n  4 -> 7 [label=\"alignment_output\"]\n  8[label=\"Samtools stats\"]\n  4 -> 8 [label=\"alignment_output\"]\n  9[label=\"Samtools view\"]\n  6 -> 9 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads \"]\n  3[label=\"Minimap2: map long reads to assembly\"]\n  2 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Racon: polish 1\"]\n  0 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"alignment_output\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Minimap2: map long reads to polished assembly 1\"]\n  2 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  4 -> 5 [label=\"consensus\"]\n  6[label=\"Racon: polish 2\"]\n  4 -> 6 [label=\"consensus\"]\n  5 -> 6 [label=\"alignment_output\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"Minimap2: map long reads to polished assembly 2\"]\n  2 -> 7 [label=\"output\"]\n  1 -> 7 [label=\"output\"]\n  6 -> 7 [label=\"consensus\"]\n  8[label=\"Racon: polish 3\"]\n  6 -> 8 [label=\"consensus\"]\n  7 -> 8 [label=\"alignment_output\"]\n  1 -> 8 [label=\"output\"]\n  9[label=\"Minimap2: map long reads to polished assembly 3\"]\n  2 -> 9 [label=\"output\"]\n  1 -> 9 [label=\"output\"]\n  8 -> 9 [label=\"consensus\"]\n  10[label=\"Racon: polish 4\"]\n  8 -> 10 [label=\"consensus\"]\n  9 -> 10 [label=\"alignment_output\"]\n  1 -> 10 [label=\"output\"]\n  kbcf0f03c595146a7aa38545aed9bc183[color=lightseagreen,label=\"Output\\nAssembly polished by long reads using Racon\"]\n  10 -> kbcf0f03c595146a7aa38545aed9bc183\n}",
                 "history": [
                     {
-                        "hash": "fc35e6581a2e34e4420f19af4619c92283609e91",
-                        "message": "add annotations",
+                        "hash": "ea8cb9df4cc68241e9b406bde825b4c16647280b",
+                        "message": "Update Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga",
+                        "num": 5,
+                        "short_hash": "ea8cb9df4",
+                        "unix": "1715074423"
+                    },
+                    {
+                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
+                        "message": "new versions of workflows",
+                        "num": 4,
+                        "short_hash": "e8ddbcdd5",
+                        "unix": "1714537936"
+                    },
+                    {
+                        "hash": "7bd7c55df24dd71009cbde6408fb87d49901a84a",
+                        "message": "Rename Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga to Galaxy-Workflow-Racon_polish_with_long_reads_x4_old.ga",
+                        "num": 3,
+                        "short_hash": "7bd7c55df",
+                        "unix": "1714537311"
+                    },
+                    {
+                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
+                        "message": "add/complete creator info on workflows",
                         "num": 2,
-                        "short_hash": "fc35e6581",
-                        "unix": "1587558793"
+                        "short_hash": "62e77944b",
+                        "unix": "1676627603"
                     },
                     {
-                        "hash": "7ed054469d1ef84a60abec55758ee2932f9a9655",
-                        "message": "readd workflows",
+                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
+                        "message": "large genome tutorial",
                         "num": 1,
-                        "short_hash": "7ed054469",
-                        "unix": "1587555276"
+                        "short_hash": "9fcb3aeec",
+                        "unix": "1665123856"
                     }
                 ],
                 "inputs": [
@@ -21224,26 +22490,26 @@
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "Collection of paired short-reads data",
-                        "name": "Input dataset collection",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Assembly to be polished"
+                            }
+                        ],
+                        "label": "Assembly to be polished",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 268.13330078125,
-                            "top": 341.41668701171875
+                            "left": 0,
+                            "top": 216.625
                         },
                         "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list:paired\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "3e7dab04-77db-4780-b1dd-c724b80a8b7b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "daba9931-3837-42b5-a93f-e2e51f5f667a"
-                            }
-                        ]
+                        "type": "data_input",
+                        "uuid": "c7796c36-adf8-49e4-a8e4-66e606d70311",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
@@ -21251,414 +22517,469 @@
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "Collection of long-reads data",
-                        "name": "Input dataset collection",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "long reads"
+                            }
+                        ],
+                        "label": "long reads",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 267.13330078125,
-                            "top": 756.4166717529297
+                            "left": 4.5,
+                            "top": 360.234375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"lis\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "bd1f5561-95a1-4fb5-af1e-f3d4cbb40639",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "7146e49b-ab4b-44a8-ac54-e98539fecb97"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nCollection of paired short-reads data\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nCollection of long-reads data\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Samtools fastx\"];\n  7 -->|outputsam| 10;\n  11[\"Samtools fastx\"];\n  9 -->|outputsam| 11;\n  12[\"Collapse Collection\"];\n  10 -->|nonspecific| 12;\n  13[\"Zip Collection\"];\n  11 -->|forward| 13;\n  11 -->|reverse| 13;\n  14[\"Collapse Collection\"];\n  11 -->|forward| 14;\n  15[\"Collapse Collection\"];\n  11 -->|reverse| 15;\n  16[\"seqtk_sample\"];\n  14 -->|output| 16;\n  17[\"seqtk_sample\"];\n  15 -->|output| 17;\n  18[\"Create assemblies with Unicycler\"];\n  12 -->|output| 18;\n  16 -->|default| 18;\n  17 -->|default| 18;\n  19[\"Bandage Info\"];\n  18 -->|assembly_graph| 19;\n  2[\"fastp: Trimmed Illumina Reads\"];\n  0 -->|output| 2;\n  20[\"Filter sequences by length\"];\n  18 -->|assembly| 20;\n  21[\"Bandage Image\"];\n  18 -->|assembly_graph| 21;\n  3[\"NanoPlot\"];\n  1 -->|output| 3;\n  4[\"Map with minimap2\"];\n  1 -->|output| 4;\n  5[\"MultiQC\"];\n  2 -->|report_json| 5;\n  6[\"Bowtie2\"];\n  2 -->|output_paired_coll| 6;\n  7[\"Samtools view\"];\n  4 -->|alignment_output| 7;\n  8[\"Samtools stats\"];\n  4 -->|alignment_output| 8;\n  9[\"Samtools view\"];\n  6 -->|output| 9;",
-                "modified": "2024-08-18 00:06:20 +0000",
-                "name": "assembly_with_preprocessing",
-                "outputs": [
+                        "type": "data_input",
+                        "uuid": "e2e4a70b-6e36-4b8b-bdf6-12b97189a6bd",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 2,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "Collection of paired short-reads data",
-                        "name": "Input dataset collection",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "minimap setting (for long reads) "
+                            }
+                        ],
+                        "label": "minimap setting (for long reads) ",
+                        "name": "Input parameter",
                         "outputs": [],
                         "position": {
-                            "left": 268.13330078125,
-                            "top": 341.41668701171875
+                            "left": 0.578125,
+                            "top": 495.859375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list:paired\"}",
+                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "3e7dab04-77db-4780-b1dd-c724b80a8b7b",
+                        "type": "parameter_input",
+                        "uuid": "fb80c05c-08d4-4ac2-b4bf-81ed906e4d72",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "daba9931-3837-42b5-a93f-e2e51f5f667a"
+                                "uuid": "3983ef22-5f05-4384-8f34-6ac8c4b2cc83"
                             }
                         ]
-                    },
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads \"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"Minimap2: map long reads to assembly\"];\n  2 -->|output| 3;\n  1 -->|output| 3;\n  0 -->|output| 3;\n  4[\"Racon: polish 1\"];\n  0 -->|output| 4;\n  3 -->|alignment_output| 4;\n  1 -->|output| 4;\n  5[\"Minimap2: map long reads to polished assembly 1\"];\n  2 -->|output| 5;\n  1 -->|output| 5;\n  4 -->|consensus| 5;\n  6[\"Racon: polish 2\"];\n  4 -->|consensus| 6;\n  5 -->|alignment_output| 6;\n  1 -->|output| 6;\n  7[\"Minimap2: map long reads to polished assembly 2\"];\n  2 -->|output| 7;\n  1 -->|output| 7;\n  6 -->|consensus| 7;\n  8[\"Racon: polish 3\"];\n  6 -->|consensus| 8;\n  7 -->|alignment_output| 8;\n  1 -->|output| 8;\n  9[\"Minimap2: map long reads to polished assembly 3\"];\n  2 -->|output| 9;\n  1 -->|output| 9;\n  8 -->|consensus| 9;\n  10[\"Racon: polish 4\"];\n  8 -->|consensus| 10;\n  9 -->|alignment_output| 10;\n  1 -->|output| 10;\n  bcf0f03c-5951-46a7-aa38-545aed9bc183[\"Output\\nAssembly polished by long reads using Racon\"];\n  10 --> bcf0f03c-5951-46a7-aa38-545aed9bc183;\n  style bcf0f03c-5951-46a7-aa38-545aed9bc183 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Racon polish with long reads, x4 - upgraded",
+                "outputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 2,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "Collection of long-reads data",
-                        "name": "Input dataset collection",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "minimap setting (for long reads) "
+                            }
+                        ],
+                        "label": "minimap setting (for long reads) ",
+                        "name": "Input parameter",
                         "outputs": [],
                         "position": {
-                            "left": 267.13330078125,
-                            "top": 756.4166717529297
+                            "left": 0.578125,
+                            "top": 495.859375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"lis\"}",
+                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "bd1f5561-95a1-4fb5-af1e-f3d4cbb40639",
+                        "type": "parameter_input",
+                        "uuid": "fb80c05c-08d4-4ac2-b4bf-81ed906e4d72",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "7146e49b-ab4b-44a8-ac54-e98539fecb97"
+                                "uuid": "3983ef22-5f05-4384-8f34-6ac8c4b2cc83"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
                         "errors": null,
                         "id": 10,
                         "input_connections": {
-                            "input": {
-                                "id": 7,
-                                "output_name": "outputsam"
+                            "corrected_reads": {
+                                "id": 8,
+                                "output_name": "consensus"
+                            },
+                            "overlaps": {
+                                "id": 9,
+                                "output_name": "alignment_output"
+                            },
+                            "reads": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Samtools fastx",
+                        "label": "Racon: polish 4",
+                        "name": "Racon",
                         "outputs": [
                             {
-                                "name": "nonspecific",
+                                "name": "consensus",
                                 "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 1333.63330078125,
-                            "top": 852.4166717529297
+                            "left": 1496.078125,
+                            "top": 431.1875
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+                        "post_job_actions": {
+                            "RenameDatasetActionconsensus": {
+                                "action_arguments": {
+                                    "newname": "Racon_long_reads_polished_assembly.fasta"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "consensus"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "a8d69aee190e",
-                            "name": "samtools_fastx",
-                            "owner": "iuc",
+                            "changeset_revision": "78c533842eeb",
+                            "name": "racon",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"copy_arb_tags\": \"\\\"\\\"\", \"__page__\": null, \"output_fmt_cond\": \"{\\\"__current_case__\\\": 2, \\\"default_quality\\\": \\\"\\\", \\\"ilumina_casava\\\": \\\"false\\\", \\\"output_fmt_select\\\": \\\"fastqsanger.gz\\\", \\\"output_quality\\\": \\\"false\\\"}\", \"idxout_cond\": \"{\\\"__current_case__\\\": 0, \\\"idxout_select\\\": \\\"no\\\"}\", \"read_numbering\": \"\\\"\\\"\", \"exclusive_filter\": \"null\", \"exclusive_filter_all\": \"null\", \"inclusive_filter\": \"null\", \"outputs\": \"[\\\"r0\\\"]\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"copy_tags\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9+galaxy1",
+                        "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.5.0+galaxy1",
                         "type": "tool",
-                        "uuid": "31e2b4e8-7631-46c0-8382-b805cee2b739",
+                        "uuid": "53f4572e-3a4a-4585-89ab-9459f8a61720",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "nonspecific",
-                                "uuid": "cfbf839f-53f0-4a82-8966-2bdb6919de5e"
+                                "label": "Assembly polished by long reads using Racon",
+                                "output_name": "consensus",
+                                "uuid": "bcf0f03c-5951-46a7-aa38-545aed9bc183"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "assembly/largegenome",
+                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga",
+                "tags": [
+                    "LG-WF",
+                    "GTN"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Racon polish with long reads, x4 - upgraded",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-racon-polish-with-long-reads-x4",
+                "tutorial_id": "largegenome",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_long_reads_x4.html",
+                "version": 2,
+                "wfid": "assembly-largegenome",
+                "wfname": "galaxy-workflow-racon-polish-with-long-reads-x4",
+                "workflow": "Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0"
+                ],
+                "workflowhub_id": "1154"
+            },
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": {
+                        "markdown": "\n# Workflow for Trim and Filter Reads\n\n## Workflow steps\n```galaxy\nworkflow_display()\n```\n\n\n\n\n"
                     },
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads R2\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  3[label=\"fastp on short reads\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  k656e413841ab4561898933de9ac9a2f3[color=lightseagreen,label=\"Output\\nfastp report on short reads html\"]\n  3 -> k656e413841ab4561898933de9ac9a2f3\n  k0d53f347036847cb953a2e4dac57e013[color=lightseagreen,label=\"Output\\nfastp filtered R1 reads\"]\n  3 -> k0d53f347036847cb953a2e4dac57e013\n  k10fbe1e5400c4ffe87949b776b0d7322[color=lightseagreen,label=\"Output\\nfastp report on short reads json\"]\n  3 -> k10fbe1e5400c4ffe87949b776b0d7322\n  k639ed3f70e514e5db6f8081378962109[color=lightseagreen,label=\"Output\\nfastp filtered R2 reads\"]\n  3 -> k639ed3f70e514e5db6f8081378962109\n  4[label=\"fastp on long reads\"]\n  2 -> 4 [label=\"output\"]\n  k5e0d2c3d41a44823ae9cb1e4d2826541[color=lightseagreen,label=\"Output\\nfastp report on long reads html\"]\n  4 -> k5e0d2c3d41a44823ae9cb1e4d2826541\n  ke6018ad686f44e788cf2ccc8b97022fe[color=lightseagreen,label=\"Output\\nfastp filtered long reads\"]\n  4 -> ke6018ad686f44e788cf2ccc8b97022fe\n  k69f8383ba1be4a7495f43dba35e01426[color=lightseagreen,label=\"Output\\nfastp report on long reads json\"]\n  4 -> k69f8383ba1be4a7495f43dba35e01426\n}",
+                "history": [
                     {
-                        "annotation": "",
-                        "content_id": "__ZIP_COLLECTION__",
-                        "errors": null,
-                        "id": 13,
-                        "input_connections": {
-                            "input_forward": {
-                                "id": 11,
-                                "output_name": "forward"
-                            },
-                            "input_reverse": {
-                                "id": 11,
-                                "output_name": "reverse"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Zip Collection",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 1754.63330078125,
-                            "top": 477.41668701171875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "__ZIP_COLLECTION__",
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_reverse\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"input_forward\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "9ba89e81-9c53-4f5b-9d61-42319b7d574c",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "ebc8f563-c45e-4e17-a541-b1275e7f61ad"
-                            }
-                        ]
+                        "hash": "1fe24b92fd7cf3bf693a850751a6215f7b9273bd",
+                        "message": "Update Galaxy-Workflow-Trim_and_filter_reads.ga",
+                        "num": 5,
+                        "short_hash": "1fe24b92f",
+                        "unix": "1715074442"
+                    },
+                    {
+                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
+                        "message": "new versions of workflows",
+                        "num": 4,
+                        "short_hash": "e8ddbcdd5",
+                        "unix": "1714537936"
+                    },
+                    {
+                        "hash": "12f721099e26ef4bd152c1c2b56ccb51e6bd31ab",
+                        "message": "Rename Galaxy-Workflow-Trim_and_filter_reads.ga to Galaxy-Workflow-Trim_and_filter_reads_old.ga",
+                        "num": 3,
+                        "short_hash": "12f721099",
+                        "unix": "1714537350"
+                    },
+                    {
+                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
+                        "message": "add/complete creator info on workflows",
+                        "num": 2,
+                        "short_hash": "62e77944b",
+                        "unix": "1676627603"
                     },
+                    {
+                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
+                        "message": "large genome tutorial",
+                        "num": 1,
+                        "short_hash": "9fcb3aeec",
+                        "unix": "1665123856"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
+                        "content_id": null,
                         "errors": null,
-                        "id": 16,
-                        "input_connections": {
-                            "in_file": {
-                                "id": 14,
-                                "output_name": "output"
-                            }
-                        },
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool seqtk_sample",
-                                "name": "in_file"
-                            }
-                        ],
-                        "label": null,
-                        "name": "seqtk_sample",
-                        "outputs": [
-                            {
-                                "name": "default",
-                                "type": "input"
+                                "description": "",
+                                "name": "Illumina reads R1"
                             }
                         ],
+                        "label": "Illumina reads R1",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2129.4166717529297,
-                            "top": 711.4166717529297
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "58c8ece95b53",
-                            "name": "seqtk",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"s\": \"\\\"4\\\"\", \"in_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"subsample_size\": \"\\\"0.1\\\"\", \"advanced\": \"{\\\"single_pass_mode\\\": \\\"false\\\"}\"}",
-                        "tool_version": "1.3.2",
-                        "type": "tool",
-                        "uuid": "4f7c9133-a664-46dc-9583-c9980d5d1011",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "default",
-                                "uuid": "be52344e-6874-431c-8d86-9d0e9371aed9"
-                            }
-                        ]
+                            "left": 0,
+                            "top": 29.045160466974437
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "00a54054-e3f7-4e4f-9195-563e54df899a",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
+                        "content_id": null,
                         "errors": null,
-                        "id": 17,
-                        "input_connections": {
-                            "in_file": {
-                                "id": 15,
-                                "output_name": "output"
-                            }
-                        },
+                        "id": 1,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool seqtk_sample",
-                                "name": "in_file"
+                                "description": "",
+                                "name": "Illumina reads R2"
                             }
                         ],
-                        "label": null,
-                        "name": "seqtk_sample",
-                        "outputs": [
+                        "label": "Illumina reads R2",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 145.03474842418325
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "14062fd8-1aa9-4a18-94d8-bbbb0e1a9262",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "default",
-                                "type": "input"
+                                "description": "",
+                                "name": "long reads"
                             }
                         ],
+                        "label": "long reads",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2116.4166717529297,
-                            "top": 859.4166717529297
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "58c8ece95b53",
-                            "name": "seqtk",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 576.5103981711648,
+                            "top": 35.50348455255681
                         },
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"s\": \"\\\"4\\\"\", \"in_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"subsample_size\": \"\\\"0.1\\\"\", \"advanced\": \"{\\\"single_pass_mode\\\": \\\"false\\\"}\"}",
-                        "tool_version": "1.3.2",
-                        "type": "tool",
-                        "uuid": "79064891-aa79-42e3-b848-7a6240022acc",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "default",
-                                "uuid": "3e196eb1-8ba1-4be5-90d0-c5b8d3df4ff0"
-                            }
-                        ]
-                    },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "08eeb0d3-6ad6-4e7f-ac6a-d00c8e87fd08",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nIllumina reads R2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"fastp on short reads\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  656e4138-41ab-4561-8989-33de9ac9a2f3[\"Output\\nfastp report on short reads html\"];\n  3 --> 656e4138-41ab-4561-8989-33de9ac9a2f3;\n  style 656e4138-41ab-4561-8989-33de9ac9a2f3 stroke:#2c3143,stroke-width:4px;\n  0d53f347-0368-47cb-953a-2e4dac57e013[\"Output\\nfastp filtered R1 reads\"];\n  3 --> 0d53f347-0368-47cb-953a-2e4dac57e013;\n  style 0d53f347-0368-47cb-953a-2e4dac57e013 stroke:#2c3143,stroke-width:4px;\n  10fbe1e5-400c-4ffe-8794-9b776b0d7322[\"Output\\nfastp report on short reads json\"];\n  3 --> 10fbe1e5-400c-4ffe-8794-9b776b0d7322;\n  style 10fbe1e5-400c-4ffe-8794-9b776b0d7322 stroke:#2c3143,stroke-width:4px;\n  639ed3f7-0e51-4e5d-b6f8-081378962109[\"Output\\nfastp filtered R2 reads\"];\n  3 --> 639ed3f7-0e51-4e5d-b6f8-081378962109;\n  style 639ed3f7-0e51-4e5d-b6f8-081378962109 stroke:#2c3143,stroke-width:4px;\n  4[\"fastp on long reads\"];\n  2 -->|output| 4;\n  5e0d2c3d-41a4-4823-ae9c-b1e4d2826541[\"Output\\nfastp report on long reads html\"];\n  4 --> 5e0d2c3d-41a4-4823-ae9c-b1e4d2826541;\n  style 5e0d2c3d-41a4-4823-ae9c-b1e4d2826541 stroke:#2c3143,stroke-width:4px;\n  e6018ad6-86f4-4e78-8cf2-ccc8b97022fe[\"Output\\nfastp filtered long reads\"];\n  4 --> e6018ad6-86f4-4e78-8cf2-ccc8b97022fe;\n  style e6018ad6-86f4-4e78-8cf2-ccc8b97022fe stroke:#2c3143,stroke-width:4px;\n  69f8383b-a1be-4a74-95f4-3dba35e01426[\"Output\\nfastp report on long reads json\"];\n  4 --> 69f8383b-a1be-4a74-95f4-3dba35e01426;\n  style 69f8383b-a1be-4a74-95f4-3dba35e01426 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Trim and filter reads - fastp - upgraded ",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
                         "errors": null,
-                        "id": 18,
+                        "id": 3,
                         "input_connections": {
-                            "long": {
-                                "id": 12,
+                            "single_paired|in1": {
+                                "id": 0,
                                 "output_name": "output"
                             },
-                            "paired_unpaired|fastq_input1": {
-                                "id": 16,
-                                "output_name": "default"
-                            },
-                            "paired_unpaired|fastq_input2": {
-                                "id": 17,
-                                "output_name": "default"
+                            "single_paired|in2": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "lr_align"
+                                "description": "runtime parameter for tool fastp",
+                                "name": "single_paired"
                             },
                             {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "long"
-                            },
+                                "description": "runtime parameter for tool fastp",
+                                "name": "single_paired"
+                            }
+                        ],
+                        "label": "fastp on short reads",
+                        "name": "fastp",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "paired_unpaired"
+                                "name": "out1",
+                                "type": "input"
                             },
                             {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "paired_unpaired"
+                                "name": "out2",
+                                "type": "input"
                             },
                             {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "rotation"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Create assemblies with Unicycler",
-                        "outputs": [
-                            {
-                                "name": "assembly_graph",
-                                "type": "tabular"
+                                "name": "report_html",
+                                "type": "html"
                             },
                             {
-                                "name": "assembly",
-                                "type": "fasta"
+                                "name": "report_json",
+                                "type": "json"
                             }
                         ],
                         "position": {
-                            "left": 2365.633331298828,
-                            "top": 706.4166717529297
+                            "left": 290.5382191051136,
+                            "top": 0
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
+                        "post_job_actions": {
+                            "DeleteIntermediatesActionout1": {
+                                "action_arguments": {},
+                                "action_type": "DeleteIntermediatesAction",
+                                "output_name": "out1"
+                            },
+                            "RenameDatasetActionout1": {
+                                "action_arguments": {
+                                    "newname": "fastp_filtered_R1.fastq.gz"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out1"
+                            },
+                            "RenameDatasetActionout2": {
+                                "action_arguments": {
+                                    "newname": "fastp_filtered_R2.fastq.gz"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out2"
+                            },
+                            "RenameDatasetActionreport_html": {
+                                "action_arguments": {
+                                    "newname": "fastp_illumina.html"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "report_html"
+                            },
+                            "RenameDatasetActionreport_json": {
+                                "action_arguments": {
+                                    "newname": "fastp_illumina.json"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "report_json"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "88c240872a65",
-                            "name": "unicycler",
+                            "changeset_revision": "c59d48774d03",
+                            "name": "fastp",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"linear_seqs\": \"\\\"1\\\"\", \"spades\": \"{\\\"depth_filter\\\": \\\"0.25\\\", \\\"kmer_count\\\": \\\"10\\\", \\\"kmers\\\": \\\"\\\", \\\"largest_component\\\": \\\"false\\\", \\\"max_kmer_frac\\\": \\\"0.95\\\", \\\"min_kmer_frac\\\": \\\"0.2\\\", \\\"no_correct\\\": \\\"false\\\"}\", \"graph_clean\": \"{\\\"min_component_size\\\": \\\"1000\\\", \\\"min_dead_end_size\\\": \\\"1000\\\"}\", \"__page__\": null, \"min_anchor_seg_len\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"lr_align\": \"{\\\"contamination\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"low_score\\\": \\\"\\\", \\\"scores\\\": \\\"3,-6,-5,-2\\\"}\", \"long\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"paired_unpaired\": \"{\\\"__current_case__\\\": 0, \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"fastq_input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired\\\"}\", \"min_fasta_length\": \"\\\"100\\\"\", \"mode\": \"\\\"normal\\\"\", \"rotation\": \"{\\\"no_rotate\\\": \\\"false\\\", \\\"start_gene_cov\\\": \\\"95.0\\\", \\\"start_gene_id\\\": \\\"90.0\\\", \\\"start_genes\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"pilon\": \"{\\\"min_polish_size\\\": \\\"1000\\\", \\\"no_pilon\\\": \\\"false\\\"}\"}",
-                        "tool_version": "0.4.8.0",
+                        "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired\", \"__current_case__\": 1, \"in1\": {\"__class__\": \"ConnectedValue\"}, \"in2\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": \"\", \"adapter_sequence2\": \"\"}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.23.4+galaxy0",
                         "type": "tool",
-                        "uuid": "851c6be6-c202-450a-9cd3-19e205dcc496",
+                        "uuid": "c38e84b3-771c-428e-9d2d-ce84d5e1153c",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "assembly",
-                                "uuid": "702dd61e-6072-49d9-a502-44e0a23f5a98"
+                                "label": "fastp report on short reads html",
+                                "output_name": "report_html",
+                                "uuid": "656e4138-41ab-4561-8989-33de9ac9a2f3"
                             },
                             {
-                                "label": null,
-                                "output_name": "assembly_graph",
-                                "uuid": "3285cc00-6b39-4f3d-87a5-87abd483ede6"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
-                        "errors": null,
-                        "id": 19,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 18,
-                                "output_name": "assembly_graph"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Bandage Info",
-                        "outputs": [
+                                "label": "fastp filtered R1 reads",
+                                "output_name": "out1",
+                                "uuid": "0d53f347-0368-47cb-953a-2e4dac57e013"
+                            },
                             {
-                                "name": "outfile",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 2665.633331298828,
-                            "top": 811.4166717529297
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b2860df42e16",
-                            "name": "bandage",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"tsv\": \"\\\"false\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
-                        "tool_version": "0.8.1+galaxy1",
-                        "type": "tool",
-                        "uuid": "4aa230bd-3269-41c3-81f5-9085fcc4001d",
-                        "workflow_outputs": [
+                                "label": "fastp report on short reads json",
+                                "output_name": "report_json",
+                                "uuid": "10fbe1e5-400c-4ffe-8794-9b776b0d7322"
+                            },
                             {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "cf5eab6a-97ae-430e-a27a-6ecc33d4b8c0"
+                                "label": "fastp filtered R2 reads",
+                                "output_name": "out2",
+                                "uuid": "639ed3f7-0e51-4e5d-b6f8-081378962109"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
                         "errors": null,
-                        "id": 2,
+                        "id": 4,
                         "input_connections": {
-                            "single_paired|paired_input": {
-                                "id": 0,
+                            "single_paired|in1": {
+                                "id": 2,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": "fastp: Trimmed Illumina Reads",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool fastp",
+                                "name": "single_paired"
+                            }
+                        ],
+                        "label": "fastp on long reads",
                         "name": "fastp",
                         "outputs": [
                             {
-                                "name": "output_paired_coll",
+                                "name": "out1",
                                 "type": "input"
                             },
                             {
@@ -21671,476 +22992,679 @@
                             }
                         ],
                         "position": {
-                            "left": 585,
-                            "top": 365.04998779296875
+                            "left": 804.010509144176,
+                            "top": 22.482646595348
                         },
                         "post_job_actions": {
-                            "HideDatasetActionreport_html": {
+                            "DeleteIntermediatesActionout1": {
                                 "action_arguments": {},
-                                "action_type": "HideDatasetAction",
+                                "action_type": "DeleteIntermediatesAction",
+                                "output_name": "out1"
+                            },
+                            "RenameDatasetActionout1": {
+                                "action_arguments": {
+                                    "newname": "fastp_filtered_long_reads.fastq.gz"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out1"
+                            },
+                            "RenameDatasetActionreport_html": {
+                                "action_arguments": {
+                                    "newname": "fastp_longreads.html"
+                                },
+                                "action_type": "RenameDatasetAction",
                                 "output_name": "report_html"
                             },
-                            "HideDatasetActionreport_json": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
+                            "RenameDatasetActionreport_json": {
+                                "action_arguments": {
+                                    "newname": "fastp_longreads.json"
+                                },
+                                "action_type": "RenameDatasetAction",
                                 "output_name": "report_json"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "1d8fe9bc4cb0",
+                            "changeset_revision": "c59d48774d03",
                             "name": "fastp",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"report_html\\\": \\\"true\\\", \\\"report_json\\\": \\\"true\\\"}\", \"single_paired\": \"{\\\"__current_case__\\\": 2, \\\"adapter_trimming_options\\\": {\\\"adapter_sequence1\\\": \\\"\\\", \\\"adapter_sequence2\\\": \\\"\\\", \\\"disable_adapter_trimming\\\": \\\"false\\\"}, \\\"global_trimming_options\\\": {\\\"trim_front1\\\": \\\"\\\", \\\"trim_front2\\\": \\\"\\\", \\\"trim_tail1\\\": \\\"\\\", \\\"trim_tail2\\\": \\\"\\\"}, \\\"paired_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"single_paired_selector\\\": \\\"paired_collection\\\"}\", \"read_mod_options\": \"{\\\"base_correction_options\\\": {\\\"correction\\\": \\\"false\\\"}, \\\"cutting_by_quality_options\\\": {\\\"cut_by_quality3\\\": \\\"false\\\", \\\"cut_by_quality5\\\": \\\"false\\\", \\\"cut_mean_quality\\\": \\\"\\\", \\\"cut_window_size\\\": \\\"\\\"}, \\\"polyg_tail_trimming\\\": {\\\"__current_case__\\\": 1, \\\"poly_g_min_len\\\": \\\"\\\", \\\"trimming_select\\\": \\\"\\\"}, \\\"polyx_tail_trimming\\\": {\\\"__current_case__\\\": 1, \\\"polyx_trimming_select\\\": \\\"\\\"}, \\\"umi_processing\\\": {\\\"umi\\\": \\\"false\\\", \\\"umi_len\\\": \\\"\\\", \\\"umi_loc\\\": \\\"\\\", \\\"umi_prefix\\\": \\\"\\\"}}\", \"overrepresented_sequence_analysis\": \"{\\\"overrepresentation_analysis\\\": \\\"false\\\", \\\"overrepresentation_sampling\\\": \\\"\\\"}\", \"filter_options\": \"{\\\"length_filtering_options\\\": {\\\"disable_length_filtering\\\": \\\"false\\\", \\\"length_required\\\": \\\"50\\\"}, \\\"low_complexity_filter\\\": {\\\"complexity_threshold\\\": \\\"\\\", \\\"enable_low_complexity_filter\\\": \\\"false\\\"}, \\\"quality_filtering_options\\\": {\\\"disable_quality_filtering\\\": \\\"false\\\", \\\"n_base_limit\\\": \\\"\\\", \\\"qualified_quality_phred\\\": \\\"20\\\", \\\"unqualified_percent_limit\\\": \\\"20\\\"}}\", \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.19.5+galaxy1",
+                        "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": true, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": true, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"-G\", \"__current_case__\": 2}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"single\", \"__current_case__\": 0, \"in1\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": true, \"adapter_sequence1\": \"\"}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.23.4+galaxy0",
                         "type": "tool",
-                        "uuid": "7508c22b-dc6a-4071-8dd0-d5616718e62b",
+                        "uuid": "93602736-2d22-43e4-a53a-803326ccab9e",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_paired_coll",
-                                "uuid": "a7be7eab-3e80-4be6-b1a4-ab303c314096"
+                                "label": "fastp report on long reads html",
+                                "output_name": "report_html",
+                                "uuid": "5e0d2c3d-41a4-4823-ae9c-b1e4d2826541"
+                            },
+                            {
+                                "label": "fastp filtered long reads",
+                                "output_name": "out1",
+                                "uuid": "e6018ad6-86f4-4e78-8cf2-ccc8b97022fe"
+                            },
+                            {
+                                "label": "fastp report on long reads json",
+                                "output_name": "report_json",
+                                "uuid": "69f8383b-a1be-4a74-95f4-3dba35e01426"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "assembly/largegenome",
+                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Trim_and_filter_reads.ga",
+                "tags": [
+                    "LG-WF",
+                    "GTN"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Trim and filter reads - fastp - upgraded ",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-trim-and-filter-reads",
+                "tutorial_id": "largegenome",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Trim_and_filter_reads.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Trim_and_filter_reads.html",
+                "version": 2,
+                "wfid": "assembly-largegenome",
+                "wfname": "galaxy-workflow-trim-and-filter-reads",
+                "workflow": "Galaxy-Workflow-Trim_and_filter_reads.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0"
+                ],
+                "workflowhub_id": "1144"
+            },
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n\r\n```galaxy\nworkflow_display()\n```\r\n"
+                    },
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"]\n  1[label=\"Meryl - count kmers\"]\n  0 -> 1 [label=\"output\"]\n  k899ddd934c0f4f81a9738120494ed983[color=lightseagreen,label=\"Output\\nMeryl on input dataset(s): read-db.meryldb\"]\n  1 -> k899ddd934c0f4f81a9738120494ed983\n  2[label=\"Meryl - generate histogram\"]\n  1 -> 2 [label=\"read_db\"]\n  3[label=\"Genomescope\"]\n  2 -> 3 [label=\"read_db_hist\"]\n  kefc727b61ef44c4c8cce35c7d3cc8aac[color=lightseagreen,label=\"Output\\nGenomeScope on input dataset(s) Transformed log plot\"]\n  3 -> kefc727b61ef44c4c8cce35c7d3cc8aac\n  k701df341576744bcade26af498ab7467[color=lightseagreen,label=\"Output\\nGenomeScope on input dataset(s) Transformed linear plot\"]\n  3 -> k701df341576744bcade26af498ab7467\n  k85fa4004b35147b384aa6788d338037a[color=lightseagreen,label=\"Output\\nGenomeScope on input dataset(s) Log plot\"]\n  3 -> k85fa4004b35147b384aa6788d338037a\n  kc71ce05598f0435493972f8833b90cc4[color=lightseagreen,label=\"Output\\nGenomeScope on input dataset(s) Linear plot\"]\n  3 -> kc71ce05598f0435493972f8833b90cc4\n}",
+                "history": [
+                    {
+                        "hash": "b74cf5a09d0d563d658d374ed6d287db85df3a8a",
+                        "message": "Update Galaxy-Workflow-kmer_counting.ga",
+                        "num": 5,
+                        "short_hash": "b74cf5a09",
+                        "unix": "1715074461"
+                    },
+                    {
+                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
+                        "message": "new versions of workflows",
+                        "num": 4,
+                        "short_hash": "e8ddbcdd5",
+                        "unix": "1714537936"
+                    },
+                    {
+                        "hash": "0be0483e2cbaa0ab18026da1f19f4b124d78e1c4",
+                        "message": "Rename Galaxy-Workflow-kmer_counting.ga to Galaxy-Workflow-kmer_counting_old.ga",
+                        "num": 3,
+                        "short_hash": "0be0483e2",
+                        "unix": "1714537366"
+                    },
+                    {
+                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
+                        "message": "add/complete creator info on workflows",
+                        "num": 2,
+                        "short_hash": "62e77944b",
+                        "unix": "1676627603"
                     },
+                    {
+                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
+                        "message": "large genome tutorial",
+                        "num": 1,
+                        "short_hash": "9fcb3aeec",
+                        "unix": "1665123856"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
+                        "content_id": null,
                         "errors": null,
-                        "id": 20,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Illumina reads R1"
+                            }
+                        ],
+                        "label": "Illumina reads R1",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 31.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "3daa3f25-6fff-4766-9d45-b991fd6751a5",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Meryl - count kmers\"];\n  0 -->|output| 1;\n  899ddd93-4c0f-4f81-a973-8120494ed983[\"Output\\nMeryl on input dataset(s): read-db.meryldb\"];\n  1 --> 899ddd93-4c0f-4f81-a973-8120494ed983;\n  style 899ddd93-4c0f-4f81-a973-8120494ed983 stroke:#2c3143,stroke-width:4px;\n  2[\"Meryl - generate histogram\"];\n  1 -->|read_db| 2;\n  3[\"Genomescope\"];\n  2 -->|read_db_hist| 3;\n  efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac[\"Output\\nGenomeScope on input dataset(s) Transformed log plot\"];\n  3 --> efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac;\n  style efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac stroke:#2c3143,stroke-width:4px;\n  701df341-5767-44bc-ade2-6af498ab7467[\"Output\\nGenomeScope on input dataset(s) Transformed linear plot\"];\n  3 --> 701df341-5767-44bc-ade2-6af498ab7467;\n  style 701df341-5767-44bc-ade2-6af498ab7467 stroke:#2c3143,stroke-width:4px;\n  85fa4004-b351-47b3-84aa-6788d338037a[\"Output\\nGenomeScope on input dataset(s) Log plot\"];\n  3 --> 85fa4004-b351-47b3-84aa-6788d338037a;\n  style 85fa4004-b351-47b3-84aa-6788d338037a stroke:#2c3143,stroke-width:4px;\n  c71ce055-98f0-4354-9397-2f8833b90cc4[\"Output\\nGenomeScope on input dataset(s) Linear plot\"];\n  3 --> c71ce055-98f0-4354-9397-2f8833b90cc4;\n  style c71ce055-98f0-4354-9397-2f8833b90cc4 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "kmer counting - meryl - upgraded",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+                        "errors": null,
+                        "id": 1,
                         "input_connections": {
-                            "input": {
-                                "id": 18,
-                                "output_name": "assembly"
+                            "operation_type|input_reads": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Filter sequences by length",
-                                "name": "input"
+                                "description": "runtime parameter for tool Meryl",
+                                "name": "operation_type"
                             }
                         ],
-                        "label": null,
-                        "name": "Filter sequences by length",
+                        "label": "Meryl - count kmers",
+                        "name": "Meryl",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "fasta"
+                                "name": "read_db",
+                                "type": "meryldb"
                             }
                         ],
                         "position": {
-                            "left": 2574.4166870117188,
-                            "top": 1254.4166870117188
+                            "left": 228,
+                            "top": 103.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
                         "tool_shed_repository": {
-                            "changeset_revision": "8cacfcf96a52",
-                            "name": "fasta_filter_by_length",
-                            "owner": "devteam",
+                            "changeset_revision": "29dabd8db6f2",
+                            "name": "meryl",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"max_length\": \"\\\"0\\\"\", \"min_length\": \"\\\"1000\\\"\"}",
-                        "tool_version": "1.2",
+                        "tool_state": "{\"operation_type\": {\"command_type\": \"count-kmers\", \"__current_case__\": 0, \"count_operations\": \"count\", \"input_reads\": {\"__class__\": \"RuntimeValue\"}, \"options_kmer_size\": {\"kmer_size\": \"provide\", \"__current_case__\": 0, \"input_kmer_size\": \"21\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3+galaxy6",
                         "type": "tool",
-                        "uuid": "3cbd67e0-3e55-4726-8dbe-0c61aec4d293",
+                        "uuid": "0a85d93b-8f53-4bc8-b89b-4be6f306f2c6",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "e4143f49-239f-4266-ba8d-e6299a331403"
+                                "label": "Meryl on input dataset(s): read-db.meryldb",
+                                "output_name": "read_db",
+                                "uuid": "899ddd93-4c0f-4f81-a973-8120494ed983"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
                         "errors": null,
-                        "id": 21,
+                        "id": 2,
                         "input_connections": {
-                            "input_file": {
-                                "id": 18,
-                                "output_name": "assembly_graph"
+                            "operation_type|input_meryldb_02": {
+                                "id": 1,
+                                "output_name": "read_db"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Bandage Image",
-                                "name": "input_file"
+                                "description": "runtime parameter for tool Meryl",
+                                "name": "operation_type"
                             }
                         ],
-                        "label": null,
-                        "name": "Bandage Image",
+                        "label": "Meryl - generate histogram",
+                        "name": "Meryl",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "jpg"
+                                "name": "read_db_hist",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 2667.4166870117188,
-                            "top": 1052.4166870117188
+                            "left": 465.5,
+                            "top": 110
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
                         "tool_shed_repository": {
-                            "changeset_revision": "b2860df42e16",
-                            "name": "bandage",
+                            "changeset_revision": "29dabd8db6f2",
+                            "name": "meryl",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"lengths\": \"\\\"true\\\"\", \"output_format\": \"\\\"jpg\\\"\", \"height\": \"\\\"1000\\\"\", \"width\": \"\\\"\\\"\", \"names\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.8.1+galaxy2",
+                        "tool_state": "{\"operation_type\": {\"command_type\": \"histogram-kmers\", \"__current_case__\": 4, \"input_meryldb_02\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3+galaxy6",
                         "type": "tool",
-                        "uuid": "ef2c6a46-8421-499e-a840-8dd03483c5c9",
+                        "uuid": "80dbb867-84f7-4349-ae1d-1c7b87d0dce7",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "5e535f98-b740-44ec-aba1-9d9090acb89a"
+                                "output_name": "read_db_hist",
+                                "uuid": "bf11e7cb-61a2-4c27-9aa1-4c7a42028330"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
                         "errors": null,
                         "id": 3,
                         "input_connections": {
-                            "mode|reads|files": {
-                                "id": 1,
-                                "output_name": "output"
+                            "input": {
+                                "id": 2,
+                                "output_name": "read_db_hist"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "NanoPlot",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "output_html",
-                                "type": "html"
-                            },
+                                "description": "runtime parameter for tool GenomeScope",
+                                "name": "input"
+                            }
+                        ],
+                        "label": "Genomescope",
+                        "name": "GenomeScope",
+                        "outputs": [
                             {
-                                "name": "nanostats",
-                                "type": "txt"
+                                "name": "linear_plot",
+                                "type": "png"
                             },
                             {
-                                "name": "nanostats_post_filtering",
-                                "type": "txt"
+                                "name": "log_plot",
+                                "type": "png"
                             },
                             {
-                                "name": "read_length",
+                                "name": "transformed_linear_plot",
                                 "type": "png"
                             },
                             {
-                                "name": "log_read_length",
+                                "name": "transformed_log_plot",
                                 "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 630,
-                            "top": 650.4666595458984
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionlog_read_length": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "log_read_length"
-                            },
-                            "HideDatasetActionnanostats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "nanostats"
                             },
-                            "HideDatasetActionnanostats_post_filtering": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "nanostats_post_filtering"
+                            {
+                                "name": "model",
+                                "type": "txt"
                             },
-                            "HideDatasetActionread_length": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "read_length"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "645159bcee2d",
-                            "name": "nanoplot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"filter\": \"{\\\"alength\\\": \\\"false\\\", \\\"barcoded\\\": \\\"false\\\", \\\"downsample\\\": \\\"\\\", \\\"drop_outliers\\\": \\\"false\\\", \\\"loglength\\\": \\\"true\\\", \\\"maxlength\\\": \\\"\\\", \\\"minlength\\\": \\\"\\\", \\\"minqual\\\": \\\"\\\", \\\"percentqual\\\": \\\"false\\\", \\\"readtype\\\": null}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"__current_case__\\\": 0, \\\"choice\\\": \\\"batch\\\", \\\"reads\\\": {\\\"__current_case__\\\": 0, \\\"files\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"type\\\": \\\"fastq\\\"}}\", \"customization\": \"{\\\"N50\\\": \\\"false\\\", \\\"color\\\": null, \\\"format\\\": \\\"png\\\", \\\"noN50\\\": \\\"false\\\", \\\"plots\\\": null}\"}",
-                        "tool_version": "1.25.0+galaxy1",
-                        "type": "tool",
-                        "uuid": "9b1d43ac-82e3-463f-9c88-08c8826a62c9",
-                        "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_html",
-                                "uuid": "cd8570c7-02db-479b-81a9-cd0d26643f71"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "fastq_input|fastq_input1": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Map with minimap2",
-                        "outputs": [
+                                "name": "summary",
+                                "type": "txt"
+                            },
                             {
-                                "name": "alignment_output",
-                                "type": "bam"
+                                "name": "progress",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 709.199951171875,
-                            "top": 1131.9666748046875
+                            "left": 699.204345703125,
+                            "top": 0
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "53c0b7a1a0c3",
-                            "name": "minimap2",
+                            "changeset_revision": "01210c4e9144",
+                            "name": "genomescope",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"alignment_options\": \"{\\\"-O2\\\": \\\"\\\", \\\"A\\\": \\\"\\\", \\\"B\\\": \\\"\\\", \\\"E\\\": \\\"\\\", \\\"E2\\\": \\\"\\\", \\\"O\\\": \\\"\\\", \\\"s\\\": \\\"\\\", \\\"u\\\": null, \\\"z\\\": \\\"\\\"}\", \"analysis_type_selector\": \"\\\"splice\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"io_options\": \"{\\\"K\\\": \\\"\\\", \\\"L\\\": \\\"false\\\", \\\"Q\\\": \\\"false\\\", \\\"Y\\\": \\\"false\\\", \\\"c\\\": \\\"false\\\", \\\"cs\\\": null, \\\"eqx\\\": \\\"false\\\", \\\"output_format\\\": \\\"BAM\\\"}\", \"mapping_options\": \"{\\\"F\\\": \\\"\\\", \\\"G\\\": \\\"\\\", \\\"N\\\": \\\"\\\", \\\"X\\\": \\\"false\\\", \\\"f\\\": \\\"\\\", \\\"g\\\": \\\"\\\", \\\"m\\\": \\\"\\\", \\\"min_occ_floor\\\": \\\"\\\", \\\"n\\\": \\\"\\\", \\\"p\\\": \\\"\\\", \\\"r\\\": \\\"\\\"}\", \"fastq_input\": \"{\\\"__current_case__\\\": 1, \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"single\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 0, \\\"ref_file\\\": \\\"hg38\\\", \\\"reference_source_selector\\\": \\\"cached\\\"}\", \"indexing_options\": \"{\\\"H\\\": \\\"false\\\", \\\"I\\\": \\\"\\\", \\\"k\\\": \\\"\\\", \\\"w\\\": \\\"\\\"}\"}",
-                        "tool_version": "2.17+galaxy1",
+                        "tool_state": "{\"advanced_options\": {\"topology\": null, \"initial_repetitiveness\": null, \"initial_heterozygosities\": \"\", \"transform_exp\": null, \"testing\": false, \"true_params\": \"\", \"trace_flag\": false, \"num_rounds\": null}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"kmer_length\": \"21\", \"lambda\": null, \"max_kmercov\": null, \"output_options\": {\"output_files\": [\"model_output\", \"summary_output\", \"progress_output\"], \"no_unique_sequence\": false}, \"ploidy\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0+galaxy2",
                         "type": "tool",
-                        "uuid": "098d2283-1218-489b-9882-8822e79d9444",
+                        "uuid": "fa7a5012-8bd0-4b35-b337-249245e0932b",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "alignment_output",
-                                "uuid": "9972015d-4bdc-440f-b8b6-84e92a64ef8f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "results_0|software_cond|input": {
-                                "id": 2,
-                                "output_name": "report_json"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "MultiQC",
-                        "outputs": [
-                            {
-                                "name": "stats",
-                                "type": "input"
+                                "output_name": "progress",
+                                "uuid": "fedca588-8be6-4e13-9ff5-62387a5a90af"
                             },
                             {
-                                "name": "html_report",
-                                "type": "html"
-                            }
-                        ],
-                        "position": {
-                            "left": 938.699951171875,
-                            "top": 250
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionstats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "stats"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b2f1f75d49c4",
-                            "name": "multiqc",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"comment\": \"\\\"\\\"\", \"__page__\": null, \"title\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"results\": \"[{\\\"__index__\\\": 0, \\\"software_cond\\\": {\\\"__current_case__\\\": 7, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"software\\\": \\\"fastp\\\"}}]\", \"saveLog\": \"\\\"false\\\"\"}",
-                        "tool_version": "1.7",
-                        "type": "tool",
-                        "uuid": "73566697-4a46-4d35-b8e2-61770acc62c0",
-                        "workflow_outputs": [
+                                "label": "GenomeScope on input dataset(s) Transformed log plot",
+                                "output_name": "transformed_log_plot",
+                                "uuid": "efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac"
+                            },
                             {
                                 "label": null,
-                                "output_name": "html_report",
-                                "uuid": "15f42a94-2c97-4932-8e3f-f26a72b58be4"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "library|input_1": {
-                                "id": 2,
-                                "output_name": "output_paired_coll"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Bowtie2",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "bam"
+                                "output_name": "summary",
+                                "uuid": "fd17af72-7c2a-4167-9880-7fbda525ccbb"
                             },
-                            {
-                                "name": "mapping_stats",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 913.9166259765625,
-                            "top": 564.6333312988281
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "749c918495f7",
-                            "name": "bowtie2",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"sam_options\": \"{\\\"__current_case__\\\": 1, \\\"sam_options_selector\\\": \\\"no\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"__current_case__\\\": 2, \\\"aligned_file\\\": \\\"false\\\", \\\"input_1\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"paired_options\\\": {\\\"__current_case__\\\": 1, \\\"paired_options_selector\\\": \\\"no\\\"}, \\\"type\\\": \\\"paired_collection\\\", \\\"unaligned_file\\\": \\\"false\\\"}\", \"reference_genome\": \"{\\\"__current_case__\\\": 0, \\\"index\\\": \\\"hg38full\\\", \\\"source\\\": \\\"indexed\\\"}\", \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"save_mapping_stats\": \"\\\"true\\\"\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"simple\\\", \\\"presets\\\": \\\"no_presets\\\"}\"}",
-                        "tool_version": "2.3.4.3+galaxy0",
-                        "type": "tool",
-                        "uuid": "43331d2c-7116-410e-a6bd-7e7520d93a52",
-                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "eeae40f6-f1b2-4c56-9860-ac7b8eb1dec0"
+                                "output_name": "model",
+                                "uuid": "ede2b1a5-4017-4aef-a6d2-bac5d17bc7b5"
                             },
                             {
-                                "label": null,
-                                "output_name": "mapping_stats",
-                                "uuid": "c567226e-efaf-4188-bdec-3ba20d0733b0"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "input": {
-                                "id": 4,
-                                "output_name": "alignment_output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Samtools stats",
-                        "outputs": [
+                                "label": "GenomeScope on input dataset(s) Transformed linear plot",
+                                "output_name": "transformed_linear_plot",
+                                "uuid": "701df341-5767-44bc-ade2-6af498ab7467"
+                            },
                             {
-                                "name": "output_collection",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 1022.4166259765625,
-                            "top": 1254.4166870117188
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "145f6d74ff5e",
-                            "name": "samtools_stats",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__page__\": null, \"coverage_cond\": \"{\\\"__current_case__\\\": 0, \\\"coverage_select\\\": \\\"no\\\"}\", \"gc_depth\": \"\\\"\\\"\", \"cov_threshold\": \"\\\"\\\"\", \"most_inserts\": \"\\\"\\\"\", \"cond_region\": \"{\\\"__current_case__\\\": 0, \\\"select_region\\\": \\\"no\\\"}\", \"split_output_cond\": \"{\\\"__current_case__\\\": 1, \\\"generate_tables\\\": [\\\"SN\\\"], \\\"split_output_selector\\\": \\\"yes\\\"}\", \"read_length\": \"\\\"\\\"\", \"trim_quality\": \"\\\"\\\"\", \"remove_overlaps\": \"\\\"false\\\"\", \"filter_by_flags\": \"{\\\"__current_case__\\\": 1, \\\"filter_flags\\\": \\\"nofilter\\\"}\", \"sparse\": \"\\\"false\\\"\", \"addref_cond\": \"{\\\"__current_case__\\\": 0, \\\"addref_select\\\": \\\"no\\\"}\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"insert_size\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"remove_dups\": \"\\\"false\\\"\"}",
-                        "tool_version": "2.0.2+galaxy2",
-                        "type": "tool",
-                        "uuid": "15f6252f-79d4-4319-855d-09665deac6a3",
-                        "workflow_outputs": [
+                                "label": "GenomeScope on input dataset(s) Log plot",
+                                "output_name": "log_plot",
+                                "uuid": "85fa4004-b351-47b3-84aa-6788d338037a"
+                            },
                             {
-                                "label": null,
-                                "output_name": "output_collection",
-                                "uuid": "faed6306-eed6-40bd-ac9f-9fb3a4e980ea"
+                                "label": "GenomeScope on input dataset(s) Linear plot",
+                                "output_name": "linear_plot",
+                                "uuid": "c71ce055-98f0-4354-9397-2f8833b90cc4"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/assembly-with-preprocessing",
-                "path": "topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing.ga",
+                "parent_id": "assembly/largegenome",
+                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-kmer_counting.ga",
                 "tags": [
                     "GTN",
-                    "assembly"
+                    "LG-WF"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "assembly_with_preprocessing",
+                "title": "kmer counting - meryl - upgraded",
                 "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-assembly-with-preprocessing/versions/assembly-with-preprocessing",
-                "tutorial_id": "assembly-with-preprocessing",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing.html",
-                "version": 1,
-                "wfid": "assembly-assembly-with-preprocessing",
-                "wfname": "assembly-with-preprocessing",
-                "workflow": "assembly_with_preprocessing.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-kmer-counting",
+                "tutorial_id": "largegenome",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-kmer_counting.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-kmer_counting.html",
+                "version": 2,
+                "wfid": "assembly-largegenome",
+                "wfname": "galaxy-workflow-kmer-counting",
+                "workflow": "Galaxy-Workflow-kmer_counting.ga",
                 "workflow_tools": [
-                    "__ZIP_COLLECTION__",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6"
                 ],
-                "workflowhub_id": "1132"
+                "workflowhub_id": "1166"
+            }
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.7055935"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "fasta_stats",
+                    "owner": "iuc",
+                    "revisions": "9c620a950d3a",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "spades",
+                    "owner": "nml",
+                    "revisions": "b7829778729f",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "velvetoptimiser",
+                    "owner": "simon-gladman",
+                    "revisions": "37d88f41c810",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fasta_stats\n  owner: iuc\n  revisions: 9c620a950d3a\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: spades\n  owner: nml\n  revisions: b7829778729f\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: velvetoptimiser\n  owner: simon-gladman\n  revisions: 37d88f41c810\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.json",
+        "contributors": [
+            {
+                "elixir_node": "au",
+                "email": "simon.gladman@unimelb.edu.au",
+                "id": "slugger70",
+                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
+                "joined": "2017-09",
+                "name": "Simon Gladman",
+                "orcid": "0000-0002-6100-4385",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            }
+        ],
+        "dir": "topics/assembly/tutorials/debruijn-graph-assembly",
+        "edam_operation": [
+            "Genome assembly",
+            "Optimisation and refinement",
+            "Sequence assembly"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "Galaxy@AuBi",
+            "UseGalaxy.be",
+            "UseGalaxy.eu",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "assembly/debruijn-graph-assembly",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "We learned about how the choice of k-mer size will affect assembly outcomes",
+            "We learned about the strategies that assemblers use to make reference genomes",
+            "We performed a number of assemblies with Velvet and SPAdes.",
+            "You should use SPAdes or another more modern assembler than Velvet for actual assemblies now."
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-02-01",
+        "objectives": [
+            "Perform an optimised Velvet assembly with the Velvet Optimiser",
+            "Compare this assembly with those we did in the basic tutorial",
+            "Perform an assembly using the SPAdes assembler."
+        ],
+        "pageviews": 5905570,
+        "pub_date": "2017-05-24",
+        "questions": [
+            "What are the factors that affect genome assembly?",
+            "How does Genome assembly work?"
+        ],
+        "short_id": "T00031",
+        "short_tools": [
+            "spades",
+            "fasta-stats",
+            "velvetoptimiser"
+        ],
+        "slides": true,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "time_estimation": "2h",
+        "title": "De Bruijn Graph Assembly",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
+            "toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/simon-gladman/velvetoptimiser/velvetoptimiser/2.2.6"
+        ],
+        "topic_name": "assembly",
+        "topic_name_human": "Assembly",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "debruijn-graph-assembly",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.json"
+        },
+        "version": 25,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 299,
+        "visitors": 2138764,
+        "workflows": [
             {
                 "creators": [],
-                "description": "Assembly with preprocessing and SRA download",
+                "description": "De Bruijn Graph Assembly",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nList of Illumina accessions\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nList of ONT accessions\"]\n  10[label=\"Samtools stats\"]\n  6 -> 10 [label=\"alignment_output\"]\n  11[label=\"Samtools view\"]\n  8 -> 11 [label=\"output\"]\n  12[label=\"Samtools fastx\"]\n  9 -> 12 [label=\"outputsam\"]\n  13[label=\"Samtools fastx\"]\n  11 -> 13 [label=\"outputsam\"]\n  14[label=\"Collapse Collection\"]\n  12 -> 14 [label=\"nonspecific\"]\n  15[label=\"Zip Collection\"]\n  13 -> 15 [label=\"forward\"]\n  13 -> 15 [label=\"reverse\"]\n  16[label=\"Collapse Collection\"]\n  13 -> 16 [label=\"forward\"]\n  17[label=\"Collapse Collection\"]\n  13 -> 17 [label=\"reverse\"]\n  18[label=\"seqtk_sample\"]\n  16 -> 18 [label=\"output\"]\n  19[label=\"seqtk_sample\"]\n  17 -> 19 [label=\"output\"]\n  2[label=\"Illumina data\"]\n  0 -> 2 [label=\"output\"]\n  20[label=\"Create assemblies with Unicycler\"]\n  14 -> 20 [label=\"output\"]\n  18 -> 20 [label=\"default\"]\n  19 -> 20 [label=\"default\"]\n  21[label=\"Bandage Info\"]\n  20 -> 21 [label=\"assembly_graph\"]\n  22[label=\"Bandage Image\"]\n  20 -> 22 [label=\"assembly_graph\"]\n  23[label=\"Filter sequences by length\"]\n  20 -> 23 [label=\"assembly\"]\n  3[label=\"ONT data\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"fastp: Trimmed Illumina Reads\"]\n  2 -> 4 [label=\"list_paired\"]\n  5[label=\"NanoPlot\"]\n  3 -> 5 [label=\"output_collection\"]\n  6[label=\"Map with minimap2\"]\n  3 -> 6 [label=\"output_collection\"]\n  7[label=\"MultiQC\"]\n  4 -> 7 [label=\"report_json\"]\n  8[label=\"Bowtie2\"]\n  4 -> 8 [label=\"output_paired_coll\"]\n  9[label=\"Samtools view\"]\n  6 -> 9 [label=\"alignment_output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmutant_R1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmutant_R2\"]\n  2[label=\"VelvetOptimiser\"]\n  0 -> 2 [label=\"output\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"SPAdes\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Fasta Statistics\"]\n  2 -> 4 [label=\"contigs\"]\n  kdacb84a554824ab081ade92af21636cd[color=lightseagreen,label=\"Output\\nfasta_stats_velvet\"]\n  4 -> kdacb84a554824ab081ade92af21636cd\n  5[label=\"Fasta Statistics\"]\n  3 -> 5 [label=\"out_contigs\"]\n  kff376be9736148c6b1c8d9f951b9c6fa[color=lightseagreen,label=\"Output\\nfasta_stats_spades\"]\n  5 -> kff376be9736148c6b1c8d9f951b9c6fa\n}",
                 "history": [
                     {
-                        "hash": "fc35e6581a2e34e4420f19af4619c92283609e91",
-                        "message": "add annotations",
+                        "hash": "b435b09a401e2f8678827dafd0e94ee51a2ff804",
+                        "message": "updated test for general-introduction, added test for debruijn-graph-assembly using planemo https://github.com/galaxyproject/planemo/pull/1028",
+                        "num": 4,
+                        "short_hash": "b435b09a4",
+                        "unix": "1595663711"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 3,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
                         "num": 2,
-                        "short_hash": "fc35e6581",
-                        "unix": "1587558793"
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
                     },
                     {
-                        "hash": "7ed054469d1ef84a60abec55758ee2932f9a9655",
-                        "message": "readd workflows",
+                        "hash": "6ce45f0c2d49dbd6e6bcb72bc3ef161c4c5a7a41",
+                        "message": "workflow",
                         "num": 1,
-                        "short_hash": "7ed054469",
-                        "unix": "1587555276"
+                        "short_hash": "6ce45f0c2",
+                        "unix": "1549974498"
                     }
                 ],
                 "inputs": [
@@ -22150,26 +23674,25 @@
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "List of Illumina accessions",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "mutant_R1.fastq"
+                            }
+                        ],
+                        "label": "mutant_R1",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 257.683349609375,
-                            "top": 215.9166259765625
+                            "left": 10,
+                            "top": 10
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"name\": \"mutant_R1.fastq\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "1a61a3b3-4515-47a1-8ee5-fb79f05a8dfa",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "ea340c2d-d9e8-4ea5-bbc0-7ee7d92a57bf"
-                            }
-                        ]
+                        "uuid": "fd0c169b-7c95-4ad9-a7c6-7e16e4eaab2e",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
@@ -22177,581 +23700,729 @@
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "List of ONT accessions",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "mutant_R2.fastq"
+                            }
+                        ],
+                        "label": "mutant_R2",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 264.9833984375,
-                            "top": 522.7166442871094
+                            "left": 10,
+                            "top": 130
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"name\": \"mutant_R2.fastq\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "0988bf07-dc80-4d7b-a62f-8e5e852b0982",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "fb053f14-71fc-45ac-83ea-a308a5c22918"
-                            }
-                        ]
+                        "uuid": "03430abb-4f48-4bb8-b294-58c4de22a85c",
+                        "workflow_outputs": []
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nList of Illumina accessions\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nList of ONT accessions\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Samtools stats\"];\n  6 -->|alignment_output| 10;\n  11[\"Samtools view\"];\n  8 -->|output| 11;\n  12[\"Samtools fastx\"];\n  9 -->|outputsam| 12;\n  13[\"Samtools fastx\"];\n  11 -->|outputsam| 13;\n  14[\"Collapse Collection\"];\n  12 -->|nonspecific| 14;\n  15[\"Zip Collection\"];\n  13 -->|forward| 15;\n  13 -->|reverse| 15;\n  16[\"Collapse Collection\"];\n  13 -->|forward| 16;\n  17[\"Collapse Collection\"];\n  13 -->|reverse| 17;\n  18[\"seqtk_sample\"];\n  16 -->|output| 18;\n  19[\"seqtk_sample\"];\n  17 -->|output| 19;\n  2[\"Illumina data\"];\n  0 -->|output| 2;\n  20[\"Create assemblies with Unicycler\"];\n  14 -->|output| 20;\n  18 -->|default| 20;\n  19 -->|default| 20;\n  21[\"Bandage Info\"];\n  20 -->|assembly_graph| 21;\n  22[\"Bandage Image\"];\n  20 -->|assembly_graph| 22;\n  23[\"Filter sequences by length\"];\n  20 -->|assembly| 23;\n  3[\"ONT data\"];\n  1 -->|output| 3;\n  4[\"fastp: Trimmed Illumina Reads\"];\n  2 -->|list_paired| 4;\n  5[\"NanoPlot\"];\n  3 -->|output_collection| 5;\n  6[\"Map with minimap2\"];\n  3 -->|output_collection| 6;\n  7[\"MultiQC\"];\n  4 -->|report_json| 7;\n  8[\"Bowtie2\"];\n  4 -->|output_paired_coll| 8;\n  9[\"Samtools view\"];\n  6 -->|alignment_output| 9;",
-                "modified": "2024-08-18 00:06:20 +0000",
-                "name": "assembly_with_preprocessing_and_sra_download",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nmutant_R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nmutant_R2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"VelvetOptimiser\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"SPAdes\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Fasta Statistics\"];\n  2 -->|contigs| 4;\n  dacb84a5-5482-4ab0-81ad-e92af21636cd[\"Output\\nfasta_stats_velvet\"];\n  4 --> dacb84a5-5482-4ab0-81ad-e92af21636cd;\n  style dacb84a5-5482-4ab0-81ad-e92af21636cd stroke:#2c3143,stroke-width:4px;\n  5[\"Fasta Statistics\"];\n  3 -->|out_contigs| 5;\n  ff376be9-7361-48c6-b1c8-d9f951b9c6fa[\"Output\\nfasta_stats_spades\"];\n  5 --> ff376be9-7361-48c6-b1c8-d9f951b9c6fa;\n  style ff376be9-7361-48c6-b1c8-d9f951b9c6fa stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Debruijn Graph",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "List of Illumina accessions",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 257.683349609375,
-                            "top": 215.9166259765625
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "1a61a3b3-4515-47a1-8ee5-fb79f05a8dfa",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "ea340c2d-d9e8-4ea5-bbc0-7ee7d92a57bf"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "List of ONT accessions",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 264.9833984375,
-                            "top": 522.7166442871094
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "0988bf07-dc80-4d7b-a62f-8e5e852b0982",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "fb053f14-71fc-45ac-83ea-a308a5c22918"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-                        "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "input": {
-                                "id": 6,
-                                "output_name": "alignment_output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Samtools stats",
-                        "outputs": [
-                            {
-                                "name": "output_collection",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 1328.4166259765625,
-                            "top": 1239.4166259765625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "145f6d74ff5e",
-                            "name": "samtools_stats",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__page__\": null, \"coverage_cond\": \"{\\\"__current_case__\\\": 0, \\\"coverage_select\\\": \\\"no\\\"}\", \"gc_depth\": \"\\\"\\\"\", \"cov_threshold\": \"\\\"\\\"\", \"most_inserts\": \"\\\"\\\"\", \"cond_region\": \"{\\\"__current_case__\\\": 0, \\\"select_region\\\": \\\"no\\\"}\", \"split_output_cond\": \"{\\\"__current_case__\\\": 1, \\\"generate_tables\\\": [\\\"SN\\\"], \\\"split_output_selector\\\": \\\"yes\\\"}\", \"read_length\": \"\\\"\\\"\", \"trim_quality\": \"\\\"\\\"\", \"remove_overlaps\": \"\\\"false\\\"\", \"filter_by_flags\": \"{\\\"__current_case__\\\": 1, \\\"filter_flags\\\": \\\"nofilter\\\"}\", \"sparse\": \"\\\"false\\\"\", \"addref_cond\": \"{\\\"__current_case__\\\": 0, \\\"addref_select\\\": \\\"no\\\"}\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"insert_size\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"remove_dups\": \"\\\"false\\\"\"}",
-                        "tool_version": "2.0.2+galaxy2",
-                        "type": "tool",
-                        "uuid": "ae176340-d7da-4c2e-851b-e6129a0c222d",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_collection",
-                                "uuid": "8652ea8a-35f5-4531-8b89-88bca189ab9f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
                         "errors": null,
-                        "id": 12,
+                        "id": 4,
                         "input_connections": {
-                            "input": {
-                                "id": 9,
-                                "output_name": "outputsam"
+                            "dataset": {
+                                "id": 2,
+                                "output_name": "contigs"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Samtools fastx",
+                        "name": "Fasta Statistics",
                         "outputs": [
                             {
-                                "name": "nonspecific",
-                                "type": "fasta"
+                                "name": "stats",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1628.4166259765625,
-                            "top": 852.4166412353516
+                            "left": 450,
+                            "top": 10
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "a8d69aee190e",
-                            "name": "samtools_fastx",
+                            "changeset_revision": "9c620a950d3a",
+                            "name": "fasta_stats",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"copy_arb_tags\": \"\\\"\\\"\", \"__page__\": null, \"output_fmt_cond\": \"{\\\"__current_case__\\\": 2, \\\"default_quality\\\": \\\"\\\", \\\"ilumina_casava\\\": \\\"false\\\", \\\"output_fmt_select\\\": \\\"fastqsanger.gz\\\", \\\"output_quality\\\": \\\"false\\\"}\", \"idxout_cond\": \"{\\\"__current_case__\\\": 0, \\\"idxout_select\\\": \\\"no\\\"}\", \"read_numbering\": \"\\\"\\\"\", \"exclusive_filter\": \"null\", \"exclusive_filter_all\": \"null\", \"inclusive_filter\": \"null\", \"outputs\": \"[\\\"r0\\\"]\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"copy_tags\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9+galaxy1",
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"dataset\": \"null\"}",
+                        "tool_version": "1.0.1",
                         "type": "tool",
-                        "uuid": "31e2b4e8-7631-46c0-8382-b805cee2b739",
+                        "uuid": "4999cd50-69fd-4e57-af95-8c73ece1fe31",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "nonspecific",
-                                "uuid": "cfbf839f-53f0-4a82-8966-2bdb6919de5e"
+                                "label": "fasta_stats_velvet",
+                                "output_name": "stats",
+                                "uuid": "dacb84a5-5482-4ab0-81ad-e92af21636cd"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "__ZIP_COLLECTION__",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
                         "errors": null,
-                        "id": 15,
+                        "id": 5,
                         "input_connections": {
-                            "input_forward": {
-                                "id": 13,
-                                "output_name": "forward"
-                            },
-                            "input_reverse": {
-                                "id": 13,
-                                "output_name": "reverse"
+                            "dataset": {
+                                "id": 3,
+                                "output_name": "out_contigs"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Zip Collection",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 2049.4166870117188,
-                            "top": 477.4166259765625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "__ZIP_COLLECTION__",
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_reverse\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"input_forward\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "9ba89e81-9c53-4f5b-9d61-42319b7d574c",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "ebc8f563-c45e-4e17-a541-b1275e7f61ad"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
-                        "errors": null,
-                        "id": 18,
-                        "input_connections": {
-                            "in_file": {
-                                "id": 16,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool seqtk_sample",
-                                "name": "in_file"
-                            }
-                        ],
-                        "label": null,
-                        "name": "seqtk_sample",
-                        "outputs": [
-                            {
-                                "name": "default",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 2438.0833282470703,
-                            "top": 688.6833190917969
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "58c8ece95b53",
-                            "name": "seqtk",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"s\": \"\\\"4\\\"\", \"in_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"subsample_size\": \"\\\"0.1\\\"\", \"advanced\": \"{\\\"single_pass_mode\\\": \\\"false\\\"}\"}",
-                        "tool_version": "1.3.2",
-                        "type": "tool",
-                        "uuid": "b4e40092-e076-4eb0-af30-c8c47885fefa",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "default",
-                                "uuid": "cf3eb8ef-fce5-42af-a14d-60ff915fbff3"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
-                        "errors": null,
-                        "id": 19,
-                        "input_connections": {
-                            "in_file": {
-                                "id": 17,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool seqtk_sample",
-                                "name": "in_file"
-                            }
-                        ],
-                        "label": null,
-                        "name": "seqtk_sample",
+                        "name": "Fasta Statistics",
                         "outputs": [
                             {
-                                "name": "default",
-                                "type": "input"
+                                "name": "stats",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 2413.0833129882812,
-                            "top": 864.6833190917969
+                            "left": 450,
+                            "top": 130
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "58c8ece95b53",
-                            "name": "seqtk",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"s\": \"\\\"4\\\"\", \"in_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"subsample_size\": \"\\\"0.1\\\"\", \"advanced\": \"{\\\"single_pass_mode\\\": \\\"false\\\"}\"}",
-                        "tool_version": "1.3.2",
-                        "type": "tool",
-                        "uuid": "1ef9ca9e-e447-4933-8871-c0e8e9a953c4",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "default",
-                                "uuid": "bf722cb7-0b06-42ed-8fbc-9dc3896e9340"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "input|file_list": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Illumina data",
-                        "name": "Faster Download and Extract Reads in FASTQ",
-                        "outputs": [
-                            {
-                                "name": "list_paired",
-                                "type": "input"
-                            },
-                            {
-                                "name": "output_collection",
-                                "type": "input"
-                            },
-                            {
-                                "name": "output_collection_other",
-                                "type": "input"
-                            },
-                            {
-                                "name": "log",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 511.783447265625,
-                            "top": 273.1666259765625
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionlog": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "log"
-                            },
-                            "HideDatasetActionoutput_collection": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_collection"
-                            },
-                            "HideDatasetActionoutput_collection_other": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_collection_other"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "aad3885b3216",
-                            "name": "sra_tools",
+                            "changeset_revision": "9c620a950d3a",
+                            "name": "fasta_stats",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": \"{\\\"minlen\\\": \\\"\\\", \\\"skip_technical\\\": \\\"true\\\", \\\"split\\\": \\\"--split-3\\\"}\", \"input\": \"{\\\"__current_case__\\\": 2, \\\"file_list\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"input_select\\\": \\\"file_list\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
-                        "tool_version": "2.10.4+galaxy1",
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"dataset\": \"null\"}",
+                        "tool_version": "1.0.1",
                         "type": "tool",
-                        "uuid": "b097b5cb-44a8-4881-9ba0-a089ef1b4ad6",
+                        "uuid": "bfc90a5a-640d-4633-b4df-2f8ccdbfe95b",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "list_paired",
-                                "uuid": "c6b4e7f2-5cf4-4051-afd1-a110381c4679"
+                                "label": "fasta_stats_spades",
+                                "output_name": "stats",
+                                "uuid": "ff376be9-7361-48c6-b1c8-d9f951b9c6fa"
                             }
                         ]
-                    },
+                    }
+                ],
+                "parent_id": "assembly/debruijn-graph-assembly",
+                "path": "topics/assembly/tutorials/debruijn-graph-assembly/workflows/debruijn-graph.ga",
+                "tags": [
+                    "assembly"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "Debruijn Graph",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-debruijn-graph-assembly/versions/debruijn-graph",
+                "tutorial_id": "debruijn-graph-assembly",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/debruijn-graph-assembly/workflows/debruijn-graph.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/debruijn-graph-assembly/workflows/debruijn-graph.html",
+                "version": 4,
+                "wfid": "assembly-debruijn-graph-assembly",
+                "wfname": "debruijn-graph",
+                "workflow": "debruijn-graph.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/simon-gladman/velvetoptimiser/velvetoptimiser/2.2.6"
+                ],
+                "workflowhub_id": "1124"
+            }
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.582600"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "unique",
+                    "owner": "bgruening",
+                    "revisions": "7ce75adb93be",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bamtools",
+                    "owner": "devteam",
+                    "revisions": "befc9dad4ca8",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bowtie2",
+                    "owner": "devteam",
+                    "revisions": "f6877ad76b00",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bowtie2",
+                    "owner": "devteam",
+                    "revisions": "03e9b2fbc005",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "3d0c7bdf12f5",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bandage",
+                    "owner": "iuc",
+                    "revisions": "21e491ad532a",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bandage",
+                    "owner": "iuc",
+                    "revisions": "21e491ad532a",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collection_column_join",
+                    "owner": "iuc",
+                    "revisions": "3ddd99c7efee",
+                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "coverm_contig",
+                    "owner": "iuc",
+                    "revisions": "6941d0d453ba",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "filter_tabular",
+                    "owner": "iuc",
+                    "revisions": "34d29339abab",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "megahit",
+                    "owner": "iuc",
+                    "revisions": "14ddfc8ffb93",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "megahit_contig2fastg",
+                    "owner": "iuc",
+                    "revisions": "4ec5b3777508",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ngsutils_bam_filter",
+                    "owner": "iuc",
+                    "revisions": "2e957d4c4b95",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "quast",
+                    "owner": "iuc",
+                    "revisions": "3061c8b029e5",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "quast",
+                    "owner": "iuc",
+                    "revisions": "72472698a2df",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seqtk",
+                    "owner": "iuc",
+                    "revisions": "3da72230c066",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "cutadapt",
+                    "owner": "lparsons",
+                    "revisions": "5915ea1ec9b1",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "metaspades",
+                    "owner": "nml",
+                    "revisions": "fd128c111ab0",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unique\n  owner: bgruening\n  revisions: 7ce75adb93be\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools\n  owner: devteam\n  revisions: befc9dad4ca8\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie2\n  owner: devteam\n  revisions: f6877ad76b00\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie2\n  owner: devteam\n  revisions: 03e9b2fbc005\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: 21e491ad532a\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: 21e491ad532a\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_column_join\n  owner: iuc\n  revisions: 3ddd99c7efee\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: coverm_contig\n  owner: iuc\n  revisions: 6941d0d453ba\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filter_tabular\n  owner: iuc\n  revisions: 34d29339abab\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: megahit\n  owner: iuc\n  revisions: 14ddfc8ffb93\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: megahit_contig2fastg\n  owner: iuc\n  revisions: 4ec5b3777508\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ngsutils_bam_filter\n  owner: iuc\n  revisions: 2e957d4c4b95\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 3061c8b029e5\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 72472698a2df\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 5915ea1ec9b1\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaspades\n  owner: nml\n  revisions: fd128c111ab0\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/metagenomics-assembly/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "plushz",
+                "bebatut"
+            ],
+            "funding": [
+                "gallantries"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "id": "plushz",
+                "joined": "2022-03",
+                "name": "Polina Polunina",
+                "orcid": "0000-0002-0507-4602",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/plushz/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/plushz.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            }
+        ],
+        "dir": "topics/assembly/tutorials/metagenomics-assembly",
+        "edam_ontology": [
+            "topic_3174",
+            "topic_0196"
+        ],
+        "edam_operation": [
+            "Data handling",
+            "Visualisation",
+            "Sequence trimming",
+            "Read mapping",
+            "Sequencing quality control",
+            "Genome assembly",
+            "Sequence alignment analysis",
+            "Sequence contamination filtering",
+            "Sequence assembly validation",
+            "Variant calling",
+            "Statistical calculation",
+            "Sequence assembly visualisation",
+            "Sequence file editing",
+            "Local alignment",
+            "Sequence composition calculation",
+            "Read pre-processing",
+            "Primer removal",
+            "Formatting"
+        ],
+        "edam_topic": [
+            "Metagenomics",
+            "Sequence assembly"
+        ],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "assembly/metagenomics-assembly",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.eu"
+        ],
+        "js_requirements": {
+            "mathjax": 25185,
+            "mermaid": false
+        },
+        "key_points": [
+            "Assembly groups reads into contigs and scafolds.",
+            "De Brujin Graphs use k-mers to assembly reads",
+            "MetaSPAdes and MEGAHIT are assemblers",
+            "Quast is the tool to assess the assembly quality"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-10-02",
+        "objectives": [
+            "Describe what an assembly is",
+            "Describe what de-replication is",
+            "Explain the difference between co-assembly and individual assembly",
+            "Explain the difference between reads, contigs and scaffolds",
+            "Explain how tools based on De Bruijn graph work",
+            "Apply appropriate tools for analyzing the quality of metagenomic data",
+            "Construct and apply simple assembly pipelines on short read data",
+            "Apply appropriate tools for analyzing the quality of metagenomic assembly",
+            "Evaluate the Quality of the Assembly with Quast, Bowtie2, and CoverM-Genome"
+        ],
+        "pageviews": 7,
+        "pub_date": "2024-10-02",
+        "questions": [
+            "Why metagenomic data should be assembled?",
+            "What is the difference between co-assembly and individual assembly?",
+            "What is the difference between reads, contigs and scaffolds?",
+            "How tools based on De Bruijn graph work?",
+            "How to assess the quality of metagenomic data assembly?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "bebatut",
+                    "sophia120199"
+                ],
+                "date": "2023-05-02",
+                "galaxy_version": "23.01",
+                "length": "1H",
+                "speakers": [
+                    "bebatut"
+                ],
+                "youtube_id": "1ZYGy85Im7w"
+            }
+        ],
+        "redirect_from": [
+            "/topics/metagenomics/tutorials/metagenomics-assembly/tutorial",
+            "/short/assembly/metagenomics-assembly",
+            "/short/T00035"
+        ],
+        "short_id": "T00035",
+        "short_tools": [
+            "ngsutils_bam_filter",
+            "tp_cat",
+            "bamtools",
+            "bandage_image",
+            "filter_tabular",
+            "megahit_contig2fastg",
+            "bandage_info",
+            "bg_uniq",
+            "quast",
+            "seqtk_subseq",
+            "cutadapt",
+            "random_lines1",
+            "collection_column_join",
+            "megahit",
+            "coverm_contig",
+            "fastqc",
+            "metaspades",
+            "bowtie2"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "metagenomics",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": true,
+        "tags": [
+            "assembly",
+            "metagenomics",
+            "microgalaxy"
+        ],
+        "time_estimation": "2H",
+        "title": "Assembly of metagenomic sequencing data",
+        "tools": [
+            "random_lines1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.2.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy10",
+            "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
+            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.15.4+galaxy2"
+        ],
+        "topic_name": "assembly",
+        "topic_name_human": "Assembly",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "metagenomics-assembly",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/metagenomics-assembly/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/metagenomics-assembly/tutorial.json"
+        },
+        "version": 0,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 23,
+        "visitors": 6,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  1[label=\"metaSPAdes\"]\n  0 -> 1 [label=\"output\"]\n  k833d79ffe16f414c9c41db8dbfa8ed6b[color=lightseagreen,label=\"Output\\nmetaSPAdes on input dataset(s): Scaffolds\"]\n  1 -> k833d79ffe16f414c9c41db8dbfa8ed6b\n  k10319152d2f947d8be41f956a57e86d3[color=lightseagreen,label=\"Output\\nmetaSPAdes on input dataset(s): Assembly graph\"]\n  1 -> k10319152d2f947d8be41f956a57e86d3\n  kb1ffc3a48e394255ac57fd7cfb9c1633[color=lightseagreen,label=\"Output\\nmetaSPAdes on input dataset(s): Assembly graph with scaffolds\"]\n  1 -> kb1ffc3a48e394255ac57fd7cfb9c1633\n  kb6b74c9d5a164725a1d111c1f05ee909[color=lightseagreen,label=\"Output\\nmetaSPAdes on input dataset(s): Contigs\"]\n  1 -> kb6b74c9d5a164725a1d111c1f05ee909\n  2[label=\"MEGAHIT\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Bowtie2\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"megahit contig2fastg\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Quast\"]\n  2 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Bandage Image\"]\n  4 -> 6 [label=\"fastg\"]\n  7[label=\"Bandage Info\"]\n  4 -> 7 [label=\"fastg\"]\n  8[label=\"Column join\"]\n  7 -> 8 [label=\"outfile\"]\n}",
+                "history": [],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 20,
-                        "input_connections": {
-                            "long": {
-                                "id": 14,
-                                "output_name": "output"
-                            },
-                            "paired_unpaired|fastq_input1": {
-                                "id": 18,
-                                "output_name": "default"
-                            },
-                            "paired_unpaired|fastq_input2": {
-                                "id": 19,
-                                "output_name": "default"
-                            }
-                        },
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "lr_align"
-                            },
-                            {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "long"
-                            },
-                            {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "paired_unpaired"
-                            },
-                            {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "paired_unpaired"
-                            },
-                            {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "rotation"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Create assemblies with Unicycler",
-                        "outputs": [
-                            {
-                                "name": "assembly_graph",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "assembly",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "Input Dataset Collection"
                             }
                         ],
+                        "label": "Input Dataset Collection",
+                        "name": "Input dataset collection",
+                        "outputs": [],
                         "position": {
-                            "left": 2673.4166717529297,
-                            "top": 699.4166412353516
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "88c240872a65",
-                            "name": "unicycler",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0.0,
+                            "top": 480
                         },
-                        "tool_state": "{\"linear_seqs\": \"\\\"1\\\"\", \"spades\": \"{\\\"depth_filter\\\": \\\"0.25\\\", \\\"kmer_count\\\": \\\"10\\\", \\\"kmers\\\": \\\"\\\", \\\"largest_component\\\": \\\"false\\\", \\\"max_kmer_frac\\\": \\\"0.95\\\", \\\"min_kmer_frac\\\": \\\"0.2\\\", \\\"no_correct\\\": \\\"false\\\"}\", \"graph_clean\": \"{\\\"min_component_size\\\": \\\"1000\\\", \\\"min_dead_end_size\\\": \\\"1000\\\"}\", \"__page__\": null, \"min_anchor_seg_len\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"lr_align\": \"{\\\"contamination\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"low_score\\\": \\\"\\\", \\\"scores\\\": \\\"3,-6,-5,-2\\\"}\", \"long\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"paired_unpaired\": \"{\\\"__current_case__\\\": 0, \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"fastq_input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired\\\"}\", \"min_fasta_length\": \"\\\"100\\\"\", \"mode\": \"\\\"normal\\\"\", \"rotation\": \"{\\\"no_rotate\\\": \\\"false\\\", \\\"start_gene_cov\\\": \\\"95.0\\\", \\\"start_gene_id\\\": \\\"90.0\\\", \\\"start_genes\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"pilon\": \"{\\\"min_polish_size\\\": \\\"1000\\\", \\\"no_pilon\\\": \\\"false\\\"}\"}",
-                        "tool_version": "0.4.8.0",
-                        "type": "tool",
-                        "uuid": "851c6be6-c202-450a-9cd3-19e205dcc496",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "cdb65097-d956-4715-9cd4-fadc9b0c07c5",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "assembly",
-                                "uuid": "17700863-7cc5-4a67-ac0f-aa5f7b258d62"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "assembly_graph",
-                                "uuid": "3285cc00-6b39-4f3d-87a5-87abd483ede6"
+                                "output_name": "output",
+                                "uuid": "c8ca2f5f-b0f4-4d90-8259-9e4796c4a35f"
                             }
                         ]
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"metaSPAdes\"];\n  0 -->|output| 1;\n  833d79ff-e16f-414c-9c41-db8dbfa8ed6b[\"Output\\nmetaSPAdes on input dataset(s): Scaffolds\"];\n  1 --> 833d79ff-e16f-414c-9c41-db8dbfa8ed6b;\n  style 833d79ff-e16f-414c-9c41-db8dbfa8ed6b stroke:#2c3143,stroke-width:4px;\n  10319152-d2f9-47d8-be41-f956a57e86d3[\"Output\\nmetaSPAdes on input dataset(s): Assembly graph\"];\n  1 --> 10319152-d2f9-47d8-be41-f956a57e86d3;\n  style 10319152-d2f9-47d8-be41-f956a57e86d3 stroke:#2c3143,stroke-width:4px;\n  b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633[\"Output\\nmetaSPAdes on input dataset(s): Assembly graph with scaffolds\"];\n  1 --> b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633;\n  style b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633 stroke:#2c3143,stroke-width:4px;\n  b6b74c9d-5a16-4725-a1d1-11c1f05ee909[\"Output\\nmetaSPAdes on input dataset(s): Contigs\"];\n  1 --> b6b74c9d-5a16-4725-a1d1-11c1f05ee909;\n  style b6b74c9d-5a16-4725-a1d1-11c1f05ee909 stroke:#2c3143,stroke-width:4px;\n  2[\"MEGAHIT\"];\n  0 -->|output| 2;\n  3[\"Bowtie2\"];\n  0 -->|output| 3;\n  2 -->|output| 3;\n  4[\"megahit contig2fastg\"];\n  2 -->|output| 4;\n  5[\"Quast\"];\n  2 -->|output| 5;\n  0 -->|output| 5;\n  6[\"Bandage Image\"];\n  4 -->|fastg| 6;\n  7[\"Bandage Info\"];\n  4 -->|fastg| 7;\n  8[\"Column join\"];\n  7 -->|outfile| 8;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Metagenomics assembly tutorial workflow",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 21,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 20,
-                                "output_name": "assembly_graph"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Bandage Info",
-                        "outputs": [
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "outfile",
-                                "type": "txt"
+                                "description": "",
+                                "name": "Input Dataset Collection"
                             }
                         ],
+                        "label": "Input Dataset Collection",
+                        "name": "Input dataset collection",
+                        "outputs": [],
                         "position": {
-                            "left": 2977.4166870117188,
-                            "top": 803.4166412353516
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b2860df42e16",
-                            "name": "bandage",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0.0,
+                            "top": 480
                         },
-                        "tool_state": "{\"tsv\": \"\\\"false\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
-                        "tool_version": "0.8.1+galaxy1",
-                        "type": "tool",
-                        "uuid": "4aa230bd-3269-41c3-81f5-9085fcc4001d",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "cdb65097-d956-4715-9cd4-fadc9b0c07c5",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "cf5eab6a-97ae-430e-a27a-6ecc33d4b8c0"
+                                "output_name": "output",
+                                "uuid": "c8ca2f5f-b0f4-4d90-8259-9e4796c4a35f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.15.4+galaxy2",
                         "errors": null,
-                        "id": 22,
+                        "id": 1,
                         "input_connections": {
-                            "input_file": {
-                                "id": 20,
-                                "output_name": "assembly_graph"
+                            "singlePaired|input": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Bandage Image",
-                                "name": "input_file"
+                                "description": "runtime parameter for tool metaSPAdes",
+                                "name": "arf"
+                            },
+                            {
+                                "description": "runtime parameter for tool metaSPAdes",
+                                "name": "arf"
+                            },
+                            {
+                                "description": "runtime parameter for tool metaSPAdes",
+                                "name": "singlePaired"
                             }
                         ],
                         "label": null,
-                        "name": "Bandage Image",
+                        "name": "metaSPAdes",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "jpg"
+                                "name": "out_ag",
+                                "type": "fastg"
+                            },
+                            {
+                                "name": "out_ags",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "out_cn",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "out_sc",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 2975.4166870117188,
-                            "top": 1017.4166412353516
+                            "left": 247.0,
+                            "top": 0
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.15.4+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "b2860df42e16",
-                            "name": "bandage",
-                            "owner": "iuc",
+                            "changeset_revision": "fd128c111ab0",
+                            "name": "metaspades",
+                            "owner": "nml",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"lengths\": \"\\\"true\\\"\", \"output_format\": \"\\\"jpg\\\"\", \"height\": \"\\\"1000\\\"\", \"width\": \"\\\"\\\"\", \"names\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.8.1+galaxy2",
+                        "tool_state": "{\"additional_reads\": {\"selector\": \"false\", \"__current_case__\": 1}, \"arf\": {\"nanopore\": {\"__class__\": \"RuntimeValue\"}, \"pacbio\": {\"__class__\": \"RuntimeValue\"}}, \"kmer_cond\": {\"kmer_sel\": \"manual\", \"__current_case__\": 1, \"manual\": \"21,33,55,77\"}, \"library_number\": \"true\", \"mode_sel\": null, \"optional_output\": [\"ag\", \"ags\", \"cn\", \"sc\"], \"phred_offset\": \"auto\", \"singlePaired\": {\"sPaired\": \"paired_collection\", \"__current_case__\": 2, \"input\": {\"__class__\": \"RuntimeValue\"}, \"type_paired\": \"pe\", \"orientation\": \"fr\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.15.4+galaxy2",
                         "type": "tool",
-                        "uuid": "7683e21a-0fe1-4871-b044-7e74321fe44b",
+                        "uuid": "7dc08460-f398-4f1d-9f30-1736cf636a13",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "12e0cc76-0374-4ce8-b882-f5f21a942ad1"
+                                "label": "metaSPAdes on input dataset(s): Scaffolds",
+                                "output_name": "out_sc",
+                                "uuid": "833d79ff-e16f-414c-9c41-db8dbfa8ed6b"
+                            },
+                            {
+                                "label": "metaSPAdes on input dataset(s): Assembly graph",
+                                "output_name": "out_ag",
+                                "uuid": "10319152-d2f9-47d8-be41-f956a57e86d3"
+                            },
+                            {
+                                "label": "metaSPAdes on input dataset(s): Assembly graph with scaffolds",
+                                "output_name": "out_ags",
+                                "uuid": "b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633"
+                            },
+                            {
+                                "label": "metaSPAdes on input dataset(s): Contigs",
+                                "output_name": "out_cn",
+                                "uuid": "b6b74c9d-5a16-4725-a1d1-11c1f05ee909"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
                         "errors": null,
-                        "id": 23,
+                        "id": 2,
                         "input_connections": {
-                            "input": {
-                                "id": 20,
-                                "output_name": "assembly"
+                            "input_option|batchmode|pair_input": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Filter sequences by length",
-                                "name": "input"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Filter sequences by length",
+                        "name": "MEGAHIT",
                         "outputs": [
                             {
                                 "name": "output",
@@ -22759,1897 +24430,1395 @@
                             }
                         ],
                         "position": {
-                            "left": 2978.4166870117188,
-                            "top": 1220.4166259765625
+                            "left": 278.0,
+                            "top": 464
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "8cacfcf96a52",
-                            "name": "fasta_filter_by_length",
-                            "owner": "devteam",
+                            "changeset_revision": "14ddfc8ffb93",
+                            "name": "megahit",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"max_length\": \"\\\"0\\\"\", \"min_length\": \"\\\"1000\\\"\"}",
-                        "tool_version": "1.2",
+                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"advanced_section\": {\"nomercy\": \"false\", \"bubble_level\": \"2\", \"merge_level\": \"20,0.95\", \"prune_level\": \"2\", \"prune_depth\": \"2\", \"disconnect_ratio\": \"0.1\", \"low_local_ratio\": \"0.2\", \"cleaning_rounds\": \"5\", \"nolocal\": \"false\", \"kmin1pass\": \"false\"}, \"basic_section\": {\"min_count\": \"2\", \"k_mer\": {\"k_mer_method\": \"klim_method\", \"__current_case__\": 1, \"k_min\": \"21\", \"k_max\": \"91\", \"k_step\": \"12\"}}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_option\": {\"choice\": \"paired_collection\", \"__current_case__\": 3, \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"pair_input\": {\"__class__\": \"ConnectedValue\"}}}, \"output_section\": {\"min_contig_len\": \"200\", \"show_intermediate_contigs\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.9+galaxy0",
                         "type": "tool",
-                        "uuid": "ef08963b-e96b-4841-b1fd-02056f6ab1f2",
+                        "uuid": "ffbb16f2-580a-4832-8b6d-e67932e24b27",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "637c866b-dc17-4c32-aa1e-5207ae2c79a0"
+                                "uuid": "061ac8dd-de43-467d-9c15-a4f46a125103"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
                         "errors": null,
                         "id": 3,
                         "input_connections": {
-                            "input|file_list": {
-                                "id": 1,
+                            "library|input_1": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "reference_genome|own_file": {
+                                "id": 2,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "ONT data",
-                        "name": "Faster Download and Extract Reads in FASTQ",
+                        "label": null,
+                        "name": "Bowtie2",
                         "outputs": [
                             {
-                                "name": "list_paired",
-                                "type": "input"
-                            },
-                            {
-                                "name": "output_collection",
-                                "type": "input"
-                            },
-                            {
-                                "name": "output_collection_other",
-                                "type": "input"
+                                "name": "output",
+                                "type": "bam"
                             },
                             {
-                                "name": "log",
+                                "name": "mapping_stats",
                                 "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 516.13330078125,
-                            "top": 540.7166442871094
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionlist_paired": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "list_paired"
-                            },
-                            "HideDatasetActionlog": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "log"
-                            },
-                            "HideDatasetActionoutput_collection_other": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_collection_other"
-                            }
+                            "left": 556.0,
+                            "top": 130
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "aad3885b3216",
-                            "name": "sra_tools",
-                            "owner": "iuc",
+                            "changeset_revision": "03e9b2fbc005",
+                            "name": "bowtie2",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": \"{\\\"minlen\\\": \\\"\\\", \\\"skip_technical\\\": \\\"true\\\", \\\"split\\\": \\\"--split-3\\\"}\", \"input\": \"{\\\"__current_case__\\\": 2, \\\"file_list\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"input_select\\\": \\\"file_list\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
-                        "tool_version": "2.10.4+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"no_presets\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": \"false\", \"aligned_file\": \"false\", \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"own_file|__identifier__\": \"ERR2231567\", \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 1, \"own_file\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.5.0+galaxy0",
                         "type": "tool",
-                        "uuid": "2ea0a236-4ecc-43b4-a815-40f37bf1bd59",
+                        "uuid": "9f445c6b-31c9-4ff0-b559-6be00fb0fc17",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_collection",
-                                "uuid": "9cd44dd5-4375-4c34-9edc-804544192c34"
+                                "output_name": "mapping_stats",
+                                "uuid": "ff350260-91cd-4f01-a82f-f64e8eddd4ed"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "2fa389b6-088a-4686-94e9-de884f86e1b7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1",
                         "errors": null,
                         "id": 4,
                         "input_connections": {
-                            "single_paired|paired_input": {
+                            "contigs": {
                                 "id": 2,
-                                "output_name": "list_paired"
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool fastp",
-                                "name": "single_paired"
-                            }
-                        ],
-                        "label": "fastp: Trimmed Illumina Reads",
-                        "name": "fastp",
+                        "inputs": [],
+                        "label": null,
+                        "name": "megahit contig2fastg",
                         "outputs": [
                             {
-                                "name": "output_paired_coll",
-                                "type": "input"
-                            },
-                            {
-                                "name": "report_json",
-                                "type": "json"
+                                "name": "fastg",
+                                "type": "fastg"
                             }
                         ],
                         "position": {
-                            "left": 879.7833251953125,
-                            "top": 365.04998779296875
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionreport_json": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "report_json"
-                            }
+                            "left": 556.0,
+                            "top": 444
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "1d8fe9bc4cb0",
-                            "name": "fastp",
+                            "changeset_revision": "4ec5b3777508",
+                            "name": "megahit_contig2fastg",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"report_html\\\": \\\"false\\\", \\\"report_json\\\": \\\"true\\\"}\", \"single_paired\": \"{\\\"__current_case__\\\": 2, \\\"adapter_trimming_options\\\": {\\\"adapter_sequence1\\\": \\\"\\\", \\\"adapter_sequence2\\\": \\\"\\\", \\\"disable_adapter_trimming\\\": \\\"false\\\"}, \\\"global_trimming_options\\\": {\\\"trim_front1\\\": \\\"\\\", \\\"trim_front2\\\": \\\"\\\", \\\"trim_tail1\\\": \\\"\\\", \\\"trim_tail2\\\": \\\"\\\"}, \\\"paired_input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"single_paired_selector\\\": \\\"paired_collection\\\"}\", \"read_mod_options\": \"{\\\"base_correction_options\\\": {\\\"correction\\\": \\\"false\\\"}, \\\"cutting_by_quality_options\\\": {\\\"cut_by_quality3\\\": \\\"false\\\", \\\"cut_by_quality5\\\": \\\"false\\\", \\\"cut_mean_quality\\\": \\\"\\\", \\\"cut_window_size\\\": \\\"\\\"}, \\\"polyg_tail_trimming\\\": {\\\"__current_case__\\\": 1, \\\"poly_g_min_len\\\": \\\"\\\", \\\"trimming_select\\\": \\\"\\\"}, \\\"polyx_tail_trimming\\\": {\\\"__current_case__\\\": 1, \\\"polyx_trimming_select\\\": \\\"\\\"}, \\\"umi_processing\\\": {\\\"umi\\\": \\\"false\\\", \\\"umi_len\\\": \\\"\\\", \\\"umi_loc\\\": \\\"\\\", \\\"umi_prefix\\\": \\\"\\\"}}\", \"overrepresented_sequence_analysis\": \"{\\\"overrepresentation_analysis\\\": \\\"false\\\", \\\"overrepresentation_sampling\\\": \\\"\\\"}\", \"filter_options\": \"{\\\"length_filtering_options\\\": {\\\"disable_length_filtering\\\": \\\"false\\\", \\\"length_required\\\": \\\"50\\\"}, \\\"low_complexity_filter\\\": {\\\"complexity_threshold\\\": \\\"\\\", \\\"enable_low_complexity_filter\\\": \\\"false\\\"}, \\\"quality_filtering_options\\\": {\\\"disable_quality_filtering\\\": \\\"false\\\", \\\"n_base_limit\\\": \\\"\\\", \\\"qualified_quality_phred\\\": \\\"20\\\", \\\"unqualified_percent_limit\\\": \\\"20\\\"}}\", \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.19.5+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"contigs\": {\"__class__\": \"ConnectedValue\"}, \"contigs|__identifier__\": \"ERR2231567\", \"kmer\": \"91\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.3+galaxy1",
                         "type": "tool",
-                        "uuid": "7508c22b-dc6a-4071-8dd0-d5616718e62b",
+                        "uuid": "c839a8b8-c719-474d-957e-d94614491f13",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_paired_coll",
-                                "uuid": "a7be7eab-3e80-4be6-b1a4-ab303c314096"
+                                "output_name": "fastg",
+                                "uuid": "91718981-2ae5-4cdd-8007-0ce9cc3c68f6"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0",
                         "errors": null,
                         "id": 5,
                         "input_connections": {
-                            "mode|reads|files": {
-                                "id": 3,
-                                "output_name": "output_collection"
+                            "in|inputs": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "reads|input_1": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "NanoPlot",
+                        "name": "Quast",
                         "outputs": [
                             {
-                                "name": "output_html",
-                                "type": "html"
+                                "name": "metrics_tabular",
+                                "type": "input"
                             },
                             {
-                                "name": "nanostats",
-                                "type": "txt"
+                                "name": "metrics_pdf",
+                                "type": "input"
                             },
                             {
-                                "name": "nanostats_post_filtering",
-                                "type": "txt"
+                                "name": "report_tabular_meta",
+                                "type": "tabular"
                             },
                             {
-                                "name": "read_length",
-                                "type": "png"
+                                "name": "report_html_meta",
+                                "type": "html"
                             },
                             {
-                                "name": "log_read_length",
-                                "type": "png"
+                                "name": "log_meta",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "krona",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 924.7833251953125,
-                            "top": 650.4666442871094
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionlog_read_length": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "log_read_length"
-                            },
-                            "HideDatasetActionnanostats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "nanostats"
-                            },
-                            "HideDatasetActionnanostats_post_filtering": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "nanostats_post_filtering"
-                            },
-                            "HideDatasetActionread_length": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "read_length"
-                            }
+                            "left": 556.0,
+                            "top": 636
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "645159bcee2d",
-                            "name": "nanoplot",
+                            "changeset_revision": "3061c8b029e5",
+                            "name": "quast",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"filter\": \"{\\\"alength\\\": \\\"false\\\", \\\"barcoded\\\": \\\"false\\\", \\\"downsample\\\": \\\"\\\", \\\"drop_outliers\\\": \\\"false\\\", \\\"loglength\\\": \\\"true\\\", \\\"maxlength\\\": \\\"\\\", \\\"minlength\\\": \\\"\\\", \\\"minqual\\\": \\\"\\\", \\\"percentqual\\\": \\\"false\\\", \\\"readtype\\\": null}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"__current_case__\\\": 0, \\\"choice\\\": \\\"batch\\\", \\\"reads\\\": {\\\"__current_case__\\\": 0, \\\"files\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"type\\\": \\\"fastq\\\"}}\", \"customization\": \"{\\\"N50\\\": \\\"false\\\", \\\"color\\\": null, \\\"format\\\": \\\"png\\\", \\\"noN50\\\": \\\"false\\\", \\\"plots\\\": null}\"}",
-                        "tool_version": "1.25.0+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": \"false\", \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": \"true\", \"fragmented_max_indent\": null, \"report_all_metrics\": \"false\", \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": \"false\", \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": \"false\", \"upper_bound_assembly\": \"false\", \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"metagenome\", \"__current_case__\": 1, \"ref\": {\"origin\": \"none\", \"__current_case__\": 3}, \"reuse_combined_alignments\": \"false\", \"min_identity\": \"90.0\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": \"false\", \"conserved_genes_finding\": \"false\"}, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"large\": \"false\", \"min_contig\": \"500\", \"output_files\": [\"html\", \"pdf\", \"tabular\", \"log\", \"summary\", \"krona\"], \"reads\": {\"reads_option\": \"paired_collection\", \"__current_case__\": 3, \"input_1\": {\"__class__\": \"ConnectedValue\"}}, \"split_scaffolds\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.2.0+galaxy0",
                         "type": "tool",
-                        "uuid": "9b1d43ac-82e3-463f-9c88-08c8826a62c9",
+                        "uuid": "12072d4c-8ad5-4de1-bbe2-3b081b8373be",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_html",
-                                "uuid": "cd8570c7-02db-479b-81a9-cd0d26643f71"
+                                "output_name": "log_meta",
+                                "uuid": "33c6424f-fceb-45d1-9462-ea3e7cda79ea"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "krona",
+                                "uuid": "44457a4b-760c-4080-b552-dc4724906b2c"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "metrics_tabular",
+                                "uuid": "9b2b72ac-a297-46a2-883f-8f1704664cf3"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "report_tabular_meta",
+                                "uuid": "1259f3a1-4952-48f1-be69-0fde3b6be9de"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "report_html_meta",
+                                "uuid": "b8f1b46c-1421-4952-9e87-1790bdd076df"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "metrics_pdf",
+                                "uuid": "ac4aa63b-5dc1-4b4c-bbb0-6afce689f0d2"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4",
                         "errors": null,
                         "id": 6,
                         "input_connections": {
-                            "fastq_input|fastq_input1": {
-                                "id": 3,
-                                "output_name": "output_collection"
+                            "input_file": {
+                                "id": 4,
+                                "output_name": "fastg"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Map with minimap2",
+                        "name": "Bandage Image",
                         "outputs": [
                             {
-                                "name": "alignment_output",
-                                "type": "bam"
+                                "name": "outfile",
+                                "type": "jpg"
                             }
                         ],
                         "position": {
-                            "left": 1003.9833984375,
-                            "top": 1131.9666442871094
+                            "left": 834.0,
+                            "top": 466
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4",
                         "tool_shed_repository": {
-                            "changeset_revision": "53c0b7a1a0c3",
-                            "name": "minimap2",
+                            "changeset_revision": "21e491ad532a",
+                            "name": "bandage",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"alignment_options\": \"{\\\"-O2\\\": \\\"\\\", \\\"A\\\": \\\"\\\", \\\"B\\\": \\\"\\\", \\\"E\\\": \\\"\\\", \\\"E2\\\": \\\"\\\", \\\"O\\\": \\\"\\\", \\\"s\\\": \\\"\\\", \\\"u\\\": null, \\\"z\\\": \\\"\\\"}\", \"analysis_type_selector\": \"\\\"splice\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"io_options\": \"{\\\"K\\\": \\\"\\\", \\\"L\\\": \\\"false\\\", \\\"Q\\\": \\\"false\\\", \\\"Y\\\": \\\"false\\\", \\\"c\\\": \\\"false\\\", \\\"cs\\\": null, \\\"eqx\\\": \\\"false\\\", \\\"output_format\\\": \\\"BAM\\\"}\", \"mapping_options\": \"{\\\"F\\\": \\\"\\\", \\\"G\\\": \\\"\\\", \\\"N\\\": \\\"\\\", \\\"X\\\": \\\"false\\\", \\\"f\\\": \\\"\\\", \\\"g\\\": \\\"\\\", \\\"m\\\": \\\"\\\", \\\"min_occ_floor\\\": \\\"\\\", \\\"n\\\": \\\"\\\", \\\"p\\\": \\\"\\\", \\\"r\\\": \\\"\\\"}\", \"fastq_input\": \"{\\\"__current_case__\\\": 1, \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"single\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 0, \\\"ref_file\\\": \\\"hg38\\\", \\\"reference_source_selector\\\": \\\"cached\\\"}\", \"indexing_options\": \"{\\\"H\\\": \\\"false\\\", \\\"I\\\": \\\"\\\", \\\"k\\\": \\\"\\\", \\\"w\\\": \\\"\\\"}\"}",
-                        "tool_version": "2.17+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fontsize\": null, \"height\": \"1000\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"input_file|__identifier__\": \"ERR2231567\", \"lengths\": \"false\", \"names\": \"false\", \"nodewidth\": null, \"output_format\": \"jpg\", \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.8.1+galaxy4",
                         "type": "tool",
-                        "uuid": "098d2283-1218-489b-9882-8822e79d9444",
+                        "uuid": "31b35530-ae7f-4e9c-8021-6983cf3f3401",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "alignment_output",
-                                "uuid": "9972015d-4bdc-440f-b8b6-84e92a64ef8f"
+                                "output_name": "outfile",
+                                "uuid": "e02c022d-3067-40ce-8bb6-4cc258d8523a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2",
                         "errors": null,
                         "id": 7,
                         "input_connections": {
-                            "results_0|software_cond|input": {
+                            "input_file": {
                                 "id": 4,
-                                "output_name": "report_json"
+                                "output_name": "fastg"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "MultiQC",
+                        "name": "Bandage Info",
                         "outputs": [
                             {
-                                "name": "stats",
-                                "type": "input"
-                            },
-                            {
-                                "name": "html_report",
-                                "type": "html"
+                                "name": "outfile",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1152.4833984375,
-                            "top": 200
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionstats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "stats"
-                            }
+                            "left": 834.0,
+                            "top": 679
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "b2f1f75d49c4",
-                            "name": "multiqc",
+                            "changeset_revision": "b9e31c5c01c7",
+                            "name": "bandage",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"comment\": \"\\\"\\\"\", \"__page__\": null, \"title\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"results\": \"[{\\\"__index__\\\": 0, \\\"software_cond\\\": {\\\"__current_case__\\\": 7, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"software\\\": \\\"fastp\\\"}}]\", \"saveLog\": \"\\\"false\\\"\"}",
-                        "tool_version": "1.7",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"input_file|__identifier__\": \"ERR2231567\", \"tsv\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.8.1+galaxy2",
                         "type": "tool",
-                        "uuid": "73566697-4a46-4d35-b8e2-61770acc62c0",
+                        "uuid": "b63e03dc-b9be-4a72-ac81-64b63ddf99f2",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "html_report",
-                                "uuid": "15f42a94-2c97-4932-8e3f-f26a72b58be4"
+                                "output_name": "outfile",
+                                "uuid": "6bd3194a-9e8c-4677-b42c-2fb3bd1116f3"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
                         "errors": null,
                         "id": 8,
                         "input_connections": {
-                            "library|input_1": {
-                                "id": 4,
-                                "output_name": "output_paired_coll"
+                            "input_tabular": {
+                                "id": 7,
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Bowtie2",
+                        "name": "Column join",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "bam"
-                            },
-                            {
-                                "name": "mapping_stats",
-                                "type": "txt"
+                                "name": "tabular_output",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1208.699951171875,
-                            "top": 564.6333160400391
+                            "left": 1112.0,
+                            "top": 732
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "749c918495f7",
-                            "name": "bowtie2",
-                            "owner": "devteam",
+                            "changeset_revision": "3ddd99c7efee",
+                            "name": "collection_column_join",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"sam_options\": \"{\\\"__current_case__\\\": 1, \\\"sam_options_selector\\\": \\\"no\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"__current_case__\\\": 2, \\\"aligned_file\\\": \\\"false\\\", \\\"input_1\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"paired_options\\\": {\\\"__current_case__\\\": 1, \\\"paired_options_selector\\\": \\\"no\\\"}, \\\"type\\\": \\\"paired_collection\\\", \\\"unaligned_file\\\": \\\"false\\\"}\", \"reference_genome\": \"{\\\"__current_case__\\\": 0, \\\"index\\\": \\\"hg38full\\\", \\\"source\\\": \\\"indexed\\\"}\", \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"save_mapping_stats\": \"\\\"true\\\"\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"simple\\\", \\\"presets\\\": \\\"no_presets\\\"}\"}",
-                        "tool_version": "2.3.4.3+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fill_char\": \".\", \"has_header\": \"0\", \"identifier_column\": \"1\", \"include_outputs\": null, \"input_tabular\": {\"__class__\": \"ConnectedValue\"}, \"old_col_in_header\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.0.3",
                         "type": "tool",
-                        "uuid": "43331d2c-7116-410e-a6bd-7e7520d93a52",
+                        "uuid": "e9dc42b2-c638-4b9c-af5f-ce84f6b0d654",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "eeae40f6-f1b2-4c56-9860-ac7b8eb1dec0"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "mapping_stats",
-                                "uuid": "c567226e-efaf-4188-bdec-3ba20d0733b0"
+                                "output_name": "tabular_output",
+                                "uuid": "fe5b4460-6fa0-48a8-84e7-b3b8270e9b8f"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/assembly-with-preprocessing",
-                "path": "topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing_and_sra_download.ga",
-                "tags": [
-                    "GTN",
-                    "assembly"
-                ],
+                "parent_id": "assembly/metagenomics-assembly",
+                "path": "topics/assembly/tutorials/metagenomics-assembly/workflows/metagenomics_assembly_tutorial_workflow.ga",
+                "tags": [],
                 "test_results": null,
                 "tests": false,
-                "title": "assembly_with_preprocessing_and_sra_download",
+                "title": "Metagenomics assembly tutorial workflow",
                 "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-assembly-with-preprocessing/versions/assembly-with-preprocessing-and-sra-download",
-                "tutorial_id": "assembly-with-preprocessing",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing_and_sra_download.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing_and_sra_download.html",
-                "version": 1,
-                "wfid": "assembly-assembly-with-preprocessing",
-                "wfname": "assembly-with-preprocessing-and-sra-download",
-                "workflow": "assembly_with_preprocessing_and_sra_download.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-metagenomics-assembly/versions/metagenomics-assembly-tutorial-workflow",
+                "tutorial_id": "metagenomics-assembly",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/metagenomics-assembly/workflows/metagenomics_assembly_tutorial_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/metagenomics-assembly/workflows/metagenomics_assembly_tutorial_workflow.html",
+                "version": 0,
+                "wfid": "assembly-metagenomics-assembly",
+                "wfname": "metagenomics-assembly-tutorial-workflow",
+                "workflow": "metagenomics_assembly_tutorial_workflow.ga",
                 "workflow_tools": [
-                    "__ZIP_COLLECTION__",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.15.4+galaxy2"
                 ],
-                "workflowhub_id": "1197"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/3732359"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "prokka",
-                    "owner": "crs4",
-                    "revisions": "bf68eb663bc3",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "e7b2202befea",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "b2f1f75d49c4",
-                    "tool_panel_section_label": "Quality Control",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "quast",
-                    "owner": "iuc",
-                    "revisions": "59db8ea8c845",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "unicycler",
-                    "owner": "iuc",
-                    "revisions": "9e3e80cc4ad4",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: prokka\n  owner: crs4\n  revisions: bf68eb663bc3\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: b2f1f75d49c4\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 59db8ea8c845\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unicycler\n  owner: iuc\n  revisions: 9e3e80cc4ad4\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/unicycler-assembly/tutorial.json",
-        "contributors": [
-            {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
-                "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
-            },
-            {
-                "email": "delphine.lariviere@galaxy.org",
-                "id": "delphine-l",
-                "joined": "2017-09",
-                "name": "Delphine Lariviere",
-                "orcid": "0000-0001-6421-3484",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
+                "workflowhub_id": "1120"
             },
-            {
-                "elixir_node": "au",
-                "email": "simon.gladman@unimelb.edu.au",
-                "id": "slugger70",
-                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
-                "joined": "2017-09",
-                "name": "Simon Gladman",
-                "orcid": "0000-0002-6100-4385",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
-            }
-        ],
-        "dir": "topics/assembly/tutorials/unicycler-assembly",
-        "edam_ontology": [
-            "topic_0196",
-            "topic_0622",
-            "topic_3301"
-        ],
-        "edam_operation": [
-            "Visualisation",
-            "Sequencing quality control",
-            "Genome annotation",
-            "Sequence assembly validation",
-            "Sequence composition calculation",
-            "Coding region prediction",
-            "Validation",
-            "Genome assembly",
-            "Gene prediction",
-            "Statistical calculation",
-            "Aggregation"
-        ],
-        "edam_topic": [
-            "Sequence assembly",
-            "Genomics",
-            "Microbiology"
-        ],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "assembly",
-                "tutorials": [
-                    "ecoli_comparison"
-                ],
-                "type": "internal"
-            }
-        ],
-        "hands_on": true,
-        "id": "assembly/unicycler-assembly",
-        "inexact_supported_servers": [
-            "GalaxyTrakr",
-            "HyPhy HIV NGS Tools",
-            "UseGalaxy.cz",
-            "UseGalaxy.fr",
-            "UseGalaxy.no"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "We learned about the strategies used by assemblers for hybrid assemblies",
-            "We performed an hybrid assembly of a bacterial genome and its annotation",
-            "Unicycler is a pipeline bases on Spades and Pilon dedicated to hybrid assembly of Small genomes",
-            "Combination of short and long reads helped us produce an almost perfect assembly"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Introductory",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-03-13",
-        "objectives": [
-            "Perform Quality Control on your reads",
-            "Perform a Small genome Assembly with Unicycler",
-            "Evaluate the Quality of the Assembly with Quast",
-            "Annotate the assembly with Prokka"
-        ],
-        "pageviews": 5746521,
-        "pub_date": "2017-10-11",
-        "questions": [
-            "I have short reads and long reads. How do I assemble a genome?"
-        ],
-        "short_id": "T00038",
-        "short_tools": [
-            "multiqc",
-            "quast",
-            "prokka",
-            "fastqc",
-            "unicycler"
-        ],
-        "slides": true,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "HyPhy HIV NGS Tools",
-                    "url": "https://galaxy.hyphy.org/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "prokaryote",
-            "microgalaxy"
-        ],
-        "time_estimation": "4h",
-        "title": "Unicycler Assembly",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0"
-        ],
-        "topic_name": "assembly",
-        "topic_name_human": "Assembly",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "unicycler-assembly",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/unicycler-assembly/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/unicycler-assembly/tutorial.json"
-        },
-        "version": 23,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 273,
-        "visitors": 2074750,
-        "workflows": [
             {
                 "creators": [],
-                "description": "Unicycler Assembly",
+                "description": "",
                 "features": {
                     "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nForward reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReverse Reads\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nLong Reads\"]\n  3[label=\"FastQC\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"FastQC\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Create assemblies with Unicycler\"]\n  2 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"MultiQC\"]\n  3 -> 6 [label=\"text_file\"]\n  4 -> 6 [label=\"text_file\"]\n  7[label=\"Quast\"]\n  5 -> 7 [label=\"assembly\"]\n  8[label=\"Prokka\"]\n  5 -> 8 [label=\"assembly\"]\n  k0d6b33c9b10549979045b86e52f00156[color=lightseagreen,label=\"Output\\ntbl\"]\n  8 -> k0d6b33c9b10549979045b86e52f00156\n  k8e08b54d87e142699b968ebf1a9bb4ab[color=lightseagreen,label=\"Output\\ngbk\"]\n  8 -> k8e08b54d87e142699b968ebf1a9bb4ab\n  k65e4ddf9f5bc40788b4e37b332e12ece[color=lightseagreen,label=\"Output\\nffn\"]\n  8 -> k65e4ddf9f5bc40788b4e37b332e12ece\n}",
-                "history": [
-                    {
-                        "hash": "232ce03723ab9acbd124828954705c1cd2679abd",
-                        "message": "removed name label bit",
-                        "num": 9,
-                        "short_hash": "232ce0372",
-                        "unix": "1581615057"
-                    },
-                    {
-                        "hash": "cccd85216e3d9baaca787eb7ae8808bd5f3fa2dc",
-                        "message": "minor tweaks and files unhidden",
-                        "num": 8,
-                        "short_hash": "cccd85216",
-                        "unix": "1581613998"
-                    },
-                    {
-                        "hash": "2a2b6329ed96aaaf214703eae87459c58d6e8702",
-                        "message": "name fixed",
-                        "num": 7,
-                        "short_hash": "2a2b6329e",
-                        "unix": "1581095735"
-                    },
-                    {
-                        "hash": "3d424d5e65326cf45c1e4d34851998ab29e6e85c",
-                        "message": "annotation fixed",
-                        "num": 6,
-                        "short_hash": "3d424d5e6",
-                        "unix": "1581014437"
-                    },
-                    {
-                        "hash": "2eade3cbf7b99b8252c3a53ac6cac59e0cacd432",
-                        "message": "tags added",
-                        "num": 5,
-                        "short_hash": "2eade3cbf",
-                        "unix": "1581004807"
-                    },
-                    {
-                        "hash": "07642064759cb13fda345ab9a687aa96b80b3004",
-                        "message": "workflows updated with newer tools, added missing",
-                        "num": 4,
-                        "short_hash": "076420647",
-                        "unix": "1580135207"
-                    },
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 3,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 2,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "02b1037e840cced4c04432f9e6e22cee7ef20392",
-                        "message": "add testing for unicycler",
-                        "num": 1,
-                        "short_hash": "02b1037e8",
-                        "unix": "1527005073"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Forward reads"
-                            }
-                        ],
-                        "label": "Forward reads",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 230.140625,
-                            "top": 404.015625
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "5152d41f-3523-496e-afa2-8d4b0af89b2a",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "e14afa81-ce6c-4577-b17e-90ef2b75c885"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Reverse Reads"
-                            }
-                        ],
-                        "label": "Reverse Reads",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 187.359375,
-                            "top": 656.765625
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "25209075-9248-4e70-9396-87e6e28995e1",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "4cade8d2-87ae-4bae-8795-b1f64c5c3cab"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Long Reads"
-                            }
-                        ],
-                        "label": "Long Reads",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 186.65625,
-                            "top": 803.734375
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "c1cfa6a5-2c17-4cd7-b582-ce85ff552b67",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "bf7b5353-30b6-471b-91b7-5fd2143bf981"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nForward reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReverse Reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nLong Reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"FastQC\"];\n  0 -->|output| 3;\n  4[\"FastQC\"];\n  1 -->|output| 4;\n  5[\"Create assemblies with Unicycler\"];\n  2 -->|output| 5;\n  0 -->|output| 5;\n  1 -->|output| 5;\n  6[\"MultiQC\"];\n  3 -->|text_file| 6;\n  4 -->|text_file| 6;\n  7[\"Quast\"];\n  5 -->|assembly| 7;\n  8[\"Prokka\"];\n  5 -->|assembly| 8;\n  0d6b33c9-b105-4997-9045-b86e52f00156[\"Output\\ntbl\"];\n  8 --> 0d6b33c9-b105-4997-9045-b86e52f00156;\n  style 0d6b33c9-b105-4997-9045-b86e52f00156 stroke:#2c3143,stroke-width:4px;\n  8e08b54d-87e1-4269-9b96-8ebf1a9bb4ab[\"Output\\ngbk\"];\n  8 --> 8e08b54d-87e1-4269-9b96-8ebf1a9bb4ab;\n  style 8e08b54d-87e1-4269-9b96-8ebf1a9bb4ab stroke:#2c3143,stroke-width:4px;\n  65e4ddf9-f5bc-4078-8b4e-37b332e12ece[\"Output\\nffn\"];\n  8 --> 65e4ddf9-f5bc-4078-8b4e-37b332e12ece;\n  style 65e4ddf9-f5bc-4078-8b4e-37b332e12ece stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Unicycler training",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Forward reads"
-                            }
-                        ],
-                        "label": "Forward reads",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 230.140625,
-                            "top": 404.015625
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "5152d41f-3523-496e-afa2-8d4b0af89b2a",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "e14afa81-ce6c-4577-b17e-90ef2b75c885"
-                            }
-                        ]
-                    },
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nERR2231567_1.fastq.gz\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nERR2231567_2.fastq.gz\"]\n  2[label=\"Cutadapt\"]\n  0 -> 2 [label=\"output\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"MEGAHIT\"]\n  2 -> 3 [label=\"out1\"]\n  2 -> 3 [label=\"out2\"]\n  4[label=\"Bowtie2\"]\n  2 -> 4 [label=\"out1\"]\n  2 -> 4 [label=\"out2\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"BAM filter\"]\n  4 -> 5 [label=\"output\"]\n  6[label=\"BAM filter\"]\n  4 -> 6 [label=\"output\"]\n  7[label=\"Convert, Merge, Randomize\"]\n  5 -> 7 [label=\"outfile\"]\n  8[label=\"Convert, Merge, Randomize\"]\n  6 -> 8 [label=\"outfile\"]\n  9[label=\"Select random lines\"]\n  7 -> 9 [label=\"out_file1\"]\n  10[label=\"Select random lines\"]\n  8 -> 10 [label=\"out_file1\"]\n  11[label=\"Filter Tabular\"]\n  9 -> 11 [label=\"out_file1\"]\n  12[label=\"Filter Tabular\"]\n  10 -> 12 [label=\"out_file1\"]\n  13[label=\"Unique\"]\n  11 -> 13 [label=\"output\"]\n  14[label=\"Unique\"]\n  12 -> 14 [label=\"output\"]\n  15[label=\"Concatenate datasets\"]\n  13 -> 15 [label=\"outfile\"]\n  14 -> 15 [label=\"outfile\"]\n  16[label=\"seqtk_subseq\"]\n  2 -> 16 [label=\"out1\"]\n  15 -> 16 [label=\"out_file1\"]\n  17[label=\"seqtk_subseq\"]\n  2 -> 17 [label=\"out2\"]\n  15 -> 17 [label=\"out_file1\"]\n  18[label=\"FastQC\"]\n  16 -> 18 [label=\"default\"]\n  19[label=\"FastQC\"]\n  17 -> 19 [label=\"default\"]\n}",
+                "history": [],
+                "inputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Reverse Reads"
+                                "name": "ERR2231567_1.fastq.gz"
                             }
                         ],
-                        "label": "Reverse Reads",
+                        "label": "ERR2231567_1.fastq.gz",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 187.359375,
-                            "top": 656.765625
+                            "left": 0,
+                            "top": 174.98046875
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "25209075-9248-4e70-9396-87e6e28995e1",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "4cade8d2-87ae-4bae-8795-b1f64c5c3cab"
-                            }
-                        ]
+                        "uuid": "ac2a7e31-6a0c-43f0-b39f-6764ae421dea",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Long Reads"
+                                "name": "ERR2231567_2.fastq.gz"
                             }
                         ],
-                        "label": "Long Reads",
+                        "label": "ERR2231567_2.fastq.gz",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 186.65625,
-                            "top": 803.734375
+                            "left": 1.03515625,
+                            "top": 365.0
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "c1cfa6a5-2c17-4cd7-b582-ce85ff552b67",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "bf7b5353-30b6-471b-91b7-5fd2143bf981"
-                            }
-                        ]
-                    },
+                        "uuid": "2e1fd5bf-3b01-49dd-a091-75c7215eb3f9",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nERR2231567_1.fastq.gz\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nERR2231567_2.fastq.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Cutadapt\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"MEGAHIT\"];\n  2 -->|out1| 3;\n  2 -->|out2| 3;\n  4[\"Bowtie2\"];\n  2 -->|out1| 4;\n  2 -->|out2| 4;\n  3 -->|output| 4;\n  5[\"BAM filter\"];\n  4 -->|output| 5;\n  6[\"BAM filter\"];\n  4 -->|output| 6;\n  7[\"Convert, Merge, Randomize\"];\n  5 -->|outfile| 7;\n  8[\"Convert, Merge, Randomize\"];\n  6 -->|outfile| 8;\n  9[\"Select random lines\"];\n  7 -->|out_file1| 9;\n  10[\"Select random lines\"];\n  8 -->|out_file1| 10;\n  11[\"Filter Tabular\"];\n  9 -->|out_file1| 11;\n  12[\"Filter Tabular\"];\n  10 -->|out_file1| 12;\n  13[\"Unique\"];\n  11 -->|output| 13;\n  14[\"Unique\"];\n  12 -->|output| 14;\n  15[\"Concatenate datasets\"];\n  13 -->|outfile| 15;\n  14 -->|outfile| 15;\n  16[\"seqtk_subseq\"];\n  2 -->|out1| 16;\n  15 -->|out_file1| 16;\n  17[\"seqtk_subseq\"];\n  2 -->|out2| 17;\n  15 -->|out_file1| 17;\n  18[\"FastQC\"];\n  16 -->|default| 18;\n  19[\"FastQC\"];\n  17 -->|default| 19;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "workflow-generate-dataset-for-assembly-tutorial",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0",
                         "errors": null,
-                        "id": 3,
+                        "id": 2,
                         "input_connections": {
-                            "input_file": {
+                            "library|input_1": {
                                 "id": 0,
                                 "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "limits"
-                            },
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "contaminants"
                             },
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "adapters"
+                            "library|input_2": {
+                                "id": 1,
+                                "output_name": "output"
                             }
-                        ],
+                        },
+                        "inputs": [],
                         "label": null,
-                        "name": "FastQC",
+                        "name": "Cutadapt",
                         "outputs": [
                             {
-                                "name": "html_file",
-                                "type": "html"
+                                "name": "out1",
+                                "type": "fastqsanger"
                             },
                             {
-                                "name": "text_file",
+                                "name": "out2",
+                                "type": "fastqsanger"
+                            },
+                            {
+                                "name": "report",
                                 "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 415.015625,
-                            "top": 199.984375
+                            "left": 248.0078125,
+                            "top": 260.0
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "e7b2202befea",
-                            "name": "fastqc",
-                            "owner": "devteam",
+                            "changeset_revision": "5915ea1ec9b1",
+                            "name": "cutadapt",
+                            "owner": "lparsons",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"min_length\": \"\", \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"adapters\": {\"__class__\": \"RuntimeValue\"}, \"nogroup\": \"false\"}",
-                        "tool_version": "0.72+galaxy1",
+                        "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"internal\": \"\", \"error_rate\": \"0.1\", \"no_indels\": \"false\", \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"revcomp\": \"false\"}, \"filter_options\": {\"discard_trimmed\": \"false\", \"discard_untrimmed\": \"false\", \"minimum_length\": \"200\", \"maximum_length\": null, \"length_R2_options\": {\"length_R2_status\": \"False\", \"__current_case__\": 1}, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"discard_cassava\": \"false\"}, \"library\": {\"type\": \"paired\", \"__current_case__\": 1, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"input_2\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}, \"r2\": {\"adapters2\": [], \"front_adapters2\": [], \"anywhere_adapters2\": [], \"cut2\": \"0\", \"quality_cutoff2\": \"\"}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"quality_cutoff\": \"20\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"strip_suffix\": \"\", \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.0+galaxy0",
                         "type": "tool",
-                        "uuid": "d0e16801-e8f6-4889-9502-c57aa6b1a436",
+                        "uuid": "67ddef5c-cde3-462d-a189-77028682a357",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "html_file",
-                                "uuid": "3c8f9841-bf87-4c4b-9af2-115a0b84f13f"
+                                "output_name": "out1",
+                                "uuid": "7b3621e4-5077-4ac8-95d3-61a94a6ee664"
                             },
                             {
                                 "label": null,
-                                "output_name": "text_file",
-                                "uuid": "5c63bd29-f9c1-423b-ad6e-4b944e32c6ac"
+                                "output_name": "out2",
+                                "uuid": "f7db5a96-f4e7-4caf-8e78-093d4e6b007c"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "report",
+                                "uuid": "ff6985ad-6afe-4cf7-9def-223fdd5e5f62"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
                         "errors": null,
-                        "id": 4,
+                        "id": 3,
                         "input_connections": {
-                            "input_file": {
-                                "id": 1,
-                                "output_name": "output"
+                            "input_option|fastq_input1": {
+                                "id": 2,
+                                "output_name": "out1"
+                            },
+                            "input_option|fastq_input2": {
+                                "id": 2,
+                                "output_name": "out2"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "MEGAHIT",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "limits"
-                            },
+                                "name": "output",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "left": 735.9765625,
+                            "top": 301.97265625
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "14ddfc8ffb93",
+                            "name": "megahit",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"advanced_section\": {\"nomercy\": \"false\", \"bubble_level\": \"2\", \"merge_level\": \"20,0.95\", \"prune_level\": \"2\", \"prune_depth\": \"2\", \"disconnect_ratio\": \"0.1\", \"low_local_ratio\": \"0.2\", \"cleaning_rounds\": \"5\", \"nolocal\": \"false\", \"kmin1pass\": \"false\"}, \"basic_section\": {\"min_count\": \"2\", \"k_mer\": {\"k_mer_method\": \"klist_method\", \"__current_case__\": 0, \"k_list\": \"21,29,39,59,79,99,119,141\"}}, \"input_option\": {\"choice\": \"paired\", \"__current_case__\": 2, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"fastq_input2\": {\"__class__\": \"ConnectedValue\"}}, \"output_section\": {\"min_contig_len\": \"200\", \"show_intermediate_contigs\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.9+galaxy0",
+                        "type": "tool",
+                        "uuid": "0e1e0ffb-4536-4802-b886-5f5f391255d1",
+                        "workflow_outputs": [
                             {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "contaminants"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "7a0e5487-3923-46e0-9976-d3fdc3fe7e09"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "library|input_1": {
+                                "id": 2,
+                                "output_name": "out1"
                             },
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "adapters"
+                            "library|input_2": {
+                                "id": 2,
+                                "output_name": "out2"
+                            },
+                            "reference_genome|own_file": {
+                                "id": 3,
+                                "output_name": "output"
                             }
-                        ],
+                        },
+                        "inputs": [],
                         "label": null,
-                        "name": "FastQC",
+                        "name": "Bowtie2",
                         "outputs": [
                             {
-                                "name": "html_file",
-                                "type": "html"
+                                "name": "output",
+                                "type": "bam"
                             },
                             {
-                                "name": "text_file",
+                                "name": "mapping_stats",
                                 "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 415.390625,
-                            "top": 410.765625
+                            "left": 979.00390625,
+                            "top": 40.9765625
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "e7b2202befea",
-                            "name": "fastqc",
+                            "changeset_revision": "f6877ad76b00",
+                            "name": "bowtie2",
                             "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"min_length\": \"\", \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"adapters\": {\"__class__\": \"RuntimeValue\"}, \"nogroup\": \"false\"}",
-                        "tool_version": "0.72+galaxy1",
+                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"no_presets\"}, \"library\": {\"type\": \"paired\", \"__current_case__\": 1, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"input_2\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": \"false\", \"aligned_file\": \"false\", \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 1, \"own_file\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.4.5+galaxy1",
                         "type": "tool",
-                        "uuid": "1f890a7b-848b-40e0-987b-26450c9f5203",
+                        "uuid": "cd8574f0-da3e-4dc1-848e-6f21c57831e6",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "html_file",
-                                "uuid": "0dee124c-9984-4c90-9a76-353ffbcea854"
+                                "output_name": "mapping_stats",
+                                "uuid": "cf119c49-eee7-448a-bfff-0f1053f87821"
                             },
                             {
                                 "label": null,
-                                "output_name": "text_file",
-                                "uuid": "f80ae006-d3ee-4794-bfe1-b656aea05823"
+                                "output_name": "output",
+                                "uuid": "44b0908f-2158-4ea2-be6f-65c0dd803bcb"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
                         "errors": null,
                         "id": 5,
                         "input_connections": {
-                            "long": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "paired_unpaired|fastq_input1": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "paired_unpaired|fastq_input2": {
-                                "id": 1,
+                            "infile": {
+                                "id": 4,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "lr_align"
+                                "description": "runtime parameter for tool BAM filter",
+                                "name": "excludebed"
                             },
                             {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "rotation"
+                                "description": "runtime parameter for tool BAM filter",
+                                "name": "includebed"
                             }
                         ],
                         "label": null,
-                        "name": "Create assemblies with Unicycler",
+                        "name": "BAM filter",
                         "outputs": [
                             {
-                                "name": "assembly_graph",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "assembly",
-                                "type": "fasta"
+                                "name": "outfile",
+                                "type": "bam"
                             }
                         ],
                         "position": {
-                            "left": 397.15625,
-                            "top": 636.984375
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionassembly_graph": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "assembly_graph"
-                            }
+                            "left": 1265.01953125,
+                            "top": 0.0
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
                         "tool_shed_repository": {
-                            "changeset_revision": "88c240872a65",
-                            "name": "unicycler",
+                            "changeset_revision": "2e957d4c4b95",
+                            "name": "ngsutils_bam_filter",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"linear_seqs\": \"0\", \"spades\": {\"no_correct\": \"false\", \"kmer_count\": \"10\", \"depth_filter\": \"0.25\", \"kmers\": \"\", \"min_kmer_frac\": \"0.2\", \"max_kmer_frac\": \"0.95\", \"largest_component\": \"false\"}, \"graph_clean\": {\"min_dead_end_size\": \"1000\", \"min_component_size\": \"1000\"}, \"__page__\": null, \"min_anchor_seg_len\": \"\", \"__rerun_remap_job_id__\": null, \"lr_align\": {\"low_score\": \"\", \"scores\": \"\", \"contamination\": {\"__class__\": \"RuntimeValue\"}}, \"long\": {\"__class__\": \"ConnectedValue\"}, \"paired_unpaired\": {\"fastq_input2\": {\"__class__\": \"ConnectedValue\"}, \"__current_case__\": 0, \"fastq_input_selector\": \"paired\", \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}}, \"min_fasta_length\": \"100\", \"mode\": \"normal\", \"rotation\": {\"start_genes\": {\"__class__\": \"RuntimeValue\"}, \"start_gene_cov\": \"95.0\", \"no_rotate\": \"false\", \"start_gene_id\": \"90.0\"}, \"pilon\": {\"no_pilon\": \"false\", \"min_polish_size\": \"1000\"}}",
-                        "tool_version": "0.4.8.0",
+                        "tool_state": "{\"excludebed\": {\"__class__\": \"RuntimeValue\"}, \"excluderef\": \"\", \"ignore_strand\": \"false\", \"includebed\": {\"__class__\": \"RuntimeValue\"}, \"includeref\": \"\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mapped\": \"false\", \"mask\": \"\", \"maximum_mismatch_ratio\": null, \"maxlen\": null, \"minlen\": null, \"mismatch\": null, \"nopcrdup\": \"false\", \"noproperpair\": \"false\", \"noqcfail\": \"false\", \"nosecondary\": \"false\", \"properpair\": \"false\", \"uniq\": \"-1\", \"uniq_start\": \"false\", \"unmapped\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.5.9",
                         "type": "tool",
-                        "uuid": "98050cb0-ca52-4a9d-a1c3-cd301f36356c",
+                        "uuid": "e2b45ca6-2a67-4b95-a454-5c67fa87bccb",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "assembly",
-                                "uuid": "c35c6740-11f7-4ca3-8b93-a1fe502b8719"
+                                "output_name": "outfile",
+                                "uuid": "c1c6c99c-c810-41f4-84f3-5998c50b1422"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
                         "errors": null,
                         "id": 6,
                         "input_connections": {
-                            "results_0|software_cond|output_0|input": {
-                                "id": 3,
-                                "output_name": "text_file"
-                            },
-                            "results_0|software_cond|output_1|input": {
+                            "infile": {
                                 "id": 4,
-                                "output_name": "text_file"
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "MultiQC",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "stats",
-                                "type": "input"
+                                "description": "runtime parameter for tool BAM filter",
+                                "name": "excludebed"
                             },
                             {
-                                "name": "html_report",
-                                "type": "html"
+                                "description": "runtime parameter for tool BAM filter",
+                                "name": "includebed"
+                            }
+                        ],
+                        "label": null,
+                        "name": "BAM filter",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "bam"
                             }
                         ],
                         "position": {
-                            "left": 650.71875,
-                            "top": 251.3125
+                            "left": 1268.0078125,
+                            "top": 354.00390625
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
                         "tool_shed_repository": {
-                            "changeset_revision": "b2f1f75d49c4",
-                            "name": "multiqc",
+                            "changeset_revision": "2e957d4c4b95",
+                            "name": "ngsutils_bam_filter",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"comment\": \"\", \"__page__\": null, \"title\": \"\", \"__rerun_remap_job_id__\": null, \"results\": [{\"__index__\": 0, \"software_cond\": {\"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}], \"__current_case__\": 8, \"software\": \"fastqc\"}}], \"saveLog\": \"false\"}",
-                        "tool_version": "1.7",
+                        "tool_state": "{\"excludebed\": {\"__class__\": \"RuntimeValue\"}, \"excluderef\": \"\", \"ignore_strand\": \"false\", \"includebed\": {\"__class__\": \"RuntimeValue\"}, \"includeref\": \"\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mapped\": \"true\", \"mask\": \"\", \"maximum_mismatch_ratio\": null, \"maxlen\": null, \"minlen\": null, \"mismatch\": null, \"nopcrdup\": \"false\", \"noproperpair\": \"false\", \"noqcfail\": \"false\", \"nosecondary\": \"false\", \"properpair\": \"false\", \"uniq\": \"-1\", \"uniq_start\": \"false\", \"unmapped\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.5.9",
                         "type": "tool",
-                        "uuid": "3277000f-cee0-4279-80d3-0b266694cce2",
+                        "uuid": "eb538482-dcf6-4509-b4b0-3da71ac6c600",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "stats",
-                                "uuid": "3bfec2db-625d-4aa5-9016-e16fe27bf466"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "html_report",
-                                "uuid": "6f40035d-5c8d-4e18-82ea-0093237d250f"
+                                "output_name": "outfile",
+                                "uuid": "b7c08a3a-296d-4352-90a6-423897d8cc74"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
                         "errors": null,
                         "id": 7,
                         "input_connections": {
-                            "in|inputs": {
+                            "input_bams": {
                                 "id": 5,
-                                "output_name": "assembly"
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Quast",
+                        "name": "Convert, Merge, Randomize",
                         "outputs": [
                             {
-                                "name": "quast_tabular",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "report_html",
-                                "type": "html"
-                            },
-                            {
-                                "name": "report_pdf",
-                                "type": "pdf"
-                            },
-                            {
-                                "name": "log",
+                                "name": "out_file1",
                                 "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 648.875,
-                            "top": 416.5
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionlog": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "log"
-                            },
-                            "HideDatasetActionquast_tabular": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "quast_tabular"
-                            },
-                            "HideDatasetActionreport_pdf": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "report_pdf"
-                            }
+                            "left": 1559.00390625,
+                            "top": 110.9765625
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "59db8ea8c845",
-                            "name": "quast",
-                            "owner": "iuc",
+                            "changeset_revision": "befc9dad4ca8",
+                            "name": "bamtools",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"scaffold_gap_max_size\": \"1000\", \"skip_unaligned_mis_contigs\": \"true\", \"assembly\": {\"ref\": {\"use_ref\": \"false\", \"est_ref_size\": \"\", \"__current_case__\": 1}, \"orga_type\": \"\", \"type\": \"genome\", \"__current_case__\": 0}, \"circos\": \"false\", \"contig_thresholds\": \"0,1000\", \"__page__\": null, \"strict_NA\": \"false\", \"__rerun_remap_job_id__\": null, \"genes\": {\"rna_finding\": \"false\", \"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"conserved_genes_finding\": \"false\"}, \"unaligned_part_size\": \"500\", \"al\": {\"upper_bound_assembly\": \"false\", \"min_identity\": \"95.0\", \"ambiguity_score\": \"0.99\", \"ambiguity_usage\": \"one\", \"upper_bound_min_con\": \"2\", \"fragmented\": \"false\", \"fragmented_max_indent\": \"50\", \"use_all_alignments\": \"false\", \"min_alignment\": \"65\"}, \"extensive_mis_size\": \"1000\", \"large\": \"false\", \"in\": {\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"__current_case__\": 1, \"custom\": \"false\"}, \"k_mer\": {\"k_mer_stats\": \"\", \"__current_case__\": 1}, \"split_scaffolds\": \"false\", \"min_contig\": \"500\"}",
-                        "tool_version": "5.0.2+galaxy0",
+                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"convert\", \"__current_case__\": 0, \"format_type\": {\"format_type_selector\": \"sam\", \"__current_case__\": 6, \"noheader\": \"false\"}}, \"input_bams\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.5.1+galaxy0",
                         "type": "tool",
-                        "uuid": "1bb7b9fa-3e76-48b6-aa08-1169710715c5",
+                        "uuid": "8dc250e9-c89b-40be-8432-08a7330d6e27",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "quast_tsv",
-                                "uuid": "22d4aad1-6145-4209-8261-8dadf4fd4c02"
-                            },
+                                "output_name": "out_file1",
+                                "uuid": "8ad07a76-7793-43b2-add3-7e236a696172"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "input_bams": {
+                                "id": 6,
+                                "output_name": "outfile"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Convert, Merge, Randomize",
+                        "outputs": [
                             {
-                                "label": null,
-                                "output_name": "report_html",
-                                "uuid": "0de88512-45db-4372-9457-94f136a77267"
-                            },
+                                "name": "out_file1",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 1548.0078125,
+                            "top": 462.98828125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "befc9dad4ca8",
+                            "name": "bamtools",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"convert\", \"__current_case__\": 0, \"format_type\": {\"format_type_selector\": \"sam\", \"__current_case__\": 6, \"noheader\": \"false\"}}, \"input_bams\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.5.1+galaxy0",
+                        "type": "tool",
+                        "uuid": "b5c1bcac-9624-477c-998f-a0988b110a26",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "icarus",
-                                "uuid": "84990237-682a-4800-9ce3-dfeb83c7042d"
+                                "output_name": "out_file1",
+                                "uuid": "9801f8ee-e700-4e9b-bbfc-7ccf7aa99372"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
+                        "content_id": "random_lines1",
                         "errors": null,
-                        "id": 8,
+                        "id": 9,
                         "input_connections": {
                             "input": {
-                                "id": 5,
-                                "output_name": "assembly"
+                                "id": 7,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Prokka",
-                                "name": "proteins"
+                                "description": "runtime parameter for tool Select random lines",
+                                "name": "input"
                             }
                         ],
                         "label": null,
-                        "name": "Prokka",
+                        "name": "Select random lines",
                         "outputs": [
                             {
-                                "name": "out_gff",
-                                "type": "gff"
-                            },
-                            {
-                                "name": "out_gbk",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "out_fna",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "out_faa",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "out_ffn",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "out_sqn",
-                                "type": "asn1"
-                            },
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1823.0078125,
+                            "top": 182.98828125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "random_lines1",
+                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"num_lines\": \"210000\", \"seed_source\": {\"seed_source_selector\": \"no_seed\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2",
+                        "type": "tool",
+                        "uuid": "88f4ed97-5899-48f1-a5de-256be6e58862",
+                        "workflow_outputs": [
                             {
-                                "name": "out_fsa",
-                                "type": "fasta"
-                            },
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "69da2900-e66d-4d95-9bdb-1d9f801097e3"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "random_lines1",
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {
+                            "input": {
+                                "id": 8,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [
                             {
-                                "name": "out_tbl",
-                                "type": "txt"
-                            },
+                                "description": "runtime parameter for tool Select random lines",
+                                "name": "input"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Select random lines",
+                        "outputs": [
                             {
-                                "name": "out_err",
-                                "type": "txt"
-                            },
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1826.9921875,
+                            "top": 535.99609375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "random_lines1",
+                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"num_lines\": \"1000000\", \"seed_source\": {\"seed_source_selector\": \"no_seed\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2",
+                        "type": "tool",
+                        "uuid": "9064c0e8-fdc9-4347-99c2-bd6d97104fc9",
+                        "workflow_outputs": [
                             {
-                                "name": "out_txt",
-                                "type": "txt"
-                            },
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "fd4f3605-1f48-4583-b11a-91a9869e7946"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
+                        "errors": null,
+                        "id": 11,
+                        "input_connections": {
+                            "input": {
+                                "id": 9,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Filter Tabular",
+                        "outputs": [
                             {
-                                "name": "out_log",
-                                "type": "txt"
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 647.125,
-                            "top": 603.75
+                            "left": 2081.015625,
+                            "top": 212.98828125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "bf68eb663bc3",
-                            "name": "prokka",
-                            "owner": "crs4",
+                            "changeset_revision": "34d29339abab",
+                            "name": "filter_tabular",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"strain\": \"C-1\", \"increment\": \"10\", \"species\": \"Coli\", \"__page__\": null, \"usegenus\": \"true\", \"evalue\": \"1e-06\", \"locustag\": \"PROKKA\", \"fast\": \"false\", \"compliant\": {\"mincontig\": \"200\", \"__current_case__\": 0, \"compliant_select\": \"no\", \"addgenes\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"kingdom\": {\"gcode\": \"11\", \"kingdom_select\": \"Bacteria\", \"__current_case__\": 1}, \"metagenome\": \"false\", \"centre\": \"\", \"outputs\": [\"gff\", \"gbk\", \"fna\", \"faa\", \"ffn\", \"sqn\", \"fsa\", \"tbl\", \"err\", \"txt\"], \"gffver\": \"3\", \"norrna\": \"false\", \"proteins\": {\"__class__\": \"RuntimeValue\"}, \"notrna\": \"false\", \"plasmid\": \"\", \"rfam\": \"false\", \"genus\": \"Escherichia\", \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.14.5",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"select_columns\", \"__current_case__\": 7, \"columns\": \"1\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.0",
                         "type": "tool",
-                        "uuid": "dd9a67df-68a8-423b-90d2-2167393949e6",
+                        "uuid": "302a62bb-98f7-4998-b290-281bb52e3c70",
                         "workflow_outputs": [
-                            {
-                                "label": "tbl",
-                                "output_name": "out_tbl",
-                                "uuid": "0d6b33c9-b105-4997-9045-b86e52f00156"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_txt",
-                                "uuid": "4b7ef57d-3075-41cf-bc75-a5fc4aa8c942"
-                            },
-                            {
-                                "label": "gbk",
-                                "output_name": "out_gbk",
-                                "uuid": "8e08b54d-87e1-4269-9b96-8ebf1a9bb4ab"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_err",
-                                "uuid": "d2cd11ae-12f9-4123-bfde-119fa409da73"
-                            },
-                            {
-                                "label": "ffn",
-                                "output_name": "out_ffn",
-                                "uuid": "65e4ddf9-f5bc-4078-8b4e-37b332e12ece"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_fsa",
-                                "uuid": "14a0d804-36f3-488f-a85d-4d18ff95d56f"
-                            },
                             {
                                 "label": null,
-                                "output_name": "out_fna",
-                                "uuid": "d494a946-ff3c-4900-a3f5-573ff1540ea3"
-                            },
+                                "output_name": "output",
+                                "uuid": "e83fbb91-742e-448f-8592-bdf37ce3cbdf"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {
+                            "input": {
+                                "id": 10,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Filter Tabular",
+                        "outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_log",
-                                "uuid": "80ed53bf-7d76-4de2-85b5-7dc487922e0e"
-                            },
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 2085,
+                            "top": 566.97265625
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "34d29339abab",
+                            "name": "filter_tabular",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"select_columns\", \"__current_case__\": 7, \"columns\": \"1\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.0",
+                        "type": "tool",
+                        "uuid": "ab1a4102-7bb2-4ba7-80d1-2a532b410201",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_faa",
-                                "uuid": "249632ad-2412-4010-a703-aa8faeecc538"
-                            },
+                                "output_name": "output",
+                                "uuid": "2701a2bd-2ec9-433a-9f26-7f35410ec018"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
+                        "errors": null,
+                        "id": 13,
+                        "input_connections": {
+                            "input": {
+                                "id": 11,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Unique",
+                        "outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_sqn",
-                                "uuid": "175956d0-42a8-4270-b976-3eefef7384ab"
-                            },
+                                "name": "outfile",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 2330,
+                            "top": 265.99609375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "7ce75adb93be",
+                            "name": "unique",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"ignore_case\": \"false\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"is_numeric\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3",
+                        "type": "tool",
+                        "uuid": "2a68a6a4-4d3d-4de3-bc64-35edc63287f9",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_gff",
-                                "uuid": "0e2ffd13-e194-4693-9adf-54e561fd24e5"
+                                "output_name": "outfile",
+                                "uuid": "b2bb66d7-fe76-4ce3-bb5b-72c979a755d1"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "assembly/unicycler-assembly",
-                "path": "topics/assembly/tutorials/unicycler-assembly/workflows/unicycler.ga",
-                "tags": [
-                    "assembly"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "Unicycler training",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-unicycler-assembly/versions/unicycler",
-                "tutorial_id": "unicycler-assembly",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/unicycler-assembly/workflows/unicycler.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/unicycler-assembly/workflows/unicycler.html",
-                "version": 4,
-                "wfid": "assembly-unicycler-assembly",
-                "wfname": "unicycler",
-                "workflow": "unicycler.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0"
-                ],
-                "workflowhub_id": "1182"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.940733"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "fasta_stats",
-                    "owner": "iuc",
-                    "revisions": "9c620a950d3a",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "spades",
-                    "owner": "nml",
-                    "revisions": "b7829778729f",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "velvetoptimiser",
-                    "owner": "simon-gladman",
-                    "revisions": "37d88f41c810",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fasta_stats\n  owner: iuc\n  revisions: 9c620a950d3a\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: spades\n  owner: nml\n  revisions: b7829778729f\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: velvetoptimiser\n  owner: simon-gladman\n  revisions: 37d88f41c810\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.json",
-        "contributors": [
-            {
-                "elixir_node": "au",
-                "email": "simon.gladman@unimelb.edu.au",
-                "id": "slugger70",
-                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
-                "joined": "2017-09",
-                "name": "Simon Gladman",
-                "orcid": "0000-0002-6100-4385",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            }
-        ],
-        "dir": "topics/assembly/tutorials/debruijn-graph-assembly",
-        "edam_operation": [
-            "Genome assembly",
-            "Sequence assembly",
-            "Optimisation and refinement"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "Galaxy@AuBi",
-            "UseGalaxy.eu",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "assembly/debruijn-graph-assembly",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "We learned about how the choice of k-mer size will affect assembly outcomes",
-            "We learned about the strategies that assemblers use to make reference genomes",
-            "We performed a number of assemblies with Velvet and SPAdes.",
-            "You should use SPAdes or another more modern assembler than Velvet for actual assemblies now."
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Introductory",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-02-01",
-        "objectives": [
-            "Perform an optimised Velvet assembly with the Velvet Optimiser",
-            "Compare this assembly with those we did in the basic tutorial",
-            "Perform an assembly using the SPAdes assembler."
-        ],
-        "pageviews": 5735100,
-        "pub_date": "2017-05-24",
-        "questions": [
-            "What are the factors that affect genome assembly?",
-            "How does Genome assembly work?"
-        ],
-        "short_id": "T00031",
-        "short_tools": [
-            "velvetoptimiser",
-            "spades",
-            "fasta-stats"
-        ],
-        "slides": true,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "time_estimation": "2h",
-        "title": "De Bruijn Graph Assembly",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
-            "toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/simon-gladman/velvetoptimiser/velvetoptimiser/2.2.6"
-        ],
-        "topic_name": "assembly",
-        "topic_name_human": "Assembly",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "debruijn-graph-assembly",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.json"
-        },
-        "version": 25,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 299,
-        "visitors": 2068785,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "De Bruijn Graph Assembly",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmutant_R1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmutant_R2\"]\n  2[label=\"VelvetOptimiser\"]\n  0 -> 2 [label=\"output\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"SPAdes\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Fasta Statistics\"]\n  2 -> 4 [label=\"contigs\"]\n  kdacb84a554824ab081ade92af21636cd[color=lightseagreen,label=\"Output\\nfasta_stats_velvet\"]\n  4 -> kdacb84a554824ab081ade92af21636cd\n  5[label=\"Fasta Statistics\"]\n  3 -> 5 [label=\"out_contigs\"]\n  kff376be9736148c6b1c8d9f951b9c6fa[color=lightseagreen,label=\"Output\\nfasta_stats_spades\"]\n  5 -> kff376be9736148c6b1c8d9f951b9c6fa\n}",
-                "history": [
-                    {
-                        "hash": "b435b09a401e2f8678827dafd0e94ee51a2ff804",
-                        "message": "updated test for general-introduction, added test for debruijn-graph-assembly using planemo https://github.com/galaxyproject/planemo/pull/1028",
-                        "num": 4,
-                        "short_hash": "b435b09a4",
-                        "unix": "1595663711"
-                    },
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 3,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 2,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "6ce45f0c2d49dbd6e6bcb72bc3ef161c4c5a7a41",
-                        "message": "workflow",
-                        "num": 1,
-                        "short_hash": "6ce45f0c2",
-                        "unix": "1549974498"
-                    }
-                ],
-                "inputs": [
+                    },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 14,
+                        "input_connections": {
+                            "input": {
+                                "id": 12,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Unique",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "mutant_R1.fastq"
+                                "name": "outfile",
+                                "type": "input"
                             }
                         ],
-                        "label": "mutant_R1",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 10
+                            "left": 2331.97265625,
+                            "top": 617.94921875
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"mutant_R1.fastq\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "fd0c169b-7c95-4ad9-a7c6-7e16e4eaab2e",
-                        "workflow_outputs": []
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "7ce75adb93be",
+                            "name": "unique",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"ignore_case\": \"false\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"is_numeric\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3",
+                        "type": "tool",
+                        "uuid": "c2d1dc5c-4d14-45e5-9bb9-bdab787ea5f3",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "df0bbae1-b735-4cf4-a5a3-ef4f8b525a4e"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 15,
+                        "input_connections": {
+                            "inputs": [
+                                {
+                                    "id": 13,
+                                    "output_name": "outfile"
+                                },
+                                {
+                                    "id": 14,
+                                    "output_name": "outfile"
+                                }
+                            ]
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Concatenate datasets",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "mutant_R2.fastq"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
-                        "label": "mutant_R2",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 130
+                            "left": 2575,
+                            "top": 417.98828125
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"mutant_R2.fastq\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "03430abb-4f48-4bb8-b294-58c4de22a85c",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nmutant_R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nmutant_R2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"VelvetOptimiser\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"SPAdes\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Fasta Statistics\"];\n  2 -->|contigs| 4;\n  dacb84a5-5482-4ab0-81ad-e92af21636cd[\"Output\\nfasta_stats_velvet\"];\n  4 --> dacb84a5-5482-4ab0-81ad-e92af21636cd;\n  style dacb84a5-5482-4ab0-81ad-e92af21636cd stroke:#2c3143,stroke-width:4px;\n  5[\"Fasta Statistics\"];\n  3 -->|out_contigs| 5;\n  ff376be9-7361-48c6-b1c8-d9f951b9c6fa[\"Output\\nfasta_stats_spades\"];\n  5 --> ff376be9-7361-48c6-b1c8-d9f951b9c6fa;\n  style ff376be9-7361-48c6-b1c8-d9f951b9c6fa stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:20 +0000",
-                "name": "Debruijn Graph",
-                "outputs": [
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f46f0e4f75c4",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.1",
+                        "type": "tool",
+                        "uuid": "bf2ba224-25ae-4ec3-9a1f-7cb1afd0aef2",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "53ae320a-b570-4985-ae2a-8344e15e43f9"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
                         "errors": null,
-                        "id": 4,
+                        "id": 16,
                         "input_connections": {
-                            "dataset": {
+                            "in_file": {
                                 "id": 2,
-                                "output_name": "contigs"
+                                "output_name": "out1"
+                            },
+                            "source|name_list": {
+                                "id": 15,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Fasta Statistics",
+                        "name": "seqtk_subseq",
                         "outputs": [
                             {
-                                "name": "stats",
-                                "type": "tabular"
+                                "name": "default",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 450,
-                            "top": 10
+                            "left": 2847.98828125,
+                            "top": 819.98046875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "9c620a950d3a",
-                            "name": "fasta_stats",
+                            "changeset_revision": "3da72230c066",
+                            "name": "seqtk",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"dataset\": \"null\"}",
-                        "tool_version": "1.0.1",
+                        "tool_state": "{\"in_file\": {\"__class__\": \"ConnectedValue\"}, \"l\": \"0\", \"source\": {\"type\": \"name\", \"__current_case__\": 1, \"name_list\": {\"__class__\": \"ConnectedValue\"}}, \"t\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3.1",
                         "type": "tool",
-                        "uuid": "4999cd50-69fd-4e57-af95-8c73ece1fe31",
+                        "uuid": "478adb2b-4910-4aed-af4e-2a66e9a1922c",
                         "workflow_outputs": [
                             {
-                                "label": "fasta_stats_velvet",
-                                "output_name": "stats",
-                                "uuid": "dacb84a5-5482-4ab0-81ad-e92af21636cd"
+                                "label": null,
+                                "output_name": "default",
+                                "uuid": "b47e4af0-c185-4b6f-a529-6f0ef96a14ab"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
                         "errors": null,
-                        "id": 5,
+                        "id": 17,
                         "input_connections": {
-                            "dataset": {
-                                "id": 3,
-                                "output_name": "out_contigs"
+                            "in_file": {
+                                "id": 2,
+                                "output_name": "out2"
+                            },
+                            "source|name_list": {
+                                "id": 15,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Fasta Statistics",
+                        "name": "seqtk_subseq",
                         "outputs": [
                             {
-                                "name": "stats",
-                                "type": "tabular"
+                                "name": "default",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 450,
-                            "top": 130
+                            "left": 2836.97265625,
+                            "top": 1019.98046875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "9c620a950d3a",
-                            "name": "fasta_stats",
+                            "changeset_revision": "3da72230c066",
+                            "name": "seqtk",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"dataset\": \"null\"}",
-                        "tool_version": "1.0.1",
+                        "tool_state": "{\"in_file\": {\"__class__\": \"ConnectedValue\"}, \"l\": \"0\", \"source\": {\"type\": \"name\", \"__current_case__\": 1, \"name_list\": {\"__class__\": \"ConnectedValue\"}}, \"t\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3.1",
                         "type": "tool",
-                        "uuid": "bfc90a5a-640d-4633-b4df-2f8ccdbfe95b",
+                        "uuid": "81ae5423-c7d0-4ceb-a6e4-168ab1f3fd35",
                         "workflow_outputs": [
                             {
-                                "label": "fasta_stats_spades",
-                                "output_name": "stats",
-                                "uuid": "ff376be9-7361-48c6-b1c8-d9f951b9c6fa"
+                                "label": null,
+                                "output_name": "default",
+                                "uuid": "c7de5bbe-f941-4772-bb32-15aeff98678a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+                        "errors": null,
+                        "id": 18,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 16,
+                                "output_name": "default"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "adapters"
+                            },
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "contaminants"
+                            },
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "limits"
+                            }
+                        ],
+                        "label": null,
+                        "name": "FastQC",
+                        "outputs": [
+                            {
+                                "name": "html_file",
+                                "type": "html"
+                            },
+                            {
+                                "name": "text_file",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 3135.9765625,
+                            "top": 775.99609375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3d0c7bdf12f5",
+                            "name": "fastqc",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adapters\": {\"__class__\": \"RuntimeValue\"}, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"min_length\": null, \"nogroup\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.73+galaxy0",
+                        "type": "tool",
+                        "uuid": "6d6cee2a-b879-463b-81d1-7ab4f72ca04b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "text_file",
+                                "uuid": "ca3ea14a-b1cc-481d-b1a3-2b46b8d24809"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "html_file",
+                                "uuid": "6849e3f4-33bc-47a9-8ef5-b7cbbdfe0d93"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+                        "errors": null,
+                        "id": 19,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 17,
+                                "output_name": "default"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "adapters"
+                            },
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "contaminants"
+                            },
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "limits"
+                            }
+                        ],
+                        "label": null,
+                        "name": "FastQC",
+                        "outputs": [
+                            {
+                                "name": "html_file",
+                                "type": "html"
+                            },
+                            {
+                                "name": "text_file",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 3133.984375,
+                            "top": 1104.98046875
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3d0c7bdf12f5",
+                            "name": "fastqc",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adapters\": {\"__class__\": \"RuntimeValue\"}, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"min_length\": null, \"nogroup\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.73+galaxy0",
+                        "type": "tool",
+                        "uuid": "54fc20b8-5520-4b93-a7d8-ed447df19b3c",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "html_file",
+                                "uuid": "a85a4180-b2ab-4cac-9c71-76aee3df673f"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "text_file",
+                                "uuid": "65e24721-ec93-4648-9310-c3c2609b7818"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/debruijn-graph-assembly",
-                "path": "topics/assembly/tutorials/debruijn-graph-assembly/workflows/debruijn-graph.ga",
-                "tags": [
-                    "assembly"
-                ],
+                "parent_id": "assembly/metagenomics-assembly",
+                "path": "topics/assembly/tutorials/metagenomics-assembly/workflows/workflow-generate-dataset-for-assembly-tutorial.ga",
+                "tags": [],
                 "test_results": null,
-                "tests": true,
-                "title": "Debruijn Graph",
+                "tests": false,
+                "title": "workflow-generate-dataset-for-assembly-tutorial",
                 "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-debruijn-graph-assembly/versions/debruijn-graph",
-                "tutorial_id": "debruijn-graph-assembly",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/debruijn-graph-assembly/workflows/debruijn-graph.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/debruijn-graph-assembly/workflows/debruijn-graph.html",
-                "version": 4,
-                "wfid": "assembly-debruijn-graph-assembly",
-                "wfname": "debruijn-graph",
-                "workflow": "debruijn-graph.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-metagenomics-assembly/versions/workflow-generate-dataset-for-assembly-tutorial",
+                "tutorial_id": "metagenomics-assembly",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/metagenomics-assembly/workflows/workflow-generate-dataset-for-assembly-tutorial.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/metagenomics-assembly/workflows/workflow-generate-dataset-for-assembly-tutorial.html",
+                "version": 0,
+                "wfid": "assembly-metagenomics-assembly",
+                "wfname": "workflow-generate-dataset-for-assembly-tutorial",
+                "workflow": "workflow-generate-dataset-for-assembly-tutorial.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/simon-gladman/velvetoptimiser/velvetoptimiser/2.2.6"
+                    "random_lines1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+                    "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0"
                 ],
-                "workflowhub_id": "1124"
+                "workflowhub_id": "1116"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.582600"
+        "zenodo_link": "https://zenodo.org/record/7818827"
     },
     {
         "admin_install": {
@@ -24657,13 +25826,6 @@
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
             "tools": [
-                {
-                    "name": "flye",
-                    "owner": "bgruening",
-                    "revisions": "3ee0ef312022",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
                 {
                     "name": "prokka",
                     "owner": "crs4",
@@ -24672,177 +25834,152 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "prokka",
-                    "owner": "crs4",
-                    "revisions": "111884f0d912",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bwa",
+                    "name": "fastqc",
                     "owner": "devteam",
-                    "revisions": "3fe632431b68",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bandage",
-                    "owner": "iuc",
-                    "revisions": "b2860df42e16",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bandage",
-                    "owner": "iuc",
-                    "revisions": "94fe43e75ddc",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_stats",
-                    "owner": "iuc",
-                    "revisions": "9c620a950d3a",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_stats",
-                    "owner": "iuc",
-                    "revisions": "0dbb995c7d35",
+                    "revisions": "e7b2202befea",
                     "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "jbrowse",
-                    "owner": "iuc",
-                    "revisions": "2bb2e07a7a21",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "jbrowse",
+                    "name": "multiqc",
                     "owner": "iuc",
-                    "revisions": "17359b808b01",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "revisions": "b2f1f75d49c4",
+                    "tool_panel_section_label": "Quality Control",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "nanoplot",
+                    "name": "quast",
                     "owner": "iuc",
-                    "revisions": "edbb6c5028f5",
-                    "tool_panel_section_label": "Nanopore",
+                    "revisions": "59db8ea8c845",
+                    "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pilon",
+                    "name": "unicycler",
                     "owner": "iuc",
-                    "revisions": "11e5408fd238",
+                    "revisions": "9e3e80cc4ad4",
                     "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: flye\n  owner: bgruening\n  revisions: 3ee0ef312022\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: prokka\n  owner: crs4\n  revisions: bf68eb663bc3\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: prokka\n  owner: crs4\n  revisions: 111884f0d912\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: 3fe632431b68\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: b2860df42e16\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: 94fe43e75ddc\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n  owner: iuc\n  revisions: 9c620a950d3a\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n  owner: iuc\n  revisions: 0dbb995c7d35\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 2bb2e07a7a21\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 17359b808b01\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: edbb6c5028f5\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pilon\n  owner: iuc\n  revisions: 11e5408fd238\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/chloroplast-assembly/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: prokka\n  owner: crs4\n  revisions: bf68eb663bc3\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: b2f1f75d49c4\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 59db8ea8c845\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unicycler\n  owner: iuc\n  revisions: 9e3e80cc4ad4\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/unicycler-assembly/tutorial.json",
         "contributors": [
             {
-                "id": "annasyme",
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
                 "joined": "2017-09",
-                "name": "Anna Syme",
-                "orcid": "0000-0002-9906-0673",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+            },
+            {
+                "email": "delphine.lariviere@galaxy.org",
+                "id": "delphine-l",
+                "joined": "2017-09",
+                "name": "Delphine Lariviere",
+                "orcid": "0000-0001-6421-3484",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
+            },
+            {
+                "elixir_node": "au",
+                "email": "simon.gladman@unimelb.edu.au",
+                "id": "slugger70",
+                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
+                "joined": "2017-09",
+                "name": "Simon Gladman",
+                "orcid": "0000-0002-6100-4385",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
             }
         ],
-        "dir": "topics/assembly/tutorials/chloroplast-assembly",
+        "dir": "topics/assembly/tutorials/unicycler-assembly",
+        "edam_ontology": [
+            "topic_0196",
+            "topic_0622",
+            "topic_3301"
+        ],
         "edam_operation": [
-            "Genome indexing",
-            "De-novo assembly",
-            "Sequence alignment",
-            "Box-Whisker plot plotting",
             "Genome annotation",
-            "Read mapping",
-            "Scatter plot plotting",
-            "Mapping assembly",
-            "Genome visualisation",
-            "Sequence assembly visualisation",
-            "Generation",
-            "Analysis",
-            "Coding region prediction",
-            "Cross-assembly",
+            "Visualisation",
             "Genome assembly",
-            "Sequence assembly",
+            "Sequencing quality control",
+            "Sequence assembly validation",
             "Gene prediction",
-            "Read alignment"
+            "Statistical calculation",
+            "Aggregation",
+            "Validation",
+            "Sequence composition calculation",
+            "Coding region prediction"
+        ],
+        "edam_topic": [
+            "Sequence assembly",
+            "Genomics",
+            "Microbiology"
         ],
-        "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "assembly",
+                "tutorials": [
+                    "ecoli_comparison"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "assembly/chloroplast-assembly",
+        "id": "assembly/unicycler-assembly",
         "inexact_supported_servers": [
             "GalaxyTrakr",
+            "HyPhy HIV NGS Tools",
+            "MISSISSIPPI",
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.no"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "A chloroplast genome can be assembled with long reads and polished with short reads",
-            "The assembly graph is useful to look at and think about genomic structure",
-            "We can map raw reads back to the assembly and investigate areas of high or low read coverage",
-            "We can view an assembly, its mapped reads, and its annotations in JBrowse"
+            "We learned about the strategies used by assemblers for hybrid assemblies",
+            "We performed an hybrid assembly of a bacterial genome and its annotation",
+            "Unicycler is a pipeline bases on Spades and Pilon dedicated to hybrid assembly of Small genomes",
+            "Combination of short and long reads helped us produce an almost perfect assembly"
         ],
         "layout": "tutorial_hands_on",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-03-13",
         "objectives": [
-            "Assemble a chloroplast genome from long reads",
-            "Polish the assembly with short reads",
-            "Annotate the assembly and view",
-            "Map reads to the assembly and view"
+            "Perform Quality Control on your reads",
+            "Perform a Small genome Assembly with Unicycler",
+            "Evaluate the Quality of the Assembly with Quast",
+            "Annotate the assembly with Prokka"
         ],
-        "pageviews": 9428,
-        "pub_date": "2020-12-04",
+        "pageviews": 5917098,
+        "pub_date": "2017-10-11",
         "questions": [
-            "How can we assemble a chloroplast genome?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "annasyme"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "35M",
-                "speakers": [
-                    "annasyme"
-                ],
-                "youtube_id": "eyfCyINTD_E"
-            }
+            "I have short reads and long reads. How do I assemble a genome?"
         ],
-        "short_id": "T00030",
+        "short_id": "T00038",
         "short_tools": [
-            "nanoplot",
-            "jbrowse",
-            "flye",
-            "fasta-stats",
             "prokka",
-            "bandage_info",
-            "bandage_image",
-            "bwa_mem",
-            "upload1",
-            "pilon"
+            "unicycler",
+            "quast",
+            "multiqc",
+            "fastqc"
         ],
-        "slides": false,
+        "slides": true,
         "slides_recordings": false,
         "supported_servers": {
             "exact": [
@@ -24850,6 +25987,16 @@
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ],
             "inexact": [
@@ -24858,6 +26005,21 @@
                     "url": "https://galaxytrakr.org/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -24872,37 +26034,22 @@
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
         "tags": [
-            "plants",
-            "nanopore",
-            "jbrowse1"
+            "prokaryote",
+            "microgalaxy"
         ],
-        "time_estimation": "2h",
-        "title": "Chloroplast genome assembly",
+        "time_estimation": "4h",
+        "title": "Unicycler Assembly",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
-            "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1",
-            "upload1"
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0"
         ],
         "topic_name": "assembly",
         "topic_name_human": "Assembly",
@@ -24912,51 +26059,93 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "chloroplast-assembly",
+        "tutorial_name": "unicycler-assembly",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/chloroplast-assembly/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/chloroplast-assembly/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/chloroplast-assembly/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/unicycler-assembly/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/unicycler-assembly/tutorial.json"
         },
-        "version": 17,
+        "version": 23,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 170,
-        "visitors": 5895,
+        "visit_duration": 274,
+        "visitors": 2144791,
         "workflows": [
             {
                 "creators": [],
-                "description": "Assembly",
+                "description": "Unicycler Assembly",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina_reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nNanopore_reads\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTiny_set_illumina_read\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTiny_set_nanopore_reads\"]\n  4[label=\"Flye assembly\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"NanoPlot\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"Map with BWA-MEM\"]\n  0 -> 6 [label=\"output\"]\n  4 -> 6 [label=\"consensus\"]\n  7[label=\"Fasta Statistics\"]\n  4 -> 7 [label=\"consensus\"]\n  8[label=\"Bandage Info\"]\n  4 -> 8 [label=\"assembly_gfa\"]\n  9[label=\"Bandage Image\"]\n  4 -> 9 [label=\"assembly_gfa\"]\n  10[label=\"pilon\"]\n  6 -> 10 [label=\"bam_output\"]\n  4 -> 10 [label=\"consensus\"]\n  11[label=\"Fasta Statistics\"]\n  10 -> 11 [label=\"output_fasta\"]\n  12[label=\"Map with BWA-MEM\"]\n  2 -> 12 [label=\"output\"]\n  10 -> 12 [label=\"output_fasta\"]\n  13[label=\"Map with BWA-MEM\"]\n  3 -> 13 [label=\"output\"]\n  10 -> 13 [label=\"output_fasta\"]\n  14[label=\"Prokka\"]\n  10 -> 14 [label=\"output_fasta\"]\n  15[label=\"JBrowse\"]\n  10 -> 15 [label=\"output_fasta\"]\n  12 -> 15 [label=\"bam_output\"]\n  13 -> 15 [label=\"bam_output\"]\n  16[label=\"JBrowse\"]\n  10 -> 16 [label=\"output_fasta\"]\n  14 -> 16 [label=\"out_gff\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nForward reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReverse Reads\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nLong Reads\"]\n  3[label=\"FastQC\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"FastQC\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Create assemblies with Unicycler\"]\n  2 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"MultiQC\"]\n  3 -> 6 [label=\"text_file\"]\n  4 -> 6 [label=\"text_file\"]\n  7[label=\"Quast\"]\n  5 -> 7 [label=\"assembly\"]\n  8[label=\"Prokka\"]\n  5 -> 8 [label=\"assembly\"]\n  k0d6b33c9b10549979045b86e52f00156[color=lightseagreen,label=\"Output\\ntbl\"]\n  8 -> k0d6b33c9b10549979045b86e52f00156\n  k8e08b54d87e142699b968ebf1a9bb4ab[color=lightseagreen,label=\"Output\\ngbk\"]\n  8 -> k8e08b54d87e142699b968ebf1a9bb4ab\n  k65e4ddf9f5bc40788b4e37b332e12ece[color=lightseagreen,label=\"Output\\nffn\"]\n  8 -> k65e4ddf9f5bc40788b4e37b332e12ece\n}",
                 "history": [
                     {
-                        "hash": "ed613d5a1151b9f28f238d38166228cd186f2462",
-                        "message": "Updated workflow with new version of Fasta Stats",
+                        "hash": "232ce03723ab9acbd124828954705c1cd2679abd",
+                        "message": "removed name label bit",
+                        "num": 9,
+                        "short_hash": "232ce0372",
+                        "unix": "1581615057"
+                    },
+                    {
+                        "hash": "cccd85216e3d9baaca787eb7ae8808bd5f3fa2dc",
+                        "message": "minor tweaks and files unhidden",
+                        "num": 8,
+                        "short_hash": "cccd85216",
+                        "unix": "1581613998"
+                    },
+                    {
+                        "hash": "2a2b6329ed96aaaf214703eae87459c58d6e8702",
+                        "message": "name fixed",
+                        "num": 7,
+                        "short_hash": "2a2b6329e",
+                        "unix": "1581095735"
+                    },
+                    {
+                        "hash": "3d424d5e65326cf45c1e4d34851998ab29e6e85c",
+                        "message": "annotation fixed",
+                        "num": 6,
+                        "short_hash": "3d424d5e6",
+                        "unix": "1581014437"
+                    },
+                    {
+                        "hash": "2eade3cbf7b99b8252c3a53ac6cac59e0cacd432",
+                        "message": "tags added",
+                        "num": 5,
+                        "short_hash": "2eade3cbf",
+                        "unix": "1581004807"
+                    },
+                    {
+                        "hash": "07642064759cb13fda345ab9a687aa96b80b3004",
+                        "message": "workflows updated with newer tools, added missing",
+                        "num": 4,
+                        "short_hash": "076420647",
+                        "unix": "1580135207"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
                         "num": 3,
-                        "short_hash": "ed613d5a1",
-                        "unix": "1683677548"
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
                     },
                     {
-                        "hash": "2b2bcd3917fafb9b8bc912598edf3ab28cee70d5",
-                        "message": "swap version of tool for one on every server",
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
                         "num": 2,
-                        "short_hash": "2b2bcd391",
-                        "unix": "1613141279"
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
                     },
                     {
-                        "hash": "ebcd3d5282b03ce89bd65e0d39748970c7738481",
-                        "message": "updated workflow added",
+                        "hash": "02b1037e840cced4c04432f9e6e22cee7ef20392",
+                        "message": "add testing for unicycler",
                         "num": 1,
-                        "short_hash": "ebcd3d528",
-                        "unix": "1611556716"
+                        "short_hash": "02b1037e8",
+                        "unix": "1527005073"
                     }
                 ],
                 "inputs": [
@@ -24969,22 +26158,28 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Illumina_reads"
+                                "name": "Forward reads"
                             }
                         ],
-                        "label": "Illumina_reads",
+                        "label": "Forward reads",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 294.1953125,
-                            "top": 123.90625
+                            "left": 230.140625,
+                            "top": 404.015625
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "35434963-8a88-47e2-99f0-ef3eb0484f7e",
-                        "workflow_outputs": []
+                        "uuid": "5152d41f-3523-496e-afa2-8d4b0af89b2a",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "e14afa81-ce6c-4577-b17e-90ef2b75c885"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
@@ -24995,685 +26190,502 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Nanopore_reads"
+                                "name": "Reverse Reads"
                             }
                         ],
-                        "label": "Nanopore_reads",
+                        "label": "Reverse Reads",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0.0,
-                            "top": 354.859375
+                            "left": 187.359375,
+                            "top": 656.765625
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "59b157b8-f5c4-498c-b66c-0d206ba06ee9",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "uuid": "25209075-9248-4e70-9396-87e6e28995e1",
+                        "workflow_outputs": [
                             {
-                                "description": "",
-                                "name": "Tiny_set_illumina_read"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "4cade8d2-87ae-4bae-8795-b1f64c5c3cab"
                             }
-                        ],
-                        "label": "Tiny_set_illumina_read",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 908.265625,
-                            "top": 919.359375
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "39c47516-8e9c-4d44-b6bc-326c4be142ee",
-                        "workflow_outputs": []
+                        ]
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Tiny_set_nanopore_reads"
+                                "name": "Long Reads"
                             }
                         ],
-                        "label": "Tiny_set_nanopore_reads",
+                        "label": "Long Reads",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 908.2734375,
-                            "top": 1040.5703125
+                            "left": 186.65625,
+                            "top": 803.734375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "1257e34e-ad76-4f76-88dc-f22c5cc60b8b",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIllumina_reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nNanopore_reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nTiny_set_illumina_read\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nTiny_set_nanopore_reads\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Flye assembly\"];\n  1 -->|output| 4;\n  5[\"NanoPlot\"];\n  1 -->|output| 5;\n  6[\"Map with BWA-MEM\"];\n  0 -->|output| 6;\n  4 -->|consensus| 6;\n  7[\"Fasta Statistics\"];\n  4 -->|consensus| 7;\n  8[\"Bandage Info\"];\n  4 -->|assembly_gfa| 8;\n  9[\"Bandage Image\"];\n  4 -->|assembly_gfa| 9;\n  10[\"pilon\"];\n  6 -->|bam_output| 10;\n  4 -->|consensus| 10;\n  11[\"Fasta Statistics\"];\n  10 -->|output_fasta| 11;\n  12[\"Map with BWA-MEM\"];\n  2 -->|output| 12;\n  10 -->|output_fasta| 12;\n  13[\"Map with BWA-MEM\"];\n  3 -->|output| 13;\n  10 -->|output_fasta| 13;\n  14[\"Prokka\"];\n  10 -->|output_fasta| 14;\n  15[\"JBrowse\"];\n  10 -->|output_fasta| 15;\n  12 -->|bam_output| 15;\n  13 -->|bam_output| 15;\n  16[\"JBrowse\"];\n  10 -->|output_fasta| 16;\n  14 -->|out_gff| 16;",
-                "modified": "2024-08-18 00:06:20 +0000",
-                "name": "Chloroplast-genome-assembly-and-annotation",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "inputs": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Flye assembly",
-                        "outputs": [
-                            {
-                                "name": "consensus",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "assembly_graph",
-                                "type": "graph_dot"
-                            },
-                            {
-                                "name": "assembly_gfa",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "assembly_info",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "flye_log",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 301.03125,
-                            "top": 244.03125
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionconsensus": {
-                                "action_arguments": {
-                                    "newname": "flye-assembly.fasta"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "consensus"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3ee0ef312022",
-                            "name": "flye",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"asm\": null, \"g\": \"160000\", \"i\": \"1\", \"inputs\": {\"__class__\": \"ConnectedValue\"}, \"m\": null, \"meta\": \"false\", \"mode\": \"--nano-raw\", \"no_trestle\": \"false\", \"plasmids\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6",
-                        "type": "tool",
-                        "uuid": "efcc01cf-bb71-4c46-9eec-83488a79859e",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "assembly_info",
-                                "uuid": "f14c4d31-93bc-4e19-9d81-f3061ed8898e"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "flye_log",
-                                "uuid": "33126b99-3149-4da0-bcaa-031156d82f09"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "consensus",
-                                "uuid": "1e33ae8a-4d67-44bf-933e-ade1a94b7f85"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "assembly_graph",
-                                "uuid": "89d53ead-feef-4079-8988-627850312bd9"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "assembly_gfa",
-                                "uuid": "de2f80a8-f73f-419c-81e2-208b63c84c1f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "mode|reads|files": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "NanoPlot",
-                        "outputs": [
-                            {
-                                "name": "output_html",
-                                "type": "html"
-                            },
-                            {
-                                "name": "nanostats",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "nanostats_post_filtering",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "read_length",
-                                "type": "png"
-                            },
-                            {
-                                "name": "log_read_length",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 315.015625,
-                            "top": 701.8125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "edbb6c5028f5",
-                            "name": "nanoplot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"customization\": {\"color\": null, \"format\": \"png\", \"plots\": null, \"N50\": \"false\"}, \"filter\": {\"maxlength\": null, \"minlength\": null, \"drop_outliers\": \"false\", \"downsample\": null, \"loglength\": \"false\", \"percentqual\": \"false\", \"alength\": \"false\", \"minqual\": null, \"readtype\": null, \"barcoded\": \"false\"}, \"mode\": {\"choice\": \"batch\", \"__current_case__\": 0, \"reads\": {\"type\": \"fastq\", \"__current_case__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.28.2+galaxy1",
-                        "type": "tool",
-                        "uuid": "655afaaf-7a0f-4103-b68c-32ad0c03a32b",
+                        "uuid": "c1cfa6a5-2c17-4cd7-b582-ce85ff552b67",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "log_read_length",
-                                "uuid": "a87ac909-55de-42d8-b637-981e0b37c062"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "nanostats_post_filtering",
-                                "uuid": "46189275-9aef-4c23-8410-d6a6eb14299d"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "nanostats",
-                                "uuid": "1f5ce9f1-eec9-48c9-b175-8d530b9d9024"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "read_length",
-                                "uuid": "18ebb4bc-a4a3-48a5-b2e2-c8f9fb801dd6"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_html",
-                                "uuid": "5192b242-50f9-4205-aac7-d1deca088724"
+                                "output_name": "output",
+                                "uuid": "bf7b5353-30b6-471b-91b7-5fd2143bf981"
                             }
                         ]
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nForward reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReverse Reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nLong Reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"FastQC\"];\n  0 -->|output| 3;\n  4[\"FastQC\"];\n  1 -->|output| 4;\n  5[\"Create assemblies with Unicycler\"];\n  2 -->|output| 5;\n  0 -->|output| 5;\n  1 -->|output| 5;\n  6[\"MultiQC\"];\n  3 -->|text_file| 6;\n  4 -->|text_file| 6;\n  7[\"Quast\"];\n  5 -->|assembly| 7;\n  8[\"Prokka\"];\n  5 -->|assembly| 8;\n  0d6b33c9-b105-4997-9045-b86e52f00156[\"Output\\ntbl\"];\n  8 --> 0d6b33c9-b105-4997-9045-b86e52f00156;\n  style 0d6b33c9-b105-4997-9045-b86e52f00156 stroke:#2c3143,stroke-width:4px;\n  8e08b54d-87e1-4269-9b96-8ebf1a9bb4ab[\"Output\\ngbk\"];\n  8 --> 8e08b54d-87e1-4269-9b96-8ebf1a9bb4ab;\n  style 8e08b54d-87e1-4269-9b96-8ebf1a9bb4ab stroke:#2c3143,stroke-width:4px;\n  65e4ddf9-f5bc-4078-8b4e-37b332e12ece[\"Output\\nffn\"];\n  8 --> 65e4ddf9-f5bc-4078-8b4e-37b332e12ece;\n  style 65e4ddf9-f5bc-4078-8b4e-37b332e12ece stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Unicycler training",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "fastq_input|fastq_input1": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "reference_source|ref_file": {
-                                "id": 4,
-                                "output_name": "consensus"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Map with BWA-MEM",
-                        "outputs": [
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "bam_output",
-                                "type": "bam"
+                                "description": "",
+                                "name": "Forward reads"
                             }
                         ],
+                        "label": "Forward reads",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 637.8359375,
-                            "top": 0.0
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionbam_output": {
-                                "action_arguments": {
-                                    "newname": "illumina.bam"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "bam_output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "dfd8b7f78c37",
-                            "name": "bwa",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 230.140625,
+                            "top": 404.015625
                         },
-                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"illumina\", \"__current_case__\": 0}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 1, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}, \"index_a\": \"auto\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.17.1",
-                        "type": "tool",
-                        "uuid": "95ed65e8-2534-4cef-888f-6de9f83a3770",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "5152d41f-3523-496e-afa2-8d4b0af89b2a",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "bam_output",
-                                "uuid": "2a0f0b99-d8b1-4585-8272-159d9f3a6a6d"
+                                "output_name": "output",
+                                "uuid": "e14afa81-ce6c-4577-b17e-90ef2b75c885"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "fasta": {
-                                "id": 4,
-                                "output_name": "consensus"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Fasta Statistics",
-                        "outputs": [
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "stats_output",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "Reverse Reads"
                             }
                         ],
+                        "label": "Reverse Reads",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 640.78125,
-                            "top": 365.859375
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionstats": {
-                                "action_arguments": {
-                                    "newname": "Fasta stats of flye assembly"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "stats"
-                            },
-                            "RenameDatasetActionstats_output": {
-                                "action_arguments": {
-                                    "newname": "Flye assembly fasta stats"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "stats_output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "0dbb995c7d35",
-                            "name": "fasta_stats",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 187.359375,
+                            "top": 656.765625
                         },
-                        "tool_state": "{\"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gaps_option\": \"false\", \"genome_size\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0",
-                        "type": "tool",
-                        "uuid": "e4b5dd88-a21b-4b20-93b6-5de72b3883e1",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "25209075-9248-4e70-9396-87e6e28995e1",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "stats_output",
-                                "uuid": "083a96d6-2e0f-408e-a343-9df5cccbcbae"
+                                "output_name": "output",
+                                "uuid": "4cade8d2-87ae-4bae-8795-b1f64c5c3cab"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 4,
-                                "output_name": "assembly_gfa"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Bandage Info",
-                        "outputs": [
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "outfile",
-                                "type": "txt"
+                                "description": "",
+                                "name": "Long Reads"
                             }
                         ],
+                        "label": "Long Reads",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 608.78125,
-                            "top": 588.5859375
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b2860df42e16",
-                            "name": "bandage",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 186.65625,
+                            "top": 803.734375
                         },
-                        "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"tsv\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.8.1+galaxy1",
-                        "type": "tool",
-                        "uuid": "11a0fc24-13ed-4199-8524-1ebc317e449e",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "c1cfa6a5-2c17-4cd7-b582-ce85ff552b67",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "5bfce93b-c6bd-42c2-8910-d99b2f472b70"
+                                "output_name": "output",
+                                "uuid": "bf7b5353-30b6-471b-91b7-5fd2143bf981"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
                         "errors": null,
-                        "id": 9,
+                        "id": 3,
                         "input_connections": {
                             "input_file": {
-                                "id": 4,
-                                "output_name": "assembly_gfa"
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "limits"
+                            },
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "contaminants"
+                            },
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "adapters"
+                            }
+                        ],
                         "label": null,
-                        "name": "Bandage Image",
+                        "name": "FastQC",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "jpg"
+                                "name": "html_file",
+                                "type": "html"
+                            },
+                            {
+                                "name": "text_file",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 605.78125,
-                            "top": 764.40625
+                            "left": 415.015625,
+                            "top": 199.984375
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "b2860df42e16",
-                            "name": "bandage",
-                            "owner": "iuc",
+                            "changeset_revision": "e7b2202befea",
+                            "name": "fastqc",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"height\": \"1000\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"lengths\": \"true\", \"names\": \"false\", \"output_format\": \"jpg\", \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.8.1+galaxy2",
+                        "tool_state": "{\"min_length\": \"\", \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"adapters\": {\"__class__\": \"RuntimeValue\"}, \"nogroup\": \"false\"}",
+                        "tool_version": "0.72+galaxy1",
                         "type": "tool",
-                        "uuid": "528ebaa8-2c95-472b-b719-4752804e2d00",
+                        "uuid": "d0e16801-e8f6-4889-9502-c57aa6b1a436",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "64a6e260-f828-42a7-9ff6-415e3fa5c496"
+                                "output_name": "html_file",
+                                "uuid": "3c8f9841-bf87-4c4b-9af2-115a0b84f13f"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "text_file",
+                                "uuid": "5c63bd29-f9c1-423b-ad6e-4b944e32c6ac"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
                         "errors": null,
-                        "id": 10,
+                        "id": 4,
                         "input_connections": {
-                            "auto_selection|bam": {
-                                "id": 6,
-                                "output_name": "bam_output"
-                            },
-                            "reference_genome|history_item": {
-                                "id": 4,
-                                "output_name": "consensus"
+                            "input_file": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "limits"
+                            },
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "contaminants"
+                            },
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "adapters"
+                            }
+                        ],
                         "label": null,
-                        "name": "pilon",
+                        "name": "FastQC",
                         "outputs": [
                             {
-                                "name": "output_changes",
-                                "type": "txt"
+                                "name": "html_file",
+                                "type": "html"
                             },
                             {
-                                "name": "output_fasta",
-                                "type": "fasta"
+                                "name": "text_file",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 886.65625,
-                            "top": 262.0625
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_fasta": {
-                                "action_arguments": {
-                                    "newname": "polished-assembly.fasta"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_fasta"
-                            }
+                            "left": 415.390625,
+                            "top": 410.765625
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "11e5408fd238",
-                            "name": "pilon",
-                            "owner": "iuc",
+                            "changeset_revision": "e7b2202befea",
+                            "name": "fastqc",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"auto_selection\": {\"auto_enabled\": \"true\", \"__current_case__\": 0, \"bam\": {\"__class__\": \"ConnectedValue\"}}, \"changes\": \"true\", \"options\": {\"selection_mode\": \"default\", \"__current_case__\": 0}, \"reference_genome\": {\"reference_genome_source\": \"history\", \"__current_case__\": 0, \"history_item\": {\"__class__\": \"ConnectedValue\"}}, \"variant\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.20.1",
+                        "tool_state": "{\"min_length\": \"\", \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"adapters\": {\"__class__\": \"RuntimeValue\"}, \"nogroup\": \"false\"}",
+                        "tool_version": "0.72+galaxy1",
                         "type": "tool",
-                        "uuid": "a445d29c-7b0c-48a0-984b-945f2acb64ac",
+                        "uuid": "1f890a7b-848b-40e0-987b-26450c9f5203",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_changes",
-                                "uuid": "d48e11c7-ea49-457b-8a96-38b6dc0f1bc2"
+                                "output_name": "html_file",
+                                "uuid": "0dee124c-9984-4c90-9a76-353ffbcea854"
                             },
                             {
                                 "label": null,
-                                "output_name": "output_fasta",
-                                "uuid": "e898b32c-b4ae-4f5a-b3be-f7a2681e4fa0"
+                                "output_name": "text_file",
+                                "uuid": "f80ae006-d3ee-4794-bfe1-b656aea05823"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
                         "errors": null,
-                        "id": 11,
+                        "id": 5,
                         "input_connections": {
-                            "fasta": {
-                                "id": 10,
-                                "output_name": "output_fasta"
+                            "long": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "paired_unpaired|fastq_input1": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "paired_unpaired|fastq_input2": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "lr_align"
+                            },
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "rotation"
+                            }
+                        ],
                         "label": null,
-                        "name": "Fasta Statistics",
+                        "name": "Create assemblies with Unicycler",
                         "outputs": [
                             {
-                                "name": "stats_output",
+                                "name": "assembly_graph",
                                 "type": "tabular"
+                            },
+                            {
+                                "name": "assembly",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 1170.40625,
-                            "top": 139.0625
+                            "left": 397.15625,
+                            "top": 636.984375
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionstats": {
-                                "action_arguments": {
-                                    "newname": "Fasta stats of polished flye assembly"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "stats"
-                            },
-                            "RenameDatasetActionstats_output": {
-                                "action_arguments": {
-                                    "newname": "Pilon polished assembly fasta stats"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "stats_output"
+                            "HideDatasetActionassembly_graph": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "assembly_graph"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "0dbb995c7d35",
-                            "name": "fasta_stats",
+                            "changeset_revision": "88c240872a65",
+                            "name": "unicycler",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gaps_option\": \"false\", \"genome_size\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0",
+                        "tool_state": "{\"linear_seqs\": \"0\", \"spades\": {\"no_correct\": \"false\", \"kmer_count\": \"10\", \"depth_filter\": \"0.25\", \"kmers\": \"\", \"min_kmer_frac\": \"0.2\", \"max_kmer_frac\": \"0.95\", \"largest_component\": \"false\"}, \"graph_clean\": {\"min_dead_end_size\": \"1000\", \"min_component_size\": \"1000\"}, \"__page__\": null, \"min_anchor_seg_len\": \"\", \"__rerun_remap_job_id__\": null, \"lr_align\": {\"low_score\": \"\", \"scores\": \"\", \"contamination\": {\"__class__\": \"RuntimeValue\"}}, \"long\": {\"__class__\": \"ConnectedValue\"}, \"paired_unpaired\": {\"fastq_input2\": {\"__class__\": \"ConnectedValue\"}, \"__current_case__\": 0, \"fastq_input_selector\": \"paired\", \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}}, \"min_fasta_length\": \"100\", \"mode\": \"normal\", \"rotation\": {\"start_genes\": {\"__class__\": \"RuntimeValue\"}, \"start_gene_cov\": \"95.0\", \"no_rotate\": \"false\", \"start_gene_id\": \"90.0\"}, \"pilon\": {\"no_pilon\": \"false\", \"min_polish_size\": \"1000\"}}",
+                        "tool_version": "0.4.8.0",
                         "type": "tool",
-                        "uuid": "465a0ecf-4f47-4679-ad02-c06eb48449fc",
+                        "uuid": "98050cb0-ca52-4a9d-a1c3-cd301f36356c",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "stats_output",
-                                "uuid": "ae93f473-d571-439c-8fa6-3927026fdb49"
+                                "output_name": "assembly",
+                                "uuid": "c35c6740-11f7-4ca3-8b93-a1fe502b8719"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
                         "errors": null,
-                        "id": 12,
+                        "id": 6,
                         "input_connections": {
-                            "fastq_input|fastq_input1": {
-                                "id": 2,
-                                "output_name": "output"
+                            "results_0|software_cond|output_0|input": {
+                                "id": 3,
+                                "output_name": "text_file"
                             },
-                            "reference_source|ref_file": {
-                                "id": 10,
-                                "output_name": "output_fasta"
+                            "results_0|software_cond|output_1|input": {
+                                "id": 4,
+                                "output_name": "text_file"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Map with BWA-MEM",
+                        "name": "MultiQC",
                         "outputs": [
                             {
-                                "name": "bam_output",
-                                "type": "bam"
+                                "name": "stats",
+                                "type": "input"
+                            },
+                            {
+                                "name": "html_report",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 1195.359375,
-                            "top": 628.0546875
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionbam_output": {
-                                "action_arguments": {
-                                    "newname": "illumina-tiny.bam"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "bam_output"
-                            }
+                            "left": 650.71875,
+                            "top": 251.3125
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
                         "tool_shed_repository": {
-                            "changeset_revision": "dfd8b7f78c37",
-                            "name": "bwa",
-                            "owner": "devteam",
+                            "changeset_revision": "b2f1f75d49c4",
+                            "name": "multiqc",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"illumina\", \"__current_case__\": 0}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 1, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}, \"index_a\": \"auto\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.17.1",
+                        "tool_state": "{\"comment\": \"\", \"__page__\": null, \"title\": \"\", \"__rerun_remap_job_id__\": null, \"results\": [{\"__index__\": 0, \"software_cond\": {\"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}], \"__current_case__\": 8, \"software\": \"fastqc\"}}], \"saveLog\": \"false\"}",
+                        "tool_version": "1.7",
                         "type": "tool",
-                        "uuid": "79954680-1c4f-4831-889c-53c4e502aa3c",
+                        "uuid": "3277000f-cee0-4279-80d3-0b266694cce2",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "bam_output",
-                                "uuid": "d2513973-0987-4260-9db6-3ac95c45c770"
+                                "output_name": "stats",
+                                "uuid": "3bfec2db-625d-4aa5-9016-e16fe27bf466"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "html_report",
+                                "uuid": "6f40035d-5c8d-4e18-82ea-0093237d250f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy0",
                         "errors": null,
-                        "id": 13,
+                        "id": 7,
                         "input_connections": {
-                            "fastq_input|fastq_input1": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "reference_source|ref_file": {
-                                "id": 10,
-                                "output_name": "output_fasta"
+                            "in|inputs": {
+                                "id": 5,
+                                "output_name": "assembly"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Map with BWA-MEM",
+                        "name": "Quast",
                         "outputs": [
                             {
-                                "name": "bam_output",
-                                "type": "bam"
+                                "name": "quast_tabular",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "report_html",
+                                "type": "html"
+                            },
+                            {
+                                "name": "report_pdf",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "log",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 1192.3828125,
-                            "top": 904.5859375
+                            "left": 648.875,
+                            "top": 416.5
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionbam_output": {
-                                "action_arguments": {
-                                    "newname": "nanopore-tiny.bam"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "bam_output"
+                            "HideDatasetActionlog": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "log"
+                            },
+                            "HideDatasetActionquast_tabular": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "quast_tabular"
+                            },
+                            "HideDatasetActionreport_pdf": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "report_pdf"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "dfd8b7f78c37",
-                            "name": "bwa",
-                            "owner": "devteam",
+                            "changeset_revision": "59db8ea8c845",
+                            "name": "quast",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"ont2d\", \"__current_case__\": 2}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 1, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}, \"index_a\": \"auto\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.17.1",
+                        "tool_state": "{\"scaffold_gap_max_size\": \"1000\", \"skip_unaligned_mis_contigs\": \"true\", \"assembly\": {\"ref\": {\"use_ref\": \"false\", \"est_ref_size\": \"\", \"__current_case__\": 1}, \"orga_type\": \"\", \"type\": \"genome\", \"__current_case__\": 0}, \"circos\": \"false\", \"contig_thresholds\": \"0,1000\", \"__page__\": null, \"strict_NA\": \"false\", \"__rerun_remap_job_id__\": null, \"genes\": {\"rna_finding\": \"false\", \"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"conserved_genes_finding\": \"false\"}, \"unaligned_part_size\": \"500\", \"al\": {\"upper_bound_assembly\": \"false\", \"min_identity\": \"95.0\", \"ambiguity_score\": \"0.99\", \"ambiguity_usage\": \"one\", \"upper_bound_min_con\": \"2\", \"fragmented\": \"false\", \"fragmented_max_indent\": \"50\", \"use_all_alignments\": \"false\", \"min_alignment\": \"65\"}, \"extensive_mis_size\": \"1000\", \"large\": \"false\", \"in\": {\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"__current_case__\": 1, \"custom\": \"false\"}, \"k_mer\": {\"k_mer_stats\": \"\", \"__current_case__\": 1}, \"split_scaffolds\": \"false\", \"min_contig\": \"500\"}",
+                        "tool_version": "5.0.2+galaxy0",
                         "type": "tool",
-                        "uuid": "c91315b3-c7f8-458c-a182-2b561d825837",
+                        "uuid": "1bb7b9fa-3e76-48b6-aa08-1169710715c5",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "bam_output",
-                                "uuid": "bebb5b25-00c2-456a-92a0-cd133a169e0e"
+                                "output_name": "quast_tsv",
+                                "uuid": "22d4aad1-6145-4209-8261-8dadf4fd4c02"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "report_html",
+                                "uuid": "0de88512-45db-4372-9457-94f136a77267"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "icarus",
+                                "uuid": "84990237-682a-4800-9ce3-dfeb83c7042d"
                             }
                         ]
                     },
@@ -25681,11 +26693,11 @@
                         "annotation": "",
                         "content_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
                         "errors": null,
-                        "id": 14,
+                        "id": 8,
                         "input_connections": {
                             "input": {
-                                "id": 10,
-                                "output_name": "output_fasta"
+                                "id": 5,
+                                "output_name": "assembly"
                             }
                         },
                         "inputs": [
@@ -25729,10 +26741,6 @@
                                 "name": "out_tbl",
                                 "type": "txt"
                             },
-                            {
-                                "name": "out_tsv",
-                                "type": "tabular"
-                            },
                             {
                                 "name": "out_err",
                                 "type": "txt"
@@ -25747,8 +26755,8 @@
                             }
                         ],
                         "position": {
-                            "left": 1704.984375,
-                            "top": 350.234375
+                            "left": 647.125,
+                            "top": 603.75
                         },
                         "post_job_actions": {},
                         "tool_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
@@ -25758,222 +26766,692 @@
                             "owner": "crs4",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"centre\": \"\", \"compliant\": {\"compliant_select\": \"no\", \"__current_case__\": 0, \"addgenes\": \"false\", \"mincontig\": \"200\"}, \"evalue\": \"1e-06\", \"fast\": \"false\", \"genus\": \"\", \"gffver\": \"3\", \"increment\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"kingdom\": {\"kingdom_select\": \"Bacteria\", \"__current_case__\": 1, \"gcode\": \"11\"}, \"locustag\": \"\", \"metagenome\": \"false\", \"norrna\": \"false\", \"notrna\": \"false\", \"outputs\": [\"gff\", \"gbk\", \"fna\", \"faa\", \"ffn\", \"sqn\", \"fsa\", \"tbl\", \"tsv\", \"err\", \"txt\"], \"plasmid\": \"\", \"proteins\": {\"__class__\": \"RuntimeValue\"}, \"rfam\": \"false\", \"species\": \"\", \"strain\": \"\", \"usegenus\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"strain\": \"C-1\", \"increment\": \"10\", \"species\": \"Coli\", \"__page__\": null, \"usegenus\": \"true\", \"evalue\": \"1e-06\", \"locustag\": \"PROKKA\", \"fast\": \"false\", \"compliant\": {\"mincontig\": \"200\", \"__current_case__\": 0, \"compliant_select\": \"no\", \"addgenes\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"kingdom\": {\"gcode\": \"11\", \"kingdom_select\": \"Bacteria\", \"__current_case__\": 1}, \"metagenome\": \"false\", \"centre\": \"\", \"outputs\": [\"gff\", \"gbk\", \"fna\", \"faa\", \"ffn\", \"sqn\", \"fsa\", \"tbl\", \"err\", \"txt\"], \"gffver\": \"3\", \"norrna\": \"false\", \"proteins\": {\"__class__\": \"RuntimeValue\"}, \"notrna\": \"false\", \"plasmid\": \"\", \"rfam\": \"false\", \"genus\": \"Escherichia\", \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.14.5",
                         "type": "tool",
-                        "uuid": "489e19de-1324-472c-8c8e-77e95572b6c3",
+                        "uuid": "dd9a67df-68a8-423b-90d2-2167393949e6",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_err",
-                                "uuid": "a5f8d2e3-b2ca-46c3-83c5-36bc15507046"
+                                "label": "tbl",
+                                "output_name": "out_tbl",
+                                "uuid": "0d6b33c9-b105-4997-9045-b86e52f00156"
                             },
                             {
                                 "label": null,
-                                "output_name": "out_fna",
-                                "uuid": "1d83fde1-6207-46cc-b65e-a71815c578d8"
+                                "output_name": "out_txt",
+                                "uuid": "4b7ef57d-3075-41cf-bc75-a5fc4aa8c942"
                             },
                             {
-                                "label": null,
-                                "output_name": "out_faa",
-                                "uuid": "8e49b1a0-fd5b-4a80-8714-5fe51e7e6096"
+                                "label": "gbk",
+                                "output_name": "out_gbk",
+                                "uuid": "8e08b54d-87e1-4269-9b96-8ebf1a9bb4ab"
                             },
                             {
                                 "label": null,
-                                "output_name": "out_tbl",
-                                "uuid": "638f81aa-0004-4497-aeb9-6c1964cb27a7"
+                                "output_name": "out_err",
+                                "uuid": "d2cd11ae-12f9-4123-bfde-119fa409da73"
                             },
                             {
-                                "label": null,
-                                "output_name": "out_fsa",
-                                "uuid": "773f3ba6-43ff-41aa-b498-ee509d71a58a"
+                                "label": "ffn",
+                                "output_name": "out_ffn",
+                                "uuid": "65e4ddf9-f5bc-4078-8b4e-37b332e12ece"
                             },
                             {
                                 "label": null,
-                                "output_name": "out_ffn",
-                                "uuid": "fd75d3c5-5cff-448e-9fd6-92b8af36e5cf"
+                                "output_name": "out_fsa",
+                                "uuid": "14a0d804-36f3-488f-a85d-4d18ff95d56f"
                             },
                             {
                                 "label": null,
-                                "output_name": "out_tsv",
-                                "uuid": "0efb82cf-84b6-49dd-bab4-d64d7356e0c7"
+                                "output_name": "out_fna",
+                                "uuid": "d494a946-ff3c-4900-a3f5-573ff1540ea3"
                             },
                             {
                                 "label": null,
-                                "output_name": "out_txt",
-                                "uuid": "da1cc1bc-e00c-4f65-afbc-1a118b23274a"
+                                "output_name": "out_log",
+                                "uuid": "80ed53bf-7d76-4de2-85b5-7dc487922e0e"
                             },
                             {
                                 "label": null,
-                                "output_name": "out_sqn",
-                                "uuid": "a5a04271-fc67-4ce3-95dc-9f01ee77775c"
+                                "output_name": "out_faa",
+                                "uuid": "249632ad-2412-4010-a703-aa8faeecc538"
                             },
                             {
                                 "label": null,
-                                "output_name": "out_log",
-                                "uuid": "ca98afab-a3d2-4beb-b3f0-de7f38bf5c6b"
+                                "output_name": "out_sqn",
+                                "uuid": "175956d0-42a8-4270-b976-3eefef7384ab"
                             },
                             {
                                 "label": null,
                                 "output_name": "out_gff",
-                                "uuid": "bae78be6-7c70-42bf-95c1-cae45c51871d"
-                            },
+                                "uuid": "0e2ffd13-e194-4693-9adf-54e561fd24e5"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "assembly/unicycler-assembly",
+                "path": "topics/assembly/tutorials/unicycler-assembly/workflows/unicycler.ga",
+                "tags": [
+                    "assembly"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "Unicycler training",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-unicycler-assembly/versions/unicycler",
+                "tutorial_id": "unicycler-assembly",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/unicycler-assembly/workflows/unicycler.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/unicycler-assembly/workflows/unicycler.html",
+                "version": 4,
+                "wfid": "assembly-unicycler-assembly",
+                "wfname": "unicycler",
+                "workflow": "unicycler.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0"
+                ],
+                "workflowhub_id": "1182"
+            }
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.940733"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "ddf54b12c295",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "add_value",
+                    "owner": "devteam",
+                    "revisions": "745871c0b055",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_compute_length",
+                    "owner": "devteam",
+                    "revisions": "de2db1bdfbf8",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_filter_by_length",
+                    "owner": "devteam",
+                    "revisions": "e626b3ff9922",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_filter_by_length",
+                    "owner": "devteam",
+                    "revisions": "8cacfcf96a52",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "lastz",
+                    "owner": "devteam",
+                    "revisions": "e7f19d6a9af8",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "merge_cols",
+                    "owner": "devteam",
+                    "revisions": "f2aac0c5c60d",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bedtools",
+                    "owner": "iuc",
+                    "revisions": "e19bebe96cd2",
+                    "tool_panel_section_label": "BED",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bedtools",
+                    "owner": "iuc",
+                    "revisions": "e19bebe96cd2",
+                    "tool_panel_section_label": "BED",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bedtools",
+                    "owner": "iuc",
+                    "revisions": "e19bebe96cd2",
+                    "tool_panel_section_label": "BED",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "circos",
+                    "owner": "iuc",
+                    "revisions": "df7356989ac1",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "circos",
+                    "owner": "iuc",
+                    "revisions": "df7356989ac1",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "datamash_ops",
+                    "owner": "iuc",
+                    "revisions": "562f3c677828",
+                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "jbrowse",
+                    "owner": "iuc",
+                    "revisions": "fd5dbf0f732e",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "25136a2b0cfe",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "830961c48e42",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: ddf54b12c295\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: add_value\n  owner: devteam\n  revisions: 745871c0b055\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_compute_length\n  owner: devteam\n  revisions: de2db1bdfbf8\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_filter_by_length\n  owner: devteam\n  revisions: e626b3ff9922\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_filter_by_length\n  owner: devteam\n  revisions: 8cacfcf96a52\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lastz\n  owner: devteam\n  revisions: e7f19d6a9af8\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merge_cols\n  owner: devteam\n  revisions: f2aac0c5c60d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: e19bebe96cd2\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: e19bebe96cd2\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: e19bebe96cd2\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: circos\n  owner: iuc\n  revisions: df7356989ac1\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: circos\n  owner: iuc\n  revisions: df7356989ac1\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 562f3c677828\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: fd5dbf0f732e\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 25136a2b0cfe\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ecoli_comparison/tutorial.json",
+        "contributors": [
+            {
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
+                "joined": "2017-09",
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+            },
+            {
+                "email": "delphine.lariviere@galaxy.org",
+                "id": "delphine-l",
+                "joined": "2017-09",
+                "name": "Delphine Lariviere",
+                "orcid": "0000-0001-6421-3484",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            }
+        ],
+        "dir": "topics/assembly/tutorials/ecoli_comparison",
+        "edam_ontology": [
+            "topic_0196",
+            "topic_0622",
+            "topic_3301"
+        ],
+        "edam_operation": [
+            "Sequence alignment",
+            "Sequence visualisation",
+            "Read mapping",
+            "Genome visualisation",
+            "Mapping"
+        ],
+        "edam_topic": [
+            "Sequence assembly",
+            "Genomics",
+            "Microbiology"
+        ],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "assembly/ecoli_comparison",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "We learned how to download large sets of completed genomes from NCBI",
+            "We learned how to use Galaxy's rule-based collection builder",
+            "We learned how to use a combination of Galaxy tools to create complex views of genome comparisons",
+            "We learned about idiosyncrasies of data formats and how to deal with them using Galaxy tools"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-24",
+        "objectives": [
+            "Identification of the most closely related genome to my new assembly",
+            "Perform sequence comparison to locate rearrangements",
+            "Identify genes located in deletions"
+        ],
+        "pageviews": 12166,
+        "pub_date": "2018-06-14",
+        "questions": [
+            "I just assembled a genome. How does it compare with already sequenced genomes?",
+            "How do I find rearranged, inserted, or deleted regions?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "assembly",
+                "tutorials": [
+                    "unicycler-assembly"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00032",
+        "short_tools": [
+            "join1",
+            "tp_sed_tool",
+            "lastz_wrapper_2",
+            "upload1",
+            "fasta_filter_by_length",
+            "bedtools_intersectbed",
+            "datamash_ops",
+            "circos_interval_to_tiles",
+            "jbrowse",
+            "tp_cat",
+            "mergeCols1",
+            "Filter1",
+            "bedtools_sortbed",
+            "tp_sort_header_tool",
+            "Grep1",
+            "Cut1",
+            "collapse_dataset",
+            "cat1",
+            "tp_replace_in_column",
+            "addValue",
+            "circos_aln_to_links",
+            "fasta_compute_length",
+            "circos",
+            "tp_grep_tool",
+            "tp_replace_in_line",
+            "random_lines1",
+            "bedtools_complementbed"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "gmod",
+            "prokaryote",
+            "microgalaxy",
+            "jbrowse1"
+        ],
+        "time_estimation": "4h",
+        "title": "Making sense of a newly assembled genome",
+        "tools": [
+            "Cut1",
+            "Filter1",
+            "Grep1",
+            "cat1",
+            "join1",
+            "random_lines1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.27.0.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.0.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7",
+            "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7",
+            "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tiles/0.69.8+galaxy7",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.8+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
+            "upload1"
+        ],
+        "topic_name": "assembly",
+        "topic_name_human": "Assembly",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "ecoli_comparison",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ecoli_comparison/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ecoli_comparison/tutorial.json"
+        },
+        "version": 29,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 181,
+        "visitors": 6026,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Making sense of a newly assembled genome",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  10[label=\"Collapse Collection\"]\n  6 -> 10 [label=\"output\"]\n  11[label=\"Text transformation\"]\n  7 -> 11 [label=\"output\"]\n  12[label=\"Add column\"]\n  8 -> 12 [label=\"out_file1\"]\n  13[label=\"LASTZ\"]\n  9 -> 13 [label=\"output\"]\n  3 -> 13 [label=\"output\"]\n  14[label=\"random_lines1\"]\n  10 -> 14 [label=\"output\"]\n  15[label=\"Filter\"]\n  10 -> 15 [label=\"output\"]\n  16[label=\"Search in textfiles\"]\n  11 -> 16 [label=\"output\"]\n  17[label=\"Concatenate datasets\"]\n  11 -> 17 [label=\"output\"]\n  9 -> 17 [label=\"output\"]\n  18[label=\"Cut\"]\n  12 -> 18 [label=\"out_file1\"]\n  19[label=\"Text transformation\"]\n  13 -> 19 [label=\"output\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  20[label=\"Datamash\"]\n  15 -> 20 [label=\"out_file1\"]\n  21[label=\"Compute sequence length\"]\n  17 -> 21 [label=\"out_file1\"]\n  22[label=\"Collapse Collection\"]\n  18 -> 22 [label=\"out_file1\"]\n  23[label=\"Merge Columns\"]\n  19 -> 23 [label=\"output\"]\n  24[label=\"Select\"]\n  20 -> 24 [label=\"out_file\"]\n  25[label=\"Sort\"]\n  21 -> 25 [label=\"output\"]\n  26[label=\"Collapse Collection\"]\n  23 -> 26 [label=\"out_file1\"]\n  27[label=\"Cut\"]\n  26 -> 27 [label=\"output\"]\n  28[label=\"Cut\"]\n  26 -> 28 [label=\"output\"]\n  29[label=\"Concatenate datasets\"]\n  27 -> 29 [label=\"out_file1\"]\n  28 -> 29 [label=\"out_file1\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  30[label=\"SortBED\"]\n  29 -> 30 [label=\"out_file1\"]\n  31[label=\"ComplementBed\"]\n  25 -> 31 [label=\"outfile\"]\n  30 -> 31 [label=\"output\"]\n  32[label=\"Filter\"]\n  31 -> 32 [label=\"output\"]\n  33[label=\"Filter\"]\n  32 -> 33 [label=\"out_file1\"]\n  34[label=\"Intersect intervals\"]\n  33 -> 34 [label=\"out_file1\"]\n  22 -> 34 [label=\"output\"]\n  35[label=\"Join two Datasets\"]\n  34 -> 35 [label=\"output\"]\n  1 -> 35 [label=\"output\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  5[label=\"Filter sequences by length\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"LASTZ\"]\n  2 -> 6 [label=\"output\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Collapse Collection\"]\n  3 -> 7 [label=\"output\"]\n  8[label=\"Select\"]\n  4 -> 8 [label=\"output\"]\n  9[label=\"Text transformation\"]\n  5 -> 9 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "48cf52ea88fe32cfc059494bc1b464c4b202bf99",
+                        "message": "on purpose mistake fixed",
+                        "num": 6,
+                        "short_hash": "48cf52ea8",
+                        "unix": "1579772724"
+                    },
+                    {
+                        "hash": "b3f79801438efc81c5f2a3f0af17a26f82e6913e",
+                        "message": "test",
+                        "num": 5,
+                        "short_hash": "b3f798014",
+                        "unix": "1579714684"
+                    },
+                    {
+                        "hash": "230f6e12fc9de41c8cb554a353e0b816eb656724",
+                        "message": "linting fix",
+                        "num": 4,
+                        "short_hash": "230f6e12f",
+                        "unix": "1579705852"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 3,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 2,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "485411d09f88e53fb83bc584da92afa171aed32a",
+                        "message": "workflow for ecoli_comparison",
+                        "num": 1,
+                        "short_hash": "485411d09",
+                        "unix": "1546963139"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Ecoli_C_assembly.fna"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 10
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Ecoli_C_assembly.fna\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "2eb3a31a-f5ec-4ce0-a4db-f421ab573412",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "out_gbk",
-                                "uuid": "9a2a7aab-fde6-4a9c-b098-17b958ff2f20"
+                                "description": "",
+                                "name": "inline-supplementary-material-7 - Table_S4_Essential genes identi.tsv"
                             }
-                        ]
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 130
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"inline-supplementary-material-7 - Table_S4_Essential genes identi.tsv\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ac567420-400d-4a74-adb5-cdaed90cebd6",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 15,
-                        "input_connections": {
-                            "reference_genome|genome": {
-                                "id": 10,
-                                "output_name": "output_fasta"
-                            },
-                            "track_groups_0|data_tracks_0|data_format|annotation": {
-                                "id": 12,
-                                "output_name": "bam_output"
-                            },
-                            "track_groups_0|data_tracks_1|data_format|annotation": {
-                                "id": 13,
-                                "output_name": "bam_output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "JBrowse",
-                        "outputs": [
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "html"
+                                "description": "",
+                                "name": "Input Dataset Collection"
                             }
                         ],
+                        "label": null,
+                        "name": "Input dataset collection",
+                        "outputs": [],
                         "position": {
-                            "left": 1469.125,
-                            "top": 558.828125
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "JBrowse-view-assembly-and-reads"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "17359b808b01",
-                            "name": "jbrowse",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 10,
+                            "top": 250
                         },
-                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"11\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Default\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"auto_snp\": \"false\", \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"force\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"auto_snp\": \"false\", \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"force\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16.9+galaxy0",
-                        "type": "tool",
-                        "uuid": "9ae0aa01-72e9-4481-b992-248f3ec20a07",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "b5c7a4ed-bb41-4486-b01f-270071e23e52"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "8cc3e0ac-13bd-4e29-83dc-8411490fc85d",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 16,
-                        "input_connections": {
-                            "reference_genome|genome": {
-                                "id": 10,
-                                "output_name": "output_fasta"
-                            },
-                            "track_groups_0|data_tracks_0|data_format|annotation": {
-                                "id": 14,
-                                "output_name": "out_gff"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "JBrowse",
-                        "outputs": [
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "html"
+                                "description": "",
+                                "name": "Input Dataset Collection"
                             }
                         ],
+                        "label": null,
+                        "name": "Input dataset collection",
+                        "outputs": [],
                         "position": {
-                            "left": 1981.40625,
-                            "top": 224.328125
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "JBrowse-view-annotations"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "17359b808b01",
-                            "name": "jbrowse",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 10,
+                            "top": 370
                         },
-                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"11\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Default\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"force\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16.9+galaxy0",
-                        "type": "tool",
-                        "uuid": "7e5c8b63-2538-4898-9644-71453e17c0ba",
-                        "workflow_outputs": [
+                        "tool_id": null,
+                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "6bc17455-70a4-48bb-a511-e484016e9ad8",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "5ad68433-82c3-47aa-b3e4-ef1b07ed790e"
+                                "description": "",
+                                "name": "Input Dataset Collection"
                             }
-                        ]
+                        ],
+                        "label": null,
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 490
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "04145efc-b9a4-4bd4-9a72-7cdf0e98e752",
+                        "workflow_outputs": []
                     }
                 ],
-                "parent_id": "assembly/chloroplast-assembly",
-                "path": "topics/assembly/tutorials/chloroplast-assembly/workflows/Galaxy-Workflow-Chloroplast-genome-assembly-and-annotation.ga",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Collapse Collection\"];\n  6 -->|output| 10;\n  11[\"Text transformation\"];\n  7 -->|output| 11;\n  12[\"Add column\"];\n  8 -->|out_file1| 12;\n  13[\"LASTZ\"];\n  9 -->|output| 13;\n  3 -->|output| 13;\n  14[\"random_lines1\"];\n  10 -->|output| 14;\n  15[\"Filter\"];\n  10 -->|output| 15;\n  16[\"Search in textfiles\"];\n  11 -->|output| 16;\n  17[\"Concatenate datasets\"];\n  11 -->|output| 17;\n  9 -->|output| 17;\n  18[\"Cut\"];\n  12 -->|out_file1| 18;\n  19[\"Text transformation\"];\n  13 -->|output| 19;\n  2[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  20[\"Datamash\"];\n  15 -->|out_file1| 20;\n  21[\"Compute sequence length\"];\n  17 -->|out_file1| 21;\n  22[\"Collapse Collection\"];\n  18 -->|out_file1| 22;\n  23[\"Merge Columns\"];\n  19 -->|output| 23;\n  24[\"Select\"];\n  20 -->|out_file| 24;\n  25[\"Sort\"];\n  21 -->|output| 25;\n  26[\"Collapse Collection\"];\n  23 -->|out_file1| 26;\n  27[\"Cut\"];\n  26 -->|output| 27;\n  28[\"Cut\"];\n  26 -->|output| 28;\n  29[\"Concatenate datasets\"];\n  27 -->|out_file1| 29;\n  28 -->|out_file1| 29;\n  3[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  30[\"SortBED\"];\n  29 -->|out_file1| 30;\n  31[\"ComplementBed\"];\n  25 -->|outfile| 31;\n  30 -->|output| 31;\n  32[\"Filter\"];\n  31 -->|output| 32;\n  33[\"Filter\"];\n  32 -->|out_file1| 33;\n  34[\"Intersect intervals\"];\n  33 -->|out_file1| 34;\n  22 -->|output| 34;\n  35[\"Join two Datasets\"];\n  34 -->|output| 35;\n  1 -->|output| 35;\n  4[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Filter sequences by length\"];\n  0 -->|output| 5;\n  6[\"LASTZ\"];\n  2 -->|output| 6;\n  0 -->|output| 6;\n  7[\"Collapse Collection\"];\n  3 -->|output| 7;\n  8[\"Select\"];\n  4 -->|output| 8;\n  9[\"Text transformation\"];\n  5 -->|output| 9;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Ecoli Comparison",
+                "outputs": [],
+                "parent_id": "assembly/ecoli_comparison",
+                "path": "topics/assembly/tutorials/ecoli_comparison/workflows/ecoli-comparison.ga",
                 "tags": [
                     "assembly"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Chloroplast-genome-assembly-and-annotation",
+                "title": "Ecoli Comparison",
                 "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-chloroplast-assembly/versions/galaxy-workflow-chloroplast-genome-assembly-and-annotation",
-                "tutorial_id": "chloroplast-assembly",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/chloroplast-assembly/workflows/Galaxy-Workflow-Chloroplast-genome-assembly-and-annotation.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/chloroplast-assembly/workflows/Galaxy-Workflow-Chloroplast-genome-assembly-and-annotation.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-ecoli_comparison/versions/ecoli-comparison",
+                "tutorial_id": "ecoli_comparison",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/ecoli_comparison/workflows/ecoli-comparison.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/ecoli_comparison/workflows/ecoli-comparison.html",
                 "version": 3,
-                "wfid": "assembly-chloroplast-assembly",
-                "wfname": "galaxy-workflow-chloroplast-genome-assembly-and-annotation",
-                "workflow": "Galaxy-Workflow-Chloroplast-genome-assembly-and-annotation.ga",
+                "wfid": "assembly-ecoli_comparison",
+                "wfname": "ecoli-comparison",
+                "workflow": "ecoli-comparison.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6",
-                    "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1"
+                    "Cut1",
+                    "Filter1",
+                    "Grep1",
+                    "cat1",
+                    "join1",
+                    "random_lines1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.27.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0"
                 ],
-                "workflowhub_id": "1139"
+                "workflowhub_id": "1113"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.3567224"
+        "zenodo_link": "https://zenodo.org/record/3382053"
     },
     {
         "admin_install": {
@@ -25983,41 +27461,8 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/get-started-genome-assembly/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "alexcorm",
-                "lleroi"
-            ],
-            "editing": [
-                "abretaud",
-                "stephanierobin",
-                "r1corre"
-            ],
-            "funding": [
-                "gallantries"
-            ]
-        },
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/algorithms-introduction/tutorial.json",
         "contributors": [
-            {
-                "email": "alexandre.cormier@ifremer.fr",
-                "id": "alexcorm",
-                "joined": "2021-11",
-                "name": "Alexandre Cormier",
-                "orcid": "0000-0002-7775-8413",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/",
-                "twitter": "allanssx",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/alexcorm.json"
-            },
-            {
-                "email": "laura.leroi@ifremer.fr",
-                "id": "lleroi",
-                "joined": "2021-11",
-                "name": "Laura Leroi",
-                "orcid": "0000-0003-3748-4179",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lleroi/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/lleroi.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
@@ -26044,60 +27489,42 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
             },
             {
-                "email": "stephanie.robin@inrae.fr",
-                "id": "stephanierobin",
-                "joined": "2021-11",
-                "name": "St\u00e9phanie Robin",
-                "orcid": "0000-0001-7379-9173",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/",
-                "twitter": "robinstphanie1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/stephanierobin.json"
+                "elixir_node": "au",
+                "email": "simon.gladman@unimelb.edu.au",
+                "id": "slugger70",
+                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
+                "joined": "2017-09",
+                "name": "Simon Gladman",
+                "orcid": "0000-0002-6100-4385",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
             },
             {
-                "email": "erwan.corre@sb-roscoff.fr",
-                "id": "r1corre",
-                "joined": "2019-04",
-                "name": "Erwan Corre",
-                "orcid": "0000-0001-6354-2278",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/r1corre/",
-                "twitter": "r1corre",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/r1corre.json"
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
+                "joined": "2017-09",
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
             },
             {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+                "email": "delphine.lariviere@galaxy.org",
+                "id": "delphine-l",
+                "joined": "2017-09",
+                "name": "Delphine Lariviere",
+                "orcid": "0000-0001-6421-3484",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
             }
         ],
-        "dir": "topics/assembly/tutorials/get-started-genome-assembly",
+        "dir": "topics/assembly/tutorials/algorithms-introduction",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": false,
-        "id": "assembly/get-started-genome-assembly",
+        "id": "assembly/algorithms-introduction",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -26108,25 +27535,19 @@
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": [
-            "We learned the definitions of bioinformatics terms used in genomes assembly and annotation",
-            "We have seen the bioinformatics file formats used for these analyses",
-            "We learned the importance of preparing the project to ensure its success",
-            "We learned the importance of surrounding ourselves with all the people who have knowledge of the different parts of the project (wet lab, sequencing, bioinformatics,...)"
-        ],
         "layout": "tutorial_slides",
-        "level": "Introductory",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
         "logo": "GTN",
-        "mod_date": "2023-10-23",
-        "pageviews": 4101826,
-        "pub_date": "2021-11-30",
+        "mod_date": "2021-01-12",
+        "pageviews": 5828618,
+        "pub_date": "2021-01-12",
         "questions": [
-            "Definitions of bioinformatics terms for assembly and annotation",
-            "What are the guidelines before starting a Genome Assembly and Annotation project?",
-            "What file formats are used for assembly and annotation?"
+            "What are the main types of assembly algorithms?",
+            "How do they perform with short and long reads?",
+            "How to improve assemblies using other technologies?"
         ],
-        "short_id": "S00034",
+        "short_id": "S00029",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
@@ -26164,8 +27585,7 @@
             ]
         },
         "symlink": null,
-        "time_estimation": "1h",
-        "title": "An introduction to get started in genome assembly and annotation",
+        "title": "Deeper look into Genome Assembly algorithms",
         "tools": [],
         "topic_name": "assembly",
         "topic_name_human": "Assembly",
@@ -26175,19 +27595,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "get-started-genome-assembly",
+        "tutorial_name": "algorithms-introduction",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/get-started-genome-assembly/slides.html",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/algorithms-introduction/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/get-started-genome-assembly/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/get-started-genome-assembly/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/algorithms-introduction/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/algorithms-introduction/slides.json"
         },
-        "version": 7,
+        "version": 1,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 149,
-        "visitors": 1577806
+        "visit_duration": 152,
+        "visitors": 2112833
     },
     {
         "admin_install": {
@@ -26197,8 +27617,41 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/algorithms-introduction/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/get-started-genome-assembly/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "alexcorm",
+                "lleroi"
+            ],
+            "editing": [
+                "abretaud",
+                "stephanierobin",
+                "r1corre"
+            ],
+            "funding": [
+                "gallantries"
+            ]
+        },
         "contributors": [
+            {
+                "email": "alexandre.cormier@ifremer.fr",
+                "id": "alexcorm",
+                "joined": "2021-11",
+                "name": "Alexandre Cormier",
+                "orcid": "0000-0002-7775-8413",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/",
+                "twitter": "allanssx",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/alexcorm.json"
+            },
+            {
+                "email": "laura.leroi@ifremer.fr",
+                "id": "lleroi",
+                "joined": "2021-11",
+                "name": "Laura Leroi",
+                "orcid": "0000-0003-3748-4179",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lleroi/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/lleroi.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
@@ -26225,42 +27678,60 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
             },
             {
-                "elixir_node": "au",
-                "email": "simon.gladman@unimelb.edu.au",
-                "id": "slugger70",
-                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
-                "joined": "2017-09",
-                "name": "Simon Gladman",
-                "orcid": "0000-0002-6100-4385",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
+                "email": "stephanie.robin@inrae.fr",
+                "id": "stephanierobin",
+                "joined": "2021-11",
+                "name": "St\u00e9phanie Robin",
+                "orcid": "0000-0001-7379-9173",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/",
+                "twitter": "robinstphanie1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/stephanierobin.json"
             },
             {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
-                "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+                "email": "erwan.corre@sb-roscoff.fr",
+                "id": "r1corre",
+                "joined": "2019-04",
+                "name": "Erwan Corre",
+                "orcid": "0000-0001-6354-2278",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/r1corre/",
+                "twitter": "r1corre",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/r1corre.json"
             },
             {
-                "email": "delphine.lariviere@galaxy.org",
-                "id": "delphine-l",
-                "joined": "2017-09",
-                "name": "Delphine Lariviere",
-                "orcid": "0000-0001-6421-3484",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/assembly/tutorials/algorithms-introduction",
+        "dir": "topics/assembly/tutorials/get-started-genome-assembly",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": false,
-        "id": "assembly/algorithms-introduction",
+        "id": "assembly/get-started-genome-assembly",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -26271,19 +27742,25 @@
             "mathjax": null,
             "mermaid": false
         },
+        "key_points": [
+            "We learned the definitions of bioinformatics terms used in genomes assembly and annotation",
+            "We have seen the bioinformatics file formats used for these analyses",
+            "We learned the importance of preparing the project to ensure its success",
+            "We learned the importance of surrounding ourselves with all the people who have knowledge of the different parts of the project (wet lab, sequencing, bioinformatics,...)"
+        ],
         "layout": "tutorial_slides",
-        "level": "Intermediate",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
         "logo": "GTN",
-        "mod_date": "2021-01-12",
-        "pageviews": 5658344,
-        "pub_date": "2021-01-12",
+        "mod_date": "2023-10-23",
+        "pageviews": 4272100,
+        "pub_date": "2021-11-30",
         "questions": [
-            "What are the main types of assembly algorithms?",
-            "How do they perform with short and long reads?",
-            "How to improve assemblies using other technologies?"
+            "Definitions of bioinformatics terms for assembly and annotation",
+            "What are the guidelines before starting a Genome Assembly and Annotation project?",
+            "What file formats are used for assembly and annotation?"
         ],
-        "short_id": "S00029",
+        "short_id": "S00034",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
@@ -26321,7 +27798,8 @@
             ]
         },
         "symlink": null,
-        "title": "Deeper look into Genome Assembly algorithms",
+        "time_estimation": "1h",
+        "title": "An introduction to get started in genome assembly and annotation",
         "tools": [],
         "topic_name": "assembly",
         "topic_name_human": "Assembly",
@@ -26331,19 +27809,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "algorithms-introduction",
+        "tutorial_name": "get-started-genome-assembly",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/algorithms-introduction/slides.html",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/get-started-genome-assembly/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/algorithms-introduction/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/algorithms-introduction/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/get-started-genome-assembly/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/get-started-genome-assembly/slides.json"
         },
-        "version": 1,
+        "version": 7,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2042097
+        "visit_duration": 149,
+        "visitors": 1647078
     },
     {
         "admin_install": {
@@ -26352,271 +27830,44 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "argo_getdata",
-                    "owner": "ecology",
-                    "revisions": "28c8f085d1b4",
-                    "tool_panel_section_label": "Get Data",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "f46f0e4f75c4",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "timeseries_extraction",
-                    "owner": "ecology",
-                    "revisions": "810820a0d45c",
-                    "tool_panel_section_label": "GIS Data Handling",
+                    "name": "ctsm_fates",
+                    "owner": "climate",
+                    "revisions": "b525b88bc941",
+                    "tool_panel_section_label": "Climate Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "xarray_coords_info",
+                    "name": "xarray_metadata_info",
                     "owner": "ecology",
-                    "revisions": "663e6f115a76",
+                    "revisions": "e8650cdf092f",
                     "tool_panel_section_label": "GIS Data Handling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "xarray_metadata_info",
+                    "name": "xarray_select",
                     "owner": "ecology",
-                    "revisions": "00de53d18b99",
+                    "revisions": "6baac361495b",
                     "tool_panel_section_label": "GIS Data Handling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: argo_getdata\n  owner: ecology\n  revisions: 28c8f085d1b4\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: timeseries_extraction\n  owner: ecology\n  revisions: 810820a0d45c\n  tool_panel_section_label: GIS Data Handling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xarray_coords_info\n  owner: ecology\n  revisions: 663e6f115a76\n  tool_panel_section_label: GIS Data Handling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xarray_metadata_info\n  owner: ecology\n  revisions: 00de53d18b99\n  tool_panel_section_label: GIS Data Handling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/argo_pangeo/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "Marie59"
-            ],
-            "funding": [
-                "fairease",
-                "eurosciencegateway"
-            ]
-        },
-        "contributors": [
-            {
-                "affiliations": [
-                    "pndb",
-                    "fairease"
-                ],
-                "email": "marie.josse@ifremer.fr",
-                "id": "Marie59",
-                "joined": "2022-03",
-                "name": "Marie Josse",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
-            },
-            {
-                "avatar": "/training-material/assets/images/fair_ease_colour.png",
-                "funder": true,
-                "funding_id": "101058785",
-                "funding_statement": "FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "fairease",
-                "joined": "2023-10",
-                "members": [
-                    "Marie59",
-                    "yvanlebras"
-                ],
-                "name": "Fair-Ease",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fairease/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/fairease.json"
-            },
-            {
-                "avatar": "/training-material/assets/images/eurosciencegateway.png",
-                "funder": true,
-                "funding_id": "101057388",
-                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "eurosciencegateway",
-                "joined": "2023-10",
-                "members": [
-                    "abretaud",
-                    "anuprulez",
-                    "bgruening",
-                    "erxleben",
-                    "pauldg",
-                    "rlibouba"
-                ],
-                "name": "EuroScienceGateway",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
-            }
-        ],
-        "dir": "topics/climate/tutorials/argo_pangeo",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "climate/argo_pangeo",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Argo data",
-            "Pangeo Ecosystem",
-            "Galaxy Earth System"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-03-24",
-        "objectives": [
-            "How to fetch Argo Data?",
-            "How to get metadata with xarray netcdf tools?",
-            "Learn to get temperature variations.",
-            "Learn to use an interactive tool to visualise Argo temperature variable on an interactive map."
-        ],
-        "pageviews": 108,
-        "pub_date": "2024-03-24",
-        "questions": [
-            "How to use the Pangeo ecosystem to analyse ocean data?",
-            "How to process Argo data to visualise ocean temperature variations?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "introduction",
-                "tutorials": [
-                    "galaxy-intro-short"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00428",
-        "short_tools": [
-            "argo_getdata",
-            "interactive_tool_odv",
-            "timeseries_extraction",
-            "xarray_metadata_info",
-            "xarray_coords_info"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
+                },
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "ggplot2_point",
+                    "owner": "iuc",
+                    "revisions": "e3a675da7fd0",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
-            ],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "earth-system",
-            "ocean",
-            "pangeo",
-            "argo"
-        ],
-        "time_estimation": "1H",
-        "title": "Analyse Argo data",
-        "tools": [
-            "interactive_tool_odv",
-            "toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ecology/timeseries_extraction/timeseries_extraction/2022.3.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/2022.3.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/2022.3.0+galaxy0"
-        ],
-        "topic_name": "climate",
-        "topic_name_human": "Climate",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "argo_pangeo",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/climate/tutorials/argo_pangeo/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/argo_pangeo/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/argo_pangeo/tutorial.json"
-        },
-        "version": 1,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 120,
-        "visitors": 85,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0009-0008-0622-604X",
-                        "name": "Marie Joss\u00e9",
-                        "url": "https://github.com/Marie59"
-                    }
-                ],
-                "description": "Process argo data with the Pangeo Ecosystem and visualise them with Ocean Data View (ODV)",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Argo data access\"]\n  1[label=\"NetCDF xarray Coordinate Info\"]\n  0 -> 1 [label=\"output_argo\"]\n  2[label=\"NetCDF xarray Metadata Info\"]\n  0 -> 2 [label=\"output_argo\"]\n  3[label=\"NetCDF timeseries Extractor\"]\n  0 -> 3 [label=\"output_argo\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"ODV\"]\n  3 -> 4 [label=\"timeseries_tabular\"]\n}",
-                "history": [
-                    {
-                        "hash": "54b194630704357541b0a560b2b5e212cbf7fa35",
-                        "message": "add new argo tuto",
-                        "num": 1,
-                        "short_hash": "54b194630",
-                        "unix": "1710791150"
-                    }
-                ],
-                "inputs": [],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"Argo data access\"];\n  1[\"NetCDF xarray Coordinate Info\"];\n  0 -->|output_argo| 1;\n  2[\"NetCDF xarray Metadata Info\"];\n  0 -->|output_argo| 2;\n  3[\"NetCDF timeseries Extractor\"];\n  0 -->|output_argo| 3;\n  2 -->|output| 3;\n  4[\"ODV\"];\n  3 -->|timeseries_tabular| 4;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Analyse Argo data ",
-                "outputs": [],
-                "parent_id": "climate/argo_pangeo",
-                "path": "topics/climate/tutorials/argo_pangeo/workflows/main_workflow.ga",
-                "tags": [
-                    "Ocean",
-                    "Pangeo",
-                    "earth-system"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Analyse Argo data ",
-                "topic_id": "climate",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/climate-argo_pangeo/versions/main-workflow",
-                "tutorial_id": "argo_pangeo",
-                "url": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/argo_pangeo/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/argo_pangeo/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "climate-argo_pangeo",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "interactive_tool_odv",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/timeseries_extraction/timeseries_extraction/2022.3.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/2022.3.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/2022.3.0+galaxy0"
-                ],
-                "workflowhub_id": "1193"
-            }
-        ]
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
+            ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/pangeo-notebook/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: f46f0e4f75c4\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ctsm_fates\n  owner: climate\n  revisions: b525b88bc941\n  tool_panel_section_label: Climate Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xarray_metadata_info\n  owner: ecology\n  revisions: e8650cdf092f\n  tool_panel_section_label: GIS Data Handling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xarray_select\n  owner: ecology\n  revisions: 6baac361495b\n  tool_panel_section_label: GIS Data Handling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ggplot2_point\n  owner: iuc\n  revisions: e3a675da7fd0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/fates/tutorial.json",
         "contributors": [
             {
                 "elixir_node": "no",
@@ -26627,133 +27878,144 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annefou/",
                 "twitter": "AnneFouilloux",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/annefou.json"
+            },
+            {
+                "id": "huitang-earth",
+                "joined": "2021-01",
+                "name": "Hui Tang",
+                "orcid": "0000-0002-8745-3859",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/huitang-earth/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/huitang-earth.json"
             }
         ],
-        "dir": "topics/climate/tutorials/pangeo-notebook",
-        "edam_operation": [],
+        "dir": "topics/climate/tutorials/fates",
+        "edam_operation": [
+            "Visualisation"
+        ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "link": "http://gallery.pangeo.io/repos/pangeo-data/pangeo-tutorial-gallery/index.html",
-                "title": "Pangeo Tutorial Gallery",
-                "type": "external"
-            },
-            {
-                "link": "http://gallery.pangeo.io/index.html",
-                "title": "Pangeo Gallery",
-                "type": "external"
-            }
-        ],
         "hands_on": true,
-        "id": "climate/pangeo-notebook",
+        "id": "climate/fates",
         "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Pangeo ecosystem enables big data analysis in geosciences",
-            "Xarray is an important Python package for big data analysis in geosciences",
-            "Xarray can be used to read, select, mask and plot netCDF data",
-            "Xarray can also be used to perform global operations such as mean, max, min or resampling data"
+            "CLM-FATES is a numerical terrestrial ecosystem model used in climate models",
+            "Panoply is a quick visualization tools for plotting your results",
+            "Multi-case simulations can be easily developed and shared with a Galaxy workflow"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
-        "notebook": {
-            "language": "python",
-            "snippet": "topics/climate/tutorials/pangeo-notebook/preamble.md"
-        },
+        "mod_date": "2024-08-08",
         "objectives": [
-            "Learn to get metadata information using Xarray Galaxy Tools",
-            "Learn to select data",
-            "Learn to visualize data",
-            "Learn to filter, make reduction operations (mean, max, min)",
-            "Learn to resample my data",
-            "Learn to cite and contribute to Pangeo"
+            "Setting up a CLM-FATES case.",
+            "Customizing your run.",
+            "Interactive visualization with Panoply.",
+            "Automating your analyzes and visualisations of your CLM-FATES case.",
+            "Creating multi-case scenarios.",
+            "Composing, executing and publishing CML-FATES workflow."
         ],
-        "pageviews": 3702313,
-        "pub_date": "2022-02-18",
+        "pageviews": 5899188,
+        "pub_date": "2020-10-25",
         "questions": [
-            "What is Pangeo notebook?",
-            "How to start Pangeo Notebook in Galaxy?",
-            "What are the main software components of the Pangeo ecosystem?",
-            "What is Xarray?",
-            "How to manipulate Xarrays?",
-            "How to print metadata information?",
-            "How to make a selection?",
-            "How to visualize?",
-            "How to filter?",
-            "How to make reduction operations (mean, max, min)?",
-            "How to resample my data?",
-            "Where to go next?"
+            "How to run CLM-FATES with the CLM-FATES Galaxy tool?",
+            "How to upload input data for running CLM-FATES?",
+            "How to customize your runs?",
+            "How to analyze your model outputs?",
+            "How to create a workflow?",
+            "How to share your workflow?"
         ],
         "recordings": [
             {
                 "captioners": [
-                    "annefou"
+                    "s3by01"
                 ],
-                "date": "2022-03-03",
-                "galaxy_version": "21.09",
-                "length": "17M",
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "1H20M",
                 "speakers": [
                     "annefou"
                 ],
-                "youtube_id": "XFF2yRcYGp0"
+                "youtube_id": "0LsEx11eLiI"
             }
         ],
         "requirements": [
             {
-                "topic_name": "data-science",
+                "topic_name": "climate",
                 "tutorials": [
-                    "python-basics"
+                    "panoply"
                 ],
                 "type": "internal"
             },
             {
-                "topic_name": "data-science",
+                "topic_name": "galaxy-interface",
                 "tutorials": [
-                    "python-plotting",
-                    "python-advanced-np-pd"
+                    "history-to-workflow"
                 ],
                 "type": "internal"
-            },
-            {
-                "link": "https://datacarpentry.org/geospatial-workshop/",
-                "title": "Data Carpentry Geospatial Workshop",
-                "type": "external"
             }
         ],
-        "short_id": "T00045",
+        "short_id": "T00042",
         "short_tools": [
-            "interactive_tool_pangeo_notebook"
+            "__EXTRACT_DATASET__",
+            "xarray_metadata_info",
+            "interactive_tool_panoply",
+            "ggplot2_point",
+            "tp_find_and_replace",
+            "ctsm_fates",
+            "xarray_select"
         ],
         "slides": true,
-        "slides_recordings": false,
+        "slides_recordings": [
+            {
+                "captioners": [
+                    "annefou"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "7M",
+                "speakers": [
+                    "awspolly"
+                ],
+                "youtube_id": "Z57C7MQG95s"
+            }
+        ],
         "supported_servers": {
             "exact": [
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 }
             ],
             "inexact": []
         },
         "symlink": null,
         "tags": [
-            "pangeo",
             "interactive-tools"
         ],
-        "time_estimation": "1H",
-        "title": "Pangeo Notebook in Galaxy - Introduction to Xarray",
+        "time_estimation": "4H",
+        "title": "Functionally Assembled Terrestrial Ecosystem Simulator (FATES)",
         "tools": [
-            "interactive_tool_pangeo_notebook"
+            "__EXTRACT_DATASET__",
+            "interactive_tool_panoply",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3",
+            "toolshed.g2.bx.psu.edu/repos/climate/ctsm_fates/ctsm_fates/2.0.1",
+            "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1",
+            "toolshed.g2.bx.psu.edu/repos/ecology/xarray_select/xarray_select/0.15.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy2"
         ],
         "topic_name": "climate",
         "topic_name_human": "Climate",
@@ -26763,131 +28025,648 @@
             "tutorial": [],
             "video": true
         },
-        "tutorial_name": "pangeo-notebook",
+        "tutorial_name": "fates",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/climate/tutorials/pangeo-notebook/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/climate/tutorials/fates/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/pangeo-notebook/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/pangeo-notebook/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/fates/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/fates/tutorial.json"
         },
-        "version": 10,
+        "version": 17,
         "video": true,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 268,
-        "visitors": 1455677,
+        "visit_duration": 273,
+        "visitors": 2134812,
         "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
                         "identifier": "https://orcid.org/0000-0002-1784-2920",
-                        "name": "Anne Fouilloux",
-                        "url": "https://github.com/annefou"
+                        "name": "Anne Fouilloux"
                     }
                 ],
-                "description": "Workflow for GTN Pangeo Notebook in Galaxy - Introduction to Xarray",
+                "description": "Functionally Assembled Terrestrial Ecosystem Simulator (FATES)",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Pangeo Jupyter for Big Data geoscience\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset for CLM-FATES\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCLM-FATES restart file\"]\n  2[label=\"CTSM/FATES-EMERALD\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Extract Dataset\"]\n  2 -> 3 [label=\"history_files\"]\n  kdebf2e31dbea46d58644586c9731cdbe[color=lightseagreen,label=\"Output\\ninput dataset(s) (extracted element)\"]\n  3 -> kdebf2e31dbea46d58644586c9731cdbe\n  4[label=\"NetCDF xarray Metadata Info\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"NetCDF xarray Selection\"]\n  3 -> 5 [label=\"output\"]\n  4 -> 5 [label=\"output\"]\n  6[label=\"Replace\"]\n  5 -> 6 [label=\"simpleoutput\"]\n  7[label=\"Scatterplot with ggplot2\"]\n  6 -> 7 [label=\"outfile\"]\n}",
                 "history": [
                     {
-                        "hash": "e1474b2a116fe585bb664fa489f11648d12be74f",
-                        "message": "Add missing annotation for pangeo-notebook workflow",
+                        "hash": "ad6ca44b0dc2aadac1598e2d9d5e3bb5e94429aa",
+                        "message": "fix wf",
+                        "num": 3,
+                        "short_hash": "ad6ca44b0",
+                        "unix": "1633952401"
+                    },
+                    {
+                        "hash": "3693396f61a109643d15e9bc1b9e21a8def0562d",
+                        "message": "add license, creator information",
                         "num": 2,
-                        "short_hash": "e1474b2a1",
-                        "unix": "1643364120"
+                        "short_hash": "3693396f6",
+                        "unix": "1633427069"
                     },
                     {
-                        "hash": "1cb326ea7de3765fc5804f168fb4d813a72676b5",
-                        "message": "split pangeo training in two (Galaxy tool and Pangeo notebook)",
+                        "hash": "969fae434066d9571160c4510b8995e99defd640",
+                        "message": "Add climate workflows from @annefou",
                         "num": 1,
-                        "short_hash": "1cb326ea7",
-                        "unix": "1640271678"
+                        "short_hash": "969fae434",
+                        "unix": "1633426896"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Input dataset for CLM-FATES"
+                            }
+                        ],
+                        "label": "Input dataset for CLM-FATES",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 389.09725189208984,
+                            "height": 81.31945037841797,
+                            "left": 340.0173645019531,
+                            "right": 540.0173797607422,
+                            "top": 307.7778015136719,
+                            "width": 200.00001525878906,
+                            "x": 340.0173645019531,
+                            "y": 307.7778015136719
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "13b908b0-6a00-437b-bc4d-6c34f6f2d390",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "424dce0e-f3f0-4095-8513-9268be9c705d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "CLM-FATES restart file"
+                            }
+                        ],
+                        "label": "CLM-FATES restart file",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 732.5695114135742,
+                            "height": 81.31945037841797,
+                            "left": 317.3958435058594,
+                            "right": 517.3958587646484,
+                            "top": 651.2500610351562,
+                            "width": 200.00001525878906,
+                            "x": 317.3958435058594,
+                            "y": 651.2500610351562
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "19770ee9-8f78-4030-a8b8-1a44dd25ed43",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "1cecc2ed-8a94-448a-90f7-e67f8e8cf117"
+                            }
+                        ]
                     }
                 ],
-                "inputs": [],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"Pangeo Jupyter for Big Data geoscience\"];",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Pangeo Jupyter Notebook",
+                "license": "Apache-2.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset for CLM-FATES\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nCLM-FATES restart file\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"CTSM/FATES-EMERALD\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Extract Dataset\"];\n  2 -->|history_files| 3;\n  debf2e31-dbea-46d5-8644-586c9731cdbe[\"Output\\ninput dataset(s) (extracted element)\"];\n  3 --> debf2e31-dbea-46d5-8644-586c9731cdbe;\n  style debf2e31-dbea-46d5-8644-586c9731cdbe stroke:#2c3143,stroke-width:4px;\n  4[\"NetCDF xarray Metadata Info\"];\n  3 -->|output| 4;\n  5[\"NetCDF xarray Selection\"];\n  3 -->|output| 5;\n  4 -->|output| 5;\n  6[\"Replace\"];\n  5 -->|simpleoutput| 6;\n  7[\"Scatterplot with ggplot2\"];\n  6 -->|outfile| 7;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "CLM-FATES_ ALP1 simulation (5 years)",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "interactive_tool_pangeo_notebook",
+                        "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Interactive Pangeo Notebook",
-                                "name": "input"
+                                "description": "",
+                                "name": "Input dataset for CLM-FATES"
                             }
                         ],
-                        "label": "Pangeo Jupyter for Big Data geoscience",
-                        "name": "Interactive Pangeo Notebook",
+                        "label": "Input dataset for CLM-FATES",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 389.09725189208984,
+                            "height": 81.31945037841797,
+                            "left": 340.0173645019531,
+                            "right": 540.0173797607422,
+                            "top": 307.7778015136719,
+                            "width": 200.00001525878906,
+                            "x": 340.0173645019531,
+                            "y": 307.7778015136719
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "13b908b0-6a00-437b-bc4d-6c34f6f2d390",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "424dce0e-f3f0-4095-8513-9268be9c705d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "CLM-FATES restart file"
+                            }
+                        ],
+                        "label": "CLM-FATES restart file",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 732.5695114135742,
+                            "height": 81.31945037841797,
+                            "left": 317.3958435058594,
+                            "right": 517.3958587646484,
+                            "top": 651.2500610351562,
+                            "width": 200.00001525878906,
+                            "x": 317.3958435058594,
+                            "y": 651.2500610351562
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "19770ee9-8f78-4030-a8b8-1a44dd25ed43",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "1cecc2ed-8a94-448a-90f7-e67f8e8cf117"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/climate/ctsm_fates/ctsm_fates/2.0.1",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "adv_period|condi_type_run|restart": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "inputdata": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "CTSM/FATES-EMERALD",
                         "outputs": [
                             {
-                                "name": "jupyter_notebook",
-                                "type": "ipynb"
+                                "name": "history_files",
+                                "type": "input"
+                            },
+                            {
+                                "name": "atm_log",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "cesm_log",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "cpl_log",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "lnd_log",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "rof_log",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "restart",
+                                "type": "tar"
+                            },
+                            {
+                                "name": "case_info",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "rinfo",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "work",
+                                "type": "tar"
                             }
                         ],
                         "position": {
-                            "bottom": 516.90625,
-                            "height": 174.734375,
-                            "left": 672,
-                            "right": 872,
-                            "top": 342.171875,
-                            "width": 200,
-                            "x": 672,
-                            "y": 342.171875
+                            "bottom": 879.3056030273438,
+                            "height": 452.4305725097656,
+                            "left": 599.1319580078125,
+                            "right": 799.1319732666016,
+                            "top": 426.8750305175781,
+                            "width": 200.00001525878906,
+                            "x": 599.1319580078125,
+                            "y": 426.8750305175781
                         },
                         "post_job_actions": {},
-                        "tool_id": "interactive_tool_pangeo_notebook",
-                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"mode\": {\"mode_select\": \"scratch\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1c0f66b",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/climate/ctsm_fates/ctsm_fates/2.0.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "b525b88bc941",
+                            "name": "ctsm_fates",
+                            "owner": "climate",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"tar\", \"adv\": {\"co2\": \"367.0\", \"condi_user_mods\": {\"add_changes\": \"no\", \"__current_case__\": 1}}, \"adv_clm\": {\"use_fates_planthydro\": \"false\", \"use_fates_cohort_age_tracking\": \"false\", \"use_fates_ed_st3\": \"false\", \"use_fates_ed_prescribed_phys\": \"false\", \"use_fates_logging\": \"false\", \"use_fates_fixed_biogeog\": \"false\", \"fates_spitfire_mode\": \"0\", \"fates_parteh_mode\": \"\"}, \"adv_period\": {\"condi_type_run\": {\"run_type\": \"hybrid\", \"__current_case__\": 2, \"run_refcase\": \"ALP1_refcase\", \"run_refdate\": \"2300-01-01\", \"run_startdate\": \"0001-01-01\", \"restart\": {\"__class__\": \"ConnectedValue\"}}, \"stopn\": \"5\", \"stop_option\": \"nyears\"}, \"casename\": \"ALP1_exp\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"inputdata\": {\"__class__\": \"ConnectedValue\"}, \"resolution\": \"1x1_ALP1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.1",
                         "type": "tool",
-                        "uuid": "e921fd5a-97f9-4364-8c8a-7f225329016a",
+                        "uuid": "91a8cda0-72a6-46cf-babe-a4c0b11731f0",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "jupyter_notebook",
-                                "uuid": "30d1f58a-ace4-4eaf-9efa-c3930d768898"
+                                "output_name": "rinfo",
+                                "uuid": "5a152c6b-5574-46be-a0fc-be24471f83f7"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "work",
+                                "uuid": "a00239c9-9d0e-46d3-970e-d2e699eb6e4f"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "rof_log",
+                                "uuid": "230f4572-a4bb-46d4-aff5-25a592b375c3"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "cpl_log",
+                                "uuid": "3d6ef14c-9ee1-4fa5-be75-91985a8bc365"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "cesm_log",
+                                "uuid": "9c0f5924-4042-4c76-8c38-b4ae523b67a1"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "atm_log",
+                                "uuid": "c8dd2197-1288-4a90-be18-9dd32a926ad5"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "restart",
+                                "uuid": "5c5a27f6-42a3-4b50-b954-54ba8e9e0c67"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "lnd_log",
+                                "uuid": "5290961c-4660-42c2-88d1-ccd8e2f78412"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "case_info",
+                                "uuid": "9dd13369-b025-4095-9842-9030623fc941"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "history_files",
+                                "uuid": "8993eb0a-6e44-4cce-b8a1-f950b96cb8a8"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "__EXTRACT_DATASET__",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "input": {
+                                "id": 2,
+                                "output_name": "history_files"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Extract Dataset",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "data"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 392.63890075683594,
+                            "height": 132.43055725097656,
+                            "left": 871.8923950195312,
+                            "right": 1071.8924102783203,
+                            "top": 260.2083435058594,
+                            "width": 200.00001525878906,
+                            "x": 871.8923950195312,
+                            "y": 260.2083435058594
+                        },
+                        "post_job_actions": {
+                            "ChangeDatatypeActionoutput": {
+                                "action_arguments": {
+                                    "newtype": "netcdf"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "__EXTRACT_DATASET__",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"first\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "efb5bd53-a220-47fe-b4e0-15dd623737a1",
+                        "workflow_outputs": [
+                            {
+                                "label": "input dataset(s) (extracted element)",
+                                "output_name": "output",
+                                "uuid": "debf2e31-dbea-46d5-8644-586c9731cdbe"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "input": {
+                                "id": 3,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "NetCDF xarray Metadata Info",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "info",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 686.1111602783203,
+                            "height": 142.43055725097656,
+                            "left": 887.951416015625,
+                            "right": 1087.951431274414,
+                            "top": 543.6806030273438,
+                            "width": 200.00001525878906,
+                            "x": 887.951416015625,
+                            "y": 543.6806030273438
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "7edbe5ae8b72",
+                            "name": "xarray_metadata_info",
+                            "owner": "ecology",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"netcdf\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.15.1",
+                        "type": "tool",
+                        "uuid": "1dce5844-3ad9-42f8-b3f3-021c20b4bff1",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "info",
+                                "uuid": "ed801226-13db-4c99-8c49-521428e96dd8"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "10127f47-1ba1-4ecf-bb1c-014b87f098cb"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_select/xarray_select/0.15.1",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "input": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "var_tab": {
+                                "id": 4,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "NetCDF xarray Selection",
+                        "outputs": [
+                            {
+                                "name": "simpleoutput",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 613.9409942626953,
+                            "height": 142.43055725097656,
+                            "left": 1162.7083740234375,
+                            "right": 1362.7083892822266,
+                            "top": 471.51043701171875,
+                            "width": 200.00001525878906,
+                            "x": 1162.7083740234375,
+                            "y": 471.51043701171875
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_select/xarray_select/0.15.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "225d0d275a24",
+                            "name": "xarray_select",
+                            "owner": "ecology",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"netcdf\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"condi_source_coord\": {\"coord_source\": \"coord_from_stdin\", \"__current_case__\": 1, \"condi_coord\": {\"coord\": \"global\", \"__current_case__\": 2}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"time\": {\"condi_datetime\": {\"datetime\": \"no\", \"__current_case__\": 0}}, \"user_choice\": [], \"var\": \"LEAFC\", \"var_tab\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.15.1",
+                        "type": "tool",
+                        "uuid": "34e85d8a-b640-41a6-b9ee-82a73f5fda43",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "simpleoutput",
+                                "uuid": "1c9a151b-50e8-439e-9586-96af577d9c27"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "infile": {
+                                "id": 5,
+                                "output_name": "simpleoutput"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Replace",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 698.3507232666016,
+                            "height": 92.43055725097656,
+                            "left": 1185.4862060546875,
+                            "right": 1385.4862213134766,
+                            "top": 605.920166015625,
+                            "width": 200.00001525878906,
+                            "x": 1185.4862060546875,
+                            "y": 605.920166015625
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"caseinsensitive\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"find_pattern\": \"00:00:00\", \"global\": \"true\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": \"false\", \"replace_pattern\": \"\", \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}, \"skip_first_line\": \"true\", \"wholewords\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.3",
+                        "type": "tool",
+                        "uuid": "f6ea58b5-a373-4cf4-884a-242dc8cc1928",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "10b70ac6-9a53-45ba-a761-71dd1e987184"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy2",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "input1": {
+                                "id": 6,
+                                "output_name": "outfile"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Scatterplot with ggplot2",
+                        "outputs": [
+                            {
+                                "name": "output1",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 815.1215362548828,
+                            "height": 152.43055725097656,
+                            "left": 1339.3751220703125,
+                            "right": 1539.3751373291016,
+                            "top": 662.6909790039062,
+                            "width": 200.00001525878906,
+                            "x": 1339.3751220703125,
+                            "y": 662.6909790039062
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "87908c76ca8d",
+                            "name": "ggplot2_point",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"adv\": {\"type\": \"pointslines\", \"points\": {\"pointoptions\": \"default\", \"__current_case__\": 0}, \"factor\": {\"factoring\": \"Default\", \"__current_case__\": 0}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"19.0\", \"height_output_dim\": \"5.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"Total carbon in live plant leaves\", \"xlab\": \"Time\", \"xplot\": \"1\", \"ylab\": \"LEAFC (kgC ha-1)\", \"yplot\": \"4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.2.1+galaxy2",
+                        "type": "tool",
+                        "uuid": "dc2790c9-e3f1-441c-8d95-2406a44bfa3e",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output1",
+                                "uuid": "2857a6af-c707-4dea-a188-dd9f2e8146e5"
                             }
                         ]
                     }
                 ],
-                "parent_id": "climate/pangeo-notebook",
-                "path": "topics/climate/tutorials/pangeo-notebook/workflows/main_workflow.ga",
+                "parent_id": "climate/fates",
+                "path": "topics/climate/tutorials/fates/workflows/CLM-FATES_ALP1_simulation_5years.ga",
                 "tags": [
-                    "pangeo",
-                    "climate",
-                    "big-data",
-                    "geosciences"
+                    "climate"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Pangeo Jupyter Notebook",
+                "title": "CLM-FATES_ ALP1 simulation (5 years)",
                 "topic_id": "climate",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/climate-pangeo-notebook/versions/main-workflow",
-                "tutorial_id": "pangeo-notebook",
-                "url": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/pangeo-notebook/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/pangeo-notebook/workflows/main_workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/climate-fates/versions/clm-fates-alp1-simulation-5years",
+                "tutorial_id": "fates",
+                "url": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/fates/workflows/CLM-FATES_ALP1_simulation_5years.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/fates/workflows/CLM-FATES_ALP1_simulation_5years.html",
                 "version": 1,
-                "wfid": "climate-pangeo-notebook",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "wfid": "climate-fates",
+                "wfname": "clm-fates-alp1-simulation-5years",
+                "workflow": "CLM-FATES_ALP1_simulation_5years.ga",
                 "workflow_tools": [
-                    "interactive_tool_pangeo_notebook"
+                    "__EXTRACT_DATASET__",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3",
+                    "toolshed.g2.bx.psu.edu/repos/climate/ctsm_fates/ctsm_fates/2.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_select/xarray_select/0.15.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy2"
                 ],
-                "workflowhub_id": "1189"
+                "workflowhub_id": "1185"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.5805953"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.4108341"
     },
     {
         "admin_install": {
@@ -26986,7 +28765,7 @@
             "Learn about the different source of climate data",
             "Learn about climate observations, reanalysis, climate predictions and climate projections"
         ],
-        "pageviews": 1191,
+        "pageviews": 1202,
         "pub_date": "2020-04-30",
         "questions": [
             "What is climate?",
@@ -26994,13 +28773,13 @@
         ],
         "short_id": "T00041",
         "short_tools": [
-            "Grep1",
-            "datamash_ops",
             "tp_awk_tool",
+            "cds_essential_variability",
             "ggplot2_point",
+            "Grep1",
             "psy_maps",
             "climate_stripes",
-            "cds_essential_variability"
+            "datamash_ops"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -27056,630 +28835,130 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 56,
-        "visitors": 841,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0002-1784-2920",
-                        "name": "Anne Fouilloux"
-                    }
-                ],
-                "description": "Visualize Climate data with Panoply netCDF viewer",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[label=\"Copernicus Essential Climate Variables\"]\n  3[label=\"climate stripes\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Select\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Datamash\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"Datamash\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"Datamash\"]\n  1 -> 7 [label=\"output\"]\n  8[label=\"Text reformatting\"]\n  1 -> 8 [label=\"output\"]\n  9[label=\"map plot\"]\n  2 -> 9 [label=\"ofilename\"]\n  10[label=\"Datamash\"]\n  8 -> 10 [label=\"outfile\"]\n  11[label=\"Datamash\"]\n  8 -> 11 [label=\"outfile\"]\n  12[label=\"Datamash\"]\n  10 -> 12 [label=\"out_file\"]\n  13[label=\"Datamash\"]\n  10 -> 13 [label=\"out_file\"]\n  14[label=\"Scatterplot w ggplot2\"]\n  11 -> 14 [label=\"out_file\"]\n}",
-                "history": [
-                    {
-                        "hash": "3693396f61a109643d15e9bc1b9e21a8def0562d",
-                        "message": "add license, creator information",
-                        "num": 2,
-                        "short_hash": "3693396f6",
-                        "unix": "1633427069"
-                    },
-                    {
-                        "hash": "969fae434066d9571160c4510b8995e99defd640",
-                        "message": "Add climate workflows from @annefou",
-                        "num": 1,
-                        "short_hash": "969fae434",
-                        "unix": "1633426896"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "ts_cities.csv"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 10
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"ts_cities.csv\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "99e7d3bd-74d3-4651-81d0-7a468624d8aa",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "tg_ens_mean_0.1deg_reg_v20.0e_Paris_daily.csv"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 130
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"tg_ens_mean_0.1deg_reg_v20.0e_Paris_daily.csv\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "0afa85cd-9b3e-44a1-a528-9e293f86b500",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Copernicus Essential Climate Variables\"];\n  3[\"climate stripes\"];\n  0 -->|output| 3;\n  4[\"Select\"];\n  1 -->|output| 4;\n  5[\"Datamash\"];\n  1 -->|output| 5;\n  6[\"Datamash\"];\n  1 -->|output| 6;\n  7[\"Datamash\"];\n  1 -->|output| 7;\n  8[\"Text reformatting\"];\n  1 -->|output| 8;\n  9[\"map plot\"];\n  2 -->|ofilename| 9;\n  10[\"Datamash\"];\n  8 -->|outfile| 10;\n  11[\"Datamash\"];\n  8 -->|outfile| 11;\n  12[\"Datamash\"];\n  10 -->|out_file| 12;\n  13[\"Datamash\"];\n  10 -->|out_file| 13;\n  14[\"Scatterplot w ggplot2\"];\n  11 -->|out_file| 14;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Climate 101",
-                "outputs": [],
-                "parent_id": "climate/climate-101",
-                "path": "topics/climate/tutorials/climate-101/workflows/climate_101_workflow.ga",
-                "tags": [
-                    "climate"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Climate 101",
-                "topic_id": "climate",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/climate-climate-101/versions/climate-101-workflow",
-                "tutorial_id": "climate-101",
-                "url": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/climate-101/workflows/climate_101_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/climate-101/workflows/climate_101_workflow.html",
-                "version": 1,
-                "wfid": "climate-climate-101",
-                "wfname": "climate-101-workflow",
-                "workflow": "climate_101_workflow.ga",
-                "workflow_tools": [
-                    "Grep1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/climate/cds_essential_variability/cds_essential_variability/0.1.4",
-                    "toolshed.g2.bx.psu.edu/repos/climate/climate_stripes/climate_stripes/1.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/climate/psy_maps/psy_maps/1.2.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy1"
-                ],
-                "workflowhub_id": "1138"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/3776500"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "divand_full_analysis",
-                    "owner": "ecology",
-                    "revisions": "484930fdc002",
-                    "tool_panel_section_label": "Climate Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: divand_full_analysis\n  owner: ecology\n  revisions: 484930fdc002\n  tool_panel_section_label: Climate Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/ocean-variables/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "Marie59"
-            ],
-            "funding": [
-                "fairease",
-                "eurosciencegateway"
-            ]
-        },
-        "contributors": [
-            {
-                "affiliations": [
-                    "pndb",
-                    "fairease"
-                ],
-                "email": "marie.josse@ifremer.fr",
-                "id": "Marie59",
-                "joined": "2022-03",
-                "name": "Marie Josse",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
-            },
-            {
-                "avatar": "/training-material/assets/images/fair_ease_colour.png",
-                "funder": true,
-                "funding_id": "101058785",
-                "funding_statement": "FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "fairease",
-                "joined": "2023-10",
-                "members": [
-                    "Marie59",
-                    "yvanlebras"
-                ],
-                "name": "Fair-Ease",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fairease/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/fairease.json"
-            },
-            {
-                "avatar": "/training-material/assets/images/eurosciencegateway.png",
-                "funder": true,
-                "funding_id": "101057388",
-                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "eurosciencegateway",
-                "joined": "2023-10",
-                "members": [
-                    "abretaud",
-                    "anuprulez",
-                    "bgruening",
-                    "erxleben",
-                    "pauldg",
-                    "rlibouba"
-                ],
-                "name": "EuroScienceGateway",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
-            }
-        ],
-        "dir": "topics/climate/tutorials/ocean-variables",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "climate/ocean-variables",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Manage ODV collection's data.",
-            "Learn to extract data and visualize them on ODV",
-            "Learn to chain ODV and DIVAnd"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-08-09",
-        "objectives": [
-            "Deals with ODV collection with data originating from Emodnet chemistry",
-            "Visualise ocean variables to study climate changes"
-        ],
-        "pageviews": 109,
-        "pub_date": "2023-11-29",
-        "questions": [
-            "How to process extract ocean's variables?",
-            "How to use ODV collections?",
-            "How to create climatological estimates?"
-        ],
-        "short_id": "T00376",
-        "short_tools": [
-            "interactive_tool_divand",
-            "divand_full_analysis",
-            "interactive_tool_odv"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "earth-system",
-            "ocean",
-            "netcdf data"
-        ],
-        "time_estimation": "1H",
-        "title": "Ocean's variables study",
-        "tools": [
-            "interactive_tool_divand",
-            "interactive_tool_odv",
-            "toolshed.g2.bx.psu.edu/repos/ecology/divand_full_analysis/divand_full_analysis/0.1.0+galaxy0"
-        ],
-        "topic_name": "climate",
-        "topic_name_human": "Climate",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "ocean-variables",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/climate/tutorials/ocean-variables/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/ocean-variables/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/ocean-variables/tutorial.json"
-        },
-        "version": 4,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 145,
-        "visitors": 84,
+        "visit_duration": 55,
+        "visitors": 852,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0009-0008-0622-604X",
-                        "name": "Marie Joss\u00e9",
-                        "url": "https://github.com/Marie59"
-                    }
-                ],
-                "description": "Subset data on the Mediterreanean see and extract and visualise the Phosphate variable",
-                "features": {
-                    "comments": true,
-                    "parameters": true,
-                    "report": {
-                        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
-                    },
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nWorflow fully interactive\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nEutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nWorkflow semi automatic\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ngebco_30sec_8.nc\"]\n  4[label=\"Ocean Data View\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Interactive DIVAnd jupyterlab\"]\n  4 -> 5 [label=\"outputs_netcdf\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"DIVAnd create a climatology\"]\n  3 -> 6 [label=\"output\"]\n  4 -> 6 [label=\"outputs_netcdf\"]\n  2 -> 6 [label=\"output\"]\n  k5996328287bf4432a7778a9b61dea03c[color=lightseagreen,label=\"Output\\nWater_body_Phosphate_Mediterranean.nc\"]\n  6 -> k5996328287bf4432a7778a9b61dea03c\n  7[label=\"ODV visualisation interactive\"]\n  5 -> 7 [label=\"output_netcdf\"]\n  kdc8316a4e57c476bb885bbe4fb84d8c7[color=lightseagreen,label=\"Output\\nOcean variables visualisation interactive\"]\n  7 -> kdc8316a4e57c476bb885bbe4fb84d8c7\n  8[label=\"ODV visualisation\"]\n  6 -> 8 [label=\"output_netcdf\"]\n  k7b0722535bf9434fb06a70b375ddaa03[color=lightseagreen,label=\"Output\\nOcean variables visualisation\"]\n  8 -> k7b0722535bf9434fb06a70b375ddaa03\n}",
-                "history": [
-                    {
-                        "hash": "1c6ee9c0d6c08affe5e54d71b4488147396ba5aa",
-                        "message": "Add new version of workflow",
-                        "num": 2,
-                        "short_hash": "1c6ee9c0d",
-                        "unix": "1723110972"
-                    },
-                    {
-                        "hash": "c51d6ffbc21866df213772767f645a889a23c70f",
-                        "message": "Add workflow",
-                        "num": 1,
-                        "short_hash": "c51d6ffbc",
-                        "unix": "1710854627"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "Choose whether you want to have only interactive tools (for more experimented user) or if you want a workflow hat combines interactive and non-interactive tools (easier)",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Choose whether you want to have only interactive tools (for more experimented user) or if you want a workflow hat combines interactive and non-interactive tools (easier)",
-                                "name": "Worflow fully interactive"
-                            }
-                        ],
-                        "label": "Worflow fully interactive",
-                        "name": "Input parameter",
-                        "outputs": [],
-                        "position": {
-                            "left": 29.80677214543107,
-                            "top": 359.1046708180256
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "250d862b-4c3d-462d-9bcd-9a5053c52b5e",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "The data here are Mediterranean Sea - Eutrophication and Acidity aggregated datasets EMODnet Chemistry.",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "The data here are Mediterranean Sea - Eutrophication and Acidity aggregated datasets EMODnet Chemistry.",
-                                "name": "Eutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip"
-                            }
-                        ],
-                        "label": "Eutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 314.4,
-                            "top": 507.4
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "b513664a-1176-4fd9-bb79-439010069177",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "Choose whether you want to have only interactive tools (for more experimented user) or if you want a workflow hat combines interactive and non-interactive tools (easier)",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Choose whether you want to have only interactive tools (for more experimented user) or if you want a workflow hat combines interactive and non-interactive tools (easier)",
-                                "name": "Workflow semi automatic"
-                            }
-                        ],
-                        "label": "Workflow semi automatic",
-                        "name": "Input parameter",
-                        "outputs": [],
-                        "position": {
-                            "left": 34.559982917236994,
-                            "top": 738.7586893348329
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "6e2ed5ec-3760-44fe-a722-4e44356f9058",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "A bathymetry file in netcdf.",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "A bathymetry file in netcdf.",
-                                "name": "gebco_30sec_8.nc"
-                            }
-                        ],
-                        "label": "gebco_30sec_8.nc",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 614.0977004616734,
-                            "top": 903.4688531054738
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "006a3936-6151-4724-9fab-6b41f869e1ee",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nWorflow fully interactive\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nEutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nWorkflow semi automatic\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\ngebco_30sec_8.nc\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Ocean Data View\"];\n  1 -->|output| 4;\n  5[\"Interactive DIVAnd jupyterlab\"];\n  4 -->|outputs_netcdf| 5;\n  0 -->|output| 5;\n  6[\"DIVAnd create a climatology\"];\n  3 -->|output| 6;\n  4 -->|outputs_netcdf| 6;\n  2 -->|output| 6;\n  59963282-87bf-4432-a777-8a9b61dea03c[\"Output\\nWater_body_Phosphate_Mediterranean.nc\"];\n  6 --> 59963282-87bf-4432-a777-8a9b61dea03c;\n  style 59963282-87bf-4432-a777-8a9b61dea03c stroke:#2c3143,stroke-width:4px;\n  7[\"ODV visualisation interactive\"];\n  5 -->|output_netcdf| 7;\n  dc8316a4-e57c-476b-b885-bbe4fb84d8c7[\"Output\\nOcean variables visualisation interactive\"];\n  7 --> dc8316a4-e57c-476b-b885-bbe4fb84d8c7;\n  style dc8316a4-e57c-476b-b885-bbe4fb84d8c7 stroke:#2c3143,stroke-width:4px;\n  8[\"ODV visualisation\"];\n  6 -->|output_netcdf| 8;\n  7b072253-5bf9-434f-b06a-70b375ddaa03[\"Output\\nOcean variables visualisation\"];\n  8 --> 7b072253-5bf9-434f-b06a-70b375ddaa03;\n  style 7b072253-5bf9-434f-b06a-70b375ddaa03 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Ocean's variables 2.0",
-                "outputs": [
-                    {
-                        "annotation": "Create a climatology (not interactively)",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/divand_full_analysis/divand_full_analysis/0.1.0+galaxy0",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "bathname": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "input_netcdf_identifier": {
-                                "id": 4,
-                                "output_name": "outputs_netcdf"
-                            },
-                            "when": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "DIVAnd (create a climatology)",
-                        "name": "DIVAnd",
-                        "outputs": [
-                            {
-                                "name": "output_netcdf",
-                                "type": "netcdf"
-                            }
-                        ],
-                        "position": {
-                            "left": 958.2529539113443,
-                            "top": 679.118779662132
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_netcdf": {
-                                "action_arguments": {
-                                    "newname": "Water_body_Phosphate_Mediterranean.nc"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_netcdf"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/divand_full_analysis/divand_full_analysis/0.1.0+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "484930fdc002",
-                            "name": "divand_full_analysis",
-                            "owner": "ecology",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"bathname\": {\"__class__\": \"ConnectedValue\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"enddate\": \"2017-01-01\", \"input_netcdf_identifier\": {\"__class__\": \"ConnectedValue\"}, \"input_netcdf_identifier|__identifier__\": \"data_from_Eutrophication_Med_profiles_2022_unrestricted.nc\", \"latmax\": \"38.0\", \"latmin\": \"32.0\", \"longmax\": \"30.0\", \"longmin\": \"19.0\", \"selmax\": \"100\", \"selmin\": \"0\", \"startdate\": \"1950-12-31\", \"varname\": \"phosphate\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.0+galaxy0",
-                        "type": "tool",
-                        "uuid": "d1c07265-1da0-40d6-9fd5-1041a9d9f658",
-                        "when": "$(inputs.when)",
-                        "workflow_outputs": [
-                            {
-                                "label": "Water_body_Phosphate_Mediterranean.nc",
-                                "output_name": "output_netcdf",
-                                "uuid": "59963282-87bf-4432-a777-8a9b61dea03c"
-                            }
-                        ]
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0002-1784-2920",
+                        "name": "Anne Fouilloux"
+                    }
+                ],
+                "description": "Visualize Climate data with Panoply netCDF viewer",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[label=\"Copernicus Essential Climate Variables\"]\n  3[label=\"climate stripes\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Select\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Datamash\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"Datamash\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"Datamash\"]\n  1 -> 7 [label=\"output\"]\n  8[label=\"Text reformatting\"]\n  1 -> 8 [label=\"output\"]\n  9[label=\"map plot\"]\n  2 -> 9 [label=\"ofilename\"]\n  10[label=\"Datamash\"]\n  8 -> 10 [label=\"outfile\"]\n  11[label=\"Datamash\"]\n  8 -> 11 [label=\"outfile\"]\n  12[label=\"Datamash\"]\n  10 -> 12 [label=\"out_file\"]\n  13[label=\"Datamash\"]\n  10 -> 13 [label=\"out_file\"]\n  14[label=\"Scatterplot w ggplot2\"]\n  11 -> 14 [label=\"out_file\"]\n}",
+                "history": [
+                    {
+                        "hash": "3693396f61a109643d15e9bc1b9e21a8def0562d",
+                        "message": "add license, creator information",
+                        "num": 2,
+                        "short_hash": "3693396f6",
+                        "unix": "1633427069"
                     },
                     {
-                        "annotation": "Final step to visualize in different way a ocean variable like the phosphate.",
-                        "content_id": "interactive_tool_odv",
+                        "hash": "969fae434066d9571160c4510b8995e99defd640",
+                        "message": "Add climate workflows from @annefou",
+                        "num": 1,
+                        "short_hash": "969fae434",
+                        "unix": "1633426896"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
                         "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "method|infiles": {
-                                "id": 5,
-                                "output_name": "output_netcdf"
-                            }
-                        },
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool ODV",
-                                "name": "method"
-                            }
-                        ],
-                        "label": "ODV (visualisation) interactive",
-                        "name": "ODV",
-                        "outputs": [
-                            {
-                                "name": "outputs_netcdf",
-                                "type": "input"
-                            },
-                            {
-                                "name": "outputs_all",
-                                "type": "input"
+                                "description": "",
+                                "name": "ts_cities.csv"
                             }
                         ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1315.0326051372172,
-                            "top": 398.52546972475403
+                            "left": 10,
+                            "top": 10
                         },
-                        "post_job_actions": {},
-                        "tool_id": "interactive_tool_odv",
-                        "tool_state": "{\"__input_ext\": \"netcdf\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"method\": {\"type\": \"own_data\", \"__current_case__\": 0, \"infiles\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.6.5.1",
-                        "type": "tool",
-                        "uuid": "50c35d61-7b8d-4706-9d56-d3bd94a46960",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Ocean variables visualisation interactive",
-                                "output_name": "outputs_all",
-                                "uuid": "dc8316a4-e57c-476b-b885-bbe4fb84d8c7"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"ts_cities.csv\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "99e7d3bd-74d3-4651-81d0-7a468624d8aa",
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "Final step to visualize in different way a ocean variable like the phosphate.",
-                        "content_id": "interactive_tool_odv",
+                        "annotation": "",
+                        "content_id": null,
                         "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "method|infiles": {
-                                "id": 6,
-                                "output_name": "output_netcdf"
-                            }
-                        },
+                        "id": 1,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool ODV",
-                                "name": "method"
-                            }
-                        ],
-                        "label": "ODV (visualisation)",
-                        "name": "ODV",
-                        "outputs": [
-                            {
-                                "name": "outputs_netcdf",
-                                "type": "input"
-                            },
-                            {
-                                "name": "outputs_all",
-                                "type": "input"
+                                "description": "",
+                                "name": "tg_ens_mean_0.1deg_reg_v20.0e_Paris_daily.csv"
                             }
                         ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1313.0264554819623,
-                            "top": 737.9220054373203
+                            "left": 10,
+                            "top": 130
                         },
-                        "post_job_actions": {},
-                        "tool_id": "interactive_tool_odv",
-                        "tool_state": "{\"__input_ext\": \"netcdf\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"method\": {\"type\": \"own_data\", \"__current_case__\": 0, \"infiles\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.6.5.1",
-                        "type": "tool",
-                        "uuid": "9bff476c-be32-4d87-a655-db241126ae49",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Ocean variables visualisation",
-                                "output_name": "outputs_all",
-                                "uuid": "7b072253-5bf9-434f-b06a-70b375ddaa03"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"tg_ens_mean_0.1deg_reg_v20.0e_Paris_daily.csv\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0afa85cd-9b3e-44a1-a528-9e293f86b500",
+                        "workflow_outputs": []
                     }
                 ],
-                "parent_id": "climate/ocean-variables",
-                "path": "topics/climate/tutorials/ocean-variables/workflows/main_workflow.ga",
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Copernicus Essential Climate Variables\"];\n  3[\"climate stripes\"];\n  0 -->|output| 3;\n  4[\"Select\"];\n  1 -->|output| 4;\n  5[\"Datamash\"];\n  1 -->|output| 5;\n  6[\"Datamash\"];\n  1 -->|output| 6;\n  7[\"Datamash\"];\n  1 -->|output| 7;\n  8[\"Text reformatting\"];\n  1 -->|output| 8;\n  9[\"map plot\"];\n  2 -->|ofilename| 9;\n  10[\"Datamash\"];\n  8 -->|outfile| 10;\n  11[\"Datamash\"];\n  8 -->|outfile| 11;\n  12[\"Datamash\"];\n  10 -->|out_file| 12;\n  13[\"Datamash\"];\n  10 -->|out_file| 13;\n  14[\"Scatterplot w ggplot2\"];\n  11 -->|out_file| 14;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Climate 101",
+                "outputs": [],
+                "parent_id": "climate/climate-101",
+                "path": "topics/climate/tutorials/climate-101/workflows/climate_101_workflow.ga",
                 "tags": [
-                    "earth-system",
-                    "Ocean"
+                    "climate"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "Ocean's variables 2.0",
+                "tests": false,
+                "title": "Climate 101",
                 "topic_id": "climate",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/climate-ocean-variables/versions/main-workflow",
-                "tutorial_id": "ocean-variables",
-                "url": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/ocean-variables/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/ocean-variables/workflows/main_workflow.html",
-                "version": 2,
-                "wfid": "climate-ocean-variables",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/climate-climate-101/versions/climate-101-workflow",
+                "tutorial_id": "climate-101",
+                "url": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/climate-101/workflows/climate_101_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/climate-101/workflows/climate_101_workflow.html",
+                "version": 1,
+                "wfid": "climate-climate-101",
+                "wfname": "climate-101-workflow",
+                "workflow": "climate_101_workflow.ga",
                 "workflow_tools": [
-                    "interactive_tool_divand",
-                    "interactive_tool_odv",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/divand_full_analysis/divand_full_analysis/0.1.0+galaxy0"
+                    "Grep1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/climate/cds_essential_variability/cds_essential_variability/0.1.4",
+                    "toolshed.g2.bx.psu.edu/repos/climate/climate_stripes/climate_stripes/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/climate/psy_maps/psy_maps/1.2.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy1"
                 ],
-                "workflowhub_id": "1200"
+                "workflowhub_id": "1138"
             }
-        ]
+        ],
+        "zenodo_link": "https://zenodo.org/record/3776500"
     },
     {
         "admin_install": {
@@ -27800,7 +29079,7 @@
             "Learn to filter, make reduction operations (mean, max, min)",
             "Learn to resample my data"
         ],
-        "pageviews": 3701863,
+        "pageviews": 3872139,
         "pub_date": "2022-02-18",
         "questions": [
             "What Xarray Galaxy Tools can I use in Galaxy and what for?",
@@ -27829,17 +29108,17 @@
         ],
         "short_id": "T00044",
         "short_tools": [
-            "xarray_select",
-            "graphicsmagick_image_montage",
+            "__EXTRACT_DATASET__",
+            "xarray_metadata_info",
             "xarray_mapplot",
+            "graphicsmagick_image_montage",
+            "xarray_netcdf2netcdf",
             "ggplot2_point",
+            "xarray_coords_info",
             "climate_stripes",
-            "xarray_netcdf2netcdf",
-            "xarray_metadata_info",
             "regexColumn1",
             "__MERGE_COLLECTION__",
-            "__EXTRACT_DATASET__",
-            "xarray_coords_info"
+            "xarray_select"
         ],
         "slides": true,
         "slides_recordings": false,
@@ -27902,8 +29181,8 @@
         "video": true,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 344,
-        "visitors": 1455499,
+        "visit_duration": 342,
+        "visitors": 1524751,
         "workflows": [
             {
                 "creators": [
@@ -28294,7 +29573,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nplot first time e.g. index=0\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nCAMS-PM2_5-20211222.netcdf\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nplot forecast time 2 days 12:00 UTC\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\ntime=5\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\ntime=6\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Parameter\\ntime=3\"];\n  style 5 fill:#ded,stroke:#393,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Parameter\\ntime=2\"];\n  style 6 fill:#ded,stroke:#393,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Parameter\\ntime=7\"];\n  style 7 fill:#ded,stroke:#393,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Parameter\\ntime=1\"];\n  style 8 fill:#ded,stroke:#393,stroke-width:4px;\n  9[\"\u2139\ufe0f Input Parameter\\ntime=4\"];\n  style 9 fill:#ded,stroke:#393,stroke-width:4px;\n  10[\"\u2139\ufe0f Input Parameter\\ntime=0\"];\n  style 10 fill:#ded,stroke:#393,stroke-width:4px;\n  11[\"NetCDF xarray Coordinate Info\"];\n  1 -->|output| 11;\n  12[\"NetCDF xarray Metadata Info\"];\n  1 -->|output| 12;\n  13[\"extract longitude\"];\n  11 -->|output_dir| 13;\n  14[\"extract latitude\"];\n  11 -->|output_dir| 14;\n  15[\"Extract time from coordinate info\"];\n  11 -->|output_dir| 15;\n  3b4968d7-8984-4e66-87a9-a3ab8fc12ca4[\"Output\\ninput dataset(s) (extracted element)\"];\n  15 --> 3b4968d7-8984-4e66-87a9-a3ab8fc12ca4;\n  style 3b4968d7-8984-4e66-87a9-a3ab8fc12ca4 stroke:#2c3143,stroke-width:4px;\n  16[\"NetCDF xarray operations\"];\n  1 -->|output| 16;\n  14 -->|output| 16;\n  13 -->|output| 16;\n  12 -->|output| 16;\n  17[\"NetCDF xarray operations\"];\n  1 -->|output| 17;\n  15 -->|output| 17;\n  12 -->|output| 17;\n  18[\"NetCDF xarray operations\"];\n  1 -->|output| 18;\n  15 -->|output| 18;\n  14 -->|output| 18;\n  13 -->|output| 18;\n  12 -->|output| 18;\n  19[\"PM2.5 CAMS Europe 0 days 00:00 UTC reference time\"];\n  15 -->|output| 19;\n  0 -->|output| 19;\n  1 -->|output| 19;\n  12 -->|output| 19;\n  42483031-21e2-4d88-8898-4a9aa9bb10e5[\"Output\\nPM2.5 reference date Europe\"];\n  19 --> 42483031-21e2-4d88-8898-4a9aa9bb10e5;\n  style 42483031-21e2-4d88-8898-4a9aa9bb10e5 stroke:#2c3143,stroke-width:4px;\n  20[\"PM2.5 CAMS forecast 2 days 12:00 UTC\"];\n  15 -->|output| 20;\n  2 -->|output| 20;\n  1 -->|output| 20;\n  12 -->|output| 20;\n  07ba8141-bad3-4a61-833d-3b3e82b53fdb[\"Output\\nPM2.5 fc 2 days 12:00 UTC Europe\"];\n  20 --> 07ba8141-bad3-4a61-833d-3b3e82b53fdb;\n  style 07ba8141-bad3-4a61-833d-3b3e82b53fdb stroke:#2c3143,stroke-width:4px;\n  21[\"NetCDF xarray Selection\"];\n  16 -->|output_netcdf| 21;\n  12 -->|output| 21;\n  22[\"NetCDF xarray Coordinate Info\"];\n  17 -->|output_netcdf| 22;\n  23[\"NetCDF xarray Coordinate Info\"];\n  18 -->|output_netcdf| 23;\n  24[\"NetCDF xarray Metadata Info\"];\n  18 -->|output_netcdf| 24;\n  25[\"Column Regex Find And Replace\"];\n  21 -->|simpleoutput| 25;\n  26[\"PM2.5 over Naples 4 days forecast\"];\n  21 -->|simpleoutput| 26;\n  8984beb4-e593-42f8-8de5-0e92631061c7[\"Output\\n1D plot PM2.5 over Naples (4 days forecast)\"];\n  26 --> 8984beb4-e593-42f8-8de5-0e92631061c7;\n  style 8984beb4-e593-42f8-8de5-0e92631061c7 stroke:#2c3143,stroke-width:4px;\n  27[\"Extract times from coordinates\"];\n  22 -->|output_dir| 27;\n  28[\"Extract time\"];\n  23 -->|output_dir| 28;\n  29[\" stripes PM2.5 over Naples 4 days forecast\"];\n  25 -->|out_file1| 29;\n  92cad576-78b5-4e07-9a07-6f05ff8f4a56[\"Output\\nPM2.5 stripes Naples for 4 days forecast from reference date\"];\n  29 --> 92cad576-78b5-4e07-9a07-6f05ff8f4a56;\n  style 92cad576-78b5-4e07-9a07-6f05ff8f4a56 stroke:#2c3143,stroke-width:4px;\n  30[\"NetCDF xarray map plotting\"];\n  27 -->|output| 30;\n  0 -->|output| 30;\n  18 -->|output_netcdf| 30;\n  24 -->|output| 30;\n  31[\"NetCDF xarray map plotting\"];\n  28 -->|output| 31;\n  6 -->|output| 31;\n  18 -->|output_netcdf| 31;\n  24 -->|output| 31;\n  32[\"NetCDF xarray map plotting\"];\n  28 -->|output| 32;\n  8 -->|output| 32;\n  18 -->|output_netcdf| 32;\n  24 -->|output| 32;\n  33[\"NetCDF xarray map plotting\"];\n  28 -->|output| 33;\n  5 -->|output| 33;\n  18 -->|output_netcdf| 33;\n  24 -->|output| 33;\n  34[\"NetCDF xarray map plotting\"];\n  28 -->|output| 34;\n  9 -->|output| 34;\n  18 -->|output_netcdf| 34;\n  24 -->|output| 34;\n  35[\"NetCDF xarray map plotting\"];\n  28 -->|output| 35;\n  4 -->|output| 35;\n  18 -->|output_netcdf| 35;\n  24 -->|output| 35;\n  36[\"NetCDF xarray map plotting\"];\n  28 -->|output| 36;\n  7 -->|output| 36;\n  18 -->|output_netcdf| 36;\n  24 -->|output| 36;\n  37[\"NetCDF xarray map plotting\"];\n  28 -->|output| 37;\n  3 -->|output| 37;\n  18 -->|output_netcdf| 37;\n  24 -->|output| 37;\n  38[\"NetCDF xarray map plotting\"];\n  28 -->|output| 38;\n  3 -->|output| 38;\n  18 -->|output_netcdf| 38;\n  24 -->|output| 38;\n  39[\"NetCDF xarray map plotting\"];\n  28 -->|output| 39;\n  4 -->|output| 39;\n  18 -->|output_netcdf| 39;\n  24 -->|output| 39;\n  40[\"NetCDF xarray map plotting\"];\n  28 -->|output| 40;\n  10 -->|output| 40;\n  18 -->|output_netcdf| 40;\n  24 -->|output| 40;\n  41[\"NetCDF xarray map plotting\"];\n  28 -->|output| 41;\n  5 -->|output| 41;\n  18 -->|output_netcdf| 41;\n  24 -->|output| 41;\n  42[\"NetCDF xarray map plotting\"];\n  28 -->|output| 42;\n  6 -->|output| 42;\n  18 -->|output_netcdf| 42;\n  24 -->|output| 42;\n  43[\"NetCDF xarray map plotting\"];\n  28 -->|output| 43;\n  10 -->|output| 43;\n  18 -->|output_netcdf| 43;\n  24 -->|output| 43;\n  44[\"NetCDF xarray map plotting\"];\n  28 -->|output| 44;\n  7 -->|output| 44;\n  18 -->|output_netcdf| 44;\n  24 -->|output| 44;\n  45[\"NetCDF xarray map plotting\"];\n  28 -->|output| 45;\n  9 -->|output| 45;\n  18 -->|output_netcdf| 45;\n  24 -->|output| 45;\n  46[\"NetCDF xarray map plotting\"];\n  28 -->|output| 46;\n  8 -->|output| 46;\n  18 -->|output_netcdf| 46;\n  24 -->|output| 46;\n  47[\"Merge collections\"];\n  30 -->|output_dir| 47;\n  32 -->|output_dir| 47;\n  31 -->|output_dir| 47;\n  33 -->|output_dir| 47;\n  34 -->|output_dir| 47;\n  37 -->|output_dir| 47;\n  35 -->|output_dir| 47;\n  36 -->|output_dir| 47;\n  48[\"Merge collections\"];\n  43 -->|output_dir| 48;\n  46 -->|output_dir| 48;\n  42 -->|output_dir| 48;\n  41 -->|output_dir| 48;\n  45 -->|output_dir| 48;\n  38 -->|output_dir| 48;\n  39 -->|output_dir| 48;\n  44 -->|output_dir| 48;\n  49[\"PM2.5 forecast 10:00 - 17:00 UTC > 30 um/m3\"];\n  47 -->|output| 49;\n  1c16eeb7-dfe1-40de-9be7-3aa2a8568308[\"Output\\nPM2.5 (values > 30 um/m3)  fc 10:00 - 17:00 UTC over Italy\"];\n  49 --> 1c16eeb7-dfe1-40de-9be7-3aa2a8568308;\n  style 1c16eeb7-dfe1-40de-9be7-3aa2a8568308 stroke:#2c3143,stroke-width:4px;\n  50[\"PM2.5 forecast 10:00 - 17:00 UTC \"];\n  48 -->|output| 50;\n  070fe227-b533-4c77-bed0-4d005b174920[\"Output\\nPM2.5 fc 10:00 - 17:00 UTC over Italy\"];\n  50 --> 070fe227-b533-4c77-bed0-4d005b174920;\n  style 070fe227-b533-4c77-bed0-4d005b174920 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
+                "modified": "2024-10-02 12:08:06 +0000",
                 "name": "GTN 'Pangeo 101 for everyone - Xarray'",
                 "outputs": [
                     {
@@ -29053,1091 +30332,790 @@
                             "x": 1680.5625,
                             "y": -1247.703125
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/climate/climate_stripes/climate_stripes/1.0.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "c6f2435d680b",
-                            "name": "climate_stripes",
-                            "owner": "climate",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adv\": {\"xname\": \"time\", \"format_date\": \"%Y%m%d %H:%M:%S.%f\", \"format_plot\": \"%d %b %H hours\", \"colormap\": \"winter\"}, \"ifilename\": {\"__class__\": \"RuntimeValue\"}, \"title\": \"PM2.5 4 days forecast from December 22 2021 over Naples\", \"variable\": \"pm2p5_conc\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.1",
-                        "type": "tool",
-                        "uuid": "d5da8203-3dab-447b-a8db-1eab85cb8174",
-                        "workflow_outputs": [
-                            {
-                                "label": "PM2.5 stripes Naples for 4 days forecast from reference date",
-                                "output_name": "ofilename",
-                                "uuid": "92cad576-78b5-4e07-9a07-6f05ff8f4a56"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0",
-                        "errors": null,
-                        "id": 40,
-                        "input_connections": {
-                            "condi_datetime|time_tab": {
-                                "id": 28,
-                                "output_name": "output"
-                            },
-                            "condi_datetime|time_values": {
-                                "id": 10,
-                                "output_name": "output"
-                            },
-                            "input": {
-                                "id": 18,
-                                "output_name": "output_netcdf"
-                            },
-                            "var_tab": {
-                                "id": 24,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "NetCDF xarray map plotting",
-                        "outputs": [
-                            {
-                                "name": "output_dir",
-                                "type": "input"
-                            },
-                            {
-                                "name": "version",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 1869.421875,
-                            "height": 235.125,
-                            "left": 1680.5625,
-                            "right": 1880.5625,
-                            "top": 1634.296875,
-                            "width": 200,
-                            "x": 1680.5625,
-                            "y": 1634.296875
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionversion": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "version"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "d7479b6dfbe8",
-                            "name": "xarray_mapplot",
-                            "owner": "ecology",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"borders\": \"0.2\", \"cmap\": \"cm.roma_r\", \"coastline\": \"0.5\", \"colorbar_label\": \"\", \"condi_datetime\": {\"datetime\": \"yes\", \"__current_case__\": 1, \"time_tab\": {\"__class__\": \"ConnectedValue\"}, \"time_values\": {\"__class__\": \"ConnectedValue\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"land\": null, \"lat_dim\": \"latitude\", \"lon_dim\": \"longitude\", \"ocean\": null, \"proj\": \"\", \"range\": \"0,35\", \"shift\": \"\", \"threshold\": \"30.0\", \"title\": \"\", \"var\": \"pm2p5_conc\", \"var_tab\": {\"__class__\": \"ConnectedValue\"}, \"xlim\": \"\", \"ylim\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.18.2+galaxy0",
-                        "type": "tool",
-                        "uuid": "16cfabc8-5374-4bb1-9f72-06a0aa832cc9",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_dir",
-                                "uuid": "e4e0322c-9e22-4cbf-8880-b0b0e4f67a9e"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "We have 8 plots, one for each forecast time for the first forecast day betwwen 100:00 and 17:00 UTC and we applied a mask e.g. only plot values great than 30 um/m3.",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage/1.3.31+galaxy1",
-                        "errors": null,
-                        "id": 49,
-                        "input_connections": {
-                            "input": {
-                                "id": 47,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Image Montage",
-                                "name": "input"
-                            }
-                        ],
-                        "label": "PM2.5 forecast 10:00 - 17:00 UTC > 30 um/m3",
-                        "name": "Image Montage",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 224.03125,
-                            "height": 174.734375,
-                            "left": 2266.5625,
-                            "right": 2466.5625,
-                            "top": 49.296875,
-                            "width": 200,
-                            "x": 2266.5625,
-                            "y": 49.296875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage/1.3.31+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "39881709807e",
-                            "name": "graphicsmagick_image_montage",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"width\": \"4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3.31+galaxy1",
-                        "type": "tool",
-                        "uuid": "8264424f-2479-4eb2-8df1-b7fde84113d7",
-                        "workflow_outputs": [
-                            {
-                                "label": "PM2.5 (values > 30 um/m3)  fc 10:00 - 17:00 UTC over Italy",
-                                "output_name": "output",
-                                "uuid": "1c16eeb7-dfe1-40de-9be7-3aa2a8568308"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "We have 8 plots, one for each forecast time. We take the forecast on day 1 between 10:00 and 17:00 UTC",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage/1.3.31+galaxy1",
-                        "errors": null,
-                        "id": 50,
-                        "input_connections": {
-                            "input": {
-                                "id": 48,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Image Montage",
-                                "name": "input"
-                            }
-                        ],
-                        "label": "PM2.5 forecast 10:00 - 17:00 UTC ",
-                        "name": "Image Montage",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 2426.25,
-                            "height": 133.953125,
-                            "left": 2266.5625,
-                            "right": 2466.5625,
-                            "top": 2292.296875,
-                            "width": 200,
-                            "x": 2266.5625,
-                            "y": 2292.296875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage/1.3.31+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "39881709807e",
-                            "name": "graphicsmagick_image_montage",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"width\": \"4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3.31+galaxy1",
-                        "type": "tool",
-                        "uuid": "84cbf552-1abd-4b4b-a022-92a5f3b15ff0",
-                        "workflow_outputs": [
-                            {
-                                "label": "PM2.5 fc 10:00 - 17:00 UTC over Italy",
-                                "output_name": "output",
-                                "uuid": "070fe227-b533-4c77-bed0-4d005b174920"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "climate/pangeo",
-                "path": "topics/climate/tutorials/pangeo/workflows/main_workflow.ga",
-                "tags": [
-                    "pangeo",
-                    "climate",
-                    "copernicus",
-                    "GTN"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "GTN 'Pangeo 101 for everyone - Xarray'",
-                "topic_id": "climate",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/climate-pangeo/versions/main-workflow",
-                "tutorial_id": "pangeo",
-                "url": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/pangeo/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/pangeo/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "climate-pangeo",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "__EXTRACT_DATASET__",
-                    "__MERGE_COLLECTION__",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage/1.3.31+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/climate/climate_stripes/climate_stripes/1.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/0.18.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_netcdf2netcdf/xarray_netcdf2netcdf/0.18.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_select/xarray_select/0.15.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy2"
-                ],
-                "workflowhub_id": "1195"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.5805953"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "f46f0e4f75c4",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ctsm_fates",
-                    "owner": "climate",
-                    "revisions": "b525b88bc941",
-                    "tool_panel_section_label": "Climate Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xarray_metadata_info",
-                    "owner": "ecology",
-                    "revisions": "e8650cdf092f",
-                    "tool_panel_section_label": "GIS Data Handling",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xarray_select",
-                    "owner": "ecology",
-                    "revisions": "6baac361495b",
-                    "tool_panel_section_label": "GIS Data Handling",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ggplot2_point",
-                    "owner": "iuc",
-                    "revisions": "e3a675da7fd0",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: f46f0e4f75c4\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ctsm_fates\n  owner: climate\n  revisions: b525b88bc941\n  tool_panel_section_label: Climate Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xarray_metadata_info\n  owner: ecology\n  revisions: e8650cdf092f\n  tool_panel_section_label: GIS Data Handling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xarray_select\n  owner: ecology\n  revisions: 6baac361495b\n  tool_panel_section_label: GIS Data Handling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ggplot2_point\n  owner: iuc\n  revisions: e3a675da7fd0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/fates/tutorial.json",
-        "contributors": [
-            {
-                "elixir_node": "no",
-                "id": "annefou",
-                "joined": "2019-07",
-                "name": "Anne Fouilloux",
-                "orcid": "0000-0002-1784-2920",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annefou/",
-                "twitter": "AnneFouilloux",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/annefou.json"
-            },
-            {
-                "id": "huitang-earth",
-                "joined": "2021-01",
-                "name": "Hui Tang",
-                "orcid": "0000-0002-8745-3859",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/huitang-earth/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/huitang-earth.json"
-            }
-        ],
-        "dir": "topics/climate/tutorials/fates",
-        "edam_operation": [
-            "Visualisation"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "climate/fates",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "CLM-FATES is a numerical terrestrial ecosystem model used in climate models",
-            "Panoply is a quick visualization tools for plotting your results",
-            "Multi-case simulations can be easily developed and shared with a Galaxy workflow"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-08-08",
-        "objectives": [
-            "Setting up a CLM-FATES case.",
-            "Customizing your run.",
-            "Interactive visualization with Panoply.",
-            "Automating your analyzes and visualisations of your CLM-FATES case.",
-            "Creating multi-case scenarios.",
-            "Composing, executing and publishing CML-FATES workflow."
-        ],
-        "pageviews": 5728870,
-        "pub_date": "2020-10-25",
-        "questions": [
-            "How to run CLM-FATES with the CLM-FATES Galaxy tool?",
-            "How to upload input data for running CLM-FATES?",
-            "How to customize your runs?",
-            "How to analyze your model outputs?",
-            "How to create a workflow?",
-            "How to share your workflow?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "s3by01"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "1H20M",
-                "speakers": [
-                    "annefou"
-                ],
-                "youtube_id": "0LsEx11eLiI"
-            }
-        ],
-        "requirements": [
-            {
-                "topic_name": "climate",
-                "tutorials": [
-                    "panoply"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "history-to-workflow"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00042",
-        "short_tools": [
-            "ctsm_fates",
-            "xarray_select",
-            "tp_find_and_replace",
-            "ggplot2_point",
-            "interactive_tool_panoply",
-            "xarray_metadata_info",
-            "__EXTRACT_DATASET__"
-        ],
-        "slides": true,
-        "slides_recordings": [
-            {
-                "captioners": [
-                    "annefou"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "7M",
-                "speakers": [
-                    "awspolly"
-                ],
-                "youtube_id": "Z57C7MQG95s"
-            }
-        ],
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "interactive-tools"
-        ],
-        "time_estimation": "4H",
-        "title": "Functionally Assembled Terrestrial Ecosystem Simulator (FATES)",
-        "tools": [
-            "__EXTRACT_DATASET__",
-            "interactive_tool_panoply",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3",
-            "toolshed.g2.bx.psu.edu/repos/climate/ctsm_fates/ctsm_fates/2.0.1",
-            "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1",
-            "toolshed.g2.bx.psu.edu/repos/ecology/xarray_select/xarray_select/0.15.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy2"
-        ],
-        "topic_name": "climate",
-        "topic_name_human": "Climate",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": true
-        },
-        "tutorial_name": "fates",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/climate/tutorials/fates/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/fates/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/fates/tutorial.json"
-        },
-        "version": 17,
-        "video": true,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 275,
-        "visitors": 2064955,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0002-1784-2920",
-                        "name": "Anne Fouilloux"
-                    }
-                ],
-                "description": "Functionally Assembled Terrestrial Ecosystem Simulator (FATES)",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset for CLM-FATES\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCLM-FATES restart file\"]\n  2[label=\"CTSM/FATES-EMERALD\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Extract Dataset\"]\n  2 -> 3 [label=\"history_files\"]\n  kdebf2e31dbea46d58644586c9731cdbe[color=lightseagreen,label=\"Output\\ninput dataset(s) (extracted element)\"]\n  3 -> kdebf2e31dbea46d58644586c9731cdbe\n  4[label=\"NetCDF xarray Metadata Info\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"NetCDF xarray Selection\"]\n  3 -> 5 [label=\"output\"]\n  4 -> 5 [label=\"output\"]\n  6[label=\"Replace\"]\n  5 -> 6 [label=\"simpleoutput\"]\n  7[label=\"Scatterplot with ggplot2\"]\n  6 -> 7 [label=\"outfile\"]\n}",
-                "history": [
-                    {
-                        "hash": "ad6ca44b0dc2aadac1598e2d9d5e3bb5e94429aa",
-                        "message": "fix wf",
-                        "num": 3,
-                        "short_hash": "ad6ca44b0",
-                        "unix": "1633952401"
-                    },
-                    {
-                        "hash": "3693396f61a109643d15e9bc1b9e21a8def0562d",
-                        "message": "add license, creator information",
-                        "num": 2,
-                        "short_hash": "3693396f6",
-                        "unix": "1633427069"
-                    },
-                    {
-                        "hash": "969fae434066d9571160c4510b8995e99defd640",
-                        "message": "Add climate workflows from @annefou",
-                        "num": 1,
-                        "short_hash": "969fae434",
-                        "unix": "1633426896"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Input dataset for CLM-FATES"
-                            }
-                        ],
-                        "label": "Input dataset for CLM-FATES",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 389.09725189208984,
-                            "height": 81.31945037841797,
-                            "left": 340.0173645019531,
-                            "right": 540.0173797607422,
-                            "top": 307.7778015136719,
-                            "width": 200.00001525878906,
-                            "x": 340.0173645019531,
-                            "y": 307.7778015136719
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "13b908b0-6a00-437b-bc4d-6c34f6f2d390",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "424dce0e-f3f0-4095-8513-9268be9c705d"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "CLM-FATES restart file"
-                            }
-                        ],
-                        "label": "CLM-FATES restart file",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 732.5695114135742,
-                            "height": 81.31945037841797,
-                            "left": 317.3958435058594,
-                            "right": 517.3958587646484,
-                            "top": 651.2500610351562,
-                            "width": 200.00001525878906,
-                            "x": 317.3958435058594,
-                            "y": 651.2500610351562
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "19770ee9-8f78-4030-a8b8-1a44dd25ed43",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1cecc2ed-8a94-448a-90f7-e67f8e8cf117"
-                            }
-                        ]
-                    }
-                ],
-                "license": "Apache-2.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset for CLM-FATES\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nCLM-FATES restart file\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"CTSM/FATES-EMERALD\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Extract Dataset\"];\n  2 -->|history_files| 3;\n  debf2e31-dbea-46d5-8644-586c9731cdbe[\"Output\\ninput dataset(s) (extracted element)\"];\n  3 --> debf2e31-dbea-46d5-8644-586c9731cdbe;\n  style debf2e31-dbea-46d5-8644-586c9731cdbe stroke:#2c3143,stroke-width:4px;\n  4[\"NetCDF xarray Metadata Info\"];\n  3 -->|output| 4;\n  5[\"NetCDF xarray Selection\"];\n  3 -->|output| 5;\n  4 -->|output| 5;\n  6[\"Replace\"];\n  5 -->|simpleoutput| 6;\n  7[\"Scatterplot with ggplot2\"];\n  6 -->|outfile| 7;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "CLM-FATES_ ALP1 simulation (5 years)",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Input dataset for CLM-FATES"
-                            }
-                        ],
-                        "label": "Input dataset for CLM-FATES",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 389.09725189208984,
-                            "height": 81.31945037841797,
-                            "left": 340.0173645019531,
-                            "right": 540.0173797607422,
-                            "top": 307.7778015136719,
-                            "width": 200.00001525878906,
-                            "x": 340.0173645019531,
-                            "y": 307.7778015136719
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "13b908b0-6a00-437b-bc4d-6c34f6f2d390",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "424dce0e-f3f0-4095-8513-9268be9c705d"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "CLM-FATES restart file"
-                            }
-                        ],
-                        "label": "CLM-FATES restart file",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 732.5695114135742,
-                            "height": 81.31945037841797,
-                            "left": 317.3958435058594,
-                            "right": 517.3958587646484,
-                            "top": 651.2500610351562,
-                            "width": 200.00001525878906,
-                            "x": 317.3958435058594,
-                            "y": 651.2500610351562
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "19770ee9-8f78-4030-a8b8-1a44dd25ed43",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1cecc2ed-8a94-448a-90f7-e67f8e8cf117"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/climate/ctsm_fates/ctsm_fates/2.0.1",
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "adv_period|condi_type_run|restart": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "inputdata": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "CTSM/FATES-EMERALD",
-                        "outputs": [
-                            {
-                                "name": "history_files",
-                                "type": "input"
-                            },
-                            {
-                                "name": "atm_log",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "cesm_log",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "cpl_log",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "lnd_log",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "rof_log",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "restart",
-                                "type": "tar"
-                            },
-                            {
-                                "name": "case_info",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "rinfo",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "work",
-                                "type": "tar"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 879.3056030273438,
-                            "height": 452.4305725097656,
-                            "left": 599.1319580078125,
-                            "right": 799.1319732666016,
-                            "top": 426.8750305175781,
-                            "width": 200.00001525878906,
-                            "x": 599.1319580078125,
-                            "y": 426.8750305175781
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/climate/ctsm_fates/ctsm_fates/2.0.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b525b88bc941",
-                            "name": "ctsm_fates",
-                            "owner": "climate",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"tar\", \"adv\": {\"co2\": \"367.0\", \"condi_user_mods\": {\"add_changes\": \"no\", \"__current_case__\": 1}}, \"adv_clm\": {\"use_fates_planthydro\": \"false\", \"use_fates_cohort_age_tracking\": \"false\", \"use_fates_ed_st3\": \"false\", \"use_fates_ed_prescribed_phys\": \"false\", \"use_fates_logging\": \"false\", \"use_fates_fixed_biogeog\": \"false\", \"fates_spitfire_mode\": \"0\", \"fates_parteh_mode\": \"\"}, \"adv_period\": {\"condi_type_run\": {\"run_type\": \"hybrid\", \"__current_case__\": 2, \"run_refcase\": \"ALP1_refcase\", \"run_refdate\": \"2300-01-01\", \"run_startdate\": \"0001-01-01\", \"restart\": {\"__class__\": \"ConnectedValue\"}}, \"stopn\": \"5\", \"stop_option\": \"nyears\"}, \"casename\": \"ALP1_exp\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"inputdata\": {\"__class__\": \"ConnectedValue\"}, \"resolution\": \"1x1_ALP1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.1",
-                        "type": "tool",
-                        "uuid": "91a8cda0-72a6-46cf-babe-a4c0b11731f0",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "rinfo",
-                                "uuid": "5a152c6b-5574-46be-a0fc-be24471f83f7"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "work",
-                                "uuid": "a00239c9-9d0e-46d3-970e-d2e699eb6e4f"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "rof_log",
-                                "uuid": "230f4572-a4bb-46d4-aff5-25a592b375c3"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "cpl_log",
-                                "uuid": "3d6ef14c-9ee1-4fa5-be75-91985a8bc365"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "cesm_log",
-                                "uuid": "9c0f5924-4042-4c76-8c38-b4ae523b67a1"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "atm_log",
-                                "uuid": "c8dd2197-1288-4a90-be18-9dd32a926ad5"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "restart",
-                                "uuid": "5c5a27f6-42a3-4b50-b954-54ba8e9e0c67"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "lnd_log",
-                                "uuid": "5290961c-4660-42c2-88d1-ccd8e2f78412"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "case_info",
-                                "uuid": "9dd13369-b025-4095-9842-9030623fc941"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "history_files",
-                                "uuid": "8993eb0a-6e44-4cce-b8a1-f950b96cb8a8"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "__EXTRACT_DATASET__",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "input": {
-                                "id": 2,
-                                "output_name": "history_files"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Extract Dataset",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "data"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 392.63890075683594,
-                            "height": 132.43055725097656,
-                            "left": 871.8923950195312,
-                            "right": 1071.8924102783203,
-                            "top": 260.2083435058594,
-                            "width": 200.00001525878906,
-                            "x": 871.8923950195312,
-                            "y": 260.2083435058594
-                        },
-                        "post_job_actions": {
-                            "ChangeDatatypeActionoutput": {
-                                "action_arguments": {
-                                    "newtype": "netcdf"
-                                },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "__EXTRACT_DATASET__",
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"first\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/climate/climate_stripes/climate_stripes/1.0.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "c6f2435d680b",
+                            "name": "climate_stripes",
+                            "owner": "climate",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv\": {\"xname\": \"time\", \"format_date\": \"%Y%m%d %H:%M:%S.%f\", \"format_plot\": \"%d %b %H hours\", \"colormap\": \"winter\"}, \"ifilename\": {\"__class__\": \"RuntimeValue\"}, \"title\": \"PM2.5 4 days forecast from December 22 2021 over Naples\", \"variable\": \"pm2p5_conc\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.1",
                         "type": "tool",
-                        "uuid": "efb5bd53-a220-47fe-b4e0-15dd623737a1",
+                        "uuid": "d5da8203-3dab-447b-a8db-1eab85cb8174",
                         "workflow_outputs": [
                             {
-                                "label": "input dataset(s) (extracted element)",
-                                "output_name": "output",
-                                "uuid": "debf2e31-dbea-46d5-8644-586c9731cdbe"
+                                "label": "PM2.5 stripes Naples for 4 days forecast from reference date",
+                                "output_name": "ofilename",
+                                "uuid": "92cad576-78b5-4e07-9a07-6f05ff8f4a56"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0",
                         "errors": null,
-                        "id": 4,
+                        "id": 40,
                         "input_connections": {
+                            "condi_datetime|time_tab": {
+                                "id": 28,
+                                "output_name": "output"
+                            },
+                            "condi_datetime|time_values": {
+                                "id": 10,
+                                "output_name": "output"
+                            },
                             "input": {
-                                "id": 3,
+                                "id": 18,
+                                "output_name": "output_netcdf"
+                            },
+                            "var_tab": {
+                                "id": 24,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "NetCDF xarray Metadata Info",
+                        "name": "NetCDF xarray map plotting",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "name": "output_dir",
+                                "type": "input"
                             },
                             {
-                                "name": "info",
-                                "type": "txt"
+                                "name": "version",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 686.1111602783203,
-                            "height": 142.43055725097656,
-                            "left": 887.951416015625,
-                            "right": 1087.951431274414,
-                            "top": 543.6806030273438,
-                            "width": 200.00001525878906,
-                            "x": 887.951416015625,
-                            "y": 543.6806030273438
+                            "bottom": 1869.421875,
+                            "height": 235.125,
+                            "left": 1680.5625,
+                            "right": 1880.5625,
+                            "top": 1634.296875,
+                            "width": 200,
+                            "x": 1680.5625,
+                            "y": 1634.296875
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1",
+                        "post_job_actions": {
+                            "HideDatasetActionversion": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "version"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "7edbe5ae8b72",
-                            "name": "xarray_metadata_info",
+                            "changeset_revision": "d7479b6dfbe8",
+                            "name": "xarray_mapplot",
                             "owner": "ecology",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"netcdf\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.15.1",
+                        "tool_state": "{\"borders\": \"0.2\", \"cmap\": \"cm.roma_r\", \"coastline\": \"0.5\", \"colorbar_label\": \"\", \"condi_datetime\": {\"datetime\": \"yes\", \"__current_case__\": 1, \"time_tab\": {\"__class__\": \"ConnectedValue\"}, \"time_values\": {\"__class__\": \"ConnectedValue\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"land\": null, \"lat_dim\": \"latitude\", \"lon_dim\": \"longitude\", \"ocean\": null, \"proj\": \"\", \"range\": \"0,35\", \"shift\": \"\", \"threshold\": \"30.0\", \"title\": \"\", \"var\": \"pm2p5_conc\", \"var_tab\": {\"__class__\": \"ConnectedValue\"}, \"xlim\": \"\", \"ylim\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.18.2+galaxy0",
                         "type": "tool",
-                        "uuid": "1dce5844-3ad9-42f8-b3f3-021c20b4bff1",
+                        "uuid": "16cfabc8-5374-4bb1-9f72-06a0aa832cc9",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "info",
-                                "uuid": "ed801226-13db-4c99-8c49-521428e96dd8"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "10127f47-1ba1-4ecf-bb1c-014b87f098cb"
+                                "output_name": "output_dir",
+                                "uuid": "e4e0322c-9e22-4cbf-8880-b0b0e4f67a9e"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_select/xarray_select/0.15.1",
+                        "annotation": "We have 8 plots, one for each forecast time for the first forecast day betwwen 100:00 and 17:00 UTC and we applied a mask e.g. only plot values great than 30 um/m3.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage/1.3.31+galaxy1",
                         "errors": null,
-                        "id": 5,
+                        "id": 49,
                         "input_connections": {
                             "input": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "var_tab": {
-                                "id": 4,
+                                "id": 47,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "NetCDF xarray Selection",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Image Montage",
+                                "name": "input"
+                            }
+                        ],
+                        "label": "PM2.5 forecast 10:00 - 17:00 UTC > 30 um/m3",
+                        "name": "Image Montage",
                         "outputs": [
                             {
-                                "name": "simpleoutput",
-                                "type": "tabular"
+                                "name": "output",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": 613.9409942626953,
-                            "height": 142.43055725097656,
-                            "left": 1162.7083740234375,
-                            "right": 1362.7083892822266,
-                            "top": 471.51043701171875,
-                            "width": 200.00001525878906,
-                            "x": 1162.7083740234375,
-                            "y": 471.51043701171875
+                            "bottom": 224.03125,
+                            "height": 174.734375,
+                            "left": 2266.5625,
+                            "right": 2466.5625,
+                            "top": 49.296875,
+                            "width": 200,
+                            "x": 2266.5625,
+                            "y": 49.296875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_select/xarray_select/0.15.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage/1.3.31+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "225d0d275a24",
-                            "name": "xarray_select",
-                            "owner": "ecology",
+                            "changeset_revision": "39881709807e",
+                            "name": "graphicsmagick_image_montage",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"netcdf\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"condi_source_coord\": {\"coord_source\": \"coord_from_stdin\", \"__current_case__\": 1, \"condi_coord\": {\"coord\": \"global\", \"__current_case__\": 2}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"time\": {\"condi_datetime\": {\"datetime\": \"no\", \"__current_case__\": 0}}, \"user_choice\": [], \"var\": \"LEAFC\", \"var_tab\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.15.1",
+                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"width\": \"4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3.31+galaxy1",
                         "type": "tool",
-                        "uuid": "34e85d8a-b640-41a6-b9ee-82a73f5fda43",
+                        "uuid": "8264424f-2479-4eb2-8df1-b7fde84113d7",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "simpleoutput",
-                                "uuid": "1c9a151b-50e8-439e-9586-96af577d9c27"
+                                "label": "PM2.5 (values > 30 um/m3)  fc 10:00 - 17:00 UTC over Italy",
+                                "output_name": "output",
+                                "uuid": "1c16eeb7-dfe1-40de-9be7-3aa2a8568308"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3",
+                        "annotation": "We have 8 plots, one for each forecast time. We take the forecast on day 1 between 10:00 and 17:00 UTC",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage/1.3.31+galaxy1",
                         "errors": null,
-                        "id": 6,
+                        "id": 50,
                         "input_connections": {
-                            "infile": {
-                                "id": 5,
-                                "output_name": "simpleoutput"
+                            "input": {
+                                "id": 48,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Replace",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Image Montage",
+                                "name": "input"
+                            }
+                        ],
+                        "label": "PM2.5 forecast 10:00 - 17:00 UTC ",
+                        "name": "Image Montage",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "input"
+                                "name": "output",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": 698.3507232666016,
-                            "height": 92.43055725097656,
-                            "left": 1185.4862060546875,
-                            "right": 1385.4862213134766,
-                            "top": 605.920166015625,
-                            "width": 200.00001525878906,
-                            "x": 1185.4862060546875,
-                            "y": 605.920166015625
+                            "bottom": 2426.25,
+                            "height": 133.953125,
+                            "left": 2266.5625,
+                            "right": 2466.5625,
+                            "top": 2292.296875,
+                            "width": 200,
+                            "x": 2266.5625,
+                            "y": 2292.296875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage/1.3.31+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
+                            "changeset_revision": "39881709807e",
+                            "name": "graphicsmagick_image_montage",
                             "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"caseinsensitive\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"find_pattern\": \"00:00:00\", \"global\": \"true\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": \"false\", \"replace_pattern\": \"\", \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}, \"skip_first_line\": \"true\", \"wholewords\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.3",
+                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"width\": \"4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3.31+galaxy1",
                         "type": "tool",
-                        "uuid": "f6ea58b5-a373-4cf4-884a-242dc8cc1928",
+                        "uuid": "84cbf552-1abd-4b4b-a022-92a5f3b15ff0",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "10b70ac6-9a53-45ba-a761-71dd1e987184"
+                                "label": "PM2.5 fc 10:00 - 17:00 UTC over Italy",
+                                "output_name": "output",
+                                "uuid": "070fe227-b533-4c77-bed0-4d005b174920"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "climate/pangeo",
+                "path": "topics/climate/tutorials/pangeo/workflows/main_workflow.ga",
+                "tags": [
+                    "pangeo",
+                    "climate",
+                    "copernicus",
+                    "GTN"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "GTN 'Pangeo 101 for everyone - Xarray'",
+                "topic_id": "climate",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/climate-pangeo/versions/main-workflow",
+                "tutorial_id": "pangeo",
+                "url": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/pangeo/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/pangeo/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "climate-pangeo",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "__EXTRACT_DATASET__",
+                    "__MERGE_COLLECTION__",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage/1.3.31+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/climate/climate_stripes/climate_stripes/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/0.18.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.18.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_netcdf2netcdf/xarray_netcdf2netcdf/0.18.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_select/xarray_select/0.15.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy2"
+                ],
+                "workflowhub_id": "1195"
+            }
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.5805953"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/pangeo-notebook/tutorial.json",
+        "contributors": [
+            {
+                "elixir_node": "no",
+                "id": "annefou",
+                "joined": "2019-07",
+                "name": "Anne Fouilloux",
+                "orcid": "0000-0002-1784-2920",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annefou/",
+                "twitter": "AnneFouilloux",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/annefou.json"
+            }
+        ],
+        "dir": "topics/climate/tutorials/pangeo-notebook",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "link": "http://gallery.pangeo.io/repos/pangeo-data/pangeo-tutorial-gallery/index.html",
+                "title": "Pangeo Tutorial Gallery",
+                "type": "external"
+            },
+            {
+                "link": "http://gallery.pangeo.io/index.html",
+                "title": "Pangeo Gallery",
+                "type": "external"
+            }
+        ],
+        "hands_on": true,
+        "id": "climate/pangeo-notebook",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Pangeo ecosystem enables big data analysis in geosciences",
+            "Xarray is an important Python package for big data analysis in geosciences",
+            "Xarray can be used to read, select, mask and plot netCDF data",
+            "Xarray can also be used to perform global operations such as mean, max, min or resampling data"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-14",
+        "notebook": {
+            "language": "python",
+            "snippet": "topics/climate/tutorials/pangeo-notebook/preamble.md"
+        },
+        "objectives": [
+            "Learn to get metadata information using Xarray Galaxy Tools",
+            "Learn to select data",
+            "Learn to visualize data",
+            "Learn to filter, make reduction operations (mean, max, min)",
+            "Learn to resample my data",
+            "Learn to cite and contribute to Pangeo"
+        ],
+        "pageviews": 3872597,
+        "pub_date": "2022-02-18",
+        "questions": [
+            "What is Pangeo notebook?",
+            "How to start Pangeo Notebook in Galaxy?",
+            "What are the main software components of the Pangeo ecosystem?",
+            "What is Xarray?",
+            "How to manipulate Xarrays?",
+            "How to print metadata information?",
+            "How to make a selection?",
+            "How to visualize?",
+            "How to filter?",
+            "How to make reduction operations (mean, max, min)?",
+            "How to resample my data?",
+            "Where to go next?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "annefou"
+                ],
+                "date": "2022-03-03",
+                "galaxy_version": "21.09",
+                "length": "17M",
+                "speakers": [
+                    "annefou"
+                ],
+                "youtube_id": "XFF2yRcYGp0"
+            }
+        ],
+        "requirements": [
+            {
+                "topic_name": "data-science",
+                "tutorials": [
+                    "python-basics"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "data-science",
+                "tutorials": [
+                    "python-plotting",
+                    "python-advanced-np-pd"
+                ],
+                "type": "internal"
+            },
+            {
+                "link": "https://datacarpentry.org/geospatial-workshop/",
+                "title": "Data Carpentry Geospatial Workshop",
+                "type": "external"
+            }
+        ],
+        "short_id": "T00045",
+        "short_tools": [
+            "interactive_tool_pangeo_notebook"
+        ],
+        "slides": true,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "pangeo",
+            "interactive-tools"
+        ],
+        "time_estimation": "1H",
+        "title": "Pangeo Notebook in Galaxy - Introduction to Xarray",
+        "tools": [
+            "interactive_tool_pangeo_notebook"
+        ],
+        "topic_name": "climate",
+        "topic_name_human": "Climate",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": true
+        },
+        "tutorial_name": "pangeo-notebook",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/climate/tutorials/pangeo-notebook/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/pangeo-notebook/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/pangeo-notebook/tutorial.json"
+        },
+        "version": 10,
+        "video": true,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 270,
+        "visitors": 1524935,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0002-1784-2920",
+                        "name": "Anne Fouilloux",
+                        "url": "https://github.com/annefou"
+                    }
+                ],
+                "description": "Workflow for GTN Pangeo Notebook in Galaxy - Introduction to Xarray",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Pangeo Jupyter for Big Data geoscience\"]\n}",
+                "history": [
+                    {
+                        "hash": "e1474b2a116fe585bb664fa489f11648d12be74f",
+                        "message": "Add missing annotation for pangeo-notebook workflow",
+                        "num": 2,
+                        "short_hash": "e1474b2a1",
+                        "unix": "1643364120"
                     },
+                    {
+                        "hash": "1cb326ea7de3765fc5804f168fb4d813a72676b5",
+                        "message": "split pangeo training in two (Galaxy tool and Pangeo notebook)",
+                        "num": 1,
+                        "short_hash": "1cb326ea7",
+                        "unix": "1640271678"
+                    }
+                ],
+                "inputs": [],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"Pangeo Jupyter for Big Data geoscience\"];",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Pangeo Jupyter Notebook",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy2",
+                        "content_id": "interactive_tool_pangeo_notebook",
                         "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "input1": {
-                                "id": 6,
-                                "output_name": "outfile"
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Interactive Pangeo Notebook",
+                                "name": "input"
                             }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scatterplot with ggplot2",
+                        ],
+                        "label": "Pangeo Jupyter for Big Data geoscience",
+                        "name": "Interactive Pangeo Notebook",
                         "outputs": [
                             {
-                                "name": "output1",
-                                "type": "png"
+                                "name": "jupyter_notebook",
+                                "type": "ipynb"
                             }
                         ],
                         "position": {
-                            "bottom": 815.1215362548828,
-                            "height": 152.43055725097656,
-                            "left": 1339.3751220703125,
-                            "right": 1539.3751373291016,
-                            "top": 662.6909790039062,
-                            "width": 200.00001525878906,
-                            "x": 1339.3751220703125,
-                            "y": 662.6909790039062
+                            "bottom": 516.90625,
+                            "height": 174.734375,
+                            "left": 672,
+                            "right": 872,
+                            "top": 342.171875,
+                            "width": 200,
+                            "x": 672,
+                            "y": 342.171875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "87908c76ca8d",
-                            "name": "ggplot2_point",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adv\": {\"type\": \"pointslines\", \"points\": {\"pointoptions\": \"default\", \"__current_case__\": 0}, \"factor\": {\"factoring\": \"Default\", \"__current_case__\": 0}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"19.0\", \"height_output_dim\": \"5.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"Total carbon in live plant leaves\", \"xlab\": \"Time\", \"xplot\": \"1\", \"ylab\": \"LEAFC (kgC ha-1)\", \"yplot\": \"4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.2.1+galaxy2",
+                        "tool_id": "interactive_tool_pangeo_notebook",
+                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"mode\": {\"mode_select\": \"scratch\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1c0f66b",
                         "type": "tool",
-                        "uuid": "dc2790c9-e3f1-441c-8d95-2406a44bfa3e",
+                        "uuid": "e921fd5a-97f9-4364-8c8a-7f225329016a",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output1",
-                                "uuid": "2857a6af-c707-4dea-a188-dd9f2e8146e5"
+                                "output_name": "jupyter_notebook",
+                                "uuid": "30d1f58a-ace4-4eaf-9efa-c3930d768898"
                             }
                         ]
                     }
                 ],
-                "parent_id": "climate/fates",
-                "path": "topics/climate/tutorials/fates/workflows/CLM-FATES_ALP1_simulation_5years.ga",
+                "parent_id": "climate/pangeo-notebook",
+                "path": "topics/climate/tutorials/pangeo-notebook/workflows/main_workflow.ga",
                 "tags": [
-                    "climate"
+                    "pangeo",
+                    "climate",
+                    "big-data",
+                    "geosciences"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "CLM-FATES_ ALP1 simulation (5 years)",
+                "title": "Pangeo Jupyter Notebook",
                 "topic_id": "climate",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/climate-fates/versions/clm-fates-alp1-simulation-5years",
-                "tutorial_id": "fates",
-                "url": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/fates/workflows/CLM-FATES_ALP1_simulation_5years.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/fates/workflows/CLM-FATES_ALP1_simulation_5years.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/climate-pangeo-notebook/versions/main-workflow",
+                "tutorial_id": "pangeo-notebook",
+                "url": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/pangeo-notebook/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/pangeo-notebook/workflows/main_workflow.html",
                 "version": 1,
-                "wfid": "climate-fates",
-                "wfname": "clm-fates-alp1-simulation-5years",
-                "workflow": "CLM-FATES_ALP1_simulation_5years.ga",
+                "wfid": "climate-pangeo-notebook",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "__EXTRACT_DATASET__",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3",
-                    "toolshed.g2.bx.psu.edu/repos/climate/ctsm_fates/ctsm_fates/2.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_select/xarray_select/0.15.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy2"
+                    "interactive_tool_pangeo_notebook"
                 ],
-                "workflowhub_id": "1185"
+                "workflowhub_id": "1189"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.4108341"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.5805953"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "argo_getdata",
+                    "owner": "ecology",
+                    "revisions": "28c8f085d1b4",
+                    "tool_panel_section_label": "Get Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "timeseries_extraction",
+                    "owner": "ecology",
+                    "revisions": "810820a0d45c",
+                    "tool_panel_section_label": "GIS Data Handling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "xarray_coords_info",
+                    "owner": "ecology",
+                    "revisions": "663e6f115a76",
+                    "tool_panel_section_label": "GIS Data Handling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "xarray_metadata_info",
+                    "owner": "ecology",
+                    "revisions": "00de53d18b99",
+                    "tool_panel_section_label": "GIS Data Handling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: argo_getdata\n  owner: ecology\n  revisions: 28c8f085d1b4\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: timeseries_extraction\n  owner: ecology\n  revisions: 810820a0d45c\n  tool_panel_section_label: GIS Data Handling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xarray_coords_info\n  owner: ecology\n  revisions: 663e6f115a76\n  tool_panel_section_label: GIS Data Handling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xarray_metadata_info\n  owner: ecology\n  revisions: 00de53d18b99\n  tool_panel_section_label: GIS Data Handling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/argo_pangeo/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "Marie59"
+            ],
+            "funding": [
+                "fairease",
+                "eurosciencegateway"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "pndb",
+                    "fairease"
+                ],
+                "email": "marie.josse@ifremer.fr",
+                "id": "Marie59",
+                "joined": "2022-03",
+                "name": "Marie Josse",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/fair_ease_colour.png",
+                "funder": true,
+                "funding_id": "101058785",
+                "funding_statement": "FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "fairease",
+                "joined": "2023-10",
+                "members": [
+                    "Marie59",
+                    "yvanlebras"
+                ],
+                "name": "Fair-Ease",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fairease/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/fairease.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/eurosciencegateway.png",
+                "funder": true,
+                "funding_id": "101057388",
+                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "eurosciencegateway",
+                "joined": "2023-10",
+                "members": [
+                    "abretaud",
+                    "anuprulez",
+                    "bgruening",
+                    "erxleben",
+                    "pauldg",
+                    "rlibouba"
+                ],
+                "name": "EuroScienceGateway",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
+            }
+        ],
+        "dir": "topics/climate/tutorials/argo_pangeo",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "climate/argo_pangeo",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Argo data",
+            "Pangeo Ecosystem",
+            "Galaxy Earth System"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-03-24",
+        "objectives": [
+            "How to fetch Argo Data?",
+            "How to get metadata with xarray netcdf tools?",
+            "Learn to get temperature variations.",
+            "Learn to use an interactive tool to visualise Argo temperature variable on an interactive map."
+        ],
+        "pageviews": 122,
+        "pub_date": "2024-03-24",
+        "questions": [
+            "How to use the Pangeo ecosystem to analyse ocean data?",
+            "How to process Argo data to visualise ocean temperature variations?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "introduction",
+                "tutorials": [
+                    "galaxy-intro-short"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00428",
+        "short_tools": [
+            "xarray_metadata_info",
+            "argo_getdata",
+            "xarray_coords_info",
+            "timeseries_extraction",
+            "interactive_tool_odv"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "earth-system",
+            "ocean",
+            "pangeo",
+            "argo"
+        ],
+        "time_estimation": "1H",
+        "title": "Analyse Argo data",
+        "tools": [
+            "interactive_tool_odv",
+            "toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/timeseries_extraction/timeseries_extraction/2022.3.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/2022.3.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/2022.3.0+galaxy0"
+        ],
+        "topic_name": "climate",
+        "topic_name_human": "Climate",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "argo_pangeo",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/climate/tutorials/argo_pangeo/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/argo_pangeo/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/argo_pangeo/tutorial.json"
+        },
+        "version": 1,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 116,
+        "visitors": 97,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0009-0008-0622-604X",
+                        "name": "Marie Joss\u00e9",
+                        "url": "https://github.com/Marie59"
+                    }
+                ],
+                "description": "Process argo data with the Pangeo Ecosystem and visualise them with Ocean Data View (ODV)",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Argo data access\"]\n  1[label=\"NetCDF xarray Coordinate Info\"]\n  0 -> 1 [label=\"output_argo\"]\n  2[label=\"NetCDF xarray Metadata Info\"]\n  0 -> 2 [label=\"output_argo\"]\n  3[label=\"NetCDF timeseries Extractor\"]\n  0 -> 3 [label=\"output_argo\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"ODV\"]\n  3 -> 4 [label=\"timeseries_tabular\"]\n}",
+                "history": [
+                    {
+                        "hash": "54b194630704357541b0a560b2b5e212cbf7fa35",
+                        "message": "add new argo tuto",
+                        "num": 1,
+                        "short_hash": "54b194630",
+                        "unix": "1710791150"
+                    }
+                ],
+                "inputs": [],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"Argo data access\"];\n  1[\"NetCDF xarray Coordinate Info\"];\n  0 -->|output_argo| 1;\n  2[\"NetCDF xarray Metadata Info\"];\n  0 -->|output_argo| 2;\n  3[\"NetCDF timeseries Extractor\"];\n  0 -->|output_argo| 3;\n  2 -->|output| 3;\n  4[\"ODV\"];\n  3 -->|timeseries_tabular| 4;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Analyse Argo data ",
+                "outputs": [],
+                "parent_id": "climate/argo_pangeo",
+                "path": "topics/climate/tutorials/argo_pangeo/workflows/main_workflow.ga",
+                "tags": [
+                    "Ocean",
+                    "Pangeo",
+                    "earth-system"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Analyse Argo data ",
+                "topic_id": "climate",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/climate-argo_pangeo/versions/main-workflow",
+                "tutorial_id": "argo_pangeo",
+                "url": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/argo_pangeo/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/argo_pangeo/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "climate-argo_pangeo",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "interactive_tool_odv",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/argo_getdata/argo_getdata/0.1.15+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/timeseries_extraction/timeseries_extraction/2022.3.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/2022.3.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/2022.3.0+galaxy0"
+                ],
+                "workflowhub_id": "1193"
+            }
+        ]
     },
     {
         "admin_install": {
@@ -30209,65 +31187,285 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
             }
         ],
-        "dir": "topics/climate/tutorials/sentinel5_data",
+        "dir": "topics/climate/tutorials/sentinel5_data",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "climate/sentinel5_data",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Manage satellite data",
+            "Visualise netcdf data",
+            "Study volcano activity"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-01-26",
+        "objectives": [
+            "Learn to use OpenEO in a jupyterlab",
+            "Learn to handle satellite data",
+            "Practice on how to visualise netcdf data with Panoply",
+            "Handle going from one interactive tool to another",
+            "Learn to visualise gases around a volcano"
+        ],
+        "pageviews": 150,
+        "pub_date": "2024-01-26",
+        "questions": [
+            "How to visualise volcanoes with Sentinel 5 data ?",
+            "How can we see the evolution of sulfur dioxide and aerosol index through time?",
+            "How can be used OpenEO ?"
+        ],
+        "short_id": "T00396",
+        "short_tools": [
+            "interactive_tool_panoply",
+            "interactive_tool_copernicus_notebook",
+            "interactive_tool_copernicus"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "earth-system",
+            "volcano",
+            "satellite data"
+        ],
+        "time_estimation": "1H",
+        "title": "Sentinel 5P data visualisation",
+        "tools": [
+            "interactive_tool_copernicus",
+            "interactive_tool_copernicus_notebook",
+            "interactive_tool_panoply"
+        ],
+        "topic_name": "climate",
+        "topic_name_human": "Climate",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "sentinel5_data",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/climate/tutorials/sentinel5_data/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/sentinel5_data/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/sentinel5_data/tutorial.json"
+        },
+        "version": 1,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 39,
+        "visitors": 127,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0009-0008-0622-604X",
+                        "name": "Marie Joss\u00e9",
+                        "url": "https://github.com/Marie59"
+                    }
+                ],
+                "description": "From Copernicus Sentinel 5P data to panoply visualization of volcanic activity impact to atmosphere",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Copernicus Data Space Ecosystem\"]\n  1[label=\"Panoply\"]\n  0 -> 1 [label=\"output_collection\"]\n}",
+                "history": [
+                    {
+                        "hash": "dc7f440762f8b8c520f88f868a2e4874a473048d",
+                        "message": "Add Sentinel5P tuto",
+                        "num": 1,
+                        "short_hash": "dc7f44076",
+                        "unix": "1706085833"
+                    }
+                ],
+                "inputs": [],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"Copernicus Data Space Ecosystem\"];\n  1[\"Panoply\"];\n  0 -->|output_collection| 1;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Sentinel5 volcanic data",
+                "outputs": [],
+                "parent_id": "climate/sentinel5_data",
+                "path": "topics/climate/tutorials/sentinel5_data/workflows/main_workflow.ga",
+                "tags": [],
+                "test_results": null,
+                "tests": false,
+                "title": "Sentinel5 volcanic data",
+                "topic_id": "climate",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/climate-sentinel5_data/versions/main-workflow",
+                "tutorial_id": "sentinel5_data",
+                "url": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/sentinel5_data/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/sentinel5_data/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "climate-sentinel5_data",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "interactive_tool_copernicus_notebook",
+                    "interactive_tool_panoply"
+                ],
+                "workflowhub_id": "1203"
+            }
+        ]
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "divand_full_analysis",
+                    "owner": "ecology",
+                    "revisions": "484930fdc002",
+                    "tool_panel_section_label": "Climate Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: divand_full_analysis\n  owner: ecology\n  revisions: 484930fdc002\n  tool_panel_section_label: Climate Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/ocean-variables/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "Marie59"
+            ],
+            "funding": [
+                "fairease",
+                "eurosciencegateway"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "pndb",
+                    "fairease"
+                ],
+                "email": "marie.josse@ifremer.fr",
+                "id": "Marie59",
+                "joined": "2022-03",
+                "name": "Marie Josse",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/fair_ease_colour.png",
+                "funder": true,
+                "funding_id": "101058785",
+                "funding_statement": "FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "fairease",
+                "joined": "2023-10",
+                "members": [
+                    "Marie59",
+                    "yvanlebras"
+                ],
+                "name": "Fair-Ease",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fairease/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/fairease.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/eurosciencegateway.png",
+                "funder": true,
+                "funding_id": "101057388",
+                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "eurosciencegateway",
+                "joined": "2023-10",
+                "members": [
+                    "abretaud",
+                    "anuprulez",
+                    "bgruening",
+                    "erxleben",
+                    "pauldg",
+                    "rlibouba"
+                ],
+                "name": "EuroScienceGateway",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
+            }
+        ],
+        "dir": "topics/climate/tutorials/ocean-variables",
         "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "climate/sentinel5_data",
+        "id": "climate/ocean-variables",
         "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Manage satellite data",
-            "Visualise netcdf data",
-            "Study volcano activity"
+            "Manage ODV collection's data.",
+            "Learn to extract data and visualize them on ODV",
+            "Learn to chain ODV and DIVAnd"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-01-26",
+        "mod_date": "2024-08-09",
         "objectives": [
-            "Learn to use OpenEO in a jupyterlab",
-            "Learn to handle satellite data",
-            "Practice on how to visualise netcdf data with Panoply",
-            "Handle going from one interactive tool to another",
-            "Learn to visualise gases around a volcano"
+            "Deals with ODV collection with data originating from Emodnet chemistry",
+            "Visualise ocean variables to study climate changes"
         ],
-        "pageviews": 113,
-        "pub_date": "2024-01-26",
+        "pageviews": 125,
+        "pub_date": "2023-11-29",
         "questions": [
-            "How to visualise volcanoes with Sentinel 5 data ?",
-            "How can we see the evolution of sulfur dioxide and aerosol index through time?",
-            "How can be used OpenEO ?"
+            "How to process extract ocean's variables?",
+            "How to use ODV collections?",
+            "How to create climatological estimates?"
         ],
-        "short_id": "T00396",
+        "short_id": "T00376",
         "short_tools": [
-            "interactive_tool_panoply",
-            "interactive_tool_copernicus",
-            "interactive_tool_copernicus_notebook"
+            "divand_full_analysis",
+            "interactive_tool_odv",
+            "interactive_tool_divand"
         ],
         "slides": false,
         "slides_recordings": false,
         "supported_servers": {
-            "exact": [],
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
             "inexact": []
         },
         "symlink": null,
         "tags": [
             "earth-system",
-            "volcano",
-            "satellite data"
+            "ocean",
+            "netcdf data"
         ],
         "time_estimation": "1H",
-        "title": "Sentinel 5P data visualisation",
+        "title": "Ocean's variables study",
         "tools": [
-            "interactive_tool_copernicus",
-            "interactive_tool_copernicus_notebook",
-            "interactive_tool_panoply"
+            "interactive_tool_divand",
+            "interactive_tool_odv",
+            "toolshed.g2.bx.psu.edu/repos/ecology/divand_full_analysis/divand_full_analysis/0.1.0+galaxy0"
         ],
         "topic_name": "climate",
         "topic_name_human": "Climate",
@@ -30277,19 +31475,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "sentinel5_data",
+        "tutorial_name": "ocean-variables",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/climate/tutorials/sentinel5_data/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/climate/tutorials/ocean-variables/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/sentinel5_data/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/sentinel5_data/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/ocean-variables/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/ocean-variables/tutorial.json"
         },
-        "version": 1,
+        "version": 4,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 37,
-        "visitors": 96,
+        "visit_duration": 130,
+        "visitors": 99,
         "workflows": [
             {
                 "creators": [
@@ -30300,49 +31498,329 @@
                         "url": "https://github.com/Marie59"
                     }
                 ],
-                "description": "From Copernicus Sentinel 5P data to panoply visualization of volcanic activity impact to atmosphere",
+                "description": "Subset data on the Mediterreanean see and extract and visualise the Phosphate variable",
                 "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
+                    "comments": true,
+                    "parameters": true,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                    },
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Copernicus Data Space Ecosystem\"]\n  1[label=\"Panoply\"]\n  0 -> 1 [label=\"output_collection\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nWorflow fully interactive\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nEutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nWorkflow semi automatic\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ngebco_30sec_8.nc\"]\n  4[label=\"Ocean Data View\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Interactive DIVAnd jupyterlab\"]\n  4 -> 5 [label=\"outputs_netcdf\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"DIVAnd create a climatology\"]\n  3 -> 6 [label=\"output\"]\n  4 -> 6 [label=\"outputs_netcdf\"]\n  2 -> 6 [label=\"output\"]\n  k5996328287bf4432a7778a9b61dea03c[color=lightseagreen,label=\"Output\\nWater_body_Phosphate_Mediterranean.nc\"]\n  6 -> k5996328287bf4432a7778a9b61dea03c\n  7[label=\"ODV visualisation interactive\"]\n  5 -> 7 [label=\"output_netcdf\"]\n  kdc8316a4e57c476bb885bbe4fb84d8c7[color=lightseagreen,label=\"Output\\nOcean variables visualisation interactive\"]\n  7 -> kdc8316a4e57c476bb885bbe4fb84d8c7\n  8[label=\"ODV visualisation\"]\n  6 -> 8 [label=\"output_netcdf\"]\n  k7b0722535bf9434fb06a70b375ddaa03[color=lightseagreen,label=\"Output\\nOcean variables visualisation\"]\n  8 -> k7b0722535bf9434fb06a70b375ddaa03\n}",
                 "history": [
                     {
-                        "hash": "dc7f440762f8b8c520f88f868a2e4874a473048d",
-                        "message": "Add Sentinel5P tuto",
+                        "hash": "1c6ee9c0d6c08affe5e54d71b4488147396ba5aa",
+                        "message": "Add new version of workflow",
+                        "num": 2,
+                        "short_hash": "1c6ee9c0d",
+                        "unix": "1723110972"
+                    },
+                    {
+                        "hash": "c51d6ffbc21866df213772767f645a889a23c70f",
+                        "message": "Add workflow",
                         "num": 1,
-                        "short_hash": "dc7f44076",
-                        "unix": "1706085833"
+                        "short_hash": "c51d6ffbc",
+                        "unix": "1710854627"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "Choose whether you want to have only interactive tools (for more experimented user) or if you want a workflow hat combines interactive and non-interactive tools (easier)",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Choose whether you want to have only interactive tools (for more experimented user) or if you want a workflow hat combines interactive and non-interactive tools (easier)",
+                                "name": "Worflow fully interactive"
+                            }
+                        ],
+                        "label": "Worflow fully interactive",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 29.80677214543107,
+                            "top": 359.1046708180256
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "250d862b-4c3d-462d-9bcd-9a5053c52b5e",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "The data here are Mediterranean Sea - Eutrophication and Acidity aggregated datasets EMODnet Chemistry.",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "The data here are Mediterranean Sea - Eutrophication and Acidity aggregated datasets EMODnet Chemistry.",
+                                "name": "Eutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip"
+                            }
+                        ],
+                        "label": "Eutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 314.4,
+                            "top": 507.4
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "b513664a-1176-4fd9-bb79-439010069177",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "Choose whether you want to have only interactive tools (for more experimented user) or if you want a workflow hat combines interactive and non-interactive tools (easier)",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Choose whether you want to have only interactive tools (for more experimented user) or if you want a workflow hat combines interactive and non-interactive tools (easier)",
+                                "name": "Workflow semi automatic"
+                            }
+                        ],
+                        "label": "Workflow semi automatic",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 34.559982917236994,
+                            "top": 738.7586893348329
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "6e2ed5ec-3760-44fe-a722-4e44356f9058",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "A bathymetry file in netcdf.",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "A bathymetry file in netcdf.",
+                                "name": "gebco_30sec_8.nc"
+                            }
+                        ],
+                        "label": "gebco_30sec_8.nc",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 614.0977004616734,
+                            "top": 903.4688531054738
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "006a3936-6151-4724-9fab-6b41f869e1ee",
+                        "when": null,
+                        "workflow_outputs": []
                     }
                 ],
-                "inputs": [],
                 "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"Copernicus Data Space Ecosystem\"];\n  1[\"Panoply\"];\n  0 -->|output_collection| 1;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Sentinel5 volcanic data",
-                "outputs": [],
-                "parent_id": "climate/sentinel5_data",
-                "path": "topics/climate/tutorials/sentinel5_data/workflows/main_workflow.ga",
-                "tags": [],
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nWorflow fully interactive\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nEutrophication_Med_profiles_2022_unrestricted_SNAPSHOT_2023-10-24T16-39-44.zip\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nWorkflow semi automatic\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\ngebco_30sec_8.nc\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Ocean Data View\"];\n  1 -->|output| 4;\n  5[\"Interactive DIVAnd jupyterlab\"];\n  4 -->|outputs_netcdf| 5;\n  0 -->|output| 5;\n  6[\"DIVAnd create a climatology\"];\n  3 -->|output| 6;\n  4 -->|outputs_netcdf| 6;\n  2 -->|output| 6;\n  59963282-87bf-4432-a777-8a9b61dea03c[\"Output\\nWater_body_Phosphate_Mediterranean.nc\"];\n  6 --> 59963282-87bf-4432-a777-8a9b61dea03c;\n  style 59963282-87bf-4432-a777-8a9b61dea03c stroke:#2c3143,stroke-width:4px;\n  7[\"ODV visualisation interactive\"];\n  5 -->|output_netcdf| 7;\n  dc8316a4-e57c-476b-b885-bbe4fb84d8c7[\"Output\\nOcean variables visualisation interactive\"];\n  7 --> dc8316a4-e57c-476b-b885-bbe4fb84d8c7;\n  style dc8316a4-e57c-476b-b885-bbe4fb84d8c7 stroke:#2c3143,stroke-width:4px;\n  8[\"ODV visualisation\"];\n  6 -->|output_netcdf| 8;\n  7b072253-5bf9-434f-b06a-70b375ddaa03[\"Output\\nOcean variables visualisation\"];\n  8 --> 7b072253-5bf9-434f-b06a-70b375ddaa03;\n  style 7b072253-5bf9-434f-b06a-70b375ddaa03 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Ocean's variables 2.0",
+                "outputs": [
+                    {
+                        "annotation": "Create a climatology (not interactively)",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/divand_full_analysis/divand_full_analysis/0.1.0+galaxy0",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "bathname": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "input_netcdf_identifier": {
+                                "id": 4,
+                                "output_name": "outputs_netcdf"
+                            },
+                            "when": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "DIVAnd (create a climatology)",
+                        "name": "DIVAnd",
+                        "outputs": [
+                            {
+                                "name": "output_netcdf",
+                                "type": "netcdf"
+                            }
+                        ],
+                        "position": {
+                            "left": 958.2529539113443,
+                            "top": 679.118779662132
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_netcdf": {
+                                "action_arguments": {
+                                    "newname": "Water_body_Phosphate_Mediterranean.nc"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_netcdf"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/divand_full_analysis/divand_full_analysis/0.1.0+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "484930fdc002",
+                            "name": "divand_full_analysis",
+                            "owner": "ecology",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"bathname\": {\"__class__\": \"ConnectedValue\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"enddate\": \"2017-01-01\", \"input_netcdf_identifier\": {\"__class__\": \"ConnectedValue\"}, \"input_netcdf_identifier|__identifier__\": \"data_from_Eutrophication_Med_profiles_2022_unrestricted.nc\", \"latmax\": \"38.0\", \"latmin\": \"32.0\", \"longmax\": \"30.0\", \"longmin\": \"19.0\", \"selmax\": \"100\", \"selmin\": \"0\", \"startdate\": \"1950-12-31\", \"varname\": \"phosphate\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0+galaxy0",
+                        "type": "tool",
+                        "uuid": "d1c07265-1da0-40d6-9fd5-1041a9d9f658",
+                        "when": "$(inputs.when)",
+                        "workflow_outputs": [
+                            {
+                                "label": "Water_body_Phosphate_Mediterranean.nc",
+                                "output_name": "output_netcdf",
+                                "uuid": "59963282-87bf-4432-a777-8a9b61dea03c"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Final step to visualize in different way a ocean variable like the phosphate.",
+                        "content_id": "interactive_tool_odv",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "method|infiles": {
+                                "id": 5,
+                                "output_name": "output_netcdf"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool ODV",
+                                "name": "method"
+                            }
+                        ],
+                        "label": "ODV (visualisation) interactive",
+                        "name": "ODV",
+                        "outputs": [
+                            {
+                                "name": "outputs_netcdf",
+                                "type": "input"
+                            },
+                            {
+                                "name": "outputs_all",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1315.0326051372172,
+                            "top": 398.52546972475403
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "interactive_tool_odv",
+                        "tool_state": "{\"__input_ext\": \"netcdf\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"method\": {\"type\": \"own_data\", \"__current_case__\": 0, \"infiles\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.6.5.1",
+                        "type": "tool",
+                        "uuid": "50c35d61-7b8d-4706-9d56-d3bd94a46960",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Ocean variables visualisation interactive",
+                                "output_name": "outputs_all",
+                                "uuid": "dc8316a4-e57c-476b-b885-bbe4fb84d8c7"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Final step to visualize in different way a ocean variable like the phosphate.",
+                        "content_id": "interactive_tool_odv",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "method|infiles": {
+                                "id": 6,
+                                "output_name": "output_netcdf"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool ODV",
+                                "name": "method"
+                            }
+                        ],
+                        "label": "ODV (visualisation)",
+                        "name": "ODV",
+                        "outputs": [
+                            {
+                                "name": "outputs_netcdf",
+                                "type": "input"
+                            },
+                            {
+                                "name": "outputs_all",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1313.0264554819623,
+                            "top": 737.9220054373203
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "interactive_tool_odv",
+                        "tool_state": "{\"__input_ext\": \"netcdf\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"method\": {\"type\": \"own_data\", \"__current_case__\": 0, \"infiles\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.6.5.1",
+                        "type": "tool",
+                        "uuid": "9bff476c-be32-4d87-a655-db241126ae49",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Ocean variables visualisation",
+                                "output_name": "outputs_all",
+                                "uuid": "7b072253-5bf9-434f-b06a-70b375ddaa03"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "climate/ocean-variables",
+                "path": "topics/climate/tutorials/ocean-variables/workflows/main_workflow.ga",
+                "tags": [
+                    "earth-system",
+                    "Ocean"
+                ],
                 "test_results": null,
-                "tests": false,
-                "title": "Sentinel5 volcanic data",
+                "tests": true,
+                "title": "Ocean's variables 2.0",
                 "topic_id": "climate",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/climate-sentinel5_data/versions/main-workflow",
-                "tutorial_id": "sentinel5_data",
-                "url": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/sentinel5_data/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/sentinel5_data/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "climate-sentinel5_data",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/climate-ocean-variables/versions/main-workflow",
+                "tutorial_id": "ocean-variables",
+                "url": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/ocean-variables/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/climate/tutorials/ocean-variables/workflows/main_workflow.html",
+                "version": 2,
+                "wfid": "climate-ocean-variables",
                 "wfname": "main-workflow",
                 "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "interactive_tool_copernicus_notebook",
-                    "interactive_tool_panoply"
+                    "interactive_tool_divand",
+                    "interactive_tool_odv",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/divand_full_analysis/divand_full_analysis/0.1.0+galaxy0"
                 ],
-                "workflowhub_id": "1203"
+                "workflowhub_id": "1200"
             }
         ]
     },
@@ -30396,7 +31874,7 @@
         "license": "CC-BY-4.0",
         "logo": "GTN",
         "mod_date": "2023-01-12",
-        "pageviews": 5726880,
+        "pageviews": 5897154,
         "priority": 1,
         "pub_date": "2020-10-11",
         "redirect_from": [
@@ -30464,7 +31942,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2063758
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -30514,7 +31992,7 @@
             "Learn to use Panoply in Galaxy to visuallize netCDF geo-referenced data",
             "Learn how Panoply plots are exported to Galaxy"
         ],
-        "pageviews": 9433,
+        "pageviews": 9530,
         "pub_date": "2020-03-05",
         "questions": [
             "How to start Panoply interactive environment in Galaxy?",
@@ -30574,7 +32052,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 51,
-        "visitors": 5546,
+        "visitors": 5632,
         "zenodo_link": "https://doi.org/10.5281/zenodo.3695482"
     },
     {
@@ -30602,6 +32080,7 @@
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.eu",
             "UseGalaxy.fr",
             "UseGalaxy.org (Main)"
@@ -30631,7 +32110,7 @@
             "Sharing CLM-FATES simulations.",
             "Composing, executing and publishing the corresponding Jupyter notebooks."
         ],
-        "pageviews": 851,
+        "pageviews": 862,
         "pub_date": "2020-10-25",
         "questions": [
             "Why and when using Galaxy Climate JupyterLab for CLM-FATES?",
@@ -30678,227 +32157,905 @@
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "interactive-tools"
+        ],
+        "time_estimation": "6H",
+        "title": "Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab",
+        "tools": [
+            "interactive_tool_jupyter_notebook"
+        ],
+        "topic_name": "climate",
+        "topic_name_human": "Climate",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "fates-jupyterlab",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/climate/tutorials/fates-jupyterlab/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/fates-jupyterlab/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/fates-jupyterlab/tutorial.json"
+        },
+        "version": 15,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 116,
+        "visitors": 469,
+        "zenodo_link": "https://doi.org/10.5281/zenodo.4108341"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/ocean-data-view/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "Marie59"
+            ],
+            "funding": [
+                "fairease",
+                "eurosciencegateway"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "pndb",
+                    "fairease"
+                ],
+                "email": "marie.josse@ifremer.fr",
+                "id": "Marie59",
+                "joined": "2022-03",
+                "name": "Marie Josse",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/fair_ease_colour.png",
+                "funder": true,
+                "funding_id": "101058785",
+                "funding_statement": "FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "fairease",
+                "joined": "2023-10",
+                "members": [
+                    "Marie59",
+                    "yvanlebras"
+                ],
+                "name": "Fair-Ease",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fairease/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/fairease.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/eurosciencegateway.png",
+                "funder": true,
+                "funding_id": "101057388",
+                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "eurosciencegateway",
+                "joined": "2023-10",
+                "members": [
+                    "abretaud",
+                    "anuprulez",
+                    "bgruening",
+                    "erxleben",
+                    "pauldg",
+                    "rlibouba"
+                ],
+                "name": "EuroScienceGateway",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
+            }
+        ],
+        "dir": "topics/climate/tutorials/ocean-data-view",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.fr"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "climate/ocean-data-view",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Manage Argo glider's data and learn to process netcdf data.",
+            "Build a map of the stations and create profiles curves with ODV",
+            "Learn to use ODV as Galaxy interactive tool"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-27",
+        "objectives": [
+            "Deal with netcdf files in ODV",
+            "Visualise ocean variables from Argo glider's data"
+        ],
+        "pageviews": 260,
+        "pub_date": "2023-11-27",
+        "questions": [
+            "How to process Argo's glider data ?",
+            "How to visualise the glider's stations",
+            "How to use make salinity temperature profiles for one or more stations ?"
+        ],
+        "short_id": "T00375",
+        "short_tools": [
+            "interactive_tool_odv"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "earth-system",
+            "ocean",
+            "geographical information system",
+            "ODV",
+            "netcdf data",
+            "maps",
+            "marine data"
+        ],
+        "time_estimation": "1H",
+        "title": "Ocean Data View (ODV)",
+        "tools": [
+            "interactive_tool_odv"
+        ],
+        "topic_name": "climate",
+        "topic_name_human": "Climate",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "ocean-data-view",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/climate/tutorials/ocean-data-view/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/ocean-data-view/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/ocean-data-view/tutorial.json"
+        },
+        "version": 1,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 80,
+        "visitors": 205
+    },
+    {
+        "abbreviations": {
+            "CoP": "Community of Practice",
+            "GCB": "Galaxy Community Board",
+            "GEB": "Galaxy Executive Board",
+            "GTB": "Galaxy Technical Board",
+            "SIG": "Special Interest Group",
+            "WG": "Working Groups"
+        },
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/community/tutorials/sig_define/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "nomadscientist"
+            ],
+            "editing": [
+                "shiltemann"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "bio": "Senior Lecturer at The Open University",
+                "elixir_node": "uk",
+                "email": "wendi.bacon@open.ac.uk",
+                "fediverse": "https://mstdn.science/@wendibacon1",
+                "fediverse_flavor": "mastodon",
+                "id": "nomadscientist",
+                "joined": "2020-03",
+                "matrix": "nomadscientist:matrix.org",
+                "name": "Wendi Bacon",
+                "orcid": "0000-0002-8170-8806",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
+                "twitter": "WendiBacon1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+            },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            }
+        ],
+        "dir": "topics/community/tutorials/sig_define",
+        "edam_operation": [],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "community",
+                "tutorials": [
+                    "sig_create"
+                ],
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "community/sig_define",
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Special Interest Groups are groups of like-minded Galaxy enthusiasts that enable global collaboration",
+            "There are many existing Special Interest Groups within Galaxy that welcome new members",
+            "If you are interacting with the Galaxy community and want to find like-minded individuals, you might want to make a Special Interest Group"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-27",
+        "objectives": [
+            "Define 'Special Interest Group'",
+            "Explain the purpose of Special Interest Groups",
+            "Learn how Special Interest Groups interact with the Galaxy governance"
+        ],
+        "pageviews": 46,
+        "priority": 1,
+        "pub_date": "2024-07-08",
+        "questions": [
+            "What is a Special Interest Group?",
+            "What is the purpose of a Special Interest Group?",
+            "How are Special Interest Groups represented in Galaxy?"
+        ],
+        "requirements": null,
+        "short_id": "T00444",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": [],
+        "symlink": null,
+        "time_estimation": "15m",
+        "title": "What's a Special Interest Group?",
+        "tools": [],
+        "topic_name": "community",
+        "topic_name_human": "Galaxy Community Building",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "sig_define",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/community/tutorials/sig_define/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/community/tutorials/sig_define/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/community/tutorials/sig_define/tutorial.json"
+        },
+        "version": 2,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 24,
+        "visitors": 22
+    },
+    {
+        "abbreviations": {
+            "CoP": "Community of Practice",
+            "GCB": "Galaxy Community Board",
+            "GEB": "Galaxy Executive Board",
+            "GTB": "Galaxy Technical Board",
+            "SIG": "Special Interest Group",
+            "WG": "Working Groups"
+        },
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/community/tutorials/sig_create/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "nomadscientist"
+            ],
+            "editing": [
+                "shiltemann"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "bio": "Senior Lecturer at The Open University",
+                "elixir_node": "uk",
+                "email": "wendi.bacon@open.ac.uk",
+                "fediverse": "https://mstdn.science/@wendibacon1",
+                "fediverse_flavor": "mastodon",
+                "id": "nomadscientist",
+                "joined": "2020-03",
+                "matrix": "nomadscientist:matrix.org",
+                "name": "Wendi Bacon",
+                "orcid": "0000-0002-8170-8806",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
+                "twitter": "WendiBacon1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+            },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            }
+        ],
+        "dir": "topics/community/tutorials/sig_create",
+        "edam_operation": [],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "community/sig_create",
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Special Interest Groups are a commitment to create and sustain.",
+            "There are centralised resources to help support running a Special Interest Group.",
+            "SIGs are joyous places for like-minded scientists to interact and share expertise."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-07-08",
+        "objectives": [
+            "Determine whether you need a Galaxy Special Interest Group",
+            "Create a Special Interest Group",
+            "Be aware of resources for expanding your Special Interest Group"
+        ],
+        "pageviews": 28,
+        "priority": 2,
+        "pub_date": "2024-07-08",
+        "questions": [
+            "Do I need to make a Special Interest Group?",
+            "What are the requirements for a Special Interest Group?",
+            "How can I create a Special Interest Group?",
+            "Where can I go to find Special Interest Group resources?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "community",
+                "tutorials": [
+                    "sig_define"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00443",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": [],
+        "symlink": null,
+        "time_estimation": "30m",
+        "title": "Creating a Special Interest Group",
+        "tools": [],
+        "topic_name": "community",
+        "topic_name_human": "Galaxy Community Building",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "sig_create",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/community/tutorials/sig_create/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/community/tutorials/sig_create/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/community/tutorials/sig_create/tutorial.json"
+        },
+        "version": 1,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 74,
+        "visitors": 25
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "autodock_vina",
+                    "owner": "bgruening",
+                    "revisions": "7a871df65202",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "autodock_vina_prepare_box",
+                    "owner": "bgruening",
+                    "revisions": "668c60aa4799",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "autodock_vina_prepare_receptor",
+                    "owner": "bgruening",
+                    "revisions": "05a13d377b28",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "chembl",
+                    "owner": "bgruening",
+                    "revisions": "a446ea7e2bc1",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "chemfp",
+                    "owner": "bgruening",
+                    "revisions": "73de2fe4bf92",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "chemfp",
+                    "owner": "bgruening",
+                    "revisions": "43a9e7d9b24f",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "chemfp",
+                    "owner": "bgruening",
+                    "revisions": "73de2fe4bf92",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "chemfp",
+                    "owner": "bgruening",
+                    "revisions": "e3a7d6cc87af",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "chemfp",
+                    "owner": "bgruening",
+                    "revisions": "73de2fe4bf92",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "chemical_data_sources",
+                    "owner": "bgruening",
+                    "revisions": "c2055dd1927b",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fpocket",
+                    "owner": "bgruening",
+                    "revisions": "4fb73be7f4cb",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "get_pdb",
+                    "owner": "bgruening",
+                    "revisions": "538790c6c21b",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "natural_product_likeness",
+                    "owner": "bgruening",
+                    "revisions": "6052dd3fa475",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openbabel_compound_convert",
+                    "owner": "bgruening",
+                    "revisions": "e2c36f62e22f",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openbabel_svg_depiction",
+                    "owner": "bgruening",
+                    "revisions": "7672039a0bb0",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sdf_to_tab",
+                    "owner": "bgruening",
+                    "revisions": "4beb3e026bbb",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "f46f0e4f75c4",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "830961c48e42",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
-            ],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "interactive-tools"
-        ],
-        "time_estimation": "6H",
-        "title": "Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab",
-        "tools": [
-            "interactive_tool_jupyter_notebook"
-        ],
-        "topic_name": "climate",
-        "topic_name_human": "Climate",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "fates-jupyterlab",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/climate/tutorials/fates-jupyterlab/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/fates-jupyterlab/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/fates-jupyterlab/tutorial.json"
-        },
-        "version": 15,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 112,
-        "visitors": 458,
-        "zenodo_link": "https://doi.org/10.5281/zenodo.4108341"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/ocean-data-view/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "Marie59"
-            ],
-            "funding": [
-                "fairease",
-                "eurosciencegateway"
             ]
         },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: autodock_vina\n  owner: bgruening\n  revisions: 7a871df65202\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: autodock_vina_prepare_box\n  owner: bgruening\n  revisions: 668c60aa4799\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: autodock_vina_prepare_receptor\n  owner: bgruening\n  revisions: 05a13d377b28\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chembl\n  owner: bgruening\n  revisions: a446ea7e2bc1\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chemfp\n  owner: bgruening\n  revisions: 73de2fe4bf92\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chemfp\n  owner: bgruening\n  revisions: 43a9e7d9b24f\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chemfp\n  owner: bgruening\n  revisions: 73de2fe4bf92\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chemfp\n  owner: bgruening\n  revisions: e3a7d6cc87af\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chemfp\n  owner: bgruening\n  revisions: 73de2fe4bf92\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chemical_data_sources\n  owner: bgruening\n  revisions: c2055dd1927b\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fpocket\n  owner: bgruening\n  revisions: 4fb73be7f4cb\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: get_pdb\n  owner: bgruening\n  revisions: 538790c6c21b\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: natural_product_likeness\n  owner: bgruening\n  revisions: 6052dd3fa475\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_compound_convert\n  owner: bgruening\n  revisions: e2c36f62e22f\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_svg_depiction\n  owner: bgruening\n  revisions: 7672039a0bb0\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sdf_to_tab\n  owner: bgruening\n  revisions: 4beb3e026bbb\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: f46f0e4f75c4\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/cheminformatics/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "pndb",
-                    "fairease"
-                ],
-                "email": "marie.josse@ifremer.fr",
-                "id": "Marie59",
-                "joined": "2022-03",
-                "name": "Marie Josse",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
-            },
-            {
-                "avatar": "/training-material/assets/images/fair_ease_colour.png",
-                "funder": true,
-                "funding_id": "101058785",
-                "funding_statement": "FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "fairease",
-                "joined": "2023-10",
-                "members": [
-                    "Marie59",
-                    "yvanlebras"
-                ],
-                "name": "Fair-Ease",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fairease/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/fairease.json"
-            },
-            {
-                "avatar": "/training-material/assets/images/eurosciencegateway.png",
-                "funder": true,
-                "funding_id": "101057388",
-                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "eurosciencegateway",
-                "joined": "2023-10",
-                "members": [
-                    "abretaud",
-                    "anuprulez",
-                    "bgruening",
-                    "erxleben",
-                    "pauldg",
-                    "rlibouba"
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
                 ],
-                "name": "EuroScienceGateway",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
+                "id": "simonbray",
+                "joined": "2019-05",
+                "name": "Simon Bray",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
             }
         ],
-        "dir": "topics/climate/tutorials/ocean-data-view",
+        "dir": "topics/computational-chemistry/tutorials/cheminformatics",
         "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.fr"
-        ],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "climate/ocean-data-view",
-        "inexact_supported_servers": [],
+        "id": "computational-chemistry/cheminformatics",
+        "inexact_supported_servers": [
+            "UseGalaxy.org (Main)"
+        ],
         "js_requirements": {
-            "mathjax": null,
+            "mathjax": 16452,
             "mermaid": false
         },
         "key_points": [
-            "Manage Argo glider's data and learn to process netcdf data.",
-            "Build a map of the stations and create profiles curves with ODV",
-            "Learn to use ODV as Galaxy interactive tool"
+            "Docking allows 'virtual screening' of drug candidates",
+            "Molecular fingerprints encode features into a bitstring",
+            "The ChemicalToolbox contains many tools for cheminformatics analysis"
         ],
         "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-27",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Deal with netcdf files in ODV",
-            "Visualise ocean variables from Argo glider's data"
+            "Create a small compound library using the ChEMBL database",
+            "Dock a variety of ligands to the active site of the Hsp90 protein"
         ],
-        "pageviews": 223,
-        "pub_date": "2023-11-27",
+        "pageviews": 27951,
+        "pub_date": "2019-10-19",
         "questions": [
-            "How to process Argo's glider data ?",
-            "How to visualise the glider's stations",
-            "How to use make salinity temperature profiles for one or more stations ?"
+            "What is cheminformatics?",
+            "What is protein-ligand docking?",
+            "How can I perform a simple docking workflow in Galaxy?"
         ],
-        "short_id": "T00375",
+        "short_id": "T00048",
         "short_tools": [
-            "interactive_tool_odv"
+            "ctb_remIons",
+            "openbabel_svg_depiction",
+            "tp_find_and_replace",
+            "ctb_remDuplicates",
+            "ctb_obgrep",
+            "ctb_np-likeness-calculator",
+            "ctb_compound_convert",
+            "ctb_online_data_fetch",
+            "ctb_chemfp_mol2fps",
+            "ctb_change_title",
+            "openbabel_compound_convert",
+            "tp_cat",
+            "ctb_chemfp_butina_clustering",
+            "docking",
+            "prepare_box",
+            "chembl",
+            "collapse_dataset",
+            "ctb_chemfp_nxn_clustering",
+            "fpocket",
+            "sdf_to_tab",
+            "get_pdb",
+            "ctb_filter",
+            "tp_grep_tool",
+            "prepare_receptor"
         ],
         "slides": false,
         "slides_recordings": false,
         "supported_servers": {
-            "exact": [
+            "exact": [],
+            "inexact": [
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
                     "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
                 }
-            ],
-            "inexact": []
+            ]
         },
         "symlink": null,
-        "tags": [
-            "earth-system",
-            "ocean",
-            "geographical information system",
-            "ODV",
-            "netcdf data",
-            "maps",
-            "marine data"
-        ],
-        "time_estimation": "1H",
-        "title": "Ocean Data View (ODV)",
+        "time_estimation": "3H",
+        "title": "Protein-ligand docking",
         "tools": [
-            "interactive_tool_odv"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/1.1.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina_prepare_box/prepare_box/2021.03.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina_prepare_receptor/prepare_receptor/1.5.7+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/chembl/chembl/0.10.1+galaxy4",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_butina_clustering/1.5",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/0.2.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/1.5",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_nxn_clustering/0.4",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_nxn_clustering/1.5.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/chemical_data_sources/ctb_online_data_fetch/0.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/fpocket/fpocket/3.1.4.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/get_pdb/get_pdb/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/natural_product_likeness/ctb_np-likeness-calculator/2.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_change_title/0.0.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_compound_convert/0.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_filter/1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_obgrep/0.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remDuplicates/1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remIons/1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_svg_depiction/openbabel_svg_depiction/3.1.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/sdf_to_tab/sdf_to_tab/2020.03.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
         ],
-        "topic_name": "climate",
-        "topic_name_human": "Climate",
+        "topic_name": "computational-chemistry",
+        "topic_name_human": "Computational chemistry",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "ocean-data-view",
+        "tutorial_name": "cheminformatics",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/climate/tutorials/ocean-data-view/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/computational-chemistry/tutorials/cheminformatics/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/ocean-data-view/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/climate/tutorials/ocean-data-view/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/cheminformatics/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/cheminformatics/tutorial.json"
         },
-        "version": 1,
+        "version": 16,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 93,
-        "visitors": 173
+        "visit_duration": 89,
+        "visitors": 15716,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "CTB Unittest workflow",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  11[label=\"Compound Search\"]\n  5 -> 11 [label=\"outfile\"]\n  13[label=\"Remove duplicated molecules\"]\n  5 -> 13 [label=\"outfile\"]\n  19[label=\"Remove counterions and fragments\"]\n  13 -> 19 [label=\"outfile\"]\n  2[label=\"Online data\"]\n  29[label=\"Filter\"]\n  19 -> 29 [label=\"outfile\"]\n  30[label=\"Compound Convert\"]\n  19 -> 30 [label=\"outfile\"]\n  31[label=\"Molecules to Fingerprints\"]\n  19 -> 31 [label=\"outfile\"]\n  39[label=\"Natural Product\"]\n  29 -> 39 [label=\"outfile\"]\n  40[label=\"Molecules to Fingerprints\"]\n  29 -> 40 [label=\"outfile\"]\n  44[label=\"NxN Clustering\"]\n  40 -> 44 [label=\"outfile\"]\n  5[label=\"Change Title\"]\n  2 -> 5 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "52ea0ed9ee0a8920a6831112d60295283db993ee",
+                        "message": "editing the workflow using the workflow editor",
+                        "num": 6,
+                        "short_hash": "52ea0ed9e",
+                        "unix": "1582108026"
+                    },
+                    {
+                        "hash": "d681f0586063602176dd9f0a0c3b6901e1252c44",
+                        "message": "disabled workflow with testtools",
+                        "num": 5,
+                        "short_hash": "d681f0586",
+                        "unix": "1579166204"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 4,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "7da80b34185f4165852feb3bfe80d692609685db",
+                        "message": "Workflows fix",
+                        "num": 3,
+                        "short_hash": "7da80b341",
+                        "unix": "1578668175"
+                    },
+                    {
+                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
+                        "message": "unflatten workflows",
+                        "num": 2,
+                        "short_hash": "faf6d298a",
+                        "unix": "1576155753"
+                    },
+                    {
+                        "hash": "aa2ef61fb0b97cf82ea068696454cf18f729f01b",
+                        "message": "initial cheminformatics commit",
+                        "num": 1,
+                        "short_hash": "aa2ef61fb",
+                        "unix": "1560350110"
+                    }
+                ],
+                "inputs": [],
+                "license": null,
+                "mermaid": "flowchart TD\n  11[\"Compound Search\"];\n  5 -->|outfile| 11;\n  13[\"Remove duplicated molecules\"];\n  5 -->|outfile| 13;\n  19[\"Remove counterions and fragments\"];\n  13 -->|outfile| 19;\n  2[\"Online data\"];\n  29[\"Filter\"];\n  19 -->|outfile| 29;\n  30[\"Compound Convert\"];\n  19 -->|outfile| 30;\n  31[\"Molecules to Fingerprints\"];\n  19 -->|outfile| 31;\n  39[\"Natural Product\"];\n  29 -->|outfile| 39;\n  40[\"Molecules to Fingerprints\"];\n  29 -->|outfile| 40;\n  44[\"NxN Clustering\"];\n  40 -->|outfile| 44;\n  5[\"Change Title\"];\n  2 -->|output| 5;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "CTB Workflow",
+                "outputs": [],
+                "parent_id": "computational-chemistry/cheminformatics",
+                "path": "topics/computational-chemistry/tutorials/cheminformatics/workflows/main_workflow.ga",
+                "tags": [
+                    "computational-chemistry"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "CTB Workflow",
+                "topic_id": "computational-chemistry",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/computational-chemistry-cheminformatics/versions/main-workflow",
+                "tutorial_id": "cheminformatics",
+                "url": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/cheminformatics/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/cheminformatics/workflows/main_workflow.html",
+                "version": 4,
+                "wfid": "computational-chemistry-cheminformatics",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/0.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_nxn_clustering/0.4",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/chemical_data_sources/ctb_online_data_fetch/0.2",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/natural_product_likeness/ctb_np-likeness-calculator/2.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_change_title/0.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_compound_convert/0.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_filter/1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_obgrep/0.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remDuplicates/1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remIons/1.0"
+                ],
+                "workflowhub_id": "1075"
+            }
+        ],
+        "zenodo_link": ""
     },
     {
-        "abbreviations": {
-            "CoP": "Community of Practice",
-            "GCB": "Galaxy Community Board",
-            "GEB": "Galaxy Executive Board",
-            "GTB": "Galaxy Technical Board",
-            "SIG": "Special Interest Group",
-            "WG": "Working Groups"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -30906,285 +33063,1154 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/community/tutorials/sig_define/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "nomadscientist"
-            ],
-            "editing": [
-                "shiltemann"
-            ]
-        },
+        "api": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/md-simulation-namd/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "bio": "Senior Lecturer at The Open University",
-                "elixir_node": "uk",
-                "email": "wendi.bacon@open.ac.uk",
-                "fediverse": "https://mstdn.science/@wendibacon1",
-                "fediverse_flavor": "mastodon",
-                "id": "nomadscientist",
-                "joined": "2020-03",
-                "matrix": "nomadscientist:matrix.org",
-                "name": "Wendi Bacon",
-                "orcid": "0000-0002-8170-8806",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
-                "twitter": "WendiBacon1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+                "id": "chrisbarnettster",
+                "joined": "2019-05",
+                "name": "Christopher Barnett",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/chrisbarnettster/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/chrisbarnettster.json"
             },
             {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
+                "id": "tsenapathi",
+                "joined": "2019-05",
+                "name": "Tharindu Senapathi",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tsenapathi/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tsenapathi.json"
+            },
+            {
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
                 ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+                "id": "simonbray",
+                "joined": "2019-05",
+                "name": "Simon Bray",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
             }
         ],
-        "dir": "topics/community/tutorials/sig_define",
+        "dir": "topics/computational-chemistry/tutorials/md-simulation-namd",
+        "draft": true,
         "edam_operation": [],
         "edam_topic": [],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "follow_up_training": [
             {
-                "topic_name": "community",
+                "topic_name": "computational-chemistry",
                 "tutorials": [
-                    "sig_create"
+                    "analysis-md-simulations"
                 ],
                 "type": "internal"
             }
         ],
         "hands_on": true,
-        "id": "community/sig_define",
+        "id": "computational-chemistry/md-simulation-namd",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Special Interest Groups are groups of like-minded Galaxy enthusiasts that enable global collaboration",
-            "There are many existing Special Interest Groups within Galaxy that welcome new members",
-            "If you are interacting with the Galaxy community and want to find like-minded individuals, you might want to make a Special Interest Group"
+            "Several MD engines are available in BRIDGE",
+            "Workflows are available for common simulations tasks such as equilibration and production dynamics for various ensembles (NVT, NPT)",
+            "You've run an equilibrium and production MD simulation using NAMD"
         ],
         "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-08",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Define 'Special Interest Group'",
-            "Explain the purpose of Special Interest Groups",
-            "Learn how Special Interest Groups interact with the Galaxy governance"
+            "Learn about the NAMD engine provided in BRIDGE"
         ],
-        "pageviews": 36,
-        "priority": 1,
-        "pub_date": "2024-07-08",
+        "pageviews": 6458,
+        "pub_date": "2019-06-03",
         "questions": [
-            "What is a Special Interest Group?",
-            "What is the purpose of a Special Interest Group?",
-            "How are Special Interest Groups represented in Galaxy?"
+            "How do I use the NAMD engine in Galaxy?",
+            "What is the correct procedure for performing a simple molecular dynamics simulation of a protein?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "computational-chemistry",
+                "tutorials": [
+                    "setting-up-molecular-systems"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00052",
+        "short_tools": [
+            "namd_nvt",
+            "setup",
+            "namd_npt",
+            "minimizer"
         ],
-        "requirements": null,
-        "short_id": "T00444",
-        "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "supported_servers": [],
+        "supported_servers": {
+            "exact": [],
+            "inexact": []
+        },
         "symlink": null,
-        "time_estimation": "15m",
-        "title": "What's a Special Interest Group?",
-        "tools": [],
-        "topic_name": "community",
-        "topic_name_human": "Galaxy Community Building",
+        "tags": [
+            "work-in-progress"
+        ],
+        "time_estimation": "3H",
+        "title": "Running molecular dynamics simulations using NAMD",
+        "tools": [
+            "minimizer",
+            "namd_npt",
+            "namd_nvt",
+            "setup"
+        ],
+        "topic_name": "computational-chemistry",
+        "topic_name_human": "Computational chemistry",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "sig_define",
+        "tutorial_name": "md-simulation-namd",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/community/tutorials/sig_define/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/computational-chemistry/tutorials/md-simulation-namd/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/community/tutorials/sig_define/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/community/tutorials/sig_define/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/md-simulation-namd/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/md-simulation-namd/tutorial.json"
         },
-        "version": 1,
+        "version": 9,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 35,
-        "visitors": 13
+        "visit_duration": 72,
+        "visitors": 3713,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Running molecular dynamics simulations using NAMD",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[label=\"System Setup\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Energy Minimizer\"]\n  2 -> 3 [label=\"setup_crd\"]\n  2 -> 3 [label=\"setup_psf\"]\n  2 -> 3 [label=\"structure_prm\"]\n  4[label=\"NAMD MD Simulator NVT\"]\n  3 -> 4 [label=\"pdbout\"]\n  3 -> 4 [label=\"pmespec\"]\n  3 -> 4 [label=\"xplorpsfout\"]\n  3 -> 4 [label=\"bbrmsd\"]\n  3 -> 4 [label=\"scrmsd\"]\n  3 -> 4 [label=\"subsrmsd\"]\n  2 -> 4 [label=\"structure_prm\"]\n  5[label=\"NAMD MD Simulator NPT\"]\n  3 -> 5 [label=\"pdbout\"]\n  3 -> 5 [label=\"pmespec\"]\n  3 -> 5 [label=\"xplorpsfout\"]\n  4 -> 5 [label=\"coorout\"]\n  4 -> 5 [label=\"velout\"]\n  4 -> 5 [label=\"xscout\"]\n  2 -> 5 [label=\"structure_prm\"]\n}",
+                "history": [
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 4,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 3,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
+                        "message": "unflatten workflows",
+                        "num": 2,
+                        "short_hash": "faf6d298a",
+                        "unix": "1576155753"
+                    },
+                    {
+                        "hash": "be6fece7faf81d375f35a35d1a115041aae6066b",
+                        "message": "Simonbray compchem (#6)",
+                        "num": 1,
+                        "short_hash": "be6fece7f",
+                        "unix": "1556962666"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "7cel.psf"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 10
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"7cel.psf\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ae09b2b3-e735-46e7-be28-eaf11cab2d24",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "7cel.crd"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 130
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"7cel.crd\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "83bc3872-4bbf-4afd-aaf8-81a03780636a",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"System Setup\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Energy Minimizer\"];\n  2 -->|setup_crd| 3;\n  2 -->|setup_psf| 3;\n  2 -->|structure_prm| 3;\n  4[\"NAMD MD Simulator NVT\"];\n  3 -->|pdbout| 4;\n  3 -->|pmespec| 4;\n  3 -->|xplorpsfout| 4;\n  3 -->|bbrmsd| 4;\n  3 -->|scrmsd| 4;\n  3 -->|subsrmsd| 4;\n  2 -->|structure_prm| 4;\n  5[\"NAMD MD Simulator NPT\"];\n  3 -->|pdbout| 5;\n  3 -->|pmespec| 5;\n  3 -->|xplorpsfout| 5;\n  4 -->|coorout| 5;\n  4 -->|velout| 5;\n  4 -->|xscout| 5;\n  2 -->|structure_prm| 5;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "MD NAMD",
+                "outputs": [],
+                "parent_id": "computational-chemistry/md-simulation-namd",
+                "path": "topics/computational-chemistry/tutorials/md-simulation-namd/workflows/main_workflow.ga",
+                "tags": [
+                    "computational-chemistry"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "MD NAMD",
+                "topic_id": "computational-chemistry",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/computational-chemistry-md-simulation-namd/versions/main-workflow",
+                "tutorial_id": "md-simulation-namd",
+                "url": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/md-simulation-namd/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/md-simulation-namd/workflows/main_workflow.html",
+                "version": 4,
+                "wfid": "computational-chemistry-md-simulation-namd",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "minimizer",
+                    "namd_npt",
+                    "namd_nvt",
+                    "setup"
+                ],
+                "workflowhub_id": "1071"
+            },
+            {
+                "creators": [],
+                "description": "Running molecular dynamics simulations using NAMD",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  4[label=\"NAMD MD Simulator NVT\"]\n  0 -> 4 [label=\"output\"]\n  2 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"NAMD MD Simulator NPT\"]\n  0 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  4 -> 5 [label=\"coorout\"]\n  4 -> 5 [label=\"velout\"]\n  4 -> 5 [label=\"xscout\"]\n  3 -> 5 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 4,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 3,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
+                        "message": "unflatten workflows",
+                        "num": 2,
+                        "short_hash": "faf6d298a",
+                        "unix": "1576155753"
+                    },
+                    {
+                        "hash": "be6fece7faf81d375f35a35d1a115041aae6066b",
+                        "message": "Simonbray compchem (#6)",
+                        "num": 1,
+                        "short_hash": "be6fece7f",
+                        "unix": "1556962666"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "step3_pbcsetup.pdb"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 10
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"step3_pbcsetup.pdb\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "180b4e05-b912-4c3e-8d7b-39027a6c9d65",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "step3_pbcsetup.xplor.ext.psf"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 130
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"step3_pbcsetup.xplor.ext.psf\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "8829a91f-e5b5-44bd-977d-c4c308453ac6",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "checkfft.str"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 250
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"checkfft.str\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "badde4ba-b790-406a-93e5-d622f4be8062",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "step2.1_waterbox.prm"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 370
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"step2.1_waterbox.prm\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "de715d6e-ffac-4e42-9166-6dfeea0c244f",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"NAMD MD Simulator NVT\"];\n  0 -->|output| 4;\n  2 -->|output| 4;\n  1 -->|output| 4;\n  3 -->|output| 4;\n  5[\"NAMD MD Simulator NPT\"];\n  0 -->|output| 5;\n  2 -->|output| 5;\n  1 -->|output| 5;\n  4 -->|coorout| 5;\n  4 -->|velout| 5;\n  4 -->|xscout| 5;\n  3 -->|output| 5;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "NAMD MD From CHARMM GUI",
+                "outputs": [],
+                "parent_id": "computational-chemistry/md-simulation-namd",
+                "path": "topics/computational-chemistry/tutorials/md-simulation-namd/workflows/main_workflow_charmmgui.ga",
+                "tags": [
+                    "computational-chemistry"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "NAMD MD From CHARMM GUI",
+                "topic_id": "computational-chemistry",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/computational-chemistry-md-simulation-namd/versions/main-workflow-charmmgui",
+                "tutorial_id": "md-simulation-namd",
+                "url": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/md-simulation-namd/workflows/main_workflow_charmmgui.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/md-simulation-namd/workflows/main_workflow_charmmgui.html",
+                "version": 4,
+                "wfid": "computational-chemistry-md-simulation-namd",
+                "wfname": "main-workflow-charmmgui",
+                "workflow": "main_workflow_charmmgui.ga",
+                "workflow_tools": [
+                    "namd_npt",
+                    "namd_nvt"
+                ],
+                "workflowhub_id": "1072"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/3234841"
     },
     {
-        "abbreviations": {
-            "CoP": "Community of Practice",
-            "GCB": "Galaxy Community Board",
-            "GEB": "Galaxy Executive Board",
-            "GTB": "Galaxy Technical Board",
-            "SIG": "Special Interest Group",
-            "WG": "Working Groups"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/community/tutorials/sig_create/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "nomadscientist"
-            ],
-            "editing": [
-                "shiltemann"
+            "tools": [
+                {
+                    "name": "get_pdb",
+                    "owner": "bgruening",
+                    "revisions": "538790c6c21b",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openbabel_compound_convert",
+                    "owner": "bgruening",
+                    "revisions": "b59c91adeac1",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openbabel_compound_convert",
+                    "owner": "bgruening",
+                    "revisions": "e2c36f62e22f",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ambertools_acpype",
+                    "owner": "chemteam",
+                    "revisions": "f4230f116196",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ambertools_acpype",
+                    "owner": "chemteam",
+                    "revisions": "6ca543ec1bf8",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bio3d_pca",
+                    "owner": "chemteam",
+                    "revisions": "24867ab16f36",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bio3d_pca_visualize",
+                    "owner": "chemteam",
+                    "revisions": "f61a718993fd",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bio3d_rmsd",
+                    "owner": "chemteam",
+                    "revisions": "77e28e1da9f4",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bio3d_rmsf",
+                    "owner": "chemteam",
+                    "revisions": "6bcb804a54c3",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gmx_editconf",
+                    "owner": "chemteam",
+                    "revisions": "3b8a9d5ced85",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gmx_editconf",
+                    "owner": "chemteam",
+                    "revisions": "0fac8e2afc13",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gmx_em",
+                    "owner": "chemteam",
+                    "revisions": "eb6564a60136",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gmx_em",
+                    "owner": "chemteam",
+                    "revisions": "f5d979cb4b54",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gmx_energy",
+                    "owner": "chemteam",
+                    "revisions": "d2f955aea23a",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gmx_merge_topology_files",
+                    "owner": "chemteam",
+                    "revisions": "d1d0efda35c0",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gmx_merge_topology_files",
+                    "owner": "chemteam",
+                    "revisions": "319a28774da9",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gmx_setup",
+                    "owner": "chemteam",
+                    "revisions": "cac1886249a2",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gmx_setup",
+                    "owner": "chemteam",
+                    "revisions": "2c349b027a01",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gmx_sim",
+                    "owner": "chemteam",
+                    "revisions": "2e219a2d9327",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gmx_sim",
+                    "owner": "chemteam",
+                    "revisions": "73008ef1f487",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gmx_solvate",
+                    "owner": "chemteam",
+                    "revisions": "1809414a9454",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gmx_solvate",
+                    "owner": "chemteam",
+                    "revisions": "2c8ed1b52bf7",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "md_converter",
+                    "owner": "chemteam",
+                    "revisions": "79e8ab8f1e81",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "md_converter",
+                    "owner": "chemteam",
+                    "revisions": "ba83f0923369",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mdanalysis_cosine_analysis",
+                    "owner": "chemteam",
+                    "revisions": "9a3a1f698fc6",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mdanalysis_cosine_analysis",
+                    "owner": "chemteam",
+                    "revisions": "48d6a6eb438b",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "vmd_hbonds",
+                    "owner": "chemteam",
+                    "revisions": "8aa5e465b043",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
             ]
         },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: get_pdb\n  owner: bgruening\n  revisions: 538790c6c21b\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_compound_convert\n  owner: bgruening\n  revisions: b59c91adeac1\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_compound_convert\n  owner: bgruening\n  revisions: e2c36f62e22f\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ambertools_acpype\n  owner: chemteam\n  revisions: f4230f116196\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ambertools_acpype\n  owner: chemteam\n  revisions: 6ca543ec1bf8\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bio3d_pca\n  owner: chemteam\n  revisions: 24867ab16f36\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bio3d_pca_visualize\n  owner: chemteam\n  revisions: f61a718993fd\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bio3d_rmsd\n  owner: chemteam\n  revisions: 77e28e1da9f4\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bio3d_rmsf\n  owner: chemteam\n  revisions: 6bcb804a54c3\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_editconf\n  owner: chemteam\n  revisions: 3b8a9d5ced85\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_editconf\n  owner: chemteam\n  revisions: 0fac8e2afc13\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_em\n  owner: chemteam\n  revisions: eb6564a60136\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_em\n  owner: chemteam\n  revisions: f5d979cb4b54\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_energy\n  owner: chemteam\n  revisions: d2f955aea23a\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_merge_topology_files\n  owner: chemteam\n  revisions: d1d0efda35c0\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_merge_topology_files\n  owner: chemteam\n  revisions: 319a28774da9\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_setup\n  owner: chemteam\n  revisions: cac1886249a2\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_setup\n  owner: chemteam\n  revisions: 2c349b027a01\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_sim\n  owner: chemteam\n  revisions: 2e219a2d9327\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_sim\n  owner: chemteam\n  revisions: 73008ef1f487\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_solvate\n  owner: chemteam\n  revisions: 1809414a9454\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_solvate\n  owner: chemteam\n  revisions: 2c8ed1b52bf7\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: md_converter\n  owner: chemteam\n  revisions: 79e8ab8f1e81\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: md_converter\n  owner: chemteam\n  revisions: ba83f0923369\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mdanalysis_cosine_analysis\n  owner: chemteam\n  revisions: 9a3a1f698fc6\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mdanalysis_cosine_analysis\n  owner: chemteam\n  revisions: 48d6a6eb438b\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: vmd_hbonds\n  owner: chemteam\n  revisions: 8aa5e465b043\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
                     "elixir-europe"
                 ],
-                "bio": "Senior Lecturer at The Open University",
-                "elixir_node": "uk",
-                "email": "wendi.bacon@open.ac.uk",
-                "fediverse": "https://mstdn.science/@wendibacon1",
-                "fediverse_flavor": "mastodon",
-                "id": "nomadscientist",
-                "joined": "2020-03",
-                "matrix": "nomadscientist:matrix.org",
-                "name": "Wendi Bacon",
-                "orcid": "0000-0002-8170-8806",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
-                "twitter": "WendiBacon1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+                "id": "simonbray",
+                "joined": "2019-05",
+                "name": "Simon Bray",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
+            },
+            {
+                "id": "tsenapathi",
+                "joined": "2019-05",
+                "name": "Tharindu Senapathi",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tsenapathi/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tsenapathi.json"
+            },
+            {
+                "id": "chrisbarnettster",
+                "joined": "2019-05",
+                "name": "Christopher Barnett",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/chrisbarnettster/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/chrisbarnettster.json"
             },
             {
                 "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
+                    "elixir-europe"
                 ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
                 "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
                 "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
+                "id": "bgruening",
                 "joined": "2017-09",
-                "linkedin": "shiltemann",
+                "linkedin": "bgruening",
                 "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
                 },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
             }
         ],
-        "dir": "topics/community/tutorials/sig_create",
+        "dir": "topics/computational-chemistry/tutorials/htmd-analysis",
         "edam_operation": [],
         "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "community/sig_create",
+        "id": "computational-chemistry/htmd-analysis",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.no"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Special Interest Groups are a commitment to create and sustain.",
-            "There are centralised resources to help support running a Special Interest Group.",
-            "SIGs are joyous places for like-minded scientists to interact and share expertise."
+            "Simulating protein-ligand systems is more complex than simply simulating protein-only systems.",
+            "There are a range of Galaxy tools for MD simulation (using GROMACS) and analysis.",
+            "Galaxy makes assembling and scaling up workflows for high-throughput MD straightforward for users."
         ],
         "layout": "tutorial_hands_on",
+        "level": "Advanced",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-08",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Determine whether you need a Galaxy Special Interest Group",
-            "Create a Special Interest Group",
-            "Be aware of resources for expanding your Special Interest Group"
+            "Learn about force-fields and MD parameterization",
+            "Learn how to conduct MD simulation and analysis for a protein-ligand system",
+            "Understand how different molecular interactions contribute to the binding affinity of various ligands for the Hsp90 protein."
         ],
-        "pageviews": 18,
-        "priority": 2,
-        "pub_date": "2024-07-08",
+        "pageviews": 15878,
+        "pub_date": "2020-05-20",
         "questions": [
-            "Do I need to make a Special Interest Group?",
-            "What are the requirements for a Special Interest Group?",
-            "How can I create a Special Interest Group?",
-            "Where can I go to find Special Interest Group resources?"
+            "How are protein-ligand systems parameterized for molecular dynamics simulation?",
+            "What kind of analysis can be carried out on molecular trajectories?",
+            "How can high-throughput MD be used to study multiple ligands?"
         ],
-        "requirements": [
+        "recordings": [
             {
-                "topic_name": "community",
-                "tutorials": [
-                    "sig_define"
+                "captioners": [
+                    "simonbray"
                 ],
-                "type": "internal"
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "1H40M",
+                "speakers": [
+                    "simonbray",
+                    "chrisbarnettster"
+                ],
+                "youtube_id": "LjW3nES04bI"
             }
         ],
-        "short_id": "T00443",
-        "short_tools": [],
+        "short_id": "T00050",
+        "short_tools": [
+            "openbabel_compound_convert",
+            "bio3d_rmsf",
+            "gmx_merge_topology_files",
+            "gmx_energy",
+            "gmx_solvate",
+            "gmx_em",
+            "get_pdb",
+            "bio3d_pca",
+            "bio3d_rmsd",
+            "tp_grep_tool",
+            "bio3d_pca_visualize",
+            "gmx_setup",
+            "md_converter",
+            "vmd_hbonds",
+            "gmx_editconf",
+            "gmx_sim",
+            "ambertools_acpype",
+            "mdanalysis_cosine_analysis"
+        ],
         "slides": false,
         "slides_recordings": false,
-        "supported_servers": [],
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                }
+            ]
+        },
         "symlink": null,
-        "time_estimation": "30m",
-        "title": "Creating a Special Interest Group",
-        "tools": [],
-        "topic_name": "community",
-        "topic_name_human": "Galaxy Community Building",
+        "time_estimation": "3H",
+        "title": "High Throughput Molecular Dynamics and Analysis",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/bgruening/get_pdb/get_pdb/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.2.2.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_acpype/ambertools_acpype/19.11",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_acpype/ambertools_acpype/21.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca/bio3d_pca/2.3.4",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca_visualize/bio3d_pca_visualize/2.3.4",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsd/bio3d_rmsd/2.3.4",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsf/bio3d_rmsf/2.3.4",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2019.1.4",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2020.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2019.1.4",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2020.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_energy/gmx_energy/2020.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_merge_topology_files/gmx_merge_topology_files/3.2.0",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_merge_topology_files/gmx_merge_topology_files/3.2.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2019.1.4",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2020.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.4.1",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.4+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2019.1.4",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2020.4+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter/1.9.3.2",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter/1.9.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_cosine_analysis/mdanalysis_cosine_analysis/0.20",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_cosine_analysis/mdanalysis_cosine_analysis/1.0.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/chemteam/vmd_hbonds/vmd_hbonds/1.9.3"
+        ],
+        "topic_name": "computational-chemistry",
+        "topic_name_human": "Computational chemistry",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "sig_create",
+        "tutorial_name": "htmd-analysis",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/community/tutorials/sig_create/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/community/tutorials/sig_create/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/community/tutorials/sig_create/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.json"
         },
-        "version": 1,
+        "version": 18,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 112,
-        "visitors": 15
+        "visit_duration": 159,
+        "visitors": 8552,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "High Throughput Molecular Dynamics and Analysis",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[label=\"GROMACS structure configuration\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"MDTraj file converter\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"RMSD Analysis\"]\n  2 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"RMSF Analysis\"]\n  2 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"output\"]\n  6[label=\"PCA\"]\n  2 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"Cosine Content\"]\n  3 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"PCA visualization\"]\n  2 -> 8 [label=\"output\"]\n  3 -> 8 [label=\"output\"]\n  9[label=\"Hydrogen Bond Analysis using VMD\"]\n  3 -> 9 [label=\"output\"]\n  2 -> 9 [label=\"output\"]\n  10[label=\"RMSD Analysis\"]\n  2 -> 10 [label=\"output\"]\n  3 -> 10 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "2a74c677081dfcdf29c3c05c38bcb07d131f412f",
+                        "message": "fix workflows",
+                        "num": 2,
+                        "short_hash": "2a74c6770",
+                        "unix": "1595329917"
+                    },
+                    {
+                        "hash": "3e9586df2283684cf7a452fb32a3ff0f69b48f4a",
+                        "message": "HTMD tutorial (#1837)",
+                        "num": 1,
+                        "short_hash": "3e9586df2",
+                        "unix": "1589995622"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Galaxy30-[GROMACS_simulation_on_data_28,_data_15,_and_data_26].gro"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 10
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Galaxy30-[GROMACS_simulation_on_data_28,_data_15,_and_data_26].gro\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "82ae4961-8bb0-440d-bed6-9206d8b9d860",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Galaxy31-[GROMACS_simulation_on_data_28,_data_15,_and_data_26].xtc"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 130
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Galaxy31-[GROMACS_simulation_on_data_28,_data_15,_and_data_26].xtc\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "f67e98b9-2b4f-4d7d-9da7-ec3c23ffbd38",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"GROMACS structure configuration\"];\n  0 -->|output| 2;\n  3[\"MDTraj file converter\"];\n  1 -->|output| 3;\n  4[\"RMSD Analysis\"];\n  2 -->|output| 4;\n  3 -->|output| 4;\n  5[\"RMSF Analysis\"];\n  2 -->|output| 5;\n  3 -->|output| 5;\n  6[\"PCA\"];\n  2 -->|output| 6;\n  3 -->|output| 6;\n  7[\"Cosine Content\"];\n  3 -->|output| 7;\n  2 -->|output| 7;\n  8[\"PCA visualization\"];\n  2 -->|output| 8;\n  3 -->|output| 8;\n  9[\"Hydrogen Bond Analysis using VMD\"];\n  3 -->|output| 9;\n  2 -->|output| 9;\n  10[\"RMSD Analysis\"];\n  2 -->|output| 10;\n  3 -->|output| 10;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Workflow constructed from history 'Hsp90-MDAnalysis'",
+                "outputs": [],
+                "parent_id": "computational-chemistry/htmd-analysis",
+                "path": "topics/computational-chemistry/tutorials/htmd-analysis/workflows/analysis_workflow.ga",
+                "tags": [
+                    "computational-chemistry"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Workflow constructed from history 'Hsp90-MDAnalysis'",
+                "topic_id": "computational-chemistry",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/computational-chemistry-htmd-analysis/versions/analysis-workflow",
+                "tutorial_id": "htmd-analysis",
+                "url": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/htmd-analysis/workflows/analysis_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/htmd-analysis/workflows/analysis_workflow.html",
+                "version": 2,
+                "wfid": "computational-chemistry-htmd-analysis",
+                "wfname": "analysis-workflow",
+                "workflow": "analysis_workflow.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca/bio3d_pca/2.3.4",
+                    "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca_visualize/bio3d_pca_visualize/2.3.4",
+                    "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsd/bio3d_rmsd/2.3.4",
+                    "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsf/bio3d_rmsf/2.3.4",
+                    "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2019.1.4",
+                    "toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter/1.9.3.2",
+                    "toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_cosine_analysis/mdanalysis_cosine_analysis/0.20",
+                    "toolshed.g2.bx.psu.edu/repos/chemteam/vmd_hbonds/vmd_hbonds/1.9.3"
+                ],
+                "workflowhub_id": "1062"
+            },
+            {
+                "creators": [],
+                "description": "High Throughput Molecular Dynamics and Analysis",
+                "features": {
+                    "comments": false,
+                    "parameters": true,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nPDB code e.g. 6hhr\"]\n  1[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nLigand name e.g. AG5E\"]\n  2[label=\"Get PDB file\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Search in textfiles\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Search in textfiles\"]\n  2 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"GROMACS initial setup\"]\n  3 -> 5 [label=\"output\"]\n  6[label=\"Compound conversion\"]\n  4 -> 6 [label=\"output\"]\n  7[label=\"Generate MD topologies for small molecules\"]\n  6 -> 7 [label=\"outfile\"]\n  8[label=\"Merge GROMACS topologies\"]\n  7 -> 8 [label=\"gro_output\"]\n  5 -> 8 [label=\"output1\"]\n  5 -> 8 [label=\"output2\"]\n  7 -> 8 [label=\"output\"]\n  9[label=\"GROMACS structure configuration\"]\n  8 -> 9 [label=\"complex_gro\"]\n  10[label=\"GROMACS solvation and adding ions\"]\n  8 -> 10 [label=\"complex_top\"]\n  9 -> 10 [label=\"output\"]\n  11[label=\"GROMACS energy minimization\"]\n  10 -> 11 [label=\"output2\"]\n  10 -> 11 [label=\"output1\"]\n  12[label=\"GROMACS simulation\"]\n  5 -> 12 [label=\"output3\"]\n  10 -> 12 [label=\"output2\"]\n  11 -> 12 [label=\"output1\"]\n  13[label=\"GROMACS simulation\"]\n  5 -> 13 [label=\"output3\"]\n  10 -> 13 [label=\"output2\"]\n  12 -> 13 [label=\"output1\"]\n  12 -> 13 [label=\"output5\"]\n  14[label=\"GROMACS simulation\"]\n  10 -> 14 [label=\"output2\"]\n  13 -> 14 [label=\"output1\"]\n  13 -> 14 [label=\"output5\"]\n}",
+                "history": [
+                    {
+                        "hash": "2a74c677081dfcdf29c3c05c38bcb07d131f412f",
+                        "message": "fix workflows",
+                        "num": 2,
+                        "short_hash": "2a74c6770",
+                        "unix": "1595329917"
+                    },
+                    {
+                        "hash": "3e9586df2283684cf7a452fb32a3ff0f69b48f4a",
+                        "message": "HTMD tutorial (#1837)",
+                        "num": 1,
+                        "short_hash": "3e9586df2",
+                        "unix": "1589995622"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "PDB code (e.g. 6hhr)",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 229.5,
+                            "top": 191.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"parameter_type\": \"text\"}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "73aff13d-acd3-41a0-8894-3104a93f9ad0",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "2a9ccaa8-d21d-4d92-8e8c-97822d8d5d9e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "Ligand name (e.g. AG5E)",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 230.5,
+                            "top": 340.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"parameter_type\": \"text\"}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "4c514954-d86b-409d-aa30-70545b8522ea",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "1fb55337-8d3f-4918-a1af-14c28986ff07"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nPDB code e.g. 6hhr\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nLigand name e.g. AG5E\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"Get PDB file\"];\n  0 -->|output| 2;\n  3[\"Search in textfiles\"];\n  2 -->|output| 3;\n  4[\"Search in textfiles\"];\n  2 -->|output| 4;\n  1 -->|output| 4;\n  5[\"GROMACS initial setup\"];\n  3 -->|output| 5;\n  6[\"Compound conversion\"];\n  4 -->|output| 6;\n  7[\"Generate MD topologies for small molecules\"];\n  6 -->|outfile| 7;\n  8[\"Merge GROMACS topologies\"];\n  7 -->|gro_output| 8;\n  5 -->|output1| 8;\n  5 -->|output2| 8;\n  7 -->|output| 8;\n  9[\"GROMACS structure configuration\"];\n  8 -->|complex_gro| 9;\n  10[\"GROMACS solvation and adding ions\"];\n  8 -->|complex_top| 10;\n  9 -->|output| 10;\n  11[\"GROMACS energy minimization\"];\n  10 -->|output2| 11;\n  10 -->|output1| 11;\n  12[\"GROMACS simulation\"];\n  5 -->|output3| 12;\n  10 -->|output2| 12;\n  11 -->|output1| 12;\n  13[\"GROMACS simulation\"];\n  5 -->|output3| 13;\n  10 -->|output2| 13;\n  12 -->|output1| 13;\n  12 -->|output5| 13;\n  14[\"GROMACS simulation\"];\n  10 -->|output2| 14;\n  13 -->|output1| 14;\n  13 -->|output5| 14;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "MD protein-ligand workflow (from PDB structure)",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "PDB code (e.g. 6hhr)",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 229.5,
+                            "top": 191.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"parameter_type\": \"text\"}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "73aff13d-acd3-41a0-8894-3104a93f9ad0",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "2a9ccaa8-d21d-4d92-8e8c-97822d8d5d9e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "Ligand name (e.g. AG5E)",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 230.5,
+                            "top": 340.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"parameter_type\": \"text\"}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "4c514954-d86b-409d-aa30-70545b8522ea",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "1fb55337-8d3f-4918-a1af-14c28986ff07"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "computational-chemistry/htmd-analysis",
+                "path": "topics/computational-chemistry/tutorials/htmd-analysis/workflows/main_workflow.ga",
+                "tags": [
+                    "cheminformatics",
+                    "moleculardynamics",
+                    "computational-chemistry"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "MD protein-ligand workflow (from PDB structure)",
+                "topic_id": "computational-chemistry",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/computational-chemistry-htmd-analysis/versions/main-workflow",
+                "tutorial_id": "htmd-analysis",
+                "url": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/htmd-analysis/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/htmd-analysis/workflows/main_workflow.html",
+                "version": 2,
+                "wfid": "computational-chemistry-htmd-analysis",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/get_pdb/get_pdb/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.2.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_acpype/ambertools_acpype/19.11",
+                    "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2019.1.4",
+                    "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2019.1.4",
+                    "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_merge_topology_files/gmx_merge_topology_files/3.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2019.1.4",
+                    "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.4.1",
+                    "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2019.1.4"
+                ],
+                "workflowhub_id": "1134"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/records/3813283"
     },
     {
         "admin_install": {
@@ -31318,6 +34344,7 @@
         "id": "computational-chemistry/md-simulation-gromacs",
         "inexact_supported_servers": [
             "Galaxy@AuBi",
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.no"
         ],
@@ -31338,7 +34365,7 @@
             "Understand the structure of the molecular dynamics workflow.",
             "Prepare a short (1 ns) trajectory for a simulation of a protein."
         ],
-        "pageviews": 43090,
+        "pageviews": 43562,
         "pub_date": "2019-06-03",
         "questions": [
             "How do I use the GROMACS engine in Galaxy?",
@@ -31346,12 +34373,12 @@
         ],
         "short_id": "T00051",
         "short_tools": [
-            "gmx_editconf",
-            "gmx_setup",
-            "tp_grep_tool",
-            "get_pdb",
-            "gmx_em",
             "gmx_solvate",
+            "gmx_em",
+            "get_pdb",
+            "tp_grep_tool",
+            "gmx_setup",
+            "gmx_editconf",
             "gmx_sim"
         ],
         "slides": false,
@@ -31380,6 +34407,11 @@
                     "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -31429,7 +34461,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 84,
-        "visitors": 23011,
+        "visitors": 23386,
         "workflows": [
             {
                 "creators": [],
@@ -31495,7 +34527,7 @@
                 "inputs": [],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"Get PDB file\"];\n  1[\"Search in textfiles\"];\n  0 -->|output| 1;\n  2[\"GROMACS initial setup\"];\n  1 -->|output| 2;\n  3[\"GROMACS structure configuration\"];\n  2 -->|output2| 3;\n  4[\"GROMACS solvation and adding ions\"];\n  2 -->|output1| 4;\n  3 -->|output| 4;\n  5[\"GROMACS energy minimization\"];\n  4 -->|output2| 5;\n  4 -->|output1| 5;\n  6[\"NVT equilibration\"];\n  2 -->|output3| 6;\n  4 -->|output2| 6;\n  5 -->|output1| 6;\n  7[\"NPT equilibration\"];\n  2 -->|output3| 7;\n  4 -->|output2| 7;\n  6 -->|output1| 7;\n  6 -->|output5| 7;\n  8[\"MD simulation\"];\n  4 -->|output2| 8;\n  7 -->|output1| 8;\n  7 -->|output5| 8;\n  027305f5-213b-40af-8e2b-c376d5d2e294[\"Output\\nxtc_output\"];\n  8 --> 027305f5-213b-40af-8e2b-c376d5d2e294;\n  style 027305f5-213b-40af-8e2b-c376d5d2e294 stroke:#2c3143,stroke-width:4px;\n  e745fd4c-f607-4215-84e4-c62587c8c07a[\"Output\\ngro_output\"];\n  8 --> e745fd4c-f607-4215-84e4-c62587c8c07a;\n  style e745fd4c-f607-4215-84e4-c62587c8c07a stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
+                "modified": "2024-10-02 12:08:06 +0000",
                 "name": "GROMACS Training Workflow",
                 "outputs": [
                     {
@@ -31769,441 +34801,6 @@
         ],
         "zenodo_link": "https://zenodo.org/record/2598415"
     },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/md-simulation-namd/tutorial.json",
-        "contributors": [
-            {
-                "id": "chrisbarnettster",
-                "joined": "2019-05",
-                "name": "Christopher Barnett",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/chrisbarnettster/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/chrisbarnettster.json"
-            },
-            {
-                "id": "tsenapathi",
-                "joined": "2019-05",
-                "name": "Tharindu Senapathi",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tsenapathi/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tsenapathi.json"
-            },
-            {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "simonbray",
-                "joined": "2019-05",
-                "name": "Simon Bray",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
-            }
-        ],
-        "dir": "topics/computational-chemistry/tutorials/md-simulation-namd",
-        "draft": true,
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "computational-chemistry",
-                "tutorials": [
-                    "analysis-md-simulations"
-                ],
-                "type": "internal"
-            }
-        ],
-        "hands_on": true,
-        "id": "computational-chemistry/md-simulation-namd",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Several MD engines are available in BRIDGE",
-            "Workflows are available for common simulations tasks such as equilibration and production dynamics for various ensembles (NVT, NPT)",
-            "You've run an equilibrium and production MD simulation using NAMD"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Learn about the NAMD engine provided in BRIDGE"
-        ],
-        "pageviews": 6361,
-        "pub_date": "2019-06-03",
-        "questions": [
-            "How do I use the NAMD engine in Galaxy?",
-            "What is the correct procedure for performing a simple molecular dynamics simulation of a protein?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "computational-chemistry",
-                "tutorials": [
-                    "setting-up-molecular-systems"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00052",
-        "short_tools": [
-            "namd_nvt",
-            "setup",
-            "namd_npt",
-            "minimizer"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "work-in-progress"
-        ],
-        "time_estimation": "3H",
-        "title": "Running molecular dynamics simulations using NAMD",
-        "tools": [
-            "minimizer",
-            "namd_npt",
-            "namd_nvt",
-            "setup"
-        ],
-        "topic_name": "computational-chemistry",
-        "topic_name_human": "Computational chemistry",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "md-simulation-namd",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/computational-chemistry/tutorials/md-simulation-namd/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/md-simulation-namd/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/md-simulation-namd/tutorial.json"
-        },
-        "version": 9,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 72,
-        "visitors": 3625,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Running molecular dynamics simulations using NAMD",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[label=\"System Setup\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Energy Minimizer\"]\n  2 -> 3 [label=\"setup_crd\"]\n  2 -> 3 [label=\"setup_psf\"]\n  2 -> 3 [label=\"structure_prm\"]\n  4[label=\"NAMD MD Simulator NVT\"]\n  3 -> 4 [label=\"pdbout\"]\n  3 -> 4 [label=\"pmespec\"]\n  3 -> 4 [label=\"xplorpsfout\"]\n  3 -> 4 [label=\"bbrmsd\"]\n  3 -> 4 [label=\"scrmsd\"]\n  3 -> 4 [label=\"subsrmsd\"]\n  2 -> 4 [label=\"structure_prm\"]\n  5[label=\"NAMD MD Simulator NPT\"]\n  3 -> 5 [label=\"pdbout\"]\n  3 -> 5 [label=\"pmespec\"]\n  3 -> 5 [label=\"xplorpsfout\"]\n  4 -> 5 [label=\"coorout\"]\n  4 -> 5 [label=\"velout\"]\n  4 -> 5 [label=\"xscout\"]\n  2 -> 5 [label=\"structure_prm\"]\n}",
-                "history": [
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 4,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 3,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
-                        "message": "unflatten workflows",
-                        "num": 2,
-                        "short_hash": "faf6d298a",
-                        "unix": "1576155753"
-                    },
-                    {
-                        "hash": "be6fece7faf81d375f35a35d1a115041aae6066b",
-                        "message": "Simonbray compchem (#6)",
-                        "num": 1,
-                        "short_hash": "be6fece7f",
-                        "unix": "1556962666"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "7cel.psf"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 10
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"7cel.psf\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ae09b2b3-e735-46e7-be28-eaf11cab2d24",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "7cel.crd"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 130
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"7cel.crd\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "83bc3872-4bbf-4afd-aaf8-81a03780636a",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"System Setup\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Energy Minimizer\"];\n  2 -->|setup_crd| 3;\n  2 -->|setup_psf| 3;\n  2 -->|structure_prm| 3;\n  4[\"NAMD MD Simulator NVT\"];\n  3 -->|pdbout| 4;\n  3 -->|pmespec| 4;\n  3 -->|xplorpsfout| 4;\n  3 -->|bbrmsd| 4;\n  3 -->|scrmsd| 4;\n  3 -->|subsrmsd| 4;\n  2 -->|structure_prm| 4;\n  5[\"NAMD MD Simulator NPT\"];\n  3 -->|pdbout| 5;\n  3 -->|pmespec| 5;\n  3 -->|xplorpsfout| 5;\n  4 -->|coorout| 5;\n  4 -->|velout| 5;\n  4 -->|xscout| 5;\n  2 -->|structure_prm| 5;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "MD NAMD",
-                "outputs": [],
-                "parent_id": "computational-chemistry/md-simulation-namd",
-                "path": "topics/computational-chemistry/tutorials/md-simulation-namd/workflows/main_workflow.ga",
-                "tags": [
-                    "computational-chemistry"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "MD NAMD",
-                "topic_id": "computational-chemistry",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/computational-chemistry-md-simulation-namd/versions/main-workflow",
-                "tutorial_id": "md-simulation-namd",
-                "url": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/md-simulation-namd/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/md-simulation-namd/workflows/main_workflow.html",
-                "version": 4,
-                "wfid": "computational-chemistry-md-simulation-namd",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "minimizer",
-                    "namd_npt",
-                    "namd_nvt",
-                    "setup"
-                ],
-                "workflowhub_id": "1071"
-            },
-            {
-                "creators": [],
-                "description": "Running molecular dynamics simulations using NAMD",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  4[label=\"NAMD MD Simulator NVT\"]\n  0 -> 4 [label=\"output\"]\n  2 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"NAMD MD Simulator NPT\"]\n  0 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  4 -> 5 [label=\"coorout\"]\n  4 -> 5 [label=\"velout\"]\n  4 -> 5 [label=\"xscout\"]\n  3 -> 5 [label=\"output\"]\n}",
-                "history": [
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 4,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 3,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
-                        "message": "unflatten workflows",
-                        "num": 2,
-                        "short_hash": "faf6d298a",
-                        "unix": "1576155753"
-                    },
-                    {
-                        "hash": "be6fece7faf81d375f35a35d1a115041aae6066b",
-                        "message": "Simonbray compchem (#6)",
-                        "num": 1,
-                        "short_hash": "be6fece7f",
-                        "unix": "1556962666"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "step3_pbcsetup.pdb"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 10
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"step3_pbcsetup.pdb\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "180b4e05-b912-4c3e-8d7b-39027a6c9d65",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "step3_pbcsetup.xplor.ext.psf"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 130
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"step3_pbcsetup.xplor.ext.psf\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "8829a91f-e5b5-44bd-977d-c4c308453ac6",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "checkfft.str"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 250
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"checkfft.str\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "badde4ba-b790-406a-93e5-d622f4be8062",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "step2.1_waterbox.prm"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 370
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"step2.1_waterbox.prm\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "de715d6e-ffac-4e42-9166-6dfeea0c244f",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"NAMD MD Simulator NVT\"];\n  0 -->|output| 4;\n  2 -->|output| 4;\n  1 -->|output| 4;\n  3 -->|output| 4;\n  5[\"NAMD MD Simulator NPT\"];\n  0 -->|output| 5;\n  2 -->|output| 5;\n  1 -->|output| 5;\n  4 -->|coorout| 5;\n  4 -->|velout| 5;\n  4 -->|xscout| 5;\n  3 -->|output| 5;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "NAMD MD From CHARMM GUI",
-                "outputs": [],
-                "parent_id": "computational-chemistry/md-simulation-namd",
-                "path": "topics/computational-chemistry/tutorials/md-simulation-namd/workflows/main_workflow_charmmgui.ga",
-                "tags": [
-                    "computational-chemistry"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "NAMD MD From CHARMM GUI",
-                "topic_id": "computational-chemistry",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/computational-chemistry-md-simulation-namd/versions/main-workflow-charmmgui",
-                "tutorial_id": "md-simulation-namd",
-                "url": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/md-simulation-namd/workflows/main_workflow_charmmgui.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/md-simulation-namd/workflows/main_workflow_charmmgui.html",
-                "version": 4,
-                "wfid": "computational-chemistry-md-simulation-namd",
-                "wfname": "main-workflow-charmmgui",
-                "workflow": "main_workflow_charmmgui.ga",
-                "workflow_tools": [
-                    "namd_npt",
-                    "namd_nvt"
-                ],
-                "workflowhub_id": "1072"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/3234841"
-    },
     {
         "admin_install": {
             "install_repository_dependencies": true,
@@ -32275,10 +34872,12 @@
         },
         "contributors": [
             {
+                "elixir_node": "uk",
                 "email": "juliajot36@gmail.com",
                 "id": "wee-snufkin",
                 "joined": "2022-06",
                 "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
             },
@@ -32356,14 +34955,14 @@
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-27",
+        "mod_date": "2024-09-13",
         "objectives": [
             "Learn some terminology from the field of medicinal chemistry",
             "Understand the idea of data-driven medicinal chemistry",
             "Explore the databases used for drug discovery and development",
             "Use Galaxy tools for data management, format conversion and simple analyses"
         ],
-        "pageviews": 212,
+        "pageviews": 226,
         "pub_date": "2024-01-08",
         "questions": [
             "Why does medicinal chemistry research produce so much data?",
@@ -32371,6 +34970,16 @@
             "What are the current publicly available databases that can be used for drug discovery and development?",
             "How to use Galaxy for data management and analysis of chemical data?"
         ],
+        "recordings": [
+            {
+                "date": "2024-09-12",
+                "length": "48M1S",
+                "speakers": [
+                    "wee-snufkin"
+                ],
+                "youtube_id": "JWV6IiD6mPE"
+            }
+        ],
         "requirements": [
             {
                 "topic_name": "fair",
@@ -32383,13 +34992,13 @@
         ],
         "short_id": "T00381",
         "short_tools": [
-            "ctb_silicos_qed",
-            "md_converter",
-            "get_pdb",
-            "ctb_im_rxn_maker",
             "openbabel_compound_convert",
+            "get_pdb",
+            "openbabel_svg_depiction",
+            "md_converter",
+            "ctb_silicos_qed",
             "chembl",
-            "openbabel_svg_depiction"
+            "ctb_im_rxn_maker"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -32457,12 +35066,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/med-chem-data/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/med-chem-data/tutorial.json"
         },
-        "version": 3,
+        "version": 4,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 131,
-        "visitors": 177,
+        "visit_duration": 148,
+        "visitors": 190,
         "workflows": [
             {
                 "creators": [
@@ -32547,7 +35156,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nBenzenesulfonyl chloride\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nEthylamine\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Compound conversion\"];\n  0 -->|output| 2;\n  aff8fa4f-c254-4f05-9560-52bad6c7e04a[\"Output\\nBenzenesulfonyl chloride SDF\"];\n  2 --> aff8fa4f-c254-4f05-9560-52bad6c7e04a;\n  style aff8fa4f-c254-4f05-9560-52bad6c7e04a stroke:#2c3143,stroke-width:4px;\n  3[\"Search ChEMBL database\"];\n  0 -->|output| 3;\n  044d2c08-92ed-45c9-9868-ee802998d92c[\"Output\\nSubstructures from ChEMBL database\"];\n  3 --> 044d2c08-92ed-45c9-9868-ee802998d92c;\n  style 044d2c08-92ed-45c9-9868-ee802998d92c stroke:#2c3143,stroke-width:4px;\n  4[\"Search ChEMBL database\"];\n  0 -->|output| 4;\n  99274b60-732d-4276-969f-ccc3673a872a[\"Output\\nLipinski substructures from ChEMBL database\"];\n  4 --> 99274b60-732d-4276-969f-ccc3673a872a;\n  style 99274b60-732d-4276-969f-ccc3673a872a stroke:#2c3143,stroke-width:4px;\n  5[\"Compound conversion\"];\n  1 -->|output| 5;\n  77ad7b99-5761-46a3-b9a6-1dd3d8e2baac[\"Output\\nEthylamine SDF\"];\n  5 --> 77ad7b99-5761-46a3-b9a6-1dd3d8e2baac;\n  style 77ad7b99-5761-46a3-b9a6-1dd3d8e2baac stroke:#2c3143,stroke-width:4px;\n  6[\"Reaction maker\"];\n  2 -->|outfile| 6;\n  5 -->|outfile| 6;\n  f9d1d7fd-e854-469b-a464-6811998e058e[\"Output\\nReaction product\"];\n  6 --> f9d1d7fd-e854-469b-a464-6811998e058e;\n  style f9d1d7fd-e854-469b-a464-6811998e058e stroke:#2c3143,stroke-width:4px;\n  b0bd7ed2-a80b-44ce-994b-999e1d472281[\"Output\\nReaction maker logfile\"];\n  6 --> b0bd7ed2-a80b-44ce-994b-999e1d472281;\n  style b0bd7ed2-a80b-44ce-994b-999e1d472281 stroke:#2c3143,stroke-width:4px;\n  7[\"Visualisation\"];\n  6 -->|outfile| 7;\n  fc618f3f-6aa5-4970-841d-56f4eabf47b7[\"Output\\nVisualisation of reaction product\"];\n  7 --> fc618f3f-6aa5-4970-841d-56f4eabf47b7;\n  style fc618f3f-6aa5-4970-841d-56f4eabf47b7 stroke:#2c3143,stroke-width:4px;\n  8[\"Drug-likeness\"];\n  6 -->|outfile| 8;\n  7ad8c184-e10d-4fce-a402-3e79da6e09ac[\"Output\\nDrug-likeness of product molecule\"];\n  8 --> 7ad8c184-e10d-4fce-a402-3e79da6e09ac;\n  style 7ad8c184-e10d-4fce-a402-3e79da6e09ac stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
+                "modified": "2024-10-02 12:08:06 +0000",
                 "name": "Data management in Medicinal Chemistry workflow",
                 "outputs": [
                     {
@@ -33103,7 +35712,7 @@
             "Learn which analysis tools are available.",
             "Analyse a protein and discuss the meaning behind each analysis."
         ],
-        "pageviews": 53658,
+        "pageviews": 54198,
         "pub_date": "2019-06-03",
         "questions": [
             "Which analysis tools are available?"
@@ -33120,14 +35729,14 @@
         ],
         "short_id": "T00047",
         "short_tools": [
+            "bio3d_rmsf",
+            "mdanalysis_dihedral",
             "mdanalysis_rdf",
-            "mdanalysis_distance",
-            "mdanalysis_cosine_analysis",
-            "bio3d_rmsd",
             "bio3d_pca",
-            "bio3d_rmsf",
+            "bio3d_rmsd",
+            "mdanalysis_distance",
             "mdanalysis_ramachandran_plot",
-            "mdanalysis_dihedral"
+            "mdanalysis_cosine_analysis"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -33203,7 +35812,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 76,
-        "visitors": 29218,
+        "visitors": 29677,
         "workflows": [
             {
                 "creators": [
@@ -33310,7 +35919,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nDCD input\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nPDB input\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"RDF Analysis\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  ab90456f-d7ae-4fb1-ba2f-978a59791acc[\"Output\\nRDF Analysis plot\"];\n  2 --> ab90456f-d7ae-4fb1-ba2f-978a59791acc;\n  style ab90456f-d7ae-4fb1-ba2f-978a59791acc stroke:#2c3143,stroke-width:4px;\n  1ee2fe4a-0e50-4a4f-828e-3b60d75120e7[\"Output\\nRDF Analysis raw data\"];\n  2 --> 1ee2fe4a-0e50-4a4f-828e-3b60d75120e7;\n  style 1ee2fe4a-0e50-4a4f-828e-3b60d75120e7 stroke:#2c3143,stroke-width:4px;\n  3[\"Cosine Content\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  5ca6c423-961b-4a55-a821-794a0d311e41[\"Output\\nCosine Content raw data\"];\n  3 --> 5ca6c423-961b-4a55-a821-794a0d311e41;\n  style 5ca6c423-961b-4a55-a821-794a0d311e41 stroke:#2c3143,stroke-width:4px;\n  7854cbf9-187f-4117-b494-73a5a404d06f[\"Output\\nCosine Content plot\"];\n  3 --> 7854cbf9-187f-4117-b494-73a5a404d06f;\n  style 7854cbf9-187f-4117-b494-73a5a404d06f stroke:#2c3143,stroke-width:4px;\n  4[\"Ramachandran Plots\"];\n  0 -->|output| 4;\n  1 -->|output| 4;\n  aa7afa97-8be6-4e6b-ad2c-5715f3c10362[\"Output\\nRamachandran Plot\"];\n  4 --> aa7afa97-8be6-4e6b-ad2c-5715f3c10362;\n  style aa7afa97-8be6-4e6b-ad2c-5715f3c10362 stroke:#2c3143,stroke-width:4px;\n  178f112a-eb0b-4299-aff5-69efd9ffb52b[\"Output\\nRamachandran Plot raw data\"];\n  4 --> 178f112a-eb0b-4299-aff5-69efd9ffb52b;\n  style 178f112a-eb0b-4299-aff5-69efd9ffb52b stroke:#2c3143,stroke-width:4px;\n  5[\"Distance Analysis\"];\n  0 -->|output| 5;\n  1 -->|output| 5;\n  eac670fb-f01e-49cd-a103-828a15149f48[\"Output\\nDistance Analysis raw data\"];\n  5 --> eac670fb-f01e-49cd-a103-828a15149f48;\n  style eac670fb-f01e-49cd-a103-828a15149f48 stroke:#2c3143,stroke-width:4px;\n  6605884d-7bfa-4f43-bbc6-2352256d2bc7[\"Output\\nDistance Analysis plot\"];\n  5 --> 6605884d-7bfa-4f43-bbc6-2352256d2bc7;\n  style 6605884d-7bfa-4f43-bbc6-2352256d2bc7 stroke:#2c3143,stroke-width:4px;\n  6[\"Dihedral Analysis\"];\n  0 -->|output| 6;\n  1 -->|output| 6;\n  755dbb99-3e3e-425b-a4b2-e375df6e39b4[\"Output\\nDihedral Analysis plot\"];\n  6 --> 755dbb99-3e3e-425b-a4b2-e375df6e39b4;\n  style 755dbb99-3e3e-425b-a4b2-e375df6e39b4 stroke:#2c3143,stroke-width:4px;\n  e0234472-cc44-483e-997b-8b0e0719c8d7[\"Output\\nDihedral Analysis raw data\"];\n  6 --> e0234472-cc44-483e-997b-8b0e0719c8d7;\n  style e0234472-cc44-483e-997b-8b0e0719c8d7 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
+                "modified": "2024-10-02 12:08:06 +0000",
                 "name": "Analysis using MDAnalysis",
                 "outputs": [
                     {
@@ -33879,7 +36488,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nprotein_mdsimulation_dcd\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nprotein_pdb\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"RMSD Analysis\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  6de2beaf-f80e-4788-8598-229a1c582757[\"Output\\nrmsd_tabular_output\"];\n  2 --> 6de2beaf-f80e-4788-8598-229a1c582757;\n  style 6de2beaf-f80e-4788-8598-229a1c582757 stroke:#2c3143,stroke-width:4px;\n  3[\"RMSF Analysis\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  1f2d715d-230a-4ec5-a509-e8ae501e7634[\"Output\\nrmsf_tabular_output\"];\n  3 --> 1f2d715d-230a-4ec5-a509-e8ae501e7634;\n  style 1f2d715d-230a-4ec5-a509-e8ae501e7634 stroke:#2c3143,stroke-width:4px;\n  4[\"PCA\"];\n  0 -->|output| 4;\n  1 -->|output| 4;\n  92b7a40f-9ffc-4f56-8cf3-deec52e7b8b5[\"Output\\npca_tabular_output\"];\n  4 --> 92b7a40f-9ffc-4f56-8cf3-deec52e7b8b5;\n  style 92b7a40f-9ffc-4f56-8cf3-deec52e7b8b5 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
+                "modified": "2024-10-02 12:08:06 +0000",
                 "name": "Simple Analysis",
                 "outputs": [
                     {
@@ -33919,829 +36528,191 @@
                                 "type": "png"
                             },
                             {
-                                "name": "rmsd_hist_plot",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 439,
-                            "top": 200
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsd/bio3d_rmsd/2.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "75fd897bd85d",
-                            "name": "bio3d_rmsd",
-                            "owner": "chemteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__page__\": null, \"rmsd\": \"{\\\"sele\\\": \\\"calpha\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"pdbin\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"dcdin\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "2.3",
-                        "type": "tool",
-                        "uuid": "5b0988f7-6cb1-4dfc-95b5-d5493d77d579",
-                        "workflow_outputs": [
-                            {
-                                "label": "rmsd_tabular_output",
-                                "output_name": "output",
-                                "uuid": "6de2beaf-f80e-4788-8598-229a1c582757"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsf/bio3d_rmsf/2.3",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "dcdin": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "pdbin": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool RMSF Analysis",
-                                "name": "pdbin"
-                            },
-                            {
-                                "description": "runtime parameter for tool RMSF Analysis",
-                                "name": "dcdin"
-                            }
-                        ],
-                        "label": null,
-                        "name": "RMSF Analysis",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "rmsf_plot",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 535,
-                            "top": 397
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsf/bio3d_rmsf/2.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "e838317708a6",
-                            "name": "bio3d_rmsf",
-                            "owner": "chemteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__page__\": null, \"rmsf\": \"{\\\"sele\\\": \\\"calpha\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"pdbin\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"dcdin\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "2.3",
-                        "type": "tool",
-                        "uuid": "aebc72d2-95bd-4b94-aa49-f8fbd55e7d54",
-                        "workflow_outputs": [
-                            {
-                                "label": "rmsf_tabular_output",
-                                "output_name": "output",
-                                "uuid": "1f2d715d-230a-4ec5-a509-e8ae501e7634"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca/bio3d_pca/2.3",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "dcdin": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "pdbin": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool PCA",
-                                "name": "pdbin"
-                            },
-                            {
-                                "description": "runtime parameter for tool PCA",
-                                "name": "dcdin"
-                            }
-                        ],
-                        "label": null,
-                        "name": "PCA",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "pca_plot",
-                                "type": "png"
-                            },
-                            {
-                                "name": "pca_cluster",
-                                "type": "png"
-                            },
-                            {
-                                "name": "pc1_rmsf",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 423,
-                            "top": 592
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca/bio3d_pca/2.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f56fb2762abb",
-                            "name": "bio3d_pca",
-                            "owner": "chemteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"dcdin\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"pdbin\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"pca\": \"{\\\"sele\\\": \\\"calpha\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"method\": \"\\\"false\\\"\"}",
-                        "tool_version": "2.3",
-                        "type": "tool",
-                        "uuid": "99415486-79b9-47d1-8111-02d0e6dcbed6",
-                        "workflow_outputs": [
-                            {
-                                "label": "pca_tabular_output",
-                                "output_name": "output",
-                                "uuid": "92b7a40f-9ffc-4f56-8cf3-deec52e7b8b5"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "computational-chemistry/analysis-md-simulations",
-                "path": "topics/computational-chemistry/tutorials/analysis-md-simulations/workflows/main_workflow.ga",
-                "tags": [
-                    "computational-chemistry"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "Simple Analysis",
-                "topic_id": "computational-chemistry",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/computational-chemistry-analysis-md-simulations/versions/main-workflow",
-                "tutorial_id": "analysis-md-simulations",
-                "url": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/analysis-md-simulations/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/analysis-md-simulations/workflows/main_workflow.html",
-                "version": 5,
-                "wfid": "computational-chemistry-analysis-md-simulations",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca/bio3d_pca/2.3",
-                    "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsd/bio3d_rmsd/2.3",
-                    "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsf/bio3d_rmsf/2.3"
-                ],
-                "workflowhub_id": "1122"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/2537734"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "align_it",
-                    "owner": "bgruening",
-                    "revisions": "06d9381593a4",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openbabel_addh",
-                    "owner": "bgruening",
-                    "revisions": "6e4b7e0c61a6",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "rdconf",
-                    "owner": "bgruening",
-                    "revisions": "5c501eb8d56c",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "split_file_to_collection",
-                    "owner": "bgruening",
-                    "revisions": "6cbe2f30c2d7",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: align_it\n  owner: bgruening\n  revisions: 06d9381593a4\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_addh\n  owner: bgruening\n  revisions: 6e4b7e0c61a6\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rdconf\n  owner: bgruening\n  revisions: 5c501eb8d56c\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_to_collection\n  owner: bgruening\n  revisions: 6cbe2f30c2d7\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/zauberkugel/tutorial.json",
-        "contributors": [
-            {
-                "email": "amaf.aurelien@yahoo.com",
-                "id": "aurelienmoumbock",
-                "joined": "2022-02",
-                "name": "Aur\u00e9lien F. A. Moumbock",
-                "orcid": "0000-0002-6034-2016",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/aurelienmoumbock/",
-                "twitter": "FMoumbock",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/aurelienmoumbock.json"
-            },
-            {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "simonbray",
-                "joined": "2019-05",
-                "name": "Simon Bray",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
-            }
-        ],
-        "dir": "topics/computational-chemistry/tutorials/zauberkugel",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "computational-chemistry/zauberkugel",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": 6049,
-            "mermaid": false
-        },
-        "key_points": [
-            "A pharmacophore is an abstract description of the molecular features of a bioactive ligand.",
-            "Pharmacophore-based target prediction is an efficient and cost-effective method."
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
-        "objectives": [
-            "Create an SMILES file of a bioactive ligand.",
-            "Screen the query ligand against a pharmacophore library.",
-            "Analyze the results of the protein target prediction."
-        ],
-        "pageviews": 1438,
-        "pub_date": "2022-02-15",
-        "questions": [
-            "What is a pharmacophore model?",
-            "How can I perform protein target prediction with a multi-step workflow or the one-step Zauberkugel workflow?"
-        ],
-        "short_id": "T00054",
-        "short_tools": [
-            "sort1",
-            "tp_cat",
-            "ctb_alignit",
-            "split_file_to_collection",
-            "rdconf",
-            "openbabel_addh"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": []
-        },
-        "symlink": null,
-        "time_estimation": "2H",
-        "title": "Protein target prediction of a bioactive ligand with Align-it and ePharmaLib",
-        "tools": [
-            "sort1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/align_it/ctb_alignit/1.0.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_addh/openbabel_addh/3.1.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/rdconf/rdconf/2020.03.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1"
-        ],
-        "topic_name": "computational-chemistry",
-        "topic_name_human": "Computational chemistry",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "zauberkugel",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/computational-chemistry/tutorials/zauberkugel/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/zauberkugel/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/zauberkugel/tutorial.json"
-        },
-        "version": 10,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 941,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "email": "mailto:amaf.aurelien@yahoo.com",
-                        "identifier": "https://orcid.org/0000-0002-6034-2016",
-                        "name": "Aur\u00e9lien F. A. Moumbock"
-                    },
-                    {
-                        "class": "Organization",
-                        "name": "Albert-Ludwigs-Universit\u00e4t Freiburg"
-                    }
-                ],
-                "description": "Protein target prediction of a bioactive ligand with Align-it and ePharmaLib",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nQuery ligand\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPharmacophore library\"]\n  2[label=\"Ligand ionization state generation\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Splitting ePharmaLib into individual pharmacophores\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\" Low-energy ligand conformer search\"]\n  2 -> 4 [label=\"outfile\"]\n  5[label=\"Pharmacophore alignment\"]\n  4 -> 5 [label=\"outfile\"]\n  3 -> 5 [label=\"list_output_generic\"]\n  6[label=\"Concatenating the pharmacophore alignment scores\"]\n  5 -> 6 [label=\"score_result_file\"]\n  7[label=\"Ranking the predicted protein targets according to the Tversky index 10th column\"]\n  6 -> 7 [label=\"out_file1\"]\n}",
-                "history": [
-                    {
-                        "hash": "b70afe30388f2cf2023a1abb8d7d6130721467b2",
-                        "message": "annotate workflow for gtn linting",
-                        "num": 3,
-                        "short_hash": "b70afe303",
-                        "unix": "1644931554"
-                    },
-                    {
-                        "hash": "506069da4d92df0665a2c7ed4de1bfc40345cf22",
-                        "message": "pretty print pharmacophore workflow",
-                        "num": 2,
-                        "short_hash": "506069da4",
-                        "unix": "1644582976"
-                    },
-                    {
-                        "hash": "fdd280bcf8dfeccdd087f4822150679914725469",
-                        "message": "Add files via upload",
-                        "num": 1,
-                        "short_hash": "fdd280bcf",
-                        "unix": "1644350636"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Query ligand"
-                            }
-                        ],
-                        "label": "Query ligand",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 747.5521469116211,
-                            "height": 62.083335876464844,
-                            "left": 559.0104370117188,
-                            "right": 759.0104522705078,
-                            "top": 685.4688110351562,
-                            "width": 200.00001525878906,
-                            "x": 559.0104370117188,
-                            "y": 685.4688110351562
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"smi\"]}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "63eee683-907c-40a4-b801-d977e0b2cb3e",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Pharmacophore library"
-                            }
-                        ],
-                        "label": "Pharmacophore library",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 1033.8889236450195,
-                            "height": 82.46527862548828,
-                            "left": 780.9375610351562,
-                            "right": 980.9375762939453,
-                            "top": 951.4236450195312,
-                            "width": 200.00001525878906,
-                            "x": 780.9375610351562,
-                            "y": 951.4236450195312
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"phar\"]}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "004f025f-dafc-4d26-8aec-88a64d013852",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQuery ligand\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nPharmacophore library\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Ligand ionization state generation\"];\n  0 -->|output| 2;\n  3[\"Splitting ePharmaLib into individual pharmacophores\"];\n  1 -->|output| 3;\n  4[\" Low-energy ligand conformer search\"];\n  2 -->|outfile| 4;\n  5[\"Pharmacophore alignment\"];\n  4 -->|outfile| 5;\n  3 -->|list_output_generic| 5;\n  6[\"Concatenating the pharmacophore alignment scores\"];\n  5 -->|score_result_file| 6;\n  7[\"Ranking the predicted protein targets according to the Tversky index 10th column\"];\n  6 -->|out_file1| 7;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Zauberkugel",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_addh/openbabel_addh/3.1.1+galaxy1",
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "infile": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Ligand ionization state generation",
-                        "name": "Add hydrogen atoms",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 746.4236679077148,
-                            "height": 113.95833587646484,
-                            "left": 776.99658203125,
-                            "right": 976.9965972900391,
-                            "top": 632.46533203125,
-                            "width": 200.00001525878906,
-                            "x": 776.99658203125,
-                            "y": 632.46533203125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_addh/openbabel_addh/3.1.1+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6e4b7e0c61a6",
-                            "name": "openbabel_addh",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"infile\": {\"__class__\": \"ConnectedValue\"}, \"pH_value\": \"7.4\", \"polar\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.1+galaxy1",
-                        "type": "tool",
-                        "uuid": "857b1ca0-d39a-463f-9840-cf2c7e6b363f",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "24b52c0f-f6e2-4d14-bd92-2aa620c91d83"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "split_parms|input": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Splitting ePharmaLib into individual pharmacophores",
-                        "name": "Split file",
-                        "outputs": [
-                            {
-                                "name": "list_output_generic",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 1036.1979370117188,
-                            "height": 154.72222900390625,
-                            "left": 1009.982666015625,
-                            "right": 1209.982681274414,
-                            "top": 881.4757080078125,
-                            "width": 200.00001525878906,
-                            "x": 1009.982666015625,
-                            "y": 881.4757080078125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6cbe2f30c2d7",
-                            "name": "split_file_to_collection",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"split_parms\": {\"select_ftype\": \"generic\", \"__current_case__\": 6, \"input\": {\"__class__\": \"ConnectedValue\"}, \"split_method\": {\"select_split_method\": \"regex\", \"__current_case__\": 0, \"generic_regex\": \"\\\\$\\\\$\\\\$\\\\$\", \"split_after\": \"true\"}, \"select_mode\": {\"mode\": \"chunk\", \"__current_case__\": 0, \"chunksize\": \"1\"}, \"newfilenames\": \"epharmalib\", \"select_allocate\": {\"allocate\": \"batch\", \"__current_case__\": 1}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.5.0",
-                        "type": "tool",
-                        "uuid": "1baf3f94-2aa7-42e9-968e-959fffcc462b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "list_output_generic",
-                                "uuid": "6d0c53e6-2607-410f-a529-3fc4cd1d70b4"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/rdconf/rdconf/2020.03.4+galaxy0",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "infile": {
-                                "id": 2,
-                                "output_name": "outfile"
-                            }
-                        },
-                        "inputs": [],
-                        "label": " Low-energy ligand conformer search",
-                        "name": "RDConf: Low-energy ligand conformer search",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "sdf"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 784.18408203125,
-                            "height": 154.72222900390625,
-                            "left": 1001.0070190429688,
-                            "right": 1201.0070343017578,
-                            "top": 629.4618530273438,
-                            "width": 200.00001525878906,
-                            "x": 1001.0070190429688,
-                            "y": 629.4618530273438
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/rdconf/rdconf/2020.03.4+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "5c501eb8d56c",
-                            "name": "rdconf",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"CNT\": \"100\", \"E\": \"10.0\", \"N\": \"1\", \"R\": \"0.7\", \"etkdg\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mmff\": \"false\", \"nomin\": \"false\", \"s\": \"9162006\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2020.03.4+galaxy0",
-                        "type": "tool",
-                        "uuid": "0c02c9e1-8579-4370-aa2e-575956b017cc",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "04f08403-a7e1-4350-94e0-17af711f0113"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/align_it/ctb_alignit/1.0.4+galaxy0",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "database": {
-                                "id": 4,
-                                "output_name": "outfile"
-                            },
-                            "reference": {
-                                "id": 3,
-                                "output_name": "list_output_generic"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Pharmacophore alignment",
-                        "outputs": [
-                            {
-                                "name": "aligned_pharmacophores",
-                                "type": "phar"
-                            },
-                            {
-                                "name": "aligned_structures",
-                                "type": "smi"
-                            },
-                            {
-                                "name": "score_result_file",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 1037.3438110351562,
-                            "height": 408.92364501953125,
-                            "left": 1244.010498046875,
-                            "right": 1444.010513305664,
-                            "top": 628.420166015625,
-                            "width": 200.00001525878906,
-                            "x": 1244.010498046875,
-                            "y": 628.420166015625
+                                "name": "rmsd_hist_plot",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 439,
+                            "top": 200
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/align_it/ctb_alignit/1.0.4+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsd/bio3d_rmsd/2.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "06d9381593a4",
-                            "name": "align_it",
-                            "owner": "bgruening",
+                            "changeset_revision": "75fd897bd85d",
+                            "name": "bio3d_rmsd",
+                            "owner": "chemteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"best\": \"1\", \"cutoff\": \"0.5\", \"database\": {\"__class__\": \"ConnectedValue\"}, \"epsilon\": \"0.5\", \"fgroups\": [\"AROM\", \"HDON\", \"HACC\", \"LIPO\", \"CHARGE\"], \"merge\": \"false\", \"noHybrid\": \"true\", \"noNormal\": \"true\", \"oformat\": \"smi\", \"rankBy\": \"TVERSKY_REF\", \"reference\": {\"__class__\": \"ConnectedValue\"}, \"scoreOnly\": \"false\", \"withExclusion\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.4+galaxy0",
+                        "tool_state": "{\"__page__\": null, \"rmsd\": \"{\\\"sele\\\": \\\"calpha\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"pdbin\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"dcdin\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "2.3",
                         "type": "tool",
-                        "uuid": "5d8f4ad4-8831-405f-8cef-7a9d0c114ddd",
+                        "uuid": "5b0988f7-6cb1-4dfc-95b5-d5493d77d579",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "aligned_pharmacophores",
-                                "uuid": "7a9ad93a-e27c-48f2-a17e-afd5afcc5c47"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "score_result_file",
-                                "uuid": "ec32ab04-d509-48ac-94c4-145a1547a134"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "aligned_structures",
-                                "uuid": "d3dd55d0-472a-4d38-b0c0-f5d61ecf167f"
+                                "label": "rmsd_tabular_output",
+                                "output_name": "output",
+                                "uuid": "6de2beaf-f80e-4788-8598-229a1c582757"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsf/bio3d_rmsf/2.3",
                         "errors": null,
-                        "id": 6,
+                        "id": 3,
                         "input_connections": {
-                            "inputs": {
-                                "id": 5,
-                                "output_name": "score_result_file"
+                            "dcdin": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "pdbin": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": "Concatenating the pharmacophore alignment scores",
-                        "name": "Concatenate datasets",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool RMSF Analysis",
+                                "name": "pdbin"
+                            },
+                            {
+                                "description": "runtime parameter for tool RMSF Analysis",
+                                "name": "dcdin"
+                            }
+                        ],
+                        "label": null,
+                        "name": "RMSF Analysis",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "output",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "rmsf_plot",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": 783.1423950195312,
-                            "height": 154.72222900390625,
-                            "left": 1475.9896240234375,
-                            "right": 1675.9896392822266,
-                            "top": 628.420166015625,
-                            "width": 200.00001525878906,
-                            "x": 1475.9896240234375,
-                            "y": 628.420166015625
+                            "left": 535,
+                            "top": 397
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsf/bio3d_rmsf/2.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "f46f0e4f75c4",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "e838317708a6",
+                            "name": "bio3d_rmsf",
+                            "owner": "chemteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.1",
+                        "tool_state": "{\"__page__\": null, \"rmsf\": \"{\\\"sele\\\": \\\"calpha\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"pdbin\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"dcdin\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "2.3",
                         "type": "tool",
-                        "uuid": "c3b7d2a3-b06e-4a4f-aee2-a2b8941ebfdb",
+                        "uuid": "aebc72d2-95bd-4b94-aa49-f8fbd55e7d54",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "9cfedc75-e78a-4425-b8dc-2019f1d8479d"
+                                "label": "rmsf_tabular_output",
+                                "output_name": "output",
+                                "uuid": "1f2d715d-230a-4ec5-a509-e8ae501e7634"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "sort1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca/bio3d_pca/2.3",
                         "errors": null,
-                        "id": 7,
+                        "id": 4,
                         "input_connections": {
-                            "input": {
-                                "id": 6,
-                                "output_name": "out_file1"
+                            "dcdin": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "pdbin": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": "Ranking the predicted protein targets according to the Tversky index (10th column)",
-                        "name": "Sort",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool PCA",
+                                "name": "pdbin"
+                            },
+                            {
+                                "description": "runtime parameter for tool PCA",
+                                "name": "dcdin"
+                            }
+                        ],
+                        "label": null,
+                        "name": "PCA",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "output",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "pca_plot",
+                                "type": "png"
+                            },
+                            {
+                                "name": "pca_cluster",
+                                "type": "png"
+                            },
+                            {
+                                "name": "pc1_rmsf",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": 782.2048950195312,
-                            "height": 154.72222900390625,
-                            "left": 1700.0001220703125,
-                            "right": 1900.0001373291016,
-                            "top": 627.482666015625,
-                            "width": 200.00001525878906,
-                            "x": 1700.0001220703125,
-                            "y": 627.482666015625
+                            "left": 423,
+                            "top": 592
                         },
-                        "post_job_actions": {
-                            "EmailActionout_file1": {
-                                "action_arguments": {},
-                                "action_type": "EmailAction",
-                                "output_name": "out_file1"
-                            }
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca/bio3d_pca/2.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f56fb2762abb",
+                            "name": "bio3d_pca",
+                            "owner": "chemteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": "sort1",
-                        "tool_state": "{\"column\": \"10\", \"column_set\": [], \"header_lines\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"order\": \"DESC\", \"style\": \"num\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.0",
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"dcdin\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"pdbin\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"pca\": \"{\\\"sele\\\": \\\"calpha\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"method\": \"\\\"false\\\"\"}",
+                        "tool_version": "2.3",
                         "type": "tool",
-                        "uuid": "3bbbee13-46e9-48ad-9ecc-c874da658723",
+                        "uuid": "99415486-79b9-47d1-8111-02d0e6dcbed6",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "f1cb518a-3021-44b3-a03c-2443d7cddc91"
+                                "label": "pca_tabular_output",
+                                "output_name": "output",
+                                "uuid": "92b7a40f-9ffc-4f56-8cf3-deec52e7b8b5"
                             }
                         ]
                     }
                 ],
-                "parent_id": "computational-chemistry/zauberkugel",
-                "path": "topics/computational-chemistry/tutorials/zauberkugel/workflows/main_workflow.ga",
+                "parent_id": "computational-chemistry/analysis-md-simulations",
+                "path": "topics/computational-chemistry/tutorials/analysis-md-simulations/workflows/main_workflow.ga",
                 "tags": [
-                    "cheminformatics",
                     "computational-chemistry"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "Zauberkugel",
+                "tests": true,
+                "title": "Simple Analysis",
                 "topic_id": "computational-chemistry",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/computational-chemistry-zauberkugel/versions/main-workflow",
-                "tutorial_id": "zauberkugel",
-                "url": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/zauberkugel/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/zauberkugel/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "computational-chemistry-zauberkugel",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/computational-chemistry-analysis-md-simulations/versions/main-workflow",
+                "tutorial_id": "analysis-md-simulations",
+                "url": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/analysis-md-simulations/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/analysis-md-simulations/workflows/main_workflow.html",
+                "version": 5,
+                "wfid": "computational-chemistry-analysis-md-simulations",
                 "wfname": "main-workflow",
                 "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "sort1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/align_it/ctb_alignit/1.0.4+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_addh/openbabel_addh/3.1.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/rdconf/rdconf/2020.03.4+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1"
+                    "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca/bio3d_pca/2.3",
+                    "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsd/bio3d_rmsd/2.3",
+                    "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsf/bio3d_rmsf/2.3"
                 ],
-                "workflowhub_id": "1082"
+                "workflowhub_id": "1122"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/6055897"
+        "zenodo_link": "https://zenodo.org/record/2537734"
     },
     {
         "admin_install": {
@@ -34905,7 +36876,7 @@
             "Replicate the study on a (very) small scale",
             "Gain familiarity with the docking and scoring techniques involved."
         ],
-        "pageviews": 4516,
+        "pageviews": 4568,
         "pub_date": "2020-03-27",
         "questions": [
             "How can candidate ligands be generated and docked to a protein in Galaxy?",
@@ -34923,18 +36894,18 @@
         ],
         "short_id": "T00049",
         "short_tools": [
-            "enumerate_charges",
-            "xchem_transfs_scoring",
-            "rdock_rbdock",
-            "rdock_rbcavity",
-            "rxdock_rbcavity",
-            "xchem_pose_scoring",
             "openbabel_compound_convert",
             "split_file_to_collection",
-            "ctb_frankenstein_ligand",
+            "enumerate_charges",
+            "rxdock_rbcavity",
             "sucos_max_score",
             "collapse_dataset",
-            "rxdock_rbdock"
+            "xchem_pose_scoring",
+            "rxdock_rbdock",
+            "ctb_frankenstein_ligand",
+            "rdock_rbdock",
+            "rdock_rbcavity",
+            "xchem_transfs_scoring"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -34987,8 +36958,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 178,
-        "visitors": 2664,
+        "visit_duration": 179,
+        "visitors": 2706,
         "workflows": [
             {
                 "creators": [],
@@ -35130,7 +37101,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nCandidates\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nMpro-x0195_0_apo-desolv.pdb\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nhits.sdf\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Enumerate changes\"];\n  0 -->|output| 3;\n  4[\"Compound conversion\"];\n  1 -->|output| 4;\n  5[\"Create Frankenstein ligand\"];\n  2 -->|output| 5;\n  6[\"Compound conversion\"];\n  3 -->|output| 6;\n  7[\"rDock cavity definition\"];\n  4 -->|outfile| 7;\n  5 -->|outfile| 7;\n  8[\"Split file\"];\n  6 -->|outfile| 8;\n  9[\"rDock docking\"];\n  4 -->|outfile| 9;\n  8 -->|list_output_sdf| 9;\n  7 -->|activesite| 9;\n  10[\"Collapse Collection\"];\n  9 -->|output| 10;\n  11[\"XChem TransFS pose scoring\"];\n  1 -->|output| 11;\n  10 -->|output| 11;\n  12[\"Max SuCOS score\"];\n  11 -->|output| 12;\n  2 -->|output| 12;",
-                "modified": "2024-08-18 00:06:21 +0000",
+                "modified": "2024-10-02 12:08:06 +0000",
                 "name": "Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring",
                 "outputs": [
                     {
@@ -35319,410 +37290,32 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "autodock_vina",
-                    "owner": "bgruening",
-                    "revisions": "7a871df65202",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "autodock_vina_prepare_box",
-                    "owner": "bgruening",
-                    "revisions": "668c60aa4799",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "autodock_vina_prepare_receptor",
-                    "owner": "bgruening",
-                    "revisions": "05a13d377b28",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "chembl",
-                    "owner": "bgruening",
-                    "revisions": "a446ea7e2bc1",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "chemfp",
-                    "owner": "bgruening",
-                    "revisions": "73de2fe4bf92",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "chemfp",
-                    "owner": "bgruening",
-                    "revisions": "43a9e7d9b24f",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "chemfp",
-                    "owner": "bgruening",
-                    "revisions": "73de2fe4bf92",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "chemfp",
-                    "owner": "bgruening",
-                    "revisions": "e3a7d6cc87af",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "chemfp",
-                    "owner": "bgruening",
-                    "revisions": "73de2fe4bf92",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "chemical_data_sources",
-                    "owner": "bgruening",
-                    "revisions": "c2055dd1927b",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fpocket",
-                    "owner": "bgruening",
-                    "revisions": "4fb73be7f4cb",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "get_pdb",
-                    "owner": "bgruening",
-                    "revisions": "538790c6c21b",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "natural_product_likeness",
-                    "owner": "bgruening",
-                    "revisions": "6052dd3fa475",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openbabel_compound_convert",
+                    "name": "align_it",
                     "owner": "bgruening",
-                    "revisions": "e2c36f62e22f",
+                    "revisions": "06d9381593a4",
                     "tool_panel_section_label": "ChemicalToolBox",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "openbabel_svg_depiction",
+                    "name": "openbabel_addh",
                     "owner": "bgruening",
-                    "revisions": "7672039a0bb0",
+                    "revisions": "7b6fd1c273cd",
                     "tool_panel_section_label": "ChemicalToolBox",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sdf_to_tab",
+                    "name": "rdconf",
                     "owner": "bgruening",
-                    "revisions": "4beb3e026bbb",
+                    "revisions": "5c501eb8d56c",
                     "tool_panel_section_label": "ChemicalToolBox",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "f46f0e4f75c4",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
+                    "name": "split_file_to_collection",
                     "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "830961c48e42",
+                    "revisions": "6cbe2f30c2d7",
                     "tool_panel_section_label": "Collection Operations",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: autodock_vina\n  owner: bgruening\n  revisions: 7a871df65202\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: autodock_vina_prepare_box\n  owner: bgruening\n  revisions: 668c60aa4799\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: autodock_vina_prepare_receptor\n  owner: bgruening\n  revisions: 05a13d377b28\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chembl\n  owner: bgruening\n  revisions: a446ea7e2bc1\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chemfp\n  owner: bgruening\n  revisions: 73de2fe4bf92\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chemfp\n  owner: bgruening\n  revisions: 43a9e7d9b24f\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chemfp\n  owner: bgruening\n  revisions: 73de2fe4bf92\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chemfp\n  owner: bgruening\n  revisions: e3a7d6cc87af\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chemfp\n  owner: bgruening\n  revisions: 73de2fe4bf92\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chemical_data_sources\n  owner: bgruening\n  revisions: c2055dd1927b\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fpocket\n  owner: bgruening\n  revisions: 4fb73be7f4cb\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: get_pdb\n  owner: bgruening\n  revisions: 538790c6c21b\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: natural_product_likeness\n  owner: bgruening\n  revisions: 6052dd3fa475\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_compound_convert\n  owner: bgruening\n  revisions: e2c36f62e22f\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_svg_depiction\n  owner: bgruening\n  revisions: 7672039a0bb0\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sdf_to_tab\n  owner: bgruening\n  revisions: 4beb3e026bbb\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: f46f0e4f75c4\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/cheminformatics/tutorial.json",
-        "contributors": [
-            {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "simonbray",
-                "joined": "2019-05",
-                "name": "Simon Bray",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
-            }
-        ],
-        "dir": "topics/computational-chemistry/tutorials/cheminformatics",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "computational-chemistry/cheminformatics",
-        "inexact_supported_servers": [
-            "UseGalaxy.org (Main)"
-        ],
-        "js_requirements": {
-            "mathjax": 16452,
-            "mermaid": false
-        },
-        "key_points": [
-            "Docking allows 'virtual screening' of drug candidates",
-            "Molecular fingerprints encode features into a bitstring",
-            "The ChemicalToolbox contains many tools for cheminformatics analysis"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Create a small compound library using the ChEMBL database",
-            "Dock a variety of ligands to the active site of the Hsp90 protein"
-        ],
-        "pageviews": 27617,
-        "pub_date": "2019-10-19",
-        "questions": [
-            "What is cheminformatics?",
-            "What is protein-ligand docking?",
-            "How can I perform a simple docking workflow in Galaxy?"
-        ],
-        "short_id": "T00048",
-        "short_tools": [
-            "ctb_remDuplicates",
-            "sdf_to_tab",
-            "ctb_chemfp_nxn_clustering",
-            "fpocket",
-            "collapse_dataset",
-            "openbabel_svg_depiction",
-            "ctb_remIons",
-            "prepare_receptor",
-            "openbabel_compound_convert",
-            "ctb_np-likeness-calculator",
-            "ctb_obgrep",
-            "tp_find_and_replace",
-            "tp_cat",
-            "chembl",
-            "ctb_chemfp_butina_clustering",
-            "prepare_box",
-            "ctb_filter",
-            "ctb_online_data_fetch",
-            "ctb_compound_convert",
-            "docking",
-            "tp_grep_tool",
-            "get_pdb",
-            "ctb_change_title",
-            "ctb_chemfp_mol2fps"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "time_estimation": "3H",
-        "title": "Protein-ligand docking",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/1.1.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina_prepare_box/prepare_box/2021.03.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina_prepare_receptor/prepare_receptor/1.5.7+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/chembl/chembl/0.10.1+galaxy4",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_butina_clustering/1.5",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/0.2.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/1.5",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_nxn_clustering/0.4",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_nxn_clustering/1.5.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/chemical_data_sources/ctb_online_data_fetch/0.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/fpocket/fpocket/3.1.4.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/get_pdb/get_pdb/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/natural_product_likeness/ctb_np-likeness-calculator/2.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_change_title/0.0.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_compound_convert/0.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_filter/1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_obgrep/0.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remDuplicates/1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remIons/1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_svg_depiction/openbabel_svg_depiction/3.1.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/sdf_to_tab/sdf_to_tab/2020.03.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
-        ],
-        "topic_name": "computational-chemistry",
-        "topic_name_human": "Computational chemistry",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "cheminformatics",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/computational-chemistry/tutorials/cheminformatics/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/cheminformatics/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/cheminformatics/tutorial.json"
-        },
-        "version": 16,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 88,
-        "visitors": 15451,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "CTB Unittest workflow",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  11[label=\"Compound Search\"]\n  5 -> 11 [label=\"outfile\"]\n  13[label=\"Remove duplicated molecules\"]\n  5 -> 13 [label=\"outfile\"]\n  19[label=\"Remove counterions and fragments\"]\n  13 -> 19 [label=\"outfile\"]\n  2[label=\"Online data\"]\n  29[label=\"Filter\"]\n  19 -> 29 [label=\"outfile\"]\n  30[label=\"Compound Convert\"]\n  19 -> 30 [label=\"outfile\"]\n  31[label=\"Molecules to Fingerprints\"]\n  19 -> 31 [label=\"outfile\"]\n  39[label=\"Natural Product\"]\n  29 -> 39 [label=\"outfile\"]\n  40[label=\"Molecules to Fingerprints\"]\n  29 -> 40 [label=\"outfile\"]\n  44[label=\"NxN Clustering\"]\n  40 -> 44 [label=\"outfile\"]\n  5[label=\"Change Title\"]\n  2 -> 5 [label=\"output\"]\n}",
-                "history": [
-                    {
-                        "hash": "52ea0ed9ee0a8920a6831112d60295283db993ee",
-                        "message": "editing the workflow using the workflow editor",
-                        "num": 6,
-                        "short_hash": "52ea0ed9e",
-                        "unix": "1582108026"
-                    },
-                    {
-                        "hash": "d681f0586063602176dd9f0a0c3b6901e1252c44",
-                        "message": "disabled workflow with testtools",
-                        "num": 5,
-                        "short_hash": "d681f0586",
-                        "unix": "1579166204"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 4,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "7da80b34185f4165852feb3bfe80d692609685db",
-                        "message": "Workflows fix",
-                        "num": 3,
-                        "short_hash": "7da80b341",
-                        "unix": "1578668175"
-                    },
-                    {
-                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
-                        "message": "unflatten workflows",
-                        "num": 2,
-                        "short_hash": "faf6d298a",
-                        "unix": "1576155753"
-                    },
-                    {
-                        "hash": "aa2ef61fb0b97cf82ea068696454cf18f729f01b",
-                        "message": "initial cheminformatics commit",
-                        "num": 1,
-                        "short_hash": "aa2ef61fb",
-                        "unix": "1560350110"
-                    }
-                ],
-                "inputs": [],
-                "license": null,
-                "mermaid": "flowchart TD\n  11[\"Compound Search\"];\n  5 -->|outfile| 11;\n  13[\"Remove duplicated molecules\"];\n  5 -->|outfile| 13;\n  19[\"Remove counterions and fragments\"];\n  13 -->|outfile| 19;\n  2[\"Online data\"];\n  29[\"Filter\"];\n  19 -->|outfile| 29;\n  30[\"Compound Convert\"];\n  19 -->|outfile| 30;\n  31[\"Molecules to Fingerprints\"];\n  19 -->|outfile| 31;\n  39[\"Natural Product\"];\n  29 -->|outfile| 39;\n  40[\"Molecules to Fingerprints\"];\n  29 -->|outfile| 40;\n  44[\"NxN Clustering\"];\n  40 -->|outfile| 44;\n  5[\"Change Title\"];\n  2 -->|output| 5;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "CTB Workflow",
-                "outputs": [],
-                "parent_id": "computational-chemistry/cheminformatics",
-                "path": "topics/computational-chemistry/tutorials/cheminformatics/workflows/main_workflow.ga",
-                "tags": [
-                    "computational-chemistry"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "CTB Workflow",
-                "topic_id": "computational-chemistry",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/computational-chemistry-cheminformatics/versions/main-workflow",
-                "tutorial_id": "cheminformatics",
-                "url": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/cheminformatics/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/cheminformatics/workflows/main_workflow.html",
-                "version": 4,
-                "wfid": "computational-chemistry-cheminformatics",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/0.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_nxn_clustering/0.4",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/chemical_data_sources/ctb_online_data_fetch/0.2",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/natural_product_likeness/ctb_np-likeness-calculator/2.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_change_title/0.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_compound_convert/0.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_filter/1.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_obgrep/0.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remDuplicates/1.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remIons/1.0"
-                ],
-                "workflowhub_id": "1075"
-            }
-        ],
-        "zenodo_link": ""
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "get_pdb",
-                    "owner": "bgruening",
-                    "revisions": "538790c6c21b",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openbabel_compound_convert",
-                    "owner": "bgruening",
-                    "revisions": "b59c91adeac1",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openbabel_compound_convert",
-                    "owner": "bgruening",
-                    "revisions": "e2c36f62e22f",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "text_processing",
@@ -35730,180 +37323,22 @@
                     "revisions": "d698c222f354",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ambertools_acpype",
-                    "owner": "chemteam",
-                    "revisions": "f4230f116196",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ambertools_acpype",
-                    "owner": "chemteam",
-                    "revisions": "6ca543ec1bf8",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bio3d_pca",
-                    "owner": "chemteam",
-                    "revisions": "24867ab16f36",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bio3d_pca_visualize",
-                    "owner": "chemteam",
-                    "revisions": "f61a718993fd",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bio3d_rmsd",
-                    "owner": "chemteam",
-                    "revisions": "77e28e1da9f4",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bio3d_rmsf",
-                    "owner": "chemteam",
-                    "revisions": "6bcb804a54c3",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gmx_editconf",
-                    "owner": "chemteam",
-                    "revisions": "3b8a9d5ced85",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gmx_editconf",
-                    "owner": "chemteam",
-                    "revisions": "0fac8e2afc13",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gmx_em",
-                    "owner": "chemteam",
-                    "revisions": "eb6564a60136",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gmx_em",
-                    "owner": "chemteam",
-                    "revisions": "f5d979cb4b54",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gmx_energy",
-                    "owner": "chemteam",
-                    "revisions": "d2f955aea23a",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gmx_merge_topology_files",
-                    "owner": "chemteam",
-                    "revisions": "d1d0efda35c0",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gmx_merge_topology_files",
-                    "owner": "chemteam",
-                    "revisions": "319a28774da9",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gmx_setup",
-                    "owner": "chemteam",
-                    "revisions": "cac1886249a2",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gmx_setup",
-                    "owner": "chemteam",
-                    "revisions": "2c349b027a01",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gmx_sim",
-                    "owner": "chemteam",
-                    "revisions": "2e219a2d9327",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gmx_sim",
-                    "owner": "chemteam",
-                    "revisions": "73008ef1f487",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gmx_solvate",
-                    "owner": "chemteam",
-                    "revisions": "1809414a9454",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gmx_solvate",
-                    "owner": "chemteam",
-                    "revisions": "2c8ed1b52bf7",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "md_converter",
-                    "owner": "chemteam",
-                    "revisions": "79e8ab8f1e81",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "md_converter",
-                    "owner": "chemteam",
-                    "revisions": "ba83f0923369",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mdanalysis_cosine_analysis",
-                    "owner": "chemteam",
-                    "revisions": "9a3a1f698fc6",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mdanalysis_cosine_analysis",
-                    "owner": "chemteam",
-                    "revisions": "48d6a6eb438b",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "vmd_hbonds",
-                    "owner": "chemteam",
-                    "revisions": "8aa5e465b043",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: get_pdb\n  owner: bgruening\n  revisions: 538790c6c21b\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_compound_convert\n  owner: bgruening\n  revisions: b59c91adeac1\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_compound_convert\n  owner: bgruening\n  revisions: e2c36f62e22f\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ambertools_acpype\n  owner: chemteam\n  revisions: f4230f116196\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ambertools_acpype\n  owner: chemteam\n  revisions: 6ca543ec1bf8\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bio3d_pca\n  owner: chemteam\n  revisions: 24867ab16f36\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bio3d_pca_visualize\n  owner: chemteam\n  revisions: f61a718993fd\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bio3d_rmsd\n  owner: chemteam\n  revisions: 77e28e1da9f4\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bio3d_rmsf\n  owner: chemteam\n  revisions: 6bcb804a54c3\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_editconf\n  owner: chemteam\n  revisions: 3b8a9d5ced85\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_editconf\n  owner: chemteam\n  revisions: 0fac8e2afc13\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_em\n  owner: chemteam\n  revisions: eb6564a60136\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_em\n  owner: chemteam\n  revisions: f5d979cb4b54\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_energy\n  owner: chemteam\n  revisions: d2f955aea23a\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_merge_topology_files\n  owner: chemteam\n  revisions: d1d0efda35c0\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_merge_topology_files\n  owner: chemteam\n  revisions: 319a28774da9\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_setup\n  owner: chemteam\n  revisions: cac1886249a2\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_setup\n  owner: chemteam\n  revisions: 2c349b027a01\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_sim\n  owner: chemteam\n  revisions: 2e219a2d9327\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_sim\n  owner: chemteam\n  revisions: 73008ef1f487\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_solvate\n  owner: chemteam\n  revisions: 1809414a9454\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gmx_solvate\n  owner: chemteam\n  revisions: 2c8ed1b52bf7\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: md_converter\n  owner: chemteam\n  revisions: 79e8ab8f1e81\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: md_converter\n  owner: chemteam\n  revisions: ba83f0923369\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mdanalysis_cosine_analysis\n  owner: chemteam\n  revisions: 9a3a1f698fc6\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mdanalysis_cosine_analysis\n  owner: chemteam\n  revisions: 48d6a6eb438b\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: vmd_hbonds\n  owner: chemteam\n  revisions: 8aa5e465b043\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: align_it\n  owner: bgruening\n  revisions: 06d9381593a4\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_addh\n  owner: bgruening\n  revisions: 7b6fd1c273cd\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rdconf\n  owner: bgruening\n  revisions: 5c501eb8d56c\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_to_collection\n  owner: bgruening\n  revisions: 6cbe2f30c2d7\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/zauberkugel/tutorial.json",
         "contributors": [
+            {
+                "email": "amaf.aurelien@yahoo.com",
+                "id": "aurelienmoumbock",
+                "joined": "2022-02",
+                "name": "Aur\u00e9lien F. A. Moumbock",
+                "orcid": "0000-0002-6034-2016",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/aurelienmoumbock/",
+                "twitter": "FMoumbock",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/aurelienmoumbock.json"
+            },
             {
                 "elixir_node": "de",
                 "former_affiliations": [
@@ -35915,146 +37350,57 @@
                 "name": "Simon Bray",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
-            },
-            {
-                "id": "tsenapathi",
-                "joined": "2019-05",
-                "name": "Tharindu Senapathi",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tsenapathi/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tsenapathi.json"
-            },
-            {
-                "id": "chrisbarnettster",
-                "joined": "2019-05",
-                "name": "Christopher Barnett",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/chrisbarnettster/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/chrisbarnettster.json"
-            },
-            {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
-                "fediverse_flavor": "mastodon",
-                "id": "bgruening",
-                "joined": "2017-09",
-                "linkedin": "bgruening",
-                "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
-                },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
             }
         ],
-        "dir": "topics/computational-chemistry/tutorials/htmd-analysis",
+        "dir": "topics/computational-chemistry/tutorials/zauberkugel",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.org (Main)",
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
             "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "computational-chemistry/htmd-analysis",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.no"
-        ],
+        "id": "computational-chemistry/zauberkugel",
+        "inexact_supported_servers": [],
         "js_requirements": {
-            "mathjax": null,
+            "mathjax": 6049,
             "mermaid": false
         },
         "key_points": [
-            "Simulating protein-ligand systems is more complex than simply simulating protein-only systems.",
-            "There are a range of Galaxy tools for MD simulation (using GROMACS) and analysis.",
-            "Galaxy makes assembling and scaling up workflows for high-throughput MD straightforward for users."
+            "A pharmacophore is an abstract description of the molecular features of a bioactive ligand.",
+            "Pharmacophore-based target prediction is an efficient and cost-effective method."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Advanced",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
         "mod_date": "2024-06-14",
         "objectives": [
-            "Learn about force-fields and MD parameterization",
-            "Learn how to conduct MD simulation and analysis for a protein-ligand system",
-            "Understand how different molecular interactions contribute to the binding affinity of various ligands for the Hsp90 protein."
+            "Create an SMILES file of a bioactive ligand.",
+            "Screen the query ligand against a pharmacophore library.",
+            "Analyze the results of the protein target prediction."
         ],
-        "pageviews": 15545,
-        "pub_date": "2020-05-20",
+        "pageviews": 1474,
+        "pub_date": "2022-02-15",
         "questions": [
-            "How are protein-ligand systems parameterized for molecular dynamics simulation?",
-            "What kind of analysis can be carried out on molecular trajectories?",
-            "How can high-throughput MD be used to study multiple ligands?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "simonbray"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "1H40M",
-                "speakers": [
-                    "simonbray",
-                    "chrisbarnettster"
-                ],
-                "youtube_id": "LjW3nES04bI"
-            }
+            "What is a pharmacophore model?",
+            "How can I perform protein target prediction with a multi-step workflow or the one-step Zauberkugel workflow?"
         ],
-        "short_id": "T00050",
+        "short_id": "T00054",
         "short_tools": [
-            "gmx_editconf",
-            "gmx_merge_topology_files",
-            "bio3d_pca_visualize",
-            "gmx_setup",
-            "vmd_hbonds",
-            "tp_grep_tool",
-            "ambertools_acpype",
-            "md_converter",
-            "get_pdb",
-            "openbabel_compound_convert",
-            "gmx_em",
-            "bio3d_rmsd",
-            "mdanalysis_cosine_analysis",
-            "bio3d_pca",
-            "bio3d_rmsf",
-            "gmx_energy",
-            "gmx_solvate",
-            "gmx_sim"
+            "tp_cat",
+            "ctb_alignit",
+            "split_file_to_collection",
+            "sort1",
+            "openbabel_addh",
+            "rdconf"
         ],
         "slides": false,
         "slides_recordings": false,
         "supported_servers": {
             "exact": [
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -36066,44 +37412,23 @@
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
-            ]
+            ],
+            "inexact": []
         },
         "symlink": null,
-        "time_estimation": "3H",
-        "title": "High Throughput Molecular Dynamics and Analysis",
+        "time_estimation": "2H",
+        "title": "Protein target prediction of a bioactive ligand with Align-it and ePharmaLib",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/get_pdb/get_pdb/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.2.2.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_acpype/ambertools_acpype/19.11",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_acpype/ambertools_acpype/21.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca/bio3d_pca/2.3.4",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca_visualize/bio3d_pca_visualize/2.3.4",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsd/bio3d_rmsd/2.3.4",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsf/bio3d_rmsf/2.3.4",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2019.1.4",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2020.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2019.1.4",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2020.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_energy/gmx_energy/2020.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_merge_topology_files/gmx_merge_topology_files/3.2.0",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_merge_topology_files/gmx_merge_topology_files/3.2.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2019.1.4",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2020.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.4.1",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.4+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2019.1.4",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2020.4+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter/1.9.3.2",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter/1.9.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_cosine_analysis/mdanalysis_cosine_analysis/0.20",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_cosine_analysis/mdanalysis_cosine_analysis/1.0.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/chemteam/vmd_hbonds/vmd_hbonds/1.9.3"
+            "sort1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/align_it/ctb_alignit/1.0.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_addh/openbabel_addh/3.1.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/rdconf/rdconf/2020.03.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1"
         ],
         "topic_name": "computational-chemistry",
         "topic_name_human": "Computational chemistry",
@@ -36113,44 +37438,62 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "htmd-analysis",
+        "tutorial_name": "zauberkugel",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/computational-chemistry/tutorials/htmd-analysis/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/computational-chemistry/tutorials/zauberkugel/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/htmd-analysis/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/zauberkugel/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/zauberkugel/tutorial.json"
         },
-        "version": 18,
+        "version": 10,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 160,
-        "visitors": 8309,
+        "visit_duration": 148,
+        "visitors": 968,
         "workflows": [
             {
-                "creators": [],
-                "description": "High Throughput Molecular Dynamics and Analysis",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "email": "mailto:amaf.aurelien@yahoo.com",
+                        "identifier": "https://orcid.org/0000-0002-6034-2016",
+                        "name": "Aur\u00e9lien F. A. Moumbock"
+                    },
+                    {
+                        "class": "Organization",
+                        "name": "Albert-Ludwigs-Universit\u00e4t Freiburg"
+                    }
+                ],
+                "description": "Protein target prediction of a bioactive ligand with Align-it and ePharmaLib",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[label=\"GROMACS structure configuration\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"MDTraj file converter\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"RMSD Analysis\"]\n  2 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"RMSF Analysis\"]\n  2 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"output\"]\n  6[label=\"PCA\"]\n  2 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"Cosine Content\"]\n  3 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"PCA visualization\"]\n  2 -> 8 [label=\"output\"]\n  3 -> 8 [label=\"output\"]\n  9[label=\"Hydrogen Bond Analysis using VMD\"]\n  3 -> 9 [label=\"output\"]\n  2 -> 9 [label=\"output\"]\n  10[label=\"RMSD Analysis\"]\n  2 -> 10 [label=\"output\"]\n  3 -> 10 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nQuery ligand\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPharmacophore library\"]\n  2[label=\"Ligand ionization state generation\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Splitting ePharmaLib into individual pharmacophores\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\" Low-energy ligand conformer search\"]\n  2 -> 4 [label=\"outfile\"]\n  5[label=\"Pharmacophore alignment\"]\n  4 -> 5 [label=\"outfile\"]\n  3 -> 5 [label=\"list_output_generic\"]\n  6[label=\"Concatenating the pharmacophore alignment scores\"]\n  5 -> 6 [label=\"score_result_file\"]\n  7[label=\"Ranking the predicted protein targets according to the Tversky index 10th column\"]\n  6 -> 7 [label=\"out_file1\"]\n}",
                 "history": [
                     {
-                        "hash": "2a74c677081dfcdf29c3c05c38bcb07d131f412f",
-                        "message": "fix workflows",
+                        "hash": "b70afe30388f2cf2023a1abb8d7d6130721467b2",
+                        "message": "annotate workflow for gtn linting",
+                        "num": 3,
+                        "short_hash": "b70afe303",
+                        "unix": "1644931554"
+                    },
+                    {
+                        "hash": "506069da4d92df0665a2c7ed4de1bfc40345cf22",
+                        "message": "pretty print pharmacophore workflow",
                         "num": 2,
-                        "short_hash": "2a74c6770",
-                        "unix": "1595329917"
+                        "short_hash": "506069da4",
+                        "unix": "1644582976"
                     },
                     {
-                        "hash": "3e9586df2283684cf7a452fb32a3ff0f69b48f4a",
-                        "message": "HTMD tutorial (#1837)",
+                        "hash": "fdd280bcf8dfeccdd087f4822150679914725469",
+                        "message": "Add files via upload",
                         "num": 1,
-                        "short_hash": "3e9586df2",
-                        "unix": "1589995622"
+                        "short_hash": "fdd280bcf",
+                        "unix": "1644350636"
                     }
                 ],
                 "inputs": [
@@ -36163,21 +37506,27 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Galaxy30-[GROMACS_simulation_on_data_28,_data_15,_and_data_26].gro"
+                                "name": "Query ligand"
                             }
                         ],
-                        "label": null,
+                        "label": "Query ligand",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 10
+                            "bottom": 747.5521469116211,
+                            "height": 62.083335876464844,
+                            "left": 559.0104370117188,
+                            "right": 759.0104522705078,
+                            "top": 685.4688110351562,
+                            "width": 200.00001525878906,
+                            "x": 559.0104370117188,
+                            "y": 685.4688110351562
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"Galaxy30-[GROMACS_simulation_on_data_28,_data_15,_and_data_26].gro\"}",
+                        "tool_state": "{\"optional\": false, \"format\": [\"smi\"]}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "82ae4961-8bb0-440d-bed6-9206d8b9d860",
+                        "uuid": "63eee683-907c-40a4-b801-d977e0b2cb3e",
                         "workflow_outputs": []
                     },
                     {
@@ -36189,235 +37538,388 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Galaxy31-[GROMACS_simulation_on_data_28,_data_15,_and_data_26].xtc"
+                                "name": "Pharmacophore library"
                             }
                         ],
-                        "label": null,
+                        "label": "Pharmacophore library",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 130
+                            "bottom": 1033.8889236450195,
+                            "height": 82.46527862548828,
+                            "left": 780.9375610351562,
+                            "right": 980.9375762939453,
+                            "top": 951.4236450195312,
+                            "width": 200.00001525878906,
+                            "x": 780.9375610351562,
+                            "y": 951.4236450195312
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"Galaxy31-[GROMACS_simulation_on_data_28,_data_15,_and_data_26].xtc\"}",
+                        "tool_state": "{\"optional\": false, \"format\": [\"phar\"]}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "f67e98b9-2b4f-4d7d-9da7-ec3c23ffbd38",
+                        "uuid": "004f025f-dafc-4d26-8aec-88a64d013852",
                         "workflow_outputs": []
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"GROMACS structure configuration\"];\n  0 -->|output| 2;\n  3[\"MDTraj file converter\"];\n  1 -->|output| 3;\n  4[\"RMSD Analysis\"];\n  2 -->|output| 4;\n  3 -->|output| 4;\n  5[\"RMSF Analysis\"];\n  2 -->|output| 5;\n  3 -->|output| 5;\n  6[\"PCA\"];\n  2 -->|output| 6;\n  3 -->|output| 6;\n  7[\"Cosine Content\"];\n  3 -->|output| 7;\n  2 -->|output| 7;\n  8[\"PCA visualization\"];\n  2 -->|output| 8;\n  3 -->|output| 8;\n  9[\"Hydrogen Bond Analysis using VMD\"];\n  3 -->|output| 9;\n  2 -->|output| 9;\n  10[\"RMSD Analysis\"];\n  2 -->|output| 10;\n  3 -->|output| 10;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Workflow constructed from history 'Hsp90-MDAnalysis'",
-                "outputs": [],
-                "parent_id": "computational-chemistry/htmd-analysis",
-                "path": "topics/computational-chemistry/tutorials/htmd-analysis/workflows/analysis_workflow.ga",
-                "tags": [
-                    "computational-chemistry"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Workflow constructed from history 'Hsp90-MDAnalysis'",
-                "topic_id": "computational-chemistry",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/computational-chemistry-htmd-analysis/versions/analysis-workflow",
-                "tutorial_id": "htmd-analysis",
-                "url": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/htmd-analysis/workflows/analysis_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/htmd-analysis/workflows/analysis_workflow.html",
-                "version": 2,
-                "wfid": "computational-chemistry-htmd-analysis",
-                "wfname": "analysis-workflow",
-                "workflow": "analysis_workflow.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca/bio3d_pca/2.3.4",
-                    "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca_visualize/bio3d_pca_visualize/2.3.4",
-                    "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsd/bio3d_rmsd/2.3.4",
-                    "toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsf/bio3d_rmsf/2.3.4",
-                    "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2019.1.4",
-                    "toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter/1.9.3.2",
-                    "toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_cosine_analysis/mdanalysis_cosine_analysis/0.20",
-                    "toolshed.g2.bx.psu.edu/repos/chemteam/vmd_hbonds/vmd_hbonds/1.9.3"
-                ],
-                "workflowhub_id": "1062"
-            },
-            {
-                "creators": [],
-                "description": "High Throughput Molecular Dynamics and Analysis",
-                "features": {
-                    "comments": false,
-                    "parameters": true,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nPDB code e.g. 6hhr\"]\n  1[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nLigand name e.g. AG5E\"]\n  2[label=\"Get PDB file\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Search in textfiles\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Search in textfiles\"]\n  2 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"GROMACS initial setup\"]\n  3 -> 5 [label=\"output\"]\n  6[label=\"Compound conversion\"]\n  4 -> 6 [label=\"output\"]\n  7[label=\"Generate MD topologies for small molecules\"]\n  6 -> 7 [label=\"outfile\"]\n  8[label=\"Merge GROMACS topologies\"]\n  7 -> 8 [label=\"gro_output\"]\n  5 -> 8 [label=\"output1\"]\n  5 -> 8 [label=\"output2\"]\n  7 -> 8 [label=\"output\"]\n  9[label=\"GROMACS structure configuration\"]\n  8 -> 9 [label=\"complex_gro\"]\n  10[label=\"GROMACS solvation and adding ions\"]\n  8 -> 10 [label=\"complex_top\"]\n  9 -> 10 [label=\"output\"]\n  11[label=\"GROMACS energy minimization\"]\n  10 -> 11 [label=\"output2\"]\n  10 -> 11 [label=\"output1\"]\n  12[label=\"GROMACS simulation\"]\n  5 -> 12 [label=\"output3\"]\n  10 -> 12 [label=\"output2\"]\n  11 -> 12 [label=\"output1\"]\n  13[label=\"GROMACS simulation\"]\n  5 -> 13 [label=\"output3\"]\n  10 -> 13 [label=\"output2\"]\n  12 -> 13 [label=\"output1\"]\n  12 -> 13 [label=\"output5\"]\n  14[label=\"GROMACS simulation\"]\n  10 -> 14 [label=\"output2\"]\n  13 -> 14 [label=\"output1\"]\n  13 -> 14 [label=\"output5\"]\n}",
-                "history": [
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQuery ligand\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nPharmacophore library\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Ligand ionization state generation\"];\n  0 -->|output| 2;\n  3[\"Splitting ePharmaLib into individual pharmacophores\"];\n  1 -->|output| 3;\n  4[\" Low-energy ligand conformer search\"];\n  2 -->|outfile| 4;\n  5[\"Pharmacophore alignment\"];\n  4 -->|outfile| 5;\n  3 -->|list_output_generic| 5;\n  6[\"Concatenating the pharmacophore alignment scores\"];\n  5 -->|score_result_file| 6;\n  7[\"Ranking the predicted protein targets according to the Tversky index 10th column\"];\n  6 -->|out_file1| 7;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Zauberkugel",
+                "outputs": [
                     {
-                        "hash": "2a74c677081dfcdf29c3c05c38bcb07d131f412f",
-                        "message": "fix workflows",
-                        "num": 2,
-                        "short_hash": "2a74c6770",
-                        "unix": "1595329917"
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_addh/openbabel_addh/3.1.1+galaxy1",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "infile": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Ligand ionization state generation",
+                        "name": "Add hydrogen atoms",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 746.4236679077148,
+                            "height": 113.95833587646484,
+                            "left": 776.99658203125,
+                            "right": 976.9965972900391,
+                            "top": 632.46533203125,
+                            "width": 200.00001525878906,
+                            "x": 776.99658203125,
+                            "y": 632.46533203125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_addh/openbabel_addh/3.1.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "6e4b7e0c61a6",
+                            "name": "openbabel_addh",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"infile\": {\"__class__\": \"ConnectedValue\"}, \"pH_value\": \"7.4\", \"polar\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.1+galaxy1",
+                        "type": "tool",
+                        "uuid": "857b1ca0-d39a-463f-9840-cf2c7e6b363f",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "24b52c0f-f6e2-4d14-bd92-2aa620c91d83"
+                            }
+                        ]
                     },
                     {
-                        "hash": "3e9586df2283684cf7a452fb32a3ff0f69b48f4a",
-                        "message": "HTMD tutorial (#1837)",
-                        "num": 1,
-                        "short_hash": "3e9586df2",
-                        "unix": "1589995622"
-                    }
-                ],
-                "inputs": [
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "split_parms|input": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Splitting ePharmaLib into individual pharmacophores",
+                        "name": "Split file",
+                        "outputs": [
+                            {
+                                "name": "list_output_generic",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 1036.1979370117188,
+                            "height": 154.72222900390625,
+                            "left": 1009.982666015625,
+                            "right": 1209.982681274414,
+                            "top": 881.4757080078125,
+                            "width": 200.00001525878906,
+                            "x": 1009.982666015625,
+                            "y": 881.4757080078125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "6cbe2f30c2d7",
+                            "name": "split_file_to_collection",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"split_parms\": {\"select_ftype\": \"generic\", \"__current_case__\": 6, \"input\": {\"__class__\": \"ConnectedValue\"}, \"split_method\": {\"select_split_method\": \"regex\", \"__current_case__\": 0, \"generic_regex\": \"\\\\$\\\\$\\\\$\\\\$\", \"split_after\": \"true\"}, \"select_mode\": {\"mode\": \"chunk\", \"__current_case__\": 0, \"chunksize\": \"1\"}, \"newfilenames\": \"epharmalib\", \"select_allocate\": {\"allocate\": \"batch\", \"__current_case__\": 1}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.5.0",
+                        "type": "tool",
+                        "uuid": "1baf3f94-2aa7-42e9-968e-959fffcc462b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "list_output_generic",
+                                "uuid": "6d0c53e6-2607-410f-a529-3fc4cd1d70b4"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/rdconf/rdconf/2020.03.4+galaxy0",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
+                        "id": 4,
+                        "input_connections": {
+                            "infile": {
+                                "id": 2,
+                                "output_name": "outfile"
+                            }
+                        },
                         "inputs": [],
-                        "label": "PDB code (e.g. 6hhr)",
-                        "name": "Input parameter",
-                        "outputs": [],
+                        "label": " Low-energy ligand conformer search",
+                        "name": "RDConf: Low-energy ligand conformer search",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "sdf"
+                            }
+                        ],
                         "position": {
-                            "left": 229.5,
-                            "top": 191.5
+                            "bottom": 784.18408203125,
+                            "height": 154.72222900390625,
+                            "left": 1001.0070190429688,
+                            "right": 1201.0070343017578,
+                            "top": 629.4618530273438,
+                            "width": 200.00001525878906,
+                            "x": 1001.0070190429688,
+                            "y": 629.4618530273438
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"parameter_type\": \"text\"}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "73aff13d-acd3-41a0-8894-3104a93f9ad0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/rdconf/rdconf/2020.03.4+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "5c501eb8d56c",
+                            "name": "rdconf",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"CNT\": \"100\", \"E\": \"10.0\", \"N\": \"1\", \"R\": \"0.7\", \"etkdg\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mmff\": \"false\", \"nomin\": \"false\", \"s\": \"9162006\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2020.03.4+galaxy0",
+                        "type": "tool",
+                        "uuid": "0c02c9e1-8579-4370-aa2e-575956b017cc",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "2a9ccaa8-d21d-4d92-8e8c-97822d8d5d9e"
+                                "output_name": "outfile",
+                                "uuid": "04f08403-a7e1-4350-94e0-17af711f0113"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/align_it/ctb_alignit/1.0.4+galaxy0",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
+                        "id": 5,
+                        "input_connections": {
+                            "database": {
+                                "id": 4,
+                                "output_name": "outfile"
+                            },
+                            "reference": {
+                                "id": 3,
+                                "output_name": "list_output_generic"
+                            }
+                        },
                         "inputs": [],
-                        "label": "Ligand name (e.g. AG5E)",
-                        "name": "Input parameter",
-                        "outputs": [],
+                        "label": null,
+                        "name": "Pharmacophore alignment",
+                        "outputs": [
+                            {
+                                "name": "aligned_pharmacophores",
+                                "type": "phar"
+                            },
+                            {
+                                "name": "aligned_structures",
+                                "type": "smi"
+                            },
+                            {
+                                "name": "score_result_file",
+                                "type": "tabular"
+                            }
+                        ],
                         "position": {
-                            "left": 230.5,
-                            "top": 340.5
+                            "bottom": 1037.3438110351562,
+                            "height": 408.92364501953125,
+                            "left": 1244.010498046875,
+                            "right": 1444.010513305664,
+                            "top": 628.420166015625,
+                            "width": 200.00001525878906,
+                            "x": 1244.010498046875,
+                            "y": 628.420166015625
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"parameter_type\": \"text\"}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "4c514954-d86b-409d-aa30-70545b8522ea",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/align_it/ctb_alignit/1.0.4+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "06d9381593a4",
+                            "name": "align_it",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"best\": \"1\", \"cutoff\": \"0.5\", \"database\": {\"__class__\": \"ConnectedValue\"}, \"epsilon\": \"0.5\", \"fgroups\": [\"AROM\", \"HDON\", \"HACC\", \"LIPO\", \"CHARGE\"], \"merge\": \"false\", \"noHybrid\": \"true\", \"noNormal\": \"true\", \"oformat\": \"smi\", \"rankBy\": \"TVERSKY_REF\", \"reference\": {\"__class__\": \"ConnectedValue\"}, \"scoreOnly\": \"false\", \"withExclusion\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.4+galaxy0",
+                        "type": "tool",
+                        "uuid": "5d8f4ad4-8831-405f-8cef-7a9d0c114ddd",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "1fb55337-8d3f-4918-a1af-14c28986ff07"
+                                "output_name": "aligned_pharmacophores",
+                                "uuid": "7a9ad93a-e27c-48f2-a17e-afd5afcc5c47"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "score_result_file",
+                                "uuid": "ec32ab04-d509-48ac-94c4-145a1547a134"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "aligned_structures",
+                                "uuid": "d3dd55d0-472a-4d38-b0c0-f5d61ecf167f"
                             }
                         ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nPDB code e.g. 6hhr\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nLigand name e.g. AG5E\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"Get PDB file\"];\n  0 -->|output| 2;\n  3[\"Search in textfiles\"];\n  2 -->|output| 3;\n  4[\"Search in textfiles\"];\n  2 -->|output| 4;\n  1 -->|output| 4;\n  5[\"GROMACS initial setup\"];\n  3 -->|output| 5;\n  6[\"Compound conversion\"];\n  4 -->|output| 6;\n  7[\"Generate MD topologies for small molecules\"];\n  6 -->|outfile| 7;\n  8[\"Merge GROMACS topologies\"];\n  7 -->|gro_output| 8;\n  5 -->|output1| 8;\n  5 -->|output2| 8;\n  7 -->|output| 8;\n  9[\"GROMACS structure configuration\"];\n  8 -->|complex_gro| 9;\n  10[\"GROMACS solvation and adding ions\"];\n  8 -->|complex_top| 10;\n  9 -->|output| 10;\n  11[\"GROMACS energy minimization\"];\n  10 -->|output2| 11;\n  10 -->|output1| 11;\n  12[\"GROMACS simulation\"];\n  5 -->|output3| 12;\n  10 -->|output2| 12;\n  11 -->|output1| 12;\n  13[\"GROMACS simulation\"];\n  5 -->|output3| 13;\n  10 -->|output2| 13;\n  12 -->|output1| 13;\n  12 -->|output5| 13;\n  14[\"GROMACS simulation\"];\n  10 -->|output2| 14;\n  13 -->|output1| 14;\n  13 -->|output5| 14;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "MD protein-ligand workflow (from PDB structure)",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
+                        "id": 6,
+                        "input_connections": {
+                            "inputs": {
+                                "id": 5,
+                                "output_name": "score_result_file"
+                            }
+                        },
                         "inputs": [],
-                        "label": "PDB code (e.g. 6hhr)",
-                        "name": "Input parameter",
-                        "outputs": [],
+                        "label": "Concatenating the pharmacophore alignment scores",
+                        "name": "Concatenate datasets",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
                         "position": {
-                            "left": 229.5,
-                            "top": 191.5
+                            "bottom": 783.1423950195312,
+                            "height": 154.72222900390625,
+                            "left": 1475.9896240234375,
+                            "right": 1675.9896392822266,
+                            "top": 628.420166015625,
+                            "width": 200.00001525878906,
+                            "x": 1475.9896240234375,
+                            "y": 628.420166015625
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"parameter_type\": \"text\"}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "73aff13d-acd3-41a0-8894-3104a93f9ad0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f46f0e4f75c4",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.1",
+                        "type": "tool",
+                        "uuid": "c3b7d2a3-b06e-4a4f-aee2-a2b8941ebfdb",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "2a9ccaa8-d21d-4d92-8e8c-97822d8d5d9e"
+                                "output_name": "out_file1",
+                                "uuid": "9cfedc75-e78a-4425-b8dc-2019f1d8479d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "sort1",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
+                        "id": 7,
+                        "input_connections": {
+                            "input": {
+                                "id": 6,
+                                "output_name": "out_file1"
+                            }
+                        },
                         "inputs": [],
-                        "label": "Ligand name (e.g. AG5E)",
-                        "name": "Input parameter",
-                        "outputs": [],
+                        "label": "Ranking the predicted protein targets according to the Tversky index (10th column)",
+                        "name": "Sort",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
                         "position": {
-                            "left": 230.5,
-                            "top": 340.5
+                            "bottom": 782.2048950195312,
+                            "height": 154.72222900390625,
+                            "left": 1700.0001220703125,
+                            "right": 1900.0001373291016,
+                            "top": 627.482666015625,
+                            "width": 200.00001525878906,
+                            "x": 1700.0001220703125,
+                            "y": 627.482666015625
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"parameter_type\": \"text\"}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "4c514954-d86b-409d-aa30-70545b8522ea",
+                        "post_job_actions": {
+                            "EmailActionout_file1": {
+                                "action_arguments": {},
+                                "action_type": "EmailAction",
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "tool_id": "sort1",
+                        "tool_state": "{\"column\": \"10\", \"column_set\": [], \"header_lines\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"order\": \"DESC\", \"style\": \"num\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.0",
+                        "type": "tool",
+                        "uuid": "3bbbee13-46e9-48ad-9ecc-c874da658723",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "1fb55337-8d3f-4918-a1af-14c28986ff07"
+                                "output_name": "out_file1",
+                                "uuid": "f1cb518a-3021-44b3-a03c-2443d7cddc91"
                             }
                         ]
                     }
                 ],
-                "parent_id": "computational-chemistry/htmd-analysis",
-                "path": "topics/computational-chemistry/tutorials/htmd-analysis/workflows/main_workflow.ga",
+                "parent_id": "computational-chemistry/zauberkugel",
+                "path": "topics/computational-chemistry/tutorials/zauberkugel/workflows/main_workflow.ga",
                 "tags": [
                     "cheminformatics",
-                    "moleculardynamics",
                     "computational-chemistry"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "MD protein-ligand workflow (from PDB structure)",
+                "title": "Zauberkugel",
                 "topic_id": "computational-chemistry",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/computational-chemistry-htmd-analysis/versions/main-workflow",
-                "tutorial_id": "htmd-analysis",
-                "url": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/htmd-analysis/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/htmd-analysis/workflows/main_workflow.html",
-                "version": 2,
-                "wfid": "computational-chemistry-htmd-analysis",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/computational-chemistry-zauberkugel/versions/main-workflow",
+                "tutorial_id": "zauberkugel",
+                "url": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/zauberkugel/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/zauberkugel/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "computational-chemistry-zauberkugel",
                 "wfname": "main-workflow",
                 "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/get_pdb/get_pdb/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.2.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_acpype/ambertools_acpype/19.11",
-                    "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2019.1.4",
-                    "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2019.1.4",
-                    "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_merge_topology_files/gmx_merge_topology_files/3.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2019.1.4",
-                    "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.4.1",
-                    "toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2019.1.4"
+                    "sort1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/align_it/ctb_alignit/1.0.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_addh/openbabel_addh/3.1.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/rdconf/rdconf/2020.03.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1"
                 ],
-                "workflowhub_id": "1134"
+                "workflowhub_id": "1082"
             }
         ],
-        "zenodo_link": "https://zenodo.org/records/3813283"
+        "zenodo_link": "https://zenodo.org/record/6055897"
     },
     {
         "admin_install": {
@@ -36499,7 +38001,7 @@
             "learn how to set up up a model protein and ligand system (with CHARMM-GUI)",
             "learn how to upload the system to Galaxy"
         ],
-        "pageviews": 1939,
+        "pageviews": 2000,
         "pub_date": "2019-06-03",
         "questions": [
             "How to get started modelling a protein and a ligand?"
@@ -36574,7 +38076,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 105,
-        "visitors": 1418,
+        "visitors": 1465,
         "zenodo_link": "https://zenodo.org/record/2600690"
     },
     {
@@ -36765,12 +38267,12 @@
         ],
         "dir": "topics/contributing/tutorials/create-new-tutorial",
         "edam_operation": [
-            "Primer removal",
-            "Read mapping",
             "Data handling",
-            "Sequence file editing",
             "Sequence trimming",
-            "Read pre-processing"
+            "Sequence file editing",
+            "Read mapping",
+            "Read pre-processing",
+            "Primer removal"
         ],
         "edam_topic": [],
         "feedback_mean_note": null,
@@ -36794,7 +38296,7 @@
             "Create hands-on",
             "Add technical support for a tutorial"
         ],
-        "pageviews": 2080,
+        "pageviews": 2148,
         "pub_date": "2018-06-20",
         "questions": [
             "How to integrate a new tutorial?",
@@ -36816,19 +38318,19 @@
         ],
         "short_id": "T00057",
         "short_tools": [
-            "cutadapt",
-            "tp_cut_tool",
-            "bowtie2",
-            "tp_cat",
-            "random_lines1",
-            "Cut1",
+            "tp_sed_tool",
+            "tp_sorted_uniq",
             "bam_to_sam",
+            "tp_cat",
+            "c3s",
             "Filter1",
-            "tp_sed_tool",
-            "fastq_to_tabular",
+            "cutadapt",
             "seqtk_subseq",
-            "tp_sorted_uniq",
-            "c3s"
+            "random_lines1",
+            "fastq_to_tabular",
+            "Cut1",
+            "tp_cut_tool",
+            "bowtie2"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -36872,7 +38374,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 315,
-        "visitors": 1367,
+        "visitors": 1415,
         "workflows": [
             {
                 "creators": [],
@@ -36970,7 +38472,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSRR891268_R1_20M.fastq.gz\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSRR891268_R2_20M.fastq.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Unique\"];\n  9 -->|out_file1| 10;\n  11[\"Text transformation\"];\n  10 -->|outfile| 11;\n  12[\"Concatenate datasets\"];\n  6 -->|out_file1| 12;\n  11 -->|output| 12;\n  13[\"Unique\"];\n  12 -->|out_file1| 13;\n  14[\"seqtk_subseq\"];\n  0 -->|output| 14;\n  13 -->|outfile| 14;\n  15[\"Text transformation\"];\n  13 -->|outfile| 15;\n  16[\"seqtk_subseq\"];\n  1 -->|output| 16;\n  15 -->|output| 16;\n  2[\"FASTQ to Tabular\"];\n  0 -->|output| 2;\n  3[\"Cutadapt\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Cut\"];\n  2 -->|output_file| 4;\n  5[\"Bowtie2\"];\n  3 -->|out1| 5;\n  3 -->|out2| 5;\n  6[\"Select random lines\"];\n  4 -->|output| 6;\n  7[\"BAM-to-SAM\"];\n  5 -->|output| 7;\n  8[\"Filter\"];\n  7 -->|output1| 8;\n  9[\"Cut\"];\n  8 -->|out_file1| 9;",
-                "modified": "2024-08-18 00:06:21 +0000",
+                "modified": "2024-10-02 12:08:06 +0000",
                 "name": "MakeAFakeInput",
                 "outputs": [],
                 "parent_id": "contributing/create-new-tutorial",
@@ -37067,7 +38569,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAPI Request file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Copernicus Climate Data Store\"];\n  0 -->|output| 1;",
-                "modified": "2024-08-18 00:06:21 +0000",
+                "modified": "2024-10-02 12:08:06 +0000",
                 "name": "Retrieve climate data from Copernicus",
                 "outputs": [
                     {
@@ -37197,208 +38699,6 @@
             }
         ]
     },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/introduction/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            }
-        ],
-        "dir": "topics/contributing/tutorials/introduction",
-        "edam_operation": [],
-        "edam_topic": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": false,
-        "id": "contributing/introduction",
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "layout": "introduction_slides",
-        "license": "CC-BY-4.0",
-        "logo": "GTN",
-        "mod_date": "2023-01-12",
-        "pageviews": 5726880,
-        "priority": 1,
-        "pub_date": "2017-06-25",
-        "redirect_from": [
-            "/topics/contributing/slides/introduction",
-            "/short/contributing/introduction/slides",
-            "/short/S00042"
-        ],
-        "short_id": "S00042",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
-        "supported_servers": [],
-        "symlink": null,
-        "title": "Overview of the Galaxy Training Material",
-        "tools": [],
-        "topic_name": "contributing",
-        "topic_name_human": "Contributing to the Galaxy Training Material",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "introduction",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/introduction/slides.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/introduction/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/introduction/slides.json"
-        },
-        "version": 1,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/github-command-line-contribution/tutorial.json",
-        "contributors": [
-            {
-                "id": "cmonjeau",
-                "joined": "2017-09",
-                "name": "Cyril Monjeaud",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cmonjeau/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/cmonjeau.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            }
-        ],
-        "dir": "topics/contributing/tutorials/github-command-line-contribution",
-        "edam_operation": [],
-        "edam_topic": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "contributing/github-command-line-contribution",
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Work on your fork",
-            "1 branch = 1 feature",
-            "1 pull request = 1 branch",
-            "Be careful of the branch you're working on",
-            "Check the automated tests"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Fork a repository on GitHub",
-            "Clone a remote repository locally",
-            "Create a branch",
-            "Commit changes",
-            "Push changes to a remote repository",
-            "Create a pull request",
-            "Update a pull request"
-        ],
-        "pageviews": 5731396,
-        "pub_date": "2017-06-12",
-        "questions": [
-            "How can I contribute to an open-source project with GitHub?",
-            "What is the GitHub flow?"
-        ],
-        "short_id": "T00064",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
-        "subtopic": "contribute",
-        "supported_servers": [],
-        "symlink": null,
-        "time_estimation": "30m",
-        "title": "Contributing with GitHub via command-line",
-        "tools": [],
-        "topic_name": "contributing",
-        "topic_name_human": "Contributing to the Galaxy Training Material",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "github-command-line-contribution",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/github-command-line-contribution/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/github-command-line-contribution/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/github-command-line-contribution/tutorial.json"
-        },
-        "version": 21,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 197,
-        "visitors": 2066555
-    },
     {
         "admin_install": {
             "install_repository_dependencies": true,
@@ -37437,329 +38737,7 @@
                 "orcid": "0000-0001-9760-8992",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            }
-        ],
-        "dir": "topics/contributing/tutorials/create-new-tutorial-slides",
-        "edam_operation": [],
-        "edam_topic": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": false,
-        "id": "contributing/create-new-tutorial-slides",
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Slides are often presented before the hands-on portion, provide relevant background information",
-            "Provide examples that are relevant to your audience"
-        ],
-        "layout": "tutorial_slides",
-        "license": "CC-BY-4.0",
-        "logo": "GTN",
-        "mod_date": "2024-08-08",
-        "objectives": [
-            "Create a new set of slides",
-            "Add presenter comments"
-        ],
-        "pageviews": 5726880,
-        "pub_date": "2018-06-13",
-        "questions": [
-            "How to format slides?",
-            "How do we add presenter notes?",
-            "How to use the features of the slide show tool?",
-            "What sort of content should be included in slides?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "shiltemann"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "5M",
-                "speakers": [
-                    "awspolly"
-                ],
-                "youtube_id": "Gm1MKAwuLxg"
-            }
-        ],
-        "short_id": "S00040",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": [
-            {
-                "captioners": [
-                    "shiltemann"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "5M",
-                "speakers": [
-                    "awspolly"
-                ],
-                "youtube_id": "Gm1MKAwuLxg"
-            }
-        ],
-        "subtopic": "writing",
-        "supported_servers": [],
-        "symlink": null,
-        "time_estimation": null,
-        "title": "Creating Slides",
-        "tools": [],
-        "topic_name": "contributing",
-        "topic_name_human": "Contributing to the Galaxy Training Material",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": true
-        },
-        "tutorial_name": "create-new-tutorial-slides",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-slides/slides.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-slides/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-slides/slides.json"
-        },
-        "version": 16,
-        "video": true,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-tours/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
-                "fediverse_flavor": "mastodon",
-                "id": "bgruening",
-                "joined": "2017-09",
-                "linkedin": "bgruening",
-                "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
-                },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            }
-        ],
-        "dir": "topics/contributing/tutorials/create-new-tutorial-tours",
-        "edam_operation": [],
-        "edam_topic": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "contributing/create-new-tutorial-tours",
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "The Interactive Tours are a good training object for self-learning at its own speed",
-            "It is now easy to create an Interactive Tour and test it"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Creating a Galaxy tour from scratch",
-            "Deploying and running a tour"
-        ],
-        "pageviews": 405,
-        "pub_date": "2017-06-25",
-        "questions": [
-            "What is a Interactive Galaxy Tour?",
-            "How can we create an Interactive Tour?"
-        ],
-        "short_id": "T00061",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": [],
-        "symlink": null,
-        "time_estimation": "15m",
-        "title": "Creating Interactive Galaxy Tours",
-        "tools": [],
-        "topic_name": "contributing",
-        "topic_name_human": "Contributing to the Galaxy Training Material",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "create-new-tutorial-tours",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-tours/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-tours/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-tours/tutorial.json"
-        },
-        "version": 12,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 167,
-        "visitors": 247
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-topic/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "bebatut"
-            ],
-            "editing": [
-                "hexylena"
-            ]
-        },
-        "contributors": [
+            },
             {
                 "affiliations": [
                     "gallantries",
@@ -37788,69 +38766,102 @@
             },
             {
                 "affiliations": [
+                    "CINECA-Project",
                     "gallantries",
-                    "by-covid",
                     "erasmusmc",
                     "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
                     "uni-freiburg"
                 ],
-                "id": "hexylena",
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
                 "joined": "2017-09",
+                "linkedin": "shiltemann",
                 "location": {
                     "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
+                    "lat": 51.912,
+                    "lon": 4.462
                 },
                 "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             }
         ],
-        "dir": "topics/contributing/tutorials/create-new-topic",
+        "dir": "topics/contributing/tutorials/create-new-tutorial-slides",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": true,
-        "id": "contributing/create-new-topic",
+        "hands_on": false,
+        "id": "contributing/create-new-tutorial-slides",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "A new topic can be easily added for new tutorials"
+            "Slides are often presented before the hands-on portion, provide relevant background information",
+            "Provide examples that are relevant to your audience"
         ],
-        "layout": "tutorial_hands_on",
+        "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-02-29",
+        "logo": "GTN",
+        "mod_date": "2024-08-08",
         "objectives": [
-            "Create a new topic",
-            "Set up the metadata for a topic"
+            "Create a new set of slides",
+            "Add presenter comments"
         ],
-        "pageviews": 1155,
-        "pub_date": "2018-06-04",
+        "pageviews": 5897155,
+        "pub_date": "2018-06-13",
         "questions": [
-            "How to include a new topic?",
-            "What kinds of Topics are possible?"
+            "How to format slides?",
+            "How do we add presenter notes?",
+            "How to use the features of the slide show tool?",
+            "What sort of content should be included in slides?"
         ],
-        "short_id": "T00056",
+        "recordings": [
+            {
+                "captioners": [
+                    "shiltemann"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "5M",
+                "speakers": [
+                    "awspolly"
+                ],
+                "youtube_id": "Gm1MKAwuLxg"
+            }
+        ],
+        "short_id": "S00040",
         "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
+        "slides": true,
+        "slides_recordings": [
+            {
+                "captioners": [
+                    "shiltemann"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "5M",
+                "speakers": [
+                    "awspolly"
+                ],
+                "youtube_id": "Gm1MKAwuLxg"
+            }
+        ],
+        "subtopic": "writing",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "30m",
-        "title": "Including a new topic",
+        "time_estimation": null,
+        "title": "Creating Slides",
         "tools": [],
         "topic_name": "contributing",
         "topic_name_human": "Contributing to the Galaxy Training Material",
@@ -37858,21 +38869,21 @@
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": false
+            "video": true
         },
-        "tutorial_name": "create-new-topic",
+        "tutorial_name": "create-new-tutorial-slides",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/create-new-topic/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-slides/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-topic/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-topic/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-slides/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-slides/slides.json"
         },
-        "version": 30,
-        "video": false,
-        "video_versions": 0,
+        "version": 16,
+        "video": true,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 27,
-        "visitors": 776
+        "visit_duration": 152,
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -37882,68 +38893,65 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/schemas/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/introduction/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
                     "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
+                    "ifb",
+                    "elixir-europe"
                 ],
-                "id": "hexylena",
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
                 "joined": "2017-09",
+                "linkedin": "berenicebatut",
                 "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
                 },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             }
         ],
-        "dir": "topics/contributing/tutorials/schemas",
+        "dir": "topics/contributing/tutorials/introduction",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": true,
-        "id": "contributing/schemas",
+        "hands_on": false,
+        "id": "contributing/introduction",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "layout": "tutorial_hands_on",
+        "layout": "introduction_slides",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-04",
-        "objectives": [
-            "Know where to find all of the available metadata, so you can reference it later."
-        ],
-        "pageviews": 259,
-        "pub_date": "2022-06-02",
-        "questions": [
-            "What metadata is required or possible to set in a Tutorial, Slide, Topic, or FAQ"
+        "logo": "GTN",
+        "mod_date": "2023-01-12",
+        "pageviews": 5897155,
+        "priority": 1,
+        "pub_date": "2017-06-25",
+        "redirect_from": [
+            "/topics/contributing/slides/introduction",
+            "/short/contributing/introduction/slides",
+            "/short/S00042"
         ],
-        "short_id": "T00070",
+        "short_id": "S00042",
         "short_tools": [],
-        "slides": false,
+        "slides": true,
         "slides_recordings": false,
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "10m",
-        "title": "GTN Metadata",
+        "title": "Overview of the Galaxy Training Material",
         "tools": [],
         "topic_name": "contributing",
         "topic_name_human": "Contributing to the Galaxy Training Material",
@@ -37953,19 +38961,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "schemas",
+        "tutorial_name": "introduction",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/schemas/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/introduction/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/schemas/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/schemas/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/introduction/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/introduction/slides.json"
         },
-        "version": 7,
+        "version": 1,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 186,
-        "visitors": 189
+        "visit_duration": 152,
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -37975,8 +38983,15 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/running-jekyll/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/github-command-line-contribution/tutorial.json",
         "contributors": [
+            {
+                "id": "cmonjeau",
+                "joined": "2017-09",
+                "name": "Cyril Monjeaud",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cmonjeau/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/cmonjeau.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
@@ -38002,105 +39017,53 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
                 "twitter": "bebatut",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
-                "fediverse_flavor": "mastodon",
-                "id": "bgruening",
-                "joined": "2017-09",
-                "linkedin": "bgruening",
-                "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
-                },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             }
         ],
-        "dir": "topics/contributing/tutorials/running-jekyll",
+        "dir": "topics/contributing/tutorials/github-command-line-contribution",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "contributing/running-jekyll",
+        "id": "contributing/github-command-line-contribution",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Checking the generated website can be done locally"
+            "Work on your fork",
+            "1 branch = 1 feature",
+            "1 pull request = 1 branch",
+            "Be careful of the branch you're working on",
+            "Check the automated tests"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-03",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Installing packages needed for rendering the webpage",
-            "Running the GTN material website locally",
-            "Tracking changes to the content live in the webbrowser"
+            "Fork a repository on GitHub",
+            "Clone a remote repository locally",
+            "Create a branch",
+            "Commit changes",
+            "Push changes to a remote repository",
+            "Create a pull request",
+            "Update a pull request"
         ],
-        "pageviews": 1492,
-        "pub_date": "2017-06-25",
+        "pageviews": 5901686,
+        "pub_date": "2017-06-12",
         "questions": [
-            "How to setup the infrastructure to build training webpages?"
+            "How can I contribute to an open-source project with GitHub?",
+            "What is the GitHub flow?"
         ],
-        "short_id": "T00069",
+        "short_id": "T00064",
         "short_tools": [],
-        "slides": false,
+        "slides": true,
         "slides_recordings": false,
-        "subtopic": "writing",
+        "subtopic": "contribute",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "15m",
-        "title": "Running the GTN website locally",
+        "time_estimation": "30m",
+        "title": "Contributing with GitHub via command-line",
         "tools": [],
         "topic_name": "contributing",
         "topic_name_human": "Contributing to the Galaxy Training Material",
@@ -38110,19 +39073,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "running-jekyll",
+        "tutorial_name": "github-command-line-contribution",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/running-jekyll/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/github-command-line-contribution/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/running-jekyll/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/running-jekyll/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/github-command-line-contribution/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/github-command-line-contribution/tutorial.json"
         },
-        "version": 25,
+        "version": 21,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 208,
-        "visitors": 1079
+        "visit_duration": 196,
+        "visitors": 2136392
     },
     {
         "admin_install": {
@@ -38279,7 +39242,7 @@
             "Explain how learning models can help you improve your teaching in the classroom",
             "List learning strategies and principles suggested by evidence-based research results"
         ],
-        "pageviews": 4820,
+        "pageviews": 5094,
         "pub_date": "2022-09-23",
         "questions": [
             "What are the main principles that drive learning?",
@@ -38356,8 +39319,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 50,
-        "visitors": 4008
+        "visit_duration": 49,
+        "visitors": 4241
     },
     {
         "admin_install": {
@@ -38367,7 +39330,18 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/admin-knitting/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/python/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "hexylena"
+            ],
+            "editing": [
+                "bazante1"
+            ],
+            "testing": [
+                "dirowa"
+            ]
+        },
         "contributors": [
             {
                 "affiliations": [
@@ -38397,44 +39371,70 @@
                 "orcid": "0000-0001-9760-8992",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "affiliations": [
+                    "avans-atgm"
+                ],
+                "id": "bazante1",
+                "joined": "2020-12",
+                "name": "Bazante Sanders",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
+            },
+            {
+                "email": "D.vrins@live.nl",
+                "former_affiliations": [
+                    "avans-atgm"
+                ],
+                "id": "dirowa",
+                "joined": "2021-10",
+                "linkedin": "Donny Vrins",
+                "name": "Donny Vrins",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dirowa/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/dirowa.json"
             }
         ],
-        "dir": "topics/contributing/tutorials/admin-knitting",
+        "dir": "topics/contributing/tutorials/python",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "contributing/admin-knitting",
+        "id": "contributing/python",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "The knitting script works OK?",
-            "Learn to rebase now, if you haven't yet",
-            "git am is not fun",
-            "If you have issues, ping me."
+            "Debugging code is an absolutely critical skill for students that they need ot become familiar with early on.",
+            "There are a lot of strategies you can teach students to give them the necessary skills for this, such as Wolf Fence debugging.",
+            "Or simply adding print statements so they can trace the code's execution.",
+            "Fading examples helps students become more independent as they work onwards through problems.",
+            "Conversely compounding problems are sometimes a good fit for homework to give numerous \"easy\" problems followed by some \"stretch\" goals that students can reach for, combining their previous work.",
+            "Pair progarmming is proven to improve student learning outcomes, when applied correctly."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2023-11-23",
         "objectives": [
-            "Update some text in an earlier commit"
+            "Learn about four different problem design ideas, and one teaching methodology."
         ],
-        "pageviews": 89,
-        "pub_date": "2021-06-07",
+        "pageviews": 440,
+        "pub_date": "2022-10-19",
         "questions": [
-            "How does it work?"
+            "What methods can I incorporate to improve student material uptake within my python courses?",
+            "How do I write problems that use these methodologies"
         ],
-        "short_id": "T00055",
+        "short_id": "T00068",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
+        "subtopic": "writing",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "5m",
-        "title": "Updating diffs in admin training",
+        "time_estimation": "2h",
+        "title": "Teaching Python",
         "tools": [],
         "topic_name": "contributing",
         "topic_name_human": "Contributing to the Galaxy Training Material",
@@ -38444,19 +39444,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "admin-knitting",
+        "tutorial_name": "python",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/admin-knitting/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/python/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/admin-knitting/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/admin-knitting/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/python/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/python/tutorial.json"
         },
-        "version": 9,
+        "version": 4,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 5,
-        "visitors": 48
+        "visit_duration": 39,
+        "visitors": 153
     },
     {
         "admin_install": {
@@ -38519,7 +39519,7 @@
             "Create a pull request",
             "Update a pull request"
         ],
-        "pageviews": 906,
+        "pageviews": 917,
         "pub_date": "2018-06-12",
         "questions": [
             "How can I contribute to an open-source project with GitHub and its interface"
@@ -38553,8 +39553,388 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 136,
-        "visitors": 572
+        "visit_duration": 135,
+        "visitors": 583
+    },
+    {
+        "abbreviations": {
+            "API": "Application Programming Interface",
+            "JSON": "JavaScript Object Notation"
+        },
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "bf675f34b056",
+                    "tool_panel_section_label": "Quality Control",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: multiqc\n  owner: iuc\n  revisions: bf675f34b056\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-content/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "bebatut",
+                "hexylena"
+            ],
+            "editing": [
+                "bgruening",
+                "shiltemann"
+            ],
+            "funding": [
+                "gallantries"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "affiliations": [
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
+                "fediverse_flavor": "mastodon",
+                "id": "bgruening",
+                "joined": "2017-09",
+                "linkedin": "bgruening",
+                "location": {
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
+                },
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+            },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            }
+        ],
+        "dir": "topics/contributing/tutorials/create-new-tutorial-content",
+        "edam_operation": [
+            "Sequencing quality control",
+            "Validation"
+        ],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "contributing/create-new-tutorial-content",
+        "js_requirements": {
+            "mathjax": 13775,
+            "mermaid": false
+        },
+        "key_points": [
+            "You can highlight questions, tools and hints with a special syntax",
+            "Self-learning can be done by questions and hidden answers"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-07-26",
+        "objectives": [
+            "Create hands-on",
+            "Use the different boxes"
+        ],
+        "pageviews": 9192,
+        "pub_date": "2017-06-25",
+        "questions": [
+            "How to write a tutorial with hands-on?",
+            "What are the different boxes?",
+            "How can I add a caption to an image?"
+        ],
+        "short_id": "T00058",
+        "short_tools": [
+            "multiqc",
+            "upload1"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "writing",
+        "supported_servers": [],
+        "symlink": null,
+        "time_estimation": "15m",
+        "title": "Creating content in Markdown",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
+            "upload1"
+        ],
+        "topic_name": "contributing",
+        "topic_name_human": "Contributing to the Galaxy Training Material",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "create-new-tutorial-content",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-content/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-content/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-content/tutorial.json"
+        },
+        "version": 81,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 123,
+        "visitors": 3303
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-topic/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "bebatut"
+            ],
+            "editing": [
+                "hexylena"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            }
+        ],
+        "dir": "topics/contributing/tutorials/create-new-topic",
+        "edam_operation": [],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "contributing/create-new-topic",
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "A new topic can be easily added for new tutorials"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-02-29",
+        "objectives": [
+            "Create a new topic",
+            "Set up the metadata for a topic"
+        ],
+        "pageviews": 1259,
+        "pub_date": "2018-06-04",
+        "questions": [
+            "How to include a new topic?",
+            "What kinds of Topics are possible?"
+        ],
+        "short_id": "T00056",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": [],
+        "symlink": null,
+        "time_estimation": "30m",
+        "title": "Including a new topic",
+        "tools": [],
+        "topic_name": "contributing",
+        "topic_name_human": "Contributing to the Galaxy Training Material",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "create-new-topic",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/create-new-topic/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-topic/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-topic/tutorial.json"
+        },
+        "version": 30,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 27,
+        "visitors": 863
     },
     {
         "admin_install": {
@@ -38704,7 +40084,7 @@
             "Distinguish different types of assessment & their role in supporting learner progression towards learning outcomes",
             "Summarise the benefits of course evaluation"
         ],
-        "pageviews": 571,
+        "pageviews": 578,
         "pub_date": "2022-09-23",
         "questions": [
             "Is the structured approach to course design?",
@@ -38784,8 +40164,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 174,
-        "visitors": 404
+        "visit_duration": 172,
+        "visitors": 411
     },
     {
         "admin_install": {
@@ -38795,68 +40175,338 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/generating-pdf/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/schemas/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            }
+        ],
+        "dir": "topics/contributing/tutorials/schemas",
+        "edam_operation": [],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "contributing/schemas",
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-07-04",
+        "objectives": [
+            "Know where to find all of the available metadata, so you can reference it later."
+        ],
+        "pageviews": 262,
+        "pub_date": "2022-06-02",
+        "questions": [
+            "What metadata is required or possible to set in a Tutorial, Slide, Topic, or FAQ"
+        ],
+        "short_id": "T00070",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": [],
+        "symlink": null,
+        "time_estimation": "10m",
+        "title": "GTN Metadata",
+        "tools": [],
+        "topic_name": "contributing",
+        "topic_name_human": "Contributing to the Galaxy Training Material",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "schemas",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/schemas/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/schemas/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/schemas/tutorial.json"
+        },
+        "version": 7,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 186,
+        "visitors": 192
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/gitpod/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            }
+        ],
+        "dir": "topics/contributing/tutorials/gitpod",
+        "edam_operation": [],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "contributing/gitpod",
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "GitPod can be used to serve the GTN training materials"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-14",
+        "objectives": [
+            "Preview the GTN website online via GitPod",
+            "Make changes to the GTN website and preview those changes"
+        ],
+        "pageviews": 1335,
+        "pub_date": "2021-06-24",
+        "questions": [
+            "How can I get a preview of the GTN website using GitPod?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "shiltemann"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "20M",
+                "speakers": [
+                    "shiltemann"
+                ],
+                "youtube_id": "_-wnsPttBCo"
+            }
+        ],
+        "short_id": "T00066",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "writing",
+        "supported_servers": [],
+        "symlink": null,
+        "time_estimation": "15m",
+        "title": "Running the GTN website online using GitPod",
+        "tools": [],
+        "topic_name": "contributing",
+        "topic_name_human": "Contributing to the Galaxy Training Material",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "gitpod",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/gitpod/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/gitpod/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/gitpod/tutorial.json"
+        },
+        "version": 9,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 167,
+        "visitors": 930
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-tours/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
                     "gallantries",
-                    "ifb",
-                    "elixir-europe"
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "affiliations": [
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
+                "fediverse_flavor": "mastodon",
+                "id": "bgruening",
+                "joined": "2017-09",
+                "linkedin": "bgruening",
+                "location": {
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
+                },
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+            },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
                 ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
                 "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
                 "fediverse_flavor": "mastodon",
-                "id": "bebatut",
+                "id": "shiltemann",
                 "joined": "2017-09",
-                "linkedin": "berenicebatut",
+                "linkedin": "shiltemann",
                 "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
                 },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             }
         ],
-        "dir": "topics/contributing/tutorials/generating-pdf",
+        "dir": "topics/contributing/tutorials/create-new-tutorial-tours",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "contributing/generating-pdf",
+        "id": "contributing/create-new-tutorial-tours",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "PDFs can be easily generated for the different tutorials to share with learnees or to keep a fixed version of a tutorial"
+            "The Interactive Tours are a good training object for self-learning at its own speed",
+            "It is now easy to create an Interactive Tour and test it"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2023-11-09",
         "objectives": [
-            "Generating PDFs"
+            "Creating a Galaxy tour from scratch",
+            "Deploying and running a tour"
         ],
-        "pageviews": 74,
-        "pub_date": "2018-06-04",
+        "pageviews": 407,
+        "pub_date": "2017-06-25",
         "questions": [
-            "How to generate PDF of the different tutorials and slides?"
+            "What is a Interactive Galaxy Tour?",
+            "How can we create an Interactive Tour?"
         ],
-        "short_id": "T00063",
+        "short_id": "T00061",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "10m",
-        "title": "Generating PDF artefacts of the website",
+        "time_estimation": "15m",
+        "title": "Creating Interactive Galaxy Tours",
         "tools": [],
         "topic_name": "contributing",
         "topic_name_human": "Contributing to the Galaxy Training Material",
@@ -38866,19 +40516,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "generating-pdf",
+        "tutorial_name": "create-new-tutorial-tours",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/generating-pdf/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-tours/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/generating-pdf/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/generating-pdf/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-tours/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-tours/tutorial.json"
         },
         "version": 12,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 217,
-        "visitors": 59
+        "visit_duration": 165,
+        "visitors": 249
     },
     {
         "admin_install": {
@@ -38888,8 +40538,95 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/slides-with-video/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-technical/tutorial.json",
         "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "affiliations": [
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
+                "fediverse_flavor": "mastodon",
+                "id": "bgruening",
+                "joined": "2017-09",
+                "linkedin": "bgruening",
+                "location": {
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
+                },
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+            },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
@@ -38920,43 +40657,50 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/contributing/tutorials/slides-with-video",
+        "dir": "topics/contributing/tutorials/create-new-tutorial-technical",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "contributing/slides-with-video",
+        "id": "contributing/create-new-tutorial-technical",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Thanks to the GTN, videos are easy to add",
-            "Be mindful of your captions. Short sentences are good!"
+            "Tools, data and workflows can be easily integrated in a Docker flavor to have a useful technical support for a tutorial",
+            "A Galaxy Docker flavor is a great support for training",
+            "A Galaxy Docker flavor can be deployed 'anywhere' and is scalable"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-03-24",
         "objectives": [
-            "Adding a video to a set of slides"
+            "Extracting the technical description for a tutorial",
+            "Populating an existing instance with the needed tools, data and workflows for a tutorial",
+            "Creating a Galaxy Docker flavor with the needed tools, data and workflows for a tutorial",
+            "Testing the Galaxy Docker flavor of a tutorial"
         ],
-        "pageviews": 312,
-        "pub_date": "2020-10-20",
+        "pageviews": 601,
+        "pub_date": "2017-06-25",
         "questions": [
-            "How can we add auto-generated video?",
-            "How does it work?",
-            "What do I need to do to make it optimal for viewers?"
+            "How can we define the technical infrastructure for a tutorial?",
+            "How to define the tools needed for a tutorial?",
+            "How to add the needed data directly in an instance?",
+            "How to add the workflows related to a tutorial?",
+            "How can we check the technical infrastructure is working?",
+            "How can we make an existing Galaxy instance able to run a tutorial?"
         ],
-        "short_id": "T00071",
+        "short_id": "T00060",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "writing",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "20m",
-        "title": "Adding auto-generated video to your slides",
+        "time_estimation": "30m",
+        "title": "Tools, Data, and Workflows for tutorials",
         "tools": [],
         "topic_name": "contributing",
         "topic_name_human": "Contributing to the Galaxy Training Material",
@@ -38966,19 +40710,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "slides-with-video",
+        "tutorial_name": "create-new-tutorial-technical",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/slides-with-video/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-technical/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/slides-with-video/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/slides-with-video/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-technical/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-technical/tutorial.json"
         },
-        "version": 12,
+        "version": 25,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 262,
-        "visitors": 235
+        "visit_duration": 109,
+        "visitors": 422
     },
     {
         "admin_install": {
@@ -38988,88 +40732,74 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/gitpod/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/admin-knitting/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
-                    "CINECA-Project",
                     "gallantries",
+                    "by-covid",
                     "erasmusmc",
                     "elixir-europe",
-                    "uni-freiburg"
+                    "elixir-converge"
                 ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
+                "contact_for_training": false,
                 "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
                 "joined": "2017-09",
-                "linkedin": "shiltemann",
                 "location": {
                     "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
+                    "lat": 51.91,
+                    "lon": 4.46
                 },
                 "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/contributing/tutorials/gitpod",
+        "dir": "topics/contributing/tutorials/admin-knitting",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "contributing/gitpod",
+        "id": "contributing/admin-knitting",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "GitPod can be used to serve the GTN training materials"
+            "The knitting script works OK?",
+            "Learn to rebase now, if you haven't yet",
+            "git am is not fun",
+            "If you have issues, ping me."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2023-11-23",
         "objectives": [
-            "Preview the GTN website online via GitPod",
-            "Make changes to the GTN website and preview those changes"
+            "Update some text in an earlier commit"
         ],
-        "pageviews": 1314,
-        "pub_date": "2021-06-24",
+        "pageviews": 89,
+        "pub_date": "2021-06-07",
         "questions": [
-            "How can I get a preview of the GTN website using GitPod?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "shiltemann"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "20M",
-                "speakers": [
-                    "shiltemann"
-                ],
-                "youtube_id": "_-wnsPttBCo"
-            }
+            "How does it work?"
         ],
-        "short_id": "T00066",
+        "short_id": "T00055",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "writing",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "15m",
-        "title": "Running the GTN website online using GitPod",
+        "time_estimation": "5m",
+        "title": "Updating diffs in admin training",
         "tools": [],
         "topic_name": "contributing",
         "topic_name_human": "Contributing to the Galaxy Training Material",
@@ -39079,19 +40809,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "gitpod",
+        "tutorial_name": "admin-knitting",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/gitpod/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/admin-knitting/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/gitpod/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/gitpod/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/admin-knitting/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/admin-knitting/tutorial.json"
         },
         "version": 9,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 168,
-        "visitors": 916
+        "visit_duration": 5,
+        "visitors": 48
     },
     {
         "admin_install": {
@@ -39101,7 +40831,7 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-quiz/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/slides-with-video/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
@@ -39133,49 +40863,43 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/contributing/tutorials/create-new-tutorial-quiz",
+        "dir": "topics/contributing/tutorials/slides-with-video",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "contributing/create-new-tutorial-quiz",
+        "id": "contributing/slides-with-video",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Quizzes are helpful for both self-directed learning, and ensuring that in synchronous classes, students are all following the material"
+            "Thanks to the GTN, videos are easy to add",
+            "Be mindful of your captions. Short sentences are good!"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2022-10-18",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Create a quiz"
+            "Adding a video to a set of slides"
         ],
-        "pageviews": 86,
-        "pub_date": "2022-05-19",
+        "pageviews": 319,
+        "pub_date": "2020-10-20",
         "questions": [
-            "How to make a quiz?"
-        ],
-        "quiz": [
-            {
-                "contributors": [
-                    "hexylena"
-                ],
-                "id": "a.yaml",
-                "path": "topics/contributing/tutorials/create-new-tutorial-quiz/quiz/a.yaml",
-                "title": "Test Quiz"
-            }
+            "How can we add auto-generated video?",
+            "How does it work?",
+            "What do I need to do to make it optimal for viewers?"
         ],
-        "short_id": "T00059",
+        "short_id": "T00071",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
+        "subtopic": "writing",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "15m",
-        "title": "Adding Quizzes to your Tutorial",
+        "time_estimation": "20m",
+        "title": "Adding auto-generated video to your slides",
         "tools": [],
         "topic_name": "contributing",
         "topic_name_human": "Contributing to the Galaxy Training Material",
@@ -39185,54 +40909,29 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "create-new-tutorial-quiz",
+        "tutorial_name": "slides-with-video",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-quiz/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/slides-with-video/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-quiz/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-quiz/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/slides-with-video/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/slides-with-video/tutorial.json"
         },
-        "version": 3,
+        "version": 12,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 16,
-        "visitors": 73
+        "visit_duration": 258,
+        "visitors": 242
     },
     {
-        "abbreviations": {
-            "API": "Application Programming Interface",
-            "JSON": "JavaScript Object Notation"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "bf675f34b056",
-                    "tool_panel_section_label": "Quality Control",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: multiqc\n  owner: iuc\n  revisions: bf675f34b056\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-content/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "bebatut",
-                "hexylena"
-            ],
-            "editing": [
-                "bgruening",
-                "shiltemann"
-            ],
-            "funding": [
-                "gallantries"
-            ]
+            "tools": []
         },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/generating-pdf/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
@@ -39259,172 +40958,42 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
                 "twitter": "bebatut",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
-                "fediverse_flavor": "mastodon",
-                "id": "bgruening",
-                "joined": "2017-09",
-                "linkedin": "bgruening",
-                "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
-                },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/contributing/tutorials/create-new-tutorial-content",
-        "edam_operation": [
-            "Sequencing quality control",
-            "Validation"
-        ],
+        "dir": "topics/contributing/tutorials/generating-pdf",
+        "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "contributing/create-new-tutorial-content",
+        "id": "contributing/generating-pdf",
         "js_requirements": {
-            "mathjax": 13775,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "You can highlight questions, tools and hints with a special syntax",
-            "Self-learning can be done by questions and hidden answers"
+            "PDFs can be easily generated for the different tutorials to share with learnees or to keep a fixed version of a tutorial"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-26",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Create hands-on",
-            "Use the different boxes"
+            "Generating PDFs"
         ],
-        "pageviews": 9110,
-        "pub_date": "2017-06-25",
+        "pageviews": 74,
+        "pub_date": "2018-06-04",
         "questions": [
-            "How to write a tutorial with hands-on?",
-            "What are the different boxes?",
-            "How can I add a caption to an image?"
-        ],
-        "short_id": "T00058",
-        "short_tools": [
-            "upload1",
-            "multiqc"
+            "How to generate PDF of the different tutorials and slides?"
         ],
+        "short_id": "T00063",
+        "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "writing",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "15m",
-        "title": "Creating content in Markdown",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
-            "upload1"
-        ],
+        "time_estimation": "10m",
+        "title": "Generating PDF artefacts of the website",
+        "tools": [],
         "topic_name": "contributing",
         "topic_name_human": "Contributing to the Galaxy Training Material",
         "tours": false,
@@ -39433,19 +41002,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "create-new-tutorial-content",
+        "tutorial_name": "generating-pdf",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-content/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/generating-pdf/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-content/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-content/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/generating-pdf/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/generating-pdf/tutorial.json"
         },
-        "version": 81,
+        "version": 12,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 122,
-        "visitors": 3243
+        "visit_duration": 217,
+        "visitors": 59
     },
     {
         "admin_install": {
@@ -39455,7 +41024,7 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-technical/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/running-jekyll/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
@@ -39543,81 +41112,44 @@
                 "orcid": "0000-0003-3803-468X",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/contributing/tutorials/create-new-tutorial-technical",
+        "dir": "topics/contributing/tutorials/running-jekyll",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "contributing/create-new-tutorial-technical",
+        "id": "contributing/running-jekyll",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Tools, data and workflows can be easily integrated in a Docker flavor to have a useful technical support for a tutorial",
-            "A Galaxy Docker flavor is a great support for training",
-            "A Galaxy Docker flavor can be deployed 'anywhere' and is scalable"
+            "Checking the generated website can be done locally"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-24",
+        "mod_date": "2024-07-03",
         "objectives": [
-            "Extracting the technical description for a tutorial",
-            "Populating an existing instance with the needed tools, data and workflows for a tutorial",
-            "Creating a Galaxy Docker flavor with the needed tools, data and workflows for a tutorial",
-            "Testing the Galaxy Docker flavor of a tutorial"
+            "Installing packages needed for rendering the webpage",
+            "Running the GTN material website locally",
+            "Tracking changes to the content live in the webbrowser"
         ],
-        "pageviews": 594,
+        "pageviews": 1540,
         "pub_date": "2017-06-25",
         "questions": [
-            "How can we define the technical infrastructure for a tutorial?",
-            "How to define the tools needed for a tutorial?",
-            "How to add the needed data directly in an instance?",
-            "How to add the workflows related to a tutorial?",
-            "How can we check the technical infrastructure is working?",
-            "How can we make an existing Galaxy instance able to run a tutorial?"
+            "How to setup the infrastructure to build training webpages?"
         ],
-        "short_id": "T00060",
+        "short_id": "T00069",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "writing",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "30m",
-        "title": "Tools, Data, and Workflows for tutorials",
+        "time_estimation": "15m",
+        "title": "Running the GTN website locally",
         "tools": [],
         "topic_name": "contributing",
         "topic_name_human": "Contributing to the Galaxy Training Material",
@@ -39627,19 +41159,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "create-new-tutorial-technical",
+        "tutorial_name": "running-jekyll",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-technical/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/running-jekyll/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-technical/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-technical/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/running-jekyll/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/running-jekyll/tutorial.json"
         },
         "version": 25,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 109,
-        "visitors": 415
+        "visit_duration": 216,
+        "visitors": 1111
     },
     {
         "admin_install": {
@@ -39649,18 +41181,7 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/python/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "hexylena"
-            ],
-            "editing": [
-                "bazante1"
-            ],
-            "testing": [
-                "dirowa"
-            ]
-        },
+        "api": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-quiz/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
@@ -39690,70 +41211,51 @@
                 "orcid": "0000-0001-9760-8992",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "affiliations": [
-                    "avans-atgm"
-                ],
-                "id": "bazante1",
-                "joined": "2020-12",
-                "name": "Bazante Sanders",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
-            },
-            {
-                "email": "D.vrins@live.nl",
-                "former_affiliations": [
-                    "avans-atgm"
-                ],
-                "id": "dirowa",
-                "joined": "2021-10",
-                "linkedin": "Donny Vrins",
-                "name": "Donny Vrins",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dirowa/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/dirowa.json"
             }
         ],
-        "dir": "topics/contributing/tutorials/python",
+        "dir": "topics/contributing/tutorials/create-new-tutorial-quiz",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "contributing/python",
+        "id": "contributing/create-new-tutorial-quiz",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Debugging code is an absolutely critical skill for students that they need ot become familiar with early on.",
-            "There are a lot of strategies you can teach students to give them the necessary skills for this, such as Wolf Fence debugging.",
-            "Or simply adding print statements so they can trace the code's execution.",
-            "Fading examples helps students become more independent as they work onwards through problems.",
-            "Conversely compounding problems are sometimes a good fit for homework to give numerous \"easy\" problems followed by some \"stretch\" goals that students can reach for, combining their previous work.",
-            "Pair progarmming is proven to improve student learning outcomes, when applied correctly."
+            "Quizzes are helpful for both self-directed learning, and ensuring that in synchronous classes, students are all following the material"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-23",
+        "mod_date": "2022-10-18",
         "objectives": [
-            "Learn about four different problem design ideas, and one teaching methodology."
+            "Create a quiz"
         ],
-        "pageviews": 429,
-        "pub_date": "2022-10-19",
+        "pageviews": 86,
+        "pub_date": "2022-05-19",
         "questions": [
-            "What methods can I incorporate to improve student material uptake within my python courses?",
-            "How do I write problems that use these methodologies"
+            "How to make a quiz?"
         ],
-        "short_id": "T00068",
+        "quiz": [
+            {
+                "contributors": [
+                    "hexylena"
+                ],
+                "id": "a.yaml",
+                "path": "topics/contributing/tutorials/create-new-tutorial-quiz/quiz/a.yaml",
+                "title": "Test Quiz"
+            }
+        ],
+        "short_id": "T00059",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "writing",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "2h",
-        "title": "Teaching Python",
+        "time_estimation": "15m",
+        "title": "Adding Quizzes to your Tutorial",
         "tools": [],
         "topic_name": "contributing",
         "topic_name_human": "Contributing to the Galaxy Training Material",
@@ -39763,19 +41265,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "python",
+        "tutorial_name": "create-new-tutorial-quiz",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/python/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/contributing/tutorials/create-new-tutorial-quiz/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/python/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/python/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-quiz/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/create-new-tutorial-quiz/tutorial.json"
         },
-        "version": 4,
+        "version": 3,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 40,
-        "visitors": 143
+        "visit_duration": 16,
+        "visitors": 73
     },
     {
         "abbreviations": {
@@ -39888,14 +41390,14 @@
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-18",
+        "mod_date": "2024-10-02",
         "objectives": [
             "Learn about metadata and findability",
             "Learn how to support system and content curation"
         ],
         "pageviews": 0,
         "priority": 3,
-        "pub_date": "2024-08-18",
+        "pub_date": "2024-10-02",
         "questions": [
             "What are the FAIR training materials?",
             "How to test, reproduce and share your content?",
@@ -39955,31 +41457,108 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "bcftools_consensus",
-                    "owner": "iuc",
-                    "revisions": "e522022137f6",
-                    "tool_panel_section_label": "Variant Calling",
+                    "name": "ctb_frankenstein_ligand",
+                    "owner": "bgruening",
+                    "revisions": "8e214e52e461",
+                    "tool_panel_section_label": "ChemicalToolBox",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "compose_text_param",
-                    "owner": "iuc",
-                    "revisions": "e188c9826e0f",
-                    "tool_panel_section_label": "Expression Tools",
+                    "name": "ctb_frankenstein_ligand",
+                    "owner": "bgruening",
+                    "revisions": "7255688c77f3",
+                    "tool_panel_section_label": "ChemicalToolBox",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pangolin",
-                    "owner": "iuc",
-                    "revisions": "b6abccb1f25b",
-                    "tool_panel_section_label": "Phylogenetics",
+                    "name": "enumerate_charges",
+                    "owner": "bgruening",
+                    "revisions": "2a868592ebcb",
+                    "tool_panel_section_label": "ChemicalToolBox",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "snpsift",
-                    "owner": "iuc",
-                    "revisions": "5fab4f81391d",
-                    "tool_panel_section_label": "Variant Calling",
+                    "name": "enumerate_charges",
+                    "owner": "bgruening",
+                    "revisions": "67ee76f0e497",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openbabel_compound_convert",
+                    "owner": "bgruening",
+                    "revisions": "b59c91adeac1",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openbabel_compound_convert",
+                    "owner": "bgruening",
+                    "revisions": "e2c36f62e22f",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rdock_rbcavity",
+                    "owner": "bgruening",
+                    "revisions": "744a777e9f90",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rdock_rbdock",
+                    "owner": "bgruening",
+                    "revisions": "a22969b08177",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rxdock_rbcavity",
+                    "owner": "bgruening",
+                    "revisions": "7fac8e7a12d5",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rxdock_rbdock",
+                    "owner": "bgruening",
+                    "revisions": "6fe6b0e10ed6",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "split_file_to_collection",
+                    "owner": "bgruening",
+                    "revisions": "0046692724f9",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "split_file_to_collection",
+                    "owner": "bgruening",
+                    "revisions": "6cbe2f30c2d7",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sucos_max_score",
+                    "owner": "bgruening",
+                    "revisions": "d4c67ced6abc",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sucos_max_score",
+                    "owner": "bgruening",
+                    "revisions": "9b48456a96fe",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "xchem_transfs_scoring",
+                    "owner": "bgruening",
+                    "revisions": "f6f9b47d02b6",
+                    "tool_panel_section_label": "ChemicalToolBox",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
@@ -39991,8 +41570,8 @@
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bcftools_consensus\n  owner: iuc\n  revisions: e522022137f6\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: compose_text_param\n  owner: iuc\n  revisions: e188c9826e0f\n  tool_panel_section_label: Expression Tools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pangolin\n  owner: iuc\n  revisions: b6abccb1f25b\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpsift\n  owner: iuc\n  revisions: 5fab4f81391d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-automation/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: ctb_frankenstein_ligand\n  owner: bgruening\n  revisions: 8e214e52e461\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ctb_frankenstein_ligand\n  owner: bgruening\n  revisions: 7255688c77f3\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: enumerate_charges\n  owner: bgruening\n  revisions: 2a868592ebcb\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: enumerate_charges\n  owner: bgruening\n  revisions: 67ee76f0e497\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_compound_convert\n  owner: bgruening\n  revisions: b59c91adeac1\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_compound_convert\n  owner: bgruening\n  revisions: e2c36f62e22f\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rdock_rbcavity\n  owner: bgruening\n  revisions: 744a777e9f90\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rdock_rbdock\n  owner: bgruening\n  revisions: a22969b08177\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rxdock_rbcavity\n  owner: bgruening\n  revisions: 7fac8e7a12d5\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rxdock_rbdock\n  owner: bgruening\n  revisions: 6fe6b0e10ed6\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_to_collection\n  owner: bgruening\n  revisions: '0046692724f9'\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_to_collection\n  owner: bgruening\n  revisions: 6cbe2f30c2d7\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sucos_max_score\n  owner: bgruening\n  revisions: d4c67ced6abc\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sucos_max_score\n  owner: bgruening\n  revisions: 9b48456a96fe\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xchem_transfs_scoring\n  owner: bgruening\n  revisions: f6f9b47d02b6\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/covid19-docking/tutorial.json",
         "contributors": [
             {
                 "elixir_node": "de",
@@ -40005,186 +41584,157 @@
                 "name": "Simon Bray",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
-            },
-            {
-                "affiliations": [
-                    "by-covid",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "fediverse": "https://scholar.social/@zerodivision",
-                "fediverse_flavor": "mastodon",
-                "id": "wm75",
-                "joined": "2017-09",
-                "matrix": "wm75:matrix.org",
-                "name": "Wolfgang Maier",
-                "orcid": "0000-0002-9464-6640",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
             }
         ],
-        "dir": "topics/galaxy-interface/tutorials/workflow-automation",
-        "edam_operation": [
-            "Variant classification",
-            "Tree-based sequence alignment"
-        ],
+        "dir": "topics/computational-chemistry/tutorials/covid19-docking",
+        "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "galaxy-interface/workflow-automation",
-        "inexact_supported_servers": [
-            "UseGalaxy.fr"
-        ],
+        "id": "computational-chemistry/covid19-docking",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Workflows can be executed not only through the web browser, but also via the command line.",
-            "Executing workflows programmatically allows automation of analyses."
+            "Galaxy can support large, rapid studies in computational chemistry",
+            "Protein-ligand docking contributes to the discovery of new drugs"
         ],
         "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Learn to use the `planemo run` subcommand to run workflows from the command line.",
-            "Be able to write simple shell scripts for running multiple workflows concurrently or sequentially.",
-            "Learn how to use Pangolin to assign annotated variants to lineages."
+            "Understand how Galaxy was used to perform docking and pose scoring on the SARS-CoV-2 main protease (MPro).",
+            "Replicate the study on a (very) small scale",
+            "Gain familiarity with the docking and scoring techniques involved."
         ],
-        "pageviews": 2720,
-        "pub_date": "2021-06-08",
+        "pageviews": 4568,
+        "pub_date": "2020-03-27",
         "questions": [
-            "How can I schedule and run tens or hundreds of Galaxy workflows easily?",
-            "How can I automate my analyses when large amounts of data are being produced daily?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "simonbray"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "30M",
-                "speakers": [
-                    "simonbray"
-                ],
-                "youtube_id": "o39QjVnLG68"
-            }
+            "How can candidate ligands be generated and docked to a protein in Galaxy?",
+            "How can the poses of the docked ligands be evaluated?",
+            "How can a workflow for drug virtual screening be constructed in Galaxy?"
         ],
         "requirements": [
             {
-                "title": "Familiarity with Galaxy and basic associated concepts, in particular workflows",
-                "type": "none"
-            },
-            {
-                "title": "Basic knowledge of the command line",
-                "type": "none"
+                "topic_name": "computational-chemistry",
+                "tutorials": [
+                    "cheminformatics"
+                ],
+                "type": "internal"
             }
         ],
-        "short_id": "T00162",
+        "short_id": "T00049",
         "short_tools": [
-            "bcftools_consensus",
-            "compose_text_param",
-            "pangolin",
-            "snpSift_filter",
-            "collapse_dataset"
+            "openbabel_compound_convert",
+            "split_file_to_collection",
+            "enumerate_charges",
+            "rxdock_rbcavity",
+            "sucos_max_score",
+            "collapse_dataset",
+            "xchem_pose_scoring",
+            "rxdock_rbdock",
+            "ctb_frankenstein_ligand",
+            "rdock_rbdock",
+            "rdock_rbcavity",
+            "xchem_transfs_scoring"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "workflows",
         "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                }
-            ]
+            "exact": [],
+            "inexact": []
         },
         "symlink": null,
         "tags": [
-            "workflows",
-            "variant-analysis",
-            "covid19"
+            "covid19",
+            "one-health"
         ],
-        "time_estimation": "2h",
-        "title": "Automating Galaxy workflows using the command line",
+        "time_estimation": "2H",
+        "title": "Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10",
-            "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/2013.1-0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/0.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/2020.03.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.2.2.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbcavity/rdock_rbcavity/0.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbdock/rdock_rbdock/0.1.4",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_rbcavity/rxdock_rbcavity/0.1.5",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_rbdock/rxdock_rbdock/0.1.5",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.4.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/sucos_max_score/sucos_max_score/0.2.3",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/sucos_max_score/sucos_max_score/2020.03.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/xchem_transfs_scoring/xchem_transfs_scoring/0.4.0",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
+            "xchem_pose_scoring"
         ],
-        "topic_name": "galaxy-interface",
-        "topic_name_human": "Using Galaxy and Managing your Data",
+        "topic_name": "computational-chemistry",
+        "topic_name_human": "Computational chemistry",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "workflow-automation",
+        "tutorial_name": "covid19-docking",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-automation/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/computational-chemistry/tutorials/covid19-docking/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-automation/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-automation/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/covid19-docking/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/covid19-docking/tutorial.json"
         },
-        "version": 8,
+        "version": 10,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 118,
-        "visitors": 2200,
+        "visit_duration": 179,
+        "visitors": 2706,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0002-9464-6640",
-                        "name": "Wolfgang Maier"
-                    }
-                ],
-                "description": "workflow-automation",
+                "creators": [],
+                "description": "Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring",
                 "features": {
                     "comments": false,
-                    "parameters": true,
+                    "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nVariant calls\"]\n  1[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nmin-AF for consensus variant\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genome\"]\n  3[label=\"Compose text parameter value\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"SnpSift Filter\"]\n  3 -> 4 [label=\"out1\"]\n  0 -> 4 [label=\"output\"]\n  kee67c5edff7c404bad2019259edbc671[color=lightseagreen,label=\"Output\\nconsensus_variants\"]\n  4 -> kee67c5edff7c404bad2019259edbc671\n  5[label=\"bcftools consensus\"]\n  4 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  k9028f80e411240d89a49f671677d304f[color=lightseagreen,label=\"Output\\nconsensus\"]\n  5 -> k9028f80e411240d89a49f671677d304f\n  6[label=\"Collapse Collection\"]\n  5 -> 6 [label=\"output_file\"]\n  k1dd7978eb90742d68fc4f6fadeefcad1[color=lightseagreen,label=\"Output\\nmultisample_consensus_fasta\"]\n  6 -> k1dd7978eb90742d68fc4f6fadeefcad1\n  7[label=\"Pangolin\"]\n  6 -> 7 [label=\"output\"]\n  ke02d2cfb98424069957c6cf4ec197056[color=lightseagreen,label=\"Output\\npangolin_results\"]\n  7 -> ke02d2cfb98424069957c6cf4ec197056\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCandidates\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMpro-x0195_0_apo-desolv.pdb\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhits.sdf\"]\n  3[label=\"Enumerate changes\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Compound conversion\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Create Frankenstein ligand\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"Compound conversion\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"rDock cavity definition\"]\n  4 -> 7 [label=\"outfile\"]\n  5 -> 7 [label=\"outfile\"]\n  8[label=\"Split file\"]\n  6 -> 8 [label=\"outfile\"]\n  9[label=\"rDock docking\"]\n  4 -> 9 [label=\"outfile\"]\n  8 -> 9 [label=\"list_output_sdf\"]\n  7 -> 9 [label=\"activesite\"]\n  10[label=\"Collapse Collection\"]\n  9 -> 10 [label=\"output\"]\n  11[label=\"XChem TransFS pose scoring\"]\n  1 -> 11 [label=\"output\"]\n  10 -> 11 [label=\"output\"]\n  12[label=\"Max SuCOS score\"]\n  11 -> 12 [label=\"output\"]\n  2 -> 12 [label=\"output\"]\n}",
                 "history": [
                     {
-                        "hash": "486585510e665c834a43668e2a769dd69654b9d6",
-                        "message": "add WF automation tutorial",
+                        "hash": "cf8b1cb0509e73e534c234076c8bd055379823c5",
+                        "message": "Update some workflow names for consistency",
+                        "num": 4,
+                        "short_hash": "cf8b1cb05",
+                        "unix": "1598836271"
+                    },
+                    {
+                        "hash": "60a21218780027dcf65a5f37b94148b0771303e1",
+                        "message": "update with covid19 tut with frankenstein ligand tool",
+                        "num": 3,
+                        "short_hash": "60a212187",
+                        "unix": "1591084355"
+                    },
+                    {
+                        "hash": "2bffcbdc75d8aaf32b06acc2f9f493931782546d",
+                        "message": "lint",
+                        "num": 2,
+                        "short_hash": "2bffcbdc7",
+                        "unix": "1585304017"
+                    },
+                    {
+                        "hash": "62d30105b34ea23f3280539d9880037639aa770e",
+                        "message": "linting covid19 cheminformatics tutorial",
                         "num": 1,
-                        "short_hash": "486585510",
-                        "unix": "1622197006"
+                        "short_hash": "62d30105b",
+                        "unix": "1585300158"
                     }
                 ],
                 "inputs": [
@@ -40197,28 +41747,28 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Variant calls"
+                                "name": "Candidates"
                             }
                         ],
-                        "label": "Variant calls",
-                        "name": "Input dataset collection",
+                        "label": "Candidates",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 425.43333435058594,
-                            "height": 61.80000305175781,
-                            "left": 297,
-                            "right": 497,
-                            "top": 363.6333312988281,
-                            "width": 200,
-                            "x": 297,
-                            "y": 363.6333312988281
+                            "left": 218,
+                            "top": 200
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"name\": \"Candidates\"}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "fca4e710-87a7-4cb6-9ff1-f9a8dc84ca37",
-                        "workflow_outputs": []
+                        "type": "data_input",
+                        "uuid": "47bf8c53-ae1e-4af6-bece-6adfd74b627c",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "cdab037e-aee1-49b8-a998-cd9fe7ddcdb7"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
@@ -40229,32 +41779,26 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "min-AF for consensus variant"
+                                "name": "Mpro-x0195_0_apo-desolv.pdb"
                             }
                         ],
-                        "label": "min-AF for consensus variant",
-                        "name": "Input parameter",
+                        "label": "Mpro-x0195_0_apo-desolv.pdb",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 619.1000061035156,
-                            "height": 102.60000610351562,
-                            "left": 295.45001220703125,
-                            "right": 495.45001220703125,
-                            "top": 516.5,
-                            "width": 200,
-                            "x": 295.45001220703125,
-                            "y": 516.5
+                            "left": 218,
+                            "top": 289.76666259765625
                         },
                         "tool_id": null,
-                        "tool_state": "{\"default\": 0.7, \"parameter_type\": \"float\", \"optional\": true}",
+                        "tool_state": "{\"name\": \"Mpro-x0195_0_apo-desolv.pdb\"}",
                         "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "52664bd7-b500-40a1-935b-8ac6df7003e5",
+                        "type": "data_input",
+                        "uuid": "156f4aeb-d160-456a-974e-7884b79cb83a",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "5db03aa3-a62d-4a39-8712-d48911abf2bb"
+                                "uuid": "1fd1c624-37c6-4874-b863-a40eac5e4994"
                             }
                         ]
                     },
@@ -40267,361 +41811,213 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Reference genome"
+                                "name": "hits.sdf"
                             }
                         ],
-                        "label": "Reference genome",
+                        "label": "hits.sdf",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 734.8500366210938,
-                            "height": 82.20001220703125,
-                            "left": 749.816650390625,
-                            "right": 949.816650390625,
-                            "top": 652.6500244140625,
-                            "width": 200,
-                            "x": 749.816650390625,
-                            "y": 652.6500244140625
+                            "left": 218,
+                            "top": 400.5333251953125
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"name\": \"hits.sdf\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "4a2c6df2-fb1e-42d8-96d5-6765ca85c214",
-                        "workflow_outputs": []
+                        "uuid": "dd2d3bc0-8138-4e66-b2d9-e5e90e27b659",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "1c8fb3cc-52ad-4f62-a00d-80b14b2c1d4a"
+                            }
+                        ]
                     }
                 ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nVariant calls\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nmin-AF for consensus variant\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Compose text parameter value\"];\n  1 -->|output| 3;\n  4[\"SnpSift Filter\"];\n  3 -->|out1| 4;\n  0 -->|output| 4;\n  ee67c5ed-ff7c-404b-ad20-19259edbc671[\"Output\\nconsensus_variants\"];\n  4 --> ee67c5ed-ff7c-404b-ad20-19259edbc671;\n  style ee67c5ed-ff7c-404b-ad20-19259edbc671 stroke:#2c3143,stroke-width:4px;\n  5[\"bcftools consensus\"];\n  4 -->|output| 5;\n  2 -->|output| 5;\n  9028f80e-4112-40d8-9a49-f671677d304f[\"Output\\nconsensus\"];\n  5 --> 9028f80e-4112-40d8-9a49-f671677d304f;\n  style 9028f80e-4112-40d8-9a49-f671677d304f stroke:#2c3143,stroke-width:4px;\n  6[\"Collapse Collection\"];\n  5 -->|output_file| 6;\n  1dd7978e-b907-42d6-8fc4-f6fadeefcad1[\"Output\\nmultisample_consensus_fasta\"];\n  6 --> 1dd7978e-b907-42d6-8fc4-f6fadeefcad1;\n  style 1dd7978e-b907-42d6-8fc4-f6fadeefcad1 stroke:#2c3143,stroke-width:4px;\n  7[\"Pangolin\"];\n  6 -->|output| 7;\n  e02d2cfb-9842-4069-957c-6cf4ec197056[\"Output\\npangolin_results\"];\n  7 --> e02d2cfb-9842-4069-957c-6cf4ec197056;\n  style e02d2cfb-9842-4069-957c-6cf4ec197056 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "vcf2lineage",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nCandidates\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nMpro-x0195_0_apo-desolv.pdb\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nhits.sdf\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Enumerate changes\"];\n  0 -->|output| 3;\n  4[\"Compound conversion\"];\n  1 -->|output| 4;\n  5[\"Create Frankenstein ligand\"];\n  2 -->|output| 5;\n  6[\"Compound conversion\"];\n  3 -->|output| 6;\n  7[\"rDock cavity definition\"];\n  4 -->|outfile| 7;\n  5 -->|outfile| 7;\n  8[\"Split file\"];\n  6 -->|outfile| 8;\n  9[\"rDock docking\"];\n  4 -->|outfile| 9;\n  8 -->|list_output_sdf| 9;\n  7 -->|activesite| 9;\n  10[\"Collapse Collection\"];\n  9 -->|output| 10;\n  11[\"XChem TransFS pose scoring\"];\n  1 -->|output| 11;\n  10 -->|output| 11;\n  12[\"Max SuCOS score\"];\n  11 -->|output| 12;\n  2 -->|output| 12;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring",
                 "outputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "min-AF for consensus variant"
+                                "name": "Candidates"
                             }
                         ],
-                        "label": "min-AF for consensus variant",
-                        "name": "Input parameter",
+                        "label": "Candidates",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 619.1000061035156,
-                            "height": 102.60000610351562,
-                            "left": 295.45001220703125,
-                            "right": 495.45001220703125,
-                            "top": 516.5,
-                            "width": 200,
-                            "x": 295.45001220703125,
-                            "y": 516.5
+                            "left": 218,
+                            "top": 200
                         },
                         "tool_id": null,
-                        "tool_state": "{\"default\": 0.7, \"parameter_type\": \"float\", \"optional\": true}",
+                        "tool_state": "{\"name\": \"Candidates\"}",
                         "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "52664bd7-b500-40a1-935b-8ac6df7003e5",
+                        "type": "data_input",
+                        "uuid": "47bf8c53-ae1e-4af6-bece-6adfd74b627c",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "5db03aa3-a62d-4a39-8712-d48911abf2bb"
+                                "uuid": "cdab037e-aee1-49b8-a998-cd9fe7ddcdb7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "filter_expression|expr": {
-                                "id": 3,
-                                "output_name": "out1"
-                            },
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "SnpSift Filter",
-                        "outputs": [
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "vcf"
+                                "description": "",
+                                "name": "Mpro-x0195_0_apo-desolv.pdb"
                             }
                         ],
+                        "label": "Mpro-x0195_0_apo-desolv.pdb",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 506.5,
-                            "height": 144,
-                            "left": 750.2833251953125,
-                            "right": 950.2833251953125,
-                            "top": 362.5,
-                            "width": 200,
-                            "x": 750.2833251953125,
-                            "y": 362.5
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Consensus variants"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2e497a770bca",
-                            "name": "snpsift",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 218,
+                            "top": 289.76666259765625
                         },
-                        "tool_state": "{\"filter_expression\": {\"type\": \"simple\", \"__current_case__\": 0, \"expr\": {\"__class__\": \"ConnectedValue\"}}, \"filtering\": {\"mode\": \"entries\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inverse\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.3+t.galaxy1",
-                        "type": "tool",
-                        "uuid": "3673b687-1ba0-42f2-ba13-fa3130462079",
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Mpro-x0195_0_apo-desolv.pdb\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "156f4aeb-d160-456a-974e-7884b79cb83a",
                         "workflow_outputs": [
                             {
-                                "label": "consensus_variants",
+                                "label": null,
                                 "output_name": "output",
-                                "uuid": "ee67c5ed-ff7c-404b-ad20-19259edbc671"
+                                "uuid": "1fd1c624-37c6-4874-b863-a40eac5e4994"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10",
+                        "content_id": null,
                         "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 4,
-                                "output_name": "output"
-                            },
-                            "reference_source|fasta_ref": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
+                        "id": 2,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool bcftools consensus",
-                                "name": "input_file"
-                            },
-                            {
-                                "description": "runtime parameter for tool bcftools consensus",
-                                "name": "reference_source"
-                            },
-                            {
-                                "description": "runtime parameter for tool bcftools consensus",
-                                "name": "sec_default"
-                            }
-                        ],
-                        "label": null,
-                        "name": "bcftools consensus",
-                        "outputs": [
-                            {
-                                "name": "output_file",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 535.5666809082031,
-                            "height": 174.39999389648438,
-                            "left": 993.8333129882812,
-                            "right": 1193.8333129882812,
-                            "top": 361.16668701171875,
-                            "width": 200,
-                            "x": 993.8333129882812,
-                            "y": 361.16668701171875
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_file": {
-                                "action_arguments": {
-                                    "newname": "Consensus sequences"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_file"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10",
-                        "tool_shed_repository": {
-                            "changeset_revision": "e522022137f6",
-                            "name": "bcftools_consensus",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"chain\": \"false\", \"input_file\": {\"__class__\": \"RuntimeValue\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"RuntimeValue\"}}, \"rename\": \"true\", \"sec_default\": {\"mask\": {\"__class__\": \"RuntimeValue\"}, \"iupac_codes\": \"false\", \"sample\": \"\", \"select_haplotype\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.10",
-                        "type": "tool",
-                        "uuid": "5d2e8bea-3e75-4453-9494-b5fd52b2f528",
-                        "workflow_outputs": [
-                            {
-                                "label": "consensus",
-                                "output_name": "output_file",
-                                "uuid": "9028f80e-4112-40d8-9a49-f671677d304f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "input_list": {
-                                "id": 5,
-                                "output_name": "output_file"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Collapse Collection",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "input"
+                                "description": "",
+                                "name": "hits.sdf"
                             }
                         ],
+                        "label": "hits.sdf",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 537.8000030517578,
-                            "height": 174.8000030517578,
-                            "left": 1223.5,
-                            "right": 1423.5,
-                            "top": 363,
-                            "width": 200,
-                            "x": 1223.5,
-                            "y": 363
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Multisample consensus FASTA"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "830961c48e42",
-                            "name": "collapse_collections",
-                            "owner": "nml",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 218,
+                            "top": 400.5333251953125
                         },
-                        "tool_state": "{\"filename\": {\"add_name\": \"false\", \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.2",
-                        "type": "tool",
-                        "uuid": "acae0f3e-448b-483e-a44a-3e09ce9b3e77",
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"hits.sdf\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "dd2d3bc0-8138-4e66-b2d9-e5e90e27b659",
                         "workflow_outputs": [
                             {
-                                "label": "multisample_consensus_fasta",
+                                "label": null,
                                 "output_name": "output",
-                                "uuid": "1dd7978e-b907-42d6-8fc4-f6fadeefcad1"
+                                "uuid": "1c8fb3cc-52ad-4f62-a00d-80b14b2c1d4a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1",
                         "errors": null,
-                        "id": 7,
+                        "id": 5,
                         "input_connections": {
-                            "input1": {
-                                "id": 6,
+                            "infile": {
+                                "id": 2,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Pangolin",
-                                "name": "input1"
+                                "description": "runtime parameter for tool Create Frankenstein ligand",
+                                "name": "infile"
                             }
                         ],
                         "label": null,
-                        "name": "Pangolin",
+                        "name": "Create Frankenstein ligand",
                         "outputs": [
                             {
-                                "name": "output1",
-                                "type": "tabular"
+                                "name": "outfile",
+                                "type": "sdf"
                             }
                         ],
                         "position": {
-                            "bottom": 512.1999969482422,
-                            "height": 93.19999694824219,
-                            "left": 1451,
-                            "right": 1651,
-                            "top": 419,
-                            "width": 200,
-                            "x": 1451,
-                            "y": 419
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput1": {
-                                "action_arguments": {
-                                    "newname": "Pangolin lineage assignments"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output1"
-                            }
+                            "left": 478.76666259765625,
+                            "top": 483.5333251953125
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "b6abccb1f25b",
-                            "name": "pangolin",
-                            "owner": "iuc",
+                            "changeset_revision": "8e214e52e461",
+                            "name": "ctb_frankenstein_ligand",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"alignment\": \"false\", \"db\": {\"source\": \"builtin\", \"__current_case__\": 1, \"db_release\": \"2021-05-11\"}, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"max_ambig\": \"0.5\", \"min_length\": \"10000\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.3.8",
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "0.1.1",
                         "type": "tool",
-                        "uuid": "bf8893e0-d08c-46c9-b384-a8ad0fc88185",
+                        "uuid": "081abe35-347a-4244-99ae-ec35329e3de0",
                         "workflow_outputs": [
                             {
-                                "label": "pangolin_results",
-                                "output_name": "output1",
-                                "uuid": "e02d2cfb-9842-4069-957c-6cf4ec197056"
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "53c557af-d5b9-4033-be54-7c197591e750"
                             }
                         ]
                     }
                 ],
-                "parent_id": "galaxy-interface/workflow-automation",
-                "path": "topics/galaxy-interface/tutorials/workflow-automation/workflows/main_workflow.ga",
+                "parent_id": "computational-chemistry/covid19-docking",
+                "path": "topics/computational-chemistry/tutorials/covid19-docking/workflows/workflow.ga",
                 "tags": [
-                    "variant-analysis",
-                    "galaxy-interface"
+                    "computational-chemistry"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "vcf2lineage",
-                "topic_id": "galaxy-interface",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/galaxy-interface-workflow-automation/versions/main-workflow",
-                "tutorial_id": "workflow-automation",
-                "url": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-automation/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-automation/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "galaxy-interface-workflow-automation",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "title": "Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring",
+                "topic_id": "computational-chemistry",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/computational-chemistry-covid19-docking/versions/workflow",
+                "tutorial_id": "covid19-docking",
+                "url": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/covid19-docking/workflows/workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/covid19-docking/workflows/workflow.html",
+                "version": 3,
+                "wfid": "computational-chemistry-covid19-docking",
+                "wfname": "workflow",
+                "workflow": "workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/0.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.2.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbcavity/rdock_rbcavity/0.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbdock/rdock_rbdock/0.1.4",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.4.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/sucos_max_score/sucos_max_score/0.2.3",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
+                    "xchem_pose_scoring"
                 ],
-                "workflowhub_id": "1293"
+                "workflowhub_id": "1079"
             }
         ],
-        "zenodo_link": ""
+        "zenodo_link": "https://zenodo.org/record/3730474"
     },
     {
         "admin_install": {
@@ -40711,7 +42107,7 @@
             "Submit raw sequencing reads and metadata to ENA's test server",
             "Submit consensus sequence and metadata to ENA's test server"
         ],
-        "pageviews": 4636019,
+        "pageviews": 4806329,
         "pub_date": "2021-08-10",
         "questions": [
             "How do you submit raw sequence reads and assembled genomes to the European Nucleotide Archive?"
@@ -40734,8 +42130,8 @@
         ],
         "short_id": "T00159",
         "short_tools": [
-            "ena_webin_cli",
-            "ena_upload"
+            "ena_upload",
+            "ena_webin_cli"
         ],
         "slides": true,
         "slides_recordings": false,
@@ -40773,8 +42169,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 238,
-        "visitors": 1741666,
+        "visit_duration": 236,
+        "visitors": 1810937,
         "workflows": [
             {
                 "creators": [],
@@ -40798,7 +42194,7 @@
                 "inputs": [],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"ENA Upload tool\"];\n  1[\"ENA Upload tool\"];",
-                "modified": "2024-08-18 00:06:23 +0000",
+                "modified": "2024-10-02 12:08:08 +0000",
                 "name": "GTN_ENA_upload_workflow",
                 "outputs": [
                     {
@@ -40915,101 +42311,31 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "bowtie2",
-                    "owner": "devteam",
-                    "revisions": "749c918495f7",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_filter_by_length",
-                    "owner": "devteam",
-                    "revisions": "8cacfcf96a52",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_stats",
-                    "owner": "devteam",
-                    "revisions": "145f6d74ff5e",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bandage",
-                    "owner": "iuc",
-                    "revisions": "b2860df42e16",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bandage",
-                    "owner": "iuc",
-                    "revisions": "94fe43e75ddc",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastp",
-                    "owner": "iuc",
-                    "revisions": "1d8fe9bc4cb0",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "minimap2",
-                    "owner": "iuc",
-                    "revisions": "53c0b7a1a0c3",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "b2f1f75d49c4",
-                    "tool_panel_section_label": "Quality Control",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "nanoplot",
-                    "owner": "iuc",
-                    "revisions": "645159bcee2d",
-                    "tool_panel_section_label": "Nanopore",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_fastx",
-                    "owner": "iuc",
-                    "revisions": "a8d69aee190e",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_view",
+                    "name": "bcftools_consensus",
                     "owner": "iuc",
-                    "revisions": "b01db2684fa5",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "revisions": "e522022137f6",
+                    "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "seqtk",
+                    "name": "compose_text_param",
                     "owner": "iuc",
-                    "revisions": "3da72230c066",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "e188c9826e0f",
+                    "tool_panel_section_label": "Expression Tools",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sra_tools",
+                    "name": "pangolin",
                     "owner": "iuc",
-                    "revisions": "aad3885b3216",
-                    "tool_panel_section_label": "Get Data",
+                    "revisions": "b6abccb1f25b",
+                    "tool_panel_section_label": "Phylogenetics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "unicycler",
+                    "name": "snpsift",
                     "owner": "iuc",
-                    "revisions": "9e3e80cc4ad4",
-                    "tool_panel_section_label": "Assembly",
+                    "revisions": "5fab4f81391d",
+                    "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
@@ -41021,9 +42347,21 @@
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bowtie2\n  owner: devteam\n  revisions: 749c918495f7\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_filter_by_length\n  owner: devteam\n  revisions: 8cacfcf96a52\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 145f6d74ff5e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: b2860df42e16\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: 94fe43e75ddc\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 1d8fe9bc4cb0\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: 53c0b7a1a0c3\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: b2f1f75d49c4\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: 645159bcee2d\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_fastx\n  owner: iuc\n  revisions: a8d69aee190e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: b01db2684fa5\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: aad3885b3216\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unicycler\n  owner: iuc\n  revisions: 9e3e80cc4ad4\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bcftools_consensus\n  owner: iuc\n  revisions: e522022137f6\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: compose_text_param\n  owner: iuc\n  revisions: e188c9826e0f\n  tool_panel_section_label: Expression Tools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pangolin\n  owner: iuc\n  revisions: b6abccb1f25b\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpsift\n  owner: iuc\n  revisions: 5fab4f81391d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-automation/tutorial.json",
         "contributors": [
+            {
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "simonbray",
+                "joined": "2019-05",
+                "name": "Simon Bray",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
+            },
             {
                 "affiliations": [
                     "by-covid",
@@ -41042,126 +42380,100 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
             }
         ],
-        "dir": "topics/assembly/tutorials/assembly-with-preprocessing",
+        "dir": "topics/galaxy-interface/tutorials/workflow-automation",
         "edam_operation": [
-            "Sequencing quality control",
-            "Sequence contamination filtering",
-            "Sequence file editing",
-            "Box-Whisker plot plotting",
-            "Read mapping",
-            "Pairwise sequence alignment",
-            "Scatter plot plotting",
-            "Sequence assembly visualisation",
-            "Data handling",
-            "Validation",
-            "Genome assembly",
-            "Aggregation"
+            "Tree-based sequence alignment",
+            "Variant classification"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.eu",
+            "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "assembly/assembly-with-preprocessing",
+        "id": "galaxy-interface/workflow-automation",
         "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)"
+            "MISSISSIPPI",
+            "UseGalaxy.fr"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Certain types of NGS samples can be heavily contaminated with sequences from other genomes",
-            "Reads from known/expected contaminating sources can be identified by mapping to the respective genomes",
-            "After mapping, use filtering tools to remove identified contaminating reads, and use conversion tools to convert remaining mapped reads back into raw sequenced reads expected by most downstream tools"
+            "Workflows can be executed not only through the web browser, but also via the command line.",
+            "Executing workflows programmatically allows automation of analyses."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
         "license": "CC-BY-4.0",
         "mod_date": "2024-06-14",
         "objectives": [
-            "Obtain viral (SARS-CoV-2) sequencing data with contaminating human reads from public sources",
-            "Organize the data into collections and check its quality",
-            "Detect and remove human reads",
-            "Assemble retained reads and explore the results"
+            "Learn to use the `planemo run` subcommand to run workflows from the command line.",
+            "Be able to write simple shell scripts for running multiple workflows concurrently or sequentially.",
+            "Learn how to use Pangolin to assign annotated variants to lineages."
         ],
-        "pageviews": 5734442,
-        "pub_date": "2020-04-21",
+        "pageviews": 2813,
+        "pub_date": "2021-06-08",
         "questions": [
-            "How can a genome of interest be assembled against a background of contaminating reads from other genomes?",
-            "How can sequencing data from public sources be turned into assembly-ready polished datasets?"
+            "How can I schedule and run tens or hundreds of Galaxy workflows easily?",
+            "How can I automate my analyses when large amounts of data are being produced daily?"
         ],
         "recordings": [
             {
                 "captioners": [
-                    "mtekman"
+                    "simonbray"
                 ],
                 "date": "2021-02-15",
                 "galaxy_version": "21.01",
-                "length": "25M",
+                "length": "30M",
                 "speakers": [
-                    "gallardoalba"
+                    "simonbray"
                 ],
-                "youtube_id": "jNFLYhjgJPs"
+                "youtube_id": "o39QjVnLG68"
             }
         ],
         "requirements": [
             {
-                "topic_name": "assembly",
-                "tutorials": [
-                    "unicycler-assembly"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "sequence-analysis",
-                "tutorials": [
-                    "mapping"
-                ],
-                "type": "internal"
+                "title": "Familiarity with Galaxy and basic associated concepts, in particular workflows",
+                "type": "none"
             },
             {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "collections"
-                ],
-                "type": "internal"
+                "title": "Basic knowledge of the command line",
+                "type": "none"
             }
         ],
-        "short_id": "T00029",
+        "short_id": "T00162",
         "short_tools": [
-            "samtools_stats",
-            "nanoplot",
-            "fastp",
-            "samtools_view",
-            "multiqc",
-            "samtools_fastx",
-            "__ZIP_COLLECTION__",
-            "bowtie2",
-            "fasterq_dump",
-            "fasta_filter_by_length",
-            "seqtk_sample",
-            "bandage_info",
-            "minimap2",
-            "bandage_image",
-            "unicycler",
+            "pangolin",
+            "bcftools_consensus",
+            "snpSift_filter",
+            "compose_text_param",
             "collapse_dataset"
         ],
-        "slides": true,
+        "slides": false,
         "slides_recordings": false,
+        "subtopic": "workflows",
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
@@ -41170,2068 +42482,1379 @@
             ],
             "inexact": [
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
                     "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.fr",
                     "url": "https://usegalaxy.fr/",
                     "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
         "tags": [
+            "workflows",
+            "variant-analysis",
             "covid19"
         ],
-        "time_estimation": "4h",
-        "title": "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads",
+        "time_estimation": "2h",
+        "title": "Automating Galaxy workflows using the command line",
         "tools": [
-            "__ZIP_COLLECTION__",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10",
+            "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
             "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
         ],
-        "topic_name": "assembly",
-        "topic_name_human": "Assembly",
+        "topic_name": "galaxy-interface",
+        "topic_name_human": "Using Galaxy and Managing your Data",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "assembly-with-preprocessing",
+        "tutorial_name": "workflow-automation",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-automation/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-automation/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-automation/tutorial.json"
         },
-        "version": 13,
+        "version": 8,
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 363,
-        "visitors": 2068028,
+        "visit_duration": 120,
+        "visitors": 2277,
         "workflows": [
             {
-                "creators": [],
-                "description": "Assembly with preprocessing",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0002-9464-6640",
+                        "name": "Wolfgang Maier"
+                    }
+                ],
+                "description": "workflow-automation",
                 "features": {
                     "comments": false,
-                    "parameters": false,
+                    "parameters": true,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nCollection of paired short-reads data\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nCollection of long-reads data\"]\n  10[label=\"Samtools fastx\"]\n  7 -> 10 [label=\"outputsam\"]\n  11[label=\"Samtools fastx\"]\n  9 -> 11 [label=\"outputsam\"]\n  12[label=\"Collapse Collection\"]\n  10 -> 12 [label=\"nonspecific\"]\n  13[label=\"Zip Collection\"]\n  11 -> 13 [label=\"forward\"]\n  11 -> 13 [label=\"reverse\"]\n  14[label=\"Collapse Collection\"]\n  11 -> 14 [label=\"forward\"]\n  15[label=\"Collapse Collection\"]\n  11 -> 15 [label=\"reverse\"]\n  16[label=\"seqtk_sample\"]\n  14 -> 16 [label=\"output\"]\n  17[label=\"seqtk_sample\"]\n  15 -> 17 [label=\"output\"]\n  18[label=\"Create assemblies with Unicycler\"]\n  12 -> 18 [label=\"output\"]\n  16 -> 18 [label=\"default\"]\n  17 -> 18 [label=\"default\"]\n  19[label=\"Bandage Info\"]\n  18 -> 19 [label=\"assembly_graph\"]\n  2[label=\"fastp: Trimmed Illumina Reads\"]\n  0 -> 2 [label=\"output\"]\n  20[label=\"Filter sequences by length\"]\n  18 -> 20 [label=\"assembly\"]\n  21[label=\"Bandage Image\"]\n  18 -> 21 [label=\"assembly_graph\"]\n  3[label=\"NanoPlot\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Map with minimap2\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"MultiQC\"]\n  2 -> 5 [label=\"report_json\"]\n  6[label=\"Bowtie2\"]\n  2 -> 6 [label=\"output_paired_coll\"]\n  7[label=\"Samtools view\"]\n  4 -> 7 [label=\"alignment_output\"]\n  8[label=\"Samtools stats\"]\n  4 -> 8 [label=\"alignment_output\"]\n  9[label=\"Samtools view\"]\n  6 -> 9 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nVariant calls\"]\n  1[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nmin-AF for consensus variant\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genome\"]\n  3[label=\"Compose text parameter value\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"SnpSift Filter\"]\n  3 -> 4 [label=\"out1\"]\n  0 -> 4 [label=\"output\"]\n  kee67c5edff7c404bad2019259edbc671[color=lightseagreen,label=\"Output\\nconsensus_variants\"]\n  4 -> kee67c5edff7c404bad2019259edbc671\n  5[label=\"bcftools consensus\"]\n  4 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  k9028f80e411240d89a49f671677d304f[color=lightseagreen,label=\"Output\\nconsensus\"]\n  5 -> k9028f80e411240d89a49f671677d304f\n  6[label=\"Collapse Collection\"]\n  5 -> 6 [label=\"output_file\"]\n  k1dd7978eb90742d68fc4f6fadeefcad1[color=lightseagreen,label=\"Output\\nmultisample_consensus_fasta\"]\n  6 -> k1dd7978eb90742d68fc4f6fadeefcad1\n  7[label=\"Pangolin\"]\n  6 -> 7 [label=\"output\"]\n  ke02d2cfb98424069957c6cf4ec197056[color=lightseagreen,label=\"Output\\npangolin_results\"]\n  7 -> ke02d2cfb98424069957c6cf4ec197056\n}",
                 "history": [
                     {
-                        "hash": "fc35e6581a2e34e4420f19af4619c92283609e91",
-                        "message": "add annotations",
-                        "num": 2,
-                        "short_hash": "fc35e6581",
-                        "unix": "1587558793"
-                    },
-                    {
-                        "hash": "7ed054469d1ef84a60abec55758ee2932f9a9655",
-                        "message": "readd workflows",
-                        "num": 1,
-                        "short_hash": "7ed054469",
-                        "unix": "1587555276"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "Collection of paired short-reads data",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 268.13330078125,
-                            "top": 341.41668701171875
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list:paired\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "3e7dab04-77db-4780-b1dd-c724b80a8b7b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "daba9931-3837-42b5-a93f-e2e51f5f667a"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "Collection of long-reads data",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 267.13330078125,
-                            "top": 756.4166717529297
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"lis\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "bd1f5561-95a1-4fb5-af1e-f3d4cbb40639",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "7146e49b-ab4b-44a8-ac54-e98539fecb97"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nCollection of paired short-reads data\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nCollection of long-reads data\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Samtools fastx\"];\n  7 -->|outputsam| 10;\n  11[\"Samtools fastx\"];\n  9 -->|outputsam| 11;\n  12[\"Collapse Collection\"];\n  10 -->|nonspecific| 12;\n  13[\"Zip Collection\"];\n  11 -->|forward| 13;\n  11 -->|reverse| 13;\n  14[\"Collapse Collection\"];\n  11 -->|forward| 14;\n  15[\"Collapse Collection\"];\n  11 -->|reverse| 15;\n  16[\"seqtk_sample\"];\n  14 -->|output| 16;\n  17[\"seqtk_sample\"];\n  15 -->|output| 17;\n  18[\"Create assemblies with Unicycler\"];\n  12 -->|output| 18;\n  16 -->|default| 18;\n  17 -->|default| 18;\n  19[\"Bandage Info\"];\n  18 -->|assembly_graph| 19;\n  2[\"fastp: Trimmed Illumina Reads\"];\n  0 -->|output| 2;\n  20[\"Filter sequences by length\"];\n  18 -->|assembly| 20;\n  21[\"Bandage Image\"];\n  18 -->|assembly_graph| 21;\n  3[\"NanoPlot\"];\n  1 -->|output| 3;\n  4[\"Map with minimap2\"];\n  1 -->|output| 4;\n  5[\"MultiQC\"];\n  2 -->|report_json| 5;\n  6[\"Bowtie2\"];\n  2 -->|output_paired_coll| 6;\n  7[\"Samtools view\"];\n  4 -->|alignment_output| 7;\n  8[\"Samtools stats\"];\n  4 -->|alignment_output| 8;\n  9[\"Samtools view\"];\n  6 -->|output| 9;",
-                "modified": "2024-08-18 00:06:20 +0000",
-                "name": "assembly_with_preprocessing",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "Collection of paired short-reads data",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 268.13330078125,
-                            "top": 341.41668701171875
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list:paired\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "3e7dab04-77db-4780-b1dd-c724b80a8b7b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "daba9931-3837-42b5-a93f-e2e51f5f667a"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "Collection of long-reads data",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 267.13330078125,
-                            "top": 756.4166717529297
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"lis\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "bd1f5561-95a1-4fb5-af1e-f3d4cbb40639",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "7146e49b-ab4b-44a8-ac54-e98539fecb97"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
-                        "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "input": {
-                                "id": 7,
-                                "output_name": "outputsam"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Samtools fastx",
-                        "outputs": [
-                            {
-                                "name": "nonspecific",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "left": 1333.63330078125,
-                            "top": 852.4166717529297
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "a8d69aee190e",
-                            "name": "samtools_fastx",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"copy_arb_tags\": \"\\\"\\\"\", \"__page__\": null, \"output_fmt_cond\": \"{\\\"__current_case__\\\": 2, \\\"default_quality\\\": \\\"\\\", \\\"ilumina_casava\\\": \\\"false\\\", \\\"output_fmt_select\\\": \\\"fastqsanger.gz\\\", \\\"output_quality\\\": \\\"false\\\"}\", \"idxout_cond\": \"{\\\"__current_case__\\\": 0, \\\"idxout_select\\\": \\\"no\\\"}\", \"read_numbering\": \"\\\"\\\"\", \"exclusive_filter\": \"null\", \"exclusive_filter_all\": \"null\", \"inclusive_filter\": \"null\", \"outputs\": \"[\\\"r0\\\"]\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"copy_tags\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9+galaxy1",
-                        "type": "tool",
-                        "uuid": "31e2b4e8-7631-46c0-8382-b805cee2b739",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "nonspecific",
-                                "uuid": "cfbf839f-53f0-4a82-8966-2bdb6919de5e"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "__ZIP_COLLECTION__",
-                        "errors": null,
-                        "id": 13,
-                        "input_connections": {
-                            "input_forward": {
-                                "id": 11,
-                                "output_name": "forward"
-                            },
-                            "input_reverse": {
-                                "id": 11,
-                                "output_name": "reverse"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Zip Collection",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 1754.63330078125,
-                            "top": 477.41668701171875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "__ZIP_COLLECTION__",
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_reverse\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"input_forward\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "9ba89e81-9c53-4f5b-9d61-42319b7d574c",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "ebc8f563-c45e-4e17-a541-b1275e7f61ad"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
-                        "errors": null,
-                        "id": 16,
-                        "input_connections": {
-                            "in_file": {
-                                "id": 14,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool seqtk_sample",
-                                "name": "in_file"
-                            }
-                        ],
-                        "label": null,
-                        "name": "seqtk_sample",
-                        "outputs": [
-                            {
-                                "name": "default",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 2129.4166717529297,
-                            "top": 711.4166717529297
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "58c8ece95b53",
-                            "name": "seqtk",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"s\": \"\\\"4\\\"\", \"in_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"subsample_size\": \"\\\"0.1\\\"\", \"advanced\": \"{\\\"single_pass_mode\\\": \\\"false\\\"}\"}",
-                        "tool_version": "1.3.2",
-                        "type": "tool",
-                        "uuid": "4f7c9133-a664-46dc-9583-c9980d5d1011",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "default",
-                                "uuid": "be52344e-6874-431c-8d86-9d0e9371aed9"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
-                        "errors": null,
-                        "id": 17,
-                        "input_connections": {
-                            "in_file": {
-                                "id": 15,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool seqtk_sample",
-                                "name": "in_file"
-                            }
-                        ],
-                        "label": null,
-                        "name": "seqtk_sample",
-                        "outputs": [
-                            {
-                                "name": "default",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 2116.4166717529297,
-                            "top": 859.4166717529297
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "58c8ece95b53",
-                            "name": "seqtk",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"s\": \"\\\"4\\\"\", \"in_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"subsample_size\": \"\\\"0.1\\\"\", \"advanced\": \"{\\\"single_pass_mode\\\": \\\"false\\\"}\"}",
-                        "tool_version": "1.3.2",
-                        "type": "tool",
-                        "uuid": "79064891-aa79-42e3-b848-7a6240022acc",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "default",
-                                "uuid": "3e196eb1-8ba1-4be5-90d0-c5b8d3df4ff0"
-                            }
-                        ]
-                    },
+                        "hash": "486585510e665c834a43668e2a769dd69654b9d6",
+                        "message": "add WF automation tutorial",
+                        "num": 1,
+                        "short_hash": "486585510",
+                        "unix": "1622197006"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 18,
-                        "input_connections": {
-                            "long": {
-                                "id": 12,
-                                "output_name": "output"
-                            },
-                            "paired_unpaired|fastq_input1": {
-                                "id": 16,
-                                "output_name": "default"
-                            },
-                            "paired_unpaired|fastq_input2": {
-                                "id": 17,
-                                "output_name": "default"
-                            }
-                        },
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "lr_align"
-                            },
-                            {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "long"
-                            },
-                            {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "paired_unpaired"
-                            },
-                            {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "paired_unpaired"
-                            },
-                            {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "rotation"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Create assemblies with Unicycler",
-                        "outputs": [
-                            {
-                                "name": "assembly_graph",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "assembly",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "Variant calls"
                             }
                         ],
+                        "label": "Variant calls",
+                        "name": "Input dataset collection",
+                        "outputs": [],
                         "position": {
-                            "left": 2365.633331298828,
-                            "top": 706.4166717529297
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "88c240872a65",
-                            "name": "unicycler",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 425.43333435058594,
+                            "height": 61.80000305175781,
+                            "left": 297,
+                            "right": 497,
+                            "top": 363.6333312988281,
+                            "width": 200,
+                            "x": 297,
+                            "y": 363.6333312988281
                         },
-                        "tool_state": "{\"linear_seqs\": \"\\\"1\\\"\", \"spades\": \"{\\\"depth_filter\\\": \\\"0.25\\\", \\\"kmer_count\\\": \\\"10\\\", \\\"kmers\\\": \\\"\\\", \\\"largest_component\\\": \\\"false\\\", \\\"max_kmer_frac\\\": \\\"0.95\\\", \\\"min_kmer_frac\\\": \\\"0.2\\\", \\\"no_correct\\\": \\\"false\\\"}\", \"graph_clean\": \"{\\\"min_component_size\\\": \\\"1000\\\", \\\"min_dead_end_size\\\": \\\"1000\\\"}\", \"__page__\": null, \"min_anchor_seg_len\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"lr_align\": \"{\\\"contamination\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"low_score\\\": \\\"\\\", \\\"scores\\\": \\\"3,-6,-5,-2\\\"}\", \"long\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"paired_unpaired\": \"{\\\"__current_case__\\\": 0, \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"fastq_input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired\\\"}\", \"min_fasta_length\": \"\\\"100\\\"\", \"mode\": \"\\\"normal\\\"\", \"rotation\": \"{\\\"no_rotate\\\": \\\"false\\\", \\\"start_gene_cov\\\": \\\"95.0\\\", \\\"start_gene_id\\\": \\\"90.0\\\", \\\"start_genes\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"pilon\": \"{\\\"min_polish_size\\\": \\\"1000\\\", \\\"no_pilon\\\": \\\"false\\\"}\"}",
-                        "tool_version": "0.4.8.0",
-                        "type": "tool",
-                        "uuid": "851c6be6-c202-450a-9cd3-19e205dcc496",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "assembly",
-                                "uuid": "702dd61e-6072-49d9-a502-44e0a23f5a98"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "assembly_graph",
-                                "uuid": "3285cc00-6b39-4f3d-87a5-87abd483ede6"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "fca4e710-87a7-4cb6-9ff1-f9a8dc84ca37",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 19,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 18,
-                                "output_name": "assembly_graph"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Bandage Info",
-                        "outputs": [
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "outfile",
-                                "type": "txt"
+                                "description": "",
+                                "name": "min-AF for consensus variant"
                             }
                         ],
+                        "label": "min-AF for consensus variant",
+                        "name": "Input parameter",
+                        "outputs": [],
                         "position": {
-                            "left": 2665.633331298828,
-                            "top": 811.4166717529297
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b2860df42e16",
-                            "name": "bandage",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 619.1000061035156,
+                            "height": 102.60000610351562,
+                            "left": 295.45001220703125,
+                            "right": 495.45001220703125,
+                            "top": 516.5,
+                            "width": 200,
+                            "x": 295.45001220703125,
+                            "y": 516.5
                         },
-                        "tool_state": "{\"tsv\": \"\\\"false\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
-                        "tool_version": "0.8.1+galaxy1",
-                        "type": "tool",
-                        "uuid": "4aa230bd-3269-41c3-81f5-9085fcc4001d",
+                        "tool_id": null,
+                        "tool_state": "{\"default\": 0.7, \"parameter_type\": \"float\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "52664bd7-b500-40a1-935b-8ac6df7003e5",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "cf5eab6a-97ae-430e-a27a-6ecc33d4b8c0"
+                                "output_name": "output",
+                                "uuid": "5db03aa3-a62d-4a39-8712-d48911abf2bb"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
+                        "content_id": null,
                         "errors": null,
                         "id": 2,
-                        "input_connections": {
-                            "single_paired|paired_input": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "fastp: Trimmed Illumina Reads",
-                        "name": "fastp",
-                        "outputs": [
-                            {
-                                "name": "output_paired_coll",
-                                "type": "input"
-                            },
-                            {
-                                "name": "report_html",
-                                "type": "html"
-                            },
-                            {
-                                "name": "report_json",
-                                "type": "json"
-                            }
-                        ],
-                        "position": {
-                            "left": 585,
-                            "top": 365.04998779296875
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionreport_html": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "report_html"
-                            },
-                            "HideDatasetActionreport_json": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "report_json"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "1d8fe9bc4cb0",
-                            "name": "fastp",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"report_html\\\": \\\"true\\\", \\\"report_json\\\": \\\"true\\\"}\", \"single_paired\": \"{\\\"__current_case__\\\": 2, \\\"adapter_trimming_options\\\": {\\\"adapter_sequence1\\\": \\\"\\\", \\\"adapter_sequence2\\\": \\\"\\\", \\\"disable_adapter_trimming\\\": \\\"false\\\"}, \\\"global_trimming_options\\\": {\\\"trim_front1\\\": \\\"\\\", \\\"trim_front2\\\": \\\"\\\", \\\"trim_tail1\\\": \\\"\\\", \\\"trim_tail2\\\": \\\"\\\"}, \\\"paired_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"single_paired_selector\\\": \\\"paired_collection\\\"}\", \"read_mod_options\": \"{\\\"base_correction_options\\\": {\\\"correction\\\": \\\"false\\\"}, \\\"cutting_by_quality_options\\\": {\\\"cut_by_quality3\\\": \\\"false\\\", \\\"cut_by_quality5\\\": \\\"false\\\", \\\"cut_mean_quality\\\": \\\"\\\", \\\"cut_window_size\\\": \\\"\\\"}, \\\"polyg_tail_trimming\\\": {\\\"__current_case__\\\": 1, \\\"poly_g_min_len\\\": \\\"\\\", \\\"trimming_select\\\": \\\"\\\"}, \\\"polyx_tail_trimming\\\": {\\\"__current_case__\\\": 1, \\\"polyx_trimming_select\\\": \\\"\\\"}, \\\"umi_processing\\\": {\\\"umi\\\": \\\"false\\\", \\\"umi_len\\\": \\\"\\\", \\\"umi_loc\\\": \\\"\\\", \\\"umi_prefix\\\": \\\"\\\"}}\", \"overrepresented_sequence_analysis\": \"{\\\"overrepresentation_analysis\\\": \\\"false\\\", \\\"overrepresentation_sampling\\\": \\\"\\\"}\", \"filter_options\": \"{\\\"length_filtering_options\\\": {\\\"disable_length_filtering\\\": \\\"false\\\", \\\"length_required\\\": \\\"50\\\"}, \\\"low_complexity_filter\\\": {\\\"complexity_threshold\\\": \\\"\\\", \\\"enable_low_complexity_filter\\\": \\\"false\\\"}, \\\"quality_filtering_options\\\": {\\\"disable_quality_filtering\\\": \\\"false\\\", \\\"n_base_limit\\\": \\\"\\\", \\\"qualified_quality_phred\\\": \\\"20\\\", \\\"unqualified_percent_limit\\\": \\\"20\\\"}}\", \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.19.5+galaxy1",
-                        "type": "tool",
-                        "uuid": "7508c22b-dc6a-4071-8dd0-d5616718e62b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_paired_coll",
-                                "uuid": "a7be7eab-3e80-4be6-b1a4-ab303c314096"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
-                        "errors": null,
-                        "id": 20,
-                        "input_connections": {
-                            "input": {
-                                "id": 18,
-                                "output_name": "assembly"
-                            }
-                        },
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Filter sequences by length",
-                                "name": "input"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Filter sequences by length",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "Reference genome"
                             }
                         ],
+                        "label": "Reference genome",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2574.4166870117188,
-                            "top": 1254.4166870117188
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "8cacfcf96a52",
-                            "name": "fasta_filter_by_length",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 734.8500366210938,
+                            "height": 82.20001220703125,
+                            "left": 749.816650390625,
+                            "right": 949.816650390625,
+                            "top": 652.6500244140625,
+                            "width": 200,
+                            "x": 749.816650390625,
+                            "y": 652.6500244140625
                         },
-                        "tool_state": "{\"__page__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"max_length\": \"\\\"0\\\"\", \"min_length\": \"\\\"1000\\\"\"}",
-                        "tool_version": "1.2",
-                        "type": "tool",
-                        "uuid": "3cbd67e0-3e55-4726-8dbe-0c61aec4d293",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "e4143f49-239f-4266-ba8d-e6299a331403"
-                            }
-                        ]
-                    },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "4a2c6df2-fb1e-42d8-96d5-6765ca85c214",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nVariant calls\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nmin-AF for consensus variant\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Compose text parameter value\"];\n  1 -->|output| 3;\n  4[\"SnpSift Filter\"];\n  3 -->|out1| 4;\n  0 -->|output| 4;\n  ee67c5ed-ff7c-404b-ad20-19259edbc671[\"Output\\nconsensus_variants\"];\n  4 --> ee67c5ed-ff7c-404b-ad20-19259edbc671;\n  style ee67c5ed-ff7c-404b-ad20-19259edbc671 stroke:#2c3143,stroke-width:4px;\n  5[\"bcftools consensus\"];\n  4 -->|output| 5;\n  2 -->|output| 5;\n  9028f80e-4112-40d8-9a49-f671677d304f[\"Output\\nconsensus\"];\n  5 --> 9028f80e-4112-40d8-9a49-f671677d304f;\n  style 9028f80e-4112-40d8-9a49-f671677d304f stroke:#2c3143,stroke-width:4px;\n  6[\"Collapse Collection\"];\n  5 -->|output_file| 6;\n  1dd7978e-b907-42d6-8fc4-f6fadeefcad1[\"Output\\nmultisample_consensus_fasta\"];\n  6 --> 1dd7978e-b907-42d6-8fc4-f6fadeefcad1;\n  style 1dd7978e-b907-42d6-8fc4-f6fadeefcad1 stroke:#2c3143,stroke-width:4px;\n  7[\"Pangolin\"];\n  6 -->|output| 7;\n  e02d2cfb-9842-4069-957c-6cf4ec197056[\"Output\\npangolin_results\"];\n  7 --> e02d2cfb-9842-4069-957c-6cf4ec197056;\n  style e02d2cfb-9842-4069-957c-6cf4ec197056 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "vcf2lineage",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+                        "content_id": null,
                         "errors": null,
-                        "id": 21,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 18,
-                                "output_name": "assembly_graph"
-                            }
-                        },
+                        "id": 1,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Bandage Image",
-                                "name": "input_file"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Bandage Image",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "jpg"
+                                "description": "",
+                                "name": "min-AF for consensus variant"
                             }
                         ],
+                        "label": "min-AF for consensus variant",
+                        "name": "Input parameter",
+                        "outputs": [],
                         "position": {
-                            "left": 2667.4166870117188,
-                            "top": 1052.4166870117188
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b2860df42e16",
-                            "name": "bandage",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 619.1000061035156,
+                            "height": 102.60000610351562,
+                            "left": 295.45001220703125,
+                            "right": 495.45001220703125,
+                            "top": 516.5,
+                            "width": 200,
+                            "x": 295.45001220703125,
+                            "y": 516.5
                         },
-                        "tool_state": "{\"__page__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"lengths\": \"\\\"true\\\"\", \"output_format\": \"\\\"jpg\\\"\", \"height\": \"\\\"1000\\\"\", \"width\": \"\\\"\\\"\", \"names\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.8.1+galaxy2",
-                        "type": "tool",
-                        "uuid": "ef2c6a46-8421-499e-a840-8dd03483c5c9",
+                        "tool_id": null,
+                        "tool_state": "{\"default\": 0.7, \"parameter_type\": \"float\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "52664bd7-b500-40a1-935b-8ac6df7003e5",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "5e535f98-b740-44ec-aba1-9d9090acb89a"
+                                "output_name": "output",
+                                "uuid": "5db03aa3-a62d-4a39-8712-d48911abf2bb"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
                         "errors": null,
-                        "id": 3,
+                        "id": 4,
                         "input_connections": {
-                            "mode|reads|files": {
-                                "id": 1,
+                            "filter_expression|expr": {
+                                "id": 3,
+                                "output_name": "out1"
+                            },
+                            "input": {
+                                "id": 0,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "NanoPlot",
+                        "name": "SnpSift Filter",
                         "outputs": [
                             {
-                                "name": "output_html",
-                                "type": "html"
-                            },
-                            {
-                                "name": "nanostats",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "nanostats_post_filtering",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "read_length",
-                                "type": "png"
-                            },
-                            {
-                                "name": "log_read_length",
-                                "type": "png"
+                                "name": "output",
+                                "type": "vcf"
                             }
                         ],
                         "position": {
-                            "left": 630,
-                            "top": 650.4666595458984
+                            "bottom": 506.5,
+                            "height": 144,
+                            "left": 750.2833251953125,
+                            "right": 950.2833251953125,
+                            "top": 362.5,
+                            "width": 200,
+                            "x": 750.2833251953125,
+                            "y": 362.5
                         },
                         "post_job_actions": {
-                            "HideDatasetActionlog_read_length": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "log_read_length"
-                            },
-                            "HideDatasetActionnanostats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "nanostats"
-                            },
-                            "HideDatasetActionnanostats_post_filtering": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "nanostats_post_filtering"
-                            },
-                            "HideDatasetActionread_length": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "read_length"
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Consensus variants"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "645159bcee2d",
-                            "name": "nanoplot",
+                            "changeset_revision": "2e497a770bca",
+                            "name": "snpsift",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"filter\": \"{\\\"alength\\\": \\\"false\\\", \\\"barcoded\\\": \\\"false\\\", \\\"downsample\\\": \\\"\\\", \\\"drop_outliers\\\": \\\"false\\\", \\\"loglength\\\": \\\"true\\\", \\\"maxlength\\\": \\\"\\\", \\\"minlength\\\": \\\"\\\", \\\"minqual\\\": \\\"\\\", \\\"percentqual\\\": \\\"false\\\", \\\"readtype\\\": null}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"__current_case__\\\": 0, \\\"choice\\\": \\\"batch\\\", \\\"reads\\\": {\\\"__current_case__\\\": 0, \\\"files\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"type\\\": \\\"fastq\\\"}}\", \"customization\": \"{\\\"N50\\\": \\\"false\\\", \\\"color\\\": null, \\\"format\\\": \\\"png\\\", \\\"noN50\\\": \\\"false\\\", \\\"plots\\\": null}\"}",
-                        "tool_version": "1.25.0+galaxy1",
+                        "tool_state": "{\"filter_expression\": {\"type\": \"simple\", \"__current_case__\": 0, \"expr\": {\"__class__\": \"ConnectedValue\"}}, \"filtering\": {\"mode\": \"entries\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inverse\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.3+t.galaxy1",
                         "type": "tool",
-                        "uuid": "9b1d43ac-82e3-463f-9c88-08c8826a62c9",
+                        "uuid": "3673b687-1ba0-42f2-ba13-fa3130462079",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_html",
-                                "uuid": "cd8570c7-02db-479b-81a9-cd0d26643f71"
+                                "label": "consensus_variants",
+                                "output_name": "output",
+                                "uuid": "ee67c5ed-ff7c-404b-ad20-19259edbc671"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10",
                         "errors": null,
-                        "id": 4,
+                        "id": 5,
                         "input_connections": {
-                            "fastq_input|fastq_input1": {
-                                "id": 1,
+                            "input_file": {
+                                "id": 4,
+                                "output_name": "output"
+                            },
+                            "reference_source|fasta_ref": {
+                                "id": 2,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Map with minimap2",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "alignment_output",
-                                "type": "bam"
-                            }
-                        ],
-                        "position": {
-                            "left": 709.199951171875,
-                            "top": 1131.9666748046875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "53c0b7a1a0c3",
-                            "name": "minimap2",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"alignment_options\": \"{\\\"-O2\\\": \\\"\\\", \\\"A\\\": \\\"\\\", \\\"B\\\": \\\"\\\", \\\"E\\\": \\\"\\\", \\\"E2\\\": \\\"\\\", \\\"O\\\": \\\"\\\", \\\"s\\\": \\\"\\\", \\\"u\\\": null, \\\"z\\\": \\\"\\\"}\", \"analysis_type_selector\": \"\\\"splice\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"io_options\": \"{\\\"K\\\": \\\"\\\", \\\"L\\\": \\\"false\\\", \\\"Q\\\": \\\"false\\\", \\\"Y\\\": \\\"false\\\", \\\"c\\\": \\\"false\\\", \\\"cs\\\": null, \\\"eqx\\\": \\\"false\\\", \\\"output_format\\\": \\\"BAM\\\"}\", \"mapping_options\": \"{\\\"F\\\": \\\"\\\", \\\"G\\\": \\\"\\\", \\\"N\\\": \\\"\\\", \\\"X\\\": \\\"false\\\", \\\"f\\\": \\\"\\\", \\\"g\\\": \\\"\\\", \\\"m\\\": \\\"\\\", \\\"min_occ_floor\\\": \\\"\\\", \\\"n\\\": \\\"\\\", \\\"p\\\": \\\"\\\", \\\"r\\\": \\\"\\\"}\", \"fastq_input\": \"{\\\"__current_case__\\\": 1, \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"single\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 0, \\\"ref_file\\\": \\\"hg38\\\", \\\"reference_source_selector\\\": \\\"cached\\\"}\", \"indexing_options\": \"{\\\"H\\\": \\\"false\\\", \\\"I\\\": \\\"\\\", \\\"k\\\": \\\"\\\", \\\"w\\\": \\\"\\\"}\"}",
-                        "tool_version": "2.17+galaxy1",
-                        "type": "tool",
-                        "uuid": "098d2283-1218-489b-9882-8822e79d9444",
-                        "workflow_outputs": [
+                                "description": "runtime parameter for tool bcftools consensus",
+                                "name": "input_file"
+                            },
                             {
-                                "label": null,
-                                "output_name": "alignment_output",
-                                "uuid": "9972015d-4bdc-440f-b8b6-84e92a64ef8f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "results_0|software_cond|input": {
-                                "id": 2,
-                                "output_name": "report_json"
+                                "description": "runtime parameter for tool bcftools consensus",
+                                "name": "reference_source"
+                            },
+                            {
+                                "description": "runtime parameter for tool bcftools consensus",
+                                "name": "sec_default"
                             }
-                        },
-                        "inputs": [],
+                        ],
                         "label": null,
-                        "name": "MultiQC",
+                        "name": "bcftools consensus",
                         "outputs": [
                             {
-                                "name": "stats",
-                                "type": "input"
-                            },
-                            {
-                                "name": "html_report",
-                                "type": "html"
+                                "name": "output_file",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 938.699951171875,
-                            "top": 250
+                            "bottom": 535.5666809082031,
+                            "height": 174.39999389648438,
+                            "left": 993.8333129882812,
+                            "right": 1193.8333129882812,
+                            "top": 361.16668701171875,
+                            "width": 200,
+                            "x": 993.8333129882812,
+                            "y": 361.16668701171875
                         },
                         "post_job_actions": {
-                            "HideDatasetActionstats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "stats"
+                            "RenameDatasetActionoutput_file": {
+                                "action_arguments": {
+                                    "newname": "Consensus sequences"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_file"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10",
                         "tool_shed_repository": {
-                            "changeset_revision": "b2f1f75d49c4",
-                            "name": "multiqc",
+                            "changeset_revision": "e522022137f6",
+                            "name": "bcftools_consensus",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"comment\": \"\\\"\\\"\", \"__page__\": null, \"title\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"results\": \"[{\\\"__index__\\\": 0, \\\"software_cond\\\": {\\\"__current_case__\\\": 7, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"software\\\": \\\"fastp\\\"}}]\", \"saveLog\": \"\\\"false\\\"\"}",
-                        "tool_version": "1.7",
+                        "tool_state": "{\"chain\": \"false\", \"input_file\": {\"__class__\": \"RuntimeValue\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"RuntimeValue\"}}, \"rename\": \"true\", \"sec_default\": {\"mask\": {\"__class__\": \"RuntimeValue\"}, \"iupac_codes\": \"false\", \"sample\": \"\", \"select_haplotype\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.10",
                         "type": "tool",
-                        "uuid": "73566697-4a46-4d35-b8e2-61770acc62c0",
+                        "uuid": "5d2e8bea-3e75-4453-9494-b5fd52b2f528",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "html_report",
-                                "uuid": "15f42a94-2c97-4932-8e3f-f26a72b58be4"
+                                "label": "consensus",
+                                "output_name": "output_file",
+                                "uuid": "9028f80e-4112-40d8-9a49-f671677d304f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
                         "errors": null,
                         "id": 6,
                         "input_connections": {
-                            "library|input_1": {
-                                "id": 2,
-                                "output_name": "output_paired_coll"
+                            "input_list": {
+                                "id": 5,
+                                "output_name": "output_file"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Bowtie2",
+                        "name": "Collapse Collection",
                         "outputs": [
                             {
                                 "name": "output",
-                                "type": "bam"
-                            },
-                            {
-                                "name": "mapping_stats",
-                                "type": "txt"
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 913.9166259765625,
-                            "top": 564.6333312988281
+                            "bottom": 537.8000030517578,
+                            "height": 174.8000030517578,
+                            "left": 1223.5,
+                            "right": 1423.5,
+                            "top": 363,
+                            "width": 200,
+                            "x": 1223.5,
+                            "y": 363
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Multisample consensus FASTA"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "749c918495f7",
-                            "name": "bowtie2",
-                            "owner": "devteam",
+                            "changeset_revision": "830961c48e42",
+                            "name": "collapse_collections",
+                            "owner": "nml",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"sam_options\": \"{\\\"__current_case__\\\": 1, \\\"sam_options_selector\\\": \\\"no\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"__current_case__\\\": 2, \\\"aligned_file\\\": \\\"false\\\", \\\"input_1\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"paired_options\\\": {\\\"__current_case__\\\": 1, \\\"paired_options_selector\\\": \\\"no\\\"}, \\\"type\\\": \\\"paired_collection\\\", \\\"unaligned_file\\\": \\\"false\\\"}\", \"reference_genome\": \"{\\\"__current_case__\\\": 0, \\\"index\\\": \\\"hg38full\\\", \\\"source\\\": \\\"indexed\\\"}\", \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"save_mapping_stats\": \"\\\"true\\\"\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"simple\\\", \\\"presets\\\": \\\"no_presets\\\"}\"}",
-                        "tool_version": "2.3.4.3+galaxy0",
+                        "tool_state": "{\"filename\": {\"add_name\": \"false\", \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.2",
                         "type": "tool",
-                        "uuid": "43331d2c-7116-410e-a6bd-7e7520d93a52",
+                        "uuid": "acae0f3e-448b-483e-a44a-3e09ce9b3e77",
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "multisample_consensus_fasta",
                                 "output_name": "output",
-                                "uuid": "eeae40f6-f1b2-4c56-9860-ac7b8eb1dec0"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "mapping_stats",
-                                "uuid": "c567226e-efaf-4188-bdec-3ba20d0733b0"
+                                "uuid": "1dd7978e-b907-42d6-8fc4-f6fadeefcad1"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8",
                         "errors": null,
-                        "id": 8,
+                        "id": 7,
                         "input_connections": {
-                            "input": {
-                                "id": 4,
-                                "output_name": "alignment_output"
+                            "input1": {
+                                "id": 6,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Pangolin",
+                                "name": "input1"
+                            }
+                        ],
                         "label": null,
-                        "name": "Samtools stats",
+                        "name": "Pangolin",
                         "outputs": [
                             {
-                                "name": "output_collection",
-                                "type": "input"
+                                "name": "output1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1022.4166259765625,
-                            "top": 1254.4166870117188
+                            "bottom": 512.1999969482422,
+                            "height": 93.19999694824219,
+                            "left": 1451,
+                            "right": 1651,
+                            "top": 419,
+                            "width": 200,
+                            "x": 1451,
+                            "y": 419
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput1": {
+                                "action_arguments": {
+                                    "newname": "Pangolin lineage assignments"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output1"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8",
                         "tool_shed_repository": {
-                            "changeset_revision": "145f6d74ff5e",
-                            "name": "samtools_stats",
-                            "owner": "devteam",
+                            "changeset_revision": "b6abccb1f25b",
+                            "name": "pangolin",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"coverage_cond\": \"{\\\"__current_case__\\\": 0, \\\"coverage_select\\\": \\\"no\\\"}\", \"gc_depth\": \"\\\"\\\"\", \"cov_threshold\": \"\\\"\\\"\", \"most_inserts\": \"\\\"\\\"\", \"cond_region\": \"{\\\"__current_case__\\\": 0, \\\"select_region\\\": \\\"no\\\"}\", \"split_output_cond\": \"{\\\"__current_case__\\\": 1, \\\"generate_tables\\\": [\\\"SN\\\"], \\\"split_output_selector\\\": \\\"yes\\\"}\", \"read_length\": \"\\\"\\\"\", \"trim_quality\": \"\\\"\\\"\", \"remove_overlaps\": \"\\\"false\\\"\", \"filter_by_flags\": \"{\\\"__current_case__\\\": 1, \\\"filter_flags\\\": \\\"nofilter\\\"}\", \"sparse\": \"\\\"false\\\"\", \"addref_cond\": \"{\\\"__current_case__\\\": 0, \\\"addref_select\\\": \\\"no\\\"}\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"insert_size\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"remove_dups\": \"\\\"false\\\"\"}",
-                        "tool_version": "2.0.2+galaxy2",
+                        "tool_state": "{\"alignment\": \"false\", \"db\": {\"source\": \"builtin\", \"__current_case__\": 1, \"db_release\": \"2021-05-11\"}, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"max_ambig\": \"0.5\", \"min_length\": \"10000\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.3.8",
                         "type": "tool",
-                        "uuid": "15f6252f-79d4-4319-855d-09665deac6a3",
+                        "uuid": "bf8893e0-d08c-46c9-b384-a8ad0fc88185",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_collection",
-                                "uuid": "faed6306-eed6-40bd-ac9f-9fb3a4e980ea"
+                                "label": "pangolin_results",
+                                "output_name": "output1",
+                                "uuid": "e02d2cfb-9842-4069-957c-6cf4ec197056"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/assembly-with-preprocessing",
-                "path": "topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing.ga",
+                "parent_id": "galaxy-interface/workflow-automation",
+                "path": "topics/galaxy-interface/tutorials/workflow-automation/workflows/main_workflow.ga",
                 "tags": [
-                    "GTN",
-                    "assembly"
+                    "variant-analysis",
+                    "galaxy-interface"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "assembly_with_preprocessing",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-assembly-with-preprocessing/versions/assembly-with-preprocessing",
-                "tutorial_id": "assembly-with-preprocessing",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing.html",
+                "title": "vcf2lineage",
+                "topic_id": "galaxy-interface",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/galaxy-interface-workflow-automation/versions/main-workflow",
+                "tutorial_id": "workflow-automation",
+                "url": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-automation/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-automation/workflows/main_workflow.html",
                 "version": 1,
-                "wfid": "assembly-assembly-with-preprocessing",
-                "wfname": "assembly-with-preprocessing",
-                "workflow": "assembly_with_preprocessing.ga",
+                "wfid": "galaxy-interface-workflow-automation",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "__ZIP_COLLECTION__",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
                     "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
                 ],
-                "workflowhub_id": "1132"
+                "workflowhub_id": "1293"
+            }
+        ],
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bwa",
+                    "owner": "devteam",
+                    "revisions": "e188dc7a68e6",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "samtools_fastx",
+                    "owner": "iuc",
+                    "revisions": "a8d69aee190e",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seqtk",
+                    "owner": "iuc",
+                    "revisions": "3da72230c066",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "trimmomatic",
+                    "owner": "pjbriggs",
+                    "revisions": "898b67846b47",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "trimmomatic",
+                    "owner": "pjbriggs",
+                    "revisions": "d94aff5ee623",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_fastx\n  owner: iuc\n  revisions: a8d69aee190e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n  owner: pjbriggs\n  revisions: 898b67846b47\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n  owner: pjbriggs\n  revisions: d94aff5ee623\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "by-covid",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "elixir_node": "de",
+                "fediverse": "https://scholar.social/@zerodivision",
+                "fediverse_flavor": "mastodon",
+                "id": "wm75",
+                "joined": "2017-09",
+                "matrix": "wm75:matrix.org",
+                "name": "Wolfgang Maier",
+                "orcid": "0000-0002-9464-6640",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
+            }
+        ],
+        "dir": "topics/sequence-analysis/tutorials/human-reads-removal",
+        "edam_operation": [
+            "Generation",
+            "Data handling",
+            "Sequence alignment",
+            "Sequence file editing",
+            "Read mapping",
+            "Genome indexing"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "sequence-analysis/human-reads-removal",
+        "inexact_supported_servers": [
+            "Galaxy@AuBi",
+            "GalaxyTrakr",
+            "MISSISSIPPI",
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Before submitting raw viral sequencing data to public databases you will want to remove human sequence traces",
+            "Human reads can be identified by mapping the data to the human reference genome",
+            "After mapping, you can extract the read identifiers of the non-human reads and use these to extract just the desired original sequenced reads from the input data"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": [
+            "Obtain viral (SARS-CoV-2) sequencing data with contaminating human reads from public sources",
+            "Organize the data into a collection",
+            "Preprocess and map the data against the human reference genome",
+            "Eliminate reads/read pairs that map to the human genome from the original data"
+        ],
+        "pageviews": 4842,
+        "pub_date": "2021-08-04",
+        "questions": [
+            "How can you remove traces of human sequence data from a sequenced viral sample?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "sequence-analysis",
+                "tutorials": [
+                    "quality-control",
+                    "mapping"
+                ],
+                "type": "internal"
             },
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "collections"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00236",
+        "short_tools": [
+            "bwa_mem",
+            "seqtk_subseq",
+            "tp_replace_in_line",
+            "samtools_fastx",
+            "Grep1",
+            "__UNZIP_COLLECTION__",
+            "trimmomatic",
+            "__ZIP_COLLECTION__"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "covid19"
+        ],
+        "time_estimation": "1h",
+        "title": "Removal of human reads from SARS-CoV-2 sequencing data",
+        "tools": [
+            "Grep1",
+            "__UNZIP_COLLECTION__",
+            "__ZIP_COLLECTION__",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+            "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
+            "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1"
+        ],
+        "topic_name": "sequence-analysis",
+        "topic_name_human": "Sequence analysis",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "human-reads-removal",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.json"
+        },
+        "version": 5,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 140,
+        "visitors": 3422,
+        "workflows": [
             {
                 "creators": [],
-                "description": "Assembly with preprocessing and SRA download",
+                "description": "Removal of human reads from SARS-CoV-2 sequencing data",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nList of Illumina accessions\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nList of ONT accessions\"]\n  10[label=\"Samtools stats\"]\n  6 -> 10 [label=\"alignment_output\"]\n  11[label=\"Samtools view\"]\n  8 -> 11 [label=\"output\"]\n  12[label=\"Samtools fastx\"]\n  9 -> 12 [label=\"outputsam\"]\n  13[label=\"Samtools fastx\"]\n  11 -> 13 [label=\"outputsam\"]\n  14[label=\"Collapse Collection\"]\n  12 -> 14 [label=\"nonspecific\"]\n  15[label=\"Zip Collection\"]\n  13 -> 15 [label=\"forward\"]\n  13 -> 15 [label=\"reverse\"]\n  16[label=\"Collapse Collection\"]\n  13 -> 16 [label=\"forward\"]\n  17[label=\"Collapse Collection\"]\n  13 -> 17 [label=\"reverse\"]\n  18[label=\"seqtk_sample\"]\n  16 -> 18 [label=\"output\"]\n  19[label=\"seqtk_sample\"]\n  17 -> 19 [label=\"output\"]\n  2[label=\"Illumina data\"]\n  0 -> 2 [label=\"output\"]\n  20[label=\"Create assemblies with Unicycler\"]\n  14 -> 20 [label=\"output\"]\n  18 -> 20 [label=\"default\"]\n  19 -> 20 [label=\"default\"]\n  21[label=\"Bandage Info\"]\n  20 -> 21 [label=\"assembly_graph\"]\n  22[label=\"Bandage Image\"]\n  20 -> 22 [label=\"assembly_graph\"]\n  23[label=\"Filter sequences by length\"]\n  20 -> 23 [label=\"assembly\"]\n  3[label=\"ONT data\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"fastp: Trimmed Illumina Reads\"]\n  2 -> 4 [label=\"list_paired\"]\n  5[label=\"NanoPlot\"]\n  3 -> 5 [label=\"output_collection\"]\n  6[label=\"Map with minimap2\"]\n  3 -> 6 [label=\"output_collection\"]\n  7[label=\"MultiQC\"]\n  4 -> 7 [label=\"report_json\"]\n  8[label=\"Bowtie2\"]\n  4 -> 8 [label=\"output_paired_coll\"]\n  9[label=\"Samtools view\"]\n  6 -> 9 [label=\"alignment_output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  1[label=\"Trimmomatic\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Unzip Collection\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Map with BWA-MEM\"]\n  1 -> 3 [label=\"fastq_out_paired\"]\n  4[label=\"Samtools fastx\"]\n  3 -> 4 [label=\"bam_output\"]\n  5[label=\"Select\"]\n  4 -> 5 [label=\"forward\"]\n  6[label=\"Replace Text\"]\n  5 -> 6 [label=\"out_file1\"]\n  7[label=\"seqtk_subseq\"]\n  2 -> 7 [label=\"forward\"]\n  6 -> 7 [label=\"outfile\"]\n  8[label=\"seqtk_subseq\"]\n  2 -> 8 [label=\"reverse\"]\n  6 -> 8 [label=\"outfile\"]\n  9[label=\"Paired-end collection of cleaned reads\"]\n  7 -> 9 [label=\"default\"]\n  8 -> 9 [label=\"default\"]\n  kf24bbf28dc51440fa758ac05033f0645[color=lightseagreen,label=\"Output\\nCleaned Data\"]\n  9 -> kf24bbf28dc51440fa758ac05033f0645\n}",
                 "history": [
-                    {
-                        "hash": "fc35e6581a2e34e4420f19af4619c92283609e91",
-                        "message": "add annotations",
-                        "num": 2,
-                        "short_hash": "fc35e6581",
-                        "unix": "1587558793"
-                    },
-                    {
-                        "hash": "7ed054469d1ef84a60abec55758ee2932f9a9655",
-                        "message": "readd workflows",
-                        "num": 1,
-                        "short_hash": "7ed054469",
-                        "unix": "1587555276"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "List of Illumina accessions",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 257.683349609375,
-                            "top": 215.9166259765625
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "1a61a3b3-4515-47a1-8ee5-fb79f05a8dfa",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "ea340c2d-d9e8-4ea5-bbc0-7ee7d92a57bf"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "List of ONT accessions",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 264.9833984375,
-                            "top": 522.7166442871094
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "0988bf07-dc80-4d7b-a62f-8e5e852b0982",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "fb053f14-71fc-45ac-83ea-a308a5c22918"
-                            }
-                        ]
+                    {
+                        "hash": "f71f6dde01e2dfe86a4b43526f119d9050693f84",
+                        "message": "Address WF linting issues",
+                        "num": 2,
+                        "short_hash": "f71f6dde0",
+                        "unix": "1628012579"
+                    },
+                    {
+                        "hash": "f232ad426455a30be4a74af21054384c23b07275",
+                        "message": "Add new tutorial for cleaning SARS-CoV-2 data",
+                        "num": 1,
+                        "short_hash": "f232ad426",
+                        "unix": "1628010649"
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nList of Illumina accessions\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nList of ONT accessions\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Samtools stats\"];\n  6 -->|alignment_output| 10;\n  11[\"Samtools view\"];\n  8 -->|output| 11;\n  12[\"Samtools fastx\"];\n  9 -->|outputsam| 12;\n  13[\"Samtools fastx\"];\n  11 -->|outputsam| 13;\n  14[\"Collapse Collection\"];\n  12 -->|nonspecific| 14;\n  15[\"Zip Collection\"];\n  13 -->|forward| 15;\n  13 -->|reverse| 15;\n  16[\"Collapse Collection\"];\n  13 -->|forward| 16;\n  17[\"Collapse Collection\"];\n  13 -->|reverse| 17;\n  18[\"seqtk_sample\"];\n  16 -->|output| 18;\n  19[\"seqtk_sample\"];\n  17 -->|output| 19;\n  2[\"Illumina data\"];\n  0 -->|output| 2;\n  20[\"Create assemblies with Unicycler\"];\n  14 -->|output| 20;\n  18 -->|default| 20;\n  19 -->|default| 20;\n  21[\"Bandage Info\"];\n  20 -->|assembly_graph| 21;\n  22[\"Bandage Image\"];\n  20 -->|assembly_graph| 22;\n  23[\"Filter sequences by length\"];\n  20 -->|assembly| 23;\n  3[\"ONT data\"];\n  1 -->|output| 3;\n  4[\"fastp: Trimmed Illumina Reads\"];\n  2 -->|list_paired| 4;\n  5[\"NanoPlot\"];\n  3 -->|output_collection| 5;\n  6[\"Map with minimap2\"];\n  3 -->|output_collection| 6;\n  7[\"MultiQC\"];\n  4 -->|report_json| 7;\n  8[\"Bowtie2\"];\n  4 -->|output_paired_coll| 8;\n  9[\"Samtools view\"];\n  6 -->|alignment_output| 9;",
-                "modified": "2024-08-18 00:06:20 +0000",
-                "name": "assembly_with_preprocessing_and_sra_download",
-                "outputs": [
+                "inputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "List of Illumina accessions",
-                        "name": "Input dataset",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Input Dataset Collection"
+                            }
+                        ],
+                        "label": "Input Dataset Collection",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 257.683349609375,
-                            "top": 215.9166259765625
+                            "bottom": 564,
+                            "height": 81,
+                            "left": 296,
+                            "right": 496,
+                            "top": 483,
+                            "width": 200,
+                            "x": 296,
+                            "y": 483
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list:paired\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "1a61a3b3-4515-47a1-8ee5-fb79f05a8dfa",
+                        "type": "data_collection_input",
+                        "uuid": "d61c43e8-23ee-4f9a-9fd8-f58ffc134735",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "ea340c2d-d9e8-4ea5-bbc0-7ee7d92a57bf"
+                                "uuid": "b14c9326-21d3-4e0e-be24-7654e6b31b43"
                             }
                         ]
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Trimmomatic\"];\n  0 -->|output| 1;\n  2[\"Unzip Collection\"];\n  0 -->|output| 2;\n  3[\"Map with BWA-MEM\"];\n  1 -->|fastq_out_paired| 3;\n  4[\"Samtools fastx\"];\n  3 -->|bam_output| 4;\n  5[\"Select\"];\n  4 -->|forward| 5;\n  6[\"Replace Text\"];\n  5 -->|out_file1| 6;\n  7[\"seqtk_subseq\"];\n  2 -->|forward| 7;\n  6 -->|outfile| 7;\n  8[\"seqtk_subseq\"];\n  2 -->|reverse| 8;\n  6 -->|outfile| 8;\n  9[\"Paired-end collection of cleaned reads\"];\n  7 -->|default| 9;\n  8 -->|default| 9;\n  f24bbf28-dc51-440f-a758-ac05033f0645[\"Output\\nCleaned Data\"];\n  9 --> f24bbf28-dc51-440f-a758-ac05033f0645;\n  style f24bbf28-dc51-440f-a758-ac05033f0645 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "GTN - Sequence Analyses - Removal of human reads from SARS-CoV-2 sequencing data",
+                "outputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 0,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "List of ONT accessions",
-                        "name": "Input dataset",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Input Dataset Collection"
+                            }
+                        ],
+                        "label": "Input Dataset Collection",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 264.9833984375,
-                            "top": 522.7166442871094
+                            "bottom": 564,
+                            "height": 81,
+                            "left": 296,
+                            "right": 496,
+                            "top": 483,
+                            "width": 200,
+                            "x": 296,
+                            "y": 483
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list:paired\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "0988bf07-dc80-4d7b-a62f-8e5e852b0982",
+                        "type": "data_collection_input",
+                        "uuid": "d61c43e8-23ee-4f9a-9fd8-f58ffc134735",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "fb053f14-71fc-45ac-83ea-a308a5c22918"
+                                "uuid": "b14c9326-21d3-4e0e-be24-7654e6b31b43"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1",
                         "errors": null,
-                        "id": 10,
+                        "id": 1,
                         "input_connections": {
-                            "input": {
-                                "id": 6,
-                                "output_name": "alignment_output"
+                            "readtype|fastq_pair": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Samtools stats",
+                        "name": "Trimmomatic",
                         "outputs": [
                             {
-                                "name": "output_collection",
+                                "name": "fastq_out_paired",
                                 "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 1328.4166259765625,
-                            "top": 1239.4166259765625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "145f6d74ff5e",
-                            "name": "samtools_stats",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__page__\": null, \"coverage_cond\": \"{\\\"__current_case__\\\": 0, \\\"coverage_select\\\": \\\"no\\\"}\", \"gc_depth\": \"\\\"\\\"\", \"cov_threshold\": \"\\\"\\\"\", \"most_inserts\": \"\\\"\\\"\", \"cond_region\": \"{\\\"__current_case__\\\": 0, \\\"select_region\\\": \\\"no\\\"}\", \"split_output_cond\": \"{\\\"__current_case__\\\": 1, \\\"generate_tables\\\": [\\\"SN\\\"], \\\"split_output_selector\\\": \\\"yes\\\"}\", \"read_length\": \"\\\"\\\"\", \"trim_quality\": \"\\\"\\\"\", \"remove_overlaps\": \"\\\"false\\\"\", \"filter_by_flags\": \"{\\\"__current_case__\\\": 1, \\\"filter_flags\\\": \\\"nofilter\\\"}\", \"sparse\": \"\\\"false\\\"\", \"addref_cond\": \"{\\\"__current_case__\\\": 0, \\\"addref_select\\\": \\\"no\\\"}\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"insert_size\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"remove_dups\": \"\\\"false\\\"\"}",
-                        "tool_version": "2.0.2+galaxy2",
-                        "type": "tool",
-                        "uuid": "ae176340-d7da-4c2e-851b-e6129a0c222d",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_collection",
-                                "uuid": "8652ea8a-35f5-4531-8b89-88bca189ab9f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
-                        "errors": null,
-                        "id": 12,
-                        "input_connections": {
-                            "input": {
-                                "id": 9,
-                                "output_name": "outputsam"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Samtools fastx",
-                        "outputs": [
-                            {
-                                "name": "nonspecific",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "left": 1628.4166259765625,
-                            "top": 852.4166412353516
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "a8d69aee190e",
-                            "name": "samtools_fastx",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"copy_arb_tags\": \"\\\"\\\"\", \"__page__\": null, \"output_fmt_cond\": \"{\\\"__current_case__\\\": 2, \\\"default_quality\\\": \\\"\\\", \\\"ilumina_casava\\\": \\\"false\\\", \\\"output_fmt_select\\\": \\\"fastqsanger.gz\\\", \\\"output_quality\\\": \\\"false\\\"}\", \"idxout_cond\": \"{\\\"__current_case__\\\": 0, \\\"idxout_select\\\": \\\"no\\\"}\", \"read_numbering\": \"\\\"\\\"\", \"exclusive_filter\": \"null\", \"exclusive_filter_all\": \"null\", \"inclusive_filter\": \"null\", \"outputs\": \"[\\\"r0\\\"]\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"copy_tags\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9+galaxy1",
-                        "type": "tool",
-                        "uuid": "31e2b4e8-7631-46c0-8382-b805cee2b739",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "nonspecific",
-                                "uuid": "cfbf839f-53f0-4a82-8966-2bdb6919de5e"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "__ZIP_COLLECTION__",
-                        "errors": null,
-                        "id": 15,
-                        "input_connections": {
-                            "input_forward": {
-                                "id": 13,
-                                "output_name": "forward"
                             },
-                            "input_reverse": {
-                                "id": 13,
-                                "output_name": "reverse"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Zip Collection",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 2049.4166870117188,
-                            "top": 477.4166259765625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "__ZIP_COLLECTION__",
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_reverse\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"input_forward\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "9ba89e81-9c53-4f5b-9d61-42319b7d574c",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "ebc8f563-c45e-4e17-a541-b1275e7f61ad"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
-                        "errors": null,
-                        "id": 18,
-                        "input_connections": {
-                            "in_file": {
-                                "id": 16,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool seqtk_sample",
-                                "name": "in_file"
-                            }
-                        ],
-                        "label": null,
-                        "name": "seqtk_sample",
-                        "outputs": [
                             {
-                                "name": "default",
+                                "name": "fastq_out_unpaired",
                                 "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 2438.0833282470703,
-                            "top": 688.6833190917969
+                            "bottom": 515,
+                            "height": 202,
+                            "left": 532,
+                            "right": 732,
+                            "top": 313,
+                            "width": 200,
+                            "x": 532,
+                            "y": 313
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "58c8ece95b53",
-                            "name": "seqtk",
-                            "owner": "iuc",
+                            "changeset_revision": "d94aff5ee623",
+                            "name": "trimmomatic",
+                            "owner": "pjbriggs",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"s\": \"\\\"4\\\"\", \"in_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"subsample_size\": \"\\\"0.1\\\"\", \"advanced\": \"{\\\"single_pass_mode\\\": \\\"false\\\"}\"}",
-                        "tool_version": "1.3.2",
+                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"illuminaclip\": {\"do_illuminaclip\": \"false\", \"__current_case__\": 1}, \"operations\": [{\"__index__\": 0, \"operation\": {\"name\": \"SLIDINGWINDOW\", \"__current_case__\": 0, \"window_size\": \"4\", \"required_quality\": \"20\"}}], \"output_err\": \"false\", \"output_logs\": \"false\", \"readtype\": {\"single_or_paired\": \"collection\", \"__current_case__\": 2, \"fastq_pair\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.38.1",
                         "type": "tool",
-                        "uuid": "b4e40092-e076-4eb0-af30-c8c47885fefa",
+                        "uuid": "ced9a15d-ca78-4cf5-b1a0-267920691879",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "default",
-                                "uuid": "cf3eb8ef-fce5-42af-a14d-60ff915fbff3"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
-                        "errors": null,
-                        "id": 19,
-                        "input_connections": {
-                            "in_file": {
-                                "id": 17,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool seqtk_sample",
-                                "name": "in_file"
-                            }
-                        ],
-                        "label": null,
-                        "name": "seqtk_sample",
-                        "outputs": [
-                            {
-                                "name": "default",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 2413.0833129882812,
-                            "top": 864.6833190917969
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "58c8ece95b53",
-                            "name": "seqtk",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"s\": \"\\\"4\\\"\", \"in_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"subsample_size\": \"\\\"0.1\\\"\", \"advanced\": \"{\\\"single_pass_mode\\\": \\\"false\\\"}\"}",
-                        "tool_version": "1.3.2",
-                        "type": "tool",
-                        "uuid": "1ef9ca9e-e447-4933-8871-c0e8e9a953c4",
-                        "workflow_outputs": [
+                                "output_name": "fastq_out_unpaired",
+                                "uuid": "88e4c149-85d2-4c19-8a53-f242a3703e5e"
+                            },
                             {
                                 "label": null,
-                                "output_name": "default",
-                                "uuid": "bf722cb7-0b06-42ed-8fbc-9dc3896e9340"
+                                "output_name": "fastq_out_paired",
+                                "uuid": "fd0243b9-ef6a-445d-8fb9-f76d47c3f6fc"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
+                        "content_id": "__UNZIP_COLLECTION__",
                         "errors": null,
                         "id": 2,
                         "input_connections": {
-                            "input|file_list": {
+                            "input": {
                                 "id": 0,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "Illumina data",
-                        "name": "Faster Download and Extract Reads in FASTQ",
+                        "label": null,
+                        "name": "Unzip Collection",
                         "outputs": [
                             {
-                                "name": "list_paired",
-                                "type": "input"
-                            },
-                            {
-                                "name": "output_collection",
+                                "name": "forward",
                                 "type": "input"
                             },
                             {
-                                "name": "output_collection_other",
+                                "name": "reverse",
                                 "type": "input"
-                            },
-                            {
-                                "name": "log",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 511.783447265625,
-                            "top": 273.1666259765625
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionlog": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "log"
-                            },
-                            "HideDatasetActionoutput_collection": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_collection"
-                            },
-                            "HideDatasetActionoutput_collection_other": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_collection_other"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "aad3885b3216",
-                            "name": "sra_tools",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adv\": \"{\\\"minlen\\\": \\\"\\\", \\\"skip_technical\\\": \\\"true\\\", \\\"split\\\": \\\"--split-3\\\"}\", \"input\": \"{\\\"__current_case__\\\": 2, \\\"file_list\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"input_select\\\": \\\"file_list\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
-                        "tool_version": "2.10.4+galaxy1",
-                        "type": "tool",
-                        "uuid": "b097b5cb-44a8-4881-9ba0-a089ef1b4ad6",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "list_paired",
-                                "uuid": "c6b4e7f2-5cf4-4051-afd1-a110381c4679"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
-                        "errors": null,
-                        "id": 20,
-                        "input_connections": {
-                            "long": {
-                                "id": 14,
-                                "output_name": "output"
-                            },
-                            "paired_unpaired|fastq_input1": {
-                                "id": 18,
-                                "output_name": "default"
-                            },
-                            "paired_unpaired|fastq_input2": {
-                                "id": 19,
-                                "output_name": "default"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "lr_align"
-                            },
-                            {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "long"
-                            },
-                            {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "paired_unpaired"
-                            },
-                            {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "paired_unpaired"
-                            },
-                            {
-                                "description": "runtime parameter for tool Create assemblies with Unicycler",
-                                "name": "rotation"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Create assemblies with Unicycler",
-                        "outputs": [
-                            {
-                                "name": "assembly_graph",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "assembly",
-                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 2673.4166717529297,
-                            "top": 699.4166412353516
+                            "bottom": 746,
+                            "height": 182,
+                            "left": 735,
+                            "right": 935,
+                            "top": 564,
+                            "width": 200,
+                            "x": 735,
+                            "y": 564
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "88c240872a65",
-                            "name": "unicycler",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"linear_seqs\": \"\\\"1\\\"\", \"spades\": \"{\\\"depth_filter\\\": \\\"0.25\\\", \\\"kmer_count\\\": \\\"10\\\", \\\"kmers\\\": \\\"\\\", \\\"largest_component\\\": \\\"false\\\", \\\"max_kmer_frac\\\": \\\"0.95\\\", \\\"min_kmer_frac\\\": \\\"0.2\\\", \\\"no_correct\\\": \\\"false\\\"}\", \"graph_clean\": \"{\\\"min_component_size\\\": \\\"1000\\\", \\\"min_dead_end_size\\\": \\\"1000\\\"}\", \"__page__\": null, \"min_anchor_seg_len\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"lr_align\": \"{\\\"contamination\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"low_score\\\": \\\"\\\", \\\"scores\\\": \\\"3,-6,-5,-2\\\"}\", \"long\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"paired_unpaired\": \"{\\\"__current_case__\\\": 0, \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"fastq_input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired\\\"}\", \"min_fasta_length\": \"\\\"100\\\"\", \"mode\": \"\\\"normal\\\"\", \"rotation\": \"{\\\"no_rotate\\\": \\\"false\\\", \\\"start_gene_cov\\\": \\\"95.0\\\", \\\"start_gene_id\\\": \\\"90.0\\\", \\\"start_genes\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"pilon\": \"{\\\"min_polish_size\\\": \\\"1000\\\", \\\"no_pilon\\\": \\\"false\\\"}\"}",
-                        "tool_version": "0.4.8.0",
+                        "tool_id": "__UNZIP_COLLECTION__",
+                        "tool_state": "{\"input\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
                         "type": "tool",
-                        "uuid": "851c6be6-c202-450a-9cd3-19e205dcc496",
+                        "uuid": "f6552b12-5845-486b-95f5-35a3eefaa109",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "assembly",
-                                "uuid": "17700863-7cc5-4a67-ac0f-aa5f7b258d62"
+                                "output_name": "forward",
+                                "uuid": "5fabd686-3611-4d28-aff3-c1286b461bbf"
                             },
                             {
                                 "label": null,
-                                "output_name": "assembly_graph",
-                                "uuid": "3285cc00-6b39-4f3d-87a5-87abd483ede6"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
-                        "errors": null,
-                        "id": 21,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 20,
-                                "output_name": "assembly_graph"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Bandage Info",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 2977.4166870117188,
-                            "top": 803.4166412353516
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b2860df42e16",
-                            "name": "bandage",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"tsv\": \"\\\"false\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
-                        "tool_version": "0.8.1+galaxy1",
-                        "type": "tool",
-                        "uuid": "4aa230bd-3269-41c3-81f5-9085fcc4001d",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "cf5eab6a-97ae-430e-a27a-6ecc33d4b8c0"
+                                "output_name": "reverse",
+                                "uuid": "9b0c1a5f-6d39-46c7-a16d-afbb9e34bcfe"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
                         "errors": null,
-                        "id": 22,
+                        "id": 3,
                         "input_connections": {
-                            "input_file": {
-                                "id": 20,
-                                "output_name": "assembly_graph"
+                            "fastq_input|fastq_input1": {
+                                "id": 1,
+                                "output_name": "fastq_out_paired"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Bandage Image",
-                                "name": "input_file"
+                                "description": "runtime parameter for tool Map with BWA-MEM",
+                                "name": "fastq_input"
                             }
                         ],
                         "label": null,
-                        "name": "Bandage Image",
+                        "name": "Map with BWA-MEM",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "jpg"
+                                "name": "bam_output",
+                                "type": "bam"
                             }
                         ],
                         "position": {
-                            "left": 2975.4166870117188,
-                            "top": 1017.4166412353516
+                            "bottom": 487,
+                            "height": 192,
+                            "left": 753,
+                            "right": 953,
+                            "top": 295,
+                            "width": 200,
+                            "x": 753,
+                            "y": 295
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "b2860df42e16",
-                            "name": "bandage",
-                            "owner": "iuc",
+                            "changeset_revision": "64f11cf59c6e",
+                            "name": "bwa",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"lengths\": \"\\\"true\\\"\", \"output_format\": \"\\\"jpg\\\"\", \"height\": \"\\\"1000\\\"\", \"width\": \"\\\"\\\"\", \"names\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.8.1+galaxy2",
+                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"illumina\", \"__current_case__\": 0}, \"fastq_input\": {\"fastq_input_selector\": \"paired_collection\", \"__current_case__\": 2, \"fastq_input1\": {\"__class__\": \"RuntimeValue\"}, \"iset_stats\": \"\"}, \"output_sort\": \"coordinate\", \"reference_source\": {\"reference_source_selector\": \"cached\", \"__current_case__\": 0, \"ref_file\": \"hg38\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.17.2",
                         "type": "tool",
-                        "uuid": "7683e21a-0fe1-4871-b044-7e74321fe44b",
+                        "uuid": "c21129e8-b54f-4a7d-9af2-b8202434c342",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "12e0cc76-0374-4ce8-b882-f5f21a942ad1"
+                                "output_name": "bam_output",
+                                "uuid": "f0ca56d9-f544-465c-ad37-6380ba0ac2ea"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
                         "errors": null,
-                        "id": 23,
+                        "id": 4,
                         "input_connections": {
                             "input": {
-                                "id": 20,
-                                "output_name": "assembly"
+                                "id": 3,
+                                "output_name": "bam_output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Filter sequences by length",
-                                "name": "input"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Filter sequences by length",
+                        "name": "Samtools fastx",
                         "outputs": [
                             {
-                                "name": "output",
+                                "name": "forward",
                                 "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 2978.4166870117188,
-                            "top": 1220.4166259765625
+                            "bottom": 447,
+                            "height": 152,
+                            "left": 973,
+                            "right": 1173,
+                            "top": 295,
+                            "width": 200,
+                            "x": 973,
+                            "y": 295
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "8cacfcf96a52",
-                            "name": "fasta_filter_by_length",
-                            "owner": "devteam",
+                            "changeset_revision": "a8d69aee190e",
+                            "name": "samtools_fastx",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"max_length\": \"\\\"0\\\"\", \"min_length\": \"\\\"1000\\\"\"}",
-                        "tool_version": "1.2",
+                        "tool_state": "{\"__input_ext\": \"bam\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"copy_arb_tags\": \"\", \"copy_tags\": \"false\", \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"idxout_cond\": {\"idxout_select\": \"no\", \"__current_case__\": 0}, \"inclusive_filter\": [\"4\", \"8\"], \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"1085990\", \"output_fmt_cond\": {\"output_fmt_select\": \"fasta\", \"__current_case__\": 1}, \"outputs\": [\"r1\"], \"read_numbering\": \"-n\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9+galaxy1",
                         "type": "tool",
-                        "uuid": "ef08963b-e96b-4841-b1fd-02056f6ab1f2",
+                        "uuid": "756ca036-b6b5-46e8-a230-81ed522ba950",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "637c866b-dc17-4c32-aa1e-5207ae2c79a0"
+                                "output_name": "forward",
+                                "uuid": "e82ae014-e75a-486c-93d6-af8cdd6e6f95"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
+                        "content_id": "Grep1",
                         "errors": null,
-                        "id": 3,
+                        "id": 5,
                         "input_connections": {
-                            "input|file_list": {
-                                "id": 1,
-                                "output_name": "output"
+                            "input": {
+                                "id": 4,
+                                "output_name": "forward"
                             }
                         },
                         "inputs": [],
-                        "label": "ONT data",
-                        "name": "Faster Download and Extract Reads in FASTQ",
+                        "label": null,
+                        "name": "Select",
                         "outputs": [
                             {
-                                "name": "list_paired",
-                                "type": "input"
-                            },
-                            {
-                                "name": "output_collection",
-                                "type": "input"
-                            },
-                            {
-                                "name": "output_collection_other",
+                                "name": "out_file1",
                                 "type": "input"
-                            },
-                            {
-                                "name": "log",
-                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 516.13330078125,
-                            "top": 540.7166442871094
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionlist_paired": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "list_paired"
-                            },
-                            "HideDatasetActionlog": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "log"
-                            },
-                            "HideDatasetActionoutput_collection_other": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_collection_other"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "aad3885b3216",
-                            "name": "sra_tools",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 387,
+                            "height": 92,
+                            "left": 1193,
+                            "right": 1393,
+                            "top": 295,
+                            "width": 200,
+                            "x": 1193,
+                            "y": 295
                         },
-                        "tool_state": "{\"adv\": \"{\\\"minlen\\\": \\\"\\\", \\\"skip_technical\\\": \\\"true\\\", \\\"split\\\": \\\"--split-3\\\"}\", \"input\": \"{\\\"__current_case__\\\": 2, \\\"file_list\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"input_select\\\": \\\"file_list\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
-                        "tool_version": "2.10.4+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "Grep1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"1085990\", \"invert\": \"\", \"keep_header\": \"false\", \"pattern\": \"^>.+\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.3",
                         "type": "tool",
-                        "uuid": "2ea0a236-4ecc-43b4-a815-40f37bf1bd59",
+                        "uuid": "5ab56d83-be12-4498-a88e-16d37ef2e904",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_collection",
-                                "uuid": "9cd44dd5-4375-4c34-9edc-804544192c34"
+                                "output_name": "out_file1",
+                                "uuid": "04aaed7c-6c4c-44d6-89b0-5bba0a58927b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
                         "errors": null,
-                        "id": 4,
+                        "id": 6,
                         "input_connections": {
-                            "single_paired|paired_input": {
-                                "id": 2,
-                                "output_name": "list_paired"
+                            "infile": {
+                                "id": 5,
+                                "output_name": "out_file1"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool fastp",
-                                "name": "single_paired"
-                            }
-                        ],
-                        "label": "fastp: Trimmed Illumina Reads",
-                        "name": "fastp",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Replace Text",
                         "outputs": [
                             {
-                                "name": "output_paired_coll",
+                                "name": "outfile",
                                 "type": "input"
-                            },
-                            {
-                                "name": "report_json",
-                                "type": "json"
                             }
                         ],
                         "position": {
-                            "left": 879.7833251953125,
-                            "top": 365.04998779296875
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionreport_json": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "report_json"
-                            }
+                            "bottom": 387,
+                            "height": 92,
+                            "left": 1413,
+                            "right": 1613,
+                            "top": 295,
+                            "width": 200,
+                            "x": 1413,
+                            "y": 295
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "1d8fe9bc4cb0",
-                            "name": "fastp",
-                            "owner": "iuc",
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"report_html\\\": \\\"false\\\", \\\"report_json\\\": \\\"true\\\"}\", \"single_paired\": \"{\\\"__current_case__\\\": 2, \\\"adapter_trimming_options\\\": {\\\"adapter_sequence1\\\": \\\"\\\", \\\"adapter_sequence2\\\": \\\"\\\", \\\"disable_adapter_trimming\\\": \\\"false\\\"}, \\\"global_trimming_options\\\": {\\\"trim_front1\\\": \\\"\\\", \\\"trim_front2\\\": \\\"\\\", \\\"trim_tail1\\\": \\\"\\\", \\\"trim_tail2\\\": \\\"\\\"}, \\\"paired_input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"single_paired_selector\\\": \\\"paired_collection\\\"}\", \"read_mod_options\": \"{\\\"base_correction_options\\\": {\\\"correction\\\": \\\"false\\\"}, \\\"cutting_by_quality_options\\\": {\\\"cut_by_quality3\\\": \\\"false\\\", \\\"cut_by_quality5\\\": \\\"false\\\", \\\"cut_mean_quality\\\": \\\"\\\", \\\"cut_window_size\\\": \\\"\\\"}, \\\"polyg_tail_trimming\\\": {\\\"__current_case__\\\": 1, \\\"poly_g_min_len\\\": \\\"\\\", \\\"trimming_select\\\": \\\"\\\"}, \\\"polyx_tail_trimming\\\": {\\\"__current_case__\\\": 1, \\\"polyx_trimming_select\\\": \\\"\\\"}, \\\"umi_processing\\\": {\\\"umi\\\": \\\"false\\\", \\\"umi_len\\\": \\\"\\\", \\\"umi_loc\\\": \\\"\\\", \\\"umi_prefix\\\": \\\"\\\"}}\", \"overrepresented_sequence_analysis\": \"{\\\"overrepresentation_analysis\\\": \\\"false\\\", \\\"overrepresentation_sampling\\\": \\\"\\\"}\", \"filter_options\": \"{\\\"length_filtering_options\\\": {\\\"disable_length_filtering\\\": \\\"false\\\", \\\"length_required\\\": \\\"50\\\"}, \\\"low_complexity_filter\\\": {\\\"complexity_threshold\\\": \\\"\\\", \\\"enable_low_complexity_filter\\\": \\\"false\\\"}, \\\"quality_filtering_options\\\": {\\\"disable_quality_filtering\\\": \\\"false\\\", \\\"n_base_limit\\\": \\\"\\\", \\\"qualified_quality_phred\\\": \\\"20\\\", \\\"unqualified_percent_limit\\\": \\\"20\\\"}}\", \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.19.5+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"infile|__identifier__\": \"1085990\", \"replacements\": [{\"__index__\": 0, \"find_pattern\": \"^>(.+)\", \"replace_pattern\": \"\\\\1\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.2",
                         "type": "tool",
-                        "uuid": "7508c22b-dc6a-4071-8dd0-d5616718e62b",
+                        "uuid": "030b177e-2375-4856-b640-8ffd7f591aaf",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_paired_coll",
-                                "uuid": "a7be7eab-3e80-4be6-b1a4-ab303c314096"
+                                "output_name": "outfile",
+                                "uuid": "f81d7560-8835-4307-b876-f56e22edf40e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
                         "errors": null,
-                        "id": 5,
+                        "id": 7,
                         "input_connections": {
-                            "mode|reads|files": {
-                                "id": 3,
-                                "output_name": "output_collection"
+                            "in_file": {
+                                "id": 2,
+                                "output_name": "forward"
+                            },
+                            "source|name_list": {
+                                "id": 6,
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "NanoPlot",
+                        "name": "seqtk_subseq",
                         "outputs": [
                             {
-                                "name": "output_html",
-                                "type": "html"
-                            },
-                            {
-                                "name": "nanostats",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "nanostats_post_filtering",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "read_length",
-                                "type": "png"
-                            },
-                            {
-                                "name": "log_read_length",
-                                "type": "png"
+                                "name": "default",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 924.7833251953125,
-                            "top": 650.4666442871094
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionlog_read_length": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "log_read_length"
-                            },
-                            "HideDatasetActionnanostats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "nanostats"
-                            },
-                            "HideDatasetActionnanostats_post_filtering": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "nanostats_post_filtering"
-                            },
-                            "HideDatasetActionread_length": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "read_length"
-                            }
+                            "bottom": 416,
+                            "height": 142,
+                            "left": 1653,
+                            "right": 1853,
+                            "top": 274,
+                            "width": 200,
+                            "x": 1653,
+                            "y": 274
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "645159bcee2d",
-                            "name": "nanoplot",
+                            "changeset_revision": "58c8ece95b53",
+                            "name": "seqtk",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"filter\": \"{\\\"alength\\\": \\\"false\\\", \\\"barcoded\\\": \\\"false\\\", \\\"downsample\\\": \\\"\\\", \\\"drop_outliers\\\": \\\"false\\\", \\\"loglength\\\": \\\"true\\\", \\\"maxlength\\\": \\\"\\\", \\\"minlength\\\": \\\"\\\", \\\"minqual\\\": \\\"\\\", \\\"percentqual\\\": \\\"false\\\", \\\"readtype\\\": null}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"__current_case__\\\": 0, \\\"choice\\\": \\\"batch\\\", \\\"reads\\\": {\\\"__current_case__\\\": 0, \\\"files\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"type\\\": \\\"fastq\\\"}}\", \"customization\": \"{\\\"N50\\\": \\\"false\\\", \\\"color\\\": null, \\\"format\\\": \\\"png\\\", \\\"noN50\\\": \\\"false\\\", \\\"plots\\\": null}\"}",
-                        "tool_version": "1.25.0+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"in_file|__identifier__\": \"1085990\", \"l\": \"0\", \"name_list|__identifier__\": \"1085990\", \"source\": {\"type\": \"name\", \"__current_case__\": 1, \"name_list\": {\"__class__\": \"ConnectedValue\"}}, \"t\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3.1",
                         "type": "tool",
-                        "uuid": "9b1d43ac-82e3-463f-9c88-08c8826a62c9",
+                        "uuid": "50599db8-7c04-4f0f-8cc7-ca9fbeb405ea",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_html",
-                                "uuid": "cd8570c7-02db-479b-81a9-cd0d26643f71"
+                                "output_name": "default",
+                                "uuid": "75989c7c-9b50-4286-b59a-e2ebefcd6206"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
                         "errors": null,
-                        "id": 6,
+                        "id": 8,
                         "input_connections": {
-                            "fastq_input|fastq_input1": {
-                                "id": 3,
-                                "output_name": "output_collection"
+                            "in_file": {
+                                "id": 2,
+                                "output_name": "reverse"
+                            },
+                            "source|name_list": {
+                                "id": 6,
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Map with minimap2",
+                        "name": "seqtk_subseq",
                         "outputs": [
                             {
-                                "name": "alignment_output",
-                                "type": "bam"
+                                "name": "default",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 1003.9833984375,
-                            "top": 1131.9666442871094
+                            "bottom": 572,
+                            "height": 142,
+                            "left": 1658,
+                            "right": 1858,
+                            "top": 430,
+                            "width": 200,
+                            "x": 1658,
+                            "y": 430
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "53c0b7a1a0c3",
-                            "name": "minimap2",
+                            "changeset_revision": "58c8ece95b53",
+                            "name": "seqtk",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"alignment_options\": \"{\\\"-O2\\\": \\\"\\\", \\\"A\\\": \\\"\\\", \\\"B\\\": \\\"\\\", \\\"E\\\": \\\"\\\", \\\"E2\\\": \\\"\\\", \\\"O\\\": \\\"\\\", \\\"s\\\": \\\"\\\", \\\"u\\\": null, \\\"z\\\": \\\"\\\"}\", \"analysis_type_selector\": \"\\\"splice\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"io_options\": \"{\\\"K\\\": \\\"\\\", \\\"L\\\": \\\"false\\\", \\\"Q\\\": \\\"false\\\", \\\"Y\\\": \\\"false\\\", \\\"c\\\": \\\"false\\\", \\\"cs\\\": null, \\\"eqx\\\": \\\"false\\\", \\\"output_format\\\": \\\"BAM\\\"}\", \"mapping_options\": \"{\\\"F\\\": \\\"\\\", \\\"G\\\": \\\"\\\", \\\"N\\\": \\\"\\\", \\\"X\\\": \\\"false\\\", \\\"f\\\": \\\"\\\", \\\"g\\\": \\\"\\\", \\\"m\\\": \\\"\\\", \\\"min_occ_floor\\\": \\\"\\\", \\\"n\\\": \\\"\\\", \\\"p\\\": \\\"\\\", \\\"r\\\": \\\"\\\"}\", \"fastq_input\": \"{\\\"__current_case__\\\": 1, \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"single\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 0, \\\"ref_file\\\": \\\"hg38\\\", \\\"reference_source_selector\\\": \\\"cached\\\"}\", \"indexing_options\": \"{\\\"H\\\": \\\"false\\\", \\\"I\\\": \\\"\\\", \\\"k\\\": \\\"\\\", \\\"w\\\": \\\"\\\"}\"}",
-                        "tool_version": "2.17+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"in_file|__identifier__\": \"1085990\", \"l\": \"0\", \"name_list|__identifier__\": \"1085990\", \"source\": {\"type\": \"name\", \"__current_case__\": 1, \"name_list\": {\"__class__\": \"ConnectedValue\"}}, \"t\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3.1",
                         "type": "tool",
-                        "uuid": "098d2283-1218-489b-9882-8822e79d9444",
+                        "uuid": "6b8ac606-6490-4355-9111-001dbe15fd22",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "alignment_output",
-                                "uuid": "9972015d-4bdc-440f-b8b6-84e92a64ef8f"
+                                "output_name": "default",
+                                "uuid": "1787644d-4796-4928-9458-7fc0779eb500"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "content_id": "__ZIP_COLLECTION__",
                         "errors": null,
-                        "id": 7,
+                        "id": 9,
                         "input_connections": {
-                            "results_0|software_cond|input": {
-                                "id": 4,
-                                "output_name": "report_json"
+                            "input_forward": {
+                                "id": 7,
+                                "output_name": "default"
+                            },
+                            "input_reverse": {
+                                "id": 8,
+                                "output_name": "default"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "MultiQC",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "stats",
-                                "type": "input"
+                                "description": "runtime parameter for tool Zip Collection",
+                                "name": "input_forward"
                             },
                             {
-                                "name": "html_report",
-                                "type": "html"
+                                "description": "runtime parameter for tool Zip Collection",
+                                "name": "input_reverse"
                             }
                         ],
-                        "position": {
-                            "left": 1152.4833984375,
-                            "top": 200
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionstats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "stats"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b2f1f75d49c4",
-                            "name": "multiqc",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"comment\": \"\\\"\\\"\", \"__page__\": null, \"title\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"results\": \"[{\\\"__index__\\\": 0, \\\"software_cond\\\": {\\\"__current_case__\\\": 7, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"software\\\": \\\"fastp\\\"}}]\", \"saveLog\": \"\\\"false\\\"\"}",
-                        "tool_version": "1.7",
-                        "type": "tool",
-                        "uuid": "73566697-4a46-4d35-b8e2-61770acc62c0",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "html_report",
-                                "uuid": "15f42a94-2c97-4932-8e3f-f26a72b58be4"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "library|input_1": {
-                                "id": 4,
-                                "output_name": "output_paired_coll"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Bowtie2",
+                        "label": "Paired-end collection of cleaned reads",
+                        "name": "Zip Collection",
                         "outputs": [
                             {
                                 "name": "output",
-                                "type": "bam"
-                            },
-                            {
-                                "name": "mapping_stats",
-                                "type": "txt"
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 1208.699951171875,
-                            "top": 564.6333160400391
+                            "bottom": 490.5,
+                            "height": 142,
+                            "left": 1939,
+                            "right": 2139,
+                            "top": 348.5,
+                            "width": 200,
+                            "x": 1939,
+                            "y": 348.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "749c918495f7",
-                            "name": "bowtie2",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"sam_options\": \"{\\\"__current_case__\\\": 1, \\\"sam_options_selector\\\": \\\"no\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"__current_case__\\\": 2, \\\"aligned_file\\\": \\\"false\\\", \\\"input_1\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"paired_options\\\": {\\\"__current_case__\\\": 1, \\\"paired_options_selector\\\": \\\"no\\\"}, \\\"type\\\": \\\"paired_collection\\\", \\\"unaligned_file\\\": \\\"false\\\"}\", \"reference_genome\": \"{\\\"__current_case__\\\": 0, \\\"index\\\": \\\"hg38full\\\", \\\"source\\\": \\\"indexed\\\"}\", \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"save_mapping_stats\": \"\\\"true\\\"\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"simple\\\", \\\"presets\\\": \\\"no_presets\\\"}\"}",
-                        "tool_version": "2.3.4.3+galaxy0",
+                        "tool_id": "__ZIP_COLLECTION__",
+                        "tool_state": "{\"input_forward\": {\"__class__\": \"RuntimeValue\"}, \"input_reverse\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
                         "type": "tool",
-                        "uuid": "43331d2c-7116-410e-a6bd-7e7520d93a52",
+                        "uuid": "381d0485-0164-410f-801d-7dfb7891663d",
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "Cleaned Data",
                                 "output_name": "output",
-                                "uuid": "eeae40f6-f1b2-4c56-9860-ac7b8eb1dec0"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "mapping_stats",
-                                "uuid": "c567226e-efaf-4188-bdec-3ba20d0733b0"
+                                "uuid": "f24bbf28-dc51-440f-a758-ac05033f0645"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/assembly-with-preprocessing",
-                "path": "topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing_and_sra_download.ga",
+                "parent_id": "sequence-analysis/human-reads-removal",
+                "path": "topics/sequence-analysis/tutorials/human-reads-removal/workflows/human-reads-removal.ga",
                 "tags": [
-                    "GTN",
-                    "assembly"
+                    "sequence-analysis"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "assembly_with_preprocessing_and_sra_download",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-assembly-with-preprocessing/versions/assembly-with-preprocessing-and-sra-download",
-                "tutorial_id": "assembly-with-preprocessing",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing_and_sra_download.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing_and_sra_download.html",
+                "title": "GTN - Sequence Analyses - Removal of human reads from SARS-CoV-2 sequencing data",
+                "topic_id": "sequence-analysis",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/sequence-analysis-human-reads-removal/versions/human-reads-removal",
+                "tutorial_id": "human-reads-removal",
+                "url": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/human-reads-removal/workflows/human-reads-removal.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/human-reads-removal/workflows/human-reads-removal.html",
                 "version": 1,
-                "wfid": "assembly-assembly-with-preprocessing",
-                "wfname": "assembly-with-preprocessing-and-sra-download",
-                "workflow": "assembly_with_preprocessing_and_sra_download.ga",
+                "wfid": "sequence-analysis-human-reads-removal",
+                "wfname": "human-reads-removal",
+                "workflow": "human-reads-removal.ga",
                 "workflow_tools": [
+                    "Grep1",
+                    "__UNZIP_COLLECTION__",
                     "__ZIP_COLLECTION__",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
                     "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+                    "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1"
                 ],
-                "workflowhub_id": "1197"
+                "workflowhub_id": "1276"
             }
-        ],
-        "zenodo_link": "https://zenodo.org/record/3732359"
+        ]
     },
     {
         "admin_install": {
@@ -43398,16 +44021,16 @@
         ],
         "dir": "topics/variant-analysis/tutorials/sars-cov-2",
         "edam_operation": [
+            "Data handling",
+            "Sequence alignment",
+            "Read mapping",
             "Sequencing quality control",
             "Sequence contamination filtering",
-            "Genome indexing",
+            "Generation",
+            "Validation",
             "SNP detection",
-            "Sequence alignment",
             "Formatting",
-            "Read mapping",
-            "Generation",
-            "Data handling",
-            "Validation"
+            "Genome indexing"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -43419,6 +44042,8 @@
         "hands_on": true,
         "id": "variant-analysis/sars-cov-2",
         "inexact_supported_servers": [
+            "MISSISSIPPI",
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.fr",
             "UseGalaxy.no",
@@ -43442,7 +44067,7 @@
             "Understand how collections enable processing of sequencing data in batches",
             "Understand the analysis steps required to identify and annotate genomic mutations from sequencing data of SARS-CoV-2 samples"
         ],
-        "pageviews": 18450,
+        "pageviews": 18698,
         "pub_date": "2020-06-24",
         "questions": [
             "How can you download public sequencing data deposited in the NCBI Sequence Read Archive (SRA) into a Galaxy history for analysis?",
@@ -43465,20 +44090,20 @@
         ],
         "short_id": "T00315",
         "short_tools": [
-            "Grep1",
-            "picard_MarkDuplicates",
+            "bwa_mem",
             "samtools_stats",
+            "picard_MarkDuplicates",
             "fastp",
+            "Filter1",
+            "lofreq_viterbi",
+            "snpeff_sars_cov_2",
             "multiqc",
-            "tp_cut_tool",
+            "lofreq_indelqual",
+            "Grep1",
             "fasterq_dump",
-            "snpSift_extractFields",
-            "Filter1",
             "lofreq_call",
-            "lofreq_indelqual",
-            "lofreq_viterbi",
-            "bwa_mem",
-            "snpeff_sars_cov_2"
+            "tp_cut_tool",
+            "snpSift_extractFields"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -43497,6 +44122,16 @@
                 }
             ],
             "inexact": [
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -43563,8 +44198,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 175,
-        "visitors": 12116,
+        "visit_duration": 174,
+        "visitors": 12309,
         "workflows": [
             {
                 "creators": [],
@@ -43695,7 +44330,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nNC_045512.2 fasta file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSRA Manifest\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Faster Download and Extract Reads in FASTQ\"];\n  1 -->|output| 2;\n  3[\"fastp\"];\n  2 -->|list_paired| 3;\n  4[\"Map with BWA-MEM\"];\n  3 -->|output_paired_coll| 4;\n  0 -->|output| 4;\n  5[\"MarkDuplicates\"];\n  4 -->|bam_output| 5;\n  6[\"Realign reads\"];\n  5 -->|outFile| 6;\n  0 -->|output| 6;\n  7[\"Samtools stats\"];\n  5 -->|outFile| 7;\n  8[\"Insert indel qualities\"];\n  6 -->|realigned| 8;\n  0 -->|output| 8;\n  2ca7c89b-999f-41dc-8037-e54e25959a7e[\"Output\\nRealigned Alignments with Indel Qualities\"];\n  8 --> 2ca7c89b-999f-41dc-8037-e54e25959a7e;\n  style 2ca7c89b-999f-41dc-8037-e54e25959a7e stroke:#2c3143,stroke-width:4px;\n  9[\"Call variants\"];\n  8 -->|output| 9;\n  0 -->|output| 9;\n  10[\"SnpEff eff:\"];\n  9 -->|variants| 10;\n  11[\"SnpSift Extract Fields\"];\n  10 -->|snpeff_output| 11;\n  06259137-eaa5-404a-923c-70ee5f1d89d4[\"Output\\nSnpSift tabular output\"];\n  11 --> 06259137-eaa5-404a-923c-70ee5f1d89d4;\n  style 06259137-eaa5-404a-923c-70ee5f1d89d4 stroke:#2c3143,stroke-width:4px;\n  12[\"MultiQC\"];\n  3 -->|report_json| 12;\n  7 -->|output| 12;\n  5 -->|metrics_file| 12;\n  10 -->|csvFile| 12;\n  758ffde5-7ddd-482a-88b2-1504f8335488[\"Output\\nMultiQC Report PE\"];\n  12 --> 758ffde5-7ddd-482a-88b2-1504f8335488;\n  style 758ffde5-7ddd-482a-88b2-1504f8335488 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
+                "modified": "2024-10-02 12:08:11 +0000",
                 "name": "Simple COVID-19 - PE Variation",
                 "outputs": [
                     {
@@ -44159,7 +44794,7 @@
                 {
                     "name": "pangolin",
                     "owner": "iuc",
-                    "revisions": "03ed9524dcd1",
+                    "revisions": "8ad84c5753ea",
                     "tool_panel_section_label": "Phylogenetics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
@@ -44172,7 +44807,7 @@
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: datamash_ops\n  owner: iuc\n  revisions: 4c07ddedc198\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nextclade\n  owner: iuc\n  revisions: 4f6349228462\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pangolin\n  owner: iuc\n  revisions: 03ed9524dcd1\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_regex_finder\n  owner: mbernt\n  revisions: 9a811adb714f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: datamash_ops\n  owner: iuc\n  revisions: 4c07ddedc198\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nextclade\n  owner: iuc\n  revisions: 4f6349228462\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pangolin\n  owner: iuc\n  revisions: 8ad84c5753ea\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_regex_finder\n  owner: mbernt\n  revisions: 9a811adb714f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
         "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.json",
         "contributions": {
             "authorship": [
@@ -44271,14 +44906,13 @@
         ],
         "dir": "topics/variant-analysis/tutorials/sars-cov-2-variant-discovery",
         "edam_operation": [
+            "Tree-based sequence alignment",
             "Variant calling",
-            "Methylation analysis",
             "Variant classification",
-            "Tree-based sequence alignment"
+            "Methylation analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.cz",
             "UseGalaxy.eu",
             "UseGalaxy.org (Main)"
         ],
@@ -44286,7 +44920,9 @@
         "feedback_number": 0,
         "hands_on": true,
         "id": "variant-analysis/sars-cov-2-variant-discovery",
-        "inexact_supported_servers": [],
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
@@ -44299,7 +44935,7 @@
         "layout": "tutorial_hands_on",
         "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-10-01",
         "objectives": [
             "Discover and obtain recommended Galaxy workflows for SARS-CoV-2 sequence data analysis through public workflow registries",
             "Choose and run a workflow to discover mutations in a batch of viral samples from sequencing data obtained through a range of different protocols and platforms",
@@ -44308,7 +44944,7 @@
             "Know different SARS-CoV-2 lineage classification systems, and use pangolin and Nextclade to assign samples to predefined lineages",
             "Combine information from different analysis steps to be able to draw appropriate conclusions about individual samples and batches of viral data"
         ],
-        "pageviews": 11912,
+        "pageviews": 12059,
         "pub_date": "2021-06-30",
         "questions": [
             "How can a complete analysis, including viral consensus sequence reconstruction and lineage assignment be performed?",
@@ -44338,6 +44974,19 @@
                     "wm75"
                 ],
                 "youtube_id": "vnFQ2fR_fzw"
+            },
+            {
+                "bot-timestamp": 1727459029,
+                "captioners": [
+                    "wm75"
+                ],
+                "date": "2024-09-27",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "55M",
+                "speakers": [
+                    "wm75"
+                ],
+                "youtube_id": "-HQB1zyWWXM"
             }
         ],
         "requirements": [
@@ -44358,23 +45007,18 @@
         ],
         "short_id": "T00316",
         "short_tools": [
-            "nextclade",
-            "datamash_ops",
-            "fasta_regex_finder",
             "pangolin",
             "Filter1",
-            "upload1"
+            "upload1",
+            "fasta_regex_finder",
+            "nextclade",
+            "datamash_ops"
         ],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "one-health",
         "supported_servers": {
             "exact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
@@ -44386,7 +45030,13 @@
                     "usegalaxy": true
                 }
             ],
-            "inexact": []
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
         },
         "symlink": null,
         "tags": [
@@ -44400,7 +45050,7 @@
             "Filter1",
             "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/iuc/nextclade/nextclade/2.7.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/4.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/4.3+galaxy2",
             "toolshed.g2.bx.psu.edu/repos/mbernt/fasta_regex_finder/fasta_regex_finder/0.1.0",
             "upload1"
         ],
@@ -44419,13 +45069,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.json"
         },
-        "version": 15,
+        "version": 17,
         "video": false,
-        "video_versions": 2,
+        "video_versions": 3,
         "video_view": 0,
-        "visit_duration": 207,
-        "visitors": 6391,
-        "zenodo_link": "https://zenodo.org/record/5036687"
+        "visit_duration": 208,
+        "visitors": 6500
     },
     {
         "admin_install": {
@@ -44434,108 +45083,101 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "ctb_frankenstein_ligand",
-                    "owner": "bgruening",
-                    "revisions": "8e214e52e461",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ctb_frankenstein_ligand",
-                    "owner": "bgruening",
-                    "revisions": "7255688c77f3",
-                    "tool_panel_section_label": "ChemicalToolBox",
+                    "name": "bowtie2",
+                    "owner": "devteam",
+                    "revisions": "749c918495f7",
+                    "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "enumerate_charges",
-                    "owner": "bgruening",
-                    "revisions": "2a868592ebcb",
-                    "tool_panel_section_label": "ChemicalToolBox",
+                    "name": "fasta_filter_by_length",
+                    "owner": "devteam",
+                    "revisions": "8cacfcf96a52",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "enumerate_charges",
-                    "owner": "bgruening",
-                    "revisions": "67ee76f0e497",
-                    "tool_panel_section_label": "ChemicalToolBox",
+                    "name": "samtools_stats",
+                    "owner": "devteam",
+                    "revisions": "145f6d74ff5e",
+                    "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "openbabel_compound_convert",
-                    "owner": "bgruening",
-                    "revisions": "b59c91adeac1",
-                    "tool_panel_section_label": "ChemicalToolBox",
+                    "name": "bandage",
+                    "owner": "iuc",
+                    "revisions": "b2860df42e16",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "openbabel_compound_convert",
-                    "owner": "bgruening",
-                    "revisions": "e2c36f62e22f",
-                    "tool_panel_section_label": "ChemicalToolBox",
+                    "name": "bandage",
+                    "owner": "iuc",
+                    "revisions": "94fe43e75ddc",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "rdock_rbcavity",
-                    "owner": "bgruening",
-                    "revisions": "744a777e9f90",
-                    "tool_panel_section_label": "ChemicalToolBox",
+                    "name": "fastp",
+                    "owner": "iuc",
+                    "revisions": "1d8fe9bc4cb0",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "rdock_rbdock",
-                    "owner": "bgruening",
-                    "revisions": "a22969b08177",
-                    "tool_panel_section_label": "ChemicalToolBox",
+                    "name": "minimap2",
+                    "owner": "iuc",
+                    "revisions": "53c0b7a1a0c3",
+                    "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "rxdock_rbcavity",
-                    "owner": "bgruening",
-                    "revisions": "7fac8e7a12d5",
-                    "tool_panel_section_label": "ChemicalToolBox",
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "b2f1f75d49c4",
+                    "tool_panel_section_label": "Quality Control",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "rxdock_rbdock",
-                    "owner": "bgruening",
-                    "revisions": "6fe6b0e10ed6",
-                    "tool_panel_section_label": "ChemicalToolBox",
+                    "name": "nanoplot",
+                    "owner": "iuc",
+                    "revisions": "645159bcee2d",
+                    "tool_panel_section_label": "Nanopore",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "split_file_to_collection",
-                    "owner": "bgruening",
-                    "revisions": "0046692724f9",
-                    "tool_panel_section_label": "Collection Operations",
+                    "name": "samtools_fastx",
+                    "owner": "iuc",
+                    "revisions": "a8d69aee190e",
+                    "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "split_file_to_collection",
-                    "owner": "bgruening",
-                    "revisions": "6cbe2f30c2d7",
-                    "tool_panel_section_label": "Collection Operations",
+                    "name": "samtools_view",
+                    "owner": "iuc",
+                    "revisions": "b01db2684fa5",
+                    "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sucos_max_score",
-                    "owner": "bgruening",
-                    "revisions": "d4c67ced6abc",
-                    "tool_panel_section_label": "ChemicalToolBox",
+                    "name": "seqtk",
+                    "owner": "iuc",
+                    "revisions": "3da72230c066",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sucos_max_score",
-                    "owner": "bgruening",
-                    "revisions": "9b48456a96fe",
-                    "tool_panel_section_label": "ChemicalToolBox",
+                    "name": "sra_tools",
+                    "owner": "iuc",
+                    "revisions": "aad3885b3216",
+                    "tool_panel_section_label": "Get Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "xchem_transfs_scoring",
-                    "owner": "bgruening",
-                    "revisions": "f6f9b47d02b6",
-                    "tool_panel_section_label": "ChemicalToolBox",
+                    "name": "unicycler",
+                    "owner": "iuc",
+                    "revisions": "9e3e80cc4ad4",
+                    "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
@@ -44547,1307 +45189,2229 @@
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: ctb_frankenstein_ligand\n  owner: bgruening\n  revisions: 8e214e52e461\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ctb_frankenstein_ligand\n  owner: bgruening\n  revisions: 7255688c77f3\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: enumerate_charges\n  owner: bgruening\n  revisions: 2a868592ebcb\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: enumerate_charges\n  owner: bgruening\n  revisions: 67ee76f0e497\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_compound_convert\n  owner: bgruening\n  revisions: b59c91adeac1\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_compound_convert\n  owner: bgruening\n  revisions: e2c36f62e22f\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rdock_rbcavity\n  owner: bgruening\n  revisions: 744a777e9f90\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rdock_rbdock\n  owner: bgruening\n  revisions: a22969b08177\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rxdock_rbcavity\n  owner: bgruening\n  revisions: 7fac8e7a12d5\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rxdock_rbdock\n  owner: bgruening\n  revisions: 6fe6b0e10ed6\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_to_collection\n  owner: bgruening\n  revisions: '0046692724f9'\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_to_collection\n  owner: bgruening\n  revisions: 6cbe2f30c2d7\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sucos_max_score\n  owner: bgruening\n  revisions: d4c67ced6abc\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sucos_max_score\n  owner: bgruening\n  revisions: 9b48456a96fe\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xchem_transfs_scoring\n  owner: bgruening\n  revisions: f6f9b47d02b6\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/covid19-docking/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bowtie2\n  owner: devteam\n  revisions: 749c918495f7\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_filter_by_length\n  owner: devteam\n  revisions: 8cacfcf96a52\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 145f6d74ff5e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: b2860df42e16\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: 94fe43e75ddc\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 1d8fe9bc4cb0\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: 53c0b7a1a0c3\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: b2f1f75d49c4\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: 645159bcee2d\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_fastx\n  owner: iuc\n  revisions: a8d69aee190e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: b01db2684fa5\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: aad3885b3216\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unicycler\n  owner: iuc\n  revisions: 9e3e80cc4ad4\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.json",
         "contributors": [
             {
-                "elixir_node": "de",
-                "former_affiliations": [
+                "affiliations": [
+                    "by-covid",
                     "uni-freiburg",
                     "elixir-europe"
                 ],
-                "id": "simonbray",
-                "joined": "2019-05",
-                "name": "Simon Bray",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
+                "elixir_node": "de",
+                "fediverse": "https://scholar.social/@zerodivision",
+                "fediverse_flavor": "mastodon",
+                "id": "wm75",
+                "joined": "2017-09",
+                "matrix": "wm75:matrix.org",
+                "name": "Wolfgang Maier",
+                "orcid": "0000-0002-9464-6640",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
             }
         ],
-        "dir": "topics/computational-chemistry/tutorials/covid19-docking",
-        "edam_operation": [],
+        "dir": "topics/assembly/tutorials/assembly-with-preprocessing",
+        "edam_operation": [
+            "Scatter plot plotting",
+            "Data handling",
+            "Read mapping",
+            "Sequencing quality control",
+            "Genome assembly",
+            "Box-Whisker plot plotting",
+            "Sequence contamination filtering",
+            "Aggregation",
+            "Sequence assembly visualisation",
+            "Pairwise sequence alignment",
+            "Validation",
+            "Sequence file editing"
+        ],
         "edam_topic": [],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org.au"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "computational-chemistry/covid19-docking",
-        "inexact_supported_servers": [],
+        "id": "assembly/assembly-with-preprocessing",
+        "inexact_supported_servers": [
+            "MISSISSIPPI",
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Galaxy can support large, rapid studies in computational chemistry",
-            "Protein-ligand docking contributes to the discovery of new drugs"
+            "Certain types of NGS samples can be heavily contaminated with sequences from other genomes",
+            "Reads from known/expected contaminating sources can be identified by mapping to the respective genomes",
+            "After mapping, use filtering tools to remove identified contaminating reads, and use conversion tools to convert remaining mapped reads back into raw sequenced reads expected by most downstream tools"
         ],
         "layout": "tutorial_hands_on",
         "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Understand how Galaxy was used to perform docking and pose scoring on the SARS-CoV-2 main protease (MPro).",
-            "Replicate the study on a (very) small scale",
-            "Gain familiarity with the docking and scoring techniques involved."
+            "Obtain viral (SARS-CoV-2) sequencing data with contaminating human reads from public sources",
+            "Organize the data into collections and check its quality",
+            "Detect and remove human reads",
+            "Assemble retained reads and explore the results"
         ],
-        "pageviews": 4516,
-        "pub_date": "2020-03-27",
+        "pageviews": 5905033,
+        "pub_date": "2020-04-21",
         "questions": [
-            "How can candidate ligands be generated and docked to a protein in Galaxy?",
-            "How can the poses of the docked ligands be evaluated?",
-            "How can a workflow for drug virtual screening be constructed in Galaxy?"
+            "How can a genome of interest be assembled against a background of contaminating reads from other genomes?",
+            "How can sequencing data from public sources be turned into assembly-ready polished datasets?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "mtekman"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "25M",
+                "speakers": [
+                    "gallardoalba"
+                ],
+                "youtube_id": "jNFLYhjgJPs"
+            }
         ],
         "requirements": [
             {
-                "topic_name": "computational-chemistry",
+                "topic_name": "assembly",
                 "tutorials": [
-                    "cheminformatics"
+                    "unicycler-assembly"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "sequence-analysis",
+                "tutorials": [
+                    "mapping"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "collections"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00049",
+        "short_id": "T00029",
         "short_tools": [
-            "enumerate_charges",
-            "xchem_transfs_scoring",
-            "rdock_rbdock",
-            "rdock_rbcavity",
-            "rxdock_rbcavity",
-            "xchem_pose_scoring",
-            "openbabel_compound_convert",
-            "split_file_to_collection",
-            "ctb_frankenstein_ligand",
-            "sucos_max_score",
+            "samtools_stats",
+            "unicycler",
+            "fastp",
+            "minimap2",
+            "bandage_image",
+            "samtools_view",
+            "fasta_filter_by_length",
+            "bandage_info",
+            "samtools_fastx",
+            "multiqc",
+            "seqtk_sample",
+            "fasterq_dump",
+            "nanoplot",
             "collapse_dataset",
-            "rxdock_rbdock"
+            "__ZIP_COLLECTION__",
+            "bowtie2"
         ],
-        "slides": false,
+        "slides": true,
         "slides_recordings": false,
         "supported_servers": {
-            "exact": [],
-            "inexact": []
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ]
         },
         "symlink": null,
         "tags": [
-            "covid19",
-            "one-health"
+            "covid19"
         ],
-        "time_estimation": "2H",
-        "title": "Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring",
+        "time_estimation": "4h",
+        "title": "Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/2013.1-0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/0.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/2020.03.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.2.2.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbcavity/rdock_rbcavity/0.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbdock/rdock_rbdock/0.1.4",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_rbcavity/rxdock_rbcavity/0.1.5",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_rbdock/rxdock_rbdock/0.1.5",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.4.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/sucos_max_score/sucos_max_score/0.2.3",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/sucos_max_score/sucos_max_score/2020.03.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/xchem_transfs_scoring/xchem_transfs_scoring/0.4.0",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
-            "xchem_pose_scoring"
+            "__ZIP_COLLECTION__",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
         ],
-        "topic_name": "computational-chemistry",
-        "topic_name_human": "Computational chemistry",
+        "topic_name": "assembly",
+        "topic_name_human": "Assembly",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "covid19-docking",
+        "tutorial_name": "assembly-with-preprocessing",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/computational-chemistry/tutorials/covid19-docking/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/covid19-docking/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/covid19-docking/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.json"
         },
-        "version": 10,
+        "version": 13,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 178,
-        "visitors": 2664,
+        "visit_duration": 364,
+        "visitors": 2138036,
         "workflows": [
             {
                 "creators": [],
-                "description": "Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring",
+                "description": "Assembly with preprocessing",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCandidates\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMpro-x0195_0_apo-desolv.pdb\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhits.sdf\"]\n  3[label=\"Enumerate changes\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Compound conversion\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Create Frankenstein ligand\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"Compound conversion\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"rDock cavity definition\"]\n  4 -> 7 [label=\"outfile\"]\n  5 -> 7 [label=\"outfile\"]\n  8[label=\"Split file\"]\n  6 -> 8 [label=\"outfile\"]\n  9[label=\"rDock docking\"]\n  4 -> 9 [label=\"outfile\"]\n  8 -> 9 [label=\"list_output_sdf\"]\n  7 -> 9 [label=\"activesite\"]\n  10[label=\"Collapse Collection\"]\n  9 -> 10 [label=\"output\"]\n  11[label=\"XChem TransFS pose scoring\"]\n  1 -> 11 [label=\"output\"]\n  10 -> 11 [label=\"output\"]\n  12[label=\"Max SuCOS score\"]\n  11 -> 12 [label=\"output\"]\n  2 -> 12 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nCollection of paired short-reads data\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nCollection of long-reads data\"]\n  10[label=\"Samtools fastx\"]\n  7 -> 10 [label=\"outputsam\"]\n  11[label=\"Samtools fastx\"]\n  9 -> 11 [label=\"outputsam\"]\n  12[label=\"Collapse Collection\"]\n  10 -> 12 [label=\"nonspecific\"]\n  13[label=\"Zip Collection\"]\n  11 -> 13 [label=\"forward\"]\n  11 -> 13 [label=\"reverse\"]\n  14[label=\"Collapse Collection\"]\n  11 -> 14 [label=\"forward\"]\n  15[label=\"Collapse Collection\"]\n  11 -> 15 [label=\"reverse\"]\n  16[label=\"seqtk_sample\"]\n  14 -> 16 [label=\"output\"]\n  17[label=\"seqtk_sample\"]\n  15 -> 17 [label=\"output\"]\n  18[label=\"Create assemblies with Unicycler\"]\n  12 -> 18 [label=\"output\"]\n  16 -> 18 [label=\"default\"]\n  17 -> 18 [label=\"default\"]\n  19[label=\"Bandage Info\"]\n  18 -> 19 [label=\"assembly_graph\"]\n  2[label=\"fastp: Trimmed Illumina Reads\"]\n  0 -> 2 [label=\"output\"]\n  20[label=\"Filter sequences by length\"]\n  18 -> 20 [label=\"assembly\"]\n  21[label=\"Bandage Image\"]\n  18 -> 21 [label=\"assembly_graph\"]\n  3[label=\"NanoPlot\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Map with minimap2\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"MultiQC\"]\n  2 -> 5 [label=\"report_json\"]\n  6[label=\"Bowtie2\"]\n  2 -> 6 [label=\"output_paired_coll\"]\n  7[label=\"Samtools view\"]\n  4 -> 7 [label=\"alignment_output\"]\n  8[label=\"Samtools stats\"]\n  4 -> 8 [label=\"alignment_output\"]\n  9[label=\"Samtools view\"]\n  6 -> 9 [label=\"output\"]\n}",
                 "history": [
                     {
-                        "hash": "cf8b1cb0509e73e534c234076c8bd055379823c5",
-                        "message": "Update some workflow names for consistency",
-                        "num": 4,
-                        "short_hash": "cf8b1cb05",
-                        "unix": "1598836271"
+                        "hash": "fc35e6581a2e34e4420f19af4619c92283609e91",
+                        "message": "add annotations",
+                        "num": 2,
+                        "short_hash": "fc35e6581",
+                        "unix": "1587558793"
                     },
                     {
-                        "hash": "60a21218780027dcf65a5f37b94148b0771303e1",
-                        "message": "update with covid19 tut with frankenstein ligand tool",
-                        "num": 3,
-                        "short_hash": "60a212187",
-                        "unix": "1591084355"
+                        "hash": "7ed054469d1ef84a60abec55758ee2932f9a9655",
+                        "message": "readd workflows",
+                        "num": 1,
+                        "short_hash": "7ed054469",
+                        "unix": "1587555276"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "Collection of paired short-reads data",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 268.13330078125,
+                            "top": 341.41668701171875
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"collection_type\": \"list:paired\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "3e7dab04-77db-4780-b1dd-c724b80a8b7b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "daba9931-3837-42b5-a93f-e2e51f5f667a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "Collection of long-reads data",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 267.13330078125,
+                            "top": 756.4166717529297
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"collection_type\": \"lis\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "bd1f5561-95a1-4fb5-af1e-f3d4cbb40639",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "7146e49b-ab4b-44a8-ac54-e98539fecb97"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nCollection of paired short-reads data\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nCollection of long-reads data\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Samtools fastx\"];\n  7 -->|outputsam| 10;\n  11[\"Samtools fastx\"];\n  9 -->|outputsam| 11;\n  12[\"Collapse Collection\"];\n  10 -->|nonspecific| 12;\n  13[\"Zip Collection\"];\n  11 -->|forward| 13;\n  11 -->|reverse| 13;\n  14[\"Collapse Collection\"];\n  11 -->|forward| 14;\n  15[\"Collapse Collection\"];\n  11 -->|reverse| 15;\n  16[\"seqtk_sample\"];\n  14 -->|output| 16;\n  17[\"seqtk_sample\"];\n  15 -->|output| 17;\n  18[\"Create assemblies with Unicycler\"];\n  12 -->|output| 18;\n  16 -->|default| 18;\n  17 -->|default| 18;\n  19[\"Bandage Info\"];\n  18 -->|assembly_graph| 19;\n  2[\"fastp: Trimmed Illumina Reads\"];\n  0 -->|output| 2;\n  20[\"Filter sequences by length\"];\n  18 -->|assembly| 20;\n  21[\"Bandage Image\"];\n  18 -->|assembly_graph| 21;\n  3[\"NanoPlot\"];\n  1 -->|output| 3;\n  4[\"Map with minimap2\"];\n  1 -->|output| 4;\n  5[\"MultiQC\"];\n  2 -->|report_json| 5;\n  6[\"Bowtie2\"];\n  2 -->|output_paired_coll| 6;\n  7[\"Samtools view\"];\n  4 -->|alignment_output| 7;\n  8[\"Samtools stats\"];\n  4 -->|alignment_output| 8;\n  9[\"Samtools view\"];\n  6 -->|output| 9;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "assembly_with_preprocessing",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "Collection of paired short-reads data",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 268.13330078125,
+                            "top": 341.41668701171875
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"collection_type\": \"list:paired\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "3e7dab04-77db-4780-b1dd-c724b80a8b7b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "daba9931-3837-42b5-a93f-e2e51f5f667a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "Collection of long-reads data",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 267.13330078125,
+                            "top": 756.4166717529297
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"collection_type\": \"lis\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "bd1f5561-95a1-4fb5-af1e-f3d4cbb40639",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "7146e49b-ab4b-44a8-ac54-e98539fecb97"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {
+                            "input": {
+                                "id": 7,
+                                "output_name": "outputsam"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Samtools fastx",
+                        "outputs": [
+                            {
+                                "name": "nonspecific",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "left": 1333.63330078125,
+                            "top": 852.4166717529297
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "a8d69aee190e",
+                            "name": "samtools_fastx",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"copy_arb_tags\": \"\\\"\\\"\", \"__page__\": null, \"output_fmt_cond\": \"{\\\"__current_case__\\\": 2, \\\"default_quality\\\": \\\"\\\", \\\"ilumina_casava\\\": \\\"false\\\", \\\"output_fmt_select\\\": \\\"fastqsanger.gz\\\", \\\"output_quality\\\": \\\"false\\\"}\", \"idxout_cond\": \"{\\\"__current_case__\\\": 0, \\\"idxout_select\\\": \\\"no\\\"}\", \"read_numbering\": \"\\\"\\\"\", \"exclusive_filter\": \"null\", \"exclusive_filter_all\": \"null\", \"inclusive_filter\": \"null\", \"outputs\": \"[\\\"r0\\\"]\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"copy_tags\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9+galaxy1",
+                        "type": "tool",
+                        "uuid": "31e2b4e8-7631-46c0-8382-b805cee2b739",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "nonspecific",
+                                "uuid": "cfbf839f-53f0-4a82-8966-2bdb6919de5e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "__ZIP_COLLECTION__",
+                        "errors": null,
+                        "id": 13,
+                        "input_connections": {
+                            "input_forward": {
+                                "id": 11,
+                                "output_name": "forward"
+                            },
+                            "input_reverse": {
+                                "id": 11,
+                                "output_name": "reverse"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Zip Collection",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1754.63330078125,
+                            "top": 477.41668701171875
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "__ZIP_COLLECTION__",
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_reverse\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"input_forward\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "9ba89e81-9c53-4f5b-9d61-42319b7d574c",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "ebc8f563-c45e-4e17-a541-b1275e7f61ad"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
+                        "errors": null,
+                        "id": 16,
+                        "input_connections": {
+                            "in_file": {
+                                "id": 14,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool seqtk_sample",
+                                "name": "in_file"
+                            }
+                        ],
+                        "label": null,
+                        "name": "seqtk_sample",
+                        "outputs": [
+                            {
+                                "name": "default",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 2129.4166717529297,
+                            "top": 711.4166717529297
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "58c8ece95b53",
+                            "name": "seqtk",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"s\": \"\\\"4\\\"\", \"in_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"subsample_size\": \"\\\"0.1\\\"\", \"advanced\": \"{\\\"single_pass_mode\\\": \\\"false\\\"}\"}",
+                        "tool_version": "1.3.2",
+                        "type": "tool",
+                        "uuid": "4f7c9133-a664-46dc-9583-c9980d5d1011",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "default",
+                                "uuid": "be52344e-6874-431c-8d86-9d0e9371aed9"
+                            }
+                        ]
                     },
                     {
-                        "hash": "2bffcbdc75d8aaf32b06acc2f9f493931782546d",
-                        "message": "lint",
-                        "num": 2,
-                        "short_hash": "2bffcbdc7",
-                        "unix": "1585304017"
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
+                        "errors": null,
+                        "id": 17,
+                        "input_connections": {
+                            "in_file": {
+                                "id": 15,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool seqtk_sample",
+                                "name": "in_file"
+                            }
+                        ],
+                        "label": null,
+                        "name": "seqtk_sample",
+                        "outputs": [
+                            {
+                                "name": "default",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 2116.4166717529297,
+                            "top": 859.4166717529297
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "58c8ece95b53",
+                            "name": "seqtk",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"s\": \"\\\"4\\\"\", \"in_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"subsample_size\": \"\\\"0.1\\\"\", \"advanced\": \"{\\\"single_pass_mode\\\": \\\"false\\\"}\"}",
+                        "tool_version": "1.3.2",
+                        "type": "tool",
+                        "uuid": "79064891-aa79-42e3-b848-7a6240022acc",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "default",
+                                "uuid": "3e196eb1-8ba1-4be5-90d0-c5b8d3df4ff0"
+                            }
+                        ]
                     },
-                    {
-                        "hash": "62d30105b34ea23f3280539d9880037639aa770e",
-                        "message": "linting covid19 cheminformatics tutorial",
-                        "num": 1,
-                        "short_hash": "62d30105b",
-                        "unix": "1585300158"
-                    }
-                ],
-                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
+                        "id": 18,
+                        "input_connections": {
+                            "long": {
+                                "id": 12,
+                                "output_name": "output"
+                            },
+                            "paired_unpaired|fastq_input1": {
+                                "id": 16,
+                                "output_name": "default"
+                            },
+                            "paired_unpaired|fastq_input2": {
+                                "id": 17,
+                                "output_name": "default"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Candidates"
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "lr_align"
+                            },
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "long"
+                            },
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "paired_unpaired"
+                            },
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "paired_unpaired"
+                            },
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "rotation"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Create assemblies with Unicycler",
+                        "outputs": [
+                            {
+                                "name": "assembly_graph",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "assembly",
+                                "type": "fasta"
                             }
                         ],
-                        "label": "Candidates",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 218,
-                            "top": 200
+                            "left": 2365.633331298828,
+                            "top": 706.4166717529297
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Candidates\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "47bf8c53-ae1e-4af6-bece-6adfd74b627c",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "88c240872a65",
+                            "name": "unicycler",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"linear_seqs\": \"\\\"1\\\"\", \"spades\": \"{\\\"depth_filter\\\": \\\"0.25\\\", \\\"kmer_count\\\": \\\"10\\\", \\\"kmers\\\": \\\"\\\", \\\"largest_component\\\": \\\"false\\\", \\\"max_kmer_frac\\\": \\\"0.95\\\", \\\"min_kmer_frac\\\": \\\"0.2\\\", \\\"no_correct\\\": \\\"false\\\"}\", \"graph_clean\": \"{\\\"min_component_size\\\": \\\"1000\\\", \\\"min_dead_end_size\\\": \\\"1000\\\"}\", \"__page__\": null, \"min_anchor_seg_len\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"lr_align\": \"{\\\"contamination\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"low_score\\\": \\\"\\\", \\\"scores\\\": \\\"3,-6,-5,-2\\\"}\", \"long\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"paired_unpaired\": \"{\\\"__current_case__\\\": 0, \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"fastq_input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired\\\"}\", \"min_fasta_length\": \"\\\"100\\\"\", \"mode\": \"\\\"normal\\\"\", \"rotation\": \"{\\\"no_rotate\\\": \\\"false\\\", \\\"start_gene_cov\\\": \\\"95.0\\\", \\\"start_gene_id\\\": \\\"90.0\\\", \\\"start_genes\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"pilon\": \"{\\\"min_polish_size\\\": \\\"1000\\\", \\\"no_pilon\\\": \\\"false\\\"}\"}",
+                        "tool_version": "0.4.8.0",
+                        "type": "tool",
+                        "uuid": "851c6be6-c202-450a-9cd3-19e205dcc496",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "cdab037e-aee1-49b8-a998-cd9fe7ddcdb7"
+                                "output_name": "assembly",
+                                "uuid": "702dd61e-6072-49d9-a502-44e0a23f5a98"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "assembly_graph",
+                                "uuid": "3285cc00-6b39-4f3d-87a5-87abd483ede6"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 19,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 18,
+                                "output_name": "assembly_graph"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Bandage Info",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Mpro-x0195_0_apo-desolv.pdb"
+                                "name": "outfile",
+                                "type": "txt"
                             }
                         ],
-                        "label": "Mpro-x0195_0_apo-desolv.pdb",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 218,
-                            "top": 289.76666259765625
+                            "left": 2665.633331298828,
+                            "top": 811.4166717529297
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Mpro-x0195_0_apo-desolv.pdb\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "156f4aeb-d160-456a-974e-7884b79cb83a",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "b2860df42e16",
+                            "name": "bandage",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"tsv\": \"\\\"false\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+                        "tool_version": "0.8.1+galaxy1",
+                        "type": "tool",
+                        "uuid": "4aa230bd-3269-41c3-81f5-9085fcc4001d",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "1fd1c624-37c6-4874-b863-a40eac5e4994"
+                                "output_name": "outfile",
+                                "uuid": "cf5eab6a-97ae-430e-a27a-6ecc33d4b8c0"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
                         "errors": null,
                         "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "input_connections": {
+                            "single_paired|paired_input": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "fastp: Trimmed Illumina Reads",
+                        "name": "fastp",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "hits.sdf"
+                                "name": "output_paired_coll",
+                                "type": "input"
+                            },
+                            {
+                                "name": "report_html",
+                                "type": "html"
+                            },
+                            {
+                                "name": "report_json",
+                                "type": "json"
                             }
                         ],
-                        "label": "hits.sdf",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 218,
-                            "top": 400.5333251953125
+                            "left": 585,
+                            "top": 365.04998779296875
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"hits.sdf\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "dd2d3bc0-8138-4e66-b2d9-e5e90e27b659",
+                        "post_job_actions": {
+                            "HideDatasetActionreport_html": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "report_html"
+                            },
+                            "HideDatasetActionreport_json": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "report_json"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "1d8fe9bc4cb0",
+                            "name": "fastp",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"report_html\\\": \\\"true\\\", \\\"report_json\\\": \\\"true\\\"}\", \"single_paired\": \"{\\\"__current_case__\\\": 2, \\\"adapter_trimming_options\\\": {\\\"adapter_sequence1\\\": \\\"\\\", \\\"adapter_sequence2\\\": \\\"\\\", \\\"disable_adapter_trimming\\\": \\\"false\\\"}, \\\"global_trimming_options\\\": {\\\"trim_front1\\\": \\\"\\\", \\\"trim_front2\\\": \\\"\\\", \\\"trim_tail1\\\": \\\"\\\", \\\"trim_tail2\\\": \\\"\\\"}, \\\"paired_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"single_paired_selector\\\": \\\"paired_collection\\\"}\", \"read_mod_options\": \"{\\\"base_correction_options\\\": {\\\"correction\\\": \\\"false\\\"}, \\\"cutting_by_quality_options\\\": {\\\"cut_by_quality3\\\": \\\"false\\\", \\\"cut_by_quality5\\\": \\\"false\\\", \\\"cut_mean_quality\\\": \\\"\\\", \\\"cut_window_size\\\": \\\"\\\"}, \\\"polyg_tail_trimming\\\": {\\\"__current_case__\\\": 1, \\\"poly_g_min_len\\\": \\\"\\\", \\\"trimming_select\\\": \\\"\\\"}, \\\"polyx_tail_trimming\\\": {\\\"__current_case__\\\": 1, \\\"polyx_trimming_select\\\": \\\"\\\"}, \\\"umi_processing\\\": {\\\"umi\\\": \\\"false\\\", \\\"umi_len\\\": \\\"\\\", \\\"umi_loc\\\": \\\"\\\", \\\"umi_prefix\\\": \\\"\\\"}}\", \"overrepresented_sequence_analysis\": \"{\\\"overrepresentation_analysis\\\": \\\"false\\\", \\\"overrepresentation_sampling\\\": \\\"\\\"}\", \"filter_options\": \"{\\\"length_filtering_options\\\": {\\\"disable_length_filtering\\\": \\\"false\\\", \\\"length_required\\\": \\\"50\\\"}, \\\"low_complexity_filter\\\": {\\\"complexity_threshold\\\": \\\"\\\", \\\"enable_low_complexity_filter\\\": \\\"false\\\"}, \\\"quality_filtering_options\\\": {\\\"disable_quality_filtering\\\": \\\"false\\\", \\\"n_base_limit\\\": \\\"\\\", \\\"qualified_quality_phred\\\": \\\"20\\\", \\\"unqualified_percent_limit\\\": \\\"20\\\"}}\", \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.19.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "7508c22b-dc6a-4071-8dd0-d5616718e62b",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "1c8fb3cc-52ad-4f62-a00d-80b14b2c1d4a"
+                                "output_name": "output_paired_coll",
+                                "uuid": "a7be7eab-3e80-4be6-b1a4-ab303c314096"
                             }
                         ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nCandidates\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nMpro-x0195_0_apo-desolv.pdb\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nhits.sdf\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Enumerate changes\"];\n  0 -->|output| 3;\n  4[\"Compound conversion\"];\n  1 -->|output| 4;\n  5[\"Create Frankenstein ligand\"];\n  2 -->|output| 5;\n  6[\"Compound conversion\"];\n  3 -->|output| 6;\n  7[\"rDock cavity definition\"];\n  4 -->|outfile| 7;\n  5 -->|outfile| 7;\n  8[\"Split file\"];\n  6 -->|outfile| 8;\n  9[\"rDock docking\"];\n  4 -->|outfile| 9;\n  8 -->|list_output_sdf| 9;\n  7 -->|activesite| 9;\n  10[\"Collapse Collection\"];\n  9 -->|output| 10;\n  11[\"XChem TransFS pose scoring\"];\n  1 -->|output| 11;\n  10 -->|output| 11;\n  12[\"Max SuCOS score\"];\n  11 -->|output| 12;\n  2 -->|output| 12;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
+                        "id": 20,
+                        "input_connections": {
+                            "input": {
+                                "id": 18,
+                                "output_name": "assembly"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Candidates"
+                                "description": "runtime parameter for tool Filter sequences by length",
+                                "name": "input"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Filter sequences by length",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "fasta"
                             }
                         ],
-                        "label": "Candidates",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 218,
-                            "top": 200
+                            "left": 2574.4166870117188,
+                            "top": 1254.4166870117188
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Candidates\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "47bf8c53-ae1e-4af6-bece-6adfd74b627c",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "8cacfcf96a52",
+                            "name": "fasta_filter_by_length",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"max_length\": \"\\\"0\\\"\", \"min_length\": \"\\\"1000\\\"\"}",
+                        "tool_version": "1.2",
+                        "type": "tool",
+                        "uuid": "3cbd67e0-3e55-4726-8dbe-0c61aec4d293",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "cdab037e-aee1-49b8-a998-cd9fe7ddcdb7"
+                                "uuid": "e4143f49-239f-4266-ba8d-e6299a331403"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
+                        "id": 21,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 18,
+                                "output_name": "assembly_graph"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Mpro-x0195_0_apo-desolv.pdb"
+                                "description": "runtime parameter for tool Bandage Image",
+                                "name": "input_file"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Bandage Image",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "jpg"
                             }
                         ],
-                        "label": "Mpro-x0195_0_apo-desolv.pdb",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 218,
-                            "top": 289.76666259765625
+                            "left": 2667.4166870117188,
+                            "top": 1052.4166870117188
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Mpro-x0195_0_apo-desolv.pdb\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "156f4aeb-d160-456a-974e-7884b79cb83a",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "b2860df42e16",
+                            "name": "bandage",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"lengths\": \"\\\"true\\\"\", \"output_format\": \"\\\"jpg\\\"\", \"height\": \"\\\"1000\\\"\", \"width\": \"\\\"\\\"\", \"names\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.8.1+galaxy2",
+                        "type": "tool",
+                        "uuid": "ef2c6a46-8421-499e-a840-8dd03483c5c9",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "1fd1c624-37c6-4874-b863-a40eac5e4994"
+                                "output_name": "outfile",
+                                "uuid": "5e535f98-b740-44ec-aba1-9d9090acb89a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 3,
+                        "input_connections": {
+                            "mode|reads|files": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "NanoPlot",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "hits.sdf"
+                                "name": "output_html",
+                                "type": "html"
+                            },
+                            {
+                                "name": "nanostats",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "nanostats_post_filtering",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "read_length",
+                                "type": "png"
+                            },
+                            {
+                                "name": "log_read_length",
+                                "type": "png"
                             }
                         ],
-                        "label": "hits.sdf",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 218,
-                            "top": 400.5333251953125
+                            "left": 630,
+                            "top": 650.4666595458984
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"hits.sdf\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "dd2d3bc0-8138-4e66-b2d9-e5e90e27b659",
+                        "post_job_actions": {
+                            "HideDatasetActionlog_read_length": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "log_read_length"
+                            },
+                            "HideDatasetActionnanostats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "nanostats"
+                            },
+                            "HideDatasetActionnanostats_post_filtering": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "nanostats_post_filtering"
+                            },
+                            "HideDatasetActionread_length": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "read_length"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "645159bcee2d",
+                            "name": "nanoplot",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"filter\": \"{\\\"alength\\\": \\\"false\\\", \\\"barcoded\\\": \\\"false\\\", \\\"downsample\\\": \\\"\\\", \\\"drop_outliers\\\": \\\"false\\\", \\\"loglength\\\": \\\"true\\\", \\\"maxlength\\\": \\\"\\\", \\\"minlength\\\": \\\"\\\", \\\"minqual\\\": \\\"\\\", \\\"percentqual\\\": \\\"false\\\", \\\"readtype\\\": null}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"__current_case__\\\": 0, \\\"choice\\\": \\\"batch\\\", \\\"reads\\\": {\\\"__current_case__\\\": 0, \\\"files\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"type\\\": \\\"fastq\\\"}}\", \"customization\": \"{\\\"N50\\\": \\\"false\\\", \\\"color\\\": null, \\\"format\\\": \\\"png\\\", \\\"noN50\\\": \\\"false\\\", \\\"plots\\\": null}\"}",
+                        "tool_version": "1.25.0+galaxy1",
+                        "type": "tool",
+                        "uuid": "9b1d43ac-82e3-463f-9c88-08c8826a62c9",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "1c8fb3cc-52ad-4f62-a00d-80b14b2c1d4a"
+                                "output_name": "output_html",
+                                "uuid": "cd8570c7-02db-479b-81a9-cd0d26643f71"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "fastq_input|fastq_input1": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Map with minimap2",
+                        "outputs": [
+                            {
+                                "name": "alignment_output",
+                                "type": "bam"
+                            }
+                        ],
+                        "position": {
+                            "left": 709.199951171875,
+                            "top": 1131.9666748046875
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "53c0b7a1a0c3",
+                            "name": "minimap2",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"alignment_options\": \"{\\\"-O2\\\": \\\"\\\", \\\"A\\\": \\\"\\\", \\\"B\\\": \\\"\\\", \\\"E\\\": \\\"\\\", \\\"E2\\\": \\\"\\\", \\\"O\\\": \\\"\\\", \\\"s\\\": \\\"\\\", \\\"u\\\": null, \\\"z\\\": \\\"\\\"}\", \"analysis_type_selector\": \"\\\"splice\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"io_options\": \"{\\\"K\\\": \\\"\\\", \\\"L\\\": \\\"false\\\", \\\"Q\\\": \\\"false\\\", \\\"Y\\\": \\\"false\\\", \\\"c\\\": \\\"false\\\", \\\"cs\\\": null, \\\"eqx\\\": \\\"false\\\", \\\"output_format\\\": \\\"BAM\\\"}\", \"mapping_options\": \"{\\\"F\\\": \\\"\\\", \\\"G\\\": \\\"\\\", \\\"N\\\": \\\"\\\", \\\"X\\\": \\\"false\\\", \\\"f\\\": \\\"\\\", \\\"g\\\": \\\"\\\", \\\"m\\\": \\\"\\\", \\\"min_occ_floor\\\": \\\"\\\", \\\"n\\\": \\\"\\\", \\\"p\\\": \\\"\\\", \\\"r\\\": \\\"\\\"}\", \"fastq_input\": \"{\\\"__current_case__\\\": 1, \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"single\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 0, \\\"ref_file\\\": \\\"hg38\\\", \\\"reference_source_selector\\\": \\\"cached\\\"}\", \"indexing_options\": \"{\\\"H\\\": \\\"false\\\", \\\"I\\\": \\\"\\\", \\\"k\\\": \\\"\\\", \\\"w\\\": \\\"\\\"}\"}",
+                        "tool_version": "2.17+galaxy1",
+                        "type": "tool",
+                        "uuid": "098d2283-1218-489b-9882-8822e79d9444",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "alignment_output",
+                                "uuid": "9972015d-4bdc-440f-b8b6-84e92a64ef8f"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
                         "errors": null,
                         "id": 5,
                         "input_connections": {
-                            "infile": {
+                            "results_0|software_cond|input": {
                                 "id": 2,
-                                "output_name": "output"
+                                "output_name": "report_json"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "MultiQC",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool Create Frankenstein ligand",
-                                "name": "infile"
+                                "name": "stats",
+                                "type": "input"
+                            },
+                            {
+                                "name": "html_report",
+                                "type": "html"
                             }
                         ],
+                        "position": {
+                            "left": 938.699951171875,
+                            "top": 250
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "tool_shed_repository": {
+                            "changeset_revision": "b2f1f75d49c4",
+                            "name": "multiqc",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"comment\": \"\\\"\\\"\", \"__page__\": null, \"title\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"results\": \"[{\\\"__index__\\\": 0, \\\"software_cond\\\": {\\\"__current_case__\\\": 7, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"software\\\": \\\"fastp\\\"}}]\", \"saveLog\": \"\\\"false\\\"\"}",
+                        "tool_version": "1.7",
+                        "type": "tool",
+                        "uuid": "73566697-4a46-4d35-b8e2-61770acc62c0",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "html_report",
+                                "uuid": "15f42a94-2c97-4932-8e3f-f26a72b58be4"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "library|input_1": {
+                                "id": 2,
+                                "output_name": "output_paired_coll"
+                            }
+                        },
+                        "inputs": [],
                         "label": null,
-                        "name": "Create Frankenstein ligand",
+                        "name": "Bowtie2",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "sdf"
+                                "name": "output",
+                                "type": "bam"
+                            },
+                            {
+                                "name": "mapping_stats",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 478.76666259765625,
-                            "top": 483.5333251953125
+                            "left": 913.9166259765625,
+                            "top": 564.6333312988281
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "8e214e52e461",
-                            "name": "ctb_frankenstein_ligand",
-                            "owner": "bgruening",
+                            "changeset_revision": "749c918495f7",
+                            "name": "bowtie2",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "0.1.1",
+                        "tool_state": "{\"sam_options\": \"{\\\"__current_case__\\\": 1, \\\"sam_options_selector\\\": \\\"no\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"__current_case__\\\": 2, \\\"aligned_file\\\": \\\"false\\\", \\\"input_1\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"paired_options\\\": {\\\"__current_case__\\\": 1, \\\"paired_options_selector\\\": \\\"no\\\"}, \\\"type\\\": \\\"paired_collection\\\", \\\"unaligned_file\\\": \\\"false\\\"}\", \"reference_genome\": \"{\\\"__current_case__\\\": 0, \\\"index\\\": \\\"hg38full\\\", \\\"source\\\": \\\"indexed\\\"}\", \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"save_mapping_stats\": \"\\\"true\\\"\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"simple\\\", \\\"presets\\\": \\\"no_presets\\\"}\"}",
+                        "tool_version": "2.3.4.3+galaxy0",
                         "type": "tool",
-                        "uuid": "081abe35-347a-4244-99ae-ec35329e3de0",
+                        "uuid": "43331d2c-7116-410e-a6bd-7e7520d93a52",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "53c557af-d5b9-4033-be54-7c197591e750"
+                                "output_name": "output",
+                                "uuid": "eeae40f6-f1b2-4c56-9860-ac7b8eb1dec0"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "mapping_stats",
+                                "uuid": "c567226e-efaf-4188-bdec-3ba20d0733b0"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "input": {
+                                "id": 4,
+                                "output_name": "alignment_output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Samtools stats",
+                        "outputs": [
+                            {
+                                "name": "output_collection",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1022.4166259765625,
+                            "top": 1254.4166870117188
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "145f6d74ff5e",
+                            "name": "samtools_stats",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"coverage_cond\": \"{\\\"__current_case__\\\": 0, \\\"coverage_select\\\": \\\"no\\\"}\", \"gc_depth\": \"\\\"\\\"\", \"cov_threshold\": \"\\\"\\\"\", \"most_inserts\": \"\\\"\\\"\", \"cond_region\": \"{\\\"__current_case__\\\": 0, \\\"select_region\\\": \\\"no\\\"}\", \"split_output_cond\": \"{\\\"__current_case__\\\": 1, \\\"generate_tables\\\": [\\\"SN\\\"], \\\"split_output_selector\\\": \\\"yes\\\"}\", \"read_length\": \"\\\"\\\"\", \"trim_quality\": \"\\\"\\\"\", \"remove_overlaps\": \"\\\"false\\\"\", \"filter_by_flags\": \"{\\\"__current_case__\\\": 1, \\\"filter_flags\\\": \\\"nofilter\\\"}\", \"sparse\": \"\\\"false\\\"\", \"addref_cond\": \"{\\\"__current_case__\\\": 0, \\\"addref_select\\\": \\\"no\\\"}\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"insert_size\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"remove_dups\": \"\\\"false\\\"\"}",
+                        "tool_version": "2.0.2+galaxy2",
+                        "type": "tool",
+                        "uuid": "15f6252f-79d4-4319-855d-09665deac6a3",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_collection",
+                                "uuid": "faed6306-eed6-40bd-ac9f-9fb3a4e980ea"
                             }
                         ]
                     }
                 ],
-                "parent_id": "computational-chemistry/covid19-docking",
-                "path": "topics/computational-chemistry/tutorials/covid19-docking/workflows/workflow.ga",
+                "parent_id": "assembly/assembly-with-preprocessing",
+                "path": "topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing.ga",
                 "tags": [
-                    "computational-chemistry"
+                    "GTN",
+                    "assembly"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring",
-                "topic_id": "computational-chemistry",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/computational-chemistry-covid19-docking/versions/workflow",
-                "tutorial_id": "covid19-docking",
-                "url": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/covid19-docking/workflows/workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/covid19-docking/workflows/workflow.html",
-                "version": 3,
-                "wfid": "computational-chemistry-covid19-docking",
-                "wfname": "workflow",
-                "workflow": "workflow.ga",
+                "title": "assembly_with_preprocessing",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-assembly-with-preprocessing/versions/assembly-with-preprocessing",
+                "tutorial_id": "assembly-with-preprocessing",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing.html",
+                "version": 1,
+                "wfid": "assembly-assembly-with-preprocessing",
+                "wfname": "assembly-with-preprocessing",
+                "workflow": "assembly_with_preprocessing.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/0.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.2.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbcavity/rdock_rbcavity/0.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbdock/rdock_rbdock/0.1.4",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.4.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/sucos_max_score/sucos_max_score/0.2.3",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
-                    "xchem_pose_scoring"
-                ],
-                "workflowhub_id": "1079"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/3730474"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bwa",
-                    "owner": "devteam",
-                    "revisions": "e188dc7a68e6",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_fastx",
-                    "owner": "iuc",
-                    "revisions": "a8d69aee190e",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "seqtk",
-                    "owner": "iuc",
-                    "revisions": "3da72230c066",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "trimmomatic",
-                    "owner": "pjbriggs",
-                    "revisions": "898b67846b47",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "trimmomatic",
-                    "owner": "pjbriggs",
-                    "revisions": "d94aff5ee623",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_fastx\n  owner: iuc\n  revisions: a8d69aee190e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n  owner: pjbriggs\n  revisions: 898b67846b47\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n  owner: pjbriggs\n  revisions: d94aff5ee623\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "by-covid",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "fediverse": "https://scholar.social/@zerodivision",
-                "fediverse_flavor": "mastodon",
-                "id": "wm75",
-                "joined": "2017-09",
-                "matrix": "wm75:matrix.org",
-                "name": "Wolfgang Maier",
-                "orcid": "0000-0002-9464-6640",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
-            }
-        ],
-        "dir": "topics/sequence-analysis/tutorials/human-reads-removal",
-        "edam_operation": [
-            "Generation",
-            "Data handling",
-            "Sequence file editing",
-            "Sequence alignment",
-            "Genome indexing",
-            "Read mapping"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "sequence-analysis/human-reads-removal",
-        "inexact_supported_servers": [
-            "Galaxy@AuBi",
-            "GalaxyTrakr",
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Before submitting raw viral sequencing data to public databases you will want to remove human sequence traces",
-            "Human reads can be identified by mapping the data to the human reference genome",
-            "After mapping, you can extract the read identifiers of the non-human reads and use these to extract just the desired original sequenced reads from the input data"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Obtain viral (SARS-CoV-2) sequencing data with contaminating human reads from public sources",
-            "Organize the data into a collection",
-            "Preprocess and map the data against the human reference genome",
-            "Eliminate reads/read pairs that map to the human genome from the original data"
-        ],
-        "pageviews": 4759,
-        "pub_date": "2021-08-04",
-        "questions": [
-            "How can you remove traces of human sequence data from a sequenced viral sample?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "sequence-analysis",
-                "tutorials": [
-                    "quality-control",
-                    "mapping"
+                    "__ZIP_COLLECTION__",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
                 ],
-                "type": "internal"
+                "workflowhub_id": "1132"
             },
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "collections"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00236",
-        "short_tools": [
-            "Grep1",
-            "__UNZIP_COLLECTION__",
-            "samtools_fastx",
-            "__ZIP_COLLECTION__",
-            "seqtk_subseq",
-            "tp_replace_in_line",
-            "bwa_mem",
-            "trimmomatic"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "covid19"
-        ],
-        "time_estimation": "1h",
-        "title": "Removal of human reads from SARS-CoV-2 sequencing data",
-        "tools": [
-            "Grep1",
-            "__UNZIP_COLLECTION__",
-            "__ZIP_COLLECTION__",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-            "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
-            "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1"
-        ],
-        "topic_name": "sequence-analysis",
-        "topic_name_human": "Sequence analysis",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "human-reads-removal",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.json"
-        },
-        "version": 5,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 141,
-        "visitors": 3347,
-        "workflows": [
             {
                 "creators": [],
-                "description": "Removal of human reads from SARS-CoV-2 sequencing data",
+                "description": "Assembly with preprocessing and SRA download",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  1[label=\"Trimmomatic\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Unzip Collection\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Map with BWA-MEM\"]\n  1 -> 3 [label=\"fastq_out_paired\"]\n  4[label=\"Samtools fastx\"]\n  3 -> 4 [label=\"bam_output\"]\n  5[label=\"Select\"]\n  4 -> 5 [label=\"forward\"]\n  6[label=\"Replace Text\"]\n  5 -> 6 [label=\"out_file1\"]\n  7[label=\"seqtk_subseq\"]\n  2 -> 7 [label=\"forward\"]\n  6 -> 7 [label=\"outfile\"]\n  8[label=\"seqtk_subseq\"]\n  2 -> 8 [label=\"reverse\"]\n  6 -> 8 [label=\"outfile\"]\n  9[label=\"Paired-end collection of cleaned reads\"]\n  7 -> 9 [label=\"default\"]\n  8 -> 9 [label=\"default\"]\n  kf24bbf28dc51440fa758ac05033f0645[color=lightseagreen,label=\"Output\\nCleaned Data\"]\n  9 -> kf24bbf28dc51440fa758ac05033f0645\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nList of Illumina accessions\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nList of ONT accessions\"]\n  10[label=\"Samtools stats\"]\n  6 -> 10 [label=\"alignment_output\"]\n  11[label=\"Samtools view\"]\n  8 -> 11 [label=\"output\"]\n  12[label=\"Samtools fastx\"]\n  9 -> 12 [label=\"outputsam\"]\n  13[label=\"Samtools fastx\"]\n  11 -> 13 [label=\"outputsam\"]\n  14[label=\"Collapse Collection\"]\n  12 -> 14 [label=\"nonspecific\"]\n  15[label=\"Zip Collection\"]\n  13 -> 15 [label=\"forward\"]\n  13 -> 15 [label=\"reverse\"]\n  16[label=\"Collapse Collection\"]\n  13 -> 16 [label=\"forward\"]\n  17[label=\"Collapse Collection\"]\n  13 -> 17 [label=\"reverse\"]\n  18[label=\"seqtk_sample\"]\n  16 -> 18 [label=\"output\"]\n  19[label=\"seqtk_sample\"]\n  17 -> 19 [label=\"output\"]\n  2[label=\"Illumina data\"]\n  0 -> 2 [label=\"output\"]\n  20[label=\"Create assemblies with Unicycler\"]\n  14 -> 20 [label=\"output\"]\n  18 -> 20 [label=\"default\"]\n  19 -> 20 [label=\"default\"]\n  21[label=\"Bandage Info\"]\n  20 -> 21 [label=\"assembly_graph\"]\n  22[label=\"Bandage Image\"]\n  20 -> 22 [label=\"assembly_graph\"]\n  23[label=\"Filter sequences by length\"]\n  20 -> 23 [label=\"assembly\"]\n  3[label=\"ONT data\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"fastp: Trimmed Illumina Reads\"]\n  2 -> 4 [label=\"list_paired\"]\n  5[label=\"NanoPlot\"]\n  3 -> 5 [label=\"output_collection\"]\n  6[label=\"Map with minimap2\"]\n  3 -> 6 [label=\"output_collection\"]\n  7[label=\"MultiQC\"]\n  4 -> 7 [label=\"report_json\"]\n  8[label=\"Bowtie2\"]\n  4 -> 8 [label=\"output_paired_coll\"]\n  9[label=\"Samtools view\"]\n  6 -> 9 [label=\"alignment_output\"]\n}",
                 "history": [
                     {
-                        "hash": "f71f6dde01e2dfe86a4b43526f119d9050693f84",
-                        "message": "Address WF linting issues",
+                        "hash": "fc35e6581a2e34e4420f19af4619c92283609e91",
+                        "message": "add annotations",
                         "num": 2,
-                        "short_hash": "f71f6dde0",
-                        "unix": "1628012579"
+                        "short_hash": "fc35e6581",
+                        "unix": "1587558793"
                     },
                     {
-                        "hash": "f232ad426455a30be4a74af21054384c23b07275",
-                        "message": "Add new tutorial for cleaning SARS-CoV-2 data",
+                        "hash": "7ed054469d1ef84a60abec55758ee2932f9a9655",
+                        "message": "readd workflows",
                         "num": 1,
-                        "short_hash": "f232ad426",
-                        "unix": "1628010649"
+                        "short_hash": "7ed054469",
+                        "unix": "1587555276"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "List of Illumina accessions",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 257.683349609375,
+                            "top": 215.9166259765625
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "1a61a3b3-4515-47a1-8ee5-fb79f05a8dfa",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "ea340c2d-d9e8-4ea5-bbc0-7ee7d92a57bf"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "List of ONT accessions",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 264.9833984375,
+                            "top": 522.7166442871094
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0988bf07-dc80-4d7b-a62f-8e5e852b0982",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "fb053f14-71fc-45ac-83ea-a308a5c22918"
+                            }
+                        ]
                     }
                 ],
-                "inputs": [
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nList of Illumina accessions\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nList of ONT accessions\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Samtools stats\"];\n  6 -->|alignment_output| 10;\n  11[\"Samtools view\"];\n  8 -->|output| 11;\n  12[\"Samtools fastx\"];\n  9 -->|outputsam| 12;\n  13[\"Samtools fastx\"];\n  11 -->|outputsam| 13;\n  14[\"Collapse Collection\"];\n  12 -->|nonspecific| 14;\n  15[\"Zip Collection\"];\n  13 -->|forward| 15;\n  13 -->|reverse| 15;\n  16[\"Collapse Collection\"];\n  13 -->|forward| 16;\n  17[\"Collapse Collection\"];\n  13 -->|reverse| 17;\n  18[\"seqtk_sample\"];\n  16 -->|output| 18;\n  19[\"seqtk_sample\"];\n  17 -->|output| 19;\n  2[\"Illumina data\"];\n  0 -->|output| 2;\n  20[\"Create assemblies with Unicycler\"];\n  14 -->|output| 20;\n  18 -->|default| 20;\n  19 -->|default| 20;\n  21[\"Bandage Info\"];\n  20 -->|assembly_graph| 21;\n  22[\"Bandage Image\"];\n  20 -->|assembly_graph| 22;\n  23[\"Filter sequences by length\"];\n  20 -->|assembly| 23;\n  3[\"ONT data\"];\n  1 -->|output| 3;\n  4[\"fastp: Trimmed Illumina Reads\"];\n  2 -->|list_paired| 4;\n  5[\"NanoPlot\"];\n  3 -->|output_collection| 5;\n  6[\"Map with minimap2\"];\n  3 -->|output_collection| 6;\n  7[\"MultiQC\"];\n  4 -->|report_json| 7;\n  8[\"Bowtie2\"];\n  4 -->|output_paired_coll| 8;\n  9[\"Samtools view\"];\n  6 -->|alignment_output| 9;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "assembly_with_preprocessing_and_sra_download",
+                "outputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Input Dataset Collection"
-                            }
-                        ],
-                        "label": "Input Dataset Collection",
-                        "name": "Input dataset collection",
+                        "inputs": [],
+                        "label": "List of Illumina accessions",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 564,
-                            "height": 81,
-                            "left": 296,
-                            "right": 496,
-                            "top": 483,
-                            "width": 200,
-                            "x": 296,
-                            "y": 483
+                            "left": 257.683349609375,
+                            "top": 215.9166259765625
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list:paired\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "d61c43e8-23ee-4f9a-9fd8-f58ffc134735",
+                        "type": "data_input",
+                        "uuid": "1a61a3b3-4515-47a1-8ee5-fb79f05a8dfa",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "b14c9326-21d3-4e0e-be24-7654e6b31b43"
+                                "uuid": "ea340c2d-d9e8-4ea5-bbc0-7ee7d92a57bf"
                             }
                         ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Trimmomatic\"];\n  0 -->|output| 1;\n  2[\"Unzip Collection\"];\n  0 -->|output| 2;\n  3[\"Map with BWA-MEM\"];\n  1 -->|fastq_out_paired| 3;\n  4[\"Samtools fastx\"];\n  3 -->|bam_output| 4;\n  5[\"Select\"];\n  4 -->|forward| 5;\n  6[\"Replace Text\"];\n  5 -->|out_file1| 6;\n  7[\"seqtk_subseq\"];\n  2 -->|forward| 7;\n  6 -->|outfile| 7;\n  8[\"seqtk_subseq\"];\n  2 -->|reverse| 8;\n  6 -->|outfile| 8;\n  9[\"Paired-end collection of cleaned reads\"];\n  7 -->|default| 9;\n  8 -->|default| 9;\n  f24bbf28-dc51-440f-a758-ac05033f0645[\"Output\\nCleaned Data\"];\n  9 --> f24bbf28-dc51-440f-a758-ac05033f0645;\n  style f24bbf28-dc51-440f-a758-ac05033f0645 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "GTN - Sequence Analyses - Removal of human reads from SARS-CoV-2 sequencing data",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 1,
                         "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Input Dataset Collection"
-                            }
-                        ],
-                        "label": "Input Dataset Collection",
-                        "name": "Input dataset collection",
+                        "inputs": [],
+                        "label": "List of ONT accessions",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 564,
-                            "height": 81,
-                            "left": 296,
-                            "right": 496,
-                            "top": 483,
-                            "width": 200,
-                            "x": 296,
-                            "y": 483
+                            "left": 264.9833984375,
+                            "top": 522.7166442871094
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list:paired\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "d61c43e8-23ee-4f9a-9fd8-f58ffc134735",
+                        "type": "data_input",
+                        "uuid": "0988bf07-dc80-4d7b-a62f-8e5e852b0982",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "b14c9326-21d3-4e0e-be24-7654e6b31b43"
+                                "uuid": "fb053f14-71fc-45ac-83ea-a308a5c22918"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
                         "errors": null,
-                        "id": 1,
+                        "id": 10,
                         "input_connections": {
-                            "readtype|fastq_pair": {
-                                "id": 0,
-                                "output_name": "output"
+                            "input": {
+                                "id": 6,
+                                "output_name": "alignment_output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Trimmomatic",
+                        "name": "Samtools stats",
                         "outputs": [
                             {
-                                "name": "fastq_out_paired",
-                                "type": "input"
-                            },
-                            {
-                                "name": "fastq_out_unpaired",
+                                "name": "output_collection",
                                 "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 515,
-                            "height": 202,
-                            "left": 532,
-                            "right": 732,
-                            "top": 313,
-                            "width": 200,
-                            "x": 532,
-                            "y": 313
+                            "left": 1328.4166259765625,
+                            "top": 1239.4166259765625
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "d94aff5ee623",
-                            "name": "trimmomatic",
-                            "owner": "pjbriggs",
+                            "changeset_revision": "145f6d74ff5e",
+                            "name": "samtools_stats",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"illuminaclip\": {\"do_illuminaclip\": \"false\", \"__current_case__\": 1}, \"operations\": [{\"__index__\": 0, \"operation\": {\"name\": \"SLIDINGWINDOW\", \"__current_case__\": 0, \"window_size\": \"4\", \"required_quality\": \"20\"}}], \"output_err\": \"false\", \"output_logs\": \"false\", \"readtype\": {\"single_or_paired\": \"collection\", \"__current_case__\": 2, \"fastq_pair\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.38.1",
+                        "tool_state": "{\"__page__\": null, \"coverage_cond\": \"{\\\"__current_case__\\\": 0, \\\"coverage_select\\\": \\\"no\\\"}\", \"gc_depth\": \"\\\"\\\"\", \"cov_threshold\": \"\\\"\\\"\", \"most_inserts\": \"\\\"\\\"\", \"cond_region\": \"{\\\"__current_case__\\\": 0, \\\"select_region\\\": \\\"no\\\"}\", \"split_output_cond\": \"{\\\"__current_case__\\\": 1, \\\"generate_tables\\\": [\\\"SN\\\"], \\\"split_output_selector\\\": \\\"yes\\\"}\", \"read_length\": \"\\\"\\\"\", \"trim_quality\": \"\\\"\\\"\", \"remove_overlaps\": \"\\\"false\\\"\", \"filter_by_flags\": \"{\\\"__current_case__\\\": 1, \\\"filter_flags\\\": \\\"nofilter\\\"}\", \"sparse\": \"\\\"false\\\"\", \"addref_cond\": \"{\\\"__current_case__\\\": 0, \\\"addref_select\\\": \\\"no\\\"}\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"insert_size\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"remove_dups\": \"\\\"false\\\"\"}",
+                        "tool_version": "2.0.2+galaxy2",
                         "type": "tool",
-                        "uuid": "ced9a15d-ca78-4cf5-b1a0-267920691879",
+                        "uuid": "ae176340-d7da-4c2e-851b-e6129a0c222d",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "fastq_out_unpaired",
-                                "uuid": "88e4c149-85d2-4c19-8a53-f242a3703e5e"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "fastq_out_paired",
-                                "uuid": "fd0243b9-ef6a-445d-8fb9-f76d47c3f6fc"
+                                "output_name": "output_collection",
+                                "uuid": "8652ea8a-35f5-4531-8b89-88bca189ab9f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "__UNZIP_COLLECTION__",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
                         "errors": null,
-                        "id": 2,
+                        "id": 12,
                         "input_connections": {
                             "input": {
-                                "id": 0,
-                                "output_name": "output"
+                                "id": 9,
+                                "output_name": "outputsam"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Unzip Collection",
+                        "name": "Samtools fastx",
                         "outputs": [
                             {
-                                "name": "forward",
-                                "type": "input"
+                                "name": "nonspecific",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "left": 1628.4166259765625,
+                            "top": 852.4166412353516
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "a8d69aee190e",
+                            "name": "samtools_fastx",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"copy_arb_tags\": \"\\\"\\\"\", \"__page__\": null, \"output_fmt_cond\": \"{\\\"__current_case__\\\": 2, \\\"default_quality\\\": \\\"\\\", \\\"ilumina_casava\\\": \\\"false\\\", \\\"output_fmt_select\\\": \\\"fastqsanger.gz\\\", \\\"output_quality\\\": \\\"false\\\"}\", \"idxout_cond\": \"{\\\"__current_case__\\\": 0, \\\"idxout_select\\\": \\\"no\\\"}\", \"read_numbering\": \"\\\"\\\"\", \"exclusive_filter\": \"null\", \"exclusive_filter_all\": \"null\", \"inclusive_filter\": \"null\", \"outputs\": \"[\\\"r0\\\"]\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"copy_tags\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9+galaxy1",
+                        "type": "tool",
+                        "uuid": "31e2b4e8-7631-46c0-8382-b805cee2b739",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "nonspecific",
+                                "uuid": "cfbf839f-53f0-4a82-8966-2bdb6919de5e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "__ZIP_COLLECTION__",
+                        "errors": null,
+                        "id": 15,
+                        "input_connections": {
+                            "input_forward": {
+                                "id": 13,
+                                "output_name": "forward"
                             },
+                            "input_reverse": {
+                                "id": 13,
+                                "output_name": "reverse"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Zip Collection",
+                        "outputs": [
                             {
-                                "name": "reverse",
+                                "name": "output",
                                 "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 746,
-                            "height": 182,
-                            "left": 735,
-                            "right": 935,
-                            "top": 564,
-                            "width": 200,
-                            "x": 735,
-                            "y": 564
+                            "left": 2049.4166870117188,
+                            "top": 477.4166259765625
                         },
                         "post_job_actions": {},
-                        "tool_id": "__UNZIP_COLLECTION__",
-                        "tool_state": "{\"input\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": "__ZIP_COLLECTION__",
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_reverse\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"input_forward\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
                         "tool_version": "1.0.0",
                         "type": "tool",
-                        "uuid": "f6552b12-5845-486b-95f5-35a3eefaa109",
+                        "uuid": "9ba89e81-9c53-4f5b-9d61-42319b7d574c",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "forward",
-                                "uuid": "5fabd686-3611-4d28-aff3-c1286b461bbf"
-                            },
+                                "output_name": "output",
+                                "uuid": "ebc8f563-c45e-4e17-a541-b1275e7f61ad"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
+                        "errors": null,
+                        "id": 18,
+                        "input_connections": {
+                            "in_file": {
+                                "id": 16,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool seqtk_sample",
+                                "name": "in_file"
+                            }
+                        ],
+                        "label": null,
+                        "name": "seqtk_sample",
+                        "outputs": [
+                            {
+                                "name": "default",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 2438.0833282470703,
+                            "top": 688.6833190917969
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "58c8ece95b53",
+                            "name": "seqtk",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"s\": \"\\\"4\\\"\", \"in_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"subsample_size\": \"\\\"0.1\\\"\", \"advanced\": \"{\\\"single_pass_mode\\\": \\\"false\\\"}\"}",
+                        "tool_version": "1.3.2",
+                        "type": "tool",
+                        "uuid": "b4e40092-e076-4eb0-af30-c8c47885fefa",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "reverse",
-                                "uuid": "9b0c1a5f-6d39-46c7-a16d-afbb9e34bcfe"
+                                "output_name": "default",
+                                "uuid": "cf3eb8ef-fce5-42af-a14d-60ff915fbff3"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
                         "errors": null,
-                        "id": 3,
+                        "id": 19,
                         "input_connections": {
-                            "fastq_input|fastq_input1": {
-                                "id": 1,
-                                "output_name": "fastq_out_paired"
+                            "in_file": {
+                                "id": 17,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Map with BWA-MEM",
-                                "name": "fastq_input"
+                                "description": "runtime parameter for tool seqtk_sample",
+                                "name": "in_file"
                             }
                         ],
                         "label": null,
-                        "name": "Map with BWA-MEM",
+                        "name": "seqtk_sample",
                         "outputs": [
                             {
-                                "name": "bam_output",
-                                "type": "bam"
+                                "name": "default",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 487,
-                            "height": 192,
-                            "left": 753,
-                            "right": 953,
-                            "top": 295,
-                            "width": 200,
-                            "x": 753,
-                            "y": 295
+                            "left": 2413.0833129882812,
+                            "top": 864.6833190917969
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "64f11cf59c6e",
-                            "name": "bwa",
-                            "owner": "devteam",
+                            "changeset_revision": "58c8ece95b53",
+                            "name": "seqtk",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"illumina\", \"__current_case__\": 0}, \"fastq_input\": {\"fastq_input_selector\": \"paired_collection\", \"__current_case__\": 2, \"fastq_input1\": {\"__class__\": \"RuntimeValue\"}, \"iset_stats\": \"\"}, \"output_sort\": \"coordinate\", \"reference_source\": {\"reference_source_selector\": \"cached\", \"__current_case__\": 0, \"ref_file\": \"hg38\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.17.2",
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"s\": \"\\\"4\\\"\", \"in_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"subsample_size\": \"\\\"0.1\\\"\", \"advanced\": \"{\\\"single_pass_mode\\\": \\\"false\\\"}\"}",
+                        "tool_version": "1.3.2",
                         "type": "tool",
-                        "uuid": "c21129e8-b54f-4a7d-9af2-b8202434c342",
+                        "uuid": "1ef9ca9e-e447-4933-8871-c0e8e9a953c4",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "bam_output",
-                                "uuid": "f0ca56d9-f544-465c-ad37-6380ba0ac2ea"
+                                "output_name": "default",
+                                "uuid": "bf722cb7-0b06-42ed-8fbc-9dc3896e9340"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
                         "errors": null,
-                        "id": 4,
+                        "id": 2,
                         "input_connections": {
-                            "input": {
-                                "id": 3,
-                                "output_name": "bam_output"
+                            "input|file_list": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
+                        "label": "Illumina data",
+                        "name": "Faster Download and Extract Reads in FASTQ",
+                        "outputs": [
+                            {
+                                "name": "list_paired",
+                                "type": "input"
+                            },
+                            {
+                                "name": "output_collection",
+                                "type": "input"
+                            },
+                            {
+                                "name": "output_collection_other",
+                                "type": "input"
+                            },
+                            {
+                                "name": "log",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 511.783447265625,
+                            "top": 273.1666259765625
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionlog": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "log"
+                            },
+                            "HideDatasetActionoutput_collection": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_collection"
+                            },
+                            "HideDatasetActionoutput_collection_other": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_collection_other"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "aad3885b3216",
+                            "name": "sra_tools",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv\": \"{\\\"minlen\\\": \\\"\\\", \\\"skip_technical\\\": \\\"true\\\", \\\"split\\\": \\\"--split-3\\\"}\", \"input\": \"{\\\"__current_case__\\\": 2, \\\"file_list\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"input_select\\\": \\\"file_list\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+                        "tool_version": "2.10.4+galaxy1",
+                        "type": "tool",
+                        "uuid": "b097b5cb-44a8-4881-9ba0-a089ef1b4ad6",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "list_paired",
+                                "uuid": "c6b4e7f2-5cf4-4051-afd1-a110381c4679"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
+                        "errors": null,
+                        "id": 20,
+                        "input_connections": {
+                            "long": {
+                                "id": 14,
+                                "output_name": "output"
+                            },
+                            "paired_unpaired|fastq_input1": {
+                                "id": 18,
+                                "output_name": "default"
+                            },
+                            "paired_unpaired|fastq_input2": {
+                                "id": 19,
+                                "output_name": "default"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "lr_align"
+                            },
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "long"
+                            },
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "paired_unpaired"
+                            },
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "paired_unpaired"
+                            },
+                            {
+                                "description": "runtime parameter for tool Create assemblies with Unicycler",
+                                "name": "rotation"
+                            }
+                        ],
                         "label": null,
-                        "name": "Samtools fastx",
+                        "name": "Create assemblies with Unicycler",
                         "outputs": [
                             {
-                                "name": "forward",
+                                "name": "assembly_graph",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "assembly",
                                 "type": "fasta"
                             }
                         ],
                         "position": {
-                            "bottom": 447,
-                            "height": 152,
-                            "left": 973,
-                            "right": 1173,
-                            "top": 295,
-                            "width": 200,
-                            "x": 973,
-                            "y": 295
+                            "left": 2673.4166717529297,
+                            "top": 699.4166412353516
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "a8d69aee190e",
-                            "name": "samtools_fastx",
+                            "changeset_revision": "88c240872a65",
+                            "name": "unicycler",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"bam\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"copy_arb_tags\": \"\", \"copy_tags\": \"false\", \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"idxout_cond\": {\"idxout_select\": \"no\", \"__current_case__\": 0}, \"inclusive_filter\": [\"4\", \"8\"], \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"1085990\", \"output_fmt_cond\": {\"output_fmt_select\": \"fasta\", \"__current_case__\": 1}, \"outputs\": [\"r1\"], \"read_numbering\": \"-n\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9+galaxy1",
+                        "tool_state": "{\"linear_seqs\": \"\\\"1\\\"\", \"spades\": \"{\\\"depth_filter\\\": \\\"0.25\\\", \\\"kmer_count\\\": \\\"10\\\", \\\"kmers\\\": \\\"\\\", \\\"largest_component\\\": \\\"false\\\", \\\"max_kmer_frac\\\": \\\"0.95\\\", \\\"min_kmer_frac\\\": \\\"0.2\\\", \\\"no_correct\\\": \\\"false\\\"}\", \"graph_clean\": \"{\\\"min_component_size\\\": \\\"1000\\\", \\\"min_dead_end_size\\\": \\\"1000\\\"}\", \"__page__\": null, \"min_anchor_seg_len\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"lr_align\": \"{\\\"contamination\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"low_score\\\": \\\"\\\", \\\"scores\\\": \\\"3,-6,-5,-2\\\"}\", \"long\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"paired_unpaired\": \"{\\\"__current_case__\\\": 0, \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"fastq_input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired\\\"}\", \"min_fasta_length\": \"\\\"100\\\"\", \"mode\": \"\\\"normal\\\"\", \"rotation\": \"{\\\"no_rotate\\\": \\\"false\\\", \\\"start_gene_cov\\\": \\\"95.0\\\", \\\"start_gene_id\\\": \\\"90.0\\\", \\\"start_genes\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"pilon\": \"{\\\"min_polish_size\\\": \\\"1000\\\", \\\"no_pilon\\\": \\\"false\\\"}\"}",
+                        "tool_version": "0.4.8.0",
                         "type": "tool",
-                        "uuid": "756ca036-b6b5-46e8-a230-81ed522ba950",
+                        "uuid": "851c6be6-c202-450a-9cd3-19e205dcc496",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "forward",
-                                "uuid": "e82ae014-e75a-486c-93d6-af8cdd6e6f95"
+                                "output_name": "assembly",
+                                "uuid": "17700863-7cc5-4a67-ac0f-aa5f7b258d62"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "assembly_graph",
+                                "uuid": "3285cc00-6b39-4f3d-87a5-87abd483ede6"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Grep1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
                         "errors": null,
-                        "id": 5,
+                        "id": 21,
                         "input_connections": {
-                            "input": {
-                                "id": 4,
-                                "output_name": "forward"
+                            "input_file": {
+                                "id": 20,
+                                "output_name": "assembly_graph"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Select",
+                        "name": "Bandage Info",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "outfile",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 387,
-                            "height": 92,
-                            "left": 1193,
-                            "right": 1393,
-                            "top": 295,
-                            "width": 200,
-                            "x": 1193,
-                            "y": 295
+                            "left": 2977.4166870117188,
+                            "top": 803.4166412353516
                         },
                         "post_job_actions": {},
-                        "tool_id": "Grep1",
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"1085990\", \"invert\": \"\", \"keep_header\": \"false\", \"pattern\": \"^>.+\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.3",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "b2860df42e16",
+                            "name": "bandage",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"tsv\": \"\\\"false\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+                        "tool_version": "0.8.1+galaxy1",
                         "type": "tool",
-                        "uuid": "5ab56d83-be12-4498-a88e-16d37ef2e904",
+                        "uuid": "4aa230bd-3269-41c3-81f5-9085fcc4001d",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "04aaed7c-6c4c-44d6-89b0-5bba0a58927b"
+                                "output_name": "outfile",
+                                "uuid": "cf5eab6a-97ae-430e-a27a-6ecc33d4b8c0"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
                         "errors": null,
-                        "id": 6,
+                        "id": 22,
                         "input_connections": {
-                            "infile": {
-                                "id": 5,
-                                "output_name": "out_file1"
+                            "input_file": {
+                                "id": 20,
+                                "output_name": "assembly_graph"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Bandage Image",
+                                "name": "input_file"
+                            }
+                        ],
                         "label": null,
-                        "name": "Replace Text",
+                        "name": "Bandage Image",
                         "outputs": [
                             {
                                 "name": "outfile",
-                                "type": "input"
+                                "type": "jpg"
                             }
                         ],
                         "position": {
-                            "bottom": 387,
-                            "height": 92,
-                            "left": 1413,
-                            "right": 1613,
-                            "top": 295,
-                            "width": 200,
-                            "x": 1413,
-                            "y": 295
+                            "left": 2975.4166870117188,
+                            "top": 1017.4166412353516
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "b2860df42e16",
+                            "name": "bandage",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"infile|__identifier__\": \"1085990\", \"replacements\": [{\"__index__\": 0, \"find_pattern\": \"^>(.+)\", \"replace_pattern\": \"\\\\1\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.2",
+                        "tool_state": "{\"__page__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"lengths\": \"\\\"true\\\"\", \"output_format\": \"\\\"jpg\\\"\", \"height\": \"\\\"1000\\\"\", \"width\": \"\\\"\\\"\", \"names\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.8.1+galaxy2",
                         "type": "tool",
-                        "uuid": "030b177e-2375-4856-b640-8ffd7f591aaf",
+                        "uuid": "7683e21a-0fe1-4871-b044-7e74321fe44b",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "outfile",
-                                "uuid": "f81d7560-8835-4307-b876-f56e22edf40e"
+                                "uuid": "12e0cc76-0374-4ce8-b882-f5f21a942ad1"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
                         "errors": null,
-                        "id": 7,
+                        "id": 23,
                         "input_connections": {
-                            "in_file": {
-                                "id": 2,
-                                "output_name": "forward"
-                            },
-                            "source|name_list": {
-                                "id": 6,
-                                "output_name": "outfile"
+                            "input": {
+                                "id": 20,
+                                "output_name": "assembly"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Filter sequences by length",
+                                "name": "input"
+                            }
+                        ],
                         "label": null,
-                        "name": "seqtk_subseq",
+                        "name": "Filter sequences by length",
                         "outputs": [
                             {
-                                "name": "default",
-                                "type": "input"
+                                "name": "output",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "bottom": 416,
-                            "height": 142,
-                            "left": 1653,
-                            "right": 1853,
-                            "top": 274,
-                            "width": 200,
-                            "x": 1653,
-                            "y": 274
+                            "left": 2978.4166870117188,
+                            "top": 1220.4166259765625
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "58c8ece95b53",
-                            "name": "seqtk",
+                            "changeset_revision": "8cacfcf96a52",
+                            "name": "fasta_filter_by_length",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"max_length\": \"\\\"0\\\"\", \"min_length\": \"\\\"1000\\\"\"}",
+                        "tool_version": "1.2",
+                        "type": "tool",
+                        "uuid": "ef08963b-e96b-4841-b1fd-02056f6ab1f2",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "637c866b-dc17-4c32-aa1e-5207ae2c79a0"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "input|file_list": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "ONT data",
+                        "name": "Faster Download and Extract Reads in FASTQ",
+                        "outputs": [
+                            {
+                                "name": "list_paired",
+                                "type": "input"
+                            },
+                            {
+                                "name": "output_collection",
+                                "type": "input"
+                            },
+                            {
+                                "name": "output_collection_other",
+                                "type": "input"
+                            },
+                            {
+                                "name": "log",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 516.13330078125,
+                            "top": 540.7166442871094
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionlist_paired": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "list_paired"
+                            },
+                            "HideDatasetActionlog": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "log"
+                            },
+                            "HideDatasetActionoutput_collection_other": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_collection_other"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "aad3885b3216",
+                            "name": "sra_tools",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"in_file|__identifier__\": \"1085990\", \"l\": \"0\", \"name_list|__identifier__\": \"1085990\", \"source\": {\"type\": \"name\", \"__current_case__\": 1, \"name_list\": {\"__class__\": \"ConnectedValue\"}}, \"t\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3.1",
+                        "tool_state": "{\"adv\": \"{\\\"minlen\\\": \\\"\\\", \\\"skip_technical\\\": \\\"true\\\", \\\"split\\\": \\\"--split-3\\\"}\", \"input\": \"{\\\"__current_case__\\\": 2, \\\"file_list\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"input_select\\\": \\\"file_list\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}",
+                        "tool_version": "2.10.4+galaxy1",
                         "type": "tool",
-                        "uuid": "50599db8-7c04-4f0f-8cc7-ca9fbeb405ea",
+                        "uuid": "2ea0a236-4ecc-43b4-a815-40f37bf1bd59",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "default",
-                                "uuid": "75989c7c-9b50-4286-b59a-e2ebefcd6206"
+                                "output_name": "output_collection",
+                                "uuid": "9cd44dd5-4375-4c34-9edc-804544192c34"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
                         "errors": null,
-                        "id": 8,
+                        "id": 4,
                         "input_connections": {
-                            "in_file": {
+                            "single_paired|paired_input": {
                                 "id": 2,
-                                "output_name": "reverse"
+                                "output_name": "list_paired"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool fastp",
+                                "name": "single_paired"
+                            }
+                        ],
+                        "label": "fastp: Trimmed Illumina Reads",
+                        "name": "fastp",
+                        "outputs": [
+                            {
+                                "name": "output_paired_coll",
+                                "type": "input"
                             },
-                            "source|name_list": {
-                                "id": 6,
-                                "output_name": "outfile"
+                            {
+                                "name": "report_json",
+                                "type": "json"
+                            }
+                        ],
+                        "position": {
+                            "left": 879.7833251953125,
+                            "top": 365.04998779296875
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionreport_json": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "report_json"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "1d8fe9bc4cb0",
+                            "name": "fastp",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"output_options\": \"{\\\"report_html\\\": \\\"false\\\", \\\"report_json\\\": \\\"true\\\"}\", \"single_paired\": \"{\\\"__current_case__\\\": 2, \\\"adapter_trimming_options\\\": {\\\"adapter_sequence1\\\": \\\"\\\", \\\"adapter_sequence2\\\": \\\"\\\", \\\"disable_adapter_trimming\\\": \\\"false\\\"}, \\\"global_trimming_options\\\": {\\\"trim_front1\\\": \\\"\\\", \\\"trim_front2\\\": \\\"\\\", \\\"trim_tail1\\\": \\\"\\\", \\\"trim_tail2\\\": \\\"\\\"}, \\\"paired_input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"single_paired_selector\\\": \\\"paired_collection\\\"}\", \"read_mod_options\": \"{\\\"base_correction_options\\\": {\\\"correction\\\": \\\"false\\\"}, \\\"cutting_by_quality_options\\\": {\\\"cut_by_quality3\\\": \\\"false\\\", \\\"cut_by_quality5\\\": \\\"false\\\", \\\"cut_mean_quality\\\": \\\"\\\", \\\"cut_window_size\\\": \\\"\\\"}, \\\"polyg_tail_trimming\\\": {\\\"__current_case__\\\": 1, \\\"poly_g_min_len\\\": \\\"\\\", \\\"trimming_select\\\": \\\"\\\"}, \\\"polyx_tail_trimming\\\": {\\\"__current_case__\\\": 1, \\\"polyx_trimming_select\\\": \\\"\\\"}, \\\"umi_processing\\\": {\\\"umi\\\": \\\"false\\\", \\\"umi_len\\\": \\\"\\\", \\\"umi_loc\\\": \\\"\\\", \\\"umi_prefix\\\": \\\"\\\"}}\", \"overrepresented_sequence_analysis\": \"{\\\"overrepresentation_analysis\\\": \\\"false\\\", \\\"overrepresentation_sampling\\\": \\\"\\\"}\", \"filter_options\": \"{\\\"length_filtering_options\\\": {\\\"disable_length_filtering\\\": \\\"false\\\", \\\"length_required\\\": \\\"50\\\"}, \\\"low_complexity_filter\\\": {\\\"complexity_threshold\\\": \\\"\\\", \\\"enable_low_complexity_filter\\\": \\\"false\\\"}, \\\"quality_filtering_options\\\": {\\\"disable_quality_filtering\\\": \\\"false\\\", \\\"n_base_limit\\\": \\\"\\\", \\\"qualified_quality_phred\\\": \\\"20\\\", \\\"unqualified_percent_limit\\\": \\\"20\\\"}}\", \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.19.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "7508c22b-dc6a-4071-8dd0-d5616718e62b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_paired_coll",
+                                "uuid": "a7be7eab-3e80-4be6-b1a4-ab303c314096"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "mode|reads|files": {
+                                "id": 3,
+                                "output_name": "output_collection"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "seqtk_subseq",
+                        "name": "NanoPlot",
                         "outputs": [
                             {
-                                "name": "default",
-                                "type": "input"
+                                "name": "output_html",
+                                "type": "html"
+                            },
+                            {
+                                "name": "nanostats",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "nanostats_post_filtering",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "read_length",
+                                "type": "png"
+                            },
+                            {
+                                "name": "log_read_length",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": 572,
-                            "height": 142,
-                            "left": 1658,
-                            "right": 1858,
-                            "top": 430,
-                            "width": 200,
-                            "x": 1658,
-                            "y": 430
+                            "left": 924.7833251953125,
+                            "top": 650.4666442871094
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionlog_read_length": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "log_read_length"
+                            },
+                            "HideDatasetActionnanostats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "nanostats"
+                            },
+                            "HideDatasetActionnanostats_post_filtering": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "nanostats_post_filtering"
+                            },
+                            "HideDatasetActionread_length": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "read_length"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "645159bcee2d",
+                            "name": "nanoplot",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"filter\": \"{\\\"alength\\\": \\\"false\\\", \\\"barcoded\\\": \\\"false\\\", \\\"downsample\\\": \\\"\\\", \\\"drop_outliers\\\": \\\"false\\\", \\\"loglength\\\": \\\"true\\\", \\\"maxlength\\\": \\\"\\\", \\\"minlength\\\": \\\"\\\", \\\"minqual\\\": \\\"\\\", \\\"percentqual\\\": \\\"false\\\", \\\"readtype\\\": null}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"__current_case__\\\": 0, \\\"choice\\\": \\\"batch\\\", \\\"reads\\\": {\\\"__current_case__\\\": 0, \\\"files\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"type\\\": \\\"fastq\\\"}}\", \"customization\": \"{\\\"N50\\\": \\\"false\\\", \\\"color\\\": null, \\\"format\\\": \\\"png\\\", \\\"noN50\\\": \\\"false\\\", \\\"plots\\\": null}\"}",
+                        "tool_version": "1.25.0+galaxy1",
+                        "type": "tool",
+                        "uuid": "9b1d43ac-82e3-463f-9c88-08c8826a62c9",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_html",
+                                "uuid": "cd8570c7-02db-479b-81a9-cd0d26643f71"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "fastq_input|fastq_input1": {
+                                "id": 3,
+                                "output_name": "output_collection"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Map with minimap2",
+                        "outputs": [
+                            {
+                                "name": "alignment_output",
+                                "type": "bam"
+                            }
+                        ],
+                        "position": {
+                            "left": 1003.9833984375,
+                            "top": 1131.9666442871094
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "58c8ece95b53",
-                            "name": "seqtk",
+                            "changeset_revision": "53c0b7a1a0c3",
+                            "name": "minimap2",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"in_file|__identifier__\": \"1085990\", \"l\": \"0\", \"name_list|__identifier__\": \"1085990\", \"source\": {\"type\": \"name\", \"__current_case__\": 1, \"name_list\": {\"__class__\": \"ConnectedValue\"}}, \"t\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3.1",
+                        "tool_state": "{\"alignment_options\": \"{\\\"-O2\\\": \\\"\\\", \\\"A\\\": \\\"\\\", \\\"B\\\": \\\"\\\", \\\"E\\\": \\\"\\\", \\\"E2\\\": \\\"\\\", \\\"O\\\": \\\"\\\", \\\"s\\\": \\\"\\\", \\\"u\\\": null, \\\"z\\\": \\\"\\\"}\", \"analysis_type_selector\": \"\\\"splice\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"io_options\": \"{\\\"K\\\": \\\"\\\", \\\"L\\\": \\\"false\\\", \\\"Q\\\": \\\"false\\\", \\\"Y\\\": \\\"false\\\", \\\"c\\\": \\\"false\\\", \\\"cs\\\": null, \\\"eqx\\\": \\\"false\\\", \\\"output_format\\\": \\\"BAM\\\"}\", \"mapping_options\": \"{\\\"F\\\": \\\"\\\", \\\"G\\\": \\\"\\\", \\\"N\\\": \\\"\\\", \\\"X\\\": \\\"false\\\", \\\"f\\\": \\\"\\\", \\\"g\\\": \\\"\\\", \\\"m\\\": \\\"\\\", \\\"min_occ_floor\\\": \\\"\\\", \\\"n\\\": \\\"\\\", \\\"p\\\": \\\"\\\", \\\"r\\\": \\\"\\\"}\", \"fastq_input\": \"{\\\"__current_case__\\\": 1, \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"single\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 0, \\\"ref_file\\\": \\\"hg38\\\", \\\"reference_source_selector\\\": \\\"cached\\\"}\", \"indexing_options\": \"{\\\"H\\\": \\\"false\\\", \\\"I\\\": \\\"\\\", \\\"k\\\": \\\"\\\", \\\"w\\\": \\\"\\\"}\"}",
+                        "tool_version": "2.17+galaxy1",
                         "type": "tool",
-                        "uuid": "6b8ac606-6490-4355-9111-001dbe15fd22",
+                        "uuid": "098d2283-1218-489b-9882-8822e79d9444",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "default",
-                                "uuid": "1787644d-4796-4928-9458-7fc0779eb500"
+                                "output_name": "alignment_output",
+                                "uuid": "9972015d-4bdc-440f-b8b6-84e92a64ef8f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "__ZIP_COLLECTION__",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
                         "errors": null,
-                        "id": 9,
+                        "id": 7,
                         "input_connections": {
-                            "input_forward": {
-                                "id": 7,
-                                "output_name": "default"
-                            },
-                            "input_reverse": {
-                                "id": 8,
-                                "output_name": "default"
+                            "results_0|software_cond|input": {
+                                "id": 4,
+                                "output_name": "report_json"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "MultiQC",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool Zip Collection",
-                                "name": "input_forward"
+                                "name": "stats",
+                                "type": "input"
                             },
                             {
-                                "description": "runtime parameter for tool Zip Collection",
-                                "name": "input_reverse"
+                                "name": "html_report",
+                                "type": "html"
                             }
                         ],
-                        "label": "Paired-end collection of cleaned reads",
-                        "name": "Zip Collection",
+                        "position": {
+                            "left": 1152.4833984375,
+                            "top": 200
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "tool_shed_repository": {
+                            "changeset_revision": "b2f1f75d49c4",
+                            "name": "multiqc",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"comment\": \"\\\"\\\"\", \"__page__\": null, \"title\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"results\": \"[{\\\"__index__\\\": 0, \\\"software_cond\\\": {\\\"__current_case__\\\": 7, \\\"input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"software\\\": \\\"fastp\\\"}}]\", \"saveLog\": \"\\\"false\\\"\"}",
+                        "tool_version": "1.7",
+                        "type": "tool",
+                        "uuid": "73566697-4a46-4d35-b8e2-61770acc62c0",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "html_report",
+                                "uuid": "15f42a94-2c97-4932-8e3f-f26a72b58be4"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "library|input_1": {
+                                "id": 4,
+                                "output_name": "output_paired_coll"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Bowtie2",
                         "outputs": [
                             {
                                 "name": "output",
-                                "type": "input"
+                                "type": "bam"
+                            },
+                            {
+                                "name": "mapping_stats",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 490.5,
-                            "height": 142,
-                            "left": 1939,
-                            "right": 2139,
-                            "top": 348.5,
-                            "width": 200,
-                            "x": 1939,
-                            "y": 348.5
+                            "left": 1208.699951171875,
+                            "top": 564.6333160400391
                         },
                         "post_job_actions": {},
-                        "tool_id": "__ZIP_COLLECTION__",
-                        "tool_state": "{\"input_forward\": {\"__class__\": \"RuntimeValue\"}, \"input_reverse\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "749c918495f7",
+                            "name": "bowtie2",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"sam_options\": \"{\\\"__current_case__\\\": 1, \\\"sam_options_selector\\\": \\\"no\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"__current_case__\\\": 2, \\\"aligned_file\\\": \\\"false\\\", \\\"input_1\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"paired_options\\\": {\\\"__current_case__\\\": 1, \\\"paired_options_selector\\\": \\\"no\\\"}, \\\"type\\\": \\\"paired_collection\\\", \\\"unaligned_file\\\": \\\"false\\\"}\", \"reference_genome\": \"{\\\"__current_case__\\\": 0, \\\"index\\\": \\\"hg38full\\\", \\\"source\\\": \\\"indexed\\\"}\", \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"save_mapping_stats\": \"\\\"true\\\"\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"simple\\\", \\\"presets\\\": \\\"no_presets\\\"}\"}",
+                        "tool_version": "2.3.4.3+galaxy0",
                         "type": "tool",
-                        "uuid": "381d0485-0164-410f-801d-7dfb7891663d",
+                        "uuid": "43331d2c-7116-410e-a6bd-7e7520d93a52",
                         "workflow_outputs": [
                             {
-                                "label": "Cleaned Data",
+                                "label": null,
                                 "output_name": "output",
-                                "uuid": "f24bbf28-dc51-440f-a758-ac05033f0645"
+                                "uuid": "eeae40f6-f1b2-4c56-9860-ac7b8eb1dec0"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "mapping_stats",
+                                "uuid": "c567226e-efaf-4188-bdec-3ba20d0733b0"
                             }
                         ]
                     }
                 ],
-                "parent_id": "sequence-analysis/human-reads-removal",
-                "path": "topics/sequence-analysis/tutorials/human-reads-removal/workflows/human-reads-removal.ga",
+                "parent_id": "assembly/assembly-with-preprocessing",
+                "path": "topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing_and_sra_download.ga",
                 "tags": [
-                    "sequence-analysis"
+                    "GTN",
+                    "assembly"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "GTN - Sequence Analyses - Removal of human reads from SARS-CoV-2 sequencing data",
-                "topic_id": "sequence-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/sequence-analysis-human-reads-removal/versions/human-reads-removal",
-                "tutorial_id": "human-reads-removal",
-                "url": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/human-reads-removal/workflows/human-reads-removal.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/human-reads-removal/workflows/human-reads-removal.html",
+                "title": "assembly_with_preprocessing_and_sra_download",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-assembly-with-preprocessing/versions/assembly-with-preprocessing-and-sra-download",
+                "tutorial_id": "assembly-with-preprocessing",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing_and_sra_download.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing_and_sra_download.html",
                 "version": 1,
-                "wfid": "sequence-analysis-human-reads-removal",
-                "wfname": "human-reads-removal",
-                "workflow": "human-reads-removal.ga",
+                "wfid": "assembly-assembly-with-preprocessing",
+                "wfname": "assembly-with-preprocessing-and-sra-download",
+                "workflow": "assembly_with_preprocessing_and_sra_download.ga",
                 "workflow_tools": [
-                    "Grep1",
-                    "__UNZIP_COLLECTION__",
                     "__ZIP_COLLECTION__",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
                     "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-                    "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
                 ],
-                "workflowhub_id": "1276"
+                "workflowhub_id": "1197"
             }
-        ]
+        ],
+        "zenodo_link": "https://zenodo.org/record/3732359"
     },
     {
         "admin_install": {
@@ -45927,11 +47491,12 @@
         ],
         "dir": "topics/galaxy-interface/tutorials/ncbi-sarf",
         "edam_operation": [
-            "Data handling",
-            "SNP detection"
+            "SNP detection",
+            "Data handling"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
@@ -45959,7 +47524,7 @@
             "Learn about SRA aligned read format and vcf files for Runs containing SARS-CoV-2 content",
             "Understand how to search the metadata for these Runs to find your dataset of interest and then import that data in your preferred format"
         ],
-        "pageviews": 4971883,
+        "pageviews": 5142208,
         "pub_date": "2021-05-31",
         "questions": [
             "How can I search SRA SARS-CoV-2 metadata from within Galaxy?",
@@ -45991,13 +47556,13 @@
         ],
         "short_id": "T00155",
         "short_tools": [
-            "fastq_to_fasta_python",
-            "tp_cat",
-            "fasterq_dump",
             "query_tabular",
-            "fastq_dump",
+            "tp_cat",
             "jq",
-            "snpeff_sars_cov_2"
+            "fastq_dump",
+            "snpeff_sars_cov_2",
+            "fastq_to_fasta_python",
+            "fasterq_dump"
         ],
         "slides": true,
         "slides_recordings": [
@@ -46017,6 +47582,11 @@
         "subtopic": "upload",
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -46081,8 +47651,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 266,
-        "visitors": 1842342
+        "visit_duration": 267,
+        "visitors": 1911645
     },
     {
         "admin_install": {
@@ -46245,14 +47815,14 @@
         ],
         "dir": "topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil",
         "edam_operation": [
-            "Sequencing quality control",
             "Generation",
-            "Read mapping",
-            "Genome visualisation",
-            "Genome indexing",
+            "Statistical calculation",
             "Sequence alignment",
+            "Read mapping",
+            "Sequencing quality control",
             "Sequence composition calculation",
-            "Statistical calculation"
+            "Genome visualisation",
+            "Genome indexing"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -46268,7 +47838,10 @@
         "id": "sequence-analysis/sars-with-galaxy-on-anvil",
         "inexact_supported_servers": [
             "Galaxy@AuBi",
+            "Galaxy@Pasteur",
             "GalaxyTrakr",
+            "MISSISSIPPI",
+            "UseGalaxy.be",
             "UseGalaxy.cz"
         ],
         "js_requirements": {
@@ -46288,7 +47861,7 @@
             "Critique large data sets and use bioinformatics to assess genetics data",
             "Tap into the interdisciplinary nature of science"
         ],
-        "pageviews": 899,
+        "pageviews": 956,
         "pub_date": "2023-07-10",
         "questions": [
             "How do I check my data quality?",
@@ -46297,8 +47870,8 @@
         ],
         "short_id": "T00356",
         "short_tools": [
-            "fastqc",
             "bwa_mem",
+            "fastqc",
             "jbrowse"
         ],
         "slides": false,
@@ -46337,11 +47910,26 @@
                     "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
                 },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "GalaxyTrakr",
                     "url": "https://galaxytrakr.org/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -46381,8 +47969,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 283,
-        "visitors": 691,
+        "visit_duration": 271,
+        "visitors": 739,
         "zenodo_link": "https://doi.org/10.5281/zenodo.8115178"
     },
     {
@@ -46581,7 +48169,7 @@
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-18",
+        "mod_date": "2024-10-02",
         "objectives": [
             "Familiarize yourself with data manipulation tools in Galaxy",
             "Perform basic text manipulation tasks in Galaxy",
@@ -46589,7 +48177,7 @@
             "Reason about the expected outcome of tools"
         ],
         "pageviews": 0,
-        "pub_date": "2024-08-18",
+        "pub_date": "2024-10-02",
         "questions": [
             "How can I do basic data manipulation in Galaxy?",
             "Which tools are available to convert, reformat, filter, sort etc my text-based data?"
@@ -46597,24 +48185,24 @@
         "short_id": "T00077",
         "short_tools": [
             "",
+            "join1",
             "Count1",
-            "Cut1",
-            "Remove beginning1",
-            "Grouping1",
+            "upload1",
+            "wc_gnu",
             "datamash_ops",
-            "Show beginning1",
-            "tp_sort_header_tool",
+            "Grouping1",
             "tp_sorted_uniq",
-            "cat1",
+            "tabular_to_csv",
             "tp_cat",
-            "wc_gnu",
             "Filter1",
+            "tp_sort_header_tool",
             "tp_split_on_column",
-            "join1",
-            "regexColumn1",
-            "upload1",
-            "tabular_to_csv",
-            "Add_a_column1"
+            "Cut1",
+            "Remove beginning1",
+            "cat1",
+            "Show beginning1",
+            "Add_a_column1",
+            "regexColumn1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -46783,7 +48371,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nolympics.tsv\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ncountry-information.tsv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nolympics_2022.tsv\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Line/Word/Character count\"];\n  0 -->|output| 3;\n  4[\"tabular-to-csv\"];\n  0 -->|output| 4;\n  5[\"Sort\"];\n  0 -->|output| 5;\n  6[\"Sort\"];\n  0 -->|output| 6;\n  7[\"Sort\"];\n  0 -->|output| 7;\n  8[\"Sort\"];\n  0 -->|output| 8;\n  9[\"Sort\"];\n  0 -->|output| 9;\n  10[\"Sort\"];\n  0 -->|output| 10;\n  11[\"Filter\"];\n  0 -->|output| 11;\n  12[\"Filter\"];\n  0 -->|output| 12;\n  13[\"Count\"];\n  0 -->|output| 13;\n  14[\"Count\"];\n  0 -->|output| 14;\n  15[\"Count\"];\n  0 -->|output| 15;\n  16[\"Count\"];\n  0 -->|output| 16;\n  17[\"Datamash\"];\n  0 -->|output| 17;\n  18[\"Count\"];\n  0 -->|output| 18;\n  19[\"Datamash\"];\n  0 -->|output| 19;\n  20[\"Filter\"];\n  0 -->|output| 20;\n  21[\"Filter\"];\n  0 -->|output| 21;\n  22[\"Filter\"];\n  0 -->|output| 22;\n  23[\"Filter\"];\n  0 -->|output| 23;\n  24[\"Filter\"];\n  0 -->|output| 24;\n  25[\"Filter\"];\n  0 -->|output| 25;\n  26[\"Filter\"];\n  0 -->|output| 26;\n  27[\"Compute\"];\n  0 -->|output| 27;\n  28[\"Compute\"];\n  0 -->|output| 28;\n  29[\"Cut\"];\n  0 -->|output| 29;\n  30[\"Column Regex Find And Replace\"];\n  0 -->|output| 30;\n  31[\"Column Regex Find And Replace\"];\n  0 -->|output| 31;\n  32[\"Column Regex Find And Replace\"];\n  0 -->|output| 32;\n  33[\"Cut\"];\n  0 -->|output| 33;\n  34[\"Cut\"];\n  0 -->|output| 34;\n  35[\"Datamash\"];\n  0 -->|output| 35;\n  36[\"Datamash\"];\n  0 -->|output| 36;\n  37[\"Datamash\"];\n  0 -->|output| 37;\n  38[\"Datamash\"];\n  0 -->|output| 38;\n  39[\"Datamash\"];\n  0 -->|output| 39;\n  40[\"Count\"];\n  0 -->|output| 40;\n  41[\"Column Regex Find And Replace\"];\n  0 -->|output| 41;\n  42[\"Split file\"];\n  0 -->|output| 42;\n  43[\"Join two Datasets\"];\n  0 -->|output| 43;\n  1 -->|output| 43;\n  44[\"Remove beginning\"];\n  2 -->|output| 44;\n  45[\"Sort\"];\n  11 -->|out_file1| 45;\n  46[\"Filter\"];\n  12 -->|out_file1| 46;\n  47[\"Cut\"];\n  28 -->|out_file1| 47;\n  48[\"Unique\"];\n  29 -->|out_file1| 48;\n  49[\"Count\"];\n  41 -->|out_file1| 49;\n  50[\"Datamash\"];\n  41 -->|out_file1| 50;\n  51[\"Concatenate datasets\"];\n  0 -->|output| 51;\n  44 -->|out_file1| 51;\n  52[\"Filter\"];\n  45 -->|outfile| 52;\n  53[\"Sort\"];\n  46 -->|out_file1| 53;\n  54[\"Remove beginning\"];\n  47 -->|out_file1| 54;\n  55[\"Select first\"];\n  47 -->|out_file1| 55;\n  56[\"Sort\"];\n  48 -->|outfile| 56;\n  57[\"Unique\"];\n  54 -->|out_file1| 57;\n  58[\"Concatenate datasets\"];\n  55 -->|out_file1| 58;\n  57 -->|outfile| 58;\n  59[\"Join two Datasets\"];\n  0 -->|output| 59;\n  58 -->|out_file1| 59;\n  60[\"Cut\"];\n  59 -->|out_file1| 60;\n  61[\"Line/Word/Character count\"];\n  60 -->|out_file1| 61;",
-                "modified": "2024-08-18 00:06:23 +0000",
+                "modified": "2024-10-02 12:08:09 +0000",
                 "name": "GTN Tutorial: Data manipulation Olympics - all steps and exercises",
                 "outputs": [],
                 "parent_id": "data-science/data-manipulation-olympics",
@@ -46827,132 +48415,6 @@
         ],
         "zenodo_link": "https://zenodo.org/record/6803028"
     },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture1/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "nekrut"
-            ]
-        },
-        "contributors": [
-            {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
-                "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
-            }
-        ],
-        "dir": "topics/data-science/tutorials/gnmx-lecture1",
-        "draft": true,
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "data-science/gnmx-lecture1",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Jim Watson did not discover DNA"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-02-20",
-        "objectives": [
-            "Have a basic understanding of history of biology from Darwin to today."
-        ],
-        "pageviews": 825832,
-        "priority": 1,
-        "pub_date": "2024-01-09",
-        "questions": [
-            "What is this course about?",
-            "What is the history of genomics?"
-        ],
-        "short_id": "T00382",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
-        "subtopic": "gnmx",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "work-in-progress"
-        ],
-        "time_estimation": "1h",
-        "title": "A (very) brief history of genomics",
-        "tools": [],
-        "topic_name": "data-science",
-        "topic_name_human": "Foundations of Data Science",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "gnmx-lecture1",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture1/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture1/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture1/tutorial.json"
-        },
-        "version": 2,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 150,
-        "visitors": 345992
-    },
     {
         "admin_install": {
             "install_repository_dependencies": true,
@@ -47058,11 +48520,10 @@
         "hands_on": true,
         "id": "data-science/online-resources-gene",
         "inexact_supported_servers": [
-            "BF2I-MAP",
-            "Center for Phage Technology (CPT)",
             "GalaxyTrakr",
+            "MISSISSIPPI",
             "PepSimili",
-            "PhagePromotor",
+            "UseGalaxy.be",
             "UseGalaxy.no"
         ],
         "js_requirements": {
@@ -47084,7 +48545,7 @@
         "objectives": [
             "Starting from a text search, navigate multiple web resources to examine multiple types of information about a gene, conveyed through multiple file formats."
         ],
-        "pageviews": 1176119,
+        "pageviews": 1346417,
         "pub_date": "2023-09-07",
         "questions": [
             "How to employ bioinformatics resources to investigate a specific protein family (opsins)?",
@@ -47134,18 +48595,13 @@
             ],
             "inexact": [
                 {
-                    "name": "BF2I-MAP",
-                    "url": "http://bf2i-galaxy.insa-lyon.fr:8080/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "Center for Phage Technology (CPT)",
-                    "url": "https://cpt.tamu.edu/galaxy-public/",
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
                     "usegalaxy": false
                 },
                 {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
                     "usegalaxy": false
                 },
                 {
@@ -47154,8 +48610,8 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "PhagePromotor",
-                    "url": "https://galaxy.bio.di.uminho.pt/",
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
                 {
@@ -47193,8 +48649,8 @@
         "video": true,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 382,
-        "visitors": 501983,
+        "visit_duration": 356,
+        "visitors": 567740,
         "zenodo_link": "https://zenodo.org/record/8304465"
     },
     {
@@ -47205,236 +48661,31 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-python/tutorial.json",
-        "contributors": [
-            {
-                "id": "carpentries",
-                "joined": "2021-09",
-                "name": "The Carpentries",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
-                "ror": "0356fgm10",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/logo-avans.png",
-                "former_members": [
-                    "dirowa",
-                    "hexylena"
-                ],
-                "id": "avans-atgm",
-                "joined": "2020-11",
-                "members": [
-                    "bazante1"
-                ],
-                "name": "Avans Hogeschool",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/",
-                "ror": "015d5s513",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
-            }
-        ],
-        "dir": "topics/data-science/tutorials/sql-python",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [],
-        "hands_on": true,
-        "id": "data-science/sql-python",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "General-purpose languages have libraries for accessing databases.",
-            "To connect to a database, a program must use a library specific to that database manager.",
-            "These libraries use a connection-and-cursor model.",
-            "Programs can read query results in batches or all at once.",
-            "Queries should be written using parameter substitution, not string formatting."
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-16",
-        "notebook": {
-            "language": "python"
-        },
-        "objectives": [
-            "Write short programs that execute SQL queries.",
-            "Trace the execution of a program that contains an SQL query.",
-            "Explain why most database applications are written in a general-purpose language rather than in SQL."
-        ],
-        "pageviews": 630,
-        "pub_date": "2021-10-11",
-        "questions": [
-            "How can I access databases from programs written in Python?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "data-science",
-                "tutorials": [
-                    "sql-advanced"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00109",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "sql",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "SQL",
-            "Python"
-        ],
-        "time_estimation": "45M",
-        "title": "SQL with Python",
-        "tools": [],
-        "topic_name": "data-science",
-        "topic_name_human": "Foundations of Data Science",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "sql-python",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/sql-python/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-python/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-python/tutorial.json"
-        },
-        "version": 7,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 25,
-        "visitors": 449,
-        "zenodo_link": null
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/git-cli/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture1/tutorial.json",
         "contributions": {
             "authorship": [
-                "hexylena"
+                "nekrut"
             ]
         },
         "contributors": [
             {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
                 "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/git-cli",
+        "dir": "topics/data-science/tutorials/gnmx-lecture1",
+        "draft": true,
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "data-science/git-cli",
+        "id": "data-science/gnmx-lecture1",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -47446,39 +48697,26 @@
             "mermaid": false
         },
         "key_points": [
-            "While git is extremely powerful, just using it for tracking changes is quite easy!",
-            "This does not take advantage of any advanced features, nor collaboration, but it is easy to expand into doing that."
+            "Jim Watson did not discover DNA"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-16",
+        "mod_date": "2024-02-20",
         "objectives": [
-            "Create a repository",
-            "Commit a file",
-            "Make some changes",
-            "Use the log to view the diff",
-            "Undo a bad change"
+            "Have a basic understanding of history of biology from Darwin to today."
         ],
-        "pageviews": 350,
-        "pub_date": "2022-06-16",
+        "pageviews": 996114,
+        "priority": 1,
+        "pub_date": "2024-01-09",
         "questions": [
-            "How can I start tracking my changes with git?",
-            "How do I commit changes?",
-            "How can I undo a mistake?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "data-science",
-                "tutorials": [
-                    "cli-basics"
-                ],
-                "type": "internal"
-            }
+            "What is this course about?",
+            "What is the history of genomics?"
         ],
-        "short_id": "T00079",
+        "short_id": "T00382",
         "short_tools": [],
-        "slides": false,
+        "slides": true,
         "slides_recordings": false,
+        "subtopic": "gnmx",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -47513,8 +48751,11 @@
             ]
         },
         "symlink": null,
-        "time_estimation": "30m",
-        "title": "Basics of using Git from the Command Line",
+        "tags": [
+            "work-in-progress"
+        ],
+        "time_estimation": "1h",
+        "title": "A (very) brief history of genomics",
         "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
@@ -47524,19 +48765,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "git-cli",
+        "tutorial_name": "gnmx-lecture1",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/git-cli/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture1/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/git-cli/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/git-cli/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture1/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture1/tutorial.json"
         },
-        "version": 6,
+        "version": 2,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 23,
-        "visitors": 108
+        "visit_duration": 151,
+        "visitors": 414805
     },
     {
         "admin_install": {
@@ -47546,16 +48787,18 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/bash-variant-calling/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/bash-git/tutorial.json",
         "contributions": {
             "authorship": [
-                "Sofokli5",
+                "Sofokli5"
+            ],
+            "editing": [
                 "fpsom",
                 "shiltemann",
-                "hexylena",
-                "carpentries"
+                "hexylena"
             ],
             "funding": [
+                "carpentries",
                 "gallantries"
             ]
         },
@@ -47680,83 +48923,106 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/bash-variant-calling",
+        "dir": "topics/data-science/tutorials/bash-git",
         "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "data-science/bash-variant-calling",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
+        "id": "data-science/bash-git",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Bioinformatic command line tools are collections of commands that can be used to carry out bioinformatic analyses.",
-            "To use most powerful bioinformatic tools, you will need to use the command line.",
-            "There are many different file formats for storing genomics data. It is important to understand what type of information is contained in each file, and how it was derived."
+            "Version control is like an unlimited 'undo'.",
+            "Version control also allows many people to work in parallel.",
+            "Use `git config` with the `--global` option to configure a user name, email address, editor, and other preferences once per machine.",
+            "`git init` initializes a repository.",
+            "Git stores all of its repository data in the `.git` directory.",
+            "`git status` shows the status of a repository.",
+            "Files can be stored in a project's working directory (which users see), the staging area (where the next commit is being built up) and the local repository (where commits are permanently recorded).",
+            "`git add` puts files in the staging area.",
+            "`git commit` saves the staged content as a new commit in the local repository.",
+            "Write a commit message that accurately describes your changes.",
+            "`git diff` displays differences between commits.",
+            "`git checkout` recovers old versions of files."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2023-10-23",
         "objectives": [
-            "Understand the steps involved in variant calling.",
-            "Describe the types of data formats encountered during variant calling.",
-            "Use command line tools to perform variant calling."
+            "Understand the benefits of an automated version control system.",
+            "Understand the basics of how automated version control systems work.",
+            "Configure `git` the first time it is used on a computer.",
+            "Understand the meaning of the `--global` configuration flag.",
+            "Create a local Git repository.",
+            "Describe the purpose of the `.git` directory.",
+            "Go through the modify-add-commit cycle for one or more files.",
+            "Explain where information is stored at each stage of that cycle.",
+            "Distinguish between descriptive and non-descriptive commit messages.",
+            "Explain what the HEAD of a repository is and how to use it.",
+            "Identify and use Git commit numbers.",
+            "Compare various versions of tracked files.",
+            "Restore old versions of files."
         ],
-        "pageviews": 7493,
-        "pub_date": "2022-07-07",
+        "pageviews": 425,
+        "pub_date": "2022-07-06",
         "questions": [
-            "How do I find sequence variants between my sample and a reference genome?"
+            "What is version control and why should I use it?",
+            "How do I get set up to use Git?",
+            "Where does Git store information?",
+            "How do I record changes in Git?",
+            "How do I check the status of my version control repository?",
+            "How do I record notes about what changes I made and why?",
+            "How can I identify old versions of files?",
+            "How do I review my changes?",
+            "How can I recover old versions of files?"
+        ],
+        "short_id": "T00072",
+        "short_tools": [
+            "interactive_tool_rstudio"
         ],
-        "short_id": "T00073",
-        "short_tools": [],
         "slides": false,
         "slides_recordings": false,
         "supported_servers": {
-            "exact": [],
-            "inexact": [
+            "exact": [
                 {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
                 {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 },
                 {
-                    "human": "Galaxy Australia",
-                    "id": "au",
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
                 }
-            ]
+            ],
+            "inexact": []
         },
         "symlink": null,
-        "time_estimation": "50M",
-        "title": "Variant Calling Workflow",
-        "tools": [],
+        "time_estimation": "65M",
+        "title": "Version Control with Git",
+        "tools": [
+            "interactive_tool_rstudio"
+        ],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
         "tours": false,
@@ -47765,21 +49031,25 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "bash-variant-calling",
+        "tutorial_name": "bash-git",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/bash-variant-calling/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/bash-git/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/bash-variant-calling/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/bash-variant-calling/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/bash-git/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/bash-git/tutorial.json"
         },
-        "version": 7,
+        "version": 6,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 118,
-        "visitors": 5656
+        "visit_duration": 46,
+        "visitors": 202
     },
     {
+        "abbreviations": {
+            "DAG": "Directed Acyclic Graph",
+            "SciWMS": "Scientific Workflow Management System"
+        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -47787,78 +49057,8 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/bash-git/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "Sofokli5"
-            ],
-            "editing": [
-                "fpsom",
-                "shiltemann",
-                "hexylena"
-            ],
-            "funding": [
-                "carpentries",
-                "gallantries"
-            ]
-        },
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/snakemake/tutorial.json",
         "contributors": [
-            {
-                "email": "sofoskeisaris@gmail.com",
-                "id": "Sofokli5",
-                "joined": "2022-05",
-                "name": "Sofoklis Keisaris",
-                "orcid": "0000-0002-4833-4726",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Sofokli5/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/Sofokli5.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "elixir-europe"
-                ],
-                "elixir_node": "gr",
-                "email": "fpsom@certh.gr",
-                "id": "fpsom",
-                "joined": "2019-03",
-                "linkedin": "fpsom",
-                "matrix": "fpsom:matrix.org",
-                "name": "Fotis E. Psomopoulos",
-                "orcid": "0000-0002-0222-4273",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
-                "twitter": "fopsom",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
@@ -47889,140 +49089,139 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
             {
-                "id": "carpentries",
-                "joined": "2021-09",
-                "name": "The Carpentries",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
-                "ror": "0356fgm10",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
+                "affiliations": [
+                    "avans-atgm"
+                ],
+                "id": "bazante1",
+                "joined": "2020-12",
+                "name": "Bazante Sanders",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
             },
             {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
+                "email": "D.vrins@live.nl",
+                "former_affiliations": [
+                    "avans-atgm"
+                ],
+                "id": "dirowa",
+                "joined": "2021-10",
+                "linkedin": "Donny Vrins",
+                "name": "Donny Vrins",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dirowa/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/dirowa.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/logo-avans.png",
+                "former_members": [
+                    "dirowa",
+                    "hexylena"
+                ],
+                "id": "avans-atgm",
+                "joined": "2020-11",
                 "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
+                    "bazante1"
                 ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+                "name": "Avans Hogeschool",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/",
+                "ror": "015d5s513",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/bash-git",
+        "dir": "topics/data-science/tutorials/snakemake",
         "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [],
         "hands_on": true,
-        "id": "data-science/bash-git",
-        "inexact_supported_servers": [],
+        "id": "data-science/snakemake",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Version control is like an unlimited 'undo'.",
-            "Version control also allows many people to work in parallel.",
-            "Use `git config` with the `--global` option to configure a user name, email address, editor, and other preferences once per machine.",
-            "`git init` initializes a repository.",
-            "Git stores all of its repository data in the `.git` directory.",
-            "`git status` shows the status of a repository.",
-            "Files can be stored in a project's working directory (which users see), the staging area (where the next commit is being built up) and the local repository (where commits are permanently recorded).",
-            "`git add` puts files in the staging area.",
-            "`git commit` saves the staged content as a new commit in the local repository.",
-            "Write a commit message that accurately describes your changes.",
-            "`git diff` displays differences between commits.",
-            "`git checkout` recovers old versions of files."
+            "Make and Snakemake are ways to write pipelines in a declarative format",
+            "Instead of writing individual actions you wish to take, you describe how to produce each file you need, and the system executes those steps only if they're needed",
+            "If you're doing scientific research you should use Snakemake",
+            "Snakemake can significantly speed up your command line pipelines by providing automatic detection of inputs, and not re-creating them if they don't need",
+            "Snakemake also provides very easy access to paralellisation without complexity.",
+            "But it is more complex than using Galaxy"
         ],
         "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-10-23",
+        "mod_date": "2024-06-11",
         "objectives": [
-            "Understand the benefits of an automated version control system.",
-            "Understand the basics of how automated version control systems work.",
-            "Configure `git` the first time it is used on a computer.",
-            "Understand the meaning of the `--global` configuration flag.",
-            "Create a local Git repository.",
-            "Describe the purpose of the `.git` directory.",
-            "Go through the modify-add-commit cycle for one or more files.",
-            "Explain where information is stored at each stage of that cycle.",
-            "Distinguish between descriptive and non-descriptive commit messages.",
-            "Explain what the HEAD of a repository is and how to use it.",
-            "Identify and use Git commit numbers.",
-            "Compare various versions of tracked files.",
-            "Restore old versions of files."
+            "Write a snakefile that does a simple QC and Mapping workflow"
         ],
-        "pageviews": 403,
-        "pub_date": "2022-07-06",
+        "pageviews": 3792,
+        "pub_date": "2021-11-18",
         "questions": [
-            "What is version control and why should I use it?",
-            "How do I get set up to use Git?",
-            "Where does Git store information?",
-            "How do I record changes in Git?",
-            "How do I check the status of my version control repository?",
-            "How do I record notes about what changes I made and why?",
-            "How can I identify old versions of files?",
-            "How do I review my changes?",
-            "How can I recover old versions of files?"
+            "What is Make & Snakemake",
+            "What is a Makefile/Snakefile",
+            "How do these improve pipelines over simple scripts?",
+            "Why is Snakemake better for scientific research and how can I use it",
+            "How do I use conda envs with Snakemake?"
         ],
-        "short_id": "T00072",
-        "short_tools": [
-            "interactive_tool_rstudio"
+        "requirements": [
+            {
+                "topic_name": "data-science",
+                "tutorials": [
+                    "cli-basics",
+                    "cli-advanced"
+                ],
+                "type": "internal"
+            }
         ],
+        "short_id": "T00105",
+        "short_tools": [],
         "slides": false,
         "slides_recordings": false,
+        "subtopic": "sciwms",
         "supported_servers": {
-            "exact": [
+            "exact": [],
+            "inexact": [
                 {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 },
                 {
+                    "human": "Galaxy Australia",
+                    "id": "au",
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
                 }
-            ],
-            "inexact": []
+            ]
         },
         "symlink": null,
-        "time_estimation": "65M",
-        "title": "Version Control with Git",
-        "tools": [
-            "interactive_tool_rstudio"
-        ],
+        "time_estimation": "3H",
+        "title": "Make & Snakemake",
+        "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
         "tours": false,
@@ -48031,24 +49230,22 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "bash-git",
+        "tutorial_name": "snakemake",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/bash-git/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/snakemake/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/bash-git/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/bash-git/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/snakemake/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/snakemake/tutorial.json"
         },
         "version": 6,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 48,
-        "visitors": 184
+        "visit_duration": 58,
+        "visitors": 2875,
+        "zenodo_link": "https://zenodo.org/record/5562251"
     },
     {
-        "abbreviations": {
-            "SQL": "Structured Query Language"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -48056,85 +49253,72 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-basic/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-basics/tutorial.json",
         "contributors": [
             {
-                "id": "carpentries",
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "gr",
+                "id": "mcmaniou",
                 "joined": "2021-09",
-                "name": "The Carpentries",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
-                "ror": "0356fgm10",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
+                "name": "Maria Christina Maniou",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mcmaniou/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mcmaniou.json"
             },
             {
                 "affiliations": [
                     "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "email": "D.vrins@live.nl",
-                "former_affiliations": [
-                    "avans-atgm"
+                    "elixir-europe"
                 ],
-                "id": "dirowa",
-                "joined": "2021-10",
-                "linkedin": "Donny Vrins",
-                "name": "Donny Vrins",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dirowa/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/dirowa.json"
+                "elixir_node": "gr",
+                "email": "fpsom@certh.gr",
+                "id": "fpsom",
+                "joined": "2019-03",
+                "linkedin": "fpsom",
+                "matrix": "fpsom:matrix.org",
+                "name": "Fotis E. Psomopoulos",
+                "orcid": "0000-0002-0222-4273",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
+                "twitter": "fopsom",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
             },
             {
-                "affiliations": [
-                    "avans-atgm"
-                ],
-                "id": "bazante1",
-                "joined": "2020-12",
-                "name": "Bazante Sanders",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
+                "id": "carpentries",
+                "joined": "2021-09",
+                "name": "The Carpentries",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
+                "ror": "0356fgm10",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
             },
             {
-                "avatar": "/training-material/shared/images/logo-avans.png",
-                "former_members": [
-                    "dirowa",
-                    "hexylena"
-                ],
-                "id": "avans-atgm",
-                "joined": "2020-11",
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
                 "members": [
-                    "bazante1"
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
                 ],
-                "name": "Avans Hogeschool",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/",
-                "ror": "015d5s513",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/sql-basic",
+        "dir": "topics/data-science/tutorials/python-basics",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -48144,13 +49328,14 @@
             {
                 "topic_name": "data-science",
                 "tutorials": [
-                    "sql-advanced"
+                    "python-plotting",
+                    "python-advanced-np-pd"
                 ],
                 "type": "internal"
             }
         ],
         "hands_on": true,
-        "id": "data-science/sql-basic",
+        "id": "data-science/python-basics",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -48162,70 +49347,32 @@
             "mermaid": false
         },
         "key_points": [
-            "A relational database stores information in tables, each of which has a fixed set of columns and a variable number of records.",
-            "A database manager is a program that manipulates information stored in a database.",
-            "We write queries in a specialized language called SQL to extract information from databases.",
-            "Use SELECT... FROM... to get values from a database table.",
-            "SQL is case-insensitive (but data is case-sensitive).",
-            "The records in a database table are not intrinsically ordered: if we want to display them in some order, we must specify that explicitly with ORDER BY.",
-            "The values in a database are not guaranteed to be unique: if we want to eliminate duplicates, we must specify that explicitly as well using DISTINCT.",
-            "Use WHERE to specify conditions that records must meet in order to be included in a query's results.",
-            "Use AND, OR, and NOT to combine tests.",
-            "Filtering is done on whole records, so conditions can use fields that are not actually displayed.",
-            "Write queries incrementally.",
-            "Queries can do the usual arithmetic operations on values.",
-            "Use UNION to combine the results of two or more queries.",
-            "Databases use a special value called NULL to represent missing information.",
-            "Almost all operations on NULL produce NULL.",
-            "Queries can test for NULLs using IS NULL and IS NOT NULL."
+            "Python is a fairly easy programming language to learn and use, but be mindful of the indexing.",
+            "Python has many libraries offering a variety of capabilities, which makes it popular for beginners, as well as, more experienced users"
         ],
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-16",
+        "mod_date": "2024-02-15",
         "notebook": {
-            "language": "sql"
+            "language": "python",
+            "pyolite": true
         },
         "objectives": [
-            "Explain the difference between a table, a record, and a field.",
-            "Explain the difference between a database and a database manager.",
-            "Write a query to select all values for specific fields from a single table.",
-            "Write queries that display results in a particular order.",
-            "Write queries that eliminate duplicate values from data.",
-            "Write queries that select records that satisfy user-specified conditions.",
-            "Explain the order in which the clauses in a query are executed.",
-            "Write queries that calculate new values for each selected record.",
-            "Explain how databases represent missing information.",
-            "Explain the three-valued logic databases use when manipulating missing information.",
-            "Write queries that handle missing information correctly."
+            "Learn the fundamentals of programming in Python"
         ],
-        "pageviews": 483,
-        "pub_date": "2021-10-11",
+        "pageviews": 1256,
+        "priority": 1,
+        "pub_date": "2021-11-08",
         "questions": [
-            "How can I get data from a database?",
-            "How can I sort a query's results?",
-            "How can I remove duplicate values from a query's results?",
-            "How can I select subsets of data?",
-            "How can I calculate new values on the fly?",
-            "How do databases represent missing information?",
-            "What special handling does missing information require?"
-        ],
-        "quiz": [
-            {
-                "contributors": [
-                    "hexylena"
-                ],
-                "id": "recap.yml",
-                "path": "topics/data-science/tutorials/sql-basic/quiz/recap.yml",
-                "title": "SQL Basics Recap"
-            }
+            "How can I run Python programs?"
         ],
         "requirements": [],
-        "short_id": "T00107",
+        "short_id": "T00083",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "sql",
+        "subtopic": "python",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -48260,11 +49407,8 @@
             ]
         },
         "symlink": null,
-        "tags": [
-            "SQL"
-        ],
-        "time_estimation": "3H",
-        "title": "Introduction to SQL",
+        "time_estimation": "5H",
+        "title": "Introduction to Python",
         "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
@@ -48274,25 +49418,21 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "sql-basic",
+        "tutorial_name": "python-basics",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/sql-basic/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/python-basics/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-basic/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-basic/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-basics/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-basics/tutorial.json"
         },
-        "version": 7,
+        "version": 6,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 101,
-        "visitors": 382,
-        "zenodo_link": null
+        "visit_duration": 115,
+        "visitors": 927
     },
     {
-        "abbreviations": {
-            "SQL": "Structured Query Language"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -48300,16 +49440,8 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-advanced/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/cli-bashcrawl/tutorial.json",
         "contributors": [
-            {
-                "id": "carpentries",
-                "joined": "2021-09",
-                "name": "The Carpentries",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
-                "ror": "0356fgm10",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
@@ -48340,39 +49472,41 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
             {
-                "avatar": "/training-material/shared/images/logo-avans.png",
-                "former_members": [
-                    "dirowa",
-                    "hexylena"
-                ],
-                "id": "avans-atgm",
-                "joined": "2020-11",
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
                 "members": [
-                    "bazante1"
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
                 ],
-                "name": "Avans Hogeschool",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/",
-                "ror": "015d5s513",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/sql-advanced",
+        "dir": "topics/data-science/tutorials/cli-bashcrawl",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "data-science",
-                "tutorials": [
-                    "sql-python"
-                ],
-                "type": "internal"
-            }
-        ],
+        "follow_up_training": [],
         "hands_on": true,
-        "id": "data-science/sql-advanced",
+        "id": "data-science/cli-bashcrawl",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -48384,97 +49518,43 @@
             "mermaid": false
         },
         "key_points": [
-            "Use aggregation functions to combine multiple values.",
-            "Aggregation functions ignore `null` values.",
-            "Aggregation happens after filtering.",
-            "Use GROUP BY to combine subsets separately.",
-            "If no aggregation function is specified for a field, the query may return an arbitrary value for that field.",
-            "Use JOIN to combine data from two tables.",
-            "Use table.field notation to refer to fields when doing joins.",
-            "Every fact should be represented in a database exactly once.",
-            "A join produces all combinations of records from one table with records from another.",
-            "A primary key is a field (or set of fields) whose values uniquely identify the records in a table.",
-            "A foreign key is a field (or set of fields) in one table whose values are a primary key in another table.",
-            "We can eliminate meaningless combinations of records by matching primary keys and foreign keys between tables.",
-            "The most common join condition is matching keys.",
-            "Every value in a database should be atomic.",
-            "Every record should have a unique primary key.",
-            "A database should not contain redundant information.",
-            "Units and similar metadata should be stored with the data.",
-            "Use CREATE and DROP to create and delete tables.",
-            "Use INSERT to add data.",
-            "Use UPDATE to modify existing data.",
-            "Use DELETE to remove data.",
-            "It is simpler and safer to modify data when every record has a unique primary key.",
-            "Do not create dangling references by deleting records that other records refer to.",
-            "General-purpose languages have libraries for accessing databases.",
-            "To connect to a database, a program must use a library specific to that database manager.",
-            "These libraries use a connection-and-cursor model.",
-            "Programs can read query results in batches or all at once.",
-            "Queries should be written using parameter substitution, not string formatting."
+            "Learning linux can be fun!"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2022-10-19",
+        "mod_date": "2023-10-23",
         "notebook": {
-            "language": "sql"
+            "language": "bash"
         },
         "objectives": [
-            "Define aggregation and give examples of its use.",
-            "Write queries that compute aggregated values.",
-            "Trace the execution of a query that performs aggregation.",
-            "Explain how missing data is handled during aggregation.",
-            "Explain the operation of a query that joins two tables.",
-            "Explain how to restrict the output of a query containing a join to only include meaningful combinations of values.",
-            "Write queries that join tables on equal keys.",
-            "Explain what primary and foreign keys are, and why they are useful.",
-            "Explain what an atomic value is.",
-            "Distinguish between atomic and non-atomic values.",
-            "Explain why every value in a database should be atomic.",
-            "Explain what a primary key is and why every record should have one.",
-            "Identify primary keys in database tables.",
-            "Explain why database entries should not contain redundant information.",
-            "Identify redundant information in databases.",
-            "Write statements that create tables.",
-            "Write statements to insert, modify, and delete records.",
-            "Write short programs that execute SQL queries.",
-            "Trace the execution of a program that contains an SQL query.",
-            "Explain why most database applications are written in a general-purpose language rather than in SQL."
+            "Explore the bash dungeon and fight monsters",
+            "Reinforce the learning of CLI basics such as how to change directories, move around, find things, and symlinkings"
         ],
-        "pageviews": 1685,
-        "pub_date": "2021-10-11",
+        "pageviews": 1878,
+        "pub_date": "2021-09-30",
         "questions": [
-            "How can I calculate sums, averages, and other summary values?",
-            "How can I combine data from multiple tables?",
-            "How should I format data in a database, and why?",
-            "How can I create, modify, and delete tables and data?",
-            "How can I access databases from programs written in Python?"
-        ],
-        "quiz": [
-            {
-                "contributors": [
-                    "hexylena"
-                ],
-                "id": "recap.yml",
-                "path": "topics/data-science/tutorials/sql-advanced/quiz/recap.yml",
-                "title": "SQL Advanced Recap"
-            }
+            "How can I move around on my computer?",
+            "How can I see what files and directories I have?",
+            "How can I specify the location of a file or directory on my computer?",
+            "How can I create, copy, and delete files and directories?",
+            "How can I edit files?"
         ],
         "requirements": [
             {
                 "topic_name": "data-science",
                 "tutorials": [
-                    "sql-basic"
+                    "cli-basics",
+                    "cli-advanced"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00106",
+        "short_id": "T00075",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "sql",
+        "subtopic": "bash",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -48510,10 +49590,11 @@
         },
         "symlink": null,
         "tags": [
-            "SQL"
+            "game",
+            "bash"
         ],
-        "time_estimation": "3H",
-        "title": "Advanced SQL",
+        "time_estimation": "2H",
+        "title": "CLI Educational Game - Bashcrawl",
         "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
@@ -48523,20 +49604,20 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "sql-advanced",
+        "tutorial_name": "cli-bashcrawl",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/sql-advanced/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/cli-bashcrawl/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-advanced/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-advanced/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/cli-bashcrawl/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/cli-bashcrawl/tutorial.json"
         },
-        "version": 7,
+        "version": 6,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 33,
-        "visitors": 1330,
-        "zenodo_link": null
+        "visit_duration": 32,
+        "visitors": 1636,
+        "zenodo_link": ""
     },
     {
         "admin_install": {
@@ -48639,7 +49720,7 @@
             "By exploring protein entries in UniProtKB, interpret protein function, taxonomy, structure, interactions, variants, and more.",
             "Use unique identifiers to connect databases, download gene and protein data, visualize and compare sequence features."
         ],
-        "pageviews": 72,
+        "pageviews": 97,
         "pub_date": "2023-09-07",
         "questions": [
             "How can you search for proteins using text, gene, or protein names?",
@@ -48724,15 +49805,11 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 77,
-        "visitors": 66,
+        "visit_duration": 90,
+        "visitors": 88,
         "zenodo_link": ""
     },
     {
-        "abbreviations": {
-            "DAG": "Directed Acyclic Graph",
-            "SciWMS": "Scientific Workflow Management System"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -48740,8 +49817,16 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/snakemake/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-r/tutorial.json",
         "contributors": [
+            {
+                "id": "carpentries",
+                "joined": "2021-09",
+                "name": "The Carpentries",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
+                "ror": "0356fgm10",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
@@ -48771,28 +49856,6 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
-            {
-                "affiliations": [
-                    "avans-atgm"
-                ],
-                "id": "bazante1",
-                "joined": "2020-12",
-                "name": "Bazante Sanders",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
-            },
-            {
-                "email": "D.vrins@live.nl",
-                "former_affiliations": [
-                    "avans-atgm"
-                ],
-                "id": "dirowa",
-                "joined": "2021-10",
-                "linkedin": "Donny Vrins",
-                "name": "Donny Vrins",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dirowa/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/dirowa.json"
-            },
             {
                 "avatar": "/training-material/shared/images/logo-avans.png",
                 "former_members": [
@@ -48810,7 +49873,7 @@
                 "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/snakemake",
+        "dir": "topics/data-science/tutorials/sql-r",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -48818,7 +49881,7 @@
         "feedback_number": 0,
         "follow_up_training": [],
         "hands_on": true,
-        "id": "data-science/snakemake",
+        "id": "data-science/sql-r",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -48830,44 +49893,52 @@
             "mermaid": false
         },
         "key_points": [
-            "Make and Snakemake are ways to write pipelines in a declarative format",
-            "Instead of writing individual actions you wish to take, you describe how to produce each file you need, and the system executes those steps only if they're needed",
-            "If you're doing scientific research you should use Snakemake",
-            "Snakemake can significantly speed up your command line pipelines by providing automatic detection of inputs, and not re-creating them if they don't need",
-            "Snakemake also provides very easy access to paralellisation without complexity.",
-            "But it is more complex than using Galaxy"
+            "Data analysis languages have libraries for accessing databases.",
+            "To connect to a database, a program must use a library specific to that database manager.",
+            "R's libraries can be used to directly query or read from a database.",
+            "Programs can read query results in batches or all at once.",
+            "Queries should be written using parameter substitution, not string formatting.",
+            "R has multiple helper functions to make working with databases easier."
         ],
         "layout": "tutorial_hands_on",
         "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-11",
+        "mod_date": "2023-11-16",
+        "notebook": {
+            "language": "r"
+        },
         "objectives": [
-            "Write a snakefile that does a simple QC and Mapping workflow"
+            "Write short programs that execute SQL queries.",
+            "Trace the execution of a program that contains an SQL query.",
+            "Explain why most database applications are written in a general-purpose language rather than in SQL."
         ],
-        "pageviews": 3709,
-        "pub_date": "2021-11-18",
+        "pageviews": 695,
+        "pub_date": "2021-10-11",
         "questions": [
-            "What is Make & Snakemake",
-            "What is a Makefile/Snakefile",
-            "How do these improve pipelines over simple scripts?",
-            "Why is Snakemake better for scientific research and how can I use it",
-            "How do I use conda envs with Snakemake?"
+            "How can I access databases from programs written in R?"
         ],
         "requirements": [
             {
                 "topic_name": "data-science",
                 "tutorials": [
-                    "cli-basics",
-                    "cli-advanced"
+                    "r-basics",
+                    "r-advanced"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "data-science",
+                "tutorials": [
+                    "sql-advanced"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00105",
+        "short_id": "T00110",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "sciwms",
+        "subtopic": "sql",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -48902,8 +49973,12 @@
             ]
         },
         "symlink": null,
-        "time_estimation": "3H",
-        "title": "Make & Snakemake",
+        "tags": [
+            "SQL",
+            "R"
+        ],
+        "time_estimation": "45M",
+        "title": "SQL with R",
         "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
@@ -48913,20 +49988,20 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "snakemake",
+        "tutorial_name": "sql-r",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/snakemake/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/sql-r/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/snakemake/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/snakemake/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-r/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-r/tutorial.json"
         },
-        "version": 6,
+        "version": 7,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 58,
-        "visitors": 2806,
-        "zenodo_link": "https://zenodo.org/record/5562251"
+        "visit_duration": 33,
+        "visitors": 537,
+        "zenodo_link": null
     },
     {
         "admin_install": {
@@ -48936,16 +50011,8 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/cli-basics/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-math/tutorial.json",
         "contributors": [
-            {
-                "id": "carpentries",
-                "joined": "2021-09",
-                "name": "The Carpentries",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
-                "ror": "0356fgm10",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
@@ -48975,6 +50042,18 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
+            {
+                "email": "D.vrins@live.nl",
+                "former_affiliations": [
+                    "avans-atgm"
+                ],
+                "id": "dirowa",
+                "joined": "2021-10",
+                "linkedin": "Donny Vrins",
+                "name": "Donny Vrins",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dirowa/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/dirowa.json"
+            },
             {
                 "affiliations": [
                     "avans-atgm"
@@ -48984,6 +50063,170 @@
                 "name": "Bazante Sanders",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
+            }
+        ],
+        "dir": "topics/data-science/tutorials/python-math",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [],
+        "hands_on": true,
+        "id": "data-science/python-math",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": 1547,
+            "mermaid": false
+        },
+        "key_points": [
+            "Converting mathematics equation to python is pretty easy!",
+            "In real life you'll occasionally need to do this, either converting from a formula you read in a paper, or a description of an algorithm, into code that you'll re-use.",
+            "Did you forget how a particular module or function works? Try `help()`"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-02-13",
+        "notebook": {
+            "language": "python",
+            "pyolite": true
+        },
+        "objectives": [
+            "Understand the fundamentals of object assignment and math in python and can write simple statements and execute calcualtions in order to be able to summarize the results of calculations and classify valid and invalid statements.",
+            "Translate some known math functions (e.g. euclidean distance, root algorithm) into python to transfer concepts from mathematics lessons directly into Python."
+        ],
+        "pageviews": 678,
+        "priority": 1,
+        "pub_date": "2022-04-25",
+        "questions": [
+            "How do I do math in Python?"
+        ],
+        "requirements": [],
+        "short_id": "T00094",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "python-modular",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "time_estimation": "30M",
+        "title": "Python - Math",
+        "tools": [],
+        "topic_name": "data-science",
+        "topic_name_human": "Foundations of Data Science",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "python-math",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/python-math/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-math/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-math/tutorial.json"
+        },
+        "version": 4,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 54,
+        "visitors": 539
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-game/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "NUKnightLab",
+                "hexylena"
+            ],
+            "funding": [
+                "gallantries",
+                "avans-atgm"
+            ]
+        },
+        "contributors": [
+            {
+                "id": "NUKnightLab",
+                "joined": "2021-10",
+                "name": "NU Knight Lab",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/NUKnightLab/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/NUKnightLab.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
             {
                 "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
@@ -49028,24 +50271,16 @@
                 "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/cli-basics",
+        "copyright": "Copyright (c) 2018 NUKnightLab",
+        "dir": "topics/data-science/tutorials/sql-game",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "data-science",
-                "tutorials": [
-                    "cli-advanced",
-                    "cli-bashcrawl"
-                ],
-                "type": "internal"
-            }
-        ],
+        "follow_up_training": [],
         "hands_on": true,
-        "id": "data-science/cli-basics",
+        "id": "data-science/sql-game",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -49057,69 +50292,39 @@
             "mermaid": false
         },
         "key_points": [
-            "A shell is a program whose primary purpose is to read commands and run other programs.",
-            "This lesson uses Bash, the default shell in many implementations of Unix.",
-            "Programs can be run in Bash by entering commands at the command-line prompt.",
-            "The shell's main advantages are its high action-to-keystroke ratio, its support for automating repetitive tasks, and its capacity to access networked machines.",
-            "The shell's main disadvantages are its primarily textual nature and how cryptic its commands and operation can be.",
-            "The file system is responsible for managing information on the disk.",
-            "Information is stored in files, which are stored in directories (folders).",
-            "Directories can also store other directories, which then form a directory tree.",
-            "`cd [path]` changes the current working directory.",
-            "`ls [path]` prints a listing of a specific file or directory; `ls` on its own lists the current working directory.",
-            "`pwd` prints the user's current working directory.",
-            "`/` on its own is the root directory of the whole file system.",
-            "Most commands take options (flags) that begin with a `-`.",
-            "A relative path specifies a location starting from the current location.",
-            "An absolute path specifies a location from the root of the file system.",
-            "Directory names in a path are separated with `/` on Unix, but `\\` on Windows.",
-            "`..` means 'the directory above the current one'; `.` on its own means 'the current directory'.",
-            "`cp [old] [new]` copies a file.",
-            "`mkdir [path]` creates a new directory.",
-            "`mv [old] [new]` moves (renames) a file or directory.",
-            "`rm [path]` removes (deletes) a file.",
-            "`*` matches zero or more characters in a filename, so `*.txt` matches all files ending in `.txt`.",
-            "`?` matches any single character in a filename, so `?.txt` matches `a.txt` but not `any.txt`.",
-            "Use of the Control key may be described in many ways, including `Ctrl-X`, `Control-X`, and `^X`.",
-            "The shell does not have a trash bin: once something is deleted, it's really gone.",
-            "Most files' names are `something.extension`. The extension isn't required, and doesn't guarantee anything, but is normally used to indicate the type of data in the file.",
-            "Depending on the type of work you do, you may need a more powerful text editor than Nano."
+            "Learning SQL can be fun!"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-10-23",
+        "level": "Intermediate",
+        "license": "MIT",
+        "mod_date": "2023-11-23",
         "notebook": {
-            "language": "bash"
+            "language": "python"
         },
         "objectives": [
-            "Explain how the shell relates to the keyboard, the screen, the operating system, and users' programs.",
-            "Explain when and why command-line interfaces should be used instead of graphical interfaces.",
-            "Explain the similarities and differences between a file and a directory.",
-            "Translate an absolute path into a relative path and vice versa.",
-            "Construct absolute and relative paths that identify specific files and directories.",
-            "Use options and arguments to change the behaviour of a shell command.",
-            "Demonstrate the use of tab completion and explain its advantages.",
-            "Create a directory hierarchy that matches a given diagram.",
-            "Create files in that hierarchy using an editor or by copying and renaming existing files.",
-            "Delete, copy and move specified files and/or directories."
+            "Explore SQL City and discover who committed the murder",
+            "Reinforce your experiences with SQL such as querying, filtering, and joining data."
         ],
-        "pageviews": 1068,
-        "pub_date": "2021-09-30",
+        "pageviews": 588,
+        "pub_date": "2021-10-11",
         "questions": [
-            "What is a command shell and why would I use one?",
-            "How can I move around on my computer?",
-            "How can I see what files and directories I have?",
-            "How can I specify the location of a file or directory on my computer?",
-            "How can I create, copy, and delete files and directories?",
-            "How can I edit files?"
+            "Who did the crime?"
         ],
-        "requirements": [],
-        "short_id": "T00076",
+        "requirements": [
+            {
+                "topic_name": "data-science",
+                "tutorials": [
+                    "sql-basic",
+                    "sql-advanced"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00108",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "bash",
+        "subtopic": "sql",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -49155,10 +50360,11 @@
         },
         "symlink": null,
         "tags": [
-            "bash"
+            "game",
+            "SQL"
         ],
-        "time_estimation": "1H",
-        "title": "CLI basics",
+        "time_estimation": "2H",
+        "title": "SQL Educational Game - Murder Mystery",
         "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
@@ -49168,19 +50374,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "cli-basics",
+        "tutorial_name": "sql-game",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/cli-basics/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/sql-game/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/cli-basics/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/cli-basics/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-game/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-game/tutorial.json"
         },
-        "version": 9,
+        "version": 6,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 164,
-        "visitors": 760,
+        "visit_duration": 19,
+        "visitors": 545,
         "zenodo_link": ""
     },
     {
@@ -49191,18 +50397,54 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-basics/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/r-basics/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "carpentries"
+            ],
+            "editing": [
+                "bebatut",
+                "fpsom",
+                "tobyhodges"
+            ],
+            "funding": [
+                "gallantries"
+            ]
+        },
         "contributors": [
+            {
+                "id": "carpentries",
+                "joined": "2021-09",
+                "name": "The Carpentries",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
+                "ror": "0356fgm10",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
+            },
             {
                 "affiliations": [
+                    "gallantries",
+                    "ifb",
                     "elixir-europe"
                 ],
-                "elixir_node": "gr",
-                "id": "mcmaniou",
-                "joined": "2021-09",
-                "name": "Maria Christina Maniou",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mcmaniou/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mcmaniou.json"
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             },
             {
                 "affiliations": [
@@ -49222,12 +50464,14 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
             },
             {
-                "id": "carpentries",
-                "joined": "2021-09",
-                "name": "The Carpentries",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
-                "ror": "0356fgm10",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
+                "email": "tbyhdgs@gmail.com",
+                "id": "tobyhodges",
+                "joined": "2019-07",
+                "name": "Toby Hodges",
+                "orcid": "0000-0003-1766-456X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tobyhodges/",
+                "twitter": "tbyhdgs",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tobyhodges.json"
             },
             {
                 "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
@@ -49256,98 +50500,123 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/python-basics",
+        "dir": "topics/data-science/tutorials/r-basics",
         "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "follow_up_training": [
             {
                 "topic_name": "data-science",
                 "tutorials": [
-                    "python-plotting",
-                    "python-advanced-np-pd"
+                    "r-advanced"
                 ],
                 "type": "internal"
             }
         ],
         "hands_on": true,
-        "id": "data-science/python-basics",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
+        "id": "data-science/r-basics",
+        "inexact_supported_servers": [],
         "js_requirements": {
-            "mathjax": null,
+            "mathjax": 11549,
             "mermaid": false
         },
         "key_points": [
-            "Python is a fairly easy programming language to learn and use, but be mindful of the indexing.",
-            "Python has many libraries offering a variety of capabilities, which makes it popular for beginners, as well as, more experienced users"
+            "It is important to understand how data are organised by R in a given object type (e.g. numeric, character, logical, etc.) and how the mode of that type determines how R will operate on that data."
         ],
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-02-15",
-        "notebook": {
-            "language": "python",
-            "pyolite": true
-        },
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Learn the fundamentals of programming in Python"
+            "Know advantages of analyzing data using R within Galaxy.",
+            "Compose an R script file containing comments, commands, objects, and functions.",
+            "Be able to work with objects (i.e. applying mathematical and logical operators, subsetting, retrieving values, etc)."
         ],
-        "pageviews": 1181,
+        "pageviews": 2990,
         "priority": 1,
-        "pub_date": "2021-11-08",
+        "pub_date": "2019-10-08",
         "questions": [
-            "How can I run Python programs?"
+            "What are the basic features and objects of the R language?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "s3by01",
+                    "annefou",
+                    "kxk302"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "50M",
+                "speakers": [
+                    "fpsom"
+                ],
+                "youtube_id": "MKkQDh5Nguc"
+            }
+        ],
+        "redirect_from": [
+            "/topics/introduction/tutorials/r-basics/tutorial",
+            "/short/data-science/r-basics",
+            "/short/T00103"
+        ],
+        "requirements": [
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "rstudio"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00103",
+        "short_tools": [
+            "interactive_tool_rstudio"
         ],
-        "requirements": [],
-        "short_id": "T00083",
-        "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "python",
+        "subtopic": "r",
         "supported_servers": {
-            "exact": [],
-            "inexact": [
+            "exact": [
                 {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
                 {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 },
                 {
-                    "human": "Galaxy Australia",
-                    "id": "au",
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
                 }
-            ]
+            ],
+            "inexact": []
         },
         "symlink": null,
-        "time_estimation": "5H",
-        "title": "Introduction to Python",
-        "tools": [],
+        "tags": [
+            "interactive-tools",
+            "R"
+        ],
+        "time_estimation": "3H",
+        "title": "R basics in Galaxy",
+        "tools": [
+            "interactive_tool_rstudio"
+        ],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
         "tours": false,
@@ -49356,21 +50625,25 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "python-basics",
+        "tutorial_name": "r-basics",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/python-basics/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/r-basics/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-basics/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-basics/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/r-basics/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/r-basics/tutorial.json"
         },
-        "version": 6,
+        "version": 11,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 100,
-        "visitors": 872
+        "visit_duration": 132,
+        "visitors": 2134,
+        "zenodo_link": ""
     },
     {
+        "abbreviations": {
+            "SQL": "Structured Query Language"
+        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -49378,8 +50651,16 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-math/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-basic/tutorial.json",
         "contributors": [
+            {
+                "id": "carpentries",
+                "joined": "2021-09",
+                "name": "The Carpentries",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
+                "ror": "0356fgm10",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
@@ -49430,17 +50711,41 @@
                 "name": "Bazante Sanders",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/logo-avans.png",
+                "former_members": [
+                    "dirowa",
+                    "hexylena"
+                ],
+                "id": "avans-atgm",
+                "joined": "2020-11",
+                "members": [
+                    "bazante1"
+                ],
+                "name": "Avans Hogeschool",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/",
+                "ror": "015d5s513",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/python-math",
+        "dir": "topics/data-science/tutorials/sql-basic",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [],
+        "follow_up_training": [
+            {
+                "topic_name": "data-science",
+                "tutorials": [
+                    "sql-advanced"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "data-science/python-math",
+        "id": "data-science/sql-basic",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -49448,38 +50753,74 @@
             "UseGalaxy.fr"
         ],
         "js_requirements": {
-            "mathjax": 1547,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Converting mathematics equation to python is pretty easy!",
-            "In real life you'll occasionally need to do this, either converting from a formula you read in a paper, or a description of an algorithm, into code that you'll re-use.",
-            "Did you forget how a particular module or function works? Try `help()`"
+            "A relational database stores information in tables, each of which has a fixed set of columns and a variable number of records.",
+            "A database manager is a program that manipulates information stored in a database.",
+            "We write queries in a specialized language called SQL to extract information from databases.",
+            "Use SELECT... FROM... to get values from a database table.",
+            "SQL is case-insensitive (but data is case-sensitive).",
+            "The records in a database table are not intrinsically ordered: if we want to display them in some order, we must specify that explicitly with ORDER BY.",
+            "The values in a database are not guaranteed to be unique: if we want to eliminate duplicates, we must specify that explicitly as well using DISTINCT.",
+            "Use WHERE to specify conditions that records must meet in order to be included in a query's results.",
+            "Use AND, OR, and NOT to combine tests.",
+            "Filtering is done on whole records, so conditions can use fields that are not actually displayed.",
+            "Write queries incrementally.",
+            "Queries can do the usual arithmetic operations on values.",
+            "Use UNION to combine the results of two or more queries.",
+            "Databases use a special value called NULL to represent missing information.",
+            "Almost all operations on NULL produce NULL.",
+            "Queries can test for NULLs using IS NULL and IS NOT NULL."
         ],
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-02-13",
+        "mod_date": "2023-11-16",
         "notebook": {
-            "language": "python",
-            "pyolite": true
+            "language": "sql"
         },
         "objectives": [
-            "Understand the fundamentals of object assignment and math in python and can write simple statements and execute calcualtions in order to be able to summarize the results of calculations and classify valid and invalid statements.",
-            "Translate some known math functions (e.g. euclidean distance, root algorithm) into python to transfer concepts from mathematics lessons directly into Python."
+            "Explain the difference between a table, a record, and a field.",
+            "Explain the difference between a database and a database manager.",
+            "Write a query to select all values for specific fields from a single table.",
+            "Write queries that display results in a particular order.",
+            "Write queries that eliminate duplicate values from data.",
+            "Write queries that select records that satisfy user-specified conditions.",
+            "Explain the order in which the clauses in a query are executed.",
+            "Write queries that calculate new values for each selected record.",
+            "Explain how databases represent missing information.",
+            "Explain the three-valued logic databases use when manipulating missing information.",
+            "Write queries that handle missing information correctly."
         ],
-        "pageviews": 599,
-        "priority": 1,
-        "pub_date": "2022-04-25",
+        "pageviews": 521,
+        "pub_date": "2021-10-11",
         "questions": [
-            "How do I do math in Python?"
+            "How can I get data from a database?",
+            "How can I sort a query's results?",
+            "How can I remove duplicate values from a query's results?",
+            "How can I select subsets of data?",
+            "How can I calculate new values on the fly?",
+            "How do databases represent missing information?",
+            "What special handling does missing information require?"
+        ],
+        "quiz": [
+            {
+                "contributors": [
+                    "hexylena"
+                ],
+                "id": "recap.yml",
+                "path": "topics/data-science/tutorials/sql-basic/quiz/recap.yml",
+                "title": "SQL Basics Recap"
+            }
         ],
         "requirements": [],
-        "short_id": "T00094",
+        "short_id": "T00107",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "python-modular",
+        "subtopic": "sql",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -49514,8 +50855,11 @@
             ]
         },
         "symlink": null,
-        "time_estimation": "30M",
-        "title": "Python - Math",
+        "tags": [
+            "SQL"
+        ],
+        "time_estimation": "3H",
+        "title": "Introduction to SQL",
         "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
@@ -49525,19 +50869,20 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "python-math",
+        "tutorial_name": "sql-basic",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/python-math/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/sql-basic/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-math/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-math/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-basic/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-basic/tutorial.json"
         },
-        "version": 4,
+        "version": 7,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 62,
-        "visitors": 471
+        "visit_duration": 98,
+        "visitors": 408,
+        "zenodo_link": null
     },
     {
         "admin_install": {
@@ -49714,7 +51059,7 @@
             "Use the output of one command as the command-line argument(s) to another command.",
             "Explain what is meant by 'text' and 'binary' files, and why many common tools don't handle the latter well."
         ],
-        "pageviews": 841,
+        "pageviews": 873,
         "pub_date": "2021-09-30",
         "questions": [
             "How can I combine existing commands to do new things?",
@@ -49795,8 +51140,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 134,
-        "visitors": 676,
+        "visit_duration": 131,
+        "visitors": 701,
         "zenodo_link": ""
     },
     {
@@ -49807,7 +51152,7 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-r/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/cli-basics/tutorial.json",
         "contributors": [
             {
                 "id": "carpentries",
@@ -49846,6 +51191,42 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
+            {
+                "affiliations": [
+                    "avans-atgm"
+                ],
+                "id": "bazante1",
+                "joined": "2020-12",
+                "name": "Bazante Sanders",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            },
             {
                 "avatar": "/training-material/shared/images/logo-avans.png",
                 "former_members": [
@@ -49863,15 +51244,24 @@
                 "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/sql-r",
+        "dir": "topics/data-science/tutorials/cli-basics",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [],
+        "follow_up_training": [
+            {
+                "topic_name": "data-science",
+                "tutorials": [
+                    "cli-advanced",
+                    "cli-bashcrawl"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "data-science/sql-r",
+        "id": "data-science/cli-basics",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -49883,52 +51273,69 @@
             "mermaid": false
         },
         "key_points": [
-            "Data analysis languages have libraries for accessing databases.",
-            "To connect to a database, a program must use a library specific to that database manager.",
-            "R's libraries can be used to directly query or read from a database.",
-            "Programs can read query results in batches or all at once.",
-            "Queries should be written using parameter substitution, not string formatting.",
-            "R has multiple helper functions to make working with databases easier."
+            "A shell is a program whose primary purpose is to read commands and run other programs.",
+            "This lesson uses Bash, the default shell in many implementations of Unix.",
+            "Programs can be run in Bash by entering commands at the command-line prompt.",
+            "The shell's main advantages are its high action-to-keystroke ratio, its support for automating repetitive tasks, and its capacity to access networked machines.",
+            "The shell's main disadvantages are its primarily textual nature and how cryptic its commands and operation can be.",
+            "The file system is responsible for managing information on the disk.",
+            "Information is stored in files, which are stored in directories (folders).",
+            "Directories can also store other directories, which then form a directory tree.",
+            "`cd [path]` changes the current working directory.",
+            "`ls [path]` prints a listing of a specific file or directory; `ls` on its own lists the current working directory.",
+            "`pwd` prints the user's current working directory.",
+            "`/` on its own is the root directory of the whole file system.",
+            "Most commands take options (flags) that begin with a `-`.",
+            "A relative path specifies a location starting from the current location.",
+            "An absolute path specifies a location from the root of the file system.",
+            "Directory names in a path are separated with `/` on Unix, but `\\` on Windows.",
+            "`..` means 'the directory above the current one'; `.` on its own means 'the current directory'.",
+            "`cp [old] [new]` copies a file.",
+            "`mkdir [path]` creates a new directory.",
+            "`mv [old] [new]` moves (renames) a file or directory.",
+            "`rm [path]` removes (deletes) a file.",
+            "`*` matches zero or more characters in a filename, so `*.txt` matches all files ending in `.txt`.",
+            "`?` matches any single character in a filename, so `?.txt` matches `a.txt` but not `any.txt`.",
+            "Use of the Control key may be described in many ways, including `Ctrl-X`, `Control-X`, and `^X`.",
+            "The shell does not have a trash bin: once something is deleted, it's really gone.",
+            "Most files' names are `something.extension`. The extension isn't required, and doesn't guarantee anything, but is normally used to indicate the type of data in the file.",
+            "Depending on the type of work you do, you may need a more powerful text editor than Nano."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-16",
+        "mod_date": "2023-10-23",
         "notebook": {
-            "language": "r"
+            "language": "bash"
         },
         "objectives": [
-            "Write short programs that execute SQL queries.",
-            "Trace the execution of a program that contains an SQL query.",
-            "Explain why most database applications are written in a general-purpose language rather than in SQL."
+            "Explain how the shell relates to the keyboard, the screen, the operating system, and users' programs.",
+            "Explain when and why command-line interfaces should be used instead of graphical interfaces.",
+            "Explain the similarities and differences between a file and a directory.",
+            "Translate an absolute path into a relative path and vice versa.",
+            "Construct absolute and relative paths that identify specific files and directories.",
+            "Use options and arguments to change the behaviour of a shell command.",
+            "Demonstrate the use of tab completion and explain its advantages.",
+            "Create a directory hierarchy that matches a given diagram.",
+            "Create files in that hierarchy using an editor or by copying and renaming existing files.",
+            "Delete, copy and move specified files and/or directories."
         ],
-        "pageviews": 670,
-        "pub_date": "2021-10-11",
+        "pageviews": 1112,
+        "pub_date": "2021-09-30",
         "questions": [
-            "How can I access databases from programs written in R?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "data-science",
-                "tutorials": [
-                    "r-basics",
-                    "r-advanced"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "data-science",
-                "tutorials": [
-                    "sql-advanced"
-                ],
-                "type": "internal"
-            }
+            "What is a command shell and why would I use one?",
+            "How can I move around on my computer?",
+            "How can I see what files and directories I have?",
+            "How can I specify the location of a file or directory on my computer?",
+            "How can I create, copy, and delete files and directories?",
+            "How can I edit files?"
         ],
-        "short_id": "T00110",
+        "requirements": [],
+        "short_id": "T00076",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "sql",
+        "subtopic": "bash",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -49964,11 +51371,10 @@
         },
         "symlink": null,
         "tags": [
-            "SQL",
-            "R"
+            "bash"
         ],
-        "time_estimation": "45M",
-        "title": "SQL with R",
+        "time_estimation": "1H",
+        "title": "CLI basics",
         "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
@@ -49978,20 +51384,20 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "sql-r",
+        "tutorial_name": "cli-basics",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/sql-r/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/cli-basics/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-r/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-r/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/cli-basics/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/cli-basics/tutorial.json"
         },
-        "version": 7,
+        "version": 9,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 35,
-        "visitors": 512,
-        "zenodo_link": null
+        "visit_duration": 167,
+        "visitors": 793,
+        "zenodo_link": ""
     },
     {
         "admin_install": {
@@ -50001,8 +51407,76 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/cli-bashcrawl/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/bash-variant-calling/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "Sofokli5",
+                "fpsom",
+                "shiltemann",
+                "hexylena",
+                "carpentries"
+            ],
+            "funding": [
+                "gallantries"
+            ]
+        },
         "contributors": [
+            {
+                "email": "sofoskeisaris@gmail.com",
+                "id": "Sofokli5",
+                "joined": "2022-05",
+                "name": "Sofoklis Keisaris",
+                "orcid": "0000-0002-4833-4726",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Sofokli5/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Sofokli5.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "elixir-europe"
+                ],
+                "elixir_node": "gr",
+                "email": "fpsom@certh.gr",
+                "id": "fpsom",
+                "joined": "2019-03",
+                "linkedin": "fpsom",
+                "matrix": "fpsom:matrix.org",
+                "name": "Fotis E. Psomopoulos",
+                "orcid": "0000-0002-0222-4273",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
+                "twitter": "fopsom",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
+            },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
@@ -50032,6 +51506,14 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
+            {
+                "id": "carpentries",
+                "joined": "2021-09",
+                "name": "The Carpentries",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
+                "ror": "0356fgm10",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
+            },
             {
                 "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
                 "end_date": "2023-09-30",
@@ -50059,15 +51541,14 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/cli-bashcrawl",
+        "dir": "topics/data-science/tutorials/bash-variant-calling",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [],
         "hands_on": true,
-        "id": "data-science/cli-bashcrawl",
+        "id": "data-science/bash-variant-calling",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -50079,43 +51560,27 @@
             "mermaid": false
         },
         "key_points": [
-            "Learning linux can be fun!"
+            "Bioinformatic command line tools are collections of commands that can be used to carry out bioinformatic analyses.",
+            "To use most powerful bioinformatic tools, you will need to use the command line.",
+            "There are many different file formats for storing genomics data. It is important to understand what type of information is contained in each file, and how it was derived."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
         "license": "CC-BY-4.0",
         "mod_date": "2023-10-23",
-        "notebook": {
-            "language": "bash"
-        },
         "objectives": [
-            "Explore the bash dungeon and fight monsters",
-            "Reinforce the learning of CLI basics such as how to change directories, move around, find things, and symlinkings"
+            "Understand the steps involved in variant calling.",
+            "Describe the types of data formats encountered during variant calling.",
+            "Use command line tools to perform variant calling."
         ],
-        "pageviews": 1800,
-        "pub_date": "2021-09-30",
+        "pageviews": 7905,
+        "pub_date": "2022-07-07",
         "questions": [
-            "How can I move around on my computer?",
-            "How can I see what files and directories I have?",
-            "How can I specify the location of a file or directory on my computer?",
-            "How can I create, copy, and delete files and directories?",
-            "How can I edit files?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "data-science",
-                "tutorials": [
-                    "cli-basics",
-                    "cli-advanced"
-                ],
-                "type": "internal"
-            }
+            "How do I find sequence variants between my sample and a reference genome?"
         ],
-        "short_id": "T00075",
+        "short_id": "T00073",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "bash",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -50150,12 +51615,8 @@
             ]
         },
         "symlink": null,
-        "tags": [
-            "game",
-            "bash"
-        ],
-        "time_estimation": "2H",
-        "title": "CLI Educational Game - Bashcrawl",
+        "time_estimation": "50M",
+        "title": "Variant Calling Workflow",
         "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
@@ -50165,22 +51626,24 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "cli-bashcrawl",
+        "tutorial_name": "bash-variant-calling",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/cli-bashcrawl/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/bash-variant-calling/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/cli-bashcrawl/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/cli-bashcrawl/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/bash-variant-calling/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/bash-variant-calling/tutorial.json"
         },
-        "version": 6,
+        "version": 7,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 33,
-        "visitors": 1566,
-        "zenodo_link": ""
+        "visit_duration": 120,
+        "visitors": 5980
     },
     {
+        "abbreviations": {
+            "SQL": "Structured Query Language"
+        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -50188,24 +51651,15 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-game/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "NUKnightLab",
-                "hexylena"
-            ],
-            "funding": [
-                "gallantries",
-                "avans-atgm"
-            ]
-        },
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-advanced/tutorial.json",
         "contributors": [
             {
-                "id": "NUKnightLab",
-                "joined": "2021-10",
-                "name": "NU Knight Lab",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/NUKnightLab/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/NUKnightLab.json"
+                "id": "carpentries",
+                "joined": "2021-09",
+                "name": "The Carpentries",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
+                "ror": "0356fgm10",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
             },
             {
                 "affiliations": [
@@ -50236,32 +51690,6 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
-            },
             {
                 "avatar": "/training-material/shared/images/logo-avans.png",
                 "former_members": [
@@ -50279,16 +51707,23 @@
                 "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
             }
         ],
-        "copyright": "Copyright (c) 2018 NUKnightLab",
-        "dir": "topics/data-science/tutorials/sql-game",
+        "dir": "topics/data-science/tutorials/sql-advanced",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [],
+        "follow_up_training": [
+            {
+                "topic_name": "data-science",
+                "tutorials": [
+                    "sql-python"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "data-science/sql-game",
+        "id": "data-science/sql-advanced",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -50300,35 +51735,93 @@
             "mermaid": false
         },
         "key_points": [
-            "Learning SQL can be fun!"
+            "Use aggregation functions to combine multiple values.",
+            "Aggregation functions ignore `null` values.",
+            "Aggregation happens after filtering.",
+            "Use GROUP BY to combine subsets separately.",
+            "If no aggregation function is specified for a field, the query may return an arbitrary value for that field.",
+            "Use JOIN to combine data from two tables.",
+            "Use table.field notation to refer to fields when doing joins.",
+            "Every fact should be represented in a database exactly once.",
+            "A join produces all combinations of records from one table with records from another.",
+            "A primary key is a field (or set of fields) whose values uniquely identify the records in a table.",
+            "A foreign key is a field (or set of fields) in one table whose values are a primary key in another table.",
+            "We can eliminate meaningless combinations of records by matching primary keys and foreign keys between tables.",
+            "The most common join condition is matching keys.",
+            "Every value in a database should be atomic.",
+            "Every record should have a unique primary key.",
+            "A database should not contain redundant information.",
+            "Units and similar metadata should be stored with the data.",
+            "Use CREATE and DROP to create and delete tables.",
+            "Use INSERT to add data.",
+            "Use UPDATE to modify existing data.",
+            "Use DELETE to remove data.",
+            "It is simpler and safer to modify data when every record has a unique primary key.",
+            "Do not create dangling references by deleting records that other records refer to.",
+            "General-purpose languages have libraries for accessing databases.",
+            "To connect to a database, a program must use a library specific to that database manager.",
+            "These libraries use a connection-and-cursor model.",
+            "Programs can read query results in batches or all at once.",
+            "Queries should be written using parameter substitution, not string formatting."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "MIT",
-        "mod_date": "2023-11-23",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-26",
         "notebook": {
-            "language": "python"
+            "language": "sql"
         },
         "objectives": [
-            "Explore SQL City and discover who committed the murder",
-            "Reinforce your experiences with SQL such as querying, filtering, and joining data."
+            "Define aggregation and give examples of its use.",
+            "Write queries that compute aggregated values.",
+            "Trace the execution of a query that performs aggregation.",
+            "Explain how missing data is handled during aggregation.",
+            "Explain the operation of a query that joins two tables.",
+            "Explain how to restrict the output of a query containing a join to only include meaningful combinations of values.",
+            "Write queries that join tables on equal keys.",
+            "Explain what primary and foreign keys are, and why they are useful.",
+            "Explain what an atomic value is.",
+            "Distinguish between atomic and non-atomic values.",
+            "Explain why every value in a database should be atomic.",
+            "Explain what a primary key is and why every record should have one.",
+            "Identify primary keys in database tables.",
+            "Explain why database entries should not contain redundant information.",
+            "Identify redundant information in databases.",
+            "Write statements that create tables.",
+            "Write statements to insert, modify, and delete records.",
+            "Write short programs that execute SQL queries.",
+            "Trace the execution of a program that contains an SQL query.",
+            "Explain why most database applications are written in a general-purpose language rather than in SQL."
         ],
-        "pageviews": 576,
+        "pageviews": 1711,
         "pub_date": "2021-10-11",
         "questions": [
-            "Who did the crime?"
+            "How can I calculate sums, averages, and other summary values?",
+            "How can I combine data from multiple tables?",
+            "How should I format data in a database, and why?",
+            "How can I create, modify, and delete tables and data?",
+            "How can I access databases from programs written in Python?"
+        ],
+        "quiz": [
+            {
+                "contributors": [
+                    "hexylena"
+                ],
+                "id": "recap.yml",
+                "path": "topics/data-science/tutorials/sql-advanced/quiz/recap.yml",
+                "title": "SQL Advanced Recap"
+            }
         ],
         "requirements": [
             {
                 "topic_name": "data-science",
                 "tutorials": [
-                    "sql-basic",
-                    "sql-advanced"
+                    "sql-basic"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00108",
+        "short_id": "T00106",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
@@ -50368,11 +51861,10 @@
         },
         "symlink": null,
         "tags": [
-            "game",
             "SQL"
         ],
-        "time_estimation": "2H",
-        "title": "SQL Educational Game - Murder Mystery",
+        "time_estimation": "3H",
+        "title": "Advanced SQL",
         "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
@@ -50382,20 +51874,20 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "sql-game",
+        "tutorial_name": "sql-advanced",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/sql-game/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/sql-advanced/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-game/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-game/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-advanced/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-advanced/tutorial.json"
         },
-        "version": 6,
+        "version": 8,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 19,
-        "visitors": 533,
-        "zenodo_link": ""
+        "visit_duration": 34,
+        "visitors": 1354,
+        "zenodo_link": null
     },
     {
         "admin_install": {
@@ -50405,20 +51897,7 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/r-basics/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "carpentries"
-            ],
-            "editing": [
-                "bebatut",
-                "fpsom",
-                "tobyhodges"
-            ],
-            "funding": [
-                "gallantries"
-            ]
-        },
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-python/tutorial.json",
         "contributors": [
             {
                 "id": "carpentries",
@@ -50431,448 +51910,147 @@
             {
                 "affiliations": [
                     "gallantries",
-                    "ifb",
-                    "elixir-europe"
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
                 ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
                 "joined": "2017-09",
-                "linkedin": "berenicebatut",
                 "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
                 },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
             {
-                "affiliations": [
-                    "gallantries",
-                    "elixir-europe"
+                "avatar": "/training-material/shared/images/logo-avans.png",
+                "former_members": [
+                    "dirowa",
+                    "hexylena"
                 ],
-                "elixir_node": "gr",
-                "email": "fpsom@certh.gr",
-                "id": "fpsom",
-                "joined": "2019-03",
-                "linkedin": "fpsom",
-                "matrix": "fpsom:matrix.org",
-                "name": "Fotis E. Psomopoulos",
-                "orcid": "0000-0002-0222-4273",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
-                "twitter": "fopsom",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
-            },
-            {
-                "email": "tbyhdgs@gmail.com",
-                "id": "tobyhodges",
-                "joined": "2019-07",
-                "name": "Toby Hodges",
-                "orcid": "0000-0003-1766-456X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tobyhodges/",
-                "twitter": "tbyhdgs",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tobyhodges.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
+                "id": "avans-atgm",
+                "joined": "2020-11",
                 "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
+                    "bazante1"
                 ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+                "name": "Avans Hogeschool",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/",
+                "ror": "015d5s513",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/r-basics",
+        "dir": "topics/data-science/tutorials/sql-python",
         "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "data-science",
-                "tutorials": [
-                    "r-advanced"
-                ],
-                "type": "internal"
-            }
-        ],
+        "follow_up_training": [],
         "hands_on": true,
-        "id": "data-science/r-basics",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": 11549,
-            "mermaid": false
-        },
-        "key_points": [
-            "It is important to understand how data are organised by R in a given object type (e.g. numeric, character, logical, etc.) and how the mode of that type determines how R will operate on that data."
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Introductory",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
-        "objectives": [
-            "Know advantages of analyzing data using R within Galaxy.",
-            "Compose an R script file containing comments, commands, objects, and functions.",
-            "Be able to work with objects (i.e. applying mathematical and logical operators, subsetting, retrieving values, etc)."
-        ],
-        "pageviews": 2887,
-        "priority": 1,
-        "pub_date": "2019-10-08",
-        "questions": [
-            "What are the basic features and objects of the R language?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "s3by01",
-                    "annefou",
-                    "kxk302"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "50M",
-                "speakers": [
-                    "fpsom"
-                ],
-                "youtube_id": "MKkQDh5Nguc"
-            }
-        ],
-        "redirect_from": [
-            "/topics/introduction/tutorials/r-basics/tutorial",
-            "/short/data-science/r-basics",
-            "/short/T00103"
-        ],
-        "requirements": [
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "rstudio"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00103",
-        "short_tools": [
-            "interactive_tool_rstudio"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "r",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "interactive-tools",
-            "R"
-        ],
-        "time_estimation": "3H",
-        "title": "R basics in Galaxy",
-        "tools": [
-            "interactive_tool_rstudio"
-        ],
-        "topic_name": "data-science",
-        "topic_name_human": "Foundations of Data Science",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "r-basics",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/r-basics/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/r-basics/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/r-basics/tutorial.json"
-        },
-        "version": 11,
-        "video": false,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 129,
-        "visitors": 2053,
-        "zenodo_link": ""
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/r-advanced/tutorial.json",
-        "contributors": [
-            {
-                "id": "carpentries",
-                "joined": "2021-09",
-                "name": "The Carpentries",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
-                "ror": "0356fgm10",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "elixir-europe"
-                ],
-                "elixir_node": "gr",
-                "email": "fpsom@certh.gr",
-                "id": "fpsom",
-                "joined": "2019-03",
-                "linkedin": "fpsom",
-                "matrix": "fpsom:matrix.org",
-                "name": "Fotis E. Psomopoulos",
-                "orcid": "0000-0002-0222-4273",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
-                "twitter": "fopsom",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
-            },
-            {
-                "email": "tbyhdgs@gmail.com",
-                "id": "tobyhodges",
-                "joined": "2019-07",
-                "name": "Toby Hodges",
-                "orcid": "0000-0003-1766-456X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tobyhodges/",
-                "twitter": "tbyhdgs",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tobyhodges.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
-            }
-        ],
-        "dir": "topics/data-science/tutorials/r-advanced",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
+        "id": "data-science/sql-python",
+        "inexact_supported_servers": [
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "transcriptomics",
-                "tutorials": [
-                    "rna-seq-counts-to-viz-in-r"
-                ],
-                "type": "internal"
-            }
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
         ],
-        "hands_on": true,
-        "id": "data-science/r-advanced",
-        "inexact_supported_servers": [],
         "js_requirements": {
-            "mathjax": 46635,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "It is easy to import data into R from tabular formats. However, you still need to check that R has imported and interpreted your data correctly.",
-            "Just like Galaxy, base R's capabilities can be further enhanced by software packages developed by the user community.",
-            "Use the `dplyr` package to manipulate data frames.",
-            "Pipes can be used to combine simple operations into complex procedures."
+            "General-purpose languages have libraries for accessing databases.",
+            "To connect to a database, a program must use a library specific to that database manager.",
+            "These libraries use a connection-and-cursor model.",
+            "Programs can read query results in batches or all at once.",
+            "Queries should be written using parameter substitution, not string formatting."
         ],
         "layout": "tutorial_hands_on",
         "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2023-11-16",
+        "notebook": {
+            "language": "python"
+        },
         "objectives": [
-            "Be able to load and explore the shape and contents of a tabular dataset using base R functions.",
-            "Understand factors and how they can be used to store and work with categorical data.",
-            "Apply common `dplyr` functions to manipulate data in R.",
-            "Employ the \u2018pipe\u2019 operator to link together a sequence of functions."
+            "Write short programs that execute SQL queries.",
+            "Trace the execution of a program that contains an SQL query.",
+            "Explain why most database applications are written in a general-purpose language rather than in SQL."
         ],
-        "pageviews": 2032,
-        "priority": 2,
-        "pub_date": "2019-12-09",
+        "pageviews": 644,
+        "pub_date": "2021-10-11",
         "questions": [
-            "How can I manipulate data using R in Galaxy?",
-            "How do I get started with tabular data from Galaxy in R?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "ksuderman",
-                    "nagoue"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "1H",
-                "speakers": [
-                    "fpsom"
-                ],
-                "youtube_id": "_hWBGdlICqg"
-            }
-        ],
-        "redirect_from": [
-            "/topics/introduction/tutorials/r-advanced/tutorial",
-            "/short/data-science/r-advanced",
-            "/short/T00102"
+            "How can I access databases from programs written in Python?"
         ],
         "requirements": [
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "rstudio"
-                ],
-                "type": "internal"
-            },
             {
                 "topic_name": "data-science",
                 "tutorials": [
-                    "r-basics"
+                    "sql-advanced"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00102",
-        "short_tools": [
-            "interactive_tool_rstudio"
-        ],
+        "short_id": "T00109",
+        "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "r",
+        "subtopic": "sql",
         "supported_servers": {
-            "exact": [
+            "exact": [],
+            "inexact": [
                 {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 },
                 {
+                    "human": "Galaxy Australia",
+                    "id": "au",
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
                 }
-            ],
-            "inexact": []
+            ]
         },
         "symlink": null,
         "tags": [
-            "R"
-        ],
-        "time_estimation": "2H",
-        "title": "Advanced R in Galaxy",
-        "tools": [
-            "interactive_tool_rstudio"
+            "SQL",
+            "Python"
         ],
+        "time_estimation": "45M",
+        "title": "SQL with Python",
+        "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
         "tours": false,
@@ -50881,20 +52059,20 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "r-advanced",
+        "tutorial_name": "sql-python",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/r-advanced/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/sql-python/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/r-advanced/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/r-advanced/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-python/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/sql-python/tutorial.json"
         },
-        "version": 10,
+        "version": 7,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 139,
-        "visitors": 1230,
-        "zenodo_link": ""
+        "visit_duration": 25,
+        "visitors": 463,
+        "zenodo_link": null
     },
     {
         "admin_install": {
@@ -50904,80 +52082,51 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-advanced-np-pd/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/git-cli/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "hexylena"
+            ]
+        },
         "contributors": [
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "gr",
-                "id": "mcmaniou",
-                "joined": "2021-09",
-                "name": "Maria Christina Maniou",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mcmaniou/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mcmaniou.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
-                    "elixir-europe"
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
                 ],
-                "elixir_node": "gr",
-                "email": "fpsom@certh.gr",
-                "id": "fpsom",
-                "joined": "2019-03",
-                "linkedin": "fpsom",
-                "matrix": "fpsom:matrix.org",
-                "name": "Fotis E. Psomopoulos",
-                "orcid": "0000-0002-0222-4273",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
-                "twitter": "fopsom",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
-            },
-            {
-                "id": "carpentries",
-                "joined": "2021-09",
-                "name": "The Carpentries",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
-                "ror": "0356fgm10",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
                 ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/python-advanced-np-pd",
+        "dir": "topics/data-science/tutorials/git-cli",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [],
         "hands_on": true,
-        "id": "data-science/python-advanced-np-pd",
+        "id": "data-science/git-cli",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -50989,41 +52138,39 @@
             "mermaid": false
         },
         "key_points": [
-            "Python has many libraries offering a variety of capabilities, which makes it popular for beginners, as well as, more experienced users",
-            "You can use scientific libraries like Numpy and Pandas to perform data analysis."
+            "While git is extremely powerful, just using it for tracking changes is quite easy!",
+            "This does not take advantage of any advanced features, nor collaboration, but it is easy to expand into doing that."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-10-23",
-        "notebook": {
-            "language": "python",
-            "pyolite": true
-        },
+        "mod_date": "2023-11-16",
         "objectives": [
-            "Use the scientific libraries pandas and numpy to explore tabular datasets",
-            "Calculate basic statistics about datasets and columns"
+            "Create a repository",
+            "Commit a file",
+            "Make some changes",
+            "Use the log to view the diff",
+            "Undo a bad change"
         ],
-        "pageviews": 548,
-        "priority": 2,
-        "pub_date": "2021-11-08",
+        "pageviews": 354,
+        "pub_date": "2022-06-16",
         "questions": [
-            "How can I analyze data using Python with Numpy and Pandas?"
+            "How can I start tracking my changes with git?",
+            "How do I commit changes?",
+            "How can I undo a mistake?"
         ],
         "requirements": [
             {
                 "topic_name": "data-science",
                 "tutorials": [
-                    "python-basics"
+                    "cli-basics"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00081",
+        "short_id": "T00079",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "python",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -51058,8 +52205,8 @@
             ]
         },
         "symlink": null,
-        "time_estimation": "3H",
-        "title": "Advanced Python",
+        "time_estimation": "30m",
+        "title": "Basics of using Git from the Command Line",
         "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
@@ -51069,20 +52216,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "python-advanced-np-pd",
+        "tutorial_name": "git-cli",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/python-advanced-np-pd/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/git-cli/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-advanced-np-pd/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-advanced-np-pd/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/git-cli/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/git-cli/tutorial.json"
         },
         "version": 6,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 79,
-        "visitors": 395,
-        "zenodo_link": "https://zenodo.org/record/3477564"
+        "visit_duration": 23,
+        "visitors": 111
     },
     {
         "abbreviations": {
@@ -51193,7 +52339,7 @@
         "objectives": [
             "Understand the structure of a \"function\" in order to be able to construct their own functions and predict which functions will not work."
         ],
-        "pageviews": 848,
+        "pageviews": 940,
         "priority": 2,
         "pub_date": "2022-04-25",
         "questions": [
@@ -51272,8 +52418,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 35,
-        "visitors": 732
+        "visit_duration": 36,
+        "visitors": 804
     },
     {
         "admin_install": {
@@ -51283,31 +52429,80 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture2/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "nekrut"
-            ]
-        },
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-advanced-np-pd/tutorial.json",
         "contributors": [
             {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
-                "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "gr",
+                "id": "mcmaniou",
+                "joined": "2021-09",
+                "name": "Maria Christina Maniou",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mcmaniou/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mcmaniou.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "elixir-europe"
+                ],
+                "elixir_node": "gr",
+                "email": "fpsom@certh.gr",
+                "id": "fpsom",
+                "joined": "2019-03",
+                "linkedin": "fpsom",
+                "matrix": "fpsom:matrix.org",
+                "name": "Fotis E. Psomopoulos",
+                "orcid": "0000-0002-0222-4273",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
+                "twitter": "fopsom",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
+            },
+            {
+                "id": "carpentries",
+                "joined": "2021-09",
+                "name": "The Carpentries",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
+                "ror": "0356fgm10",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/gnmx-lecture2",
-        "draft": true,
+        "dir": "topics/data-science/tutorials/python-advanced-np-pd",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [],
         "hands_on": true,
-        "id": "data-science/gnmx-lecture2",
+        "id": "data-science/python-advanced-np-pd",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -51315,37 +52510,45 @@
             "UseGalaxy.fr"
         ],
         "js_requirements": {
-            "mathjax": 12768,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Sanger sequencing is sequencing by synthesis",
-            "Python is powerful"
+            "Python has many libraries offering a variety of capabilities, which makes it popular for beginners, as well as, more experienced users",
+            "You can use scientific libraries like Numpy and Pandas to perform data analysis."
         ],
         "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-02-20",
+        "mod_date": "2023-10-23",
         "notebook": {
             "language": "python",
             "pyolite": true
         },
         "objectives": [
-            "Have a basic understanding of the history of sequencing",
-            "Understand Python basics"
+            "Use the scientific libraries pandas and numpy to explore tabular datasets",
+            "Calculate basic statistics about datasets and columns"
         ],
-        "pageviews": 56,
+        "pageviews": 583,
         "priority": 2,
-        "pub_date": "2024-01-23",
+        "pub_date": "2021-11-08",
         "questions": [
-            "What are the origins of Sanger sequencing",
-            "How did sequencing machines evolve?",
-            "How can we simulate Sanger sequencing with Python?"
+            "How can I analyze data using Python with Numpy and Pandas?"
         ],
-        "short_id": "T00397",
+        "requirements": [
+            {
+                "topic_name": "data-science",
+                "tutorials": [
+                    "python-basics"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00081",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "gnmx",
+        "subtopic": "python",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -51380,11 +52583,8 @@
             ]
         },
         "symlink": null,
-        "tags": [
-            "work-in-progress"
-        ],
-        "time_estimation": "1h",
-        "title": "Introduction to sequencing with Python (part one)",
+        "time_estimation": "3H",
+        "title": "Advanced Python",
         "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
@@ -51394,19 +52594,20 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "gnmx-lecture2",
+        "tutorial_name": "python-advanced-np-pd",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture2/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/python-advanced-np-pd/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture2/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture2/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-advanced-np-pd/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-advanced-np-pd/tutorial.json"
         },
-        "version": 2,
+        "version": 6,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 133,
-        "visitors": 49
+        "visit_duration": 78,
+        "visitors": 417,
+        "zenodo_link": "https://zenodo.org/record/3477564"
     },
     {
         "admin_install": {
@@ -51567,7 +52768,7 @@
             "Modify the aesthetics of an existing ggplot plot (including axis labels and color).",
             "Build complex and customized plots from data in a data frame."
         ],
-        "pageviews": 319,
+        "pageviews": 374,
         "priority": 2,
         "pub_date": "2023-06-16",
         "questions": [
@@ -51640,10 +52841,524 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 66,
-        "visitors": 277,
+        "visit_duration": 59,
+        "visitors": 330,
         "zenodo_link": "https://zenodo.org/record/6803028"
     },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/r-advanced/tutorial.json",
+        "contributors": [
+            {
+                "id": "carpentries",
+                "joined": "2021-09",
+                "name": "The Carpentries",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
+                "ror": "0356fgm10",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "elixir-europe"
+                ],
+                "elixir_node": "gr",
+                "email": "fpsom@certh.gr",
+                "id": "fpsom",
+                "joined": "2019-03",
+                "linkedin": "fpsom",
+                "matrix": "fpsom:matrix.org",
+                "name": "Fotis E. Psomopoulos",
+                "orcid": "0000-0002-0222-4273",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
+                "twitter": "fopsom",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
+            },
+            {
+                "email": "tbyhdgs@gmail.com",
+                "id": "tobyhodges",
+                "joined": "2019-07",
+                "name": "Toby Hodges",
+                "orcid": "0000-0003-1766-456X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tobyhodges/",
+                "twitter": "tbyhdgs",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tobyhodges.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            }
+        ],
+        "dir": "topics/data-science/tutorials/r-advanced",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "transcriptomics",
+                "tutorials": [
+                    "rna-seq-counts-to-viz-in-r"
+                ],
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "data-science/r-advanced",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": 46635,
+            "mermaid": false
+        },
+        "key_points": [
+            "It is easy to import data into R from tabular formats. However, you still need to check that R has imported and interpreted your data correctly.",
+            "Just like Galaxy, base R's capabilities can be further enhanced by software packages developed by the user community.",
+            "Use the `dplyr` package to manipulate data frames.",
+            "Pipes can be used to combine simple operations into complex procedures."
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-14",
+        "objectives": [
+            "Be able to load and explore the shape and contents of a tabular dataset using base R functions.",
+            "Understand factors and how they can be used to store and work with categorical data.",
+            "Apply common `dplyr` functions to manipulate data in R.",
+            "Employ the \u2018pipe\u2019 operator to link together a sequence of functions."
+        ],
+        "pageviews": 2086,
+        "priority": 2,
+        "pub_date": "2019-12-09",
+        "questions": [
+            "How can I manipulate data using R in Galaxy?",
+            "How do I get started with tabular data from Galaxy in R?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "ksuderman",
+                    "nagoue"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "1H",
+                "speakers": [
+                    "fpsom"
+                ],
+                "youtube_id": "_hWBGdlICqg"
+            }
+        ],
+        "redirect_from": [
+            "/topics/introduction/tutorials/r-advanced/tutorial",
+            "/short/data-science/r-advanced",
+            "/short/T00102"
+        ],
+        "requirements": [
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "rstudio"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "data-science",
+                "tutorials": [
+                    "r-basics"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00102",
+        "short_tools": [
+            "interactive_tool_rstudio"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "r",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "R"
+        ],
+        "time_estimation": "2H",
+        "title": "Advanced R in Galaxy",
+        "tools": [
+            "interactive_tool_rstudio"
+        ],
+        "topic_name": "data-science",
+        "topic_name_human": "Foundations of Data Science",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "r-advanced",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/r-advanced/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/r-advanced/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/r-advanced/tutorial.json"
+        },
+        "version": 10,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 138,
+        "visitors": 1271,
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture2/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "nekrut"
+            ]
+        },
+        "contributors": [
+            {
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
+                "joined": "2017-09",
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+            }
+        ],
+        "dir": "topics/data-science/tutorials/gnmx-lecture2",
+        "draft": true,
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "data-science/gnmx-lecture2",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": 12768,
+            "mermaid": false
+        },
+        "key_points": [
+            "Sanger sequencing is sequencing by synthesis",
+            "Python is powerful"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-02-20",
+        "notebook": {
+            "language": "python",
+            "pyolite": true
+        },
+        "objectives": [
+            "Have a basic understanding of the history of sequencing",
+            "Understand Python basics"
+        ],
+        "pageviews": 64,
+        "priority": 2,
+        "pub_date": "2024-01-23",
+        "questions": [
+            "What are the origins of Sanger sequencing",
+            "How did sequencing machines evolve?",
+            "How can we simulate Sanger sequencing with Python?"
+        ],
+        "short_id": "T00397",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "gnmx",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "work-in-progress"
+        ],
+        "time_estimation": "1h",
+        "title": "Introduction to sequencing with Python (part one)",
+        "tools": [],
+        "topic_name": "data-science",
+        "topic_name_human": "Foundations of Data Science",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "gnmx-lecture2",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture2/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture2/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture2/tutorial.json"
+        },
+        "version": 2,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 120,
+        "visitors": 57
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture3/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "nekrut"
+            ]
+        },
+        "contributors": [
+            {
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
+                "joined": "2017-09",
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+            }
+        ],
+        "dir": "topics/data-science/tutorials/gnmx-lecture3",
+        "draft": true,
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "data-science/gnmx-lecture3",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Python can be used to parse FASTQ easily",
+            "One can readily visualize quality values"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-02-20",
+        "notebook": {
+            "language": "python",
+            "pyolite": true
+        },
+        "objectives": [
+            "Understand manipulation of FASTQ data in Python",
+            "Understand quality metrics"
+        ],
+        "pageviews": 41,
+        "priority": 3,
+        "pub_date": "2024-01-23",
+        "questions": [
+            "What is FASTQ format",
+            "How do I parse FASTQ format with Python",
+            "How do I decide whether my data is good or not?"
+        ],
+        "short_id": "T00398",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "gnmx",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "work-in-progress"
+        ],
+        "time_estimation": "1h",
+        "title": "Introduction to sequencing with Python (part two)",
+        "tools": [],
+        "topic_name": "data-science",
+        "topic_name_human": "Foundations of Data Science",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "gnmx-lecture3",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture3/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture3/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture3/tutorial.json"
+        },
+        "version": 3,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 51,
+        "visitors": 37
+    },
     {
         "admin_install": {
             "install_repository_dependencies": true,
@@ -51751,7 +53466,7 @@
         "objectives": [
             "Use the scientific library matplolib to explore tabular datasets"
         ],
-        "pageviews": 546,
+        "pageviews": 579,
         "priority": 3,
         "pub_date": "2021-11-08",
         "questions": [
@@ -51827,8 +53542,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 41,
-        "visitors": 452,
+        "visit_duration": 48,
+        "visitors": 473,
         "zenodo_link": "https://zenodo.org/record/3477564"
     },
     {
@@ -51943,7 +53658,7 @@
             "Explain key differences between numbers and character strings.",
             "Use built-in functions to convert between integers, floating point numbers, and strings."
         ],
-        "pageviews": 203,
+        "pageviews": 544,
         "priority": 3,
         "pub_date": "2022-04-25",
         "questions": [
@@ -52012,13 +53727,10 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 78,
-        "visitors": 166
+        "visit_duration": 384,
+        "visitors": 299
     },
     {
-        "abbreviations": {
-            "SQL": "Structured Query Language"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -52026,47 +53738,8 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/data-manipulation-olympics-sql/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "shiltemann",
-                "hexylena"
-            ],
-            "funding": [
-                "gallantries"
-            ]
-        },
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/r-dplyr/tutorial.json",
         "contributors": [
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
@@ -52121,16 +53794,33 @@
                 "short_name": "Gallantries",
                 "start_date": "2020-09-01",
                 "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/logo-avans.png",
+                "former_members": [
+                    "dirowa",
+                    "hexylena"
+                ],
+                "id": "avans-atgm",
+                "joined": "2020-11",
+                "members": [
+                    "bazante1"
+                ],
+                "name": "Avans Hogeschool",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/",
+                "ror": "015d5s513",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/data-manipulation-olympics-sql",
+        "dir": "topics/data-science/tutorials/r-dplyr",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [],
         "hands_on": true,
-        "id": "data-science/data-manipulation-olympics-sql",
+        "id": "data-science/r-dplyr",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -52138,175 +53828,47 @@
             "UseGalaxy.fr"
         ],
         "js_requirements": {
-            "mathjax": 28620,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Basic data manipulation is often needed between steps in a larger scientific analysis in order to connect outputs from one tool to input of another.",
-            "There are often multiple ways/tools to achieve the same end result",
-            "Having a basic understanding of data manipulation tools will make it easier to do exploratory data analysis",
-            "Always read the help text of the tool before using it to get a full understanding of its workings",
-            "Always try to formulate the output you are expecting from a tool. This will make it easier to spot mistakes as soon as possible."
+            "Dplyr and tidyverse make it a lot easier to process data",
+            "The functions for selecting data are a lot easier to understand than R's built in alternatives."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-05-07",
+        "level": "Advanced",
+        "license": "MIT",
+        "mod_date": "2023-10-23",
         "notebook": {
-            "language": "sql"
+            "language": "r"
         },
         "objectives": [
-            "Familiarize yourself with data manipulation in SQL",
-            "Perform basic SQL query tasks in Galaxy",
-            "Reason about the expected outcome of tools"
+            "Read data with the built-in `read.csv`",
+            "Read data with dplyr's `read_csv`",
+            "Use dplyr and tidyverse functions to cleanup data."
         ],
-        "pageviews": 461,
+        "pageviews": 671,
         "priority": 3,
-        "pub_date": "2023-06-16",
+        "pub_date": "2021-10-20",
         "questions": [
-            "How can I do basic data manipulation in SQL?",
-            "Which functions are available to convert, reformat, filter, sort etc my data stored in a database?"
-        ],
-        "short_id": "T00078",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "next-steps",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "cyoa",
-            "sql"
+            "How can I load tabular data into R?",
+            "How can I slice and dice the data to ask questions?"
         ],
-        "time_estimation": "1h",
-        "title": "Data Manipulation Olympics - SQL",
-        "tools": [],
-        "topic_name": "data-science",
-        "topic_name_human": "Foundations of Data Science",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "data-manipulation-olympics-sql",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/data-manipulation-olympics-sql/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/data-manipulation-olympics-sql/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/data-manipulation-olympics-sql/tutorial.json"
-        },
-        "version": 4,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 42,
-        "visitors": 398,
-        "zenodo_link": "https://zenodo.org/record/6803028"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture3/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "nekrut"
-            ]
-        },
-        "contributors": [
+        "requirements": [
             {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
-                "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+                "topic_name": "data-science",
+                "tutorials": [
+                    "r-basics",
+                    "r-advanced"
+                ],
+                "type": "internal"
             }
         ],
-        "dir": "topics/data-science/tutorials/gnmx-lecture3",
-        "draft": true,
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "data-science/gnmx-lecture3",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Python can be used to parse FASTQ easily",
-            "One can readily visualize quality values"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-02-20",
-        "notebook": {
-            "language": "python",
-            "pyolite": true
-        },
-        "objectives": [
-            "Understand manipulation of FASTQ data in Python",
-            "Understand quality metrics"
-        ],
-        "pageviews": 27,
-        "priority": 3,
-        "pub_date": "2024-01-23",
-        "questions": [
-            "What is FASTQ format",
-            "How do I parse FASTQ format with Python",
-            "How do I decide whether my data is good or not?"
-        ],
-        "short_id": "T00398",
+        "short_id": "T00104",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "gnmx",
+        "subtopic": "r",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -52342,10 +53904,10 @@
         },
         "symlink": null,
         "tags": [
-            "work-in-progress"
+            "R"
         ],
-        "time_estimation": "1h",
-        "title": "Introduction to sequencing with Python (part two)",
+        "time_estimation": "1H",
+        "title": "dplyr & tidyverse for data processing",
         "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
@@ -52355,21 +53917,25 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "gnmx-lecture3",
+        "tutorial_name": "r-dplyr",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture3/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/r-dplyr/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture3/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture3/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/r-dplyr/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/r-dplyr/tutorial.json"
         },
-        "version": 3,
+        "version": 5,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 70,
-        "visitors": 24
+        "visit_duration": 54,
+        "visitors": 497,
+        "zenodo_link": null
     },
     {
+        "abbreviations": {
+            "SQL": "Structured Query Language"
+        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -52377,8 +53943,47 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/r-dplyr/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/data-manipulation-olympics-sql/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "shiltemann",
+                "hexylena"
+            ],
+            "funding": [
+                "gallantries"
+            ]
+        },
         "contributors": [
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
@@ -52433,33 +54038,16 @@
                 "short_name": "Gallantries",
                 "start_date": "2020-09-01",
                 "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/logo-avans.png",
-                "former_members": [
-                    "dirowa",
-                    "hexylena"
-                ],
-                "id": "avans-atgm",
-                "joined": "2020-11",
-                "members": [
-                    "bazante1"
-                ],
-                "name": "Avans Hogeschool",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/",
-                "ror": "015d5s513",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/r-dplyr",
+        "dir": "topics/data-science/tutorials/data-manipulation-olympics-sql",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [],
         "hands_on": true,
-        "id": "data-science/r-dplyr",
+        "id": "data-science/data-manipulation-olympics-sql",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -52467,47 +54055,40 @@
             "UseGalaxy.fr"
         ],
         "js_requirements": {
-            "mathjax": null,
+            "mathjax": 28620,
             "mermaid": false
         },
         "key_points": [
-            "Dplyr and tidyverse make it a lot easier to process data",
-            "The functions for selecting data are a lot easier to understand than R's built in alternatives."
+            "Basic data manipulation is often needed between steps in a larger scientific analysis in order to connect outputs from one tool to input of another.",
+            "There are often multiple ways/tools to achieve the same end result",
+            "Having a basic understanding of data manipulation tools will make it easier to do exploratory data analysis",
+            "Always read the help text of the tool before using it to get a full understanding of its workings",
+            "Always try to formulate the output you are expecting from a tool. This will make it easier to spot mistakes as soon as possible."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Advanced",
-        "license": "MIT",
-        "mod_date": "2023-10-23",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-05-07",
         "notebook": {
-            "language": "r"
+            "language": "sql"
         },
         "objectives": [
-            "Read data with the built-in `read.csv`",
-            "Read data with dplyr's `read_csv`",
-            "Use dplyr and tidyverse functions to cleanup data."
+            "Familiarize yourself with data manipulation in SQL",
+            "Perform basic SQL query tasks in Galaxy",
+            "Reason about the expected outcome of tools"
         ],
-        "pageviews": 649,
+        "pageviews": 533,
         "priority": 3,
-        "pub_date": "2021-10-20",
+        "pub_date": "2023-06-16",
         "questions": [
-            "How can I load tabular data into R?",
-            "How can I slice and dice the data to ask questions?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "data-science",
-                "tutorials": [
-                    "r-basics",
-                    "r-advanced"
-                ],
-                "type": "internal"
-            }
+            "How can I do basic data manipulation in SQL?",
+            "Which functions are available to convert, reformat, filter, sort etc my data stored in a database?"
         ],
-        "short_id": "T00104",
+        "short_id": "T00078",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "r",
+        "subtopic": "next-steps",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -52543,10 +54124,11 @@
         },
         "symlink": null,
         "tags": [
-            "R"
+            "cyoa",
+            "sql"
         ],
-        "time_estimation": "1H",
-        "title": "dplyr & tidyverse for data processing",
+        "time_estimation": "1h",
+        "title": "Data Manipulation Olympics - SQL",
         "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
@@ -52556,20 +54138,20 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "r-dplyr",
+        "tutorial_name": "data-manipulation-olympics-sql",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/r-dplyr/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/data-manipulation-olympics-sql/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/r-dplyr/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/r-dplyr/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/data-manipulation-olympics-sql/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/data-manipulation-olympics-sql/tutorial.json"
         },
-        "version": 5,
+        "version": 4,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 55,
-        "visitors": 484,
-        "zenodo_link": null
+        "visit_duration": 44,
+        "visitors": 463,
+        "zenodo_link": "https://zenodo.org/record/6803028"
     },
     {
         "admin_install": {
@@ -52712,7 +54294,7 @@
             "Become comfortable converting JSON-based files in a variety of ways.",
             "Reason about the expected outcome of tools"
         ],
-        "pageviews": 254,
+        "pageviews": 278,
         "priority": 4,
         "pub_date": "2023-06-16",
         "questions": [
@@ -52784,8 +54366,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 53,
-        "visitors": 219,
+        "visit_duration": 47,
+        "visitors": 241,
         "zenodo_link": "https://zenodo.org/record/6803028"
     },
     {
@@ -52901,7 +54483,7 @@
             "Explain why programs need collections of values.",
             "Write programs that create flat lists, index them, slice them, and modify them through assignment and method calls."
         ],
-        "pageviews": 1865,
+        "pageviews": 2090,
         "priority": 4,
         "pub_date": "2022-04-25",
         "questions": [
@@ -52969,8 +54551,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 17,
-        "visitors": 1600
+        "visit_duration": 27,
+        "visitors": 1768
     },
     {
         "admin_install": {
@@ -53030,7 +54612,7 @@
             "Learning about dynamic programming",
             "Learning about how to translate DNA in Python"
         ],
-        "pageviews": 13,
+        "pageviews": 21,
         "priority": 4,
         "pub_date": "2024-02-06",
         "questions": [
@@ -53102,8 +54684,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 17,
-        "visitors": 11
+        "visit_duration": 8,
+        "visitors": 18
     },
     {
         "admin_install": {
@@ -53216,7 +54798,7 @@
             "Write conditional statements including `if`, `elif`, and `else` branches.",
             "Correctly evaluate expressions containing `and` and `or`."
         ],
-        "pageviews": 203,
+        "pageviews": 234,
         "priority": 5,
         "pub_date": "2022-04-25",
         "questions": [
@@ -53262,140 +54844,8 @@
             ]
         },
         "symlink": null,
-        "time_estimation": "40M",
-        "title": "Python - Flow Control",
-        "tools": [],
-        "topic_name": "data-science",
-        "topic_name_human": "Foundations of Data Science",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "python-flow",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/python-flow/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-flow/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-flow/tutorial.json"
-        },
-        "version": 3,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 36,
-        "visitors": 173
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture5/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "nekrut"
-            ]
-        },
-        "contributors": [
-            {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
-                "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
-            }
-        ],
-        "dir": "topics/data-science/tutorials/gnmx-lecture5",
-        "draft": true,
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "data-science/gnmx-lecture5",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Python can be used to read and write files"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-02-20",
-        "notebook": {
-            "language": "python",
-            "pyolite": true
-        },
-        "objectives": [
-            "Understand manipulation of files in Python"
-        ],
-        "pageviews": 19,
-        "priority": 5,
-        "pub_date": "2024-02-13",
-        "questions": [
-            "How to manipulate files in Python",
-            "How to read and write FASTA",
-            "How to read and write FASTQ",
-            "How to read and write SAM"
-        ],
-        "short_id": "T00411",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "gnmx",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "work-in-progress"
-        ],
-        "time_estimation": "1h",
-        "title": "Introduction to sequencing with Python (part four)",
+        "time_estimation": "40M",
+        "title": "Python - Flow Control",
         "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
@@ -53405,19 +54855,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "gnmx-lecture5",
+        "tutorial_name": "python-flow",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture5/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/python-flow/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture5/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture5/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-flow/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-flow/tutorial.json"
         },
-        "version": 2,
+        "version": 3,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 29,
-        "visitors": 19
+        "visit_duration": 46,
+        "visitors": 195
     },
     {
         "admin_install": {
@@ -53427,77 +54877,31 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-loops/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture5/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "nekrut"
+            ]
+        },
         "contributors": [
             {
-                "id": "carpentries",
-                "joined": "2021-09",
-                "name": "The Carpentries",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
-                "ror": "0356fgm10",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
                 "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "email": "D.vrins@live.nl",
-                "former_affiliations": [
-                    "avans-atgm"
-                ],
-                "id": "dirowa",
-                "joined": "2021-10",
-                "linkedin": "Donny Vrins",
-                "name": "Donny Vrins",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dirowa/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/dirowa.json"
-            },
-            {
-                "affiliations": [
-                    "avans-atgm"
-                ],
-                "id": "bazante1",
-                "joined": "2020-12",
-                "name": "Bazante Sanders",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/python-loops",
+        "dir": "topics/data-science/tutorials/gnmx-lecture5",
+        "draft": true,
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [],
         "hands_on": true,
-        "id": "data-science/python-loops",
+        "id": "data-science/gnmx-lecture5",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -53509,49 +54913,32 @@
             "mermaid": false
         },
         "key_points": [
-            "A *for loop* executes commands once for each value in a collection.",
-            "A `for` loop is made up of a collection, a loop variable, and a body.",
-            "The first line of the `for` loop must end with a colon, and the body must be indented.",
-            "Indentation is always meaningful in Python.",
-            "Loop variables can be called anything (but it is strongly advised to have a meaningful name to the looping variable).",
-            "The body of a loop can contain many statements.",
-            "Use `range` to iterate over a sequence of numbers.",
-            "The Accumulator pattern turns many values into one."
+            "Python can be used to read and write files"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-02-13",
+        "mod_date": "2024-02-20",
         "notebook": {
             "language": "python",
             "pyolite": true
         },
         "objectives": [
-            "Explain what for loops are normally used for.",
-            "Trace the execution of a simple (unnested) loop and correctly state the values of variables in each iteration.",
-            "Write for loops that use the Accumulator pattern to aggregate values."
+            "Understand manipulation of files in Python"
         ],
-        "pageviews": 361,
-        "priority": 6,
-        "pub_date": "2022-04-25",
+        "pageviews": 25,
+        "priority": 5,
+        "pub_date": "2024-02-13",
         "questions": [
-            "How can I make a program do many things?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "data-science",
-                "tutorials": [
-                    "python-iterables",
-                    "python-flow"
-                ],
-                "type": "internal"
-            }
+            "How to manipulate files in Python",
+            "How to read and write FASTA",
+            "How to read and write FASTQ",
+            "How to read and write SAM"
         ],
-        "short_id": "T00093",
+        "short_id": "T00411",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "python-modular",
+        "subtopic": "gnmx",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -53586,8 +54973,11 @@
             ]
         },
         "symlink": null,
-        "time_estimation": "40M",
-        "title": "Python - Loops",
+        "tags": [
+            "work-in-progress"
+        ],
+        "time_estimation": "1h",
+        "title": "Introduction to sequencing with Python (part four)",
         "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
@@ -53597,19 +54987,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "python-loops",
+        "tutorial_name": "gnmx-lecture5",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/python-loops/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture5/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-loops/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-loops/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture5/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture5/tutorial.json"
         },
-        "version": 3,
+        "version": 2,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 108,
-        "visitors": 301
+        "visit_duration": 21,
+        "visitors": 25
     },
     {
         "admin_install": {
@@ -53667,7 +55057,7 @@
         "objectives": [
             "Understand data manipulation in Pandas"
         ],
-        "pageviews": 11,
+        "pageviews": 13,
         "priority": 6,
         "pub_date": "2024-02-20",
         "questions": [
@@ -53739,8 +55129,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 51,
-        "visitors": 8
+        "visit_duration": 38,
+        "visitors": 10
     },
     {
         "admin_install": {
@@ -53750,31 +55140,77 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture7/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "nekrut"
-            ]
-        },
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-loops/tutorial.json",
         "contributors": [
             {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
+                "id": "carpentries",
+                "joined": "2021-09",
+                "name": "The Carpentries",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
+                "ror": "0356fgm10",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
                 "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "email": "D.vrins@live.nl",
+                "former_affiliations": [
+                    "avans-atgm"
+                ],
+                "id": "dirowa",
+                "joined": "2021-10",
+                "linkedin": "Donny Vrins",
+                "name": "Donny Vrins",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dirowa/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/dirowa.json"
+            },
+            {
+                "affiliations": [
+                    "avans-atgm"
+                ],
+                "id": "bazante1",
+                "joined": "2020-12",
+                "name": "Bazante Sanders",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/gnmx-lecture7",
-        "draft": true,
+        "dir": "topics/data-science/tutorials/python-loops",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [],
         "hands_on": true,
-        "id": "data-science/gnmx-lecture7",
+        "id": "data-science/python-loops",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -53786,28 +55222,49 @@
             "mermaid": false
         },
         "key_points": [
-            "No git, no life"
+            "A *for loop* executes commands once for each value in a collection.",
+            "A `for` loop is made up of a collection, a loop variable, and a body.",
+            "The first line of the `for` loop must end with a colon, and the body must be indented.",
+            "Indentation is always meaningful in Python.",
+            "Loop variables can be called anything (but it is strongly advised to have a meaningful name to the looping variable).",
+            "The body of a loop can contain many statements.",
+            "Use `range` to iterate over a sequence of numbers.",
+            "The Accumulator pattern turns many values into one."
         ],
         "layout": "tutorial_hands_on",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-12",
+        "mod_date": "2023-02-13",
+        "notebook": {
+            "language": "python",
+            "pyolite": true
+        },
         "objectives": [
-            "Get a basic understanding of git and version control"
+            "Explain what for loops are normally used for.",
+            "Trace the execution of a simple (unnested) loop and correctly state the values of variables in each iteration.",
+            "Write for loops that use the Accumulator pattern to aggregate values."
         ],
-        "pageviews": 3,
-        "priority": 7,
-        "pub_date": "2024-03-12",
+        "pageviews": 385,
+        "priority": 6,
+        "pub_date": "2022-04-25",
         "questions": [
-            "What is git",
-            "How is git different from GitHub?",
-            "What is branch?",
-            "How to uise git as a time machine"
+            "How can I make a program do many things?"
         ],
-        "short_id": "T00425",
+        "requirements": [
+            {
+                "topic_name": "data-science",
+                "tutorials": [
+                    "python-iterables",
+                    "python-flow"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00093",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "gnmx",
+        "subtopic": "python-modular",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -53842,11 +55299,8 @@
             ]
         },
         "symlink": null,
-        "tags": [
-            "work-in-progress"
-        ],
-        "time_estimation": "1h",
-        "title": "Versioning your code and data with git",
+        "time_estimation": "40M",
+        "title": "Python - Loops",
         "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
@@ -53856,19 +55310,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "gnmx-lecture7",
+        "tutorial_name": "python-loops",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture7/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/python-loops/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture7/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture7/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-loops/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-loops/tutorial.json"
         },
-        "version": 1,
+        "version": 3,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 0,
-        "visitors": 3
+        "visit_duration": 107,
+        "visitors": 316
     },
     {
         "admin_install": {
@@ -53971,7 +55425,7 @@
             "Use `with` to ensure the file is closed properly.",
             "Use the CSV module to parse comma and tab separated datasets."
         ],
-        "pageviews": 519,
+        "pageviews": 564,
         "priority": 7,
         "pub_date": "2022-04-25",
         "questions": [
@@ -54041,8 +55495,136 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 37,
-        "visitors": 447
+        "visit_duration": 40,
+        "visitors": 475
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture7/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "nekrut"
+            ]
+        },
+        "contributors": [
+            {
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
+                "joined": "2017-09",
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+            }
+        ],
+        "dir": "topics/data-science/tutorials/gnmx-lecture7",
+        "draft": true,
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "data-science/gnmx-lecture7",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "No git, no life"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-03-12",
+        "objectives": [
+            "Get a basic understanding of git and version control"
+        ],
+        "pageviews": 3,
+        "priority": 7,
+        "pub_date": "2024-03-12",
+        "questions": [
+            "What is git",
+            "How is git different from GitHub?",
+            "What is branch?",
+            "How to uise git as a time machine"
+        ],
+        "short_id": "T00425",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "gnmx",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "work-in-progress"
+        ],
+        "time_estimation": "1h",
+        "title": "Versioning your code and data with git",
+        "tools": [],
+        "topic_name": "data-science",
+        "topic_name_human": "Foundations of Data Science",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "gnmx-lecture7",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/gnmx-lecture7/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture7/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/gnmx-lecture7/tutorial.json"
+        },
+        "version": 1,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 0,
+        "visitors": 3
     },
     {
         "admin_install": {
@@ -54143,7 +55725,7 @@
             "catch an exception",
             "raise your own exception"
         ],
-        "pageviews": 423,
+        "pageviews": 471,
         "priority": 8,
         "pub_date": "2022-04-25",
         "questions": [
@@ -54213,8 +55795,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 14,
-        "visitors": 367
+        "visit_duration": 15,
+        "visitors": 407
     },
     {
         "abbreviations": {
@@ -54313,7 +55895,7 @@
             "Recap all previous modules.",
             "Use exercises to ensure that all previous knowledge is sufficiently covered."
         ],
-        "pageviews": 204,
+        "pageviews": 222,
         "priority": 9,
         "pub_date": "2022-04-25",
         "questions": [
@@ -54396,8 +55978,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 83,
-        "visitors": 169
+        "visit_duration": 104,
+        "visitors": 183
     },
     {
         "admin_install": {
@@ -54547,7 +56129,7 @@
             "Describe the three main types of tests and what each are used for",
             "Implement and run unit tests to verify the correct behaviour of program functions"
         ],
-        "pageviews": 173,
+        "pageviews": 194,
         "priority": 10,
         "pub_date": "2022-10-19",
         "questions": [
@@ -54617,8 +56199,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 33,
-        "visitors": 153
+        "visit_duration": 30,
+        "visitors": 173
     },
     {
         "admin_install": {
@@ -54741,7 +56323,7 @@
             "Set up a Python virtual environment for our software project using `venv` and `pip`.",
             "Run our software from the command line."
         ],
-        "pageviews": 108,
+        "pageviews": 112,
         "priority": 10,
         "pub_date": "2022-10-19",
         "questions": [
@@ -54810,8 +56392,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 96,
-        "visitors": 95
+        "visit_duration": 95,
+        "visitors": 99
     },
     {
         "admin_install": {
@@ -54821,22 +56403,26 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-typing/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-conda/tutorial.json",
         "contributions": {
             "authorship": [
+                "carpentries",
                 "hexylena"
             ],
-            "editing": [
-                "mvdbeek",
-                "pvanheus",
-                "dirowa",
-                "bazante1"
-            ],
             "funding": [
+                "carpentries",
                 "avans-atgm"
             ]
         },
         "contributors": [
+            {
+                "id": "carpentries",
+                "joined": "2021-09",
+                "name": "The Carpentries",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
+                "ror": "0356fgm10",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
@@ -54867,43 +56453,12 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
             {
-                "id": "mvdbeek",
-                "joined": "2018-06",
-                "name": "Marius van den Beek",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
-            },
-            {
-                "bio": "Research at the South African National Bioinformatics Institute",
-                "id": "pvanheus",
-                "joined": "2017-09",
-                "name": "Peter van Heusden",
-                "orcid": "0000-0001-6553-5274",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/",
-                "twitter": "pvanheus",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pvanheus.json"
-            },
-            {
-                "email": "D.vrins@live.nl",
-                "former_affiliations": [
-                    "avans-atgm"
-                ],
-                "id": "dirowa",
-                "joined": "2021-10",
-                "linkedin": "Donny Vrins",
-                "name": "Donny Vrins",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dirowa/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/dirowa.json"
-            },
-            {
-                "affiliations": [
-                    "avans-atgm"
-                ],
-                "id": "bazante1",
-                "joined": "2020-12",
-                "name": "Bazante Sanders",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
+                "id": "carpentries",
+                "joined": "2021-09",
+                "name": "The Carpentries",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
+                "ror": "0356fgm10",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
             },
             {
                 "avatar": "/training-material/shared/images/logo-avans.png",
@@ -54922,7 +56477,7 @@
                 "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/python-typing",
+        "dir": "topics/data-science/tutorials/python-conda",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -54930,7 +56485,7 @@
         "feedback_number": 0,
         "follow_up_training": [],
         "hands_on": true,
-        "id": "data-science/python-typing",
+        "id": "data-science/python-conda",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -54942,31 +56497,34 @@
             "mermaid": false
         },
         "key_points": [
-            "Typing improves the correctness and quality of your code",
-            "It can ensure that editor provided hints are better and more accurate."
+            "Environments keep Python versions and dependencies required by different projects separate.",
+            "An environment is itself a directory structure of software and libraries",
+            "Use `conda create -n <name>` to create and manage environments.",
+            "Use `conda install` to install and manage additional external (third-party) libraries.",
+            "Conda allows you to declare all dependencies for a project in a separate file (by convention called `environment.yml`) which can be shared with collaborators/users and used to replicate an environment.",
+            "Use `conda env export > environment.yml` to take snapshot of your project's dependencies.",
+            "Use `conda env create -f environment.yml` to replicate someone else's environment on your machine from the `environment.yml` file."
         ],
         "layout": "tutorial_hands_on",
         "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-02-13",
+        "mod_date": "2023-05-18",
         "notebook": {
-            "language": "python",
-            "pyolite": true
+            "language": "bash"
         },
         "objectives": [
-            "Understand the utility of annotating types on one's code",
-            "Understand the limits of type annotations in python"
+            "Set up a Conda environment for our software project using `conda`.",
+            "Run our software from the command line."
         ],
-        "pageviews": 478,
+        "pageviews": 513,
         "priority": 10,
         "pub_date": "2022-10-19",
         "questions": [
-            "What is typing?",
-            "How does it improve code?",
-            "Can it help me?"
+            "What are Conda environments in software development and why you should use them?",
+            "How can we manage Conda environments and external (third-party) libraries via Conda?"
         ],
         "requirements": [],
-        "short_id": "T00100",
+        "short_id": "T00085",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
@@ -55005,8 +56563,11 @@
             ]
         },
         "symlink": null,
+        "tags": [
+            "conda"
+        ],
         "time_estimation": "30M",
-        "title": "Python - Type annotations",
+        "title": "Conda Environments For Software Development",
         "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
@@ -55016,19 +56577,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "python-typing",
+        "tutorial_name": "python-conda",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/python-typing/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/python-conda/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-typing/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-typing/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-conda/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-conda/tutorial.json"
         },
-        "version": 2,
+        "version": 3,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 13,
-        "visitors": 453
+        "visit_duration": 23,
+        "visitors": 471
     },
     {
         "admin_install": {
@@ -55038,26 +56599,22 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-conda/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-argparse/tutorial.json",
         "contributions": {
             "authorship": [
-                "carpentries",
                 "hexylena"
             ],
+            "editing": [
+                "bazante1"
+            ],
             "funding": [
-                "carpentries",
                 "avans-atgm"
+            ],
+            "testing": [
+                "dirowa"
             ]
         },
         "contributors": [
-            {
-                "id": "carpentries",
-                "joined": "2021-09",
-                "name": "The Carpentries",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
-                "ror": "0356fgm10",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
@@ -55088,12 +56645,26 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
             {
-                "id": "carpentries",
-                "joined": "2021-09",
-                "name": "The Carpentries",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
-                "ror": "0356fgm10",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
+                "affiliations": [
+                    "avans-atgm"
+                ],
+                "id": "bazante1",
+                "joined": "2020-12",
+                "name": "Bazante Sanders",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
+            },
+            {
+                "email": "D.vrins@live.nl",
+                "former_affiliations": [
+                    "avans-atgm"
+                ],
+                "id": "dirowa",
+                "joined": "2021-10",
+                "linkedin": "Donny Vrins",
+                "name": "Donny Vrins",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dirowa/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/dirowa.json"
             },
             {
                 "avatar": "/training-material/shared/images/logo-avans.png",
@@ -55112,7 +56683,7 @@
                 "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/python-conda",
+        "dir": "topics/data-science/tutorials/python-argparse",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -55120,7 +56691,7 @@
         "feedback_number": 0,
         "follow_up_training": [],
         "hands_on": true,
-        "id": "data-science/python-conda",
+        "id": "data-science/python-argparse",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -55132,34 +56703,31 @@
             "mermaid": false
         },
         "key_points": [
-            "Environments keep Python versions and dependencies required by different projects separate.",
-            "An environment is itself a directory structure of software and libraries",
-            "Use `conda create -n <name>` to create and manage environments.",
-            "Use `conda install` to install and manage additional external (third-party) libraries.",
-            "Conda allows you to declare all dependencies for a project in a separate file (by convention called `environment.yml`) which can be shared with collaborators/users and used to replicate an environment.",
-            "Use `conda env export > environment.yml` to take snapshot of your project's dependencies.",
-            "Use `conda env create -f environment.yml` to replicate someone else's environment on your machine from the `environment.yml` file."
+            "If you are writing a command line script, no matter how small, use argparse.",
+            "`--help` is even written for us, without us writing any special code to handle that case",
+            "It handles a lot of cases and input validation for you",
+            "It produces a nice `--help` text that can help you if you've forgotten what your tool does",
+            "It's nice for users of your scripts! They don't have to read the code to know how it behaves if you document it well."
         ],
         "layout": "tutorial_hands_on",
         "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-05-18",
-        "notebook": {
-            "language": "bash"
-        },
+        "mod_date": "2023-01-24",
         "objectives": [
-            "Set up a Conda environment for our software project using `conda`.",
-            "Run our software from the command line."
+            "Learn how sys.argv works",
+            "Write a simple command line program that sums some numbers",
+            "Use argparse to make it nicer."
         ],
-        "pageviews": 479,
+        "pageviews": 1271,
         "priority": 10,
-        "pub_date": "2022-10-19",
+        "pub_date": "2022-04-25",
         "questions": [
-            "What are Conda environments in software development and why you should use them?",
-            "How can we manage Conda environments and external (third-party) libraries via Conda?"
+            "How do I make a proper command line script",
+            "How do I use argparse?",
+            "What problems does it solve?"
         ],
         "requirements": [],
-        "short_id": "T00085",
+        "short_id": "T00082",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
@@ -55198,11 +56766,8 @@
             ]
         },
         "symlink": null,
-        "tags": [
-            "conda"
-        ],
         "time_estimation": "30M",
-        "title": "Conda Environments For Software Development",
+        "title": "Python - Argparse",
         "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
@@ -55212,19 +56777,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "python-conda",
+        "tutorial_name": "python-argparse",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/python-conda/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/python-argparse/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-conda/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-conda/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-argparse/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-argparse/tutorial.json"
         },
-        "version": 3,
+        "version": 5,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 24,
-        "visitors": 441
+        "visitors": 1168
     },
     {
         "admin_install": {
@@ -55234,19 +56799,19 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-argparse/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-typing/tutorial.json",
         "contributions": {
             "authorship": [
                 "hexylena"
             ],
             "editing": [
+                "mvdbeek",
+                "pvanheus",
+                "dirowa",
                 "bazante1"
             ],
             "funding": [
                 "avans-atgm"
-            ],
-            "testing": [
-                "dirowa"
             ]
         },
         "contributors": [
@@ -55280,14 +56845,21 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
             {
-                "affiliations": [
-                    "avans-atgm"
-                ],
-                "id": "bazante1",
-                "joined": "2020-12",
-                "name": "Bazante Sanders",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
+                "id": "mvdbeek",
+                "joined": "2018-06",
+                "name": "Marius van den Beek",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
+            },
+            {
+                "bio": "Research at the South African National Bioinformatics Institute",
+                "id": "pvanheus",
+                "joined": "2017-09",
+                "name": "Peter van Heusden",
+                "orcid": "0000-0001-6553-5274",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/",
+                "twitter": "pvanheus",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pvanheus.json"
             },
             {
                 "email": "D.vrins@live.nl",
@@ -55301,6 +56873,16 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dirowa/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/dirowa.json"
             },
+            {
+                "affiliations": [
+                    "avans-atgm"
+                ],
+                "id": "bazante1",
+                "joined": "2020-12",
+                "name": "Bazante Sanders",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
+            },
             {
                 "avatar": "/training-material/shared/images/logo-avans.png",
                 "former_members": [
@@ -55318,7 +56900,7 @@
                 "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
             }
         ],
-        "dir": "topics/data-science/tutorials/python-argparse",
+        "dir": "topics/data-science/tutorials/python-typing",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -55326,7 +56908,7 @@
         "feedback_number": 0,
         "follow_up_training": [],
         "hands_on": true,
-        "id": "data-science/python-argparse",
+        "id": "data-science/python-typing",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -55338,31 +56920,31 @@
             "mermaid": false
         },
         "key_points": [
-            "If you are writing a command line script, no matter how small, use argparse.",
-            "`--help` is even written for us, without us writing any special code to handle that case",
-            "It handles a lot of cases and input validation for you",
-            "It produces a nice `--help` text that can help you if you've forgotten what your tool does",
-            "It's nice for users of your scripts! They don't have to read the code to know how it behaves if you document it well."
+            "Typing improves the correctness and quality of your code",
+            "It can ensure that editor provided hints are better and more accurate."
         ],
         "layout": "tutorial_hands_on",
         "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-01-24",
+        "mod_date": "2023-02-13",
+        "notebook": {
+            "language": "python",
+            "pyolite": true
+        },
         "objectives": [
-            "Learn how sys.argv works",
-            "Write a simple command line program that sums some numbers",
-            "Use argparse to make it nicer."
+            "Understand the utility of annotating types on one's code",
+            "Understand the limits of type annotations in python"
         ],
-        "pageviews": 1230,
+        "pageviews": 509,
         "priority": 10,
-        "pub_date": "2022-04-25",
+        "pub_date": "2022-10-19",
         "questions": [
-            "How do I make a proper command line script",
-            "How do I use argparse?",
-            "What problems does it solve?"
+            "What is typing?",
+            "How does it improve code?",
+            "Can it help me?"
         ],
         "requirements": [],
-        "short_id": "T00082",
+        "short_id": "T00100",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
@@ -55402,7 +56984,7 @@
         },
         "symlink": null,
         "time_estimation": "30M",
-        "title": "Python - Argparse",
+        "title": "Python - Type annotations",
         "tools": [],
         "topic_name": "data-science",
         "topic_name_human": "Foundations of Data Science",
@@ -55412,19 +56994,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "python-argparse",
+        "tutorial_name": "python-typing",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/python-argparse/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/python-typing/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-argparse/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-argparse/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-typing/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-typing/tutorial.json"
         },
-        "version": 5,
+        "version": 2,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 24,
-        "visitors": 1129
+        "visit_duration": 13,
+        "visitors": 481
     },
     {
         "admin_install": {
@@ -55522,7 +57104,7 @@
             "Use glob to collect a list of files",
             "Learn about the potential pitfalls of glob"
         ],
-        "pageviews": 418,
+        "pageviews": 455,
         "priority": 11,
         "pub_date": "2022-04-25",
         "questions": [
@@ -55590,8 +57172,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 28,
-        "visitors": 388
+        "visit_duration": 26,
+        "visitors": 419
     },
     {
         "admin_install": {
@@ -55694,7 +57276,7 @@
             "Learn about `check_call` and `check_output` and when to use each of these.",
             "Read it's output."
         ],
-        "pageviews": 1134,
+        "pageviews": 1168,
         "priority": 12,
         "pub_date": "2022-04-25",
         "questions": [
@@ -55763,7 +57345,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 17,
-        "visitors": 956
+        "visitors": 988
     },
     {
         "abbreviations": {
@@ -55891,7 +57473,7 @@
         "objectives": [
             "Understand the benefits of following community coding conventions"
         ],
-        "pageviews": 102,
+        "pageviews": 111,
         "priority": 13,
         "pub_date": "2022-11-03",
         "questions": [
@@ -55961,8 +57543,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 69,
-        "visitors": 90
+        "visit_duration": 66,
+        "visitors": 99
     },
     {
         "abbreviations": {
@@ -56091,7 +57673,7 @@
             "Understanding how to paralellise code to make it run faster.",
             "Identifying how to decompose code into a parallel unit."
         ],
-        "pageviews": 708,
+        "pageviews": 761,
         "priority": 20,
         "pub_date": "2022-10-19",
         "questions": [
@@ -56149,19 +57731,134 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "python-multiprocessing",
+        "tutorial_name": "python-multiprocessing",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/python-multiprocessing/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-multiprocessing/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-multiprocessing/tutorial.json"
+        },
+        "version": 4,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 20,
+        "visitors": 702
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/visualization-generic/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
+            {
+                "id": "yhoogstrate",
+                "joined": "2017-09",
+                "name": "Youri Hoogstrate",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yhoogstrate/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/yhoogstrate.json"
+            }
+        ],
+        "dir": "topics/dev/tutorials/visualization-generic",
+        "edam_operation": [],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "dev/visualization-generic",
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Visualizations require a different way of thinking: server and client side; downloading files rather than system level access",
+            "Interactivity is what makes visualizations different from static tools",
+            "Requires understanding of both the Galaxy ecosystem as well as HTML5/JS",
+            "Performance is more important than for static Galaxy tools"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": [
+            "Implement a first Galaxy visualization",
+            "Understand the client side vs. server side principle"
+        ],
+        "pageviews": 5897608,
+        "pub_date": "2016-09-30",
+        "questions": [
+            "How can visualization plugins benefit science?"
+        ],
+        "requirements": [
+            {
+                "title": "Javascript knowledge",
+                "type": "none"
+            }
+        ],
+        "short_id": "T00121",
+        "short_tools": [],
+        "slides": true,
+        "slides_recordings": false,
+        "subtopic": "viz",
+        "supported_servers": [],
+        "symlink": null,
+        "time_estimation": "90m",
+        "title": "Generic plugins",
+        "tools": [],
+        "topic_name": "dev",
+        "topic_name_human": "Development in Galaxy",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "visualization-generic",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/python-multiprocessing/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/dev/tutorials/visualization-generic/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-multiprocessing/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/python-multiprocessing/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/visualization-generic/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/visualization-generic/tutorial.json"
         },
-        "version": 4,
+        "version": 21,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 21,
-        "visitors": 652
+        "visit_duration": 274,
+        "visitors": 2133883
     },
     {
         "admin_install": {
@@ -56171,137 +57868,81 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/conda/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/conda_sys/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
-                    "earlham",
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "fediverse": "https://mstdn.science/@nsoranzo",
-                "fediverse_flavor": "mastodon",
-                "id": "nsoranzo",
-                "joined": "2017-09",
-                "linkedin": "nicola-soranzo-7884125",
-                "matrix": "nsoranzo:matrix.org",
-                "name": "Nicola Soranzo",
-                "orcid": "0000-0003-3627-5340",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
-                "twitter": "NicolaSoranzo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
-            },
-            {
-                "email": "jmchilton@gmail.com",
-                "id": "jmchilton",
-                "joined": "2017-09",
-                "matrix": "jmchilton:matrix.org",
-                "name": "John Chilton",
-                "orcid": "0000-0002-6794-0756",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jmchilton/",
-                "twitter": "jmchilton",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jmchilton.json"
-            },
-            {
-                "affiliations": [
+                    "gallantries",
                     "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
                     "elixir-europe"
                 ],
                 "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
+                "elixir_node": "fr",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
                 "fediverse_flavor": "mastodon",
-                "id": "bgruening",
+                "id": "abretaud",
                 "joined": "2017-09",
-                "linkedin": "bgruening",
                 "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
+                    "country": "FR",
+                    "lat": 48.11,
+                    "lon": -1.64
                 },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
             },
             {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "fr",
-                "id": "hmenager",
+                "id": "cmonjeau",
                 "joined": "2017-09",
-                "name": "Herv\u00e9 M\u00e9nager",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hmenager/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hmenager.json"
+                "name": "Cyril Monjeaud",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cmonjeau/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/cmonjeau.json"
             }
         ],
-        "dir": "topics/dev/tutorials/conda",
+        "dir": "topics/dev/tutorials/conda_sys",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": false,
-        "id": "dev/conda",
+        "id": "dev/conda_sys",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Conda and Bioconda are Galaxy best practices for connecting Galaxy tools to underlying applications and libraries.",
-            "Leveraging Conda allows easy installation of your tool's dependencies by Galaxy deployers.",
-            "The Planemo commands `conda_search`, `conda_init`, `conda_install`, `lint`, `test`, and `serve` make it easy to search and use existing Conda recipes when developing tools.",
-            "Conda recipe skeletons, `conda build`, and with `planemo conda_install --conda_use_local` allow easy development of new Conda recipes at the same time as Galaxy tools that wrap them.",
-            "Bioconda is a Galaxy best practice Conda channel for recipe publication.",
-            "Bioconda has easy to follow contribution guidelines and is very welcoming to new contributors."
+            "There is a common procedure to compile and install many tools: `./configure && make && make install`",
+            "Some exotic tools require adjustements to compile or install properly",
+            "Pay attention to INSTALL and README files, and to documentation"
         ],
         "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
         "logo": "GTN",
-        "mod_date": "2023-04-14",
+        "mod_date": "2021-05-28",
         "objectives": [
-            "Learn to use existing Conda recipes to enable best practice tool dependency management in Galaxy.",
-            "Learn the basics of building Conda recipes and contributing to Bioconda.",
-            "Learn to use Planemo to assist in developing Galaxy tools from existing and new Conda recipes."
+            "Learn how to compile and install tools using standard procedures.",
+            "Learn needed tricks to write conda build.sh files."
         ],
-        "pageviews": 5726881,
-        "pub_date": "2017-06-20",
+        "pageviews": 5897164,
+        "pub_date": "2018-02-15",
         "questions": [
-            "How can I connect tools to applications and libraries?",
-            "What are the advantages of declaring dependencies for my tool?",
-            "What are Conda and Bioconda?",
-            "What are Conda recipes and environments?",
-            "How do I find and use existing Conda recipes?",
-            "How do I develop Conda recipes for use within Galaxy tools?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "dev",
-                "tutorials": [
-                    "tool-integration",
-                    "conda_sys"
-                ],
-                "type": "internal"
-            }
+            "What does 'installing a software' means on a Linux architecture?",
+            "Why my compilations always fail?",
+            "How to solve common compiling and installation issues?"
         ],
-        "short_id": "S00045",
+        "short_id": "S00046",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
         "subtopic": "dependencies",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "75m",
-        "title": "Tool Dependencies and Conda",
+        "time_estimation": "1h",
+        "title": "Prerequisites for building software/conda packages",
         "tools": [],
         "topic_name": "dev",
         "topic_name_human": "Development in Galaxy",
@@ -56311,19 +57952,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "conda",
+        "tutorial_name": "conda_sys",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/dev/tutorials/conda/slides.html",
+        "url": "https://training.galaxyproject.org//topics/dev/tutorials/conda_sys/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/conda/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/conda/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/conda_sys/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/conda_sys/slides.json"
         },
-        "version": 33,
+        "version": 6,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2063758
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -56333,115 +57974,115 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/webhooks/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/toolshed/tutorial.json",
         "contributors": [
-            {
-                "elixir_node": "de",
-                "email": "blankclemens@gmail.com",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "blankclemens",
-                "joined": "2017-09",
-                "name": "Clemens Blank",
-                "orcid": "0000-0002-1726-2256",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankclemens/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankclemens.json"
-            },
             {
                 "affiliations": [
+                    "gallantries",
+                    "eurosciencegateway",
                     "elixir-europe"
                 ],
                 "contact_for_training": true,
-                "elixir_node": "cz",
-                "email": "marten@bx.psu.edu",
-                "fediverse": "https://mastodon.world/@martenson",
+                "elixir_node": "fr",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
                 "fediverse_flavor": "mastodon",
-                "id": "martenson",
+                "id": "abretaud",
                 "joined": "2017-09",
                 "location": {
-                    "country": "USA",
-                    "lat": 37.0,
-                    "lon": -122.0
+                    "country": "FR",
+                    "lat": 48.11,
+                    "lon": -1.64
                 },
-                "matrix": "martenson:matrix.org",
-                "name": "Martin \u010cech",
-                "orcid": "0000-0002-9318-1781",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/martenson/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/martenson.json"
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+            },
+            {
+                "id": "loraine-gueguen",
+                "joined": "2017-09",
+                "name": "Loraine Gu\u00e9guen",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/loraine-gueguen/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/loraine-gueguen.json"
+            },
+            {
+                "id": "slegras",
+                "joined": "2017-09",
+                "name": "St\u00e9phanie Legras",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slegras/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/slegras.json"
             },
             {
                 "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
+                    "gallantries",
+                    "ifb",
                     "elixir-europe"
                 ],
                 "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
                 "fediverse_flavor": "mastodon",
-                "id": "bgruening",
+                "id": "bebatut",
                 "joined": "2017-09",
-                "linkedin": "bgruening",
+                "linkedin": "berenicebatut",
                 "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
                 },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             }
         ],
-        "dir": "topics/dev/tutorials/webhooks",
+        "dir": "topics/dev/tutorials/toolshed",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": true,
-        "id": "dev/webhooks",
+        "hands_on": false,
+        "id": "dev/toolshed",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "A Galaxy Webhook provides an easy way to customize the Galaxy UI with plugins",
-            "Right now there are 4 entry points: tool, workflow, masthead, history-menu",
-            "With a minimal amount of code you can extend Galaxy's user-interace."
+            "Use Planemo",
+            "Contribute to the Main Tool Shed"
         ],
-        "layout": "tutorial_hands_on",
+        "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-24",
+        "logo": "GTN",
+        "mod_date": "2022-10-18",
         "objectives": [
-            "Discover what Galaxy Webhooks are",
-            "Be able to create Webhooks",
-            "Be able to add a Galaxy Webhook in a Galaxy instance"
+            "Discover what is a Tool Shed",
+            "Be able to install tools and workflows from a Tool Shed into a Galaxy instance",
+            "Be able to publish tools with Planemo"
         ],
-        "pageviews": 5727095,
-        "pub_date": "2017-04-03",
+        "pageviews": 5897164,
+        "pub_date": "2017-06-12",
         "questions": [
-            "What are Galaxy Webhooks?",
-            "How to create them?"
+            "What is a Tool Shed?",
+            "How to install tools and workflows from a Tool Shed into a Galaxy instance?",
+            "What are the Tool Shed repository types?",
+            "How to publish with Planemo?"
         ],
-        "short_id": "T00122",
+        "short_id": "S00052",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
-        "subtopic": "advanced",
+        "subtopic": "tooldev",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "1h",
-        "title": "Galaxy Webhooks",
+        "time_estimation": "3h",
+        "title": "Tool Shed: sharing Galaxy tools",
         "tools": [],
         "topic_name": "dev",
         "topic_name_human": "Development in Galaxy",
@@ -56451,19 +58092,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "webhooks",
+        "tutorial_name": "toolshed",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/dev/tutorials/webhooks/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/dev/tutorials/toolshed/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/webhooks/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/webhooks/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/toolshed/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/toolshed/slides.json"
         },
-        "version": 16,
+        "version": 15,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 200,
-        "visitors": 2063912
+        "visit_duration": 152,
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -56553,7 +58194,7 @@
             "Modify and re-generate them to see how the changes affect the tool",
             "Generate new simple Galaxy tools using your own scripts"
         ],
-        "pageviews": 4997387,
+        "pageviews": 5167701,
         "pub_date": "2021-05-26",
         "questions": [
             "What options exist for new-to-Galaxy developers to convert functioning command line scripts into Galaxy tools?",
@@ -56622,8 +58263,8 @@
         "video": true,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 304,
-        "visitors": 1850073
+        "visit_duration": 299,
+        "visitors": 1919340
     },
     {
         "admin_install": {
@@ -56633,117 +58274,43 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-integration/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/webhooks/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
+                "elixir_node": "de",
+                "email": "blankclemens@gmail.com",
+                "former_affiliations": [
+                    "uni-freiburg",
                     "elixir-europe"
                 ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
+                "id": "blankclemens",
                 "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+                "name": "Clemens Blank",
+                "orcid": "0000-0002-1726-2256",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankclemens/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankclemens.json"
             },
             {
                 "affiliations": [
-                    "gallantries",
-                    "eurosciencegateway",
                     "elixir-europe"
                 ],
                 "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
+                "elixir_node": "cz",
+                "email": "marten@bx.psu.edu",
+                "fediverse": "https://mastodon.world/@martenson",
                 "fediverse_flavor": "mastodon",
-                "id": "abretaud",
+                "id": "martenson",
                 "joined": "2017-09",
                 "location": {
-                    "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
+                    "country": "USA",
+                    "lat": 37.0,
+                    "lon": -122.0
                 },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
-            },
-            {
-                "email": "jmchilton@gmail.com",
-                "id": "jmchilton",
-                "joined": "2017-09",
-                "matrix": "jmchilton:matrix.org",
-                "name": "John Chilton",
-                "orcid": "0000-0002-6794-0756",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jmchilton/",
-                "twitter": "jmchilton",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jmchilton.json"
-            },
-            {
-                "affiliations": [
-                    "earlham",
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "fediverse": "https://mstdn.science/@nsoranzo",
-                "fediverse_flavor": "mastodon",
-                "id": "nsoranzo",
-                "joined": "2017-09",
-                "linkedin": "nicola-soranzo-7884125",
-                "matrix": "nsoranzo:matrix.org",
-                "name": "Nicola Soranzo",
-                "orcid": "0000-0003-3627-5340",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
-                "twitter": "NicolaSoranzo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
+                "matrix": "martenson:matrix.org",
+                "name": "Martin \u010cech",
+                "orcid": "0000-0002-9318-1781",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/martenson/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/martenson.json"
             },
             {
                 "affiliations": [
@@ -56775,75 +58342,47 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
                 "twitter": "bjoerngruening",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "fr",
-                "id": "lecorguille",
-                "joined": "2017-09",
-                "name": "Gildas Le Corguill\u00e9",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
             }
         ],
-        "dir": "topics/dev/tutorials/tool-integration",
+        "dir": "topics/dev/tutorials/webhooks",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "dev",
-                "tutorials": [
-                    "conda"
-                ],
-                "type": "internal"
-            }
-        ],
-        "hands_on": "external",
-        "hands_on_url": "http://planemo.readthedocs.io/en/latest/writing_standalone.html",
-        "id": "dev/tool-integration",
+        "hands_on": true,
+        "id": "dev/webhooks",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Galaxy Tool Syntax",
-            "Use Planemo",
-            "Use Conda",
-            "Use GitHub",
-            "Use GitHub Actions",
-            "No more excuse to develop crappy Galaxy tools"
+            "A Galaxy Webhook provides an easy way to customize the Galaxy UI with plugins",
+            "Right now there are 4 entry points: tool, workflow, masthead, history-menu",
+            "With a minimal amount of code you can extend Galaxy's user-interace."
         ],
-        "layout": "tutorial_slides",
+        "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "logo": "GTN",
-        "mod_date": "2023-04-21",
+        "mod_date": "2024-06-24",
         "objectives": [
-            "Learn what a tool is and its structure",
-            "Use the Planemo utilities to develop a tool",
-            "Deal with the dependencies",
-            "Write functional tests",
-            "Make a tool ready for publishing in a ToolShed"
+            "Discover what Galaxy Webhooks are",
+            "Be able to create Webhooks",
+            "Be able to add a Galaxy Webhook in a Galaxy instance"
         ],
-        "pageviews": 5726884,
-        "pub_date": "2016-09-30",
+        "pageviews": 5897385,
+        "pub_date": "2017-04-03",
         "questions": [
-            "What is a tool for Galaxy?",
-            "How to write a best-practice tool?",
-            "How to deal with the tool environment?"
+            "What are Galaxy Webhooks?",
+            "How to create them?"
         ],
-        "short_id": "S00051",
+        "short_id": "T00122",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
-        "subtopic": "tooldev",
+        "subtopic": "advanced",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "6h",
-        "title": "Tool development and integration into Galaxy",
+        "time_estimation": "1h",
+        "title": "Galaxy Webhooks",
         "tools": [],
         "topic_name": "dev",
         "topic_name_human": "Development in Galaxy",
@@ -56853,19 +58392,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "tool-integration",
+        "tutorial_name": "webhooks",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/dev/tutorials/tool-integration/slides.html",
+        "url": "https://training.galaxyproject.org//topics/dev/tutorials/webhooks/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-integration/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-integration/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/webhooks/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/webhooks/tutorial.json"
         },
-        "version": 29,
+        "version": 16,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063760
+        "visit_duration": 198,
+        "visitors": 2133742
     },
     {
         "admin_install": {
@@ -56980,7 +58519,7 @@
         "objectives": [
             "Interact with Galaxy via BioBlend."
         ],
-        "pageviews": 5727485,
+        "pageviews": 5897804,
         "pub_date": "2017-01-17",
         "questions": [
             "What is a REST API?",
@@ -57017,8 +58556,8 @@
         "video": true,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 311,
-        "visitors": 2064202
+        "visit_duration": 304,
+        "visitors": 2134053
     },
     {
         "admin_install": {
@@ -57028,37 +58567,33 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/interactive-environments/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/interactive-tours/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
-                    "CINECA-Project",
                     "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
+                    "ifb",
+                    "elixir-europe"
                 ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
                 "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
                 "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
+                "id": "bebatut",
                 "joined": "2017-09",
-                "linkedin": "shiltemann",
+                "linkedin": "berenicebatut",
                 "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
                 },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             },
             {
                 "affiliations": [
@@ -57090,85 +58625,48 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
                 "twitter": "bjoerngruening",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/dev/tutorials/interactive-environments",
-        "draft": true,
+        "dir": "topics/dev/tutorials/interactive-tours",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": false,
-        "id": "dev/interactive-environments",
+        "id": "dev/interactive-tours",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Interactive Environments offer access to third-party applications within Galaxy",
-            "Interactive Environments run in a docker images for sandboxing and easy dependency management"
+            "An Interactive Tour is easy to create: just a yaml file to fill",
+            "Use the Developper Tools of find the JQuery Selector",
+            "Help yourself by using the available web plugins and record an interactive tour"
         ],
         "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
         "logo": "GTN",
-        "mod_date": "2023-02-17",
+        "mod_date": "2021-07-27",
         "objectives": [
-            "Implement a Hello-World Galaxy Interactive Environment"
+            "Discover what is a Galaxy Interactive Tour",
+            "Be able to create a Galaxy Interactive Tour",
+            "Be able to add a Galaxy Interactive Tour in a Galaxy instance"
         ],
-        "pageviews": 5726881,
-        "pub_date": "2017-02-05",
+        "pageviews": 5897164,
+        "pub_date": "2017-01-12",
         "questions": [
-            "What are Galaxy Interactive Environments (GIEs)?",
-            "How to enable GIEs in Galaxy?",
-            "How to develop your own GIE?"
-        ],
-        "requirements": [
-            {
-                "title": "Docker basics",
-                "type": "none"
-            }
+            "What is a Galaxy Interactive Tour?",
+            "How to create a Galaxy Interactive Tour?"
         ],
-        "short_id": "S00048",
+        "short_id": "S00049",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
         "subtopic": "advanced",
         "supported_servers": [],
         "symlink": null,
-        "tags": [
-            "work-in-progress"
-        ],
-        "time_estimation": "90m",
-        "title": "Galaxy Interactive Environments",
+        "time_estimation": "3h",
+        "title": "Galaxy Interactive Tours",
         "tools": [],
         "topic_name": "dev",
         "topic_name_human": "Development in Galaxy",
@@ -57178,19 +58676,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "interactive-environments",
+        "tutorial_name": "interactive-tours",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/dev/tutorials/interactive-environments/slides.html",
+        "url": "https://training.galaxyproject.org//topics/dev/tutorials/interactive-tours/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/interactive-environments/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/interactive-environments/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/interactive-tours/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/interactive-tours/slides.json"
         },
-        "version": 16,
+        "version": 14,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2063758
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -57200,18 +58698,44 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/containers/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/visualization-charts/tutorial.json",
         "contributors": [
             {
-                "email": "jmchilton@gmail.com",
-                "id": "jmchilton",
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
                 "joined": "2017-09",
-                "matrix": "jmchilton:matrix.org",
-                "name": "John Chilton",
-                "orcid": "0000-0002-6794-0756",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jmchilton/",
-                "twitter": "jmchilton",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jmchilton.json"
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
+            {
+                "id": "yhoogstrate",
+                "joined": "2017-09",
+                "name": "Youri Hoogstrate",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yhoogstrate/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/yhoogstrate.json"
             },
             {
                 "affiliations": [
@@ -57243,59 +58767,57 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
                 "twitter": "bjoerngruening",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+            },
+            {
+                "id": "guerler",
+                "joined": "2017-09",
+                "name": "Aysam Guerler",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/guerler/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/guerler.json"
+            },
+            {
+                "id": "dannon",
+                "joined": "2017-09",
+                "name": "Dannon Baker",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dannon/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/dannon.json"
             }
         ],
-        "dir": "topics/dev/tutorials/containers",
+        "dir": "topics/dev/tutorials/visualization-charts",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": false,
-        "id": "dev/containers",
+        "hands_on": true,
+        "id": "dev/visualization-charts",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "It is becoming easier, more advantageous, and more common for Galaxy admins to run all tools within their own container.",
-            "You can explicitly define a container for your tool - but it is easier and more reproducible to let Galaxy find or build one using your tool's best practice requirements.",
-            "The Galaxy community will infrastructure to automatically build and/or publish containers for your tool as long as it defines best practice Conda dependencies.",
-            "Planemo makes it easy to test your tool inside of containers."
+            "Demonstrating a pluggable extension system for JavaScript visualizations",
+            "With three primary files we can integrate any JavaScript visualization into Galaxy"
         ],
-        "layout": "tutorial_slides",
+        "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "logo": "GTN",
-        "mod_date": "2022-10-18",
+        "mod_date": "2024-07-08",
         "objectives": [
-            "Explore the differences between containerizing Galaxy and tool execution.",
-            "Discuss the advantages of containerizing tools.",
-            "Learn to build best practice tools ready to be containerized."
+            "Learn how to add JavaScript plugins to Galaxy using the Charts visualization framework"
         ],
-        "pageviews": 5726881,
-        "pub_date": "2017-06-20",
+        "pageviews": 5897882,
+        "pub_date": "2017-06-22",
         "questions": [
-            "What are the advantages of running my Galaxy tool inside of a container?",
-            "How does Galaxy find a container to run my tool in?",
-            "What are BioContainers and how are they related to Galaxy?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "dev",
-                "tutorials": [
-                    "tool-integration"
-                ],
-                "type": "internal"
-            }
+            "How can I make a custom visualization plugin for Galaxy?"
         ],
-        "short_id": "S00047",
+        "short_id": "T00120",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
-        "subtopic": "dependencies",
+        "subtopic": "viz",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "45m",
-        "title": "Tool Dependencies and Containers",
+        "time_estimation": "1h",
+        "title": "JavaScript plugins",
         "tools": [],
         "topic_name": "dev",
         "topic_name_human": "Development in Galaxy",
@@ -57305,19 +58827,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "containers",
+        "tutorial_name": "visualization-charts",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/dev/tutorials/containers/slides.html",
+        "url": "https://training.galaxyproject.org//topics/dev/tutorials/visualization-charts/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/containers/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/containers/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/visualization-charts/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/visualization-charts/tutorial.json"
         },
-        "version": 14,
+        "version": 19,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758
+        "visit_duration": 205,
+        "visitors": 2134178
     },
     {
         "admin_install": {
@@ -57327,33 +58849,36 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/interactive-tours/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/conda/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
-                    "gallantries",
-                    "ifb",
+                    "earlham",
                     "elixir-europe"
                 ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
+                "elixir_node": "uk",
+                "fediverse": "https://mstdn.science/@nsoranzo",
                 "fediverse_flavor": "mastodon",
-                "id": "bebatut",
+                "id": "nsoranzo",
                 "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+                "linkedin": "nicola-soranzo-7884125",
+                "matrix": "nsoranzo:matrix.org",
+                "name": "Nicola Soranzo",
+                "orcid": "0000-0003-3627-5340",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
+                "twitter": "NicolaSoranzo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
+            },
+            {
+                "email": "jmchilton@gmail.com",
+                "id": "jmchilton",
+                "joined": "2017-09",
+                "matrix": "jmchilton:matrix.org",
+                "name": "John Chilton",
+                "orcid": "0000-0002-6794-0756",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jmchilton/",
+                "twitter": "jmchilton",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jmchilton.json"
             },
             {
                 "affiliations": [
@@ -57385,48 +58910,76 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
                 "twitter": "bjoerngruening",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "fr",
+                "id": "hmenager",
+                "joined": "2017-09",
+                "name": "Herv\u00e9 M\u00e9nager",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hmenager/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hmenager.json"
             }
         ],
-        "dir": "topics/dev/tutorials/interactive-tours",
+        "dir": "topics/dev/tutorials/conda",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": false,
-        "id": "dev/interactive-tours",
+        "id": "dev/conda",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "An Interactive Tour is easy to create: just a yaml file to fill",
-            "Use the Developper Tools of find the JQuery Selector",
-            "Help yourself by using the available web plugins and record an interactive tour"
+            "Conda and Bioconda are Galaxy best practices for connecting Galaxy tools to underlying applications and libraries.",
+            "Leveraging Conda allows easy installation of your tool's dependencies by Galaxy deployers.",
+            "The Planemo commands `conda_search`, `conda_init`, `conda_install`, `lint`, `test`, and `serve` make it easy to search and use existing Conda recipes when developing tools.",
+            "Conda recipe skeletons, `conda build`, and with `planemo conda_install --conda_use_local` allow easy development of new Conda recipes at the same time as Galaxy tools that wrap them.",
+            "Bioconda is a Galaxy best practice Conda channel for recipe publication.",
+            "Bioconda has easy to follow contribution guidelines and is very welcoming to new contributors."
         ],
         "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
         "logo": "GTN",
-        "mod_date": "2021-07-27",
+        "mod_date": "2023-04-14",
         "objectives": [
-            "Discover what is a Galaxy Interactive Tour",
-            "Be able to create a Galaxy Interactive Tour",
-            "Be able to add a Galaxy Interactive Tour in a Galaxy instance"
+            "Learn to use existing Conda recipes to enable best practice tool dependency management in Galaxy.",
+            "Learn the basics of building Conda recipes and contributing to Bioconda.",
+            "Learn to use Planemo to assist in developing Galaxy tools from existing and new Conda recipes."
         ],
-        "pageviews": 5726881,
-        "pub_date": "2017-01-12",
+        "pageviews": 5897164,
+        "pub_date": "2017-06-20",
         "questions": [
-            "What is a Galaxy Interactive Tour?",
-            "How to create a Galaxy Interactive Tour?"
+            "How can I connect tools to applications and libraries?",
+            "What are the advantages of declaring dependencies for my tool?",
+            "What are Conda and Bioconda?",
+            "What are Conda recipes and environments?",
+            "How do I find and use existing Conda recipes?",
+            "How do I develop Conda recipes for use within Galaxy tools?"
         ],
-        "short_id": "S00049",
+        "requirements": [
+            {
+                "topic_name": "dev",
+                "tutorials": [
+                    "tool-integration",
+                    "conda_sys"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "S00045",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
-        "subtopic": "advanced",
+        "subtopic": "dependencies",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "3h",
-        "title": "Galaxy Interactive Tours",
+        "time_estimation": "75m",
+        "title": "Tool Dependencies and Conda",
         "tools": [],
         "topic_name": "dev",
         "topic_name_human": "Development in Galaxy",
@@ -57436,19 +58989,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "interactive-tours",
+        "tutorial_name": "conda",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/dev/tutorials/interactive-tours/slides.html",
+        "url": "https://training.galaxyproject.org//topics/dev/tutorials/conda/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/interactive-tours/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/interactive-tours/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/conda/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/conda/slides.json"
         },
-        "version": 14,
+        "version": 33,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2063758
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -57458,8 +59011,64 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/conda_sys/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-integration/tutorial.json",
         "contributors": [
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
@@ -57485,87 +59094,6 @@
                 "twitter": "abretau",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
             },
-            {
-                "id": "cmonjeau",
-                "joined": "2017-09",
-                "name": "Cyril Monjeaud",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cmonjeau/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/cmonjeau.json"
-            }
-        ],
-        "dir": "topics/dev/tutorials/conda_sys",
-        "edam_operation": [],
-        "edam_topic": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": false,
-        "id": "dev/conda_sys",
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "There is a common procedure to compile and install many tools: `./configure && make && make install`",
-            "Some exotic tools require adjustements to compile or install properly",
-            "Pay attention to INSTALL and README files, and to documentation"
-        ],
-        "layout": "tutorial_slides",
-        "license": "CC-BY-4.0",
-        "logo": "GTN",
-        "mod_date": "2021-05-28",
-        "objectives": [
-            "Learn how to compile and install tools using standard procedures.",
-            "Learn needed tricks to write conda build.sh files."
-        ],
-        "pageviews": 5726881,
-        "pub_date": "2018-02-15",
-        "questions": [
-            "What does 'installing a software' means on a Linux architecture?",
-            "Why my compilations always fail?",
-            "How to solve common compiling and installation issues?"
-        ],
-        "short_id": "S00046",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
-        "subtopic": "dependencies",
-        "supported_servers": [],
-        "symlink": null,
-        "time_estimation": "1h",
-        "title": "Prerequisites for building software/conda packages",
-        "tools": [],
-        "topic_name": "dev",
-        "topic_name_human": "Development in Galaxy",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "conda_sys",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/dev/tutorials/conda_sys/slides.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/conda_sys/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/conda_sys/slides.json"
-        },
-        "version": 6,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/architecture/tutorial.json",
-        "contributors": [
             {
                 "email": "jmchilton@gmail.com",
                 "id": "jmchilton",
@@ -57577,6 +59105,24 @@
                 "twitter": "jmchilton",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/jmchilton.json"
             },
+            {
+                "affiliations": [
+                    "earlham",
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "fediverse": "https://mstdn.science/@nsoranzo",
+                "fediverse_flavor": "mastodon",
+                "id": "nsoranzo",
+                "joined": "2017-09",
+                "linkedin": "nicola-soranzo-7884125",
+                "matrix": "nsoranzo:matrix.org",
+                "name": "Nicola Soranzo",
+                "orcid": "0000-0003-3627-5340",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
+                "twitter": "NicolaSoranzo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
+            },
             {
                 "affiliations": [
                     "eurosciencegateway",
@@ -57607,51 +59153,75 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
                 "twitter": "bjoerngruening",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "fr",
+                "id": "lecorguille",
+                "joined": "2017-09",
+                "name": "Gildas Le Corguill\u00e9",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
             }
         ],
-        "dir": "topics/dev/tutorials/architecture",
+        "dir": "topics/dev/tutorials/tool-integration",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": false,
-        "id": "dev/architecture",
+        "follow_up_training": [
+            {
+                "topic_name": "dev",
+                "tutorials": [
+                    "conda"
+                ],
+                "type": "internal"
+            }
+        ],
+        "hands_on": "external",
+        "hands_on_url": "http://planemo.readthedocs.io/en/latest/writing_standalone.html",
+        "id": "dev/tool-integration",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Galaxy runs out of the box and fetches all needed dependencies.",
-            "Running Galaxy in production requires configuration.",
-            "The architecture is designed to be pluggable and extensible.",
-            "Learn more about different Galaxy aspects in our [development section](/topics/dev/)."
+            "Galaxy Tool Syntax",
+            "Use Planemo",
+            "Use Conda",
+            "Use GitHub",
+            "Use GitHub Actions",
+            "No more excuse to develop crappy Galaxy tools"
         ],
         "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
         "logo": "GTN",
-        "mod_date": "2024-06-14",
+        "mod_date": "2023-04-21",
         "objectives": [
-            "Explore various aspects of the Galaxy codebase.",
-            "Understand the various top-level files and modules in Galaxy.",
-            "Understand how dependencies work in Galaxy's frontend and backend."
+            "Learn what a tool is and its structure",
+            "Use the Planemo utilities to develop a tool",
+            "Deal with the dependencies",
+            "Write functional tests",
+            "Make a tool ready for publishing in a ToolShed"
         ],
-        "pageviews": 5726881,
-        "pub_date": "2017-06-20",
+        "pageviews": 5897167,
+        "pub_date": "2016-09-30",
         "questions": [
-            "How is the Galaxy code structured?",
-            "What do the various other projects related to Galaxy do?",
-            "What happens when I start Galaxy?"
+            "What is a tool for Galaxy?",
+            "How to write a best-practice tool?",
+            "How to deal with the tool environment?"
         ],
-        "requirements": null,
-        "short_id": "S00043",
+        "short_id": "S00051",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
-        "subtopic": "core",
+        "subtopic": "tooldev",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "150m",
-        "title": "Galaxy Code Architecture",
+        "time_estimation": "6h",
+        "title": "Tool development and integration into Galaxy",
         "tools": [],
         "topic_name": "dev",
         "topic_name_human": "Development in Galaxy",
@@ -57661,19 +59231,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "architecture",
+        "tutorial_name": "tool-integration",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/dev/tutorials/architecture/slides.html",
+        "url": "https://training.galaxyproject.org//topics/dev/tutorials/tool-integration/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/architecture/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/architecture/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-integration/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-integration/slides.json"
         },
-        "version": 34,
+        "version": 29,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2063758
+        "visitors": 2133584
     },
     {
         "admin_install": {
@@ -57683,115 +59253,102 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/toolshed/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/containers/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "gallantries",
-                    "eurosciencegateway",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
-                "fediverse_flavor": "mastodon",
-                "id": "abretaud",
-                "joined": "2017-09",
-                "location": {
-                    "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
-                },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
-            },
-            {
-                "id": "loraine-gueguen",
-                "joined": "2017-09",
-                "name": "Loraine Gu\u00e9guen",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/loraine-gueguen/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/loraine-gueguen.json"
-            },
-            {
-                "id": "slegras",
+                "email": "jmchilton@gmail.com",
+                "id": "jmchilton",
                 "joined": "2017-09",
-                "name": "St\u00e9phanie Legras",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slegras/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/slegras.json"
+                "matrix": "jmchilton:matrix.org",
+                "name": "John Chilton",
+                "orcid": "0000-0002-6794-0756",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jmchilton/",
+                "twitter": "jmchilton",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jmchilton.json"
             },
             {
                 "affiliations": [
-                    "gallantries",
-                    "ifb",
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
                     "elixir-europe"
                 ],
                 "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
                 "fediverse_flavor": "mastodon",
-                "id": "bebatut",
+                "id": "bgruening",
                 "joined": "2017-09",
-                "linkedin": "berenicebatut",
+                "linkedin": "bgruening",
                 "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
                 },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
             }
         ],
-        "dir": "topics/dev/tutorials/toolshed",
+        "dir": "topics/dev/tutorials/containers",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": false,
-        "id": "dev/toolshed",
+        "id": "dev/containers",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Use Planemo",
-            "Contribute to the Main Tool Shed"
+            "It is becoming easier, more advantageous, and more common for Galaxy admins to run all tools within their own container.",
+            "You can explicitly define a container for your tool - but it is easier and more reproducible to let Galaxy find or build one using your tool's best practice requirements.",
+            "The Galaxy community will infrastructure to automatically build and/or publish containers for your tool as long as it defines best practice Conda dependencies.",
+            "Planemo makes it easy to test your tool inside of containers."
         ],
         "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
         "logo": "GTN",
         "mod_date": "2022-10-18",
         "objectives": [
-            "Discover what is a Tool Shed",
-            "Be able to install tools and workflows from a Tool Shed into a Galaxy instance",
-            "Be able to publish tools with Planemo"
+            "Explore the differences between containerizing Galaxy and tool execution.",
+            "Discuss the advantages of containerizing tools.",
+            "Learn to build best practice tools ready to be containerized."
         ],
-        "pageviews": 5726881,
-        "pub_date": "2017-06-12",
+        "pageviews": 5897164,
+        "pub_date": "2017-06-20",
         "questions": [
-            "What is a Tool Shed?",
-            "How to install tools and workflows from a Tool Shed into a Galaxy instance?",
-            "What are the Tool Shed repository types?",
-            "How to publish with Planemo?"
+            "What are the advantages of running my Galaxy tool inside of a container?",
+            "How does Galaxy find a container to run my tool in?",
+            "What are BioContainers and how are they related to Galaxy?"
         ],
-        "short_id": "S00052",
+        "requirements": [
+            {
+                "topic_name": "dev",
+                "tutorials": [
+                    "tool-integration"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "S00047",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
-        "subtopic": "tooldev",
+        "subtopic": "dependencies",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "3h",
-        "title": "Tool Shed: sharing Galaxy tools",
+        "time_estimation": "45m",
+        "title": "Tool Dependencies and Containers",
         "tools": [],
         "topic_name": "dev",
         "topic_name_human": "Development in Galaxy",
@@ -57801,19 +59358,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "toolshed",
+        "tutorial_name": "containers",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/dev/tutorials/toolshed/slides.html",
+        "url": "https://training.galaxyproject.org//topics/dev/tutorials/containers/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/toolshed/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/toolshed/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/containers/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/containers/slides.json"
         },
-        "version": 15,
+        "version": 14,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2063758
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -57823,7 +59380,7 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/visualization-charts/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/interactive-environments/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
@@ -57855,13 +59412,6 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             },
-            {
-                "id": "yhoogstrate",
-                "joined": "2017-09",
-                "name": "Youri Hoogstrate",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yhoogstrate/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/yhoogstrate.json"
-            },
             {
                 "affiliations": [
                     "eurosciencegateway",
@@ -57894,55 +59444,83 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
             },
             {
-                "id": "guerler",
-                "joined": "2017-09",
-                "name": "Aysam Guerler",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/guerler/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/guerler.json"
-            },
-            {
-                "id": "dannon",
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
                 "joined": "2017-09",
-                "name": "Dannon Baker",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dannon/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/dannon.json"
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/dev/tutorials/visualization-charts",
+        "dir": "topics/dev/tutorials/interactive-environments",
+        "draft": true,
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": true,
-        "id": "dev/visualization-charts",
+        "hands_on": false,
+        "id": "dev/interactive-environments",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Demonstrating a pluggable extension system for JavaScript visualizations",
-            "With three primary files we can integrate any JavaScript visualization into Galaxy"
+            "Interactive Environments offer access to third-party applications within Galaxy",
+            "Interactive Environments run in a docker images for sandboxing and easy dependency management"
         ],
-        "layout": "tutorial_hands_on",
+        "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-08",
+        "logo": "GTN",
+        "mod_date": "2023-02-17",
         "objectives": [
-            "Learn how to add JavaScript plugins to Galaxy using the Charts visualization framework"
+            "Implement a Hello-World Galaxy Interactive Environment"
         ],
-        "pageviews": 5727572,
-        "pub_date": "2017-06-22",
+        "pageviews": 5897164,
+        "pub_date": "2017-02-05",
         "questions": [
-            "How can I make a custom visualization plugin for Galaxy?"
+            "What are Galaxy Interactive Environments (GIEs)?",
+            "How to enable GIEs in Galaxy?",
+            "How to develop your own GIE?"
         ],
-        "short_id": "T00120",
+        "requirements": [
+            {
+                "title": "Docker basics",
+                "type": "none"
+            }
+        ],
+        "short_id": "S00048",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
-        "subtopic": "viz",
+        "subtopic": "advanced",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "1h",
-        "title": "JavaScript plugins",
+        "tags": [
+            "work-in-progress"
+        ],
+        "time_estimation": "90m",
+        "title": "Galaxy Interactive Environments",
         "tools": [],
         "topic_name": "dev",
         "topic_name_human": "Development in Galaxy",
@@ -57952,19 +59530,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "visualization-charts",
+        "tutorial_name": "interactive-environments",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/dev/tutorials/visualization-charts/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/dev/tutorials/interactive-environments/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/visualization-charts/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/visualization-charts/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/interactive-environments/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/interactive-environments/slides.json"
         },
-        "version": 19,
+        "version": 16,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 206,
-        "visitors": 2064328
+        "visit_duration": 152,
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -57974,90 +59552,94 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/visualization-generic/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/architecture/tutorial.json",
         "contributors": [
+            {
+                "email": "jmchilton@gmail.com",
+                "id": "jmchilton",
+                "joined": "2017-09",
+                "matrix": "jmchilton:matrix.org",
+                "name": "John Chilton",
+                "orcid": "0000-0002-6794-0756",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jmchilton/",
+                "twitter": "jmchilton",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jmchilton.json"
+            },
             {
                 "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
+                    "elixir-europe"
                 ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
                 "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
                 "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
+                "id": "bgruening",
                 "joined": "2017-09",
-                "linkedin": "shiltemann",
+                "linkedin": "bgruening",
                 "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
                 },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
-            {
-                "id": "yhoogstrate",
-                "joined": "2017-09",
-                "name": "Youri Hoogstrate",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yhoogstrate/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/yhoogstrate.json"
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
             }
         ],
-        "dir": "topics/dev/tutorials/visualization-generic",
+        "dir": "topics/dev/tutorials/architecture",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": true,
-        "id": "dev/visualization-generic",
+        "hands_on": false,
+        "id": "dev/architecture",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Visualizations require a different way of thinking: server and client side; downloading files rather than system level access",
-            "Interactivity is what makes visualizations different from static tools",
-            "Requires understanding of both the Galaxy ecosystem as well as HTML5/JS",
-            "Performance is more important than for static Galaxy tools"
+            "Galaxy runs out of the box and fetches all needed dependencies.",
+            "Running Galaxy in production requires configuration.",
+            "The architecture is designed to be pluggable and extensible.",
+            "Learn more about different Galaxy aspects in our [development section](/topics/dev/)."
         ],
-        "layout": "tutorial_hands_on",
+        "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "logo": "GTN",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Implement a first Galaxy visualization",
-            "Understand the client side vs. server side principle"
+            "Explore various aspects of the Galaxy codebase.",
+            "Understand the various top-level files and modules in Galaxy.",
+            "Understand how dependencies work in Galaxy's frontend and backend."
         ],
-        "pageviews": 5727324,
-        "pub_date": "2016-09-30",
+        "pageviews": 5897164,
+        "pub_date": "2017-06-20",
         "questions": [
-            "How can visualization plugins benefit science?"
-        ],
-        "requirements": [
-            {
-                "title": "Javascript knowledge",
-                "type": "none"
-            }
+            "How is the Galaxy code structured?",
+            "What do the various other projects related to Galaxy do?",
+            "What happens when I start Galaxy?"
         ],
-        "short_id": "T00121",
+        "requirements": null,
+        "short_id": "S00043",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
-        "subtopic": "viz",
+        "subtopic": "core",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "90m",
-        "title": "Generic plugins",
+        "time_estimation": "150m",
+        "title": "Galaxy Code Architecture",
         "tools": [],
         "topic_name": "dev",
         "topic_name_human": "Development in Galaxy",
@@ -58067,19 +59649,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "visualization-generic",
+        "tutorial_name": "architecture",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/dev/tutorials/visualization-generic/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/dev/tutorials/architecture/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/visualization-generic/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/visualization-generic/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/architecture/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/architecture/slides.json"
         },
-        "version": 21,
+        "version": 34,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 274,
-        "visitors": 2064058
+        "visit_duration": 152,
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -58089,112 +59671,83 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-annotation/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "bebatut",
-                "supernord",
-                "paulzierep"
-            ]
-        },
+        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/core-contributing/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
+                "email": "jmchilton@gmail.com",
+                "id": "jmchilton",
                 "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "au",
-                "id": "supernord",
-                "joined": "2024-02",
-                "name": "Johan Gustafsson",
-                "orcid": "0000-0002-2977-5032",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/supernord/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/supernord.json"
+                "matrix": "jmchilton:matrix.org",
+                "name": "John Chilton",
+                "orcid": "0000-0002-6794-0756",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jmchilton/",
+                "twitter": "jmchilton",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jmchilton.json"
             },
             {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "email": "zierep@informatik.uni-freiburg.de",
-                "id": "paulzierep",
-                "joined": "2023-02",
-                "name": "Paul Zierep",
-                "orcid": "0000-0003-2982-388X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json"
+                "email": "jdavcs@gmail.com",
+                "id": "jdavcs",
+                "joined": "2019-06",
+                "name": "John Davis",
+                "orcid": "0000-0002-1363-1245",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jdavcs/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jdavcs.json"
             }
         ],
-        "dir": "topics/dev/tutorials/tool-annotation",
+        "dir": "topics/dev/tutorials/core-contributing",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "dev/tool-annotation",
+        "id": "dev/core-contributing",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Galaxy tools can get EDAM ontology terms from bio.tools",
-            "bio.tools entry can be created and modified to provide the best EDAM annotations",
-            "An up-to-date bio.tools entry provides readily accessible metadata that can help users find and understand tools that are available on Galaxy",
-            "bio.tools entry can easily be added to a Galaxy tool"
+            "Galaxy database interactions are mitigated via SQLAlchemy code in lib/galaxy/model.",
+            "Galaxy API endpoints are implemented in lib/galaxy/webapps/galaxy, but generally defer to application logic in lib/galaxy/managers.",
+            "Galaxy client code should do its best to separate API interaction logic from display components."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-24",
+        "mod_date": "2024-06-30",
         "objectives": [
-            "Identify Galaxy tools without bio.tools entry",
-            "Create a bio.tools entry",
-            "Update a bio.tools entry",
-            "Add EDAM ontology terms to a bio.tools entry",
-            "Link a Galaxy tool to its corresponding bio.tools entry"
+            "Learn to develop extensions to the Galaxy data model",
+            "Learn to implement new API functionality within Galaxy",
+            "Learn to extend the Galaxy user interface with VueJS components"
         ],
-        "pageviews": 99,
-        "pub_date": "2024-03-06",
+        "pageviews": 808,
+        "pub_date": "2021-06-08",
         "questions": [
-            "How are Galaxy tools linked to EDAM ontology?",
-            "How to connect Galaxy tools to bio.tools?",
-            "What is bio.tools?",
-            "How to add, and update, entries in bio.tools?"
+            "How can I add a new feature to Galaxy that involves modifications to the database, the API, and the UI?"
         ],
-        "short_id": "T00421",
+        "requirements": [
+            {
+                "topic_name": "contributing",
+                "tutorials": [
+                    "github-command-line-contribution"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "dev",
+                "tutorials": [
+                    "architecture"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00113",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "tooldev",
+        "subtopic": "core",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "1H",
-        "title": "Adding and updating best practice metadata for Galaxy tools using the bio.tools registry",
+        "time_estimation": "3H",
+        "title": "Contributing a New Feature to Galaxy Core",
         "tools": [],
         "topic_name": "dev",
         "topic_name_human": "Development in Galaxy",
@@ -58204,19 +59757,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "tool-annotation",
+        "tutorial_name": "core-contributing",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/dev/tutorials/tool-annotation/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/dev/tutorials/core-contributing/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-annotation/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-annotation/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/core-contributing/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/core-contributing/tutorial.json"
         },
-        "version": 2,
+        "version": 8,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 170,
-        "visitors": 82
+        "visit_duration": 143,
+        "visitors": 512
     },
     {
         "admin_install": {
@@ -58370,7 +59923,7 @@
             "Be able to test and debug a new GxIT locally and on a Galaxy server",
             "Be able to distribute a new GxIT for others to use"
         ],
-        "pageviews": 1011,
+        "pageviews": 1033,
         "pub_date": "2022-03-02",
         "questions": [
             "What is an Interactive Tool on Galaxy (GxIT)?",
@@ -58419,18 +59972,10 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 170,
-        "visitors": 729
+        "visit_duration": 169,
+        "visitors": 749
     },
     {
-        "abbreviations": {
-            "API": "Application Programming Interface",
-            "HDA": "History Dataset Association",
-            "HDCA": "History Dataset Collection Association",
-            "LDA": "Library Dataset Association",
-            "LDCA": "Library Dataset Collection Association",
-            "PR": "Pull Request"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -58438,83 +59983,90 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/bioblend-dev/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/writing_tests/tutorial.json",
         "contributors": [
             {
-                "id": "rikeshi",
-                "joined": "2021-05",
-                "name": "Erik Schill",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/rikeshi/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/rikeshi.json"
+                "email": "jdavcs@gmail.com",
+                "id": "jdavcs",
+                "joined": "2019-06",
+                "name": "John Davis",
+                "orcid": "0000-0002-1363-1245",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jdavcs/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jdavcs.json"
             },
             {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "simonbray",
-                "joined": "2019-05",
-                "name": "Simon Bray",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
+                "email": "jmchilton@gmail.com",
+                "id": "jmchilton",
+                "joined": "2017-09",
+                "matrix": "jmchilton:matrix.org",
+                "name": "John Chilton",
+                "orcid": "0000-0002-6794-0756",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jmchilton/",
+                "twitter": "jmchilton",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jmchilton.json"
             }
         ],
-        "dir": "topics/dev/tutorials/bioblend-dev",
+        "dir": "topics/dev/tutorials/writing_tests",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "dev/bioblend-dev",
+        "id": "dev/writing_tests",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "BioBlend is a Python library that provides methods for easy interaction with the Galaxy API.",
-            "Implementing BioBlend methods is generally quite an easy process, making it well suited to beginners and a viable stepping stone into Galaxy development."
+            "Read the Writing Tests for Galaxy documentation article",
+            "Check for existing examples of similar tests before implementing your own",
+            "Prefer Galaxy's abstractions to writing low level code whenever possible",
+            "Write tests that do not depend on each other or the state of the database",
+            "When testing the API, verify the return status code before checking the response data",
+            "Refactor the code under test if that's needed to make it testable",
+            "Move redundant setup code into fixtures",
+            "Use test doubles (mocks, stubs, etc.) sparingly"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-06-25",
         "objectives": [
-            "Learn the basics behind BioBlend and the Galaxy API from a developer perspective.",
-            "Learn how to implement a simple method in BioBlend.",
-            "Learn how to run the BioBlend test suite."
-        ],
-        "pageviews": 248,
-        "pub_date": "2021-05-25",
-        "questions": [
-            "How to get started making contributions to BioBlend?"
+            "Learn about the different types of automated tests in Galaxy",
+            "Learn to write API tests",
+            "Learn to write unit tests"
         ],
+        "pageviews": 613,
+        "pub_date": "2022-07-15",
         "requirements": [
             {
-                "title": "Basic command line knowledge",
+                "title": "Familiarity with basic Git commands",
                 "type": "none"
             },
             {
-                "title": "Familiarity with git and access to a GitHub account",
+                "title": "Basic knowledge of Python and JavaScript",
                 "type": "none"
             },
             {
-                "title": "Familiarity with the Python programming language",
+                "title": "Mac OS or Linux that can run Galaxy & your favorite IDE or editor",
                 "type": "none"
             },
             {
-                "title": "Familiarity with HTTP methods and JavaScript Object Notation (JSON)",
-                "type": "none"
+                "topic_name": "dev",
+                "tutorials": [
+                    "architecture"
+                ],
+                "type": "internal"
             }
         ],
-        "short_id": "T00112",
+        "short_id": "T00123",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "api",
+        "subtopic": "core",
         "supported_servers": [],
         "symlink": null,
         "time_estimation": "3h",
-        "title": "Contributing to BioBlend as a developer",
+        "title": "Writing Automated Tests for Galaxy",
         "tools": [],
         "topic_name": "dev",
         "topic_name_human": "Development in Galaxy",
@@ -58524,19 +60076,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "bioblend-dev",
+        "tutorial_name": "writing_tests",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/dev/tutorials/bioblend-dev/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/dev/tutorials/writing_tests/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/bioblend-dev/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/bioblend-dev/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/writing_tests/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/writing_tests/tutorial.json"
         },
-        "version": 8,
+        "version": 5,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 208,
-        "visitors": 171
+        "visit_duration": 156,
+        "visitors": 191
     },
     {
         "admin_install": {
@@ -58546,8 +60098,162 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/writing_tests/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-from-scratch/tutorial.json",
+        "contributors": [
+            {
+                "email": "a.ostrovsky@mac.com",
+                "id": "astrovsky01",
+                "joined": "2019-06",
+                "name": "Alex Ostrovsky",
+                "orcid": "0000-0002-7901-7109",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/astrovsky01/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/astrovsky01.json"
+            },
+            {
+                "id": "davebx",
+                "joined": "2021-06",
+                "name": "Dave B.",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/davebx/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/davebx.json"
+            },
+            {
+                "elixir_node": "de",
+                "id": "bernt-matthias",
+                "joined": "2017-09",
+                "name": "Matthias Bernt",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bernt-matthias/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bernt-matthias.json"
+            }
+        ],
+        "dir": "topics/dev/tutorials/tool-from-scratch",
+        "edam_operation": [],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "dev/tool-from-scratch",
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Galaxy tools are made in 3 parts -- Conda, tool wrappers, and planemo",
+            "Anyone can write and deploy a tool wrapper!"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-27",
+        "objectives": [
+            "Learn how to make and deploy a conda package",
+            "Understand how to write a Galaxy tool wrapper",
+            "Be able to use a tool wrapper locally",
+            "Be able to test the tool wrapper",
+            "Learn how to add tools to the Galaxy toolshed and make them available to any user"
+        ],
+        "pageviews": 3708,
+        "pub_date": "2021-06-15",
+        "questions": [
+            "How do you create a conda package used as a dependency in a Galaxy tool wrapper?",
+            "How do you create a Galaxy tool wrapper and all of its requirements?",
+            "How do you test a Galaxy tool wrapper after it's written?",
+            "How do you deploy a Galaxy tool wrapper?",
+            "How to do you make a Galaxy tool wrapper publicly available?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "gallardoalba",
+                    "astrovsky01"
+                ],
+                "date": "2023-05-18",
+                "galaxy_version": "22.01",
+                "length": "50M",
+                "speakers": [
+                    "gallardoalba",
+                    "astrovsky01"
+                ],
+                "youtube_id": "QRoY1pFUY30"
+            },
+            {
+                "captioners": [
+                    "gallardoalba"
+                ],
+                "date": "2022-03-11",
+                "galaxy_version": "22.01",
+                "length": "40M",
+                "speakers": [
+                    "gallardoalba"
+                ],
+                "youtube_id": "33L4B9ir0aQ"
+            },
+            {
+                "captioners": [
+                    "davebx",
+                    "astrovsky01",
+                    "bernt-matthias"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "1H40M",
+                "speakers": [
+                    "davebx",
+                    "astrovsky01",
+                    "bernt-matthias"
+                ],
+                "youtube_id": "videoseries?list=PLNFLKDpdM3B9GhA0FryVV2YX3YL35rENK"
+            }
+        ],
+        "short_id": "T00117",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "tooldev",
+        "supported_servers": [],
+        "symlink": null,
+        "time_estimation": "3H",
+        "title": "Creating Galaxy tools from Conda Through Deployment",
+        "tools": [],
+        "topic_name": "dev",
+        "topic_name_human": "Development in Galaxy",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "tool-from-scratch",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/dev/tutorials/tool-from-scratch/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-from-scratch/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-from-scratch/tutorial.json"
+        },
+        "version": 14,
+        "video": false,
+        "video_versions": 3,
+        "video_view": 0,
+        "visit_duration": 164,
+        "visitors": 2231,
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/debugging/tutorial.json",
         "contributors": [
+            {
+                "email": "assuntad23@gmail.com",
+                "id": "assuntad23",
+                "joined": "2021-05",
+                "name": "Assunta DeSanto",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/assuntad23/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/assuntad23.json"
+            },
             {
                 "email": "jdavcs@gmail.com",
                 "id": "jdavcs",
@@ -58569,37 +60275,43 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/jmchilton.json"
             }
         ],
-        "dir": "topics/dev/tutorials/writing_tests",
+        "dir": "topics/dev/tutorials/debugging",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "dev/writing_tests",
+        "id": "dev/debugging",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Read the Writing Tests for Galaxy documentation article",
-            "Check for existing examples of similar tests before implementing your own",
-            "Prefer Galaxy's abstractions to writing low level code whenever possible",
-            "Write tests that do not depend on each other or the state of the database",
-            "When testing the API, verify the return status code before checking the response data",
-            "Refactor the code under test if that's needed to make it testable",
-            "Move redundant setup code into fixtures",
-            "Use test doubles (mocks, stubs, etc.) sparingly"
+            "Always run individual failing tests locally to minimize the feedback loop.",
+            "To fix a bug, start by looking for the precise location in the code where the unexpected result is being produced, starting from the failing test or the error message in the log. Once the location is identified, finding and correcting the error is often trivial.",
+            "When debugging an API test failure, first determine what endpoint is being utilized; then look in `lib/galaxy/webapps/galaxy/api/` to locate the controller that handles that enpoint. The controller will point you to a manager module, which is where you're most likely to find the bug.",
+            "To locate the probable cause of a Selenium test failure, run Selenium with `GALAXY_TEST_SELENIUM_HEADLESS=false` to watch the browser step through the test.",
+            "When debugging a runtime error, use pdb or any other interactive Python debugger to step through the code to identify the location of the error. Remember to use `GALAXY_CONFIG_DEBUG=1` to enable debugging.",
+            "If you find a bug in a code block that is not covered by a test, before you fix the bug, write a test exposing the bug; run the test to ensure it fails; then fix the bug; then run the test again to ensure it passes.",
+            "Write useful and property formatted commit messages.",
+            "Pdb is your friend."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-25",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Learn about the different types of automated tests in Galaxy",
-            "Learn to write API tests",
-            "Learn to write unit tests"
+            "Fix a broken branch",
+            "Interpret the results of failed tests on GitHub",
+            "Run individual tests locally",
+            "Fix errors identified by failing tests",
+            "Debug simple runtime errors using the Python debugger",
+            "Write tests exposing the identified bug"
+        ],
+        "pageviews": 1075,
+        "pub_date": "2021-06-15",
+        "questions": [
+            "How do I debug Galaxy?"
         ],
-        "pageviews": 605,
-        "pub_date": "2022-07-15",
         "requirements": [
             {
                 "title": "Familiarity with basic Git commands",
@@ -58621,15 +60333,15 @@
                 "type": "internal"
             }
         ],
-        "short_id": "T00123",
+        "short_id": "T00115",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "core",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "3h",
-        "title": "Writing Automated Tests for Galaxy",
+        "time_estimation": "4h",
+        "title": "Debugging Galaxy",
         "tools": [],
         "topic_name": "dev",
         "topic_name_human": "Development in Galaxy",
@@ -58639,19 +60351,156 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "writing_tests",
+        "tutorial_name": "debugging",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/dev/tutorials/writing_tests/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/dev/tutorials/debugging/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/writing_tests/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/writing_tests/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/debugging/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/debugging/tutorial.json"
         },
-        "version": 5,
+        "version": 14,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 160,
-        "visitors": 184
+        "visit_duration": 181,
+        "visitors": 479
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-annotation/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "bebatut",
+                "supernord",
+                "paulzierep"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "au",
+                "id": "supernord",
+                "joined": "2024-02",
+                "name": "Johan Gustafsson",
+                "orcid": "0000-0002-2977-5032",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/supernord/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/supernord.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "email": "zierep@informatik.uni-freiburg.de",
+                "id": "paulzierep",
+                "joined": "2023-02",
+                "name": "Paul Zierep",
+                "orcid": "0000-0003-2982-388X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json"
+            }
+        ],
+        "dir": "topics/dev/tutorials/tool-annotation",
+        "edam_operation": [],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "dev/tool-annotation",
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Galaxy tools can get EDAM ontology terms from bio.tools",
+            "bio.tools entry can be created and modified to provide the best EDAM annotations",
+            "An up-to-date bio.tools entry provides readily accessible metadata that can help users find and understand tools that are available on Galaxy",
+            "bio.tools entry can easily be added to a Galaxy tool"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-27",
+        "objectives": [
+            "Identify Galaxy tools without bio.tools entry",
+            "Create a bio.tools entry",
+            "Update a bio.tools entry",
+            "Add EDAM ontology terms to a bio.tools entry",
+            "Link a Galaxy tool to its corresponding bio.tools entry"
+        ],
+        "pageviews": 108,
+        "pub_date": "2024-03-06",
+        "questions": [
+            "How are Galaxy tools linked to EDAM ontology?",
+            "How to connect Galaxy tools to bio.tools?",
+            "What is bio.tools?",
+            "How to add, and update, entries in bio.tools?"
+        ],
+        "short_id": "T00421",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "tooldev",
+        "supported_servers": [],
+        "symlink": null,
+        "time_estimation": "1H",
+        "title": "Adding and updating best practice metadata for Galaxy tools using the bio.tools registry",
+        "tools": [],
+        "topic_name": "dev",
+        "topic_name_human": "Development in Galaxy",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "tool-annotation",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/dev/tutorials/tool-annotation/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-annotation/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-annotation/tutorial.json"
+        },
+        "version": 3,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 177,
+        "visitors": 91
     },
     {
         "admin_install": {
@@ -58782,7 +60631,7 @@
         "license": "CC-BY-4.0",
         "mod_date": "2022-10-18",
         "objectives": null,
-        "pageviews": 280,
+        "pageviews": 284,
         "pub_date": "2016-09-30",
         "questions": [
             "How can I write a tool that can import data into Galaxy from an external database?",
@@ -58818,8 +60667,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 204,
-        "visitors": 174
+        "visit_duration": 201,
+        "visitors": 177
     },
     {
         "admin_install": {
@@ -58829,120 +60678,93 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-from-scratch/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-generators-advanced/tutorial.json",
         "contributors": [
             {
-                "email": "a.ostrovsky@mac.com",
-                "id": "astrovsky01",
-                "joined": "2019-06",
-                "name": "Alex Ostrovsky",
-                "orcid": "0000-0002-7901-7109",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/astrovsky01/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/astrovsky01.json"
-            },
-            {
-                "id": "davebx",
-                "joined": "2021-06",
-                "name": "Dave B.",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/davebx/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/davebx.json"
-            },
-            {
-                "elixir_node": "de",
-                "id": "bernt-matthias",
-                "joined": "2017-09",
-                "name": "Matthias Bernt",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bernt-matthias/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bernt-matthias.json"
+                "elixir_node": "au",
+                "email": "ross.lazarus@gmail.com",
+                "id": "fubar2",
+                "joined": "2021-02",
+                "name": "Ross Lazarus",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fubar2/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/fubar2.json"
             }
         ],
-        "dir": "topics/dev/tutorials/tool-from-scratch",
+        "dir": "topics/dev/tutorials/tool-generators-advanced",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "dev/tool-from-scratch",
+        "id": "dev/tool-generators-advanced",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Galaxy tools are made in 3 parts -- Conda, tool wrappers, and planemo",
-            "Anyone can write and deploy a tool wrapper!"
+            "The ToolFactory Appliance includes an automated form driven tool generator.",
+            "It produces new tools as Toolshed ready archives",
+            "It was designed for scientists and developers who routinely write scripts for their analyses.",
+            "It can quickly turn a working command line script into a working Galaxy tool.",
+            "It generates tools from information entered on a Galaxy form in the familiar UI.",
+            "The new tool is installed in the appliance after generation so can be used and explored immediately.",
+            "New tools can be adjusted as needed by re-running the job that generated the tool and updating the form settings to suit.",
+            "Adding a test to the toolshed archive takes a minute or so and is only needed when the new tool is ready to export for sharing.",
+            "Experimenting with the ToolFactory samples will help acquire insight and skills useful for manual tool building."
         ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
-        "objectives": [
-            "Learn how to make and deploy a conda package",
-            "Understand how to write a Galaxy tool wrapper",
-            "Be able to use a tool wrapper locally",
-            "Be able to test the tool wrapper",
-            "Learn how to add tools to the Galaxy toolshed and make them available to any user"
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-27",
+        "objectives": [
+            "Further develop your ToolFactory Skills"
         ],
-        "pageviews": 3634,
-        "pub_date": "2021-06-15",
+        "pageviews": 375,
+        "pub_date": "2021-05-26",
         "questions": [
-            "How do you create a conda package used as a dependency in a Galaxy tool wrapper?",
-            "How do you create a Galaxy tool wrapper and all of its requirements?",
-            "How do you test a Galaxy tool wrapper after it's written?",
-            "How do you deploy a Galaxy tool wrapper?",
-            "How to do you make a Galaxy tool wrapper publicly available?"
+            "What else can I do with the ToolFactory?"
         ],
         "recordings": [
             {
                 "captioners": [
-                    "gallardoalba",
-                    "astrovsky01"
+                    "fubar2"
                 ],
-                "date": "2023-05-18",
-                "galaxy_version": "22.01",
-                "length": "50M",
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "7M",
                 "speakers": [
-                    "gallardoalba",
-                    "astrovsky01"
+                    "fubar2"
                 ],
-                "youtube_id": "QRoY1pFUY30"
-            },
+                "youtube_id": "DK1eKz5TRs4"
+            }
+        ],
+        "requirements": [
             {
-                "captioners": [
-                    "gallardoalba"
-                ],
-                "date": "2022-03-11",
-                "galaxy_version": "22.01",
-                "length": "40M",
-                "speakers": [
-                    "gallardoalba"
+                "topic_name": "introduction",
+                "tutorials": [
+                    "galaxy-intro-short",
+                    "galaxy-intro-101-everyone"
                 ],
-                "youtube_id": "33L4B9ir0aQ"
+                "type": "internal"
             },
             {
-                "captioners": [
-                    "davebx",
-                    "astrovsky01",
-                    "bernt-matthias"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "1H40M",
-                "speakers": [
-                    "davebx",
-                    "astrovsky01",
-                    "bernt-matthias"
+                "topic_name": "dev",
+                "tutorials": [
+                    "tool-integration",
+                    "interactive-environments",
+                    "tool-generators"
                 ],
-                "youtube_id": "videoseries?list=PLNFLKDpdM3B9GhA0FryVV2YX3YL35rENK"
+                "type": "internal"
             }
         ],
-        "short_id": "T00117",
+        "short_id": "T00119",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "tooldev",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "3H",
-        "title": "Creating Galaxy tools from Conda Through Deployment",
+        "time_estimation": "1H",
+        "title": "ToolFactory: Generating Tools From More Complex Scripts",
         "tools": [],
         "topic_name": "dev",
         "topic_name_human": "Development in Galaxy",
@@ -58952,20 +60774,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "tool-from-scratch",
+        "tutorial_name": "tool-generators-advanced",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/dev/tutorials/tool-from-scratch/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/dev/tutorials/tool-generators-advanced/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-from-scratch/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-from-scratch/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-generators-advanced/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-generators-advanced/tutorial.json"
         },
-        "version": 13,
+        "version": 12,
         "video": false,
-        "video_versions": 3,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 168,
-        "visitors": 2166,
-        "zenodo_link": ""
+        "visit_duration": 131,
+        "visitors": 307
     },
     {
         "admin_install": {
@@ -59028,12 +60849,12 @@
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-24",
+        "mod_date": "2024-09-27",
         "objectives": [
             "Create a community reviewed table for Galaxy tools within a specific scientific domain",
             "Embed an interactive table in a community page"
         ],
-        "pageviews": 59,
+        "pageviews": 63,
         "pub_date": "2024-03-13",
         "questions": [
             "Is it possible to have an overview of all Galaxy tools for a specific scientific domain?",
@@ -59068,14 +60889,22 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/community-tool-table/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/community-tool-table/tutorial.json"
         },
-        "version": 3,
+        "version": 4,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 505,
-        "visitors": 50
+        "visit_duration": 482,
+        "visitors": 54
     },
     {
+        "abbreviations": {
+            "API": "Application Programming Interface",
+            "HDA": "History Dataset Association",
+            "HDCA": "History Dataset Collection Association",
+            "LDA": "Library Dataset Association",
+            "LDCA": "Library Dataset Collection Association",
+            "PR": "Pull Request"
+        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -59083,83 +60912,83 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/core-contributing/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/bioblend-dev/tutorial.json",
         "contributors": [
             {
-                "email": "jmchilton@gmail.com",
-                "id": "jmchilton",
-                "joined": "2017-09",
-                "matrix": "jmchilton:matrix.org",
-                "name": "John Chilton",
-                "orcid": "0000-0002-6794-0756",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jmchilton/",
-                "twitter": "jmchilton",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jmchilton.json"
+                "id": "rikeshi",
+                "joined": "2021-05",
+                "name": "Erik Schill",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/rikeshi/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/rikeshi.json"
             },
             {
-                "email": "jdavcs@gmail.com",
-                "id": "jdavcs",
-                "joined": "2019-06",
-                "name": "John Davis",
-                "orcid": "0000-0002-1363-1245",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jdavcs/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jdavcs.json"
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "simonbray",
+                "joined": "2019-05",
+                "name": "Simon Bray",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
             }
         ],
-        "dir": "topics/dev/tutorials/core-contributing",
+        "dir": "topics/dev/tutorials/bioblend-dev",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "dev/core-contributing",
+        "id": "dev/bioblend-dev",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Galaxy database interactions are mitigated via SQLAlchemy code in lib/galaxy/model.",
-            "Galaxy API endpoints are implemented in lib/galaxy/webapps/galaxy, but generally defer to application logic in lib/galaxy/managers.",
-            "Galaxy client code should do its best to separate API interaction logic from display components."
+            "BioBlend is a Python library that provides methods for easy interaction with the Galaxy API.",
+            "Implementing BioBlend methods is generally quite an easy process, making it well suited to beginners and a viable stepping stone into Galaxy development."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-30",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Learn to develop extensions to the Galaxy data model",
-            "Learn to implement new API functionality within Galaxy",
-            "Learn to extend the Galaxy user interface with VueJS components"
+            "Learn the basics behind BioBlend and the Galaxy API from a developer perspective.",
+            "Learn how to implement a simple method in BioBlend.",
+            "Learn how to run the BioBlend test suite."
         ],
-        "pageviews": 782,
-        "pub_date": "2021-06-08",
+        "pageviews": 255,
+        "pub_date": "2021-05-25",
         "questions": [
-            "How can I add a new feature to Galaxy that involves modifications to the database, the API, and the UI?"
+            "How to get started making contributions to BioBlend?"
         ],
         "requirements": [
             {
-                "topic_name": "contributing",
-                "tutorials": [
-                    "github-command-line-contribution"
-                ],
-                "type": "internal"
+                "title": "Basic command line knowledge",
+                "type": "none"
             },
             {
-                "topic_name": "dev",
-                "tutorials": [
-                    "architecture"
-                ],
-                "type": "internal"
+                "title": "Familiarity with git and access to a GitHub account",
+                "type": "none"
+            },
+            {
+                "title": "Familiarity with the Python programming language",
+                "type": "none"
+            },
+            {
+                "title": "Familiarity with HTTP methods and JavaScript Object Notation (JSON)",
+                "type": "none"
             }
         ],
-        "short_id": "T00113",
+        "short_id": "T00112",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "core",
+        "subtopic": "api",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "3H",
-        "title": "Contributing a New Feature to Galaxy Core",
+        "time_estimation": "3h",
+        "title": "Contributing to BioBlend as a developer",
         "tools": [],
         "topic_name": "dev",
         "topic_name_human": "Development in Galaxy",
@@ -59169,266 +60998,549 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "core-contributing",
+        "tutorial_name": "bioblend-dev",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/dev/tutorials/core-contributing/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/dev/tutorials/bioblend-dev/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/core-contributing/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/core-contributing/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/bioblend-dev/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/bioblend-dev/tutorial.json"
         },
         "version": 8,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 126,
-        "visitors": 490
+        "visit_duration": 208,
+        "visitors": 175
     },
     {
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": []
+            "tools": [
+                {
+                    "name": "srs_diversity_maps",
+                    "owner": "ecology",
+                    "revisions": "9adccd3da70c",
+                    "tool_panel_section_label": "Compute indicators for satellite remote sensing",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "srs_global_indices",
+                    "owner": "ecology",
+                    "revisions": "5cae678042ec",
+                    "tool_panel_section_label": "Compute indicators for satellite remote sensing",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "srs_pca",
+                    "owner": "ecology",
+                    "revisions": "21e21363a8b4",
+                    "tool_panel_section_label": "Compute indicators for satellite remote sensing",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "srs_preprocess_s2",
+                    "owner": "ecology",
+                    "revisions": "33a1e15f7252",
+                    "tool_panel_section_label": "Compute indicators for satellite remote sensing",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "srs_process_data",
+                    "owner": "ecology",
+                    "revisions": "cf69ad260611",
+                    "tool_panel_section_label": "Compute indicators for satellite remote sensing",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "srs_spectral_indices",
+                    "owner": "ecology",
+                    "revisions": "b40aba3d9e5c",
+                    "tool_panel_section_label": "Compute indicators for satellite remote sensing",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-generators-advanced/tutorial.json",
-        "contributors": [
-            {
-                "elixir_node": "au",
-                "email": "ross.lazarus@gmail.com",
-                "id": "fubar2",
-                "joined": "2021-02",
-                "name": "Ross Lazarus",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fubar2/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/fubar2.json"
-            }
-        ],
-        "dir": "topics/dev/tutorials/tool-generators-advanced",
-        "edam_operation": [],
-        "edam_topic": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "dev/tool-generators-advanced",
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: srs_diversity_maps\n  owner: ecology\n  revisions: 9adccd3da70c\n  tool_panel_section_label: Compute indicators for satellite remote sensing\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: srs_global_indices\n  owner: ecology\n  revisions: 5cae678042ec\n  tool_panel_section_label: Compute indicators for satellite remote sensing\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: srs_pca\n  owner: ecology\n  revisions: 21e21363a8b4\n  tool_panel_section_label: Compute indicators for satellite remote sensing\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: srs_preprocess_s2\n  owner: ecology\n  revisions: 33a1e15f7252\n  tool_panel_section_label: Compute indicators for satellite remote sensing\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: srs_process_data\n  owner: ecology\n  revisions: cf69ad260611\n  tool_panel_section_label: Compute indicators for satellite remote sensing\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: srs_spectral_indices\n  owner: ecology\n  revisions: b40aba3d9e5c\n  tool_panel_section_label: Compute indicators for satellite remote sensing\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/remote-sensing/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "Marie59",
+                "yvanlebras"
+            ],
+            "funding": [
+                "pndb"
+            ]
         },
-        "key_points": [
-            "The ToolFactory Appliance includes an automated form driven tool generator.",
-            "It produces new tools as Toolshed ready archives",
-            "It was designed for scientists and developers who routinely write scripts for their analyses.",
-            "It can quickly turn a working command line script into a working Galaxy tool.",
-            "It generates tools from information entered on a Galaxy form in the familiar UI.",
-            "The new tool is installed in the appliance after generation so can be used and explored immediately.",
-            "New tools can be adjusted as needed by re-running the job that generated the tool and updating the form settings to suit.",
-            "Adding a test to the toolshed archive takes a minute or so and is only needed when the new tool is ready to export for sharing.",
-            "Experimenting with the ToolFactory samples will help acquire insight and skills useful for manual tool building."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-25",
-        "objectives": [
-            "Further develop your ToolFactory Skills"
-        ],
-        "pageviews": 369,
-        "pub_date": "2021-05-26",
-        "questions": [
-            "What else can I do with the ToolFactory?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "fubar2"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "7M",
-                "speakers": [
-                    "fubar2"
-                ],
-                "youtube_id": "DK1eKz5TRs4"
-            }
-        ],
-        "requirements": [
+        "contributors": [
             {
-                "topic_name": "introduction",
-                "tutorials": [
-                    "galaxy-intro-short",
-                    "galaxy-intro-101-everyone"
+                "affiliations": [
+                    "pndb",
+                    "fairease"
                 ],
-                "type": "internal"
+                "email": "marie.josse@ifremer.fr",
+                "id": "Marie59",
+                "joined": "2022-03",
+                "name": "Marie Josse",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
             },
             {
-                "topic_name": "dev",
-                "tutorials": [
-                    "tool-integration",
-                    "interactive-environments",
-                    "tool-generators"
+                "affiliations": [
+                    "pndb",
+                    "gallantries",
+                    "fairease",
+                    "fnso2019",
+                    "elixir-europe"
                 ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00119",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "tooldev",
-        "supported_servers": [],
-        "symlink": null,
-        "time_estimation": "1H",
-        "title": "ToolFactory: Generating Tools From More Complex Scripts",
-        "tools": [],
-        "topic_name": "dev",
-        "topic_name_human": "Development in Galaxy",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "tool-generators-advanced",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/dev/tutorials/tool-generators-advanced/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-generators-advanced/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/tool-generators-advanced/tutorial.json"
-        },
-        "version": 11,
-        "video": false,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 133,
-        "visitors": 302
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/debugging/tutorial.json",
-        "contributors": [
-            {
-                "email": "assuntad23@gmail.com",
-                "id": "assuntad23",
-                "joined": "2021-05",
-                "name": "Assunta DeSanto",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/assuntad23/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/assuntad23.json"
-            },
-            {
-                "email": "jdavcs@gmail.com",
-                "id": "jdavcs",
-                "joined": "2019-06",
-                "name": "John Davis",
-                "orcid": "0000-0002-1363-1245",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jdavcs/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jdavcs.json"
+                "elixir_node": "fr",
+                "email": "yvan.le-bras@mnhn.fr",
+                "id": "yvanlebras",
+                "joined": "2017-09",
+                "matrix": "yvanlebras:matrix.org",
+                "name": "Yvan Le Bras",
+                "orcid": "0000-0002-8504-068X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
+                "twitter": "Yvan2935",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
             },
             {
-                "email": "jmchilton@gmail.com",
-                "id": "jmchilton",
-                "joined": "2017-09",
-                "matrix": "jmchilton:matrix.org",
-                "name": "John Chilton",
-                "orcid": "0000-0002-6794-0756",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jmchilton/",
-                "twitter": "jmchilton",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jmchilton.json"
+                "avatar": "/training-material/shared/images/PNDB_sub.png",
+                "github": false,
+                "id": "pndb",
+                "members": [
+                    "colineroyaux",
+                    "Marie59",
+                    "ThibaudGlinez",
+                    "yvanlebras"
+                ],
+                "name": "P\u00f4le National de Donn\u00e9es de Biodiversit\u00e9",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pndb/",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/pndb.json"
             }
         ],
-        "dir": "topics/dev/tutorials/debugging",
+        "dir": "topics/ecology/tutorials/remote-sensing",
         "edam_operation": [],
         "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.fr"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "dev/debugging",
+        "id": "ecology/remote-sensing",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Always run individual failing tests locally to minimize the feedback loop.",
-            "To fix a bug, start by looking for the precise location in the code where the unexpected result is being produced, starting from the failing test or the error message in the log. Once the location is identified, finding and correcting the error is often trivial.",
-            "When debugging an API test failure, first determine what endpoint is being utilized; then look in `lib/galaxy/webapps/galaxy/api/` to locate the controller that handles that enpoint. The controller will point you to a manager module, which is where you're most likely to find the bug.",
-            "To locate the probable cause of a Selenium test failure, run Selenium with `GALAXY_TEST_SELENIUM_HEADLESS=false` to watch the browser step through the test.",
-            "When debugging a runtime error, use pdb or any other interactive Python debugger to step through the code to identify the location of the error. Remember to use `GALAXY_CONFIG_DEBUG=1` to enable debugging.",
-            "If you find a bug in a code block that is not covered by a test, before you fix the bug, write a test exposing the bug; run the test to ensure it fails; then fix the bug; then run the test again to ensure it passes.",
-            "Write useful and property formatted commit messages.",
-            "Pdb is your friend."
+            "Remote sensing data can be useful to find hotspots of biodiversity.",
+            "Spectral indices are of key importance to asset vegetation well-being.",
+            "Always keep in mind that remote sensing and in-situ data are complementary."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-06-27",
         "objectives": [
-            "Fix a broken branch",
-            "Interpret the results of failed tests on GitHub",
-            "Run individual tests locally",
-            "Fix errors identified by failing tests",
-            "Debug simple runtime errors using the Python debugger",
-            "Write tests exposing the identified bug"
+            "Getting Sentinel 2 data and reformatting them in a generalized way",
+            "Computing spectral indices such as the NDVI",
+            "Calculating and visualizing biodiversity indicators",
+            "Comparing with in-situ data"
         ],
-        "pageviews": 1068,
-        "pub_date": "2021-06-15",
+        "pageviews": 425,
+        "pub_date": "2023-04-13",
         "questions": [
-            "How do I debug Galaxy?"
+            "How to get spectral and biodiversity indicators from remote sensing data ?",
+            "Which kind of ecosystem are you studying ? global or canopy data ?"
         ],
-        "requirements": [
-            {
-                "title": "Familiarity with basic Git commands",
-                "type": "none"
-            },
-            {
-                "title": "Basic knowledge of Python and JavaScript",
-                "type": "none"
-            },
-            {
-                "title": "Mac OS or Linux that can run Galaxy & your favorite IDE or editor",
-                "type": "none"
-            },
-            {
-                "topic_name": "dev",
-                "tutorials": [
-                    "architecture"
-                ],
-                "type": "internal"
-            }
+        "short_id": "T00333",
+        "short_tools": [
+            "srs_spectral_indices",
+            "srs_process_data",
+            "srs_diversity_maps",
+            "srs_preprocess_s2",
+            "srs_pca",
+            "srs_global_indices"
         ],
-        "short_id": "T00115",
-        "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "core",
-        "supported_servers": [],
+        "subtopic": "ecologyanalysis",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                }
+            ],
+            "inexact": []
+        },
         "symlink": null,
-        "time_estimation": "4h",
-        "title": "Debugging Galaxy",
-        "tools": [],
-        "topic_name": "dev",
-        "topic_name_human": "Development in Galaxy",
+        "tags": [
+            "Remote sensing"
+        ],
+        "time_estimation": "48H",
+        "title": "Sentinel 2 biodiversity",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/ecology/srs_diversity_maps/srs_diversity_maps/0.0.1",
+            "toolshed.g2.bx.psu.edu/repos/ecology/srs_global_indices/srs_global_indices/0.0.1",
+            "toolshed.g2.bx.psu.edu/repos/ecology/srs_pca/srs_pca/0.0.1",
+            "toolshed.g2.bx.psu.edu/repos/ecology/srs_preprocess_s2/srs_preprocess_s2/0.0.1",
+            "toolshed.g2.bx.psu.edu/repos/ecology/srs_process_data/srs_process_data/0.0.1",
+            "toolshed.g2.bx.psu.edu/repos/ecology/srs_spectral_indices/srs_spectral_indices/0.0.1"
+        ],
+        "topic_name": "ecology",
+        "topic_name_human": "Ecology",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "debugging",
+        "tutorial_name": "remote-sensing",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/dev/tutorials/debugging/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/remote-sensing/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/debugging/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/dev/tutorials/debugging/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/remote-sensing/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/remote-sensing/tutorial.json"
         },
-        "version": 14,
+        "version": 5,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 183,
-        "visitors": 472
+        "visit_duration": 88,
+        "visitors": 330,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "email": "mailto:marie14.josse@gmail.com",
+                        "identifier": "Marie59",
+                        "name": "Marie Josse"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSENTINEL2A_20230214-105638-781_L2A_T31UET_D.zip\"]\n  1[label=\"Preprocess sentinel 2 data\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Compute spectral indices\"]\n  1 -> 2 [label=\"output_refl\"]\n  3[label=\"Compute biodiversity indices\"]\n  1 -> 3 [label=\"output_refl\"]\n  4[label=\"Map diversity\"]\n  1 -> 4 [label=\"output_refl\"]\n}",
+                "history": [
+                    {
+                        "hash": "9ec32f916371d75664d87bfc61c7209b16224f0d",
+                        "message": "Add workflow",
+                        "num": 1,
+                        "short_hash": "9ec32f916",
+                        "unix": "1681207567"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "SENTINEL2A_20230214-105638-781_L2A_T31UET_D.zip"
+                            }
+                        ],
+                        "label": "SENTINEL2A_20230214-105638-781_L2A_T31UET_D.zip",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 95.67931487630185
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "bcaa7cfd-1850-48f5-9f3c-d476805764b5",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSENTINEL2A_20230214-105638-781_L2A_T31UET_D.zip\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Preprocess sentinel 2 data\"];\n  0 -->|output| 1;\n  2[\"Compute spectral indices\"];\n  1 -->|output_refl| 2;\n  3[\"Compute biodiversity indices\"];\n  1 -->|output_refl| 3;\n  4[\"Map diversity\"];\n  1 -->|output_refl| 4;",
+                "modified": "2024-10-02 12:08:07 +0000",
+                "name": "Sentinel 2 example",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/srs_preprocess_s2/srs_preprocess_s2/0.0.1",
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Preprocess sentinel 2 data",
+                                "name": "input"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Preprocess sentinel 2 data",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "csv"
+                            },
+                            {
+                                "name": "output_refl",
+                                "type": "zip"
+                            },
+                            {
+                                "name": "output_cloud",
+                                "type": "zip"
+                            }
+                        ],
+                        "position": {
+                            "left": 338.55905768840034,
+                            "top": 133.4050064677535
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/srs_preprocess_s2/srs_preprocess_s2/0.0.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "33a1e15f7252",
+                            "name": "srs_preprocess_s2",
+                            "owner": "ecology",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"source_s2\": \"SAFE\", \"type_s2\": \"2A\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.0.1",
+                        "type": "tool",
+                        "uuid": "5d5d8bc5-db29-41d5-8c49-ee27a480f5f7",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "77639f71-b4de-4cf7-a753-82ac095f640b"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_refl",
+                                "uuid": "724fb3dc-e0e2-4f6c-a377-ad47c1b6306c"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_cloud",
+                                "uuid": "af28d52b-ef5c-4bd8-817f-6881e4f6bdcc"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/srs_spectral_indices/srs_spectral_indices/0.0.1",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "method|input": {
+                                "id": 1,
+                                "output_name": "output_refl"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Compute spectral indices",
+                        "outputs": [
+                            {
+                                "name": "plots",
+                                "type": "input"
+                            },
+                            {
+                                "name": "output_indices",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 646.041836526378,
+                            "top": 0
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/srs_spectral_indices/srs_spectral_indices/0.0.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "a8dabbf47e15",
+                            "name": "srs_spectral_indices",
+                            "owner": "ecology",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"choice\": \"N\", \"input_indice\": [\"NDVI\"], \"method\": {\"type\": \"zipper\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.0.1",
+                        "type": "tool",
+                        "uuid": "a71dbaa9-14b9-4d71-8dc7-0b8c01da6de1",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_indices",
+                                "uuid": "413c3c32-93a8-42f2-9a5f-515583743c6a"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "plots",
+                                "uuid": "8156dd15-cabc-46b4-a483-1460e3ff87eb"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/srs_global_indices/srs_global_indices/0.0.1",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "method|input": {
+                                "id": 1,
+                                "output_name": "output_refl"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Compute biodiversity indices",
+                        "outputs": [
+                            {
+                                "name": "plots_png",
+                                "type": "input"
+                            },
+                            {
+                                "name": "output_indices",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 643.2986798909894,
+                            "top": 200.60987670512733
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/srs_global_indices/srs_global_indices/0.0.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "5cae678042ec",
+                            "name": "srs_global_indices",
+                            "owner": "ecology",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"alpha\": \"2\", \"method\": {\"type\": \"zipper\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.0.1",
+                        "type": "tool",
+                        "uuid": "5f001f10-d438-408e-b768-6b128fc997b1",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "plots_png",
+                                "uuid": "8a821365-181c-4e39-adda-db360859a4b9"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_indices",
+                                "uuid": "1d529bee-5bda-43f8-9baa-a56ac64dc270"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/srs_diversity_maps/srs_diversity_maps/0.0.1",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "method|input": {
+                                "id": 1,
+                                "output_name": "output_refl"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Map diversity",
+                        "outputs": [
+                            {
+                                "name": "plots",
+                                "type": "input"
+                            },
+                            {
+                                "name": "output_beta",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 641.2327166372127,
+                            "top": 393.50916884961316
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/srs_diversity_maps/srs_diversity_maps/0.0.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "9adccd3da70c",
+                            "name": "srs_diversity_maps",
+                            "owner": "ecology",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"method\": {\"origin\": \"zipper\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"type\": \"beta\", \"typepca\": \"SPCA\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.0.1",
+                        "type": "tool",
+                        "uuid": "e2b9f2a3-2feb-4630-881e-7514f6728207",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "plots",
+                                "uuid": "95fb8122-582a-4e01-b6b9-beae1920d0b6"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_beta",
+                                "uuid": "6d5a4bb8-6abb-4581-842c-85ea3d05a5ab"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "ecology/remote-sensing",
+                "path": "topics/ecology/tutorials/remote-sensing/workflows/Sentinel-2-example.ga",
+                "tags": [],
+                "test_results": null,
+                "tests": true,
+                "title": "Sentinel 2 example",
+                "topic_id": "ecology",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-remote-sensing/versions/sentinel-2-example",
+                "tutorial_id": "remote-sensing",
+                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/remote-sensing/workflows/Sentinel-2-example.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/remote-sensing/workflows/Sentinel-2-example.html",
+                "version": 1,
+                "wfid": "ecology-remote-sensing",
+                "wfname": "sentinel-2-example",
+                "workflow": "Sentinel-2-example.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/ecology/srs_diversity_maps/srs_diversity_maps/0.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/srs_global_indices/srs_global_indices/0.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/srs_preprocess_s2/srs_preprocess_s2/0.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/srs_spectral_indices/srs_spectral_indices/0.0.1"
+                ],
+                "workflowhub_id": "1211"
+            }
+        ],
+        "zenodo_link": ""
     },
     {
         "admin_install": {
@@ -59503,8 +61615,8 @@
                 "members": [
                     "colineroyaux",
                     "Marie59",
-                    "yvanlebras",
-                    "ThibaudGlinez"
+                    "ThibaudGlinez",
+                    "yvanlebras"
                 ],
                 "name": "P\u00f4le National de Donn\u00e9es de Biodiversit\u00e9",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pndb/",
@@ -59540,7 +61652,7 @@
             "Visualize the data to understand them",
             "Clean GBIF dataset for further analyses"
         ],
-        "pageviews": 488,
+        "pageviews": 508,
         "pub_date": "2022-10-28",
         "questions": [
             "How can I get ecological data from GBIF?",
@@ -59549,11 +61661,11 @@
         ],
         "short_id": "T00129",
         "short_tools": [
-            "gdal_ogr2ogr",
+            "Summary_Statistics1",
             "Count1",
-            "spocc_occ",
             "Filter1",
-            "Summary_Statistics1"
+            "gdal_ogr2ogr",
+            "spocc_occ"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -59617,8 +61729,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 63,
-        "visitors": 368,
+        "visit_duration": 61,
+        "visitors": 387,
         "workflows": [
             {
                 "creators": [],
@@ -59649,7 +61761,7 @@
                 "inputs": [],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"Get species occurrences data\"];\n  1[\"Filter\"];\n  0 -->|output| 1;\n  2[\"Count\"];\n  0 -->|output| 2;\n  3[\"Summary Statistics\"];\n  1 -->|out_file1| 3;\n  4[\"Summary Statistics\"];\n  1 -->|out_file1| 4;\n  5[\"Filter\"];\n  1 -->|out_file1| 5;\n  6[\"Filter\"];\n  5 -->|out_file1| 6;\n  7[\"Count\"];\n  6 -->|out_file1| 7;\n  8[\"Filter\"];\n  6 -->|out_file1| 8;\n  9[\"OGR2ogr\"];\n  8 -->|out_file1| 9;\n  10[\"OGR2ogr\"];\n  8 -->|out_file1| 10;",
-                "modified": "2024-08-18 00:06:22 +0000",
+                "modified": "2024-10-02 12:08:07 +0000",
                 "name": "GBIF data Quality check and filtering workflow Feb-2020",
                 "outputs": [],
                 "parent_id": "ecology/gbif_cleaning",
@@ -59679,7 +61791,226 @@
                 "workflowhub_id": "1268"
             }
         ],
-        "zenodo_link": ""
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/Metashrimps_tutorial/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "TanguyGen",
+                "yvanlebras"
+            ],
+            "editing": [
+                "yvanlebras",
+                "hexylena"
+            ],
+            "funding": [
+                "fnso2019",
+                "pndb"
+            ]
+        },
+        "contributors": [
+            {
+                "id": "TanguyGen",
+                "joined": "2023-06",
+                "name": "Tanguy Genthon",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/TanguyGen/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/TanguyGen.json"
+            },
+            {
+                "affiliations": [
+                    "pndb",
+                    "gallantries",
+                    "fairease",
+                    "fnso2019",
+                    "elixir-europe"
+                ],
+                "elixir_node": "fr",
+                "email": "yvan.le-bras@mnhn.fr",
+                "id": "yvanlebras",
+                "joined": "2017-09",
+                "matrix": "yvanlebras:matrix.org",
+                "name": "Yvan Le Bras",
+                "orcid": "0000-0002-8504-068X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
+                "twitter": "Yvan2935",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
+            },
+            {
+                "affiliations": [
+                    "pndb",
+                    "gallantries",
+                    "fairease",
+                    "fnso2019",
+                    "elixir-europe"
+                ],
+                "elixir_node": "fr",
+                "email": "yvan.le-bras@mnhn.fr",
+                "id": "yvanlebras",
+                "joined": "2017-09",
+                "matrix": "yvanlebras:matrix.org",
+                "name": "Yvan Le Bras",
+                "orcid": "0000-0002-8504-068X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
+                "twitter": "Yvan2935",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/fnso.png",
+                "funder": true,
+                "funder_name": "National Fund for Open Science",
+                "funding_id": "AAPFNSO2019OpenMetaPaper-14026",
+                "funding_statement": "This project (<a href=\"https://www.ouvrirlascience.fr/submit-your-data-its-published/\"><code class=\"language-plaintext highlighter-rouge\">AAPFNSO2019OpenMetaPaper-14026</code></a>) is funded with the support of the national Fund for Open Science programme of the French Minister of Higher Education, Research and Innovation. Their funding has supported development of data/metadata management tools and related tutorial for Ecology and FAIR topics.\n<img src=\"https://lamy-environnement.com/wp-content/uploads/2023/03/Logo-MESR.png\" alt=\"French research ministry flag with the text: with the support of the National Fund for Open Science programme of french Minister of Higher Education, Research and Innovation\" />\n<img src=\"/training-material/shared/images/fnso.png\" alt=\"FNSO logo\" />",
+                "github": false,
+                "id": "fnso2019",
+                "joined": "2023-05",
+                "members": [
+                    "yvanlebras"
+                ],
+                "name": "OpenMetaPaper",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fnso2019/",
+                "short_name": "FNSO",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/fnso2019.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/PNDB_sub.png",
+                "github": false,
+                "id": "pndb",
+                "members": [
+                    "colineroyaux",
+                    "Marie59",
+                    "ThibaudGlinez",
+                    "yvanlebras"
+                ],
+                "name": "P\u00f4le National de Donn\u00e9es de Biodiversit\u00e9",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pndb/",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/pndb.json"
+            }
+        ],
+        "dir": "topics/ecology/tutorials/Metashrimps_tutorial",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "ecology/Metashrimps_tutorial",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "This tool aims to improve FAIR quality of metadata",
+            "Creating metadata as FAIR as possible is a must",
+            "Be carefull of the format and standard of metadata used only EML metadata will work"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-27",
+        "objectives": [
+            "Learn how to use the interactive tool Metashrimps",
+            "Understand the challenges MetaShRIMPS is trying to respond to",
+            "Learn how to create a FAIR Quality assessment report from a metadata using EML standard",
+            "Understand the concept of Data Paper and learn how to produce it",
+            "Explain the necessity of using such tools when producing ecological metadata"
+        ],
+        "pageviews": 39,
+        "pub_date": "2024-01-22",
+        "questions": [
+            "How to improve the FAIR quality of an EML metadata ?",
+            "How to use metadata for machine actionnable processes ?",
+            "What is the point of having a FAIR metadata ?"
+        ],
+        "short_id": "T00399",
+        "short_tools": [
+            "interactive_tool_metashrimps"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "ecologymetadatamgt",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "Metadata",
+            "EML",
+            "FAIR",
+            "Data Paper"
+        ],
+        "time_estimation": "30M",
+        "title": "Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS",
+        "tools": [
+            "interactive_tool_metashrimps"
+        ],
+        "topic_name": "ecology",
+        "topic_name_human": "Ecology",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "Metashrimps_tutorial",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/Metashrimps_tutorial/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/Metashrimps_tutorial/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/Metashrimps_tutorial/tutorial.json"
+        },
+        "version": 4,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 160,
+        "visitors": 36,
+        "zenodo_link": "https://doi.org/10.5281/zenodo.8130567"
     },
     {
         "admin_install": {
@@ -59687,6 +62018,20 @@
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
             "tools": [
+                {
+                    "name": "glimmer_gbk_to_orf",
+                    "owner": "bgruening",
+                    "revisions": "04861c9bbf45",
+                    "tool_panel_section_label": "Ecology",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "repeat_masker",
+                    "owner": "bgruening",
+                    "revisions": "39b40a9a6296",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
@@ -59695,196 +62040,153 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "12615d397df7",
+                    "name": "clustalw",
+                    "owner": "devteam",
+                    "revisions": "d6694932c5e0",
+                    "tool_panel_section_label": "Multiple Alignments",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "regex_find_replace",
+                    "owner": "galaxyp",
+                    "revisions": "ae8c4b2488e7",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "obis_data",
-                    "owner": "ecology",
-                    "revisions": "1fcd81d65467",
-                    "tool_panel_section_label": "Get Data",
+                    "name": "busco",
+                    "owner": "iuc",
+                    "revisions": "602fb8e63aa7",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "obisindicators",
-                    "owner": "ecology",
-                    "revisions": "1015a0070bac",
-                    "tool_panel_section_label": "Biodiversity data exploration",
+                    "name": "funannotate_predict",
+                    "owner": "iuc",
+                    "revisions": "2bba2ff070d9",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "obisindicators",
-                    "owner": "ecology",
-                    "revisions": "393957ecc97d",
-                    "tool_panel_section_label": "Biodiversity data exploration",
+                    "name": "proteinortho",
+                    "owner": "iuc",
+                    "revisions": "4850f0d15f01",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "830961c48e42",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "clipkit",
+                    "owner": "padge",
+                    "revisions": "770695339600",
+                    "tool_panel_section_label": "Phylogenetics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "phykit",
+                    "owner": "padge",
+                    "revisions": "1ac6ee298657",
+                    "tool_panel_section_label": "Ecology",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 12615d397df7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obis_data\n  owner: ecology\n  revisions: 1fcd81d65467\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obisindicators\n  owner: ecology\n  revisions: 1015a0070bac\n  tool_panel_section_label: Biodiversity data exploration\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obisindicators\n  owner: ecology\n  revisions: 393957ecc97d\n  tool_panel_section_label: Biodiversity data exploration\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/obisindicators/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "Marie59",
-                "yvanlebras"
-            ],
-            "funding": [
-                "gallantries",
-                "fairease",
-                "eurosciencegateway",
-                "pndb"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: glimmer_gbk_to_orf\n  owner: bgruening\n  revisions: '04861c9bbf45'\n  tool_panel_section_label: Ecology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: repeat_masker\n  owner: bgruening\n  revisions: 39b40a9a6296\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clustalw\n  owner: devteam\n  revisions: d6694932c5e0\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: ae8c4b2488e7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 602fb8e63aa7\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_predict\n  owner: iuc\n  revisions: 2bba2ff070d9\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteinortho\n  owner: iuc\n  revisions: 4850f0d15f01\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clipkit\n  owner: padge\n  revisions: '770695339600'\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: phykit\n  owner: padge\n  revisions: 1ac6ee298657\n  tool_panel_section_label: Ecology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/phylogeny-data-prep/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "pndb",
-                    "fairease"
-                ],
-                "email": "marie.josse@ifremer.fr",
-                "id": "Marie59",
-                "joined": "2022-03",
-                "name": "Marie Josse",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
-            },
-            {
-                "affiliations": [
-                    "pndb",
-                    "gallantries",
-                    "fairease",
-                    "fnso2019",
-                    "elixir-europe"
-                ],
-                "elixir_node": "fr",
-                "email": "yvan.le-bras@mnhn.fr",
-                "id": "yvanlebras",
-                "joined": "2017-09",
-                "matrix": "yvanlebras:matrix.org",
-                "name": "Yvan Le Bras",
-                "orcid": "0000-0002-8504-068X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
-                "twitter": "Yvan2935",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
-            },
-            {
-                "avatar": "/training-material/assets/images/fair_ease_colour.png",
-                "funder": true,
-                "funding_id": "101058785",
-                "funding_statement": "FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "fairease",
-                "joined": "2023-10",
-                "members": [
-                    "Marie59",
-                    "yvanlebras"
-                ],
-                "name": "Fair-Ease",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fairease/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/fairease.json"
-            },
-            {
-                "avatar": "/training-material/assets/images/eurosciencegateway.png",
-                "funder": true,
-                "funding_id": "101057388",
-                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "eurosciencegateway",
-                "joined": "2023-10",
-                "members": [
-                    "abretaud",
-                    "anuprulez",
-                    "bgruening",
-                    "erxleben",
-                    "pauldg",
-                    "rlibouba"
-                ],
-                "name": "EuroScienceGateway",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
+                "email": "miguel.roncoroni@elixir-belgium.org",
+                "id": "roncoronimiguel",
+                "joined": "2021-08",
+                "name": "Miguel Roncoroni",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/roncoronimiguel/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/roncoronimiguel.json"
             },
             {
-                "avatar": "/training-material/shared/images/PNDB_sub.png",
-                "github": false,
-                "id": "pndb",
-                "members": [
-                    "colineroyaux",
-                    "Marie59",
-                    "yvanlebras",
-                    "ThibaudGlinez"
-                ],
-                "name": "P\u00f4le National de Donn\u00e9es de Biodiversit\u00e9",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pndb/",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/pndb.json"
+                "id": "brigidagallone",
+                "joined": "2022-05",
+                "name": "Brigida Gallone",
+                "orcid": "0000-0003-3045-5949",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/brigidagallone/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/brigidagallone.json"
             }
         ],
-        "dir": "topics/ecology/tutorials/obisindicators",
-        "edam_operation": [],
+        "dir": "topics/ecology/tutorials/phylogeny-data-prep",
+        "edam_operation": [
+            "Genome annotation",
+            "Genome assembly",
+            "Sequence analysis",
+            "Multiple sequence alignment",
+            "Sequence assembly validation",
+            "Scaffolding",
+            "Transcriptome assembly",
+            "Genetic variation analysis",
+            "Sequence clustering"
+        ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.be"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "ecology/obisindicators",
+        "id": "ecology/phylogeny-data-prep",
         "inexact_supported_servers": [],
         "js_requirements": {
-            "mathjax": 8847,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Marine data",
-            "Diversity indicators"
+            "You now are able to",
+            "Predict proteins in a nucleotide sequence *de-novo* using **funannotate_predict**",
+            "Find orthologs across different samples with **orthofinder**",
+            "Align orthologs with **ClustalW** in preparation for phylogeny reconstruction <!-- link to phylogeny reconstruction training. -->"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2024-06-27",
         "objectives": [
-            "Calculating and vizualizing marine biodiversity indicators"
+            "Mask repetitive elements from a genome",
+            "Annotate (predict protein-coding genes) the genomes of the samples to compare",
+            "Find a set of common proteins across the samples (orthologs)",
+            "Align orthologs across samples"
         ],
-        "pageviews": 202,
-        "pub_date": "2023-04-11",
+        "pageviews": 2073,
+        "pub_date": "2022-10-21",
         "questions": [
-            "How to retrieve Obis data with Galaxy ?",
-            "How can you analyse and visualise them ?"
+            "How do I find a set of common proteins (orthologs) across related species or strains?",
+            "How do I organize a set of orthologs to infer evolutionary relations between species or strains (phylogenetic reconstruction)?"
         ],
-        "short_id": "T00332",
+        "requirements": [
+            {
+                "topic_name": "assembly",
+                "tutorials": [
+                    "general-introduction"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00132",
         "short_tools": [
-            "obis_data",
-            "tp_cut_tool",
-            "obisindicators"
+            "phykit_alignment_based",
+            "repeatmasker_wrapper",
+            "glimmer_gbk_to_orf",
+            "Filter1",
+            "proteinortho",
+            "busco",
+            "proteinortho_grab_proteins",
+            "tp_replace_in_line",
+            "funannotate_predict",
+            "clipkit",
+            "collapse_dataset",
+            "clustalw",
+            "regex1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -59892,28 +62194,35 @@
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
                 }
             ],
             "inexact": []
         },
         "symlink": null,
         "tags": [
-            "earth-system",
-            "ocean",
-            "marine omics",
-            "biodiversity"
+            "phylogeny",
+            "data handling",
+            "functional annotation"
         ],
-        "time_estimation": "1H",
-        "title": "Obis marine indicators",
+        "time_estimation": "3H",
+        "title": "Preparing genomic data for phylogeny reconstruction",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2",
-            "toolshed.g2.bx.psu.edu/repos/ecology/obisindicators/obisindicators/0.0.1",
-            "toolshed.g2.bx.psu.edu/repos/ecology/obisindicators/obisindicators/0.0.2"
+            "Filter1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/glimmer_gbk_to_orf/glimmer_gbk_to_orf/3.02",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.2-p1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.9+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/proteinortho/proteinortho/6.0.14+galaxy2.9.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.0.14+galaxy2.9.1",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
+            "toolshed.g2.bx.psu.edu/repos/padge/clipkit/clipkit/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/padge/phykit/phykit_alignment_based/0.1.0"
         ],
         "topic_name": "ecology",
         "topic_name_human": "Ecology",
@@ -59923,757 +62232,1049 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "obisindicators",
+        "tutorial_name": "phylogeny-data-prep",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/obisindicators/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/phylogeny-data-prep/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/obisindicators/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/obisindicators/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/phylogeny-data-prep/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/phylogeny-data-prep/tutorial.json"
         },
-        "version": 8,
+        "version": 4,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 136,
-        "visitors": 164,
+        "visit_duration": 167,
+        "visitors": 1531,
         "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "0009-0008-0622-604X",
-                        "name": "Marie Joss\u00e9",
-                        "url": "https://github.com/Marie59"
+                        "identifier": "",
+                        "name": "Miguel Roncoroni"
                     }
                 ],
-                "description": "From Obis data to Biodiversity indicators",
+                "description": "This workflow begins from a set of genome assemblies of different samples, strains, species. The genome is first annotated with Funnanotate. Predicted proteins are furtner annotated with Busco. Next, 'ProteinOrtho' finds orthologs across the samples and makes orthogroups. Orthogroups where all samples are represented are extracted. Orthologs in each orthogroup are aligned with ClustalW. The alignments are cleaned with ClipKIT and the concatenation matrix is built using PhyKit. This can be used for phylogeny reconstruction.",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"OBIS occurences\"]\n  1[label=\"Advanced Cut\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Ocean biodiversity indicators\"]\n  1 -> 2 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput genomes as collection\"]\n  1[label=\"Replace Text\"]\n  0 -> 1 [label=\"output\"]\n  k6a2d3fcdb5574440910db4c537feef20[color=lightseagreen,label=\"Output\\nheaders_shortened\"]\n  1 -> k6a2d3fcdb5574440910db4c537feef20\n  2[label=\"RepeatMasker\"]\n  1 -> 2 [label=\"outfile\"]\n  k1db6607a343a4a619a3b43101eb8223b[color=lightseagreen,label=\"Output\\nrepeat_masked\"]\n  2 -> k1db6607a343a4a619a3b43101eb8223b\n  3[label=\"Funannotate predict annotation\"]\n  2 -> 3 [label=\"output_masked_genome\"]\n  k642c1c0982f44ef4bd53d14a583044e2[color=lightseagreen,label=\"Output\\nfunannotate_predicted_proteins\"]\n  3 -> k642c1c0982f44ef4bd53d14a583044e2\n  4[label=\"Extract ORF\"]\n  3 -> 4 [label=\"annot_gbk\"]\n  k07fb8c04990e4bc7b6079c4161b4786d[color=lightseagreen,label=\"Output\\nextracted_ORFs\"]\n  4 -> k07fb8c04990e4bc7b6079c4161b4786d\n  5[label=\"Regex Find And Replace\"]\n  4 -> 5 [label=\"aa_output\"]\n  k8dc378a8d48542df83226cf8230257a0[color=lightseagreen,label=\"Output\\nsample_names_to_headers\"]\n  5 -> k8dc378a8d48542df83226cf8230257a0\n  6[label=\"Collapse Collection\"]\n  5 -> 6 [label=\"out_file1\"]\n  ke9a554594a2c42388494e99ec67307ea[color=lightseagreen,label=\"Output\\nproteomes_to_one_file\"]\n  6 -> ke9a554594a2c42388494e99ec67307ea\n  7[label=\"Proteinortho\"]\n  5 -> 7 [label=\"out_file1\"]\n  kee688b7a2a9e4480a27adb8cf795b635[color=lightseagreen,label=\"Output\\nProteinortho on input dataset(s): orthology-groups\"]\n  7 -> kee688b7a2a9e4480a27adb8cf795b635\n  8[label=\"Busco\"]\n  5 -> 8 [label=\"out_file1\"]\n  9[label=\"Filter\"]\n  7 -> 9 [label=\"proteinortho\"]\n  10[label=\"Proteinortho grab proteins\"]\n  6 -> 10 [label=\"output\"]\n  9 -> 10 [label=\"out_file1\"]\n  k8625e8b1e3af4afabf851a3258cbbfb2[color=lightseagreen,label=\"Output\\nProteinortho_extract_by_orthogroup\"]\n  10 -> k8625e8b1e3af4afabf851a3258cbbfb2\n  11[label=\"Regex Find And Replace\"]\n  10 -> 11 [label=\"listproteinorthograbproteins\"]\n  kb072d32ef7254833af0b74f4df526d9a[color=lightseagreen,label=\"Output\\nfasta_header_cleaned\"]\n  11 -> kb072d32ef7254833af0b74f4df526d9a\n  12[label=\"ClustalW\"]\n  11 -> 12 [label=\"out_file1\"]\n  kf704b4b2521443938a856274bda27c8c[color=lightseagreen,label=\"Output\\nClustalW on input dataset(s): clustal\"]\n  12 -> kf704b4b2521443938a856274bda27c8c\n  13[label=\"ClipKIT. Alignment trimming software for phylogenetics.\"]\n  12 -> 13 [label=\"output\"]\n  k37092981191a44138f6051802dd95f9c[color=lightseagreen,label=\"Output\\nTrimmed alignment.\"]\n  13 -> k37092981191a44138f6051802dd95f9c\n  14[label=\"PhyKit - Alignment-based functions\"]\n  13 -> 14 [label=\"trimmed_output\"]\n  k09ad25e3cd684fb49c573e79212b8e01[color=lightseagreen,label=\"Output\\nConcatenated fasta alignment file\"]\n  14 -> k09ad25e3cd684fb49c573e79212b8e01\n  k1d546e4c7e3c499d870c4846feb7a46d[color=lightseagreen,label=\"Output\\nA partition file ready for input into RAxML or IQ-tree\"]\n  14 -> k1d546e4c7e3c499d870c4846feb7a46d\n  k26846814d43a4ce79f26cfb70f184dce[color=lightseagreen,label=\"Output\\nAn occupancy file that summarizes the taxon occupancy per sequence\"]\n  14 -> k26846814d43a4ce79f26cfb70f184dce\n}",
                 "history": [
                     {
-                        "hash": "00a713cdfff3d5ee4c936e563aac9e9b17fe087e",
-                        "message": "updated workflow",
-                        "num": 3,
-                        "short_hash": "00a713cdf",
-                        "unix": "1710839703"
+                        "hash": "f7b9464bb24007d8f974decd05b331b67ff877ab",
+                        "message": "Update main_workflow.ga",
+                        "num": 2,
+                        "short_hash": "f7b9464bb",
+                        "unix": "1656489327"
+                    },
+                    {
+                        "hash": "d6ad32e2684e4274d081b593df3966220a6e0d55",
+                        "message": "create phylogenetic-data-prep training backbone",
+                        "num": 1,
+                        "short_hash": "d6ad32e26",
+                        "unix": "1651848710"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Input genomes as collection"
+                            }
+                        ],
+                        "label": "Input genomes as collection",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 309.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 387,
+                            "right": 587,
+                            "top": 227,
+                            "width": 200,
+                            "x": 387,
+                            "y": 227
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "3ae6fd26-b1ef-4339-b84b-82463a3575cf",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput genomes as collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Replace Text\"];\n  0 -->|output| 1;\n  6a2d3fcd-b557-4440-910d-b4c537feef20[\"Output\\nheaders_shortened\"];\n  1 --> 6a2d3fcd-b557-4440-910d-b4c537feef20;\n  style 6a2d3fcd-b557-4440-910d-b4c537feef20 stroke:#2c3143,stroke-width:4px;\n  2[\"RepeatMasker\"];\n  1 -->|outfile| 2;\n  1db6607a-343a-4a61-9a3b-43101eb8223b[\"Output\\nrepeat_masked\"];\n  2 --> 1db6607a-343a-4a61-9a3b-43101eb8223b;\n  style 1db6607a-343a-4a61-9a3b-43101eb8223b stroke:#2c3143,stroke-width:4px;\n  3[\"Funannotate predict annotation\"];\n  2 -->|output_masked_genome| 3;\n  642c1c09-82f4-4ef4-bd53-d14a583044e2[\"Output\\nfunannotate_predicted_proteins\"];\n  3 --> 642c1c09-82f4-4ef4-bd53-d14a583044e2;\n  style 642c1c09-82f4-4ef4-bd53-d14a583044e2 stroke:#2c3143,stroke-width:4px;\n  4[\"Extract ORF\"];\n  3 -->|annot_gbk| 4;\n  07fb8c04-990e-4bc7-b607-9c4161b4786d[\"Output\\nextracted_ORFs\"];\n  4 --> 07fb8c04-990e-4bc7-b607-9c4161b4786d;\n  style 07fb8c04-990e-4bc7-b607-9c4161b4786d stroke:#2c3143,stroke-width:4px;\n  5[\"Regex Find And Replace\"];\n  4 -->|aa_output| 5;\n  8dc378a8-d485-42df-8322-6cf8230257a0[\"Output\\nsample_names_to_headers\"];\n  5 --> 8dc378a8-d485-42df-8322-6cf8230257a0;\n  style 8dc378a8-d485-42df-8322-6cf8230257a0 stroke:#2c3143,stroke-width:4px;\n  6[\"Collapse Collection\"];\n  5 -->|out_file1| 6;\n  e9a55459-4a2c-4238-8494-e99ec67307ea[\"Output\\nproteomes_to_one_file\"];\n  6 --> e9a55459-4a2c-4238-8494-e99ec67307ea;\n  style e9a55459-4a2c-4238-8494-e99ec67307ea stroke:#2c3143,stroke-width:4px;\n  7[\"Proteinortho\"];\n  5 -->|out_file1| 7;\n  ee688b7a-2a9e-4480-a27a-db8cf795b635[\"Output\\nProteinortho on input dataset(s): orthology-groups\"];\n  7 --> ee688b7a-2a9e-4480-a27a-db8cf795b635;\n  style ee688b7a-2a9e-4480-a27a-db8cf795b635 stroke:#2c3143,stroke-width:4px;\n  8[\"Busco\"];\n  5 -->|out_file1| 8;\n  9[\"Filter\"];\n  7 -->|proteinortho| 9;\n  10[\"Proteinortho grab proteins\"];\n  6 -->|output| 10;\n  9 -->|out_file1| 10;\n  8625e8b1-e3af-4afa-bf85-1a3258cbbfb2[\"Output\\nProteinortho_extract_by_orthogroup\"];\n  10 --> 8625e8b1-e3af-4afa-bf85-1a3258cbbfb2;\n  style 8625e8b1-e3af-4afa-bf85-1a3258cbbfb2 stroke:#2c3143,stroke-width:4px;\n  11[\"Regex Find And Replace\"];\n  10 -->|listproteinorthograbproteins| 11;\n  b072d32e-f725-4833-af0b-74f4df526d9a[\"Output\\nfasta_header_cleaned\"];\n  11 --> b072d32e-f725-4833-af0b-74f4df526d9a;\n  style b072d32e-f725-4833-af0b-74f4df526d9a stroke:#2c3143,stroke-width:4px;\n  12[\"ClustalW\"];\n  11 -->|out_file1| 12;\n  f704b4b2-5214-4393-8a85-6274bda27c8c[\"Output\\nClustalW on input dataset(s): clustal\"];\n  12 --> f704b4b2-5214-4393-8a85-6274bda27c8c;\n  style f704b4b2-5214-4393-8a85-6274bda27c8c stroke:#2c3143,stroke-width:4px;\n  13[\"ClipKIT. Alignment trimming software for phylogenetics.\"];\n  12 -->|output| 13;\n  37092981-191a-4413-8f60-51802dd95f9c[\"Output\\nTrimmed alignment.\"];\n  13 --> 37092981-191a-4413-8f60-51802dd95f9c;\n  style 37092981-191a-4413-8f60-51802dd95f9c stroke:#2c3143,stroke-width:4px;\n  14[\"PhyKit - Alignment-based functions\"];\n  13 -->|trimmed_output| 14;\n  09ad25e3-cd68-4fb4-9c57-3e79212b8e01[\"Output\\nConcatenated fasta alignment file\"];\n  14 --> 09ad25e3-cd68-4fb4-9c57-3e79212b8e01;\n  style 09ad25e3-cd68-4fb4-9c57-3e79212b8e01 stroke:#2c3143,stroke-width:4px;\n  1d546e4c-7e3c-499d-870c-4846feb7a46d[\"Output\\nA partition file ready for input into RAxML or IQ-tree\"];\n  14 --> 1d546e4c-7e3c-499d-870c-4846feb7a46d;\n  style 1d546e4c-7e3c-499d-870c-4846feb7a46d stroke:#2c3143,stroke-width:4px;\n  26846814-d43a-4ce7-9f26-cfb70f184dce[\"Output\\nAn occupancy file that summarizes the taxon occupancy per sequence\"];\n  14 --> 26846814-d43a-4ce7-9f26-cfb70f184dce;\n  style 26846814-d43a-4ce7-9f26-cfb70f184dce stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:07 +0000",
+                "name": "preparing genomic data for phylogeny recostruction (GTN)",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {
+                            "infile": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Replace Text",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 359.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": 780.5,
+                            "right": 980.5,
+                            "top": 246,
+                            "width": 200,
+                            "x": 780.5,
+                            "y": 246
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutfile": {
+                                "action_arguments": {
+                                    "newname": "#{infile}"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "outfile"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"find_pattern\": \"(>[^ ]+).+\", \"replace_pattern\": \"\\\\1\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.2",
+                        "type": "tool",
+                        "uuid": "2192525a-028a-4fb3-a772-5ccface42221",
+                        "workflow_outputs": [
+                            {
+                                "label": "headers_shortened",
+                                "output_name": "outfile",
+                                "uuid": "6a2d3fcd-b557-4440-910d-b4c537feef20"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.2-p1+galaxy0",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "input_fasta": {
+                                "id": 1,
+                                "output_name": "outfile"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool RepeatMasker",
+                                "name": "input_fasta"
+                            }
+                        ],
+                        "label": null,
+                        "name": "RepeatMasker",
+                        "outputs": [
+                            {
+                                "name": "output_masked_genome",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "output_log",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "output_table",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "output_repeat_catalog",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 669.3999938964844,
+                            "height": 286.3999938964844,
+                            "left": 1078.5,
+                            "right": 1278.5,
+                            "top": 383,
+                            "width": 200,
+                            "x": 1078.5,
+                            "y": 383
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionoutput_log": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_log"
+                            },
+                            "HideDatasetActionoutput_repeat_catalog": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_repeat_catalog"
+                            },
+                            "HideDatasetActionoutput_table": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_table"
+                            },
+                            "RenameDatasetActionoutput_masked_genome": {
+                                "action_arguments": {
+                                    "newname": "#{input_fasta}"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_masked_genome"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.2-p1+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "39b40a9a6296",
+                            "name": "repeat_masker",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"advanced\": {\"is_only\": \"false\", \"is_clip\": \"false\", \"no_is\": \"false\", \"rodspec\": \"false\", \"primspec\": \"false\", \"nolow\": \"false\", \"noint\": \"false\", \"norna\": \"false\", \"alu\": \"false\", \"div\": \"false\", \"search_speed\": \"\", \"frag\": \"40000\", \"gc\": null, \"gccalc\": \"false\", \"nocut\": \"false\", \"xout\": \"false\", \"keep_alignments\": \"false\", \"invert_alignments\": \"false\", \"xsmall\": \"false\", \"poly\": \"false\"}, \"excln\": \"true\", \"gff\": \"false\", \"input_fasta\": {\"__class__\": \"RuntimeValue\"}, \"repeat_source\": {\"source_type\": \"dfam\", \"__current_case__\": 0, \"species_source\": {\"species_from_list\": \"no\", \"__current_case__\": 1, \"species_name\": \"Saccharomyces cerevisiae\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.1.2-p1+galaxy0",
+                        "type": "tool",
+                        "uuid": "2c65b372-4d50-46a0-8a41-fc9e903956b8",
+                        "workflow_outputs": [
+                            {
+                                "label": "repeat_masked",
+                                "output_name": "output_masked_genome",
+                                "uuid": "1db6607a-343a-4a61-9a3b-43101eb8223b"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.9+galaxy2",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "input": {
+                                "id": 2,
+                                "output_name": "output_masked_genome"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "evidences"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "evidences"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "genemark"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "genemark"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "other_predictors"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "other_predictors"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "other_predictors"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "other_predictors"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "parameters"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Funannotate predict annotation",
+                        "outputs": [
+                            {
+                                "name": "annot_gbk",
+                                "type": "genbank"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 978.2000122070312,
+                            "height": 591.2000122070312,
+                            "left": 1417.5,
+                            "right": 1617.5,
+                            "top": 387,
+                            "width": 200,
+                            "x": 1417.5,
+                            "y": 387
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionannot_gbk": {
+                                "action_arguments": {
+                                    "newname": "#{input}"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "annot_gbk"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.9+galaxy2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2bba2ff070d9",
+                            "name": "funannotate_predict",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"augustus\": {\"augustus_species\": \"none\", \"min_training_models\": \"15\", \"optimize_augustus\": \"false\"}, \"busco\": {\"busco_db\": \"saccharomycetes\", \"busco_seed_species\": \"saccharomyces\"}, \"database\": \"2022-03-24-174412\", \"evidences\": {\"rna_bam\": {\"__class__\": \"RuntimeValue\"}, \"transcript_evidence\": {\"__class__\": \"RuntimeValue\"}, \"prot_evidence\": {\"prot_evidence_source\": \"uniprot\", \"__current_case__\": 0}, \"p2g_pident\": \"80\", \"p2g_prefilter\": \"diamond\"}, \"evm\": {\"repeats2evm\": \"false\", \"evm_partitioning\": {\"evm_partition\": \"yes\", \"__current_case__\": 0, \"evm_partition_interval\": \"1500\"}, \"weights\": \"\"}, \"filtering\": {\"min_intronlen\": \"10\", \"max_intronlen\": \"3000\", \"min_protlen\": \"50\", \"keep_no_stops\": \"false\", \"repeat_filter\": \"overlap blast\"}, \"force\": \"true\", \"genemark\": {\"genemark_license\": {\"__class__\": \"RuntimeValue\"}, \"genemark_mode\": \"ES\", \"genemark_mod\": {\"__class__\": \"RuntimeValue\"}, \"soft_mask\": \"2000\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"organism\": {\"species\": \"Saccharomyces cerevisiae\", \"isolate\": \"\", \"strain\": \"\", \"organism\": \"true\", \"ploidy\": \"1\", \"SeqCenter\": \"CFMR\", \"SeqAccession\": \"12345\", \"name\": \"FUN_\", \"numbering\": \"1\"}, \"other_predictors\": {\"stringtie\": {\"__class__\": \"RuntimeValue\"}, \"maker_gff\": {\"__class__\": \"RuntimeValue\"}, \"pasa_gff\": {\"__class__\": \"RuntimeValue\"}, \"pasa_gff_weight\": \"1\", \"other_gff\": {\"__class__\": \"RuntimeValue\"}, \"other_gff_weight\": \"1\"}, \"outputs\": [\"gbk\"], \"parameters\": {\"__class__\": \"RuntimeValue\"}, \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.9+galaxy2",
+                        "type": "tool",
+                        "uuid": "760b55d2-5e23-41f5-9766-e939fe5e6d9b",
+                        "workflow_outputs": [
+                            {
+                                "label": "funannotate_predicted_proteins",
+                                "output_name": "annot_gbk",
+                                "uuid": "642c1c09-82f4-4ef4-bd53-d14a583044e2"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/glimmer_gbk_to_orf/glimmer_gbk_to_orf/3.02",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "infile": {
+                                "id": 3,
+                                "output_name": "annot_gbk"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Extract ORF",
+                        "outputs": [
+                            {
+                                "name": "aa_output",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "nc_output",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 763.6000061035156,
+                            "height": 123.60000610351562,
+                            "left": 1705.5,
+                            "right": 1905.5,
+                            "top": 640,
+                            "width": 200,
+                            "x": 1705.5,
+                            "y": 640
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionaa_output": {
+                                "action_arguments": {
+                                    "newname": "#{infile}"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "aa_output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/glimmer_gbk_to_orf/glimmer_gbk_to_orf/3.02",
+                        "tool_shed_repository": {
+                            "changeset_revision": "04861c9bbf45",
+                            "name": "glimmer_gbk_to_orf",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.02",
+                        "type": "tool",
+                        "uuid": "ac2baad9-7cdd-4c59-a260-492d4f54bed4",
+                        "workflow_outputs": [
+                            {
+                                "label": "extracted_ORFs",
+                                "output_name": "aa_output",
+                                "uuid": "07fb8c04-990e-4bc7-b607-9c4161b4786d"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "nc_output",
+                                "uuid": "3b303171-139b-45dc-943b-8a425f679f46"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "input": {
+                                "id": 4,
+                                "output_name": "aa_output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Regex Find And Replace",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 794.3999938964844,
+                            "height": 154.39999389648438,
+                            "left": 1992,
+                            "right": 2192,
+                            "top": 640,
+                            "width": 200,
+                            "x": 1992,
+                            "y": 640
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "#{input}"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ae8c4b2488e7",
+                            "name": "regex_find_replace",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \">([^ ]+).+\", \"replacement\": \">#{input_name}_\\\\1\"}], \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.1",
+                        "type": "tool",
+                        "uuid": "adaf4b62-fe6a-4881-a6af-1e2afb87bfe9",
+                        "workflow_outputs": [
+                            {
+                                "label": "sample_names_to_headers",
+                                "output_name": "out_file1",
+                                "uuid": "8dc378a8-d485-42df-8322-6cf8230257a0"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "input_list": {
+                                "id": 5,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Collapse Collection",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 494.3999938964844,
+                            "height": 154.39999389648438,
+                            "left": 2314.966552734375,
+                            "right": 2514.966552734375,
+                            "top": 340,
+                            "width": 200,
+                            "x": 2314.966552734375,
+                            "y": 340
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "830961c48e42",
+                            "name": "collapse_collections",
+                            "owner": "nml",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"filename\": {\"add_name\": \"false\", \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.2",
+                        "type": "tool",
+                        "uuid": "ae4ddb2f-104b-409f-9d91-07c4410ba00a",
+                        "workflow_outputs": [
+                            {
+                                "label": "proteomes_to_one_file",
+                                "output_name": "output",
+                                "uuid": "e9a55459-4a2c-4238-8494-e99ec67307ea"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/proteinortho/proteinortho/6.0.14+galaxy2.9.1",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "input_files": {
+                                "id": 5,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Proteinortho",
+                        "outputs": [
+                            {
+                                "name": "blastgraph",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "proteinortho",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "proteinorthograph",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 826.3333129882812,
+                            "height": 296.79998779296875,
+                            "left": 2307.966552734375,
+                            "right": 2507.966552734375,
+                            "top": 529.5333251953125,
+                            "width": 200,
+                            "x": 2307.966552734375,
+                            "y": 529.5333251953125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/proteinortho/proteinortho/6.0.14+galaxy2.9.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "4850f0d15f01",
+                            "name": "proteinortho",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"conn\": \"0.1\", \"evalue\": \"0.001\", \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"more_options\": {\"cov\": \"50\", \"sim\": \"95\", \"identity\": \"25\", \"selfblast\": \"false\", \"singles\": \"false\", \"isoform\": \"no\"}, \"p\": \"diamond\", \"synteny\": {\"synteny_options\": \"no\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "6.0.14+galaxy2.9.1",
+                        "type": "tool",
+                        "uuid": "2d05e13f-4cb1-4d86-800f-3e743b50fab8",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "proteinorthograph",
+                                "uuid": "42f51f73-f573-4d2f-a703-04dd329dfd4b"
+                            },
+                            {
+                                "label": "Proteinortho on input dataset(s): orthology-groups",
+                                "output_name": "proteinortho",
+                                "uuid": "ee688b7a-2a9e-4480-a27a-db8cf795b635"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "blastgraph",
+                                "uuid": "e2b3b5ba-33ec-4330-bebc-2bb7f3c2b360"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "input": {
+                                "id": 5,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Busco",
+                        "outputs": [
+                            {
+                                "name": "busco_sum",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "busco_table",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "busco_missing",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 1122.3999938964844,
+                            "height": 276.3999938964844,
+                            "left": 2316.466552734375,
+                            "right": 2516.466552734375,
+                            "top": 846,
+                            "width": 200,
+                            "x": 2316.466552734375,
+                            "y": 846
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "602fb8e63aa7",
+                            "name": "busco",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"chromInfo\": \"/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"CM005299.1\", \"lineage_dataset\": \"saccharomycetes_odb10\", \"mode\": \"prot\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.1.4",
+                        "type": "tool",
+                        "uuid": "174f50d8-09bd-48b9-afcd-44468e41a0c3",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "busco_sum",
+                                "uuid": "471d5e9e-db3e-44ee-9936-22f5e9072fd1"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "busco_missing",
+                                "uuid": "2195fc7f-ae89-43e8-ba1e-d45955b8856e"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "busco_table",
+                                "uuid": "76879cb7-9b5f-443b-84a4-414e2fe0b14d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "Filter1",
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {
+                            "input": {
+                                "id": 7,
+                                "output_name": "proteinortho"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Filter",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 785.7333221435547,
+                            "height": 93.19999694824219,
+                            "left": 2585,
+                            "right": 2785,
+                            "top": 692.5333251953125,
+                            "width": 200,
+                            "x": 2585,
+                            "y": 692.5333251953125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"cond\": \"c1==4 and c2==4\", \"header_lines\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
+                        "type": "tool",
+                        "uuid": "b4758296-c3c9-4c3c-bb2d-2f637f8702b5",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "c03839b1-17e0-4fb1-8b53-d3fd2a89aaba"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.0.14+galaxy2.9.1",
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {
+                            "input_files": {
+                                "id": 6,
+                                "output_name": "output"
+                            },
+                            "query|queryfile": {
+                                "id": 9,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Proteinortho grab proteins",
+                        "outputs": [
+                            {
+                                "name": "listproteinorthograbproteins",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 597.8000030517578,
+                            "height": 184.8000030517578,
+                            "left": 2850,
+                            "right": 3050,
+                            "top": 413,
+                            "width": 200,
+                            "x": 2850,
+                            "y": 413
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionlistproteinorthograbproteins": {
+                                "action_arguments": {
+                                    "newname": "#{query.queryfile}"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "listproteinorthograbproteins"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.0.14+galaxy2.9.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "d348c3a151d9",
+                            "name": "proteinortho_grab_proteins",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input_files\": {\"__class__\": \"ConnectedValue\"}, \"query\": {\"querytype\": \"file\", \"__current_case__\": 1, \"queryfile\": {\"__class__\": \"ConnectedValue\"}}, \"regex\": \"false\", \"source\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "6.0.14+galaxy2.9.1",
+                        "type": "tool",
+                        "uuid": "78e25a29-21b2-47ab-ac0e-a5b958258086",
+                        "workflow_outputs": [
+                            {
+                                "label": "Proteinortho_extract_by_orthogroup",
+                                "output_name": "listproteinorthograbproteins",
+                                "uuid": "8625e8b1-e3af-4afa-bf85-1a3258cbbfb2"
+                            }
+                        ]
                     },
                     {
-                        "hash": "ce566378abf7d51f9aee0f33727e8573c71b698f",
-                        "message": "Add files via upload",
-                        "num": 2,
-                        "short_hash": "ce566378a",
-                        "unix": "1680848192"
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1",
+                        "errors": null,
+                        "id": 11,
+                        "input_connections": {
+                            "input": {
+                                "id": 10,
+                                "output_name": "listproteinorthograbproteins"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Regex Find And Replace",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 541,
+                            "height": 134,
+                            "left": 3151,
+                            "right": 3351,
+                            "top": 407,
+                            "width": 200,
+                            "x": 3151,
+                            "y": 407
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "#{input}"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ae8c4b2488e7",
+                            "name": "regex_find_replace",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \"(>[^_]+).+\", \"replacement\": \"\\\\1\"}], \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.1",
+                        "type": "tool",
+                        "uuid": "c99a9988-fa6a-4366-8c9f-9195e7f77b19",
+                        "workflow_outputs": [
+                            {
+                                "label": "fasta_header_cleaned",
+                                "output_name": "out_file1",
+                                "uuid": "b072d32e-f725-4833-af0b-74f4df526d9a"
+                            }
+                        ]
                     },
                     {
-                        "hash": "5cf36e64c0a8b287d9e108919e23581c6fa4aa5b",
-                        "message": "Add files via upload",
-                        "num": 1,
-                        "short_hash": "5cf36e64c",
-                        "unix": "1680787259"
-                    }
-                ],
-                "inputs": [],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"OBIS occurences\"];\n  1[\"Advanced Cut\"];\n  0 -->|output| 1;\n  2[\"Ocean biodiversity indicators\"];\n  1 -->|output| 2;",
-                "modified": "2024-08-18 00:06:22 +0000",
-                "name": "Marine Omics visualisation",
-                "outputs": [],
-                "parent_id": "ecology/obisindicators",
-                "path": "topics/ecology/tutorials/obisindicators/workflows/Obis-indicators.ga",
-                "tags": [
-                    "Ocean",
-                    "Marineomics",
-                    "earth-system"
-                ],
-                "test_results": {
-                    "eu": {
-                        "summary": {
-                            "num_errors": 0,
-                            "num_failures": 0,
-                            "num_skips": 0,
-                            "num_tests": 1
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {
+                            "input": {
+                                "id": 11,
+                                "output_name": "out_file1"
+                            }
                         },
-                        "tests": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "ClustalW",
+                        "outputs": [
                             {
-                                "data": {
-                                    "end_datetime": "2023-05-23T13:01:11.109149",
-                                    "inputs": {
-                                        "Occurrence.csv": {
-                                            "class": "File",
-                                            "filetype": "csv",
-                                            "path": "test-data/Occurrence.csv.csv"
-                                        }
-                                    },
-                                    "invocation_details": {
-                                        "details": {
-                                            "error_message": "",
-                                            "history_id": "18649784ceeae594",
-                                            "history_state": "ok",
-                                            "invocation_id": "5416bcf2f590c4c2",
-                                            "invocation_state": "scheduled",
-                                            "workflow_id": "fbbe3ba09fea56a3"
-                                        },
-                                        "steps": {
-                                            "0. Occurrence.csv": {
-                                                "action": null,
-                                                "id": "081be084fdd665d8",
-                                                "job_id": null,
-                                                "jobs": [],
-                                                "model_class": "WorkflowInvocationStep",
-                                                "order_index": 0,
-                                                "output_collections": {},
-                                                "outputs": {
-                                                    "output": {
-                                                        "id": "4838ba20a6d867651377ade0c55e4376",
-                                                        "src": "hda",
-                                                        "uuid": "0ba0ffa3-b7b6-4f70-a9f5-b635cd06615d"
-                                                    }
-                                                },
-                                                "state": "scheduled",
-                                                "subworkflow": null,
-                                                "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-23T10:58:01.456172",
-                                                "workflow_step_id": "6919056b5db62ca4",
-                                                "workflow_step_label": "Occurrence.csv",
-                                                "workflow_step_uuid": "cf8be611-fbf7-428b-b1f6-113c1c2e1eae"
-                                            },
-                                            "1. Unnamed step": {
-                                                "action": null,
-                                                "id": "9029b42bf346eab8",
-                                                "job_id": "11ac94870d0bb33aaf0d076bb75012e2",
-                                                "jobs": [
-                                                    {
-                                                        "command_line": "python '/opt/galaxy/server/lib/galaxy/datatypes/converters/tabular_csv.py' -o '/data/jwd01/main/060/156/60156723/outputs/galaxy_dataset_e3394d0e-14f6-44d6-9752-82710416346b.dat' -i '/data/dnb08/galaxy_db/files/0/b/a/dataset_0ba0ffa3-b7b6-4f70-a9f5-b635cd06615d.dat'",
-                                                        "command_version": null,
-                                                        "create_time": "2023-05-23T10:58:01.450496",
-                                                        "dependencies": [
-                                                            {
-                                                                "cacheable": false,
-                                                                "dependency_resolver": {
-                                                                    "auto_init": true,
-                                                                    "auto_install": false,
-                                                                    "can_uninstall_dependencies": true,
-                                                                    "ensure_channels": "conda-forge,bioconda",
-                                                                    "model_class": "CondaDependencyResolver",
-                                                                    "prefix": "/usr/local/tools/_conda",
-                                                                    "read_only": false,
-                                                                    "resolver_type": "conda",
-                                                                    "resolves_simple_dependencies": true,
-                                                                    "use_local": false,
-                                                                    "versionless": false
-                                                                },
-                                                                "dependency_type": "conda",
-                                                                "environment_path": "/usr/local/tools/_conda/envs/__python@3.7",
-                                                                "exact": true,
-                                                                "model_class": "MergedCondaDependency",
-                                                                "name": "python",
-                                                                "version": "3.7"
-                                                            }
-                                                        ],
-                                                        "exit_code": 0,
-                                                        "external_id": "43631290",
-                                                        "galaxy_version": "23.0",
-                                                        "history_id": "18649784ceeae594",
-                                                        "id": "11ac94870d0bb33aaf0d076bb75012e2",
-                                                        "inputs": {
-                                                            "csv": {
-                                                                "id": "4838ba20a6d867651377ade0c55e4376",
-                                                                "src": "hda",
-                                                                "uuid": "0ba0ffa3-b7b6-4f70-a9f5-b635cd06615d"
-                                                            }
-                                                        },
-                                                        "job_messages": [],
-                                                        "job_metrics": [
-                                                            {
-                                                                "name": "hostname",
-                                                                "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c36m100-6296.novalocal",
-                                                                "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c36m100-6296.novalocal"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_slots",
-                                                                "plugin": "core",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "Cores Allocated",
-                                                                "value": "1"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_memory_mb",
-                                                                "plugin": "core",
-                                                                "raw_value": "3891.0000000",
-                                                                "title": "Memory Allocated (MB)",
-                                                                "value": "3891"
-                                                            },
-                                                            {
-                                                                "name": "start_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684839498.0000000",
-                                                                "title": "Job Start Time",
-                                                                "value": "2023-05-23 12:58:18"
-                                                            },
-                                                            {
-                                                                "name": "end_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684839529.0000000",
-                                                                "title": "Job End Time",
-                                                                "value": "2023-05-23 12:58:49"
-                                                            },
-                                                            {
-                                                                "name": "runtime_seconds",
-                                                                "plugin": "core",
-                                                                "raw_value": "31.0000000",
-                                                                "title": "Job Runtime (Wall Clock)",
-                                                                "value": "31 seconds"
-                                                            },
-                                                            {
-                                                                "name": "cpuacct.usage",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "14969322405.0000000",
-                                                                "title": "CPU Time",
-                                                                "value": "14.969322405 seconds"
-                                                            },
-                                                            {
-                                                                "name": "memory.failcnt",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Failed to allocate memory count",
-                                                                "value": 0.0
-                                                            },
-                                                            {
-                                                                "name": "memory.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "4160749568.0000000",
-                                                                "title": "Memory limit on cgroup (MEM)",
-                                                                "value": "3.9 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "210845696.0000000",
-                                                                "title": "Max memory usage (MEM)",
-                                                                "value": "201.1 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "4219351040.0000000",
-                                                                "title": "Memory limit on cgroup (MEM+SWP)",
-                                                                "value": "3.9 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "210845696.0000000",
-                                                                "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "201.1 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.oom_kill_disable",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "OOM Control enabled",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.under_oom",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Was OOM Killer active?",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.soft_limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Memory softlimit on cgroup",
-                                                                "value": "0 bytes"
-                                                            }
-                                                        ],
-                                                        "job_stderr": "",
-                                                        "job_stdout": "",
-                                                        "model_class": "Job",
-                                                        "output_collections": {},
-                                                        "outputs": {
-                                                            "tabular": {
-                                                                "id": "4838ba20a6d867659478aa0f23a27d78",
-                                                                "src": "hda",
-                                                                "uuid": "e3394d0e-14f6-44d6-9752-82710416346b"
-                                                            }
-                                                        },
-                                                        "params": {
-                                                            "__input_ext": "\"input\"",
-                                                            "__target_datatype__": "\"tabular\"",
-                                                            "__workflow_invocation_uuid__": "\"a98238aaf95811ed822c001e67d2ec02\"",
-                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
-                                                            "dbkey": "\"?\""
-                                                        },
-                                                        "state": "ok",
-                                                        "stderr": "",
-                                                        "stdout": "",
-                                                        "tool_id": "csv_to_tabular",
-                                                        "tool_stderr": "",
-                                                        "tool_stdout": "",
-                                                        "traceback": null,
-                                                        "update_time": "2023-05-23T10:58:53.605766",
-                                                        "user_email": "hxr@informatik.uni-freiburg.de"
-                                                    }
-                                                ],
-                                                "model_class": "WorkflowInvocationStep",
-                                                "order_index": 1,
-                                                "output_collections": {},
-                                                "outputs": {
-                                                    "tabular": {
-                                                        "id": "4838ba20a6d867659478aa0f23a27d78",
-                                                        "src": "hda",
-                                                        "uuid": "e3394d0e-14f6-44d6-9752-82710416346b"
-                                                    }
-                                                },
-                                                "state": "scheduled",
-                                                "subworkflow": null,
-                                                "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-23T10:58:53.286673",
-                                                "workflow_step_id": "901c22ecf4799bd6",
-                                                "workflow_step_label": null,
-                                                "workflow_step_uuid": "68d37ef8-8a10-46ba-8bce-4cda1bdab0e1"
-                                            },
-                                            "2. Unnamed step": {
-                                                "action": null,
-                                                "id": "347cfc8750f2fe94",
-                                                "job_id": "11ac94870d0bb33a413dde79a1714548",
-                                                "jobs": [
-                                                    {
-                                                        "command_line": "cut  -f '1,3,4,9,95' '/data/dnb08/galaxy_db/files/e/3/3/dataset_e3394d0e-14f6-44d6-9752-82710416346b.dat' > '/data/jwd02f/main/060/156/60156724/outputs/galaxy_dataset_c3b48c80-ad5e-4f84-b68d-db94fd9f4ec7.dat'",
-                                                        "command_version": "cut (GNU coreutils) 8.25",
-                                                        "create_time": "2023-05-23T10:58:01.530299",
-                                                        "dependencies": [],
-                                                        "exit_code": 0,
-                                                        "external_id": "43631331",
-                                                        "galaxy_version": "23.0",
-                                                        "history_id": "18649784ceeae594",
-                                                        "id": "11ac94870d0bb33a413dde79a1714548",
-                                                        "inputs": {
-                                                            "input": {
-                                                                "id": "4838ba20a6d867659478aa0f23a27d78",
-                                                                "src": "hda",
-                                                                "uuid": "e3394d0e-14f6-44d6-9752-82710416346b"
-                                                            }
-                                                        },
-                                                        "job_messages": [],
-                                                        "job_metrics": [
-                                                            {
-                                                                "name": "hostname",
-                                                                "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c36m975-5969.novalocal",
-                                                                "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c36m975-5969.novalocal"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_slots",
-                                                                "plugin": "core",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "Cores Allocated",
-                                                                "value": "1"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_memory_mb",
-                                                                "plugin": "core",
-                                                                "raw_value": "3891.0000000",
-                                                                "title": "Memory Allocated (MB)",
-                                                                "value": "3891"
-                                                            },
-                                                            {
-                                                                "name": "start_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684839542.0000000",
-                                                                "title": "Job Start Time",
-                                                                "value": "2023-05-23 12:59:02"
-                                                            },
-                                                            {
-                                                                "name": "end_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684839558.0000000",
-                                                                "title": "Job End Time",
-                                                                "value": "2023-05-23 12:59:18"
-                                                            },
-                                                            {
-                                                                "name": "runtime_seconds",
-                                                                "plugin": "core",
-                                                                "raw_value": "16.0000000",
-                                                                "title": "Job Runtime (Wall Clock)",
-                                                                "value": "16 seconds"
-                                                            },
-                                                            {
-                                                                "name": "cpuacct.usage",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "10210526103.0000000",
-                                                                "title": "CPU Time",
-                                                                "value": "10.210526103 seconds"
-                                                            },
-                                                            {
-                                                                "name": "memory.failcnt",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Failed to allocate memory count",
-                                                                "value": 0.0
-                                                            },
-                                                            {
-                                                                "name": "memory.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "9223372036854771712.0000000",
-                                                                "title": "Memory limit on cgroup (MEM)",
-                                                                "value": "8.0 EB"
-                                                            },
-                                                            {
-                                                                "name": "memory.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "195211264.0000000",
-                                                                "title": "Max memory usage (MEM)",
-                                                                "value": "186.2 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "9223372036854771712.0000000",
-                                                                "title": "Memory limit on cgroup (MEM+SWP)",
-                                                                "value": "8.0 EB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "195211264.0000000",
-                                                                "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "186.2 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.oom_kill_disable",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "OOM Control enabled",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.under_oom",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Was OOM Killer active?",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.soft_limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "4160749568.0000000",
-                                                                "title": "Memory softlimit on cgroup",
-                                                                "value": "3.9 GB"
-                                                            }
-                                                        ],
-                                                        "job_stderr": "",
-                                                        "job_stdout": "",
-                                                        "model_class": "Job",
-                                                        "output_collections": {},
-                                                        "outputs": {
-                                                            "output": {
-                                                                "id": "4838ba20a6d8676581b548fa09109a8c",
-                                                                "src": "hda",
-                                                                "uuid": "c3b48c80-ad5e-4f84-b68d-db94fd9f4ec7"
-                                                            }
-                                                        },
-                                                        "params": {
-                                                            "__input_ext": "\"tabular\"",
-                                                            "__workflow_invocation_uuid__": "\"a98238aaf95811ed822c001e67d2ec02\"",
-                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
-                                                            "complement": "\"\"",
-                                                            "cut_type_options": "{\"__current_case__\": 0, \"cut_element\": \"-f\", \"list\": [\"1\", \"3\", \"4\", \"9\", \"95\"]}",
-                                                            "dbkey": "\"?\"",
-                                                            "delimiter": "\"\""
-                                                        },
-                                                        "state": "ok",
-                                                        "stderr": "",
-                                                        "stdout": "",
-                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-                                                        "tool_stderr": "",
-                                                        "tool_stdout": "",
-                                                        "traceback": null,
-                                                        "update_time": "2023-05-23T10:59:20.902960",
-                                                        "user_email": "hxr@informatik.uni-freiburg.de"
-                                                    }
-                                                ],
-                                                "model_class": "WorkflowInvocationStep",
-                                                "order_index": 2,
-                                                "output_collections": {},
-                                                "outputs": {
-                                                    "output": {
-                                                        "id": "4838ba20a6d8676581b548fa09109a8c",
-                                                        "src": "hda",
-                                                        "uuid": "c3b48c80-ad5e-4f84-b68d-db94fd9f4ec7"
-                                                    }
-                                                },
-                                                "state": "scheduled",
-                                                "subworkflow": null,
-                                                "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-23T10:59:20.871746",
-                                                "workflow_step_id": "8221333250114ef6",
-                                                "workflow_step_label": null,
-                                                "workflow_step_uuid": "f268a9c2-c603-4746-8f7c-9e06742934b5"
-                                            },
-                                            "3. Unnamed step": {
-                                                "action": null,
-                                                "id": "3d1f5a3044f2e3db",
-                                                "job_id": "11ac94870d0bb33a13d697639a952600",
-                                                "jobs": [
-                                                    {
-                                                        "command_line": "Rscript '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ecology/obisindicators/d7b6ff32d072/obisindicators/obisindicators.r' '/data/dnb08/galaxy_db/files/c/3/b/dataset_c3b48c80-ad5e-4f84-b68d-db94fd9f4ec7.dat' 'true' 't' '2' '3' '4' '5' '0' '10' '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ecology/obisindicators/d7b6ff32d072/obisindicators/analyze.r' '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ecology/obisindicators/d7b6ff32d072/obisindicators/visualize.r' '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ecology/obisindicators/d7b6ff32d072/obisindicators/data.r' '/data/jwd05e/main/060/156/60156725/outputs/galaxy_dataset_91bb988c-8725-4295-828d-1ac13db8a60f.dat' '<galaxy.tools.wrappers.DatasetCollectionWrapper object at 0x7fd2902529a0>'",
-                                                        "command_version": null,
-                                                        "create_time": "2023-05-23T10:58:01.621838",
-                                                        "dependencies": [],
-                                                        "exit_code": 0,
-                                                        "external_id": "43631352",
-                                                        "galaxy_version": "23.0",
-                                                        "history_id": "18649784ceeae594",
-                                                        "id": "11ac94870d0bb33a13d697639a952600",
-                                                        "inputs": {
-                                                            "input": {
-                                                                "id": "4838ba20a6d8676581b548fa09109a8c",
-                                                                "src": "hda",
-                                                                "uuid": "c3b48c80-ad5e-4f84-b68d-db94fd9f4ec7"
-                                                            }
-                                                        },
-                                                        "job_messages": [],
-                                                        "job_metrics": [
-                                                            {
-                                                                "name": "hostname",
-                                                                "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c36m975-0315.novalocal",
-                                                                "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c36m975-0315.novalocal"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_slots",
-                                                                "plugin": "core",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "Cores Allocated",
-                                                                "value": "1"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_memory_mb",
-                                                                "plugin": "core",
-                                                                "raw_value": "3891.0000000",
-                                                                "title": "Memory Allocated (MB)",
-                                                                "value": "3891"
-                                                            },
-                                                            {
-                                                                "name": "start_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684839564.0000000",
-                                                                "title": "Job Start Time",
-                                                                "value": "2023-05-23 12:59:24"
-                                                            },
-                                                            {
-                                                                "name": "end_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684839655.0000000",
-                                                                "title": "Job End Time",
-                                                                "value": "2023-05-23 13:00:55"
-                                                            },
-                                                            {
-                                                                "name": "runtime_seconds",
-                                                                "plugin": "core",
-                                                                "raw_value": "91.0000000",
-                                                                "title": "Job Runtime (Wall Clock)",
-                                                                "value": "1 minute"
-                                                            },
-                                                            {
-                                                                "name": "cpuacct.usage",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "28077674459.0000000",
-                                                                "title": "CPU Time",
-                                                                "value": "28.077674459 seconds"
-                                                            },
-                                                            {
-                                                                "name": "memory.failcnt",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Failed to allocate memory count",
-                                                                "value": 0.0
-                                                            },
-                                                            {
-                                                                "name": "memory.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "9223372036854771712.0000000",
-                                                                "title": "Memory limit on cgroup (MEM)",
-                                                                "value": "8.0 EB"
-                                                            },
-                                                            {
-                                                                "name": "memory.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "338599936.0000000",
-                                                                "title": "Max memory usage (MEM)",
-                                                                "value": "322.9 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "9223372036854771712.0000000",
-                                                                "title": "Memory limit on cgroup (MEM+SWP)",
-                                                                "value": "8.0 EB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "338599936.0000000",
-                                                                "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "322.9 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.oom_kill_disable",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "OOM Control enabled",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.under_oom",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Was OOM Killer active?",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.soft_limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "4160749568.0000000",
-                                                                "title": "Memory softlimit on cgroup",
-                                                                "value": "3.9 GB"
-                                                            }
-                                                        ],
-                                                        "job_stderr": "",
-                                                        "job_stdout": "",
-                                                        "model_class": "Job",
-                                                        "output_collections": {
-                                                            "plots": {
-                                                                "id": "13968361629db34c",
-                                                                "src": "hdca"
-                                                            }
-                                                        },
-                                                        "outputs": {
-                                                            "__new_primary_file_plots|ES_50__": {
-                                                                "id": "4838ba20a6d86765eaf3f31461579100",
-                                                                "src": "hda",
-                                                                "uuid": "81032c7a-1351-4267-8189-cbc5d2455632"
-                                                            },
-                                                            "__new_primary_file_plots|Maxp__": {
-                                                                "id": "4838ba20a6d8676574439f4e43ad19ae",
-                                                                "src": "hda",
-                                                                "uuid": "c45d82ae-a267-42a9-b1da-0c2aa492f4fc"
-                                                            },
-                                                            "__new_primary_file_plots|Records__": {
-                                                                "id": "4838ba20a6d867659af91628bbf2fd3d",
-                                                                "src": "hda",
-                                                                "uuid": "42320b99-2b25-4b11-b245-2b9e75869619"
-                                                            },
-                                                            "__new_primary_file_plots|Shannon_index__": {
-                                                                "id": "4838ba20a6d86765d225dba0fa1f54ea",
-                                                                "src": "hda",
-                                                                "uuid": "e5e7a500-230d-453b-8f90-1f2fe2aeb17d"
-                                                            },
-                                                            "__new_primary_file_plots|Simpson_index__": {
-                                                                "id": "4838ba20a6d867653fb9e294c0047986",
-                                                                "src": "hda",
-                                                                "uuid": "fdb2f88a-6c14-4382-b955-45f242a7367c"
-                                                            },
-                                                            "output_index": {
-                                                                "id": "4838ba20a6d86765db55ac8f682db95c",
-                                                                "src": "hda",
-                                                                "uuid": "91bb988c-8725-4295-828d-1ac13db8a60f"
-                                                            }
-                                                        },
-                                                        "params": {
-                                                            "__input_ext": "\"input\"",
-                                                            "__workflow_invocation_uuid__": "\"a98238aaf95811ed822c001e67d2ec02\"",
-                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
-                                                            "colnames": "true",
-                                                            "dbkey": "\"?\"",
-                                                            "latitude": "\"3\"",
-                                                            "longitude": "\"2\"",
-                                                            "records": "\"5\"",
-                                                            "resolution": "\"10\"",
-                                                            "separator": "\"t\"",
-                                                            "species": "\"4\"",
-                                                            "type": "\"0\""
-                                                        },
-                                                        "state": "ok",
-                                                        "stderr": "Warning message:\n`aes_string()` was deprecated in ggplot2 3.0.0.\n\u2139 Please use tidy evaluation ideoms with `aes()` \n",
-                                                        "stdout": "[1] \"ES_50.png\"\n[1] \"Shannon_index.png\"\n[1] \"Simpson_index.png\"\n[1] \"Maxp.png\"\n[1] \"Records.png\"\n",
-                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/obisindicators/obisindicators/0.0.2",
-                                                        "tool_stderr": "Warning message:\n`aes_string()` was deprecated in ggplot2 3.0.0.\n\u2139 Please use tidy evaluation ideoms with `aes()` \n",
-                                                        "tool_stdout": "[1] \"ES_50.png\"\n[1] \"Shannon_index.png\"\n[1] \"Simpson_index.png\"\n[1] \"Maxp.png\"\n[1] \"Records.png\"\n",
-                                                        "traceback": null,
-                                                        "update_time": "2023-05-23T11:00:57.908654",
-                                                        "user_email": "hxr@informatik.uni-freiburg.de"
-                                                    }
-                                                ],
-                                                "model_class": "WorkflowInvocationStep",
-                                                "order_index": 3,
-                                                "output_collections": {
-                                                    "plots": {
-                                                        "id": "13968361629db34c",
-                                                        "src": "hdca"
-                                                    }
-                                                },
-                                                "outputs": {
-                                                    "output_index": {
-                                                        "id": "4838ba20a6d86765db55ac8f682db95c",
-                                                        "src": "hda",
-                                                        "uuid": "91bb988c-8725-4295-828d-1ac13db8a60f"
-                                                    }
-                                                },
-                                                "state": "scheduled",
-                                                "subworkflow": null,
-                                                "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-23T11:00:57.878144",
-                                                "workflow_step_id": "f05cffad898145a3",
-                                                "workflow_step_label": null,
-                                                "workflow_step_uuid": "86cf1452-ed27-4ba0-b8cb-e1aa5c5584a5"
-                                            }
-                                        }
-                                    },
-                                    "problem_log": "No log for this engine type.",
-                                    "start_datetime": "2023-05-23T12:56:33.104415",
-                                    "status": "success"
+                                "name": "output",
+                                "type": "clustal"
+                            },
+                            {
+                                "name": "dnd",
+                                "type": "nhx"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 593.3333129882812,
+                            "height": 184.79998779296875,
+                            "left": 3431,
+                            "right": 3631,
+                            "top": 408.5333251953125,
+                            "width": 200,
+                            "x": 3431,
+                            "y": 408.5333251953125
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActiondnd": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "dnd"
+                            },
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "#{input}"
                                 },
-                                "doc": "Test outline for Obis-indicators",
-                                "has_data": true,
-                                "id": "Obis-indicators.ga_0",
-                                "test_type": "galaxy_workflow"
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "d6694932c5e0",
+                            "name": "clustalw",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"dnarna\": \"PROTEIN\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"out_order\": \"ALIGNED\", \"outcontrol\": {\"outform\": \"fasta\", \"__current_case__\": 0}, \"range\": {\"mode\": \"complete\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1",
+                        "type": "tool",
+                        "uuid": "8ead7ee6-fe67-4479-a8dd-722e8247cb0e",
+                        "workflow_outputs": [
+                            {
+                                "label": "ClustalW on input dataset(s): clustal",
+                                "output_name": "output",
+                                "uuid": "f704b4b2-5214-4393-8a85-6274bda27c8c"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/padge/clipkit/clipkit/0.1.0",
+                        "errors": null,
+                        "id": 13,
+                        "input_connections": {
+                            "input1": {
+                                "id": 12,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "ClipKIT. Alignment trimming software for phylogenetics.",
+                        "outputs": [
+                            {
+                                "name": "trimmed_output",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "log_output",
+                                "type": "txt"
                             }
                         ],
-                        "version": "0.1"
+                        "position": {
+                            "bottom": 611.1999969482422,
+                            "height": 205.1999969482422,
+                            "left": 3710,
+                            "right": 3910,
+                            "top": 406,
+                            "width": 200,
+                            "x": 3710,
+                            "y": 406
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionlog_output": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "log_output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/padge/clipkit/clipkit/0.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "770695339600",
+                            "name": "clipkit",
+                            "owner": "padge",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"complement\": \"false\", \"gaps\": \"0.9\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"mode_selector\": \"smart-gap\", \"out_format_selector\": \"fasta\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0",
+                        "type": "tool",
+                        "uuid": "ee4b18ee-b6df-46ad-a808-cc78783fc773",
+                        "workflow_outputs": [
+                            {
+                                "label": "Trimmed alignment.",
+                                "output_name": "trimmed_output",
+                                "uuid": "37092981-191a-4413-8f60-51802dd95f9c"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/padge/phykit/phykit_alignment_based/0.1.0",
+                        "errors": null,
+                        "id": 14,
+                        "input_connections": {
+                            "tools|input1": {
+                                "id": 13,
+                                "output_name": "trimmed_output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "PhyKit - Alignment-based functions",
+                        "outputs": [
+                            {
+                                "name": "fasta",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "partition",
+                                "type": "iqtree"
+                            },
+                            {
+                                "name": "occupancy",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 806.7999877929688,
+                            "height": 398.79998779296875,
+                            "left": 3990,
+                            "right": 4190,
+                            "top": 408,
+                            "width": 200,
+                            "x": 3990,
+                            "y": 408
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionfasta": {
+                                "action_arguments": {
+                                    "newname": "#{tools.input1}"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "fasta"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/padge/phykit/phykit_alignment_based/0.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "1ac6ee298657",
+                            "name": "phykit",
+                            "owner": "padge",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"tools\": {\"tool_selector\": \"create_concat\", \"__current_case__\": 0, \"input1\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0",
+                        "type": "tool",
+                        "uuid": "9077044b-7125-4381-858c-d7078d37c529",
+                        "workflow_outputs": [
+                            {
+                                "label": "Concatenated fasta alignment file",
+                                "output_name": "fasta",
+                                "uuid": "09ad25e3-cd68-4fb4-9c57-3e79212b8e01"
+                            },
+                            {
+                                "label": "A partition file ready for input into RAxML or IQ-tree",
+                                "output_name": "partition",
+                                "uuid": "1d546e4c-7e3c-499d-870c-4846feb7a46d"
+                            },
+                            {
+                                "label": "An occupancy file that summarizes the taxon occupancy per sequence",
+                                "output_name": "occupancy",
+                                "uuid": "26846814-d43a-4ce7-9f26-cfb70f184dce"
+                            }
+                        ]
                     }
-                },
-                "tests": true,
-                "title": "Marine Omics visualisation",
-                "topic_id": "ecology",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-obisindicators/versions/obis-indicators",
-                "tutorial_id": "obisindicators",
-                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/obisindicators/workflows/Obis-indicators.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/obisindicators/workflows/Obis-indicators.html",
-                "version": 2,
-                "wfid": "ecology-obisindicators",
-                "wfname": "obis-indicators",
-                "workflow": "Obis-indicators.ga",
+                ],
+                "parent_id": "ecology/phylogeny-data-prep",
+                "path": "topics/ecology/tutorials/phylogeny-data-prep/workflows/main_workflow.ga",
+                "tags": [
+                    "ecology"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "preparing genomic data for phylogeny recostruction (GTN)",
+                "topic_id": "ecology",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-phylogeny-data-prep/versions/main-workflow",
+                "tutorial_id": "phylogeny-data-prep",
+                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/phylogeny-data-prep/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/phylogeny-data-prep/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "ecology-phylogeny-data-prep",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/obisindicators/obisindicators/0.0.2"
+                    "Filter1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/glimmer_gbk_to_orf/glimmer_gbk_to_orf/3.02",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.2-p1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.9+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/proteinortho/proteinortho/6.0.14+galaxy2.9.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.0.14+galaxy2.9.1",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
+                    "toolshed.g2.bx.psu.edu/repos/padge/clipkit/clipkit/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/padge/phykit/phykit_alignment_based/0.1.0"
                 ],
-                "workflowhub_id": "1252"
+                "workflowhub_id": "1264"
             }
-        ]
+        ],
+        "zenodo_link": "https://zenodo.org/record/6610704"
     },
     {
         "admin_install": {
@@ -60682,158 +63283,24 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "fastq_groomer",
-                    "owner": "devteam",
-                    "revisions": "47e5dbc3e790",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "3d0c7bdf12f5",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ncbi_blast_plus",
-                    "owner": "devteam",
-                    "revisions": "5edc472ec434",
-                    "tool_panel_section_label": "NCBI Blast",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "unzip",
-                    "owner": "imgteam",
-                    "revisions": "38eec75fbe9b",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "obi_annotate",
-                    "owner": "iuc",
-                    "revisions": "d50dc96e3ce9",
-                    "tool_panel_section_label": "DNA Metabarcoding",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "obi_clean",
-                    "owner": "iuc",
-                    "revisions": "08d873cdd5f6",
-                    "tool_panel_section_label": "DNA Metabarcoding",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "obi_grep",
-                    "owner": "iuc",
-                    "revisions": "02bab5ff7c37",
-                    "tool_panel_section_label": "DNA Metabarcoding",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "obi_illumina_pairend",
-                    "owner": "iuc",
-                    "revisions": "8cb6bd511879",
-                    "tool_panel_section_label": "DNA Metabarcoding",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "obi_ngsfilter",
-                    "owner": "iuc",
-                    "revisions": "91a1ed0b486f",
-                    "tool_panel_section_label": "DNA Metabarcoding",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "obi_stat",
-                    "owner": "iuc",
-                    "revisions": "5f4544915893",
-                    "tool_panel_section_label": "DNA Metabarcoding",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "obi_tab",
+                    "name": "stacks_denovomap",
                     "owner": "iuc",
-                    "revisions": "4cf47c504672",
-                    "tool_panel_section_label": "DNA Metabarcoding",
+                    "revisions": "fdbcc560c691",
+                    "tool_panel_section_label": "RAD-seq",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "obi_uniq",
+                    "name": "stacks_genotypes",
                     "owner": "iuc",
-                    "revisions": "d4bea99366f9",
-                    "tool_panel_section_label": "DNA Metabarcoding",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "seq_filter_by_id",
-                    "owner": "peterjc",
-                    "revisions": "141612f8c3e3",
-                    "tool_panel_section_label": "Filter and Sort",
+                    "revisions": "62a4b8e5e139",
+                    "tool_panel_section_label": "RAD-seq",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastq_groomer\n  owner: devteam\n  revisions: 47e5dbc3e790\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: 5edc472ec434\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unzip\n  owner: imgteam\n  revisions: 38eec75fbe9b\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obi_annotate\n  owner: iuc\n  revisions: d50dc96e3ce9\n  tool_panel_section_label: DNA Metabarcoding\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obi_clean\n  owner: iuc\n  revisions: '08d873cdd5f6'\n  tool_panel_section_label: DNA Metabarcoding\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obi_grep\n  owner: iuc\n  revisions: 02bab5ff7c37\n  tool_panel_section_label: DNA Metabarcoding\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obi_illumina_pairend\n  owner: iuc\n  revisions: 8cb6bd511879\n  tool_panel_section_label: DNA Metabarcoding\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obi_ngsfilter\n  owner: iuc\n  revisions: 91a1ed0b486f\n  tool_panel_section_label: DNA Metabarcoding\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obi_stat\n  owner: iuc\n  revisions: 5f4544915893\n  tool_panel_section_label: DNA Metabarcoding\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obi_tab\n  owner: iuc\n  revisions: 4cf47c504672\n  tool_panel_section_label: DNA Metabarcoding\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obi_uniq\n  owner: iuc\n  revisions: d4bea99366f9\n  tool_panel_section_label: DNA Metabarcoding\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seq_filter_by_id\n  owner: peterjc\n  revisions: 141612f8c3e3\n  tool_panel_section_label: Filter and Sort\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "colineroyaux",
-                "onorvez",
-                "ecoissac",
-                "fboyer",
-                "yvanlebras"
-            ],
-            "funding": [
-                "gallantries",
-                "pndb"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: stacks_denovomap\n  owner: iuc\n  revisions: fdbcc560c691\n  tool_panel_section_label: RAD-seq\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_genotypes\n  owner: iuc\n  revisions: 62a4b8e5e139\n  tool_panel_section_label: RAD-seq\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/genetic-map-rad-seq/tutorial.json",
         "contributors": [
-            {
-                "affiliations": [
-                    "pndb",
-                    "gallantries",
-                    "elixir-europe"
-                ],
-                "elixir_node": "fr",
-                "email": "coline.royaux@mnhn.fr",
-                "id": "colineroyaux",
-                "joined": "2020-11",
-                "name": "Coline Royaux",
-                "orcid": "0000-0003-4308-5617",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/",
-                "twitter": "ColineRoyaux",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/colineroyaux.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "fr",
-                "email": "olivier.norvez@mnhn.fr",
-                "id": "onorvez",
-                "joined": "2022-02",
-                "name": "Olivier Norvez",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/onorvez/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/onorvez.json"
-            },
-            {
-                "github": false,
-                "id": "ecoissac",
-                "joined": "2022-02",
-                "name": "Eric Coissac",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ecoissac/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/ecoissac.json"
-            },
-            {
-                "github": false,
-                "id": "fboyer",
-                "joined": "2022-02",
-                "name": "Fr\u00e9d\u00e9ric Boyer",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fboyer/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/fboyer.json"
-            },
             {
                 "affiliations": [
                     "pndb",
@@ -60852,57 +63319,16 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
                 "twitter": "Yvan2935",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/PNDB_sub.png",
-                "github": false,
-                "id": "pndb",
-                "members": [
-                    "colineroyaux",
-                    "Marie59",
-                    "yvanlebras",
-                    "ThibaudGlinez"
-                ],
-                "name": "P\u00f4le National de Donn\u00e9es de Biodiversit\u00e9",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pndb/",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/pndb.json"
             }
         ],
-        "dir": "topics/ecology/tutorials/Obitools-metabarcoding",
+        "dir": "topics/ecology/tutorials/genetic-map-rad-seq",
         "edam_operation": [
-            "Sequencing quality control",
-            "Sequence analysis",
-            "Sequence composition calculation",
-            "Statistical calculation"
+            "Data handling"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
             "UseGalaxy.eu",
             "UseGalaxy.no",
             "UseGalaxy.org.au"
@@ -60910,69 +63336,51 @@
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "ecology/Obitools-metabarcoding",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.fr"
-        ],
+        "id": "ecology/genetic-map-rad-seq",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": [
-            "From raw reads you can process, clean and filter data to obtain a list of species from environmental DNA (eDNA) samples."
-        ],
+        "key_points": null,
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2024-06-27",
         "objectives": [
-            "Deal with paired-end data to create consensus sequences",
-            "Clean, filter and anlayse data to obtain strong results"
+            "SNP calling from RAD sequencing data",
+            "Find and correct haplotypes",
+            "Create input files for genetic map building software"
         ],
-        "pageviews": 4050,
-        "pub_date": "2022-02-28",
+        "pageviews": 1105,
+        "pub_date": "2017-02-14",
         "questions": [
-            "how to analyze DNA metabarcoding / eDNA data produced on Illumina sequencers using the OBITools?"
+            "How to analyze RAD sequencing data for a genetic map study?"
         ],
-        "recordings": [
-            {
-                "captioners": [
-                    "yvanlebras"
-                ],
-                "date": "2022-03-03",
-                "galaxy_version": "21.09",
-                "length": "1H15M",
-                "speakers": [
-                    "yvanlebras"
-                ],
-                "youtube_id": "o2cUvb_lmLs"
-            }
+        "redirect_from": [
+            "/topics/sequence-analysis/tutorials/genetic-map-rad-seq/tutorial",
+            "/short/ecology/genetic-map-rad-seq",
+            "/short/T00130"
         ],
-        "short_id": "T00124",
+        "short_id": "T00130",
         "short_tools": [
-            "obi_tab",
-            "obi_illumina_pairend",
-            "obi_clean",
-            "obi_ngsfilter",
-            "wc_gnu",
-            "obi_stat",
-            "Cut1",
-            "fastqc",
-            "ncbi_blastn_wrapper",
-            "unzip",
-            "Filter1",
-            "obi_grep",
-            "obi_uniq",
-            "seq_filter_by_id",
-            "fastq_groomer",
-            "join1",
-            "obi_annotate"
+            "stacks_denovomap",
+            "stacks_genotypes"
         ],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "ecologyanalysis",
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
@@ -60989,48 +63397,20 @@
                     "usegalaxy": true
                 }
             ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                }
-            ]
+            "inexact": []
         },
         "symlink": null,
         "tags": [
+            "RAD-seq",
             "Genetic composition EBV class",
-            "Community composition EBV class",
             "EBV dataset",
-            "EBV workflow",
-            "eDNA",
-            "Metabarcoding"
+            "EBV workflow"
         ],
-        "time_estimation": "1H",
-        "title": "Metabarcoding/eDNA through Obitools",
+        "time_estimation": "8h",
+        "title": "RAD-Seq to construct genetic maps",
         "tools": [
-            "Cut1",
-            "Filter1",
-            "join1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/0.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/obi_annotate/obi_annotate/1.2.13",
-            "toolshed.g2.bx.psu.edu/repos/iuc/obi_clean/obi_clean/1.2.13",
-            "toolshed.g2.bx.psu.edu/repos/iuc/obi_grep/obi_grep/1.2.13",
-            "toolshed.g2.bx.psu.edu/repos/iuc/obi_illumina_pairend/obi_illumina_pairend/1.2.13",
-            "toolshed.g2.bx.psu.edu/repos/iuc/obi_ngsfilter/obi_ngsfilter/1.2.13",
-            "toolshed.g2.bx.psu.edu/repos/iuc/obi_stat/obi_stat/1.2.13",
-            "toolshed.g2.bx.psu.edu/repos/iuc/obi_tab/obi_tab/1.2.13",
-            "toolshed.g2.bx.psu.edu/repos/iuc/obi_uniq/obi_uniq/1.2.13",
-            "toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7",
-            "wc_gnu"
+            "toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/1.46.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/stacks_genotypes/stacks_genotypes/1.46.0"
         ],
         "topic_name": "ecology",
         "topic_name_human": "Ecology",
@@ -61040,51 +63420,51 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "Obitools-metabarcoding",
+        "tutorial_name": "genetic-map-rad-seq",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/genetic-map-rad-seq/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/genetic-map-rad-seq/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/genetic-map-rad-seq/tutorial.json"
         },
-        "version": 11,
+        "version": 12,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 120,
-        "visitors": 2814,
+        "visit_duration": 81,
+        "visitors": 761,
         "workflows": [
             {
                 "creators": [],
-                "description": "Metabarcoding/eDNA through Obitools",
+                "description": "RAD-Seq to construct genetic maps",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nwolf_tutorial.zip?download=1\"]\n  1[label=\"Illuminapairedend\"]\n  2[label=\"Unzip\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"FastQC\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"FASTQ Groomer\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"obigrep\"]\n  4 -> 5 [label=\"output_file\"]\n  6[label=\"Line/Word/Character count\"]\n  4 -> 6 [label=\"output_file\"]\n  7[label=\"Line/Word/Character count\"]\n  5 -> 7 [label=\"output\"]\n  8[label=\"NGSfilter\"]\n  5 -> 8 [label=\"output\"]\n  9[label=\"obiuniq\"]\n  8 -> 9 [label=\"output\"]\n  10[label=\"obiannotate\"]\n  9 -> 10 [label=\"output\"]\n  11[label=\"obistat\"]\n  10 -> 11 [label=\"output\"]\n  12[label=\"obigrep\"]\n  10 -> 12 [label=\"output\"]\n  13[label=\"obigrep\"]\n  12 -> 13 [label=\"output\"]\n  14[label=\"obiclean\"]\n  13 -> 14 [label=\"output\"]\n  15[label=\"NCBI BLAST+ blastn\"]\n  14 -> 15 [label=\"output\"]\n  16[label=\"Filter sequences by ID\"]\n  15 -> 16 [label=\"output1\"]\n  17[label=\"Filter sequences by ID\"]\n  15 -> 17 [label=\"output1\"]\n  14 -> 17 [label=\"output\"]\n  18[label=\"obitab\"]\n  16 -> 18 [label=\"output_pos\"]\n  19[label=\"obitab\"]\n  17 -> 19 [label=\"output_pos\"]\n  20[label=\"Join two Datasets\"]\n  19 -> 20 [label=\"output\"]\n  15 -> 20 [label=\"output1\"]\n  21[label=\"Join two Datasets\"]\n  20 -> 21 [label=\"out_file1\"]\n  18 -> 21 [label=\"output\"]\n  22[label=\"Cut\"]\n  21 -> 22 [label=\"out_file1\"]\n  23[label=\"Filter\"]\n  22 -> 23 [label=\"out_file1\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  9[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  10[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  11[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  12[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  13[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  14[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  15[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  16[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  17[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  18[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  19[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  20[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  21[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  22[label=\"Stacks: de novo map\"]\n  1 -> 22 [label=\"output\"]\n  0 -> 22 [label=\"output\"]\n  15 -> 22 [label=\"output\"]\n  14 -> 22 [label=\"output\"]\n  13 -> 22 [label=\"output\"]\n  12 -> 22 [label=\"output\"]\n  11 -> 22 [label=\"output\"]\n  10 -> 22 [label=\"output\"]\n  9 -> 22 [label=\"output\"]\n  8 -> 22 [label=\"output\"]\n  7 -> 22 [label=\"output\"]\n  6 -> 22 [label=\"output\"]\n  5 -> 22 [label=\"output\"]\n  4 -> 22 [label=\"output\"]\n  3 -> 22 [label=\"output\"]\n  2 -> 22 [label=\"output\"]\n  17 -> 22 [label=\"output\"]\n  18 -> 22 [label=\"output\"]\n  19 -> 22 [label=\"output\"]\n  20 -> 22 [label=\"output\"]\n  21 -> 22 [label=\"output\"]\n  16 -> 22 [label=\"output\"]\n  23[label=\"Stacks: genotypes\"]\n  22 -> 23 [label=\"all_output\"]\n}",
                 "history": [
                     {
-                        "hash": "20d3c8ceff4b1be65ec450a24c19e4541dc1817d",
-                        "message": "fix workflow linting",
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
                         "num": 3,
-                        "short_hash": "20d3c8cef",
-                        "unix": "1645781525"
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
                     },
                     {
-                        "hash": "931fb1735a5b24da90bcaa5a63a23ac4b5abf790",
-                        "message": "update workflow",
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
                         "num": 2,
-                        "short_hash": "931fb1735",
-                        "unix": "1645228612"
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
                     },
                     {
-                        "hash": "45ca3bc6d72f0eb5c43d19929da4730ec9c838db",
-                        "message": "Add files via upload",
+                        "hash": "bfc1c8c3f8660106a468dbfbc3af09af3e48da72",
+                        "message": "Move RAD-Seq tutorials to ecology topic",
                         "num": 1,
-                        "short_hash": "45ca3bc6d",
-                        "unix": "1643659846"
+                        "short_hash": "bfc1c8c3f",
+                        "unix": "1568279010"
                     }
                 ],
                 "inputs": [
@@ -61097,10 +63477,10 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "wolf_tutorial.zip?download=1"
+                                "name": "female.fa"
                             }
                         ],
-                        "label": "wolf_tutorial.zip?download=1",
+                        "label": null,
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
@@ -61108,58 +63488,589 @@
                             "top": 10
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"name\": \"female.fa\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "427d6f7d-b819-45fc-8d2a-c6d3b52c6aca",
+                        "uuid": "2c38288c-adb6-4ac2-99a7-1f2bbb97e366",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "male.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 130
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"male.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "cfa7a746-2f03-4eca-bea8-2c6a14173e3c",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_1.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 250
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_1.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "07615ec4-10af-4a33-a3b4-12cb107ede8f",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_2.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 370
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_2.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "e1ecc352-8a19-409a-a5a6-282721ffd482",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_3.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 490
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_3.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "21648aa0-f3e7-4378-ba1f-f8cdca509d61",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_4.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 610
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_4.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ca90884a-02b6-4685-95c1-62aed3267897",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_5.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 730
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_5.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "cb156339-4a67-4539-943a-15de7e5880fc",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_6.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 850
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_6.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "dfc34c06-efcc-40d8-a4d5-665629f25a0f",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_7.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 970
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_7.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "f30601cb-218c-4f1c-a5ec-1d97bea49294",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_8.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 1090
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_8.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "bcc298aa-5437-4cca-a8d4-f1414bd70455",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_9.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 1210
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_9.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0c0ad65a-2df5-4aef-bcd2-db4a570aed81",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 11,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_10.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 1330
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_10.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "3de49992-fc60-43c6-a8f5-dd34c29ace1c",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_11.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 1450
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_11.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "9d20cab4-c732-45bd-9b68-7bf5b0a2c9c0",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 13,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_12.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 1570
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_12.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "c1786041-32ff-4079-b653-5cfe682bc041",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 14,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_13.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 1690
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_13.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "89f8ce6d-21ea-4f07-9b15-58882b39d0ca",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 15,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_14.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 1810
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_14.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "6f7e59de-f796-4c80-a8aa-e70efe9c022b",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 16,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_15.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 1930
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_15.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "91e4dc8a-84a2-4530-aeab-2130270c7514",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 17,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_16.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 2050
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_16.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "cb53dbf8-f79a-4374-bef4-8eec9adef44e",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 18,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_17.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 2170
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_17.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "4a8a8a60-e631-473c-aaaa-e61f627da84d",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 19,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_18.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 2290
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_18.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "e9235e06-b5ca-432a-8723-41134cc00832",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 20,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_19.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 2410
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_19.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "d6ceab00-6bff-474a-9e4e-21e1a9997756",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 21,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "progeny_20.fa"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 2530
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"progeny_20.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "b293304f-da0b-45ef-a2b9-94a9a747bfa5",
                         "workflow_outputs": []
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nwolf_tutorial.zip?download=1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Illuminapairedend\"];\n  2[\"Unzip\"];\n  0 -->|output| 2;\n  3[\"FastQC\"];\n  1 -->|output| 3;\n  4[\"FASTQ Groomer\"];\n  1 -->|output| 4;\n  5[\"obigrep\"];\n  4 -->|output_file| 5;\n  6[\"Line/Word/Character count\"];\n  4 -->|output_file| 6;\n  7[\"Line/Word/Character count\"];\n  5 -->|output| 7;\n  8[\"NGSfilter\"];\n  5 -->|output| 8;\n  9[\"obiuniq\"];\n  8 -->|output| 9;\n  10[\"obiannotate\"];\n  9 -->|output| 10;\n  11[\"obistat\"];\n  10 -->|output| 11;\n  12[\"obigrep\"];\n  10 -->|output| 12;\n  13[\"obigrep\"];\n  12 -->|output| 13;\n  14[\"obiclean\"];\n  13 -->|output| 14;\n  15[\"NCBI BLAST+ blastn\"];\n  14 -->|output| 15;\n  16[\"Filter sequences by ID\"];\n  15 -->|output1| 16;\n  17[\"Filter sequences by ID\"];\n  15 -->|output1| 17;\n  14 -->|output| 17;\n  18[\"obitab\"];\n  16 -->|output_pos| 18;\n  19[\"obitab\"];\n  17 -->|output_pos| 19;\n  20[\"Join two Datasets\"];\n  19 -->|output| 20;\n  15 -->|output1| 20;\n  21[\"Join two Datasets\"];\n  20 -->|out_file1| 21;\n  18 -->|output| 21;\n  22[\"Cut\"];\n  21 -->|out_file1| 22;\n  23[\"Filter\"];\n  22 -->|out_file1| 23;",
-                "modified": "2024-08-18 00:06:22 +0000",
-                "name": "Workflow constructed from history 'Tuto Obitools'",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 9 stroke:#2c3143,stroke-width:4px;\n  10[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 10 stroke:#2c3143,stroke-width:4px;\n  11[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 11 stroke:#2c3143,stroke-width:4px;\n  12[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 12 stroke:#2c3143,stroke-width:4px;\n  13[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 13 stroke:#2c3143,stroke-width:4px;\n  14[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 14 stroke:#2c3143,stroke-width:4px;\n  15[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 15 stroke:#2c3143,stroke-width:4px;\n  16[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 16 stroke:#2c3143,stroke-width:4px;\n  17[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 17 stroke:#2c3143,stroke-width:4px;\n  18[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 18 stroke:#2c3143,stroke-width:4px;\n  19[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 19 stroke:#2c3143,stroke-width:4px;\n  20[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 20 stroke:#2c3143,stroke-width:4px;\n  21[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 21 stroke:#2c3143,stroke-width:4px;\n  22[\"Stacks: de novo map\"];\n  1 -->|output| 22;\n  0 -->|output| 22;\n  15 -->|output| 22;\n  14 -->|output| 22;\n  13 -->|output| 22;\n  12 -->|output| 22;\n  11 -->|output| 22;\n  10 -->|output| 22;\n  9 -->|output| 22;\n  8 -->|output| 22;\n  7 -->|output| 22;\n  6 -->|output| 22;\n  5 -->|output| 22;\n  4 -->|output| 22;\n  3 -->|output| 22;\n  2 -->|output| 22;\n  17 -->|output| 22;\n  18 -->|output| 22;\n  19 -->|output| 22;\n  20 -->|output| 22;\n  21 -->|output| 22;\n  16 -->|output| 22;\n  23[\"Stacks: genotypes\"];\n  22 -->|all_output| 23;",
+                "modified": "2024-10-02 12:08:07 +0000",
+                "name": "Genetic Map Rad Seq Workflow",
                 "outputs": [],
-                "parent_id": "ecology/Obitools-metabarcoding",
-                "path": "topics/ecology/tutorials/Obitools-metabarcoding/workflows/main_workflow.ga",
+                "parent_id": "ecology/genetic-map-rad-seq",
+                "path": "topics/ecology/tutorials/genetic-map-rad-seq/workflows/genetic-map-rad-seq.ga",
                 "tags": [
                     "ecology"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Workflow constructed from history 'Tuto Obitools'",
+                "title": "Genetic Map Rad Seq Workflow",
                 "topic_id": "ecology",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-Obitools-metabarcoding/versions/main-workflow",
-                "tutorial_id": "Obitools-metabarcoding",
-                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/Obitools-metabarcoding/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/Obitools-metabarcoding/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "ecology-Obitools-metabarcoding",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-genetic-map-rad-seq/versions/genetic-map-rad-seq",
+                "tutorial_id": "genetic-map-rad-seq",
+                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/genetic-map-rad-seq/workflows/genetic-map-rad-seq.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/genetic-map-rad-seq/workflows/genetic-map-rad-seq.html",
+                "version": 3,
+                "wfid": "ecology-genetic-map-rad-seq",
+                "wfname": "genetic-map-rad-seq",
+                "workflow": "genetic-map-rad-seq.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "Filter1",
-                    "join1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/0.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/obi_annotate/obi_annotate/1.2.13",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/obi_clean/obi_clean/1.2.13",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/obi_grep/obi_grep/1.2.13",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/obi_illumina_pairend/obi_illumina_pairend/1.2.13",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/obi_ngsfilter/obi_ngsfilter/1.2.13",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/obi_stat/obi_stat/1.2.13",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/obi_tab/obi_tab/1.2.13",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/obi_uniq/obi_uniq/1.2.13",
-                    "toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7",
-                    "wc_gnu"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/1.46.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_genotypes/stacks_genotypes/1.46.0"
                 ],
-                "workflowhub_id": "1274"
+                "workflowhub_id": "1216"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/5932108"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.1219888"
     },
     {
         "admin_install": {
@@ -61168,17 +64079,10 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "glimmer_gbk_to_orf",
-                    "owner": "bgruening",
-                    "revisions": "04861c9bbf45",
-                    "tool_panel_section_label": "Ecology",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "repeat_masker",
+                    "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "39b40a9a6296",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "74a8bef53a00",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
@@ -61189,151 +64093,148 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "clustalw",
+                    "name": "bwa",
                     "owner": "devteam",
-                    "revisions": "d6694932c5e0",
-                    "tool_panel_section_label": "Multiple Alignments",
+                    "revisions": "64f11cf59c6e",
+                    "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "regex_find_replace",
-                    "owner": "galaxyp",
-                    "revisions": "ae8c4b2488e7",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "bwa_wrappers",
+                    "owner": "devteam",
+                    "revisions": "b4427dbb6ced",
+                    "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "busco",
-                    "owner": "iuc",
-                    "revisions": "602fb8e63aa7",
-                    "tool_panel_section_label": "Annotation",
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "ff9530579d1f",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "funannotate_predict",
+                    "name": "multiqc",
                     "owner": "iuc",
-                    "revisions": "2bba2ff070d9",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "1c2db0054039",
+                    "tool_panel_section_label": "Quality Control",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "proteinortho",
+                    "name": "stacks_populations",
                     "owner": "iuc",
-                    "revisions": "4850f0d15f01",
-                    "tool_panel_section_label": "Proteomics",
+                    "revisions": "45db1ba16163",
+                    "tool_panel_section_label": "RAD-seq",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "830961c48e42",
-                    "tool_panel_section_label": "Collection Operations",
+                    "name": "stacks_procrad",
+                    "owner": "iuc",
+                    "revisions": "eded025438db",
+                    "tool_panel_section_label": "RAD-seq",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "clipkit",
-                    "owner": "padge",
-                    "revisions": "770695339600",
-                    "tool_panel_section_label": "Phylogenetics",
+                    "name": "stacks_refmap",
+                    "owner": "iuc",
+                    "revisions": "d7a482f44e08",
+                    "tool_panel_section_label": "RAD-seq",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "phykit",
-                    "owner": "padge",
-                    "revisions": "1ac6ee298657",
-                    "tool_panel_section_label": "Ecology",
+                    "name": "regex_replace",
+                    "owner": "kellrott",
+                    "revisions": "9a77d5fca67c",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: glimmer_gbk_to_orf\n  owner: bgruening\n  revisions: '04861c9bbf45'\n  tool_panel_section_label: Ecology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: repeat_masker\n  owner: bgruening\n  revisions: 39b40a9a6296\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clustalw\n  owner: devteam\n  revisions: d6694932c5e0\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: ae8c4b2488e7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 602fb8e63aa7\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_predict\n  owner: iuc\n  revisions: 2bba2ff070d9\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteinortho\n  owner: iuc\n  revisions: 4850f0d15f01\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clipkit\n  owner: padge\n  revisions: '770695339600'\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: phykit\n  owner: padge\n  revisions: 1ac6ee298657\n  tool_panel_section_label: Ecology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/phylogeny-data-prep/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: 74a8bef53a00\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: 64f11cf59c6e\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_wrappers\n  owner: devteam\n  revisions: b4427dbb6ced\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: ff9530579d1f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 1c2db0054039\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_populations\n  owner: iuc\n  revisions: 45db1ba16163\n  tool_panel_section_label: RAD-seq\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_procrad\n  owner: iuc\n  revisions: eded025438db\n  tool_panel_section_label: RAD-seq\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_refmap\n  owner: iuc\n  revisions: d7a482f44e08\n  tool_panel_section_label: RAD-seq\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_replace\n  owner: kellrott\n  revisions: 9a77d5fca67c\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/ref-based-rad-seq/tutorial.json",
         "contributors": [
             {
-                "email": "miguel.roncoroni@elixir-belgium.org",
-                "id": "roncoronimiguel",
-                "joined": "2021-08",
-                "name": "Miguel Roncoroni",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/roncoronimiguel/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/roncoronimiguel.json"
-            },
-            {
-                "id": "brigidagallone",
-                "joined": "2022-05",
-                "name": "Brigida Gallone",
-                "orcid": "0000-0003-3045-5949",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/brigidagallone/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/brigidagallone.json"
+                "affiliations": [
+                    "pndb",
+                    "gallantries",
+                    "fairease",
+                    "fnso2019",
+                    "elixir-europe"
+                ],
+                "elixir_node": "fr",
+                "email": "yvan.le-bras@mnhn.fr",
+                "id": "yvanlebras",
+                "joined": "2017-09",
+                "matrix": "yvanlebras:matrix.org",
+                "name": "Yvan Le Bras",
+                "orcid": "0000-0002-8504-068X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
+                "twitter": "Yvan2935",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
             }
         ],
-        "dir": "topics/ecology/tutorials/phylogeny-data-prep",
+        "dir": "topics/ecology/tutorials/ref-based-rad-seq",
         "edam_operation": [
-            "Genetic variation analysis",
-            "Sequence analysis",
-            "Genome annotation",
-            "Sequence assembly validation",
-            "Multiple sequence alignment",
-            "Transcriptome assembly",
-            "Genome assembly",
-            "Sequence clustering",
-            "Scaffolding"
+            "Data handling",
+            "Sequence alignment",
+            "Read mapping",
+            "Sequencing quality control",
+            "Generation",
+            "Statistical calculation",
+            "Validation",
+            "Sequence composition calculation",
+            "Genome indexing"
         ],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "ecology/phylogeny-data-prep",
+        "id": "ecology/ref-based-rad-seq",
         "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": [
-            "You now are able to",
-            "Predict proteins in a nucleotide sequence *de-novo* using **funannotate_predict**",
-            "Find orthologs across different samples with **orthofinder**",
-            "Align orthologs with **ClustalW** in preparation for phylogeny reconstruction <!-- link to phylogeny reconstruction training. -->"
-        ],
+        "key_points": null,
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2024-06-27",
         "objectives": [
-            "Mask repetitive elements from a genome",
-            "Annotate (predict protein-coding genes) the genomes of the samples to compare",
-            "Find a set of common proteins across the samples (orthologs)",
-            "Align orthologs across samples"
+            "Analysis of RAD sequencing data using a reference genome",
+            "SNP calling from RAD sequencing data",
+            "Calculate population genomics statistics from RAD sequencing data"
         ],
-        "pageviews": 2012,
-        "pub_date": "2022-10-21",
+        "pageviews": 3808,
+        "pub_date": "2017-02-14",
         "questions": [
-            "How do I find a set of common proteins (orthologs) across related species or strains?",
-            "How do I organize a set of orthologs to infer evolutionary relations between species or strains (phylogenetic reconstruction)?"
+            "How to analyze RAD sequencing data using a reference genome for a population genomics study?"
         ],
-        "requirements": [
-            {
-                "topic_name": "assembly",
-                "tutorials": [
-                    "general-introduction"
-                ],
-                "type": "internal"
-            }
+        "redirect_from": [
+            "/topics/sequence-analysis/tutorials/ref-based-rad-seq/tutorial",
+            "/short/ecology/ref-based-rad-seq",
+            "/short/T00133"
         ],
-        "short_id": "T00132",
+        "short_id": "T00133",
         "short_tools": [
-            "repeatmasker_wrapper",
-            "regex1",
-            "busco",
-            "clipkit",
-            "phykit_alignment_based",
-            "funannotate_predict",
-            "proteinortho_grab_proteins",
-            "glimmer_gbk_to_orf",
+            "stacks_procrad",
+            "Count1",
+            "Summary_Statistics1",
             "Filter1",
+            "Convert characters1",
+            "tp_sort_header_tool",
+            "stacks_refmap",
             "tp_replace_in_line",
-            "clustalw",
-            "collapse_dataset",
-            "proteinortho"
+            "multiqc",
+            "bwa_wrapper",
+            "Grep1",
+            "Cut1",
+            "bwa",
+            "stacks_populations",
+            "regex_replace",
+            "fastqc",
+            "cat1",
+            "addValue"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -61344,26 +64245,33 @@
         },
         "symlink": null,
         "tags": [
-            "phylogeny",
-            "data handling",
-            "functional annotation"
+            "RAD-seq",
+            "Genetic composition EBV class",
+            "Species population EBV class",
+            "EBV dataset",
+            "EBV workflow"
         ],
-        "time_estimation": "3H",
-        "title": "Preparing genomic data for phylogeny reconstruction",
+        "time_estimation": "8h",
+        "title": "RAD-Seq Reference-based data analysis",
         "tools": [
+            "Convert characters1",
+            "Count1",
+            "Cut1",
             "Filter1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/glimmer_gbk_to_orf/glimmer_gbk_to_orf/3.02",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.2-p1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.9+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/proteinortho/proteinortho/6.0.14+galaxy2.9.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.0.14+galaxy2.9.1",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
-            "toolshed.g2.bx.psu.edu/repos/padge/clipkit/clipkit/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/padge/phykit/phykit_alignment_based/0.1.0"
+            "Grep1",
+            "Summary_Statistics1",
+            "addValue",
+            "cat1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6",
+            "toolshed.g2.bx.psu.edu/repos/iuc/stacks_populations/stacks_populations/1.46.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/stacks_refmap/stacks_refmap/1.46.0",
+            "toolshed.g2.bx.psu.edu/repos/kellrott/regex_replace/regex_replace/1.0.0"
         ],
         "topic_name": "ecology",
         "topic_name_human": "Ecology",
@@ -61373,50 +64281,65 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "phylogeny-data-prep",
+        "tutorial_name": "ref-based-rad-seq",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/phylogeny-data-prep/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/ref-based-rad-seq/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/phylogeny-data-prep/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/phylogeny-data-prep/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/ref-based-rad-seq/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/ref-based-rad-seq/tutorial.json"
         },
-        "version": 4,
+        "version": 11,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 167,
-        "visitors": 1478,
+        "visit_duration": 104,
+        "visitors": 2275,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "",
-                        "name": "Miguel Roncoroni"
-                    }
-                ],
-                "description": "This workflow begins from a set of genome assemblies of different samples, strains, species. The genome is first annotated with Funnanotate. Predicted proteins are furtner annotated with Busco. Next, 'ProteinOrtho' finds orthologs across the samples and makes orthogroups. Orthogroups where all samples are represented are extracted. Orthologs in each orthogroup are aligned with ClustalW. The alignments are cleaned with ClipKIT and the concatenation matrix is built using PhyKit. This can be used for phylogeny reconstruction.",
+                "creators": [],
+                "description": "RAD-Seq Reference-based data analysis",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput genomes as collection\"]\n  1[label=\"Replace Text\"]\n  0 -> 1 [label=\"output\"]\n  k6a2d3fcdb5574440910db4c537feef20[color=lightseagreen,label=\"Output\\nheaders_shortened\"]\n  1 -> k6a2d3fcdb5574440910db4c537feef20\n  2[label=\"RepeatMasker\"]\n  1 -> 2 [label=\"outfile\"]\n  k1db6607a343a4a619a3b43101eb8223b[color=lightseagreen,label=\"Output\\nrepeat_masked\"]\n  2 -> k1db6607a343a4a619a3b43101eb8223b\n  3[label=\"Funannotate predict annotation\"]\n  2 -> 3 [label=\"output_masked_genome\"]\n  k642c1c0982f44ef4bd53d14a583044e2[color=lightseagreen,label=\"Output\\nfunannotate_predicted_proteins\"]\n  3 -> k642c1c0982f44ef4bd53d14a583044e2\n  4[label=\"Extract ORF\"]\n  3 -> 4 [label=\"annot_gbk\"]\n  k07fb8c04990e4bc7b6079c4161b4786d[color=lightseagreen,label=\"Output\\nextracted_ORFs\"]\n  4 -> k07fb8c04990e4bc7b6079c4161b4786d\n  5[label=\"Regex Find And Replace\"]\n  4 -> 5 [label=\"aa_output\"]\n  k8dc378a8d48542df83226cf8230257a0[color=lightseagreen,label=\"Output\\nsample_names_to_headers\"]\n  5 -> k8dc378a8d48542df83226cf8230257a0\n  6[label=\"Collapse Collection\"]\n  5 -> 6 [label=\"out_file1\"]\n  ke9a554594a2c42388494e99ec67307ea[color=lightseagreen,label=\"Output\\nproteomes_to_one_file\"]\n  6 -> ke9a554594a2c42388494e99ec67307ea\n  7[label=\"Proteinortho\"]\n  5 -> 7 [label=\"out_file1\"]\n  kee688b7a2a9e4480a27adb8cf795b635[color=lightseagreen,label=\"Output\\nProteinortho on input dataset(s): orthology-groups\"]\n  7 -> kee688b7a2a9e4480a27adb8cf795b635\n  8[label=\"Busco\"]\n  5 -> 8 [label=\"out_file1\"]\n  9[label=\"Filter\"]\n  7 -> 9 [label=\"proteinortho\"]\n  10[label=\"Proteinortho grab proteins\"]\n  6 -> 10 [label=\"output\"]\n  9 -> 10 [label=\"out_file1\"]\n  k8625e8b1e3af4afabf851a3258cbbfb2[color=lightseagreen,label=\"Output\\nProteinortho_extract_by_orthogroup\"]\n  10 -> k8625e8b1e3af4afabf851a3258cbbfb2\n  11[label=\"Regex Find And Replace\"]\n  10 -> 11 [label=\"listproteinorthograbproteins\"]\n  kb072d32ef7254833af0b74f4df526d9a[color=lightseagreen,label=\"Output\\nfasta_header_cleaned\"]\n  11 -> kb072d32ef7254833af0b74f4df526d9a\n  12[label=\"ClustalW\"]\n  11 -> 12 [label=\"out_file1\"]\n  kf704b4b2521443938a856274bda27c8c[color=lightseagreen,label=\"Output\\nClustalW on input dataset(s): clustal\"]\n  12 -> kf704b4b2521443938a856274bda27c8c\n  13[label=\"ClipKIT. Alignment trimming software for phylogenetics.\"]\n  12 -> 13 [label=\"output\"]\n  k37092981191a44138f6051802dd95f9c[color=lightseagreen,label=\"Output\\nTrimmed alignment.\"]\n  13 -> k37092981191a44138f6051802dd95f9c\n  14[label=\"PhyKit - Alignment-based functions\"]\n  13 -> 14 [label=\"trimmed_output\"]\n  k09ad25e3cd684fb49c573e79212b8e01[color=lightseagreen,label=\"Output\\nConcatenated fasta alignment file\"]\n  14 -> k09ad25e3cd684fb49c573e79212b8e01\n  k1d546e4c7e3c499d870c4846feb7a46d[color=lightseagreen,label=\"Output\\nA partition file ready for input into RAxML or IQ-tree\"]\n  14 -> k1d546e4c7e3c499d870c4846feb7a46d\n  k26846814d43a4ce79f26cfb70f184dce[color=lightseagreen,label=\"Output\\nAn occupancy file that summarizes the taxon occupancy per sequence\"]\n  14 -> k26846814d43a4ce79f26cfb70f184dce\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nEBI SRA: SRR034310 File: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR034/SRR034310/SRR034310.fastq.gz\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/1134547/files/Barcode_SRR034310.txt\"]\n  10[label=\"FastQC\"]\n  5 -> 10 [label=\"demultiplexed\"]\n  11[label=\"Map with BWA\"]\n  5 -> 11 [label=\"demultiplexed\"]\n  3 -> 11 [label=\"output\"]\n  12[label=\"Select\"]\n  6 -> 12 [label=\"output_log\"]\n  13[label=\"Select\"]\n  6 -> 13 [label=\"output_log\"]\n  14[label=\"Replace Text\"]\n  7 -> 14 [label=\"outfile\"]\n  15[label=\"Replace Text\"]\n  8 -> 15 [label=\"out_file1\"]\n  16[label=\"Replace Text\"]\n  9 -> 16 [label=\"out_file1\"]\n  17[label=\"MultiQC\"]\n  10 -> 17 [label=\"text_file\"]\n  18[label=\"Replace Text\"]\n  12 -> 18 [label=\"out_file1\"]\n  19[label=\"Replace Text\"]\n  13 -> 19 [label=\"out_file1\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/1134547/files/Details_Barcode_Population_SRR034310.txt\"]\n  20[label=\"Add column\"]\n  14 -> 20 [label=\"outfile\"]\n  21[label=\"Concatenate datasets\"]\n  19 -> 21 [label=\"outfile\"]\n  15 -> 21 [label=\"outfile\"]\n  16 -> 21 [label=\"outfile\"]\n  18 -> 21 [label=\"outfile\"]\n  22[label=\"Cut\"]\n  20 -> 22 [label=\"out_file1\"]\n  23[label=\"Convert\"]\n  21 -> 23 [label=\"out_file1\"]\n  24[label=\"Regex Replace\"]\n  22 -> 24 [label=\"out_file1\"]\n  25[label=\"Stacks: reference map\"]\n  11 -> 25 [label=\"bam_output\"]\n  24 -> 25 [label=\"outfile\"]\n  26[label=\"Stacks: populations\"]\n  25 -> 26 [label=\"all_output\"]\n  24 -> 26 [label=\"outfile\"]\n  27[label=\"Summary Statistics\"]\n  26 -> 27 [label=\"out_fstats\"]\n  28[label=\"Sort\"]\n  26 -> 28 [label=\"out_fstats\"]\n  29[label=\"Count\"]\n  26 -> 29 [label=\"out_fstats\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/1134547/files/Reference_genome_11_chromosomes.fasta\"]\n  30[label=\"Filter\"]\n  26 -> 30 [label=\"out_fstats\"]\n  4[label=\"Stacks: process radtags\"]\n  1 -> 4 [label=\"output\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Stacks: process radtags\"]\n  1 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Stacks: process radtags\"]\n  1 -> 6 [label=\"output\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Replace Text\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"Select\"]\n  4 -> 8 [label=\"output_log\"]\n  9[label=\"Select\"]\n  5 -> 9 [label=\"output_log\"]\n}",
                 "history": [
                     {
-                        "hash": "f7b9464bb24007d8f974decd05b331b67ff877ab",
-                        "message": "Update main_workflow.ga",
+                        "hash": "00cfc1f0873c7eee656d05fd549f5cd3eae6a8da",
+                        "message": "out_fastp\u0125ase",
+                        "num": 5,
+                        "short_hash": "00cfc1f08",
+                        "unix": "1579699186"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 4,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "ea197f141d3c4fcf8f8e424604a5d40bf9125ce6",
+                        "message": "small changes",
+                        "num": 3,
+                        "short_hash": "ea197f141",
+                        "unix": "1579091409"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
                         "num": 2,
-                        "short_hash": "f7b9464bb",
-                        "unix": "1656489327"
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
                     },
                     {
-                        "hash": "d6ad32e2684e4274d081b593df3966220a6e0d55",
-                        "message": "create phylogenetic-data-prep training backbone",
+                        "hash": "bfc1c8c3f8660106a468dbfbc3af09af3e48da72",
+                        "message": "Move RAD-Seq tutorials to ecology topic",
                         "num": 1,
-                        "short_hash": "d6ad32e26",
-                        "unix": "1651848710"
+                        "short_hash": "bfc1c8c3f",
+                        "unix": "1568279010"
                     }
                 ],
                 "inputs": [
@@ -61429,1044 +64352,1044 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Input genomes as collection"
+                                "name": "EBI SRA: SRR034310 File: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR034/SRR034310/SRR034310.fastq.gz"
                             }
                         ],
-                        "label": "Input genomes as collection",
-                        "name": "Input dataset collection",
+                        "label": "EBI SRA: SRR034310 File: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR034/SRR034310/SRR034310.fastq.gz",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 309.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 387,
-                            "right": 587,
-                            "top": 227,
-                            "width": 200,
-                            "x": 387,
-                            "y": 227
+                            "left": 200.00001525878906,
+                            "top": 200.00001525878906
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"name\": \"EBI SRA: SRR034310 File: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR034/SRR034310/SRR034310.fastq.gz\"}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "3ae6fd26-b1ef-4339-b84b-82463a3575cf",
+                        "type": "data_input",
+                        "uuid": "4be2b939-61bf-4ed9-b134-5307c5127fe8",
                         "workflow_outputs": []
-                    }
-                ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput genomes as collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Replace Text\"];\n  0 -->|output| 1;\n  6a2d3fcd-b557-4440-910d-b4c537feef20[\"Output\\nheaders_shortened\"];\n  1 --> 6a2d3fcd-b557-4440-910d-b4c537feef20;\n  style 6a2d3fcd-b557-4440-910d-b4c537feef20 stroke:#2c3143,stroke-width:4px;\n  2[\"RepeatMasker\"];\n  1 -->|outfile| 2;\n  1db6607a-343a-4a61-9a3b-43101eb8223b[\"Output\\nrepeat_masked\"];\n  2 --> 1db6607a-343a-4a61-9a3b-43101eb8223b;\n  style 1db6607a-343a-4a61-9a3b-43101eb8223b stroke:#2c3143,stroke-width:4px;\n  3[\"Funannotate predict annotation\"];\n  2 -->|output_masked_genome| 3;\n  642c1c09-82f4-4ef4-bd53-d14a583044e2[\"Output\\nfunannotate_predicted_proteins\"];\n  3 --> 642c1c09-82f4-4ef4-bd53-d14a583044e2;\n  style 642c1c09-82f4-4ef4-bd53-d14a583044e2 stroke:#2c3143,stroke-width:4px;\n  4[\"Extract ORF\"];\n  3 -->|annot_gbk| 4;\n  07fb8c04-990e-4bc7-b607-9c4161b4786d[\"Output\\nextracted_ORFs\"];\n  4 --> 07fb8c04-990e-4bc7-b607-9c4161b4786d;\n  style 07fb8c04-990e-4bc7-b607-9c4161b4786d stroke:#2c3143,stroke-width:4px;\n  5[\"Regex Find And Replace\"];\n  4 -->|aa_output| 5;\n  8dc378a8-d485-42df-8322-6cf8230257a0[\"Output\\nsample_names_to_headers\"];\n  5 --> 8dc378a8-d485-42df-8322-6cf8230257a0;\n  style 8dc378a8-d485-42df-8322-6cf8230257a0 stroke:#2c3143,stroke-width:4px;\n  6[\"Collapse Collection\"];\n  5 -->|out_file1| 6;\n  e9a55459-4a2c-4238-8494-e99ec67307ea[\"Output\\nproteomes_to_one_file\"];\n  6 --> e9a55459-4a2c-4238-8494-e99ec67307ea;\n  style e9a55459-4a2c-4238-8494-e99ec67307ea stroke:#2c3143,stroke-width:4px;\n  7[\"Proteinortho\"];\n  5 -->|out_file1| 7;\n  ee688b7a-2a9e-4480-a27a-db8cf795b635[\"Output\\nProteinortho on input dataset(s): orthology-groups\"];\n  7 --> ee688b7a-2a9e-4480-a27a-db8cf795b635;\n  style ee688b7a-2a9e-4480-a27a-db8cf795b635 stroke:#2c3143,stroke-width:4px;\n  8[\"Busco\"];\n  5 -->|out_file1| 8;\n  9[\"Filter\"];\n  7 -->|proteinortho| 9;\n  10[\"Proteinortho grab proteins\"];\n  6 -->|output| 10;\n  9 -->|out_file1| 10;\n  8625e8b1-e3af-4afa-bf85-1a3258cbbfb2[\"Output\\nProteinortho_extract_by_orthogroup\"];\n  10 --> 8625e8b1-e3af-4afa-bf85-1a3258cbbfb2;\n  style 8625e8b1-e3af-4afa-bf85-1a3258cbbfb2 stroke:#2c3143,stroke-width:4px;\n  11[\"Regex Find And Replace\"];\n  10 -->|listproteinorthograbproteins| 11;\n  b072d32e-f725-4833-af0b-74f4df526d9a[\"Output\\nfasta_header_cleaned\"];\n  11 --> b072d32e-f725-4833-af0b-74f4df526d9a;\n  style b072d32e-f725-4833-af0b-74f4df526d9a stroke:#2c3143,stroke-width:4px;\n  12[\"ClustalW\"];\n  11 -->|out_file1| 12;\n  f704b4b2-5214-4393-8a85-6274bda27c8c[\"Output\\nClustalW on input dataset(s): clustal\"];\n  12 --> f704b4b2-5214-4393-8a85-6274bda27c8c;\n  style f704b4b2-5214-4393-8a85-6274bda27c8c stroke:#2c3143,stroke-width:4px;\n  13[\"ClipKIT. Alignment trimming software for phylogenetics.\"];\n  12 -->|output| 13;\n  37092981-191a-4413-8f60-51802dd95f9c[\"Output\\nTrimmed alignment.\"];\n  13 --> 37092981-191a-4413-8f60-51802dd95f9c;\n  style 37092981-191a-4413-8f60-51802dd95f9c stroke:#2c3143,stroke-width:4px;\n  14[\"PhyKit - Alignment-based functions\"];\n  13 -->|trimmed_output| 14;\n  09ad25e3-cd68-4fb4-9c57-3e79212b8e01[\"Output\\nConcatenated fasta alignment file\"];\n  14 --> 09ad25e3-cd68-4fb4-9c57-3e79212b8e01;\n  style 09ad25e3-cd68-4fb4-9c57-3e79212b8e01 stroke:#2c3143,stroke-width:4px;\n  1d546e4c-7e3c-499d-870c-4846feb7a46d[\"Output\\nA partition file ready for input into RAxML or IQ-tree\"];\n  14 --> 1d546e4c-7e3c-499d-870c-4846feb7a46d;\n  style 1d546e4c-7e3c-499d-870c-4846feb7a46d stroke:#2c3143,stroke-width:4px;\n  26846814-d43a-4ce7-9f26-cfb70f184dce[\"Output\\nAn occupancy file that summarizes the taxon occupancy per sequence\"];\n  14 --> 26846814-d43a-4ce7-9f26-cfb70f184dce;\n  style 26846814-d43a-4ce7-9f26-cfb70f184dce stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:22 +0000",
-                "name": "preparing genomic data for phylogeny recostruction (GTN)",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                        "content_id": null,
                         "errors": null,
                         "id": 1,
-                        "input_connections": {
-                            "infile": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Replace Text",
-                        "outputs": [
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "outfile",
-                                "type": "input"
+                                "description": "",
+                                "name": "https://zenodo.org/record/1134547/files/Barcode_SRR034310.txt"
                             }
                         ],
+                        "label": "https://zenodo.org/record/1134547/files/Barcode_SRR034310.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 359.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": 780.5,
-                            "right": 980.5,
-                            "top": 246,
-                            "width": 200,
-                            "x": 780.5,
-                            "y": 246
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutfile": {
-                                "action_arguments": {
-                                    "newname": "#{infile}"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "outfile"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 200.00001525878906,
+                            "top": 320.00001525878906
                         },
-                        "tool_state": "{\"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"find_pattern\": \"(>[^ ]+).+\", \"replace_pattern\": \"\\\\1\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.2",
-                        "type": "tool",
-                        "uuid": "2192525a-028a-4fb3-a772-5ccface42221",
-                        "workflow_outputs": [
-                            {
-                                "label": "headers_shortened",
-                                "output_name": "outfile",
-                                "uuid": "6a2d3fcd-b557-4440-910d-b4c537feef20"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"https://zenodo.org/record/1134547/files/Barcode_SRR034310.txt\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "95b8e56e-433d-4014-9dee-d9310863a20d",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.2-p1+galaxy0",
+                        "content_id": null,
                         "errors": null,
                         "id": 2,
-                        "input_connections": {
-                            "input_fasta": {
-                                "id": 1,
-                                "output_name": "outfile"
-                            }
-                        },
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool RepeatMasker",
-                                "name": "input_fasta"
-                            }
-                        ],
-                        "label": null,
-                        "name": "RepeatMasker",
-                        "outputs": [
-                            {
-                                "name": "output_masked_genome",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "output_log",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "output_table",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "output_repeat_catalog",
-                                "type": "txt"
+                                "description": "",
+                                "name": "https://zenodo.org/record/1134547/files/Details_Barcode_Population_SRR034310.txt"
                             }
                         ],
+                        "label": "https://zenodo.org/record/1134547/files/Details_Barcode_Population_SRR034310.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 669.3999938964844,
-                            "height": 286.3999938964844,
-                            "left": 1078.5,
-                            "right": 1278.5,
-                            "top": 383,
-                            "width": 200,
-                            "x": 1078.5,
-                            "y": 383
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionoutput_log": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_log"
-                            },
-                            "HideDatasetActionoutput_repeat_catalog": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_repeat_catalog"
-                            },
-                            "HideDatasetActionoutput_table": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_table"
-                            },
-                            "RenameDatasetActionoutput_masked_genome": {
-                                "action_arguments": {
-                                    "newname": "#{input_fasta}"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_masked_genome"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.2-p1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "39b40a9a6296",
-                            "name": "repeat_masker",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 200.00001525878906,
+                            "top": 440.0000305175781
                         },
-                        "tool_state": "{\"advanced\": {\"is_only\": \"false\", \"is_clip\": \"false\", \"no_is\": \"false\", \"rodspec\": \"false\", \"primspec\": \"false\", \"nolow\": \"false\", \"noint\": \"false\", \"norna\": \"false\", \"alu\": \"false\", \"div\": \"false\", \"search_speed\": \"\", \"frag\": \"40000\", \"gc\": null, \"gccalc\": \"false\", \"nocut\": \"false\", \"xout\": \"false\", \"keep_alignments\": \"false\", \"invert_alignments\": \"false\", \"xsmall\": \"false\", \"poly\": \"false\"}, \"excln\": \"true\", \"gff\": \"false\", \"input_fasta\": {\"__class__\": \"RuntimeValue\"}, \"repeat_source\": {\"source_type\": \"dfam\", \"__current_case__\": 0, \"species_source\": {\"species_from_list\": \"no\", \"__current_case__\": 1, \"species_name\": \"Saccharomyces cerevisiae\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.1.2-p1+galaxy0",
-                        "type": "tool",
-                        "uuid": "2c65b372-4d50-46a0-8a41-fc9e903956b8",
-                        "workflow_outputs": [
-                            {
-                                "label": "repeat_masked",
-                                "output_name": "output_masked_genome",
-                                "uuid": "1db6607a-343a-4a61-9a3b-43101eb8223b"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"https://zenodo.org/record/1134547/files/Details_Barcode_Population_SRR034310.txt\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "43ca52f2-f60d-4fa6-9608-65ac4cc471b9",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.9+galaxy2",
+                        "content_id": null,
                         "errors": null,
                         "id": 3,
-                        "input_connections": {
-                            "input": {
-                                "id": 2,
-                                "output_name": "output_masked_genome"
-                            }
-                        },
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "evidences"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "evidences"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "genemark"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "genemark"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "other_predictors"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "other_predictors"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "other_predictors"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "other_predictors"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "parameters"
+                                "description": "",
+                                "name": "https://zenodo.org/record/1134547/files/Reference_genome_11_chromosomes.fasta"
                             }
                         ],
-                        "label": null,
-                        "name": "Funannotate predict annotation",
-                        "outputs": [
+                        "label": "https://zenodo.org/record/1134547/files/Reference_genome_11_chromosomes.fasta",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 200.00001525878906,
+                            "top": 577.9861450195312
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"https://zenodo.org/record/1134547/files/Reference_genome_11_chromosomes.fasta\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "7c1d53db-b81d-40ab-8a75-221a94eb09ff",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nEBI SRA: SRR034310 File: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR034/SRR034310/SRR034310.fastq.gz\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/1134547/files/Barcode_SRR034310.txt\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"FastQC\"];\n  5 -->|demultiplexed| 10;\n  11[\"Map with BWA\"];\n  5 -->|demultiplexed| 11;\n  3 -->|output| 11;\n  12[\"Select\"];\n  6 -->|output_log| 12;\n  13[\"Select\"];\n  6 -->|output_log| 13;\n  14[\"Replace Text\"];\n  7 -->|outfile| 14;\n  15[\"Replace Text\"];\n  8 -->|out_file1| 15;\n  16[\"Replace Text\"];\n  9 -->|out_file1| 16;\n  17[\"MultiQC\"];\n  10 -->|text_file| 17;\n  18[\"Replace Text\"];\n  12 -->|out_file1| 18;\n  19[\"Replace Text\"];\n  13 -->|out_file1| 19;\n  2[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/1134547/files/Details_Barcode_Population_SRR034310.txt\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  20[\"Add column\"];\n  14 -->|outfile| 20;\n  21[\"Concatenate datasets\"];\n  19 -->|outfile| 21;\n  15 -->|outfile| 21;\n  16 -->|outfile| 21;\n  18 -->|outfile| 21;\n  22[\"Cut\"];\n  20 -->|out_file1| 22;\n  23[\"Convert\"];\n  21 -->|out_file1| 23;\n  24[\"Regex Replace\"];\n  22 -->|out_file1| 24;\n  25[\"Stacks: reference map\"];\n  11 -->|bam_output| 25;\n  24 -->|outfile| 25;\n  26[\"Stacks: populations\"];\n  25 -->|all_output| 26;\n  24 -->|outfile| 26;\n  27[\"Summary Statistics\"];\n  26 -->|out_fstats| 27;\n  28[\"Sort\"];\n  26 -->|out_fstats| 28;\n  29[\"Count\"];\n  26 -->|out_fstats| 29;\n  3[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/1134547/files/Reference_genome_11_chromosomes.fasta\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  30[\"Filter\"];\n  26 -->|out_fstats| 30;\n  4[\"Stacks: process radtags\"];\n  1 -->|output| 4;\n  0 -->|output| 4;\n  5[\"Stacks: process radtags\"];\n  1 -->|output| 5;\n  0 -->|output| 5;\n  6[\"Stacks: process radtags\"];\n  1 -->|output| 6;\n  0 -->|output| 6;\n  7[\"Replace Text\"];\n  2 -->|output| 7;\n  8[\"Select\"];\n  4 -->|output_log| 8;\n  9[\"Select\"];\n  5 -->|output_log| 9;",
+                "modified": "2024-10-02 12:08:07 +0000",
+                "name": "Workflow Constructed From History 'STACKS RAD: Population Genomics With Reference Genome'",
+                "outputs": [],
+                "parent_id": "ecology/ref-based-rad-seq",
+                "path": "topics/ecology/tutorials/ref-based-rad-seq/workflows/Galaxy-Workflow-Workflow_constructed_from_history__STACKS_RAD__population_genomics_with_reference_genome_.ga",
+                "tags": [
+                    "ecology"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Workflow Constructed From History 'STACKS RAD: Population Genomics With Reference Genome'",
+                "topic_id": "ecology",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-ref-based-rad-seq/versions/galaxy-workflow-workflow-constructed-from-history--stacks-rad--population-genomics-with-reference-genome-",
+                "tutorial_id": "ref-based-rad-seq",
+                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ref-based-rad-seq/workflows/Galaxy-Workflow-Workflow_constructed_from_history__STACKS_RAD__population_genomics_with_reference_genome_.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ref-based-rad-seq/workflows/Galaxy-Workflow-Workflow_constructed_from_history__STACKS_RAD__population_genomics_with_reference_genome_.html",
+                "version": 3,
+                "wfid": "ecology-ref-based-rad-seq",
+                "wfname": "galaxy-workflow-workflow-constructed-from-history--stacks-rad--population-genomics-with-reference-genome-",
+                "workflow": "Galaxy-Workflow-Workflow_constructed_from_history__STACKS_RAD__population_genomics_with_reference_genome_.ga",
+                "workflow_tools": [
+                    "Convert characters1",
+                    "Count1",
+                    "Cut1",
+                    "Filter1",
+                    "Grep1",
+                    "Summary_Statistics1",
+                    "addValue",
+                    "cat1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_populations/stacks_populations/1.46.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_refmap/stacks_refmap/1.46.0",
+                    "toolshed.g2.bx.psu.edu/repos/kellrott/regex_replace/regex_replace/1.0.0"
+                ],
+                "workflowhub_id": "1250"
+            },
+            {
+                "creators": [],
+                "description": "RAD-Seq Reference-based data analysis",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nref_genome_chromFa.tar\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPopulation_map.txt\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBarcodes_SRR034310.tabular\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSRR034310.fastq\"]\n  4[label=\"Stacks: process radtags\"]\n  2 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"Stacks: process radtags\"]\n  2 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"output\"]\n  6[label=\"Stacks: process radtags\"]\n  2 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"Map with BWA for Illumina\"]\n  0 -> 7 [label=\"output\"]\n  4 -> 7 [label=\"demultiplexed\"]\n  8[label=\"Stacks: reference map\"]\n  7 -> 8 [label=\"output\"]\n  1 -> 8 [label=\"output\"]\n  9[label=\"Stacks: populations\"]\n  8 -> 9 [label=\"all_output\"]\n  1 -> 9 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "00cfc1f0873c7eee656d05fd549f5cd3eae6a8da",
+                        "message": "out_fastp\u0125ase",
+                        "num": 5,
+                        "short_hash": "00cfc1f08",
+                        "unix": "1579699186"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 4,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "ea197f141d3c4fcf8f8e424604a5d40bf9125ce6",
+                        "message": "small changes",
+                        "num": 3,
+                        "short_hash": "ea197f141",
+                        "unix": "1579091409"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 2,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "bfc1c8c3f8660106a468dbfbc3af09af3e48da72",
+                        "message": "Move RAD-Seq tutorials to ecology topic",
+                        "num": 1,
+                        "short_hash": "bfc1c8c3f",
+                        "unix": "1568279010"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "annot_gbk",
-                                "type": "genbank"
+                                "description": "",
+                                "name": "ref_genome_chromFa.tar"
                             }
                         ],
+                        "label": "ref_genome_chromFa.tar",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 978.2000122070312,
-                            "height": 591.2000122070312,
-                            "left": 1417.5,
-                            "right": 1617.5,
-                            "top": 387,
-                            "width": 200,
-                            "x": 1417.5,
-                            "y": 387
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionannot_gbk": {
-                                "action_arguments": {
-                                    "newname": "#{input}"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "annot_gbk"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.9+galaxy2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2bba2ff070d9",
-                            "name": "funannotate_predict",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 200.00001525878906,
+                            "top": 200.00001525878906
                         },
-                        "tool_state": "{\"augustus\": {\"augustus_species\": \"none\", \"min_training_models\": \"15\", \"optimize_augustus\": \"false\"}, \"busco\": {\"busco_db\": \"saccharomycetes\", \"busco_seed_species\": \"saccharomyces\"}, \"database\": \"2022-03-24-174412\", \"evidences\": {\"rna_bam\": {\"__class__\": \"RuntimeValue\"}, \"transcript_evidence\": {\"__class__\": \"RuntimeValue\"}, \"prot_evidence\": {\"prot_evidence_source\": \"uniprot\", \"__current_case__\": 0}, \"p2g_pident\": \"80\", \"p2g_prefilter\": \"diamond\"}, \"evm\": {\"repeats2evm\": \"false\", \"evm_partitioning\": {\"evm_partition\": \"yes\", \"__current_case__\": 0, \"evm_partition_interval\": \"1500\"}, \"weights\": \"\"}, \"filtering\": {\"min_intronlen\": \"10\", \"max_intronlen\": \"3000\", \"min_protlen\": \"50\", \"keep_no_stops\": \"false\", \"repeat_filter\": \"overlap blast\"}, \"force\": \"true\", \"genemark\": {\"genemark_license\": {\"__class__\": \"RuntimeValue\"}, \"genemark_mode\": \"ES\", \"genemark_mod\": {\"__class__\": \"RuntimeValue\"}, \"soft_mask\": \"2000\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"organism\": {\"species\": \"Saccharomyces cerevisiae\", \"isolate\": \"\", \"strain\": \"\", \"organism\": \"true\", \"ploidy\": \"1\", \"SeqCenter\": \"CFMR\", \"SeqAccession\": \"12345\", \"name\": \"FUN_\", \"numbering\": \"1\"}, \"other_predictors\": {\"stringtie\": {\"__class__\": \"RuntimeValue\"}, \"maker_gff\": {\"__class__\": \"RuntimeValue\"}, \"pasa_gff\": {\"__class__\": \"RuntimeValue\"}, \"pasa_gff_weight\": \"1\", \"other_gff\": {\"__class__\": \"RuntimeValue\"}, \"other_gff_weight\": \"1\"}, \"outputs\": [\"gbk\"], \"parameters\": {\"__class__\": \"RuntimeValue\"}, \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.9+galaxy2",
-                        "type": "tool",
-                        "uuid": "760b55d2-5e23-41f5-9766-e939fe5e6d9b",
-                        "workflow_outputs": [
-                            {
-                                "label": "funannotate_predicted_proteins",
-                                "output_name": "annot_gbk",
-                                "uuid": "642c1c09-82f4-4ef4-bd53-d14a583044e2"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"ref_genome_chromFa.tar\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "d41b8a08-8893-4fe4-86c1-21caa8e95cb9",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/glimmer_gbk_to_orf/glimmer_gbk_to_orf/3.02",
+                        "content_id": null,
                         "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "infile": {
-                                "id": 3,
-                                "output_name": "annot_gbk"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Extract ORF",
-                        "outputs": [
-                            {
-                                "name": "aa_output",
-                                "type": "fasta"
-                            },
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "nc_output",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "Population_map.txt"
                             }
                         ],
+                        "label": "Population_map.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 763.6000061035156,
-                            "height": 123.60000610351562,
-                            "left": 1705.5,
-                            "right": 1905.5,
-                            "top": 640,
-                            "width": 200,
-                            "x": 1705.5,
-                            "y": 640
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionaa_output": {
-                                "action_arguments": {
-                                    "newname": "#{infile}"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "aa_output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/glimmer_gbk_to_orf/glimmer_gbk_to_orf/3.02",
-                        "tool_shed_repository": {
-                            "changeset_revision": "04861c9bbf45",
-                            "name": "glimmer_gbk_to_orf",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 200.00001525878906,
+                            "top": 320.00001525878906
                         },
-                        "tool_state": "{\"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.02",
-                        "type": "tool",
-                        "uuid": "ac2baad9-7cdd-4c59-a260-492d4f54bed4",
-                        "workflow_outputs": [
-                            {
-                                "label": "extracted_ORFs",
-                                "output_name": "aa_output",
-                                "uuid": "07fb8c04-990e-4bc7-b607-9c4161b4786d"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "nc_output",
-                                "uuid": "3b303171-139b-45dc-943b-8a425f679f46"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Population_map.txt\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "59b48fd7-4a76-4683-8e5b-b8db033e4f5d",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "input": {
-                                "id": 4,
-                                "output_name": "aa_output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Regex Find And Replace",
-                        "outputs": [
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "description": "",
+                                "name": "Barcodes_SRR034310.tabular"
                             }
                         ],
+                        "label": "Barcodes_SRR034310.tabular",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 794.3999938964844,
-                            "height": 154.39999389648438,
-                            "left": 1992,
-                            "right": 2192,
-                            "top": 640,
-                            "width": 200,
-                            "x": 1992,
-                            "y": 640
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "#{input}"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ae8c4b2488e7",
-                            "name": "regex_find_replace",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 200.00001525878906,
+                            "top": 440.00001525878906
                         },
-                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \">([^ ]+).+\", \"replacement\": \">#{input_name}_\\\\1\"}], \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.1",
-                        "type": "tool",
-                        "uuid": "adaf4b62-fe6a-4881-a6af-1e2afb87bfe9",
-                        "workflow_outputs": [
-                            {
-                                "label": "sample_names_to_headers",
-                                "output_name": "out_file1",
-                                "uuid": "8dc378a8-d485-42df-8322-6cf8230257a0"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Barcodes_SRR034310.tabular\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "c7ea916e-f493-4e53-bbf5-1d9b0ab34c18",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "SRR034310.fastq"
+                            }
+                        ],
+                        "label": "SRR034310.fastq",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 200.00001525878906,
+                            "top": 560.0000457763672
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"SRR034310.fastq\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "8dcf8e48-fc08-4c2c-9aad-477de98b41d1",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nref_genome_chromFa.tar\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nPopulation_map.txt\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nBarcodes_SRR034310.tabular\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nSRR034310.fastq\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Stacks: process radtags\"];\n  2 -->|output| 4;\n  3 -->|output| 4;\n  5[\"Stacks: process radtags\"];\n  2 -->|output| 5;\n  3 -->|output| 5;\n  6[\"Stacks: process radtags\"];\n  2 -->|output| 6;\n  3 -->|output| 6;\n  7[\"Map with BWA for Illumina\"];\n  0 -->|output| 7;\n  4 -->|demultiplexed| 7;\n  8[\"Stacks: reference map\"];\n  7 -->|output| 8;\n  1 -->|output| 8;\n  9[\"Stacks: populations\"];\n  8 -->|all_output| 9;\n  1 -->|output| 9;",
+                "modified": "2024-10-02 12:08:07 +0000",
+                "name": "Ref Based Rad Seq",
+                "outputs": [],
+                "parent_id": "ecology/ref-based-rad-seq",
+                "path": "topics/ecology/tutorials/ref-based-rad-seq/workflows/workflow.ga",
+                "tags": [
+                    "ecology"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Ref Based Rad Seq",
+                "topic_id": "ecology",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-ref-based-rad-seq/versions/workflow",
+                "tutorial_id": "ref-based-rad-seq",
+                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ref-based-rad-seq/workflows/workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ref-based-rad-seq/workflows/workflow.html",
+                "version": 3,
+                "wfid": "ecology-ref-based-rad-seq",
+                "wfname": "workflow",
+                "workflow": "workflow.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_populations/stacks_populations/1.46.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_refmap/stacks_refmap/1.46.0"
+                ],
+                "workflowhub_id": "1245"
+            }
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.1134547"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "graphicsmagick_image_montage",
+                    "owner": "bgruening",
+                    "revisions": "a0f01c777820",
+                    "tool_panel_section_label": "Convert Formats",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "cdo_operations",
+                    "owner": "climate",
+                    "revisions": "d5355f6fa02b",
+                    "tool_panel_section_label": "Climate Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "xarray_coords_info",
+                    "owner": "ecology",
+                    "revisions": "3e73f657a998",
+                    "tool_panel_section_label": "GIS Data Handling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "xarray_mapplot",
+                    "owner": "ecology",
+                    "revisions": "dc05bf0af58f",
+                    "tool_panel_section_label": "GIS Data Handling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "xarray_metadata_info",
+                    "owner": "ecology",
+                    "revisions": "e8650cdf092f",
+                    "tool_panel_section_label": "GIS Data Handling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: graphicsmagick_image_montage\n  owner: bgruening\n  revisions: a0f01c777820\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cdo_operations\n  owner: climate\n  revisions: d5355f6fa02b\n  tool_panel_section_label: Climate Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xarray_coords_info\n  owner: ecology\n  revisions: 3e73f657a998\n  tool_panel_section_label: GIS Data Handling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xarray_mapplot\n  owner: ecology\n  revisions: dc05bf0af58f\n  tool_panel_section_label: GIS Data Handling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xarray_metadata_info\n  owner: ecology\n  revisions: e8650cdf092f\n  tool_panel_section_label: GIS Data Handling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/x-array-map-plot/tutorial.json",
+        "contributors": [
+            {
+                "id": "Quickbeasts51429",
+                "joined": "2022-06",
+                "name": "Soumya Jha",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Quickbeasts51429/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Quickbeasts51429.json"
+            }
+        ],
+        "dir": "topics/ecology/tutorials/x-array-map-plot",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "ecology/x-array-map-plot",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "NetCDF xarray climate data visualization",
+            "NetCDF xarray map plotting projections",
+            "NetCDF xarray map plotting colormaps"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-27",
+        "objectives": [
+            "Learn about plotting Climate Data",
+            "Learn about NetCDF xarray map plotting tool",
+            "Learn about visualizing the climate data using NetCDF xarray map plotting using the different kinds of projections and colormap options"
+        ],
+        "pageviews": 2315,
+        "pub_date": "2022-10-26",
+        "questions": [
+            "What is xarray map plotting?",
+            "How to plot NetCDF data using xarray map plotting tool?",
+            "What are the different types of projections and colormap options available in the tool?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "climate",
+                "tutorials": [
+                    "climate-101"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00136",
+        "short_tools": [
+            "xarray_metadata_info",
+            "xarray_mapplot",
+            "graphicsmagick_image_montage",
+            "cdo_operations",
+            "xarray_coords_info"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "ecologyviz",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "pangeo"
+        ],
+        "time_estimation": "1H",
+        "title": "Visualization of Climate Data using  NetCDF xarray Map Plotting",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage/1.3.31+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/climate/cdo_operations/cdo_operations/2.0.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/0.20.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.20.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1"
+        ],
+        "topic_name": "ecology",
+        "topic_name_human": "Ecology",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "x-array-map-plot",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/x-array-map-plot/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/x-array-map-plot/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/x-array-map-plot/tutorial.json"
+        },
+        "version": 9,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 31,
+        "visitors": 1976,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "Quickbeasts51429",
+                        "name": "Soumya Jha"
+                    }
+                ],
+                "description": "Visualization of Climate Data using NetCDF Xarray Map Plotting",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nair_temperature_at_2_metres.nc\"]\n  1[label=\"NetCDF xarray Coordinate Info\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"NetCDF xarray Metadata Info\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"CDO Operations\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"CDO Operations\"]\n  3 -> 4 [label=\"output_files\"]\n  5[label=\"NetCDF xarray Metadata Info\"]\n  4 -> 5 [label=\"output_files\"]\n  6[label=\"NetCDF xarray map plotting\"]\n  4 -> 6 [label=\"output_files\"]\n  5 -> 6 [label=\"output\"]\n  7[label=\"NetCDF xarray map plotting\"]\n  4 -> 7 [label=\"output_files\"]\n  5 -> 7 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "ce9cd3e8d3c5487ed4bbce32d5d889ee84e91e9d",
+                        "message": "Tutorial added to ecology folder: \"Visualization of Climate Data using NetCDF Xarray Map Plotting\"  (#3481)",
+                        "num": 1,
+                        "short_hash": "ce9cd3e8d",
+                        "unix": "1666808431"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "Upload the dataset : air temperatures at 2  metres , from the 'remote datasets'",
+                        "content_id": null,
                         "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "input_list": {
-                                "id": 5,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Collapse Collection",
-                        "outputs": [
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "input"
+                                "description": "Upload the dataset : air temperatures at 2  metres , from the 'remote datasets'",
+                                "name": "air_temperature_at_2_metres.nc"
                             }
                         ],
+                        "label": "air_temperature_at_2_metres.nc",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 494.3999938964844,
-                            "height": 154.39999389648438,
-                            "left": 2314.966552734375,
-                            "right": 2514.966552734375,
-                            "top": 340,
-                            "width": 200,
-                            "x": 2314.966552734375,
-                            "y": 340
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "830961c48e42",
-                            "name": "collapse_collections",
-                            "owner": "nml",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": -16.41666666666667,
+                            "height": 76.96875,
+                            "left": -247.125,
+                            "right": -97.125,
+                            "top": -93.38541666666667,
+                            "width": 150,
+                            "x": -247.125,
+                            "y": -93.38541666666667
                         },
-                        "tool_state": "{\"filename\": {\"add_name\": \"false\", \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.2",
-                        "type": "tool",
-                        "uuid": "ae4ddb2f-104b-409f-9d91-07c4410ba00a",
-                        "workflow_outputs": [
-                            {
-                                "label": "proteomes_to_one_file",
-                                "output_name": "output",
-                                "uuid": "e9a55459-4a2c-4238-8494-e99ec67307ea"
-                            }
-                        ]
-                    },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"input\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "f1e7e3ca-c219-42e5-ab29-86be86e3a49c",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nair_temperature_at_2_metres.nc\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"NetCDF xarray Coordinate Info\"];\n  0 -->|output| 1;\n  2[\"NetCDF xarray Metadata Info\"];\n  0 -->|output| 2;\n  3[\"CDO Operations\"];\n  0 -->|output| 3;\n  4[\"CDO Operations\"];\n  3 -->|output_files| 4;\n  5[\"NetCDF xarray Metadata Info\"];\n  4 -->|output_files| 5;\n  6[\"NetCDF xarray map plotting\"];\n  4 -->|output_files| 6;\n  5 -->|output| 6;\n  7[\"NetCDF xarray map plotting\"];\n  4 -->|output_files| 7;\n  5 -->|output| 7;",
+                "modified": "2024-10-02 12:08:07 +0000",
+                "name": "Xarray_Map_Plotting_Workflow",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/proteinortho/proteinortho/6.0.14+galaxy2.9.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/0.20.2+galaxy0",
                         "errors": null,
-                        "id": 7,
+                        "id": 1,
                         "input_connections": {
-                            "input_files": {
-                                "id": 5,
-                                "output_name": "out_file1"
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Proteinortho",
+                        "name": "NetCDF xarray Coordinate Info",
                         "outputs": [
                             {
-                                "name": "blastgraph",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "proteinortho",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "proteinorthograph",
-                                "type": "tabular"
+                                "name": "output_dir",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 826.3333129882812,
-                            "height": 296.79998779296875,
-                            "left": 2307.966552734375,
-                            "right": 2507.966552734375,
-                            "top": 529.5333251953125,
-                            "width": 200,
-                            "x": 2307.966552734375,
-                            "y": 529.5333251953125
+                            "bottom": 112.39583333333333,
+                            "height": 85.21875,
+                            "left": 101.77083333333333,
+                            "right": 251.77083333333331,
+                            "top": 27.177083333333332,
+                            "width": 150,
+                            "x": 101.77083333333333,
+                            "y": 27.177083333333332
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/proteinortho/proteinortho/6.0.14+galaxy2.9.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/0.20.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "4850f0d15f01",
-                            "name": "proteinortho",
-                            "owner": "iuc",
+                            "changeset_revision": "3e73f657a998",
+                            "name": "xarray_coords_info",
+                            "owner": "ecology",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"conn\": \"0.1\", \"evalue\": \"0.001\", \"input_files\": {\"__class__\": \"ConnectedValue\"}, \"more_options\": {\"cov\": \"50\", \"sim\": \"95\", \"identity\": \"25\", \"selfblast\": \"false\", \"singles\": \"false\", \"isoform\": \"no\"}, \"p\": \"diamond\", \"synteny\": {\"synteny_options\": \"no\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "6.0.14+galaxy2.9.1",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.20.2+galaxy0",
                         "type": "tool",
-                        "uuid": "2d05e13f-4cb1-4d86-800f-3e743b50fab8",
+                        "uuid": "6f17f1e4-27d1-49af-a15d-080826d7a36b",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "proteinorthograph",
-                                "uuid": "42f51f73-f573-4d2f-a703-04dd329dfd4b"
-                            },
-                            {
-                                "label": "Proteinortho on input dataset(s): orthology-groups",
-                                "output_name": "proteinortho",
-                                "uuid": "ee688b7a-2a9e-4480-a27a-db8cf795b635"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "blastgraph",
-                                "uuid": "e2b3b5ba-33ec-4330-bebc-2bb7f3c2b360"
+                                "output_name": "output_dir",
+                                "uuid": "c60539a8-ee7d-479a-81e9-486d0f8221d9"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1",
                         "errors": null,
-                        "id": 8,
+                        "id": 2,
                         "input_connections": {
                             "input": {
-                                "id": 5,
-                                "output_name": "out_file1"
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Busco",
+                        "name": "NetCDF xarray Metadata Info",
                         "outputs": [
                             {
-                                "name": "busco_sum",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "busco_table",
+                                "name": "output",
                                 "type": "tabular"
                             },
                             {
-                                "name": "busco_missing",
-                                "type": "tabular"
+                                "name": "info",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 1122.3999938964844,
-                            "height": 276.3999938964844,
-                            "left": 2316.466552734375,
-                            "right": 2516.466552734375,
-                            "top": 846,
-                            "width": 200,
-                            "x": 2316.466552734375,
-                            "y": 846
+                            "bottom": -29.4765625,
+                            "height": 108.0234375,
+                            "left": 59.333333333333336,
+                            "right": 209.33333333333334,
+                            "top": -137.5,
+                            "width": 150,
+                            "x": 59.333333333333336,
+                            "y": -137.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "602fb8e63aa7",
-                            "name": "busco",
-                            "owner": "iuc",
+                            "changeset_revision": "e8650cdf092f",
+                            "name": "xarray_metadata_info",
+                            "owner": "ecology",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"chromInfo\": \"/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"CM005299.1\", \"lineage_dataset\": \"saccharomycetes_odb10\", \"mode\": \"prot\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.1.4",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.15.1",
                         "type": "tool",
-                        "uuid": "174f50d8-09bd-48b9-afcd-44468e41a0c3",
+                        "uuid": "a7264ebe-3a2a-4289-a441-6d1c6069c308",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "busco_sum",
-                                "uuid": "471d5e9e-db3e-44ee-9936-22f5e9072fd1"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "busco_missing",
-                                "uuid": "2195fc7f-ae89-43e8-ba1e-d45955b8856e"
+                                "output_name": "output",
+                                "uuid": "9d7ca599-cbeb-4015-9906-45d3381b5fee"
                             },
                             {
                                 "label": null,
-                                "output_name": "busco_table",
-                                "uuid": "76879cb7-9b5f-443b-84a4-414e2fe0b14d"
+                                "output_name": "info",
+                                "uuid": "930410e1-a49f-4484-9e71-d8d3a15fde9a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Filter1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/climate/cdo_operations/cdo_operations/2.0.0+galaxy0",
                         "errors": null,
-                        "id": 9,
+                        "id": 3,
                         "input_connections": {
-                            "input": {
-                                "id": 7,
-                                "output_name": "proteinortho"
+                            "section_operators_0|operator|add_file": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Filter",
+                        "name": "CDO Operations",
                         "outputs": [
                             {
-                                "name": "out_file1",
+                                "name": "output_files",
                                 "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 785.7333221435547,
-                            "height": 93.19999694824219,
-                            "left": 2585,
-                            "right": 2785,
-                            "top": 692.5333251953125,
-                            "width": 200,
-                            "x": 2585,
-                            "y": 692.5333251953125
+                            "bottom": 282.34895833333337,
+                            "height": 115.828125,
+                            "left": 119.98958333333333,
+                            "right": 269.9895833333333,
+                            "top": 166.52083333333334,
+                            "width": 150,
+                            "x": 119.98958333333333,
+                            "y": 166.52083333333334
                         },
                         "post_job_actions": {},
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"cond\": \"c1==4 and c2==4\", \"header_lines\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/climate/cdo_operations/cdo_operations/2.0.0+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "d5355f6fa02b",
+                            "name": "cdo_operations",
+                            "owner": "climate",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"section_operators\": [{\"__index__\": 0, \"operator\": {\"opt\": \"seltimestep\", \"__current_case__\": 27, \"params\": \"594/595\", \"add_file\": {\"__class__\": \"RuntimeValue\"}}}], \"section_option\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.0+galaxy0",
                         "type": "tool",
-                        "uuid": "b4758296-c3c9-4c3c-bb2d-2f637f8702b5",
+                        "uuid": "c0830da8-262f-4ac2-ad4f-c4f283ab344a",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "c03839b1-17e0-4fb1-8b53-d3fd2a89aaba"
+                                "output_name": "output_files",
+                                "uuid": "9fb668b7-381d-4af9-9128-8e8d06c18023"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.0.14+galaxy2.9.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/climate/cdo_operations/cdo_operations/2.0.0+galaxy0",
                         "errors": null,
-                        "id": 10,
+                        "id": 4,
                         "input_connections": {
-                            "input_files": {
-                                "id": 6,
-                                "output_name": "output"
-                            },
-                            "query|queryfile": {
-                                "id": 9,
-                                "output_name": "out_file1"
+                            "section_operators_0|operator|add_file": {
+                                "id": 3,
+                                "output_name": "output_files"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Proteinortho grab proteins",
+                        "name": "CDO Operations",
                         "outputs": [
                             {
-                                "name": "listproteinorthograbproteins",
+                                "name": "output_files",
                                 "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 597.8000030517578,
-                            "height": 184.8000030517578,
-                            "left": 2850,
-                            "right": 3050,
-                            "top": 413,
-                            "width": 200,
-                            "x": 2850,
-                            "y": 413
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionlistproteinorthograbproteins": {
-                                "action_arguments": {
-                                    "newname": "#{query.queryfile}"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "listproteinorthograbproteins"
-                            }
+                            "bottom": 304.46354166666663,
+                            "height": 115.828125,
+                            "left": 407.3333333333333,
+                            "right": 557.3333333333333,
+                            "top": 188.63541666666666,
+                            "width": 150,
+                            "x": 407.3333333333333,
+                            "y": 188.63541666666666
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.0.14+galaxy2.9.1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/climate/cdo_operations/cdo_operations/2.0.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "d348c3a151d9",
-                            "name": "proteinortho_grab_proteins",
-                            "owner": "iuc",
+                            "changeset_revision": "d5355f6fa02b",
+                            "name": "cdo_operations",
+                            "owner": "climate",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input_files\": {\"__class__\": \"ConnectedValue\"}, \"query\": {\"querytype\": \"file\", \"__current_case__\": 1, \"queryfile\": {\"__class__\": \"ConnectedValue\"}}, \"regex\": \"false\", \"source\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "6.0.14+galaxy2.9.1",
+                        "tool_state": "{\"section_operators\": [{\"__index__\": 0, \"operator\": {\"opt\": \"splithour\", \"__current_case__\": 14, \"add_file\": {\"__class__\": \"RuntimeValue\"}}}], \"section_option\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.0+galaxy0",
                         "type": "tool",
-                        "uuid": "78e25a29-21b2-47ab-ac0e-a5b958258086",
+                        "uuid": "dbd1ef36-61b8-497a-859c-61640ec2c2ac",
                         "workflow_outputs": [
                             {
-                                "label": "Proteinortho_extract_by_orthogroup",
-                                "output_name": "listproteinorthograbproteins",
-                                "uuid": "8625e8b1-e3af-4afa-bf85-1a3258cbbfb2"
+                                "label": null,
+                                "output_name": "output_files",
+                                "uuid": "b02a9565-40e3-4042-ae0b-e8dadc595082"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1",
                         "errors": null,
-                        "id": 11,
+                        "id": 5,
                         "input_connections": {
                             "input": {
-                                "id": 10,
-                                "output_name": "listproteinorthograbproteins"
+                                "id": 4,
+                                "output_name": "output_files"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Regex Find And Replace",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "description": "runtime parameter for tool NetCDF xarray Metadata Info",
+                                "name": "input"
                             }
                         ],
-                        "position": {
-                            "bottom": 541,
-                            "height": 134,
-                            "left": 3151,
-                            "right": 3351,
-                            "top": 407,
-                            "width": 200,
-                            "x": 3151,
-                            "y": 407
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "#{input}"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ae8c4b2488e7",
-                            "name": "regex_find_replace",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \"(>[^_]+).+\", \"replacement\": \"\\\\1\"}], \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.1",
-                        "type": "tool",
-                        "uuid": "c99a9988-fa6a-4366-8c9f-9195e7f77b19",
-                        "workflow_outputs": [
-                            {
-                                "label": "fasta_header_cleaned",
-                                "output_name": "out_file1",
-                                "uuid": "b072d32e-f725-4833-af0b-74f4df526d9a"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
-                        "errors": null,
-                        "id": 12,
-                        "input_connections": {
-                            "input": {
-                                "id": 11,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
                         "label": null,
-                        "name": "ClustalW",
+                        "name": "NetCDF xarray Metadata Info",
                         "outputs": [
                             {
                                 "name": "output",
-                                "type": "clustal"
+                                "type": "tabular"
                             },
                             {
-                                "name": "dnd",
-                                "type": "nhx"
+                                "name": "info",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 593.3333129882812,
-                            "height": 184.79998779296875,
-                            "left": 3431,
-                            "right": 3631,
-                            "top": 408.5333251953125,
-                            "width": 200,
-                            "x": 3431,
-                            "y": 408.5333251953125
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActiondnd": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "dnd"
-                            },
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "#{input}"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
+                            "bottom": 559.6484375,
+                            "height": 108.0234375,
+                            "left": 669.9791666666666,
+                            "right": 819.9791666666666,
+                            "top": 451.625,
+                            "width": 150,
+                            "x": 669.9791666666666,
+                            "y": 451.625
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "d6694932c5e0",
-                            "name": "clustalw",
-                            "owner": "devteam",
+                            "changeset_revision": "e8650cdf092f",
+                            "name": "xarray_metadata_info",
+                            "owner": "ecology",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"dnarna\": \"PROTEIN\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"out_order\": \"ALIGNED\", \"outcontrol\": {\"outform\": \"fasta\", \"__current_case__\": 0}, \"range\": {\"mode\": \"complete\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1",
+                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.15.1",
                         "type": "tool",
-                        "uuid": "8ead7ee6-fe67-4479-a8dd-722e8247cb0e",
+                        "uuid": "388764c7-3d2f-448f-833e-63520411263e",
                         "workflow_outputs": [
                             {
-                                "label": "ClustalW on input dataset(s): clustal",
+                                "label": null,
                                 "output_name": "output",
-                                "uuid": "f704b4b2-5214-4393-8a85-6274bda27c8c"
+                                "uuid": "eac57113-dab5-4047-9e3e-082aa04375c9"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "info",
+                                "uuid": "f629b534-e0fb-4dbc-8c4c-72b5f2105119"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/padge/clipkit/clipkit/0.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.20.2+galaxy0",
                         "errors": null,
-                        "id": 13,
+                        "id": 6,
                         "input_connections": {
-                            "input1": {
-                                "id": 12,
+                            "input": {
+                                "id": 4,
+                                "output_name": "output_files"
+                            },
+                            "var_tab": {
+                                "id": 5,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool NetCDF xarray map plotting",
+                                "name": "input"
+                            },
+                            {
+                                "description": "runtime parameter for tool NetCDF xarray map plotting",
+                                "name": "var_tab"
+                            }
+                        ],
                         "label": null,
-                        "name": "ClipKIT. Alignment trimming software for phylogenetics.",
+                        "name": "NetCDF xarray map plotting",
                         "outputs": [
                             {
-                                "name": "trimmed_output",
-                                "type": "fasta"
+                                "name": "output_dir",
+                                "type": "input"
                             },
                             {
-                                "name": "log_output",
-                                "type": "txt"
+                                "name": "version",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 611.1999969482422,
-                            "height": 205.1999969482422,
-                            "left": 3710,
-                            "right": 3910,
-                            "top": 406,
-                            "width": 200,
-                            "x": 3710,
-                            "y": 406
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionlog_output": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "log_output"
-                            }
+                            "bottom": 332.015625,
+                            "height": 130.828125,
+                            "left": 1004.7604166666666,
+                            "right": 1154.7604166666665,
+                            "top": 201.1875,
+                            "width": 150,
+                            "x": 1004.7604166666666,
+                            "y": 201.1875
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/padge/clipkit/clipkit/0.1.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.20.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "770695339600",
-                            "name": "clipkit",
-                            "owner": "padge",
+                            "changeset_revision": "dc05bf0af58f",
+                            "name": "xarray_mapplot",
+                            "owner": "ecology",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"complement\": \"false\", \"gaps\": \"0.9\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"mode_selector\": \"smart-gap\", \"out_format_selector\": \"fasta\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.0",
+                        "tool_state": "{\"borders\": \"1.0\", \"cmap\": \"cm.lajolla\", \"coastline\": \"1.0\", \"colorbar_label\": \"\", \"condi_datetime\": {\"datetime\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"land\": null, \"lat_dim\": \"lat\", \"lon_dim\": \"lon\", \"ocean\": \"1.0\", \"proj\": \"{'proj': 'Mercator', 'central_longitude': 12.0}\", \"range\": \"220,320\", \"shift\": \"\", \"threshold\": null, \"title\": \"Projection :  Mercator 17:00 UTC \", \"var\": \"air_temperature_at_2_metres\", \"var_tab\": {\"__class__\": \"RuntimeValue\"}, \"xlim\": \"\", \"ylim\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.20.2+galaxy0",
                         "type": "tool",
-                        "uuid": "ee4b18ee-b6df-46ad-a808-cc78783fc773",
+                        "uuid": "bd88b706-c6b1-4a39-a0f5-24d2d306d3bc",
                         "workflow_outputs": [
                             {
-                                "label": "Trimmed alignment.",
-                                "output_name": "trimmed_output",
-                                "uuid": "37092981-191a-4413-8f60-51802dd95f9c"
+                                "label": null,
+                                "output_name": "output_dir",
+                                "uuid": "7540245d-ebf3-4446-b8f2-71dfa0410b2d"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "version",
+                                "uuid": "8a0f1cb9-67bc-4554-9473-e10f482d3f79"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/padge/phykit/phykit_alignment_based/0.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.20.2+galaxy0",
                         "errors": null,
-                        "id": 14,
+                        "id": 7,
                         "input_connections": {
-                            "tools|input1": {
-                                "id": 13,
-                                "output_name": "trimmed_output"
+                            "input": {
+                                "id": 4,
+                                "output_name": "output_files"
+                            },
+                            "var_tab": {
+                                "id": 5,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "PhyKit - Alignment-based functions",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "fasta",
-                                "type": "fasta"
+                                "description": "runtime parameter for tool NetCDF xarray map plotting",
+                                "name": "input"
                             },
                             {
-                                "name": "partition",
-                                "type": "iqtree"
+                                "description": "runtime parameter for tool NetCDF xarray map plotting",
+                                "name": "var_tab"
+                            }
+                        ],
+                        "label": null,
+                        "name": "NetCDF xarray map plotting",
+                        "outputs": [
+                            {
+                                "name": "output_dir",
+                                "type": "input"
                             },
                             {
-                                "name": "occupancy",
+                                "name": "version",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 806.7999877929688,
-                            "height": 398.79998779296875,
-                            "left": 3990,
-                            "right": 4190,
-                            "top": 408,
-                            "width": 200,
-                            "x": 3990,
-                            "y": 408
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionfasta": {
-                                "action_arguments": {
-                                    "newname": "#{tools.input1}"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "fasta"
-                            }
+                            "bottom": 523.796875,
+                            "height": 130.828125,
+                            "left": 1005.3333333333334,
+                            "right": 1155.3333333333335,
+                            "top": 392.96875,
+                            "width": 150,
+                            "x": 1005.3333333333334,
+                            "y": 392.96875
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/padge/phykit/phykit_alignment_based/0.1.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.20.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "1ac6ee298657",
-                            "name": "phykit",
-                            "owner": "padge",
+                            "changeset_revision": "dc05bf0af58f",
+                            "name": "xarray_mapplot",
+                            "owner": "ecology",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"tools\": {\"tool_selector\": \"create_concat\", \"__current_case__\": 0, \"input1\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.0",
+                        "tool_state": "{\"borders\": \"1.0\", \"cmap\": \"cm.lajolla\", \"coastline\": \"1.0\", \"colorbar_label\": \"\", \"condi_datetime\": {\"datetime\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"land\": null, \"lat_dim\": \"lat\", \"lon_dim\": \"lon\", \"ocean\": \"1.0\", \"proj\": \"{'proj': 'Mercator', 'central_longitude': 12.0}\", \"range\": \"220,320\", \"shift\": \"\", \"threshold\": null, \"title\": \"Projection :  Mercator 18:00 UTC \", \"var\": \"air_temperature_at_2_metres\", \"var_tab\": {\"__class__\": \"RuntimeValue\"}, \"xlim\": \"\", \"ylim\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.20.2+galaxy0",
                         "type": "tool",
-                        "uuid": "9077044b-7125-4381-858c-d7078d37c529",
+                        "uuid": "1ec4337e-4927-4666-b2a7-f4cfe3eec203",
                         "workflow_outputs": [
                             {
-                                "label": "Concatenated fasta alignment file",
-                                "output_name": "fasta",
-                                "uuid": "09ad25e3-cd68-4fb4-9c57-3e79212b8e01"
-                            },
-                            {
-                                "label": "A partition file ready for input into RAxML or IQ-tree",
-                                "output_name": "partition",
-                                "uuid": "1d546e4c-7e3c-499d-870c-4846feb7a46d"
+                                "label": null,
+                                "output_name": "output_dir",
+                                "uuid": "d16f3d0e-1319-4534-bf43-e5f2068fb196"
                             },
                             {
-                                "label": "An occupancy file that summarizes the taxon occupancy per sequence",
-                                "output_name": "occupancy",
-                                "uuid": "26846814-d43a-4ce7-9f26-cfb70f184dce"
+                                "label": null,
+                                "output_name": "version",
+                                "uuid": "040771d9-9700-4457-a50a-44a957fea91f"
                             }
                         ]
                     }
                 ],
-                "parent_id": "ecology/phylogeny-data-prep",
-                "path": "topics/ecology/tutorials/phylogeny-data-prep/workflows/main_workflow.ga",
+                "parent_id": "ecology/x-array-map-plot",
+                "path": "topics/ecology/tutorials/x-array-map-plot/workflows/main-workflow.ga",
                 "tags": [
-                    "ecology"
+                    "ecology",
+                    "climate"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "preparing genomic data for phylogeny recostruction (GTN)",
+                "title": "Xarray_Map_Plotting_Workflow",
                 "topic_id": "ecology",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-phylogeny-data-prep/versions/main-workflow",
-                "tutorial_id": "phylogeny-data-prep",
-                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/phylogeny-data-prep/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/phylogeny-data-prep/workflows/main_workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-x-array-map-plot/versions/main-workflow",
+                "tutorial_id": "x-array-map-plot",
+                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/x-array-map-plot/workflows/main-workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/x-array-map-plot/workflows/main-workflow.html",
                 "version": 1,
-                "wfid": "ecology-phylogeny-data-prep",
+                "wfid": "ecology-x-array-map-plot",
                 "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "workflow": "main-workflow.ga",
                 "workflow_tools": [
-                    "Filter1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/glimmer_gbk_to_orf/glimmer_gbk_to_orf/3.02",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.2-p1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.9+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/proteinortho/proteinortho/6.0.14+galaxy2.9.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.0.14+galaxy2.9.1",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
-                    "toolshed.g2.bx.psu.edu/repos/padge/clipkit/clipkit/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/padge/phykit/phykit_alignment_based/0.1.0"
+                    "toolshed.g2.bx.psu.edu/repos/climate/cdo_operations/cdo_operations/2.0.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/0.20.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.20.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1"
                 ],
-                "workflowhub_id": "1264"
+                "workflowhub_id": "1260"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/6610704"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.6621460"
     },
     {
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/Metashrimps_tutorial/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "TanguyGen",
-                "yvanlebras"
-            ],
-            "editing": [
-                "yvanlebras",
-                "hexylena"
-            ],
-            "funding": [
-                "fnso2019",
-                "pndb"
+            "tools": [
+                {
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "f2e8552cf1d0",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "stacks_denovomap",
+                    "owner": "iuc",
+                    "revisions": "fdbcc560c691",
+                    "tool_panel_section_label": "RAD-seq",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "stacks_populations",
+                    "owner": "iuc",
+                    "revisions": "45db1ba16163",
+                    "tool_panel_section_label": "RAD-seq",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "stacks_procrad",
+                    "owner": "iuc",
+                    "revisions": "eded025438db",
+                    "tool_panel_section_label": "RAD-seq",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
             ]
         },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastqc\n  owner: devteam\n  revisions: f2e8552cf1d0\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_denovomap\n  owner: iuc\n  revisions: fdbcc560c691\n  tool_panel_section_label: RAD-seq\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_populations\n  owner: iuc\n  revisions: 45db1ba16163\n  tool_panel_section_label: RAD-seq\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_procrad\n  owner: iuc\n  revisions: eded025438db\n  tool_panel_section_label: RAD-seq\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/de-novo-rad-seq/tutorial.json",
         "contributors": [
-            {
-                "id": "TanguyGen",
-                "joined": "2023-06",
-                "name": "Tanguy Genthon",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/TanguyGen/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/TanguyGen.json"
-            },
-            {
-                "affiliations": [
-                    "pndb",
-                    "gallantries",
-                    "fairease",
-                    "fnso2019",
-                    "elixir-europe"
-                ],
-                "elixir_node": "fr",
-                "email": "yvan.le-bras@mnhn.fr",
-                "id": "yvanlebras",
-                "joined": "2017-09",
-                "matrix": "yvanlebras:matrix.org",
-                "name": "Yvan Le Bras",
-                "orcid": "0000-0002-8504-068X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
-                "twitter": "Yvan2935",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
-            },
             {
                 "affiliations": [
                     "pndb",
@@ -62485,156 +65408,316 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
                 "twitter": "Yvan2935",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
+            }
+        ],
+        "dir": "topics/ecology/tutorials/de-novo-rad-seq",
+        "edam_operation": [
+            "Statistical calculation",
+            "Data handling",
+            "Sequencing quality control",
+            "Sequence composition calculation"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.eu"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "ecology/de-novo-rad-seq",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": null,
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-27",
+        "objectives": [
+            "Analysis of RAD sequencing data without a reference genome",
+            "SNP calling from RAD sequencing data",
+            "Calculate population genomics statistics from RAD sequencing data"
+        ],
+        "pageviews": 3862,
+        "pub_date": "2017-02-14",
+        "questions": [
+            "How to analyze RAD sequencing data without a reference genome for a population genomics study?"
+        ],
+        "redirect_from": [
+            "/topics/sequence-analysis/tutorials/de-novo-rad-seq/tutorial",
+            "/short/ecology/de-novo-rad-seq",
+            "/short/T00128"
+        ],
+        "short_id": "T00128",
+        "short_tools": [
+            "fastqc",
+            "stacks_procrad",
+            "stacks_populations",
+            "stacks_denovomap"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "ecologyanalysis",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
                 },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "RAD-seq",
+            "Genetic composition EBV class",
+            "Species populations EBV class",
+            "EBV dataset",
+            "EBV workflow"
+        ],
+        "time_estimation": "8h",
+        "title": "RAD-Seq de-novo data analysis",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69",
+            "toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/1.46.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/stacks_populations/stacks_populations/1.46.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0"
+        ],
+        "topic_name": "ecology",
+        "topic_name_human": "Ecology",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "de-novo-rad-seq",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/de-novo-rad-seq/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/de-novo-rad-seq/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/de-novo-rad-seq/tutorial.json"
+        },
+        "version": 12,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 129,
+        "visitors": 2343,
+        "workflows": [
             {
-                "avatar": "/training-material/shared/images/fnso.png",
-                "funder": true,
-                "funder_name": "National Fund for Open Science",
-                "funding_id": "AAPFNSO2019OpenMetaPaper-14026",
-                "funding_statement": "This project (<a href=\"https://www.ouvrirlascience.fr/submit-your-data-its-published/\"><code class=\"language-plaintext highlighter-rouge\">AAPFNSO2019OpenMetaPaper-14026</code></a>) is funded with the support of the national Fund for Open Science programme of the French Minister of Higher Education, Research and Innovation. Their funding has supported development of data/metadata management tools and related tutorial for Ecology and FAIR topics.\n<img src=\"https://lamy-environnement.com/wp-content/uploads/2023/03/Logo-MESR.png\" alt=\"French research ministry flag with the text: with the support of the National Fund for Open Science programme of french Minister of Higher Education, Research and Innovation\" />\n<img src=\"/training-material/shared/images/fnso.png\" alt=\"FNSO logo\" />",
-                "github": false,
-                "id": "fnso2019",
-                "joined": "2023-05",
-                "members": [
-                    "yvanlebras"
+                "creators": [],
+                "description": "RAD-Seq de-novo data analysis",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPopulation_map.txt\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBarcodes_SRR034310.tabular\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSRR034310.fastq\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nref_genome_chromFa.tar\"]\n  4[label=\"Stacks: process radtags\"]\n  1 -> 4 [label=\"output\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Stacks: process radtags\"]\n  1 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"Stacks: process radtags\"]\n  1 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"FastQC\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"Stacks: de novo map\"]\n  4 -> 8 [label=\"demultiplexed\"]\n  0 -> 8 [label=\"output\"]\n  9[label=\"Stacks: populations\"]\n  8 -> 9 [label=\"all_output\"]\n  0 -> 9 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "00cfc1f0873c7eee656d05fd549f5cd3eae6a8da",
+                        "message": "out_fastp\u0125ase",
+                        "num": 5,
+                        "short_hash": "00cfc1f08",
+                        "unix": "1579699186"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 4,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "ea197f141d3c4fcf8f8e424604a5d40bf9125ce6",
+                        "message": "small changes",
+                        "num": 3,
+                        "short_hash": "ea197f141",
+                        "unix": "1579091409"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 2,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "bfc1c8c3f8660106a468dbfbc3af09af3e48da72",
+                        "message": "Move RAD-Seq tutorials to ecology topic",
+                        "num": 1,
+                        "short_hash": "bfc1c8c3f",
+                        "unix": "1568279010"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Population_map.txt"
+                            }
+                        ],
+                        "label": "Population_map.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 200
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Population_map.txt\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "c070e872-bf5b-4690-85f8-20435bce6495",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Barcodes_SRR034310.tabular"
+                            }
+                        ],
+                        "label": "Barcodes_SRR034310.tabular",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 320
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Barcodes_SRR034310.tabular\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "27073ffe-9a96-4cee-a9c5-a95b9ab1e7c7",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "SRR034310.fastq"
+                            }
+                        ],
+                        "label": "SRR034310.fastq",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 560
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"SRR034310.fastq\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "16c3fb88-cdf5-418a-8e32-154bf142cca6",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "ref_genome_chromFa.tar"
+                            }
+                        ],
+                        "label": "ref_genome_chromFa.tar",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 440
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"ref_genome_chromFa.tar\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "50b66134-d154-425e-a66f-51e05f5edb58",
+                        "workflow_outputs": []
+                    }
                 ],
-                "name": "OpenMetaPaper",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fnso2019/",
-                "short_name": "FNSO",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/fnso2019.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/PNDB_sub.png",
-                "github": false,
-                "id": "pndb",
-                "members": [
-                    "colineroyaux",
-                    "Marie59",
-                    "yvanlebras",
-                    "ThibaudGlinez"
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPopulation_map.txt\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nBarcodes_SRR034310.tabular\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nSRR034310.fastq\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nref_genome_chromFa.tar\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Stacks: process radtags\"];\n  1 -->|output| 4;\n  2 -->|output| 4;\n  5[\"Stacks: process radtags\"];\n  1 -->|output| 5;\n  2 -->|output| 5;\n  6[\"Stacks: process radtags\"];\n  1 -->|output| 6;\n  2 -->|output| 6;\n  7[\"FastQC\"];\n  2 -->|output| 7;\n  8[\"Stacks: de novo map\"];\n  4 -->|demultiplexed| 8;\n  0 -->|output| 8;\n  9[\"Stacks: populations\"];\n  8 -->|all_output| 9;\n  0 -->|output| 9;",
+                "modified": "2024-10-02 12:08:07 +0000",
+                "name": "de novo Rad Seq",
+                "outputs": [],
+                "parent_id": "ecology/de-novo-rad-seq",
+                "path": "topics/ecology/tutorials/de-novo-rad-seq/workflows/Galaxy-Workflow-de-novo-rad-seq.ga",
+                "tags": [
+                    "ecology"
                 ],
-                "name": "P\u00f4le National de Donn\u00e9es de Biodiversit\u00e9",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pndb/",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/pndb.json"
+                "test_results": null,
+                "tests": false,
+                "title": "de novo Rad Seq",
+                "topic_id": "ecology",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-de-novo-rad-seq/versions/galaxy-workflow-de-novo-rad-seq",
+                "tutorial_id": "de-novo-rad-seq",
+                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/de-novo-rad-seq/workflows/Galaxy-Workflow-de-novo-rad-seq.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/de-novo-rad-seq/workflows/Galaxy-Workflow-de-novo-rad-seq.html",
+                "version": 3,
+                "wfid": "ecology-de-novo-rad-seq",
+                "wfname": "galaxy-workflow-de-novo-rad-seq",
+                "workflow": "Galaxy-Workflow-de-novo-rad-seq.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/1.46.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_populations/stacks_populations/1.46.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0"
+                ],
+                "workflowhub_id": "1286"
             }
         ],
-        "dir": "topics/ecology/tutorials/Metashrimps_tutorial",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "ecology/Metashrimps_tutorial",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "This tool aims to improve FAIR quality of metadata",
-            "Creating metadata as FAIR as possible is a must",
-            "Be carefull of the format and standard of metadata used only EML metadata will work"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-27",
-        "objectives": [
-            "Learn how to use the interactive tool Metashrimps",
-            "Understand the challenges MetaShRIMPS is trying to respond to",
-            "Learn how to create a FAIR Quality assessment report from a metadata using EML standard",
-            "Understand the concept of Data Paper and learn how to produce it",
-            "Explain the necessity of using such tools when producing ecological metadata"
-        ],
-        "pageviews": 31,
-        "pub_date": "2024-01-22",
-        "questions": [
-            "How to improve the FAIR quality of an EML metadata ?",
-            "How to use metadata for machine actionnable processes ?",
-            "What is the point of having a FAIR metadata ?"
-        ],
-        "short_id": "T00399",
-        "short_tools": [
-            "interactive_tool_metashrimps"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "ecologymetadatamgt",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "Metadata",
-            "EML",
-            "FAIR",
-            "Data Paper"
-        ],
-        "time_estimation": "30M",
-        "title": "Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS",
-        "tools": [
-            "interactive_tool_metashrimps"
-        ],
-        "topic_name": "ecology",
-        "topic_name_human": "Ecology",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "Metashrimps_tutorial",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/Metashrimps_tutorial/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/Metashrimps_tutorial/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/Metashrimps_tutorial/tutorial.json"
-        },
-        "version": 4,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 160,
-        "visitors": 30,
-        "zenodo_link": "https://doi.org/10.5281/zenodo.8130567"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.1134547"
     },
     {
         "admin_install": {
@@ -62837,30 +65920,30 @@
             "Compute and visualize phenology of a species through the years",
             "Compute temporal abundance trends"
         ],
-        "pageviews": 368,
+        "pageviews": 378,
         "pub_date": "2019-07-04",
         "questions": [
             "What are abundance and trends of a butterfly species?"
         ],
         "short_id": "T00134",
         "short_tools": [
-            "tab2csv_R",
-            "regionalgam_gls",
+            "Count1",
+            "mergeCols1",
             "regionalgam_glmmpql",
-            "csv2tab_R",
-            "Paste1",
-            "regionalgam_flight_curve",
+            "Filter1",
             "tp_awk_tool",
+            "Paste1",
+            "regionalgam_plot_trend",
             "flight-curve",
-            "Count1",
-            "regionalgam_autocor_acf",
             "ggplot2_point",
-            "Filter1",
-            "regionalgam_ab_index",
-            "Remove beginning1",
-            "regionalgam_plot_trend",
+            "tab2csv_R",
+            "csv2tab_R",
+            "regionalgam_gls",
+            "regionalgam_flight_curve",
             "regexColumn1",
-            "mergeCols1"
+            "Remove beginning1",
+            "regionalgam_ab_index",
+            "regionalgam_autocor_acf"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -62916,8 +65999,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 218,
-        "visitors": 262,
+        "visit_duration": 214,
+        "visitors": 272,
         "workflows": [
             {
                 "creators": [],
@@ -62984,7 +66067,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAbundance index file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Filter\"];\n  0 -->|output| 1;\n  2[\"Filter\"];\n  0 -->|output| 2;\n  3[\"Filter\"];\n  0 -->|output| 3;\n  4[\"Filter\"];\n  0 -->|output| 4;\n  5[\"Filter\"];\n  0 -->|output| 5;\n  6[\"Paste\"];\n  1 -->|out_file1| 6;\n  2 -->|out_file1| 6;\n  7[\"Paste\"];\n  3 -->|out_file1| 7;\n  4 -->|out_file1| 7;\n  8[\"Paste\"];\n  6 -->|out_file1| 8;\n  7 -->|out_file1| 8;\n  9[\"Paste\"];\n  8 -->|out_file1| 9;\n  5 -->|out_file1| 9;",
-                "modified": "2024-08-18 00:06:22 +0000",
+                "modified": "2024-10-02 12:08:07 +0000",
                 "name": "Abundance Index \"stacked\" Visualization Creation",
                 "outputs": [],
                 "parent_id": "ecology/regionalGAM",
@@ -63075,7 +66158,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nFlight curve dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Filter\"];\n  0 -->|output| 1;\n  2[\"Filter\"];\n  0 -->|output| 2;\n  3[\"Paste\"];\n  1 -->|out_file1| 3;\n  2 -->|out_file1| 3;",
-                "modified": "2024-08-18 00:06:22 +0000",
+                "modified": "2024-10-02 12:08:07 +0000",
                 "name": "Phenology \"stacked\" Visualization Creation",
                 "outputs": [],
                 "parent_id": "ecology/regionalGAM",
@@ -63171,7 +66254,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"CSV to Tabular\"];\n  0 -->|output| 1;\n  10[\"Count\"];\n  8 -->|output| 10;\n  11[\"Column Regex Find And Replace\"];\n  8 -->|output| 11;\n  12[\"Count\"];\n  9 -->|output| 12;\n  13[\"Column Regex Find And Replace\"];\n  9 -->|output| 13;\n  14[\"Merge Columns\"];\n  11 -->|out_file1| 14;\n  15[\"Merge Columns\"];\n  13 -->|out_file1| 15;\n  16[\"Remove beginning\"];\n  14 -->|out_file1| 16;\n  17[\"Remove beginning\"];\n  15 -->|out_file1| 17;\n  18[\"Paste\"];\n  16 -->|out_file1| 18;\n  17 -->|out_file1| 18;\n  2[\"Column Regex Find And Replace\"];\n  1 -->|output| 2;\n  3[\"Count\"];\n  2 -->|out_file1| 3;\n  4[\"Filter\"];\n  2 -->|out_file1| 4;\n  5[\"Filter\"];\n  2 -->|out_file1| 5;\n  6[\"Tabular to CSV\"];\n  4 -->|out_file1| 6;\n  7[\"Tabular to CSV\"];\n  5 -->|out_file1| 7;\n  8[\"Flight curve\"];\n  6 -->|output| 8;\n  9[\"Flight curve\"];\n  7 -->|output| 9;",
-                "modified": "2024-08-18 00:06:22 +0000",
+                "modified": "2024-10-02 12:08:07 +0000",
                 "name": "Tutorial regionalGAM Complete Multispecies",
                 "outputs": [],
                 "parent_id": "ecology/regionalGAM",
@@ -63281,7 +66364,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nregionalGAM.csv\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Text reformatting\"];\n  0 -->|output| 1;\n  2[\"Count\"];\n  1 -->|outfile| 2;\n  3[\"Flight curve\"];\n  2 -->|out_file1| 3;\n  4[\"Abundance index\"];\n  2 -->|out_file1| 4;\n  3 -->|output| 4;\n  5[\"Scatterplot w ggplot2\"];\n  3 -->|output| 5;\n  6[\"Expected temporal trend\"];\n  4 -->|output| 6;\n  7[\"Model temporal trend\"];\n  4 -->|output| 7;\n  6 -->|output2| 7;\n  8[\"Autocorrelation test\"];\n  7 -->|output2| 8;\n  9[\"Plot abundance\"];\n  4 -->|output| 9;\n  7 -->|output2| 9;",
-                "modified": "2024-08-18 00:06:22 +0000",
+                "modified": "2024-10-02 12:08:07 +0000",
                 "name": "Regional GAM Workflow",
                 "outputs": [
                     {
@@ -63679,162 +66762,141 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "74a8bef53a00",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
+                    "name": "interproscan",
                     "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bwa",
-                    "owner": "devteam",
-                    "revisions": "64f11cf59c6e",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bwa_wrappers",
-                    "owner": "devteam",
-                    "revisions": "b4427dbb6ced",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "ff9530579d1f",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "1c2db0054039",
-                    "tool_panel_section_label": "Quality Control",
+                    "revisions": "74810db257cc",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "stacks_populations",
-                    "owner": "iuc",
-                    "revisions": "45db1ba16163",
-                    "tool_panel_section_label": "RAD-seq",
+                    "name": "sanntis_marine",
+                    "owner": "ecology",
+                    "revisions": "9d689f8c9ce4",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "stacks_procrad",
-                    "owner": "iuc",
-                    "revisions": "eded025438db",
-                    "tool_panel_section_label": "RAD-seq",
+                    "name": "regex_find_replace",
+                    "owner": "galaxyp",
+                    "revisions": "503bcd6ebe4b",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "stacks_refmap",
+                    "name": "prodigal",
                     "owner": "iuc",
-                    "revisions": "d7a482f44e08",
-                    "tool_panel_section_label": "RAD-seq",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "regex_replace",
-                    "owner": "kellrott",
-                    "revisions": "9a77d5fca67c",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "revisions": "91791b6ecd38",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: 74a8bef53a00\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: 64f11cf59c6e\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_wrappers\n  owner: devteam\n  revisions: b4427dbb6ced\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: ff9530579d1f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 1c2db0054039\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_populations\n  owner: iuc\n  revisions: 45db1ba16163\n  tool_panel_section_label: RAD-seq\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_procrad\n  owner: iuc\n  revisions: eded025438db\n  tool_panel_section_label: RAD-seq\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_refmap\n  owner: iuc\n  revisions: d7a482f44e08\n  tool_panel_section_label: RAD-seq\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_replace\n  owner: kellrott\n  revisions: 9a77d5fca67c\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/ref-based-rad-seq/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: interproscan\n  owner: bgruening\n  revisions: 74810db257cc\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sanntis_marine\n  owner: ecology\n  revisions: 9d689f8c9ce4\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 503bcd6ebe4b\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: prodigal\n  owner: iuc\n  revisions: 91791b6ecd38\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/marine_omics_bgc/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "Marie59"
+            ],
+            "funding": [
+                "fairease",
+                "eurosciencegateway"
+            ]
+        },
         "contributors": [
             {
                 "affiliations": [
                     "pndb",
-                    "gallantries",
-                    "fairease",
-                    "fnso2019",
-                    "elixir-europe"
+                    "fairease"
                 ],
-                "elixir_node": "fr",
-                "email": "yvan.le-bras@mnhn.fr",
-                "id": "yvanlebras",
-                "joined": "2017-09",
-                "matrix": "yvanlebras:matrix.org",
-                "name": "Yvan Le Bras",
-                "orcid": "0000-0002-8504-068X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
-                "twitter": "Yvan2935",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
+                "email": "marie.josse@ifremer.fr",
+                "id": "Marie59",
+                "joined": "2022-03",
+                "name": "Marie Josse",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/fair_ease_colour.png",
+                "funder": true,
+                "funding_id": "101058785",
+                "funding_statement": "FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "fairease",
+                "joined": "2023-10",
+                "members": [
+                    "Marie59",
+                    "yvanlebras"
+                ],
+                "name": "Fair-Ease",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fairease/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/fairease.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/eurosciencegateway.png",
+                "funder": true,
+                "funding_id": "101057388",
+                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "eurosciencegateway",
+                "joined": "2023-10",
+                "members": [
+                    "abretaud",
+                    "anuprulez",
+                    "bgruening",
+                    "erxleben",
+                    "pauldg",
+                    "rlibouba"
+                ],
+                "name": "EuroScienceGateway",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
             }
         ],
-        "dir": "topics/ecology/tutorials/ref-based-rad-seq",
+        "dir": "topics/ecology/tutorials/marine_omics_bgc",
         "edam_operation": [
-            "Sequencing quality control",
-            "Genome indexing",
-            "Sequence alignment",
-            "Sequence composition calculation",
-            "Read mapping",
-            "Generation",
-            "Data handling",
-            "Validation",
-            "Statistical calculation"
+            "Sequence motif recognition",
+            "Genome annotation",
+            "Protein feature detection"
         ],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "ecology/ref-based-rad-seq",
+        "id": "ecology/marine_omics_bgc",
         "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": null,
+        "key_points": [
+            "SMBGC annotation",
+            "Marine omics analysis"
+        ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-27",
+        "mod_date": "2024-09-16",
         "objectives": [
-            "Analysis of RAD sequencing data using a reference genome",
-            "SNP calling from RAD sequencing data",
-            "Calculate population genomics statistics from RAD sequencing data"
+            "Follow a marine omics analysis",
+            "Learn to conduct a secondary metabolite biosynthetic gene cluster (SMBGC) Annotation",
+            "Discover SanntiS a tool for identifying BGCs in genomic & metagenomic data",
+            "Manage fasta files"
         ],
-        "pageviews": 3737,
-        "pub_date": "2017-02-14",
+        "pageviews": 24,
+        "pub_date": "2024-08-19",
         "questions": [
-            "How to analyze RAD sequencing data using a reference genome for a population genomics study?"
-        ],
-        "redirect_from": [
-            "/topics/sequence-analysis/tutorials/ref-based-rad-seq/tutorial",
-            "/short/ecology/ref-based-rad-seq",
-            "/short/T00133"
+            "Which biological questions are addressed by the tutorial?",
+            "Which bioinformatics techniques are important to know for this type of data?"
         ],
-        "short_id": "T00133",
+        "short_id": "T00450",
         "short_tools": [
-            "Grep1",
-            "stacks_populations",
-            "cat1",
-            "multiqc",
-            "bwa_wrapper",
-            "stacks_refmap",
-            "regex_replace",
-            "Convert characters1",
-            "Count1",
-            "stacks_procrad",
-            "Cut1",
-            "fastqc",
-            "Filter1",
-            "tp_sort_header_tool",
-            "tp_replace_in_line",
-            "bwa",
-            "Summary_Statistics1",
-            "addValue"
+            "SanntiS_marine",
+            "sanntis_marine",
+            "interproscan",
+            "prodigal",
+            "regex1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -63845,33 +66907,18 @@
         },
         "symlink": null,
         "tags": [
-            "RAD-seq",
-            "Genetic composition EBV class",
-            "Species population EBV class",
-            "EBV dataset",
-            "EBV workflow"
+            "earth-system",
+            "ocean",
+            "marine omics"
         ],
-        "time_estimation": "8h",
-        "title": "RAD-Seq Reference-based data analysis",
+        "time_estimation": "3H",
+        "title": "Marine Omics identifying biosynthetic gene clusters",
         "tools": [
-            "Convert characters1",
-            "Count1",
-            "Cut1",
-            "Filter1",
-            "Grep1",
-            "Summary_Statistics1",
-            "addValue",
-            "cat1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6",
-            "toolshed.g2.bx.psu.edu/repos/iuc/stacks_populations/stacks_populations/1.46.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/stacks_refmap/stacks_refmap/1.46.0",
-            "toolshed.g2.bx.psu.edu/repos/kellrott/regex_replace/regex_replace/1.0.0"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/ecology/SanntiS_marine/SanntiS_marine/0.9.3.5+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/ecology/sanntis_marine/sanntis_marine/0.9.3.5+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/2.6.3+galaxy0"
         ],
         "topic_name": "ecology",
         "topic_name_human": "Ecology",
@@ -63881,234 +66928,588 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "ref-based-rad-seq",
+        "tutorial_name": "marine_omics_bgc",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/ref-based-rad-seq/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/marine_omics_bgc/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/ref-based-rad-seq/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/ref-based-rad-seq/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/marine_omics_bgc/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/marine_omics_bgc/tutorial.json"
         },
-        "version": 11,
+        "version": 2,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 106,
-        "visitors": 2212,
+        "visit_duration": 92,
+        "visitors": 18,
         "workflows": [
             {
-                "creators": [],
-                "description": "RAD-Seq Reference-based data analysis",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0009-0008-0622-604X",
+                        "name": "Marie Joss\u00e9",
+                        "url": "https://github.com/Marie59"
+                    }
+                ],
+                "description": "Secondary metabolite biosynthetic gene cluster (SMBGC) Annotation using Neural Networks Trained on Interpro Signatures ",
                 "features": {
-                    "comments": false,
+                    "comments": true,
                     "parameters": false,
-                    "report": null,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                    },
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nEBI SRA: SRR034310 File: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR034/SRR034310/SRR034310.fastq.gz\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/1134547/files/Barcode_SRR034310.txt\"]\n  10[label=\"FastQC\"]\n  5 -> 10 [label=\"demultiplexed\"]\n  11[label=\"Map with BWA\"]\n  5 -> 11 [label=\"demultiplexed\"]\n  3 -> 11 [label=\"output\"]\n  12[label=\"Select\"]\n  6 -> 12 [label=\"output_log\"]\n  13[label=\"Select\"]\n  6 -> 13 [label=\"output_log\"]\n  14[label=\"Replace Text\"]\n  7 -> 14 [label=\"outfile\"]\n  15[label=\"Replace Text\"]\n  8 -> 15 [label=\"out_file1\"]\n  16[label=\"Replace Text\"]\n  9 -> 16 [label=\"out_file1\"]\n  17[label=\"MultiQC\"]\n  10 -> 17 [label=\"text_file\"]\n  18[label=\"Replace Text\"]\n  12 -> 18 [label=\"out_file1\"]\n  19[label=\"Replace Text\"]\n  13 -> 19 [label=\"out_file1\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/1134547/files/Details_Barcode_Population_SRR034310.txt\"]\n  20[label=\"Add column\"]\n  14 -> 20 [label=\"outfile\"]\n  21[label=\"Concatenate datasets\"]\n  19 -> 21 [label=\"outfile\"]\n  15 -> 21 [label=\"outfile\"]\n  16 -> 21 [label=\"outfile\"]\n  18 -> 21 [label=\"outfile\"]\n  22[label=\"Cut\"]\n  20 -> 22 [label=\"out_file1\"]\n  23[label=\"Convert\"]\n  21 -> 23 [label=\"out_file1\"]\n  24[label=\"Regex Replace\"]\n  22 -> 24 [label=\"out_file1\"]\n  25[label=\"Stacks: reference map\"]\n  11 -> 25 [label=\"bam_output\"]\n  24 -> 25 [label=\"outfile\"]\n  26[label=\"Stacks: populations\"]\n  25 -> 26 [label=\"all_output\"]\n  24 -> 26 [label=\"outfile\"]\n  27[label=\"Summary Statistics\"]\n  26 -> 27 [label=\"out_fstats\"]\n  28[label=\"Sort\"]\n  26 -> 28 [label=\"out_fstats\"]\n  29[label=\"Count\"]\n  26 -> 29 [label=\"out_fstats\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/1134547/files/Reference_genome_11_chromosomes.fasta\"]\n  30[label=\"Filter\"]\n  26 -> 30 [label=\"out_fstats\"]\n  4[label=\"Stacks: process radtags\"]\n  1 -> 4 [label=\"output\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Stacks: process radtags\"]\n  1 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Stacks: process radtags\"]\n  1 -> 6 [label=\"output\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Replace Text\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"Select\"]\n  4 -> 8 [label=\"output_log\"]\n  9[label=\"Select\"]\n  5 -> 9 [label=\"output_log\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nFasta nucelotide file\"]\n  1[label=\"Prodigal Gene Predictor \"]\n  0 -> 1 [label=\"output\"]\n  k351cf550c05d4bad9394fe9b45ef6298[color=lightseagreen,label=\"Output\\nProtein fasta file\"]\n  1 -> k351cf550c05d4bad9394fe9b45ef6298\n  2[label=\"Sanntis: Build Genbank \"]\n  0 -> 2 [label=\"output\"]\n  1 -> 2 [label=\"output_faa\"]\n  k1b9f0275191a4e90b4b47b10475f4602[color=lightseagreen,label=\"Output\\nGenbank file\"]\n  2 -> k1b9f0275191a4e90b4b47b10475f4602\n  3[label=\"Regex Find And Replace\"]\n  1 -> 3 [label=\"output_faa\"]\n  ke41e8fb9c5f6425fa351f8fa92f7821d[color=lightseagreen,label=\"Output\\nClean protein fasta file\"]\n  3 -> ke41e8fb9c5f6425fa351f8fa92f7821d\n  4[label=\" InterProScan\"]\n  3 -> 4 [label=\"out_file1\"]\n  k522b49db765041e7b88801bb3cb1b451[color=lightseagreen,label=\"Output\\nTabular file (.tsv)\"]\n  4 -> k522b49db765041e7b88801bb3cb1b451\n  5[label=\"Sanntis: identify biosynthetic gene clusters\"]\n  2 -> 5 [label=\"output_sanntis_gb\"]\n  4 -> 5 [label=\"outfile_tsv\"]\n  kc96c8c7e0a504506a1449d941f50eb5e[color=lightseagreen,label=\"Output\\n SMBGC Annotation\"]\n  5 -> kc96c8c7e0a504506a1449d941f50eb5e\n}",
                 "history": [
                     {
-                        "hash": "00cfc1f0873c7eee656d05fd549f5cd3eae6a8da",
-                        "message": "out_fastp\u0125ase",
-                        "num": 5,
-                        "short_hash": "00cfc1f08",
-                        "unix": "1579699186"
-                    },
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 4,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "ea197f141d3c4fcf8f8e424604a5d40bf9125ce6",
-                        "message": "small changes",
+                        "hash": "f2570ea6f8219fd9d8f9e88c5ca75946854261bb",
+                        "message": "add again workflow with test",
                         "num": 3,
-                        "short_hash": "ea197f141",
-                        "unix": "1579091409"
+                        "short_hash": "f2570ea6f",
+                        "unix": "1723454213"
                     },
                     {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
+                        "hash": "25c640725d83d35f1b7153da26c906f1727f8b82",
+                        "message": "Delete topics/ecology/tutorials/marine_omics_bgc/workflows/main_workflow.ga",
                         "num": 2,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
+                        "short_hash": "25c640725",
+                        "unix": "1723454186"
                     },
                     {
-                        "hash": "bfc1c8c3f8660106a468dbfbc3af09af3e48da72",
-                        "message": "Move RAD-Seq tutorials to ecology topic",
+                        "hash": "ded4748a79e38531cc0f028b9cb7026902238791",
+                        "message": "add marine omics tuto",
                         "num": 1,
-                        "short_hash": "bfc1c8c3f",
-                        "unix": "1568279010"
+                        "short_hash": "ded4748a7",
+                        "unix": "1723452341"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "",
+                        "annotation": "BGC0001472.fna",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "EBI SRA: SRR034310 File: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR034/SRR034310/SRR034310.fastq.gz"
+                                "description": "BGC0001472.fna",
+                                "name": "Fasta nucelotide file"
                             }
                         ],
-                        "label": "EBI SRA: SRR034310 File: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR034/SRR034310/SRR034310.fastq.gz",
+                        "label": "Fasta nucelotide file",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200.00001525878906,
-                            "top": 200.00001525878906
+                            "left": 0.0,
+                            "top": 237.1372700459935
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"EBI SRA: SRR034310 File: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR034/SRR034310/SRR034310.fastq.gz\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "4be2b939-61bf-4ed9-b134-5307c5127fe8",
+                        "uuid": "0d5808da-76d5-42d7-a669-59f8887514b5",
+                        "when": null,
                         "workflow_outputs": []
-                    },
+                    }
+                ],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nFasta nucelotide file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Prodigal Gene Predictor \"];\n  0 -->|output| 1;\n  351cf550-c05d-4bad-9394-fe9b45ef6298[\"Output\\nProtein fasta file\"];\n  1 --> 351cf550-c05d-4bad-9394-fe9b45ef6298;\n  style 351cf550-c05d-4bad-9394-fe9b45ef6298 stroke:#2c3143,stroke-width:4px;\n  2[\"Sanntis: Build Genbank \"];\n  0 -->|output| 2;\n  1 -->|output_faa| 2;\n  1b9f0275-191a-4e90-b4b4-7b10475f4602[\"Output\\nGenbank file\"];\n  2 --> 1b9f0275-191a-4e90-b4b4-7b10475f4602;\n  style 1b9f0275-191a-4e90-b4b4-7b10475f4602 stroke:#2c3143,stroke-width:4px;\n  3[\"Regex Find And Replace\"];\n  1 -->|output_faa| 3;\n  e41e8fb9-c5f6-425f-a351-f8fa92f7821d[\"Output\\nClean protein fasta file\"];\n  3 --> e41e8fb9-c5f6-425f-a351-f8fa92f7821d;\n  style e41e8fb9-c5f6-425f-a351-f8fa92f7821d stroke:#2c3143,stroke-width:4px;\n  4[\" InterProScan\"];\n  3 -->|out_file1| 4;\n  522b49db-7650-41e7-b888-01bb3cb1b451[\"Output\\nTabular file (.tsv)\"];\n  4 --> 522b49db-7650-41e7-b888-01bb3cb1b451;\n  style 522b49db-7650-41e7-b888-01bb3cb1b451 stroke:#2c3143,stroke-width:4px;\n  5[\"Sanntis: identify biosynthetic gene clusters\"];\n  2 -->|output_sanntis_gb| 5;\n  4 -->|outfile_tsv| 5;\n  c96c8c7e-0a50-4506-a144-9d941f50eb5e[\"Output\\n SMBGC Annotation\"];\n  5 --> c96c8c7e-0a50-4506-a144-9d941f50eb5e;\n  style c96c8c7e-0a50-4506-a144-9d941f50eb5e stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:07 +0000",
+                "name": "Marine Omics identifying biosynthetic gene clusters",
+                "outputs": [
                     {
-                        "annotation": "",
-                        "content_id": null,
+                        "annotation": "Create the protein fasta file",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/2.6.3+galaxy0",
                         "errors": null,
                         "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "input_connections": {
+                            "input_fa": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Prodigal Gene Predictor ",
+                        "name": "Prodigal Gene Predictor",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "https://zenodo.org/record/1134547/files/Barcode_SRR034310.txt"
+                                "name": "output",
+                                "type": "genbank"
+                            },
+                            {
+                                "name": "output_faa",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "output_fnn",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "output_start",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "https://zenodo.org/record/1134547/files/Barcode_SRR034310.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 200.00001525878906,
-                            "top": 320.00001525878906
+                            "left": 250.3965410835214,
+                            "top": 441.31949463344165
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"https://zenodo.org/record/1134547/files/Barcode_SRR034310.txt\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "95b8e56e-433d-4014-9dee-d9310863a20d",
-                        "workflow_outputs": []
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/2.6.3+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "91791b6ecd38",
+                            "name": "prodigal",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"closed\": false, \"force_nonsd\": false, \"input_fa\": {\"__class__\": \"ConnectedValue\"}, \"input_train\": null, \"masked_seq\": false, \"out_format\": \"gbk\", \"procedure\": \"meta\", \"trans_table\": \"11\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.3+galaxy0",
+                        "type": "tool",
+                        "uuid": "16fe7e1b-364c-4a90-90b4-1ab32b6484f7",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Protein fasta file",
+                                "output_name": "output_faa",
+                                "uuid": "351cf550-c05d-4bad-9394-fe9b45ef6298"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
+                        "annotation": "Use of Sanntis",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/sanntis_marine/sanntis_marine/0.9.3.5+galaxy1",
                         "errors": null,
                         "id": 2,
-                        "input_connections": {},
+                        "input_connections": {
+                            "selection|input_nuc": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "selection|input_prot": {
+                                "id": 1,
+                                "output_name": "output_faa"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "https://zenodo.org/record/1134547/files/Details_Barcode_Population_SRR034310.txt"
+                                "description": "runtime parameter for tool Sanntis biosynthetic gene clusters",
+                                "name": "selection"
+                            },
+                            {
+                                "description": "runtime parameter for tool Sanntis biosynthetic gene clusters",
+                                "name": "selection"
+                            }
+                        ],
+                        "label": "Sanntis: Build Genbank ",
+                        "name": "Sanntis biosynthetic gene clusters",
+                        "outputs": [
+                            {
+                                "name": "output_sanntis_gb",
+                                "type": "genbank"
                             }
                         ],
-                        "label": "https://zenodo.org/record/1134547/files/Details_Barcode_Population_SRR034310.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 200.00001525878906,
-                            "top": 440.0000305175781
+                            "left": 715.403011844556,
+                            "top": 236.8431499791749
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"https://zenodo.org/record/1134547/files/Details_Barcode_Population_SRR034310.txt\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "43ca52f2-f60d-4fa6-9608-65ac4cc471b9",
-                        "workflow_outputs": []
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/sanntis_marine/sanntis_marine/0.9.3.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "9d689f8c9ce4",
+                            "name": "sanntis_marine",
+                            "owner": "ecology",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"selection\": {\"which_sanntis\": \"genbank\", \"__current_case__\": 1, \"input_nuc\": {\"__class__\": \"ConnectedValue\"}, \"input_prot\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.9.3.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "7938a6b6-e603-41d2-b15f-904d6199d6ec",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Genbank file",
+                                "output_name": "output_sanntis_gb",
+                                "uuid": "1b9f0275-191a-4e90-b4b4-7b10475f4602"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
+                        "annotation": "Remove useless * in the protein fasta file",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3",
                         "errors": null,
                         "id": 3,
-                        "input_connections": {},
+                        "input_connections": {
+                            "input": {
+                                "id": 1,
+                                "output_name": "output_faa"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Regex Find And Replace",
+                        "name": "Regex Find And Replace",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 590.0224617880027,
+                            "top": 608.4869646334582
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "503bcd6ebe4b",
+                            "name": "regex_find_replace",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"checks\": [{\"__index__\": 0, \"pattern\": \"\\\\*$\", \"replacement\": \"\"}], \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.3",
+                        "type": "tool",
+                        "uuid": "696cbe41-e2df-4ed1-971e-d53db4afb3bd",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Clean protein fasta file",
+                                "output_name": "out_file1",
+                                "uuid": "e41e8fb9-c5f6-425f-a351-f8fa92f7821d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Create TSV file for Sanntis",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "input": {
+                                "id": 3,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": " InterProScan",
+                        "name": "InterProScan",
+                        "outputs": [
+                            {
+                                "name": "outfile_tsv",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 888.2399382143647,
+                            "top": 606.9532717459192
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "74810db257cc",
+                            "name": "interproscan",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"applications\": [\"TIGRFAM\", \"FunFam\", \"SFLD\", \"SUPERFAMILY\", \"PANTHER\", \"Gene3D\", \"Hamap\", \"PrositeProfiles\", \"Coils\", \"SMART\", \"CDD\", \"PRINTS\", \"PIRSR\", \"PrositePatterns\", \"AntiFam\", \"Pfam\", \"MobiDBLite\", \"PIRSF\"], \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"database\": \"5.59-91.0\", \"goterms\": true, \"input\": {\"__class__\": \"ConnectedValue\"}, \"iprlookup\": false, \"licensed\": {\"use\": \"false\", \"__current_case__\": 0}, \"oformat\": \"TSV\", \"pathways\": true, \"seqtype\": \"p\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.59-91.0+galaxy3",
+                        "type": "tool",
+                        "uuid": "aa635573-d4ec-4b7e-af6f-573c197f6dc9",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Tabular file (.tsv)",
+                                "output_name": "outfile_tsv",
+                                "uuid": "522b49db-7650-41e7-b888-01bb3cb1b451"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/sanntis_marine/sanntis_marine/0.9.3.5+galaxy1",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "selection|input_genbank": {
+                                "id": 2,
+                                "output_name": "output_sanntis_gb"
+                            },
+                            "selection|input_interpro": {
+                                "id": 4,
+                                "output_name": "outfile_tsv"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "https://zenodo.org/record/1134547/files/Reference_genome_11_chromosomes.fasta"
+                                "description": "runtime parameter for tool Sanntis biosynthetic gene clusters",
+                                "name": "selection"
+                            },
+                            {
+                                "description": "runtime parameter for tool Sanntis biosynthetic gene clusters",
+                                "name": "selection"
+                            }
+                        ],
+                        "label": "Sanntis: identify biosynthetic gene clusters",
+                        "name": "Sanntis biosynthetic gene clusters",
+                        "outputs": [
+                            {
+                                "name": "output_sanntis",
+                                "type": "gff3"
                             }
                         ],
-                        "label": "https://zenodo.org/record/1134547/files/Reference_genome_11_chromosomes.fasta",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 200.00001525878906,
-                            "top": 577.9861450195312
+                            "left": 1151.9503777422938,
+                            "top": 319.39463092564574
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"https://zenodo.org/record/1134547/files/Reference_genome_11_chromosomes.fasta\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "7c1d53db-b81d-40ab-8a75-221a94eb09ff",
-                        "workflow_outputs": []
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/sanntis_marine/sanntis_marine/0.9.3.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "9d689f8c9ce4",
+                            "name": "sanntis_marine",
+                            "owner": "ecology",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"selection\": {\"which_sanntis\": \"sanntis\", \"__current_case__\": 0, \"input_interpro\": {\"__class__\": \"ConnectedValue\"}, \"input_genbank\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.9.3.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "a5d9a6b6-4bb4-4fa3-893c-b0ad3794027e",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": " SMBGC Annotation",
+                                "output_name": "output_sanntis",
+                                "uuid": "c96c8c7e-0a50-4506-a144-9d941f50eb5e"
+                            }
+                        ]
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nEBI SRA: SRR034310 File: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR034/SRR034310/SRR034310.fastq.gz\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/1134547/files/Barcode_SRR034310.txt\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"FastQC\"];\n  5 -->|demultiplexed| 10;\n  11[\"Map with BWA\"];\n  5 -->|demultiplexed| 11;\n  3 -->|output| 11;\n  12[\"Select\"];\n  6 -->|output_log| 12;\n  13[\"Select\"];\n  6 -->|output_log| 13;\n  14[\"Replace Text\"];\n  7 -->|outfile| 14;\n  15[\"Replace Text\"];\n  8 -->|out_file1| 15;\n  16[\"Replace Text\"];\n  9 -->|out_file1| 16;\n  17[\"MultiQC\"];\n  10 -->|text_file| 17;\n  18[\"Replace Text\"];\n  12 -->|out_file1| 18;\n  19[\"Replace Text\"];\n  13 -->|out_file1| 19;\n  2[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/1134547/files/Details_Barcode_Population_SRR034310.txt\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  20[\"Add column\"];\n  14 -->|outfile| 20;\n  21[\"Concatenate datasets\"];\n  19 -->|outfile| 21;\n  15 -->|outfile| 21;\n  16 -->|outfile| 21;\n  18 -->|outfile| 21;\n  22[\"Cut\"];\n  20 -->|out_file1| 22;\n  23[\"Convert\"];\n  21 -->|out_file1| 23;\n  24[\"Regex Replace\"];\n  22 -->|out_file1| 24;\n  25[\"Stacks: reference map\"];\n  11 -->|bam_output| 25;\n  24 -->|outfile| 25;\n  26[\"Stacks: populations\"];\n  25 -->|all_output| 26;\n  24 -->|outfile| 26;\n  27[\"Summary Statistics\"];\n  26 -->|out_fstats| 27;\n  28[\"Sort\"];\n  26 -->|out_fstats| 28;\n  29[\"Count\"];\n  26 -->|out_fstats| 29;\n  3[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/1134547/files/Reference_genome_11_chromosomes.fasta\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  30[\"Filter\"];\n  26 -->|out_fstats| 30;\n  4[\"Stacks: process radtags\"];\n  1 -->|output| 4;\n  0 -->|output| 4;\n  5[\"Stacks: process radtags\"];\n  1 -->|output| 5;\n  0 -->|output| 5;\n  6[\"Stacks: process radtags\"];\n  1 -->|output| 6;\n  0 -->|output| 6;\n  7[\"Replace Text\"];\n  2 -->|output| 7;\n  8[\"Select\"];\n  4 -->|output_log| 8;\n  9[\"Select\"];\n  5 -->|output_log| 9;",
-                "modified": "2024-08-18 00:06:22 +0000",
-                "name": "Workflow Constructed From History 'STACKS RAD: Population Genomics With Reference Genome'",
-                "outputs": [],
-                "parent_id": "ecology/ref-based-rad-seq",
-                "path": "topics/ecology/tutorials/ref-based-rad-seq/workflows/Galaxy-Workflow-Workflow_constructed_from_history__STACKS_RAD__population_genomics_with_reference_genome_.ga",
+                "parent_id": "ecology/marine_omics_bgc",
+                "path": "topics/ecology/tutorials/marine_omics_bgc/workflows/main_workflow.ga",
                 "tags": [
-                    "ecology"
+                    "earth-system",
+                    "Ocean",
+                    "Marineomics"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "Workflow Constructed From History 'STACKS RAD: Population Genomics With Reference Genome'",
+                "tests": true,
+                "title": "Marine Omics identifying biosynthetic gene clusters",
                 "topic_id": "ecology",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-ref-based-rad-seq/versions/galaxy-workflow-workflow-constructed-from-history--stacks-rad--population-genomics-with-reference-genome-",
-                "tutorial_id": "ref-based-rad-seq",
-                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ref-based-rad-seq/workflows/Galaxy-Workflow-Workflow_constructed_from_history__STACKS_RAD__population_genomics_with_reference_genome_.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ref-based-rad-seq/workflows/Galaxy-Workflow-Workflow_constructed_from_history__STACKS_RAD__population_genomics_with_reference_genome_.html",
-                "version": 3,
-                "wfid": "ecology-ref-based-rad-seq",
-                "wfname": "galaxy-workflow-workflow-constructed-from-history--stacks-rad--population-genomics-with-reference-genome-",
-                "workflow": "Galaxy-Workflow-Workflow_constructed_from_history__STACKS_RAD__population_genomics_with_reference_genome_.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-marine_omics_bgc/versions/main-workflow",
+                "tutorial_id": "marine_omics_bgc",
+                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/marine_omics_bgc/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/marine_omics_bgc/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "ecology-marine_omics_bgc",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "Convert characters1",
-                    "Count1",
-                    "Cut1",
-                    "Filter1",
-                    "Grep1",
-                    "Summary_Statistics1",
-                    "addValue",
-                    "cat1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_populations/stacks_populations/1.46.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_refmap/stacks_refmap/1.46.0",
-                    "toolshed.g2.bx.psu.edu/repos/kellrott/regex_replace/regex_replace/1.0.0"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/sanntis_marine/sanntis_marine/0.9.3.5+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/2.6.3+galaxy0"
                 ],
-                "workflowhub_id": "1250"
+                "workflowhub_id": "1357"
+            }
+        ],
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "0a8c6b61f0f4",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "spocc_occ",
+                    "owner": "ecology",
+                    "revisions": "f9d76a46799a",
+                    "tool_panel_section_label": "Get Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 0a8c6b61f0f4\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: spocc_occ\n  owner: ecology\n  revisions: f9d76a46799a\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/species-distribution-modeling/tutorial.json",
+        "contributors": [
+            {
+                "id": "emichn",
+                "joined": "2019-03",
+                "name": "Elisa Michon",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/emichn/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/emichn.json"
+            },
+            {
+                "affiliations": [
+                    "pndb",
+                    "gallantries",
+                    "fairease",
+                    "fnso2019",
+                    "elixir-europe"
+                ],
+                "elixir_node": "fr",
+                "email": "yvan.le-bras@mnhn.fr",
+                "id": "yvanlebras",
+                "joined": "2017-09",
+                "matrix": "yvanlebras:matrix.org",
+                "name": "Yvan Le Bras",
+                "orcid": "0000-0002-8504-068X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
+                "twitter": "Yvan2935",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
             },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            }
+        ],
+        "dir": "topics/ecology/tutorials/species-distribution-modeling",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.fr"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "ecology/species-distribution-modeling",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Use 'classical' Galaxy tools in combination with Interactive tools",
+            "Identify general steps of a species distribution modeling aproach"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-27",
+        "objectives": [
+            "Find and download occurrences data from GBIF",
+            "Find and download environmental data",
+            "Process both occurrences and environmental data",
+            "Partition occurrence data",
+            "Model a theoretical ecological niche and predict species distribution in a future climate scenario by using SDM"
+        ],
+        "pageviews": 4208,
+        "pub_date": "2019-07-04",
+        "questions": [
+            "How to build & evaluate a niche model, visualize and project it?"
+        ],
+        "requirements": null,
+        "short_id": "T00135",
+        "short_tools": [
+            "tabular_to_csv",
+            "Filter1",
+            "interactive_tool_wallace",
+            "spocc_occ",
+            "tp_find_and_replace",
+            "tp_cut_tool"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "ecologyanalysis",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "interactive-tools",
+            "modeling",
+            "gbif",
+            "species populations EBV class"
+        ],
+        "time_estimation": "1h",
+        "title": "Species distribution modeling",
+        "tools": [
+            "Filter1",
+            "interactive_tool_wallace",
+            "tabular_to_csv",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/ecology/spocc_occ/spocc_occ/0.9.0"
+        ],
+        "topic_name": "ecology",
+        "topic_name_human": "Ecology",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "species-distribution-modeling",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/species-distribution-modeling/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/species-distribution-modeling/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/species-distribution-modeling/tutorial.json"
+        },
+        "version": 17,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 69,
+        "visitors": 2666,
+        "workflows": [
             {
                 "creators": [],
-                "description": "RAD-Seq Reference-based data analysis",
+                "description": "Species distribution modeling",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nref_genome_chromFa.tar\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPopulation_map.txt\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBarcodes_SRR034310.tabular\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSRR034310.fastq\"]\n  4[label=\"Stacks: process radtags\"]\n  2 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"Stacks: process radtags\"]\n  2 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"output\"]\n  6[label=\"Stacks: process radtags\"]\n  2 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"Map with BWA for Illumina\"]\n  0 -> 7 [label=\"output\"]\n  4 -> 7 [label=\"demultiplexed\"]\n  8[label=\"Stacks: reference map\"]\n  7 -> 8 [label=\"output\"]\n  1 -> 8 [label=\"output\"]\n  9[label=\"Stacks: populations\"]\n  8 -> 9 [label=\"all_output\"]\n  1 -> 9 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Get species occurrences data\"]\n  1[label=\"Wallace\"]\n  2[label=\"Cut\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Filter\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Convert tabular to CSV\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"Replace\"]\n  4 -> 5 [label=\"csv\"]\n}",
                 "history": [
-                    {
-                        "hash": "00cfc1f0873c7eee656d05fd549f5cd3eae6a8da",
-                        "message": "out_fastp\u0125ase",
-                        "num": 5,
-                        "short_hash": "00cfc1f08",
-                        "unix": "1579699186"
-                    },
                     {
                         "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
                         "message": "annotation",
@@ -64116,166 +67517,96 @@
                         "short_hash": "667ff3de9",
                         "unix": "1579690769"
                     },
-                    {
-                        "hash": "ea197f141d3c4fcf8f8e424604a5d40bf9125ce6",
-                        "message": "small changes",
-                        "num": 3,
-                        "short_hash": "ea197f141",
-                        "unix": "1579091409"
-                    },
                     {
                         "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
                         "message": "Workflow renaming",
-                        "num": 2,
+                        "num": 3,
                         "short_hash": "eb4d724e0",
                         "unix": "1579084895"
                     },
                     {
-                        "hash": "bfc1c8c3f8660106a468dbfbc3af09af3e48da72",
-                        "message": "Move RAD-Seq tutorials to ecology topic",
+                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
+                        "message": "unflatten workflows",
+                        "num": 2,
+                        "short_hash": "faf6d298a",
+                        "unix": "1576155753"
+                    },
+                    {
+                        "hash": "de727da9edf3f1567430727c681c1eba5f4e9c90",
+                        "message": "add SDM ecology.usegalaxy.eu workflow",
                         "num": 1,
-                        "short_hash": "bfc1c8c3f",
-                        "unix": "1568279010"
+                        "short_hash": "de727da9e",
+                        "unix": "1575551509"
                     }
                 ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "ref_genome_chromFa.tar"
-                            }
-                        ],
-                        "label": "ref_genome_chromFa.tar",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 200.00001525878906,
-                            "top": 200.00001525878906
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"ref_genome_chromFa.tar\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "d41b8a08-8893-4fe4-86c1-21caa8e95cb9",
-                        "workflow_outputs": []
-                    },
+                "inputs": [],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"Get species occurrences data\"];\n  1[\"Wallace\"];\n  2[\"Cut\"];\n  0 -->|output| 2;\n  3[\"Filter\"];\n  2 -->|output| 3;\n  4[\"Convert tabular to CSV\"];\n  3 -->|out_file1| 4;\n  5[\"Replace\"];\n  4 -->|csv| 5;",
+                "modified": "2024-10-02 12:08:07 +0000",
+                "name": "Species Distribution Modeling With Wallace From GBIF - Training Material",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "interactive_tool_wallace",
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Population_map.txt"
-                            }
-                        ],
-                        "label": "Population_map.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 200.00001525878906,
-                            "top": 320.00001525878906
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Population_map.txt\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "59b48fd7-4a76-4683-8e5b-b8db033e4f5d",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Barcodes_SRR034310.tabular"
-                            }
-                        ],
-                        "label": "Barcodes_SRR034310.tabular",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 200.00001525878906,
-                            "top": 440.00001525878906
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Barcodes_SRR034310.tabular\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "c7ea916e-f493-4e53-bbf5-1d9b0ab34c18",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Wallace",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "SRR034310.fastq"
+                                "name": "outfile",
+                                "type": "txt"
                             }
                         ],
-                        "label": "SRR034310.fastq",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 200.00001525878906,
-                            "top": 560.0000457763672
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"SRR034310.fastq\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "8dcf8e48-fc08-4c2c-9aad-477de98b41d1",
-                        "workflow_outputs": []
+                            "left": 1077.5,
+                            "top": 400.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "interactive_tool_wallace",
+                        "tool_state": "{}",
+                        "tool_version": "0.1",
+                        "type": "tool",
+                        "uuid": "fe5c0b4c-b5ee-4c41-8145-bd9e610fd066",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "c9ce6982-0192-413d-a476-71c45c15ce4b"
+                            }
+                        ]
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nref_genome_chromFa.tar\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nPopulation_map.txt\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nBarcodes_SRR034310.tabular\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nSRR034310.fastq\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Stacks: process radtags\"];\n  2 -->|output| 4;\n  3 -->|output| 4;\n  5[\"Stacks: process radtags\"];\n  2 -->|output| 5;\n  3 -->|output| 5;\n  6[\"Stacks: process radtags\"];\n  2 -->|output| 6;\n  3 -->|output| 6;\n  7[\"Map with BWA for Illumina\"];\n  0 -->|output| 7;\n  4 -->|demultiplexed| 7;\n  8[\"Stacks: reference map\"];\n  7 -->|output| 8;\n  1 -->|output| 8;\n  9[\"Stacks: populations\"];\n  8 -->|all_output| 9;\n  1 -->|output| 9;",
-                "modified": "2024-08-18 00:06:22 +0000",
-                "name": "Ref Based Rad Seq",
-                "outputs": [],
-                "parent_id": "ecology/ref-based-rad-seq",
-                "path": "topics/ecology/tutorials/ref-based-rad-seq/workflows/workflow.ga",
+                "parent_id": "ecology/species-distribution-modeling",
+                "path": "topics/ecology/tutorials/species-distribution-modeling/workflows/Galaxy-Workflow-Species_Distribution_Modeling_with_Wallace_from_GBIF_-_Training_material.ga",
                 "tags": [
                     "ecology"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Ref Based Rad Seq",
+                "title": "Species Distribution Modeling With Wallace From GBIF - Training Material",
                 "topic_id": "ecology",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-ref-based-rad-seq/versions/workflow",
-                "tutorial_id": "ref-based-rad-seq",
-                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ref-based-rad-seq/workflows/workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ref-based-rad-seq/workflows/workflow.html",
-                "version": 3,
-                "wfid": "ecology-ref-based-rad-seq",
-                "wfname": "workflow",
-                "workflow": "workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-species-distribution-modeling/versions/galaxy-workflow-species-distribution-modeling-with-wallace-from-gbif---training-material",
+                "tutorial_id": "species-distribution-modeling",
+                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/species-distribution-modeling/workflows/Galaxy-Workflow-Species_Distribution_Modeling_with_Wallace_from_GBIF_-_Training_material.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/species-distribution-modeling/workflows/Galaxy-Workflow-Species_Distribution_Modeling_with_Wallace_from_GBIF_-_Training_material.html",
+                "version": 4,
+                "wfid": "ecology-species-distribution-modeling",
+                "wfname": "galaxy-workflow-species-distribution-modeling-with-wallace-from-gbif---training-material",
+                "workflow": "Galaxy-Workflow-Species_Distribution_Modeling_with_Wallace_from_GBIF_-_Training_material.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_populations/stacks_populations/1.46.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_refmap/stacks_refmap/1.46.0"
+                    "Filter1",
+                    "interactive_tool_wallace",
+                    "tabular_to_csv",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/spocc_occ/spocc_occ/0.9.0"
                 ],
-                "workflowhub_id": "1245"
+                "workflowhub_id": "1235"
             }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.1134547"
+        ]
     },
     {
         "admin_install": {
@@ -64284,209 +67615,237 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "bracken",
-                    "owner": "iuc",
-                    "revisions": "1d4bd12f01cf",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "fbf99087e067",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "kraken2",
-                    "owner": "iuc",
-                    "revisions": "20e2f64aa1fe",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "name": "merge_cols",
+                    "owner": "devteam",
+                    "revisions": "dd40b1e9eebe",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "recentrifuge",
+                    "name": "ecoregion_brt_analysis",
+                    "owner": "ecology",
+                    "revisions": "2129484beb61",
+                    "tool_panel_section_label": "Ecoregionalization",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ecoregion_clara_cluster",
+                    "owner": "ecology",
+                    "revisions": "844b5bf84164",
+                    "tool_panel_section_label": "Ecoregionalization",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ecoregion_cluster_estimate",
+                    "owner": "ecology",
+                    "revisions": "001d7d101915",
+                    "tool_panel_section_label": "Ecoregionalization",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ecoregion_eco_map",
+                    "owner": "ecology",
+                    "revisions": "c6b1bf7b0ac6",
+                    "tool_panel_section_label": "Ecoregionalization",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ecoregion_geonearestneighbor",
+                    "owner": "ecology",
+                    "revisions": "36637718c51d",
+                    "tool_panel_section_label": "Ecoregionalization",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ecoregion_taxa_seeker",
+                    "owner": "ecology",
+                    "revisions": "18c4cd785a74",
+                    "tool_panel_section_label": "Ecoregionalization",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "regex_find_replace",
+                    "owner": "galaxyp",
+                    "revisions": "503bcd6ebe4b",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "unzip",
+                    "owner": "imgteam",
+                    "revisions": "57f0914ddb7b",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "filter_tabular",
                     "owner": "iuc",
-                    "revisions": "b5407cc2bf51",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "revisions": "557ec8d7087d",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bracken\n  owner: iuc\n  revisions: 1d4bd12f01cf\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: 20e2f64aa1fe\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: recentrifuge\n  owner: iuc\n  revisions: b5407cc2bf51\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merge_cols\n  owner: devteam\n  revisions: dd40b1e9eebe\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ecoregion_brt_analysis\n  owner: ecology\n  revisions: 2129484beb61\n  tool_panel_section_label: Ecoregionalization\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ecoregion_clara_cluster\n  owner: ecology\n  revisions: 844b5bf84164\n  tool_panel_section_label: Ecoregionalization\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ecoregion_cluster_estimate\n  owner: ecology\n  revisions: 001d7d101915\n  tool_panel_section_label: Ecoregionalization\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ecoregion_eco_map\n  owner: ecology\n  revisions: c6b1bf7b0ac6\n  tool_panel_section_label: Ecoregionalization\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ecoregion_geonearestneighbor\n  owner: ecology\n  revisions: 36637718c51d\n  tool_panel_section_label: Ecoregionalization\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ecoregion_taxa_seeker\n  owner: ecology\n  revisions: 18c4cd785a74\n  tool_panel_section_label: Ecoregionalization\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 503bcd6ebe4b\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unzip\n  owner: imgteam\n  revisions: 57f0914ddb7b\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filter_tabular\n  owner: iuc\n  revisions: 557ec8d7087d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.json",
         "contributions": {
             "authorship": [
-                "bebatut"
-            ],
-            "editing": [
-                "clsiguret"
+                "PaulineSGN"
             ],
-            "funding": [
-                "abromics"
+            "testing": [
+                "yvanlebras",
+                "Marie59",
+                "Rassine"
             ]
         },
         "contributors": [
+            {
+                "email": "pauline.seguineau@mnhn.fr",
+                "id": "PaulineSGN",
+                "joined": "2024-01",
+                "name": "Pauline Seguineau",
+                "orcid": "0009-0009-5969-8478",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/PaulineSGN/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/PaulineSGN.json"
+            },
             {
                 "affiliations": [
+                    "pndb",
                     "gallantries",
-                    "ifb",
+                    "fairease",
+                    "fnso2019",
                     "elixir-europe"
                 ],
-                "contact_for_training": true,
                 "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
+                "email": "yvan.le-bras@mnhn.fr",
+                "id": "yvanlebras",
                 "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+                "matrix": "yvanlebras:matrix.org",
+                "name": "Yvan Le Bras",
+                "orcid": "0000-0002-8504-068X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
+                "twitter": "Yvan2935",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
             },
             {
                 "affiliations": [
-                    "ifb",
-                    "elixir-europe"
+                    "pndb",
+                    "fairease"
                 ],
-                "elixir_node": "fr",
-                "email": "clea.siguret@gmail.com",
-                "id": "clsiguret",
-                "joined": "2024-04",
-                "linkedin": "cl\u00e9a-siguret-58423b107",
-                "matrix": "clsiguret:matrix.org",
-                "name": "Clea Siguret",
-                "orcid": "0009-0005-6140-0379",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/clsiguret/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/clsiguret.json"
+                "email": "marie.josse@ifremer.fr",
+                "id": "Marie59",
+                "joined": "2022-03",
+                "name": "Marie Josse",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
             },
             {
-                "avatar": "/training-material/assets/images/abromics.png",
-                "funder": true,
-                "github": false,
-                "id": "abromics",
-                "joined": "2024-01",
-                "name": "ABRomics",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abromics/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/abromics.json"
+                "email": "yassine.ankerl@live.fr",
+                "id": "Rassine",
+                "joined": "2024-07",
+                "name": "Ankerl Yassine",
+                "orcid": "0009-0007-1538-2303",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Rassine/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Rassine.json"
             }
         ],
-        "dir": "topics/ecology/tutorials/bacterial-isolate-species-contamination-checking",
-        "edam_ontology": [
-            "topic_3673",
-            "topic_0622",
-            "topic_3301",
-            "topic_3697"
-        ],
-        "edam_operation": [
-            "Cross-assembly",
-            "Taxonomic classification",
-            "Expression analysis",
-            "Statistical calculation"
-        ],
-        "edam_topic": [
-            "Whole genome sequencing",
-            "Genomics",
-            "Microbiology",
-            "Microbial ecology"
-        ],
+        "dir": "topics/ecology/tutorials/Ecoregionalization_tutorial",
+        "edam_operation": [],
+        "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.fr"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "ecology/bacterial-isolate-species-contamination-checking",
-        "inexact_supported_servers": [
-            "Galaxy@AuBi",
-            "GalaxyTrakr",
-            "UseGalaxy.cz",
-            "UseGalaxy.org (Main)"
-        ],
+        "id": "ecology/Ecoregionalization_tutorial",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Kraken assigns taxons to sequences",
-            "Bracken extracts species from Kraken assignations",
-            "Recentrifuge extracts stats and creates visualization from Kraken report"
+            "Get raw data from research data wharehouse",
+            "Clean data content to be used by an existing workflow",
+            "Evaluate the best number of cluster to cut a dataset"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-27",
+        "mod_date": "2024-09-19",
         "objectives": [
-            "Run a series of tool to identify species in bacterial isolate sequencing data",
-            "Visualize the species abundance"
-        ],
-        "pageviews": 302,
-        "pub_date": "2024-03-04",
+            "Learning how to use the ecoregionalization workflow.",
+            "Learning about boosted regression trees algorithm.",
+            "Learning about Silhouette index and select an appropriate number of cluster",
+            "Learning about Clara clustering algorithm (PAM for large datasets)",
+            "Create an ecoregionalization map"
+        ],
+        "pageviews": 64,
+        "pub_date": "2024-09-16",
         "questions": [
-            "What are the species in bacterial isolate sequencing data?"
+            "How to use the ecoregionalization workflow?",
+            "How to construct ecoregions from occurrences species data and environmental data?"
         ],
-        "short_id": "T00423",
+        "short_id": "T00455",
         "short_tools": [
-            "est_abundance",
-            "upload1",
-            "kraken2",
-            "recentrifuge"
+            "interactive_tool_jupyter_notebook",
+            "ecoregion_clara_cluster",
+            "ecoregion_taxa_seeker",
+            "mergeCols1",
+            "filter_tabular",
+            "ecoregion_GeoNearestNeighbor",
+            "unzip",
+            "ecoregion_cluster_estimate",
+            "tp_cut_tool",
+            "ecoregion_eco_map",
+            "ecoregion_brt_analysis",
+            "regexColumn1"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "ecologypreprocess",
+        "subtopic": "ecologyanalysis",
         "supported_servers": {
             "exact": [
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
                 }
             ],
-            "inexact": [
-                {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ]
+            "inexact": []
         },
         "symlink": null,
         "tags": [
-            "illumina",
-            "bacteria",
-            "microgalaxy"
+            "ecology",
+            "taxonomic data",
+            "EBV workflow",
+            "modeling",
+            "gbif",
+            "ocean",
+            "earth-system",
+            "interactive-tools"
         ],
-        "time_estimation": "1H",
-        "title": "Checking expected species and contamination in bacterial isolate",
+        "time_estimation": "2H",
+        "title": "Ecoregionalization workflow tutorial",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0",
-            "upload1"
+            "interactive_tool_jupyter_notebook",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.2",
+            "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_brt_analysis/ecoregion_brt_analysis/0.1.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_clara_cluster/ecoregion_clara_cluster/0.1.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_cluster_estimate/ecoregion_cluster_estimate/0.1.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_eco_map/ecoregion_eco_map/0.1.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_geonearestneighbor/ecoregion_GeoNearestNeighbor/0.1.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_taxa_seeker/ecoregion_taxa_seeker/0.1.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.0"
         ],
         "topic_name": "ecology",
         "topic_name_human": "Ecology",
@@ -64496,450 +67855,703 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "bacterial-isolate-species-contamination-checking",
+        "tutorial_name": "Ecoregionalization_tutorial",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/Ecoregionalization_tutorial/tutorial.json"
         },
-        "version": 4,
+        "version": 5,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 237,
-        "visitors": 229,
+        "visit_duration": 209,
+        "visitors": 35,
         "workflows": [
             {
                 "creators": [
-                    {
-                        "alternateName": "pimarin",
-                        "class": "Person",
-                        "email": "mailto:pierre.marin@france-bioinformatique.fr",
-                        "familyName": "MARIN",
-                        "identifier": "0000-0002-8304-138X",
-                        "name": "Pierre"
-                    },
                     {
                         "class": "Person",
-                        "identifier": "https://orcid.org/0000-0001-9852-1987",
-                        "name": "B\u00e9r\u00e9nice Batut"
+                        "identifier": "0009-0009-5969-8478",
+                        "name": "Seguineau Pauline"
                     }
                 ],
-                "description": "Checking expected species and contamination in bacterial isolate",
+                "description": "",
                 "features": {
-                    "comments": false,
+                    "comments": true,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreverse_reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nforward_reads\"]\n  2[label=\"Kraken2\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  ka408a64458cd4f5eaf2515b5ea63aa76[color=lightseagreen,label=\"Output\\nkraken_report_reads\"]\n  2 -> ka408a64458cd4f5eaf2515b5ea63aa76\n  k54b85a5372ee4b73b1867fd55e8aab9b[color=lightseagreen,label=\"Output\\nkraken_report_tabular\"]\n  2 -> k54b85a5372ee4b73b1867fd55e8aab9b\n  3[label=\"Bracken\"]\n  2 -> 3 [label=\"report_output\"]\n  kae6c6464f5f54e5bb616d38166fc0133[color=lightseagreen,label=\"Output\\nbracken_report_tsv\"]\n  3 -> kae6c6464f5f54e5bb616d38166fc0133\n  k8ca52af9f83942b6aa74f1a6a1dfbbc8[color=lightseagreen,label=\"Output\\nbracken_kraken_report\"]\n  3 -> k8ca52af9f83942b6aa74f1a6a1dfbbc8\n  4[label=\"Recentrifuge\"]\n  2 -> 4 [label=\"output\"]\n  kb5694f2dc8cd4460bfff74fd0792ecb3[color=lightseagreen,label=\"Output\\nrecentrifuge_stats_tabular\"]\n  4 -> kb5694f2dc8cd4460bfff74fd0792ecb3\n  kbd947a1d0443465f86585d76d9ce69f8[color=lightseagreen,label=\"Output\\nrecentrifuge_report_html\"]\n  4 -> kbd947a1d0443465f86585d76d9ce69f8\n  kc7457acb41bc4191b3fb6716e15fbe57[color=lightseagreen,label=\"Output\\nrecentrifuge_data_tabular\"]\n  4 -> kc7457acb41bc4191b3fb6716e15fbe57\n  k94f6ff070e0647ad88f8a058d0808537[color=lightseagreen,label=\"Output\\nrecentrifuge_logfile\"]\n  4 -> k94f6ff070e0647ad88f8a058d0808537\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\noccurrence.txt\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\npivot_wider_jupytool_notebook.ipynb\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nceamarc_env.tsv\"]\n  3[label=\"Advanced Cut\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Column Regex Find And Replace\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"Column Regex Find And Replace\"]\n  4 -> 5 [label=\"out_file1\"]\n  6[label=\"Column Regex Find And Replace\"]\n  5 -> 6 [label=\"out_file1\"]\n  7[label=\"Column Regex Find And Replace\"]\n  6 -> 7 [label=\"out_file1\"]\n  8[label=\"Filter Tabular\"]\n  7 -> 8 [label=\"out_file1\"]\n  9[label=\"Column Regex Find And Replace\"]\n  8 -> 9 [label=\"output\"]\n  10[label=\"Column Regex Find And Replace\"]\n  9 -> 10 [label=\"out_file1\"]\n  11[label=\"Column Regex Find And Replace\"]\n  10 -> 11 [label=\"out_file1\"]\n  12[label=\"Column Regex Find And Replace\"]\n  11 -> 12 [label=\"out_file1\"]\n  13[label=\"Column Regex Find And Replace\"]\n  12 -> 13 [label=\"out_file1\"]\n  14[label=\"Merge Columns\"]\n  13 -> 14 [label=\"out_file1\"]\n  15[label=\"Advanced Cut\"]\n  14 -> 15 [label=\"out_file1\"]\n  16[label=\"Interactive JupyTool and notebook\"]\n  1 -> 16 [label=\"output\"]\n  15 -> 16 [label=\"output\"]\n  kb3689891b1e54af7aa8aa01cfdd249e6[color=lightseagreen,label=\"Output\\nocc_out\"]\n  16 -> kb3689891b1e54af7aa8aa01cfdd249e6\n  17[label=\"GeoNearestNeighbor\"]\n  2 -> 17 [label=\"output\"]\n  16 -> 17 [label=\"output_dataset\"]\n  k3d871fdd1ca84ca580ddb50ec7193a09[color=lightseagreen,label=\"Output\\nocc_env_out\"]\n  17 -> k3d871fdd1ca84ca580ddb50ec7193a09\n  k23ef2c886caa4a4abf3334e51ea63787[color=lightseagreen,label=\"Output\\ninfo_out\"]\n  17 -> k23ef2c886caa4a4abf3334e51ea63787\n  18[label=\"BRT tool prediction\"]\n  2 -> 18 [label=\"output\"]\n  17 -> 18 [label=\"occ_env_out\"]\n  k5003067a90e64b6fbcb515c7f07a587b[color=lightseagreen,label=\"Output\\ncoll_pred\"]\n  18 -> k5003067a90e64b6fbcb515c7f07a587b\n  k2588bbcf106443c19eb3aaa9a699be61[color=lightseagreen,label=\"Output\\ncoll_val\"]\n  18 -> k2588bbcf106443c19eb3aaa9a699be61\n  k7d4abdef22d740e09d4551a8151a6ab5[color=lightseagreen,label=\"Output\\ncoll_distri\"]\n  18 -> k7d4abdef22d740e09d4551a8151a6ab5\n  kd4f30afaddd74be3827b504c9b152e79[color=lightseagreen,label=\"Output\\ncoll_plots\"]\n  18 -> kd4f30afaddd74be3827b504c9b152e79\n  19[label=\"TaxaSeeker\"]\n  2 -> 19 [label=\"output\"]\n  17 -> 19 [label=\"occ_env_out\"]\n  18 -> 19 [label=\"outputpred\"]\n  k5109d04069324a698a7a01372852ec58[color=lightseagreen,label=\"Output\\nsummary\"]\n  19 -> k5109d04069324a698a7a01372852ec58\n  k66fd292ac5424e7ba8cb124095e6e8ed[color=lightseagreen,label=\"Output\\ntaxa\"]\n  19 -> k66fd292ac5424e7ba8cb124095e6e8ed\n  ka4c7a093d64046ba86815bd09c899215[color=lightseagreen,label=\"Output\\ntaxa_clean\"]\n  19 -> ka4c7a093d64046ba86815bd09c899215\n  20[label=\"ClusterEstimate\"]\n  2 -> 20 [label=\"output\"]\n  18 -> 20 [label=\"outputpred\"]\n  19 -> 20 [label=\"output2\"]\n  kfd5e25b231b8446bbbde33f4978cbbce[color=lightseagreen,label=\"Output\\nSIH_index\"]\n  20 -> kfd5e25b231b8446bbbde33f4978cbbce\n  kada14639f7a0454ca0b9a6efdf019186[color=lightseagreen,label=\"Output\\ndata_to_clus\"]\n  20 -> kada14639f7a0454ca0b9a6efdf019186\n  k7556cf4a92f7443fa43fcc011a4eea8f[color=lightseagreen,label=\"Output\\ndatabio_table\"]\n  20 -> k7556cf4a92f7443fa43fcc011a4eea8f\n  21[label=\"ClaraClust\"]\n  2 -> 21 [label=\"output\"]\n  20 -> 21 [label=\"output3\"]\n  20 -> 21 [label=\"output2\"]\n  k65123e97b2fa429dbf325733ccb17fb5[color=lightseagreen,label=\"Output\\nSIH_plot\"]\n  21 -> k65123e97b2fa429dbf325733ccb17fb5\n  k38a7227ba1f54728bdac87d0764c3a29[color=lightseagreen,label=\"Output\\ncluster_points\"]\n  21 -> k38a7227ba1f54728bdac87d0764c3a29\n  k592084ea4cbe477db826e01ec4f52650[color=lightseagreen,label=\"Output\\ncluster_info\"]\n  21 -> k592084ea4cbe477db826e01ec4f52650\n  22[label=\"EcoMap\"]\n  21 -> 22 [label=\"output2\"]\n  k2f8feb4ced0a4bfc89e8e7befd040ada[color=lightseagreen,label=\"Output\\neco_map\"]\n  22 -> k2f8feb4ced0a4bfc89e8e7befd040ada\n}",
                 "history": [
                     {
-                        "hash": "4854483dab21555869c5c49b91fa3113146c07dc",
-                        "message": "Update Bracken version toolshed",
-                        "num": 3,
-                        "short_hash": "4854483da",
-                        "unix": "1712233925"
-                    },
-                    {
-                        "hash": "96c80b0ad7e5179b3d43364e789efee1adeea130",
-                        "message": "Update workflow creators",
-                        "num": 2,
-                        "short_hash": "96c80b0ad",
-                        "unix": "1706542936"
-                    },
-                    {
-                        "hash": "96df58f868367e22ade2e451a1d9ecacba822bcc",
-                        "message": "Create new tutorial for checking expected species and contamination in bacterial isolate",
+                        "hash": "106094184ea15924f444a0b076b0afecd065494a",
+                        "message": "Update workflow",
                         "num": 1,
-                        "short_hash": "96df58f86",
-                        "unix": "1706542439"
+                        "short_hash": "106094184",
+                        "unix": "1718800835"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "reverse_reads",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "reverse_reads",
-                                "name": "reverse_reads"
+                                "description": "",
+                                "name": "occurrence.txt"
                             }
                         ],
-                        "label": "reverse_reads",
+                        "label": "occurrence.txt",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 56
+                            "left": 20,
+                            "top": 260
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fastq\", \"fastq.gz\", \"fastqsanger\", \"fastqsanger.gz\"], \"tag\": \"\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "a39893cf-49cb-4c5c-9e71-0f8004a2a1ee",
+                        "uuid": "2c6ad1a0-b36d-4fac-a0e3-5d5d89435886",
                         "when": null,
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "forward_reads",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "forward_reads",
-                                "name": "forward_reads"
+                                "description": "",
+                                "name": "pivot_wider_jupytool_notebook.ipynb"
                             }
                         ],
-                        "label": "forward_reads",
+                        "label": "pivot_wider_jupytool_notebook.ipynb",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 179
+                            "left": 2290,
+                            "top": 250
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fastq\", \"fastq.gz\", \"fastqsanger\", \"fastqsanger.gz\"], \"tag\": \"\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ca539dfd-e173-42d6-998a-0fc4c5f3d5b8",
+                        "uuid": "3f8f2445-d193-4cd0-9880-fb61b5e8ab66",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "ceamarc_env.tsv"
+                            }
+                        ],
+                        "label": "ceamarc_env.tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 2850.0099833137524,
+                            "top": 56.75797316712817
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "c9e7efc5-0fde-4ced-be6b-5d39c36ff72b",
                         "when": null,
                         "workflow_outputs": []
                     }
                 ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nreverse_reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nforward_reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Kraken2\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  a408a644-58cd-4f5e-af25-15b5ea63aa76[\"Output\\nkraken_report_reads\"];\n  2 --> a408a644-58cd-4f5e-af25-15b5ea63aa76;\n  style a408a644-58cd-4f5e-af25-15b5ea63aa76 stroke:#2c3143,stroke-width:4px;\n  54b85a53-72ee-4b73-b186-7fd55e8aab9b[\"Output\\nkraken_report_tabular\"];\n  2 --> 54b85a53-72ee-4b73-b186-7fd55e8aab9b;\n  style 54b85a53-72ee-4b73-b186-7fd55e8aab9b stroke:#2c3143,stroke-width:4px;\n  3[\"Bracken\"];\n  2 -->|report_output| 3;\n  ae6c6464-f5f5-4e5b-b616-d38166fc0133[\"Output\\nbracken_report_tsv\"];\n  3 --> ae6c6464-f5f5-4e5b-b616-d38166fc0133;\n  style ae6c6464-f5f5-4e5b-b616-d38166fc0133 stroke:#2c3143,stroke-width:4px;\n  8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8[\"Output\\nbracken_kraken_report\"];\n  3 --> 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8;\n  style 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8 stroke:#2c3143,stroke-width:4px;\n  4[\"Recentrifuge\"];\n  2 -->|output| 4;\n  b5694f2d-c8cd-4460-bfff-74fd0792ecb3[\"Output\\nrecentrifuge_stats_tabular\"];\n  4 --> b5694f2d-c8cd-4460-bfff-74fd0792ecb3;\n  style b5694f2d-c8cd-4460-bfff-74fd0792ecb3 stroke:#2c3143,stroke-width:4px;\n  bd947a1d-0443-465f-8658-5d76d9ce69f8[\"Output\\nrecentrifuge_report_html\"];\n  4 --> bd947a1d-0443-465f-8658-5d76d9ce69f8;\n  style bd947a1d-0443-465f-8658-5d76d9ce69f8 stroke:#2c3143,stroke-width:4px;\n  c7457acb-41bc-4191-b3fb-6716e15fbe57[\"Output\\nrecentrifuge_data_tabular\"];\n  4 --> c7457acb-41bc-4191-b3fb-6716e15fbe57;\n  style c7457acb-41bc-4191-b3fb-6716e15fbe57 stroke:#2c3143,stroke-width:4px;\n  94f6ff07-0e06-47ad-88f8-a058d0808537[\"Output\\nrecentrifuge_logfile\"];\n  4 --> 94f6ff07-0e06-47ad-88f8-a058d0808537;\n  style 94f6ff07-0e06-47ad-88f8-a058d0808537 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:22 +0000",
-                "name": "Checking expected species and contamination in bacterial isolate",
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\noccurrence.txt\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\npivot_wider_jupytool_notebook.ipynb\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nceamarc_env.tsv\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Advanced Cut\"];\n  0 -->|output| 3;\n  4[\"Column Regex Find And Replace\"];\n  3 -->|output| 4;\n  5[\"Column Regex Find And Replace\"];\n  4 -->|out_file1| 5;\n  6[\"Column Regex Find And Replace\"];\n  5 -->|out_file1| 6;\n  7[\"Column Regex Find And Replace\"];\n  6 -->|out_file1| 7;\n  8[\"Filter Tabular\"];\n  7 -->|out_file1| 8;\n  9[\"Column Regex Find And Replace\"];\n  8 -->|output| 9;\n  10[\"Column Regex Find And Replace\"];\n  9 -->|out_file1| 10;\n  11[\"Column Regex Find And Replace\"];\n  10 -->|out_file1| 11;\n  12[\"Column Regex Find And Replace\"];\n  11 -->|out_file1| 12;\n  13[\"Column Regex Find And Replace\"];\n  12 -->|out_file1| 13;\n  14[\"Merge Columns\"];\n  13 -->|out_file1| 14;\n  15[\"Advanced Cut\"];\n  14 -->|out_file1| 15;\n  16[\"Interactive JupyTool and notebook\"];\n  1 -->|output| 16;\n  15 -->|output| 16;\n  b3689891-b1e5-4af7-aa8a-a01cfdd249e6[\"Output\\nocc_out\"];\n  16 --> b3689891-b1e5-4af7-aa8a-a01cfdd249e6;\n  style b3689891-b1e5-4af7-aa8a-a01cfdd249e6 stroke:#2c3143,stroke-width:4px;\n  17[\"GeoNearestNeighbor\"];\n  2 -->|output| 17;\n  16 -->|output_dataset| 17;\n  3d871fdd-1ca8-4ca5-80dd-b50ec7193a09[\"Output\\nocc_env_out\"];\n  17 --> 3d871fdd-1ca8-4ca5-80dd-b50ec7193a09;\n  style 3d871fdd-1ca8-4ca5-80dd-b50ec7193a09 stroke:#2c3143,stroke-width:4px;\n  23ef2c88-6caa-4a4a-bf33-34e51ea63787[\"Output\\ninfo_out\"];\n  17 --> 23ef2c88-6caa-4a4a-bf33-34e51ea63787;\n  style 23ef2c88-6caa-4a4a-bf33-34e51ea63787 stroke:#2c3143,stroke-width:4px;\n  18[\"BRT tool prediction\"];\n  2 -->|output| 18;\n  17 -->|occ_env_out| 18;\n  5003067a-90e6-4b6f-bcb5-15c7f07a587b[\"Output\\ncoll_pred\"];\n  18 --> 5003067a-90e6-4b6f-bcb5-15c7f07a587b;\n  style 5003067a-90e6-4b6f-bcb5-15c7f07a587b stroke:#2c3143,stroke-width:4px;\n  2588bbcf-1064-43c1-9eb3-aaa9a699be61[\"Output\\ncoll_val\"];\n  18 --> 2588bbcf-1064-43c1-9eb3-aaa9a699be61;\n  style 2588bbcf-1064-43c1-9eb3-aaa9a699be61 stroke:#2c3143,stroke-width:4px;\n  7d4abdef-22d7-40e0-9d45-51a8151a6ab5[\"Output\\ncoll_distri\"];\n  18 --> 7d4abdef-22d7-40e0-9d45-51a8151a6ab5;\n  style 7d4abdef-22d7-40e0-9d45-51a8151a6ab5 stroke:#2c3143,stroke-width:4px;\n  d4f30afa-ddd7-4be3-827b-504c9b152e79[\"Output\\ncoll_plots\"];\n  18 --> d4f30afa-ddd7-4be3-827b-504c9b152e79;\n  style d4f30afa-ddd7-4be3-827b-504c9b152e79 stroke:#2c3143,stroke-width:4px;\n  19[\"TaxaSeeker\"];\n  2 -->|output| 19;\n  17 -->|occ_env_out| 19;\n  18 -->|outputpred| 19;\n  5109d040-6932-4a69-8a7a-01372852ec58[\"Output\\nsummary\"];\n  19 --> 5109d040-6932-4a69-8a7a-01372852ec58;\n  style 5109d040-6932-4a69-8a7a-01372852ec58 stroke:#2c3143,stroke-width:4px;\n  66fd292a-c542-4e7b-a8cb-124095e6e8ed[\"Output\\ntaxa\"];\n  19 --> 66fd292a-c542-4e7b-a8cb-124095e6e8ed;\n  style 66fd292a-c542-4e7b-a8cb-124095e6e8ed stroke:#2c3143,stroke-width:4px;\n  a4c7a093-d640-46ba-8681-5bd09c899215[\"Output\\ntaxa_clean\"];\n  19 --> a4c7a093-d640-46ba-8681-5bd09c899215;\n  style a4c7a093-d640-46ba-8681-5bd09c899215 stroke:#2c3143,stroke-width:4px;\n  20[\"ClusterEstimate\"];\n  2 -->|output| 20;\n  18 -->|outputpred| 20;\n  19 -->|output2| 20;\n  fd5e25b2-31b8-446b-bbde-33f4978cbbce[\"Output\\nSIH_index\"];\n  20 --> fd5e25b2-31b8-446b-bbde-33f4978cbbce;\n  style fd5e25b2-31b8-446b-bbde-33f4978cbbce stroke:#2c3143,stroke-width:4px;\n  ada14639-f7a0-454c-a0b9-a6efdf019186[\"Output\\ndata_to_clus\"];\n  20 --> ada14639-f7a0-454c-a0b9-a6efdf019186;\n  style ada14639-f7a0-454c-a0b9-a6efdf019186 stroke:#2c3143,stroke-width:4px;\n  7556cf4a-92f7-443f-a43f-cc011a4eea8f[\"Output\\ndatabio_table\"];\n  20 --> 7556cf4a-92f7-443f-a43f-cc011a4eea8f;\n  style 7556cf4a-92f7-443f-a43f-cc011a4eea8f stroke:#2c3143,stroke-width:4px;\n  21[\"ClaraClust\"];\n  2 -->|output| 21;\n  20 -->|output3| 21;\n  20 -->|output2| 21;\n  65123e97-b2fa-429d-bf32-5733ccb17fb5[\"Output\\nSIH_plot\"];\n  21 --> 65123e97-b2fa-429d-bf32-5733ccb17fb5;\n  style 65123e97-b2fa-429d-bf32-5733ccb17fb5 stroke:#2c3143,stroke-width:4px;\n  38a7227b-a1f5-4728-bdac-87d0764c3a29[\"Output\\ncluster_points\"];\n  21 --> 38a7227b-a1f5-4728-bdac-87d0764c3a29;\n  style 38a7227b-a1f5-4728-bdac-87d0764c3a29 stroke:#2c3143,stroke-width:4px;\n  592084ea-4cbe-477d-b826-e01ec4f52650[\"Output\\ncluster_info\"];\n  21 --> 592084ea-4cbe-477d-b826-e01ec4f52650;\n  style 592084ea-4cbe-477d-b826-e01ec4f52650 stroke:#2c3143,stroke-width:4px;\n  22[\"EcoMap\"];\n  21 -->|output2| 22;\n  2f8feb4c-ed0a-4bfc-89e8-e7befd040ada[\"Output\\neco_map\"];\n  22 --> 2f8feb4c-ed0a-4bfc-89e8-e7befd040ada;\n  style 2f8feb4c-ed0a-4bfc-89e8-e7befd040ada stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:07 +0000",
+                "name": "Ecoregionalization workflow",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                        "content_id": "interactive_tool_jupyter_notebook",
                         "errors": null,
-                        "id": 2,
+                        "id": 16,
                         "input_connections": {
-                            "single_paired|forward_input": {
+                            "mode|ipynb": {
                                 "id": 1,
                                 "output_name": "output"
                             },
-                            "single_paired|reverse_input": {
-                                "id": 0,
+                            "user_inputs_0|input_type|input_value": {
+                                "id": 15,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Interactive JupyTool and notebook",
+                                "name": "mode"
+                            }
+                        ],
                         "label": null,
-                        "name": "Kraken2",
+                        "name": "Interactive JupyTool and notebook",
                         "outputs": [
                             {
-                                "name": "report_output",
+                                "name": "output_collection",
+                                "type": "input"
+                            },
+                            {
+                                "name": "jupyter_notebook",
+                                "type": "ipynb"
+                            },
+                            {
+                                "name": "output_dataset",
+                                "type": "data"
+                            }
+                        ],
+                        "position": {
+                            "left": 2550,
+                            "top": 280
+                        },
+                        "post_job_actions": {
+                            "ChangeDatatypeActionoutput_dataset": {
+                                "action_arguments": {
+                                    "newtype": "tabular"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "output_dataset"
+                            }
+                        },
+                        "tool_id": "interactive_tool_jupyter_notebook",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"mode\": {\"mode_select\": \"previous\", \"__current_case__\": 1, \"ipynb\": {\"__class__\": \"ConnectedValue\"}, \"run_it\": true}, \"user_inputs\": [{\"__index__\": 0, \"input_name\": \"Input file\", \"description\": null, \"input_type\": {\"input_type_selector\": \"dataset\", \"__current_case__\": 0, \"input_value\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "13e9ad8f-74ee-44f9-a4c9-efc377fe7c5e",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "occ_out",
+                                "output_name": "output_dataset",
+                                "uuid": "b3689891-b1e5-4af7-aa8a-a01cfdd249e6"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_geonearestneighbor/ecoregion_GeoNearestNeighbor/0.1.0+galaxy0",
+                        "errors": null,
+                        "id": 17,
+                        "input_connections": {
+                            "env_file|env": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "occ_file|occ": {
+                                "id": 16,
+                                "output_name": "output_dataset"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool GeoNearestNeighbor",
+                                "name": "env_file"
+                            },
+                            {
+                                "description": "runtime parameter for tool GeoNearestNeighbor",
+                                "name": "occ_file"
+                            }
+                        ],
+                        "label": null,
+                        "name": "GeoNearestNeighbor",
+                        "outputs": [
+                            {
+                                "name": "occ_env_out",
                                 "type": "tabular"
                             },
                             {
-                                "name": "output",
+                                "name": "info_out",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 280,
-                            "top": 0
+                            "left": 2894.5877827929194,
+                            "top": 408.1579568910865
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_geonearestneighbor/ecoregion_GeoNearestNeighbor/0.1.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "e674066930b2",
-                            "name": "kraken2",
-                            "owner": "iuc",
+                            "changeset_revision": "5cde56683579",
+                            "name": "ecoregion_geonearestneighbor",
+                            "owner": "ecology",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"confidence\": \"0.0\", \"kraken2_database\": \"2023-08-24T153645Z_standard_prebuilt_pluspf_16gb_2022-06-07\", \"min_base_quality\": \"10\", \"minimum_hit_groups\": \"2\", \"quick\": false, \"report\": {\"create_report\": true, \"use_mpa_style\": false, \"report_zero_counts\": false, \"report_minimizer_data\": false}, \"single_paired\": {\"single_paired_selector\": \"yes\", \"__current_case__\": 1, \"forward_input\": {\"__class__\": \"ConnectedValue\"}, \"reverse_input\": {\"__class__\": \"ConnectedValue\"}}, \"split_reads\": false, \"use_names\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.1+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"env_file\": {\"env\": {\"__class__\": \"ConnectedValue\"}, \"envgeolat\": \"2\", \"envgeolong\": \"1\"}, \"occ_file\": {\"occ\": {\"__class__\": \"ConnectedValue\"}, \"occgeolat\": \"1\", \"occgeolong\": \"2\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0+galaxy0",
                         "type": "tool",
-                        "uuid": "75b7f2b8-2b63-4f1a-a877-4babef16a08b",
+                        "uuid": "9a90d520-1415-4e61-b182-bc901419017d",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "kraken_report_reads",
-                                "output_name": "output",
-                                "uuid": "a408a644-58cd-4f5e-af25-15b5ea63aa76"
+                                "label": "occ_env_out",
+                                "output_name": "occ_env_out",
+                                "uuid": "3d871fdd-1ca8-4ca5-80dd-b50ec7193a09"
                             },
                             {
-                                "label": "kraken_report_tabular",
-                                "output_name": "report_output",
-                                "uuid": "54b85a53-72ee-4b73-b186-7fd55e8aab9b"
+                                "label": "info_out",
+                                "output_name": "info_out",
+                                "uuid": "23ef2c88-6caa-4a4a-bf33-34e51ea63787"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_brt_analysis/ecoregion_brt_analysis/0.1.0+galaxy0",
                         "errors": null,
-                        "id": 3,
+                        "id": 18,
                         "input_connections": {
-                            "input": {
+                            "enviro": {
                                 "id": 2,
-                                "output_name": "report_output"
+                                "output_name": "output"
+                            },
+                            "species_files": {
+                                "id": 17,
+                                "output_name": "occ_env_out"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Bracken",
+                        "name": "BRT tool prediction",
                         "outputs": [
                             {
-                                "name": "report",
-                                "type": "tabular"
+                                "name": "outputpred",
+                                "type": "input"
                             },
                             {
-                                "name": "kraken_report",
-                                "type": "tabular"
+                                "name": "outputval",
+                                "type": "input"
+                            },
+                            {
+                                "name": "outputspdistri",
+                                "type": "input"
+                            },
+                            {
+                                "name": "outputplots",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 560,
-                            "top": 40
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionkraken_report": {
-                                "action_arguments": {
-                                    "newname": "bracken_kraken_report"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "kraken_report"
-                            },
-                            "RenameDatasetActionreport": {
-                                "action_arguments": {
-                                    "newname": "bracken_report_tsv"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "report"
-                            }
+                            "left": 3193.504075252652,
+                            "top": 541.7185497919073
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_brt_analysis/ecoregion_brt_analysis/0.1.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "0357fb68688c419f",
-                            "name": "bracken",
-                            "owner": "iuc",
+                            "changeset_revision": "f8962f1c832a",
+                            "name": "ecoregion_brt_analysis",
+                            "owner": "ecology",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"kmer_distr\": \"bf6177af-7f5b-4005-9bec-fc7c89c3cb1c\", \"level\": \"S\", \"logfile_output\": false, \"out_report\": true, \"threshold\": \"10\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.8+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"abioticname\": [\"3\", \"4\", \"5\", \"6\", \"7\", \"8\", \"9\", \"10\", \"11\", \"12\", \"13\", \"14\", \"15\", \"16\", \"17\", \"18\", \"19\"], \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"dec_env\": \".\", \"dec_species\": \".\", \"enviro\": {\"__class__\": \"ConnectedValue\"}, \"species_files\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0+galaxy0",
                         "type": "tool",
-                        "uuid": "53b9c80b-f5f4-4fee-9778-fb4fd6b76165",
+                        "uuid": "31b18fc8-1e4d-493c-984e-4258f1a4f2c6",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "bracken_report_tsv",
-                                "output_name": "report",
-                                "uuid": "ae6c6464-f5f5-4e5b-b616-d38166fc0133"
+                                "label": "coll_pred",
+                                "output_name": "outputpred",
+                                "uuid": "5003067a-90e6-4b6f-bcb5-15c7f07a587b"
                             },
                             {
-                                "label": "bracken_kraken_report",
-                                "output_name": "kraken_report",
-                                "uuid": "8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8"
+                                "label": "coll_val",
+                                "output_name": "outputval",
+                                "uuid": "2588bbcf-1064-43c1-9eb3-aaa9a699be61"
+                            },
+                            {
+                                "label": "coll_distri",
+                                "output_name": "outputspdistri",
+                                "uuid": "7d4abdef-22d7-40e0-9d45-51a8151a6ab5"
+                            },
+                            {
+                                "label": "coll_plots",
+                                "output_name": "outputplots",
+                                "uuid": "d4f30afa-ddd7-4be3-827b-504c9b152e79"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_taxa_seeker/ecoregion_taxa_seeker/0.1.0+galaxy0",
                         "errors": null,
-                        "id": 4,
+                        "id": 19,
                         "input_connections": {
-                            "input_file": {
+                            "envfile": {
                                 "id": 2,
                                 "output_name": "output"
+                            },
+                            "occurencefile": {
+                                "id": 17,
+                                "output_name": "occ_env_out"
+                            },
+                            "predictionfile": {
+                                "id": 18,
+                                "output_name": "outputpred"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Recentrifuge",
+                        "name": "TaxaSeeker",
                         "outputs": [
                             {
-                                "name": "html_report",
-                                "type": "html"
+                                "name": "output1",
+                                "type": "tabular"
                             },
                             {
-                                "name": "logfile",
+                                "name": "output2",
                                 "type": "txt"
                             },
                             {
-                                "name": "data_tsv",
+                                "name": "output3",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 3433.8698763810016,
+                            "top": 237.72007897217372
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_taxa_seeker/ecoregion_taxa_seeker/0.1.0+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "788b118910a7",
+                            "name": "ecoregion_taxa_seeker",
+                            "owner": "ecology",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"envfile\": {\"__class__\": \"ConnectedValue\"}, \"occurencefile\": {\"__class__\": \"ConnectedValue\"}, \"predictionfile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0+galaxy0",
+                        "type": "tool",
+                        "uuid": "5fcebc7f-6c64-4d03-ba84-4698bec4972f",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "summary",
+                                "output_name": "output1",
+                                "uuid": "5109d040-6932-4a69-8a7a-01372852ec58"
+                            },
+                            {
+                                "label": "taxa",
+                                "output_name": "output2",
+                                "uuid": "66fd292a-c542-4e7b-a8cb-124095e6e8ed"
+                            },
+                            {
+                                "label": "taxa_clean",
+                                "output_name": "output3",
+                                "uuid": "a4c7a093-d640-46ba-8681-5bd09c899215"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_cluster_estimate/ecoregion_cluster_estimate/0.1.0+galaxy0",
+                        "errors": null,
+                        "id": 20,
+                        "input_connections": {
+                            "envfile": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "predictionfile": {
+                                "id": 18,
+                                "output_name": "outputpred"
+                            },
+                            "taxafile": {
+                                "id": 19,
+                                "output_name": "output2"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "ClusterEstimate",
+                        "outputs": [
+                            {
+                                "name": "output1",
+                                "type": "png"
+                            },
+                            {
+                                "name": "output2",
                                 "type": "tabular"
                             },
                             {
-                                "name": "stat_tsv",
+                                "name": "output3",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 560,
-                            "top": 329
+                            "left": 3874.7,
+                            "top": 200
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActiondata_tsv": {
-                                "action_arguments": {
-                                    "newname": "recentrifuge_data_tabular"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "data_tsv"
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_cluster_estimate/ecoregion_cluster_estimate/0.1.0+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "1b9522671e90",
+                            "name": "ecoregion_cluster_estimate",
+                            "owner": "ecology",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"envfile\": {\"__class__\": \"ConnectedValue\"}, \"max_k\": \"10\", \"metric\": \"manhattan\", \"predictionfile\": {\"__class__\": \"ConnectedValue\"}, \"sample\": \"10\", \"taxafile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0+galaxy0",
+                        "type": "tool",
+                        "uuid": "eb37099c-77b2-4bd2-b1f9-11f0a46ba7ab",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "SIH_index",
+                                "output_name": "output1",
+                                "uuid": "fd5e25b2-31b8-446b-bbde-33f4978cbbce"
                             },
-                            "RenameDatasetActionhtml_report": {
-                                "action_arguments": {
-                                    "newname": "recentrifuge_report_html"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "html_report"
+                            {
+                                "label": "data_to_clus",
+                                "output_name": "output2",
+                                "uuid": "ada14639-f7a0-454c-a0b9-a6efdf019186"
                             },
-                            "RenameDatasetActionlogfile": {
-                                "action_arguments": {
-                                    "newname": "recentrifuge_logfile"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "logfile"
+                            {
+                                "label": "databio_table",
+                                "output_name": "output3",
+                                "uuid": "7556cf4a-92f7-443f-a43f-cc011a4eea8f"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Please ensure that the parameter 'Number of Clusters Wanted' reflects your actual desired number. To determine this parameter, refer to your SIH index plot from the ClusterEstimate step.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_clara_cluster/ecoregion_clara_cluster/0.1.0+galaxy0",
+                        "errors": null,
+                        "id": 21,
+                        "input_connections": {
+                            "envfile": {
+                                "id": 2,
+                                "output_name": "output"
                             },
-                            "RenameDatasetActionstat_tsv": {
-                                "action_arguments": {
-                                    "newname": "recentrifuge_stats_tabular"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "stat_tsv"
+                            "predictionfile": {
+                                "id": 20,
+                                "output_name": "output3"
+                            },
+                            "predictionmatrix": {
+                                "id": 20,
+                                "output_name": "output2"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0",
+                        "inputs": [],
+                        "label": null,
+                        "name": "ClaraClust",
+                        "outputs": [
+                            {
+                                "name": "output1",
+                                "type": "png"
+                            },
+                            {
+                                "name": "output2",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "output3",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 4289.178352338062,
+                            "top": 39.984930695645005
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_clara_cluster/ecoregion_clara_cluster/0.1.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "b5407cc2bf51",
-                            "name": "recentrifuge",
-                            "owner": "iuc",
+                            "changeset_revision": "24a81631a8b5",
+                            "name": "ecoregion_clara_cluster",
+                            "owner": "ecology",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_option\": {\"controls\": \"0\", \"scoring\": null, \"minscore_value\": \"0\", \"mintaxa\": \"0\", \"exclude_taxa_name\": null, \"include_taxa_name\": null, \"avoidcross\": false}, \"database\": {\"database_name\": \"ncbi-2023-06-27\"}, \"file_type\": {\"filetype\": \"kraken\", \"__current_case__\": 3}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"more_advanced_option\": {\"ctrlminscore\": \"0\", \"ctrlmintaxa\": \"0\", \"summary\": \"ADD\", \"takeoutroot\": false, \"nokollapse\": false, \"strain\": true, \"sequential\": false}, \"output_option\": {\"extra\": \"TSV\", \"nohtml\": false, \"no_logfile\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.12.1+galaxy0",
+                        "tool_state": "{\"envfile\": {\"__class__\": \"ConnectedValue\"}, \"k\": \"7\", \"metric\": \"manhattan\", \"predictionfile\": {\"__class__\": \"ConnectedValue\"}, \"predictionmatrix\": {\"__class__\": \"ConnectedValue\"}, \"sample\": \"10\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0+galaxy0",
                         "type": "tool",
-                        "uuid": "4b3b34ad-2352-4e93-abbc-69da3ab9ee3a",
+                        "uuid": "7cd94343-68e1-48d6-8ad1-6bced0b2e78f",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "recentrifuge_stats_tabular",
-                                "output_name": "stat_tsv",
-                                "uuid": "b5694f2d-c8cd-4460-bfff-74fd0792ecb3"
+                                "label": "SIH_plot",
+                                "output_name": "output1",
+                                "uuid": "65123e97-b2fa-429d-bf32-5733ccb17fb5"
                             },
                             {
-                                "label": "recentrifuge_report_html",
-                                "output_name": "html_report",
-                                "uuid": "bd947a1d-0443-465f-8658-5d76d9ce69f8"
+                                "label": "cluster_points",
+                                "output_name": "output2",
+                                "uuid": "38a7227b-a1f5-4728-bdac-87d0764c3a29"
                             },
                             {
-                                "label": "recentrifuge_data_tabular",
-                                "output_name": "data_tsv",
-                                "uuid": "c7457acb-41bc-4191-b3fb-6716e15fbe57"
-                            },
+                                "label": "cluster_info",
+                                "output_name": "output3",
+                                "uuid": "592084ea-4cbe-477d-b826-e01ec4f52650"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_eco_map/ecoregion_eco_map/0.1.0+galaxy0",
+                        "errors": null,
+                        "id": 22,
+                        "input_connections": {
+                            "cluster": {
+                                "id": 21,
+                                "output_name": "output2"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "EcoMap",
+                        "outputs": [
                             {
-                                "label": "recentrifuge_logfile",
-                                "output_name": "logfile",
-                                "uuid": "94f6ff07-0e06-47ad-88f8-a058d0808537"
+                                "name": "output",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 4527.826706775709,
+                            "top": 284.3215296781037
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_eco_map/ecoregion_eco_map/0.1.0+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "374555fc30bd",
+                            "name": "ecoregion_eco_map",
+                            "owner": "ecology",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cluster\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0+galaxy0",
+                        "type": "tool",
+                        "uuid": "173e238c-b551-40bf-9ada-302f6a2f8537",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "eco_map",
+                                "output_name": "output",
+                                "uuid": "2f8feb4c-ed0a-4bfc-89e8-e7befd040ada"
                             }
                         ]
                     }
                 ],
-                "parent_id": "ecology/bacterial-isolate-species-contamination-checking",
-                "path": "topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/workflows/Checking-expected-species-and-contamination-in-bacterial-isolate.ga",
-                "tags": [
-                    "ecology"
-                ],
+                "parent_id": "ecology/Ecoregionalization_tutorial",
+                "path": "topics/ecology/tutorials/Ecoregionalization_tutorial/workflows/Ecoregionalization_workflow.ga",
+                "tags": [],
                 "test_results": null,
                 "tests": true,
-                "title": "Checking expected species and contamination in bacterial isolate",
+                "title": "Ecoregionalization workflow",
                 "topic_id": "ecology",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-bacterial-isolate-species-contamination-checking/versions/checking-expected-species-and-contamination-in-bacterial-isolate",
-                "tutorial_id": "bacterial-isolate-species-contamination-checking",
-                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/workflows/Checking-expected-species-and-contamination-in-bacterial-isolate.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/workflows/Checking-expected-species-and-contamination-in-bacterial-isolate.html",
-                "version": 2,
-                "wfid": "ecology-bacterial-isolate-species-contamination-checking",
-                "wfname": "checking-expected-species-and-contamination-in-bacterial-isolate",
-                "workflow": "Checking-expected-species-and-contamination-in-bacterial-isolate.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-Ecoregionalization_tutorial/versions/ecoregionalization-workflow",
+                "tutorial_id": "Ecoregionalization_tutorial",
+                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/Ecoregionalization_tutorial/workflows/Ecoregionalization_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/Ecoregionalization_tutorial/workflows/Ecoregionalization_workflow.html",
+                "version": 1,
+                "wfid": "ecology-Ecoregionalization_tutorial",
+                "wfname": "ecoregionalization-workflow",
+                "workflow": "Ecoregionalization_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0"
+                    "interactive_tool_jupyter_notebook",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_brt_analysis/ecoregion_brt_analysis/0.1.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_clara_cluster/ecoregion_clara_cluster/0.1.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_cluster_estimate/ecoregion_cluster_estimate/0.1.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_eco_map/ecoregion_eco_map/0.1.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_geonearestneighbor/ecoregion_GeoNearestNeighbor/0.1.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/ecoregion_taxa_seeker/ecoregion_taxa_seeker/0.1.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.0"
                 ],
-                "workflowhub_id": "1217"
+                "workflowhub_id": "1363"
             }
-        ],
-        "zenodo_link": "https://zenodo.org/record/10572227"
+        ]
     },
     {
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "f2e8552cf1d0",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "stacks_denovomap",
-                    "owner": "iuc",
-                    "revisions": "fdbcc560c691",
-                    "tool_panel_section_label": "RAD-seq",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "stacks_populations",
-                    "owner": "iuc",
-                    "revisions": "45db1ba16163",
-                    "tool_panel_section_label": "RAD-seq",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "stacks_procrad",
-                    "owner": "iuc",
-                    "revisions": "eded025438db",
-                    "tool_panel_section_label": "RAD-seq",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/ndvi_openeo/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "Marie59"
+            ],
+            "funding": [
+                "fairease",
+                "eurosciencegateway"
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastqc\n  owner: devteam\n  revisions: f2e8552cf1d0\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_denovomap\n  owner: iuc\n  revisions: fdbcc560c691\n  tool_panel_section_label: RAD-seq\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_populations\n  owner: iuc\n  revisions: 45db1ba16163\n  tool_panel_section_label: RAD-seq\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_procrad\n  owner: iuc\n  revisions: eded025438db\n  tool_panel_section_label: RAD-seq\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/de-novo-rad-seq/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
                     "pndb",
-                    "gallantries",
-                    "fairease",
-                    "fnso2019",
-                    "elixir-europe"
+                    "fairease"
                 ],
-                "elixir_node": "fr",
-                "email": "yvan.le-bras@mnhn.fr",
-                "id": "yvanlebras",
-                "joined": "2017-09",
-                "matrix": "yvanlebras:matrix.org",
-                "name": "Yvan Le Bras",
-                "orcid": "0000-0002-8504-068X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
-                "twitter": "Yvan2935",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
+                "email": "marie.josse@ifremer.fr",
+                "id": "Marie59",
+                "joined": "2022-03",
+                "name": "Marie Josse",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/fair_ease_colour.png",
+                "funder": true,
+                "funding_id": "101058785",
+                "funding_statement": "FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "fairease",
+                "joined": "2023-10",
+                "members": [
+                    "Marie59",
+                    "yvanlebras"
+                ],
+                "name": "Fair-Ease",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fairease/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/fairease.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/eurosciencegateway.png",
+                "funder": true,
+                "funding_id": "101057388",
+                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "eurosciencegateway",
+                "joined": "2023-10",
+                "members": [
+                    "abretaud",
+                    "anuprulez",
+                    "bgruening",
+                    "erxleben",
+                    "pauldg",
+                    "rlibouba"
+                ],
+                "name": "EuroScienceGateway",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
             }
         ],
-        "dir": "topics/ecology/tutorials/de-novo-rad-seq",
-        "edam_operation": [
-            "Sequencing quality control",
-            "Data handling",
-            "Sequence composition calculation",
-            "Statistical calculation"
-        ],
+        "dir": "topics/ecology/tutorials/ndvi_openeo",
+        "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu"
@@ -64947,41 +68559,35 @@
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "ecology/de-novo-rad-seq",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
-        ],
+        "id": "ecology/ndvi_openeo",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": null,
+        "key_points": [
+            "Manage NDVI data",
+            "Handle jupyterlab tools"
+        ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-27",
+        "mod_date": "2024-06-29",
         "objectives": [
-            "Analysis of RAD sequencing data without a reference genome",
-            "SNP calling from RAD sequencing data",
-            "Calculate population genomics statistics from RAD sequencing data"
+            "Use OpenEo technologies and learn how to download data with them",
+            "Learn to use Holoviz environment to process csv data",
+            "Create timeseries and visualisation of the NDVI",
+            "Handle going form one interactive tool to another"
         ],
-        "pageviews": 3812,
-        "pub_date": "2017-02-14",
+        "pageviews": 100,
+        "pub_date": "2024-01-24",
         "questions": [
-            "How to analyze RAD sequencing data without a reference genome for a population genomics study?"
-        ],
-        "redirect_from": [
-            "/topics/sequence-analysis/tutorials/de-novo-rad-seq/tutorial",
-            "/short/ecology/de-novo-rad-seq",
-            "/short/T00128"
+            "What's the NDVI ?",
+            "How to evaluate the NDVI through out time ?"
         ],
-        "short_id": "T00128",
+        "short_id": "T00400",
         "short_tools": [
-            "stacks_denovomap",
-            "fastqc",
-            "stacks_populations",
-            "stacks_procrad"
+            "interactive_tool_holoviz",
+            "interactive_tool_copernicus_notebook"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -64994,39 +68600,21 @@
                     "usegalaxy": true
                 }
             ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
+            "inexact": []
         },
         "symlink": null,
         "tags": [
-            "RAD-seq",
-            "Genetic composition EBV class",
-            "Species populations EBV class",
-            "EBV dataset",
-            "EBV workflow"
+            "earth-system",
+            "land degradation",
+            "NDVI",
+            "copernicus",
+            "holoviews"
         ],
-        "time_estimation": "8h",
-        "title": "RAD-Seq de-novo data analysis",
+        "time_estimation": "1H",
+        "title": "From NDVI data with OpenEO to time series visualisation with Holoviews",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69",
-            "toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/1.46.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/stacks_populations/stacks_populations/1.46.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0"
+            "interactive_tool_copernicus_notebook",
+            "interactive_tool_holoviz"
         ],
         "topic_name": "ecology",
         "topic_name_human": "Ecology",
@@ -65036,205 +68624,169 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "de-novo-rad-seq",
+        "tutorial_name": "ndvi_openeo",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/de-novo-rad-seq/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/ndvi_openeo/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/de-novo-rad-seq/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/de-novo-rad-seq/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/ndvi_openeo/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/ndvi_openeo/tutorial.json"
         },
-        "version": 12,
+        "version": 3,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 130,
-        "visitors": 2302,
+        "visit_duration": 53,
+        "visitors": 85,
         "workflows": [
             {
-                "creators": [],
-                "description": "RAD-Seq de-novo data analysis",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0009-0008-0622-604X",
+                        "name": "Marie Joss\u00e9",
+                        "url": "https://github.com/Marie59"
+                    }
+                ],
+                "description": "",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPopulation_map.txt\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBarcodes_SRR034310.tabular\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSRR034310.fastq\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nref_genome_chromFa.tar\"]\n  4[label=\"Stacks: process radtags\"]\n  1 -> 4 [label=\"output\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Stacks: process radtags\"]\n  1 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"Stacks: process radtags\"]\n  1 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"FastQC\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"Stacks: de novo map\"]\n  4 -> 8 [label=\"demultiplexed\"]\n  0 -> 8 [label=\"output\"]\n  9[label=\"Stacks: populations\"]\n  8 -> 9 [label=\"all_output\"]\n  0 -> 9 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Copernicus Data Space Ecosystem\"]\n  1[label=\"Holoviz\"]\n  0 -> 1 [label=\"output_collection\"]\n}",
+                "history": [
+                    {
+                        "hash": "76cb605583a35eb62c395933f9798887f5dd2164",
+                        "message": "fix license test",
+                        "num": 2,
+                        "short_hash": "76cb60558",
+                        "unix": "1705331890"
+                    },
+                    {
+                        "hash": "1b86f105a7a072e2405b937e816e682617fe779d",
+                        "message": "add test files",
+                        "num": 1,
+                        "short_hash": "1b86f105a",
+                        "unix": "1705326039"
+                    }
+                ],
+                "inputs": [],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"Copernicus Data Space Ecosystem\"];\n  1[\"Holoviz\"];\n  0 -->|output_collection| 1;",
+                "modified": "2024-10-02 12:08:07 +0000",
+                "name": "NDVI with OpenEO",
+                "outputs": [],
+                "parent_id": "ecology/ndvi_openeo",
+                "path": "topics/ecology/tutorials/ndvi_openeo/workflows/NDVI-with-OpenEO.ga",
+                "tags": [],
+                "test_results": null,
+                "tests": true,
+                "title": "NDVI with OpenEO",
+                "topic_id": "ecology",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-ndvi_openeo/versions/ndvi-with-openeo",
+                "tutorial_id": "ndvi_openeo",
+                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ndvi_openeo/workflows/NDVI-with-OpenEO.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ndvi_openeo/workflows/NDVI-with-OpenEO.html",
+                "version": 1,
+                "wfid": "ecology-ndvi_openeo",
+                "wfname": "ndvi-with-openeo",
+                "workflow": "NDVI-with-OpenEO.ga",
+                "workflow_tools": [
+                    "interactive_tool_copernicus_notebook",
+                    "interactive_tool_holoviz"
+                ],
+                "workflowhub_id": "1242"
+            },
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0009-0008-0622-604X",
+                        "name": "Marie Joss\u00e9",
+                        "url": "https://github.com/Marie59"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Copernicus Data Space Ecosystem\"]\n  1[label=\"Holoviz\"]\n  0 -> 1 [label=\"output_collection\"]\n}",
                 "history": [
                     {
-                        "hash": "00cfc1f0873c7eee656d05fd549f5cd3eae6a8da",
-                        "message": "out_fastp\u0125ase",
+                        "hash": "c9e46f370f0170707bf194000ba7d81dedb1eb56",
+                        "message": "fix license",
+                        "num": 6,
+                        "short_hash": "c9e46f370",
+                        "unix": "1705331825"
+                    },
+                    {
+                        "hash": "fb3bcc497acebb64dfa435efd224496615913356",
+                        "message": "add workflow",
                         "num": 5,
-                        "short_hash": "00cfc1f08",
-                        "unix": "1579699186"
+                        "short_hash": "fb3bcc497",
+                        "unix": "1705324903"
                     },
                     {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
+                        "hash": "0f88c406dde20fdb8f822000a7a6f10802d6d644",
+                        "message": "Delete topics/ecology/tutorials/ndvi_openeo/workflows/main_workflow.ga",
                         "num": 4,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
+                        "short_hash": "0f88c406d",
+                        "unix": "1705324823"
                     },
                     {
-                        "hash": "ea197f141d3c4fcf8f8e424604a5d40bf9125ce6",
-                        "message": "small changes",
+                        "hash": "9336c867093f14929f5eeb2f8ac7ca7e3484f4f0",
+                        "message": "add new workflow",
                         "num": 3,
-                        "short_hash": "ea197f141",
-                        "unix": "1579091409"
+                        "short_hash": "9336c8670",
+                        "unix": "1705317870"
                     },
                     {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
+                        "hash": "c8b1d5f64271724fb617321c267940f72c1cb062",
+                        "message": "Delete topics/ecology/tutorials/ndvi_openeo/workflows/main_workflow.ga",
                         "num": 2,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
+                        "short_hash": "c8b1d5f64",
+                        "unix": "1705317845"
                     },
                     {
-                        "hash": "bfc1c8c3f8660106a468dbfbc3af09af3e48da72",
-                        "message": "Move RAD-Seq tutorials to ecology topic",
+                        "hash": "9346f227c4a55267bedf0c2a76fb0c2b3fec185b",
+                        "message": "add ndvi openeo tuto",
                         "num": 1,
-                        "short_hash": "bfc1c8c3f",
-                        "unix": "1568279010"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Population_map.txt"
-                            }
-                        ],
-                        "label": "Population_map.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 200
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Population_map.txt\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "c070e872-bf5b-4690-85f8-20435bce6495",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Barcodes_SRR034310.tabular"
-                            }
-                        ],
-                        "label": "Barcodes_SRR034310.tabular",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 320
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Barcodes_SRR034310.tabular\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "27073ffe-9a96-4cee-a9c5-a95b9ab1e7c7",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "SRR034310.fastq"
-                            }
-                        ],
-                        "label": "SRR034310.fastq",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 560
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"SRR034310.fastq\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "16c3fb88-cdf5-418a-8e32-154bf142cca6",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "ref_genome_chromFa.tar"
-                            }
-                        ],
-                        "label": "ref_genome_chromFa.tar",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 440
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"ref_genome_chromFa.tar\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "50b66134-d154-425e-a66f-51e05f5edb58",
-                        "workflow_outputs": []
+                        "short_hash": "9346f227c",
+                        "unix": "1705076722"
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPopulation_map.txt\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nBarcodes_SRR034310.tabular\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nSRR034310.fastq\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nref_genome_chromFa.tar\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Stacks: process radtags\"];\n  1 -->|output| 4;\n  2 -->|output| 4;\n  5[\"Stacks: process radtags\"];\n  1 -->|output| 5;\n  2 -->|output| 5;\n  6[\"Stacks: process radtags\"];\n  1 -->|output| 6;\n  2 -->|output| 6;\n  7[\"FastQC\"];\n  2 -->|output| 7;\n  8[\"Stacks: de novo map\"];\n  4 -->|demultiplexed| 8;\n  0 -->|output| 8;\n  9[\"Stacks: populations\"];\n  8 -->|all_output| 9;\n  0 -->|output| 9;",
-                "modified": "2024-08-18 00:06:22 +0000",
-                "name": "de novo Rad Seq",
+                "inputs": [],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"Copernicus Data Space Ecosystem\"];\n  1[\"Holoviz\"];\n  0 -->|output_collection| 1;",
+                "modified": "2024-10-02 12:08:07 +0000",
+                "name": "NDVI with OpenEO",
                 "outputs": [],
-                "parent_id": "ecology/de-novo-rad-seq",
-                "path": "topics/ecology/tutorials/de-novo-rad-seq/workflows/Galaxy-Workflow-de-novo-rad-seq.ga",
-                "tags": [
-                    "ecology"
-                ],
+                "parent_id": "ecology/ndvi_openeo",
+                "path": "topics/ecology/tutorials/ndvi_openeo/workflows/main_workflow.ga",
+                "tags": [],
                 "test_results": null,
                 "tests": false,
-                "title": "de novo Rad Seq",
+                "title": "NDVI with OpenEO",
                 "topic_id": "ecology",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-de-novo-rad-seq/versions/galaxy-workflow-de-novo-rad-seq",
-                "tutorial_id": "de-novo-rad-seq",
-                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/de-novo-rad-seq/workflows/Galaxy-Workflow-de-novo-rad-seq.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/de-novo-rad-seq/workflows/Galaxy-Workflow-de-novo-rad-seq.html",
-                "version": 3,
-                "wfid": "ecology-de-novo-rad-seq",
-                "wfname": "galaxy-workflow-de-novo-rad-seq",
-                "workflow": "Galaxy-Workflow-de-novo-rad-seq.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-ndvi_openeo/versions/main-workflow",
+                "tutorial_id": "ndvi_openeo",
+                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ndvi_openeo/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ndvi_openeo/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "ecology-ndvi_openeo",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/1.46.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_populations/stacks_populations/1.46.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0"
+                    "interactive_tool_copernicus_notebook",
+                    "interactive_tool_holoviz"
                 ],
-                "workflowhub_id": "1286"
+                "workflowhub_id": "1239"
             }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.1134547"
+        ]
     },
     {
         "admin_install": {
@@ -65243,24 +68795,136 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "stacks_denovomap",
-                    "owner": "iuc",
-                    "revisions": "fdbcc560c691",
-                    "tool_panel_section_label": "RAD-seq",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "ddf54b12c295",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "stacks_genotypes",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "merge_cols",
+                    "owner": "devteam",
+                    "revisions": "dd40b1e9eebe",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pampa_communitymetrics",
+                    "owner": "ecology",
+                    "revisions": "c67ece97d4b1",
+                    "tool_panel_section_label": "Species abundance",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pampa_glmcomm",
+                    "owner": "ecology",
+                    "revisions": "b40fecef616b",
+                    "tool_panel_section_label": "Species abundance",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pampa_glmsp",
+                    "owner": "ecology",
+                    "revisions": "7a69e1c8ba46",
+                    "tool_panel_section_label": "Species abundance",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pampa_plotglm",
+                    "owner": "ecology",
+                    "revisions": "c448e026f122",
+                    "tool_panel_section_label": "Species abundance",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pampa_presabs",
+                    "owner": "ecology",
+                    "revisions": "1ebb70b59037",
+                    "tool_panel_section_label": "Species abundance",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "regex_find_replace",
+                    "owner": "galaxyp",
+                    "revisions": "209b7c5ee9d7",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "regex_find_replace",
+                    "owner": "galaxyp",
+                    "revisions": "209b7c5ee9d7",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "regex_find_replace",
+                    "owner": "galaxyp",
+                    "revisions": "ae8c4b2488e7",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "datamash_transpose",
                     "owner": "iuc",
-                    "revisions": "62a4b8e5e139",
-                    "tool_panel_section_label": "RAD-seq",
+                    "revisions": "22c2a1ac7ae3",
+                    "tool_panel_section_label": "Join, Subtract and Group",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: stacks_denovomap\n  owner: iuc\n  revisions: fdbcc560c691\n  tool_panel_section_label: RAD-seq\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stacks_genotypes\n  owner: iuc\n  revisions: 62a4b8e5e139\n  tool_panel_section_label: RAD-seq\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/genetic-map-rad-seq/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: ddf54b12c295\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merge_cols\n  owner: devteam\n  revisions: dd40b1e9eebe\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pampa_communitymetrics\n  owner: ecology\n  revisions: c67ece97d4b1\n  tool_panel_section_label: Species abundance\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pampa_glmcomm\n  owner: ecology\n  revisions: b40fecef616b\n  tool_panel_section_label: Species abundance\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pampa_glmsp\n  owner: ecology\n  revisions: 7a69e1c8ba46\n  tool_panel_section_label: Species abundance\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pampa_plotglm\n  owner: ecology\n  revisions: c448e026f122\n  tool_panel_section_label: Species abundance\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pampa_presabs\n  owner: ecology\n  revisions: 1ebb70b59037\n  tool_panel_section_label: Species abundance\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 209b7c5ee9d7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 209b7c5ee9d7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: ae8c4b2488e7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_transpose\n  owner: iuc\n  revisions: 22c2a1ac7ae3\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "colineroyaux",
+                "yvanlebras",
+                "dpelletier",
+                "jbmihoub"
+            ],
+            "funding": [
+                "gallantries",
+                "pndb"
+            ]
+        },
         "contributors": [
+            {
+                "affiliations": [
+                    "pndb",
+                    "gallantries",
+                    "elixir-europe"
+                ],
+                "elixir_node": "fr",
+                "email": "coline.royaux@mnhn.fr",
+                "id": "colineroyaux",
+                "joined": "2020-11",
+                "name": "Coline Royaux",
+                "orcid": "0000-0003-4308-5617",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/",
+                "twitter": "ColineRoyaux",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/colineroyaux.json"
+            },
             {
                 "affiliations": [
                     "pndb",
@@ -65279,70 +68943,159 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
                 "twitter": "Yvan2935",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
+            },
+            {
+                "id": "dpelletier",
+                "joined": "2022-03",
+                "name": "Dominique Pelletier",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dpelletier/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/dpelletier.json"
+            },
+            {
+                "email": "jean-baptiste.mihoub@mnhn.fr",
+                "id": "jbmihoub",
+                "joined": "2022-03",
+                "name": "Jean-Baptiste Mihoub",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jbmihoub/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jbmihoub.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/PNDB_sub.png",
+                "github": false,
+                "id": "pndb",
+                "members": [
+                    "colineroyaux",
+                    "Marie59",
+                    "ThibaudGlinez",
+                    "yvanlebras"
+                ],
+                "name": "P\u00f4le National de Donn\u00e9es de Biodiversit\u00e9",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pndb/",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/pndb.json"
             }
         ],
-        "dir": "topics/ecology/tutorials/genetic-map-rad-seq",
-        "edam_operation": [
-            "Data handling"
-        ],
+        "dir": "topics/ecology/tutorials/PAMPA-toolsuite-tutorial",
+        "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "ecology/genetic-map-rad-seq",
-        "inexact_supported_servers": [],
+        "id": "ecology/PAMPA-toolsuite-tutorial",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.fr",
+            "UseGalaxy.org.au"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": null,
+        "key_points": [
+            "Pre-process abundance data",
+            "Compute Community and Population metrics",
+            "Construct a GL(M)M with common biodiversity metrics",
+            "Interpret (and correct if needed) GL(M)M results",
+            "Learn about and interpret common tests to evaluate the quality of your GL(M)M",
+            "Use an Essential Biodiversity Variables workflow"
+        ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2024-06-27",
         "objectives": [
-            "SNP calling from RAD sequencing data",
-            "Find and correct haplotypes",
-            "Create input files for genetic map building software"
+            "Upload data from DATRAS portal of ICES",
+            "Pre-process population data with Galaxy",
+            "Learning how to use an ecological analysis workflow from raw data to graphical representations",
+            "Learning how to construct a Generalized Linear (Mixed) Model from a usual ecological question",
+            "Learning how to interpret a Generalized Linear (Mixed) Model"
         ],
-        "pageviews": 1088,
-        "pub_date": "2017-02-14",
+        "pageviews": 1285,
+        "pub_date": "2020-11-19",
         "questions": [
-            "How to analyze RAD sequencing data for a genetic map study?"
+            "How to evaluate properly populations and communities biological state with abundance data?",
+            "How does trawl exploited populations of Baltic sea, Southern Atlantic and Scotland are doing over time?",
+            "How to compute and analyze biodiversity metrics from abundance data?"
         ],
-        "redirect_from": [
-            "/topics/sequence-analysis/tutorials/genetic-map-rad-seq/tutorial",
-            "/short/ecology/genetic-map-rad-seq",
-            "/short/T00130"
+        "recordings": [
+            {
+                "captioners": [
+                    "colineroyaux"
+                ],
+                "date": "2022-03-03",
+                "galaxy_version": "21.09",
+                "length": "2H",
+                "speakers": [
+                    "colineroyaux"
+                ],
+                "youtube_id": "leMPC2Ckehc"
+            }
         ],
-        "short_id": "T00130",
+        "short_id": "T00125",
         "short_tools": [
-            "stacks_denovomap",
-            "stacks_genotypes"
+            "Count1",
+            "tp_easyjoin_tool",
+            "tp_cat",
+            "mergeCols1",
+            "Filter1",
+            "pampa_glmcomm",
+            "pampa_plotglm",
+            "tp_sort_header_tool",
+            "pampa_glmsp",
+            "pampa_presabs",
+            "datamash_transpose",
+            "regexColumn1",
+            "tp_cut_tool",
+            "pampa_communitymetrics",
+            "regex1"
         ],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "ecologyanalysis",
         "supported_servers": {
             "exact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
                     "usegalaxy": false
                 },
                 {
@@ -65350,21 +69103,35 @@
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
                 }
-            ],
-            "inexact": []
+            ]
         },
         "symlink": null,
         "tags": [
-            "RAD-seq",
-            "Genetic composition EBV class",
+            "Species population EBV class",
+            "Community composition EBV class",
             "EBV dataset",
-            "EBV workflow"
+            "EBV workflow",
+            "modeling"
         ],
-        "time_estimation": "8h",
-        "title": "RAD-Seq to construct genetic maps",
+        "time_estimation": "2H",
+        "title": "Compute and analyze biodiversity metrics with PAMPA toolsuite",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/1.46.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/stacks_genotypes/stacks_genotypes/1.46.0"
+            "Count1",
+            "Filter1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.2",
+            "toolshed.g2.bx.psu.edu/repos/ecology/pampa_communitymetrics/pampa_communitymetrics/0.0.2",
+            "toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmcomm/pampa_glmcomm/0.0.2",
+            "toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmsp/pampa_glmsp/0.0.2",
+            "toolshed.g2.bx.psu.edu/repos/ecology/pampa_plotglm/pampa_plotglm/0.0.2",
+            "toolshed.g2.bx.psu.edu/repos/ecology/pampa_presabs/pampa_presabs/0.0.2",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0"
         ],
         "topic_name": "ecology",
         "topic_name_human": "Ecology",
@@ -65374,558 +69141,78 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "genetic-map-rad-seq",
+        "tutorial_name": "PAMPA-toolsuite-tutorial",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/genetic-map-rad-seq/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/genetic-map-rad-seq/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/genetic-map-rad-seq/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.json"
         },
-        "version": 12,
+        "version": 21,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 83,
-        "visitors": 747,
+        "visit_duration": 109,
+        "visitors": 962,
         "workflows": [
             {
                 "creators": [],
-                "description": "RAD-Seq to construct genetic maps",
+                "description": "Compute and analyze biodiversity metrics with PAMPA toolsuite",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  9[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  10[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  11[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  12[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  13[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  14[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  15[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  16[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  17[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  18[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  19[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  20[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  21[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  22[label=\"Stacks: de novo map\"]\n  1 -> 22 [label=\"output\"]\n  0 -> 22 [label=\"output\"]\n  15 -> 22 [label=\"output\"]\n  14 -> 22 [label=\"output\"]\n  13 -> 22 [label=\"output\"]\n  12 -> 22 [label=\"output\"]\n  11 -> 22 [label=\"output\"]\n  10 -> 22 [label=\"output\"]\n  9 -> 22 [label=\"output\"]\n  8 -> 22 [label=\"output\"]\n  7 -> 22 [label=\"output\"]\n  6 -> 22 [label=\"output\"]\n  5 -> 22 [label=\"output\"]\n  4 -> 22 [label=\"output\"]\n  3 -> 22 [label=\"output\"]\n  2 -> 22 [label=\"output\"]\n  17 -> 22 [label=\"output\"]\n  18 -> 22 [label=\"output\"]\n  19 -> 22 [label=\"output\"]\n  20 -> 22 [label=\"output\"]\n  21 -> 22 [label=\"output\"]\n  16 -> 22 [label=\"output\"]\n  23[label=\"Stacks: genotypes\"]\n  22 -> 23 [label=\"all_output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  3[label=\"Column Regex Find And Replace\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Column Regex Find And Replace\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Concatenate datasets\"]\n  2 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Column Regex Find And Replace\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"Merge Columns\"]\n  3 -> 7 [label=\"out_file1\"]\n  8[label=\"Merge Columns\"]\n  4 -> 8 [label=\"out_file1\"]\n  9[label=\"Count\"]\n  5 -> 9 [label=\"out_file1\"]\n  10[label=\"Filter\"]\n  5 -> 10 [label=\"out_file1\"]\n  11[label=\"Merge Columns\"]\n  6 -> 11 [label=\"out_file1\"]\n  12[label=\"Regex Find And Replace\"]\n  7 -> 12 [label=\"out_file1\"]\n  13[label=\"Regex Find And Replace\"]\n  8 -> 13 [label=\"out_file1\"]\n  14[label=\"Column Regex Find And Replace\"]\n  10 -> 14 [label=\"out_file1\"]\n  15[label=\"Regex Find And Replace\"]\n  11 -> 15 [label=\"out_file1\"]\n  16[label=\"Calculate presence absence table\"]\n  12 -> 16 [label=\"out_file1\"]\n  17[label=\"Calculate presence absence table\"]\n  13 -> 17 [label=\"out_file1\"]\n  18[label=\"Merge Columns\"]\n  14 -> 18 [label=\"out_file1\"]\n  19[label=\"Calculate presence absence table\"]\n  15 -> 19 [label=\"out_file1\"]\n  20[label=\"Regex Find And Replace\"]\n  18 -> 20 [label=\"out_file1\"]\n  21[label=\"Calculate community metrics\"]\n  20 -> 21 [label=\"out_file1\"]\n  22[label=\"Column Regex Find And Replace\"]\n  20 -> 22 [label=\"out_file1\"]\n  23[label=\"Merge Columns\"]\n  22 -> 23 [label=\"out_file1\"]\n  24[label=\"Column Regex Find And Replace\"]\n  23 -> 24 [label=\"out_file1\"]\n  25[label=\"Advanced Cut\"]\n  24 -> 25 [label=\"out_file1\"]\n  26[label=\"Sort\"]\n  25 -> 26 [label=\"output\"]\n  27[label=\"Regex Find And Replace\"]\n  26 -> 27 [label=\"outfile\"]\n  28[label=\"Compute GLM on community data\"]\n  21 -> 28 [label=\"output_community\"]\n  27 -> 28 [label=\"out_file1\"]\n  29[label=\"Compute GLM on population data\"]\n  16 -> 29 [label=\"output_presabs\"]\n  27 -> 29 [label=\"out_file1\"]\n  30[label=\"Compute GLM on population data\"]\n  17 -> 30 [label=\"output_presabs\"]\n  27 -> 30 [label=\"out_file1\"]\n  31[label=\"Compute GLM on population data\"]\n  19 -> 31 [label=\"output_presabs\"]\n  27 -> 31 [label=\"out_file1\"]\n  32[label=\"Transpose\"]\n  28 -> 32 [label=\"output_summary\"]\n  33[label=\"Create a plot from GLM data\"]\n  21 -> 33 [label=\"output_community\"]\n  28 -> 33 [label=\"output_summary\"]\n  27 -> 33 [label=\"out_file1\"]\n  34[label=\"Transpose\"]\n  29 -> 34 [label=\"output_summary\"]\n  35[label=\"Create a plot from GLM data\"]\n  16 -> 35 [label=\"output_presabs\"]\n  29 -> 35 [label=\"output_summary\"]\n  27 -> 35 [label=\"out_file1\"]\n  36[label=\"Transpose\"]\n  30 -> 36 [label=\"output_summary\"]\n  37[label=\"Create a plot from GLM data\"]\n  17 -> 37 [label=\"output_presabs\"]\n  30 -> 37 [label=\"output_summary\"]\n  27 -> 37 [label=\"out_file1\"]\n  38[label=\"Transpose\"]\n  31 -> 38 [label=\"output_summary\"]\n  39[label=\"Create a plot from GLM data\"]\n  19 -> 39 [label=\"output_presabs\"]\n  31 -> 39 [label=\"output_summary\"]\n  27 -> 39 [label=\"out_file1\"]\n}",
                 "history": [
                     {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 3,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 2,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "bfc1c8c3f8660106a468dbfbc3af09af3e48da72",
-                        "message": "Move RAD-Seq tutorials to ecology topic",
-                        "num": 1,
-                        "short_hash": "bfc1c8c3f",
-                        "unix": "1568279010"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "female.fa"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 10
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"female.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "2c38288c-adb6-4ac2-99a7-1f2bbb97e366",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "male.fa"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 130
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"male.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "cfa7a746-2f03-4eca-bea8-2c6a14173e3c",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "progeny_1.fa"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 250
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_1.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "07615ec4-10af-4a33-a3b4-12cb107ede8f",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "progeny_2.fa"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 370
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_2.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "e1ecc352-8a19-409a-a5a6-282721ffd482",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "progeny_3.fa"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 490
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_3.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "21648aa0-f3e7-4378-ba1f-f8cdca509d61",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "progeny_4.fa"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 610
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_4.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ca90884a-02b6-4685-95c1-62aed3267897",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "progeny_5.fa"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 730
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_5.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "cb156339-4a67-4539-943a-15de7e5880fc",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "progeny_6.fa"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 850
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_6.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "dfc34c06-efcc-40d8-a4d5-665629f25a0f",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "progeny_7.fa"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 970
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_7.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f30601cb-218c-4f1c-a5ec-1d97bea49294",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "progeny_8.fa"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 1090
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_8.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "bcc298aa-5437-4cca-a8d4-f1414bd70455",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 10,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "progeny_9.fa"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 1210
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_9.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "0c0ad65a-2df5-4aef-bcd2-db4a570aed81",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 11,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "progeny_10.fa"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 1330
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_10.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "3de49992-fc60-43c6-a8f5-dd34c29ace1c",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 12,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "progeny_11.fa"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 1450
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_11.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "9d20cab4-c732-45bd-9b68-7bf5b0a2c9c0",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 13,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "progeny_12.fa"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 1570
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_12.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "c1786041-32ff-4079-b653-5cfe682bc041",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 14,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "progeny_13.fa"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 1690
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_13.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "89f8ce6d-21ea-4f07-9b15-58882b39d0ca",
-                        "workflow_outputs": []
+                        "hash": "59d712ff30d5e8f4a5355ce2b2822e412b669f5c",
+                        "message": "Third version with good tag",
+                        "num": 5,
+                        "short_hash": "59d712ff3",
+                        "unix": "1614183047"
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 15,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "progeny_14.fa"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 1810
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_14.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "6f7e59de-f796-4c80-a8aa-e70efe9c022b",
-                        "workflow_outputs": []
+                        "hash": "76a4fcec2322203b57409cde43b42061d5342467",
+                        "message": "Delete Galaxy-Workflow-Compute_and_analyze_biodiversity_metrics_with_PAMPA_toolsuite.ga",
+                        "num": 4,
+                        "short_hash": "76a4fcec2",
+                        "unix": "1614183020"
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 16,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "progeny_15.fa"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 1930
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_15.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "91e4dc8a-84a2-4530-aeab-2130270c7514",
-                        "workflow_outputs": []
+                        "hash": "5dc93ca540b20999ab654de39a3a117ea0e48342",
+                        "message": "Add updated workflow",
+                        "num": 3,
+                        "short_hash": "5dc93ca54",
+                        "unix": "1614182846"
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 17,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "progeny_16.fa"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 2050
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_16.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "cb53dbf8-f79a-4374-bef4-8eec9adef44e",
-                        "workflow_outputs": []
+                        "hash": "a4b073fcc3bb5affb1f9bf70f3c659b6a80efdbf",
+                        "message": "Delete Galaxy-Workflow-Compute_and_analyze_biodiversity_metrics_with_PAMPA_toolsuite.ga",
+                        "num": 2,
+                        "short_hash": "a4b073fcc",
+                        "unix": "1614182812"
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 18,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "progeny_17.fa"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 2170
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_17.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "4a8a8a60-e631-473c-aaaa-e61f627da84d",
-                        "workflow_outputs": []
-                    },
+                        "hash": "87b82c19f54fa91e697b2ecd8b70b61a61e0d57e",
+                        "message": "Add tutorial workflow",
+                        "num": 1,
+                        "short_hash": "87b82c19f",
+                        "unix": "1614181101"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 19,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "progeny_18.fa"
+                                "name": "https://zenodo.org/record/4264936/files/CPUE%20per%20length%20per%20area_A.csv?download=1"
                             }
                         ],
                         "label": null,
@@ -65933,25 +69220,25 @@
                         "outputs": [],
                         "position": {
                             "left": 10,
-                            "top": 2290
+                            "top": 10
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_18.fa\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "e9235e06-b5ca-432a-8723-41134cc00832",
+                        "uuid": "07e9c5f6-f826-496c-b900-5c22fd643fb4",
                         "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 20,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "progeny_19.fa"
+                                "name": "https://zenodo.org/record/4264936/files/CPUE%20per%20length%20per%20area_B.csv?download=1"
                             }
                         ],
                         "label": null,
@@ -65959,25 +69246,25 @@
                         "outputs": [],
                         "position": {
                             "left": 10,
-                            "top": 2410
+                            "top": 130
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_19.fa\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "d6ceab00-6bff-474a-9e4e-21e1a9997756",
+                        "uuid": "9ad55992-d9e2-4263-bbe7-31dc551f81fd",
                         "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 21,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "progeny_20.fa"
+                                "name": "https://zenodo.org/record/4264936/files/CPUE%20per%20length%20per%20area_C.csv?download=1"
                             }
                         ],
                         "label": null,
@@ -65985,46 +69272,59 @@
                         "outputs": [],
                         "position": {
                             "left": 10,
-                            "top": 2530
+                            "top": 250
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"progeny_20.fa\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "b293304f-da0b-45ef-a2b9-94a9a747bfa5",
+                        "uuid": "d80371d8-924c-4f37-8081-cc3a9201ba4a",
                         "workflow_outputs": []
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 9 stroke:#2c3143,stroke-width:4px;\n  10[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 10 stroke:#2c3143,stroke-width:4px;\n  11[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 11 stroke:#2c3143,stroke-width:4px;\n  12[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 12 stroke:#2c3143,stroke-width:4px;\n  13[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 13 stroke:#2c3143,stroke-width:4px;\n  14[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 14 stroke:#2c3143,stroke-width:4px;\n  15[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 15 stroke:#2c3143,stroke-width:4px;\n  16[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 16 stroke:#2c3143,stroke-width:4px;\n  17[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 17 stroke:#2c3143,stroke-width:4px;\n  18[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 18 stroke:#2c3143,stroke-width:4px;\n  19[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 19 stroke:#2c3143,stroke-width:4px;\n  20[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 20 stroke:#2c3143,stroke-width:4px;\n  21[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 21 stroke:#2c3143,stroke-width:4px;\n  22[\"Stacks: de novo map\"];\n  1 -->|output| 22;\n  0 -->|output| 22;\n  15 -->|output| 22;\n  14 -->|output| 22;\n  13 -->|output| 22;\n  12 -->|output| 22;\n  11 -->|output| 22;\n  10 -->|output| 22;\n  9 -->|output| 22;\n  8 -->|output| 22;\n  7 -->|output| 22;\n  6 -->|output| 22;\n  5 -->|output| 22;\n  4 -->|output| 22;\n  3 -->|output| 22;\n  2 -->|output| 22;\n  17 -->|output| 22;\n  18 -->|output| 22;\n  19 -->|output| 22;\n  20 -->|output| 22;\n  21 -->|output| 22;\n  16 -->|output| 22;\n  23[\"Stacks: genotypes\"];\n  22 -->|all_output| 23;",
-                "modified": "2024-08-18 00:06:22 +0000",
-                "name": "Genetic Map Rad Seq Workflow",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Column Regex Find And Replace\"];\n  0 -->|output| 3;\n  4[\"Column Regex Find And Replace\"];\n  1 -->|output| 4;\n  5[\"Concatenate datasets\"];\n  2 -->|output| 5;\n  1 -->|output| 5;\n  0 -->|output| 5;\n  6[\"Column Regex Find And Replace\"];\n  2 -->|output| 6;\n  7[\"Merge Columns\"];\n  3 -->|out_file1| 7;\n  8[\"Merge Columns\"];\n  4 -->|out_file1| 8;\n  9[\"Count\"];\n  5 -->|out_file1| 9;\n  10[\"Filter\"];\n  5 -->|out_file1| 10;\n  11[\"Merge Columns\"];\n  6 -->|out_file1| 11;\n  12[\"Regex Find And Replace\"];\n  7 -->|out_file1| 12;\n  13[\"Regex Find And Replace\"];\n  8 -->|out_file1| 13;\n  14[\"Column Regex Find And Replace\"];\n  10 -->|out_file1| 14;\n  15[\"Regex Find And Replace\"];\n  11 -->|out_file1| 15;\n  16[\"Calculate presence absence table\"];\n  12 -->|out_file1| 16;\n  17[\"Calculate presence absence table\"];\n  13 -->|out_file1| 17;\n  18[\"Merge Columns\"];\n  14 -->|out_file1| 18;\n  19[\"Calculate presence absence table\"];\n  15 -->|out_file1| 19;\n  20[\"Regex Find And Replace\"];\n  18 -->|out_file1| 20;\n  21[\"Calculate community metrics\"];\n  20 -->|out_file1| 21;\n  22[\"Column Regex Find And Replace\"];\n  20 -->|out_file1| 22;\n  23[\"Merge Columns\"];\n  22 -->|out_file1| 23;\n  24[\"Column Regex Find And Replace\"];\n  23 -->|out_file1| 24;\n  25[\"Advanced Cut\"];\n  24 -->|out_file1| 25;\n  26[\"Sort\"];\n  25 -->|output| 26;\n  27[\"Regex Find And Replace\"];\n  26 -->|outfile| 27;\n  28[\"Compute GLM on community data\"];\n  21 -->|output_community| 28;\n  27 -->|out_file1| 28;\n  29[\"Compute GLM on population data\"];\n  16 -->|output_presabs| 29;\n  27 -->|out_file1| 29;\n  30[\"Compute GLM on population data\"];\n  17 -->|output_presabs| 30;\n  27 -->|out_file1| 30;\n  31[\"Compute GLM on population data\"];\n  19 -->|output_presabs| 31;\n  27 -->|out_file1| 31;\n  32[\"Transpose\"];\n  28 -->|output_summary| 32;\n  33[\"Create a plot from GLM data\"];\n  21 -->|output_community| 33;\n  28 -->|output_summary| 33;\n  27 -->|out_file1| 33;\n  34[\"Transpose\"];\n  29 -->|output_summary| 34;\n  35[\"Create a plot from GLM data\"];\n  16 -->|output_presabs| 35;\n  29 -->|output_summary| 35;\n  27 -->|out_file1| 35;\n  36[\"Transpose\"];\n  30 -->|output_summary| 36;\n  37[\"Create a plot from GLM data\"];\n  17 -->|output_presabs| 37;\n  30 -->|output_summary| 37;\n  27 -->|out_file1| 37;\n  38[\"Transpose\"];\n  31 -->|output_summary| 38;\n  39[\"Create a plot from GLM data\"];\n  19 -->|output_presabs| 39;\n  31 -->|output_summary| 39;\n  27 -->|out_file1| 39;",
+                "modified": "2024-10-02 12:08:07 +0000",
+                "name": "Compute and analyze biodiversity metrics with PAMPA toolsuite",
                 "outputs": [],
-                "parent_id": "ecology/genetic-map-rad-seq",
-                "path": "topics/ecology/tutorials/genetic-map-rad-seq/workflows/genetic-map-rad-seq.ga",
+                "parent_id": "ecology/PAMPA-toolsuite-tutorial",
+                "path": "topics/ecology/tutorials/PAMPA-toolsuite-tutorial/workflows/Galaxy-Workflow-Compute_and_analyze_biodiversity_metrics_with_PAMPA_toolsuite.ga",
                 "tags": [
                     "ecology"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Genetic Map Rad Seq Workflow",
+                "title": "Compute and analyze biodiversity metrics with PAMPA toolsuite",
                 "topic_id": "ecology",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-genetic-map-rad-seq/versions/genetic-map-rad-seq",
-                "tutorial_id": "genetic-map-rad-seq",
-                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/genetic-map-rad-seq/workflows/genetic-map-rad-seq.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/genetic-map-rad-seq/workflows/genetic-map-rad-seq.html",
-                "version": 3,
-                "wfid": "ecology-genetic-map-rad-seq",
-                "wfname": "genetic-map-rad-seq",
-                "workflow": "genetic-map-rad-seq.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-PAMPA-toolsuite-tutorial/versions/galaxy-workflow-compute-and-analyze-biodiversity-metrics-with-pampa-toolsuite",
+                "tutorial_id": "PAMPA-toolsuite-tutorial",
+                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/workflows/Galaxy-Workflow-Compute_and_analyze_biodiversity_metrics_with_PAMPA_toolsuite.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/workflows/Galaxy-Workflow-Compute_and_analyze_biodiversity_metrics_with_PAMPA_toolsuite.html",
+                "version": 1,
+                "wfid": "ecology-PAMPA-toolsuite-tutorial",
+                "wfname": "galaxy-workflow-compute-and-analyze-biodiversity-metrics-with-pampa-toolsuite",
+                "workflow": "Galaxy-Workflow-Compute_and_analyze_biodiversity_metrics_with_PAMPA_toolsuite.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/1.46.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/stacks_genotypes/stacks_genotypes/1.46.0"
+                    "Count1",
+                    "Filter1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/pampa_communitymetrics/pampa_communitymetrics/0.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmcomm/pampa_glmcomm/0.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmsp/pampa_glmsp/0.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/pampa_plotglm/pampa_plotglm/0.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/pampa_presabs/pampa_presabs/0.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0"
                 ],
-                "workflowhub_id": "1216"
+                "workflowhub_id": "1283"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.1219888"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.4264936"
     },
     {
         "admin_install": {
@@ -66033,54 +69333,168 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "graphicsmagick_image_montage",
+                    "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "a0f01c777820",
-                    "tool_panel_section_label": "Convert Formats",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cdo_operations",
-                    "owner": "climate",
-                    "revisions": "d5355f6fa02b",
-                    "tool_panel_section_label": "Climate Analysis",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "12615d397df7",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "xarray_coords_info",
+                    "name": "obis_data",
                     "owner": "ecology",
-                    "revisions": "3e73f657a998",
-                    "tool_panel_section_label": "GIS Data Handling",
+                    "revisions": "1fcd81d65467",
+                    "tool_panel_section_label": "Get Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "xarray_mapplot",
+                    "name": "obisindicators",
                     "owner": "ecology",
-                    "revisions": "dc05bf0af58f",
-                    "tool_panel_section_label": "GIS Data Handling",
+                    "revisions": "1015a0070bac",
+                    "tool_panel_section_label": "Biodiversity data exploration",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "xarray_metadata_info",
+                    "name": "obisindicators",
                     "owner": "ecology",
-                    "revisions": "e8650cdf092f",
-                    "tool_panel_section_label": "GIS Data Handling",
+                    "revisions": "393957ecc97d",
+                    "tool_panel_section_label": "Biodiversity data exploration",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: graphicsmagick_image_montage\n  owner: bgruening\n  revisions: a0f01c777820\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cdo_operations\n  owner: climate\n  revisions: d5355f6fa02b\n  tool_panel_section_label: Climate Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xarray_coords_info\n  owner: ecology\n  revisions: 3e73f657a998\n  tool_panel_section_label: GIS Data Handling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xarray_mapplot\n  owner: ecology\n  revisions: dc05bf0af58f\n  tool_panel_section_label: GIS Data Handling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xarray_metadata_info\n  owner: ecology\n  revisions: e8650cdf092f\n  tool_panel_section_label: GIS Data Handling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/x-array-map-plot/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 12615d397df7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obis_data\n  owner: ecology\n  revisions: 1fcd81d65467\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obisindicators\n  owner: ecology\n  revisions: 1015a0070bac\n  tool_panel_section_label: Biodiversity data exploration\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obisindicators\n  owner: ecology\n  revisions: 393957ecc97d\n  tool_panel_section_label: Biodiversity data exploration\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/obisindicators/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "Marie59",
+                "yvanlebras"
+            ],
+            "funding": [
+                "gallantries",
+                "fairease",
+                "eurosciencegateway",
+                "pndb"
+            ]
+        },
         "contributors": [
             {
-                "id": "Quickbeasts51429",
-                "joined": "2022-06",
-                "name": "Soumya Jha",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Quickbeasts51429/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/Quickbeasts51429.json"
+                "affiliations": [
+                    "pndb",
+                    "fairease"
+                ],
+                "email": "marie.josse@ifremer.fr",
+                "id": "Marie59",
+                "joined": "2022-03",
+                "name": "Marie Josse",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
+            },
+            {
+                "affiliations": [
+                    "pndb",
+                    "gallantries",
+                    "fairease",
+                    "fnso2019",
+                    "elixir-europe"
+                ],
+                "elixir_node": "fr",
+                "email": "yvan.le-bras@mnhn.fr",
+                "id": "yvanlebras",
+                "joined": "2017-09",
+                "matrix": "yvanlebras:matrix.org",
+                "name": "Yvan Le Bras",
+                "orcid": "0000-0002-8504-068X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
+                "twitter": "Yvan2935",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/fair_ease_colour.png",
+                "funder": true,
+                "funding_id": "101058785",
+                "funding_statement": "FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "fairease",
+                "joined": "2023-10",
+                "members": [
+                    "Marie59",
+                    "yvanlebras"
+                ],
+                "name": "Fair-Ease",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fairease/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/fairease.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/eurosciencegateway.png",
+                "funder": true,
+                "funding_id": "101057388",
+                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "eurosciencegateway",
+                "joined": "2023-10",
+                "members": [
+                    "abretaud",
+                    "anuprulez",
+                    "bgruening",
+                    "erxleben",
+                    "pauldg",
+                    "rlibouba"
+                ],
+                "name": "EuroScienceGateway",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/PNDB_sub.png",
+                "github": false,
+                "id": "pndb",
+                "members": [
+                    "colineroyaux",
+                    "Marie59",
+                    "ThibaudGlinez",
+                    "yvanlebras"
+                ],
+                "name": "P\u00f4le National de Donn\u00e9es de Biodiversit\u00e9",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pndb/",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/pndb.json"
             }
         ],
-        "dir": "topics/ecology/tutorials/x-array-map-plot",
+        "dir": "topics/ecology/tutorials/obisindicators",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -66089,55 +69503,37 @@
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "ecology/x-array-map-plot",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz"
-        ],
+        "id": "ecology/obisindicators",
+        "inexact_supported_servers": [],
         "js_requirements": {
-            "mathjax": null,
+            "mathjax": 8847,
             "mermaid": false
         },
         "key_points": [
-            "NetCDF xarray climate data visualization",
-            "NetCDF xarray map plotting projections",
-            "NetCDF xarray map plotting colormaps"
+            "Marine data",
+            "Diversity indicators"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
         "license": "CC-BY-4.0",
         "mod_date": "2024-06-27",
         "objectives": [
-            "Learn about plotting Climate Data",
-            "Learn about NetCDF xarray map plotting tool",
-            "Learn about visualizing the climate data using NetCDF xarray map plotting using the different kinds of projections and colormap options"
+            "Calculating and vizualizing marine biodiversity indicators"
         ],
-        "pageviews": 2253,
-        "pub_date": "2022-10-26",
+        "pageviews": 220,
+        "pub_date": "2023-04-11",
         "questions": [
-            "What is xarray map plotting?",
-            "How to plot NetCDF data using xarray map plotting tool?",
-            "What are the different types of projections and colormap options available in the tool?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "climate",
-                "tutorials": [
-                    "climate-101"
-                ],
-                "type": "internal"
-            }
+            "How to retrieve Obis data with Galaxy ?",
+            "How can you analyse and visualise them ?"
         ],
-        "short_id": "T00136",
+        "short_id": "T00332",
         "short_tools": [
-            "cdo_operations",
-            "graphicsmagick_image_montage",
-            "xarray_coords_info",
-            "xarray_metadata_info",
-            "xarray_mapplot"
+            "tp_cut_tool",
+            "obis_data",
+            "obisindicators"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "ecologyviz",
+        "subtopic": "ecologyanalysis",
         "supported_servers": {
             "exact": [
                 {
@@ -66146,26 +69542,23 @@
                     "usegalaxy": true
                 }
             ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                }
-            ]
+            "inexact": []
         },
         "symlink": null,
         "tags": [
-            "pangeo"
+            "earth-system",
+            "ocean",
+            "marine omics",
+            "biodiversity"
         ],
         "time_estimation": "1H",
-        "title": "Visualization of Climate Data using  NetCDF xarray Map Plotting",
+        "title": "Obis marine indicators",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage/1.3.31+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/climate/cdo_operations/cdo_operations/2.0.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/0.20.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.20.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2",
+            "toolshed.g2.bx.psu.edu/repos/ecology/obisindicators/obisindicators/0.0.1",
+            "toolshed.g2.bx.psu.edu/repos/ecology/obisindicators/obisindicators/0.0.2"
         ],
         "topic_name": "ecology",
         "topic_name_human": "Ecology",
@@ -66175,530 +69568,757 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "x-array-map-plot",
+        "tutorial_name": "obisindicators",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/x-array-map-plot/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/obisindicators/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/x-array-map-plot/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/x-array-map-plot/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/obisindicators/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/obisindicators/tutorial.json"
         },
-        "version": 9,
+        "version": 8,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 31,
-        "visitors": 1924,
+        "visit_duration": 126,
+        "visitors": 180,
         "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "Quickbeasts51429",
-                        "name": "Soumya Jha"
+                        "identifier": "0009-0008-0622-604X",
+                        "name": "Marie Joss\u00e9",
+                        "url": "https://github.com/Marie59"
                     }
                 ],
-                "description": "Visualization of Climate Data using NetCDF Xarray Map Plotting",
+                "description": "From Obis data to Biodiversity indicators",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nair_temperature_at_2_metres.nc\"]\n  1[label=\"NetCDF xarray Coordinate Info\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"NetCDF xarray Metadata Info\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"CDO Operations\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"CDO Operations\"]\n  3 -> 4 [label=\"output_files\"]\n  5[label=\"NetCDF xarray Metadata Info\"]\n  4 -> 5 [label=\"output_files\"]\n  6[label=\"NetCDF xarray map plotting\"]\n  4 -> 6 [label=\"output_files\"]\n  5 -> 6 [label=\"output\"]\n  7[label=\"NetCDF xarray map plotting\"]\n  4 -> 7 [label=\"output_files\"]\n  5 -> 7 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"OBIS occurences\"]\n  1[label=\"Advanced Cut\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Ocean biodiversity indicators\"]\n  1 -> 2 [label=\"output\"]\n}",
                 "history": [
                     {
-                        "hash": "ce9cd3e8d3c5487ed4bbce32d5d889ee84e91e9d",
-                        "message": "Tutorial added to ecology folder: \"Visualization of Climate Data using NetCDF Xarray Map Plotting\"  (#3481)",
-                        "num": 1,
-                        "short_hash": "ce9cd3e8d",
-                        "unix": "1666808431"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "Upload the dataset : air temperatures at 2  metres , from the 'remote datasets'",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Upload the dataset : air temperatures at 2  metres , from the 'remote datasets'",
-                                "name": "air_temperature_at_2_metres.nc"
-                            }
-                        ],
-                        "label": "air_temperature_at_2_metres.nc",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": -16.41666666666667,
-                            "height": 76.96875,
-                            "left": -247.125,
-                            "right": -97.125,
-                            "top": -93.38541666666667,
-                            "width": 150,
-                            "x": -247.125,
-                            "y": -93.38541666666667
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"input\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f1e7e3ca-c219-42e5-ab29-86be86e3a49c",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nair_temperature_at_2_metres.nc\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"NetCDF xarray Coordinate Info\"];\n  0 -->|output| 1;\n  2[\"NetCDF xarray Metadata Info\"];\n  0 -->|output| 2;\n  3[\"CDO Operations\"];\n  0 -->|output| 3;\n  4[\"CDO Operations\"];\n  3 -->|output_files| 4;\n  5[\"NetCDF xarray Metadata Info\"];\n  4 -->|output_files| 5;\n  6[\"NetCDF xarray map plotting\"];\n  4 -->|output_files| 6;\n  5 -->|output| 6;\n  7[\"NetCDF xarray map plotting\"];\n  4 -->|output_files| 7;\n  5 -->|output| 7;",
-                "modified": "2024-08-18 00:06:22 +0000",
-                "name": "Xarray_Map_Plotting_Workflow",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/0.20.2+galaxy0",
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "NetCDF xarray Coordinate Info",
-                        "outputs": [
-                            {
-                                "name": "output_dir",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 112.39583333333333,
-                            "height": 85.21875,
-                            "left": 101.77083333333333,
-                            "right": 251.77083333333331,
-                            "top": 27.177083333333332,
-                            "width": 150,
-                            "x": 101.77083333333333,
-                            "y": 27.177083333333332
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/0.20.2+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3e73f657a998",
-                            "name": "xarray_coords_info",
-                            "owner": "ecology",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.20.2+galaxy0",
-                        "type": "tool",
-                        "uuid": "6f17f1e4-27d1-49af-a15d-080826d7a36b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_dir",
-                                "uuid": "c60539a8-ee7d-479a-81e9-486d0f8221d9"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1",
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "NetCDF xarray Metadata Info",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "info",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "bottom": -29.4765625,
-                            "height": 108.0234375,
-                            "left": 59.333333333333336,
-                            "right": 209.33333333333334,
-                            "top": -137.5,
-                            "width": 150,
-                            "x": 59.333333333333336,
-                            "y": -137.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "e8650cdf092f",
-                            "name": "xarray_metadata_info",
-                            "owner": "ecology",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.15.1",
-                        "type": "tool",
-                        "uuid": "a7264ebe-3a2a-4289-a441-6d1c6069c308",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "9d7ca599-cbeb-4015-9906-45d3381b5fee"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "info",
-                                "uuid": "930410e1-a49f-4484-9e71-d8d3a15fde9a"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/climate/cdo_operations/cdo_operations/2.0.0+galaxy0",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "section_operators_0|operator|add_file": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "CDO Operations",
-                        "outputs": [
-                            {
-                                "name": "output_files",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 282.34895833333337,
-                            "height": 115.828125,
-                            "left": 119.98958333333333,
-                            "right": 269.9895833333333,
-                            "top": 166.52083333333334,
-                            "width": 150,
-                            "x": 119.98958333333333,
-                            "y": 166.52083333333334
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/climate/cdo_operations/cdo_operations/2.0.0+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "d5355f6fa02b",
-                            "name": "cdo_operations",
-                            "owner": "climate",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"section_operators\": [{\"__index__\": 0, \"operator\": {\"opt\": \"seltimestep\", \"__current_case__\": 27, \"params\": \"594/595\", \"add_file\": {\"__class__\": \"RuntimeValue\"}}}], \"section_option\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.0+galaxy0",
-                        "type": "tool",
-                        "uuid": "c0830da8-262f-4ac2-ad4f-c4f283ab344a",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_files",
-                                "uuid": "9fb668b7-381d-4af9-9128-8e8d06c18023"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/climate/cdo_operations/cdo_operations/2.0.0+galaxy0",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "section_operators_0|operator|add_file": {
-                                "id": 3,
-                                "output_name": "output_files"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "CDO Operations",
-                        "outputs": [
-                            {
-                                "name": "output_files",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 304.46354166666663,
-                            "height": 115.828125,
-                            "left": 407.3333333333333,
-                            "right": 557.3333333333333,
-                            "top": 188.63541666666666,
-                            "width": 150,
-                            "x": 407.3333333333333,
-                            "y": 188.63541666666666
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/climate/cdo_operations/cdo_operations/2.0.0+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "d5355f6fa02b",
-                            "name": "cdo_operations",
-                            "owner": "climate",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"section_operators\": [{\"__index__\": 0, \"operator\": {\"opt\": \"splithour\", \"__current_case__\": 14, \"add_file\": {\"__class__\": \"RuntimeValue\"}}}], \"section_option\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.0+galaxy0",
-                        "type": "tool",
-                        "uuid": "dbd1ef36-61b8-497a-859c-61640ec2c2ac",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_files",
-                                "uuid": "b02a9565-40e3-4042-ae0b-e8dadc595082"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "input": {
-                                "id": 4,
-                                "output_name": "output_files"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool NetCDF xarray Metadata Info",
-                                "name": "input"
-                            }
-                        ],
-                        "label": null,
-                        "name": "NetCDF xarray Metadata Info",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "info",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 559.6484375,
-                            "height": 108.0234375,
-                            "left": 669.9791666666666,
-                            "right": 819.9791666666666,
-                            "top": 451.625,
-                            "width": 150,
-                            "x": 669.9791666666666,
-                            "y": 451.625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "e8650cdf092f",
-                            "name": "xarray_metadata_info",
-                            "owner": "ecology",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.15.1",
-                        "type": "tool",
-                        "uuid": "388764c7-3d2f-448f-833e-63520411263e",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "eac57113-dab5-4047-9e3e-082aa04375c9"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "info",
-                                "uuid": "f629b534-e0fb-4dbc-8c4c-72b5f2105119"
-                            }
-                        ]
+                        "hash": "00a713cdfff3d5ee4c936e563aac9e9b17fe087e",
+                        "message": "updated workflow",
+                        "num": 3,
+                        "short_hash": "00a713cdf",
+                        "unix": "1710839703"
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.20.2+galaxy0",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "input": {
-                                "id": 4,
-                                "output_name": "output_files"
-                            },
-                            "var_tab": {
-                                "id": 5,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool NetCDF xarray map plotting",
-                                "name": "input"
-                            },
-                            {
-                                "description": "runtime parameter for tool NetCDF xarray map plotting",
-                                "name": "var_tab"
-                            }
-                        ],
-                        "label": null,
-                        "name": "NetCDF xarray map plotting",
-                        "outputs": [
-                            {
-                                "name": "output_dir",
-                                "type": "input"
-                            },
-                            {
-                                "name": "version",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 332.015625,
-                            "height": 130.828125,
-                            "left": 1004.7604166666666,
-                            "right": 1154.7604166666665,
-                            "top": 201.1875,
-                            "width": 150,
-                            "x": 1004.7604166666666,
-                            "y": 201.1875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.20.2+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "dc05bf0af58f",
-                            "name": "xarray_mapplot",
-                            "owner": "ecology",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"borders\": \"1.0\", \"cmap\": \"cm.lajolla\", \"coastline\": \"1.0\", \"colorbar_label\": \"\", \"condi_datetime\": {\"datetime\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"land\": null, \"lat_dim\": \"lat\", \"lon_dim\": \"lon\", \"ocean\": \"1.0\", \"proj\": \"{'proj': 'Mercator', 'central_longitude': 12.0}\", \"range\": \"220,320\", \"shift\": \"\", \"threshold\": null, \"title\": \"Projection :  Mercator 17:00 UTC \", \"var\": \"air_temperature_at_2_metres\", \"var_tab\": {\"__class__\": \"RuntimeValue\"}, \"xlim\": \"\", \"ylim\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.20.2+galaxy0",
-                        "type": "tool",
-                        "uuid": "bd88b706-c6b1-4a39-a0f5-24d2d306d3bc",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_dir",
-                                "uuid": "7540245d-ebf3-4446-b8f2-71dfa0410b2d"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "version",
-                                "uuid": "8a0f1cb9-67bc-4554-9473-e10f482d3f79"
-                            }
-                        ]
+                        "hash": "ce566378abf7d51f9aee0f33727e8573c71b698f",
+                        "message": "Add files via upload",
+                        "num": 2,
+                        "short_hash": "ce566378a",
+                        "unix": "1680848192"
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.20.2+galaxy0",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "input": {
-                                "id": 4,
-                                "output_name": "output_files"
-                            },
-                            "var_tab": {
-                                "id": 5,
-                                "output_name": "output"
-                            }
+                        "hash": "5cf36e64c0a8b287d9e108919e23581c6fa4aa5b",
+                        "message": "Add files via upload",
+                        "num": 1,
+                        "short_hash": "5cf36e64c",
+                        "unix": "1680787259"
+                    }
+                ],
+                "inputs": [],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"OBIS occurences\"];\n  1[\"Advanced Cut\"];\n  0 -->|output| 1;\n  2[\"Ocean biodiversity indicators\"];\n  1 -->|output| 2;",
+                "modified": "2024-10-02 12:08:07 +0000",
+                "name": "Marine Omics visualisation",
+                "outputs": [],
+                "parent_id": "ecology/obisindicators",
+                "path": "topics/ecology/tutorials/obisindicators/workflows/Obis-indicators.ga",
+                "tags": [
+                    "Ocean",
+                    "Marineomics",
+                    "earth-system"
+                ],
+                "test_results": {
+                    "eu": {
+                        "summary": {
+                            "num_errors": 0,
+                            "num_failures": 0,
+                            "num_skips": 0,
+                            "num_tests": 1
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool NetCDF xarray map plotting",
-                                "name": "input"
-                            },
-                            {
-                                "description": "runtime parameter for tool NetCDF xarray map plotting",
-                                "name": "var_tab"
-                            }
-                        ],
-                        "label": null,
-                        "name": "NetCDF xarray map plotting",
-                        "outputs": [
-                            {
-                                "name": "output_dir",
-                                "type": "input"
-                            },
+                        "tests": [
                             {
-                                "name": "version",
-                                "type": "tabular"
+                                "data": {
+                                    "end_datetime": "2023-05-23T13:01:11.109149",
+                                    "inputs": {
+                                        "Occurrence.csv": {
+                                            "class": "File",
+                                            "filetype": "csv",
+                                            "path": "test-data/Occurrence.csv.csv"
+                                        }
+                                    },
+                                    "invocation_details": {
+                                        "details": {
+                                            "error_message": "",
+                                            "history_id": "18649784ceeae594",
+                                            "history_state": "ok",
+                                            "invocation_id": "5416bcf2f590c4c2",
+                                            "invocation_state": "scheduled",
+                                            "workflow_id": "fbbe3ba09fea56a3"
+                                        },
+                                        "steps": {
+                                            "0. Occurrence.csv": {
+                                                "action": null,
+                                                "id": "081be084fdd665d8",
+                                                "job_id": null,
+                                                "jobs": [],
+                                                "model_class": "WorkflowInvocationStep",
+                                                "order_index": 0,
+                                                "output_collections": {},
+                                                "outputs": {
+                                                    "output": {
+                                                        "id": "4838ba20a6d867651377ade0c55e4376",
+                                                        "src": "hda",
+                                                        "uuid": "0ba0ffa3-b7b6-4f70-a9f5-b635cd06615d"
+                                                    }
+                                                },
+                                                "state": "scheduled",
+                                                "subworkflow": null,
+                                                "subworkflow_invocation_id": null,
+                                                "update_time": "2023-05-23T10:58:01.456172",
+                                                "workflow_step_id": "6919056b5db62ca4",
+                                                "workflow_step_label": "Occurrence.csv",
+                                                "workflow_step_uuid": "cf8be611-fbf7-428b-b1f6-113c1c2e1eae"
+                                            },
+                                            "1. Unnamed step": {
+                                                "action": null,
+                                                "id": "9029b42bf346eab8",
+                                                "job_id": "11ac94870d0bb33aaf0d076bb75012e2",
+                                                "jobs": [
+                                                    {
+                                                        "command_line": "python '/opt/galaxy/server/lib/galaxy/datatypes/converters/tabular_csv.py' -o '/data/jwd01/main/060/156/60156723/outputs/galaxy_dataset_e3394d0e-14f6-44d6-9752-82710416346b.dat' -i '/data/dnb08/galaxy_db/files/0/b/a/dataset_0ba0ffa3-b7b6-4f70-a9f5-b635cd06615d.dat'",
+                                                        "command_version": null,
+                                                        "create_time": "2023-05-23T10:58:01.450496",
+                                                        "dependencies": [
+                                                            {
+                                                                "cacheable": false,
+                                                                "dependency_resolver": {
+                                                                    "auto_init": true,
+                                                                    "auto_install": false,
+                                                                    "can_uninstall_dependencies": true,
+                                                                    "ensure_channels": "conda-forge,bioconda",
+                                                                    "model_class": "CondaDependencyResolver",
+                                                                    "prefix": "/usr/local/tools/_conda",
+                                                                    "read_only": false,
+                                                                    "resolver_type": "conda",
+                                                                    "resolves_simple_dependencies": true,
+                                                                    "use_local": false,
+                                                                    "versionless": false
+                                                                },
+                                                                "dependency_type": "conda",
+                                                                "environment_path": "/usr/local/tools/_conda/envs/__python@3.7",
+                                                                "exact": true,
+                                                                "model_class": "MergedCondaDependency",
+                                                                "name": "python",
+                                                                "version": "3.7"
+                                                            }
+                                                        ],
+                                                        "exit_code": 0,
+                                                        "external_id": "43631290",
+                                                        "galaxy_version": "23.0",
+                                                        "history_id": "18649784ceeae594",
+                                                        "id": "11ac94870d0bb33aaf0d076bb75012e2",
+                                                        "inputs": {
+                                                            "csv": {
+                                                                "id": "4838ba20a6d867651377ade0c55e4376",
+                                                                "src": "hda",
+                                                                "uuid": "0ba0ffa3-b7b6-4f70-a9f5-b635cd06615d"
+                                                            }
+                                                        },
+                                                        "job_messages": [],
+                                                        "job_metrics": [
+                                                            {
+                                                                "name": "hostname",
+                                                                "plugin": "hostname",
+                                                                "raw_value": "vgcnbwc-worker-c36m100-6296.novalocal",
+                                                                "title": "hostname",
+                                                                "value": "vgcnbwc-worker-c36m100-6296.novalocal"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_slots",
+                                                                "plugin": "core",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "Cores Allocated",
+                                                                "value": "1"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_memory_mb",
+                                                                "plugin": "core",
+                                                                "raw_value": "3891.0000000",
+                                                                "title": "Memory Allocated (MB)",
+                                                                "value": "3891"
+                                                            },
+                                                            {
+                                                                "name": "start_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684839498.0000000",
+                                                                "title": "Job Start Time",
+                                                                "value": "2023-05-23 12:58:18"
+                                                            },
+                                                            {
+                                                                "name": "end_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684839529.0000000",
+                                                                "title": "Job End Time",
+                                                                "value": "2023-05-23 12:58:49"
+                                                            },
+                                                            {
+                                                                "name": "runtime_seconds",
+                                                                "plugin": "core",
+                                                                "raw_value": "31.0000000",
+                                                                "title": "Job Runtime (Wall Clock)",
+                                                                "value": "31 seconds"
+                                                            },
+                                                            {
+                                                                "name": "cpuacct.usage",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "14969322405.0000000",
+                                                                "title": "CPU Time",
+                                                                "value": "14.969322405 seconds"
+                                                            },
+                                                            {
+                                                                "name": "memory.failcnt",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Failed to allocate memory count",
+                                                                "value": 0.0
+                                                            },
+                                                            {
+                                                                "name": "memory.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "4160749568.0000000",
+                                                                "title": "Memory limit on cgroup (MEM)",
+                                                                "value": "3.9 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "210845696.0000000",
+                                                                "title": "Max memory usage (MEM)",
+                                                                "value": "201.1 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "4219351040.0000000",
+                                                                "title": "Memory limit on cgroup (MEM+SWP)",
+                                                                "value": "3.9 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "210845696.0000000",
+                                                                "title": "Max memory usage (MEM+SWP)",
+                                                                "value": "201.1 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.oom_kill_disable",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "OOM Control enabled",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.under_oom",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Was OOM Killer active?",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.soft_limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Memory softlimit on cgroup",
+                                                                "value": "0 bytes"
+                                                            }
+                                                        ],
+                                                        "job_stderr": "",
+                                                        "job_stdout": "",
+                                                        "model_class": "Job",
+                                                        "output_collections": {},
+                                                        "outputs": {
+                                                            "tabular": {
+                                                                "id": "4838ba20a6d867659478aa0f23a27d78",
+                                                                "src": "hda",
+                                                                "uuid": "e3394d0e-14f6-44d6-9752-82710416346b"
+                                                            }
+                                                        },
+                                                        "params": {
+                                                            "__input_ext": "\"input\"",
+                                                            "__target_datatype__": "\"tabular\"",
+                                                            "__workflow_invocation_uuid__": "\"a98238aaf95811ed822c001e67d2ec02\"",
+                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
+                                                            "dbkey": "\"?\""
+                                                        },
+                                                        "state": "ok",
+                                                        "stderr": "",
+                                                        "stdout": "",
+                                                        "tool_id": "csv_to_tabular",
+                                                        "tool_stderr": "",
+                                                        "tool_stdout": "",
+                                                        "traceback": null,
+                                                        "update_time": "2023-05-23T10:58:53.605766",
+                                                        "user_email": "hxr@informatik.uni-freiburg.de"
+                                                    }
+                                                ],
+                                                "model_class": "WorkflowInvocationStep",
+                                                "order_index": 1,
+                                                "output_collections": {},
+                                                "outputs": {
+                                                    "tabular": {
+                                                        "id": "4838ba20a6d867659478aa0f23a27d78",
+                                                        "src": "hda",
+                                                        "uuid": "e3394d0e-14f6-44d6-9752-82710416346b"
+                                                    }
+                                                },
+                                                "state": "scheduled",
+                                                "subworkflow": null,
+                                                "subworkflow_invocation_id": null,
+                                                "update_time": "2023-05-23T10:58:53.286673",
+                                                "workflow_step_id": "901c22ecf4799bd6",
+                                                "workflow_step_label": null,
+                                                "workflow_step_uuid": "68d37ef8-8a10-46ba-8bce-4cda1bdab0e1"
+                                            },
+                                            "2. Unnamed step": {
+                                                "action": null,
+                                                "id": "347cfc8750f2fe94",
+                                                "job_id": "11ac94870d0bb33a413dde79a1714548",
+                                                "jobs": [
+                                                    {
+                                                        "command_line": "cut  -f '1,3,4,9,95' '/data/dnb08/galaxy_db/files/e/3/3/dataset_e3394d0e-14f6-44d6-9752-82710416346b.dat' > '/data/jwd02f/main/060/156/60156724/outputs/galaxy_dataset_c3b48c80-ad5e-4f84-b68d-db94fd9f4ec7.dat'",
+                                                        "command_version": "cut (GNU coreutils) 8.25",
+                                                        "create_time": "2023-05-23T10:58:01.530299",
+                                                        "dependencies": [],
+                                                        "exit_code": 0,
+                                                        "external_id": "43631331",
+                                                        "galaxy_version": "23.0",
+                                                        "history_id": "18649784ceeae594",
+                                                        "id": "11ac94870d0bb33a413dde79a1714548",
+                                                        "inputs": {
+                                                            "input": {
+                                                                "id": "4838ba20a6d867659478aa0f23a27d78",
+                                                                "src": "hda",
+                                                                "uuid": "e3394d0e-14f6-44d6-9752-82710416346b"
+                                                            }
+                                                        },
+                                                        "job_messages": [],
+                                                        "job_metrics": [
+                                                            {
+                                                                "name": "hostname",
+                                                                "plugin": "hostname",
+                                                                "raw_value": "vgcnbwc-worker-c36m975-5969.novalocal",
+                                                                "title": "hostname",
+                                                                "value": "vgcnbwc-worker-c36m975-5969.novalocal"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_slots",
+                                                                "plugin": "core",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "Cores Allocated",
+                                                                "value": "1"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_memory_mb",
+                                                                "plugin": "core",
+                                                                "raw_value": "3891.0000000",
+                                                                "title": "Memory Allocated (MB)",
+                                                                "value": "3891"
+                                                            },
+                                                            {
+                                                                "name": "start_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684839542.0000000",
+                                                                "title": "Job Start Time",
+                                                                "value": "2023-05-23 12:59:02"
+                                                            },
+                                                            {
+                                                                "name": "end_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684839558.0000000",
+                                                                "title": "Job End Time",
+                                                                "value": "2023-05-23 12:59:18"
+                                                            },
+                                                            {
+                                                                "name": "runtime_seconds",
+                                                                "plugin": "core",
+                                                                "raw_value": "16.0000000",
+                                                                "title": "Job Runtime (Wall Clock)",
+                                                                "value": "16 seconds"
+                                                            },
+                                                            {
+                                                                "name": "cpuacct.usage",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "10210526103.0000000",
+                                                                "title": "CPU Time",
+                                                                "value": "10.210526103 seconds"
+                                                            },
+                                                            {
+                                                                "name": "memory.failcnt",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Failed to allocate memory count",
+                                                                "value": 0.0
+                                                            },
+                                                            {
+                                                                "name": "memory.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "9223372036854771712.0000000",
+                                                                "title": "Memory limit on cgroup (MEM)",
+                                                                "value": "8.0 EB"
+                                                            },
+                                                            {
+                                                                "name": "memory.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "195211264.0000000",
+                                                                "title": "Max memory usage (MEM)",
+                                                                "value": "186.2 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "9223372036854771712.0000000",
+                                                                "title": "Memory limit on cgroup (MEM+SWP)",
+                                                                "value": "8.0 EB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "195211264.0000000",
+                                                                "title": "Max memory usage (MEM+SWP)",
+                                                                "value": "186.2 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.oom_kill_disable",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "OOM Control enabled",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.under_oom",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Was OOM Killer active?",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.soft_limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "4160749568.0000000",
+                                                                "title": "Memory softlimit on cgroup",
+                                                                "value": "3.9 GB"
+                                                            }
+                                                        ],
+                                                        "job_stderr": "",
+                                                        "job_stdout": "",
+                                                        "model_class": "Job",
+                                                        "output_collections": {},
+                                                        "outputs": {
+                                                            "output": {
+                                                                "id": "4838ba20a6d8676581b548fa09109a8c",
+                                                                "src": "hda",
+                                                                "uuid": "c3b48c80-ad5e-4f84-b68d-db94fd9f4ec7"
+                                                            }
+                                                        },
+                                                        "params": {
+                                                            "__input_ext": "\"tabular\"",
+                                                            "__workflow_invocation_uuid__": "\"a98238aaf95811ed822c001e67d2ec02\"",
+                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
+                                                            "complement": "\"\"",
+                                                            "cut_type_options": "{\"__current_case__\": 0, \"cut_element\": \"-f\", \"list\": [\"1\", \"3\", \"4\", \"9\", \"95\"]}",
+                                                            "dbkey": "\"?\"",
+                                                            "delimiter": "\"\""
+                                                        },
+                                                        "state": "ok",
+                                                        "stderr": "",
+                                                        "stdout": "",
+                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                                                        "tool_stderr": "",
+                                                        "tool_stdout": "",
+                                                        "traceback": null,
+                                                        "update_time": "2023-05-23T10:59:20.902960",
+                                                        "user_email": "hxr@informatik.uni-freiburg.de"
+                                                    }
+                                                ],
+                                                "model_class": "WorkflowInvocationStep",
+                                                "order_index": 2,
+                                                "output_collections": {},
+                                                "outputs": {
+                                                    "output": {
+                                                        "id": "4838ba20a6d8676581b548fa09109a8c",
+                                                        "src": "hda",
+                                                        "uuid": "c3b48c80-ad5e-4f84-b68d-db94fd9f4ec7"
+                                                    }
+                                                },
+                                                "state": "scheduled",
+                                                "subworkflow": null,
+                                                "subworkflow_invocation_id": null,
+                                                "update_time": "2023-05-23T10:59:20.871746",
+                                                "workflow_step_id": "8221333250114ef6",
+                                                "workflow_step_label": null,
+                                                "workflow_step_uuid": "f268a9c2-c603-4746-8f7c-9e06742934b5"
+                                            },
+                                            "3. Unnamed step": {
+                                                "action": null,
+                                                "id": "3d1f5a3044f2e3db",
+                                                "job_id": "11ac94870d0bb33a13d697639a952600",
+                                                "jobs": [
+                                                    {
+                                                        "command_line": "Rscript '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ecology/obisindicators/d7b6ff32d072/obisindicators/obisindicators.r' '/data/dnb08/galaxy_db/files/c/3/b/dataset_c3b48c80-ad5e-4f84-b68d-db94fd9f4ec7.dat' 'true' 't' '2' '3' '4' '5' '0' '10' '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ecology/obisindicators/d7b6ff32d072/obisindicators/analyze.r' '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ecology/obisindicators/d7b6ff32d072/obisindicators/visualize.r' '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ecology/obisindicators/d7b6ff32d072/obisindicators/data.r' '/data/jwd05e/main/060/156/60156725/outputs/galaxy_dataset_91bb988c-8725-4295-828d-1ac13db8a60f.dat' '<galaxy.tools.wrappers.DatasetCollectionWrapper object at 0x7fd2902529a0>'",
+                                                        "command_version": null,
+                                                        "create_time": "2023-05-23T10:58:01.621838",
+                                                        "dependencies": [],
+                                                        "exit_code": 0,
+                                                        "external_id": "43631352",
+                                                        "galaxy_version": "23.0",
+                                                        "history_id": "18649784ceeae594",
+                                                        "id": "11ac94870d0bb33a13d697639a952600",
+                                                        "inputs": {
+                                                            "input": {
+                                                                "id": "4838ba20a6d8676581b548fa09109a8c",
+                                                                "src": "hda",
+                                                                "uuid": "c3b48c80-ad5e-4f84-b68d-db94fd9f4ec7"
+                                                            }
+                                                        },
+                                                        "job_messages": [],
+                                                        "job_metrics": [
+                                                            {
+                                                                "name": "hostname",
+                                                                "plugin": "hostname",
+                                                                "raw_value": "vgcnbwc-worker-c36m975-0315.novalocal",
+                                                                "title": "hostname",
+                                                                "value": "vgcnbwc-worker-c36m975-0315.novalocal"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_slots",
+                                                                "plugin": "core",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "Cores Allocated",
+                                                                "value": "1"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_memory_mb",
+                                                                "plugin": "core",
+                                                                "raw_value": "3891.0000000",
+                                                                "title": "Memory Allocated (MB)",
+                                                                "value": "3891"
+                                                            },
+                                                            {
+                                                                "name": "start_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684839564.0000000",
+                                                                "title": "Job Start Time",
+                                                                "value": "2023-05-23 12:59:24"
+                                                            },
+                                                            {
+                                                                "name": "end_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684839655.0000000",
+                                                                "title": "Job End Time",
+                                                                "value": "2023-05-23 13:00:55"
+                                                            },
+                                                            {
+                                                                "name": "runtime_seconds",
+                                                                "plugin": "core",
+                                                                "raw_value": "91.0000000",
+                                                                "title": "Job Runtime (Wall Clock)",
+                                                                "value": "1 minute"
+                                                            },
+                                                            {
+                                                                "name": "cpuacct.usage",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "28077674459.0000000",
+                                                                "title": "CPU Time",
+                                                                "value": "28.077674459 seconds"
+                                                            },
+                                                            {
+                                                                "name": "memory.failcnt",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Failed to allocate memory count",
+                                                                "value": 0.0
+                                                            },
+                                                            {
+                                                                "name": "memory.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "9223372036854771712.0000000",
+                                                                "title": "Memory limit on cgroup (MEM)",
+                                                                "value": "8.0 EB"
+                                                            },
+                                                            {
+                                                                "name": "memory.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "338599936.0000000",
+                                                                "title": "Max memory usage (MEM)",
+                                                                "value": "322.9 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "9223372036854771712.0000000",
+                                                                "title": "Memory limit on cgroup (MEM+SWP)",
+                                                                "value": "8.0 EB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "338599936.0000000",
+                                                                "title": "Max memory usage (MEM+SWP)",
+                                                                "value": "322.9 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.oom_kill_disable",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "OOM Control enabled",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.under_oom",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Was OOM Killer active?",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.soft_limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "4160749568.0000000",
+                                                                "title": "Memory softlimit on cgroup",
+                                                                "value": "3.9 GB"
+                                                            }
+                                                        ],
+                                                        "job_stderr": "",
+                                                        "job_stdout": "",
+                                                        "model_class": "Job",
+                                                        "output_collections": {
+                                                            "plots": {
+                                                                "id": "13968361629db34c",
+                                                                "src": "hdca"
+                                                            }
+                                                        },
+                                                        "outputs": {
+                                                            "__new_primary_file_plots|ES_50__": {
+                                                                "id": "4838ba20a6d86765eaf3f31461579100",
+                                                                "src": "hda",
+                                                                "uuid": "81032c7a-1351-4267-8189-cbc5d2455632"
+                                                            },
+                                                            "__new_primary_file_plots|Maxp__": {
+                                                                "id": "4838ba20a6d8676574439f4e43ad19ae",
+                                                                "src": "hda",
+                                                                "uuid": "c45d82ae-a267-42a9-b1da-0c2aa492f4fc"
+                                                            },
+                                                            "__new_primary_file_plots|Records__": {
+                                                                "id": "4838ba20a6d867659af91628bbf2fd3d",
+                                                                "src": "hda",
+                                                                "uuid": "42320b99-2b25-4b11-b245-2b9e75869619"
+                                                            },
+                                                            "__new_primary_file_plots|Shannon_index__": {
+                                                                "id": "4838ba20a6d86765d225dba0fa1f54ea",
+                                                                "src": "hda",
+                                                                "uuid": "e5e7a500-230d-453b-8f90-1f2fe2aeb17d"
+                                                            },
+                                                            "__new_primary_file_plots|Simpson_index__": {
+                                                                "id": "4838ba20a6d867653fb9e294c0047986",
+                                                                "src": "hda",
+                                                                "uuid": "fdb2f88a-6c14-4382-b955-45f242a7367c"
+                                                            },
+                                                            "output_index": {
+                                                                "id": "4838ba20a6d86765db55ac8f682db95c",
+                                                                "src": "hda",
+                                                                "uuid": "91bb988c-8725-4295-828d-1ac13db8a60f"
+                                                            }
+                                                        },
+                                                        "params": {
+                                                            "__input_ext": "\"input\"",
+                                                            "__workflow_invocation_uuid__": "\"a98238aaf95811ed822c001e67d2ec02\"",
+                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
+                                                            "colnames": "true",
+                                                            "dbkey": "\"?\"",
+                                                            "latitude": "\"3\"",
+                                                            "longitude": "\"2\"",
+                                                            "records": "\"5\"",
+                                                            "resolution": "\"10\"",
+                                                            "separator": "\"t\"",
+                                                            "species": "\"4\"",
+                                                            "type": "\"0\""
+                                                        },
+                                                        "state": "ok",
+                                                        "stderr": "Warning message:\n`aes_string()` was deprecated in ggplot2 3.0.0.\n\u2139 Please use tidy evaluation ideoms with `aes()` \n",
+                                                        "stdout": "[1] \"ES_50.png\"\n[1] \"Shannon_index.png\"\n[1] \"Simpson_index.png\"\n[1] \"Maxp.png\"\n[1] \"Records.png\"\n",
+                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/obisindicators/obisindicators/0.0.2",
+                                                        "tool_stderr": "Warning message:\n`aes_string()` was deprecated in ggplot2 3.0.0.\n\u2139 Please use tidy evaluation ideoms with `aes()` \n",
+                                                        "tool_stdout": "[1] \"ES_50.png\"\n[1] \"Shannon_index.png\"\n[1] \"Simpson_index.png\"\n[1] \"Maxp.png\"\n[1] \"Records.png\"\n",
+                                                        "traceback": null,
+                                                        "update_time": "2023-05-23T11:00:57.908654",
+                                                        "user_email": "hxr@informatik.uni-freiburg.de"
+                                                    }
+                                                ],
+                                                "model_class": "WorkflowInvocationStep",
+                                                "order_index": 3,
+                                                "output_collections": {
+                                                    "plots": {
+                                                        "id": "13968361629db34c",
+                                                        "src": "hdca"
+                                                    }
+                                                },
+                                                "outputs": {
+                                                    "output_index": {
+                                                        "id": "4838ba20a6d86765db55ac8f682db95c",
+                                                        "src": "hda",
+                                                        "uuid": "91bb988c-8725-4295-828d-1ac13db8a60f"
+                                                    }
+                                                },
+                                                "state": "scheduled",
+                                                "subworkflow": null,
+                                                "subworkflow_invocation_id": null,
+                                                "update_time": "2023-05-23T11:00:57.878144",
+                                                "workflow_step_id": "f05cffad898145a3",
+                                                "workflow_step_label": null,
+                                                "workflow_step_uuid": "86cf1452-ed27-4ba0-b8cb-e1aa5c5584a5"
+                                            }
+                                        }
+                                    },
+                                    "problem_log": "No log for this engine type.",
+                                    "start_datetime": "2023-05-23T12:56:33.104415",
+                                    "status": "success"
+                                },
+                                "doc": "Test outline for Obis-indicators",
+                                "has_data": true,
+                                "id": "Obis-indicators.ga_0",
+                                "test_type": "galaxy_workflow"
                             }
                         ],
-                        "position": {
-                            "bottom": 523.796875,
-                            "height": 130.828125,
-                            "left": 1005.3333333333334,
-                            "right": 1155.3333333333335,
-                            "top": 392.96875,
-                            "width": 150,
-                            "x": 1005.3333333333334,
-                            "y": 392.96875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.20.2+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "dc05bf0af58f",
-                            "name": "xarray_mapplot",
-                            "owner": "ecology",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"borders\": \"1.0\", \"cmap\": \"cm.lajolla\", \"coastline\": \"1.0\", \"colorbar_label\": \"\", \"condi_datetime\": {\"datetime\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"land\": null, \"lat_dim\": \"lat\", \"lon_dim\": \"lon\", \"ocean\": \"1.0\", \"proj\": \"{'proj': 'Mercator', 'central_longitude': 12.0}\", \"range\": \"220,320\", \"shift\": \"\", \"threshold\": null, \"title\": \"Projection :  Mercator 18:00 UTC \", \"var\": \"air_temperature_at_2_metres\", \"var_tab\": {\"__class__\": \"RuntimeValue\"}, \"xlim\": \"\", \"ylim\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.20.2+galaxy0",
-                        "type": "tool",
-                        "uuid": "1ec4337e-4927-4666-b2a7-f4cfe3eec203",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_dir",
-                                "uuid": "d16f3d0e-1319-4534-bf43-e5f2068fb196"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "version",
-                                "uuid": "040771d9-9700-4457-a50a-44a957fea91f"
-                            }
-                        ]
+                        "version": "0.1"
                     }
-                ],
-                "parent_id": "ecology/x-array-map-plot",
-                "path": "topics/ecology/tutorials/x-array-map-plot/workflows/main-workflow.ga",
-                "tags": [
-                    "ecology",
-                    "climate"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Xarray_Map_Plotting_Workflow",
+                },
+                "tests": true,
+                "title": "Marine Omics visualisation",
                 "topic_id": "ecology",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-x-array-map-plot/versions/main-workflow",
-                "tutorial_id": "x-array-map-plot",
-                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/x-array-map-plot/workflows/main-workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/x-array-map-plot/workflows/main-workflow.html",
-                "version": 1,
-                "wfid": "ecology-x-array-map-plot",
-                "wfname": "main-workflow",
-                "workflow": "main-workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-obisindicators/versions/obis-indicators",
+                "tutorial_id": "obisindicators",
+                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/obisindicators/workflows/Obis-indicators.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/obisindicators/workflows/Obis-indicators.html",
+                "version": 2,
+                "wfid": "ecology-obisindicators",
+                "wfname": "obis-indicators",
+                "workflow": "Obis-indicators.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/climate/cdo_operations/cdo_operations/2.0.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/0.20.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.20.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/obis_data/obis_data/0.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/obisindicators/obisindicators/0.0.2"
                 ],
-                "workflowhub_id": "1260"
+                "workflowhub_id": "1252"
             }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.6621460"
+        ]
     },
     {
         "admin_install": {
@@ -66707,36 +70327,110 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "cb_dissim",
-                    "owner": "ecology",
-                    "revisions": "8dc082da41c1",
-                    "tool_panel_section_label": "Compute indicators for turnover boulders fields",
+                    "name": "fastq_groomer",
+                    "owner": "devteam",
+                    "revisions": "47e5dbc3e790",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cb_div",
-                    "owner": "ecology",
-                    "revisions": "5b31641e6d30",
-                    "tool_panel_section_label": "Biodiversity data exploration",
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "3d0c7bdf12f5",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cb_ivr",
-                    "owner": "ecology",
-                    "revisions": "bcbad4f83dec",
-                    "tool_panel_section_label": "Compute indicators for turnover boulders fields",
+                    "name": "ncbi_blast_plus",
+                    "owner": "devteam",
+                    "revisions": "5edc472ec434",
+                    "tool_panel_section_label": "NCBI Blast",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "unzip",
+                    "owner": "imgteam",
+                    "revisions": "38eec75fbe9b",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "obi_annotate",
+                    "owner": "iuc",
+                    "revisions": "d50dc96e3ce9",
+                    "tool_panel_section_label": "DNA Metabarcoding",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "obi_clean",
+                    "owner": "iuc",
+                    "revisions": "08d873cdd5f6",
+                    "tool_panel_section_label": "DNA Metabarcoding",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "obi_grep",
+                    "owner": "iuc",
+                    "revisions": "02bab5ff7c37",
+                    "tool_panel_section_label": "DNA Metabarcoding",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "obi_illumina_pairend",
+                    "owner": "iuc",
+                    "revisions": "8cb6bd511879",
+                    "tool_panel_section_label": "DNA Metabarcoding",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "obi_ngsfilter",
+                    "owner": "iuc",
+                    "revisions": "91a1ed0b486f",
+                    "tool_panel_section_label": "DNA Metabarcoding",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "obi_stat",
+                    "owner": "iuc",
+                    "revisions": "5f4544915893",
+                    "tool_panel_section_label": "DNA Metabarcoding",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "obi_tab",
+                    "owner": "iuc",
+                    "revisions": "4cf47c504672",
+                    "tool_panel_section_label": "DNA Metabarcoding",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "obi_uniq",
+                    "owner": "iuc",
+                    "revisions": "d4bea99366f9",
+                    "tool_panel_section_label": "DNA Metabarcoding",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seq_filter_by_id",
+                    "owner": "peterjc",
+                    "revisions": "141612f8c3e3",
+                    "tool_panel_section_label": "Filter and Sort",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: cb_dissim\n  owner: ecology\n  revisions: 8dc082da41c1\n  tool_panel_section_label: Compute indicators for turnover boulders fields\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cb_div\n  owner: ecology\n  revisions: 5b31641e6d30\n  tool_panel_section_label: Biodiversity data exploration\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cb_ivr\n  owner: ecology\n  revisions: bcbad4f83dec\n  tool_panel_section_label: Compute indicators for turnover boulders fields\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/champs-blocs/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastq_groomer\n  owner: devteam\n  revisions: 47e5dbc3e790\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: 5edc472ec434\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unzip\n  owner: imgteam\n  revisions: 38eec75fbe9b\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obi_annotate\n  owner: iuc\n  revisions: d50dc96e3ce9\n  tool_panel_section_label: DNA Metabarcoding\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obi_clean\n  owner: iuc\n  revisions: '08d873cdd5f6'\n  tool_panel_section_label: DNA Metabarcoding\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obi_grep\n  owner: iuc\n  revisions: 02bab5ff7c37\n  tool_panel_section_label: DNA Metabarcoding\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obi_illumina_pairend\n  owner: iuc\n  revisions: 8cb6bd511879\n  tool_panel_section_label: DNA Metabarcoding\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obi_ngsfilter\n  owner: iuc\n  revisions: 91a1ed0b486f\n  tool_panel_section_label: DNA Metabarcoding\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obi_stat\n  owner: iuc\n  revisions: 5f4544915893\n  tool_panel_section_label: DNA Metabarcoding\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obi_tab\n  owner: iuc\n  revisions: 4cf47c504672\n  tool_panel_section_label: DNA Metabarcoding\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: obi_uniq\n  owner: iuc\n  revisions: d4bea99366f9\n  tool_panel_section_label: DNA Metabarcoding\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seq_filter_by_id\n  owner: peterjc\n  revisions: 141612f8c3e3\n  tool_panel_section_label: Filter and Sort\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.json",
         "contributions": {
             "authorship": [
-                "Marie59",
+                "colineroyaux",
+                "onorvez",
+                "ecoissac",
+                "fboyer",
                 "yvanlebras"
             ],
             "funding": [
+                "gallantries",
                 "pndb"
             ]
         },
@@ -66744,14 +70438,46 @@
             {
                 "affiliations": [
                     "pndb",
-                    "fairease"
+                    "gallantries",
+                    "elixir-europe"
                 ],
-                "email": "marie.josse@ifremer.fr",
-                "id": "Marie59",
-                "joined": "2022-03",
-                "name": "Marie Josse",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
+                "elixir_node": "fr",
+                "email": "coline.royaux@mnhn.fr",
+                "id": "colineroyaux",
+                "joined": "2020-11",
+                "name": "Coline Royaux",
+                "orcid": "0000-0003-4308-5617",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/",
+                "twitter": "ColineRoyaux",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/colineroyaux.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "fr",
+                "email": "olivier.norvez@mnhn.fr",
+                "id": "onorvez",
+                "joined": "2022-02",
+                "name": "Olivier Norvez",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/onorvez/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/onorvez.json"
+            },
+            {
+                "github": false,
+                "id": "ecoissac",
+                "joined": "2022-02",
+                "name": "Eric Coissac",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ecoissac/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/ecoissac.json"
+            },
+            {
+                "github": false,
+                "id": "fboyer",
+                "joined": "2022-02",
+                "name": "Fr\u00e9d\u00e9ric Boyer",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fboyer/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/fboyer.json"
             },
             {
                 "affiliations": [
@@ -66772,6 +70498,32 @@
                 "twitter": "Yvan2935",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
             },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            },
             {
                 "avatar": "/training-material/shared/images/PNDB_sub.png",
                 "github": false,
@@ -66779,350 +70531,208 @@
                 "members": [
                     "colineroyaux",
                     "Marie59",
-                    "yvanlebras",
-                    "ThibaudGlinez"
+                    "ThibaudGlinez",
+                    "yvanlebras"
                 ],
                 "name": "P\u00f4le National de Donn\u00e9es de Biodiversit\u00e9",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pndb/",
                 "url": "https://training.galaxyproject.org/training-material/api/organisations/pndb.json"
             }
         ],
-        "dir": "topics/ecology/tutorials/champs-blocs",
-        "edam_operation": [],
+        "dir": "topics/ecology/tutorials/Obitools-metabarcoding",
+        "edam_operation": [
+            "Statistical calculation",
+            "Sequencing quality control",
+            "Sequence composition calculation",
+            "Sequence analysis"
+        ],
         "edam_topic": [],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "ecology/champs-blocs",
-        "inexact_supported_servers": [],
+        "id": "ecology/Obitools-metabarcoding",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.fr"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Diversity indicators",
-            "Champs Blocs",
-            "Boulder Fields"
+            "From raw reads you can process, clean and filter data to obtain a list of species from environmental DNA (eDNA) samples."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2024-06-27",
         "objectives": [
-            "Calculate IVR (Visual Rollover Indicator)",
-            "Compute dissimilarity indice",
-            "Vizualize some diversity indices"
+            "Deal with paired-end data to create consensus sequences",
+            "Clean, filter and anlayse data to obtain strong results"
         ],
-        "pageviews": 223,
-        "pub_date": "2023-01-04",
+        "pageviews": 4327,
+        "pub_date": "2022-02-28",
         "questions": [
-            "Which biological questions are addressed by the tutorial?",
-            "Which bioinformatics techniques are important to know for this type of data?"
+            "how to analyze DNA metabarcoding / eDNA data produced on Illumina sequencers using the OBITools?"
         ],
-        "short_id": "T00127",
+        "recordings": [
+            {
+                "captioners": [
+                    "yvanlebras"
+                ],
+                "date": "2022-03-03",
+                "galaxy_version": "21.09",
+                "length": "1H15M",
+                "speakers": [
+                    "yvanlebras"
+                ],
+                "youtube_id": "o2cUvb_lmLs"
+            }
+        ],
+        "short_id": "T00124",
         "short_tools": [
-            "cb_eco",
-            "cb_div",
-            "cb_ivr",
-            "cb_qecb",
-            "cb_dissim"
+            "obi_ngsfilter",
+            "join1",
+            "fastq_groomer",
+            "Filter1",
+            "obi_grep",
+            "obi_illumina_pairend",
+            "unzip",
+            "obi_annotate",
+            "wc_gnu",
+            "Cut1",
+            "obi_clean",
+            "seq_filter_by_id",
+            "fastqc",
+            "obi_uniq",
+            "obi_tab",
+            "ncbi_blastn_wrapper",
+            "obi_stat"
         ],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "ecologyanalysis",
         "supported_servers": {
-            "exact": [],
-            "inexact": []
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                }
+            ]
         },
         "symlink": null,
+        "tags": [
+            "Genetic composition EBV class",
+            "Community composition EBV class",
+            "EBV dataset",
+            "EBV workflow",
+            "eDNA",
+            "Metabarcoding"
+        ],
         "time_estimation": "1H",
-        "title": "Champs blocs indicators",
+        "title": "Metabarcoding/eDNA through Obitools",
         "tools": [
-            "cb_eco",
-            "cb_ivr",
-            "cb_qecb",
-            "toolshed.g2.bx.psu.edu/repos/ecology/cb_dissim/cb_dissim/0.0.0",
-            "toolshed.g2.bx.psu.edu/repos/ecology/cb_div/cb_div/0.0.0",
-            "toolshed.g2.bx.psu.edu/repos/ecology/cb_ivr/cb_ivr/0.0.0"
+            "Cut1",
+            "Filter1",
+            "join1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/0.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/obi_annotate/obi_annotate/1.2.13",
+            "toolshed.g2.bx.psu.edu/repos/iuc/obi_clean/obi_clean/1.2.13",
+            "toolshed.g2.bx.psu.edu/repos/iuc/obi_grep/obi_grep/1.2.13",
+            "toolshed.g2.bx.psu.edu/repos/iuc/obi_illumina_pairend/obi_illumina_pairend/1.2.13",
+            "toolshed.g2.bx.psu.edu/repos/iuc/obi_ngsfilter/obi_ngsfilter/1.2.13",
+            "toolshed.g2.bx.psu.edu/repos/iuc/obi_stat/obi_stat/1.2.13",
+            "toolshed.g2.bx.psu.edu/repos/iuc/obi_tab/obi_tab/1.2.13",
+            "toolshed.g2.bx.psu.edu/repos/iuc/obi_uniq/obi_uniq/1.2.13",
+            "toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7",
+            "wc_gnu"
         ],
         "topic_name": "ecology",
         "topic_name_human": "Ecology",
         "tours": false,
         "translations": {
             "slides": [],
-            "tutorial": [
-                "fr"
-            ],
+            "tutorial": [],
             "video": false
         },
-        "tutorial_name": "champs-blocs",
+        "tutorial_name": "Obitools-metabarcoding",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/champs-blocs/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/champs-blocs/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/champs-blocs/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.json"
         },
-        "version": 9,
+        "version": 11,
         "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 178,
-        "visitors": 88,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Compute indicators for Champs blocs",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nchampbloc_ivr_val.csv\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nchampbloc_ivr.csv\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nficheterrain_val.csv\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nficheterrain.csv\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nchampbloc_qecb_val.csv\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nchampbloc_qecb.csv\"]\n  6[label=\"IVR\"]\n  3 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  0 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"QECB\"]\n  3 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  4 -> 7 [label=\"output\"]\n  5 -> 7 [label=\"output\"]\n  8[label=\"Champs blocs indicators\"]\n  7 -> 8 [label=\"output_rds\"]\n}",
-                "history": [
-                    {
-                        "hash": "0b6778b7f1da935c60f9d7cbd6e8f2c9993bde5c",
-                        "message": "Add champ bloc tutorial",
-                        "num": 1,
-                        "short_hash": "0b6778b7f",
-                        "unix": "1670507254"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "champbloc_ivr_val.csv"
-                            }
-                        ],
-                        "label": "champbloc_ivr_val.csv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 217.671875,
-                            "height": 82.171875,
-                            "left": 386,
-                            "right": 586,
-                            "top": 135.5,
-                            "width": 200,
-                            "x": 386,
-                            "y": 135.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "eeb5efda-5d7d-4220-8e0f-2587fdf3ad7d",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "5fcbefd3-c2d2-4e85-8b90-8f1227afbd62"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "champbloc_ivr.csv"
-                            }
-                        ],
-                        "label": "champbloc_ivr.csv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 305.671875,
-                            "height": 82.171875,
-                            "left": 383,
-                            "right": 583,
-                            "top": 223.5,
-                            "width": 200,
-                            "x": 383,
-                            "y": 223.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "5a645b0a-9709-45d2-84d2-a334316ca860",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "4580be50-8a61-4930-b031-e63701223b3b"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "ficheterrain_val.csv"
-                            }
-                        ],
-                        "label": "ficheterrain_val.csv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 400.671875,
-                            "height": 82.171875,
-                            "left": 380,
-                            "right": 580,
-                            "top": 318.5,
-                            "width": 200,
-                            "x": 380,
-                            "y": 318.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "dad7d6cf-b728-4e05-bf85-437bb84d71cd",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "16a16950-c439-4f47-9d23-e433152ac9e3"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "ficheterrain.csv"
-                            }
-                        ],
-                        "label": "ficheterrain.csv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 481.28125,
-                            "height": 61.78125,
-                            "left": 380,
-                            "right": 580,
-                            "top": 419.5,
-                            "width": 200,
-                            "x": 380,
-                            "y": 419.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "82b42eb2-7530-4b90-884e-5f837b027dc7",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "ba5ad2d3-b368-45ad-8a68-f4150f74b505"
-                            }
-                        ]
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 118,
+        "visitors": 3031,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Metabarcoding/eDNA through Obitools",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nwolf_tutorial.zip?download=1\"]\n  1[label=\"Illuminapairedend\"]\n  2[label=\"Unzip\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"FastQC\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"FASTQ Groomer\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"obigrep\"]\n  4 -> 5 [label=\"output_file\"]\n  6[label=\"Line/Word/Character count\"]\n  4 -> 6 [label=\"output_file\"]\n  7[label=\"Line/Word/Character count\"]\n  5 -> 7 [label=\"output\"]\n  8[label=\"NGSfilter\"]\n  5 -> 8 [label=\"output\"]\n  9[label=\"obiuniq\"]\n  8 -> 9 [label=\"output\"]\n  10[label=\"obiannotate\"]\n  9 -> 10 [label=\"output\"]\n  11[label=\"obistat\"]\n  10 -> 11 [label=\"output\"]\n  12[label=\"obigrep\"]\n  10 -> 12 [label=\"output\"]\n  13[label=\"obigrep\"]\n  12 -> 13 [label=\"output\"]\n  14[label=\"obiclean\"]\n  13 -> 14 [label=\"output\"]\n  15[label=\"NCBI BLAST+ blastn\"]\n  14 -> 15 [label=\"output\"]\n  16[label=\"Filter sequences by ID\"]\n  15 -> 16 [label=\"output1\"]\n  17[label=\"Filter sequences by ID\"]\n  15 -> 17 [label=\"output1\"]\n  14 -> 17 [label=\"output\"]\n  18[label=\"obitab\"]\n  16 -> 18 [label=\"output_pos\"]\n  19[label=\"obitab\"]\n  17 -> 19 [label=\"output_pos\"]\n  20[label=\"Join two Datasets\"]\n  19 -> 20 [label=\"output\"]\n  15 -> 20 [label=\"output1\"]\n  21[label=\"Join two Datasets\"]\n  20 -> 21 [label=\"out_file1\"]\n  18 -> 21 [label=\"output\"]\n  22[label=\"Cut\"]\n  21 -> 22 [label=\"out_file1\"]\n  23[label=\"Filter\"]\n  22 -> 23 [label=\"out_file1\"]\n}",
+                "history": [
+                    {
+                        "hash": "20d3c8ceff4b1be65ec450a24c19e4541dc1817d",
+                        "message": "fix workflow linting",
+                        "num": 3,
+                        "short_hash": "20d3c8cef",
+                        "unix": "1645781525"
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "champbloc_qecb_val.csv"
-                            }
-                        ],
-                        "label": "champbloc_qecb_val.csv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 579.671875,
-                            "height": 82.171875,
-                            "left": 379,
-                            "right": 579,
-                            "top": 497.5,
-                            "width": 200,
-                            "x": 379,
-                            "y": 497.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "34ec646b-ef25-4263-94db-d082e546a69f",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "5a2619ce-3765-47c8-9d22-11903e0552a4"
-                            }
-                        ]
+                        "hash": "931fb1735a5b24da90bcaa5a63a23ac4b5abf790",
+                        "message": "update workflow",
+                        "num": 2,
+                        "short_hash": "931fb1735",
+                        "unix": "1645228612"
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "champbloc_qecb.csv"
-                            }
-                        ],
-                        "label": "champbloc_qecb.csv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 680.671875,
-                            "height": 82.171875,
-                            "left": 379,
-                            "right": 579,
-                            "top": 598.5,
-                            "width": 200,
-                            "x": 379,
-                            "y": 598.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "cb4cf37d-788d-42e5-9810-77b2ca4d190e",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "b1b2286a-a7af-4b5a-9ea0-c9ea60a48ba0"
-                            }
-                        ]
+                        "hash": "45ca3bc6d72f0eb5c43d19929da4730ec9c838db",
+                        "message": "Add files via upload",
+                        "num": 1,
+                        "short_hash": "45ca3bc6d",
+                        "unix": "1643659846"
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nchampbloc_ivr_val.csv\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nchampbloc_ivr.csv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nficheterrain_val.csv\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nficheterrain.csv\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nchampbloc_qecb_val.csv\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nchampbloc_qecb.csv\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"IVR\"];\n  3 -->|output| 6;\n  2 -->|output| 6;\n  0 -->|output| 6;\n  1 -->|output| 6;\n  7[\"QECB\"];\n  3 -->|output| 7;\n  2 -->|output| 7;\n  4 -->|output| 7;\n  5 -->|output| 7;\n  8[\"Champs blocs indicators\"];\n  7 -->|output_rds| 8;",
-                "modified": "2024-08-18 00:06:22 +0000",
-                "name": "Champs blocs indicators",
-                "outputs": [
+                "inputs": [
                     {
                         "annotation": "",
                         "content_id": null,
@@ -67132,500 +70742,69 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "champbloc_ivr_val.csv"
-                            }
-                        ],
-                        "label": "champbloc_ivr_val.csv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 217.671875,
-                            "height": 82.171875,
-                            "left": 386,
-                            "right": 586,
-                            "top": 135.5,
-                            "width": 200,
-                            "x": 386,
-                            "y": 135.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "eeb5efda-5d7d-4220-8e0f-2587fdf3ad7d",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "5fcbefd3-c2d2-4e85-8b90-8f1227afbd62"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "champbloc_ivr.csv"
-                            }
-                        ],
-                        "label": "champbloc_ivr.csv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 305.671875,
-                            "height": 82.171875,
-                            "left": 383,
-                            "right": 583,
-                            "top": 223.5,
-                            "width": 200,
-                            "x": 383,
-                            "y": 223.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "5a645b0a-9709-45d2-84d2-a334316ca860",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "4580be50-8a61-4930-b031-e63701223b3b"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "ficheterrain_val.csv"
-                            }
-                        ],
-                        "label": "ficheterrain_val.csv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 400.671875,
-                            "height": 82.171875,
-                            "left": 380,
-                            "right": 580,
-                            "top": 318.5,
-                            "width": 200,
-                            "x": 380,
-                            "y": 318.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "dad7d6cf-b728-4e05-bf85-437bb84d71cd",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "16a16950-c439-4f47-9d23-e433152ac9e3"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "ficheterrain.csv"
-                            }
-                        ],
-                        "label": "ficheterrain.csv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 481.28125,
-                            "height": 61.78125,
-                            "left": 380,
-                            "right": 580,
-                            "top": 419.5,
-                            "width": 200,
-                            "x": 380,
-                            "y": 419.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "82b42eb2-7530-4b90-884e-5f837b027dc7",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "ba5ad2d3-b368-45ad-8a68-f4150f74b505"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "champbloc_qecb_val.csv"
-                            }
-                        ],
-                        "label": "champbloc_qecb_val.csv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 579.671875,
-                            "height": 82.171875,
-                            "left": 379,
-                            "right": 579,
-                            "top": 497.5,
-                            "width": 200,
-                            "x": 379,
-                            "y": 497.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "34ec646b-ef25-4263-94db-d082e546a69f",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "5a2619ce-3765-47c8-9d22-11903e0552a4"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "champbloc_qecb.csv"
+                                "name": "wolf_tutorial.zip?download=1"
                             }
                         ],
-                        "label": "champbloc_qecb.csv",
+                        "label": "wolf_tutorial.zip?download=1",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 680.671875,
-                            "height": 82.171875,
-                            "left": 379,
-                            "right": 579,
-                            "top": 598.5,
-                            "width": 200,
-                            "x": 379,
-                            "y": 598.5
+                            "left": 10,
+                            "top": 10
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "cb4cf37d-788d-42e5-9810-77b2ca4d190e",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "b1b2286a-a7af-4b5a-9ea0-c9ea60a48ba0"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "cb_ivr",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "fiche_term": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "fiche_val": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "input_data": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "input_data2": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool IVR",
-                                "name": "fiche_term"
-                            },
-                            {
-                                "description": "runtime parameter for tool IVR",
-                                "name": "fiche_val"
-                            },
-                            {
-                                "description": "runtime parameter for tool IVR",
-                                "name": "input_data"
-                            },
-                            {
-                                "description": "runtime parameter for tool IVR",
-                                "name": "input_data2"
-                            }
-                        ],
-                        "label": null,
-                        "name": "IVR",
-                        "outputs": [
-                            {
-                                "name": "plots",
-                                "type": "input"
-                            },
-                            {
-                                "name": "output_rds",
-                                "type": "input"
-                            },
-                            {
-                                "name": "output_ivr",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 392.625,
-                            "height": 245.125,
-                            "left": 1079,
-                            "right": 1279,
-                            "top": 147.5,
-                            "width": 200,
-                            "x": 1079,
-                            "y": 147.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "cb_ivr",
-                        "tool_state": "{\"fiche_term\": {\"__class__\": \"RuntimeValue\"}, \"fiche_val\": {\"__class__\": \"RuntimeValue\"}, \"input_data\": {\"__class__\": \"RuntimeValue\"}, \"input_data2\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.0.0",
-                        "type": "tool",
-                        "uuid": "7a3c6336-6af4-4122-82a9-2b1476f471bd",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "plots",
-                                "uuid": "81408705-3fb8-41af-b329-fc9fbd360f52"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_rds",
-                                "uuid": "e2dc091a-bb27-4132-9196-95a44ef78597"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_ivr",
-                                "uuid": "60b6f4c5-a080-4daf-9f28-0c03132d42f2"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "cb_qecb",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "fiche_term": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "fiche_val": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "input_data": {
-                                "id": 4,
-                                "output_name": "output"
-                            },
-                            "input_data2": {
-                                "id": 5,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool QECB",
-                                "name": "fiche_term"
-                            },
-                            {
-                                "description": "runtime parameter for tool QECB",
-                                "name": "fiche_val"
-                            },
-                            {
-                                "description": "runtime parameter for tool QECB",
-                                "name": "input_data"
-                            },
-                            {
-                                "description": "runtime parameter for tool QECB",
-                                "name": "input_data2"
-                            }
-                        ],
-                        "label": null,
-                        "name": "QECB",
-                        "outputs": [
-                            {
-                                "name": "plots",
-                                "type": "input"
-                            },
-                            {
-                                "name": "output_rds",
-                                "type": "input"
-                            },
-                            {
-                                "name": "output_qecb",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 663.625,
-                            "height": 245.125,
-                            "left": 1092,
-                            "right": 1292,
-                            "top": 418.5,
-                            "width": 200,
-                            "x": 1092,
-                            "y": 418.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "cb_qecb",
-                        "tool_state": "{\"fiche_term\": {\"__class__\": \"RuntimeValue\"}, \"fiche_val\": {\"__class__\": \"RuntimeValue\"}, \"input_data\": {\"__class__\": \"RuntimeValue\"}, \"input_data2\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.0.0",
-                        "type": "tool",
-                        "uuid": "615551d9-0f93-4801-9a53-645448ee83db",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "plots",
-                                "uuid": "3f823485-3454-4b57-a9f0-5071ae870aa0"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_rds",
-                                "uuid": "6ba691f4-0a10-46c2-8737-1a7405becf8f"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_qecb",
-                                "uuid": "de7b3d96-08d8-4f9e-884a-d1eefde7a670"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "cb_eco",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "input_data": {
-                                "id": 7,
-                                "output_name": "output_rds"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Ecology",
-                                "name": "input_data"
-                            }
-                        ],
-                        "label": "Champs blocs indicators",
-                        "name": "Ecology",
-                        "outputs": [
-                            {
-                                "name": "plots",
-                                "type": "input"
-                            },
-                            {
-                                "name": "output_rds",
-                                "type": "input"
-                            },
-                            {
-                                "name": "output_eco",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 659.84375,
-                            "height": 174.34375,
-                            "left": 1404,
-                            "right": 1604,
-                            "top": 485.5,
-                            "width": 200,
-                            "x": 1404,
-                            "y": 485.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "cb_eco",
-                        "tool_state": "{\"input_data\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.0.0",
-                        "type": "tool",
-                        "uuid": "d4897790-0e61-425a-a7d8-3120e653de81",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "plots",
-                                "uuid": "6ba51e6e-8183-478d-a1f6-adee124a18aa"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_rds",
-                                "uuid": "14901eab-4866-4d92-ac9e-e79390cd6b4d"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_eco",
-                                "uuid": "ef6de5cf-0d90-47f1-bda9-0f44a7837555"
-                            }
-                        ]
+                        "uuid": "427d6f7d-b819-45fc-8d2a-c6d3b52c6aca",
+                        "workflow_outputs": []
                     }
                 ],
-                "parent_id": "ecology/champs-blocs",
-                "path": "topics/ecology/tutorials/champs-blocs/workflows/main_workflow.ga",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nwolf_tutorial.zip?download=1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Illuminapairedend\"];\n  2[\"Unzip\"];\n  0 -->|output| 2;\n  3[\"FastQC\"];\n  1 -->|output| 3;\n  4[\"FASTQ Groomer\"];\n  1 -->|output| 4;\n  5[\"obigrep\"];\n  4 -->|output_file| 5;\n  6[\"Line/Word/Character count\"];\n  4 -->|output_file| 6;\n  7[\"Line/Word/Character count\"];\n  5 -->|output| 7;\n  8[\"NGSfilter\"];\n  5 -->|output| 8;\n  9[\"obiuniq\"];\n  8 -->|output| 9;\n  10[\"obiannotate\"];\n  9 -->|output| 10;\n  11[\"obistat\"];\n  10 -->|output| 11;\n  12[\"obigrep\"];\n  10 -->|output| 12;\n  13[\"obigrep\"];\n  12 -->|output| 13;\n  14[\"obiclean\"];\n  13 -->|output| 14;\n  15[\"NCBI BLAST+ blastn\"];\n  14 -->|output| 15;\n  16[\"Filter sequences by ID\"];\n  15 -->|output1| 16;\n  17[\"Filter sequences by ID\"];\n  15 -->|output1| 17;\n  14 -->|output| 17;\n  18[\"obitab\"];\n  16 -->|output_pos| 18;\n  19[\"obitab\"];\n  17 -->|output_pos| 19;\n  20[\"Join two Datasets\"];\n  19 -->|output| 20;\n  15 -->|output1| 20;\n  21[\"Join two Datasets\"];\n  20 -->|out_file1| 21;\n  18 -->|output| 21;\n  22[\"Cut\"];\n  21 -->|out_file1| 22;\n  23[\"Filter\"];\n  22 -->|out_file1| 23;",
+                "modified": "2024-10-02 12:08:07 +0000",
+                "name": "Workflow constructed from history 'Tuto Obitools'",
+                "outputs": [],
+                "parent_id": "ecology/Obitools-metabarcoding",
+                "path": "topics/ecology/tutorials/Obitools-metabarcoding/workflows/main_workflow.ga",
                 "tags": [
                     "ecology"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Champs blocs indicators",
+                "title": "Workflow constructed from history 'Tuto Obitools'",
                 "topic_id": "ecology",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-champs-blocs/versions/main-workflow",
-                "tutorial_id": "champs-blocs",
-                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/champs-blocs/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/champs-blocs/workflows/main_workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-Obitools-metabarcoding/versions/main-workflow",
+                "tutorial_id": "Obitools-metabarcoding",
+                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/Obitools-metabarcoding/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/Obitools-metabarcoding/workflows/main_workflow.html",
                 "version": 1,
-                "wfid": "ecology-champs-blocs",
+                "wfid": "ecology-Obitools-metabarcoding",
                 "wfname": "main-workflow",
                 "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "cb_eco",
-                    "cb_ivr",
-                    "cb_qecb"
+                    "Cut1",
+                    "Filter1",
+                    "join1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/0.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/obi_annotate/obi_annotate/1.2.13",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/obi_clean/obi_clean/1.2.13",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/obi_grep/obi_grep/1.2.13",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/obi_illumina_pairend/obi_illumina_pairend/1.2.13",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/obi_ngsfilter/obi_ngsfilter/1.2.13",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/obi_stat/obi_stat/1.2.13",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/obi_tab/obi_tab/1.2.13",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/obi_uniq/obi_uniq/1.2.13",
+                    "toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7",
+                    "wc_gnu"
                 ],
-                "workflowhub_id": "1256"
+                "workflowhub_id": "1274"
             }
-        ]
+        ],
+        "zenodo_link": "https://zenodo.org/record/5932108"
     },
     {
         "admin_install": {
@@ -67634,61 +70813,92 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "srs_diversity_maps",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ecology_beta_diversity",
                     "owner": "ecology",
-                    "revisions": "9adccd3da70c",
-                    "tool_panel_section_label": "Compute indicators for satellite remote sensing",
+                    "revisions": "fb7b2cbd80bb",
+                    "tool_panel_section_label": "Biodiversity data exploration",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "srs_global_indices",
+                    "name": "ecology_homogeneity_normality",
                     "owner": "ecology",
-                    "revisions": "5cae678042ec",
-                    "tool_panel_section_label": "Compute indicators for satellite remote sensing",
+                    "revisions": "3df8937fd6fd",
+                    "tool_panel_section_label": "Biodiversity data exploration",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "srs_pca",
+                    "name": "ecology_link_between_var",
                     "owner": "ecology",
-                    "revisions": "21e21363a8b4",
-                    "tool_panel_section_label": "Compute indicators for satellite remote sensing",
+                    "revisions": "8e8867bf491a",
+                    "tool_panel_section_label": "Biodiversity data exploration",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "srs_preprocess_s2",
+                    "name": "ecology_presence_abs_abund",
                     "owner": "ecology",
-                    "revisions": "33a1e15f7252",
-                    "tool_panel_section_label": "Compute indicators for satellite remote sensing",
+                    "revisions": "4ed07d2d442b",
+                    "tool_panel_section_label": "Biodiversity data exploration",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "srs_process_data",
+                    "name": "ecology_stat_presence_abs",
                     "owner": "ecology",
-                    "revisions": "cf69ad260611",
-                    "tool_panel_section_label": "Compute indicators for satellite remote sensing",
+                    "revisions": "9a2e0195bb43",
+                    "tool_panel_section_label": "Biodiversity data exploration",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "srs_spectral_indices",
+                    "name": "tool_anonymization",
                     "owner": "ecology",
-                    "revisions": "b40aba3d9e5c",
-                    "tool_panel_section_label": "Compute indicators for satellite remote sensing",
+                    "revisions": "726a387cfdc2",
+                    "tool_panel_section_label": "Biodiversity data exploration",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "regex_find_replace",
+                    "owner": "galaxyp",
+                    "revisions": "209b7c5ee9d7",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: srs_diversity_maps\n  owner: ecology\n  revisions: 9adccd3da70c\n  tool_panel_section_label: Compute indicators for satellite remote sensing\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: srs_global_indices\n  owner: ecology\n  revisions: 5cae678042ec\n  tool_panel_section_label: Compute indicators for satellite remote sensing\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: srs_pca\n  owner: ecology\n  revisions: 21e21363a8b4\n  tool_panel_section_label: Compute indicators for satellite remote sensing\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: srs_preprocess_s2\n  owner: ecology\n  revisions: 33a1e15f7252\n  tool_panel_section_label: Compute indicators for satellite remote sensing\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: srs_process_data\n  owner: ecology\n  revisions: cf69ad260611\n  tool_panel_section_label: Compute indicators for satellite remote sensing\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: srs_spectral_indices\n  owner: ecology\n  revisions: b40aba3d9e5c\n  tool_panel_section_label: Compute indicators for satellite remote sensing\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/remote-sensing/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ecology_beta_diversity\n  owner: ecology\n  revisions: fb7b2cbd80bb\n  tool_panel_section_label: Biodiversity data exploration\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ecology_homogeneity_normality\n  owner: ecology\n  revisions: 3df8937fd6fd\n  tool_panel_section_label: Biodiversity data exploration\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ecology_link_between_var\n  owner: ecology\n  revisions: 8e8867bf491a\n  tool_panel_section_label: Biodiversity data exploration\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ecology_presence_abs_abund\n  owner: ecology\n  revisions: 4ed07d2d442b\n  tool_panel_section_label: Biodiversity data exploration\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ecology_stat_presence_abs\n  owner: ecology\n  revisions: 9a2e0195bb43\n  tool_panel_section_label: Biodiversity data exploration\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tool_anonymization\n  owner: ecology\n  revisions: 726a387cfdc2\n  tool_panel_section_label: Biodiversity data exploration\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 209b7c5ee9d7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.json",
         "contributions": {
             "authorship": [
+                "onorvez",
                 "Marie59",
+                "colineroyaux",
                 "yvanlebras"
             ],
             "funding": [
-                "pndb"
+                "pndb",
+                "gallantries",
+                "pndb",
+                "fnso2019"
             ]
         },
         "contributors": [
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "fr",
+                "email": "olivier.norvez@mnhn.fr",
+                "id": "onorvez",
+                "joined": "2022-02",
+                "name": "Olivier Norvez",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/onorvez/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/onorvez.json"
+            },
             {
                 "affiliations": [
                     "pndb",
@@ -67701,6 +70911,22 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
             },
+            {
+                "affiliations": [
+                    "pndb",
+                    "gallantries",
+                    "elixir-europe"
+                ],
+                "elixir_node": "fr",
+                "email": "coline.royaux@mnhn.fr",
+                "id": "colineroyaux",
+                "joined": "2020-11",
+                "name": "Coline Royaux",
+                "orcid": "0000-0003-4308-5617",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/",
+                "twitter": "ColineRoyaux",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/colineroyaux.json"
+            },
             {
                 "affiliations": [
                     "pndb",
@@ -67727,96 +70953,173 @@
                 "members": [
                     "colineroyaux",
                     "Marie59",
-                    "yvanlebras",
-                    "ThibaudGlinez"
+                    "ThibaudGlinez",
+                    "yvanlebras"
+                ],
+                "name": "P\u00f4le National de Donn\u00e9es de Biodiversit\u00e9",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pndb/",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/pndb.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/PNDB_sub.png",
+                "github": false,
+                "id": "pndb",
+                "members": [
+                    "colineroyaux",
+                    "Marie59",
+                    "ThibaudGlinez",
+                    "yvanlebras"
                 ],
                 "name": "P\u00f4le National de Donn\u00e9es de Biodiversit\u00e9",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pndb/",
                 "url": "https://training.galaxyproject.org/training-material/api/organisations/pndb.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/fnso.png",
+                "funder": true,
+                "funder_name": "National Fund for Open Science",
+                "funding_id": "AAPFNSO2019OpenMetaPaper-14026",
+                "funding_statement": "This project (<a href=\"https://www.ouvrirlascience.fr/submit-your-data-its-published/\"><code class=\"language-plaintext highlighter-rouge\">AAPFNSO2019OpenMetaPaper-14026</code></a>) is funded with the support of the national Fund for Open Science programme of the French Minister of Higher Education, Research and Innovation. Their funding has supported development of data/metadata management tools and related tutorial for Ecology and FAIR topics.\n<img src=\"https://lamy-environnement.com/wp-content/uploads/2023/03/Logo-MESR.png\" alt=\"French research ministry flag with the text: with the support of the National Fund for Open Science programme of french Minister of Higher Education, Research and Innovation\" />\n<img src=\"/training-material/shared/images/fnso.png\" alt=\"FNSO logo\" />",
+                "github": false,
+                "id": "fnso2019",
+                "joined": "2023-05",
+                "members": [
+                    "yvanlebras"
+                ],
+                "name": "OpenMetaPaper",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fnso2019/",
+                "short_name": "FNSO",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/fnso2019.json"
             }
         ],
-        "dir": "topics/ecology/tutorials/remote-sensing",
+        "dir": "topics/ecology/tutorials/biodiversity-data-exploration",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "ecology/remote-sensing",
-        "inexact_supported_servers": [],
+        "id": "ecology/biodiversity-data-exploration",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.fr"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Remote sensing data can be useful to find hotspots of biodiversity.",
-            "Spectral indices are of key importance to asset vegetation well-being.",
-            "Always keep in mind that remote sensing and in-situ data are complementary."
+            "Explore your data before diving into deep analysis"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2024-06-27",
         "objectives": [
-            "Getting Sentinel 2 data and reformatting them in a generalized way",
-            "Computing spectral indices such as the NDVI",
-            "Calculating and visualizing biodiversity indicators",
-            "Comparing with in-situ data"
+            "Explore Biodiversity data with taxonomic, temporal and geographical informations",
+            "Have an idea about quality content of the data regarding statistical tests like normality or homoscedasticity and coverage like temporal or geographical coverage"
         ],
-        "pageviews": 365,
-        "pub_date": "2023-04-13",
+        "pageviews": 1713,
+        "pub_date": "2022-03-01",
         "questions": [
-            "How to get spectral and biodiversity indicators from remote sensing data ?",
-            "Which kind of ecosystem are you studying ? global or canopy data ?"
+            "How to explore biodiversity data?",
+            "How to look at Homoscedasticity, normality or collinearity of presences-absence or abundance data?",
+            "How to compare beta diversity taking into account space, time and species components?"
         ],
-        "short_id": "T00333",
+        "recordings": [
+            {
+                "captioners": [
+                    "onorvez"
+                ],
+                "date": "2022-03-03",
+                "galaxy_version": "21.09",
+                "length": "1H",
+                "speakers": [
+                    "onorvez"
+                ],
+                "youtube_id": "rWfPr-5F3GQ"
+            }
+        ],
+        "short_id": "T00126",
         "short_tools": [
-            "srs_pca",
-            "srs_preprocess_s2",
-            "srs_spectral_indices",
-            "srs_global_indices",
-            "srs_diversity_maps",
-            "srs_process_data"
+            "ecology_beta_diversity",
+            "ecology_stat_presence_abs",
+            "tool_anonymization",
+            "ecology_link_between_var",
+            "ecology_presence_abs_abund",
+            "tp_cut_tool",
+            "ecology_homogeneity_normality",
+            "Remove beginning1",
+            "regexColumn1"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "ecologyanalysis",
+        "subtopic": "ecologypreprocess",
         "supported_servers": {
             "exact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.fr",
                     "url": "https://usegalaxy.fr/",
                     "usegalaxy": false
                 }
-            ],
-            "inexact": []
+            ]
         },
         "symlink": null,
         "tags": [
-            "Remote sensing"
+            "taxonomic data",
+            "data quality"
         ],
-        "time_estimation": "48H",
-        "title": "Sentinel 2 biodiversity",
+        "time_estimation": "1H",
+        "title": "Biodiversity data exploration",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/ecology/srs_diversity_maps/srs_diversity_maps/0.0.1",
-            "toolshed.g2.bx.psu.edu/repos/ecology/srs_global_indices/srs_global_indices/0.0.1",
-            "toolshed.g2.bx.psu.edu/repos/ecology/srs_pca/srs_pca/0.0.1",
-            "toolshed.g2.bx.psu.edu/repos/ecology/srs_preprocess_s2/srs_preprocess_s2/0.0.1",
-            "toolshed.g2.bx.psu.edu/repos/ecology/srs_process_data/srs_process_data/0.0.1",
-            "toolshed.g2.bx.psu.edu/repos/ecology/srs_spectral_indices/srs_spectral_indices/0.0.1"
+            "Remove beginning1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/ecology_beta_diversity/ecology_beta_diversity/0.0.0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/ecology_homogeneity_normality/ecology_homogeneity_normality/0.0.0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/ecology_link_between_var/ecology_link_between_var/0.0.0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/ecology_presence_abs_abund/ecology_presence_abs_abund/0.0.0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/ecology_stat_presence_abs/ecology_stat_presence_abs/0.0.0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/tool_anonymization/tool_anonymization/0.0.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0"
         ],
         "topic_name": "ecology",
         "topic_name_human": "Ecology",
@@ -67826,44 +71129,37 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "remote-sensing",
+        "tutorial_name": "biodiversity-data-exploration",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/remote-sensing/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/biodiversity-data-exploration/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/remote-sensing/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/remote-sensing/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.json"
         },
-        "version": 5,
+        "version": 14,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 89,
-        "visitors": 287,
+        "visit_duration": 168,
+        "visitors": 1170,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "email": "mailto:marie14.josse@gmail.com",
-                        "identifier": "Marie59",
-                        "name": "Marie Josse"
-                    }
-                ],
-                "description": "",
+                "creators": [],
+                "description": "Biodiversity data exploration",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSENTINEL2A_20230214-105638-781_L2A_T31UET_D.zip\"]\n  1[label=\"Preprocess sentinel 2 data\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Compute spectral indices\"]\n  1 -> 2 [label=\"output_refl\"]\n  3[label=\"Compute biodiversity indices\"]\n  1 -> 3 [label=\"output_refl\"]\n  4[label=\"Map diversity\"]\n  1 -> 4 [label=\"output_refl\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReel_life_survey_fish_modif.tabular\"]\n  1[label=\"Spatial coordinates anonymization\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Homoscedasticity and normality\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Variables exploration\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Presence-absence and abundance\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Statistics on presence-absence\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Local Contributions to Beta Diversity LCBD\"]\n  0 -> 6 [label=\"output\"]\n}",
                 "history": [
                     {
-                        "hash": "9ec32f916371d75664d87bfc61c7209b16224f0d",
-                        "message": "Add workflow",
+                        "hash": "00c1aaba1d1373e4f148e8312a54ae9cd4a38876",
+                        "message": "Make some renames for the gtn",
                         "num": 1,
-                        "short_hash": "9ec32f916",
-                        "unix": "1681207567"
+                        "short_hash": "00c1aaba1",
+                        "unix": "1646129123"
                     }
                 ],
                 "inputs": [
@@ -67876,33 +71172,82 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "SENTINEL2A_20230214-105638-781_L2A_T31UET_D.zip"
+                                "name": "Reel_life_survey_fish_modif.tabular"
                             }
                         ],
-                        "label": "SENTINEL2A_20230214-105638-781_L2A_T31UET_D.zip",
+                        "label": "Reel_life_survey_fish_modif.tabular",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 95.67931487630185
+                            "bottom": 226.44445037841797,
+                            "height": 102.55555725097656,
+                            "left": 393,
+                            "right": 593,
+                            "top": 123.8888931274414,
+                            "width": 200,
+                            "x": 393,
+                            "y": 123.8888931274414
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "bcaa7cfd-1850-48f5-9f3c-d476805764b5",
-                        "when": null,
-                        "workflow_outputs": []
+                        "uuid": "01b5e1a1-50d0-46d2-8b68-1cbeaa4a929a",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "97fc5a7d-db66-4c7d-8d58-97a167c4867e"
+                            }
+                        ]
                     }
                 ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSENTINEL2A_20230214-105638-781_L2A_T31UET_D.zip\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Preprocess sentinel 2 data\"];\n  0 -->|output| 1;\n  2[\"Compute spectral indices\"];\n  1 -->|output_refl| 2;\n  3[\"Compute biodiversity indices\"];\n  1 -->|output_refl| 3;\n  4[\"Map diversity\"];\n  1 -->|output_refl| 4;",
-                "modified": "2024-08-18 00:06:22 +0000",
-                "name": "Sentinel 2 example",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nReel_life_survey_fish_modif.tabular\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Spatial coordinates anonymization\"];\n  0 -->|output| 1;\n  2[\"Homoscedasticity and normality\"];\n  0 -->|output| 2;\n  3[\"Variables exploration\"];\n  0 -->|output| 3;\n  4[\"Presence-absence and abundance\"];\n  0 -->|output| 4;\n  5[\"Statistics on presence-absence\"];\n  0 -->|output| 5;\n  6[\"Local Contributions to Beta Diversity LCBD\"];\n  0 -->|output| 6;",
+                "modified": "2024-10-02 12:08:07 +0000",
+                "name": "Workflow 'Biodiversity data exploration tuto'",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/srs_preprocess_s2/srs_preprocess_s2/0.0.1",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Reel_life_survey_fish_modif.tabular"
+                            }
+                        ],
+                        "label": "Reel_life_survey_fish_modif.tabular",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 226.44445037841797,
+                            "height": 102.55555725097656,
+                            "left": 393,
+                            "right": 593,
+                            "top": 123.8888931274414,
+                            "width": 200,
+                            "x": 393,
+                            "y": 123.8888931274414
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "01b5e1a1-50d0-46d2-8b68-1cbeaa4a929a",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "97fc5a7d-db66-4c7d-8d58-97a167c4867e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/tool_anonymization/tool_anonymization/0.0.0",
                         "errors": null,
                         "id": 1,
                         "input_connections": {
@@ -67913,545 +71258,405 @@
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Preprocess sentinel 2 data",
+                                "description": "runtime parameter for tool Spatial coordinates anonymization",
+                                "name": "input"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Spatial coordinates anonymization",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 240.44445037841797,
+                            "height": 113.55555725097656,
+                            "left": 610,
+                            "right": 810,
+                            "top": 126.8888931274414,
+                            "width": 200,
+                            "x": 610,
+                            "y": 126.8888931274414
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/tool_anonymization/tool_anonymization/0.0.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "726a387cfdc2",
+                            "name": "tool_anonymization",
+                            "owner": "ecology",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"colnames\": \"true\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"latitude\": \"9\", \"longitude\": \"10\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.0.0",
+                        "type": "tool",
+                        "uuid": "c629e167-96eb-48e3-b1fe-a6d1d315acb0",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "5deea508-0542-4eb8-ac66-84ac0a7162c2"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_homogeneity_normality/ecology_homogeneity_normality/0.0.0",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Homoscedasticity and normality",
                                 "name": "input"
                             }
                         ],
                         "label": null,
-                        "name": "Preprocess sentinel 2 data",
+                        "name": "Homoscedasticity and normality",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "csv"
+                                "name": "plots",
+                                "type": "input"
                             },
                             {
-                                "name": "output_refl",
-                                "type": "zip"
+                                "name": "output_levene",
+                                "type": "txt"
                             },
                             {
-                                "name": "output_cloud",
-                                "type": "zip"
+                                "name": "output_ks",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 338.55905768840034,
-                            "top": 133.4050064677535
+                            "bottom": 414.3888854980469,
+                            "height": 235.5,
+                            "left": 617,
+                            "right": 817,
+                            "top": 178.88888549804688,
+                            "width": 200,
+                            "x": 617,
+                            "y": 178.88888549804688
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/srs_preprocess_s2/srs_preprocess_s2/0.0.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_homogeneity_normality/ecology_homogeneity_normality/0.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "33a1e15f7252",
-                            "name": "srs_preprocess_s2",
+                            "changeset_revision": "3df8937fd6fd",
+                            "name": "ecology_homogeneity_normality",
                             "owner": "ecology",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"source_s2\": \"SAFE\", \"type_s2\": \"2A\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.0.1",
+                        "tool_state": "{\"colnames\": \"true\", \"date\": \"11\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"species\": \"16\", \"variable\": \"18\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.0.0",
                         "type": "tool",
-                        "uuid": "5d5d8bc5-db29-41d5-8c49-ee27a480f5f7",
-                        "when": null,
+                        "uuid": "06eb8a3f-1702-4ca5-8124-f501adbb4acc",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "77639f71-b4de-4cf7-a753-82ac095f640b"
+                                "output_name": "output_levene",
+                                "uuid": "30bc9ecc-c9de-4e74-bc9d-284f2d5a60aa"
                             },
                             {
                                 "label": null,
-                                "output_name": "output_refl",
-                                "uuid": "724fb3dc-e0e2-4f6c-a377-ad47c1b6306c"
+                                "output_name": "output_ks",
+                                "uuid": "df48b84c-5bc3-4eca-bbde-dbf21e708959"
                             },
                             {
                                 "label": null,
-                                "output_name": "output_cloud",
-                                "uuid": "af28d52b-ef5c-4bd8-817f-6881e4f6bdcc"
+                                "output_name": "plots",
+                                "uuid": "08790bfd-cfb2-44cb-a156-a71abcd91369"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/srs_spectral_indices/srs_spectral_indices/0.0.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_link_between_var/ecology_link_between_var/0.0.0",
                         "errors": null,
-                        "id": 2,
+                        "id": 3,
                         "input_connections": {
-                            "method|input": {
-                                "id": 1,
-                                "output_name": "output_refl"
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Compute spectral indices",
+                        "name": "Variables exploration",
                         "outputs": [
                             {
                                 "name": "plots",
                                 "type": "input"
                             },
                             {
-                                "name": "output_indices",
-                                "type": "tabular"
+                                "name": "output_coli",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 646.041836526378,
-                            "top": 0
+                            "bottom": 408.2222137451172,
+                            "height": 164.3333282470703,
+                            "left": 613,
+                            "right": 813,
+                            "top": 243.88888549804688,
+                            "width": 200,
+                            "x": 613,
+                            "y": 243.88888549804688
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/srs_spectral_indices/srs_spectral_indices/0.0.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_link_between_var/ecology_link_between_var/0.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "a8dabbf47e15",
-                            "name": "srs_spectral_indices",
+                            "changeset_revision": "8e8867bf491a",
+                            "name": "ecology_link_between_var",
                             "owner": "ecology",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"choice\": \"N\", \"input_indice\": [\"NDVI\"], \"method\": {\"type\": \"zipper\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.0.1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"colnames\": \"true\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"method\": {\"type\": \"collinearity\", \"__current_case__\": 0, \"species\": \"16\", \"columns\": [\"12\", \"17\", \"18\"]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.0.0",
                         "type": "tool",
-                        "uuid": "a71dbaa9-14b9-4d71-8dc7-0b8c01da6de1",
-                        "when": null,
+                        "uuid": "83cdbf22-ac7e-4ddf-a444-3de0b347d613",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_indices",
-                                "uuid": "413c3c32-93a8-42f2-9a5f-515583743c6a"
+                                "output_name": "output_coli",
+                                "uuid": "a8a2bbd3-aedc-4b40-adb1-abdac7e95034"
                             },
                             {
                                 "label": null,
                                 "output_name": "plots",
-                                "uuid": "8156dd15-cabc-46b4-a483-1460e3ff87eb"
+                                "uuid": "0f18247b-f4a3-45c5-9053-bfd3fb2ad6a1"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/srs_global_indices/srs_global_indices/0.0.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_presence_abs_abund/ecology_presence_abs_abund/0.0.0",
                         "errors": null,
-                        "id": 3,
+                        "id": 4,
                         "input_connections": {
-                            "method|input": {
-                                "id": 1,
-                                "output_name": "output_refl"
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Compute biodiversity indices",
+                        "name": "Presence-absence and abundance",
                         "outputs": [
                             {
-                                "name": "plots_png",
+                                "name": "plots",
                                 "type": "input"
                             },
                             {
-                                "name": "output_indices",
-                                "type": "tabular"
+                                "name": "output_abund",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 643.2986798909894,
-                            "top": 200.60987670512733
+                            "bottom": 507.8333282470703,
+                            "height": 143.94444274902344,
+                            "left": 613,
+                            "right": 813,
+                            "top": 363.8888854980469,
+                            "width": 200,
+                            "x": 613,
+                            "y": 363.8888854980469
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/srs_global_indices/srs_global_indices/0.0.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_presence_abs_abund/ecology_presence_abs_abund/0.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "5cae678042ec",
-                            "name": "srs_global_indices",
+                            "changeset_revision": "4ed07d2d442b",
+                            "name": "ecology_presence_abs_abund",
                             "owner": "ecology",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"alpha\": \"2\", \"method\": {\"type\": \"zipper\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.0.1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"abundance\": \"18\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"colnames\": \"true\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"method\": {\"type\": \"abund\", \"__current_case__\": 0, \"latitude\": \"9\", \"longitude\": \"10\", \"individual\": \"fishes\", \"species\": \"16\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.0.0",
                         "type": "tool",
-                        "uuid": "5f001f10-d438-408e-b768-6b128fc997b1",
-                        "when": null,
+                        "uuid": "46f4249f-7a72-4d75-8a3f-a1fa62cba536",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "plots_png",
-                                "uuid": "8a821365-181c-4e39-adda-db360859a4b9"
+                                "output_name": "output_abund",
+                                "uuid": "83036527-2e15-4c84-b521-262c88fe5657"
                             },
                             {
                                 "label": null,
-                                "output_name": "output_indices",
-                                "uuid": "1d529bee-5bda-43f8-9baa-a56ac64dc270"
+                                "output_name": "plots",
+                                "uuid": "7ecccacc-3ab4-449e-bb61-5378d14fb42b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/srs_diversity_maps/srs_diversity_maps/0.0.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_stat_presence_abs/ecology_stat_presence_abs/0.0.0",
                         "errors": null,
-                        "id": 4,
+                        "id": 5,
                         "input_connections": {
-                            "method|input": {
-                                "id": 1,
-                                "output_name": "output_refl"
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Map diversity",
+                        "name": "Statistics on presence-absence",
                         "outputs": [
                             {
-                                "name": "plots",
-                                "type": "input"
+                                "name": "output_md",
+                                "type": "png"
                             },
                             {
-                                "name": "output_beta",
-                                "type": "tabular"
+                                "name": "output_0",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 641.2327166372127,
-                            "top": 393.50916884961316
+                            "bottom": 668.6111145019531,
+                            "height": 184.72222900390625,
+                            "left": 613,
+                            "right": 813,
+                            "top": 483.8888854980469,
+                            "width": 200,
+                            "x": 613,
+                            "y": 483.8888854980469
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/srs_diversity_maps/srs_diversity_maps/0.0.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_stat_presence_abs/ecology_stat_presence_abs/0.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "9adccd3da70c",
-                            "name": "srs_diversity_maps",
+                            "changeset_revision": "9a2e0195bb43",
+                            "name": "ecology_stat_presence_abs",
                             "owner": "ecology",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"method\": {\"origin\": \"zipper\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"type\": \"beta\", \"typepca\": \"SPCA\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.0.1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"colnames\": \"true\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"location\": \"8\", \"species\": \"16\", \"time\": \"11\", \"variable1\": \"18\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.0.0",
                         "type": "tool",
-                        "uuid": "e2b9f2a3-2feb-4630-881e-7514f6728207",
-                        "when": null,
+                        "uuid": "d8d3a4db-e5e3-4453-87e0-592d987987a6",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "plots",
-                                "uuid": "95fb8122-582a-4e01-b6b9-beae1920d0b6"
+                                "output_name": "output_0",
+                                "uuid": "494e4e8d-93ca-466e-a0ea-3ea83f59d64a"
                             },
                             {
                                 "label": null,
-                                "output_name": "output_beta",
-                                "uuid": "6d5a4bb8-6abb-4581-842c-85ea3d05a5ab"
+                                "output_name": "output_md",
+                                "uuid": "74b67cb1-d5d6-418b-a56a-645d0b17f559"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "ecology/remote-sensing",
-                "path": "topics/ecology/tutorials/remote-sensing/workflows/Sentinel-2-example.ga",
-                "tags": [],
-                "test_results": null,
-                "tests": true,
-                "title": "Sentinel 2 example",
-                "topic_id": "ecology",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-remote-sensing/versions/sentinel-2-example",
-                "tutorial_id": "remote-sensing",
-                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/remote-sensing/workflows/Sentinel-2-example.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/remote-sensing/workflows/Sentinel-2-example.html",
-                "version": 1,
-                "wfid": "ecology-remote-sensing",
-                "wfname": "sentinel-2-example",
-                "workflow": "Sentinel-2-example.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/ecology/srs_diversity_maps/srs_diversity_maps/0.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/srs_global_indices/srs_global_indices/0.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/srs_preprocess_s2/srs_preprocess_s2/0.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/srs_spectral_indices/srs_spectral_indices/0.0.1"
-                ],
-                "workflowhub_id": "1211"
-            }
-        ],
-        "zenodo_link": ""
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "0a8c6b61f0f4",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "spocc_occ",
-                    "owner": "ecology",
-                    "revisions": "f9d76a46799a",
-                    "tool_panel_section_label": "Get Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 0a8c6b61f0f4\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: spocc_occ\n  owner: ecology\n  revisions: f9d76a46799a\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/species-distribution-modeling/tutorial.json",
-        "contributors": [
-            {
-                "id": "emichn",
-                "joined": "2019-03",
-                "name": "Elisa Michon",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/emichn/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/emichn.json"
-            },
-            {
-                "affiliations": [
-                    "pndb",
-                    "gallantries",
-                    "fairease",
-                    "fnso2019",
-                    "elixir-europe"
-                ],
-                "elixir_node": "fr",
-                "email": "yvan.le-bras@mnhn.fr",
-                "id": "yvanlebras",
-                "joined": "2017-09",
-                "matrix": "yvanlebras:matrix.org",
-                "name": "Yvan Le Bras",
-                "orcid": "0000-0002-8504-068X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
-                "twitter": "Yvan2935",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            }
-        ],
-        "dir": "topics/ecology/tutorials/species-distribution-modeling",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.fr"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "ecology/species-distribution-modeling",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Use 'classical' Galaxy tools in combination with Interactive tools",
-            "Identify general steps of a species distribution modeling aproach"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-27",
-        "objectives": [
-            "Find and download occurrences data from GBIF",
-            "Find and download environmental data",
-            "Process both occurrences and environmental data",
-            "Partition occurrence data",
-            "Model a theoretical ecological niche and predict species distribution in a future climate scenario by using SDM"
-        ],
-        "pageviews": 4127,
-        "pub_date": "2019-07-04",
-        "questions": [
-            "How to build & evaluate a niche model, visualize and project it?"
-        ],
-        "requirements": null,
-        "short_id": "T00135",
-        "short_tools": [
-            "tp_find_and_replace",
-            "tp_cut_tool",
-            "interactive_tool_wallace",
-            "tabular_to_csv",
-            "Filter1",
-            "spocc_occ"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "ecologyanalysis",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                }
-            ],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "interactive-tools",
-            "modeling",
-            "gbif",
-            "species populations EBV class"
-        ],
-        "time_estimation": "1h",
-        "title": "Species distribution modeling",
-        "tools": [
-            "Filter1",
-            "interactive_tool_wallace",
-            "tabular_to_csv",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/ecology/spocc_occ/spocc_occ/0.9.0"
-        ],
-        "topic_name": "ecology",
-        "topic_name_human": "Ecology",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "species-distribution-modeling",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/species-distribution-modeling/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/species-distribution-modeling/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/species-distribution-modeling/tutorial.json"
-        },
-        "version": 17,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 67,
-        "visitors": 2598,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Species distribution modeling",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Get species occurrences data\"]\n  1[label=\"Wallace\"]\n  2[label=\"Cut\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Filter\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Convert tabular to CSV\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"Replace\"]\n  4 -> 5 [label=\"csv\"]\n}",
-                "history": [
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 4,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 3,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
-                        "message": "unflatten workflows",
-                        "num": 2,
-                        "short_hash": "faf6d298a",
-                        "unix": "1576155753"
                     },
-                    {
-                        "hash": "de727da9edf3f1567430727c681c1eba5f4e9c90",
-                        "message": "add SDM ecology.usegalaxy.eu workflow",
-                        "num": 1,
-                        "short_hash": "de727da9e",
-                        "unix": "1575551509"
-                    }
-                ],
-                "inputs": [],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"Get species occurrences data\"];\n  1[\"Wallace\"];\n  2[\"Cut\"];\n  0 -->|output| 2;\n  3[\"Filter\"];\n  2 -->|output| 3;\n  4[\"Convert tabular to CSV\"];\n  3 -->|out_file1| 4;\n  5[\"Replace\"];\n  4 -->|csv| 5;",
-                "modified": "2024-08-18 00:06:22 +0000",
-                "name": "Species Distribution Modeling With Wallace From GBIF - Training Material",
-                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "interactive_tool_wallace",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_beta_diversity/ecology_beta_diversity/0.0.0",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
+                        "id": 6,
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
                         "inputs": [],
                         "label": null,
-                        "name": "Wallace",
+                        "name": "Local Contributions to Beta Diversity (LCBD)",
                         "outputs": [
                             {
-                                "name": "outfile",
+                                "name": "plots",
+                                "type": "input"
+                            },
+                            {
+                                "name": "output_lcbd",
                                 "type": "txt"
+                            },
+                            {
+                                "name": "output_scbd",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "output_beta",
+                                "type": "Rdata"
                             }
                         ],
                         "position": {
-                            "left": 1077.5,
-                            "top": 400.5
+                            "bottom": 890.1666870117188,
+                            "height": 286.27777099609375,
+                            "left": 613,
+                            "right": 813,
+                            "top": 603.888916015625,
+                            "width": 200,
+                            "x": 613,
+                            "y": 603.888916015625
                         },
                         "post_job_actions": {},
-                        "tool_id": "interactive_tool_wallace",
-                        "tool_state": "{}",
-                        "tool_version": "0.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_beta_diversity/ecology_beta_diversity/0.0.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "fb7b2cbd80bb",
+                            "name": "ecology_beta_diversity",
+                            "owner": "ecology",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"abundance\": \"18\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"colnames\": \"true\", \"date\": \"11\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"location\": \"8\", \"method\": {\"type\": \"Graph\", \"__current_case__\": 0, \"latitude\": \"9\", \"longitude\": \"10\"}, \"rdata\": \"true\", \"species\": \"16\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.0.0",
                         "type": "tool",
-                        "uuid": "fe5c0b4c-b5ee-4c41-8145-bd9e610fd066",
+                        "uuid": "16c310f1-d14c-4778-a5cf-4798e3eb7043",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "c9ce6982-0192-413d-a476-71c45c15ce4b"
+                                "output_name": "plots",
+                                "uuid": "d6465151-e83a-4031-bd96-8a8f3d999bbb"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_lcbd",
+                                "uuid": "418fbdae-1a70-4e8c-a645-9e34b009f976"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_scbd",
+                                "uuid": "dd87eda6-8f3c-4e76-b3ae-f5c464697956"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_beta",
+                                "uuid": "acf06966-78ec-4013-a32b-061b385808cf"
                             }
                         ]
                     }
                 ],
-                "parent_id": "ecology/species-distribution-modeling",
-                "path": "topics/ecology/tutorials/species-distribution-modeling/workflows/Galaxy-Workflow-Species_Distribution_Modeling_with_Wallace_from_GBIF_-_Training_material.ga",
+                "parent_id": "ecology/biodiversity-data-exploration",
+                "path": "topics/ecology/tutorials/biodiversity-data-exploration/workflows/main_workflow.ga",
                 "tags": [
                     "ecology"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Species Distribution Modeling With Wallace From GBIF - Training Material",
+                "title": "Workflow 'Biodiversity data exploration tuto'",
                 "topic_id": "ecology",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-species-distribution-modeling/versions/galaxy-workflow-species-distribution-modeling-with-wallace-from-gbif---training-material",
-                "tutorial_id": "species-distribution-modeling",
-                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/species-distribution-modeling/workflows/Galaxy-Workflow-Species_Distribution_Modeling_with_Wallace_from_GBIF_-_Training_material.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/species-distribution-modeling/workflows/Galaxy-Workflow-Species_Distribution_Modeling_with_Wallace_from_GBIF_-_Training_material.html",
-                "version": 4,
-                "wfid": "ecology-species-distribution-modeling",
-                "wfname": "galaxy-workflow-species-distribution-modeling-with-wallace-from-gbif---training-material",
-                "workflow": "Galaxy-Workflow-Species_Distribution_Modeling_with_Wallace_from_GBIF_-_Training_material.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-biodiversity-data-exploration/versions/main-workflow",
+                "tutorial_id": "biodiversity-data-exploration",
+                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/biodiversity-data-exploration/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/biodiversity-data-exploration/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "ecology-biodiversity-data-exploration",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "Filter1",
-                    "interactive_tool_wallace",
-                    "tabular_to_csv",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/spocc_occ/spocc_occ/0.9.0"
+                    "toolshed.g2.bx.psu.edu/repos/ecology/ecology_beta_diversity/ecology_beta_diversity/0.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/ecology_homogeneity_normality/ecology_homogeneity_normality/0.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/ecology_link_between_var/ecology_link_between_var/0.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/ecology_presence_abs_abund/ecology_presence_abs_abund/0.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/ecology_stat_presence_abs/ecology_stat_presence_abs/0.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/tool_anonymization/tool_anonymization/0.0.0"
                 ],
-                "workflowhub_id": "1235"
+                "workflowhub_id": "1278"
             }
-        ]
+        ],
+        "zenodo_link": "https://zenodo.org/record/6107457"
     },
     {
         "admin_install": {
@@ -68597,8 +71802,8 @@
                 "members": [
                     "colineroyaux",
                     "Marie59",
-                    "yvanlebras",
-                    "ThibaudGlinez"
+                    "ThibaudGlinez",
+                    "yvanlebras"
                 ],
                 "name": "P\u00f4le National de Donn\u00e9es de Biodiversit\u00e9",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pndb/",
@@ -68606,7 +71811,6 @@
             }
         ],
         "dir": "topics/ecology/tutorials/MetaShARK_tutorial",
-        "draft": true,
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -68629,13 +71833,13 @@
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-27",
+        "mod_date": "2024-09-10",
         "objectives": [
             "Explain the necessity of using such tools when producing ecological metadata",
             "Learn how to create rich metadata using Ecological Metadata Language (EML) standard",
             "Learn how to update EML metadata"
         ],
-        "pageviews": 83,
+        "pageviews": 90,
         "pub_date": "2024-03-04",
         "questions": [
             "How to generate detailled metadata easily from biodiversity datasets ?",
@@ -68671,8 +71875,7 @@
             "Ecology",
             "Biodiversity",
             "FAIR",
-            "Data Paper",
-            "work-in-progress"
+            "Data Paper"
         ],
         "time_estimation": "30M",
         "title": "Creating metadata using Ecological Metadata Language (EML) standard with EML Assembly Line functionalities",
@@ -68694,12 +71897,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/MetaShARK_tutorial/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/MetaShARK_tutorial/tutorial.json"
         },
-        "version": 6,
+        "version": 7,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 159,
-        "visitors": 57,
+        "visit_duration": 173,
+        "visitors": 62,
         "zenodo_link": "https://zenodo.org/records/10663465"
     },
     {
@@ -68707,136 +71910,211 @@
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": []
+            "tools": [
+                {
+                    "name": "bracken",
+                    "owner": "iuc",
+                    "revisions": "1d4bd12f01cf",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "kraken2",
+                    "owner": "iuc",
+                    "revisions": "20e2f64aa1fe",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "recentrifuge",
+                    "owner": "iuc",
+                    "revisions": "b5407cc2bf51",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/ndvi_openeo/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bracken\n  owner: iuc\n  revisions: 1d4bd12f01cf\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: 20e2f64aa1fe\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: recentrifuge\n  owner: iuc\n  revisions: b5407cc2bf51\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.json",
         "contributions": {
             "authorship": [
-                "Marie59"
+                "bebatut"
+            ],
+            "editing": [
+                "clsiguret"
             ],
             "funding": [
-                "fairease",
-                "eurosciencegateway"
+                "abromics"
             ]
         },
         "contributors": [
             {
                 "affiliations": [
-                    "pndb",
-                    "fairease"
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
                 ],
-                "email": "marie.josse@ifremer.fr",
-                "id": "Marie59",
-                "joined": "2022-03",
-                "name": "Marie Josse",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             },
             {
-                "avatar": "/training-material/assets/images/fair_ease_colour.png",
-                "funder": true,
-                "funding_id": "101058785",
-                "funding_statement": "FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "fairease",
-                "joined": "2023-10",
-                "members": [
-                    "Marie59",
-                    "yvanlebras"
+                "affiliations": [
+                    "ifb",
+                    "elixir-europe"
                 ],
-                "name": "Fair-Ease",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fairease/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/fairease.json"
+                "elixir_node": "fr",
+                "email": "clea.siguret@gmail.com",
+                "id": "clsiguret",
+                "joined": "2024-04",
+                "linkedin": "cl\u00e9a-siguret-58423b107",
+                "matrix": "clsiguret:matrix.org",
+                "name": "Clea Siguret",
+                "orcid": "0009-0005-6140-0379",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/clsiguret/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/clsiguret.json"
             },
             {
-                "avatar": "/training-material/assets/images/eurosciencegateway.png",
+                "avatar": "/training-material/assets/images/abromics.png",
                 "funder": true,
-                "funding_id": "101057388",
-                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
-                "funding_system": "cordis",
                 "github": false,
-                "id": "eurosciencegateway",
-                "joined": "2023-10",
-                "members": [
-                    "abretaud",
-                    "anuprulez",
-                    "bgruening",
-                    "erxleben",
-                    "pauldg",
-                    "rlibouba"
-                ],
-                "name": "EuroScienceGateway",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
+                "id": "abromics",
+                "joined": "2024-01",
+                "name": "ABRomics",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abromics/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/abromics.json"
             }
         ],
-        "dir": "topics/ecology/tutorials/ndvi_openeo",
-        "edam_operation": [],
-        "edam_topic": [],
+        "dir": "topics/ecology/tutorials/bacterial-isolate-species-contamination-checking",
+        "edam_ontology": [
+            "topic_3673",
+            "topic_0622",
+            "topic_3301",
+            "topic_3697"
+        ],
+        "edam_operation": [
+            "Statistical calculation",
+            "Taxonomic classification",
+            "Cross-assembly",
+            "Expression analysis"
+        ],
+        "edam_topic": [
+            "Whole genome sequencing",
+            "Genomics",
+            "Microbiology",
+            "Microbial ecology"
+        ],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.eu",
+            "UseGalaxy.fr"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "ecology/ndvi_openeo",
-        "inexact_supported_servers": [],
+        "id": "ecology/bacterial-isolate-species-contamination-checking",
+        "inexact_supported_servers": [
+            "Galaxy@AuBi",
+            "GalaxyTrakr",
+            "UseGalaxy.cz",
+            "UseGalaxy.org (Main)"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Manage NDVI data",
-            "Handle jupyterlab tools"
+            "Kraken assigns taxons to sequences",
+            "Bracken extracts species from Kraken assignations",
+            "Recentrifuge extracts stats and creates visualization from Kraken report"
         ],
         "layout": "tutorial_hands_on",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-29",
+        "mod_date": "2024-06-27",
         "objectives": [
-            "Use OpenEo technologies and learn how to download data with them",
-            "Learn to use Holoviz environment to process csv data",
-            "Create timeseries and visualisation of the NDVI",
-            "Handle going form one interactive tool to another"
+            "Run a series of tool to identify species in bacterial isolate sequencing data",
+            "Visualize the species abundance"
         ],
-        "pageviews": 78,
-        "pub_date": "2024-01-24",
+        "pageviews": 343,
+        "pub_date": "2024-03-04",
         "questions": [
-            "What's the NDVI ?",
-            "How to evaluate the NDVI through out time ?"
+            "What are the species in bacterial isolate sequencing data?"
         ],
-        "short_id": "T00400",
+        "short_id": "T00423",
         "short_tools": [
-            "interactive_tool_holoviz",
-            "interactive_tool_copernicus_notebook"
+            "recentrifuge",
+            "kraken2",
+            "upload1",
+            "est_abundance"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "ecologyanalysis",
+        "subtopic": "ecologypreprocess",
         "supported_servers": {
             "exact": [
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
                 }
             ],
-            "inexact": []
+            "inexact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ]
         },
         "symlink": null,
         "tags": [
-            "earth-system",
-            "land degradation",
-            "NDVI",
-            "copernicus",
-            "holoviews"
+            "illumina",
+            "bacteria",
+            "microgalaxy"
         ],
         "time_estimation": "1H",
-        "title": "From NDVI data with OpenEO to time series visualisation with Holoviews",
+        "title": "Checking expected species and contamination in bacterial isolate",
         "tools": [
-            "interactive_tool_copernicus_notebook",
-            "interactive_tool_holoviz"
+            "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0",
+            "upload1"
         ],
         "topic_name": "ecology",
         "topic_name_human": "Ecology",
@@ -68846,169 +72124,383 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "ndvi_openeo",
+        "tutorial_name": "bacterial-isolate-species-contamination-checking",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/ndvi_openeo/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/ndvi_openeo/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/ndvi_openeo/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.json"
         },
-        "version": 3,
+        "version": 4,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 67,
-        "visitors": 66,
+        "visit_duration": 212,
+        "visitors": 260,
         "workflows": [
             {
                 "creators": [
                     {
+                        "alternateName": "pimarin",
                         "class": "Person",
-                        "identifier": "0009-0008-0622-604X",
-                        "name": "Marie Joss\u00e9",
-                        "url": "https://github.com/Marie59"
+                        "email": "mailto:pierre.marin@france-bioinformatique.fr",
+                        "familyName": "MARIN",
+                        "identifier": "0000-0002-8304-138X",
+                        "name": "Pierre"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0001-9852-1987",
+                        "name": "B\u00e9r\u00e9nice Batut"
                     }
                 ],
-                "description": "",
+                "description": "Checking expected species and contamination in bacterial isolate",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Copernicus Data Space Ecosystem\"]\n  1[label=\"Holoviz\"]\n  0 -> 1 [label=\"output_collection\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreverse_reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nforward_reads\"]\n  2[label=\"Kraken2\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  ka408a64458cd4f5eaf2515b5ea63aa76[color=lightseagreen,label=\"Output\\nkraken_report_reads\"]\n  2 -> ka408a64458cd4f5eaf2515b5ea63aa76\n  k54b85a5372ee4b73b1867fd55e8aab9b[color=lightseagreen,label=\"Output\\nkraken_report_tabular\"]\n  2 -> k54b85a5372ee4b73b1867fd55e8aab9b\n  3[label=\"Bracken\"]\n  2 -> 3 [label=\"report_output\"]\n  kae6c6464f5f54e5bb616d38166fc0133[color=lightseagreen,label=\"Output\\nbracken_report_tsv\"]\n  3 -> kae6c6464f5f54e5bb616d38166fc0133\n  k8ca52af9f83942b6aa74f1a6a1dfbbc8[color=lightseagreen,label=\"Output\\nbracken_kraken_report\"]\n  3 -> k8ca52af9f83942b6aa74f1a6a1dfbbc8\n  4[label=\"Recentrifuge\"]\n  2 -> 4 [label=\"output\"]\n  kb5694f2dc8cd4460bfff74fd0792ecb3[color=lightseagreen,label=\"Output\\nrecentrifuge_stats_tabular\"]\n  4 -> kb5694f2dc8cd4460bfff74fd0792ecb3\n  kbd947a1d0443465f86585d76d9ce69f8[color=lightseagreen,label=\"Output\\nrecentrifuge_report_html\"]\n  4 -> kbd947a1d0443465f86585d76d9ce69f8\n  kc7457acb41bc4191b3fb6716e15fbe57[color=lightseagreen,label=\"Output\\nrecentrifuge_data_tabular\"]\n  4 -> kc7457acb41bc4191b3fb6716e15fbe57\n  k94f6ff070e0647ad88f8a058d0808537[color=lightseagreen,label=\"Output\\nrecentrifuge_logfile\"]\n  4 -> k94f6ff070e0647ad88f8a058d0808537\n}",
                 "history": [
                     {
-                        "hash": "76cb605583a35eb62c395933f9798887f5dd2164",
-                        "message": "fix license test",
+                        "hash": "4854483dab21555869c5c49b91fa3113146c07dc",
+                        "message": "Update Bracken version toolshed",
+                        "num": 3,
+                        "short_hash": "4854483da",
+                        "unix": "1712233925"
+                    },
+                    {
+                        "hash": "96c80b0ad7e5179b3d43364e789efee1adeea130",
+                        "message": "Update workflow creators",
                         "num": 2,
-                        "short_hash": "76cb60558",
-                        "unix": "1705331890"
+                        "short_hash": "96c80b0ad",
+                        "unix": "1706542936"
                     },
                     {
-                        "hash": "1b86f105a7a072e2405b937e816e682617fe779d",
-                        "message": "add test files",
+                        "hash": "96df58f868367e22ade2e451a1d9ecacba822bcc",
+                        "message": "Create new tutorial for checking expected species and contamination in bacterial isolate",
                         "num": 1,
-                        "short_hash": "1b86f105a",
-                        "unix": "1705326039"
-                    }
-                ],
-                "inputs": [],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"Copernicus Data Space Ecosystem\"];\n  1[\"Holoviz\"];\n  0 -->|output_collection| 1;",
-                "modified": "2024-08-18 00:06:22 +0000",
-                "name": "NDVI with OpenEO",
-                "outputs": [],
-                "parent_id": "ecology/ndvi_openeo",
-                "path": "topics/ecology/tutorials/ndvi_openeo/workflows/NDVI-with-OpenEO.ga",
-                "tags": [],
-                "test_results": null,
-                "tests": true,
-                "title": "NDVI with OpenEO",
-                "topic_id": "ecology",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-ndvi_openeo/versions/ndvi-with-openeo",
-                "tutorial_id": "ndvi_openeo",
-                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ndvi_openeo/workflows/NDVI-with-OpenEO.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ndvi_openeo/workflows/NDVI-with-OpenEO.html",
-                "version": 1,
-                "wfid": "ecology-ndvi_openeo",
-                "wfname": "ndvi-with-openeo",
-                "workflow": "NDVI-with-OpenEO.ga",
-                "workflow_tools": [
-                    "interactive_tool_copernicus_notebook",
-                    "interactive_tool_holoviz"
-                ],
-                "workflowhub_id": "1242"
-            },
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0009-0008-0622-604X",
-                        "name": "Marie Joss\u00e9",
-                        "url": "https://github.com/Marie59"
+                        "short_hash": "96df58f86",
+                        "unix": "1706542439"
                     }
                 ],
-                "description": "",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Copernicus Data Space Ecosystem\"]\n  1[label=\"Holoviz\"]\n  0 -> 1 [label=\"output_collection\"]\n}",
-                "history": [
-                    {
-                        "hash": "c9e46f370f0170707bf194000ba7d81dedb1eb56",
-                        "message": "fix license",
-                        "num": 6,
-                        "short_hash": "c9e46f370",
-                        "unix": "1705331825"
-                    },
+                "inputs": [
                     {
-                        "hash": "fb3bcc497acebb64dfa435efd224496615913356",
-                        "message": "add workflow",
-                        "num": 5,
-                        "short_hash": "fb3bcc497",
-                        "unix": "1705324903"
+                        "annotation": "reverse_reads",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "reverse_reads",
+                                "name": "reverse_reads"
+                            }
+                        ],
+                        "label": "reverse_reads",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 56
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fastq\", \"fastq.gz\", \"fastqsanger\", \"fastqsanger.gz\"], \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "a39893cf-49cb-4c5c-9e71-0f8004a2a1ee",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
-                        "hash": "0f88c406dde20fdb8f822000a7a6f10802d6d644",
-                        "message": "Delete topics/ecology/tutorials/ndvi_openeo/workflows/main_workflow.ga",
-                        "num": 4,
-                        "short_hash": "0f88c406d",
-                        "unix": "1705324823"
-                    },
+                        "annotation": "forward_reads",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "forward_reads",
+                                "name": "forward_reads"
+                            }
+                        ],
+                        "label": "forward_reads",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 179
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fastq\", \"fastq.gz\", \"fastqsanger\", \"fastqsanger.gz\"], \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ca539dfd-e173-42d6-998a-0fc4c5f3d5b8",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nreverse_reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nforward_reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Kraken2\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  a408a644-58cd-4f5e-af25-15b5ea63aa76[\"Output\\nkraken_report_reads\"];\n  2 --> a408a644-58cd-4f5e-af25-15b5ea63aa76;\n  style a408a644-58cd-4f5e-af25-15b5ea63aa76 stroke:#2c3143,stroke-width:4px;\n  54b85a53-72ee-4b73-b186-7fd55e8aab9b[\"Output\\nkraken_report_tabular\"];\n  2 --> 54b85a53-72ee-4b73-b186-7fd55e8aab9b;\n  style 54b85a53-72ee-4b73-b186-7fd55e8aab9b stroke:#2c3143,stroke-width:4px;\n  3[\"Bracken\"];\n  2 -->|report_output| 3;\n  ae6c6464-f5f5-4e5b-b616-d38166fc0133[\"Output\\nbracken_report_tsv\"];\n  3 --> ae6c6464-f5f5-4e5b-b616-d38166fc0133;\n  style ae6c6464-f5f5-4e5b-b616-d38166fc0133 stroke:#2c3143,stroke-width:4px;\n  8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8[\"Output\\nbracken_kraken_report\"];\n  3 --> 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8;\n  style 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8 stroke:#2c3143,stroke-width:4px;\n  4[\"Recentrifuge\"];\n  2 -->|output| 4;\n  b5694f2d-c8cd-4460-bfff-74fd0792ecb3[\"Output\\nrecentrifuge_stats_tabular\"];\n  4 --> b5694f2d-c8cd-4460-bfff-74fd0792ecb3;\n  style b5694f2d-c8cd-4460-bfff-74fd0792ecb3 stroke:#2c3143,stroke-width:4px;\n  bd947a1d-0443-465f-8658-5d76d9ce69f8[\"Output\\nrecentrifuge_report_html\"];\n  4 --> bd947a1d-0443-465f-8658-5d76d9ce69f8;\n  style bd947a1d-0443-465f-8658-5d76d9ce69f8 stroke:#2c3143,stroke-width:4px;\n  c7457acb-41bc-4191-b3fb-6716e15fbe57[\"Output\\nrecentrifuge_data_tabular\"];\n  4 --> c7457acb-41bc-4191-b3fb-6716e15fbe57;\n  style c7457acb-41bc-4191-b3fb-6716e15fbe57 stroke:#2c3143,stroke-width:4px;\n  94f6ff07-0e06-47ad-88f8-a058d0808537[\"Output\\nrecentrifuge_logfile\"];\n  4 --> 94f6ff07-0e06-47ad-88f8-a058d0808537;\n  style 94f6ff07-0e06-47ad-88f8-a058d0808537 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:07 +0000",
+                "name": "Checking expected species and contamination in bacterial isolate",
+                "outputs": [
                     {
-                        "hash": "9336c867093f14929f5eeb2f8ac7ca7e3484f4f0",
-                        "message": "add new workflow",
-                        "num": 3,
-                        "short_hash": "9336c8670",
-                        "unix": "1705317870"
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "single_paired|forward_input": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "single_paired|reverse_input": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Kraken2",
+                        "outputs": [
+                            {
+                                "name": "report_output",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 280,
+                            "top": 0
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e674066930b2",
+                            "name": "kraken2",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"confidence\": \"0.0\", \"kraken2_database\": \"2023-08-24T153645Z_standard_prebuilt_pluspf_16gb_2022-06-07\", \"min_base_quality\": \"10\", \"minimum_hit_groups\": \"2\", \"quick\": false, \"report\": {\"create_report\": true, \"use_mpa_style\": false, \"report_zero_counts\": false, \"report_minimizer_data\": false}, \"single_paired\": {\"single_paired_selector\": \"yes\", \"__current_case__\": 1, \"forward_input\": {\"__class__\": \"ConnectedValue\"}, \"reverse_input\": {\"__class__\": \"ConnectedValue\"}}, \"split_reads\": false, \"use_names\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.1+galaxy1",
+                        "type": "tool",
+                        "uuid": "75b7f2b8-2b63-4f1a-a877-4babef16a08b",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "kraken_report_reads",
+                                "output_name": "output",
+                                "uuid": "a408a644-58cd-4f5e-af25-15b5ea63aa76"
+                            },
+                            {
+                                "label": "kraken_report_tabular",
+                                "output_name": "report_output",
+                                "uuid": "54b85a53-72ee-4b73-b186-7fd55e8aab9b"
+                            }
+                        ]
                     },
                     {
-                        "hash": "c8b1d5f64271724fb617321c267940f72c1cb062",
-                        "message": "Delete topics/ecology/tutorials/ndvi_openeo/workflows/main_workflow.ga",
-                        "num": 2,
-                        "short_hash": "c8b1d5f64",
-                        "unix": "1705317845"
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "input": {
+                                "id": 2,
+                                "output_name": "report_output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Bracken",
+                        "outputs": [
+                            {
+                                "name": "report",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "kraken_report",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 560,
+                            "top": 40
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionkraken_report": {
+                                "action_arguments": {
+                                    "newname": "bracken_kraken_report"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "kraken_report"
+                            },
+                            "RenameDatasetActionreport": {
+                                "action_arguments": {
+                                    "newname": "bracken_report_tsv"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "report"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "0357fb68688c419f",
+                            "name": "bracken",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"kmer_distr\": \"bf6177af-7f5b-4005-9bec-fc7c89c3cb1c\", \"level\": \"S\", \"logfile_output\": false, \"out_report\": true, \"threshold\": \"10\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.8+galaxy0",
+                        "type": "tool",
+                        "uuid": "53b9c80b-f5f4-4fee-9778-fb4fd6b76165",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "bracken_report_tsv",
+                                "output_name": "report",
+                                "uuid": "ae6c6464-f5f5-4e5b-b616-d38166fc0133"
+                            },
+                            {
+                                "label": "bracken_kraken_report",
+                                "output_name": "kraken_report",
+                                "uuid": "8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8"
+                            }
+                        ]
                     },
                     {
-                        "hash": "9346f227c4a55267bedf0c2a76fb0c2b3fec185b",
-                        "message": "add ndvi openeo tuto",
-                        "num": 1,
-                        "short_hash": "9346f227c",
-                        "unix": "1705076722"
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Recentrifuge",
+                        "outputs": [
+                            {
+                                "name": "html_report",
+                                "type": "html"
+                            },
+                            {
+                                "name": "logfile",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "data_tsv",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "stat_tsv",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 560,
+                            "top": 329
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActiondata_tsv": {
+                                "action_arguments": {
+                                    "newname": "recentrifuge_data_tabular"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "data_tsv"
+                            },
+                            "RenameDatasetActionhtml_report": {
+                                "action_arguments": {
+                                    "newname": "recentrifuge_report_html"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "html_report"
+                            },
+                            "RenameDatasetActionlogfile": {
+                                "action_arguments": {
+                                    "newname": "recentrifuge_logfile"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "logfile"
+                            },
+                            "RenameDatasetActionstat_tsv": {
+                                "action_arguments": {
+                                    "newname": "recentrifuge_stats_tabular"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "stat_tsv"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "b5407cc2bf51",
+                            "name": "recentrifuge",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"advanced_option\": {\"controls\": \"0\", \"scoring\": null, \"minscore_value\": \"0\", \"mintaxa\": \"0\", \"exclude_taxa_name\": null, \"include_taxa_name\": null, \"avoidcross\": false}, \"database\": {\"database_name\": \"ncbi-2023-06-27\"}, \"file_type\": {\"filetype\": \"kraken\", \"__current_case__\": 3}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"more_advanced_option\": {\"ctrlminscore\": \"0\", \"ctrlmintaxa\": \"0\", \"summary\": \"ADD\", \"takeoutroot\": false, \"nokollapse\": false, \"strain\": true, \"sequential\": false}, \"output_option\": {\"extra\": \"TSV\", \"nohtml\": false, \"no_logfile\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.12.1+galaxy0",
+                        "type": "tool",
+                        "uuid": "4b3b34ad-2352-4e93-abbc-69da3ab9ee3a",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "recentrifuge_stats_tabular",
+                                "output_name": "stat_tsv",
+                                "uuid": "b5694f2d-c8cd-4460-bfff-74fd0792ecb3"
+                            },
+                            {
+                                "label": "recentrifuge_report_html",
+                                "output_name": "html_report",
+                                "uuid": "bd947a1d-0443-465f-8658-5d76d9ce69f8"
+                            },
+                            {
+                                "label": "recentrifuge_data_tabular",
+                                "output_name": "data_tsv",
+                                "uuid": "c7457acb-41bc-4191-b3fb-6716e15fbe57"
+                            },
+                            {
+                                "label": "recentrifuge_logfile",
+                                "output_name": "logfile",
+                                "uuid": "94f6ff07-0e06-47ad-88f8-a058d0808537"
+                            }
+                        ]
                     }
                 ],
-                "inputs": [],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"Copernicus Data Space Ecosystem\"];\n  1[\"Holoviz\"];\n  0 -->|output_collection| 1;",
-                "modified": "2024-08-18 00:06:22 +0000",
-                "name": "NDVI with OpenEO",
-                "outputs": [],
-                "parent_id": "ecology/ndvi_openeo",
-                "path": "topics/ecology/tutorials/ndvi_openeo/workflows/main_workflow.ga",
-                "tags": [],
+                "parent_id": "ecology/bacterial-isolate-species-contamination-checking",
+                "path": "topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/workflows/Checking-expected-species-and-contamination-in-bacterial-isolate.ga",
+                "tags": [
+                    "ecology"
+                ],
                 "test_results": null,
-                "tests": false,
-                "title": "NDVI with OpenEO",
+                "tests": true,
+                "title": "Checking expected species and contamination in bacterial isolate",
                 "topic_id": "ecology",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-ndvi_openeo/versions/main-workflow",
-                "tutorial_id": "ndvi_openeo",
-                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ndvi_openeo/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ndvi_openeo/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "ecology-ndvi_openeo",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-bacterial-isolate-species-contamination-checking/versions/checking-expected-species-and-contamination-in-bacterial-isolate",
+                "tutorial_id": "bacterial-isolate-species-contamination-checking",
+                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/workflows/Checking-expected-species-and-contamination-in-bacterial-isolate.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/workflows/Checking-expected-species-and-contamination-in-bacterial-isolate.html",
+                "version": 2,
+                "wfid": "ecology-bacterial-isolate-species-contamination-checking",
+                "wfname": "checking-expected-species-and-contamination-in-bacterial-isolate",
+                "workflow": "Checking-expected-species-and-contamination-in-bacterial-isolate.ga",
                 "workflow_tools": [
-                    "interactive_tool_copernicus_notebook",
-                    "interactive_tool_holoviz"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0"
                 ],
-                "workflowhub_id": "1239"
+                "workflowhub_id": "1217"
             }
-        ]
+        ],
+        "zenodo_link": "https://zenodo.org/record/10572227"
     },
     {
         "admin_install": {
@@ -69017,92 +72509,40 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ecology_beta_diversity",
-                    "owner": "ecology",
-                    "revisions": "fb7b2cbd80bb",
-                    "tool_panel_section_label": "Biodiversity data exploration",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ecology_homogeneity_normality",
-                    "owner": "ecology",
-                    "revisions": "3df8937fd6fd",
-                    "tool_panel_section_label": "Biodiversity data exploration",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ecology_link_between_var",
-                    "owner": "ecology",
-                    "revisions": "8e8867bf491a",
-                    "tool_panel_section_label": "Biodiversity data exploration",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ecology_presence_abs_abund",
+                    "name": "cb_dissim",
                     "owner": "ecology",
-                    "revisions": "4ed07d2d442b",
-                    "tool_panel_section_label": "Biodiversity data exploration",
+                    "revisions": "8dc082da41c1",
+                    "tool_panel_section_label": "Compute indicators for turnover boulders fields",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ecology_stat_presence_abs",
+                    "name": "cb_div",
                     "owner": "ecology",
-                    "revisions": "9a2e0195bb43",
+                    "revisions": "5b31641e6d30",
                     "tool_panel_section_label": "Biodiversity data exploration",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "tool_anonymization",
+                    "name": "cb_ivr",
                     "owner": "ecology",
-                    "revisions": "726a387cfdc2",
-                    "tool_panel_section_label": "Biodiversity data exploration",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "regex_find_replace",
-                    "owner": "galaxyp",
-                    "revisions": "209b7c5ee9d7",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "revisions": "bcbad4f83dec",
+                    "tool_panel_section_label": "Compute indicators for turnover boulders fields",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ecology_beta_diversity\n  owner: ecology\n  revisions: fb7b2cbd80bb\n  tool_panel_section_label: Biodiversity data exploration\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ecology_homogeneity_normality\n  owner: ecology\n  revisions: 3df8937fd6fd\n  tool_panel_section_label: Biodiversity data exploration\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ecology_link_between_var\n  owner: ecology\n  revisions: 8e8867bf491a\n  tool_panel_section_label: Biodiversity data exploration\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ecology_presence_abs_abund\n  owner: ecology\n  revisions: 4ed07d2d442b\n  tool_panel_section_label: Biodiversity data exploration\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ecology_stat_presence_abs\n  owner: ecology\n  revisions: 9a2e0195bb43\n  tool_panel_section_label: Biodiversity data exploration\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tool_anonymization\n  owner: ecology\n  revisions: 726a387cfdc2\n  tool_panel_section_label: Biodiversity data exploration\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 209b7c5ee9d7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: cb_dissim\n  owner: ecology\n  revisions: 8dc082da41c1\n  tool_panel_section_label: Compute indicators for turnover boulders fields\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cb_div\n  owner: ecology\n  revisions: 5b31641e6d30\n  tool_panel_section_label: Biodiversity data exploration\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cb_ivr\n  owner: ecology\n  revisions: bcbad4f83dec\n  tool_panel_section_label: Compute indicators for turnover boulders fields\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/champs-blocs/tutorial.json",
         "contributions": {
             "authorship": [
-                "onorvez",
                 "Marie59",
-                "colineroyaux",
                 "yvanlebras"
             ],
             "funding": [
-                "pndb",
-                "gallantries",
-                "pndb",
-                "fnso2019"
+                "pndb"
             ]
         },
         "contributors": [
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "fr",
-                "email": "olivier.norvez@mnhn.fr",
-                "id": "onorvez",
-                "joined": "2022-02",
-                "name": "Olivier Norvez",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/onorvez/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/onorvez.json"
-            },
             {
                 "affiliations": [
                     "pndb",
@@ -69115,22 +72555,6 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
             },
-            {
-                "affiliations": [
-                    "pndb",
-                    "gallantries",
-                    "elixir-europe"
-                ],
-                "elixir_node": "fr",
-                "email": "coline.royaux@mnhn.fr",
-                "id": "colineroyaux",
-                "joined": "2020-11",
-                "name": "Coline Royaux",
-                "orcid": "0000-0003-4308-5617",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/",
-                "twitter": "ColineRoyaux",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/colineroyaux.json"
-            },
             {
                 "affiliations": [
                     "pndb",
@@ -69157,213 +72581,119 @@
                 "members": [
                     "colineroyaux",
                     "Marie59",
-                    "yvanlebras",
-                    "ThibaudGlinez"
-                ],
-                "name": "P\u00f4le National de Donn\u00e9es de Biodiversit\u00e9",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pndb/",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/pndb.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
+                    "ThibaudGlinez",
                     "yvanlebras"
                 ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/PNDB_sub.png",
-                "github": false,
-                "id": "pndb",
-                "members": [
-                    "colineroyaux",
-                    "Marie59",
-                    "yvanlebras",
-                    "ThibaudGlinez"
-                ],
                 "name": "P\u00f4le National de Donn\u00e9es de Biodiversit\u00e9",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pndb/",
                 "url": "https://training.galaxyproject.org/training-material/api/organisations/pndb.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/fnso.png",
-                "funder": true,
-                "funder_name": "National Fund for Open Science",
-                "funding_id": "AAPFNSO2019OpenMetaPaper-14026",
-                "funding_statement": "This project (<a href=\"https://www.ouvrirlascience.fr/submit-your-data-its-published/\"><code class=\"language-plaintext highlighter-rouge\">AAPFNSO2019OpenMetaPaper-14026</code></a>) is funded with the support of the national Fund for Open Science programme of the French Minister of Higher Education, Research and Innovation. Their funding has supported development of data/metadata management tools and related tutorial for Ecology and FAIR topics.\n<img src=\"https://lamy-environnement.com/wp-content/uploads/2023/03/Logo-MESR.png\" alt=\"French research ministry flag with the text: with the support of the National Fund for Open Science programme of french Minister of Higher Education, Research and Innovation\" />\n<img src=\"/training-material/shared/images/fnso.png\" alt=\"FNSO logo\" />",
-                "github": false,
-                "id": "fnso2019",
-                "joined": "2023-05",
-                "members": [
-                    "yvanlebras"
-                ],
-                "name": "OpenMetaPaper",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fnso2019/",
-                "short_name": "FNSO",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/fnso2019.json"
             }
         ],
-        "dir": "topics/ecology/tutorials/biodiversity-data-exploration",
+        "dir": "topics/ecology/tutorials/champs-blocs",
         "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "ecology/biodiversity-data-exploration",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.fr"
-        ],
+        "id": "ecology/champs-blocs",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Explore your data before diving into deep analysis"
+            "Diversity indicators",
+            "Champs Blocs",
+            "Boulder Fields"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-27",
+        "mod_date": "2024-09-19",
         "objectives": [
-            "Explore Biodiversity data with taxonomic, temporal and geographical informations",
-            "Have an idea about quality content of the data regarding statistical tests like normality or homoscedasticity and coverage like temporal or geographical coverage"
+            "Calculate IVR (Visual Rollover Indicator)",
+            "Compute dissimilarity indice",
+            "Vizualize some diversity indices"
         ],
-        "pageviews": 1665,
-        "pub_date": "2022-03-01",
+        "pageviews": 229,
+        "pub_date": "2023-01-04",
         "questions": [
-            "How to explore biodiversity data?",
-            "How to look at Homoscedasticity, normality or collinearity of presences-absence or abundance data?",
-            "How to compare beta diversity taking into account space, time and species components?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "onorvez"
-                ],
-                "date": "2022-03-03",
-                "galaxy_version": "21.09",
-                "length": "1H",
-                "speakers": [
-                    "onorvez"
-                ],
-                "youtube_id": "rWfPr-5F3GQ"
-            }
+            "Which biological questions are addressed by the tutorial?",
+            "Which bioinformatics techniques are important to know for this type of data?"
         ],
-        "short_id": "T00126",
+        "short_id": "T00127",
         "short_tools": [
-            "ecology_beta_diversity",
-            "ecology_stat_presence_abs",
-            "tp_cut_tool",
-            "ecology_presence_abs_abund",
-            "ecology_link_between_var",
-            "tool_anonymization",
-            "Remove beginning1",
-            "regexColumn1",
-            "ecology_homogeneity_normality"
+            "cb_eco",
+            "cb_ivr",
+            "cb_div",
+            "cb_dissim",
+            "cb_qecb"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "ecologypreprocess",
+        "subtopic": "ecologyanalysis",
         "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                }
-            ]
+            "exact": [],
+            "inexact": []
         },
         "symlink": null,
         "tags": [
-            "taxonomic data",
-            "data quality"
+            "Ecosystem EBV class",
+            "EBV dataset",
+            "EBV workflow",
+            "Marine ecosystems"
         ],
         "time_estimation": "1H",
-        "title": "Biodiversity data exploration",
+        "title": "Champs blocs indicators",
         "tools": [
-            "Remove beginning1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/ecology/ecology_beta_diversity/ecology_beta_diversity/0.0.0",
-            "toolshed.g2.bx.psu.edu/repos/ecology/ecology_homogeneity_normality/ecology_homogeneity_normality/0.0.0",
-            "toolshed.g2.bx.psu.edu/repos/ecology/ecology_link_between_var/ecology_link_between_var/0.0.0",
-            "toolshed.g2.bx.psu.edu/repos/ecology/ecology_presence_abs_abund/ecology_presence_abs_abund/0.0.0",
-            "toolshed.g2.bx.psu.edu/repos/ecology/ecology_stat_presence_abs/ecology_stat_presence_abs/0.0.0",
-            "toolshed.g2.bx.psu.edu/repos/ecology/tool_anonymization/tool_anonymization/0.0.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0"
+            "cb_eco",
+            "cb_ivr",
+            "cb_qecb",
+            "toolshed.g2.bx.psu.edu/repos/ecology/cb_dissim/cb_dissim/0.0.0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/cb_div/cb_div/0.0.0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/cb_ivr/cb_ivr/0.0.0"
         ],
         "topic_name": "ecology",
         "topic_name_human": "Ecology",
         "tours": false,
         "translations": {
             "slides": [],
-            "tutorial": [],
+            "tutorial": [
+                "fr"
+            ],
             "video": false
         },
-        "tutorial_name": "biodiversity-data-exploration",
+        "tutorial_name": "champs-blocs",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/biodiversity-data-exploration/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/champs-blocs/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/biodiversity-data-exploration/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/champs-blocs/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/champs-blocs/tutorial.json"
         },
-        "version": 14,
+        "version": 10,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
         "visit_duration": 173,
-        "visitors": 1133,
+        "visitors": 93,
         "workflows": [
             {
                 "creators": [],
-                "description": "Biodiversity data exploration",
+                "description": "Compute indicators for Champs blocs",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReel_life_survey_fish_modif.tabular\"]\n  1[label=\"Spatial coordinates anonymization\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Homoscedasticity and normality\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Variables exploration\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Presence-absence and abundance\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Statistics on presence-absence\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Local Contributions to Beta Diversity LCBD\"]\n  0 -> 6 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nchampbloc_ivr_val.csv\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nchampbloc_ivr.csv\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nficheterrain_val.csv\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nficheterrain.csv\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nchampbloc_qecb_val.csv\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nchampbloc_qecb.csv\"]\n  6[label=\"IVR\"]\n  3 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  0 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"QECB\"]\n  3 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  4 -> 7 [label=\"output\"]\n  5 -> 7 [label=\"output\"]\n  8[label=\"Champs blocs indicators\"]\n  7 -> 8 [label=\"output_rds\"]\n}",
                 "history": [
                     {
-                        "hash": "00c1aaba1d1373e4f148e8312a54ae9cd4a38876",
-                        "message": "Make some renames for the gtn",
+                        "hash": "0b6778b7f1da935c60f9d7cbd6e8f2c9993bde5c",
+                        "message": "Add champ bloc tutorial",
                         "num": 1,
-                        "short_hash": "00c1aaba1",
-                        "unix": "1646129123"
+                        "short_hash": "0b6778b7f",
+                        "unix": "1670507254"
                     }
                 ],
                 "inputs": [
@@ -69376,628 +72706,772 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Reel_life_survey_fish_modif.tabular"
+                                "name": "champbloc_ivr_val.csv"
                             }
                         ],
-                        "label": "Reel_life_survey_fish_modif.tabular",
+                        "label": "champbloc_ivr_val.csv",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 226.44445037841797,
-                            "height": 102.55555725097656,
-                            "left": 393,
-                            "right": 593,
-                            "top": 123.8888931274414,
+                            "bottom": 217.671875,
+                            "height": 82.171875,
+                            "left": 386,
+                            "right": 586,
+                            "top": 135.5,
                             "width": 200,
-                            "x": 393,
-                            "y": 123.8888931274414
+                            "x": 386,
+                            "y": 135.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "01b5e1a1-50d0-46d2-8b68-1cbeaa4a929a",
+                        "uuid": "eeb5efda-5d7d-4220-8e0f-2587fdf3ad7d",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "97fc5a7d-db66-4c7d-8d58-97a167c4867e"
+                                "uuid": "5fcbefd3-c2d2-4e85-8b90-8f1227afbd62"
                             }
                         ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nReel_life_survey_fish_modif.tabular\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Spatial coordinates anonymization\"];\n  0 -->|output| 1;\n  2[\"Homoscedasticity and normality\"];\n  0 -->|output| 2;\n  3[\"Variables exploration\"];\n  0 -->|output| 3;\n  4[\"Presence-absence and abundance\"];\n  0 -->|output| 4;\n  5[\"Statistics on presence-absence\"];\n  0 -->|output| 5;\n  6[\"Local Contributions to Beta Diversity LCBD\"];\n  0 -->|output| 6;",
-                "modified": "2024-08-18 00:06:22 +0000",
-                "name": "Workflow 'Biodiversity data exploration tuto'",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Reel_life_survey_fish_modif.tabular"
+                                "name": "champbloc_ivr.csv"
                             }
                         ],
-                        "label": "Reel_life_survey_fish_modif.tabular",
+                        "label": "champbloc_ivr.csv",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 226.44445037841797,
-                            "height": 102.55555725097656,
-                            "left": 393,
-                            "right": 593,
-                            "top": 123.8888931274414,
+                            "bottom": 305.671875,
+                            "height": 82.171875,
+                            "left": 383,
+                            "right": 583,
+                            "top": 223.5,
                             "width": 200,
-                            "x": 393,
-                            "y": 123.8888931274414
+                            "x": 383,
+                            "y": 223.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "01b5e1a1-50d0-46d2-8b68-1cbeaa4a929a",
+                        "uuid": "5a645b0a-9709-45d2-84d2-a334316ca860",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "97fc5a7d-db66-4c7d-8d58-97a167c4867e"
+                                "uuid": "4580be50-8a61-4930-b031-e63701223b3b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/tool_anonymization/tool_anonymization/0.0.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "ficheterrain_val.csv"
                             }
+                        ],
+                        "label": "ficheterrain_val.csv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 400.671875,
+                            "height": 82.171875,
+                            "left": 380,
+                            "right": 580,
+                            "top": 318.5,
+                            "width": 200,
+                            "x": 380,
+                            "y": 318.5
                         },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "dad7d6cf-b728-4e05-bf85-437bb84d71cd",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "16a16950-c439-4f47-9d23-e433152ac9e3"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Spatial coordinates anonymization",
-                                "name": "input"
+                                "description": "",
+                                "name": "ficheterrain.csv"
                             }
                         ],
-                        "label": null,
-                        "name": "Spatial coordinates anonymization",
-                        "outputs": [
+                        "label": "ficheterrain.csv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 481.28125,
+                            "height": 61.78125,
+                            "left": 380,
+                            "right": 580,
+                            "top": 419.5,
+                            "width": 200,
+                            "x": 380,
+                            "y": 419.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "82b42eb2-7530-4b90-884e-5f837b027dc7",
+                        "workflow_outputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "ba5ad2d3-b368-45ad-8a68-f4150f74b505"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "champbloc_qecb_val.csv"
                             }
                         ],
+                        "label": "champbloc_qecb_val.csv",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 240.44445037841797,
-                            "height": 113.55555725097656,
-                            "left": 610,
-                            "right": 810,
-                            "top": 126.8888931274414,
+                            "bottom": 579.671875,
+                            "height": 82.171875,
+                            "left": 379,
+                            "right": 579,
+                            "top": 497.5,
                             "width": 200,
-                            "x": 610,
-                            "y": 126.8888931274414
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/tool_anonymization/tool_anonymization/0.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "726a387cfdc2",
-                            "name": "tool_anonymization",
-                            "owner": "ecology",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "x": 379,
+                            "y": 497.5
                         },
-                        "tool_state": "{\"colnames\": \"true\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"latitude\": \"9\", \"longitude\": \"10\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.0.0",
-                        "type": "tool",
-                        "uuid": "c629e167-96eb-48e3-b1fe-a6d1d315acb0",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "34ec646b-ef25-4263-94db-d082e546a69f",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "5deea508-0542-4eb8-ac66-84ac0a7162c2"
+                                "uuid": "5a2619ce-3765-47c8-9d22-11903e0552a4"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_homogeneity_normality/ecology_homogeneity_normality/0.0.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
+                        "id": 5,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "champbloc_qecb.csv"
                             }
+                        ],
+                        "label": "champbloc_qecb.csv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 680.671875,
+                            "height": 82.171875,
+                            "left": 379,
+                            "right": 579,
+                            "top": 598.5,
+                            "width": 200,
+                            "x": 379,
+                            "y": 598.5
                         },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "cb4cf37d-788d-42e5-9810-77b2ca4d190e",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "b1b2286a-a7af-4b5a-9ea0-c9ea60a48ba0"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nchampbloc_ivr_val.csv\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nchampbloc_ivr.csv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nficheterrain_val.csv\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nficheterrain.csv\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nchampbloc_qecb_val.csv\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nchampbloc_qecb.csv\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"IVR\"];\n  3 -->|output| 6;\n  2 -->|output| 6;\n  0 -->|output| 6;\n  1 -->|output| 6;\n  7[\"QECB\"];\n  3 -->|output| 7;\n  2 -->|output| 7;\n  4 -->|output| 7;\n  5 -->|output| 7;\n  8[\"Champs blocs indicators\"];\n  7 -->|output_rds| 8;",
+                "modified": "2024-10-02 12:08:07 +0000",
+                "name": "Champs blocs indicators",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Homoscedasticity and normality",
-                                "name": "input"
+                                "description": "",
+                                "name": "champbloc_ivr_val.csv"
                             }
                         ],
-                        "label": null,
-                        "name": "Homoscedasticity and normality",
-                        "outputs": [
-                            {
-                                "name": "plots",
-                                "type": "input"
-                            },
+                        "label": "champbloc_ivr_val.csv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 217.671875,
+                            "height": 82.171875,
+                            "left": 386,
+                            "right": 586,
+                            "top": 135.5,
+                            "width": 200,
+                            "x": 386,
+                            "y": 135.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "eeb5efda-5d7d-4220-8e0f-2587fdf3ad7d",
+                        "workflow_outputs": [
                             {
-                                "name": "output_levene",
-                                "type": "txt"
-                            },
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "5fcbefd3-c2d2-4e85-8b90-8f1227afbd62"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output_ks",
-                                "type": "txt"
+                                "description": "",
+                                "name": "champbloc_ivr.csv"
                             }
                         ],
+                        "label": "champbloc_ivr.csv",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 414.3888854980469,
-                            "height": 235.5,
-                            "left": 617,
-                            "right": 817,
-                            "top": 178.88888549804688,
+                            "bottom": 305.671875,
+                            "height": 82.171875,
+                            "left": 383,
+                            "right": 583,
+                            "top": 223.5,
                             "width": 200,
-                            "x": 617,
-                            "y": 178.88888549804688
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_homogeneity_normality/ecology_homogeneity_normality/0.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3df8937fd6fd",
-                            "name": "ecology_homogeneity_normality",
-                            "owner": "ecology",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "x": 383,
+                            "y": 223.5
                         },
-                        "tool_state": "{\"colnames\": \"true\", \"date\": \"11\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"species\": \"16\", \"variable\": \"18\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.0.0",
-                        "type": "tool",
-                        "uuid": "06eb8a3f-1702-4ca5-8124-f501adbb4acc",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "5a645b0a-9709-45d2-84d2-a334316ca860",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_levene",
-                                "uuid": "30bc9ecc-c9de-4e74-bc9d-284f2d5a60aa"
-                            },
+                                "output_name": "output",
+                                "uuid": "4580be50-8a61-4930-b031-e63701223b3b"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "output_ks",
-                                "uuid": "df48b84c-5bc3-4eca-bbde-dbf21e708959"
-                            },
+                                "description": "",
+                                "name": "ficheterrain_val.csv"
+                            }
+                        ],
+                        "label": "ficheterrain_val.csv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 400.671875,
+                            "height": 82.171875,
+                            "left": 380,
+                            "right": 580,
+                            "top": 318.5,
+                            "width": 200,
+                            "x": 380,
+                            "y": 318.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "dad7d6cf-b728-4e05-bf85-437bb84d71cd",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "plots",
-                                "uuid": "08790bfd-cfb2-44cb-a156-a71abcd91369"
+                                "output_name": "output",
+                                "uuid": "16a16950-c439-4f47-9d23-e433152ac9e3"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_link_between_var/ecology_link_between_var/0.0.0",
+                        "content_id": null,
                         "errors": null,
                         "id": 3,
-                        "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "ficheterrain.csv"
                             }
+                        ],
+                        "label": "ficheterrain.csv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 481.28125,
+                            "height": 61.78125,
+                            "left": 380,
+                            "right": 580,
+                            "top": 419.5,
+                            "width": 200,
+                            "x": 380,
+                            "y": 419.5
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Variables exploration",
-                        "outputs": [
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "82b42eb2-7530-4b90-884e-5f837b027dc7",
+                        "workflow_outputs": [
                             {
-                                "name": "plots",
-                                "type": "input"
-                            },
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "ba5ad2d3-b368-45ad-8a68-f4150f74b505"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output_coli",
-                                "type": "txt"
+                                "description": "",
+                                "name": "champbloc_qecb_val.csv"
                             }
                         ],
+                        "label": "champbloc_qecb_val.csv",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 408.2222137451172,
-                            "height": 164.3333282470703,
-                            "left": 613,
-                            "right": 813,
-                            "top": 243.88888549804688,
+                            "bottom": 579.671875,
+                            "height": 82.171875,
+                            "left": 379,
+                            "right": 579,
+                            "top": 497.5,
                             "width": 200,
-                            "x": 613,
-                            "y": 243.88888549804688
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_link_between_var/ecology_link_between_var/0.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "8e8867bf491a",
-                            "name": "ecology_link_between_var",
-                            "owner": "ecology",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "x": 379,
+                            "y": 497.5
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"colnames\": \"true\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"method\": {\"type\": \"collinearity\", \"__current_case__\": 0, \"species\": \"16\", \"columns\": [\"12\", \"17\", \"18\"]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.0.0",
-                        "type": "tool",
-                        "uuid": "83cdbf22-ac7e-4ddf-a444-3de0b347d613",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "34ec646b-ef25-4263-94db-d082e546a69f",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_coli",
-                                "uuid": "a8a2bbd3-aedc-4b40-adb1-abdac7e95034"
-                            },
+                                "output_name": "output",
+                                "uuid": "5a2619ce-3765-47c8-9d22-11903e0552a4"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "champbloc_qecb.csv"
+                            }
+                        ],
+                        "label": "champbloc_qecb.csv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 680.671875,
+                            "height": 82.171875,
+                            "left": 379,
+                            "right": 579,
+                            "top": 598.5,
+                            "width": 200,
+                            "x": 379,
+                            "y": 598.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "cb4cf37d-788d-42e5-9810-77b2ca4d190e",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "plots",
-                                "uuid": "0f18247b-f4a3-45c5-9053-bfd3fb2ad6a1"
+                                "output_name": "output",
+                                "uuid": "b1b2286a-a7af-4b5a-9ea0-c9ea60a48ba0"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_presence_abs_abund/ecology_presence_abs_abund/0.0.0",
+                        "content_id": "cb_ivr",
                         "errors": null,
-                        "id": 4,
+                        "id": 6,
                         "input_connections": {
-                            "input": {
+                            "fiche_term": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "fiche_val": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "input_data": {
                                 "id": 0,
                                 "output_name": "output"
+                            },
+                            "input_data2": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool IVR",
+                                "name": "fiche_term"
+                            },
+                            {
+                                "description": "runtime parameter for tool IVR",
+                                "name": "fiche_val"
+                            },
+                            {
+                                "description": "runtime parameter for tool IVR",
+                                "name": "input_data"
+                            },
+                            {
+                                "description": "runtime parameter for tool IVR",
+                                "name": "input_data2"
+                            }
+                        ],
                         "label": null,
-                        "name": "Presence-absence and abundance",
+                        "name": "IVR",
                         "outputs": [
                             {
                                 "name": "plots",
                                 "type": "input"
                             },
                             {
-                                "name": "output_abund",
-                                "type": "txt"
+                                "name": "output_rds",
+                                "type": "input"
+                            },
+                            {
+                                "name": "output_ivr",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 507.8333282470703,
-                            "height": 143.94444274902344,
-                            "left": 613,
-                            "right": 813,
-                            "top": 363.8888854980469,
+                            "bottom": 392.625,
+                            "height": 245.125,
+                            "left": 1079,
+                            "right": 1279,
+                            "top": 147.5,
                             "width": 200,
-                            "x": 613,
-                            "y": 363.8888854980469
+                            "x": 1079,
+                            "y": 147.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_presence_abs_abund/ecology_presence_abs_abund/0.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "4ed07d2d442b",
-                            "name": "ecology_presence_abs_abund",
-                            "owner": "ecology",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"abundance\": \"18\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"colnames\": \"true\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"method\": {\"type\": \"abund\", \"__current_case__\": 0, \"latitude\": \"9\", \"longitude\": \"10\", \"individual\": \"fishes\", \"species\": \"16\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": "cb_ivr",
+                        "tool_state": "{\"fiche_term\": {\"__class__\": \"RuntimeValue\"}, \"fiche_val\": {\"__class__\": \"RuntimeValue\"}, \"input_data\": {\"__class__\": \"RuntimeValue\"}, \"input_data2\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "0.0.0",
                         "type": "tool",
-                        "uuid": "46f4249f-7a72-4d75-8a3f-a1fa62cba536",
+                        "uuid": "7a3c6336-6af4-4122-82a9-2b1476f471bd",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_abund",
-                                "uuid": "83036527-2e15-4c84-b521-262c88fe5657"
+                                "output_name": "plots",
+                                "uuid": "81408705-3fb8-41af-b329-fc9fbd360f52"
                             },
                             {
                                 "label": null,
-                                "output_name": "plots",
-                                "uuid": "7ecccacc-3ab4-449e-bb61-5378d14fb42b"
+                                "output_name": "output_rds",
+                                "uuid": "e2dc091a-bb27-4132-9196-95a44ef78597"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_ivr",
+                                "uuid": "60b6f4c5-a080-4daf-9f28-0c03132d42f2"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_stat_presence_abs/ecology_stat_presence_abs/0.0.0",
+                        "content_id": "cb_qecb",
                         "errors": null,
-                        "id": 5,
+                        "id": 7,
                         "input_connections": {
-                            "input": {
-                                "id": 0,
+                            "fiche_term": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "fiche_val": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "input_data": {
+                                "id": 4,
+                                "output_name": "output"
+                            },
+                            "input_data2": {
+                                "id": 5,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool QECB",
+                                "name": "fiche_term"
+                            },
+                            {
+                                "description": "runtime parameter for tool QECB",
+                                "name": "fiche_val"
+                            },
+                            {
+                                "description": "runtime parameter for tool QECB",
+                                "name": "input_data"
+                            },
+                            {
+                                "description": "runtime parameter for tool QECB",
+                                "name": "input_data2"
+                            }
+                        ],
                         "label": null,
-                        "name": "Statistics on presence-absence",
+                        "name": "QECB",
                         "outputs": [
                             {
-                                "name": "output_md",
-                                "type": "png"
+                                "name": "plots",
+                                "type": "input"
                             },
                             {
-                                "name": "output_0",
-                                "type": "png"
+                                "name": "output_rds",
+                                "type": "input"
+                            },
+                            {
+                                "name": "output_qecb",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 668.6111145019531,
-                            "height": 184.72222900390625,
-                            "left": 613,
-                            "right": 813,
-                            "top": 483.8888854980469,
+                            "bottom": 663.625,
+                            "height": 245.125,
+                            "left": 1092,
+                            "right": 1292,
+                            "top": 418.5,
                             "width": 200,
-                            "x": 613,
-                            "y": 483.8888854980469
+                            "x": 1092,
+                            "y": 418.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_stat_presence_abs/ecology_stat_presence_abs/0.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9a2e0195bb43",
-                            "name": "ecology_stat_presence_abs",
-                            "owner": "ecology",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"colnames\": \"true\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"location\": \"8\", \"species\": \"16\", \"time\": \"11\", \"variable1\": \"18\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": "cb_qecb",
+                        "tool_state": "{\"fiche_term\": {\"__class__\": \"RuntimeValue\"}, \"fiche_val\": {\"__class__\": \"RuntimeValue\"}, \"input_data\": {\"__class__\": \"RuntimeValue\"}, \"input_data2\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "0.0.0",
                         "type": "tool",
-                        "uuid": "d8d3a4db-e5e3-4453-87e0-592d987987a6",
+                        "uuid": "615551d9-0f93-4801-9a53-645448ee83db",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_0",
-                                "uuid": "494e4e8d-93ca-466e-a0ea-3ea83f59d64a"
+                                "output_name": "plots",
+                                "uuid": "3f823485-3454-4b57-a9f0-5071ae870aa0"
                             },
                             {
                                 "label": null,
-                                "output_name": "output_md",
-                                "uuid": "74b67cb1-d5d6-418b-a56a-645d0b17f559"
+                                "output_name": "output_rds",
+                                "uuid": "6ba691f4-0a10-46c2-8737-1a7405becf8f"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_qecb",
+                                "uuid": "de7b3d96-08d8-4f9e-884a-d1eefde7a670"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_beta_diversity/ecology_beta_diversity/0.0.0",
+                        "content_id": "cb_eco",
                         "errors": null,
-                        "id": 6,
+                        "id": 8,
                         "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
+                            "input_data": {
+                                "id": 7,
+                                "output_name": "output_rds"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Local Contributions to Beta Diversity (LCBD)",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Ecology",
+                                "name": "input_data"
+                            }
+                        ],
+                        "label": "Champs blocs indicators",
+                        "name": "Ecology",
                         "outputs": [
                             {
                                 "name": "plots",
                                 "type": "input"
                             },
                             {
-                                "name": "output_lcbd",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "output_scbd",
-                                "type": "txt"
+                                "name": "output_rds",
+                                "type": "input"
                             },
                             {
-                                "name": "output_beta",
-                                "type": "Rdata"
+                                "name": "output_eco",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 890.1666870117188,
-                            "height": 286.27777099609375,
-                            "left": 613,
-                            "right": 813,
-                            "top": 603.888916015625,
+                            "bottom": 659.84375,
+                            "height": 174.34375,
+                            "left": 1404,
+                            "right": 1604,
+                            "top": 485.5,
                             "width": 200,
-                            "x": 613,
-                            "y": 603.888916015625
+                            "x": 1404,
+                            "y": 485.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/ecology_beta_diversity/ecology_beta_diversity/0.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "fb7b2cbd80bb",
-                            "name": "ecology_beta_diversity",
-                            "owner": "ecology",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"abundance\": \"18\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"colnames\": \"true\", \"date\": \"11\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"location\": \"8\", \"method\": {\"type\": \"Graph\", \"__current_case__\": 0, \"latitude\": \"9\", \"longitude\": \"10\"}, \"rdata\": \"true\", \"species\": \"16\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": "cb_eco",
+                        "tool_state": "{\"input_data\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "0.0.0",
                         "type": "tool",
-                        "uuid": "16c310f1-d14c-4778-a5cf-4798e3eb7043",
+                        "uuid": "d4897790-0e61-425a-a7d8-3120e653de81",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "plots",
-                                "uuid": "d6465151-e83a-4031-bd96-8a8f3d999bbb"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_lcbd",
-                                "uuid": "418fbdae-1a70-4e8c-a645-9e34b009f976"
+                                "uuid": "6ba51e6e-8183-478d-a1f6-adee124a18aa"
                             },
                             {
                                 "label": null,
-                                "output_name": "output_scbd",
-                                "uuid": "dd87eda6-8f3c-4e76-b3ae-f5c464697956"
+                                "output_name": "output_rds",
+                                "uuid": "14901eab-4866-4d92-ac9e-e79390cd6b4d"
                             },
                             {
                                 "label": null,
-                                "output_name": "output_beta",
-                                "uuid": "acf06966-78ec-4013-a32b-061b385808cf"
+                                "output_name": "output_eco",
+                                "uuid": "ef6de5cf-0d90-47f1-bda9-0f44a7837555"
                             }
                         ]
                     }
                 ],
-                "parent_id": "ecology/biodiversity-data-exploration",
-                "path": "topics/ecology/tutorials/biodiversity-data-exploration/workflows/main_workflow.ga",
+                "parent_id": "ecology/champs-blocs",
+                "path": "topics/ecology/tutorials/champs-blocs/workflows/main_workflow.ga",
                 "tags": [
                     "ecology"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Workflow 'Biodiversity data exploration tuto'",
+                "title": "Champs blocs indicators",
                 "topic_id": "ecology",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-biodiversity-data-exploration/versions/main-workflow",
-                "tutorial_id": "biodiversity-data-exploration",
-                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/biodiversity-data-exploration/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/biodiversity-data-exploration/workflows/main_workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-champs-blocs/versions/main-workflow",
+                "tutorial_id": "champs-blocs",
+                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/champs-blocs/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/champs-blocs/workflows/main_workflow.html",
                 "version": 1,
-                "wfid": "ecology-biodiversity-data-exploration",
+                "wfid": "ecology-champs-blocs",
                 "wfname": "main-workflow",
                 "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/ecology/ecology_beta_diversity/ecology_beta_diversity/0.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/ecology_homogeneity_normality/ecology_homogeneity_normality/0.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/ecology_link_between_var/ecology_link_between_var/0.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/ecology_presence_abs_abund/ecology_presence_abs_abund/0.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/ecology_stat_presence_abs/ecology_stat_presence_abs/0.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/tool_anonymization/tool_anonymization/0.0.0"
+                    "cb_eco",
+                    "cb_ivr",
+                    "cb_qecb"
                 ],
-                "workflowhub_id": "1278"
+                "workflowhub_id": "1256"
             }
-        ],
-        "zenodo_link": "https://zenodo.org/record/6107457"
+        ]
     },
     {
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "ddf54b12c295",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "merge_cols",
-                    "owner": "devteam",
-                    "revisions": "dd40b1e9eebe",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pampa_communitymetrics",
-                    "owner": "ecology",
-                    "revisions": "c67ece97d4b1",
-                    "tool_panel_section_label": "Species abundance",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pampa_glmcomm",
-                    "owner": "ecology",
-                    "revisions": "b40fecef616b",
-                    "tool_panel_section_label": "Species abundance",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pampa_glmsp",
-                    "owner": "ecology",
-                    "revisions": "7a69e1c8ba46",
-                    "tool_panel_section_label": "Species abundance",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pampa_plotglm",
-                    "owner": "ecology",
-                    "revisions": "c448e026f122",
-                    "tool_panel_section_label": "Species abundance",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pampa_presabs",
-                    "owner": "ecology",
-                    "revisions": "1ebb70b59037",
-                    "tool_panel_section_label": "Species abundance",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "regex_find_replace",
-                    "owner": "galaxyp",
-                    "revisions": "209b7c5ee9d7",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "regex_find_replace",
-                    "owner": "galaxyp",
-                    "revisions": "209b7c5ee9d7",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "regex_find_replace",
-                    "owner": "galaxyp",
-                    "revisions": "ae8c4b2488e7",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "datamash_transpose",
-                    "owner": "iuc",
-                    "revisions": "22c2a1ac7ae3",
-                    "tool_panel_section_label": "Join, Subtract and Group",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
+            "tools": []
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: ddf54b12c295\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merge_cols\n  owner: devteam\n  revisions: dd40b1e9eebe\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pampa_communitymetrics\n  owner: ecology\n  revisions: c67ece97d4b1\n  tool_panel_section_label: Species abundance\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pampa_glmcomm\n  owner: ecology\n  revisions: b40fecef616b\n  tool_panel_section_label: Species abundance\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pampa_glmsp\n  owner: ecology\n  revisions: 7a69e1c8ba46\n  tool_panel_section_label: Species abundance\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pampa_plotglm\n  owner: ecology\n  revisions: c448e026f122\n  tool_panel_section_label: Species abundance\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pampa_presabs\n  owner: ecology\n  revisions: 1ebb70b59037\n  tool_panel_section_label: Species abundance\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 209b7c5ee9d7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 209b7c5ee9d7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: ae8c4b2488e7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_transpose\n  owner: iuc\n  revisions: 22c2a1ac7ae3\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/panoply_ebv/tutorial.json",
         "contributions": {
             "authorship": [
-                "colineroyaux",
+                "pndb",
                 "yvanlebras",
-                "dpelletier",
-                "jbmihoub"
+                "colineroyaux",
+                "Marie59",
+                "annefou"
             ],
             "funding": [
                 "gallantries",
+                "fairease",
                 "pndb"
             ]
         },
         "contributors": [
             {
-                "affiliations": [
-                    "pndb",
-                    "gallantries",
-                    "elixir-europe"
+                "avatar": "/training-material/shared/images/PNDB_sub.png",
+                "github": false,
+                "id": "pndb",
+                "members": [
+                    "colineroyaux",
+                    "Marie59",
+                    "ThibaudGlinez",
+                    "yvanlebras"
                 ],
-                "elixir_node": "fr",
-                "email": "coline.royaux@mnhn.fr",
-                "id": "colineroyaux",
-                "joined": "2020-11",
-                "name": "Coline Royaux",
-                "orcid": "0000-0003-4308-5617",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/",
-                "twitter": "ColineRoyaux",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/colineroyaux.json"
+                "name": "P\u00f4le National de Donn\u00e9es de Biodiversit\u00e9",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pndb/",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/pndb.json"
             },
             {
                 "affiliations": [
@@ -70019,19 +73493,42 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
             },
             {
-                "id": "dpelletier",
-                "joined": "2022-03",
-                "name": "Dominique Pelletier",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dpelletier/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/dpelletier.json"
+                "affiliations": [
+                    "pndb",
+                    "gallantries",
+                    "elixir-europe"
+                ],
+                "elixir_node": "fr",
+                "email": "coline.royaux@mnhn.fr",
+                "id": "colineroyaux",
+                "joined": "2020-11",
+                "name": "Coline Royaux",
+                "orcid": "0000-0003-4308-5617",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/",
+                "twitter": "ColineRoyaux",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/colineroyaux.json"
             },
             {
-                "email": "jean-baptiste.mihoub@mnhn.fr",
-                "id": "jbmihoub",
+                "affiliations": [
+                    "pndb",
+                    "fairease"
+                ],
+                "email": "marie.josse@ifremer.fr",
+                "id": "Marie59",
                 "joined": "2022-03",
-                "name": "Jean-Baptiste Mihoub",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jbmihoub/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jbmihoub.json"
+                "name": "Marie Josse",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
+            },
+            {
+                "elixir_node": "no",
+                "id": "annefou",
+                "joined": "2019-07",
+                "name": "Anne Fouilloux",
+                "orcid": "0000-0002-1784-2920",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annefou/",
+                "twitter": "AnneFouilloux",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/annefou.json"
             },
             {
                 "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
@@ -70059,6 +73556,23 @@
                 "start_date": "2020-09-01",
                 "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             },
+            {
+                "avatar": "/training-material/assets/images/fair_ease_colour.png",
+                "funder": true,
+                "funding_id": "101058785",
+                "funding_statement": "FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "fairease",
+                "joined": "2023-10",
+                "members": [
+                    "Marie59",
+                    "yvanlebras"
+                ],
+                "name": "Fair-Ease",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fairease/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/fairease.json"
+            },
             {
                 "avatar": "/training-material/shared/images/PNDB_sub.png",
                 "github": false,
@@ -70066,146 +73580,83 @@
                 "members": [
                     "colineroyaux",
                     "Marie59",
-                    "yvanlebras",
-                    "ThibaudGlinez"
+                    "ThibaudGlinez",
+                    "yvanlebras"
                 ],
                 "name": "P\u00f4le National de Donn\u00e9es de Biodiversit\u00e9",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pndb/",
                 "url": "https://training.galaxyproject.org/training-material/api/organisations/pndb.json"
             }
         ],
-        "dir": "topics/ecology/tutorials/PAMPA-toolsuite-tutorial",
+        "dir": "topics/ecology/tutorials/panoply_ebv",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "ecology/PAMPA-toolsuite-tutorial",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.fr",
-            "UseGalaxy.org.au"
-        ],
+        "id": "ecology/panoply_ebv",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Pre-process abundance data",
-            "Compute Community and Population metrics",
-            "Construct a GL(M)M with common biodiversity metrics",
-            "Interpret (and correct if needed) GL(M)M results",
-            "Learn about and interpret common tests to evaluate the quality of your GL(M)M",
-            "Use an Essential Biodiversity Variables workflow"
+            "Inspect and view EBV cube netCDF data with Panoply",
+            "Interact with Galaxy to save your plots"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2024-06-27",
         "objectives": [
-            "Upload data from DATRAS portal of ICES",
-            "Pre-process population data with Galaxy",
-            "Learning how to use an ecological analysis workflow from raw data to graphical representations",
-            "Learning how to construct a Generalized Linear (Mixed) Model from a usual ecological question",
-            "Learning how to interpret a Generalized Linear (Mixed) Model"
+            "Learn to use Panoply in Galaxy to visuallize EBV cube netCDF geo-referenced data",
+            "Learn how Panoply plots are exported to Galaxy"
         ],
-        "pageviews": 1262,
-        "pub_date": "2020-11-19",
+        "pageviews": 220,
+        "pub_date": "2022-10-28",
         "questions": [
-            "How to evaluate properly populations and communities biological state with abundance data?",
-            "How does trawl exploited populations of Baltic sea, Southern Atlantic and Scotland are doing over time?",
-            "How to compute and analyze biodiversity metrics from abundance data?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "colineroyaux"
-                ],
-                "date": "2022-03-03",
-                "galaxy_version": "21.09",
-                "length": "2H",
-                "speakers": [
-                    "colineroyaux"
-                ],
-                "youtube_id": "leMPC2Ckehc"
-            }
+            "How to start Panoply interactive environment in Galaxy?",
+            "How to inspect EBV cube netCDF data?",
+            "How to make a plot with Panoply?",
+            "Where to save your plots in Panoply?",
+            "How to customize plots in Panoply?",
+            "How to generate animation in Panoply?"
         ],
-        "short_id": "T00125",
+        "short_id": "T00131",
         "short_tools": [
-            "pampa_plotglm",
-            "pampa_glmcomm",
-            "tp_cut_tool",
-            "tp_cat",
-            "pampa_presabs",
-            "tp_easyjoin_tool",
-            "Count1",
-            "datamash_transpose",
-            "Filter1",
-            "tp_sort_header_tool",
-            "pampa_communitymetrics",
-            "regex1",
-            "regexColumn1",
-            "pampa_glmsp",
-            "mergeCols1"
+            "interactive_tool_panoply"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "ecologyanalysis",
+        "subtopic": "ecologyviz",
         "supported_servers": {
             "exact": [
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 }
-            ]
+            ],
+            "inexact": []
         },
         "symlink": null,
         "tags": [
-            "Species population EBV class",
-            "Community composition EBV class",
-            "EBV dataset",
-            "EBV workflow",
-            "modeling"
+            "interactive-tools",
+            "EBV cube",
+            "Data visualization"
         ],
-        "time_estimation": "2H",
-        "title": "Compute and analyze biodiversity metrics with PAMPA toolsuite",
+        "time_estimation": "1H",
+        "title": "Visualize EBV cube data with Panoply netCDF viewer",
         "tools": [
-            "Count1",
-            "Filter1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.2",
-            "toolshed.g2.bx.psu.edu/repos/ecology/pampa_communitymetrics/pampa_communitymetrics/0.0.2",
-            "toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmcomm/pampa_glmcomm/0.0.2",
-            "toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmsp/pampa_glmsp/0.0.2",
-            "toolshed.g2.bx.psu.edu/repos/ecology/pampa_plotglm/pampa_plotglm/0.0.2",
-            "toolshed.g2.bx.psu.edu/repos/ecology/pampa_presabs/pampa_presabs/0.0.2",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0"
+            "interactive_tool_panoply"
         ],
         "topic_name": "ecology",
         "topic_name_human": "Ecology",
@@ -70215,190 +73666,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "PAMPA-toolsuite-tutorial",
+        "tutorial_name": "panoply_ebv",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/panoply_ebv/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/panoply_ebv/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/panoply_ebv/tutorial.json"
         },
-        "version": 21,
+        "version": 9,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 111,
-        "visitors": 944,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Compute and analyze biodiversity metrics with PAMPA toolsuite",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  3[label=\"Column Regex Find And Replace\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Column Regex Find And Replace\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Concatenate datasets\"]\n  2 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Column Regex Find And Replace\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"Merge Columns\"]\n  3 -> 7 [label=\"out_file1\"]\n  8[label=\"Merge Columns\"]\n  4 -> 8 [label=\"out_file1\"]\n  9[label=\"Count\"]\n  5 -> 9 [label=\"out_file1\"]\n  10[label=\"Filter\"]\n  5 -> 10 [label=\"out_file1\"]\n  11[label=\"Merge Columns\"]\n  6 -> 11 [label=\"out_file1\"]\n  12[label=\"Regex Find And Replace\"]\n  7 -> 12 [label=\"out_file1\"]\n  13[label=\"Regex Find And Replace\"]\n  8 -> 13 [label=\"out_file1\"]\n  14[label=\"Column Regex Find And Replace\"]\n  10 -> 14 [label=\"out_file1\"]\n  15[label=\"Regex Find And Replace\"]\n  11 -> 15 [label=\"out_file1\"]\n  16[label=\"Calculate presence absence table\"]\n  12 -> 16 [label=\"out_file1\"]\n  17[label=\"Calculate presence absence table\"]\n  13 -> 17 [label=\"out_file1\"]\n  18[label=\"Merge Columns\"]\n  14 -> 18 [label=\"out_file1\"]\n  19[label=\"Calculate presence absence table\"]\n  15 -> 19 [label=\"out_file1\"]\n  20[label=\"Regex Find And Replace\"]\n  18 -> 20 [label=\"out_file1\"]\n  21[label=\"Calculate community metrics\"]\n  20 -> 21 [label=\"out_file1\"]\n  22[label=\"Column Regex Find And Replace\"]\n  20 -> 22 [label=\"out_file1\"]\n  23[label=\"Merge Columns\"]\n  22 -> 23 [label=\"out_file1\"]\n  24[label=\"Column Regex Find And Replace\"]\n  23 -> 24 [label=\"out_file1\"]\n  25[label=\"Advanced Cut\"]\n  24 -> 25 [label=\"out_file1\"]\n  26[label=\"Sort\"]\n  25 -> 26 [label=\"output\"]\n  27[label=\"Regex Find And Replace\"]\n  26 -> 27 [label=\"outfile\"]\n  28[label=\"Compute GLM on community data\"]\n  21 -> 28 [label=\"output_community\"]\n  27 -> 28 [label=\"out_file1\"]\n  29[label=\"Compute GLM on population data\"]\n  16 -> 29 [label=\"output_presabs\"]\n  27 -> 29 [label=\"out_file1\"]\n  30[label=\"Compute GLM on population data\"]\n  17 -> 30 [label=\"output_presabs\"]\n  27 -> 30 [label=\"out_file1\"]\n  31[label=\"Compute GLM on population data\"]\n  19 -> 31 [label=\"output_presabs\"]\n  27 -> 31 [label=\"out_file1\"]\n  32[label=\"Transpose\"]\n  28 -> 32 [label=\"output_summary\"]\n  33[label=\"Create a plot from GLM data\"]\n  21 -> 33 [label=\"output_community\"]\n  28 -> 33 [label=\"output_summary\"]\n  27 -> 33 [label=\"out_file1\"]\n  34[label=\"Transpose\"]\n  29 -> 34 [label=\"output_summary\"]\n  35[label=\"Create a plot from GLM data\"]\n  16 -> 35 [label=\"output_presabs\"]\n  29 -> 35 [label=\"output_summary\"]\n  27 -> 35 [label=\"out_file1\"]\n  36[label=\"Transpose\"]\n  30 -> 36 [label=\"output_summary\"]\n  37[label=\"Create a plot from GLM data\"]\n  17 -> 37 [label=\"output_presabs\"]\n  30 -> 37 [label=\"output_summary\"]\n  27 -> 37 [label=\"out_file1\"]\n  38[label=\"Transpose\"]\n  31 -> 38 [label=\"output_summary\"]\n  39[label=\"Create a plot from GLM data\"]\n  19 -> 39 [label=\"output_presabs\"]\n  31 -> 39 [label=\"output_summary\"]\n  27 -> 39 [label=\"out_file1\"]\n}",
-                "history": [
-                    {
-                        "hash": "59d712ff30d5e8f4a5355ce2b2822e412b669f5c",
-                        "message": "Third version with good tag",
-                        "num": 5,
-                        "short_hash": "59d712ff3",
-                        "unix": "1614183047"
-                    },
-                    {
-                        "hash": "76a4fcec2322203b57409cde43b42061d5342467",
-                        "message": "Delete Galaxy-Workflow-Compute_and_analyze_biodiversity_metrics_with_PAMPA_toolsuite.ga",
-                        "num": 4,
-                        "short_hash": "76a4fcec2",
-                        "unix": "1614183020"
-                    },
-                    {
-                        "hash": "5dc93ca540b20999ab654de39a3a117ea0e48342",
-                        "message": "Add updated workflow",
-                        "num": 3,
-                        "short_hash": "5dc93ca54",
-                        "unix": "1614182846"
-                    },
-                    {
-                        "hash": "a4b073fcc3bb5affb1f9bf70f3c659b6a80efdbf",
-                        "message": "Delete Galaxy-Workflow-Compute_and_analyze_biodiversity_metrics_with_PAMPA_toolsuite.ga",
-                        "num": 2,
-                        "short_hash": "a4b073fcc",
-                        "unix": "1614182812"
-                    },
-                    {
-                        "hash": "87b82c19f54fa91e697b2ecd8b70b61a61e0d57e",
-                        "message": "Add tutorial workflow",
-                        "num": 1,
-                        "short_hash": "87b82c19f",
-                        "unix": "1614181101"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "https://zenodo.org/record/4264936/files/CPUE%20per%20length%20per%20area_A.csv?download=1"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 10
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "07e9c5f6-f826-496c-b900-5c22fd643fb4",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "https://zenodo.org/record/4264936/files/CPUE%20per%20length%20per%20area_B.csv?download=1"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 130
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "9ad55992-d9e2-4263-bbe7-31dc551f81fd",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "https://zenodo.org/record/4264936/files/CPUE%20per%20length%20per%20area_C.csv?download=1"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 250
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "d80371d8-924c-4f37-8081-cc3a9201ba4a",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Column Regex Find And Replace\"];\n  0 -->|output| 3;\n  4[\"Column Regex Find And Replace\"];\n  1 -->|output| 4;\n  5[\"Concatenate datasets\"];\n  2 -->|output| 5;\n  1 -->|output| 5;\n  0 -->|output| 5;\n  6[\"Column Regex Find And Replace\"];\n  2 -->|output| 6;\n  7[\"Merge Columns\"];\n  3 -->|out_file1| 7;\n  8[\"Merge Columns\"];\n  4 -->|out_file1| 8;\n  9[\"Count\"];\n  5 -->|out_file1| 9;\n  10[\"Filter\"];\n  5 -->|out_file1| 10;\n  11[\"Merge Columns\"];\n  6 -->|out_file1| 11;\n  12[\"Regex Find And Replace\"];\n  7 -->|out_file1| 12;\n  13[\"Regex Find And Replace\"];\n  8 -->|out_file1| 13;\n  14[\"Column Regex Find And Replace\"];\n  10 -->|out_file1| 14;\n  15[\"Regex Find And Replace\"];\n  11 -->|out_file1| 15;\n  16[\"Calculate presence absence table\"];\n  12 -->|out_file1| 16;\n  17[\"Calculate presence absence table\"];\n  13 -->|out_file1| 17;\n  18[\"Merge Columns\"];\n  14 -->|out_file1| 18;\n  19[\"Calculate presence absence table\"];\n  15 -->|out_file1| 19;\n  20[\"Regex Find And Replace\"];\n  18 -->|out_file1| 20;\n  21[\"Calculate community metrics\"];\n  20 -->|out_file1| 21;\n  22[\"Column Regex Find And Replace\"];\n  20 -->|out_file1| 22;\n  23[\"Merge Columns\"];\n  22 -->|out_file1| 23;\n  24[\"Column Regex Find And Replace\"];\n  23 -->|out_file1| 24;\n  25[\"Advanced Cut\"];\n  24 -->|out_file1| 25;\n  26[\"Sort\"];\n  25 -->|output| 26;\n  27[\"Regex Find And Replace\"];\n  26 -->|outfile| 27;\n  28[\"Compute GLM on community data\"];\n  21 -->|output_community| 28;\n  27 -->|out_file1| 28;\n  29[\"Compute GLM on population data\"];\n  16 -->|output_presabs| 29;\n  27 -->|out_file1| 29;\n  30[\"Compute GLM on population data\"];\n  17 -->|output_presabs| 30;\n  27 -->|out_file1| 30;\n  31[\"Compute GLM on population data\"];\n  19 -->|output_presabs| 31;\n  27 -->|out_file1| 31;\n  32[\"Transpose\"];\n  28 -->|output_summary| 32;\n  33[\"Create a plot from GLM data\"];\n  21 -->|output_community| 33;\n  28 -->|output_summary| 33;\n  27 -->|out_file1| 33;\n  34[\"Transpose\"];\n  29 -->|output_summary| 34;\n  35[\"Create a plot from GLM data\"];\n  16 -->|output_presabs| 35;\n  29 -->|output_summary| 35;\n  27 -->|out_file1| 35;\n  36[\"Transpose\"];\n  30 -->|output_summary| 36;\n  37[\"Create a plot from GLM data\"];\n  17 -->|output_presabs| 37;\n  30 -->|output_summary| 37;\n  27 -->|out_file1| 37;\n  38[\"Transpose\"];\n  31 -->|output_summary| 38;\n  39[\"Create a plot from GLM data\"];\n  19 -->|output_presabs| 39;\n  31 -->|output_summary| 39;\n  27 -->|out_file1| 39;",
-                "modified": "2024-08-18 00:06:22 +0000",
-                "name": "Compute and analyze biodiversity metrics with PAMPA toolsuite",
-                "outputs": [],
-                "parent_id": "ecology/PAMPA-toolsuite-tutorial",
-                "path": "topics/ecology/tutorials/PAMPA-toolsuite-tutorial/workflows/Galaxy-Workflow-Compute_and_analyze_biodiversity_metrics_with_PAMPA_toolsuite.ga",
-                "tags": [
-                    "ecology"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Compute and analyze biodiversity metrics with PAMPA toolsuite",
-                "topic_id": "ecology",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/ecology-PAMPA-toolsuite-tutorial/versions/galaxy-workflow-compute-and-analyze-biodiversity-metrics-with-pampa-toolsuite",
-                "tutorial_id": "PAMPA-toolsuite-tutorial",
-                "url": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/workflows/Galaxy-Workflow-Compute_and_analyze_biodiversity_metrics_with_PAMPA_toolsuite.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/workflows/Galaxy-Workflow-Compute_and_analyze_biodiversity_metrics_with_PAMPA_toolsuite.html",
-                "version": 1,
-                "wfid": "ecology-PAMPA-toolsuite-tutorial",
-                "wfname": "galaxy-workflow-compute-and-analyze-biodiversity-metrics-with-pampa-toolsuite",
-                "workflow": "Galaxy-Workflow-Compute_and_analyze_biodiversity_metrics_with_PAMPA_toolsuite.ga",
-                "workflow_tools": [
-                    "Count1",
-                    "Filter1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.2",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/pampa_communitymetrics/pampa_communitymetrics/0.0.2",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmcomm/pampa_glmcomm/0.0.2",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/pampa_glmsp/pampa_glmsp/0.0.2",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/pampa_plotglm/pampa_plotglm/0.0.2",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/pampa_presabs/pampa_presabs/0.0.2",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0"
-                ],
-                "workflowhub_id": "1283"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.4264936"
+        "visit_duration": 103,
+        "visitors": 161
     },
     {
         "admin_install": {
@@ -70519,8 +73799,8 @@
                 "members": [
                     "colineroyaux",
                     "Marie59",
-                    "yvanlebras",
-                    "ThibaudGlinez"
+                    "ThibaudGlinez",
+                    "yvanlebras"
                 ],
                 "name": "P\u00f4le National de Donn\u00e9es de Biodiversit\u00e9",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pndb/",
@@ -70552,7 +73832,7 @@
             "Deal with QGIS execution management",
             "Access, filter, and import GIS data using WFS webservice"
         ],
-        "pageviews": 141,
+        "pageviews": 166,
         "pub_date": "2023-10-11",
         "questions": [
             "How to use WFS webservice to access and import GIS data through Galaxy"
@@ -70608,253 +73888,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 66,
-        "visitors": 118
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/panoply_ebv/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "pndb",
-                "yvanlebras",
-                "colineroyaux",
-                "Marie59",
-                "annefou"
-            ],
-            "funding": [
-                "gallantries",
-                "fairease",
-                "pndb"
-            ]
-        },
-        "contributors": [
-            {
-                "avatar": "/training-material/shared/images/PNDB_sub.png",
-                "github": false,
-                "id": "pndb",
-                "members": [
-                    "colineroyaux",
-                    "Marie59",
-                    "yvanlebras",
-                    "ThibaudGlinez"
-                ],
-                "name": "P\u00f4le National de Donn\u00e9es de Biodiversit\u00e9",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pndb/",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/pndb.json"
-            },
-            {
-                "affiliations": [
-                    "pndb",
-                    "gallantries",
-                    "fairease",
-                    "fnso2019",
-                    "elixir-europe"
-                ],
-                "elixir_node": "fr",
-                "email": "yvan.le-bras@mnhn.fr",
-                "id": "yvanlebras",
-                "joined": "2017-09",
-                "matrix": "yvanlebras:matrix.org",
-                "name": "Yvan Le Bras",
-                "orcid": "0000-0002-8504-068X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
-                "twitter": "Yvan2935",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
-            },
-            {
-                "affiliations": [
-                    "pndb",
-                    "gallantries",
-                    "elixir-europe"
-                ],
-                "elixir_node": "fr",
-                "email": "coline.royaux@mnhn.fr",
-                "id": "colineroyaux",
-                "joined": "2020-11",
-                "name": "Coline Royaux",
-                "orcid": "0000-0003-4308-5617",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/",
-                "twitter": "ColineRoyaux",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/colineroyaux.json"
-            },
-            {
-                "affiliations": [
-                    "pndb",
-                    "fairease"
-                ],
-                "email": "marie.josse@ifremer.fr",
-                "id": "Marie59",
-                "joined": "2022-03",
-                "name": "Marie Josse",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
-            },
-            {
-                "elixir_node": "no",
-                "id": "annefou",
-                "joined": "2019-07",
-                "name": "Anne Fouilloux",
-                "orcid": "0000-0002-1784-2920",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annefou/",
-                "twitter": "AnneFouilloux",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/annefou.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
-            },
-            {
-                "avatar": "/training-material/assets/images/fair_ease_colour.png",
-                "funder": true,
-                "funding_id": "101058785",
-                "funding_statement": "FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "fairease",
-                "joined": "2023-10",
-                "members": [
-                    "Marie59",
-                    "yvanlebras"
-                ],
-                "name": "Fair-Ease",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fairease/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/fairease.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/PNDB_sub.png",
-                "github": false,
-                "id": "pndb",
-                "members": [
-                    "colineroyaux",
-                    "Marie59",
-                    "yvanlebras",
-                    "ThibaudGlinez"
-                ],
-                "name": "P\u00f4le National de Donn\u00e9es de Biodiversit\u00e9",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pndb/",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/pndb.json"
-            }
-        ],
-        "dir": "topics/ecology/tutorials/panoply_ebv",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "ecology/panoply_ebv",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Inspect and view EBV cube netCDF data with Panoply",
-            "Interact with Galaxy to save your plots"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-27",
-        "objectives": [
-            "Learn to use Panoply in Galaxy to visuallize EBV cube netCDF geo-referenced data",
-            "Learn how Panoply plots are exported to Galaxy"
-        ],
-        "pageviews": 212,
-        "pub_date": "2022-10-28",
-        "questions": [
-            "How to start Panoply interactive environment in Galaxy?",
-            "How to inspect EBV cube netCDF data?",
-            "How to make a plot with Panoply?",
-            "Where to save your plots in Panoply?",
-            "How to customize plots in Panoply?",
-            "How to generate animation in Panoply?"
-        ],
-        "short_id": "T00131",
-        "short_tools": [
-            "interactive_tool_panoply"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "ecologyviz",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "interactive-tools",
-            "EBV cube",
-            "Data visualization"
-        ],
-        "time_estimation": "1H",
-        "title": "Visualize EBV cube data with Panoply netCDF viewer",
-        "tools": [
-            "interactive_tool_panoply"
-        ],
-        "topic_name": "ecology",
-        "topic_name_human": "Ecology",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "panoply_ebv",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/ecology/tutorials/panoply_ebv/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/panoply_ebv/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/panoply_ebv/tutorial.json"
-        },
-        "version": 9,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 108,
-        "visitors": 153
+        "visit_duration": 74,
+        "visitors": 139
     },
     {
         "admin_install": {
@@ -71049,17 +74084,17 @@
         ],
         "dir": "topics/epigenetics/tutorials/formation_of_super-structures_on_xi",
         "edam_operation": [
-            "Sequencing quality control",
-            "Primer removal",
             "Peak calling",
-            "Enrichment analysis",
-            "Mapping",
+            "Sequence trimming",
             "Read mapping",
+            "Sequencing quality control",
+            "Statistical calculation",
+            "Gene regulatory network analysis",
             "Sequence composition calculation",
+            "Mapping",
             "Read pre-processing",
-            "Gene regulatory network analysis",
-            "Sequence trimming",
-            "Statistical calculation"
+            "Primer removal",
+            "Enrichment analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -71074,6 +74109,7 @@
         "id": "epigenetics/formation_of_super-structures_on_xi",
         "inexact_supported_servers": [
             "Galaxy@AuBi",
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.no"
         ],
@@ -71097,7 +74133,7 @@
             "Extract coverage files",
             "Call enriched regions or peaks"
         ],
-        "pageviews": 5736884,
+        "pageviews": 5907301,
         "pub_date": "2018-09-17",
         "questions": [
             "Histone modification?",
@@ -71111,21 +74147,21 @@
         ],
         "short_id": "T00140",
         "short_tools": [
-            "bedtools_mergebed",
             "deeptools_plot_correlation",
+            "deeptools_plot_fingerprint",
+            "macs2_callpeak",
+            "deeptools_bam_compare",
+            "Filter1",
+            "bedtools_sortbed",
+            "fastqc",
+            "deeptools_plot_heatmap",
             "deeptools_multi_bam_summary",
-            "cat1",
+            "samtools_idxstats",
+            "bedtools_mergebed",
             "bowtie2",
             "deeptools_bam_coverage",
-            "bedtools_sortbed",
-            "deeptools_bam_compare",
             "deeptools_compute_matrix",
-            "deeptools_plot_heatmap",
-            "fastqc",
-            "samtools_idxstats",
-            "Filter1",
-            "deeptools_plot_fingerprint",
-            "macs2_callpeak",
+            "cat1",
             "trim_galore"
         ],
         "slides": true,
@@ -71159,6 +74195,11 @@
                     "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -71214,8 +74255,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 383,
-        "visitors": 2068456,
+        "visit_duration": 380,
+        "visitors": 2138387,
         "workflows": [
             {
                 "creators": [
@@ -71588,7 +74629,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nwt_H3K4me3_read2.fastq.gz\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nwt_H3K4me3_read1.fastq.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nwt_input_rep1.bam\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nwt_H3K4me3_rep1.bam\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nwt_CTCF_rep1.bam\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nwt_H3K27me3_rep1.bam\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nwt_input_rep2.bam\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nwt_H3K4me3_rep2.bam\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nwt_CTCF_rep2.bam\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"\u2139\ufe0f Input Dataset\\nwt_H3K27me3_rep2.bam\"];\n  style 9 stroke:#2c3143,stroke-width:4px;\n  10[\"FastQC\"];\n  0 -->|output| 10;\n  892e22b2-3194-4076-af80-357530c17186[\"Output\\nwt_H3K4me3_rep1_read2_fastqc\"];\n  10 --> 892e22b2-3194-4076-af80-357530c17186;\n  style 892e22b2-3194-4076-af80-357530c17186 stroke:#2c3143,stroke-width:4px;\n  11[\"Trim Galore!\"];\n  1 -->|output| 11;\n  0 -->|output| 11;\n  a66a6432-690f-4e66-88c0-7eba0a014677[\"Output\\nwt_H3K4me3_rep1_trim_galore\"];\n  11 --> a66a6432-690f-4e66-88c0-7eba0a014677;\n  style a66a6432-690f-4e66-88c0-7eba0a014677 stroke:#2c3143,stroke-width:4px;\n  12[\"FastQC\"];\n  1 -->|output| 12;\n  da453096-fdd9-44ee-b83b-e4eca5c800f9[\"Output\\nwt_H3K4me3_rep1_read1_fastqc\"];\n  12 --> da453096-fdd9-44ee-b83b-e4eca5c800f9;\n  style da453096-fdd9-44ee-b83b-e4eca5c800f9 stroke:#2c3143,stroke-width:4px;\n  13[\"Samtools idxstats\"];\n  2 -->|output| 13;\n  14[\"bamCoverage\"];\n  2 -->|output| 14;\n  15[\"bamCoverage\"];\n  3 -->|output| 15;\n  16[\"bamCoverage\"];\n  3 -->|output| 16;\n  73e2f018-d9e4-4f74-8110-598b9b43a940[\"Output\\nwt_H3K4me3_rep1_bamcoverage\"];\n  16 --> 73e2f018-d9e4-4f74-8110-598b9b43a940;\n  style 73e2f018-d9e4-4f74-8110-598b9b43a940 stroke:#2c3143,stroke-width:4px;\n  17[\"Samtools idxstats\"];\n  3 -->|output| 17;\n  09449d6f-ce88-4448-9928-064c729c32d1[\"Output\\nwt_H3K4me3_rep1_idxstats\"];\n  17 --> 09449d6f-ce88-4448-9928-064c729c32d1;\n  style 09449d6f-ce88-4448-9928-064c729c32d1 stroke:#2c3143,stroke-width:4px;\n  18[\"plotFingerprint\"];\n  3 -->|output| 18;\n  2 -->|output| 18;\n  19[\"bamCompare\"];\n  3 -->|output| 19;\n  2 -->|output| 19;\n  20[\"MACS2 callpeak\"];\n  2 -->|output| 20;\n  3 -->|output| 20;\n  a36b5a6c-d992-4a2d-8fd8-95e8eac74cbd[\"Output\\nwt_H3K4me3_input_rep1_macs2\"];\n  20 --> a36b5a6c-d992-4a2d-8fd8-95e8eac74cbd;\n  style a36b5a6c-d992-4a2d-8fd8-95e8eac74cbd stroke:#2c3143,stroke-width:4px;\n  21[\"bamCompare\"];\n  3 -->|output| 21;\n  2 -->|output| 21;\n  5174d1aa-21f6-4187-8935-70ba8bd0f6e0[\"Output\\nwt_H3K4me3_input_rep1_bamcompare\"];\n  21 --> 5174d1aa-21f6-4187-8935-70ba8bd0f6e0;\n  style 5174d1aa-21f6-4187-8935-70ba8bd0f6e0 stroke:#2c3143,stroke-width:4px;\n  22[\"bamCompare\"];\n  4 -->|output| 22;\n  2 -->|output| 22;\n  23[\"MACS2 callpeak\"];\n  2 -->|output| 23;\n  4 -->|output| 23;\n  24[\"bamCompare\"];\n  4 -->|output| 24;\n  2 -->|output| 24;\n  25[\"bamCompare\"];\n  5 -->|output| 25;\n  2 -->|output| 25;\n  26[\"MACS2 callpeak\"];\n  2 -->|output| 26;\n  5 -->|output| 26;\n  27[\"bamCompare\"];\n  7 -->|output| 27;\n  6 -->|output| 27;\n  28[\"MACS2 callpeak\"];\n  6 -->|output| 28;\n  7 -->|output| 28;\n  29[\"bamCompare\"];\n  8 -->|output| 29;\n  6 -->|output| 29;\n  30[\"MACS2 callpeak\"];\n  6 -->|output| 30;\n  8 -->|output| 30;\n  31[\"multiBamSummary\"];\n  2 -->|output| 31;\n  3 -->|output| 31;\n  4 -->|output| 31;\n  5 -->|output| 31;\n  6 -->|output| 31;\n  7 -->|output| 31;\n  8 -->|output| 31;\n  9 -->|output| 31;\n  32[\"bamCompare\"];\n  9 -->|output| 32;\n  6 -->|output| 32;\n  33[\"MACS2 callpeak\"];\n  6 -->|output| 33;\n  9 -->|output| 33;\n  34[\"Bowtie2\"];\n  11 -->|trimmed_reads_pair1| 34;\n  11 -->|trimmed_reads_pair2| 34;\n  4c3ca5b1-2298-4bb4-8d2f-f62619f35158[\"Output\\nwt_H3K4me3_rep1_bowtie2\"];\n  34 --> 4c3ca5b1-2298-4bb4-8d2f-f62619f35158;\n  style 4c3ca5b1-2298-4bb4-8d2f-f62619f35158 stroke:#2c3143,stroke-width:4px;\n  35[\"Concatenate datasets\"];\n  20 -->|output_narrowpeaks| 35;\n  23 -->|output_narrowpeaks| 35;\n  36[\"plotCorrelation\"];\n  31 -->|outFile| 36;\n  37[\"Concatenate datasets\"];\n  20 -->|output_narrowpeaks| 37;\n  23 -->|output_narrowpeaks| 37;\n  26 -->|output_narrowpeaks| 37;\n  28 -->|output_narrowpeaks| 37;\n  30 -->|output_narrowpeaks| 37;\n  33 -->|output_narrowpeaks| 37;\n  38[\"bedtools SortBED\"];\n  35 -->|out_file1| 38;\n  39[\"bedtools SortBED\"];\n  37 -->|out_file1| 39;\n  40[\"bedtools MergeBED\"];\n  38 -->|output| 40;\n  931eb26a-0e5d-4556-b67f-1c37372aaf28[\"Output\\nwt_H3K4me3_CTCF_rep1_mergebed\"];\n  40 --> 931eb26a-0e5d-4556-b67f-1c37372aaf28;\n  style 931eb26a-0e5d-4556-b67f-1c37372aaf28 stroke:#2c3143,stroke-width:4px;\n  41[\"bedtools MergeBED\"];\n  39 -->|output| 41;\n  9c4c5a1f-f2c1-4e83-b1f9-ff32ee48baeb[\"Output\\nwt_all_mergebed\"];\n  41 --> 9c4c5a1f-f2c1-4e83-b1f9-ff32ee48baeb;\n  style 9c4c5a1f-f2c1-4e83-b1f9-ff32ee48baeb stroke:#2c3143,stroke-width:4px;\n  42[\"computeMatrix\"];\n  19 -->|outFileName| 42;\n  22 -->|outFileName| 42;\n  40 -->|output| 42;\n  43[\"computeMatrix\"];\n  19 -->|outFileName| 43;\n  22 -->|outFileName| 43;\n  25 -->|outFileName| 43;\n  27 -->|outFileName| 43;\n  29 -->|outFileName| 43;\n  32 -->|outFileName| 43;\n  41 -->|output| 43;\n  44[\"plotHeatmap\"];\n  42 -->|outFileName| 44;\n  45[\"plotHeatmap\"];\n  43 -->|outFileName| 45;",
-                "modified": "2024-08-18 00:06:23 +0000",
+                "modified": "2024-10-02 12:08:08 +0000",
                 "name": "GTN - ChIP Seq - Formation Of Super Structures On Xi",
                 "outputs": [
                     {
@@ -72122,12 +75163,6 @@
         "zenodo_link": "https://zenodo.org/record/1324070"
     },
     {
-        "abbreviations": {
-            "CUT&RUN": "Cleavage Under Targets and Release Using Nuclease",
-            "POI": "protein of interest",
-            "TF": "transcription factors",
-            "pA(G)-MNase": "protein A(-protein G hybrid)-micrococcal nuclease"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -72148,16 +75183,16 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bamtools_filter",
-                    "owner": "devteam",
-                    "revisions": "cb20f99fd45b",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "bamtools_filter",
                     "owner": "devteam",
-                    "revisions": "1dfd95ee241e",
+                    "revisions": "cb20f99fd45b",
                     "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
@@ -72168,13 +75203,6 @@
                     "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
-                {
-                    "name": "bowtie2",
-                    "owner": "devteam",
-                    "revisions": "f6877ad76b00",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
                 {
                     "name": "fastqc",
                     "owner": "devteam",
@@ -72182,13 +75210,6 @@
                     "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "3d0c7bdf12f5",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
                 {
                     "name": "picard",
                     "owner": "devteam",
@@ -72197,10 +75218,10 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "picard",
+                    "name": "samtools_idxstats",
                     "owner": "devteam",
-                    "revisions": "b502c227b5e6",
-                    "tool_panel_section_label": "Picard",
+                    "revisions": "7a6034296ae9",
+                    "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
@@ -72210,13 +75231,6 @@
                     "tool_panel_section_label": "BED",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
-                {
-                    "name": "bedtools",
-                    "owner": "iuc",
-                    "revisions": "a1a923cd89e8",
-                    "tool_panel_section_label": "BED",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
                 {
                     "name": "bedtools",
                     "owner": "iuc",
@@ -72224,27 +75238,6 @@
                     "tool_panel_section_label": "BED",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
-                {
-                    "name": "bedtools",
-                    "owner": "iuc",
-                    "revisions": "a1a923cd89e8",
-                    "tool_panel_section_label": "BED",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "extract_genomic_dna",
-                    "owner": "iuc",
-                    "revisions": "5cc8e93ee98f",
-                    "tool_panel_section_label": "Fetch Sequences/Alignments",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "idr",
-                    "owner": "iuc",
-                    "revisions": "de7795890bc5",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
                 {
                     "name": "macs2",
                     "owner": "iuc",
@@ -72252,20 +75245,6 @@
                     "tool_panel_section_label": "Peak Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
-                {
-                    "name": "macs2",
-                    "owner": "iuc",
-                    "revisions": "640d3af5d833",
-                    "tool_panel_section_label": "Peak Calling",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "meme_chip",
-                    "owner": "iuc",
-                    "revisions": "cc100e0f61f4",
-                    "tool_panel_section_label": "Motif Tools",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
                 {
                     "name": "pe_histogram",
                     "owner": "iuc",
@@ -72289,60 +75268,9 @@
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: deeptools_compute_matrix\n  owner: bgruening\n  revisions: 514fa53b5efb\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_plot_heatmap\n  owner: bgruening\n  revisions: a4dfb122e52b\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_filter\n  owner: devteam\n  revisions: cb20f99fd45b\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_filter\n  owner: devteam\n  revisions: 1dfd95ee241e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie2\n  owner: devteam\n  revisions: a6d65b0c67af\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie2\n  owner: devteam\n  revisions: f6877ad76b00\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: a1f0b3f4b781\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: b502c227b5e6\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: ce3c7f062223\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: a1a923cd89e8\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: a68aa6c1204a\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: a1a923cd89e8\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: extract_genomic_dna\n  owner: iuc\n  revisions: 5cc8e93ee98f\n  tool_panel_section_label: Fetch Sequences/Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: idr\n  owner: iuc\n  revisions: de7795890bc5\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: macs2\n  owner: iuc\n  revisions: 424aefbd7777\n  tool_panel_section_label: Peak Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: macs2\n  owner: iuc\n  revisions: 640d3af5d833\n  tool_panel_section_label: Peak Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meme_chip\n  owner: iuc\n  revisions: cc100e0f61f4\n  tool_panel_section_label: Motif Tools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pe_histogram\n  owner: iuc\n  revisions: bd1416eea1f0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pygenometracks\n  owner: iuc\n  revisions: 2824d77cd8f8\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 49370cb85f0f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/cut_and_run/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "heylf"
-            ],
-            "editing": [
-                "hexylena",
-                "lldelisle"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: deeptools_compute_matrix\n  owner: bgruening\n  revisions: 514fa53b5efb\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_plot_heatmap\n  owner: bgruening\n  revisions: a4dfb122e52b\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_filter\n  owner: devteam\n  revisions: cb20f99fd45b\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie2\n  owner: devteam\n  revisions: a6d65b0c67af\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: a1f0b3f4b781\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_idxstats\n  owner: devteam\n  revisions: 7a6034296ae9\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: ce3c7f062223\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: a68aa6c1204a\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: macs2\n  owner: iuc\n  revisions: 424aefbd7777\n  tool_panel_section_label: Peak Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pe_histogram\n  owner: iuc\n  revisions: bd1416eea1f0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pygenometracks\n  owner: iuc\n  revisions: 2824d77cd8f8\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 49370cb85f0f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/atac-seq/tutorial.json",
         "contributors": [
-            {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "heylf",
-                "joined": "2018-08",
-                "name": "Florian Heyl",
-                "orcid": "0000-0002-3651-5685",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/heylf/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/heylf.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
             {
                 "affiliations": [
                     "elixir-europe"
@@ -72361,120 +75289,165 @@
                 "orcid": "0000-0002-1964-4960",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/lldelisle.json"
+            },
+            {
+                "id": "mblue9",
+                "joined": "2018-09",
+                "name": "Maria Doyle",
+                "orcid": "0000-0003-4847-8436",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
+            },
+            {
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "heylf",
+                "joined": "2018-08",
+                "name": "Florian Heyl",
+                "orcid": "0000-0002-3651-5685",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/heylf/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/heylf.json"
             }
         ],
-        "dir": "topics/epigenetics/tutorials/cut_and_run",
-        "draft": true,
+        "dir": "topics/epigenetics/tutorials/atac-seq",
         "edam_operation": [
-            "Visualisation",
-            "Primer removal",
-            "Sequencing quality control",
+            "Data handling",
             "Peak calling",
-            "Enrichment analysis",
-            "Formatting",
+            "Visualisation",
+            "Sequence trimming",
             "Read mapping",
-            "Mapping",
-            "Sequence alignment analysis",
-            "Read pre-processing",
+            "Sequencing quality control",
             "Sequence composition calculation",
+            "Sequence alignment analysis",
+            "Statistical calculation",
             "Gene regulatory network analysis",
-            "Data handling",
-            "Sequence trimming",
-            "Statistical calculation"
+            "Mapping",
+            "Read pre-processing",
+            "Primer removal",
+            "Enrichment analysis",
+            "Formatting"
         ],
         "edam_topic": [],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "UseGalaxy.be"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "epigenetics/cut_and_run",
-        "inexact_supported_servers": [],
+        "id": "epigenetics/atac-seq",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "CUT&RUN can be used to identify binding regions for DNA binding proteins.",
+            "ATAC-Seq can be used to identify accessible gene promoters and enhancers",
             "Several filters are applied to the reads, such as removing those mapped to mitochondria",
-            "Fragment distribution can help determine whether an CUT&RUN experiment has worked well",
-            "A robust peak detection removes noise from the data"
+            "Fragment distribution can help determine whether an ATAC-Seq experiment has worked well"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-06",
+        "mod_date": "2024-08-08",
         "objectives": [
-            "Apply appropriate analysis and quality control steps for CUT&RUN",
-            "Apply an enrichment analysis and a robust peak detection",
-            "Find protein binding motifs"
+            "Apply appropriate analysis and quality control steps for ATAC-Seq",
+            "Generate a heatmap of transcription start site accessibility",
+            "Visualise peaks for specific regions"
         ],
-        "pageviews": 1723,
-        "pub_date": "2024-03-06",
+        "pageviews": 5998000,
+        "pub_date": "2019-09-02",
         "questions": [
-            "Which binding motif has the transcription factor GATA1?",
-            "What kind of quality control do I have to do?",
-            "How to analyse and visualise CUT&RUN data?"
+            "Which DNA regions are accessible in the human lymphoblastoid cell line GM12878?",
+            "How to analyse and visualise ATAC-Seq data?"
         ],
-        "short_id": "T00424",
+        "recordings": [
+            {
+                "captioners": [
+                    "hrhotz"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "1H50M",
+                "speakers": [
+                    "heylf"
+                ],
+                "youtube_id": "Zc-bl6ZfcX4"
+            }
+        ],
+        "short_id": "T00137",
         "short_tools": [
-            "deeptools_compute_matrix",
-            "__EXTRACT_DATASET__",
-            "Grep1",
-            "meme_chip",
-            "deeptools_plot_heatmap",
-            "macs2_callpeak",
-            "wig_to_bigWig",
-            "trim_galore",
+            "picard_MarkDuplicates",
             "pygenomeTracks",
-            "bowtie2",
             "Filter1",
+            "tp_sort_header_tool",
             "cutadapt",
-            "picard_MarkDuplicates",
-            "bedtools_intersectbed",
+            "deeptools_plot_heatmap",
             "bamFilter",
+            "samtools_idxstats",
+            "bedtools_intersectbed",
+            "Grep1",
+            "Cut1",
             "bedtools_bamtobed",
-            "fastqc",
-            "idr",
             "pe_histogram",
-            "Extract genomic DNA 1",
-            "__FLATTEN__"
+            "macs2_callpeak",
+            "fastqc",
+            "wig_to_bigWig",
+            "deeptools_compute_matrix",
+            "bowtie2"
+        ],
+        "slides": true,
+        "slides_recordings": [
+            {
+                "captioners": [
+                    "lldelisle"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "15M",
+                "speakers": [
+                    "lldelisle"
+                ],
+                "youtube_id": "2jPNNd5YJNM"
+            }
         ],
-        "slides": false,
-        "slides_recordings": false,
         "supported_servers": {
-            "exact": [],
-            "inexact": []
+            "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
         },
         "symlink": null,
-        "tags": [
-            "work-in-progress"
-        ],
         "time_estimation": "3h",
-        "title": "CUT&RUN data analysis",
+        "title": "ATAC-Seq data analysis",
         "tools": [
-            " https://toolshed.g2.bx.psu.edu/view/bgruening/trim_galore/cd7e644cae1d",
+            "Cut1",
             "Filter1",
             "Grep1",
-            "__EXTRACT_DATASET__",
-            "__FLATTEN__",
             "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0",
             "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
             "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.1+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
             "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3",
             "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2",
             "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/idr/idr/2.0.3",
             "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6",
-            "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1",
             "toolshed.g2.bx.psu.edu/repos/iuc/pe_histogram/pe_histogram/1.0.1",
             "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6",
             "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
@@ -72486,21 +75459,21 @@
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": false
+            "video": true
         },
-        "tutorial_name": "cut_and_run",
+        "tutorial_name": "atac-seq",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/epigenetics/tutorials/cut_and_run/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/epigenetics/tutorials/atac-seq/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/cut_and_run/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/cut_and_run/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/atac-seq/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/atac-seq/tutorial.json"
         },
-        "version": 1,
-        "video": false,
-        "video_versions": 0,
+        "version": 23,
+        "video": true,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 91,
-        "visitors": 1300,
+        "visit_duration": 264,
+        "visitors": 2186389,
         "workflows": [
             {
                 "creators": [],
@@ -72514,11 +75487,144 @@
                 "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nbed file with genes\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nctcf peaks\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nATAC R2 read in fastq.gz format\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nATAC R1 read in fastq.gz format\"]\n  4[label=\"Filter\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"FastQC\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"ATAC remove nextera adapters with cutadapt\"]\n  3 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"FastQC\"]\n  3 -> 7 [label=\"output\"]\n  8[label=\"bedtools Intersect intervals\"]\n  4 -> 8 [label=\"out_file1\"]\n  0 -> 8 [label=\"output\"]\n  9[label=\"FastQC\"]\n  6 -> 9 [label=\"out2\"]\n  10[label=\"Bowtie2\"]\n  6 -> 10 [label=\"out1\"]\n  6 -> 10 [label=\"out2\"]\n  11[label=\"FastQC\"]\n  6 -> 11 [label=\"out1\"]\n  12[label=\"Filter BAM ATAC\"]\n  10 -> 12 [label=\"output\"]\n  13[label=\"MarkDuplicates\"]\n  12 -> 13 [label=\"out_file1\"]\n  14[label=\"bedtools BAM to BED\"]\n  13 -> 14 [label=\"outFile\"]\n  15[label=\"Paired-end histogram\"]\n  13 -> 15 [label=\"outFile\"]\n  16[label=\"MACS2 callpeak\"]\n  14 -> 16 [label=\"output\"]\n  17[label=\"Wig/BedGraph-to-bigWig\"]\n  16 -> 17 [label=\"output_treat_pileup\"]\n  18[label=\"computeMatrix\"]\n  17 -> 18 [label=\"out_file1\"]\n  0 -> 18 [label=\"output\"]\n  19[label=\"pyGenomeTracks\"]\n  17 -> 19 [label=\"out_file1\"]\n  16 -> 19 [label=\"output_narrowpeaks\"]\n  0 -> 19 [label=\"output\"]\n  1 -> 19 [label=\"output\"]\n  20[label=\"computeMatrix\"]\n  17 -> 20 [label=\"out_file1\"]\n  8 -> 20 [label=\"output\"]\n  k65159c9c050b406987048f66c0563a98[color=lightseagreen,label=\"Output\\ncomputeMatrix on input dataset(s): Matrix\"]\n  20 -> k65159c9c050b406987048f66c0563a98\n  21[label=\"plotHeatmap\"]\n  18 -> 21 [label=\"outFileName\"]\n  22[label=\"plotHeatmap\"]\n  20 -> 22 [label=\"outFileName\"]\n  k74a36643b88f43788f9cc1b20ee2651e[color=lightseagreen,label=\"Output\\nplotHeatmap on input dataset(s): Image\"]\n  22 -> k74a36643b88f43788f9cc1b20ee2651e\n}",
                 "history": [
                     {
-                        "hash": "c32dabaf3de77d6f436f0bc58b0b7735f64767c8",
-                        "message": "Adding cut and run",
+                        "hash": "96d212779f2fbe4abf7c850b750ca5e163e88361",
+                        "message": "update deeptools tools + parameters",
+                        "num": 20,
+                        "short_hash": "96d212779",
+                        "unix": "1619713579"
+                    },
+                    {
+                        "hash": "ba3bf335e18101d6178afceebe7226c14c1153c4",
+                        "message": "use pygenometracks 3.6",
+                        "num": 19,
+                        "short_hash": "ba3bf335e",
+                        "unix": "1618238510"
+                    },
+                    {
+                        "hash": "af99da9c03f900d2c078b704c84993c64d9cf722",
+                        "message": "update the workflow",
+                        "num": 18,
+                        "short_hash": "af99da9c0",
+                        "unix": "1617381749"
+                    },
+                    {
+                        "hash": "d5cd0ab560e9922b159174141905919870659041",
+                        "message": "update tutorial",
+                        "num": 17,
+                        "short_hash": "d5cd0ab56",
+                        "unix": "1617118406"
+                    },
+                    {
+                        "hash": "d4aee8b0dee08824c24db20abb73078b27d46b2e",
+                        "message": "change bedtools to allow to sort encodePeak",
+                        "num": 16,
+                        "short_hash": "d4aee8b0d",
+                        "unix": "1592298126"
+                    },
+                    {
+                        "hash": "c1cf1143c8c7aa6fbd822761682cd94d95588b82",
+                        "message": "macs2 to MACS2 in figures and workflow",
+                        "num": 15,
+                        "short_hash": "c1cf1143c",
+                        "unix": "1591860137"
+                    },
+                    {
+                        "hash": "69d703ece4379791461043ed5d78dee4b2a9a724",
+                        "message": "add tag and annotation",
+                        "num": 14,
+                        "short_hash": "69d703ece",
+                        "unix": "1591855841"
+                    },
+                    {
+                        "hash": "83f254a2b6d7ab6dd0677111eca534d4fd70aa21",
+                        "message": "update new version of pgt",
+                        "num": 13,
+                        "short_hash": "83f254a2b",
+                        "unix": "1591824498"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 12,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 11,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "05fb8eedbed86a986f9bc87a8bdfedd4093acc75",
+                        "message": "New workflows unflattened",
+                        "num": 10,
+                        "short_hash": "05fb8eedb",
+                        "unix": "1576835747"
+                    },
+                    {
+                        "hash": "2ebad4e591be9976da3c76fac328910cbb532b53",
+                        "message": "rebase",
+                        "num": 9,
+                        "short_hash": "2ebad4e59",
+                        "unix": "1576835604"
+                    },
+                    {
+                        "hash": "bc9c7ce8a01c0205beb6267bcd866330acc1747f",
+                        "message": "changed awk step",
+                        "num": 8,
+                        "short_hash": "bc9c7ce8a",
+                        "unix": "1576770705"
+                    },
+                    {
+                        "hash": "1bef60c2de1f1a8f7b43814a18a9b4378a7433ba",
+                        "message": "updated workflow",
+                        "num": 7,
+                        "short_hash": "1bef60c2d",
+                        "unix": "1576768651"
+                    },
+                    {
+                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
+                        "message": "unflatten workflows",
+                        "num": 6,
+                        "short_hash": "faf6d298a",
+                        "unix": "1576155753"
+                    },
+                    {
+                        "hash": "397de5ef9638f7e38137e143e575a87e13443089",
+                        "message": "modified version of genrich and pygenometracks",
+                        "num": 5,
+                        "short_hash": "397de5ef9",
+                        "unix": "1566912825"
+                    },
+                    {
+                        "hash": "93027360bcbac79c5e7d2eec481679d9ab09a159",
+                        "message": "Changes to workflow atac",
+                        "num": 4,
+                        "short_hash": "93027360b",
+                        "unix": "1565856529"
+                    },
+                    {
+                        "hash": "b2bcfc0d7fbfc45e055185515a5ba99b86ba4b00",
+                        "message": "Add visualisation step to workflow (pygenometracks)",
+                        "num": 3,
+                        "short_hash": "b2bcfc0d7",
+                        "unix": "1562416848"
+                    },
+                    {
+                        "hash": "7dec9b919382dc05ac8e1a717ca8e70078ea343e",
+                        "message": "Updates to workflow",
+                        "num": 2,
+                        "short_hash": "7dec9b919",
+                        "unix": "1562336122"
+                    },
+                    {
+                        "hash": "bb008c8c916d026929795969c28763b1cddfbfd1",
+                        "message": "First draft of ATAC-seq tut from CoFest (WIP)",
                         "num": 1,
-                        "short_hash": "c32dabaf3",
-                        "unix": "1627297960"
+                        "short_hash": "bb008c8c9",
+                        "unix": "1562333044"
                     }
                 ],
                 "inputs": [
@@ -72653,7 +75759,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nbed file with genes\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nctcf peaks\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nATAC R2 read in fastq.gz format\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nATAC R1 read in fastq.gz format\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Filter\"];\n  1 -->|output| 4;\n  5[\"FastQC\"];\n  2 -->|output| 5;\n  6[\"ATAC remove nextera adapters with cutadapt\"];\n  3 -->|output| 6;\n  2 -->|output| 6;\n  7[\"FastQC\"];\n  3 -->|output| 7;\n  8[\"bedtools Intersect intervals\"];\n  4 -->|out_file1| 8;\n  0 -->|output| 8;\n  9[\"FastQC\"];\n  6 -->|out2| 9;\n  10[\"Bowtie2\"];\n  6 -->|out1| 10;\n  6 -->|out2| 10;\n  11[\"FastQC\"];\n  6 -->|out1| 11;\n  12[\"Filter BAM ATAC\"];\n  10 -->|output| 12;\n  13[\"MarkDuplicates\"];\n  12 -->|out_file1| 13;\n  14[\"bedtools BAM to BED\"];\n  13 -->|outFile| 14;\n  15[\"Paired-end histogram\"];\n  13 -->|outFile| 15;\n  16[\"MACS2 callpeak\"];\n  14 -->|output| 16;\n  17[\"Wig/BedGraph-to-bigWig\"];\n  16 -->|output_treat_pileup| 17;\n  18[\"computeMatrix\"];\n  17 -->|out_file1| 18;\n  0 -->|output| 18;\n  19[\"pyGenomeTracks\"];\n  17 -->|out_file1| 19;\n  16 -->|output_narrowpeaks| 19;\n  0 -->|output| 19;\n  1 -->|output| 19;\n  20[\"computeMatrix\"];\n  17 -->|out_file1| 20;\n  8 -->|output| 20;\n  65159c9c-050b-4069-8704-8f66c0563a98[\"Output\\ncomputeMatrix on input dataset(s): Matrix\"];\n  20 --> 65159c9c-050b-4069-8704-8f66c0563a98;\n  style 65159c9c-050b-4069-8704-8f66c0563a98 stroke:#2c3143,stroke-width:4px;\n  21[\"plotHeatmap\"];\n  18 -->|outFileName| 21;\n  22[\"plotHeatmap\"];\n  20 -->|outFileName| 22;\n  74a36643-b88f-4378-8f9c-c1b20ee2651e[\"Output\\nplotHeatmap on input dataset(s): Image\"];\n  22 --> 74a36643-b88f-4378-8f9c-c1b20ee2651e;\n  style 74a36643-b88f-4378-8f9c-c1b20ee2651e stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:22 +0000",
+                "modified": "2024-10-02 12:08:07 +0000",
                 "name": "ATAC-seq GTM",
                 "outputs": [
                     {
@@ -73949,8 +77055,8 @@
                         ]
                     }
                 ],
-                "parent_id": "epigenetics/cut_and_run",
-                "path": "topics/epigenetics/tutorials/cut_and_run/workflows/main_workflow.ga",
+                "parent_id": "epigenetics/atac-seq",
+                "path": "topics/epigenetics/tutorials/atac-seq/workflows/main_workflow.ga",
                 "tags": [
                     "epigenetics"
                 ],
@@ -73958,12 +77064,12 @@
                 "tests": false,
                 "title": "ATAC-seq GTM",
                 "topic_id": "epigenetics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/epigenetics-cut_and_run/versions/main-workflow",
-                "tutorial_id": "cut_and_run",
-                "url": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/cut_and_run/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/cut_and_run/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "epigenetics-cut_and_run",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/epigenetics-atac-seq/versions/main-workflow",
+                "tutorial_id": "atac-seq",
+                "url": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/workflows/main_workflow.html",
+                "version": 10,
+                "wfid": "epigenetics-atac-seq",
                 "wfname": "main-workflow",
                 "workflow": "main_workflow.ga",
                 "workflow_tools": [
@@ -73982,7 +77088,7 @@
                     "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
                     "wig_to_bigWig"
                 ],
-                "workflowhub_id": "1161"
+                "workflowhub_id": "1169"
             }
         ],
         "zenodo_link": "https://zenodo.org/record/3862793"
@@ -73994,125 +77100,287 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "chipeakanno_annopeaks",
-                    "owner": "kpbioteam",
-                    "revisions": "104882a2de00",
-                    "tool_panel_section_label": "Test Tools",
+                    "name": "deeptools_bam_compare",
+                    "owner": "bgruening",
+                    "revisions": "e821645ef8fc",
+                    "tool_panel_section_label": "deepTools",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "clusterprofiler_bitr",
-                    "owner": "kpbioteam",
-                    "revisions": "762c61c71874",
-                    "tool_panel_section_label": "Test Tools",
+                    "name": "deeptools_compute_gc_bias",
+                    "owner": "bgruening",
+                    "revisions": "2bc10a9ca58b",
+                    "tool_panel_section_label": "deepTools",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "clusterprofiler_go",
-                    "owner": "kpbioteam",
-                    "revisions": "5299be80cafb",
-                    "tool_panel_section_label": "Test Tools",
+                    "name": "deeptools_compute_matrix",
+                    "owner": "bgruening",
+                    "revisions": "514fa53b5efb",
+                    "tool_panel_section_label": "deepTools",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ewastools",
-                    "owner": "kpbioteam",
-                    "revisions": "369fef559cfc",
-                    "tool_panel_section_label": "Epigenetics",
+                    "name": "deeptools_correct_gc_bias",
+                    "owner": "bgruening",
+                    "revisions": "2c37ce318bc3",
+                    "tool_panel_section_label": "deepTools",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "deeptools_multi_bam_summary",
+                    "owner": "bgruening",
+                    "revisions": "78f405266706",
+                    "tool_panel_section_label": "deepTools",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "deeptools_plot_correlation",
+                    "owner": "bgruening",
+                    "revisions": "32e451def88c",
+                    "tool_panel_section_label": "deepTools",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "deeptools_plot_fingerprint",
+                    "owner": "bgruening",
+                    "revisions": "2da482e408b8",
+                    "tool_panel_section_label": "deepTools",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "deeptools_plot_heatmap",
+                    "owner": "bgruening",
+                    "revisions": "a4dfb122e52b",
+                    "tool_panel_section_label": "deepTools",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bwa",
+                    "owner": "devteam",
+                    "revisions": "64f11cf59c6e",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "e7b2202befea",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "samtools_idxstats",
+                    "owner": "devteam",
+                    "revisions": "7a6034296ae9",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bedtools",
+                    "owner": "iuc",
+                    "revisions": "b28e0cfa7ba1",
+                    "tool_panel_section_label": "BED",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "macs2",
+                    "owner": "iuc",
+                    "revisions": "424aefbd7777",
+                    "tool_panel_section_label": "Peak Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "trimmomatic",
+                    "owner": "pjbriggs",
+                    "revisions": "898b67846b47",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: chipeakanno_annopeaks\n  owner: kpbioteam\n  revisions: 104882a2de00\n  tool_panel_section_label: Test Tools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clusterprofiler_bitr\n  owner: kpbioteam\n  revisions: 762c61c71874\n  tool_panel_section_label: Test Tools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clusterprofiler_go\n  owner: kpbioteam\n  revisions: 5299be80cafb\n  tool_panel_section_label: Test Tools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ewastools\n  owner: kpbioteam\n  revisions: 369fef559cfc\n  tool_panel_section_label: Epigenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/ewas-suite/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: deeptools_bam_compare\n  owner: bgruening\n  revisions: e821645ef8fc\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_compute_gc_bias\n  owner: bgruening\n  revisions: 2bc10a9ca58b\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_compute_matrix\n  owner: bgruening\n  revisions: 514fa53b5efb\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_correct_gc_bias\n  owner: bgruening\n  revisions: 2c37ce318bc3\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_multi_bam_summary\n  owner: bgruening\n  revisions: 78f405266706\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_plot_correlation\n  owner: bgruening\n  revisions: 32e451def88c\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_plot_fingerprint\n  owner: bgruening\n  revisions: 2da482e408b8\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_plot_heatmap\n  owner: bgruening\n  revisions: a4dfb122e52b\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: 64f11cf59c6e\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_idxstats\n  owner: devteam\n  revisions: 7a6034296ae9\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: b28e0cfa7ba1\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: macs2\n  owner: iuc\n  revisions: 424aefbd7777\n  tool_panel_section_label: Peak Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n  owner: pjbriggs\n  revisions: 898b67846b47\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "id": "kkamieniecka",
-                "joined": "2018-08",
-                "name": "Katarzyna Kamieniecka",
-                "orcid": "0009-0004-2454-5950",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/",
-                "twitter": "katemurat",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
+                "id": "malloryfreeberg",
+                "joined": "2017-09",
+                "name": "Mallory Freeberg",
+                "orcid": "0000-0003-2949-3921",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/malloryfreeberg/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/malloryfreeberg.json"
             },
             {
-                "affiliations": [
+                "email": "mheydarian@gmail.com",
+                "id": "moheydarian",
+                "joined": "2017-09",
+                "name": "Mo Heydarian",
+                "orcid": "0000-0001-9449-9364",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/moheydarian/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/moheydarian.json"
+            },
+            {
+                "id": "vivekbhr",
+                "joined": "2017-09",
+                "name": "Vivek Bhardwaj",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/vivekbhr/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/vivekbhr.json"
+            },
+            {
+                "elixir_node": "de",
+                "email": "wolffj@informatik.uni-freiburg.de",
+                "former_affiliations": [
+                    "uni-freiburg",
                     "elixir-europe"
                 ],
-                "elixir_node": "uk",
-                "email": "k.jumah@bradford.ac.uk",
-                "id": "khaled196",
-                "joined": "2022-09",
-                "name": "Khaled Jum\u2019ah",
-                "orcid": "0000-0001-5481-8893",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/khaled196/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/khaled196.json"
+                "id": "joachimwolff",
+                "joined": "2017-09",
+                "name": "Joachim Wolff",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/joachimwolff.json"
             },
             {
                 "affiliations": [
+                    "eurosciencegateway",
+                    "uni-freiburg",
                     "elixir-europe"
                 ],
-                "elixir_node": "uk",
-                "id": "poterlowicz-lab",
+                "elixir_node": "de",
+                "email": "anikaerxleben@gmail.com",
+                "id": "erxleben",
                 "joined": "2017-09",
-                "name": "Krzysztof Poterlowicz",
-                "orcid": "0000-0001-6173-5674",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/poterlowicz-lab/",
-                "twitter": "bioinfbrad",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/poterlowicz-lab.json"
+                "name": "Anika Erxleben",
+                "orcid": "0000-0002-7427-6478",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/erxleben/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/erxleben.json"
             }
         ],
-        "dir": "topics/epigenetics/tutorials/ewas-suite",
-        "edam_operation": [],
-        "edam_topic": [],
+        "dir": "topics/epigenetics/tutorials/tal1-binding-site-identification",
+        "edam_ontology": [
+            "topic_3169"
+        ],
+        "edam_operation": [
+            "Peak calling",
+            "Sequence alignment",
+            "Read mapping",
+            "Sequencing quality control",
+            "Sequence composition calculation",
+            "Genome indexing",
+            "Generation",
+            "Statistical calculation",
+            "Gene regulatory network analysis",
+            "Mapping",
+            "Enrichment analysis"
+        ],
+        "edam_topic": [
+            "ChIP-seq"
+        ],
         "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.no"
+            "UseGalaxy.be",
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "epigenetics/ewas-suite",
-        "inexact_supported_servers": [],
+        "id": "epigenetics/tal1-binding-site-identification",
+        "inexact_supported_servers": [
+            "Galaxy@AuBi",
+            "MISSISSIPPI",
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Infinium Human Methylation BeadChip is an array based technology to generate DNA methylation profiling at individual CpG loci in the human genome based on Illumina\u2019s bead technology.",
-            "Time and cost efficiency followed by high sample output, and overall quantitative accuracy and reproducibility made Infinium Human Methylation BeadChip one of the most widely used arrays on the market."
+            "Sophisticated analysis of ChIP-seq data is possible using tools hosted by Galaxy.",
+            "Genomic dataset analyses require multiple methods of quality assessment to ensure that the data are appropriate for answering the biology question of interest.",
+            "By using the sharable and transparent Galaxy platform, data analyses can easily be shared and reproduced."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-26",
+        "mod_date": "2024-06-25",
         "objectives": [
-            "Learn how to perform reproducible Infinium Human Methylation BeadChip analysis",
-            "Visualise differentially methylated positions using UCSC browser"
+            "Inspect read quality with FastQC",
+            "Perform read trimming with Trimmomatic",
+            "Align trimmed reads with BWA",
+            "Assess quality and reproducibility of experiments",
+            "Identify TAL1 binding sites with MACS2",
+            "Determine unique/common TAL1 binding sites from G1E and Megakaryocytes",
+            "Identify unique/common TAL1 peaks occupying gene promoters",
+            "Visually inspect TAL1 peaks with Trackster"
         ],
-        "pageviews": 5729674,
-        "pub_date": "2018-08-27",
+        "pageviews": 11314,
+        "pub_date": "2016-12-20",
         "questions": [
-            "Which DNA regions and positions are diffrentialy methylated in pre MAPKi treatment and post MAPKi resistance Melanomas GSE65183?",
-            "How to analyse and visualise Infinium Human Methylation BeadChip's?"
+            "How is raw ChIP-seq data processed and analyzed?",
+            "What are the binding sites of TAL1?",
+            "Which genes are regulated by TAL1?"
         ],
-        "short_id": "T00139",
+        "redirect_from": [
+            "/topics/chip-seq/tutorials/tal1-binding-site-identification/tutorial",
+            "/short/epigenetics/tal1-binding-site-identification",
+            "/short/T00143"
+        ],
+        "requirements": [
+            {
+                "link": "https://wiki.galaxyproject.org/Learn/Visualization",
+                "title": "Trackster",
+                "type": "external"
+            }
+        ],
+        "short_id": "T00143",
         "short_tools": [
-            "clusterprofiler_go",
-            "clusterprofiler_bitr",
-            "Cut1",
-            "minfi_analysis",
-            "Remove beginning1",
-            "chipeakanno_annopeaks"
+            "deeptools_plot_correlation",
+            "deeptools_plot_fingerprint",
+            "deeptools_bam_compare",
+            "deeptools_compute_gc_bias",
+            "deeptools_plot_heatmap",
+            "deeptools_correct_gc_bias",
+            "deeptools_multi_bam_summary",
+            "samtools_idxstats",
+            "bedtools_intersectbed",
+            "bwa",
+            "macs2_callpeak",
+            "fastqc",
+            "trimmomatic",
+            "deeptools_compute_matrix"
         ],
-        "slides": true,
+        "slides": false,
         "slides_recordings": false,
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -74127,20 +77395,35 @@
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
-            ],
-            "inexact": []
+            ]
         },
         "symlink": null,
-        "time_estimation": "1h",
-        "title": "Infinium Human Methylation BeadChip",
+        "tags": [
+            "ChIP-seq"
+        ],
+        "time_estimation": "3h",
+        "title": "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)",
         "tools": [
-            "Cut1",
-            "Remove beginning1",
-            "toolshed.g2.bx.psu.edu/repos/kpbioteam/chipeakanno_annopeaks/chipeakanno_annopeaks/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_bitr/clusterprofiler_bitr/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_go/clusterprofiler_go/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/kpbioteam/ewastools/minfi_analysis/2.1.0"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.3.2.0.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.3.2.0.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.3.2.0.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.3.2.0.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.3.2.0.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6",
+            "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0"
         ],
         "topic_name": "epigenetics",
         "topic_name_human": "Epigenetics",
@@ -74150,74 +77433,65 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "ewas-suite",
+        "tutorial_name": "tal1-binding-site-identification",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/epigenetics/tutorials/ewas-suite/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/ewas-suite/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/ewas-suite/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.json"
         },
-        "version": 19,
+        "version": 10,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 268,
-        "visitors": 2065448,
+        "visit_duration": 203,
+        "visitors": 5959,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0009-0004-2454-5950",
-                        "name": "Katarzyna Kamieniecka"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0001-5481-8893",
-                        "name": "Khaled Jum'ah"
-                    },
-                    {
-                        "class": "Organization",
-                        "name": "poterlowicz-lab",
-                        "url": "https://github.com/ELIXIR-UK-DaSH"
-                    }
-                ],
-                "description": "The workflow containes the step to perpare the data for and run Galaxy Infinium Human Methylation BeadChip tool that represents many popular algorithms for detecting somatic genetic alterations from genome and exome data",
+                "creators": [],
+                "description": "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR01C02_Red.idat\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR02C02_Red.idat\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR05C02_Red.idat\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR06C02_Red.idat\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR01C02_Green.idat\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR02C02_Green.idat\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR05C02_Green.idat\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR06C02_Green.idat\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nphenotype Table txt file\"]\n  9[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nUCSC Main on Human\"]\n  10[label=\"Infinium Human Methylation BeadChip\"]\n  4 -> 10 [label=\"output\"]\n  5 -> 10 [label=\"output\"]\n  6 -> 10 [label=\"output\"]\n  7 -> 10 [label=\"output\"]\n  0 -> 10 [label=\"output\"]\n  1 -> 10 [label=\"output\"]\n  2 -> 10 [label=\"output\"]\n  3 -> 10 [label=\"output\"]\n  8 -> 10 [label=\"output\"]\n  9 -> 10 [label=\"output\"]\n  k2ac7dd5ded744d58b1cbbe7dcca9154a[color=lightseagreen,label=\"Output\\nSNPInfo Table\"]\n  10 -> k2ac7dd5ded744d58b1cbbe7dcca9154a\n  kd1732a9818614612bdaaf68861c22f56[color=lightseagreen,label=\"Output\\nDifferentially Methylated Regions\"]\n  10 -> kd1732a9818614612bdaaf68861c22f56\n  k9aa8b4a9611e4a39864f400f17866a9e[color=lightseagreen,label=\"Output\\nDifferentially Methylated Positions\"]\n  10 -> k9aa8b4a9611e4a39864f400f17866a9e\n  k14ddb6f7637e4193bfb580aeae4fab64[color=lightseagreen,label=\"Output\\nQuality Control Report\"]\n  10 -> k14ddb6f7637e4193bfb580aeae4fab64\n  kc8c37ff8716d4c23a84f7cebcb4b6c9d[color=lightseagreen,label=\"Output\\nQuality Control Plot\"]\n  10 -> kc8c37ff8716d4c23a84f7cebcb4b6c9d\n  11[label=\"ChIPpeakAnno annoPeaks\"]\n  10 -> 11 [label=\"dmp\"]\n  kbedf4346da4d4e1abf3ca7d20f3ec3c5[color=lightseagreen,label=\"Output\\nTable of Annotated Peaks\"]\n  11 -> kbedf4346da4d4e1abf3ca7d20f3ec3c5\n  12[label=\"Cut\"]\n  11 -> 12 [label=\"tab\"]\n  k0b54dfe5f84a4288b631ae4dc2384a17[color=lightseagreen,label=\"Output\\nCut on Table of Annotated Peaks\"]\n  12 -> k0b54dfe5f84a4288b631ae4dc2384a17\n  13[label=\"Remove beginning\"]\n  12 -> 13 [label=\"out_file1\"]\n  k8f65cf8274274273ba0ba6673ee1ff2d[color=lightseagreen,label=\"Output\\nRemove beginning on the cut output\"]\n  13 -> k8f65cf8274274273ba0ba6673ee1ff2d\n  14[label=\"Cluster Profiler Bitr\"]\n  13 -> 14 [label=\"out_file1\"]\n  k7989f80a3e794d2fbbe4e4d641eebd6a[color=lightseagreen,label=\"Output\\nTable of Translated Gene ID's\"]\n  14 -> k7989f80a3e794d2fbbe4e4d641eebd6a\n  15[label=\"Cluster Profiler GO\"]\n  14 -> 15 [label=\"translation\"]\n  kff6c7018b8214ade9931fa99aeb0a86c[color=lightseagreen,label=\"Output\\nGO Enrichment Analysis of a Gene Set\"]\n  15 -> kff6c7018b8214ade9931fa99aeb0a86c\n  k03b88399095b4bd59693528c60338407[color=lightseagreen,label=\"Output\\nGO Enrichment Analysis Visualization\"]\n  15 -> k03b88399095b4bd59693528c60338407\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nG1E_input_R1_downsampled_SRR507859.fastqsanger\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nG1E_input_R2_downsampled_SRR507860.fastqsanger\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nG1E_Tal1_R1_downsampled_SRR492444.fastqsanger\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nG1E_Tal1_R2_downsampled_SRR492445.fastqsanger\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_input_R1_downsampled_SRR492453.fastqsanger\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_input_R2_downsampled_SRR492454.fastqsanger\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMegakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nRefSeq_gene_annotations_mm10.bed\"]\n  9[label=\"FastQC\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"Trimmomatic\"]\n  0 -> 10 [label=\"output\"]\n  11[label=\"FastQC\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"Trimmomatic\"]\n  1 -> 12 [label=\"output\"]\n  13[label=\"FastQC\"]\n  2 -> 13 [label=\"output\"]\n  14[label=\"Trimmomatic\"]\n  2 -> 14 [label=\"output\"]\n  15[label=\"FastQC\"]\n  3 -> 15 [label=\"output\"]\n  16[label=\"Trimmomatic\"]\n  3 -> 16 [label=\"output\"]\n  17[label=\"FastQC\"]\n  4 -> 17 [label=\"output\"]\n  18[label=\"Trimmomatic\"]\n  4 -> 18 [label=\"output\"]\n  19[label=\"FastQC\"]\n  5 -> 19 [label=\"output\"]\n  20[label=\"Trimmomatic\"]\n  5 -> 20 [label=\"output\"]\n  21[label=\"FastQC\"]\n  6 -> 21 [label=\"output\"]\n  22[label=\"Trimmomatic\"]\n  6 -> 22 [label=\"output\"]\n  23[label=\"FastQC\"]\n  7 -> 23 [label=\"output\"]\n  24[label=\"Trimmomatic\"]\n  7 -> 24 [label=\"output\"]\n  25[label=\"FastQC\"]\n  10 -> 25 [label=\"fastq_out\"]\n  26[label=\"Map with BWA\"]\n  10 -> 26 [label=\"fastq_out\"]\n  27[label=\"FastQC\"]\n  12 -> 27 [label=\"fastq_out\"]\n  28[label=\"Map with BWA\"]\n  12 -> 28 [label=\"fastq_out\"]\n  29[label=\"FastQC\"]\n  14 -> 29 [label=\"fastq_out\"]\n  30[label=\"Map with BWA\"]\n  14 -> 30 [label=\"fastq_out\"]\n  31[label=\"FastQC\"]\n  16 -> 31 [label=\"fastq_out\"]\n  32[label=\"Map with BWA\"]\n  16 -> 32 [label=\"fastq_out\"]\n  33[label=\"FastQC\"]\n  18 -> 33 [label=\"fastq_out\"]\n  34[label=\"Map with BWA\"]\n  18 -> 34 [label=\"fastq_out\"]\n  35[label=\"FastQC\"]\n  20 -> 35 [label=\"fastq_out\"]\n  36[label=\"Map with BWA\"]\n  20 -> 36 [label=\"fastq_out\"]\n  37[label=\"FastQC\"]\n  22 -> 37 [label=\"fastq_out\"]\n  38[label=\"Map with BWA\"]\n  22 -> 38 [label=\"fastq_out\"]\n  39[label=\"FastQC\"]\n  24 -> 39 [label=\"fastq_out\"]\n  40[label=\"Map with BWA\"]\n  24 -> 40 [label=\"fastq_out\"]\n  41[label=\"Samtools idxstats\"]\n  26 -> 41 [label=\"bam_output\"]\n  42[label=\"Samtools idxstats\"]\n  28 -> 42 [label=\"bam_output\"]\n  43[label=\"Samtools idxstats\"]\n  30 -> 43 [label=\"bam_output\"]\n  44[label=\"bamCompare\"]\n  30 -> 44 [label=\"bam_output\"]\n  26 -> 44 [label=\"bam_output\"]\n  45[label=\"Samtools idxstats\"]\n  32 -> 45 [label=\"bam_output\"]\n  46[label=\"plotFingerprint\"]\n  26 -> 46 [label=\"bam_output\"]\n  28 -> 46 [label=\"bam_output\"]\n  30 -> 46 [label=\"bam_output\"]\n  32 -> 46 [label=\"bam_output\"]\n  47[label=\"MACS2 callpeak\"]\n  26 -> 47 [label=\"bam_output\"]\n  28 -> 47 [label=\"bam_output\"]\n  30 -> 47 [label=\"bam_output\"]\n  32 -> 47 [label=\"bam_output\"]\n  48[label=\"bamCompare\"]\n  32 -> 48 [label=\"bam_output\"]\n  28 -> 48 [label=\"bam_output\"]\n  49[label=\"Samtools idxstats\"]\n  34 -> 49 [label=\"bam_output\"]\n  50[label=\"Samtools idxstats\"]\n  36 -> 50 [label=\"bam_output\"]\n  51[label=\"Samtools idxstats\"]\n  38 -> 51 [label=\"bam_output\"]\n  52[label=\"bamCompare\"]\n  38 -> 52 [label=\"bam_output\"]\n  34 -> 52 [label=\"bam_output\"]\n  53[label=\"Samtools idxstats\"]\n  40 -> 53 [label=\"bam_output\"]\n  54[label=\"multiBamSummary\"]\n  26 -> 54 [label=\"bam_output\"]\n  28 -> 54 [label=\"bam_output\"]\n  30 -> 54 [label=\"bam_output\"]\n  32 -> 54 [label=\"bam_output\"]\n  34 -> 54 [label=\"bam_output\"]\n  36 -> 54 [label=\"bam_output\"]\n  38 -> 54 [label=\"bam_output\"]\n  40 -> 54 [label=\"bam_output\"]\n  55[label=\"plotFingerprint\"]\n  34 -> 55 [label=\"bam_output\"]\n  36 -> 55 [label=\"bam_output\"]\n  38 -> 55 [label=\"bam_output\"]\n  40 -> 55 [label=\"bam_output\"]\n  56[label=\"MACS2 callpeak\"]\n  34 -> 56 [label=\"bam_output\"]\n  36 -> 56 [label=\"bam_output\"]\n  38 -> 56 [label=\"bam_output\"]\n  40 -> 56 [label=\"bam_output\"]\n  57[label=\"bamCompare\"]\n  40 -> 57 [label=\"bam_output\"]\n  36 -> 57 [label=\"bam_output\"]\n  58[label=\"computeMatrix\"]\n  44 -> 58 [label=\"outFileName\"]\n  48 -> 58 [label=\"outFileName\"]\n  47 -> 58 [label=\"output_narrowpeaks\"]\n  59[label=\"plotCorrelation\"]\n  54 -> 59 [label=\"outFile\"]\n  60[label=\"bedtools Intersect intervals\"]\n  47 -> 60 [label=\"output_narrowpeaks\"]\n  56 -> 60 [label=\"output_narrowpeaks\"]\n  k0b9a3e20a9d6446485f0012664b895ff[color=lightseagreen,label=\"Output\\noutput_overlapping_peaks\"]\n  60 -> k0b9a3e20a9d6446485f0012664b895ff\n  61[label=\"bedtools Intersect intervals\"]\n  47 -> 61 [label=\"output_narrowpeaks\"]\n  56 -> 61 [label=\"output_narrowpeaks\"]\n  k609ee90a2c9e4bde82d65f59516c3bad[color=lightseagreen,label=\"Output\\noutput_g1e_peaks\"]\n  61 -> k609ee90a2c9e4bde82d65f59516c3bad\n  62[label=\"bedtools Intersect intervals\"]\n  56 -> 62 [label=\"output_narrowpeaks\"]\n  47 -> 62 [label=\"output_narrowpeaks\"]\n  k0bb490b277e54b5982eb6a2b918c2788[color=lightseagreen,label=\"Output\\noutput_megakaryocyte_peaks\"]\n  62 -> k0bb490b277e54b5982eb6a2b918c2788\n  63[label=\"computeMatrix\"]\n  52 -> 63 [label=\"outFileName\"]\n  57 -> 63 [label=\"outFileName\"]\n  56 -> 63 [label=\"output_narrowpeaks\"]\n  64[label=\"plotHeatmap\"]\n  58 -> 64 [label=\"outFileName\"]\n  65[label=\"plotHeatmap\"]\n  63 -> 65 [label=\"outFileName\"]\n}",
                 "history": [
                     {
-                        "hash": "4f69ebe91fffffe057c1f187bc83e1562369defd",
-                        "message": "fix workflow",
+                        "hash": "818f002190ef7fb261a841024556075ceff1df49",
+                        "message": "Fixed JSON format.",
+                        "num": 5,
+                        "short_hash": "818f00219",
+                        "unix": "1602017176"
+                    },
+                    {
+                        "hash": "473da245d41207021918c79019a3e5833873c82f",
+                        "message": "Updated outputs in workflow and test.yml.",
                         "num": 4,
-                        "short_hash": "4f69ebe91",
-                        "unix": "1698053430"
+                        "short_hash": "473da245d",
+                        "unix": "1602015752"
                     },
                     {
-                        "hash": "8f19faceda02e93f48bb3fe0e7fffa533685d99d",
-                        "message": "fix",
+                        "hash": "3bee4c5377363dbf60c059683f0f972a343c3cbc",
+                        "message": "Updated inputs in workflow and test.yml.",
                         "num": 3,
-                        "short_hash": "8f19faced",
-                        "unix": "1697725863"
+                        "short_hash": "3bee4c537",
+                        "unix": "1602012514"
                     },
                     {
-                        "hash": "568e22f2036d5cfb1cd3d3454d0b50e3c6ca54ca",
-                        "message": "add license",
+                        "hash": "e9f2fa109479668f2d020a75f3496a3db5fdcedd",
+                        "message": "Updated workflow with tags.",
                         "num": 2,
-                        "short_hash": "568e22f20",
-                        "unix": "1697724380"
+                        "short_hash": "e9f2fa109",
+                        "unix": "1601981292"
                     },
                     {
-                        "hash": "451efca00587e14a69d8df6096d0297e739d1f27",
-                        "message": "remove pictures and add output tests",
+                        "hash": "7fe3ca36a9a8b8022922de0f9c2d7385628b2e5c",
+                        "message": "Added workflow.",
                         "num": 1,
-                        "short_hash": "451efca00",
-                        "unix": "1697723365"
+                        "short_hash": "7fe3ca36a",
+                        "unix": "1601924809"
                     }
                 ],
                 "inputs": [
@@ -74230,22 +77504,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "R01C02_Red.idat"
+                                "name": "G1E_input_R1_downsampled_SRR507859.fastqsanger"
                             }
                         ],
-                        "label": "R01C02_Red.idat",
-                        "name": "Input dataset",
+                        "label": "G1E_input_R1_downsampled_SRR507859.fastqsanger",
+                        "name": "G1E_input_R1_downsampled_SRR507859.fastqsanger",
                         "outputs": [],
                         "position": {
-                            "left": 1.885486970465422e-05,
-                            "top": 3
+                            "left": 10,
+                            "top": 10
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{\"name\": \"G1E_input_R1_downsampled_SRR507859.fastqsanger\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "71c54456-73d3-4af4-8d89-ab81d0feb88d",
-                        "when": null,
+                        "uuid": "72908882-dad9-452e-9ed6-42aa567c7b6d",
                         "workflow_outputs": []
                     },
                     {
@@ -74257,22 +77530,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "R02C02_Red.idat"
+                                "name": "G1E_input_R2_downsampled_SRR507860.fastqsanger"
                             }
                         ],
-                        "label": "R02C02_Red.idat",
-                        "name": "Input dataset",
+                        "label": "G1E_input_R2_downsampled_SRR507860.fastqsanger",
+                        "name": "G1E_input_R2_downsampled_SRR507860.fastqsanger",
                         "outputs": [],
                         "position": {
-                            "left": 1.885486970465422e-05,
-                            "top": 123
+                            "left": 10,
+                            "top": 130
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{\"name\": \"G1E_input_R2_downsampled_SRR507860.fastqsanger\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "2521d0ca-a0d8-416f-8735-0a6c441812fc",
-                        "when": null,
+                        "uuid": "f9264f2a-fd66-40ef-8d19-88de9e5adcf0",
                         "workflow_outputs": []
                     },
                     {
@@ -74284,675 +77556,365 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "R05C02_Red.idat"
-                            }
-                        ],
-                        "label": "R05C02_Red.idat",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 1.885486970465422e-05,
-                            "top": 243
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f3068f86-caf3-4e26-a51b-3c6c6683ce84",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "R06C02_Red.idat"
-                            }
-                        ],
-                        "label": "R06C02_Red.idat",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 362.99997401229103
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ef39313e-8463-444e-8d91-ebebfc16e124",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "R01C02_Green.idat"
-                            }
-                        ],
-                        "label": "R01C02_Green.idat",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 1.885486970465422e-05,
-                            "top": 483
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "738cbcf1-2bc8-438d-b539-bc6e762af030",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "R02C02_Green.idat"
-                            }
-                        ],
-                        "label": "R02C02_Green.idat",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 1.885486970465422e-05,
-                            "top": 603
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "4d8bb323-db45-4f9d-b846-fde1c4f08b13",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "R05C02_Green.idat"
-                            }
-                        ],
-                        "label": "R05C02_Green.idat",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 6.401854712230744,
-                            "top": 721.3996100720306
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "c47087fa-a5df-4ec4-8142-e2352e620e4f",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "R06C02_Green.idat"
-                            }
-                        ],
-                        "label": "R06C02_Green.idat",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 1.885486970465422e-05,
-                            "top": 843
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "3b510a95-0b47-4d90-b499-4c33e4914954",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "phenotype Table txt file"
-                            }
-                        ],
-                        "label": "phenotype Table txt file",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 1.885486970465422e-05,
-                            "top": 963
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "0c5e494f-b987-4f48-a667-b9e8a259794e",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "UCSC Main on Human"
+                                "name": "G1E_Tal1_R1_downsampled_SRR492444.fastqsanger"
                             }
                         ],
-                        "label": "UCSC Main on Human",
-                        "name": "Input dataset",
+                        "label": "G1E_Tal1_R1_downsampled_SRR492444.fastqsanger",
+                        "name": "G1E_Tal1_R1_downsampled_SRR492444.fastqsanger",
                         "outputs": [],
                         "position": {
-                            "left": 1.885486970465422e-05,
-                            "top": 1083
+                            "left": 10,
+                            "top": 250
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"name\": \"G1E_Tal1_R1_downsampled_SRR492444.fastqsanger\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "04bc7d9a-d7ae-46fe-9eaf-85d6c47c57a5",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "AGPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nR01C02_Red.idat\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nR02C02_Red.idat\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nR05C02_Red.idat\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nR06C02_Red.idat\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nR01C02_Green.idat\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nR02C02_Green.idat\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nR05C02_Green.idat\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nR06C02_Green.idat\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nphenotype Table txt file\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"\u2139\ufe0f Input Dataset\\nUCSC Main on Human\"];\n  style 9 stroke:#2c3143,stroke-width:4px;\n  10[\"Infinium Human Methylation BeadChip\"];\n  4 -->|output| 10;\n  5 -->|output| 10;\n  6 -->|output| 10;\n  7 -->|output| 10;\n  0 -->|output| 10;\n  1 -->|output| 10;\n  2 -->|output| 10;\n  3 -->|output| 10;\n  8 -->|output| 10;\n  9 -->|output| 10;\n  2ac7dd5d-ed74-4d58-b1cb-be7dcca9154a[\"Output\\nSNPInfo Table\"];\n  10 --> 2ac7dd5d-ed74-4d58-b1cb-be7dcca9154a;\n  style 2ac7dd5d-ed74-4d58-b1cb-be7dcca9154a stroke:#2c3143,stroke-width:4px;\n  d1732a98-1861-4612-bdaa-f68861c22f56[\"Output\\nDifferentially Methylated Regions\"];\n  10 --> d1732a98-1861-4612-bdaa-f68861c22f56;\n  style d1732a98-1861-4612-bdaa-f68861c22f56 stroke:#2c3143,stroke-width:4px;\n  9aa8b4a9-611e-4a39-864f-400f17866a9e[\"Output\\nDifferentially Methylated Positions\"];\n  10 --> 9aa8b4a9-611e-4a39-864f-400f17866a9e;\n  style 9aa8b4a9-611e-4a39-864f-400f17866a9e stroke:#2c3143,stroke-width:4px;\n  14ddb6f7-637e-4193-bfb5-80aeae4fab64[\"Output\\nQuality Control Report\"];\n  10 --> 14ddb6f7-637e-4193-bfb5-80aeae4fab64;\n  style 14ddb6f7-637e-4193-bfb5-80aeae4fab64 stroke:#2c3143,stroke-width:4px;\n  c8c37ff8-716d-4c23-a84f-7cebcb4b6c9d[\"Output\\nQuality Control Plot\"];\n  10 --> c8c37ff8-716d-4c23-a84f-7cebcb4b6c9d;\n  style c8c37ff8-716d-4c23-a84f-7cebcb4b6c9d stroke:#2c3143,stroke-width:4px;\n  11[\"ChIPpeakAnno annoPeaks\"];\n  10 -->|dmp| 11;\n  bedf4346-da4d-4e1a-bf3c-a7d20f3ec3c5[\"Output\\nTable of Annotated Peaks\"];\n  11 --> bedf4346-da4d-4e1a-bf3c-a7d20f3ec3c5;\n  style bedf4346-da4d-4e1a-bf3c-a7d20f3ec3c5 stroke:#2c3143,stroke-width:4px;\n  12[\"Cut\"];\n  11 -->|tab| 12;\n  0b54dfe5-f84a-4288-b631-ae4dc2384a17[\"Output\\nCut on Table of Annotated Peaks\"];\n  12 --> 0b54dfe5-f84a-4288-b631-ae4dc2384a17;\n  style 0b54dfe5-f84a-4288-b631-ae4dc2384a17 stroke:#2c3143,stroke-width:4px;\n  13[\"Remove beginning\"];\n  12 -->|out_file1| 13;\n  8f65cf82-7427-4273-ba0b-a6673ee1ff2d[\"Output\\nRemove beginning on the cut output\"];\n  13 --> 8f65cf82-7427-4273-ba0b-a6673ee1ff2d;\n  style 8f65cf82-7427-4273-ba0b-a6673ee1ff2d stroke:#2c3143,stroke-width:4px;\n  14[\"Cluster Profiler Bitr\"];\n  13 -->|out_file1| 14;\n  7989f80a-3e79-4d2f-bbe4-e4d641eebd6a[\"Output\\nTable of Translated Gene ID's\"];\n  14 --> 7989f80a-3e79-4d2f-bbe4-e4d641eebd6a;\n  style 7989f80a-3e79-4d2f-bbe4-e4d641eebd6a stroke:#2c3143,stroke-width:4px;\n  15[\"Cluster Profiler GO\"];\n  14 -->|translation| 15;\n  ff6c7018-b821-4ade-9931-fa99aeb0a86c[\"Output\\nGO Enrichment Analysis of a Gene Set\"];\n  15 --> ff6c7018-b821-4ade-9931-fa99aeb0a86c;\n  style ff6c7018-b821-4ade-9931-fa99aeb0a86c stroke:#2c3143,stroke-width:4px;\n  03b88399-095b-4bd5-9693-528c60338407[\"Output\\nGO Enrichment Analysis Visualization\"];\n  15 --> 03b88399-095b-4bd5-9693-528c60338407;\n  style 03b88399-095b-4bd5-9693-528c60338407 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:22 +0000",
-                "name": "Infinium Human Methylation BeadChip",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/kpbioteam/ewastools/minfi_analysis/2.1.0",
-                        "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "files_grn": [
-                                {
-                                    "id": 4,
-                                    "output_name": "output"
-                                },
-                                {
-                                    "id": 5,
-                                    "output_name": "output"
-                                },
-                                {
-                                    "id": 6,
-                                    "output_name": "output"
-                                },
-                                {
-                                    "id": 7,
-                                    "output_name": "output"
-                                }
-                            ],
-                            "files_red": [
-                                {
-                                    "id": 0,
-                                    "output_name": "output"
-                                },
-                                {
-                                    "id": 1,
-                                    "output_name": "output"
-                                },
-                                {
-                                    "id": 2,
-                                    "output_name": "output"
-                                },
-                                {
-                                    "id": 3,
-                                    "output_name": "output"
-                                }
-                            ],
-                            "phenotype_table": {
-                                "id": 8,
-                                "output_name": "output"
-                            },
-                            "ucsc_genome": {
-                                "id": 9,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Infinium Human Methylation BeadChip",
-                        "outputs": [
-                            {
-                                "name": "qctab",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "qcpng",
-                                "type": "png"
-                            },
-                            {
-                                "name": "table",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "dmr",
-                                "type": "bed"
-                            },
-                            {
-                                "name": "dmp",
-                                "type": "bed"
-                            }
-                        ],
-                        "position": {
-                            "left": 220.0000188548697,
-                            "top": 3
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActiondmp": {
-                                "action_arguments": {
-                                    "newname": "Differentially Methylated Positions"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "dmp"
-                            },
-                            "RenameDatasetActiondmr": {
-                                "action_arguments": {
-                                    "newname": "Differentially Methylated Regions"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "dmr"
-                            },
-                            "RenameDatasetActionqcpng": {
-                                "action_arguments": {
-                                    "newname": "Quality Control Plot"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "qcpng"
-                            },
-                            "RenameDatasetActionqctab": {
-                                "action_arguments": {
-                                    "newname": "Quality Control Report"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "qctab"
-                            },
-                            "RenameDatasetActiontable": {
-                                "action_arguments": {
-                                    "newname": "SNPInfo Table"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "table"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/kpbioteam/ewastools/minfi_analysis/2.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "369fef559cfc",
-                            "name": "ewastools",
-                            "owner": "kpbioteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"idat\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/hg19.len\", \"cutoff_size\": \"0.1\", \"files_grn\": {\"__class__\": \"ConnectedValue\"}, \"files_red\": {\"__class__\": \"ConnectedValue\"}, \"maxgap_size\": \"250\", \"null_method\": \"permutation\", \"number_of_resamples\": \"0\", \"optpp\": \"ppsnp\", \"phenotype\": \"categorical\", \"phenotype_table\": {\"__class__\": \"ConnectedValue\"}, \"q_cutoff\": \"0.5\", \"ucsc_genome\": {\"__class__\": \"ConnectedValue\"}, \"variance_shrinkage\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.0",
-                        "type": "tool",
-                        "uuid": "99026073-61d1-408d-b7a7-50fe91530aa5",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "SNPInfo Table",
-                                "output_name": "table",
-                                "uuid": "2ac7dd5d-ed74-4d58-b1cb-be7dcca9154a"
-                            },
-                            {
-                                "label": "Differentially Methylated Regions",
-                                "output_name": "dmr",
-                                "uuid": "d1732a98-1861-4612-bdaa-f68861c22f56"
-                            },
-                            {
-                                "label": "Differentially Methylated Positions",
-                                "output_name": "dmp",
-                                "uuid": "9aa8b4a9-611e-4a39-864f-400f17866a9e"
-                            },
-                            {
-                                "label": "Quality Control Report",
-                                "output_name": "qctab",
-                                "uuid": "14ddb6f7-637e-4193-bfb5-80aeae4fab64"
-                            },
-                            {
-                                "label": "Quality Control Plot",
-                                "output_name": "qcpng",
-                                "uuid": "c8c37ff8-716d-4c23-a84f-7cebcb4b6c9d"
-                            }
-                        ]
+                        "uuid": "2f74715c-df91-46a4-8845-1d4463c4f0c0",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/kpbioteam/chipeakanno_annopeaks/chipeakanno_annopeaks/0.1.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 11,
-                        "input_connections": {
-                            "dmp": {
-                                "id": 10,
-                                "output_name": "dmp"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "ChIPpeakAnno annoPeaks",
-                        "outputs": [
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "tab",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "G1E_Tal1_R2_downsampled_SRR492445.fastqsanger"
                             }
                         ],
+                        "label": "G1E_Tal1_R2_downsampled_SRR492445.fastqsanger",
+                        "name": "G1E_Tal1_R2_downsampled_SRR492445.fastqsanger",
+                        "outputs": [],
                         "position": {
-                            "left": 452,
-                            "top": 0
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActiontab": {
-                                "action_arguments": {
-                                    "newname": "Table of Annotated Peaks"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "tab"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/kpbioteam/chipeakanno_annopeaks/chipeakanno_annopeaks/0.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "104882a2de00",
-                            "name": "chipeakanno_annopeaks",
-                            "owner": "kpbioteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 10,
+                            "top": 370
                         },
-                        "tool_state": "{\"__input_ext\": \"bed\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/hg19.len\", \"dmp\": {\"__class__\": \"ConnectedValue\"}, \"end\": \"3000\", \"score\": \"5\", \"start\": \"-5000\", \"type\": \"startSite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.0",
-                        "type": "tool",
-                        "uuid": "3a83a9ba-d58c-455a-84b0-8f25e95cc4f3",
-                        "when": null,
-                        "workflow_outputs": [
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"G1E_Tal1_R2_downsampled_SRR492445.fastqsanger\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0fc34c4d-c3d6-44b4-a683-521d707f06f1",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": "Table of Annotated Peaks",
-                                "output_name": "tab",
-                                "uuid": "bedf4346-da4d-4e1a-bf3c-a7d20f3ec3c5"
+                                "description": "",
+                                "name": "Megakaryocyte_input_R1_downsampled_SRR492453.fastqsanger"
                             }
-                        ]
+                        ],
+                        "label": "Megakaryocyte_input_R1_downsampled_SRR492453.fastqsanger",
+                        "name": "Megakaryocyte_input_R1_downsampled_SRR492453.fastqsanger",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 490
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Megakaryocyte_input_R1_downsampled_SRR492453.fastqsanger\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "92c034ae-9c9e-4dcc-98a4-556d314a7bba",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "Cut1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 12,
-                        "input_connections": {
-                            "input": {
-                                "id": 11,
-                                "output_name": "tab"
+                        "id": 5,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Megakaryocyte_input_R2_downsampled_SRR492454.fastqsanger"
                             }
+                        ],
+                        "label": "Megakaryocyte_input_R2_downsampled_SRR492454.fastqsanger",
+                        "name": "Megakaryocyte_input_R2_downsampled_SRR492454.fastqsanger",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 610
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cut",
-                        "outputs": [
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Megakaryocyte_input_R2_downsampled_SRR492454.fastqsanger\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "7bb71d6b-de12-485c-83c9-ed75af5f7fac",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "Megakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger"
                             }
                         ],
+                        "label": "Megakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger",
+                        "name": "Megakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger",
+                        "outputs": [],
                         "position": {
-                            "left": 660.0000188548697,
-                            "top": 3
+                            "left": 10,
+                            "top": 730
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Cut on Table of Annotated Peaks"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Megakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "dd716dbd-e466-40c8-88bf-88febc0b2119",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Megakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger"
                             }
+                        ],
+                        "label": "Megakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger",
+                        "name": "Megakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 850
                         },
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/hg19.len\", \"columnList\": \"c16\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2",
-                        "type": "tool",
-                        "uuid": "6af6eed4-d83b-42de-a72f-67443b9c63ea",
-                        "when": null,
-                        "workflow_outputs": [
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Megakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "5695db81-e17a-4242-aa28-c703b2988666",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": "Cut on Table of Annotated Peaks",
-                                "output_name": "out_file1",
-                                "uuid": "0b54dfe5-f84a-4288-b631-ae4dc2384a17"
+                                "description": "",
+                                "name": "RefSeq_gene_annotations_mm10.bed"
                             }
-                        ]
-                    },
+                        ],
+                        "label": "RefSeq_gene_annotations_mm10.bed",
+                        "name": "RefSeq_gene_annotations_mm10.bed",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 970
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"RefSeq_gene_annotations_mm10.bed\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "bc0fc125-1b3c-489f-ae71-ef6320c1ccad",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nG1E_input_R1_downsampled_SRR507859.fastqsanger\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nG1E_input_R2_downsampled_SRR507860.fastqsanger\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nG1E_Tal1_R1_downsampled_SRR492444.fastqsanger\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nG1E_Tal1_R2_downsampled_SRR492445.fastqsanger\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_input_R1_downsampled_SRR492453.fastqsanger\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_input_R2_downsampled_SRR492454.fastqsanger\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nMegakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nRefSeq_gene_annotations_mm10.bed\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"FastQC\"];\n  0 -->|output| 9;\n  10[\"Trimmomatic\"];\n  0 -->|output| 10;\n  11[\"FastQC\"];\n  1 -->|output| 11;\n  12[\"Trimmomatic\"];\n  1 -->|output| 12;\n  13[\"FastQC\"];\n  2 -->|output| 13;\n  14[\"Trimmomatic\"];\n  2 -->|output| 14;\n  15[\"FastQC\"];\n  3 -->|output| 15;\n  16[\"Trimmomatic\"];\n  3 -->|output| 16;\n  17[\"FastQC\"];\n  4 -->|output| 17;\n  18[\"Trimmomatic\"];\n  4 -->|output| 18;\n  19[\"FastQC\"];\n  5 -->|output| 19;\n  20[\"Trimmomatic\"];\n  5 -->|output| 20;\n  21[\"FastQC\"];\n  6 -->|output| 21;\n  22[\"Trimmomatic\"];\n  6 -->|output| 22;\n  23[\"FastQC\"];\n  7 -->|output| 23;\n  24[\"Trimmomatic\"];\n  7 -->|output| 24;\n  25[\"FastQC\"];\n  10 -->|fastq_out| 25;\n  26[\"Map with BWA\"];\n  10 -->|fastq_out| 26;\n  27[\"FastQC\"];\n  12 -->|fastq_out| 27;\n  28[\"Map with BWA\"];\n  12 -->|fastq_out| 28;\n  29[\"FastQC\"];\n  14 -->|fastq_out| 29;\n  30[\"Map with BWA\"];\n  14 -->|fastq_out| 30;\n  31[\"FastQC\"];\n  16 -->|fastq_out| 31;\n  32[\"Map with BWA\"];\n  16 -->|fastq_out| 32;\n  33[\"FastQC\"];\n  18 -->|fastq_out| 33;\n  34[\"Map with BWA\"];\n  18 -->|fastq_out| 34;\n  35[\"FastQC\"];\n  20 -->|fastq_out| 35;\n  36[\"Map with BWA\"];\n  20 -->|fastq_out| 36;\n  37[\"FastQC\"];\n  22 -->|fastq_out| 37;\n  38[\"Map with BWA\"];\n  22 -->|fastq_out| 38;\n  39[\"FastQC\"];\n  24 -->|fastq_out| 39;\n  40[\"Map with BWA\"];\n  24 -->|fastq_out| 40;\n  41[\"Samtools idxstats\"];\n  26 -->|bam_output| 41;\n  42[\"Samtools idxstats\"];\n  28 -->|bam_output| 42;\n  43[\"Samtools idxstats\"];\n  30 -->|bam_output| 43;\n  44[\"bamCompare\"];\n  30 -->|bam_output| 44;\n  26 -->|bam_output| 44;\n  45[\"Samtools idxstats\"];\n  32 -->|bam_output| 45;\n  46[\"plotFingerprint\"];\n  26 -->|bam_output| 46;\n  28 -->|bam_output| 46;\n  30 -->|bam_output| 46;\n  32 -->|bam_output| 46;\n  47[\"MACS2 callpeak\"];\n  26 -->|bam_output| 47;\n  28 -->|bam_output| 47;\n  30 -->|bam_output| 47;\n  32 -->|bam_output| 47;\n  48[\"bamCompare\"];\n  32 -->|bam_output| 48;\n  28 -->|bam_output| 48;\n  49[\"Samtools idxstats\"];\n  34 -->|bam_output| 49;\n  50[\"Samtools idxstats\"];\n  36 -->|bam_output| 50;\n  51[\"Samtools idxstats\"];\n  38 -->|bam_output| 51;\n  52[\"bamCompare\"];\n  38 -->|bam_output| 52;\n  34 -->|bam_output| 52;\n  53[\"Samtools idxstats\"];\n  40 -->|bam_output| 53;\n  54[\"multiBamSummary\"];\n  26 -->|bam_output| 54;\n  28 -->|bam_output| 54;\n  30 -->|bam_output| 54;\n  32 -->|bam_output| 54;\n  34 -->|bam_output| 54;\n  36 -->|bam_output| 54;\n  38 -->|bam_output| 54;\n  40 -->|bam_output| 54;\n  55[\"plotFingerprint\"];\n  34 -->|bam_output| 55;\n  36 -->|bam_output| 55;\n  38 -->|bam_output| 55;\n  40 -->|bam_output| 55;\n  56[\"MACS2 callpeak\"];\n  34 -->|bam_output| 56;\n  36 -->|bam_output| 56;\n  38 -->|bam_output| 56;\n  40 -->|bam_output| 56;\n  57[\"bamCompare\"];\n  40 -->|bam_output| 57;\n  36 -->|bam_output| 57;\n  58[\"computeMatrix\"];\n  44 -->|outFileName| 58;\n  48 -->|outFileName| 58;\n  47 -->|output_narrowpeaks| 58;\n  59[\"plotCorrelation\"];\n  54 -->|outFile| 59;\n  60[\"bedtools Intersect intervals\"];\n  47 -->|output_narrowpeaks| 60;\n  56 -->|output_narrowpeaks| 60;\n  0b9a3e20-a9d6-4464-85f0-012664b895ff[\"Output\\noutput_overlapping_peaks\"];\n  60 --> 0b9a3e20-a9d6-4464-85f0-012664b895ff;\n  style 0b9a3e20-a9d6-4464-85f0-012664b895ff stroke:#2c3143,stroke-width:4px;\n  61[\"bedtools Intersect intervals\"];\n  47 -->|output_narrowpeaks| 61;\n  56 -->|output_narrowpeaks| 61;\n  609ee90a-2c9e-4bde-82d6-5f59516c3bad[\"Output\\noutput_g1e_peaks\"];\n  61 --> 609ee90a-2c9e-4bde-82d6-5f59516c3bad;\n  style 609ee90a-2c9e-4bde-82d6-5f59516c3bad stroke:#2c3143,stroke-width:4px;\n  62[\"bedtools Intersect intervals\"];\n  56 -->|output_narrowpeaks| 62;\n  47 -->|output_narrowpeaks| 62;\n  0bb490b2-77e5-4b59-82eb-6a2b918c2788[\"Output\\noutput_megakaryocyte_peaks\"];\n  62 --> 0bb490b2-77e5-4b59-82eb-6a2b918c2788;\n  style 0bb490b2-77e5-4b59-82eb-6a2b918c2788 stroke:#2c3143,stroke-width:4px;\n  63[\"computeMatrix\"];\n  52 -->|outFileName| 63;\n  57 -->|outFileName| 63;\n  56 -->|output_narrowpeaks| 63;\n  64[\"plotHeatmap\"];\n  58 -->|outFileName| 64;\n  65[\"plotHeatmap\"];\n  63 -->|outFileName| 65;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "Remove beginning1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0",
                         "errors": null,
-                        "id": 13,
+                        "id": 60,
                         "input_connections": {
-                            "input": {
-                                "id": 12,
-                                "output_name": "out_file1"
+                            "inputA": {
+                                "id": 47,
+                                "output_name": "output_narrowpeaks"
+                            },
+                            "reduce_or_iterate|inputB": {
+                                "id": 56,
+                                "output_name": "output_narrowpeaks"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Remove beginning",
+                        "name": "bedtools Intersect intervals",
                         "outputs": [
                             {
-                                "name": "out_file1",
+                                "name": "output",
                                 "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 880.0000188548697,
-                            "top": 3
+                            "left": 890,
+                            "top": 130
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Remove beginning on the cut output"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "b28e0cfa7ba1",
+                            "name": "bedtools",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": "Remove beginning1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/hg19.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"num_lines\": \"1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
+                        "tool_state": "{\"__input_ext\": \"bed\", \"bed\": \"false\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len\", \"count\": \"false\", \"fraction_cond\": {\"fraction_select\": \"default\", \"__current_case__\": 0}, \"header\": \"false\", \"inputA\": null, \"invert\": \"false\", \"once\": \"false\", \"overlap_mode\": null, \"reduce_or_iterate\": {\"reduce_or_iterate_selector\": \"iterate\", \"__current_case__\": 0, \"inputB\": null}, \"sorted\": \"false\", \"split\": \"false\", \"strand\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.29.0",
                         "type": "tool",
-                        "uuid": "8eaba4e8-a8a4-4123-80c7-ef822bd19bb3",
-                        "when": null,
+                        "uuid": "34bf938f-c70a-4bca-b5ca-cf4ea480bc90",
                         "workflow_outputs": [
                             {
-                                "label": "Remove beginning on the cut output",
-                                "output_name": "out_file1",
-                                "uuid": "8f65cf82-7427-4273-ba0b-a6673ee1ff2d"
+                                "label": "output_overlapping_peaks",
+                                "output_name": "output",
+                                "uuid": "0b9a3e20-a9d6-4464-85f0-012664b895ff"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_bitr/clusterprofiler_bitr/0.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0",
                         "errors": null,
-                        "id": 14,
+                        "id": 61,
                         "input_connections": {
-                            "genelist": {
-                                "id": 13,
-                                "output_name": "out_file1"
+                            "inputA": {
+                                "id": 47,
+                                "output_name": "output_narrowpeaks"
+                            },
+                            "reduce_or_iterate|inputB": {
+                                "id": 56,
+                                "output_name": "output_narrowpeaks"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Cluster Profiler Bitr",
+                        "name": "bedtools Intersect intervals",
                         "outputs": [
                             {
-                                "name": "translation",
-                                "type": "txt"
+                                "name": "output",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 1100.0000188548697,
-                            "top": 3
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActiontranslation": {
-                                "action_arguments": {
-                                    "newname": "Table of Translated Gene ID's"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "translation"
-                            }
+                            "left": 890,
+                            "top": 250
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_bitr/clusterprofiler_bitr/0.1.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "762c61c71874",
-                            "name": "clusterprofiler_bitr",
-                            "owner": "kpbioteam",
+                            "changeset_revision": "b28e0cfa7ba1",
+                            "name": "bedtools",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/hg19.len\", \"fromType\": \"SYMBOL\", \"genelist\": {\"__class__\": \"ConnectedValue\"}, \"toType\": \"ENTREZID\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.0",
+                        "tool_state": "{\"__input_ext\": \"bed\", \"bed\": \"false\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len\", \"count\": \"false\", \"fraction_cond\": {\"fraction_select\": \"default\", \"__current_case__\": 0}, \"header\": \"false\", \"inputA\": null, \"invert\": \"true\", \"once\": \"false\", \"overlap_mode\": null, \"reduce_or_iterate\": {\"reduce_or_iterate_selector\": \"iterate\", \"__current_case__\": 0, \"inputB\": null}, \"sorted\": \"false\", \"split\": \"false\", \"strand\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.29.0",
                         "type": "tool",
-                        "uuid": "2fe5dfd4-a3b7-42c9-9831-13bf2400d2bf",
-                        "when": null,
+                        "uuid": "52bfc6e7-7515-41c3-9d4d-c13a2f754cc6",
                         "workflow_outputs": [
                             {
-                                "label": "Table of Translated Gene ID's",
-                                "output_name": "translation",
-                                "uuid": "7989f80a-3e79-4d2f-bbe4-e4d641eebd6a"
+                                "label": "output_g1e_peaks",
+                                "output_name": "output",
+                                "uuid": "609ee90a-2c9e-4bde-82d6-5f59516c3bad"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_go/clusterprofiler_go/0.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0",
                         "errors": null,
-                        "id": 15,
+                        "id": 62,
                         "input_connections": {
-                            "entrezid": {
-                                "id": 14,
-                                "output_name": "translation"
+                            "inputA": {
+                                "id": 56,
+                                "output_name": "output_narrowpeaks"
+                            },
+                            "reduce_or_iterate|inputB": {
+                                "id": 47,
+                                "output_name": "output_narrowpeaks"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Cluster Profiler GO",
+                        "name": "bedtools Intersect intervals",
                         "outputs": [
                             {
-                                "name": "table",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "plot",
-                                "type": "pdf"
+                                "name": "output",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 1320.0000188548697,
-                            "top": 3
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionplot": {
-                                "action_arguments": {
-                                    "newname": "GO Enrichment Analysis Visualization"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "plot"
-                            },
-                            "RenameDatasetActiontable": {
-                                "action_arguments": {
-                                    "newname": "GO Enrichment Analysis of a Gene Set"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "table"
-                            }
+                            "left": 890,
+                            "top": 370
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_go/clusterprofiler_go/0.1.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "5299be80cafb",
-                            "name": "clusterprofiler_go",
-                            "owner": "kpbioteam",
+                            "changeset_revision": "b28e0cfa7ba1",
+                            "name": "bedtools",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/hg19.len\", \"entrezid\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.0",
+                        "tool_state": "{\"__input_ext\": \"bed\", \"bed\": \"false\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len\", \"count\": \"false\", \"fraction_cond\": {\"fraction_select\": \"default\", \"__current_case__\": 0}, \"header\": \"false\", \"inputA\": null, \"invert\": \"true\", \"once\": \"false\", \"overlap_mode\": null, \"reduce_or_iterate\": {\"reduce_or_iterate_selector\": \"iterate\", \"__current_case__\": 0, \"inputB\": null}, \"sorted\": \"false\", \"split\": \"false\", \"strand\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.29.0",
                         "type": "tool",
-                        "uuid": "53573a62-88a2-41f3-b3ed-a2afc511f0dd",
-                        "when": null,
+                        "uuid": "39089148-e7ee-4b44-8b55-973fb6864d57",
                         "workflow_outputs": [
                             {
-                                "label": "GO Enrichment Analysis of a Gene Set",
-                                "output_name": "table",
-                                "uuid": "ff6c7018-b821-4ade-9931-fa99aeb0a86c"
-                            },
-                            {
-                                "label": "GO Enrichment Analysis Visualization",
-                                "output_name": "plot",
-                                "uuid": "03b88399-095b-4bd5-9693-528c60338407"
+                                "label": "output_megakaryocyte_peaks",
+                                "output_name": "output",
+                                "uuid": "0bb490b2-77e5-4b59-82eb-6a2b918c2788"
                             }
                         ]
                     }
                 ],
-                "parent_id": "epigenetics/ewas-suite",
-                "path": "topics/epigenetics/tutorials/ewas-suite/workflows/Infinium-Human-Methylation-BeadChip.ga",
+                "parent_id": "epigenetics/tal1-binding-site-identification",
+                "path": "topics/epigenetics/tutorials/tal1-binding-site-identification/workflows/tal1-binding-site-identification-workflow.ga",
                 "tags": [
                     "epigenetics"
                 ],
                 "test_results": null,
                 "tests": true,
-                "title": "Infinium Human Methylation BeadChip",
+                "title": "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)",
                 "topic_id": "epigenetics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/epigenetics-ewas-suite/versions/infinium-human-methylation-beadchip",
-                "tutorial_id": "ewas-suite",
-                "url": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/ewas-suite/workflows/Infinium-Human-Methylation-BeadChip.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/ewas-suite/workflows/Infinium-Human-Methylation-BeadChip.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/epigenetics-tal1-binding-site-identification/versions/tal1-binding-site-identification-workflow",
+                "tutorial_id": "tal1-binding-site-identification",
+                "url": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/tal1-binding-site-identification/workflows/tal1-binding-site-identification-workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/tal1-binding-site-identification/workflows/tal1-binding-site-identification-workflow.html",
                 "version": 1,
-                "wfid": "epigenetics-ewas-suite",
-                "wfname": "infinium-human-methylation-beadchip",
-                "workflow": "Infinium-Human-Methylation-BeadChip.ga",
+                "wfid": "epigenetics-tal1-binding-site-identification",
+                "wfname": "tal1-binding-site-identification-workflow",
+                "workflow": "tal1-binding-site-identification-workflow.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "Remove beginning1",
-                    "toolshed.g2.bx.psu.edu/repos/kpbioteam/chipeakanno_annopeaks/chipeakanno_annopeaks/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_bitr/clusterprofiler_bitr/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_go/clusterprofiler_go/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/kpbioteam/ewastools/minfi_analysis/2.1.0"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.3.2.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.3.2.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.3.2.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6",
+                    "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0"
                 ],
-                "workflowhub_id": "1165"
+                "workflowhub_id": "1175"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/1251211"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.197100"
     },
     {
         "admin_install": {
@@ -75055,8 +78017,8 @@
         ],
         "edam_operation": [
             "Sequencing quality control",
-            "Sequence composition calculation",
-            "Statistical calculation"
+            "Statistical calculation",
+            "Sequence composition calculation"
         ],
         "edam_topic": [
             "Epigenomics"
@@ -75071,6 +78033,7 @@
         "id": "epigenetics/methylation-seq",
         "inexact_supported_servers": [
             "HyPhy HIV NGS Tools",
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.no",
             "UseGalaxy.org.au"
@@ -75091,7 +78054,7 @@
             "Learn how to analyse methylation data",
             "Get a first intuition what are common pitfalls."
         ],
-        "pageviews": 19773,
+        "pageviews": 20136,
         "pub_date": "2017-02-16",
         "questions": [
             "What is methylation and why it cannot be recognised by a normal NGS procedure?",
@@ -75100,15 +78063,15 @@
         ],
         "short_id": "T00142",
         "short_tools": [
+            "pileometh",
             "replace_column_with_key_value_file",
-            "tp_awk_tool",
+            "deeptools_plot_profile",
             "bwameth",
-            "tp_tail_tool",
-            "deeptools_compute_matrix",
+            "tp_awk_tool",
             "fastqc",
-            "pileometh",
-            "deeptools_plot_profile",
-            "metilene"
+            "metilene",
+            "deeptools_compute_matrix",
+            "tp_tail_tool"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -75131,6 +78094,11 @@
                     "url": "https://galaxy.hyphy.org/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -75181,8 +78149,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 127,
-        "visitors": 11091,
+        "visit_duration": 126,
+        "visitors": 11375,
         "workflows": [
             {
                 "creators": [],
@@ -75193,7 +78161,7 @@
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  9[label=\"FastQC\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"FastQC\"]\n  1 -> 10 [label=\"output\"]\n  11[label=\"bwameth\"]\n  0 -> 11 [label=\"output\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"Replace column\"]\n  3 -> 12 [label=\"output\"]\n  4 -> 12 [label=\"output\"]\n  13[label=\"metilene\"]\n  2 -> 13 [label=\"output\"]\n  5 -> 13 [label=\"output\"]\n  3 -> 13 [label=\"output\"]\n  8 -> 13 [label=\"output\"]\n  7 -> 13 [label=\"output\"]\n  6 -> 13 [label=\"output\"]\n  14[label=\"MethylDackel\"]\n  11 -> 14 [label=\"output\"]\n  15[label=\"MethylDackel\"]\n  11 -> 15 [label=\"output\"]\n  16[label=\"Select last\"]\n  12 -> 16 [label=\"outfile_replace\"]\n  17[label=\"Select last\"]\n  15 -> 17 [label=\"outFileExtractCpGFraction\"]\n  18[label=\"computeMatrix\"]\n  16 -> 18 [label=\"outfile\"]\n  2 -> 18 [label=\"output\"]\n  19[label=\"Text reformatting\"]\n  17 -> 19 [label=\"outfile\"]\n  20[label=\"computeMatrix\"]\n  19 -> 20 [label=\"outfile\"]\n  2 -> 20 [label=\"output\"]\n  21[label=\"plotProfile\"]\n  20 -> 21 [label=\"outFileName\"]\n  k5b647979e90244b0a07a262f8044c75d[color=lightseagreen,label=\"Output\\nplot_profile_tabular\"]\n  21 -> k5b647979e90244b0a07a262f8044c75d\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  9[label=\"FastQC\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"FastQC\"]\n  1 -> 10 [label=\"output\"]\n  11[label=\"bwameth\"]\n  0 -> 11 [label=\"output\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"Replace column\"]\n  3 -> 12 [label=\"output\"]\n  4 -> 12 [label=\"output\"]\n  13[label=\"metilene\"]\n  2 -> 13 [label=\"output\"]\n  5 -> 13 [label=\"output\"]\n  3 -> 13 [label=\"output\"]\n  8 -> 13 [label=\"output\"]\n  7 -> 13 [label=\"output\"]\n  6 -> 13 [label=\"output\"]\n  14[label=\"MethylDackel\"]\n  11 -> 14 [label=\"output\"]\n  15[label=\"MethylDackel\"]\n  11 -> 15 [label=\"output\"]\n  16[label=\"Select last\"]\n  12 -> 16 [label=\"outfile_replace\"]\n  17[label=\"Select last\"]\n  15 -> 17 [label=\"outFileExtractCpGFraction\"]\n  18[label=\"computeMatrix\"]\n  16 -> 18 [label=\"outfile\"]\n  2 -> 18 [label=\"output\"]\n  19[label=\"Text reformatting\"]\n  17 -> 19 [label=\"outfile\"]\n  20[label=\"computeMatrix\"]\n  19 -> 20 [label=\"outfile\"]\n  2 -> 20 [label=\"output\"]\n  21[label=\"plotProfile\"]\n  20 -> 21 [label=\"outFileName\"]\n  k2259f2ac153844ce8c84e6de532838fc[color=lightseagreen,label=\"Output\\nplot_profile_tabular\"]\n  21 -> k2259f2ac153844ce8c84e6de532838fc\n}",
                 "history": [
                     {
                         "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
@@ -75289,267 +78257,1234 @@
                                 "name": "CpGIslands.bed"
                             }
                         ],
-                        "label": null,
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 250
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"CpGIslands.bed\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "e9c54940-b612-40cc-a58e-c14bc3945ed6",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "NB1_CpG.meth.bedGraph"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 370
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"NB1_CpG.meth.bedGraph\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "6f1eb0a2-5719-4f24-9933-3b28034e70ab",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "GRCh38_ensembl2UCSC.txt"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 490
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"GRCh38_ensembl2UCSC.txt\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "c7238557-c79b-41e5-aa38-68b27ca88d2e",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "NB2_CpG.meth.bedGraph"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 610
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"NB2_CpG.meth.bedGraph\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0cab2494-32bc-4732-86e4-a10cb0edfeff",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "BT089_CpG.meth.bedGraph"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 730
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"BT089_CpG.meth.bedGraph\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "bbd85ab1-a5cb-4db6-b05f-78c90eb7b0d6",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "BT126_CpG.meth.bedGraph"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 850
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"BT126_CpG.meth.bedGraph\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ba585cf0-5d2c-4894-ad69-18e7f5a182d4",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "BT198_CpG.meth.bedGraph"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 970
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"BT198_CpG.meth.bedGraph\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "da460b45-dc16-4806-975c-361ac13e2156",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"FastQC\"];\n  0 -->|output| 9;\n  10[\"FastQC\"];\n  1 -->|output| 10;\n  11[\"bwameth\"];\n  0 -->|output| 11;\n  1 -->|output| 11;\n  12[\"Replace column\"];\n  3 -->|output| 12;\n  4 -->|output| 12;\n  13[\"metilene\"];\n  2 -->|output| 13;\n  5 -->|output| 13;\n  3 -->|output| 13;\n  8 -->|output| 13;\n  7 -->|output| 13;\n  6 -->|output| 13;\n  14[\"MethylDackel\"];\n  11 -->|output| 14;\n  15[\"MethylDackel\"];\n  11 -->|output| 15;\n  16[\"Select last\"];\n  12 -->|outfile_replace| 16;\n  17[\"Select last\"];\n  15 -->|outFileExtractCpGFraction| 17;\n  18[\"computeMatrix\"];\n  16 -->|outfile| 18;\n  2 -->|output| 18;\n  19[\"Text reformatting\"];\n  17 -->|outfile| 19;\n  20[\"computeMatrix\"];\n  19 -->|outfile| 20;\n  2 -->|output| 20;\n  21[\"plotProfile\"];\n  20 -->|outFileName| 21;\n  2259f2ac-1538-44ce-8c84-e6de532838fc[\"Output\\nplot_profile_tabular\"];\n  21 --> 2259f2ac-1538-44ce-8c84-e6de532838fc;\n  style 2259f2ac-1538-44ce-8c84-e6de532838fc stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Workflow Methylation Seq",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.1.1.0",
+                        "errors": null,
+                        "id": 21,
+                        "input_connections": {
+                            "matrixFile": {
+                                "id": 20,
+                                "output_name": "outFileName"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "plotProfile",
+                        "outputs": [
+                            {
+                                "name": "outFileName",
+                                "type": "png"
+                            },
+                            {
+                                "name": "outFileSortedRegions",
+                                "type": "bed"
+                            },
+                            {
+                                "name": "output_outFileNameData",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 1330,
+                            "top": 10
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.1.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "aac8444d6681",
+                            "name": "deeptools_plot_profile",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"matrixFile\": \"null\", \"scaleRegions\": \"{\\\"showScaleRegionsOpt\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"output\": \"{\\\"showOutputSettings\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"advancedOpt\": \"{\\\"showAdvancedOpt\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg38.len\\\"\"}",
+                        "tool_version": "2.5.1.1.0",
+                        "type": "tool",
+                        "uuid": "0f49a7fe-0f63-4ab6-8e70-f9207b5098af",
+                        "workflow_outputs": [
+                            {
+                                "label": "plot_profile_tabular",
+                                "output_name": "output_outFileNameData",
+                                "uuid": "2259f2ac-1538-44ce-8c84-e6de532838fc"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "epigenetics/methylation-seq",
+                "path": "topics/epigenetics/tutorials/methylation-seq/workflows/methylation-seq.ga",
+                "tags": [
+                    "epigenetics"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "Workflow Methylation Seq",
+                "topic_id": "epigenetics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/epigenetics-methylation-seq/versions/methylation-seq",
+                "tutorial_id": "methylation-seq",
+                "url": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/methylation-seq/workflows/methylation-seq.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/methylation-seq/workflows/methylation-seq.html",
+                "version": 3,
+                "wfid": "epigenetics-methylation-seq",
+                "wfname": "methylation-seq",
+                "workflow": "methylation-seq.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.5.1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/pileometh/pileometh/0.3.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.68",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.0.3",
+                    "toolshed.g2.bx.psu.edu/repos/rnateam/metilene/metilene/0.2.6.1"
+                ],
+                "workflowhub_id": "1157"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/557099"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "chipeakanno_annopeaks",
+                    "owner": "kpbioteam",
+                    "revisions": "104882a2de00",
+                    "tool_panel_section_label": "Test Tools",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "clusterprofiler_bitr",
+                    "owner": "kpbioteam",
+                    "revisions": "762c61c71874",
+                    "tool_panel_section_label": "Test Tools",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "clusterprofiler_go",
+                    "owner": "kpbioteam",
+                    "revisions": "5299be80cafb",
+                    "tool_panel_section_label": "Test Tools",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ewastools",
+                    "owner": "kpbioteam",
+                    "revisions": "369fef559cfc",
+                    "tool_panel_section_label": "Epigenetics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: chipeakanno_annopeaks\n  owner: kpbioteam\n  revisions: 104882a2de00\n  tool_panel_section_label: Test Tools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clusterprofiler_bitr\n  owner: kpbioteam\n  revisions: 762c61c71874\n  tool_panel_section_label: Test Tools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clusterprofiler_go\n  owner: kpbioteam\n  revisions: 5299be80cafb\n  tool_panel_section_label: Test Tools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ewastools\n  owner: kpbioteam\n  revisions: 369fef559cfc\n  tool_panel_section_label: Epigenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/ewas-suite/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "id": "kkamieniecka",
+                "joined": "2018-08",
+                "name": "Katarzyna Kamieniecka",
+                "orcid": "0009-0004-2454-5950",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/",
+                "twitter": "katemurat",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "email": "k.jumah@bradford.ac.uk",
+                "id": "khaled196",
+                "joined": "2022-09",
+                "name": "Khaled Jum\u2019ah",
+                "orcid": "0000-0001-5481-8893",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/khaled196/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/khaled196.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "id": "poterlowicz-lab",
+                "joined": "2017-09",
+                "name": "Krzysztof Poterlowicz",
+                "orcid": "0000-0001-6173-5674",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/poterlowicz-lab/",
+                "twitter": "bioinfbrad",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/poterlowicz-lab.json"
+            }
+        ],
+        "dir": "topics/epigenetics/tutorials/ewas-suite",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.no"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "epigenetics/ewas-suite",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Infinium Human Methylation BeadChip is an array based technology to generate DNA methylation profiling at individual CpG loci in the human genome based on Illumina\u2019s bead technology.",
+            "Time and cost efficiency followed by high sample output, and overall quantitative accuracy and reproducibility made Infinium Human Methylation BeadChip one of the most widely used arrays on the market."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-03-26",
+        "objectives": [
+            "Learn how to perform reproducible Infinium Human Methylation BeadChip analysis",
+            "Visualise differentially methylated positions using UCSC browser"
+        ],
+        "pageviews": 5900005,
+        "pub_date": "2018-08-27",
+        "questions": [
+            "Which DNA regions and positions are diffrentialy methylated in pre MAPKi treatment and post MAPKi resistance Melanomas GSE65183?",
+            "How to analyse and visualise Infinium Human Methylation BeadChip's?"
+        ],
+        "short_id": "T00139",
+        "short_tools": [
+            "chipeakanno_annopeaks",
+            "clusterprofiler_go",
+            "clusterprofiler_bitr",
+            "Cut1",
+            "minfi_analysis",
+            "Remove beginning1"
+        ],
+        "slides": true,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "time_estimation": "1h",
+        "title": "Infinium Human Methylation BeadChip",
+        "tools": [
+            "Cut1",
+            "Remove beginning1",
+            "toolshed.g2.bx.psu.edu/repos/kpbioteam/chipeakanno_annopeaks/chipeakanno_annopeaks/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_bitr/clusterprofiler_bitr/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_go/clusterprofiler_go/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/kpbioteam/ewastools/minfi_analysis/2.1.0"
+        ],
+        "topic_name": "epigenetics",
+        "topic_name_human": "Epigenetics",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "ewas-suite",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/epigenetics/tutorials/ewas-suite/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/ewas-suite/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/ewas-suite/tutorial.json"
+        },
+        "version": 19,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 267,
+        "visitors": 2135314,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0009-0004-2454-5950",
+                        "name": "Katarzyna Kamieniecka"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0001-5481-8893",
+                        "name": "Khaled Jum'ah"
+                    },
+                    {
+                        "class": "Organization",
+                        "name": "poterlowicz-lab",
+                        "url": "https://github.com/ELIXIR-UK-DaSH"
+                    }
+                ],
+                "description": "The workflow containes the step to perpare the data for and run Galaxy Infinium Human Methylation BeadChip tool that represents many popular algorithms for detecting somatic genetic alterations from genome and exome data",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR01C02_Red.idat\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR02C02_Red.idat\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR05C02_Red.idat\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR06C02_Red.idat\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR01C02_Green.idat\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR02C02_Green.idat\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR05C02_Green.idat\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR06C02_Green.idat\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nphenotype Table txt file\"]\n  9[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nUCSC Main on Human\"]\n  10[label=\"Infinium Human Methylation BeadChip\"]\n  4 -> 10 [label=\"output\"]\n  5 -> 10 [label=\"output\"]\n  6 -> 10 [label=\"output\"]\n  7 -> 10 [label=\"output\"]\n  0 -> 10 [label=\"output\"]\n  1 -> 10 [label=\"output\"]\n  2 -> 10 [label=\"output\"]\n  3 -> 10 [label=\"output\"]\n  8 -> 10 [label=\"output\"]\n  9 -> 10 [label=\"output\"]\n  k2ac7dd5ded744d58b1cbbe7dcca9154a[color=lightseagreen,label=\"Output\\nSNPInfo Table\"]\n  10 -> k2ac7dd5ded744d58b1cbbe7dcca9154a\n  kd1732a9818614612bdaaf68861c22f56[color=lightseagreen,label=\"Output\\nDifferentially Methylated Regions\"]\n  10 -> kd1732a9818614612bdaaf68861c22f56\n  k9aa8b4a9611e4a39864f400f17866a9e[color=lightseagreen,label=\"Output\\nDifferentially Methylated Positions\"]\n  10 -> k9aa8b4a9611e4a39864f400f17866a9e\n  k14ddb6f7637e4193bfb580aeae4fab64[color=lightseagreen,label=\"Output\\nQuality Control Report\"]\n  10 -> k14ddb6f7637e4193bfb580aeae4fab64\n  kc8c37ff8716d4c23a84f7cebcb4b6c9d[color=lightseagreen,label=\"Output\\nQuality Control Plot\"]\n  10 -> kc8c37ff8716d4c23a84f7cebcb4b6c9d\n  11[label=\"ChIPpeakAnno annoPeaks\"]\n  10 -> 11 [label=\"dmp\"]\n  kbedf4346da4d4e1abf3ca7d20f3ec3c5[color=lightseagreen,label=\"Output\\nTable of Annotated Peaks\"]\n  11 -> kbedf4346da4d4e1abf3ca7d20f3ec3c5\n  12[label=\"Cut\"]\n  11 -> 12 [label=\"tab\"]\n  k0b54dfe5f84a4288b631ae4dc2384a17[color=lightseagreen,label=\"Output\\nCut on Table of Annotated Peaks\"]\n  12 -> k0b54dfe5f84a4288b631ae4dc2384a17\n  13[label=\"Remove beginning\"]\n  12 -> 13 [label=\"out_file1\"]\n  k8f65cf8274274273ba0ba6673ee1ff2d[color=lightseagreen,label=\"Output\\nRemove beginning on the cut output\"]\n  13 -> k8f65cf8274274273ba0ba6673ee1ff2d\n  14[label=\"Cluster Profiler Bitr\"]\n  13 -> 14 [label=\"out_file1\"]\n  k7989f80a3e794d2fbbe4e4d641eebd6a[color=lightseagreen,label=\"Output\\nTable of Translated Gene ID's\"]\n  14 -> k7989f80a3e794d2fbbe4e4d641eebd6a\n  15[label=\"Cluster Profiler GO\"]\n  14 -> 15 [label=\"translation\"]\n  kff6c7018b8214ade9931fa99aeb0a86c[color=lightseagreen,label=\"Output\\nGO Enrichment Analysis of a Gene Set\"]\n  15 -> kff6c7018b8214ade9931fa99aeb0a86c\n  k03b88399095b4bd59693528c60338407[color=lightseagreen,label=\"Output\\nGO Enrichment Analysis Visualization\"]\n  15 -> k03b88399095b4bd59693528c60338407\n}",
+                "history": [
+                    {
+                        "hash": "4f69ebe91fffffe057c1f187bc83e1562369defd",
+                        "message": "fix workflow",
+                        "num": 4,
+                        "short_hash": "4f69ebe91",
+                        "unix": "1698053430"
+                    },
+                    {
+                        "hash": "8f19faceda02e93f48bb3fe0e7fffa533685d99d",
+                        "message": "fix",
+                        "num": 3,
+                        "short_hash": "8f19faced",
+                        "unix": "1697725863"
+                    },
+                    {
+                        "hash": "568e22f2036d5cfb1cd3d3454d0b50e3c6ca54ca",
+                        "message": "add license",
+                        "num": 2,
+                        "short_hash": "568e22f20",
+                        "unix": "1697724380"
+                    },
+                    {
+                        "hash": "451efca00587e14a69d8df6096d0297e739d1f27",
+                        "message": "remove pictures and add output tests",
+                        "num": 1,
+                        "short_hash": "451efca00",
+                        "unix": "1697723365"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "R01C02_Red.idat"
+                            }
+                        ],
+                        "label": "R01C02_Red.idat",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 1.885486970465422e-05,
+                            "top": 3
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "71c54456-73d3-4af4-8d89-ab81d0feb88d",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "R02C02_Red.idat"
+                            }
+                        ],
+                        "label": "R02C02_Red.idat",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 1.885486970465422e-05,
+                            "top": 123
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "2521d0ca-a0d8-416f-8735-0a6c441812fc",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "R05C02_Red.idat"
+                            }
+                        ],
+                        "label": "R05C02_Red.idat",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 1.885486970465422e-05,
+                            "top": 243
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "f3068f86-caf3-4e26-a51b-3c6c6683ce84",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "R06C02_Red.idat"
+                            }
+                        ],
+                        "label": "R06C02_Red.idat",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 250
+                            "left": 0,
+                            "top": 362.99997401229103
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"CpGIslands.bed\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "e9c54940-b612-40cc-a58e-c14bc3945ed6",
+                        "uuid": "ef39313e-8463-444e-8d91-ebebfc16e124",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 4,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "NB1_CpG.meth.bedGraph"
+                                "name": "R01C02_Green.idat"
                             }
                         ],
-                        "label": null,
+                        "label": "R01C02_Green.idat",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 370
+                            "left": 1.885486970465422e-05,
+                            "top": 483
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"NB1_CpG.meth.bedGraph\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "6f1eb0a2-5719-4f24-9933-3b28034e70ab",
+                        "uuid": "738cbcf1-2bc8-438d-b539-bc6e762af030",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 4,
+                        "id": 5,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "GRCh38_ensembl2UCSC.txt"
+                                "name": "R02C02_Green.idat"
                             }
                         ],
-                        "label": null,
+                        "label": "R02C02_Green.idat",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 490
+                            "left": 1.885486970465422e-05,
+                            "top": 603
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"GRCh38_ensembl2UCSC.txt\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "c7238557-c79b-41e5-aa38-68b27ca88d2e",
+                        "uuid": "4d8bb323-db45-4f9d-b846-fde1c4f08b13",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 5,
+                        "id": 6,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "NB2_CpG.meth.bedGraph"
+                                "name": "R05C02_Green.idat"
                             }
                         ],
-                        "label": null,
+                        "label": "R05C02_Green.idat",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 610
+                            "left": 6.401854712230744,
+                            "top": 721.3996100720306
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"NB2_CpG.meth.bedGraph\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "0cab2494-32bc-4732-86e4-a10cb0edfeff",
+                        "uuid": "c47087fa-a5df-4ec4-8142-e2352e620e4f",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 6,
+                        "id": 7,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "BT089_CpG.meth.bedGraph"
+                                "name": "R06C02_Green.idat"
                             }
                         ],
-                        "label": null,
+                        "label": "R06C02_Green.idat",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 730
+                            "left": 1.885486970465422e-05,
+                            "top": 843
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"BT089_CpG.meth.bedGraph\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "bbd85ab1-a5cb-4db6-b05f-78c90eb7b0d6",
+                        "uuid": "3b510a95-0b47-4d90-b499-4c33e4914954",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 7,
+                        "id": 8,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "BT126_CpG.meth.bedGraph"
+                                "name": "phenotype Table txt file"
                             }
                         ],
-                        "label": null,
+                        "label": "phenotype Table txt file",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 850
+                            "left": 1.885486970465422e-05,
+                            "top": 963
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"BT126_CpG.meth.bedGraph\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ba585cf0-5d2c-4894-ad69-18e7f5a182d4",
+                        "uuid": "0c5e494f-b987-4f48-a667-b9e8a259794e",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 8,
+                        "id": 9,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "BT198_CpG.meth.bedGraph"
+                                "name": "UCSC Main on Human"
                             }
                         ],
-                        "label": null,
+                        "label": "UCSC Main on Human",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 970
+                            "left": 1.885486970465422e-05,
+                            "top": 1083
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"BT198_CpG.meth.bedGraph\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "da460b45-dc16-4806-975c-361ac13e2156",
+                        "uuid": "04bc7d9a-d7ae-46fe-9eaf-85d6c47c57a5",
+                        "when": null,
                         "workflow_outputs": []
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"FastQC\"];\n  0 -->|output| 9;\n  10[\"FastQC\"];\n  1 -->|output| 10;\n  11[\"bwameth\"];\n  0 -->|output| 11;\n  1 -->|output| 11;\n  12[\"Replace column\"];\n  3 -->|output| 12;\n  4 -->|output| 12;\n  13[\"metilene\"];\n  2 -->|output| 13;\n  5 -->|output| 13;\n  3 -->|output| 13;\n  8 -->|output| 13;\n  7 -->|output| 13;\n  6 -->|output| 13;\n  14[\"MethylDackel\"];\n  11 -->|output| 14;\n  15[\"MethylDackel\"];\n  11 -->|output| 15;\n  16[\"Select last\"];\n  12 -->|outfile_replace| 16;\n  17[\"Select last\"];\n  15 -->|outFileExtractCpGFraction| 17;\n  18[\"computeMatrix\"];\n  16 -->|outfile| 18;\n  2 -->|output| 18;\n  19[\"Text reformatting\"];\n  17 -->|outfile| 19;\n  20[\"computeMatrix\"];\n  19 -->|outfile| 20;\n  2 -->|output| 20;\n  21[\"plotProfile\"];\n  20 -->|outFileName| 21;\n  5b647979-e902-44b0-a07a-262f8044c75d[\"Output\\nplot_profile_tabular\"];\n  21 --> 5b647979-e902-44b0-a07a-262f8044c75d;\n  style 5b647979-e902-44b0-a07a-262f8044c75d stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Workflow Methylation Seq",
+                "license": "AGPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nR01C02_Red.idat\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nR02C02_Red.idat\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nR05C02_Red.idat\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nR06C02_Red.idat\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nR01C02_Green.idat\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nR02C02_Green.idat\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nR05C02_Green.idat\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nR06C02_Green.idat\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nphenotype Table txt file\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"\u2139\ufe0f Input Dataset\\nUCSC Main on Human\"];\n  style 9 stroke:#2c3143,stroke-width:4px;\n  10[\"Infinium Human Methylation BeadChip\"];\n  4 -->|output| 10;\n  5 -->|output| 10;\n  6 -->|output| 10;\n  7 -->|output| 10;\n  0 -->|output| 10;\n  1 -->|output| 10;\n  2 -->|output| 10;\n  3 -->|output| 10;\n  8 -->|output| 10;\n  9 -->|output| 10;\n  2ac7dd5d-ed74-4d58-b1cb-be7dcca9154a[\"Output\\nSNPInfo Table\"];\n  10 --> 2ac7dd5d-ed74-4d58-b1cb-be7dcca9154a;\n  style 2ac7dd5d-ed74-4d58-b1cb-be7dcca9154a stroke:#2c3143,stroke-width:4px;\n  d1732a98-1861-4612-bdaa-f68861c22f56[\"Output\\nDifferentially Methylated Regions\"];\n  10 --> d1732a98-1861-4612-bdaa-f68861c22f56;\n  style d1732a98-1861-4612-bdaa-f68861c22f56 stroke:#2c3143,stroke-width:4px;\n  9aa8b4a9-611e-4a39-864f-400f17866a9e[\"Output\\nDifferentially Methylated Positions\"];\n  10 --> 9aa8b4a9-611e-4a39-864f-400f17866a9e;\n  style 9aa8b4a9-611e-4a39-864f-400f17866a9e stroke:#2c3143,stroke-width:4px;\n  14ddb6f7-637e-4193-bfb5-80aeae4fab64[\"Output\\nQuality Control Report\"];\n  10 --> 14ddb6f7-637e-4193-bfb5-80aeae4fab64;\n  style 14ddb6f7-637e-4193-bfb5-80aeae4fab64 stroke:#2c3143,stroke-width:4px;\n  c8c37ff8-716d-4c23-a84f-7cebcb4b6c9d[\"Output\\nQuality Control Plot\"];\n  10 --> c8c37ff8-716d-4c23-a84f-7cebcb4b6c9d;\n  style c8c37ff8-716d-4c23-a84f-7cebcb4b6c9d stroke:#2c3143,stroke-width:4px;\n  11[\"ChIPpeakAnno annoPeaks\"];\n  10 -->|dmp| 11;\n  bedf4346-da4d-4e1a-bf3c-a7d20f3ec3c5[\"Output\\nTable of Annotated Peaks\"];\n  11 --> bedf4346-da4d-4e1a-bf3c-a7d20f3ec3c5;\n  style bedf4346-da4d-4e1a-bf3c-a7d20f3ec3c5 stroke:#2c3143,stroke-width:4px;\n  12[\"Cut\"];\n  11 -->|tab| 12;\n  0b54dfe5-f84a-4288-b631-ae4dc2384a17[\"Output\\nCut on Table of Annotated Peaks\"];\n  12 --> 0b54dfe5-f84a-4288-b631-ae4dc2384a17;\n  style 0b54dfe5-f84a-4288-b631-ae4dc2384a17 stroke:#2c3143,stroke-width:4px;\n  13[\"Remove beginning\"];\n  12 -->|out_file1| 13;\n  8f65cf82-7427-4273-ba0b-a6673ee1ff2d[\"Output\\nRemove beginning on the cut output\"];\n  13 --> 8f65cf82-7427-4273-ba0b-a6673ee1ff2d;\n  style 8f65cf82-7427-4273-ba0b-a6673ee1ff2d stroke:#2c3143,stroke-width:4px;\n  14[\"Cluster Profiler Bitr\"];\n  13 -->|out_file1| 14;\n  7989f80a-3e79-4d2f-bbe4-e4d641eebd6a[\"Output\\nTable of Translated Gene ID's\"];\n  14 --> 7989f80a-3e79-4d2f-bbe4-e4d641eebd6a;\n  style 7989f80a-3e79-4d2f-bbe4-e4d641eebd6a stroke:#2c3143,stroke-width:4px;\n  15[\"Cluster Profiler GO\"];\n  14 -->|translation| 15;\n  ff6c7018-b821-4ade-9931-fa99aeb0a86c[\"Output\\nGO Enrichment Analysis of a Gene Set\"];\n  15 --> ff6c7018-b821-4ade-9931-fa99aeb0a86c;\n  style ff6c7018-b821-4ade-9931-fa99aeb0a86c stroke:#2c3143,stroke-width:4px;\n  03b88399-095b-4bd5-9693-528c60338407[\"Output\\nGO Enrichment Analysis Visualization\"];\n  15 --> 03b88399-095b-4bd5-9693-528c60338407;\n  style 03b88399-095b-4bd5-9693-528c60338407 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:07 +0000",
+                "name": "Infinium Human Methylation BeadChip",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.1.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/kpbioteam/ewastools/minfi_analysis/2.1.0",
                         "errors": null,
-                        "id": 21,
+                        "id": 10,
                         "input_connections": {
-                            "matrixFile": {
-                                "id": 20,
-                                "output_name": "outFileName"
+                            "files_grn": [
+                                {
+                                    "id": 4,
+                                    "output_name": "output"
+                                },
+                                {
+                                    "id": 5,
+                                    "output_name": "output"
+                                },
+                                {
+                                    "id": 6,
+                                    "output_name": "output"
+                                },
+                                {
+                                    "id": 7,
+                                    "output_name": "output"
+                                }
+                            ],
+                            "files_red": [
+                                {
+                                    "id": 0,
+                                    "output_name": "output"
+                                },
+                                {
+                                    "id": 1,
+                                    "output_name": "output"
+                                },
+                                {
+                                    "id": 2,
+                                    "output_name": "output"
+                                },
+                                {
+                                    "id": 3,
+                                    "output_name": "output"
+                                }
+                            ],
+                            "phenotype_table": {
+                                "id": 8,
+                                "output_name": "output"
+                            },
+                            "ucsc_genome": {
+                                "id": 9,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "plotProfile",
+                        "name": "Infinium Human Methylation BeadChip",
                         "outputs": [
                             {
-                                "name": "outFileName",
+                                "name": "qctab",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "qcpng",
                                 "type": "png"
                             },
                             {
-                                "name": "outFileSortedRegions",
+                                "name": "table",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "dmr",
                                 "type": "bed"
                             },
                             {
-                                "name": "output_outFileNameData",
+                                "name": "dmp",
+                                "type": "bed"
+                            }
+                        ],
+                        "position": {
+                            "left": 220.0000188548697,
+                            "top": 3
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActiondmp": {
+                                "action_arguments": {
+                                    "newname": "Differentially Methylated Positions"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "dmp"
+                            },
+                            "RenameDatasetActiondmr": {
+                                "action_arguments": {
+                                    "newname": "Differentially Methylated Regions"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "dmr"
+                            },
+                            "RenameDatasetActionqcpng": {
+                                "action_arguments": {
+                                    "newname": "Quality Control Plot"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "qcpng"
+                            },
+                            "RenameDatasetActionqctab": {
+                                "action_arguments": {
+                                    "newname": "Quality Control Report"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "qctab"
+                            },
+                            "RenameDatasetActiontable": {
+                                "action_arguments": {
+                                    "newname": "SNPInfo Table"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "table"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/kpbioteam/ewastools/minfi_analysis/2.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "369fef559cfc",
+                            "name": "ewastools",
+                            "owner": "kpbioteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"idat\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/hg19.len\", \"cutoff_size\": \"0.1\", \"files_grn\": {\"__class__\": \"ConnectedValue\"}, \"files_red\": {\"__class__\": \"ConnectedValue\"}, \"maxgap_size\": \"250\", \"null_method\": \"permutation\", \"number_of_resamples\": \"0\", \"optpp\": \"ppsnp\", \"phenotype\": \"categorical\", \"phenotype_table\": {\"__class__\": \"ConnectedValue\"}, \"q_cutoff\": \"0.5\", \"ucsc_genome\": {\"__class__\": \"ConnectedValue\"}, \"variance_shrinkage\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.0",
+                        "type": "tool",
+                        "uuid": "99026073-61d1-408d-b7a7-50fe91530aa5",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "SNPInfo Table",
+                                "output_name": "table",
+                                "uuid": "2ac7dd5d-ed74-4d58-b1cb-be7dcca9154a"
+                            },
+                            {
+                                "label": "Differentially Methylated Regions",
+                                "output_name": "dmr",
+                                "uuid": "d1732a98-1861-4612-bdaa-f68861c22f56"
+                            },
+                            {
+                                "label": "Differentially Methylated Positions",
+                                "output_name": "dmp",
+                                "uuid": "9aa8b4a9-611e-4a39-864f-400f17866a9e"
+                            },
+                            {
+                                "label": "Quality Control Report",
+                                "output_name": "qctab",
+                                "uuid": "14ddb6f7-637e-4193-bfb5-80aeae4fab64"
+                            },
+                            {
+                                "label": "Quality Control Plot",
+                                "output_name": "qcpng",
+                                "uuid": "c8c37ff8-716d-4c23-a84f-7cebcb4b6c9d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/kpbioteam/chipeakanno_annopeaks/chipeakanno_annopeaks/0.1.0",
+                        "errors": null,
+                        "id": 11,
+                        "input_connections": {
+                            "dmp": {
+                                "id": 10,
+                                "output_name": "dmp"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "ChIPpeakAnno annoPeaks",
+                        "outputs": [
+                            {
+                                "name": "tab",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1330,
-                            "top": 10
+                            "left": 452,
+                            "top": 0
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.1.1.0",
+                        "post_job_actions": {
+                            "RenameDatasetActiontab": {
+                                "action_arguments": {
+                                    "newname": "Table of Annotated Peaks"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "tab"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/kpbioteam/chipeakanno_annopeaks/chipeakanno_annopeaks/0.1.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "aac8444d6681",
-                            "name": "deeptools_plot_profile",
-                            "owner": "bgruening",
+                            "changeset_revision": "104882a2de00",
+                            "name": "chipeakanno_annopeaks",
+                            "owner": "kpbioteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"matrixFile\": \"null\", \"scaleRegions\": \"{\\\"showScaleRegionsOpt\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"output\": \"{\\\"showOutputSettings\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"advancedOpt\": \"{\\\"showAdvancedOpt\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg38.len\\\"\"}",
-                        "tool_version": "2.5.1.1.0",
+                        "tool_state": "{\"__input_ext\": \"bed\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/hg19.len\", \"dmp\": {\"__class__\": \"ConnectedValue\"}, \"end\": \"3000\", \"score\": \"5\", \"start\": \"-5000\", \"type\": \"startSite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0",
                         "type": "tool",
-                        "uuid": "0f49a7fe-0f63-4ab6-8e70-f9207b5098af",
+                        "uuid": "3a83a9ba-d58c-455a-84b0-8f25e95cc4f3",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "plot_profile_tabular",
-                                "output_name": "output_outFileNameData",
-                                "uuid": "5b647979-e902-44b0-a07a-262f8044c75d"
+                                "label": "Table of Annotated Peaks",
+                                "output_name": "tab",
+                                "uuid": "bedf4346-da4d-4e1a-bf3c-a7d20f3ec3c5"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "Cut1",
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {
+                            "input": {
+                                "id": 11,
+                                "output_name": "tab"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Cut",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 660.0000188548697,
+                            "top": 3
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Cut on Table of Annotated Peaks"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/hg19.len\", \"columnList\": \"c16\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2",
+                        "type": "tool",
+                        "uuid": "6af6eed4-d83b-42de-a72f-67443b9c63ea",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Cut on Table of Annotated Peaks",
+                                "output_name": "out_file1",
+                                "uuid": "0b54dfe5-f84a-4288-b631-ae4dc2384a17"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "Remove beginning1",
+                        "errors": null,
+                        "id": 13,
+                        "input_connections": {
+                            "input": {
+                                "id": 12,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Remove beginning",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 880.0000188548697,
+                            "top": 3
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Remove beginning on the cut output"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "tool_id": "Remove beginning1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/hg19.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"num_lines\": \"1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "8eaba4e8-a8a4-4123-80c7-ef822bd19bb3",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Remove beginning on the cut output",
+                                "output_name": "out_file1",
+                                "uuid": "8f65cf82-7427-4273-ba0b-a6673ee1ff2d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_bitr/clusterprofiler_bitr/0.1.0",
+                        "errors": null,
+                        "id": 14,
+                        "input_connections": {
+                            "genelist": {
+                                "id": 13,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Cluster Profiler Bitr",
+                        "outputs": [
+                            {
+                                "name": "translation",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 1100.0000188548697,
+                            "top": 3
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActiontranslation": {
+                                "action_arguments": {
+                                    "newname": "Table of Translated Gene ID's"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "translation"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_bitr/clusterprofiler_bitr/0.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "762c61c71874",
+                            "name": "clusterprofiler_bitr",
+                            "owner": "kpbioteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/hg19.len\", \"fromType\": \"SYMBOL\", \"genelist\": {\"__class__\": \"ConnectedValue\"}, \"toType\": \"ENTREZID\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0",
+                        "type": "tool",
+                        "uuid": "2fe5dfd4-a3b7-42c9-9831-13bf2400d2bf",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Table of Translated Gene ID's",
+                                "output_name": "translation",
+                                "uuid": "7989f80a-3e79-4d2f-bbe4-e4d641eebd6a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_go/clusterprofiler_go/0.1.0",
+                        "errors": null,
+                        "id": 15,
+                        "input_connections": {
+                            "entrezid": {
+                                "id": 14,
+                                "output_name": "translation"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Cluster Profiler GO",
+                        "outputs": [
+                            {
+                                "name": "table",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "plot",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "left": 1320.0000188548697,
+                            "top": 3
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionplot": {
+                                "action_arguments": {
+                                    "newname": "GO Enrichment Analysis Visualization"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "plot"
+                            },
+                            "RenameDatasetActiontable": {
+                                "action_arguments": {
+                                    "newname": "GO Enrichment Analysis of a Gene Set"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "table"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_go/clusterprofiler_go/0.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "5299be80cafb",
+                            "name": "clusterprofiler_go",
+                            "owner": "kpbioteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"txt\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/hg19.len\", \"entrezid\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0",
+                        "type": "tool",
+                        "uuid": "53573a62-88a2-41f3-b3ed-a2afc511f0dd",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "GO Enrichment Analysis of a Gene Set",
+                                "output_name": "table",
+                                "uuid": "ff6c7018-b821-4ade-9931-fa99aeb0a86c"
+                            },
+                            {
+                                "label": "GO Enrichment Analysis Visualization",
+                                "output_name": "plot",
+                                "uuid": "03b88399-095b-4bd5-9693-528c60338407"
                             }
                         ]
                     }
                 ],
-                "parent_id": "epigenetics/methylation-seq",
-                "path": "topics/epigenetics/tutorials/methylation-seq/workflows/methylation-seq.ga",
+                "parent_id": "epigenetics/ewas-suite",
+                "path": "topics/epigenetics/tutorials/ewas-suite/workflows/Infinium-Human-Methylation-BeadChip.ga",
                 "tags": [
                     "epigenetics"
                 ],
                 "test_results": null,
                 "tests": true,
-                "title": "Workflow Methylation Seq",
+                "title": "Infinium Human Methylation BeadChip",
                 "topic_id": "epigenetics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/epigenetics-methylation-seq/versions/methylation-seq",
-                "tutorial_id": "methylation-seq",
-                "url": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/methylation-seq/workflows/methylation-seq.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/methylation-seq/workflows/methylation-seq.html",
-                "version": 3,
-                "wfid": "epigenetics-methylation-seq",
-                "wfname": "methylation-seq",
-                "workflow": "methylation-seq.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/epigenetics-ewas-suite/versions/infinium-human-methylation-beadchip",
+                "tutorial_id": "ewas-suite",
+                "url": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/ewas-suite/workflows/Infinium-Human-Methylation-BeadChip.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/ewas-suite/workflows/Infinium-Human-Methylation-BeadChip.html",
+                "version": 1,
+                "wfid": "epigenetics-ewas-suite",
+                "wfname": "infinium-human-methylation-beadchip",
+                "workflow": "Infinium-Human-Methylation-BeadChip.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.5.1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/pileometh/pileometh/0.3.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.68",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.0.3",
-                    "toolshed.g2.bx.psu.edu/repos/rnateam/metilene/metilene/0.2.6.1"
+                    "Cut1",
+                    "Remove beginning1",
+                    "toolshed.g2.bx.psu.edu/repos/kpbioteam/chipeakanno_annopeaks/chipeakanno_annopeaks/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_bitr/clusterprofiler_bitr/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/kpbioteam/clusterprofiler_go/clusterprofiler_go/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/kpbioteam/ewastools/minfi_analysis/2.1.0"
                 ],
-                "workflowhub_id": "1157"
+                "workflowhub_id": "1165"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/557099"
+        "zenodo_link": "https://zenodo.org/record/1251211"
     },
     {
         "admin_install": {
@@ -75651,10 +79586,10 @@
         ],
         "dir": "topics/epigenetics/tutorials/hicexplorer",
         "edam_operation": [
+            "Generation",
             "Sequence alignment",
-            "Read mapping",
             "Genome indexing",
-            "Generation"
+            "Read mapping"
         ],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -75675,7 +79610,7 @@
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2023-11-09",
-        "pageviews": 10386,
+        "pageviews": 10656,
         "pub_date": "2018-02-23",
         "questions": [
             "Why is a Hi-C analysis useful?",
@@ -75684,14 +79619,14 @@
         ],
         "short_id": "T00141",
         "short_tools": [
-            "hicexplorer_hicbuildmatrix",
-            "hicexplorer_hicfindtads",
+            "bwa_mem",
+            "hicexplorer_hicmergematrixbins",
             "hicexplorer_hicpca",
-            "hicexplorer_hicplottads",
-            "hicexplorer_hiccorrectmatrix",
+            "hicexplorer_hicfindtads",
             "hicexplorer_hicplotmatrix",
-            "bwa_mem",
-            "hicexplorer_hicmergematrixbins"
+            "hicexplorer_hicplottads",
+            "hicexplorer_hicbuildmatrix",
+            "hicexplorer_hiccorrectmatrix"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -75731,8 +79666,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 96,
-        "visitors": 5725,
+        "visit_duration": 95,
+        "visitors": 5935,
         "workflows": [
             {
                 "creators": [],
@@ -75962,7 +79897,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nR1.fastq\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nR2.fastq\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nH3K27me3.bw\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nH3K36me3.bw\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nH4K16ac.bw\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\ndm3_genes.bed\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"Map with BWA-MEM\"];\n  0 -->|output| 6;\n  7[\"Map with BWA-MEM\"];\n  1 -->|output| 7;\n  8[\"hicBuildMatrix\"];\n  7 -->|output| 8;\n  6 -->|output| 8;\n  9[\"hicMergeMatrixBins\"];\n  8 -->|outFileName| 9;\n  10[\"hicCorrectMatrix\"];\n  8 -->|outFileName| 10;\n  11[\"hicCorrectMatrix\"];\n  8 -->|outFileName| 11;\n  12[\"hicPlotMatrix\"];\n  9 -->|outFileName| 12;\n  13[\"hicPlotMatrix\"];\n  11 -->|outFileName| 13;\n  14[\"hicFindTADs\"];\n  11 -->|outFileName| 14;\n  15[\"hicPCA\"];\n  14 -->|matrix_output| 15;\n  16[\"hicPlotTADs\"];\n  14 -->|domains| 16;\n  11 -->|outFileName| 16;\n  14 -->|tad_score| 16;\n  15 -->|pca1| 16;\n  15 -->|pca2| 16;\n  3 -->|output| 16;\n  2 -->|output| 16;\n  4 -->|output| 16;\n  5 -->|output| 16;",
-                "modified": "2024-08-18 00:06:23 +0000",
+                "modified": "2024-10-02 12:08:08 +0000",
                 "name": "Galaxy Workflow Galaxy Hi C",
                 "outputs": [],
                 "parent_id": "epigenetics/hicexplorer",
@@ -75998,6 +79933,12 @@
         "zenodo_link": "https://doi.org/10.5281/zenodo.1183661"
     },
     {
+        "abbreviations": {
+            "CUT&RUN": "Cleavage Under Targets and Release Using Nuclease",
+            "POI": "protein of interest",
+            "TF": "transcription factors",
+            "pA(G)-MNase": "protein A(-protein G hybrid)-micrococcal nuclease"
+        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -76018,16 +79959,16 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "bamtools_filter",
+                    "owner": "devteam",
+                    "revisions": "cb20f99fd45b",
+                    "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "bamtools_filter",
                     "owner": "devteam",
-                    "revisions": "cb20f99fd45b",
+                    "revisions": "1dfd95ee241e",
                     "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
@@ -76038,6 +79979,13 @@
                     "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "bowtie2",
+                    "owner": "devteam",
+                    "revisions": "f6877ad76b00",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "fastqc",
                     "owner": "devteam",
@@ -76045,6 +79993,13 @@
                     "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "3d0c7bdf12f5",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "picard",
                     "owner": "devteam",
@@ -76053,10 +80008,10 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "samtools_idxstats",
+                    "name": "picard",
                     "owner": "devteam",
-                    "revisions": "7a6034296ae9",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "revisions": "b502c227b5e6",
+                    "tool_panel_section_label": "Picard",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
@@ -76066,6 +80021,13 @@
                     "tool_panel_section_label": "BED",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "bedtools",
+                    "owner": "iuc",
+                    "revisions": "a1a923cd89e8",
+                    "tool_panel_section_label": "BED",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "bedtools",
                     "owner": "iuc",
@@ -76073,6 +80035,27 @@
                     "tool_panel_section_label": "BED",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "bedtools",
+                    "owner": "iuc",
+                    "revisions": "a1a923cd89e8",
+                    "tool_panel_section_label": "BED",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "extract_genomic_dna",
+                    "owner": "iuc",
+                    "revisions": "5cc8e93ee98f",
+                    "tool_panel_section_label": "Fetch Sequences/Alignments",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "idr",
+                    "owner": "iuc",
+                    "revisions": "de7795890bc5",
+                    "tool_panel_section_label": "RNA Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "macs2",
                     "owner": "iuc",
@@ -76080,6 +80063,20 @@
                     "tool_panel_section_label": "Peak Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "macs2",
+                    "owner": "iuc",
+                    "revisions": "640d3af5d833",
+                    "tool_panel_section_label": "Peak Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "meme_chip",
+                    "owner": "iuc",
+                    "revisions": "cc100e0f61f4",
+                    "tool_panel_section_label": "Motif Tools",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "pe_histogram",
                     "owner": "iuc",
@@ -76103,9 +80100,60 @@
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: deeptools_compute_matrix\n  owner: bgruening\n  revisions: 514fa53b5efb\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_plot_heatmap\n  owner: bgruening\n  revisions: a4dfb122e52b\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_filter\n  owner: devteam\n  revisions: cb20f99fd45b\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie2\n  owner: devteam\n  revisions: a6d65b0c67af\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: a1f0b3f4b781\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_idxstats\n  owner: devteam\n  revisions: 7a6034296ae9\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: ce3c7f062223\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: a68aa6c1204a\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: macs2\n  owner: iuc\n  revisions: 424aefbd7777\n  tool_panel_section_label: Peak Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pe_histogram\n  owner: iuc\n  revisions: bd1416eea1f0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pygenometracks\n  owner: iuc\n  revisions: 2824d77cd8f8\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 49370cb85f0f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/atac-seq/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: deeptools_compute_matrix\n  owner: bgruening\n  revisions: 514fa53b5efb\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_plot_heatmap\n  owner: bgruening\n  revisions: a4dfb122e52b\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_filter\n  owner: devteam\n  revisions: cb20f99fd45b\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_filter\n  owner: devteam\n  revisions: 1dfd95ee241e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie2\n  owner: devteam\n  revisions: a6d65b0c67af\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie2\n  owner: devteam\n  revisions: f6877ad76b00\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: a1f0b3f4b781\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: b502c227b5e6\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: ce3c7f062223\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: a1a923cd89e8\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: a68aa6c1204a\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: a1a923cd89e8\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: extract_genomic_dna\n  owner: iuc\n  revisions: 5cc8e93ee98f\n  tool_panel_section_label: Fetch Sequences/Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: idr\n  owner: iuc\n  revisions: de7795890bc5\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: macs2\n  owner: iuc\n  revisions: 424aefbd7777\n  tool_panel_section_label: Peak Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: macs2\n  owner: iuc\n  revisions: 640d3af5d833\n  tool_panel_section_label: Peak Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meme_chip\n  owner: iuc\n  revisions: cc100e0f61f4\n  tool_panel_section_label: Motif Tools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pe_histogram\n  owner: iuc\n  revisions: bd1416eea1f0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pygenometracks\n  owner: iuc\n  revisions: 2824d77cd8f8\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 49370cb85f0f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/cut_and_run/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "heylf"
+            ],
+            "editing": [
+                "hexylena",
+                "lldelisle"
+            ]
+        },
         "contributors": [
+            {
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "heylf",
+                "joined": "2018-08",
+                "name": "Florian Heyl",
+                "orcid": "0000-0002-3651-5685",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/heylf/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/heylf.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
             {
                 "affiliations": [
                     "elixir-europe"
@@ -76124,157 +80172,120 @@
                 "orcid": "0000-0002-1964-4960",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/lldelisle.json"
-            },
-            {
-                "id": "mblue9",
-                "joined": "2018-09",
-                "name": "Maria Doyle",
-                "orcid": "0000-0003-4847-8436",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
-            },
-            {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "heylf",
-                "joined": "2018-08",
-                "name": "Florian Heyl",
-                "orcid": "0000-0002-3651-5685",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/heylf/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/heylf.json"
             }
         ],
-        "dir": "topics/epigenetics/tutorials/atac-seq",
+        "dir": "topics/epigenetics/tutorials/cut_and_run",
+        "draft": true,
         "edam_operation": [
-            "Visualisation",
-            "Sequencing quality control",
-            "Primer removal",
+            "Data handling",
             "Peak calling",
-            "Enrichment analysis",
-            "Formatting",
+            "Visualisation",
+            "Sequence trimming",
             "Read mapping",
-            "Sequence alignment analysis",
-            "Mapping",
+            "Sequencing quality control",
             "Sequence composition calculation",
+            "Sequence alignment analysis",
+            "Statistical calculation",
             "Read pre-processing",
             "Gene regulatory network analysis",
-            "Data handling",
-            "Sequence trimming",
-            "Statistical calculation"
+            "Mapping",
+            "Formatting",
+            "Primer removal",
+            "Enrichment analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "epigenetics/atac-seq",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz"
-        ],
+        "id": "epigenetics/cut_and_run",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "ATAC-Seq can be used to identify accessible gene promoters and enhancers",
+            "CUT&RUN can be used to identify binding regions for DNA binding proteins.",
             "Several filters are applied to the reads, such as removing those mapped to mitochondria",
-            "Fragment distribution can help determine whether an ATAC-Seq experiment has worked well"
+            "Fragment distribution can help determine whether an CUT&RUN experiment has worked well",
+            "A robust peak detection removes noise from the data"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-08",
+        "mod_date": "2024-03-06",
         "objectives": [
-            "Apply appropriate analysis and quality control steps for ATAC-Seq",
-            "Generate a heatmap of transcription start site accessibility",
-            "Visualise peaks for specific regions"
+            "Apply appropriate analysis and quality control steps for CUT&RUN",
+            "Apply an enrichment analysis and a robust peak detection",
+            "Find protein binding motifs"
         ],
-        "pageviews": 5826101,
-        "pub_date": "2019-09-02",
+        "pageviews": 2162,
+        "pub_date": "2024-03-06",
         "questions": [
-            "Which DNA regions are accessible in the human lymphoblastoid cell line GM12878?",
-            "How to analyse and visualise ATAC-Seq data?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "hrhotz"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "1H50M",
-                "speakers": [
-                    "heylf"
-                ],
-                "youtube_id": "Zc-bl6ZfcX4"
-            }
+            "Which binding motif has the transcription factor GATA1?",
+            "What kind of quality control do I have to do?",
+            "How to analyse and visualise CUT&RUN data?"
         ],
-        "short_id": "T00137",
+        "short_id": "T00424",
         "short_tools": [
-            "Grep1",
             "picard_MarkDuplicates",
             "pygenomeTracks",
-            "bedtools_intersectbed",
-            "bowtie2",
-            "bamFilter",
-            "deeptools_compute_matrix",
-            "Cut1",
             "deeptools_plot_heatmap",
+            "bamFilter",
+            "bedtools_intersectbed",
+            "macs2_callpeak",
+            "wig_to_bigWig",
+            "meme_chip",
+            "Extract genomic DNA 1",
+            "pe_histogram",
             "fastqc",
-            "samtools_idxstats",
+            "deeptools_compute_matrix",
+            "bowtie2",
+            "idr",
+            "__EXTRACT_DATASET__",
             "Filter1",
-            "tp_sort_header_tool",
+            "cutadapt",
+            "Grep1",
             "bedtools_bamtobed",
-            "macs2_callpeak",
-            "pe_histogram",
-            "wig_to_bigWig",
-            "cutadapt"
-        ],
-        "slides": true,
-        "slides_recordings": [
-            {
-                "captioners": [
-                    "lldelisle"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "15M",
-                "speakers": [
-                    "lldelisle"
-                ],
-                "youtube_id": "2jPNNd5YJNM"
-            }
+            "__FLATTEN__",
+            "trim_galore"
         ],
+        "slides": false,
+        "slides_recordings": false,
         "supported_servers": {
             "exact": [],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                }
-            ]
+            "inexact": []
         },
         "symlink": null,
+        "tags": [
+            "work-in-progress"
+        ],
         "time_estimation": "3h",
-        "title": "ATAC-Seq data analysis",
+        "title": "CUT&RUN data analysis",
         "tools": [
-            "Cut1",
+            " https://toolshed.g2.bx.psu.edu/view/bgruening/trim_galore/cd7e644cae1d",
             "Filter1",
             "Grep1",
+            "__EXTRACT_DATASET__",
+            "__FLATTEN__",
             "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0",
             "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
             "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.1+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
             "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3",
+            "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3",
             "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2",
             "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/idr/idr/2.0.3",
             "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6",
+            "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1",
             "toolshed.g2.bx.psu.edu/repos/iuc/pe_histogram/pe_histogram/1.0.1",
             "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.6",
             "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
@@ -76286,21 +80297,21 @@
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": true
+            "video": false
         },
-        "tutorial_name": "atac-seq",
+        "tutorial_name": "cut_and_run",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/epigenetics/tutorials/atac-seq/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/epigenetics/tutorials/cut_and_run/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/atac-seq/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/atac-seq/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/cut_and_run/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/cut_and_run/tutorial.json"
         },
-        "version": 23,
-        "video": true,
-        "video_versions": 1,
+        "version": 1,
+        "video": false,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 265,
-        "visitors": 2115259,
+        "visit_duration": 86,
+        "visitors": 1659,
         "workflows": [
             {
                 "creators": [],
@@ -76314,144 +80325,11 @@
                 "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nbed file with genes\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nctcf peaks\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nATAC R2 read in fastq.gz format\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nATAC R1 read in fastq.gz format\"]\n  4[label=\"Filter\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"FastQC\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"ATAC remove nextera adapters with cutadapt\"]\n  3 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"FastQC\"]\n  3 -> 7 [label=\"output\"]\n  8[label=\"bedtools Intersect intervals\"]\n  4 -> 8 [label=\"out_file1\"]\n  0 -> 8 [label=\"output\"]\n  9[label=\"FastQC\"]\n  6 -> 9 [label=\"out2\"]\n  10[label=\"Bowtie2\"]\n  6 -> 10 [label=\"out1\"]\n  6 -> 10 [label=\"out2\"]\n  11[label=\"FastQC\"]\n  6 -> 11 [label=\"out1\"]\n  12[label=\"Filter BAM ATAC\"]\n  10 -> 12 [label=\"output\"]\n  13[label=\"MarkDuplicates\"]\n  12 -> 13 [label=\"out_file1\"]\n  14[label=\"bedtools BAM to BED\"]\n  13 -> 14 [label=\"outFile\"]\n  15[label=\"Paired-end histogram\"]\n  13 -> 15 [label=\"outFile\"]\n  16[label=\"MACS2 callpeak\"]\n  14 -> 16 [label=\"output\"]\n  17[label=\"Wig/BedGraph-to-bigWig\"]\n  16 -> 17 [label=\"output_treat_pileup\"]\n  18[label=\"computeMatrix\"]\n  17 -> 18 [label=\"out_file1\"]\n  0 -> 18 [label=\"output\"]\n  19[label=\"pyGenomeTracks\"]\n  17 -> 19 [label=\"out_file1\"]\n  16 -> 19 [label=\"output_narrowpeaks\"]\n  0 -> 19 [label=\"output\"]\n  1 -> 19 [label=\"output\"]\n  20[label=\"computeMatrix\"]\n  17 -> 20 [label=\"out_file1\"]\n  8 -> 20 [label=\"output\"]\n  k65159c9c050b406987048f66c0563a98[color=lightseagreen,label=\"Output\\ncomputeMatrix on input dataset(s): Matrix\"]\n  20 -> k65159c9c050b406987048f66c0563a98\n  21[label=\"plotHeatmap\"]\n  18 -> 21 [label=\"outFileName\"]\n  22[label=\"plotHeatmap\"]\n  20 -> 22 [label=\"outFileName\"]\n  k74a36643b88f43788f9cc1b20ee2651e[color=lightseagreen,label=\"Output\\nplotHeatmap on input dataset(s): Image\"]\n  22 -> k74a36643b88f43788f9cc1b20ee2651e\n}",
                 "history": [
                     {
-                        "hash": "96d212779f2fbe4abf7c850b750ca5e163e88361",
-                        "message": "update deeptools tools + parameters",
-                        "num": 20,
-                        "short_hash": "96d212779",
-                        "unix": "1619713579"
-                    },
-                    {
-                        "hash": "ba3bf335e18101d6178afceebe7226c14c1153c4",
-                        "message": "use pygenometracks 3.6",
-                        "num": 19,
-                        "short_hash": "ba3bf335e",
-                        "unix": "1618238510"
-                    },
-                    {
-                        "hash": "af99da9c03f900d2c078b704c84993c64d9cf722",
-                        "message": "update the workflow",
-                        "num": 18,
-                        "short_hash": "af99da9c0",
-                        "unix": "1617381749"
-                    },
-                    {
-                        "hash": "d5cd0ab560e9922b159174141905919870659041",
-                        "message": "update tutorial",
-                        "num": 17,
-                        "short_hash": "d5cd0ab56",
-                        "unix": "1617118406"
-                    },
-                    {
-                        "hash": "d4aee8b0dee08824c24db20abb73078b27d46b2e",
-                        "message": "change bedtools to allow to sort encodePeak",
-                        "num": 16,
-                        "short_hash": "d4aee8b0d",
-                        "unix": "1592298126"
-                    },
-                    {
-                        "hash": "c1cf1143c8c7aa6fbd822761682cd94d95588b82",
-                        "message": "macs2 to MACS2 in figures and workflow",
-                        "num": 15,
-                        "short_hash": "c1cf1143c",
-                        "unix": "1591860137"
-                    },
-                    {
-                        "hash": "69d703ece4379791461043ed5d78dee4b2a9a724",
-                        "message": "add tag and annotation",
-                        "num": 14,
-                        "short_hash": "69d703ece",
-                        "unix": "1591855841"
-                    },
-                    {
-                        "hash": "83f254a2b6d7ab6dd0677111eca534d4fd70aa21",
-                        "message": "update new version of pgt",
-                        "num": 13,
-                        "short_hash": "83f254a2b",
-                        "unix": "1591824498"
-                    },
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 12,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 11,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "05fb8eedbed86a986f9bc87a8bdfedd4093acc75",
-                        "message": "New workflows unflattened",
-                        "num": 10,
-                        "short_hash": "05fb8eedb",
-                        "unix": "1576835747"
-                    },
-                    {
-                        "hash": "2ebad4e591be9976da3c76fac328910cbb532b53",
-                        "message": "rebase",
-                        "num": 9,
-                        "short_hash": "2ebad4e59",
-                        "unix": "1576835604"
-                    },
-                    {
-                        "hash": "bc9c7ce8a01c0205beb6267bcd866330acc1747f",
-                        "message": "changed awk step",
-                        "num": 8,
-                        "short_hash": "bc9c7ce8a",
-                        "unix": "1576770705"
-                    },
-                    {
-                        "hash": "1bef60c2de1f1a8f7b43814a18a9b4378a7433ba",
-                        "message": "updated workflow",
-                        "num": 7,
-                        "short_hash": "1bef60c2d",
-                        "unix": "1576768651"
-                    },
-                    {
-                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
-                        "message": "unflatten workflows",
-                        "num": 6,
-                        "short_hash": "faf6d298a",
-                        "unix": "1576155753"
-                    },
-                    {
-                        "hash": "397de5ef9638f7e38137e143e575a87e13443089",
-                        "message": "modified version of genrich and pygenometracks",
-                        "num": 5,
-                        "short_hash": "397de5ef9",
-                        "unix": "1566912825"
-                    },
-                    {
-                        "hash": "93027360bcbac79c5e7d2eec481679d9ab09a159",
-                        "message": "Changes to workflow atac",
-                        "num": 4,
-                        "short_hash": "93027360b",
-                        "unix": "1565856529"
-                    },
-                    {
-                        "hash": "b2bcfc0d7fbfc45e055185515a5ba99b86ba4b00",
-                        "message": "Add visualisation step to workflow (pygenometracks)",
-                        "num": 3,
-                        "short_hash": "b2bcfc0d7",
-                        "unix": "1562416848"
-                    },
-                    {
-                        "hash": "7dec9b919382dc05ac8e1a717ca8e70078ea343e",
-                        "message": "Updates to workflow",
-                        "num": 2,
-                        "short_hash": "7dec9b919",
-                        "unix": "1562336122"
-                    },
-                    {
-                        "hash": "bb008c8c916d026929795969c28763b1cddfbfd1",
-                        "message": "First draft of ATAC-seq tut from CoFest (WIP)",
+                        "hash": "c32dabaf3de77d6f436f0bc58b0b7735f64767c8",
+                        "message": "Adding cut and run",
                         "num": 1,
-                        "short_hash": "bb008c8c9",
-                        "unix": "1562333044"
+                        "short_hash": "c32dabaf3",
+                        "unix": "1627297960"
                     }
                 ],
                 "inputs": [
@@ -76586,7 +80464,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nbed file with genes\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nctcf peaks\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nATAC R2 read in fastq.gz format\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nATAC R1 read in fastq.gz format\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Filter\"];\n  1 -->|output| 4;\n  5[\"FastQC\"];\n  2 -->|output| 5;\n  6[\"ATAC remove nextera adapters with cutadapt\"];\n  3 -->|output| 6;\n  2 -->|output| 6;\n  7[\"FastQC\"];\n  3 -->|output| 7;\n  8[\"bedtools Intersect intervals\"];\n  4 -->|out_file1| 8;\n  0 -->|output| 8;\n  9[\"FastQC\"];\n  6 -->|out2| 9;\n  10[\"Bowtie2\"];\n  6 -->|out1| 10;\n  6 -->|out2| 10;\n  11[\"FastQC\"];\n  6 -->|out1| 11;\n  12[\"Filter BAM ATAC\"];\n  10 -->|output| 12;\n  13[\"MarkDuplicates\"];\n  12 -->|out_file1| 13;\n  14[\"bedtools BAM to BED\"];\n  13 -->|outFile| 14;\n  15[\"Paired-end histogram\"];\n  13 -->|outFile| 15;\n  16[\"MACS2 callpeak\"];\n  14 -->|output| 16;\n  17[\"Wig/BedGraph-to-bigWig\"];\n  16 -->|output_treat_pileup| 17;\n  18[\"computeMatrix\"];\n  17 -->|out_file1| 18;\n  0 -->|output| 18;\n  19[\"pyGenomeTracks\"];\n  17 -->|out_file1| 19;\n  16 -->|output_narrowpeaks| 19;\n  0 -->|output| 19;\n  1 -->|output| 19;\n  20[\"computeMatrix\"];\n  17 -->|out_file1| 20;\n  8 -->|output| 20;\n  65159c9c-050b-4069-8704-8f66c0563a98[\"Output\\ncomputeMatrix on input dataset(s): Matrix\"];\n  20 --> 65159c9c-050b-4069-8704-8f66c0563a98;\n  style 65159c9c-050b-4069-8704-8f66c0563a98 stroke:#2c3143,stroke-width:4px;\n  21[\"plotHeatmap\"];\n  18 -->|outFileName| 21;\n  22[\"plotHeatmap\"];\n  20 -->|outFileName| 22;\n  74a36643-b88f-4378-8f9c-c1b20ee2651e[\"Output\\nplotHeatmap on input dataset(s): Image\"];\n  22 --> 74a36643-b88f-4378-8f9c-c1b20ee2651e;\n  style 74a36643-b88f-4378-8f9c-c1b20ee2651e stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:22 +0000",
+                "modified": "2024-10-02 12:08:07 +0000",
                 "name": "ATAC-seq GTM",
                 "outputs": [
                     {
@@ -77882,8 +81760,8 @@
                         ]
                     }
                 ],
-                "parent_id": "epigenetics/atac-seq",
-                "path": "topics/epigenetics/tutorials/atac-seq/workflows/main_workflow.ga",
+                "parent_id": "epigenetics/cut_and_run",
+                "path": "topics/epigenetics/tutorials/cut_and_run/workflows/main_workflow.ga",
                 "tags": [
                     "epigenetics"
                 ],
@@ -77891,12 +81769,12 @@
                 "tests": false,
                 "title": "ATAC-seq GTM",
                 "topic_id": "epigenetics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/epigenetics-atac-seq/versions/main-workflow",
-                "tutorial_id": "atac-seq",
-                "url": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/workflows/main_workflow.html",
-                "version": 10,
-                "wfid": "epigenetics-atac-seq",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/epigenetics-cut_and_run/versions/main-workflow",
+                "tutorial_id": "cut_and_run",
+                "url": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/cut_and_run/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/cut_and_run/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "epigenetics-cut_and_run",
                 "wfname": "main-workflow",
                 "workflow": "main_workflow.ga",
                 "workflow_tools": [
@@ -77915,822 +81793,11 @@
                     "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
                     "wig_to_bigWig"
                 ],
-                "workflowhub_id": "1169"
+                "workflowhub_id": "1161"
             }
         ],
         "zenodo_link": "https://zenodo.org/record/3862793"
     },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "deeptools_bam_compare",
-                    "owner": "bgruening",
-                    "revisions": "e821645ef8fc",
-                    "tool_panel_section_label": "deepTools",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "deeptools_compute_gc_bias",
-                    "owner": "bgruening",
-                    "revisions": "2bc10a9ca58b",
-                    "tool_panel_section_label": "deepTools",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "deeptools_compute_matrix",
-                    "owner": "bgruening",
-                    "revisions": "514fa53b5efb",
-                    "tool_panel_section_label": "deepTools",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "deeptools_correct_gc_bias",
-                    "owner": "bgruening",
-                    "revisions": "2c37ce318bc3",
-                    "tool_panel_section_label": "deepTools",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "deeptools_multi_bam_summary",
-                    "owner": "bgruening",
-                    "revisions": "78f405266706",
-                    "tool_panel_section_label": "deepTools",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "deeptools_plot_correlation",
-                    "owner": "bgruening",
-                    "revisions": "32e451def88c",
-                    "tool_panel_section_label": "deepTools",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "deeptools_plot_fingerprint",
-                    "owner": "bgruening",
-                    "revisions": "2da482e408b8",
-                    "tool_panel_section_label": "deepTools",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "deeptools_plot_heatmap",
-                    "owner": "bgruening",
-                    "revisions": "a4dfb122e52b",
-                    "tool_panel_section_label": "deepTools",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bwa",
-                    "owner": "devteam",
-                    "revisions": "64f11cf59c6e",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "e7b2202befea",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_idxstats",
-                    "owner": "devteam",
-                    "revisions": "7a6034296ae9",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bedtools",
-                    "owner": "iuc",
-                    "revisions": "b28e0cfa7ba1",
-                    "tool_panel_section_label": "BED",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "macs2",
-                    "owner": "iuc",
-                    "revisions": "424aefbd7777",
-                    "tool_panel_section_label": "Peak Calling",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "trimmomatic",
-                    "owner": "pjbriggs",
-                    "revisions": "898b67846b47",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: deeptools_bam_compare\n  owner: bgruening\n  revisions: e821645ef8fc\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_compute_gc_bias\n  owner: bgruening\n  revisions: 2bc10a9ca58b\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_compute_matrix\n  owner: bgruening\n  revisions: 514fa53b5efb\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_correct_gc_bias\n  owner: bgruening\n  revisions: 2c37ce318bc3\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_multi_bam_summary\n  owner: bgruening\n  revisions: 78f405266706\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_plot_correlation\n  owner: bgruening\n  revisions: 32e451def88c\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_plot_fingerprint\n  owner: bgruening\n  revisions: 2da482e408b8\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deeptools_plot_heatmap\n  owner: bgruening\n  revisions: a4dfb122e52b\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: 64f11cf59c6e\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_idxstats\n  owner: devteam\n  revisions: 7a6034296ae9\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: b28e0cfa7ba1\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: macs2\n  owner: iuc\n  revisions: 424aefbd7777\n  tool_panel_section_label: Peak Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n  owner: pjbriggs\n  revisions: 898b67846b47\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.json",
-        "contributors": [
-            {
-                "id": "malloryfreeberg",
-                "joined": "2017-09",
-                "name": "Mallory Freeberg",
-                "orcid": "0000-0003-2949-3921",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/malloryfreeberg/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/malloryfreeberg.json"
-            },
-            {
-                "email": "mheydarian@gmail.com",
-                "id": "moheydarian",
-                "joined": "2017-09",
-                "name": "Mo Heydarian",
-                "orcid": "0000-0001-9449-9364",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/moheydarian/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/moheydarian.json"
-            },
-            {
-                "id": "vivekbhr",
-                "joined": "2017-09",
-                "name": "Vivek Bhardwaj",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/vivekbhr/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/vivekbhr.json"
-            },
-            {
-                "elixir_node": "de",
-                "email": "wolffj@informatik.uni-freiburg.de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "joachimwolff",
-                "joined": "2017-09",
-                "name": "Joachim Wolff",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/joachimwolff.json"
-            },
-            {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "email": "anikaerxleben@gmail.com",
-                "id": "erxleben",
-                "joined": "2017-09",
-                "name": "Anika Erxleben",
-                "orcid": "0000-0002-7427-6478",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/erxleben/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/erxleben.json"
-            }
-        ],
-        "dir": "topics/epigenetics/tutorials/tal1-binding-site-identification",
-        "edam_ontology": [
-            "topic_3169"
-        ],
-        "edam_operation": [
-            "Sequencing quality control",
-            "Genome indexing",
-            "Peak calling",
-            "Sequence alignment",
-            "Mapping",
-            "Read mapping",
-            "Sequence composition calculation",
-            "Enrichment analysis",
-            "Gene regulatory network analysis",
-            "Generation",
-            "Statistical calculation"
-        ],
-        "edam_topic": [
-            "ChIP-seq"
-        ],
-        "exact_supported_servers": [
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "epigenetics/tal1-binding-site-identification",
-        "inexact_supported_servers": [
-            "Galaxy@AuBi",
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Sophisticated analysis of ChIP-seq data is possible using tools hosted by Galaxy.",
-            "Genomic dataset analyses require multiple methods of quality assessment to ensure that the data are appropriate for answering the biology question of interest.",
-            "By using the sharable and transparent Galaxy platform, data analyses can easily be shared and reproduced."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-25",
-        "objectives": [
-            "Inspect read quality with FastQC",
-            "Perform read trimming with Trimmomatic",
-            "Align trimmed reads with BWA",
-            "Assess quality and reproducibility of experiments",
-            "Identify TAL1 binding sites with MACS2",
-            "Determine unique/common TAL1 binding sites from G1E and Megakaryocytes",
-            "Identify unique/common TAL1 peaks occupying gene promoters",
-            "Visually inspect TAL1 peaks with Trackster"
-        ],
-        "pageviews": 11153,
-        "pub_date": "2016-12-20",
-        "questions": [
-            "How is raw ChIP-seq data processed and analyzed?",
-            "What are the binding sites of TAL1?",
-            "Which genes are regulated by TAL1?"
-        ],
-        "redirect_from": [
-            "/topics/chip-seq/tutorials/tal1-binding-site-identification/tutorial",
-            "/short/epigenetics/tal1-binding-site-identification",
-            "/short/T00143"
-        ],
-        "requirements": [
-            {
-                "link": "https://wiki.galaxyproject.org/Learn/Visualization",
-                "title": "Trackster",
-                "type": "external"
-            }
-        ],
-        "short_id": "T00143",
-        "short_tools": [
-            "deeptools_plot_correlation",
-            "deeptools_multi_bam_summary",
-            "bedtools_intersectbed",
-            "deeptools_correct_gc_bias",
-            "bwa",
-            "deeptools_bam_compare",
-            "deeptools_compute_matrix",
-            "deeptools_plot_heatmap",
-            "fastqc",
-            "samtools_idxstats",
-            "macs2_callpeak",
-            "deeptools_plot_fingerprint",
-            "deeptools_compute_gc_bias",
-            "trimmomatic"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "ChIP-seq"
-        ],
-        "time_estimation": "3h",
-        "title": "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.3.2.0.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.3.2.0.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.3.2.0.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.3.2.0.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.3.2.0.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6",
-            "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0"
-        ],
-        "topic_name": "epigenetics",
-        "topic_name_human": "Epigenetics",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "tal1-binding-site-identification",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.json"
-        },
-        "version": 10,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 202,
-        "visitors": 5835,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nG1E_input_R1_downsampled_SRR507859.fastqsanger\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nG1E_input_R2_downsampled_SRR507860.fastqsanger\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nG1E_Tal1_R1_downsampled_SRR492444.fastqsanger\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nG1E_Tal1_R2_downsampled_SRR492445.fastqsanger\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_input_R1_downsampled_SRR492453.fastqsanger\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_input_R2_downsampled_SRR492454.fastqsanger\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMegakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nRefSeq_gene_annotations_mm10.bed\"]\n  9[label=\"FastQC\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"Trimmomatic\"]\n  0 -> 10 [label=\"output\"]\n  11[label=\"FastQC\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"Trimmomatic\"]\n  1 -> 12 [label=\"output\"]\n  13[label=\"FastQC\"]\n  2 -> 13 [label=\"output\"]\n  14[label=\"Trimmomatic\"]\n  2 -> 14 [label=\"output\"]\n  15[label=\"FastQC\"]\n  3 -> 15 [label=\"output\"]\n  16[label=\"Trimmomatic\"]\n  3 -> 16 [label=\"output\"]\n  17[label=\"FastQC\"]\n  4 -> 17 [label=\"output\"]\n  18[label=\"Trimmomatic\"]\n  4 -> 18 [label=\"output\"]\n  19[label=\"FastQC\"]\n  5 -> 19 [label=\"output\"]\n  20[label=\"Trimmomatic\"]\n  5 -> 20 [label=\"output\"]\n  21[label=\"FastQC\"]\n  6 -> 21 [label=\"output\"]\n  22[label=\"Trimmomatic\"]\n  6 -> 22 [label=\"output\"]\n  23[label=\"FastQC\"]\n  7 -> 23 [label=\"output\"]\n  24[label=\"Trimmomatic\"]\n  7 -> 24 [label=\"output\"]\n  25[label=\"FastQC\"]\n  10 -> 25 [label=\"fastq_out\"]\n  26[label=\"Map with BWA\"]\n  10 -> 26 [label=\"fastq_out\"]\n  27[label=\"FastQC\"]\n  12 -> 27 [label=\"fastq_out\"]\n  28[label=\"Map with BWA\"]\n  12 -> 28 [label=\"fastq_out\"]\n  29[label=\"FastQC\"]\n  14 -> 29 [label=\"fastq_out\"]\n  30[label=\"Map with BWA\"]\n  14 -> 30 [label=\"fastq_out\"]\n  31[label=\"FastQC\"]\n  16 -> 31 [label=\"fastq_out\"]\n  32[label=\"Map with BWA\"]\n  16 -> 32 [label=\"fastq_out\"]\n  33[label=\"FastQC\"]\n  18 -> 33 [label=\"fastq_out\"]\n  34[label=\"Map with BWA\"]\n  18 -> 34 [label=\"fastq_out\"]\n  35[label=\"FastQC\"]\n  20 -> 35 [label=\"fastq_out\"]\n  36[label=\"Map with BWA\"]\n  20 -> 36 [label=\"fastq_out\"]\n  37[label=\"FastQC\"]\n  22 -> 37 [label=\"fastq_out\"]\n  38[label=\"Map with BWA\"]\n  22 -> 38 [label=\"fastq_out\"]\n  39[label=\"FastQC\"]\n  24 -> 39 [label=\"fastq_out\"]\n  40[label=\"Map with BWA\"]\n  24 -> 40 [label=\"fastq_out\"]\n  41[label=\"Samtools idxstats\"]\n  26 -> 41 [label=\"bam_output\"]\n  42[label=\"Samtools idxstats\"]\n  28 -> 42 [label=\"bam_output\"]\n  43[label=\"Samtools idxstats\"]\n  30 -> 43 [label=\"bam_output\"]\n  44[label=\"bamCompare\"]\n  30 -> 44 [label=\"bam_output\"]\n  26 -> 44 [label=\"bam_output\"]\n  45[label=\"Samtools idxstats\"]\n  32 -> 45 [label=\"bam_output\"]\n  46[label=\"plotFingerprint\"]\n  26 -> 46 [label=\"bam_output\"]\n  28 -> 46 [label=\"bam_output\"]\n  30 -> 46 [label=\"bam_output\"]\n  32 -> 46 [label=\"bam_output\"]\n  47[label=\"MACS2 callpeak\"]\n  26 -> 47 [label=\"bam_output\"]\n  28 -> 47 [label=\"bam_output\"]\n  30 -> 47 [label=\"bam_output\"]\n  32 -> 47 [label=\"bam_output\"]\n  48[label=\"bamCompare\"]\n  32 -> 48 [label=\"bam_output\"]\n  28 -> 48 [label=\"bam_output\"]\n  49[label=\"Samtools idxstats\"]\n  34 -> 49 [label=\"bam_output\"]\n  50[label=\"Samtools idxstats\"]\n  36 -> 50 [label=\"bam_output\"]\n  51[label=\"Samtools idxstats\"]\n  38 -> 51 [label=\"bam_output\"]\n  52[label=\"bamCompare\"]\n  38 -> 52 [label=\"bam_output\"]\n  34 -> 52 [label=\"bam_output\"]\n  53[label=\"Samtools idxstats\"]\n  40 -> 53 [label=\"bam_output\"]\n  54[label=\"multiBamSummary\"]\n  26 -> 54 [label=\"bam_output\"]\n  28 -> 54 [label=\"bam_output\"]\n  30 -> 54 [label=\"bam_output\"]\n  32 -> 54 [label=\"bam_output\"]\n  34 -> 54 [label=\"bam_output\"]\n  36 -> 54 [label=\"bam_output\"]\n  38 -> 54 [label=\"bam_output\"]\n  40 -> 54 [label=\"bam_output\"]\n  55[label=\"plotFingerprint\"]\n  34 -> 55 [label=\"bam_output\"]\n  36 -> 55 [label=\"bam_output\"]\n  38 -> 55 [label=\"bam_output\"]\n  40 -> 55 [label=\"bam_output\"]\n  56[label=\"MACS2 callpeak\"]\n  34 -> 56 [label=\"bam_output\"]\n  36 -> 56 [label=\"bam_output\"]\n  38 -> 56 [label=\"bam_output\"]\n  40 -> 56 [label=\"bam_output\"]\n  57[label=\"bamCompare\"]\n  40 -> 57 [label=\"bam_output\"]\n  36 -> 57 [label=\"bam_output\"]\n  58[label=\"computeMatrix\"]\n  44 -> 58 [label=\"outFileName\"]\n  48 -> 58 [label=\"outFileName\"]\n  47 -> 58 [label=\"output_narrowpeaks\"]\n  59[label=\"plotCorrelation\"]\n  54 -> 59 [label=\"outFile\"]\n  60[label=\"bedtools Intersect intervals\"]\n  47 -> 60 [label=\"output_narrowpeaks\"]\n  56 -> 60 [label=\"output_narrowpeaks\"]\n  k0d2260b8138a4ca99fb22ba391f7517a[color=lightseagreen,label=\"Output\\noutput_overlapping_peaks\"]\n  60 -> k0d2260b8138a4ca99fb22ba391f7517a\n  61[label=\"bedtools Intersect intervals\"]\n  47 -> 61 [label=\"output_narrowpeaks\"]\n  56 -> 61 [label=\"output_narrowpeaks\"]\n  k2cd86f4ca1f442a89bbd82ef8f156dac[color=lightseagreen,label=\"Output\\noutput_g1e_peaks\"]\n  61 -> k2cd86f4ca1f442a89bbd82ef8f156dac\n  62[label=\"bedtools Intersect intervals\"]\n  56 -> 62 [label=\"output_narrowpeaks\"]\n  47 -> 62 [label=\"output_narrowpeaks\"]\n  kf8a16be5f7ae4fecb67b91c4532a43d2[color=lightseagreen,label=\"Output\\noutput_megakaryocyte_peaks\"]\n  62 -> kf8a16be5f7ae4fecb67b91c4532a43d2\n  63[label=\"computeMatrix\"]\n  52 -> 63 [label=\"outFileName\"]\n  57 -> 63 [label=\"outFileName\"]\n  56 -> 63 [label=\"output_narrowpeaks\"]\n  64[label=\"plotHeatmap\"]\n  58 -> 64 [label=\"outFileName\"]\n  65[label=\"plotHeatmap\"]\n  63 -> 65 [label=\"outFileName\"]\n}",
-                "history": [
-                    {
-                        "hash": "818f002190ef7fb261a841024556075ceff1df49",
-                        "message": "Fixed JSON format.",
-                        "num": 5,
-                        "short_hash": "818f00219",
-                        "unix": "1602017176"
-                    },
-                    {
-                        "hash": "473da245d41207021918c79019a3e5833873c82f",
-                        "message": "Updated outputs in workflow and test.yml.",
-                        "num": 4,
-                        "short_hash": "473da245d",
-                        "unix": "1602015752"
-                    },
-                    {
-                        "hash": "3bee4c5377363dbf60c059683f0f972a343c3cbc",
-                        "message": "Updated inputs in workflow and test.yml.",
-                        "num": 3,
-                        "short_hash": "3bee4c537",
-                        "unix": "1602012514"
-                    },
-                    {
-                        "hash": "e9f2fa109479668f2d020a75f3496a3db5fdcedd",
-                        "message": "Updated workflow with tags.",
-                        "num": 2,
-                        "short_hash": "e9f2fa109",
-                        "unix": "1601981292"
-                    },
-                    {
-                        "hash": "7fe3ca36a9a8b8022922de0f9c2d7385628b2e5c",
-                        "message": "Added workflow.",
-                        "num": 1,
-                        "short_hash": "7fe3ca36a",
-                        "unix": "1601924809"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "G1E_input_R1_downsampled_SRR507859.fastqsanger"
-                            }
-                        ],
-                        "label": "G1E_input_R1_downsampled_SRR507859.fastqsanger",
-                        "name": "G1E_input_R1_downsampled_SRR507859.fastqsanger",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 10
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"G1E_input_R1_downsampled_SRR507859.fastqsanger\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "72908882-dad9-452e-9ed6-42aa567c7b6d",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "G1E_input_R2_downsampled_SRR507860.fastqsanger"
-                            }
-                        ],
-                        "label": "G1E_input_R2_downsampled_SRR507860.fastqsanger",
-                        "name": "G1E_input_R2_downsampled_SRR507860.fastqsanger",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 130
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"G1E_input_R2_downsampled_SRR507860.fastqsanger\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f9264f2a-fd66-40ef-8d19-88de9e5adcf0",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "G1E_Tal1_R1_downsampled_SRR492444.fastqsanger"
-                            }
-                        ],
-                        "label": "G1E_Tal1_R1_downsampled_SRR492444.fastqsanger",
-                        "name": "G1E_Tal1_R1_downsampled_SRR492444.fastqsanger",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 250
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"G1E_Tal1_R1_downsampled_SRR492444.fastqsanger\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "2f74715c-df91-46a4-8845-1d4463c4f0c0",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "G1E_Tal1_R2_downsampled_SRR492445.fastqsanger"
-                            }
-                        ],
-                        "label": "G1E_Tal1_R2_downsampled_SRR492445.fastqsanger",
-                        "name": "G1E_Tal1_R2_downsampled_SRR492445.fastqsanger",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 370
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"G1E_Tal1_R2_downsampled_SRR492445.fastqsanger\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "0fc34c4d-c3d6-44b4-a683-521d707f06f1",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Megakaryocyte_input_R1_downsampled_SRR492453.fastqsanger"
-                            }
-                        ],
-                        "label": "Megakaryocyte_input_R1_downsampled_SRR492453.fastqsanger",
-                        "name": "Megakaryocyte_input_R1_downsampled_SRR492453.fastqsanger",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 490
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Megakaryocyte_input_R1_downsampled_SRR492453.fastqsanger\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "92c034ae-9c9e-4dcc-98a4-556d314a7bba",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Megakaryocyte_input_R2_downsampled_SRR492454.fastqsanger"
-                            }
-                        ],
-                        "label": "Megakaryocyte_input_R2_downsampled_SRR492454.fastqsanger",
-                        "name": "Megakaryocyte_input_R2_downsampled_SRR492454.fastqsanger",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 610
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Megakaryocyte_input_R2_downsampled_SRR492454.fastqsanger\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "7bb71d6b-de12-485c-83c9-ed75af5f7fac",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Megakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger"
-                            }
-                        ],
-                        "label": "Megakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger",
-                        "name": "Megakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 730
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Megakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "dd716dbd-e466-40c8-88bf-88febc0b2119",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Megakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger"
-                            }
-                        ],
-                        "label": "Megakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger",
-                        "name": "Megakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 850
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Megakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "5695db81-e17a-4242-aa28-c703b2988666",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "RefSeq_gene_annotations_mm10.bed"
-                            }
-                        ],
-                        "label": "RefSeq_gene_annotations_mm10.bed",
-                        "name": "RefSeq_gene_annotations_mm10.bed",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 970
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"RefSeq_gene_annotations_mm10.bed\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "bc0fc125-1b3c-489f-ae71-ef6320c1ccad",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nG1E_input_R1_downsampled_SRR507859.fastqsanger\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nG1E_input_R2_downsampled_SRR507860.fastqsanger\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nG1E_Tal1_R1_downsampled_SRR492444.fastqsanger\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nG1E_Tal1_R2_downsampled_SRR492445.fastqsanger\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_input_R1_downsampled_SRR492453.fastqsanger\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_input_R2_downsampled_SRR492454.fastqsanger\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nMegakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nRefSeq_gene_annotations_mm10.bed\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"FastQC\"];\n  0 -->|output| 9;\n  10[\"Trimmomatic\"];\n  0 -->|output| 10;\n  11[\"FastQC\"];\n  1 -->|output| 11;\n  12[\"Trimmomatic\"];\n  1 -->|output| 12;\n  13[\"FastQC\"];\n  2 -->|output| 13;\n  14[\"Trimmomatic\"];\n  2 -->|output| 14;\n  15[\"FastQC\"];\n  3 -->|output| 15;\n  16[\"Trimmomatic\"];\n  3 -->|output| 16;\n  17[\"FastQC\"];\n  4 -->|output| 17;\n  18[\"Trimmomatic\"];\n  4 -->|output| 18;\n  19[\"FastQC\"];\n  5 -->|output| 19;\n  20[\"Trimmomatic\"];\n  5 -->|output| 20;\n  21[\"FastQC\"];\n  6 -->|output| 21;\n  22[\"Trimmomatic\"];\n  6 -->|output| 22;\n  23[\"FastQC\"];\n  7 -->|output| 23;\n  24[\"Trimmomatic\"];\n  7 -->|output| 24;\n  25[\"FastQC\"];\n  10 -->|fastq_out| 25;\n  26[\"Map with BWA\"];\n  10 -->|fastq_out| 26;\n  27[\"FastQC\"];\n  12 -->|fastq_out| 27;\n  28[\"Map with BWA\"];\n  12 -->|fastq_out| 28;\n  29[\"FastQC\"];\n  14 -->|fastq_out| 29;\n  30[\"Map with BWA\"];\n  14 -->|fastq_out| 30;\n  31[\"FastQC\"];\n  16 -->|fastq_out| 31;\n  32[\"Map with BWA\"];\n  16 -->|fastq_out| 32;\n  33[\"FastQC\"];\n  18 -->|fastq_out| 33;\n  34[\"Map with BWA\"];\n  18 -->|fastq_out| 34;\n  35[\"FastQC\"];\n  20 -->|fastq_out| 35;\n  36[\"Map with BWA\"];\n  20 -->|fastq_out| 36;\n  37[\"FastQC\"];\n  22 -->|fastq_out| 37;\n  38[\"Map with BWA\"];\n  22 -->|fastq_out| 38;\n  39[\"FastQC\"];\n  24 -->|fastq_out| 39;\n  40[\"Map with BWA\"];\n  24 -->|fastq_out| 40;\n  41[\"Samtools idxstats\"];\n  26 -->|bam_output| 41;\n  42[\"Samtools idxstats\"];\n  28 -->|bam_output| 42;\n  43[\"Samtools idxstats\"];\n  30 -->|bam_output| 43;\n  44[\"bamCompare\"];\n  30 -->|bam_output| 44;\n  26 -->|bam_output| 44;\n  45[\"Samtools idxstats\"];\n  32 -->|bam_output| 45;\n  46[\"plotFingerprint\"];\n  26 -->|bam_output| 46;\n  28 -->|bam_output| 46;\n  30 -->|bam_output| 46;\n  32 -->|bam_output| 46;\n  47[\"MACS2 callpeak\"];\n  26 -->|bam_output| 47;\n  28 -->|bam_output| 47;\n  30 -->|bam_output| 47;\n  32 -->|bam_output| 47;\n  48[\"bamCompare\"];\n  32 -->|bam_output| 48;\n  28 -->|bam_output| 48;\n  49[\"Samtools idxstats\"];\n  34 -->|bam_output| 49;\n  50[\"Samtools idxstats\"];\n  36 -->|bam_output| 50;\n  51[\"Samtools idxstats\"];\n  38 -->|bam_output| 51;\n  52[\"bamCompare\"];\n  38 -->|bam_output| 52;\n  34 -->|bam_output| 52;\n  53[\"Samtools idxstats\"];\n  40 -->|bam_output| 53;\n  54[\"multiBamSummary\"];\n  26 -->|bam_output| 54;\n  28 -->|bam_output| 54;\n  30 -->|bam_output| 54;\n  32 -->|bam_output| 54;\n  34 -->|bam_output| 54;\n  36 -->|bam_output| 54;\n  38 -->|bam_output| 54;\n  40 -->|bam_output| 54;\n  55[\"plotFingerprint\"];\n  34 -->|bam_output| 55;\n  36 -->|bam_output| 55;\n  38 -->|bam_output| 55;\n  40 -->|bam_output| 55;\n  56[\"MACS2 callpeak\"];\n  34 -->|bam_output| 56;\n  36 -->|bam_output| 56;\n  38 -->|bam_output| 56;\n  40 -->|bam_output| 56;\n  57[\"bamCompare\"];\n  40 -->|bam_output| 57;\n  36 -->|bam_output| 57;\n  58[\"computeMatrix\"];\n  44 -->|outFileName| 58;\n  48 -->|outFileName| 58;\n  47 -->|output_narrowpeaks| 58;\n  59[\"plotCorrelation\"];\n  54 -->|outFile| 59;\n  60[\"bedtools Intersect intervals\"];\n  47 -->|output_narrowpeaks| 60;\n  56 -->|output_narrowpeaks| 60;\n  0d2260b8-138a-4ca9-9fb2-2ba391f7517a[\"Output\\noutput_overlapping_peaks\"];\n  60 --> 0d2260b8-138a-4ca9-9fb2-2ba391f7517a;\n  style 0d2260b8-138a-4ca9-9fb2-2ba391f7517a stroke:#2c3143,stroke-width:4px;\n  61[\"bedtools Intersect intervals\"];\n  47 -->|output_narrowpeaks| 61;\n  56 -->|output_narrowpeaks| 61;\n  2cd86f4c-a1f4-42a8-9bbd-82ef8f156dac[\"Output\\noutput_g1e_peaks\"];\n  61 --> 2cd86f4c-a1f4-42a8-9bbd-82ef8f156dac;\n  style 2cd86f4c-a1f4-42a8-9bbd-82ef8f156dac stroke:#2c3143,stroke-width:4px;\n  62[\"bedtools Intersect intervals\"];\n  56 -->|output_narrowpeaks| 62;\n  47 -->|output_narrowpeaks| 62;\n  f8a16be5-f7ae-4fec-b67b-91c4532a43d2[\"Output\\noutput_megakaryocyte_peaks\"];\n  62 --> f8a16be5-f7ae-4fec-b67b-91c4532a43d2;\n  style f8a16be5-f7ae-4fec-b67b-91c4532a43d2 stroke:#2c3143,stroke-width:4px;\n  63[\"computeMatrix\"];\n  52 -->|outFileName| 63;\n  57 -->|outFileName| 63;\n  56 -->|output_narrowpeaks| 63;\n  64[\"plotHeatmap\"];\n  58 -->|outFileName| 64;\n  65[\"plotHeatmap\"];\n  63 -->|outFileName| 65;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0",
-                        "errors": null,
-                        "id": 60,
-                        "input_connections": {
-                            "inputA": {
-                                "id": 47,
-                                "output_name": "output_narrowpeaks"
-                            },
-                            "reduce_or_iterate|inputB": {
-                                "id": 56,
-                                "output_name": "output_narrowpeaks"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "bedtools Intersect intervals",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 890,
-                            "top": 130
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b28e0cfa7ba1",
-                            "name": "bedtools",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"bed\", \"bed\": \"false\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len\", \"count\": \"false\", \"fraction_cond\": {\"fraction_select\": \"default\", \"__current_case__\": 0}, \"header\": \"false\", \"inputA\": null, \"invert\": \"false\", \"once\": \"false\", \"overlap_mode\": null, \"reduce_or_iterate\": {\"reduce_or_iterate_selector\": \"iterate\", \"__current_case__\": 0, \"inputB\": null}, \"sorted\": \"false\", \"split\": \"false\", \"strand\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.29.0",
-                        "type": "tool",
-                        "uuid": "34bf938f-c70a-4bca-b5ca-cf4ea480bc90",
-                        "workflow_outputs": [
-                            {
-                                "label": "output_overlapping_peaks",
-                                "output_name": "output",
-                                "uuid": "0d2260b8-138a-4ca9-9fb2-2ba391f7517a"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0",
-                        "errors": null,
-                        "id": 61,
-                        "input_connections": {
-                            "inputA": {
-                                "id": 47,
-                                "output_name": "output_narrowpeaks"
-                            },
-                            "reduce_or_iterate|inputB": {
-                                "id": 56,
-                                "output_name": "output_narrowpeaks"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "bedtools Intersect intervals",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 890,
-                            "top": 250
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b28e0cfa7ba1",
-                            "name": "bedtools",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"bed\", \"bed\": \"false\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len\", \"count\": \"false\", \"fraction_cond\": {\"fraction_select\": \"default\", \"__current_case__\": 0}, \"header\": \"false\", \"inputA\": null, \"invert\": \"true\", \"once\": \"false\", \"overlap_mode\": null, \"reduce_or_iterate\": {\"reduce_or_iterate_selector\": \"iterate\", \"__current_case__\": 0, \"inputB\": null}, \"sorted\": \"false\", \"split\": \"false\", \"strand\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.29.0",
-                        "type": "tool",
-                        "uuid": "52bfc6e7-7515-41c3-9d4d-c13a2f754cc6",
-                        "workflow_outputs": [
-                            {
-                                "label": "output_g1e_peaks",
-                                "output_name": "output",
-                                "uuid": "2cd86f4c-a1f4-42a8-9bbd-82ef8f156dac"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0",
-                        "errors": null,
-                        "id": 62,
-                        "input_connections": {
-                            "inputA": {
-                                "id": 56,
-                                "output_name": "output_narrowpeaks"
-                            },
-                            "reduce_or_iterate|inputB": {
-                                "id": 47,
-                                "output_name": "output_narrowpeaks"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "bedtools Intersect intervals",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 890,
-                            "top": 370
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b28e0cfa7ba1",
-                            "name": "bedtools",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"bed\", \"bed\": \"false\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/mm10.len\", \"count\": \"false\", \"fraction_cond\": {\"fraction_select\": \"default\", \"__current_case__\": 0}, \"header\": \"false\", \"inputA\": null, \"invert\": \"true\", \"once\": \"false\", \"overlap_mode\": null, \"reduce_or_iterate\": {\"reduce_or_iterate_selector\": \"iterate\", \"__current_case__\": 0, \"inputB\": null}, \"sorted\": \"false\", \"split\": \"false\", \"strand\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.29.0",
-                        "type": "tool",
-                        "uuid": "39089148-e7ee-4b44-8b55-973fb6864d57",
-                        "workflow_outputs": [
-                            {
-                                "label": "output_megakaryocyte_peaks",
-                                "output_name": "output",
-                                "uuid": "f8a16be5-f7ae-4fec-b67b-91c4532a43d2"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "epigenetics/tal1-binding-site-identification",
-                "path": "topics/epigenetics/tutorials/tal1-binding-site-identification/workflows/tal1-binding-site-identification-workflow.ga",
-                "tags": [
-                    "epigenetics"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)",
-                "topic_id": "epigenetics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/epigenetics-tal1-binding-site-identification/versions/tal1-binding-site-identification-workflow",
-                "tutorial_id": "tal1-binding-site-identification",
-                "url": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/tal1-binding-site-identification/workflows/tal1-binding-site-identification-workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/tal1-binding-site-identification/workflows/tal1-binding-site-identification-workflow.html",
-                "version": 1,
-                "wfid": "epigenetics-tal1-binding-site-identification",
-                "wfname": "tal1-binding-site-identification-workflow",
-                "workflow": "tal1-binding-site-identification-workflow.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.3.2.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.3.2.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.3.2.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6",
-                    "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0"
-                ],
-                "workflowhub_id": "1175"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.197100"
-    },
     {
         "admin_install": {
             "install_repository_dependencies": true,
@@ -78906,19 +81973,21 @@
         "dir": "topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification",
         "draft": true,
         "edam_operation": [
-            "Sequencing quality control",
-            "Primer removal",
             "Peak calling",
-            "Enrichment analysis",
+            "Sequence trimming",
             "Read mapping",
+            "Sequencing quality control",
             "Sequence composition calculation",
-            "Read pre-processing",
+            "Statistical calculation",
             "Gene regulatory network analysis",
-            "Sequence trimming",
-            "Statistical calculation"
+            "Read pre-processing",
+            "Primer removal",
+            "Enrichment analysis"
         ],
         "edam_topic": [],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "UseGalaxy.be"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
@@ -78950,7 +82019,7 @@
             "Extract coverage files",
             "Call enriched regions or peaks"
         ],
-        "pageviews": 2364,
+        "pageviews": 2415,
         "pub_date": "2017-09-18",
         "questions": [
             "How is raw ChIP-seq data processed and analyzed?",
@@ -78964,24 +82033,30 @@
         "short_id": "T00138",
         "short_tools": [
             "deeptools_plot_correlation",
-            "deeptools_multi_bam_summary",
-            "bowtie2",
-            "deeptools_bam_coverage",
+            "deeptools_plot_fingerprint",
             "deeptools_bam_compare",
-            "deeptools_compute_matrix",
-            "deeptools_plot_heatmap",
             "bam_to_sam",
             "fastqc",
+            "deeptools_compute_gc_bias",
+            "deeptools_plot_heatmap",
+            "deeptools_multi_bam_summary",
             "samtools_idxstats",
-            "deeptools_plot_fingerprint",
             "macs2_callpeak",
-            "deeptools_compute_gc_bias",
+            "deeptools_bam_coverage",
+            "deeptools_compute_matrix",
+            "bowtie2",
             "trim_galore"
         ],
         "slides": false,
         "slides_recordings": false,
         "supported_servers": {
-            "exact": [],
+            "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                }
+            ],
             "inexact": [
                 {
                     "name": "Galaxy@AuBi",
@@ -79058,7 +82133,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 168,
-        "visitors": 1526,
+        "visitors": 1566,
         "workflows": [
             {
                 "creators": [],
@@ -79338,7 +82413,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"IdxStats\"];\n  0 -->|output| 9;\n  10[\"bamCoverage\"];\n  0 -->|output| 10;\n  11[\"bamCoverage\"];\n  0 -->|output| 11;\n  12[\"plotFingerprint\"];\n  4 -->|output| 12;\n  0 -->|output| 12;\n  13[\"computeGCBias\"];\n  4 -->|output| 13;\n  14[\"IdxStats\"];\n  4 -->|output| 14;\n  15[\"bamCoverage\"];\n  4 -->|output| 15;\n  16[\"bamCoverage\"];\n  4 -->|output| 16;\n  17[\"bamCompare\"];\n  0 -->|output| 17;\n  4 -->|output| 17;\n  18[\"bamCompare\"];\n  0 -->|output| 18;\n  4 -->|output| 18;\n  19[\"MACS2 callpeak\"];\n  4 -->|output| 19;\n  0 -->|output| 19;\n  20[\"multiBamSummary\"];\n  7 -->|output| 20;\n  6 -->|output| 20;\n  5 -->|output| 20;\n  4 -->|output| 20;\n  3 -->|output| 20;\n  2 -->|output| 20;\n  1 -->|output| 20;\n  0 -->|output| 20;\n  21[\"computeMatrix\"];\n  18 -->|outFileName| 21;\n  8 -->|output| 21;\n  22[\"computeMatrix\"];\n  18 -->|outFileName| 22;\n  8 -->|output| 22;\n  23[\"plotCorrelation\"];\n  20 -->|outFile| 23;\n  24[\"plotHeatmap\"];\n  21 -->|outFileName| 24;\n  25[\"plotHeatmap\"];\n  22 -->|outFileName| 25;",
-                "modified": "2024-08-18 00:06:22 +0000",
+                "modified": "2024-10-02 12:08:07 +0000",
                 "name": "Identification Of The Binding Sites Of The Estrogen Receptor - Chip Seq",
                 "outputs": [],
                 "parent_id": "epigenetics/estrogen-receptor-binding-site-identification",
@@ -79442,7 +82517,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"FastQC\"];\n  0 -->|output| 1;\n  2[\"Trim Galore!\"];\n  0 -->|output| 2;\n  3[\"Bowtie2\"];\n  2 -->|trimmed_reads_single| 3;\n  4[\"BAM-to-SAM\"];\n  3 -->|output| 4;",
-                "modified": "2024-08-18 00:06:22 +0000",
+                "modified": "2024-10-02 12:08:07 +0000",
                 "name": "Identification Of The Binding Sites Of The Estrogen Receptor - Qc Mapping",
                 "outputs": [],
                 "parent_id": "epigenetics/estrogen-receptor-binding-site-identification",
@@ -79481,49 +82556,43 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/introduction-dna-methylation/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/introduction-chip-seq/tutorial.json",
         "contributors": [
-            {
-                "elixir_node": "de",
-                "email": "wolffj@informatik.uni-freiburg.de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "joachimwolff",
-                "joined": "2017-09",
-                "name": "Joachim Wolff",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/joachimwolff.json"
-            },
             {
                 "affiliations": [
-                    "pndb",
                     "gallantries",
-                    "fairease",
-                    "fnso2019",
+                    "ifb",
                     "elixir-europe"
                 ],
+                "contact_for_training": true,
                 "elixir_node": "fr",
-                "email": "yvan.le-bras@mnhn.fr",
-                "id": "yvanlebras",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
                 "joined": "2017-09",
-                "matrix": "yvanlebras:matrix.org",
-                "name": "Yvan Le Bras",
-                "orcid": "0000-0002-8504-068X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
-                "twitter": "Yvan2935",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             }
         ],
-        "dir": "topics/epigenetics/tutorials/introduction-dna-methylation",
+        "dir": "topics/epigenetics/tutorials/introduction-chip-seq",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": false,
-        "id": "epigenetics/introduction-dna-methylation",
+        "id": "epigenetics/introduction-chip-seq",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -79538,15 +82607,15 @@
         "license": "CC-BY-4.0",
         "logo": "GTN",
         "mod_date": "2024-03-05",
-        "pageviews": 5726883,
+        "pageviews": 5897165,
         "priority": 1,
-        "pub_date": "2016-10-05",
+        "pub_date": "2017-06-12",
         "redirect_from": [
-            "/topics/epigenetics/slides/introduction-dna-methylation",
-            "/short/epigenetics/introduction-dna-methylation/slides",
-            "/short/S00060"
+            "/topics/epigenetics/slides/introduction-chip-seq",
+            "/short/epigenetics/introduction-chip-seq/slides",
+            "/short/S00059"
         ],
-        "short_id": "S00060",
+        "short_id": "S00059",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
@@ -79584,7 +82653,7 @@
             ]
         },
         "symlink": null,
-        "title": "Introduction to DNA Methylation data analysis",
+        "title": "Introduction to ChIP-Seq data analysis",
         "tools": [],
         "topic_name": "epigenetics",
         "topic_name_human": "Epigenetics",
@@ -79594,19 +82663,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "introduction-dna-methylation",
+        "tutorial_name": "introduction-chip-seq",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/epigenetics/tutorials/introduction-dna-methylation/slides.html",
+        "url": "https://training.galaxyproject.org//topics/epigenetics/tutorials/introduction-chip-seq/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/introduction-dna-methylation/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/introduction-dna-methylation/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/introduction-chip-seq/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/introduction-chip-seq/slides.json"
         },
         "version": 2,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2063758
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -79616,43 +82685,49 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/introduction-chip-seq/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/introduction-dna-methylation/tutorial.json",
         "contributors": [
+            {
+                "elixir_node": "de",
+                "email": "wolffj@informatik.uni-freiburg.de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "joachimwolff",
+                "joined": "2017-09",
+                "name": "Joachim Wolff",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/joachimwolff.json"
+            },
             {
                 "affiliations": [
+                    "pndb",
                     "gallantries",
-                    "ifb",
+                    "fairease",
+                    "fnso2019",
                     "elixir-europe"
                 ],
-                "contact_for_training": true,
                 "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
+                "email": "yvan.le-bras@mnhn.fr",
+                "id": "yvanlebras",
                 "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+                "matrix": "yvanlebras:matrix.org",
+                "name": "Yvan Le Bras",
+                "orcid": "0000-0002-8504-068X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/",
+                "twitter": "Yvan2935",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/yvanlebras.json"
             }
         ],
-        "dir": "topics/epigenetics/tutorials/introduction-chip-seq",
+        "dir": "topics/epigenetics/tutorials/introduction-dna-methylation",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": false,
-        "id": "epigenetics/introduction-chip-seq",
+        "id": "epigenetics/introduction-dna-methylation",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -79667,15 +82742,15 @@
         "license": "CC-BY-4.0",
         "logo": "GTN",
         "mod_date": "2024-03-05",
-        "pageviews": 5726883,
+        "pageviews": 5897165,
         "priority": 1,
-        "pub_date": "2017-06-12",
+        "pub_date": "2016-10-05",
         "redirect_from": [
-            "/topics/epigenetics/slides/introduction-chip-seq",
-            "/short/epigenetics/introduction-chip-seq/slides",
-            "/short/S00059"
+            "/topics/epigenetics/slides/introduction-dna-methylation",
+            "/short/epigenetics/introduction-dna-methylation/slides",
+            "/short/S00060"
         ],
-        "short_id": "S00059",
+        "short_id": "S00060",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
@@ -79713,7 +82788,7 @@
             ]
         },
         "symlink": null,
-        "title": "Introduction to ChIP-Seq data analysis",
+        "title": "Introduction to DNA Methylation data analysis",
         "tools": [],
         "topic_name": "epigenetics",
         "topic_name_human": "Epigenetics",
@@ -79723,19 +82798,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "introduction-chip-seq",
+        "tutorial_name": "introduction-dna-methylation",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/epigenetics/tutorials/introduction-chip-seq/slides.html",
+        "url": "https://training.galaxyproject.org//topics/epigenetics/tutorials/introduction-dna-methylation/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/introduction-chip-seq/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/introduction-chip-seq/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/introduction-dna-methylation/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/epigenetics/tutorials/introduction-dna-methylation/slides.json"
         },
         "version": 2,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2063758
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -79829,14 +82904,14 @@
         ],
         "dir": "topics/evolution/tutorials/abc_intro_phylo",
         "edam_operation": [
+            "Phylogenetic tree analysis",
+            "Phylogenetic tree generation",
             "Multiple sequence alignment",
+            "Phylogenetic analysis",
             "Phylogenetic tree generation (from molecular sequences)",
-            "Phylogenetic tree generation",
+            "Phylogenetic tree reconstruction",
             "Sequence analysis",
-            "Phylogenetic analysis",
-            "Phylogenetic tree generation (maximum likelihood and Bayesian methods)",
-            "Phylogenetic tree analysis",
-            "Phylogenetic tree reconstruction"
+            "Phylogenetic tree generation (maximum likelihood and Bayesian methods)"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -79850,6 +82925,7 @@
         "id": "evolution/abc_intro_phylo",
         "inexact_supported_servers": [
             "GalaxyTrakr",
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.no"
         ],
@@ -79870,7 +82946,7 @@
             "Assess the reliability of estimated phylogenies with bootstrapping",
             "Explore phylogenetic signal using phylogenetic networks"
         ],
-        "pageviews": 967,
+        "pageviews": 1370,
         "priority": 0,
         "pub_date": "2024-05-10",
         "questions": [
@@ -79881,10 +82957,10 @@
         ],
         "short_id": "T00440",
         "short_tools": [
-            "fasttree",
-            "newick_display",
             "rbc_mafft",
-            "iqtree"
+            "iqtree",
+            "newick_display",
+            "fasttree"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -79913,6 +82989,11 @@
                     "url": "https://galaxytrakr.org/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -79957,8 +83038,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 142,
-        "visitors": 701,
+        "visit_duration": 128,
+        "visitors": 1020,
         "workflows": [
             {
                 "creators": [
@@ -80035,7 +83116,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput FASTA Sequence File\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"MAFFT\"];\n  0 -->|output| 1;\n  e5d56101-daff-420b-82e9-dc6cc923f7ab[\"Output\\noutputAlignment\"];\n  1 --> e5d56101-daff-420b-82e9-dc6cc923f7ab;\n  style e5d56101-daff-420b-82e9-dc6cc923f7ab stroke:#2c3143,stroke-width:4px;\n  2[\"FASTTREE\"];\n  1 -->|outputAlignment| 2;\n  632ce28d-3086-490e-bd97-949eb2cb385a[\"Output\\noutput\"];\n  2 --> 632ce28d-3086-490e-bd97-949eb2cb385a;\n  style 632ce28d-3086-490e-bd97-949eb2cb385a stroke:#2c3143,stroke-width:4px;\n  3[\"IQ-TREE\"];\n  1 -->|outputAlignment| 3;\n  b8434b2b-2001-4b1a-bd06-faeab18519a4[\"Output\\ntreefile\"];\n  3 --> b8434b2b-2001-4b1a-bd06-faeab18519a4;\n  style b8434b2b-2001-4b1a-bd06-faeab18519a4 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
+                "modified": "2024-10-02 12:08:08 +0000",
                 "name": "Tree Building (imported from uploaded file)",
                 "outputs": [
                     {
@@ -80235,6 +83316,404 @@
         ],
         "zenodo_link": "https://zenodo.org/records/11089653"
     },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "raxml",
+                    "owner": "iuc",
+                    "revisions": "ea30d3089354",
+                    "tool_panel_section_label": "Phylogenetics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "raxml",
+                    "owner": "iuc",
+                    "revisions": "73a469f7dc96",
+                    "tool_panel_section_label": "Phylogenetics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: raxml\n  owner: iuc\n  revisions: ea30d3089354\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: raxml\n  owner: iuc\n  revisions: 73a469f7dc96\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/evolution/tutorials/mtb_phylogeny/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "cstritt",
+                "dbrites",
+                "GaloGS"
+            ],
+            "editing": [
+                "wm75"
+            ]
+        },
+        "contributors": [
+            {
+                "id": "cstritt",
+                "joined": "2022-03",
+                "name": "Christoph Stritt",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cstritt/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/cstritt.json"
+            },
+            {
+                "id": "dbrites",
+                "joined": "2022-03",
+                "name": "Daniela Brites",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dbrites/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/dbrites.json"
+            },
+            {
+                "id": "GaloGS",
+                "joined": "2022-03",
+                "name": "Galo A. Goig",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/GaloGS/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/GaloGS.json"
+            },
+            {
+                "affiliations": [
+                    "by-covid",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "elixir_node": "de",
+                "fediverse": "https://scholar.social/@zerodivision",
+                "fediverse_flavor": "mastodon",
+                "id": "wm75",
+                "joined": "2017-09",
+                "matrix": "wm75:matrix.org",
+                "name": "Wolfgang Maier",
+                "orcid": "0000-0002-9464-6640",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
+            }
+        ],
+        "dir": "topics/evolution/tutorials/mtb_phylogeny",
+        "edam_ontology": [
+            "topic_0622",
+            "topic_3301",
+            "topic_0084",
+            "topic_3324"
+        ],
+        "edam_operation": [
+            "Phylogenetic tree analysis",
+            "Sequence analysis"
+        ],
+        "edam_topic": [
+            "Genomics",
+            "Microbiology",
+            "Phylogeny",
+            "Infectious disease"
+        ],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "evolution/mtb_phylogeny",
+        "inexact_supported_servers": [
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "layout": "tutorial_hands_on",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-03-12",
+        "objectives": [
+            "Understand the basic concepts behind phylogenetic trees, as applied to *Mycobacterium tuberculosis*",
+            "Be able to read and interrogate a phylogeny encountered in the literature"
+        ],
+        "pageviews": 2071,
+        "pub_date": "2022-03-16",
+        "questions": [
+            "What information can I get from a phylogenetic tree?",
+            "How do I estimate a phylogeny?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "variant-analysis",
+                "tutorials": [
+                    "tb-variant-analysis"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "evolution",
+                "tutorials": [
+                    "mtb_transmission"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00144",
+        "short_tools": [
+            "upload1",
+            "interactive_tool_rstudio",
+            "raxml"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "prokaryote",
+            "one-health",
+            "phylogenetics",
+            "microgalaxy"
+        ],
+        "time_estimation": "1H",
+        "title": "Tree thinking for tuberculosis evolution and epidemiology",
+        "tools": [
+            "interactive_tool_rstudio",
+            "toolshed.g2.bx.psu.edu/repos/iuc/raxml/raxml/8.2.12+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/raxml/raxml/8.2.4+galaxy2",
+            "upload1"
+        ],
+        "topic_name": "evolution",
+        "topic_name_human": "Evolution",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "mtb_phylogeny",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/evolution/tutorials/mtb_phylogeny/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/evolution/tutorials/mtb_phylogeny/tutorial.json"
+        },
+        "version": 11,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 134,
+        "visitors": 1373,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Estimate a phylogenetic tree from whole genome sequencing data for M. tuberculosis",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput alignment\"]\n  1[label=\"RStudio\"]\n  2[label=\"Estimate phylogeny with RAxML\"]\n  0 -> 2 [label=\"output\"]\n  k9f8ae577c5834a2db64d14c25fb859d9[color=lightseagreen,label=\"Output\\nBest-scoring ML Tree\"]\n  2 -> k9f8ae577c5834a2db64d14c25fb859d9\n  kbdb8cf2fb5534a968b5538b4b499ab88[color=lightseagreen,label=\"Output\\nInfo\"]\n  2 -> kbdb8cf2fb5534a968b5538b4b499ab88\n}",
+                "history": [
+                    {
+                        "hash": "afdd9be4b6e36ae6eafd8b9a9a98e215f1546961",
+                        "message": "add tag",
+                        "num": 3,
+                        "short_hash": "afdd9be4b",
+                        "unix": "1647422954"
+                    },
+                    {
+                        "hash": "946859f788400ae6b40df5b7a08a07fd6fe44edf",
+                        "message": "prettyprint workflow",
+                        "num": 2,
+                        "short_hash": "946859f78",
+                        "unix": "1647422932"
+                    },
+                    {
+                        "hash": "2e7ba78522415b81e10f3f5a74144f4f419b218d",
+                        "message": "tweak",
+                        "num": 1,
+                        "short_hash": "2e7ba7852",
+                        "unix": "1647422653"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "Alignment in fasta format, containing variable positions from  variant calling",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Alignment in fasta format, containing variable positions from  variant calling",
+                                "name": "Input alignment"
+                            }
+                        ],
+                        "label": "Input alignment",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 433.31666564941406,
+                            "height": 82.19999694824219,
+                            "left": 392.7166748046875,
+                            "right": 592.7166748046875,
+                            "top": 351.1166687011719,
+                            "width": 200,
+                            "x": 392.7166748046875,
+                            "y": 351.1166687011719
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "94b1ea1c-8a3a-4fb7-9cfe-40a1c1c1833d",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput alignment\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"RStudio\"];\n  2[\"Estimate phylogeny with RAxML\"];\n  0 -->|output| 2;\n  9f8ae577-c583-4a2d-b64d-14c25fb859d9[\"Output\\nBest-scoring ML Tree\"];\n  2 --> 9f8ae577-c583-4a2d-b64d-14c25fb859d9;\n  style 9f8ae577-c583-4a2d-b64d-14c25fb859d9 stroke:#2c3143,stroke-width:4px;\n  bdb8cf2f-b553-4a96-8b55-38b4b499ab88[\"Output\\nInfo\"];\n  2 --> bdb8cf2f-b553-4a96-8b55-38b4b499ab88;\n  style bdb8cf2f-b553-4a96-8b55-38b4b499ab88 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Mtb phylogeny",
+                "outputs": [
+                    {
+                        "annotation": "Maximum likelihood-based inference of a phylogenetic tree",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/raxml/raxml/8.2.4+galaxy2",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "infile": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Phyogenetic reconstruction with RAxML",
+                                "name": "infile"
+                            }
+                        ],
+                        "label": "Estimate phylogeny with RAxML",
+                        "name": "Phyogenetic reconstruction with RAxML",
+                        "outputs": [
+                            {
+                                "name": "info",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "logReq",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "parsimonyTreeReq",
+                                "type": "nhx"
+                            },
+                            {
+                                "name": "resultReq",
+                                "type": "nhx"
+                            },
+                            {
+                                "name": "bestTree",
+                                "type": "nhx"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 629.4500122070312,
+                            "height": 276,
+                            "left": 678.2166748046875,
+                            "right": 878.2166748046875,
+                            "top": 353.45001220703125,
+                            "width": 200,
+                            "x": 678.2166748046875,
+                            "y": 353.45001220703125
+                        },
+                        "post_job_actions": {
+                            "DeleteIntermediatesActioninfo": {
+                                "action_arguments": {},
+                                "action_type": "DeleteIntermediatesAction",
+                                "output_name": "info"
+                            },
+                            "HideDatasetActionlogReq": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "logReq"
+                            },
+                            "HideDatasetActionparsimonyTreeReq": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "parsimonyTreeReq"
+                            },
+                            "HideDatasetActionresultReq": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "resultReq"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/raxml/raxml/8.2.4+galaxy2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "73a469f7dc96",
+                            "name": "raxml",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"infile\": {\"__class__\": \"RuntimeValue\"}, \"random_seed\": \"1234567890\", \"search_model_selector\": {\"model_type\": \"nucleotide\", \"__current_case__\": 0, \"base_model\": \"GTRGAMMA\"}, \"selExtraOpts\": {\"extraOptions\": \"required\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "8.2.4+galaxy2",
+                        "type": "tool",
+                        "uuid": "057bd38a-20c2-4713-ba6f-964f15904b37",
+                        "workflow_outputs": [
+                            {
+                                "label": "Best-scoring ML Tree",
+                                "output_name": "bestTree",
+                                "uuid": "9f8ae577-c583-4a2d-b64d-14c25fb859d9"
+                            },
+                            {
+                                "label": "Info",
+                                "output_name": "info",
+                                "uuid": "bdb8cf2f-b553-4a96-8b55-38b4b499ab88"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "evolution/mtb_phylogeny",
+                "path": "topics/evolution/tutorials/mtb_phylogeny/workflows/main_workflow.ga",
+                "tags": [
+                    "evolution"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Mtb phylogeny",
+                "topic_id": "evolution",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/evolution-mtb_phylogeny/versions/main-workflow",
+                "tutorial_id": "mtb_phylogeny",
+                "url": "https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_phylogeny/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_phylogeny/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "evolution-mtb_phylogeny",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "interactive_tool_rstudio",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/raxml/raxml/8.2.4+galaxy2"
+                ],
+                "workflowhub_id": "1300"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/6010176"
+    },
     {
         "admin_install": {
             "install_repository_dependencies": true,
@@ -80279,7 +83758,7 @@
                 {
                     "name": "bcftools_consensus",
                     "owner": "iuc",
-                    "revisions": "1171446da5db",
+                    "revisions": "da0bf365652d",
                     "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
@@ -80383,7 +83862,7 @@
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_consensus\n  owner: iuc\n  revisions: 1171446da5db\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_consensus\n  owner: iuc\n  revisions: a87ae767b01d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: 0dbf49c414ae\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snippy\n  owner: iuc\n  revisions: c9a8ef2aa380\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snippy\n  owner: iuc\n  revisions: d220115f882b\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snp_dists\n  owner: iuc\n  revisions: 1959cc43b414\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snp_dists\n  owner: iuc\n  revisions: f78492521996\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snp_sites\n  owner: iuc\n  revisions: 5804f786060d\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tb_variant_filter\n  owner: iuc\n  revisions: 3b1e7c170b10\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tb_variant_filter\n  owner: iuc\n  revisions: e7aff4a85df5\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tb_variant_filter\n  owner: iuc\n  revisions: ee4a90760848\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbprofiler\n  owner: iuc\n  revisions: 809dfc93d593\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: add_input_name_as_column\n  owner: mvdbeek\n  revisions: 3284b72eef56\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n  owner: pjbriggs\n  revisions: d94aff5ee623\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_consensus\n  owner: iuc\n  revisions: da0bf365652d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_consensus\n  owner: iuc\n  revisions: a87ae767b01d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: 0dbf49c414ae\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snippy\n  owner: iuc\n  revisions: c9a8ef2aa380\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snippy\n  owner: iuc\n  revisions: d220115f882b\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snp_dists\n  owner: iuc\n  revisions: 1959cc43b414\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snp_dists\n  owner: iuc\n  revisions: f78492521996\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snp_sites\n  owner: iuc\n  revisions: 5804f786060d\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tb_variant_filter\n  owner: iuc\n  revisions: 3b1e7c170b10\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tb_variant_filter\n  owner: iuc\n  revisions: e7aff4a85df5\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tb_variant_filter\n  owner: iuc\n  revisions: ee4a90760848\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbprofiler\n  owner: iuc\n  revisions: 809dfc93d593\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: add_input_name_as_column\n  owner: mvdbeek\n  revisions: 3284b72eef56\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n  owner: pjbriggs\n  revisions: d94aff5ee623\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
         "api": "https://training.galaxyproject.org/training-material/api/topics/evolution/tutorials/mtb_transmission/tutorial.json",
         "contributions": {
             "authorship": [
@@ -80443,10 +83922,10 @@
             "topic_2885"
         ],
         "edam_operation": [
-            "Variant calling",
             "Phylogenetic tree visualisation",
-            "Phylogenetic tree generation",
-            "Antimicrobial resistance prediction"
+            "Variant calling",
+            "Antimicrobial resistance prediction",
+            "Phylogenetic tree generation"
         ],
         "edam_topic": [
             "Genomics",
@@ -80486,7 +83965,7 @@
             "Identify transmission clusters based on SNP distances",
             "Study the emergence and spread of drug resistance based on transmission analysis."
         ],
-        "pageviews": 2414,
+        "pageviews": 2499,
         "pub_date": "2022-03-16",
         "requirements": [
             {
@@ -80506,24 +83985,24 @@
         ],
         "short_id": "T00145",
         "short_tools": [
-            "Grep1",
+            "tp_sed_tool",
+            "tp_easyjoin_tool",
+            "tp_cat",
             "bcftools_consensus",
-            "tb_variant_filter",
-            "upload1",
             "samtools_view",
-            "snp_sites",
-            "tb_profiler_profile",
-            "tp_grep_tool",
-            "tp_cat",
+            "upload1",
             "snippy",
-            "tp_easyjoin_tool",
-            "addName",
-            "tp_sed_tool",
+            "tp_grep_tool",
             "tp_replace_in_line",
             "snp_dists",
+            "Grep1",
+            "tb_variant_filter",
+            "tb_profiler_profile",
             "collapse_dataset",
+            "snp_sites",
+            "trimmomatic",
             "__MERGE_COLLECTION__",
-            "trimmomatic"
+            "addName"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -80605,8 +84084,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 188,
-        "visitors": 1533,
+        "visit_duration": 183,
+        "visitors": 1605,
         "workflows": [
             {
                 "creators": [],
@@ -80702,7 +84181,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nMTB single-end BAMs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nMTB paired-end BAMs\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Merge collections\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"Samtools view BAM > SAM\"];\n  2 -->|output| 3;\n  aa220027-9d10-4328-b2c2-e4d139d5d5bd[\"Output\\nSamtools view on input dataset(s): filtered alignments\"];\n  3 --> aa220027-9d10-4328-b2c2-e4d139d5d5bd;\n  style aa220027-9d10-4328-b2c2-e4d139d5d5bd stroke:#2c3143,stroke-width:4px;\n  4[\"Sed MTB_anc to Chromosome\"];\n  3 -->|outputsam| 4;\n  5[\"Samtools view SAM > BAM\"];\n  4 -->|output| 5;\n  6[\"TB-profiler\"];\n  5 -->|outputsam| 6;\n  7[\"Get drug resistance profile\"];\n  6 -->|output_txt| 7;\n  8[\"Add Sample Name\"];\n  7 -->|output| 8;\n  9[\"Concatenate DR profiles in a single table\"];\n  8 -->|output| 9;\n  10[\"Cleanup the table\"];\n  9 -->|out_file1| 10;",
-                "modified": "2024-08-18 00:06:23 +0000",
+                "modified": "2024-10-02 12:08:08 +0000",
                 "name": "From BAMs to drug resistance prediction with TB-profiler",
                 "outputs": [
                     {
@@ -81337,7 +84816,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nSingle-End FASTQs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nPaired-End FASTQs\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nMycobacterium_tuberculosis_ancestral_reference.gbk\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Trimmomatic\"];\n  0 -->|output| 3;\n  4[\"Trimmomatic\"];\n  1 -->|output| 4;\n  5[\"Mapping and variant calling of SINGLE END FASTQs with snippy\"];\n  3 -->|fastq_out| 5;\n  2 -->|output| 5;\n  6[\"Mapping and variant calling of PAIRED END FASTQs with snippy\"];\n  4 -->|fastq_out_paired| 6;\n  2 -->|output| 6;\n  7[\"Merge PE/SE VCFs in a single collection with all samples\"];\n  5 -->|snpvcf| 7;\n  6 -->|snpvcf| 7;\n  8[\"Merge PE/SE BAMs in a single collection with all samples Part the workflow \u201dIdentifying DR with TB-profiler\"];\n  5 -->|snpsbam| 8;\n  6 -->|snpsbam| 8;\n  9[\"TB Variant Filter\"];\n  7 -->|output| 9;",
-                "modified": "2024-08-18 00:06:23 +0000",
+                "modified": "2024-10-02 12:08:08 +0000",
                 "name": "From Fastqs to VCFs and BAMs",
                 "outputs": [
                     {
@@ -81817,7 +85296,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nCollection of VCFs to analyze\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference genome of the MTBC ancestor\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Filter TB variants\"];\n  0 -->|output| 2;\n  3[\"Generate the complete genome of each of the samples\"];\n  2 -->|output1| 3;\n  1 -->|output| 3;\n  ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a[\"Output\\n#{input_file}\"];\n  3 --> ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a;\n  style ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a stroke:#2c3143,stroke-width:4px;\n  4[\"Concatenate genomes to build a MSA\"];\n  3 -->|output_file| 4;\n  5[\"Keep only variable positions\"];\n  4 -->|out_file1| 5;\n  6[\"Calculate SNP distances\"];\n  5 -->|output_fasta| 6;",
-                "modified": "2024-08-18 00:06:23 +0000",
+                "modified": "2024-10-02 12:08:08 +0000",
                 "name": "From VCFs to SNP distance matrix",
                 "outputs": [
                     {
@@ -82148,404 +85627,6 @@
         ],
         "zenodo_link": "https://zenodo.org/record/6010176"
     },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "raxml",
-                    "owner": "iuc",
-                    "revisions": "ea30d3089354",
-                    "tool_panel_section_label": "Phylogenetics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "raxml",
-                    "owner": "iuc",
-                    "revisions": "73a469f7dc96",
-                    "tool_panel_section_label": "Phylogenetics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: raxml\n  owner: iuc\n  revisions: ea30d3089354\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: raxml\n  owner: iuc\n  revisions: 73a469f7dc96\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/evolution/tutorials/mtb_phylogeny/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "cstritt",
-                "dbrites",
-                "GaloGS"
-            ],
-            "editing": [
-                "wm75"
-            ]
-        },
-        "contributors": [
-            {
-                "id": "cstritt",
-                "joined": "2022-03",
-                "name": "Christoph Stritt",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cstritt/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/cstritt.json"
-            },
-            {
-                "id": "dbrites",
-                "joined": "2022-03",
-                "name": "Daniela Brites",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dbrites/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/dbrites.json"
-            },
-            {
-                "id": "GaloGS",
-                "joined": "2022-03",
-                "name": "Galo A. Goig",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/GaloGS/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/GaloGS.json"
-            },
-            {
-                "affiliations": [
-                    "by-covid",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "fediverse": "https://scholar.social/@zerodivision",
-                "fediverse_flavor": "mastodon",
-                "id": "wm75",
-                "joined": "2017-09",
-                "matrix": "wm75:matrix.org",
-                "name": "Wolfgang Maier",
-                "orcid": "0000-0002-9464-6640",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
-            }
-        ],
-        "dir": "topics/evolution/tutorials/mtb_phylogeny",
-        "edam_ontology": [
-            "topic_0622",
-            "topic_3301",
-            "topic_0084",
-            "topic_3324"
-        ],
-        "edam_operation": [
-            "Sequence analysis",
-            "Phylogenetic tree analysis"
-        ],
-        "edam_topic": [
-            "Genomics",
-            "Microbiology",
-            "Phylogeny",
-            "Infectious disease"
-        ],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "evolution/mtb_phylogeny",
-        "inexact_supported_servers": [
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "layout": "tutorial_hands_on",
-        "level": "Introductory",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-03-12",
-        "objectives": [
-            "Understand the basic concepts behind phylogenetic trees, as applied to *Mycobacterium tuberculosis*",
-            "Be able to read and interrogate a phylogeny encountered in the literature"
-        ],
-        "pageviews": 1983,
-        "pub_date": "2022-03-16",
-        "questions": [
-            "What information can I get from a phylogenetic tree?",
-            "How do I estimate a phylogeny?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "variant-analysis",
-                "tutorials": [
-                    "tb-variant-analysis"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "evolution",
-                "tutorials": [
-                    "mtb_transmission"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00144",
-        "short_tools": [
-            "interactive_tool_rstudio",
-            "upload1",
-            "raxml"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "prokaryote",
-            "one-health",
-            "phylogenetics",
-            "microgalaxy"
-        ],
-        "time_estimation": "1H",
-        "title": "Tree thinking for tuberculosis evolution and epidemiology",
-        "tools": [
-            "interactive_tool_rstudio",
-            "toolshed.g2.bx.psu.edu/repos/iuc/raxml/raxml/8.2.12+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/raxml/raxml/8.2.4+galaxy2",
-            "upload1"
-        ],
-        "topic_name": "evolution",
-        "topic_name_human": "Evolution",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "mtb_phylogeny",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/evolution/tutorials/mtb_phylogeny/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/evolution/tutorials/mtb_phylogeny/tutorial.json"
-        },
-        "version": 11,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 131,
-        "visitors": 1308,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Estimate a phylogenetic tree from whole genome sequencing data for M. tuberculosis",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput alignment\"]\n  1[label=\"RStudio\"]\n  2[label=\"Estimate phylogeny with RAxML\"]\n  0 -> 2 [label=\"output\"]\n  k9f8ae577c5834a2db64d14c25fb859d9[color=lightseagreen,label=\"Output\\nBest-scoring ML Tree\"]\n  2 -> k9f8ae577c5834a2db64d14c25fb859d9\n  kbdb8cf2fb5534a968b5538b4b499ab88[color=lightseagreen,label=\"Output\\nInfo\"]\n  2 -> kbdb8cf2fb5534a968b5538b4b499ab88\n}",
-                "history": [
-                    {
-                        "hash": "afdd9be4b6e36ae6eafd8b9a9a98e215f1546961",
-                        "message": "add tag",
-                        "num": 3,
-                        "short_hash": "afdd9be4b",
-                        "unix": "1647422954"
-                    },
-                    {
-                        "hash": "946859f788400ae6b40df5b7a08a07fd6fe44edf",
-                        "message": "prettyprint workflow",
-                        "num": 2,
-                        "short_hash": "946859f78",
-                        "unix": "1647422932"
-                    },
-                    {
-                        "hash": "2e7ba78522415b81e10f3f5a74144f4f419b218d",
-                        "message": "tweak",
-                        "num": 1,
-                        "short_hash": "2e7ba7852",
-                        "unix": "1647422653"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "Alignment in fasta format, containing variable positions from  variant calling",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Alignment in fasta format, containing variable positions from  variant calling",
-                                "name": "Input alignment"
-                            }
-                        ],
-                        "label": "Input alignment",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 433.31666564941406,
-                            "height": 82.19999694824219,
-                            "left": 392.7166748046875,
-                            "right": 592.7166748046875,
-                            "top": 351.1166687011719,
-                            "width": 200,
-                            "x": 392.7166748046875,
-                            "y": 351.1166687011719
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "94b1ea1c-8a3a-4fb7-9cfe-40a1c1c1833d",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput alignment\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"RStudio\"];\n  2[\"Estimate phylogeny with RAxML\"];\n  0 -->|output| 2;\n  9f8ae577-c583-4a2d-b64d-14c25fb859d9[\"Output\\nBest-scoring ML Tree\"];\n  2 --> 9f8ae577-c583-4a2d-b64d-14c25fb859d9;\n  style 9f8ae577-c583-4a2d-b64d-14c25fb859d9 stroke:#2c3143,stroke-width:4px;\n  bdb8cf2f-b553-4a96-8b55-38b4b499ab88[\"Output\\nInfo\"];\n  2 --> bdb8cf2f-b553-4a96-8b55-38b4b499ab88;\n  style bdb8cf2f-b553-4a96-8b55-38b4b499ab88 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Mtb phylogeny",
-                "outputs": [
-                    {
-                        "annotation": "Maximum likelihood-based inference of a phylogenetic tree",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/raxml/raxml/8.2.4+galaxy2",
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "infile": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Phyogenetic reconstruction with RAxML",
-                                "name": "infile"
-                            }
-                        ],
-                        "label": "Estimate phylogeny with RAxML",
-                        "name": "Phyogenetic reconstruction with RAxML",
-                        "outputs": [
-                            {
-                                "name": "info",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "logReq",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "parsimonyTreeReq",
-                                "type": "nhx"
-                            },
-                            {
-                                "name": "resultReq",
-                                "type": "nhx"
-                            },
-                            {
-                                "name": "bestTree",
-                                "type": "nhx"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 629.4500122070312,
-                            "height": 276,
-                            "left": 678.2166748046875,
-                            "right": 878.2166748046875,
-                            "top": 353.45001220703125,
-                            "width": 200,
-                            "x": 678.2166748046875,
-                            "y": 353.45001220703125
-                        },
-                        "post_job_actions": {
-                            "DeleteIntermediatesActioninfo": {
-                                "action_arguments": {},
-                                "action_type": "DeleteIntermediatesAction",
-                                "output_name": "info"
-                            },
-                            "HideDatasetActionlogReq": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "logReq"
-                            },
-                            "HideDatasetActionparsimonyTreeReq": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "parsimonyTreeReq"
-                            },
-                            "HideDatasetActionresultReq": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "resultReq"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/raxml/raxml/8.2.4+galaxy2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "73a469f7dc96",
-                            "name": "raxml",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"infile\": {\"__class__\": \"RuntimeValue\"}, \"random_seed\": \"1234567890\", \"search_model_selector\": {\"model_type\": \"nucleotide\", \"__current_case__\": 0, \"base_model\": \"GTRGAMMA\"}, \"selExtraOpts\": {\"extraOptions\": \"required\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "8.2.4+galaxy2",
-                        "type": "tool",
-                        "uuid": "057bd38a-20c2-4713-ba6f-964f15904b37",
-                        "workflow_outputs": [
-                            {
-                                "label": "Best-scoring ML Tree",
-                                "output_name": "bestTree",
-                                "uuid": "9f8ae577-c583-4a2d-b64d-14c25fb859d9"
-                            },
-                            {
-                                "label": "Info",
-                                "output_name": "info",
-                                "uuid": "bdb8cf2f-b553-4a96-8b55-38b4b499ab88"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "evolution/mtb_phylogeny",
-                "path": "topics/evolution/tutorials/mtb_phylogeny/workflows/main_workflow.ga",
-                "tags": [
-                    "evolution"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Mtb phylogeny",
-                "topic_id": "evolution",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/evolution-mtb_phylogeny/versions/main-workflow",
-                "tutorial_id": "mtb_phylogeny",
-                "url": "https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_phylogeny/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_phylogeny/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "evolution-mtb_phylogeny",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "interactive_tool_rstudio",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/raxml/raxml/8.2.4+galaxy2"
-                ],
-                "workflowhub_id": "1300"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/6010176"
-    },
     {
         "admin_install": {
             "install_repository_dependencies": true,
@@ -82590,7 +85671,7 @@
         "license": "CC-BY-4.0",
         "logo": "shared/images/biocommons-utas.png",
         "mod_date": "2024-05-10",
-        "pageviews": 348186,
+        "pageviews": 518468,
         "priority": 1,
         "pub_date": "2024-05-10",
         "short_id": "S00116",
@@ -82654,7 +85735,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 153,
-        "visitors": 142604,
+        "visitors": 212297,
         "zenodo_link": ""
     },
     {
@@ -82701,7 +85782,7 @@
         "license": "CC-BY-4.0",
         "logo": "shared/images/biocommons-utas.png",
         "mod_date": "2024-05-10",
-        "pageviews": 348186,
+        "pageviews": 518468,
         "priority": 2,
         "pub_date": "2024-05-10",
         "short_id": "S00120",
@@ -82765,7 +85846,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 153,
-        "visitors": 142604,
+        "visitors": 212297,
         "zenodo_link": ""
     },
     {
@@ -82812,7 +85893,7 @@
         "license": "CC-BY-4.0",
         "logo": "shared/images/biocommons-utas.png",
         "mod_date": "2024-05-10",
-        "pageviews": 348186,
+        "pageviews": 518468,
         "priority": 3,
         "pub_date": "2024-05-10",
         "short_id": "S00118",
@@ -82876,7 +85957,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 153,
-        "visitors": 142604,
+        "visitors": 212297,
         "zenodo_link": ""
     },
     {
@@ -82923,7 +86004,7 @@
         "license": "CC-BY-4.0",
         "logo": "shared/images/biocommons-utas.png",
         "mod_date": "2024-05-10",
-        "pageviews": 348186,
+        "pageviews": 518468,
         "priority": 4,
         "pub_date": "2024-05-10",
         "short_id": "S00121",
@@ -82987,7 +86068,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 153,
-        "visitors": 142604,
+        "visitors": 212297,
         "zenodo_link": ""
     },
     {
@@ -83034,7 +86115,7 @@
         "license": "CC-BY-4.0",
         "logo": "shared/images/biocommons-utas.png",
         "mod_date": "2024-05-10",
-        "pageviews": 348186,
+        "pageviews": 518468,
         "priority": 5,
         "pub_date": "2024-05-10",
         "short_id": "S00117",
@@ -83098,7 +86179,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 153,
-        "visitors": 142604,
+        "visitors": 212297,
         "zenodo_link": ""
     },
     {
@@ -83145,7 +86226,7 @@
         "license": "CC-BY-4.0",
         "logo": "shared/images/biocommons-utas.png",
         "mod_date": "2024-05-10",
-        "pageviews": 348186,
+        "pageviews": 518468,
         "priority": 6,
         "pub_date": "2024-05-10",
         "short_id": "S00119",
@@ -83209,7 +86290,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 153,
-        "visitors": 142604,
+        "visitors": 212297,
         "zenodo_link": ""
     },
     {
@@ -83283,10 +86364,12 @@
         },
         "contributors": [
             {
+                "elixir_node": "uk",
                 "email": "juliajot36@gmail.com",
                 "id": "wee-snufkin",
                 "joined": "2022-06",
                 "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
             },
@@ -83364,21 +86447,31 @@
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-18",
+        "mod_date": "2024-10-02",
         "objectives": [
             "Learn some terminology from the field of medicinal chemistry",
             "Understand the idea of data-driven medicinal chemistry",
             "Explore the databases used for drug discovery and development",
             "Use Galaxy tools for data management, format conversion and simple analyses"
         ],
-        "pageviews": 0,
-        "pub_date": "2024-08-18",
+        "pageviews": 2,
+        "pub_date": "2024-10-02",
         "questions": [
             "Why does medicinal chemistry research produce so much data?",
             "How can big data be useful for medicinal chemists?",
             "What are the current publicly available databases that can be used for drug discovery and development?",
             "How to use Galaxy for data management and analysis of chemical data?"
         ],
+        "recordings": [
+            {
+                "date": "2024-09-12",
+                "length": "48M1S",
+                "speakers": [
+                    "wee-snufkin"
+                ],
+                "youtube_id": "JWV6IiD6mPE"
+            }
+        ],
         "requirements": [
             {
                 "topic_name": "fair",
@@ -83391,13 +86484,13 @@
         ],
         "short_id": "T00429",
         "short_tools": [
-            "ctb_silicos_qed",
-            "md_converter",
-            "get_pdb",
-            "ctb_im_rxn_maker",
             "openbabel_compound_convert",
+            "get_pdb",
+            "openbabel_svg_depiction",
+            "md_converter",
+            "ctb_silicos_qed",
             "chembl",
-            "openbabel_svg_depiction"
+            "ctb_im_rxn_maker"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -83467,10 +86560,10 @@
         },
         "version": 0,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
         "visit_duration": 0,
-        "visitors": 0,
+        "visitors": 1,
         "workflows": [
             {
                 "creators": [
@@ -83547,7 +86640,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nBenzenesulfonyl chloride\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nEthylamine\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Compound conversion\"];\n  0 -->|output| 2;\n  aff8fa4f-c254-4f05-9560-52bad6c7e04a[\"Output\\nBenzenesulfonyl chloride SDF\"];\n  2 --> aff8fa4f-c254-4f05-9560-52bad6c7e04a;\n  style aff8fa4f-c254-4f05-9560-52bad6c7e04a stroke:#2c3143,stroke-width:4px;\n  3[\"Search ChEMBL database\"];\n  0 -->|output| 3;\n  044d2c08-92ed-45c9-9868-ee802998d92c[\"Output\\nSubstructures from ChEMBL database\"];\n  3 --> 044d2c08-92ed-45c9-9868-ee802998d92c;\n  style 044d2c08-92ed-45c9-9868-ee802998d92c stroke:#2c3143,stroke-width:4px;\n  4[\"Search ChEMBL database\"];\n  0 -->|output| 4;\n  99274b60-732d-4276-969f-ccc3673a872a[\"Output\\nLipinski substructures from ChEMBL database\"];\n  4 --> 99274b60-732d-4276-969f-ccc3673a872a;\n  style 99274b60-732d-4276-969f-ccc3673a872a stroke:#2c3143,stroke-width:4px;\n  5[\"Compound conversion\"];\n  1 -->|output| 5;\n  77ad7b99-5761-46a3-b9a6-1dd3d8e2baac[\"Output\\nEthylamine SDF\"];\n  5 --> 77ad7b99-5761-46a3-b9a6-1dd3d8e2baac;\n  style 77ad7b99-5761-46a3-b9a6-1dd3d8e2baac stroke:#2c3143,stroke-width:4px;\n  6[\"Reaction maker\"];\n  2 -->|outfile| 6;\n  5 -->|outfile| 6;\n  f9d1d7fd-e854-469b-a464-6811998e058e[\"Output\\nReaction product\"];\n  6 --> f9d1d7fd-e854-469b-a464-6811998e058e;\n  style f9d1d7fd-e854-469b-a464-6811998e058e stroke:#2c3143,stroke-width:4px;\n  b0bd7ed2-a80b-44ce-994b-999e1d472281[\"Output\\nReaction maker logfile\"];\n  6 --> b0bd7ed2-a80b-44ce-994b-999e1d472281;\n  style b0bd7ed2-a80b-44ce-994b-999e1d472281 stroke:#2c3143,stroke-width:4px;\n  7[\"Visualisation\"];\n  6 -->|outfile| 7;\n  fc618f3f-6aa5-4970-841d-56f4eabf47b7[\"Output\\nVisualisation of reaction product\"];\n  7 --> fc618f3f-6aa5-4970-841d-56f4eabf47b7;\n  style fc618f3f-6aa5-4970-841d-56f4eabf47b7 stroke:#2c3143,stroke-width:4px;\n  8[\"Drug-likeness\"];\n  6 -->|outfile| 8;\n  7ad8c184-e10d-4fce-a402-3e79da6e09ac[\"Output\\nDrug-likeness of product molecule\"];\n  8 --> 7ad8c184-e10d-4fce-a402-3e79da6e09ac;\n  style 7ad8c184-e10d-4fce-a402-3e79da6e09ac stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
+                "modified": "2024-10-02 12:08:06 +0000",
                 "name": "Data management in Medicinal Chemistry workflow",
                 "outputs": [
                     {
@@ -83939,6 +87032,7 @@
     },
     {
         "abbreviations": {
+            "DMP": "Data Management Plan",
             "FAIR": "Findable, Accessible, Interoperable, Reusable"
         },
         "admin_install": {
@@ -83948,20 +87042,30 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-intro/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/data-management-peatlands/tutorial.json",
         "contributions": {
             "authorship": [
+                "GabrielaLopez",
                 "kkamieniecka",
+                "robertmand",
+                "angiolini",
                 "poterlowicz-lab"
             ],
             "editing": [
                 "hexylena"
-            ],
-            "funding": [
-                "elixir-uk-dash"
             ]
         },
         "contributors": [
+            {
+                "elixir_node": "uk",
+                "id": "GabrielaLopez",
+                "joined": "2023-01",
+                "name": "Gabriela Lopez-Gonzalez",
+                "orcid": "0000-0002-0814-8830",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/GabrielaLopez/",
+                "twitter": "GabyBelicosa",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/GabrielaLopez.json"
+            },
             {
                 "affiliations": [
                     "elixir-europe"
@@ -83975,6 +87079,29 @@
                 "twitter": "katemurat",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
             },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "email": "andrewsr9@cardiff.ac.uk",
+                "id": "robertmand",
+                "joined": "2021-10",
+                "name": "Robert Andrews",
+                "orcid": "0000-0002-3491-2361",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/robertmand/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/robertmand.json"
+            },
+            {
+                "elixir_node": "uk",
+                "github": false,
+                "id": "angiolini",
+                "joined": "2024-05",
+                "name": "Emily Angiolini",
+                "orcid": "0000-0002-0814-8830",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/angiolini/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/angiolini.json"
+            },
             {
                 "affiliations": [
                     "elixir-europe"
@@ -84016,29 +87143,16 @@
                 "orcid": "0000-0001-9760-8992",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/dash.png",
-                "funder": true,
-                "funding_id": "MR/V038966/1",
-                "funding_statement": "This Fellowship was funded through the ELIXIR-UK DaSH project as part of the UKRI Innovation Scholars: Data Science Training in Health and Bioscience call (DaSH). (MR/V038966/1). The project aims to embed Research Data Management (RDM) know-how into UK universities and institutes by producing and delivering training in FAIR data stewardship using ELIXIR-UK knowledge and resources.",
-                "funding_system": "ukri",
-                "github": false,
-                "id": "elixir-uk-dash",
-                "joined": "2023-10",
-                "name": "DASH UK",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-uk-dash/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-uk-dash.json"
             }
         ],
-        "dir": "topics/fair/tutorials/fair-intro",
+        "dir": "topics/fair/tutorials/data-management-peatlands",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "fair/fair-intro",
+        "id": "fair/data-management-peatlands",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -84050,181 +87164,43 @@
             "mermaid": false
         },
         "key_points": [
-            "FAIR data are data which meet principles of findability, accessibility, interoperability, and reusability (FAIR).",
-            "FAIR data are as open as possible, and as closed as necessary.",
-            "The main objective of FAIR data is to increase data reuse by researchers."
+            "A Data Management Plan (DMP) is a live document that provides a framework for managing data material during and after the research project.",
+            "FAIR data are data which meet principles of findability, accessibility, interoperability, and reusability (FAIR)."
         ],
         "layout": "tutorial_hands_on",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-04-30",
+        "mod_date": "2024-09-13",
         "objectives": [
-            "Learn the FAIR principles",
-            "Recognise the relationship between FAIR and Open data"
+            "Understand the importance of data management in peatland research.",
+            "Learn how to create a data management plan (DMP) for peatland research",
+            "Create a first draft of a data management plan for peatland research"
         ],
-        "pageviews": 518,
+        "pageviews": 8,
         "priority": 1,
-        "pub_date": "2023-05-30",
+        "pub_date": "2024-09-13",
         "questions": [
-            "What do the FAIR principles stand for [Wilkinson et al. 2016](https://www.nature.com/articles/sdata201618)?",
-            "How to make data FAIR?"
-        ],
-        "short_id": "T00351",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "fair-data",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "fair",
-            "open",
-            "data stewardship"
+            "Why create a DMP for peatland research?",
+            "How to apply FAIR data management solutions for peatland research?"
         ],
-        "time_estimation": "10M",
-        "title": "FAIR in a nutshell",
-        "tools": [],
-        "topic_name": "fair",
-        "topic_name_human": "FAIR Data, Workflows, and Research",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "fair-intro",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/fair/tutorials/fair-intro/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-intro/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-intro/tutorial.json"
-        },
-        "version": 6,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 88,
-        "visitors": 389,
-        "zenodo_link": ""
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-workflow-run-ro-crate/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "simleo"
-            ],
-            "funding": [
-                "by-covid"
-            ]
-        },
-        "contributors": [
+        "recordings": [
             {
-                "affiliations": [
-                    "by-covid",
-                    "elixir-europe"
+                "captioners": [
+                    "kkamieniecka"
                 ],
-                "elixir_node": "it",
-                "id": "simleo",
-                "joined": "2023-04",
-                "name": "Simone Leo",
-                "orcid": "0000-0001-8271-5429",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simleo/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/simleo.json"
-            },
-            {
-                "funder": true,
-                "funding_id": "101046203",
-                "funding_statement": "BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response.\n\nThis project has received funding from the European Union\u2019s Horizon Europe research and innovation programme under grant agreement \u2116 101046203 (BY-COVID)",
-                "funding_system": "cordis",
-                "id": "by-covid",
-                "joined": "2023-04",
-                "members": [
-                    "bgruening",
-                    "hexylena",
-                    "ilveroluca",
-                    "kikkomep",
-                    "mbaardwijk",
-                    "PapXis",
-                    "pauldg",
-                    "simleo",
-                    "stain",
-                    "wm75"
+                "date": "2024-09-12",
+                "length": "1H1M41S",
+                "speakers": [
+                    "GabrielaLopez"
                 ],
-                "name": "BeYond-COVID",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/by-covid/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/by-covid.json"
+                "youtube_id": "MX-4AWyKP8E"
             }
         ],
-        "dir": "topics/fair/tutorials/ro-crate-workflow-run-ro-crate",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "fair/ro-crate-workflow-run-ro-crate",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [],
-        "layout": "tutorial_hands_on",
-        "license": "Apache-2.0",
-        "mod_date": "2023-05-11",
-        "objectives": [],
-        "pageviews": 239,
-        "priority": 1,
-        "pub_date": "2023-05-11",
-        "questions": [],
-        "short_id": "T00343",
+        "short_id": "T00454",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "ro-crate",
+        "subtopic": "fair-data",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -84260,10 +87236,12 @@
         },
         "symlink": null,
         "tags": [
-            "ro-crate"
+            "fair",
+            "open",
+            "data management plan"
         ],
         "time_estimation": "30M",
-        "title": "Workflow Run RO-Crate Introduction",
+        "title": "Introduction to Data Management Plan (DMP) for Peatland Research and PeatDataHub",
         "tools": [],
         "topic_name": "fair",
         "topic_name_human": "FAIR Data, Workflows, and Research",
@@ -84273,23 +87251,23 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "ro-crate-workflow-run-ro-crate",
+        "tutorial_name": "data-management-peatlands",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-workflow-run-ro-crate/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/fair/tutorials/data-management-peatlands/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-workflow-run-ro-crate/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-workflow-run-ro-crate/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/data-management-peatlands/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/data-management-peatlands/tutorial.json"
         },
         "version": 1,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 79,
-        "visitors": 181
+        "visit_duration": 17,
+        "visitors": 7,
+        "zenodo_link": ""
     },
     {
         "abbreviations": {
-            "DOI": "Digital Object Identifier",
             "FAIR": "Findable, Accessible, Interoperable, Reusable"
         },
         "admin_install": {
@@ -84299,14 +87277,24 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-clinical/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-origin/tutorial.json",
         "contributions": {
             "authorship": [
-                "SNG888"
-            ],
-            "editing": [
+                "robertmand",
+                "nsjuty",
+                "smza",
+                "nsoranzo",
+                "saramorsy",
+                "kellsnow",
+                "khens",
+                "proccaserra",
+                "lcooper",
+                "sitjart",
+                "asmasonomics",
+                "bfranicevic",
+                "saskia-lawson-tovey",
                 "kkamieniecka",
-                "tb143",
+                "khaled196",
                 "poterlowicz-lab"
             ],
             "funding": [
@@ -84314,208 +87302,137 @@
             ]
         },
         "contributors": [
-            {
-                "email": "s.ng@qmul.ac.uk",
-                "id": "SNG888",
-                "joined": "2023-07",
-                "name": "Sandra Ng",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/SNG888/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/SNG888.json"
-            },
             {
                 "affiliations": [
                     "elixir-europe"
                 ],
                 "elixir_node": "uk",
-                "id": "kkamieniecka",
-                "joined": "2018-08",
-                "name": "Katarzyna Kamieniecka",
-                "orcid": "0009-0004-2454-5950",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/",
-                "twitter": "katemurat",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
+                "email": "andrewsr9@cardiff.ac.uk",
+                "id": "robertmand",
+                "joined": "2021-10",
+                "name": "Robert Andrews",
+                "orcid": "0000-0002-3491-2361",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/robertmand/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/robertmand.json"
             },
             {
-                "id": "tb143",
+                "id": "nsjuty",
+                "joined": "2024-04",
+                "name": "Nick Juty",
+                "orcid": "0000-0002-2036-8350",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsjuty/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsjuty.json"
+            },
+            {
+                "id": "smza",
                 "joined": "2023-09",
-                "name": "Tim Beck",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tb143/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tb143.json"
+                "name": "Munazah Andrabi",
+                "orcid": "0000-0002-7718-5109",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/smza/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/smza.json"
             },
             {
                 "affiliations": [
+                    "earlham",
                     "elixir-europe"
                 ],
                 "elixir_node": "uk",
-                "id": "poterlowicz-lab",
+                "fediverse": "https://mstdn.science/@nsoranzo",
+                "fediverse_flavor": "mastodon",
+                "id": "nsoranzo",
                 "joined": "2017-09",
-                "name": "Krzysztof Poterlowicz",
-                "orcid": "0000-0001-6173-5674",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/poterlowicz-lab/",
-                "twitter": "bioinfbrad",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/poterlowicz-lab.json"
+                "linkedin": "nicola-soranzo-7884125",
+                "matrix": "nsoranzo:matrix.org",
+                "name": "Nicola Soranzo",
+                "orcid": "0000-0003-3627-5340",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
+                "twitter": "NicolaSoranzo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
+            },
+            {
+                "elixir_node": "uk",
+                "id": "saramorsy",
+                "joined": "2021-10",
+                "name": "Sara Morsy",
+                "orcid": "0000-0002-2477-1139",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/saramorsy/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/saramorsy.json"
+            },
+            {
+                "id": "kellsnow",
+                "joined": "2024-03",
+                "name": "Kellie Snow",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kellsnow/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/kellsnow.json"
             },
             {
-                "avatar": "/training-material/shared/images/dash.png",
-                "funder": true,
-                "funding_id": "MR/V038966/1",
-                "funding_statement": "This Fellowship was funded through the ELIXIR-UK DaSH project as part of the UKRI Innovation Scholars: Data Science Training in Health and Bioscience call (DaSH). (MR/V038966/1). The project aims to embed Research Data Management (RDM) know-how into UK universities and institutes by producing and delivering training in FAIR data stewardship using ELIXIR-UK knowledge and resources.",
-                "funding_system": "ukri",
                 "github": false,
-                "id": "elixir-uk-dash",
-                "joined": "2023-10",
-                "name": "DASH UK",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-uk-dash/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-uk-dash.json"
-            }
-        ],
-        "dir": "topics/fair/tutorials/fair-clinical",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "fair/fair-clinical",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "FAIR data are data that meet principles of findability, accessibility, interoperability, and reusability (FAIR)."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-03-27",
-        "objectives": [
-            "Learn how to make clinical datasets FAIR",
-            "Recognise why FAIR datasets are important"
-        ],
-        "pageviews": 235,
-        "priority": 1,
-        "pub_date": "2023-10-24",
-        "questions": [
-            "Why make clinical data FAIR?",
-            "How to make clinical data FAIR?",
-            "test"
-        ],
-        "requirements": [
+                "id": "khens",
+                "joined": "2024-03",
+                "name": "Korneel Hens",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/khens/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/khens.json"
+            },
             {
-                "topic_name": "fair",
-                "tutorials": [
-                    "fair-intro"
+                "affiliations": [
+                    "elixir-europe"
                 ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00368",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "fair-data",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "fair",
-            "open",
-            "data stewardship"
-        ],
-        "time_estimation": "1H",
-        "title": "Making clinical datasets FAIR",
-        "tools": [],
-        "topic_name": "fair",
-        "topic_name_human": "FAIR Data, Workflows, and Research",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "fair-clinical",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/fair/tutorials/fair-clinical/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-clinical/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-clinical/tutorial.json"
-        },
-        "version": 4,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 119,
-        "visitors": 172,
-        "zenodo_link": ""
-    },
-    {
-        "abbreviations": {
-            "ENA": "European Nucleotide Archive"
-        },
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-ena/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "sonalhenson"
-            ],
-            "editing": [
-                "kkamieniecka",
-                "smza",
-                "poterlowicz-lab"
-            ],
-            "funding": [
-                "elixir-uk-dash"
-            ]
-        },
-        "contributors": [
+                "elixir_node": "uk",
+                "id": "proccaserra",
+                "joined": "2024-03",
+                "name": "Philippe Rocca-Serra",
+                "orcid": "0000-0001-9853-5668",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/proccaserra/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/proccaserra.json"
+            },
             {
-                "id": "sonalhenson",
-                "joined": "2023-09",
-                "name": "Sonal Henson",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/sonalhenson/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/sonalhenson.json"
+                "github": false,
+                "id": "lcooper",
+                "joined": "2024-03",
+                "name": "Laura Cooper",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lcooper/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/lcooper.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "id": "sitjart",
+                "joined": "2024-03",
+                "name": "Xenia Perez Sitja",
+                "orcid": "0000-0002-7166-0183",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/sitjart/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/sitjart.json"
+            },
+            {
+                "elixir_node": "uk",
+                "id": "asmasonomics",
+                "joined": "2024-02",
+                "name": "Andrew Mason",
+                "orcid": "0000-0002-8222-3974",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/asmasonomics/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/asmasonomics.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "id": "bfranicevic",
+                "joined": "2021-10",
+                "name": "Branka Franicevic",
+                "orcid": "0000-0002-3440-6581",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bfranicevic/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bfranicevic.json"
+            },
+            {
+                "id": "saskia-lawson-tovey",
+                "joined": "2024-03",
+                "name": "Saskia Lawson-Tovey",
+                "orcid": "0000-0002-8611-162X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/saskia-lawson-tovey/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/saskia-lawson-tovey.json"
             },
             {
                 "affiliations": [
@@ -84531,12 +87448,17 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
             },
             {
-                "id": "smza",
-                "joined": "2023-09",
-                "name": "Munazah Andrabi",
-                "orcid": "0000-0002-7718-5109",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/smza/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/smza.json"
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "email": "k.jumah@bradford.ac.uk",
+                "id": "khaled196",
+                "joined": "2022-09",
+                "name": "Khaled Jum\u2019ah",
+                "orcid": "0000-0001-5481-8893",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/khaled196/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/khaled196.json"
             },
             {
                 "affiliations": [
@@ -84565,14 +87487,23 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-uk-dash.json"
             }
         ],
-        "dir": "topics/fair/tutorials/fair-ena",
+        "dir": "topics/fair/tutorials/fair-origin",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "fair",
+                "tutorials": [
+                    "fair-metadata"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "fair/fair-ena",
+        "id": "fair/fair-origin",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -84580,47 +87511,43 @@
             "UseGalaxy.fr"
         ],
         "js_requirements": {
-            "mathjax": 13181,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Use ENA Webin interactive portal to submit metadata",
-            "Preparation of metadata and sequence data for the submission",
-            "Use cURL to submit read fastq files"
+            "FAIR stands for Findable, Accessible, Interoperable and Reusable.",
+            "Metadata, Identifiers, Registration and Access are 4 key components in the process of FAIRification.",
+            "FAIR data is as open as possible, and as closed as necessary."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-25",
+        "mod_date": "2024-03-27",
         "objectives": [
-            "To populate ENA metadata objects through the Webin portal",
-            "To submit raw reads to ENA using FTP"
+            "Identify the FAIR principles and their origin.",
+            "Explain the difference between FAIR and open data.",
+            "Contextualise the main principles of FAIR around the common characteristics of identifiers, access, metadata and registration."
         ],
-        "pageviews": 242,
+        "pageviews": 59,
         "priority": 1,
-        "pub_date": "2023-11-01",
+        "pub_date": "2024-03-26",
         "questions": [
-            "I am new to sequence submission to a repository.",
-            "How do I submit sequences and metadata to ENA using the Webin portal and cURL?"
+            "What is FAIR and the FAIR Guiding Principles?",
+            "Where does FAIR come from?"
         ],
         "requirements": [
             {
-                "title": "Web browser",
-                "type": "none"
-            },
-            {
-                "title": "A linux-based machine or linux emulator",
-                "type": "none"
-            },
-            {
-                "title": "Read data in fastq format",
-                "type": "none"
+                "topic_name": "fair",
+                "tutorials": [
+                    "fair-intro"
+                ],
+                "type": "internal"
             }
         ],
-        "short_id": "T00369",
+        "short_id": "T00433",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "fair-data",
+        "subtopic": "pointers",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -84656,11 +87583,12 @@
         },
         "symlink": null,
         "tags": [
-            "FAIR",
-            "ENA"
+            "fair",
+            "dmp",
+            "data stewardship"
         ],
-        "time_estimation": "1H",
-        "title": "Sequence data submission to ENA",
+        "time_estimation": "40M",
+        "title": "FAIR and its Origins",
         "tools": [],
         "topic_name": "fair",
         "topic_name_human": "FAIR Data, Workflows, and Research",
@@ -84670,19 +87598,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "fair-ena",
+        "tutorial_name": "fair-origin",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/fair/tutorials/fair-ena/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/fair/tutorials/fair-origin/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-ena/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-ena/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-origin/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-origin/tutorial.json"
         },
-        "version": 5,
+        "version": 2,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 56,
-        "visitors": 197,
+        "visit_duration": 111,
+        "visitors": 49,
         "zenodo_link": ""
     },
     {
@@ -84769,7 +87697,7 @@
             "Learn basic JSON-LD to create FAIR metadata",
             "Connect different parts of the Research Object using identifiers"
         ],
-        "pageviews": 430,
+        "pageviews": 474,
         "priority": 1,
         "pub_date": "2023-05-23",
         "questions": [
@@ -84874,13 +87802,10 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 100,
-        "visitors": 293
+        "visit_duration": 102,
+        "visitors": 334
     },
     {
-        "abbreviations": {
-            "FAIR": "Findable, Accessible, Interoperable, Reusable"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -84888,163 +87813,172 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-origin/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-workflow-run-ro-crate/tutorial.json",
         "contributions": {
             "authorship": [
-                "robertmand",
-                "nsjuty",
-                "smza",
-                "nsoranzo",
-                "saramorsy",
-                "kellsnow",
-                "khens",
-                "proccaserra",
-                "lcooper",
-                "sitjart",
-                "asmasonomics",
-                "bfranicevic",
-                "saskia-lawson-tovey",
-                "kkamieniecka",
-                "khaled196",
-                "poterlowicz-lab"
+                "simleo"
             ],
             "funding": [
-                "elixir-uk-dash"
+                "by-covid"
             ]
         },
         "contributors": [
             {
                 "affiliations": [
+                    "by-covid",
                     "elixir-europe"
                 ],
-                "elixir_node": "uk",
-                "email": "andrewsr9@cardiff.ac.uk",
-                "id": "robertmand",
-                "joined": "2021-10",
-                "name": "Robert Andrews",
-                "orcid": "0000-0002-3491-2361",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/robertmand/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/robertmand.json"
-            },
-            {
-                "id": "nsjuty",
-                "joined": "2024-04",
-                "name": "Nick Juty",
-                "orcid": "0000-0002-2036-8350",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsjuty/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsjuty.json"
-            },
-            {
-                "id": "smza",
-                "joined": "2023-09",
-                "name": "Munazah Andrabi",
-                "orcid": "0000-0002-7718-5109",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/smza/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/smza.json"
-            },
-            {
-                "affiliations": [
-                    "earlham",
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "fediverse": "https://mstdn.science/@nsoranzo",
-                "fediverse_flavor": "mastodon",
-                "id": "nsoranzo",
-                "joined": "2017-09",
-                "linkedin": "nicola-soranzo-7884125",
-                "matrix": "nsoranzo:matrix.org",
-                "name": "Nicola Soranzo",
-                "orcid": "0000-0003-3627-5340",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
-                "twitter": "NicolaSoranzo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
-            },
-            {
-                "elixir_node": "uk",
-                "id": "saramorsy",
-                "joined": "2021-10",
-                "name": "Sara Morsy",
-                "orcid": "0000-0002-2477-1139",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/saramorsy/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/saramorsy.json"
-            },
-            {
-                "id": "kellsnow",
-                "joined": "2024-03",
-                "name": "Kellie Snow",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kellsnow/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/kellsnow.json"
-            },
-            {
-                "github": false,
-                "id": "khens",
-                "joined": "2024-03",
-                "name": "Korneel Hens",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/khens/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/khens.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "id": "proccaserra",
-                "joined": "2024-03",
-                "name": "Philippe Rocca-Serra",
-                "orcid": "0000-0001-9853-5668",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/proccaserra/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/proccaserra.json"
-            },
-            {
-                "github": false,
-                "id": "lcooper",
-                "joined": "2024-03",
-                "name": "Laura Cooper",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lcooper/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/lcooper.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "id": "sitjart",
-                "joined": "2024-03",
-                "name": "Xenia Perez Sitja",
-                "orcid": "0000-0002-7166-0183",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/sitjart/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/sitjart.json"
-            },
-            {
-                "elixir_node": "uk",
-                "id": "asmasonomics",
-                "joined": "2024-02",
-                "name": "Andrew Mason",
-                "orcid": "0000-0002-8222-3974",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/asmasonomics/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/asmasonomics.json"
+                "elixir_node": "it",
+                "id": "simleo",
+                "joined": "2023-04",
+                "name": "Simone Leo",
+                "orcid": "0000-0001-8271-5429",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simleo/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/simleo.json"
             },
             {
-                "affiliations": [
-                    "elixir-europe"
+                "funder": true,
+                "funding_id": "101046203",
+                "funding_statement": "BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response.\n\nThis project has received funding from the European Union\u2019s Horizon Europe research and innovation programme under grant agreement \u2116 101046203 (BY-COVID)",
+                "funding_system": "cordis",
+                "id": "by-covid",
+                "joined": "2023-04",
+                "members": [
+                    "bgruening",
+                    "hexylena",
+                    "ilveroluca",
+                    "kikkomep",
+                    "mbaardwijk",
+                    "PapXis",
+                    "pauldg",
+                    "simleo",
+                    "stain",
+                    "wm75"
                 ],
-                "elixir_node": "uk",
-                "id": "bfranicevic",
-                "joined": "2021-10",
-                "name": "Branka Franicevic",
-                "orcid": "0000-0002-3440-6581",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bfranicevic/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bfranicevic.json"
-            },
-            {
-                "id": "saskia-lawson-tovey",
-                "joined": "2024-03",
-                "name": "Saskia Lawson-Tovey",
-                "orcid": "0000-0002-8611-162X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/saskia-lawson-tovey/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/saskia-lawson-tovey.json"
-            },
+                "name": "BeYond-COVID",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/by-covid/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/by-covid.json"
+            }
+        ],
+        "dir": "topics/fair/tutorials/ro-crate-workflow-run-ro-crate",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "fair/ro-crate-workflow-run-ro-crate",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [],
+        "layout": "tutorial_hands_on",
+        "license": "Apache-2.0",
+        "mod_date": "2023-05-11",
+        "objectives": [],
+        "pageviews": 260,
+        "priority": 1,
+        "pub_date": "2023-05-11",
+        "questions": [],
+        "short_id": "T00343",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "ro-crate",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "ro-crate"
+        ],
+        "time_estimation": "30M",
+        "title": "Workflow Run RO-Crate Introduction",
+        "tools": [],
+        "topic_name": "fair",
+        "topic_name_human": "FAIR Data, Workflows, and Research",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "ro-crate-workflow-run-ro-crate",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-workflow-run-ro-crate/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-workflow-run-ro-crate/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-workflow-run-ro-crate/tutorial.json"
+        },
+        "version": 1,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 89,
+        "visitors": 199
+    },
+    {
+        "abbreviations": {
+            "FAIR": "Findable, Accessible, Interoperable, Reusable"
+        },
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-intro/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "kkamieniecka",
+                "poterlowicz-lab"
+            ],
+            "editing": [
+                "hexylena"
+            ],
+            "funding": [
+                "elixir-uk-dash"
+            ]
+        },
+        "contributors": [
             {
                 "affiliations": [
                     "elixir-europe"
@@ -85058,19 +87992,6 @@
                 "twitter": "katemurat",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
             },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "email": "k.jumah@bradford.ac.uk",
-                "id": "khaled196",
-                "joined": "2022-09",
-                "name": "Khaled Jum\u2019ah",
-                "orcid": "0000-0001-5481-8893",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/khaled196/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/khaled196.json"
-            },
             {
                 "affiliations": [
                     "elixir-europe"
@@ -85084,6 +88005,35 @@
                 "twitter": "bioinfbrad",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/poterlowicz-lab.json"
             },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
             {
                 "avatar": "/training-material/shared/images/dash.png",
                 "funder": true,
@@ -85098,23 +88048,14 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-uk-dash.json"
             }
         ],
-        "dir": "topics/fair/tutorials/fair-origin",
+        "dir": "topics/fair/tutorials/fair-intro",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "fair",
-                "tutorials": [
-                    "fair-metadata"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "fair/fair-origin",
+        "id": "fair/fair-intro",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -85126,39 +88067,29 @@
             "mermaid": false
         },
         "key_points": [
-            "FAIR stands for Findable, Accessible, Interoperable and Reusable.",
-            "Metadata, Identifiers, Registration and Access are 4 key components in the process of FAIRification.",
-            "FAIR data is as open as possible, and as closed as necessary."
+            "FAIR data are data which meet principles of findability, accessibility, interoperability, and reusability (FAIR).",
+            "FAIR data are as open as possible, and as closed as necessary.",
+            "The main objective of FAIR data is to increase data reuse by researchers."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-27",
+        "mod_date": "2024-04-30",
         "objectives": [
-            "Identify the FAIR principles and their origin.",
-            "Explain the difference between FAIR and open data.",
-            "Contextualise the main principles of FAIR around the common characteristics of identifiers, access, metadata and registration."
+            "Learn the FAIR principles",
+            "Recognise the relationship between FAIR and Open data"
         ],
-        "pageviews": 43,
+        "pageviews": 562,
         "priority": 1,
-        "pub_date": "2024-03-26",
+        "pub_date": "2023-05-30",
         "questions": [
-            "What is FAIR and the FAIR Guiding Principles?",
-            "Where does FAIR come from?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "fair",
-                "tutorials": [
-                    "fair-intro"
-                ],
-                "type": "internal"
-            }
+            "What do the FAIR principles stand for [Wilkinson et al. 2016](https://www.nature.com/articles/sdata201618)?",
+            "How to make data FAIR?"
         ],
-        "short_id": "T00433",
+        "short_id": "T00351",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "pointers",
+        "subtopic": "fair-data",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -85195,11 +88126,11 @@
         "symlink": null,
         "tags": [
             "fair",
-            "dmp",
+            "open",
             "data stewardship"
         ],
-        "time_estimation": "40M",
-        "title": "FAIR and its Origins",
+        "time_estimation": "10M",
+        "title": "FAIR in a nutshell",
         "tools": [],
         "topic_name": "fair",
         "topic_name_human": "FAIR Data, Workflows, and Research",
@@ -85209,23 +88140,24 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "fair-origin",
+        "tutorial_name": "fair-intro",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/fair/tutorials/fair-origin/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/fair/tutorials/fair-intro/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-origin/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-origin/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-intro/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-intro/tutorial.json"
         },
-        "version": 2,
+        "version": 6,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 0,
-        "visitors": 37,
+        "visit_duration": 110,
+        "visitors": 423,
         "zenodo_link": ""
     },
     {
         "abbreviations": {
+            "DOI": "Digital Object Identifier",
             "FAIR": "Findable, Accessible, Interoperable, Reusable"
         },
         "admin_install": {
@@ -85235,24 +88167,14 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-metadata/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-clinical/tutorial.json",
         "contributions": {
             "authorship": [
-                "robertmand",
-                "nsjuty",
-                "smza",
-                "nsoranzo",
-                "saramorsy",
-                "kellsnow",
-                "khens",
-                "proccaserra",
-                "lcooper",
-                "sitjart",
-                "asmasonomics",
-                "bfranicevic",
-                "saskia-lawson-tovey",
+                "SNG888"
+            ],
+            "editing": [
                 "kkamieniecka",
-                "khaled196",
+                "tb143",
                 "poterlowicz-lab"
             ],
             "funding": [
@@ -85261,136 +88183,12 @@
         },
         "contributors": [
             {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "email": "andrewsr9@cardiff.ac.uk",
-                "id": "robertmand",
-                "joined": "2021-10",
-                "name": "Robert Andrews",
-                "orcid": "0000-0002-3491-2361",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/robertmand/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/robertmand.json"
-            },
-            {
-                "id": "nsjuty",
-                "joined": "2024-04",
-                "name": "Nick Juty",
-                "orcid": "0000-0002-2036-8350",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsjuty/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsjuty.json"
-            },
-            {
-                "id": "smza",
-                "joined": "2023-09",
-                "name": "Munazah Andrabi",
-                "orcid": "0000-0002-7718-5109",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/smza/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/smza.json"
-            },
-            {
-                "affiliations": [
-                    "earlham",
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "fediverse": "https://mstdn.science/@nsoranzo",
-                "fediverse_flavor": "mastodon",
-                "id": "nsoranzo",
-                "joined": "2017-09",
-                "linkedin": "nicola-soranzo-7884125",
-                "matrix": "nsoranzo:matrix.org",
-                "name": "Nicola Soranzo",
-                "orcid": "0000-0003-3627-5340",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
-                "twitter": "NicolaSoranzo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
-            },
-            {
-                "elixir_node": "uk",
-                "id": "saramorsy",
-                "joined": "2021-10",
-                "name": "Sara Morsy",
-                "orcid": "0000-0002-2477-1139",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/saramorsy/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/saramorsy.json"
-            },
-            {
-                "id": "kellsnow",
-                "joined": "2024-03",
-                "name": "Kellie Snow",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kellsnow/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/kellsnow.json"
-            },
-            {
-                "github": false,
-                "id": "khens",
-                "joined": "2024-03",
-                "name": "Korneel Hens",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/khens/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/khens.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "id": "proccaserra",
-                "joined": "2024-03",
-                "name": "Philippe Rocca-Serra",
-                "orcid": "0000-0001-9853-5668",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/proccaserra/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/proccaserra.json"
-            },
-            {
-                "github": false,
-                "id": "lcooper",
-                "joined": "2024-03",
-                "name": "Laura Cooper",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lcooper/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/lcooper.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "id": "sitjart",
-                "joined": "2024-03",
-                "name": "Xenia Perez Sitja",
-                "orcid": "0000-0002-7166-0183",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/sitjart/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/sitjart.json"
-            },
-            {
-                "elixir_node": "uk",
-                "id": "asmasonomics",
-                "joined": "2024-02",
-                "name": "Andrew Mason",
-                "orcid": "0000-0002-8222-3974",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/asmasonomics/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/asmasonomics.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "id": "bfranicevic",
-                "joined": "2021-10",
-                "name": "Branka Franicevic",
-                "orcid": "0000-0002-3440-6581",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bfranicevic/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bfranicevic.json"
-            },
-            {
-                "id": "saskia-lawson-tovey",
-                "joined": "2024-03",
-                "name": "Saskia Lawson-Tovey",
-                "orcid": "0000-0002-8611-162X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/saskia-lawson-tovey/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/saskia-lawson-tovey.json"
+                "email": "s.ng@qmul.ac.uk",
+                "id": "SNG888",
+                "joined": "2023-07",
+                "name": "Sandra Ng",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/SNG888/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/SNG888.json"
             },
             {
                 "affiliations": [
@@ -85406,17 +88204,11 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
             },
             {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "email": "k.jumah@bradford.ac.uk",
-                "id": "khaled196",
-                "joined": "2022-09",
-                "name": "Khaled Jum\u2019ah",
-                "orcid": "0000-0001-5481-8893",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/khaled196/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/khaled196.json"
+                "id": "tb143",
+                "joined": "2023-09",
+                "name": "Tim Beck",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tb143/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tb143.json"
             },
             {
                 "affiliations": [
@@ -85445,23 +88237,14 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-uk-dash.json"
             }
         ],
-        "dir": "topics/fair/tutorials/fair-metadata",
+        "dir": "topics/fair/tutorials/fair-clinical",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "fair",
-                "tutorials": [
-                    "fair-data-registration"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "fair/fair-metadata",
+        "id": "fair/fair-clinical",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -85473,40 +88256,47 @@
             "mermaid": false
         },
         "key_points": [
-            "Metadata is data about data.",
-            "Metadata is used to help you find and interpret data.",
-            "Domain-relevant community standards help researchers write better, interoperable metadata."
+            "FAIR data are data that meet principles of findability, accessibility, interoperability, and reusability (FAIR)."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-27",
+        "mod_date": "2024-09-13",
         "objectives": [
-            "Define the term \u2018metadata\u2019.",
-            "Recall examples of community/domain standards that apply to data and metadata."
+            "Learn how to make clinical datasets FAIR",
+            "Recognise why FAIR datasets are important"
         ],
-        "pageviews": 69,
-        "priority": 2,
-        "pub_date": "2024-03-26",
+        "pageviews": 253,
+        "priority": 1,
+        "pub_date": "2023-10-24",
         "questions": [
-            "What is metadata?",
-            "What is good metadata?",
-            "Using community standards to write (meta)data"
+            "Why make clinical data FAIR?",
+            "How to make clinical data FAIR?",
+            "test"
+        ],
+        "recordings": [
+            {
+                "date": "2024-09-12",
+                "length": "1H2M54S",
+                "speakers": [
+                    "SNG888"
+                ],
+                "youtube_id": "48hRQM0yvao"
+            }
         ],
         "requirements": [
             {
                 "topic_name": "fair",
                 "tutorials": [
-                    "fair-intro",
-                    "fair-origin"
+                    "fair-intro"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00432",
+        "short_id": "T00368",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "pointers",
+        "subtopic": "fair-data",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -85543,11 +88333,11 @@
         "symlink": null,
         "tags": [
             "fair",
-            "dmp",
+            "open",
             "data stewardship"
         ],
-        "time_estimation": "40M",
-        "title": "Metadata",
+        "time_estimation": "1H",
+        "title": "Making clinical datasets FAIR",
         "tools": [],
         "topic_name": "fair",
         "topic_name_human": "FAIR Data, Workflows, and Research",
@@ -85557,22 +88347,25 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "fair-metadata",
+        "tutorial_name": "fair-clinical",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/fair/tutorials/fair-metadata/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/fair/tutorials/fair-clinical/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-metadata/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-metadata/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-clinical/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-clinical/tutorial.json"
         },
-        "version": 2,
+        "version": 5,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 130,
-        "visitors": 55,
+        "visit_duration": 124,
+        "visitors": 186,
         "zenodo_link": ""
     },
     {
+        "abbreviations": {
+            "ENA": "European Nucleotide Archive"
+        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -85580,128 +88373,84 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-in-python/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-ena/tutorial.json",
         "contributions": {
             "authorship": [
-                "simleo",
-                "kinow"
+                "sonalhenson"
             ],
             "editing": [
-                "hexylena",
-                "elichad"
+                "kkamieniecka",
+                "smza",
+                "poterlowicz-lab"
             ],
             "funding": [
-                "by-covid"
-            ],
-            "testing": [
-                "elichad"
+                "elixir-uk-dash"
             ]
         },
         "contributors": [
             {
-                "affiliations": [
-                    "by-covid",
-                    "elixir-europe"
-                ],
-                "elixir_node": "it",
-                "id": "simleo",
-                "joined": "2023-04",
-                "name": "Simone Leo",
-                "orcid": "0000-0001-8271-5429",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simleo/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/simleo.json"
+                "id": "sonalhenson",
+                "joined": "2023-09",
+                "name": "Sonal Henson",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/sonalhenson/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/sonalhenson.json"
             },
             {
                 "affiliations": [
                     "elixir-europe"
                 ],
-                "elixir_node": "es",
-                "id": "kinow",
-                "joined": "2023-04",
-                "name": "Bruno P. Kinoshita",
-                "orcid": "0000-0001-8250-4074",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kinow/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/kinow.json"
+                "elixir_node": "uk",
+                "id": "kkamieniecka",
+                "joined": "2018-08",
+                "name": "Katarzyna Kamieniecka",
+                "orcid": "0009-0004-2454-5950",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/",
+                "twitter": "katemurat",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
+            },
+            {
+                "id": "smza",
+                "joined": "2023-09",
+                "name": "Munazah Andrabi",
+                "orcid": "0000-0002-7718-5109",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/smza/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/smza.json"
             },
             {
                 "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
+                    "elixir-europe"
                 ],
-                "id": "hexylena",
+                "elixir_node": "uk",
+                "id": "poterlowicz-lab",
                 "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "email": "eli.chadwick@manchester.ac.uk",
-                "id": "elichad",
-                "joined": "2022-11",
-                "name": "Eli Chadwick",
-                "orcid": "0000-0002-0035-6475",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elichad/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/elichad.json"
-            },
-            {
-                "email": "eli.chadwick@manchester.ac.uk",
-                "id": "elichad",
-                "joined": "2022-11",
-                "name": "Eli Chadwick",
-                "orcid": "0000-0002-0035-6475",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elichad/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/elichad.json"
+                "name": "Krzysztof Poterlowicz",
+                "orcid": "0000-0001-6173-5674",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/poterlowicz-lab/",
+                "twitter": "bioinfbrad",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/poterlowicz-lab.json"
             },
             {
+                "avatar": "/training-material/shared/images/dash.png",
                 "funder": true,
-                "funding_id": "101046203",
-                "funding_statement": "BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response.\n\nThis project has received funding from the European Union\u2019s Horizon Europe research and innovation programme under grant agreement \u2116 101046203 (BY-COVID)",
-                "funding_system": "cordis",
-                "id": "by-covid",
-                "joined": "2023-04",
-                "members": [
-                    "bgruening",
-                    "hexylena",
-                    "ilveroluca",
-                    "kikkomep",
-                    "mbaardwijk",
-                    "PapXis",
-                    "pauldg",
-                    "simleo",
-                    "stain",
-                    "wm75"
-                ],
-                "name": "BeYond-COVID",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/by-covid/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/by-covid.json"
+                "funding_id": "MR/V038966/1",
+                "funding_statement": "This Fellowship was funded through the ELIXIR-UK DaSH project as part of the UKRI Innovation Scholars: Data Science Training in Health and Bioscience call (DaSH). (MR/V038966/1). The project aims to embed Research Data Management (RDM) know-how into UK universities and institutes by producing and delivering training in FAIR data stewardship using ELIXIR-UK knowledge and resources.",
+                "funding_system": "ukri",
+                "github": false,
+                "id": "elixir-uk-dash",
+                "joined": "2023-10",
+                "name": "DASH UK",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-uk-dash/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-uk-dash.json"
             }
         ],
-        "dir": "topics/fair/tutorials/ro-crate-in-python",
+        "dir": "topics/fair/tutorials/fair-ena",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "fair/ro-crate-in-python",
+        "id": "fair/fair-ena",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -85709,35 +88458,47 @@
             "UseGalaxy.fr"
         ],
         "js_requirements": {
-            "mathjax": null,
+            "mathjax": 13181,
             "mermaid": false
         },
         "key_points": [
-            "RO-Crates can be created by hand with essentially arbitrary data, using the rocrate python module",
-            "However the rocrate command line tool adds several commands to make it easier to automatically generate crates based on existing folder structures."
+            "Use ENA Webin interactive portal to submit metadata",
+            "Preparation of metadata and sequence data for the submission",
+            "Use cURL to submit read fastq files"
         ],
         "layout": "tutorial_hands_on",
-        "license": "Apache-2.0",
-        "mod_date": "2024-03-27",
-        "notebook": {
-            "language": "python"
-        },
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-25",
         "objectives": [
-            "Create a custom, annotated RO-Crate",
-            "Use ORCIDs and other linked data to annotate datasets contained within the crate"
+            "To populate ENA metadata objects through the Webin portal",
+            "To submit raw reads to ENA using FTP"
         ],
-        "pageviews": 126,
-        "priority": 2,
-        "pub_date": "2023-05-11",
+        "pageviews": 279,
+        "priority": 1,
+        "pub_date": "2023-11-01",
         "questions": [
-            "What data is contained within an RO-Crate",
-            "How can I create an RO-Crate myself?"
+            "I am new to sequence submission to a repository.",
+            "How do I submit sequences and metadata to ENA using the Webin portal and cURL?"
         ],
-        "short_id": "T00341",
+        "requirements": [
+            {
+                "title": "Web browser",
+                "type": "none"
+            },
+            {
+                "title": "A linux-based machine or linux emulator",
+                "type": "none"
+            },
+            {
+                "title": "Read data in fastq format",
+                "type": "none"
+            }
+        ],
+        "short_id": "T00369",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "ro-crate",
+        "subtopic": "fair-data",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -85773,10 +88534,11 @@
         },
         "symlink": null,
         "tags": [
-            "ro-crate"
+            "FAIR",
+            "ENA"
         ],
-        "time_estimation": "30M",
-        "title": "RO-Crate in Python",
+        "time_estimation": "1H",
+        "title": "Sequence data submission to ENA",
         "tools": [],
         "topic_name": "fair",
         "topic_name_human": "FAIR Data, Workflows, and Research",
@@ -85786,26 +88548,22 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "ro-crate-in-python",
+        "tutorial_name": "fair-ena",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-in-python/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/fair/tutorials/fair-ena/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-in-python/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-in-python/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-ena/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-ena/tutorial.json"
         },
-        "version": 4,
+        "version": 5,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 136,
-        "visitors": 110
+        "visit_duration": 56,
+        "visitors": 227,
+        "zenodo_link": ""
     },
     {
-        "abbreviations": {
-            "DMP": "Data Management Plan",
-            "FAIR": "Findable, Accessible, Interoperable, Reusable",
-            "PID": "Persistent Identifier"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -85813,97 +88571,101 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/data-management/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-in-galaxy/tutorial.json",
         "contributions": {
             "authorship": [
-                "kkamieniecka",
-                "poterlowicz-lab"
+                "pauldg"
             ],
             "editing": [
-                "hexylena"
+                "Marie59"
             ],
             "funding": [
-                "elixir-uk-dash"
+                "by-covid",
+                "eurosciencegateway"
             ]
         },
         "contributors": [
             {
                 "affiliations": [
+                    "by-covid",
+                    "vib",
+                    "eurosciencegateway",
                     "elixir-europe"
                 ],
-                "elixir_node": "uk",
-                "id": "kkamieniecka",
-                "joined": "2018-08",
-                "name": "Katarzyna Kamieniecka",
-                "orcid": "0009-0004-2454-5950",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/",
-                "twitter": "katemurat",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
+                "elixir_node": "be",
+                "id": "pauldg",
+                "joined": "2023-04",
+                "matrix": "padge:matrix.org",
+                "name": "Paul De Geest",
+                "orcid": "0000-0002-8940-4946",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pauldg/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pauldg.json"
             },
             {
                 "affiliations": [
-                    "elixir-europe"
+                    "pndb",
+                    "fairease"
                 ],
-                "elixir_node": "uk",
-                "id": "poterlowicz-lab",
-                "joined": "2017-09",
-                "name": "Krzysztof Poterlowicz",
-                "orcid": "0000-0001-6173-5674",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/poterlowicz-lab/",
-                "twitter": "bioinfbrad",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/poterlowicz-lab.json"
+                "email": "marie.josse@ifremer.fr",
+                "id": "Marie59",
+                "joined": "2022-03",
+                "name": "Marie Josse",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
             },
             {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
+                "funder": true,
+                "funding_id": "101046203",
+                "funding_statement": "BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response.\n\nThis project has received funding from the European Union\u2019s Horizon Europe research and innovation programme under grant agreement \u2116 101046203 (BY-COVID)",
+                "funding_system": "cordis",
+                "id": "by-covid",
+                "joined": "2023-04",
+                "members": [
+                    "bgruening",
+                    "hexylena",
+                    "ilveroluca",
+                    "kikkomep",
+                    "mbaardwijk",
+                    "PapXis",
+                    "pauldg",
+                    "simleo",
+                    "stain",
+                    "wm75"
                 ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+                "name": "BeYond-COVID",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/by-covid/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/by-covid.json"
             },
             {
-                "avatar": "/training-material/shared/images/dash.png",
+                "avatar": "/training-material/assets/images/eurosciencegateway.png",
                 "funder": true,
-                "funding_id": "MR/V038966/1",
-                "funding_statement": "This Fellowship was funded through the ELIXIR-UK DaSH project as part of the UKRI Innovation Scholars: Data Science Training in Health and Bioscience call (DaSH). (MR/V038966/1). The project aims to embed Research Data Management (RDM) know-how into UK universities and institutes by producing and delivering training in FAIR data stewardship using ELIXIR-UK knowledge and resources.",
-                "funding_system": "ukri",
+                "funding_id": "101057388",
+                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
+                "funding_system": "cordis",
                 "github": false,
-                "id": "elixir-uk-dash",
+                "id": "eurosciencegateway",
                 "joined": "2023-10",
-                "name": "DASH UK",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-uk-dash/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-uk-dash.json"
+                "members": [
+                    "abretaud",
+                    "anuprulez",
+                    "bgruening",
+                    "erxleben",
+                    "pauldg",
+                    "rlibouba"
+                ],
+                "name": "EuroScienceGateway",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
             }
         ],
-        "dir": "topics/fair/tutorials/data-management",
+        "dir": "topics/fair/tutorials/ro-crate-in-galaxy",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "fair/data-management",
+        "id": "fair/ro-crate-in-galaxy",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -85915,36 +88677,38 @@
             "mermaid": false
         },
         "key_points": [
-            "FAIR data management allows machines to automatically find and use the data accordingly."
+            "Galaxy Workflow Run Crates help you keep provenance of a workflow run / invocation.",
+            "Galaxy Workflow Run Crates give extra context to the standard workflow run export",
+            "Galaxy Workflow Run Crates can be exported from the top menu, **User -> Workflow Invocations**."
         ],
         "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-03-27",
+        "license": "Apache-2.0",
+        "mod_date": "2024-08-26",
         "objectives": [
-            "Learn best practices in data management",
-            "Learn how to introduce computational reproducibility in your research"
+            "Understanding, viewing and creating Galaxy Workflow Run Crates"
         ],
-        "pageviews": 275,
+        "pageviews": 176,
         "priority": 2,
-        "pub_date": "2023-05-30",
+        "pub_date": "2023-05-11",
         "questions": [
-            "Is there a reproducibility crisis?",
-            "What can go wrong with data analysis?"
+            "What is a Workflow Run Crate?",
+            "How can I export a Galaxy Workflow Run Crate?"
         ],
         "requirements": [
             {
-                "topic_name": "fair",
+                "topic_name": "galaxy-interface",
                 "tutorials": [
-                    "fair-intro"
+                    "workflow-editor",
+                    "history-to-workflow"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00349",
+        "short_id": "T00340",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "fair-data",
+        "subtopic": "ro-crate",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -85980,12 +88744,11 @@
         },
         "symlink": null,
         "tags": [
-            "fair",
-            "dmp",
-            "data stewardship"
+            "ro-crate",
+            "workflows"
         ],
-        "time_estimation": "10M",
-        "title": "FAIR data management solutions",
+        "time_estimation": "30m",
+        "title": "Exporting Workflow Run RO-Crates from Galaxy",
         "tools": [],
         "topic_name": "fair",
         "topic_name_human": "FAIR Data, Workflows, and Research",
@@ -85995,20 +88758,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "data-management",
+        "tutorial_name": "ro-crate-in-galaxy",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/fair/tutorials/data-management/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-in-galaxy/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/data-management/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/data-management/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-in-galaxy/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-in-galaxy/tutorial.json"
         },
-        "version": 4,
+        "version": 8,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 178,
-        "visitors": 213,
-        "zenodo_link": ""
+        "visit_duration": 97,
+        "visitors": 141
     },
     {
         "admin_install": {
@@ -86018,47 +88780,95 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-in-galaxy/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-in-python/tutorial.json",
         "contributions": {
             "authorship": [
-                "pauldg"
+                "simleo",
+                "kinow"
             ],
             "editing": [
-                "Marie59"
+                "hexylena",
+                "elichad"
             ],
             "funding": [
-                "by-covid",
-                "eurosciencegateway"
+                "by-covid"
+            ],
+            "testing": [
+                "elichad"
             ]
         },
         "contributors": [
             {
                 "affiliations": [
                     "by-covid",
-                    "vib",
-                    "eurosciencegateway",
                     "elixir-europe"
                 ],
-                "elixir_node": "be",
-                "id": "pauldg",
+                "elixir_node": "it",
+                "id": "simleo",
                 "joined": "2023-04",
-                "matrix": "padge:matrix.org",
-                "name": "Paul De Geest",
-                "orcid": "0000-0002-8940-4946",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pauldg/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pauldg.json"
+                "name": "Simone Leo",
+                "orcid": "0000-0001-8271-5429",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simleo/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/simleo.json"
             },
             {
                 "affiliations": [
-                    "pndb",
-                    "fairease"
+                    "elixir-europe"
                 ],
-                "email": "marie.josse@ifremer.fr",
-                "id": "Marie59",
-                "joined": "2022-03",
-                "name": "Marie Josse",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Marie59/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/Marie59.json"
+                "elixir_node": "es",
+                "id": "kinow",
+                "joined": "2023-04",
+                "name": "Bruno P. Kinoshita",
+                "orcid": "0000-0001-8250-4074",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kinow/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/kinow.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "email": "eli.chadwick@manchester.ac.uk",
+                "id": "elichad",
+                "joined": "2022-11",
+                "name": "Eli Chadwick",
+                "orcid": "0000-0002-0035-6475",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elichad/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/elichad.json"
+            },
+            {
+                "email": "eli.chadwick@manchester.ac.uk",
+                "id": "elichad",
+                "joined": "2022-11",
+                "name": "Eli Chadwick",
+                "orcid": "0000-0002-0035-6475",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elichad/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/elichad.json"
             },
             {
                 "funder": true,
@@ -86082,37 +88892,16 @@
                 "name": "BeYond-COVID",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/by-covid/",
                 "url": "https://training.galaxyproject.org/training-material/api/funders/by-covid.json"
-            },
-            {
-                "avatar": "/training-material/assets/images/eurosciencegateway.png",
-                "funder": true,
-                "funding_id": "101057388",
-                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "eurosciencegateway",
-                "joined": "2023-10",
-                "members": [
-                    "abretaud",
-                    "anuprulez",
-                    "bgruening",
-                    "erxleben",
-                    "pauldg",
-                    "rlibouba"
-                ],
-                "name": "EuroScienceGateway",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
             }
         ],
-        "dir": "topics/fair/tutorials/ro-crate-in-galaxy",
+        "dir": "topics/fair/tutorials/ro-crate-in-python",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "fair/ro-crate-in-galaxy",
+        "id": "fair/ro-crate-in-python",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -86124,34 +88913,27 @@
             "mermaid": false
         },
         "key_points": [
-            "Galaxy Workflow Run Crates help you keep provenance of a workflow run / invocation.",
-            "Galaxy Workflow Run Crates give extra context to the standard workflow run export",
-            "Galaxy Workflow Run Crates can be exported from the top menu, **User -> Workflow Invocations**."
+            "RO-Crates can be created by hand with essentially arbitrary data, using the rocrate python module",
+            "However the rocrate command line tool adds several commands to make it easier to automatically generate crates based on existing folder structures."
         ],
         "layout": "tutorial_hands_on",
         "license": "Apache-2.0",
-        "mod_date": "2024-08-14",
+        "mod_date": "2024-03-27",
+        "notebook": {
+            "language": "python"
+        },
         "objectives": [
-            "Understanding, viewing and creating Galaxy Workflow Run Crates"
+            "Create a custom, annotated RO-Crate",
+            "Use ORCIDs and other linked data to annotate datasets contained within the crate"
         ],
-        "pageviews": 153,
+        "pageviews": 138,
         "priority": 2,
         "pub_date": "2023-05-11",
         "questions": [
-            "What is a Workflow Run Crate?",
-            "How can I export a Galaxy Workflow Run Crate?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "workflow-editor",
-                    "history-to-workflow"
-                ],
-                "type": "internal"
-            }
+            "What data is contained within an RO-Crate",
+            "How can I create an RO-Crate myself?"
         ],
-        "short_id": "T00340",
+        "short_id": "T00341",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
@@ -86191,11 +88973,10 @@
         },
         "symlink": null,
         "tags": [
-            "ro-crate",
-            "workflows"
+            "ro-crate"
         ],
-        "time_estimation": "30m",
-        "title": "Exporting Workflow Run RO-Crates from Galaxy",
+        "time_estimation": "30M",
+        "title": "RO-Crate in Python",
         "tools": [],
         "topic_name": "fair",
         "topic_name_human": "FAIR Data, Workflows, and Research",
@@ -86205,19 +88986,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "ro-crate-in-galaxy",
+        "tutorial_name": "ro-crate-in-python",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-in-galaxy/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-in-python/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-in-galaxy/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-in-galaxy/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-in-python/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-in-python/tutorial.json"
         },
-        "version": 7,
+        "version": 4,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 94,
-        "visitors": 125
+        "visit_duration": 125,
+        "visitors": 121
     },
     {
         "abbreviations": {
@@ -86230,7 +89011,7 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-data-registration/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-metadata/tutorial.json",
         "contributions": {
             "authorship": [
                 "robertmand",
@@ -86440,7 +89221,7 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-uk-dash.json"
             }
         ],
-        "dir": "topics/fair/tutorials/fair-data-registration",
+        "dir": "topics/fair/tutorials/fair-metadata",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -86450,13 +89231,13 @@
             {
                 "topic_name": "fair",
                 "tutorials": [
-                    "fair-access"
+                    "fair-data-registration"
                 ],
                 "type": "internal"
             }
         ],
         "hands_on": true,
-        "id": "fair/fair-data-registration",
+        "id": "fair/fair-metadata",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -86468,38 +89249,36 @@
             "mermaid": false
         },
         "key_points": [
-            "A good way to FAIRify your (meta)data is through submission to a public repository if it indexes and exposes the appropriate level of metadata to serve your specific use case or serve your envisaged users.",
-            "Use Repositories that  support controlled access to data if necessary.",
-            "FAIRsharing is a useful resource to locate relevant public repositories."
+            "Metadata is data about data.",
+            "Metadata is used to help you find and interpret data.",
+            "Domain-relevant community standards help researchers write better, interoperable metadata."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2024-03-27",
         "objectives": [
-            "Describe why indexed data repositories are important.",
-            "Summarise resources enabling you to choose a searchable repository."
+            "Define the term \u2018metadata\u2019.",
+            "Recall examples of community/domain standards that apply to data and metadata."
         ],
-        "pageviews": 18,
-        "priority": 3,
+        "pageviews": 79,
+        "priority": 2,
         "pub_date": "2024-03-26",
         "questions": [
-            "What is data registration?",
-            "Why should you upload your data to a data repository?",
-            "What types of data repositories are there?",
-            "How to choose the right repository for your dataset?"
+            "What is metadata?",
+            "What is good metadata?",
+            "Using community standards to write (meta)data"
         ],
         "requirements": [
             {
                 "topic_name": "fair",
                 "tutorials": [
                     "fair-intro",
-                    "fair-origin",
-                    "fair-metadata"
+                    "fair-origin"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00431",
+        "short_id": "T00432",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
@@ -86544,7 +89323,7 @@
             "data stewardship"
         ],
         "time_estimation": "40M",
-        "title": "Data Registration",
+        "title": "Metadata",
         "tools": [],
         "topic_name": "fair",
         "topic_name_human": "FAIR Data, Workflows, and Research",
@@ -86554,25 +89333,26 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "fair-data-registration",
+        "tutorial_name": "fair-metadata",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/fair/tutorials/fair-data-registration/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/fair/tutorials/fair-metadata/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-data-registration/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-data-registration/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-metadata/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-metadata/tutorial.json"
         },
         "version": 2,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 0,
-        "visitors": 15,
+        "visit_duration": 131,
+        "visitors": 63,
         "zenodo_link": ""
     },
     {
         "abbreviations": {
+            "DMP": "Data Management Plan",
             "FAIR": "Findable, Accessible, Interoperable, Reusable",
-            "GTN": "Galaxy Training Network"
+            "PID": "Persistent Identifier"
         },
         "admin_install": {
             "install_repository_dependencies": true,
@@ -86581,7 +89361,7 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-gtn/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/data-management/tutorial.json",
         "contributions": {
             "authorship": [
                 "kkamieniecka",
@@ -86664,14 +89444,14 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-uk-dash.json"
             }
         ],
-        "dir": "topics/fair/tutorials/fair-gtn",
+        "dir": "topics/fair/tutorials/data-management",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "fair/fair-gtn",
+        "id": "fair/data-management",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -86683,22 +89463,21 @@
             "mermaid": false
         },
         "key_points": [
-            "FAIR principles in Galaxy training development and content creation."
+            "FAIR data management allows machines to automatically find and use the data accordingly."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2024-03-27",
         "objectives": [
-            "Learn about metadata and findability",
-            "Learn how to support system and content curation"
+            "Learn best practices in data management",
+            "Learn how to introduce computational reproducibility in your research"
         ],
-        "pageviews": 118,
-        "priority": 3,
+        "pageviews": 289,
+        "priority": 2,
         "pub_date": "2023-05-30",
         "questions": [
-            "What are the FAIR training materials?",
-            "How to test, reproduce and share your content?",
-            "How to collaborate and don\u2019t duplicate?"
+            "Is there a reproducibility crisis?",
+            "What can go wrong with data analysis?"
         ],
         "requirements": [
             {
@@ -86709,7 +89488,7 @@
                 "type": "internal"
             }
         ],
-        "short_id": "T00350",
+        "short_id": "T00349",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
@@ -86750,11 +89529,11 @@
         "symlink": null,
         "tags": [
             "fair",
-            "gtn",
-            "training"
+            "dmp",
+            "data stewardship"
         ],
-        "time_estimation": "30M",
-        "title": "FAIR Galaxy Training Material",
+        "time_estimation": "10M",
+        "title": "FAIR data management solutions",
         "tools": [],
         "topic_name": "fair",
         "topic_name_human": "FAIR Data, Workflows, and Research",
@@ -86764,22 +89543,26 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "fair-gtn",
+        "tutorial_name": "data-management",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/fair/tutorials/fair-gtn/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/fair/tutorials/data-management/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-gtn/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-gtn/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/data-management/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/data-management/tutorial.json"
         },
-        "version": 5,
+        "version": 4,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 175,
-        "visitors": 101,
+        "visit_duration": 172,
+        "visitors": 227,
         "zenodo_link": ""
     },
     {
+        "abbreviations": {
+            "FAIR": "Findable, Accessible, Interoperable, Reusable",
+            "GTN": "Galaxy Training Network"
+        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -86787,61 +89570,97 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-galaxy-best-practices/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-gtn/tutorial.json",
         "contributions": {
             "authorship": [
-                "simleo"
+                "kkamieniecka",
+                "poterlowicz-lab"
+            ],
+            "editing": [
+                "hexylena"
             ],
             "funding": [
-                "by-covid"
+                "elixir-uk-dash"
             ]
         },
         "contributors": [
             {
                 "affiliations": [
-                    "by-covid",
                     "elixir-europe"
                 ],
-                "elixir_node": "it",
-                "id": "simleo",
-                "joined": "2023-04",
-                "name": "Simone Leo",
-                "orcid": "0000-0001-8271-5429",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simleo/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/simleo.json"
+                "elixir_node": "uk",
+                "id": "kkamieniecka",
+                "joined": "2018-08",
+                "name": "Katarzyna Kamieniecka",
+                "orcid": "0009-0004-2454-5950",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/",
+                "twitter": "katemurat",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
             },
             {
-                "funder": true,
-                "funding_id": "101046203",
-                "funding_statement": "BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response.\n\nThis project has received funding from the European Union\u2019s Horizon Europe research and innovation programme under grant agreement \u2116 101046203 (BY-COVID)",
-                "funding_system": "cordis",
-                "id": "by-covid",
-                "joined": "2023-04",
-                "members": [
-                    "bgruening",
-                    "hexylena",
-                    "ilveroluca",
-                    "kikkomep",
-                    "mbaardwijk",
-                    "PapXis",
-                    "pauldg",
-                    "simleo",
-                    "stain",
-                    "wm75"
+                "affiliations": [
+                    "elixir-europe"
                 ],
-                "name": "BeYond-COVID",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/by-covid/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/by-covid.json"
+                "elixir_node": "uk",
+                "id": "poterlowicz-lab",
+                "joined": "2017-09",
+                "name": "Krzysztof Poterlowicz",
+                "orcid": "0000-0001-6173-5674",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/poterlowicz-lab/",
+                "twitter": "bioinfbrad",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/poterlowicz-lab.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/dash.png",
+                "funder": true,
+                "funding_id": "MR/V038966/1",
+                "funding_statement": "This Fellowship was funded through the ELIXIR-UK DaSH project as part of the UKRI Innovation Scholars: Data Science Training in Health and Bioscience call (DaSH). (MR/V038966/1). The project aims to embed Research Data Management (RDM) know-how into UK universities and institutes by producing and delivering training in FAIR data stewardship using ELIXIR-UK knowledge and resources.",
+                "funding_system": "ukri",
+                "github": false,
+                "id": "elixir-uk-dash",
+                "joined": "2023-10",
+                "name": "DASH UK",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-uk-dash/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-uk-dash.json"
             }
         ],
-        "dir": "topics/fair/tutorials/ro-crate-galaxy-best-practices",
+        "dir": "topics/fair/tutorials/fair-gtn",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "fair/ro-crate-galaxy-best-practices",
+        "id": "fair/fair-gtn",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -86853,31 +89672,37 @@
             "mermaid": false
         },
         "key_points": [
-            "repo2rocrate lets you easily generate templated out metadata for your workflow",
-            "Generating tests is easy and something everyone should do."
+            "FAIR principles in Galaxy training development and content creation."
         ],
         "layout": "tutorial_hands_on",
-        "license": "Apache-2.0",
-        "mod_date": "2023-06-02",
-        "notebook": {
-            "language": "bash"
-        },
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-03-27",
         "objectives": [
-            "Generate a workflow test using Planemo",
-            "Understand how testing can be automated with GitHub Actions"
+            "Learn about metadata and findability",
+            "Learn how to support system and content curation"
         ],
-        "pageviews": 199,
+        "pageviews": 124,
         "priority": 3,
-        "pub_date": "2023-05-11",
+        "pub_date": "2023-05-30",
         "questions": [
-            "What are Workflow Best Practices",
-            "How does RO-Crate help?"
+            "What are the FAIR training materials?",
+            "How to test, reproduce and share your content?",
+            "How to collaborate and don\u2019t duplicate?"
         ],
-        "short_id": "T00339",
+        "requirements": [
+            {
+                "topic_name": "fair",
+                "tutorials": [
+                    "fair-intro"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00350",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "ro-crate",
+        "subtopic": "fair-data",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -86913,10 +89738,12 @@
         },
         "symlink": null,
         "tags": [
-            "ro-crate"
+            "fair",
+            "gtn",
+            "training"
         ],
         "time_estimation": "30M",
-        "title": "Best practices for workflows in GitHub repositories",
+        "title": "FAIR Galaxy Training Material",
         "tools": [],
         "topic_name": "fair",
         "topic_name_human": "FAIR Data, Workflows, and Research",
@@ -86926,24 +89753,22 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "ro-crate-galaxy-best-practices",
+        "tutorial_name": "fair-gtn",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-galaxy-best-practices/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/fair/tutorials/fair-gtn/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-galaxy-best-practices/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-galaxy-best-practices/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-gtn/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-gtn/tutorial.json"
         },
-        "version": 2,
+        "version": 5,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 65,
-        "visitors": 179
+        "visit_duration": 175,
+        "visitors": 105,
+        "zenodo_link": ""
     },
     {
-        "abbreviations": {
-            "LM": "Life Monitor"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -86951,32 +89776,17 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-submitting-life-monitor/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-galaxy-best-practices/tutorial.json",
         "contributions": {
             "authorship": [
-                "ilveroluca",
                 "simleo",
-                "kikkomep"
-            ],
-            "editing": [
-                "hexylena"
+                "elichad"
             ],
             "funding": [
                 "by-covid"
             ]
         },
         "contributors": [
-            {
-                "affiliations": [
-                    "by-covid"
-                ],
-                "id": "ilveroluca",
-                "joined": "2023-04",
-                "name": "Luca Pireddu",
-                "orcid": "0000-0002-4663-5613",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ilveroluca/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/ilveroluca.json"
-            },
             {
                 "affiliations": [
                     "by-covid",
@@ -86991,46 +89801,13 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/simleo.json"
             },
             {
-                "affiliations": [
-                    "by-covid",
-                    "elixir-europe"
-                ],
-                "elixir_node": "it",
-                "id": "kikkomep",
-                "joined": "2023-04",
-                "name": "Marco Enrico Piras",
-                "orcid": "0000-0002-5207-0030",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kikkomep/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/kikkomep.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+                "email": "eli.chadwick@manchester.ac.uk",
+                "id": "elichad",
+                "joined": "2022-11",
+                "name": "Eli Chadwick",
+                "orcid": "0000-0002-0035-6475",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elichad/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/elichad.json"
             },
             {
                 "funder": true,
@@ -87056,14 +89833,14 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/by-covid.json"
             }
         ],
-        "dir": "topics/fair/tutorials/ro-crate-submitting-life-monitor",
+        "dir": "topics/fair/tutorials/ro-crate-galaxy-best-practices",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "fair/ro-crate-submitting-life-monitor",
+        "id": "fair/ro-crate-galaxy-best-practices",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -87075,34 +89852,27 @@
             "mermaid": false
         },
         "key_points": [
-            "Automation helps us keep workflows re-usable and reproducible.",
-            "LifeMonitor helps you monitor and periodically test your workflow.",
-            "New workflow releases will automatically be propagated to WorkflowHub, saving you time."
+            "repo2rocrate lets you easily generate templated out metadata for your workflow",
+            "Generating tests is easy and something everyone should do."
         ],
         "layout": "tutorial_hands_on",
         "license": "Apache-2.0",
-        "mod_date": "2023-06-02",
+        "mod_date": "2024-09-30",
+        "notebook": {
+            "language": "bash"
+        },
         "objectives": [
-            "Setup Life Monitor"
+            "Generate a workflow test using Planemo",
+            "Understand how testing can be automated with GitHub Actions"
         ],
-        "pageviews": 32,
-        "priority": 4,
+        "pageviews": 213,
+        "priority": 3,
         "pub_date": "2023-05-11",
         "questions": [
-            "What is LifeMonitor?",
-            "How is it useful to me?",
-            "How can I automate things?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "fair",
-                "tutorials": [
-                    "ro-crate-galaxy-best-practices"
-                ],
-                "type": "internal"
-            }
+            "What are Workflow Best Practices",
+            "How does RO-Crate help?"
         ],
-        "short_id": "T00342",
+        "short_id": "T00339",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
@@ -87145,7 +89915,7 @@
             "ro-crate"
         ],
         "time_estimation": "30M",
-        "title": "Submitting workflows to LifeMonitor",
+        "title": "Best practices for workflows in GitHub repositories",
         "tools": [],
         "topic_name": "fair",
         "topic_name_human": "FAIR Data, Workflows, and Research",
@@ -87155,21 +89925,24 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "ro-crate-submitting-life-monitor",
+        "tutorial_name": "ro-crate-galaxy-best-practices",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-submitting-life-monitor/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-galaxy-best-practices/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-submitting-life-monitor/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-submitting-life-monitor/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-galaxy-best-practices/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-galaxy-best-practices/tutorial.json"
         },
-        "version": 3,
+        "version": 5,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 657,
-        "visitors": 27
+        "visit_duration": 63,
+        "visitors": 189
     },
     {
+        "abbreviations": {
+            "FAIR": "Findable, Accessible, Interoperable, Reusable"
+        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -87177,12 +89950,24 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/bioimage-metadata/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-data-registration/tutorial.json",
         "contributions": {
             "authorship": [
-                "wee-snufkin",
-                "Laura190",
+                "robertmand",
+                "nsjuty",
+                "smza",
+                "nsoranzo",
+                "saramorsy",
+                "kellsnow",
+                "khens",
+                "proccaserra",
+                "lcooper",
+                "sitjart",
+                "asmasonomics",
+                "bfranicevic",
+                "saskia-lawson-tovey",
                 "kkamieniecka",
+                "khaled196",
                 "poterlowicz-lab"
             ],
             "funding": [
@@ -87191,20 +89976,136 @@
         },
         "contributors": [
             {
-                "email": "juliajot36@gmail.com",
-                "id": "wee-snufkin",
-                "joined": "2022-06",
-                "name": "Julia Jakiela",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "email": "andrewsr9@cardiff.ac.uk",
+                "id": "robertmand",
+                "joined": "2021-10",
+                "name": "Robert Andrews",
+                "orcid": "0000-0002-3491-2361",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/robertmand/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/robertmand.json"
             },
             {
-                "email": "L.Cooper.5@warwick.ac.uk",
-                "id": "Laura190",
-                "joined": "2023-08",
+                "id": "nsjuty",
+                "joined": "2024-04",
+                "name": "Nick Juty",
+                "orcid": "0000-0002-2036-8350",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsjuty/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsjuty.json"
+            },
+            {
+                "id": "smza",
+                "joined": "2023-09",
+                "name": "Munazah Andrabi",
+                "orcid": "0000-0002-7718-5109",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/smza/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/smza.json"
+            },
+            {
+                "affiliations": [
+                    "earlham",
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "fediverse": "https://mstdn.science/@nsoranzo",
+                "fediverse_flavor": "mastodon",
+                "id": "nsoranzo",
+                "joined": "2017-09",
+                "linkedin": "nicola-soranzo-7884125",
+                "matrix": "nsoranzo:matrix.org",
+                "name": "Nicola Soranzo",
+                "orcid": "0000-0003-3627-5340",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
+                "twitter": "NicolaSoranzo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
+            },
+            {
+                "elixir_node": "uk",
+                "id": "saramorsy",
+                "joined": "2021-10",
+                "name": "Sara Morsy",
+                "orcid": "0000-0002-2477-1139",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/saramorsy/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/saramorsy.json"
+            },
+            {
+                "id": "kellsnow",
+                "joined": "2024-03",
+                "name": "Kellie Snow",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kellsnow/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/kellsnow.json"
+            },
+            {
+                "github": false,
+                "id": "khens",
+                "joined": "2024-03",
+                "name": "Korneel Hens",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/khens/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/khens.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "id": "proccaserra",
+                "joined": "2024-03",
+                "name": "Philippe Rocca-Serra",
+                "orcid": "0000-0001-9853-5668",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/proccaserra/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/proccaserra.json"
+            },
+            {
+                "github": false,
+                "id": "lcooper",
+                "joined": "2024-03",
                 "name": "Laura Cooper",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Laura190/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/Laura190.json"
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lcooper/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/lcooper.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "id": "sitjart",
+                "joined": "2024-03",
+                "name": "Xenia Perez Sitja",
+                "orcid": "0000-0002-7166-0183",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/sitjart/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/sitjart.json"
+            },
+            {
+                "elixir_node": "uk",
+                "id": "asmasonomics",
+                "joined": "2024-02",
+                "name": "Andrew Mason",
+                "orcid": "0000-0002-8222-3974",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/asmasonomics/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/asmasonomics.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "id": "bfranicevic",
+                "joined": "2021-10",
+                "name": "Branka Franicevic",
+                "orcid": "0000-0002-3440-6581",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bfranicevic/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bfranicevic.json"
+            },
+            {
+                "id": "saskia-lawson-tovey",
+                "joined": "2024-03",
+                "name": "Saskia Lawson-Tovey",
+                "orcid": "0000-0002-8611-162X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/saskia-lawson-tovey/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/saskia-lawson-tovey.json"
             },
             {
                 "affiliations": [
@@ -87219,6 +90120,19 @@
                 "twitter": "katemurat",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
             },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "email": "k.jumah@bradford.ac.uk",
+                "id": "khaled196",
+                "joined": "2022-09",
+                "name": "Khaled Jum\u2019ah",
+                "orcid": "0000-0001-5481-8893",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/khaled196/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/khaled196.json"
+            },
             {
                 "affiliations": [
                     "elixir-europe"
@@ -87246,7 +90160,7 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-uk-dash.json"
             }
         ],
-        "dir": "topics/fair/tutorials/bioimage-metadata",
+        "dir": "topics/fair/tutorials/fair-data-registration",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -87256,17 +90170,13 @@
             {
                 "topic_name": "fair",
                 "tutorials": [
-                    "bioimage-REMBI"
+                    "fair-access"
                 ],
                 "type": "internal"
-            },
-            {
-                "topic_name": "imaging",
-                "type": "internal"
             }
         ],
         "hands_on": true,
-        "id": "fair/bioimage-metadata",
+        "id": "fair/fair-data-registration",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -87278,41 +90188,42 @@
             "mermaid": false
         },
         "key_points": [
-            "Data repositories such as BioImage Archive, Electron Microscopy Public Image Archive (EMPIAR) and Image Data Repository (IDR) are available to help make bioimaging data FAIR.",
-            "Find out what are the repository's requirements to help decide which is suitable for your data.",
-            "All repositories require some metadata, so collecting the metadata alongside data acquisition will make this process easier."
+            "A good way to FAIRify your (meta)data is through submission to a public repository if it indexes and exposes the appropriate level of metadata to serve your specific use case or serve your envisaged users.",
+            "Use Repositories that  support controlled access to data if necessary.",
+            "FAIRsharing is a useful resource to locate relevant public repositories."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-27",
+        "mod_date": "2024-09-27",
         "objectives": [
-            "Locate bioimage data repositories",
-            "Compare repositories to find which are suitable for your data",
-            "Find out what the requirements are for submitting"
+            "Describe why indexed data repositories are important.",
+            "Summarise resources enabling you to choose a searchable repository."
         ],
-        "pageviews": 150,
-        "priority": 4,
-        "pub_date": "2023-09-13",
+        "pageviews": 21,
+        "priority": 3,
+        "pub_date": "2024-03-26",
         "questions": [
-            "What are the commonly used repositories for bioimaging data?",
-            "Which repositories are suitable for my data?",
-            "What are the requirements for submitting?"
+            "What is data registration?",
+            "Why should you upload your data to a data repository?",
+            "What types of data repositories are there?",
+            "How to choose the right repository for your dataset?"
         ],
         "requirements": [
             {
                 "topic_name": "fair",
                 "tutorials": [
                     "fair-intro",
-                    "data-management"
+                    "fair-origin",
+                    "fair-metadata"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00362",
+        "short_id": "T00431",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "fair-data",
+        "subtopic": "pointers",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -87349,11 +90260,11 @@
         "symlink": null,
         "tags": [
             "fair",
-            "data management",
-            "bioimaging"
+            "dmp",
+            "data stewardship"
         ],
-        "time_estimation": "15m",
-        "title": "FAIR Bioimage Metadata",
+        "time_estimation": "40M",
+        "title": "Data Registration",
         "tools": [],
         "topic_name": "fair",
         "topic_name_human": "FAIR Data, Workflows, and Research",
@@ -87363,19 +90274,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "bioimage-metadata",
+        "tutorial_name": "fair-data-registration",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/fair/tutorials/bioimage-metadata/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/fair/tutorials/fair-data-registration/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/bioimage-metadata/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/bioimage-metadata/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-data-registration/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-data-registration/tutorial.json"
         },
         "version": 3,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 176,
-        "visitors": 118,
+        "visit_duration": 0,
+        "visitors": 18,
         "zenodo_link": ""
     },
     {
@@ -87639,7 +90550,7 @@
             "To illustrate data access in terms of the FAIR Principles using companion terms including communications protocol and authentication.",
             "To interpret the data usage licence associated with different data sets."
         ],
-        "pageviews": 22,
+        "pageviews": 29,
         "priority": 4,
         "pub_date": "2024-03-26",
         "questions": [
@@ -87701,11 +90612,222 @@
         "symlink": null,
         "tags": [
             "fair",
-            "dmp",
-            "data stewardship"
+            "dmp",
+            "data stewardship"
+        ],
+        "time_estimation": "50M",
+        "title": "Access",
+        "tools": [],
+        "topic_name": "fair",
+        "topic_name_human": "FAIR Data, Workflows, and Research",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "fair-access",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/fair/tutorials/fair-access/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-access/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-access/tutorial.json"
+        },
+        "version": 2,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 247,
+        "visitors": 22,
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/bioimage-metadata/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "wee-snufkin",
+                "Laura190",
+                "kkamieniecka",
+                "poterlowicz-lab"
+            ],
+            "funding": [
+                "elixir-uk-dash"
+            ]
+        },
+        "contributors": [
+            {
+                "elixir_node": "uk",
+                "email": "juliajot36@gmail.com",
+                "id": "wee-snufkin",
+                "joined": "2022-06",
+                "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
+            },
+            {
+                "email": "L.Cooper.5@warwick.ac.uk",
+                "id": "Laura190",
+                "joined": "2023-08",
+                "name": "Laura Cooper",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Laura190/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Laura190.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "id": "kkamieniecka",
+                "joined": "2018-08",
+                "name": "Katarzyna Kamieniecka",
+                "orcid": "0009-0004-2454-5950",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/",
+                "twitter": "katemurat",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "id": "poterlowicz-lab",
+                "joined": "2017-09",
+                "name": "Krzysztof Poterlowicz",
+                "orcid": "0000-0001-6173-5674",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/poterlowicz-lab/",
+                "twitter": "bioinfbrad",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/poterlowicz-lab.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/dash.png",
+                "funder": true,
+                "funding_id": "MR/V038966/1",
+                "funding_statement": "This Fellowship was funded through the ELIXIR-UK DaSH project as part of the UKRI Innovation Scholars: Data Science Training in Health and Bioscience call (DaSH). (MR/V038966/1). The project aims to embed Research Data Management (RDM) know-how into UK universities and institutes by producing and delivering training in FAIR data stewardship using ELIXIR-UK knowledge and resources.",
+                "funding_system": "ukri",
+                "github": false,
+                "id": "elixir-uk-dash",
+                "joined": "2023-10",
+                "name": "DASH UK",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-uk-dash/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-uk-dash.json"
+            }
+        ],
+        "dir": "topics/fair/tutorials/bioimage-metadata",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "fair",
+                "tutorials": [
+                    "bioimage-REMBI"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "imaging",
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "fair/bioimage-metadata",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Data repositories such as BioImage Archive, Electron Microscopy Public Image Archive (EMPIAR) and Image Data Repository (IDR) are available to help make bioimaging data FAIR.",
+            "Find out what are the repository's requirements to help decide which is suitable for your data.",
+            "All repositories require some metadata, so collecting the metadata alongside data acquisition will make this process easier."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-03-27",
+        "objectives": [
+            "Locate bioimage data repositories",
+            "Compare repositories to find which are suitable for your data",
+            "Find out what the requirements are for submitting"
+        ],
+        "pageviews": 165,
+        "priority": 4,
+        "pub_date": "2023-09-13",
+        "questions": [
+            "What are the commonly used repositories for bioimaging data?",
+            "Which repositories are suitable for my data?",
+            "What are the requirements for submitting?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "fair",
+                "tutorials": [
+                    "fair-intro",
+                    "data-management"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00362",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "fair-data",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "fair",
+            "data management",
+            "bioimaging"
         ],
-        "time_estimation": "50M",
-        "title": "Access",
+        "time_estimation": "15m",
+        "title": "FAIR Bioimage Metadata",
         "tools": [],
         "topic_name": "fair",
         "topic_name_human": "FAIR Data, Workflows, and Research",
@@ -87715,21 +90837,250 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "fair-access",
+        "tutorial_name": "bioimage-metadata",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/fair/tutorials/fair-access/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/fair/tutorials/bioimage-metadata/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-access/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-access/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/bioimage-metadata/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/bioimage-metadata/tutorial.json"
         },
-        "version": 2,
+        "version": 3,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 414,
-        "visitors": 17,
+        "visit_duration": 163,
+        "visitors": 132,
         "zenodo_link": ""
     },
+    {
+        "abbreviations": {
+            "LM": "Life Monitor"
+        },
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-submitting-life-monitor/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "ilveroluca",
+                "simleo",
+                "kikkomep"
+            ],
+            "editing": [
+                "hexylena"
+            ],
+            "funding": [
+                "by-covid"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "by-covid"
+                ],
+                "id": "ilveroluca",
+                "joined": "2023-04",
+                "name": "Luca Pireddu",
+                "orcid": "0000-0002-4663-5613",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ilveroluca/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/ilveroluca.json"
+            },
+            {
+                "affiliations": [
+                    "by-covid",
+                    "elixir-europe"
+                ],
+                "elixir_node": "it",
+                "id": "simleo",
+                "joined": "2023-04",
+                "name": "Simone Leo",
+                "orcid": "0000-0001-8271-5429",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simleo/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/simleo.json"
+            },
+            {
+                "affiliations": [
+                    "by-covid",
+                    "elixir-europe"
+                ],
+                "elixir_node": "it",
+                "id": "kikkomep",
+                "joined": "2023-04",
+                "name": "Marco Enrico Piras",
+                "orcid": "0000-0002-5207-0030",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kikkomep/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/kikkomep.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "funder": true,
+                "funding_id": "101046203",
+                "funding_statement": "BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response.\n\nThis project has received funding from the European Union\u2019s Horizon Europe research and innovation programme under grant agreement \u2116 101046203 (BY-COVID)",
+                "funding_system": "cordis",
+                "id": "by-covid",
+                "joined": "2023-04",
+                "members": [
+                    "bgruening",
+                    "hexylena",
+                    "ilveroluca",
+                    "kikkomep",
+                    "mbaardwijk",
+                    "PapXis",
+                    "pauldg",
+                    "simleo",
+                    "stain",
+                    "wm75"
+                ],
+                "name": "BeYond-COVID",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/by-covid/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/by-covid.json"
+            }
+        ],
+        "dir": "topics/fair/tutorials/ro-crate-submitting-life-monitor",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "fair/ro-crate-submitting-life-monitor",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Automation helps us keep workflows re-usable and reproducible.",
+            "LifeMonitor helps you monitor and periodically test your workflow.",
+            "New workflow releases will automatically be propagated to WorkflowHub, saving you time."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "Apache-2.0",
+        "mod_date": "2024-09-26",
+        "objectives": [
+            "Setup Life Monitor"
+        ],
+        "pageviews": 33,
+        "priority": 4,
+        "pub_date": "2023-05-11",
+        "questions": [
+            "What is LifeMonitor?",
+            "How is it useful to me?",
+            "How can I automate things?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "fair",
+                "tutorials": [
+                    "ro-crate-galaxy-best-practices"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00342",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "ro-crate",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "ro-crate"
+        ],
+        "time_estimation": "30M",
+        "title": "Submitting workflows to LifeMonitor",
+        "tools": [],
+        "topic_name": "fair",
+        "topic_name_human": "FAIR Data, Workflows, and Research",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "ro-crate-submitting-life-monitor",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-submitting-life-monitor/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-submitting-life-monitor/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/ro-crate-submitting-life-monitor/tutorial.json"
+        },
+        "version": 4,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 584,
+        "visitors": 28
+    },
     {
         "admin_install": {
             "install_repository_dependencies": true,
@@ -87752,10 +91103,12 @@
         },
         "contributors": [
             {
+                "elixir_node": "uk",
                 "email": "juliajot36@gmail.com",
                 "id": "wee-snufkin",
                 "joined": "2022-06",
                 "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
             },
@@ -87836,20 +91189,30 @@
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-05-07",
+        "mod_date": "2024-09-13",
         "objectives": [
             "Organise bioimage metadata",
             "Find out what REMBI is and why it is useful",
             "Categorise what metadata belongs to each of the submodules of REMBI",
             "Gather the metadata for an example bioimage dataset"
         ],
-        "pageviews": 144,
+        "pageviews": 160,
         "priority": 5,
         "pub_date": "2023-09-13",
         "questions": [
             "What is REMBI and why should I use it?",
             "What information should be included when collecting bioimage data?"
         ],
+        "recordings": [
+            {
+                "date": "2024-09-12",
+                "length": "48M14S",
+                "speakers": [
+                    "lcooper"
+                ],
+                "youtube_id": "QA82MzWle_w"
+            }
+        ],
         "requirements": [
             {
                 "topic_name": "fair",
@@ -87923,12 +91286,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/bioimage-REMBI/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/bioimage-REMBI/tutorial.json"
         },
-        "version": 4,
+        "version": 5,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 206,
-        "visitors": 126,
+        "visit_duration": 181,
+        "visitors": 140,
         "zenodo_link": ""
     },
     {
@@ -88182,7 +91545,7 @@
             "Illustrate what are the persistent identifiers.",
             "Give examples of the structure of persistent identifiers."
         ],
-        "pageviews": 47,
+        "pageviews": 56,
         "priority": 5,
         "pub_date": "2024-03-26",
         "questions": [
@@ -88269,8 +91632,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 36,
-        "visitors": 40,
+        "visit_duration": 30,
+        "visitors": 48,
         "zenodo_link": ""
     },
     {
@@ -88449,7 +91812,7 @@
         "objectives": [
             "To be able to map each of the FAIR principles to a dataset in the public domain"
         ],
-        "pageviews": 97,
+        "pageviews": 101,
         "priority": 6,
         "pub_date": "2024-03-27",
         "questions": [
@@ -88535,8 +91898,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 74,
-        "visitors": 74,
+        "visit_duration": 85,
+        "visitors": 78,
         "zenodo_link": ""
     },
     {
@@ -88546,146 +91909,229 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "bcftools_consensus",
-                    "owner": "iuc",
-                    "revisions": "e522022137f6",
-                    "tool_panel_section_label": "Variant Calling",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "compose_text_param",
-                    "owner": "iuc",
-                    "revisions": "e188c9826e0f",
-                    "tool_panel_section_label": "Expression Tools",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pangolin",
+                    "name": "datamash_ops",
                     "owner": "iuc",
-                    "revisions": "b6abccb1f25b",
-                    "tool_panel_section_label": "Phylogenetics",
+                    "revisions": "562f3c677828",
+                    "tool_panel_section_label": "Join, Subtract and Group",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "snpsift",
+                    "name": "ggplot2_point",
                     "owner": "iuc",
-                    "revisions": "5fab4f81391d",
-                    "tool_panel_section_label": "Variant Calling",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "830961c48e42",
-                    "tool_panel_section_label": "Collection Operations",
+                    "revisions": "1acf88921176",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bcftools_consensus\n  owner: iuc\n  revisions: e522022137f6\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: compose_text_param\n  owner: iuc\n  revisions: e188c9826e0f\n  tool_panel_section_label: Expression Tools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pangolin\n  owner: iuc\n  revisions: b6abccb1f25b\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpsift\n  owner: iuc\n  revisions: 5fab4f81391d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-automation/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 562f3c677828\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ggplot2_point\n  owner: iuc\n  revisions: 1acf88921176\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-reports/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "shiltemann"
+            ],
+            "funding": [
+                "gallantries"
+            ],
+            "infrastructure": [
+                "jmchilton",
+                "guerler",
+                "mvdbeek"
+            ],
+            "testing": [
+                "hexylena"
+            ]
+        },
         "contributors": [
             {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
                 ],
-                "id": "simonbray",
-                "joined": "2019-05",
-                "name": "Simon Bray",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             },
             {
                 "affiliations": [
+                    "gallantries",
                     "by-covid",
-                    "uni-freiburg",
-                    "elixir-europe"
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "email": "jmchilton@gmail.com",
+                "id": "jmchilton",
+                "joined": "2017-09",
+                "matrix": "jmchilton:matrix.org",
+                "name": "John Chilton",
+                "orcid": "0000-0002-6794-0756",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jmchilton/",
+                "twitter": "jmchilton",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jmchilton.json"
+            },
+            {
+                "id": "guerler",
+                "joined": "2017-09",
+                "name": "Aysam Guerler",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/guerler/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/guerler.json"
+            },
+            {
+                "id": "mvdbeek",
+                "joined": "2018-06",
+                "name": "Marius van den Beek",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
                 ],
-                "elixir_node": "de",
-                "fediverse": "https://scholar.social/@zerodivision",
-                "fediverse_flavor": "mastodon",
-                "id": "wm75",
-                "joined": "2017-09",
-                "matrix": "wm75:matrix.org",
-                "name": "Wolfgang Maier",
-                "orcid": "0000-0002-9464-6640",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/galaxy-interface/tutorials/workflow-automation",
+        "dir": "topics/galaxy-interface/tutorials/workflow-reports",
         "edam_operation": [
-            "Variant classification",
-            "Tree-based sequence alignment"
+            "Visualisation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "galaxy-interface/workflow-automation",
+        "id": "galaxy-interface/workflow-reports",
         "inexact_supported_servers": [
-            "UseGalaxy.fr"
+            "Galaxy@AuBi",
+            "MISSISSIPPI",
+            "UseGalaxy.be",
+            "UseGalaxy.cz"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Workflows can be executed not only through the web browser, but also via the command line.",
-            "Executing workflows programmatically allows automation of analyses."
+            "Workflow reports help you display the most important results of a workflow in an organized fashion.",
+            "Workflow reports are configured as part of the workflow definition, for every run of the workflow, a report will be automatically created",
+            "Workflow reports can be viewed from the top menu, **User -> Workflow Invocations**.",
+            "Labels must be added to workflow outputs before they can be included",
+            "Many different components can be added to a workflow report (datasets, images, links to datasets, job metrics, text and sections, visualisations, and much more!)",
+            "Workflow reports can be shared as Galaxy Pages."
         ],
         "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
         "mod_date": "2024-06-14",
         "objectives": [
-            "Learn to use the `planemo run` subcommand to run workflows from the command line.",
-            "Be able to write simple shell scripts for running multiple workflows concurrently or sequentially.",
-            "Learn how to use Pangolin to assign annotated variants to lineages."
+            "Understanding, viewing and creating workflow reports"
         ],
-        "pageviews": 2720,
-        "pub_date": "2021-06-08",
+        "pageviews": 891,
+        "pub_date": "2022-06-02",
         "questions": [
-            "How can I schedule and run tens or hundreds of Galaxy workflows easily?",
-            "How can I automate my analyses when large amounts of data are being produced daily?"
+            "What are workflow reports?",
+            "How can I view a workflow report?",
+            "How can I customize a workflow report?",
+            "How can I share a workflow report with others?"
         ],
         "recordings": [
             {
                 "captioners": [
-                    "simonbray"
+                    "shiltemann"
                 ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
+                "date": "2022-07-06",
                 "length": "30M",
                 "speakers": [
-                    "simonbray"
+                    "shiltemann"
                 ],
-                "youtube_id": "o39QjVnLG68"
-            }
-        ],
-        "requirements": [
-            {
-                "title": "Familiarity with Galaxy and basic associated concepts, in particular workflows",
-                "type": "none"
-            },
-            {
-                "title": "Basic knowledge of the command line",
-                "type": "none"
+                "youtube_id": "hrZhpsiGaPM"
             }
         ],
-        "short_id": "T00162",
+        "short_id": "T00165",
         "short_tools": [
-            "bcftools_consensus",
-            "compose_text_param",
-            "pangolin",
-            "snpSift_filter",
-            "collapse_dataset"
+            "tp_sorted_uniq",
+            "csv_to_tabular",
+            "upload1",
+            "ggplot2_point",
+            "Cut1",
+            "Remove beginning1",
+            "datamash_ops",
+            "Grouping1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -88698,38 +92144,59 @@
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 }
             ],
             "inexact": [
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 }
             ]
         },
         "symlink": null,
         "tags": [
-            "workflows",
-            "variant-analysis",
-            "covid19"
+            "workflows"
         ],
-        "time_estimation": "2h",
-        "title": "Automating Galaxy workflows using the command line",
+        "time_estimation": "30m",
+        "title": "Workflow Reports",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10",
-            "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
+            "Cut1",
+            "Grouping1",
+            "Remove beginning1",
+            "csv_to_tabular",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
+            "upload1"
         ],
         "topic_name": "galaxy-interface",
         "topic_name_human": "Using Galaxy and Managing your Data",
@@ -88739,43 +92206,51 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "workflow-automation",
+        "tutorial_name": "workflow-reports",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-automation/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-reports/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-automation/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-automation/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-reports/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-reports/tutorial.json"
         },
-        "version": 8,
+        "version": 9,
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 118,
-        "visitors": 2200,
+        "visit_duration": 180,
+        "visitors": 621,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0002-9464-6640",
-                        "name": "Wolfgang Maier"
-                    }
-                ],
-                "description": "workflow-automation",
+                "creators": [],
+                "description": "introduction",
                 "features": {
                     "comments": false,
-                    "parameters": true,
+                    "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nVariant calls\"]\n  1[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nmin-AF for consensus variant\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genome\"]\n  3[label=\"Compose text parameter value\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"SnpSift Filter\"]\n  3 -> 4 [label=\"out1\"]\n  0 -> 4 [label=\"output\"]\n  kee67c5edff7c404bad2019259edbc671[color=lightseagreen,label=\"Output\\nconsensus_variants\"]\n  4 -> kee67c5edff7c404bad2019259edbc671\n  5[label=\"bcftools consensus\"]\n  4 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  k9028f80e411240d89a49f671677d304f[color=lightseagreen,label=\"Output\\nconsensus\"]\n  5 -> k9028f80e411240d89a49f671677d304f\n  6[label=\"Collapse Collection\"]\n  5 -> 6 [label=\"output_file\"]\n  k1dd7978eb90742d68fc4f6fadeefcad1[color=lightseagreen,label=\"Output\\nmultisample_consensus_fasta\"]\n  6 -> k1dd7978eb90742d68fc4f6fadeefcad1\n  7[label=\"Pangolin\"]\n  6 -> 7 [label=\"output\"]\n  ke02d2cfb98424069957c6cf4ec197056[color=lightseagreen,label=\"Output\\npangolin_results\"]\n  7 -> ke02d2cfb98424069957c6cf4ec197056\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIris Dataset\"]\n  1[label=\"Convert CSV to tabular\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Datamash\"]\n  1 -> 2 [label=\"tabular\"]\n  k5fc8c705b9e24008aa85e84504b8395f[color=lightseagreen,label=\"Output\\ndatamash_output\"]\n  2 -> k5fc8c705b9e24008aa85e84504b8395f\n  3[label=\"Remove beginning\"]\n  1 -> 3 [label=\"tabular\"]\n  4[label=\"Cut\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"Group\"]\n  3 -> 5 [label=\"out_file1\"]\n  k7e07839ce8ca46928b8e6eb3607066de[color=lightseagreen,label=\"Output\\ngroup1\"]\n  5 -> k7e07839ce8ca46928b8e6eb3607066de\n  6[label=\"Group\"]\n  3 -> 6 [label=\"out_file1\"]\n  k9cb98227aa5b4b77933cffba1e98566e[color=lightseagreen,label=\"Output\\ngroup2\"]\n  6 -> k9cb98227aa5b4b77933cffba1e98566e\n  7[label=\"Scatterplot with ggplot2\"]\n  3 -> 7 [label=\"out_file1\"]\n  8[label=\"Scatterplot with ggplot2\"]\n  3 -> 8 [label=\"out_file1\"]\n  9[label=\"Unique\"]\n  4 -> 9 [label=\"out_file1\"]\n  kfc73409c78784391bc91f99a5be0ba06[color=lightseagreen,label=\"Output\\nunique_output\"]\n  9 -> kfc73409c78784391bc91f99a5be0ba06\n}",
                 "history": [
                     {
-                        "hash": "486585510e665c834a43668e2a769dd69654b9d6",
-                        "message": "add WF automation tutorial",
+                        "hash": "bffad533763a3daa41aa8d7d083c978f46598355",
+                        "message": "update worfklow to not hide png output",
+                        "num": 3,
+                        "short_hash": "bffad5337",
+                        "unix": "1657113550"
+                    },
+                    {
+                        "hash": "56ef1bde9ab0a1e9493989335f23daecaf16510d",
+                        "message": "update topic tag on workflow",
+                        "num": 2,
+                        "short_hash": "56ef1bde9",
+                        "unix": "1654089632"
+                    },
+                    {
+                        "hash": "b200300b458fdfb7d025ece2746ec08134e8ccbd",
+                        "message": "start workflow reports tutorial",
                         "num": 1,
-                        "short_hash": "486585510",
-                        "unix": "1622197006"
+                        "short_hash": "b200300b4",
+                        "unix": "1654074124"
                     }
                 ],
                 "inputs": [
@@ -88788,428 +92263,776 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Variant calls"
+                                "name": "Iris Dataset"
                             }
                         ],
-                        "label": "Variant calls",
-                        "name": "Input dataset collection",
+                        "label": "Iris Dataset",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 425.43333435058594,
+                            "bottom": 205.8000030517578,
                             "height": 61.80000305175781,
-                            "left": 297,
-                            "right": 497,
-                            "top": 363.6333312988281,
+                            "left": 292,
+                            "right": 492,
+                            "top": 144,
                             "width": 200,
-                            "x": 297,
-                            "y": 363.6333312988281
+                            "x": 292,
+                            "y": 144
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "fca4e710-87a7-4cb6-9ff1-f9a8dc84ca37",
+                        "type": "data_input",
+                        "uuid": "6a8d8ca9-8bb9-414b-af8f-50d07721b363",
                         "workflow_outputs": []
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIris Dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Convert CSV to tabular\"];\n  0 -->|output| 1;\n  2[\"Datamash\"];\n  1 -->|tabular| 2;\n  5fc8c705-b9e2-4008-aa85-e84504b8395f[\"Output\\ndatamash_output\"];\n  2 --> 5fc8c705-b9e2-4008-aa85-e84504b8395f;\n  style 5fc8c705-b9e2-4008-aa85-e84504b8395f stroke:#2c3143,stroke-width:4px;\n  3[\"Remove beginning\"];\n  1 -->|tabular| 3;\n  4[\"Cut\"];\n  3 -->|out_file1| 4;\n  5[\"Group\"];\n  3 -->|out_file1| 5;\n  7e07839c-e8ca-4692-8b8e-6eb3607066de[\"Output\\ngroup1\"];\n  5 --> 7e07839c-e8ca-4692-8b8e-6eb3607066de;\n  style 7e07839c-e8ca-4692-8b8e-6eb3607066de stroke:#2c3143,stroke-width:4px;\n  6[\"Group\"];\n  3 -->|out_file1| 6;\n  9cb98227-aa5b-4b77-933c-ffba1e98566e[\"Output\\ngroup2\"];\n  6 --> 9cb98227-aa5b-4b77-933c-ffba1e98566e;\n  style 9cb98227-aa5b-4b77-933c-ffba1e98566e stroke:#2c3143,stroke-width:4px;\n  7[\"Scatterplot with ggplot2\"];\n  3 -->|out_file1| 7;\n  8[\"Scatterplot with ggplot2\"];\n  3 -->|out_file1| 8;\n  9[\"Unique\"];\n  4 -->|out_file1| 9;\n  fc73409c-7878-4391-bc91-f99a5be0ba06[\"Output\\nunique_output\"];\n  9 --> fc73409c-7878-4391-bc91-f99a5be0ba06;\n  style fc73409c-7878-4391-bc91-f99a5be0ba06 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "GTN Training: Workflow Reports - Galaxy 101 For Everyone",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 2,
+                        "input_connections": {
+                            "in_file": {
+                                "id": 1,
+                                "output_name": "tabular"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Datamash",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "min-AF for consensus variant"
+                                "name": "out_file",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "min-AF for consensus variant",
-                        "name": "Input parameter",
-                        "outputs": [],
                         "position": {
-                            "bottom": 619.1000061035156,
-                            "height": 102.60000610351562,
-                            "left": 295.45001220703125,
-                            "right": 495.45001220703125,
-                            "top": 516.5,
+                            "bottom": 52.600006103515625,
+                            "height": 113.60000610351562,
+                            "left": 639,
+                            "right": 839,
+                            "top": -61,
                             "width": 200,
-                            "x": 295.45001220703125,
-                            "y": 516.5
+                            "x": 639,
+                            "y": -61
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": 0.7, \"parameter_type\": \"float\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "52664bd7-b500-40a1-935b-8ac6df7003e5",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "562f3c677828",
+                            "name": "datamash_ops",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"grouping\": \"5\", \"header_in\": \"true\", \"header_out\": \"true\", \"ignore_case\": \"true\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"need_sort\": \"true\", \"operations\": [{\"__index__\": 0, \"op_name\": \"mean\", \"op_column\": \"1\"}, {\"__index__\": 1, \"op_name\": \"sstdev\", \"op_column\": \"1\"}, {\"__index__\": 2, \"op_name\": \"mean\", \"op_column\": \"2\"}, {\"__index__\": 3, \"op_name\": \"sstdev\", \"op_column\": \"2\"}, {\"__index__\": 4, \"op_name\": \"mean\", \"op_column\": \"3\"}, {\"__index__\": 5, \"op_name\": \"sstdev\", \"op_column\": \"3\"}, {\"__index__\": 6, \"op_name\": \"mean\", \"op_column\": \"4\"}, {\"__index__\": 7, \"op_name\": \"sstdev\", \"op_column\": \"4\"}], \"print_full_line\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.0",
+                        "type": "tool",
+                        "uuid": "e1a58a79-5102-450e-bfe0-200f0e64139d",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "5db03aa3-a62d-4a39-8712-d48911abf2bb"
+                                "label": "datamash_output",
+                                "output_name": "out_file",
+                                "uuid": "5fc8c705-b9e2-4008-aa85-e84504b8395f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "Grouping1",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 5,
+                        "input_connections": {
+                            "input1": {
+                                "id": 3,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Group",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Reference genome"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "Reference genome",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 734.8500366210938,
-                            "height": 82.20001220703125,
-                            "left": 749.816650390625,
-                            "right": 949.816650390625,
-                            "top": 652.6500244140625,
+                            "bottom": 496.1999969482422,
+                            "height": 93.19999694824219,
+                            "left": 1059,
+                            "right": 1259,
+                            "top": 403,
                             "width": 200,
-                            "x": 749.816650390625,
-                            "y": 652.6500244140625
+                            "x": 1059,
+                            "y": 403
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "4a2c6df2-fb1e-42d8-96d5-6765ca85c214",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nVariant calls\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nmin-AF for consensus variant\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Compose text parameter value\"];\n  1 -->|output| 3;\n  4[\"SnpSift Filter\"];\n  3 -->|out1| 4;\n  0 -->|output| 4;\n  ee67c5ed-ff7c-404b-ad20-19259edbc671[\"Output\\nconsensus_variants\"];\n  4 --> ee67c5ed-ff7c-404b-ad20-19259edbc671;\n  style ee67c5ed-ff7c-404b-ad20-19259edbc671 stroke:#2c3143,stroke-width:4px;\n  5[\"bcftools consensus\"];\n  4 -->|output| 5;\n  2 -->|output| 5;\n  9028f80e-4112-40d8-9a49-f671677d304f[\"Output\\nconsensus\"];\n  5 --> 9028f80e-4112-40d8-9a49-f671677d304f;\n  style 9028f80e-4112-40d8-9a49-f671677d304f stroke:#2c3143,stroke-width:4px;\n  6[\"Collapse Collection\"];\n  5 -->|output_file| 6;\n  1dd7978e-b907-42d6-8fc4-f6fadeefcad1[\"Output\\nmultisample_consensus_fasta\"];\n  6 --> 1dd7978e-b907-42d6-8fc4-f6fadeefcad1;\n  style 1dd7978e-b907-42d6-8fc4-f6fadeefcad1 stroke:#2c3143,stroke-width:4px;\n  7[\"Pangolin\"];\n  6 -->|output| 7;\n  e02d2cfb-9842-4069-957c-6cf4ec197056[\"Output\\npangolin_results\"];\n  7 --> e02d2cfb-9842-4069-957c-6cf4ec197056;\n  style e02d2cfb-9842-4069-957c-6cf4ec197056 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "vcf2lineage",
-                "outputs": [
+                        "post_job_actions": {},
+                        "tool_id": "Grouping1",
+                        "tool_state": "{\"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"groupcol\": \"5\", \"ignorecase\": \"false\", \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.4",
+                        "type": "tool",
+                        "uuid": "dcd3ddc6-d871-45dd-94ed-3eae56dd56db",
+                        "workflow_outputs": [
+                            {
+                                "label": "group1",
+                                "output_name": "out_file1",
+                                "uuid": "7e07839c-e8ca-4692-8b8e-6eb3607066de"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "Grouping1",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 6,
+                        "input_connections": {
+                            "input1": {
+                                "id": 3,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Group",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "min-AF for consensus variant"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "min-AF for consensus variant",
-                        "name": "Input parameter",
-                        "outputs": [],
                         "position": {
-                            "bottom": 619.1000061035156,
-                            "height": 102.60000610351562,
-                            "left": 295.45001220703125,
-                            "right": 495.45001220703125,
-                            "top": 516.5,
+                            "bottom": 616.1999969482422,
+                            "height": 93.19999694824219,
+                            "left": 1059,
+                            "right": 1259,
+                            "top": 523,
                             "width": 200,
-                            "x": 295.45001220703125,
-                            "y": 516.5
+                            "x": 1059,
+                            "y": 523
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": 0.7, \"parameter_type\": \"float\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "52664bd7-b500-40a1-935b-8ac6df7003e5",
+                        "post_job_actions": {},
+                        "tool_id": "Grouping1",
+                        "tool_state": "{\"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"groupcol\": \"5\", \"ignorecase\": \"false\", \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [{\"__index__\": 0, \"optype\": \"length\", \"opcol\": \"1\", \"opround\": \"no\", \"opdefault\": null}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.4",
+                        "type": "tool",
+                        "uuid": "285a3852-71cb-4137-be1d-b0ec0a59d9e9",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "5db03aa3-a62d-4a39-8712-d48911abf2bb"
+                                "label": "group2",
+                                "output_name": "out_file1",
+                                "uuid": "9cb98227-aa5b-4b77-933c-ffba1e98566e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
                         "errors": null,
-                        "id": 4,
+                        "id": 7,
                         "input_connections": {
-                            "filter_expression|expr": {
+                            "input1": {
                                 "id": 3,
-                                "output_name": "out1"
-                            },
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
+                                "output_name": "out_file1"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Scatterplot with ggplot2",
+                                "name": "input1"
+                            }
+                        ],
                         "label": null,
-                        "name": "SnpSift Filter",
+                        "name": "Scatterplot with ggplot2",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "vcf"
+                                "name": "output1",
+                                "type": "png"
+                            },
+                            {
+                                "name": "output2",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "bottom": 506.5,
-                            "height": 144,
-                            "left": 750.2833251953125,
-                            "right": 950.2833251953125,
-                            "top": 362.5,
+                            "bottom": 889,
+                            "height": 246,
+                            "left": 1059,
+                            "right": 1259,
+                            "top": 643,
                             "width": 200,
-                            "x": 750.2833251953125,
-                            "y": 362.5
+                            "x": 1059,
+                            "y": 643
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Consensus variants"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
+                            "HideDatasetActionoutput2": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output2"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "2e497a770bca",
-                            "name": "snpsift",
+                            "changeset_revision": "1acf88921176",
+                            "name": "ggplot2_point",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"filter_expression\": {\"type\": \"simple\", \"__current_case__\": 0, \"expr\": {\"__class__\": \"ConnectedValue\"}}, \"filtering\": {\"mode\": \"entries\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inverse\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.3+t.galaxy1",
+                        "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"points\", \"__current_case__\": 0, \"points\": {\"pointoptions\": \"default\", \"__current_case__\": 0}}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"5\", \"colors\": \"Set2\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"7.0\", \"height_output_dim\": \"7.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"pdf\"}, \"title\": \"Sepal length as a function of sepal width\", \"xlab\": \"Sepal length\", \"xplot\": \"1\", \"ylab\": \"Sepal width\", \"yplot\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.3.5+galaxy0",
                         "type": "tool",
-                        "uuid": "3673b687-1ba0-42f2-ba13-fa3130462079",
+                        "uuid": "fa412209-5e3a-448e-8b0b-fa88870e19c1",
                         "workflow_outputs": [
                             {
-                                "label": "consensus_variants",
-                                "output_name": "output",
-                                "uuid": "ee67c5ed-ff7c-404b-ad20-19259edbc671"
+                                "label": null,
+                                "output_name": "output1",
+                                "uuid": "edb75294-0687-433e-821e-cffc03c7c103"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
                         "errors": null,
-                        "id": 5,
+                        "id": 8,
                         "input_connections": {
-                            "input_file": {
-                                "id": 4,
-                                "output_name": "output"
-                            },
-                            "reference_source|fasta_ref": {
-                                "id": 2,
-                                "output_name": "output"
+                            "input1": {
+                                "id": 3,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool bcftools consensus",
-                                "name": "input_file"
-                            },
-                            {
-                                "description": "runtime parameter for tool bcftools consensus",
-                                "name": "reference_source"
-                            },
-                            {
-                                "description": "runtime parameter for tool bcftools consensus",
-                                "name": "sec_default"
+                                "description": "runtime parameter for tool Scatterplot with ggplot2",
+                                "name": "input1"
                             }
                         ],
                         "label": null,
-                        "name": "bcftools consensus",
+                        "name": "Scatterplot with ggplot2",
                         "outputs": [
                             {
-                                "name": "output_file",
-                                "type": "fasta"
+                                "name": "output1",
+                                "type": "png"
+                            },
+                            {
+                                "name": "output2",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "bottom": 535.5666809082031,
-                            "height": 174.39999389648438,
-                            "left": 993.8333129882812,
-                            "right": 1193.8333129882812,
-                            "top": 361.16668701171875,
+                            "bottom": 1009,
+                            "height": 246,
+                            "left": 1059,
+                            "right": 1259,
+                            "top": 763,
                             "width": 200,
-                            "x": 993.8333129882812,
-                            "y": 361.16668701171875
+                            "x": 1059,
+                            "y": 763
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput_file": {
-                                "action_arguments": {
-                                    "newname": "Consensus sequences"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_file"
+                            "HideDatasetActionoutput2": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output2"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "e522022137f6",
-                            "name": "bcftools_consensus",
+                            "changeset_revision": "1acf88921176",
+                            "name": "ggplot2_point",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"chain\": \"false\", \"input_file\": {\"__class__\": \"RuntimeValue\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"RuntimeValue\"}}, \"rename\": \"true\", \"sec_default\": {\"mask\": {\"__class__\": \"RuntimeValue\"}, \"iupac_codes\": \"false\", \"sample\": \"\", \"select_haplotype\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.10",
+                        "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"points\", \"__current_case__\": 0, \"points\": {\"pointoptions\": \"default\", \"__current_case__\": 0}}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"5\", \"colors\": \"Set2\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"7.0\", \"height_output_dim\": \"7.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"pdf\"}, \"title\": \"Petal length as a function of petal width\", \"xlab\": \"Petal length\", \"xplot\": \"3\", \"ylab\": \"Petal width\", \"yplot\": \"4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.3.5+galaxy0",
                         "type": "tool",
-                        "uuid": "5d2e8bea-3e75-4453-9494-b5fd52b2f528",
+                        "uuid": "8e7b3f8d-2b8b-46cb-93d4-0d74bf54441e",
                         "workflow_outputs": [
                             {
-                                "label": "consensus",
-                                "output_name": "output_file",
-                                "uuid": "9028f80e-4112-40d8-9a49-f671677d304f"
+                                "label": null,
+                                "output_name": "output1",
+                                "uuid": "9e55c569-0443-4b96-b34a-e37a8416cd22"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
                         "errors": null,
-                        "id": 6,
+                        "id": 9,
                         "input_connections": {
-                            "input_list": {
-                                "id": 5,
-                                "output_name": "output_file"
+                            "infile": {
+                                "id": 4,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Collapse Collection",
+                        "name": "Unique",
                         "outputs": [
                             {
-                                "name": "output",
+                                "name": "outfile",
                                 "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 537.8000030517578,
-                            "height": 174.8000030517578,
-                            "left": 1223.5,
-                            "right": 1423.5,
-                            "top": 363,
+                            "bottom": 276.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": 1279,
+                            "right": 1479,
+                            "top": 163,
                             "width": 200,
-                            "x": 1223.5,
-                            "y": 363
+                            "x": 1279,
+                            "y": 163
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Multisample consensus FASTA"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_numeric\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.0",
+                        "type": "tool",
+                        "uuid": "3e2d84e9-2fff-4321-9db6-41af99367162",
+                        "workflow_outputs": [
+                            {
+                                "label": "unique_output",
+                                "output_name": "outfile",
+                                "uuid": "fc73409c-7878-4391-bc91-f99a5be0ba06"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "galaxy-interface/workflow-reports",
+                "path": "topics/galaxy-interface/tutorials/workflow-reports/workflows/galaxy-101-everyone.ga",
+                "tags": [
+                    "galaxy-interface"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "GTN Training: Workflow Reports - Galaxy 101 For Everyone",
+                "topic_id": "galaxy-interface",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/galaxy-interface-workflow-reports/versions/galaxy-101-everyone",
+                "tutorial_id": "workflow-reports",
+                "url": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-reports/workflows/galaxy-101-everyone.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-reports/workflows/galaxy-101-everyone.html",
+                "version": 2,
+                "wfid": "galaxy-interface-workflow-reports",
+                "wfname": "galaxy-101-everyone",
+                "workflow": "galaxy-101-everyone.ga",
+                "workflow_tools": [
+                    "Cut1",
+                    "Grouping1",
+                    "Remove beginning1",
+                    "csv_to_tabular",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0"
+                ],
+                "workflowhub_id": "1301"
+            },
+            {
+                "creators": [],
+                "description": "introduction",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": {
+                        "markdown": "# Iris Analysis\n\nBelow are the results for the Iris analysis workflow.\n\nThis workflow was run on:\n\n```galaxy\ngenerate_time()\n```\n\nWith Galaxy version:\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n# Results\n\n## Species detected\n\ndisplay:\n```galaxy\nhistory_dataset_display(output=\"Iris Species\")\n```\n\n## Sepal plot\n\n```galaxy\nhistory_dataset_as_image(output=\"Sepal Plot (PNG)\")\n```\n\n## Petal Plot\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Petal Plot (PNG)\")\n```\n\n\n\n\n"
+                    },
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIris Dataset\"]\n  1[label=\"Convert CSV to tabular\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Datamash\"]\n  1 -> 2 [label=\"tabular\"]\n  k5381f9b05170484c828e4469ec27ab3e[color=lightseagreen,label=\"Output\\ndatamash_output\"]\n  2 -> k5381f9b05170484c828e4469ec27ab3e\n  3[label=\"Remove beginning\"]\n  1 -> 3 [label=\"tabular\"]\n  4[label=\"Cut\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"Group\"]\n  3 -> 5 [label=\"out_file1\"]\n  k836a57b33657435bb396869af7e2f35e[color=lightseagreen,label=\"Output\\ngroup1\"]\n  5 -> k836a57b33657435bb396869af7e2f35e\n  6[label=\"Group\"]\n  3 -> 6 [label=\"out_file1\"]\n  k82e163a48fc54b8e81869fc66cd75b1d[color=lightseagreen,label=\"Output\\ngroup2\"]\n  6 -> k82e163a48fc54b8e81869fc66cd75b1d\n  7[label=\"Scatterplot with ggplot2\"]\n  3 -> 7 [label=\"out_file1\"]\n  kbbbac6ca64fb46ad87986c7c5369ccaf[color=lightseagreen,label=\"Output\\nSepal Plot (PNG)\"]\n  7 -> kbbbac6ca64fb46ad87986c7c5369ccaf\n  8[label=\"Scatterplot with ggplot2\"]\n  3 -> 8 [label=\"out_file1\"]\n  k74ee0c3c53c244cfb0e82a10c24166c9[color=lightseagreen,label=\"Output\\nPetal Plot (PNG)\"]\n  8 -> k74ee0c3c53c244cfb0e82a10c24166c9\n  9[label=\"Unique\"]\n  4 -> 9 [label=\"out_file1\"]\n  k6bcc2f96255e48f5a37b7d6a2c123493[color=lightseagreen,label=\"Output\\nIris Species\"]\n  9 -> k6bcc2f96255e48f5a37b7d6a2c123493\n}",
+                "history": [
+                    {
+                        "hash": "a8cea912fc5b649e72e07b366c1a53299559c901",
+                        "message": "add final workflow with report",
+                        "num": 1,
+                        "short_hash": "a8cea912f",
+                        "unix": "1654092494"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Iris Dataset"
+                            }
+                        ],
+                        "label": "Iris Dataset",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 383.8000030517578,
+                            "height": 61.80000305175781,
+                            "left": -119.5,
+                            "right": 80.5,
+                            "top": 322,
+                            "width": 200,
+                            "x": -119.5,
+                            "y": 322
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "6a8d8ca9-8bb9-414b-af8f-50d07721b363",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIris Dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Convert CSV to tabular\"];\n  0 -->|output| 1;\n  2[\"Datamash\"];\n  1 -->|tabular| 2;\n  5381f9b0-5170-484c-828e-4469ec27ab3e[\"Output\\ndatamash_output\"];\n  2 --> 5381f9b0-5170-484c-828e-4469ec27ab3e;\n  style 5381f9b0-5170-484c-828e-4469ec27ab3e stroke:#2c3143,stroke-width:4px;\n  3[\"Remove beginning\"];\n  1 -->|tabular| 3;\n  4[\"Cut\"];\n  3 -->|out_file1| 4;\n  5[\"Group\"];\n  3 -->|out_file1| 5;\n  836a57b3-3657-435b-b396-869af7e2f35e[\"Output\\ngroup1\"];\n  5 --> 836a57b3-3657-435b-b396-869af7e2f35e;\n  style 836a57b3-3657-435b-b396-869af7e2f35e stroke:#2c3143,stroke-width:4px;\n  6[\"Group\"];\n  3 -->|out_file1| 6;\n  82e163a4-8fc5-4b8e-8186-9fc66cd75b1d[\"Output\\ngroup2\"];\n  6 --> 82e163a4-8fc5-4b8e-8186-9fc66cd75b1d;\n  style 82e163a4-8fc5-4b8e-8186-9fc66cd75b1d stroke:#2c3143,stroke-width:4px;\n  7[\"Scatterplot with ggplot2\"];\n  3 -->|out_file1| 7;\n  bbbac6ca-64fb-46ad-8798-6c7c5369ccaf[\"Output\\nSepal Plot (PNG)\"];\n  7 --> bbbac6ca-64fb-46ad-8798-6c7c5369ccaf;\n  style bbbac6ca-64fb-46ad-8798-6c7c5369ccaf stroke:#2c3143,stroke-width:4px;\n  8[\"Scatterplot with ggplot2\"];\n  3 -->|out_file1| 8;\n  74ee0c3c-53c2-44cf-b0e8-2a10c24166c9[\"Output\\nPetal Plot (PNG)\"];\n  8 --> 74ee0c3c-53c2-44cf-b0e8-2a10c24166c9;\n  style 74ee0c3c-53c2-44cf-b0e8-2a10c24166c9 stroke:#2c3143,stroke-width:4px;\n  9[\"Unique\"];\n  4 -->|out_file1| 9;\n  6bcc2f96-255e-48f5-a37b-7d6a2c123493[\"Output\\nIris Species\"];\n  9 --> 6bcc2f96-255e-48f5-a37b-7d6a2c123493;\n  style 6bcc2f96-255e-48f5-a37b-7d6a2c123493 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "GTN Training: Workflow Reports",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "in_file": {
+                                "id": 1,
+                                "output_name": "tabular"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Datamash",
+                        "outputs": [
+                            {
+                                "name": "out_file",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 278.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": 372.5,
+                            "right": 572.5,
+                            "top": 165,
+                            "width": 200,
+                            "x": 372.5,
+                            "y": 165
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "830961c48e42",
-                            "name": "collapse_collections",
-                            "owner": "nml",
+                            "changeset_revision": "562f3c677828",
+                            "name": "datamash_ops",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"filename\": {\"add_name\": \"false\", \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.2",
+                        "tool_state": "{\"grouping\": \"5\", \"header_in\": \"true\", \"header_out\": \"true\", \"ignore_case\": \"true\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"need_sort\": \"true\", \"operations\": [{\"__index__\": 0, \"op_name\": \"mean\", \"op_column\": \"1\"}, {\"__index__\": 1, \"op_name\": \"sstdev\", \"op_column\": \"1\"}, {\"__index__\": 2, \"op_name\": \"mean\", \"op_column\": \"2\"}, {\"__index__\": 3, \"op_name\": \"sstdev\", \"op_column\": \"2\"}, {\"__index__\": 4, \"op_name\": \"mean\", \"op_column\": \"3\"}, {\"__index__\": 5, \"op_name\": \"sstdev\", \"op_column\": \"3\"}, {\"__index__\": 6, \"op_name\": \"mean\", \"op_column\": \"4\"}, {\"__index__\": 7, \"op_name\": \"sstdev\", \"op_column\": \"4\"}], \"print_full_line\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.0",
                         "type": "tool",
-                        "uuid": "acae0f3e-448b-483e-a44a-3e09ce9b3e77",
+                        "uuid": "e1a58a79-5102-450e-bfe0-200f0e64139d",
                         "workflow_outputs": [
                             {
-                                "label": "multisample_consensus_fasta",
-                                "output_name": "output",
-                                "uuid": "1dd7978e-b907-42d6-8fc4-f6fadeefcad1"
+                                "label": "datamash_output",
+                                "output_name": "out_file",
+                                "uuid": "5381f9b0-5170-484c-828e-4469ec27ab3e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8",
+                        "content_id": "Grouping1",
                         "errors": null,
-                        "id": 7,
+                        "id": 5,
                         "input_connections": {
                             "input1": {
-                                "id": 6,
-                                "output_name": "output"
+                                "id": 3,
+                                "output_name": "out_file1"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Group",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool Pangolin",
-                                "name": "input1"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
+                        "position": {
+                            "bottom": 538.1999969482422,
+                            "height": 93.19999694824219,
+                            "left": 668.5,
+                            "right": 868.5,
+                            "top": 445,
+                            "width": 200,
+                            "x": 668.5,
+                            "y": 445
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "Grouping1",
+                        "tool_state": "{\"groupcol\": \"5\", \"ignorecase\": \"false\", \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.4",
+                        "type": "tool",
+                        "uuid": "dcd3ddc6-d871-45dd-94ed-3eae56dd56db",
+                        "workflow_outputs": [
+                            {
+                                "label": "group1",
+                                "output_name": "out_file1",
+                                "uuid": "836a57b3-3657-435b-b396-869af7e2f35e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "Grouping1",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "input1": {
+                                "id": 3,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
                         "label": null,
-                        "name": "Pangolin",
+                        "name": "Group",
                         "outputs": [
                             {
-                                "name": "output1",
+                                "name": "out_file1",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 512.1999969482422,
+                            "bottom": 683.1999969482422,
                             "height": 93.19999694824219,
-                            "left": 1451,
-                            "right": 1651,
-                            "top": 419,
+                            "left": 667.5,
+                            "right": 867.5,
+                            "top": 590,
                             "width": 200,
-                            "x": 1451,
-                            "y": 419
+                            "x": 667.5,
+                            "y": 590
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput1": {
-                                "action_arguments": {
-                                    "newname": "Pangolin lineage assignments"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output1"
+                        "post_job_actions": {},
+                        "tool_id": "Grouping1",
+                        "tool_state": "{\"groupcol\": \"5\", \"ignorecase\": \"false\", \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [{\"__index__\": 0, \"optype\": \"length\", \"opcol\": \"1\", \"opround\": \"no\", \"opdefault\": null}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.4",
+                        "type": "tool",
+                        "uuid": "285a3852-71cb-4137-be1d-b0ec0a59d9e9",
+                        "workflow_outputs": [
+                            {
+                                "label": "group2",
+                                "output_name": "out_file1",
+                                "uuid": "82e163a4-8fc5-4b8e-8186-9fc66cd75b1d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "input1": {
+                                "id": 3,
+                                "output_name": "out_file1"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Scatterplot with ggplot2",
+                        "outputs": [
+                            {
+                                "name": "output1",
+                                "type": "png"
+                            },
+                            {
+                                "name": "output2",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 924.1999969482422,
+                            "height": 205.1999969482422,
+                            "left": 971.5,
+                            "right": 1171.5,
+                            "top": 719,
+                            "width": 200,
+                            "x": 971.5,
+                            "y": 719
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "b6abccb1f25b",
-                            "name": "pangolin",
+                            "changeset_revision": "1acf88921176",
+                            "name": "ggplot2_point",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"alignment\": \"false\", \"db\": {\"source\": \"builtin\", \"__current_case__\": 1, \"db_release\": \"2021-05-11\"}, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"max_ambig\": \"0.5\", \"min_length\": \"10000\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.3.8",
+                        "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"points\", \"__current_case__\": 0, \"points\": {\"pointoptions\": \"default\", \"__current_case__\": 0}}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"5\", \"colors\": \"Set2\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"7.0\", \"height_output_dim\": \"7.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"pdf\"}, \"title\": \"Sepal length as a function of sepal width\", \"xlab\": \"Sepal length\", \"xplot\": \"1\", \"ylab\": \"Sepal width\", \"yplot\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.3.5+galaxy0",
                         "type": "tool",
-                        "uuid": "bf8893e0-d08c-46c9-b384-a8ad0fc88185",
+                        "uuid": "fa412209-5e3a-448e-8b0b-fa88870e19c1",
                         "workflow_outputs": [
                             {
-                                "label": "pangolin_results",
+                                "label": null,
+                                "output_name": "output2",
+                                "uuid": "d8dd48e7-e9e0-4b5c-8d9f-4b47be570e31"
+                            },
+                            {
+                                "label": "Sepal Plot (PNG)",
                                 "output_name": "output1",
-                                "uuid": "e02d2cfb-9842-4069-957c-6cf4ec197056"
+                                "uuid": "bbbac6ca-64fb-46ad-8798-6c7c5369ccaf"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "input1": {
+                                "id": 3,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Scatterplot with ggplot2",
+                        "outputs": [
+                            {
+                                "name": "output1",
+                                "type": "png"
+                            },
+                            {
+                                "name": "output2",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 1210.1999969482422,
+                            "height": 205.1999969482422,
+                            "left": 677.5,
+                            "right": 877.5,
+                            "top": 1005,
+                            "width": 200,
+                            "x": 677.5,
+                            "y": 1005
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "1acf88921176",
+                            "name": "ggplot2_point",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"points\", \"__current_case__\": 0, \"points\": {\"pointoptions\": \"default\", \"__current_case__\": 0}}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"5\", \"colors\": \"Set2\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"7.0\", \"height_output_dim\": \"7.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"pdf\"}, \"title\": \"Petal length as a function of petal width\", \"xlab\": \"Petal length\", \"xplot\": \"3\", \"ylab\": \"Petal width\", \"yplot\": \"4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.3.5+galaxy0",
+                        "type": "tool",
+                        "uuid": "8e7b3f8d-2b8b-46cb-93d4-0d74bf54441e",
+                        "workflow_outputs": [
+                            {
+                                "label": "Petal Plot (PNG)",
+                                "output_name": "output1",
+                                "uuid": "74ee0c3c-53c2-44cf-b0e8-2a10c24166c9"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output2",
+                                "uuid": "54f6cc43-48a3-495d-9f11-4f03e19d56ef"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {
+                            "infile": {
+                                "id": 4,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Unique",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 382.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": 922.5,
+                            "right": 1122.5,
+                            "top": 269,
+                            "width": 200,
+                            "x": 922.5,
+                            "y": 269
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_numeric\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.0",
+                        "type": "tool",
+                        "uuid": "3e2d84e9-2fff-4321-9db6-41af99367162",
+                        "workflow_outputs": [
+                            {
+                                "label": "Iris Species",
+                                "output_name": "outfile",
+                                "uuid": "6bcc2f96-255e-48f5-a37b-7d6a2c123493"
                             }
                         ]
                     }
                 ],
-                "parent_id": "galaxy-interface/workflow-automation",
-                "path": "topics/galaxy-interface/tutorials/workflow-automation/workflows/main_workflow.ga",
+                "parent_id": "galaxy-interface/workflow-reports",
+                "path": "topics/galaxy-interface/tutorials/workflow-reports/workflows/workflow_reports_final_workflow.ga",
                 "tags": [
-                    "variant-analysis",
                     "galaxy-interface"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "vcf2lineage",
+                "title": "GTN Training: Workflow Reports",
                 "topic_id": "galaxy-interface",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/galaxy-interface-workflow-automation/versions/main-workflow",
-                "tutorial_id": "workflow-automation",
-                "url": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-automation/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-automation/workflows/main_workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/galaxy-interface-workflow-reports/versions/workflow-reports-final-workflow",
+                "tutorial_id": "workflow-reports",
+                "url": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-reports/workflows/workflow_reports_final_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-reports/workflows/workflow_reports_final_workflow.html",
                 "version": 1,
-                "wfid": "galaxy-interface-workflow-automation",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "wfid": "galaxy-interface-workflow-reports",
+                "wfname": "workflow-reports-final-workflow",
+                "workflow": "workflow_reports_final_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
+                    "Cut1",
+                    "Grouping1",
+                    "Remove beginning1",
+                    "csv_to_tabular",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0"
                 ],
-                "workflowhub_id": "1293"
+                "workflowhub_id": "1297"
             }
         ],
         "zenodo_link": ""
@@ -89257,6 +93080,7 @@
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.eu",
             "UseGalaxy.no",
@@ -89279,7 +93103,7 @@
             "Learn how to import/export data from/to InterMine instances",
             "Understand the InterMine Interchange Dataset"
         ],
-        "pageviews": 185,
+        "pageviews": 195,
         "pub_date": "2020-12-09",
         "questions": [
             "How to export your query results from your InterMine of choice to Galaxy?",
@@ -89295,6 +93119,11 @@
         "subtopic": "analyse",
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -89353,8 +93182,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 149,
-        "visitors": 134,
+        "visit_duration": 136,
+        "visitors": 144,
         "workflows": [
             {
                 "creators": [],
@@ -89413,7 +93242,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Create InterMine Interchange\"];\n  0 -->|output| 1;",
-                "modified": "2024-08-18 00:06:23 +0000",
+                "modified": "2024-10-02 12:08:08 +0000",
                 "name": "Intermine import/export",
                 "outputs": [
                     {
@@ -89549,6 +93378,7 @@
         "edam_topic": [],
         "exact_supported_servers": [
             "Galaxy@AuBi",
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.eu",
             "UseGalaxy.fr",
@@ -89560,7 +93390,9 @@
         "feedback_number": 0,
         "hands_on": true,
         "id": "galaxy-interface/workflow-editor",
-        "inexact_supported_servers": [],
+        "inexact_supported_servers": [
+            "MISSISSIPPI"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
@@ -89576,7 +93408,7 @@
             "Understand key aspects of workflows",
             "Create clean, non-repetitive workflows"
         ],
-        "pageviews": 5647,
+        "pageviews": 5838,
         "pub_date": "2020-07-17",
         "questions": [
             "How can you construct Galaxy workflows from scratch?",
@@ -89602,6 +93434,11 @@
                     "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -89633,7 +93470,13 @@
                     "usegalaxy": true
                 }
             ],
-            "inexact": []
+            "inexact": [
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                }
+            ]
         },
         "symlink": null,
         "tags": [
@@ -89665,8 +93508,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 177,
-        "visitors": 4433,
+        "visit_duration": 179,
+        "visitors": 4590,
         "workflows": [
             {
                 "creators": [],
@@ -89738,7 +93581,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Reverse dataset\"];\n  0 -->|output| 1;\n  2[\"Select first lines\"];\n  1 -->|outfile| 2;\n  daf1abd9-a5c8-4b25-add1-5475e594f187[\"Output\\nFirst lines\"];\n  2 --> daf1abd9-a5c8-4b25-add1-5475e594f187;\n  style daf1abd9-a5c8-4b25-add1-5475e594f187 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
+                "modified": "2024-10-02 12:08:08 +0000",
                 "name": "Tutorial workflow",
                 "outputs": [
                     {
@@ -89920,7 +93763,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\ud83d\udee0\ufe0f Subworkflow\\nworkflow 1\"];\n  style 1 fill:#edd,stroke:#900,stroke-width:4px;\n  0 -->|output| 1;\n  88160926-01a6-4903-8737-1f3d65449e12[\"Output\\nFirst lines\"];\n  1 --> 88160926-01a6-4903-8737-1f3d65449e12;\n  style 88160926-01a6-4903-8737-1f3d65449e12 stroke:#2c3143,stroke-width:4px;\n  2[\"\ud83d\udee0\ufe0f Subworkflow\\nworkflow 2\"];\n  style 2 fill:#edd,stroke:#900,stroke-width:4px;\n  0 -->|output| 2;\n  f18ca9d2-a8bb-4317-86cb-bad2ef3d2fba[\"Output\\nFirst lines\"];\n  2 --> f18ca9d2-a8bb-4317-86cb-bad2ef3d2fba;\n  style f18ca9d2-a8bb-4317-86cb-bad2ef3d2fba stroke:#2c3143,stroke-width:4px;\n  3[\"Paste\"];\n  1 -->|First lines| 3;\n  2 -->|First lines| 3;",
-                "modified": "2024-08-18 00:06:23 +0000",
+                "modified": "2024-10-02 12:08:08 +0000",
                 "name": "Subworkflow",
                 "outputs": [
                     {
@@ -90430,362 +94273,6 @@
         ],
         "zenodo_link": ""
     },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-parameters/tutorial.json",
-        "contributors": [
-            {
-                "id": "mvdbeek",
-                "joined": "2018-06",
-                "name": "Marius van den Beek",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            }
-        ],
-        "dir": "topics/galaxy-interface/tutorials/workflow-parameters",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "Galaxy@AuBi",
-            "GalaxyTrakr",
-            "HyPhy HIV NGS Tools",
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "galaxy-interface/workflow-parameters",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Use Workflow Parameters to make your Workflows more versatile"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
-        "objectives": [
-            "Learn how to use Workflow Parameters to improve your Workflows"
-        ],
-        "pageviews": 2009,
-        "pub_date": "2019-06-27",
-        "questions": [
-            "What are Workflow Parameters",
-            "How can I define and use Workflow Parameters",
-            "How can I read Parameters from Datasets"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "mvdbeek"
-                ],
-                "date": "2022-07-06",
-                "length": "30M",
-                "speakers": [
-                    "mvdbeek"
-                ],
-                "youtube_id": "otvEuDlCye0"
-            }
-        ],
-        "redirect_from": [
-            "/topics/galaxy-ui/tutorials/workflow-parameters/tutorial",
-            "/short/galaxy-interface/workflow-parameters",
-            "/short/T00164"
-        ],
-        "short_id": "T00164",
-        "short_tools": [
-            "tp_head_tool"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "workflows",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "HyPhy HIV NGS Tools",
-                    "url": "https://galaxy.hyphy.org/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "workflows"
-        ],
-        "time_estimation": "30m",
-        "title": "Using Workflow Parameters",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0"
-        ],
-        "topic_name": "galaxy-interface",
-        "topic_name_human": "Using Galaxy and Managing your Data",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "workflow-parameters",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-parameters/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-parameters/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-parameters/tutorial.json"
-        },
-        "version": 15,
-        "video": false,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 129,
-        "visitors": 1553,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Workflows: Using Workflow Parameters",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[label=\"Select first\"]\n  0 -> 1 [label=\"output\"]\n}",
-                "history": [
-                    {
-                        "hash": "dfe28b422df8f2d253c12f50c87ac20353493eea",
-                        "message": "Completely merge topics",
-                        "num": 1,
-                        "short_hash": "dfe28b422",
-                        "unix": "1592211035"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 162.9609375,
-                            "top": 199.9921875
-                        },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ac600c9c-04f0-4e2d-9bd7-636de8a7ae56",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "3e5ff777-86d7-4510-8f63-d0c6379656fe"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Select first\"];\n  0 -->|output| 1;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Select First N Lines",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 162.9609375,
-                            "top": 199.9921875
-                        },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ac600c9c-04f0-4e2d-9bd7-636de8a7ae56",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "3e5ff777-86d7-4510-8f63-d0c6379656fe"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0",
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {
-                            "infile": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Select first",
-                                "name": "infile"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Select first",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 463.9453125,
-                            "top": 197.9765625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "0a8c6b61f0f4",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"complement\": \"\\\"\\\"\", \"count\": \"\\\"10\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.0",
-                        "type": "tool",
-                        "uuid": "6ef9506c-cf7b-48c9-889f-db7dfb97389a",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "6f9509ee-42cd-4c3d-81fc-22c3a95de600"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "galaxy-interface/workflow-parameters",
-                "path": "topics/galaxy-interface/tutorials/workflow-parameters/workflows/cut_n_lines.ga",
-                "tags": [
-                    "galaxy-interface"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Select First N Lines",
-                "topic_id": "galaxy-interface",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/galaxy-interface-workflow-parameters/versions/cut-n-lines",
-                "tutorial_id": "workflow-parameters",
-                "url": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-parameters/workflows/cut_n_lines.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-parameters/workflows/cut_n_lines.html",
-                "version": 1,
-                "wfid": "galaxy-interface-workflow-parameters",
-                "wfname": "cut-n-lines",
-                "workflow": "cut_n_lines.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0"
-                ],
-                "workflowhub_id": "1304"
-            }
-        ],
-        "zenodo_link": ""
-    },
     {
         "admin_install": {
             "install_repository_dependencies": true,
@@ -90874,7 +94361,7 @@
             "Submit raw sequencing reads and metadata to ENA's test server",
             "Submit consensus sequence and metadata to ENA's test server"
         ],
-        "pageviews": 4636021,
+        "pageviews": 4806337,
         "pub_date": "2021-08-10",
         "questions": [
             "How do you submit raw sequence reads and assembled genomes to the European Nucleotide Archive?"
@@ -90897,8 +94384,8 @@
         ],
         "short_id": "T00159",
         "short_tools": [
-            "ena_webin_cli",
-            "ena_upload"
+            "ena_upload",
+            "ena_webin_cli"
         ],
         "slides": true,
         "slides_recordings": false,
@@ -90936,8 +94423,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 238,
-        "visitors": 1741666,
+        "visit_duration": 236,
+        "visitors": 1810937,
         "workflows": [
             {
                 "creators": [],
@@ -90961,7 +94448,7 @@
                 "inputs": [],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"ENA Upload tool\"];\n  1[\"ENA Upload tool\"];",
-                "modified": "2024-08-18 00:06:23 +0000",
+                "modified": "2024-10-02 12:08:08 +0000",
                 "name": "GTN_ENA_upload_workflow",
                 "outputs": [
                     {
@@ -91078,227 +94565,148 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "bcftools_consensus",
+                    "owner": "iuc",
+                    "revisions": "e522022137f6",
+                    "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "datamash_ops",
+                    "name": "compose_text_param",
                     "owner": "iuc",
-                    "revisions": "562f3c677828",
-                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "revisions": "e188c9826e0f",
+                    "tool_panel_section_label": "Expression Tools",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ggplot2_point",
+                    "name": "pangolin",
                     "owner": "iuc",
-                    "revisions": "1acf88921176",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "revisions": "b6abccb1f25b",
+                    "tool_panel_section_label": "Phylogenetics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "snpsift",
+                    "owner": "iuc",
+                    "revisions": "5fab4f81391d",
+                    "tool_panel_section_label": "Variant Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "830961c48e42",
+                    "tool_panel_section_label": "Collection Operations",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 562f3c677828\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ggplot2_point\n  owner: iuc\n  revisions: 1acf88921176\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-reports/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "shiltemann"
-            ],
-            "funding": [
-                "gallantries"
-            ],
-            "infrastructure": [
-                "jmchilton",
-                "guerler",
-                "mvdbeek"
-            ],
-            "testing": [
-                "hexylena"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bcftools_consensus\n  owner: iuc\n  revisions: e522022137f6\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: compose_text_param\n  owner: iuc\n  revisions: e188c9826e0f\n  tool_panel_section_label: Expression Tools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pangolin\n  owner: iuc\n  revisions: b6abccb1f25b\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpsift\n  owner: iuc\n  revisions: 5fab4f81391d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-automation/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
                 ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+                "id": "simonbray",
+                "joined": "2019-05",
+                "name": "Simon Bray",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
             },
             {
                 "affiliations": [
-                    "gallantries",
                     "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
+                    "uni-freiburg",
+                    "elixir-europe"
                 ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "email": "jmchilton@gmail.com",
-                "id": "jmchilton",
-                "joined": "2017-09",
-                "matrix": "jmchilton:matrix.org",
-                "name": "John Chilton",
-                "orcid": "0000-0002-6794-0756",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jmchilton/",
-                "twitter": "jmchilton",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jmchilton.json"
-            },
-            {
-                "id": "guerler",
+                "elixir_node": "de",
+                "fediverse": "https://scholar.social/@zerodivision",
+                "fediverse_flavor": "mastodon",
+                "id": "wm75",
                 "joined": "2017-09",
-                "name": "Aysam Guerler",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/guerler/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/guerler.json"
-            },
-            {
-                "id": "mvdbeek",
-                "joined": "2018-06",
-                "name": "Marius van den Beek",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+                "matrix": "wm75:matrix.org",
+                "name": "Wolfgang Maier",
+                "orcid": "0000-0002-9464-6640",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
             }
         ],
-        "dir": "topics/galaxy-interface/tutorials/workflow-reports",
+        "dir": "topics/galaxy-interface/tutorials/workflow-automation",
         "edam_operation": [
-            "Visualisation"
+            "Tree-based sequence alignment",
+            "Variant classification"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "galaxy-interface/workflow-reports",
+        "id": "galaxy-interface/workflow-automation",
         "inexact_supported_servers": [
-            "Galaxy@AuBi",
-            "UseGalaxy.cz"
+            "MISSISSIPPI",
+            "UseGalaxy.fr"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Workflow reports help you display the most important results of a workflow in an organized fashion.",
-            "Workflow reports are configured as part of the workflow definition, for every run of the workflow, a report will be automatically created",
-            "Workflow reports can be viewed from the top menu, **User -> Workflow Invocations**.",
-            "Labels must be added to workflow outputs before they can be included",
-            "Many different components can be added to a workflow report (datasets, images, links to datasets, job metrics, text and sections, visualisations, and much more!)",
-            "Workflow reports can be shared as Galaxy Pages."
+            "Workflows can be executed not only through the web browser, but also via the command line.",
+            "Executing workflows programmatically allows automation of analyses."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
         "license": "CC-BY-4.0",
         "mod_date": "2024-06-14",
         "objectives": [
-            "Understanding, viewing and creating workflow reports"
+            "Learn to use the `planemo run` subcommand to run workflows from the command line.",
+            "Be able to write simple shell scripts for running multiple workflows concurrently or sequentially.",
+            "Learn how to use Pangolin to assign annotated variants to lineages."
         ],
-        "pageviews": 864,
-        "pub_date": "2022-06-02",
+        "pageviews": 2813,
+        "pub_date": "2021-06-08",
         "questions": [
-            "What are workflow reports?",
-            "How can I view a workflow report?",
-            "How can I customize a workflow report?",
-            "How can I share a workflow report with others?"
+            "How can I schedule and run tens or hundreds of Galaxy workflows easily?",
+            "How can I automate my analyses when large amounts of data are being produced daily?"
         ],
         "recordings": [
             {
                 "captioners": [
-                    "shiltemann"
+                    "simonbray"
                 ],
-                "date": "2022-07-06",
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
                 "length": "30M",
                 "speakers": [
-                    "shiltemann"
+                    "simonbray"
                 ],
-                "youtube_id": "hrZhpsiGaPM"
+                "youtube_id": "o39QjVnLG68"
             }
         ],
-        "short_id": "T00165",
+        "requirements": [
+            {
+                "title": "Familiarity with Galaxy and basic associated concepts, in particular workflows",
+                "type": "none"
+            },
+            {
+                "title": "Basic knowledge of the command line",
+                "type": "none"
+            }
+        ],
+        "short_id": "T00162",
         "short_tools": [
-            "Grouping1",
-            "datamash_ops",
-            "ggplot2_point",
-            "Cut1",
-            "csv_to_tabular",
-            "Remove beginning1",
-            "tp_sorted_uniq",
-            "upload1"
+            "pangolin",
+            "bcftools_consensus",
+            "snpSift_filter",
+            "compose_text_param",
+            "collapse_dataset"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -91306,54 +94714,53 @@
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
                 },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ],
             "inexact": [
                 {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
                     "usegalaxy": false
                 }
             ]
         },
         "symlink": null,
         "tags": [
-            "workflows"
+            "workflows",
+            "variant-analysis",
+            "covid19"
         ],
-        "time_estimation": "30m",
-        "title": "Workflow Reports",
+        "time_estimation": "2h",
+        "title": "Automating Galaxy workflows using the command line",
         "tools": [
-            "Cut1",
-            "Grouping1",
-            "Remove beginning1",
-            "csv_to_tabular",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
-            "upload1"
+            "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10",
+            "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
         ],
         "topic_name": "galaxy-interface",
         "topic_name_human": "Using Galaxy and Managing your Data",
@@ -91363,1234 +94770,479 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "workflow-reports",
+        "tutorial_name": "workflow-automation",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-reports/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-automation/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-reports/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-reports/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-automation/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-automation/tutorial.json"
         },
-        "version": 9,
+        "version": 8,
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 179,
-        "visitors": 597,
+        "visit_duration": 120,
+        "visitors": 2277,
         "workflows": [
             {
-                "creators": [],
-                "description": "introduction",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIris Dataset\"]\n  1[label=\"Convert CSV to tabular\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Datamash\"]\n  1 -> 2 [label=\"tabular\"]\n  k5fc8c705b9e24008aa85e84504b8395f[color=lightseagreen,label=\"Output\\ndatamash_output\"]\n  2 -> k5fc8c705b9e24008aa85e84504b8395f\n  3[label=\"Remove beginning\"]\n  1 -> 3 [label=\"tabular\"]\n  4[label=\"Cut\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"Group\"]\n  3 -> 5 [label=\"out_file1\"]\n  k7e07839ce8ca46928b8e6eb3607066de[color=lightseagreen,label=\"Output\\ngroup1\"]\n  5 -> k7e07839ce8ca46928b8e6eb3607066de\n  6[label=\"Group\"]\n  3 -> 6 [label=\"out_file1\"]\n  k9cb98227aa5b4b77933cffba1e98566e[color=lightseagreen,label=\"Output\\ngroup2\"]\n  6 -> k9cb98227aa5b4b77933cffba1e98566e\n  7[label=\"Scatterplot with ggplot2\"]\n  3 -> 7 [label=\"out_file1\"]\n  8[label=\"Scatterplot with ggplot2\"]\n  3 -> 8 [label=\"out_file1\"]\n  9[label=\"Unique\"]\n  4 -> 9 [label=\"out_file1\"]\n  kfc73409c78784391bc91f99a5be0ba06[color=lightseagreen,label=\"Output\\nunique_output\"]\n  9 -> kfc73409c78784391bc91f99a5be0ba06\n}",
-                "history": [
-                    {
-                        "hash": "bffad533763a3daa41aa8d7d083c978f46598355",
-                        "message": "update worfklow to not hide png output",
-                        "num": 3,
-                        "short_hash": "bffad5337",
-                        "unix": "1657113550"
-                    },
-                    {
-                        "hash": "56ef1bde9ab0a1e9493989335f23daecaf16510d",
-                        "message": "update topic tag on workflow",
-                        "num": 2,
-                        "short_hash": "56ef1bde9",
-                        "unix": "1654089632"
-                    },
-                    {
-                        "hash": "b200300b458fdfb7d025ece2746ec08134e8ccbd",
-                        "message": "start workflow reports tutorial",
-                        "num": 1,
-                        "short_hash": "b200300b4",
-                        "unix": "1654074124"
-                    }
-                ],
-                "inputs": [
+                "creators": [
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Iris Dataset"
-                            }
-                        ],
-                        "label": "Iris Dataset",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 205.8000030517578,
-                            "height": 61.80000305175781,
-                            "left": 292,
-                            "right": 492,
-                            "top": 144,
-                            "width": 200,
-                            "x": 292,
-                            "y": 144
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "6a8d8ca9-8bb9-414b-af8f-50d07721b363",
-                        "workflow_outputs": []
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0002-9464-6640",
+                        "name": "Wolfgang Maier"
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIris Dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Convert CSV to tabular\"];\n  0 -->|output| 1;\n  2[\"Datamash\"];\n  1 -->|tabular| 2;\n  5fc8c705-b9e2-4008-aa85-e84504b8395f[\"Output\\ndatamash_output\"];\n  2 --> 5fc8c705-b9e2-4008-aa85-e84504b8395f;\n  style 5fc8c705-b9e2-4008-aa85-e84504b8395f stroke:#2c3143,stroke-width:4px;\n  3[\"Remove beginning\"];\n  1 -->|tabular| 3;\n  4[\"Cut\"];\n  3 -->|out_file1| 4;\n  5[\"Group\"];\n  3 -->|out_file1| 5;\n  7e07839c-e8ca-4692-8b8e-6eb3607066de[\"Output\\ngroup1\"];\n  5 --> 7e07839c-e8ca-4692-8b8e-6eb3607066de;\n  style 7e07839c-e8ca-4692-8b8e-6eb3607066de stroke:#2c3143,stroke-width:4px;\n  6[\"Group\"];\n  3 -->|out_file1| 6;\n  9cb98227-aa5b-4b77-933c-ffba1e98566e[\"Output\\ngroup2\"];\n  6 --> 9cb98227-aa5b-4b77-933c-ffba1e98566e;\n  style 9cb98227-aa5b-4b77-933c-ffba1e98566e stroke:#2c3143,stroke-width:4px;\n  7[\"Scatterplot with ggplot2\"];\n  3 -->|out_file1| 7;\n  8[\"Scatterplot with ggplot2\"];\n  3 -->|out_file1| 8;\n  9[\"Unique\"];\n  4 -->|out_file1| 9;\n  fc73409c-7878-4391-bc91-f99a5be0ba06[\"Output\\nunique_output\"];\n  9 --> fc73409c-7878-4391-bc91-f99a5be0ba06;\n  style fc73409c-7878-4391-bc91-f99a5be0ba06 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "GTN Training: Workflow Reports - Galaxy 101 For Everyone",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "in_file": {
-                                "id": 1,
-                                "output_name": "tabular"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Datamash",
-                        "outputs": [
-                            {
-                                "name": "out_file",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 52.600006103515625,
-                            "height": 113.60000610351562,
-                            "left": 639,
-                            "right": 839,
-                            "top": -61,
-                            "width": 200,
-                            "x": 639,
-                            "y": -61
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "562f3c677828",
-                            "name": "datamash_ops",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"grouping\": \"5\", \"header_in\": \"true\", \"header_out\": \"true\", \"ignore_case\": \"true\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"need_sort\": \"true\", \"operations\": [{\"__index__\": 0, \"op_name\": \"mean\", \"op_column\": \"1\"}, {\"__index__\": 1, \"op_name\": \"sstdev\", \"op_column\": \"1\"}, {\"__index__\": 2, \"op_name\": \"mean\", \"op_column\": \"2\"}, {\"__index__\": 3, \"op_name\": \"sstdev\", \"op_column\": \"2\"}, {\"__index__\": 4, \"op_name\": \"mean\", \"op_column\": \"3\"}, {\"__index__\": 5, \"op_name\": \"sstdev\", \"op_column\": \"3\"}, {\"__index__\": 6, \"op_name\": \"mean\", \"op_column\": \"4\"}, {\"__index__\": 7, \"op_name\": \"sstdev\", \"op_column\": \"4\"}], \"print_full_line\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.0",
-                        "type": "tool",
-                        "uuid": "e1a58a79-5102-450e-bfe0-200f0e64139d",
-                        "workflow_outputs": [
-                            {
-                                "label": "datamash_output",
-                                "output_name": "out_file",
-                                "uuid": "5fc8c705-b9e2-4008-aa85-e84504b8395f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "Grouping1",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "input1": {
-                                "id": 3,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Group",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 496.1999969482422,
-                            "height": 93.19999694824219,
-                            "left": 1059,
-                            "right": 1259,
-                            "top": 403,
-                            "width": 200,
-                            "x": 1059,
-                            "y": 403
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "Grouping1",
-                        "tool_state": "{\"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"groupcol\": \"5\", \"ignorecase\": \"false\", \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.4",
-                        "type": "tool",
-                        "uuid": "dcd3ddc6-d871-45dd-94ed-3eae56dd56db",
-                        "workflow_outputs": [
-                            {
-                                "label": "group1",
-                                "output_name": "out_file1",
-                                "uuid": "7e07839c-e8ca-4692-8b8e-6eb3607066de"
-                            }
-                        ]
-                    },
+                "description": "workflow-automation",
+                "features": {
+                    "comments": false,
+                    "parameters": true,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nVariant calls\"]\n  1[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nmin-AF for consensus variant\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genome\"]\n  3[label=\"Compose text parameter value\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"SnpSift Filter\"]\n  3 -> 4 [label=\"out1\"]\n  0 -> 4 [label=\"output\"]\n  kee67c5edff7c404bad2019259edbc671[color=lightseagreen,label=\"Output\\nconsensus_variants\"]\n  4 -> kee67c5edff7c404bad2019259edbc671\n  5[label=\"bcftools consensus\"]\n  4 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  k9028f80e411240d89a49f671677d304f[color=lightseagreen,label=\"Output\\nconsensus\"]\n  5 -> k9028f80e411240d89a49f671677d304f\n  6[label=\"Collapse Collection\"]\n  5 -> 6 [label=\"output_file\"]\n  k1dd7978eb90742d68fc4f6fadeefcad1[color=lightseagreen,label=\"Output\\nmultisample_consensus_fasta\"]\n  6 -> k1dd7978eb90742d68fc4f6fadeefcad1\n  7[label=\"Pangolin\"]\n  6 -> 7 [label=\"output\"]\n  ke02d2cfb98424069957c6cf4ec197056[color=lightseagreen,label=\"Output\\npangolin_results\"]\n  7 -> ke02d2cfb98424069957c6cf4ec197056\n}",
+                "history": [
                     {
-                        "annotation": "",
-                        "content_id": "Grouping1",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "input1": {
-                                "id": 3,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Group",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 616.1999969482422,
-                            "height": 93.19999694824219,
-                            "left": 1059,
-                            "right": 1259,
-                            "top": 523,
-                            "width": 200,
-                            "x": 1059,
-                            "y": 523
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "Grouping1",
-                        "tool_state": "{\"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"groupcol\": \"5\", \"ignorecase\": \"false\", \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [{\"__index__\": 0, \"optype\": \"length\", \"opcol\": \"1\", \"opround\": \"no\", \"opdefault\": null}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.4",
-                        "type": "tool",
-                        "uuid": "285a3852-71cb-4137-be1d-b0ec0a59d9e9",
-                        "workflow_outputs": [
-                            {
-                                "label": "group2",
-                                "output_name": "out_file1",
-                                "uuid": "9cb98227-aa5b-4b77-933c-ffba1e98566e"
-                            }
-                        ]
-                    },
+                        "hash": "486585510e665c834a43668e2a769dd69654b9d6",
+                        "message": "add WF automation tutorial",
+                        "num": 1,
+                        "short_hash": "486585510",
+                        "unix": "1622197006"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "input1": {
-                                "id": 3,
-                                "output_name": "out_file1"
-                            }
-                        },
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Scatterplot with ggplot2",
-                                "name": "input1"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Scatterplot with ggplot2",
-                        "outputs": [
-                            {
-                                "name": "output1",
-                                "type": "png"
-                            },
-                            {
-                                "name": "output2",
-                                "type": "pdf"
+                                "description": "",
+                                "name": "Variant calls"
                             }
                         ],
+                        "label": "Variant calls",
+                        "name": "Input dataset collection",
+                        "outputs": [],
                         "position": {
-                            "bottom": 889,
-                            "height": 246,
-                            "left": 1059,
-                            "right": 1259,
-                            "top": 643,
+                            "bottom": 425.43333435058594,
+                            "height": 61.80000305175781,
+                            "left": 297,
+                            "right": 497,
+                            "top": 363.6333312988281,
                             "width": 200,
-                            "x": 1059,
-                            "y": 643
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionoutput2": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output2"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "1acf88921176",
-                            "name": "ggplot2_point",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "x": 297,
+                            "y": 363.6333312988281
                         },
-                        "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"points\", \"__current_case__\": 0, \"points\": {\"pointoptions\": \"default\", \"__current_case__\": 0}}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"5\", \"colors\": \"Set2\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"7.0\", \"height_output_dim\": \"7.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"pdf\"}, \"title\": \"Sepal length as a function of sepal width\", \"xlab\": \"Sepal length\", \"xplot\": \"1\", \"ylab\": \"Sepal width\", \"yplot\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.3.5+galaxy0",
-                        "type": "tool",
-                        "uuid": "fa412209-5e3a-448e-8b0b-fa88870e19c1",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output1",
-                                "uuid": "edb75294-0687-433e-821e-cffc03c7c103"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "fca4e710-87a7-4cb6-9ff1-f9a8dc84ca37",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "input1": {
-                                "id": 3,
-                                "output_name": "out_file1"
-                            }
-                        },
+                        "id": 1,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Scatterplot with ggplot2",
-                                "name": "input1"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Scatterplot with ggplot2",
-                        "outputs": [
-                            {
-                                "name": "output1",
-                                "type": "png"
-                            },
-                            {
-                                "name": "output2",
-                                "type": "pdf"
+                                "description": "",
+                                "name": "min-AF for consensus variant"
                             }
                         ],
+                        "label": "min-AF for consensus variant",
+                        "name": "Input parameter",
+                        "outputs": [],
                         "position": {
-                            "bottom": 1009,
-                            "height": 246,
-                            "left": 1059,
-                            "right": 1259,
-                            "top": 763,
+                            "bottom": 619.1000061035156,
+                            "height": 102.60000610351562,
+                            "left": 295.45001220703125,
+                            "right": 495.45001220703125,
+                            "top": 516.5,
                             "width": 200,
-                            "x": 1059,
-                            "y": 763
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionoutput2": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output2"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "1acf88921176",
-                            "name": "ggplot2_point",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "x": 295.45001220703125,
+                            "y": 516.5
                         },
-                        "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"points\", \"__current_case__\": 0, \"points\": {\"pointoptions\": \"default\", \"__current_case__\": 0}}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"5\", \"colors\": \"Set2\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"7.0\", \"height_output_dim\": \"7.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"pdf\"}, \"title\": \"Petal length as a function of petal width\", \"xlab\": \"Petal length\", \"xplot\": \"3\", \"ylab\": \"Petal width\", \"yplot\": \"4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.3.5+galaxy0",
-                        "type": "tool",
-                        "uuid": "8e7b3f8d-2b8b-46cb-93d4-0d74bf54441e",
+                        "tool_id": null,
+                        "tool_state": "{\"default\": 0.7, \"parameter_type\": \"float\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "52664bd7-b500-40a1-935b-8ac6df7003e5",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output1",
-                                "uuid": "9e55c569-0443-4b96-b34a-e37a8416cd22"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "infile": {
-                                "id": 4,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Unique",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 276.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": 1279,
-                            "right": 1479,
-                            "top": 163,
-                            "width": 200,
-                            "x": 1279,
-                            "y": 163
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_numeric\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.0",
-                        "type": "tool",
-                        "uuid": "3e2d84e9-2fff-4321-9db6-41af99367162",
-                        "workflow_outputs": [
-                            {
-                                "label": "unique_output",
-                                "output_name": "outfile",
-                                "uuid": "fc73409c-7878-4391-bc91-f99a5be0ba06"
+                                "output_name": "output",
+                                "uuid": "5db03aa3-a62d-4a39-8712-d48911abf2bb"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "galaxy-interface/workflow-reports",
-                "path": "topics/galaxy-interface/tutorials/workflow-reports/workflows/galaxy-101-everyone.ga",
-                "tags": [
-                    "galaxy-interface"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "GTN Training: Workflow Reports - Galaxy 101 For Everyone",
-                "topic_id": "galaxy-interface",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/galaxy-interface-workflow-reports/versions/galaxy-101-everyone",
-                "tutorial_id": "workflow-reports",
-                "url": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-reports/workflows/galaxy-101-everyone.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-reports/workflows/galaxy-101-everyone.html",
-                "version": 2,
-                "wfid": "galaxy-interface-workflow-reports",
-                "wfname": "galaxy-101-everyone",
-                "workflow": "galaxy-101-everyone.ga",
-                "workflow_tools": [
-                    "Cut1",
-                    "Grouping1",
-                    "Remove beginning1",
-                    "csv_to_tabular",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0"
-                ],
-                "workflowhub_id": "1301"
-            },
-            {
-                "creators": [],
-                "description": "introduction",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": {
-                        "markdown": "# Iris Analysis\n\nBelow are the results for the Iris analysis workflow.\n\nThis workflow was run on:\n\n```galaxy\ngenerate_time()\n```\n\nWith Galaxy version:\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n# Results\n\n## Species detected\n\ndisplay:\n```galaxy\nhistory_dataset_display(output=\"Iris Species\")\n```\n\n## Sepal plot\n\n```galaxy\nhistory_dataset_as_image(output=\"Sepal Plot (PNG)\")\n```\n\n## Petal Plot\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Petal Plot (PNG)\")\n```\n\n\n\n\n"
                     },
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIris Dataset\"]\n  1[label=\"Convert CSV to tabular\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Datamash\"]\n  1 -> 2 [label=\"tabular\"]\n  k5381f9b05170484c828e4469ec27ab3e[color=lightseagreen,label=\"Output\\ndatamash_output\"]\n  2 -> k5381f9b05170484c828e4469ec27ab3e\n  3[label=\"Remove beginning\"]\n  1 -> 3 [label=\"tabular\"]\n  4[label=\"Cut\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"Group\"]\n  3 -> 5 [label=\"out_file1\"]\n  k836a57b33657435bb396869af7e2f35e[color=lightseagreen,label=\"Output\\ngroup1\"]\n  5 -> k836a57b33657435bb396869af7e2f35e\n  6[label=\"Group\"]\n  3 -> 6 [label=\"out_file1\"]\n  k82e163a48fc54b8e81869fc66cd75b1d[color=lightseagreen,label=\"Output\\ngroup2\"]\n  6 -> k82e163a48fc54b8e81869fc66cd75b1d\n  7[label=\"Scatterplot with ggplot2\"]\n  3 -> 7 [label=\"out_file1\"]\n  kbbbac6ca64fb46ad87986c7c5369ccaf[color=lightseagreen,label=\"Output\\nSepal Plot (PNG)\"]\n  7 -> kbbbac6ca64fb46ad87986c7c5369ccaf\n  8[label=\"Scatterplot with ggplot2\"]\n  3 -> 8 [label=\"out_file1\"]\n  k74ee0c3c53c244cfb0e82a10c24166c9[color=lightseagreen,label=\"Output\\nPetal Plot (PNG)\"]\n  8 -> k74ee0c3c53c244cfb0e82a10c24166c9\n  9[label=\"Unique\"]\n  4 -> 9 [label=\"out_file1\"]\n  k6bcc2f96255e48f5a37b7d6a2c123493[color=lightseagreen,label=\"Output\\nIris Species\"]\n  9 -> k6bcc2f96255e48f5a37b7d6a2c123493\n}",
-                "history": [
-                    {
-                        "hash": "a8cea912fc5b649e72e07b366c1a53299559c901",
-                        "message": "add final workflow with report",
-                        "num": 1,
-                        "short_hash": "a8cea912f",
-                        "unix": "1654092494"
-                    }
-                ],
-                "inputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Iris Dataset"
+                                "name": "Reference genome"
                             }
                         ],
-                        "label": "Iris Dataset",
+                        "label": "Reference genome",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 383.8000030517578,
-                            "height": 61.80000305175781,
-                            "left": -119.5,
-                            "right": 80.5,
-                            "top": 322,
+                            "bottom": 734.8500366210938,
+                            "height": 82.20001220703125,
+                            "left": 749.816650390625,
+                            "right": 949.816650390625,
+                            "top": 652.6500244140625,
                             "width": 200,
-                            "x": -119.5,
-                            "y": 322
+                            "x": 749.816650390625,
+                            "y": 652.6500244140625
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "6a8d8ca9-8bb9-414b-af8f-50d07721b363",
+                        "uuid": "4a2c6df2-fb1e-42d8-96d5-6765ca85c214",
                         "workflow_outputs": []
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIris Dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Convert CSV to tabular\"];\n  0 -->|output| 1;\n  2[\"Datamash\"];\n  1 -->|tabular| 2;\n  5381f9b0-5170-484c-828e-4469ec27ab3e[\"Output\\ndatamash_output\"];\n  2 --> 5381f9b0-5170-484c-828e-4469ec27ab3e;\n  style 5381f9b0-5170-484c-828e-4469ec27ab3e stroke:#2c3143,stroke-width:4px;\n  3[\"Remove beginning\"];\n  1 -->|tabular| 3;\n  4[\"Cut\"];\n  3 -->|out_file1| 4;\n  5[\"Group\"];\n  3 -->|out_file1| 5;\n  836a57b3-3657-435b-b396-869af7e2f35e[\"Output\\ngroup1\"];\n  5 --> 836a57b3-3657-435b-b396-869af7e2f35e;\n  style 836a57b3-3657-435b-b396-869af7e2f35e stroke:#2c3143,stroke-width:4px;\n  6[\"Group\"];\n  3 -->|out_file1| 6;\n  82e163a4-8fc5-4b8e-8186-9fc66cd75b1d[\"Output\\ngroup2\"];\n  6 --> 82e163a4-8fc5-4b8e-8186-9fc66cd75b1d;\n  style 82e163a4-8fc5-4b8e-8186-9fc66cd75b1d stroke:#2c3143,stroke-width:4px;\n  7[\"Scatterplot with ggplot2\"];\n  3 -->|out_file1| 7;\n  bbbac6ca-64fb-46ad-8798-6c7c5369ccaf[\"Output\\nSepal Plot (PNG)\"];\n  7 --> bbbac6ca-64fb-46ad-8798-6c7c5369ccaf;\n  style bbbac6ca-64fb-46ad-8798-6c7c5369ccaf stroke:#2c3143,stroke-width:4px;\n  8[\"Scatterplot with ggplot2\"];\n  3 -->|out_file1| 8;\n  74ee0c3c-53c2-44cf-b0e8-2a10c24166c9[\"Output\\nPetal Plot (PNG)\"];\n  8 --> 74ee0c3c-53c2-44cf-b0e8-2a10c24166c9;\n  style 74ee0c3c-53c2-44cf-b0e8-2a10c24166c9 stroke:#2c3143,stroke-width:4px;\n  9[\"Unique\"];\n  4 -->|out_file1| 9;\n  6bcc2f96-255e-48f5-a37b-7d6a2c123493[\"Output\\nIris Species\"];\n  9 --> 6bcc2f96-255e-48f5-a37b-7d6a2c123493;\n  style 6bcc2f96-255e-48f5-a37b-7d6a2c123493 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "GTN Training: Workflow Reports",
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nVariant calls\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nmin-AF for consensus variant\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Compose text parameter value\"];\n  1 -->|output| 3;\n  4[\"SnpSift Filter\"];\n  3 -->|out1| 4;\n  0 -->|output| 4;\n  ee67c5ed-ff7c-404b-ad20-19259edbc671[\"Output\\nconsensus_variants\"];\n  4 --> ee67c5ed-ff7c-404b-ad20-19259edbc671;\n  style ee67c5ed-ff7c-404b-ad20-19259edbc671 stroke:#2c3143,stroke-width:4px;\n  5[\"bcftools consensus\"];\n  4 -->|output| 5;\n  2 -->|output| 5;\n  9028f80e-4112-40d8-9a49-f671677d304f[\"Output\\nconsensus\"];\n  5 --> 9028f80e-4112-40d8-9a49-f671677d304f;\n  style 9028f80e-4112-40d8-9a49-f671677d304f stroke:#2c3143,stroke-width:4px;\n  6[\"Collapse Collection\"];\n  5 -->|output_file| 6;\n  1dd7978e-b907-42d6-8fc4-f6fadeefcad1[\"Output\\nmultisample_consensus_fasta\"];\n  6 --> 1dd7978e-b907-42d6-8fc4-f6fadeefcad1;\n  style 1dd7978e-b907-42d6-8fc4-f6fadeefcad1 stroke:#2c3143,stroke-width:4px;\n  7[\"Pangolin\"];\n  6 -->|output| 7;\n  e02d2cfb-9842-4069-957c-6cf4ec197056[\"Output\\npangolin_results\"];\n  7 --> e02d2cfb-9842-4069-957c-6cf4ec197056;\n  style e02d2cfb-9842-4069-957c-6cf4ec197056 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "vcf2lineage",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "in_file": {
-                                "id": 1,
-                                "output_name": "tabular"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Datamash",
-                        "outputs": [
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "min-AF for consensus variant"
                             }
                         ],
+                        "label": "min-AF for consensus variant",
+                        "name": "Input parameter",
+                        "outputs": [],
                         "position": {
-                            "bottom": 278.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": 372.5,
-                            "right": 572.5,
-                            "top": 165,
+                            "bottom": 619.1000061035156,
+                            "height": 102.60000610351562,
+                            "left": 295.45001220703125,
+                            "right": 495.45001220703125,
+                            "top": 516.5,
                             "width": 200,
-                            "x": 372.5,
-                            "y": 165
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "562f3c677828",
-                            "name": "datamash_ops",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "x": 295.45001220703125,
+                            "y": 516.5
                         },
-                        "tool_state": "{\"grouping\": \"5\", \"header_in\": \"true\", \"header_out\": \"true\", \"ignore_case\": \"true\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"need_sort\": \"true\", \"operations\": [{\"__index__\": 0, \"op_name\": \"mean\", \"op_column\": \"1\"}, {\"__index__\": 1, \"op_name\": \"sstdev\", \"op_column\": \"1\"}, {\"__index__\": 2, \"op_name\": \"mean\", \"op_column\": \"2\"}, {\"__index__\": 3, \"op_name\": \"sstdev\", \"op_column\": \"2\"}, {\"__index__\": 4, \"op_name\": \"mean\", \"op_column\": \"3\"}, {\"__index__\": 5, \"op_name\": \"sstdev\", \"op_column\": \"3\"}, {\"__index__\": 6, \"op_name\": \"mean\", \"op_column\": \"4\"}, {\"__index__\": 7, \"op_name\": \"sstdev\", \"op_column\": \"4\"}], \"print_full_line\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.0",
-                        "type": "tool",
-                        "uuid": "e1a58a79-5102-450e-bfe0-200f0e64139d",
+                        "tool_id": null,
+                        "tool_state": "{\"default\": 0.7, \"parameter_type\": \"float\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "52664bd7-b500-40a1-935b-8ac6df7003e5",
                         "workflow_outputs": [
                             {
-                                "label": "datamash_output",
-                                "output_name": "out_file",
-                                "uuid": "5381f9b0-5170-484c-828e-4469ec27ab3e"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "5db03aa3-a62d-4a39-8712-d48911abf2bb"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Grouping1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
                         "errors": null,
-                        "id": 5,
+                        "id": 4,
                         "input_connections": {
-                            "input1": {
+                            "filter_expression|expr": {
                                 "id": 3,
-                                "output_name": "out_file1"
+                                "output_name": "out1"
+                            },
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Group",
+                        "name": "SnpSift Filter",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "tabular"
+                                "name": "output",
+                                "type": "vcf"
                             }
                         ],
                         "position": {
-                            "bottom": 538.1999969482422,
-                            "height": 93.19999694824219,
-                            "left": 668.5,
-                            "right": 868.5,
-                            "top": 445,
+                            "bottom": 506.5,
+                            "height": 144,
+                            "left": 750.2833251953125,
+                            "right": 950.2833251953125,
+                            "top": 362.5,
                             "width": 200,
-                            "x": 668.5,
-                            "y": 445
+                            "x": 750.2833251953125,
+                            "y": 362.5
                         },
-                        "post_job_actions": {},
-                        "tool_id": "Grouping1",
-                        "tool_state": "{\"groupcol\": \"5\", \"ignorecase\": \"false\", \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.4",
-                        "type": "tool",
-                        "uuid": "dcd3ddc6-d871-45dd-94ed-3eae56dd56db",
-                        "workflow_outputs": [
-                            {
-                                "label": "group1",
-                                "output_name": "out_file1",
-                                "uuid": "836a57b3-3657-435b-b396-869af7e2f35e"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "Grouping1",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "input1": {
-                                "id": 3,
-                                "output_name": "out_file1"
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Consensus variants"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Group",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 683.1999969482422,
-                            "height": 93.19999694824219,
-                            "left": 667.5,
-                            "right": 867.5,
-                            "top": 590,
-                            "width": 200,
-                            "x": 667.5,
-                            "y": 590
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2e497a770bca",
+                            "name": "snpsift",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "post_job_actions": {},
-                        "tool_id": "Grouping1",
-                        "tool_state": "{\"groupcol\": \"5\", \"ignorecase\": \"false\", \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [{\"__index__\": 0, \"optype\": \"length\", \"opcol\": \"1\", \"opround\": \"no\", \"opdefault\": null}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.4",
+                        "tool_state": "{\"filter_expression\": {\"type\": \"simple\", \"__current_case__\": 0, \"expr\": {\"__class__\": \"ConnectedValue\"}}, \"filtering\": {\"mode\": \"entries\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inverse\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.3+t.galaxy1",
                         "type": "tool",
-                        "uuid": "285a3852-71cb-4137-be1d-b0ec0a59d9e9",
+                        "uuid": "3673b687-1ba0-42f2-ba13-fa3130462079",
                         "workflow_outputs": [
                             {
-                                "label": "group2",
-                                "output_name": "out_file1",
-                                "uuid": "82e163a4-8fc5-4b8e-8186-9fc66cd75b1d"
+                                "label": "consensus_variants",
+                                "output_name": "output",
+                                "uuid": "ee67c5ed-ff7c-404b-ad20-19259edbc671"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10",
                         "errors": null,
-                        "id": 7,
+                        "id": 5,
                         "input_connections": {
-                            "input1": {
-                                "id": 3,
-                                "output_name": "out_file1"
+                            "input_file": {
+                                "id": 4,
+                                "output_name": "output"
+                            },
+                            "reference_source|fasta_ref": {
+                                "id": 2,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scatterplot with ggplot2",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "output1",
-                                "type": "png"
+                                "description": "runtime parameter for tool bcftools consensus",
+                                "name": "input_file"
                             },
                             {
-                                "name": "output2",
-                                "type": "pdf"
+                                "description": "runtime parameter for tool bcftools consensus",
+                                "name": "reference_source"
+                            },
+                            {
+                                "description": "runtime parameter for tool bcftools consensus",
+                                "name": "sec_default"
+                            }
+                        ],
+                        "label": null,
+                        "name": "bcftools consensus",
+                        "outputs": [
+                            {
+                                "name": "output_file",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "bottom": 924.1999969482422,
-                            "height": 205.1999969482422,
-                            "left": 971.5,
-                            "right": 1171.5,
-                            "top": 719,
+                            "bottom": 535.5666809082031,
+                            "height": 174.39999389648438,
+                            "left": 993.8333129882812,
+                            "right": 1193.8333129882812,
+                            "top": 361.16668701171875,
                             "width": 200,
-                            "x": 971.5,
-                            "y": 719
+                            "x": 993.8333129882812,
+                            "y": 361.16668701171875
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_file": {
+                                "action_arguments": {
+                                    "newname": "Consensus sequences"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_file"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10",
                         "tool_shed_repository": {
-                            "changeset_revision": "1acf88921176",
-                            "name": "ggplot2_point",
+                            "changeset_revision": "e522022137f6",
+                            "name": "bcftools_consensus",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"points\", \"__current_case__\": 0, \"points\": {\"pointoptions\": \"default\", \"__current_case__\": 0}}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"5\", \"colors\": \"Set2\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"7.0\", \"height_output_dim\": \"7.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"pdf\"}, \"title\": \"Sepal length as a function of sepal width\", \"xlab\": \"Sepal length\", \"xplot\": \"1\", \"ylab\": \"Sepal width\", \"yplot\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.3.5+galaxy0",
+                        "tool_state": "{\"chain\": \"false\", \"input_file\": {\"__class__\": \"RuntimeValue\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"RuntimeValue\"}}, \"rename\": \"true\", \"sec_default\": {\"mask\": {\"__class__\": \"RuntimeValue\"}, \"iupac_codes\": \"false\", \"sample\": \"\", \"select_haplotype\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.10",
                         "type": "tool",
-                        "uuid": "fa412209-5e3a-448e-8b0b-fa88870e19c1",
+                        "uuid": "5d2e8bea-3e75-4453-9494-b5fd52b2f528",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output2",
-                                "uuid": "d8dd48e7-e9e0-4b5c-8d9f-4b47be570e31"
-                            },
-                            {
-                                "label": "Sepal Plot (PNG)",
-                                "output_name": "output1",
-                                "uuid": "bbbac6ca-64fb-46ad-8798-6c7c5369ccaf"
+                                "label": "consensus",
+                                "output_name": "output_file",
+                                "uuid": "9028f80e-4112-40d8-9a49-f671677d304f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
                         "errors": null,
-                        "id": 8,
+                        "id": 6,
                         "input_connections": {
-                            "input1": {
-                                "id": 3,
-                                "output_name": "out_file1"
+                            "input_list": {
+                                "id": 5,
+                                "output_name": "output_file"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Scatterplot with ggplot2",
+                        "name": "Collapse Collection",
                         "outputs": [
                             {
-                                "name": "output1",
-                                "type": "png"
-                            },
-                            {
-                                "name": "output2",
-                                "type": "pdf"
+                                "name": "output",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 1210.1999969482422,
-                            "height": 205.1999969482422,
-                            "left": 677.5,
-                            "right": 877.5,
-                            "top": 1005,
+                            "bottom": 537.8000030517578,
+                            "height": 174.8000030517578,
+                            "left": 1223.5,
+                            "right": 1423.5,
+                            "top": 363,
                             "width": 200,
-                            "x": 677.5,
-                            "y": 1005
+                            "x": 1223.5,
+                            "y": 363
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Multisample consensus FASTA"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "1acf88921176",
-                            "name": "ggplot2_point",
-                            "owner": "iuc",
+                            "changeset_revision": "830961c48e42",
+                            "name": "collapse_collections",
+                            "owner": "nml",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"points\", \"__current_case__\": 0, \"points\": {\"pointoptions\": \"default\", \"__current_case__\": 0}}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"5\", \"colors\": \"Set2\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"7.0\", \"height_output_dim\": \"7.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"pdf\"}, \"title\": \"Petal length as a function of petal width\", \"xlab\": \"Petal length\", \"xplot\": \"3\", \"ylab\": \"Petal width\", \"yplot\": \"4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.3.5+galaxy0",
+                        "tool_state": "{\"filename\": {\"add_name\": \"false\", \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.2",
                         "type": "tool",
-                        "uuid": "8e7b3f8d-2b8b-46cb-93d4-0d74bf54441e",
+                        "uuid": "acae0f3e-448b-483e-a44a-3e09ce9b3e77",
                         "workflow_outputs": [
                             {
-                                "label": "Petal Plot (PNG)",
-                                "output_name": "output1",
-                                "uuid": "74ee0c3c-53c2-44cf-b0e8-2a10c24166c9"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output2",
-                                "uuid": "54f6cc43-48a3-495d-9f11-4f03e19d56ef"
+                                "label": "multisample_consensus_fasta",
+                                "output_name": "output",
+                                "uuid": "1dd7978e-b907-42d6-8fc4-f6fadeefcad1"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8",
                         "errors": null,
-                        "id": 9,
+                        "id": 7,
                         "input_connections": {
-                            "infile": {
-                                "id": 4,
-                                "output_name": "out_file1"
+                            "input1": {
+                                "id": 6,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Pangolin",
+                                "name": "input1"
+                            }
+                        ],
                         "label": null,
-                        "name": "Unique",
+                        "name": "Pangolin",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "input"
+                                "name": "output1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 382.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": 922.5,
-                            "right": 1122.5,
-                            "top": 269,
+                            "bottom": 512.1999969482422,
+                            "height": 93.19999694824219,
+                            "left": 1451,
+                            "right": 1651,
+                            "top": 419,
                             "width": 200,
-                            "x": 922.5,
-                            "y": 269
+                            "x": 1451,
+                            "y": 419
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput1": {
+                                "action_arguments": {
+                                    "newname": "Pangolin lineage assignments"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output1"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8",
                         "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "b6abccb1f25b",
+                            "name": "pangolin",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_numeric\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.0",
+                        "tool_state": "{\"alignment\": \"false\", \"db\": {\"source\": \"builtin\", \"__current_case__\": 1, \"db_release\": \"2021-05-11\"}, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"max_ambig\": \"0.5\", \"min_length\": \"10000\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.3.8",
                         "type": "tool",
-                        "uuid": "3e2d84e9-2fff-4321-9db6-41af99367162",
+                        "uuid": "bf8893e0-d08c-46c9-b384-a8ad0fc88185",
                         "workflow_outputs": [
                             {
-                                "label": "Iris Species",
-                                "output_name": "outfile",
-                                "uuid": "6bcc2f96-255e-48f5-a37b-7d6a2c123493"
+                                "label": "pangolin_results",
+                                "output_name": "output1",
+                                "uuid": "e02d2cfb-9842-4069-957c-6cf4ec197056"
                             }
                         ]
                     }
                 ],
-                "parent_id": "galaxy-interface/workflow-reports",
-                "path": "topics/galaxy-interface/tutorials/workflow-reports/workflows/workflow_reports_final_workflow.ga",
+                "parent_id": "galaxy-interface/workflow-automation",
+                "path": "topics/galaxy-interface/tutorials/workflow-automation/workflows/main_workflow.ga",
                 "tags": [
+                    "variant-analysis",
                     "galaxy-interface"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "GTN Training: Workflow Reports",
+                "title": "vcf2lineage",
                 "topic_id": "galaxy-interface",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/galaxy-interface-workflow-reports/versions/workflow-reports-final-workflow",
-                "tutorial_id": "workflow-reports",
-                "url": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-reports/workflows/workflow_reports_final_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-reports/workflows/workflow_reports_final_workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/galaxy-interface-workflow-automation/versions/main-workflow",
+                "tutorial_id": "workflow-automation",
+                "url": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-automation/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-automation/workflows/main_workflow.html",
                 "version": 1,
-                "wfid": "galaxy-interface-workflow-reports",
-                "wfname": "workflow-reports-final-workflow",
-                "workflow": "workflow_reports_final_workflow.ga",
-                "workflow_tools": [
-                    "Cut1",
-                    "Grouping1",
-                    "Remove beginning1",
-                    "csv_to_tabular",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0"
-                ],
-                "workflowhub_id": "1297"
-            }
-        ],
-        "zenodo_link": ""
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "ddf54b12c295",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastqtofasta",
-                    "owner": "devteam",
-                    "revisions": "297962e79f39",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "jq",
-                    "owner": "iuc",
-                    "revisions": "5ff75eb1a893",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "query_tabular",
-                    "owner": "iuc",
-                    "revisions": "33d61c89fb8d",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "snpeff_sars_cov_2",
-                    "owner": "iuc",
-                    "revisions": "2a3a00c1fa0a",
-                    "tool_panel_section_label": "Variant Calling",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "sra_tools",
-                    "owner": "iuc",
-                    "revisions": "69ebb7f46e45",
-                    "tool_panel_section_label": "Get Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "sra_tools",
-                    "owner": "iuc",
-                    "revisions": "83c7d564b128",
-                    "tool_panel_section_label": "Get Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: ddf54b12c295\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqtofasta\n  owner: devteam\n  revisions: 297962e79f39\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jq\n  owner: iuc\n  revisions: 5ff75eb1a893\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n  owner: iuc\n  revisions: 33d61c89fb8d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff_sars_cov_2\n  owner: iuc\n  revisions: 2a3a00c1fa0a\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: 69ebb7f46e45\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: 83c7d564b128\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.json",
-        "contributors": [
-            {
-                "github": false,
-                "id": "jontrow",
-                "joined": "2021-05",
-                "name": "Jon Trow",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jontrow/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jontrow.json"
-            },
-            {
-                "id": "RareSeas",
-                "joined": "2021-05",
-                "name": "Adelaide Rhodes",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/RareSeas/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/RareSeas.json"
-            }
-        ],
-        "dir": "topics/galaxy-interface/tutorials/ncbi-sarf",
-        "edam_operation": [
-            "Data handling",
-            "SNP detection"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "galaxy-interface/ncbi-sarf",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.no"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "NCBI Publishes datasets in the cloud that you can easily process with Galaxy",
-            "The Rule Based Uploader simplifies processing and downloading large numbers of files"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
-        "objectives": [
-            "Learn about SRA aligned read format and vcf files for Runs containing SARS-CoV-2 content",
-            "Understand how to search the metadata for these Runs to find your dataset of interest and then import that data in your preferred format"
-        ],
-        "pageviews": 4971885,
-        "pub_date": "2021-05-31",
-        "questions": [
-            "How can I search SRA SARS-CoV-2 metadata from within Galaxy?",
-            "How can I import SRA aligned read files and extract the data in my format of choice?",
-            "How can I import vcf files into Galaxy that have been generated for these Runs?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "prodromus"
-                ],
-                "date": "2021-05-15",
-                "galaxy_version": "21.01",
-                "length": "40M",
-                "speakers": [
-                    "prodromus"
-                ],
-                "youtube_id": "ogu-NBTP-DM"
-            }
-        ],
-        "requirements": [
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "upload-rules"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00155",
-        "short_tools": [
-            "fastq_to_fasta_python",
-            "tp_cat",
-            "fasterq_dump",
-            "query_tabular",
-            "fastq_dump",
-            "jq",
-            "snpeff_sars_cov_2"
-        ],
-        "slides": true,
-        "slides_recordings": [
-            {
-                "captioners": [
-                    "prodromus"
-                ],
-                "date": "2021-05-15",
-                "galaxy_version": "21.01",
-                "length": "15M",
-                "speakers": [
-                    "prodromus"
-                ],
-                "youtube_id": "siLP71B9gm4"
-            }
-        ],
-        "subtopic": "upload",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "ncbi",
-            "covid19"
-        ],
-        "time_estimation": "30m",
-        "title": "SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
-            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0"
-        ],
-        "topic_name": "galaxy-interface",
-        "topic_name_human": "Using Galaxy and Managing your Data",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "ncbi-sarf",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.json"
-        },
-        "version": 12,
-        "video": false,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 266,
-        "visitors": 1842342
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/get-data/tutorial.json",
-        "contributors": [
-            {
-                "id": "pajanne",
-                "joined": "2017-09",
-                "name": "Anne Pajon",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pajanne/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pajanne.json"
-            },
-            {
-                "id": "tnabtaf",
-                "joined": "2017-09",
-                "name": "Dave Clements",
-                "orcid": "0000-0002-9970-6657",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
-            },
-            {
-                "id": "mblue9",
-                "joined": "2018-09",
-                "name": "Maria Doyle",
-                "orcid": "0000-0003-4847-8436",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
+                "wfid": "galaxy-interface-workflow-automation",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
                 ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+                "workflowhub_id": "1293"
             }
         ],
-        "dir": "topics/galaxy-interface/tutorials/get-data",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": false,
-        "id": "galaxy-interface/get-data",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": null,
-        "layout": "tutorial_slides",
-        "license": "CC-BY-4.0",
-        "logo": "GTN",
-        "mod_date": "2022-10-18",
-        "objectives": null,
-        "pageviews": 5726883,
-        "pub_date": "2017-05-24",
-        "questions": [
-            "How do I get my data into Galaxy?",
-            "How do I get public data into Galaxy?"
-        ],
-        "redirect_from": [
-            "/topics/galaxy-data-manipulation/tutorials/get-data/slides",
-            "/short/galaxy-interface/get-data/slides",
-            "/short/S00062"
-        ],
-        "short_id": "S00062",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
-        "subtopic": "upload",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "time_estimation": null,
-        "title": "Getting data into Galaxy",
-        "tools": [],
-        "topic_name": "galaxy-interface",
-        "topic_name_human": "Using Galaxy and Managing your Data",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "get-data",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/get-data/slides.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/get-data/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/get-data/slides.json"
-        },
-        "version": 4,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758,
         "zenodo_link": ""
     },
     {
@@ -92598,301 +95250,25 @@
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/galaxy-on-dockstore/tutorial.json",
-        "contributors": [
-            {
-                "email": "akhadilk@ucsc.edu",
-                "id": "avani-k",
-                "joined": "2021-12",
-                "name": "Avani Khadilkar",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avani-k/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/avani-k.json"
-            },
-            {
-                "email": "esheets@ucsc.edu",
-                "id": "bethsheets",
-                "joined": "2021-12",
-                "name": "Elizabeth Sheets",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bethsheets/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bethsheets.json"
-            },
-            {
-                "email": "coverbec@ucsc.edu",
-                "id": "coverbeck",
-                "joined": "2021-12",
-                "name": "Charles Overbeck",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/coverbeck/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/coverbeck.json"
-            },
-            {
-                "id": "afgane",
-                "joined": "2018-06",
-                "name": "Enis Afgan",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/afgane/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/afgane.json"
-            }
-        ],
-        "dir": "topics/galaxy-interface/tutorials/galaxy-on-dockstore",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": false,
-        "id": "galaxy-interface/galaxy-on-dockstore",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "layout": "tutorial_slides",
-        "license": "CC-BY-4.0",
-        "logo": "GTN",
-        "mod_date": "2022-10-27",
-        "objectives": [
-            "What is Dockstore?",
-            "Why use Dockstore?",
-            "How to find workflows on Dockstore?",
-            "How to launch workflows from Dockstore?",
-            "Getting started with Galaxy workflows on Dockstore",
-            "Register your Galaxy workflow on Dockstore"
-        ],
-        "pageviews": 3890903,
-        "pub_date": "2022-01-14",
-        "short_id": "S00061",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
-        "subtopic": "workflows",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
+            "tools": [
                 {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "symlink": null,
-        "title": "Galaxy workflows in Dockstore",
-        "tools": [],
-        "topic_name": "galaxy-interface",
-        "topic_name_human": "Using Galaxy and Managing your Data",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "galaxy-on-dockstore",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/galaxy-on-dockstore/slides.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/galaxy-on-dockstore/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/galaxy-on-dockstore/slides.json"
-        },
-        "version": 4,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 148,
-        "visitors": 1513885
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/history/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "nekrut"
-            ],
-            "editing": [
-                "polkhe",
-                "martenson",
-                "gallardoalba",
-                "shiltemann",
-                "bebatut",
-                "bgruening",
-                "hexylena"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-parameters/tutorial.json",
         "contributors": [
             {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
-                "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "id": "polkhe",
-                "joined": "2017-09",
-                "name": "Ekaterina Polkh",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/polkhe/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/polkhe.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "cz",
-                "email": "marten@bx.psu.edu",
-                "fediverse": "https://mastodon.world/@martenson",
-                "fediverse_flavor": "mastodon",
-                "id": "martenson",
-                "joined": "2017-09",
-                "location": {
-                    "country": "USA",
-                    "lat": 37.0,
-                    "lon": -122.0
-                },
-                "matrix": "martenson:matrix.org",
-                "name": "Martin \u010cech",
-                "orcid": "0000-0002-9318-1781",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/martenson/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/martenson.json"
-            },
-            {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "gallardoalba",
-                "joined": "2020-11",
-                "name": "Crist\u00f3bal Gallardo",
-                "orcid": "0000-0002-5752-2155",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
-                "fediverse_flavor": "mastodon",
-                "id": "bgruening",
-                "joined": "2017-09",
-                "linkedin": "bgruening",
-                "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
-                },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+                "id": "mvdbeek",
+                "joined": "2018-06",
+                "name": "Marius van den Beek",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
             },
             {
                 "affiliations": [
@@ -92924,274 +95300,101 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/galaxy-interface/tutorials/history",
+        "dir": "topics/galaxy-interface/tutorials/workflow-parameters",
         "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "Galaxy@AuBi",
+            "GalaxyTrakr",
+            "HyPhy HIV NGS Tools",
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "galaxy-interface/history",
+        "id": "galaxy-interface/workflow-parameters",
         "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
+            "MISSISSIPPI"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "In Galaxy, data is stored in datasets and organized in histories",
-            "The right pane shows the current history. It displays the name of the history, the tags and annotations assigned to it, and the size of the data in it",
-            "The datasets are shown differently depending on their status: queued, running, ok, error, or paused",
-            "The summary view for each dataset can be expanded to show additional information",
-            "Datasets deleted are hidden from history. They can be restored to the history, or permanently deleted from the server, or purged. Purged files cannot be restored",
-            "Histories can also be deleted and purged, similar to datasets",
-            "Datasets can be organized into collections within a history with search and multi-select. Jobs applied to collections use the same settings for each dataset in the collection"
+            "Use Workflow Parameters to make your Workflows more versatile"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-02",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Gain understanding on navigating and manipulating histories"
+            "Learn how to use Workflow Parameters to improve your Workflows"
         ],
-        "pageviews": 5096,
-        "pub_date": "2017-02-20",
+        "pageviews": 2067,
+        "pub_date": "2019-06-27",
         "questions": [
-            "How do Galaxy histories work?"
+            "What are Workflow Parameters",
+            "How can I define and use Workflow Parameters",
+            "How can I read Parameters from Datasets"
         ],
         "recordings": [
             {
                 "captioners": [
-                    "shiltemann"
+                    "mvdbeek"
                 ],
-                "date": "2023-05-19",
-                "galaxy_version": "23.01",
-                "length": "18M",
+                "date": "2022-07-06",
+                "length": "30M",
                 "speakers": [
-                    "shiltemann"
+                    "mvdbeek"
                 ],
-                "youtube_id": "C3_HSgbbDWc"
+                "youtube_id": "otvEuDlCye0"
             }
         ],
         "redirect_from": [
-            "/topics/galaxy-ui/tutorials/history/tutorial",
-            "/short/galaxy-interface/history",
-            "/short/T00150"
+            "/topics/galaxy-ui/tutorials/workflow-parameters/tutorial",
+            "/short/galaxy-interface/workflow-parameters",
+            "/short/T00164"
+        ],
+        "short_id": "T00164",
+        "short_tools": [
+            "tp_head_tool"
         ],
-        "short_id": "T00150",
-        "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "histories",
+        "subtopic": "workflows",
         "supported_servers": {
-            "exact": [],
-            "inexact": [
+            "exact": [
                 {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
                 },
                 {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
                 },
                 {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
                 },
                 {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "time_estimation": "30m",
-        "title": "Understanding Galaxy history system",
-        "tools": [],
-        "topic_name": "galaxy-interface",
-        "topic_name_human": "Using Galaxy and Managing your Data",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "history",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/history/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/history/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/history/tutorial.json"
-        },
-        "version": 8,
-        "video": false,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 161,
-        "visitors": 3886,
-        "zenodo_link": ""
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/rstudio/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
                 },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "elixir-europe"
-                ],
-                "elixir_node": "gr",
-                "email": "fpsom@certh.gr",
-                "id": "fpsom",
-                "joined": "2019-03",
-                "linkedin": "fpsom",
-                "matrix": "fpsom:matrix.org",
-                "name": "Fotis E. Psomopoulos",
-                "orcid": "0000-0002-0222-4273",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
-                "twitter": "fopsom",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
-            },
-            {
-                "email": "tbyhdgs@gmail.com",
-                "id": "tobyhodges",
-                "joined": "2019-07",
-                "name": "Toby Hodges",
-                "orcid": "0000-0003-1766-456X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tobyhodges/",
-                "twitter": "tbyhdgs",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tobyhodges.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
-            }
-        ],
-        "dir": "topics/galaxy-interface/tutorials/rstudio",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "data-science",
-                "tutorials": [
-                    "r-basics"
-                ],
-                "type": "internal"
-            }
-        ],
-        "hands_on": true,
-        "id": "galaxy-interface/rstudio",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Why it's helpful to be able to work with R interactively within Galaxy"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Launch RStudio in Galaxy"
-        ],
-        "pageviews": 6706,
-        "pub_date": "2019-10-08",
-        "questions": [
-            "How can I manipulate data using R in Galaxy?"
-        ],
-        "redirect_from": [
-            "/topics/galaxy-ui/tutorials/rstudio/tutorial",
-            "/short/galaxy-interface/rstudio",
-            "/short/T00157"
-        ],
-        "short_id": "T00157",
-        "short_tools": [
-            "interactive_tool_rstudio"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "analyse",
-        "supported_servers": {
-            "exact": [
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
@@ -93202,6 +95405,11 @@
                     "url": "https://usegalaxy.fr/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -93213,16 +95421,22 @@
                     "usegalaxy": true
                 }
             ],
-            "inexact": []
+            "inexact": [
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                }
+            ]
         },
         "symlink": null,
         "tags": [
-            "interactive-tools"
+            "workflows"
         ],
-        "time_estimation": "3H",
-        "title": "RStudio in Galaxy",
+        "time_estimation": "30m",
+        "title": "Using Workflow Parameters",
         "tools": [
-            "interactive_tool_rstudio"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0"
         ],
         "topic_name": "galaxy-interface",
         "topic_name_human": "Using Galaxy and Managing your Data",
@@ -93232,19 +95446,173 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "rstudio",
+        "tutorial_name": "workflow-parameters",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/rstudio/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-parameters/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/rstudio/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/rstudio/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-parameters/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-parameters/tutorial.json"
         },
-        "version": 12,
+        "version": 15,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 125,
-        "visitors": 4124,
+        "visit_duration": 135,
+        "visitors": 1594,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Workflows: Using Workflow Parameters",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[label=\"Select first\"]\n  0 -> 1 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "dfe28b422df8f2d253c12f50c87ac20353493eea",
+                        "message": "Completely merge topics",
+                        "num": 1,
+                        "short_hash": "dfe28b422",
+                        "unix": "1592211035"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 162.9609375,
+                            "top": 199.9921875
+                        },
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ac600c9c-04f0-4e2d-9bd7-636de8a7ae56",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "3e5ff777-86d7-4510-8f63-d0c6379656fe"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Select first\"];\n  0 -->|output| 1;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Select First N Lines",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 162.9609375,
+                            "top": 199.9921875
+                        },
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ac600c9c-04f0-4e2d-9bd7-636de8a7ae56",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "3e5ff777-86d7-4510-8f63-d0c6379656fe"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0",
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {
+                            "infile": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Select first",
+                                "name": "infile"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Select first",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 463.9453125,
+                            "top": 197.9765625
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "0a8c6b61f0f4",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"complement\": \"\\\"\\\"\", \"count\": \"\\\"10\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.0",
+                        "type": "tool",
+                        "uuid": "6ef9506c-cf7b-48c9-889f-db7dfb97389a",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "6f9509ee-42cd-4c3d-81fc-22c3a95de600"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "galaxy-interface/workflow-parameters",
+                "path": "topics/galaxy-interface/tutorials/workflow-parameters/workflows/cut_n_lines.ga",
+                "tags": [
+                    "galaxy-interface"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Select First N Lines",
+                "topic_id": "galaxy-interface",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/galaxy-interface-workflow-parameters/versions/cut-n-lines",
+                "tutorial_id": "workflow-parameters",
+                "url": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-parameters/workflows/cut_n_lines.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-parameters/workflows/cut_n_lines.html",
+                "version": 1,
+                "wfid": "galaxy-interface-workflow-parameters",
+                "wfname": "cut-n-lines",
+                "workflow": "cut_n_lines.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0"
+                ],
+                "workflowhub_id": "1304"
+            }
+        ],
         "zenodo_link": ""
     },
     {
@@ -93255,136 +95623,113 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/jupyterlab/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "annefou"
-            ],
-            "editing": [
-                "hexylena"
-            ]
-        },
+        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/galaxy-on-dockstore/tutorial.json",
         "contributors": [
             {
-                "elixir_node": "no",
-                "id": "annefou",
-                "joined": "2019-07",
-                "name": "Anne Fouilloux",
-                "orcid": "0000-0002-1784-2920",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annefou/",
-                "twitter": "AnneFouilloux",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/annefou.json"
+                "email": "akhadilk@ucsc.edu",
+                "id": "avani-k",
+                "joined": "2021-12",
+                "name": "Avani Khadilkar",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avani-k/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/avani-k.json"
             },
             {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+                "email": "esheets@ucsc.edu",
+                "id": "bethsheets",
+                "joined": "2021-12",
+                "name": "Elizabeth Sheets",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bethsheets/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bethsheets.json"
+            },
+            {
+                "email": "coverbec@ucsc.edu",
+                "id": "coverbeck",
+                "joined": "2021-12",
+                "name": "Charles Overbeck",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/coverbeck/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/coverbeck.json"
+            },
+            {
+                "id": "afgane",
+                "joined": "2018-06",
+                "name": "Enis Afgan",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/afgane/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/afgane.json"
             }
         ],
-        "dir": "topics/galaxy-interface/tutorials/jupyterlab",
+        "dir": "topics/galaxy-interface/tutorials/galaxy-on-dockstore",
         "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)"
-        ],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": true,
-        "id": "galaxy-interface/jupyterlab",
-        "inexact_supported_servers": [],
+        "hands_on": false,
+        "id": "galaxy-interface/galaxy-on-dockstore",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": [
-            "How to work with JupyterLab interactively within Galaxy"
-        ],
-        "layout": "tutorial_hands_on",
+        "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
-        "mod_date": "2022-10-18",
+        "logo": "GTN",
+        "mod_date": "2022-10-27",
         "objectives": [
-            "Launch JupyterLab in Galaxy",
-            "Start a notebook",
-            "Import libraries",
-            "Use get() to import datasets from your history to the notebook",
-            "Use put() to export datasets from the notebook to your history",
-            "Save your notebook into your history"
-        ],
-        "pageviews": 2642,
-        "pub_date": "2020-03-05",
-        "questions": [
-            "How can I manipulate data using JupyterLab in Galaxy?",
-            "How can I start a notebook in JupyterLab?",
-            "How can I import/export dataset from/to my history to/from the notebook?",
-            "How can I save my notebook to my history?"
-        ],
-        "redirect_from": [
-            "/topics/galaxy-ui/tutorials/jupyterlab/tutorial",
-            "/short/galaxy-interface/jupyterlab",
-            "/short/T00153"
-        ],
-        "short_id": "T00153",
-        "short_tools": [
-            "interactive_tool_jupyter_notebook"
+            "What is Dockstore?",
+            "Why use Dockstore?",
+            "How to find workflows on Dockstore?",
+            "How to launch workflows from Dockstore?",
+            "Getting started with Galaxy workflows on Dockstore",
+            "Register your Galaxy workflow on Dockstore"
         ],
-        "slides": false,
+        "pageviews": 4061190,
+        "pub_date": "2022-01-14",
+        "short_id": "S00061",
+        "short_tools": [],
+        "slides": true,
         "slides_recordings": false,
-        "subtopic": "analyse",
+        "subtopic": "workflows",
         "supported_servers": {
-            "exact": [
+            "exact": [],
+            "inexact": [
                 {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
                     "usegalaxy": true
                 }
-            ],
-            "inexact": []
+            ]
         },
         "symlink": null,
-        "tags": [
-            "interactive-tools"
-        ],
-        "time_estimation": "1H",
-        "title": "JupyterLab in Galaxy",
-        "tools": [
-            "interactive_tool_jupyter_notebook"
-        ],
+        "title": "Galaxy workflows in Dockstore",
+        "tools": [],
         "topic_name": "galaxy-interface",
         "topic_name_human": "Using Galaxy and Managing your Data",
         "tours": false,
@@ -93393,20 +95738,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "jupyterlab",
+        "tutorial_name": "galaxy-on-dockstore",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/jupyterlab/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/galaxy-on-dockstore/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/jupyterlab/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/jupyterlab/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/galaxy-on-dockstore/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/galaxy-on-dockstore/slides.json"
         },
-        "version": 8,
+        "version": 4,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 148,
-        "visitors": 1537,
-        "zenodo_link": ""
+        "visitors": 1583144
     },
     {
         "admin_install": {
@@ -93415,80 +95759,93 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "graphicsmagick_image_convert",
+                    "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "5376a7767fb3",
-                    "tool_panel_section_label": "Convert Formats",
+                    "revisions": "ddf54b12c295",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastqtofasta",
+                    "owner": "devteam",
+                    "revisions": "297962e79f39",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "jq",
+                    "owner": "iuc",
+                    "revisions": "5ff75eb1a893",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "query_tabular",
+                    "owner": "iuc",
+                    "revisions": "33d61c89fb8d",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "snpeff_sars_cov_2",
+                    "owner": "iuc",
+                    "revisions": "2a3a00c1fa0a",
+                    "tool_panel_section_label": "Variant Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sra_tools",
+                    "owner": "iuc",
+                    "revisions": "69ebb7f46e45",
+                    "tool_panel_section_label": "Get Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sra_tools",
+                    "owner": "iuc",
+                    "revisions": "83c7d564b128",
+                    "tool_panel_section_label": "Get Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: graphicsmagick_image_convert\n  owner: bgruening\n  revisions: 5376a7767fb3\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-posters/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "ElectronicBlueberry"
-            ],
-            "editing": [
-                "hexylena"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: ddf54b12c295\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqtofasta\n  owner: devteam\n  revisions: 297962e79f39\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jq\n  owner: iuc\n  revisions: 5ff75eb1a893\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n  owner: iuc\n  revisions: 33d61c89fb8d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff_sars_cov_2\n  owner: iuc\n  revisions: 2a3a00c1fa0a\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: 69ebb7f46e45\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: 83c7d564b128\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "id": "ElectronicBlueberry",
-                "joined": "2023-04",
-                "name": "Laila Los",
-                "orcid": "0000-0002-2362-9720",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ElectronicBlueberry/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/ElectronicBlueberry.json"
+                "github": false,
+                "id": "jontrow",
+                "joined": "2021-05",
+                "name": "Jon Trow",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jontrow/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jontrow.json"
             },
             {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+                "id": "RareSeas",
+                "joined": "2021-05",
+                "name": "Adelaide Rhodes",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/RareSeas/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/RareSeas.json"
             }
         ],
-        "dir": "topics/galaxy-interface/tutorials/workflow-posters",
-        "edam_operation": [],
+        "dir": "topics/galaxy-interface/tutorials/ncbi-sarf",
+        "edam_operation": [
+            "SNP detection",
+            "Data handling"
+        ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.be",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "galaxy-interface/workflow-posters",
+        "id": "galaxy-interface/ncbi-sarf",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
+            "UseGalaxy.eu",
             "UseGalaxy.no"
         ],
         "js_requirements": {
@@ -93496,43 +95853,87 @@
             "mermaid": false
         },
         "key_points": [
-            "Print ready screenshots",
-            "Basic image compression"
+            "NCBI Publishes datasets in the cloud that you can easily process with Galaxy",
+            "The Rule Based Uploader simplifies processing and downloading large numbers of files"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-02-05",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Create a high resolution image of your Workflow, ready for a poster",
-            "Learn how to utilize external tools to make high resolution images of your Workflow",
-            "Learn how to compress high resolution Workflow images to share them in the web"
+            "Learn about SRA aligned read format and vcf files for Runs containing SARS-CoV-2 content",
+            "Understand how to search the metadata for these Runs to find your dataset of interest and then import that data in your preferred format"
         ],
-        "pageviews": 76,
-        "pub_date": "2024-02-05",
+        "pageviews": 5142217,
+        "pub_date": "2021-05-31",
         "questions": [
-            "How can I print or screenshot my Workflow in high resolution for a poster or presentation?",
-            "How can I share high detail images of my Workflows?"
+            "How can I search SRA SARS-CoV-2 metadata from within Galaxy?",
+            "How can I import SRA aligned read files and extract the data in my format of choice?",
+            "How can I import vcf files into Galaxy that have been generated for these Runs?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "prodromus"
+                ],
+                "date": "2021-05-15",
+                "galaxy_version": "21.01",
+                "length": "40M",
+                "speakers": [
+                    "prodromus"
+                ],
+                "youtube_id": "ogu-NBTP-DM"
+            }
         ],
         "requirements": [
             {
-                "link": "https://www.mozilla.org/en-US/firefox/new/",
-                "title": "The Firefox Browser (this will not work in Chrome)",
-                "type": "external"
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "upload-rules"
+                ],
+                "type": "internal"
             }
         ],
-        "short_id": "T00405",
+        "short_id": "T00155",
         "short_tools": [
-            "graphicsmagick_image_convert"
+            "query_tabular",
+            "tp_cat",
+            "jq",
+            "fastq_dump",
+            "snpeff_sars_cov_2",
+            "fastq_to_fasta_python",
+            "fasterq_dump"
         ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "workflows",
+        "slides": true,
+        "slides_recordings": [
+            {
+                "captioners": [
+                    "prodromus"
+                ],
+                "date": "2021-05-15",
+                "galaxy_version": "21.01",
+                "length": "15M",
+                "speakers": [
+                    "prodromus"
+                ],
+                "youtube_id": "siLP71B9gm4"
+            }
+        ],
+        "subtopic": "upload",
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
                 }
             ],
@@ -93542,6 +95943,11 @@
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -93551,12 +95957,19 @@
         },
         "symlink": null,
         "tags": [
-            "workflows"
+            "ncbi",
+            "covid19"
         ],
-        "time_estimation": "30M",
-        "title": "Creating high resolution images of Galaxy Workflows",
+        "time_estimation": "30m",
+        "title": "SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_convert/graphicsmagick_image_convert/1.3.40+galaxy0"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
+            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.11.0+galaxy0"
         ],
         "topic_name": "galaxy-interface",
         "topic_name_human": "Using Galaxy and Managing your Data",
@@ -93566,19 +95979,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "workflow-posters",
+        "tutorial_name": "ncbi-sarf",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-posters/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-posters/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-posters/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/ncbi-sarf/tutorial.json"
         },
-        "version": 1,
+        "version": 12,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 182,
-        "visitors": 61
+        "visit_duration": 267,
+        "visitors": 1911645
     },
     {
         "admin_install": {
@@ -93588,211 +96001,70 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/name-tags/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/get-data/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
+                "id": "pajanne",
                 "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            }
-        ],
-        "dir": "topics/galaxy-interface/tutorials/name-tags",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "galaxy-interface/name-tags",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Naming your datasets clearly is good practice, but name tags provide an easier alternative to the amount of effort required to rename 100s of datasets.",
-            "Name tags allow you to follow the flow of data throughout your history"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Learn how to set name tags",
-            "Learn how they are propagated"
-        ],
-        "pageviews": 1779,
-        "pub_date": "2019-04-08",
-        "questions": [
-            "What are name tags or hash tags?",
-            "How can I use them to keep track of my data?"
-        ],
-        "redirect_from": [
-            "/topics/galaxy-data-manipulation/tutorials/name-tags/tutorial",
-            "/short/galaxy-interface/name-tags",
-            "/short/T00154"
-        ],
-        "short_id": "T00154",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "manage",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "time_estimation": "20m",
-        "title": "Name tags for following complex histories",
-        "tools": [],
-        "topic_name": "galaxy-interface",
-        "topic_name_human": "Using Galaxy and Managing your Data",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "name-tags",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/name-tags/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/name-tags/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/name-tags/tutorial.json"
-        },
-        "version": 8,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 176,
-        "visitors": 1277,
-        "zenodo_link": ""
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/upload-rules/tutorial.json",
-        "contributors": [
+                "name": "Anne Pajon",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pajanne/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pajanne.json"
+            },
             {
-                "email": "jmchilton@gmail.com",
-                "id": "jmchilton",
+                "id": "tnabtaf",
                 "joined": "2017-09",
-                "matrix": "jmchilton:matrix.org",
-                "name": "John Chilton",
-                "orcid": "0000-0002-6794-0756",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jmchilton/",
-                "twitter": "jmchilton",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jmchilton.json"
+                "name": "Dave Clements",
+                "orcid": "0000-0002-9970-6657",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
+            },
+            {
+                "id": "mblue9",
+                "joined": "2018-09",
+                "name": "Maria Doyle",
+                "orcid": "0000-0003-4847-8436",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
             },
             {
                 "affiliations": [
+                    "CINECA-Project",
                     "gallantries",
-                    "by-covid",
                     "erasmusmc",
                     "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
                     "uni-freiburg"
                 ],
-                "id": "hexylena",
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
                 "joined": "2017-09",
+                "linkedin": "shiltemann",
                 "location": {
                     "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
+                    "lat": 51.912,
+                    "lon": 4.462
                 },
                 "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             }
         ],
-        "dir": "topics/galaxy-interface/tutorials/upload-rules",
+        "dir": "topics/galaxy-interface/tutorials/get-data",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "upload-rules-advanced"
-                ],
-                "type": "internal"
-            }
-        ],
-        "hands_on": true,
-        "id": "galaxy-interface/upload-rules",
+        "hands_on": false,
+        "id": "galaxy-interface/get-data",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -93804,49 +96076,25 @@
             "mermaid": false
         },
         "key_points": null,
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
+        "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
-        "objectives": [
-            "Learn about the Rule Based Uploader"
-        ],
-        "pageviews": 3832,
-        "pub_date": "2020-07-04",
+        "logo": "GTN",
+        "mod_date": "2022-10-18",
+        "objectives": null,
+        "pageviews": 5897170,
+        "pub_date": "2017-05-24",
         "questions": [
-            "How to use the rule based uploader to create complex collections"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "assuntad23"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "22M",
-                "speakers": [
-                    "assuntad23"
-                ],
-                "youtube_id": "1MWHVRWXpyA"
-            }
+            "How do I get my data into Galaxy?",
+            "How do I get public data into Galaxy?"
         ],
         "redirect_from": [
-            "/topics/galaxy-data-manipulation/tutorials/upload-rules/tutorial",
-            "/short/galaxy-interface/upload-rules",
-            "/short/T00160"
-        ],
-        "requirements": [
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "collections"
-                ],
-                "type": "internal"
-            }
+            "/topics/galaxy-data-manipulation/tutorials/get-data/slides",
+            "/short/galaxy-interface/get-data/slides",
+            "/short/S00062"
         ],
-        "short_id": "T00160",
+        "short_id": "S00062",
         "short_tools": [],
-        "slides": false,
+        "slides": true,
         "slides_recordings": false,
         "subtopic": "upload",
         "supported_servers": {
@@ -93883,12 +96131,8 @@
             ]
         },
         "symlink": null,
-        "tags": [
-            "collections",
-            "tags"
-        ],
-        "time_estimation": "20m",
-        "title": "Rule Based Uploader",
+        "time_estimation": null,
+        "title": "Getting data into Galaxy",
         "tools": [],
         "topic_name": "galaxy-interface",
         "topic_name_human": "Using Galaxy and Managing your Data",
@@ -93898,20 +96142,20 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "upload-rules",
+        "tutorial_name": "get-data",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/upload-rules/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/get-data/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/upload-rules/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/upload-rules/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/get-data/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/get-data/slides.json"
         },
-        "version": 11,
+        "version": 4,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 273,
-        "visitors": 2735,
-        "zenodo_link": "https://zenodo.org/records/3263975"
+        "visit_duration": 152,
+        "visitors": 2133582,
+        "zenodo_link": ""
     },
     {
         "admin_install": {
@@ -93963,7 +96207,7 @@
         "license": "CC-BY-4.0",
         "mod_date": "2024-06-25",
         "objectives": null,
-        "pageviews": 1697,
+        "pageviews": 1730,
         "pub_date": "2016-07-11",
         "questions": null,
         "redirect_from": [
@@ -94035,8 +96279,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 161,
-        "visitors": 1220,
+        "visit_duration": 158,
+        "visitors": 1252,
         "zenodo_link": ""
     },
     {
@@ -94047,8 +96291,19 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/search/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/upload-rules/tutorial.json",
         "contributors": [
+            {
+                "email": "jmchilton@gmail.com",
+                "id": "jmchilton",
+                "joined": "2017-09",
+                "matrix": "jmchilton:matrix.org",
+                "name": "John Chilton",
+                "orcid": "0000-0002-6794-0756",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jmchilton/",
+                "twitter": "jmchilton",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jmchilton.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
@@ -94077,24 +96332,25 @@
                 "orcid": "0000-0001-9760-8992",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
-                "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
             }
         ],
-        "dir": "topics/galaxy-interface/tutorials/search",
+        "dir": "topics/galaxy-interface/tutorials/upload-rules",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "upload-rules-advanced"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "galaxy-interface/search",
+        "id": "galaxy-interface/upload-rules",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -94105,29 +96361,52 @@
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": [
-            "Searching is easy and powerful",
-            "It will help you manage large histories with complex analyses"
-        ],
+        "key_points": null,
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-16",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Feel confident in searching your history"
+            "Learn about the Rule Based Uploader"
         ],
-        "pageviews": 518,
-        "pub_date": "2020-07-15",
+        "pageviews": 3928,
+        "pub_date": "2020-07-04",
         "questions": [
-            "How can you find your datasets?",
-            "How to search by file type?",
-            "What filters are available to you?"
+            "How to use the rule based uploader to create complex collections"
         ],
-        "short_id": "T00158",
+        "recordings": [
+            {
+                "captioners": [
+                    "assuntad23"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "22M",
+                "speakers": [
+                    "assuntad23"
+                ],
+                "youtube_id": "1MWHVRWXpyA"
+            }
+        ],
+        "redirect_from": [
+            "/topics/galaxy-data-manipulation/tutorials/upload-rules/tutorial",
+            "/short/galaxy-interface/upload-rules",
+            "/short/T00160"
+        ],
+        "requirements": [
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "collections"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00160",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "histories",
+        "subtopic": "upload",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -94162,8 +96441,12 @@
             ]
         },
         "symlink": null,
-        "time_estimation": "5m",
-        "title": "Searching Your History",
+        "tags": [
+            "collections",
+            "tags"
+        ],
+        "time_estimation": "20m",
+        "title": "Rule Based Uploader",
         "tools": [],
         "topic_name": "galaxy-interface",
         "topic_name_human": "Using Galaxy and Managing your Data",
@@ -94173,20 +96456,20 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "search",
+        "tutorial_name": "upload-rules",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/search/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/upload-rules/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/search/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/search/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/upload-rules/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/upload-rules/tutorial.json"
         },
-        "version": 4,
+        "version": 11,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 153,
-        "visitors": 318,
-        "zenodo_link": ""
+        "visit_duration": 278,
+        "visitors": 2812,
+        "zenodo_link": "https://zenodo.org/records/3263975"
     },
     {
         "admin_install": {
@@ -94196,26 +96479,25 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/galaxy-intro-jupyter/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/history-to-workflow/tutorial.json",
         "contributors": [
             {
-                "email": "delphine.lariviere@galaxy.org",
-                "id": "delphine-l",
+                "id": "tnabtaf",
                 "joined": "2017-09",
-                "name": "Delphine Lariviere",
-                "orcid": "0000-0001-6421-3484",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
+                "name": "Dave Clements",
+                "orcid": "0000-0002-9970-6657",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
             }
         ],
-        "dir": "topics/galaxy-interface/tutorials/galaxy-intro-jupyter",
+        "dir": "topics/galaxy-interface/tutorials/history-to-workflow",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "galaxy-interface/galaxy-intro-jupyter",
+        "id": "galaxy-interface/history-to-workflow",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -94227,33 +96509,35 @@
             "mermaid": false
         },
         "key_points": [
-            "Start Jupyter from the Visualize tab or from a dataset",
-            "Install Libraries with pip or Conda",
-            "Use get() to import datasets from your history to the notebook",
-            "Use put() to export datasets from the notebook to your history",
-            "Save your notebook into your history"
+            "Workflows allow you to easily repeat your analyses on different input datasets",
+            "Workflows can be automatically extracted from your analysis history",
+            "You can perform your analysis manually once, then automatically extract the recipe for repeating this analysis on other datasets",
+            "Workflows capture all the tools and parameter settings needed to perform an analysis",
+            "Workflows can be edited or created from scratch using the workflow editor"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-05",
+        "mod_date": "2023-02-03",
         "objectives": [
-            "Learn about the Jupyter Interactive Environment"
+            "Learn how to extract a workflow from a Galaxy history",
+            "Learn how to change a workflow using the workflow editor"
         ],
-        "pageviews": 2189,
-        "pub_date": "2018-07-02",
+        "pageviews": 3415,
+        "pub_date": "2017-10-18",
         "questions": [
-            "How to use a Jupyter Notebook in Galaxy"
+            "What is a workflow?",
+            "How can I create a workflow based on my analysis history?"
         ],
         "redirect_from": [
-            "/topics/galaxy-ui/tutorials/galaxy-intro-jupyter/tutorial",
-            "/short/galaxy-interface/galaxy-intro-jupyter",
-            "/short/T00148"
+            "/topics/galaxy-ui/tutorials/history-to-workflow/tutorial",
+            "/short/galaxy-interface/history-to-workflow",
+            "/short/T00151"
         ],
-        "short_id": "T00148",
+        "short_id": "T00151",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "analyse",
+        "subtopic": "workflows",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -94288,8 +96572,11 @@
             ]
         },
         "symlink": null,
+        "tags": [
+            "workflows"
+        ],
         "time_estimation": "30m",
-        "title": "Use Jupyter notebooks in Galaxy",
+        "title": "Extracting Workflows from Histories",
         "tools": [],
         "topic_name": "galaxy-interface",
         "topic_name_human": "Using Galaxy and Managing your Data",
@@ -94299,20 +96586,20 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "galaxy-intro-jupyter",
+        "tutorial_name": "history-to-workflow",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/galaxy-intro-jupyter/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/history-to-workflow/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/galaxy-intro-jupyter/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/galaxy-intro-jupyter/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/history-to-workflow/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/history-to-workflow/tutorial.json"
         },
         "version": 7,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 131,
-        "visitors": 1617,
-        "zenodo_link": "https://zenodo.org/record/1185122"
+        "visit_duration": 224,
+        "visitors": 2607,
+        "zenodo_link": ""
     },
     {
         "admin_install": {
@@ -94322,97 +96609,142 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/group-tags/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/jupyterlab/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "annefou"
+            ],
+            "editing": [
+                "hexylena"
+            ]
+        },
         "contributors": [
             {
-                "id": "mvdbeek",
-                "joined": "2018-06",
-                "name": "Marius van den Beek",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
+                "elixir_node": "no",
+                "id": "annefou",
+                "joined": "2019-07",
+                "name": "Anne Fouilloux",
+                "orcid": "0000-0002-1784-2920",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annefou/",
+                "twitter": "AnneFouilloux",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/annefou.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/galaxy-interface/tutorials/group-tags",
+        "dir": "topics/galaxy-interface/tutorials/jupyterlab",
         "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "galaxy-interface/group-tags",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
+        "id": "galaxy-interface/jupyterlab",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Group tags allow complex analyses without reshaping or unhiding datasets in a collection"
+            "How to work with JupyterLab interactively within Galaxy"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2022-10-18",
         "objectives": [
-            "Learn how to set group tags",
-            "Learn how to select group tags in tools"
+            "Launch JupyterLab in Galaxy",
+            "Start a notebook",
+            "Import libraries",
+            "Use get() to import datasets from your history to the notebook",
+            "Use put() to export datasets from the notebook to your history",
+            "Save your notebook into your history"
         ],
-        "pageviews": 3314,
-        "pub_date": "2019-03-06",
+        "pageviews": 2704,
+        "pub_date": "2020-03-05",
         "questions": [
-            "What are group tags?",
-            "How can I use group tags to perform multi-factor analyses with collections"
+            "How can I manipulate data using JupyterLab in Galaxy?",
+            "How can I start a notebook in JupyterLab?",
+            "How can I import/export dataset from/to my history to/from the notebook?",
+            "How can I save my notebook to my history?"
         ],
         "redirect_from": [
-            "/topics/galaxy-data-manipulation/tutorials/group-tags/tutorial",
-            "/short/galaxy-interface/group-tags",
-            "/short/T00149"
+            "/topics/galaxy-ui/tutorials/jupyterlab/tutorial",
+            "/short/galaxy-interface/jupyterlab",
+            "/short/T00153"
+        ],
+        "short_id": "T00153",
+        "short_tools": [
+            "interactive_tool_jupyter_notebook"
         ],
-        "short_id": "T00149",
-        "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "manage",
+        "subtopic": "analyse",
         "supported_servers": {
-            "exact": [],
-            "inexact": [
+            "exact": [
                 {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
                 },
                 {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
                 {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
                 },
                 {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 }
-            ]
+            ],
+            "inexact": []
         },
         "symlink": null,
-        "time_estimation": "10m",
-        "title": "Group tags for complex experimental designs",
-        "tools": [],
+        "tags": [
+            "interactive-tools"
+        ],
+        "time_estimation": "1H",
+        "title": "JupyterLab in Galaxy",
+        "tools": [
+            "interactive_tool_jupyter_notebook"
+        ],
         "topic_name": "galaxy-interface",
         "topic_name_human": "Using Galaxy and Managing your Data",
         "tours": false,
@@ -94421,19 +96753,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "group-tags",
+        "tutorial_name": "jupyterlab",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/group-tags/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/jupyterlab/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/group-tags/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/group-tags/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/jupyterlab/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/jupyterlab/tutorial.json"
         },
-        "version": 11,
+        "version": 8,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 199,
-        "visitors": 2412,
+        "visit_duration": 158,
+        "visitors": 1584,
         "zenodo_link": ""
     },
     {
@@ -94444,25 +96776,57 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/history-to-workflow/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/upload-rules-advanced/tutorial.json",
         "contributors": [
             {
-                "id": "tnabtaf",
+                "email": "jmchilton@gmail.com",
+                "id": "jmchilton",
                 "joined": "2017-09",
-                "name": "Dave Clements",
-                "orcid": "0000-0002-9970-6657",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
+                "matrix": "jmchilton:matrix.org",
+                "name": "John Chilton",
+                "orcid": "0000-0002-6794-0756",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jmchilton/",
+                "twitter": "jmchilton",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jmchilton.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/galaxy-interface/tutorials/history-to-workflow",
+        "dir": "topics/galaxy-interface/tutorials/upload-rules-advanced",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "galaxy-interface/history-to-workflow",
+        "id": "galaxy-interface/upload-rules-advanced",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -94473,36 +96837,48 @@
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": [
-            "Workflows allow you to easily repeat your analyses on different input datasets",
-            "Workflows can be automatically extracted from your analysis history",
-            "You can perform your analysis manually once, then automatically extract the recipe for repeating this analysis on other datasets",
-            "Workflows capture all the tools and parameter settings needed to perform an analysis",
-            "Workflows can be edited or created from scratch using the workflow editor"
-        ],
+        "key_points": null,
         "layout": "tutorial_hands_on",
+        "level": "Advanced",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-02-03",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Learn how to extract a workflow from a Galaxy history",
-            "Learn how to change a workflow using the workflow editor"
+            "Learn even more about the Rule Based Uploader"
         ],
-        "pageviews": 3344,
-        "pub_date": "2017-10-18",
+        "pageviews": 835,
+        "pub_date": "2018-05-25",
         "questions": [
-            "What is a workflow?",
-            "How can I create a workflow based on my analysis history?"
+            "How to use the rule based uploader to create complex collections"
         ],
-        "redirect_from": [
-            "/topics/galaxy-ui/tutorials/history-to-workflow/tutorial",
-            "/short/galaxy-interface/history-to-workflow",
-            "/short/T00151"
+        "recordings": [
+            {
+                "captioners": [
+                    "assuntad23"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "22M",
+                "speakers": [
+                    "assuntad23"
+                ],
+                "youtube_id": "1MWHVRWXpyA"
+            }
         ],
-        "short_id": "T00151",
+        "requirements": [
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "collections",
+                    "upload-rules"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00161",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "workflows",
+        "subtopic": "upload",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -94538,10 +96914,11 @@
         },
         "symlink": null,
         "tags": [
-            "workflows"
+            "collections",
+            "tags"
         ],
-        "time_estimation": "30m",
-        "title": "Extracting Workflows from Histories",
+        "time_estimation": "20m",
+        "title": "Rule Based Uploader: Advanced",
         "tools": [],
         "topic_name": "galaxy-interface",
         "topic_name_human": "Using Galaxy and Managing your Data",
@@ -94551,19 +96928,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "history-to-workflow",
+        "tutorial_name": "upload-rules-advanced",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/history-to-workflow/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/upload-rules-advanced/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/history-to-workflow/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/history-to-workflow/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/upload-rules-advanced/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/upload-rules-advanced/tutorial.json"
         },
-        "version": 7,
+        "version": 11,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 228,
-        "visitors": 2550,
+        "visit_duration": 356,
+        "visitors": 610,
         "zenodo_link": ""
     },
     {
@@ -94616,10 +96993,10 @@
         ],
         "dir": "topics/galaxy-interface/tutorials/collections",
         "edam_operation": [
+            "Generation",
             "Sequence alignment",
-            "Read mapping",
             "Genome indexing",
-            "Generation"
+            "Read mapping"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -94634,6 +97011,8 @@
         "inexact_supported_servers": [
             "GalaxyTrakr",
             "HyPhy HIV NGS Tools",
+            "MISSISSIPPI",
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.fr",
             "UseGalaxy.no"
@@ -94655,7 +97034,7 @@
         "objectives": [
             "Understand and master dataset collections"
         ],
-        "pageviews": 16178,
+        "pageviews": 16713,
         "pub_date": "2016-09-30",
         "questions": [
             "How to manipulate large numbers of datasets at once?"
@@ -94692,10 +97071,10 @@
         ],
         "short_id": "T00146",
         "short_tools": [
-            "snpSift_extractFields",
             "bwa_mem",
-            "collapse_dataset",
-            "lofreq_call"
+            "snpSift_extractFields",
+            "lofreq_call",
+            "collapse_dataset"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -94729,6 +97108,16 @@
                     "url": "https://galaxy.hyphy.org/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -94778,7 +97167,7 @@
         "video_versions": 2,
         "video_view": 0,
         "visit_duration": 173,
-        "visitors": 11542,
+        "visitors": 11953,
         "zenodo_link": "https://doi.org/10.5281/zenodo.5119008"
     },
     {
@@ -94789,19 +97178,8 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/upload-rules-advanced/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/name-tags/tutorial.json",
         "contributors": [
-            {
-                "email": "jmchilton@gmail.com",
-                "id": "jmchilton",
-                "joined": "2017-09",
-                "matrix": "jmchilton:matrix.org",
-                "name": "John Chilton",
-                "orcid": "0000-0002-6794-0756",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jmchilton/",
-                "twitter": "jmchilton",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jmchilton.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
@@ -94832,14 +97210,14 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/galaxy-interface/tutorials/upload-rules-advanced",
+        "dir": "topics/galaxy-interface/tutorials/name-tags",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "galaxy-interface/upload-rules-advanced",
+        "id": "galaxy-interface/name-tags",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -94850,48 +97228,33 @@
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": null,
+        "key_points": [
+            "Naming your datasets clearly is good practice, but name tags provide an easier alternative to the amount of effort required to rename 100s of datasets.",
+            "Name tags allow you to follow the flow of data throughout your history"
+        ],
         "layout": "tutorial_hands_on",
-        "level": "Advanced",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Learn even more about the Rule Based Uploader"
+            "Learn how to set name tags",
+            "Learn how they are propagated"
         ],
-        "pageviews": 816,
-        "pub_date": "2018-05-25",
+        "pageviews": 1831,
+        "pub_date": "2019-04-08",
         "questions": [
-            "How to use the rule based uploader to create complex collections"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "assuntad23"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "22M",
-                "speakers": [
-                    "assuntad23"
-                ],
-                "youtube_id": "1MWHVRWXpyA"
-            }
+            "What are name tags or hash tags?",
+            "How can I use them to keep track of my data?"
         ],
-        "requirements": [
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "collections",
-                    "upload-rules"
-                ],
-                "type": "internal"
-            }
+        "redirect_from": [
+            "/topics/galaxy-data-manipulation/tutorials/name-tags/tutorial",
+            "/short/galaxy-interface/name-tags",
+            "/short/T00154"
         ],
-        "short_id": "T00161",
+        "short_id": "T00154",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "upload",
+        "subtopic": "manage",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -94926,12 +97289,8 @@
             ]
         },
         "symlink": null,
-        "tags": [
-            "collections",
-            "tags"
-        ],
         "time_estimation": "20m",
-        "title": "Rule Based Uploader: Advanced",
+        "title": "Name tags for following complex histories",
         "tools": [],
         "topic_name": "galaxy-interface",
         "topic_name_human": "Using Galaxy and Managing your Data",
@@ -94941,19 +97300,219 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "upload-rules-advanced",
+        "tutorial_name": "name-tags",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/upload-rules-advanced/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/name-tags/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/upload-rules-advanced/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/upload-rules-advanced/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/name-tags/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/name-tags/tutorial.json"
         },
-        "version": 11,
+        "version": 8,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 173,
+        "visitors": 1321,
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/rstudio/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "elixir-europe"
+                ],
+                "elixir_node": "gr",
+                "email": "fpsom@certh.gr",
+                "id": "fpsom",
+                "joined": "2019-03",
+                "linkedin": "fpsom",
+                "matrix": "fpsom:matrix.org",
+                "name": "Fotis E. Psomopoulos",
+                "orcid": "0000-0002-0222-4273",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
+                "twitter": "fopsom",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
+            },
+            {
+                "email": "tbyhdgs@gmail.com",
+                "id": "tobyhodges",
+                "joined": "2019-07",
+                "name": "Toby Hodges",
+                "orcid": "0000-0003-1766-456X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tobyhodges/",
+                "twitter": "tbyhdgs",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tobyhodges.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            }
+        ],
+        "dir": "topics/galaxy-interface/tutorials/rstudio",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "data-science",
+                "tutorials": [
+                    "r-basics"
+                ],
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "galaxy-interface/rstudio",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Why it's helpful to be able to work with R interactively within Galaxy"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": [
+            "Launch RStudio in Galaxy"
+        ],
+        "pageviews": 6875,
+        "pub_date": "2019-10-08",
+        "questions": [
+            "How can I manipulate data using R in Galaxy?"
+        ],
+        "redirect_from": [
+            "/topics/galaxy-ui/tutorials/rstudio/tutorial",
+            "/short/galaxy-interface/rstudio",
+            "/short/T00157"
+        ],
+        "short_id": "T00157",
+        "short_tools": [
+            "interactive_tool_rstudio"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "analyse",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "interactive-tools"
+        ],
+        "time_estimation": "3H",
+        "title": "RStudio in Galaxy",
+        "tools": [
+            "interactive_tool_rstudio"
+        ],
+        "topic_name": "galaxy-interface",
+        "topic_name_human": "Using Galaxy and Managing your Data",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "rstudio",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/rstudio/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/rstudio/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/rstudio/tutorial.json"
+        },
+        "version": 12,
+        "video": false,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 365,
-        "visitors": 592,
+        "visit_duration": 125,
+        "visitors": 4256,
         "zenodo_link": ""
     },
     {
@@ -95037,7 +97596,7 @@
             "Have a greater knowledge of how Galaxy handles data downloads and deletions",
             "Be able to successfully download and delete their own data"
         ],
-        "pageviews": 8319,
+        "pageviews": 8472,
         "pub_date": "2019-10-17",
         "questions": [
             "How can I efficiently download my data from Galaxy once I've completed my analyses?",
@@ -95109,8 +97668,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 92,
-        "visitors": 6149,
+        "visit_duration": 93,
+        "visitors": 6277,
         "zenodo_link": ""
     },
     {
@@ -95118,1475 +97677,685 @@
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": [
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/group-tags/tutorial.json",
+        "contributors": [
+            {
+                "id": "mvdbeek",
+                "joined": "2018-06",
+                "name": "Marius van den Beek",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
+            }
+        ],
+        "dir": "topics/galaxy-interface/tutorials/group-tags",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "galaxy-interface/group-tags",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Group tags allow complex analyses without reshaping or unhiding datasets in a collection"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": [
+            "Learn how to set group tags",
+            "Learn how to select group tags in tools"
+        ],
+        "pageviews": 3345,
+        "pub_date": "2019-03-06",
+        "questions": [
+            "What are group tags?",
+            "How can I use group tags to perform multi-factor analyses with collections"
+        ],
+        "redirect_from": [
+            "/topics/galaxy-data-manipulation/tutorials/group-tags/tutorial",
+            "/short/galaxy-interface/group-tags",
+            "/short/T00149"
+        ],
+        "short_id": "T00149",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "manage",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
                 {
-                    "name": "prokka",
-                    "owner": "crs4",
-                    "revisions": "bf68eb663bc3",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
                 },
                 {
-                    "name": "prokka",
-                    "owner": "crs4",
-                    "revisions": "111884f0d912",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 },
                 {
-                    "name": "jbrowse",
-                    "owner": "iuc",
-                    "revisions": "a6e57ff585c0",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: prokka\n  owner: crs4\n  revisions: bf68eb663bc3\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: prokka\n  owner: crs4\n  revisions: 111884f0d912\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.json",
+        "symlink": null,
+        "time_estimation": "10m",
+        "title": "Group tags for complex experimental designs",
+        "tools": [],
+        "topic_name": "galaxy-interface",
+        "topic_name_human": "Using Galaxy and Managing your Data",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "group-tags",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/group-tags/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/group-tags/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/group-tags/tutorial.json"
+        },
+        "version": 11,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 199,
+        "visitors": 2442,
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/search/tutorial.json",
         "contributors": [
-            {
-                "id": "annasyme",
-                "joined": "2017-09",
-                "name": "Anna Syme",
-                "orcid": "0000-0002-9906-0673",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
-            },
             {
                 "affiliations": [
-                    "elixir-europe"
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
                 ],
-                "elixir_node": "au",
-                "id": "tseemann",
-                "joined": "2018-06",
-                "name": "Torsten Seemann",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tseemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tseemann.json"
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
             {
-                "elixir_node": "au",
-                "email": "simon.gladman@unimelb.edu.au",
-                "id": "slugger70",
-                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
                 "joined": "2017-09",
-                "name": "Simon Gladman",
-                "orcid": "0000-0002-6100-4385",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
             }
         ],
-        "dir": "topics/genome-annotation/tutorials/annotation-with-prokka",
-        "edam_ontology": [
-            "topic_0622",
-            "topic_3301",
-            "topic_0623",
-            "topic_0080"
-        ],
-        "edam_operation": [
-            "Genome visualisation",
-            "Genome annotation",
-            "Gene prediction",
-            "Coding region prediction"
-        ],
-        "edam_topic": [
-            "Genomics",
-            "Microbiology",
-            "Gene and protein families",
-            "Sequence analysis"
-        ],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)"
-        ],
+        "dir": "topics/galaxy-interface/tutorials/search",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "genome-annotation",
-                "tutorials": [
-                    "apollo"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "genome-annotation/annotation-with-prokka",
+        "id": "galaxy-interface/search",
         "inexact_supported_servers": [
-            "Galaxy@AuBi",
-            "GalaxyTrakr",
-            "UseGalaxy.cz",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Prokka is a useful tool to annotate a bacterial genome.",
-            "JBrowse can be used to inspect the annotation of a genome."
+            "Searching is easy and powerful",
+            "It will help you manage large histories with complex analyses"
         ],
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-08",
+        "mod_date": "2023-11-16",
         "objectives": [
-            "Load genome into Galaxy",
-            "Annotate genome with Prokka",
-            "View annotations in JBrowse"
+            "Feel confident in searching your history"
         ],
-        "pageviews": 5754405,
-        "pub_date": "2018-03-06",
+        "pageviews": 528,
+        "pub_date": "2020-07-15",
         "questions": [
-            "How can we annotate a bacterial genome?",
-            "How can we visualize annotated genomic features?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "abretaud"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "20M",
-                "speakers": [
-                    "abretaud"
-                ],
-                "youtube_id": "B8pIQZPf21Y"
-            }
-        ],
-        "short_id": "T00168",
-        "short_tools": [
-            "prokka",
-            "jbrowse"
-        ],
-        "slides": true,
-        "slides_recordings": [
-            {
-                "captioners": [
-                    "abretaud"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "3M",
-                "speakers": [
-                    "awspolly"
-                ],
-                "youtube_id": "eqHy-Cc7k4Q"
-            }
+            "How can you find your datasets?",
+            "How to search by file type?",
+            "What filters are available to you?"
         ],
-        "subtopic": "prokaryote",
+        "short_id": "T00158",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "histories",
         "supported_servers": {
-            "exact": [
+            "exact": [],
+            "inexact": [
                 {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.org (Main)",
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 },
                 {
+                    "human": "Galaxy France",
+                    "id": "fr",
                     "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
+                    "url": "https://usegalaxy.fr",
                     "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
-        "tags": [
-            "gmod",
-            "prokaryote",
-            "microgalaxy",
-            "jbrowse1"
-        ],
-        "time_estimation": "1h",
-        "title": "Genome annotation with Prokka",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
-            "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1"
-        ],
-        "topic_name": "genome-annotation",
-        "topic_name_human": "Genome Annotation",
+        "time_estimation": "5m",
+        "title": "Searching Your History",
+        "tools": [],
+        "topic_name": "galaxy-interface",
+        "topic_name_human": "Using Galaxy and Managing your Data",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": true
+            "video": false
         },
-        "tutorial_name": "annotation-with-prokka",
+        "tutorial_name": "search",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/search/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/search/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/search/tutorial.json"
         },
-        "version": 25,
-        "video": true,
-        "video_versions": 1,
+        "version": 4,
+        "video": false,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 260,
-        "visitors": 2079352,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0001-6046-610X",
-                        "name": "Torsten Seemann"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-6100-4385",
-                        "name": "Simon Gladman"
-                    }
-                ],
-                "description": "Genome annotation with Prokka",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontigs.fasta\"]\n  1[label=\"Prokka\"]\n  0 -> 1 [label=\"output\"]\n  ka336c364e69e47ebace6a7fe46d285fe[color=lightseagreen,label=\"Output\\ngff_output\"]\n  1 -> ka336c364e69e47ebace6a7fe46d285fe\n  2[label=\"JBrowse\"]\n  1 -> 2 [label=\"out_fna\"]\n  1 -> 2 [label=\"out_gff\"]\n}",
-                "history": [
-                    {
-                        "hash": "70a555355ed2ebc563a4388cd1da50f7f1a5952f",
-                        "message": "Update topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
-                        "num": 10,
-                        "short_hash": "70a555355",
-                        "unix": "1715074163"
-                    },
-                    {
-                        "hash": "466b451a082b7d2d5e60777a45289874bbbde721",
-                        "message": "Add creators and license to workflow",
-                        "num": 9,
-                        "short_hash": "466b451a0",
-                        "unix": "1714990318"
-                    },
-                    {
-                        "hash": "499e257dee992b4645adf4c79844b8cc89e68c24",
-                        "message": "update prokka workflow",
-                        "num": 8,
-                        "short_hash": "499e257de",
-                        "unix": "1714456964"
-                    },
-                    {
-                        "hash": "56413bab75ab75be269668d70e3929e01bbaa5fb",
-                        "message": "Add workflow test.",
-                        "num": 7,
-                        "short_hash": "56413bab7",
-                        "unix": "1603310943"
-                    },
-                    {
-                        "hash": "a3829a12322232647926a394b1ecae3af17a858b",
-                        "message": "Update Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
-                        "num": 6,
-                        "short_hash": "a3829a123",
-                        "unix": "1580832292"
-                    },
-                    {
-                        "hash": "bab7ab72c6a4436a3ac3e6745b364696332399b5",
-                        "message": "prokka@1.14.5 jbrowse@1.16.5+galaxy7",
-                        "num": 5,
-                        "short_hash": "bab7ab72c",
-                        "unix": "1580433748"
-                    },
-                    {
-                        "hash": "c69f09dd0cb211d5621af293fe400892e343f78e",
-                        "message": "Adding tag",
-                        "num": 4,
-                        "short_hash": "c69f09dd0",
-                        "unix": "1579796672"
-                    },
-                    {
-                        "hash": "920732bc2295d6120b075934b758290ad56f5759",
-                        "message": "Updated prokka workflow to newest tool versions",
-                        "num": 3,
-                        "short_hash": "920732bc2",
-                        "unix": "1579634888"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 2,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "b9a6072964bce056112a36326600e4c80bd133ec",
-                        "message": "move tutorials to new topic",
-                        "num": 1,
-                        "short_hash": "b9a607296",
-                        "unix": "1528898987"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "contigs.fasta"
-                            }
-                        ],
-                        "label": "contigs.fasta",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 76.845458984375
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "79e73b85-8d44-413f-83b7-c0e668ec963c",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ncontigs.fasta\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Prokka\"];\n  0 -->|output| 1;\n  a336c364-e69e-47eb-ace6-a7fe46d285fe[\"Output\\ngff_output\"];\n  1 --> a336c364-e69e-47eb-ace6-a7fe46d285fe;\n  style a336c364-e69e-47eb-ace6-a7fe46d285fe stroke:#2c3143,stroke-width:4px;\n  2[\"JBrowse\"];\n  1 -->|out_fna| 2;\n  1 -->|out_gff| 2;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Genome Annotation with Prokka ",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Prokka",
-                        "outputs": [
-                            {
-                                "name": "out_gff",
-                                "type": "gff"
-                            },
-                            {
-                                "name": "out_gbk",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "out_fna",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "out_faa",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "out_ffn",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "out_sqn",
-                                "type": "asn1"
-                            },
-                            {
-                                "name": "out_fsa",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "out_tbl",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "out_err",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "out_txt",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "out_log",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 254.117919921875,
-                            "top": 0.0
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
-                        "tool_shed_repository": {
-                            "changeset_revision": "bf68eb663bc3",
-                            "name": "prokka",
-                            "owner": "crs4",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"__workflow_invocation_uuid__\": \"5dc31c9443c711eabead005056ba55fb\", \"centre\": \"V\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"compliant\": {\"compliant_select\": \"no\", \"__current_case__\": 0, \"addgenes\": false, \"mincontig\": \"200\"}, \"evalue\": \"1e-06\", \"fast\": false, \"genus\": \"Staphylococcus\", \"gffver\": \"3\", \"increment\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"kingdom\": {\"kingdom_select\": \"Bacteria\", \"__current_case__\": 1, \"gcode\": \"11\"}, \"locustag\": \"P\", \"metagenome\": false, \"norrna\": false, \"notrna\": false, \"outputs\": [\"gff\", \"gbk\", \"fna\", \"faa\", \"ffn\", \"sqn\", \"fsa\", \"tbl\", \"err\", \"txt\"], \"plasmid\": \"\", \"proteins\": null, \"rfam\": false, \"species\": \"aureus\", \"strain\": \"\", \"usegenus\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.14.5",
-                        "type": "tool",
-                        "uuid": "28efec53-71bb-4aaa-993d-03b78d493570",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "gff_output",
-                                "output_name": "out_gff",
-                                "uuid": "a336c364-e69e-47eb-ace6-a7fe46d285fe"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "genome-annotation/annotation-with-prokka",
-                "path": "topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
-                "tags": [
-                    "genome-annotation",
-                    "GTN"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "Genome Annotation with Prokka ",
-                "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-annotation-with-prokka/versions/galaxy-workflow-workflow-constructed-from-history--prokka-workflow-",
-                "tutorial_id": "annotation-with-prokka",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.html",
-                "version": 6,
-                "wfid": "genome-annotation-annotation-with-prokka",
-                "wfname": "galaxy-workflow-workflow-constructed-from-history--prokka-workflow-",
-                "workflow": "Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1"
-                ],
-                "workflowhub_id": "1186"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.1156405"
+        "visit_duration": 153,
+        "visitors": 328,
+        "zenodo_link": ""
     },
     {
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/history/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "nekrut"
+            ],
+            "editing": [
+                "polkhe",
+                "martenson",
+                "gallardoalba",
+                "shiltemann",
+                "bebatut",
+                "bgruening",
+                "hexylena",
+                "ahmedhamidawan"
+            ]
+        },
+        "contributors": [
+            {
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
+                "joined": "2017-09",
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "id": "polkhe",
+                "joined": "2017-09",
+                "name": "Ekaterina Polkh",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/polkhe/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/polkhe.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "cz",
+                "email": "marten@bx.psu.edu",
+                "fediverse": "https://mastodon.world/@martenson",
+                "fediverse_flavor": "mastodon",
+                "id": "martenson",
+                "joined": "2017-09",
+                "location": {
+                    "country": "USA",
+                    "lat": 37.0,
+                    "lon": -122.0
+                },
+                "matrix": "martenson:matrix.org",
+                "name": "Martin \u010cech",
+                "orcid": "0000-0002-9318-1781",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/martenson/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/martenson.json"
+            },
+            {
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "gallardoalba",
+                "joined": "2020-11",
+                "name": "Crist\u00f3bal Gallardo",
+                "orcid": "0000-0002-5752-2155",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
+            },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
                 },
-                {
-                    "name": "clustalw",
-                    "owner": "devteam",
-                    "revisions": "d6694932c5e0",
-                    "tool_panel_section_label": "Multiple Alignments",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "affiliations": [
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
+                "fediverse_flavor": "mastodon",
+                "id": "bgruening",
+                "joined": "2017-09",
+                "linkedin": "bgruening",
+                "location": {
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
                 },
-                {
-                    "name": "chromeister",
-                    "owner": "iuc",
-                    "revisions": "e483be1014b6",
-                    "tool_panel_section_label": "Multiple Alignments",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
                 },
-                {
-                    "name": "gecko",
-                    "owner": "iuc",
-                    "revisions": "5efbd15675ca",
-                    "tool_panel_section_label": "Multiple Alignments",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clustalw\n  owner: devteam\n  revisions: d6694932c5e0\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chromeister\n  owner: iuc\n  revisions: e483be1014b6\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gecko\n  owner: iuc\n  revisions: 5efbd15675ca\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.json",
-        "contributors": [
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
             {
-                "elixir_node": "es",
-                "email": "estebanpw@uma.es",
-                "id": "estebanpw",
-                "joined": "2020-11",
-                "name": "Esteban Perez-Wohlfeil",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/estebanpw/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/estebanpw.json"
+                "email": "aawan7@jhu.edu",
+                "id": "ahmedhamidawan",
+                "joined": "2024-08",
+                "linkedin": "ahmed-awan-70a20919a",
+                "matrix": "ahmedhamidawan:matrix.org",
+                "name": "Ahmed Hamid Awan",
+                "orcid": "0009-0003-2600-6152",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ahmedhamidawan/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/ahmedhamidawan.json"
             }
         ],
-        "dir": "topics/genome-annotation/tutorials/hpc-for-lsgc",
-        "edam_operation": [
-            "Multiple sequence alignment"
-        ],
+        "dir": "topics/galaxy-interface/tutorials/history",
+        "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org.au"
-        ],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "genome-annotation/hpc-for-lsgc",
+        "id": "galaxy-interface/history",
         "inexact_supported_servers": [
-            "GalaxyTrakr",
-            "UseGalaxy.cz"
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
         ],
         "js_requirements": {
-            "mathjax": 10229,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "We learnt that sequence comparison is a demanding problem and that there are several ways to approach it",
-            "We learnt how to run sequence comparisons in Galaxy with different levels of precision, particularly fine-grained and coarse-grained sequence comparison using GECKO and CHROMEISTER for smaller and larger sequences, respectively",
-            "We learnt how to post-process our comparison by extracting alignments, fine-tuning with multiple sequence alignment, detecting rearrangements, etc."
+            "In Galaxy, data is stored in datasets and organized in histories",
+            "The right pane shows the current history. It displays the name of the history, the tags and annotations assigned to it, and the size of the data in it",
+            "The datasets are shown differently depending on their status: queued, running, ok, error, or paused",
+            "The summary view for each dataset can be expanded to show additional information",
+            "Datasets deleted are hidden from history. They can be restored to the history, or permanently deleted from the server, or purged. Purged files cannot be restored",
+            "Histories can also be deleted and purged, similar to datasets",
+            "Datasets can be organized into collections within a history with search and multi-select. Jobs applied to collections use the same settings for each dataset in the collection"
         ],
         "layout": "tutorial_hands_on",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-31",
+        "mod_date": "2024-09-18",
         "objectives": [
-            "Learn the basics of pairwise sequence comparison",
-            "Learn how to run different tools in Galaxy to perform sequence comparison at fine and coarse-grained levels",
-            "Learn how to post-process your sequence comparisons"
+            "Gain understanding on navigating and manipulating histories"
         ],
-        "pageviews": 5565092,
-        "pub_date": "2021-02-08",
+        "pageviews": 5256,
+        "pub_date": "2017-02-20",
         "questions": [
-            "How can we run pairwise genome comparisons using Galaxy?",
-            "How can we run massive chromosome comparisons in Galaxy?",
-            "How can we quickly visualize genome comparisons in Galaxy?"
+            "How do Galaxy histories work?"
         ],
-        "requirements": [
+        "recordings": [
             {
-                "topic_name": "introduction",
-                "tutorials": [
-                    "galaxy-intro-101"
+                "captioners": [
+                    "shiltemann"
                 ],
-                "type": "internal"
+                "date": "2023-05-19",
+                "galaxy_version": "23.01",
+                "length": "18M",
+                "speakers": [
+                    "shiltemann"
+                ],
+                "youtube_id": "C3_HSgbbDWc"
+            },
+            {
+                "bot-timestamp": 1725682847,
+                "captioners": [
+                    "ahmedhamidawan"
+                ],
+                "date": "2024-09-07",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "23M",
+                "speakers": [
+                    "ahmedhamidawan"
+                ],
+                "youtube_id": "InBwrXde-g4"
             }
         ],
-        "short_id": "T00176",
-        "short_tools": [
-            "clustalw",
-            "gecko",
-            "tp_awk_tool",
-            "chromeister"
+        "redirect_from": [
+            "/topics/galaxy-ui/tutorials/history/tutorial",
+            "/short/galaxy-interface/history",
+            "/short/T00150"
         ],
-        "slides": true,
+        "short_id": "T00150",
+        "short_tools": [],
+        "slides": false,
         "slides_recordings": false,
+        "subtopic": "histories",
         "supported_servers": {
-            "exact": [
+            "exact": [],
+            "inexact": [
                 {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
                     "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "plants",
-            "prokaryote"
-        ],
-        "time_estimation": "2H",
-        "title": "From small to large-scale genome comparison",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a",
-            "toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2"
-        ],
-        "topic_name": "genome-annotation",
-        "topic_name_human": "Genome Annotation",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "hpc-for-lsgc",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.json"
-        },
-        "version": 8,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 282,
-        "visitors": 2016344,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "A workflow designed to compare chromosomes and study large-scale rearrangements using CHROMEISTER",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nQuery chromosome\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference chromosome\"]\n  2[label=\"Chromeister\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  k58cf0c0c92004ba497276d908ccdfa9a[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Detected events\"]\n  2 -> k58cf0c0c92004ba497276d908ccdfa9a\n  k2afd0e7cd1cf4bfdbec66cc237ff3e2c[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Comparison metainformation\"]\n  2 -> k2afd0e7cd1cf4bfdbec66cc237ff3e2c\n  kc248576c1c39416c99d040c520e3da67[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Comparison dotplot\"]\n  2 -> kc248576c1c39416c99d040c520e3da67\n  k5f9aad77f9ee4932ab22bb5fd83f416c[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Comparison matrix\"]\n  2 -> k5f9aad77f9ee4932ab22bb5fd83f416c\n  kdea450c2712643dcaf7a9f2b704c76dd[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Comparison score\"]\n  2 -> kdea450c2712643dcaf7a9f2b704c76dd\n  k9a03f72255884a3fb70e0ec9979c16dd[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Detected events plot\"]\n  2 -> k9a03f72255884a3fb70e0ec9979c16dd\n}",
-                "history": [
-                    {
-                        "hash": "ae7dbf55cc79f67b32661f650f26d5baad4779b3",
-                        "message": "added workflow for chromeister",
-                        "num": 1,
-                        "short_hash": "ae7dbf55c",
-                        "unix": "1612266607"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Query chromosome"
-                            }
-                        ],
-                        "label": "Query chromosome",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 345.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 446,
-                            "right": 646,
-                            "top": 263,
-                            "width": 200,
-                            "x": 446,
-                            "y": 263
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "fdde703b-e59f-403b-be56-28b4fde66d17",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "e6b6ae7f-73c3-450e-a997-103138788bc6"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Reference chromosome"
-                            }
-                        ],
-                        "label": "Reference chromosome",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 445.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 448,
-                            "right": 648,
-                            "top": 363,
-                            "width": 200,
-                            "x": 448,
-                            "y": 363
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "43a48ede-1c2e-4b0d-bf74-da212443a7de",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1007eb1e-be5f-4f22-9d42-046f5e695dc4"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQuery chromosome\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference chromosome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Chromeister\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  58cf0c0c-9200-4ba4-9727-6d908ccdfa9a[\"Output\\nChromeister on input dataset(s): Detected events\"];\n  2 --> 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a;\n  style 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a stroke:#2c3143,stroke-width:4px;\n  2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c[\"Output\\nChromeister on input dataset(s): Comparison metainformation\"];\n  2 --> 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c;\n  style 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c stroke:#2c3143,stroke-width:4px;\n  c248576c-1c39-416c-99d0-40c520e3da67[\"Output\\nChromeister on input dataset(s): Comparison dotplot\"];\n  2 --> c248576c-1c39-416c-99d0-40c520e3da67;\n  style c248576c-1c39-416c-99d0-40c520e3da67 stroke:#2c3143,stroke-width:4px;\n  5f9aad77-f9ee-4932-ab22-bb5fd83f416c[\"Output\\nChromeister on input dataset(s): Comparison matrix\"];\n  2 --> 5f9aad77-f9ee-4932-ab22-bb5fd83f416c;\n  style 5f9aad77-f9ee-4932-ab22-bb5fd83f416c stroke:#2c3143,stroke-width:4px;\n  dea450c2-7126-43dc-af7a-9f2b704c76dd[\"Output\\nChromeister on input dataset(s): Comparison score\"];\n  2 --> dea450c2-7126-43dc-af7a-9f2b704c76dd;\n  style dea450c2-7126-43dc-af7a-9f2b704c76dd stroke:#2c3143,stroke-width:4px;\n  9a03f722-5588-4a3f-b70e-0ec9979c16dd[\"Output\\nChromeister on input dataset(s): Detected events plot\"];\n  2 --> 9a03f722-5588-4a3f-b70e-0ec9979c16dd;\n  style 9a03f722-5588-4a3f-b70e-0ec9979c16dd stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "CHROMEISTER chromosome comparison",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Query chromosome"
-                            }
-                        ],
-                        "label": "Query chromosome",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 345.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 446,
-                            "right": 646,
-                            "top": 263,
-                            "width": 200,
-                            "x": 446,
-                            "y": 263
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "fdde703b-e59f-403b-be56-28b4fde66d17",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "e6b6ae7f-73c3-450e-a997-103138788bc6"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Reference chromosome"
-                            }
-                        ],
-                        "label": "Reference chromosome",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 445.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 448,
-                            "right": 648,
-                            "top": 363,
-                            "width": 200,
-                            "x": 448,
-                            "y": 363
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "43a48ede-1c2e-4b0d-bf74-da212443a7de",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1007eb1e-be5f-4f22-9d42-046f5e695dc4"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a",
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "db": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "query": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Chromeister",
-                                "name": "db"
-                            },
-                            {
-                                "description": "runtime parameter for tool Chromeister",
-                                "name": "query"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Chromeister",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "output_imagen",
-                                "type": "png"
-                            },
-                            {
-                                "name": "output_csv",
-                                "type": "csv"
-                            },
-                            {
-                                "name": "output_events",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "output_events_png",
-                                "type": "png"
-                            },
-                            {
-                                "name": "output_score",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 793.4000244140625,
-                            "height": 520.4000244140625,
-                            "left": 851,
-                            "right": 1051,
-                            "top": 273,
-                            "width": 200,
-                            "x": 851,
-                            "y": 273
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a",
-                        "tool_shed_repository": {
-                            "changeset_revision": "a6d1f83c46b4",
-                            "name": "chromeister",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"db\": {\"__class__\": \"RuntimeValue\"}, \"diffuse\": \"4\", \"dimension\": \"1000\", \"grid\": \"true\", \"kmer\": \"32\", \"pngevents\": \"true\", \"query\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.5.a",
-                        "type": "tool",
-                        "uuid": "79507815-b059-4f21-b74e-8e390fbb4bf2",
-                        "workflow_outputs": [
-                            {
-                                "label": "Chromeister on input dataset(s): Detected events",
-                                "output_name": "output_events",
-                                "uuid": "58cf0c0c-9200-4ba4-9727-6d908ccdfa9a"
-                            },
-                            {
-                                "label": "Chromeister on input dataset(s): Comparison metainformation",
-                                "output_name": "output_csv",
-                                "uuid": "2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c"
-                            },
-                            {
-                                "label": "Chromeister on input dataset(s): Comparison dotplot",
-                                "output_name": "output_imagen",
-                                "uuid": "c248576c-1c39-416c-99d0-40c520e3da67"
-                            },
-                            {
-                                "label": "Chromeister on input dataset(s): Comparison matrix",
-                                "output_name": "output",
-                                "uuid": "5f9aad77-f9ee-4932-ab22-bb5fd83f416c"
-                            },
-                            {
-                                "label": "Chromeister on input dataset(s): Comparison score",
-                                "output_name": "output_score",
-                                "uuid": "dea450c2-7126-43dc-af7a-9f2b704c76dd"
-                            },
-                            {
-                                "label": "Chromeister on input dataset(s): Detected events plot",
-                                "output_name": "output_events_png",
-                                "uuid": "9a03f722-5588-4a3f-b70e-0ec9979c16dd"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "genome-annotation/hpc-for-lsgc",
-                "path": "topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/CHROMEISTER_chromosome_comparison.ga",
-                "tags": [
-                    "genome-annotation"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "CHROMEISTER chromosome comparison",
-                "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-hpc-for-lsgc/versions/chromeister-chromosome-comparison",
-                "tutorial_id": "hpc-for-lsgc",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/CHROMEISTER_chromosome_comparison.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/CHROMEISTER_chromosome_comparison.html",
-                "version": 1,
-                "wfid": "genome-annotation-hpc-for-lsgc",
-                "wfname": "chromeister-chromosome-comparison",
-                "workflow": "CHROMEISTER_chromosome_comparison.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a"
-                ],
-                "workflowhub_id": "1156"
-            },
-            {
-                "creators": [],
-                "description": "A workflow designed to compare two sequences using GECKO, extract repeats and perform multiple sequence alignment",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nQuery sequence\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference sequence\"]\n  2[label=\"Gecko\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  k6275abc1d74e45a7b8ab3c88426cc488[color=lightseagreen,label=\"Output\\nGecko on input dataset(s): CSV\"]\n  2 -> k6275abc1d74e45a7b8ab3c88426cc488\n  3[label=\"Text reformatting\"]\n  2 -> 3 [label=\"alignments2\"]\n  4[label=\"ClustalW\"]\n  3 -> 4 [label=\"outfile\"]\n  kd63c1172a5914bf6b307052ca19e7098[color=lightseagreen,label=\"Output\\nClustalW on input dataset(s): clustal\"]\n  4 -> kd63c1172a5914bf6b307052ca19e7098\n  kd7758e3a522d44398c9a03f784284ebd[color=lightseagreen,label=\"Output\\nClustalW on input dataset(s): dnd\"]\n  4 -> kd7758e3a522d44398c9a03f784284ebd\n}",
-                "history": [
-                    {
-                        "hash": "ae7dbf55cc79f67b32661f650f26d5baad4779b3",
-                        "message": "added workflow for chromeister",
-                        "num": 2,
-                        "short_hash": "ae7dbf55c",
-                        "unix": "1612266607"
-                    },
-                    {
-                        "hash": "42c257d5c78780b24fb384627c26488a90eeda4f",
-                        "message": "changed topic to genome-annotation",
-                        "num": 1,
-                        "short_hash": "42c257d5c",
-                        "unix": "1612264525"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Query sequence"
-                            }
-                        ],
-                        "label": "Query sequence",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 473.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 481,
-                            "right": 681,
-                            "top": 391,
-                            "width": 200,
-                            "x": 481,
-                            "y": 391
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "63490a28-7edf-4e4f-8697-5cbf621b0768",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "f1c8c4bf-126f-4c4b-8e5a-512cd0d270cd"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Reference sequence"
-                            }
-                        ],
-                        "label": "Reference sequence",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 598.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 482,
-                            "right": 682,
-                            "top": 516,
-                            "width": 200,
-                            "x": 482,
-                            "y": 516
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f49e63f9-977e-4a1f-bf43-9a50cfa14ee3",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "0867afff-2445-4a26-b21c-2476606adb88"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQuery sequence\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference sequence\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Gecko\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  6275abc1-d74e-45a7-b8ab-3c88426cc488[\"Output\\nGecko on input dataset(s): CSV\"];\n  2 --> 6275abc1-d74e-45a7-b8ab-3c88426cc488;\n  style 6275abc1-d74e-45a7-b8ab-3c88426cc488 stroke:#2c3143,stroke-width:4px;\n  3[\"Text reformatting\"];\n  2 -->|alignments2| 3;\n  4[\"ClustalW\"];\n  3 -->|outfile| 4;\n  d63c1172-a591-4bf6-b307-052ca19e7098[\"Output\\nClustalW on input dataset(s): clustal\"];\n  4 --> d63c1172-a591-4bf6-b307-052ca19e7098;\n  style d63c1172-a591-4bf6-b307-052ca19e7098 stroke:#2c3143,stroke-width:4px;\n  d7758e3a-522d-4439-8c9a-03f784284ebd[\"Output\\nClustalW on input dataset(s): dnd\"];\n  4 --> d7758e3a-522d-4439-8c9a-03f784284ebd;\n  style d7758e3a-522d-4439-8c9a-03f784284ebd stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "GECKO pairwise comparison",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Query sequence"
-                            }
-                        ],
-                        "label": "Query sequence",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 473.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 481,
-                            "right": 681,
-                            "top": 391,
-                            "width": 200,
-                            "x": 481,
-                            "y": 391
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "63490a28-7edf-4e4f-8697-5cbf621b0768",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "f1c8c4bf-126f-4c4b-8e5a-512cd0d270cd"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Reference sequence"
-                            }
-                        ],
-                        "label": "Reference sequence",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 598.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 482,
-                            "right": 682,
-                            "top": 516,
-                            "width": 200,
-                            "x": 482,
-                            "y": 516
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f49e63f9-977e-4a1f-bf43-9a50cfa14ee3",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "0867afff-2445-4a26-b21c-2476606adb88"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2",
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "db": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "query": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Gecko",
-                        "outputs": [
-                            {
-                                "name": "csv_output1",
-                                "type": "csv"
-                            },
-                            {
-                                "name": "alignments2",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 709.8000030517578,
-                            "height": 194.8000030517578,
-                            "left": 841,
-                            "right": 1041,
-                            "top": 515,
-                            "width": 200,
-                            "x": 841,
-                            "y": 515
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "5efbd15675ca",
-                            "name": "gecko",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"db\": {\"__class__\": \"ConnectedValue\"}, \"kmer\": \"16\", \"minlen\": \"50\", \"options\": {\"selection_mode\": \"alignments\", \"__current_case__\": 0}, \"query\": {\"__class__\": \"ConnectedValue\"}, \"similarity\": \"60\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2",
-                        "type": "tool",
-                        "uuid": "217b825b-dfa8-4443-95cb-ea55dd499397",
-                        "workflow_outputs": [
-                            {
-                                "label": "Gecko on input dataset(s): CSV",
-                                "output_name": "csv_output1",
-                                "uuid": "6275abc1-d74e-45a7-b8ab-3c88426cc488"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "alignments2",
-                                "uuid": "643f73a5-9648-4b78-8b39-4643a0f4438a"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "infile": {
-                                "id": 2,
-                                "output_name": "alignments2"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Text reformatting",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 740.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": 1162,
-                            "right": 1362,
-                            "top": 627,
-                            "width": 200,
-                            "x": 1162,
-                            "y": 627
-                        },
-                        "post_job_actions": {
-                            "ChangeDatatypeActionoutfile": {
-                                "action_arguments": {
-                                    "newtype": "fasta"
-                                },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "outfile"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"code\": \"BEGIN{FS=\\\" \\\"} /@\\\\(196[0-9][0-9]/ { printf(\\\">sequence%s%s\\\\n\\\", $(NF-1), $NF); getline; while(substr($0,1,1) != \\\">\\\"){ if(substr($0,1,1) ==\\\"Y\\\"){ print $2; } getline; } } \", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.2",
-                        "type": "tool",
-                        "uuid": "ac13faf0-b6dc-48fa-b5b4-31fec9a4733f",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "789a050e-0ab3-4296-b64d-9b7ad67af768"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "input": {
-                                "id": 3,
-                                "output_name": "outfile"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "ClustalW",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "clustal"
-                            },
-                            {
-                                "name": "dnd",
-                                "type": "nhx"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 864.8000030517578,
-                            "height": 184.8000030517578,
-                            "left": 1536,
-                            "right": 1736,
-                            "top": 680,
-                            "width": 200,
-                            "x": 1536,
-                            "y": 680
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "d6694932c5e0",
-                            "name": "clustalw",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"dnarna\": \"DNA\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"out_order\": \"ALIGNED\", \"outcontrol\": {\"outform\": \"clustal\", \"__current_case__\": 2, \"out_seqnos\": \"false\"}, \"range\": {\"mode\": \"complete\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1",
-                        "type": "tool",
-                        "uuid": "b95c1c44-a967-47fd-a85c-3a3121163486",
-                        "workflow_outputs": [
-                            {
-                                "label": "ClustalW on input dataset(s): clustal",
-                                "output_name": "output",
-                                "uuid": "d63c1172-a591-4bf6-b307-052ca19e7098"
-                            },
-                            {
-                                "label": "ClustalW on input dataset(s): dnd",
-                                "output_name": "dnd",
-                                "uuid": "d7758e3a-522d-4439-8c9a-03f784284ebd"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "genome-annotation/hpc-for-lsgc",
-                "path": "topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/GECKO_pairwise_comparison.ga",
-                "tags": [
-                    "genome-annotation"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "GECKO pairwise comparison",
-                "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-hpc-for-lsgc/versions/gecko-pairwise-comparison",
-                "tutorial_id": "hpc-for-lsgc",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/GECKO_pairwise_comparison.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/GECKO_pairwise_comparison.html",
-                "version": 1,
-                "wfid": "genome-annotation-hpc-for-lsgc",
-                "wfname": "gecko-pairwise-comparison",
-                "workflow": "GECKO_pairwise_comparison.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2"
-                ],
-                "workflowhub_id": "1160"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.4485547"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "antismash",
-                    "owner": "bgruening",
-                    "revisions": "bc88856eddab",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "chemfp",
-                    "owner": "bgruening",
-                    "revisions": "73de2fe4bf92",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "natural_product_likeness",
-                    "owner": "bgruening",
-                    "revisions": "6052dd3fa475",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openbabel_remduplicates",
-                    "owner": "bgruening",
-                    "revisions": "b2569e22b40c",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "qed",
-                    "owner": "bgruening",
-                    "revisions": "52a8d34dd08f",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "simsearch",
-                    "owner": "bgruening",
-                    "revisions": "0892f7ced10c",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cpt_gbk_to_gff",
-                    "owner": "cpt",
-                    "revisions": "a921d6148d88",
-                    "tool_panel_section_label": "Convert Formats",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bp_genbank2gff3",
-                    "owner": "iuc",
-                    "revisions": "11c3eb512633",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 },
                 {
-                    "name": "ncbi_acc_download",
-                    "owner": "iuc",
-                    "revisions": "e063168e0a81",
-                    "tool_panel_section_label": "Get Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "time_estimation": "30m",
+        "title": "Understanding Galaxy history system",
+        "tools": [],
+        "topic_name": "galaxy-interface",
+        "topic_name_human": "Using Galaxy and Managing your Data",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "history",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/history/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/history/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/history/tutorial.json"
+        },
+        "version": 10,
+        "video": false,
+        "video_versions": 2,
+        "video_view": 0,
+        "visit_duration": 161,
+        "visitors": 4031,
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
                 {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "90981f86000f",
-                    "tool_panel_section_label": "Collection Operations",
+                    "name": "graphicsmagick_image_convert",
+                    "owner": "bgruening",
+                    "revisions": "5376a7767fb3",
+                    "tool_panel_section_label": "Convert Formats",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: antismash\n  owner: bgruening\n  revisions: bc88856eddab\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chemfp\n  owner: bgruening\n  revisions: 73de2fe4bf92\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: natural_product_likeness\n  owner: bgruening\n  revisions: 6052dd3fa475\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_remduplicates\n  owner: bgruening\n  revisions: b2569e22b40c\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qed\n  owner: bgruening\n  revisions: 52a8d34dd08f\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: simsearch\n  owner: bgruening\n  revisions: '0892f7ced10c'\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cpt_gbk_to_gff\n  owner: cpt\n  revisions: a921d6148d88\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bp_genbank2gff3\n  owner: iuc\n  revisions: 11c3eb512633\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_acc_download\n  owner: iuc\n  revisions: e063168e0a81\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: graphicsmagick_image_convert\n  owner: bgruening\n  revisions: 5376a7767fb3\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-posters/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "ElectronicBlueberry"
+            ],
+            "editing": [
+                "hexylena"
+            ]
+        },
         "contributors": [
             {
                 "affiliations": [
                     "uni-freiburg",
                     "elixir-europe"
                 ],
-                "email": "zierep@informatik.uni-freiburg.de",
-                "id": "paulzierep",
-                "joined": "2023-02",
-                "name": "Paul Zierep",
-                "orcid": "0000-0003-2982-388X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json"
+                "elixir_node": "de",
+                "id": "ElectronicBlueberry",
+                "joined": "2023-04",
+                "name": "Laila Los",
+                "orcid": "0000-0002-2362-9720",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ElectronicBlueberry/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/ElectronicBlueberry.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/genome-annotation/tutorials/secondary-metabolite-discovery",
-        "draft": true,
-        "edam_operation": [
-            "Gene prediction",
-            "Service invocation",
-            "Data handling",
-            "Differential gene expression analysis",
-            "Sequence clustering"
-        ],
+        "dir": "topics/galaxy-interface/tutorials/workflow-posters",
+        "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu"
@@ -96594,50 +98363,49 @@
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "genome-annotation/secondary-metabolite-discovery",
-        "inexact_supported_servers": [],
+        "id": "galaxy-interface/workflow-posters",
+        "inexact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.no"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Gene cluster prediction that can be performed for any assembly or genome of microorganisms (procaryotes and fungi).",
-            "Bridging of gene annotation and cheminformatics.",
-            "Usage of custom script to bridge workflow steps."
+            "Print ready screenshots",
+            "Basic image compression"
         ],
         "layout": "tutorial_hands_on",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-02-21",
+        "mod_date": "2024-02-05",
         "objectives": [
-            "Gene cluster prediction using antiSMAHS.",
-            "Extraction of gene cluster products using a custom script.",
-            "Query of the products in compound libraries using cheminformatic tools."
+            "Create a high resolution image of your Workflow, ready for a poster",
+            "Learn how to utilize external tools to make high resolution images of your Workflow",
+            "Learn how to compress high resolution Workflow images to share them in the web"
         ],
-        "pageviews": 233,
-        "pub_date": "2024-02-21",
+        "pageviews": 91,
+        "pub_date": "2024-02-05",
         "questions": [
-            "How to discover secondary metabolites produced by microorganisms ?",
-            "How to identify the discovered secondary metabolites in compound libraries ?",
-            "How to bridge workflow steps using custom scripts ?"
+            "How can I print or screenshot my Workflow in high resolution for a poster or presentation?",
+            "How can I share high detail images of my Workflows?"
         ],
-        "short_id": "T00420",
+        "requirements": [
+            {
+                "link": "https://www.mozilla.org/en-US/firefox/new/",
+                "title": "The Firefox Browser (this will not work in Chrome)",
+                "type": "external"
+            }
+        ],
+        "short_id": "T00405",
         "short_tools": [
-            "ctb_silicos_qed",
-            "interactive_tool_jupyter_notebook",
-            "tp_awk_tool",
-            "ctb_np-likeness-calculator",
-            "antismash",
-            "ctb_simsearch",
-            "edu.tamu.cpt.gff3.customGbkToGff",
-            "ncbi_acc_download",
-            "Remove beginning1",
-            "bp_genbank2gff3",
-            "collapse_dataset",
-            "openbabel_remDuplicates",
-            "ctb_chemfp_mol2fps"
+            "graphicsmagick_image_convert"
         ],
         "slides": false,
         "slides_recordings": false,
+        "subtopic": "workflows",
         "supported_servers": {
             "exact": [
                 {
@@ -96646,427 +98414,199 @@
                     "usegalaxy": true
                 }
             ],
-            "inexact": []
+            "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                }
+            ]
         },
         "symlink": null,
         "tags": [
-            "work-in-progress"
+            "workflows"
         ],
-        "time_estimation": "3H",
-        "title": "Secondary metabolite discovery",
+        "time_estimation": "30M",
+        "title": "Creating high resolution images of Galaxy Workflows",
         "tools": [
-            "Remove beginning1",
-            "interactive_tool_jupyter_notebook",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/6.1.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/1.5",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/natural_product_likeness/ctb_np-likeness-calculator/2.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_remduplicates/openbabel_remDuplicates/3.1.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/qed/ctb_silicos_qed/2021.03.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/simsearch/ctb_simsearch/0.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/cpt/cpt_gbk_to_gff/edu.tamu.cpt.gff3.customGbkToGff/20.1.0.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bp_genbank2gff3/bp_genbank2gff3/1.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_convert/graphicsmagick_image_convert/1.3.40+galaxy0"
         ],
-        "topic_name": "genome-annotation",
-        "topic_name_human": "Genome Annotation",
+        "topic_name": "galaxy-interface",
+        "topic_name_human": "Using Galaxy and Managing your Data",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "secondary-metabolite-discovery",
+        "tutorial_name": "workflow-posters",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-posters/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-posters/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/workflow-posters/tutorial.json"
         },
         "version": 1,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 51,
-        "visitors": 179,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "",
-                "features": {
-                    "comments": false,
-                    "parameters": true,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nQuery Genomes\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nJupyter Notebook Genbank2Features\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTarget Molecules Natural Compound Library\"]\n  3[label=\"NCBI Accession Download\"]\n  0 -> 3 [label=\"output\"]\n  kfaecdec3711d43babb9138a4b4b3932d[color=lightseagreen,label=\"Output\\nNCBI Accession Download on input dataset(s): Log\"]\n  3 -> kfaecdec3711d43babb9138a4b4b3932d\n  kc8857c6fec994d298c98be7a63a9f029[color=lightseagreen,label=\"Output\\nNCBI Accession Download on input dataset(s): Downloaded Files\"]\n  3 -> kc8857c6fec994d298c98be7a63a9f029\n  4[label=\"Molecule to fingerprint\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Antismash\"]\n  3 -> 5 [label=\"output\"]\n  kcc813ad7f4234cb8ba798201abab206a[color=lightseagreen,label=\"Output\\nAntismash on input dataset(s): HTML report\"]\n  5 -> kcc813ad7f4234cb8ba798201abab206a\n  6[label=\"Collapse clusters in one Genbank entry\"]\n  5 -> 6 [label=\"genbank\"]\n  7[label=\"Extract SMILES qualifiers\"]\n  1 -> 7 [label=\"output\"]\n  6 -> 7 [label=\"output\"]\n  8[label=\"Convert table to smi format\"]\n  7 -> 8 [label=\"output_collection\"]\n  9[label=\"Remove beginning\"]\n  8 -> 9 [label=\"outfile\"]\n  10[label=\"Remove duplicated molecules\"]\n  9 -> 10 [label=\"out_file1\"]\n  11[label=\"Molecule to fingerprint\"]\n  10 -> 11 [label=\"outfile\"]\n  12[label=\"Natural Product\"]\n  10 -> 12 [label=\"outfile\"]\n  13[label=\"Drug-likeness\"]\n  10 -> 13 [label=\"outfile\"]\n  14[label=\"Similarity Search\"]\n  11 -> 14 [label=\"outfile\"]\n  4 -> 14 [label=\"outfile\"]\n}",
-                "history": [
-                    {
-                        "hash": "af81c1a8eee9601fc595b636e052099a41c98493",
-                        "message": "init",
-                        "num": 1,
-                        "short_hash": "af81c1a8e",
-                        "unix": "1707812500"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Query Genomes"
-                            }
-                        ],
-                        "label": "Query Genomes",
-                        "name": "Input parameter",
-                        "outputs": [],
-                        "position": {
-                            "left": 0.0,
-                            "top": 138.68778864733008
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": \"AL645882.2\", \"parameter_type\": \"text\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "34c92bcf-3ff2-4364-8dd8-0320ea449c09",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Jupyter Notebook Genbank2Features"
-                            }
-                        ],
-                        "label": "Jupyter Notebook Genbank2Features",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 1000.13886850544,
-                            "top": 967.9040340744108
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "5abb2d68-5c14-43af-9878-bf2b51bda3c5",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Target Molecules (Natural Compound Library)"
-                            }
-                        ],
-                        "label": "Target Molecules (Natural Compound Library)",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 999.7029249019243,
-                            "top": 1102.574230607614
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "41f458be-660b-40f7-abef-c57489b3099c",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nQuery Genomes\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nJupyter Notebook Genbank2Features\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nTarget Molecules Natural Compound Library\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"NCBI Accession Download\"];\n  0 -->|output| 3;\n  faecdec3-711d-43ba-bb91-38a4b4b3932d[\"Output\\nNCBI Accession Download on input dataset(s): Log\"];\n  3 --> faecdec3-711d-43ba-bb91-38a4b4b3932d;\n  style faecdec3-711d-43ba-bb91-38a4b4b3932d stroke:#2c3143,stroke-width:4px;\n  c8857c6f-ec99-4d29-8c98-be7a63a9f029[\"Output\\nNCBI Accession Download on input dataset(s): Downloaded Files\"];\n  3 --> c8857c6f-ec99-4d29-8c98-be7a63a9f029;\n  style c8857c6f-ec99-4d29-8c98-be7a63a9f029 stroke:#2c3143,stroke-width:4px;\n  4[\"Molecule to fingerprint\"];\n  2 -->|output| 4;\n  5[\"Antismash\"];\n  3 -->|output| 5;\n  cc813ad7-f423-4cb8-ba79-8201abab206a[\"Output\\nAntismash on input dataset(s): HTML report\"];\n  5 --> cc813ad7-f423-4cb8-ba79-8201abab206a;\n  style cc813ad7-f423-4cb8-ba79-8201abab206a stroke:#2c3143,stroke-width:4px;\n  6[\"Collapse clusters in one Genbank entry\"];\n  5 -->|genbank| 6;\n  7[\"Extract SMILES qualifiers\"];\n  1 -->|output| 7;\n  6 -->|output| 7;\n  8[\"Convert table to smi format\"];\n  7 -->|output_collection| 8;\n  9[\"Remove beginning\"];\n  8 -->|outfile| 9;\n  10[\"Remove duplicated molecules\"];\n  9 -->|out_file1| 10;\n  11[\"Molecule to fingerprint\"];\n  10 -->|outfile| 11;\n  12[\"Natural Product\"];\n  10 -->|outfile| 12;\n  13[\"Drug-likeness\"];\n  10 -->|outfile| 13;\n  14[\"Similarity Search\"];\n  11 -->|outfile| 14;\n  4 -->|outfile| 14;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Gene Cluster Product Similarity Search ",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "query_source|accession_list": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "NCBI Accession Download",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "input"
-                            },
-                            {
-                                "name": "error_log",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 295.1263437181945,
-                            "top": 125.66098683332416
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "e063168e0a81",
-                            "name": "ncbi_acc_download",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"ignore_failed\": \"0\", \"molecule\": {\"select\": \"nucleotide\", \"__current_case__\": 0, \"format\": \"fasta\"}, \"query_source\": {\"select\": \"accession_list\", \"__current_case__\": 1, \"accession_list\": {\"__class__\": \"ConnectedValue\"}}, \"range\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.2.8+galaxy0",
-                        "type": "tool",
-                        "uuid": "5586d5e9-ea6f-4e01-8e41-c3fe790535a3",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "NCBI Accession Download on input dataset(s): Log",
-                                "output_name": "error_log",
-                                "uuid": "faecdec3-711d-43ba-bb91-38a4b4b3932d"
-                            },
-                            {
-                                "label": "NCBI Accession Download on input dataset(s): Downloaded Files",
-                                "output_name": "output",
-                                "uuid": "c8857c6f-ec99-4d29-8c98-be7a63a9f029"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/6.1.1+galaxy1",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "infile": {
-                                "id": 3,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Antismash",
-                                "name": "genefinding_gff3"
-                            },
-                            {
-                                "description": "runtime parameter for tool Antismash",
-                                "name": "sideload"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Antismash",
-                        "outputs": [
-                            {
-                                "name": "genecluster_tabular",
-                                "type": "input"
-                            },
-                            {
-                                "name": "genbank",
-                                "type": "input"
-                            },
-                            {
-                                "name": "embl",
-                                "type": "input"
-                            },
-                            {
-                                "name": "archive",
-                                "type": "input"
-                            },
-                            {
-                                "name": "html",
-                                "type": "html"
-                            },
-                            {
-                                "name": "log",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 639.6596780017987,
-                            "top": 0
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/6.1.1+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "bc88856eddab",
-                            "name": "antismash",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"advanced_options\": {\"minlength\": \"1000\", \"hmmdetection_strictness\": \"relaxed\", \"cb_nclusters\": \"10\", \"cb_min_homology_scale\": \"0.0\", \"rre_cutoff\": \"25.0\", \"rre_minlength\": \"50\"}, \"asf\": true, \"cb_general\": false, \"cb_knownclusters\": true, \"cb_subclusters\": true, \"cc_mibig\": false, \"clusterhmmer\": false, \"cond_taxon\": {\"taxon\": \"bacteria\", \"__current_case__\": 0, \"genefinding_tool\": \"prodigal\", \"tigrfam\": false}, \"fullhmmer\": false, \"genefinding_gff3\": {\"__class__\": \"RuntimeValue\"}, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"outputs\": [\"html\", \"all\", \"embl\", \"gb\", \"genecluster_tabular\", \"log\"], \"pfam2go\": true, \"rre\": true, \"sideload\": {\"file\": {\"__class__\": \"RuntimeValue\"}, \"format\": \"harmonize\"}, \"smcog_trees\": true, \"tta_threshold\": \"0.65\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "6.1.1+galaxy1",
-                        "type": "tool",
-                        "uuid": "0f476190-2ca9-4b60-b6af-9c6ac4e12d0b",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "log",
-                                "uuid": "26f7288b-d497-4680-af57-169bf7d8a22a"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "genbank",
-                                "uuid": "607063ee-4d4c-40d0-b355-cff12b9de2a9"
-                            },
-                            {
-                                "label": "Antismash on input dataset(s): HTML report",
-                                "output_name": "html",
-                                "uuid": "cc813ad7-f423-4cb8-ba79-8201abab206a"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "archive",
-                                "uuid": "a8a9e6d6-652d-44b5-ba4f-60aff9c9999f"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "embl",
-                                "uuid": "7c948135-1c3a-43eb-9a40-a5fe28334f58"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "genecluster_tabular",
-                                "uuid": "5bfc66a2-bec6-4818-9fa8-ad42b3b73dc8"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "input_list": {
-                                "id": 5,
-                                "output_name": "genbank"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Collapse clusters in one Genbank entry",
-                        "name": "Collapse Collection",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 963.0516444199695,
-                            "top": 145.633549188099
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "90981f86000f",
-                            "name": "collapse_collections",
-                            "owner": "nml",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"filename\": {\"add_name\": true, \"__current_case__\": 0, \"place_name\": \"above\"}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.1.0",
-                        "type": "tool",
-                        "uuid": "fe07e889-e6a5-48bc-9f61-1676b3cc6641",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "dc73d9e2-5338-4fa7-90c0-6b03b4181457"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "genome-annotation/secondary-metabolite-discovery",
-                "path": "topics/genome-annotation/tutorials/secondary-metabolite-discovery/workflows/main_workflow.ga",
-                "tags": [
-                    "sempi3"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Gene Cluster Product Similarity Search ",
-                "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-secondary-metabolite-discovery/versions/main-workflow",
-                "tutorial_id": "secondary-metabolite-discovery",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/secondary-metabolite-discovery/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/secondary-metabolite-discovery/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "genome-annotation-secondary-metabolite-discovery",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "Remove beginning1",
-                    "interactive_tool_jupyter_notebook",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/6.1.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/1.5",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/natural_product_likeness/ctb_np-likeness-calculator/2.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_remduplicates/openbabel_remDuplicates/3.1.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/qed/ctb_silicos_qed/2021.03.4+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/simsearch/ctb_simsearch/0.2",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
-                ],
-                "workflowhub_id": "1145"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/records/10652998"
+        "visit_duration": 157,
+        "visitors": 75
     },
     {
-        "abbreviations": {
-            "OGS": "Official Gene Set"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": [
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/galaxy-intro-jupyter/tutorial.json",
+        "contributors": [
+            {
+                "email": "delphine.lariviere@galaxy.org",
+                "id": "delphine-l",
+                "joined": "2017-09",
+                "name": "Delphine Lariviere",
+                "orcid": "0000-0001-6421-3484",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
+            }
+        ],
+        "dir": "topics/galaxy-interface/tutorials/galaxy-intro-jupyter",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "galaxy-interface/galaxy-intro-jupyter",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Start Jupyter from the Visualize tab or from a dataset",
+            "Install Libraries with pip or Conda",
+            "Use get() to import datasets from your history to the notebook",
+            "Use put() to export datasets from the notebook to your history",
+            "Save your notebook into your history"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-03-05",
+        "objectives": [
+            "Learn about the Jupyter Interactive Environment"
+        ],
+        "pageviews": 2242,
+        "pub_date": "2018-07-02",
+        "questions": [
+            "How to use a Jupyter Notebook in Galaxy"
+        ],
+        "redirect_from": [
+            "/topics/galaxy-ui/tutorials/galaxy-intro-jupyter/tutorial",
+            "/short/galaxy-interface/galaxy-intro-jupyter",
+            "/short/T00148"
+        ],
+        "short_id": "T00148",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "analyse",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
                 {
-                    "name": "apollo_create_account",
-                    "owner": "gga",
-                    "revisions": "e80d29fd2a33",
-                    "tool_panel_section_label": "Apollo",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
                 },
                 {
-                    "name": "apollo_create_or_update",
-                    "owner": "gga",
-                    "revisions": "4abaab60f9e1",
-                    "tool_panel_section_label": "Apollo",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 },
                 {
-                    "name": "apollo_iframe",
-                    "owner": "gga",
-                    "revisions": "f4e3f9480307",
-                    "tool_panel_section_label": "Apollo",
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "time_estimation": "30m",
+        "title": "Use Jupyter notebooks in Galaxy",
+        "tools": [],
+        "topic_name": "galaxy-interface",
+        "topic_name_human": "Using Galaxy and Managing your Data",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "galaxy-intro-jupyter",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/galaxy-intro-jupyter/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/galaxy-intro-jupyter/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/galaxy-intro-jupyter/tutorial.json"
+        },
+        "version": 7,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 131,
+        "visitors": 1663,
+        "zenodo_link": "https://zenodo.org/record/1185122"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "prokka",
+                    "owner": "crs4",
+                    "revisions": "bf68eb663bc3",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "apollo_list_organism",
-                    "owner": "gga",
-                    "revisions": "2c749ed310da",
-                    "tool_panel_section_label": "Apollo",
+                    "name": "prokka",
+                    "owner": "crs4",
+                    "revisions": "111884f0d912",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
@@ -97078,146 +98618,41 @@
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: apollo_create_account\n  owner: gga\n  revisions: e80d29fd2a33\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: apollo_create_or_update\n  owner: gga\n  revisions: 4abaab60f9e1\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: apollo_iframe\n  owner: gga\n  revisions: f4e3f9480307\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: apollo_list_organism\n  owner: gga\n  revisions: 2c749ed310da\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "abretaud",
-                "hexylena",
-                "nathandunn",
-                "mboudet"
-            ],
-            "funding": [
-                "gallantries",
-                "eurosciencegateway"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: prokka\n  owner: crs4\n  revisions: bf68eb663bc3\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: prokka\n  owner: crs4\n  revisions: 111884f0d912\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "gallantries",
-                    "eurosciencegateway",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
-                "fediverse_flavor": "mastodon",
-                "id": "abretaud",
-                "joined": "2017-09",
-                "location": {
-                    "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
-                },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
+                "id": "annasyme",
                 "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "email": "nathandunn@lbl.gov",
-                "id": "nathandunn",
-                "joined": "2019-07",
-                "name": "Nathan Dunn",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nathandunn/",
-                "twitter": "precogincog",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nathandunn.json"
+                "name": "Anna Syme",
+                "orcid": "0000-0002-9906-0673",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
             },
             {
                 "affiliations": [
                     "elixir-europe"
                 ],
-                "elixir_node": "fr",
-                "email": "mateo.boudet@inrae.fr",
-                "id": "mboudet",
-                "joined": "2021-05",
-                "name": "Mateo Boudet",
-                "orcid": "0000-0002-7028-7620",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mboudet/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mboudet.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+                "elixir_node": "au",
+                "id": "tseemann",
+                "joined": "2018-06",
+                "name": "Torsten Seemann",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tseemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tseemann.json"
             },
             {
-                "avatar": "/training-material/assets/images/eurosciencegateway.png",
-                "funder": true,
-                "funding_id": "101057388",
-                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "eurosciencegateway",
-                "joined": "2023-10",
-                "members": [
-                    "abretaud",
-                    "anuprulez",
-                    "bgruening",
-                    "erxleben",
-                    "pauldg",
-                    "rlibouba"
-                ],
-                "name": "EuroScienceGateway",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
+                "elixir_node": "au",
+                "email": "simon.gladman@unimelb.edu.au",
+                "id": "slugger70",
+                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
+                "joined": "2017-09",
+                "name": "Simon Gladman",
+                "orcid": "0000-0002-6100-4385",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
             }
         ],
-        "dir": "topics/genome-annotation/tutorials/apollo",
+        "dir": "topics/genome-annotation/tutorials/annotation-with-prokka",
         "edam_ontology": [
             "topic_0622",
             "topic_3301",
@@ -97225,7 +98660,10 @@
             "topic_0080"
         ],
         "edam_operation": [
-            "Genome visualisation"
+            "Genome visualisation",
+            "Gene prediction",
+            "Genome annotation",
+            "Coding region prediction"
         ],
         "edam_topic": [
             "Genomics",
@@ -97233,44 +98671,55 @@
             "Gene and protein families",
             "Sequence analysis"
         ],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "genome-annotation",
+                "tutorials": [
+                    "apollo"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "genome-annotation/apollo",
+        "id": "genome-annotation/annotation-with-prokka",
         "inexact_supported_servers": [
+            "Galaxy@AuBi",
+            "GalaxyTrakr",
+            "MISSISSIPPI",
+            "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.no"
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Apollo is the Google Docs of the genome annotation world, real-time collaborative genome annotation.",
-            "Apollo allows a group to view and manually refine predicted genome annotations",
-            "Use Apollo to edit annotations within your group.",
-            "Export manual annotations as GFF3."
+            "Prokka is a useful tool to annotate a bacterial genome.",
+            "JBrowse can be used to inspect the annotation of a genome."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
         "mod_date": "2024-08-08",
         "objectives": [
-            "Load a genome into Galaxy",
-            "View annotations in JBrowse",
-            "Learn how to load JBrowse data into Apollo",
-            "Learn how to manually refine genome annotations within Apollo",
-            "Export refined genome annotations"
+            "Load genome into Galaxy",
+            "Annotate genome with Prokka",
+            "View annotations in JBrowse"
         ],
-        "pageviews": 4949160,
-        "pub_date": "2021-06-04",
+        "pageviews": 5925124,
+        "pub_date": "2018-03-06",
         "questions": [
-            "How to visualize your genome after automated annotations have been performed?",
-            "How to manually annotate genome after automated annotations have been performed?",
-            "How to evaluate and visualize annotated genomic features?",
-            "How do I collaborate when doing genome annotation?"
+            "How can we annotate a bacterial genome?",
+            "How can we visualize annotated genomic features?"
         ],
         "recordings": [
             {
@@ -97279,36 +98728,17 @@
                 ],
                 "date": "2021-02-15",
                 "galaxy_version": "21.01",
-                "length": "1H",
+                "length": "20M",
                 "speakers": [
                     "abretaud"
                 ],
-                "youtube_id": "ywK1fhM-QFU"
-            }
-        ],
-        "requirements": [
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "upload-rules"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "genome-annotation",
-                "tutorials": [
-                    "annotation-with-prokka"
-                ],
-                "type": "internal"
+                "youtube_id": "B8pIQZPf21Y"
             }
         ],
-        "short_id": "T00169",
+        "short_id": "T00168",
         "short_tools": [
             "jbrowse",
-            "create_or_update",
-            "list_organism",
-            "iframe",
-            "create_account"
+            "prokka"
         ],
         "slides": true,
         "slides_recordings": [
@@ -97318,31 +98748,67 @@
                 ],
                 "date": "2021-02-15",
                 "galaxy_version": "21.01",
-                "length": "5M",
+                "length": "3M",
                 "speakers": [
                     "awspolly"
                 ],
-                "youtube_id": "ailUycRVHtE"
+                "youtube_id": "eqHy-Cc7k4Q"
             }
         ],
         "subtopic": "prokaryote",
         "supported_servers": {
-            "exact": [],
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
             "inexact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ]
         },
@@ -97351,16 +98817,13 @@
             "gmod",
             "prokaryote",
             "microgalaxy",
-            "jbrowse1",
-            "apollo2"
+            "jbrowse1"
         ],
-        "time_estimation": "3h",
-        "title": "Refining Genome Annotations with Apollo (prokaryotes)",
+        "time_estimation": "1h",
+        "title": "Genome annotation with Prokka",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_account/create_account/3.1",
-            "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
-            "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
-            "toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1",
+            "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
+            "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1"
         ],
         "topic_name": "genome-annotation",
@@ -97371,952 +98834,432 @@
             "tutorial": [],
             "video": true
         },
-        "tutorial_name": "apollo",
+        "tutorial_name": "annotation-with-prokka",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.json"
         },
-        "version": 20,
+        "version": 25,
         "video": true,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 297,
-        "visitors": 1836817,
+        "visit_duration": 259,
+        "visitors": 2149523,
         "workflows": [
             {
-                "creators": [],
-                "description": "Refining Genome Annotations with Apollo",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0001-6046-610X",
+                        "name": "Torsten Seemann"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-6100-4385",
+                        "name": "Simon Gladman"
+                    }
+                ],
+                "description": "Genome annotation with Prokka",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager.bw\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam\"]\n  4[label=\"Register Account\"]\n  5[label=\"List Organisms\"]\n  6[label=\"JBrowse\"]\n  0 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"Create or Update Organism\"]\n  6 -> 7 [label=\"output\"]\n  8[label=\"Annotate\"]\n  7 -> 8 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontigs.fasta\"]\n  1[label=\"Prokka\"]\n  0 -> 1 [label=\"output\"]\n  ka336c364e69e47ebace6a7fe46d285fe[color=lightseagreen,label=\"Output\\ngff_output\"]\n  1 -> ka336c364e69e47ebace6a7fe46d285fe\n  2[label=\"JBrowse\"]\n  1 -> 2 [label=\"out_fna\"]\n  1 -> 2 [label=\"out_gff\"]\n}",
                 "history": [
                     {
-                        "hash": "6bc77b7441375cd57ea1d73e9fe2f80ef550891a",
-                        "message": "wf annotation",
-                        "num": 3,
-                        "short_hash": "6bc77b744",
-                        "unix": "1622101979"
+                        "hash": "70a555355ed2ebc563a4388cd1da50f7f1a5952f",
+                        "message": "Update topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
+                        "num": 10,
+                        "short_hash": "70a555355",
+                        "unix": "1715074163"
                     },
                     {
-                        "hash": "9ced3a95cd725623c7c1f2664b0174a14cd59337",
-                        "message": "update workflow",
-                        "num": 2,
-                        "short_hash": "9ced3a95c",
-                        "unix": "1622043687"
+                        "hash": "466b451a082b7d2d5e60777a45289874bbbde721",
+                        "message": "Add creators and license to workflow",
+                        "num": 9,
+                        "short_hash": "466b451a0",
+                        "unix": "1714990318"
                     },
                     {
-                        "hash": "32f41f6fe47606c12d4574551233e4a2583df189",
-                        "message": "rewrite bits v2",
-                        "num": 1,
-                        "short_hash": "32f41f6fe",
-                        "unix": "1571055596"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "https://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1"
-                            }
-                        ],
-                        "label": "https://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 354.8999938964844,
-                            "height": 143.39999389648438,
-                            "left": 488,
-                            "right": 688,
-                            "top": 211.5,
-                            "width": 200,
-                            "x": 488,
-                            "y": 211.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "fa88b9bb-b87e-457b-a836-a8f1b25e520b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "82c708ee-87a4-45a2-abf0-911309e218fd"
-                            }
-                        ]
+                        "hash": "499e257dee992b4645adf4c79844b8cc89e68c24",
+                        "message": "update prokka workflow",
+                        "num": 8,
+                        "short_hash": "499e257de",
+                        "unix": "1714456964"
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "https://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1"
-                            }
-                        ],
-                        "label": "https://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 527.8999938964844,
-                            "height": 143.39999389648438,
-                            "left": 510,
-                            "right": 710,
-                            "top": 384.5,
-                            "width": 200,
-                            "x": 510,
-                            "y": 384.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "1afd430b-6250-4eb2-8cf2-a83adf022e4b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "cbbb4914-0c3d-4857-8c3a-f43b3f0c39f9"
-                            }
-                        ]
+                        "hash": "56413bab75ab75be269668d70e3929e01bbaa5fb",
+                        "message": "Add workflow test.",
+                        "num": 7,
+                        "short_hash": "56413bab7",
+                        "unix": "1603310943"
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "https://zenodo.org/record/3270822/files/forager.bw"
-                            }
-                        ],
-                        "label": "https://zenodo.org/record/3270822/files/forager.bw",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 659.1000061035156,
-                            "height": 102.60000610351562,
-                            "left": 493,
-                            "right": 693,
-                            "top": 556.5,
-                            "width": 200,
-                            "x": 493,
-                            "y": 556.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "091ca713-0096-419c-8cb7-7e83a41aab37",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "f4c19cc0-5099-4514-af29-52a3933b28f9"
-                            }
-                        ]
+                        "hash": "a3829a12322232647926a394b1ecae3af17a858b",
+                        "message": "Update Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
+                        "num": 6,
+                        "short_hash": "a3829a123",
+                        "unix": "1580832292"
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "https://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam"
-                            }
-                        ],
-                        "label": "https://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 858.8999938964844,
-                            "height": 143.39999389648438,
-                            "left": 563,
-                            "right": 763,
-                            "top": 715.5,
-                            "width": 200,
-                            "x": 563,
-                            "y": 715.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "13d26450-8b30-42d4-9822-f697217818b1",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "464904cb-5608-4f5d-b282-a09be9d3dbbb"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager.bw\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Register Account\"];\n  5[\"List Organisms\"];\n  6[\"JBrowse\"];\n  0 -->|output| 6;\n  1 -->|output| 6;\n  3 -->|output| 6;\n  2 -->|output| 6;\n  7[\"Create or Update Organism\"];\n  6 -->|output| 7;\n  8[\"Annotate\"];\n  7 -->|output| 8;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Apollo Load Test",
-                "outputs": [
+                        "hash": "bab7ab72c6a4436a3ac3e6745b364696332399b5",
+                        "message": "prokka@1.14.5 jbrowse@1.16.5+galaxy7",
+                        "num": 5,
+                        "short_hash": "bab7ab72c",
+                        "unix": "1580433748"
+                    },
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "https://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1"
-                            }
-                        ],
-                        "label": "https://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 354.8999938964844,
-                            "height": 143.39999389648438,
-                            "left": 488,
-                            "right": 688,
-                            "top": 211.5,
-                            "width": 200,
-                            "x": 488,
-                            "y": 211.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "fa88b9bb-b87e-457b-a836-a8f1b25e520b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "82c708ee-87a4-45a2-abf0-911309e218fd"
-                            }
-                        ]
+                        "hash": "c69f09dd0cb211d5621af293fe400892e343f78e",
+                        "message": "Adding tag",
+                        "num": 4,
+                        "short_hash": "c69f09dd0",
+                        "unix": "1579796672"
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "https://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1"
-                            }
-                        ],
-                        "label": "https://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 527.8999938964844,
-                            "height": 143.39999389648438,
-                            "left": 510,
-                            "right": 710,
-                            "top": 384.5,
-                            "width": 200,
-                            "x": 510,
-                            "y": 384.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "1afd430b-6250-4eb2-8cf2-a83adf022e4b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "cbbb4914-0c3d-4857-8c3a-f43b3f0c39f9"
-                            }
-                        ]
+                        "hash": "920732bc2295d6120b075934b758290ad56f5759",
+                        "message": "Updated prokka workflow to newest tool versions",
+                        "num": 3,
+                        "short_hash": "920732bc2",
+                        "unix": "1579634888"
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "https://zenodo.org/record/3270822/files/forager.bw"
-                            }
-                        ],
-                        "label": "https://zenodo.org/record/3270822/files/forager.bw",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 659.1000061035156,
-                            "height": 102.60000610351562,
-                            "left": 493,
-                            "right": 693,
-                            "top": 556.5,
-                            "width": 200,
-                            "x": 493,
-                            "y": 556.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "091ca713-0096-419c-8cb7-7e83a41aab37",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "f4c19cc0-5099-4514-af29-52a3933b28f9"
-                            }
-                        ]
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 2,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
                     },
+                    {
+                        "hash": "b9a6072964bce056112a36326600e4c80bd133ec",
+                        "message": "move tutorials to new topic",
+                        "num": 1,
+                        "short_hash": "b9a607296",
+                        "unix": "1528898987"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "https://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam"
+                                "name": "contigs.fasta"
                             }
                         ],
-                        "label": "https://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam",
+                        "label": "contigs.fasta",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 858.8999938964844,
-                            "height": 143.39999389648438,
-                            "left": 563,
-                            "right": 763,
-                            "top": 715.5,
-                            "width": 200,
-                            "x": 563,
-                            "y": 715.5
+                            "left": 0,
+                            "top": 76.845458984375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "13d26450-8b30-42d4-9822-f697217818b1",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "464904cb-5608-4f5d-b282-a09be9d3dbbb"
-                            }
-                        ]
-                    },
+                        "uuid": "79e73b85-8d44-413f-83b7-c0e668ec963c",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ncontigs.fasta\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Prokka\"];\n  0 -->|output| 1;\n  a336c364-e69e-47eb-ace6-a7fe46d285fe[\"Output\\ngff_output\"];\n  1 --> a336c364-e69e-47eb-ace6-a7fe46d285fe;\n  style a336c364-e69e-47eb-ace6-a7fe46d285fe stroke:#2c3143,stroke-width:4px;\n  2[\"JBrowse\"];\n  1 -->|out_fna| 2;\n  1 -->|out_gff| 2;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Genome Annotation with Prokka ",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_account/create_account/3.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
                         "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "Register Account",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "txt"
+                        "id": 1,
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
                             }
-                        ],
-                        "position": {
-                            "bottom": 1038.6999969482422,
-                            "height": 82.19999694824219,
-                            "left": 644,
-                            "right": 844,
-                            "top": 956.5,
-                            "width": 200,
-                            "x": 644,
-                            "y": 956.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_account/create_account/3.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "e80d29fd2a33",
-                            "name": "apollo_create_account",
-                            "owner": "gga",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"first\": \"Nathan\", \"last\": \"Dunn\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1",
-                        "type": "tool",
-                        "uuid": "82f0b666-8743-4cdc-9682-feb10c35b0c6",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "dc1e2c2f-c566-48e0-95c7-327adb229fb5"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {},
                         "inputs": [],
                         "label": null,
-                        "name": "List Organisms",
+                        "name": "Prokka",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "json"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 1158.6999969482422,
-                            "height": 82.19999694824219,
-                            "left": 644,
-                            "right": 844,
-                            "top": 1076.5,
-                            "width": 200,
-                            "x": 644,
-                            "y": 1076.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2c749ed310da",
-                            "name": "apollo_list_organism",
-                            "owner": "gga",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"chromInfo\": \"\\\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
-                        "tool_version": "3.1",
-                        "type": "tool",
-                        "uuid": "3fc26308-b331-4286-863a-d31ac5b6fb03",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "d7cc17cb-e3e2-4adf-857c-8d3583e57fdd"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "reference_genome|genome": {
-                                "id": 0,
-                                "output_name": "output"
+                                "name": "out_gff",
+                                "type": "gff"
                             },
-                            "track_groups_0|data_tracks_0|data_format|annotation": {
-                                "id": 1,
-                                "output_name": "output"
+                            {
+                                "name": "out_gbk",
+                                "type": "txt"
                             },
-                            "track_groups_1|data_tracks_0|data_format|annotation": {
-                                "id": 3,
-                                "output_name": "output"
+                            {
+                                "name": "out_fna",
+                                "type": "fasta"
                             },
-                            "track_groups_1|data_tracks_1|data_format|annotation": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
                             {
-                                "description": "runtime parameter for tool JBrowse",
-                                "name": "reference_genome"
-                            }
-                        ],
-                        "label": null,
-                        "name": "JBrowse",
-                        "outputs": [
+                                "name": "out_faa",
+                                "type": "fasta"
+                            },
                             {
-                                "name": "output",
-                                "type": "html"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 650.2999877929688,
-                            "height": 306.79998779296875,
-                            "left": 821,
-                            "right": 1021,
-                            "top": 343.5,
-                            "width": 200,
-                            "x": 821,
-                            "y": 343.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "a6e57ff585c0",
-                            "name": "jbrowse",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"true\", \"track_groups\": [{\"__index__\": 0, \"category\": \"OGS 3.2\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_on\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 1, \"category\": \"Reads\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"auto_snp\": \"true\", \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 4, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"xyplot\": \"false\", \"var_band\": \"false\", \"scaling\": {\"scale_select\": \"auto_local\", \"__current_case__\": 0}, \"scale_select2\": \"linear\", \"MultiBigWig\": \"false\", \"jbcolor\": {\"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}, \"bicolor_pivot\": {\"bicolor_pivot_select\": \"zero\", \"__current_case__\": 0}}, \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16.11+galaxy1",
-                        "type": "tool",
-                        "uuid": "2e2723bf-9597-4c96-9980-33220e3b849a",
-                        "workflow_outputs": [
+                                "name": "out_ffn",
+                                "type": "fasta"
+                            },
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "9514c32e-2376-44ee-b368-beb25bf77ad7"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "jbrowse": {
-                                "id": 6,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
+                                "name": "out_sqn",
+                                "type": "asn1"
+                            },
                             {
-                                "description": "runtime parameter for tool Create or Update Organism",
-                                "name": "jbrowse"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Create or Update Organism",
-                        "outputs": [
+                                "name": "out_fsa",
+                                "type": "fasta"
+                            },
                             {
-                                "name": "output",
-                                "type": "json"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 506.1000061035156,
-                            "height": 113.60000610351562,
-                            "left": 1405,
-                            "right": 1605,
-                            "top": 392.5,
-                            "width": 200,
-                            "x": 1405,
-                            "y": 392.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
-                        "tool_shed_repository": {
-                            "changeset_revision": "4abaab60f9e1",
-                            "name": "apollo_create_or_update",
-                            "owner": "gga",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"genus\": \"Apis\", \"group\": null, \"jbrowse\": {\"__class__\": \"RuntimeValue\"}, \"no_reload_sequences\": \"false\", \"org_source\": {\"source_select\": \"direct\", \"__current_case__\": 1, \"org_raw\": \"Honeybee\"}, \"public\": \"true\", \"remove_old_directory\": \"true\", \"species\": \"Mellifera\", \"test_hack\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.2.5",
-                        "type": "tool",
-                        "uuid": "72c53f14-4e91-40c1-a4e9-325b6c2a3105",
-                        "workflow_outputs": [
+                                "name": "out_tbl",
+                                "type": "txt"
+                            },
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "10c77447-f92c-44b0-8a04-151eef670244"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "json_file": {
-                                "id": 7,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
+                                "name": "out_err",
+                                "type": "txt"
+                            },
                             {
-                                "description": "runtime parameter for tool Annotate",
-                                "name": "json_file"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Annotate",
-                        "outputs": [
+                                "name": "out_txt",
+                                "type": "txt"
+                            },
                             {
-                                "name": "output",
-                                "type": "html"
+                                "name": "out_log",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 502.6999969482422,
-                            "height": 93.19999694824219,
-                            "left": 1703,
-                            "right": 1903,
-                            "top": 409.5,
-                            "width": 200,
-                            "x": 1703,
-                            "y": 409.5
+                            "left": 254.117919921875,
+                            "top": 0.0
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
                         "tool_shed_repository": {
-                            "changeset_revision": "f4e3f9480307",
-                            "name": "apollo_iframe",
-                            "owner": "gga",
+                            "changeset_revision": "bf68eb663bc3",
+                            "name": "prokka",
+                            "owner": "crs4",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"json_file\": {\"__class__\": \"RuntimeValue\"}, \"tracklist\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.2.5",
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"__workflow_invocation_uuid__\": \"5dc31c9443c711eabead005056ba55fb\", \"centre\": \"V\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"compliant\": {\"compliant_select\": \"no\", \"__current_case__\": 0, \"addgenes\": false, \"mincontig\": \"200\"}, \"evalue\": \"1e-06\", \"fast\": false, \"genus\": \"Staphylococcus\", \"gffver\": \"3\", \"increment\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"kingdom\": {\"kingdom_select\": \"Bacteria\", \"__current_case__\": 1, \"gcode\": \"11\"}, \"locustag\": \"P\", \"metagenome\": false, \"norrna\": false, \"notrna\": false, \"outputs\": [\"gff\", \"gbk\", \"fna\", \"faa\", \"ffn\", \"sqn\", \"fsa\", \"tbl\", \"err\", \"txt\"], \"plasmid\": \"\", \"proteins\": null, \"rfam\": false, \"species\": \"aureus\", \"strain\": \"\", \"usegenus\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.14.5",
                         "type": "tool",
-                        "uuid": "2cfe94b1-f9cb-4df6-a3fd-b9356ea2423f",
+                        "uuid": "28efec53-71bb-4aaa-993d-03b78d493570",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "4eaf137c-b5fd-4cdd-9fa7-ed973e2302f3"
+                                "label": "gff_output",
+                                "output_name": "out_gff",
+                                "uuid": "a336c364-e69e-47eb-ace6-a7fe46d285fe"
                             }
                         ]
                     }
                 ],
-                "parent_id": "genome-annotation/apollo",
-                "path": "topics/genome-annotation/tutorials/apollo/workflows/main_workflow.ga",
+                "parent_id": "genome-annotation/annotation-with-prokka",
+                "path": "topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
                 "tags": [
-                    "genome-annotation"
+                    "genome-annotation",
+                    "GTN"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "Apollo Load Test",
+                "tests": true,
+                "title": "Genome Annotation with Prokka ",
                 "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-apollo/versions/main-workflow",
-                "tutorial_id": "apollo",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/apollo/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/apollo/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "genome-annotation-apollo",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-annotation-with-prokka/versions/galaxy-workflow-workflow-constructed-from-history--prokka-workflow-",
+                "tutorial_id": "annotation-with-prokka",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.html",
+                "version": 6,
+                "wfid": "genome-annotation-annotation-with-prokka",
+                "wfname": "galaxy-workflow-workflow-constructed-from-history--prokka-workflow-",
+                "workflow": "Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_account/create_account/3.1",
-                    "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
-                    "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
-                    "toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1",
+                    "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
                     "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1"
                 ],
-                "workflowhub_id": "1190"
+                "workflowhub_id": "1186"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/4889110"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.1156405"
     },
     {
-        "abbreviations": {
-            "LINEs": "Long Interspersed Nuclear Elements",
-            "SINEs": "Short Interspersed Nuclear Elements"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "repeat_masker",
+                    "name": "antismash",
                     "owner": "bgruening",
-                    "revisions": "ba6d2c32f797",
+                    "revisions": "bc88856eddab",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "repeatmodeler",
-                    "owner": "csbl",
-                    "revisions": "8661b2607b7e",
-                    "tool_panel_section_label": "Annotation",
+                    "name": "chemfp",
+                    "owner": "bgruening",
+                    "revisions": "73de2fe4bf92",
+                    "tool_panel_section_label": "ChemicalToolBox",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bedtools",
-                    "owner": "iuc",
-                    "revisions": "a1a923cd89e8",
-                    "tool_panel_section_label": "BED",
+                    "name": "natural_product_likeness",
+                    "owner": "bgruening",
+                    "revisions": "6052dd3fa475",
+                    "tool_panel_section_label": "ChemicalToolBox",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "red",
+                    "name": "openbabel_remduplicates",
+                    "owner": "bgruening",
+                    "revisions": "c5de6c19eb06",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "qed",
+                    "owner": "bgruening",
+                    "revisions": "52a8d34dd08f",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "simsearch",
+                    "owner": "bgruening",
+                    "revisions": "0892f7ced10c",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "cpt_gbk_to_gff",
+                    "owner": "cpt",
+                    "revisions": "a921d6148d88",
+                    "tool_panel_section_label": "Convert Formats",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bp_genbank2gff3",
                     "owner": "iuc",
-                    "revisions": "db57bc3b57af",
+                    "revisions": "11c3eb512633",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ncbi_acc_download",
+                    "owner": "iuc",
+                    "revisions": "e063168e0a81",
+                    "tool_panel_section_label": "Get Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "90981f86000f",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: repeat_masker\n  owner: bgruening\n  revisions: ba6d2c32f797\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: repeatmodeler\n  owner: csbl\n  revisions: 8661b2607b7e\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: a1a923cd89e8\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: red\n  owner: iuc\n  revisions: db57bc3b57af\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/repeatmasker/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "abretaud",
-                "alexcorm",
-                "lleroi",
-                "r1corre",
-                "stephanierobin",
-                "jkreplak"
-            ],
-            "funding": [
-                "gallantries",
-                "eurosciencegateway"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: antismash\n  owner: bgruening\n  revisions: bc88856eddab\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chemfp\n  owner: bgruening\n  revisions: 73de2fe4bf92\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: natural_product_likeness\n  owner: bgruening\n  revisions: 6052dd3fa475\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_remduplicates\n  owner: bgruening\n  revisions: c5de6c19eb06\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qed\n  owner: bgruening\n  revisions: 52a8d34dd08f\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: simsearch\n  owner: bgruening\n  revisions: '0892f7ced10c'\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cpt_gbk_to_gff\n  owner: cpt\n  revisions: a921d6148d88\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bp_genbank2gff3\n  owner: iuc\n  revisions: 11c3eb512633\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_acc_download\n  owner: iuc\n  revisions: e063168e0a81\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
-                    "gallantries",
-                    "eurosciencegateway",
+                    "uni-freiburg",
                     "elixir-europe"
                 ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
-                "fediverse_flavor": "mastodon",
-                "id": "abretaud",
-                "joined": "2017-09",
-                "location": {
-                    "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
-                },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
-            },
-            {
-                "email": "alexandre.cormier@ifremer.fr",
-                "id": "alexcorm",
-                "joined": "2021-11",
-                "name": "Alexandre Cormier",
-                "orcid": "0000-0002-7775-8413",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/",
-                "twitter": "allanssx",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/alexcorm.json"
-            },
-            {
-                "email": "laura.leroi@ifremer.fr",
-                "id": "lleroi",
-                "joined": "2021-11",
-                "name": "Laura Leroi",
-                "orcid": "0000-0003-3748-4179",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lleroi/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/lleroi.json"
-            },
-            {
-                "email": "erwan.corre@sb-roscoff.fr",
-                "id": "r1corre",
-                "joined": "2019-04",
-                "name": "Erwan Corre",
-                "orcid": "0000-0001-6354-2278",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/r1corre/",
-                "twitter": "r1corre",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/r1corre.json"
-            },
-            {
-                "email": "stephanie.robin@inrae.fr",
-                "id": "stephanierobin",
-                "joined": "2021-11",
-                "name": "St\u00e9phanie Robin",
-                "orcid": "0000-0001-7379-9173",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/",
-                "twitter": "robinstphanie1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/stephanierobin.json"
-            },
-            {
-                "email": "jonathan.kreplak@inrae.fr",
-                "id": "jkreplak",
-                "joined": "2020-09",
-                "name": "Jonathan Kreplak",
-                "orcid": "0000-0001-5563-1932",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jkreplak/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jkreplak.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
-            },
-            {
-                "avatar": "/training-material/assets/images/eurosciencegateway.png",
-                "funder": true,
-                "funding_id": "101057388",
-                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "eurosciencegateway",
-                "joined": "2023-10",
-                "members": [
-                    "abretaud",
-                    "anuprulez",
-                    "bgruening",
-                    "erxleben",
-                    "pauldg",
-                    "rlibouba"
-                ],
-                "name": "EuroScienceGateway",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
+                "email": "zierep@informatik.uni-freiburg.de",
+                "id": "paulzierep",
+                "joined": "2023-02",
+                "name": "Paul Zierep",
+                "orcid": "0000-0003-2982-388X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json"
             }
         ],
-        "dir": "topics/genome-annotation/tutorials/repeatmasker",
+        "dir": "topics/genome-annotation/tutorials/secondary-metabolite-discovery",
+        "draft": true,
         "edam_operation": [
-            "Editing",
-            "RNA-Seq analysis",
-            "Genome annotation",
-            "Mapping",
-            "Repeat sequence detection"
+            "Gene prediction",
+            "Data handling",
+            "Service invocation",
+            "Differential gene expression analysis",
+            "Sequence clustering"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "genome-annotation",
-                "tutorials": [
-                    "funannotate"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "genome-annotation/repeatmasker",
+        "id": "genome-annotation/secondary-metabolite-discovery",
         "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "RepeatMasker can be used to soft-mask a genome",
-            "It is an essential first step before running structural annotation pipelines"
+            "Gene cluster prediction that can be performed for any assembly or genome of microorganisms (procaryotes and fungi).",
+            "Bridging of gene annotation and cheminformatics.",
+            "Usage of custom script to bridge workflow steps."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-09-27",
         "objectives": [
-            "Use Red and RepeatMasker to soft-mask a newly assembled genome"
+            "Gene cluster prediction using antiSMAHS.",
+            "Extraction of gene cluster products using a custom script.",
+            "Query of the products in compound libraries using cheminformatic tools."
         ],
-        "pageviews": 9312,
-        "priority": 1,
-        "pub_date": "2021-11-29",
+        "pageviews": 285,
+        "pub_date": "2024-02-21",
         "questions": [
-            "How to mask repeats in a genome?",
-            "What is the difference between hard and soft-masking?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "abretaud"
-                ],
-                "date": "2023-05-10",
-                "galaxy_version": "23.01",
-                "length": "18M",
-                "speakers": [
-                    "abretaud"
-                ],
-                "youtube_id": "7tYEDmAvHD4"
-            },
-            {
-                "captioners": [
-                    "abretaud"
-                ],
-                "date": "2022-03-03",
-                "galaxy_version": "21.09",
-                "length": "16M",
-                "speakers": [
-                    "abretaud"
-                ],
-                "youtube_id": "AYAvjwm4cnM"
-            }
+            "How to discover secondary metabolites produced by microorganisms ?",
+            "How to identify the discovered secondary metabolites in compound libraries ?",
+            "How to bridge workflow steps using custom scripts ?"
         ],
-        "short_id": "T00178",
+        "short_id": "T00420",
         "short_tools": [
-            "bedtools_maskfastabed",
-            "repeatmodeler",
-            "repeatmasker_wrapper",
-            "red"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "eukaryote",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
+            "ctb_np-likeness-calculator",
+            "interactive_tool_jupyter_notebook",
+            "antismash",
+            "ctb_simsearch",
+            "tp_awk_tool",
+            "bp_genbank2gff3",
+            "ctb_chemfp_mol2fps",
+            "openbabel_remDuplicates",
+            "ncbi_acc_download",
+            "collapse_dataset",
+            "ctb_silicos_qed",
+            "edu.tamu.cpt.gff3.customGbkToGff",
+            "Remove beginning1"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
                 {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 }
             ],
@@ -98324,15 +99267,24 @@
         },
         "symlink": null,
         "tags": [
-            "eukaryote"
+            "work-in-progress"
         ],
-        "time_estimation": "1H",
-        "title": "Masking repeats with RepeatMasker",
+        "time_estimation": "3H",
+        "title": "Secondary metabolite discovery",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/2.0.4+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/red/red/2018.09.10+galaxy1"
+            "Remove beginning1",
+            "interactive_tool_jupyter_notebook",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/6.1.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/1.5",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/natural_product_likeness/ctb_np-likeness-calculator/2.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_remduplicates/openbabel_remDuplicates/3.1.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/qed/ctb_silicos_qed/2021.03.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/simsearch/ctb_simsearch/0.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/cpt/cpt_gbk_to_gff/edu.tamu.cpt.gff3.customGbkToGff/20.1.0.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bp_genbank2gff3/bp_genbank2gff3/1.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
         ],
         "topic_name": "genome-annotation",
         "topic_name_human": "Genome Annotation",
@@ -98342,238 +99294,360 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "repeatmasker",
+        "tutorial_name": "secondary-metabolite-discovery",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/repeatmasker/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/repeatmasker/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/repeatmasker/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/secondary-metabolite-discovery/tutorial.json"
         },
-        "version": 20,
+        "version": 2,
         "video": false,
-        "video_versions": 2,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 83,
-        "visitors": 7110,
+        "visit_duration": 57,
+        "visitors": 217,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0003-0914-2470",
-                        "name": "Anthony Bretaudeau"
-                    }
-                ],
-                "description": "Masking repeats in a genome using RepeatMasker",
+                "creators": [],
+                "description": "",
                 "features": {
                     "comments": false,
-                    "parameters": false,
+                    "parameters": true,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nRaw genome sequence\"]\n  1[label=\"Red\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"RepeatMasker\"]\n  0 -> 2 [label=\"output\"]\n  k3d7a51a241f9426fb9e8082fab12d6e2[color=lightseagreen,label=\"Output\\nRepeatMasker repeat catalogue on input dataset(s)\"]\n  2 -> k3d7a51a241f9426fb9e8082fab12d6e2\n  k3f0c419c7bd24378b174fe11e52bbf61[color=lightseagreen,label=\"Output\\nRepeatMasker masked sequence on input dataset(s)\"]\n  2 -> k3f0c419c7bd24378b174fe11e52bbf61\n  k342d5065122b437a8f78a636c5f2b7f6[color=lightseagreen,label=\"Output\\nRepeatMasker output log on input dataset(s)\"]\n  2 -> k342d5065122b437a8f78a636c5f2b7f6\n  k4a157f800d75425b858d49c4a12f91a0[color=lightseagreen,label=\"Output\\nRepeatMasker repeat statistics on input dataset(s)\"]\n  2 -> k4a157f800d75425b858d49c4a12f91a0\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nQuery Genomes\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nJupyter Notebook Genbank2Features\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTarget Molecules Natural Compound Library\"]\n  3[label=\"NCBI Accession Download\"]\n  0 -> 3 [label=\"output\"]\n  kfaecdec3711d43babb9138a4b4b3932d[color=lightseagreen,label=\"Output\\nNCBI Accession Download on input dataset(s): Log\"]\n  3 -> kfaecdec3711d43babb9138a4b4b3932d\n  kc8857c6fec994d298c98be7a63a9f029[color=lightseagreen,label=\"Output\\nNCBI Accession Download on input dataset(s): Downloaded Files\"]\n  3 -> kc8857c6fec994d298c98be7a63a9f029\n  4[label=\"Molecule to fingerprint\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Antismash\"]\n  3 -> 5 [label=\"output\"]\n  kcc813ad7f4234cb8ba798201abab206a[color=lightseagreen,label=\"Output\\nAntismash on input dataset(s): HTML report\"]\n  5 -> kcc813ad7f4234cb8ba798201abab206a\n  6[label=\"Collapse clusters in one Genbank entry\"]\n  5 -> 6 [label=\"genbank\"]\n  7[label=\"Extract SMILES qualifiers\"]\n  1 -> 7 [label=\"output\"]\n  6 -> 7 [label=\"output\"]\n  8[label=\"Convert table to smi format\"]\n  7 -> 8 [label=\"output_collection\"]\n  9[label=\"Remove beginning\"]\n  8 -> 9 [label=\"outfile\"]\n  10[label=\"Remove duplicated molecules\"]\n  9 -> 10 [label=\"out_file1\"]\n  11[label=\"Molecule to fingerprint\"]\n  10 -> 11 [label=\"outfile\"]\n  12[label=\"Natural Product\"]\n  10 -> 12 [label=\"outfile\"]\n  13[label=\"Drug-likeness\"]\n  10 -> 13 [label=\"outfile\"]\n  14[label=\"Similarity Search\"]\n  11 -> 14 [label=\"outfile\"]\n  4 -> 14 [label=\"outfile\"]\n}",
                 "history": [
                     {
-                        "hash": "c62f8399d7c3d6e04e1f8db85543ba9162e902d8",
-                        "message": "workflow test",
+                        "hash": "af81c1a8eee9601fc595b636e052099a41c98493",
+                        "message": "init",
                         "num": 1,
-                        "short_hash": "c62f8399d",
-                        "unix": "1682350616"
+                        "short_hash": "af81c1a8e",
+                        "unix": "1707812500"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "The raw (not masked) genome sequence in fasta format",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "The raw (not masked) genome sequence in fasta format",
-                                "name": "Raw genome sequence"
+                                "description": "",
+                                "name": "Query Genomes"
                             }
                         ],
-                        "label": "Raw genome sequence",
+                        "label": "Query Genomes",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 0.0,
+                            "top": 138.68778864733008
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"default\": \"AL645882.2\", \"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "34c92bcf-3ff2-4364-8dd8-0320ea449c09",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Jupyter Notebook Genbank2Features"
+                            }
+                        ],
+                        "label": "Jupyter Notebook Genbank2Features",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 77.5
+                            "left": 1000.13886850544,
+                            "top": 967.9040340744108
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "c26e06b1-39a6-43f4-a83f-7daeba257011",
+                        "uuid": "5abb2d68-5c14-43af-9878-bf2b51bda3c5",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Target Molecules (Natural Compound Library)"
+                            }
+                        ],
+                        "label": "Target Molecules (Natural Compound Library)",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 999.7029249019243,
+                            "top": 1102.574230607614
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "41f458be-660b-40f7-abef-c57489b3099c",
+                        "when": null,
                         "workflow_outputs": []
                     }
                 ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nRaw genome sequence\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Red\"];\n  0 -->|output| 1;\n  2[\"RepeatMasker\"];\n  0 -->|output| 2;\n  3d7a51a2-41f9-426f-b9e8-082fab12d6e2[\"Output\\nRepeatMasker repeat catalogue on input dataset(s)\"];\n  2 --> 3d7a51a2-41f9-426f-b9e8-082fab12d6e2;\n  style 3d7a51a2-41f9-426f-b9e8-082fab12d6e2 stroke:#2c3143,stroke-width:4px;\n  3f0c419c-7bd2-4378-b174-fe11e52bbf61[\"Output\\nRepeatMasker masked sequence on input dataset(s)\"];\n  2 --> 3f0c419c-7bd2-4378-b174-fe11e52bbf61;\n  style 3f0c419c-7bd2-4378-b174-fe11e52bbf61 stroke:#2c3143,stroke-width:4px;\n  342d5065-122b-437a-8f78-a636c5f2b7f6[\"Output\\nRepeatMasker output log on input dataset(s)\"];\n  2 --> 342d5065-122b-437a-8f78-a636c5f2b7f6;\n  style 342d5065-122b-437a-8f78-a636c5f2b7f6 stroke:#2c3143,stroke-width:4px;\n  4a157f80-0d75-425b-858d-49c4a12f91a0[\"Output\\nRepeatMasker repeat statistics on input dataset(s)\"];\n  2 --> 4a157f80-0d75-425b-858d-49c4a12f91a0;\n  style 4a157f80-0d75-425b-858d-49c4a12f91a0 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "RepeatMasker",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nQuery Genomes\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nJupyter Notebook Genbank2Features\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nTarget Molecules Natural Compound Library\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"NCBI Accession Download\"];\n  0 -->|output| 3;\n  faecdec3-711d-43ba-bb91-38a4b4b3932d[\"Output\\nNCBI Accession Download on input dataset(s): Log\"];\n  3 --> faecdec3-711d-43ba-bb91-38a4b4b3932d;\n  style faecdec3-711d-43ba-bb91-38a4b4b3932d stroke:#2c3143,stroke-width:4px;\n  c8857c6f-ec99-4d29-8c98-be7a63a9f029[\"Output\\nNCBI Accession Download on input dataset(s): Downloaded Files\"];\n  3 --> c8857c6f-ec99-4d29-8c98-be7a63a9f029;\n  style c8857c6f-ec99-4d29-8c98-be7a63a9f029 stroke:#2c3143,stroke-width:4px;\n  4[\"Molecule to fingerprint\"];\n  2 -->|output| 4;\n  5[\"Antismash\"];\n  3 -->|output| 5;\n  cc813ad7-f423-4cb8-ba79-8201abab206a[\"Output\\nAntismash on input dataset(s): HTML report\"];\n  5 --> cc813ad7-f423-4cb8-ba79-8201abab206a;\n  style cc813ad7-f423-4cb8-ba79-8201abab206a stroke:#2c3143,stroke-width:4px;\n  6[\"Collapse clusters in one Genbank entry\"];\n  5 -->|genbank| 6;\n  7[\"Extract SMILES qualifiers\"];\n  1 -->|output| 7;\n  6 -->|output| 7;\n  8[\"Convert table to smi format\"];\n  7 -->|output_collection| 8;\n  9[\"Remove beginning\"];\n  8 -->|outfile| 9;\n  10[\"Remove duplicated molecules\"];\n  9 -->|out_file1| 10;\n  11[\"Molecule to fingerprint\"];\n  10 -->|outfile| 11;\n  12[\"Natural Product\"];\n  10 -->|outfile| 12;\n  13[\"Drug-likeness\"];\n  10 -->|outfile| 13;\n  14[\"Similarity Search\"];\n  11 -->|outfile| 14;\n  4 -->|outfile| 14;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Gene Cluster Product Similarity Search ",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/red/red/2018.09.10+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0",
                         "errors": null,
-                        "id": 1,
+                        "id": 3,
                         "input_connections": {
-                            "input": {
+                            "query_source|accession_list": {
                                 "id": 0,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Red",
-                                "name": "input"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Red",
+                        "name": "NCBI Accession Download",
                         "outputs": [
                             {
-                                "name": "masked",
-                                "type": "fasta"
+                                "name": "output",
+                                "type": "input"
                             },
                             {
-                                "name": "bed",
-                                "type": "bed"
+                                "name": "error_log",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 354,
-                            "top": 0
+                            "left": 295.1263437181945,
+                            "top": 125.66098683332416
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/red/red/2018.09.10+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "18a46265455b",
-                            "name": "red",
+                            "changeset_revision": "e063168e0a81",
+                            "name": "ncbi_acc_download",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2018.09.10+galaxy1",
+                        "tool_state": "{\"ignore_failed\": \"0\", \"molecule\": {\"select\": \"nucleotide\", \"__current_case__\": 0, \"format\": \"fasta\"}, \"query_source\": {\"select\": \"accession_list\", \"__current_case__\": 1, \"accession_list\": {\"__class__\": \"ConnectedValue\"}}, \"range\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.2.8+galaxy0",
                         "type": "tool",
-                        "uuid": "8e20207e-cee6-42fc-afd0-6bed48afe669",
+                        "uuid": "5586d5e9-ea6f-4e01-8e41-c3fe790535a3",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "masked",
-                                "uuid": "344db107-2ffa-4389-91d8-bd1505707369"
+                                "label": "NCBI Accession Download on input dataset(s): Log",
+                                "output_name": "error_log",
+                                "uuid": "faecdec3-711d-43ba-bb91-38a4b4b3932d"
                             },
                             {
-                                "label": null,
-                                "output_name": "bed",
-                                "uuid": "6414050e-9640-490a-a39b-26c582bd8f91"
+                                "label": "NCBI Accession Download on input dataset(s): Downloaded Files",
+                                "output_name": "output",
+                                "uuid": "c8857c6f-ec99-4d29-8c98-be7a63a9f029"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.5+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/6.1.1+galaxy1",
                         "errors": null,
-                        "id": 2,
+                        "id": 5,
                         "input_connections": {
-                            "input_fasta": {
-                                "id": 0,
+                            "infile": {
+                                "id": 3,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool RepeatMasker",
-                                "name": "input_fasta"
+                                "description": "runtime parameter for tool Antismash",
+                                "name": "genefinding_gff3"
+                            },
+                            {
+                                "description": "runtime parameter for tool Antismash",
+                                "name": "sideload"
                             }
                         ],
                         "label": null,
-                        "name": "RepeatMasker",
+                        "name": "Antismash",
                         "outputs": [
                             {
-                                "name": "output_masked_genome",
-                                "type": "fasta"
+                                "name": "genecluster_tabular",
+                                "type": "input"
                             },
                             {
-                                "name": "output_log",
-                                "type": "tabular"
+                                "name": "genbank",
+                                "type": "input"
                             },
                             {
-                                "name": "output_table",
-                                "type": "txt"
+                                "name": "embl",
+                                "type": "input"
                             },
                             {
-                                "name": "output_repeat_catalog",
+                                "name": "archive",
+                                "type": "input"
+                            },
+                            {
+                                "name": "html",
+                                "type": "html"
+                            },
+                            {
+                                "name": "log",
                                 "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 355,
-                            "top": 144.5
+                            "left": 639.6596780017987,
+                            "top": 0
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.5+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/6.1.1+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "ba6d2c32f797",
-                            "name": "repeat_masker",
+                            "changeset_revision": "bc88856eddab",
+                            "name": "antismash",
                             "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced\": {\"is_only\": \"false\", \"is_clip\": \"false\", \"no_is\": \"false\", \"rodspec\": \"false\", \"primspec\": \"false\", \"nolow\": \"false\", \"noint\": \"false\", \"norna\": \"false\", \"alu\": \"false\", \"div\": \"false\", \"search_speed\": \"\", \"frag\": \"40000\", \"gc\": null, \"gccalc\": \"false\", \"nocut\": \"false\", \"xout\": \"false\", \"keep_alignments\": \"false\", \"invert_alignments\": \"false\", \"poly\": \"false\"}, \"excln\": \"true\", \"gff\": \"false\", \"input_fasta\": {\"__class__\": \"RuntimeValue\"}, \"repeat_source\": {\"source_type\": \"dfam\", \"__current_case__\": 0, \"species_source\": {\"species_from_list\": \"yes\", \"__current_case__\": 0, \"species_list\": \"human\"}}, \"xsmall\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.1.5+galaxy0",
+                        "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"advanced_options\": {\"minlength\": \"1000\", \"hmmdetection_strictness\": \"relaxed\", \"cb_nclusters\": \"10\", \"cb_min_homology_scale\": \"0.0\", \"rre_cutoff\": \"25.0\", \"rre_minlength\": \"50\"}, \"asf\": true, \"cb_general\": false, \"cb_knownclusters\": true, \"cb_subclusters\": true, \"cc_mibig\": false, \"clusterhmmer\": false, \"cond_taxon\": {\"taxon\": \"bacteria\", \"__current_case__\": 0, \"genefinding_tool\": \"prodigal\", \"tigrfam\": false}, \"fullhmmer\": false, \"genefinding_gff3\": {\"__class__\": \"RuntimeValue\"}, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"outputs\": [\"html\", \"all\", \"embl\", \"gb\", \"genecluster_tabular\", \"log\"], \"pfam2go\": true, \"rre\": true, \"sideload\": {\"file\": {\"__class__\": \"RuntimeValue\"}, \"format\": \"harmonize\"}, \"smcog_trees\": true, \"tta_threshold\": \"0.65\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "6.1.1+galaxy1",
                         "type": "tool",
-                        "uuid": "f7ef7c85-b782-468b-94a2-076efc91920c",
+                        "uuid": "0f476190-2ca9-4b60-b6af-9c6ac4e12d0b",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "RepeatMasker repeat catalogue on input dataset(s)",
-                                "output_name": "output_repeat_catalog",
-                                "uuid": "3d7a51a2-41f9-426f-b9e8-082fab12d6e2"
+                                "label": null,
+                                "output_name": "log",
+                                "uuid": "26f7288b-d497-4680-af57-169bf7d8a22a"
                             },
                             {
-                                "label": "RepeatMasker masked sequence on input dataset(s)",
-                                "output_name": "output_masked_genome",
-                                "uuid": "3f0c419c-7bd2-4378-b174-fe11e52bbf61"
+                                "label": null,
+                                "output_name": "genbank",
+                                "uuid": "607063ee-4d4c-40d0-b355-cff12b9de2a9"
                             },
                             {
-                                "label": "RepeatMasker output log on input dataset(s)",
-                                "output_name": "output_log",
-                                "uuid": "342d5065-122b-437a-8f78-a636c5f2b7f6"
+                                "label": "Antismash on input dataset(s): HTML report",
+                                "output_name": "html",
+                                "uuid": "cc813ad7-f423-4cb8-ba79-8201abab206a"
                             },
                             {
-                                "label": "RepeatMasker repeat statistics on input dataset(s)",
-                                "output_name": "output_table",
-                                "uuid": "4a157f80-0d75-425b-858d-49c4a12f91a0"
+                                "label": null,
+                                "output_name": "archive",
+                                "uuid": "a8a9e6d6-652d-44b5-ba4f-60aff9c9999f"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "embl",
+                                "uuid": "7c948135-1c3a-43eb-9a40-a5fe28334f58"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "genecluster_tabular",
+                                "uuid": "5bfc66a2-bec6-4818-9fa8-ad42b3b73dc8"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "input_list": {
+                                "id": 5,
+                                "output_name": "genbank"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Collapse clusters in one Genbank entry",
+                        "name": "Collapse Collection",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 963.0516444199695,
+                            "top": 145.633549188099
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "90981f86000f",
+                            "name": "collapse_collections",
+                            "owner": "nml",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"filename\": {\"add_name\": true, \"__current_case__\": 0, \"place_name\": \"above\"}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.1.0",
+                        "type": "tool",
+                        "uuid": "fe07e889-e6a5-48bc-9f61-1676b3cc6641",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "dc73d9e2-5338-4fa7-90c0-6b03b4181457"
                             }
                         ]
                     }
                 ],
-                "parent_id": "genome-annotation/repeatmasker",
-                "path": "topics/genome-annotation/tutorials/repeatmasker/workflows/RepeatMasker.ga",
+                "parent_id": "genome-annotation/secondary-metabolite-discovery",
+                "path": "topics/genome-annotation/tutorials/secondary-metabolite-discovery/workflows/main_workflow.ga",
                 "tags": [
-                    "genome-annotation"
+                    "sempi3"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "RepeatMasker",
+                "tests": false,
+                "title": "Gene Cluster Product Similarity Search ",
                 "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-repeatmasker/versions/repeatmasker",
-                "tutorial_id": "repeatmasker",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/repeatmasker/workflows/RepeatMasker.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/repeatmasker/workflows/RepeatMasker.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-secondary-metabolite-discovery/versions/main-workflow",
+                "tutorial_id": "secondary-metabolite-discovery",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/secondary-metabolite-discovery/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/secondary-metabolite-discovery/workflows/main_workflow.html",
                 "version": 1,
-                "wfid": "genome-annotation-repeatmasker",
-                "wfname": "repeatmasker",
-                "workflow": "RepeatMasker.ga",
+                "wfid": "genome-annotation-secondary-metabolite-discovery",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/red/red/2018.09.10+galaxy1"
+                    "Remove beginning1",
+                    "interactive_tool_jupyter_notebook",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/6.1.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/1.5",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/natural_product_likeness/ctb_np-likeness-calculator/2.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_remduplicates/openbabel_remDuplicates/3.1.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/qed/ctb_silicos_qed/2021.03.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/simsearch/ctb_simsearch/0.2",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
                 ],
-                "workflowhub_id": "1198"
+                "workflowhub_id": "1145"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/7085837"
+        "zenodo_link": "https://zenodo.org/records/10652998"
     },
     {
         "admin_install": {
@@ -98828,7 +99902,8 @@
         "hands_on": true,
         "id": "genome-annotation/amr-gene-detection",
         "inexact_supported_servers": [
-            "Galaxy@AuBi"
+            "Galaxy@AuBi",
+            "UseGalaxy.org (Main)"
         ],
         "js_requirements": {
             "mathjax": null,
@@ -98841,27 +99916,42 @@
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-13",
+        "mod_date": "2024-09-27",
         "objectives": [
             "Run a series of tool to assess the presence of antimicrobial resistance genes (ARG)",
             "Get information about ARGs",
             "Visualize the ARGs and plasmid genes in their genomic context"
         ],
-        "pageviews": 1368,
+        "pageviews": 1576,
         "pub_date": "2024-01-23",
         "questions": [
             "Which resistance genes are on a bacterial genome?",
             "Where are the genes located on the genome?"
         ],
+        "recordings": [
+            {
+                "bot-timestamp": 1727199012,
+                "captioners": [
+                    "SaimMomin12"
+                ],
+                "date": "2024-09-24",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "26M",
+                "speakers": [
+                    "SaimMomin12"
+                ],
+                "youtube_id": "hfiYCIcD0ww"
+            }
+        ],
         "short_id": "T00401",
         "short_tools": [
-            "Grep1",
             "jbrowse",
-            "bowtie2",
             "tbl2gff3",
-            "bakta",
+            "upload1",
+            "Grep1",
             "staramr_search",
-            "upload1"
+            "bakta",
+            "bowtie2"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -98889,6 +99979,11 @@
                     "name": "Galaxy@AuBi",
                     "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 }
             ]
         },
@@ -98927,12 +100022,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.json"
         },
-        "version": 5,
+        "version": 6,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 176,
-        "visitors": 967,
+        "visit_duration": 165,
+        "visitors": 1138,
         "workflows": [
             {
                 "creators": [
@@ -98954,7 +100049,7 @@
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontigs\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nforward_reads\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreverse_reads\"]\n  3[label=\"staramr\"]\n  0 -> 3 [label=\"output\"]\n  k7a18df3cf28045aa92e427b79f10a005[color=lightseagreen,label=\"Output\\nstararm_detailed_summary\"]\n  3 -> k7a18df3cf28045aa92e427b79f10a005\n  4[label=\"Bakta\"]\n  0 -> 4 [label=\"output\"]\n  kead94d4086b04cf0aee2cf72a8f47933[color=lightseagreen,label=\"Output\\nbakta_annotation_summary\"]\n  4 -> kead94d4086b04cf0aee2cf72a8f47933\n  5[label=\"Bowtie2\"]\n  1 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  k0639b4672e624a52b72f35bf9f46f6a3[color=lightseagreen,label=\"Output\\nbowtie_mapping_stats\"]\n  5 -> k0639b4672e624a52b72f35bf9f46f6a3\n  6[label=\"Select\"]\n  3 -> 6 [label=\"detailed_summary\"]\n  7[label=\"Table to GFF3\"]\n  6 -> 7 [label=\"out_file1\"]\n  8[label=\"JBrowse\"]\n  4 -> 8 [label=\"annotation_gff3\"]\n  7 -> 8 [label=\"output\"]\n  5 -> 8 [label=\"output\"]\n  k910a35522a224279b15930379b31496f[color=lightseagreen,label=\"Output\\njbrowse_output\"]\n  8 -> k910a35522a224279b15930379b31496f\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontigs\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nforward_reads\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreverse_reads\"]\n  3[label=\"staramr\"]\n  0 -> 3 [label=\"output\"]\n  k000e2ab992db45bba0efecccf06da616[color=lightseagreen,label=\"Output\\nstararm_detailed_summary\"]\n  3 -> k000e2ab992db45bba0efecccf06da616\n  4[label=\"Bakta\"]\n  0 -> 4 [label=\"output\"]\n  kc848b1eb72624627b7a705a13b968935[color=lightseagreen,label=\"Output\\nbakta_annotation_summary\"]\n  4 -> kc848b1eb72624627b7a705a13b968935\n  5[label=\"Bowtie2\"]\n  1 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  k352e63d38aca4dff878c10497f65bb74[color=lightseagreen,label=\"Output\\nbowtie_mapping_stats\"]\n  5 -> k352e63d38aca4dff878c10497f65bb74\n  6[label=\"Select\"]\n  3 -> 6 [label=\"detailed_summary\"]\n  7[label=\"Table to GFF3\"]\n  6 -> 7 [label=\"out_file1\"]\n  8[label=\"JBrowse\"]\n  4 -> 8 [label=\"annotation_gff3\"]\n  7 -> 8 [label=\"output\"]\n  5 -> 8 [label=\"output\"]\n  k3c3bd5fd419c45b2afcdc6d02af82695[color=lightseagreen,label=\"Output\\njbrowse_output\"]\n  8 -> k3c3bd5fd419c45b2afcdc6d02af82695\n}",
                 "history": [
                     {
                         "hash": "597f8ce954083c7cd4e43765b6c4709619637e6a",
@@ -99069,8 +100164,8 @@
                     }
                 ],
                 "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nforward_reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nreverse_reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"staramr\"];\n  0 -->|output| 3;\n  7a18df3c-f280-45aa-92e4-27b79f10a005[\"Output\\nstararm_detailed_summary\"];\n  3 --> 7a18df3c-f280-45aa-92e4-27b79f10a005;\n  style 7a18df3c-f280-45aa-92e4-27b79f10a005 stroke:#2c3143,stroke-width:4px;\n  4[\"Bakta\"];\n  0 -->|output| 4;\n  ead94d40-86b0-4cf0-aee2-cf72a8f47933[\"Output\\nbakta_annotation_summary\"];\n  4 --> ead94d40-86b0-4cf0-aee2-cf72a8f47933;\n  style ead94d40-86b0-4cf0-aee2-cf72a8f47933 stroke:#2c3143,stroke-width:4px;\n  5[\"Bowtie2\"];\n  1 -->|output| 5;\n  2 -->|output| 5;\n  0 -->|output| 5;\n  0639b467-2e62-4a52-b72f-35bf9f46f6a3[\"Output\\nbowtie_mapping_stats\"];\n  5 --> 0639b467-2e62-4a52-b72f-35bf9f46f6a3;\n  style 0639b467-2e62-4a52-b72f-35bf9f46f6a3 stroke:#2c3143,stroke-width:4px;\n  6[\"Select\"];\n  3 -->|detailed_summary| 6;\n  7[\"Table to GFF3\"];\n  6 -->|out_file1| 7;\n  8[\"JBrowse\"];\n  4 -->|annotation_gff3| 8;\n  7 -->|output| 8;\n  5 -->|output| 8;\n  910a3552-2a22-4279-b159-30379b31496f[\"Output\\njbrowse_output\"];\n  8 --> 910a3552-2a22-4279-b159-30379b31496f;\n  style 910a3552-2a22-4279-b159-30379b31496f stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nforward_reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nreverse_reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"staramr\"];\n  0 -->|output| 3;\n  000e2ab9-92db-45bb-a0ef-ecccf06da616[\"Output\\nstararm_detailed_summary\"];\n  3 --> 000e2ab9-92db-45bb-a0ef-ecccf06da616;\n  style 000e2ab9-92db-45bb-a0ef-ecccf06da616 stroke:#2c3143,stroke-width:4px;\n  4[\"Bakta\"];\n  0 -->|output| 4;\n  c848b1eb-7262-4627-b7a7-05a13b968935[\"Output\\nbakta_annotation_summary\"];\n  4 --> c848b1eb-7262-4627-b7a7-05a13b968935;\n  style c848b1eb-7262-4627-b7a7-05a13b968935 stroke:#2c3143,stroke-width:4px;\n  5[\"Bowtie2\"];\n  1 -->|output| 5;\n  2 -->|output| 5;\n  0 -->|output| 5;\n  352e63d3-8aca-4dff-878c-10497f65bb74[\"Output\\nbowtie_mapping_stats\"];\n  5 --> 352e63d3-8aca-4dff-878c-10497f65bb74;\n  style 352e63d3-8aca-4dff-878c-10497f65bb74 stroke:#2c3143,stroke-width:4px;\n  6[\"Select\"];\n  3 -->|detailed_summary| 6;\n  7[\"Table to GFF3\"];\n  6 -->|out_file1| 7;\n  8[\"JBrowse\"];\n  4 -->|annotation_gff3| 8;\n  7 -->|output| 8;\n  5 -->|output| 8;\n  3c3bd5fd-419c-45b2-afcd-c6d02af82695[\"Output\\njbrowse_output\"];\n  8 --> 3c3bd5fd-419c-45b2-afcd-c6d02af82695;\n  style 3c3bd5fd-419c-45b2-afcd-c6d02af82695 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
                 "name": "mrsa AMR gene detection",
                 "outputs": [
                     {
@@ -99142,7 +100237,7 @@
                             {
                                 "label": "stararm_detailed_summary",
                                 "output_name": "detailed_summary",
-                                "uuid": "7a18df3c-f280-45aa-92e4-27b79f10a005"
+                                "uuid": "000e2ab9-92db-45bb-a0ef-ecccf06da616"
                             }
                         ]
                     },
@@ -99216,7 +100311,7 @@
                             {
                                 "label": "bakta_annotation_summary",
                                 "output_name": "annotation_tsv",
-                                "uuid": "ead94d40-86b0-4cf0-aee2-cf72a8f47933"
+                                "uuid": "c848b1eb-7262-4627-b7a7-05a13b968935"
                             }
                         ]
                     },
@@ -99273,7 +100368,7 @@
                             {
                                 "label": "bowtie_mapping_stats",
                                 "output_name": "mapping_stats",
-                                "uuid": "0639b467-2e62-4a52-b72f-35bf9f46f6a3"
+                                "uuid": "352e63d3-8aca-4dff-878c-10497f65bb74"
                             }
                         ]
                     },
@@ -99326,7 +100421,7 @@
                             {
                                 "label": "jbrowse_output",
                                 "output_name": "output",
-                                "uuid": "910a3552-2a22-4279-b159-30379b31496f"
+                                "uuid": "3c3bd5fd-419c-45b2-afcd-c6d02af82695"
                             }
                         ]
                     }
@@ -99371,232 +100466,128 @@
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "fbf99087e067",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "fbf99087e067",
+                    "revisions": "d698c222f354",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bakta",
-                    "owner": "iuc",
-                    "revisions": "ba6990f72184",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "integron_finder",
-                    "owner": "iuc",
-                    "revisions": "bfd290fe1588",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "isescan",
-                    "owner": "iuc",
-                    "revisions": "9e776e7fab4f",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "jbrowse",
-                    "owner": "iuc",
-                    "revisions": "a6e57ff585c0",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "name": "clustalw",
+                    "owner": "devteam",
+                    "revisions": "d6694932c5e0",
+                    "tool_panel_section_label": "Multiple Alignments",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "plasmidfinder",
+                    "name": "chromeister",
                     "owner": "iuc",
-                    "revisions": "7075b7a5441b",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "e483be1014b6",
+                    "tool_panel_section_label": "Multiple Alignments",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "tbl2gff3",
+                    "name": "gecko",
                     "owner": "iuc",
-                    "revisions": "4a7f4b0cc0a3",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "5efbd15675ca",
+                    "tool_panel_section_label": "Multiple Alignments",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bakta\n  owner: iuc\n  revisions: ba6990f72184\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: integron_finder\n  owner: iuc\n  revisions: bfd290fe1588\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: isescan\n  owner: iuc\n  revisions: 9e776e7fab4f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: plasmidfinder\n  owner: iuc\n  revisions: 7075b7a5441b\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbl2gff3\n  owner: iuc\n  revisions: 4a7f4b0cc0a3\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "bebatut"
-            ],
-            "funding": [
-                "abromics"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clustalw\n  owner: devteam\n  revisions: d6694932c5e0\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chromeister\n  owner: iuc\n  revisions: e483be1014b6\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gecko\n  owner: iuc\n  revisions: 5efbd15675ca\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "avatar": "/training-material/assets/images/abromics.png",
-                "funder": true,
-                "github": false,
-                "id": "abromics",
-                "joined": "2024-01",
-                "name": "ABRomics",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abromics/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/abromics.json"
+                "elixir_node": "es",
+                "email": "estebanpw@uma.es",
+                "id": "estebanpw",
+                "joined": "2020-11",
+                "name": "Esteban Perez-Wohlfeil",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/estebanpw/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/estebanpw.json"
             }
         ],
-        "dir": "topics/genome-annotation/tutorials/bacterial-genome-annotation",
-        "edam_ontology": [
-            "topic_0622",
-            "topic_3301",
-            "topic_0623",
-            "topic_0080",
-            "topic_3673",
-            "topic_0085",
-            "topic_0798"
-        ],
+        "dir": "topics/genome-annotation/tutorials/hpc-for-lsgc",
         "edam_operation": [
-            "Genome assembly",
-            "Sequence motif recognition",
-            "Genome annotation",
-            "Nucleic acid feature detection",
-            "Structural variation detection",
-            "Multilocus sequence typing",
-            "Genome visualisation",
-            "Protein feature detection",
-            "Scaffolding"
-        ],
-        "edam_topic": [
-            "Genomics",
-            "Microbiology",
-            "Gene and protein families",
-            "Sequence analysis",
-            "Whole genome sequencing",
-            "Functional genomics",
-            "Mobile genetic elements"
+            "Multiple sequence alignment"
         ],
+        "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.eu",
-            "UseGalaxy.fr"
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "genome-annotation",
-                "tutorials": [
-                    "apollo"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "visualisation",
-                "tutorials": [
-                    "circos",
-                    "jbrowse"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "history-to-workflow"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "genome-annotation/bacterial-genome-annotation",
+        "id": "genome-annotation/hpc-for-lsgc",
         "inexact_supported_servers": [
-            "Galaxy@AuBi",
+            "GalaxyTrakr",
             "UseGalaxy.cz"
         ],
         "js_requirements": {
-            "mathjax": null,
+            "mathjax": 10229,
             "mermaid": false
         },
         "key_points": [
-            "Bakta is a powerful tool to annotate a bacterial genome",
-            "Annotation can be easily visualized to understand the genomic context and help making sense of the annotations"
+            "We learnt that sequence comparison is a demanding problem and that there are several ways to approach it",
+            "We learnt how to run sequence comparisons in Galaxy with different levels of precision, particularly fine-grained and coarse-grained sequence comparison using GECKO and CHROMEISTER for smaller and larger sequences, respectively",
+            "We learnt how to post-process our comparison by extracting alignments, fine-tuning with multiple sequence alignment, detecting rearrangements, etc."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-01",
+        "mod_date": "2024-07-31",
         "objectives": [
-            "Run a series of tool to annotate a draft bacterial genome for different types of genomic components",
-            "Evaluate the annotation",
-            "Process the outputs to formate them for visualization needs",
-            "Visualize a draft bacterial genome and its annotations"
+            "Learn the basics of pairwise sequence comparison",
+            "Learn how to run different tools in Galaxy to perform sequence comparison at fine and coarse-grained levels",
+            "Learn how to post-process your sequence comparisons"
         ],
-        "pageviews": 2378,
-        "pub_date": "2024-02-01",
+        "pageviews": 5735585,
+        "pub_date": "2021-02-08",
         "questions": [
-            "Which genes are on a draft bacterial genome?",
-            "Which other genomic components can be found on a draft bacterial genome?"
+            "How can we run pairwise genome comparisons using Galaxy?",
+            "How can we run massive chromosome comparisons in Galaxy?",
+            "How can we quickly visualize genome comparisons in Galaxy?"
         ],
-        "short_id": "T00403",
+        "requirements": [
+            {
+                "topic_name": "introduction",
+                "tutorials": [
+                    "galaxy-intro-101"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00176",
         "short_tools": [
-            "Grouping1",
-            "jbrowse",
-            "upload1",
-            "integron_finder",
-            "isescan",
-            "tp_tail_tool",
-            "plasmidfinder",
-            "tbl2gff3",
-            "bakta",
-            "tp_replace_in_column"
+            "tp_awk_tool",
+            "gecko",
+            "clustalw",
+            "chromeister"
         ],
-        "slides": false,
+        "slides": true,
         "slides_recordings": false,
-        "subtopic": "prokaryote",
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ],
             "inexact": [
                 {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
                     "usegalaxy": false
                 },
                 {
@@ -99608,25 +100599,16 @@
         },
         "symlink": null,
         "tags": [
-            "gmod",
-            "illumina",
-            "bacteria",
-            "microgalaxy",
-            "jbrowse1"
+            "plants",
+            "prokaryote"
         ],
-        "time_estimation": "3H",
-        "title": "Bacterial Genome Annotation",
+        "time_estimation": "2H",
+        "title": "From small to large-scale genome comparison",
         "tools": [
-            "Grouping1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2",
-            "upload1"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a",
+            "toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2"
         ],
         "topic_name": "genome-annotation",
         "topic_name_human": "Genome Annotation",
@@ -99636,855 +100618,725 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "bacterial-genome-annotation",
+        "tutorial_name": "hpc-for-lsgc",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.json"
         },
-        "version": 4,
+        "version": 8,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 140,
-        "visitors": 1800,
+        "visit_duration": 283,
+        "visitors": 2085776,
         "workflows": [
             {
-                "creators": [
+                "creators": [],
+                "description": "A workflow designed to compare chromosomes and study large-scale rearrangements using CHROMEISTER",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nQuery chromosome\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference chromosome\"]\n  2[label=\"Chromeister\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  k58cf0c0c92004ba497276d908ccdfa9a[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Detected events\"]\n  2 -> k58cf0c0c92004ba497276d908ccdfa9a\n  k2afd0e7cd1cf4bfdbec66cc237ff3e2c[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Comparison metainformation\"]\n  2 -> k2afd0e7cd1cf4bfdbec66cc237ff3e2c\n  kc248576c1c39416c99d040c520e3da67[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Comparison dotplot\"]\n  2 -> kc248576c1c39416c99d040c520e3da67\n  k5f9aad77f9ee4932ab22bb5fd83f416c[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Comparison matrix\"]\n  2 -> k5f9aad77f9ee4932ab22bb5fd83f416c\n  kdea450c2712643dcaf7a9f2b704c76dd[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Comparison score\"]\n  2 -> kdea450c2712643dcaf7a9f2b704c76dd\n  k9a03f72255884a3fb70e0ec9979c16dd[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Detected events plot\"]\n  2 -> k9a03f72255884a3fb70e0ec9979c16dd\n}",
+                "history": [
                     {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0001-9852-1987",
-                        "name": "B\u00e9r\u00e9nice Batut"
+                        "hash": "ae7dbf55cc79f67b32661f650f26d5baad4779b3",
+                        "message": "added workflow for chromeister",
+                        "num": 1,
+                        "short_hash": "ae7dbf55c",
+                        "unix": "1612266607"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Query chromosome"
+                            }
+                        ],
+                        "label": "Query chromosome",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 345.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 446,
+                            "right": 646,
+                            "top": 263,
+                            "width": 200,
+                            "x": 446,
+                            "y": 263
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "fdde703b-e59f-403b-be56-28b4fde66d17",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "e6b6ae7f-73c3-450e-a997-103138788bc6"
+                            }
+                        ]
                     },
                     {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0002-8304-138X",
-                        "name": "Pierre Marin"
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Reference chromosome"
+                            }
+                        ],
+                        "label": "Reference chromosome",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 445.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 448,
+                            "right": 648,
+                            "top": 363,
+                            "width": 200,
+                            "x": 448,
+                            "y": 363
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "43a48ede-1c2e-4b0d-bf74-da212443a7de",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "1007eb1e-be5f-4f22-9d42-046f5e695dc4"
+                            }
+                        ]
                     }
                 ],
-                "description": "Bacterial Genome Annotation",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQuery chromosome\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference chromosome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Chromeister\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  58cf0c0c-9200-4ba4-9727-6d908ccdfa9a[\"Output\\nChromeister on input dataset(s): Detected events\"];\n  2 --> 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a;\n  style 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a stroke:#2c3143,stroke-width:4px;\n  2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c[\"Output\\nChromeister on input dataset(s): Comparison metainformation\"];\n  2 --> 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c;\n  style 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c stroke:#2c3143,stroke-width:4px;\n  c248576c-1c39-416c-99d0-40c520e3da67[\"Output\\nChromeister on input dataset(s): Comparison dotplot\"];\n  2 --> c248576c-1c39-416c-99d0-40c520e3da67;\n  style c248576c-1c39-416c-99d0-40c520e3da67 stroke:#2c3143,stroke-width:4px;\n  5f9aad77-f9ee-4932-ab22-bb5fd83f416c[\"Output\\nChromeister on input dataset(s): Comparison matrix\"];\n  2 --> 5f9aad77-f9ee-4932-ab22-bb5fd83f416c;\n  style 5f9aad77-f9ee-4932-ab22-bb5fd83f416c stroke:#2c3143,stroke-width:4px;\n  dea450c2-7126-43dc-af7a-9f2b704c76dd[\"Output\\nChromeister on input dataset(s): Comparison score\"];\n  2 --> dea450c2-7126-43dc-af7a-9f2b704c76dd;\n  style dea450c2-7126-43dc-af7a-9f2b704c76dd stroke:#2c3143,stroke-width:4px;\n  9a03f722-5588-4a3f-b70e-0ec9979c16dd[\"Output\\nChromeister on input dataset(s): Detected events plot\"];\n  2 --> 9a03f722-5588-4a3f-b70e-0ec9979c16dd;\n  style 9a03f722-5588-4a3f-b70e-0ec9979c16dd stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "CHROMEISTER chromosome comparison",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Query chromosome"
+                            }
+                        ],
+                        "label": "Query chromosome",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 345.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 446,
+                            "right": 646,
+                            "top": 263,
+                            "width": 200,
+                            "x": 446,
+                            "y": 263
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "fdde703b-e59f-403b-be56-28b4fde66d17",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "e6b6ae7f-73c3-450e-a997-103138788bc6"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Reference chromosome"
+                            }
+                        ],
+                        "label": "Reference chromosome",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 445.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 448,
+                            "right": 648,
+                            "top": 363,
+                            "width": 200,
+                            "x": 448,
+                            "y": 363
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "43a48ede-1c2e-4b0d-bf74-da212443a7de",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "1007eb1e-be5f-4f22-9d42-046f5e695dc4"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "db": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "query": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Chromeister",
+                                "name": "db"
+                            },
+                            {
+                                "description": "runtime parameter for tool Chromeister",
+                                "name": "query"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Chromeister",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "output_imagen",
+                                "type": "png"
+                            },
+                            {
+                                "name": "output_csv",
+                                "type": "csv"
+                            },
+                            {
+                                "name": "output_events",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "output_events_png",
+                                "type": "png"
+                            },
+                            {
+                                "name": "output_score",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 793.4000244140625,
+                            "height": 520.4000244140625,
+                            "left": 851,
+                            "right": 1051,
+                            "top": 273,
+                            "width": 200,
+                            "x": 851,
+                            "y": 273
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a",
+                        "tool_shed_repository": {
+                            "changeset_revision": "a6d1f83c46b4",
+                            "name": "chromeister",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"db\": {\"__class__\": \"RuntimeValue\"}, \"diffuse\": \"4\", \"dimension\": \"1000\", \"grid\": \"true\", \"kmer\": \"32\", \"pngevents\": \"true\", \"query\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.5.a",
+                        "type": "tool",
+                        "uuid": "79507815-b059-4f21-b74e-8e390fbb4bf2",
+                        "workflow_outputs": [
+                            {
+                                "label": "Chromeister on input dataset(s): Detected events",
+                                "output_name": "output_events",
+                                "uuid": "58cf0c0c-9200-4ba4-9727-6d908ccdfa9a"
+                            },
+                            {
+                                "label": "Chromeister on input dataset(s): Comparison metainformation",
+                                "output_name": "output_csv",
+                                "uuid": "2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c"
+                            },
+                            {
+                                "label": "Chromeister on input dataset(s): Comparison dotplot",
+                                "output_name": "output_imagen",
+                                "uuid": "c248576c-1c39-416c-99d0-40c520e3da67"
+                            },
+                            {
+                                "label": "Chromeister on input dataset(s): Comparison matrix",
+                                "output_name": "output",
+                                "uuid": "5f9aad77-f9ee-4932-ab22-bb5fd83f416c"
+                            },
+                            {
+                                "label": "Chromeister on input dataset(s): Comparison score",
+                                "output_name": "output_score",
+                                "uuid": "dea450c2-7126-43dc-af7a-9f2b704c76dd"
+                            },
+                            {
+                                "label": "Chromeister on input dataset(s): Detected events plot",
+                                "output_name": "output_events_png",
+                                "uuid": "9a03f722-5588-4a3f-b70e-0ec9979c16dd"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "genome-annotation/hpc-for-lsgc",
+                "path": "topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/CHROMEISTER_chromosome_comparison.ga",
+                "tags": [
+                    "genome-annotation"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "CHROMEISTER chromosome comparison",
+                "topic_id": "genome-annotation",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-hpc-for-lsgc/versions/chromeister-chromosome-comparison",
+                "tutorial_id": "hpc-for-lsgc",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/CHROMEISTER_chromosome_comparison.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/CHROMEISTER_chromosome_comparison.html",
+                "version": 1,
+                "wfid": "genome-annotation-hpc-for-lsgc",
+                "wfname": "chromeister-chromosome-comparison",
+                "workflow": "CHROMEISTER_chromosome_comparison.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a"
+                ],
+                "workflowhub_id": "1156"
+            },
+            {
+                "creators": [],
+                "description": "A workflow designed to compare two sequences using GECKO, extract repeats and perform multiple sequence alignment",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontigs\"]\n  1[label=\"ISEScan\"]\n  0 -> 1 [label=\"output\"]\n  k2bb672cb453646b08a228590a0ca36c7[color=lightseagreen,label=\"Output\\nisescan_results\"]\n  1 -> k2bb672cb453646b08a228590a0ca36c7\n  2[label=\"PlasmidFinder\"]\n  0 -> 2 [label=\"output\"]\n  k614064e64b0f4e38b04ee3f61ba41b46[color=lightseagreen,label=\"Output\\nplasmidfinder_results\"]\n  2 -> k614064e64b0f4e38b04ee3f61ba41b46\n  3[label=\"Integron Finder\"]\n  0 -> 3 [label=\"output\"]\n  kd26788cf24414f29ac39b6be96f192eb[color=lightseagreen,label=\"Output\\nintegronfinder_summary\"]\n  3 -> kd26788cf24414f29ac39b6be96f192eb\n  4[label=\"Bakta\"]\n  0 -> 4 [label=\"output\"]\n  kd3a40a8b1bd142b6a91e756379b86d94[color=lightseagreen,label=\"Output\\nbakta_summary\"]\n  4 -> kd3a40a8b1bd142b6a91e756379b86d94\n  5[label=\"Group\"]\n  1 -> 5 [label=\"all_results\"]\n  6[label=\"Group\"]\n  1 -> 6 [label=\"all_results\"]\n  7[label=\"Replace Text\"]\n  2 -> 7 [label=\"result_file\"]\n  8[label=\"Select last\"]\n  7 -> 8 [label=\"outfile\"]\n  9[label=\"Table to GFF3\"]\n  8 -> 9 [label=\"outfile\"]\n  10[label=\"JBrowse\"]\n  0 -> 10 [label=\"output\"]\n  4 -> 10 [label=\"annotation_gff3\"]\n  9 -> 10 [label=\"output\"]\n  1 -> 10 [label=\"annotation\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nQuery sequence\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference sequence\"]\n  2[label=\"Gecko\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  k6275abc1d74e45a7b8ab3c88426cc488[color=lightseagreen,label=\"Output\\nGecko on input dataset(s): CSV\"]\n  2 -> k6275abc1d74e45a7b8ab3c88426cc488\n  3[label=\"Text reformatting\"]\n  2 -> 3 [label=\"alignments2\"]\n  4[label=\"ClustalW\"]\n  3 -> 4 [label=\"outfile\"]\n  kd63c1172a5914bf6b307052ca19e7098[color=lightseagreen,label=\"Output\\nClustalW on input dataset(s): clustal\"]\n  4 -> kd63c1172a5914bf6b307052ca19e7098\n  kd7758e3a522d44398c9a03f784284ebd[color=lightseagreen,label=\"Output\\nClustalW on input dataset(s): dnd\"]\n  4 -> kd7758e3a522d44398c9a03f784284ebd\n}",
                 "history": [
                     {
-                        "hash": "87968f9a6953ebf322d9fb0fae3a4193b6222288",
-                        "message": "Update tool versions",
+                        "hash": "ae7dbf55cc79f67b32661f650f26d5baad4779b3",
+                        "message": "added workflow for chromeister",
                         "num": 2,
-                        "short_hash": "87968f9a6",
-                        "unix": "1722510143"
+                        "short_hash": "ae7dbf55c",
+                        "unix": "1612266607"
+                    },
+                    {
+                        "hash": "42c257d5c78780b24fb384627c26488a90eeda4f",
+                        "message": "changed topic to genome-annotation",
+                        "num": 1,
+                        "short_hash": "42c257d5c",
+                        "unix": "1612264525"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Query sequence"
+                            }
+                        ],
+                        "label": "Query sequence",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 473.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 481,
+                            "right": 681,
+                            "top": 391,
+                            "width": 200,
+                            "x": 481,
+                            "y": 391
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "63490a28-7edf-4e4f-8697-5cbf621b0768",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "f1c8c4bf-126f-4c4b-8e5a-512cd0d270cd"
+                            }
+                        ]
                     },
                     {
-                        "hash": "217f251aaa898a91dbb18b5cec3daebaf582c712",
-                        "message": "Update worklow and add tests",
-                        "num": 1,
-                        "short_hash": "217f251aa",
-                        "unix": "1706526984"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "contigs",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "contigs",
-                                "name": "contigs"
+                                "description": "",
+                                "name": "Reference sequence"
                             }
                         ],
-                        "label": "contigs",
+                        "label": "Reference sequence",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 424
+                            "bottom": 598.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 482,
+                            "right": 682,
+                            "top": 516,
+                            "width": 200,
+                            "x": 482,
+                            "y": 516
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "8cde8af1-c277-4b9f-97f7-54f5997f2c5d",
-                        "when": null,
-                        "workflow_outputs": []
+                        "uuid": "f49e63f9-977e-4a1f-bf43-9a50cfa14ee3",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "0867afff-2445-4a26-b21c-2476606adb88"
+                            }
+                        ]
                     }
                 ],
-                "license": "AGPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"ISEScan\"];\n  0 -->|output| 1;\n  2bb672cb-4536-46b0-8a22-8590a0ca36c7[\"Output\\nisescan_results\"];\n  1 --> 2bb672cb-4536-46b0-8a22-8590a0ca36c7;\n  style 2bb672cb-4536-46b0-8a22-8590a0ca36c7 stroke:#2c3143,stroke-width:4px;\n  2[\"PlasmidFinder\"];\n  0 -->|output| 2;\n  614064e6-4b0f-4e38-b04e-e3f61ba41b46[\"Output\\nplasmidfinder_results\"];\n  2 --> 614064e6-4b0f-4e38-b04e-e3f61ba41b46;\n  style 614064e6-4b0f-4e38-b04e-e3f61ba41b46 stroke:#2c3143,stroke-width:4px;\n  3[\"Integron Finder\"];\n  0 -->|output| 3;\n  d26788cf-2441-4f29-ac39-b6be96f192eb[\"Output\\nintegronfinder_summary\"];\n  3 --> d26788cf-2441-4f29-ac39-b6be96f192eb;\n  style d26788cf-2441-4f29-ac39-b6be96f192eb stroke:#2c3143,stroke-width:4px;\n  4[\"Bakta\"];\n  0 -->|output| 4;\n  d3a40a8b-1bd1-42b6-a91e-756379b86d94[\"Output\\nbakta_summary\"];\n  4 --> d3a40a8b-1bd1-42b6-a91e-756379b86d94;\n  style d3a40a8b-1bd1-42b6-a91e-756379b86d94 stroke:#2c3143,stroke-width:4px;\n  5[\"Group\"];\n  1 -->|all_results| 5;\n  6[\"Group\"];\n  1 -->|all_results| 6;\n  7[\"Replace Text\"];\n  2 -->|result_file| 7;\n  8[\"Select last\"];\n  7 -->|outfile| 8;\n  9[\"Table to GFF3\"];\n  8 -->|outfile| 9;\n  10[\"JBrowse\"];\n  0 -->|output| 10;\n  4 -->|annotation_gff3| 10;\n  9 -->|output| 10;\n  1 -->|annotation| 10;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Bacterial Genome Annotation",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQuery sequence\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference sequence\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Gecko\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  6275abc1-d74e-45a7-b8ab-3c88426cc488[\"Output\\nGecko on input dataset(s): CSV\"];\n  2 --> 6275abc1-d74e-45a7-b8ab-3c88426cc488;\n  style 6275abc1-d74e-45a7-b8ab-3c88426cc488 stroke:#2c3143,stroke-width:4px;\n  3[\"Text reformatting\"];\n  2 -->|alignments2| 3;\n  4[\"ClustalW\"];\n  3 -->|outfile| 4;\n  d63c1172-a591-4bf6-b307-052ca19e7098[\"Output\\nClustalW on input dataset(s): clustal\"];\n  4 --> d63c1172-a591-4bf6-b307-052ca19e7098;\n  style d63c1172-a591-4bf6-b307-052ca19e7098 stroke:#2c3143,stroke-width:4px;\n  d7758e3a-522d-4439-8c9a-03f784284ebd[\"Output\\nClustalW on input dataset(s): dnd\"];\n  4 --> d7758e3a-522d-4439-8c9a-03f784284ebd;\n  style d7758e3a-522d-4439-8c9a-03f784284ebd stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "GECKO pairwise comparison",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 0,
-                                "output_name": "output"
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Query sequence"
                             }
+                        ],
+                        "label": "Query sequence",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 473.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 481,
+                            "right": 681,
+                            "top": 391,
+                            "width": 200,
+                            "x": 481,
+                            "y": 391
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "ISEScan",
-                        "outputs": [
-                            {
-                                "name": "summary",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "all_results",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "annotation",
-                                "type": "gff"
-                            },
-                            {
-                                "name": "is_fasta",
-                                "type": "fasta"
-                            },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "63490a28-7edf-4e4f-8697-5cbf621b0768",
+                        "workflow_outputs": [
                             {
-                                "name": "orf_fna",
-                                "type": "fasta"
-                            },
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "f1c8c4bf-126f-4c4b-8e5a-512cd0d270cd"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "orf_faa",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "Reference sequence"
                             }
                         ],
+                        "label": "Reference sequence",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 280,
-                            "top": 133
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "19f42b3ea391",
-                            "name": "isescan",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 598.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 482,
+                            "right": 682,
+                            "top": 516,
+                            "width": 200,
+                            "x": 482,
+                            "y": 516
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"log_activate\": false, \"remove_short_is\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.2.3+galaxy1",
-                        "type": "tool",
-                        "uuid": "334b327f-be00-4e75-ae01-c3ba674dbc9b",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "f49e63f9-977e-4a1f-bf43-9a50cfa14ee3",
                         "workflow_outputs": [
                             {
-                                "label": "isescan_results",
-                                "output_name": "all_results",
-                                "uuid": "2bb672cb-4536-46b0-8a22-8590a0ca36c7"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "0867afff-2445-4a26-b21c-2476606adb88"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2",
                         "errors": null,
                         "id": 2,
                         "input_connections": {
-                            "input|input_file": {
+                            "db": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "query": {
                                 "id": 0,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "PlasmidFinder",
+                        "name": "Gecko",
                         "outputs": [
                             {
-                                "name": "hit_file",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "plasmid_file",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "result_file",
-                                "type": "tabular"
+                                "name": "csv_output1",
+                                "type": "csv"
                             },
                             {
-                                "name": "raw_file",
+                                "name": "alignments2",
                                 "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 280,
-                            "top": 420
+                            "bottom": 709.8000030517578,
+                            "height": 194.8000030517578,
+                            "left": 841,
+                            "right": 1041,
+                            "top": 515,
+                            "width": 200,
+                            "x": 841,
+                            "y": 515
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "7075b7a5441b",
-                            "name": "plasmidfinder",
+                            "changeset_revision": "5efbd15675ca",
+                            "name": "gecko",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"database_name\": \"plasmidfinder_1307168_2019_08_28\"}, \"options\": {\"min_cov\": \"0.6\", \"threshold\": \"0.95\"}, \"output_files\": {\"output_selection\": [\"hit_fasta\", \"plasmid_fasta\", \"result_tsv\", \"result_txt\"]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.6+galaxy1",
+                        "tool_state": "{\"db\": {\"__class__\": \"ConnectedValue\"}, \"kmer\": \"16\", \"minlen\": \"50\", \"options\": {\"selection_mode\": \"alignments\", \"__current_case__\": 0}, \"query\": {\"__class__\": \"ConnectedValue\"}, \"similarity\": \"60\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2",
                         "type": "tool",
-                        "uuid": "484ea537-4097-4097-b19c-84fef6c7de9a",
-                        "when": null,
+                        "uuid": "217b825b-dfa8-4443-95cb-ea55dd499397",
                         "workflow_outputs": [
                             {
-                                "label": "plasmidfinder_results",
-                                "output_name": "result_file",
-                                "uuid": "614064e6-4b0f-4e38-b04e-e3f61ba41b46"
+                                "label": "Gecko on input dataset(s): CSV",
+                                "output_name": "csv_output1",
+                                "uuid": "6275abc1-d74e-45a7-b8ab-3c88426cc488"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "alignments2",
+                                "uuid": "643f73a5-9648-4b78-8b39-4643a0f4438a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
                         "errors": null,
                         "id": 3,
                         "input_connections": {
-                            "sequence": {
-                                "id": 0,
-                                "output_name": "output"
+                            "infile": {
+                                "id": 2,
+                                "output_name": "alignments2"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Integron Finder",
+                        "name": "Text reformatting",
                         "outputs": [
                             {
-                                "name": "integrons_table",
-                                "type": "tsv"
-                            },
-                            {
-                                "name": "summary",
-                                "type": "tsv"
+                                "name": "outfile",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 280,
-                            "top": 665
+                            "bottom": 740.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": 1162,
+                            "right": 1362,
+                            "top": 627,
+                            "width": 200,
+                            "x": 1162,
+                            "y": 627
                         },
                         "post_job_actions": {
-                            "ChangeDatatypeActionintegrons_table": {
+                            "ChangeDatatypeActionoutfile": {
                                 "action_arguments": {
-                                    "newtype": "tabular"
+                                    "newtype": "fasta"
                                 },
                                 "action_type": "ChangeDatatypeAction",
-                                "output_name": "integrons_table"
+                                "output_name": "outfile"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "4768f7f8e93f",
-                            "name": "integron_finder",
-                            "owner": "iuc",
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"gbk\": false, \"local_max\": true, \"no_logfile\": true, \"pdf\": false, \"promoter_attI\": true, \"sequence\": {\"__class__\": \"ConnectedValue\"}, \"settings\": {\"attc_settings\": {\"dist_thresh\": \"4000\", \"calin_threshold\": \"2\", \"max_attc_size\": \"200\", \"min_attc_size\": \"40\", \"keep_palindromes\": false, \"covar_matrix\": null}, \"protein_settings\": {\"no_proteins\": false, \"union_integrases\": false, \"func_annot\": false}}, \"topology_file\": null, \"type_replicon\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.5+galaxy0",
+                        "tool_state": "{\"code\": \"BEGIN{FS=\\\" \\\"} /@\\\\(196[0-9][0-9]/ { printf(\\\">sequence%s%s\\\\n\\\", $(NF-1), $NF); getline; while(substr($0,1,1) != \\\">\\\"){ if(substr($0,1,1) ==\\\"Y\\\"){ print $2; } getline; } } \", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.2",
                         "type": "tool",
-                        "uuid": "29a9252c-5c3b-4024-99ff-637d0572320a",
-                        "when": null,
+                        "uuid": "ac13faf0-b6dc-48fa-b5b4-31fec9a4733f",
                         "workflow_outputs": [
                             {
-                                "label": "integronfinder_summary",
-                                "output_name": "summary",
-                                "uuid": "d26788cf-2441-4f29-ac39-b6be96f192eb"
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "789a050e-0ab3-4296-b64d-9b7ad67af768"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
                         "errors": null,
                         "id": 4,
                         "input_connections": {
-                            "input_option|input_file": {
-                                "id": 0,
-                                "output_name": "output"
+                            "input": {
+                                "id": 3,
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Bakta",
+                        "name": "ClustalW",
                         "outputs": [
                             {
-                                "name": "annotation_tsv",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "annotation_gff3",
-                                "type": "gff3"
-                            },
-                            {
-                                "name": "annotation_ffn",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "summary_txt",
-                                "type": "txt"
+                                "name": "output",
+                                "type": "clustal"
                             },
                             {
-                                "name": "annotation_plot",
-                                "type": "svg"
+                                "name": "dnd",
+                                "type": "nhx"
                             }
                         ],
                         "position": {
-                            "left": 850,
-                            "top": 0
+                            "bottom": 864.8000030517578,
+                            "height": 184.8000030517578,
+                            "left": 1536,
+                            "right": 1736,
+                            "top": 680,
+                            "width": 200,
+                            "x": 1536,
+                            "y": 680
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "728dacaf08a9",
-                            "name": "bakta",
-                            "owner": "iuc",
+                            "changeset_revision": "d6694932c5e0",
+                            "name": "clustalw",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"annotation\": {\"complete\": false, \"prodigal\": null, \"translation_table\": \"11\", \"keep_contig_headers\": true, \"replicons\": null, \"compliant\": false, \"proteins\": null, \"meta\": false}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input_option\": {\"bakta_db_select\": \"V5.0_2023-02-20\", \"amrfinder_db_select\": \"amrfinderplus_V3.11_2022-12-19.1\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"min_contig_length\": null}, \"organism\": {\"genus\": null, \"species\": null, \"strain\": null, \"plasmid\": null}, \"output_files\": {\"output_selection\": [\"file_tsv\", \"file_gff3\", \"file_ffn\", \"file_plot\", \"sum_txt\"]}, \"workflow\": {\"skip_analysis\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.3+galaxy0",
+                        "tool_state": "{\"dnarna\": \"DNA\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"out_order\": \"ALIGNED\", \"outcontrol\": {\"outform\": \"clustal\", \"__current_case__\": 2, \"out_seqnos\": \"false\"}, \"range\": {\"mode\": \"complete\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1",
                         "type": "tool",
-                        "uuid": "181220e7-9082-48bc-b855-f10baf78fc2a",
-                        "when": null,
+                        "uuid": "b95c1c44-a967-47fd-a85c-3a3121163486",
                         "workflow_outputs": [
                             {
-                                "label": "bakta_summary",
-                                "output_name": "summary_txt",
-                                "uuid": "d3a40a8b-1bd1-42b6-a91e-756379b86d94"
+                                "label": "ClustalW on input dataset(s): clustal",
+                                "output_name": "output",
+                                "uuid": "d63c1172-a591-4bf6-b307-052ca19e7098"
+                            },
+                            {
+                                "label": "ClustalW on input dataset(s): dnd",
+                                "output_name": "dnd",
+                                "uuid": "d7758e3a-522d-4439-8c9a-03f784284ebd"
                             }
                         ]
                     }
                 ],
-                "parent_id": "genome-annotation/bacterial-genome-annotation",
-                "path": "topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.ga",
+                "parent_id": "genome-annotation/hpc-for-lsgc",
+                "path": "topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/GECKO_pairwise_comparison.ga",
                 "tags": [
                     "genome-annotation"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "Bacterial Genome Annotation",
+                "tests": false,
+                "title": "GECKO pairwise comparison",
                 "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-bacterial-genome-annotation/versions/bacterial-genome-annotation",
-                "tutorial_id": "bacterial-genome-annotation",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.html",
-                "version": 2,
-                "wfid": "genome-annotation-bacterial-genome-annotation",
-                "wfname": "bacterial-genome-annotation",
-                "workflow": "Bacterial-Genome-Annotation.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-hpc-for-lsgc/versions/gecko-pairwise-comparison",
+                "tutorial_id": "hpc-for-lsgc",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/GECKO_pairwise_comparison.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/GECKO_pairwise_comparison.html",
+                "version": 1,
+                "wfid": "genome-annotation-hpc-for-lsgc",
+                "wfname": "gecko-pairwise-comparison",
+                "workflow": "GECKO_pairwise_comparison.ga",
                 "workflow_tools": [
-                    "Grouping1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2"
-                ],
-                "workflowhub_id": "1136"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/10572227"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/introduction/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "gallantries",
-                    "eurosciencegateway",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
-                "fediverse_flavor": "mastodon",
-                "id": "abretaud",
-                "joined": "2017-09",
-                "location": {
-                    "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
-                },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            }
-        ],
-        "dir": "topics/genome-annotation/tutorials/introduction",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": false,
-        "id": "genome-annotation/introduction",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "layout": "introduction_slides",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "logo": "GTN",
-        "mod_date": "2024-05-31",
-        "pageviews": 5726884,
-        "priority": 1,
-        "pub_date": "2019-05-13",
-        "redirect_from": [
-            "/topics/genome-annotation/slides/introduction",
-            "/short/genome-annotation/introduction/slides",
-            "/short/S00069"
-        ],
-        "short_id": "S00069",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
-        "subtopic": "intro",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "title": "Introduction to Genome Annotation",
-        "tools": [],
-        "topic_name": "genome-annotation",
-        "topic_name_human": "Genome Annotation",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "introduction",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/introduction/slides.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/introduction/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/introduction/slides.json"
-        },
-        "version": 3,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/official-gene-set/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "abretaud"
-            ],
-            "funding": [
-                "gallantries"
-            ]
-        },
-        "contributors": [
-            {
-                "affiliations": [
-                    "gallantries",
-                    "eurosciencegateway",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
-                "fediverse_flavor": "mastodon",
-                "id": "abretaud",
-                "joined": "2017-09",
-                "location": {
-                    "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
-                },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
-            }
-        ],
-        "dir": "topics/genome-annotation/tutorials/official-gene-set",
-        "draft": true,
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "genome-annotation/official-gene-set",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Genoest' OGS Tools makes it easy to validate and release a build of your genome and its annotations."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-02-29",
-        "objectives": [
-            "Validate your genes and create an official gene set from them."
-        ],
-        "pageviews": 9,
-        "pub_date": "2023-11-02",
-        "questions": [
-            "I have several genomes assemblies that are not annotated (or I do not trust annotations)",
-            "I am interested to compare structure of a particular gene across these genome assemblies",
-            "How do I do that?"
-        ],
-        "short_id": "T00370",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "gmod",
-            "apollo2",
-            "work-in-progress"
-        ],
-        "time_estimation": "30M",
-        "title": "Creating an Official Gene Set",
-        "tools": [],
-        "topic_name": "genome-annotation",
-        "topic_name_human": "Genome Annotation",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "official-gene-set",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/official-gene-set/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/official-gene-set/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/official-gene-set/tutorial.json"
-        },
-        "version": 2,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 0,
-        "visitors": 7,
-        "zenodo_link": ""
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/genome-annotation/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "email": "anikaerxleben@gmail.com",
-                "id": "erxleben",
-                "joined": "2017-09",
-                "name": "Anika Erxleben",
-                "orcid": "0000-0002-7427-6478",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/erxleben/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/erxleben.json"
-            },
-            {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
-                    "elixir-europe"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2"
                 ],
-                "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
-                "fediverse_flavor": "mastodon",
-                "id": "bgruening",
-                "joined": "2017-09",
-                "linkedin": "bgruening",
-                "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
-                },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+                "workflowhub_id": "1160"
             }
         ],
-        "dir": "topics/genome-annotation/tutorials/genome-annotation",
-        "draft": true,
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "genome-annotation/genome-annotation",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": null,
-        "layout": "tutorial_hands_on",
-        "level": "Introductory",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": null,
-        "pageviews": 61166,
-        "pub_date": "2015-06-29",
-        "questions": null,
-        "short_id": "T00175",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "prokaryote",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "prokaryote",
-            "work-in-progress"
-        ],
-        "time_estimation": "2H",
-        "title": "Genome Annotation",
-        "tools": [],
-        "topic_name": "genome-annotation",
-        "topic_name_human": "Genome Annotation",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "genome-annotation",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/genome-annotation/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/genome-annotation/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/genome-annotation/tutorial.json"
-        },
-        "version": 16,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 85,
-        "visitors": 32874,
-        "zenodo_link": "https://doi.org/10.5281/zenodo.1250793"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.4485547"
     },
     {
         "abbreviations": {
-            "NMDS": "Non-metric multidimensional scaling"
+            "OGS": "Official Gene Set"
         },
         "admin_install": {
             "install_repository_dependencies": true,
@@ -100492,80 +101344,31 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "interproscan",
-                    "owner": "bgruening",
-                    "revisions": "74810db257cc",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "picard",
-                    "owner": "devteam",
-                    "revisions": "f9242e01365a",
-                    "tool_panel_section_label": "Picard",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "eggnog_mapper",
-                    "owner": "galaxyp",
-                    "revisions": "844fa988236b",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "aegean_parseval",
-                    "owner": "iuc",
-                    "revisions": "1b52f0c8ad7f",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "busco",
-                    "owner": "iuc",
-                    "revisions": "94170eee0ad8",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "funannotate_annotate",
-                    "owner": "iuc",
-                    "revisions": "9feee7fc49a1",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "funannotate_annotate",
-                    "owner": "iuc",
-                    "revisions": "582fd74dc2a1",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "funannotate_compare",
-                    "owner": "iuc",
-                    "revisions": "a7ce2601500c",
-                    "tool_panel_section_label": "Annotation",
+                    "name": "apollo_create_account",
+                    "owner": "gga",
+                    "revisions": "e80d29fd2a33",
+                    "tool_panel_section_label": "Apollo",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "funannotate_compare",
-                    "owner": "iuc",
-                    "revisions": "30f08d74024f",
-                    "tool_panel_section_label": "Annotation",
+                    "name": "apollo_create_or_update",
+                    "owner": "gga",
+                    "revisions": "4abaab60f9e1",
+                    "tool_panel_section_label": "Apollo",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "funannotate_predict",
-                    "owner": "iuc",
-                    "revisions": "51b6ee65ef7f",
-                    "tool_panel_section_label": "Annotation",
+                    "name": "apollo_iframe",
+                    "owner": "gga",
+                    "revisions": "f4e3f9480307",
+                    "tool_panel_section_label": "Apollo",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "funannotate_predict",
-                    "owner": "iuc",
-                    "revisions": "f31125bb85ea",
-                    "tool_panel_section_label": "Annotation",
+                    "name": "apollo_list_organism",
+                    "owner": "gga",
+                    "revisions": "2c749ed310da",
+                    "tool_panel_section_label": "Apollo",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
@@ -100574,34 +101377,17 @@
                     "revisions": "a6e57ff585c0",
                     "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "rgrnastar",
-                    "owner": "iuc",
-                    "revisions": "3ea5a2a63fa2",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "rgrnastar",
-                    "owner": "iuc",
-                    "revisions": "4074fc1940e2",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: interproscan\n  owner: bgruening\n  revisions: 74810db257cc\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: f9242e01365a\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: eggnog_mapper\n  owner: galaxyp\n  revisions: 844fa988236b\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: aegean_parseval\n  owner: iuc\n  revisions: 1b52f0c8ad7f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 94170eee0ad8\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_annotate\n  owner: iuc\n  revisions: 9feee7fc49a1\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_annotate\n  owner: iuc\n  revisions: 582fd74dc2a1\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_compare\n  owner: iuc\n  revisions: a7ce2601500c\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_compare\n  owner: iuc\n  revisions: 30f08d74024f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_predict\n  owner: iuc\n  revisions: 51b6ee65ef7f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_predict\n  owner: iuc\n  revisions: f31125bb85ea\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n  owner: iuc\n  revisions: 3ea5a2a63fa2\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n  owner: iuc\n  revisions: 4074fc1940e2\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/funannotate/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: apollo_create_account\n  owner: gga\n  revisions: e80d29fd2a33\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: apollo_create_or_update\n  owner: gga\n  revisions: 4abaab60f9e1\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: apollo_iframe\n  owner: gga\n  revisions: f4e3f9480307\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: apollo_list_organism\n  owner: gga\n  revisions: 2c749ed310da\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo/tutorial.json",
         "contributions": {
             "authorship": [
-                "abretaud"
-            ],
-            "editing": [
-                "alexcorm",
-                "lleroi",
-                "r1corre",
-                "stephanierobin"
+                "abretaud",
+                "hexylena",
+                "nathandunn",
+                "mboudet"
             ],
             "funding": [
                 "gallantries",
@@ -100635,43 +101421,55 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
             },
             {
-                "email": "alexandre.cormier@ifremer.fr",
-                "id": "alexcorm",
-                "joined": "2021-11",
-                "name": "Alexandre Cormier",
-                "orcid": "0000-0002-7775-8413",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/",
-                "twitter": "allanssx",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/alexcorm.json"
-            },
-            {
-                "email": "laura.leroi@ifremer.fr",
-                "id": "lleroi",
-                "joined": "2021-11",
-                "name": "Laura Leroi",
-                "orcid": "0000-0003-3748-4179",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lleroi/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/lleroi.json"
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
             {
-                "email": "erwan.corre@sb-roscoff.fr",
-                "id": "r1corre",
-                "joined": "2019-04",
-                "name": "Erwan Corre",
-                "orcid": "0000-0001-6354-2278",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/r1corre/",
-                "twitter": "r1corre",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/r1corre.json"
+                "email": "nathandunn@lbl.gov",
+                "id": "nathandunn",
+                "joined": "2019-07",
+                "name": "Nathan Dunn",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nathandunn/",
+                "twitter": "precogincog",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nathandunn.json"
             },
             {
-                "email": "stephanie.robin@inrae.fr",
-                "id": "stephanierobin",
-                "joined": "2021-11",
-                "name": "St\u00e9phanie Robin",
-                "orcid": "0000-0001-7379-9173",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/",
-                "twitter": "robinstphanie1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/stephanierobin.json"
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "fr",
+                "email": "mateo.boudet@inrae.fr",
+                "id": "mboudet",
+                "joined": "2021-05",
+                "name": "Mateo Boudet",
+                "orcid": "0000-0002-7028-7620",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mboudet/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mboudet.json"
             },
             {
                 "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
@@ -100721,146 +101519,117 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
             }
         ],
-        "dir": "topics/genome-annotation/tutorials/funannotate",
+        "dir": "topics/genome-annotation/tutorials/apollo",
+        "edam_ontology": [
+            "topic_0622",
+            "topic_3301",
+            "topic_0623",
+            "topic_0080"
+        ],
         "edam_operation": [
-            "Sequence motif recognition",
-            "Sequence alignment",
-            "Genome annotation",
-            "Sequence assembly validation",
-            "Homology-based gene prediction",
-            "Fold recognition",
-            "Formatting",
-            "Information extraction",
-            "Genome visualisation",
-            "Transcriptome assembly",
-            "Sequence annotation",
-            "Genome assembly",
-            "Protein feature detection",
-            "Query and retrieval",
-            "Scaffolding"
+            "Genome visualisation"
         ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)"
+        "edam_topic": [
+            "Genomics",
+            "Microbiology",
+            "Gene and protein families",
+            "Sequence analysis"
         ],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "genome-annotation",
-                "tutorials": [
-                    "apollo"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "genome-annotation/funannotate",
+        "id": "genome-annotation/apollo",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.org.au"
+            "UseGalaxy.eu",
+            "UseGalaxy.no"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Funannotate allows to perform structural annotation of an eukaryotic genome.",
-            "Functional annotation can be performed using EggNOG-mapper and InterProScan.",
-            "BUSCO and JBrowse allow to inspect the quality of an annotation.",
-            "Funannotate allows to format an annotation for sumission at NCBI."
+            "Apollo is the Google Docs of the genome annotation world, real-time collaborative genome annotation.",
+            "Apollo allows a group to view and manually refine predicted genome annotations",
+            "Use Apollo to edit annotations within your group.",
+            "Export manual annotations as GFF3."
         ],
         "layout": "tutorial_hands_on",
         "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-08-08",
         "objectives": [
-            "Load genome into Galaxy",
-            "Annotate genome with Funannotate",
-            "Perform functional annotation using EggNOG-mapper and InterProScan",
-            "Evaluate annotation quality with BUSCO",
-            "View annotations in JBrowse"
+            "Load a genome into Galaxy",
+            "View annotations in JBrowse",
+            "Learn how to load JBrowse data into Apollo",
+            "Learn how to manually refine genome annotations within Apollo",
+            "Export refined genome annotations"
         ],
-        "pageviews": 10392,
-        "priority": 2,
-        "pub_date": "2021-11-29",
+        "pageviews": 5119567,
+        "pub_date": "2021-06-04",
         "questions": [
-            "How to annotate an eukaryotic genome with Funannotate?",
-            "How to perform functional annotation?",
+            "How to visualize your genome after automated annotations have been performed?",
+            "How to manually annotate genome after automated annotations have been performed?",
             "How to evaluate and visualize annotated genomic features?",
-            "How to format the annotation for submission at NCBI?"
+            "How do I collaborate when doing genome annotation?"
         ],
         "recordings": [
             {
                 "captioners": [
                     "abretaud"
                 ],
-                "date": "2023-05-12",
-                "galaxy_version": "23.01",
-                "length": "1H10M",
-                "speakers": [
-                    "abretaud"
-                ],
-                "youtube_id": "p0NBxZk5964"
-            },
-            {
-                "captioners": [
-                    "abretaud"
-                ],
-                "date": "2022-03-03",
-                "galaxy_version": "21.09",
-                "length": "1H10M",
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "1H",
                 "speakers": [
                     "abretaud"
                 ],
-                "youtube_id": "r-wU6BhqIpk"
+                "youtube_id": "ywK1fhM-QFU"
             }
         ],
         "requirements": [
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "upload-rules"
+                ],
+                "type": "internal"
+            },
             {
                 "topic_name": "genome-annotation",
                 "tutorials": [
-                    "repeatmasker"
+                    "annotation-with-prokka"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00172",
+        "short_id": "T00169",
         "short_tools": [
             "jbrowse",
-            "busco",
-            "eggnog_mapper",
-            "picard_MergeSamFiles",
-            "funannotate_annotate",
-            "funannotate_predict",
-            "aegean_parseval",
-            "funannotate_compare",
-            "interproscan",
-            "rna_star"
+            "create_or_update",
+            "iframe",
+            "list_organism",
+            "create_account"
         ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "eukaryote",
+        "slides": true,
+        "slides_recordings": [
+            {
+                "captioners": [
+                    "abretaud"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "5M",
+                "speakers": [
+                    "awspolly"
+                ],
+                "youtube_id": "ailUycRVHtE"
+            }
+        ],
+        "subtopic": "prokaryote",
         "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
+            "exact": [],
             "inexact": [
                 {
                     "name": "UseGalaxy.cz",
@@ -100868,35 +101637,33 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
                 }
             ]
         },
         "symlink": null,
         "tags": [
             "gmod",
-            "eukaryote",
-            "jbrowse1"
+            "prokaryote",
+            "microgalaxy",
+            "jbrowse1",
+            "apollo2"
         ],
-        "time_estimation": "8h",
-        "title": "Genome annotation with Funannotate",
+        "time_estimation": "3h",
+        "title": "Refining Genome Annotations with Apollo (prokaryotes)",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy0"
+            "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_account/create_account/3.1",
+            "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
+            "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
+            "toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1"
         ],
         "topic_name": "genome-annotation",
         "topic_name_human": "Genome Annotation",
@@ -100904,847 +101671,453 @@
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": false
+            "video": true
         },
-        "tutorial_name": "funannotate",
+        "tutorial_name": "apollo",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/funannotate/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/funannotate/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/funannotate/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo/tutorial.json"
         },
-        "version": 22,
-        "video": false,
-        "video_versions": 2,
+        "version": 20,
+        "video": true,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 129,
-        "visitors": 6817,
+        "visit_duration": 299,
+        "visitors": 1906178,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0003-0914-2470",
-                        "name": "Anthony Bretaudeau"
-                    }
-                ],
-                "description": "Structural and functional genome annotation with Funannotate",
+                "creators": [],
+                "description": "Refining Genome Annotations with Apollo",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenome assembly\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nRNASeq reads forward\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nRNASeq reads reverse\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nProtein evidence sequences\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nNCBI submission template\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAlternate annotation gbk\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAlternate annotation gff3\"]\n  7[label=\"RNA STAR\"]\n  0 -> 7 [label=\"output\"]\n  1 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  k79cf59ea3aef4cb89c705b42e03a5da9[color=lightseagreen,label=\"Output\\nMapped RNASeq\"]\n  7 -> k79cf59ea3aef4cb89c705b42e03a5da9\n  8[label=\"Funannotate predict annotation\"]\n  3 -> 8 [label=\"output\"]\n  7 -> 8 [label=\"mapped_reads\"]\n  0 -> 8 [label=\"output\"]\n  9[label=\"eggNOG Mapper\"]\n  8 -> 9 [label=\"fasta_proteins\"]\n  10[label=\"InterProScan\"]\n  8 -> 10 [label=\"fasta_proteins\"]\n  11[label=\"Funannotate functional\"]\n  9 -> 11 [label=\"annotations\"]\n  8 -> 11 [label=\"annot_gbk\"]\n  10 -> 11 [label=\"outfile_xml\"]\n  4 -> 11 [label=\"output\"]\n  kd0694cd16d814d7283b994cb57dc1502[color=lightseagreen,label=\"Output\\nFinal annotation (genbank)\"]\n  11 -> kd0694cd16d814d7283b994cb57dc1502\n  k9a1e7b70109041ed863765b7372a9f6c[color=lightseagreen,label=\"Output\\nFinal annotation (CDS sequences)\"]\n  11 -> k9a1e7b70109041ed863765b7372a9f6c\n  k99fffa402196491d9a66559ebf2d9561[color=lightseagreen,label=\"Output\\nFinal annotation (mRNA sequences)\"]\n  11 -> k99fffa402196491d9a66559ebf2d9561\n  k17b03b7704854176b2b303bfa2d3bcb0[color=lightseagreen,label=\"Output\\nFinal annotation (protein sequences)\"]\n  11 -> k17b03b7704854176b2b303bfa2d3bcb0\n  k4a0602fce6d243fc9957344707c22c05[color=lightseagreen,label=\"Output\\nFinal annotation (GFF3)\"]\n  11 -> k4a0602fce6d243fc9957344707c22c05\n  12[label=\"JBrowse\"]\n  0 -> 12 [label=\"output\"]\n  11 -> 12 [label=\"gff3\"]\n  7 -> 12 [label=\"mapped_reads\"]\n  kac4d8805f12344d2b30f8ac906cc471f[color=lightseagreen,label=\"Output\\nJBrowse\"]\n  12 -> kac4d8805f12344d2b30f8ac906cc471f\n  13[label=\"Funannotate compare\"]\n  5 -> 13 [label=\"output\"]\n  11 -> 13 [label=\"gbk\"]\n  ke531c81ff6b74c82a712c562873ff714[color=lightseagreen,label=\"Output\\nFunannotate compare report\"]\n  13 -> ke531c81ff6b74c82a712c562873ff714\n  14[label=\"AEGeAn ParsEval\"]\n  6 -> 14 [label=\"output\"]\n  11 -> 14 [label=\"gff3\"]\n  k0d776b462c1c40839f9da213fa62eb81[color=lightseagreen,label=\"Output\\nAEGeAN report\"]\n  14 -> k0d776b462c1c40839f9da213fa62eb81\n  15[label=\"Busco\"]\n  11 -> 15 [label=\"fa_proteins\"]\n  k57a619f5b3314ca68e6e72eb61860032[color=lightseagreen,label=\"Output\\nBusco summary\"]\n  15 -> k57a619f5b3314ca68e6e72eb61860032\n  k97d23764ad4a4d69948cc81afb76fbaf[color=lightseagreen,label=\"Output\\nBusco image\"]\n  15 -> k97d23764ad4a4d69948cc81afb76fbaf\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager.bw\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam\"]\n  4[label=\"Register Account\"]\n  5[label=\"List Organisms\"]\n  6[label=\"JBrowse\"]\n  0 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"Create or Update Organism\"]\n  6 -> 7 [label=\"output\"]\n  8[label=\"Annotate\"]\n  7 -> 8 [label=\"output\"]\n}",
                 "history": [
                     {
-                        "hash": "ed3325d60843b30358cdb704f83ad9ea4b6c149f",
-                        "message": "update funannotate tuto",
+                        "hash": "6bc77b7441375cd57ea1d73e9fe2f80ef550891a",
+                        "message": "wf annotation",
+                        "num": 3,
+                        "short_hash": "6bc77b744",
+                        "unix": "1622101979"
+                    },
+                    {
+                        "hash": "9ced3a95cd725623c7c1f2664b0174a14cd59337",
+                        "message": "update workflow",
+                        "num": 2,
+                        "short_hash": "9ced3a95c",
+                        "unix": "1622043687"
+                    },
+                    {
+                        "hash": "32f41f6fe47606c12d4574551233e4a2583df189",
+                        "message": "rewrite bits v2",
                         "num": 1,
-                        "short_hash": "ed3325d60",
-                        "unix": "1682519007"
+                        "short_hash": "32f41f6fe",
+                        "unix": "1571055596"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "The genome sequence that you wish to annotate, in fasta format. It needs to be soft masked beforehand.",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "The genome sequence that you wish to annotate, in fasta format. It needs to be soft masked beforehand.",
-                                "name": "Genome assembly"
+                                "description": "",
+                                "name": "https://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1"
                             }
                         ],
-                        "label": "Genome assembly",
+                        "label": "https://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 7.75
+                            "bottom": 354.8999938964844,
+                            "height": 143.39999389648438,
+                            "left": 488,
+                            "right": 688,
+                            "top": 211.5,
+                            "width": 200,
+                            "x": 488,
+                            "y": 211.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "cca15c08-8dd9-424a-8260-4c02a94c2612",
-                        "workflow_outputs": []
+                        "uuid": "fa88b9bb-b87e-457b-a836-a8f1b25e520b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "82c708ee-87a4-45a2-abf0-911309e218fd"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "Some RNASeq data, forward reads, in fastq format",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Some RNASeq data, forward reads, in fastq format",
-                                "name": "RNASeq reads forward"
+                                "description": "",
+                                "name": "https://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1"
                             }
                         ],
-                        "label": "RNASeq reads forward",
+                        "label": "https://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 3.45001220703125,
-                            "top": 164.33334350585938
+                            "bottom": 527.8999938964844,
+                            "height": 143.39999389648438,
+                            "left": 510,
+                            "right": 710,
+                            "top": 384.5,
+                            "width": 200,
+                            "x": 510,
+                            "y": 384.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "6681e7b9-68f6-46e4-811f-60473d23fe0f",
-                        "workflow_outputs": []
+                        "uuid": "1afd430b-6250-4eb2-8cf2-a83adf022e4b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "cbbb4914-0c3d-4857-8c3a-f43b3f0c39f9"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "Some RNASeq data, reverse reads, in fastq format",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Some RNASeq data, reverse reads, in fastq format",
-                                "name": "RNASeq reads reverse"
+                                "description": "",
+                                "name": "https://zenodo.org/record/3270822/files/forager.bw"
                             }
                         ],
-                        "label": "RNASeq reads reverse",
+                        "label": "https://zenodo.org/record/3270822/files/forager.bw",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 6,
-                            "top": 310.6666564941406
+                            "bottom": 659.1000061035156,
+                            "height": 102.60000610351562,
+                            "left": 493,
+                            "right": 693,
+                            "top": 556.5,
+                            "width": 200,
+                            "x": 493,
+                            "y": 556.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "160023e3-250f-424d-abe5-f7e3978768f0",
-                        "workflow_outputs": []
+                        "uuid": "091ca713-0096-419c-8cb7-7e83a41aab37",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "f4c19cc0-5099-4514-af29-52a3933b28f9"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "Some protein sequences to align on the genome to help annotation",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 3,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Some protein sequences to align on the genome to help annotation",
-                                "name": "Protein evidence sequences"
+                                "description": "",
+                                "name": "https://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam"
                             }
                         ],
-                        "label": "Protein evidence sequences",
+                        "label": "https://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 7.116668701171875,
-                            "top": 441.4166564941406
+                            "bottom": 858.8999938964844,
+                            "height": 143.39999389648438,
+                            "left": 563,
+                            "right": 763,
+                            "top": 715.5,
+                            "width": 200,
+                            "x": 563,
+                            "y": 715.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "abb56aaf-5988-4fb8-a68f-0edaee00f445",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "A submission template retrieved from NCBI (generate it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/)",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
+                        "uuid": "13d26450-8b30-42d4-9822-f697217818b1",
+                        "workflow_outputs": [
                             {
-                                "description": "A submission template retrieved from NCBI (generate it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/)",
-                                "name": "NCBI submission template"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "464904cb-5608-4f5d-b282-a09be9d3dbbb"
                             }
-                        ],
-                        "label": "NCBI submission template",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 2.45001220703125,
-                            "top": 580.4833068847656
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "537f8bb4-4986-4d8d-a49b-1842dfaa739a",
-                        "workflow_outputs": []
-                    },
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager.bw\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Register Account\"];\n  5[\"List Organisms\"];\n  6[\"JBrowse\"];\n  0 -->|output| 6;\n  1 -->|output| 6;\n  3 -->|output| 6;\n  2 -->|output| 6;\n  7[\"Create or Update Organism\"];\n  6 -->|output| 7;\n  8[\"Annotate\"];\n  7 -->|output| 8;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Apollo Load Test",
+                "outputs": [
                     {
-                        "annotation": "The genbank output of an alternate annotation (for comparison)",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 5,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "The genbank output of an alternate annotation (for comparison)",
-                                "name": "Alternate annotation gbk"
+                                "description": "",
+                                "name": "https://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1"
                             }
                         ],
-                        "label": "Alternate annotation gbk",
+                        "label": "https://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 727.7333068847656
+                            "bottom": 354.8999938964844,
+                            "height": 143.39999389648438,
+                            "left": 488,
+                            "right": 688,
+                            "top": 211.5,
+                            "width": 200,
+                            "x": 488,
+                            "y": 211.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "51a62e82-d478-45c3-bcbc-f38f1fd85974",
-                        "workflow_outputs": []
+                        "uuid": "fa88b9bb-b87e-457b-a836-a8f1b25e520b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "82c708ee-87a4-45a2-abf0-911309e218fd"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "The gff3 output of an alternate annotation (for comparison)",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 6,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "The gff3 output of an alternate annotation (for comparison)",
-                                "name": "Alternate annotation gff3"
+                                "description": "",
+                                "name": "https://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1"
                             }
                         ],
-                        "label": "Alternate annotation gff3",
+                        "label": "https://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0.4666748046875,
-                            "top": 845.7500305175781
+                            "bottom": 527.8999938964844,
+                            "height": 143.39999389648438,
+                            "left": 510,
+                            "right": 710,
+                            "top": 384.5,
+                            "width": 200,
+                            "x": 510,
+                            "y": 384.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "e4367779-3fc7-4eec-8e45-86158b3950bc",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGenome assembly\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nRNASeq reads forward\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nRNASeq reads reverse\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nProtein evidence sequences\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nNCBI submission template\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nAlternate annotation gbk\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nAlternate annotation gff3\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"RNA STAR\"];\n  0 -->|output| 7;\n  1 -->|output| 7;\n  2 -->|output| 7;\n  79cf59ea-3aef-4cb8-9c70-5b42e03a5da9[\"Output\\nMapped RNASeq\"];\n  7 --> 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9;\n  style 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9 stroke:#2c3143,stroke-width:4px;\n  8[\"Funannotate predict annotation\"];\n  3 -->|output| 8;\n  7 -->|mapped_reads| 8;\n  0 -->|output| 8;\n  9[\"eggNOG Mapper\"];\n  8 -->|fasta_proteins| 9;\n  10[\"InterProScan\"];\n  8 -->|fasta_proteins| 10;\n  11[\"Funannotate functional\"];\n  9 -->|annotations| 11;\n  8 -->|annot_gbk| 11;\n  10 -->|outfile_xml| 11;\n  4 -->|output| 11;\n  d0694cd1-6d81-4d72-83b9-94cb57dc1502[\"Output\\nFinal annotation (genbank)\"];\n  11 --> d0694cd1-6d81-4d72-83b9-94cb57dc1502;\n  style d0694cd1-6d81-4d72-83b9-94cb57dc1502 stroke:#2c3143,stroke-width:4px;\n  9a1e7b70-1090-41ed-8637-65b7372a9f6c[\"Output\\nFinal annotation (CDS sequences)\"];\n  11 --> 9a1e7b70-1090-41ed-8637-65b7372a9f6c;\n  style 9a1e7b70-1090-41ed-8637-65b7372a9f6c stroke:#2c3143,stroke-width:4px;\n  99fffa40-2196-491d-9a66-559ebf2d9561[\"Output\\nFinal annotation (mRNA sequences)\"];\n  11 --> 99fffa40-2196-491d-9a66-559ebf2d9561;\n  style 99fffa40-2196-491d-9a66-559ebf2d9561 stroke:#2c3143,stroke-width:4px;\n  17b03b77-0485-4176-b2b3-03bfa2d3bcb0[\"Output\\nFinal annotation (protein sequences)\"];\n  11 --> 17b03b77-0485-4176-b2b3-03bfa2d3bcb0;\n  style 17b03b77-0485-4176-b2b3-03bfa2d3bcb0 stroke:#2c3143,stroke-width:4px;\n  4a0602fc-e6d2-43fc-9957-344707c22c05[\"Output\\nFinal annotation (GFF3)\"];\n  11 --> 4a0602fc-e6d2-43fc-9957-344707c22c05;\n  style 4a0602fc-e6d2-43fc-9957-344707c22c05 stroke:#2c3143,stroke-width:4px;\n  12[\"JBrowse\"];\n  0 -->|output| 12;\n  11 -->|gff3| 12;\n  7 -->|mapped_reads| 12;\n  ac4d8805-f123-44d2-b30f-8ac906cc471f[\"Output\\nJBrowse\"];\n  12 --> ac4d8805-f123-44d2-b30f-8ac906cc471f;\n  style ac4d8805-f123-44d2-b30f-8ac906cc471f stroke:#2c3143,stroke-width:4px;\n  13[\"Funannotate compare\"];\n  5 -->|output| 13;\n  11 -->|gbk| 13;\n  e531c81f-f6b7-4c82-a712-c562873ff714[\"Output\\nFunannotate compare report\"];\n  13 --> e531c81f-f6b7-4c82-a712-c562873ff714;\n  style e531c81f-f6b7-4c82-a712-c562873ff714 stroke:#2c3143,stroke-width:4px;\n  14[\"AEGeAn ParsEval\"];\n  6 -->|output| 14;\n  11 -->|gff3| 14;\n  0d776b46-2c1c-4083-9f9d-a213fa62eb81[\"Output\\nAEGeAN report\"];\n  14 --> 0d776b46-2c1c-4083-9f9d-a213fa62eb81;\n  style 0d776b46-2c1c-4083-9f9d-a213fa62eb81 stroke:#2c3143,stroke-width:4px;\n  15[\"Busco\"];\n  11 -->|fa_proteins| 15;\n  57a619f5-b331-4ca6-8e6e-72eb61860032[\"Output\\nBusco summary\"];\n  15 --> 57a619f5-b331-4ca6-8e6e-72eb61860032;\n  style 57a619f5-b331-4ca6-8e6e-72eb61860032 stroke:#2c3143,stroke-width:4px;\n  97d23764-ad4a-4d69-948c-c81afb76fbaf[\"Output\\nBusco image\"];\n  15 --> 97d23764-ad4a-4d69-948c-c81afb76fbaf;\n  style 97d23764-ad4a-4d69-948c-c81afb76fbaf stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Funannotate",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "refGenomeSource|genomeFastaFiles": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "singlePaired|input1": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "singlePaired|input2": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool RNA STAR",
-                                "name": "refGenomeSource"
-                            },
-                            {
-                                "description": "runtime parameter for tool RNA STAR",
-                                "name": "singlePaired"
-                            },
-                            {
-                                "description": "runtime parameter for tool RNA STAR",
-                                "name": "singlePaired"
-                            }
-                        ],
-                        "label": null,
-                        "name": "RNA STAR",
-                        "outputs": [
-                            {
-                                "name": "output_log",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "splice_junctions",
-                                "type": "interval"
-                            },
-                            {
-                                "name": "mapped_reads",
-                                "type": "bam"
-                            }
-                        ],
-                        "position": {
-                            "left": 766.699951171875,
-                            "top": 239.0
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionoutput_log": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_log"
-                            },
-                            "HideDatasetActionsplice_junctions": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "splice_junctions"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3ea5a2a63fa2",
-                            "name": "rgrnastar",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"algo\": {\"params\": {\"settingsType\": \"default\", \"__current_case__\": 0}}, \"chimOutType\": \"\", \"filter\": {\"basic_filters\": [\"exclude_unmapped\"], \"output_params2\": {\"output_select2\": \"no\", \"__current_case__\": 1}}, \"oformat\": {\"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"ch\"], \"HI_offset\": \"1\", \"outSAMprimaryFlag\": \"OneBestScore\", \"outSAMmapqUnique\": \"60\"}, \"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"perf\": {\"outBAMsortingBinsN\": \"50\", \"winAnchorMultimapNmax\": \"50\"}, \"refGenomeSource\": {\"geneSource\": \"history\", \"__current_case__\": 1, \"genomeFastaFiles\": {\"__class__\": \"RuntimeValue\"}, \"genomeSAindexNbases\": \"11\", \"GTFconditional\": {\"GTFselect\": \"without-gtf\", \"__current_case__\": 1, \"quantmode_output\": {\"quantMode\": \"-\", \"__current_case__\": 0}}}, \"singlePaired\": {\"sPaired\": \"paired\", \"__current_case__\": 1, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"input2\": {\"__class__\": \"RuntimeValue\"}}, \"twopass\": {\"twopassMode\": \"None\", \"__current_case__\": 0, \"twopass_read_subset\": \"\", \"sj_precalculated\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.7.10b+galaxy3",
-                        "type": "tool",
-                        "uuid": "269a3794-e421-4826-a5de-8a328fd194bd",
+                        "uuid": "1afd430b-6250-4eb2-8cf2-a83adf022e4b",
                         "workflow_outputs": [
                             {
-                                "label": "Mapped RNASeq",
-                                "output_name": "mapped_reads",
-                                "uuid": "79cf59ea-3aef-4cb8-9c70-5b42e03a5da9"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "cbbb4914-0c3d-4857-8c3a-f43b3f0c39f9"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "evidences|prot_evidence|protein_evidence": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "evidences|rna_bam": {
-                                "id": 7,
-                                "output_name": "mapped_reads"
-                            },
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
+                        "id": 2,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "database"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "evidences"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "evidences"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "genemark"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "genemark"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "input"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "other_predictors"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "other_predictors"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "other_predictors"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "other_predictors"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "parameters"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Funannotate predict annotation",
-                        "outputs": [
-                            {
-                                "name": "annot_gbk",
-                                "type": "genbank"
-                            },
-                            {
-                                "name": "annot_tbl",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "annot_gff3",
-                                "type": "gff3"
-                            },
-                            {
-                                "name": "fasta_proteins",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "fasta_transcripts_mrna",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "fasta_transcripts_cds",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "tbl2asn_report",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "tbl2asn_error",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "tbl2asn_validation",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "stats",
-                                "type": "json"
+                                "description": "",
+                                "name": "https://zenodo.org/record/3270822/files/forager.bw"
                             }
                         ],
+                        "label": "https://zenodo.org/record/3270822/files/forager.bw",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1055.2666015625,
-                            "top": 65.88333129882812
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionannot_gbk": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "annot_gbk"
-                            },
-                            "HideDatasetActionannot_gff3": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "annot_gff3"
-                            },
-                            "HideDatasetActionannot_tbl": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "annot_tbl"
-                            },
-                            "HideDatasetActionfasta_transcripts_cds": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "fasta_transcripts_cds"
-                            },
-                            "HideDatasetActionfasta_transcripts_mrna": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "fasta_transcripts_mrna"
-                            },
-                            "HideDatasetActionstats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "stats"
-                            },
-                            "HideDatasetActiontbl2asn_error": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "tbl2asn_error"
-                            },
-                            "HideDatasetActiontbl2asn_report": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "tbl2asn_report"
-                            },
-                            "HideDatasetActiontbl2asn_validation": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "tbl2asn_validation"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "51b6ee65ef7f",
-                            "name": "funannotate_predict",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 659.1000061035156,
+                            "height": 102.60000610351562,
+                            "left": 493,
+                            "right": 693,
+                            "top": 556.5,
+                            "width": 200,
+                            "x": 493,
+                            "y": 556.5
                         },
-                        "tool_state": "{\"augustus\": {\"augustus_species\": \"none\", \"min_training_models\": \"200\", \"optimize_augustus\": \"false\"}, \"busco\": {\"busco_db\": \"mucorales_odb10\", \"busco_seed_species\": \"rhizopus_oryzae\"}, \"database\": {\"__class__\": \"RuntimeValue\"}, \"evidences\": {\"rna_bam\": {\"__class__\": \"RuntimeValue\"}, \"transcript_evidence\": {\"__class__\": \"RuntimeValue\"}, \"prot_evidence\": {\"prot_evidence_source\": \"custom\", \"__current_case__\": 1, \"protein_evidence\": {\"__class__\": \"RuntimeValue\"}}, \"p2g_pident\": \"80\", \"p2g_prefilter\": \"diamond\"}, \"evm\": {\"repeats2evm\": \"false\", \"evm_partitioning\": {\"evm_partition\": \"yes\", \"__current_case__\": 0, \"evm_partition_interval\": \"1500\"}, \"weights\": \"\"}, \"filtering\": {\"min_intronlen\": \"10\", \"max_intronlen\": \"3000\", \"min_protlen\": \"50\", \"keep_no_stops\": \"false\", \"repeat_filter\": \"overlap blast\"}, \"force\": \"true\", \"genemark\": {\"genemark_license\": {\"__class__\": \"RuntimeValue\"}, \"genemark_mode\": \"ES\", \"genemark_mod\": {\"__class__\": \"RuntimeValue\"}, \"soft_mask\": \"2000\"}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"organism\": {\"species\": \"Mucor mucedo\", \"isolate\": \"\", \"strain\": \"muc1\", \"organism\": \"false\", \"ploidy\": \"1\", \"SeqCenter\": \"CFMR\", \"SeqAccession\": \"12345\", \"name\": \"FUN_\", \"numbering\": \"1\"}, \"other_predictors\": {\"stringtie\": {\"__class__\": \"RuntimeValue\"}, \"maker_gff\": {\"__class__\": \"RuntimeValue\"}, \"pasa_gff\": {\"__class__\": \"RuntimeValue\"}, \"pasa_gff_weight\": \"1\", \"other_gff\": {\"__class__\": \"RuntimeValue\"}, \"other_gff_weight\": \"1\"}, \"outputs\": [\"gbk\", \"tbl\", \"gff3\", \"proteins_fa\", \"mrna_transcripts_fa\", \"cds_transcripts_fa\", \"tbl2asn_report\", \"tbl2asn_error\", \"tbl2asn_validation\", \"stats\"], \"parameters\": {\"__class__\": \"RuntimeValue\"}, \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.15+galaxy0",
-                        "type": "tool",
-                        "uuid": "aefc0275-b611-4ede-9650-2e16553a7352",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "091ca713-0096-419c-8cb7-7e83a41aab37",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "fasta_proteins",
-                                "uuid": "aa7fb986-b7db-4353-a83b-3f1591911388"
+                                "output_name": "output",
+                                "uuid": "f4c19cc0-5099-4514-af29-52a3933b28f9"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
+                        "content_id": null,
                         "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "ortho_method|input": {
-                                "id": 8,
-                                "output_name": "fasta_proteins"
-                            }
-                        },
+                        "id": 3,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool eggNOG Mapper",
-                                "name": "ortho_method"
-                            }
-                        ],
-                        "label": null,
-                        "name": "eggNOG Mapper",
-                        "outputs": [
-                            {
-                                "name": "seed_orthologs",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "annotations",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "https://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam"
                             }
                         ],
+                        "label": "https://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1444.9666748046875,
-                            "top": 418.7333068847656
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionseed_orthologs": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "seed_orthologs"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9d1fbff733cf",
-                            "name": "eggnog_mapper",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 858.8999938964844,
+                            "height": 143.39999389648438,
+                            "left": 563,
+                            "right": 763,
+                            "top": 715.5,
+                            "width": 200,
+                            "x": 563,
+                            "y": 715.5
                         },
-                        "tool_state": "{\"annotation_options\": {\"no_annot\": \"\", \"__current_case__\": 0, \"seed_ortholog_evalue\": \"0.001\", \"seed_ortholog_score\": null, \"tax_scope\": null, \"target_orthologs\": \"all\", \"go_evidence\": \"non-electronic\"}, \"eggnog_data\": \"5.0.2\", \"ortho_method\": {\"m\": \"diamond\", \"__current_case__\": 0, \"input\": {\"__class__\": \"RuntimeValue\"}, \"input_trans\": {\"itype\": \"proteins\", \"__current_case__\": 0}, \"matrix_gapcosts\": {\"matrix\": \"BLOSUM62\", \"__current_case__\": 2, \"gap_costs\": \"--gapopen 11 --gapextend 1\"}, \"sensmode\": \"sensitive\", \"dmnd_iterate\": \"false\", \"dmnd_ignore_warnings\": \"false\", \"query_cover\": null, \"subject_cover\": null, \"pident\": null, \"evalue\": null, \"score\": \"0.001\"}, \"output_options\": {\"no_file_comments\": \"false\", \"report_orthologs\": \"false\", \"md5\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.8+galaxy3",
-                        "type": "tool",
-                        "uuid": "0d9f93f0-88b3-406b-b8f9-ecb2d74c61e9",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "13d26450-8b30-42d4-9822-f697217818b1",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "annotations",
-                                "uuid": "521fe026-4958-4965-9414-e7074aea7860"
+                                "output_name": "output",
+                                "uuid": "464904cb-5608-4f5d-b282-a09be9d3dbbb"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_account/create_account/3.1",
                         "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "input": {
-                                "id": 8,
-                                "output_name": "fasta_proteins"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool InterProScan",
-                                "name": "input"
-                            }
-                        ],
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [],
                         "label": null,
-                        "name": "InterProScan",
+                        "name": "Register Account",
                         "outputs": [
                             {
-                                "name": "outfile_tsv",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "outfile_xml",
-                                "type": "xml"
+                                "name": "output",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 1475.8499755859375,
-                            "top": 817.8666687011719
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionoutfile_xml": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "outfile_xml"
-                            }
+                            "bottom": 1038.6999969482422,
+                            "height": 82.19999694824219,
+                            "left": 644,
+                            "right": 844,
+                            "top": 956.5,
+                            "width": 200,
+                            "x": 644,
+                            "y": 956.5
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_account/create_account/3.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "74810db257cc",
-                            "name": "interproscan",
-                            "owner": "bgruening",
+                            "changeset_revision": "e80d29fd2a33",
+                            "name": "apollo_create_account",
+                            "owner": "gga",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"applications\": [\"TIGRFAM\", \"SFLD\", \"SUPERFAMILY\", \"PANTHER\", \"Gene3D\", \"Hamap\", \"PrositeProfiles\", \"Coils\", \"SMART\", \"CDD\", \"PRINTS\", \"PIRSR\", \"PrositePatterns\", \"Pfam\", \"MobiDBLite\", \"PIRSF\"], \"database\": \"5.59-91.0\", \"goterms\": \"true\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"iprlookup\": \"false\", \"licensed\": {\"use\": \"true\", \"__current_case__\": 1, \"applications_licensed\": [\"Phobius\", \"SignalP_EUK\", \"TMHMM\"]}, \"oformat\": [\"TSV\", \"XML\"], \"pathways\": \"true\", \"seqtype\": \"p\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.59-91.0+galaxy3",
+                        "tool_state": "{\"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"first\": \"Nathan\", \"last\": \"Dunn\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1",
                         "type": "tool",
-                        "uuid": "cb7a1910-3c31-47d9-835b-f1bd16a1c3ff",
+                        "uuid": "82f0b666-8743-4cdc-9682-feb10c35b0c6",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile_tsv",
-                                "uuid": "65e267a7-d3c6-410d-9b44-f655d70d7d9a"
+                                "output_name": "output",
+                                "uuid": "dc1e2c2f-c566-48e0-95c7-327adb229fb5"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1",
                         "errors": null,
-                        "id": 11,
-                        "input_connections": {
-                            "eggnog": {
-                                "id": 9,
-                                "output_name": "annotations"
-                            },
-                            "input|genbank": {
-                                "id": 8,
-                                "output_name": "annot_gbk"
-                            },
-                            "iprscan": {
-                                "id": 10,
-                                "output_name": "outfile_xml"
-                            },
-                            "sbt": {
-                                "id": 4,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "annotations"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "antismash"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "database"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "eggnog"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "fix"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "input"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "iprscan"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "phobius"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "remove"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "sbt"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Funannotate functional",
-                        "outputs": [
-                            {
-                                "name": "gbk",
-                                "type": "genbank"
-                            },
-                            {
-                                "name": "annot",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "contigs_fsa",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "agp",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "tbl",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "sqn",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "fa_scaffolds",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "fa_proteins",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "fa_transcripts_mrna",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "fa_transcripts_cds",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "gff3",
-                                "type": "gff3"
-                            },
-                            {
-                                "name": "tbl2asn_report",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "stats",
-                                "type": "json"
-                            },
-                            {
-                                "name": "must_fix",
-                                "type": "json"
-                            },
-                            {
-                                "name": "need_curating",
-                                "type": "json"
-                            },
+                        "id": 5,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": null,
+                        "name": "List Organisms",
+                        "outputs": [
                             {
-                                "name": "new_names_passed",
+                                "name": "output",
                                 "type": "json"
                             }
                         ],
                         "position": {
-                            "left": 1877.11669921875,
-                            "top": 101.59999084472656
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionagp": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "agp"
-                            },
-                            "HideDatasetActionannot": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "annot"
-                            },
-                            "HideDatasetActioncontigs_fsa": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "contigs_fsa"
-                            },
-                            "HideDatasetActionfa_scaffolds": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "fa_scaffolds"
-                            },
-                            "HideDatasetActionmust_fix": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "must_fix"
-                            },
-                            "HideDatasetActionneed_curating": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "need_curating"
-                            },
-                            "HideDatasetActionnew_names_passed": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "new_names_passed"
-                            },
-                            "HideDatasetActionsqn": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "sqn"
-                            },
-                            "HideDatasetActiontbl": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "tbl"
-                            }
+                            "bottom": 1158.6999969482422,
+                            "height": 82.19999694824219,
+                            "left": 644,
+                            "right": 844,
+                            "top": 1076.5,
+                            "width": 200,
+                            "x": 644,
+                            "y": 1076.5
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "9feee7fc49a1",
-                            "name": "funannotate_annotate",
-                            "owner": "iuc",
+                            "changeset_revision": "2c749ed310da",
+                            "name": "apollo_list_organism",
+                            "owner": "gga",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"annotations\": {\"__class__\": \"RuntimeValue\"}, \"antismash\": {\"__class__\": \"RuntimeValue\"}, \"busco_db\": \"mucorales_odb10\", \"database\": {\"__class__\": \"RuntimeValue\"}, \"eggnog\": {\"__class__\": \"RuntimeValue\"}, \"fix\": {\"__class__\": \"RuntimeValue\"}, \"input\": {\"input_type\": \"gbk\", \"__current_case__\": 0, \"genbank\": {\"__class__\": \"RuntimeValue\"}}, \"iprscan\": {\"__class__\": \"RuntimeValue\"}, \"isolate\": \"\", \"outputs\": [\"gbk\", \"annotations\", \"contigs_fsa\", \"agp\", \"tbl\", \"sqn\", \"scaffolds_fa\", \"proteins_fa\", \"mrna_transcripts_fa\", \"cds_transcripts_fa\", \"gff3\", \"discrepency\", \"stats\", \"must_fix\", \"need_curating\", \"new_names_passed\"], \"phobius\": {\"__class__\": \"RuntimeValue\"}, \"remove\": {\"__class__\": \"RuntimeValue\"}, \"rename\": \"\", \"sbt\": {\"__class__\": \"RuntimeValue\"}, \"strain\": \"muc1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.15+galaxy0",
+                        "tool_state": "{\"chromInfo\": \"\\\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
+                        "tool_version": "3.1",
                         "type": "tool",
-                        "uuid": "e07de1e0-8f91-4477-b951-7d97dba2e397",
+                        "uuid": "3fc26308-b331-4286-863a-d31ac5b6fb03",
                         "workflow_outputs": [
-                            {
-                                "label": "Final annotation (genbank)",
-                                "output_name": "gbk",
-                                "uuid": "d0694cd1-6d81-4d72-83b9-94cb57dc1502"
-                            },
-                            {
-                                "label": "Final annotation (CDS sequences)",
-                                "output_name": "fa_transcripts_cds",
-                                "uuid": "9a1e7b70-1090-41ed-8637-65b7372a9f6c"
-                            },
-                            {
-                                "label": "Final annotation (mRNA sequences)",
-                                "output_name": "fa_transcripts_mrna",
-                                "uuid": "99fffa40-2196-491d-9a66-559ebf2d9561"
-                            },
-                            {
-                                "label": "Final annotation (protein sequences)",
-                                "output_name": "fa_proteins",
-                                "uuid": "17b03b77-0485-4176-b2b3-03bfa2d3bcb0"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "tbl2asn_report",
-                                "uuid": "d3d4daec-75fe-4071-af37-c2907e46f5c1"
-                            },
                             {
                                 "label": null,
-                                "output_name": "stats",
-                                "uuid": "4a682ab6-8a6f-4a0f-bb0e-ba796f587ddc"
-                            },
-                            {
-                                "label": "Final annotation (GFF3)",
-                                "output_name": "gff3",
-                                "uuid": "4a0602fc-e6d2-43fc-9957-344707c22c05"
+                                "output_name": "output",
+                                "uuid": "d7cc17cb-e3e2-4adf-857c-8d3583e57fdd"
                             }
                         ]
                     },
@@ -101752,19 +102125,23 @@
                         "annotation": "",
                         "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
                         "errors": null,
-                        "id": 12,
+                        "id": 6,
                         "input_connections": {
                             "reference_genome|genome": {
                                 "id": 0,
                                 "output_name": "output"
                             },
                             "track_groups_0|data_tracks_0|data_format|annotation": {
-                                "id": 11,
-                                "output_name": "gff3"
+                                "id": 1,
+                                "output_name": "output"
                             },
                             "track_groups_1|data_tracks_0|data_format|annotation": {
-                                "id": 7,
-                                "output_name": "mapped_reads"
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "track_groups_1|data_tracks_1|data_format|annotation": {
+                                "id": 2,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [
@@ -101782,8 +102159,14 @@
                             }
                         ],
                         "position": {
-                            "left": 2152.60009765625,
-                            "top": 0.0
+                            "bottom": 650.2999877929688,
+                            "height": 306.79998779296875,
+                            "left": 821,
+                            "right": 1021,
+                            "top": 343.5,
+                            "width": 200,
+                            "x": 821,
+                            "y": 343.5
                         },
                         "post_job_actions": {},
                         "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
@@ -101793,230 +102176,162 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 1, \"category\": \"RNASeq\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"auto_snp\": \"true\", \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"true\", \"track_groups\": [{\"__index__\": 0, \"category\": \"OGS 3.2\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_on\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 1, \"category\": \"Reads\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"auto_snp\": \"true\", \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 4, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"xyplot\": \"false\", \"var_band\": \"false\", \"scaling\": {\"scale_select\": \"auto_local\", \"__current_case__\": 0}, \"scale_select2\": \"linear\", \"MultiBigWig\": \"false\", \"jbcolor\": {\"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}, \"bicolor_pivot\": {\"bicolor_pivot_select\": \"zero\", \"__current_case__\": 0}}, \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.16.11+galaxy1",
                         "type": "tool",
-                        "uuid": "e6d0e687-1a13-482b-a00a-28c7304d59ac",
+                        "uuid": "2e2723bf-9597-4c96-9980-33220e3b849a",
                         "workflow_outputs": [
                             {
-                                "label": "JBrowse",
+                                "label": null,
                                 "output_name": "output",
-                                "uuid": "ac4d8805-f123-44d2-b30f-8ac906cc471f"
+                                "uuid": "9514c32e-2376-44ee-b368-beb25bf77ad7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
                         "errors": null,
-                        "id": 13,
+                        "id": 7,
                         "input_connections": {
-                            "input": [
-                                {
-                                    "id": 5,
-                                    "output_name": "output"
-                                },
-                                {
-                                    "id": 11,
-                                    "output_name": "gbk"
-                                }
-                            ]
+                            "jbrowse": {
+                                "id": 6,
+                                "output_name": "output"
+                            }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Funannotate compare",
-                                "name": "database"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate compare",
-                                "name": "proteinortho"
+                                "description": "runtime parameter for tool Create or Update Organism",
+                                "name": "jbrowse"
                             }
                         ],
                         "label": null,
-                        "name": "Funannotate compare",
+                        "name": "Create or Update Organism",
                         "outputs": [
                             {
                                 "name": "output",
-                                "type": "html"
+                                "type": "json"
                             }
                         ],
                         "position": {
-                            "left": 2318,
-                            "top": 403.7333068847656
+                            "bottom": 506.1000061035156,
+                            "height": 113.60000610351562,
+                            "left": 1405,
+                            "right": 1605,
+                            "top": 392.5,
+                            "width": 200,
+                            "x": 1405,
+                            "y": 392.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
                         "tool_shed_repository": {
-                            "changeset_revision": "a7ce2601500c",
-                            "name": "funannotate_compare",
-                            "owner": "iuc",
+                            "changeset_revision": "4abaab60f9e1",
+                            "name": "apollo_create_or_update",
+                            "owner": "gga",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"database\": {\"__class__\": \"RuntimeValue\"}, \"go_fdr\": \"0.05\", \"heatmap_stdev\": \"1.0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"ml\": {\"ml_method\": \"iqtree\", \"__current_case__\": 0}, \"num_orthos\": \"500\", \"proteinortho\": {\"__class__\": \"RuntimeValue\"}, \"run_dnds\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.15+galaxy0",
+                        "tool_state": "{\"genus\": \"Apis\", \"group\": null, \"jbrowse\": {\"__class__\": \"RuntimeValue\"}, \"no_reload_sequences\": \"false\", \"org_source\": {\"source_select\": \"direct\", \"__current_case__\": 1, \"org_raw\": \"Honeybee\"}, \"public\": \"true\", \"remove_old_directory\": \"true\", \"species\": \"Mellifera\", \"test_hack\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.2.5",
                         "type": "tool",
-                        "uuid": "750137e5-2cac-4bec-8337-03dab562a7a5",
+                        "uuid": "72c53f14-4e91-40c1-a4e9-325b6c2a3105",
                         "workflow_outputs": [
                             {
-                                "label": "Funannotate compare report",
+                                "label": null,
                                 "output_name": "output",
-                                "uuid": "e531c81f-f6b7-4c82-a712-c562873ff714"
+                                "uuid": "10c77447-f92c-44b0-8a04-151eef670244"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
                         "errors": null,
-                        "id": 14,
+                        "id": 8,
                         "input_connections": {
-                            "predictiongff3": {
-                                "id": 6,
+                            "json_file": {
+                                "id": 7,
                                 "output_name": "output"
-                            },
-                            "referencegff3": {
-                                "id": 11,
-                                "output_name": "gff3"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "AEGeAn ParsEval",
-                        "outputs": [
-                            {
-                                "name": "output_html",
-                                "type": "html"
-                            }
-                        ],
-                        "position": {
-                            "left": 2318.5,
-                            "top": 643.7333068847656
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "1b52f0c8ad7f",
-                            "name": "aegean_parseval",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"delta\": \"0\", \"maxtrans\": \"32\", \"output_type\": \"html\", \"predictiongff3\": {\"__class__\": \"ConnectedValue\"}, \"predlabel\": \"\", \"referencegff3\": {\"__class__\": \"ConnectedValue\"}, \"refrlabel\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.16.0",
-                        "type": "tool",
-                        "uuid": "b5870c4b-d799-4da0-83cc-7dd5a0b049e4",
-                        "workflow_outputs": [
-                            {
-                                "label": "AEGeAN report",
-                                "output_name": "output_html",
-                                "uuid": "0d776b46-2c1c-4083-9f9d-a213fa62eb81"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0",
-                        "errors": null,
-                        "id": 15,
-                        "input_connections": {
-                            "input": {
-                                "id": 11,
-                                "output_name": "fa_proteins"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Busco",
-                                "name": "input"
+                                "description": "runtime parameter for tool Annotate",
+                                "name": "json_file"
                             }
                         ],
                         "label": null,
-                        "name": "Busco",
+                        "name": "Annotate",
                         "outputs": [
                             {
-                                "name": "busco_sum",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "busco_table",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "summary_image",
-                                "type": "png"
+                                "name": "output",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 2252.2666015625,
-                            "top": 1072.0666809082031
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionbusco_table": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "busco_table"
-                            }
+                            "bottom": 502.6999969482422,
+                            "height": 93.19999694824219,
+                            "left": 1703,
+                            "right": 1903,
+                            "top": 409.5,
+                            "width": 200,
+                            "x": 1703,
+                            "y": 409.5
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
                         "tool_shed_repository": {
-                            "changeset_revision": "94170eee0ad8",
-                            "name": "busco",
-                            "owner": "iuc",
+                            "changeset_revision": "f4e3f9480307",
+                            "name": "apollo_iframe",
+                            "owner": "gga",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\"}, \"busco_mode\": {\"mode\": \"prot\", \"__current_case__\": 2}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": \"mucorales_odb10\"}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"image\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.4.6+galaxy0",
+                        "tool_state": "{\"json_file\": {\"__class__\": \"RuntimeValue\"}, \"tracklist\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.2.5",
                         "type": "tool",
-                        "uuid": "bec3d4d9-88e6-4ea0-beb6-219d5c727290",
+                        "uuid": "2cfe94b1-f9cb-4df6-a3fd-b9356ea2423f",
                         "workflow_outputs": [
                             {
-                                "label": "Busco summary",
-                                "output_name": "busco_sum",
-                                "uuid": "57a619f5-b331-4ca6-8e6e-72eb61860032"
-                            },
-                            {
-                                "label": "Busco image",
-                                "output_name": "summary_image",
-                                "uuid": "97d23764-ad4a-4d69-948c-c81afb76fbaf"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "4eaf137c-b5fd-4cdd-9fa7-ed973e2302f3"
                             }
                         ]
                     }
                 ],
-                "parent_id": "genome-annotation/funannotate",
-                "path": "topics/genome-annotation/tutorials/funannotate/workflows/funannotate.ga",
+                "parent_id": "genome-annotation/apollo",
+                "path": "topics/genome-annotation/tutorials/apollo/workflows/main_workflow.ga",
                 "tags": [
                     "genome-annotation"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "Funannotate",
+                "tests": false,
+                "title": "Apollo Load Test",
                 "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-funannotate/versions/funannotate",
-                "tutorial_id": "funannotate",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/funannotate/workflows/funannotate.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/funannotate/workflows/funannotate.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-apollo/versions/main-workflow",
+                "tutorial_id": "apollo",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/apollo/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/apollo/workflows/main_workflow.html",
                 "version": 1,
-                "wfid": "genome-annotation-funannotate",
-                "wfname": "funannotate",
-                "workflow": "funannotate.ga",
+                "wfid": "genome-annotation-apollo",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3"
+                    "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_account/create_account/3.1",
+                    "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
+                    "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
+                    "toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1"
                 ],
-                "workflowhub_id": "1202"
+                "workflowhub_id": "1190"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/7867921"
+        "zenodo_link": "https://zenodo.org/record/4889110"
     },
     {
         "abbreviations": {
-            "ORF": "Open Reading Frame"
+            "LINEs": "Long Interspersed Nuclear Elements",
+            "SINEs": "Short Interspersed Nuclear Elements"
         },
         "admin_install": {
             "install_repository_dependencies": true,
@@ -102024,252 +102339,302 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "diamond",
-                    "owner": "bgruening",
-                    "revisions": "e8ac2b53f262",
-                    "tool_panel_section_label": "NCBI Blast",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "diamond",
-                    "owner": "bgruening",
-                    "revisions": "e8ac2b53f262",
-                    "tool_panel_section_label": "NCBI Blast",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "diamond",
-                    "owner": "bgruening",
-                    "revisions": "e8ac2b53f262",
-                    "tool_panel_section_label": "NCBI Blast",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "split_file_on_column",
+                    "name": "repeat_masker",
                     "owner": "bgruening",
-                    "revisions": "37a53100b67e",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "column_maker",
-                    "owner": "devteam",
-                    "revisions": "02026300aa45",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "column_maker",
-                    "owner": "devteam",
-                    "revisions": "6595517c2dd8",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "intersect",
-                    "owner": "devteam",
-                    "revisions": "69c10b56f46d",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "tabular_to_fasta",
-                    "owner": "devteam",
-                    "revisions": "0a7799698fe5",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "ba6d2c32f797",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "regex_find_replace",
-                    "owner": "galaxyp",
-                    "revisions": "ae8c4b2488e7",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "repeatmodeler",
+                    "owner": "csbl",
+                    "revisions": "8661b2607b7e",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "orfipy",
+                    "name": "bedtools",
                     "owner": "iuc",
-                    "revisions": "c147914c9f02",
-                    "tool_panel_section_label": "Extract Features",
+                    "revisions": "a1a923cd89e8",
+                    "tool_panel_section_label": "BED",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "rapidnj",
+                    "name": "red",
                     "owner": "iuc",
-                    "revisions": "9f4a66e22580",
-                    "tool_panel_section_label": "Evolution",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "90981f86000f",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mafft",
-                    "owner": "rnateam",
-                    "revisions": "f1a5908ea2cb",
-                    "tool_panel_section_label": "Multiple Alignments",
+                    "revisions": "db57bc3b57af",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: diamond\n  owner: bgruening\n  revisions: e8ac2b53f262\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: diamond\n  owner: bgruening\n  revisions: e8ac2b53f262\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: diamond\n  owner: bgruening\n  revisions: e8ac2b53f262\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_on_column\n  owner: bgruening\n  revisions: 37a53100b67e\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 02026300aa45\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 6595517c2dd8\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: intersect\n  owner: devteam\n  revisions: 69c10b56f46d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tabular_to_fasta\n  owner: devteam\n  revisions: 0a7799698fe5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: ae8c4b2488e7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: orfipy\n  owner: iuc\n  revisions: c147914c9f02\n  tool_panel_section_label: Extract Features\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rapidnj\n  owner: iuc\n  revisions: 9f4a66e22580\n  tool_panel_section_label: Evolution\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mafft\n  owner: rnateam\n  revisions: f1a5908ea2cb\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/gene-centric/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: repeat_masker\n  owner: bgruening\n  revisions: ba6d2c32f797\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: repeatmodeler\n  owner: csbl\n  revisions: 8661b2607b7e\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: a1a923cd89e8\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: red\n  owner: iuc\n  revisions: db57bc3b57af\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/repeatmasker/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "abretaud",
+                "alexcorm",
+                "lleroi",
+                "r1corre",
+                "stephanierobin",
+                "jkreplak"
+            ],
+            "funding": [
+                "gallantries",
+                "eurosciencegateway"
+            ]
+        },
         "contributors": [
             {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
+                "affiliations": [
+                    "gallantries",
+                    "eurosciencegateway",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
+                "fediverse_flavor": "mastodon",
+                "id": "abretaud",
                 "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+                "location": {
+                    "country": "FR",
+                    "lat": 48.11,
+                    "lon": -1.64
+                },
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+            },
+            {
+                "email": "alexandre.cormier@ifremer.fr",
+                "id": "alexcorm",
+                "joined": "2021-11",
+                "name": "Alexandre Cormier",
+                "orcid": "0000-0002-7775-8413",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/",
+                "twitter": "allanssx",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/alexcorm.json"
+            },
+            {
+                "email": "laura.leroi@ifremer.fr",
+                "id": "lleroi",
+                "joined": "2021-11",
+                "name": "Laura Leroi",
+                "orcid": "0000-0003-3748-4179",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lleroi/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/lleroi.json"
+            },
+            {
+                "email": "erwan.corre@sb-roscoff.fr",
+                "id": "r1corre",
+                "joined": "2019-04",
+                "name": "Erwan Corre",
+                "orcid": "0000-0001-6354-2278",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/r1corre/",
+                "twitter": "r1corre",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/r1corre.json"
+            },
+            {
+                "email": "stephanie.robin@inrae.fr",
+                "id": "stephanierobin",
+                "joined": "2021-11",
+                "name": "St\u00e9phanie Robin",
+                "orcid": "0000-0001-7379-9173",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/",
+                "twitter": "robinstphanie1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/stephanierobin.json"
+            },
+            {
+                "email": "jonathan.kreplak@inrae.fr",
+                "id": "jkreplak",
+                "joined": "2020-09",
+                "name": "Jonathan Kreplak",
+                "orcid": "0000-0001-5563-1932",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jkreplak/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jkreplak.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/eurosciencegateway.png",
+                "funder": true,
+                "funding_id": "101057388",
+                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "eurosciencegateway",
+                "joined": "2023-10",
+                "members": [
+                    "abretaud",
+                    "anuprulez",
+                    "bgruening",
+                    "erxleben",
+                    "pauldg",
+                    "rlibouba"
+                ],
+                "name": "EuroScienceGateway",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
             }
         ],
-        "dir": "topics/genome-annotation/tutorials/gene-centric",
-        "edam_ontology": [
-            "topic_0622",
-            "topic_0623",
-            "topic_0080",
-            "topic_0084"
-        ],
+        "dir": "topics/genome-annotation/tutorials/repeatmasker",
         "edam_operation": [
-            "Multiple sequence alignment",
-            "Database search",
-            "Transcriptome assembly",
-            "Coding region prediction",
-            "De-novo assembly",
-            "Sequence alignment analysis",
-            "Phylogenetic tree generation"
-        ],
-        "edam_topic": [
-            "Genomics",
-            "Gene and protein families",
-            "Sequence analysis",
-            "Phylogeny"
+            "Genome annotation",
+            "Editing",
+            "Repeat sequence detection",
+            "RNA-Seq analysis",
+            "Mapping"
         ],
+        "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": true,
-        "id": "genome-annotation/gene-centric",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz"
+        "follow_up_training": [
+            {
+                "topic_name": "genome-annotation",
+                "tutorials": [
+                    "funannotate"
+                ],
+                "type": "internal"
+            }
         ],
+        "hands_on": true,
+        "id": "genome-annotation/repeatmasker",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "You can locate gene of interest in unannotated genomes and compare its structure across multiple species"
+            "RepeatMasker can be used to soft-mask a genome",
+            "It is an essential first step before running structural annotation pipelines"
         ],
         "layout": "tutorial_hands_on",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-18",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Provide a quick method for identifying genes of interest in unannotated or newly assembled genomes"
+            "Use Red and RepeatMasker to soft-mask a newly assembled genome"
         ],
-        "pageviews": 1476,
-        "priority": 2,
-        "pub_date": "2022-09-08",
+        "pageviews": 9655,
+        "priority": 1,
+        "pub_date": "2021-11-29",
         "questions": [
-            "I have several genomes assemblies that are not annotated (or I do not trust annotations)",
-            "I am interested to compare structure of a particular gene across these genome assemblies",
-            "How do I do that?"
+            "How to mask repeats in a genome?",
+            "What is the difference between hard and soft-masking?"
         ],
-        "requirements": [
+        "recordings": [
             {
-                "topic_name": "introduction",
-                "tutorials": [
-                    "galaxy-intro-101"
+                "captioners": [
+                    "abretaud"
                 ],
-                "type": "internal"
+                "date": "2023-05-10",
+                "galaxy_version": "23.01",
+                "length": "18M",
+                "speakers": [
+                    "abretaud"
+                ],
+                "youtube_id": "7tYEDmAvHD4"
             },
             {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "collections"
+                "captioners": [
+                    "abretaud"
                 ],
-                "type": "internal"
+                "date": "2022-03-03",
+                "galaxy_version": "21.09",
+                "length": "16M",
+                "speakers": [
+                    "abretaud"
+                ],
+                "youtube_id": "AYAvjwm4cnM"
             }
         ],
-        "short_id": "T00174",
+        "short_id": "T00178",
         "short_tools": [
-            "tab2fasta",
-            "cat1",
-            "orfipy",
-            "Add_a_column1",
-            "rbc_mafft",
-            "rapidnj",
-            "bg_diamond_view",
-            "regexColumn1",
-            "Cut1",
-            "bg_diamond_makedb",
-            "Filter1",
-            "bg_diamond",
-            "tp_split_on_column",
-            "join1",
-            "gops_intersect_1",
-            "collapse_dataset"
+            "bedtools_maskfastabed",
+            "repeatmodeler",
+            "red",
+            "repeatmasker_wrapper"
         ],
         "slides": false,
         "slides_recordings": false,
+        "subtopic": "eukaryote",
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
-                }
-            ],
-            "inexact": [
+                },
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
-            ]
+            ],
+            "inexact": []
         },
         "symlink": null,
         "tags": [
-            "evolution",
-            "annotation",
-            "vgp",
-            "cookbook",
-            "eukaryote",
-            "prokaryote",
-            "microgalaxy"
+            "eukaryote"
         ],
-        "time_estimation": "30M",
-        "title": "Comparative gene analysis in unannotated genomes",
+        "time_estimation": "1H",
+        "title": "Masking repeats with RepeatMasker",
         "tools": [
-            "Cut1",
-            "Filter1",
-            "cat1",
-            "join1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_makedb/2.0.15+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_view/2.0.15+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4",
-            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
-            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/orfipy/orfipy/0.0.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/rapidnj/rapidnj/2.3.2",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
-            "toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/2.0.4+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.30.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/red/red/2018.09.10+galaxy1"
         ],
         "topic_name": "genome-annotation",
         "topic_name_human": "Genome Annotation",
@@ -102279,277 +102644,244 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "gene-centric",
+        "tutorial_name": "repeatmasker",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/repeatmasker/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/gene-centric/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/gene-centric/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/repeatmasker/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/repeatmasker/tutorial.json"
         },
-        "version": 8,
+        "version": 20,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 186,
-        "visitors": 974,
+        "visit_duration": 82,
+        "visitors": 7397,
         "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "0000-0002-5987-8032",
-                        "name": "Anton Nekrutenko"
+                        "identifier": "https://orcid.org/0000-0003-0914-2470",
+                        "name": "Anthony Bretaudeau"
                     }
                 ],
-                "description": "Workflows for comparison of genes in annotated genomes",
+                "description": "Masking repeats in a genome using RepeatMasker",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nExons\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nDiamond makedb\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nORFipy BED\"]\n  3[label=\"Diamond: Find hits in ORFs\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Column Regex Find And Replace\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Alignments\"]\n  3 -> 5 [label=\"daa_output\"]\n  6[label=\"Cut\"]\n  4 -> 6 [label=\"out_file1\"]\n  7[label=\"Alignments + BED\"]\n  6 -> 7 [label=\"out_file1\"]\n  5 -> 7 [label=\"blast_tabular\"]\n  8[label=\"Cut\"]\n  7 -> 8 [label=\"out_file1\"]\n  9[label=\"Collapse Collection\"]\n  7 -> 9 [label=\"out_file1\"]\n  10[label=\"Intersect\"]\n  6 -> 10 [label=\"out_file1\"]\n  8 -> 10 [label=\"out_file1\"]\n  11[label=\"Filter\"]\n  9 -> 11 [label=\"output\"]\n  12[label=\"Overlapping ORFs\"]\n  10 -> 12 [label=\"output\"]\n  13[label=\"Cut\"]\n  11 -> 13 [label=\"out_file1\"]\n  14[label=\"Compute\"]\n  12 -> 14 [label=\"output\"]\n  15[label=\"Compute\"]\n  13 -> 15 [label=\"out_file1\"]\n  16[label=\"Split file\"]\n  15 -> 16 [label=\"out_file1\"]\n  17[label=\"Report\"]\n  15 -> 17 [label=\"out_file1\"]\n  18[label=\"Tabular-to-FASTA\"]\n  16 -> 18 [label=\"split_output\"]\n  19[label=\"Cut\"]\n  17 -> 19 [label=\"out_file1\"]\n  20[label=\"MAFFT\"]\n  18 -> 20 [label=\"output\"]\n  21[label=\"Filter: Plus strand matches\"]\n  19 -> 21 [label=\"out_file1\"]\n  22[label=\"Filter: Minus strand matches\"]\n  19 -> 22 [label=\"out_file1\"]\n  23[label=\"Join neighbors\"]\n  20 -> 23 [label=\"outputAlignment\"]\n  k54ea37cc63d1422a9f5e124b8d39e6bd[color=lightseagreen,label=\"Output\\nJoin neighbors on input dataset(s): Calculated distances\"]\n  23 -> k54ea37cc63d1422a9f5e124b8d39e6bd\n  24[label=\"Compute\"]\n  21 -> 24 [label=\"out_file1\"]\n  25[label=\"Compute\"]\n  22 -> 25 [label=\"out_file1\"]\n  26[label=\"Concatenate datasets\"]\n  24 -> 26 [label=\"out_file1\"]\n  25 -> 26 [label=\"out_file1\"]\n  27[label=\"Compute\"]\n  26 -> 27 [label=\"out_file1\"]\n  28[label=\"Cut\"]\n  27 -> 28 [label=\"out_file1\"]\n  29[label=\"Compute\"]\n  28 -> 29 [label=\"out_file1\"]\n  30[label=\"Join two Datasets\"]\n  14 -> 30 [label=\"out_file1\"]\n  29 -> 30 [label=\"out_file1\"]\n  31[label=\"Mapping report\"]\n  30 -> 31 [label=\"out_file1\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nRaw genome sequence\"]\n  1[label=\"Red\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"RepeatMasker\"]\n  0 -> 2 [label=\"output\"]\n  k3d7a51a241f9426fb9e8082fab12d6e2[color=lightseagreen,label=\"Output\\nRepeatMasker repeat catalogue on input dataset(s)\"]\n  2 -> k3d7a51a241f9426fb9e8082fab12d6e2\n  k3f0c419c7bd24378b174fe11e52bbf61[color=lightseagreen,label=\"Output\\nRepeatMasker masked sequence on input dataset(s)\"]\n  2 -> k3f0c419c7bd24378b174fe11e52bbf61\n  k342d5065122b437a8f78a636c5f2b7f6[color=lightseagreen,label=\"Output\\nRepeatMasker output log on input dataset(s)\"]\n  2 -> k342d5065122b437a8f78a636c5f2b7f6\n  k4a157f800d75425b858d49c4a12f91a0[color=lightseagreen,label=\"Output\\nRepeatMasker repeat statistics on input dataset(s)\"]\n  2 -> k4a157f800d75425b858d49c4a12f91a0\n}",
                 "history": [
                     {
-                        "hash": "476d3d57ff2b0ce249879b60aa03500ab62685d6",
-                        "message": "workflow update",
+                        "hash": "c62f8399d7c3d6e04e1f8db85543ba9162e902d8",
+                        "message": "workflow test",
                         "num": 1,
-                        "short_hash": "476d3d57f",
-                        "unix": "1662055154"
+                        "short_hash": "c62f8399d",
+                        "unix": "1682350616"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "Amino acid sequences of CDS exons from the gene of interest",
+                        "annotation": "The raw (not masked) genome sequence in fasta format",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Amino acid sequences of CDS exons from the gene of interest",
-                                "name": "Exons"
+                                "description": "The raw (not masked) genome sequence in fasta format",
+                                "name": "Raw genome sequence"
                             }
                         ],
-                        "label": "Exons",
+                        "label": "Raw genome sequence",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 1.90625,
-                            "top": 74.21875
+                            "left": 0,
+                            "top": 77.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": \"\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "107c06e7-51a6-41a1-a026-45a9dddf29a9",
+                        "uuid": "c26e06b1-39a6-43f4-a83f-7daeba257011",
                         "workflow_outputs": []
-                    },
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nRaw genome sequence\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Red\"];\n  0 -->|output| 1;\n  2[\"RepeatMasker\"];\n  0 -->|output| 2;\n  3d7a51a2-41f9-426f-b9e8-082fab12d6e2[\"Output\\nRepeatMasker repeat catalogue on input dataset(s)\"];\n  2 --> 3d7a51a2-41f9-426f-b9e8-082fab12d6e2;\n  style 3d7a51a2-41f9-426f-b9e8-082fab12d6e2 stroke:#2c3143,stroke-width:4px;\n  3f0c419c-7bd2-4378-b174-fe11e52bbf61[\"Output\\nRepeatMasker masked sequence on input dataset(s)\"];\n  2 --> 3f0c419c-7bd2-4378-b174-fe11e52bbf61;\n  style 3f0c419c-7bd2-4378-b174-fe11e52bbf61 stroke:#2c3143,stroke-width:4px;\n  342d5065-122b-437a-8f78-a636c5f2b7f6[\"Output\\nRepeatMasker output log on input dataset(s)\"];\n  2 --> 342d5065-122b-437a-8f78-a636c5f2b7f6;\n  style 342d5065-122b-437a-8f78-a636c5f2b7f6 stroke:#2c3143,stroke-width:4px;\n  4a157f80-0d75-425b-858d-49c4a12f91a0[\"Output\\nRepeatMasker repeat statistics on input dataset(s)\"];\n  2 --> 4a157f80-0d75-425b-858d-49c4a12f91a0;\n  style 4a157f80-0d75-425b-858d-49c4a12f91a0 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "RepeatMasker",
+                "outputs": [
                     {
-                        "annotation": "Diamond DB created from ORF predicted from genomes used in the analysis",
-                        "content_id": null,
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/red/red/2018.09.10+galaxy1",
                         "errors": null,
                         "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Diamond DB created from ORF predicted from genomes used in the analysis",
-                                "name": "Diamond makedb"
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
                             }
-                        ],
-                        "label": "Diamond makedb",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 0.0,
-                            "top": 185.71875
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "0acc2c20-91fb-4470-80ac-2eeb7e2f32ae",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "BED dataset containing information about ORFs predicted in genomes of interest",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "BED dataset containing information about ORFs predicted in genomes of interest",
-                                "name": "ORFipy BED"
+                                "description": "runtime parameter for tool Red",
+                                "name": "input"
                             }
                         ],
-                        "label": "ORFipy BED",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 1.90625,
-                            "top": 313.203125
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\", \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "329b3c07-f0ee-4882-abf7-1215062a0fec",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nExons\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nDiamond makedb\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nORFipy BED\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Diamond: Find hits in ORFs\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Column Regex Find And Replace\"];\n  2 -->|output| 4;\n  5[\"Alignments\"];\n  3 -->|daa_output| 5;\n  6[\"Cut\"];\n  4 -->|out_file1| 6;\n  7[\"Alignments + BED\"];\n  6 -->|out_file1| 7;\n  5 -->|blast_tabular| 7;\n  8[\"Cut\"];\n  7 -->|out_file1| 8;\n  9[\"Collapse Collection\"];\n  7 -->|out_file1| 9;\n  10[\"Intersect\"];\n  6 -->|out_file1| 10;\n  8 -->|out_file1| 10;\n  11[\"Filter\"];\n  9 -->|output| 11;\n  12[\"Overlapping ORFs\"];\n  10 -->|output| 12;\n  13[\"Cut\"];\n  11 -->|out_file1| 13;\n  14[\"Compute\"];\n  12 -->|output| 14;\n  15[\"Compute\"];\n  13 -->|out_file1| 15;\n  16[\"Split file\"];\n  15 -->|out_file1| 16;\n  17[\"Report\"];\n  15 -->|out_file1| 17;\n  18[\"Tabular-to-FASTA\"];\n  16 -->|split_output| 18;\n  19[\"Cut\"];\n  17 -->|out_file1| 19;\n  20[\"MAFFT\"];\n  18 -->|output| 20;\n  21[\"Filter: Plus strand matches\"];\n  19 -->|out_file1| 21;\n  22[\"Filter: Minus strand matches\"];\n  19 -->|out_file1| 22;\n  23[\"Join neighbors\"];\n  20 -->|outputAlignment| 23;\n  54ea37cc-63d1-422a-9f5e-124b8d39e6bd[\"Output\\nJoin neighbors on input dataset(s): Calculated distances\"];\n  23 --> 54ea37cc-63d1-422a-9f5e-124b8d39e6bd;\n  style 54ea37cc-63d1-422a-9f5e-124b8d39e6bd stroke:#2c3143,stroke-width:4px;\n  24[\"Compute\"];\n  21 -->|out_file1| 24;\n  25[\"Compute\"];\n  22 -->|out_file1| 25;\n  26[\"Concatenate datasets\"];\n  24 -->|out_file1| 26;\n  25 -->|out_file1| 26;\n  27[\"Compute\"];\n  26 -->|out_file1| 27;\n  28[\"Cut\"];\n  27 -->|out_file1| 28;\n  29[\"Compute\"];\n  28 -->|out_file1| 29;\n  30[\"Join two Datasets\"];\n  14 -->|out_file1| 30;\n  29 -->|out_file1| 30;\n  31[\"Mapping report\"];\n  30 -->|out_file1| 31;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Comparative gene analysis",
-                "outputs": [
-                    {
-                        "annotation": "Compute NJ phylogenetic trees",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rapidnj/rapidnj/2.3.2",
-                        "errors": null,
-                        "id": 23,
-                        "input_connections": {
-                            "alignments": {
-                                "id": 20,
-                                "output_name": "outputAlignment"
-                            }
-                        },
-                        "inputs": [],
                         "label": null,
-                        "name": "Join neighbors",
+                        "name": "Red",
                         "outputs": [
                             {
-                                "name": "distances",
-                                "type": "nhx"
+                                "name": "masked",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "bed",
+                                "type": "bed"
                             }
                         ],
                         "position": {
-                            "left": 2200.03125,
+                            "left": 354,
                             "top": 0
                         },
-                        "post_job_actions": {
-                            "TagDatasetActiondistances": {
-                                "action_arguments": {
-                                    "tags": "Trees"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "distances"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rapidnj/rapidnj/2.3.2",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/red/red/2018.09.10+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "9f4a66e22580",
-                            "name": "rapidnj",
+                            "changeset_revision": "18a46265455b",
+                            "name": "red",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"alignment_type\": \"p\", \"alignments\": {\"__class__\": \"ConnectedValue\"}, \"bootstrap\": null, \"evolution_model\": \"kim\", \"no_negative_length\": \"false\", \"output_format\": \"t\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.3.2",
+                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2018.09.10+galaxy1",
                         "type": "tool",
-                        "uuid": "a9f1ebbf-4a88-4ddb-aec7-6a1c3a3921db",
+                        "uuid": "8e20207e-cee6-42fc-afd0-6bed48afe669",
                         "workflow_outputs": [
                             {
-                                "label": "Join neighbors on input dataset(s): Calculated distances",
-                                "output_name": "distances",
-                                "uuid": "54ea37cc-63d1-422a-9f5e-124b8d39e6bd"
+                                "label": null,
+                                "output_name": "masked",
+                                "uuid": "344db107-2ffa-4389-91d8-bd1505707369"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "bed",
+                                "uuid": "6414050e-9640-490a-a39b-26c582bd8f91"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Cut1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.5+galaxy0",
                         "errors": null,
-                        "id": 31,
+                        "id": 2,
                         "input_connections": {
-                            "input": {
-                                "id": 30,
-                                "output_name": "out_file1"
+                            "input_fasta": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": "Mapping report",
-                        "name": "Cut",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool RepeatMasker",
+                                "name": "input_fasta"
+                            }
+                        ],
+                        "label": null,
+                        "name": "RepeatMasker",
                         "outputs": [
                             {
-                                "name": "out_file1",
+                                "name": "output_masked_genome",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "output_log",
                                 "type": "tabular"
+                            },
+                            {
+                                "name": "output_table",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "output_repeat_catalog",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 3450.75,
-                            "top": 1309.90625
+                            "left": 355,
+                            "top": 144.5
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Mapping report"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            },
-                            "TagDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "tags": "PlottingData"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "out_file1"
-                            }
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.5+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ba6d2c32f797",
+                            "name": "repeat_masker",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"columnList\": \"c1,c2,c3,c4,c5,c6,c7,c11,c12,c13,c14,c15\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2",
+                        "tool_state": "{\"advanced\": {\"is_only\": \"false\", \"is_clip\": \"false\", \"no_is\": \"false\", \"rodspec\": \"false\", \"primspec\": \"false\", \"nolow\": \"false\", \"noint\": \"false\", \"norna\": \"false\", \"alu\": \"false\", \"div\": \"false\", \"search_speed\": \"\", \"frag\": \"40000\", \"gc\": null, \"gccalc\": \"false\", \"nocut\": \"false\", \"xout\": \"false\", \"keep_alignments\": \"false\", \"invert_alignments\": \"false\", \"poly\": \"false\"}, \"excln\": \"true\", \"gff\": \"false\", \"input_fasta\": {\"__class__\": \"RuntimeValue\"}, \"repeat_source\": {\"source_type\": \"dfam\", \"__current_case__\": 0, \"species_source\": {\"species_from_list\": \"yes\", \"__current_case__\": 0, \"species_list\": \"human\"}}, \"xsmall\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.1.5+galaxy0",
                         "type": "tool",
-                        "uuid": "341c7257-c027-421b-afc1-a8dc11d2f6cd",
+                        "uuid": "f7ef7c85-b782-468b-94a2-076efc91920c",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "bb199f1a-1402-4f00-9a02-e5743a8662b6"
+                                "label": "RepeatMasker repeat catalogue on input dataset(s)",
+                                "output_name": "output_repeat_catalog",
+                                "uuid": "3d7a51a2-41f9-426f-b9e8-082fab12d6e2"
+                            },
+                            {
+                                "label": "RepeatMasker masked sequence on input dataset(s)",
+                                "output_name": "output_masked_genome",
+                                "uuid": "3f0c419c-7bd2-4378-b174-fe11e52bbf61"
+                            },
+                            {
+                                "label": "RepeatMasker output log on input dataset(s)",
+                                "output_name": "output_log",
+                                "uuid": "342d5065-122b-437a-8f78-a636c5f2b7f6"
+                            },
+                            {
+                                "label": "RepeatMasker repeat statistics on input dataset(s)",
+                                "output_name": "output_table",
+                                "uuid": "4a157f80-0d75-425b-858d-49c4a12f91a0"
                             }
                         ]
                     }
                 ],
-                "parent_id": "genome-annotation/gene-centric",
-                "path": "topics/genome-annotation/tutorials/gene-centric/workflows/Comparative-gene-analysis.ga",
+                "parent_id": "genome-annotation/repeatmasker",
+                "path": "topics/genome-annotation/tutorials/repeatmasker/workflows/RepeatMasker.ga",
                 "tags": [
-                    "vgp",
                     "genome-annotation"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "Comparative gene analysis",
-                "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-gene-centric/versions/comparative-gene-analysis",
-                "tutorial_id": "gene-centric",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/gene-centric/workflows/Comparative-gene-analysis.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/gene-centric/workflows/Comparative-gene-analysis.html",
+                "tests": true,
+                "title": "RepeatMasker",
+                "topic_id": "genome-annotation",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-repeatmasker/versions/repeatmasker",
+                "tutorial_id": "repeatmasker",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/repeatmasker/workflows/RepeatMasker.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/repeatmasker/workflows/RepeatMasker.html",
                 "version": 1,
-                "wfid": "genome-annotation-gene-centric",
-                "wfname": "comparative-gene-analysis",
-                "workflow": "Comparative-gene-analysis.ga",
+                "wfid": "genome-annotation-repeatmasker",
+                "wfname": "repeatmasker",
+                "workflow": "RepeatMasker.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "Filter1",
-                    "cat1",
-                    "join1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_view/2.0.15+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/rapidnj/rapidnj/2.3.2",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/red/red/2018.09.10+galaxy1"
                 ],
-                "workflowhub_id": "1173"
+                "workflowhub_id": "1198"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/7034885"
+        "zenodo_link": "https://zenodo.org/record/7085837"
     },
     {
+        "abbreviations": {
+            "GPU": "Graphics Processing Unit",
+            "UTR": "Untranslated region"
+        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
@@ -102558,57 +102890,73 @@
                 {
                     "name": "gffread",
                     "owner": "devteam",
-                    "revisions": "0232f19d300f",
+                    "revisions": "3e436657dcd0",
                     "tool_panel_section_label": "Convert Formats",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "busco",
-                    "owner": "iuc",
-                    "revisions": "1440ae06552f",
+                    "name": "helixer",
+                    "owner": "genouest",
+                    "revisions": "c2fc4ac35199",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "jbrowse",
-                    "owner": "iuc",
-                    "revisions": "2bb2e07a7a21",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "jcvi_gff_stats",
+                    "name": "busco",
                     "owner": "iuc",
-                    "revisions": "8cffbd184762",
+                    "revisions": "ea8146ee148f",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "maker",
+                    "name": "compleasm",
                     "owner": "iuc",
-                    "revisions": "96ac930d84fa",
+                    "revisions": "47f9f4d13d2c",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "maker_map_ids",
+                    "name": "jbrowse",
                     "owner": "iuc",
-                    "revisions": "326f9c294b09",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "a6e57ff585c0",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fasta_stats",
-                    "owner": "simon-gladman",
-                    "revisions": "20ca2574216a",
+                    "name": "jcvi_gff_stats",
+                    "owner": "iuc",
+                    "revisions": "8cffbd184762",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: gffread\n  owner: devteam\n  revisions: 0232f19d300f\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 1440ae06552f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 2bb2e07a7a21\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jcvi_gff_stats\n  owner: iuc\n  revisions: 8cffbd184762\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker\n  owner: iuc\n  revisions: 96ac930d84fa\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker_map_ids\n  owner: iuc\n  revisions: 326f9c294b09\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n  owner: simon-gladman\n  revisions: 20ca2574216a\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: gffread\n  owner: devteam\n  revisions: 3e436657dcd0\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: helixer\n  owner: genouest\n  revisions: c2fc4ac35199\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: ea8146ee148f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: compleasm\n  owner: iuc\n  revisions: 47f9f4d13d2c\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jcvi_gff_stats\n  owner: iuc\n  revisions: 8cffbd184762\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/helixer/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "rlibouba",
+                "abretaud"
+            ],
+            "funding": [
+                "eurosciencegateway"
+            ]
+        },
         "contributors": [
+            {
+                "affiliations": [
+                    "eurosciencegateway",
+                    "elixir-europe"
+                ],
+                "email": "romane.libouban@irisa.fr",
+                "id": "rlibouba",
+                "joined": "2023-03",
+                "matrix": "rlibouban:matrix.org",
+                "name": "Romane LIBOUBAN",
+                "orcid": "0009-0001-4920-9951",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/rlibouba/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/rlibouba.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
@@ -102633,59 +102981,92 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
                 "twitter": "abretau",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/eurosciencegateway.png",
+                "funder": true,
+                "funding_id": "101057388",
+                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "eurosciencegateway",
+                "joined": "2023-10",
+                "members": [
+                    "abretaud",
+                    "anuprulez",
+                    "bgruening",
+                    "erxleben",
+                    "pauldg",
+                    "rlibouba"
+                ],
+                "name": "EuroScienceGateway",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
             }
         ],
-        "dir": "topics/genome-annotation/tutorials/annotation-with-maker-short",
+        "dir": "topics/genome-annotation/tutorials/helixer",
+        "edam_ontology": [
+            "topic_0362"
+        ],
         "edam_operation": [
-            "Genome assembly",
-            "Sequence annotation",
-            "Transcriptome assembly",
-            "Genome visualisation",
             "Genome annotation",
+            "Genome visualisation",
+            "Genome assembly",
+            "Sequence analysis",
             "Sequence assembly validation",
-            "Scaffolding"
+            "Gene prediction",
+            "Scaffolding",
+            "Sequence annotation",
+            "Transcriptome assembly"
         ],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "genome-annotation/annotation-with-maker-short",
+        "id": "genome-annotation/helixer",
         "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Maker allows to annotate a eukaryotic genome.",
-            "BUSCO and JBrowse allow to inspect the quality of an annotation."
+            "Helixer allows to perform structural annotation of an eukaryotic genome",
+            "BUSCO allows to inspect the quality of an annotation"
         ],
         "layout": "tutorial_hands_on",
         "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-02-29",
+        "mod_date": "2024-08-28",
         "objectives": [
             "Load genome into Galaxy",
-            "Annotate genome with Maker",
+            "Annotate genome with Helixer",
             "Evaluate annotation quality with BUSCO",
             "View annotations in JBrowse"
         ],
-        "pageviews": 4070,
-        "priority": 3,
-        "pub_date": "2021-01-12",
+        "pageviews": 103,
+        "pub_date": "2024-08-21",
         "questions": [
-            "How to annotate an eukaryotic genome?",
+            "How to annotate an eukaryotic genome with Helixer?",
             "How to evaluate and visualize annotated genomic features?"
         ],
-        "short_id": "T00167",
+        "requirements": [
+            {
+                "topic_name": "genome-annotation",
+                "tutorials": [
+                    "repeatmasker"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00451",
         "short_tools": [
-            "jcvi_gff_stats",
-            "gffread",
             "jbrowse",
+            "compleasm",
             "busco",
-            "fasta-stats",
-            "maker",
-            "maker_map_ids"
+            "jcvi_gff_stats",
+            "gffread",
+            "helixer"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -102696,21 +103077,20 @@
         },
         "symlink": null,
         "tags": [
-            "gmod",
-            "eukaryote",
-            "maker",
+            "eukaryota",
+            "helixer",
             "jbrowse1"
         ],
-        "time_estimation": "2h",
-        "title": "Genome annotation with Maker (short)",
+        "time_estimation": "4h",
+        "title": "Genome annotation with Helixer",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/genouest/helixer/helixer/0.3.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
             "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.10",
-            "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10",
-            "toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0"
+            "toolshed.g2.bx.psu.edu/view/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4"
         ],
         "topic_name": "genome-annotation",
         "topic_name_human": "Genome Annotation",
@@ -102720,1155 +103100,2014 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "annotation-with-maker-short",
+        "tutorial_name": "helixer",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/helixer/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/helixer/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/helixer/tutorial.json"
         },
         "version": 3,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 192,
-        "visitors": 2763,
+        "visit_duration": 157,
+        "visitors": 86,
         "workflows": [
             {
-                "creators": [],
-                "description": "Genome annotation with Maker (short)",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0009-0001-4920-9951",
+                        "name": "Romane Libouban"
+                    }
+                ],
+                "description": "Structural genome annotation with Helixer",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenome sequence\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nProteins\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSNAP model\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAugustus model\"]\n  5[label=\"Fasta Statistics\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Busco\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Maker\"]\n  4 -> 7 [label=\"output\"]\n  3 -> 7 [label=\"output\"]\n  1 -> 7 [label=\"output\"]\n  0 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"Map annotation ids\"]\n  7 -> 8 [label=\"output_gff\"]\n  9[label=\"Genome annotation statistics\"]\n  8 -> 9 [label=\"renamed\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"gffread\"]\n  8 -> 10 [label=\"renamed\"]\n  0 -> 10 [label=\"output\"]\n  11[label=\"JBrowse\"]\n  0 -> 11 [label=\"output\"]\n  8 -> 11 [label=\"renamed\"]\n  7 -> 11 [label=\"output_evidences\"]\n  12[label=\"Busco\"]\n  10 -> 12 [label=\"output_exons\"]\n  k6951417bee0b4e0398e467d262e086dc[color=lightseagreen,label=\"Output\\nBusco summary final round\"]\n  12 -> k6951417bee0b4e0398e467d262e086dc\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenome\"]\n  1[label=\"Helixer\"]\n  0 -> 1 [label=\"output\"]\n  k9ebeb90d1528494ca88d50f28836d7c7[color=lightseagreen,label=\"Output\\nHelixer\"]\n  1 -> k9ebeb90d1528494ca88d50f28836d7c7\n  2[label=\"compleasm\"]\n  0 -> 2 [label=\"output\"]\n  ke0d3aa0bd18b41afa6fc28a8688fe9a5[color=lightseagreen,label=\"Output\\ncompleasm miniprot\"]\n  2 -> ke0d3aa0bd18b41afa6fc28a8688fe9a5\n  k93b908a5e39f4cfb84c3edf4ab8b71cf[color=lightseagreen,label=\"Output\\ncompleasm full table\"]\n  2 -> k93b908a5e39f4cfb84c3edf4ab8b71cf\n  k7c9cb7e2dfac4aa1b87df6a2eb7e21a5[color=lightseagreen,label=\"Output\\ncompleasm full table busco\"]\n  2 -> k7c9cb7e2dfac4aa1b87df6a2eb7e21a5\n  k9215afe64aad4d43a3a1c2c5ab0ea1e2[color=lightseagreen,label=\"Output\\ncompleasm translated protein\"]\n  2 -> k9215afe64aad4d43a3a1c2c5ab0ea1e2\n  3[label=\"BUSCO\"]\n  0 -> 3 [label=\"output\"]\n  k703a797f428b4c41984f1283bb8eecaa[color=lightseagreen,label=\"Output\\nBUSCO sum\"]\n  3 -> k703a797f428b4c41984f1283bb8eecaa\n  ke3879637613a45cf90a03eecab2e0981[color=lightseagreen,label=\"Output\\nBUSCO miniprot\"]\n  3 -> ke3879637613a45cf90a03eecab2e0981\n  kacbfdee0cafd46e881e98a1fd22ee758[color=lightseagreen,label=\"Output\\nBUSCO gff3\"]\n  3 -> kacbfdee0cafd46e881e98a1fd22ee758\n  k5574f029f31d4d20a8474d1818f95707[color=lightseagreen,label=\"Output\\nBUSCO summary image\"]\n  3 -> k5574f029f31d4d20a8474d1818f95707\n  kb19bfb5f901f4568a46153bfc980bdcc[color=lightseagreen,label=\"Output\\nBUSCO missing\"]\n  3 -> kb19bfb5f901f4568a46153bfc980bdcc\n  k0ba757ff6c1b496ba288335369058923[color=lightseagreen,label=\"Output\\nBUSCO table\"]\n  3 -> k0ba757ff6c1b496ba288335369058923\n  4[label=\"Genome annotation statistics Helixer\"]\n  1 -> 4 [label=\"output\"]\n  0 -> 4 [label=\"output\"]\n  ka445f12b685d47afb40790fa7ea935b1[color=lightseagreen,label=\"Output\\ngraphs helixer\"]\n  4 -> ka445f12b685d47afb40790fa7ea935b1\n  k8eae8a88c73d42dcad0d62d2f1d29c6a[color=lightseagreen,label=\"Output\\nsummary helixer\"]\n  4 -> k8eae8a88c73d42dcad0d62d2f1d29c6a\n  5[label=\"JBrowse\"]\n  0 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  k2bac35a7837942699769e0e0c541f4a3[color=lightseagreen,label=\"Output\\nJBrowse output\"]\n  5 -> k2bac35a7837942699769e0e0c541f4a3\n}",
                 "history": [
                     {
-                        "hash": "005d964a2e8cb80f8d1bf0b304adc8f9d7c9ff76",
-                        "message": "fix workflows",
+                        "hash": "405592af154c2f5d5f62897c1da5e4c77e25df2c",
+                        "message": "Helixer tutorial review",
                         "num": 2,
-                        "short_hash": "005d964a2",
-                        "unix": "1609752597"
+                        "short_hash": "405592af1",
+                        "unix": "1724251469"
                     },
                     {
-                        "hash": "774f2aa374452d48fd29ee85513c3dc3a7f137f5",
-                        "message": "update maker tutorial and add a short version",
+                        "hash": "151f64c69534af5d50eee436735bceec6ddacf69",
+                        "message": "add Helixer training",
                         "num": 1,
-                        "short_hash": "774f2aa37",
-                        "unix": "1609431273"
+                        "short_hash": "151f64c69",
+                        "unix": "1712059634"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "",
+                        "annotation": "Genome input (fasta format)",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Genome sequence"
+                                "description": "Genome input (fasta format)",
+                                "name": "Genome"
                             }
                         ],
-                        "label": "Genome sequence",
+                        "label": "Genome",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 94.08332824707031,
-                            "height": 82.19999694824219,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 11.883331298828125,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 11.883331298828125
+                            "left": 0.0,
+                            "top": 393.5426496082689
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "a361a75e-5fa4-44ca-a4b7-cc9054a73054",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "9a09d16c-18af-4605-8416-4966fe918677"
-                            }
-                        ]
-                    },
+                        "uuid": "332fb9cd-3819-4e81-8aa5-c6cc6fbda4f7",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGenome\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Helixer\"];\n  0 -->|output| 1;\n  9ebeb90d-1528-494c-a88d-50f28836d7c7[\"Output\\nHelixer\"];\n  1 --> 9ebeb90d-1528-494c-a88d-50f28836d7c7;\n  style 9ebeb90d-1528-494c-a88d-50f28836d7c7 stroke:#2c3143,stroke-width:4px;\n  2[\"compleasm\"];\n  0 -->|output| 2;\n  e0d3aa0b-d18b-41af-a6fc-28a8688fe9a5[\"Output\\ncompleasm miniprot\"];\n  2 --> e0d3aa0b-d18b-41af-a6fc-28a8688fe9a5;\n  style e0d3aa0b-d18b-41af-a6fc-28a8688fe9a5 stroke:#2c3143,stroke-width:4px;\n  93b908a5-e39f-4cfb-84c3-edf4ab8b71cf[\"Output\\ncompleasm full table\"];\n  2 --> 93b908a5-e39f-4cfb-84c3-edf4ab8b71cf;\n  style 93b908a5-e39f-4cfb-84c3-edf4ab8b71cf stroke:#2c3143,stroke-width:4px;\n  7c9cb7e2-dfac-4aa1-b87d-f6a2eb7e21a5[\"Output\\ncompleasm full table busco\"];\n  2 --> 7c9cb7e2-dfac-4aa1-b87d-f6a2eb7e21a5;\n  style 7c9cb7e2-dfac-4aa1-b87d-f6a2eb7e21a5 stroke:#2c3143,stroke-width:4px;\n  9215afe6-4aad-4d43-a3a1-c2c5ab0ea1e2[\"Output\\ncompleasm translated protein\"];\n  2 --> 9215afe6-4aad-4d43-a3a1-c2c5ab0ea1e2;\n  style 9215afe6-4aad-4d43-a3a1-c2c5ab0ea1e2 stroke:#2c3143,stroke-width:4px;\n  3[\"BUSCO\"];\n  0 -->|output| 3;\n  703a797f-428b-4c41-984f-1283bb8eecaa[\"Output\\nBUSCO sum\"];\n  3 --> 703a797f-428b-4c41-984f-1283bb8eecaa;\n  style 703a797f-428b-4c41-984f-1283bb8eecaa stroke:#2c3143,stroke-width:4px;\n  e3879637-613a-45cf-90a0-3eecab2e0981[\"Output\\nBUSCO miniprot\"];\n  3 --> e3879637-613a-45cf-90a0-3eecab2e0981;\n  style e3879637-613a-45cf-90a0-3eecab2e0981 stroke:#2c3143,stroke-width:4px;\n  acbfdee0-cafd-46e8-81e9-8a1fd22ee758[\"Output\\nBUSCO gff3\"];\n  3 --> acbfdee0-cafd-46e8-81e9-8a1fd22ee758;\n  style acbfdee0-cafd-46e8-81e9-8a1fd22ee758 stroke:#2c3143,stroke-width:4px;\n  5574f029-f31d-4d20-a847-4d1818f95707[\"Output\\nBUSCO summary image\"];\n  3 --> 5574f029-f31d-4d20-a847-4d1818f95707;\n  style 5574f029-f31d-4d20-a847-4d1818f95707 stroke:#2c3143,stroke-width:4px;\n  b19bfb5f-901f-4568-a461-53bfc980bdcc[\"Output\\nBUSCO missing\"];\n  3 --> b19bfb5f-901f-4568-a461-53bfc980bdcc;\n  style b19bfb5f-901f-4568-a461-53bfc980bdcc stroke:#2c3143,stroke-width:4px;\n  0ba757ff-6c1b-496b-a288-335369058923[\"Output\\nBUSCO table\"];\n  3 --> 0ba757ff-6c1b-496b-a288-335369058923;\n  style 0ba757ff-6c1b-496b-a288-335369058923 stroke:#2c3143,stroke-width:4px;\n  4[\"Genome annotation statistics Helixer\"];\n  1 -->|output| 4;\n  0 -->|output| 4;\n  a445f12b-685d-47af-b407-90fa7ea935b1[\"Output\\ngraphs helixer\"];\n  4 --> a445f12b-685d-47af-b407-90fa7ea935b1;\n  style a445f12b-685d-47af-b407-90fa7ea935b1 stroke:#2c3143,stroke-width:4px;\n  8eae8a88-c73d-42dc-ad0d-62d2f1d29c6a[\"Output\\nsummary helixer\"];\n  4 --> 8eae8a88-c73d-42dc-ad0d-62d2f1d29c6a;\n  style 8eae8a88-c73d-42dc-ad0d-62d2f1d29c6a stroke:#2c3143,stroke-width:4px;\n  5[\"JBrowse\"];\n  0 -->|output| 5;\n  1 -->|output| 5;\n  2bac35a7-8379-4269-9769-e0e0c541f4a3[\"Output\\nJBrowse output\"];\n  5 --> 2bac35a7-8379-4269-9769-e0e0c541f4a3;\n  style 2bac35a7-8379-4269-9769-e0e0c541f4a3 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Training - Helixer",
+                "outputs": [
                     {
-                        "annotation": "",
-                        "content_id": null,
+                        "annotation": "Structural annotation step",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/genouest/helixer/helixer/0.3.3+galaxy1",
                         "errors": null,
                         "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "EST and/or cDNA"
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
                             }
-                        ],
-                        "label": "EST and/or cDNA",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 214.0833282470703,
-                            "height": 82.19999694824219,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 131.88333129882812,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 131.88333129882812
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "6b3edbe9-085d-46ae-9ae3-96e876c003e0",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "c5c5fb8f-9932-499c-b404-c142aedd1aa5"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Proteins"
+                                "description": "runtime parameter for tool Helixer",
+                                "name": "input"
                             }
                         ],
-                        "label": "Proteins",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 313.68333435058594,
-                            "height": 61.80000305175781,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 251.88333129882812,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 251.88333129882812
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ce4ee756-1713-4e6a-898c-b85a834712bc",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "cbbe9e59-ccd5-4925-a7a3-e1d094284fca"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
+                        "label": "Helixer",
+                        "name": "Helixer",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "SNAP model"
+                                "name": "output",
+                                "type": "gff3"
                             }
                         ],
-                        "label": "SNAP model",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 413.68333435058594,
-                            "height": 61.80000305175781,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 351.8833312988281,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 351.8833312988281
+                            "left": 495.6559490752344,
+                            "top": 126.52477912175132
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ebf1f01c-e804-462a-92cf-670012b103b3",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/genouest/helixer/helixer/0.3.3+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e3846dc36c4d",
+                            "name": "helixer",
+                            "owner": "genouest",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"lineages\": \"fungi\", \"option_overlap\": {\"use_overlap\": \"true\", \"__current_case__\": 0, \"overlap_offset\": null, \"overlap_core_length\": null}, \"post_processing\": {\"window_size\": \"100\", \"edge_threshold\": \"0.1\", \"peak_threshold\": \"0.8\", \"min_coding_length\": \"100\"}, \"size\": \"8\", \"species\": null, \"subsequence_length\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3.3+galaxy1",
+                        "type": "tool",
+                        "uuid": "c151bbb2-deb9-4fb6-a047-7a92ede3171a",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "Helixer",
                                 "output_name": "output",
-                                "uuid": "ecfd7af4-f95c-4b2d-9f06-8e851a0c4d9e"
+                                "uuid": "9ebeb90d-1528-494c-a88d-50f28836d7c7"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
+                        "annotation": "Compleam is described as a faster and more accurate reimplementation of Busco.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.5+galaxy0",
                         "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Augustus model"
+                        "id": 2,
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
                             }
-                        ],
-                        "label": "Augustus model",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 554.0833282470703,
-                            "height": 82.19999694824219,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 471.8833312988281,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 471.8833312988281
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "586af078-09ce-476b-9eb7-55e443a8eeaf",
-                        "workflow_outputs": [
+                        "inputs": [],
+                        "label": "compleasm",
+                        "name": "compleasm",
+                        "outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "7259eb8b-9c2d-4eff-a49d-1b447e905314"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGenome sequence\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nProteins\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nSNAP model\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nAugustus model\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Fasta Statistics\"];\n  0 -->|output| 5;\n  6[\"Busco\"];\n  0 -->|output| 6;\n  7[\"Maker\"];\n  4 -->|output| 7;\n  3 -->|output| 7;\n  1 -->|output| 7;\n  0 -->|output| 7;\n  2 -->|output| 7;\n  8[\"Map annotation ids\"];\n  7 -->|output_gff| 8;\n  9[\"Genome annotation statistics\"];\n  8 -->|renamed| 9;\n  0 -->|output| 9;\n  10[\"gffread\"];\n  8 -->|renamed| 10;\n  0 -->|output| 10;\n  11[\"JBrowse\"];\n  0 -->|output| 11;\n  8 -->|renamed| 11;\n  7 -->|output_evidences| 11;\n  12[\"Busco\"];\n  10 -->|output_exons| 12;\n  6951417b-ee0b-4e03-98e4-67d262e086dc[\"Output\\nBusco summary final round\"];\n  12 --> 6951417b-ee0b-4e03-98e4-67d262e086dc;\n  style 6951417b-ee0b-4e03-98e4-67d262e086dc stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Genome annotation with Maker (short)",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                                "name": "full_table_busco",
+                                "type": "tsv"
+                            },
                             {
-                                "description": "",
-                                "name": "Genome sequence"
+                                "name": "full_table",
+                                "type": "tsv"
+                            },
+                            {
+                                "name": "miniprot",
+                                "type": "gff3"
+                            },
+                            {
+                                "name": "translated_protein",
+                                "type": "fasta"
                             }
                         ],
-                        "label": "Genome sequence",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 94.08332824707031,
-                            "height": 82.19999694824219,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 11.883331298828125,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 11.883331298828125
+                            "left": 677.3732598347183,
+                            "top": 639.0246967831238
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "a361a75e-5fa4-44ca-a4b7-cc9054a73054",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.5+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "47f9f4d13d2c",
+                            "name": "compleasm",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"busco_database\": \"v5\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"mucorales_odb10\", \"mode\": \"busco\", \"outputs\": [\"full_table_busco\", \"full_table\", \"miniprot\", \"translated_protein\"], \"specified_contigs\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.2.5+galaxy0",
+                        "type": "tool",
+                        "uuid": "e95adff9-488d-41af-b55c-c137ab9667cf",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "9a09d16c-18af-4605-8416-4966fe918677"
+                                "label": "compleasm miniprot",
+                                "output_name": "miniprot",
+                                "uuid": "e0d3aa0b-d18b-41af-a6fc-28a8688fe9a5"
+                            },
+                            {
+                                "label": "compleasm full table",
+                                "output_name": "full_table",
+                                "uuid": "93b908a5-e39f-4cfb-84c3-edf4ab8b71cf"
+                            },
+                            {
+                                "label": "compleasm full table busco",
+                                "output_name": "full_table_busco",
+                                "uuid": "7c9cb7e2-dfac-4aa1-b87d-f6a2eb7e21a5"
+                            },
+                            {
+                                "label": "compleasm translated protein",
+                                "output_name": "translated_protein",
+                                "uuid": "9215afe6-4aad-4d43-a3a1-c2c5ab0ea1e2"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
+                        "annotation": "BSUCO assesses the quality of genomic data. The tool inspects the transcription sequences of predicted genes.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
+                        "id": 3,
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "EST and/or cDNA"
+                                "description": "runtime parameter for tool Busco",
+                                "name": "input"
                             }
                         ],
-                        "label": "EST and/or cDNA",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 214.0833282470703,
-                            "height": 82.19999694824219,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 131.88333129882812,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 131.88333129882812
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "6b3edbe9-085d-46ae-9ae3-96e876c003e0",
-                        "workflow_outputs": [
+                        "label": "BUSCO",
+                        "name": "Busco",
+                        "outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "c5c5fb8f-9932-499c-b404-c142aedd1aa5"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                                "name": "busco_sum",
+                                "type": "txt"
+                            },
                             {
-                                "description": "",
-                                "name": "Proteins"
+                                "name": "busco_table",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "busco_missing",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "summary_image",
+                                "type": "png"
+                            },
+                            {
+                                "name": "busco_gff",
+                                "type": "gff3"
+                            },
+                            {
+                                "name": "busco_miniprot",
+                                "type": "gff3"
                             }
                         ],
-                        "label": "Proteins",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 313.68333435058594,
-                            "height": 61.80000305175781,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 251.88333129882812,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 251.88333129882812
+                            "left": 948.5586447752132,
+                            "top": 415.14516016871283
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ce4ee756-1713-4e6a-898c-b85a834712bc",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ea8146ee148f",
+                            "name": "busco",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": true, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": \"mucorales_odb10\"}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"missing\", \"image\", \"gff\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.5.0+galaxy0",
+                        "type": "tool",
+                        "uuid": "af725f3e-ee5a-485b-af11-d87a8ecf9aeb",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "cbbe9e59-ccd5-4925-a7a3-e1d094284fca"
+                                "label": "BUSCO sum",
+                                "output_name": "busco_sum",
+                                "uuid": "703a797f-428b-4c41-984f-1283bb8eecaa"
+                            },
+                            {
+                                "label": "BUSCO miniprot",
+                                "output_name": "busco_miniprot",
+                                "uuid": "e3879637-613a-45cf-90a0-3eecab2e0981"
+                            },
+                            {
+                                "label": "BUSCO gff3",
+                                "output_name": "busco_gff",
+                                "uuid": "acbfdee0-cafd-46e8-81e9-8a1fd22ee758"
+                            },
+                            {
+                                "label": "BUSCO summary image",
+                                "output_name": "summary_image",
+                                "uuid": "5574f029-f31d-4d20-a847-4d1818f95707"
+                            },
+                            {
+                                "label": "BUSCO missing",
+                                "output_name": "busco_missing",
+                                "uuid": "b19bfb5f-901f-4568-a461-53bfc980bdcc"
+                            },
+                            {
+                                "label": "BUSCO table",
+                                "output_name": "busco_table",
+                                "uuid": "0ba757ff-6c1b-496b-a288-335369058923"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
+                        "annotation": "Calculate statistics from a genome annotation in GFF3 format",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
                         "errors": null,
-                        "id": 3,
-                        "input_connections": {},
+                        "id": 4,
+                        "input_connections": {
+                            "gff": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "ref_genome|genome": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "SNAP model"
+                                "description": "runtime parameter for tool Genome annotation statistics",
+                                "name": "gff"
+                            },
+                            {
+                                "description": "runtime parameter for tool Genome annotation statistics",
+                                "name": "ref_genome"
                             }
                         ],
-                        "label": "SNAP model",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 413.68333435058594,
-                            "height": 61.80000305175781,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 351.8833312988281,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 351.8833312988281
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ebf1f01c-e804-462a-92cf-670012b103b3",
-                        "workflow_outputs": [
+                        "label": "Genome annotation statistics Helixer",
+                        "name": "Genome annotation statistics",
+                        "outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "ecfd7af4-f95c-4b2d-9f06-8e851a0c4d9e"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
+                                "name": "summary",
+                                "type": "txt"
+                            },
                             {
-                                "description": "",
-                                "name": "Augustus model"
+                                "name": "graphs",
+                                "type": "pdf"
                             }
                         ],
-                        "label": "Augustus model",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 554.0833282470703,
-                            "height": 82.19999694824219,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 471.8833312988281,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 471.8833312988281
+                            "left": 1011.9681945236466,
+                            "top": 0.0
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "586af078-09ce-476b-9eb7-55e443a8eeaf",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "8cffbd184762",
+                            "name": "jcvi_gff_stats",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"gff\": {\"__class__\": \"RuntimeValue\"}, \"ref_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.8.4",
+                        "type": "tool",
+                        "uuid": "64572fdd-797c-44e9-8662-2ae4d51528c1",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "7259eb8b-9c2d-4eff-a49d-1b447e905314"
+                                "label": "graphs helixer",
+                                "output_name": "graphs",
+                                "uuid": "a445f12b-685d-47af-b407-90fa7ea935b1"
+                            },
+                            {
+                                "label": "summary helixer",
+                                "output_name": "summary",
+                                "uuid": "8eae8a88-c73d-42dc-ad0d-62d2f1d29c6a"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0",
+                        "annotation": "Visualization",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
                         "errors": null,
                         "id": 5,
                         "input_connections": {
-                            "dataset": {
+                            "reference_genome|genome": {
                                 "id": 0,
                                 "output_name": "output"
+                            },
+                            "track_groups_0|data_tracks_0|data_format|annotation": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Fasta Statistics",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool JBrowse",
+                                "name": "reference_genome"
+                            }
+                        ],
+                        "label": "JBrowse",
+                        "name": "JBrowse",
                         "outputs": [
                             {
-                                "name": "stats",
-                                "type": "tabular"
+                                "name": "output",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "bottom": 34.28334045410156,
-                            "height": 154.40000915527344,
-                            "left": -15.350006103515625,
-                            "right": 184.64999389648438,
-                            "top": -120.11666870117188,
-                            "width": 200,
-                            "x": -15.350006103515625,
-                            "y": -120.11666870117188
+                            "left": 1175.5063439719256,
+                            "top": 231.38681642718768
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "20ca2574216a",
-                            "name": "fasta_stats",
-                            "owner": "simon-gladman",
+                            "changeset_revision": "a6e57ff585c0",
+                            "name": "jbrowse",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
+                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": true, \"aboutDescription\": \"\", \"show_tracklist\": true, \"show_nav\": true, \"show_overview\": true, \"show_menu\": true, \"hideGenomeOptions\": false}, \"plugins\": {\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": false, \"__current_case__\": 1}, \"index\": false, \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.11+galaxy1",
                         "type": "tool",
-                        "uuid": "43cab601-f700-4278-bd0a-7f0997cf75cf",
+                        "uuid": "f77404b0-6e49-4951-9553-65ef0a24499a",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "stats",
-                                "uuid": "7840b5e6-2a7e-4b3c-bea3-4a0d70fea21b"
+                                "label": "JBrowse output",
+                                "output_name": "output",
+                                "uuid": "2bac35a7-8379-4269-9769-e0e0c541f4a3"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "genome-annotation/helixer",
+                "path": "topics/genome-annotation/tutorials/helixer/workflows/Helixer.ga",
+                "tags": [],
+                "test_results": null,
+                "tests": true,
+                "title": "Training - Helixer",
+                "topic_id": "genome-annotation",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-helixer/versions/helixer",
+                "tutorial_id": "helixer",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/helixer/workflows/Helixer.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/helixer/workflows/Helixer.html",
+                "version": 1,
+                "wfid": "genome-annotation-helixer",
+                "wfname": "helixer",
+                "workflow": "Helixer.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/genouest/helixer/helixer/0.3.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/compleasm/compleasm/0.2.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4"
+                ],
+                "workflowhub_id": "1358"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/7867921"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "86755160afbf",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "86755160afbf",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bakta",
+                    "owner": "iuc",
+                    "revisions": "ba6990f72184",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "integron_finder",
+                    "owner": "iuc",
+                    "revisions": "bfd290fe1588",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "isescan",
+                    "owner": "iuc",
+                    "revisions": "9e776e7fab4f",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "jbrowse",
+                    "owner": "iuc",
+                    "revisions": "a6e57ff585c0",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "plasmidfinder",
+                    "owner": "iuc",
+                    "revisions": "7075b7a5441b",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "tbl2gff3",
+                    "owner": "iuc",
+                    "revisions": "4a7f4b0cc0a3",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bakta\n  owner: iuc\n  revisions: ba6990f72184\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: integron_finder\n  owner: iuc\n  revisions: bfd290fe1588\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: isescan\n  owner: iuc\n  revisions: 9e776e7fab4f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: plasmidfinder\n  owner: iuc\n  revisions: 7075b7a5441b\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbl2gff3\n  owner: iuc\n  revisions: 4a7f4b0cc0a3\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "bebatut"
+            ],
+            "funding": [
+                "abromics"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/abromics.png",
+                "funder": true,
+                "github": false,
+                "id": "abromics",
+                "joined": "2024-01",
+                "name": "ABRomics",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abromics/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/abromics.json"
+            }
+        ],
+        "dir": "topics/genome-annotation/tutorials/bacterial-genome-annotation",
+        "edam_ontology": [
+            "topic_0622",
+            "topic_3301",
+            "topic_0623",
+            "topic_0080",
+            "topic_3673",
+            "topic_0085",
+            "topic_0798"
+        ],
+        "edam_operation": [
+            "Genome annotation",
+            "Nucleic acid feature detection",
+            "Multilocus sequence typing",
+            "Genome visualisation",
+            "Genome assembly",
+            "Sequence motif recognition",
+            "Structural variation detection",
+            "Scaffolding",
+            "Protein feature detection"
+        ],
+        "edam_topic": [
+            "Genomics",
+            "Microbiology",
+            "Gene and protein families",
+            "Sequence analysis",
+            "Whole genome sequencing",
+            "Functional genomics",
+            "Mobile genetic elements"
+        ],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.fr"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "genome-annotation",
+                "tutorials": [
+                    "apollo"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "visualisation",
+                "tutorials": [
+                    "circos",
+                    "jbrowse"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "history-to-workflow"
+                ],
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "genome-annotation/bacterial-genome-annotation",
+        "inexact_supported_servers": [
+            "Galaxy@AuBi",
+            "UseGalaxy.cz",
+            "UseGalaxy.org (Main)"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Bakta is a powerful tool to annotate a bacterial genome",
+            "Annotation can be easily visualized to understand the genomic context and help making sense of the annotations"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-08",
+        "objectives": [
+            "Run a series of tool to annotate a draft bacterial genome for different types of genomic components",
+            "Evaluate the annotation",
+            "Process the outputs to formate them for visualization needs",
+            "Visualize a draft bacterial genome and its annotations"
+        ],
+        "pageviews": 2969,
+        "pub_date": "2024-02-01",
+        "questions": [
+            "Which genes are on a draft bacterial genome?",
+            "Which other genomic components can be found on a draft bacterial genome?"
+        ],
+        "recordings": [
+            {
+                "bot-timestamp": 1725267714,
+                "captioners": [
+                    "bebatut"
+                ],
+                "date": "2024-09-02",
+                "galaxy_version": "24.0.4.dev0",
+                "length": "44M",
+                "speakers": [
+                    "bebatut"
+                ],
+                "youtube_id": "VOwplmv0vNs"
+            }
+        ],
+        "short_id": "T00403",
+        "short_tools": [
+            "jbrowse",
+            "tbl2gff3",
+            "plasmidfinder",
+            "integron_finder",
+            "upload1",
+            "isescan",
+            "tp_tail_tool",
+            "bakta",
+            "tp_replace_in_column",
+            "Grouping1"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "prokaryote",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "gmod",
+            "illumina",
+            "bacteria",
+            "microgalaxy",
+            "jbrowse1"
+        ],
+        "time_estimation": "3H",
+        "title": "Bacterial Genome Annotation",
+        "tools": [
+            "Grouping1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2",
+            "upload1"
+        ],
+        "topic_name": "genome-annotation",
+        "topic_name_human": "Genome Annotation",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "bacterial-genome-annotation",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.json"
+        },
+        "version": 5,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 140,
+        "visitors": 2243,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0001-9852-1987",
+                        "name": "B\u00e9r\u00e9nice Batut"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0002-8304-138X",
+                        "name": "Pierre Marin"
+                    }
+                ],
+                "description": "Bacterial Genome Annotation",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontigs\"]\n  1[label=\"ISEScan\"]\n  0 -> 1 [label=\"output\"]\n  k2bb672cb453646b08a228590a0ca36c7[color=lightseagreen,label=\"Output\\nisescan_results\"]\n  1 -> k2bb672cb453646b08a228590a0ca36c7\n  2[label=\"PlasmidFinder\"]\n  0 -> 2 [label=\"output\"]\n  k614064e64b0f4e38b04ee3f61ba41b46[color=lightseagreen,label=\"Output\\nplasmidfinder_results\"]\n  2 -> k614064e64b0f4e38b04ee3f61ba41b46\n  3[label=\"Integron Finder\"]\n  0 -> 3 [label=\"output\"]\n  kd26788cf24414f29ac39b6be96f192eb[color=lightseagreen,label=\"Output\\nintegronfinder_summary\"]\n  3 -> kd26788cf24414f29ac39b6be96f192eb\n  4[label=\"Bakta\"]\n  0 -> 4 [label=\"output\"]\n  kd3a40a8b1bd142b6a91e756379b86d94[color=lightseagreen,label=\"Output\\nbakta_summary\"]\n  4 -> kd3a40a8b1bd142b6a91e756379b86d94\n  5[label=\"Group\"]\n  1 -> 5 [label=\"all_results\"]\n  6[label=\"Group\"]\n  1 -> 6 [label=\"all_results\"]\n  7[label=\"Replace Text\"]\n  2 -> 7 [label=\"result_file\"]\n  8[label=\"Select last\"]\n  7 -> 8 [label=\"outfile\"]\n  9[label=\"Table to GFF3\"]\n  8 -> 9 [label=\"outfile\"]\n  10[label=\"JBrowse\"]\n  0 -> 10 [label=\"output\"]\n  4 -> 10 [label=\"annotation_gff3\"]\n  9 -> 10 [label=\"output\"]\n  1 -> 10 [label=\"annotation\"]\n}",
+                "history": [
+                    {
+                        "hash": "87968f9a6953ebf322d9fb0fae3a4193b6222288",
+                        "message": "Update tool versions",
+                        "num": 2,
+                        "short_hash": "87968f9a6",
+                        "unix": "1722510143"
+                    },
+                    {
+                        "hash": "217f251aaa898a91dbb18b5cec3daebaf582c712",
+                        "message": "Update worklow and add tests",
+                        "num": 1,
+                        "short_hash": "217f251aa",
+                        "unix": "1706526984"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "contigs",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "contigs",
+                                "name": "contigs"
                             }
-                        ]
-                    },
+                        ],
+                        "label": "contigs",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 424
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "8cde8af1-c277-4b9f-97f7-54f5997f2c5d",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "AGPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"ISEScan\"];\n  0 -->|output| 1;\n  2bb672cb-4536-46b0-8a22-8590a0ca36c7[\"Output\\nisescan_results\"];\n  1 --> 2bb672cb-4536-46b0-8a22-8590a0ca36c7;\n  style 2bb672cb-4536-46b0-8a22-8590a0ca36c7 stroke:#2c3143,stroke-width:4px;\n  2[\"PlasmidFinder\"];\n  0 -->|output| 2;\n  614064e6-4b0f-4e38-b04e-e3f61ba41b46[\"Output\\nplasmidfinder_results\"];\n  2 --> 614064e6-4b0f-4e38-b04e-e3f61ba41b46;\n  style 614064e6-4b0f-4e38-b04e-e3f61ba41b46 stroke:#2c3143,stroke-width:4px;\n  3[\"Integron Finder\"];\n  0 -->|output| 3;\n  d26788cf-2441-4f29-ac39-b6be96f192eb[\"Output\\nintegronfinder_summary\"];\n  3 --> d26788cf-2441-4f29-ac39-b6be96f192eb;\n  style d26788cf-2441-4f29-ac39-b6be96f192eb stroke:#2c3143,stroke-width:4px;\n  4[\"Bakta\"];\n  0 -->|output| 4;\n  d3a40a8b-1bd1-42b6-a91e-756379b86d94[\"Output\\nbakta_summary\"];\n  4 --> d3a40a8b-1bd1-42b6-a91e-756379b86d94;\n  style d3a40a8b-1bd1-42b6-a91e-756379b86d94 stroke:#2c3143,stroke-width:4px;\n  5[\"Group\"];\n  1 -->|all_results| 5;\n  6[\"Group\"];\n  1 -->|all_results| 6;\n  7[\"Replace Text\"];\n  2 -->|result_file| 7;\n  8[\"Select last\"];\n  7 -->|outfile| 8;\n  9[\"Table to GFF3\"];\n  8 -->|outfile| 9;\n  10[\"JBrowse\"];\n  0 -->|output| 10;\n  4 -->|annotation_gff3| 10;\n  9 -->|output| 10;\n  1 -->|annotation| 10;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Bacterial Genome Annotation",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
                         "errors": null,
-                        "id": 6,
+                        "id": 1,
                         "input_connections": {
-                            "input": {
+                            "input_file": {
                                 "id": 0,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Busco",
+                        "name": "ISEScan",
                         "outputs": [
                             {
-                                "name": "busco_sum",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "busco_table",
+                                "name": "summary",
                                 "type": "tabular"
                             },
                             {
-                                "name": "busco_missing",
+                                "name": "all_results",
                                 "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": -157.71664428710938,
-                            "height": 276.4000244140625,
-                            "left": -15.350006103515625,
-                            "right": 184.64999389648438,
-                            "top": -434.1166687011719,
-                            "width": 200,
-                            "x": -15.350006103515625,
-                            "y": -434.1166687011719
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "602fb8e63aa7",
-                            "name": "busco",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"geno\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.1.4",
-                        "type": "tool",
-                        "uuid": "876334be-d7e5-4504-bb1b-727472839c02",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "busco_sum",
-                                "uuid": "59ce9dc8-762f-4c38-aded-5d031db50609"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "busco_missing",
-                                "uuid": "9b000535-1702-4888-951c-4cc8e782a511"
                             },
                             {
-                                "label": null,
-                                "output_name": "busco_table",
-                                "uuid": "76c0d8fc-4e81-4ba0-b8b2-ebfda0ba5786"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "maker_gff": {
-                                "id": 7,
-                                "output_name": "output_gff"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Map annotation ids",
-                        "outputs": [
-                            {
-                                "name": "renamed",
+                                "name": "annotation",
                                 "type": "gff"
                             },
                             {
-                                "name": "id_map",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 318.8833312988281,
-                            "height": 246,
-                            "left": 272.66668701171875,
-                            "right": 472.66668701171875,
-                            "top": 72.88333129882812,
-                            "width": 200,
-                            "x": 272.66668701171875,
-                            "y": 72.88333129882812
-                        },
-                        "post_job_actions": {
-                            "ChangeDatatypeActionrenamed": {
-                                "action_arguments": {
-                                    "newtype": "gff3"
-                                },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "renamed"
-                            },
-                            "HideDatasetActionid_map": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "id_map"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f1912d5575df",
-                            "name": "maker_map_ids",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"justify\": \"6\", \"maker_gff\": {\"__class__\": \"ConnectedValue\"}, \"prefix\": \"TEST\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.31.11",
-                        "type": "tool",
-                        "uuid": "b1127093-0aae-4bfa-b474-042b838a8299",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "renamed",
-                                "uuid": "e8686326-b443-402b-bb0e-b4a02a8815a7"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "gff": {
-                                "id": 8,
-                                "output_name": "renamed"
+                                "name": "is_fasta",
+                                "type": "fasta"
                             },
-                            "ref_genome|genome": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Genome annotation statistics",
-                        "outputs": [
                             {
-                                "name": "summary",
-                                "type": "txt"
+                                "name": "orf_fna",
+                                "type": "fasta"
                             },
                             {
-                                "name": "graphs",
-                                "type": "pdf"
+                                "name": "orf_faa",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "bottom": 363.2833557128906,
-                            "height": 276.4000244140625,
-                            "left": 560.6500244140625,
-                            "right": 760.6500244140625,
-                            "top": 86.88333129882812,
-                            "width": 200,
-                            "x": 560.6500244140625,
-                            "y": 86.88333129882812
+                            "left": 280,
+                            "top": 133
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "8cffbd184762",
-                            "name": "jcvi_gff_stats",
+                            "changeset_revision": "19f42b3ea391",
+                            "name": "isescan",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"gff\": {\"__class__\": \"ConnectedValue\"}, \"ref_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.8.4",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"log_activate\": false, \"remove_short_is\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.2.3+galaxy1",
                         "type": "tool",
-                        "uuid": "14236032-ec57-4beb-ab0a-e44bf845643c",
+                        "uuid": "334b327f-be00-4e75-ae01-c3ba674dbc9b",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "graphs",
-                                "uuid": "782e21db-4be6-4230-92b5-3ea9004dda04"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "summary",
-                                "uuid": "a4dff39c-0479-4a25-ac62-b132c1083604"
+                                "label": "isescan_results",
+                                "output_name": "all_results",
+                                "uuid": "2bb672cb-4536-46b0-8a22-8590a0ca36c7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1",
                         "errors": null,
-                        "id": 10,
+                        "id": 2,
                         "input_connections": {
-                            "input": {
-                                "id": 8,
-                                "output_name": "renamed"
-                            },
-                            "reference_genome|genome_fasta": {
+                            "input|input_file": {
                                 "id": 0,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool gffread",
-                                "name": "chr_replace"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "gffread",
+                        "name": "PlasmidFinder",
                         "outputs": [
                             {
-                                "name": "output_exons",
+                                "name": "hit_file",
                                 "type": "fasta"
                             },
                             {
-                                "name": "output_cds",
+                                "name": "plasmid_file",
                                 "type": "fasta"
                             },
                             {
-                                "name": "output_pep",
-                                "type": "fasta"
+                                "name": "result_file",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "raw_file",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 48.683319091796875,
-                            "height": 316.79998779296875,
-                            "left": 560.6500244140625,
-                            "right": 760.6500244140625,
-                            "top": -268.1166687011719,
-                            "width": 200,
-                            "x": 560.6500244140625,
-                            "y": -268.1166687011719
+                            "left": 280,
+                            "top": 420
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "0232f19d300f",
-                            "name": "gffread",
-                            "owner": "devteam",
+                            "changeset_revision": "7075b7a5441b",
+                            "name": "plasmidfinder",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"chr_replace\": {\"__class__\": \"RuntimeValue\"}, \"decode_url\": \"false\", \"expose\": \"false\", \"filtering\": null, \"full_gff_attribute_preservation\": \"false\", \"gffs\": {\"gff_fmt\": \"none\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"maxintron\": \"\", \"merging\": {\"merge_sel\": \"none\", \"__current_case__\": 0}, \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 2, \"genome_fasta\": {\"__class__\": \"ConnectedValue\"}, \"ref_filtering\": null, \"fa_outputs\": [\"-w exons.fa\", \"-x cds.fa\", \"-y pep.fa\"]}, \"region\": {\"region_filter\": \"none\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.2.1.1",
+                        "tool_state": "{\"input\": {\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"database_name\": \"plasmidfinder_1307168_2019_08_28\"}, \"options\": {\"min_cov\": \"0.6\", \"threshold\": \"0.95\"}, \"output_files\": {\"output_selection\": [\"hit_fasta\", \"plasmid_fasta\", \"result_tsv\", \"result_txt\"]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.6+galaxy1",
                         "type": "tool",
-                        "uuid": "3b5ecaf4-2d08-42f8-a6f0-f05ad9e5fe92",
+                        "uuid": "484ea537-4097-4097-b19c-84fef6c7de9a",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_cds",
-                                "uuid": "0df7b9b5-1ed1-4cf4-b483-a604862f4540"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_exons",
-                                "uuid": "f485f8fe-0d63-49ba-a88d-dfc8e03db553"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_pep",
-                                "uuid": "7430528c-9af5-4e05-ba6c-bbf95f19ad7e"
+                                "label": "plasmidfinder_results",
+                                "output_name": "result_file",
+                                "uuid": "614064e6-4b0f-4e38-b04e-e3f61ba41b46"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
                         "errors": null,
-                        "id": 11,
+                        "id": 3,
                         "input_connections": {
-                            "reference_genome|genome": {
+                            "sequence": {
                                 "id": 0,
                                 "output_name": "output"
-                            },
-                            "track_groups_0|data_tracks_0|data_format|annotation": {
-                                "id": 8,
-                                "output_name": "renamed"
-                            },
-                            "track_groups_1|data_tracks_0|data_format|annotation": {
-                                "id": 7,
-                                "output_name": "output_evidences"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool JBrowse",
-                                "name": "reference_genome"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "JBrowse",
+                        "name": "Integron Finder",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "html"
+                                "name": "integrons_table",
+                                "type": "tsv"
+                            },
+                            {
+                                "name": "summary",
+                                "type": "tsv"
                             }
                         ],
                         "position": {
-                            "bottom": 677.2833557128906,
-                            "height": 276.4000244140625,
-                            "left": 560.6500244140625,
-                            "right": 760.6500244140625,
-                            "top": 400.8833312988281,
-                            "width": 200,
-                            "x": 560.6500244140625,
-                            "y": 400.8833312988281
+                            "left": 280,
+                            "top": 665
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3",
+                        "post_job_actions": {
+                            "ChangeDatatypeActionintegrons_table": {
+                                "action_arguments": {
+                                    "newtype": "tabular"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "integrons_table"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "8774b28235bb",
-                            "name": "jbrowse",
+                            "changeset_revision": "4768f7f8e93f",
+                            "name": "integron_finder",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Maker annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 1, \"category\": \"Maker evidences\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"true\", \"__current_case__\": 0, \"name\": {\"__class__\": \"RuntimeValue\"}}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16.10+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"gbk\": false, \"local_max\": true, \"no_logfile\": true, \"pdf\": false, \"promoter_attI\": true, \"sequence\": {\"__class__\": \"ConnectedValue\"}, \"settings\": {\"attc_settings\": {\"dist_thresh\": \"4000\", \"calin_threshold\": \"2\", \"max_attc_size\": \"200\", \"min_attc_size\": \"40\", \"keep_palindromes\": false, \"covar_matrix\": null}, \"protein_settings\": {\"no_proteins\": false, \"union_integrases\": false, \"func_annot\": false}}, \"topology_file\": null, \"type_replicon\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.5+galaxy0",
                         "type": "tool",
-                        "uuid": "5a978f9d-7adc-4e30-8b20-dcfa27f18dfa",
+                        "uuid": "29a9252c-5c3b-4024-99ff-637d0572320a",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "c7432de7-b6b4-457a-8c0a-69c44418234d"
+                                "label": "integronfinder_summary",
+                                "output_name": "summary",
+                                "uuid": "d26788cf-2441-4f29-ac39-b6be96f192eb"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0",
                         "errors": null,
-                        "id": 12,
+                        "id": 4,
                         "input_connections": {
-                            "input": {
-                                "id": 10,
-                                "output_name": "output_exons"
+                            "input_option|input_file": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Busco",
+                        "name": "Bakta",
                         "outputs": [
                             {
-                                "name": "busco_sum",
-                                "type": "txt"
+                                "name": "annotation_tsv",
+                                "type": "tabular"
                             },
                             {
-                                "name": "busco_table",
-                                "type": "tabular"
+                                "name": "annotation_gff3",
+                                "type": "gff3"
                             },
                             {
-                                "name": "busco_missing",
-                                "type": "tabular"
+                                "name": "annotation_ffn",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "summary_txt",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "annotation_plot",
+                                "type": "svg"
                             }
                         ],
                         "position": {
-                            "bottom": 100.88333129882812,
-                            "height": 256,
-                            "left": 838.6666870117188,
-                            "right": 1038.6666870117188,
-                            "top": -155.11666870117188,
-                            "width": 200,
-                            "x": 838.6666870117188,
-                            "y": -155.11666870117188
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionbusco_missing": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "busco_missing"
-                            },
-                            "HideDatasetActionbusco_table": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "busco_table"
-                            }
+                            "left": 850,
+                            "top": 0
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "602fb8e63aa7",
-                            "name": "busco",
+                            "changeset_revision": "728dacaf08a9",
+                            "name": "bakta",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"tran\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.1.4",
+                        "tool_state": "{\"__input_ext\": \"input\", \"annotation\": {\"complete\": false, \"prodigal\": null, \"translation_table\": \"11\", \"keep_contig_headers\": true, \"replicons\": null, \"compliant\": false, \"proteins\": null, \"meta\": false}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input_option\": {\"bakta_db_select\": \"V5.0_2023-02-20\", \"amrfinder_db_select\": \"amrfinderplus_V3.11_2022-12-19.1\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"min_contig_length\": null}, \"organism\": {\"genus\": null, \"species\": null, \"strain\": null, \"plasmid\": null}, \"output_files\": {\"output_selection\": [\"file_tsv\", \"file_gff3\", \"file_ffn\", \"file_plot\", \"sum_txt\"]}, \"workflow\": {\"skip_analysis\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.3+galaxy0",
                         "type": "tool",
-                        "uuid": "dee27b5d-de92-4e99-898c-3bf3fea6ee72",
+                        "uuid": "181220e7-9082-48bc-b855-f10baf78fc2a",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Busco summary final round",
-                                "output_name": "busco_sum",
-                                "uuid": "6951417b-ee0b-4e03-98e4-67d262e086dc"
+                                "label": "bakta_summary",
+                                "output_name": "summary_txt",
+                                "uuid": "d3a40a8b-1bd1-42b6-a91e-756379b86d94"
                             }
                         ]
                     }
                 ],
-                "parent_id": "genome-annotation/annotation-with-maker-short",
-                "path": "topics/genome-annotation/tutorials/annotation-with-maker-short/workflows/main_workflow.ga",
+                "parent_id": "genome-annotation/bacterial-genome-annotation",
+                "path": "topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.ga",
                 "tags": [
                     "genome-annotation"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "Genome annotation with Maker (short)",
+                "tests": true,
+                "title": "Bacterial Genome Annotation",
                 "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-annotation-with-maker-short/versions/main-workflow",
-                "tutorial_id": "annotation-with-maker-short",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-maker-short/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-maker-short/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "genome-annotation-annotation-with-maker-short",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-bacterial-genome-annotation/versions/bacterial-genome-annotation",
+                "tutorial_id": "bacterial-genome-annotation",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.html",
+                "version": 2,
+                "wfid": "genome-annotation-bacterial-genome-annotation",
+                "wfname": "bacterial-genome-annotation",
+                "workflow": "Bacterial-Genome-Annotation.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.10",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10",
-                    "toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0"
+                    "Grouping1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2"
                 ],
-                "workflowhub_id": "1194"
+                "workflowhub_id": "1136"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.4406623"
+        "zenodo_link": "https://zenodo.org/record/10572227"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/introduction/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "eurosciencegateway",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
+                "fediverse_flavor": "mastodon",
+                "id": "abretaud",
+                "joined": "2017-09",
+                "location": {
+                    "country": "FR",
+                    "lat": 48.11,
+                    "lon": -1.64
+                },
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            }
+        ],
+        "dir": "topics/genome-annotation/tutorials/introduction",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": false,
+        "id": "genome-annotation/introduction",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "layout": "introduction_slides",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "logo": "GTN",
+        "mod_date": "2024-05-31",
+        "pageviews": 5897171,
+        "priority": 1,
+        "pub_date": "2019-05-13",
+        "redirect_from": [
+            "/topics/genome-annotation/slides/introduction",
+            "/short/genome-annotation/introduction/slides",
+            "/short/S00069"
+        ],
+        "short_id": "S00069",
+        "short_tools": [],
+        "slides": true,
+        "slides_recordings": false,
+        "subtopic": "intro",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "title": "Introduction to Genome Annotation",
+        "tools": [],
+        "topic_name": "genome-annotation",
+        "topic_name_human": "Genome Annotation",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "introduction",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/introduction/slides.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/introduction/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/introduction/slides.json"
+        },
+        "version": 3,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 152,
+        "visitors": 2133582
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/official-gene-set/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "abretaud"
+            ],
+            "funding": [
+                "gallantries"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "eurosciencegateway",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
+                "fediverse_flavor": "mastodon",
+                "id": "abretaud",
+                "joined": "2017-09",
+                "location": {
+                    "country": "FR",
+                    "lat": 48.11,
+                    "lon": -1.64
+                },
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            }
+        ],
+        "dir": "topics/genome-annotation/tutorials/official-gene-set",
+        "draft": true,
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "genome-annotation/official-gene-set",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Genoest' OGS Tools makes it easy to validate and release a build of your genome and its annotations."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-02-29",
+        "objectives": [
+            "Validate your genes and create an official gene set from them."
+        ],
+        "pageviews": 12,
+        "pub_date": "2023-11-02",
+        "questions": [
+            "I have several genomes assemblies that are not annotated (or I do not trust annotations)",
+            "I am interested to compare structure of a particular gene across these genome assemblies",
+            "How do I do that?"
+        ],
+        "short_id": "T00370",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "gmod",
+            "apollo2",
+            "work-in-progress"
+        ],
+        "time_estimation": "30M",
+        "title": "Creating an Official Gene Set",
+        "tools": [],
+        "topic_name": "genome-annotation",
+        "topic_name_human": "Genome Annotation",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "official-gene-set",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/official-gene-set/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/official-gene-set/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/official-gene-set/tutorial.json"
+        },
+        "version": 2,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 0,
+        "visitors": 10,
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/genome-annotation/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "eurosciencegateway",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "elixir_node": "de",
+                "email": "anikaerxleben@gmail.com",
+                "id": "erxleben",
+                "joined": "2017-09",
+                "name": "Anika Erxleben",
+                "orcid": "0000-0002-7427-6478",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/erxleben/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/erxleben.json"
+            },
+            {
+                "affiliations": [
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
+                "fediverse_flavor": "mastodon",
+                "id": "bgruening",
+                "joined": "2017-09",
+                "linkedin": "bgruening",
+                "location": {
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
+                },
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+            }
+        ],
+        "dir": "topics/genome-annotation/tutorials/genome-annotation",
+        "draft": true,
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "genome-annotation/genome-annotation",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": null,
+        "layout": "tutorial_hands_on",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": null,
+        "pageviews": 61614,
+        "pub_date": "2015-06-29",
+        "questions": null,
+        "short_id": "T00175",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "prokaryote",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "prokaryote",
+            "work-in-progress"
+        ],
+        "time_estimation": "2H",
+        "title": "Genome Annotation",
+        "tools": [],
+        "topic_name": "genome-annotation",
+        "topic_name_human": "Genome Annotation",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "genome-annotation",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/genome-annotation/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/genome-annotation/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/genome-annotation/tutorial.json"
+        },
+        "version": 16,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 86,
+        "visitors": 33198,
+        "zenodo_link": "https://doi.org/10.5281/zenodo.1250793"
     },
     {
+        "abbreviations": {
+            "NMDS": "Non-metric multidimensional scaling"
+        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "deeptools_bam_coverage",
+                    "name": "interproscan",
                     "owner": "bgruening",
-                    "revisions": "bb1e4f63e0e6",
-                    "tool_panel_section_label": "deepTools",
+                    "revisions": "74810db257cc",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "find_subsequences",
-                    "owner": "bgruening",
-                    "revisions": "d882a0a75759",
+                    "name": "picard",
+                    "owner": "devteam",
+                    "revisions": "f9242e01365a",
+                    "tool_panel_section_label": "Picard",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "eggnog_mapper",
+                    "owner": "galaxyp",
+                    "revisions": "844fa988236b",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "aegean_parseval",
+                    "owner": "iuc",
+                    "revisions": "1b52f0c8ad7f",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "busco",
+                    "owner": "iuc",
+                    "revisions": "94170eee0ad8",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "funannotate_annotate",
+                    "owner": "iuc",
+                    "revisions": "9feee7fc49a1",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bowtie_wrappers",
-                    "owner": "devteam",
-                    "revisions": "b46e7d48076a",
-                    "tool_panel_section_label": "Mapping",
+                    "name": "funannotate_annotate",
+                    "owner": "iuc",
+                    "revisions": "582fd74dc2a1",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "funannotate_compare",
+                    "owner": "iuc",
+                    "revisions": "a7ce2601500c",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "funannotate_compare",
+                    "owner": "iuc",
+                    "revisions": "30f08d74024f",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "column_maker",
-                    "owner": "devteam",
-                    "revisions": "be25c075ed54",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "funannotate_predict",
+                    "owner": "iuc",
+                    "revisions": "51b6ee65ef7f",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "gff_to_prot",
+                    "name": "funannotate_predict",
                     "owner": "iuc",
-                    "revisions": "07d7991bf205",
+                    "revisions": "f31125bb85ea",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "transit_gumbel",
+                    "name": "jbrowse",
                     "owner": "iuc",
-                    "revisions": "f50807720df1",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "a6e57ff585c0",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cutadapt",
-                    "owner": "lparsons",
-                    "revisions": "49370cb85f0f",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "rgrnastar",
+                    "owner": "iuc",
+                    "revisions": "3ea5a2a63fa2",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rgrnastar",
+                    "owner": "iuc",
+                    "revisions": "4074fc1940e2",
+                    "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: deeptools_bam_coverage\n  owner: bgruening\n  revisions: bb1e4f63e0e6\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: find_subsequences\n  owner: bgruening\n  revisions: d882a0a75759\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie_wrappers\n  owner: devteam\n  revisions: b46e7d48076a\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: be25c075ed54\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gff_to_prot\n  owner: iuc\n  revisions: 07d7991bf205\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: transit_gumbel\n  owner: iuc\n  revisions: f50807720df1\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 49370cb85f0f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/tnseq/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: interproscan\n  owner: bgruening\n  revisions: 74810db257cc\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: f9242e01365a\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: eggnog_mapper\n  owner: galaxyp\n  revisions: 844fa988236b\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: aegean_parseval\n  owner: iuc\n  revisions: 1b52f0c8ad7f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 94170eee0ad8\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_annotate\n  owner: iuc\n  revisions: 9feee7fc49a1\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_annotate\n  owner: iuc\n  revisions: 582fd74dc2a1\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_compare\n  owner: iuc\n  revisions: a7ce2601500c\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_compare\n  owner: iuc\n  revisions: 30f08d74024f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_predict\n  owner: iuc\n  revisions: 51b6ee65ef7f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_predict\n  owner: iuc\n  revisions: f31125bb85ea\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n  owner: iuc\n  revisions: 3ea5a2a63fa2\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n  owner: iuc\n  revisions: 4074fc1940e2\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/funannotate/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "abretaud"
+            ],
+            "editing": [
+                "alexcorm",
+                "lleroi",
+                "r1corre",
+                "stephanierobin"
+            ],
+            "funding": [
+                "gallantries",
+                "eurosciencegateway"
+            ]
+        },
         "contributors": [
-            {
-                "email": "delphine.lariviere@galaxy.org",
-                "id": "delphine-l",
-                "joined": "2017-09",
-                "name": "Delphine Lariviere",
-                "orcid": "0000-0001-6421-3484",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
-                    "ifb",
+                    "eurosciencegateway",
                     "elixir-europe"
                 ],
                 "contact_for_training": true,
                 "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
                 "fediverse_flavor": "mastodon",
-                "id": "bebatut",
+                "id": "abretaud",
                 "joined": "2017-09",
-                "linkedin": "berenicebatut",
                 "location": {
                     "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
+                    "lat": 48.11,
+                    "lon": -1.64
                 },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+            },
+            {
+                "email": "alexandre.cormier@ifremer.fr",
+                "id": "alexcorm",
+                "joined": "2021-11",
+                "name": "Alexandre Cormier",
+                "orcid": "0000-0002-7775-8413",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/",
+                "twitter": "allanssx",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/alexcorm.json"
+            },
+            {
+                "email": "laura.leroi@ifremer.fr",
+                "id": "lleroi",
+                "joined": "2021-11",
+                "name": "Laura Leroi",
+                "orcid": "0000-0003-3748-4179",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lleroi/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/lleroi.json"
+            },
+            {
+                "email": "erwan.corre@sb-roscoff.fr",
+                "id": "r1corre",
+                "joined": "2019-04",
+                "name": "Erwan Corre",
+                "orcid": "0000-0001-6354-2278",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/r1corre/",
+                "twitter": "r1corre",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/r1corre.json"
+            },
+            {
+                "email": "stephanie.robin@inrae.fr",
+                "id": "stephanierobin",
+                "joined": "2021-11",
+                "name": "St\u00e9phanie Robin",
+                "orcid": "0000-0001-7379-9173",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/",
+                "twitter": "robinstphanie1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/stephanierobin.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/eurosciencegateway.png",
+                "funder": true,
+                "funding_id": "101057388",
+                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "eurosciencegateway",
+                "joined": "2023-10",
+                "members": [
+                    "abretaud",
+                    "anuprulez",
+                    "bgruening",
+                    "erxleben",
+                    "pauldg",
+                    "rlibouba"
+                ],
+                "name": "EuroScienceGateway",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
             }
         ],
-        "dir": "topics/genome-annotation/tutorials/tnseq",
-        "edam_ontology": [
-            "topic_0622",
-            "topic_3301",
-            "topic_0080",
-            "topic_0798"
-        ],
+        "dir": "topics/genome-annotation/tutorials/funannotate",
         "edam_operation": [
-            "Transposon prediction",
-            "Primer removal",
-            "Sequence trimming",
-            "Read pre-processing"
-        ],
-        "edam_topic": [
-            "Genomics",
-            "Microbiology",
-            "Sequence analysis",
-            "Mobile genetic elements"
+            "Genome annotation",
+            "Sequence alignment",
+            "Genome visualisation",
+            "Genome assembly",
+            "Sequence motif recognition",
+            "Query and retrieval",
+            "Fold recognition",
+            "Homology-based gene prediction",
+            "Sequence assembly validation",
+            "Scaffolding",
+            "Information extraction",
+            "Sequence annotation",
+            "Transcriptome assembly",
+            "Protein feature detection",
+            "Formatting"
         ],
+        "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "genome-annotation",
+                "tutorials": [
+                    "apollo"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "genome-annotation/tnseq",
+        "id": "genome-annotation/funannotate",
         "inexact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.eu"
+            "UseGalaxy.org.au"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "TnSeq is a useful analysis to detect essential genes and conditional essential genes",
-            "The saturation of the library must be sufficient so that every gene must have been impacted at least once",
-            "Be sure you have removed every transposon sequence before starting your analysis",
-            "Verify the results manually do separate domain essential and essential genes"
+            "Funannotate allows to perform structural annotation of an eukaryotic genome.",
+            "Functional annotation can be performed using EggNOG-mapper and InterProScan.",
+            "BUSCO and JBrowse allow to inspect the quality of an annotation.",
+            "Funannotate allows to format an annotation for sumission at NCBI."
         ],
         "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-18",
+        "mod_date": "2024-08-21",
         "objectives": [
-            "Understand the read structure of TnSeq analyses",
-            "Predict Essential genes with Transit",
-            "Compare gene essentiality in control sample and an different experimental condition"
+            "Load genome into Galaxy",
+            "Annotate genome with Funannotate",
+            "Perform functional annotation using EggNOG-mapper and InterProScan",
+            "Evaluate annotation quality with BUSCO",
+            "View annotations in JBrowse"
         ],
-        "pageviews": 5739476,
-        "priority": 4,
-        "pub_date": "2019-07-02",
+        "pageviews": 10859,
+        "priority": 2,
+        "pub_date": "2021-11-29",
         "questions": [
-            "What is Transposon insertion Sequencing?",
-            "How to get TA sites Coverage ? ",
-            "How to predict essential genes ?"
+            "How to annotate an eukaryotic genome with Funannotate?",
+            "How to perform functional annotation?",
+            "How to evaluate and visualize annotated genomic features?",
+            "How to format the annotation for submission at NCBI?"
         ],
-        "short_id": "T00179",
+        "recordings": [
+            {
+                "captioners": [
+                    "abretaud"
+                ],
+                "date": "2023-05-12",
+                "galaxy_version": "23.01",
+                "length": "1H10M",
+                "speakers": [
+                    "abretaud"
+                ],
+                "youtube_id": "p0NBxZk5964"
+            },
+            {
+                "captioners": [
+                    "abretaud"
+                ],
+                "date": "2022-03-03",
+                "galaxy_version": "21.09",
+                "length": "1H10M",
+                "speakers": [
+                    "abretaud"
+                ],
+                "youtube_id": "r-wU6BhqIpk"
+            }
+        ],
+        "requirements": [
+            {
+                "topic_name": "genome-annotation",
+                "tutorials": [
+                    "repeatmasker"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00172",
         "short_tools": [
-            "transit_gumbel",
-            "Add_a_column1",
-            "deeptools_bam_coverage",
-            "tp_easyjoin_tool",
-            "bg_find_subsequences",
-            "Cut1",
-            "Filter1",
-            "tp_sort_header_tool",
-            "bowtie_wrapper",
-            "gff_to_prot",
-            "cutadapt",
-            "__EXTRACT_DATASET__"
+            "jbrowse",
+            "rna_star",
+            "eggnog_mapper",
+            "funannotate_compare",
+            "busco",
+            "funannotate_predict",
+            "picard_MergeSamFiles",
+            "interproscan",
+            "funannotate_annotate",
+            "aegean_parseval"
         ],
-        "slides": true,
+        "slides": false,
         "slides_recordings": false,
-        "subtopic": "prokaryote",
+        "subtopic": "eukaryote",
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 }
             ],
             "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
         "tags": [
-            "bacteria",
-            "tnseq",
-            "essential genes",
-            "microgalaxy"
+            "gmod",
+            "eukaryote",
+            "jbrowse1"
         ],
-        "time_estimation": "7H",
-        "title": "Essential genes detection with Transposon insertion sequencing",
+        "time_estimation": "8h",
+        "title": "Genome annotation with Funannotate",
         "tools": [
-            "Cut1",
-            "Filter1",
-            "__EXTRACT_DATASET__",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/find_subsequences/bg_find_subsequences/0.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/gff_to_prot/gff_to_prot/3.0.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/3.0.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy0"
         ],
         "topic_name": "genome-annotation",
         "topic_name_human": "Genome Annotation",
@@ -103878,1930 +105117,2743 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "tnseq",
+        "tutorial_name": "funannotate",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/funannotate/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/tnseq/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/tnseq/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/funannotate/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/funannotate/tutorial.json"
         },
-        "version": 12,
+        "version": 23,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 255,
-        "visitors": 2070408,
+        "visit_duration": 127,
+        "visitors": 7195,
         "workflows": [
             {
-                "creators": [],
-                "description": "Essential genes detection with Transposon insertion sequencing",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0003-0914-2470",
+                        "name": "Anthony Bretaudeau"
+                    }
+                ],
+                "description": "Structural and functional genome annotation with Funannotate",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTnseq-Tutorial-reads.fastqsanger.gz\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncondition_barcodes.fasta\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nconstruct_barcodes.fasta\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nstaph_aur.fasta\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nstaph_aur.gff3\"]\n  5[label=\"Cutadapt\"]\n  0 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"Nucleotide subsequence search\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"Convert GFF3\"]\n  4 -> 7 [label=\"output\"]\n  8[label=\"Cutadapt\"]\n  5 -> 8 [label=\"split_output\"]\n  9[label=\"Cut\"]\n  6 -> 9 [label=\"output\"]\n  10[label=\"Cut\"]\n  6 -> 10 [label=\"output\"]\n  11[label=\"Cutadapt\"]\n  8 -> 11 [label=\"out1\"]\n  12[label=\"Compute\"]\n  10 -> 12 [label=\"out_file1\"]\n  13[label=\"Cutadapt\"]\n  11 -> 13 [label=\"out1\"]\n  2 -> 13 [label=\"output\"]\n  14[label=\"Cut\"]\n  12 -> 14 [label=\"out_file1\"]\n  15[label=\"Cutadapt\"]\n  13 -> 15 [label=\"split_output\"]\n  16[label=\"Map with Bowtie for Illumina\"]\n  3 -> 16 [label=\"output\"]\n  15 -> 16 [label=\"out1\"]\n  17[label=\"bamCoverage\"]\n  16 -> 17 [label=\"output\"]\n  18[label=\"Join\"]\n  17 -> 18 [label=\"outFileName\"]\n  9 -> 18 [label=\"out_file1\"]\n  19[label=\"Join\"]\n  17 -> 19 [label=\"outFileName\"]\n  14 -> 19 [label=\"out_file1\"]\n  20[label=\"Cut\"]\n  18 -> 20 [label=\"output\"]\n  21[label=\"Cut\"]\n  19 -> 21 [label=\"output\"]\n  22[label=\"Sort\"]\n  20 -> 22 [label=\"out_file1\"]\n  23[label=\"Compute\"]\n  21 -> 23 [label=\"out_file1\"]\n  24[label=\"Cut\"]\n  23 -> 24 [label=\"out_file1\"]\n  25[label=\"Sort\"]\n  24 -> 25 [label=\"out_file1\"]\n  26[label=\"Join\"]\n  22 -> 26 [label=\"outfile\"]\n  25 -> 26 [label=\"outfile\"]\n  27[label=\"Compute\"]\n  26 -> 27 [label=\"output\"]\n  28[label=\"Cut\"]\n  27 -> 28 [label=\"out_file1\"]\n  29[label=\"Sort\"]\n  28 -> 29 [label=\"out_file1\"]\n  30[label=\"Gumbel\"]\n  7 -> 30 [label=\"output\"]\n  29 -> 30 [label=\"outfile\"]\n  31[label=\"Filter\"]\n  30 -> 31 [label=\"sites\"]\n  32[label=\"Extract Dataset\"]\n  31 -> 32 [label=\"out_file1\"]\n  k8796f62f46764ad2b0857597f894c32c[color=lightseagreen,label=\"Output\\ncontrol\"]\n  32 -> k8796f62f46764ad2b0857597f894c32c\n  33[label=\"Extract Dataset\"]\n  31 -> 33 [label=\"out_file1\"]\n  kbd014de4708e419cbd1e8bf350661aad[color=lightseagreen,label=\"Output\\ncondition\"]\n  33 -> kbd014de4708e419cbd1e8bf350661aad\n  34[label=\"Join\"]\n  32 -> 34 [label=\"output\"]\n  33 -> 34 [label=\"output\"]\n  k5cdfb5c9c67741dca838c4a61d62f5be[color=lightseagreen,label=\"Output\\nessential_both\"]\n  34 -> k5cdfb5c9c67741dca838c4a61d62f5be\n  35[label=\"Join\"]\n  32 -> 35 [label=\"output\"]\n  33 -> 35 [label=\"output\"]\n  k8b2b65ea37c343d2b41638f8f920fbd9[color=lightseagreen,label=\"Output\\nessential_control\"]\n  35 -> k8b2b65ea37c343d2b41638f8f920fbd9\n  36[label=\"Join\"]\n  32 -> 36 [label=\"output\"]\n  33 -> 36 [label=\"output\"]\n  k37639319b0534fbcbf61fd3e38263502[color=lightseagreen,label=\"Output\\nessential_condition\"]\n  36 -> k37639319b0534fbcbf61fd3e38263502\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenome assembly\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nRNASeq reads forward\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nRNASeq reads reverse\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nProtein evidence sequences\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nNCBI submission template\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAlternate annotation gbk\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAlternate annotation gff3\"]\n  7[label=\"RNA STAR\"]\n  0 -> 7 [label=\"output\"]\n  1 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  k79cf59ea3aef4cb89c705b42e03a5da9[color=lightseagreen,label=\"Output\\nMapped RNASeq\"]\n  7 -> k79cf59ea3aef4cb89c705b42e03a5da9\n  8[label=\"Funannotate predict annotation\"]\n  3 -> 8 [label=\"output\"]\n  7 -> 8 [label=\"mapped_reads\"]\n  0 -> 8 [label=\"output\"]\n  9[label=\"eggNOG Mapper\"]\n  8 -> 9 [label=\"fasta_proteins\"]\n  10[label=\"InterProScan\"]\n  8 -> 10 [label=\"fasta_proteins\"]\n  11[label=\"Funannotate functional\"]\n  9 -> 11 [label=\"annotations\"]\n  8 -> 11 [label=\"annot_gbk\"]\n  10 -> 11 [label=\"outfile_xml\"]\n  4 -> 11 [label=\"output\"]\n  kd0694cd16d814d7283b994cb57dc1502[color=lightseagreen,label=\"Output\\nFinal annotation (genbank)\"]\n  11 -> kd0694cd16d814d7283b994cb57dc1502\n  k9a1e7b70109041ed863765b7372a9f6c[color=lightseagreen,label=\"Output\\nFinal annotation (CDS sequences)\"]\n  11 -> k9a1e7b70109041ed863765b7372a9f6c\n  k99fffa402196491d9a66559ebf2d9561[color=lightseagreen,label=\"Output\\nFinal annotation (mRNA sequences)\"]\n  11 -> k99fffa402196491d9a66559ebf2d9561\n  k17b03b7704854176b2b303bfa2d3bcb0[color=lightseagreen,label=\"Output\\nFinal annotation (protein sequences)\"]\n  11 -> k17b03b7704854176b2b303bfa2d3bcb0\n  k4a0602fce6d243fc9957344707c22c05[color=lightseagreen,label=\"Output\\nFinal annotation (GFF3)\"]\n  11 -> k4a0602fce6d243fc9957344707c22c05\n  12[label=\"JBrowse\"]\n  0 -> 12 [label=\"output\"]\n  11 -> 12 [label=\"gff3\"]\n  7 -> 12 [label=\"mapped_reads\"]\n  kac4d8805f12344d2b30f8ac906cc471f[color=lightseagreen,label=\"Output\\nJBrowse\"]\n  12 -> kac4d8805f12344d2b30f8ac906cc471f\n  13[label=\"Funannotate compare\"]\n  5 -> 13 [label=\"output\"]\n  11 -> 13 [label=\"gbk\"]\n  ke531c81ff6b74c82a712c562873ff714[color=lightseagreen,label=\"Output\\nFunannotate compare report\"]\n  13 -> ke531c81ff6b74c82a712c562873ff714\n  14[label=\"AEGeAn ParsEval\"]\n  6 -> 14 [label=\"output\"]\n  11 -> 14 [label=\"gff3\"]\n  k0d776b462c1c40839f9da213fa62eb81[color=lightseagreen,label=\"Output\\nAEGeAN report\"]\n  14 -> k0d776b462c1c40839f9da213fa62eb81\n  15[label=\"Busco\"]\n  11 -> 15 [label=\"fa_proteins\"]\n  k57a619f5b3314ca68e6e72eb61860032[color=lightseagreen,label=\"Output\\nBusco summary\"]\n  15 -> k57a619f5b3314ca68e6e72eb61860032\n  k97d23764ad4a4d69948cc81afb76fbaf[color=lightseagreen,label=\"Output\\nBusco image\"]\n  15 -> k97d23764ad4a4d69948cc81afb76fbaf\n}",
                 "history": [
                     {
-                        "hash": "bc41adb9e901759a7013cebea286e631df2325e9",
-                        "message": "Rename workflow.",
-                        "num": 3,
-                        "short_hash": "bc41adb9e",
-                        "unix": "1603052556"
-                    },
-                    {
-                        "hash": "50c52377ea0c134e400a00e0d89e1973c203fa6c",
-                        "message": "Update workflow test.",
-                        "num": 2,
-                        "short_hash": "50c52377e",
-                        "unix": "1603048372"
-                    },
-                    {
-                        "hash": "708ae9c5d8f8a740f948382c3fd5e7c935685d64",
-                        "message": "Updated workflow and test.",
+                        "hash": "ed3325d60843b30358cdb704f83ad9ea4b6c149f",
+                        "message": "update funannotate tuto",
                         "num": 1,
-                        "short_hash": "708ae9c5d",
-                        "unix": "1603017659"
+                        "short_hash": "ed3325d60",
+                        "unix": "1682519007"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "",
+                        "annotation": "The genome sequence that you wish to annotate, in fasta format. It needs to be soft masked beforehand.",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Tnseq-Tutorial-reads.fastqsanger.gz"
+                                "description": "The genome sequence that you wish to annotate, in fasta format. It needs to be soft masked beforehand.",
+                                "name": "Genome assembly"
                             }
                         ],
-                        "label": "Tnseq-Tutorial-reads.fastqsanger.gz",
-                        "name": "Tnseq-Tutorial-reads.fastqsanger.gz",
+                        "label": "Genome assembly",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 204,
-                            "top": 204
+                            "left": 0,
+                            "top": 7.75
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"Tnseq-Tutorial-reads.fastqsanger.gz\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "299514db-9c70-4ef6-8414-a343c9721121",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "9a01ba0a-25c6-4bed-9ead-21b9298585d9"
-                            }
-                        ]
+                        "uuid": "cca15c08-8dd9-424a-8260-4c02a94c2612",
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Some RNASeq data, forward reads, in fastq format",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "condition_barcodes.fasta"
+                                "description": "Some RNASeq data, forward reads, in fastq format",
+                                "name": "RNASeq reads forward"
                             }
                         ],
-                        "label": "condition_barcodes.fasta",
-                        "name": "condition_barcodes.fasta",
+                        "label": "RNASeq reads forward",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 202,
-                            "top": 326
+                            "left": 3.45001220703125,
+                            "top": 164.33334350585938
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"condition_barcodes.fasta\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "2e5a56b4-93d7-4fba-b165-5feb86deb7c2",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "51bba64c-6acc-4ebf-971d-b1f2ee9adcc6"
-                            }
-                        ]
+                        "uuid": "6681e7b9-68f6-46e4-811f-60473d23fe0f",
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Some RNASeq data, reverse reads, in fastq format",
                         "content_id": null,
                         "errors": null,
                         "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "construct_barcodes.fasta"
+                                "description": "Some RNASeq data, reverse reads, in fastq format",
+                                "name": "RNASeq reads reverse"
                             }
                         ],
-                        "label": "construct_barcodes.fasta",
-                        "name": "construct_barcodes.fasta",
+                        "label": "RNASeq reads reverse",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 440
+                            "left": 6,
+                            "top": 310.6666564941406
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"construct_barcodes.fasta\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "7af899e7-676b-46ef-8c15-ff7b73b0fe76",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "e850fc22-c77f-4bbe-968f-ba44dea4caaf"
-                            }
-                        ]
+                        "uuid": "160023e3-250f-424d-abe5-f7e3978768f0",
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Some protein sequences to align on the genome to help annotation",
                         "content_id": null,
                         "errors": null,
                         "id": 3,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "staph_aur.fasta"
+                                "description": "Some protein sequences to align on the genome to help annotation",
+                                "name": "Protein evidence sequences"
                             }
                         ],
-                        "label": "staph_aur.fasta",
-                        "name": "staph_aur.fasta",
+                        "label": "Protein evidence sequences",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 183,
-                            "top": 550
+                            "left": 7.116668701171875,
+                            "top": 441.4166564941406
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"staph_aur.fasta\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "b522e8dc-3f8f-4e6d-9a2d-c970e25bf6f9",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "793cf25f-49a3-4afa-8165-c5c54e581864"
-                            }
-                        ]
+                        "uuid": "abb56aaf-5988-4fb8-a68f-0edaee00f445",
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "A submission template retrieved from NCBI (generate it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/)",
                         "content_id": null,
                         "errors": null,
                         "id": 4,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "staph_aur.gff3"
-                            }
-                        ],
-                        "label": "staph_aur.gff3",
-                        "name": "staph_aur.gff3",
-                        "outputs": [],
-                        "position": {
-                            "left": 183,
-                            "top": 694
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"staph_aur.gff3\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "e523846f-d4bf-43a8-a6f6-5763dba67f8f",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "2e39f099-2536-4a11-add0-9cf3576f1d68"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nTnseq-Tutorial-reads.fastqsanger.gz\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ncondition_barcodes.fasta\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nconstruct_barcodes.fasta\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nstaph_aur.fasta\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nstaph_aur.gff3\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Cutadapt\"];\n  0 -->|output| 5;\n  1 -->|output| 5;\n  6[\"Nucleotide subsequence search\"];\n  3 -->|output| 6;\n  7[\"Convert GFF3\"];\n  4 -->|output| 7;\n  8[\"Cutadapt\"];\n  5 -->|split_output| 8;\n  9[\"Cut\"];\n  6 -->|output| 9;\n  10[\"Cut\"];\n  6 -->|output| 10;\n  11[\"Cutadapt\"];\n  8 -->|out1| 11;\n  12[\"Compute\"];\n  10 -->|out_file1| 12;\n  13[\"Cutadapt\"];\n  11 -->|out1| 13;\n  2 -->|output| 13;\n  14[\"Cut\"];\n  12 -->|out_file1| 14;\n  15[\"Cutadapt\"];\n  13 -->|split_output| 15;\n  16[\"Map with Bowtie for Illumina\"];\n  3 -->|output| 16;\n  15 -->|out1| 16;\n  17[\"bamCoverage\"];\n  16 -->|output| 17;\n  18[\"Join\"];\n  17 -->|outFileName| 18;\n  9 -->|out_file1| 18;\n  19[\"Join\"];\n  17 -->|outFileName| 19;\n  14 -->|out_file1| 19;\n  20[\"Cut\"];\n  18 -->|output| 20;\n  21[\"Cut\"];\n  19 -->|output| 21;\n  22[\"Sort\"];\n  20 -->|out_file1| 22;\n  23[\"Compute\"];\n  21 -->|out_file1| 23;\n  24[\"Cut\"];\n  23 -->|out_file1| 24;\n  25[\"Sort\"];\n  24 -->|out_file1| 25;\n  26[\"Join\"];\n  22 -->|outfile| 26;\n  25 -->|outfile| 26;\n  27[\"Compute\"];\n  26 -->|output| 27;\n  28[\"Cut\"];\n  27 -->|out_file1| 28;\n  29[\"Sort\"];\n  28 -->|out_file1| 29;\n  30[\"Gumbel\"];\n  7 -->|output| 30;\n  29 -->|outfile| 30;\n  31[\"Filter\"];\n  30 -->|sites| 31;\n  32[\"Extract Dataset\"];\n  31 -->|out_file1| 32;\n  8796f62f-4676-4ad2-b085-7597f894c32c[\"Output\\ncontrol\"];\n  32 --> 8796f62f-4676-4ad2-b085-7597f894c32c;\n  style 8796f62f-4676-4ad2-b085-7597f894c32c stroke:#2c3143,stroke-width:4px;\n  33[\"Extract Dataset\"];\n  31 -->|out_file1| 33;\n  bd014de4-708e-419c-bd1e-8bf350661aad[\"Output\\ncondition\"];\n  33 --> bd014de4-708e-419c-bd1e-8bf350661aad;\n  style bd014de4-708e-419c-bd1e-8bf350661aad stroke:#2c3143,stroke-width:4px;\n  34[\"Join\"];\n  32 -->|output| 34;\n  33 -->|output| 34;\n  5cdfb5c9-c677-41dc-a838-c4a61d62f5be[\"Output\\nessential_both\"];\n  34 --> 5cdfb5c9-c677-41dc-a838-c4a61d62f5be;\n  style 5cdfb5c9-c677-41dc-a838-c4a61d62f5be stroke:#2c3143,stroke-width:4px;\n  35[\"Join\"];\n  32 -->|output| 35;\n  33 -->|output| 35;\n  8b2b65ea-37c3-43d2-b416-38f8f920fbd9[\"Output\\nessential_control\"];\n  35 --> 8b2b65ea-37c3-43d2-b416-38f8f920fbd9;\n  style 8b2b65ea-37c3-43d2-b416-38f8f920fbd9 stroke:#2c3143,stroke-width:4px;\n  36[\"Join\"];\n  32 -->|output| 36;\n  33 -->|output| 36;\n  37639319-b053-4fbc-bf61-fd3e38263502[\"Output\\nessential_condition\"];\n  36 --> 37639319-b053-4fbc-bf61-fd3e38263502;\n  style 37639319-b053-4fbc-bf61-fd3e38263502 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Essential genes detection with Transposon insertion sequencing",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Tnseq-Tutorial-reads.fastqsanger.gz"
-                            }
-                        ],
-                        "label": "Tnseq-Tutorial-reads.fastqsanger.gz",
-                        "name": "Tnseq-Tutorial-reads.fastqsanger.gz",
-                        "outputs": [],
-                        "position": {
-                            "left": 204,
-                            "top": 204
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Tnseq-Tutorial-reads.fastqsanger.gz\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "299514db-9c70-4ef6-8414-a343c9721121",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "9a01ba0a-25c6-4bed-9ead-21b9298585d9"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "condition_barcodes.fasta"
-                            }
-                        ],
-                        "label": "condition_barcodes.fasta",
-                        "name": "condition_barcodes.fasta",
-                        "outputs": [],
-                        "position": {
-                            "left": 202,
-                            "top": 326
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"condition_barcodes.fasta\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "2e5a56b4-93d7-4fba-b165-5feb86deb7c2",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "51bba64c-6acc-4ebf-971d-b1f2ee9adcc6"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "construct_barcodes.fasta"
+                                "description": "A submission template retrieved from NCBI (generate it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/)",
+                                "name": "NCBI submission template"
                             }
                         ],
-                        "label": "construct_barcodes.fasta",
-                        "name": "construct_barcodes.fasta",
+                        "label": "NCBI submission template",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 440
+                            "left": 2.45001220703125,
+                            "top": 580.4833068847656
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"construct_barcodes.fasta\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "7af899e7-676b-46ef-8c15-ff7b73b0fe76",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "e850fc22-c77f-4bbe-968f-ba44dea4caaf"
-                            }
-                        ]
+                        "uuid": "537f8bb4-4986-4d8d-a49b-1842dfaa739a",
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "The genbank output of an alternate annotation (for comparison)",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 5,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "staph_aur.fasta"
+                                "description": "The genbank output of an alternate annotation (for comparison)",
+                                "name": "Alternate annotation gbk"
                             }
                         ],
-                        "label": "staph_aur.fasta",
-                        "name": "staph_aur.fasta",
+                        "label": "Alternate annotation gbk",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 183,
-                            "top": 550
+                            "left": 0,
+                            "top": 727.7333068847656
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"staph_aur.fasta\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "b522e8dc-3f8f-4e6d-9a2d-c970e25bf6f9",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "793cf25f-49a3-4afa-8165-c5c54e581864"
-                            }
-                        ]
+                        "uuid": "51a62e82-d478-45c3-bcbc-f38f1fd85974",
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "The gff3 output of an alternate annotation (for comparison)",
                         "content_id": null,
                         "errors": null,
-                        "id": 4,
+                        "id": 6,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "staph_aur.gff3"
+                                "description": "The gff3 output of an alternate annotation (for comparison)",
+                                "name": "Alternate annotation gff3"
                             }
                         ],
-                        "label": "staph_aur.gff3",
-                        "name": "staph_aur.gff3",
+                        "label": "Alternate annotation gff3",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 183,
-                            "top": 694
+                            "left": 0.4666748046875,
+                            "top": 845.7500305175781
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"staph_aur.gff3\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "e523846f-d4bf-43a8-a6f6-5763dba67f8f",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "2e39f099-2536-4a11-add0-9cf3576f1d68"
-                            }
-                        ]
-                    },
+                        "uuid": "e4367779-3fc7-4eec-8e45-86158b3950bc",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGenome assembly\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nRNASeq reads forward\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nRNASeq reads reverse\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nProtein evidence sequences\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nNCBI submission template\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nAlternate annotation gbk\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nAlternate annotation gff3\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"RNA STAR\"];\n  0 -->|output| 7;\n  1 -->|output| 7;\n  2 -->|output| 7;\n  79cf59ea-3aef-4cb8-9c70-5b42e03a5da9[\"Output\\nMapped RNASeq\"];\n  7 --> 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9;\n  style 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9 stroke:#2c3143,stroke-width:4px;\n  8[\"Funannotate predict annotation\"];\n  3 -->|output| 8;\n  7 -->|mapped_reads| 8;\n  0 -->|output| 8;\n  9[\"eggNOG Mapper\"];\n  8 -->|fasta_proteins| 9;\n  10[\"InterProScan\"];\n  8 -->|fasta_proteins| 10;\n  11[\"Funannotate functional\"];\n  9 -->|annotations| 11;\n  8 -->|annot_gbk| 11;\n  10 -->|outfile_xml| 11;\n  4 -->|output| 11;\n  d0694cd1-6d81-4d72-83b9-94cb57dc1502[\"Output\\nFinal annotation (genbank)\"];\n  11 --> d0694cd1-6d81-4d72-83b9-94cb57dc1502;\n  style d0694cd1-6d81-4d72-83b9-94cb57dc1502 stroke:#2c3143,stroke-width:4px;\n  9a1e7b70-1090-41ed-8637-65b7372a9f6c[\"Output\\nFinal annotation (CDS sequences)\"];\n  11 --> 9a1e7b70-1090-41ed-8637-65b7372a9f6c;\n  style 9a1e7b70-1090-41ed-8637-65b7372a9f6c stroke:#2c3143,stroke-width:4px;\n  99fffa40-2196-491d-9a66-559ebf2d9561[\"Output\\nFinal annotation (mRNA sequences)\"];\n  11 --> 99fffa40-2196-491d-9a66-559ebf2d9561;\n  style 99fffa40-2196-491d-9a66-559ebf2d9561 stroke:#2c3143,stroke-width:4px;\n  17b03b77-0485-4176-b2b3-03bfa2d3bcb0[\"Output\\nFinal annotation (protein sequences)\"];\n  11 --> 17b03b77-0485-4176-b2b3-03bfa2d3bcb0;\n  style 17b03b77-0485-4176-b2b3-03bfa2d3bcb0 stroke:#2c3143,stroke-width:4px;\n  4a0602fc-e6d2-43fc-9957-344707c22c05[\"Output\\nFinal annotation (GFF3)\"];\n  11 --> 4a0602fc-e6d2-43fc-9957-344707c22c05;\n  style 4a0602fc-e6d2-43fc-9957-344707c22c05 stroke:#2c3143,stroke-width:4px;\n  12[\"JBrowse\"];\n  0 -->|output| 12;\n  11 -->|gff3| 12;\n  7 -->|mapped_reads| 12;\n  ac4d8805-f123-44d2-b30f-8ac906cc471f[\"Output\\nJBrowse\"];\n  12 --> ac4d8805-f123-44d2-b30f-8ac906cc471f;\n  style ac4d8805-f123-44d2-b30f-8ac906cc471f stroke:#2c3143,stroke-width:4px;\n  13[\"Funannotate compare\"];\n  5 -->|output| 13;\n  11 -->|gbk| 13;\n  e531c81f-f6b7-4c82-a712-c562873ff714[\"Output\\nFunannotate compare report\"];\n  13 --> e531c81f-f6b7-4c82-a712-c562873ff714;\n  style e531c81f-f6b7-4c82-a712-c562873ff714 stroke:#2c3143,stroke-width:4px;\n  14[\"AEGeAn ParsEval\"];\n  6 -->|output| 14;\n  11 -->|gff3| 14;\n  0d776b46-2c1c-4083-9f9d-a213fa62eb81[\"Output\\nAEGeAN report\"];\n  14 --> 0d776b46-2c1c-4083-9f9d-a213fa62eb81;\n  style 0d776b46-2c1c-4083-9f9d-a213fa62eb81 stroke:#2c3143,stroke-width:4px;\n  15[\"Busco\"];\n  11 -->|fa_proteins| 15;\n  57a619f5-b331-4ca6-8e6e-72eb61860032[\"Output\\nBusco summary\"];\n  15 --> 57a619f5-b331-4ca6-8e6e-72eb61860032;\n  style 57a619f5-b331-4ca6-8e6e-72eb61860032 stroke:#2c3143,stroke-width:4px;\n  97d23764-ad4a-4d69-948c-c81afb76fbaf[\"Output\\nBusco image\"];\n  15 --> 97d23764-ad4a-4d69-948c-c81afb76fbaf;\n  style 97d23764-ad4a-4d69-948c-c81afb76fbaf stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Funannotate",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3",
                         "errors": null,
-                        "id": 5,
+                        "id": 7,
                         "input_connections": {
-                            "library|input_1": {
+                            "refGenomeSource|genomeFastaFiles": {
                                 "id": 0,
                                 "output_name": "output"
                             },
-                            "library|r1|front_adapters_0|front_adapter_source|front_adapter_file": {
+                            "singlePaired|input1": {
                                 "id": 1,
                                 "output_name": "output"
+                            },
+                            "singlePaired|input2": {
+                                "id": 2,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cutadapt",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "split_output",
-                                "type": "input"
+                                "description": "runtime parameter for tool RNA STAR",
+                                "name": "refGenomeSource"
                             },
                             {
-                                "name": "report",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 442,
-                            "top": 190
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
-                        "tool_shed_repository": {
-                            "changeset_revision": "49370cb85f0f",
-                            "name": "cutadapt",
-                            "owner": "lparsons",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adapter_options\": {\"error_rate\": \"0.15\", \"no_indels\": \"false\", \"count\": \"3\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"no_trim\": \"false\", \"mask_adapter\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"discard\": \"false\", \"discard_untrimmed\": \"false\", \"min\": \"0\", \"max\": \"0\", \"max_n\": \"\", \"pair_filter\": \"any\"}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [{\"__index__\": 0, \"front_adapter_source\": {\"front_adapter_source_list\": \"file\", \"__current_case__\": 2, \"front_adapter_file\": {\"__class__\": \"ConnectedValue\"}}}], \"anywhere_adapters\": [], \"cut\": \"0\"}}, \"output_options\": {\"report\": \"true\", \"info_file\": \"false\", \"rest_file\": \"false\", \"wildcard_file\": \"false\", \"too_short_file\": \"false\", \"too_long_file\": \"false\", \"untrimmed_file\": \"false\", \"multiple_output\": \"true\"}, \"read_mod_options\": {\"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"prefix\": \"\", \"suffix\": \"\", \"strip_suffix\": \"\", \"length\": \"0\", \"length_tag\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
-                        "type": "tool",
-                        "uuid": "88a0eb99-bd98-4016-b0ee-6fca1043db7b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "split_output",
-                                "uuid": "292be5db-6a3d-4ccd-b766-8c2348f59a46"
+                                "description": "runtime parameter for tool RNA STAR",
+                                "name": "singlePaired"
                             },
                             {
-                                "label": null,
-                                "output_name": "report",
-                                "uuid": "8ae622ce-4da5-43f7-8f45-ba95ff557050"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/find_subsequences/bg_find_subsequences/0.2",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "input": {
-                                "id": 3,
-                                "output_name": "output"
+                                "description": "runtime parameter for tool RNA STAR",
+                                "name": "singlePaired"
                             }
-                        },
-                        "inputs": [],
+                        ],
                         "label": null,
-                        "name": "Nucleotide subsequence search",
+                        "name": "RNA STAR",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "bed"
+                                "name": "output_log",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "splice_junctions",
+                                "type": "interval"
+                            },
+                            {
+                                "name": "mapped_reads",
+                                "type": "bam"
                             }
                         ],
                         "position": {
-                            "left": 437,
-                            "top": 534
+                            "left": 766.699951171875,
+                            "top": 239.0
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/find_subsequences/bg_find_subsequences/0.2",
+                        "post_job_actions": {
+                            "HideDatasetActionoutput_log": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_log"
+                            },
+                            "HideDatasetActionsplice_junctions": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "splice_junctions"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3",
                         "tool_shed_repository": {
-                            "changeset_revision": "d882a0a75759",
-                            "name": "find_subsequences",
-                            "owner": "bgruening",
+                            "changeset_revision": "3ea5a2a63fa2",
+                            "name": "rgrnastar",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"pattern_conditional\": {\"pattern_conditional_select\": \"user\", \"__current_case__\": 1, \"pattern\": \"TA\"}, \"strand\": \"forward\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"algo\": {\"params\": {\"settingsType\": \"default\", \"__current_case__\": 0}}, \"chimOutType\": \"\", \"filter\": {\"basic_filters\": [\"exclude_unmapped\"], \"output_params2\": {\"output_select2\": \"no\", \"__current_case__\": 1}}, \"oformat\": {\"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"ch\"], \"HI_offset\": \"1\", \"outSAMprimaryFlag\": \"OneBestScore\", \"outSAMmapqUnique\": \"60\"}, \"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"perf\": {\"outBAMsortingBinsN\": \"50\", \"winAnchorMultimapNmax\": \"50\"}, \"refGenomeSource\": {\"geneSource\": \"history\", \"__current_case__\": 1, \"genomeFastaFiles\": {\"__class__\": \"RuntimeValue\"}, \"genomeSAindexNbases\": \"11\", \"GTFconditional\": {\"GTFselect\": \"without-gtf\", \"__current_case__\": 1, \"quantmode_output\": {\"quantMode\": \"-\", \"__current_case__\": 0}}}, \"singlePaired\": {\"sPaired\": \"paired\", \"__current_case__\": 1, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"input2\": {\"__class__\": \"RuntimeValue\"}}, \"twopass\": {\"twopassMode\": \"None\", \"__current_case__\": 0, \"twopass_read_subset\": \"\", \"sj_precalculated\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.7.10b+galaxy3",
                         "type": "tool",
-                        "uuid": "d72aa8a7-e558-4c97-9ccf-6f7cce88105c",
+                        "uuid": "269a3794-e421-4826-a5de-8a328fd194bd",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "12e30ef1-fe37-47f5-9879-ed7e375d4bb2"
+                                "label": "Mapped RNASeq",
+                                "output_name": "mapped_reads",
+                                "uuid": "79cf59ea-3aef-4cb8-9c70-5b42e03a5da9"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gff_to_prot/gff_to_prot/3.0.2+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0",
                         "errors": null,
-                        "id": 7,
+                        "id": 8,
                         "input_connections": {
+                            "evidences|prot_evidence|protein_evidence": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "evidences|rna_bam": {
+                                "id": 7,
+                                "output_name": "mapped_reads"
+                            },
                             "input": {
-                                "id": 4,
+                                "id": 0,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Convert GFF3",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 3582,
-                            "top": 443
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gff_to_prot/gff_to_prot/3.0.2+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2aea122fbd25",
-                            "name": "gff_to_prot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
-                        "type": "tool",
-                        "uuid": "3db46674-95fe-4285-a23a-a5cbeb185cf8",
-                        "workflow_outputs": [
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "database"
+                            },
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "eb959619-62d7-4e16-b5f4-067851b05581"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "library|input_1": {
-                                "id": 5,
-                                "output_name": "split_output"
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "evidences"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "evidences"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "genemark"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "genemark"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "input"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "other_predictors"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "other_predictors"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "other_predictors"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "other_predictors"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "parameters"
                             }
-                        },
-                        "inputs": [],
+                        ],
                         "label": null,
-                        "name": "Cutadapt",
+                        "name": "Funannotate predict annotation",
                         "outputs": [
                             {
-                                "name": "out1",
-                                "type": "fastqsanger"
+                                "name": "annot_gbk",
+                                "type": "genbank"
                             },
                             {
-                                "name": "report",
+                                "name": "annot_tbl",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "annot_gff3",
+                                "type": "gff3"
+                            },
+                            {
+                                "name": "fasta_proteins",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "fasta_transcripts_mrna",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "fasta_transcripts_cds",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "tbl2asn_report",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "tbl2asn_error",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "tbl2asn_validation",
                                 "type": "txt"
+                            },
+                            {
+                                "name": "stats",
+                                "type": "json"
                             }
                         ],
                         "position": {
-                            "left": 673,
-                            "top": 184
+                            "left": 1055.2666015625,
+                            "top": 65.88333129882812
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
+                        "post_job_actions": {
+                            "HideDatasetActionannot_gbk": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "annot_gbk"
+                            },
+                            "HideDatasetActionannot_gff3": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "annot_gff3"
+                            },
+                            "HideDatasetActionannot_tbl": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "annot_tbl"
+                            },
+                            "HideDatasetActionfasta_transcripts_cds": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "fasta_transcripts_cds"
+                            },
+                            "HideDatasetActionfasta_transcripts_mrna": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "fasta_transcripts_mrna"
+                            },
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "HideDatasetActiontbl2asn_error": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "tbl2asn_error"
+                            },
+                            "HideDatasetActiontbl2asn_report": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "tbl2asn_report"
+                            },
+                            "HideDatasetActiontbl2asn_validation": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "tbl2asn_validation"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "49370cb85f0f",
-                            "name": "cutadapt",
-                            "owner": "lparsons",
+                            "changeset_revision": "51b6ee65ef7f",
+                            "name": "funannotate_predict",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adapter_options\": {\"error_rate\": \"0.1\", \"no_indels\": \"false\", \"count\": \"3\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"no_trim\": \"false\", \"mask_adapter\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"discard\": \"false\", \"discard_untrimmed\": \"false\", \"min\": \"0\", \"max\": \"0\", \"max_n\": \"\", \"pair_filter\": \"any\"}, \"input_1|__identifier__\": \"control\", \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"\", \"adapter\": \"CGTTATGGCACGC\"}}], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}}, \"output_options\": {\"report\": \"true\", \"info_file\": \"false\", \"rest_file\": \"false\", \"wildcard_file\": \"false\", \"too_short_file\": \"false\", \"too_long_file\": \"false\", \"untrimmed_file\": \"false\", \"multiple_output\": \"false\"}, \"read_mod_options\": {\"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"prefix\": \"\", \"suffix\": \"\", \"strip_suffix\": \"\", \"length\": \"0\", \"length_tag\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"augustus\": {\"augustus_species\": \"none\", \"min_training_models\": \"200\", \"optimize_augustus\": \"false\"}, \"busco\": {\"busco_db\": \"mucorales_odb10\", \"busco_seed_species\": \"rhizopus_oryzae\"}, \"database\": {\"__class__\": \"RuntimeValue\"}, \"evidences\": {\"rna_bam\": {\"__class__\": \"RuntimeValue\"}, \"transcript_evidence\": {\"__class__\": \"RuntimeValue\"}, \"prot_evidence\": {\"prot_evidence_source\": \"custom\", \"__current_case__\": 1, \"protein_evidence\": {\"__class__\": \"RuntimeValue\"}}, \"p2g_pident\": \"80\", \"p2g_prefilter\": \"diamond\"}, \"evm\": {\"repeats2evm\": \"false\", \"evm_partitioning\": {\"evm_partition\": \"yes\", \"__current_case__\": 0, \"evm_partition_interval\": \"1500\"}, \"weights\": \"\"}, \"filtering\": {\"min_intronlen\": \"10\", \"max_intronlen\": \"3000\", \"min_protlen\": \"50\", \"keep_no_stops\": \"false\", \"repeat_filter\": \"overlap blast\"}, \"force\": \"true\", \"genemark\": {\"genemark_license\": {\"__class__\": \"RuntimeValue\"}, \"genemark_mode\": \"ES\", \"genemark_mod\": {\"__class__\": \"RuntimeValue\"}, \"soft_mask\": \"2000\"}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"organism\": {\"species\": \"Mucor mucedo\", \"isolate\": \"\", \"strain\": \"muc1\", \"organism\": \"false\", \"ploidy\": \"1\", \"SeqCenter\": \"CFMR\", \"SeqAccession\": \"12345\", \"name\": \"FUN_\", \"numbering\": \"1\"}, \"other_predictors\": {\"stringtie\": {\"__class__\": \"RuntimeValue\"}, \"maker_gff\": {\"__class__\": \"RuntimeValue\"}, \"pasa_gff\": {\"__class__\": \"RuntimeValue\"}, \"pasa_gff_weight\": \"1\", \"other_gff\": {\"__class__\": \"RuntimeValue\"}, \"other_gff_weight\": \"1\"}, \"outputs\": [\"gbk\", \"tbl\", \"gff3\", \"proteins_fa\", \"mrna_transcripts_fa\", \"cds_transcripts_fa\", \"tbl2asn_report\", \"tbl2asn_error\", \"tbl2asn_validation\", \"stats\"], \"parameters\": {\"__class__\": \"RuntimeValue\"}, \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.15+galaxy0",
                         "type": "tool",
-                        "uuid": "4fd67900-a4a7-4f36-b738-310f413fcbc7",
+                        "uuid": "aefc0275-b611-4ede-9650-2e16553a7352",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out1",
-                                "uuid": "d3d7c441-23c8-4a69-b893-08ae55da0989"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "report",
-                                "uuid": "0d77a42f-4f4e-40ab-928c-42f616ca87e2"
+                                "output_name": "fasta_proteins",
+                                "uuid": "aa7fb986-b7db-4353-a83b-3f1591911388"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Cut1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
                         "errors": null,
                         "id": 9,
                         "input_connections": {
-                            "input": {
-                                "id": 6,
-                                "output_name": "output"
+                            "ortho_method|input": {
+                                "id": 8,
+                                "output_name": "fasta_proteins"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool eggNOG Mapper",
+                                "name": "ortho_method"
+                            }
+                        ],
                         "label": null,
-                        "name": "Cut",
+                        "name": "eggNOG Mapper",
                         "outputs": [
                             {
-                                "name": "out_file1",
+                                "name": "seed_orthologs",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "annotations",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 683,
-                            "top": 443
+                            "left": 1444.9666748046875,
+                            "top": 418.7333068847656
                         },
-                        "post_job_actions": {},
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"__input_ext\": \"bed\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c2\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "post_job_actions": {
+                            "HideDatasetActionseed_orthologs": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "seed_orthologs"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "9d1fbff733cf",
+                            "name": "eggnog_mapper",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"annotation_options\": {\"no_annot\": \"\", \"__current_case__\": 0, \"seed_ortholog_evalue\": \"0.001\", \"seed_ortholog_score\": null, \"tax_scope\": null, \"target_orthologs\": \"all\", \"go_evidence\": \"non-electronic\"}, \"eggnog_data\": \"5.0.2\", \"ortho_method\": {\"m\": \"diamond\", \"__current_case__\": 0, \"input\": {\"__class__\": \"RuntimeValue\"}, \"input_trans\": {\"itype\": \"proteins\", \"__current_case__\": 0}, \"matrix_gapcosts\": {\"matrix\": \"BLOSUM62\", \"__current_case__\": 2, \"gap_costs\": \"--gapopen 11 --gapextend 1\"}, \"sensmode\": \"sensitive\", \"dmnd_iterate\": \"false\", \"dmnd_ignore_warnings\": \"false\", \"query_cover\": null, \"subject_cover\": null, \"pident\": null, \"evalue\": null, \"score\": \"0.001\"}, \"output_options\": {\"no_file_comments\": \"false\", \"report_orthologs\": \"false\", \"md5\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.8+galaxy3",
                         "type": "tool",
-                        "uuid": "a5312714-814a-4c22-a56d-ac5eb6056443",
+                        "uuid": "0d9f93f0-88b3-406b-b8f9-ecb2d74c61e9",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "c84ab194-b4ca-462b-9aca-b9e0c679cfda"
+                                "output_name": "annotations",
+                                "uuid": "521fe026-4958-4965-9414-e7074aea7860"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Cut1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
                         "errors": null,
                         "id": 10,
                         "input_connections": {
                             "input": {
-                                "id": 6,
-                                "output_name": "output"
+                                "id": 8,
+                                "output_name": "fasta_proteins"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool InterProScan",
+                                "name": "input"
+                            }
+                        ],
                         "label": null,
-                        "name": "Cut",
+                        "name": "InterProScan",
                         "outputs": [
                             {
-                                "name": "out_file1",
+                                "name": "outfile_tsv",
                                 "type": "tabular"
+                            },
+                            {
+                                "name": "outfile_xml",
+                                "type": "xml"
                             }
                         ],
                         "position": {
-                            "left": 730,
-                            "top": 581
+                            "left": 1475.8499755859375,
+                            "top": 817.8666687011719
                         },
-                        "post_job_actions": {},
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"__input_ext\": \"bed\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c1,c3\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "post_job_actions": {
+                            "HideDatasetActionoutfile_xml": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "outfile_xml"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "74810db257cc",
+                            "name": "interproscan",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"applications\": [\"TIGRFAM\", \"SFLD\", \"SUPERFAMILY\", \"PANTHER\", \"Gene3D\", \"Hamap\", \"PrositeProfiles\", \"Coils\", \"SMART\", \"CDD\", \"PRINTS\", \"PIRSR\", \"PrositePatterns\", \"Pfam\", \"MobiDBLite\", \"PIRSF\"], \"database\": \"5.59-91.0\", \"goterms\": \"true\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"iprlookup\": \"false\", \"licensed\": {\"use\": \"true\", \"__current_case__\": 1, \"applications_licensed\": [\"Phobius\", \"SignalP_EUK\", \"TMHMM\"]}, \"oformat\": [\"TSV\", \"XML\"], \"pathways\": \"true\", \"seqtype\": \"p\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.59-91.0+galaxy3",
                         "type": "tool",
-                        "uuid": "db5bcbb6-8922-4189-9a27-5785442cd08f",
+                        "uuid": "cb7a1910-3c31-47d9-835b-f1bd16a1c3ff",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "a8d013af-90a3-4838-a328-9c9ebc308c91"
+                                "output_name": "outfile_tsv",
+                                "uuid": "65e267a7-d3c6-410d-9b44-f655d70d7d9a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0",
                         "errors": null,
                         "id": 11,
                         "input_connections": {
-                            "library|input_1": {
+                            "eggnog": {
+                                "id": 9,
+                                "output_name": "annotations"
+                            },
+                            "input|genbank": {
                                 "id": 8,
-                                "output_name": "out1"
+                                "output_name": "annot_gbk"
+                            },
+                            "iprscan": {
+                                "id": 10,
+                                "output_name": "outfile_xml"
+                            },
+                            "sbt": {
+                                "id": 4,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "annotations"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "antismash"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "database"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "eggnog"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "fix"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "input"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "iprscan"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "phobius"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "remove"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "sbt"
+                            }
+                        ],
                         "label": null,
-                        "name": "Cutadapt",
+                        "name": "Funannotate functional",
                         "outputs": [
                             {
-                                "name": "out1",
-                                "type": "fastqsanger"
+                                "name": "gbk",
+                                "type": "genbank"
                             },
                             {
-                                "name": "report",
+                                "name": "annot",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "contigs_fsa",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "agp",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "tbl",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "sqn",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "fa_scaffolds",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "fa_proteins",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "fa_transcripts_mrna",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "fa_transcripts_cds",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "gff3",
+                                "type": "gff3"
+                            },
+                            {
+                                "name": "tbl2asn_report",
                                 "type": "txt"
+                            },
+                            {
+                                "name": "stats",
+                                "type": "json"
+                            },
+                            {
+                                "name": "must_fix",
+                                "type": "json"
+                            },
+                            {
+                                "name": "need_curating",
+                                "type": "json"
+                            },
+                            {
+                                "name": "new_names_passed",
+                                "type": "json"
                             }
                         ],
                         "position": {
-                            "left": 906,
-                            "top": 186
+                            "left": 1877.11669921875,
+                            "top": 101.59999084472656
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
+                        "post_job_actions": {
+                            "HideDatasetActionagp": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "agp"
+                            },
+                            "HideDatasetActionannot": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "annot"
+                            },
+                            "HideDatasetActioncontigs_fsa": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "contigs_fsa"
+                            },
+                            "HideDatasetActionfa_scaffolds": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "fa_scaffolds"
+                            },
+                            "HideDatasetActionmust_fix": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "must_fix"
+                            },
+                            "HideDatasetActionneed_curating": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "need_curating"
+                            },
+                            "HideDatasetActionnew_names_passed": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "new_names_passed"
+                            },
+                            "HideDatasetActionsqn": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "sqn"
+                            },
+                            "HideDatasetActiontbl": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "tbl"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "49370cb85f0f",
-                            "name": "cutadapt",
-                            "owner": "lparsons",
+                            "changeset_revision": "9feee7fc49a1",
+                            "name": "funannotate_annotate",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adapter_options\": {\"error_rate\": \"0.1\", \"no_indels\": \"false\", \"count\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"no_trim\": \"false\", \"mask_adapter\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"discard\": \"false\", \"discard_untrimmed\": \"false\", \"min\": \"64\", \"max\": \"70\", \"max_n\": \"\", \"pair_filter\": \"any\"}, \"input_1|__identifier__\": \"control\", \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}}, \"output_options\": {\"report\": \"true\", \"info_file\": \"false\", \"rest_file\": \"false\", \"wildcard_file\": \"false\", \"too_short_file\": \"false\", \"too_long_file\": \"false\", \"untrimmed_file\": \"false\", \"multiple_output\": \"false\"}, \"read_mod_options\": {\"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"prefix\": \"\", \"suffix\": \"\", \"strip_suffix\": \"\", \"length\": \"0\", \"length_tag\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"annotations\": {\"__class__\": \"RuntimeValue\"}, \"antismash\": {\"__class__\": \"RuntimeValue\"}, \"busco_db\": \"mucorales_odb10\", \"database\": {\"__class__\": \"RuntimeValue\"}, \"eggnog\": {\"__class__\": \"RuntimeValue\"}, \"fix\": {\"__class__\": \"RuntimeValue\"}, \"input\": {\"input_type\": \"gbk\", \"__current_case__\": 0, \"genbank\": {\"__class__\": \"RuntimeValue\"}}, \"iprscan\": {\"__class__\": \"RuntimeValue\"}, \"isolate\": \"\", \"outputs\": [\"gbk\", \"annotations\", \"contigs_fsa\", \"agp\", \"tbl\", \"sqn\", \"scaffolds_fa\", \"proteins_fa\", \"mrna_transcripts_fa\", \"cds_transcripts_fa\", \"gff3\", \"discrepency\", \"stats\", \"must_fix\", \"need_curating\", \"new_names_passed\"], \"phobius\": {\"__class__\": \"RuntimeValue\"}, \"remove\": {\"__class__\": \"RuntimeValue\"}, \"rename\": \"\", \"sbt\": {\"__class__\": \"RuntimeValue\"}, \"strain\": \"muc1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.15+galaxy0",
                         "type": "tool",
-                        "uuid": "43159e62-7eda-4f71-a6be-9c5a46222c51",
+                        "uuid": "e07de1e0-8f91-4477-b951-7d97dba2e397",
                         "workflow_outputs": [
+                            {
+                                "label": "Final annotation (genbank)",
+                                "output_name": "gbk",
+                                "uuid": "d0694cd1-6d81-4d72-83b9-94cb57dc1502"
+                            },
+                            {
+                                "label": "Final annotation (CDS sequences)",
+                                "output_name": "fa_transcripts_cds",
+                                "uuid": "9a1e7b70-1090-41ed-8637-65b7372a9f6c"
+                            },
+                            {
+                                "label": "Final annotation (mRNA sequences)",
+                                "output_name": "fa_transcripts_mrna",
+                                "uuid": "99fffa40-2196-491d-9a66-559ebf2d9561"
+                            },
+                            {
+                                "label": "Final annotation (protein sequences)",
+                                "output_name": "fa_proteins",
+                                "uuid": "17b03b77-0485-4176-b2b3-03bfa2d3bcb0"
+                            },
                             {
                                 "label": null,
-                                "output_name": "report",
-                                "uuid": "15e3858e-5c79-4d31-a76b-423be5855479"
+                                "output_name": "tbl2asn_report",
+                                "uuid": "d3d4daec-75fe-4071-af37-c2907e46f5c1"
                             },
                             {
                                 "label": null,
-                                "output_name": "out1",
-                                "uuid": "e9511fc9-50b9-4a63-be4a-3022031091de"
+                                "output_name": "stats",
+                                "uuid": "4a682ab6-8a6f-4a0f-bb0e-ba796f587ddc"
+                            },
+                            {
+                                "label": "Final annotation (GFF3)",
+                                "output_name": "gff3",
+                                "uuid": "4a0602fc-e6d2-43fc-9957-344707c22c05"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
                         "errors": null,
                         "id": 12,
                         "input_connections": {
-                            "input": {
-                                "id": 10,
-                                "output_name": "out_file1"
+                            "reference_genome|genome": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "track_groups_0|data_tracks_0|data_format|annotation": {
+                                "id": 11,
+                                "output_name": "gff3"
+                            },
+                            "track_groups_1|data_tracks_0|data_format|annotation": {
+                                "id": 7,
+                                "output_name": "mapped_reads"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool JBrowse",
+                                "name": "reference_genome"
+                            }
+                        ],
                         "label": null,
-                        "name": "Compute",
+                        "name": "JBrowse",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "output",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 997,
-                            "top": 511
+                            "left": 2152.60009765625,
+                            "top": 0.0
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "be25c075ed54",
-                            "name": "column_maker",
-                            "owner": "devteam",
+                            "changeset_revision": "a6e57ff585c0",
+                            "name": "jbrowse",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"avoid_scientific_notation\": \"no\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c2-1\", \"header_lines_conditional\": {\"header_lines_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"round\": \"yes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 1, \"category\": \"RNASeq\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"auto_snp\": \"true\", \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.11+galaxy1",
                         "type": "tool",
-                        "uuid": "862f354c-4fd7-41df-88a9-47e3cea4227b",
+                        "uuid": "e6d0e687-1a13-482b-a00a-28c7304d59ac",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "7ecdf545-74b5-423a-ac04-8dff265fb11e"
+                                "label": "JBrowse",
+                                "output_name": "output",
+                                "uuid": "ac4d8805-f123-44d2-b30f-8ac906cc471f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0",
                         "errors": null,
                         "id": 13,
                         "input_connections": {
-                            "library|input_1": {
-                                "id": 11,
-                                "output_name": "out1"
+                            "input": [
+                                {
+                                    "id": 5,
+                                    "output_name": "output"
+                                },
+                                {
+                                    "id": 11,
+                                    "output_name": "gbk"
+                                }
+                            ]
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Funannotate compare",
+                                "name": "database"
                             },
-                            "library|r1|adapters_0|adapter_source|adapter_file": {
-                                "id": 2,
-                                "output_name": "output"
+                            {
+                                "description": "runtime parameter for tool Funannotate compare",
+                                "name": "proteinortho"
                             }
-                        },
-                        "inputs": [],
+                        ],
                         "label": null,
-                        "name": "Cutadapt",
+                        "name": "Funannotate compare",
                         "outputs": [
                             {
-                                "name": "split_output",
-                                "type": "input"
-                            },
-                            {
-                                "name": "report",
-                                "type": "txt"
+                                "name": "output",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 1129,
-                            "top": 214
+                            "left": 2318,
+                            "top": 403.7333068847656
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "49370cb85f0f",
-                            "name": "cutadapt",
-                            "owner": "lparsons",
+                            "changeset_revision": "a7ce2601500c",
+                            "name": "funannotate_compare",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adapter_options\": {\"error_rate\": \"0.1\", \"no_indels\": \"false\", \"count\": \"3\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"no_trim\": \"false\", \"mask_adapter\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"discard\": \"false\", \"discard_untrimmed\": \"false\", \"min\": \"0\", \"max\": \"0\", \"max_n\": \"\", \"pair_filter\": \"any\"}, \"input_1|__identifier__\": \"control\", \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"file\", \"__current_case__\": 2, \"adapter_file\": {\"__class__\": \"ConnectedValue\"}}}], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}}, \"output_options\": {\"report\": \"true\", \"info_file\": \"false\", \"rest_file\": \"false\", \"wildcard_file\": \"false\", \"too_short_file\": \"false\", \"too_long_file\": \"false\", \"untrimmed_file\": \"false\", \"multiple_output\": \"true\"}, \"read_mod_options\": {\"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"prefix\": \"\", \"suffix\": \"\", \"strip_suffix\": \"\", \"length\": \"0\", \"length_tag\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"database\": {\"__class__\": \"RuntimeValue\"}, \"go_fdr\": \"0.05\", \"heatmap_stdev\": \"1.0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"ml\": {\"ml_method\": \"iqtree\", \"__current_case__\": 0}, \"num_orthos\": \"500\", \"proteinortho\": {\"__class__\": \"RuntimeValue\"}, \"run_dnds\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.15+galaxy0",
                         "type": "tool",
-                        "uuid": "f27ae319-a997-42ed-856b-13c6a687f3b3",
+                        "uuid": "750137e5-2cac-4bec-8337-03dab562a7a5",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "split_output",
-                                "uuid": "8b9cd027-9d39-43ae-b31e-089210c7208f"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "report",
-                                "uuid": "7818fffe-b449-4ec9-9d9c-54400e921a1d"
+                                "label": "Funannotate compare report",
+                                "output_name": "output",
+                                "uuid": "e531c81f-f6b7-4c82-a712-c562873ff714"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Cut1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0",
                         "errors": null,
                         "id": 14,
                         "input_connections": {
-                            "input": {
-                                "id": 12,
-                                "output_name": "out_file1"
+                            "predictiongff3": {
+                                "id": 6,
+                                "output_name": "output"
+                            },
+                            "referencegff3": {
+                                "id": 11,
+                                "output_name": "gff3"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Cut",
+                        "name": "AEGeAn ParsEval",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "tabular"
+                                "name": "output_html",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 1279,
-                            "top": 512
+                            "left": 2318.5,
+                            "top": 643.7333068847656
                         },
                         "post_job_actions": {},
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c3\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "1b52f0c8ad7f",
+                            "name": "aegean_parseval",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"delta\": \"0\", \"maxtrans\": \"32\", \"output_type\": \"html\", \"predictiongff3\": {\"__class__\": \"ConnectedValue\"}, \"predlabel\": \"\", \"referencegff3\": {\"__class__\": \"ConnectedValue\"}, \"refrlabel\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.16.0",
                         "type": "tool",
-                        "uuid": "5e32b04b-a6a7-409c-855c-706188e4ce13",
+                        "uuid": "b5870c4b-d799-4da0-83cc-7dd5a0b049e4",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "48313713-24eb-4d80-9683-914b90b56f74"
+                                "label": "AEGeAN report",
+                                "output_name": "output_html",
+                                "uuid": "0d776b46-2c1c-4083-9f9d-a213fa62eb81"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0",
                         "errors": null,
                         "id": 15,
                         "input_connections": {
-                            "library|input_1": {
-                                "id": 13,
-                                "output_name": "split_output"
+                            "input": {
+                                "id": 11,
+                                "output_name": "fa_proteins"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Busco",
+                                "name": "input"
+                            }
+                        ],
                         "label": null,
-                        "name": "Cutadapt",
+                        "name": "Busco",
                         "outputs": [
                             {
-                                "name": "out1",
-                                "type": "fastqsanger"
+                                "name": "busco_sum",
+                                "type": "txt"
                             },
                             {
-                                "name": "report",
-                                "type": "txt"
+                                "name": "busco_table",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "summary_image",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 1361,
-                            "top": 199
+                            "left": 2252.2666015625,
+                            "top": 1072.0666809082031
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
+                        "post_job_actions": {
+                            "HideDatasetActionbusco_table": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "busco_table"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "49370cb85f0f",
-                            "name": "cutadapt",
-                            "owner": "lparsons",
+                            "changeset_revision": "94170eee0ad8",
+                            "name": "busco",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adapter_options\": {\"error_rate\": \"0.15\", \"no_indels\": \"false\", \"count\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"no_trim\": \"false\", \"mask_adapter\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"discard\": \"false\", \"discard_untrimmed\": \"false\", \"min\": \"0\", \"max\": \"0\", \"max_n\": \"\", \"pair_filter\": \"any\"}, \"input_1|__identifier__\": \"unknown\", \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"\", \"adapter\": \"ACAGGTTGGATGATAAGTCCCCGGTCTATATTGAGAGTAACTACATTT\"}}], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}}, \"output_options\": {\"report\": \"true\", \"info_file\": \"false\", \"rest_file\": \"false\", \"wildcard_file\": \"false\", \"too_short_file\": \"false\", \"too_long_file\": \"false\", \"untrimmed_file\": \"false\", \"multiple_output\": \"false\"}, \"read_mod_options\": {\"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"prefix\": \"\", \"suffix\": \"\", \"strip_suffix\": \"\", \"length\": \"0\", \"length_tag\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\"}, \"busco_mode\": {\"mode\": \"prot\", \"__current_case__\": 2}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": \"mucorales_odb10\"}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"image\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.4.6+galaxy0",
                         "type": "tool",
-                        "uuid": "c4379b3f-de3d-4eca-96ca-cdaba4006736",
+                        "uuid": "bec3d4d9-88e6-4ea0-beb6-219d5c727290",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out1",
-                                "uuid": "8acb6fcd-1665-4269-8170-203c3e04f6c0"
+                                "label": "Busco summary",
+                                "output_name": "busco_sum",
+                                "uuid": "57a619f5-b331-4ca6-8e6e-72eb61860032"
                             },
                             {
-                                "label": null,
-                                "output_name": "report",
-                                "uuid": "83580f2a-2641-4127-9152-69a2ac1e044f"
+                                "label": "Busco image",
+                                "output_name": "summary_image",
+                                "uuid": "97d23764-ad4a-4d69-948c-c81afb76fbaf"
                             }
                         ]
-                    },
+                    }
+                ],
+                "parent_id": "genome-annotation/funannotate",
+                "path": "topics/genome-annotation/tutorials/funannotate/workflows/funannotate.ga",
+                "tags": [
+                    "genome-annotation"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "Funannotate",
+                "topic_id": "genome-annotation",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-funannotate/versions/funannotate",
+                "tutorial_id": "funannotate",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/funannotate/workflows/funannotate.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/funannotate/workflows/funannotate.html",
+                "version": 1,
+                "wfid": "genome-annotation-funannotate",
+                "wfname": "funannotate",
+                "workflow": "funannotate.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3"
+                ],
+                "workflowhub_id": "1202"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/7867921"
+    },
+    {
+        "abbreviations": {
+            "ORF": "Open Reading Frame"
+        },
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "diamond",
+                    "owner": "bgruening",
+                    "revisions": "e8ac2b53f262",
+                    "tool_panel_section_label": "NCBI Blast",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "diamond",
+                    "owner": "bgruening",
+                    "revisions": "e8ac2b53f262",
+                    "tool_panel_section_label": "NCBI Blast",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "diamond",
+                    "owner": "bgruening",
+                    "revisions": "e8ac2b53f262",
+                    "tool_panel_section_label": "NCBI Blast",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "split_file_on_column",
+                    "owner": "bgruening",
+                    "revisions": "37a53100b67e",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "column_maker",
+                    "owner": "devteam",
+                    "revisions": "02026300aa45",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "column_maker",
+                    "owner": "devteam",
+                    "revisions": "6595517c2dd8",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "intersect",
+                    "owner": "devteam",
+                    "revisions": "69c10b56f46d",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "tabular_to_fasta",
+                    "owner": "devteam",
+                    "revisions": "0a7799698fe5",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "regex_find_replace",
+                    "owner": "galaxyp",
+                    "revisions": "ae8c4b2488e7",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "orfipy",
+                    "owner": "iuc",
+                    "revisions": "c147914c9f02",
+                    "tool_panel_section_label": "Extract Features",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rapidnj",
+                    "owner": "iuc",
+                    "revisions": "9f4a66e22580",
+                    "tool_panel_section_label": "Evolution",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "90981f86000f",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mafft",
+                    "owner": "rnateam",
+                    "revisions": "f1a5908ea2cb",
+                    "tool_panel_section_label": "Multiple Alignments",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: diamond\n  owner: bgruening\n  revisions: e8ac2b53f262\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: diamond\n  owner: bgruening\n  revisions: e8ac2b53f262\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: diamond\n  owner: bgruening\n  revisions: e8ac2b53f262\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_on_column\n  owner: bgruening\n  revisions: 37a53100b67e\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 02026300aa45\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 6595517c2dd8\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: intersect\n  owner: devteam\n  revisions: 69c10b56f46d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tabular_to_fasta\n  owner: devteam\n  revisions: 0a7799698fe5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: ae8c4b2488e7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: orfipy\n  owner: iuc\n  revisions: c147914c9f02\n  tool_panel_section_label: Extract Features\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rapidnj\n  owner: iuc\n  revisions: 9f4a66e22580\n  tool_panel_section_label: Evolution\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mafft\n  owner: rnateam\n  revisions: f1a5908ea2cb\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/gene-centric/tutorial.json",
+        "contributors": [
+            {
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
+                "joined": "2017-09",
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+            }
+        ],
+        "dir": "topics/genome-annotation/tutorials/gene-centric",
+        "edam_ontology": [
+            "topic_0622",
+            "topic_0623",
+            "topic_0080",
+            "topic_0084"
+        ],
+        "edam_operation": [
+            "Database search",
+            "Transcriptome assembly",
+            "Phylogenetic tree generation",
+            "De-novo assembly",
+            "Sequence alignment analysis",
+            "Multiple sequence alignment",
+            "Coding region prediction"
+        ],
+        "edam_topic": [
+            "Genomics",
+            "Gene and protein families",
+            "Sequence analysis",
+            "Phylogeny"
+        ],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "genome-annotation/gene-centric",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "You can locate gene of interest in unannotated genomes and compare its structure across multiple species"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-03-18",
+        "objectives": [
+            "Provide a quick method for identifying genes of interest in unannotated or newly assembled genomes"
+        ],
+        "pageviews": 1602,
+        "priority": 2,
+        "pub_date": "2022-09-08",
+        "questions": [
+            "I have several genomes assemblies that are not annotated (or I do not trust annotations)",
+            "I am interested to compare structure of a particular gene across these genome assemblies",
+            "How do I do that?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "introduction",
+                "tutorials": [
+                    "galaxy-intro-101"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "collections"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00174",
+        "short_tools": [
+            "orfipy",
+            "rapidnj",
+            "join1",
+            "bg_diamond_makedb",
+            "Filter1",
+            "tp_split_on_column",
+            "tab2fasta",
+            "collapse_dataset",
+            "rbc_mafft",
+            "bg_diamond_view",
+            "Cut1",
+            "Add_a_column1",
+            "bg_diamond",
+            "regexColumn1",
+            "gops_intersect_1",
+            "cat1"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "evolution",
+            "annotation",
+            "vgp",
+            "cookbook",
+            "eukaryote",
+            "prokaryote",
+            "microgalaxy"
+        ],
+        "time_estimation": "30M",
+        "title": "Comparative gene analysis in unannotated genomes",
+        "tools": [
+            "Cut1",
+            "Filter1",
+            "cat1",
+            "join1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_makedb/2.0.15+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_view/2.0.15+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4",
+            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
+            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/orfipy/orfipy/0.0.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/rapidnj/rapidnj/2.3.2",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
+            "toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0"
+        ],
+        "topic_name": "genome-annotation",
+        "topic_name_human": "Genome Annotation",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "gene-centric",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/gene-centric/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/gene-centric/tutorial.json"
+        },
+        "version": 8,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 215,
+        "visitors": 1045,
+        "workflows": [
+            {
+                "creators": [
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0",
+                        "class": "Person",
+                        "identifier": "0000-0002-5987-8032",
+                        "name": "Anton Nekrutenko"
+                    }
+                ],
+                "description": "Workflows for comparison of genes in annotated genomes",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nExons\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nDiamond makedb\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nORFipy BED\"]\n  3[label=\"Diamond: Find hits in ORFs\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Column Regex Find And Replace\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Alignments\"]\n  3 -> 5 [label=\"daa_output\"]\n  6[label=\"Cut\"]\n  4 -> 6 [label=\"out_file1\"]\n  7[label=\"Alignments + BED\"]\n  6 -> 7 [label=\"out_file1\"]\n  5 -> 7 [label=\"blast_tabular\"]\n  8[label=\"Cut\"]\n  7 -> 8 [label=\"out_file1\"]\n  9[label=\"Collapse Collection\"]\n  7 -> 9 [label=\"out_file1\"]\n  10[label=\"Intersect\"]\n  6 -> 10 [label=\"out_file1\"]\n  8 -> 10 [label=\"out_file1\"]\n  11[label=\"Filter\"]\n  9 -> 11 [label=\"output\"]\n  12[label=\"Overlapping ORFs\"]\n  10 -> 12 [label=\"output\"]\n  13[label=\"Cut\"]\n  11 -> 13 [label=\"out_file1\"]\n  14[label=\"Compute\"]\n  12 -> 14 [label=\"output\"]\n  15[label=\"Compute\"]\n  13 -> 15 [label=\"out_file1\"]\n  16[label=\"Split file\"]\n  15 -> 16 [label=\"out_file1\"]\n  17[label=\"Report\"]\n  15 -> 17 [label=\"out_file1\"]\n  18[label=\"Tabular-to-FASTA\"]\n  16 -> 18 [label=\"split_output\"]\n  19[label=\"Cut\"]\n  17 -> 19 [label=\"out_file1\"]\n  20[label=\"MAFFT\"]\n  18 -> 20 [label=\"output\"]\n  21[label=\"Filter: Plus strand matches\"]\n  19 -> 21 [label=\"out_file1\"]\n  22[label=\"Filter: Minus strand matches\"]\n  19 -> 22 [label=\"out_file1\"]\n  23[label=\"Join neighbors\"]\n  20 -> 23 [label=\"outputAlignment\"]\n  k54ea37cc63d1422a9f5e124b8d39e6bd[color=lightseagreen,label=\"Output\\nJoin neighbors on input dataset(s): Calculated distances\"]\n  23 -> k54ea37cc63d1422a9f5e124b8d39e6bd\n  24[label=\"Compute\"]\n  21 -> 24 [label=\"out_file1\"]\n  25[label=\"Compute\"]\n  22 -> 25 [label=\"out_file1\"]\n  26[label=\"Concatenate datasets\"]\n  24 -> 26 [label=\"out_file1\"]\n  25 -> 26 [label=\"out_file1\"]\n  27[label=\"Compute\"]\n  26 -> 27 [label=\"out_file1\"]\n  28[label=\"Cut\"]\n  27 -> 28 [label=\"out_file1\"]\n  29[label=\"Compute\"]\n  28 -> 29 [label=\"out_file1\"]\n  30[label=\"Join two Datasets\"]\n  14 -> 30 [label=\"out_file1\"]\n  29 -> 30 [label=\"out_file1\"]\n  31[label=\"Mapping report\"]\n  30 -> 31 [label=\"out_file1\"]\n}",
+                "history": [
+                    {
+                        "hash": "476d3d57ff2b0ce249879b60aa03500ab62685d6",
+                        "message": "workflow update",
+                        "num": 1,
+                        "short_hash": "476d3d57f",
+                        "unix": "1662055154"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "Amino acid sequences of CDS exons from the gene of interest",
+                        "content_id": null,
                         "errors": null,
-                        "id": 16,
-                        "input_connections": {
-                            "refGenomeSource|ownFile": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "singlePaired|sInput1": {
-                                "id": 15,
-                                "output_name": "out1"
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Amino acid sequences of CDS exons from the gene of interest",
+                                "name": "Exons"
                             }
+                        ],
+                        "label": "Exons",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 1.90625,
+                            "top": 74.21875
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Map with Bowtie for Illumina",
-                        "outputs": [
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "107c06e7-51a6-41a1-a026-45a9dddf29a9",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "Diamond DB created from ORF predicted from genomes used in the analysis",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "sam"
+                                "description": "Diamond DB created from ORF predicted from genomes used in the analysis",
+                                "name": "Diamond makedb"
                             }
                         ],
+                        "label": "Diamond makedb",
+                        "name": "Input dataset collection",
+                        "outputs": [],
                         "position": {
-                            "left": 1594,
-                            "top": 201
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b46e7d48076a",
-                            "name": "bowtie_wrappers",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0.0,
+                            "top": 185.71875
                         },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"refGenomeSource\": {\"genomeSource\": \"history\", \"__current_case__\": 1, \"ownFile\": {\"__class__\": \"ConnectedValue\"}, \"indexParams\": {\"indexSettings\": \"indexPreSet\", \"__current_case__\": 0}}, \"save_mapping_stats\": \"false\", \"singlePaired\": {\"sPaired\": \"single\", \"__current_case__\": 0, \"sInput1\": {\"__class__\": \"ConnectedValue\"}, \"sParams\": {\"sSettingsType\": \"full\", \"__current_case__\": 1, \"sSkip\": \"0\", \"sAlignLimit\": \"-1\", \"sTrimH\": \"0\", \"sTrimL\": \"0\", \"alignModeOption\": {\"alignMode\": \"nMode\", \"__current_case__\": 0, \"sMismatchSeed\": \"0\", \"sMismatchQual\": \"70\", \"sSeedLen\": \"17\", \"sRounding\": \"round\"}, \"sForwardAlign\": \"forward\", \"sReverseAlign\": \"reverse\", \"sBestOption\": {\"sBest\": \"doBest\", \"__current_case__\": 1, \"sdStrata\": \"noStrata\", \"sTryHardOption\": {\"sTryHard\": \"doTryHard\", \"__current_case__\": 1}}, \"sAllValAlignsOption\": {\"sAllValAligns\": \"noAllValAligns\", \"__current_case__\": 0, \"sValAlign\": \"1\"}, \"sSuppressAlign\": \"-1\", \"sMaxFile\": \"false\", \"sUnmappedFile\": \"false\", \"sOffrate\": \"-1\", \"sSeed\": \"-1\"}}, \"suppressHeader\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "9cd2e25c-9bc6-4136-9a10-3192c9e41841",
-                        "workflow_outputs": [
+                        "type": "data_collection_input",
+                        "uuid": "0acc2c20-91fb-4470-80ac-2eeb7e2f32ae",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "BED dataset containing information about ORFs predicted in genomes of interest",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "7e683afc-5d1f-48f9-a4f1-daedee314672"
+                                "description": "BED dataset containing information about ORFs predicted in genomes of interest",
+                                "name": "ORFipy BED"
                             }
-                        ]
-                    },
+                        ],
+                        "label": "ORFipy BED",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 1.90625,
+                            "top": 313.203125
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"bed\"], \"tag\": \"\", \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "329b3c07-f0ee-4882-abf7-1215062a0fec",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nExons\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nDiamond makedb\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nORFipy BED\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Diamond: Find hits in ORFs\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Column Regex Find And Replace\"];\n  2 -->|output| 4;\n  5[\"Alignments\"];\n  3 -->|daa_output| 5;\n  6[\"Cut\"];\n  4 -->|out_file1| 6;\n  7[\"Alignments + BED\"];\n  6 -->|out_file1| 7;\n  5 -->|blast_tabular| 7;\n  8[\"Cut\"];\n  7 -->|out_file1| 8;\n  9[\"Collapse Collection\"];\n  7 -->|out_file1| 9;\n  10[\"Intersect\"];\n  6 -->|out_file1| 10;\n  8 -->|out_file1| 10;\n  11[\"Filter\"];\n  9 -->|output| 11;\n  12[\"Overlapping ORFs\"];\n  10 -->|output| 12;\n  13[\"Cut\"];\n  11 -->|out_file1| 13;\n  14[\"Compute\"];\n  12 -->|output| 14;\n  15[\"Compute\"];\n  13 -->|out_file1| 15;\n  16[\"Split file\"];\n  15 -->|out_file1| 16;\n  17[\"Report\"];\n  15 -->|out_file1| 17;\n  18[\"Tabular-to-FASTA\"];\n  16 -->|split_output| 18;\n  19[\"Cut\"];\n  17 -->|out_file1| 19;\n  20[\"MAFFT\"];\n  18 -->|output| 20;\n  21[\"Filter: Plus strand matches\"];\n  19 -->|out_file1| 21;\n  22[\"Filter: Minus strand matches\"];\n  19 -->|out_file1| 22;\n  23[\"Join neighbors\"];\n  20 -->|outputAlignment| 23;\n  54ea37cc-63d1-422a-9f5e-124b8d39e6bd[\"Output\\nJoin neighbors on input dataset(s): Calculated distances\"];\n  23 --> 54ea37cc-63d1-422a-9f5e-124b8d39e6bd;\n  style 54ea37cc-63d1-422a-9f5e-124b8d39e6bd stroke:#2c3143,stroke-width:4px;\n  24[\"Compute\"];\n  21 -->|out_file1| 24;\n  25[\"Compute\"];\n  22 -->|out_file1| 25;\n  26[\"Concatenate datasets\"];\n  24 -->|out_file1| 26;\n  25 -->|out_file1| 26;\n  27[\"Compute\"];\n  26 -->|out_file1| 27;\n  28[\"Cut\"];\n  27 -->|out_file1| 28;\n  29[\"Compute\"];\n  28 -->|out_file1| 29;\n  30[\"Join two Datasets\"];\n  14 -->|out_file1| 30;\n  29 -->|out_file1| 30;\n  31[\"Mapping report\"];\n  30 -->|out_file1| 31;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Comparative gene analysis",
+                "outputs": [
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0",
+                        "annotation": "Compute NJ phylogenetic trees",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rapidnj/rapidnj/2.3.2",
                         "errors": null,
-                        "id": 17,
+                        "id": 23,
                         "input_connections": {
-                            "bamInput": {
-                                "id": 16,
-                                "output_name": "output"
+                            "alignments": {
+                                "id": 20,
+                                "output_name": "outputAlignment"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "bamCoverage",
+                        "name": "Join neighbors",
                         "outputs": [
                             {
-                                "name": "outFileName",
-                                "type": "bigwig"
+                                "name": "distances",
+                                "type": "nhx"
                             }
                         ],
                         "position": {
-                            "left": 1846,
-                            "top": 196
+                            "left": 2200.03125,
+                            "top": 0
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0",
+                        "post_job_actions": {
+                            "TagDatasetActiondistances": {
+                                "action_arguments": {
+                                    "tags": "Trees"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "distances"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rapidnj/rapidnj/2.3.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "bb1e4f63e0e6",
-                            "name": "deeptools_bam_coverage",
-                            "owner": "bgruening",
+                            "changeset_revision": "9f4a66e22580",
+                            "name": "rapidnj",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"bam\", \"advancedOpt\": {\"showAdvancedOpt\": \"yes\", \"__current_case__\": 1, \"scaleFactor\": \"1.0\", \"smoothLength\": \"\", \"ignoreForNormalization\": \"\", \"skipNAs\": \"true\", \"doExtendCustom\": {\"doExtend\": \"no\", \"__current_case__\": 0}, \"ignoreDuplicates\": \"false\", \"centerReads\": \"false\", \"minMappingQuality\": \"1\", \"samFlagInclude\": \"\", \"samFlagExclude\": \"\", \"minFragmentLength\": \"0\", \"maxFragmentLength\": \"0\", \"MNase\": \"false\", \"Offset\": \"-1\", \"filterRNAstrand\": \"no\", \"blackListFileName\": null}, \"bamInput\": {\"__class__\": \"ConnectedValue\"}, \"binSize\": \"1\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"exactScaling\": \"false\", \"outFileFormat\": \"bedgraph\", \"region\": \"\", \"scaling\": {\"type\": \"no\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"alignment_type\": \"p\", \"alignments\": {\"__class__\": \"ConnectedValue\"}, \"bootstrap\": null, \"evolution_model\": \"kim\", \"no_negative_length\": \"false\", \"output_format\": \"t\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.3.2",
                         "type": "tool",
-                        "uuid": "8355bf16-b3bf-4361-b2f1-f1504154a4ee",
+                        "uuid": "a9f1ebbf-4a88-4ddb-aec7-6a1c3a3921db",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "outFileName",
-                                "uuid": "63663acf-5780-492b-8b01-e958cf47617f"
+                                "label": "Join neighbors on input dataset(s): Calculated distances",
+                                "output_name": "distances",
+                                "uuid": "54ea37cc-63d1-422a-9f5e-124b8d39e6bd"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "content_id": "Cut1",
                         "errors": null,
-                        "id": 18,
+                        "id": 31,
                         "input_connections": {
-                            "infile1": {
-                                "id": 17,
-                                "output_name": "outFileName"
-                            },
-                            "infile2": {
-                                "id": 9,
+                            "input": {
+                                "id": 30,
                                 "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Join",
+                        "label": "Mapping report",
+                        "name": "Cut",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "input"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 2113,
-                            "top": 204
+                            "left": 3450.75,
+                            "top": 1309.90625
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9ff72e942410",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Mapping report"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            },
+                            "TagDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "tags": "PlottingData"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "out_file1"
+                            }
                         },
-                        "tool_state": "{\"__input_ext\": \"bedgraph\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"column1\": \"2\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": \"false\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile1|__identifier__\": \"unknown\", \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \"-a 2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"columnList\": \"c1,c2,c3,c4,c5,c6,c7,c11,c12,c13,c14,c15\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2",
                         "type": "tool",
-                        "uuid": "095dd2dd-5082-419a-9743-0b6ac031392d",
+                        "uuid": "341c7257-c027-421b-afc1-a8dc11d2f6cd",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "89f48391-502f-4bc1-8755-fd3faf3245dc"
+                                "output_name": "out_file1",
+                                "uuid": "bb199f1a-1402-4f00-9a02-e5743a8662b6"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "genome-annotation/gene-centric",
+                "path": "topics/genome-annotation/tutorials/gene-centric/workflows/Comparative-gene-analysis.ga",
+                "tags": [
+                    "vgp",
+                    "genome-annotation"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Comparative gene analysis",
+                "topic_id": "genome-annotation",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-gene-centric/versions/comparative-gene-analysis",
+                "tutorial_id": "gene-centric",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/gene-centric/workflows/Comparative-gene-analysis.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/gene-centric/workflows/Comparative-gene-analysis.html",
+                "version": 1,
+                "wfid": "genome-annotation-gene-centric",
+                "wfname": "comparative-gene-analysis",
+                "workflow": "Comparative-gene-analysis.ga",
+                "workflow_tools": [
+                    "Cut1",
+                    "Filter1",
+                    "cat1",
+                    "join1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_view/2.0.15+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/rapidnj/rapidnj/2.3.2",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.489+galaxy0"
+                ],
+                "workflowhub_id": "1173"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/7034885"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "gffread",
+                    "owner": "devteam",
+                    "revisions": "0232f19d300f",
+                    "tool_panel_section_label": "Convert Formats",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "busco",
+                    "owner": "iuc",
+                    "revisions": "1440ae06552f",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "jbrowse",
+                    "owner": "iuc",
+                    "revisions": "2bb2e07a7a21",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "jcvi_gff_stats",
+                    "owner": "iuc",
+                    "revisions": "8cffbd184762",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "maker",
+                    "owner": "iuc",
+                    "revisions": "96ac930d84fa",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "maker_map_ids",
+                    "owner": "iuc",
+                    "revisions": "326f9c294b09",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_stats",
+                    "owner": "simon-gladman",
+                    "revisions": "20ca2574216a",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: gffread\n  owner: devteam\n  revisions: 0232f19d300f\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 1440ae06552f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 2bb2e07a7a21\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jcvi_gff_stats\n  owner: iuc\n  revisions: 8cffbd184762\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker\n  owner: iuc\n  revisions: 96ac930d84fa\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker_map_ids\n  owner: iuc\n  revisions: 326f9c294b09\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n  owner: simon-gladman\n  revisions: 20ca2574216a\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "eurosciencegateway",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
+                "fediverse_flavor": "mastodon",
+                "id": "abretaud",
+                "joined": "2017-09",
+                "location": {
+                    "country": "FR",
+                    "lat": 48.11,
+                    "lon": -1.64
+                },
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+            }
+        ],
+        "dir": "topics/genome-annotation/tutorials/annotation-with-maker-short",
+        "edam_operation": [
+            "Sequence assembly validation",
+            "Genome annotation",
+            "Scaffolding",
+            "Sequence annotation",
+            "Transcriptome assembly",
+            "Genome assembly",
+            "Genome visualisation"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "genome-annotation/annotation-with-maker-short",
+        "inexact_supported_servers": [
+            "UseGalaxy.be"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Maker allows to annotate a eukaryotic genome.",
+            "BUSCO and JBrowse allow to inspect the quality of an annotation."
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-02-29",
+        "objectives": [
+            "Load genome into Galaxy",
+            "Annotate genome with Maker",
+            "Evaluate annotation quality with BUSCO",
+            "View annotations in JBrowse"
+        ],
+        "pageviews": 4148,
+        "priority": 3,
+        "pub_date": "2021-01-12",
+        "questions": [
+            "How to annotate an eukaryotic genome?",
+            "How to evaluate and visualize annotated genomic features?"
+        ],
+        "short_id": "T00167",
+        "short_tools": [
+            "jbrowse",
+            "busco",
+            "fasta-stats",
+            "maker_map_ids",
+            "jcvi_gff_stats",
+            "gffread",
+            "maker"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "eukaryote",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "gmod",
+            "eukaryote",
+            "maker",
+            "jbrowse1"
+        ],
+        "time_estimation": "2h",
+        "title": "Genome annotation with Maker (short)",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.10",
+            "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10",
+            "toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0"
+        ],
+        "topic_name": "genome-annotation",
+        "topic_name_human": "Genome Annotation",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "annotation-with-maker-short",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.json"
+        },
+        "version": 3,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 189,
+        "visitors": 2836,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Genome annotation with Maker (short)",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenome sequence\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nProteins\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSNAP model\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAugustus model\"]\n  5[label=\"Fasta Statistics\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Busco\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Maker\"]\n  4 -> 7 [label=\"output\"]\n  3 -> 7 [label=\"output\"]\n  1 -> 7 [label=\"output\"]\n  0 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"Map annotation ids\"]\n  7 -> 8 [label=\"output_gff\"]\n  9[label=\"Genome annotation statistics\"]\n  8 -> 9 [label=\"renamed\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"gffread\"]\n  8 -> 10 [label=\"renamed\"]\n  0 -> 10 [label=\"output\"]\n  11[label=\"JBrowse\"]\n  0 -> 11 [label=\"output\"]\n  8 -> 11 [label=\"renamed\"]\n  7 -> 11 [label=\"output_evidences\"]\n  12[label=\"Busco\"]\n  10 -> 12 [label=\"output_exons\"]\n  k6951417bee0b4e0398e467d262e086dc[color=lightseagreen,label=\"Output\\nBusco summary final round\"]\n  12 -> k6951417bee0b4e0398e467d262e086dc\n}",
+                "history": [
+                    {
+                        "hash": "005d964a2e8cb80f8d1bf0b304adc8f9d7c9ff76",
+                        "message": "fix workflows",
+                        "num": 2,
+                        "short_hash": "005d964a2",
+                        "unix": "1609752597"
                     },
+                    {
+                        "hash": "774f2aa374452d48fd29ee85513c3dc3a7f137f5",
+                        "message": "update maker tutorial and add a short version",
+                        "num": 1,
+                        "short_hash": "774f2aa37",
+                        "unix": "1609431273"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "content_id": null,
                         "errors": null,
-                        "id": 19,
-                        "input_connections": {
-                            "infile1": {
-                                "id": 17,
-                                "output_name": "outFileName"
-                            },
-                            "infile2": {
-                                "id": 14,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Join",
-                        "outputs": [
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "input"
+                                "description": "",
+                                "name": "Genome sequence"
                             }
                         ],
+                        "label": "Genome sequence",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2137,
-                            "top": 366
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9ff72e942410",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 94.08332824707031,
+                            "height": 82.19999694824219,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 11.883331298828125,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 11.883331298828125
                         },
-                        "tool_state": "{\"__input_ext\": \"bedgraph\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"column1\": \"2\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": \"false\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile1|__identifier__\": \"unknown\", \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \"-a 2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "fc70f1e1-17dd-4287-8dfb-c7f86b71d645",
+                        "type": "data_input",
+                        "uuid": "a361a75e-5fa4-44ca-a4b7-cc9054a73054",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "bf190ec2-215f-4404-b3e3-c230f84c6939"
+                                "uuid": "9a09d16c-18af-4605-8416-4966fe918677"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Cut1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 20,
-                        "input_connections": {
-                            "input": {
-                                "id": 18,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cut",
-                        "outputs": [
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "EST and/or cDNA"
                             }
                         ],
+                        "label": "EST and/or cDNA",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2443,
-                            "top": 205
+                            "bottom": 214.0833282470703,
+                            "height": 82.19999694824219,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 131.88333129882812,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 131.88333129882812
                         },
-                        "post_job_actions": {},
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"__input_ext\": \"bedgraph\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c1,c4\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"unknown\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "43459cad-a7b6-412f-8975-bc73f9127e12",
+                        "type": "data_input",
+                        "uuid": "6b3edbe9-085d-46ae-9ae3-96e876c003e0",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "205cebe3-e508-4a9b-8429-78d624b27028"
+                                "output_name": "output",
+                                "uuid": "c5c5fb8f-9932-499c-b404-c142aedd1aa5"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Cut1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 21,
-                        "input_connections": {
-                            "input": {
-                                "id": 19,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cut",
-                        "outputs": [
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "Proteins"
                             }
                         ],
+                        "label": "Proteins",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2311,
-                            "top": 537
+                            "bottom": 313.68333435058594,
+                            "height": 61.80000305175781,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 251.88333129882812,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 251.88333129882812
                         },
-                        "post_job_actions": {},
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"__input_ext\": \"bedgraph\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c1,c4\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"unknown\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "b9d313a5-f9c1-4209-9235-1c7ba2aa6e2c",
+                        "type": "data_input",
+                        "uuid": "ce4ee756-1713-4e6a-898c-b85a834712bc",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "be1284e3-bc3c-40c9-98cd-f3489b5addbf"
+                                "output_name": "output",
+                                "uuid": "cbbe9e59-ccd5-4925-a7a3-e1d094284fca"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 22,
-                        "input_connections": {
-                            "infile": {
-                                "id": 20,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Sort",
-                        "outputs": [
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "outfile",
-                                "type": "input"
+                                "description": "",
+                                "name": "SNAP model"
                             }
                         ],
+                        "label": "SNAP model",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2731,
-                            "top": 189
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "74a8bef53a00",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 413.68333435058594,
+                            "height": 61.80000305175781,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 351.8833312988281,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 351.8833312988281
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"header\": \"0\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"infile|__identifier__\": \"unknown\", \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"n\"}], \"unique\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "5bd821e2-8e48-4bc5-b7ce-6e4d9459764b",
+                        "type": "data_input",
+                        "uuid": "ebf1f01c-e804-462a-92cf-670012b103b3",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "95ac6ae6-6620-4809-9fcf-90f2ffe0ef90"
+                                "output_name": "output",
+                                "uuid": "ecfd7af4-f95c-4b2d-9f06-8e851a0c4d9e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 23,
-                        "input_connections": {
-                            "input": {
-                                "id": 21,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Compute",
-                        "outputs": [
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "description": "",
+                                "name": "Augustus model"
                             }
                         ],
+                        "label": "Augustus model",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2504,
-                            "top": 384
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "be25c075ed54",
-                            "name": "column_maker",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 554.0833282470703,
+                            "height": 82.19999694824219,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 471.8833312988281,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 471.8833312988281
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"avoid_scientific_notation\": \"no\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c1-1\", \"header_lines_conditional\": {\"header_lines_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"unknown\", \"round\": \"yes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "55059dd9-d9e5-4ec2-8756-af9ec8239924",
+                        "type": "data_input",
+                        "uuid": "586af078-09ce-476b-9eb7-55e443a8eeaf",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "9efd613c-1f50-4e3c-b007-4196b9eefc69"
+                                "output_name": "output",
+                                "uuid": "7259eb8b-9c2d-4eff-a49d-1b447e905314"
                             }
                         ]
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGenome sequence\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nProteins\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nSNAP model\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nAugustus model\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Fasta Statistics\"];\n  0 -->|output| 5;\n  6[\"Busco\"];\n  0 -->|output| 6;\n  7[\"Maker\"];\n  4 -->|output| 7;\n  3 -->|output| 7;\n  1 -->|output| 7;\n  0 -->|output| 7;\n  2 -->|output| 7;\n  8[\"Map annotation ids\"];\n  7 -->|output_gff| 8;\n  9[\"Genome annotation statistics\"];\n  8 -->|renamed| 9;\n  0 -->|output| 9;\n  10[\"gffread\"];\n  8 -->|renamed| 10;\n  0 -->|output| 10;\n  11[\"JBrowse\"];\n  0 -->|output| 11;\n  8 -->|renamed| 11;\n  7 -->|output_evidences| 11;\n  12[\"Busco\"];\n  10 -->|output_exons| 12;\n  6951417b-ee0b-4e03-98e4-67d262e086dc[\"Output\\nBusco summary final round\"];\n  12 --> 6951417b-ee0b-4e03-98e4-67d262e086dc;\n  style 6951417b-ee0b-4e03-98e4-67d262e086dc stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Genome annotation with Maker (short)",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "Cut1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 24,
-                        "input_connections": {
-                            "input": {
-                                "id": 23,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cut",
-                        "outputs": [
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "Genome sequence"
                             }
                         ],
+                        "label": "Genome sequence",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2641,
-                            "top": 523
+                            "bottom": 94.08332824707031,
+                            "height": 82.19999694824219,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 11.883331298828125,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 11.883331298828125
                         },
-                        "post_job_actions": {},
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c3,c2\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"unknown\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "54b3489e-f6ec-44de-8bbb-493c972e3666",
+                        "type": "data_input",
+                        "uuid": "a361a75e-5fa4-44ca-a4b7-cc9054a73054",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "48b2b3cd-45f4-43fe-aaaf-83ca18b7bf9d"
+                                "output_name": "output",
+                                "uuid": "9a09d16c-18af-4605-8416-4966fe918677"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 25,
-                        "input_connections": {
-                            "infile": {
-                                "id": 24,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Sort",
-                        "outputs": [
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "outfile",
-                                "type": "input"
+                                "description": "",
+                                "name": "EST and/or cDNA"
                             }
                         ],
+                        "label": "EST and/or cDNA",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2841,
-                            "top": 389
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "74a8bef53a00",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 214.0833282470703,
+                            "height": 82.19999694824219,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 131.88333129882812,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 131.88333129882812
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"header\": \"0\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"infile|__identifier__\": \"unknown\", \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"n\"}], \"unique\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "06aa9c94-2850-41d2-bc52-a7a954d2ca70",
+                        "type": "data_input",
+                        "uuid": "6b3edbe9-085d-46ae-9ae3-96e876c003e0",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "3b7302f9-16c5-464f-866b-df392abe0fbf"
+                                "output_name": "output",
+                                "uuid": "c5c5fb8f-9932-499c-b404-c142aedd1aa5"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "content_id": null,
                         "errors": null,
-                        "id": 26,
-                        "input_connections": {
-                            "infile1": {
-                                "id": 22,
-                                "output_name": "outfile"
-                            },
-                            "infile2": {
-                                "id": 25,
-                                "output_name": "outfile"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Join",
-                        "outputs": [
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "input"
+                                "description": "",
+                                "name": "Proteins"
                             }
                         ],
+                        "label": "Proteins",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 3185,
-                            "top": 209
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9ff72e942410",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 313.68333435058594,
+                            "height": 61.80000305175781,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 251.88333129882812,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 251.88333129882812
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \".\", \"header\": \"false\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile1|__identifier__\": \"unknown\", \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"infile2|__identifier__\": \"unknown\", \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "4668ac5e-a567-4107-80e4-b6fe91f762ce",
+                        "type": "data_input",
+                        "uuid": "ce4ee756-1713-4e6a-898c-b85a834712bc",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "fa45da27-d946-4d8c-8ef6-339d95e8b183"
+                                "uuid": "cbbe9e59-ccd5-4925-a7a3-e1d094284fca"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 27,
-                        "input_connections": {
-                            "input": {
-                                "id": 26,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Compute",
-                        "outputs": [
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "description": "",
+                                "name": "SNAP model"
                             }
                         ],
+                        "label": "SNAP model",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 3438,
-                            "top": 151
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "be25c075ed54",
-                            "name": "column_maker",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 413.68333435058594,
+                            "height": 61.80000305175781,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 351.8833312988281,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 351.8833312988281
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"avoid_scientific_notation\": \"no\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c2+c3\", \"header_lines_conditional\": {\"header_lines_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"unknown\", \"round\": \"yes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "8ea3f455-800b-423d-99dd-827b8a91d079",
+                        "type": "data_input",
+                        "uuid": "ebf1f01c-e804-462a-92cf-670012b103b3",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "9d672d8f-f57f-49df-a2fb-0bc9daae2591"
+                                "output_name": "output",
+                                "uuid": "ecfd7af4-f95c-4b2d-9f06-8e851a0c4d9e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Cut1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 28,
-                        "input_connections": {
-                            "input": {
-                                "id": 27,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cut",
-                        "outputs": [
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "Augustus model"
                             }
                         ],
+                        "label": "Augustus model",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 3597,
-                            "top": 319
+                            "bottom": 554.0833282470703,
+                            "height": 82.19999694824219,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 471.8833312988281,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 471.8833312988281
                         },
-                        "post_job_actions": {},
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c1,c4\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"unknown\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "b57d2009-2255-4aba-89dd-edd902fa21c4",
+                        "type": "data_input",
+                        "uuid": "586af078-09ce-476b-9eb7-55e443a8eeaf",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "f6051684-f77b-4895-8424-361bd399da4b"
+                                "output_name": "output",
+                                "uuid": "7259eb8b-9c2d-4eff-a49d-1b447e905314"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0",
                         "errors": null,
-                        "id": 29,
+                        "id": 5,
                         "input_connections": {
-                            "infile": {
-                                "id": 28,
-                                "output_name": "out_file1"
+                            "dataset": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Sort",
+                        "name": "Fasta Statistics",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "input"
+                                "name": "stats",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 3811,
-                            "top": 161
+                            "bottom": 34.28334045410156,
+                            "height": 154.40000915527344,
+                            "left": -15.350006103515625,
+                            "right": 184.64999389648438,
+                            "top": -120.11666870117188,
+                            "width": 200,
+                            "x": -15.350006103515625,
+                            "y": -120.11666870117188
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "74a8bef53a00",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "20ca2574216a",
+                            "name": "fasta_stats",
+                            "owner": "simon-gladman",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"header\": \"0\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"infile|__identifier__\": \"unknown\", \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"n\"}], \"unique\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
                         "type": "tool",
-                        "uuid": "180421e5-45e7-4d88-be28-15d682f5e392",
+                        "uuid": "43cab601-f700-4278-bd0a-7f0997cf75cf",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "8543b2f7-cf8e-43f5-a06a-a7a20f180946"
+                                "output_name": "stats",
+                                "uuid": "7840b5e6-2a7e-4b3c-bea3-4a0d70fea21b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/3.0.2+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
                         "errors": null,
-                        "id": 30,
+                        "id": 6,
                         "input_connections": {
-                            "annotation": {
-                                "id": 7,
+                            "input": {
+                                "id": 0,
                                 "output_name": "output"
-                            },
-                            "mode|inputs": {
-                                "id": 29,
-                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Gumbel",
+                        "name": "Busco",
                         "outputs": [
                             {
-                                "name": "sites",
+                                "name": "busco_sum",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "busco_table",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "busco_missing",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 4067,
-                            "top": 266
+                            "bottom": -157.71664428710938,
+                            "height": 276.4000244140625,
+                            "left": -15.350006103515625,
+                            "right": 184.64999389648438,
+                            "top": -434.1166687011719,
+                            "width": 200,
+                            "x": -15.350006103515625,
+                            "y": -434.1166687011719
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/3.0.2+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "f50807720df1",
-                            "name": "transit_gumbel",
+                            "changeset_revision": "602fb8e63aa7",
+                            "name": "busco",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"annotation\": {\"__class__\": \"ConnectedValue\"}, \"burnin\": \"500\", \"cterm\": \"0.1\", \"handle_replicates\": \"Sum\", \"mode\": {\"replicates\": \"Replicates\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"normalization\": \"TTR\", \"nterm\": \"0.1\", \"samples\": \"10000\", \"smallest\": \"2\", \"trim\": \"1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"geno\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.1.4",
                         "type": "tool",
-                        "uuid": "70b9679b-e15b-4756-8ae7-0457944dabbc",
+                        "uuid": "876334be-d7e5-4504-bb1b-727472839c02",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "sites",
-                                "uuid": "a46ddc5a-f542-49ac-bb67-f23f734dabf4"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "Filter1",
-                        "errors": null,
-                        "id": 31,
-                        "input_connections": {
-                            "input": {
-                                "id": 30,
-                                "output_name": "sites"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Filter",
-                        "outputs": [
+                                "output_name": "busco_sum",
+                                "uuid": "59ce9dc8-762f-4c38-aded-5d031db50609"
+                            },
                             {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 4335,
-                            "top": 269
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"cond\": \"c9=='E'\", \"header_lines\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
-                        "type": "tool",
-                        "uuid": "42633d45-79c3-48ba-810d-5fe839a621d6",
-                        "workflow_outputs": [
+                                "label": null,
+                                "output_name": "busco_missing",
+                                "uuid": "9b000535-1702-4888-951c-4cc8e782a511"
+                            },
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "cb86d7f5-8c93-40bc-9836-1e68756c0e5e"
+                                "output_name": "busco_table",
+                                "uuid": "76c0d8fc-4e81-4ba0-b8b2-ebfda0ba5786"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "__EXTRACT_DATASET__",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10",
                         "errors": null,
-                        "id": 32,
+                        "id": 8,
                         "input_connections": {
-                            "input": {
-                                "id": 31,
-                                "output_name": "out_file1"
+                            "maker_gff": {
+                                "id": 7,
+                                "output_name": "output_gff"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Extract Dataset",
+                        "name": "Map annotation ids",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "data"
+                                "name": "renamed",
+                                "type": "gff"
+                            },
+                            {
+                                "name": "id_map",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 4607,
-                            "top": 266
+                            "bottom": 318.8833312988281,
+                            "height": 246,
+                            "left": 272.66668701171875,
+                            "right": 472.66668701171875,
+                            "top": 72.88333129882812,
+                            "width": 200,
+                            "x": 272.66668701171875,
+                            "y": 72.88333129882812
                         },
                         "post_job_actions": {
-                            "ChangeDatatypeActionoutput": {
+                            "ChangeDatatypeActionrenamed": {
                                 "action_arguments": {
-                                    "newtype": "tabular"
+                                    "newtype": "gff3"
                                 },
                                 "action_type": "ChangeDatatypeAction",
-                                "output_name": "output"
+                                "output_name": "renamed"
                             },
-                            "TagDatasetActionoutput": {
-                                "action_arguments": {
-                                    "tags": "#control"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "output"
+                            "HideDatasetActionid_map": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "id_map"
                             }
                         },
-                        "tool_id": "__EXTRACT_DATASET__",
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"by_index\", \"__current_case__\": 2, \"index\": \"1\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f1912d5575df",
+                            "name": "maker_map_ids",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"justify\": \"6\", \"maker_gff\": {\"__class__\": \"ConnectedValue\"}, \"prefix\": \"TEST\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.31.11",
                         "type": "tool",
-                        "uuid": "886a7aec-fa32-410d-b82a-02f2c0722ff4",
+                        "uuid": "b1127093-0aae-4bfa-b474-042b838a8299",
                         "workflow_outputs": [
                             {
-                                "label": "control",
-                                "output_name": "output",
-                                "uuid": "8796f62f-4676-4ad2-b085-7597f894c32c"
+                                "label": null,
+                                "output_name": "renamed",
+                                "uuid": "e8686326-b443-402b-bb0e-b4a02a8815a7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "__EXTRACT_DATASET__",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
                         "errors": null,
-                        "id": 33,
+                        "id": 9,
                         "input_connections": {
-                            "input": {
-                                "id": 31,
-                                "output_name": "out_file1"
+                            "gff": {
+                                "id": 8,
+                                "output_name": "renamed"
+                            },
+                            "ref_genome|genome": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Extract Dataset",
+                        "name": "Genome annotation statistics",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "data"
+                                "name": "summary",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "graphs",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "left": 4607,
-                            "top": 465
+                            "bottom": 363.2833557128906,
+                            "height": 276.4000244140625,
+                            "left": 560.6500244140625,
+                            "right": 760.6500244140625,
+                            "top": 86.88333129882812,
+                            "width": 200,
+                            "x": 560.6500244140625,
+                            "y": 86.88333129882812
                         },
-                        "post_job_actions": {
-                            "ChangeDatatypeActionoutput": {
-                                "action_arguments": {
-                                    "newtype": "tabular"
-                                },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "output"
-                            },
-                            "TagDatasetActionoutput": {
-                                "action_arguments": {
-                                    "tags": "#condition"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "output"
-                            }
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "8cffbd184762",
+                            "name": "jcvi_gff_stats",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": "__EXTRACT_DATASET__",
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"by_index\", \"__current_case__\": 2, \"index\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"gff\": {\"__class__\": \"ConnectedValue\"}, \"ref_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.8.4",
                         "type": "tool",
-                        "uuid": "7b09fd71-c2d4-48a8-ba5a-ef9acba7e6b8",
+                        "uuid": "14236032-ec57-4beb-ab0a-e44bf845643c",
                         "workflow_outputs": [
                             {
-                                "label": "condition",
-                                "output_name": "output",
-                                "uuid": "bd014de4-708e-419c-bd1e-8bf350661aad"
+                                "label": null,
+                                "output_name": "graphs",
+                                "uuid": "782e21db-4be6-4230-92b5-3ea9004dda04"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "summary",
+                                "uuid": "a4dff39c-0479-4a25-ac62-b132c1083604"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1",
                         "errors": null,
-                        "id": 34,
+                        "id": 10,
                         "input_connections": {
-                            "infile1": {
-                                "id": 32,
-                                "output_name": "output"
+                            "input": {
+                                "id": 8,
+                                "output_name": "renamed"
                             },
-                            "infile2": {
-                                "id": 33,
+                            "reference_genome|genome_fasta": {
+                                "id": 0,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Join",
-                                "name": "infile1"
-                            },
-                            {
-                                "description": "runtime parameter for tool Join",
-                                "name": "infile2"
+                                "description": "runtime parameter for tool gffread",
+                                "name": "chr_replace"
                             }
                         ],
                         "label": null,
-                        "name": "Join",
+                        "name": "gffread",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "input"
+                                "name": "output_exons",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "output_cds",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "output_pep",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 4890,
-                            "top": 254
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Essential genes in both"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
+                            "bottom": 48.683319091796875,
+                            "height": 316.79998779296875,
+                            "left": 560.6500244140625,
+                            "right": 760.6500244140625,
+                            "top": -268.1166687011719,
+                            "width": 200,
+                            "x": 560.6500244140625,
+                            "y": -268.1166687011719
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "9ff72e942410",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "0232f19d300f",
+                            "name": "gffread",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \".\", \"header\": \"false\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"RuntimeValue\"}, \"infile2\": {\"__class__\": \"RuntimeValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"chr_replace\": {\"__class__\": \"RuntimeValue\"}, \"decode_url\": \"false\", \"expose\": \"false\", \"filtering\": null, \"full_gff_attribute_preservation\": \"false\", \"gffs\": {\"gff_fmt\": \"none\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"maxintron\": \"\", \"merging\": {\"merge_sel\": \"none\", \"__current_case__\": 0}, \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 2, \"genome_fasta\": {\"__class__\": \"ConnectedValue\"}, \"ref_filtering\": null, \"fa_outputs\": [\"-w exons.fa\", \"-x cds.fa\", \"-y pep.fa\"]}, \"region\": {\"region_filter\": \"none\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.2.1.1",
                         "type": "tool",
-                        "uuid": "e3079b53-7fa1-43d1-820c-dbcded909b75",
+                        "uuid": "3b5ecaf4-2d08-42f8-a6f0-f05ad9e5fe92",
                         "workflow_outputs": [
                             {
-                                "label": "essential_both",
-                                "output_name": "output",
-                                "uuid": "5cdfb5c9-c677-41dc-a838-c4a61d62f5be"
+                                "label": null,
+                                "output_name": "output_cds",
+                                "uuid": "0df7b9b5-1ed1-4cf4-b483-a604862f4540"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_exons",
+                                "uuid": "f485f8fe-0d63-49ba-a88d-dfc8e03db553"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_pep",
+                                "uuid": "7430528c-9af5-4e05-ba6c-bbf95f19ad7e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3",
                         "errors": null,
-                        "id": 35,
+                        "id": 11,
                         "input_connections": {
-                            "infile1": {
-                                "id": 32,
+                            "reference_genome|genome": {
+                                "id": 0,
                                 "output_name": "output"
                             },
-                            "infile2": {
-                                "id": 33,
-                                "output_name": "output"
+                            "track_groups_0|data_tracks_0|data_format|annotation": {
+                                "id": 8,
+                                "output_name": "renamed"
+                            },
+                            "track_groups_1|data_tracks_0|data_format|annotation": {
+                                "id": 7,
+                                "output_name": "output_evidences"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Join",
-                                "name": "infile1"
-                            },
-                            {
-                                "description": "runtime parameter for tool Join",
-                                "name": "infile2"
+                                "description": "runtime parameter for tool JBrowse",
+                                "name": "reference_genome"
                             }
                         ],
                         "label": null,
-                        "name": "Join",
+                        "name": "JBrowse",
                         "outputs": [
                             {
                                 "name": "output",
-                                "type": "input"
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 4895,
-                            "top": 412
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Essential genes only in control"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
+                            "bottom": 677.2833557128906,
+                            "height": 276.4000244140625,
+                            "left": 560.6500244140625,
+                            "right": 760.6500244140625,
+                            "top": 400.8833312988281,
+                            "width": 200,
+                            "x": 560.6500244140625,
+                            "y": 400.8833312988281
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3",
                         "tool_shed_repository": {
-                            "changeset_revision": "9ff72e942410",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "8774b28235bb",
+                            "name": "jbrowse",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \".\", \"header\": \"false\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"RuntimeValue\"}, \"infile2\": {\"__class__\": \"RuntimeValue\"}, \"jointype\": \"-v 1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Maker annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 1, \"category\": \"Maker evidences\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"true\", \"__current_case__\": 0, \"name\": {\"__class__\": \"RuntimeValue\"}}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.10+galaxy0",
                         "type": "tool",
-                        "uuid": "10ed907c-d126-47f8-b91a-ddf45f0e0c9e",
+                        "uuid": "5a978f9d-7adc-4e30-8b20-dcfa27f18dfa",
                         "workflow_outputs": [
                             {
-                                "label": "essential_control",
+                                "label": null,
                                 "output_name": "output",
-                                "uuid": "8b2b65ea-37c3-43d2-b416-38f8f920fbd9"
+                                "uuid": "c7432de7-b6b4-457a-8c0a-69c44418234d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
                         "errors": null,
-                        "id": 36,
+                        "id": 12,
                         "input_connections": {
-                            "infile1": {
-                                "id": 32,
-                                "output_name": "output"
-                            },
-                            "infile2": {
-                                "id": 33,
-                                "output_name": "output"
+                            "input": {
+                                "id": 10,
+                                "output_name": "output_exons"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Busco",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool Join",
-                                "name": "infile1"
+                                "name": "busco_sum",
+                                "type": "txt"
                             },
                             {
-                                "description": "runtime parameter for tool Join",
-                                "name": "infile2"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Join",
-                        "outputs": [
+                                "name": "busco_table",
+                                "type": "tabular"
+                            },
                             {
-                                "name": "output",
-                                "type": "input"
+                                "name": "busco_missing",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 4896,
-                            "top": 566
+                            "bottom": 100.88333129882812,
+                            "height": 256,
+                            "left": 838.6666870117188,
+                            "right": 1038.6666870117188,
+                            "top": -155.11666870117188,
+                            "width": 200,
+                            "x": 838.6666870117188,
+                            "y": -155.11666870117188
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Essential genes only in condition"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
+                            "HideDatasetActionbusco_missing": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "busco_missing"
+                            },
+                            "HideDatasetActionbusco_table": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "busco_table"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "9ff72e942410",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "602fb8e63aa7",
+                            "name": "busco",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \".\", \"header\": \"false\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"RuntimeValue\"}, \"infile2\": {\"__class__\": \"RuntimeValue\"}, \"jointype\": \"-v 2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"tran\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.1.4",
                         "type": "tool",
-                        "uuid": "c1e1e08c-c12a-4ea0-a166-0e45c1044463",
+                        "uuid": "dee27b5d-de92-4e99-898c-3bf3fea6ee72",
                         "workflow_outputs": [
                             {
-                                "label": "essential_condition",
-                                "output_name": "output",
-                                "uuid": "37639319-b053-4fbc-bf61-fd3e38263502"
+                                "label": "Busco summary final round",
+                                "output_name": "busco_sum",
+                                "uuid": "6951417b-ee0b-4e03-98e4-67d262e086dc"
                             }
                         ]
                     }
                 ],
-                "parent_id": "genome-annotation/tnseq",
-                "path": "topics/genome-annotation/tutorials/tnseq/workflows/essential-genes-detection-transposon-insertion-sequencing-workflow.ga",
+                "parent_id": "genome-annotation/annotation-with-maker-short",
+                "path": "topics/genome-annotation/tutorials/annotation-with-maker-short/workflows/main_workflow.ga",
                 "tags": [
                     "genome-annotation"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "Essential genes detection with Transposon insertion sequencing",
+                "tests": false,
+                "title": "Genome annotation with Maker (short)",
                 "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-tnseq/versions/essential-genes-detection-transposon-insertion-sequencing-workflow",
-                "tutorial_id": "tnseq",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/tnseq/workflows/essential-genes-detection-transposon-insertion-sequencing-workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/tnseq/workflows/essential-genes-detection-transposon-insertion-sequencing-workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-annotation-with-maker-short/versions/main-workflow",
+                "tutorial_id": "annotation-with-maker-short",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-maker-short/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-maker-short/workflows/main_workflow.html",
                 "version": 1,
-                "wfid": "genome-annotation-tnseq",
-                "wfname": "essential-genes-detection-transposon-insertion-sequencing-workflow",
-                "workflow": "essential-genes-detection-transposon-insertion-sequencing-workflow.ga",
+                "wfid": "genome-annotation-annotation-with-maker-short",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "Filter1",
-                    "__EXTRACT_DATASET__",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/find_subsequences/bg_find_subsequences/0.2",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/gff_to_prot/gff_to_prot/3.0.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/3.0.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5"
+                    "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.10",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10",
+                    "toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0"
                 ],
-                "workflowhub_id": "1149"
+                "workflowhub_id": "1194"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.2579335"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.4406623"
     },
     {
         "admin_install": {
@@ -105810,173 +107862,191 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "augustus_training",
+                    "name": "deeptools_bam_coverage",
                     "owner": "bgruening",
-                    "revisions": "6519ebe25019",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "bb1e4f63e0e6",
+                    "tool_panel_section_label": "deepTools",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "gffread",
-                    "owner": "devteam",
-                    "revisions": "69e0806b63a4",
-                    "tool_panel_section_label": "Convert Formats",
+                    "name": "find_subsequences",
+                    "owner": "bgruening",
+                    "revisions": "d882a0a75759",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "busco",
-                    "owner": "iuc",
-                    "revisions": "602fb8e63aa7",
-                    "tool_panel_section_label": "Annotation",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fasta_stats",
-                    "owner": "iuc",
-                    "revisions": "9c620a950d3a",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "jbrowse",
-                    "owner": "iuc",
-                    "revisions": "6cd09d7b5f37",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "name": "bowtie_wrappers",
+                    "owner": "devteam",
+                    "revisions": "b46e7d48076a",
+                    "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "jcvi_gff_stats",
-                    "owner": "iuc",
-                    "revisions": "8cffbd184762",
-                    "tool_panel_section_label": "Annotation",
+                    "name": "column_maker",
+                    "owner": "devteam",
+                    "revisions": "be25c075ed54",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "maker",
+                    "name": "gff_to_prot",
                     "owner": "iuc",
-                    "revisions": "d46d803ca6cc",
+                    "revisions": "07d7991bf205",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "maker_map_ids",
+                    "name": "transit_gumbel",
                     "owner": "iuc",
-                    "revisions": "e906fa778440",
+                    "revisions": "f50807720df1",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "snap_training",
-                    "owner": "iuc",
-                    "revisions": "2a598c0aa042",
-                    "tool_panel_section_label": "Annotation",
+                    "name": "cutadapt",
+                    "owner": "lparsons",
+                    "revisions": "49370cb85f0f",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: augustus_training\n  owner: bgruening\n  revisions: 6519ebe25019\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gffread\n  owner: devteam\n  revisions: 69e0806b63a4\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 602fb8e63aa7\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n  owner: iuc\n  revisions: 9c620a950d3a\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 6cd09d7b5f37\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jcvi_gff_stats\n  owner: iuc\n  revisions: 8cffbd184762\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker\n  owner: iuc\n  revisions: d46d803ca6cc\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker_map_ids\n  owner: iuc\n  revisions: e906fa778440\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snap_training\n  owner: iuc\n  revisions: 2a598c0aa042\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: deeptools_bam_coverage\n  owner: bgruening\n  revisions: bb1e4f63e0e6\n  tool_panel_section_label: deepTools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: find_subsequences\n  owner: bgruening\n  revisions: d882a0a75759\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie_wrappers\n  owner: devteam\n  revisions: b46e7d48076a\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: be25c075ed54\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gff_to_prot\n  owner: iuc\n  revisions: 07d7991bf205\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: transit_gumbel\n  owner: iuc\n  revisions: f50807720df1\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 49370cb85f0f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/tnseq/tutorial.json",
         "contributors": [
+            {
+                "email": "delphine.lariviere@galaxy.org",
+                "id": "delphine-l",
+                "joined": "2017-09",
+                "name": "Delphine Lariviere",
+                "orcid": "0000-0001-6421-3484",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
-                    "eurosciencegateway",
+                    "ifb",
                     "elixir-europe"
                 ],
                 "contact_for_training": true,
                 "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
                 "fediverse_flavor": "mastodon",
-                "id": "abretaud",
+                "id": "bebatut",
                 "joined": "2017-09",
+                "linkedin": "berenicebatut",
                 "location": {
                     "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
+                    "lat": 45.77,
+                    "lon": 3.08
                 },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             }
         ],
-        "dir": "topics/genome-annotation/tutorials/annotation-with-maker",
+        "dir": "topics/genome-annotation/tutorials/tnseq",
+        "edam_ontology": [
+            "topic_0622",
+            "topic_3301",
+            "topic_0080",
+            "topic_0798"
+        ],
         "edam_operation": [
-            "Ab-initio gene prediction",
-            "Genome annotation",
-            "Sequence assembly validation",
-            "Homology-based gene prediction",
-            "Genome visualisation",
-            "Operation",
-            "Transcriptome assembly",
-            "Sequence annotation",
-            "Genome assembly",
-            "Gene prediction",
-            "Scaffolding"
+            "Sequence trimming",
+            "Transposon prediction",
+            "Read pre-processing",
+            "Primer removal"
+        ],
+        "edam_topic": [
+            "Genomics",
+            "Microbiology",
+            "Sequence analysis",
+            "Mobile genetic elements"
         ],
-        "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
+            "UseGalaxy.be",
             "UseGalaxy.no",
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "genome-annotation/annotation-with-maker",
+        "id": "genome-annotation/tnseq",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.org.au"
+            "UseGalaxy.eu"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Maker allows to annotate a eukaryotic genome.",
-            "BUSCO and JBrowse allow to inspect the quality of an annotation."
+            "TnSeq is a useful analysis to detect essential genes and conditional essential genes",
+            "The saturation of the library must be sufficient so that every gene must have been impacted at least once",
+            "Be sure you have removed every transposon sequence before starting your analysis",
+            "Verify the results manually do separate domain essential and essential genes"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Advanced",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-02-29",
+        "mod_date": "2024-03-18",
         "objectives": [
-            "Load genome into Galaxy",
-            "Annotate genome with Maker",
-            "Evaluate annotation quality with BUSCO",
-            "View annotations in JBrowse"
+            "Understand the read structure of TnSeq analyses",
+            "Predict Essential genes with Transit",
+            "Compare gene essentiality in control sample and an different experimental condition"
         ],
-        "pageviews": 21535,
+        "pageviews": 5910080,
         "priority": 4,
-        "pub_date": "2018-09-24",
+        "pub_date": "2019-07-02",
         "questions": [
-            "How to annotate an eukaryotic genome?",
-            "How to evaluate and visualize annotated genomic features?"
+            "What is Transposon insertion Sequencing?",
+            "How to get TA sites Coverage ? ",
+            "How to predict essential genes ?"
         ],
-        "short_id": "T00166",
+        "short_id": "T00179",
         "short_tools": [
-            "jcvi_gff_stats",
-            "gffread",
-            "jbrowse",
-            "busco",
-            "fasta-stats",
-            "snap_training",
-            "maker",
-            "augustus_training",
-            "maker_map_ids"
+            "__EXTRACT_DATASET__",
+            "bowtie_wrapper",
+            "gff_to_prot",
+            "tp_easyjoin_tool",
+            "Filter1",
+            "transit_gumbel",
+            "bg_find_subsequences",
+            "tp_sort_header_tool",
+            "cutadapt",
+            "Cut1",
+            "Add_a_column1",
+            "deeptools_bam_coverage"
         ],
-        "slides": false,
+        "slides": true,
         "slides_recordings": false,
-        "subtopic": "eukaryote",
+        "subtopic": "prokaryote",
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.no",
@@ -105984,8 +108054,8 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
                 }
             ],
@@ -105996,31 +108066,34 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
         "tags": [
-            "gmod",
-            "eukaryote",
-            "jbrowse1",
-            "maker"
+            "bacteria",
+            "tnseq",
+            "essential genes",
+            "microgalaxy"
         ],
-        "time_estimation": "4h",
-        "title": "Genome annotation with Maker",
+        "time_estimation": "7H",
+        "title": "Essential genes detection with Transposon insertion sequencing",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3",
-            "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.11",
-            "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1"
+            "Cut1",
+            "Filter1",
+            "__EXTRACT_DATASET__",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/find_subsequences/bg_find_subsequences/0.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/gff_to_prot/gff_to_prot/3.0.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/3.0.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5"
         ],
         "topic_name": "genome-annotation",
         "topic_name_human": "Genome Annotation",
@@ -106030,2317 +108103,1569 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "annotation-with-maker",
+        "tutorial_name": "tnseq",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/tnseq/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/tnseq/tutorial.json"
         },
-        "version": 14,
+        "version": 12,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 114,
-        "visitors": 11527,
+        "visit_duration": 256,
+        "visitors": 2140389,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0003-0914-2470",
-                        "name": "Anthony Bretaudeau"
-                    },
-                    {
-                        "class": "Organization",
-                        "name": "French National Institute for Agriculture, Food, and Environment (INRAE)"
-                    }
-                ],
-                "description": "Genome annotation with Maker",
+                "creators": [],
+                "description": "Essential genes detection with Transposon insertion sequencing",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nProtein sequences\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenome sequence\"]\n  3[label=\"Maker\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Fasta Statistics\"]\n  2 -> 4 [label=\"output\"]\n  k2d3829e6f5b946d183e317efff814e09[color=lightseagreen,label=\"Output\\nFasta Statistics on input dataset(s): Fasta summary stats\"]\n  4 -> k2d3829e6f5b946d183e317efff814e09\n  5[label=\"Busco\"]\n  2 -> 5 [label=\"output\"]\n  ka15e121423a2484b9c751635fcd61fe3[color=lightseagreen,label=\"Output\\nBUSCO: short summary\"]\n  5 -> ka15e121423a2484b9c751635fcd61fe3\n  k7806088df65743899d546a3bdfa233b2[color=lightseagreen,label=\"Output\\nBUSCO: list of missing ortholog genes\"]\n  5 -> k7806088df65743899d546a3bdfa233b2\n  k6a27d0f6d83c42b1a7af5f99ba5debe2[color=lightseagreen,label=\"Output\\nBUSCO: full table\"]\n  5 -> k6a27d0f6d83c42b1a7af5f99ba5debe2\n  6[label=\"Train Augustus\"]\n  2 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output_gff\"]\n  7[label=\"Genome annotation statistics\"]\n  3 -> 7 [label=\"output_gff\"]\n  2 -> 7 [label=\"output\"]\n  k2bed9aa65f22494d9caaf0ece8464f15[color=lightseagreen,label=\"Output\\nGenome annotation statistics: graphs (first round)\"]\n  7 -> k2bed9aa65f22494d9caaf0ece8464f15\n  k71d41ce2e90d435b9b64ab4320524770[color=lightseagreen,label=\"Output\\nGenome annotation statistics: summary (first round)\"]\n  7 -> k71d41ce2e90d435b9b64ab4320524770\n  8[label=\"gffread\"]\n  3 -> 8 [label=\"output_gff\"]\n  2 -> 8 [label=\"output\"]\n  9[label=\"Train SNAP\"]\n  2 -> 9 [label=\"output\"]\n  3 -> 9 [label=\"output_gff\"]\n  10[label=\"Busco\"]\n  8 -> 10 [label=\"output_exons\"]\n  ka79ab19d980242ca8ffa8c197a16c8b8[color=lightseagreen,label=\"Output\\nBusco summary first round\"]\n  10 -> ka79ab19d980242ca8ffa8c197a16c8b8\n  11[label=\"Maker\"]\n  6 -> 11 [label=\"output_tar\"]\n  9 -> 11 [label=\"output\"]\n  2 -> 11 [label=\"output\"]\n  3 -> 11 [label=\"output_full\"]\n  12[label=\"gffread\"]\n  11 -> 12 [label=\"output_gff\"]\n  2 -> 12 [label=\"output\"]\n  13[label=\"Train Augustus\"]\n  2 -> 13 [label=\"output\"]\n  11 -> 13 [label=\"output_gff\"]\n  k42d5aadd3a8c441d913fee8745a99b0b[color=lightseagreen,label=\"Output\\nAugus: trained model\"]\n  13 -> k42d5aadd3a8c441d913fee8745a99b0b\n  14[label=\"Genome annotation statistics\"]\n  11 -> 14 [label=\"output_gff\"]\n  2 -> 14 [label=\"output\"]\n  k9def2c6efd3c4969b5d4d13c187c1144[color=lightseagreen,label=\"Output\\nGenome annotation statistics: graphs (second round)\"]\n  14 -> k9def2c6efd3c4969b5d4d13c187c1144\n  k61f7a150a4a246b189f52170d466656e[color=lightseagreen,label=\"Output\\nGenome annotation statistics: summary (second round)\"]\n  14 -> k61f7a150a4a246b189f52170d466656e\n  15[label=\"Train SNAP\"]\n  2 -> 15 [label=\"output\"]\n  11 -> 15 [label=\"output_gff\"]\n  k458887f706614bdeab1a875aac6caed8[color=lightseagreen,label=\"Output\\nSNAP: trained model\"]\n  15 -> k458887f706614bdeab1a875aac6caed8\n  16[label=\"Busco\"]\n  12 -> 16 [label=\"output_exons\"]\n  kf52b1b410ea54384bd434927273c909c[color=lightseagreen,label=\"Output\\nBusco summary second round\"]\n  16 -> kf52b1b410ea54384bd434927273c909c\n  17[label=\"Maker\"]\n  13 -> 17 [label=\"output_tar\"]\n  15 -> 17 [label=\"output\"]\n  2 -> 17 [label=\"output\"]\n  11 -> 17 [label=\"output_full\"]\n  18[label=\"Map annotation ids\"]\n  17 -> 18 [label=\"output_gff\"]\n  k63575dcf54d14cb1b5fba2810b4da807[color=lightseagreen,label=\"Output\\nMap annotation ids: renamed GFF\"]\n  18 -> k63575dcf54d14cb1b5fba2810b4da807\n  19[label=\"JBrowse\"]\n  2 -> 19 [label=\"output\"]\n  3 -> 19 [label=\"output_gff\"]\n  18 -> 19 [label=\"renamed\"]\n  11 -> 19 [label=\"output_gff\"]\n  3 -> 19 [label=\"output_evidences\"]\n  11 -> 19 [label=\"output_evidences\"]\n  17 -> 19 [label=\"output_evidences\"]\n  k5a38ae83e17745f3aa9f4c1844584fa5[color=lightseagreen,label=\"Output\\nJBrowse: report\"]\n  19 -> k5a38ae83e17745f3aa9f4c1844584fa5\n  20[label=\"gffread\"]\n  18 -> 20 [label=\"renamed\"]\n  2 -> 20 [label=\"output\"]\n  k52fcac23b6124377a19a2e3b667a23e3[color=lightseagreen,label=\"Output\\nGffread: exons\"]\n  20 -> k52fcac23b6124377a19a2e3b667a23e3\n  k5c47c25e0ddb4adea5d0873ff4add28c[color=lightseagreen,label=\"Output\\nGffread: translation of cds\"]\n  20 -> k5c47c25e0ddb4adea5d0873ff4add28c\n  k84d9183b9589464b9f824dae7f87133e[color=lightseagreen,label=\"Output\\nGffread: cds\"]\n  20 -> k84d9183b9589464b9f824dae7f87133e\n  21[label=\"Genome annotation statistics\"]\n  18 -> 21 [label=\"renamed\"]\n  2 -> 21 [label=\"output\"]\n  kf5d4a6bf1ff8435a80847921e25bff3a[color=lightseagreen,label=\"Output\\nGenome annotation statistics: graphs (third round)\"]\n  21 -> kf5d4a6bf1ff8435a80847921e25bff3a\n  k5a863bd410f24ac881b6ce8b7f663e42[color=lightseagreen,label=\"Output\\nGenome annotation statistics: summary (third round)\"]\n  21 -> k5a863bd410f24ac881b6ce8b7f663e42\n  22[label=\"Busco\"]\n  20 -> 22 [label=\"output_exons\"]\n  k0bc78676eecc4168894d34c4ca07cdf3[color=lightseagreen,label=\"Output\\nBusco summary final round\"]\n  22 -> k0bc78676eecc4168894d34c4ca07cdf3\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTnseq-Tutorial-reads.fastqsanger.gz\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncondition_barcodes.fasta\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nconstruct_barcodes.fasta\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nstaph_aur.fasta\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nstaph_aur.gff3\"]\n  5[label=\"Cutadapt\"]\n  0 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"Nucleotide subsequence search\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"Convert GFF3\"]\n  4 -> 7 [label=\"output\"]\n  8[label=\"Cutadapt\"]\n  5 -> 8 [label=\"split_output\"]\n  9[label=\"Cut\"]\n  6 -> 9 [label=\"output\"]\n  10[label=\"Cut\"]\n  6 -> 10 [label=\"output\"]\n  11[label=\"Cutadapt\"]\n  8 -> 11 [label=\"out1\"]\n  12[label=\"Compute\"]\n  10 -> 12 [label=\"out_file1\"]\n  13[label=\"Cutadapt\"]\n  11 -> 13 [label=\"out1\"]\n  2 -> 13 [label=\"output\"]\n  14[label=\"Cut\"]\n  12 -> 14 [label=\"out_file1\"]\n  15[label=\"Cutadapt\"]\n  13 -> 15 [label=\"split_output\"]\n  16[label=\"Map with Bowtie for Illumina\"]\n  3 -> 16 [label=\"output\"]\n  15 -> 16 [label=\"out1\"]\n  17[label=\"bamCoverage\"]\n  16 -> 17 [label=\"output\"]\n  18[label=\"Join\"]\n  17 -> 18 [label=\"outFileName\"]\n  9 -> 18 [label=\"out_file1\"]\n  19[label=\"Join\"]\n  17 -> 19 [label=\"outFileName\"]\n  14 -> 19 [label=\"out_file1\"]\n  20[label=\"Cut\"]\n  18 -> 20 [label=\"output\"]\n  21[label=\"Cut\"]\n  19 -> 21 [label=\"output\"]\n  22[label=\"Sort\"]\n  20 -> 22 [label=\"out_file1\"]\n  23[label=\"Compute\"]\n  21 -> 23 [label=\"out_file1\"]\n  24[label=\"Cut\"]\n  23 -> 24 [label=\"out_file1\"]\n  25[label=\"Sort\"]\n  24 -> 25 [label=\"out_file1\"]\n  26[label=\"Join\"]\n  22 -> 26 [label=\"outfile\"]\n  25 -> 26 [label=\"outfile\"]\n  27[label=\"Compute\"]\n  26 -> 27 [label=\"output\"]\n  28[label=\"Cut\"]\n  27 -> 28 [label=\"out_file1\"]\n  29[label=\"Sort\"]\n  28 -> 29 [label=\"out_file1\"]\n  30[label=\"Gumbel\"]\n  7 -> 30 [label=\"output\"]\n  29 -> 30 [label=\"outfile\"]\n  31[label=\"Filter\"]\n  30 -> 31 [label=\"sites\"]\n  32[label=\"Extract Dataset\"]\n  31 -> 32 [label=\"out_file1\"]\n  k8796f62f46764ad2b0857597f894c32c[color=lightseagreen,label=\"Output\\ncontrol\"]\n  32 -> k8796f62f46764ad2b0857597f894c32c\n  33[label=\"Extract Dataset\"]\n  31 -> 33 [label=\"out_file1\"]\n  kbd014de4708e419cbd1e8bf350661aad[color=lightseagreen,label=\"Output\\ncondition\"]\n  33 -> kbd014de4708e419cbd1e8bf350661aad\n  34[label=\"Join\"]\n  32 -> 34 [label=\"output\"]\n  33 -> 34 [label=\"output\"]\n  k5cdfb5c9c67741dca838c4a61d62f5be[color=lightseagreen,label=\"Output\\nessential_both\"]\n  34 -> k5cdfb5c9c67741dca838c4a61d62f5be\n  35[label=\"Join\"]\n  32 -> 35 [label=\"output\"]\n  33 -> 35 [label=\"output\"]\n  k8b2b65ea37c343d2b41638f8f920fbd9[color=lightseagreen,label=\"Output\\nessential_control\"]\n  35 -> k8b2b65ea37c343d2b41638f8f920fbd9\n  36[label=\"Join\"]\n  32 -> 36 [label=\"output\"]\n  33 -> 36 [label=\"output\"]\n  k37639319b0534fbcbf61fd3e38263502[color=lightseagreen,label=\"Output\\nessential_condition\"]\n  36 -> k37639319b0534fbcbf61fd3e38263502\n}",
                 "history": [
                     {
-                        "hash": "e61e9eba49f4c255dd46e1094355f61a770ba14e",
-                        "message": "Fix workflow",
-                        "num": 12,
-                        "short_hash": "e61e9eba4",
-                        "unix": "1625849450"
-                    },
-                    {
-                        "hash": "106af0888f3f8cbc7040c20b62adbf52ddfe2186",
-                        "message": "Update maker workflow",
-                        "num": 11,
-                        "short_hash": "106af0888",
-                        "unix": "1625842677"
-                    },
-                    {
-                        "hash": "005d964a2e8cb80f8d1bf0b304adc8f9d7c9ff76",
-                        "message": "fix workflows",
-                        "num": 10,
-                        "short_hash": "005d964a2",
-                        "unix": "1609752597"
-                    },
-                    {
-                        "hash": "774f2aa374452d48fd29ee85513c3dc3a7f137f5",
-                        "message": "update maker tutorial and add a short version",
-                        "num": 9,
-                        "short_hash": "774f2aa37",
-                        "unix": "1609431273"
-                    },
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 8,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 7,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "1a3049ca861744336a01f79b6ae1bc8bc46e2b12",
-                        "message": "typos + update workflow",
-                        "num": 6,
-                        "short_hash": "1a3049ca8",
-                        "unix": "1558343672"
-                    },
-                    {
-                        "hash": "2318b970d421c42bbced1799cfca63ce056ad01f",
-                        "message": "udpate workflow",
-                        "num": 5,
-                        "short_hash": "2318b970d",
-                        "unix": "1557415647"
-                    },
-                    {
-                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
-                        "message": "Changed format of workflows",
-                        "num": 4,
-                        "short_hash": "361236c41",
-                        "unix": "1554368414"
-                    },
-                    {
-                        "hash": "6eef55b7e8306d8ce46ac08e7799f6f65ae106aa",
-                        "message": "Updated install_tutorial_requirements.sh + minor fixes (#1275)",
+                        "hash": "bc41adb9e901759a7013cebea286e631df2325e9",
+                        "message": "Rename workflow.",
                         "num": 3,
-                        "short_hash": "6eef55b7e",
-                        "unix": "1551293676"
+                        "short_hash": "bc41adb9e",
+                        "unix": "1603052556"
                     },
                     {
-                        "hash": "bc6d0ddca2ce262deb405fd92e0dab955488eb49",
-                        "message": "jbrowse part",
+                        "hash": "50c52377ea0c134e400a00e0d89e1973c203fa6c",
+                        "message": "Update workflow test.",
                         "num": 2,
-                        "short_hash": "bc6d0ddca",
-                        "unix": "1536669505"
+                        "short_hash": "50c52377e",
+                        "unix": "1603048372"
                     },
                     {
-                        "hash": "7b73f26f84bc0e9dc9e771f7dd89be3e6daddd66",
-                        "message": "update wf",
+                        "hash": "708ae9c5d8f8a740f948382c3fd5e7c935685d64",
+                        "message": "Updated workflow and test.",
                         "num": 1,
-                        "short_hash": "7b73f26f8",
-                        "unix": "1536594667"
+                        "short_hash": "708ae9c5d",
+                        "unix": "1603017659"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "It contains the sequences used by Maker to construct gene models.",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "It contains the sequences used by Maker to construct gene models.",
-                                "name": "EST and/or cDNA"
+                                "description": "",
+                                "name": "Tnseq-Tutorial-reads.fastqsanger.gz"
                             }
                         ],
-                        "label": "EST and/or cDNA",
-                        "name": "Input dataset",
+                        "label": "Tnseq-Tutorial-reads.fastqsanger.gz",
+                        "name": "Tnseq-Tutorial-reads.fastqsanger.gz",
                         "outputs": [],
                         "position": {
-                            "bottom": 287.875,
-                            "height": 81,
-                            "left": 661.46875,
-                            "right": 861.46875,
-                            "top": 206.875,
-                            "width": 200,
-                            "x": 661.46875,
-                            "y": 206.875
+                            "left": 204,
+                            "top": 204
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"name\": \"Tnseq-Tutorial-reads.fastqsanger.gz\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "397d1af7-4d12-43d6-955c-e3122978fc92",
-                        "workflow_outputs": []
+                        "uuid": "299514db-9c70-4ef6-8414-a343c9721121",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "9a01ba0a-25c6-4bed-9ead-21b9298585d9"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "A set of protein sequences, usually from closely related species or from a curated sequence database like UniProt/SwissProt.",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "A set of protein sequences, usually from closely related species or from a curated sequence database like UniProt/SwissProt.",
-                                "name": "Protein sequences"
+                                "description": "",
+                                "name": "condition_barcodes.fasta"
                             }
                         ],
-                        "label": "Protein sequences",
-                        "name": "Input dataset",
+                        "label": "condition_barcodes.fasta",
+                        "name": "condition_barcodes.fasta",
                         "outputs": [],
                         "position": {
-                            "bottom": 459,
-                            "height": 81,
-                            "left": 659.5,
-                            "right": 859.5,
-                            "top": 378,
-                            "width": 200,
-                            "x": 659.5,
-                            "y": 378
+                            "left": 202,
+                            "top": 326
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"name\": \"condition_barcodes.fasta\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "418c68b0-b726-4f5e-b53c-480f1e7d43b5",
-                        "workflow_outputs": []
+                        "uuid": "2e5a56b4-93d7-4fba-b165-5feb86deb7c2",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "51bba64c-6acc-4ebf-971d-b1f2ee9adcc6"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "This file corresponds to the sequence to be annotated.",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "This file corresponds to the sequence to be annotated.",
-                                "name": "Genome sequence"
+                                "description": "",
+                                "name": "construct_barcodes.fasta"
                             }
                         ],
-                        "label": "Genome sequence",
-                        "name": "Input dataset",
+                        "label": "construct_barcodes.fasta",
+                        "name": "construct_barcodes.fasta",
                         "outputs": [],
                         "position": {
-                            "bottom": 1797.03125,
-                            "height": 81,
-                            "left": 661.46875,
-                            "right": 861.46875,
-                            "top": 1716.03125,
-                            "width": 200,
-                            "x": 661.46875,
-                            "y": 1716.03125
+                            "left": 200,
+                            "top": 440
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"name\": \"construct_barcodes.fasta\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "e03b5775-bd22-4528-9f21-20cd396dc6cc",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nProtein sequences\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nGenome sequence\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Maker\"];\n  0 -->|output| 3;\n  2 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Fasta Statistics\"];\n  2 -->|output| 4;\n  2d3829e6-f5b9-46d1-83e3-17efff814e09[\"Output\\nFasta Statistics on input dataset(s): Fasta summary stats\"];\n  4 --> 2d3829e6-f5b9-46d1-83e3-17efff814e09;\n  style 2d3829e6-f5b9-46d1-83e3-17efff814e09 stroke:#2c3143,stroke-width:4px;\n  5[\"Busco\"];\n  2 -->|output| 5;\n  a15e1214-23a2-484b-9c75-1635fcd61fe3[\"Output\\nBUSCO: short summary\"];\n  5 --> a15e1214-23a2-484b-9c75-1635fcd61fe3;\n  style a15e1214-23a2-484b-9c75-1635fcd61fe3 stroke:#2c3143,stroke-width:4px;\n  7806088d-f657-4389-9d54-6a3bdfa233b2[\"Output\\nBUSCO: list of missing ortholog genes\"];\n  5 --> 7806088d-f657-4389-9d54-6a3bdfa233b2;\n  style 7806088d-f657-4389-9d54-6a3bdfa233b2 stroke:#2c3143,stroke-width:4px;\n  6a27d0f6-d83c-42b1-a7af-5f99ba5debe2[\"Output\\nBUSCO: full table\"];\n  5 --> 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2;\n  style 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2 stroke:#2c3143,stroke-width:4px;\n  6[\"Train Augustus\"];\n  2 -->|output| 6;\n  3 -->|output_gff| 6;\n  7[\"Genome annotation statistics\"];\n  3 -->|output_gff| 7;\n  2 -->|output| 7;\n  2bed9aa6-5f22-494d-9caa-f0ece8464f15[\"Output\\nGenome annotation statistics: graphs (first round)\"];\n  7 --> 2bed9aa6-5f22-494d-9caa-f0ece8464f15;\n  style 2bed9aa6-5f22-494d-9caa-f0ece8464f15 stroke:#2c3143,stroke-width:4px;\n  71d41ce2-e90d-435b-9b64-ab4320524770[\"Output\\nGenome annotation statistics: summary (first round)\"];\n  7 --> 71d41ce2-e90d-435b-9b64-ab4320524770;\n  style 71d41ce2-e90d-435b-9b64-ab4320524770 stroke:#2c3143,stroke-width:4px;\n  8[\"gffread\"];\n  3 -->|output_gff| 8;\n  2 -->|output| 8;\n  9[\"Train SNAP\"];\n  2 -->|output| 9;\n  3 -->|output_gff| 9;\n  10[\"Busco\"];\n  8 -->|output_exons| 10;\n  a79ab19d-9802-42ca-8ffa-8c197a16c8b8[\"Output\\nBusco summary first round\"];\n  10 --> a79ab19d-9802-42ca-8ffa-8c197a16c8b8;\n  style a79ab19d-9802-42ca-8ffa-8c197a16c8b8 stroke:#2c3143,stroke-width:4px;\n  11[\"Maker\"];\n  6 -->|output_tar| 11;\n  9 -->|output| 11;\n  2 -->|output| 11;\n  3 -->|output_full| 11;\n  12[\"gffread\"];\n  11 -->|output_gff| 12;\n  2 -->|output| 12;\n  13[\"Train Augustus\"];\n  2 -->|output| 13;\n  11 -->|output_gff| 13;\n  42d5aadd-3a8c-441d-913f-ee8745a99b0b[\"Output\\nAugus: trained model\"];\n  13 --> 42d5aadd-3a8c-441d-913f-ee8745a99b0b;\n  style 42d5aadd-3a8c-441d-913f-ee8745a99b0b stroke:#2c3143,stroke-width:4px;\n  14[\"Genome annotation statistics\"];\n  11 -->|output_gff| 14;\n  2 -->|output| 14;\n  9def2c6e-fd3c-4969-b5d4-d13c187c1144[\"Output\\nGenome annotation statistics: graphs (second round)\"];\n  14 --> 9def2c6e-fd3c-4969-b5d4-d13c187c1144;\n  style 9def2c6e-fd3c-4969-b5d4-d13c187c1144 stroke:#2c3143,stroke-width:4px;\n  61f7a150-a4a2-46b1-89f5-2170d466656e[\"Output\\nGenome annotation statistics: summary (second round)\"];\n  14 --> 61f7a150-a4a2-46b1-89f5-2170d466656e;\n  style 61f7a150-a4a2-46b1-89f5-2170d466656e stroke:#2c3143,stroke-width:4px;\n  15[\"Train SNAP\"];\n  2 -->|output| 15;\n  11 -->|output_gff| 15;\n  458887f7-0661-4bde-ab1a-875aac6caed8[\"Output\\nSNAP: trained model\"];\n  15 --> 458887f7-0661-4bde-ab1a-875aac6caed8;\n  style 458887f7-0661-4bde-ab1a-875aac6caed8 stroke:#2c3143,stroke-width:4px;\n  16[\"Busco\"];\n  12 -->|output_exons| 16;\n  f52b1b41-0ea5-4384-bd43-4927273c909c[\"Output\\nBusco summary second round\"];\n  16 --> f52b1b41-0ea5-4384-bd43-4927273c909c;\n  style f52b1b41-0ea5-4384-bd43-4927273c909c stroke:#2c3143,stroke-width:4px;\n  17[\"Maker\"];\n  13 -->|output_tar| 17;\n  15 -->|output| 17;\n  2 -->|output| 17;\n  11 -->|output_full| 17;\n  18[\"Map annotation ids\"];\n  17 -->|output_gff| 18;\n  63575dcf-54d1-4cb1-b5fb-a2810b4da807[\"Output\\nMap annotation ids: renamed GFF\"];\n  18 --> 63575dcf-54d1-4cb1-b5fb-a2810b4da807;\n  style 63575dcf-54d1-4cb1-b5fb-a2810b4da807 stroke:#2c3143,stroke-width:4px;\n  19[\"JBrowse\"];\n  2 -->|output| 19;\n  3 -->|output_gff| 19;\n  18 -->|renamed| 19;\n  11 -->|output_gff| 19;\n  3 -->|output_evidences| 19;\n  11 -->|output_evidences| 19;\n  17 -->|output_evidences| 19;\n  5a38ae83-e177-45f3-aa9f-4c1844584fa5[\"Output\\nJBrowse: report\"];\n  19 --> 5a38ae83-e177-45f3-aa9f-4c1844584fa5;\n  style 5a38ae83-e177-45f3-aa9f-4c1844584fa5 stroke:#2c3143,stroke-width:4px;\n  20[\"gffread\"];\n  18 -->|renamed| 20;\n  2 -->|output| 20;\n  52fcac23-b612-4377-a19a-2e3b667a23e3[\"Output\\nGffread: exons\"];\n  20 --> 52fcac23-b612-4377-a19a-2e3b667a23e3;\n  style 52fcac23-b612-4377-a19a-2e3b667a23e3 stroke:#2c3143,stroke-width:4px;\n  5c47c25e-0ddb-4ade-a5d0-873ff4add28c[\"Output\\nGffread: translation of cds\"];\n  20 --> 5c47c25e-0ddb-4ade-a5d0-873ff4add28c;\n  style 5c47c25e-0ddb-4ade-a5d0-873ff4add28c stroke:#2c3143,stroke-width:4px;\n  84d9183b-9589-464b-9f82-4dae7f87133e[\"Output\\nGffread: cds\"];\n  20 --> 84d9183b-9589-464b-9f82-4dae7f87133e;\n  style 84d9183b-9589-464b-9f82-4dae7f87133e stroke:#2c3143,stroke-width:4px;\n  21[\"Genome annotation statistics\"];\n  18 -->|renamed| 21;\n  2 -->|output| 21;\n  f5d4a6bf-1ff8-435a-8084-7921e25bff3a[\"Output\\nGenome annotation statistics: graphs (third round)\"];\n  21 --> f5d4a6bf-1ff8-435a-8084-7921e25bff3a;\n  style f5d4a6bf-1ff8-435a-8084-7921e25bff3a stroke:#2c3143,stroke-width:4px;\n  5a863bd4-10f2-4ac8-81b6-ce8b7f663e42[\"Output\\nGenome annotation statistics: summary (third round)\"];\n  21 --> 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42;\n  style 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42 stroke:#2c3143,stroke-width:4px;\n  22[\"Busco\"];\n  20 -->|output_exons| 22;\n  0bc78676-eecc-4168-894d-34c4ca07cdf3[\"Output\\nBusco summary final round\"];\n  22 --> 0bc78676-eecc-4168-894d-34c4ca07cdf3;\n  style 0bc78676-eecc-4168-894d-34c4ca07cdf3 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Genome annotation with Maker ",
-                "outputs": [
+                        "uuid": "7af899e7-676b-46ef-8c15-ff7b73b0fe76",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "e850fc22-c77f-4bbe-968f-ba44dea4caaf"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "dataset": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Fasta Statistics",
-                        "outputs": [
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "stats",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "staph_aur.fasta"
                             }
                         ],
+                        "label": "staph_aur.fasta",
+                        "name": "staph_aur.fasta",
+                        "outputs": [],
                         "position": {
-                            "bottom": 1526.4375,
-                            "height": 152,
-                            "left": 722.921875,
-                            "right": 922.921875,
-                            "top": 1374.4375,
-                            "width": 200,
-                            "x": 722.921875,
-                            "y": 1374.4375
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9c620a950d3a",
-                            "name": "fasta_stats",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 183,
+                            "top": 550
                         },
-                        "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.1",
-                        "type": "tool",
-                        "uuid": "9cd9564b-b447-4a93-9445-ae3583137010",
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"staph_aur.fasta\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "b522e8dc-3f8f-4e6d-9a2d-c970e25bf6f9",
                         "workflow_outputs": [
                             {
-                                "label": "Fasta Statistics on input dataset(s): Fasta summary stats",
-                                "output_name": "stats",
-                                "uuid": "2d3829e6-f5b9-46d1-83e3-17efff814e09"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "793cf25f-49a3-4afa-8165-c5c54e581864"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                        "content_id": null,
                         "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "input": {
-                                "id": 2,
-                                "output_name": "output"
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "staph_aur.gff3"
                             }
+                        ],
+                        "label": "staph_aur.gff3",
+                        "name": "staph_aur.gff3",
+                        "outputs": [],
+                        "position": {
+                            "left": 183,
+                            "top": 694
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Busco",
-                        "outputs": [
-                            {
-                                "name": "busco_sum",
-                                "type": "txt"
-                            },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"staph_aur.gff3\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "e523846f-d4bf-43a8-a6f6-5763dba67f8f",
+                        "workflow_outputs": [
                             {
-                                "name": "busco_table",
-                                "type": "tabular"
-                            },
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "2e39f099-2536-4a11-add0-9cf3576f1d68"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nTnseq-Tutorial-reads.fastqsanger.gz\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ncondition_barcodes.fasta\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nconstruct_barcodes.fasta\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nstaph_aur.fasta\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nstaph_aur.gff3\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Cutadapt\"];\n  0 -->|output| 5;\n  1 -->|output| 5;\n  6[\"Nucleotide subsequence search\"];\n  3 -->|output| 6;\n  7[\"Convert GFF3\"];\n  4 -->|output| 7;\n  8[\"Cutadapt\"];\n  5 -->|split_output| 8;\n  9[\"Cut\"];\n  6 -->|output| 9;\n  10[\"Cut\"];\n  6 -->|output| 10;\n  11[\"Cutadapt\"];\n  8 -->|out1| 11;\n  12[\"Compute\"];\n  10 -->|out_file1| 12;\n  13[\"Cutadapt\"];\n  11 -->|out1| 13;\n  2 -->|output| 13;\n  14[\"Cut\"];\n  12 -->|out_file1| 14;\n  15[\"Cutadapt\"];\n  13 -->|split_output| 15;\n  16[\"Map with Bowtie for Illumina\"];\n  3 -->|output| 16;\n  15 -->|out1| 16;\n  17[\"bamCoverage\"];\n  16 -->|output| 17;\n  18[\"Join\"];\n  17 -->|outFileName| 18;\n  9 -->|out_file1| 18;\n  19[\"Join\"];\n  17 -->|outFileName| 19;\n  14 -->|out_file1| 19;\n  20[\"Cut\"];\n  18 -->|output| 20;\n  21[\"Cut\"];\n  19 -->|output| 21;\n  22[\"Sort\"];\n  20 -->|out_file1| 22;\n  23[\"Compute\"];\n  21 -->|out_file1| 23;\n  24[\"Cut\"];\n  23 -->|out_file1| 24;\n  25[\"Sort\"];\n  24 -->|out_file1| 25;\n  26[\"Join\"];\n  22 -->|outfile| 26;\n  25 -->|outfile| 26;\n  27[\"Compute\"];\n  26 -->|output| 27;\n  28[\"Cut\"];\n  27 -->|out_file1| 28;\n  29[\"Sort\"];\n  28 -->|out_file1| 29;\n  30[\"Gumbel\"];\n  7 -->|output| 30;\n  29 -->|outfile| 30;\n  31[\"Filter\"];\n  30 -->|sites| 31;\n  32[\"Extract Dataset\"];\n  31 -->|out_file1| 32;\n  8796f62f-4676-4ad2-b085-7597f894c32c[\"Output\\ncontrol\"];\n  32 --> 8796f62f-4676-4ad2-b085-7597f894c32c;\n  style 8796f62f-4676-4ad2-b085-7597f894c32c stroke:#2c3143,stroke-width:4px;\n  33[\"Extract Dataset\"];\n  31 -->|out_file1| 33;\n  bd014de4-708e-419c-bd1e-8bf350661aad[\"Output\\ncondition\"];\n  33 --> bd014de4-708e-419c-bd1e-8bf350661aad;\n  style bd014de4-708e-419c-bd1e-8bf350661aad stroke:#2c3143,stroke-width:4px;\n  34[\"Join\"];\n  32 -->|output| 34;\n  33 -->|output| 34;\n  5cdfb5c9-c677-41dc-a838-c4a61d62f5be[\"Output\\nessential_both\"];\n  34 --> 5cdfb5c9-c677-41dc-a838-c4a61d62f5be;\n  style 5cdfb5c9-c677-41dc-a838-c4a61d62f5be stroke:#2c3143,stroke-width:4px;\n  35[\"Join\"];\n  32 -->|output| 35;\n  33 -->|output| 35;\n  8b2b65ea-37c3-43d2-b416-38f8f920fbd9[\"Output\\nessential_control\"];\n  35 --> 8b2b65ea-37c3-43d2-b416-38f8f920fbd9;\n  style 8b2b65ea-37c3-43d2-b416-38f8f920fbd9 stroke:#2c3143,stroke-width:4px;\n  36[\"Join\"];\n  32 -->|output| 36;\n  33 -->|output| 36;\n  37639319-b053-4fbc-bf61-fd3e38263502[\"Output\\nessential_condition\"];\n  36 --> 37639319-b053-4fbc-bf61-fd3e38263502;\n  style 37639319-b053-4fbc-bf61-fd3e38263502 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Essential genes detection with Transposon insertion sequencing",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "busco_missing",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "Tnseq-Tutorial-reads.fastqsanger.gz"
                             }
                         ],
+                        "label": "Tnseq-Tutorial-reads.fastqsanger.gz",
+                        "name": "Tnseq-Tutorial-reads.fastqsanger.gz",
+                        "outputs": [],
                         "position": {
-                            "bottom": 1989.015625,
-                            "height": 212,
-                            "left": 939.484375,
-                            "right": 1139.484375,
-                            "top": 1777.015625,
-                            "width": 200,
-                            "x": 939.484375,
-                            "y": 1777.015625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
-                        "tool_shed_repository": {
-                            "changeset_revision": "602fb8e63aa7",
-                            "name": "busco",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 204,
+                            "top": 204
                         },
-                        "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"geno\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.1.4",
-                        "type": "tool",
-                        "uuid": "2e99d9de-b48b-4f0f-99da-5f727ad023cc",
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Tnseq-Tutorial-reads.fastqsanger.gz\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "299514db-9c70-4ef6-8414-a343c9721121",
                         "workflow_outputs": [
                             {
-                                "label": "BUSCO: short summary",
-                                "output_name": "busco_sum",
-                                "uuid": "a15e1214-23a2-484b-9c75-1635fcd61fe3"
-                            },
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "9a01ba0a-25c6-4bed-9ead-21b9298585d9"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": "BUSCO: list of missing ortholog genes",
-                                "output_name": "busco_missing",
-                                "uuid": "7806088d-f657-4389-9d54-6a3bdfa233b2"
-                            },
+                                "description": "",
+                                "name": "condition_barcodes.fasta"
+                            }
+                        ],
+                        "label": "condition_barcodes.fasta",
+                        "name": "condition_barcodes.fasta",
+                        "outputs": [],
+                        "position": {
+                            "left": 202,
+                            "top": 326
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"condition_barcodes.fasta\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "2e5a56b4-93d7-4fba-b165-5feb86deb7c2",
+                        "workflow_outputs": [
                             {
-                                "label": "BUSCO: full table",
-                                "output_name": "busco_table",
-                                "uuid": "6a27d0f6-d83c-42b1-a7af-5f99ba5debe2"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "51bba64c-6acc-4ebf-971d-b1f2ee9adcc6"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                        "content_id": null,
                         "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "gff": {
-                                "id": 3,
-                                "output_name": "output_gff"
-                            },
-                            "ref_genome|genome": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Genome annotation statistics",
-                        "outputs": [
-                            {
-                                "name": "summary",
-                                "type": "txt"
-                            },
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "graphs",
-                                "type": "pdf"
+                                "description": "",
+                                "name": "construct_barcodes.fasta"
                             }
                         ],
+                        "label": "construct_barcodes.fasta",
+                        "name": "construct_barcodes.fasta",
+                        "outputs": [],
                         "position": {
-                            "bottom": 1247.015625,
-                            "height": 272,
-                            "left": 1247.5,
-                            "right": 1447.5,
-                            "top": 975.015625,
-                            "width": 200,
-                            "x": 1247.5,
-                            "y": 975.015625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
-                        "tool_shed_repository": {
-                            "changeset_revision": "8cffbd184762",
-                            "name": "jcvi_gff_stats",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 200,
+                            "top": 440
                         },
-                        "tool_state": "{\"gff\": {\"__class__\": \"ConnectedValue\"}, \"ref_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.8.4",
-                        "type": "tool",
-                        "uuid": "af60c4d9-58f2-4f41-a2a3-6458cdcfd404",
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"construct_barcodes.fasta\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "7af899e7-676b-46ef-8c15-ff7b73b0fe76",
                         "workflow_outputs": [
                             {
-                                "label": "Genome annotation statistics: graphs (first round)",
-                                "output_name": "graphs",
-                                "uuid": "2bed9aa6-5f22-494d-9caa-f0ece8464f15"
-                            },
-                            {
-                                "label": "Genome annotation statistics: summary (first round)",
-                                "output_name": "summary",
-                                "uuid": "71d41ce2-e90d-435b-9b64-ab4320524770"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "e850fc22-c77f-4bbe-968f-ba44dea4caaf"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                        "content_id": null,
                         "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "input": {
-                                "id": 8,
-                                "output_name": "output_exons"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Busco",
-                        "outputs": [
-                            {
-                                "name": "busco_sum",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "busco_table",
-                                "type": "tabular"
-                            },
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "busco_missing",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "staph_aur.fasta"
                             }
                         ],
+                        "label": "staph_aur.fasta",
+                        "name": "staph_aur.fasta",
+                        "outputs": [],
                         "position": {
-                            "bottom": 1738.03125,
-                            "height": 252,
-                            "left": 1545.5,
-                            "right": 1745.5,
-                            "top": 1486.03125,
-                            "width": 200,
-                            "x": 1545.5,
-                            "y": 1486.03125
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionbusco_missing": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "busco_missing"
-                            },
-                            "HideDatasetActionbusco_table": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "busco_table"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
-                        "tool_shed_repository": {
-                            "changeset_revision": "602fb8e63aa7",
-                            "name": "busco",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 183,
+                            "top": 550
                         },
-                        "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"tran\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.1.4",
-                        "type": "tool",
-                        "uuid": "a83a2b48-7787-4b53-a592-339f5134e168",
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"staph_aur.fasta\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "b522e8dc-3f8f-4e6d-9a2d-c970e25bf6f9",
                         "workflow_outputs": [
                             {
-                                "label": "Busco summary first round",
-                                "output_name": "busco_sum",
-                                "uuid": "a79ab19d-9802-42ca-8ffa-8c197a16c8b8"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "793cf25f-49a3-4afa-8165-c5c54e581864"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3",
+                        "content_id": null,
                         "errors": null,
-                        "id": 13,
-                        "input_connections": {
-                            "genome": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "maker_gff": {
-                                "id": 11,
-                                "output_name": "output_gff"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Train Augustus",
-                        "outputs": [
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output_tar",
-                                "type": "augustus"
+                                "description": "",
+                                "name": "staph_aur.gff3"
                             }
                         ],
+                        "label": "staph_aur.gff3",
+                        "name": "staph_aur.gff3",
+                        "outputs": [],
                         "position": {
-                            "bottom": 1259.03125,
-                            "height": 182,
-                            "left": 1863.5,
-                            "right": 2063.5,
-                            "top": 1077.03125,
-                            "width": 200,
-                            "x": 1863.5,
-                            "y": 1077.03125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6519ebe25019",
-                            "name": "augustus_training",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 183,
+                            "top": 694
                         },
-                        "tool_state": "{\"genome\": {\"__class__\": \"ConnectedValue\"}, \"maker_gff\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.3.3",
-                        "type": "tool",
-                        "uuid": "b347da09-05a2-4d30-a103-dbeb5853efcd",
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"staph_aur.gff3\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "e523846f-d4bf-43a8-a6f6-5763dba67f8f",
                         "workflow_outputs": [
                             {
-                                "label": "Augus: trained model",
-                                "output_name": "output_tar",
-                                "uuid": "42d5aadd-3a8c-441d-913f-ee8745a99b0b"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "2e39f099-2536-4a11-add0-9cf3576f1d68"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
                         "errors": null,
-                        "id": 14,
+                        "id": 5,
                         "input_connections": {
-                            "gff": {
-                                "id": 11,
-                                "output_name": "output_gff"
+                            "library|input_1": {
+                                "id": 0,
+                                "output_name": "output"
                             },
-                            "ref_genome|genome": {
-                                "id": 2,
+                            "library|r1|front_adapters_0|front_adapter_source|front_adapter_file": {
+                                "id": 1,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Genome annotation statistics",
+                        "name": "Cutadapt",
                         "outputs": [
                             {
-                                "name": "summary",
-                                "type": "txt"
+                                "name": "split_output",
+                                "type": "input"
                             },
                             {
-                                "name": "graphs",
-                                "type": "pdf"
+                                "name": "report",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 1569.03125,
-                            "height": 272,
-                            "left": 1863.5,
-                            "right": 2063.5,
-                            "top": 1297.03125,
-                            "width": 200,
-                            "x": 1863.5,
-                            "y": 1297.03125
+                            "left": 442,
+                            "top": 190
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
                         "tool_shed_repository": {
-                            "changeset_revision": "8cffbd184762",
-                            "name": "jcvi_gff_stats",
-                            "owner": "iuc",
+                            "changeset_revision": "49370cb85f0f",
+                            "name": "cutadapt",
+                            "owner": "lparsons",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"gff\": {\"__class__\": \"ConnectedValue\"}, \"ref_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.8.4",
+                        "tool_state": "{\"__input_ext\": \"input\", \"adapter_options\": {\"error_rate\": \"0.15\", \"no_indels\": \"false\", \"count\": \"3\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"no_trim\": \"false\", \"mask_adapter\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"discard\": \"false\", \"discard_untrimmed\": \"false\", \"min\": \"0\", \"max\": \"0\", \"max_n\": \"\", \"pair_filter\": \"any\"}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [{\"__index__\": 0, \"front_adapter_source\": {\"front_adapter_source_list\": \"file\", \"__current_case__\": 2, \"front_adapter_file\": {\"__class__\": \"ConnectedValue\"}}}], \"anywhere_adapters\": [], \"cut\": \"0\"}}, \"output_options\": {\"report\": \"true\", \"info_file\": \"false\", \"rest_file\": \"false\", \"wildcard_file\": \"false\", \"too_short_file\": \"false\", \"too_long_file\": \"false\", \"untrimmed_file\": \"false\", \"multiple_output\": \"true\"}, \"read_mod_options\": {\"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"prefix\": \"\", \"suffix\": \"\", \"strip_suffix\": \"\", \"length\": \"0\", \"length_tag\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "5a3899b6-a669-4a36-990e-01e6cac6410d",
+                        "uuid": "88a0eb99-bd98-4016-b0ee-6fca1043db7b",
                         "workflow_outputs": [
                             {
-                                "label": "Genome annotation statistics: graphs (second round)",
-                                "output_name": "graphs",
-                                "uuid": "9def2c6e-fd3c-4969-b5d4-d13c187c1144"
+                                "label": null,
+                                "output_name": "split_output",
+                                "uuid": "292be5db-6a3d-4ccd-b766-8c2348f59a46"
                             },
                             {
-                                "label": "Genome annotation statistics: summary (second round)",
-                                "output_name": "summary",
-                                "uuid": "61f7a150-a4a2-46b1-89f5-2170d466656e"
+                                "label": null,
+                                "output_name": "report",
+                                "uuid": "8ae622ce-4da5-43f7-8f45-ba95ff557050"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/find_subsequences/bg_find_subsequences/0.2",
                         "errors": null,
-                        "id": 15,
+                        "id": 6,
                         "input_connections": {
-                            "genome": {
-                                "id": 2,
+                            "input": {
+                                "id": 3,
                                 "output_name": "output"
-                            },
-                            "maker_gff": {
-                                "id": 11,
-                                "output_name": "output_gff"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Train SNAP",
+                        "name": "Nucleotide subsequence search",
                         "outputs": [
                             {
                                 "name": "output",
-                                "type": "snaphmm"
+                                "type": "bed"
                             }
                         ],
                         "position": {
-                            "bottom": 1770.03125,
-                            "height": 162,
-                            "left": 1863.5,
-                            "right": 2063.5,
-                            "top": 1608.03125,
-                            "width": 200,
-                            "x": 1863.5,
-                            "y": 1608.03125
+                            "left": 437,
+                            "top": 534
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/find_subsequences/bg_find_subsequences/0.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "2a598c0aa042",
-                            "name": "snap_training",
-                            "owner": "iuc",
+                            "changeset_revision": "d882a0a75759",
+                            "name": "find_subsequences",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"gene_num\": \"1000\", \"genome\": {\"__class__\": \"ConnectedValue\"}, \"maker_gff\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2013_11_29+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"pattern_conditional\": {\"pattern_conditional_select\": \"user\", \"__current_case__\": 1, \"pattern\": \"TA\"}, \"strand\": \"forward\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "97cec0ac-e731-4b55-859d-773a7c88bc26",
+                        "uuid": "d72aa8a7-e558-4c97-9ccf-6f7cce88105c",
                         "workflow_outputs": [
                             {
-                                "label": "SNAP: trained model",
+                                "label": null,
                                 "output_name": "output",
-                                "uuid": "458887f7-0661-4bde-ab1a-875aac6caed8"
+                                "uuid": "12e30ef1-fe37-47f5-9879-ed7e375d4bb2"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gff_to_prot/gff_to_prot/3.0.2+galaxy0",
                         "errors": null,
-                        "id": 16,
+                        "id": 7,
                         "input_connections": {
                             "input": {
-                                "id": 12,
-                                "output_name": "output_exons"
+                                "id": 4,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Busco",
+                        "name": "Convert GFF3",
                         "outputs": [
                             {
-                                "name": "busco_sum",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "busco_table",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "busco_missing",
+                                "name": "output",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 870.03125,
-                            "height": 252,
-                            "left": 2161.484375,
-                            "right": 2361.484375,
-                            "top": 618.03125,
-                            "width": 200,
-                            "x": 2161.484375,
-                            "y": 618.03125
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionbusco_missing": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "busco_missing"
-                            },
-                            "HideDatasetActionbusco_table": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "busco_table"
-                            }
+                            "left": 3582,
+                            "top": 443
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gff_to_prot/gff_to_prot/3.0.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "602fb8e63aa7",
-                            "name": "busco",
+                            "changeset_revision": "2aea122fbd25",
+                            "name": "gff_to_prot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"tran\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.1.4",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "9b04f806-0275-4939-bf74-b8c58ae2bffa",
+                        "uuid": "3db46674-95fe-4285-a23a-a5cbeb185cf8",
                         "workflow_outputs": [
                             {
-                                "label": "Busco summary second round",
-                                "output_name": "busco_sum",
-                                "uuid": "f52b1b41-0ea5-4384-bd43-4927273c909c"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "eb959619-62d7-4e16-b5f4-067851b05581"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
                         "errors": null,
-                        "id": 18,
+                        "id": 8,
                         "input_connections": {
-                            "maker_gff": {
-                                "id": 17,
-                                "output_name": "output_gff"
+                            "library|input_1": {
+                                "id": 5,
+                                "output_name": "split_output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Map annotation ids",
+                        "name": "Cutadapt",
                         "outputs": [
                             {
-                                "name": "renamed",
-                                "type": "gff"
+                                "name": "out1",
+                                "type": "fastqsanger"
                             },
                             {
-                                "name": "id_map",
-                                "type": "tabular"
+                                "name": "report",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 1637.03125,
-                            "height": 222,
-                            "left": 2439.5,
-                            "right": 2639.5,
-                            "top": 1415.03125,
-                            "width": 200,
-                            "x": 2439.5,
-                            "y": 1415.03125
-                        },
-                        "post_job_actions": {
-                            "ChangeDatatypeActionrenamed": {
-                                "action_arguments": {
-                                    "newtype": "gff3"
-                                },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "renamed"
-                            },
-                            "HideDatasetActionid_map": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "id_map"
-                            }
+                            "left": 673,
+                            "top": 184
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
                         "tool_shed_repository": {
-                            "changeset_revision": "2e3535db1bfa",
-                            "name": "maker_map_ids",
-                            "owner": "iuc",
+                            "changeset_revision": "49370cb85f0f",
+                            "name": "cutadapt",
+                            "owner": "lparsons",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"justify\": \"6\", \"maker_gff\": {\"__class__\": \"ConnectedValue\"}, \"prefix\": \"TEST\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.31.11",
+                        "tool_state": "{\"__input_ext\": \"input\", \"adapter_options\": {\"error_rate\": \"0.1\", \"no_indels\": \"false\", \"count\": \"3\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"no_trim\": \"false\", \"mask_adapter\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"discard\": \"false\", \"discard_untrimmed\": \"false\", \"min\": \"0\", \"max\": \"0\", \"max_n\": \"\", \"pair_filter\": \"any\"}, \"input_1|__identifier__\": \"control\", \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"\", \"adapter\": \"CGTTATGGCACGC\"}}], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}}, \"output_options\": {\"report\": \"true\", \"info_file\": \"false\", \"rest_file\": \"false\", \"wildcard_file\": \"false\", \"too_short_file\": \"false\", \"too_long_file\": \"false\", \"untrimmed_file\": \"false\", \"multiple_output\": \"false\"}, \"read_mod_options\": {\"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"prefix\": \"\", \"suffix\": \"\", \"strip_suffix\": \"\", \"length\": \"0\", \"length_tag\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "d7101291-76ac-48ec-9fb3-89ca5554e8ea",
+                        "uuid": "4fd67900-a4a7-4f36-b738-310f413fcbc7",
                         "workflow_outputs": [
                             {
-                                "label": "Map annotation ids: renamed GFF",
-                                "output_name": "renamed",
-                                "uuid": "63575dcf-54d1-4cb1-b5fb-a2810b4da807"
+                                "label": null,
+                                "output_name": "out1",
+                                "uuid": "d3d7c441-23c8-4a69-b893-08ae55da0989"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "report",
+                                "uuid": "0d77a42f-4f4e-40ab-928c-42f616ca87e2"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
+                        "content_id": "Cut1",
                         "errors": null,
-                        "id": 19,
+                        "id": 9,
                         "input_connections": {
-                            "reference_genome|genome": {
-                                "id": 2,
+                            "input": {
+                                "id": 6,
                                 "output_name": "output"
-                            },
-                            "track_groups_0|data_tracks_0|data_format|annotation": [
-                                {
-                                    "id": 3,
-                                    "output_name": "output_gff"
-                                },
-                                {
-                                    "id": 18,
-                                    "output_name": "renamed"
-                                },
-                                {
-                                    "id": 11,
-                                    "output_name": "output_gff"
-                                }
-                            ],
-                            "track_groups_1|data_tracks_0|data_format|annotation": [
-                                {
-                                    "id": 3,
-                                    "output_name": "output_evidences"
-                                },
-                                {
-                                    "id": 11,
-                                    "output_name": "output_evidences"
-                                },
-                                {
-                                    "id": 17,
-                                    "output_name": "output_evidences"
-                                }
-                            ]
+                            }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "JBrowse",
+                        "name": "Cut",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "html"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 775.015625,
-                            "height": 292,
-                            "left": 2747.5,
-                            "right": 2947.5,
-                            "top": 483.015625,
-                            "width": 200,
-                            "x": 2747.5,
-                            "y": 483.015625
+                            "left": 683,
+                            "top": 443
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6cd09d7b5f37",
-                            "name": "jbrowse",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Maker annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 1, \"category\": \"Maker evidences\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"match_part\": {\"match_part_select\": \"true\", \"__current_case__\": 0, \"name\": {\"__class__\": \"RuntimeValue\"}}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16.10+galaxy0",
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"__input_ext\": \"bed\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c2\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "4585ada8-27ac-4632-8ac4-76f452316f21",
+                        "uuid": "a5312714-814a-4c22-a56d-ac5eb6056443",
                         "workflow_outputs": [
                             {
-                                "label": "JBrowse: report",
-                                "output_name": "output",
-                                "uuid": "5a38ae83-e177-45f3-aa9f-4c1844584fa5"
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "c84ab194-b4ca-462b-9aca-b9e0c679cfda"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2",
+                        "content_id": "Cut1",
                         "errors": null,
-                        "id": 20,
+                        "id": 10,
                         "input_connections": {
                             "input": {
-                                "id": 18,
-                                "output_name": "renamed"
-                            },
-                            "reference_genome|genome_fasta": {
-                                "id": 2,
+                                "id": 6,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool gffread",
-                                "name": "chr_replace"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "gffread",
+                        "name": "Cut",
                         "outputs": [
                             {
-                                "name": "output_exons",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "output_cds",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "output_pep",
-                                "type": "fasta"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 1085.015625,
-                            "height": 272,
-                            "left": 2747.5,
-                            "right": 2947.5,
-                            "top": 813.015625,
-                            "width": 200,
-                            "x": 2747.5,
-                            "y": 813.015625
+                            "left": 730,
+                            "top": 581
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "69e0806b63a4",
-                            "name": "gffread",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"chr_replace\": {\"__class__\": \"RuntimeValue\"}, \"decode_url\": \"false\", \"expose\": \"false\", \"filtering\": null, \"full_gff_attribute_preservation\": \"false\", \"gffs\": {\"gff_fmt\": \"none\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"maxintron\": null, \"merging\": {\"merge_sel\": \"none\", \"__current_case__\": 0}, \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 2, \"genome_fasta\": {\"__class__\": \"ConnectedValue\"}, \"ref_filtering\": null, \"fa_outputs\": [\"-w exons.fa\", \"-x cds.fa\", \"-y pep.fa\"]}, \"region\": {\"region_filter\": \"none\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.2.1.2",
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"__input_ext\": \"bed\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c1,c3\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "51674c8f-f50e-430f-b0ff-49b1b96887aa",
+                        "uuid": "db5bcbb6-8922-4189-9a27-5785442cd08f",
                         "workflow_outputs": [
                             {
-                                "label": "Gffread: exons",
-                                "output_name": "output_exons",
-                                "uuid": "52fcac23-b612-4377-a19a-2e3b667a23e3"
-                            },
-                            {
-                                "label": "Gffread: translation of cds",
-                                "output_name": "output_pep",
-                                "uuid": "5c47c25e-0ddb-4ade-a5d0-873ff4add28c"
-                            },
-                            {
-                                "label": "Gffread: cds",
-                                "output_name": "output_cds",
-                                "uuid": "84d9183b-9589-464b-9f82-4dae7f87133e"
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "a8d013af-90a3-4838-a328-9c9ebc308c91"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
                         "errors": null,
-                        "id": 21,
+                        "id": 11,
                         "input_connections": {
-                            "gff": {
-                                "id": 18,
-                                "output_name": "renamed"
-                            },
-                            "ref_genome|genome": {
-                                "id": 2,
-                                "output_name": "output"
+                            "library|input_1": {
+                                "id": 8,
+                                "output_name": "out1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Genome annotation statistics",
+                        "name": "Cutadapt",
                         "outputs": [
                             {
-                                "name": "summary",
-                                "type": "txt"
+                                "name": "out1",
+                                "type": "fastqsanger"
                             },
                             {
-                                "name": "graphs",
-                                "type": "pdf"
+                                "name": "report",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 1954.03125,
-                            "height": 272,
-                            "left": 2747.5,
-                            "right": 2947.5,
-                            "top": 1682.03125,
-                            "width": 200,
-                            "x": 2747.5,
-                            "y": 1682.03125
+                            "left": 906,
+                            "top": 186
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
                         "tool_shed_repository": {
-                            "changeset_revision": "8cffbd184762",
-                            "name": "jcvi_gff_stats",
-                            "owner": "iuc",
+                            "changeset_revision": "49370cb85f0f",
+                            "name": "cutadapt",
+                            "owner": "lparsons",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"gff\": {\"__class__\": \"ConnectedValue\"}, \"ref_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.8.4",
+                        "tool_state": "{\"__input_ext\": \"input\", \"adapter_options\": {\"error_rate\": \"0.1\", \"no_indels\": \"false\", \"count\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"no_trim\": \"false\", \"mask_adapter\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"discard\": \"false\", \"discard_untrimmed\": \"false\", \"min\": \"64\", \"max\": \"70\", \"max_n\": \"\", \"pair_filter\": \"any\"}, \"input_1|__identifier__\": \"control\", \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}}, \"output_options\": {\"report\": \"true\", \"info_file\": \"false\", \"rest_file\": \"false\", \"wildcard_file\": \"false\", \"too_short_file\": \"false\", \"too_long_file\": \"false\", \"untrimmed_file\": \"false\", \"multiple_output\": \"false\"}, \"read_mod_options\": {\"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"prefix\": \"\", \"suffix\": \"\", \"strip_suffix\": \"\", \"length\": \"0\", \"length_tag\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "d5c389a7-0746-49da-ad3d-e206b5506acc",
+                        "uuid": "43159e62-7eda-4f71-a6be-9c5a46222c51",
                         "workflow_outputs": [
                             {
-                                "label": "Genome annotation statistics: graphs (third round)",
-                                "output_name": "graphs",
-                                "uuid": "f5d4a6bf-1ff8-435a-8084-7921e25bff3a"
+                                "label": null,
+                                "output_name": "report",
+                                "uuid": "15e3858e-5c79-4d31-a76b-423be5855479"
                             },
                             {
-                                "label": "Genome annotation statistics: summary (third round)",
-                                "output_name": "summary",
-                                "uuid": "5a863bd4-10f2-4ac8-81b6-ce8b7f663e42"
+                                "label": null,
+                                "output_name": "out1",
+                                "uuid": "e9511fc9-50b9-4a63-be4a-3022031091de"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
                         "errors": null,
-                        "id": 22,
+                        "id": 12,
                         "input_connections": {
                             "input": {
-                                "id": 20,
-                                "output_name": "output_exons"
+                                "id": 10,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Busco",
+                        "name": "Compute",
                         "outputs": [
                             {
-                                "name": "busco_sum",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "busco_table",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "busco_missing",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 1156.03125,
-                            "height": 252,
-                            "left": 3025.5,
-                            "right": 3225.5,
-                            "top": 904.03125,
-                            "width": 200,
-                            "x": 3025.5,
-                            "y": 904.03125
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionbusco_missing": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "busco_missing"
-                            },
-                            "HideDatasetActionbusco_table": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "busco_table"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
-                        "tool_shed_repository": {
-                            "changeset_revision": "602fb8e63aa7",
-                            "name": "busco",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"tran\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.1.4",
-                        "type": "tool",
-                        "uuid": "94dac116-5e62-487c-912a-a63ca53c17e7",
-                        "workflow_outputs": [
-                            {
-                                "label": "Busco summary final round",
-                                "output_name": "busco_sum",
-                                "uuid": "0bc78676-eecc-4168-894d-34c4ca07cdf3"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "genome-annotation/annotation-with-maker",
-                "path": "topics/genome-annotation/tutorials/annotation-with-maker/workflows/main_workflow.ga",
-                "tags": [
-                    "genome-annotation"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Genome annotation with Maker ",
-                "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-annotation-with-maker/versions/main-workflow",
-                "tutorial_id": "annotation-with-maker",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-maker/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-maker/workflows/main_workflow.html",
-                "version": 10,
-                "wfid": "genome-annotation-annotation-with-maker",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.11",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1"
-                ],
-                "workflowhub_id": "1164"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.4406623"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "diamond",
-                    "owner": "bgruening",
-                    "revisions": "e8ac2b53f262",
-                    "tool_panel_section_label": "NCBI Blast",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "interproscan",
-                    "owner": "bgruening",
-                    "revisions": "74810db257cc",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ncbi_blast_plus",
-                    "owner": "devteam",
-                    "revisions": "0e3cf9594bb7",
-                    "tool_panel_section_label": "NCBI Blast",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "eggnog_mapper",
-                    "owner": "galaxyp",
-                    "revisions": "844fa988236b",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: diamond\n  owner: bgruening\n  revisions: e8ac2b53f262\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: interproscan\n  owner: bgruening\n  revisions: 74810db257cc\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: 0e3cf9594bb7\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: eggnog_mapper\n  owner: galaxyp\n  revisions: 844fa988236b\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/functional/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "abretaud"
-            ],
-            "funding": [
-                "gallantries",
-                "eurosciencegateway"
-            ]
-        },
-        "contributors": [
-            {
-                "affiliations": [
-                    "gallantries",
-                    "eurosciencegateway",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
-                "fediverse_flavor": "mastodon",
-                "id": "abretaud",
-                "joined": "2017-09",
-                "location": {
-                    "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
-                },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
-            },
-            {
-                "avatar": "/training-material/assets/images/eurosciencegateway.png",
-                "funder": true,
-                "funding_id": "101057388",
-                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "eurosciencegateway",
-                "joined": "2023-10",
-                "members": [
-                    "abretaud",
-                    "anuprulez",
-                    "bgruening",
-                    "erxleben",
-                    "pauldg",
-                    "rlibouba"
-                ],
-                "name": "EuroScienceGateway",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
-            }
-        ],
-        "dir": "topics/genome-annotation/tutorials/functional",
-        "edam_operation": [
-            "Information extraction",
-            "Sequence alignment analysis",
-            "Sequence motif recognition",
-            "Genome annotation",
-            "Protein feature detection",
-            "Homology-based gene prediction",
-            "Query and retrieval",
-            "Fold recognition"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "genome-annotation/functional",
-        "inexact_supported_servers": [
-            "UseGalaxy.no"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "EggNOG Mapper compares sequences to a database of annotated orthologous sequences",
-            "InterProScan detects known motifs in protein sequences"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Introductory",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-01-09",
-        "objectives": [
-            "Perform functional annotation using EggNOG-mapper and InterProScan"
-        ],
-        "pageviews": 3302,
-        "priority": 6,
-        "pub_date": "2022-07-20",
-        "questions": [
-            "How to perform functional annotation on protein sequences?"
-        ],
-        "short_id": "T00173",
-        "short_tools": [
-            "eggnog_mapper",
-            "interproscan",
-            "ncbi_blastp_wrapper",
-            "bg_diamond"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "eukaryote",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "eukaryote"
-        ],
-        "time_estimation": "1h",
-        "title": "Functional annotation of protein sequences",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/2.10.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3"
-        ],
-        "topic_name": "genome-annotation",
-        "topic_name_human": "Genome Annotation",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "functional",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/functional/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/functional/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/functional/tutorial.json"
-        },
-        "version": 9,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 106,
-        "visitors": 2227,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0003-0914-2470",
-                        "name": "Anthony Bretaudeau"
-                    }
-                ],
-                "description": "Functional annotation of protein sequences",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nProtein sequences\"]\n  1[label=\"eggNOG Mapper\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"InterProScan\"]\n  0 -> 2 [label=\"output\"]\n}",
-                "history": [
-                    {
-                        "hash": "f618c506c91dba9edce85bd76d1fb1d4a1c45eda",
-                        "message": "rename wf",
-                        "num": 1,
-                        "short_hash": "f618c506c",
-                        "unix": "1683023161"
-                    }
-                ],
-                "inputs": [
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 997,
+                            "top": 511
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "be25c075ed54",
+                            "name": "column_maker",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"avoid_scientific_notation\": \"no\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c2-1\", \"header_lines_conditional\": {\"header_lines_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"round\": \"yes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "862f354c-4fd7-41df-88a9-47e3cea4227b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "7ecdf545-74b5-423a-ac04-8dff265fb11e"
+                            }
+                        ]
+                    },
                     {
-                        "annotation": "Some protein sequences to functionally annotate",
-                        "content_id": null,
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 13,
+                        "input_connections": {
+                            "library|input_1": {
+                                "id": 11,
+                                "output_name": "out1"
+                            },
+                            "library|r1|adapters_0|adapter_source|adapter_file": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Cutadapt",
+                        "outputs": [
                             {
-                                "description": "Some protein sequences to functionally annotate",
-                                "name": "Protein sequences"
+                                "name": "split_output",
+                                "type": "input"
+                            },
+                            {
+                                "name": "report",
+                                "type": "txt"
                             }
                         ],
-                        "label": "Protein sequences",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 315.5999984741211,
-                            "height": 65.76666259765625,
-                            "left": 726.3958740234375,
-                            "right": 886.3958740234375,
-                            "top": 249.83333587646484,
-                            "width": 160,
-                            "x": 726.3958740234375,
-                            "y": 249.83333587646484
+                            "left": 1129,
+                            "top": 214
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
+                        "tool_shed_repository": {
+                            "changeset_revision": "49370cb85f0f",
+                            "name": "cutadapt",
+                            "owner": "lparsons",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"adapter_options\": {\"error_rate\": \"0.1\", \"no_indels\": \"false\", \"count\": \"3\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"no_trim\": \"false\", \"mask_adapter\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"discard\": \"false\", \"discard_untrimmed\": \"false\", \"min\": \"0\", \"max\": \"0\", \"max_n\": \"\", \"pair_filter\": \"any\"}, \"input_1|__identifier__\": \"control\", \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"file\", \"__current_case__\": 2, \"adapter_file\": {\"__class__\": \"ConnectedValue\"}}}], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}}, \"output_options\": {\"report\": \"true\", \"info_file\": \"false\", \"rest_file\": \"false\", \"wildcard_file\": \"false\", \"too_short_file\": \"false\", \"too_long_file\": \"false\", \"untrimmed_file\": \"false\", \"multiple_output\": \"true\"}, \"read_mod_options\": {\"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"prefix\": \"\", \"suffix\": \"\", \"strip_suffix\": \"\", \"length\": \"0\", \"length_tag\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "abb56aaf-5988-4fb8-a68f-0edaee00f445",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nProtein sequences\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"eggNOG Mapper\"];\n  0 -->|output| 1;\n  2[\"InterProScan\"];\n  0 -->|output| 2;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Functional annotation",
-                "outputs": [
+                        "type": "tool",
+                        "uuid": "f27ae319-a997-42ed-856b-13c6a687f3b3",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "split_output",
+                                "uuid": "8b9cd027-9d39-43ae-b31e-089210c7208f"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "report",
+                                "uuid": "7818fffe-b449-4ec9-9d9c-54400e921a1d"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
+                        "content_id": "Cut1",
                         "errors": null,
-                        "id": 1,
+                        "id": 14,
                         "input_connections": {
                             "input": {
-                                "id": 0,
-                                "output_name": "output"
+                                "id": 12,
+                                "output_name": "out_file1"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Cut",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool eggNOG Mapper",
-                                "name": "input"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
+                        "position": {
+                            "left": 1279,
+                            "top": 512
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c3\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "5e32b04b-a6a7-409c-855c-706188e4ce13",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "48313713-24eb-4d80-9683-914b90b56f74"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
+                        "errors": null,
+                        "id": 15,
+                        "input_connections": {
+                            "library|input_1": {
+                                "id": 13,
+                                "output_name": "split_output"
+                            }
+                        },
+                        "inputs": [],
                         "label": null,
-                        "name": "eggNOG Mapper",
+                        "name": "Cutadapt",
                         "outputs": [
                             {
-                                "name": "seed_orthologs",
-                                "type": "tabular"
+                                "name": "out1",
+                                "type": "fastqsanger"
                             },
                             {
-                                "name": "annotations",
-                                "type": "tabular"
+                                "name": "report",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 435.17499923706055,
-                            "height": 196.8000030517578,
-                            "left": 1194.4791412353516,
-                            "right": 1354.4791412353516,
-                            "top": 238.37499618530273,
-                            "width": 160,
-                            "x": 1194.4791412353516,
-                            "y": 238.37499618530273
+                            "left": 1361,
+                            "top": 199
                         },
-                        "post_job_actions": {
-                            "HideDatasetActionseed_orthologs": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "seed_orthologs"
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
+                        "tool_shed_repository": {
+                            "changeset_revision": "49370cb85f0f",
+                            "name": "cutadapt",
+                            "owner": "lparsons",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"adapter_options\": {\"error_rate\": \"0.15\", \"no_indels\": \"false\", \"count\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"no_trim\": \"false\", \"mask_adapter\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"discard\": \"false\", \"discard_untrimmed\": \"false\", \"min\": \"0\", \"max\": \"0\", \"max_n\": \"\", \"pair_filter\": \"any\"}, \"input_1|__identifier__\": \"unknown\", \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"\", \"adapter\": \"ACAGGTTGGATGATAAGTCCCCGGTCTATATTGAGAGTAACTACATTT\"}}], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}}, \"output_options\": {\"report\": \"true\", \"info_file\": \"false\", \"rest_file\": \"false\", \"wildcard_file\": \"false\", \"too_short_file\": \"false\", \"too_long_file\": \"false\", \"untrimmed_file\": \"false\", \"multiple_output\": \"false\"}, \"read_mod_options\": {\"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"prefix\": \"\", \"suffix\": \"\", \"strip_suffix\": \"\", \"length\": \"0\", \"length_tag\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "c4379b3f-de3d-4eca-96ca-cdaba4006736",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out1",
+                                "uuid": "8acb6fcd-1665-4269-8170-203c3e04f6c0"
                             },
-                            "RenameDatasetActionannotations": {
-                                "action_arguments": {
-                                    "newname": "EggNOG Mapper annotations"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "annotations"
+                            {
+                                "label": null,
+                                "output_name": "report",
+                                "uuid": "83580f2a-2641-4127-9152-69a2ac1e044f"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0",
+                        "errors": null,
+                        "id": 16,
+                        "input_connections": {
+                            "refGenomeSource|ownFile": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "singlePaired|sInput1": {
+                                "id": 15,
+                                "output_name": "out1"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Map with Bowtie for Illumina",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "sam"
+                            }
+                        ],
+                        "position": {
+                            "left": 1594,
+                            "top": 201
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "5a30ae278db0",
-                            "name": "eggnog_mapper",
-                            "owner": "galaxyp",
+                            "changeset_revision": "b46e7d48076a",
+                            "name": "bowtie_wrappers",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"annotation_options\": {\"tax_scope\": null, \"target_orthologs\": \"all\", \"go_evidence\": \"non-electronic\"}, \"eggnog_data\": \"5.0.2\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"input_trans\": {\"itype\": \"proteins\", \"__current_case__\": 0}, \"output_options\": {\"no_file_comments\": \"false\", \"no_annot\": \"false\", \"report_orthologs\": \"false\"}, \"seed_ortho_options\": {\"ortho_method\": {\"m\": \"diamond\", \"__current_case__\": 0, \"matrix_gapcosts\": {\"matrix\": \"BLOSUM62\", \"__current_case__\": 2, \"gap_costs\": \"--gapopen 11 --gapextend 1\"}, \"sensmode\": \"sensitive\", \"dmnd_iterate\": \"false\", \"dmnd_ignore_warnings\": \"false\"}, \"query_cover\": null, \"subject_cover\": null, \"pident\": null}, \"seed_ortholog_options\": {\"seed_ortholog_evalue\": \"0.001\", \"seed_ortholog_score\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.8+galaxy3",
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"refGenomeSource\": {\"genomeSource\": \"history\", \"__current_case__\": 1, \"ownFile\": {\"__class__\": \"ConnectedValue\"}, \"indexParams\": {\"indexSettings\": \"indexPreSet\", \"__current_case__\": 0}}, \"save_mapping_stats\": \"false\", \"singlePaired\": {\"sPaired\": \"single\", \"__current_case__\": 0, \"sInput1\": {\"__class__\": \"ConnectedValue\"}, \"sParams\": {\"sSettingsType\": \"full\", \"__current_case__\": 1, \"sSkip\": \"0\", \"sAlignLimit\": \"-1\", \"sTrimH\": \"0\", \"sTrimL\": \"0\", \"alignModeOption\": {\"alignMode\": \"nMode\", \"__current_case__\": 0, \"sMismatchSeed\": \"0\", \"sMismatchQual\": \"70\", \"sSeedLen\": \"17\", \"sRounding\": \"round\"}, \"sForwardAlign\": \"forward\", \"sReverseAlign\": \"reverse\", \"sBestOption\": {\"sBest\": \"doBest\", \"__current_case__\": 1, \"sdStrata\": \"noStrata\", \"sTryHardOption\": {\"sTryHard\": \"doTryHard\", \"__current_case__\": 1}}, \"sAllValAlignsOption\": {\"sAllValAligns\": \"noAllValAligns\", \"__current_case__\": 0, \"sValAlign\": \"1\"}, \"sSuppressAlign\": \"-1\", \"sMaxFile\": \"false\", \"sUnmappedFile\": \"false\", \"sOffrate\": \"-1\", \"sSeed\": \"-1\"}}, \"suppressHeader\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "0d9f93f0-88b3-406b-b8f9-ecb2d74c61e9",
+                        "uuid": "9cd2e25c-9bc6-4136-9a10-3192c9e41841",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "annotations",
-                                "uuid": "bc64d801-036f-4608-8ba1-74f16fddb574"
+                                "output_name": "output",
+                                "uuid": "7e683afc-5d1f-48f9-a4f1-daedee314672"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0",
                         "errors": null,
-                        "id": 2,
+                        "id": 17,
                         "input_connections": {
-                            "input": {
-                                "id": 0,
+                            "bamInput": {
+                                "id": 16,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "bamCoverage",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool InterProScan",
-                                "name": "input"
+                                "name": "outFileName",
+                                "type": "bigwig"
                             }
                         ],
-                        "label": null,
-                        "name": "InterProScan",
-                        "outputs": [
+                        "position": {
+                            "left": 1846,
+                            "top": 196
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "bb1e4f63e0e6",
+                            "name": "deeptools_bam_coverage",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"bam\", \"advancedOpt\": {\"showAdvancedOpt\": \"yes\", \"__current_case__\": 1, \"scaleFactor\": \"1.0\", \"smoothLength\": \"\", \"ignoreForNormalization\": \"\", \"skipNAs\": \"true\", \"doExtendCustom\": {\"doExtend\": \"no\", \"__current_case__\": 0}, \"ignoreDuplicates\": \"false\", \"centerReads\": \"false\", \"minMappingQuality\": \"1\", \"samFlagInclude\": \"\", \"samFlagExclude\": \"\", \"minFragmentLength\": \"0\", \"maxFragmentLength\": \"0\", \"MNase\": \"false\", \"Offset\": \"-1\", \"filterRNAstrand\": \"no\", \"blackListFileName\": null}, \"bamInput\": {\"__class__\": \"ConnectedValue\"}, \"binSize\": \"1\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"exactScaling\": \"false\", \"outFileFormat\": \"bedgraph\", \"region\": \"\", \"scaling\": {\"type\": \"no\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "8355bf16-b3bf-4361-b2f1-f1504154a4ee",
+                        "workflow_outputs": [
                             {
-                                "name": "outfile_tsv",
-                                "type": "tabular"
+                                "label": null,
+                                "output_name": "outFileName",
+                                "uuid": "63663acf-5780-492b-8b01-e958cf47617f"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "errors": null,
+                        "id": 18,
+                        "input_connections": {
+                            "infile1": {
+                                "id": 17,
+                                "output_name": "outFileName"
                             },
+                            "infile2": {
+                                "id": 9,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Join",
+                        "outputs": [
                             {
-                                "name": "outfile_xml",
-                                "type": "xml"
+                                "name": "output",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 646.2666473388672,
-                            "height": 131.51666259765625,
-                            "left": 1197.1041870117188,
-                            "right": 1357.1041870117188,
-                            "top": 514.7499847412109,
-                            "width": 160,
-                            "x": 1197.1041870117188,
-                            "y": 514.7499847412109
+                            "left": 2113,
+                            "top": 204
                         },
-                        "post_job_actions": {
-                            "HideDatasetActionoutfile_xml": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "outfile_xml"
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "9ff72e942410",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"bedgraph\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"column1\": \"2\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": \"false\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile1|__identifier__\": \"unknown\", \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \"-a 2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "095dd2dd-5082-419a-9743-0b6ac031392d",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "89f48391-502f-4bc1-8755-fd3faf3245dc"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "errors": null,
+                        "id": 19,
+                        "input_connections": {
+                            "infile1": {
+                                "id": 17,
+                                "output_name": "outFileName"
                             },
-                            "RenameDatasetActionoutfile_tsv": {
-                                "action_arguments": {
-                                    "newname": "InterProScan annotations (tsv)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "outfile_tsv"
+                            "infile2": {
+                                "id": 14,
+                                "output_name": "out_file1"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Join",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 2137,
+                            "top": 366
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "98cafcbd2578",
-                            "name": "interproscan",
+                            "changeset_revision": "9ff72e942410",
+                            "name": "text_processing",
                             "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"applications\": [\"TIGRFAM\", \"SFLD\", \"SUPERFAMILY\", \"PANTHER\", \"Gene3D\", \"Hamap\", \"PrositeProfiles\", \"Coils\", \"SMART\", \"CDD\", \"PRINTS\", \"PIRSR\", \"PrositePatterns\", \"Pfam\", \"MobiDBLite\", \"PIRSF\"], \"database\": \"5.59-91.0\", \"goterms\": \"true\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"iprlookup\": \"false\", \"licensed\": {\"use\": \"true\", \"__current_case__\": 1, \"applications_licensed\": [\"Phobius\", \"SignalP_EUK\", \"TMHMM\"]}, \"oformat\": [\"TSV\", \"XML\"], \"pathways\": \"true\", \"seqtype\": \"p\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.59-91.0+galaxy3",
+                        "tool_state": "{\"__input_ext\": \"bedgraph\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"column1\": \"2\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": \"false\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile1|__identifier__\": \"unknown\", \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \"-a 2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "cb7a1910-3c31-47d9-835b-f1bd16a1c3ff",
+                        "uuid": "fc70f1e1-17dd-4287-8dfb-c7f86b71d645",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile_tsv",
-                                "uuid": "b5a0e608-3bed-4fb2-9d47-d6bd521aee14"
+                                "output_name": "output",
+                                "uuid": "bf190ec2-215f-4404-b3e3-c230f84c6939"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "genome-annotation/functional",
-                "path": "topics/genome-annotation/tutorials/functional/workflows/functional.ga",
-                "tags": [
-                    "genome-annotation"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "Functional annotation",
-                "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-functional/versions/functional",
-                "tutorial_id": "functional",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/functional/workflows/functional.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/functional/workflows/functional.html",
-                "version": 1,
-                "wfid": "genome-annotation-functional",
-                "wfname": "functional",
-                "workflow": "functional.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3"
-                ],
-                "workflowhub_id": "1183"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/6861851"
-    },
-    {
-        "abbreviations": {
-            "OGS": "Official Gene Set"
-        },
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "apollo_create_or_update",
-                    "owner": "gga",
-                    "revisions": "4abaab60f9e1",
-                    "tool_panel_section_label": "Apollo",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "apollo_iframe",
-                    "owner": "gga",
-                    "revisions": "f4e3f9480307",
-                    "tool_panel_section_label": "Apollo",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "jbrowse",
-                    "owner": "iuc",
-                    "revisions": "a6e57ff585c0",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: apollo_create_or_update\n  owner: gga\n  revisions: 4abaab60f9e1\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: apollo_iframe\n  owner: gga\n  revisions: f4e3f9480307\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo-euk/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "abretaud"
-            ],
-            "funding": [
-                "gallantries",
-                "eurosciencegateway"
-            ]
-        },
-        "contributors": [
-            {
-                "affiliations": [
-                    "gallantries",
-                    "eurosciencegateway",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
-                "fediverse_flavor": "mastodon",
-                "id": "abretaud",
-                "joined": "2017-09",
-                "location": {
-                    "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
-                },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
-            },
-            {
-                "avatar": "/training-material/assets/images/eurosciencegateway.png",
-                "funder": true,
-                "funding_id": "101057388",
-                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "eurosciencegateway",
-                "joined": "2023-10",
-                "members": [
-                    "abretaud",
-                    "anuprulez",
-                    "bgruening",
-                    "erxleben",
-                    "pauldg",
-                    "rlibouba"
-                ],
-                "name": "EuroScienceGateway",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
-            }
-        ],
-        "dir": "topics/genome-annotation/tutorials/apollo-euk",
-        "edam_operation": [
-            "Genome visualisation"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.no"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "genome-annotation/apollo-euk",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Apollo is the Google Docs of the genome annotation world, real-time collaborative genome annotation.",
-            "Apollo allows a group to view and manually refine predicted genome annotations",
-            "Use Apollo to edit annotations within your group.",
-            "Export manual annotations as GFF3."
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-02-29",
-        "objectives": [
-            "Load a genome into Galaxy",
-            "View annotations in JBrowse",
-            "Learn how to load JBrowse data into Apollo",
-            "Learn how to manually refine genome annotations within Apollo",
-            "Export refined genome annotations"
-        ],
-        "pageviews": 1546,
-        "priority": 6,
-        "pub_date": "2022-08-22",
-        "questions": [
-            "How to visualize your genome after automated annotations have been performed?",
-            "How to manually annotate genome after automated annotations have been performed?",
-            "How to evaluate and visualize annotated genomic features?",
-            "How do I collaborate when doing genome annotation?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "upload-rules"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "genome-annotation",
-                "tutorials": [
-                    "funannotate"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00170",
-        "short_tools": [
-            "create_or_update",
-            "iframe",
-            "jbrowse"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "eukaryote",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "gmod",
-            "eukaryote",
-            "cyoa",
-            "jbrowse1",
-            "apollo2"
-        ],
-        "time_estimation": "3h",
-        "title": "Refining Genome Annotations with Apollo (eukaryotes)",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
-            "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1"
-        ],
-        "topic_name": "genome-annotation",
-        "topic_name_human": "Genome Annotation",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "apollo-euk",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo-euk/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo-euk/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo-euk/tutorial.json"
-        },
-        "version": 13,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 158,
-        "visitors": 871,
-        "zenodo_link": "https://zenodo.org/record/3270822"
-    },
-    {
-        "abbreviations": {
-            "LncRNAs": "Long non-coding RNAs",
-            "lncRNAs": "long non-coding RNAs",
-            "mRNAs": "Messenger RNAs"
-        },
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gffread",
-                    "owner": "devteam",
-                    "revisions": "154d00cbbf2d",
-                    "tool_panel_section_label": "Convert Formats",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "feelnc",
-                    "owner": "iuc",
-                    "revisions": "67af24676bd6",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "stringtie",
-                    "owner": "iuc",
-                    "revisions": "eba36e001f45",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "stringtie",
-                    "owner": "iuc",
-                    "revisions": "cef79931dda5",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gffread\n  owner: devteam\n  revisions: 154d00cbbf2d\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: feelnc\n  owner: iuc\n  revisions: 67af24676bd6\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stringtie\n  owner: iuc\n  revisions: eba36e001f45\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stringtie\n  owner: iuc\n  revisions: cef79931dda5\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/lncrna/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "stephanierobin"
-            ],
-            "editing": [
-                "abretaud"
-            ]
-        },
-        "contributors": [
-            {
-                "email": "stephanie.robin@inrae.fr",
-                "id": "stephanierobin",
-                "joined": "2021-11",
-                "name": "St\u00e9phanie Robin",
-                "orcid": "0000-0001-7379-9173",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/",
-                "twitter": "robinstphanie1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/stephanierobin.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "eurosciencegateway",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
-                "fediverse_flavor": "mastodon",
-                "id": "abretaud",
-                "joined": "2017-09",
-                "location": {
-                    "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
-                },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
-            }
-        ],
-        "dir": "topics/genome-annotation/tutorials/lncrna",
-        "edam_operation": [
-            "Classification",
-            "Transcriptome assembly",
-            "Sequence annotation",
-            "RNA-Seq analysis",
-            "Annotation"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "genome-annotation/lncrna",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "StringTie allows to perform a transcriptome assembly using mapped RNASeq data and provides an annotation file containing trancripts description.",
-            "FEELnc pipeline allows to perform annotation of long non-coding RNAs (lncRNAs).",
-            "Annotation is based on reconstructed transcripts from RNA-seq data (either with or without a reference genome)",
-            "Annotation can be performed without any training set of non-coding RNAs.",
-            "FEELnc provides the localisation and the direction of transcription of proximal RNA transcripts of lncRNAs."
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-03",
-        "objectives": [
-            "Load data (genome assembly, annotation and mapped RNASeq) into Galaxy",
-            "Perform a transcriptome assembly with StringTie",
-            "Annotate lncRNAs with FEELnc",
-            "Classify lncRNAs according to their location",
-            "Update genome annotation with lncRNAs"
-        ],
-        "pageviews": 1242,
-        "priority": 7,
-        "pub_date": "2022-09-23",
-        "questions": [
-            "How to annotate lncRNAs with FEELnc?",
-            "How to classify lncRNAs according to their localisation and direction of transcription of proximal RNA transcripts?",
-            "How to update genome annotation with these annotated lncRNAs?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "genome-annotation",
-                "tutorials": [
-                    "funannotate"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00177",
-        "short_tools": [
-            "gffread",
-            "tp_cat",
-            "Extract_features1",
-            "stringtie",
-            "feelnc"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "eukaryote",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "eukaryote"
-        ],
-        "time_estimation": "2h",
-        "title": "Long non-coding RNAs (lncRNAs) annotation with FEELnc",
-        "tools": [
-            "Extract_features1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/feelnc/feelnc/0.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.6",
-            "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.7+galaxy1"
-        ],
-        "topic_name": "genome-annotation",
-        "topic_name_human": "Genome Annotation",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "lncrna",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/lncrna/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/lncrna/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/lncrna/tutorial.json"
-        },
-        "version": 8,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 128,
-        "visitors": 913,
-        "workflows": [
-            {
-                "creators": [
+                    },
                     {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0001-7379-9173",
-                        "name": "St\u00e9phanie Robin"
-                    }
-                ],
-                "description": "Long non-coding RNAs (lncRNAs) annotation with FEELnc",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmapped_RNASeq.bam\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ngenome_annotation.gff3\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ngenome_assembly.fasta\"]\n  3[label=\"StringTie\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"gffread\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"FEELnc\"]\n  3 -> 5 [label=\"output_gtf\"]\n  2 -> 5 [label=\"output\"]\n  4 -> 5 [label=\"output_gtf\"]\n  k4055b259173c492d86a45e662b663421[color=lightseagreen,label=\"Output\\nmRNAs\"]\n  5 -> k4055b259173c492d86a45e662b663421\n  kabc029bab7ba458688b45e5d758c2f39[color=lightseagreen,label=\"Output\\nlncRNAs\"]\n  5 -> kabc029bab7ba458688b45e5d758c2f39\n  k93ff3464d1bb405986af3e703da3e542[color=lightseagreen,label=\"Output\\nClassifier output\"]\n  5 -> k93ff3464d1bb405986af3e703da3e542\n  6[label=\"Concatenate datasets\"]\n  4 -> 6 [label=\"output_gtf\"]\n  5 -> 6 [label=\"candidate_lncRNA\"]\n  k7b91b6a4ef6743599c93eabcc021b0fc[color=lightseagreen,label=\"Output\\nfinal_annotation\"]\n  6 -> k7b91b6a4ef6743599c93eabcc021b0fc\n}",
-                "history": [
+                        "annotation": "",
+                        "content_id": "Cut1",
+                        "errors": null,
+                        "id": 20,
+                        "input_connections": {
+                            "input": {
+                                "id": 18,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Cut",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 2443,
+                            "top": 205
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"__input_ext\": \"bedgraph\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c1,c4\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"unknown\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "43459cad-a7b6-412f-8975-bc73f9127e12",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "205cebe3-e508-4a9b-8429-78d624b27028"
+                            }
+                        ]
+                    },
                     {
-                        "hash": "8b70507229249bc44854bb8f23a50a6448cdd517",
-                        "message": "Add a new tutorial about lncRNAs annotation (with FEELnc) (#3623)",
-                        "num": 1,
-                        "short_hash": "8b7050722",
-                        "unix": "1663943586"
-                    }
-                ],
-                "inputs": [
+                        "annotation": "",
+                        "content_id": "Cut1",
+                        "errors": null,
+                        "id": 21,
+                        "input_connections": {
+                            "input": {
+                                "id": 19,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Cut",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 2311,
+                            "top": 537
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"__input_ext\": \"bedgraph\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c1,c4\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"unknown\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "b9d313a5-f9c1-4209-9235-1c7ba2aa6e2c",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "be1284e3-bc3c-40c9-98cd-f3489b5addbf"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                        "errors": null,
+                        "id": 22,
+                        "input_connections": {
+                            "infile": {
+                                "id": 20,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Sort",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 2731,
+                            "top": 189
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "74a8bef53a00",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"header\": \"0\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"infile|__identifier__\": \"unknown\", \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"n\"}], \"unique\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "5bd821e2-8e48-4bc5-b7ce-6e4d9459764b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "95ac6ae6-6620-4809-9fcf-90f2ffe0ef90"
+                            }
+                        ]
+                    },
                     {
-                        "annotation": "RNASeq data mapped on the genome",
-                        "content_id": null,
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 23,
+                        "input_connections": {
+                            "input": {
+                                "id": 21,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Compute",
+                        "outputs": [
                             {
-                                "description": "RNASeq data mapped on the genome",
-                                "name": "mapped_RNASeq.bam"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
-                        "label": "mapped_RNASeq.bam",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 342.40000915527344,
-                            "height": 82.19999694824219,
-                            "left": 297.5,
-                            "right": 497.5,
-                            "top": 260.20001220703125,
-                            "width": 200,
-                            "x": 297.5,
-                            "y": 260.20001220703125
+                            "left": 2504,
+                            "top": 384
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"bam\"], \"tag\": \"\"}",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "be25c075ed54",
+                            "name": "column_maker",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"avoid_scientific_notation\": \"no\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c1-1\", \"header_lines_conditional\": {\"header_lines_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"unknown\", \"round\": \"yes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "0d6d7a64-f5f5-4d80-8e76-72859ae6fa1b",
-                        "workflow_outputs": []
+                        "type": "tool",
+                        "uuid": "55059dd9-d9e5-4ec2-8756-af9ec8239924",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "9efd613c-1f50-4e3c-b007-4196b9eefc69"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "Original structural annotation",
-                        "content_id": null,
+                        "annotation": "",
+                        "content_id": "Cut1",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 24,
+                        "input_connections": {
+                            "input": {
+                                "id": 23,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Cut",
+                        "outputs": [
                             {
-                                "description": "Original structural annotation",
-                                "name": "genome_annotation.gff3"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "genome_annotation.gff3",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 448.40000915527344,
-                            "height": 82.19999694824219,
-                            "left": 297,
-                            "right": 497,
-                            "top": 366.20001220703125,
-                            "width": 200,
-                            "x": 297,
-                            "y": 366.20001220703125
+                            "left": 2641,
+                            "top": 523
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"gff3\"], \"tag\": \"\"}",
+                        "post_job_actions": {},
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c3,c2\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"unknown\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "4cc3b4aa-b54d-4652-bd14-9611bece1ca8",
-                        "workflow_outputs": []
+                        "type": "tool",
+                        "uuid": "54b3489e-f6ec-44de-8bbb-493c972e3666",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "48b2b3cd-45f4-43fe-aaaf-83ca18b7bf9d"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "Genome sequence",
-                        "content_id": null,
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 25,
+                        "input_connections": {
+                            "infile": {
+                                "id": 24,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Sort",
+                        "outputs": [
                             {
-                                "description": "Genome sequence",
-                                "name": "genome_assembly.fasta"
+                                "name": "outfile",
+                                "type": "input"
                             }
                         ],
-                        "label": "genome_assembly.fasta",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 546.4000091552734,
-                            "height": 82.19999694824219,
-                            "left": 298,
-                            "right": 498,
-                            "top": 464.20001220703125,
-                            "width": 200,
-                            "x": 298,
-                            "y": 464.20001220703125
+                            "left": 2841,
+                            "top": 389
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "74a8bef53a00",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"header\": \"0\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"infile|__identifier__\": \"unknown\", \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"n\"}], \"unique\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "580a4505-ee23-4a3a-ac37-7e83cef79a0a",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nmapped_RNASeq.bam\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ngenome_annotation.gff3\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ngenome_assembly.fasta\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"StringTie\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  4[\"gffread\"];\n  1 -->|output| 4;\n  5[\"FEELnc\"];\n  3 -->|output_gtf| 5;\n  2 -->|output| 5;\n  4 -->|output_gtf| 5;\n  4055b259-173c-492d-86a4-5e662b663421[\"Output\\nmRNAs\"];\n  5 --> 4055b259-173c-492d-86a4-5e662b663421;\n  style 4055b259-173c-492d-86a4-5e662b663421 stroke:#2c3143,stroke-width:4px;\n  abc029ba-b7ba-4586-88b4-5e5d758c2f39[\"Output\\nlncRNAs\"];\n  5 --> abc029ba-b7ba-4586-88b4-5e5d758c2f39;\n  style abc029ba-b7ba-4586-88b4-5e5d758c2f39 stroke:#2c3143,stroke-width:4px;\n  93ff3464-d1bb-4059-86af-3e703da3e542[\"Output\\nClassifier output\"];\n  5 --> 93ff3464-d1bb-4059-86af-3e703da3e542;\n  style 93ff3464-d1bb-4059-86af-3e703da3e542 stroke:#2c3143,stroke-width:4px;\n  6[\"Concatenate datasets\"];\n  4 -->|output_gtf| 6;\n  5 -->|candidate_lncRNA| 6;\n  7b91b6a4-ef67-4359-9c93-eabcc021b0fc[\"Output\\nfinal_annotation\"];\n  6 --> 7b91b6a4-ef67-4359-9c93-eabcc021b0fc;\n  style 7b91b6a4-ef67-4359-9c93-eabcc021b0fc stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Long non-coding RNAs (lncRNAs) annotation with FEELnc",
-                "outputs": [
+                        "type": "tool",
+                        "uuid": "06aa9c94-2850-41d2-bc52-a7a954d2ca70",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "3b7302f9-16c5-464f-866b-df392abe0fbf"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/feelnc/feelnc/0.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
                         "errors": null,
-                        "id": 5,
+                        "id": 26,
                         "input_connections": {
-                            "candidate": {
-                                "id": 3,
-                                "output_name": "output_gtf"
-                            },
-                            "genome": {
-                                "id": 2,
-                                "output_name": "output"
+                            "infile1": {
+                                "id": 22,
+                                "output_name": "outfile"
                             },
-                            "reference": {
-                                "id": 4,
-                                "output_name": "output_gtf"
+                            "infile2": {
+                                "id": 25,
+                                "output_name": "outfile"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Join",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool FEELnc",
-                                "name": "candidate"
-                            },
+                                "name": "output",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 3185,
+                            "top": 209
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "9ff72e942410",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \".\", \"header\": \"false\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile1|__identifier__\": \"unknown\", \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"infile2|__identifier__\": \"unknown\", \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "4668ac5e-a567-4107-80e4-b6fe91f762ce",
+                        "workflow_outputs": [
                             {
-                                "description": "runtime parameter for tool FEELnc",
-                                "name": "genome"
-                            },
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "fa45da27-d946-4d8c-8ef6-339d95e8b183"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                        "errors": null,
+                        "id": 27,
+                        "input_connections": {
+                            "input": {
+                                "id": 26,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Compute",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool FEELnc",
-                                "name": "reference"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
+                        "position": {
+                            "left": 3438,
+                            "top": 151
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "be25c075ed54",
+                            "name": "column_maker",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"avoid_scientific_notation\": \"no\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c2+c3\", \"header_lines_conditional\": {\"header_lines_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"unknown\", \"round\": \"yes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "8ea3f455-800b-423d-99dd-827b8a91d079",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "9d672d8f-f57f-49df-a2fb-0bc9daae2591"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "Cut1",
+                        "errors": null,
+                        "id": 28,
+                        "input_connections": {
+                            "input": {
+                                "id": 27,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
                         "label": null,
-                        "name": "FEELnc",
+                        "name": "Cut",
                         "outputs": [
                             {
-                                "name": "candidate_lncRNA",
-                                "type": "gtf"
-                            },
+                                "name": "out_file1",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 3597,
+                            "top": 319
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c1,c4\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"unknown\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "b57d2009-2255-4aba-89dd-edd902fa21c4",
+                        "workflow_outputs": [
                             {
-                                "name": "candidate_mRNA",
-                                "type": "gtf"
-                            },
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "f6051684-f77b-4895-8424-361bd399da4b"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                        "errors": null,
+                        "id": 29,
+                        "input_connections": {
+                            "infile": {
+                                "id": 28,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Sort",
+                        "outputs": [
                             {
-                                "name": "classifier",
-                                "type": "txt"
+                                "name": "outfile",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 529.0000152587891,
-                            "height": 214.8000030517578,
-                            "left": 922,
-                            "right": 1122,
-                            "top": 314.20001220703125,
-                            "width": 200,
-                            "x": 922,
-                            "y": 314.20001220703125
+                            "left": 3811,
+                            "top": 161
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/feelnc/feelnc/0.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "67af24676bd6",
-                            "name": "feelnc",
-                            "owner": "iuc",
+                            "changeset_revision": "74a8bef53a00",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"candidate\": {\"__class__\": \"RuntimeValue\"}, \"genome\": {\"__class__\": \"RuntimeValue\"}, \"reference\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.2",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"header\": \"0\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"infile|__identifier__\": \"unknown\", \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"n\"}], \"unique\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "74ebae55-e16d-4884-bd59-0d6775bb731a",
+                        "uuid": "180421e5-45e7-4d88-be28-15d682f5e392",
                         "workflow_outputs": [
                             {
-                                "label": "mRNAs",
-                                "output_name": "candidate_mRNA",
-                                "uuid": "4055b259-173c-492d-86a4-5e662b663421"
-                            },
-                            {
-                                "label": "lncRNAs",
-                                "output_name": "candidate_lncRNA",
-                                "uuid": "abc029ba-b7ba-4586-88b4-5e5d758c2f39"
-                            },
-                            {
-                                "label": "Classifier output",
-                                "output_name": "classifier",
-                                "uuid": "93ff3464-d1bb-4059-86af-3e703da3e542"
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "8543b2f7-cf8e-43f5-a06a-a7a20f180946"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/3.0.2+galaxy0",
                         "errors": null,
-                        "id": 6,
+                        "id": 30,
                         "input_connections": {
-                            "inputs": {
-                                "id": 4,
-                                "output_name": "output_gtf"
+                            "annotation": {
+                                "id": 7,
+                                "output_name": "output"
                             },
-                            "queries_0|inputs2": {
-                                "id": 5,
-                                "output_name": "candidate_lncRNA"
+                            "mode|inputs": {
+                                "id": 29,
+                                "output_name": "outfile"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Gumbel",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool Concatenate datasets",
-                                "name": "inputs"
+                                "name": "sites",
+                                "type": "tabular"
                             }
                         ],
+                        "position": {
+                            "left": 4067,
+                            "top": 266
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/3.0.2+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f50807720df1",
+                            "name": "transit_gumbel",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"annotation\": {\"__class__\": \"ConnectedValue\"}, \"burnin\": \"500\", \"cterm\": \"0.1\", \"handle_replicates\": \"Sum\", \"mode\": {\"replicates\": \"Replicates\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"normalization\": \"TTR\", \"nterm\": \"0.1\", \"samples\": \"10000\", \"smallest\": \"2\", \"trim\": \"1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "70b9679b-e15b-4756-8ae7-0457944dabbc",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "sites",
+                                "uuid": "a46ddc5a-f542-49ac-bb67-f23f734dabf4"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "Filter1",
+                        "errors": null,
+                        "id": 31,
+                        "input_connections": {
+                            "input": {
+                                "id": 30,
+                                "output_name": "sites"
+                            }
+                        },
+                        "inputs": [],
                         "label": null,
-                        "name": "Concatenate datasets",
+                        "name": "Filter",
                         "outputs": [
                             {
                                 "name": "out_file1",
@@ -108348,519 +109673,360 @@
                             }
                         ],
                         "position": {
-                            "bottom": 758.2000122070312,
-                            "height": 144,
-                            "left": 1234,
-                            "right": 1434,
-                            "top": 614.2000122070312,
-                            "width": 200,
-                            "x": 1234,
-                            "y": 614.2000122070312
+                            "left": 4335,
+                            "top": 269
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"cond\": \"c9=='E'\", \"header_lines\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "42633d45-79c3-48ba-810d-5fe839a621d6",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "cb86d7f5-8c93-40bc-9836-1e68756c0e5e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "__EXTRACT_DATASET__",
+                        "errors": null,
+                        "id": 32,
+                        "input_connections": {
+                            "input": {
+                                "id": 31,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Extract Dataset",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "data"
+                            }
+                        ],
+                        "position": {
+                            "left": 4607,
+                            "top": 266
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
+                            "ChangeDatatypeActionoutput": {
                                 "action_arguments": {
-                                    "newname": "final_annotation"
+                                    "newtype": "tabular"
                                 },
-                                "action_type": "RenameDatasetAction",
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "output"
+                            },
+                            "TagDatasetActionoutput": {
+                                "action_arguments": {
+                                    "tags": "#control"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "__EXTRACT_DATASET__",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"by_index\", \"__current_case__\": 2, \"index\": \"1\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "886a7aec-fa32-410d-b82a-02f2c0722ff4",
+                        "workflow_outputs": [
+                            {
+                                "label": "control",
+                                "output_name": "output",
+                                "uuid": "8796f62f-4676-4ad2-b085-7597f894c32c"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "__EXTRACT_DATASET__",
+                        "errors": null,
+                        "id": 33,
+                        "input_connections": {
+                            "input": {
+                                "id": 31,
                                 "output_name": "out_file1"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f46f0e4f75c4",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        "inputs": [],
+                        "label": null,
+                        "name": "Extract Dataset",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "data"
+                            }
+                        ],
+                        "position": {
+                            "left": 4607,
+                            "top": 465
                         },
-                        "tool_state": "{\"inputs\": {\"__class__\": \"RuntimeValue\"}, \"queries\": [{\"__index__\": 0, \"inputs2\": {\"__class__\": \"RuntimeValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.1",
+                        "post_job_actions": {
+                            "ChangeDatatypeActionoutput": {
+                                "action_arguments": {
+                                    "newtype": "tabular"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "output"
+                            },
+                            "TagDatasetActionoutput": {
+                                "action_arguments": {
+                                    "tags": "#condition"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "__EXTRACT_DATASET__",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"by_index\", \"__current_case__\": 2, \"index\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "d6f07c9d-56db-43f9-b0e3-09db582015fd",
+                        "uuid": "7b09fd71-c2d4-48a8-ba5a-ef9acba7e6b8",
                         "workflow_outputs": [
                             {
-                                "label": "final_annotation",
-                                "output_name": "out_file1",
-                                "uuid": "7b91b6a4-ef67-4359-9c93-eabcc021b0fc"
+                                "label": "condition",
+                                "output_name": "output",
+                                "uuid": "bd014de4-708e-419c-bd1e-8bf350661aad"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "genome-annotation/lncrna",
-                "path": "topics/genome-annotation/tutorials/lncrna/workflows/main_workflow.ga",
-                "tags": [
-                    "genome-annotation"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Long non-coding RNAs (lncRNAs) annotation with FEELnc",
-                "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-lncrna/versions/main-workflow",
-                "tutorial_id": "lncrna",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/lncrna/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/lncrna/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "genome-annotation-lncrna",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/feelnc/feelnc/0.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.6"
-                ],
-                "workflowhub_id": "1141"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/records/11367439"
-    },
-    {
-        "abbreviations": {
-            "CRISPR": "Clustered Regularly Interspaced Short Palindromic Repeats",
-            "MAGeCK": "Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout"
-        },
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "e7b2202befea",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "3d0c7bdf12f5",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mageck_count",
-                    "owner": "iuc",
-                    "revisions": "e329d44424d7",
-                    "tool_panel_section_label": "Genome Editing",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mageck_mle",
-                    "owner": "iuc",
-                    "revisions": "26126538a86f",
-                    "tool_panel_section_label": "Genome Editing",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mageck_test",
-                    "owner": "iuc",
-                    "revisions": "9b4f4533c9ee",
-                    "tool_panel_section_label": "Genome Editing",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "9a913cdee30e",
-                    "tool_panel_section_label": "Quality Control",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "75c93c70d094",
-                    "tool_panel_section_label": "Quality Control",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "volcanoplot",
-                    "owner": "iuc",
-                    "revisions": "83c573f2e73c",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cutadapt",
-                    "owner": "lparsons",
-                    "revisions": "4e5056fefd88",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cutadapt",
-                    "owner": "lparsons",
-                    "revisions": "de6cebe3c043",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mageck_count\n  owner: iuc\n  revisions: e329d44424d7\n  tool_panel_section_label: Genome Editing\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mageck_mle\n  owner: iuc\n  revisions: 26126538a86f\n  tool_panel_section_label: Genome Editing\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mageck_test\n  owner: iuc\n  revisions: 9b4f4533c9ee\n  tool_panel_section_label: Genome Editing\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 9a913cdee30e\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 75c93c70d094\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: volcanoplot\n  owner: iuc\n  revisions: 83c573f2e73c\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 4e5056fefd88\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: de6cebe3c043\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/crispr-screen/tutorial.json",
-        "contributors": [
-            {
-                "id": "mblue9",
-                "joined": "2018-09",
-                "name": "Maria Doyle",
-                "orcid": "0000-0003-4847-8436",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
-            },
-            {
-                "github": false,
-                "id": "kenjifujihara",
-                "joined": "2021-10",
-                "name": "Kenji Fujihara",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kenjifujihara/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/kenjifujihara.json"
-            },
-            {
-                "github": false,
-                "id": "twishigulati",
-                "joined": "2021-11",
-                "name": "Twishi Gulati",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/twishigulati/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/twishigulati.json"
-            }
-        ],
-        "dir": "topics/genome-annotation/tutorials/crispr-screen",
-        "edam_operation": [
-            "Sequencing quality control",
-            "Primer removal",
-            "Validation",
-            "Genetic variation analysis",
-            "Sequence trimming",
-            "Sequence composition calculation",
-            "Read pre-processing",
-            "Statistical calculation"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "genome-annotation/crispr-screen",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.no"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "CRISPR screen data can be analysed using MAGeCK and standard read quality tools"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-08-08",
-        "objectives": [
-            "Apply appropriate analysis and quality control steps for CRISPR screen data",
-            "Identify differentially enriched genes across conditions",
-            "Generate volcano plot to visualise results"
-        ],
-        "pageviews": 4353732,
-        "priority": 8,
-        "pub_date": "2021-10-15",
-        "questions": [
-            "What are the steps to process CRISPR screen data?",
-            "How to identify essential genes across experimental conditions?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "mblue9"
-                ],
-                "date": "2022-03-10",
-                "galaxy_version": "21.09",
-                "length": "45M",
-                "speakers": [
-                    "mblue9"
-                ],
-                "youtube_id": "wavAf_2ytWg"
-            }
-        ],
-        "redirect_from": [
-            "/topics/genome-editing/tutorials/crispr-screen/tutorial",
-            "/short/genome-annotation/crispr-screen",
-            "/short/T00171"
-        ],
-        "requirements": [
-            {
-                "topic_name": "sequence-analysis",
-                "tutorials": [
-                    "quality-control"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "collections",
-                    "upload-rules"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00171",
-        "short_tools": [
-            "multiqc",
-            "mageck_count",
-            "mageck_test",
-            "tp_awk_tool",
-            "mageck_mle",
-            "fastqc",
-            "volcanoplot",
-            "cutadapt"
-        ],
-        "slides": true,
-        "slides_recordings": [
-            {
-                "captioners": [
-                    "mblue9"
-                ],
-                "date": "2022-03-10",
-                "galaxy_version": "21.09",
-                "length": "3M",
-                "speakers": [
-                    "awspolly"
-                ],
-                "youtube_id": "MNT9gB5_RMg"
-            }
-        ],
-        "subtopic": "eukaryote",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "genome editing",
-            "CRISPR",
-            "essential genes",
-            "cell line"
-        ],
-        "time_estimation": "2H",
-        "title": "CRISPR screen analysis",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mageck_count/mageck_count/0.5.9.2.4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mageck_mle/mageck_mle/0.5.9.2.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mageck_test/mageck_test/0.5.9.2.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5",
-            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.4+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy0"
-        ],
-        "topic_name": "genome-annotation",
-        "topic_name_human": "Genome Annotation",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": true
-        },
-        "tutorial_name": "crispr-screen",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/crispr-screen/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/crispr-screen/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/crispr-screen/tutorial.json"
-        },
-        "version": 12,
-        "video": true,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 274,
-        "visitors": 1660992,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "CRISPR screen analysis",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nbroadgpp-brunello-library-contents.csv\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCalabrese_SetA_Guides_Reference.csv\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  3[label=\"FastQC\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Cutadapt\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"MultiQC\"]\n  3 -> 5 [label=\"text_file\"]\n  6[label=\"MAGeCK count\"]\n  4 -> 6 [label=\"out1\"]\n  7[label=\"MAGeCKs test\"]\n  6 -> 7 [label=\"counts\"]\n}",
-                "history": [
-                    {
-                        "hash": "6de3720bca01013738f2c7a888d8f801b152cad0",
-                        "message": "fix tagging",
-                        "num": 2,
-                        "short_hash": "6de3720bc",
-                        "unix": "1646669939"
                     },
-                    {
-                        "hash": "25fe77f9e08a7d086221d60a37e4e538db380c29",
-                        "message": "Migrate to GA",
-                        "num": 1,
-                        "short_hash": "25fe77f9e",
-                        "unix": "1646669586"
-                    }
-                ],
-                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
+                        "id": 34,
+                        "input_connections": {
+                            "infile1": {
+                                "id": 32,
+                                "output_name": "output"
+                            },
+                            "infile2": {
+                                "id": 33,
+                                "output_name": "output"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "broadgpp-brunello-library-contents.csv"
+                                "description": "runtime parameter for tool Join",
+                                "name": "infile1"
+                            },
+                            {
+                                "description": "runtime parameter for tool Join",
+                                "name": "infile2"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Join",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "input"
                             }
                         ],
-                        "label": "broadgpp-brunello-library-contents.csv",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 10
+                            "left": 4890,
+                            "top": 254
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Essential genes in both"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "9ff72e942410",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \".\", \"header\": \"false\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"RuntimeValue\"}, \"infile2\": {\"__class__\": \"RuntimeValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "2d894130-2416-4418-98bd-0f62d0ce3288",
-                        "workflow_outputs": []
+                        "type": "tool",
+                        "uuid": "e3079b53-7fa1-43d1-820c-dbcded909b75",
+                        "workflow_outputs": [
+                            {
+                                "label": "essential_both",
+                                "output_name": "output",
+                                "uuid": "5cdfb5c9-c677-41dc-a838-c4a61d62f5be"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
+                        "id": 35,
+                        "input_connections": {
+                            "infile1": {
+                                "id": 32,
+                                "output_name": "output"
+                            },
+                            "infile2": {
+                                "id": 33,
+                                "output_name": "output"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Calabrese_SetA_Guides_Reference.csv"
+                                "description": "runtime parameter for tool Join",
+                                "name": "infile1"
+                            },
+                            {
+                                "description": "runtime parameter for tool Join",
+                                "name": "infile2"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Join",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "input"
                             }
                         ],
-                        "label": "Calabrese_SetA_Guides_Reference.csv",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 130
+                            "left": 4895,
+                            "top": 412
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Essential genes only in control"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "9ff72e942410",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \".\", \"header\": \"false\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"RuntimeValue\"}, \"infile2\": {\"__class__\": \"RuntimeValue\"}, \"jointype\": \"-v 1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f79b3850-c8b6-4ca7-8406-c795702195ae",
-                        "workflow_outputs": []
+                        "type": "tool",
+                        "uuid": "10ed907c-d126-47f8-b91a-ddf45f0e0c9e",
+                        "workflow_outputs": [
+                            {
+                                "label": "essential_control",
+                                "output_name": "output",
+                                "uuid": "8b2b65ea-37c3-43d2-b416-38f8f920fbd9"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
+                        "id": 36,
+                        "input_connections": {
+                            "infile1": {
+                                "id": 32,
+                                "output_name": "output"
+                            },
+                            "infile2": {
+                                "id": 33,
+                                "output_name": "output"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Input Dataset Collection"
+                                "description": "runtime parameter for tool Join",
+                                "name": "infile1"
+                            },
+                            {
+                                "description": "runtime parameter for tool Join",
+                                "name": "infile2"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Join",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "input"
                             }
                         ],
-                        "label": "Input Dataset Collection",
-                        "name": "Input dataset collection",
-                        "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 250
+                            "left": 4896,
+                            "top": 566
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Essential genes only in condition"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "9ff72e942410",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \".\", \"header\": \"false\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"RuntimeValue\"}, \"infile2\": {\"__class__\": \"RuntimeValue\"}, \"jointype\": \"-v 2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "699e7c6b-5248-484a-a06c-bae15497e74e",
-                        "workflow_outputs": []
+                        "type": "tool",
+                        "uuid": "c1e1e08c-c12a-4ea0-a166-0e45c1044463",
+                        "workflow_outputs": [
+                            {
+                                "label": "essential_condition",
+                                "output_name": "output",
+                                "uuid": "37639319-b053-4fbc-bf61-fd3e38263502"
+                            }
+                        ]
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nbroadgpp-brunello-library-contents.csv\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nCalabrese_SetA_Guides_Reference.csv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"FastQC\"];\n  2 -->|output| 3;\n  4[\"Cutadapt\"];\n  2 -->|output| 4;\n  5[\"MultiQC\"];\n  3 -->|text_file| 5;\n  6[\"MAGeCK count\"];\n  4 -->|out1| 6;\n  7[\"MAGeCKs test\"];\n  6 -->|counts| 7;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Workflow constructed from history 'CRISPR tutorial Kenji'",
-                "outputs": [],
-                "parent_id": "genome-annotation/crispr-screen",
-                "path": "topics/genome-annotation/tutorials/crispr-screen/workflows/main_workflow.ga",
+                "parent_id": "genome-annotation/tnseq",
+                "path": "topics/genome-annotation/tutorials/tnseq/workflows/essential-genes-detection-transposon-insertion-sequencing-workflow.ga",
                 "tags": [
                     "genome-annotation"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "Workflow constructed from history 'CRISPR tutorial Kenji'",
+                "tests": true,
+                "title": "Essential genes detection with Transposon insertion sequencing",
                 "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-crispr-screen/versions/main-workflow",
-                "tutorial_id": "crispr-screen",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/crispr-screen/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/crispr-screen/workflows/main_workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-tnseq/versions/essential-genes-detection-transposon-insertion-sequencing-workflow",
+                "tutorial_id": "tnseq",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/tnseq/workflows/essential-genes-detection-transposon-insertion-sequencing-workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/tnseq/workflows/essential-genes-detection-transposon-insertion-sequencing-workflow.html",
                 "version": 1,
-                "wfid": "genome-annotation-crispr-screen",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "wfid": "genome-annotation-tnseq",
+                "wfname": "essential-genes-detection-transposon-insertion-sequencing-workflow",
+                "workflow": "essential-genes-detection-transposon-insertion-sequencing-workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mageck_count/mageck_count/0.5.9.2.4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mageck_test/mageck_test/0.5.9.2.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.4+galaxy1"
+                    "Cut1",
+                    "Filter1",
+                    "__EXTRACT_DATASET__",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/find_subsequences/bg_find_subsequences/0.2",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/gff_to_prot/gff_to_prot/3.0.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/3.0.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5"
                 ],
-                "workflowhub_id": "1179"
+                "workflowhub_id": "1149"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/5750854"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.2579335"
     },
     {
         "admin_install": {
@@ -108869,104 +110035,126 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "prokka",
-                    "owner": "crs4",
-                    "revisions": "bf68eb663bc3",
+                    "name": "augustus_training",
+                    "owner": "bgruening",
+                    "revisions": "6519ebe25019",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "prokka",
-                    "owner": "crs4",
-                    "revisions": "111884f0d912",
+                    "name": "gffread",
+                    "owner": "devteam",
+                    "revisions": "69e0806b63a4",
+                    "tool_panel_section_label": "Convert Formats",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "busco",
+                    "owner": "iuc",
+                    "revisions": "602fb8e63aa7",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "fasta_stats",
+                    "owner": "iuc",
+                    "revisions": "9c620a950d3a",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "jbrowse",
                     "owner": "iuc",
-                    "revisions": "a6e57ff585c0",
+                    "revisions": "6cd09d7b5f37",
                     "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "jcvi_gff_stats",
+                    "owner": "iuc",
+                    "revisions": "8cffbd184762",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "maker",
+                    "owner": "iuc",
+                    "revisions": "d46d803ca6cc",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "maker_map_ids",
+                    "owner": "iuc",
+                    "revisions": "e906fa778440",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "snap_training",
+                    "owner": "iuc",
+                    "revisions": "2a598c0aa042",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: prokka\n  owner: crs4\n  revisions: bf68eb663bc3\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: prokka\n  owner: crs4\n  revisions: 111884f0d912\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: augustus_training\n  owner: bgruening\n  revisions: 6519ebe25019\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gffread\n  owner: devteam\n  revisions: 69e0806b63a4\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 602fb8e63aa7\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n  owner: iuc\n  revisions: 9c620a950d3a\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 6cd09d7b5f37\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jcvi_gff_stats\n  owner: iuc\n  revisions: 8cffbd184762\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker\n  owner: iuc\n  revisions: d46d803ca6cc\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker_map_ids\n  owner: iuc\n  revisions: e906fa778440\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snap_training\n  owner: iuc\n  revisions: 2a598c0aa042\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.json",
         "contributors": [
-            {
-                "id": "annasyme",
-                "joined": "2017-09",
-                "name": "Anna Syme",
-                "orcid": "0000-0002-9906-0673",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
-            },
             {
                 "affiliations": [
+                    "gallantries",
+                    "eurosciencegateway",
                     "elixir-europe"
                 ],
-                "elixir_node": "au",
-                "id": "tseemann",
-                "joined": "2018-06",
-                "name": "Torsten Seemann",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tseemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tseemann.json"
-            },
-            {
-                "elixir_node": "au",
-                "email": "simon.gladman@unimelb.edu.au",
-                "id": "slugger70",
-                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
+                "fediverse_flavor": "mastodon",
+                "id": "abretaud",
                 "joined": "2017-09",
-                "name": "Simon Gladman",
-                "orcid": "0000-0002-6100-4385",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
+                "location": {
+                    "country": "FR",
+                    "lat": 48.11,
+                    "lon": -1.64
+                },
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
             }
         ],
-        "dir": "topics/genome-annotation/tutorials/annotation-with-prokka",
-        "edam_ontology": [
-            "topic_0622",
-            "topic_3301",
-            "topic_0623",
-            "topic_0080"
-        ],
+        "dir": "topics/genome-annotation/tutorials/annotation-with-maker",
         "edam_operation": [
-            "Genome visualisation",
             "Genome annotation",
+            "Ab-initio gene prediction",
+            "Genome visualisation",
+            "Genome assembly",
+            "Sequence assembly validation",
             "Gene prediction",
-            "Coding region prediction"
-        ],
-        "edam_topic": [
-            "Genomics",
-            "Microbiology",
-            "Gene and protein families",
-            "Sequence analysis"
+            "Homology-based gene prediction",
+            "Scaffolding",
+            "Sequence annotation",
+            "Operation",
+            "Transcriptome assembly"
         ],
+        "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.eu",
+            "UseGalaxy.no",
             "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "genome-annotation",
-                "tutorials": [
-                    "apollo"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "genome-annotation/annotation-with-prokka",
+        "id": "genome-annotation/annotation-with-maker",
         "inexact_supported_servers": [
-            "Galaxy@AuBi",
-            "GalaxyTrakr",
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
             "UseGalaxy.org.au"
         ],
         "js_requirements": {
@@ -108974,66 +110162,58 @@
             "mermaid": false
         },
         "key_points": [
-            "Prokka is a useful tool to annotate a bacterial genome.",
-            "JBrowse can be used to inspect the annotation of a genome."
+            "Maker allows to annotate a eukaryotic genome.",
+            "BUSCO and JBrowse allow to inspect the quality of an annotation."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
+        "level": "Advanced",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-08",
+        "mod_date": "2024-02-29",
         "objectives": [
             "Load genome into Galaxy",
-            "Annotate genome with Prokka",
+            "Annotate genome with Maker",
+            "Evaluate annotation quality with BUSCO",
             "View annotations in JBrowse"
         ],
-        "pageviews": 5754405,
-        "pub_date": "2018-03-06",
+        "pageviews": 21813,
+        "priority": 4,
+        "pub_date": "2018-09-24",
         "questions": [
-            "How can we annotate a bacterial genome?",
-            "How can we visualize annotated genomic features?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "abretaud"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "20M",
-                "speakers": [
-                    "abretaud"
-                ],
-                "youtube_id": "B8pIQZPf21Y"
-            }
+            "How to annotate an eukaryotic genome?",
+            "How to evaluate and visualize annotated genomic features?"
         ],
-        "short_id": "T00168",
+        "short_id": "T00166",
         "short_tools": [
-            "prokka",
-            "jbrowse"
-        ],
-        "slides": true,
-        "slides_recordings": [
-            {
-                "captioners": [
-                    "abretaud"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "3M",
-                "speakers": [
-                    "awspolly"
-                ],
-                "youtube_id": "eqHy-Cc7k4Q"
-            }
+            "jbrowse",
+            "augustus_training",
+            "busco",
+            "fasta-stats",
+            "maker_map_ids",
+            "jcvi_gff_stats",
+            "snap_training",
+            "gffread",
+            "maker"
         ],
-        "subtopic": "prokaryote",
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "eukaryote",
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -109041,31 +110221,11 @@
                 }
             ],
             "inexact": [
-                {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
@@ -109076,16 +110236,22 @@
         "symlink": null,
         "tags": [
             "gmod",
-            "prokaryote",
-            "microgalaxy",
-            "jbrowse1"
+            "eukaryote",
+            "jbrowse1",
+            "maker"
         ],
-        "time_estimation": "1h",
-        "title": "Genome annotation with Prokka",
+        "time_estimation": "4h",
+        "title": "Genome annotation with Maker",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
-            "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3",
+            "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.11",
+            "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1"
         ],
         "topic_name": "genome-annotation",
         "topic_name_human": "Genome Annotation",
@@ -109093,1458 +110259,1850 @@
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": true
+            "video": false
         },
-        "tutorial_name": "annotation-with-prokka",
+        "tutorial_name": "annotation-with-maker",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.json"
         },
-        "version": 25,
-        "video": true,
-        "video_versions": 1,
+        "version": 14,
+        "video": false,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 260,
-        "visitors": 2079352,
+        "visit_duration": 113,
+        "visitors": 11759,
         "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0001-6046-610X",
-                        "name": "Torsten Seemann"
+                        "identifier": "0000-0003-0914-2470",
+                        "name": "Anthony Bretaudeau"
                     },
                     {
-                        "class": "Person",
-                        "identifier": "0000-0002-6100-4385",
-                        "name": "Simon Gladman"
+                        "class": "Organization",
+                        "name": "French National Institute for Agriculture, Food, and Environment (INRAE)"
                     }
                 ],
-                "description": "Genome annotation with Prokka",
+                "description": "Genome annotation with Maker",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontigs.fasta\"]\n  1[label=\"Prokka\"]\n  0 -> 1 [label=\"output\"]\n  ka336c364e69e47ebace6a7fe46d285fe[color=lightseagreen,label=\"Output\\ngff_output\"]\n  1 -> ka336c364e69e47ebace6a7fe46d285fe\n  2[label=\"JBrowse\"]\n  1 -> 2 [label=\"out_fna\"]\n  1 -> 2 [label=\"out_gff\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nProtein sequences\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenome sequence\"]\n  3[label=\"Maker\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Fasta Statistics\"]\n  2 -> 4 [label=\"output\"]\n  k2d3829e6f5b946d183e317efff814e09[color=lightseagreen,label=\"Output\\nFasta Statistics on input dataset(s): Fasta summary stats\"]\n  4 -> k2d3829e6f5b946d183e317efff814e09\n  5[label=\"Busco\"]\n  2 -> 5 [label=\"output\"]\n  ka15e121423a2484b9c751635fcd61fe3[color=lightseagreen,label=\"Output\\nBUSCO: short summary\"]\n  5 -> ka15e121423a2484b9c751635fcd61fe3\n  k7806088df65743899d546a3bdfa233b2[color=lightseagreen,label=\"Output\\nBUSCO: list of missing ortholog genes\"]\n  5 -> k7806088df65743899d546a3bdfa233b2\n  k6a27d0f6d83c42b1a7af5f99ba5debe2[color=lightseagreen,label=\"Output\\nBUSCO: full table\"]\n  5 -> k6a27d0f6d83c42b1a7af5f99ba5debe2\n  6[label=\"Train Augustus\"]\n  2 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output_gff\"]\n  7[label=\"Genome annotation statistics\"]\n  3 -> 7 [label=\"output_gff\"]\n  2 -> 7 [label=\"output\"]\n  k2bed9aa65f22494d9caaf0ece8464f15[color=lightseagreen,label=\"Output\\nGenome annotation statistics: graphs (first round)\"]\n  7 -> k2bed9aa65f22494d9caaf0ece8464f15\n  k71d41ce2e90d435b9b64ab4320524770[color=lightseagreen,label=\"Output\\nGenome annotation statistics: summary (first round)\"]\n  7 -> k71d41ce2e90d435b9b64ab4320524770\n  8[label=\"gffread\"]\n  3 -> 8 [label=\"output_gff\"]\n  2 -> 8 [label=\"output\"]\n  9[label=\"Train SNAP\"]\n  2 -> 9 [label=\"output\"]\n  3 -> 9 [label=\"output_gff\"]\n  10[label=\"Busco\"]\n  8 -> 10 [label=\"output_exons\"]\n  ka79ab19d980242ca8ffa8c197a16c8b8[color=lightseagreen,label=\"Output\\nBusco summary first round\"]\n  10 -> ka79ab19d980242ca8ffa8c197a16c8b8\n  11[label=\"Maker\"]\n  6 -> 11 [label=\"output_tar\"]\n  9 -> 11 [label=\"output\"]\n  2 -> 11 [label=\"output\"]\n  3 -> 11 [label=\"output_full\"]\n  12[label=\"gffread\"]\n  11 -> 12 [label=\"output_gff\"]\n  2 -> 12 [label=\"output\"]\n  13[label=\"Train Augustus\"]\n  2 -> 13 [label=\"output\"]\n  11 -> 13 [label=\"output_gff\"]\n  k42d5aadd3a8c441d913fee8745a99b0b[color=lightseagreen,label=\"Output\\nAugus: trained model\"]\n  13 -> k42d5aadd3a8c441d913fee8745a99b0b\n  14[label=\"Genome annotation statistics\"]\n  11 -> 14 [label=\"output_gff\"]\n  2 -> 14 [label=\"output\"]\n  k9def2c6efd3c4969b5d4d13c187c1144[color=lightseagreen,label=\"Output\\nGenome annotation statistics: graphs (second round)\"]\n  14 -> k9def2c6efd3c4969b5d4d13c187c1144\n  k61f7a150a4a246b189f52170d466656e[color=lightseagreen,label=\"Output\\nGenome annotation statistics: summary (second round)\"]\n  14 -> k61f7a150a4a246b189f52170d466656e\n  15[label=\"Train SNAP\"]\n  2 -> 15 [label=\"output\"]\n  11 -> 15 [label=\"output_gff\"]\n  k458887f706614bdeab1a875aac6caed8[color=lightseagreen,label=\"Output\\nSNAP: trained model\"]\n  15 -> k458887f706614bdeab1a875aac6caed8\n  16[label=\"Busco\"]\n  12 -> 16 [label=\"output_exons\"]\n  kf52b1b410ea54384bd434927273c909c[color=lightseagreen,label=\"Output\\nBusco summary second round\"]\n  16 -> kf52b1b410ea54384bd434927273c909c\n  17[label=\"Maker\"]\n  13 -> 17 [label=\"output_tar\"]\n  15 -> 17 [label=\"output\"]\n  2 -> 17 [label=\"output\"]\n  11 -> 17 [label=\"output_full\"]\n  18[label=\"Map annotation ids\"]\n  17 -> 18 [label=\"output_gff\"]\n  k63575dcf54d14cb1b5fba2810b4da807[color=lightseagreen,label=\"Output\\nMap annotation ids: renamed GFF\"]\n  18 -> k63575dcf54d14cb1b5fba2810b4da807\n  19[label=\"JBrowse\"]\n  2 -> 19 [label=\"output\"]\n  3 -> 19 [label=\"output_gff\"]\n  18 -> 19 [label=\"renamed\"]\n  11 -> 19 [label=\"output_gff\"]\n  3 -> 19 [label=\"output_evidences\"]\n  11 -> 19 [label=\"output_evidences\"]\n  17 -> 19 [label=\"output_evidences\"]\n  k5a38ae83e17745f3aa9f4c1844584fa5[color=lightseagreen,label=\"Output\\nJBrowse: report\"]\n  19 -> k5a38ae83e17745f3aa9f4c1844584fa5\n  20[label=\"gffread\"]\n  18 -> 20 [label=\"renamed\"]\n  2 -> 20 [label=\"output\"]\n  k52fcac23b6124377a19a2e3b667a23e3[color=lightseagreen,label=\"Output\\nGffread: exons\"]\n  20 -> k52fcac23b6124377a19a2e3b667a23e3\n  k5c47c25e0ddb4adea5d0873ff4add28c[color=lightseagreen,label=\"Output\\nGffread: translation of cds\"]\n  20 -> k5c47c25e0ddb4adea5d0873ff4add28c\n  k84d9183b9589464b9f824dae7f87133e[color=lightseagreen,label=\"Output\\nGffread: cds\"]\n  20 -> k84d9183b9589464b9f824dae7f87133e\n  21[label=\"Genome annotation statistics\"]\n  18 -> 21 [label=\"renamed\"]\n  2 -> 21 [label=\"output\"]\n  kf5d4a6bf1ff8435a80847921e25bff3a[color=lightseagreen,label=\"Output\\nGenome annotation statistics: graphs (third round)\"]\n  21 -> kf5d4a6bf1ff8435a80847921e25bff3a\n  k5a863bd410f24ac881b6ce8b7f663e42[color=lightseagreen,label=\"Output\\nGenome annotation statistics: summary (third round)\"]\n  21 -> k5a863bd410f24ac881b6ce8b7f663e42\n  22[label=\"Busco\"]\n  20 -> 22 [label=\"output_exons\"]\n  k0bc78676eecc4168894d34c4ca07cdf3[color=lightseagreen,label=\"Output\\nBusco summary final round\"]\n  22 -> k0bc78676eecc4168894d34c4ca07cdf3\n}",
                 "history": [
                     {
-                        "hash": "70a555355ed2ebc563a4388cd1da50f7f1a5952f",
-                        "message": "Update topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
+                        "hash": "e61e9eba49f4c255dd46e1094355f61a770ba14e",
+                        "message": "Fix workflow",
+                        "num": 12,
+                        "short_hash": "e61e9eba4",
+                        "unix": "1625849450"
+                    },
+                    {
+                        "hash": "106af0888f3f8cbc7040c20b62adbf52ddfe2186",
+                        "message": "Update maker workflow",
+                        "num": 11,
+                        "short_hash": "106af0888",
+                        "unix": "1625842677"
+                    },
+                    {
+                        "hash": "005d964a2e8cb80f8d1bf0b304adc8f9d7c9ff76",
+                        "message": "fix workflows",
                         "num": 10,
-                        "short_hash": "70a555355",
-                        "unix": "1715074163"
+                        "short_hash": "005d964a2",
+                        "unix": "1609752597"
                     },
                     {
-                        "hash": "466b451a082b7d2d5e60777a45289874bbbde721",
-                        "message": "Add creators and license to workflow",
+                        "hash": "774f2aa374452d48fd29ee85513c3dc3a7f137f5",
+                        "message": "update maker tutorial and add a short version",
                         "num": 9,
-                        "short_hash": "466b451a0",
-                        "unix": "1714990318"
+                        "short_hash": "774f2aa37",
+                        "unix": "1609431273"
                     },
                     {
-                        "hash": "499e257dee992b4645adf4c79844b8cc89e68c24",
-                        "message": "update prokka workflow",
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
                         "num": 8,
-                        "short_hash": "499e257de",
-                        "unix": "1714456964"
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
                     },
                     {
-                        "hash": "56413bab75ab75be269668d70e3929e01bbaa5fb",
-                        "message": "Add workflow test.",
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
                         "num": 7,
-                        "short_hash": "56413bab7",
-                        "unix": "1603310943"
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
                     },
                     {
-                        "hash": "a3829a12322232647926a394b1ecae3af17a858b",
-                        "message": "Update Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
+                        "hash": "1a3049ca861744336a01f79b6ae1bc8bc46e2b12",
+                        "message": "typos + update workflow",
                         "num": 6,
-                        "short_hash": "a3829a123",
-                        "unix": "1580832292"
+                        "short_hash": "1a3049ca8",
+                        "unix": "1558343672"
                     },
                     {
-                        "hash": "bab7ab72c6a4436a3ac3e6745b364696332399b5",
-                        "message": "prokka@1.14.5 jbrowse@1.16.5+galaxy7",
+                        "hash": "2318b970d421c42bbced1799cfca63ce056ad01f",
+                        "message": "udpate workflow",
                         "num": 5,
-                        "short_hash": "bab7ab72c",
-                        "unix": "1580433748"
+                        "short_hash": "2318b970d",
+                        "unix": "1557415647"
                     },
                     {
-                        "hash": "c69f09dd0cb211d5621af293fe400892e343f78e",
-                        "message": "Adding tag",
+                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
+                        "message": "Changed format of workflows",
                         "num": 4,
-                        "short_hash": "c69f09dd0",
-                        "unix": "1579796672"
+                        "short_hash": "361236c41",
+                        "unix": "1554368414"
                     },
                     {
-                        "hash": "920732bc2295d6120b075934b758290ad56f5759",
-                        "message": "Updated prokka workflow to newest tool versions",
+                        "hash": "6eef55b7e8306d8ce46ac08e7799f6f65ae106aa",
+                        "message": "Updated install_tutorial_requirements.sh + minor fixes (#1275)",
                         "num": 3,
-                        "short_hash": "920732bc2",
-                        "unix": "1579634888"
+                        "short_hash": "6eef55b7e",
+                        "unix": "1551293676"
                     },
                     {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
+                        "hash": "bc6d0ddca2ce262deb405fd92e0dab955488eb49",
+                        "message": "jbrowse part",
                         "num": 2,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
+                        "short_hash": "bc6d0ddca",
+                        "unix": "1536669505"
+                    },
+                    {
+                        "hash": "7b73f26f84bc0e9dc9e771f7dd89be3e6daddd66",
+                        "message": "update wf",
+                        "num": 1,
+                        "short_hash": "7b73f26f8",
+                        "unix": "1536594667"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "It contains the sequences used by Maker to construct gene models.",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "It contains the sequences used by Maker to construct gene models.",
+                                "name": "EST and/or cDNA"
+                            }
+                        ],
+                        "label": "EST and/or cDNA",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 287.875,
+                            "height": 81,
+                            "left": 661.46875,
+                            "right": 861.46875,
+                            "top": 206.875,
+                            "width": 200,
+                            "x": 661.46875,
+                            "y": 206.875
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "397d1af7-4d12-43d6-955c-e3122978fc92",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "A set of protein sequences, usually from closely related species or from a curated sequence database like UniProt/SwissProt.",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "A set of protein sequences, usually from closely related species or from a curated sequence database like UniProt/SwissProt.",
+                                "name": "Protein sequences"
+                            }
+                        ],
+                        "label": "Protein sequences",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 459,
+                            "height": 81,
+                            "left": 659.5,
+                            "right": 859.5,
+                            "top": 378,
+                            "width": 200,
+                            "x": 659.5,
+                            "y": 378
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "418c68b0-b726-4f5e-b53c-480f1e7d43b5",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "This file corresponds to the sequence to be annotated.",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "This file corresponds to the sequence to be annotated.",
+                                "name": "Genome sequence"
+                            }
+                        ],
+                        "label": "Genome sequence",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 1797.03125,
+                            "height": 81,
+                            "left": 661.46875,
+                            "right": 861.46875,
+                            "top": 1716.03125,
+                            "width": 200,
+                            "x": 661.46875,
+                            "y": 1716.03125
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "e03b5775-bd22-4528-9f21-20cd396dc6cc",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nProtein sequences\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nGenome sequence\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Maker\"];\n  0 -->|output| 3;\n  2 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Fasta Statistics\"];\n  2 -->|output| 4;\n  2d3829e6-f5b9-46d1-83e3-17efff814e09[\"Output\\nFasta Statistics on input dataset(s): Fasta summary stats\"];\n  4 --> 2d3829e6-f5b9-46d1-83e3-17efff814e09;\n  style 2d3829e6-f5b9-46d1-83e3-17efff814e09 stroke:#2c3143,stroke-width:4px;\n  5[\"Busco\"];\n  2 -->|output| 5;\n  a15e1214-23a2-484b-9c75-1635fcd61fe3[\"Output\\nBUSCO: short summary\"];\n  5 --> a15e1214-23a2-484b-9c75-1635fcd61fe3;\n  style a15e1214-23a2-484b-9c75-1635fcd61fe3 stroke:#2c3143,stroke-width:4px;\n  7806088d-f657-4389-9d54-6a3bdfa233b2[\"Output\\nBUSCO: list of missing ortholog genes\"];\n  5 --> 7806088d-f657-4389-9d54-6a3bdfa233b2;\n  style 7806088d-f657-4389-9d54-6a3bdfa233b2 stroke:#2c3143,stroke-width:4px;\n  6a27d0f6-d83c-42b1-a7af-5f99ba5debe2[\"Output\\nBUSCO: full table\"];\n  5 --> 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2;\n  style 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2 stroke:#2c3143,stroke-width:4px;\n  6[\"Train Augustus\"];\n  2 -->|output| 6;\n  3 -->|output_gff| 6;\n  7[\"Genome annotation statistics\"];\n  3 -->|output_gff| 7;\n  2 -->|output| 7;\n  2bed9aa6-5f22-494d-9caa-f0ece8464f15[\"Output\\nGenome annotation statistics: graphs (first round)\"];\n  7 --> 2bed9aa6-5f22-494d-9caa-f0ece8464f15;\n  style 2bed9aa6-5f22-494d-9caa-f0ece8464f15 stroke:#2c3143,stroke-width:4px;\n  71d41ce2-e90d-435b-9b64-ab4320524770[\"Output\\nGenome annotation statistics: summary (first round)\"];\n  7 --> 71d41ce2-e90d-435b-9b64-ab4320524770;\n  style 71d41ce2-e90d-435b-9b64-ab4320524770 stroke:#2c3143,stroke-width:4px;\n  8[\"gffread\"];\n  3 -->|output_gff| 8;\n  2 -->|output| 8;\n  9[\"Train SNAP\"];\n  2 -->|output| 9;\n  3 -->|output_gff| 9;\n  10[\"Busco\"];\n  8 -->|output_exons| 10;\n  a79ab19d-9802-42ca-8ffa-8c197a16c8b8[\"Output\\nBusco summary first round\"];\n  10 --> a79ab19d-9802-42ca-8ffa-8c197a16c8b8;\n  style a79ab19d-9802-42ca-8ffa-8c197a16c8b8 stroke:#2c3143,stroke-width:4px;\n  11[\"Maker\"];\n  6 -->|output_tar| 11;\n  9 -->|output| 11;\n  2 -->|output| 11;\n  3 -->|output_full| 11;\n  12[\"gffread\"];\n  11 -->|output_gff| 12;\n  2 -->|output| 12;\n  13[\"Train Augustus\"];\n  2 -->|output| 13;\n  11 -->|output_gff| 13;\n  42d5aadd-3a8c-441d-913f-ee8745a99b0b[\"Output\\nAugus: trained model\"];\n  13 --> 42d5aadd-3a8c-441d-913f-ee8745a99b0b;\n  style 42d5aadd-3a8c-441d-913f-ee8745a99b0b stroke:#2c3143,stroke-width:4px;\n  14[\"Genome annotation statistics\"];\n  11 -->|output_gff| 14;\n  2 -->|output| 14;\n  9def2c6e-fd3c-4969-b5d4-d13c187c1144[\"Output\\nGenome annotation statistics: graphs (second round)\"];\n  14 --> 9def2c6e-fd3c-4969-b5d4-d13c187c1144;\n  style 9def2c6e-fd3c-4969-b5d4-d13c187c1144 stroke:#2c3143,stroke-width:4px;\n  61f7a150-a4a2-46b1-89f5-2170d466656e[\"Output\\nGenome annotation statistics: summary (second round)\"];\n  14 --> 61f7a150-a4a2-46b1-89f5-2170d466656e;\n  style 61f7a150-a4a2-46b1-89f5-2170d466656e stroke:#2c3143,stroke-width:4px;\n  15[\"Train SNAP\"];\n  2 -->|output| 15;\n  11 -->|output_gff| 15;\n  458887f7-0661-4bde-ab1a-875aac6caed8[\"Output\\nSNAP: trained model\"];\n  15 --> 458887f7-0661-4bde-ab1a-875aac6caed8;\n  style 458887f7-0661-4bde-ab1a-875aac6caed8 stroke:#2c3143,stroke-width:4px;\n  16[\"Busco\"];\n  12 -->|output_exons| 16;\n  f52b1b41-0ea5-4384-bd43-4927273c909c[\"Output\\nBusco summary second round\"];\n  16 --> f52b1b41-0ea5-4384-bd43-4927273c909c;\n  style f52b1b41-0ea5-4384-bd43-4927273c909c stroke:#2c3143,stroke-width:4px;\n  17[\"Maker\"];\n  13 -->|output_tar| 17;\n  15 -->|output| 17;\n  2 -->|output| 17;\n  11 -->|output_full| 17;\n  18[\"Map annotation ids\"];\n  17 -->|output_gff| 18;\n  63575dcf-54d1-4cb1-b5fb-a2810b4da807[\"Output\\nMap annotation ids: renamed GFF\"];\n  18 --> 63575dcf-54d1-4cb1-b5fb-a2810b4da807;\n  style 63575dcf-54d1-4cb1-b5fb-a2810b4da807 stroke:#2c3143,stroke-width:4px;\n  19[\"JBrowse\"];\n  2 -->|output| 19;\n  3 -->|output_gff| 19;\n  18 -->|renamed| 19;\n  11 -->|output_gff| 19;\n  3 -->|output_evidences| 19;\n  11 -->|output_evidences| 19;\n  17 -->|output_evidences| 19;\n  5a38ae83-e177-45f3-aa9f-4c1844584fa5[\"Output\\nJBrowse: report\"];\n  19 --> 5a38ae83-e177-45f3-aa9f-4c1844584fa5;\n  style 5a38ae83-e177-45f3-aa9f-4c1844584fa5 stroke:#2c3143,stroke-width:4px;\n  20[\"gffread\"];\n  18 -->|renamed| 20;\n  2 -->|output| 20;\n  52fcac23-b612-4377-a19a-2e3b667a23e3[\"Output\\nGffread: exons\"];\n  20 --> 52fcac23-b612-4377-a19a-2e3b667a23e3;\n  style 52fcac23-b612-4377-a19a-2e3b667a23e3 stroke:#2c3143,stroke-width:4px;\n  5c47c25e-0ddb-4ade-a5d0-873ff4add28c[\"Output\\nGffread: translation of cds\"];\n  20 --> 5c47c25e-0ddb-4ade-a5d0-873ff4add28c;\n  style 5c47c25e-0ddb-4ade-a5d0-873ff4add28c stroke:#2c3143,stroke-width:4px;\n  84d9183b-9589-464b-9f82-4dae7f87133e[\"Output\\nGffread: cds\"];\n  20 --> 84d9183b-9589-464b-9f82-4dae7f87133e;\n  style 84d9183b-9589-464b-9f82-4dae7f87133e stroke:#2c3143,stroke-width:4px;\n  21[\"Genome annotation statistics\"];\n  18 -->|renamed| 21;\n  2 -->|output| 21;\n  f5d4a6bf-1ff8-435a-8084-7921e25bff3a[\"Output\\nGenome annotation statistics: graphs (third round)\"];\n  21 --> f5d4a6bf-1ff8-435a-8084-7921e25bff3a;\n  style f5d4a6bf-1ff8-435a-8084-7921e25bff3a stroke:#2c3143,stroke-width:4px;\n  5a863bd4-10f2-4ac8-81b6-ce8b7f663e42[\"Output\\nGenome annotation statistics: summary (third round)\"];\n  21 --> 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42;\n  style 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42 stroke:#2c3143,stroke-width:4px;\n  22[\"Busco\"];\n  20 -->|output_exons| 22;\n  0bc78676-eecc-4168-894d-34c4ca07cdf3[\"Output\\nBusco summary final round\"];\n  22 --> 0bc78676-eecc-4168-894d-34c4ca07cdf3;\n  style 0bc78676-eecc-4168-894d-34c4ca07cdf3 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Genome annotation with Maker ",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "dataset": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Fasta Statistics",
+                        "outputs": [
+                            {
+                                "name": "stats",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 1526.4375,
+                            "height": 152,
+                            "left": 722.921875,
+                            "right": 922.921875,
+                            "top": 1374.4375,
+                            "width": 200,
+                            "x": 722.921875,
+                            "y": 1374.4375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "9c620a950d3a",
+                            "name": "fasta_stats",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.1",
+                        "type": "tool",
+                        "uuid": "9cd9564b-b447-4a93-9445-ae3583137010",
+                        "workflow_outputs": [
+                            {
+                                "label": "Fasta Statistics on input dataset(s): Fasta summary stats",
+                                "output_name": "stats",
+                                "uuid": "2d3829e6-f5b9-46d1-83e3-17efff814e09"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "input": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Busco",
+                        "outputs": [
+                            {
+                                "name": "busco_sum",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "busco_table",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "busco_missing",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 1989.015625,
+                            "height": 212,
+                            "left": 939.484375,
+                            "right": 1139.484375,
+                            "top": 1777.015625,
+                            "width": 200,
+                            "x": 939.484375,
+                            "y": 1777.015625
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "602fb8e63aa7",
+                            "name": "busco",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"geno\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.1.4",
+                        "type": "tool",
+                        "uuid": "2e99d9de-b48b-4f0f-99da-5f727ad023cc",
+                        "workflow_outputs": [
+                            {
+                                "label": "BUSCO: short summary",
+                                "output_name": "busco_sum",
+                                "uuid": "a15e1214-23a2-484b-9c75-1635fcd61fe3"
+                            },
+                            {
+                                "label": "BUSCO: list of missing ortholog genes",
+                                "output_name": "busco_missing",
+                                "uuid": "7806088d-f657-4389-9d54-6a3bdfa233b2"
+                            },
+                            {
+                                "label": "BUSCO: full table",
+                                "output_name": "busco_table",
+                                "uuid": "6a27d0f6-d83c-42b1-a7af-5f99ba5debe2"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "gff": {
+                                "id": 3,
+                                "output_name": "output_gff"
+                            },
+                            "ref_genome|genome": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Genome annotation statistics",
+                        "outputs": [
+                            {
+                                "name": "summary",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "graphs",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 1247.015625,
+                            "height": 272,
+                            "left": 1247.5,
+                            "right": 1447.5,
+                            "top": 975.015625,
+                            "width": 200,
+                            "x": 1247.5,
+                            "y": 975.015625
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "8cffbd184762",
+                            "name": "jcvi_gff_stats",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"gff\": {\"__class__\": \"ConnectedValue\"}, \"ref_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.8.4",
+                        "type": "tool",
+                        "uuid": "af60c4d9-58f2-4f41-a2a3-6458cdcfd404",
+                        "workflow_outputs": [
+                            {
+                                "label": "Genome annotation statistics: graphs (first round)",
+                                "output_name": "graphs",
+                                "uuid": "2bed9aa6-5f22-494d-9caa-f0ece8464f15"
+                            },
+                            {
+                                "label": "Genome annotation statistics: summary (first round)",
+                                "output_name": "summary",
+                                "uuid": "71d41ce2-e90d-435b-9b64-ab4320524770"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {
+                            "input": {
+                                "id": 8,
+                                "output_name": "output_exons"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Busco",
+                        "outputs": [
+                            {
+                                "name": "busco_sum",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "busco_table",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "busco_missing",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 1738.03125,
+                            "height": 252,
+                            "left": 1545.5,
+                            "right": 1745.5,
+                            "top": 1486.03125,
+                            "width": 200,
+                            "x": 1545.5,
+                            "y": 1486.03125
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionbusco_missing": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "busco_missing"
+                            },
+                            "HideDatasetActionbusco_table": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "busco_table"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "602fb8e63aa7",
+                            "name": "busco",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"tran\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.1.4",
+                        "type": "tool",
+                        "uuid": "a83a2b48-7787-4b53-a592-339f5134e168",
+                        "workflow_outputs": [
+                            {
+                                "label": "Busco summary first round",
+                                "output_name": "busco_sum",
+                                "uuid": "a79ab19d-9802-42ca-8ffa-8c197a16c8b8"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3",
+                        "errors": null,
+                        "id": 13,
+                        "input_connections": {
+                            "genome": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "maker_gff": {
+                                "id": 11,
+                                "output_name": "output_gff"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Train Augustus",
+                        "outputs": [
+                            {
+                                "name": "output_tar",
+                                "type": "augustus"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 1259.03125,
+                            "height": 182,
+                            "left": 1863.5,
+                            "right": 2063.5,
+                            "top": 1077.03125,
+                            "width": 200,
+                            "x": 1863.5,
+                            "y": 1077.03125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "6519ebe25019",
+                            "name": "augustus_training",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"genome\": {\"__class__\": \"ConnectedValue\"}, \"maker_gff\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.3.3",
+                        "type": "tool",
+                        "uuid": "b347da09-05a2-4d30-a103-dbeb5853efcd",
+                        "workflow_outputs": [
+                            {
+                                "label": "Augus: trained model",
+                                "output_name": "output_tar",
+                                "uuid": "42d5aadd-3a8c-441d-913f-ee8745a99b0b"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                        "errors": null,
+                        "id": 14,
+                        "input_connections": {
+                            "gff": {
+                                "id": 11,
+                                "output_name": "output_gff"
+                            },
+                            "ref_genome|genome": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Genome annotation statistics",
+                        "outputs": [
+                            {
+                                "name": "summary",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "graphs",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 1569.03125,
+                            "height": 272,
+                            "left": 1863.5,
+                            "right": 2063.5,
+                            "top": 1297.03125,
+                            "width": 200,
+                            "x": 1863.5,
+                            "y": 1297.03125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "8cffbd184762",
+                            "name": "jcvi_gff_stats",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"gff\": {\"__class__\": \"ConnectedValue\"}, \"ref_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.8.4",
+                        "type": "tool",
+                        "uuid": "5a3899b6-a669-4a36-990e-01e6cac6410d",
+                        "workflow_outputs": [
+                            {
+                                "label": "Genome annotation statistics: graphs (second round)",
+                                "output_name": "graphs",
+                                "uuid": "9def2c6e-fd3c-4969-b5d4-d13c187c1144"
+                            },
+                            {
+                                "label": "Genome annotation statistics: summary (second round)",
+                                "output_name": "summary",
+                                "uuid": "61f7a150-a4a2-46b1-89f5-2170d466656e"
+                            }
+                        ]
                     },
-                    {
-                        "hash": "b9a6072964bce056112a36326600e4c80bd133ec",
-                        "message": "move tutorials to new topic",
-                        "num": 1,
-                        "short_hash": "b9a607296",
-                        "unix": "1528898987"
-                    }
-                ],
-                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 15,
+                        "input_connections": {
+                            "genome": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "maker_gff": {
+                                "id": 11,
+                                "output_name": "output_gff"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Train SNAP",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "contigs.fasta"
+                                "name": "output",
+                                "type": "snaphmm"
                             }
                         ],
-                        "label": "contigs.fasta",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 76.845458984375
+                            "bottom": 1770.03125,
+                            "height": 162,
+                            "left": 1863.5,
+                            "right": 2063.5,
+                            "top": 1608.03125,
+                            "width": 200,
+                            "x": 1863.5,
+                            "y": 1608.03125
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "79e73b85-8d44-413f-83b7-c0e668ec963c",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ncontigs.fasta\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Prokka\"];\n  0 -->|output| 1;\n  a336c364-e69e-47eb-ace6-a7fe46d285fe[\"Output\\ngff_output\"];\n  1 --> a336c364-e69e-47eb-ace6-a7fe46d285fe;\n  style a336c364-e69e-47eb-ace6-a7fe46d285fe stroke:#2c3143,stroke-width:4px;\n  2[\"JBrowse\"];\n  1 -->|out_fna| 2;\n  1 -->|out_gff| 2;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Genome Annotation with Prokka ",
-                "outputs": [
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2a598c0aa042",
+                            "name": "snap_training",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"gene_num\": \"1000\", \"genome\": {\"__class__\": \"ConnectedValue\"}, \"maker_gff\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2013_11_29+galaxy1",
+                        "type": "tool",
+                        "uuid": "97cec0ac-e731-4b55-859d-773a7c88bc26",
+                        "workflow_outputs": [
+                            {
+                                "label": "SNAP: trained model",
+                                "output_name": "output",
+                                "uuid": "458887f7-0661-4bde-ab1a-875aac6caed8"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
                         "errors": null,
-                        "id": 1,
+                        "id": 16,
                         "input_connections": {
                             "input": {
-                                "id": 0,
-                                "output_name": "output"
+                                "id": 12,
+                                "output_name": "output_exons"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Prokka",
+                        "name": "Busco",
                         "outputs": [
                             {
-                                "name": "out_gff",
-                                "type": "gff"
-                            },
-                            {
-                                "name": "out_gbk",
+                                "name": "busco_sum",
                                 "type": "txt"
                             },
                             {
-                                "name": "out_fna",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "out_faa",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "out_ffn",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "out_sqn",
-                                "type": "asn1"
-                            },
-                            {
-                                "name": "out_fsa",
-                                "type": "fasta"
+                                "name": "busco_table",
+                                "type": "tabular"
                             },
                             {
-                                "name": "out_tbl",
-                                "type": "txt"
+                                "name": "busco_missing",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 870.03125,
+                            "height": 252,
+                            "left": 2161.484375,
+                            "right": 2361.484375,
+                            "top": 618.03125,
+                            "width": 200,
+                            "x": 2161.484375,
+                            "y": 618.03125
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionbusco_missing": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "busco_missing"
                             },
+                            "HideDatasetActionbusco_table": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "busco_table"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "602fb8e63aa7",
+                            "name": "busco",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"tran\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.1.4",
+                        "type": "tool",
+                        "uuid": "9b04f806-0275-4939-bf74-b8c58ae2bffa",
+                        "workflow_outputs": [
                             {
-                                "name": "out_err",
-                                "type": "txt"
-                            },
+                                "label": "Busco summary second round",
+                                "output_name": "busco_sum",
+                                "uuid": "f52b1b41-0ea5-4384-bd43-4927273c909c"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11",
+                        "errors": null,
+                        "id": 18,
+                        "input_connections": {
+                            "maker_gff": {
+                                "id": 17,
+                                "output_name": "output_gff"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Map annotation ids",
+                        "outputs": [
                             {
-                                "name": "out_txt",
-                                "type": "txt"
+                                "name": "renamed",
+                                "type": "gff"
                             },
                             {
-                                "name": "out_log",
-                                "type": "txt"
+                                "name": "id_map",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 254.117919921875,
-                            "top": 0.0
+                            "bottom": 1637.03125,
+                            "height": 222,
+                            "left": 2439.5,
+                            "right": 2639.5,
+                            "top": 1415.03125,
+                            "width": 200,
+                            "x": 2439.5,
+                            "y": 1415.03125
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
+                        "post_job_actions": {
+                            "ChangeDatatypeActionrenamed": {
+                                "action_arguments": {
+                                    "newtype": "gff3"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "renamed"
+                            },
+                            "HideDatasetActionid_map": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "id_map"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11",
                         "tool_shed_repository": {
-                            "changeset_revision": "bf68eb663bc3",
-                            "name": "prokka",
-                            "owner": "crs4",
+                            "changeset_revision": "2e3535db1bfa",
+                            "name": "maker_map_ids",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"__workflow_invocation_uuid__\": \"5dc31c9443c711eabead005056ba55fb\", \"centre\": \"V\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"compliant\": {\"compliant_select\": \"no\", \"__current_case__\": 0, \"addgenes\": false, \"mincontig\": \"200\"}, \"evalue\": \"1e-06\", \"fast\": false, \"genus\": \"Staphylococcus\", \"gffver\": \"3\", \"increment\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"kingdom\": {\"kingdom_select\": \"Bacteria\", \"__current_case__\": 1, \"gcode\": \"11\"}, \"locustag\": \"P\", \"metagenome\": false, \"norrna\": false, \"notrna\": false, \"outputs\": [\"gff\", \"gbk\", \"fna\", \"faa\", \"ffn\", \"sqn\", \"fsa\", \"tbl\", \"err\", \"txt\"], \"plasmid\": \"\", \"proteins\": null, \"rfam\": false, \"species\": \"aureus\", \"strain\": \"\", \"usegenus\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.14.5",
+                        "tool_state": "{\"justify\": \"6\", \"maker_gff\": {\"__class__\": \"ConnectedValue\"}, \"prefix\": \"TEST\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.31.11",
                         "type": "tool",
-                        "uuid": "28efec53-71bb-4aaa-993d-03b78d493570",
-                        "when": null,
+                        "uuid": "d7101291-76ac-48ec-9fb3-89ca5554e8ea",
                         "workflow_outputs": [
                             {
-                                "label": "gff_output",
-                                "output_name": "out_gff",
-                                "uuid": "a336c364-e69e-47eb-ace6-a7fe46d285fe"
+                                "label": "Map annotation ids: renamed GFF",
+                                "output_name": "renamed",
+                                "uuid": "63575dcf-54d1-4cb1-b5fb-a2810b4da807"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "genome-annotation/annotation-with-prokka",
-                "path": "topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
-                "tags": [
-                    "genome-annotation",
-                    "GTN"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "Genome Annotation with Prokka ",
-                "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-annotation-with-prokka/versions/galaxy-workflow-workflow-constructed-from-history--prokka-workflow-",
-                "tutorial_id": "annotation-with-prokka",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.html",
-                "version": 6,
-                "wfid": "genome-annotation-annotation-with-prokka",
-                "wfname": "galaxy-workflow-workflow-constructed-from-history--prokka-workflow-",
-                "workflow": "Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1"
-                ],
-                "workflowhub_id": "1186"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.1156405"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "intermine_galaxy_exchange",
-                    "owner": "iuc",
-                    "revisions": "c24014d80001",
-                    "tool_panel_section_label": "Convert Formats",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: intermine_galaxy_exchange\n  owner: iuc\n  revisions: c24014d80001\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/intermine/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "danielabutano",
-                "yochannah"
-            ]
-        },
-        "contributors": [
-            {
-                "id": "danielabutano",
-                "joined": "2019-09",
-                "name": "Daniela Butano",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/danielabutano/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/danielabutano.json"
-            },
-            {
-                "id": "yochannah",
-                "joined": "2019-09",
-                "name": "Yo Yehudi",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yochannah/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/yochannah.json"
-            }
-        ],
-        "dir": "topics/galaxy-interface/tutorials/intermine",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "galaxy-interface/intermine",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-02-29",
-        "objectives": [
-            "Learn how to import/export data from/to InterMine instances",
-            "Understand the InterMine Interchange Dataset"
-        ],
-        "pageviews": 185,
-        "pub_date": "2020-12-09",
-        "questions": [
-            "How to export your query results from your InterMine of choice to Galaxy?",
-            "How to export a list of identifiers from Galaxy to your InterMine of choice?"
-        ],
-        "short_id": "T00152",
-        "short_tools": [
-            "intermine",
-            "galaxy_intermine_exchange"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "analyse",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "gmod",
-            "intermine"
-        ],
-        "time_estimation": "1h",
-        "title": "InterMine integration with Galaxy",
-        "tools": [
-            "intermine",
-            "toolshed.g2.bx.psu.edu/repos/iuc/intermine_galaxy_exchange/galaxy_intermine_exchange/0.0.1"
-        ],
-        "topic_name": "galaxy-interface",
-        "topic_name_human": "Using Galaxy and Managing your Data",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "intermine",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/intermine/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/intermine/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/intermine/tutorial.json"
-        },
-        "version": 9,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 149,
-        "visitors": 134,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Intermine import/export",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[label=\"Create InterMine Interchange\"]\n  0 -> 1 [label=\"output\"]\n}",
-                "history": [
-                    {
-                        "hash": "6a3063bce6a3990aefa6facf94d34a08bf4eea6f",
-                        "message": "more small edits",
-                        "num": 2,
-                        "short_hash": "6a3063bce",
-                        "unix": "1607081036"
                     },
-                    {
-                        "hash": "de251b5d774f97b4dcb70121c68ea01eba22536d",
-                        "message": "move folder",
-                        "num": 1,
-                        "short_hash": "de251b5d7",
-                        "unix": "1607080170"
-                    }
-                ],
-                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
+                        "id": 19,
+                        "input_connections": {
+                            "reference_genome|genome": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "track_groups_0|data_tracks_0|data_format|annotation": [
+                                {
+                                    "id": 3,
+                                    "output_name": "output_gff"
+                                },
+                                {
+                                    "id": 18,
+                                    "output_name": "renamed"
+                                },
+                                {
+                                    "id": 11,
+                                    "output_name": "output_gff"
+                                }
+                            ],
+                            "track_groups_1|data_tracks_0|data_format|annotation": [
+                                {
+                                    "id": 3,
+                                    "output_name": "output_evidences"
+                                },
+                                {
+                                    "id": 11,
+                                    "output_name": "output_evidences"
+                                },
+                                {
+                                    "id": 17,
+                                    "output_name": "output_evidences"
+                                }
+                            ]
+                        },
                         "inputs": [],
                         "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
+                        "name": "JBrowse",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "html"
+                            }
+                        ],
                         "position": {
-                            "left": 257,
-                            "top": 403.5
+                            "bottom": 775.015625,
+                            "height": 292,
+                            "left": 2747.5,
+                            "right": 2947.5,
+                            "top": 483.015625,
+                            "width": 200,
+                            "x": 2747.5,
+                            "y": 483.015625
                         },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "13261ad4-770b-4728-9068-d9941d07abf7",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "6cd09d7b5f37",
+                            "name": "jbrowse",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Maker annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 1, \"category\": \"Maker evidences\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"match_part\": {\"match_part_select\": \"true\", \"__current_case__\": 0, \"name\": {\"__class__\": \"RuntimeValue\"}}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.10+galaxy0",
+                        "type": "tool",
+                        "uuid": "4585ada8-27ac-4632-8ac4-76f452316f21",
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "JBrowse: report",
                                 "output_name": "output",
-                                "uuid": "3df15ab7-6fb7-4a90-81e9-f25868067b8e"
+                                "uuid": "5a38ae83-e177-45f3-aa9f-4c1844584fa5"
                             }
                         ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Create InterMine Interchange\"];\n  0 -->|output| 1;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Intermine import/export",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [],
+                        "id": 20,
+                        "input_connections": {
+                            "input": {
+                                "id": 18,
+                                "output_name": "renamed"
+                            },
+                            "reference_genome|genome_fasta": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool gffread",
+                                "name": "chr_replace"
+                            }
+                        ],
                         "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
+                        "name": "gffread",
+                        "outputs": [
+                            {
+                                "name": "output_exons",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "output_cds",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "output_pep",
+                                "type": "fasta"
+                            }
+                        ],
                         "position": {
-                            "left": 257,
-                            "top": 403.5
+                            "bottom": 1085.015625,
+                            "height": 272,
+                            "left": 2747.5,
+                            "right": 2947.5,
+                            "top": 813.015625,
+                            "width": 200,
+                            "x": 2747.5,
+                            "y": 813.015625
                         },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "13261ad4-770b-4728-9068-d9941d07abf7",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "69e0806b63a4",
+                            "name": "gffread",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"chr_replace\": {\"__class__\": \"RuntimeValue\"}, \"decode_url\": \"false\", \"expose\": \"false\", \"filtering\": null, \"full_gff_attribute_preservation\": \"false\", \"gffs\": {\"gff_fmt\": \"none\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"maxintron\": null, \"merging\": {\"merge_sel\": \"none\", \"__current_case__\": 0}, \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 2, \"genome_fasta\": {\"__class__\": \"ConnectedValue\"}, \"ref_filtering\": null, \"fa_outputs\": [\"-w exons.fa\", \"-x cds.fa\", \"-y pep.fa\"]}, \"region\": {\"region_filter\": \"none\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.2.1.2",
+                        "type": "tool",
+                        "uuid": "51674c8f-f50e-430f-b0ff-49b1b96887aa",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "3df15ab7-6fb7-4a90-81e9-f25868067b8e"
+                                "label": "Gffread: exons",
+                                "output_name": "output_exons",
+                                "uuid": "52fcac23-b612-4377-a19a-2e3b667a23e3"
+                            },
+                            {
+                                "label": "Gffread: translation of cds",
+                                "output_name": "output_pep",
+                                "uuid": "5c47c25e-0ddb-4ade-a5d0-873ff4add28c"
+                            },
+                            {
+                                "label": "Gffread: cds",
+                                "output_name": "output_cds",
+                                "uuid": "84d9183b-9589-464b-9f82-4dae7f87133e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/intermine_galaxy_exchange/galaxy_intermine_exchange/0.0.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
                         "errors": null,
-                        "id": 1,
+                        "id": 21,
                         "input_connections": {
-                            "input_tabular": {
-                                "id": 0,
+                            "gff": {
+                                "id": 18,
+                                "output_name": "renamed"
+                            },
+                            "ref_genome|genome": {
+                                "id": 2,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Genome annotation statistics",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool Create InterMine Interchange",
-                                "name": "input_tabular"
+                                "name": "summary",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "graphs",
+                                "type": "pdf"
                             }
                         ],
+                        "position": {
+                            "bottom": 1954.03125,
+                            "height": 272,
+                            "left": 2747.5,
+                            "right": 2947.5,
+                            "top": 1682.03125,
+                            "width": 200,
+                            "x": 2747.5,
+                            "y": 1682.03125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "8cffbd184762",
+                            "name": "jcvi_gff_stats",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"gff\": {\"__class__\": \"ConnectedValue\"}, \"ref_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.8.4",
+                        "type": "tool",
+                        "uuid": "d5c389a7-0746-49da-ad3d-e206b5506acc",
+                        "workflow_outputs": [
+                            {
+                                "label": "Genome annotation statistics: graphs (third round)",
+                                "output_name": "graphs",
+                                "uuid": "f5d4a6bf-1ff8-435a-8084-7921e25bff3a"
+                            },
+                            {
+                                "label": "Genome annotation statistics: summary (third round)",
+                                "output_name": "summary",
+                                "uuid": "5a863bd4-10f2-4ac8-81b6-ce8b7f663e42"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                        "errors": null,
+                        "id": 22,
+                        "input_connections": {
+                            "input": {
+                                "id": 20,
+                                "output_name": "output_exons"
+                            }
+                        },
+                        "inputs": [],
                         "label": null,
-                        "name": "Create InterMine Interchange",
+                        "name": "Busco",
                         "outputs": [
                             {
-                                "name": "intermine_output",
-                                "type": "intermine_tabular"
+                                "name": "busco_sum",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "busco_table",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "busco_missing",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 509,
-                            "top": 402.5
+                            "bottom": 1156.03125,
+                            "height": 252,
+                            "left": 3025.5,
+                            "right": 3225.5,
+                            "top": 904.03125,
+                            "width": 200,
+                            "x": 3025.5,
+                            "y": 904.03125
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/intermine_galaxy_exchange/galaxy_intermine_exchange/0.0.1",
+                        "post_job_actions": {
+                            "HideDatasetActionbusco_missing": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "busco_missing"
+                            },
+                            "HideDatasetActionbusco_table": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "busco_table"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
                         "tool_shed_repository": {
-                            "changeset_revision": "c24014d80001",
-                            "name": "intermine_galaxy_exchange",
+                            "changeset_revision": "602fb8e63aa7",
+                            "name": "busco",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"feature_id_column\": \"\\\"2\\\"\", \"feature_id_text\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"feature_column\": \"\\\"1\\\"\", \"input_tabular\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"feature_text\": \"\\\"Gene\\\"\", \"organism_text\": \"\\\"\\\"\", \"organism_column\": \"\\\"3\\\"\"}",
-                        "tool_version": "0.0.1",
+                        "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"tran\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.1.4",
                         "type": "tool",
-                        "uuid": "8e5e0134-7b2a-43c4-b1d4-4d4b62b6af3c",
+                        "uuid": "94dac116-5e62-487c-912a-a63ca53c17e7",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "intermine_output",
-                                "uuid": "bfa0f275-4aee-4d3f-8b7c-4e32e8cc9710"
+                                "label": "Busco summary final round",
+                                "output_name": "busco_sum",
+                                "uuid": "0bc78676-eecc-4168-894d-34c4ca07cdf3"
                             }
                         ]
                     }
                 ],
-                "parent_id": "galaxy-interface/intermine",
-                "path": "topics/galaxy-interface/tutorials/intermine/workflows/main_workflow.ga",
+                "parent_id": "genome-annotation/annotation-with-maker",
+                "path": "topics/genome-annotation/tutorials/annotation-with-maker/workflows/main_workflow.ga",
                 "tags": [
-                    "galaxy-interface"
+                    "genome-annotation"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Intermine import/export",
-                "topic_id": "galaxy-interface",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/galaxy-interface-intermine/versions/main-workflow",
-                "tutorial_id": "intermine",
-                "url": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/intermine/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/intermine/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "galaxy-interface-intermine",
+                "title": "Genome annotation with Maker ",
+                "topic_id": "genome-annotation",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-annotation-with-maker/versions/main-workflow",
+                "tutorial_id": "annotation-with-maker",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-maker/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-maker/workflows/main_workflow.html",
+                "version": 10,
+                "wfid": "genome-annotation-annotation-with-maker",
                 "wfname": "main-workflow",
                 "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/intermine_galaxy_exchange/galaxy_intermine_exchange/0.0.1"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.11",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1"
                 ],
-                "workflowhub_id": "1290"
+                "workflowhub_id": "1164"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/3407174"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.4406623"
     },
     {
-        "abbreviations": {
-            "SVs": "Structural Variations"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "flye",
+                    "name": "diamond",
                     "owner": "bgruening",
-                    "revisions": "cb8dfd28c16f",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "5ec9f6bceaee",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bandage",
-                    "owner": "iuc",
-                    "revisions": "ddddce450736",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bwa_mem2",
-                    "owner": "iuc",
-                    "revisions": "bfaa0d22c2e4",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastp",
-                    "owner": "iuc",
-                    "revisions": "65b93b623c77",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "filtlong",
-                    "owner": "iuc",
-                    "revisions": "8880fb74ef56",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "filtlong",
-                    "owner": "iuc",
-                    "revisions": "1f296803dfa3",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "nanoplot",
-                    "owner": "iuc",
-                    "revisions": "0f1c34698076",
-                    "tool_panel_section_label": "Nanopore",
+                    "revisions": "e8ac2b53f262",
+                    "tool_panel_section_label": "NCBI Blast",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "polypolish",
-                    "owner": "iuc",
-                    "revisions": "f355085dd2aa",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "name": "interproscan",
+                    "owner": "bgruening",
+                    "revisions": "74810db257cc",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "porechop",
-                    "owner": "iuc",
-                    "revisions": "93d623d9979c",
-                    "tool_panel_section_label": "Nanopore",
+                    "name": "ncbi_blast_plus",
+                    "owner": "devteam",
+                    "revisions": "0e3cf9594bb7",
+                    "tool_panel_section_label": "NCBI Blast",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "quast",
-                    "owner": "iuc",
-                    "revisions": "72472698a2df",
-                    "tool_panel_section_label": "Assembly",
+                    "name": "eggnog_mapper",
+                    "owner": "galaxyp",
+                    "revisions": "844fa988236b",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: flye\n  owner: bgruening\n  revisions: cb8dfd28c16f\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_mem2\n  owner: iuc\n  revisions: bfaa0d22c2e4\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filtlong\n  owner: iuc\n  revisions: 8880fb74ef56\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filtlong\n  owner: iuc\n  revisions: 1f296803dfa3\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: 0f1c34698076\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: polypolish\n  owner: iuc\n  revisions: f355085dd2aa\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: porechop\n  owner: iuc\n  revisions: 93d623d9979c\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 72472698a2df\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-nanopore/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: diamond\n  owner: bgruening\n  revisions: e8ac2b53f262\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: interproscan\n  owner: bgruening\n  revisions: 74810db257cc\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: 0e3cf9594bb7\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: eggnog_mapper\n  owner: galaxyp\n  revisions: 844fa988236b\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/functional/tutorial.json",
         "contributions": {
             "authorship": [
-                "bazante1",
-                "bebatut"
-            ],
-            "editing": [
-                "hexylena",
-                "bazante1",
-                "shiltemann",
-                "miaomiaozhou88"
+                "abretaud"
             ],
             "funding": [
-                "avans-atgm",
-                "abromics"
+                "gallantries",
+                "eurosciencegateway"
             ]
         },
         "contributors": [
-            {
-                "affiliations": [
-                    "avans-atgm"
-                ],
-                "id": "bazante1",
-                "joined": "2020-12",
-                "name": "Bazante Sanders",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
-                    "ifb",
+                    "eurosciencegateway",
                     "elixir-europe"
                 ],
                 "contact_for_training": true,
                 "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
                 "fediverse_flavor": "mastodon",
-                "id": "bebatut",
+                "id": "abretaud",
                 "joined": "2017-09",
-                "linkedin": "berenicebatut",
                 "location": {
                     "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "affiliations": [
-                    "avans-atgm"
-                ],
-                "id": "bazante1",
-                "joined": "2020-12",
-                "name": "Bazante Sanders",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
+                    "lat": 48.11,
+                    "lon": -1.64
                 },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
-            {
-                "email": "m.zhou1@avans.nl",
-                "id": "miaomiaozhou88",
-                "joined": "2020-12",
-                "name": "Miaomiao Zhou",
-                "orcid": "0000-0003-4426-1758",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/miaomiaozhou88/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/miaomiaozhou88.json"
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
             },
             {
-                "avatar": "/training-material/shared/images/logo-avans.png",
-                "former_members": [
-                    "dirowa",
-                    "hexylena"
-                ],
-                "id": "avans-atgm",
-                "joined": "2020-11",
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
                 "members": [
-                    "bazante1"
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
                 ],
-                "name": "Avans Hogeschool",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/",
-                "ror": "015d5s513",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             },
             {
-                "avatar": "/training-material/assets/images/abromics.png",
+                "avatar": "/training-material/assets/images/eurosciencegateway.png",
                 "funder": true,
+                "funding_id": "101057388",
+                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
+                "funding_system": "cordis",
                 "github": false,
-                "id": "abromics",
-                "joined": "2024-01",
-                "name": "ABRomics",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abromics/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/abromics.json"
+                "id": "eurosciencegateway",
+                "joined": "2023-10",
+                "members": [
+                    "abretaud",
+                    "anuprulez",
+                    "bgruening",
+                    "erxleben",
+                    "pauldg",
+                    "rlibouba"
+                ],
+                "name": "EuroScienceGateway",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
             }
         ],
-        "dir": "topics/assembly/tutorials/mrsa-nanopore",
-        "edam_ontology": [
-            "topic_0196",
-            "topic_3673",
-            "topic_3305",
-            "topic_0622",
-            "topic_3301",
-            "topic_4013"
-        ],
+        "dir": "topics/genome-annotation/tutorials/functional",
         "edam_operation": [
-            "Visualisation",
-            "Sequencing quality control",
-            "Sequence contamination filtering",
-            "Genome assembly",
-            "De-novo assembly",
-            "Sequence alignment",
-            "Box-Whisker plot plotting",
-            "Sequence assembly validation",
-            "Sequence composition calculation",
-            "Read mapping",
-            "Scatter plot plotting",
-            "Mapping assembly",
-            "Sequencing error detection",
-            "Sequence assembly visualisation",
-            "Cross-assembly",
-            "Filtering",
-            "Statistical calculation"
-        ],
-        "edam_topic": [
-            "Sequence assembly",
-            "Whole genome sequencing",
-            "Public health and epidemiology",
-            "Genomics",
-            "Microbiology",
-            "Antimicrobial Resistance"
+            "Fold recognition",
+            "Homology-based gene prediction",
+            "Genome annotation",
+            "Information extraction",
+            "Protein feature detection",
+            "Sequence motif recognition",
+            "Sequence alignment analysis",
+            "Query and retrieval"
         ],
+        "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "genome-annotation",
-                "tutorials": [
-                    "amr-gene-detection"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "history-to-workflow"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "assembly/mrsa-nanopore",
+        "id": "genome-annotation/functional",
         "inexact_supported_servers": [
-            "UseGalaxy.cz"
+            "UseGalaxy.no"
         ],
         "js_requirements": {
-            "mathjax": 11271,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Nanopore produces fantastic assemblies but with low quality data",
-            "Annotation with Prokka is very easy"
+            "EggNOG Mapper compares sequences to a database of annotated orthologous sequences",
+            "InterProScan detects known motifs in protein sequences"
         ],
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-13",
+        "mod_date": "2024-01-09",
         "objectives": [
-            "Run tools to evaluate sequencing data on quality and quantity",
-            "Process the output of quality control tools",
-            "Improve the quality of sequencing data",
-            "Run a tool to assemble a bacterial genome using short reads",
-            "Run tools to assess the quality of an assembly",
-            "Understand the outputs of tools to assess the quality of an assembly"
+            "Perform functional annotation using EggNOG-mapper and InterProScan"
         ],
-        "pageviews": 10571,
-        "pub_date": "2021-03-24",
+        "pageviews": 3511,
+        "priority": 6,
+        "pub_date": "2022-07-20",
         "questions": [
-            "How to check the quality of the MinION data (together with Illumina data)?",
-            "How to perform an assembly of a bacterial genome with MinION data?",
-            "How to check the quality of an assembly?"
+            "How to perform functional annotation on protein sequences?"
         ],
-        "short_id": "T00037",
+        "short_id": "T00173",
         "short_tools": [
-            "nanoplot",
-            "fastp",
-            "CONVERTER_bz2_to_uncompressed",
-            "filtlong",
-            "flye",
-            "bwa_mem2",
-            "quast",
-            "fastqc",
-            "polypolish",
-            "bandage_image",
-            "upload1",
-            "porechop"
+            "ncbi_blastp_wrapper",
+            "eggnog_mapper",
+            "interproscan",
+            "bg_diamond"
         ],
         "slides": false,
         "slides_recordings": false,
+        "subtopic": "eukaryote",
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ],
             "inexact": [
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 }
             ]
         },
         "symlink": null,
         "tags": [
-            "nanopore",
-            "assembly",
-            "amr",
-            "gmod",
-            "jbrowse1",
-            "microgalaxy"
+            "eukaryote"
         ],
-        "time_estimation": "2h",
-        "title": "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)",
+        "time_estimation": "1h",
+        "title": "Functional annotation of protein sequences",
         "tools": [
-            "CONVERTER_bz2_to_uncompressed",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/polypolish/polypolish/0.5.0+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
-            "upload1"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/2.10.1+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3"
         ],
-        "topic_name": "assembly",
-        "topic_name_human": "Assembly",
+        "topic_name": "genome-annotation",
+        "topic_name_human": "Genome Annotation",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "mrsa-nanopore",
+        "tutorial_name": "functional",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/functional/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-nanopore/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-nanopore/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/functional/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/functional/tutorial.json"
         },
-        "version": 14,
+        "version": 9,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 206,
-        "visitors": 6851,
+        "visit_duration": 103,
+        "visitors": 2405,
         "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "https://orcid.org/0000-0003-2255-1631",
-                        "name": "Bazante Sanders"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0001-9852-1987",
-                        "name": "B\u00e9r\u00e9nice Batut"
+                        "identifier": "https://orcid.org/0000-0003-0914-2470",
+                        "name": "Anthony Bretaudeau"
                     }
                 ],
-                "description": "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)",
+                "description": "Functional annotation of protein sequences",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nNanopore raw reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina forward raw reads\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reverse raw reads\"]\n  3[label=\"Convert compressed file to uncompressed.\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"FastQC\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"fastp\"]\n  1 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"NanoPlot\"]\n  3 -> 6 [label=\"output1\"]\n  ka97e6f3381824a3386dd6cfbb83a842d[color=lightseagreen,label=\"Output\\nnanoplot_before_filtering\"]\n  6 -> ka97e6f3381824a3386dd6cfbb83a842d\n  7[label=\"filtlong\"]\n  5 -> 7 [label=\"out1\"]\n  5 -> 7 [label=\"out2\"]\n  0 -> 7 [label=\"output\"]\n  8[label=\"Flye\"]\n  7 -> 8 [label=\"outfile\"]\n  kf12e718f1bd5490dbd41f0747aaa41a6[color=lightseagreen,label=\"Output\\nflye_assembly_info\"]\n  8 -> kf12e718f1bd5490dbd41f0747aaa41a6\n  9[label=\"NanoPlot\"]\n  7 -> 9 [label=\"outfile\"]\n  k89524090f590434d89e266f0b1a23c7c[color=lightseagreen,label=\"Output\\nnanoplot_after_filtering\"]\n  9 -> k89524090f590434d89e266f0b1a23c7c\n  10[label=\"Bandage Image\"]\n  8 -> 10 [label=\"assembly_gfa\"]\n  11[label=\"BWA-MEM2\"]\n  5 -> 11 [label=\"out2\"]\n  8 -> 11 [label=\"consensus\"]\n  12[label=\"Quast\"]\n  8 -> 12 [label=\"consensus\"]\n  kdabfb8fd87914959a9dc9b3c1e57a69c[color=lightseagreen,label=\"Output\\nquast_report_before_polishing\"]\n  12 -> kdabfb8fd87914959a9dc9b3c1e57a69c\n  13[label=\"BWA-MEM2\"]\n  5 -> 13 [label=\"out1\"]\n  8 -> 13 [label=\"consensus\"]\n  14[label=\"Polypolish\"]\n  8 -> 14 [label=\"consensus\"]\n  13 -> 14 [label=\"bam_output\"]\n  11 -> 14 [label=\"bam_output\"]\n  15[label=\"Quast\"]\n  14 -> 15 [label=\"polished_fasta\"]\n  8 -> 15 [label=\"consensus\"]\n  k4e465b5168bf42039a7c897f46c70277[color=lightseagreen,label=\"Output\\nquast_report_after_polishing\"]\n  15 -> k4e465b5168bf42039a7c897f46c70277\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nProtein sequences\"]\n  1[label=\"eggNOG Mapper\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"InterProScan\"]\n  0 -> 2 [label=\"output\"]\n}",
                 "history": [
                     {
-                        "hash": "96393a7fcb4d6dc37d86866cf8a61c931293502f",
-                        "message": "Add MRSA Nanopore assembly tutorial to AMR learning pathway",
+                        "hash": "f618c506c91dba9edce85bd76d1fb1d4a1c45eda",
+                        "message": "rename wf",
                         "num": 1,
-                        "short_hash": "96393a7fc",
-                        "unix": "1709135526"
+                        "short_hash": "f618c506c",
+                        "unix": "1683023161"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "Nanopore raw reads",
+                        "annotation": "Some protein sequences to functionally annotate",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Nanopore raw reads",
-                                "name": "Nanopore raw reads"
-                            }
-                        ],
-                        "label": "Nanopore raw reads",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 65.66800632871802,
-                            "top": 217.27323322511424
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "cd4fd302-af94-4771-9b80-7c7acb6619d4",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "Illumina forward raw reads",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Illumina forward raw reads",
-                                "name": "Illumina forward raw reads"
-                            }
-                        ],
-                        "label": "Illumina forward raw reads",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 479
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "b3fe89da-544c-4066-abcb-b33d4f005796",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "Illumina reverse raw reads",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Illumina reverse raw reads",
-                                "name": "Illumina reverse raw reads"
+                                "description": "Some protein sequences to functionally annotate",
+                                "name": "Protein sequences"
                             }
                         ],
-                        "label": "Illumina reverse raw reads",
+                        "label": "Protein sequences",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 602
+                            "bottom": 315.5999984741211,
+                            "height": 65.76666259765625,
+                            "left": 726.3958740234375,
+                            "right": 886.3958740234375,
+                            "top": 249.83333587646484,
+                            "width": 160,
+                            "x": 726.3958740234375,
+                            "y": 249.83333587646484
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "16545abc-0513-4a32-9ea5-4a168875a854",
-                        "when": null,
+                        "uuid": "abb56aaf-5988-4fb8-a68f-0edaee00f445",
                         "workflow_outputs": []
                     }
                 ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nNanopore raw reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nIllumina forward raw reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nIllumina reverse raw reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Convert compressed file to uncompressed.\"];\n  0 -->|output| 3;\n  4[\"FastQC\"];\n  0 -->|output| 4;\n  5[\"fastp\"];\n  1 -->|output| 5;\n  2 -->|output| 5;\n  6[\"NanoPlot\"];\n  3 -->|output1| 6;\n  a97e6f33-8182-4a33-86dd-6cfbb83a842d[\"Output\\nnanoplot_before_filtering\"];\n  6 --> a97e6f33-8182-4a33-86dd-6cfbb83a842d;\n  style a97e6f33-8182-4a33-86dd-6cfbb83a842d stroke:#2c3143,stroke-width:4px;\n  7[\"filtlong\"];\n  5 -->|out1| 7;\n  5 -->|out2| 7;\n  0 -->|output| 7;\n  8[\"Flye\"];\n  7 -->|outfile| 8;\n  f12e718f-1bd5-490d-bd41-f0747aaa41a6[\"Output\\nflye_assembly_info\"];\n  8 --> f12e718f-1bd5-490d-bd41-f0747aaa41a6;\n  style f12e718f-1bd5-490d-bd41-f0747aaa41a6 stroke:#2c3143,stroke-width:4px;\n  9[\"NanoPlot\"];\n  7 -->|outfile| 9;\n  89524090-f590-434d-89e2-66f0b1a23c7c[\"Output\\nnanoplot_after_filtering\"];\n  9 --> 89524090-f590-434d-89e2-66f0b1a23c7c;\n  style 89524090-f590-434d-89e2-66f0b1a23c7c stroke:#2c3143,stroke-width:4px;\n  10[\"Bandage Image\"];\n  8 -->|assembly_gfa| 10;\n  11[\"BWA-MEM2\"];\n  5 -->|out2| 11;\n  8 -->|consensus| 11;\n  12[\"Quast\"];\n  8 -->|consensus| 12;\n  dabfb8fd-8791-4959-a9dc-9b3c1e57a69c[\"Output\\nquast_report_before_polishing\"];\n  12 --> dabfb8fd-8791-4959-a9dc-9b3c1e57a69c;\n  style dabfb8fd-8791-4959-a9dc-9b3c1e57a69c stroke:#2c3143,stroke-width:4px;\n  13[\"BWA-MEM2\"];\n  5 -->|out1| 13;\n  8 -->|consensus| 13;\n  14[\"Polypolish\"];\n  8 -->|consensus| 14;\n  13 -->|bam_output| 14;\n  11 -->|bam_output| 14;\n  15[\"Quast\"];\n  14 -->|polished_fasta| 15;\n  8 -->|consensus| 15;\n  4e465b51-68bf-4203-9a7c-897f46c70277[\"Output\\nquast_report_after_polishing\"];\n  15 --> 4e465b51-68bf-4203-9a7c-897f46c70277;\n  style 4e465b51-68bf-4203-9a7c-897f46c70277 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available)",
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nProtein sequences\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"eggNOG Mapper\"];\n  0 -->|output| 1;\n  2[\"InterProScan\"];\n  0 -->|output| 2;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Functional annotation",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
                         "errors": null,
-                        "id": 6,
+                        "id": 1,
                         "input_connections": {
-                            "mode|reads|files": {
-                                "id": 3,
-                                "output_name": "output1"
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool eggNOG Mapper",
+                                "name": "input"
+                            }
+                        ],
                         "label": null,
-                        "name": "NanoPlot",
+                        "name": "eggNOG Mapper",
                         "outputs": [
                             {
-                                "name": "output_html",
-                                "type": "html"
-                            },
-                            {
-                                "name": "nanostats",
+                                "name": "seed_orthologs",
                                 "type": "tabular"
                             },
                             {
-                                "name": "nanostats_post_filtering",
+                                "name": "annotations",
                                 "type": "tabular"
-                            },
-                            {
-                                "name": "read_length",
-                                "type": "png"
-                            },
-                            {
-                                "name": "log_read_length",
-                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 598.8807084399002,
-                            "top": 268.83097889129806
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "0f1c34698076",
-                            "name": "nanoplot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"customization\": {\"color\": null, \"plots\": null, \"N50\": true}, \"filter\": {\"maxlength\": null, \"minlength\": null, \"drop_outliers\": false, \"downsample\": null, \"loglength\": false, \"percentqual\": false, \"alength\": false, \"minqual\": null, \"runtime_until\": null, \"readtype\": null, \"barcoded\": false, \"no_supplementary\": false}, \"mode\": {\"choice\": \"batch\", \"__current_case__\": 0, \"reads\": {\"type\": \"fastq\", \"__current_case__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.41.0+galaxy0",
-                        "type": "tool",
-                        "uuid": "ad46f297-04f2-4959-aa09-db88cd91cc27",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "nanoplot_before_filtering",
-                                "output_name": "nanostats",
-                                "uuid": "a97e6f33-8182-4a33-86dd-6cfbb83a842d"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "inputs": {
-                                "id": 7,
-                                "output_name": "outfile"
-                            }
+                            "bottom": 435.17499923706055,
+                            "height": 196.8000030517578,
+                            "left": 1194.4791412353516,
+                            "right": 1354.4791412353516,
+                            "top": 238.37499618530273,
+                            "width": 160,
+                            "x": 1194.4791412353516,
+                            "y": 238.37499618530273
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Flye",
-                        "outputs": [
-                            {
-                                "name": "consensus",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "assembly_graph",
-                                "type": "graph_dot"
-                            },
-                            {
-                                "name": "assembly_gfa",
-                                "type": "txt"
+                        "post_job_actions": {
+                            "HideDatasetActionseed_orthologs": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "seed_orthologs"
                             },
-                            {
-                                "name": "assembly_info",
-                                "type": "tabular"
+                            "RenameDatasetActionannotations": {
+                                "action_arguments": {
+                                    "newname": "EggNOG Mapper annotations"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "annotations"
                             }
-                        ],
-                        "position": {
-                            "left": 850.0098909589506,
-                            "top": 593
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
                         "tool_shed_repository": {
-                            "changeset_revision": "cb8dfd28c16f",
-                            "name": "flye",
-                            "owner": "bgruening",
+                            "changeset_revision": "5a30ae278db0",
+                            "name": "eggnog_mapper",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"asm\": {\"asm_select\": \"false\", \"__current_case__\": 1}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"generate_log\": false, \"inputs\": {\"__class__\": \"ConnectedValue\"}, \"iterations\": \"1\", \"keep_haplotypes\": false, \"meta\": false, \"min_overlap\": null, \"mode_conditional\": {\"mode\": \"--nano-corr\", \"__current_case__\": 1}, \"no_alt_contigs\": false, \"scaffold\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.9.1+galaxy0",
+                        "tool_state": "{\"annotation_options\": {\"tax_scope\": null, \"target_orthologs\": \"all\", \"go_evidence\": \"non-electronic\"}, \"eggnog_data\": \"5.0.2\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"input_trans\": {\"itype\": \"proteins\", \"__current_case__\": 0}, \"output_options\": {\"no_file_comments\": \"false\", \"no_annot\": \"false\", \"report_orthologs\": \"false\"}, \"seed_ortho_options\": {\"ortho_method\": {\"m\": \"diamond\", \"__current_case__\": 0, \"matrix_gapcosts\": {\"matrix\": \"BLOSUM62\", \"__current_case__\": 2, \"gap_costs\": \"--gapopen 11 --gapextend 1\"}, \"sensmode\": \"sensitive\", \"dmnd_iterate\": \"false\", \"dmnd_ignore_warnings\": \"false\"}, \"query_cover\": null, \"subject_cover\": null, \"pident\": null}, \"seed_ortholog_options\": {\"seed_ortholog_evalue\": \"0.001\", \"seed_ortholog_score\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.8+galaxy3",
                         "type": "tool",
-                        "uuid": "8cf7ff30-4007-49cb-a959-e25c337f05be",
-                        "when": null,
+                        "uuid": "0d9f93f0-88b3-406b-b8f9-ecb2d74c61e9",
                         "workflow_outputs": [
                             {
-                                "label": "flye_assembly_info",
-                                "output_name": "assembly_info",
-                                "uuid": "f12e718f-1bd5-490d-bd41-f0747aaa41a6"
+                                "label": null,
+                                "output_name": "annotations",
+                                "uuid": "bc64d801-036f-4608-8ba1-74f16fddb574"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
                         "errors": null,
-                        "id": 9,
+                        "id": 2,
                         "input_connections": {
-                            "mode|reads|files": {
-                                "id": 7,
-                                "output_name": "outfile"
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "NanoPlot",
-                        "outputs": [
-                            {
-                                "name": "output_html",
-                                "type": "html"
-                            },
-                            {
-                                "name": "nanostats",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "nanostats_post_filtering",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "read_length",
-                                "type": "png"
-                            },
+                        "inputs": [
                             {
-                                "name": "log_read_length",
-                                "type": "png"
+                                "description": "runtime parameter for tool InterProScan",
+                                "name": "input"
                             }
                         ],
-                        "position": {
-                            "left": 850.0098909589506,
-                            "top": 859
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "0f1c34698076",
-                            "name": "nanoplot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"customization\": {\"color\": null, \"plots\": null, \"N50\": true}, \"filter\": {\"maxlength\": null, \"minlength\": null, \"drop_outliers\": false, \"downsample\": null, \"loglength\": false, \"percentqual\": false, \"alength\": false, \"minqual\": null, \"runtime_until\": null, \"readtype\": null, \"barcoded\": false, \"no_supplementary\": false}, \"mode\": {\"choice\": \"batch\", \"__current_case__\": 0, \"reads\": {\"type\": \"fastq\", \"__current_case__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.41.0+galaxy0",
-                        "type": "tool",
-                        "uuid": "467fca53-715f-4717-ab4c-c4410d321086",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "nanoplot_after_filtering",
-                                "output_name": "nanostats",
-                                "uuid": "89524090-f590-434d-89e2-66f0b1a23c7c"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
-                        "errors": null,
-                        "id": 12,
-                        "input_connections": {
-                            "mode|in|inputs": {
-                                "id": 8,
-                                "output_name": "consensus"
-                            }
-                        },
-                        "inputs": [],
                         "label": null,
-                        "name": "Quast",
+                        "name": "InterProScan",
                         "outputs": [
                             {
-                                "name": "report_html",
-                                "type": "html"
+                                "name": "outfile_tsv",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "outfile_xml",
+                                "type": "xml"
                             }
                         ],
                         "position": {
-                            "left": 1140.0069535390257,
-                            "top": 767
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "72472698a2df",
-                            "name": "quast",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 646.2666473388672,
+                            "height": 131.51666259765625,
+                            "left": 1197.1041870117188,
+                            "right": 1357.1041870117188,
+                            "top": 514.7499847412109,
+                            "width": 160,
+                            "x": 1197.1041870117188,
+                            "y": 514.7499847412109
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"false\", \"__current_case__\": 1, \"est_ref_size\": null}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": false}, \"large\": false, \"min_contig\": \"500\", \"mode\": {\"mode\": \"co\", \"__current_case__\": 1, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": \"html\", \"split_scaffolds\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.2.0+galaxy1",
-                        "type": "tool",
-                        "uuid": "6949cf20-419e-4cee-86fa-3b08ab60cb9f",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "quast_report_before_polishing",
-                                "output_name": "report_html",
-                                "uuid": "dabfb8fd-8791-4959-a9dc-9b3c1e57a69c"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
-                        "errors": null,
-                        "id": 15,
-                        "input_connections": {
-                            "mode|in|inputs": [
-                                {
-                                    "id": 14,
-                                    "output_name": "polished_fasta"
+                        "post_job_actions": {
+                            "HideDatasetActionoutfile_xml": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "outfile_xml"
+                            },
+                            "RenameDatasetActionoutfile_tsv": {
+                                "action_arguments": {
+                                    "newname": "InterProScan annotations (tsv)"
                                 },
-                                {
-                                    "id": 8,
-                                    "output_name": "consensus"
-                                }
-                            ]
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Quast",
-                        "outputs": [
-                            {
-                                "name": "report_html",
-                                "type": "html"
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "outfile_tsv"
                             }
-                        ],
-                        "position": {
-                            "left": 1700.001078699176,
-                            "top": 853
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
                         "tool_shed_repository": {
-                            "changeset_revision": "72472698a2df",
-                            "name": "quast",
-                            "owner": "iuc",
+                            "changeset_revision": "98cafcbd2578",
+                            "name": "interproscan",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"false\", \"__current_case__\": 1, \"est_ref_size\": null}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": false}, \"large\": false, \"min_contig\": \"500\", \"mode\": {\"mode\": \"co\", \"__current_case__\": 1, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": \"html\", \"split_scaffolds\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.2.0+galaxy1",
+                        "tool_state": "{\"applications\": [\"TIGRFAM\", \"SFLD\", \"SUPERFAMILY\", \"PANTHER\", \"Gene3D\", \"Hamap\", \"PrositeProfiles\", \"Coils\", \"SMART\", \"CDD\", \"PRINTS\", \"PIRSR\", \"PrositePatterns\", \"Pfam\", \"MobiDBLite\", \"PIRSF\"], \"database\": \"5.59-91.0\", \"goterms\": \"true\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"iprlookup\": \"false\", \"licensed\": {\"use\": \"true\", \"__current_case__\": 1, \"applications_licensed\": [\"Phobius\", \"SignalP_EUK\", \"TMHMM\"]}, \"oformat\": [\"TSV\", \"XML\"], \"pathways\": \"true\", \"seqtype\": \"p\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.59-91.0+galaxy3",
                         "type": "tool",
-                        "uuid": "866187e0-dd7c-40d5-b121-a8ef4a281c80",
-                        "when": null,
+                        "uuid": "cb7a1910-3c31-47d9-835b-f1bd16a1c3ff",
                         "workflow_outputs": [
                             {
-                                "label": "quast_report_after_polishing",
-                                "output_name": "report_html",
-                                "uuid": "4e465b51-68bf-4203-9a7c-897f46c70277"
+                                "label": null,
+                                "output_name": "outfile_tsv",
+                                "uuid": "b5a0e608-3bed-4fb2-9d47-d6bd521aee14"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/mrsa-nanopore",
-                "path": "topics/assembly/tutorials/mrsa-nanopore/workflows/main-workflow.ga",
+                "parent_id": "genome-annotation/functional",
+                "path": "topics/genome-annotation/tutorials/functional/workflows/functional.ga",
                 "tags": [
-                    "Assembly"
+                    "genome-annotation"
                 ],
                 "test_results": null,
                 "tests": true,
-                "title": "Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available)",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-mrsa-nanopore/versions/main-workflow",
-                "tutorial_id": "mrsa-nanopore",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/mrsa-nanopore/workflows/main-workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/mrsa-nanopore/workflows/main-workflow.html",
+                "title": "Functional annotation",
+                "topic_id": "genome-annotation",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-functional/versions/functional",
+                "tutorial_id": "functional",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/functional/workflows/functional.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/functional/workflows/functional.html",
                 "version": 1,
-                "wfid": "assembly-mrsa-nanopore",
-                "wfname": "main-workflow",
-                "workflow": "main-workflow.ga",
+                "wfid": "genome-annotation-functional",
+                "wfname": "functional",
+                "workflow": "functional.ga",
                 "workflow_tools": [
-                    "CONVERTER_bz2_to_uncompressed",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/polypolish/polypolish/0.5.0+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3"
                 ],
-                "workflowhub_id": "1178"
+                "workflowhub_id": "1183"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/10669812"
+        "zenodo_link": "https://zenodo.org/record/6861851"
     },
     {
+        "abbreviations": {
+            "OGS": "Official Gene Set"
+        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "ddf54b12c295",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "apollo_create_or_update",
+                    "owner": "gga",
+                    "revisions": "4abaab60f9e1",
+                    "tool_panel_section_label": "Apollo",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "apollo_iframe",
+                    "owner": "gga",
+                    "revisions": "f4e3f9480307",
+                    "tool_panel_section_label": "Apollo",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "jbrowse",
+                    "owner": "iuc",
+                    "revisions": "a6e57ff585c0",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: apollo_create_or_update\n  owner: gga\n  revisions: 4abaab60f9e1\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: apollo_iframe\n  owner: gga\n  revisions: f4e3f9480307\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo-euk/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "abretaud"
+            ],
+            "funding": [
+                "gallantries",
+                "eurosciencegateway"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "eurosciencegateway",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
+                "fediverse_flavor": "mastodon",
+                "id": "abretaud",
+                "joined": "2017-09",
+                "location": {
+                    "country": "FR",
+                    "lat": 48.11,
+                    "lon": -1.64
                 },
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/eurosciencegateway.png",
+                "funder": true,
+                "funding_id": "101057388",
+                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "eurosciencegateway",
+                "joined": "2023-10",
+                "members": [
+                    "abretaud",
+                    "anuprulez",
+                    "bgruening",
+                    "erxleben",
+                    "pauldg",
+                    "rlibouba"
+                ],
+                "name": "EuroScienceGateway",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
+            }
+        ],
+        "dir": "topics/genome-annotation/tutorials/apollo-euk",
+        "edam_operation": [
+            "Genome visualisation"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.no"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "genome-annotation/apollo-euk",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.eu"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Apollo is the Google Docs of the genome annotation world, real-time collaborative genome annotation.",
+            "Apollo allows a group to view and manually refine predicted genome annotations",
+            "Use Apollo to edit annotations within your group.",
+            "Export manual annotations as GFF3."
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-02-29",
+        "objectives": [
+            "Load a genome into Galaxy",
+            "View annotations in JBrowse",
+            "Learn how to load JBrowse data into Apollo",
+            "Learn how to manually refine genome annotations within Apollo",
+            "Export refined genome annotations"
+        ],
+        "pageviews": 1584,
+        "priority": 6,
+        "pub_date": "2022-08-22",
+        "questions": [
+            "How to visualize your genome after automated annotations have been performed?",
+            "How to manually annotate genome after automated annotations have been performed?",
+            "How to evaluate and visualize annotated genomic features?",
+            "How do I collaborate when doing genome annotation?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "upload-rules"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "genome-annotation",
+                "tutorials": [
+                    "funannotate"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00170",
+        "short_tools": [
+            "jbrowse",
+            "create_or_update",
+            "iframe"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "eukaryote",
+        "supported_servers": {
+            "exact": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                }
+            ],
+            "inexact": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "gmod",
+            "eukaryote",
+            "cyoa",
+            "jbrowse1",
+            "apollo2"
+        ],
+        "time_estimation": "3h",
+        "title": "Refining Genome Annotations with Apollo (eukaryotes)",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
+            "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1"
+        ],
+        "topic_name": "genome-annotation",
+        "topic_name_human": "Genome Annotation",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "apollo-euk",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo-euk/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo-euk/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo-euk/tutorial.json"
+        },
+        "version": 13,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 156,
+        "visitors": 900,
+        "zenodo_link": "https://zenodo.org/record/3270822"
+    },
+    {
+        "abbreviations": {
+            "LncRNAs": "Long non-coding RNAs",
+            "lncRNAs": "long non-coding RNAs",
+            "mRNAs": "Messenger RNAs"
+        },
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
@@ -110553,694 +112111,814 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "add_value",
-                    "owner": "devteam",
-                    "revisions": "745871c0b055",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_compute_length",
-                    "owner": "devteam",
-                    "revisions": "de2db1bdfbf8",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_filter_by_length",
-                    "owner": "devteam",
-                    "revisions": "e626b3ff9922",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_filter_by_length",
-                    "owner": "devteam",
-                    "revisions": "8cacfcf96a52",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "lastz",
+                    "name": "gffread",
                     "owner": "devteam",
-                    "revisions": "e7f19d6a9af8",
-                    "tool_panel_section_label": "Mapping",
+                    "revisions": "154d00cbbf2d",
+                    "tool_panel_section_label": "Convert Formats",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "merge_cols",
+                    "name": "gffread",
                     "owner": "devteam",
-                    "revisions": "f2aac0c5c60d",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bedtools",
-                    "owner": "iuc",
-                    "revisions": "e19bebe96cd2",
-                    "tool_panel_section_label": "BED",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bedtools",
-                    "owner": "iuc",
-                    "revisions": "e19bebe96cd2",
-                    "tool_panel_section_label": "BED",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bedtools",
-                    "owner": "iuc",
-                    "revisions": "e19bebe96cd2",
-                    "tool_panel_section_label": "BED",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "circos",
-                    "owner": "iuc",
-                    "revisions": "df7356989ac1",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "circos",
-                    "owner": "iuc",
-                    "revisions": "df7356989ac1",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "revisions": "3e436657dcd0",
+                    "tool_panel_section_label": "Convert Formats",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "datamash_ops",
+                    "name": "feelnc",
                     "owner": "iuc",
-                    "revisions": "562f3c677828",
-                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "revisions": "67af24676bd6",
+                    "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "jbrowse",
+                    "name": "stringtie",
                     "owner": "iuc",
-                    "revisions": "fd5dbf0f732e",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "25136a2b0cfe",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "830961c48e42",
-                    "tool_panel_section_label": "Collection Operations",
+                    "revisions": "eba36e001f45",
+                    "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: ddf54b12c295\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: add_value\n  owner: devteam\n  revisions: 745871c0b055\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_compute_length\n  owner: devteam\n  revisions: de2db1bdfbf8\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_filter_by_length\n  owner: devteam\n  revisions: e626b3ff9922\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_filter_by_length\n  owner: devteam\n  revisions: 8cacfcf96a52\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lastz\n  owner: devteam\n  revisions: e7f19d6a9af8\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merge_cols\n  owner: devteam\n  revisions: f2aac0c5c60d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: e19bebe96cd2\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: e19bebe96cd2\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: e19bebe96cd2\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: circos\n  owner: iuc\n  revisions: df7356989ac1\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: circos\n  owner: iuc\n  revisions: df7356989ac1\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 562f3c677828\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: fd5dbf0f732e\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 25136a2b0cfe\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ecoli_comparison/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gffread\n  owner: devteam\n  revisions: 154d00cbbf2d\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gffread\n  owner: devteam\n  revisions: 3e436657dcd0\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: feelnc\n  owner: iuc\n  revisions: 67af24676bd6\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stringtie\n  owner: iuc\n  revisions: eba36e001f45\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/lncrna/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "stephanierobin"
+            ],
+            "editing": [
+                "abretaud"
+            ]
+        },
         "contributors": [
             {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
-                "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
-            },
-            {
-                "email": "delphine.lariviere@galaxy.org",
-                "id": "delphine-l",
-                "joined": "2017-09",
-                "name": "Delphine Lariviere",
-                "orcid": "0000-0001-6421-3484",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
+                "email": "stephanie.robin@inrae.fr",
+                "id": "stephanierobin",
+                "joined": "2021-11",
+                "name": "St\u00e9phanie Robin",
+                "orcid": "0000-0001-7379-9173",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/",
+                "twitter": "robinstphanie1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/stephanierobin.json"
             },
             {
                 "affiliations": [
                     "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
+                    "eurosciencegateway",
+                    "elixir-europe"
                 ],
-                "id": "hexylena",
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
+                "fediverse_flavor": "mastodon",
+                "id": "abretaud",
                 "joined": "2017-09",
                 "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
+                    "country": "FR",
+                    "lat": 48.11,
+                    "lon": -1.64
                 },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
             }
         ],
-        "dir": "topics/assembly/tutorials/ecoli_comparison",
-        "edam_ontology": [
-            "topic_0196",
-            "topic_0622",
-            "topic_3301"
-        ],
+        "dir": "topics/genome-annotation/tutorials/lncrna",
         "edam_operation": [
-            "Genome visualisation",
-            "Sequence alignment",
-            "Mapping",
-            "Read mapping",
-            "Sequence visualisation"
-        ],
-        "edam_topic": [
-            "Sequence assembly",
-            "Genomics",
-            "Microbiology"
+            "Sequence annotation",
+            "Classification",
+            "Transcriptome assembly",
+            "Annotation",
+            "RNA-Seq analysis"
         ],
+        "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "assembly/ecoli_comparison",
-        "inexact_supported_servers": [],
+        "id": "genome-annotation/lncrna",
+        "inexact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "We learned how to download large sets of completed genomes from NCBI",
-            "We learned how to use Galaxy's rule-based collection builder",
-            "We learned how to use a combination of Galaxy tools to create complex views of genome comparisons",
-            "We learned about idiosyncrasies of data formats and how to deal with them using Galaxy tools"
+            "StringTie allows to perform a transcriptome assembly using mapped RNASeq data and provides an annotation file containing trancripts description.",
+            "FEELnc pipeline allows to perform annotation of long non-coding RNAs (lncRNAs).",
+            "Annotation is based on reconstructed transcripts from RNA-seq data (either with or without a reference genome)",
+            "Annotation can be performed without any training set of non-coding RNAs.",
+            "FEELnc provides the localisation and the direction of transcription of proximal RNA transcripts of lncRNAs."
         ],
         "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-24",
+        "mod_date": "2024-09-18",
         "objectives": [
-            "Identification of the most closely related genome to my new assembly",
-            "Perform sequence comparison to locate rearrangements",
-            "Identify genes located in deletions"
+            "Load data (genome assembly, annotation and mapped RNASeq) into Galaxy",
+            "Perform a transcriptome assembly with StringTie",
+            "Annotate lncRNAs with FEELnc",
+            "Classify lncRNAs according to their location",
+            "Update genome annotation with lncRNAs"
         ],
-        "pageviews": 12067,
-        "pub_date": "2018-06-14",
+        "pageviews": 1367,
+        "priority": 7,
+        "pub_date": "2022-09-23",
         "questions": [
-            "I just assembled a genome. How does it compare with already sequenced genomes?",
-            "How do I find rearranged, inserted, or deleted regions?"
+            "How to annotate lncRNAs with FEELnc?",
+            "How to classify lncRNAs according to their localisation and direction of transcription of proximal RNA transcripts?",
+            "How to update genome annotation with these annotated lncRNAs?"
+        ],
+        "recordings": [
+            {
+                "bot-timestamp": 1726077703,
+                "captioners": [
+                    "stephanierobin",
+                    "abretaud"
+                ],
+                "date": "2024-09-11",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "11M",
+                "speakers": [
+                    "rlibouba"
+                ],
+                "youtube_id": "U5WZMWd-3kk"
+            }
         ],
         "requirements": [
             {
-                "topic_name": "assembly",
+                "topic_name": "genome-annotation",
                 "tutorials": [
-                    "unicycler-assembly"
+                    "funannotate"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00032",
+        "short_id": "T00177",
         "short_tools": [
-            "circos",
-            "lastz_wrapper_2",
-            "random_lines1",
-            "Cut1",
-            "circos_interval_to_tiles",
-            "addValue",
-            "collapse_dataset",
-            "Grep1",
-            "datamash_ops",
-            "bedtools_sortbed",
-            "tp_sort_header_tool",
-            "bedtools_complementbed",
-            "tp_replace_in_column",
-            "circos_aln_to_links",
-            "cat1",
             "tp_cat",
-            "fasta_filter_by_length",
-            "Filter1",
-            "tp_sed_tool",
-            "fasta_compute_length",
-            "tp_replace_in_line",
-            "join1",
-            "upload1",
-            "jbrowse",
-            "bedtools_intersectbed",
-            "tp_grep_tool",
-            "mergeCols1"
+            "Extract_features1",
+            "stringtie",
+            "feelnc",
+            "gffread"
         ],
         "slides": false,
         "slides_recordings": false,
+        "subtopic": "eukaryote",
         "supported_servers": {
             "exact": [],
-            "inexact": []
+            "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
         },
         "symlink": null,
         "tags": [
-            "gmod",
-            "prokaryote",
-            "microgalaxy",
-            "jbrowse1"
+            "eukaryote"
         ],
-        "time_estimation": "4h",
-        "title": "Making sense of a newly assembled genome",
+        "time_estimation": "2h",
+        "title": "Long non-coding RNAs (lncRNAs) annotation with FEELnc",
         "tools": [
-            "Cut1",
-            "Filter1",
-            "Grep1",
-            "cat1",
-            "join1",
-            "random_lines1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.27.0.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.0.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7",
-            "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7",
-            "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tiles/0.69.8+galaxy7",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.8+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
-            "upload1"
+            "Extract_features1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/1.0.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/feelnc/feelnc/0.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/feelnc/feelnc/0.2.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.6",
+            "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy1"
         ],
-        "topic_name": "assembly",
-        "topic_name_human": "Assembly",
+        "topic_name": "genome-annotation",
+        "topic_name_human": "Genome Annotation",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "ecoli_comparison",
+        "tutorial_name": "lncrna",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/lncrna/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ecoli_comparison/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ecoli_comparison/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/lncrna/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/lncrna/tutorial.json"
         },
-        "version": 29,
+        "version": 11,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 182,
-        "visitors": 5938,
+        "visit_duration": 122,
+        "visitors": 1008,
         "workflows": [
             {
-                "creators": [],
-                "description": "Making sense of a newly assembled genome",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0001-7379-9173",
+                        "name": "St\u00e9phanie Robin"
+                    }
+                ],
+                "description": "Long non-coding RNAs (lncRNAs) annotation with FEELnc",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  10[label=\"Collapse Collection\"]\n  6 -> 10 [label=\"output\"]\n  11[label=\"Text transformation\"]\n  7 -> 11 [label=\"output\"]\n  12[label=\"Add column\"]\n  8 -> 12 [label=\"out_file1\"]\n  13[label=\"LASTZ\"]\n  9 -> 13 [label=\"output\"]\n  3 -> 13 [label=\"output\"]\n  14[label=\"random_lines1\"]\n  10 -> 14 [label=\"output\"]\n  15[label=\"Filter\"]\n  10 -> 15 [label=\"output\"]\n  16[label=\"Search in textfiles\"]\n  11 -> 16 [label=\"output\"]\n  17[label=\"Concatenate datasets\"]\n  11 -> 17 [label=\"output\"]\n  9 -> 17 [label=\"output\"]\n  18[label=\"Cut\"]\n  12 -> 18 [label=\"out_file1\"]\n  19[label=\"Text transformation\"]\n  13 -> 19 [label=\"output\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  20[label=\"Datamash\"]\n  15 -> 20 [label=\"out_file1\"]\n  21[label=\"Compute sequence length\"]\n  17 -> 21 [label=\"out_file1\"]\n  22[label=\"Collapse Collection\"]\n  18 -> 22 [label=\"out_file1\"]\n  23[label=\"Merge Columns\"]\n  19 -> 23 [label=\"output\"]\n  24[label=\"Select\"]\n  20 -> 24 [label=\"out_file\"]\n  25[label=\"Sort\"]\n  21 -> 25 [label=\"output\"]\n  26[label=\"Collapse Collection\"]\n  23 -> 26 [label=\"out_file1\"]\n  27[label=\"Cut\"]\n  26 -> 27 [label=\"output\"]\n  28[label=\"Cut\"]\n  26 -> 28 [label=\"output\"]\n  29[label=\"Concatenate datasets\"]\n  27 -> 29 [label=\"out_file1\"]\n  28 -> 29 [label=\"out_file1\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  30[label=\"SortBED\"]\n  29 -> 30 [label=\"out_file1\"]\n  31[label=\"ComplementBed\"]\n  25 -> 31 [label=\"outfile\"]\n  30 -> 31 [label=\"output\"]\n  32[label=\"Filter\"]\n  31 -> 32 [label=\"output\"]\n  33[label=\"Filter\"]\n  32 -> 33 [label=\"out_file1\"]\n  34[label=\"Intersect intervals\"]\n  33 -> 34 [label=\"out_file1\"]\n  22 -> 34 [label=\"output\"]\n  35[label=\"Join two Datasets\"]\n  34 -> 35 [label=\"output\"]\n  1 -> 35 [label=\"output\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  5[label=\"Filter sequences by length\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"LASTZ\"]\n  2 -> 6 [label=\"output\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Collapse Collection\"]\n  3 -> 7 [label=\"output\"]\n  8[label=\"Select\"]\n  4 -> 8 [label=\"output\"]\n  9[label=\"Text transformation\"]\n  5 -> 9 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmapped_RNASeq.bam\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ngenome_annotation.gff3\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ngenome_assembly.fasta\"]\n  3[label=\"StringTie\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"gffread\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"FEELnc\"]\n  3 -> 5 [label=\"output_gtf\"]\n  2 -> 5 [label=\"output\"]\n  4 -> 5 [label=\"output_gtf\"]\n  k4055b259173c492d86a45e662b663421[color=lightseagreen,label=\"Output\\nmRNAs\"]\n  5 -> k4055b259173c492d86a45e662b663421\n  kabc029bab7ba458688b45e5d758c2f39[color=lightseagreen,label=\"Output\\nlncRNAs\"]\n  5 -> kabc029bab7ba458688b45e5d758c2f39\n  k93ff3464d1bb405986af3e703da3e542[color=lightseagreen,label=\"Output\\nClassifier output\"]\n  5 -> k93ff3464d1bb405986af3e703da3e542\n  6[label=\"Concatenate datasets\"]\n  4 -> 6 [label=\"output_gtf\"]\n  5 -> 6 [label=\"candidate_lncRNA\"]\n  k7b91b6a4ef6743599c93eabcc021b0fc[color=lightseagreen,label=\"Output\\nfinal_annotation\"]\n  6 -> k7b91b6a4ef6743599c93eabcc021b0fc\n}",
                 "history": [
                     {
-                        "hash": "48cf52ea88fe32cfc059494bc1b464c4b202bf99",
-                        "message": "on purpose mistake fixed",
-                        "num": 6,
-                        "short_hash": "48cf52ea8",
-                        "unix": "1579772724"
-                    },
-                    {
-                        "hash": "b3f79801438efc81c5f2a3f0af17a26f82e6913e",
-                        "message": "test",
-                        "num": 5,
-                        "short_hash": "b3f798014",
-                        "unix": "1579714684"
-                    },
-                    {
-                        "hash": "230f6e12fc9de41c8cb554a353e0b816eb656724",
-                        "message": "linting fix",
-                        "num": 4,
-                        "short_hash": "230f6e12f",
-                        "unix": "1579705852"
-                    },
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 3,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 2,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "485411d09f88e53fb83bc584da92afa171aed32a",
-                        "message": "workflow for ecoli_comparison",
+                        "hash": "8b70507229249bc44854bb8f23a50a6448cdd517",
+                        "message": "Add a new tutorial about lncRNAs annotation (with FEELnc) (#3623)",
                         "num": 1,
-                        "short_hash": "485411d09",
-                        "unix": "1546963139"
+                        "short_hash": "8b7050722",
+                        "unix": "1663943586"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "",
+                        "annotation": "RNASeq data mapped on the genome",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Ecoli_C_assembly.fna"
+                                "description": "RNASeq data mapped on the genome",
+                                "name": "mapped_RNASeq.bam"
                             }
                         ],
-                        "label": null,
+                        "label": "mapped_RNASeq.bam",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 10
+                            "bottom": 342.40000915527344,
+                            "height": 82.19999694824219,
+                            "left": 297.5,
+                            "right": 497.5,
+                            "top": 260.20001220703125,
+                            "width": 200,
+                            "x": 297.5,
+                            "y": 260.20001220703125
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"Ecoli_C_assembly.fna\"}",
+                        "tool_state": "{\"optional\": false, \"format\": [\"bam\"], \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "2eb3a31a-f5ec-4ce0-a4db-f421ab573412",
+                        "uuid": "0d6d7a64-f5f5-4d80-8e76-72859ae6fa1b",
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Original structural annotation",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "inline-supplementary-material-7 - Table_S4_Essential genes identi.tsv"
+                                "description": "Original structural annotation",
+                                "name": "genome_annotation.gff3"
                             }
                         ],
-                        "label": null,
+                        "label": "genome_annotation.gff3",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 130
+                            "bottom": 448.40000915527344,
+                            "height": 82.19999694824219,
+                            "left": 297,
+                            "right": 497,
+                            "top": 366.20001220703125,
+                            "width": 200,
+                            "x": 297,
+                            "y": 366.20001220703125
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"inline-supplementary-material-7 - Table_S4_Essential genes identi.tsv\"}",
+                        "tool_state": "{\"optional\": false, \"format\": [\"gff3\"], \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ac567420-400d-4a74-adb5-cdaed90cebd6",
+                        "uuid": "4cc3b4aa-b54d-4652-bd14-9611bece1ca8",
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Genome sequence",
                         "content_id": null,
                         "errors": null,
                         "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Input Dataset Collection"
+                                "description": "Genome sequence",
+                                "name": "genome_assembly.fasta"
                             }
                         ],
-                        "label": null,
-                        "name": "Input dataset collection",
+                        "label": "genome_assembly.fasta",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 250
+                            "bottom": 546.4000091552734,
+                            "height": 82.19999694824219,
+                            "left": 298,
+                            "right": 498,
+                            "top": 464.20001220703125,
+                            "width": 200,
+                            "x": 298,
+                            "y": 464.20001220703125
                         },
                         "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "8cc3e0ac-13bd-4e29-83dc-8411490fc85d",
+                        "type": "data_input",
+                        "uuid": "580a4505-ee23-4a3a-ac37-7e83cef79a0a",
                         "workflow_outputs": []
-                    },
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nmapped_RNASeq.bam\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ngenome_annotation.gff3\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ngenome_assembly.fasta\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"StringTie\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  4[\"gffread\"];\n  1 -->|output| 4;\n  5[\"FEELnc\"];\n  3 -->|output_gtf| 5;\n  2 -->|output| 5;\n  4 -->|output_gtf| 5;\n  4055b259-173c-492d-86a4-5e662b663421[\"Output\\nmRNAs\"];\n  5 --> 4055b259-173c-492d-86a4-5e662b663421;\n  style 4055b259-173c-492d-86a4-5e662b663421 stroke:#2c3143,stroke-width:4px;\n  abc029ba-b7ba-4586-88b4-5e5d758c2f39[\"Output\\nlncRNAs\"];\n  5 --> abc029ba-b7ba-4586-88b4-5e5d758c2f39;\n  style abc029ba-b7ba-4586-88b4-5e5d758c2f39 stroke:#2c3143,stroke-width:4px;\n  93ff3464-d1bb-4059-86af-3e703da3e542[\"Output\\nClassifier output\"];\n  5 --> 93ff3464-d1bb-4059-86af-3e703da3e542;\n  style 93ff3464-d1bb-4059-86af-3e703da3e542 stroke:#2c3143,stroke-width:4px;\n  6[\"Concatenate datasets\"];\n  4 -->|output_gtf| 6;\n  5 -->|candidate_lncRNA| 6;\n  7b91b6a4-ef67-4359-9c93-eabcc021b0fc[\"Output\\nfinal_annotation\"];\n  6 --> 7b91b6a4-ef67-4359-9c93-eabcc021b0fc;\n  style 7b91b6a4-ef67-4359-9c93-eabcc021b0fc stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Long non-coding RNAs (lncRNAs) annotation with FEELnc",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/feelnc/feelnc/0.2",
                         "errors": null,
-                        "id": 3,
-                        "input_connections": {},
+                        "id": 5,
+                        "input_connections": {
+                            "candidate": {
+                                "id": 3,
+                                "output_name": "output_gtf"
+                            },
+                            "genome": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "reference": {
+                                "id": 4,
+                                "output_name": "output_gtf"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Input Dataset Collection"
+                                "description": "runtime parameter for tool FEELnc",
+                                "name": "candidate"
+                            },
+                            {
+                                "description": "runtime parameter for tool FEELnc",
+                                "name": "genome"
+                            },
+                            {
+                                "description": "runtime parameter for tool FEELnc",
+                                "name": "reference"
                             }
                         ],
                         "label": null,
-                        "name": "Input dataset collection",
-                        "outputs": [],
+                        "name": "FEELnc",
+                        "outputs": [
+                            {
+                                "name": "candidate_lncRNA",
+                                "type": "gtf"
+                            },
+                            {
+                                "name": "candidate_mRNA",
+                                "type": "gtf"
+                            },
+                            {
+                                "name": "classifier",
+                                "type": "txt"
+                            }
+                        ],
                         "position": {
-                            "left": 10,
-                            "top": 370
+                            "bottom": 529.0000152587891,
+                            "height": 214.8000030517578,
+                            "left": 922,
+                            "right": 1122,
+                            "top": 314.20001220703125,
+                            "width": 200,
+                            "x": 922,
+                            "y": 314.20001220703125
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "6bc17455-70a4-48bb-a511-e484016e9ad8",
-                        "workflow_outputs": []
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/feelnc/feelnc/0.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "67af24676bd6",
+                            "name": "feelnc",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"candidate\": {\"__class__\": \"RuntimeValue\"}, \"genome\": {\"__class__\": \"RuntimeValue\"}, \"reference\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.2",
+                        "type": "tool",
+                        "uuid": "74ebae55-e16d-4884-bd59-0d6775bb731a",
+                        "workflow_outputs": [
+                            {
+                                "label": "mRNAs",
+                                "output_name": "candidate_mRNA",
+                                "uuid": "4055b259-173c-492d-86a4-5e662b663421"
+                            },
+                            {
+                                "label": "lncRNAs",
+                                "output_name": "candidate_lncRNA",
+                                "uuid": "abc029ba-b7ba-4586-88b4-5e5d758c2f39"
+                            },
+                            {
+                                "label": "Classifier output",
+                                "output_name": "classifier",
+                                "uuid": "93ff3464-d1bb-4059-86af-3e703da3e542"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
                         "errors": null,
-                        "id": 4,
-                        "input_connections": {},
+                        "id": 6,
+                        "input_connections": {
+                            "inputs": {
+                                "id": 4,
+                                "output_name": "output_gtf"
+                            },
+                            "queries_0|inputs2": {
+                                "id": 5,
+                                "output_name": "candidate_lncRNA"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Input Dataset Collection"
+                                "description": "runtime parameter for tool Concatenate datasets",
+                                "name": "inputs"
                             }
                         ],
                         "label": null,
-                        "name": "Input dataset collection",
-                        "outputs": [],
+                        "name": "Concatenate datasets",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
                         "position": {
-                            "left": 10,
-                            "top": 490
+                            "bottom": 758.2000122070312,
+                            "height": 144,
+                            "left": 1234,
+                            "right": 1434,
+                            "top": 614.2000122070312,
+                            "width": 200,
+                            "x": 1234,
+                            "y": 614.2000122070312
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "04145efc-b9a4-4bd4-9a72-7cdf0e98e752",
-                        "workflow_outputs": []
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "final_annotation"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f46f0e4f75c4",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"inputs\": {\"__class__\": \"RuntimeValue\"}, \"queries\": [{\"__index__\": 0, \"inputs2\": {\"__class__\": \"RuntimeValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.1",
+                        "type": "tool",
+                        "uuid": "d6f07c9d-56db-43f9-b0e3-09db582015fd",
+                        "workflow_outputs": [
+                            {
+                                "label": "final_annotation",
+                                "output_name": "out_file1",
+                                "uuid": "7b91b6a4-ef67-4359-9c93-eabcc021b0fc"
+                            }
+                        ]
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Collapse Collection\"];\n  6 -->|output| 10;\n  11[\"Text transformation\"];\n  7 -->|output| 11;\n  12[\"Add column\"];\n  8 -->|out_file1| 12;\n  13[\"LASTZ\"];\n  9 -->|output| 13;\n  3 -->|output| 13;\n  14[\"random_lines1\"];\n  10 -->|output| 14;\n  15[\"Filter\"];\n  10 -->|output| 15;\n  16[\"Search in textfiles\"];\n  11 -->|output| 16;\n  17[\"Concatenate datasets\"];\n  11 -->|output| 17;\n  9 -->|output| 17;\n  18[\"Cut\"];\n  12 -->|out_file1| 18;\n  19[\"Text transformation\"];\n  13 -->|output| 19;\n  2[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  20[\"Datamash\"];\n  15 -->|out_file1| 20;\n  21[\"Compute sequence length\"];\n  17 -->|out_file1| 21;\n  22[\"Collapse Collection\"];\n  18 -->|out_file1| 22;\n  23[\"Merge Columns\"];\n  19 -->|output| 23;\n  24[\"Select\"];\n  20 -->|out_file| 24;\n  25[\"Sort\"];\n  21 -->|output| 25;\n  26[\"Collapse Collection\"];\n  23 -->|out_file1| 26;\n  27[\"Cut\"];\n  26 -->|output| 27;\n  28[\"Cut\"];\n  26 -->|output| 28;\n  29[\"Concatenate datasets\"];\n  27 -->|out_file1| 29;\n  28 -->|out_file1| 29;\n  3[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  30[\"SortBED\"];\n  29 -->|out_file1| 30;\n  31[\"ComplementBed\"];\n  25 -->|outfile| 31;\n  30 -->|output| 31;\n  32[\"Filter\"];\n  31 -->|output| 32;\n  33[\"Filter\"];\n  32 -->|out_file1| 33;\n  34[\"Intersect intervals\"];\n  33 -->|out_file1| 34;\n  22 -->|output| 34;\n  35[\"Join two Datasets\"];\n  34 -->|output| 35;\n  1 -->|output| 35;\n  4[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Filter sequences by length\"];\n  0 -->|output| 5;\n  6[\"LASTZ\"];\n  2 -->|output| 6;\n  0 -->|output| 6;\n  7[\"Collapse Collection\"];\n  3 -->|output| 7;\n  8[\"Select\"];\n  4 -->|output| 8;\n  9[\"Text transformation\"];\n  5 -->|output| 9;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Ecoli Comparison",
-                "outputs": [],
-                "parent_id": "assembly/ecoli_comparison",
-                "path": "topics/assembly/tutorials/ecoli_comparison/workflows/ecoli-comparison.ga",
+                "parent_id": "genome-annotation/lncrna",
+                "path": "topics/genome-annotation/tutorials/lncrna/workflows/main_workflow.ga",
                 "tags": [
-                    "assembly"
+                    "genome-annotation"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Ecoli Comparison",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-ecoli_comparison/versions/ecoli-comparison",
-                "tutorial_id": "ecoli_comparison",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/ecoli_comparison/workflows/ecoli-comparison.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/ecoli_comparison/workflows/ecoli-comparison.html",
-                "version": 3,
-                "wfid": "assembly-ecoli_comparison",
-                "wfname": "ecoli-comparison",
-                "workflow": "ecoli-comparison.ga",
+                "title": "Long non-coding RNAs (lncRNAs) annotation with FEELnc",
+                "topic_id": "genome-annotation",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-lncrna/versions/main-workflow",
+                "tutorial_id": "lncrna",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/lncrna/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/lncrna/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "genome-annotation-lncrna",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "Filter1",
-                    "Grep1",
-                    "cat1",
-                    "join1",
-                    "random_lines1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.27.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/feelnc/feelnc/0.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.6"
                 ],
-                "workflowhub_id": "1113"
+                "workflowhub_id": "1141"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/3382053"
+        "zenodo_link": "https://zenodo.org/records/11367439"
     },
     {
+        "abbreviations": {
+            "CRISPR": "Clustered Regularly Interspaced Short Palindromic Repeats",
+            "MAGeCK": "Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout"
+        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "jbrowse",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "e7b2202befea",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "3d0c7bdf12f5",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mageck_count",
                     "owner": "iuc",
-                    "revisions": "836d1aa3e89a",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "revisions": "e329d44424d7",
+                    "tool_panel_section_label": "Genome Editing",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "snippy",
+                    "name": "mageck_mle",
                     "owner": "iuc",
-                    "revisions": "c9a8ef2aa380",
-                    "tool_panel_section_label": "Variant Calling",
+                    "revisions": "26126538a86f",
+                    "tool_panel_section_label": "Genome Editing",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mageck_test",
+                    "owner": "iuc",
+                    "revisions": "9b4f4533c9ee",
+                    "tool_panel_section_label": "Genome Editing",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "9a913cdee30e",
+                    "tool_panel_section_label": "Quality Control",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "75c93c70d094",
+                    "tool_panel_section_label": "Quality Control",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "volcanoplot",
+                    "owner": "iuc",
+                    "revisions": "83c573f2e73c",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "cutadapt",
+                    "owner": "lparsons",
+                    "revisions": "4e5056fefd88",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "cutadapt",
+                    "owner": "lparsons",
+                    "revisions": "de6cebe3c043",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: jbrowse\n  owner: iuc\n  revisions: 836d1aa3e89a\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snippy\n  owner: iuc\n  revisions: c9a8ef2aa380\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/microbial-variants/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mageck_count\n  owner: iuc\n  revisions: e329d44424d7\n  tool_panel_section_label: Genome Editing\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mageck_mle\n  owner: iuc\n  revisions: 26126538a86f\n  tool_panel_section_label: Genome Editing\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mageck_test\n  owner: iuc\n  revisions: 9b4f4533c9ee\n  tool_panel_section_label: Genome Editing\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 9a913cdee30e\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 75c93c70d094\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: volcanoplot\n  owner: iuc\n  revisions: 83c573f2e73c\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 4e5056fefd88\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: de6cebe3c043\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/crispr-screen/tutorial.json",
         "contributors": [
             {
-                "id": "annasyme",
-                "joined": "2017-09",
-                "name": "Anna Syme",
-                "orcid": "0000-0002-9906-0673",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
+                "id": "mblue9",
+                "joined": "2018-09",
+                "name": "Maria Doyle",
+                "orcid": "0000-0003-4847-8436",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
             },
             {
-                "elixir_node": "au",
-                "email": "simon.gladman@unimelb.edu.au",
-                "id": "slugger70",
-                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
-                "joined": "2017-09",
-                "name": "Simon Gladman",
-                "orcid": "0000-0002-6100-4385",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
+                "github": false,
+                "id": "kenjifujihara",
+                "joined": "2021-10",
+                "name": "Kenji Fujihara",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kenjifujihara/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/kenjifujihara.json"
             },
             {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "au",
-                "id": "tseemann",
-                "joined": "2018-06",
-                "name": "Torsten Seemann",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tseemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tseemann.json"
+                "github": false,
+                "id": "twishigulati",
+                "joined": "2021-11",
+                "name": "Twishi Gulati",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/twishigulati/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/twishigulati.json"
             }
         ],
-        "dir": "topics/variant-analysis/tutorials/microbial-variants",
-        "edam_ontology": [
-            "topic_0622",
-            "topic_0196",
-            "topic_2885",
-            "topic_3301",
-            "topic_0080",
-            "topic_0199"
-        ],
+        "dir": "topics/genome-annotation/tutorials/crispr-screen",
         "edam_operation": [
-            "Genome visualisation",
-            "Variant calling",
-            "Phylogenetic tree generation",
-            "Phylogenetic tree visualisation"
-        ],
-        "edam_topic": [
-            "Genomics",
-            "Sequence assembly",
-            "DNA polymorphism",
-            "Microbiology",
-            "Sequence analysis",
-            "Genetic variation"
+            "Sequence trimming",
+            "Sequencing quality control",
+            "Statistical calculation",
+            "Validation",
+            "Sequence composition calculation",
+            "Genetic variation analysis",
+            "Read pre-processing",
+            "Primer removal"
         ],
+        "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "variant-analysis/microbial-variants",
+        "id": "genome-annotation/crispr-screen",
         "inexact_supported_servers": [
-            "GalaxyTrakr",
+            "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
+            "UseGalaxy.eu",
+            "UseGalaxy.no"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "We used a tool called Snippy to call variants between our reads and our reference genome.",
-            "As our reference genome had annotations, we could see what effect the changes have on the features as annotated in the reference and therefore make inferences on the possible changes to the phenotype.",
-            "We used the JBrowse genome browser to visualise what these changes look like."
+            "CRISPR screen data can be analysed using MAGeCK and standard read quality tools"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-15",
+        "mod_date": "2024-08-08",
         "objectives": [
-            "Find variants between a reference genome and a set of reads",
-            "Visualise the SNP in context of the reads aligned to the genome",
-            "Determine the effect of those variants on genomic features",
-            "Understand if the SNP is potentially affecting the phenotype"
+            "Apply appropriate analysis and quality control steps for CRISPR screen data",
+            "Identify differentially enriched genes across conditions",
+            "Generate volcano plot to visualise results"
         ],
-        "pageviews": 20322,
-        "pub_date": "2018-02-26",
+        "pageviews": 4524944,
+        "priority": 8,
+        "pub_date": "2021-10-15",
         "questions": [
-            "How do we detect differences between a set of reads from a microorganism and a reference genome"
+            "What are the steps to process CRISPR screen data?",
+            "How to identify essential genes across experimental conditions?"
         ],
-        "short_id": "T00313",
+        "recordings": [
+            {
+                "captioners": [
+                    "mblue9"
+                ],
+                "date": "2022-03-10",
+                "galaxy_version": "21.09",
+                "length": "45M",
+                "speakers": [
+                    "mblue9"
+                ],
+                "youtube_id": "wavAf_2ytWg"
+            }
+        ],
+        "redirect_from": [
+            "/topics/genome-editing/tutorials/crispr-screen/tutorial",
+            "/short/genome-annotation/crispr-screen",
+            "/short/T00171"
+        ],
+        "requirements": [
+            {
+                "topic_name": "sequence-analysis",
+                "tutorials": [
+                    "quality-control"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "collections",
+                    "upload-rules"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00171",
         "short_tools": [
-            "jbrowse",
-            "snippy"
+            "mageck_test",
+            "mageck_mle",
+            "tp_awk_tool",
+            "volcanoplot",
+            "cutadapt",
+            "multiqc",
+            "mageck_count",
+            "fastqc"
         ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "introduction",
+        "slides": true,
+        "slides_recordings": [
+            {
+                "captioners": [
+                    "mblue9"
+                ],
+                "date": "2022-03-10",
+                "galaxy_version": "21.09",
+                "length": "3M",
+                "speakers": [
+                    "awspolly"
+                ],
+                "youtube_id": "MNT9gB5_RMg"
+            }
+        ],
+        "subtopic": "eukaryote",
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ],
             "inexact": [
                 {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
                 {
@@ -111249,102 +112927,85 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
                 },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
         "tags": [
-            "prokaryote",
-            "microgalaxy",
-            "gmod",
-            "jbrowse1"
+            "genome editing",
+            "CRISPR",
+            "essential genes",
+            "cell line"
         ],
-        "time_estimation": "45m",
-        "title": "Microbial Variant Calling",
+        "time_estimation": "2H",
+        "title": "CRISPR screen analysis",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/0.7.0.3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mageck_count/mageck_count/0.5.9.2.4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mageck_mle/mageck_mle/0.5.9.2.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mageck_test/mageck_test/0.5.9.2.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5",
+            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.4+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy0"
         ],
-        "topic_name": "variant-analysis",
-        "topic_name_human": "Variant Analysis",
+        "topic_name": "genome-annotation",
+        "topic_name_human": "Genome Annotation",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": false
+            "video": true
         },
-        "tutorial_name": "microbial-variants",
+        "tutorial_name": "crispr-screen",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/crispr-screen/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/microbial-variants/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/microbial-variants/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/crispr-screen/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/crispr-screen/tutorial.json"
         },
-        "version": 23,
-        "video": false,
-        "video_versions": 0,
+        "version": 12,
+        "video": true,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 120,
-        "visitors": 12166,
+        "visit_duration": 274,
+        "visitors": 1730919,
         "workflows": [
             {
                 "creators": [],
-                "description": "Microbial Variant Calling",
+                "description": "CRISPR screen analysis",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  5[label=\"snippy\"]\n  0 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"output\"]\n  k58cbabf03a3c4ec5b16a40d19fc82aae[color=lightseagreen,label=\"Output\\nsnippy_fasta\"]\n  5 -> k58cbabf03a3c4ec5b16a40d19fc82aae\n  k4002677b75f248f49d5332ab4dd44165[color=lightseagreen,label=\"Output\\nsnippy_tabular\"]\n  5 -> k4002677b75f248f49d5332ab4dd44165\n  6[label=\"JBrowse\"]\n  5 -> 6 [label=\"snpgff\"]\n  4 -> 6 [label=\"output\"]\n  5 -> 6 [label=\"snpsbam\"]\n  2 -> 6 [label=\"output\"]\n  kadfd738e00464e26a338254cdcb175af[color=lightseagreen,label=\"Output\\njbrowse_html\"]\n  6 -> kadfd738e00464e26a338254cdcb175af\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nbroadgpp-brunello-library-contents.csv\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCalabrese_SetA_Guides_Reference.csv\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  3[label=\"FastQC\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Cutadapt\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"MultiQC\"]\n  3 -> 5 [label=\"text_file\"]\n  6[label=\"MAGeCK count\"]\n  4 -> 6 [label=\"out1\"]\n  7[label=\"MAGeCKs test\"]\n  6 -> 7 [label=\"counts\"]\n}",
                 "history": [
                     {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 5,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 4,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "dfb97360348d32210f7c4bae68f1154a2336e520",
-                        "message": "annotate workflow outputs",
-                        "num": 3,
-                        "short_hash": "dfb973603",
-                        "unix": "1526109637"
-                    },
-                    {
-                        "hash": "8803cca01f5e6e62243a1cefbe21e701e89151af",
-                        "message": "pretty'fy workflow",
+                        "hash": "6de3720bca01013738f2c7a888d8f801b152cad0",
+                        "message": "fix tagging",
                         "num": 2,
-                        "short_hash": "8803cca01",
-                        "unix": "1526109452"
+                        "short_hash": "6de3720bc",
+                        "unix": "1646669939"
                     },
                     {
-                        "hash": "5a1bff42297572d14d33b4e41de89694a6957676",
-                        "message": "Add some love to microbial variant calling tutorial (#732)",
+                        "hash": "25fe77f9e08a7d086221d60a37e4e538db380c29",
+                        "message": "Migrate to GA",
                         "num": 1,
-                        "short_hash": "5a1bff422",
-                        "unix": "1523043969"
+                        "short_hash": "25fe77f9e",
+                        "unix": "1646669586"
                     }
                 ],
                 "inputs": [
@@ -111357,344 +113018,128 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "mutant_R1"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 10
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"mutant_R1\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f78a5562-288a-49fa-a8e4-a6facf09bffe",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "mutant_R2"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 130
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"mutant_R2\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "9f0aa29d-da56-4535-96ce-696a721d1d76",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "wildtype.fna"
+                                "name": "broadgpp-brunello-library-contents.csv"
                             }
                         ],
-                        "label": null,
+                        "label": "broadgpp-brunello-library-contents.csv",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
                             "left": 10,
-                            "top": 250
+                            "top": 10
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"wildtype.fna\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "1ad30281-3ee6-4725-8515-8db4936de0ff",
+                        "uuid": "2d894130-2416-4418-98bd-0f62d0ce3288",
                         "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "wildtype.gbk"
+                                "name": "Calabrese_SetA_Guides_Reference.csv"
                             }
                         ],
-                        "label": null,
+                        "label": "Calabrese_SetA_Guides_Reference.csv",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
                             "left": 10,
-                            "top": 370
+                            "top": 130
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"wildtype.gbk\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "3c0c913a-7106-4ac7-b653-a0a0da1d14f8",
+                        "uuid": "f79b3850-c8b6-4ca7-8406-c795702195ae",
                         "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 4,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "wildtype.gff"
+                                "name": "Input Dataset Collection"
                             }
                         ],
-                        "label": null,
-                        "name": "Input dataset",
+                        "label": "Input Dataset Collection",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
                             "left": 10,
-                            "top": 490
+                            "top": 250
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"wildtype.gff\"}",
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "0a4f5c3d-4f34-4461-8114-98f3bb0a4cf8",
+                        "type": "data_collection_input",
+                        "uuid": "699e7c6b-5248-484a-a06c-bae15497e74e",
                         "workflow_outputs": []
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"snippy\"];\n  0 -->|output| 5;\n  1 -->|output| 5;\n  3 -->|output| 5;\n  58cbabf0-3a3c-4ec5-b16a-40d19fc82aae[\"Output\\nsnippy_fasta\"];\n  5 --> 58cbabf0-3a3c-4ec5-b16a-40d19fc82aae;\n  style 58cbabf0-3a3c-4ec5-b16a-40d19fc82aae stroke:#2c3143,stroke-width:4px;\n  4002677b-75f2-48f4-9d53-32ab4dd44165[\"Output\\nsnippy_tabular\"];\n  5 --> 4002677b-75f2-48f4-9d53-32ab4dd44165;\n  style 4002677b-75f2-48f4-9d53-32ab4dd44165 stroke:#2c3143,stroke-width:4px;\n  6[\"JBrowse\"];\n  5 -->|snpgff| 6;\n  4 -->|output| 6;\n  5 -->|snpsbam| 6;\n  2 -->|output| 6;\n  adfd738e-0046-4e26-a338-254cdcb175af[\"Output\\njbrowse_html\"];\n  6 --> adfd738e-0046-4e26-a338-254cdcb175af;\n  style adfd738e-0046-4e26-a338-254cdcb175af stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "Microbial Variant Calling",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "fastq_input|fastq_input1": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "fastq_input|fastq_input2": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "ref": {
-                                "id": 3,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "snippy",
-                        "outputs": [
-                            {
-                                "name": "snpvcf",
-                                "type": "vcf"
-                            },
-                            {
-                                "name": "snpgff",
-                                "type": "gff3"
-                            },
-                            {
-                                "name": "snptab",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "snpsum",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "snplog",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "snpalign",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "snpconsensus",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "snpsdepth",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "snpsbam",
-                                "type": "bam"
-                            },
-                            {
-                                "name": "outdir",
-                                "type": "zip"
-                            }
-                        ],
-                        "position": {
-                            "left": 230,
-                            "top": 10
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "c9a8ef2aa380",
-                            "name": "snippy",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adv\": \"{\\\"mapqual\\\": \\\"60\\\", \\\"bwaopt\\\": \\\"\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\", \\\"mincov\\\": \\\"10\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outgff\\\", \\\"outtab\\\", \\\"outsum\\\", \\\"outlog\\\", \\\"outaln\\\", \\\"outcon\\\", \\\"outdep\\\", \\\"outbam\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"fastq_input2\\\": null, \\\"__current_case__\\\": 0, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"fastq_input1\\\": null}\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"ref\": \"null\"}",
-                        "tool_version": "3.2",
-                        "type": "tool",
-                        "uuid": "5f5638b5-3553-4522-9cfa-d47dd45e8c42",
-                        "workflow_outputs": [
-                            {
-                                "label": "snippy_fasta",
-                                "output_name": "snpconsensus",
-                                "uuid": "58cbabf0-3a3c-4ec5-b16a-40d19fc82aae"
-                            },
-                            {
-                                "label": "snippy_tabular",
-                                "output_name": "snpsum",
-                                "uuid": "4002677b-75f2-48f4-9d53-32ab4dd44165"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/0.7.0.3",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "reference_genome|genomes": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "track_groups_0|data_tracks_0|data_format|annotation": {
-                                "id": 5,
-                                "output_name": "snpsbam"
-                            },
-                            "track_groups_1|data_tracks_0|data_format|annotation": {
-                                "id": 5,
-                                "output_name": "snpgff"
-                            },
-                            "track_groups_2|data_tracks_0|data_format|annotation": {
-                                "id": 4,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "JBrowse",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "html"
-                            }
-                        ],
-                        "position": {
-                            "left": 450,
-                            "top": 10
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/0.7.0.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "836d1aa3e89a",
-                            "name": "jbrowse",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__page__\": null, \"standalone\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"reference_genome\": \"{\\\"genomes\\\": null, \\\"__current_case__\\\": 1, \\\"genome_type_select\\\": \\\"history\\\"}\", \"track_groups\": \"[{\\\"category\\\": \\\"sequence reads\\\", \\\"__index__\\\": 0, \\\"data_tracks\\\": [{\\\"__index__\\\": 0, \\\"data_format\\\": {\\\"auto_snp\\\": \\\"true\\\", \\\"track_visibility\\\": \\\"default_on\\\", \\\"override_apollo_drag\\\": \\\"False\\\", \\\"__current_case__\\\": 3, \\\"override_apollo_plugins\\\": \\\"False\\\", \\\"annotation\\\": null, \\\"data_format_select\\\": \\\"pileup\\\"}}]}, {\\\"category\\\": \\\"variants\\\", \\\"__index__\\\": 1, \\\"data_tracks\\\": [{\\\"__index__\\\": 0, \\\"data_format\\\": {\\\"index\\\": \\\"false\\\", \\\"match_part\\\": {\\\"match_part_select\\\": \\\"false\\\", \\\"__current_case__\\\": 1}, \\\"jbstyle\\\": {\\\"style_classname\\\": \\\"feature\\\", \\\"style_description\\\": \\\"note,description\\\", \\\"style_height\\\": \\\"10px\\\", \\\"max_height\\\": \\\"600\\\", \\\"style_label\\\": \\\"product,name,id\\\"}, \\\"track_visibility\\\": \\\"default_on\\\", \\\"track_config\\\": {\\\"track_class\\\": \\\"JBrowse/View/Track/CanvasFeatures\\\", \\\"canvas_options\\\": {\\\"transcriptType\\\": \\\"\\\", \\\"subParts\\\": \\\"\\\", \\\"impliedUTRs\\\": \\\"false\\\"}, \\\"__current_case__\\\": 0}, \\\"jbcolor_scale\\\": {\\\"color_score\\\": {\\\"color\\\": {\\\"color_select\\\": \\\"automatic\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 0, \\\"color_score_select\\\": \\\"none\\\"}}, \\\"override_apollo_drag\\\": \\\"False\\\", \\\"__current_case__\\\": 2, \\\"override_apollo_plugins\\\": \\\"False\\\", \\\"jbmenu\\\": {\\\"track_menu\\\": []}, \\\"annotation\\\": null, \\\"data_format_select\\\": \\\"gene_calls\\\"}}]}, {\\\"category\\\": \\\"annotated reference\\\", \\\"__index__\\\": 2, \\\"data_tracks\\\": [{\\\"__index__\\\": 0, \\\"data_format\\\": {\\\"index\\\": \\\"false\\\", \\\"match_part\\\": {\\\"match_part_select\\\": \\\"false\\\", \\\"__current_case__\\\": 1}, \\\"jbstyle\\\": {\\\"style_classname\\\": \\\"feature\\\", \\\"style_description\\\": \\\"product\\\", \\\"style_height\\\": \\\"10px\\\", \\\"max_height\\\": \\\"600\\\", \\\"style_label\\\": \\\"product\\\"}, \\\"track_visibility\\\": \\\"default_on\\\", \\\"track_config\\\": {\\\"track_class\\\": \\\"JBrowse/View/Track/CanvasFeatures\\\", \\\"canvas_options\\\": {\\\"transcriptType\\\": \\\"\\\", \\\"subParts\\\": \\\"\\\", \\\"impliedUTRs\\\": \\\"false\\\"}, \\\"__current_case__\\\": 0}, \\\"jbcolor_scale\\\": {\\\"color_score\\\": {\\\"color\\\": {\\\"color_select\\\": \\\"automatic\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 0, \\\"color_score_select\\\": \\\"none\\\"}}, \\\"override_apollo_drag\\\": \\\"False\\\", \\\"__current_case__\\\": 2, \\\"override_apollo_plugins\\\": \\\"False\\\", \\\"jbmenu\\\": {\\\"track_menu\\\": []}, \\\"annotation\\\": null, \\\"data_format_select\\\": \\\"gene_calls\\\"}}]}]\", \"plugins\": \"{\\\"GCContent\\\": \\\"false\\\", \\\"Bookmarks\\\": \\\"false\\\", \\\"theme\\\": \\\"\\\", \\\"ComboTrackSelector\\\": \\\"false\\\"}\", \"action\": \"{\\\"action_select\\\": \\\"create\\\", \\\"__current_case__\\\": 0}\", \"gencode\": \"\\\"11\\\"\", \"uglyTestingHack\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"jbgen\": \"{\\\"trackPadding\\\": \\\"20\\\", \\\"show_tracklist\\\": \\\"true\\\", \\\"show_overview\\\": \\\"true\\\", \\\"show_nav\\\": \\\"true\\\", \\\"aboutDescription\\\": \\\"\\\", \\\"defaultLocation\\\": \\\"\\\", \\\"hideGenomeOptions\\\": \\\"false\\\", \\\"shareLink\\\": \\\"true\\\", \\\"show_menu\\\": \\\"true\\\"}\"}",
-                        "tool_version": "0.7.0.3",
-                        "type": "tool",
-                        "uuid": "2a2aad62-4281-4bd1-bb5c-cd8bc078ec85",
-                        "workflow_outputs": [
-                            {
-                                "label": "jbrowse_html",
-                                "output_name": "output",
-                                "uuid": "adfd738e-0046-4e26-a338-254cdcb175af"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "variant-analysis/microbial-variants",
-                "path": "topics/variant-analysis/tutorials/microbial-variants/workflows/microbial_variant_calling.ga",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nbroadgpp-brunello-library-contents.csv\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nCalabrese_SetA_Guides_Reference.csv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"FastQC\"];\n  2 -->|output| 3;\n  4[\"Cutadapt\"];\n  2 -->|output| 4;\n  5[\"MultiQC\"];\n  3 -->|text_file| 5;\n  6[\"MAGeCK count\"];\n  4 -->|out1| 6;\n  7[\"MAGeCKs test\"];\n  6 -->|counts| 7;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Workflow constructed from history 'CRISPR tutorial Kenji'",
+                "outputs": [],
+                "parent_id": "genome-annotation/crispr-screen",
+                "path": "topics/genome-annotation/tutorials/crispr-screen/workflows/main_workflow.ga",
                 "tags": [
-                    "variant-analysis"
+                    "genome-annotation"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "Microbial Variant Calling",
-                "topic_id": "variant-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-microbial-variants/versions/microbial-variant-calling",
-                "tutorial_id": "microbial-variants",
-                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/microbial-variants/workflows/microbial_variant_calling.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/microbial-variants/workflows/microbial_variant_calling.html",
-                "version": 4,
-                "wfid": "variant-analysis-microbial-variants",
-                "wfname": "microbial-variant-calling",
-                "workflow": "microbial_variant_calling.ga",
+                "tests": false,
+                "title": "Workflow constructed from history 'CRISPR tutorial Kenji'",
+                "topic_id": "genome-annotation",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-crispr-screen/versions/main-workflow",
+                "tutorial_id": "crispr-screen",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/crispr-screen/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/crispr-screen/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "genome-annotation-crispr-screen",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/0.7.0.3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2"
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mageck_count/mageck_count/0.5.9.2.4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mageck_test/mageck_test/0.5.9.2.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.4+galaxy1"
                 ],
-                "workflowhub_id": "1093"
+                "workflowhub_id": "1179"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.582600"
+        "zenodo_link": "https://zenodo.org/record/5750854"
     },
     {
-        "abbreviations": {
-            "OGS": "Official Gene Set"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "apollo_create_account",
-                    "owner": "gga",
-                    "revisions": "e80d29fd2a33",
-                    "tool_panel_section_label": "Apollo",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "apollo_create_or_update",
-                    "owner": "gga",
-                    "revisions": "4abaab60f9e1",
-                    "tool_panel_section_label": "Apollo",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "apollo_iframe",
-                    "owner": "gga",
-                    "revisions": "f4e3f9480307",
-                    "tool_panel_section_label": "Apollo",
+                    "name": "prokka",
+                    "owner": "crs4",
+                    "revisions": "bf68eb663bc3",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "apollo_list_organism",
-                    "owner": "gga",
-                    "revisions": "2c749ed310da",
-                    "tool_panel_section_label": "Apollo",
+                    "name": "prokka",
+                    "owner": "crs4",
+                    "revisions": "111884f0d912",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
@@ -111706,146 +113151,41 @@
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: apollo_create_account\n  owner: gga\n  revisions: e80d29fd2a33\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: apollo_create_or_update\n  owner: gga\n  revisions: 4abaab60f9e1\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: apollo_iframe\n  owner: gga\n  revisions: f4e3f9480307\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: apollo_list_organism\n  owner: gga\n  revisions: 2c749ed310da\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "abretaud",
-                "hexylena",
-                "nathandunn",
-                "mboudet"
-            ],
-            "funding": [
-                "gallantries",
-                "eurosciencegateway"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: prokka\n  owner: crs4\n  revisions: bf68eb663bc3\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: prokka\n  owner: crs4\n  revisions: 111884f0d912\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "gallantries",
-                    "eurosciencegateway",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
-                "fediverse_flavor": "mastodon",
-                "id": "abretaud",
-                "joined": "2017-09",
-                "location": {
-                    "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
-                },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
+                "id": "annasyme",
                 "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "email": "nathandunn@lbl.gov",
-                "id": "nathandunn",
-                "joined": "2019-07",
-                "name": "Nathan Dunn",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nathandunn/",
-                "twitter": "precogincog",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nathandunn.json"
+                "name": "Anna Syme",
+                "orcid": "0000-0002-9906-0673",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
             },
             {
                 "affiliations": [
                     "elixir-europe"
                 ],
-                "elixir_node": "fr",
-                "email": "mateo.boudet@inrae.fr",
-                "id": "mboudet",
-                "joined": "2021-05",
-                "name": "Mateo Boudet",
-                "orcid": "0000-0002-7028-7620",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mboudet/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mboudet.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+                "elixir_node": "au",
+                "id": "tseemann",
+                "joined": "2018-06",
+                "name": "Torsten Seemann",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tseemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tseemann.json"
             },
             {
-                "avatar": "/training-material/assets/images/eurosciencegateway.png",
-                "funder": true,
-                "funding_id": "101057388",
-                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "eurosciencegateway",
-                "joined": "2023-10",
-                "members": [
-                    "abretaud",
-                    "anuprulez",
-                    "bgruening",
-                    "erxleben",
-                    "pauldg",
-                    "rlibouba"
-                ],
-                "name": "EuroScienceGateway",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
+                "elixir_node": "au",
+                "email": "simon.gladman@unimelb.edu.au",
+                "id": "slugger70",
+                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
+                "joined": "2017-09",
+                "name": "Simon Gladman",
+                "orcid": "0000-0002-6100-4385",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
             }
         ],
-        "dir": "topics/genome-annotation/tutorials/apollo",
+        "dir": "topics/genome-annotation/tutorials/annotation-with-prokka",
         "edam_ontology": [
             "topic_0622",
             "topic_3301",
@@ -111853,7 +113193,10 @@
             "topic_0080"
         ],
         "edam_operation": [
-            "Genome visualisation"
+            "Genome visualisation",
+            "Gene prediction",
+            "Genome annotation",
+            "Coding region prediction"
         ],
         "edam_topic": [
             "Genomics",
@@ -111861,44 +113204,55 @@
             "Gene and protein families",
             "Sequence analysis"
         ],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "genome-annotation",
+                "tutorials": [
+                    "apollo"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "genome-annotation/apollo",
+        "id": "genome-annotation/annotation-with-prokka",
         "inexact_supported_servers": [
+            "Galaxy@AuBi",
+            "GalaxyTrakr",
+            "MISSISSIPPI",
+            "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.no"
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Apollo is the Google Docs of the genome annotation world, real-time collaborative genome annotation.",
-            "Apollo allows a group to view and manually refine predicted genome annotations",
-            "Use Apollo to edit annotations within your group.",
-            "Export manual annotations as GFF3."
+            "Prokka is a useful tool to annotate a bacterial genome.",
+            "JBrowse can be used to inspect the annotation of a genome."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
         "mod_date": "2024-08-08",
         "objectives": [
-            "Load a genome into Galaxy",
-            "View annotations in JBrowse",
-            "Learn how to load JBrowse data into Apollo",
-            "Learn how to manually refine genome annotations within Apollo",
-            "Export refined genome annotations"
+            "Load genome into Galaxy",
+            "Annotate genome with Prokka",
+            "View annotations in JBrowse"
         ],
-        "pageviews": 4949160,
-        "pub_date": "2021-06-04",
+        "pageviews": 5925127,
+        "pub_date": "2018-03-06",
         "questions": [
-            "How to visualize your genome after automated annotations have been performed?",
-            "How to manually annotate genome after automated annotations have been performed?",
-            "How to evaluate and visualize annotated genomic features?",
-            "How do I collaborate when doing genome annotation?"
+            "How can we annotate a bacterial genome?",
+            "How can we visualize annotated genomic features?"
         ],
         "recordings": [
             {
@@ -111907,36 +113261,17 @@
                 ],
                 "date": "2021-02-15",
                 "galaxy_version": "21.01",
-                "length": "1H",
+                "length": "20M",
                 "speakers": [
                     "abretaud"
                 ],
-                "youtube_id": "ywK1fhM-QFU"
-            }
-        ],
-        "requirements": [
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "upload-rules"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "genome-annotation",
-                "tutorials": [
-                    "annotation-with-prokka"
-                ],
-                "type": "internal"
+                "youtube_id": "B8pIQZPf21Y"
             }
         ],
-        "short_id": "T00169",
+        "short_id": "T00168",
         "short_tools": [
             "jbrowse",
-            "create_or_update",
-            "list_organism",
-            "iframe",
-            "create_account"
+            "prokka"
         ],
         "slides": true,
         "slides_recordings": [
@@ -111946,31 +113281,67 @@
                 ],
                 "date": "2021-02-15",
                 "galaxy_version": "21.01",
-                "length": "5M",
+                "length": "3M",
                 "speakers": [
                     "awspolly"
                 ],
-                "youtube_id": "ailUycRVHtE"
+                "youtube_id": "eqHy-Cc7k4Q"
             }
         ],
         "subtopic": "prokaryote",
         "supported_servers": {
-            "exact": [],
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
             "inexact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ]
         },
@@ -111979,16 +113350,13 @@
             "gmod",
             "prokaryote",
             "microgalaxy",
-            "jbrowse1",
-            "apollo2"
+            "jbrowse1"
         ],
-        "time_estimation": "3h",
-        "title": "Refining Genome Annotations with Apollo (prokaryotes)",
+        "time_estimation": "1h",
+        "title": "Genome annotation with Prokka",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_account/create_account/3.1",
-            "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
-            "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
-            "toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1",
+            "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
+            "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1"
         ],
         "topic_name": "genome-annotation",
@@ -111999,660 +113367,264 @@
             "tutorial": [],
             "video": true
         },
-        "tutorial_name": "apollo",
+        "tutorial_name": "annotation-with-prokka",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.json"
         },
-        "version": 20,
+        "version": 25,
         "video": true,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 297,
-        "visitors": 1836817,
+        "visit_duration": 259,
+        "visitors": 2149523,
         "workflows": [
             {
-                "creators": [],
-                "description": "Refining Genome Annotations with Apollo",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager.bw\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam\"]\n  4[label=\"Register Account\"]\n  5[label=\"List Organisms\"]\n  6[label=\"JBrowse\"]\n  0 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"Create or Update Organism\"]\n  6 -> 7 [label=\"output\"]\n  8[label=\"Annotate\"]\n  7 -> 8 [label=\"output\"]\n}",
-                "history": [
+                "creators": [
                     {
-                        "hash": "6bc77b7441375cd57ea1d73e9fe2f80ef550891a",
-                        "message": "wf annotation",
-                        "num": 3,
-                        "short_hash": "6bc77b744",
-                        "unix": "1622101979"
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
                     },
                     {
-                        "hash": "9ced3a95cd725623c7c1f2664b0174a14cd59337",
-                        "message": "update workflow",
-                        "num": 2,
-                        "short_hash": "9ced3a95c",
-                        "unix": "1622043687"
+                        "class": "Person",
+                        "identifier": "0000-0001-6046-610X",
+                        "name": "Torsten Seemann"
                     },
                     {
-                        "hash": "32f41f6fe47606c12d4574551233e4a2583df189",
-                        "message": "rewrite bits v2",
-                        "num": 1,
-                        "short_hash": "32f41f6fe",
-                        "unix": "1571055596"
+                        "class": "Person",
+                        "identifier": "0000-0002-6100-4385",
+                        "name": "Simon Gladman"
                     }
                 ],
-                "inputs": [
+                "description": "Genome annotation with Prokka",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontigs.fasta\"]\n  1[label=\"Prokka\"]\n  0 -> 1 [label=\"output\"]\n  ka336c364e69e47ebace6a7fe46d285fe[color=lightseagreen,label=\"Output\\ngff_output\"]\n  1 -> ka336c364e69e47ebace6a7fe46d285fe\n  2[label=\"JBrowse\"]\n  1 -> 2 [label=\"out_fna\"]\n  1 -> 2 [label=\"out_gff\"]\n}",
+                "history": [
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "https://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1"
-                            }
-                        ],
-                        "label": "https://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 354.8999938964844,
-                            "height": 143.39999389648438,
-                            "left": 488,
-                            "right": 688,
-                            "top": 211.5,
-                            "width": 200,
-                            "x": 488,
-                            "y": 211.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "fa88b9bb-b87e-457b-a836-a8f1b25e520b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "82c708ee-87a4-45a2-abf0-911309e218fd"
-                            }
-                        ]
+                        "hash": "70a555355ed2ebc563a4388cd1da50f7f1a5952f",
+                        "message": "Update topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
+                        "num": 10,
+                        "short_hash": "70a555355",
+                        "unix": "1715074163"
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "https://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1"
-                            }
-                        ],
-                        "label": "https://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 527.8999938964844,
-                            "height": 143.39999389648438,
-                            "left": 510,
-                            "right": 710,
-                            "top": 384.5,
-                            "width": 200,
-                            "x": 510,
-                            "y": 384.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "1afd430b-6250-4eb2-8cf2-a83adf022e4b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "cbbb4914-0c3d-4857-8c3a-f43b3f0c39f9"
-                            }
-                        ]
+                        "hash": "466b451a082b7d2d5e60777a45289874bbbde721",
+                        "message": "Add creators and license to workflow",
+                        "num": 9,
+                        "short_hash": "466b451a0",
+                        "unix": "1714990318"
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "https://zenodo.org/record/3270822/files/forager.bw"
-                            }
-                        ],
-                        "label": "https://zenodo.org/record/3270822/files/forager.bw",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 659.1000061035156,
-                            "height": 102.60000610351562,
-                            "left": 493,
-                            "right": 693,
-                            "top": 556.5,
-                            "width": 200,
-                            "x": 493,
-                            "y": 556.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "091ca713-0096-419c-8cb7-7e83a41aab37",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "f4c19cc0-5099-4514-af29-52a3933b28f9"
-                            }
-                        ]
+                        "hash": "499e257dee992b4645adf4c79844b8cc89e68c24",
+                        "message": "update prokka workflow",
+                        "num": 8,
+                        "short_hash": "499e257de",
+                        "unix": "1714456964"
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "https://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam"
-                            }
-                        ],
-                        "label": "https://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 858.8999938964844,
-                            "height": 143.39999389648438,
-                            "left": 563,
-                            "right": 763,
-                            "top": 715.5,
-                            "width": 200,
-                            "x": 563,
-                            "y": 715.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "13d26450-8b30-42d4-9822-f697217818b1",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "464904cb-5608-4f5d-b282-a09be9d3dbbb"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager.bw\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Register Account\"];\n  5[\"List Organisms\"];\n  6[\"JBrowse\"];\n  0 -->|output| 6;\n  1 -->|output| 6;\n  3 -->|output| 6;\n  2 -->|output| 6;\n  7[\"Create or Update Organism\"];\n  6 -->|output| 7;\n  8[\"Annotate\"];\n  7 -->|output| 8;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Apollo Load Test",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "https://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1"
-                            }
-                        ],
-                        "label": "https://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 354.8999938964844,
-                            "height": 143.39999389648438,
-                            "left": 488,
-                            "right": 688,
-                            "top": 211.5,
-                            "width": 200,
-                            "x": 488,
-                            "y": 211.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "fa88b9bb-b87e-457b-a836-a8f1b25e520b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "82c708ee-87a4-45a2-abf0-911309e218fd"
-                            }
-                        ]
+                        "hash": "56413bab75ab75be269668d70e3929e01bbaa5fb",
+                        "message": "Add workflow test.",
+                        "num": 7,
+                        "short_hash": "56413bab7",
+                        "unix": "1603310943"
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "https://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1"
-                            }
-                        ],
-                        "label": "https://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 527.8999938964844,
-                            "height": 143.39999389648438,
-                            "left": 510,
-                            "right": 710,
-                            "top": 384.5,
-                            "width": 200,
-                            "x": 510,
-                            "y": 384.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "1afd430b-6250-4eb2-8cf2-a83adf022e4b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "cbbb4914-0c3d-4857-8c3a-f43b3f0c39f9"
-                            }
-                        ]
+                        "hash": "a3829a12322232647926a394b1ecae3af17a858b",
+                        "message": "Update Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
+                        "num": 6,
+                        "short_hash": "a3829a123",
+                        "unix": "1580832292"
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "https://zenodo.org/record/3270822/files/forager.bw"
-                            }
-                        ],
-                        "label": "https://zenodo.org/record/3270822/files/forager.bw",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 659.1000061035156,
-                            "height": 102.60000610351562,
-                            "left": 493,
-                            "right": 693,
-                            "top": 556.5,
-                            "width": 200,
-                            "x": 493,
-                            "y": 556.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "091ca713-0096-419c-8cb7-7e83a41aab37",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "f4c19cc0-5099-4514-af29-52a3933b28f9"
-                            }
-                        ]
+                        "hash": "bab7ab72c6a4436a3ac3e6745b364696332399b5",
+                        "message": "prokka@1.14.5 jbrowse@1.16.5+galaxy7",
+                        "num": 5,
+                        "short_hash": "bab7ab72c",
+                        "unix": "1580433748"
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "https://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam"
-                            }
-                        ],
-                        "label": "https://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 858.8999938964844,
-                            "height": 143.39999389648438,
-                            "left": 563,
-                            "right": 763,
-                            "top": 715.5,
-                            "width": 200,
-                            "x": 563,
-                            "y": 715.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "13d26450-8b30-42d4-9822-f697217818b1",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "464904cb-5608-4f5d-b282-a09be9d3dbbb"
-                            }
-                        ]
+                        "hash": "c69f09dd0cb211d5621af293fe400892e343f78e",
+                        "message": "Adding tag",
+                        "num": 4,
+                        "short_hash": "c69f09dd0",
+                        "unix": "1579796672"
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_account/create_account/3.1",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "Register Account",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 1038.6999969482422,
-                            "height": 82.19999694824219,
-                            "left": 644,
-                            "right": 844,
-                            "top": 956.5,
-                            "width": 200,
-                            "x": 644,
-                            "y": 956.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_account/create_account/3.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "e80d29fd2a33",
-                            "name": "apollo_create_account",
-                            "owner": "gga",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"first\": \"Nathan\", \"last\": \"Dunn\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1",
-                        "type": "tool",
-                        "uuid": "82f0b666-8743-4cdc-9682-feb10c35b0c6",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "dc1e2c2f-c566-48e0-95c7-327adb229fb5"
-                            }
-                        ]
+                        "hash": "920732bc2295d6120b075934b758290ad56f5759",
+                        "message": "Updated prokka workflow to newest tool versions",
+                        "num": 3,
+                        "short_hash": "920732bc2",
+                        "unix": "1579634888"
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "List Organisms",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "json"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 1158.6999969482422,
-                            "height": 82.19999694824219,
-                            "left": 644,
-                            "right": 844,
-                            "top": 1076.5,
-                            "width": 200,
-                            "x": 644,
-                            "y": 1076.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2c749ed310da",
-                            "name": "apollo_list_organism",
-                            "owner": "gga",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"chromInfo\": \"\\\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
-                        "tool_version": "3.1",
-                        "type": "tool",
-                        "uuid": "3fc26308-b331-4286-863a-d31ac5b6fb03",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "d7cc17cb-e3e2-4adf-857c-8d3583e57fdd"
-                            }
-                        ]
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 2,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
                     },
+                    {
+                        "hash": "b9a6072964bce056112a36326600e4c80bd133ec",
+                        "message": "move tutorials to new topic",
+                        "num": 1,
+                        "short_hash": "b9a607296",
+                        "unix": "1528898987"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "reference_genome|genome": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "track_groups_0|data_tracks_0|data_format|annotation": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "track_groups_1|data_tracks_0|data_format|annotation": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "track_groups_1|data_tracks_1|data_format|annotation": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool JBrowse",
-                                "name": "reference_genome"
-                            }
-                        ],
-                        "label": null,
-                        "name": "JBrowse",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "html"
+                                "description": "",
+                                "name": "contigs.fasta"
                             }
                         ],
+                        "label": "contigs.fasta",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 650.2999877929688,
-                            "height": 306.79998779296875,
-                            "left": 821,
-                            "right": 1021,
-                            "top": 343.5,
-                            "width": 200,
-                            "x": 821,
-                            "y": 343.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "a6e57ff585c0",
-                            "name": "jbrowse",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 76.845458984375
                         },
-                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"true\", \"track_groups\": [{\"__index__\": 0, \"category\": \"OGS 3.2\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_on\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 1, \"category\": \"Reads\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"auto_snp\": \"true\", \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 4, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"xyplot\": \"false\", \"var_band\": \"false\", \"scaling\": {\"scale_select\": \"auto_local\", \"__current_case__\": 0}, \"scale_select2\": \"linear\", \"MultiBigWig\": \"false\", \"jbcolor\": {\"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}, \"bicolor_pivot\": {\"bicolor_pivot_select\": \"zero\", \"__current_case__\": 0}}, \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16.11+galaxy1",
-                        "type": "tool",
-                        "uuid": "2e2723bf-9597-4c96-9980-33220e3b849a",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "9514c32e-2376-44ee-b368-beb25bf77ad7"
-                            }
-                        ]
-                    },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "79e73b85-8d44-413f-83b7-c0e668ec963c",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ncontigs.fasta\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Prokka\"];\n  0 -->|output| 1;\n  a336c364-e69e-47eb-ace6-a7fe46d285fe[\"Output\\ngff_output\"];\n  1 --> a336c364-e69e-47eb-ace6-a7fe46d285fe;\n  style a336c364-e69e-47eb-ace6-a7fe46d285fe stroke:#2c3143,stroke-width:4px;\n  2[\"JBrowse\"];\n  1 -->|out_fna| 2;\n  1 -->|out_gff| 2;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Genome Annotation with Prokka ",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
                         "errors": null,
-                        "id": 7,
+                        "id": 1,
                         "input_connections": {
-                            "jbrowse": {
-                                "id": 6,
+                            "input": {
+                                "id": 0,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Create or Update Organism",
-                                "name": "jbrowse"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Create or Update Organism",
+                        "name": "Prokka",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "json"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 506.1000061035156,
-                            "height": 113.60000610351562,
-                            "left": 1405,
-                            "right": 1605,
-                            "top": 392.5,
-                            "width": 200,
-                            "x": 1405,
-                            "y": 392.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
-                        "tool_shed_repository": {
-                            "changeset_revision": "4abaab60f9e1",
-                            "name": "apollo_create_or_update",
-                            "owner": "gga",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"genus\": \"Apis\", \"group\": null, \"jbrowse\": {\"__class__\": \"RuntimeValue\"}, \"no_reload_sequences\": \"false\", \"org_source\": {\"source_select\": \"direct\", \"__current_case__\": 1, \"org_raw\": \"Honeybee\"}, \"public\": \"true\", \"remove_old_directory\": \"true\", \"species\": \"Mellifera\", \"test_hack\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.2.5",
-                        "type": "tool",
-                        "uuid": "72c53f14-4e91-40c1-a4e9-325b6c2a3105",
-                        "workflow_outputs": [
+                                "name": "out_gff",
+                                "type": "gff"
+                            },
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "10c77447-f92c-44b0-8a04-151eef670244"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "json_file": {
-                                "id": 7,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
+                                "name": "out_gbk",
+                                "type": "txt"
+                            },
                             {
-                                "description": "runtime parameter for tool Annotate",
-                                "name": "json_file"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Annotate",
-                        "outputs": [
+                                "name": "out_fna",
+                                "type": "fasta"
+                            },
                             {
-                                "name": "output",
-                                "type": "html"
+                                "name": "out_faa",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "out_ffn",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "out_sqn",
+                                "type": "asn1"
+                            },
+                            {
+                                "name": "out_fsa",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "out_tbl",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "out_err",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "out_txt",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "out_log",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 502.6999969482422,
-                            "height": 93.19999694824219,
-                            "left": 1703,
-                            "right": 1903,
-                            "top": 409.5,
-                            "width": 200,
-                            "x": 1703,
-                            "y": 409.5
+                            "left": 254.117919921875,
+                            "top": 0.0
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
                         "tool_shed_repository": {
-                            "changeset_revision": "f4e3f9480307",
-                            "name": "apollo_iframe",
-                            "owner": "gga",
+                            "changeset_revision": "bf68eb663bc3",
+                            "name": "prokka",
+                            "owner": "crs4",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"json_file\": {\"__class__\": \"RuntimeValue\"}, \"tracklist\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.2.5",
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"__workflow_invocation_uuid__\": \"5dc31c9443c711eabead005056ba55fb\", \"centre\": \"V\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"compliant\": {\"compliant_select\": \"no\", \"__current_case__\": 0, \"addgenes\": false, \"mincontig\": \"200\"}, \"evalue\": \"1e-06\", \"fast\": false, \"genus\": \"Staphylococcus\", \"gffver\": \"3\", \"increment\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"kingdom\": {\"kingdom_select\": \"Bacteria\", \"__current_case__\": 1, \"gcode\": \"11\"}, \"locustag\": \"P\", \"metagenome\": false, \"norrna\": false, \"notrna\": false, \"outputs\": [\"gff\", \"gbk\", \"fna\", \"faa\", \"ffn\", \"sqn\", \"fsa\", \"tbl\", \"err\", \"txt\"], \"plasmid\": \"\", \"proteins\": null, \"rfam\": false, \"species\": \"aureus\", \"strain\": \"\", \"usegenus\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.14.5",
                         "type": "tool",
-                        "uuid": "2cfe94b1-f9cb-4df6-a3fd-b9356ea2423f",
+                        "uuid": "28efec53-71bb-4aaa-993d-03b78d493570",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "4eaf137c-b5fd-4cdd-9fa7-ed973e2302f3"
+                                "label": "gff_output",
+                                "output_name": "out_gff",
+                                "uuid": "a336c364-e69e-47eb-ace6-a7fe46d285fe"
                             }
                         ]
                     }
                 ],
-                "parent_id": "genome-annotation/apollo",
-                "path": "topics/genome-annotation/tutorials/apollo/workflows/main_workflow.ga",
+                "parent_id": "genome-annotation/annotation-with-prokka",
+                "path": "topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
                 "tags": [
-                    "genome-annotation"
+                    "genome-annotation",
+                    "GTN"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "Apollo Load Test",
+                "tests": true,
+                "title": "Genome Annotation with Prokka ",
                 "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-apollo/versions/main-workflow",
-                "tutorial_id": "apollo",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/apollo/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/apollo/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "genome-annotation-apollo",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-annotation-with-prokka/versions/galaxy-workflow-workflow-constructed-from-history--prokka-workflow-",
+                "tutorial_id": "annotation-with-prokka",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.html",
+                "version": 6,
+                "wfid": "genome-annotation-annotation-with-prokka",
+                "wfname": "galaxy-workflow-workflow-constructed-from-history--prokka-workflow-",
+                "workflow": "Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_account/create_account/3.1",
-                    "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
-                    "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
-                    "toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1",
+                    "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
                     "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1"
                 ],
-                "workflowhub_id": "1190"
+                "workflowhub_id": "1186"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/4889110"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.1156405"
     },
     {
         "admin_install": {
@@ -112907,7 +113879,8 @@
         "hands_on": true,
         "id": "genome-annotation/amr-gene-detection",
         "inexact_supported_servers": [
-            "Galaxy@AuBi"
+            "Galaxy@AuBi",
+            "UseGalaxy.org (Main)"
         ],
         "js_requirements": {
             "mathjax": null,
@@ -112920,27 +113893,42 @@
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-13",
+        "mod_date": "2024-09-27",
         "objectives": [
             "Run a series of tool to assess the presence of antimicrobial resistance genes (ARG)",
             "Get information about ARGs",
             "Visualize the ARGs and plasmid genes in their genomic context"
         ],
-        "pageviews": 1368,
+        "pageviews": 1576,
         "pub_date": "2024-01-23",
         "questions": [
             "Which resistance genes are on a bacterial genome?",
             "Where are the genes located on the genome?"
         ],
+        "recordings": [
+            {
+                "bot-timestamp": 1727199012,
+                "captioners": [
+                    "SaimMomin12"
+                ],
+                "date": "2024-09-24",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "26M",
+                "speakers": [
+                    "SaimMomin12"
+                ],
+                "youtube_id": "hfiYCIcD0ww"
+            }
+        ],
         "short_id": "T00401",
         "short_tools": [
-            "Grep1",
             "jbrowse",
-            "bowtie2",
             "tbl2gff3",
-            "bakta",
+            "upload1",
+            "Grep1",
             "staramr_search",
-            "upload1"
+            "bakta",
+            "bowtie2"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -112968,6 +113956,11 @@
                     "name": "Galaxy@AuBi",
                     "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 }
             ]
         },
@@ -113006,12 +113999,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.json"
         },
-        "version": 5,
+        "version": 6,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 176,
-        "visitors": 967,
+        "visit_duration": 165,
+        "visitors": 1138,
         "workflows": [
             {
                 "creators": [
@@ -113033,7 +114026,7 @@
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontigs\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nforward_reads\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreverse_reads\"]\n  3[label=\"staramr\"]\n  0 -> 3 [label=\"output\"]\n  k7a18df3cf28045aa92e427b79f10a005[color=lightseagreen,label=\"Output\\nstararm_detailed_summary\"]\n  3 -> k7a18df3cf28045aa92e427b79f10a005\n  4[label=\"Bakta\"]\n  0 -> 4 [label=\"output\"]\n  kead94d4086b04cf0aee2cf72a8f47933[color=lightseagreen,label=\"Output\\nbakta_annotation_summary\"]\n  4 -> kead94d4086b04cf0aee2cf72a8f47933\n  5[label=\"Bowtie2\"]\n  1 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  k0639b4672e624a52b72f35bf9f46f6a3[color=lightseagreen,label=\"Output\\nbowtie_mapping_stats\"]\n  5 -> k0639b4672e624a52b72f35bf9f46f6a3\n  6[label=\"Select\"]\n  3 -> 6 [label=\"detailed_summary\"]\n  7[label=\"Table to GFF3\"]\n  6 -> 7 [label=\"out_file1\"]\n  8[label=\"JBrowse\"]\n  4 -> 8 [label=\"annotation_gff3\"]\n  7 -> 8 [label=\"output\"]\n  5 -> 8 [label=\"output\"]\n  k910a35522a224279b15930379b31496f[color=lightseagreen,label=\"Output\\njbrowse_output\"]\n  8 -> k910a35522a224279b15930379b31496f\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontigs\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nforward_reads\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreverse_reads\"]\n  3[label=\"staramr\"]\n  0 -> 3 [label=\"output\"]\n  k000e2ab992db45bba0efecccf06da616[color=lightseagreen,label=\"Output\\nstararm_detailed_summary\"]\n  3 -> k000e2ab992db45bba0efecccf06da616\n  4[label=\"Bakta\"]\n  0 -> 4 [label=\"output\"]\n  kc848b1eb72624627b7a705a13b968935[color=lightseagreen,label=\"Output\\nbakta_annotation_summary\"]\n  4 -> kc848b1eb72624627b7a705a13b968935\n  5[label=\"Bowtie2\"]\n  1 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  k352e63d38aca4dff878c10497f65bb74[color=lightseagreen,label=\"Output\\nbowtie_mapping_stats\"]\n  5 -> k352e63d38aca4dff878c10497f65bb74\n  6[label=\"Select\"]\n  3 -> 6 [label=\"detailed_summary\"]\n  7[label=\"Table to GFF3\"]\n  6 -> 7 [label=\"out_file1\"]\n  8[label=\"JBrowse\"]\n  4 -> 8 [label=\"annotation_gff3\"]\n  7 -> 8 [label=\"output\"]\n  5 -> 8 [label=\"output\"]\n  k3c3bd5fd419c45b2afcdc6d02af82695[color=lightseagreen,label=\"Output\\njbrowse_output\"]\n  8 -> k3c3bd5fd419c45b2afcdc6d02af82695\n}",
                 "history": [
                     {
                         "hash": "597f8ce954083c7cd4e43765b6c4709619637e6a",
@@ -113148,8 +114141,8 @@
                     }
                 ],
                 "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nforward_reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nreverse_reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"staramr\"];\n  0 -->|output| 3;\n  7a18df3c-f280-45aa-92e4-27b79f10a005[\"Output\\nstararm_detailed_summary\"];\n  3 --> 7a18df3c-f280-45aa-92e4-27b79f10a005;\n  style 7a18df3c-f280-45aa-92e4-27b79f10a005 stroke:#2c3143,stroke-width:4px;\n  4[\"Bakta\"];\n  0 -->|output| 4;\n  ead94d40-86b0-4cf0-aee2-cf72a8f47933[\"Output\\nbakta_annotation_summary\"];\n  4 --> ead94d40-86b0-4cf0-aee2-cf72a8f47933;\n  style ead94d40-86b0-4cf0-aee2-cf72a8f47933 stroke:#2c3143,stroke-width:4px;\n  5[\"Bowtie2\"];\n  1 -->|output| 5;\n  2 -->|output| 5;\n  0 -->|output| 5;\n  0639b467-2e62-4a52-b72f-35bf9f46f6a3[\"Output\\nbowtie_mapping_stats\"];\n  5 --> 0639b467-2e62-4a52-b72f-35bf9f46f6a3;\n  style 0639b467-2e62-4a52-b72f-35bf9f46f6a3 stroke:#2c3143,stroke-width:4px;\n  6[\"Select\"];\n  3 -->|detailed_summary| 6;\n  7[\"Table to GFF3\"];\n  6 -->|out_file1| 7;\n  8[\"JBrowse\"];\n  4 -->|annotation_gff3| 8;\n  7 -->|output| 8;\n  5 -->|output| 8;\n  910a3552-2a22-4279-b159-30379b31496f[\"Output\\njbrowse_output\"];\n  8 --> 910a3552-2a22-4279-b159-30379b31496f;\n  style 910a3552-2a22-4279-b159-30379b31496f stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nforward_reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nreverse_reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"staramr\"];\n  0 -->|output| 3;\n  000e2ab9-92db-45bb-a0ef-ecccf06da616[\"Output\\nstararm_detailed_summary\"];\n  3 --> 000e2ab9-92db-45bb-a0ef-ecccf06da616;\n  style 000e2ab9-92db-45bb-a0ef-ecccf06da616 stroke:#2c3143,stroke-width:4px;\n  4[\"Bakta\"];\n  0 -->|output| 4;\n  c848b1eb-7262-4627-b7a7-05a13b968935[\"Output\\nbakta_annotation_summary\"];\n  4 --> c848b1eb-7262-4627-b7a7-05a13b968935;\n  style c848b1eb-7262-4627-b7a7-05a13b968935 stroke:#2c3143,stroke-width:4px;\n  5[\"Bowtie2\"];\n  1 -->|output| 5;\n  2 -->|output| 5;\n  0 -->|output| 5;\n  352e63d3-8aca-4dff-878c-10497f65bb74[\"Output\\nbowtie_mapping_stats\"];\n  5 --> 352e63d3-8aca-4dff-878c-10497f65bb74;\n  style 352e63d3-8aca-4dff-878c-10497f65bb74 stroke:#2c3143,stroke-width:4px;\n  6[\"Select\"];\n  3 -->|detailed_summary| 6;\n  7[\"Table to GFF3\"];\n  6 -->|out_file1| 7;\n  8[\"JBrowse\"];\n  4 -->|annotation_gff3| 8;\n  7 -->|output| 8;\n  5 -->|output| 8;\n  3c3bd5fd-419c-45b2-afcd-c6d02af82695[\"Output\\njbrowse_output\"];\n  8 --> 3c3bd5fd-419c-45b2-afcd-c6d02af82695;\n  style 3c3bd5fd-419c-45b2-afcd-c6d02af82695 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
                 "name": "mrsa AMR gene detection",
                 "outputs": [
                     {
@@ -113221,7 +114214,7 @@
                             {
                                 "label": "stararm_detailed_summary",
                                 "output_name": "detailed_summary",
-                                "uuid": "7a18df3c-f280-45aa-92e4-27b79f10a005"
+                                "uuid": "000e2ab9-92db-45bb-a0ef-ecccf06da616"
                             }
                         ]
                     },
@@ -113295,7 +114288,7 @@
                             {
                                 "label": "bakta_annotation_summary",
                                 "output_name": "annotation_tsv",
-                                "uuid": "ead94d40-86b0-4cf0-aee2-cf72a8f47933"
+                                "uuid": "c848b1eb-7262-4627-b7a7-05a13b968935"
                             }
                         ]
                     },
@@ -113352,7 +114345,7 @@
                             {
                                 "label": "bowtie_mapping_stats",
                                 "output_name": "mapping_stats",
-                                "uuid": "0639b467-2e62-4a52-b72f-35bf9f46f6a3"
+                                "uuid": "352e63d3-8aca-4dff-878c-10497f65bb74"
                             }
                         ]
                     },
@@ -113405,7 +114398,7 @@
                             {
                                 "label": "jbrowse_output",
                                 "output_name": "output",
-                                "uuid": "910a3552-2a22-4279-b159-30379b31496f"
+                                "uuid": "3c3bd5fd-419c-45b2-afcd-c6d02af82695"
                             }
                         ]
                     }
@@ -113442,44 +114435,40 @@
         "zenodo_link": "https://zenodo.org/record/10572227"
     },
     {
+        "abbreviations": {
+            "OGS": "Official Gene Set"
+        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "fbf99087e067",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "fbf99087e067",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "apollo_create_account",
+                    "owner": "gga",
+                    "revisions": "e80d29fd2a33",
+                    "tool_panel_section_label": "Apollo",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bakta",
-                    "owner": "iuc",
-                    "revisions": "ba6990f72184",
-                    "tool_panel_section_label": "Annotation",
+                    "name": "apollo_create_or_update",
+                    "owner": "gga",
+                    "revisions": "4abaab60f9e1",
+                    "tool_panel_section_label": "Apollo",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "integron_finder",
-                    "owner": "iuc",
-                    "revisions": "bfd290fe1588",
-                    "tool_panel_section_label": "Annotation",
+                    "name": "apollo_iframe",
+                    "owner": "gga",
+                    "revisions": "f4e3f9480307",
+                    "tool_panel_section_label": "Apollo",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "isescan",
-                    "owner": "iuc",
-                    "revisions": "9e776e7fab4f",
-                    "tool_panel_section_label": "Annotation",
+                    "name": "apollo_list_organism",
+                    "owner": "gga",
+                    "revisions": "2c749ed310da",
+                    "tool_panel_section_label": "Apollo",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
@@ -113488,199 +114477,273 @@
                     "revisions": "a6e57ff585c0",
                     "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "plasmidfinder",
-                    "owner": "iuc",
-                    "revisions": "7075b7a5441b",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "tbl2gff3",
-                    "owner": "iuc",
-                    "revisions": "4a7f4b0cc0a3",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bakta\n  owner: iuc\n  revisions: ba6990f72184\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: integron_finder\n  owner: iuc\n  revisions: bfd290fe1588\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: isescan\n  owner: iuc\n  revisions: 9e776e7fab4f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: plasmidfinder\n  owner: iuc\n  revisions: 7075b7a5441b\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbl2gff3\n  owner: iuc\n  revisions: 4a7f4b0cc0a3\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: apollo_create_account\n  owner: gga\n  revisions: e80d29fd2a33\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: apollo_create_or_update\n  owner: gga\n  revisions: 4abaab60f9e1\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: apollo_iframe\n  owner: gga\n  revisions: f4e3f9480307\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: apollo_list_organism\n  owner: gga\n  revisions: 2c749ed310da\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo/tutorial.json",
         "contributions": {
             "authorship": [
-                "bebatut"
+                "abretaud",
+                "hexylena",
+                "nathandunn",
+                "mboudet"
             ],
             "funding": [
-                "abromics"
+                "gallantries",
+                "eurosciencegateway"
             ]
         },
         "contributors": [
             {
                 "affiliations": [
                     "gallantries",
-                    "ifb",
+                    "eurosciencegateway",
                     "elixir-europe"
                 ],
                 "contact_for_training": true,
                 "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
                 "fediverse_flavor": "mastodon",
-                "id": "bebatut",
+                "id": "abretaud",
                 "joined": "2017-09",
-                "linkedin": "berenicebatut",
                 "location": {
                     "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
+                    "lat": 48.11,
+                    "lon": -1.64
                 },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
             },
             {
-                "avatar": "/training-material/assets/images/abromics.png",
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "email": "nathandunn@lbl.gov",
+                "id": "nathandunn",
+                "joined": "2019-07",
+                "name": "Nathan Dunn",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nathandunn/",
+                "twitter": "precogincog",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nathandunn.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "fr",
+                "email": "mateo.boudet@inrae.fr",
+                "id": "mboudet",
+                "joined": "2021-05",
+                "name": "Mateo Boudet",
+                "orcid": "0000-0002-7028-7620",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mboudet/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mboudet.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/eurosciencegateway.png",
                 "funder": true,
+                "funding_id": "101057388",
+                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
+                "funding_system": "cordis",
                 "github": false,
-                "id": "abromics",
-                "joined": "2024-01",
-                "name": "ABRomics",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abromics/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/abromics.json"
+                "id": "eurosciencegateway",
+                "joined": "2023-10",
+                "members": [
+                    "abretaud",
+                    "anuprulez",
+                    "bgruening",
+                    "erxleben",
+                    "pauldg",
+                    "rlibouba"
+                ],
+                "name": "EuroScienceGateway",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
             }
         ],
-        "dir": "topics/genome-annotation/tutorials/bacterial-genome-annotation",
+        "dir": "topics/genome-annotation/tutorials/apollo",
         "edam_ontology": [
             "topic_0622",
             "topic_3301",
             "topic_0623",
-            "topic_0080",
-            "topic_3673",
-            "topic_0085",
-            "topic_0798"
+            "topic_0080"
         ],
         "edam_operation": [
-            "Genome assembly",
-            "Sequence motif recognition",
-            "Genome annotation",
-            "Nucleic acid feature detection",
-            "Structural variation detection",
-            "Multilocus sequence typing",
-            "Genome visualisation",
-            "Protein feature detection",
-            "Scaffolding"
+            "Genome visualisation"
         ],
         "edam_topic": [
             "Genomics",
             "Microbiology",
             "Gene and protein families",
-            "Sequence analysis",
-            "Whole genome sequencing",
-            "Functional genomics",
-            "Mobile genetic elements"
-        ],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.fr"
+            "Sequence analysis"
         ],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "genome-annotation",
-                "tutorials": [
-                    "apollo"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "visualisation",
-                "tutorials": [
-                    "circos",
-                    "jbrowse"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "history-to-workflow"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "genome-annotation/bacterial-genome-annotation",
+        "id": "genome-annotation/apollo",
         "inexact_supported_servers": [
-            "Galaxy@AuBi",
-            "UseGalaxy.cz"
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.no"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Bakta is a powerful tool to annotate a bacterial genome",
-            "Annotation can be easily visualized to understand the genomic context and help making sense of the annotations"
+            "Apollo is the Google Docs of the genome annotation world, real-time collaborative genome annotation.",
+            "Apollo allows a group to view and manually refine predicted genome annotations",
+            "Use Apollo to edit annotations within your group.",
+            "Export manual annotations as GFF3."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-01",
+        "mod_date": "2024-08-08",
         "objectives": [
-            "Run a series of tool to annotate a draft bacterial genome for different types of genomic components",
-            "Evaluate the annotation",
-            "Process the outputs to formate them for visualization needs",
-            "Visualize a draft bacterial genome and its annotations"
+            "Load a genome into Galaxy",
+            "View annotations in JBrowse",
+            "Learn how to load JBrowse data into Apollo",
+            "Learn how to manually refine genome annotations within Apollo",
+            "Export refined genome annotations"
         ],
-        "pageviews": 2378,
-        "pub_date": "2024-02-01",
+        "pageviews": 5119570,
+        "pub_date": "2021-06-04",
         "questions": [
-            "Which genes are on a draft bacterial genome?",
-            "Which other genomic components can be found on a draft bacterial genome?"
+            "How to visualize your genome after automated annotations have been performed?",
+            "How to manually annotate genome after automated annotations have been performed?",
+            "How to evaluate and visualize annotated genomic features?",
+            "How do I collaborate when doing genome annotation?"
         ],
-        "short_id": "T00403",
+        "recordings": [
+            {
+                "captioners": [
+                    "abretaud"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "1H",
+                "speakers": [
+                    "abretaud"
+                ],
+                "youtube_id": "ywK1fhM-QFU"
+            }
+        ],
+        "requirements": [
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "upload-rules"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "genome-annotation",
+                "tutorials": [
+                    "annotation-with-prokka"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00169",
         "short_tools": [
-            "Grouping1",
             "jbrowse",
-            "upload1",
-            "integron_finder",
-            "isescan",
-            "tp_tail_tool",
-            "plasmidfinder",
-            "tbl2gff3",
-            "bakta",
-            "tp_replace_in_column"
+            "create_or_update",
+            "iframe",
+            "list_organism",
+            "create_account"
+        ],
+        "slides": true,
+        "slides_recordings": [
+            {
+                "captioners": [
+                    "abretaud"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "5M",
+                "speakers": [
+                    "awspolly"
+                ],
+                "youtube_id": "ailUycRVHtE"
+            }
         ],
-        "slides": false,
-        "slides_recordings": false,
         "subtopic": "prokaryote",
         "supported_servers": {
-            "exact": [
+            "exact": [],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 }
             ]
@@ -113688,24 +114751,19 @@
         "symlink": null,
         "tags": [
             "gmod",
-            "illumina",
-            "bacteria",
+            "prokaryote",
             "microgalaxy",
-            "jbrowse1"
+            "jbrowse1",
+            "apollo2"
         ],
-        "time_estimation": "3H",
-        "title": "Bacterial Genome Annotation",
+        "time_estimation": "3h",
+        "title": "Refining Genome Annotations with Apollo (prokaryotes)",
         "tools": [
-            "Grouping1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2",
-            "upload1"
+            "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_account/create_account/3.1",
+            "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
+            "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
+            "toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1"
         ],
         "topic_name": "genome-annotation",
         "topic_name_human": "Genome Annotation",
@@ -113713,1157 +114771,701 @@
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": false
+            "video": true
         },
-        "tutorial_name": "bacterial-genome-annotation",
+        "tutorial_name": "apollo",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo/tutorial.json"
         },
-        "version": 4,
-        "video": false,
-        "video_versions": 0,
+        "version": 20,
+        "video": true,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 140,
-        "visitors": 1800,
+        "visit_duration": 299,
+        "visitors": 1906178,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0001-9852-1987",
-                        "name": "B\u00e9r\u00e9nice Batut"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0002-8304-138X",
-                        "name": "Pierre Marin"
-                    }
-                ],
-                "description": "Bacterial Genome Annotation",
+                "creators": [],
+                "description": "Refining Genome Annotations with Apollo",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontigs\"]\n  1[label=\"ISEScan\"]\n  0 -> 1 [label=\"output\"]\n  k2bb672cb453646b08a228590a0ca36c7[color=lightseagreen,label=\"Output\\nisescan_results\"]\n  1 -> k2bb672cb453646b08a228590a0ca36c7\n  2[label=\"PlasmidFinder\"]\n  0 -> 2 [label=\"output\"]\n  k614064e64b0f4e38b04ee3f61ba41b46[color=lightseagreen,label=\"Output\\nplasmidfinder_results\"]\n  2 -> k614064e64b0f4e38b04ee3f61ba41b46\n  3[label=\"Integron Finder\"]\n  0 -> 3 [label=\"output\"]\n  kd26788cf24414f29ac39b6be96f192eb[color=lightseagreen,label=\"Output\\nintegronfinder_summary\"]\n  3 -> kd26788cf24414f29ac39b6be96f192eb\n  4[label=\"Bakta\"]\n  0 -> 4 [label=\"output\"]\n  kd3a40a8b1bd142b6a91e756379b86d94[color=lightseagreen,label=\"Output\\nbakta_summary\"]\n  4 -> kd3a40a8b1bd142b6a91e756379b86d94\n  5[label=\"Group\"]\n  1 -> 5 [label=\"all_results\"]\n  6[label=\"Group\"]\n  1 -> 6 [label=\"all_results\"]\n  7[label=\"Replace Text\"]\n  2 -> 7 [label=\"result_file\"]\n  8[label=\"Select last\"]\n  7 -> 8 [label=\"outfile\"]\n  9[label=\"Table to GFF3\"]\n  8 -> 9 [label=\"outfile\"]\n  10[label=\"JBrowse\"]\n  0 -> 10 [label=\"output\"]\n  4 -> 10 [label=\"annotation_gff3\"]\n  9 -> 10 [label=\"output\"]\n  1 -> 10 [label=\"annotation\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager.bw\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam\"]\n  4[label=\"Register Account\"]\n  5[label=\"List Organisms\"]\n  6[label=\"JBrowse\"]\n  0 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"Create or Update Organism\"]\n  6 -> 7 [label=\"output\"]\n  8[label=\"Annotate\"]\n  7 -> 8 [label=\"output\"]\n}",
                 "history": [
                     {
-                        "hash": "87968f9a6953ebf322d9fb0fae3a4193b6222288",
-                        "message": "Update tool versions",
+                        "hash": "6bc77b7441375cd57ea1d73e9fe2f80ef550891a",
+                        "message": "wf annotation",
+                        "num": 3,
+                        "short_hash": "6bc77b744",
+                        "unix": "1622101979"
+                    },
+                    {
+                        "hash": "9ced3a95cd725623c7c1f2664b0174a14cd59337",
+                        "message": "update workflow",
                         "num": 2,
-                        "short_hash": "87968f9a6",
-                        "unix": "1722510143"
+                        "short_hash": "9ced3a95c",
+                        "unix": "1622043687"
                     },
                     {
-                        "hash": "217f251aaa898a91dbb18b5cec3daebaf582c712",
-                        "message": "Update worklow and add tests",
+                        "hash": "32f41f6fe47606c12d4574551233e4a2583df189",
+                        "message": "rewrite bits v2",
                         "num": 1,
-                        "short_hash": "217f251aa",
-                        "unix": "1706526984"
+                        "short_hash": "32f41f6fe",
+                        "unix": "1571055596"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "contigs",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "contigs",
-                                "name": "contigs"
+                                "description": "",
+                                "name": "https://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1"
                             }
                         ],
-                        "label": "contigs",
+                        "label": "https://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 354.8999938964844,
+                            "height": 143.39999389648438,
+                            "left": 488,
+                            "right": 688,
+                            "top": 211.5,
+                            "width": 200,
+                            "x": 488,
+                            "y": 211.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "fa88b9bb-b87e-457b-a836-a8f1b25e520b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "82c708ee-87a4-45a2-abf0-911309e218fd"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "https://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1"
+                            }
+                        ],
+                        "label": "https://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 527.8999938964844,
+                            "height": 143.39999389648438,
+                            "left": 510,
+                            "right": 710,
+                            "top": 384.5,
+                            "width": 200,
+                            "x": 510,
+                            "y": 384.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "1afd430b-6250-4eb2-8cf2-a83adf022e4b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "cbbb4914-0c3d-4857-8c3a-f43b3f0c39f9"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "https://zenodo.org/record/3270822/files/forager.bw"
+                            }
+                        ],
+                        "label": "https://zenodo.org/record/3270822/files/forager.bw",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 659.1000061035156,
+                            "height": 102.60000610351562,
+                            "left": 493,
+                            "right": 693,
+                            "top": 556.5,
+                            "width": 200,
+                            "x": 493,
+                            "y": 556.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "091ca713-0096-419c-8cb7-7e83a41aab37",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "f4c19cc0-5099-4514-af29-52a3933b28f9"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "https://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam"
+                            }
+                        ],
+                        "label": "https://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 858.8999938964844,
+                            "height": 143.39999389648438,
+                            "left": 563,
+                            "right": 763,
+                            "top": 715.5,
+                            "width": 200,
+                            "x": 563,
+                            "y": 715.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "13d26450-8b30-42d4-9822-f697217818b1",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "464904cb-5608-4f5d-b282-a09be9d3dbbb"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager.bw\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nhttps://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Register Account\"];\n  5[\"List Organisms\"];\n  6[\"JBrowse\"];\n  0 -->|output| 6;\n  1 -->|output| 6;\n  3 -->|output| 6;\n  2 -->|output| 6;\n  7[\"Create or Update Organism\"];\n  6 -->|output| 7;\n  8[\"Annotate\"];\n  7 -->|output| 8;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Apollo Load Test",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "https://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1"
+                            }
+                        ],
+                        "label": "https://zenodo.org/record/3270822/files/Amel_4.5_scaffolds.fa.gz?download=1",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 354.8999938964844,
+                            "height": 143.39999389648438,
+                            "left": 488,
+                            "right": 688,
+                            "top": 211.5,
+                            "width": 200,
+                            "x": 488,
+                            "y": 211.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "fa88b9bb-b87e-457b-a836-a8f1b25e520b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "82c708ee-87a4-45a2-abf0-911309e218fd"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "https://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1"
+                            }
+                        ],
+                        "label": "https://zenodo.org/record/3270822/files/amel_OGSv3.2.gff3.gz?download=1",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 527.8999938964844,
+                            "height": 143.39999389648438,
+                            "left": 510,
+                            "right": 710,
+                            "top": 384.5,
+                            "width": 200,
+                            "x": 510,
+                            "y": 384.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "1afd430b-6250-4eb2-8cf2-a83adf022e4b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "cbbb4914-0c3d-4857-8c3a-f43b3f0c39f9"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "https://zenodo.org/record/3270822/files/forager.bw"
+                            }
+                        ],
+                        "label": "https://zenodo.org/record/3270822/files/forager.bw",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 659.1000061035156,
+                            "height": 102.60000610351562,
+                            "left": 493,
+                            "right": 693,
+                            "top": 556.5,
+                            "width": 200,
+                            "x": 493,
+                            "y": 556.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "091ca713-0096-419c-8cb7-7e83a41aab37",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "f4c19cc0-5099-4514-af29-52a3933b28f9"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "https://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam"
+                            }
+                        ],
+                        "label": "https://zenodo.org/record/3270822/files/forager_Amel4.5_accepted_hits.bam",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 424
+                            "bottom": 858.8999938964844,
+                            "height": 143.39999389648438,
+                            "left": 563,
+                            "right": 763,
+                            "top": 715.5,
+                            "width": 200,
+                            "x": 563,
+                            "y": 715.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "8cde8af1-c277-4b9f-97f7-54f5997f2c5d",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "AGPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"ISEScan\"];\n  0 -->|output| 1;\n  2bb672cb-4536-46b0-8a22-8590a0ca36c7[\"Output\\nisescan_results\"];\n  1 --> 2bb672cb-4536-46b0-8a22-8590a0ca36c7;\n  style 2bb672cb-4536-46b0-8a22-8590a0ca36c7 stroke:#2c3143,stroke-width:4px;\n  2[\"PlasmidFinder\"];\n  0 -->|output| 2;\n  614064e6-4b0f-4e38-b04e-e3f61ba41b46[\"Output\\nplasmidfinder_results\"];\n  2 --> 614064e6-4b0f-4e38-b04e-e3f61ba41b46;\n  style 614064e6-4b0f-4e38-b04e-e3f61ba41b46 stroke:#2c3143,stroke-width:4px;\n  3[\"Integron Finder\"];\n  0 -->|output| 3;\n  d26788cf-2441-4f29-ac39-b6be96f192eb[\"Output\\nintegronfinder_summary\"];\n  3 --> d26788cf-2441-4f29-ac39-b6be96f192eb;\n  style d26788cf-2441-4f29-ac39-b6be96f192eb stroke:#2c3143,stroke-width:4px;\n  4[\"Bakta\"];\n  0 -->|output| 4;\n  d3a40a8b-1bd1-42b6-a91e-756379b86d94[\"Output\\nbakta_summary\"];\n  4 --> d3a40a8b-1bd1-42b6-a91e-756379b86d94;\n  style d3a40a8b-1bd1-42b6-a91e-756379b86d94 stroke:#2c3143,stroke-width:4px;\n  5[\"Group\"];\n  1 -->|all_results| 5;\n  6[\"Group\"];\n  1 -->|all_results| 6;\n  7[\"Replace Text\"];\n  2 -->|result_file| 7;\n  8[\"Select last\"];\n  7 -->|outfile| 8;\n  9[\"Table to GFF3\"];\n  8 -->|outfile| 9;\n  10[\"JBrowse\"];\n  0 -->|output| 10;\n  4 -->|annotation_gff3| 10;\n  9 -->|output| 10;\n  1 -->|annotation| 10;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Bacterial Genome Annotation",
-                "outputs": [
+                        "uuid": "13d26450-8b30-42d4-9822-f697217818b1",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "464904cb-5608-4f5d-b282-a09be9d3dbbb"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_account/create_account/3.1",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
+                        "id": 4,
+                        "input_connections": {},
                         "inputs": [],
                         "label": null,
-                        "name": "ISEScan",
+                        "name": "Register Account",
                         "outputs": [
                             {
-                                "name": "summary",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "all_results",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "annotation",
-                                "type": "gff"
-                            },
-                            {
-                                "name": "is_fasta",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "orf_fna",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "orf_faa",
-                                "type": "fasta"
+                                "name": "output",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 280,
-                            "top": 133
+                            "bottom": 1038.6999969482422,
+                            "height": 82.19999694824219,
+                            "left": 644,
+                            "right": 844,
+                            "top": 956.5,
+                            "width": 200,
+                            "x": 644,
+                            "y": 956.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_account/create_account/3.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "19f42b3ea391",
-                            "name": "isescan",
-                            "owner": "iuc",
+                            "changeset_revision": "e80d29fd2a33",
+                            "name": "apollo_create_account",
+                            "owner": "gga",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"log_activate\": false, \"remove_short_is\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.2.3+galaxy1",
+                        "tool_state": "{\"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"first\": \"Nathan\", \"last\": \"Dunn\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1",
                         "type": "tool",
-                        "uuid": "334b327f-be00-4e75-ae01-c3ba674dbc9b",
-                        "when": null,
+                        "uuid": "82f0b666-8743-4cdc-9682-feb10c35b0c6",
                         "workflow_outputs": [
                             {
-                                "label": "isescan_results",
-                                "output_name": "all_results",
-                                "uuid": "2bb672cb-4536-46b0-8a22-8590a0ca36c7"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "dc1e2c2f-c566-48e0-95c7-327adb229fb5"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "input|input_file": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
+                        "id": 5,
+                        "input_connections": {},
                         "inputs": [],
                         "label": null,
-                        "name": "PlasmidFinder",
+                        "name": "List Organisms",
                         "outputs": [
                             {
-                                "name": "hit_file",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "plasmid_file",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "result_file",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "raw_file",
-                                "type": "txt"
+                                "name": "output",
+                                "type": "json"
                             }
                         ],
                         "position": {
-                            "left": 280,
-                            "top": 420
+                            "bottom": 1158.6999969482422,
+                            "height": 82.19999694824219,
+                            "left": 644,
+                            "right": 844,
+                            "top": 1076.5,
+                            "width": 200,
+                            "x": 644,
+                            "y": 1076.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "7075b7a5441b",
-                            "name": "plasmidfinder",
-                            "owner": "iuc",
+                            "changeset_revision": "2c749ed310da",
+                            "name": "apollo_list_organism",
+                            "owner": "gga",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"database_name\": \"plasmidfinder_1307168_2019_08_28\"}, \"options\": {\"min_cov\": \"0.6\", \"threshold\": \"0.95\"}, \"output_files\": {\"output_selection\": [\"hit_fasta\", \"plasmid_fasta\", \"result_tsv\", \"result_txt\"]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.6+galaxy1",
+                        "tool_state": "{\"chromInfo\": \"\\\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
+                        "tool_version": "3.1",
                         "type": "tool",
-                        "uuid": "484ea537-4097-4097-b19c-84fef6c7de9a",
-                        "when": null,
+                        "uuid": "3fc26308-b331-4286-863a-d31ac5b6fb03",
                         "workflow_outputs": [
                             {
-                                "label": "plasmidfinder_results",
-                                "output_name": "result_file",
-                                "uuid": "614064e6-4b0f-4e38-b04e-e3f61ba41b46"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "d7cc17cb-e3e2-4adf-857c-8d3583e57fdd"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
                         "errors": null,
-                        "id": 3,
+                        "id": 6,
                         "input_connections": {
-                            "sequence": {
+                            "reference_genome|genome": {
                                 "id": 0,
                                 "output_name": "output"
+                            },
+                            "track_groups_0|data_tracks_0|data_format|annotation": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "track_groups_1|data_tracks_0|data_format|annotation": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "track_groups_1|data_tracks_1|data_format|annotation": {
+                                "id": 2,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool JBrowse",
+                                "name": "reference_genome"
+                            }
+                        ],
                         "label": null,
-                        "name": "Integron Finder",
+                        "name": "JBrowse",
                         "outputs": [
                             {
-                                "name": "integrons_table",
-                                "type": "tsv"
-                            },
-                            {
-                                "name": "summary",
-                                "type": "tsv"
+                                "name": "output",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 280,
-                            "top": 665
-                        },
-                        "post_job_actions": {
-                            "ChangeDatatypeActionintegrons_table": {
-                                "action_arguments": {
-                                    "newtype": "tabular"
-                                },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "integrons_table"
-                            }
+                            "bottom": 650.2999877929688,
+                            "height": 306.79998779296875,
+                            "left": 821,
+                            "right": 1021,
+                            "top": 343.5,
+                            "width": 200,
+                            "x": 821,
+                            "y": 343.5
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "4768f7f8e93f",
-                            "name": "integron_finder",
+                            "changeset_revision": "a6e57ff585c0",
+                            "name": "jbrowse",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"gbk\": false, \"local_max\": true, \"no_logfile\": true, \"pdf\": false, \"promoter_attI\": true, \"sequence\": {\"__class__\": \"ConnectedValue\"}, \"settings\": {\"attc_settings\": {\"dist_thresh\": \"4000\", \"calin_threshold\": \"2\", \"max_attc_size\": \"200\", \"min_attc_size\": \"40\", \"keep_palindromes\": false, \"covar_matrix\": null}, \"protein_settings\": {\"no_proteins\": false, \"union_integrases\": false, \"func_annot\": false}}, \"topology_file\": null, \"type_replicon\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.5+galaxy0",
+                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"true\", \"track_groups\": [{\"__index__\": 0, \"category\": \"OGS 3.2\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_on\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 1, \"category\": \"Reads\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"auto_snp\": \"true\", \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"wiggle\", \"__current_case__\": 4, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"xyplot\": \"false\", \"var_band\": \"false\", \"scaling\": {\"scale_select\": \"auto_local\", \"__current_case__\": 0}, \"scale_select2\": \"linear\", \"MultiBigWig\": \"false\", \"jbcolor\": {\"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}, \"bicolor_pivot\": {\"bicolor_pivot_select\": \"zero\", \"__current_case__\": 0}}, \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.11+galaxy1",
                         "type": "tool",
-                        "uuid": "29a9252c-5c3b-4024-99ff-637d0572320a",
-                        "when": null,
+                        "uuid": "2e2723bf-9597-4c96-9980-33220e3b849a",
                         "workflow_outputs": [
                             {
-                                "label": "integronfinder_summary",
-                                "output_name": "summary",
-                                "uuid": "d26788cf-2441-4f29-ac39-b6be96f192eb"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "9514c32e-2376-44ee-b368-beb25bf77ad7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
                         "errors": null,
-                        "id": 4,
+                        "id": 7,
                         "input_connections": {
-                            "input_option|input_file": {
-                                "id": 0,
+                            "jbrowse": {
+                                "id": 6,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Create or Update Organism",
+                                "name": "jbrowse"
+                            }
+                        ],
                         "label": null,
-                        "name": "Bakta",
+                        "name": "Create or Update Organism",
                         "outputs": [
                             {
-                                "name": "annotation_tsv",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "annotation_gff3",
-                                "type": "gff3"
-                            },
-                            {
-                                "name": "annotation_ffn",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "summary_txt",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "annotation_plot",
-                                "type": "svg"
+                                "name": "output",
+                                "type": "json"
                             }
                         ],
                         "position": {
-                            "left": 850,
-                            "top": 0
+                            "bottom": 506.1000061035156,
+                            "height": 113.60000610351562,
+                            "left": 1405,
+                            "right": 1605,
+                            "top": 392.5,
+                            "width": 200,
+                            "x": 1405,
+                            "y": 392.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
                         "tool_shed_repository": {
-                            "changeset_revision": "728dacaf08a9",
-                            "name": "bakta",
-                            "owner": "iuc",
+                            "changeset_revision": "4abaab60f9e1",
+                            "name": "apollo_create_or_update",
+                            "owner": "gga",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"annotation\": {\"complete\": false, \"prodigal\": null, \"translation_table\": \"11\", \"keep_contig_headers\": true, \"replicons\": null, \"compliant\": false, \"proteins\": null, \"meta\": false}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input_option\": {\"bakta_db_select\": \"V5.0_2023-02-20\", \"amrfinder_db_select\": \"amrfinderplus_V3.11_2022-12-19.1\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"min_contig_length\": null}, \"organism\": {\"genus\": null, \"species\": null, \"strain\": null, \"plasmid\": null}, \"output_files\": {\"output_selection\": [\"file_tsv\", \"file_gff3\", \"file_ffn\", \"file_plot\", \"sum_txt\"]}, \"workflow\": {\"skip_analysis\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.3+galaxy0",
+                        "tool_state": "{\"genus\": \"Apis\", \"group\": null, \"jbrowse\": {\"__class__\": \"RuntimeValue\"}, \"no_reload_sequences\": \"false\", \"org_source\": {\"source_select\": \"direct\", \"__current_case__\": 1, \"org_raw\": \"Honeybee\"}, \"public\": \"true\", \"remove_old_directory\": \"true\", \"species\": \"Mellifera\", \"test_hack\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.2.5",
                         "type": "tool",
-                        "uuid": "181220e7-9082-48bc-b855-f10baf78fc2a",
-                        "when": null,
+                        "uuid": "72c53f14-4e91-40c1-a4e9-325b6c2a3105",
                         "workflow_outputs": [
                             {
-                                "label": "bakta_summary",
-                                "output_name": "summary_txt",
-                                "uuid": "d3a40a8b-1bd1-42b6-a91e-756379b86d94"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "10c77447-f92c-44b0-8a04-151eef670244"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "genome-annotation/bacterial-genome-annotation",
-                "path": "topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.ga",
-                "tags": [
-                    "genome-annotation"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "Bacterial Genome Annotation",
-                "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-bacterial-genome-annotation/versions/bacterial-genome-annotation",
-                "tutorial_id": "bacterial-genome-annotation",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.html",
-                "version": 2,
-                "wfid": "genome-annotation-bacterial-genome-annotation",
-                "wfname": "bacterial-genome-annotation",
-                "workflow": "Bacterial-Genome-Annotation.ga",
-                "workflow_tools": [
-                    "Grouping1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2"
-                ],
-                "workflowhub_id": "1136"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/10572227"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "jbrowse",
-                    "owner": "iuc",
-                    "revisions": "17359b808b01",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: jbrowse\n  owner: iuc\n  revisions: 17359b808b01\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/jbrowse/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
-            }
-        ],
-        "dir": "topics/visualisation/tutorials/jbrowse",
-        "edam_operation": [
-            "Genome visualisation"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "Galaxy@AuBi",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "visualisation/jbrowse",
-        "inexact_supported_servers": [
-            "GalaxyTrakr",
-            "UseGalaxy.cz"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "This tutorial can not exhaustively cover every data type, but maybe it provides inspiration for your own analyses",
-            "JBrowse is a great, workflow-compatible alternative to other genome browsers",
-            "You can build visualisations that summarise dozens of analyses in one visualisation"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-02-29",
-        "objectives": [
-            "Build several visualisations in JBrowse",
-            "Have basic familiarity with moving around JBrowse, and loading several data tracks"
-        ],
-        "pageviews": 5732004,
-        "pub_date": "2020-01-10",
-        "questions": [
-            "How can I visualise features or blast data?",
-            "How can I visualise sequencing data in a workflow"
-        ],
-        "short_id": "T00322",
-        "short_tools": [
-            "jbrowse"
-        ],
-        "slides": true,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "gmod",
-            "jbrowse1"
-        ],
-        "time_estimation": "1h",
-        "title": "Genomic Data Visualisation with JBrowse",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0"
-        ],
-        "topic_name": "visualisation",
-        "topic_name_human": "Visualisation",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "jbrowse",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/visualisation/tutorials/jbrowse/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/jbrowse/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/jbrowse/tutorial.json"
-        },
-        "version": 15,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 287,
-        "visitors": 2067558,
-        "zenodo_link": "https://doi.org/10.5281/zenodo.3591856"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/official-gene-set/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "abretaud"
-            ],
-            "funding": [
-                "gallantries"
-            ]
-        },
-        "contributors": [
-            {
-                "affiliations": [
-                    "gallantries",
-                    "eurosciencegateway",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
-                "fediverse_flavor": "mastodon",
-                "id": "abretaud",
-                "joined": "2017-09",
-                "location": {
-                    "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
-                },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
-            }
-        ],
-        "dir": "topics/genome-annotation/tutorials/official-gene-set",
-        "draft": true,
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "genome-annotation/official-gene-set",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Genoest' OGS Tools makes it easy to validate and release a build of your genome and its annotations."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-02-29",
-        "objectives": [
-            "Validate your genes and create an official gene set from them."
-        ],
-        "pageviews": 9,
-        "pub_date": "2023-11-02",
-        "questions": [
-            "I have several genomes assemblies that are not annotated (or I do not trust annotations)",
-            "I am interested to compare structure of a particular gene across these genome assemblies",
-            "How do I do that?"
-        ],
-        "short_id": "T00370",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "gmod",
-            "apollo2",
-            "work-in-progress"
-        ],
-        "time_estimation": "30M",
-        "title": "Creating an Official Gene Set",
-        "tools": [],
-        "topic_name": "genome-annotation",
-        "topic_name_human": "Genome Annotation",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "official-gene-set",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/official-gene-set/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/official-gene-set/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/official-gene-set/tutorial.json"
-        },
-        "version": 2,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 0,
-        "visitors": 7,
-        "zenodo_link": ""
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "bwa",
-                    "owner": "devteam",
-                    "revisions": "e188dc7a68e6",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "3d0c7bdf12f5",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "jbrowse",
-                    "owner": "iuc",
-                    "revisions": "17359b808b01",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 17359b808b01\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "nakucher",
-                "avahoffman",
-                "robertmeller"
-            ],
-            "editing": [
-                "katherinecox",
-                "cutsort",
-                "nakucher"
-            ],
-            "funding": [
-                "nhgri-gdscn",
-                "nhgri-anvil"
-            ],
-            "infrastructure": [
-                "cansavvy",
-                "avahoffman",
-                "katherinecox",
-                "ehumph",
-                "cutsort"
-            ]
-        },
-        "contributors": [
-            {
-                "email": "nkucher3@jhu.edu",
-                "id": "nakucher",
-                "joined": "2023-06",
-                "name": "Natalie Kucher",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nakucher/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nakucher.json"
-            },
-            {
-                "id": "avahoffman",
-                "joined": "2023-06",
-                "name": "Ava Hoffman",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avahoffman/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/avahoffman.json"
-            },
-            {
-                "id": "robertmeller",
-                "joined": "2023-06",
-                "name": "Robert Meller",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/robertmeller/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/robertmeller.json"
-            },
-            {
-                "id": "katherinecox",
-                "joined": "2023-06",
-                "name": "Katherine Cox",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/katherinecox/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/katherinecox.json"
-            },
-            {
-                "id": "cutsort",
-                "joined": "2023-06",
-                "name": "Frederick Tan",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cutsort/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/cutsort.json"
-            },
-            {
-                "email": "nkucher3@jhu.edu",
-                "id": "nakucher",
-                "joined": "2023-06",
-                "name": "Natalie Kucher",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nakucher/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nakucher.json"
-            },
-            {
-                "id": "cansavvy",
-                "joined": "2023-06",
-                "name": "Candace Savonen",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cansavvy/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/cansavvy.json"
-            },
-            {
-                "id": "avahoffman",
-                "joined": "2023-06",
-                "name": "Ava Hoffman",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avahoffman/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/avahoffman.json"
-            },
-            {
-                "id": "katherinecox",
-                "joined": "2023-06",
-                "name": "Katherine Cox",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/katherinecox/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/katherinecox.json"
-            },
-            {
-                "id": "ehumph",
-                "joined": "2023-06",
-                "name": "Elizabeth Humphries",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ehumph/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/ehumph.json"
-            },
-            {
-                "id": "cutsort",
-                "joined": "2023-06",
-                "name": "Frederick Tan",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cutsort/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/cutsort.json"
-            },
-            {
-                "avatar": "https://www.ashg.org/wp-content/uploads/2021/07/nhgri-logo-800x167-1.png",
-                "funder": true,
-                "funding_id": "75N92022P00232",
-                "github": false,
-                "id": "nhgri-gdscn",
-                "joined": "2023-06",
-                "name": "National Human Genome Research Institute Genomic Data Science Community Network",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nhgri-gdscn/",
-                "short_name": "NHGRI GDS Community Network",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/nhgri-gdscn.json"
-            },
-            {
-                "avatar": "https://www.ashg.org/wp-content/uploads/2021/07/nhgri-logo-800x167-1.png",
-                "funder": true,
-                "funding_id": "U24HG010263",
-                "github": false,
-                "id": "nhgri-anvil",
-                "joined": "2023-06",
-                "name": "National Human Genome Research Institute Genomic Data Science Analysis, Visualization, and Informatics Lab-Space",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nhgri-anvil/",
-                "short_name": "NHGRI ANVIL",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/nhgri-anvil.json"
-            }
-        ],
-        "dir": "topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil",
-        "edam_operation": [
-            "Sequencing quality control",
-            "Generation",
-            "Read mapping",
-            "Genome visualisation",
-            "Genome indexing",
-            "Sequence alignment",
-            "Sequence composition calculation",
-            "Statistical calculation"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "sequence-analysis/sars-with-galaxy-on-anvil",
-        "inexact_supported_servers": [
-            "Galaxy@AuBi",
-            "GalaxyTrakr",
-            "UseGalaxy.cz"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Use Galaxy on the AnVIL cloud computing resource to check data, perform an alignment, and visualize the results."
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Introductory",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-02-29",
-        "objectives": [
-            "Gather and evaluate experimental evidence, including qualitative and quantitative data",
-            "Generate and interpret graphs displaying experimental results",
-            "Critique large data sets and use bioinformatics to assess genetics data",
-            "Tap into the interdisciplinary nature of science"
-        ],
-        "pageviews": 899,
-        "pub_date": "2023-07-10",
-        "questions": [
-            "How do I check my data quality?",
-            "How do I put together my dataset of fragmented sequences into a full sequence?",
-            "How do I visually explore the variants in my SARS-CoV-2 sample?"
-        ],
-        "short_id": "T00356",
-        "short_tools": [
-            "fastqc",
-            "bwa_mem",
-            "jbrowse"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "covid19",
-            "gmod",
-            "jbrowse1"
-        ],
-        "time_estimation": "1H",
-        "title": "SARS-CoV-2 Viral Sample Alignment and Variant Visualization",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0"
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "json_file": {
+                                "id": 7,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Annotate",
+                                "name": "json_file"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Annotate",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "html"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 502.6999969482422,
+                            "height": 93.19999694824219,
+                            "left": 1703,
+                            "right": 1903,
+                            "top": 409.5,
+                            "width": 200,
+                            "x": 1703,
+                            "y": 409.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f4e3f9480307",
+                            "name": "apollo_iframe",
+                            "owner": "gga",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"json_file\": {\"__class__\": \"RuntimeValue\"}, \"tracklist\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.2.5",
+                        "type": "tool",
+                        "uuid": "2cfe94b1-f9cb-4df6-a3fd-b9356ea2423f",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "4eaf137c-b5fd-4cdd-9fa7-ed973e2302f3"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "genome-annotation/apollo",
+                "path": "topics/genome-annotation/tutorials/apollo/workflows/main_workflow.ga",
+                "tags": [
+                    "genome-annotation"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Apollo Load Test",
+                "topic_id": "genome-annotation",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-apollo/versions/main-workflow",
+                "tutorial_id": "apollo",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/apollo/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/apollo/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "genome-annotation-apollo",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_account/create_account/3.1",
+                    "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
+                    "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
+                    "toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1"
+                ],
+                "workflowhub_id": "1190"
+            }
         ],
-        "topic_name": "sequence-analysis",
-        "topic_name_human": "Sequence analysis",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "sars-with-galaxy-on-anvil",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.json"
-        },
-        "version": 2,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 283,
-        "visitors": 691,
-        "zenodo_link": "https://doi.org/10.5281/zenodo.8115178"
+        "zenodo_link": "https://zenodo.org/record/4889110"
     },
     {
-        "abbreviations": {
-            "NMDS": "Non-metric multidimensional scaling"
-        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "interproscan",
+                    "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "74810db257cc",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "picard",
-                    "owner": "devteam",
-                    "revisions": "f9242e01365a",
-                    "tool_panel_section_label": "Picard",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "eggnog_mapper",
-                    "owner": "galaxyp",
-                    "revisions": "844fa988236b",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "aegean_parseval",
-                    "owner": "iuc",
-                    "revisions": "1b52f0c8ad7f",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "busco",
-                    "owner": "iuc",
-                    "revisions": "94170eee0ad8",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "funannotate_annotate",
-                    "owner": "iuc",
-                    "revisions": "9feee7fc49a1",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "funannotate_annotate",
-                    "owner": "iuc",
-                    "revisions": "582fd74dc2a1",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "86755160afbf",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "funannotate_compare",
-                    "owner": "iuc",
-                    "revisions": "a7ce2601500c",
-                    "tool_panel_section_label": "Annotation",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "86755160afbf",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "funannotate_compare",
+                    "name": "bakta",
                     "owner": "iuc",
-                    "revisions": "30f08d74024f",
+                    "revisions": "ba6990f72184",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "funannotate_predict",
+                    "name": "integron_finder",
                     "owner": "iuc",
-                    "revisions": "51b6ee65ef7f",
+                    "revisions": "bfd290fe1588",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "funannotate_predict",
+                    "name": "isescan",
                     "owner": "iuc",
-                    "revisions": "f31125bb85ea",
+                    "revisions": "9e776e7fab4f",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
@@ -114875,174 +115477,102 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "rgrnastar",
+                    "name": "plasmidfinder",
                     "owner": "iuc",
-                    "revisions": "3ea5a2a63fa2",
-                    "tool_panel_section_label": "Mapping",
+                    "revisions": "7075b7a5441b",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "rgrnastar",
+                    "name": "tbl2gff3",
                     "owner": "iuc",
-                    "revisions": "4074fc1940e2",
-                    "tool_panel_section_label": "Mapping",
+                    "revisions": "4a7f4b0cc0a3",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: interproscan\n  owner: bgruening\n  revisions: 74810db257cc\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: f9242e01365a\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: eggnog_mapper\n  owner: galaxyp\n  revisions: 844fa988236b\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: aegean_parseval\n  owner: iuc\n  revisions: 1b52f0c8ad7f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 94170eee0ad8\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_annotate\n  owner: iuc\n  revisions: 9feee7fc49a1\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_annotate\n  owner: iuc\n  revisions: 582fd74dc2a1\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_compare\n  owner: iuc\n  revisions: a7ce2601500c\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_compare\n  owner: iuc\n  revisions: 30f08d74024f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_predict\n  owner: iuc\n  revisions: 51b6ee65ef7f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_predict\n  owner: iuc\n  revisions: f31125bb85ea\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n  owner: iuc\n  revisions: 3ea5a2a63fa2\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n  owner: iuc\n  revisions: 4074fc1940e2\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/funannotate/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bakta\n  owner: iuc\n  revisions: ba6990f72184\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: integron_finder\n  owner: iuc\n  revisions: bfd290fe1588\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: isescan\n  owner: iuc\n  revisions: 9e776e7fab4f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: plasmidfinder\n  owner: iuc\n  revisions: 7075b7a5441b\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbl2gff3\n  owner: iuc\n  revisions: 4a7f4b0cc0a3\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.json",
         "contributions": {
             "authorship": [
-                "abretaud"
-            ],
-            "editing": [
-                "alexcorm",
-                "lleroi",
-                "r1corre",
-                "stephanierobin"
+                "bebatut"
             ],
             "funding": [
-                "gallantries",
-                "eurosciencegateway"
+                "abromics"
             ]
         },
         "contributors": [
             {
                 "affiliations": [
                     "gallantries",
-                    "eurosciencegateway",
+                    "ifb",
                     "elixir-europe"
                 ],
                 "contact_for_training": true,
                 "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
                 "fediverse_flavor": "mastodon",
-                "id": "abretaud",
+                "id": "bebatut",
                 "joined": "2017-09",
+                "linkedin": "berenicebatut",
                 "location": {
                     "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
+                    "lat": 45.77,
+                    "lon": 3.08
                 },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
-            },
-            {
-                "email": "alexandre.cormier@ifremer.fr",
-                "id": "alexcorm",
-                "joined": "2021-11",
-                "name": "Alexandre Cormier",
-                "orcid": "0000-0002-7775-8413",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/",
-                "twitter": "allanssx",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/alexcorm.json"
-            },
-            {
-                "email": "laura.leroi@ifremer.fr",
-                "id": "lleroi",
-                "joined": "2021-11",
-                "name": "Laura Leroi",
-                "orcid": "0000-0003-3748-4179",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lleroi/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/lleroi.json"
-            },
-            {
-                "email": "erwan.corre@sb-roscoff.fr",
-                "id": "r1corre",
-                "joined": "2019-04",
-                "name": "Erwan Corre",
-                "orcid": "0000-0001-6354-2278",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/r1corre/",
-                "twitter": "r1corre",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/r1corre.json"
-            },
-            {
-                "email": "stephanie.robin@inrae.fr",
-                "id": "stephanierobin",
-                "joined": "2021-11",
-                "name": "St\u00e9phanie Robin",
-                "orcid": "0000-0001-7379-9173",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/",
-                "twitter": "robinstphanie1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/stephanierobin.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             },
             {
-                "avatar": "/training-material/assets/images/eurosciencegateway.png",
+                "avatar": "/training-material/assets/images/abromics.png",
                 "funder": true,
-                "funding_id": "101057388",
-                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
-                "funding_system": "cordis",
                 "github": false,
-                "id": "eurosciencegateway",
-                "joined": "2023-10",
-                "members": [
-                    "abretaud",
-                    "anuprulez",
-                    "bgruening",
-                    "erxleben",
-                    "pauldg",
-                    "rlibouba"
-                ],
-                "name": "EuroScienceGateway",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
+                "id": "abromics",
+                "joined": "2024-01",
+                "name": "ABRomics",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abromics/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/abromics.json"
             }
         ],
-        "dir": "topics/genome-annotation/tutorials/funannotate",
+        "dir": "topics/genome-annotation/tutorials/bacterial-genome-annotation",
+        "edam_ontology": [
+            "topic_0622",
+            "topic_3301",
+            "topic_0623",
+            "topic_0080",
+            "topic_3673",
+            "topic_0085",
+            "topic_0798"
+        ],
         "edam_operation": [
-            "Sequence motif recognition",
-            "Sequence alignment",
             "Genome annotation",
-            "Sequence assembly validation",
-            "Homology-based gene prediction",
-            "Fold recognition",
-            "Formatting",
-            "Information extraction",
+            "Nucleic acid feature detection",
+            "Multilocus sequence typing",
             "Genome visualisation",
-            "Transcriptome assembly",
-            "Sequence annotation",
             "Genome assembly",
-            "Protein feature detection",
-            "Query and retrieval",
-            "Scaffolding"
+            "Sequence motif recognition",
+            "Structural variation detection",
+            "Scaffolding",
+            "Protein feature detection"
+        ],
+        "edam_topic": [
+            "Genomics",
+            "Microbiology",
+            "Gene and protein families",
+            "Sequence analysis",
+            "Whole genome sequencing",
+            "Functional genomics",
+            "Mobile genetic elements"
         ],
-        "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.fr"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
@@ -115053,95 +115583,85 @@
                     "apollo"
                 ],
                 "type": "internal"
+            },
+            {
+                "topic_name": "visualisation",
+                "tutorials": [
+                    "circos",
+                    "jbrowse"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "history-to-workflow"
+                ],
+                "type": "internal"
             }
         ],
         "hands_on": true,
-        "id": "genome-annotation/funannotate",
+        "id": "genome-annotation/bacterial-genome-annotation",
         "inexact_supported_servers": [
+            "Galaxy@AuBi",
             "UseGalaxy.cz",
-            "UseGalaxy.org.au"
+            "UseGalaxy.org (Main)"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Funannotate allows to perform structural annotation of an eukaryotic genome.",
-            "Functional annotation can be performed using EggNOG-mapper and InterProScan.",
-            "BUSCO and JBrowse allow to inspect the quality of an annotation.",
-            "Funannotate allows to format an annotation for sumission at NCBI."
+            "Bakta is a powerful tool to annotate a bacterial genome",
+            "Annotation can be easily visualized to understand the genomic context and help making sense of the annotations"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-09-08",
         "objectives": [
-            "Load genome into Galaxy",
-            "Annotate genome with Funannotate",
-            "Perform functional annotation using EggNOG-mapper and InterProScan",
-            "Evaluate annotation quality with BUSCO",
-            "View annotations in JBrowse"
+            "Run a series of tool to annotate a draft bacterial genome for different types of genomic components",
+            "Evaluate the annotation",
+            "Process the outputs to formate them for visualization needs",
+            "Visualize a draft bacterial genome and its annotations"
         ],
-        "pageviews": 10392,
-        "priority": 2,
-        "pub_date": "2021-11-29",
+        "pageviews": 2969,
+        "pub_date": "2024-02-01",
         "questions": [
-            "How to annotate an eukaryotic genome with Funannotate?",
-            "How to perform functional annotation?",
-            "How to evaluate and visualize annotated genomic features?",
-            "How to format the annotation for submission at NCBI?"
+            "Which genes are on a draft bacterial genome?",
+            "Which other genomic components can be found on a draft bacterial genome?"
         ],
         "recordings": [
             {
+                "bot-timestamp": 1725267714,
                 "captioners": [
-                    "abretaud"
-                ],
-                "date": "2023-05-12",
-                "galaxy_version": "23.01",
-                "length": "1H10M",
-                "speakers": [
-                    "abretaud"
-                ],
-                "youtube_id": "p0NBxZk5964"
-            },
-            {
-                "captioners": [
-                    "abretaud"
+                    "bebatut"
                 ],
-                "date": "2022-03-03",
-                "galaxy_version": "21.09",
-                "length": "1H10M",
+                "date": "2024-09-02",
+                "galaxy_version": "24.0.4.dev0",
+                "length": "44M",
                 "speakers": [
-                    "abretaud"
-                ],
-                "youtube_id": "r-wU6BhqIpk"
-            }
-        ],
-        "requirements": [
-            {
-                "topic_name": "genome-annotation",
-                "tutorials": [
-                    "repeatmasker"
+                    "bebatut"
                 ],
-                "type": "internal"
+                "youtube_id": "VOwplmv0vNs"
             }
         ],
-        "short_id": "T00172",
+        "short_id": "T00403",
         "short_tools": [
             "jbrowse",
-            "busco",
-            "eggnog_mapper",
-            "picard_MergeSamFiles",
-            "funannotate_annotate",
-            "funannotate_predict",
-            "aegean_parseval",
-            "funannotate_compare",
-            "interproscan",
-            "rna_star"
+            "tbl2gff3",
+            "plasmidfinder",
+            "integron_finder",
+            "upload1",
+            "isescan",
+            "tp_tail_tool",
+            "bakta",
+            "tp_replace_in_column",
+            "Grouping1"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "eukaryote",
+        "subtopic": "prokaryote",
         "supported_servers": {
             "exact": [
                 {
@@ -115153,22 +115673,22 @@
                     "name": "UseGalaxy.fr",
                     "url": "https://usegalaxy.fr/",
                     "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
                 }
             ],
             "inexact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 }
             ]
@@ -115176,26 +115696,24 @@
         "symlink": null,
         "tags": [
             "gmod",
-            "eukaryote",
+            "illumina",
+            "bacteria",
+            "microgalaxy",
             "jbrowse1"
         ],
-        "time_estimation": "8h",
-        "title": "Genome annotation with Funannotate",
+        "time_estimation": "3H",
+        "title": "Bacterial Genome Annotation",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy1",
+            "Grouping1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
             "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy0"
+            "toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2",
+            "upload1"
         ],
         "topic_name": "genome-annotation",
         "topic_name_human": "Genome Annotation",
@@ -115205,1113 +115723,674 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "funannotate",
+        "tutorial_name": "bacterial-genome-annotation",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/funannotate/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/funannotate/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/funannotate/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.json"
         },
-        "version": 22,
+        "version": 5,
         "video": false,
-        "video_versions": 2,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 129,
-        "visitors": 6817,
+        "visit_duration": 140,
+        "visitors": 2243,
         "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "https://orcid.org/0000-0003-0914-2470",
-                        "name": "Anthony Bretaudeau"
+                        "identifier": "https://orcid.org/0000-0001-9852-1987",
+                        "name": "B\u00e9r\u00e9nice Batut"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0002-8304-138X",
+                        "name": "Pierre Marin"
                     }
                 ],
-                "description": "Structural and functional genome annotation with Funannotate",
+                "description": "Bacterial Genome Annotation",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenome assembly\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nRNASeq reads forward\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nRNASeq reads reverse\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nProtein evidence sequences\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nNCBI submission template\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAlternate annotation gbk\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAlternate annotation gff3\"]\n  7[label=\"RNA STAR\"]\n  0 -> 7 [label=\"output\"]\n  1 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  k79cf59ea3aef4cb89c705b42e03a5da9[color=lightseagreen,label=\"Output\\nMapped RNASeq\"]\n  7 -> k79cf59ea3aef4cb89c705b42e03a5da9\n  8[label=\"Funannotate predict annotation\"]\n  3 -> 8 [label=\"output\"]\n  7 -> 8 [label=\"mapped_reads\"]\n  0 -> 8 [label=\"output\"]\n  9[label=\"eggNOG Mapper\"]\n  8 -> 9 [label=\"fasta_proteins\"]\n  10[label=\"InterProScan\"]\n  8 -> 10 [label=\"fasta_proteins\"]\n  11[label=\"Funannotate functional\"]\n  9 -> 11 [label=\"annotations\"]\n  8 -> 11 [label=\"annot_gbk\"]\n  10 -> 11 [label=\"outfile_xml\"]\n  4 -> 11 [label=\"output\"]\n  kd0694cd16d814d7283b994cb57dc1502[color=lightseagreen,label=\"Output\\nFinal annotation (genbank)\"]\n  11 -> kd0694cd16d814d7283b994cb57dc1502\n  k9a1e7b70109041ed863765b7372a9f6c[color=lightseagreen,label=\"Output\\nFinal annotation (CDS sequences)\"]\n  11 -> k9a1e7b70109041ed863765b7372a9f6c\n  k99fffa402196491d9a66559ebf2d9561[color=lightseagreen,label=\"Output\\nFinal annotation (mRNA sequences)\"]\n  11 -> k99fffa402196491d9a66559ebf2d9561\n  k17b03b7704854176b2b303bfa2d3bcb0[color=lightseagreen,label=\"Output\\nFinal annotation (protein sequences)\"]\n  11 -> k17b03b7704854176b2b303bfa2d3bcb0\n  k4a0602fce6d243fc9957344707c22c05[color=lightseagreen,label=\"Output\\nFinal annotation (GFF3)\"]\n  11 -> k4a0602fce6d243fc9957344707c22c05\n  12[label=\"JBrowse\"]\n  0 -> 12 [label=\"output\"]\n  11 -> 12 [label=\"gff3\"]\n  7 -> 12 [label=\"mapped_reads\"]\n  kac4d8805f12344d2b30f8ac906cc471f[color=lightseagreen,label=\"Output\\nJBrowse\"]\n  12 -> kac4d8805f12344d2b30f8ac906cc471f\n  13[label=\"Funannotate compare\"]\n  5 -> 13 [label=\"output\"]\n  11 -> 13 [label=\"gbk\"]\n  ke531c81ff6b74c82a712c562873ff714[color=lightseagreen,label=\"Output\\nFunannotate compare report\"]\n  13 -> ke531c81ff6b74c82a712c562873ff714\n  14[label=\"AEGeAn ParsEval\"]\n  6 -> 14 [label=\"output\"]\n  11 -> 14 [label=\"gff3\"]\n  k0d776b462c1c40839f9da213fa62eb81[color=lightseagreen,label=\"Output\\nAEGeAN report\"]\n  14 -> k0d776b462c1c40839f9da213fa62eb81\n  15[label=\"Busco\"]\n  11 -> 15 [label=\"fa_proteins\"]\n  k57a619f5b3314ca68e6e72eb61860032[color=lightseagreen,label=\"Output\\nBusco summary\"]\n  15 -> k57a619f5b3314ca68e6e72eb61860032\n  k97d23764ad4a4d69948cc81afb76fbaf[color=lightseagreen,label=\"Output\\nBusco image\"]\n  15 -> k97d23764ad4a4d69948cc81afb76fbaf\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontigs\"]\n  1[label=\"ISEScan\"]\n  0 -> 1 [label=\"output\"]\n  k2bb672cb453646b08a228590a0ca36c7[color=lightseagreen,label=\"Output\\nisescan_results\"]\n  1 -> k2bb672cb453646b08a228590a0ca36c7\n  2[label=\"PlasmidFinder\"]\n  0 -> 2 [label=\"output\"]\n  k614064e64b0f4e38b04ee3f61ba41b46[color=lightseagreen,label=\"Output\\nplasmidfinder_results\"]\n  2 -> k614064e64b0f4e38b04ee3f61ba41b46\n  3[label=\"Integron Finder\"]\n  0 -> 3 [label=\"output\"]\n  kd26788cf24414f29ac39b6be96f192eb[color=lightseagreen,label=\"Output\\nintegronfinder_summary\"]\n  3 -> kd26788cf24414f29ac39b6be96f192eb\n  4[label=\"Bakta\"]\n  0 -> 4 [label=\"output\"]\n  kd3a40a8b1bd142b6a91e756379b86d94[color=lightseagreen,label=\"Output\\nbakta_summary\"]\n  4 -> kd3a40a8b1bd142b6a91e756379b86d94\n  5[label=\"Group\"]\n  1 -> 5 [label=\"all_results\"]\n  6[label=\"Group\"]\n  1 -> 6 [label=\"all_results\"]\n  7[label=\"Replace Text\"]\n  2 -> 7 [label=\"result_file\"]\n  8[label=\"Select last\"]\n  7 -> 8 [label=\"outfile\"]\n  9[label=\"Table to GFF3\"]\n  8 -> 9 [label=\"outfile\"]\n  10[label=\"JBrowse\"]\n  0 -> 10 [label=\"output\"]\n  4 -> 10 [label=\"annotation_gff3\"]\n  9 -> 10 [label=\"output\"]\n  1 -> 10 [label=\"annotation\"]\n}",
                 "history": [
                     {
-                        "hash": "ed3325d60843b30358cdb704f83ad9ea4b6c149f",
-                        "message": "update funannotate tuto",
+                        "hash": "87968f9a6953ebf322d9fb0fae3a4193b6222288",
+                        "message": "Update tool versions",
+                        "num": 2,
+                        "short_hash": "87968f9a6",
+                        "unix": "1722510143"
+                    },
+                    {
+                        "hash": "217f251aaa898a91dbb18b5cec3daebaf582c712",
+                        "message": "Update worklow and add tests",
                         "num": 1,
-                        "short_hash": "ed3325d60",
-                        "unix": "1682519007"
+                        "short_hash": "217f251aa",
+                        "unix": "1706526984"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "The genome sequence that you wish to annotate, in fasta format. It needs to be soft masked beforehand.",
+                        "annotation": "contigs",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "The genome sequence that you wish to annotate, in fasta format. It needs to be soft masked beforehand.",
-                                "name": "Genome assembly"
-                            }
-                        ],
-                        "label": "Genome assembly",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 7.75
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "cca15c08-8dd9-424a-8260-4c02a94c2612",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "Some RNASeq data, forward reads, in fastq format",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Some RNASeq data, forward reads, in fastq format",
-                                "name": "RNASeq reads forward"
-                            }
-                        ],
-                        "label": "RNASeq reads forward",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 3.45001220703125,
-                            "top": 164.33334350585938
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "6681e7b9-68f6-46e4-811f-60473d23fe0f",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "Some RNASeq data, reverse reads, in fastq format",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Some RNASeq data, reverse reads, in fastq format",
-                                "name": "RNASeq reads reverse"
-                            }
-                        ],
-                        "label": "RNASeq reads reverse",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 6,
-                            "top": 310.6666564941406
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "160023e3-250f-424d-abe5-f7e3978768f0",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "Some protein sequences to align on the genome to help annotation",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Some protein sequences to align on the genome to help annotation",
-                                "name": "Protein evidence sequences"
-                            }
-                        ],
-                        "label": "Protein evidence sequences",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 7.116668701171875,
-                            "top": 441.4166564941406
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "abb56aaf-5988-4fb8-a68f-0edaee00f445",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "A submission template retrieved from NCBI (generate it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/)",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "A submission template retrieved from NCBI (generate it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/)",
-                                "name": "NCBI submission template"
-                            }
-                        ],
-                        "label": "NCBI submission template",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 2.45001220703125,
-                            "top": 580.4833068847656
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "537f8bb4-4986-4d8d-a49b-1842dfaa739a",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "The genbank output of an alternate annotation (for comparison)",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "The genbank output of an alternate annotation (for comparison)",
-                                "name": "Alternate annotation gbk"
+                                "description": "contigs",
+                                "name": "contigs"
                             }
                         ],
-                        "label": "Alternate annotation gbk",
+                        "label": "contigs",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
                             "left": 0,
-                            "top": 727.7333068847656
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "51a62e82-d478-45c3-bcbc-f38f1fd85974",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "The gff3 output of an alternate annotation (for comparison)",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "The gff3 output of an alternate annotation (for comparison)",
-                                "name": "Alternate annotation gff3"
-                            }
-                        ],
-                        "label": "Alternate annotation gff3",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0.4666748046875,
-                            "top": 845.7500305175781
+                            "top": 424
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "e4367779-3fc7-4eec-8e45-86158b3950bc",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGenome assembly\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nRNASeq reads forward\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nRNASeq reads reverse\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nProtein evidence sequences\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nNCBI submission template\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nAlternate annotation gbk\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nAlternate annotation gff3\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"RNA STAR\"];\n  0 -->|output| 7;\n  1 -->|output| 7;\n  2 -->|output| 7;\n  79cf59ea-3aef-4cb8-9c70-5b42e03a5da9[\"Output\\nMapped RNASeq\"];\n  7 --> 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9;\n  style 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9 stroke:#2c3143,stroke-width:4px;\n  8[\"Funannotate predict annotation\"];\n  3 -->|output| 8;\n  7 -->|mapped_reads| 8;\n  0 -->|output| 8;\n  9[\"eggNOG Mapper\"];\n  8 -->|fasta_proteins| 9;\n  10[\"InterProScan\"];\n  8 -->|fasta_proteins| 10;\n  11[\"Funannotate functional\"];\n  9 -->|annotations| 11;\n  8 -->|annot_gbk| 11;\n  10 -->|outfile_xml| 11;\n  4 -->|output| 11;\n  d0694cd1-6d81-4d72-83b9-94cb57dc1502[\"Output\\nFinal annotation (genbank)\"];\n  11 --> d0694cd1-6d81-4d72-83b9-94cb57dc1502;\n  style d0694cd1-6d81-4d72-83b9-94cb57dc1502 stroke:#2c3143,stroke-width:4px;\n  9a1e7b70-1090-41ed-8637-65b7372a9f6c[\"Output\\nFinal annotation (CDS sequences)\"];\n  11 --> 9a1e7b70-1090-41ed-8637-65b7372a9f6c;\n  style 9a1e7b70-1090-41ed-8637-65b7372a9f6c stroke:#2c3143,stroke-width:4px;\n  99fffa40-2196-491d-9a66-559ebf2d9561[\"Output\\nFinal annotation (mRNA sequences)\"];\n  11 --> 99fffa40-2196-491d-9a66-559ebf2d9561;\n  style 99fffa40-2196-491d-9a66-559ebf2d9561 stroke:#2c3143,stroke-width:4px;\n  17b03b77-0485-4176-b2b3-03bfa2d3bcb0[\"Output\\nFinal annotation (protein sequences)\"];\n  11 --> 17b03b77-0485-4176-b2b3-03bfa2d3bcb0;\n  style 17b03b77-0485-4176-b2b3-03bfa2d3bcb0 stroke:#2c3143,stroke-width:4px;\n  4a0602fc-e6d2-43fc-9957-344707c22c05[\"Output\\nFinal annotation (GFF3)\"];\n  11 --> 4a0602fc-e6d2-43fc-9957-344707c22c05;\n  style 4a0602fc-e6d2-43fc-9957-344707c22c05 stroke:#2c3143,stroke-width:4px;\n  12[\"JBrowse\"];\n  0 -->|output| 12;\n  11 -->|gff3| 12;\n  7 -->|mapped_reads| 12;\n  ac4d8805-f123-44d2-b30f-8ac906cc471f[\"Output\\nJBrowse\"];\n  12 --> ac4d8805-f123-44d2-b30f-8ac906cc471f;\n  style ac4d8805-f123-44d2-b30f-8ac906cc471f stroke:#2c3143,stroke-width:4px;\n  13[\"Funannotate compare\"];\n  5 -->|output| 13;\n  11 -->|gbk| 13;\n  e531c81f-f6b7-4c82-a712-c562873ff714[\"Output\\nFunannotate compare report\"];\n  13 --> e531c81f-f6b7-4c82-a712-c562873ff714;\n  style e531c81f-f6b7-4c82-a712-c562873ff714 stroke:#2c3143,stroke-width:4px;\n  14[\"AEGeAn ParsEval\"];\n  6 -->|output| 14;\n  11 -->|gff3| 14;\n  0d776b46-2c1c-4083-9f9d-a213fa62eb81[\"Output\\nAEGeAN report\"];\n  14 --> 0d776b46-2c1c-4083-9f9d-a213fa62eb81;\n  style 0d776b46-2c1c-4083-9f9d-a213fa62eb81 stroke:#2c3143,stroke-width:4px;\n  15[\"Busco\"];\n  11 -->|fa_proteins| 15;\n  57a619f5-b331-4ca6-8e6e-72eb61860032[\"Output\\nBusco summary\"];\n  15 --> 57a619f5-b331-4ca6-8e6e-72eb61860032;\n  style 57a619f5-b331-4ca6-8e6e-72eb61860032 stroke:#2c3143,stroke-width:4px;\n  97d23764-ad4a-4d69-948c-c81afb76fbaf[\"Output\\nBusco image\"];\n  15 --> 97d23764-ad4a-4d69-948c-c81afb76fbaf;\n  style 97d23764-ad4a-4d69-948c-c81afb76fbaf stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Funannotate",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "refGenomeSource|genomeFastaFiles": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "singlePaired|input1": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "singlePaired|input2": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool RNA STAR",
-                                "name": "refGenomeSource"
-                            },
-                            {
-                                "description": "runtime parameter for tool RNA STAR",
-                                "name": "singlePaired"
-                            },
-                            {
-                                "description": "runtime parameter for tool RNA STAR",
-                                "name": "singlePaired"
-                            }
-                        ],
-                        "label": null,
-                        "name": "RNA STAR",
-                        "outputs": [
-                            {
-                                "name": "output_log",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "splice_junctions",
-                                "type": "interval"
-                            },
-                            {
-                                "name": "mapped_reads",
-                                "type": "bam"
-                            }
-                        ],
-                        "position": {
-                            "left": 766.699951171875,
-                            "top": 239.0
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionoutput_log": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_log"
-                            },
-                            "HideDatasetActionsplice_junctions": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "splice_junctions"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3ea5a2a63fa2",
-                            "name": "rgrnastar",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"algo\": {\"params\": {\"settingsType\": \"default\", \"__current_case__\": 0}}, \"chimOutType\": \"\", \"filter\": {\"basic_filters\": [\"exclude_unmapped\"], \"output_params2\": {\"output_select2\": \"no\", \"__current_case__\": 1}}, \"oformat\": {\"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"ch\"], \"HI_offset\": \"1\", \"outSAMprimaryFlag\": \"OneBestScore\", \"outSAMmapqUnique\": \"60\"}, \"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"perf\": {\"outBAMsortingBinsN\": \"50\", \"winAnchorMultimapNmax\": \"50\"}, \"refGenomeSource\": {\"geneSource\": \"history\", \"__current_case__\": 1, \"genomeFastaFiles\": {\"__class__\": \"RuntimeValue\"}, \"genomeSAindexNbases\": \"11\", \"GTFconditional\": {\"GTFselect\": \"without-gtf\", \"__current_case__\": 1, \"quantmode_output\": {\"quantMode\": \"-\", \"__current_case__\": 0}}}, \"singlePaired\": {\"sPaired\": \"paired\", \"__current_case__\": 1, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"input2\": {\"__class__\": \"RuntimeValue\"}}, \"twopass\": {\"twopassMode\": \"None\", \"__current_case__\": 0, \"twopass_read_subset\": \"\", \"sj_precalculated\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.7.10b+galaxy3",
-                        "type": "tool",
-                        "uuid": "269a3794-e421-4826-a5de-8a328fd194bd",
-                        "workflow_outputs": [
-                            {
-                                "label": "Mapped RNASeq",
-                                "output_name": "mapped_reads",
-                                "uuid": "79cf59ea-3aef-4cb8-9c70-5b42e03a5da9"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "evidences|prot_evidence|protein_evidence": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "evidences|rna_bam": {
-                                "id": 7,
-                                "output_name": "mapped_reads"
-                            },
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "database"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "evidences"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "evidences"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "genemark"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "genemark"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "input"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "other_predictors"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "other_predictors"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "other_predictors"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "other_predictors"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate predict annotation",
-                                "name": "parameters"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Funannotate predict annotation",
-                        "outputs": [
-                            {
-                                "name": "annot_gbk",
-                                "type": "genbank"
-                            },
-                            {
-                                "name": "annot_tbl",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "annot_gff3",
-                                "type": "gff3"
-                            },
-                            {
-                                "name": "fasta_proteins",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "fasta_transcripts_mrna",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "fasta_transcripts_cds",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "tbl2asn_report",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "tbl2asn_error",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "tbl2asn_validation",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "stats",
-                                "type": "json"
-                            }
-                        ],
-                        "position": {
-                            "left": 1055.2666015625,
-                            "top": 65.88333129882812
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionannot_gbk": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "annot_gbk"
-                            },
-                            "HideDatasetActionannot_gff3": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "annot_gff3"
-                            },
-                            "HideDatasetActionannot_tbl": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "annot_tbl"
-                            },
-                            "HideDatasetActionfasta_transcripts_cds": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "fasta_transcripts_cds"
-                            },
-                            "HideDatasetActionfasta_transcripts_mrna": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "fasta_transcripts_mrna"
-                            },
-                            "HideDatasetActionstats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "stats"
-                            },
-                            "HideDatasetActiontbl2asn_error": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "tbl2asn_error"
-                            },
-                            "HideDatasetActiontbl2asn_report": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "tbl2asn_report"
-                            },
-                            "HideDatasetActiontbl2asn_validation": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "tbl2asn_validation"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "51b6ee65ef7f",
-                            "name": "funannotate_predict",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"augustus\": {\"augustus_species\": \"none\", \"min_training_models\": \"200\", \"optimize_augustus\": \"false\"}, \"busco\": {\"busco_db\": \"mucorales_odb10\", \"busco_seed_species\": \"rhizopus_oryzae\"}, \"database\": {\"__class__\": \"RuntimeValue\"}, \"evidences\": {\"rna_bam\": {\"__class__\": \"RuntimeValue\"}, \"transcript_evidence\": {\"__class__\": \"RuntimeValue\"}, \"prot_evidence\": {\"prot_evidence_source\": \"custom\", \"__current_case__\": 1, \"protein_evidence\": {\"__class__\": \"RuntimeValue\"}}, \"p2g_pident\": \"80\", \"p2g_prefilter\": \"diamond\"}, \"evm\": {\"repeats2evm\": \"false\", \"evm_partitioning\": {\"evm_partition\": \"yes\", \"__current_case__\": 0, \"evm_partition_interval\": \"1500\"}, \"weights\": \"\"}, \"filtering\": {\"min_intronlen\": \"10\", \"max_intronlen\": \"3000\", \"min_protlen\": \"50\", \"keep_no_stops\": \"false\", \"repeat_filter\": \"overlap blast\"}, \"force\": \"true\", \"genemark\": {\"genemark_license\": {\"__class__\": \"RuntimeValue\"}, \"genemark_mode\": \"ES\", \"genemark_mod\": {\"__class__\": \"RuntimeValue\"}, \"soft_mask\": \"2000\"}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"organism\": {\"species\": \"Mucor mucedo\", \"isolate\": \"\", \"strain\": \"muc1\", \"organism\": \"false\", \"ploidy\": \"1\", \"SeqCenter\": \"CFMR\", \"SeqAccession\": \"12345\", \"name\": \"FUN_\", \"numbering\": \"1\"}, \"other_predictors\": {\"stringtie\": {\"__class__\": \"RuntimeValue\"}, \"maker_gff\": {\"__class__\": \"RuntimeValue\"}, \"pasa_gff\": {\"__class__\": \"RuntimeValue\"}, \"pasa_gff_weight\": \"1\", \"other_gff\": {\"__class__\": \"RuntimeValue\"}, \"other_gff_weight\": \"1\"}, \"outputs\": [\"gbk\", \"tbl\", \"gff3\", \"proteins_fa\", \"mrna_transcripts_fa\", \"cds_transcripts_fa\", \"tbl2asn_report\", \"tbl2asn_error\", \"tbl2asn_validation\", \"stats\"], \"parameters\": {\"__class__\": \"RuntimeValue\"}, \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.15+galaxy0",
-                        "type": "tool",
-                        "uuid": "aefc0275-b611-4ede-9650-2e16553a7352",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "fasta_proteins",
-                                "uuid": "aa7fb986-b7db-4353-a83b-3f1591911388"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "ortho_method|input": {
-                                "id": 8,
-                                "output_name": "fasta_proteins"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool eggNOG Mapper",
-                                "name": "ortho_method"
-                            }
-                        ],
-                        "label": null,
-                        "name": "eggNOG Mapper",
-                        "outputs": [
-                            {
-                                "name": "seed_orthologs",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "annotations",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 1444.9666748046875,
-                            "top": 418.7333068847656
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionseed_orthologs": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "seed_orthologs"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9d1fbff733cf",
-                            "name": "eggnog_mapper",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"annotation_options\": {\"no_annot\": \"\", \"__current_case__\": 0, \"seed_ortholog_evalue\": \"0.001\", \"seed_ortholog_score\": null, \"tax_scope\": null, \"target_orthologs\": \"all\", \"go_evidence\": \"non-electronic\"}, \"eggnog_data\": \"5.0.2\", \"ortho_method\": {\"m\": \"diamond\", \"__current_case__\": 0, \"input\": {\"__class__\": \"RuntimeValue\"}, \"input_trans\": {\"itype\": \"proteins\", \"__current_case__\": 0}, \"matrix_gapcosts\": {\"matrix\": \"BLOSUM62\", \"__current_case__\": 2, \"gap_costs\": \"--gapopen 11 --gapextend 1\"}, \"sensmode\": \"sensitive\", \"dmnd_iterate\": \"false\", \"dmnd_ignore_warnings\": \"false\", \"query_cover\": null, \"subject_cover\": null, \"pident\": null, \"evalue\": null, \"score\": \"0.001\"}, \"output_options\": {\"no_file_comments\": \"false\", \"report_orthologs\": \"false\", \"md5\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.8+galaxy3",
-                        "type": "tool",
-                        "uuid": "0d9f93f0-88b3-406b-b8f9-ecb2d74c61e9",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "annotations",
-                                "uuid": "521fe026-4958-4965-9414-e7074aea7860"
-                            }
-                        ]
-                    },
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "8cde8af1-c277-4b9f-97f7-54f5997f2c5d",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "AGPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"ISEScan\"];\n  0 -->|output| 1;\n  2bb672cb-4536-46b0-8a22-8590a0ca36c7[\"Output\\nisescan_results\"];\n  1 --> 2bb672cb-4536-46b0-8a22-8590a0ca36c7;\n  style 2bb672cb-4536-46b0-8a22-8590a0ca36c7 stroke:#2c3143,stroke-width:4px;\n  2[\"PlasmidFinder\"];\n  0 -->|output| 2;\n  614064e6-4b0f-4e38-b04e-e3f61ba41b46[\"Output\\nplasmidfinder_results\"];\n  2 --> 614064e6-4b0f-4e38-b04e-e3f61ba41b46;\n  style 614064e6-4b0f-4e38-b04e-e3f61ba41b46 stroke:#2c3143,stroke-width:4px;\n  3[\"Integron Finder\"];\n  0 -->|output| 3;\n  d26788cf-2441-4f29-ac39-b6be96f192eb[\"Output\\nintegronfinder_summary\"];\n  3 --> d26788cf-2441-4f29-ac39-b6be96f192eb;\n  style d26788cf-2441-4f29-ac39-b6be96f192eb stroke:#2c3143,stroke-width:4px;\n  4[\"Bakta\"];\n  0 -->|output| 4;\n  d3a40a8b-1bd1-42b6-a91e-756379b86d94[\"Output\\nbakta_summary\"];\n  4 --> d3a40a8b-1bd1-42b6-a91e-756379b86d94;\n  style d3a40a8b-1bd1-42b6-a91e-756379b86d94 stroke:#2c3143,stroke-width:4px;\n  5[\"Group\"];\n  1 -->|all_results| 5;\n  6[\"Group\"];\n  1 -->|all_results| 6;\n  7[\"Replace Text\"];\n  2 -->|result_file| 7;\n  8[\"Select last\"];\n  7 -->|outfile| 8;\n  9[\"Table to GFF3\"];\n  8 -->|outfile| 9;\n  10[\"JBrowse\"];\n  0 -->|output| 10;\n  4 -->|annotation_gff3| 10;\n  9 -->|output| 10;\n  1 -->|annotation| 10;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Bacterial Genome Annotation",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
                         "errors": null,
-                        "id": 10,
+                        "id": 1,
                         "input_connections": {
-                            "input": {
-                                "id": 8,
-                                "output_name": "fasta_proteins"
+                            "input_file": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool InterProScan",
-                                "name": "input"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "InterProScan",
+                        "name": "ISEScan",
                         "outputs": [
                             {
-                                "name": "outfile_tsv",
+                                "name": "summary",
                                 "type": "tabular"
                             },
                             {
-                                "name": "outfile_xml",
-                                "type": "xml"
+                                "name": "all_results",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "annotation",
+                                "type": "gff"
+                            },
+                            {
+                                "name": "is_fasta",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "orf_fna",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "orf_faa",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 1475.8499755859375,
-                            "top": 817.8666687011719
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionoutfile_xml": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "outfile_xml"
-                            }
+                            "left": 280,
+                            "top": 133
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "74810db257cc",
-                            "name": "interproscan",
-                            "owner": "bgruening",
+                            "changeset_revision": "19f42b3ea391",
+                            "name": "isescan",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"applications\": [\"TIGRFAM\", \"SFLD\", \"SUPERFAMILY\", \"PANTHER\", \"Gene3D\", \"Hamap\", \"PrositeProfiles\", \"Coils\", \"SMART\", \"CDD\", \"PRINTS\", \"PIRSR\", \"PrositePatterns\", \"Pfam\", \"MobiDBLite\", \"PIRSF\"], \"database\": \"5.59-91.0\", \"goterms\": \"true\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"iprlookup\": \"false\", \"licensed\": {\"use\": \"true\", \"__current_case__\": 1, \"applications_licensed\": [\"Phobius\", \"SignalP_EUK\", \"TMHMM\"]}, \"oformat\": [\"TSV\", \"XML\"], \"pathways\": \"true\", \"seqtype\": \"p\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.59-91.0+galaxy3",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"log_activate\": false, \"remove_short_is\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.2.3+galaxy1",
                         "type": "tool",
-                        "uuid": "cb7a1910-3c31-47d9-835b-f1bd16a1c3ff",
+                        "uuid": "334b327f-be00-4e75-ae01-c3ba674dbc9b",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "outfile_tsv",
-                                "uuid": "65e267a7-d3c6-410d-9b44-f655d70d7d9a"
+                                "label": "isescan_results",
+                                "output_name": "all_results",
+                                "uuid": "2bb672cb-4536-46b0-8a22-8590a0ca36c7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1",
                         "errors": null,
-                        "id": 11,
+                        "id": 2,
                         "input_connections": {
-                            "eggnog": {
-                                "id": 9,
-                                "output_name": "annotations"
-                            },
-                            "input|genbank": {
-                                "id": 8,
-                                "output_name": "annot_gbk"
-                            },
-                            "iprscan": {
-                                "id": 10,
-                                "output_name": "outfile_xml"
-                            },
-                            "sbt": {
-                                "id": 4,
+                            "input|input_file": {
+                                "id": 0,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "annotations"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "antismash"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "database"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "eggnog"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "fix"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "input"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "iprscan"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "phobius"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "remove"
-                            },
-                            {
-                                "description": "runtime parameter for tool Funannotate functional",
-                                "name": "sbt"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Funannotate functional",
+                        "name": "PlasmidFinder",
                         "outputs": [
                             {
-                                "name": "gbk",
-                                "type": "genbank"
-                            },
-                            {
-                                "name": "annot",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "contigs_fsa",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "agp",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "tbl",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "sqn",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "fa_scaffolds",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "fa_proteins",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "fa_transcripts_mrna",
+                                "name": "hit_file",
                                 "type": "fasta"
                             },
                             {
-                                "name": "fa_transcripts_cds",
+                                "name": "plasmid_file",
                                 "type": "fasta"
                             },
                             {
-                                "name": "gff3",
-                                "type": "gff3"
+                                "name": "result_file",
+                                "type": "tabular"
                             },
                             {
-                                "name": "tbl2asn_report",
+                                "name": "raw_file",
                                 "type": "txt"
-                            },
-                            {
-                                "name": "stats",
-                                "type": "json"
-                            },
-                            {
-                                "name": "must_fix",
-                                "type": "json"
-                            },
-                            {
-                                "name": "need_curating",
-                                "type": "json"
-                            },
-                            {
-                                "name": "new_names_passed",
-                                "type": "json"
                             }
                         ],
                         "position": {
-                            "left": 1877.11669921875,
-                            "top": 101.59999084472656
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionagp": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "agp"
-                            },
-                            "HideDatasetActionannot": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "annot"
-                            },
-                            "HideDatasetActioncontigs_fsa": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "contigs_fsa"
-                            },
-                            "HideDatasetActionfa_scaffolds": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "fa_scaffolds"
-                            },
-                            "HideDatasetActionmust_fix": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "must_fix"
-                            },
-                            "HideDatasetActionneed_curating": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "need_curating"
-                            },
-                            "HideDatasetActionnew_names_passed": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "new_names_passed"
-                            },
-                            "HideDatasetActionsqn": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "sqn"
-                            },
-                            "HideDatasetActiontbl": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "tbl"
-                            }
+                            "left": 280,
+                            "top": 420
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "9feee7fc49a1",
-                            "name": "funannotate_annotate",
+                            "changeset_revision": "7075b7a5441b",
+                            "name": "plasmidfinder",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"annotations\": {\"__class__\": \"RuntimeValue\"}, \"antismash\": {\"__class__\": \"RuntimeValue\"}, \"busco_db\": \"mucorales_odb10\", \"database\": {\"__class__\": \"RuntimeValue\"}, \"eggnog\": {\"__class__\": \"RuntimeValue\"}, \"fix\": {\"__class__\": \"RuntimeValue\"}, \"input\": {\"input_type\": \"gbk\", \"__current_case__\": 0, \"genbank\": {\"__class__\": \"RuntimeValue\"}}, \"iprscan\": {\"__class__\": \"RuntimeValue\"}, \"isolate\": \"\", \"outputs\": [\"gbk\", \"annotations\", \"contigs_fsa\", \"agp\", \"tbl\", \"sqn\", \"scaffolds_fa\", \"proteins_fa\", \"mrna_transcripts_fa\", \"cds_transcripts_fa\", \"gff3\", \"discrepency\", \"stats\", \"must_fix\", \"need_curating\", \"new_names_passed\"], \"phobius\": {\"__class__\": \"RuntimeValue\"}, \"remove\": {\"__class__\": \"RuntimeValue\"}, \"rename\": \"\", \"sbt\": {\"__class__\": \"RuntimeValue\"}, \"strain\": \"muc1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.15+galaxy0",
+                        "tool_state": "{\"input\": {\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"database_name\": \"plasmidfinder_1307168_2019_08_28\"}, \"options\": {\"min_cov\": \"0.6\", \"threshold\": \"0.95\"}, \"output_files\": {\"output_selection\": [\"hit_fasta\", \"plasmid_fasta\", \"result_tsv\", \"result_txt\"]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.6+galaxy1",
                         "type": "tool",
-                        "uuid": "e07de1e0-8f91-4477-b951-7d97dba2e397",
+                        "uuid": "484ea537-4097-4097-b19c-84fef6c7de9a",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Final annotation (genbank)",
-                                "output_name": "gbk",
-                                "uuid": "d0694cd1-6d81-4d72-83b9-94cb57dc1502"
-                            },
-                            {
-                                "label": "Final annotation (CDS sequences)",
-                                "output_name": "fa_transcripts_cds",
-                                "uuid": "9a1e7b70-1090-41ed-8637-65b7372a9f6c"
-                            },
-                            {
-                                "label": "Final annotation (mRNA sequences)",
-                                "output_name": "fa_transcripts_mrna",
-                                "uuid": "99fffa40-2196-491d-9a66-559ebf2d9561"
-                            },
-                            {
-                                "label": "Final annotation (protein sequences)",
-                                "output_name": "fa_proteins",
-                                "uuid": "17b03b77-0485-4176-b2b3-03bfa2d3bcb0"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "tbl2asn_report",
-                                "uuid": "d3d4daec-75fe-4071-af37-c2907e46f5c1"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "stats",
-                                "uuid": "4a682ab6-8a6f-4a0f-bb0e-ba796f587ddc"
-                            },
-                            {
-                                "label": "Final annotation (GFF3)",
-                                "output_name": "gff3",
-                                "uuid": "4a0602fc-e6d2-43fc-9957-344707c22c05"
+                                "label": "plasmidfinder_results",
+                                "output_name": "result_file",
+                                "uuid": "614064e6-4b0f-4e38-b04e-e3f61ba41b46"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
                         "errors": null,
-                        "id": 12,
+                        "id": 3,
                         "input_connections": {
-                            "reference_genome|genome": {
+                            "sequence": {
                                 "id": 0,
                                 "output_name": "output"
-                            },
-                            "track_groups_0|data_tracks_0|data_format|annotation": {
-                                "id": 11,
-                                "output_name": "gff3"
-                            },
-                            "track_groups_1|data_tracks_0|data_format|annotation": {
-                                "id": 7,
-                                "output_name": "mapped_reads"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool JBrowse",
-                                "name": "reference_genome"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "JBrowse",
+                        "name": "Integron Finder",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "html"
+                                "name": "integrons_table",
+                                "type": "tsv"
+                            },
+                            {
+                                "name": "summary",
+                                "type": "tsv"
                             }
                         ],
                         "position": {
-                            "left": 2152.60009765625,
-                            "top": 0.0
+                            "left": 280,
+                            "top": 665
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
+                        "post_job_actions": {
+                            "ChangeDatatypeActionintegrons_table": {
+                                "action_arguments": {
+                                    "newtype": "tabular"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "integrons_table"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "a6e57ff585c0",
-                            "name": "jbrowse",
+                            "changeset_revision": "4768f7f8e93f",
+                            "name": "integron_finder",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 1, \"category\": \"RNASeq\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"auto_snp\": \"true\", \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16.11+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"gbk\": false, \"local_max\": true, \"no_logfile\": true, \"pdf\": false, \"promoter_attI\": true, \"sequence\": {\"__class__\": \"ConnectedValue\"}, \"settings\": {\"attc_settings\": {\"dist_thresh\": \"4000\", \"calin_threshold\": \"2\", \"max_attc_size\": \"200\", \"min_attc_size\": \"40\", \"keep_palindromes\": false, \"covar_matrix\": null}, \"protein_settings\": {\"no_proteins\": false, \"union_integrases\": false, \"func_annot\": false}}, \"topology_file\": null, \"type_replicon\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.5+galaxy0",
                         "type": "tool",
-                        "uuid": "e6d0e687-1a13-482b-a00a-28c7304d59ac",
+                        "uuid": "29a9252c-5c3b-4024-99ff-637d0572320a",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "JBrowse",
-                                "output_name": "output",
-                                "uuid": "ac4d8805-f123-44d2-b30f-8ac906cc471f"
+                                "label": "integronfinder_summary",
+                                "output_name": "summary",
+                                "uuid": "d26788cf-2441-4f29-ac39-b6be96f192eb"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0",
                         "errors": null,
-                        "id": 13,
+                        "id": 4,
                         "input_connections": {
-                            "input": [
-                                {
-                                    "id": 5,
-                                    "output_name": "output"
-                                },
-                                {
-                                    "id": 11,
-                                    "output_name": "gbk"
-                                }
-                            ]
+                            "input_option|input_file": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Bakta",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool Funannotate compare",
-                                "name": "database"
+                                "name": "annotation_tsv",
+                                "type": "tabular"
                             },
                             {
-                                "description": "runtime parameter for tool Funannotate compare",
-                                "name": "proteinortho"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Funannotate compare",
-                        "outputs": [
+                                "name": "annotation_gff3",
+                                "type": "gff3"
+                            },
                             {
-                                "name": "output",
-                                "type": "html"
+                                "name": "annotation_ffn",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "summary_txt",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "annotation_plot",
+                                "type": "svg"
                             }
                         ],
                         "position": {
-                            "left": 2318,
-                            "top": 403.7333068847656
+                            "left": 850,
+                            "top": 0
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "a7ce2601500c",
-                            "name": "funannotate_compare",
+                            "changeset_revision": "728dacaf08a9",
+                            "name": "bakta",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"database\": {\"__class__\": \"RuntimeValue\"}, \"go_fdr\": \"0.05\", \"heatmap_stdev\": \"1.0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"ml\": {\"ml_method\": \"iqtree\", \"__current_case__\": 0}, \"num_orthos\": \"500\", \"proteinortho\": {\"__class__\": \"RuntimeValue\"}, \"run_dnds\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.15+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"annotation\": {\"complete\": false, \"prodigal\": null, \"translation_table\": \"11\", \"keep_contig_headers\": true, \"replicons\": null, \"compliant\": false, \"proteins\": null, \"meta\": false}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input_option\": {\"bakta_db_select\": \"V5.0_2023-02-20\", \"amrfinder_db_select\": \"amrfinderplus_V3.11_2022-12-19.1\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"min_contig_length\": null}, \"organism\": {\"genus\": null, \"species\": null, \"strain\": null, \"plasmid\": null}, \"output_files\": {\"output_selection\": [\"file_tsv\", \"file_gff3\", \"file_ffn\", \"file_plot\", \"sum_txt\"]}, \"workflow\": {\"skip_analysis\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.3+galaxy0",
                         "type": "tool",
-                        "uuid": "750137e5-2cac-4bec-8337-03dab562a7a5",
+                        "uuid": "181220e7-9082-48bc-b855-f10baf78fc2a",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Funannotate compare report",
-                                "output_name": "output",
-                                "uuid": "e531c81f-f6b7-4c82-a712-c562873ff714"
+                                "label": "bakta_summary",
+                                "output_name": "summary_txt",
+                                "uuid": "d3a40a8b-1bd1-42b6-a91e-756379b86d94"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "genome-annotation/bacterial-genome-annotation",
+                "path": "topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.ga",
+                "tags": [
+                    "genome-annotation"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "Bacterial Genome Annotation",
+                "topic_id": "genome-annotation",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-bacterial-genome-annotation/versions/bacterial-genome-annotation",
+                "tutorial_id": "bacterial-genome-annotation",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/bacterial-genome-annotation/workflows/Bacterial-Genome-Annotation.html",
+                "version": 2,
+                "wfid": "genome-annotation-bacterial-genome-annotation",
+                "wfname": "bacterial-genome-annotation",
+                "workflow": "Bacterial-Genome-Annotation.ga",
+                "workflow_tools": [
+                    "Grouping1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.9.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2"
+                ],
+                "workflowhub_id": "1136"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/10572227"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "intermine_galaxy_exchange",
+                    "owner": "iuc",
+                    "revisions": "c24014d80001",
+                    "tool_panel_section_label": "Convert Formats",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: intermine_galaxy_exchange\n  owner: iuc\n  revisions: c24014d80001\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/intermine/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "danielabutano",
+                "yochannah"
+            ]
+        },
+        "contributors": [
+            {
+                "id": "danielabutano",
+                "joined": "2019-09",
+                "name": "Daniela Butano",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/danielabutano/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/danielabutano.json"
+            },
+            {
+                "id": "yochannah",
+                "joined": "2019-09",
+                "name": "Yo Yehudi",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yochannah/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/yochannah.json"
+            }
+        ],
+        "dir": "topics/galaxy-interface/tutorials/intermine",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "galaxy-interface/intermine",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-02-29",
+        "objectives": [
+            "Learn how to import/export data from/to InterMine instances",
+            "Understand the InterMine Interchange Dataset"
+        ],
+        "pageviews": 195,
+        "pub_date": "2020-12-09",
+        "questions": [
+            "How to export your query results from your InterMine of choice to Galaxy?",
+            "How to export a list of identifiers from Galaxy to your InterMine of choice?"
+        ],
+        "short_id": "T00152",
+        "short_tools": [
+            "intermine",
+            "galaxy_intermine_exchange"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "analyse",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "gmod",
+            "intermine"
+        ],
+        "time_estimation": "1h",
+        "title": "InterMine integration with Galaxy",
+        "tools": [
+            "intermine",
+            "toolshed.g2.bx.psu.edu/repos/iuc/intermine_galaxy_exchange/galaxy_intermine_exchange/0.0.1"
+        ],
+        "topic_name": "galaxy-interface",
+        "topic_name_human": "Using Galaxy and Managing your Data",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "intermine",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/galaxy-interface/tutorials/intermine/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/intermine/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/intermine/tutorial.json"
+        },
+        "version": 9,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 136,
+        "visitors": 144,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Intermine import/export",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[label=\"Create InterMine Interchange\"]\n  0 -> 1 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "6a3063bce6a3990aefa6facf94d34a08bf4eea6f",
+                        "message": "more small edits",
+                        "num": 2,
+                        "short_hash": "6a3063bce",
+                        "unix": "1607081036"
                     },
+                    {
+                        "hash": "de251b5d774f97b4dcb70121c68ea01eba22536d",
+                        "message": "move folder",
+                        "num": 1,
+                        "short_hash": "de251b5d7",
+                        "unix": "1607080170"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 14,
-                        "input_connections": {
-                            "predictiongff3": {
-                                "id": 6,
-                                "output_name": "output"
-                            },
-                            "referencegff3": {
-                                "id": 11,
-                                "output_name": "gff3"
-                            }
-                        },
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [],
                         "label": null,
-                        "name": "AEGeAn ParsEval",
-                        "outputs": [
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 257,
+                            "top": 403.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "13261ad4-770b-4728-9068-d9941d07abf7",
+                        "workflow_outputs": [
                             {
-                                "name": "output_html",
-                                "type": "html"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "3df15ab7-6fb7-4a90-81e9-f25868067b8e"
                             }
-                        ],
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Create InterMine Interchange\"];\n  0 -->|output| 1;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Intermine import/export",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2318.5,
-                            "top": 643.7333068847656
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "1b52f0c8ad7f",
-                            "name": "aegean_parseval",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 257,
+                            "top": 403.5
                         },
-                        "tool_state": "{\"delta\": \"0\", \"maxtrans\": \"32\", \"output_type\": \"html\", \"predictiongff3\": {\"__class__\": \"ConnectedValue\"}, \"predlabel\": \"\", \"referencegff3\": {\"__class__\": \"ConnectedValue\"}, \"refrlabel\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.16.0",
-                        "type": "tool",
-                        "uuid": "b5870c4b-d799-4da0-83cc-7dd5a0b049e4",
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "13261ad4-770b-4728-9068-d9941d07abf7",
                         "workflow_outputs": [
                             {
-                                "label": "AEGeAN report",
-                                "output_name": "output_html",
-                                "uuid": "0d776b46-2c1c-4083-9f9d-a213fa62eb81"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "3df15ab7-6fb7-4a90-81e9-f25868067b8e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/intermine_galaxy_exchange/galaxy_intermine_exchange/0.0.1",
                         "errors": null,
-                        "id": 15,
+                        "id": 1,
                         "input_connections": {
-                            "input": {
-                                "id": 11,
-                                "output_name": "fa_proteins"
+                            "input_tabular": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Busco",
-                                "name": "input"
+                                "description": "runtime parameter for tool Create InterMine Interchange",
+                                "name": "input_tabular"
                             }
                         ],
                         "label": null,
-                        "name": "Busco",
+                        "name": "Create InterMine Interchange",
                         "outputs": [
                             {
-                                "name": "busco_sum",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "busco_table",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "summary_image",
-                                "type": "png"
+                                "name": "intermine_output",
+                                "type": "intermine_tabular"
                             }
                         ],
                         "position": {
-                            "left": 2252.2666015625,
-                            "top": 1072.0666809082031
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionbusco_table": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "busco_table"
-                            }
+                            "left": 509,
+                            "top": 402.5
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/intermine_galaxy_exchange/galaxy_intermine_exchange/0.0.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "94170eee0ad8",
-                            "name": "busco",
+                            "changeset_revision": "c24014d80001",
+                            "name": "intermine_galaxy_exchange",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\"}, \"busco_mode\": {\"mode\": \"prot\", \"__current_case__\": 2}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": \"mucorales_odb10\"}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"image\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.4.6+galaxy0",
+                        "tool_state": "{\"__page__\": null, \"feature_id_column\": \"\\\"2\\\"\", \"feature_id_text\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"feature_column\": \"\\\"1\\\"\", \"input_tabular\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"feature_text\": \"\\\"Gene\\\"\", \"organism_text\": \"\\\"\\\"\", \"organism_column\": \"\\\"3\\\"\"}",
+                        "tool_version": "0.0.1",
                         "type": "tool",
-                        "uuid": "bec3d4d9-88e6-4ea0-beb6-219d5c727290",
+                        "uuid": "8e5e0134-7b2a-43c4-b1d4-4d4b62b6af3c",
                         "workflow_outputs": [
                             {
-                                "label": "Busco summary",
-                                "output_name": "busco_sum",
-                                "uuid": "57a619f5-b331-4ca6-8e6e-72eb61860032"
-                            },
-                            {
-                                "label": "Busco image",
-                                "output_name": "summary_image",
-                                "uuid": "97d23764-ad4a-4d69-948c-c81afb76fbaf"
+                                "label": null,
+                                "output_name": "intermine_output",
+                                "uuid": "bfa0f275-4aee-4d3f-8b7c-4e32e8cc9710"
                             }
                         ]
                     }
                 ],
-                "parent_id": "genome-annotation/funannotate",
-                "path": "topics/genome-annotation/tutorials/funannotate/workflows/funannotate.ga",
+                "parent_id": "galaxy-interface/intermine",
+                "path": "topics/galaxy-interface/tutorials/intermine/workflows/main_workflow.ga",
                 "tags": [
-                    "genome-annotation"
+                    "galaxy-interface"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "Funannotate",
-                "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-funannotate/versions/funannotate",
-                "tutorial_id": "funannotate",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/funannotate/workflows/funannotate.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/funannotate/workflows/funannotate.html",
+                "tests": false,
+                "title": "Intermine import/export",
+                "topic_id": "galaxy-interface",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/galaxy-interface-intermine/versions/main-workflow",
+                "tutorial_id": "intermine",
+                "url": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/intermine/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/intermine/workflows/main_workflow.html",
                 "version": 1,
-                "wfid": "genome-annotation-funannotate",
-                "wfname": "funannotate",
-                "workflow": "funannotate.ga",
+                "wfid": "galaxy-interface-intermine",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/intermine_galaxy_exchange/galaxy_intermine_exchange/0.0.1"
                 ],
-                "workflowhub_id": "1202"
+                "workflowhub_id": "1290"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/7867921"
+        "zenodo_link": "https://zenodo.org/record/3407174"
     },
     {
         "admin_install": {
@@ -116319,209 +116398,252 @@
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
             "tools": [
-                {
-                    "name": "gffread",
-                    "owner": "devteam",
-                    "revisions": "0232f19d300f",
-                    "tool_panel_section_label": "Convert Formats",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "busco",
-                    "owner": "iuc",
-                    "revisions": "1440ae06552f",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
                 {
                     "name": "jbrowse",
                     "owner": "iuc",
-                    "revisions": "2bb2e07a7a21",
+                    "revisions": "836d1aa3e89a",
                     "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "jcvi_gff_stats",
-                    "owner": "iuc",
-                    "revisions": "8cffbd184762",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "maker",
-                    "owner": "iuc",
-                    "revisions": "96ac930d84fa",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "maker_map_ids",
+                    "name": "snippy",
                     "owner": "iuc",
-                    "revisions": "326f9c294b09",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_stats",
-                    "owner": "simon-gladman",
-                    "revisions": "20ca2574216a",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "c9a8ef2aa380",
+                    "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: gffread\n  owner: devteam\n  revisions: 0232f19d300f\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 1440ae06552f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 2bb2e07a7a21\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jcvi_gff_stats\n  owner: iuc\n  revisions: 8cffbd184762\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker\n  owner: iuc\n  revisions: 96ac930d84fa\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker_map_ids\n  owner: iuc\n  revisions: 326f9c294b09\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n  owner: simon-gladman\n  revisions: 20ca2574216a\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: jbrowse\n  owner: iuc\n  revisions: 836d1aa3e89a\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snippy\n  owner: iuc\n  revisions: c9a8ef2aa380\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/microbial-variants/tutorial.json",
         "contributors": [
+            {
+                "id": "annasyme",
+                "joined": "2017-09",
+                "name": "Anna Syme",
+                "orcid": "0000-0002-9906-0673",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
+            },
+            {
+                "elixir_node": "au",
+                "email": "simon.gladman@unimelb.edu.au",
+                "id": "slugger70",
+                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
+                "joined": "2017-09",
+                "name": "Simon Gladman",
+                "orcid": "0000-0002-6100-4385",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
+            },
             {
                 "affiliations": [
-                    "gallantries",
-                    "eurosciencegateway",
                     "elixir-europe"
                 ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
-                "fediverse_flavor": "mastodon",
-                "id": "abretaud",
-                "joined": "2017-09",
-                "location": {
-                    "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
-                },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+                "elixir_node": "au",
+                "id": "tseemann",
+                "joined": "2018-06",
+                "name": "Torsten Seemann",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tseemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tseemann.json"
             }
         ],
-        "dir": "topics/genome-annotation/tutorials/annotation-with-maker-short",
+        "dir": "topics/variant-analysis/tutorials/microbial-variants",
+        "edam_ontology": [
+            "topic_0622",
+            "topic_0196",
+            "topic_2885",
+            "topic_3301",
+            "topic_0080",
+            "topic_0199"
+        ],
         "edam_operation": [
-            "Genome assembly",
-            "Sequence annotation",
-            "Transcriptome assembly",
             "Genome visualisation",
-            "Genome annotation",
-            "Sequence assembly validation",
-            "Scaffolding"
+            "Variant calling",
+            "Phylogenetic tree visualisation",
+            "Phylogenetic tree generation"
+        ],
+        "edam_topic": [
+            "Genomics",
+            "Sequence assembly",
+            "DNA polymorphism",
+            "Microbiology",
+            "Sequence analysis",
+            "Genetic variation"
+        ],
+        "exact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)"
         ],
-        "edam_topic": [],
-        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "genome-annotation/annotation-with-maker-short",
-        "inexact_supported_servers": [],
+        "id": "variant-analysis/microbial-variants",
+        "inexact_supported_servers": [
+            "GalaxyTrakr",
+            "UseGalaxy.cz",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Maker allows to annotate a eukaryotic genome.",
-            "BUSCO and JBrowse allow to inspect the quality of an annotation."
+            "We used a tool called Snippy to call variants between our reads and our reference genome.",
+            "As our reference genome had annotations, we could see what effect the changes have on the features as annotated in the reference and therefore make inferences on the possible changes to the phenotype.",
+            "We used the JBrowse genome browser to visualise what these changes look like."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-02-29",
+        "mod_date": "2024-03-15",
         "objectives": [
-            "Load genome into Galaxy",
-            "Annotate genome with Maker",
-            "Evaluate annotation quality with BUSCO",
-            "View annotations in JBrowse"
+            "Find variants between a reference genome and a set of reads",
+            "Visualise the SNP in context of the reads aligned to the genome",
+            "Determine the effect of those variants on genomic features",
+            "Understand if the SNP is potentially affecting the phenotype"
         ],
-        "pageviews": 4070,
-        "priority": 3,
-        "pub_date": "2021-01-12",
+        "pageviews": 20692,
+        "pub_date": "2018-02-26",
         "questions": [
-            "How to annotate an eukaryotic genome?",
-            "How to evaluate and visualize annotated genomic features?"
+            "How do we detect differences between a set of reads from a microorganism and a reference genome"
         ],
-        "short_id": "T00167",
+        "short_id": "T00313",
         "short_tools": [
-            "jcvi_gff_stats",
-            "gffread",
             "jbrowse",
-            "busco",
-            "fasta-stats",
-            "maker",
-            "maker_map_ids"
+            "snippy"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "eukaryote",
+        "subtopic": "introduction",
         "supported_servers": {
-            "exact": [],
-            "inexact": []
+            "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
         },
         "symlink": null,
         "tags": [
+            "prokaryote",
+            "microgalaxy",
             "gmod",
-            "eukaryote",
-            "maker",
             "jbrowse1"
         ],
-        "time_estimation": "2h",
-        "title": "Genome annotation with Maker (short)",
+        "time_estimation": "45m",
+        "title": "Microbial Variant Calling",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.10",
-            "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10",
-            "toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0"
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/0.7.0.3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2"
         ],
-        "topic_name": "genome-annotation",
-        "topic_name_human": "Genome Annotation",
+        "topic_name": "variant-analysis",
+        "topic_name_human": "Variant Analysis",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "annotation-with-maker-short",
+        "tutorial_name": "microbial-variants",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/microbial-variants/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/microbial-variants/tutorial.json"
         },
-        "version": 3,
+        "version": 23,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 192,
-        "visitors": 2763,
+        "visit_duration": 119,
+        "visitors": 12475,
         "workflows": [
             {
                 "creators": [],
-                "description": "Genome annotation with Maker (short)",
+                "description": "Microbial Variant Calling",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenome sequence\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nProteins\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSNAP model\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAugustus model\"]\n  5[label=\"Fasta Statistics\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Busco\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Maker\"]\n  4 -> 7 [label=\"output\"]\n  3 -> 7 [label=\"output\"]\n  1 -> 7 [label=\"output\"]\n  0 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"Map annotation ids\"]\n  7 -> 8 [label=\"output_gff\"]\n  9[label=\"Genome annotation statistics\"]\n  8 -> 9 [label=\"renamed\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"gffread\"]\n  8 -> 10 [label=\"renamed\"]\n  0 -> 10 [label=\"output\"]\n  11[label=\"JBrowse\"]\n  0 -> 11 [label=\"output\"]\n  8 -> 11 [label=\"renamed\"]\n  7 -> 11 [label=\"output_evidences\"]\n  12[label=\"Busco\"]\n  10 -> 12 [label=\"output_exons\"]\n  k6951417bee0b4e0398e467d262e086dc[color=lightseagreen,label=\"Output\\nBusco summary final round\"]\n  12 -> k6951417bee0b4e0398e467d262e086dc\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  5[label=\"snippy\"]\n  0 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"output\"]\n  k419ad933d100406bbd61a70885eec0f8[color=lightseagreen,label=\"Output\\nsnippy_fasta\"]\n  5 -> k419ad933d100406bbd61a70885eec0f8\n  k47781ae9a68240a9aa61b972e5e5c9af[color=lightseagreen,label=\"Output\\nsnippy_tabular\"]\n  5 -> k47781ae9a68240a9aa61b972e5e5c9af\n  6[label=\"JBrowse\"]\n  5 -> 6 [label=\"snpgff\"]\n  4 -> 6 [label=\"output\"]\n  5 -> 6 [label=\"snpsbam\"]\n  2 -> 6 [label=\"output\"]\n  k6d6b366134ed417ab7b6394afe7a0edd[color=lightseagreen,label=\"Output\\njbrowse_html\"]\n  6 -> k6d6b366134ed417ab7b6394afe7a0edd\n}",
                 "history": [
                     {
-                        "hash": "005d964a2e8cb80f8d1bf0b304adc8f9d7c9ff76",
-                        "message": "fix workflows",
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 5,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 4,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "dfb97360348d32210f7c4bae68f1154a2336e520",
+                        "message": "annotate workflow outputs",
+                        "num": 3,
+                        "short_hash": "dfb973603",
+                        "unix": "1526109637"
+                    },
+                    {
+                        "hash": "8803cca01f5e6e62243a1cefbe21e701e89151af",
+                        "message": "pretty'fy workflow",
                         "num": 2,
-                        "short_hash": "005d964a2",
-                        "unix": "1609752597"
+                        "short_hash": "8803cca01",
+                        "unix": "1526109452"
                     },
                     {
-                        "hash": "774f2aa374452d48fd29ee85513c3dc3a7f137f5",
-                        "message": "update maker tutorial and add a short version",
+                        "hash": "5a1bff42297572d14d33b4e41de89694a6957676",
+                        "message": "Add some love to microbial variant calling tutorial (#732)",
                         "num": 1,
-                        "short_hash": "774f2aa37",
-                        "unix": "1609431273"
+                        "short_hash": "5a1bff422",
+                        "unix": "1523043969"
                     }
                 ],
                 "inputs": [
@@ -116534,34 +116656,22 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Genome sequence"
+                                "name": "mutant_R1"
                             }
                         ],
-                        "label": "Genome sequence",
+                        "label": null,
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 94.08332824707031,
-                            "height": 82.19999694824219,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 11.883331298828125,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 11.883331298828125
+                            "left": 10,
+                            "top": 10
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"name\": \"mutant_R1\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "a361a75e-5fa4-44ca-a4b7-cc9054a73054",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "9a09d16c-18af-4605-8416-4966fe918677"
-                            }
-                        ]
+                        "uuid": "f78a5562-288a-49fa-a8e4-a6facf09bffe",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
@@ -116572,34 +116682,22 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "EST and/or cDNA"
+                                "name": "mutant_R2"
                             }
                         ],
-                        "label": "EST and/or cDNA",
+                        "label": null,
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 214.0833282470703,
-                            "height": 82.19999694824219,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 131.88333129882812,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 131.88333129882812
+                            "left": 10,
+                            "top": 130
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"name\": \"mutant_R2\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "6b3edbe9-085d-46ae-9ae3-96e876c003e0",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "c5c5fb8f-9932-499c-b404-c142aedd1aa5"
-                            }
-                        ]
+                        "uuid": "9f0aa29d-da56-4535-96ce-696a721d1d76",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
@@ -116610,34 +116708,22 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Proteins"
+                                "name": "wildtype.fna"
                             }
                         ],
-                        "label": "Proteins",
+                        "label": null,
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 313.68333435058594,
-                            "height": 61.80000305175781,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 251.88333129882812,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 251.88333129882812
+                            "left": 10,
+                            "top": 250
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"name\": \"wildtype.fna\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ce4ee756-1713-4e6a-898c-b85a834712bc",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "cbbe9e59-ccd5-4925-a7a3-e1d094284fca"
-                            }
-                        ]
+                        "uuid": "1ad30281-3ee6-4725-8515-8db4936de0ff",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
@@ -116648,34 +116734,22 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "SNAP model"
+                                "name": "wildtype.gbk"
                             }
                         ],
-                        "label": "SNAP model",
+                        "label": null,
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 413.68333435058594,
-                            "height": 61.80000305175781,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 351.8833312988281,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 351.8833312988281
+                            "left": 10,
+                            "top": 370
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"name\": \"wildtype.gbk\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ebf1f01c-e804-462a-92cf-670012b103b3",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "ecfd7af4-f95c-4b2d-9f06-8e851a0c4d9e"
-                            }
-                        ]
+                        "uuid": "3c0c913a-7106-4ac7-b653-a0a0da1d14f8",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
@@ -116686,719 +116760,2070 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Augustus model"
+                                "name": "wildtype.gff"
                             }
                         ],
-                        "label": "Augustus model",
+                        "label": null,
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 554.0833282470703,
-                            "height": 82.19999694824219,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 471.8833312988281,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 471.8833312988281
+                            "left": 10,
+                            "top": 490
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"name\": \"wildtype.gff\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "586af078-09ce-476b-9eb7-55e443a8eeaf",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "7259eb8b-9c2d-4eff-a49d-1b447e905314"
-                            }
-                        ]
+                        "uuid": "0a4f5c3d-4f34-4461-8114-98f3bb0a4cf8",
+                        "workflow_outputs": []
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGenome sequence\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nProteins\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nSNAP model\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nAugustus model\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Fasta Statistics\"];\n  0 -->|output| 5;\n  6[\"Busco\"];\n  0 -->|output| 6;\n  7[\"Maker\"];\n  4 -->|output| 7;\n  3 -->|output| 7;\n  1 -->|output| 7;\n  0 -->|output| 7;\n  2 -->|output| 7;\n  8[\"Map annotation ids\"];\n  7 -->|output_gff| 8;\n  9[\"Genome annotation statistics\"];\n  8 -->|renamed| 9;\n  0 -->|output| 9;\n  10[\"gffread\"];\n  8 -->|renamed| 10;\n  0 -->|output| 10;\n  11[\"JBrowse\"];\n  0 -->|output| 11;\n  8 -->|renamed| 11;\n  7 -->|output_evidences| 11;\n  12[\"Busco\"];\n  10 -->|output_exons| 12;\n  6951417b-ee0b-4e03-98e4-67d262e086dc[\"Output\\nBusco summary final round\"];\n  12 --> 6951417b-ee0b-4e03-98e4-67d262e086dc;\n  style 6951417b-ee0b-4e03-98e4-67d262e086dc stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Genome annotation with Maker (short)",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"snippy\"];\n  0 -->|output| 5;\n  1 -->|output| 5;\n  3 -->|output| 5;\n  419ad933-d100-406b-bd61-a70885eec0f8[\"Output\\nsnippy_fasta\"];\n  5 --> 419ad933-d100-406b-bd61-a70885eec0f8;\n  style 419ad933-d100-406b-bd61-a70885eec0f8 stroke:#2c3143,stroke-width:4px;\n  47781ae9-a682-40a9-aa61-b972e5e5c9af[\"Output\\nsnippy_tabular\"];\n  5 --> 47781ae9-a682-40a9-aa61-b972e5e5c9af;\n  style 47781ae9-a682-40a9-aa61-b972e5e5c9af stroke:#2c3143,stroke-width:4px;\n  6[\"JBrowse\"];\n  5 -->|snpgff| 6;\n  4 -->|output| 6;\n  5 -->|snpsbam| 6;\n  2 -->|output| 6;\n  6d6b3661-34ed-417a-b7b6-394afe7a0edd[\"Output\\njbrowse_html\"];\n  6 --> 6d6b3661-34ed-417a-b7b6-394afe7a0edd;\n  style 6d6b3661-34ed-417a-b7b6-394afe7a0edd stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "Microbial Variant Calling",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 5,
+                        "input_connections": {
+                            "fastq_input|fastq_input1": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "fastq_input|fastq_input2": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "ref": {
+                                "id": 3,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "snippy",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Genome sequence"
+                                "name": "snpvcf",
+                                "type": "vcf"
+                            },
+                            {
+                                "name": "snpgff",
+                                "type": "gff3"
+                            },
+                            {
+                                "name": "snptab",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "snpsum",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "snplog",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "snpalign",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "snpconsensus",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "snpsdepth",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "snpsbam",
+                                "type": "bam"
+                            },
+                            {
+                                "name": "outdir",
+                                "type": "zip"
                             }
                         ],
-                        "label": "Genome sequence",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 94.08332824707031,
-                            "height": 82.19999694824219,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 11.883331298828125,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 11.883331298828125
+                            "left": 230,
+                            "top": 10
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "a361a75e-5fa4-44ca-a4b7-cc9054a73054",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "c9a8ef2aa380",
+                            "name": "snippy",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv\": \"{\\\"mapqual\\\": \\\"60\\\", \\\"bwaopt\\\": \\\"\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"rgid\\\": \\\"\\\", \\\"mincov\\\": \\\"10\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outgff\\\", \\\"outtab\\\", \\\"outsum\\\", \\\"outlog\\\", \\\"outaln\\\", \\\"outcon\\\", \\\"outdep\\\", \\\"outbam\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"fastq_input2\\\": null, \\\"__current_case__\\\": 0, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"fastq_input1\\\": null}\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"ref\": \"null\"}",
+                        "tool_version": "3.2",
+                        "type": "tool",
+                        "uuid": "5f5638b5-3553-4522-9cfa-d47dd45e8c42",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "9a09d16c-18af-4605-8416-4966fe918677"
+                                "label": "snippy_fasta",
+                                "output_name": "snpconsensus",
+                                "uuid": "419ad933-d100-406b-bd61-a70885eec0f8"
+                            },
+                            {
+                                "label": "snippy_tabular",
+                                "output_name": "snpsum",
+                                "uuid": "47781ae9-a682-40a9-aa61-b972e5e5c9af"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/0.7.0.3",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 6,
+                        "input_connections": {
+                            "reference_genome|genomes": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "track_groups_0|data_tracks_0|data_format|annotation": {
+                                "id": 5,
+                                "output_name": "snpsbam"
+                            },
+                            "track_groups_1|data_tracks_0|data_format|annotation": {
+                                "id": 5,
+                                "output_name": "snpgff"
+                            },
+                            "track_groups_2|data_tracks_0|data_format|annotation": {
+                                "id": 4,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "JBrowse",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "EST and/or cDNA"
+                                "name": "output",
+                                "type": "html"
                             }
                         ],
-                        "label": "EST and/or cDNA",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 214.0833282470703,
-                            "height": 82.19999694824219,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 131.88333129882812,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 131.88333129882812
+                            "left": 450,
+                            "top": 10
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "6b3edbe9-085d-46ae-9ae3-96e876c003e0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/0.7.0.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "836d1aa3e89a",
+                            "name": "jbrowse",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"standalone\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"reference_genome\": \"{\\\"genomes\\\": null, \\\"__current_case__\\\": 1, \\\"genome_type_select\\\": \\\"history\\\"}\", \"track_groups\": \"[{\\\"category\\\": \\\"sequence reads\\\", \\\"__index__\\\": 0, \\\"data_tracks\\\": [{\\\"__index__\\\": 0, \\\"data_format\\\": {\\\"auto_snp\\\": \\\"true\\\", \\\"track_visibility\\\": \\\"default_on\\\", \\\"override_apollo_drag\\\": \\\"False\\\", \\\"__current_case__\\\": 3, \\\"override_apollo_plugins\\\": \\\"False\\\", \\\"annotation\\\": null, \\\"data_format_select\\\": \\\"pileup\\\"}}]}, {\\\"category\\\": \\\"variants\\\", \\\"__index__\\\": 1, \\\"data_tracks\\\": [{\\\"__index__\\\": 0, \\\"data_format\\\": {\\\"index\\\": \\\"false\\\", \\\"match_part\\\": {\\\"match_part_select\\\": \\\"false\\\", \\\"__current_case__\\\": 1}, \\\"jbstyle\\\": {\\\"style_classname\\\": \\\"feature\\\", \\\"style_description\\\": \\\"note,description\\\", \\\"style_height\\\": \\\"10px\\\", \\\"max_height\\\": \\\"600\\\", \\\"style_label\\\": \\\"product,name,id\\\"}, \\\"track_visibility\\\": \\\"default_on\\\", \\\"track_config\\\": {\\\"track_class\\\": \\\"JBrowse/View/Track/CanvasFeatures\\\", \\\"canvas_options\\\": {\\\"transcriptType\\\": \\\"\\\", \\\"subParts\\\": \\\"\\\", \\\"impliedUTRs\\\": \\\"false\\\"}, \\\"__current_case__\\\": 0}, \\\"jbcolor_scale\\\": {\\\"color_score\\\": {\\\"color\\\": {\\\"color_select\\\": \\\"automatic\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 0, \\\"color_score_select\\\": \\\"none\\\"}}, \\\"override_apollo_drag\\\": \\\"False\\\", \\\"__current_case__\\\": 2, \\\"override_apollo_plugins\\\": \\\"False\\\", \\\"jbmenu\\\": {\\\"track_menu\\\": []}, \\\"annotation\\\": null, \\\"data_format_select\\\": \\\"gene_calls\\\"}}]}, {\\\"category\\\": \\\"annotated reference\\\", \\\"__index__\\\": 2, \\\"data_tracks\\\": [{\\\"__index__\\\": 0, \\\"data_format\\\": {\\\"index\\\": \\\"false\\\", \\\"match_part\\\": {\\\"match_part_select\\\": \\\"false\\\", \\\"__current_case__\\\": 1}, \\\"jbstyle\\\": {\\\"style_classname\\\": \\\"feature\\\", \\\"style_description\\\": \\\"product\\\", \\\"style_height\\\": \\\"10px\\\", \\\"max_height\\\": \\\"600\\\", \\\"style_label\\\": \\\"product\\\"}, \\\"track_visibility\\\": \\\"default_on\\\", \\\"track_config\\\": {\\\"track_class\\\": \\\"JBrowse/View/Track/CanvasFeatures\\\", \\\"canvas_options\\\": {\\\"transcriptType\\\": \\\"\\\", \\\"subParts\\\": \\\"\\\", \\\"impliedUTRs\\\": \\\"false\\\"}, \\\"__current_case__\\\": 0}, \\\"jbcolor_scale\\\": {\\\"color_score\\\": {\\\"color\\\": {\\\"color_select\\\": \\\"automatic\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 0, \\\"color_score_select\\\": \\\"none\\\"}}, \\\"override_apollo_drag\\\": \\\"False\\\", \\\"__current_case__\\\": 2, \\\"override_apollo_plugins\\\": \\\"False\\\", \\\"jbmenu\\\": {\\\"track_menu\\\": []}, \\\"annotation\\\": null, \\\"data_format_select\\\": \\\"gene_calls\\\"}}]}]\", \"plugins\": \"{\\\"GCContent\\\": \\\"false\\\", \\\"Bookmarks\\\": \\\"false\\\", \\\"theme\\\": \\\"\\\", \\\"ComboTrackSelector\\\": \\\"false\\\"}\", \"action\": \"{\\\"action_select\\\": \\\"create\\\", \\\"__current_case__\\\": 0}\", \"gencode\": \"\\\"11\\\"\", \"uglyTestingHack\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"jbgen\": \"{\\\"trackPadding\\\": \\\"20\\\", \\\"show_tracklist\\\": \\\"true\\\", \\\"show_overview\\\": \\\"true\\\", \\\"show_nav\\\": \\\"true\\\", \\\"aboutDescription\\\": \\\"\\\", \\\"defaultLocation\\\": \\\"\\\", \\\"hideGenomeOptions\\\": \\\"false\\\", \\\"shareLink\\\": \\\"true\\\", \\\"show_menu\\\": \\\"true\\\"}\"}",
+                        "tool_version": "0.7.0.3",
+                        "type": "tool",
+                        "uuid": "2a2aad62-4281-4bd1-bb5c-cd8bc078ec85",
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "jbrowse_html",
                                 "output_name": "output",
-                                "uuid": "c5c5fb8f-9932-499c-b404-c142aedd1aa5"
+                                "uuid": "6d6b3661-34ed-417a-b7b6-394afe7a0edd"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "variant-analysis/microbial-variants",
+                "path": "topics/variant-analysis/tutorials/microbial-variants/workflows/microbial_variant_calling.ga",
+                "tags": [
+                    "variant-analysis"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "Microbial Variant Calling",
+                "topic_id": "variant-analysis",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-microbial-variants/versions/microbial-variant-calling",
+                "tutorial_id": "microbial-variants",
+                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/microbial-variants/workflows/microbial_variant_calling.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/microbial-variants/workflows/microbial_variant_calling.html",
+                "version": 4,
+                "wfid": "variant-analysis-microbial-variants",
+                "wfname": "microbial-variant-calling",
+                "workflow": "microbial_variant_calling.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/0.7.0.3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2"
+                ],
+                "workflowhub_id": "1093"
+            }
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.582600"
+    },
+    {
+        "abbreviations": {
+            "SVs": "Structural Variations"
+        },
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "flye",
+                    "owner": "bgruening",
+                    "revisions": "cb8dfd28c16f",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "5ec9f6bceaee",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bandage",
+                    "owner": "iuc",
+                    "revisions": "ddddce450736",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bwa_mem2",
+                    "owner": "iuc",
+                    "revisions": "bfaa0d22c2e4",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastp",
+                    "owner": "iuc",
+                    "revisions": "65b93b623c77",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "filtlong",
+                    "owner": "iuc",
+                    "revisions": "8880fb74ef56",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "filtlong",
+                    "owner": "iuc",
+                    "revisions": "1f296803dfa3",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "nanoplot",
+                    "owner": "iuc",
+                    "revisions": "0f1c34698076",
+                    "tool_panel_section_label": "Nanopore",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "polypolish",
+                    "owner": "iuc",
+                    "revisions": "f355085dd2aa",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "porechop",
+                    "owner": "iuc",
+                    "revisions": "93d623d9979c",
+                    "tool_panel_section_label": "Nanopore",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "quast",
+                    "owner": "iuc",
+                    "revisions": "72472698a2df",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: flye\n  owner: bgruening\n  revisions: cb8dfd28c16f\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_mem2\n  owner: iuc\n  revisions: bfaa0d22c2e4\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filtlong\n  owner: iuc\n  revisions: 8880fb74ef56\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filtlong\n  owner: iuc\n  revisions: 1f296803dfa3\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: 0f1c34698076\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: polypolish\n  owner: iuc\n  revisions: f355085dd2aa\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: porechop\n  owner: iuc\n  revisions: 93d623d9979c\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 72472698a2df\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-nanopore/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "bazante1",
+                "bebatut"
+            ],
+            "editing": [
+                "hexylena",
+                "bazante1",
+                "shiltemann",
+                "miaomiaozhou88"
+            ],
+            "funding": [
+                "avans-atgm",
+                "abromics"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "avans-atgm"
+                ],
+                "id": "bazante1",
+                "joined": "2020-12",
+                "name": "Bazante Sanders",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "affiliations": [
+                    "avans-atgm"
+                ],
+                "id": "bazante1",
+                "joined": "2020-12",
+                "name": "Bazante Sanders",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
+            },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
+            {
+                "email": "m.zhou1@avans.nl",
+                "id": "miaomiaozhou88",
+                "joined": "2020-12",
+                "name": "Miaomiao Zhou",
+                "orcid": "0000-0003-4426-1758",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/miaomiaozhou88/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/miaomiaozhou88.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/logo-avans.png",
+                "former_members": [
+                    "dirowa",
+                    "hexylena"
+                ],
+                "id": "avans-atgm",
+                "joined": "2020-11",
+                "members": [
+                    "bazante1"
+                ],
+                "name": "Avans Hogeschool",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/",
+                "ror": "015d5s513",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/abromics.png",
+                "funder": true,
+                "github": false,
+                "id": "abromics",
+                "joined": "2024-01",
+                "name": "ABRomics",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abromics/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/abromics.json"
+            }
+        ],
+        "dir": "topics/assembly/tutorials/mrsa-nanopore",
+        "edam_ontology": [
+            "topic_0196",
+            "topic_3673",
+            "topic_3305",
+            "topic_0622",
+            "topic_3301",
+            "topic_4013"
+        ],
+        "edam_operation": [
+            "Scatter plot plotting",
+            "Sequencing error detection",
+            "Sequence alignment",
+            "Visualisation",
+            "Cross-assembly",
+            "Read mapping",
+            "Sequencing quality control",
+            "Genome assembly",
+            "De-novo assembly",
+            "Box-Whisker plot plotting",
+            "Sequence contamination filtering",
+            "Sequence assembly validation",
+            "Mapping assembly",
+            "Statistical calculation",
+            "Sequence assembly visualisation",
+            "Filtering",
+            "Sequence composition calculation"
+        ],
+        "edam_topic": [
+            "Sequence assembly",
+            "Whole genome sequencing",
+            "Public health and epidemiology",
+            "Genomics",
+            "Microbiology",
+            "Antimicrobial Resistance"
+        ],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "genome-annotation",
+                "tutorials": [
+                    "amr-gene-detection"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "history-to-workflow"
+                ],
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "assembly/mrsa-nanopore",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": 11271,
+            "mermaid": false
+        },
+        "key_points": [
+            "Nanopore produces fantastic assemblies but with low quality data",
+            "Annotation with Prokka is very easy"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-03-13",
+        "objectives": [
+            "Run tools to evaluate sequencing data on quality and quantity",
+            "Process the output of quality control tools",
+            "Improve the quality of sequencing data",
+            "Run a tool to assemble a bacterial genome using short reads",
+            "Run tools to assess the quality of an assembly",
+            "Understand the outputs of tools to assess the quality of an assembly"
+        ],
+        "pageviews": 10977,
+        "pub_date": "2021-03-24",
+        "questions": [
+            "How to check the quality of the MinION data (together with Illumina data)?",
+            "How to perform an assembly of a bacterial genome with MinION data?",
+            "How to check the quality of an assembly?"
+        ],
+        "short_id": "T00037",
+        "short_tools": [
+            "CONVERTER_bz2_to_uncompressed",
+            "fastp",
+            "filtlong",
+            "bandage_image",
+            "porechop",
+            "upload1",
+            "quast",
+            "flye",
+            "nanoplot",
+            "bwa_mem2",
+            "polypolish",
+            "fastqc"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "nanopore",
+            "assembly",
+            "amr",
+            "gmod",
+            "jbrowse1",
+            "microgalaxy"
+        ],
+        "time_estimation": "2h",
+        "title": "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)",
+        "tools": [
+            "CONVERTER_bz2_to_uncompressed",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/polypolish/polypolish/0.5.0+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+            "upload1"
+        ],
+        "topic_name": "assembly",
+        "topic_name_human": "Assembly",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "mrsa-nanopore",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-nanopore/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/mrsa-nanopore/tutorial.json"
+        },
+        "version": 14,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 204,
+        "visitors": 7148,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0003-2255-1631",
+                        "name": "Bazante Sanders"
                     },
                     {
-                        "annotation": "",
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0001-9852-1987",
+                        "name": "B\u00e9r\u00e9nice Batut"
+                    }
+                ],
+                "description": "Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nNanopore raw reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina forward raw reads\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reverse raw reads\"]\n  3[label=\"Convert compressed file to uncompressed.\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"FastQC\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"fastp\"]\n  1 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"NanoPlot\"]\n  3 -> 6 [label=\"output1\"]\n  ka97e6f3381824a3386dd6cfbb83a842d[color=lightseagreen,label=\"Output\\nnanoplot_before_filtering\"]\n  6 -> ka97e6f3381824a3386dd6cfbb83a842d\n  7[label=\"filtlong\"]\n  5 -> 7 [label=\"out1\"]\n  5 -> 7 [label=\"out2\"]\n  0 -> 7 [label=\"output\"]\n  8[label=\"Flye\"]\n  7 -> 8 [label=\"outfile\"]\n  kf12e718f1bd5490dbd41f0747aaa41a6[color=lightseagreen,label=\"Output\\nflye_assembly_info\"]\n  8 -> kf12e718f1bd5490dbd41f0747aaa41a6\n  9[label=\"NanoPlot\"]\n  7 -> 9 [label=\"outfile\"]\n  k89524090f590434d89e266f0b1a23c7c[color=lightseagreen,label=\"Output\\nnanoplot_after_filtering\"]\n  9 -> k89524090f590434d89e266f0b1a23c7c\n  10[label=\"Bandage Image\"]\n  8 -> 10 [label=\"assembly_gfa\"]\n  11[label=\"BWA-MEM2\"]\n  5 -> 11 [label=\"out2\"]\n  8 -> 11 [label=\"consensus\"]\n  12[label=\"Quast\"]\n  8 -> 12 [label=\"consensus\"]\n  kdabfb8fd87914959a9dc9b3c1e57a69c[color=lightseagreen,label=\"Output\\nquast_report_before_polishing\"]\n  12 -> kdabfb8fd87914959a9dc9b3c1e57a69c\n  13[label=\"BWA-MEM2\"]\n  5 -> 13 [label=\"out1\"]\n  8 -> 13 [label=\"consensus\"]\n  14[label=\"Polypolish\"]\n  8 -> 14 [label=\"consensus\"]\n  13 -> 14 [label=\"bam_output\"]\n  11 -> 14 [label=\"bam_output\"]\n  15[label=\"Quast\"]\n  14 -> 15 [label=\"polished_fasta\"]\n  8 -> 15 [label=\"consensus\"]\n  k4e465b5168bf42039a7c897f46c70277[color=lightseagreen,label=\"Output\\nquast_report_after_polishing\"]\n  15 -> k4e465b5168bf42039a7c897f46c70277\n}",
+                "history": [
+                    {
+                        "hash": "96393a7fcb4d6dc37d86866cf8a61c931293502f",
+                        "message": "Add MRSA Nanopore assembly tutorial to AMR learning pathway",
+                        "num": 1,
+                        "short_hash": "96393a7fc",
+                        "unix": "1709135526"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "Nanopore raw reads",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Proteins"
+                                "description": "Nanopore raw reads",
+                                "name": "Nanopore raw reads"
                             }
                         ],
-                        "label": "Proteins",
+                        "label": "Nanopore raw reads",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 313.68333435058594,
-                            "height": 61.80000305175781,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 251.88333129882812,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 251.88333129882812
+                            "left": 65.66800632871802,
+                            "top": 217.27323322511424
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ce4ee756-1713-4e6a-898c-b85a834712bc",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "cbbe9e59-ccd5-4925-a7a3-e1d094284fca"
-                            }
-                        ]
+                        "uuid": "cd4fd302-af94-4771-9b80-7c7acb6619d4",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Illumina forward raw reads",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "SNAP model"
+                                "description": "Illumina forward raw reads",
+                                "name": "Illumina forward raw reads"
                             }
                         ],
-                        "label": "SNAP model",
+                        "label": "Illumina forward raw reads",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 413.68333435058594,
-                            "height": 61.80000305175781,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 351.8833312988281,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 351.8833312988281
+                            "left": 0,
+                            "top": 479
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ebf1f01c-e804-462a-92cf-670012b103b3",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "ecfd7af4-f95c-4b2d-9f06-8e851a0c4d9e"
-                            }
-                        ]
+                        "uuid": "b3fe89da-544c-4066-abcb-b33d4f005796",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Illumina reverse raw reads",
                         "content_id": null,
                         "errors": null,
-                        "id": 4,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Augustus model"
+                                "description": "Illumina reverse raw reads",
+                                "name": "Illumina reverse raw reads"
                             }
                         ],
-                        "label": "Augustus model",
+                        "label": "Illumina reverse raw reads",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 554.0833282470703,
-                            "height": 82.19999694824219,
-                            "left": -313.33331298828125,
-                            "right": -113.33331298828125,
-                            "top": 471.8833312988281,
-                            "width": 200,
-                            "x": -313.33331298828125,
-                            "y": 471.8833312988281
+                            "left": 0,
+                            "top": 602
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "586af078-09ce-476b-9eb7-55e443a8eeaf",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "7259eb8b-9c2d-4eff-a49d-1b447e905314"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "dataset": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Fasta Statistics",
-                        "outputs": [
-                            {
-                                "name": "stats",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 34.28334045410156,
-                            "height": 154.40000915527344,
-                            "left": -15.350006103515625,
-                            "right": 184.64999389648438,
-                            "top": -120.11666870117188,
-                            "width": 200,
-                            "x": -15.350006103515625,
-                            "y": -120.11666870117188
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "20ca2574216a",
-                            "name": "fasta_stats",
-                            "owner": "simon-gladman",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "43cab601-f700-4278-bd0a-7f0997cf75cf",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "stats",
-                                "uuid": "7840b5e6-2a7e-4b3c-bea3-4a0d70fea21b"
-                            }
-                        ]
-                    },
+                        "uuid": "16545abc-0513-4a32-9ea5-4a168875a854",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nNanopore raw reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nIllumina forward raw reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nIllumina reverse raw reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Convert compressed file to uncompressed.\"];\n  0 -->|output| 3;\n  4[\"FastQC\"];\n  0 -->|output| 4;\n  5[\"fastp\"];\n  1 -->|output| 5;\n  2 -->|output| 5;\n  6[\"NanoPlot\"];\n  3 -->|output1| 6;\n  a97e6f33-8182-4a33-86dd-6cfbb83a842d[\"Output\\nnanoplot_before_filtering\"];\n  6 --> a97e6f33-8182-4a33-86dd-6cfbb83a842d;\n  style a97e6f33-8182-4a33-86dd-6cfbb83a842d stroke:#2c3143,stroke-width:4px;\n  7[\"filtlong\"];\n  5 -->|out1| 7;\n  5 -->|out2| 7;\n  0 -->|output| 7;\n  8[\"Flye\"];\n  7 -->|outfile| 8;\n  f12e718f-1bd5-490d-bd41-f0747aaa41a6[\"Output\\nflye_assembly_info\"];\n  8 --> f12e718f-1bd5-490d-bd41-f0747aaa41a6;\n  style f12e718f-1bd5-490d-bd41-f0747aaa41a6 stroke:#2c3143,stroke-width:4px;\n  9[\"NanoPlot\"];\n  7 -->|outfile| 9;\n  89524090-f590-434d-89e2-66f0b1a23c7c[\"Output\\nnanoplot_after_filtering\"];\n  9 --> 89524090-f590-434d-89e2-66f0b1a23c7c;\n  style 89524090-f590-434d-89e2-66f0b1a23c7c stroke:#2c3143,stroke-width:4px;\n  10[\"Bandage Image\"];\n  8 -->|assembly_gfa| 10;\n  11[\"BWA-MEM2\"];\n  5 -->|out2| 11;\n  8 -->|consensus| 11;\n  12[\"Quast\"];\n  8 -->|consensus| 12;\n  dabfb8fd-8791-4959-a9dc-9b3c1e57a69c[\"Output\\nquast_report_before_polishing\"];\n  12 --> dabfb8fd-8791-4959-a9dc-9b3c1e57a69c;\n  style dabfb8fd-8791-4959-a9dc-9b3c1e57a69c stroke:#2c3143,stroke-width:4px;\n  13[\"BWA-MEM2\"];\n  5 -->|out1| 13;\n  8 -->|consensus| 13;\n  14[\"Polypolish\"];\n  8 -->|consensus| 14;\n  13 -->|bam_output| 14;\n  11 -->|bam_output| 14;\n  15[\"Quast\"];\n  14 -->|polished_fasta| 15;\n  8 -->|consensus| 15;\n  4e465b51-68bf-4203-9a7c-897f46c70277[\"Output\\nquast_report_after_polishing\"];\n  15 --> 4e465b51-68bf-4203-9a7c-897f46c70277;\n  style 4e465b51-68bf-4203-9a7c-897f46c70277 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available)",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
                         "errors": null,
                         "id": 6,
                         "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
+                            "mode|reads|files": {
+                                "id": 3,
+                                "output_name": "output1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Busco",
+                        "name": "NanoPlot",
                         "outputs": [
                             {
-                                "name": "busco_sum",
-                                "type": "txt"
+                                "name": "output_html",
+                                "type": "html"
                             },
                             {
-                                "name": "busco_table",
+                                "name": "nanostats",
                                 "type": "tabular"
                             },
                             {
-                                "name": "busco_missing",
+                                "name": "nanostats_post_filtering",
                                 "type": "tabular"
+                            },
+                            {
+                                "name": "read_length",
+                                "type": "png"
+                            },
+                            {
+                                "name": "log_read_length",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": -157.71664428710938,
-                            "height": 276.4000244140625,
-                            "left": -15.350006103515625,
-                            "right": 184.64999389648438,
-                            "top": -434.1166687011719,
-                            "width": 200,
-                            "x": -15.350006103515625,
-                            "y": -434.1166687011719
+                            "left": 598.8807084399002,
+                            "top": 268.83097889129806
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "602fb8e63aa7",
-                            "name": "busco",
+                            "changeset_revision": "0f1c34698076",
+                            "name": "nanoplot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"geno\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.1.4",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"customization\": {\"color\": null, \"plots\": null, \"N50\": true}, \"filter\": {\"maxlength\": null, \"minlength\": null, \"drop_outliers\": false, \"downsample\": null, \"loglength\": false, \"percentqual\": false, \"alength\": false, \"minqual\": null, \"runtime_until\": null, \"readtype\": null, \"barcoded\": false, \"no_supplementary\": false}, \"mode\": {\"choice\": \"batch\", \"__current_case__\": 0, \"reads\": {\"type\": \"fastq\", \"__current_case__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.41.0+galaxy0",
                         "type": "tool",
-                        "uuid": "876334be-d7e5-4504-bb1b-727472839c02",
+                        "uuid": "ad46f297-04f2-4959-aa09-db88cd91cc27",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "busco_sum",
-                                "uuid": "59ce9dc8-762f-4c38-aded-5d031db50609"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "busco_missing",
-                                "uuid": "9b000535-1702-4888-951c-4cc8e782a511"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "busco_table",
-                                "uuid": "76c0d8fc-4e81-4ba0-b8b2-ebfda0ba5786"
+                                "label": "nanoplot_before_filtering",
+                                "output_name": "nanostats",
+                                "uuid": "a97e6f33-8182-4a33-86dd-6cfbb83a842d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0",
                         "errors": null,
                         "id": 8,
                         "input_connections": {
-                            "maker_gff": {
+                            "inputs": {
                                 "id": 7,
-                                "output_name": "output_gff"
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Map annotation ids",
+                        "name": "Flye",
                         "outputs": [
                             {
-                                "name": "renamed",
-                                "type": "gff"
+                                "name": "consensus",
+                                "type": "fasta"
                             },
                             {
-                                "name": "id_map",
+                                "name": "assembly_graph",
+                                "type": "graph_dot"
+                            },
+                            {
+                                "name": "assembly_gfa",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "assembly_info",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 318.8833312988281,
-                            "height": 246,
-                            "left": 272.66668701171875,
-                            "right": 472.66668701171875,
-                            "top": 72.88333129882812,
-                            "width": 200,
-                            "x": 272.66668701171875,
-                            "y": 72.88333129882812
-                        },
-                        "post_job_actions": {
-                            "ChangeDatatypeActionrenamed": {
-                                "action_arguments": {
-                                    "newtype": "gff3"
-                                },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "renamed"
-                            },
-                            "HideDatasetActionid_map": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "id_map"
-                            }
+                            "left": 850.0098909589506,
+                            "top": 593
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "f1912d5575df",
-                            "name": "maker_map_ids",
-                            "owner": "iuc",
+                            "changeset_revision": "cb8dfd28c16f",
+                            "name": "flye",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"justify\": \"6\", \"maker_gff\": {\"__class__\": \"ConnectedValue\"}, \"prefix\": \"TEST\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.31.11",
+                        "tool_state": "{\"__input_ext\": \"input\", \"asm\": {\"asm_select\": \"false\", \"__current_case__\": 1}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"generate_log\": false, \"inputs\": {\"__class__\": \"ConnectedValue\"}, \"iterations\": \"1\", \"keep_haplotypes\": false, \"meta\": false, \"min_overlap\": null, \"mode_conditional\": {\"mode\": \"--nano-corr\", \"__current_case__\": 1}, \"no_alt_contigs\": false, \"scaffold\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.9.1+galaxy0",
                         "type": "tool",
-                        "uuid": "b1127093-0aae-4bfa-b474-042b838a8299",
+                        "uuid": "8cf7ff30-4007-49cb-a959-e25c337f05be",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "renamed",
-                                "uuid": "e8686326-b443-402b-bb0e-b4a02a8815a7"
+                                "label": "flye_assembly_info",
+                                "output_name": "assembly_info",
+                                "uuid": "f12e718f-1bd5-490d-bd41-f0747aaa41a6"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
                         "errors": null,
                         "id": 9,
                         "input_connections": {
-                            "gff": {
-                                "id": 8,
-                                "output_name": "renamed"
-                            },
-                            "ref_genome|genome": {
-                                "id": 0,
-                                "output_name": "output"
+                            "mode|reads|files": {
+                                "id": 7,
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Genome annotation statistics",
+                        "name": "NanoPlot",
                         "outputs": [
                             {
-                                "name": "summary",
-                                "type": "txt"
+                                "name": "output_html",
+                                "type": "html"
                             },
                             {
-                                "name": "graphs",
-                                "type": "pdf"
+                                "name": "nanostats",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "nanostats_post_filtering",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "read_length",
+                                "type": "png"
+                            },
+                            {
+                                "name": "log_read_length",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": 363.2833557128906,
-                            "height": 276.4000244140625,
-                            "left": 560.6500244140625,
-                            "right": 760.6500244140625,
-                            "top": 86.88333129882812,
-                            "width": 200,
-                            "x": 560.6500244140625,
-                            "y": 86.88333129882812
+                            "left": 850.0098909589506,
+                            "top": 859
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "8cffbd184762",
-                            "name": "jcvi_gff_stats",
+                            "changeset_revision": "0f1c34698076",
+                            "name": "nanoplot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"gff\": {\"__class__\": \"ConnectedValue\"}, \"ref_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.8.4",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"customization\": {\"color\": null, \"plots\": null, \"N50\": true}, \"filter\": {\"maxlength\": null, \"minlength\": null, \"drop_outliers\": false, \"downsample\": null, \"loglength\": false, \"percentqual\": false, \"alength\": false, \"minqual\": null, \"runtime_until\": null, \"readtype\": null, \"barcoded\": false, \"no_supplementary\": false}, \"mode\": {\"choice\": \"batch\", \"__current_case__\": 0, \"reads\": {\"type\": \"fastq\", \"__current_case__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.41.0+galaxy0",
                         "type": "tool",
-                        "uuid": "14236032-ec57-4beb-ab0a-e44bf845643c",
+                        "uuid": "467fca53-715f-4717-ab4c-c4410d321086",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "graphs",
-                                "uuid": "782e21db-4be6-4230-92b5-3ea9004dda04"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "summary",
-                                "uuid": "a4dff39c-0479-4a25-ac62-b132c1083604"
+                                "label": "nanoplot_after_filtering",
+                                "output_name": "nanostats",
+                                "uuid": "89524090-f590-434d-89e2-66f0b1a23c7c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
                         "errors": null,
-                        "id": 10,
+                        "id": 12,
                         "input_connections": {
-                            "input": {
+                            "mode|in|inputs": {
                                 "id": 8,
-                                "output_name": "renamed"
-                            },
-                            "reference_genome|genome_fasta": {
-                                "id": 0,
-                                "output_name": "output"
+                                "output_name": "consensus"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool gffread",
-                                "name": "chr_replace"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "gffread",
+                        "name": "Quast",
                         "outputs": [
                             {
-                                "name": "output_exons",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "output_cds",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "output_pep",
-                                "type": "fasta"
+                                "name": "report_html",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "bottom": 48.683319091796875,
-                            "height": 316.79998779296875,
-                            "left": 560.6500244140625,
-                            "right": 760.6500244140625,
-                            "top": -268.1166687011719,
-                            "width": 200,
-                            "x": 560.6500244140625,
-                            "y": -268.1166687011719
+                            "left": 1140.0069535390257,
+                            "top": 767
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "0232f19d300f",
-                            "name": "gffread",
-                            "owner": "devteam",
+                            "changeset_revision": "72472698a2df",
+                            "name": "quast",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"chr_replace\": {\"__class__\": \"RuntimeValue\"}, \"decode_url\": \"false\", \"expose\": \"false\", \"filtering\": null, \"full_gff_attribute_preservation\": \"false\", \"gffs\": {\"gff_fmt\": \"none\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"maxintron\": \"\", \"merging\": {\"merge_sel\": \"none\", \"__current_case__\": 0}, \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 2, \"genome_fasta\": {\"__class__\": \"ConnectedValue\"}, \"ref_filtering\": null, \"fa_outputs\": [\"-w exons.fa\", \"-x cds.fa\", \"-y pep.fa\"]}, \"region\": {\"region_filter\": \"none\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.2.1.1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"false\", \"__current_case__\": 1, \"est_ref_size\": null}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": false}, \"large\": false, \"min_contig\": \"500\", \"mode\": {\"mode\": \"co\", \"__current_case__\": 1, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": \"html\", \"split_scaffolds\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.2.0+galaxy1",
                         "type": "tool",
-                        "uuid": "3b5ecaf4-2d08-42f8-a6f0-f05ad9e5fe92",
+                        "uuid": "6949cf20-419e-4cee-86fa-3b08ab60cb9f",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_cds",
-                                "uuid": "0df7b9b5-1ed1-4cf4-b483-a604862f4540"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_exons",
-                                "uuid": "f485f8fe-0d63-49ba-a88d-dfc8e03db553"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_pep",
-                                "uuid": "7430528c-9af5-4e05-ba6c-bbf95f19ad7e"
+                                "label": "quast_report_before_polishing",
+                                "output_name": "report_html",
+                                "uuid": "dabfb8fd-8791-4959-a9dc-9b3c1e57a69c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
                         "errors": null,
-                        "id": 11,
+                        "id": 15,
                         "input_connections": {
-                            "reference_genome|genome": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "track_groups_0|data_tracks_0|data_format|annotation": {
-                                "id": 8,
-                                "output_name": "renamed"
-                            },
-                            "track_groups_1|data_tracks_0|data_format|annotation": {
-                                "id": 7,
-                                "output_name": "output_evidences"
-                            }
+                            "mode|in|inputs": [
+                                {
+                                    "id": 14,
+                                    "output_name": "polished_fasta"
+                                },
+                                {
+                                    "id": 8,
+                                    "output_name": "consensus"
+                                }
+                            ]
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool JBrowse",
-                                "name": "reference_genome"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "JBrowse",
+                        "name": "Quast",
                         "outputs": [
                             {
-                                "name": "output",
+                                "name": "report_html",
                                 "type": "html"
                             }
                         ],
                         "position": {
-                            "bottom": 677.2833557128906,
-                            "height": 276.4000244140625,
-                            "left": 560.6500244140625,
-                            "right": 760.6500244140625,
-                            "top": 400.8833312988281,
-                            "width": 200,
-                            "x": 560.6500244140625,
-                            "y": 400.8833312988281
+                            "left": 1700.001078699176,
+                            "top": 853
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "8774b28235bb",
-                            "name": "jbrowse",
+                            "changeset_revision": "72472698a2df",
+                            "name": "quast",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Maker annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 1, \"category\": \"Maker evidences\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"true\", \"__current_case__\": 0, \"name\": {\"__class__\": \"RuntimeValue\"}}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16.10+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"false\", \"__current_case__\": 1, \"est_ref_size\": null}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": false}, \"large\": false, \"min_contig\": \"500\", \"mode\": {\"mode\": \"co\", \"__current_case__\": 1, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": \"html\", \"split_scaffolds\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.2.0+galaxy1",
                         "type": "tool",
-                        "uuid": "5a978f9d-7adc-4e30-8b20-dcfa27f18dfa",
+                        "uuid": "866187e0-dd7c-40d5-b121-a8ef4a281c80",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "c7432de7-b6b4-457a-8c0a-69c44418234d"
+                                "label": "quast_report_after_polishing",
+                                "output_name": "report_html",
+                                "uuid": "4e465b51-68bf-4203-9a7c-897f46c70277"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "assembly/mrsa-nanopore",
+                "path": "topics/assembly/tutorials/mrsa-nanopore/workflows/main-workflow.ga",
+                "tags": [
+                    "Assembly"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available)",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-mrsa-nanopore/versions/main-workflow",
+                "tutorial_id": "mrsa-nanopore",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/mrsa-nanopore/workflows/main-workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/mrsa-nanopore/workflows/main-workflow.html",
+                "version": 1,
+                "wfid": "assembly-mrsa-nanopore",
+                "wfname": "main-workflow",
+                "workflow": "main-workflow.ga",
+                "workflow_tools": [
+                    "CONVERTER_bz2_to_uncompressed",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/polypolish/polypolish/0.5.0+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
+                ],
+                "workflowhub_id": "1178"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/10669812"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "ddf54b12c295",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "add_value",
+                    "owner": "devteam",
+                    "revisions": "745871c0b055",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_compute_length",
+                    "owner": "devteam",
+                    "revisions": "de2db1bdfbf8",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_filter_by_length",
+                    "owner": "devteam",
+                    "revisions": "e626b3ff9922",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_filter_by_length",
+                    "owner": "devteam",
+                    "revisions": "8cacfcf96a52",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "lastz",
+                    "owner": "devteam",
+                    "revisions": "e7f19d6a9af8",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "merge_cols",
+                    "owner": "devteam",
+                    "revisions": "f2aac0c5c60d",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bedtools",
+                    "owner": "iuc",
+                    "revisions": "e19bebe96cd2",
+                    "tool_panel_section_label": "BED",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bedtools",
+                    "owner": "iuc",
+                    "revisions": "e19bebe96cd2",
+                    "tool_panel_section_label": "BED",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bedtools",
+                    "owner": "iuc",
+                    "revisions": "e19bebe96cd2",
+                    "tool_panel_section_label": "BED",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "circos",
+                    "owner": "iuc",
+                    "revisions": "df7356989ac1",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "circos",
+                    "owner": "iuc",
+                    "revisions": "df7356989ac1",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "datamash_ops",
+                    "owner": "iuc",
+                    "revisions": "562f3c677828",
+                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "jbrowse",
+                    "owner": "iuc",
+                    "revisions": "fd5dbf0f732e",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "25136a2b0cfe",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "830961c48e42",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: ddf54b12c295\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: add_value\n  owner: devteam\n  revisions: 745871c0b055\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_compute_length\n  owner: devteam\n  revisions: de2db1bdfbf8\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_filter_by_length\n  owner: devteam\n  revisions: e626b3ff9922\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_filter_by_length\n  owner: devteam\n  revisions: 8cacfcf96a52\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lastz\n  owner: devteam\n  revisions: e7f19d6a9af8\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merge_cols\n  owner: devteam\n  revisions: f2aac0c5c60d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: e19bebe96cd2\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: e19bebe96cd2\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: e19bebe96cd2\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: circos\n  owner: iuc\n  revisions: df7356989ac1\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: circos\n  owner: iuc\n  revisions: df7356989ac1\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 562f3c677828\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: fd5dbf0f732e\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 25136a2b0cfe\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ecoli_comparison/tutorial.json",
+        "contributors": [
+            {
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
+                "joined": "2017-09",
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+            },
+            {
+                "email": "delphine.lariviere@galaxy.org",
+                "id": "delphine-l",
+                "joined": "2017-09",
+                "name": "Delphine Lariviere",
+                "orcid": "0000-0001-6421-3484",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            }
+        ],
+        "dir": "topics/assembly/tutorials/ecoli_comparison",
+        "edam_ontology": [
+            "topic_0196",
+            "topic_0622",
+            "topic_3301"
+        ],
+        "edam_operation": [
+            "Sequence alignment",
+            "Sequence visualisation",
+            "Read mapping",
+            "Genome visualisation",
+            "Mapping"
+        ],
+        "edam_topic": [
+            "Sequence assembly",
+            "Genomics",
+            "Microbiology"
+        ],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "assembly/ecoli_comparison",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "We learned how to download large sets of completed genomes from NCBI",
+            "We learned how to use Galaxy's rule-based collection builder",
+            "We learned how to use a combination of Galaxy tools to create complex views of genome comparisons",
+            "We learned about idiosyncrasies of data formats and how to deal with them using Galaxy tools"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-24",
+        "objectives": [
+            "Identification of the most closely related genome to my new assembly",
+            "Perform sequence comparison to locate rearrangements",
+            "Identify genes located in deletions"
+        ],
+        "pageviews": 12166,
+        "pub_date": "2018-06-14",
+        "questions": [
+            "I just assembled a genome. How does it compare with already sequenced genomes?",
+            "How do I find rearranged, inserted, or deleted regions?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "assembly",
+                "tutorials": [
+                    "unicycler-assembly"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00032",
+        "short_tools": [
+            "join1",
+            "tp_sed_tool",
+            "lastz_wrapper_2",
+            "upload1",
+            "fasta_filter_by_length",
+            "bedtools_intersectbed",
+            "datamash_ops",
+            "circos_interval_to_tiles",
+            "jbrowse",
+            "tp_cat",
+            "mergeCols1",
+            "Filter1",
+            "bedtools_sortbed",
+            "tp_sort_header_tool",
+            "Grep1",
+            "Cut1",
+            "collapse_dataset",
+            "cat1",
+            "tp_replace_in_column",
+            "addValue",
+            "circos_aln_to_links",
+            "fasta_compute_length",
+            "circos",
+            "tp_grep_tool",
+            "tp_replace_in_line",
+            "random_lines1",
+            "bedtools_complementbed"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "gmod",
+            "prokaryote",
+            "microgalaxy",
+            "jbrowse1"
+        ],
+        "time_estimation": "4h",
+        "title": "Making sense of a newly assembled genome",
+        "tools": [
+            "Cut1",
+            "Filter1",
+            "Grep1",
+            "cat1",
+            "join1",
+            "random_lines1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.27.0.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.0.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy7",
+            "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_aln_to_links/0.69.8+galaxy7",
+            "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tiles/0.69.8+galaxy7",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.8+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
+            "upload1"
+        ],
+        "topic_name": "assembly",
+        "topic_name_human": "Assembly",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "ecoli_comparison",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ecoli_comparison/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ecoli_comparison/tutorial.json"
+        },
+        "version": 29,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 181,
+        "visitors": 6026,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Making sense of a newly assembled genome",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  10[label=\"Collapse Collection\"]\n  6 -> 10 [label=\"output\"]\n  11[label=\"Text transformation\"]\n  7 -> 11 [label=\"output\"]\n  12[label=\"Add column\"]\n  8 -> 12 [label=\"out_file1\"]\n  13[label=\"LASTZ\"]\n  9 -> 13 [label=\"output\"]\n  3 -> 13 [label=\"output\"]\n  14[label=\"random_lines1\"]\n  10 -> 14 [label=\"output\"]\n  15[label=\"Filter\"]\n  10 -> 15 [label=\"output\"]\n  16[label=\"Search in textfiles\"]\n  11 -> 16 [label=\"output\"]\n  17[label=\"Concatenate datasets\"]\n  11 -> 17 [label=\"output\"]\n  9 -> 17 [label=\"output\"]\n  18[label=\"Cut\"]\n  12 -> 18 [label=\"out_file1\"]\n  19[label=\"Text transformation\"]\n  13 -> 19 [label=\"output\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  20[label=\"Datamash\"]\n  15 -> 20 [label=\"out_file1\"]\n  21[label=\"Compute sequence length\"]\n  17 -> 21 [label=\"out_file1\"]\n  22[label=\"Collapse Collection\"]\n  18 -> 22 [label=\"out_file1\"]\n  23[label=\"Merge Columns\"]\n  19 -> 23 [label=\"output\"]\n  24[label=\"Select\"]\n  20 -> 24 [label=\"out_file\"]\n  25[label=\"Sort\"]\n  21 -> 25 [label=\"output\"]\n  26[label=\"Collapse Collection\"]\n  23 -> 26 [label=\"out_file1\"]\n  27[label=\"Cut\"]\n  26 -> 27 [label=\"output\"]\n  28[label=\"Cut\"]\n  26 -> 28 [label=\"output\"]\n  29[label=\"Concatenate datasets\"]\n  27 -> 29 [label=\"out_file1\"]\n  28 -> 29 [label=\"out_file1\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  30[label=\"SortBED\"]\n  29 -> 30 [label=\"out_file1\"]\n  31[label=\"ComplementBed\"]\n  25 -> 31 [label=\"outfile\"]\n  30 -> 31 [label=\"output\"]\n  32[label=\"Filter\"]\n  31 -> 32 [label=\"output\"]\n  33[label=\"Filter\"]\n  32 -> 33 [label=\"out_file1\"]\n  34[label=\"Intersect intervals\"]\n  33 -> 34 [label=\"out_file1\"]\n  22 -> 34 [label=\"output\"]\n  35[label=\"Join two Datasets\"]\n  34 -> 35 [label=\"output\"]\n  1 -> 35 [label=\"output\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  5[label=\"Filter sequences by length\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"LASTZ\"]\n  2 -> 6 [label=\"output\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Collapse Collection\"]\n  3 -> 7 [label=\"output\"]\n  8[label=\"Select\"]\n  4 -> 8 [label=\"output\"]\n  9[label=\"Text transformation\"]\n  5 -> 9 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "48cf52ea88fe32cfc059494bc1b464c4b202bf99",
+                        "message": "on purpose mistake fixed",
+                        "num": 6,
+                        "short_hash": "48cf52ea8",
+                        "unix": "1579772724"
+                    },
+                    {
+                        "hash": "b3f79801438efc81c5f2a3f0af17a26f82e6913e",
+                        "message": "test",
+                        "num": 5,
+                        "short_hash": "b3f798014",
+                        "unix": "1579714684"
+                    },
+                    {
+                        "hash": "230f6e12fc9de41c8cb554a353e0b816eb656724",
+                        "message": "linting fix",
+                        "num": 4,
+                        "short_hash": "230f6e12f",
+                        "unix": "1579705852"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 3,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 2,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
                     },
+                    {
+                        "hash": "485411d09f88e53fb83bc584da92afa171aed32a",
+                        "message": "workflow for ecoli_comparison",
+                        "num": 1,
+                        "short_hash": "485411d09",
+                        "unix": "1546963139"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 12,
-                        "input_connections": {
-                            "input": {
-                                "id": 10,
-                                "output_name": "output_exons"
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Ecoli_C_assembly.fna"
                             }
-                        },
-                        "inputs": [],
+                        ],
                         "label": null,
-                        "name": "Busco",
-                        "outputs": [
-                            {
-                                "name": "busco_sum",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "busco_table",
-                                "type": "tabular"
-                            },
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 10
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Ecoli_C_assembly.fna\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "2eb3a31a-f5ec-4ce0-a4db-f421ab573412",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "busco_missing",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "inline-supplementary-material-7 - Table_S4_Essential genes identi.tsv"
                             }
                         ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 100.88333129882812,
-                            "height": 256,
-                            "left": 838.6666870117188,
-                            "right": 1038.6666870117188,
-                            "top": -155.11666870117188,
-                            "width": 200,
-                            "x": 838.6666870117188,
-                            "y": -155.11666870117188
+                            "left": 10,
+                            "top": 130
                         },
-                        "post_job_actions": {
-                            "HideDatasetActionbusco_missing": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "busco_missing"
-                            },
-                            "HideDatasetActionbusco_table": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "busco_table"
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"inline-supplementary-material-7 - Table_S4_Essential genes identi.tsv\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ac567420-400d-4a74-adb5-cdaed90cebd6",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Input Dataset Collection"
                             }
+                        ],
+                        "label": null,
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 250
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "602fb8e63aa7",
-                            "name": "busco",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        "tool_id": null,
+                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "8cc3e0ac-13bd-4e29-83dc-8411490fc85d",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Input Dataset Collection"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 370
                         },
-                        "tool_state": "{\"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"tran\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.1.4",
-                        "type": "tool",
-                        "uuid": "dee27b5d-de92-4e99-898c-3bf3fea6ee72",
-                        "workflow_outputs": [
+                        "tool_id": null,
+                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "6bc17455-70a4-48bb-a511-e484016e9ad8",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": "Busco summary final round",
-                                "output_name": "busco_sum",
-                                "uuid": "6951417b-ee0b-4e03-98e4-67d262e086dc"
+                                "description": "",
+                                "name": "Input Dataset Collection"
                             }
-                        ]
+                        ],
+                        "label": null,
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 490
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "04145efc-b9a4-4bd4-9a72-7cdf0e98e752",
+                        "workflow_outputs": []
                     }
                 ],
-                "parent_id": "genome-annotation/annotation-with-maker-short",
-                "path": "topics/genome-annotation/tutorials/annotation-with-maker-short/workflows/main_workflow.ga",
-                "tags": [
-                    "genome-annotation"
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Collapse Collection\"];\n  6 -->|output| 10;\n  11[\"Text transformation\"];\n  7 -->|output| 11;\n  12[\"Add column\"];\n  8 -->|out_file1| 12;\n  13[\"LASTZ\"];\n  9 -->|output| 13;\n  3 -->|output| 13;\n  14[\"random_lines1\"];\n  10 -->|output| 14;\n  15[\"Filter\"];\n  10 -->|output| 15;\n  16[\"Search in textfiles\"];\n  11 -->|output| 16;\n  17[\"Concatenate datasets\"];\n  11 -->|output| 17;\n  9 -->|output| 17;\n  18[\"Cut\"];\n  12 -->|out_file1| 18;\n  19[\"Text transformation\"];\n  13 -->|output| 19;\n  2[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  20[\"Datamash\"];\n  15 -->|out_file1| 20;\n  21[\"Compute sequence length\"];\n  17 -->|out_file1| 21;\n  22[\"Collapse Collection\"];\n  18 -->|out_file1| 22;\n  23[\"Merge Columns\"];\n  19 -->|output| 23;\n  24[\"Select\"];\n  20 -->|out_file| 24;\n  25[\"Sort\"];\n  21 -->|output| 25;\n  26[\"Collapse Collection\"];\n  23 -->|out_file1| 26;\n  27[\"Cut\"];\n  26 -->|output| 27;\n  28[\"Cut\"];\n  26 -->|output| 28;\n  29[\"Concatenate datasets\"];\n  27 -->|out_file1| 29;\n  28 -->|out_file1| 29;\n  3[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  30[\"SortBED\"];\n  29 -->|out_file1| 30;\n  31[\"ComplementBed\"];\n  25 -->|outfile| 31;\n  30 -->|output| 31;\n  32[\"Filter\"];\n  31 -->|output| 32;\n  33[\"Filter\"];\n  32 -->|out_file1| 33;\n  34[\"Intersect intervals\"];\n  33 -->|out_file1| 34;\n  22 -->|output| 34;\n  35[\"Join two Datasets\"];\n  34 -->|output| 35;\n  1 -->|output| 35;\n  4[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Filter sequences by length\"];\n  0 -->|output| 5;\n  6[\"LASTZ\"];\n  2 -->|output| 6;\n  0 -->|output| 6;\n  7[\"Collapse Collection\"];\n  3 -->|output| 7;\n  8[\"Select\"];\n  4 -->|output| 8;\n  9[\"Text transformation\"];\n  5 -->|output| 9;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Ecoli Comparison",
+                "outputs": [],
+                "parent_id": "assembly/ecoli_comparison",
+                "path": "topics/assembly/tutorials/ecoli_comparison/workflows/ecoli-comparison.ga",
+                "tags": [
+                    "assembly"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Ecoli Comparison",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-ecoli_comparison/versions/ecoli-comparison",
+                "tutorial_id": "ecoli_comparison",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/ecoli_comparison/workflows/ecoli-comparison.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/ecoli_comparison/workflows/ecoli-comparison.html",
+                "version": 3,
+                "wfid": "assembly-ecoli_comparison",
+                "wfname": "ecoli-comparison",
+                "workflow": "ecoli-comparison.ga",
+                "workflow_tools": [
+                    "Cut1",
+                    "Filter1",
+                    "Grep1",
+                    "cat1",
+                    "join1",
+                    "random_lines1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.27.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0"
+                ],
+                "workflowhub_id": "1113"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/3382053"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "jbrowse",
+                    "owner": "iuc",
+                    "revisions": "17359b808b01",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: jbrowse\n  owner: iuc\n  revisions: 17359b808b01\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/jbrowse/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
                 ],
-                "test_results": null,
-                "tests": false,
-                "title": "Genome annotation with Maker (short)",
-                "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-annotation-with-maker-short/versions/main-workflow",
-                "tutorial_id": "annotation-with-maker-short",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-maker-short/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-maker-short/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "genome-annotation-annotation-with-maker-short",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.10",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10",
-                    "toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0"
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
                 ],
-                "workflowhub_id": "1194"
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.4406623"
+        "dir": "topics/visualisation/tutorials/jbrowse",
+        "edam_operation": [
+            "Genome visualisation"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "Galaxy@AuBi",
+            "UseGalaxy.be",
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "visualisation/jbrowse",
+        "inexact_supported_servers": [
+            "Galaxy@Pasteur",
+            "GalaxyTrakr",
+            "MISSISSIPPI",
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "This tutorial can not exhaustively cover every data type, but maybe it provides inspiration for your own analyses",
+            "JBrowse is a great, workflow-compatible alternative to other genome browsers",
+            "You can build visualisations that summarise dozens of analyses in one visualisation"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-17",
+        "objectives": [
+            "Build several visualisations in JBrowse",
+            "Have basic familiarity with moving around JBrowse, and loading several data tracks"
+        ],
+        "pageviews": 5902528,
+        "pub_date": "2020-01-10",
+        "questions": [
+            "How can I visualise features or blast data?",
+            "How can I visualise sequencing data in a workflow"
+        ],
+        "short_id": "T00322",
+        "short_tools": [
+            "jbrowse"
+        ],
+        "slides": true,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "gmod",
+            "jbrowse1"
+        ],
+        "time_estimation": "1h",
+        "title": "Genomic Data Visualisation with JBrowse",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0"
+        ],
+        "topic_name": "visualisation",
+        "topic_name_human": "Visualisation",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "jbrowse",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/visualisation/tutorials/jbrowse/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/jbrowse/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/jbrowse/tutorial.json"
+        },
+        "version": 16,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 287,
+        "visitors": 2137509,
+        "zenodo_link": "https://doi.org/10.5281/zenodo.3591856"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/official-gene-set/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "abretaud"
+            ],
+            "funding": [
+                "gallantries"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "eurosciencegateway",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
+                "fediverse_flavor": "mastodon",
+                "id": "abretaud",
+                "joined": "2017-09",
+                "location": {
+                    "country": "FR",
+                    "lat": 48.11,
+                    "lon": -1.64
+                },
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            }
+        ],
+        "dir": "topics/genome-annotation/tutorials/official-gene-set",
+        "draft": true,
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "genome-annotation/official-gene-set",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Genoest' OGS Tools makes it easy to validate and release a build of your genome and its annotations."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-02-29",
+        "objectives": [
+            "Validate your genes and create an official gene set from them."
+        ],
+        "pageviews": 12,
+        "pub_date": "2023-11-02",
+        "questions": [
+            "I have several genomes assemblies that are not annotated (or I do not trust annotations)",
+            "I am interested to compare structure of a particular gene across these genome assemblies",
+            "How do I do that?"
+        ],
+        "short_id": "T00370",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "gmod",
+            "apollo2",
+            "work-in-progress"
+        ],
+        "time_estimation": "30M",
+        "title": "Creating an Official Gene Set",
+        "tools": [],
+        "topic_name": "genome-annotation",
+        "topic_name_human": "Genome Annotation",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "official-gene-set",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/official-gene-set/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/official-gene-set/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/official-gene-set/tutorial.json"
+        },
+        "version": 2,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 0,
+        "visitors": 10,
+        "zenodo_link": ""
     },
     {
         "admin_install": {
@@ -117407,72 +118832,444 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "augustus_training",
+                    "name": "bwa",
+                    "owner": "devteam",
+                    "revisions": "e188dc7a68e6",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "3d0c7bdf12f5",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "jbrowse",
+                    "owner": "iuc",
+                    "revisions": "17359b808b01",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 17359b808b01\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "nakucher",
+                "avahoffman",
+                "robertmeller"
+            ],
+            "editing": [
+                "katherinecox",
+                "cutsort",
+                "nakucher"
+            ],
+            "funding": [
+                "nhgri-gdscn",
+                "nhgri-anvil"
+            ],
+            "infrastructure": [
+                "cansavvy",
+                "avahoffman",
+                "katherinecox",
+                "ehumph",
+                "cutsort"
+            ]
+        },
+        "contributors": [
+            {
+                "email": "nkucher3@jhu.edu",
+                "id": "nakucher",
+                "joined": "2023-06",
+                "name": "Natalie Kucher",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nakucher/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nakucher.json"
+            },
+            {
+                "id": "avahoffman",
+                "joined": "2023-06",
+                "name": "Ava Hoffman",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avahoffman/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/avahoffman.json"
+            },
+            {
+                "id": "robertmeller",
+                "joined": "2023-06",
+                "name": "Robert Meller",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/robertmeller/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/robertmeller.json"
+            },
+            {
+                "id": "katherinecox",
+                "joined": "2023-06",
+                "name": "Katherine Cox",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/katherinecox/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/katherinecox.json"
+            },
+            {
+                "id": "cutsort",
+                "joined": "2023-06",
+                "name": "Frederick Tan",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cutsort/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/cutsort.json"
+            },
+            {
+                "email": "nkucher3@jhu.edu",
+                "id": "nakucher",
+                "joined": "2023-06",
+                "name": "Natalie Kucher",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nakucher/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nakucher.json"
+            },
+            {
+                "id": "cansavvy",
+                "joined": "2023-06",
+                "name": "Candace Savonen",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cansavvy/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/cansavvy.json"
+            },
+            {
+                "id": "avahoffman",
+                "joined": "2023-06",
+                "name": "Ava Hoffman",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avahoffman/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/avahoffman.json"
+            },
+            {
+                "id": "katherinecox",
+                "joined": "2023-06",
+                "name": "Katherine Cox",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/katherinecox/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/katherinecox.json"
+            },
+            {
+                "id": "ehumph",
+                "joined": "2023-06",
+                "name": "Elizabeth Humphries",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ehumph/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/ehumph.json"
+            },
+            {
+                "id": "cutsort",
+                "joined": "2023-06",
+                "name": "Frederick Tan",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cutsort/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/cutsort.json"
+            },
+            {
+                "avatar": "https://www.ashg.org/wp-content/uploads/2021/07/nhgri-logo-800x167-1.png",
+                "funder": true,
+                "funding_id": "75N92022P00232",
+                "github": false,
+                "id": "nhgri-gdscn",
+                "joined": "2023-06",
+                "name": "National Human Genome Research Institute Genomic Data Science Community Network",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nhgri-gdscn/",
+                "short_name": "NHGRI GDS Community Network",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/nhgri-gdscn.json"
+            },
+            {
+                "avatar": "https://www.ashg.org/wp-content/uploads/2021/07/nhgri-logo-800x167-1.png",
+                "funder": true,
+                "funding_id": "U24HG010263",
+                "github": false,
+                "id": "nhgri-anvil",
+                "joined": "2023-06",
+                "name": "National Human Genome Research Institute Genomic Data Science Analysis, Visualization, and Informatics Lab-Space",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nhgri-anvil/",
+                "short_name": "NHGRI ANVIL",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/nhgri-anvil.json"
+            }
+        ],
+        "dir": "topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil",
+        "edam_operation": [
+            "Generation",
+            "Statistical calculation",
+            "Sequence alignment",
+            "Read mapping",
+            "Sequencing quality control",
+            "Sequence composition calculation",
+            "Genome visualisation",
+            "Genome indexing"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "sequence-analysis/sars-with-galaxy-on-anvil",
+        "inexact_supported_servers": [
+            "Galaxy@AuBi",
+            "Galaxy@Pasteur",
+            "GalaxyTrakr",
+            "MISSISSIPPI",
+            "UseGalaxy.be",
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Use Galaxy on the AnVIL cloud computing resource to check data, perform an alignment, and visualize the results."
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-02-29",
+        "objectives": [
+            "Gather and evaluate experimental evidence, including qualitative and quantitative data",
+            "Generate and interpret graphs displaying experimental results",
+            "Critique large data sets and use bioinformatics to assess genetics data",
+            "Tap into the interdisciplinary nature of science"
+        ],
+        "pageviews": 956,
+        "pub_date": "2023-07-10",
+        "questions": [
+            "How do I check my data quality?",
+            "How do I put together my dataset of fragmented sequences into a full sequence?",
+            "How do I visually explore the variants in my SARS-CoV-2 sample?"
+        ],
+        "short_id": "T00356",
+        "short_tools": [
+            "bwa_mem",
+            "fastqc",
+            "jbrowse"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "covid19",
+            "gmod",
+            "jbrowse1"
+        ],
+        "time_estimation": "1H",
+        "title": "SARS-CoV-2 Viral Sample Alignment and Variant Visualization",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0"
+        ],
+        "topic_name": "sequence-analysis",
+        "topic_name_human": "Sequence analysis",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "sars-with-galaxy-on-anvil",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.json"
+        },
+        "version": 2,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 271,
+        "visitors": 739,
+        "zenodo_link": "https://doi.org/10.5281/zenodo.8115178"
+    },
+    {
+        "abbreviations": {
+            "NMDS": "Non-metric multidimensional scaling"
+        },
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "interproscan",
                     "owner": "bgruening",
-                    "revisions": "6519ebe25019",
+                    "revisions": "74810db257cc",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "gffread",
+                    "name": "picard",
                     "owner": "devteam",
-                    "revisions": "69e0806b63a4",
-                    "tool_panel_section_label": "Convert Formats",
+                    "revisions": "f9242e01365a",
+                    "tool_panel_section_label": "Picard",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "eggnog_mapper",
+                    "owner": "galaxyp",
+                    "revisions": "844fa988236b",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "aegean_parseval",
+                    "owner": "iuc",
+                    "revisions": "1b52f0c8ad7f",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "busco",
                     "owner": "iuc",
-                    "revisions": "602fb8e63aa7",
+                    "revisions": "94170eee0ad8",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fasta_stats",
+                    "name": "funannotate_annotate",
                     "owner": "iuc",
-                    "revisions": "9c620a950d3a",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "9feee7fc49a1",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "jbrowse",
+                    "name": "funannotate_annotate",
                     "owner": "iuc",
-                    "revisions": "6cd09d7b5f37",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "revisions": "582fd74dc2a1",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "jcvi_gff_stats",
+                    "name": "funannotate_compare",
                     "owner": "iuc",
-                    "revisions": "8cffbd184762",
+                    "revisions": "a7ce2601500c",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "maker",
+                    "name": "funannotate_compare",
                     "owner": "iuc",
-                    "revisions": "d46d803ca6cc",
+                    "revisions": "30f08d74024f",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "maker_map_ids",
+                    "name": "funannotate_predict",
                     "owner": "iuc",
-                    "revisions": "e906fa778440",
+                    "revisions": "51b6ee65ef7f",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "snap_training",
+                    "name": "funannotate_predict",
                     "owner": "iuc",
-                    "revisions": "2a598c0aa042",
+                    "revisions": "f31125bb85ea",
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "jbrowse",
+                    "owner": "iuc",
+                    "revisions": "a6e57ff585c0",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rgrnastar",
+                    "owner": "iuc",
+                    "revisions": "3ea5a2a63fa2",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rgrnastar",
+                    "owner": "iuc",
+                    "revisions": "4074fc1940e2",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: augustus_training\n  owner: bgruening\n  revisions: 6519ebe25019\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gffread\n  owner: devteam\n  revisions: 69e0806b63a4\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 602fb8e63aa7\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n  owner: iuc\n  revisions: 9c620a950d3a\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 6cd09d7b5f37\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jcvi_gff_stats\n  owner: iuc\n  revisions: 8cffbd184762\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker\n  owner: iuc\n  revisions: d46d803ca6cc\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker_map_ids\n  owner: iuc\n  revisions: e906fa778440\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snap_training\n  owner: iuc\n  revisions: 2a598c0aa042\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: interproscan\n  owner: bgruening\n  revisions: 74810db257cc\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: f9242e01365a\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: eggnog_mapper\n  owner: galaxyp\n  revisions: 844fa988236b\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: aegean_parseval\n  owner: iuc\n  revisions: 1b52f0c8ad7f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 94170eee0ad8\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_annotate\n  owner: iuc\n  revisions: 9feee7fc49a1\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_annotate\n  owner: iuc\n  revisions: 582fd74dc2a1\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_compare\n  owner: iuc\n  revisions: a7ce2601500c\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_compare\n  owner: iuc\n  revisions: 30f08d74024f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_predict\n  owner: iuc\n  revisions: 51b6ee65ef7f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: funannotate_predict\n  owner: iuc\n  revisions: f31125bb85ea\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n  owner: iuc\n  revisions: 3ea5a2a63fa2\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n  owner: iuc\n  revisions: 4074fc1940e2\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/funannotate/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "abretaud"
+            ],
+            "editing": [
+                "alexcorm",
+                "lleroi",
+                "r1corre",
+                "stephanierobin"
+            ],
+            "funding": [
+                "gallantries",
+                "eurosciencegateway"
+            ]
+        },
         "contributors": [
             {
                 "affiliations": [
@@ -117498,33 +119295,133 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
                 "twitter": "abretau",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+            },
+            {
+                "email": "alexandre.cormier@ifremer.fr",
+                "id": "alexcorm",
+                "joined": "2021-11",
+                "name": "Alexandre Cormier",
+                "orcid": "0000-0002-7775-8413",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/",
+                "twitter": "allanssx",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/alexcorm.json"
+            },
+            {
+                "email": "laura.leroi@ifremer.fr",
+                "id": "lleroi",
+                "joined": "2021-11",
+                "name": "Laura Leroi",
+                "orcid": "0000-0003-3748-4179",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lleroi/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/lleroi.json"
+            },
+            {
+                "email": "erwan.corre@sb-roscoff.fr",
+                "id": "r1corre",
+                "joined": "2019-04",
+                "name": "Erwan Corre",
+                "orcid": "0000-0001-6354-2278",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/r1corre/",
+                "twitter": "r1corre",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/r1corre.json"
+            },
+            {
+                "email": "stephanie.robin@inrae.fr",
+                "id": "stephanierobin",
+                "joined": "2021-11",
+                "name": "St\u00e9phanie Robin",
+                "orcid": "0000-0001-7379-9173",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/",
+                "twitter": "robinstphanie1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/stephanierobin.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/eurosciencegateway.png",
+                "funder": true,
+                "funding_id": "101057388",
+                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "eurosciencegateway",
+                "joined": "2023-10",
+                "members": [
+                    "abretaud",
+                    "anuprulez",
+                    "bgruening",
+                    "erxleben",
+                    "pauldg",
+                    "rlibouba"
+                ],
+                "name": "EuroScienceGateway",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
             }
         ],
-        "dir": "topics/genome-annotation/tutorials/annotation-with-maker",
+        "dir": "topics/genome-annotation/tutorials/funannotate",
         "edam_operation": [
-            "Ab-initio gene prediction",
             "Genome annotation",
-            "Sequence assembly validation",
-            "Homology-based gene prediction",
+            "Sequence alignment",
             "Genome visualisation",
-            "Operation",
-            "Transcriptome assembly",
-            "Sequence annotation",
             "Genome assembly",
-            "Gene prediction",
-            "Scaffolding"
+            "Sequence motif recognition",
+            "Query and retrieval",
+            "Fold recognition",
+            "Homology-based gene prediction",
+            "Sequence assembly validation",
+            "Scaffolding",
+            "Information extraction",
+            "Sequence annotation",
+            "Transcriptome assembly",
+            "Protein feature detection",
+            "Formatting"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu",
-            "UseGalaxy.no",
+            "UseGalaxy.fr",
             "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "genome-annotation",
+                "tutorials": [
+                    "apollo"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "genome-annotation/annotation-with-maker",
+        "id": "genome-annotation/funannotate",
         "inexact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.org.au"
         ],
@@ -117533,37 +119430,78 @@
             "mermaid": false
         },
         "key_points": [
-            "Maker allows to annotate a eukaryotic genome.",
-            "BUSCO and JBrowse allow to inspect the quality of an annotation."
+            "Funannotate allows to perform structural annotation of an eukaryotic genome.",
+            "Functional annotation can be performed using EggNOG-mapper and InterProScan.",
+            "BUSCO and JBrowse allow to inspect the quality of an annotation.",
+            "Funannotate allows to format an annotation for sumission at NCBI."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Advanced",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-02-29",
+        "mod_date": "2024-08-21",
         "objectives": [
             "Load genome into Galaxy",
-            "Annotate genome with Maker",
+            "Annotate genome with Funannotate",
+            "Perform functional annotation using EggNOG-mapper and InterProScan",
             "Evaluate annotation quality with BUSCO",
             "View annotations in JBrowse"
         ],
-        "pageviews": 21535,
-        "priority": 4,
-        "pub_date": "2018-09-24",
+        "pageviews": 10859,
+        "priority": 2,
+        "pub_date": "2021-11-29",
         "questions": [
-            "How to annotate an eukaryotic genome?",
-            "How to evaluate and visualize annotated genomic features?"
+            "How to annotate an eukaryotic genome with Funannotate?",
+            "How to perform functional annotation?",
+            "How to evaluate and visualize annotated genomic features?",
+            "How to format the annotation for submission at NCBI?"
         ],
-        "short_id": "T00166",
+        "recordings": [
+            {
+                "captioners": [
+                    "abretaud"
+                ],
+                "date": "2023-05-12",
+                "galaxy_version": "23.01",
+                "length": "1H10M",
+                "speakers": [
+                    "abretaud"
+                ],
+                "youtube_id": "p0NBxZk5964"
+            },
+            {
+                "captioners": [
+                    "abretaud"
+                ],
+                "date": "2022-03-03",
+                "galaxy_version": "21.09",
+                "length": "1H10M",
+                "speakers": [
+                    "abretaud"
+                ],
+                "youtube_id": "r-wU6BhqIpk"
+            }
+        ],
+        "requirements": [
+            {
+                "topic_name": "genome-annotation",
+                "tutorials": [
+                    "repeatmasker"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00172",
         "short_tools": [
-            "jcvi_gff_stats",
-            "gffread",
             "jbrowse",
+            "rna_star",
+            "eggnog_mapper",
+            "funannotate_compare",
             "busco",
-            "fasta-stats",
-            "snap_training",
-            "maker",
-            "augustus_training",
-            "maker_map_ids"
+            "funannotate_predict",
+            "picard_MergeSamFiles",
+            "interproscan",
+            "funannotate_annotate",
+            "aegean_parseval"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -117576,8 +119514,8 @@
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
                     "usegalaxy": false
                 },
                 {
@@ -117587,6 +119525,11 @@
                 }
             ],
             "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -117603,21 +119546,25 @@
         "tags": [
             "gmod",
             "eukaryote",
-            "jbrowse1",
-            "maker"
-        ],
-        "time_estimation": "4h",
-        "title": "Genome annotation with Maker",
+            "jbrowse1"
+        ],
+        "time_estimation": "8h",
+        "title": "Genome annotation with Funannotate",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3",
-            "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.11",
-            "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy0"
         ],
         "topic_name": "genome-annotation",
         "topic_name_human": "Genome Annotation",
@@ -117627,1903 +119574,1113 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "annotation-with-maker",
+        "tutorial_name": "funannotate",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/funannotate/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/funannotate/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/funannotate/tutorial.json"
         },
-        "version": 14,
+        "version": 23,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 114,
-        "visitors": 11527,
+        "visit_duration": 127,
+        "visitors": 7195,
         "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "0000-0003-0914-2470",
+                        "identifier": "https://orcid.org/0000-0003-0914-2470",
                         "name": "Anthony Bretaudeau"
-                    },
-                    {
-                        "class": "Organization",
-                        "name": "French National Institute for Agriculture, Food, and Environment (INRAE)"
                     }
                 ],
-                "description": "Genome annotation with Maker",
+                "description": "Structural and functional genome annotation with Funannotate",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nProtein sequences\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenome sequence\"]\n  3[label=\"Maker\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Fasta Statistics\"]\n  2 -> 4 [label=\"output\"]\n  k2d3829e6f5b946d183e317efff814e09[color=lightseagreen,label=\"Output\\nFasta Statistics on input dataset(s): Fasta summary stats\"]\n  4 -> k2d3829e6f5b946d183e317efff814e09\n  5[label=\"Busco\"]\n  2 -> 5 [label=\"output\"]\n  ka15e121423a2484b9c751635fcd61fe3[color=lightseagreen,label=\"Output\\nBUSCO: short summary\"]\n  5 -> ka15e121423a2484b9c751635fcd61fe3\n  k7806088df65743899d546a3bdfa233b2[color=lightseagreen,label=\"Output\\nBUSCO: list of missing ortholog genes\"]\n  5 -> k7806088df65743899d546a3bdfa233b2\n  k6a27d0f6d83c42b1a7af5f99ba5debe2[color=lightseagreen,label=\"Output\\nBUSCO: full table\"]\n  5 -> k6a27d0f6d83c42b1a7af5f99ba5debe2\n  6[label=\"Train Augustus\"]\n  2 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output_gff\"]\n  7[label=\"Genome annotation statistics\"]\n  3 -> 7 [label=\"output_gff\"]\n  2 -> 7 [label=\"output\"]\n  k2bed9aa65f22494d9caaf0ece8464f15[color=lightseagreen,label=\"Output\\nGenome annotation statistics: graphs (first round)\"]\n  7 -> k2bed9aa65f22494d9caaf0ece8464f15\n  k71d41ce2e90d435b9b64ab4320524770[color=lightseagreen,label=\"Output\\nGenome annotation statistics: summary (first round)\"]\n  7 -> k71d41ce2e90d435b9b64ab4320524770\n  8[label=\"gffread\"]\n  3 -> 8 [label=\"output_gff\"]\n  2 -> 8 [label=\"output\"]\n  9[label=\"Train SNAP\"]\n  2 -> 9 [label=\"output\"]\n  3 -> 9 [label=\"output_gff\"]\n  10[label=\"Busco\"]\n  8 -> 10 [label=\"output_exons\"]\n  ka79ab19d980242ca8ffa8c197a16c8b8[color=lightseagreen,label=\"Output\\nBusco summary first round\"]\n  10 -> ka79ab19d980242ca8ffa8c197a16c8b8\n  11[label=\"Maker\"]\n  6 -> 11 [label=\"output_tar\"]\n  9 -> 11 [label=\"output\"]\n  2 -> 11 [label=\"output\"]\n  3 -> 11 [label=\"output_full\"]\n  12[label=\"gffread\"]\n  11 -> 12 [label=\"output_gff\"]\n  2 -> 12 [label=\"output\"]\n  13[label=\"Train Augustus\"]\n  2 -> 13 [label=\"output\"]\n  11 -> 13 [label=\"output_gff\"]\n  k42d5aadd3a8c441d913fee8745a99b0b[color=lightseagreen,label=\"Output\\nAugus: trained model\"]\n  13 -> k42d5aadd3a8c441d913fee8745a99b0b\n  14[label=\"Genome annotation statistics\"]\n  11 -> 14 [label=\"output_gff\"]\n  2 -> 14 [label=\"output\"]\n  k9def2c6efd3c4969b5d4d13c187c1144[color=lightseagreen,label=\"Output\\nGenome annotation statistics: graphs (second round)\"]\n  14 -> k9def2c6efd3c4969b5d4d13c187c1144\n  k61f7a150a4a246b189f52170d466656e[color=lightseagreen,label=\"Output\\nGenome annotation statistics: summary (second round)\"]\n  14 -> k61f7a150a4a246b189f52170d466656e\n  15[label=\"Train SNAP\"]\n  2 -> 15 [label=\"output\"]\n  11 -> 15 [label=\"output_gff\"]\n  k458887f706614bdeab1a875aac6caed8[color=lightseagreen,label=\"Output\\nSNAP: trained model\"]\n  15 -> k458887f706614bdeab1a875aac6caed8\n  16[label=\"Busco\"]\n  12 -> 16 [label=\"output_exons\"]\n  kf52b1b410ea54384bd434927273c909c[color=lightseagreen,label=\"Output\\nBusco summary second round\"]\n  16 -> kf52b1b410ea54384bd434927273c909c\n  17[label=\"Maker\"]\n  13 -> 17 [label=\"output_tar\"]\n  15 -> 17 [label=\"output\"]\n  2 -> 17 [label=\"output\"]\n  11 -> 17 [label=\"output_full\"]\n  18[label=\"Map annotation ids\"]\n  17 -> 18 [label=\"output_gff\"]\n  k63575dcf54d14cb1b5fba2810b4da807[color=lightseagreen,label=\"Output\\nMap annotation ids: renamed GFF\"]\n  18 -> k63575dcf54d14cb1b5fba2810b4da807\n  19[label=\"JBrowse\"]\n  2 -> 19 [label=\"output\"]\n  3 -> 19 [label=\"output_gff\"]\n  18 -> 19 [label=\"renamed\"]\n  11 -> 19 [label=\"output_gff\"]\n  3 -> 19 [label=\"output_evidences\"]\n  11 -> 19 [label=\"output_evidences\"]\n  17 -> 19 [label=\"output_evidences\"]\n  k5a38ae83e17745f3aa9f4c1844584fa5[color=lightseagreen,label=\"Output\\nJBrowse: report\"]\n  19 -> k5a38ae83e17745f3aa9f4c1844584fa5\n  20[label=\"gffread\"]\n  18 -> 20 [label=\"renamed\"]\n  2 -> 20 [label=\"output\"]\n  k52fcac23b6124377a19a2e3b667a23e3[color=lightseagreen,label=\"Output\\nGffread: exons\"]\n  20 -> k52fcac23b6124377a19a2e3b667a23e3\n  k5c47c25e0ddb4adea5d0873ff4add28c[color=lightseagreen,label=\"Output\\nGffread: translation of cds\"]\n  20 -> k5c47c25e0ddb4adea5d0873ff4add28c\n  k84d9183b9589464b9f824dae7f87133e[color=lightseagreen,label=\"Output\\nGffread: cds\"]\n  20 -> k84d9183b9589464b9f824dae7f87133e\n  21[label=\"Genome annotation statistics\"]\n  18 -> 21 [label=\"renamed\"]\n  2 -> 21 [label=\"output\"]\n  kf5d4a6bf1ff8435a80847921e25bff3a[color=lightseagreen,label=\"Output\\nGenome annotation statistics: graphs (third round)\"]\n  21 -> kf5d4a6bf1ff8435a80847921e25bff3a\n  k5a863bd410f24ac881b6ce8b7f663e42[color=lightseagreen,label=\"Output\\nGenome annotation statistics: summary (third round)\"]\n  21 -> k5a863bd410f24ac881b6ce8b7f663e42\n  22[label=\"Busco\"]\n  20 -> 22 [label=\"output_exons\"]\n  k0bc78676eecc4168894d34c4ca07cdf3[color=lightseagreen,label=\"Output\\nBusco summary final round\"]\n  22 -> k0bc78676eecc4168894d34c4ca07cdf3\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenome assembly\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nRNASeq reads forward\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nRNASeq reads reverse\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nProtein evidence sequences\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nNCBI submission template\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAlternate annotation gbk\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAlternate annotation gff3\"]\n  7[label=\"RNA STAR\"]\n  0 -> 7 [label=\"output\"]\n  1 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  k79cf59ea3aef4cb89c705b42e03a5da9[color=lightseagreen,label=\"Output\\nMapped RNASeq\"]\n  7 -> k79cf59ea3aef4cb89c705b42e03a5da9\n  8[label=\"Funannotate predict annotation\"]\n  3 -> 8 [label=\"output\"]\n  7 -> 8 [label=\"mapped_reads\"]\n  0 -> 8 [label=\"output\"]\n  9[label=\"eggNOG Mapper\"]\n  8 -> 9 [label=\"fasta_proteins\"]\n  10[label=\"InterProScan\"]\n  8 -> 10 [label=\"fasta_proteins\"]\n  11[label=\"Funannotate functional\"]\n  9 -> 11 [label=\"annotations\"]\n  8 -> 11 [label=\"annot_gbk\"]\n  10 -> 11 [label=\"outfile_xml\"]\n  4 -> 11 [label=\"output\"]\n  kd0694cd16d814d7283b994cb57dc1502[color=lightseagreen,label=\"Output\\nFinal annotation (genbank)\"]\n  11 -> kd0694cd16d814d7283b994cb57dc1502\n  k9a1e7b70109041ed863765b7372a9f6c[color=lightseagreen,label=\"Output\\nFinal annotation (CDS sequences)\"]\n  11 -> k9a1e7b70109041ed863765b7372a9f6c\n  k99fffa402196491d9a66559ebf2d9561[color=lightseagreen,label=\"Output\\nFinal annotation (mRNA sequences)\"]\n  11 -> k99fffa402196491d9a66559ebf2d9561\n  k17b03b7704854176b2b303bfa2d3bcb0[color=lightseagreen,label=\"Output\\nFinal annotation (protein sequences)\"]\n  11 -> k17b03b7704854176b2b303bfa2d3bcb0\n  k4a0602fce6d243fc9957344707c22c05[color=lightseagreen,label=\"Output\\nFinal annotation (GFF3)\"]\n  11 -> k4a0602fce6d243fc9957344707c22c05\n  12[label=\"JBrowse\"]\n  0 -> 12 [label=\"output\"]\n  11 -> 12 [label=\"gff3\"]\n  7 -> 12 [label=\"mapped_reads\"]\n  kac4d8805f12344d2b30f8ac906cc471f[color=lightseagreen,label=\"Output\\nJBrowse\"]\n  12 -> kac4d8805f12344d2b30f8ac906cc471f\n  13[label=\"Funannotate compare\"]\n  5 -> 13 [label=\"output\"]\n  11 -> 13 [label=\"gbk\"]\n  ke531c81ff6b74c82a712c562873ff714[color=lightseagreen,label=\"Output\\nFunannotate compare report\"]\n  13 -> ke531c81ff6b74c82a712c562873ff714\n  14[label=\"AEGeAn ParsEval\"]\n  6 -> 14 [label=\"output\"]\n  11 -> 14 [label=\"gff3\"]\n  k0d776b462c1c40839f9da213fa62eb81[color=lightseagreen,label=\"Output\\nAEGeAN report\"]\n  14 -> k0d776b462c1c40839f9da213fa62eb81\n  15[label=\"Busco\"]\n  11 -> 15 [label=\"fa_proteins\"]\n  k57a619f5b3314ca68e6e72eb61860032[color=lightseagreen,label=\"Output\\nBusco summary\"]\n  15 -> k57a619f5b3314ca68e6e72eb61860032\n  k97d23764ad4a4d69948cc81afb76fbaf[color=lightseagreen,label=\"Output\\nBusco image\"]\n  15 -> k97d23764ad4a4d69948cc81afb76fbaf\n}",
                 "history": [
                     {
-                        "hash": "e61e9eba49f4c255dd46e1094355f61a770ba14e",
-                        "message": "Fix workflow",
-                        "num": 12,
-                        "short_hash": "e61e9eba4",
-                        "unix": "1625849450"
-                    },
-                    {
-                        "hash": "106af0888f3f8cbc7040c20b62adbf52ddfe2186",
-                        "message": "Update maker workflow",
-                        "num": 11,
-                        "short_hash": "106af0888",
-                        "unix": "1625842677"
-                    },
-                    {
-                        "hash": "005d964a2e8cb80f8d1bf0b304adc8f9d7c9ff76",
-                        "message": "fix workflows",
-                        "num": 10,
-                        "short_hash": "005d964a2",
-                        "unix": "1609752597"
-                    },
-                    {
-                        "hash": "774f2aa374452d48fd29ee85513c3dc3a7f137f5",
-                        "message": "update maker tutorial and add a short version",
-                        "num": 9,
-                        "short_hash": "774f2aa37",
-                        "unix": "1609431273"
-                    },
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 8,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 7,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "1a3049ca861744336a01f79b6ae1bc8bc46e2b12",
-                        "message": "typos + update workflow",
-                        "num": 6,
-                        "short_hash": "1a3049ca8",
-                        "unix": "1558343672"
-                    },
-                    {
-                        "hash": "2318b970d421c42bbced1799cfca63ce056ad01f",
-                        "message": "udpate workflow",
-                        "num": 5,
-                        "short_hash": "2318b970d",
-                        "unix": "1557415647"
-                    },
-                    {
-                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
-                        "message": "Changed format of workflows",
-                        "num": 4,
-                        "short_hash": "361236c41",
-                        "unix": "1554368414"
-                    },
-                    {
-                        "hash": "6eef55b7e8306d8ce46ac08e7799f6f65ae106aa",
-                        "message": "Updated install_tutorial_requirements.sh + minor fixes (#1275)",
-                        "num": 3,
-                        "short_hash": "6eef55b7e",
-                        "unix": "1551293676"
-                    },
-                    {
-                        "hash": "bc6d0ddca2ce262deb405fd92e0dab955488eb49",
-                        "message": "jbrowse part",
-                        "num": 2,
-                        "short_hash": "bc6d0ddca",
-                        "unix": "1536669505"
-                    },
-                    {
-                        "hash": "7b73f26f84bc0e9dc9e771f7dd89be3e6daddd66",
-                        "message": "update wf",
+                        "hash": "ed3325d60843b30358cdb704f83ad9ea4b6c149f",
+                        "message": "update funannotate tuto",
                         "num": 1,
-                        "short_hash": "7b73f26f8",
-                        "unix": "1536594667"
+                        "short_hash": "ed3325d60",
+                        "unix": "1682519007"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "It contains the sequences used by Maker to construct gene models.",
+                        "annotation": "The genome sequence that you wish to annotate, in fasta format. It needs to be soft masked beforehand.",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "It contains the sequences used by Maker to construct gene models.",
-                                "name": "EST and/or cDNA"
+                                "description": "The genome sequence that you wish to annotate, in fasta format. It needs to be soft masked beforehand.",
+                                "name": "Genome assembly"
                             }
                         ],
-                        "label": "EST and/or cDNA",
+                        "label": "Genome assembly",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 287.875,
-                            "height": 81,
-                            "left": 661.46875,
-                            "right": 861.46875,
-                            "top": 206.875,
-                            "width": 200,
-                            "x": 661.46875,
-                            "y": 206.875
+                            "left": 0,
+                            "top": 7.75
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "397d1af7-4d12-43d6-955c-e3122978fc92",
+                        "uuid": "cca15c08-8dd9-424a-8260-4c02a94c2612",
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "A set of protein sequences, usually from closely related species or from a curated sequence database like UniProt/SwissProt.",
+                        "annotation": "Some RNASeq data, forward reads, in fastq format",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "A set of protein sequences, usually from closely related species or from a curated sequence database like UniProt/SwissProt.",
-                                "name": "Protein sequences"
+                                "description": "Some RNASeq data, forward reads, in fastq format",
+                                "name": "RNASeq reads forward"
                             }
                         ],
-                        "label": "Protein sequences",
+                        "label": "RNASeq reads forward",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 459,
-                            "height": 81,
-                            "left": 659.5,
-                            "right": 859.5,
-                            "top": 378,
-                            "width": 200,
-                            "x": 659.5,
-                            "y": 378
+                            "left": 3.45001220703125,
+                            "top": 164.33334350585938
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "418c68b0-b726-4f5e-b53c-480f1e7d43b5",
+                        "uuid": "6681e7b9-68f6-46e4-811f-60473d23fe0f",
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "This file corresponds to the sequence to be annotated.",
+                        "annotation": "Some RNASeq data, reverse reads, in fastq format",
                         "content_id": null,
                         "errors": null,
                         "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "This file corresponds to the sequence to be annotated.",
-                                "name": "Genome sequence"
+                                "description": "Some RNASeq data, reverse reads, in fastq format",
+                                "name": "RNASeq reads reverse"
                             }
                         ],
-                        "label": "Genome sequence",
+                        "label": "RNASeq reads reverse",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 1797.03125,
-                            "height": 81,
-                            "left": 661.46875,
-                            "right": 861.46875,
-                            "top": 1716.03125,
-                            "width": 200,
-                            "x": 661.46875,
-                            "y": 1716.03125
+                            "left": 6,
+                            "top": 310.6666564941406
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "e03b5775-bd22-4528-9f21-20cd396dc6cc",
+                        "uuid": "160023e3-250f-424d-abe5-f7e3978768f0",
                         "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nProtein sequences\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nGenome sequence\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Maker\"];\n  0 -->|output| 3;\n  2 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Fasta Statistics\"];\n  2 -->|output| 4;\n  2d3829e6-f5b9-46d1-83e3-17efff814e09[\"Output\\nFasta Statistics on input dataset(s): Fasta summary stats\"];\n  4 --> 2d3829e6-f5b9-46d1-83e3-17efff814e09;\n  style 2d3829e6-f5b9-46d1-83e3-17efff814e09 stroke:#2c3143,stroke-width:4px;\n  5[\"Busco\"];\n  2 -->|output| 5;\n  a15e1214-23a2-484b-9c75-1635fcd61fe3[\"Output\\nBUSCO: short summary\"];\n  5 --> a15e1214-23a2-484b-9c75-1635fcd61fe3;\n  style a15e1214-23a2-484b-9c75-1635fcd61fe3 stroke:#2c3143,stroke-width:4px;\n  7806088d-f657-4389-9d54-6a3bdfa233b2[\"Output\\nBUSCO: list of missing ortholog genes\"];\n  5 --> 7806088d-f657-4389-9d54-6a3bdfa233b2;\n  style 7806088d-f657-4389-9d54-6a3bdfa233b2 stroke:#2c3143,stroke-width:4px;\n  6a27d0f6-d83c-42b1-a7af-5f99ba5debe2[\"Output\\nBUSCO: full table\"];\n  5 --> 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2;\n  style 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2 stroke:#2c3143,stroke-width:4px;\n  6[\"Train Augustus\"];\n  2 -->|output| 6;\n  3 -->|output_gff| 6;\n  7[\"Genome annotation statistics\"];\n  3 -->|output_gff| 7;\n  2 -->|output| 7;\n  2bed9aa6-5f22-494d-9caa-f0ece8464f15[\"Output\\nGenome annotation statistics: graphs (first round)\"];\n  7 --> 2bed9aa6-5f22-494d-9caa-f0ece8464f15;\n  style 2bed9aa6-5f22-494d-9caa-f0ece8464f15 stroke:#2c3143,stroke-width:4px;\n  71d41ce2-e90d-435b-9b64-ab4320524770[\"Output\\nGenome annotation statistics: summary (first round)\"];\n  7 --> 71d41ce2-e90d-435b-9b64-ab4320524770;\n  style 71d41ce2-e90d-435b-9b64-ab4320524770 stroke:#2c3143,stroke-width:4px;\n  8[\"gffread\"];\n  3 -->|output_gff| 8;\n  2 -->|output| 8;\n  9[\"Train SNAP\"];\n  2 -->|output| 9;\n  3 -->|output_gff| 9;\n  10[\"Busco\"];\n  8 -->|output_exons| 10;\n  a79ab19d-9802-42ca-8ffa-8c197a16c8b8[\"Output\\nBusco summary first round\"];\n  10 --> a79ab19d-9802-42ca-8ffa-8c197a16c8b8;\n  style a79ab19d-9802-42ca-8ffa-8c197a16c8b8 stroke:#2c3143,stroke-width:4px;\n  11[\"Maker\"];\n  6 -->|output_tar| 11;\n  9 -->|output| 11;\n  2 -->|output| 11;\n  3 -->|output_full| 11;\n  12[\"gffread\"];\n  11 -->|output_gff| 12;\n  2 -->|output| 12;\n  13[\"Train Augustus\"];\n  2 -->|output| 13;\n  11 -->|output_gff| 13;\n  42d5aadd-3a8c-441d-913f-ee8745a99b0b[\"Output\\nAugus: trained model\"];\n  13 --> 42d5aadd-3a8c-441d-913f-ee8745a99b0b;\n  style 42d5aadd-3a8c-441d-913f-ee8745a99b0b stroke:#2c3143,stroke-width:4px;\n  14[\"Genome annotation statistics\"];\n  11 -->|output_gff| 14;\n  2 -->|output| 14;\n  9def2c6e-fd3c-4969-b5d4-d13c187c1144[\"Output\\nGenome annotation statistics: graphs (second round)\"];\n  14 --> 9def2c6e-fd3c-4969-b5d4-d13c187c1144;\n  style 9def2c6e-fd3c-4969-b5d4-d13c187c1144 stroke:#2c3143,stroke-width:4px;\n  61f7a150-a4a2-46b1-89f5-2170d466656e[\"Output\\nGenome annotation statistics: summary (second round)\"];\n  14 --> 61f7a150-a4a2-46b1-89f5-2170d466656e;\n  style 61f7a150-a4a2-46b1-89f5-2170d466656e stroke:#2c3143,stroke-width:4px;\n  15[\"Train SNAP\"];\n  2 -->|output| 15;\n  11 -->|output_gff| 15;\n  458887f7-0661-4bde-ab1a-875aac6caed8[\"Output\\nSNAP: trained model\"];\n  15 --> 458887f7-0661-4bde-ab1a-875aac6caed8;\n  style 458887f7-0661-4bde-ab1a-875aac6caed8 stroke:#2c3143,stroke-width:4px;\n  16[\"Busco\"];\n  12 -->|output_exons| 16;\n  f52b1b41-0ea5-4384-bd43-4927273c909c[\"Output\\nBusco summary second round\"];\n  16 --> f52b1b41-0ea5-4384-bd43-4927273c909c;\n  style f52b1b41-0ea5-4384-bd43-4927273c909c stroke:#2c3143,stroke-width:4px;\n  17[\"Maker\"];\n  13 -->|output_tar| 17;\n  15 -->|output| 17;\n  2 -->|output| 17;\n  11 -->|output_full| 17;\n  18[\"Map annotation ids\"];\n  17 -->|output_gff| 18;\n  63575dcf-54d1-4cb1-b5fb-a2810b4da807[\"Output\\nMap annotation ids: renamed GFF\"];\n  18 --> 63575dcf-54d1-4cb1-b5fb-a2810b4da807;\n  style 63575dcf-54d1-4cb1-b5fb-a2810b4da807 stroke:#2c3143,stroke-width:4px;\n  19[\"JBrowse\"];\n  2 -->|output| 19;\n  3 -->|output_gff| 19;\n  18 -->|renamed| 19;\n  11 -->|output_gff| 19;\n  3 -->|output_evidences| 19;\n  11 -->|output_evidences| 19;\n  17 -->|output_evidences| 19;\n  5a38ae83-e177-45f3-aa9f-4c1844584fa5[\"Output\\nJBrowse: report\"];\n  19 --> 5a38ae83-e177-45f3-aa9f-4c1844584fa5;\n  style 5a38ae83-e177-45f3-aa9f-4c1844584fa5 stroke:#2c3143,stroke-width:4px;\n  20[\"gffread\"];\n  18 -->|renamed| 20;\n  2 -->|output| 20;\n  52fcac23-b612-4377-a19a-2e3b667a23e3[\"Output\\nGffread: exons\"];\n  20 --> 52fcac23-b612-4377-a19a-2e3b667a23e3;\n  style 52fcac23-b612-4377-a19a-2e3b667a23e3 stroke:#2c3143,stroke-width:4px;\n  5c47c25e-0ddb-4ade-a5d0-873ff4add28c[\"Output\\nGffread: translation of cds\"];\n  20 --> 5c47c25e-0ddb-4ade-a5d0-873ff4add28c;\n  style 5c47c25e-0ddb-4ade-a5d0-873ff4add28c stroke:#2c3143,stroke-width:4px;\n  84d9183b-9589-464b-9f82-4dae7f87133e[\"Output\\nGffread: cds\"];\n  20 --> 84d9183b-9589-464b-9f82-4dae7f87133e;\n  style 84d9183b-9589-464b-9f82-4dae7f87133e stroke:#2c3143,stroke-width:4px;\n  21[\"Genome annotation statistics\"];\n  18 -->|renamed| 21;\n  2 -->|output| 21;\n  f5d4a6bf-1ff8-435a-8084-7921e25bff3a[\"Output\\nGenome annotation statistics: graphs (third round)\"];\n  21 --> f5d4a6bf-1ff8-435a-8084-7921e25bff3a;\n  style f5d4a6bf-1ff8-435a-8084-7921e25bff3a stroke:#2c3143,stroke-width:4px;\n  5a863bd4-10f2-4ac8-81b6-ce8b7f663e42[\"Output\\nGenome annotation statistics: summary (third round)\"];\n  21 --> 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42;\n  style 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42 stroke:#2c3143,stroke-width:4px;\n  22[\"Busco\"];\n  20 -->|output_exons| 22;\n  0bc78676-eecc-4168-894d-34c4ca07cdf3[\"Output\\nBusco summary final round\"];\n  22 --> 0bc78676-eecc-4168-894d-34c4ca07cdf3;\n  style 0bc78676-eecc-4168-894d-34c4ca07cdf3 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Genome annotation with Maker ",
-                "outputs": [
+                    },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
+                        "annotation": "Some protein sequences to align on the genome to help annotation",
+                        "content_id": null,
                         "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "dataset": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Fasta Statistics",
-                        "outputs": [
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "stats",
-                                "type": "tabular"
+                                "description": "Some protein sequences to align on the genome to help annotation",
+                                "name": "Protein evidence sequences"
                             }
                         ],
+                        "label": "Protein evidence sequences",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 1526.4375,
-                            "height": 152,
-                            "left": 722.921875,
-                            "right": 922.921875,
-                            "top": 1374.4375,
-                            "width": 200,
-                            "x": 722.921875,
-                            "y": 1374.4375
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9c620a950d3a",
-                            "name": "fasta_stats",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 7.116668701171875,
+                            "top": 441.4166564941406
                         },
-                        "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.1",
-                        "type": "tool",
-                        "uuid": "9cd9564b-b447-4a93-9445-ae3583137010",
-                        "workflow_outputs": [
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "abb56aaf-5988-4fb8-a68f-0edaee00f445",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "A submission template retrieved from NCBI (generate it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/)",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": "Fasta Statistics on input dataset(s): Fasta summary stats",
-                                "output_name": "stats",
-                                "uuid": "2d3829e6-f5b9-46d1-83e3-17efff814e09"
+                                "description": "A submission template retrieved from NCBI (generate it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/)",
+                                "name": "NCBI submission template"
                             }
-                        ]
+                        ],
+                        "label": "NCBI submission template",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 2.45001220703125,
+                            "top": 580.4833068847656
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "537f8bb4-4986-4d8d-a49b-1842dfaa739a",
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                        "annotation": "The genbank output of an alternate annotation (for comparison)",
+                        "content_id": null,
                         "errors": null,
                         "id": 5,
-                        "input_connections": {
-                            "input": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Busco",
-                        "outputs": [
-                            {
-                                "name": "busco_sum",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "busco_table",
-                                "type": "tabular"
-                            },
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "busco_missing",
-                                "type": "tabular"
+                                "description": "The genbank output of an alternate annotation (for comparison)",
+                                "name": "Alternate annotation gbk"
                             }
                         ],
+                        "label": "Alternate annotation gbk",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 1989.015625,
-                            "height": 212,
-                            "left": 939.484375,
-                            "right": 1139.484375,
-                            "top": 1777.015625,
-                            "width": 200,
-                            "x": 939.484375,
-                            "y": 1777.015625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
-                        "tool_shed_repository": {
-                            "changeset_revision": "602fb8e63aa7",
-                            "name": "busco",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 727.7333068847656
                         },
-                        "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"geno\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.1.4",
-                        "type": "tool",
-                        "uuid": "2e99d9de-b48b-4f0f-99da-5f727ad023cc",
-                        "workflow_outputs": [
-                            {
-                                "label": "BUSCO: short summary",
-                                "output_name": "busco_sum",
-                                "uuid": "a15e1214-23a2-484b-9c75-1635fcd61fe3"
-                            },
-                            {
-                                "label": "BUSCO: list of missing ortholog genes",
-                                "output_name": "busco_missing",
-                                "uuid": "7806088d-f657-4389-9d54-6a3bdfa233b2"
-                            },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "51a62e82-d478-45c3-bcbc-f38f1fd85974",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "The gff3 output of an alternate annotation (for comparison)",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": "BUSCO: full table",
-                                "output_name": "busco_table",
-                                "uuid": "6a27d0f6-d83c-42b1-a7af-5f99ba5debe2"
+                                "description": "The gff3 output of an alternate annotation (for comparison)",
+                                "name": "Alternate annotation gff3"
                             }
-                        ]
-                    },
+                        ],
+                        "label": "Alternate annotation gff3",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0.4666748046875,
+                            "top": 845.7500305175781
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "e4367779-3fc7-4eec-8e45-86158b3950bc",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGenome assembly\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nRNASeq reads forward\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nRNASeq reads reverse\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nProtein evidence sequences\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nNCBI submission template\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nAlternate annotation gbk\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nAlternate annotation gff3\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"RNA STAR\"];\n  0 -->|output| 7;\n  1 -->|output| 7;\n  2 -->|output| 7;\n  79cf59ea-3aef-4cb8-9c70-5b42e03a5da9[\"Output\\nMapped RNASeq\"];\n  7 --> 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9;\n  style 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9 stroke:#2c3143,stroke-width:4px;\n  8[\"Funannotate predict annotation\"];\n  3 -->|output| 8;\n  7 -->|mapped_reads| 8;\n  0 -->|output| 8;\n  9[\"eggNOG Mapper\"];\n  8 -->|fasta_proteins| 9;\n  10[\"InterProScan\"];\n  8 -->|fasta_proteins| 10;\n  11[\"Funannotate functional\"];\n  9 -->|annotations| 11;\n  8 -->|annot_gbk| 11;\n  10 -->|outfile_xml| 11;\n  4 -->|output| 11;\n  d0694cd1-6d81-4d72-83b9-94cb57dc1502[\"Output\\nFinal annotation (genbank)\"];\n  11 --> d0694cd1-6d81-4d72-83b9-94cb57dc1502;\n  style d0694cd1-6d81-4d72-83b9-94cb57dc1502 stroke:#2c3143,stroke-width:4px;\n  9a1e7b70-1090-41ed-8637-65b7372a9f6c[\"Output\\nFinal annotation (CDS sequences)\"];\n  11 --> 9a1e7b70-1090-41ed-8637-65b7372a9f6c;\n  style 9a1e7b70-1090-41ed-8637-65b7372a9f6c stroke:#2c3143,stroke-width:4px;\n  99fffa40-2196-491d-9a66-559ebf2d9561[\"Output\\nFinal annotation (mRNA sequences)\"];\n  11 --> 99fffa40-2196-491d-9a66-559ebf2d9561;\n  style 99fffa40-2196-491d-9a66-559ebf2d9561 stroke:#2c3143,stroke-width:4px;\n  17b03b77-0485-4176-b2b3-03bfa2d3bcb0[\"Output\\nFinal annotation (protein sequences)\"];\n  11 --> 17b03b77-0485-4176-b2b3-03bfa2d3bcb0;\n  style 17b03b77-0485-4176-b2b3-03bfa2d3bcb0 stroke:#2c3143,stroke-width:4px;\n  4a0602fc-e6d2-43fc-9957-344707c22c05[\"Output\\nFinal annotation (GFF3)\"];\n  11 --> 4a0602fc-e6d2-43fc-9957-344707c22c05;\n  style 4a0602fc-e6d2-43fc-9957-344707c22c05 stroke:#2c3143,stroke-width:4px;\n  12[\"JBrowse\"];\n  0 -->|output| 12;\n  11 -->|gff3| 12;\n  7 -->|mapped_reads| 12;\n  ac4d8805-f123-44d2-b30f-8ac906cc471f[\"Output\\nJBrowse\"];\n  12 --> ac4d8805-f123-44d2-b30f-8ac906cc471f;\n  style ac4d8805-f123-44d2-b30f-8ac906cc471f stroke:#2c3143,stroke-width:4px;\n  13[\"Funannotate compare\"];\n  5 -->|output| 13;\n  11 -->|gbk| 13;\n  e531c81f-f6b7-4c82-a712-c562873ff714[\"Output\\nFunannotate compare report\"];\n  13 --> e531c81f-f6b7-4c82-a712-c562873ff714;\n  style e531c81f-f6b7-4c82-a712-c562873ff714 stroke:#2c3143,stroke-width:4px;\n  14[\"AEGeAn ParsEval\"];\n  6 -->|output| 14;\n  11 -->|gff3| 14;\n  0d776b46-2c1c-4083-9f9d-a213fa62eb81[\"Output\\nAEGeAN report\"];\n  14 --> 0d776b46-2c1c-4083-9f9d-a213fa62eb81;\n  style 0d776b46-2c1c-4083-9f9d-a213fa62eb81 stroke:#2c3143,stroke-width:4px;\n  15[\"Busco\"];\n  11 -->|fa_proteins| 15;\n  57a619f5-b331-4ca6-8e6e-72eb61860032[\"Output\\nBusco summary\"];\n  15 --> 57a619f5-b331-4ca6-8e6e-72eb61860032;\n  style 57a619f5-b331-4ca6-8e6e-72eb61860032 stroke:#2c3143,stroke-width:4px;\n  97d23764-ad4a-4d69-948c-c81afb76fbaf[\"Output\\nBusco image\"];\n  15 --> 97d23764-ad4a-4d69-948c-c81afb76fbaf;\n  style 97d23764-ad4a-4d69-948c-c81afb76fbaf stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Funannotate",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3",
                         "errors": null,
                         "id": 7,
                         "input_connections": {
-                            "gff": {
-                                "id": 3,
-                                "output_name": "output_gff"
+                            "refGenomeSource|genomeFastaFiles": {
+                                "id": 0,
+                                "output_name": "output"
                             },
-                            "ref_genome|genome": {
+                            "singlePaired|input1": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "singlePaired|input2": {
                                 "id": 2,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Genome annotation statistics",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "summary",
-                                "type": "txt"
+                                "description": "runtime parameter for tool RNA STAR",
+                                "name": "refGenomeSource"
                             },
                             {
-                                "name": "graphs",
-                                "type": "pdf"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 1247.015625,
-                            "height": 272,
-                            "left": 1247.5,
-                            "right": 1447.5,
-                            "top": 975.015625,
-                            "width": 200,
-                            "x": 1247.5,
-                            "y": 975.015625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
-                        "tool_shed_repository": {
-                            "changeset_revision": "8cffbd184762",
-                            "name": "jcvi_gff_stats",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"gff\": {\"__class__\": \"ConnectedValue\"}, \"ref_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.8.4",
-                        "type": "tool",
-                        "uuid": "af60c4d9-58f2-4f41-a2a3-6458cdcfd404",
-                        "workflow_outputs": [
-                            {
-                                "label": "Genome annotation statistics: graphs (first round)",
-                                "output_name": "graphs",
-                                "uuid": "2bed9aa6-5f22-494d-9caa-f0ece8464f15"
+                                "description": "runtime parameter for tool RNA STAR",
+                                "name": "singlePaired"
                             },
                             {
-                                "label": "Genome annotation statistics: summary (first round)",
-                                "output_name": "summary",
-                                "uuid": "71d41ce2-e90d-435b-9b64-ab4320524770"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
-                        "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "input": {
-                                "id": 8,
-                                "output_name": "output_exons"
+                                "description": "runtime parameter for tool RNA STAR",
+                                "name": "singlePaired"
                             }
-                        },
-                        "inputs": [],
+                        ],
                         "label": null,
-                        "name": "Busco",
+                        "name": "RNA STAR",
                         "outputs": [
                             {
-                                "name": "busco_sum",
+                                "name": "output_log",
                                 "type": "txt"
                             },
                             {
-                                "name": "busco_table",
-                                "type": "tabular"
+                                "name": "splice_junctions",
+                                "type": "interval"
                             },
                             {
-                                "name": "busco_missing",
-                                "type": "tabular"
+                                "name": "mapped_reads",
+                                "type": "bam"
                             }
                         ],
                         "position": {
-                            "bottom": 1738.03125,
-                            "height": 252,
-                            "left": 1545.5,
-                            "right": 1745.5,
-                            "top": 1486.03125,
-                            "width": 200,
-                            "x": 1545.5,
-                            "y": 1486.03125
+                            "left": 766.699951171875,
+                            "top": 239.0
                         },
                         "post_job_actions": {
-                            "HideDatasetActionbusco_missing": {
+                            "HideDatasetActionoutput_log": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "busco_missing"
+                                "output_name": "output_log"
                             },
-                            "HideDatasetActionbusco_table": {
+                            "HideDatasetActionsplice_junctions": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "busco_table"
+                                "output_name": "splice_junctions"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3",
                         "tool_shed_repository": {
-                            "changeset_revision": "602fb8e63aa7",
-                            "name": "busco",
+                            "changeset_revision": "3ea5a2a63fa2",
+                            "name": "rgrnastar",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"tran\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.1.4",
+                        "tool_state": "{\"algo\": {\"params\": {\"settingsType\": \"default\", \"__current_case__\": 0}}, \"chimOutType\": \"\", \"filter\": {\"basic_filters\": [\"exclude_unmapped\"], \"output_params2\": {\"output_select2\": \"no\", \"__current_case__\": 1}}, \"oformat\": {\"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"ch\"], \"HI_offset\": \"1\", \"outSAMprimaryFlag\": \"OneBestScore\", \"outSAMmapqUnique\": \"60\"}, \"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"perf\": {\"outBAMsortingBinsN\": \"50\", \"winAnchorMultimapNmax\": \"50\"}, \"refGenomeSource\": {\"geneSource\": \"history\", \"__current_case__\": 1, \"genomeFastaFiles\": {\"__class__\": \"RuntimeValue\"}, \"genomeSAindexNbases\": \"11\", \"GTFconditional\": {\"GTFselect\": \"without-gtf\", \"__current_case__\": 1, \"quantmode_output\": {\"quantMode\": \"-\", \"__current_case__\": 0}}}, \"singlePaired\": {\"sPaired\": \"paired\", \"__current_case__\": 1, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"input2\": {\"__class__\": \"RuntimeValue\"}}, \"twopass\": {\"twopassMode\": \"None\", \"__current_case__\": 0, \"twopass_read_subset\": \"\", \"sj_precalculated\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.7.10b+galaxy3",
                         "type": "tool",
-                        "uuid": "a83a2b48-7787-4b53-a592-339f5134e168",
+                        "uuid": "269a3794-e421-4826-a5de-8a328fd194bd",
                         "workflow_outputs": [
                             {
-                                "label": "Busco summary first round",
-                                "output_name": "busco_sum",
-                                "uuid": "a79ab19d-9802-42ca-8ffa-8c197a16c8b8"
+                                "label": "Mapped RNASeq",
+                                "output_name": "mapped_reads",
+                                "uuid": "79cf59ea-3aef-4cb8-9c70-5b42e03a5da9"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0",
                         "errors": null,
-                        "id": 13,
+                        "id": 8,
                         "input_connections": {
-                            "genome": {
-                                "id": 2,
+                            "evidences|prot_evidence|protein_evidence": {
+                                "id": 3,
                                 "output_name": "output"
                             },
-                            "maker_gff": {
-                                "id": 11,
-                                "output_name": "output_gff"
+                            "evidences|rna_bam": {
+                                "id": 7,
+                                "output_name": "mapped_reads"
+                            },
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Train Augustus",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "output_tar",
-                                "type": "augustus"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 1259.03125,
-                            "height": 182,
-                            "left": 1863.5,
-                            "right": 2063.5,
-                            "top": 1077.03125,
-                            "width": 200,
-                            "x": 1863.5,
-                            "y": 1077.03125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6519ebe25019",
-                            "name": "augustus_training",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"genome\": {\"__class__\": \"ConnectedValue\"}, \"maker_gff\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.3.3",
-                        "type": "tool",
-                        "uuid": "b347da09-05a2-4d30-a103-dbeb5853efcd",
-                        "workflow_outputs": [
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "database"
+                            },
                             {
-                                "label": "Augus: trained model",
-                                "output_name": "output_tar",
-                                "uuid": "42d5aadd-3a8c-441d-913f-ee8745a99b0b"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
-                        "errors": null,
-                        "id": 14,
-                        "input_connections": {
-                            "gff": {
-                                "id": 11,
-                                "output_name": "output_gff"
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "evidences"
                             },
-                            "ref_genome|genome": {
-                                "id": 2,
-                                "output_name": "output"
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "evidences"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "genemark"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "genemark"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "input"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "other_predictors"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "other_predictors"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "other_predictors"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "other_predictors"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate predict annotation",
+                                "name": "parameters"
                             }
-                        },
-                        "inputs": [],
+                        ],
                         "label": null,
-                        "name": "Genome annotation statistics",
+                        "name": "Funannotate predict annotation",
                         "outputs": [
                             {
-                                "name": "summary",
+                                "name": "annot_gbk",
+                                "type": "genbank"
+                            },
+                            {
+                                "name": "annot_tbl",
                                 "type": "txt"
                             },
                             {
-                                "name": "graphs",
-                                "type": "pdf"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 1569.03125,
-                            "height": 272,
-                            "left": 1863.5,
-                            "right": 2063.5,
-                            "top": 1297.03125,
-                            "width": 200,
-                            "x": 1863.5,
-                            "y": 1297.03125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
-                        "tool_shed_repository": {
-                            "changeset_revision": "8cffbd184762",
-                            "name": "jcvi_gff_stats",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"gff\": {\"__class__\": \"ConnectedValue\"}, \"ref_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.8.4",
-                        "type": "tool",
-                        "uuid": "5a3899b6-a669-4a36-990e-01e6cac6410d",
-                        "workflow_outputs": [
+                                "name": "annot_gff3",
+                                "type": "gff3"
+                            },
                             {
-                                "label": "Genome annotation statistics: graphs (second round)",
-                                "output_name": "graphs",
-                                "uuid": "9def2c6e-fd3c-4969-b5d4-d13c187c1144"
+                                "name": "fasta_proteins",
+                                "type": "fasta"
                             },
                             {
-                                "label": "Genome annotation statistics: summary (second round)",
-                                "output_name": "summary",
-                                "uuid": "61f7a150-a4a2-46b1-89f5-2170d466656e"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1",
-                        "errors": null,
-                        "id": 15,
-                        "input_connections": {
-                            "genome": {
-                                "id": 2,
-                                "output_name": "output"
+                                "name": "fasta_transcripts_mrna",
+                                "type": "fasta"
                             },
-                            "maker_gff": {
-                                "id": 11,
-                                "output_name": "output_gff"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Train SNAP",
-                        "outputs": [
                             {
-                                "name": "output",
-                                "type": "snaphmm"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 1770.03125,
-                            "height": 162,
-                            "left": 1863.5,
-                            "right": 2063.5,
-                            "top": 1608.03125,
-                            "width": 200,
-                            "x": 1863.5,
-                            "y": 1608.03125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2a598c0aa042",
-                            "name": "snap_training",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"gene_num\": \"1000\", \"genome\": {\"__class__\": \"ConnectedValue\"}, \"maker_gff\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2013_11_29+galaxy1",
-                        "type": "tool",
-                        "uuid": "97cec0ac-e731-4b55-859d-773a7c88bc26",
-                        "workflow_outputs": [
+                                "name": "fasta_transcripts_cds",
+                                "type": "fasta"
+                            },
                             {
-                                "label": "SNAP: trained model",
-                                "output_name": "output",
-                                "uuid": "458887f7-0661-4bde-ab1a-875aac6caed8"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
-                        "errors": null,
-                        "id": 16,
-                        "input_connections": {
-                            "input": {
-                                "id": 12,
-                                "output_name": "output_exons"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Busco",
-                        "outputs": [
+                                "name": "tbl2asn_report",
+                                "type": "txt"
+                            },
                             {
-                                "name": "busco_sum",
+                                "name": "tbl2asn_error",
                                 "type": "txt"
                             },
                             {
-                                "name": "busco_table",
-                                "type": "tabular"
+                                "name": "tbl2asn_validation",
+                                "type": "txt"
                             },
                             {
-                                "name": "busco_missing",
-                                "type": "tabular"
+                                "name": "stats",
+                                "type": "json"
                             }
                         ],
                         "position": {
-                            "bottom": 870.03125,
-                            "height": 252,
-                            "left": 2161.484375,
-                            "right": 2361.484375,
-                            "top": 618.03125,
-                            "width": 200,
-                            "x": 2161.484375,
-                            "y": 618.03125
+                            "left": 1055.2666015625,
+                            "top": 65.88333129882812
                         },
                         "post_job_actions": {
-                            "HideDatasetActionbusco_missing": {
+                            "HideDatasetActionannot_gbk": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "busco_missing"
+                                "output_name": "annot_gbk"
                             },
-                            "HideDatasetActionbusco_table": {
+                            "HideDatasetActionannot_gff3": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "busco_table"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
-                        "tool_shed_repository": {
-                            "changeset_revision": "602fb8e63aa7",
-                            "name": "busco",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"tran\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.1.4",
-                        "type": "tool",
-                        "uuid": "9b04f806-0275-4939-bf74-b8c58ae2bffa",
-                        "workflow_outputs": [
-                            {
-                                "label": "Busco summary second round",
-                                "output_name": "busco_sum",
-                                "uuid": "f52b1b41-0ea5-4384-bd43-4927273c909c"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11",
-                        "errors": null,
-                        "id": 18,
-                        "input_connections": {
-                            "maker_gff": {
-                                "id": 17,
-                                "output_name": "output_gff"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Map annotation ids",
-                        "outputs": [
-                            {
-                                "name": "renamed",
-                                "type": "gff"
+                                "output_name": "annot_gff3"
                             },
-                            {
-                                "name": "id_map",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 1637.03125,
-                            "height": 222,
-                            "left": 2439.5,
-                            "right": 2639.5,
-                            "top": 1415.03125,
-                            "width": 200,
-                            "x": 2439.5,
-                            "y": 1415.03125
-                        },
-                        "post_job_actions": {
-                            "ChangeDatatypeActionrenamed": {
-                                "action_arguments": {
-                                    "newtype": "gff3"
-                                },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "renamed"
+                            "HideDatasetActionannot_tbl": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "annot_tbl"
                             },
-                            "HideDatasetActionid_map": {
+                            "HideDatasetActionfasta_transcripts_cds": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "id_map"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2e3535db1bfa",
-                            "name": "maker_map_ids",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"justify\": \"6\", \"maker_gff\": {\"__class__\": \"ConnectedValue\"}, \"prefix\": \"TEST\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.31.11",
-                        "type": "tool",
-                        "uuid": "d7101291-76ac-48ec-9fb3-89ca5554e8ea",
-                        "workflow_outputs": [
-                            {
-                                "label": "Map annotation ids: renamed GFF",
-                                "output_name": "renamed",
-                                "uuid": "63575dcf-54d1-4cb1-b5fb-a2810b4da807"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
-                        "errors": null,
-                        "id": 19,
-                        "input_connections": {
-                            "reference_genome|genome": {
-                                "id": 2,
-                                "output_name": "output"
+                                "output_name": "fasta_transcripts_cds"
                             },
-                            "track_groups_0|data_tracks_0|data_format|annotation": [
-                                {
-                                    "id": 3,
-                                    "output_name": "output_gff"
-                                },
-                                {
-                                    "id": 18,
-                                    "output_name": "renamed"
-                                },
-                                {
-                                    "id": 11,
-                                    "output_name": "output_gff"
-                                }
-                            ],
-                            "track_groups_1|data_tracks_0|data_format|annotation": [
-                                {
-                                    "id": 3,
-                                    "output_name": "output_evidences"
-                                },
-                                {
-                                    "id": 11,
-                                    "output_name": "output_evidences"
-                                },
-                                {
-                                    "id": 17,
-                                    "output_name": "output_evidences"
-                                }
-                            ]
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "JBrowse",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "html"
+                            "HideDatasetActionfasta_transcripts_mrna": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "fasta_transcripts_mrna"
+                            },
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "HideDatasetActiontbl2asn_error": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "tbl2asn_error"
+                            },
+                            "HideDatasetActiontbl2asn_report": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "tbl2asn_report"
+                            },
+                            "HideDatasetActiontbl2asn_validation": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "tbl2asn_validation"
                             }
-                        ],
-                        "position": {
-                            "bottom": 775.015625,
-                            "height": 292,
-                            "left": 2747.5,
-                            "right": 2947.5,
-                            "top": 483.015625,
-                            "width": 200,
-                            "x": 2747.5,
-                            "y": 483.015625
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "6cd09d7b5f37",
-                            "name": "jbrowse",
+                            "changeset_revision": "51b6ee65ef7f",
+                            "name": "funannotate_predict",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Maker annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 1, \"category\": \"Maker evidences\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"match_part\": {\"match_part_select\": \"true\", \"__current_case__\": 0, \"name\": {\"__class__\": \"RuntimeValue\"}}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16.10+galaxy0",
+                        "tool_state": "{\"augustus\": {\"augustus_species\": \"none\", \"min_training_models\": \"200\", \"optimize_augustus\": \"false\"}, \"busco\": {\"busco_db\": \"mucorales_odb10\", \"busco_seed_species\": \"rhizopus_oryzae\"}, \"database\": {\"__class__\": \"RuntimeValue\"}, \"evidences\": {\"rna_bam\": {\"__class__\": \"RuntimeValue\"}, \"transcript_evidence\": {\"__class__\": \"RuntimeValue\"}, \"prot_evidence\": {\"prot_evidence_source\": \"custom\", \"__current_case__\": 1, \"protein_evidence\": {\"__class__\": \"RuntimeValue\"}}, \"p2g_pident\": \"80\", \"p2g_prefilter\": \"diamond\"}, \"evm\": {\"repeats2evm\": \"false\", \"evm_partitioning\": {\"evm_partition\": \"yes\", \"__current_case__\": 0, \"evm_partition_interval\": \"1500\"}, \"weights\": \"\"}, \"filtering\": {\"min_intronlen\": \"10\", \"max_intronlen\": \"3000\", \"min_protlen\": \"50\", \"keep_no_stops\": \"false\", \"repeat_filter\": \"overlap blast\"}, \"force\": \"true\", \"genemark\": {\"genemark_license\": {\"__class__\": \"RuntimeValue\"}, \"genemark_mode\": \"ES\", \"genemark_mod\": {\"__class__\": \"RuntimeValue\"}, \"soft_mask\": \"2000\"}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"organism\": {\"species\": \"Mucor mucedo\", \"isolate\": \"\", \"strain\": \"muc1\", \"organism\": \"false\", \"ploidy\": \"1\", \"SeqCenter\": \"CFMR\", \"SeqAccession\": \"12345\", \"name\": \"FUN_\", \"numbering\": \"1\"}, \"other_predictors\": {\"stringtie\": {\"__class__\": \"RuntimeValue\"}, \"maker_gff\": {\"__class__\": \"RuntimeValue\"}, \"pasa_gff\": {\"__class__\": \"RuntimeValue\"}, \"pasa_gff_weight\": \"1\", \"other_gff\": {\"__class__\": \"RuntimeValue\"}, \"other_gff_weight\": \"1\"}, \"outputs\": [\"gbk\", \"tbl\", \"gff3\", \"proteins_fa\", \"mrna_transcripts_fa\", \"cds_transcripts_fa\", \"tbl2asn_report\", \"tbl2asn_error\", \"tbl2asn_validation\", \"stats\"], \"parameters\": {\"__class__\": \"RuntimeValue\"}, \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.15+galaxy0",
                         "type": "tool",
-                        "uuid": "4585ada8-27ac-4632-8ac4-76f452316f21",
+                        "uuid": "aefc0275-b611-4ede-9650-2e16553a7352",
                         "workflow_outputs": [
                             {
-                                "label": "JBrowse: report",
-                                "output_name": "output",
-                                "uuid": "5a38ae83-e177-45f3-aa9f-4c1844584fa5"
+                                "label": null,
+                                "output_name": "fasta_proteins",
+                                "uuid": "aa7fb986-b7db-4353-a83b-3f1591911388"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
                         "errors": null,
-                        "id": 20,
+                        "id": 9,
                         "input_connections": {
-                            "input": {
-                                "id": 18,
-                                "output_name": "renamed"
-                            },
-                            "reference_genome|genome_fasta": {
-                                "id": 2,
-                                "output_name": "output"
+                            "ortho_method|input": {
+                                "id": 8,
+                                "output_name": "fasta_proteins"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool gffread",
-                                "name": "chr_replace"
+                                "description": "runtime parameter for tool eggNOG Mapper",
+                                "name": "ortho_method"
                             }
                         ],
                         "label": null,
-                        "name": "gffread",
+                        "name": "eggNOG Mapper",
                         "outputs": [
                             {
-                                "name": "output_exons",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "output_cds",
-                                "type": "fasta"
+                                "name": "seed_orthologs",
+                                "type": "tabular"
                             },
                             {
-                                "name": "output_pep",
-                                "type": "fasta"
+                                "name": "annotations",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 1085.015625,
-                            "height": 272,
-                            "left": 2747.5,
-                            "right": 2947.5,
-                            "top": 813.015625,
-                            "width": 200,
-                            "x": 2747.5,
-                            "y": 813.015625
+                            "left": 1444.9666748046875,
+                            "top": 418.7333068847656
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2",
+                        "post_job_actions": {
+                            "HideDatasetActionseed_orthologs": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "seed_orthologs"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
                         "tool_shed_repository": {
-                            "changeset_revision": "69e0806b63a4",
-                            "name": "gffread",
-                            "owner": "devteam",
+                            "changeset_revision": "9d1fbff733cf",
+                            "name": "eggnog_mapper",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"chr_replace\": {\"__class__\": \"RuntimeValue\"}, \"decode_url\": \"false\", \"expose\": \"false\", \"filtering\": null, \"full_gff_attribute_preservation\": \"false\", \"gffs\": {\"gff_fmt\": \"none\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"maxintron\": null, \"merging\": {\"merge_sel\": \"none\", \"__current_case__\": 0}, \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 2, \"genome_fasta\": {\"__class__\": \"ConnectedValue\"}, \"ref_filtering\": null, \"fa_outputs\": [\"-w exons.fa\", \"-x cds.fa\", \"-y pep.fa\"]}, \"region\": {\"region_filter\": \"none\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.2.1.2",
+                        "tool_state": "{\"annotation_options\": {\"no_annot\": \"\", \"__current_case__\": 0, \"seed_ortholog_evalue\": \"0.001\", \"seed_ortholog_score\": null, \"tax_scope\": null, \"target_orthologs\": \"all\", \"go_evidence\": \"non-electronic\"}, \"eggnog_data\": \"5.0.2\", \"ortho_method\": {\"m\": \"diamond\", \"__current_case__\": 0, \"input\": {\"__class__\": \"RuntimeValue\"}, \"input_trans\": {\"itype\": \"proteins\", \"__current_case__\": 0}, \"matrix_gapcosts\": {\"matrix\": \"BLOSUM62\", \"__current_case__\": 2, \"gap_costs\": \"--gapopen 11 --gapextend 1\"}, \"sensmode\": \"sensitive\", \"dmnd_iterate\": \"false\", \"dmnd_ignore_warnings\": \"false\", \"query_cover\": null, \"subject_cover\": null, \"pident\": null, \"evalue\": null, \"score\": \"0.001\"}, \"output_options\": {\"no_file_comments\": \"false\", \"report_orthologs\": \"false\", \"md5\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.8+galaxy3",
                         "type": "tool",
-                        "uuid": "51674c8f-f50e-430f-b0ff-49b1b96887aa",
+                        "uuid": "0d9f93f0-88b3-406b-b8f9-ecb2d74c61e9",
                         "workflow_outputs": [
                             {
-                                "label": "Gffread: exons",
-                                "output_name": "output_exons",
-                                "uuid": "52fcac23-b612-4377-a19a-2e3b667a23e3"
-                            },
-                            {
-                                "label": "Gffread: translation of cds",
-                                "output_name": "output_pep",
-                                "uuid": "5c47c25e-0ddb-4ade-a5d0-873ff4add28c"
-                            },
-                            {
-                                "label": "Gffread: cds",
-                                "output_name": "output_cds",
-                                "uuid": "84d9183b-9589-464b-9f82-4dae7f87133e"
+                                "label": null,
+                                "output_name": "annotations",
+                                "uuid": "521fe026-4958-4965-9414-e7074aea7860"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
                         "errors": null,
-                        "id": 21,
+                        "id": 10,
                         "input_connections": {
-                            "gff": {
-                                "id": 18,
-                                "output_name": "renamed"
-                            },
-                            "ref_genome|genome": {
-                                "id": 2,
-                                "output_name": "output"
+                            "input": {
+                                "id": 8,
+                                "output_name": "fasta_proteins"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool InterProScan",
+                                "name": "input"
+                            }
+                        ],
                         "label": null,
-                        "name": "Genome annotation statistics",
+                        "name": "InterProScan",
                         "outputs": [
                             {
-                                "name": "summary",
-                                "type": "txt"
+                                "name": "outfile_tsv",
+                                "type": "tabular"
                             },
                             {
-                                "name": "graphs",
-                                "type": "pdf"
+                                "name": "outfile_xml",
+                                "type": "xml"
                             }
                         ],
                         "position": {
-                            "bottom": 1954.03125,
-                            "height": 272,
-                            "left": 2747.5,
-                            "right": 2947.5,
-                            "top": 1682.03125,
-                            "width": 200,
-                            "x": 2747.5,
-                            "y": 1682.03125
+                            "left": 1475.8499755859375,
+                            "top": 817.8666687011719
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                        "post_job_actions": {
+                            "HideDatasetActionoutfile_xml": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "outfile_xml"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
                         "tool_shed_repository": {
-                            "changeset_revision": "8cffbd184762",
-                            "name": "jcvi_gff_stats",
-                            "owner": "iuc",
+                            "changeset_revision": "74810db257cc",
+                            "name": "interproscan",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"gff\": {\"__class__\": \"ConnectedValue\"}, \"ref_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.8.4",
+                        "tool_state": "{\"applications\": [\"TIGRFAM\", \"SFLD\", \"SUPERFAMILY\", \"PANTHER\", \"Gene3D\", \"Hamap\", \"PrositeProfiles\", \"Coils\", \"SMART\", \"CDD\", \"PRINTS\", \"PIRSR\", \"PrositePatterns\", \"Pfam\", \"MobiDBLite\", \"PIRSF\"], \"database\": \"5.59-91.0\", \"goterms\": \"true\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"iprlookup\": \"false\", \"licensed\": {\"use\": \"true\", \"__current_case__\": 1, \"applications_licensed\": [\"Phobius\", \"SignalP_EUK\", \"TMHMM\"]}, \"oformat\": [\"TSV\", \"XML\"], \"pathways\": \"true\", \"seqtype\": \"p\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.59-91.0+galaxy3",
                         "type": "tool",
-                        "uuid": "d5c389a7-0746-49da-ad3d-e206b5506acc",
+                        "uuid": "cb7a1910-3c31-47d9-835b-f1bd16a1c3ff",
                         "workflow_outputs": [
                             {
-                                "label": "Genome annotation statistics: graphs (third round)",
-                                "output_name": "graphs",
-                                "uuid": "f5d4a6bf-1ff8-435a-8084-7921e25bff3a"
-                            },
-                            {
-                                "label": "Genome annotation statistics: summary (third round)",
-                                "output_name": "summary",
-                                "uuid": "5a863bd4-10f2-4ac8-81b6-ce8b7f663e42"
+                                "label": null,
+                                "output_name": "outfile_tsv",
+                                "uuid": "65e267a7-d3c6-410d-9b44-f655d70d7d9a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0",
                         "errors": null,
-                        "id": 22,
+                        "id": 11,
                         "input_connections": {
-                            "input": {
-                                "id": 20,
-                                "output_name": "output_exons"
+                            "eggnog": {
+                                "id": 9,
+                                "output_name": "annotations"
+                            },
+                            "input|genbank": {
+                                "id": 8,
+                                "output_name": "annot_gbk"
+                            },
+                            "iprscan": {
+                                "id": 10,
+                                "output_name": "outfile_xml"
+                            },
+                            "sbt": {
+                                "id": 4,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "annotations"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "antismash"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "database"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "eggnog"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "fix"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "input"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "iprscan"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "phobius"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "remove"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate functional",
+                                "name": "sbt"
+                            }
+                        ],
                         "label": null,
-                        "name": "Busco",
+                        "name": "Funannotate functional",
                         "outputs": [
                             {
-                                "name": "busco_sum",
-                                "type": "txt"
+                                "name": "gbk",
+                                "type": "genbank"
                             },
                             {
-                                "name": "busco_table",
+                                "name": "annot",
                                 "type": "tabular"
                             },
                             {
-                                "name": "busco_missing",
+                                "name": "contigs_fsa",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "agp",
                                 "type": "tabular"
+                            },
+                            {
+                                "name": "tbl",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "sqn",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "fa_scaffolds",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "fa_proteins",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "fa_transcripts_mrna",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "fa_transcripts_cds",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "gff3",
+                                "type": "gff3"
+                            },
+                            {
+                                "name": "tbl2asn_report",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "stats",
+                                "type": "json"
+                            },
+                            {
+                                "name": "must_fix",
+                                "type": "json"
+                            },
+                            {
+                                "name": "need_curating",
+                                "type": "json"
+                            },
+                            {
+                                "name": "new_names_passed",
+                                "type": "json"
                             }
                         ],
                         "position": {
-                            "bottom": 1156.03125,
-                            "height": 252,
-                            "left": 3025.5,
-                            "right": 3225.5,
-                            "top": 904.03125,
-                            "width": 200,
-                            "x": 3025.5,
-                            "y": 904.03125
+                            "left": 1877.11669921875,
+                            "top": 101.59999084472656
                         },
                         "post_job_actions": {
-                            "HideDatasetActionbusco_missing": {
+                            "HideDatasetActionagp": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "busco_missing"
+                                "output_name": "agp"
                             },
-                            "HideDatasetActionbusco_table": {
+                            "HideDatasetActionannot": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "busco_table"
+                                "output_name": "annot"
+                            },
+                            "HideDatasetActioncontigs_fsa": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "contigs_fsa"
+                            },
+                            "HideDatasetActionfa_scaffolds": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "fa_scaffolds"
+                            },
+                            "HideDatasetActionmust_fix": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "must_fix"
+                            },
+                            "HideDatasetActionneed_curating": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "need_curating"
+                            },
+                            "HideDatasetActionnew_names_passed": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "new_names_passed"
+                            },
+                            "HideDatasetActionsqn": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "sqn"
+                            },
+                            "HideDatasetActiontbl": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "tbl"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "602fb8e63aa7",
-                            "name": "busco",
+                            "changeset_revision": "9feee7fc49a1",
+                            "name": "funannotate_annotate",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"tran\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.1.4",
+                        "tool_state": "{\"annotations\": {\"__class__\": \"RuntimeValue\"}, \"antismash\": {\"__class__\": \"RuntimeValue\"}, \"busco_db\": \"mucorales_odb10\", \"database\": {\"__class__\": \"RuntimeValue\"}, \"eggnog\": {\"__class__\": \"RuntimeValue\"}, \"fix\": {\"__class__\": \"RuntimeValue\"}, \"input\": {\"input_type\": \"gbk\", \"__current_case__\": 0, \"genbank\": {\"__class__\": \"RuntimeValue\"}}, \"iprscan\": {\"__class__\": \"RuntimeValue\"}, \"isolate\": \"\", \"outputs\": [\"gbk\", \"annotations\", \"contigs_fsa\", \"agp\", \"tbl\", \"sqn\", \"scaffolds_fa\", \"proteins_fa\", \"mrna_transcripts_fa\", \"cds_transcripts_fa\", \"gff3\", \"discrepency\", \"stats\", \"must_fix\", \"need_curating\", \"new_names_passed\"], \"phobius\": {\"__class__\": \"RuntimeValue\"}, \"remove\": {\"__class__\": \"RuntimeValue\"}, \"rename\": \"\", \"sbt\": {\"__class__\": \"RuntimeValue\"}, \"strain\": \"muc1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.15+galaxy0",
                         "type": "tool",
-                        "uuid": "94dac116-5e62-487c-912a-a63ca53c17e7",
+                        "uuid": "e07de1e0-8f91-4477-b951-7d97dba2e397",
                         "workflow_outputs": [
                             {
-                                "label": "Busco summary final round",
-                                "output_name": "busco_sum",
-                                "uuid": "0bc78676-eecc-4168-894d-34c4ca07cdf3"
+                                "label": "Final annotation (genbank)",
+                                "output_name": "gbk",
+                                "uuid": "d0694cd1-6d81-4d72-83b9-94cb57dc1502"
+                            },
+                            {
+                                "label": "Final annotation (CDS sequences)",
+                                "output_name": "fa_transcripts_cds",
+                                "uuid": "9a1e7b70-1090-41ed-8637-65b7372a9f6c"
+                            },
+                            {
+                                "label": "Final annotation (mRNA sequences)",
+                                "output_name": "fa_transcripts_mrna",
+                                "uuid": "99fffa40-2196-491d-9a66-559ebf2d9561"
+                            },
+                            {
+                                "label": "Final annotation (protein sequences)",
+                                "output_name": "fa_proteins",
+                                "uuid": "17b03b77-0485-4176-b2b3-03bfa2d3bcb0"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "tbl2asn_report",
+                                "uuid": "d3d4daec-75fe-4071-af37-c2907e46f5c1"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "stats",
+                                "uuid": "4a682ab6-8a6f-4a0f-bb0e-ba796f587ddc"
+                            },
+                            {
+                                "label": "Final annotation (GFF3)",
+                                "output_name": "gff3",
+                                "uuid": "4a0602fc-e6d2-43fc-9957-344707c22c05"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "genome-annotation/annotation-with-maker",
-                "path": "topics/genome-annotation/tutorials/annotation-with-maker/workflows/main_workflow.ga",
-                "tags": [
-                    "genome-annotation"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Genome annotation with Maker ",
-                "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-annotation-with-maker/versions/main-workflow",
-                "tutorial_id": "annotation-with-maker",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-maker/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-maker/workflows/main_workflow.html",
-                "version": 10,
-                "wfid": "genome-annotation-annotation-with-maker",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.11",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1"
-                ],
-                "workflowhub_id": "1164"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.4406623"
-    },
-    {
-        "abbreviations": {
-            "OGS": "Official Gene Set"
-        },
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "apollo_create_or_update",
-                    "owner": "gga",
-                    "revisions": "4abaab60f9e1",
-                    "tool_panel_section_label": "Apollo",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "apollo_iframe",
-                    "owner": "gga",
-                    "revisions": "f4e3f9480307",
-                    "tool_panel_section_label": "Apollo",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "jbrowse",
-                    "owner": "iuc",
-                    "revisions": "a6e57ff585c0",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: apollo_create_or_update\n  owner: gga\n  revisions: 4abaab60f9e1\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: apollo_iframe\n  owner: gga\n  revisions: f4e3f9480307\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo-euk/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "abretaud"
-            ],
-            "funding": [
-                "gallantries",
-                "eurosciencegateway"
-            ]
-        },
-        "contributors": [
-            {
-                "affiliations": [
-                    "gallantries",
-                    "eurosciencegateway",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
-                "fediverse_flavor": "mastodon",
-                "id": "abretaud",
-                "joined": "2017-09",
-                "location": {
-                    "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
-                },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
-            },
-            {
-                "avatar": "/training-material/assets/images/eurosciencegateway.png",
-                "funder": true,
-                "funding_id": "101057388",
-                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "eurosciencegateway",
-                "joined": "2023-10",
-                "members": [
-                    "abretaud",
-                    "anuprulez",
-                    "bgruening",
-                    "erxleben",
-                    "pauldg",
-                    "rlibouba"
-                ],
-                "name": "EuroScienceGateway",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
-            }
-        ],
-        "dir": "topics/genome-annotation/tutorials/apollo-euk",
-        "edam_operation": [
-            "Genome visualisation"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.no"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "genome-annotation/apollo-euk",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Apollo is the Google Docs of the genome annotation world, real-time collaborative genome annotation.",
-            "Apollo allows a group to view and manually refine predicted genome annotations",
-            "Use Apollo to edit annotations within your group.",
-            "Export manual annotations as GFF3."
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-02-29",
-        "objectives": [
-            "Load a genome into Galaxy",
-            "View annotations in JBrowse",
-            "Learn how to load JBrowse data into Apollo",
-            "Learn how to manually refine genome annotations within Apollo",
-            "Export refined genome annotations"
-        ],
-        "pageviews": 1546,
-        "priority": 6,
-        "pub_date": "2022-08-22",
-        "questions": [
-            "How to visualize your genome after automated annotations have been performed?",
-            "How to manually annotate genome after automated annotations have been performed?",
-            "How to evaluate and visualize annotated genomic features?",
-            "How do I collaborate when doing genome annotation?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "upload-rules"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "genome-annotation",
-                "tutorials": [
-                    "funannotate"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00170",
-        "short_tools": [
-            "create_or_update",
-            "iframe",
-            "jbrowse"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "eukaryote",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "gmod",
-            "eukaryote",
-            "cyoa",
-            "jbrowse1",
-            "apollo2"
-        ],
-        "time_estimation": "3h",
-        "title": "Refining Genome Annotations with Apollo (eukaryotes)",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
-            "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1"
-        ],
-        "topic_name": "genome-annotation",
-        "topic_name_human": "Genome Annotation",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "apollo-euk",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo-euk/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo-euk/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo-euk/tutorial.json"
-        },
-        "version": 13,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 158,
-        "visitors": 871,
-        "zenodo_link": "https://zenodo.org/record/3270822"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "2d_auto_threshold",
-                    "owner": "imgteam",
-                    "revisions": "0c777d708acc",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "2d_auto_threshold",
-                    "owner": "imgteam",
-                    "revisions": "3df9f0a4bf34",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "2d_histogram_equalization",
-                    "owner": "imgteam",
-                    "revisions": "70316d792fc9",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "2d_histogram_equalization",
-                    "owner": "imgteam",
-                    "revisions": "77f7159d775a",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "2d_simple_filter",
-                    "owner": "imgteam",
-                    "revisions": "dba87c4b32d3",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "2d_simple_filter",
-                    "owner": "imgteam",
-                    "revisions": "f70b215d155c",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bfconvert",
-                    "owner": "imgteam",
-                    "revisions": "10eed33aa9b2",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bfconvert",
-                    "owner": "imgteam",
-                    "revisions": "85edbb7a436b",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "binary2labelimage",
-                    "owner": "imgteam",
-                    "revisions": "6e65fd971e13",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "binary2labelimage",
-                    "owner": "imgteam",
-                    "revisions": "9bb446db4a1e",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "count_objects",
-                    "owner": "imgteam",
-                    "revisions": "5bf8eb50b280",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "count_objects",
-                    "owner": "imgteam",
-                    "revisions": "b58447a2eed2",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "image_info",
-                    "owner": "imgteam",
-                    "revisions": "7b6d9412c7f8",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "overlay_images",
-                    "owner": "imgteam",
-                    "revisions": "b74693340624",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "overlay_images",
-                    "owner": "imgteam",
-                    "revisions": "22ff7c705a83",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "unzip",
-                    "owner": "imgteam",
-                    "revisions": "57f0914ddb7b",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: 2d_auto_threshold\n  owner: imgteam\n  revisions: 0c777d708acc\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_auto_threshold\n  owner: imgteam\n  revisions: 3df9f0a4bf34\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_histogram_equalization\n  owner: imgteam\n  revisions: 70316d792fc9\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_histogram_equalization\n  owner: imgteam\n  revisions: 77f7159d775a\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_simple_filter\n  owner: imgteam\n  revisions: dba87c4b32d3\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_simple_filter\n  owner: imgteam\n  revisions: f70b215d155c\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bfconvert\n  owner: imgteam\n  revisions: 10eed33aa9b2\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bfconvert\n  owner: imgteam\n  revisions: 85edbb7a436b\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: binary2labelimage\n  owner: imgteam\n  revisions: 6e65fd971e13\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: binary2labelimage\n  owner: imgteam\n  revisions: 9bb446db4a1e\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: count_objects\n  owner: imgteam\n  revisions: 5bf8eb50b280\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: count_objects\n  owner: imgteam\n  revisions: b58447a2eed2\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: image_info\n  owner: imgteam\n  revisions: 7b6d9412c7f8\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: overlay_images\n  owner: imgteam\n  revisions: b74693340624\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: overlay_images\n  owner: imgteam\n  revisions: 22ff7c705a83\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unzip\n  owner: imgteam\n  revisions: 57f0914ddb7b\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/imaging-introduction/tutorial.json",
-        "contributors": [
-            {
-                "former_affiliations": [
-                    "deNBI",
-                    "elixir-europe"
-                ],
-                "id": "thomaswollmann",
-                "joined": "2019-08",
-                "name": "Thomas Wollmann",
-                "orcid": "0000-0002-4741-3844",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/thomaswollmann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/thomaswollmann.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe",
-                    "deNBI"
-                ],
-                "elixir_node": "de",
-                "email": "leonid.kostrykin@bioquant.uni-heidelberg.de",
-                "id": "kostrykin",
-                "joined": "2023-08",
-                "linkedin": "kostrykin",
-                "name": "Leonid Kostrykin",
-                "orcid": "0000-0003-1323-3762",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kostrykin/",
-                "twitter": "l_kostrykin",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/kostrykin.json"
-            }
-        ],
-        "dir": "topics/imaging/tutorials/imaging-introduction",
-        "edam_operation": [
-            "Visualisation",
-            "Image analysis",
-            "Image annotation",
-            "Data handling"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "imaging",
-                "tutorials": [
-                    "hela-screen-analysis"
-                ],
-                "type": "internal"
-            }
-        ],
-        "hands_on": true,
-        "id": "imaging/imaging-introduction",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.org.au"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "The **Image Info** tool can provide valuable metadata information of an image.",
-            "TIFF files cannot viewed directly in most web browser, but have to be converted.",
-            "For visualization, images with a bit-depth more than 8-bit have to be histogram equalized."
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Introductory",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-14",
-        "objectives": [
-            "How to handle images in Galaxy.",
-            "How to perform basic image processing in Galaxy."
-        ],
-        "pageviews": 2880,
-        "pub_date": "2019-08-13",
-        "questions": [
-            "How do I use Galaxy with imaging data?",
-            "How do I convert images using Galaxy?",
-            "How do I display images in Galaxy?",
-            "How do I filter images in Galaxy?",
-            "How do I segment simple images in Galaxy?"
-        ],
-        "short_id": "T00181",
-        "short_tools": [
-            "ip_convertimage",
-            "ip_filter_standard",
-            "ip_histogram_equalization",
-            "ip_count_objects",
-            "ip_threshold",
-            "ip_overlay_images",
-            "unzip",
-            "ip_imageinfo",
-            "ip_binary_to_labelimage"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "HeLa"
-        ],
-        "time_estimation": "1H",
-        "title": "Introduction to image analysis using Galaxy",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.0.5",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.0.5-2",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.0.1",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.0.1-2",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/0.0.3",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/0.0.3-2",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/0.0.3-3",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.4",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.4-2",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5-2",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/image_info/ip_imageinfo/0.2",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.3",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.3-3",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy0"
-        ],
-        "topic_name": "imaging",
-        "topic_name_human": "Imaging",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "imaging-introduction",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/imaging/tutorials/imaging-introduction/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/imaging-introduction/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/imaging-introduction/tutorial.json"
-        },
-        "version": 11,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 98,
-        "visitors": 1978,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0002-2315-9247",
-                        "name": "Till Korten",
-                        "url": "https://github.com/thawn/"
-                    }
-                ],
-                "description": "",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ninput_image\"]\n  1[label=\"Histogram equalization\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Image Info\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Filter Image\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Filter Image\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Convert image\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Convert image\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"Auto Threshold\"]\n  3 -> 7 [label=\"output\"]\n  8[label=\"Histogram equalization\"]\n  3 -> 8 [label=\"output\"]\n  9[label=\"Binary 2 Label\"]\n  7 -> 9 [label=\"output\"]\n  10[label=\"Convert image\"]\n  8 -> 10 [label=\"output\"]\n  11[label=\"Overlay Images\"]\n  6 -> 11 [label=\"output\"]\n  9 -> 11 [label=\"output\"]\n  k85029ccbebb34a919ba3d1daefd13efc[color=lightseagreen,label=\"Output\\nout\"]\n  11 -> k85029ccbebb34a919ba3d1daefd13efc\n  12[label=\"Convert image\"]\n  9 -> 12 [label=\"output\"]\n  13[label=\"Count Objects\"]\n  9 -> 13 [label=\"output\"]\n  k1446f4bfb031405a84f088acc1a5c8a3[color=lightseagreen,label=\"Output\\noutput\"]\n  13 -> k1446f4bfb031405a84f088acc1a5c8a3\n}",
-                "history": [
-                    {
-                        "hash": "417cff2ccf2bd267e63d478bec4fec85b8fc04b1",
-                        "message": "fixed json syntax",
-                        "num": 8,
-                        "short_hash": "417cff2cc",
-                        "unix": "1699440926"
-                    },
-                    {
-                        "hash": "9fd3cf532f4cbe3feff9ee7561ccc45fca40e4ea",
-                        "message": "added `creator` and `license` fields",
-                        "num": 7,
-                        "short_hash": "9fd3cf532",
-                        "unix": "1699440835"
-                    },
-                    {
-                        "hash": "f1edf310368eae3320d7cad61b45da646dcb24f8",
-                        "message": "updated ga file",
-                        "num": 6,
-                        "short_hash": "f1edf3103",
-                        "unix": "1699371738"
-                    },
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 5,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 4,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
-                        "message": "unflatten workflows",
-                        "num": 3,
-                        "short_hash": "faf6d298a",
-                        "unix": "1576155753"
                     },
                     {
-                        "hash": "5eca26d3a4b208e631bbf18232cb1a6727ec99db",
-                        "message": "update images, workflow, and final hands on box",
-                        "num": 2,
-                        "short_hash": "5eca26d3a",
-                        "unix": "1565346764"
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {
+                            "reference_genome|genome": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "track_groups_0|data_tracks_0|data_format|annotation": {
+                                "id": 11,
+                                "output_name": "gff3"
+                            },
+                            "track_groups_1|data_tracks_0|data_format|annotation": {
+                                "id": 7,
+                                "output_name": "mapped_reads"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool JBrowse",
+                                "name": "reference_genome"
+                            }
+                        ],
+                        "label": null,
+                        "name": "JBrowse",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "html"
+                            }
+                        ],
+                        "position": {
+                            "left": 2152.60009765625,
+                            "top": 0.0
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "a6e57ff585c0",
+                            "name": "jbrowse",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 1, \"category\": \"RNASeq\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"auto_snp\": \"true\", \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.11+galaxy1",
+                        "type": "tool",
+                        "uuid": "e6d0e687-1a13-482b-a00a-28c7304d59ac",
+                        "workflow_outputs": [
+                            {
+                                "label": "JBrowse",
+                                "output_name": "output",
+                                "uuid": "ac4d8805-f123-44d2-b30f-8ac906cc471f"
+                            }
+                        ]
                     },
-                    {
-                        "hash": "2e42bf8893d877437f600ea4e849c169cbcbb263",
-                        "message": "add workflow",
-                        "num": 1,
-                        "short_hash": "2e42bf889",
-                        "unix": "1565003060"
-                    }
-                ],
-                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
+                        "id": 13,
+                        "input_connections": {
+                            "input": [
+                                {
+                                    "id": 5,
+                                    "output_name": "output"
+                                },
+                                {
+                                    "id": 11,
+                                    "output_name": "gbk"
+                                }
+                            ]
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "input_image"
+                                "description": "runtime parameter for tool Funannotate compare",
+                                "name": "database"
+                            },
+                            {
+                                "description": "runtime parameter for tool Funannotate compare",
+                                "name": "proteinortho"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Funannotate compare",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "html"
                             }
                         ],
-                        "label": "input_image",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 0.0,
-                            "top": 184.22997472088954
+                            "left": 2318,
+                            "top": 403.7333068847656
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "3414473c-85fe-41b7-9492-61afc45dd847",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ninput_image\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Histogram equalization\"];\n  0 -->|output| 1;\n  2[\"Image Info\"];\n  0 -->|output| 2;\n  3[\"Filter Image\"];\n  0 -->|output| 3;\n  4[\"Filter Image\"];\n  0 -->|output| 4;\n  5[\"Convert image\"];\n  0 -->|output| 5;\n  6[\"Convert image\"];\n  1 -->|output| 6;\n  7[\"Auto Threshold\"];\n  3 -->|output| 7;\n  8[\"Histogram equalization\"];\n  3 -->|output| 8;\n  9[\"Binary 2 Label\"];\n  7 -->|output| 9;\n  10[\"Convert image\"];\n  8 -->|output| 10;\n  11[\"Overlay Images\"];\n  6 -->|output| 11;\n  9 -->|output| 11;\n  85029ccb-ebb3-4a91-9ba3-d1daefd13efc[\"Output\\nout\"];\n  11 --> 85029ccb-ebb3-4a91-9ba3-d1daefd13efc;\n  style 85029ccb-ebb3-4a91-9ba3-d1daefd13efc stroke:#2c3143,stroke-width:4px;\n  12[\"Convert image\"];\n  9 -->|output| 12;\n  13[\"Count Objects\"];\n  9 -->|output| 13;\n  1446f4bf-b031-405a-84f0-88acc1a5c8a3[\"Output\\noutput\"];\n  13 --> 1446f4bf-b031-405a-84f0-88acc1a5c8a3;\n  style 1446f4bf-b031-405a-84f0-88acc1a5c8a3 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Workflow constructed from Tutorial 'Introduction to image analysis using Galaxy'",
-                "outputs": [
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "a7ce2601500c",
+                            "name": "funannotate_compare",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"database\": {\"__class__\": \"RuntimeValue\"}, \"go_fdr\": \"0.05\", \"heatmap_stdev\": \"1.0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"ml\": {\"ml_method\": \"iqtree\", \"__current_case__\": 0}, \"num_orthos\": \"500\", \"proteinortho\": {\"__class__\": \"RuntimeValue\"}, \"run_dnds\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.15+galaxy0",
+                        "type": "tool",
+                        "uuid": "750137e5-2cac-4bec-8337-03dab562a7a5",
+                        "workflow_outputs": [
+                            {
+                                "label": "Funannotate compare report",
+                                "output_name": "output",
+                                "uuid": "e531c81f-f6b7-4c82-a712-c562873ff714"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0",
                         "errors": null,
-                        "id": 11,
+                        "id": 14,
                         "input_connections": {
-                            "method_option|im1": {
+                            "predictiongff3": {
                                 "id": 6,
                                 "output_name": "output"
                             },
-                            "method_option|im2": {
-                                "id": 9,
-                                "output_name": "output"
+                            "referencegff3": {
+                                "id": 11,
+                                "output_name": "gff3"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Overlay Images",
+                        "name": "AEGeAn ParsEval",
                         "outputs": [
                             {
-                                "name": "out",
-                                "type": "tiff"
+                                "name": "output_html",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 1103.1565029542078,
-                            "top": 4.927314536610737
+                            "left": 2318.5,
+                            "top": 643.7333068847656
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.3",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "b74693340624",
-                            "name": "overlay_images",
-                            "owner": "imgteam",
+                            "changeset_revision": "1b52f0c8ad7f",
+                            "name": "aegean_parseval",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"method_option\": {\"method\": \"seg_contour\", \"__current_case__\": 2, \"im1\": {\"__class__\": \"ConnectedValue\"}, \"im2\": {\"__class__\": \"ConnectedValue\"}, \"thickness\": \"2\", \"color\": \"#ff0000\", \"show_label\": true, \"label_color\": \"#ffff00\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.0.3",
+                        "tool_state": "{\"delta\": \"0\", \"maxtrans\": \"32\", \"output_type\": \"html\", \"predictiongff3\": {\"__class__\": \"ConnectedValue\"}, \"predlabel\": \"\", \"referencegff3\": {\"__class__\": \"ConnectedValue\"}, \"refrlabel\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.16.0",
                         "type": "tool",
-                        "uuid": "e6920848-10eb-406c-939e-6bfae3041346",
-                        "when": null,
+                        "uuid": "b5870c4b-d799-4da0-83cc-7dd5a0b049e4",
                         "workflow_outputs": [
                             {
-                                "label": "out",
-                                "output_name": "out",
-                                "uuid": "85029ccb-ebb3-4a91-9ba3-d1daefd13efc"
+                                "label": "AEGeAN report",
+                                "output_name": "output_html",
+                                "uuid": "0d776b46-2c1c-4083-9f9d-a213fa62eb81"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0",
                         "errors": null,
-                        "id": 13,
+                        "id": 15,
                         "input_connections": {
                             "input": {
-                                "id": 9,
-                                "output_name": "output"
+                                "id": 11,
+                                "output_name": "fa_proteins"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Busco",
+                                "name": "input"
+                            }
+                        ],
                         "label": null,
-                        "name": "Count Objects",
+                        "name": "Busco",
                         "outputs": [
                             {
-                                "name": "output",
+                                "name": "busco_sum",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "busco_table",
                                 "type": "tabular"
+                            },
+                            {
+                                "name": "summary_image",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 1172.3462617863868,
-                            "top": 500.229868675786
+                            "left": 2252.2666015625,
+                            "top": 1072.0666809082031
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5",
+                        "post_job_actions": {
+                            "HideDatasetActionbusco_table": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "busco_table"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "5bf8eb50b280",
-                            "name": "count_objects",
-                            "owner": "imgteam",
+                            "changeset_revision": "94170eee0ad8",
+                            "name": "busco",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tiff\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.0.5",
+                        "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\"}, \"busco_mode\": {\"mode\": \"prot\", \"__current_case__\": 2}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": \"mucorales_odb10\"}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"image\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.4.6+galaxy0",
                         "type": "tool",
-                        "uuid": "3c7f2b09-2fd6-452a-983d-ca120067c1a4",
-                        "when": null,
+                        "uuid": "bec3d4d9-88e6-4ea0-beb6-219d5c727290",
                         "workflow_outputs": [
                             {
-                                "label": "output",
-                                "output_name": "output",
-                                "uuid": "1446f4bf-b031-405a-84f0-88acc1a5c8a3"
+                                "label": "Busco summary",
+                                "output_name": "busco_sum",
+                                "uuid": "57a619f5-b331-4ca6-8e6e-72eb61860032"
+                            },
+                            {
+                                "label": "Busco image",
+                                "output_name": "summary_image",
+                                "uuid": "97d23764-ad4a-4d69-948c-c81afb76fbaf"
                             }
                         ]
                     }
                 ],
-                "parent_id": "imaging/imaging-introduction",
-                "path": "topics/imaging/tutorials/imaging-introduction/workflows/Galaxy-Workflow-GTN_Tutorial__Introduction_to_Imaging.ga",
-                "tags": [],
+                "parent_id": "genome-annotation/funannotate",
+                "path": "topics/genome-annotation/tutorials/funannotate/workflows/funannotate.ga",
+                "tags": [
+                    "genome-annotation"
+                ],
                 "test_results": null,
                 "tests": true,
-                "title": "Workflow constructed from Tutorial 'Introduction to image analysis using Galaxy'",
-                "topic_id": "imaging",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/imaging-imaging-introduction/versions/galaxy-workflow-gtn-tutorial--introduction-to-imaging",
-                "tutorial_id": "imaging-introduction",
-                "url": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/imaging-introduction/workflows/Galaxy-Workflow-GTN_Tutorial__Introduction_to_Imaging.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/imaging-introduction/workflows/Galaxy-Workflow-GTN_Tutorial__Introduction_to_Imaging.html",
-                "version": 5,
-                "wfid": "imaging-imaging-introduction",
-                "wfname": "galaxy-workflow-gtn-tutorial--introduction-to-imaging",
-                "workflow": "Galaxy-Workflow-GTN_Tutorial__Introduction_to_Imaging.ga",
+                "title": "Funannotate",
+                "topic_id": "genome-annotation",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-funannotate/versions/funannotate",
+                "tutorial_id": "funannotate",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/funannotate/workflows/funannotate.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/funannotate/workflows/funannotate.html",
+                "version": 1,
+                "wfid": "genome-annotation-funannotate",
+                "wfname": "funannotate",
+                "workflow": "funannotate.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.0.5",
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/0.0.3",
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.4",
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5",
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/image_info/ip_imageinfo/0.2",
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.3"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_compare/funannotate_compare/1.8.15+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.15+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3"
                 ],
-                "workflowhub_id": "1258"
+                "workflowhub_id": "1202"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/3362976"
+        "zenodo_link": "https://zenodo.org/record/7867921"
     },
     {
         "admin_install": {
@@ -119532,1561 +120689,2674 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "cp_cellprofiler",
-                    "owner": "bgruening",
-                    "revisions": "e917a2424690",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cp_common",
-                    "owner": "bgruening",
-                    "revisions": "e7273daa5ae2",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cp_convert_objects_to_image",
-                    "owner": "bgruening",
-                    "revisions": "df3ad3ba5c6f",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cp_display_data_on_image",
-                    "owner": "bgruening",
-                    "revisions": "2484086dee41",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cp_enhance_or_suppress_features",
-                    "owner": "bgruening",
-                    "revisions": "f2ed92b011a9",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cp_export_to_spreadsheet",
-                    "owner": "bgruening",
-                    "revisions": "f8fa0f6718a3",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cp_gray_to_color",
-                    "owner": "bgruening",
-                    "revisions": "31d195bedf6d",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cp_identify_primary_objects",
-                    "owner": "bgruening",
-                    "revisions": "993faa34333b",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cp_image_math",
-                    "owner": "bgruening",
-                    "revisions": "c09dcda1143f",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cp_mask_image",
-                    "owner": "bgruening",
-                    "revisions": "3a05117669cf",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cp_measure_granularity",
-                    "owner": "bgruening",
-                    "revisions": "a1a961c46d4b",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cp_measure_image_area_occupied",
-                    "owner": "bgruening",
-                    "revisions": "20dbb1f7ec7b",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cp_measure_image_intensity",
-                    "owner": "bgruening",
-                    "revisions": "5499dc6f8ac1",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cp_measure_image_quality",
-                    "owner": "bgruening",
-                    "revisions": "e972e07c7845",
-                    "tool_panel_section_label": "Imaging",
+                    "name": "gffread",
+                    "owner": "devteam",
+                    "revisions": "0232f19d300f",
+                    "tool_panel_section_label": "Convert Formats",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cp_measure_object_intensity",
-                    "owner": "bgruening",
-                    "revisions": "980aed9e8fd5",
-                    "tool_panel_section_label": "Imaging",
+                    "name": "busco",
+                    "owner": "iuc",
+                    "revisions": "1440ae06552f",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cp_measure_object_size_shape",
-                    "owner": "bgruening",
-                    "revisions": "79e10d12d90a",
-                    "tool_panel_section_label": "Imaging",
+                    "name": "jbrowse",
+                    "owner": "iuc",
+                    "revisions": "2bb2e07a7a21",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cp_measure_texture",
-                    "owner": "bgruening",
-                    "revisions": "035a58c7f54a",
-                    "tool_panel_section_label": "Imaging",
+                    "name": "jcvi_gff_stats",
+                    "owner": "iuc",
+                    "revisions": "8cffbd184762",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cp_relate_objects",
-                    "owner": "bgruening",
-                    "revisions": "8083a87d2fdf",
-                    "tool_panel_section_label": "Imaging",
+                    "name": "maker",
+                    "owner": "iuc",
+                    "revisions": "96ac930d84fa",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cp_save_images",
-                    "owner": "bgruening",
-                    "revisions": "4ecf93628f97",
-                    "tool_panel_section_label": "Imaging",
+                    "name": "maker_map_ids",
+                    "owner": "iuc",
+                    "revisions": "326f9c294b09",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "idr_download_by_ids",
-                    "owner": "iuc",
-                    "revisions": "e08b1dc0480c",
-                    "tool_panel_section_label": "Imaging",
+                    "name": "fasta_stats",
+                    "owner": "simon-gladman",
+                    "revisions": "20ca2574216a",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: cp_cellprofiler\n  owner: bgruening\n  revisions: e917a2424690\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_common\n  owner: bgruening\n  revisions: e7273daa5ae2\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_convert_objects_to_image\n  owner: bgruening\n  revisions: df3ad3ba5c6f\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_display_data_on_image\n  owner: bgruening\n  revisions: 2484086dee41\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_enhance_or_suppress_features\n  owner: bgruening\n  revisions: f2ed92b011a9\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_export_to_spreadsheet\n  owner: bgruening\n  revisions: f8fa0f6718a3\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_gray_to_color\n  owner: bgruening\n  revisions: 31d195bedf6d\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_identify_primary_objects\n  owner: bgruening\n  revisions: 993faa34333b\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_image_math\n  owner: bgruening\n  revisions: c09dcda1143f\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_mask_image\n  owner: bgruening\n  revisions: 3a05117669cf\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_measure_granularity\n  owner: bgruening\n  revisions: a1a961c46d4b\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_measure_image_area_occupied\n  owner: bgruening\n  revisions: 20dbb1f7ec7b\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_measure_image_intensity\n  owner: bgruening\n  revisions: 5499dc6f8ac1\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_measure_image_quality\n  owner: bgruening\n  revisions: e972e07c7845\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_measure_object_intensity\n  owner: bgruening\n  revisions: 980aed9e8fd5\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_measure_object_size_shape\n  owner: bgruening\n  revisions: 79e10d12d90a\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_measure_texture\n  owner: bgruening\n  revisions: 035a58c7f54a\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_relate_objects\n  owner: bgruening\n  revisions: 8083a87d2fdf\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_save_images\n  owner: bgruening\n  revisions: 4ecf93628f97\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: idr_download_by_ids\n  owner: iuc\n  revisions: e08b1dc0480c\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/tutorial-CP/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: gffread\n  owner: devteam\n  revisions: 0232f19d300f\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 1440ae06552f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 2bb2e07a7a21\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jcvi_gff_stats\n  owner: iuc\n  revisions: 8cffbd184762\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker\n  owner: iuc\n  revisions: 96ac930d84fa\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker_map_ids\n  owner: iuc\n  revisions: 326f9c294b09\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n  owner: simon-gladman\n  revisions: 20ca2574216a\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.json",
         "contributors": [
             {
-                "email": "beatrizserrano.galaxy@gmail.com",
-                "id": "beatrizserrano",
-                "joined": "2020-07",
-                "linkedin": "beatriz-serrano",
-                "matrix": "beatrizserrano:matrix.org",
-                "name": "Beatriz Serrano-Solano",
-                "orcid": "0000-0002-5862-6132",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/beatrizserrano/",
-                "twitter": "BSerranoSolano",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/beatrizserrano.json"
-            },
-            {
-                "id": "jkh1",
-                "joined": "2020-07",
-                "name": "Jean-Karim H\u00e9rich\u00e9",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jkh1/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jkh1.json"
+                "affiliations": [
+                    "gallantries",
+                    "eurosciencegateway",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
+                "fediverse_flavor": "mastodon",
+                "id": "abretaud",
+                "joined": "2017-09",
+                "location": {
+                    "country": "FR",
+                    "lat": 48.11,
+                    "lon": -1.64
+                },
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
             }
         ],
-        "dir": "topics/imaging/tutorials/tutorial-CP",
+        "dir": "topics/genome-annotation/tutorials/annotation-with-maker-short",
         "edam_operation": [
-            "Parsing",
-            "Image analysis",
-            "Quantification"
+            "Sequence assembly validation",
+            "Genome annotation",
+            "Scaffolding",
+            "Sequence annotation",
+            "Transcriptome assembly",
+            "Genome assembly",
+            "Genome visualisation"
         ],
         "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "imaging/tutorial-CP",
+        "id": "genome-annotation/annotation-with-maker-short",
         "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
+            "UseGalaxy.be"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Galaxy workflows can download images from the IDR, selecting specific channels, time points, z-stack positions and crop the image in different ways.",
-            "CellProfiler in Galaxy can segment and extract features of any object of interest.",
-            "The features and masks can be exported for further analysis."
+            "Maker allows to annotate a eukaryotic genome.",
+            "BUSCO and JBrowse allow to inspect the quality of an annotation."
         ],
         "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-02-29",
         "objectives": [
-            "How to download images from a public image repository.",
-            "How to segment cell nuclei using CellProfiler in Galaxy.",
-            "How to segment cell nucleoli using CellProfiler in Galaxy.",
-            "How to extract features for images, nuclei and nucleoli."
+            "Load genome into Galaxy",
+            "Annotate genome with Maker",
+            "Evaluate annotation quality with BUSCO",
+            "View annotations in JBrowse"
         ],
-        "pageviews": 5731803,
-        "pub_date": "2020-07-01",
+        "pageviews": 4148,
+        "priority": 3,
+        "pub_date": "2021-01-12",
         "questions": [
-            "How do I run an image analysis pipeline on public data using CellProfiler?",
-            "How do I analyse the DNA channel of fluorescence siRNA screens?",
-            "How do I download public image data into my history?",
-            "How do I segment and label cell nuclei?",
-            "How do I segment nucleoli (as the absence of DNA)?",
-            "How do I combine nuclei and nucleoli into one segmentation mask?",
-            "How do I extract the background of an image?",
-            "How do I relate the nucleoli to their parent nucleus?",
-            "How do I measure the image and object features?",
-            "How do I measure the image quality?"
+            "How to annotate an eukaryotic genome?",
+            "How to evaluate and visualize annotated genomic features?"
         ],
-        "short_id": "T00183",
+        "short_id": "T00167",
         "short_tools": [
-            "cp_display_data_on_image",
-            "cp_gray_to_color",
-            "cp_identify_primary_objects",
-            "idr_download_by_ids",
-            "cp_measure_image_intensity",
-            "cp_measure_image_area_occupied",
-            "cp_measure_image_quality",
-            "cp_common",
-            "cp_measure_granularity",
-            "cp_enhance_or_suppress_features",
-            "cp_measure_texture",
-            "cp_convert_objects_to_image",
-            "cp_cellprofiler",
-            "cp_measure_object_intensity",
-            "cp_export_to_spreadsheet",
-            "cp_relate_objects",
-            "cp_measure_object_size_shape",
-            "cp_save_images",
-            "cp_mask_image",
-            "cp_image_math"
+            "jbrowse",
+            "busco",
+            "fasta-stats",
+            "maker_map_ids",
+            "jcvi_gff_stats",
+            "gffread",
+            "maker"
         ],
-        "slides": true,
+        "slides": false,
         "slides_recordings": false,
+        "subtopic": "eukaryote",
         "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ],
+            "exact": [],
             "inexact": [
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
-        "time_estimation": "4H",
-        "title": "Nucleoli segmentation and feature extraction using CellProfiler",
+        "tags": [
+            "gmod",
+            "eukaryote",
+            "maker",
+            "jbrowse1"
+        ],
+        "time_estimation": "2h",
+        "title": "Genome annotation with Maker (short)",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_display_data_on_image/cp_display_data_on_image/3.1.9",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_enhance_or_suppress_features/cp_enhance_or_suppress_features/3.1.9",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_gray_to_color/cp_gray_to_color/3.1.9",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_image_math/cp_image_math/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_mask_image/cp_mask_image/3.1.9",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_granularity/cp_measure_granularity/3.1.9",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_area_occupied/cp_measure_image_area_occupied/3.1.9",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_intensity/cp_measure_image_intensity/3.1.9",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_quality/cp_measure_image_quality/3.1.9",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_texture/cp_measure_texture/3.1.9",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_relate_objects/cp_relate_objects/3.1.9",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9",
-            "toolshed.g2.bx.psu.edu/repos/iuc/idr_download_by_ids/idr_download_by_ids/0.41"
+            "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.10",
+            "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10",
+            "toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0"
         ],
-        "topic_name": "imaging",
-        "topic_name_human": "Imaging",
+        "topic_name": "genome-annotation",
+        "topic_name_human": "Genome Annotation",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "tutorial-CP",
+        "tutorial_name": "annotation-with-maker-short",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/imaging/tutorials/tutorial-CP/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/tutorial-CP/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/tutorial-CP/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker-short/tutorial.json"
         },
-        "version": 8,
+        "version": 3,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 229,
-        "visitors": 2067019,
+        "visit_duration": 189,
+        "visitors": 2836,
         "workflows": [
             {
                 "creators": [],
-                "description": "Nucleoli segmentation and feature extraction using CellProfiler",
+                "description": "Genome annotation with Maker (short)",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Starting modules\"]\n  1[label=\"Download images\"]\n  2[label=\"Segment complete nuclei\"]\n  0 -> 2 [label=\"output_pipeline\"]\n  3[label=\"Segmentation mask complete nuclei\"]\n  2 -> 3 [label=\"output_pipeline\"]\n  4[label=\"Label nuclei\"]\n  3 -> 4 [label=\"output_pipeline\"]\n  5[label=\"Save labelled nuclei\"]\n  4 -> 5 [label=\"output_pipeline\"]\n  6[label=\"Detect dark holes in nuclei\"]\n  5 -> 6 [label=\"output_pipeline\"]\n  7[label=\"Segment nucleoli that fall inside nuclei\"]\n  6 -> 7 [label=\"output_pipeline\"]\n  8[label=\"Segment nucleoli\"]\n  7 -> 8 [label=\"output_pipeline\"]\n  9[label=\"Convert the segmented nucleoli into an image\"]\n  8 -> 9 [label=\"output_pipeline\"]\n  10[label=\"Combine masks nuclei + nucleoli\"]\n  9 -> 10 [label=\"output_pipeline\"]\n  11[label=\"Save combined segmentation masks\"]\n  10 -> 11 [label=\"output_pipeline\"]\n  12[label=\"Segment all nuclei\"]\n  11 -> 12 [label=\"output_pipeline\"]\n  13[label=\"Segmentation mask nucleoli including cells touching borders\"]\n  12 -> 13 [label=\"output_pipeline\"]\n  14[label=\"Extract background\"]\n  13 -> 14 [label=\"output_pipeline\"]\n  15[label=\"Measure the image granularity\"]\n  14 -> 15 [label=\"output_pipeline\"]\n  16[label=\"Measure the nuclei texture\"]\n  15 -> 16 [label=\"output_pipeline\"]\n  17[label=\"Measure the nuclei intensity\"]\n  16 -> 17 [label=\"output_pipeline\"]\n  18[label=\"Measure size and shape of nuclei and nucleoli\"]\n  17 -> 18 [label=\"output_pipeline\"]\n  19[label=\"Relate nucleoli with their parent nuclei\"]\n  18 -> 19 [label=\"output_pipeline\"]\n  20[label=\"Measure the image quality\"]\n  19 -> 20 [label=\"output_pipeline\"]\n  21[label=\"Measure the area occupied by nuclei and nucleoli\"]\n  20 -> 21 [label=\"output_pipeline\"]\n  22[label=\"Measure the image intensity\"]\n  21 -> 22 [label=\"output_pipeline\"]\n  23[label=\"Export measurements\"]\n  22 -> 23 [label=\"output_pipeline\"]\n  24[label=\"Run CellProfiler\"]\n  1 -> 24 [label=\"output_tar\"]\n  23 -> 24 [label=\"output_pipeline\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenome sequence\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nProteins\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSNAP model\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAugustus model\"]\n  5[label=\"Fasta Statistics\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Busco\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Maker\"]\n  4 -> 7 [label=\"output\"]\n  3 -> 7 [label=\"output\"]\n  1 -> 7 [label=\"output\"]\n  0 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"Map annotation ids\"]\n  7 -> 8 [label=\"output_gff\"]\n  9[label=\"Genome annotation statistics\"]\n  8 -> 9 [label=\"renamed\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"gffread\"]\n  8 -> 10 [label=\"renamed\"]\n  0 -> 10 [label=\"output\"]\n  11[label=\"JBrowse\"]\n  0 -> 11 [label=\"output\"]\n  8 -> 11 [label=\"renamed\"]\n  7 -> 11 [label=\"output_evidences\"]\n  12[label=\"Busco\"]\n  10 -> 12 [label=\"output_exons\"]\n  k6951417bee0b4e0398e467d262e086dc[color=lightseagreen,label=\"Output\\nBusco summary final round\"]\n  12 -> k6951417bee0b4e0398e467d262e086dc\n}",
                 "history": [
                     {
-                        "hash": "bd719212c3b71090065923e9941d9f5efbb4e3e3",
-                        "message": "Update main_workflow.ga",
-                        "num": 7,
-                        "short_hash": "bd719212c",
-                        "unix": "1604492160"
+                        "hash": "005d964a2e8cb80f8d1bf0b304adc8f9d7c9ff76",
+                        "message": "fix workflows",
+                        "num": 2,
+                        "short_hash": "005d964a2",
+                        "unix": "1609752597"
                     },
                     {
-                        "hash": "e060051254138ba425caa5775fc10bc5ac93c33e",
-                        "message": "add missing annotation field",
-                        "num": 6,
-                        "short_hash": "e06005125",
-                        "unix": "1604488703"
-                    },
+                        "hash": "774f2aa374452d48fd29ee85513c3dc3a7f137f5",
+                        "message": "update maker tutorial and add a short version",
+                        "num": 1,
+                        "short_hash": "774f2aa37",
+                        "unix": "1609431273"
+                    }
+                ],
+                "inputs": [
                     {
-                        "hash": "ceef3fe076a86ac8ecc50eba9b77ff192385ab60",
-                        "message": "add tag imaging",
-                        "num": 5,
-                        "short_hash": "ceef3fe07",
-                        "unix": "1604444072"
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Genome sequence"
+                            }
+                        ],
+                        "label": "Genome sequence",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 94.08332824707031,
+                            "height": 82.19999694824219,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 11.883331298828125,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 11.883331298828125
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "a361a75e-5fa4-44ca-a4b7-cc9054a73054",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "9a09d16c-18af-4605-8416-4966fe918677"
+                            }
+                        ]
                     },
                     {
-                        "hash": "28a7fb28b785ae9b4804700a389d2334dc0eeb63",
-                        "message": "Update main_workflow.ga",
-                        "num": 4,
-                        "short_hash": "28a7fb28b",
-                        "unix": "1604443613"
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "EST and/or cDNA"
+                            }
+                        ],
+                        "label": "EST and/or cDNA",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 214.0833282470703,
+                            "height": 82.19999694824219,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 131.88333129882812,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 131.88333129882812
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "6b3edbe9-085d-46ae-9ae3-96e876c003e0",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "c5c5fb8f-9932-499c-b404-c142aedd1aa5"
+                            }
+                        ]
                     },
                     {
-                        "hash": "a3a14fb9052dfae1f59ddec213fe4850779b2f1e",
-                        "message": "add annotation and tags to the wf",
-                        "num": 3,
-                        "short_hash": "a3a14fb90",
-                        "unix": "1593000970"
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Proteins"
+                            }
+                        ],
+                        "label": "Proteins",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 313.68333435058594,
+                            "height": 61.80000305175781,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 251.88333129882812,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 251.88333129882812
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ce4ee756-1713-4e6a-898c-b85a834712bc",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "cbbe9e59-ccd5-4925-a7a3-e1d094284fca"
+                            }
+                        ]
                     },
                     {
-                        "hash": "8fdf6cf2d432e514ebb2fd0a79ede703f2f36efb",
-                        "message": "format wf",
-                        "num": 2,
-                        "short_hash": "8fdf6cf2d",
-                        "unix": "1592999030"
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "SNAP model"
+                            }
+                        ],
+                        "label": "SNAP model",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 413.68333435058594,
+                            "height": 61.80000305175781,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 351.8833312988281,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 351.8833312988281
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ebf1f01c-e804-462a-92cf-670012b103b3",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "ecfd7af4-f95c-4b2d-9f06-8e851a0c4d9e"
+                            }
+                        ]
                     },
                     {
-                        "hash": "82051aef73313659e45e3e3fa243c84ca022dce4",
-                        "message": "training_init",
-                        "num": 1,
-                        "short_hash": "82051aef7",
-                        "unix": "1592558689"
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Augustus model"
+                            }
+                        ],
+                        "label": "Augustus model",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 554.0833282470703,
+                            "height": 82.19999694824219,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 471.8833312988281,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 471.8833312988281
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "586af078-09ce-476b-9eb7-55e443a8eeaf",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "7259eb8b-9c2d-4eff-a49d-1b447e905314"
+                            }
+                        ]
                     }
                 ],
-                "inputs": [],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"Starting modules\"];\n  1[\"Download images\"];\n  2[\"Segment complete nuclei\"];\n  0 -->|output_pipeline| 2;\n  3[\"Segmentation mask complete nuclei\"];\n  2 -->|output_pipeline| 3;\n  4[\"Label nuclei\"];\n  3 -->|output_pipeline| 4;\n  5[\"Save labelled nuclei\"];\n  4 -->|output_pipeline| 5;\n  6[\"Detect dark holes in nuclei\"];\n  5 -->|output_pipeline| 6;\n  7[\"Segment nucleoli that fall inside nuclei\"];\n  6 -->|output_pipeline| 7;\n  8[\"Segment nucleoli\"];\n  7 -->|output_pipeline| 8;\n  9[\"Convert the segmented nucleoli into an image\"];\n  8 -->|output_pipeline| 9;\n  10[\"Combine masks nuclei + nucleoli\"];\n  9 -->|output_pipeline| 10;\n  11[\"Save combined segmentation masks\"];\n  10 -->|output_pipeline| 11;\n  12[\"Segment all nuclei\"];\n  11 -->|output_pipeline| 12;\n  13[\"Segmentation mask nucleoli including cells touching borders\"];\n  12 -->|output_pipeline| 13;\n  14[\"Extract background\"];\n  13 -->|output_pipeline| 14;\n  15[\"Measure the image granularity\"];\n  14 -->|output_pipeline| 15;\n  16[\"Measure the nuclei texture\"];\n  15 -->|output_pipeline| 16;\n  17[\"Measure the nuclei intensity\"];\n  16 -->|output_pipeline| 17;\n  18[\"Measure size and shape of nuclei and nucleoli\"];\n  17 -->|output_pipeline| 18;\n  19[\"Relate nucleoli with their parent nuclei\"];\n  18 -->|output_pipeline| 19;\n  20[\"Measure the image quality\"];\n  19 -->|output_pipeline| 20;\n  21[\"Measure the area occupied by nuclei and nucleoli\"];\n  20 -->|output_pipeline| 21;\n  22[\"Measure the image intensity\"];\n  21 -->|output_pipeline| 22;\n  23[\"Export measurements\"];\n  22 -->|output_pipeline| 23;\n  24[\"Run CellProfiler\"];\n  1 -->|output_tar| 24;\n  23 -->|output_pipeline| 24;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "CP_pipeline_IDR_training",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGenome sequence\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nProteins\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nSNAP model\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nAugustus model\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Fasta Statistics\"];\n  0 -->|output| 5;\n  6[\"Busco\"];\n  0 -->|output| 6;\n  7[\"Maker\"];\n  4 -->|output| 7;\n  3 -->|output| 7;\n  1 -->|output| 7;\n  0 -->|output| 7;\n  2 -->|output| 7;\n  8[\"Map annotation ids\"];\n  7 -->|output_gff| 8;\n  9[\"Genome annotation statistics\"];\n  8 -->|renamed| 9;\n  0 -->|output| 9;\n  10[\"gffread\"];\n  8 -->|renamed| 10;\n  0 -->|output| 10;\n  11[\"JBrowse\"];\n  0 -->|output| 11;\n  8 -->|renamed| 11;\n  7 -->|output_evidences| 11;\n  12[\"Busco\"];\n  10 -->|output_exons| 12;\n  6951417b-ee0b-4e03-98e4-67d262e086dc[\"Output\\nBusco summary final round\"];\n  12 --> 6951417b-ee0b-4e03-98e4-67d262e086dc;\n  style 6951417b-ee0b-4e03-98e4-67d262e086dc stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Genome annotation with Maker (short)",
                 "outputs": [
                     {
-                        "annotation": "Detail the metadata associated to the images that will be processed",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9",
+                        "annotation": "",
+                        "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "Starting modules",
-                        "name": "Starting Modules",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "output_pipeline",
-                                "type": "txt"
+                                "description": "",
+                                "name": "Genome sequence"
                             }
                         ],
+                        "label": "Genome sequence",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 219
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9",
-                        "tool_shed_repository": {
-                            "changeset_revision": "27396311a314",
-                            "name": "cp_common",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 94.08332824707031,
+                            "height": 82.19999694824219,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 11.883331298828125,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 11.883331298828125
                         },
-                        "tool_state": "{\"groups\": {\"con_groups\": {\"group_images\": \"Yes\", \"__current_case__\": 0, \"group_category\": \"field1\"}}, \"images\": {\"filter_images\": \"Images only\"}, \"metadata\": {\"con_metadata_extraction\": {\"extract\": \"Yes\", \"__current_case__\": 0, \"extraction_method\": [{\"__index__\": 0, \"metadata_extraction_method\": \"Extract from file/folder names\", \"con_metadata_source\": {\"metadata_source\": \"File name\", \"__current_case__\": 0, \"file_name_regex\": \"(?P<field1>.*)__(?P<field2>[a-zA-Z0-9]+)__(?P<field3>[a-zA-Z0-9]+)__(?P<field4>[a-zA-Z0-9]+)__(?P<field5>[a-zA-Z0-9]+)__(?P<field6>[a-zA-Z0-9]+)\"}, \"con_metadata_extract_from\": {\"extract_metadata_from\": \"All images\", \"__current_case__\": 1}}]}}, \"nameandtypes\": {\"pixel_space\": {\"process_3d\": \"No\", \"__current_case__\": 1}, \"con_assign_a_name_to\": {\"assign_a_name_to\": \"All images\", \"__current_case__\": 0, \"name_to_assign\": \"DNA\", \"con_select_image_type\": {\"select_image_type\": \"Grayscale image\", \"__current_case__\": 0, \"con_set_intensity\": {\"set_intensity_range_from\": \"Image metadata\", \"__current_case__\": 1}}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
-                        "type": "tool",
-                        "uuid": "9cb7aa2c-b60c-4a5b-9653-fa41ab465e94",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "a361a75e-5fa4-44ca-a4b7-cc9054a73054",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "6e8dc853-a475-401f-b276-c6ab024681fc"
+                                "output_name": "output",
+                                "uuid": "9a09d16c-18af-4605-8416-4966fe918677"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/idr_download_by_ids/idr_download_by_ids/0.41",
+                        "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "Download images",
-                        "name": "IDR Download",
-                        "outputs": [
-                            {
-                                "name": "out_log",
-                                "type": "txt"
-                            },
+                        "inputs": [
                             {
-                                "name": "output_tar",
-                                "type": "tar"
+                                "description": "",
+                                "name": "EST and/or cDNA"
                             }
                         ],
+                        "label": "EST and/or cDNA",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 241.25
-                        },
-                        "post_job_actions": {
-                            "EmailActionout_log": {
-                                "action_arguments": {},
-                                "action_type": "EmailAction",
-                                "output_name": "out_log"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/idr_download_by_ids/idr_download_by_ids/0.41",
-                        "tool_shed_repository": {
-                            "changeset_revision": "e08b1dc0480c",
-                            "name": "idr_download_by_ids",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 214.0833282470703,
+                            "height": 82.19999694824219,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 131.88333129882812,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 131.88333129882812
                         },
-                        "tool_state": "{\"channel\": \"Cy3\", \"clip_image\": {\"select\": \"\", \"__current_case__\": 0}, \"download_tar\": \"true\", \"frame\": \"0\", \"image_ids\": {\"source\": \"link\", \"__current_case__\": 0, \"id_spec\": \"http://idr.openmicroscopy.org/webclient/?show=image-295900|image-295905|image-295910|image-295918|image-295928|image-295934\"}, \"skip_failed\": \"true\", \"z_section\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.41",
-                        "type": "tool",
-                        "uuid": "682880bc-d35f-4f77-996e-7600de735da6",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "6b3edbe9-085d-46ae-9ae3-96e876c003e0",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_log",
-                                "uuid": "ff013d1c-7570-4720-8b15-6689021807d5"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_tar",
-                                "uuid": "b94d5196-23db-4340-aa58-c082fc5ca449"
+                                "output_name": "output",
+                                "uuid": "c5c5fb8f-9932-499c-b404-c142aedd1aa5"
                             }
                         ]
                     },
                     {
-                        "annotation": "Incomplete nuclei that are touching the borders of the image are ignored and therefore, not segmented. It doesn't include the nuclei outside the diameter range either.",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9",
+                        "annotation": "",
+                        "content_id": null,
                         "errors": null,
                         "id": 2,
-                        "input_connections": {
-                            "input_pipeline": {
-                                "id": 0,
-                                "output_name": "output_pipeline"
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Proteins"
                             }
+                        ],
+                        "label": "Proteins",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 313.68333435058594,
+                            "height": 61.80000305175781,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 251.88333129882812,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 251.88333129882812
                         },
-                        "inputs": [],
-                        "label": "Segment complete nuclei",
-                        "name": "IdentifyPrimaryObjects",
-                        "outputs": [
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ce4ee756-1713-4e6a-898c-b85a834712bc",
+                        "workflow_outputs": [
                             {
-                                "name": "output_pipeline",
-                                "type": "txt"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "cbbe9e59-ccd5-4925-a7a3-e1d094284fca"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "SNAP model"
                             }
                         ],
+                        "label": "SNAP model",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 272.75,
-                            "top": 219
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9",
-                        "tool_shed_repository": {
-                            "changeset_revision": "52c01fb29b2a",
-                            "name": "cp_identify_primary_objects",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"con_advanced\": {\"advanced\": \"Yes\", \"__current_case__\": 1, \"input_from_nat\": \"DNA\", \"name_to_be_identified\": \"Nuclei\", \"min_diameter\": \"15\", \"max_diameter\": \"200\", \"discard_outside_border\": \"Yes\", \"discard_touching_border\": \"Yes\", \"con_threshold_strategy\": {\"threshold_strategy\": \"Global\", \"__current_case__\": 1, \"con_threshold_method\": {\"threshold_method\": \"Otsu\", \"__current_case__\": 0, \"con_threshold_class\": {\"threshold_class\": \"Two classes\", \"__current_case__\": 1}, \"threshold_smoothing_scale\": \"1.3488\", \"threshold_correction_factor\": \"0.9\", \"threshold_lower\": \"0.0\", \"threshold_upper\": \"1.0\"}}, \"con_distinguish_clumped_objects\": {\"distinguish_clumped_objects\": \"Shape\", \"__current_case__\": 0, \"con_dividing_lines\": {\"dividing_lines\": \"Shape\", \"__current_case__\": 0, \"con_smoothing_filter\": {\"smoothing_filter\": \"Yes\", \"__current_case__\": 1}, \"con_min_distance\": {\"min_distance\": \"Yes\", \"__current_case__\": 1}, \"speed_up\": \"Yes\"}}, \"fill_hole\": \"After both thresholding and declumping\", \"con_handling_excessive\": {\"excessive_handling\": \"Continue\", \"__current_case__\": 1}}, \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
-                        "type": "tool",
-                        "uuid": "1614fb83-6565-4534-9a42-03e9d5c21a75",
+                            "bottom": 413.68333435058594,
+                            "height": 61.80000305175781,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 351.8833312988281,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 351.8833312988281
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ebf1f01c-e804-462a-92cf-670012b103b3",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "efff5d2f-aa7d-406a-8927-f373feb57837"
+                                "output_name": "output",
+                                "uuid": "ecfd7af4-f95c-4b2d-9f06-8e851a0c4d9e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9",
+                        "content_id": null,
                         "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "input_pipeline": {
-                                "id": 2,
-                                "output_name": "output_pipeline"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Segmentation mask complete nuclei",
-                        "name": "ConvertObjectsToImage",
-                        "outputs": [
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output_pipeline",
-                                "type": "txt"
+                                "description": "",
+                                "name": "Augustus model"
                             }
                         ],
+                        "label": "Augustus model",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 353.5,
-                            "top": 219
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2690da374874",
-                            "name": "cp_convert_objects_to_image",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 554.0833282470703,
+                            "height": 82.19999694824219,
+                            "left": -313.33331298828125,
+                            "right": -113.33331298828125,
+                            "top": 471.8833312988281,
+                            "width": 200,
+                            "x": -313.33331298828125,
+                            "y": 471.8833312988281
                         },
-                        "tool_state": "{\"con_color_format\": {\"color_format\": \"Binary (black & white)\", \"__current_case__\": 0}, \"input_object\": \"Nuclei\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"name_output_image\": \"MaskNuclei\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
-                        "type": "tool",
-                        "uuid": "dc500b23-6fb7-4daa-85f1-53f66b034826",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "586af078-09ce-476b-9eb7-55e443a8eeaf",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "3c7575e4-4094-4e19-9778-801325f82df9"
+                                "output_name": "output",
+                                "uuid": "7259eb8b-9c2d-4eff-a49d-1b447e905314"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_display_data_on_image/cp_display_data_on_image/3.1.9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0",
                         "errors": null,
-                        "id": 4,
+                        "id": 5,
                         "input_connections": {
-                            "input_pipeline": {
-                                "id": 3,
-                                "output_name": "output_pipeline"
+                            "dataset": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "Label nuclei",
-                        "name": "DisplayDataOnImage",
+                        "label": null,
+                        "name": "Fasta Statistics",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
-                                "type": "txt"
+                                "name": "stats",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 434.25,
-                            "top": 219
+                            "bottom": 34.28334045410156,
+                            "height": 154.40000915527344,
+                            "left": -15.350006103515625,
+                            "right": 184.64999389648438,
+                            "top": -120.11666870117188,
+                            "width": 200,
+                            "x": -15.350006103515625,
+                            "y": -120.11666870117188
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_display_data_on_image/cp_display_data_on_image/3.1.9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "4e12ef887a2a",
-                            "name": "cp_display_data_on_image",
-                            "owner": "bgruening",
+                            "changeset_revision": "20ca2574216a",
+                            "name": "fasta_stats",
+                            "owner": "simon-gladman",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"con_display_mode\": {\"display_mode\": \"Text\", \"__current_case__\": 0, \"text_color\": \"#ff0000\", \"font_size\": \"11\", \"number_of_decimals\": \"0\", \"annotation_offset\": \"0\"}, \"con_display_obj_image\": {\"display_obj_image\": \"Object\", \"__current_case__\": 0, \"select_input_obj\": \"Nuclei\", \"con_obj_measurement_category\": {\"measurement_category\": \"Number\", \"__current_case__\": 0, \"measurement\": \"Object_Number\"}}, \"display_background_image\": \"Yes\", \"element_to_save\": \"Image\", \"image_to_display_measurements\": \"DNA\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"name_output_image\": \"ImageDisplay\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
+                        "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
                         "type": "tool",
-                        "uuid": "d74959c7-b1f5-47a4-8272-b3de8adaf04a",
+                        "uuid": "43cab601-f700-4278-bd0a-7f0997cf75cf",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "113e8d23-a9e2-45a1-9d40-1e26d4f23456"
+                                "output_name": "stats",
+                                "uuid": "7840b5e6-2a7e-4b3c-bea3-4a0d70fea21b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
                         "errors": null,
-                        "id": 5,
+                        "id": 6,
                         "input_connections": {
-                            "input_pipeline": {
-                                "id": 4,
-                                "output_name": "output_pipeline"
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "Save labelled nuclei",
-                        "name": "SaveImages",
+                        "label": null,
+                        "name": "Busco",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
+                                "name": "busco_sum",
                                 "type": "txt"
+                            },
+                            {
+                                "name": "busco_table",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "busco_missing",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 515,
-                            "top": 219
+                            "bottom": -157.71664428710938,
+                            "height": 276.4000244140625,
+                            "left": -15.350006103515625,
+                            "right": 184.64999389648438,
+                            "top": -434.1166687011719,
+                            "width": 200,
+                            "x": -15.350006103515625,
+                            "y": -434.1166687011719
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "a45d360ae9d9",
-                            "name": "cp_save_images",
-                            "owner": "bgruening",
+                            "changeset_revision": "602fb8e63aa7",
+                            "name": "busco",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"con_method_for_constructing\": {\"method_for_constructing\": \"From image filename\", \"__current_case__\": 0, \"name_for_file_prefix\": \"DNA\", \"con_append_suffix\": {\"append_suffix\": \"Yes\", \"__current_case__\": 0, \"text_to_append\": \"_nucleiNumbers\"}}, \"con_type_of_image\": {\"type_of_image\": \"Image\", \"__current_case__\": 0, \"con_save_file_format\": {\"file_format\": \"tiff\", \"__current_case__\": 0, \"bit_depth\": \"8-bit integer\"}}, \"image_to_save\": \"ImageDisplay\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"overwrite_without_warning\": \"Yes\", \"record_info\": \"No\", \"when_to_save\": \"Every cycle\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
+                        "tool_state": "{\"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"geno\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.1.4",
                         "type": "tool",
-                        "uuid": "32d4b134-e681-484b-a46d-6fb511358a39",
+                        "uuid": "876334be-d7e5-4504-bb1b-727472839c02",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "b1aa7814-3057-4f2f-8c8d-48aa7c1a7fa5"
+                                "output_name": "busco_sum",
+                                "uuid": "59ce9dc8-762f-4c38-aded-5d031db50609"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "busco_missing",
+                                "uuid": "9b000535-1702-4888-951c-4cc8e782a511"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "busco_table",
+                                "uuid": "76c0d8fc-4e81-4ba0-b8b2-ebfda0ba5786"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_enhance_or_suppress_features/cp_enhance_or_suppress_features/3.1.9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10",
                         "errors": null,
-                        "id": 6,
+                        "id": 8,
                         "input_connections": {
-                            "input_pipeline": {
-                                "id": 5,
-                                "output_name": "output_pipeline"
+                            "maker_gff": {
+                                "id": 7,
+                                "output_name": "output_gff"
                             }
                         },
                         "inputs": [],
-                        "label": "Detect dark holes in nuclei",
-                        "name": "EnhanceOrSuppressFeatures",
+                        "label": null,
+                        "name": "Map annotation ids",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
-                                "type": "txt"
+                                "name": "renamed",
+                                "type": "gff"
+                            },
+                            {
+                                "name": "id_map",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 595.75,
-                            "top": 219
+                            "bottom": 318.8833312988281,
+                            "height": 246,
+                            "left": 272.66668701171875,
+                            "right": 472.66668701171875,
+                            "top": 72.88333129882812,
+                            "width": 200,
+                            "x": 272.66668701171875,
+                            "y": 72.88333129882812
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_enhance_or_suppress_features/cp_enhance_or_suppress_features/3.1.9",
+                        "post_job_actions": {
+                            "ChangeDatatypeActionrenamed": {
+                                "action_arguments": {
+                                    "newtype": "gff3"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "renamed"
+                            },
+                            "HideDatasetActionid_map": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "id_map"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10",
                         "tool_shed_repository": {
-                            "changeset_revision": "3f9747bda8c4",
-                            "name": "cp_enhance_or_suppress_features",
-                            "owner": "bgruening",
+                            "changeset_revision": "f1912d5575df",
+                            "name": "maker_map_ids",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"con_enhance_suppress\": {\"select_operation\": \"Enhance\", \"__current_case__\": 0, \"con_feature_type\": {\"feature_type\": \"Dark holes\", \"__current_case__\": 2, \"min_hole_size\": \"1\", \"max_hole_size\": \"15\"}}, \"input_image\": \"DNA\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"name_output_image\": \"DNAdarkholes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
+                        "tool_state": "{\"justify\": \"6\", \"maker_gff\": {\"__class__\": \"ConnectedValue\"}, \"prefix\": \"TEST\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.31.11",
                         "type": "tool",
-                        "uuid": "2704e748-66d4-4a32-a9eb-459f65f58eb0",
+                        "uuid": "b1127093-0aae-4bfa-b474-042b838a8299",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "fd53651d-06fb-4d6a-b65b-dd686dcb0fcc"
+                                "output_name": "renamed",
+                                "uuid": "e8686326-b443-402b-bb0e-b4a02a8815a7"
                             }
                         ]
                     },
                     {
-                        "annotation": "The dark holes enhanced in the previous step are segmented only if they are inside a nuclei",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_mask_image/cp_mask_image/3.1.9",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
                         "errors": null,
-                        "id": 7,
+                        "id": 9,
                         "input_connections": {
-                            "input_pipeline": {
-                                "id": 6,
-                                "output_name": "output_pipeline"
+                            "gff": {
+                                "id": 8,
+                                "output_name": "renamed"
+                            },
+                            "ref_genome|genome": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "Segment nucleoli that fall inside nuclei",
-                        "name": "MaskImage",
+                        "label": null,
+                        "name": "Genome annotation statistics",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
+                                "name": "summary",
                                 "type": "txt"
+                            },
+                            {
+                                "name": "graphs",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "left": 677.75,
-                            "top": 219
+                            "bottom": 363.2833557128906,
+                            "height": 276.4000244140625,
+                            "left": 560.6500244140625,
+                            "right": 760.6500244140625,
+                            "top": 86.88333129882812,
+                            "width": 200,
+                            "x": 560.6500244140625,
+                            "y": 86.88333129882812
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_mask_image/cp_mask_image/3.1.9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
                         "tool_shed_repository": {
-                            "changeset_revision": "ca1421f7e3ed",
-                            "name": "cp_mask_image",
-                            "owner": "bgruening",
+                            "changeset_revision": "8cffbd184762",
+                            "name": "jcvi_gff_stats",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"con_img_obj\": {\"img_obj\": \"Objects\", \"__current_case__\": 0, \"select_obj\": \"Nuclei\"}, \"input_image\": \"DNAdarkholes\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"invert_mask\": \"No\", \"name_output_image\": \"MaskDNAdarkholes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
+                        "tool_state": "{\"gff\": {\"__class__\": \"ConnectedValue\"}, \"ref_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.8.4",
                         "type": "tool",
-                        "uuid": "32492729-4cd6-419e-9429-4fdf91410591",
+                        "uuid": "14236032-ec57-4beb-ab0a-e44bf845643c",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "da3978ac-fb7a-4095-80d8-df2fad05b747"
+                                "output_name": "graphs",
+                                "uuid": "782e21db-4be6-4230-92b5-3ea9004dda04"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "summary",
+                                "uuid": "a4dff39c-0479-4a25-ac62-b132c1083604"
                             }
                         ]
                     },
                     {
-                        "annotation": "The segmentation only affects those inside the nuclei",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1",
                         "errors": null,
-                        "id": 8,
+                        "id": 10,
                         "input_connections": {
-                            "input_pipeline": {
-                                "id": 7,
-                                "output_name": "output_pipeline"
+                            "input": {
+                                "id": 8,
+                                "output_name": "renamed"
+                            },
+                            "reference_genome|genome_fasta": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": "Segment nucleoli",
-                        "name": "IdentifyPrimaryObjects",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool gffread",
+                                "name": "chr_replace"
+                            }
+                        ],
+                        "label": null,
+                        "name": "gffread",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
-                                "type": "txt"
+                                "name": "output_exons",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "output_cds",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "output_pep",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 758.5,
-                            "top": 219
+                            "bottom": 48.683319091796875,
+                            "height": 316.79998779296875,
+                            "left": 560.6500244140625,
+                            "right": 760.6500244140625,
+                            "top": -268.1166687011719,
+                            "width": 200,
+                            "x": 560.6500244140625,
+                            "y": -268.1166687011719
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "52c01fb29b2a",
-                            "name": "cp_identify_primary_objects",
-                            "owner": "bgruening",
+                            "changeset_revision": "0232f19d300f",
+                            "name": "gffread",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"con_advanced\": {\"advanced\": \"Yes\", \"__current_case__\": 1, \"input_from_nat\": \"MaskDNAdarkholes\", \"name_to_be_identified\": \"Nucleoli\", \"min_diameter\": \"2\", \"max_diameter\": \"15\", \"discard_outside_border\": \"Yes\", \"discard_touching_border\": \"No\", \"con_threshold_strategy\": {\"threshold_strategy\": \"Global\", \"__current_case__\": 1, \"con_threshold_method\": {\"threshold_method\": \"Otsu\", \"__current_case__\": 0, \"con_threshold_class\": {\"threshold_class\": \"Two classes\", \"__current_case__\": 1}, \"threshold_smoothing_scale\": \"1.3488\", \"threshold_correction_factor\": \"0.9\", \"threshold_lower\": \"0.0\", \"threshold_upper\": \"1.0\"}}, \"con_distinguish_clumped_objects\": {\"distinguish_clumped_objects\": \"Shape\", \"__current_case__\": 0, \"con_dividing_lines\": {\"dividing_lines\": \"Shape\", \"__current_case__\": 0, \"con_smoothing_filter\": {\"smoothing_filter\": \"Yes\", \"__current_case__\": 1}, \"con_min_distance\": {\"min_distance\": \"Yes\", \"__current_case__\": 1}, \"speed_up\": \"Yes\"}}, \"fill_hole\": \"After both thresholding and declumping\", \"con_handling_excessive\": {\"excessive_handling\": \"Continue\", \"__current_case__\": 1}}, \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
+                        "tool_state": "{\"chr_replace\": {\"__class__\": \"RuntimeValue\"}, \"decode_url\": \"false\", \"expose\": \"false\", \"filtering\": null, \"full_gff_attribute_preservation\": \"false\", \"gffs\": {\"gff_fmt\": \"none\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"maxintron\": \"\", \"merging\": {\"merge_sel\": \"none\", \"__current_case__\": 0}, \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 2, \"genome_fasta\": {\"__class__\": \"ConnectedValue\"}, \"ref_filtering\": null, \"fa_outputs\": [\"-w exons.fa\", \"-x cds.fa\", \"-y pep.fa\"]}, \"region\": {\"region_filter\": \"none\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.2.1.1",
                         "type": "tool",
-                        "uuid": "d9cd434a-3fca-4e45-8e73-6c8791af8304",
+                        "uuid": "3b5ecaf4-2d08-42f8-a6f0-f05ad9e5fe92",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "dbf37c30-6e43-4d38-9584-b40946194283"
+                                "output_name": "output_cds",
+                                "uuid": "0df7b9b5-1ed1-4cf4-b483-a604862f4540"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_exons",
+                                "uuid": "f485f8fe-0d63-49ba-a88d-dfc8e03db553"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_pep",
+                                "uuid": "7430528c-9af5-4e05-ba6c-bbf95f19ad7e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3",
                         "errors": null,
-                        "id": 9,
+                        "id": 11,
                         "input_connections": {
-                            "input_pipeline": {
+                            "reference_genome|genome": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "track_groups_0|data_tracks_0|data_format|annotation": {
                                 "id": 8,
-                                "output_name": "output_pipeline"
+                                "output_name": "renamed"
+                            },
+                            "track_groups_1|data_tracks_0|data_format|annotation": {
+                                "id": 7,
+                                "output_name": "output_evidences"
                             }
                         },
-                        "inputs": [],
-                        "label": "Convert the segmented nucleoli into an image",
-                        "name": "ConvertObjectsToImage",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool JBrowse",
+                                "name": "reference_genome"
+                            }
+                        ],
+                        "label": null,
+                        "name": "JBrowse",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
-                                "type": "txt"
+                                "name": "output",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 839.25,
-                            "top": 219
+                            "bottom": 677.2833557128906,
+                            "height": 276.4000244140625,
+                            "left": 560.6500244140625,
+                            "right": 760.6500244140625,
+                            "top": 400.8833312988281,
+                            "width": 200,
+                            "x": 560.6500244140625,
+                            "y": 400.8833312988281
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3",
                         "tool_shed_repository": {
-                            "changeset_revision": "2690da374874",
-                            "name": "cp_convert_objects_to_image",
-                            "owner": "bgruening",
+                            "changeset_revision": "8774b28235bb",
+                            "name": "jbrowse",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"con_color_format\": {\"color_format\": \"Binary (black & white)\", \"__current_case__\": 0}, \"input_object\": \"Nucleoli\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"name_output_image\": \"MaskNucleoli\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
+                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Maker annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 1, \"category\": \"Maker evidences\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"true\", \"__current_case__\": 0, \"name\": {\"__class__\": \"RuntimeValue\"}}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.10+galaxy0",
                         "type": "tool",
-                        "uuid": "549c3604-1951-49d5-b170-de37f295f3ac",
+                        "uuid": "5a978f9d-7adc-4e30-8b20-dcfa27f18dfa",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "9082f1cc-35ee-4993-975e-592fe84143a9"
+                                "output_name": "output",
+                                "uuid": "c7432de7-b6b4-457a-8c0a-69c44418234d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_gray_to_color/cp_gray_to_color/3.1.9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
                         "errors": null,
-                        "id": 10,
+                        "id": 12,
                         "input_connections": {
-                            "input_pipeline": {
-                                "id": 9,
-                                "output_name": "output_pipeline"
+                            "input": {
+                                "id": 10,
+                                "output_name": "output_exons"
                             }
                         },
                         "inputs": [],
-                        "label": "Combine masks (nuclei + nucleoli)",
-                        "name": "GrayToColor",
+                        "label": null,
+                        "name": "Busco",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
+                                "name": "busco_sum",
                                 "type": "txt"
+                            },
+                            {
+                                "name": "busco_table",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "busco_missing",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 920,
-                            "top": 219
+                            "bottom": 100.88333129882812,
+                            "height": 256,
+                            "left": 838.6666870117188,
+                            "right": 1038.6666870117188,
+                            "top": -155.11666870117188,
+                            "width": 200,
+                            "x": 838.6666870117188,
+                            "y": -155.11666870117188
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_gray_to_color/cp_gray_to_color/3.1.9",
+                        "post_job_actions": {
+                            "HideDatasetActionbusco_missing": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "busco_missing"
+                            },
+                            "HideDatasetActionbusco_table": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "busco_table"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "bbf1ef17c01b",
-                            "name": "cp_gray_to_color",
-                            "owner": "bgruening",
+                            "changeset_revision": "602fb8e63aa7",
+                            "name": "busco",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"con_color_scheme\": {\"color_scheme\": \"RGB\", \"__current_case__\": 0, \"rgb_red\": \"MaskNucleoli\", \"rgb_red_weight\": \"0.8\", \"rgb_green\": \"Leave this black\", \"rgb_green_weight\": \"1.0\", \"rgb_blue\": \"MaskNuclei\", \"rgb_blue_weight\": \"0.5\"}, \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"name_output_image\": \"CombinedMask\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
+                        "tool_state": "{\"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"tran\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.1.4",
                         "type": "tool",
-                        "uuid": "0e09f485-e2ff-4610-bf71-31cf1168ee6d",
+                        "uuid": "dee27b5d-de92-4e99-898c-3bf3fea6ee72",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "1a8affd0-4d20-4335-845a-367f12879a2f"
+                                "label": "Busco summary final round",
+                                "output_name": "busco_sum",
+                                "uuid": "6951417b-ee0b-4e03-98e4-67d262e086dc"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "genome-annotation/annotation-with-maker-short",
+                "path": "topics/genome-annotation/tutorials/annotation-with-maker-short/workflows/main_workflow.ga",
+                "tags": [
+                    "genome-annotation"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Genome annotation with Maker (short)",
+                "topic_id": "genome-annotation",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-annotation-with-maker-short/versions/main-workflow",
+                "tutorial_id": "annotation-with-maker-short",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-maker-short/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-maker-short/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "genome-annotation-annotation-with-maker-short",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.4+galaxy3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.10",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10",
+                    "toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0"
+                ],
+                "workflowhub_id": "1194"
+            }
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.4406623"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "augustus_training",
+                    "owner": "bgruening",
+                    "revisions": "6519ebe25019",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gffread",
+                    "owner": "devteam",
+                    "revisions": "69e0806b63a4",
+                    "tool_panel_section_label": "Convert Formats",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "busco",
+                    "owner": "iuc",
+                    "revisions": "602fb8e63aa7",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_stats",
+                    "owner": "iuc",
+                    "revisions": "9c620a950d3a",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "jbrowse",
+                    "owner": "iuc",
+                    "revisions": "6cd09d7b5f37",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "jcvi_gff_stats",
+                    "owner": "iuc",
+                    "revisions": "8cffbd184762",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "maker",
+                    "owner": "iuc",
+                    "revisions": "d46d803ca6cc",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "maker_map_ids",
+                    "owner": "iuc",
+                    "revisions": "e906fa778440",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "snap_training",
+                    "owner": "iuc",
+                    "revisions": "2a598c0aa042",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: augustus_training\n  owner: bgruening\n  revisions: 6519ebe25019\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gffread\n  owner: devteam\n  revisions: 69e0806b63a4\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 602fb8e63aa7\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n  owner: iuc\n  revisions: 9c620a950d3a\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 6cd09d7b5f37\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jcvi_gff_stats\n  owner: iuc\n  revisions: 8cffbd184762\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker\n  owner: iuc\n  revisions: d46d803ca6cc\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maker_map_ids\n  owner: iuc\n  revisions: e906fa778440\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snap_training\n  owner: iuc\n  revisions: 2a598c0aa042\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "eurosciencegateway",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
+                "fediverse_flavor": "mastodon",
+                "id": "abretaud",
+                "joined": "2017-09",
+                "location": {
+                    "country": "FR",
+                    "lat": 48.11,
+                    "lon": -1.64
+                },
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+            }
+        ],
+        "dir": "topics/genome-annotation/tutorials/annotation-with-maker",
+        "edam_operation": [
+            "Genome annotation",
+            "Ab-initio gene prediction",
+            "Genome visualisation",
+            "Genome assembly",
+            "Sequence assembly validation",
+            "Gene prediction",
+            "Homology-based gene prediction",
+            "Scaffolding",
+            "Sequence annotation",
+            "Operation",
+            "Transcriptome assembly"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.eu",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "genome-annotation/annotation-with-maker",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.org.au"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Maker allows to annotate a eukaryotic genome.",
+            "BUSCO and JBrowse allow to inspect the quality of an annotation."
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Advanced",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-02-29",
+        "objectives": [
+            "Load genome into Galaxy",
+            "Annotate genome with Maker",
+            "Evaluate annotation quality with BUSCO",
+            "View annotations in JBrowse"
+        ],
+        "pageviews": 21813,
+        "priority": 4,
+        "pub_date": "2018-09-24",
+        "questions": [
+            "How to annotate an eukaryotic genome?",
+            "How to evaluate and visualize annotated genomic features?"
+        ],
+        "short_id": "T00166",
+        "short_tools": [
+            "jbrowse",
+            "augustus_training",
+            "busco",
+            "fasta-stats",
+            "maker_map_ids",
+            "jcvi_gff_stats",
+            "snap_training",
+            "gffread",
+            "maker"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "eukaryote",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "gmod",
+            "eukaryote",
+            "jbrowse1",
+            "maker"
+        ],
+        "time_estimation": "4h",
+        "title": "Genome annotation with Maker",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3",
+            "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.11",
+            "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1"
+        ],
+        "topic_name": "genome-annotation",
+        "topic_name_human": "Genome Annotation",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "annotation-with-maker",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.json"
+        },
+        "version": 14,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 113,
+        "visitors": 11759,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0003-0914-2470",
+                        "name": "Anthony Bretaudeau"
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9",
+                        "class": "Organization",
+                        "name": "French National Institute for Agriculture, Food, and Environment (INRAE)"
+                    }
+                ],
+                "description": "Genome annotation with Maker",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nProtein sequences\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenome sequence\"]\n  3[label=\"Maker\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Fasta Statistics\"]\n  2 -> 4 [label=\"output\"]\n  k2d3829e6f5b946d183e317efff814e09[color=lightseagreen,label=\"Output\\nFasta Statistics on input dataset(s): Fasta summary stats\"]\n  4 -> k2d3829e6f5b946d183e317efff814e09\n  5[label=\"Busco\"]\n  2 -> 5 [label=\"output\"]\n  ka15e121423a2484b9c751635fcd61fe3[color=lightseagreen,label=\"Output\\nBUSCO: short summary\"]\n  5 -> ka15e121423a2484b9c751635fcd61fe3\n  k7806088df65743899d546a3bdfa233b2[color=lightseagreen,label=\"Output\\nBUSCO: list of missing ortholog genes\"]\n  5 -> k7806088df65743899d546a3bdfa233b2\n  k6a27d0f6d83c42b1a7af5f99ba5debe2[color=lightseagreen,label=\"Output\\nBUSCO: full table\"]\n  5 -> k6a27d0f6d83c42b1a7af5f99ba5debe2\n  6[label=\"Train Augustus\"]\n  2 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output_gff\"]\n  7[label=\"Genome annotation statistics\"]\n  3 -> 7 [label=\"output_gff\"]\n  2 -> 7 [label=\"output\"]\n  k2bed9aa65f22494d9caaf0ece8464f15[color=lightseagreen,label=\"Output\\nGenome annotation statistics: graphs (first round)\"]\n  7 -> k2bed9aa65f22494d9caaf0ece8464f15\n  k71d41ce2e90d435b9b64ab4320524770[color=lightseagreen,label=\"Output\\nGenome annotation statistics: summary (first round)\"]\n  7 -> k71d41ce2e90d435b9b64ab4320524770\n  8[label=\"gffread\"]\n  3 -> 8 [label=\"output_gff\"]\n  2 -> 8 [label=\"output\"]\n  9[label=\"Train SNAP\"]\n  2 -> 9 [label=\"output\"]\n  3 -> 9 [label=\"output_gff\"]\n  10[label=\"Busco\"]\n  8 -> 10 [label=\"output_exons\"]\n  ka79ab19d980242ca8ffa8c197a16c8b8[color=lightseagreen,label=\"Output\\nBusco summary first round\"]\n  10 -> ka79ab19d980242ca8ffa8c197a16c8b8\n  11[label=\"Maker\"]\n  6 -> 11 [label=\"output_tar\"]\n  9 -> 11 [label=\"output\"]\n  2 -> 11 [label=\"output\"]\n  3 -> 11 [label=\"output_full\"]\n  12[label=\"gffread\"]\n  11 -> 12 [label=\"output_gff\"]\n  2 -> 12 [label=\"output\"]\n  13[label=\"Train Augustus\"]\n  2 -> 13 [label=\"output\"]\n  11 -> 13 [label=\"output_gff\"]\n  k42d5aadd3a8c441d913fee8745a99b0b[color=lightseagreen,label=\"Output\\nAugus: trained model\"]\n  13 -> k42d5aadd3a8c441d913fee8745a99b0b\n  14[label=\"Genome annotation statistics\"]\n  11 -> 14 [label=\"output_gff\"]\n  2 -> 14 [label=\"output\"]\n  k9def2c6efd3c4969b5d4d13c187c1144[color=lightseagreen,label=\"Output\\nGenome annotation statistics: graphs (second round)\"]\n  14 -> k9def2c6efd3c4969b5d4d13c187c1144\n  k61f7a150a4a246b189f52170d466656e[color=lightseagreen,label=\"Output\\nGenome annotation statistics: summary (second round)\"]\n  14 -> k61f7a150a4a246b189f52170d466656e\n  15[label=\"Train SNAP\"]\n  2 -> 15 [label=\"output\"]\n  11 -> 15 [label=\"output_gff\"]\n  k458887f706614bdeab1a875aac6caed8[color=lightseagreen,label=\"Output\\nSNAP: trained model\"]\n  15 -> k458887f706614bdeab1a875aac6caed8\n  16[label=\"Busco\"]\n  12 -> 16 [label=\"output_exons\"]\n  kf52b1b410ea54384bd434927273c909c[color=lightseagreen,label=\"Output\\nBusco summary second round\"]\n  16 -> kf52b1b410ea54384bd434927273c909c\n  17[label=\"Maker\"]\n  13 -> 17 [label=\"output_tar\"]\n  15 -> 17 [label=\"output\"]\n  2 -> 17 [label=\"output\"]\n  11 -> 17 [label=\"output_full\"]\n  18[label=\"Map annotation ids\"]\n  17 -> 18 [label=\"output_gff\"]\n  k63575dcf54d14cb1b5fba2810b4da807[color=lightseagreen,label=\"Output\\nMap annotation ids: renamed GFF\"]\n  18 -> k63575dcf54d14cb1b5fba2810b4da807\n  19[label=\"JBrowse\"]\n  2 -> 19 [label=\"output\"]\n  3 -> 19 [label=\"output_gff\"]\n  18 -> 19 [label=\"renamed\"]\n  11 -> 19 [label=\"output_gff\"]\n  3 -> 19 [label=\"output_evidences\"]\n  11 -> 19 [label=\"output_evidences\"]\n  17 -> 19 [label=\"output_evidences\"]\n  k5a38ae83e17745f3aa9f4c1844584fa5[color=lightseagreen,label=\"Output\\nJBrowse: report\"]\n  19 -> k5a38ae83e17745f3aa9f4c1844584fa5\n  20[label=\"gffread\"]\n  18 -> 20 [label=\"renamed\"]\n  2 -> 20 [label=\"output\"]\n  k52fcac23b6124377a19a2e3b667a23e3[color=lightseagreen,label=\"Output\\nGffread: exons\"]\n  20 -> k52fcac23b6124377a19a2e3b667a23e3\n  k5c47c25e0ddb4adea5d0873ff4add28c[color=lightseagreen,label=\"Output\\nGffread: translation of cds\"]\n  20 -> k5c47c25e0ddb4adea5d0873ff4add28c\n  k84d9183b9589464b9f824dae7f87133e[color=lightseagreen,label=\"Output\\nGffread: cds\"]\n  20 -> k84d9183b9589464b9f824dae7f87133e\n  21[label=\"Genome annotation statistics\"]\n  18 -> 21 [label=\"renamed\"]\n  2 -> 21 [label=\"output\"]\n  kf5d4a6bf1ff8435a80847921e25bff3a[color=lightseagreen,label=\"Output\\nGenome annotation statistics: graphs (third round)\"]\n  21 -> kf5d4a6bf1ff8435a80847921e25bff3a\n  k5a863bd410f24ac881b6ce8b7f663e42[color=lightseagreen,label=\"Output\\nGenome annotation statistics: summary (third round)\"]\n  21 -> k5a863bd410f24ac881b6ce8b7f663e42\n  22[label=\"Busco\"]\n  20 -> 22 [label=\"output_exons\"]\n  k0bc78676eecc4168894d34c4ca07cdf3[color=lightseagreen,label=\"Output\\nBusco summary final round\"]\n  22 -> k0bc78676eecc4168894d34c4ca07cdf3\n}",
+                "history": [
+                    {
+                        "hash": "e61e9eba49f4c255dd46e1094355f61a770ba14e",
+                        "message": "Fix workflow",
+                        "num": 12,
+                        "short_hash": "e61e9eba4",
+                        "unix": "1625849450"
+                    },
+                    {
+                        "hash": "106af0888f3f8cbc7040c20b62adbf52ddfe2186",
+                        "message": "Update maker workflow",
+                        "num": 11,
+                        "short_hash": "106af0888",
+                        "unix": "1625842677"
+                    },
+                    {
+                        "hash": "005d964a2e8cb80f8d1bf0b304adc8f9d7c9ff76",
+                        "message": "fix workflows",
+                        "num": 10,
+                        "short_hash": "005d964a2",
+                        "unix": "1609752597"
+                    },
+                    {
+                        "hash": "774f2aa374452d48fd29ee85513c3dc3a7f137f5",
+                        "message": "update maker tutorial and add a short version",
+                        "num": 9,
+                        "short_hash": "774f2aa37",
+                        "unix": "1609431273"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 8,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 7,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "1a3049ca861744336a01f79b6ae1bc8bc46e2b12",
+                        "message": "typos + update workflow",
+                        "num": 6,
+                        "short_hash": "1a3049ca8",
+                        "unix": "1558343672"
+                    },
+                    {
+                        "hash": "2318b970d421c42bbced1799cfca63ce056ad01f",
+                        "message": "udpate workflow",
+                        "num": 5,
+                        "short_hash": "2318b970d",
+                        "unix": "1557415647"
+                    },
+                    {
+                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
+                        "message": "Changed format of workflows",
+                        "num": 4,
+                        "short_hash": "361236c41",
+                        "unix": "1554368414"
+                    },
+                    {
+                        "hash": "6eef55b7e8306d8ce46ac08e7799f6f65ae106aa",
+                        "message": "Updated install_tutorial_requirements.sh + minor fixes (#1275)",
+                        "num": 3,
+                        "short_hash": "6eef55b7e",
+                        "unix": "1551293676"
+                    },
+                    {
+                        "hash": "bc6d0ddca2ce262deb405fd92e0dab955488eb49",
+                        "message": "jbrowse part",
+                        "num": 2,
+                        "short_hash": "bc6d0ddca",
+                        "unix": "1536669505"
+                    },
+                    {
+                        "hash": "7b73f26f84bc0e9dc9e771f7dd89be3e6daddd66",
+                        "message": "update wf",
+                        "num": 1,
+                        "short_hash": "7b73f26f8",
+                        "unix": "1536594667"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "It contains the sequences used by Maker to construct gene models.",
+                        "content_id": null,
                         "errors": null,
-                        "id": 11,
-                        "input_connections": {
-                            "input_pipeline": {
-                                "id": 10,
-                                "output_name": "output_pipeline"
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "It contains the sequences used by Maker to construct gene models.",
+                                "name": "EST and/or cDNA"
                             }
+                        ],
+                        "label": "EST and/or cDNA",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 287.875,
+                            "height": 81,
+                            "left": 661.46875,
+                            "right": 861.46875,
+                            "top": 206.875,
+                            "width": 200,
+                            "x": 661.46875,
+                            "y": 206.875
                         },
-                        "inputs": [],
-                        "label": "Save combined segmentation masks",
-                        "name": "SaveImages",
-                        "outputs": [
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "397d1af7-4d12-43d6-955c-e3122978fc92",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "A set of protein sequences, usually from closely related species or from a curated sequence database like UniProt/SwissProt.",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output_pipeline",
-                                "type": "txt"
+                                "description": "A set of protein sequences, usually from closely related species or from a curated sequence database like UniProt/SwissProt.",
+                                "name": "Protein sequences"
                             }
                         ],
+                        "label": "Protein sequences",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1000.75,
-                            "top": 219
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9",
-                        "tool_shed_repository": {
-                            "changeset_revision": "a45d360ae9d9",
-                            "name": "cp_save_images",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 459,
+                            "height": 81,
+                            "left": 659.5,
+                            "right": 859.5,
+                            "top": 378,
+                            "width": 200,
+                            "x": 659.5,
+                            "y": 378
                         },
-                        "tool_state": "{\"con_method_for_constructing\": {\"method_for_constructing\": \"From image filename\", \"__current_case__\": 0, \"name_for_file_prefix\": \"DNA\", \"con_append_suffix\": {\"append_suffix\": \"Yes\", \"__current_case__\": 0, \"text_to_append\": \"_combinedMask\"}}, \"con_type_of_image\": {\"type_of_image\": \"Image\", \"__current_case__\": 0, \"con_save_file_format\": {\"file_format\": \"tiff\", \"__current_case__\": 0, \"bit_depth\": \"8-bit integer\"}}, \"image_to_save\": \"CombinedMask\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"overwrite_without_warning\": \"Yes\", \"record_info\": \"No\", \"when_to_save\": \"Every cycle\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
-                        "type": "tool",
-                        "uuid": "46a80d5c-29ee-45ae-9e5b-93099e8eadc2",
-                        "workflow_outputs": [
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "418c68b0-b726-4f5e-b53c-480f1e7d43b5",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "This file corresponds to the sequence to be annotated.",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "5888c4cd-9a64-40f9-82c6-629f211fb04f"
+                                "description": "This file corresponds to the sequence to be annotated.",
+                                "name": "Genome sequence"
                             }
-                        ]
-                    },
+                        ],
+                        "label": "Genome sequence",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 1797.03125,
+                            "height": 81,
+                            "left": 661.46875,
+                            "right": 861.46875,
+                            "top": 1716.03125,
+                            "width": 200,
+                            "x": 661.46875,
+                            "y": 1716.03125
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "e03b5775-bd22-4528-9f21-20cd396dc6cc",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nProtein sequences\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nGenome sequence\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Maker\"];\n  0 -->|output| 3;\n  2 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Fasta Statistics\"];\n  2 -->|output| 4;\n  2d3829e6-f5b9-46d1-83e3-17efff814e09[\"Output\\nFasta Statistics on input dataset(s): Fasta summary stats\"];\n  4 --> 2d3829e6-f5b9-46d1-83e3-17efff814e09;\n  style 2d3829e6-f5b9-46d1-83e3-17efff814e09 stroke:#2c3143,stroke-width:4px;\n  5[\"Busco\"];\n  2 -->|output| 5;\n  a15e1214-23a2-484b-9c75-1635fcd61fe3[\"Output\\nBUSCO: short summary\"];\n  5 --> a15e1214-23a2-484b-9c75-1635fcd61fe3;\n  style a15e1214-23a2-484b-9c75-1635fcd61fe3 stroke:#2c3143,stroke-width:4px;\n  7806088d-f657-4389-9d54-6a3bdfa233b2[\"Output\\nBUSCO: list of missing ortholog genes\"];\n  5 --> 7806088d-f657-4389-9d54-6a3bdfa233b2;\n  style 7806088d-f657-4389-9d54-6a3bdfa233b2 stroke:#2c3143,stroke-width:4px;\n  6a27d0f6-d83c-42b1-a7af-5f99ba5debe2[\"Output\\nBUSCO: full table\"];\n  5 --> 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2;\n  style 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2 stroke:#2c3143,stroke-width:4px;\n  6[\"Train Augustus\"];\n  2 -->|output| 6;\n  3 -->|output_gff| 6;\n  7[\"Genome annotation statistics\"];\n  3 -->|output_gff| 7;\n  2 -->|output| 7;\n  2bed9aa6-5f22-494d-9caa-f0ece8464f15[\"Output\\nGenome annotation statistics: graphs (first round)\"];\n  7 --> 2bed9aa6-5f22-494d-9caa-f0ece8464f15;\n  style 2bed9aa6-5f22-494d-9caa-f0ece8464f15 stroke:#2c3143,stroke-width:4px;\n  71d41ce2-e90d-435b-9b64-ab4320524770[\"Output\\nGenome annotation statistics: summary (first round)\"];\n  7 --> 71d41ce2-e90d-435b-9b64-ab4320524770;\n  style 71d41ce2-e90d-435b-9b64-ab4320524770 stroke:#2c3143,stroke-width:4px;\n  8[\"gffread\"];\n  3 -->|output_gff| 8;\n  2 -->|output| 8;\n  9[\"Train SNAP\"];\n  2 -->|output| 9;\n  3 -->|output_gff| 9;\n  10[\"Busco\"];\n  8 -->|output_exons| 10;\n  a79ab19d-9802-42ca-8ffa-8c197a16c8b8[\"Output\\nBusco summary first round\"];\n  10 --> a79ab19d-9802-42ca-8ffa-8c197a16c8b8;\n  style a79ab19d-9802-42ca-8ffa-8c197a16c8b8 stroke:#2c3143,stroke-width:4px;\n  11[\"Maker\"];\n  6 -->|output_tar| 11;\n  9 -->|output| 11;\n  2 -->|output| 11;\n  3 -->|output_full| 11;\n  12[\"gffread\"];\n  11 -->|output_gff| 12;\n  2 -->|output| 12;\n  13[\"Train Augustus\"];\n  2 -->|output| 13;\n  11 -->|output_gff| 13;\n  42d5aadd-3a8c-441d-913f-ee8745a99b0b[\"Output\\nAugus: trained model\"];\n  13 --> 42d5aadd-3a8c-441d-913f-ee8745a99b0b;\n  style 42d5aadd-3a8c-441d-913f-ee8745a99b0b stroke:#2c3143,stroke-width:4px;\n  14[\"Genome annotation statistics\"];\n  11 -->|output_gff| 14;\n  2 -->|output| 14;\n  9def2c6e-fd3c-4969-b5d4-d13c187c1144[\"Output\\nGenome annotation statistics: graphs (second round)\"];\n  14 --> 9def2c6e-fd3c-4969-b5d4-d13c187c1144;\n  style 9def2c6e-fd3c-4969-b5d4-d13c187c1144 stroke:#2c3143,stroke-width:4px;\n  61f7a150-a4a2-46b1-89f5-2170d466656e[\"Output\\nGenome annotation statistics: summary (second round)\"];\n  14 --> 61f7a150-a4a2-46b1-89f5-2170d466656e;\n  style 61f7a150-a4a2-46b1-89f5-2170d466656e stroke:#2c3143,stroke-width:4px;\n  15[\"Train SNAP\"];\n  2 -->|output| 15;\n  11 -->|output_gff| 15;\n  458887f7-0661-4bde-ab1a-875aac6caed8[\"Output\\nSNAP: trained model\"];\n  15 --> 458887f7-0661-4bde-ab1a-875aac6caed8;\n  style 458887f7-0661-4bde-ab1a-875aac6caed8 stroke:#2c3143,stroke-width:4px;\n  16[\"Busco\"];\n  12 -->|output_exons| 16;\n  f52b1b41-0ea5-4384-bd43-4927273c909c[\"Output\\nBusco summary second round\"];\n  16 --> f52b1b41-0ea5-4384-bd43-4927273c909c;\n  style f52b1b41-0ea5-4384-bd43-4927273c909c stroke:#2c3143,stroke-width:4px;\n  17[\"Maker\"];\n  13 -->|output_tar| 17;\n  15 -->|output| 17;\n  2 -->|output| 17;\n  11 -->|output_full| 17;\n  18[\"Map annotation ids\"];\n  17 -->|output_gff| 18;\n  63575dcf-54d1-4cb1-b5fb-a2810b4da807[\"Output\\nMap annotation ids: renamed GFF\"];\n  18 --> 63575dcf-54d1-4cb1-b5fb-a2810b4da807;\n  style 63575dcf-54d1-4cb1-b5fb-a2810b4da807 stroke:#2c3143,stroke-width:4px;\n  19[\"JBrowse\"];\n  2 -->|output| 19;\n  3 -->|output_gff| 19;\n  18 -->|renamed| 19;\n  11 -->|output_gff| 19;\n  3 -->|output_evidences| 19;\n  11 -->|output_evidences| 19;\n  17 -->|output_evidences| 19;\n  5a38ae83-e177-45f3-aa9f-4c1844584fa5[\"Output\\nJBrowse: report\"];\n  19 --> 5a38ae83-e177-45f3-aa9f-4c1844584fa5;\n  style 5a38ae83-e177-45f3-aa9f-4c1844584fa5 stroke:#2c3143,stroke-width:4px;\n  20[\"gffread\"];\n  18 -->|renamed| 20;\n  2 -->|output| 20;\n  52fcac23-b612-4377-a19a-2e3b667a23e3[\"Output\\nGffread: exons\"];\n  20 --> 52fcac23-b612-4377-a19a-2e3b667a23e3;\n  style 52fcac23-b612-4377-a19a-2e3b667a23e3 stroke:#2c3143,stroke-width:4px;\n  5c47c25e-0ddb-4ade-a5d0-873ff4add28c[\"Output\\nGffread: translation of cds\"];\n  20 --> 5c47c25e-0ddb-4ade-a5d0-873ff4add28c;\n  style 5c47c25e-0ddb-4ade-a5d0-873ff4add28c stroke:#2c3143,stroke-width:4px;\n  84d9183b-9589-464b-9f82-4dae7f87133e[\"Output\\nGffread: cds\"];\n  20 --> 84d9183b-9589-464b-9f82-4dae7f87133e;\n  style 84d9183b-9589-464b-9f82-4dae7f87133e stroke:#2c3143,stroke-width:4px;\n  21[\"Genome annotation statistics\"];\n  18 -->|renamed| 21;\n  2 -->|output| 21;\n  f5d4a6bf-1ff8-435a-8084-7921e25bff3a[\"Output\\nGenome annotation statistics: graphs (third round)\"];\n  21 --> f5d4a6bf-1ff8-435a-8084-7921e25bff3a;\n  style f5d4a6bf-1ff8-435a-8084-7921e25bff3a stroke:#2c3143,stroke-width:4px;\n  5a863bd4-10f2-4ac8-81b6-ce8b7f663e42[\"Output\\nGenome annotation statistics: summary (third round)\"];\n  21 --> 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42;\n  style 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42 stroke:#2c3143,stroke-width:4px;\n  22[\"Busco\"];\n  20 -->|output_exons| 22;\n  0bc78676-eecc-4168-894d-34c4ca07cdf3[\"Output\\nBusco summary final round\"];\n  22 --> 0bc78676-eecc-4168-894d-34c4ca07cdf3;\n  style 0bc78676-eecc-4168-894d-34c4ca07cdf3 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Genome annotation with Maker ",
+                "outputs": [
                     {
-                        "annotation": "Incomplete nuclei that are touching the borders of the image are segmented, also the nuclei outside the diameter range.",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
                         "errors": null,
-                        "id": 12,
+                        "id": 4,
                         "input_connections": {
-                            "input_pipeline": {
-                                "id": 11,
-                                "output_name": "output_pipeline"
+                            "dataset": {
+                                "id": 2,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "Segment all nuclei",
-                        "name": "IdentifyPrimaryObjects",
+                        "label": null,
+                        "name": "Fasta Statistics",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
-                                "type": "txt"
+                                "name": "stats",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1081.5,
-                            "top": 219
+                            "bottom": 1526.4375,
+                            "height": 152,
+                            "left": 722.921875,
+                            "right": 922.921875,
+                            "top": 1374.4375,
+                            "width": 200,
+                            "x": 722.921875,
+                            "y": 1374.4375
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "52c01fb29b2a",
-                            "name": "cp_identify_primary_objects",
-                            "owner": "bgruening",
+                            "changeset_revision": "9c620a950d3a",
+                            "name": "fasta_stats",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"con_advanced\": {\"advanced\": \"Yes\", \"__current_case__\": 1, \"input_from_nat\": \"DNA\", \"name_to_be_identified\": \"NucleiIncludingTouchingBorders\", \"min_diameter\": \"15\", \"max_diameter\": \"200\", \"discard_outside_border\": \"No\", \"discard_touching_border\": \"No\", \"con_threshold_strategy\": {\"threshold_strategy\": \"Global\", \"__current_case__\": 1, \"con_threshold_method\": {\"threshold_method\": \"Otsu\", \"__current_case__\": 0, \"con_threshold_class\": {\"threshold_class\": \"Two classes\", \"__current_case__\": 1}, \"threshold_smoothing_scale\": \"1.3488\", \"threshold_correction_factor\": \"0.9\", \"threshold_lower\": \"0.0\", \"threshold_upper\": \"1.0\"}}, \"con_distinguish_clumped_objects\": {\"distinguish_clumped_objects\": \"Shape\", \"__current_case__\": 0, \"con_dividing_lines\": {\"dividing_lines\": \"Shape\", \"__current_case__\": 0, \"con_smoothing_filter\": {\"smoothing_filter\": \"Yes\", \"__current_case__\": 1}, \"con_min_distance\": {\"min_distance\": \"Yes\", \"__current_case__\": 1}, \"speed_up\": \"Yes\"}}, \"fill_hole\": \"After both thresholding and declumping\", \"con_handling_excessive\": {\"excessive_handling\": \"Continue\", \"__current_case__\": 1}}, \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
+                        "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.1",
                         "type": "tool",
-                        "uuid": "b6f8fb6c-4278-4b17-ba76-c949f87fee51",
+                        "uuid": "9cd9564b-b447-4a93-9445-ae3583137010",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "c96b7030-c091-4961-801c-dc3e72b4a357"
+                                "label": "Fasta Statistics on input dataset(s): Fasta summary stats",
+                                "output_name": "stats",
+                                "uuid": "2d3829e6-f5b9-46d1-83e3-17efff814e09"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
                         "errors": null,
-                        "id": 13,
+                        "id": 5,
                         "input_connections": {
-                            "input_pipeline": {
-                                "id": 12,
-                                "output_name": "output_pipeline"
+                            "input": {
+                                "id": 2,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "Segmentation mask nucleoli including cells touching borders",
-                        "name": "ConvertObjectsToImage",
+                        "label": null,
+                        "name": "Busco",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
+                                "name": "busco_sum",
                                 "type": "txt"
+                            },
+                            {
+                                "name": "busco_table",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "busco_missing",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1162.25,
-                            "top": 219
+                            "bottom": 1989.015625,
+                            "height": 212,
+                            "left": 939.484375,
+                            "right": 1139.484375,
+                            "top": 1777.015625,
+                            "width": 200,
+                            "x": 939.484375,
+                            "y": 1777.015625
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
                         "tool_shed_repository": {
-                            "changeset_revision": "2690da374874",
-                            "name": "cp_convert_objects_to_image",
-                            "owner": "bgruening",
+                            "changeset_revision": "602fb8e63aa7",
+                            "name": "busco",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"con_color_format\": {\"color_format\": \"Binary (black & white)\", \"__current_case__\": 0}, \"input_object\": \"NucleiIncludingTouchingBorders\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"name_output_image\": \"Image_NucleiIncludingTouchingBorders\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
+                        "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"geno\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.1.4",
                         "type": "tool",
-                        "uuid": "adc8a062-58ee-4285-a4f2-fcf423f30bdd",
+                        "uuid": "2e99d9de-b48b-4f0f-99da-5f727ad023cc",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "a9f1d26d-ad3d-4984-b15b-76d1e3309833"
+                                "label": "BUSCO: short summary",
+                                "output_name": "busco_sum",
+                                "uuid": "a15e1214-23a2-484b-9c75-1635fcd61fe3"
+                            },
+                            {
+                                "label": "BUSCO: list of missing ortholog genes",
+                                "output_name": "busco_missing",
+                                "uuid": "7806088d-f657-4389-9d54-6a3bdfa233b2"
+                            },
+                            {
+                                "label": "BUSCO: full table",
+                                "output_name": "busco_table",
+                                "uuid": "6a27d0f6-d83c-42b1-a7af-5f99ba5debe2"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_image_math/cp_image_math/0.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
                         "errors": null,
-                        "id": 14,
+                        "id": 7,
                         "input_connections": {
-                            "input_pipeline": {
-                                "id": 13,
-                                "output_name": "output_pipeline"
+                            "gff": {
+                                "id": 3,
+                                "output_name": "output_gff"
+                            },
+                            "ref_genome|genome": {
+                                "id": 2,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "Extract background",
-                        "name": "ImageMath",
+                        "label": null,
+                        "name": "Genome annotation statistics",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
+                                "name": "summary",
                                 "type": "txt"
+                            },
+                            {
+                                "name": "graphs",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "left": 1243,
-                            "top": 219
+                            "bottom": 1247.015625,
+                            "height": 272,
+                            "left": 1247.5,
+                            "right": 1447.5,
+                            "top": 975.015625,
+                            "width": 200,
+                            "x": 1247.5,
+                            "y": 975.015625
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_image_math/cp_image_math/0.1.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
                         "tool_shed_repository": {
-                            "changeset_revision": "6d3851ac885f",
-                            "name": "cp_image_math",
-                            "owner": "bgruening",
+                            "changeset_revision": "8cffbd184762",
+                            "name": "jcvi_gff_stats",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"ignore_the_image_masks\": \"No\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"name_output_image\": \"BG\", \"operation\": {\"operation\": \"subtract\", \"__current_case__\": 1, \"first_image\": {\"image_or_measurement_first\": {\"image_or_measurement_first\": \"Image\", \"__current_case__\": 0, \"select_the_first_image\": \"DNA\"}, \"multiply_the_first_image_by\": \"1.0\"}, \"second_image\": {\"image_or_measurement_second\": {\"image_or_measurement_second\": \"Image\", \"__current_case__\": 0, \"select_the_second_image\": \"Image_NucleiIncludingTouchingBorders\"}, \"multiply_the_second_image_by\": \"1.0\"}, \"op_results\": {\"raise_the_power_of_the_result_by\": \"1.0\", \"multiply_the_result_by\": \"1.0\", \"add_to_result\": \"0.0\", \"set_values_less_than_0_equal_to_0\": \"Yes\", \"set_values_greater_than_1_equal_to_1\": \"Yes\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.0",
+                        "tool_state": "{\"gff\": {\"__class__\": \"ConnectedValue\"}, \"ref_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.8.4",
                         "type": "tool",
-                        "uuid": "549ce202-f817-48e7-90cb-2e3766c67e4b",
+                        "uuid": "af60c4d9-58f2-4f41-a2a3-6458cdcfd404",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "b64b6fc5-593f-4755-9531-3d4b2d47cc61"
+                                "label": "Genome annotation statistics: graphs (first round)",
+                                "output_name": "graphs",
+                                "uuid": "2bed9aa6-5f22-494d-9caa-f0ece8464f15"
+                            },
+                            {
+                                "label": "Genome annotation statistics: summary (first round)",
+                                "output_name": "summary",
+                                "uuid": "71d41ce2-e90d-435b-9b64-ab4320524770"
                             }
                         ]
                     },
                     {
-                        "annotation": "This step measures the granularity of the original image",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_granularity/cp_measure_granularity/3.1.9",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
                         "errors": null,
-                        "id": 15,
+                        "id": 10,
                         "input_connections": {
-                            "input_pipeline": {
-                                "id": 14,
-                                "output_name": "output_pipeline"
+                            "input": {
+                                "id": 8,
+                                "output_name": "output_exons"
                             }
                         },
                         "inputs": [],
-                        "label": "Measure the image granularity",
-                        "name": "MeasureGranularity",
+                        "label": null,
+                        "name": "Busco",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
+                                "name": "busco_sum",
                                 "type": "txt"
+                            },
+                            {
+                                "name": "busco_table",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "busco_missing",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1323.75,
-                            "top": 219
+                            "bottom": 1738.03125,
+                            "height": 252,
+                            "left": 1545.5,
+                            "right": 1745.5,
+                            "top": 1486.03125,
+                            "width": 200,
+                            "x": 1545.5,
+                            "y": 1486.03125
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_granularity/cp_measure_granularity/3.1.9",
+                        "post_job_actions": {
+                            "HideDatasetActionbusco_missing": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "busco_missing"
+                            },
+                            "HideDatasetActionbusco_table": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "busco_table"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
                         "tool_shed_repository": {
-                            "changeset_revision": "382413f8ec1d",
-                            "name": "cp_measure_granularity",
-                            "owner": "bgruening",
+                            "changeset_revision": "602fb8e63aa7",
+                            "name": "busco",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"rpt_image\": [{\"__index__\": 0, \"image_to_measure\": \"DNA\", \"subsampling_factor_granularity\": \"0.25\", \"subsampling_factor_background_reduction\": \"0.25\", \"radius\": \"10\", \"range_granular_spectrum\": \"16\", \"rpt_object\": []}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
+                        "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"tran\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.1.4",
                         "type": "tool",
-                        "uuid": "facc511c-7f3e-48bc-8330-e9bb5b4a6b1e",
+                        "uuid": "a83a2b48-7787-4b53-a592-339f5134e168",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "b157d712-698d-46e6-b042-913748e44f89"
+                                "label": "Busco summary first round",
+                                "output_name": "busco_sum",
+                                "uuid": "a79ab19d-9802-42ca-8ffa-8c197a16c8b8"
                             }
                         ]
                     },
                     {
-                        "annotation": "This step measures the texture of the original image and nuclei in it",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_texture/cp_measure_texture/3.1.9",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3",
                         "errors": null,
-                        "id": 16,
+                        "id": 13,
                         "input_connections": {
-                            "input_pipeline": {
-                                "id": 15,
-                                "output_name": "output_pipeline"
+                            "genome": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "maker_gff": {
+                                "id": 11,
+                                "output_name": "output_gff"
                             }
                         },
                         "inputs": [],
-                        "label": "Measure the nuclei texture",
-                        "name": "MeasureTexture",
+                        "label": null,
+                        "name": "Train Augustus",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
-                                "type": "txt"
+                                "name": "output_tar",
+                                "type": "augustus"
                             }
                         ],
                         "position": {
-                            "left": 1404.5,
-                            "top": 219
+                            "bottom": 1259.03125,
+                            "height": 182,
+                            "left": 1863.5,
+                            "right": 2063.5,
+                            "top": 1077.03125,
+                            "width": 200,
+                            "x": 1863.5,
+                            "y": 1077.03125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_texture/cp_measure_texture/3.1.9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "658a2a451aec",
-                            "name": "cp_measure_texture",
+                            "changeset_revision": "6519ebe25019",
+                            "name": "augustus_training",
                             "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"con_img_obj\": {\"img_obj\": \"Objects\", \"__current_case__\": 0, \"rpt_obj_to_measure\": [{\"__index__\": 0, \"obj_to_measure\": \"Nuclei\"}]}, \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"rpt_image_to_measure\": [{\"__index__\": 0, \"image_to_measure\": \"DNA\"}], \"rpt_scale_to_measure\": [{\"__index__\": 0, \"scale_to_measure\": \"3\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
+                        "tool_state": "{\"genome\": {\"__class__\": \"ConnectedValue\"}, \"maker_gff\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.3.3",
                         "type": "tool",
-                        "uuid": "ae3973f7-8c6e-410e-828a-633b59839fe6",
+                        "uuid": "b347da09-05a2-4d30-a103-dbeb5853efcd",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "5d4d6e55-44cf-4611-bcd8-bda8a9df7286"
+                                "label": "Augus: trained model",
+                                "output_name": "output_tar",
+                                "uuid": "42d5aadd-3a8c-441d-913f-ee8745a99b0b"
                             }
                         ]
                     },
                     {
-                        "annotation": "This step measures the intensity of the original image and the nuclei",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
                         "errors": null,
-                        "id": 17,
+                        "id": 14,
                         "input_connections": {
-                            "input_pipeline": {
-                                "id": 16,
-                                "output_name": "output_pipeline"
+                            "gff": {
+                                "id": 11,
+                                "output_name": "output_gff"
+                            },
+                            "ref_genome|genome": {
+                                "id": 2,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "Measure the nuclei intensity",
-                        "name": "MeasureObjectIntensity",
+                        "label": null,
+                        "name": "Genome annotation statistics",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
+                                "name": "summary",
                                 "type": "txt"
+                            },
+                            {
+                                "name": "graphs",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "left": 1485.25,
-                            "top": 219
+                            "bottom": 1569.03125,
+                            "height": 272,
+                            "left": 1863.5,
+                            "right": 2063.5,
+                            "top": 1297.03125,
+                            "width": 200,
+                            "x": 1863.5,
+                            "y": 1297.03125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
                         "tool_shed_repository": {
-                            "changeset_revision": "b867e9317a06",
-                            "name": "cp_measure_object_intensity",
-                            "owner": "bgruening",
+                            "changeset_revision": "8cffbd184762",
+                            "name": "jcvi_gff_stats",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"rpt_image\": [{\"__index__\": 0, \"image_to_measure\": \"DNA\"}], \"rpt_object\": [{\"__index__\": 0, \"objects_to_measure\": \"Nuclei\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
+                        "tool_state": "{\"gff\": {\"__class__\": \"ConnectedValue\"}, \"ref_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.8.4",
                         "type": "tool",
-                        "uuid": "0ac29831-ed29-4294-95b5-ba2400408dab",
+                        "uuid": "5a3899b6-a669-4a36-990e-01e6cac6410d",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "d26c927d-f6c3-4c53-873b-015d8fe59d0f"
+                                "label": "Genome annotation statistics: graphs (second round)",
+                                "output_name": "graphs",
+                                "uuid": "9def2c6e-fd3c-4969-b5d4-d13c187c1144"
+                            },
+                            {
+                                "label": "Genome annotation statistics: summary (second round)",
+                                "output_name": "summary",
+                                "uuid": "61f7a150-a4a2-46b1-89f5-2170d466656e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1",
                         "errors": null,
-                        "id": 18,
+                        "id": 15,
                         "input_connections": {
-                            "input_pipeline": {
-                                "id": 17,
-                                "output_name": "output_pipeline"
+                            "genome": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "maker_gff": {
+                                "id": 11,
+                                "output_name": "output_gff"
                             }
                         },
                         "inputs": [],
-                        "label": "Measure size and shape of nuclei and nucleoli",
-                        "name": "MeasureObjectSizeShape",
+                        "label": null,
+                        "name": "Train SNAP",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
-                                "type": "txt"
+                                "name": "output",
+                                "type": "snaphmm"
                             }
                         ],
                         "position": {
-                            "left": 1566,
-                            "top": 219
+                            "bottom": 1770.03125,
+                            "height": 162,
+                            "left": 1863.5,
+                            "right": 2063.5,
+                            "top": 1608.03125,
+                            "width": 200,
+                            "x": 1863.5,
+                            "y": 1608.03125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "5c9549983af8",
-                            "name": "cp_measure_object_size_shape",
-                            "owner": "bgruening",
+                            "changeset_revision": "2a598c0aa042",
+                            "name": "snap_training",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"rpt_object\": [{\"__index__\": 0, \"objects_to_measure\": \"Nuclei\"}, {\"__index__\": 1, \"objects_to_measure\": \"Nucleoli\"}], \"zernike_feature\": \"Yes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
+                        "tool_state": "{\"gene_num\": \"1000\", \"genome\": {\"__class__\": \"ConnectedValue\"}, \"maker_gff\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2013_11_29+galaxy1",
                         "type": "tool",
-                        "uuid": "580e3cc4-48f3-48d2-9d69-8bb6c3d79be9",
+                        "uuid": "97cec0ac-e731-4b55-859d-773a7c88bc26",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "289985e1-f94e-4223-bc1b-64ac4eadf40e"
+                                "label": "SNAP: trained model",
+                                "output_name": "output",
+                                "uuid": "458887f7-0661-4bde-ab1a-875aac6caed8"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_relate_objects/cp_relate_objects/3.1.9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
                         "errors": null,
-                        "id": 19,
+                        "id": 16,
                         "input_connections": {
-                            "input_pipeline": {
-                                "id": 18,
-                                "output_name": "output_pipeline"
+                            "input": {
+                                "id": 12,
+                                "output_name": "output_exons"
                             }
                         },
                         "inputs": [],
-                        "label": "Relate nucleoli with their parent nuclei",
-                        "name": "RelateObjects",
+                        "label": null,
+                        "name": "Busco",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
+                                "name": "busco_sum",
                                 "type": "txt"
+                            },
+                            {
+                                "name": "busco_table",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "busco_missing",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1648,
-                            "top": 219
+                            "bottom": 870.03125,
+                            "height": 252,
+                            "left": 2161.484375,
+                            "right": 2361.484375,
+                            "top": 618.03125,
+                            "width": 200,
+                            "x": 2161.484375,
+                            "y": 618.03125
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_relate_objects/cp_relate_objects/3.1.9",
+                        "post_job_actions": {
+                            "HideDatasetActionbusco_missing": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "busco_missing"
+                            },
+                            "HideDatasetActionbusco_table": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "busco_table"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
                         "tool_shed_repository": {
-                            "changeset_revision": "f3f45c42bc36",
-                            "name": "cp_relate_objects",
-                            "owner": "bgruening",
+                            "changeset_revision": "602fb8e63aa7",
+                            "name": "busco",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"child_objects\": \"Nucleoli\", \"con_dist\": {\"calc_dist\": \"Both\", \"__current_case__\": 2, \"con_other_parent_dist\": {\"calc_dist_to_others\": \"No\", \"__current_case__\": 1}}, \"con_save_child\": {\"save_child_as_new\": \"Yes\", \"__current_case__\": 0, \"name_output\": \"RelateObjects\"}, \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"means_for_all\": \"Yes\", \"parent_objects\": \"Nuclei\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
+                        "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"tran\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.1.4",
                         "type": "tool",
-                        "uuid": "d776a7aa-7154-401d-8ff5-15e986f29597",
+                        "uuid": "9b04f806-0275-4939-bf74-b8c58ae2bffa",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "48df535c-abd3-423e-b6c4-e3e6a2579eb7"
+                                "label": "Busco summary second round",
+                                "output_name": "busco_sum",
+                                "uuid": "f52b1b41-0ea5-4384-bd43-4927273c909c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_quality/cp_measure_image_quality/3.1.9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11",
                         "errors": null,
-                        "id": 20,
+                        "id": 18,
                         "input_connections": {
-                            "input_pipeline": {
-                                "id": 19,
-                                "output_name": "output_pipeline"
+                            "maker_gff": {
+                                "id": 17,
+                                "output_name": "output_gff"
                             }
                         },
                         "inputs": [],
-                        "label": "Measure the image quality",
-                        "name": "MeasureImageQuality",
+                        "label": null,
+                        "name": "Map annotation ids",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
-                                "type": "txt"
+                                "name": "renamed",
+                                "type": "gff"
+                            },
+                            {
+                                "name": "id_map",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1728.75,
-                            "top": 219
+                            "bottom": 1637.03125,
+                            "height": 222,
+                            "left": 2439.5,
+                            "right": 2639.5,
+                            "top": 1415.03125,
+                            "width": 200,
+                            "x": 2439.5,
+                            "y": 1415.03125
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_quality/cp_measure_image_quality/3.1.9",
+                        "post_job_actions": {
+                            "ChangeDatatypeActionrenamed": {
+                                "action_arguments": {
+                                    "newtype": "gff3"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "renamed"
+                            },
+                            "HideDatasetActionid_map": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "id_map"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11",
                         "tool_shed_repository": {
-                            "changeset_revision": "08a2cf887a44",
-                            "name": "cp_measure_image_quality",
-                            "owner": "bgruening",
+                            "changeset_revision": "2e3535db1bfa",
+                            "name": "maker_map_ids",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"calc_for_images\": \"All loaded images\", \"calc_intensity_metrics\": \"Yes\", \"calc_saturation_metrics\": \"Yes\", \"con_calc_blur_metrics\": {\"calc_blur_metrics\": \"Yes\", \"__current_case__\": 0, \"rpt_blur_measurements\": [{\"__index__\": 0, \"blur_measurements\": \"20\"}]}, \"con_calc_threshold\": {\"calc_threshold\": \"Yes\", \"__current_case__\": 0, \"con_use_all_methods\": {\"use_all_methods\": \"No\", \"__current_case__\": 1, \"rpt_threshold_method\": [{\"__index__\": 0, \"con_threshold_methods\": {\"select_threshold_method\": \"Otsu\", \"__current_case__\": 0, \"otsu_weighted_entropy\": \"Weighted variance\", \"con_threshold_classes\": {\"threshold_classes\": \"Two classes\", \"__current_case__\": 1}}}]}}, \"include_rescaling_value\": \"Yes\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
+                        "tool_state": "{\"justify\": \"6\", \"maker_gff\": {\"__class__\": \"ConnectedValue\"}, \"prefix\": \"TEST\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.31.11",
                         "type": "tool",
-                        "uuid": "3b81db10-c6dd-4ff0-8b2d-58ab00f80260",
+                        "uuid": "d7101291-76ac-48ec-9fb3-89ca5554e8ea",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "db6c90c4-44cd-405d-94f2-00f9c93a120c"
+                                "label": "Map annotation ids: renamed GFF",
+                                "output_name": "renamed",
+                                "uuid": "63575dcf-54d1-4cb1-b5fb-a2810b4da807"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_area_occupied/cp_measure_image_area_occupied/3.1.9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
                         "errors": null,
-                        "id": 21,
+                        "id": 19,
                         "input_connections": {
-                            "input_pipeline": {
-                                "id": 20,
-                                "output_name": "output_pipeline"
-                            }
+                            "reference_genome|genome": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "track_groups_0|data_tracks_0|data_format|annotation": [
+                                {
+                                    "id": 3,
+                                    "output_name": "output_gff"
+                                },
+                                {
+                                    "id": 18,
+                                    "output_name": "renamed"
+                                },
+                                {
+                                    "id": 11,
+                                    "output_name": "output_gff"
+                                }
+                            ],
+                            "track_groups_1|data_tracks_0|data_format|annotation": [
+                                {
+                                    "id": 3,
+                                    "output_name": "output_evidences"
+                                },
+                                {
+                                    "id": 11,
+                                    "output_name": "output_evidences"
+                                },
+                                {
+                                    "id": 17,
+                                    "output_name": "output_evidences"
+                                }
+                            ]
                         },
                         "inputs": [],
-                        "label": "Measure the area occupied by nuclei and nucleoli",
-                        "name": "MeasureImageAreaOccupied",
+                        "label": null,
+                        "name": "JBrowse",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
-                                "type": "txt"
+                                "name": "output",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 1809.5,
-                            "top": 219
+                            "bottom": 775.015625,
+                            "height": 292,
+                            "left": 2747.5,
+                            "right": 2947.5,
+                            "top": 483.015625,
+                            "width": 200,
+                            "x": 2747.5,
+                            "y": 483.015625
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_area_occupied/cp_measure_image_area_occupied/3.1.9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "7a08edbc790e",
-                            "name": "cp_measure_image_area_occupied",
-                            "owner": "bgruening",
+                            "changeset_revision": "6cd09d7b5f37",
+                            "name": "jbrowse",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"rpt_area\": [{\"__index__\": 0, \"con_area\": {\"objects_or_image\": \"Objects\", \"__current_case__\": 0, \"objects_to_measure\": \"Nuclei\"}}, {\"__index__\": 1, \"con_area\": {\"objects_or_image\": \"Objects\", \"__current_case__\": 0, \"objects_to_measure\": \"Nucleoli\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
+                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Maker annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 1, \"category\": \"Maker evidences\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"match_part\": {\"match_part_select\": \"true\", \"__current_case__\": 0, \"name\": {\"__class__\": \"RuntimeValue\"}}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.10+galaxy0",
                         "type": "tool",
-                        "uuid": "3df981d5-142e-4cb5-b897-05afcb201811",
+                        "uuid": "4585ada8-27ac-4632-8ac4-76f452316f21",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "58cdfb31-71f2-44ef-a385-f62188f8d2a3"
+                                "label": "JBrowse: report",
+                                "output_name": "output",
+                                "uuid": "5a38ae83-e177-45f3-aa9f-4c1844584fa5"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_intensity/cp_measure_image_intensity/3.1.9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2",
                         "errors": null,
-                        "id": 22,
+                        "id": 20,
                         "input_connections": {
-                            "input_pipeline": {
-                                "id": 21,
-                                "output_name": "output_pipeline"
+                            "input": {
+                                "id": 18,
+                                "output_name": "renamed"
+                            },
+                            "reference_genome|genome_fasta": {
+                                "id": 2,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": "Measure the image intensity",
-                        "name": "MeasureImageIntensity",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool gffread",
+                                "name": "chr_replace"
+                            }
+                        ],
+                        "label": null,
+                        "name": "gffread",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
-                                "type": "txt"
+                                "name": "output_exons",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "output_cds",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "output_pep",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 1891.5,
-                            "top": 219
+                            "bottom": 1085.015625,
+                            "height": 272,
+                            "left": 2747.5,
+                            "right": 2947.5,
+                            "top": 813.015625,
+                            "width": 200,
+                            "x": 2747.5,
+                            "y": 813.015625
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_intensity/cp_measure_image_intensity/3.1.9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "2681008d726f",
-                            "name": "cp_measure_image_intensity",
-                            "owner": "bgruening",
+                            "changeset_revision": "69e0806b63a4",
+                            "name": "gffread",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"rpt_intensity\": [{\"__index__\": 0, \"image_to_measure\": \"DNA\", \"con_intensity\": {\"only_from_objects\": \"No\", \"__current_case__\": 1}}, {\"__index__\": 1, \"image_to_measure\": \"DNA\", \"con_intensity\": {\"only_from_objects\": \"Yes\", \"__current_case__\": 0, \"input_objects\": \"Nuclei\"}}, {\"__index__\": 2, \"image_to_measure\": \"BG\", \"con_intensity\": {\"only_from_objects\": \"No\", \"__current_case__\": 1}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
+                        "tool_state": "{\"chr_replace\": {\"__class__\": \"RuntimeValue\"}, \"decode_url\": \"false\", \"expose\": \"false\", \"filtering\": null, \"full_gff_attribute_preservation\": \"false\", \"gffs\": {\"gff_fmt\": \"none\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"maxintron\": null, \"merging\": {\"merge_sel\": \"none\", \"__current_case__\": 0}, \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 2, \"genome_fasta\": {\"__class__\": \"ConnectedValue\"}, \"ref_filtering\": null, \"fa_outputs\": [\"-w exons.fa\", \"-x cds.fa\", \"-y pep.fa\"]}, \"region\": {\"region_filter\": \"none\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.2.1.2",
                         "type": "tool",
-                        "uuid": "5aa9619d-a11a-4b22-8d13-0b39eff4f665",
+                        "uuid": "51674c8f-f50e-430f-b0ff-49b1b96887aa",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "64333743-a286-4ecb-85be-4203f31d566c"
+                                "label": "Gffread: exons",
+                                "output_name": "output_exons",
+                                "uuid": "52fcac23-b612-4377-a19a-2e3b667a23e3"
+                            },
+                            {
+                                "label": "Gffread: translation of cds",
+                                "output_name": "output_pep",
+                                "uuid": "5c47c25e-0ddb-4ade-a5d0-873ff4add28c"
+                            },
+                            {
+                                "label": "Gffread: cds",
+                                "output_name": "output_cds",
+                                "uuid": "84d9183b-9589-464b-9f82-4dae7f87133e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
                         "errors": null,
-                        "id": 23,
+                        "id": 21,
                         "input_connections": {
-                            "input_pipeline": {
-                                "id": 22,
-                                "output_name": "output_pipeline"
+                            "gff": {
+                                "id": 18,
+                                "output_name": "renamed"
+                            },
+                            "ref_genome|genome": {
+                                "id": 2,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "Export measurements",
-                        "name": "ExportToSpreadsheet",
+                        "label": null,
+                        "name": "Genome annotation statistics",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
+                                "name": "summary",
                                 "type": "txt"
+                            },
+                            {
+                                "name": "graphs",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "left": 1972.25,
-                            "top": 219
+                            "bottom": 1954.03125,
+                            "height": 272,
+                            "left": 2747.5,
+                            "right": 2947.5,
+                            "top": 1682.03125,
+                            "width": 200,
+                            "x": 2747.5,
+                            "y": 1682.03125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
                         "tool_shed_repository": {
-                            "changeset_revision": "72a7f23f3a79",
-                            "name": "cp_export_to_spreadsheet",
-                            "owner": "bgruening",
+                            "changeset_revision": "8cffbd184762",
+                            "name": "jcvi_gff_stats",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"add_metadata_column_to_object\": \"Yes\", \"calc_mean\": \"Yes\", \"calc_median\": \"Yes\", \"calc_standard_deviation\": \"Yes\", \"con_create_gene_pattern\": {\"create_gene_pattern\": \"No\", \"__current_case__\": 1}, \"con_export_all_measurements\": {\"export_all_measurements\": \"Yes\", \"__current_case__\": 1}, \"con_prefix\": {\"add_prefix\": \"No\", \"__current_case__\": 1}, \"delimiter\": \"Tab\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"overwrite_existing_file\": \"Yes\", \"represent_nan\": \"NaN\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
+                        "tool_state": "{\"gff\": {\"__class__\": \"ConnectedValue\"}, \"ref_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.8.4",
                         "type": "tool",
-                        "uuid": "fe3256bd-e219-48ba-9588-87ccd061ce46",
+                        "uuid": "d5c389a7-0746-49da-ad3d-e206b5506acc",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "70625d77-224f-405a-ab93-3f55d644d9bd"
+                                "label": "Genome annotation statistics: graphs (third round)",
+                                "output_name": "graphs",
+                                "uuid": "f5d4a6bf-1ff8-435a-8084-7921e25bff3a"
+                            },
+                            {
+                                "label": "Genome annotation statistics: summary (third round)",
+                                "output_name": "summary",
+                                "uuid": "5a863bd4-10f2-4ac8-81b6-ce8b7f663e42"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
                         "errors": null,
-                        "id": 24,
+                        "id": 22,
                         "input_connections": {
-                            "con_input_type|input_images": {
-                                "id": 1,
-                                "output_name": "output_tar"
-                            },
-                            "pipeline": {
-                                "id": 23,
-                                "output_name": "output_pipeline"
+                            "input": {
+                                "id": 20,
+                                "output_name": "output_exons"
                             }
                         },
                         "inputs": [],
-                        "label": "Run CellProfiler",
-                        "name": "CellProfiler",
+                        "label": null,
+                        "name": "Busco",
                         "outputs": [
                             {
-                                "name": "pipeline_output",
-                                "type": "input"
+                                "name": "busco_sum",
+                                "type": "txt"
                             },
                             {
-                                "name": "logs",
-                                "type": "txt"
+                                "name": "busco_table",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "busco_missing",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 2053,
-                            "top": 219
+                            "bottom": 1156.03125,
+                            "height": 252,
+                            "left": 3025.5,
+                            "right": 3225.5,
+                            "top": 904.03125,
+                            "width": 200,
+                            "x": 3025.5,
+                            "y": 904.03125
                         },
                         "post_job_actions": {
-                            "EmailActionpipeline_output": {
+                            "HideDatasetActionbusco_missing": {
                                 "action_arguments": {},
-                                "action_type": "EmailAction",
-                                "output_name": "pipeline_output"
+                                "action_type": "HideDatasetAction",
+                                "output_name": "busco_missing"
                             },
-                            "HideDatasetActionlogs": {
+                            "HideDatasetActionbusco_table": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "logs"
+                                "output_name": "busco_table"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
                         "tool_shed_repository": {
-                            "changeset_revision": "fca368c99299",
-                            "name": "cp_cellprofiler",
-                            "owner": "bgruening",
+                            "changeset_revision": "602fb8e63aa7",
+                            "name": "busco",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"con_input_type\": {\"input_type\": \"yes\", \"__current_case__\": 1, \"input_images\": {\"__class__\": \"ConnectedValue\"}}, \"detailed_output\": \"true\", \"pipeline\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9",
+                        "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adv\": {\"evalue\": \"0.01\", \"limit\": \"3\", \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage_dataset\": \"fungi_odb10\", \"mode\": \"tran\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.1.4",
                         "type": "tool",
-                        "uuid": "5e893441-7a89-44ce-afe8-29959465f0ee",
+                        "uuid": "94dac116-5e62-487c-912a-a63ca53c17e7",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "pipeline_output",
-                                "uuid": "30778509-8776-4c05-8d4e-6823532a9c41"
+                                "label": "Busco summary final round",
+                                "output_name": "busco_sum",
+                                "uuid": "0bc78676-eecc-4168-894d-34c4ca07cdf3"
                             }
                         ]
                     }
                 ],
-                "parent_id": "imaging/tutorial-CP",
-                "path": "topics/imaging/tutorials/tutorial-CP/workflows/main_workflow.ga",
+                "parent_id": "genome-annotation/annotation-with-maker",
+                "path": "topics/genome-annotation/tutorials/annotation-with-maker/workflows/main_workflow.ga",
                 "tags": [
-                    "CellProfiler",
-                    "imaging"
+                    "genome-annotation"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "CP_pipeline_IDR_training",
-                "topic_id": "imaging",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/imaging-tutorial-CP/versions/main-workflow",
-                "tutorial_id": "tutorial-CP",
-                "url": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/tutorial-CP/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/tutorial-CP/workflows/main_workflow.html",
-                "version": 3,
-                "wfid": "imaging-tutorial-CP",
+                "title": "Genome annotation with Maker ",
+                "topic_id": "genome-annotation",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-annotation-with-maker/versions/main-workflow",
+                "tutorial_id": "annotation-with-maker",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-maker/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-maker/workflows/main_workflow.html",
+                "version": 10,
+                "wfid": "genome-annotation-annotation-with-maker",
                 "wfname": "main-workflow",
                 "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_display_data_on_image/cp_display_data_on_image/3.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_enhance_or_suppress_features/cp_enhance_or_suppress_features/3.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_gray_to_color/cp_gray_to_color/3.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_image_math/cp_image_math/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_mask_image/cp_mask_image/3.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_granularity/cp_measure_granularity/3.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_area_occupied/cp_measure_image_area_occupied/3.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_intensity/cp_measure_image_intensity/3.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_quality/cp_measure_image_quality/3.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_texture/cp_measure_texture/3.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_relate_objects/cp_relate_objects/3.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/idr_download_by_ids/idr_download_by_ids/0.41"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.11",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1"
+                ],
+                "workflowhub_id": "1164"
+            }
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.4406623"
+    },
+    {
+        "abbreviations": {
+            "OGS": "Official Gene Set"
+        },
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "apollo_create_or_update",
+                    "owner": "gga",
+                    "revisions": "4abaab60f9e1",
+                    "tool_panel_section_label": "Apollo",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "apollo_iframe",
+                    "owner": "gga",
+                    "revisions": "f4e3f9480307",
+                    "tool_panel_section_label": "Apollo",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "jbrowse",
+                    "owner": "iuc",
+                    "revisions": "a6e57ff585c0",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: apollo_create_or_update\n  owner: gga\n  revisions: 4abaab60f9e1\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: apollo_iframe\n  owner: gga\n  revisions: f4e3f9480307\n  tool_panel_section_label: Apollo\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo-euk/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "abretaud"
+            ],
+            "funding": [
+                "gallantries",
+                "eurosciencegateway"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "eurosciencegateway",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
+                "fediverse_flavor": "mastodon",
+                "id": "abretaud",
+                "joined": "2017-09",
+                "location": {
+                    "country": "FR",
+                    "lat": 48.11,
+                    "lon": -1.64
+                },
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/eurosciencegateway.png",
+                "funder": true,
+                "funding_id": "101057388",
+                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "eurosciencegateway",
+                "joined": "2023-10",
+                "members": [
+                    "abretaud",
+                    "anuprulez",
+                    "bgruening",
+                    "erxleben",
+                    "pauldg",
+                    "rlibouba"
+                ],
+                "name": "EuroScienceGateway",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
+            }
+        ],
+        "dir": "topics/genome-annotation/tutorials/apollo-euk",
+        "edam_operation": [
+            "Genome visualisation"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.no"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "genome-annotation/apollo-euk",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.eu"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Apollo is the Google Docs of the genome annotation world, real-time collaborative genome annotation.",
+            "Apollo allows a group to view and manually refine predicted genome annotations",
+            "Use Apollo to edit annotations within your group.",
+            "Export manual annotations as GFF3."
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-02-29",
+        "objectives": [
+            "Load a genome into Galaxy",
+            "View annotations in JBrowse",
+            "Learn how to load JBrowse data into Apollo",
+            "Learn how to manually refine genome annotations within Apollo",
+            "Export refined genome annotations"
+        ],
+        "pageviews": 1584,
+        "priority": 6,
+        "pub_date": "2022-08-22",
+        "questions": [
+            "How to visualize your genome after automated annotations have been performed?",
+            "How to manually annotate genome after automated annotations have been performed?",
+            "How to evaluate and visualize annotated genomic features?",
+            "How do I collaborate when doing genome annotation?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "upload-rules"
                 ],
-                "workflowhub_id": "1262"
+                "type": "internal"
+            },
+            {
+                "topic_name": "genome-annotation",
+                "tutorials": [
+                    "funannotate"
+                ],
+                "type": "internal"
             }
         ],
-        "zenodo_link": ""
+        "short_id": "T00170",
+        "short_tools": [
+            "jbrowse",
+            "create_or_update",
+            "iframe"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "eukaryote",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "gmod",
+            "eukaryote",
+            "cyoa",
+            "jbrowse1",
+            "apollo2"
+        ],
+        "time_estimation": "3h",
+        "title": "Refining Genome Annotations with Apollo (eukaryotes)",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_or_update/create_or_update/4.2.5",
+            "toolshed.g2.bx.psu.edu/repos/gga/apollo_iframe/iframe/4.2.5",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1"
+        ],
+        "topic_name": "genome-annotation",
+        "topic_name_human": "Genome Annotation",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "apollo-euk",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo-euk/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo-euk/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/apollo-euk/tutorial.json"
+        },
+        "version": 13,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 156,
+        "visitors": 900,
+        "zenodo_link": "https://zenodo.org/record/3270822"
     },
     {
         "admin_install": {
@@ -121214,8 +123484,8 @@
         "dir": "topics/imaging/tutorials/object-tracking-using-cell-profiler",
         "edam_operation": [
             "Parsing",
-            "Image analysis",
-            "Quantification"
+            "Quantification",
+            "Image analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -121243,7 +123513,7 @@
             "Segment fluorescent objects using CellProfiler in Galaxy",
             "Track objects over multiple frames using CellProfiler in Galaxy"
         ],
-        "pageviews": 2270,
+        "pageviews": 2318,
         "pub_date": "2021-03-17",
         "questions": [
             "How to segment and track objects in fluorescence time-lapse microscopy images?"
@@ -121259,18 +123529,18 @@
         ],
         "short_id": "T00182",
         "short_tools": [
-            "cp_color_to_gray",
+            "cp_overlay_outlines",
             "cp_common",
-            "cp_identify_primary_objects",
-            "cp_measure_object_size_shape",
-            "cp_cellprofiler",
             "cp_save_images",
+            "cp_identify_primary_objects",
             "cp_tile",
-            "unzip",
-            "cp_track_objects",
-            "cp_overlay_outlines",
+            "cp_cellprofiler",
             "cp_measure_object_intensity",
-            "cp_export_to_spreadsheet"
+            "unzip",
+            "cp_export_to_spreadsheet",
+            "cp_color_to_gray",
+            "cp_measure_object_size_shape",
+            "cp_track_objects"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -121331,8 +123601,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 61,
-        "visitors": 1802,
+        "visit_duration": 62,
+        "visitors": 1841,
         "workflows": [
             {
                 "creators": [],
@@ -121411,7 +123681,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"Starting Modules\"];\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"ColorToGray\"];\n  0 -->|output_pipeline| 2;\n  3[\"Unzip\"];\n  1 -->|output| 3;\n  4[\"IdentifyPrimaryObjects\"];\n  2 -->|output_pipeline| 4;\n  5[\"MeasureObjectSizeShape\"];\n  4 -->|output_pipeline| 5;\n  6[\"MeasureObjectIntensity\"];\n  5 -->|output_pipeline| 6;\n  7[\"TrackObjects\"];\n  6 -->|output_pipeline| 7;\n  8[\"OverlayOutlines\"];\n  7 -->|output_pipeline| 8;\n  9[\"Tile\"];\n  8 -->|output_pipeline| 9;\n  10[\"SaveImages\"];\n  9 -->|output_pipeline| 10;\n  11[\"ExportToSpreadsheet\"];\n  10 -->|output_pipeline| 11;\n  12[\"CellProfiler\"];\n  3 -->|unzipped| 12;\n  11 -->|output_pipeline| 12;\n  dab4a9ee-fb53-4c74-93f5-8a0c7f7eb13e[\"Output\\nCellProfiler pipeline output files\"];\n  12 --> dab4a9ee-fb53-4c74-93f5-8a0c7f7eb13e;\n  style dab4a9ee-fb53-4c74-93f5-8a0c7f7eb13e stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
+                "modified": "2024-10-02 12:08:08 +0000",
                 "name": "CP_object_tracking_example",
                 "outputs": [
                     {
@@ -121608,1543 +123878,495 @@
                         "name": "IdentifyPrimaryObjects",
                         "outputs": [
                             {
-                                "name": "output_pipeline",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "bottom": -91.13333129882812,
-                            "height": 134,
-                            "left": -62.100006103515625,
-                            "right": 137.89999389648438,
-                            "top": -225.13333129882812,
-                            "width": 200,
-                            "x": -62.100006103515625,
-                            "y": -225.13333129882812
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b6eec6087271",
-                            "name": "cp_identify_primary_objects",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"con_advanced\": {\"advanced\": \"Yes\", \"__current_case__\": 1, \"input_from_nat\": \"OrigGray\", \"name_to_be_identified\": \"Nuclei\", \"min_diameter\": \"30\", \"max_diameter\": \"9999\", \"discard_outside_border\": \"Yes\", \"discard_touching_border\": \"Yes\", \"con_threshold_strategy\": {\"threshold_strategy\": \"Global\", \"__current_case__\": 1, \"con_threshold_method\": {\"threshold_method\": \"Otsu\", \"__current_case__\": 0, \"con_threshold_class\": {\"threshold_class\": \"Three classes\", \"__current_case__\": 0, \"assign_pixel\": \"Background\"}, \"threshold_smoothing_scale\": \"1.3488\", \"threshold_correction_factor\": \"1.0\", \"threshold_lower\": \"0.01\", \"threshold_upper\": \"1.0\"}}, \"con_distinguish_clumped_objects\": {\"distinguish_clumped_objects\": \"Intensity\", \"__current_case__\": 1, \"con_dividing_lines\": {\"dividing_lines\": \"Intensity\", \"__current_case__\": 1, \"con_smoothing_filter\": {\"smoothing_filter\": \"Yes\", \"__current_case__\": 1}, \"con_min_distance\": {\"min_distance\": \"Yes\", \"__current_case__\": 1}, \"speed_up\": \"Yes\"}}, \"fill_hole\": \"After both thresholding and declumping\", \"con_handling_excessive\": {\"excessive_handling\": \"Continue\", \"__current_case__\": 1}}, \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9+galaxy1",
-                        "type": "tool",
-                        "uuid": "8b8c952e-c9f2-483b-84b9-365162987b51",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "1988a994-a7f4-4abf-b7dc-3cffcd7d0331"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9+galaxy0",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "input_pipeline": {
-                                "id": 4,
-                                "output_name": "output_pipeline"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "MeasureObjectSizeShape",
-                        "outputs": [
-                            {
-                                "name": "output_pipeline",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 87.66667175292969,
-                            "height": 134,
-                            "left": 75.30000305175781,
-                            "right": 275.3000030517578,
-                            "top": -46.33332824707031,
-                            "width": 200,
-                            "x": 75.30000305175781,
-                            "y": -46.33332824707031
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "acf3aa487283",
-                            "name": "cp_measure_object_size_shape",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"rpt_object\": [{\"__index__\": 0, \"objects_to_measure\": \"Nuclei\"}], \"zernike_feature\": \"No\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9+galaxy0",
-                        "type": "tool",
-                        "uuid": "9366dc9d-f4aa-4930-b50d-e1bffe20da6e",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "a4fc756b-790d-42e8-8637-2ac9a54caa01"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9+galaxy0",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "input_pipeline": {
-                                "id": 5,
-                                "output_name": "output_pipeline"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "MeasureObjectIntensity",
-                        "outputs": [
-                            {
-                                "name": "output_pipeline",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 94.5,
-                            "height": 134,
-                            "left": 314.1166687011719,
-                            "right": 514.1166687011719,
-                            "top": -39.5,
-                            "width": 200,
-                            "x": 314.1166687011719,
-                            "y": -39.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "407925835dd9",
-                            "name": "cp_measure_object_intensity",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"rpt_image\": [{\"__index__\": 0, \"image_to_measure\": \"OrigGray\"}], \"rpt_object\": [{\"__index__\": 0, \"objects_to_measure\": \"Nuclei\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9+galaxy0",
-                        "type": "tool",
-                        "uuid": "47e32310-e656-411a-a34b-a80ef90b4596",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "83dd3bbf-cf0b-4581-a73e-dedf91383a61"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_track_objects/cp_track_objects/3.1.9+galaxy0",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "input_pipeline": {
-                                "id": 6,
-                                "output_name": "output_pipeline"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "TrackObjects",
-                        "outputs": [
-                            {
-                                "name": "output_pipeline",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 265.75,
-                            "height": 134,
-                            "left": 469.6333312988281,
-                            "right": 669.6333312988281,
-                            "top": 131.75,
-                            "width": 200,
-                            "x": 469.6333312988281,
-                            "y": 131.75
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_track_objects/cp_track_objects/3.1.9+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "1fd453cd757b",
-                            "name": "cp_track_objects",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"con_tracking_method\": {\"tracking_method\": \"Overlap\", \"__current_case__\": 0, \"max_distance\": \"50\", \"con_filter_by_lifetime\": {\"filter_by_lifetime\": \"No\", \"__current_case__\": 1}, \"display_option\": \"Color and Number\", \"con_save_coded_img\": {\"save_coded_img\": \"Yes\", \"__current_case__\": 0, \"name_output_img\": \"TrackedCells\"}}, \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"object_to_track\": \"Nuclei\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9+galaxy0",
-                        "type": "tool",
-                        "uuid": "39cf58a1-e5e5-4fd4-abc7-12fa772877e7",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "327ce30c-a4c9-4dff-99f1-cdcc82ce101d"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_overlay_outlines/cp_overlay_outlines/3.1.9+galaxy0",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "input_pipeline": {
-                                "id": 7,
-                                "output_name": "output_pipeline"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "OverlayOutlines",
-                        "outputs": [
-                            {
-                                "name": "output_pipeline",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 443.04998779296875,
-                            "height": 134,
-                            "left": 595.9666748046875,
-                            "right": 795.9666748046875,
-                            "top": 309.04998779296875,
-                            "width": 200,
-                            "x": 595.9666748046875,
-                            "y": 309.04998779296875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_overlay_outlines/cp_overlay_outlines/3.1.9+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "91560258e972",
-                            "name": "cp_overlay_outlines",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"con_blank_img\": {\"blank_img\": \"No\", \"__current_case__\": 1, \"image_to_outline\": \"OrigGray\", \"con_display_mode\": {\"display_mode\": \"Color\", \"__current_case__\": 0, \"rpt_obj_to_display\": [{\"__index__\": 0, \"obj_to_display\": \"Nuclei\", \"outline_color\": \"#ff0000\"}]}}, \"howto_outline\": \"Inner\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"name_output_image\": \"OutlineImage\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9+galaxy0",
-                        "type": "tool",
-                        "uuid": "725e19a9-31dc-463f-ba04-9704626e6077",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "c0550e15-158b-4a4d-a1cc-a4877e1bb77a"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_tile/cp_tile/3.1.9+galaxy0",
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "input_pipeline": {
-                                "id": 8,
-                                "output_name": "output_pipeline"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Tile",
-                        "outputs": [
-                            {
-                                "name": "output_pipeline",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 431.0166778564453,
-                            "height": 113.59999084472656,
-                            "left": 829.0999755859375,
-                            "right": 1029.0999755859375,
-                            "top": 317.41668701171875,
-                            "width": 200,
-                            "x": 829.0999755859375,
-                            "y": 317.41668701171875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_tile/cp_tile/3.1.9+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "878bafb411dd",
-                            "name": "cp_tile",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"con_assembly_method\": {\"assembly_method\": \"Within cycles\", \"__current_case__\": 0, \"con_calc_no_row\": {\"calc_no_row\": \"No\", \"__current_case__\": 1, \"no_of_row\": \"1\"}, \"con_calc_no_cols\": {\"calc_no_cols\": \"Yes\", \"__current_case__\": 0}, \"corner_to_begin\": \"top left\", \"direction\": \"row\", \"meander_mode\": \"No\", \"rpt_additional_image\": [{\"__index__\": 0, \"additional_img\": \"OutlineImage\"}, {\"__index__\": 1, \"additional_img\": \"TrackedCells\"}]}, \"input_image\": \"OrigColor\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"output_image_name\": \"TiledImages\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9+galaxy0",
-                        "type": "tool",
-                        "uuid": "210b3d0d-1139-4934-886b-805c1fcfa3de",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "83dbb3d1-3126-4e95-a2ea-d8f9a6ed5722"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9+galaxy1",
-                        "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "input_pipeline": {
-                                "id": 9,
-                                "output_name": "output_pipeline"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool SaveImages",
-                                "name": "input_pipeline"
-                            }
-                        ],
-                        "label": null,
-                        "name": "SaveImages",
-                        "outputs": [
-                            {
-                                "name": "output_pipeline",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 591.4833374023438,
-                            "height": 113.60000610351562,
-                            "left": 887.566650390625,
-                            "right": 1087.566650390625,
-                            "top": 477.8833312988281,
-                            "width": 200,
-                            "x": 887.566650390625,
-                            "y": 477.8833312988281
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "33f4fa1413fb",
-                            "name": "cp_save_images",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"con_method_for_constructing\": {\"method_for_constructing\": \"From image filename\", \"__current_case__\": 0, \"name_for_file_prefix\": \"OrigColor\", \"con_append_suffix\": {\"append_suffix\": \"Yes\", \"__current_case__\": 0, \"text_to_append\": \"\"}}, \"con_type_of_image\": {\"type_of_image\": \"Image\", \"__current_case__\": 0, \"con_save_file_format\": {\"file_format\": \"png\", \"__current_case__\": 3}}, \"image_to_save\": \"TiledImages\", \"input_pipeline\": {\"__class__\": \"RuntimeValue\"}, \"overwrite_without_warning\": \"Yes\", \"record_info\": \"No\", \"when_to_save\": \"Every cycle\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9+galaxy1",
-                        "type": "tool",
-                        "uuid": "86647f83-5316-4577-be99-1d966eb2f92a",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "1c29a3c6-ebb0-4ece-b2cf-aeeb0cdf6e1e"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9+galaxy1",
-                        "errors": null,
-                        "id": 11,
-                        "input_connections": {
-                            "input_pipeline": {
-                                "id": 10,
-                                "output_name": "output_pipeline"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "ExportToSpreadsheet",
-                        "outputs": [
-                            {
-                                "name": "output_pipeline",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 586.816650390625,
-                            "height": 134,
-                            "left": 1144.7833251953125,
-                            "right": 1344.7833251953125,
-                            "top": 452.816650390625,
-                            "width": 200,
-                            "x": 1144.7833251953125,
-                            "y": 452.816650390625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "d0178bdcd00e",
-                            "name": "cp_export_to_spreadsheet",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"add_metadata_column_to_object\": \"Yes\", \"calc_mean\": \"Yes\", \"calc_median\": \"No\", \"calc_standard_deviation\": \"No\", \"con_create_gene_pattern\": {\"create_gene_pattern\": \"No\", \"__current_case__\": 1}, \"con_export_all_measurements\": {\"__current_case__\": 1, \"export_all_measurements\": \"Yes\"}, \"con_prefix\": {\"add_prefix\": \"No\", \"__current_case__\": 1}, \"delimiter\": \"Comma (\\\",\\\")\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"overwrite_existing_file\": \"Yes\", \"represent_nan\": \"NaN\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9+galaxy1",
-                        "type": "tool",
-                        "uuid": "c08309b4-101c-4150-bb88-c2856bb2636e",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_pipeline",
-                                "uuid": "52f72fd2-726e-40b1-b168-7396a64f7a16"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9+galaxy0",
-                        "errors": null,
-                        "id": 12,
-                        "input_connections": {
-                            "con_input_type|input_images": {
-                                "id": 3,
-                                "output_name": "unzipped"
-                            },
-                            "pipeline": {
-                                "id": 11,
-                                "output_name": "output_pipeline"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "CellProfiler",
-                        "outputs": [
-                            {
-                                "name": "pipeline_output",
-                                "type": "input"
-                            },
-                            {
-                                "name": "logs",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 808.9333190917969,
-                            "height": 174.39999389648438,
-                            "left": 1371.8333740234375,
-                            "right": 1571.8333740234375,
-                            "top": 634.5333251953125,
-                            "width": 200,
-                            "x": 1371.8333740234375,
-                            "y": 634.5333251953125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "0e4dccaafef5",
-                            "name": "cp_cellprofiler",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"con_input_type\": {\"input_type\": \"no\", \"__current_case__\": 0, \"input_images\": {\"__class__\": \"ConnectedValue\"}}, \"detailed_output\": \"true\", \"pipeline\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.1.9+galaxy0",
-                        "type": "tool",
-                        "uuid": "da0bad08-2691-40e5-b2ae-24890ea16e7b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "logs",
-                                "uuid": "ca4a668b-b33c-41fa-a427-ad3b83c2d07f"
-                            },
-                            {
-                                "label": "CellProfiler pipeline output files",
-                                "output_name": "pipeline_output",
-                                "uuid": "dab4a9ee-fb53-4c74-93f5-8a0c7f7eb13e"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "imaging/object-tracking-using-cell-profiler",
-                "path": "topics/imaging/tutorials/object-tracking-using-cell-profiler/workflows/main_workflow.ga",
-                "tags": [
-                    "CellProfiler",
-                    "imaging"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "CP_object_tracking_example",
-                "topic_id": "imaging",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/imaging-object-tracking-using-cell-profiler/versions/main-workflow",
-                "tutorial_id": "object-tracking-using-cell-profiler",
-                "url": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/object-tracking-using-cell-profiler/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/object-tracking-using-cell-profiler/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "imaging-object-tracking-using-cell-profiler",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_color_to_gray/cp_color_to_gray/3.1.9+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_overlay_outlines/cp_overlay_outlines/3.1.9+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_tile/cp_tile/3.1.9+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_track_objects/cp_track_objects/3.1.9+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/0.2"
-                ],
-                "workflowhub_id": "1254"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.4567084"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "mesmer",
-                    "owner": "goeckslab",
-                    "revisions": "187918c47051",
-                    "tool_panel_section_label": "Spatial Omics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "rename_tiff_channels",
-                    "owner": "goeckslab",
-                    "revisions": "09e240a12897",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scimap_mcmicro_to_anndata",
-                    "owner": "goeckslab",
-                    "revisions": "8ca435ec19be",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scimap_phenotyping",
-                    "owner": "goeckslab",
-                    "revisions": "dcfcad35e847",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "vitessce_spatial",
-                    "owner": "goeckslab",
-                    "revisions": "9f60ef2d586e",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bfconvert",
-                    "owner": "imgteam",
-                    "revisions": "f3360fbeda64",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ashlar",
-                    "owner": "perssond",
-                    "revisions": "33ab2058c6d9",
-                    "tool_panel_section_label": "Spatial Omics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "basic_illumination",
-                    "owner": "perssond",
-                    "revisions": "acc6f509968c",
-                    "tool_panel_section_label": "Spatial Omics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "coreograph",
-                    "owner": "perssond",
-                    "revisions": "ee92746d141a",
-                    "tool_panel_section_label": "Spatial Omics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "quantification",
-                    "owner": "perssond",
-                    "revisions": "3a916c4e9f5f",
-                    "tool_panel_section_label": "Spatial Omics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: mesmer\n  owner: goeckslab\n  revisions: 187918c47051\n  tool_panel_section_label: Spatial Omics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rename_tiff_channels\n  owner: goeckslab\n  revisions: '09e240a12897'\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scimap_mcmicro_to_anndata\n  owner: goeckslab\n  revisions: 8ca435ec19be\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scimap_phenotyping\n  owner: goeckslab\n  revisions: dcfcad35e847\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: vitessce_spatial\n  owner: goeckslab\n  revisions: 9f60ef2d586e\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bfconvert\n  owner: imgteam\n  revisions: f3360fbeda64\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ashlar\n  owner: perssond\n  revisions: 33ab2058c6d9\n  tool_panel_section_label: Spatial Omics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: basic_illumination\n  owner: perssond\n  revisions: acc6f509968c\n  tool_panel_section_label: Spatial Omics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: coreograph\n  owner: perssond\n  revisions: ee92746d141a\n  tool_panel_section_label: Spatial Omics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quantification\n  owner: perssond\n  revisions: 3a916c4e9f5f\n  tool_panel_section_label: Spatial Omics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.json",
-        "contributors": [
-            {
-                "email": "watsocam@ohsu.edu",
-                "id": "CameronFRWatson",
-                "joined": "2022-07",
-                "name": "Cameron Watson",
-                "orcid": "0000-0002-6942-2469",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/CameronFRWatson/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/CameronFRWatson.json"
-            },
-            {
-                "email": "creason@ohsu.edu",
-                "id": "alliecreason",
-                "joined": "2023-02",
-                "name": "Allison Creason",
-                "orcid": "0000-0001-5724-1276",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/alliecreason/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/alliecreason.json"
-            }
-        ],
-        "dir": "topics/imaging/tutorials/multiplex-tissue-imaging-TMA",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "imaging/multiplex-tissue-imaging-TMA",
-        "inexact_supported_servers": [
-            "UseGalaxy.no"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Galaxy has tools and workflows that can be used to process and analyze multiplex tissue images",
-            "Cell feature tables produced by the Galaxy TMA workflow can be used for downstream single-cell and spatial analyses",
-            "There are powerful interactive visualization tools available in Galaxy that can combine the real images with associated data",
-            "Tissue Microarray data can be analyzed using workflows that invoke MTI tools in batch",
-            "Segmentation quality can vary significantly depending on features of the input image, tool used, and parameters"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Understand the tools available in Galaxy for multiplex tissue imaging analysis",
-            "Analyze and visualize publicly available TMA data using Galaxy"
-        ],
-        "pageviews": 1005,
-        "pub_date": "2023-02-14",
-        "questions": [
-            "What tools are available for pre-processing multiplex tissue images in Galaxy?",
-            "What tools are available for downstream analysis of multiplex tissue images in Galaxy?",
-            "How do I pre-process and analyze Tissue Microarray data?",
-            "How can I visualize multiplex tissue images and associated data?",
-            "How can I assign phenotypes to cells in an MTI dataset?"
-        ],
-        "short_id": "T00334",
-        "short_tools": [
-            "basic_illumination",
-            "ip_convertimage",
-            "vitessce_spatial",
-            "scimap_mcmicro_to_anndata",
-            "unet_coreograph",
-            "rename_tiff_channels",
-            "mesmer",
-            "quantification",
-            "ashlar",
-            "scimap_phenotyping"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "time_estimation": "3H",
-        "title": "End-to-End Tissue Microarray Image Analysis with Galaxy-ME",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/goeckslab/mesmer/mesmer/0.12.3+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/goeckslab/rename_tiff_channels/rename_tiff_channels/0.0.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata/0.17.7+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_phenotyping/scimap_phenotyping/0.17.7+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/1.0.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/perssond/ashlar/ashlar/1.14.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/basic_illumination/1.0.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/perssond/coreograph/unet_coreograph/2.2.8+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/perssond/quantification/quantification/1.5.3+galaxy1"
-        ],
-        "topic_name": "imaging",
-        "topic_name_human": "Imaging",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "multiplex-tissue-imaging-TMA",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.json"
-        },
-        "version": 3,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 110,
-        "visitors": 729,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "End-to-End Tissue Microarray Analysis with Galaxy-ME",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmarkers.csv\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPhenotypeWorkflow\"]\n  3[label=\"BaSiC Illumination\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"ASHLAR\"]\n  3 -> 4 [label=\"output_dfp\"]\n  3 -> 4 [label=\"output_ffp\"]\n  0 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"UNetCoreograph\"]\n  4 -> 5 [label=\"output\"]\n  6[label=\"Mesmer\"]\n  5 -> 6 [label=\"tma_sections\"]\n  kee73bee359e74e1c87fd197b8eac7e15[color=lightseagreen,label=\"Output\\nMesmer on input dataset(s): Mask\"]\n  6 -> kee73bee359e74e1c87fd197b8eac7e15\n  7[label=\"Convert image\"]\n  5 -> 7 [label=\"tma_sections\"]\n  8[label=\"MCQUANT\"]\n  1 -> 8 [label=\"output\"]\n  5 -> 8 [label=\"tma_sections\"]\n  6 -> 8 [label=\"mask\"]\n  kfe28534a2b3f4ecc8ba9a106b2d1425c[color=lightseagreen,label=\"Output\\nPrimary Mask Quantification\"]\n  8 -> kfe28534a2b3f4ecc8ba9a106b2d1425c\n  9[label=\"Rename OME-TIFF Channels\"]\n  1 -> 9 [label=\"output\"]\n  7 -> 9 [label=\"output\"]\n  10[label=\"Convert McMicro Output to Anndata\"]\n  8 -> 10 [label=\"cellmask\"]\n  11[label=\"Single Cell Phenotyping\"]\n  10 -> 11 [label=\"outfile\"]\n  2 -> 11 [label=\"output\"]\n  12[label=\"Vitessce Visualization\"]\n  11 -> 12 [label=\"output\"]\n  9 -> 12 [label=\"renamed_image\"]\n  6 -> 12 [label=\"mask\"]\n}",
-                "history": [
-                    {
-                        "hash": "74c571972f6c9c00bca6242b05cab50a0c947af0",
-                        "message": "update tool IDs, params to tutorial; add updated workflow; add hands-on avivator example to tutorial",
-                        "num": 3,
-                        "short_hash": "74c571972",
-                        "unix": "1675987355"
-                    },
-                    {
-                        "hash": "b0bac741569e5790eca8b5f21619220cea4ab902",
-                        "message": "update tool IDs in MTI workflow for linting",
-                        "num": 2,
-                        "short_hash": "b0bac7415",
-                        "unix": "1657213046"
-                    },
-                    {
-                        "hash": "aa2aba190643cbb000c0c2916d4c3656c1988e2d",
-                        "message": "Multiplex Imaging tutorial - initial push",
-                        "num": 1,
-                        "short_hash": "aa2aba190",
-                        "unix": "1656910720"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Input Dataset Collection"
-                            }
-                        ],
-                        "label": "Input Dataset Collection",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 371.28125,
-                            "height": 82.1953125,
-                            "left": -742,
-                            "right": -542,
-                            "top": 289.0859375,
-                            "width": 200,
-                            "x": -742,
-                            "y": 289.0859375
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "df4b5b73-b816-4362-b95b-f4571766abfe",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "markers.csv"
-                            }
-                        ],
-                        "label": "markers.csv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 760.8828125,
-                            "height": 61.796875,
-                            "left": -408,
-                            "right": -208,
-                            "top": 699.0859375,
-                            "width": 200,
-                            "x": -408,
-                            "y": 699.0859375
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "8d2425da-b96c-4955-81c3-9303bec9cf9a",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "PhenotypeWorkflow"
-                            }
-                        ],
-                        "label": "PhenotypeWorkflow",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 704.28125,
-                            "height": 82.1953125,
-                            "left": 911,
-                            "right": 1111,
-                            "top": 622.0859375,
-                            "width": 200,
-                            "x": 911,
-                            "y": 622.0859375
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"csv\"], \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "9748c022-951a-40b6-9371-fc35ee908110",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nmarkers.csv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nPhenotypeWorkflow\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"BaSiC Illumination\"];\n  0 -->|output| 3;\n  4[\"ASHLAR\"];\n  3 -->|output_dfp| 4;\n  3 -->|output_ffp| 4;\n  0 -->|output| 4;\n  1 -->|output| 4;\n  5[\"UNetCoreograph\"];\n  4 -->|output| 5;\n  6[\"Mesmer\"];\n  5 -->|tma_sections| 6;\n  ee73bee3-59e7-4e1c-87fd-197b8eac7e15[\"Output\\nMesmer on input dataset(s): Mask\"];\n  6 --> ee73bee3-59e7-4e1c-87fd-197b8eac7e15;\n  style ee73bee3-59e7-4e1c-87fd-197b8eac7e15 stroke:#2c3143,stroke-width:4px;\n  7[\"Convert image\"];\n  5 -->|tma_sections| 7;\n  8[\"MCQUANT\"];\n  1 -->|output| 8;\n  5 -->|tma_sections| 8;\n  6 -->|mask| 8;\n  fe28534a-2b3f-4ecc-8ba9-a106b2d1425c[\"Output\\nPrimary Mask Quantification\"];\n  8 --> fe28534a-2b3f-4ecc-8ba9-a106b2d1425c;\n  style fe28534a-2b3f-4ecc-8ba9-a106b2d1425c stroke:#2c3143,stroke-width:4px;\n  9[\"Rename OME-TIFF Channels\"];\n  1 -->|output| 9;\n  7 -->|output| 9;\n  10[\"Convert McMicro Output to Anndata\"];\n  8 -->|cellmask| 10;\n  11[\"Single Cell Phenotyping\"];\n  10 -->|outfile| 11;\n  2 -->|output| 11;\n  12[\"Vitessce Visualization\"];\n  11 -->|output| 12;\n  9 -->|renamed_image| 12;\n  6 -->|mask| 12;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "GTN_Exemplar_002_TMA_workflow",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/basic_illumination/1.0.3+galaxy1",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "in_files": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool BaSiC Illumination",
-                                "name": "in_files"
-                            }
-                        ],
-                        "label": null,
-                        "name": "BaSiC Illumination",
-                        "outputs": [
-                            {
-                                "name": "output_dfp",
-                                "type": "tiff"
-                            },
-                            {
-                                "name": "output_ffp",
-                                "type": "tiff"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 475.875,
-                            "height": 184.7890625,
-                            "left": -430,
-                            "right": -230,
-                            "top": 291.0859375,
-                            "width": 200,
-                            "x": -430,
-                            "y": 291.0859375
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/basic_illumination/1.0.3+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "acc6f509968c",
-                            "name": "basic_illumination",
-                            "owner": "perssond",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"in_files\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
-                        "type": "tool",
-                        "uuid": "d8dcb396-6420-4fd4-9ac8-8b4a86bc1767",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_dfp",
-                                "uuid": "1c6a93d0-6f2b-442a-a255-bfea77cb9c4f"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_ffp",
-                                "uuid": "b30ada0d-9d98-4cb4-aeac-570d42683135"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/perssond/ashlar/ashlar/1.14.0+galaxy1",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "ldfp": {
-                                "id": 3,
-                                "output_name": "output_dfp"
-                            },
-                            "lffp": {
-                                "id": 3,
-                                "output_name": "output_ffp"
-                            },
-                            "lraw": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "upgrade|markers_file": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool ASHLAR",
-                                "name": "ldfp"
-                            },
-                            {
-                                "description": "runtime parameter for tool ASHLAR",
-                                "name": "lffp"
-                            },
-                            {
-                                "description": "runtime parameter for tool ASHLAR",
-                                "name": "lraw"
-                            },
-                            {
-                                "description": "runtime parameter for tool ASHLAR",
-                                "name": "upgrade"
-                            }
-                        ],
-                        "label": null,
-                        "name": "ASHLAR",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "ome.tiff"
+                                "name": "output_pipeline",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 493.875,
-                            "height": 204.7890625,
-                            "left": -168,
-                            "right": 32,
-                            "top": 289.0859375,
+                            "bottom": -91.13333129882812,
+                            "height": 134,
+                            "left": -62.100006103515625,
+                            "right": 137.89999389648438,
+                            "top": -225.13333129882812,
                             "width": 200,
-                            "x": -168,
-                            "y": 289.0859375
+                            "x": -62.100006103515625,
+                            "y": -225.13333129882812
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/perssond/ashlar/ashlar/1.14.0+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "33ab2058c6d9",
-                            "name": "ashlar",
-                            "owner": "perssond",
+                            "changeset_revision": "b6eec6087271",
+                            "name": "cp_identify_primary_objects",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"align_channel\": \"0\", \"filter_sigma\": null, \"tile_size\": null, \"flip_mosaic_x\": \"false\", \"flip_mosaic_y\": \"false\", \"pyramid\": \"true\"}, \"flip_x\": \"false\", \"flip_y\": \"false\", \"ldfp\": {\"__class__\": \"RuntimeValue\"}, \"lffp\": {\"__class__\": \"RuntimeValue\"}, \"lraw\": {\"__class__\": \"RuntimeValue\"}, \"max_shift\": \"30\", \"upgrade\": {\"decide\": \"do_upgrade\", \"__current_case__\": 0, \"markers_file\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"con_advanced\": {\"advanced\": \"Yes\", \"__current_case__\": 1, \"input_from_nat\": \"OrigGray\", \"name_to_be_identified\": \"Nuclei\", \"min_diameter\": \"30\", \"max_diameter\": \"9999\", \"discard_outside_border\": \"Yes\", \"discard_touching_border\": \"Yes\", \"con_threshold_strategy\": {\"threshold_strategy\": \"Global\", \"__current_case__\": 1, \"con_threshold_method\": {\"threshold_method\": \"Otsu\", \"__current_case__\": 0, \"con_threshold_class\": {\"threshold_class\": \"Three classes\", \"__current_case__\": 0, \"assign_pixel\": \"Background\"}, \"threshold_smoothing_scale\": \"1.3488\", \"threshold_correction_factor\": \"1.0\", \"threshold_lower\": \"0.01\", \"threshold_upper\": \"1.0\"}}, \"con_distinguish_clumped_objects\": {\"distinguish_clumped_objects\": \"Intensity\", \"__current_case__\": 1, \"con_dividing_lines\": {\"dividing_lines\": \"Intensity\", \"__current_case__\": 1, \"con_smoothing_filter\": {\"smoothing_filter\": \"Yes\", \"__current_case__\": 1}, \"con_min_distance\": {\"min_distance\": \"Yes\", \"__current_case__\": 1}, \"speed_up\": \"Yes\"}}, \"fill_hole\": \"After both thresholding and declumping\", \"con_handling_excessive\": {\"excessive_handling\": \"Continue\", \"__current_case__\": 1}}, \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9+galaxy1",
                         "type": "tool",
-                        "uuid": "01551249-f885-48f6-95de-45d12c255066",
+                        "uuid": "8b8c952e-c9f2-483b-84b9-365162987b51",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "d86f47ed-259c-47f9-b61c-1538653c0733"
+                                "output_name": "output_pipeline",
+                                "uuid": "1988a994-a7f4-4abf-b7dc-3cffcd7d0331"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/perssond/coreograph/unet_coreograph/2.2.8+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9+galaxy0",
                         "errors": null,
                         "id": 5,
                         "input_connections": {
-                            "source_image": {
+                            "input_pipeline": {
                                 "id": 4,
-                                "output_name": "output"
+                                "output_name": "output_pipeline"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool UNetCoreograph",
-                                "name": "source_image"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "UNetCoreograph",
+                        "name": "MeasureObjectSizeShape",
                         "outputs": [
                             {
-                                "name": "tma_sections",
-                                "type": "input"
-                            },
-                            {
-                                "name": "masks",
-                                "type": "input"
-                            },
-                            {
-                                "name": "TMA_MAP",
-                                "type": "tiff"
+                                "name": "output_pipeline",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 585.8671875,
-                            "height": 296.78125,
-                            "left": 81,
-                            "right": 281,
-                            "top": 289.0859375,
+                            "bottom": 87.66667175292969,
+                            "height": 134,
+                            "left": 75.30000305175781,
+                            "right": 275.3000030517578,
+                            "top": -46.33332824707031,
                             "width": 200,
-                            "x": 81,
-                            "y": 289.0859375
+                            "x": 75.30000305175781,
+                            "y": -46.33332824707031
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/perssond/coreograph/unet_coreograph/2.2.8+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "ee92746d141a",
-                            "name": "coreograph",
-                            "owner": "perssond",
+                            "changeset_revision": "acf3aa487283",
+                            "name": "cp_measure_object_size_shape",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"buffer\": \"2.0\", \"channel\": \"0\", \"cluster\": \"false\", \"downsamplefactor\": \"5\", \"sensitivity\": \"0.3\", \"source_image\": {\"__class__\": \"RuntimeValue\"}, \"tissue\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"rpt_object\": [{\"__index__\": 0, \"objects_to_measure\": \"Nuclei\"}], \"zernike_feature\": \"No\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9+galaxy0",
                         "type": "tool",
-                        "uuid": "307e61ea-1b23-41dc-82c8-3df1988179c1",
+                        "uuid": "9366dc9d-f4aa-4930-b50d-e1bffe20da6e",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "masks",
-                                "uuid": "69ca4dab-bd1f-49bc-84c5-71360be56577"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "TMA_MAP",
-                                "uuid": "e4f74e11-7d44-4cea-a065-8c15af8171df"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "tma_sections",
-                                "uuid": "b031e518-f1cc-4bef-9b90-429d36234b1b"
+                                "output_name": "output_pipeline",
+                                "uuid": "a4fc756b-790d-42e8-8637-2ac9a54caa01"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/mesmer/mesmer/0.12.3+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9+galaxy0",
                         "errors": null,
                         "id": 6,
                         "input_connections": {
-                            "image": {
+                            "input_pipeline": {
                                 "id": 5,
-                                "output_name": "tma_sections"
+                                "output_name": "output_pipeline"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Mesmer",
-                                "name": "image"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Mesmer",
+                        "name": "MeasureObjectIntensity",
                         "outputs": [
                             {
-                                "name": "mask",
-                                "type": "tiff"
+                                "name": "output_pipeline",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 422.9921875,
-                            "height": 133.9921875,
-                            "left": 371,
-                            "right": 571,
-                            "top": 289,
+                            "bottom": 94.5,
+                            "height": 134,
+                            "left": 314.1166687011719,
+                            "right": 514.1166687011719,
+                            "top": -39.5,
                             "width": 200,
-                            "x": 371,
-                            "y": 289
+                            "x": 314.1166687011719,
+                            "y": -39.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/mesmer/mesmer/0.12.3+galaxy2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "187918c47051",
-                            "name": "mesmer",
-                            "owner": "goeckslab",
+                            "changeset_revision": "407925835dd9",
+                            "name": "cp_measure_object_intensity",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"compartment_select\": {\"compartment\": \"nuclear\", \"__current_case__\": 0, \"nuclear_options\": {\"pixel_expansion\": null, \"maxima_threshold\": \"0.1\", \"adv_options\": {\"maxima_smooth\": \"0\", \"interior_threshold\": \"0.2\", \"interior_smooth\": \"2\", \"small_objects_threshold\": \"15\", \"fill_holes_threshold\": \"15\", \"radius\": \"1\"}}}, \"image\": {\"__class__\": \"RuntimeValue\"}, \"image_mpp\": \"0.65\", \"nuclear_channels\": \"0\", \"squeeze\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"rpt_image\": [{\"__index__\": 0, \"image_to_measure\": \"OrigGray\"}], \"rpt_object\": [{\"__index__\": 0, \"objects_to_measure\": \"Nuclei\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9+galaxy0",
                         "type": "tool",
-                        "uuid": "d15a2489-42d5-47f2-8da2-a4d86c293af0",
+                        "uuid": "47e32310-e656-411a-a34b-a80ef90b4596",
                         "workflow_outputs": [
                             {
-                                "label": "Mesmer on input dataset(s): Mask",
-                                "output_name": "mask",
-                                "uuid": "ee73bee3-59e7-4e1c-87fd-197b8eac7e15"
+                                "label": null,
+                                "output_name": "output_pipeline",
+                                "uuid": "83dd3bbf-cf0b-4581-a73e-dedf91383a61"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_track_objects/cp_track_objects/3.1.9+galaxy0",
                         "errors": null,
                         "id": 7,
                         "input_connections": {
-                            "input_file": {
-                                "id": 5,
-                                "output_name": "tma_sections"
+                            "input_pipeline": {
+                                "id": 6,
+                                "output_name": "output_pipeline"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Convert image",
-                                "name": "input_file"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Convert image",
+                        "name": "TrackObjects",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "tiff"
+                                "name": "output_pipeline",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 729.59375,
-                            "height": 113.59375,
-                            "left": 345,
-                            "right": 545,
-                            "top": 616,
+                            "bottom": 265.75,
+                            "height": 134,
+                            "left": 469.6333312988281,
+                            "right": 669.6333312988281,
+                            "top": 131.75,
                             "width": 200,
-                            "x": 345,
-                            "y": 616
+                            "x": 469.6333312988281,
+                            "y": 131.75
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_track_objects/cp_track_objects/3.1.9+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "f3360fbeda64",
-                            "name": "bfconvert",
-                            "owner": "imgteam",
+                            "changeset_revision": "1fd453cd757b",
+                            "name": "cp_track_objects",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"bigtiff\": \"false\", \"channel_options\": {\"extract\": \"False\", \"__current_case__\": 0}, \"compression\": \"False\", \"crop_options\": {\"extract\": \"False\", \"__current_case__\": 0}, \"input_file\": {\"__class__\": \"RuntimeValue\"}, \"noflat\": \"true\", \"out_format\": \"ome.tiff\", \"pyramid_options\": {\"generate\": \"True\", \"__current_case__\": 0, \"pyramid_resolutions\": \"4\", \"pyramid_scale\": \"2\"}, \"range_options\": {\"extract\": \"False\", \"__current_case__\": 0}, \"series_options\": {\"extract\": \"False\", \"__current_case__\": 0}, \"tile_options\": {\"extract\": \"True\", \"__current_case__\": 1, \"tile_x\": \"512\", \"tile_y\": \"512\"}, \"timepoint_options\": {\"extract\": \"False\", \"__current_case__\": 0}, \"z_options\": {\"extract\": \"False\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"con_tracking_method\": {\"tracking_method\": \"Overlap\", \"__current_case__\": 0, \"max_distance\": \"50\", \"con_filter_by_lifetime\": {\"filter_by_lifetime\": \"No\", \"__current_case__\": 1}, \"display_option\": \"Color and Number\", \"con_save_coded_img\": {\"save_coded_img\": \"Yes\", \"__current_case__\": 0, \"name_output_img\": \"TrackedCells\"}}, \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"object_to_track\": \"Nuclei\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9+galaxy0",
                         "type": "tool",
-                        "uuid": "0bb1cbe2-35ee-4711-a37c-8ffe769a953a",
+                        "uuid": "39cf58a1-e5e5-4fd4-abc7-12fa772877e7",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "e4bd4c1a-00b4-47f9-8e75-7968b5824e19"
+                                "output_name": "output_pipeline",
+                                "uuid": "327ce30c-a4c9-4dff-99f1-cdcc82ce101d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/perssond/quantification/quantification/1.5.3+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_overlay_outlines/cp_overlay_outlines/3.1.9+galaxy0",
                         "errors": null,
                         "id": 8,
                         "input_connections": {
-                            "channel_names": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "image": {
-                                "id": 5,
-                                "output_name": "tma_sections"
-                            },
-                            "primary_mask": {
-                                "id": 6,
-                                "output_name": "mask"
+                            "input_pipeline": {
+                                "id": 7,
+                                "output_name": "output_pipeline"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool MCQUANT",
-                                "name": "channel_names"
-                            },
-                            {
-                                "description": "runtime parameter for tool MCQUANT",
-                                "name": "image"
-                            },
-                            {
-                                "description": "runtime parameter for tool MCQUANT",
-                                "name": "primary_mask"
-                            },
-                            {
-                                "description": "runtime parameter for tool MCQUANT",
-                                "name": "supp_mask"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "MCQUANT",
+                        "name": "OverlayOutlines",
                         "outputs": [
                             {
-                                "name": "cellmask",
-                                "type": "csv"
-                            },
-                            {
-                                "name": "suppmask",
-                                "type": "csv"
+                                "name": "output_pipeline",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 544.5859375,
-                            "height": 255.5859375,
-                            "left": 638,
-                            "right": 838,
-                            "top": 289,
+                            "bottom": 443.04998779296875,
+                            "height": 134,
+                            "left": 595.9666748046875,
+                            "right": 795.9666748046875,
+                            "top": 309.04998779296875,
                             "width": 200,
-                            "x": 638,
-                            "y": 289
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionsuppmask": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "suppmask"
-                            }
+                            "x": 595.9666748046875,
+                            "y": 309.04998779296875
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/perssond/quantification/quantification/1.5.3+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_overlay_outlines/cp_overlay_outlines/3.1.9+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "3a916c4e9f5f",
-                            "name": "quantification",
-                            "owner": "perssond",
+                            "changeset_revision": "91560258e972",
+                            "name": "cp_overlay_outlines",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"channel_names\": {\"__class__\": \"RuntimeValue\"}, \"image\": {\"__class__\": \"RuntimeValue\"}, \"intensity_props\": \"\", \"mask_props\": \"\", \"primary_mask\": {\"__class__\": \"RuntimeValue\"}, \"supp_mask\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"con_blank_img\": {\"blank_img\": \"No\", \"__current_case__\": 1, \"image_to_outline\": \"OrigGray\", \"con_display_mode\": {\"display_mode\": \"Color\", \"__current_case__\": 0, \"rpt_obj_to_display\": [{\"__index__\": 0, \"obj_to_display\": \"Nuclei\", \"outline_color\": \"#ff0000\"}]}}, \"howto_outline\": \"Inner\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"name_output_image\": \"OutlineImage\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9+galaxy0",
                         "type": "tool",
-                        "uuid": "e743e3d4-538c-475c-95be-94af7805246c",
+                        "uuid": "725e19a9-31dc-463f-ba04-9704626e6077",
                         "workflow_outputs": [
                             {
-                                "label": "Primary Mask Quantification",
-                                "output_name": "cellmask",
-                                "uuid": "fe28534a-2b3f-4ecc-8ba9-a106b2d1425c"
+                                "label": null,
+                                "output_name": "output_pipeline",
+                                "uuid": "c0550e15-158b-4a4d-a1cc-a4877e1bb77a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/rename_tiff_channels/rename_tiff_channels/0.0.1+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_tile/cp_tile/3.1.9+galaxy0",
                         "errors": null,
                         "id": 9,
                         "input_connections": {
-                            "channel_csv": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "image": {
-                                "id": 7,
-                                "output_name": "output"
+                            "input_pipeline": {
+                                "id": 8,
+                                "output_name": "output_pipeline"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Rename OME-TIFF Channels",
-                                "name": "channel_csv"
-                            },
-                            {
-                                "description": "runtime parameter for tool Rename OME-TIFF Channels",
-                                "name": "image"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Rename OME-TIFF Channels",
+                        "name": "Tile",
                         "outputs": [
                             {
-                                "name": "renamed_image",
-                                "type": "ome.tiff"
+                                "name": "output_pipeline",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 825.1875,
-                            "height": 205.1875,
-                            "left": 651,
-                            "right": 851,
-                            "top": 620,
+                            "bottom": 431.0166778564453,
+                            "height": 113.59999084472656,
+                            "left": 829.0999755859375,
+                            "right": 1029.0999755859375,
+                            "top": 317.41668701171875,
                             "width": 200,
-                            "x": 651,
-                            "y": 620
+                            "x": 829.0999755859375,
+                            "y": 317.41668701171875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/rename_tiff_channels/rename_tiff_channels/0.0.1+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_tile/cp_tile/3.1.9+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "09e240a12897",
-                            "name": "rename_tiff_channels",
-                            "owner": "goeckslab",
+                            "changeset_revision": "878bafb411dd",
+                            "name": "cp_tile",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"channel_csv\": {\"__class__\": \"RuntimeValue\"}, \"image\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"con_assembly_method\": {\"assembly_method\": \"Within cycles\", \"__current_case__\": 0, \"con_calc_no_row\": {\"calc_no_row\": \"No\", \"__current_case__\": 1, \"no_of_row\": \"1\"}, \"con_calc_no_cols\": {\"calc_no_cols\": \"Yes\", \"__current_case__\": 0}, \"corner_to_begin\": \"top left\", \"direction\": \"row\", \"meander_mode\": \"No\", \"rpt_additional_image\": [{\"__index__\": 0, \"additional_img\": \"OutlineImage\"}, {\"__index__\": 1, \"additional_img\": \"TrackedCells\"}]}, \"input_image\": \"OrigColor\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"output_image_name\": \"TiledImages\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9+galaxy0",
                         "type": "tool",
-                        "uuid": "48533f44-e13e-4dc2-aa36-c8b2ab7fc18f",
+                        "uuid": "210b3d0d-1139-4934-886b-805c1fcfa3de",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "renamed_image",
-                                "uuid": "4d9e9fea-2636-4b36-9b8c-d8db49dedb23"
+                                "output_name": "output_pipeline",
+                                "uuid": "83dbb3d1-3126-4e95-a2ea-d8f9a6ed5722"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata/0.17.7+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9+galaxy1",
                         "errors": null,
                         "id": 10,
                         "input_connections": {
-                            "image_path": {
-                                "id": 8,
-                                "output_name": "cellmask"
+                            "input_pipeline": {
+                                "id": 9,
+                                "output_name": "output_pipeline"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Convert McMicro Output to Anndata",
-                                "name": "image_path"
+                                "description": "runtime parameter for tool SaveImages",
+                                "name": "input_pipeline"
                             }
                         ],
                         "label": null,
-                        "name": "Convert McMicro Output to Anndata",
+                        "name": "SaveImages",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "h5ad"
+                                "name": "output_pipeline",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 423.9921875,
-                            "height": 133.9921875,
-                            "left": 929,
-                            "right": 1129,
-                            "top": 290,
+                            "bottom": 591.4833374023438,
+                            "height": 113.60000610351562,
+                            "left": 887.566650390625,
+                            "right": 1087.566650390625,
+                            "top": 477.8833312988281,
                             "width": 200,
-                            "x": 929,
-                            "y": 290
+                            "x": 887.566650390625,
+                            "y": 477.8833312988281
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata/0.17.7+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "8ca435ec19be",
-                            "name": "scimap_mcmicro_to_anndata",
-                            "owner": "goeckslab",
+                            "changeset_revision": "33f4fa1413fb",
+                            "name": "cp_save_images",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"drop_markers\": \"\", \"image_path\": {\"__class__\": \"RuntimeValue\"}, \"options\": {\"remove_dna\": \"false\", \"remove_string_from_name\": \"\", \"log\": \"true\", \"random_sample\": null, \"CellId\": \"CellID\", \"unique_CellId\": \"false\", \"split\": \"X_centroid\", \"custom_imageid\": \"\", \"min_cells\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"con_method_for_constructing\": {\"method_for_constructing\": \"From image filename\", \"__current_case__\": 0, \"name_for_file_prefix\": \"OrigColor\", \"con_append_suffix\": {\"append_suffix\": \"Yes\", \"__current_case__\": 0, \"text_to_append\": \"\"}}, \"con_type_of_image\": {\"type_of_image\": \"Image\", \"__current_case__\": 0, \"con_save_file_format\": {\"file_format\": \"png\", \"__current_case__\": 3}}, \"image_to_save\": \"TiledImages\", \"input_pipeline\": {\"__class__\": \"RuntimeValue\"}, \"overwrite_without_warning\": \"Yes\", \"record_info\": \"No\", \"when_to_save\": \"Every cycle\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9+galaxy1",
                         "type": "tool",
-                        "uuid": "9d492127-f07a-4d1b-8e0f-f40ddcdc657a",
+                        "uuid": "86647f83-5316-4577-be99-1d966eb2f92a",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "f798992e-0612-4a4d-9e33-8ee4075eb74a"
+                                "output_name": "output_pipeline",
+                                "uuid": "1c29a3c6-ebb0-4ece-b2cf-aeeb0cdf6e1e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_phenotyping/scimap_phenotyping/0.17.7+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9+galaxy1",
                         "errors": null,
                         "id": 11,
                         "input_connections": {
-                            "anndata": {
+                            "input_pipeline": {
                                 "id": 10,
-                                "output_name": "outfile"
-                            },
-                            "gating_workflow": {
-                                "id": 2,
-                                "output_name": "output"
+                                "output_name": "output_pipeline"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Single Cell Phenotyping",
-                                "name": "anndata"
-                            },
-                            {
-                                "description": "runtime parameter for tool Single Cell Phenotyping",
-                                "name": "gating_workflow"
-                            },
-                            {
-                                "description": "runtime parameter for tool Single Cell Phenotyping",
-                                "name": "manual_gates"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Single Cell Phenotyping",
+                        "name": "ExportToSpreadsheet",
                         "outputs": [
                             {
-                                "name": "gmm_plots",
-                                "type": "input"
-                            },
-                            {
-                                "name": "output",
-                                "type": "h5ad"
+                                "name": "output_pipeline",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 581.3828125,
-                            "height": 286.3828125,
-                            "left": 1192,
-                            "right": 1392,
-                            "top": 295,
+                            "bottom": 586.816650390625,
+                            "height": 134,
+                            "left": 1144.7833251953125,
+                            "right": 1344.7833251953125,
+                            "top": 452.816650390625,
                             "width": 200,
-                            "x": 1192,
-                            "y": 295
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActiongmm_plots": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "gmm_plots"
-                            }
+                            "x": 1144.7833251953125,
+                            "y": 452.816650390625
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_phenotyping/scimap_phenotyping/0.17.7+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "dcfcad35e847",
-                            "name": "scimap_phenotyping",
-                            "owner": "goeckslab",
+                            "changeset_revision": "d0178bdcd00e",
+                            "name": "cp_export_to_spreadsheet",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"anndata\": {\"__class__\": \"RuntimeValue\"}, \"gating_workflow\": {\"__class__\": \"RuntimeValue\"}, \"manual_gates\": {\"__class__\": \"RuntimeValue\"}, \"rescale_plots\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"add_metadata_column_to_object\": \"Yes\", \"calc_mean\": \"Yes\", \"calc_median\": \"No\", \"calc_standard_deviation\": \"No\", \"con_create_gene_pattern\": {\"create_gene_pattern\": \"No\", \"__current_case__\": 1}, \"con_export_all_measurements\": {\"__current_case__\": 1, \"export_all_measurements\": \"Yes\"}, \"con_prefix\": {\"add_prefix\": \"No\", \"__current_case__\": 1}, \"delimiter\": \"Comma (\\\",\\\")\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"overwrite_existing_file\": \"Yes\", \"represent_nan\": \"NaN\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9+galaxy1",
                         "type": "tool",
-                        "uuid": "c0617ff6-1681-4ab2-a217-b61d71e50e5d",
+                        "uuid": "c08309b4-101c-4150-bb88-c2856bb2636e",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "2e53afc6-9a31-43fd-8795-92889b92bcea"
+                                "output_name": "output_pipeline",
+                                "uuid": "52f72fd2-726e-40b1-b168-7396a64f7a16"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/1.0.4+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9+galaxy0",
                         "errors": null,
                         "id": 12,
                         "input_connections": {
-                            "do_phenotyping|anndata": {
-                                "id": 11,
-                                "output_name": "output"
-                            },
-                            "image": {
-                                "id": 9,
-                                "output_name": "renamed_image"
+                            "con_input_type|input_images": {
+                                "id": 3,
+                                "output_name": "unzipped"
                             },
-                            "masks": {
-                                "id": 6,
-                                "output_name": "mask"
+                            "pipeline": {
+                                "id": 11,
+                                "output_name": "output_pipeline"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Vitessce Visualization",
-                                "name": "do_phenotyping"
-                            },
-                            {
-                                "description": "runtime parameter for tool Vitessce Visualization",
-                                "name": "image"
-                            },
-                            {
-                                "description": "runtime parameter for tool Vitessce Visualization",
-                                "name": "masks"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Vitessce Visualization",
+                        "name": "CellProfiler",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "html"
+                                "name": "pipeline_output",
+                                "type": "input"
+                            },
+                            {
+                                "name": "logs",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 533.5859375,
-                            "height": 235.5859375,
-                            "left": 1455,
-                            "right": 1655,
-                            "top": 298,
+                            "bottom": 808.9333190917969,
+                            "height": 174.39999389648438,
+                            "left": 1371.8333740234375,
+                            "right": 1571.8333740234375,
+                            "top": 634.5333251953125,
                             "width": 200,
-                            "x": 1455,
-                            "y": 298
+                            "x": 1371.8333740234375,
+                            "y": 634.5333251953125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/1.0.4+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "9f60ef2d586e",
-                            "name": "vitessce_spatial",
-                            "owner": "goeckslab",
+                            "changeset_revision": "0e4dccaafef5",
+                            "name": "cp_cellprofiler",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"do_phenotyping\": {\"phenotyping_choice\": \"true\", \"__current_case__\": 0, \"anndata\": {\"__class__\": \"RuntimeValue\"}, \"scatterplot_embeddings\": {\"embedding\": \"umap\", \"__current_case__\": 0, \"options\": {\"n_neighbors\": \"30\", \"n_pcs\": \"10\", \"knn\": \"true\", \"random_state\": \"0\"}}, \"phenotype_factory\": {\"phenotype_mode\": \"choices\", \"__current_case__\": 0, \"phenotypes\": [\"phenotype\"]}}, \"image\": {\"__class__\": \"RuntimeValue\"}, \"masks\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"con_input_type\": {\"input_type\": \"no\", \"__current_case__\": 0, \"input_images\": {\"__class__\": \"ConnectedValue\"}}, \"detailed_output\": \"true\", \"pipeline\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9+galaxy0",
                         "type": "tool",
-                        "uuid": "8f4881b5-437e-4ef5-a10f-7ae2275fe758",
+                        "uuid": "da0bad08-2691-40e5-b2ae-24890ea16e7b",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "8f6096d5-f5ae-4eb5-a8bd-d1f79b9b2e47"
+                                "output_name": "logs",
+                                "uuid": "ca4a668b-b33c-41fa-a427-ad3b83c2d07f"
+                            },
+                            {
+                                "label": "CellProfiler pipeline output files",
+                                "output_name": "pipeline_output",
+                                "uuid": "dab4a9ee-fb53-4c74-93f5-8a0c7f7eb13e"
                             }
                         ]
                     }
                 ],
-                "parent_id": "imaging/multiplex-tissue-imaging-TMA",
-                "path": "topics/imaging/tutorials/multiplex-tissue-imaging-TMA/workflows/main_workflow.ga",
+                "parent_id": "imaging/object-tracking-using-cell-profiler",
+                "path": "topics/imaging/tutorials/object-tracking-using-cell-profiler/workflows/main_workflow.ga",
                 "tags": [
+                    "CellProfiler",
                     "imaging"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "GTN_Exemplar_002_TMA_workflow",
+                "title": "CP_object_tracking_example",
                 "topic_id": "imaging",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/imaging-multiplex-tissue-imaging-TMA/versions/main-workflow",
-                "tutorial_id": "multiplex-tissue-imaging-TMA",
-                "url": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/workflows/main_workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/imaging-object-tracking-using-cell-profiler/versions/main-workflow",
+                "tutorial_id": "object-tracking-using-cell-profiler",
+                "url": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/object-tracking-using-cell-profiler/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/object-tracking-using-cell-profiler/workflows/main_workflow.html",
                 "version": 1,
-                "wfid": "imaging-multiplex-tissue-imaging-TMA",
+                "wfid": "imaging-object-tracking-using-cell-profiler",
                 "wfname": "main-workflow",
                 "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/goeckslab/mesmer/mesmer/0.12.3+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/goeckslab/rename_tiff_channels/rename_tiff_channels/0.0.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata/0.17.7+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_phenotyping/scimap_phenotyping/0.17.7+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/1.0.4+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/perssond/ashlar/ashlar/1.14.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/basic_illumination/1.0.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/perssond/coreograph/unet_coreograph/2.2.8+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/perssond/quantification/quantification/1.5.3+galaxy1"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_color_to_gray/cp_color_to_gray/3.1.9+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_overlay_outlines/cp_overlay_outlines/3.1.9+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_tile/cp_tile/3.1.9+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_track_objects/cp_track_objects/3.1.9+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/0.2"
                 ],
-                "workflowhub_id": "1267"
+                "workflowhub_id": "1254"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.7622545"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.4567084"
     },
     {
         "admin_install": {
@@ -123167,65 +124389,107 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "2d_feature_extraction",
+                    "name": "2d_histogram_equalization",
                     "owner": "imgteam",
-                    "revisions": "5791a7f65275",
+                    "revisions": "70316d792fc9",
                     "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "2d_feature_extraction",
+                    "name": "2d_histogram_equalization",
                     "owner": "imgteam",
-                    "revisions": "0a53256b48c6",
+                    "revisions": "77f7159d775a",
                     "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "2d_filter_segmentation_by_features",
+                    "name": "2d_simple_filter",
                     "owner": "imgteam",
-                    "revisions": "e576b73a2e2f",
+                    "revisions": "dba87c4b32d3",
                     "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "2d_simple_filter",
                     "owner": "imgteam",
-                    "revisions": "dba87c4b32d3",
+                    "revisions": "f70b215d155c",
                     "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "2d_simple_filter",
+                    "name": "bfconvert",
                     "owner": "imgteam",
-                    "revisions": "f70b215d155c",
+                    "revisions": "10eed33aa9b2",
                     "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "2d_split_binaryimage_by_watershed",
+                    "name": "bfconvert",
                     "owner": "imgteam",
-                    "revisions": "f8f7987586b7",
+                    "revisions": "85edbb7a436b",
                     "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "unzip",
+                    "name": "binary2labelimage",
                     "owner": "imgteam",
-                    "revisions": "57f0914ddb7b",
-                    "tool_panel_section_label": "Collection Operations",
+                    "revisions": "6e65fd971e13",
+                    "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "90981f86000f",
+                    "name": "binary2labelimage",
+                    "owner": "imgteam",
+                    "revisions": "9bb446db4a1e",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "count_objects",
+                    "owner": "imgteam",
+                    "revisions": "5bf8eb50b280",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "count_objects",
+                    "owner": "imgteam",
+                    "revisions": "b58447a2eed2",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "image_info",
+                    "owner": "imgteam",
+                    "revisions": "7b6d9412c7f8",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "overlay_images",
+                    "owner": "imgteam",
+                    "revisions": "b74693340624",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "overlay_images",
+                    "owner": "imgteam",
+                    "revisions": "22ff7c705a83",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "unzip",
+                    "owner": "imgteam",
+                    "revisions": "57f0914ddb7b",
                     "tool_panel_section_label": "Collection Operations",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: 2d_auto_threshold\n  owner: imgteam\n  revisions: 0c777d708acc\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_auto_threshold\n  owner: imgteam\n  revisions: 3df9f0a4bf34\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_feature_extraction\n  owner: imgteam\n  revisions: 5791a7f65275\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_feature_extraction\n  owner: imgteam\n  revisions: 0a53256b48c6\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_filter_segmentation_by_features\n  owner: imgteam\n  revisions: e576b73a2e2f\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_simple_filter\n  owner: imgteam\n  revisions: dba87c4b32d3\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_simple_filter\n  owner: imgteam\n  revisions: f70b215d155c\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_split_binaryimage_by_watershed\n  owner: imgteam\n  revisions: f8f7987586b7\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unzip\n  owner: imgteam\n  revisions: 57f0914ddb7b\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/hela-screen-analysis/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: 2d_auto_threshold\n  owner: imgteam\n  revisions: 0c777d708acc\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_auto_threshold\n  owner: imgteam\n  revisions: 3df9f0a4bf34\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_histogram_equalization\n  owner: imgteam\n  revisions: 70316d792fc9\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_histogram_equalization\n  owner: imgteam\n  revisions: 77f7159d775a\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_simple_filter\n  owner: imgteam\n  revisions: dba87c4b32d3\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_simple_filter\n  owner: imgteam\n  revisions: f70b215d155c\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bfconvert\n  owner: imgteam\n  revisions: 10eed33aa9b2\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bfconvert\n  owner: imgteam\n  revisions: 85edbb7a436b\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: binary2labelimage\n  owner: imgteam\n  revisions: 6e65fd971e13\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: binary2labelimage\n  owner: imgteam\n  revisions: 9bb446db4a1e\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: count_objects\n  owner: imgteam\n  revisions: 5bf8eb50b280\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: count_objects\n  owner: imgteam\n  revisions: b58447a2eed2\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: image_info\n  owner: imgteam\n  revisions: 7b6d9412c7f8\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: overlay_images\n  owner: imgteam\n  revisions: b74693340624\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: overlay_images\n  owner: imgteam\n  revisions: 22ff7c705a83\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unzip\n  owner: imgteam\n  revisions: 57f0914ddb7b\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/imaging-introduction/tutorial.json",
         "contributors": [
             {
                 "former_affiliations": [
@@ -123239,6 +124503,36 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/thomaswollmann/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/thomaswollmann.json"
             },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
             {
                 "affiliations": [
                     "elixir-europe",
@@ -123256,12 +124550,12 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/kostrykin.json"
             }
         ],
-        "dir": "topics/imaging/tutorials/hela-screen-analysis",
+        "dir": "topics/imaging/tutorials/imaging-introduction",
         "edam_operation": [
+            "Data handling",
             "Visualisation",
-            "Image analysis",
             "Image annotation",
-            "Data handling"
+            "Image analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -123269,19 +124563,18 @@
         "feedback_number": 0,
         "follow_up_training": [
             {
-                "topic_name": "statistics",
+                "topic_name": "imaging",
                 "tutorials": [
-                    "machinelearning"
+                    "hela-screen-analysis"
                 ],
                 "type": "internal"
             }
         ],
         "hands_on": true,
-        "id": "imaging/hela-screen-analysis",
+        "id": "imaging/imaging-introduction",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.no",
             "UseGalaxy.org.au"
         ],
         "js_requirements": {
@@ -123289,49 +124582,38 @@
             "mermaid": false
         },
         "key_points": [
-            "Galaxy workflows can be used to scale image analysis pipelines to whole screens.",
-            "Segmented objects can be filtered using the **Filter label map by rules** tool.",
-            "Galaxy charts can be used to compare features extracted from screens showing cells with different treatments."
+            "The **Image Info** tool can provide valuable metadata information of an image.",
+            "TIFF files cannot viewed directly in most web browser, but have to be converted.",
+            "For visualization, images with a bit-depth more than 8-bit have to be histogram equalized."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
         "mod_date": "2023-11-14",
         "objectives": [
-            "How to segment cell nuclei in Galaxy.",
-            "How to extract features from segmentations in Galaxy.",
-            "How to filter segmentations by morphological features in Galaxy.",
-            "How to extract features from an imaging screen in Galaxy.",
-            "How to analyse extracted features from an imaging screen in Galaxy."
+            "How to handle images in Galaxy.",
+            "How to perform basic image processing in Galaxy."
         ],
-        "pageviews": 713,
+        "pageviews": 2945,
         "pub_date": "2019-08-13",
         "questions": [
-            "How do I analyze a HeLa fluorescence siRNA screen?",
-            "How do I segment cell nuclei?",
-            "How do I extract features from segmentations?",
-            "How do I filter segmentations by morphological features?",
-            "How do I apply a feature extraction workflow to a screen?",
-            "How do I visualize feature extraction results?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "imaging",
-                "tutorials": [
-                    "imaging-introduction"
-                ],
-                "type": "internal"
-            }
+            "How do I use Galaxy with imaging data?",
+            "How do I convert images using Galaxy?",
+            "How do I display images in Galaxy?",
+            "How do I filter images in Galaxy?",
+            "How do I segment simple images in Galaxy?"
         ],
-        "short_id": "T00180",
+        "short_id": "T00181",
         "short_tools": [
-            "ip_filter_standard",
             "ip_threshold",
+            "ip_overlay_images",
+            "ip_histogram_equalization",
+            "ip_binary_to_labelimage",
             "unzip",
-            "ip_2d_filter_segmentation_by_features",
-            "ip_2d_split_binaryimage_by_watershed",
-            "collapse_dataset",
-            "ip_2d_feature_extraction"
+            "ip_imageinfo",
+            "ip_filter_standard",
+            "ip_count_objects",
+            "ip_convertimage"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -123348,11 +124630,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
@@ -123365,247 +124642,48 @@
             "HeLa"
         ],
         "time_estimation": "1H",
-        "title": "Analyse HeLa fluorescence siRNA screen",
+        "title": "Introduction to image analysis using Galaxy",
         "tools": [
             "toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.0.5",
             "toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.0.5-2",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.1.1",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.1.1-2",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_filter_segmentation_by_features/ip_2d_filter_segmentation_by_features/0.0.1",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.0.1",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.0.1-2",
             "toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/0.0.3",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/0.0.3-2",
             "toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/0.0.3-3",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_split_binaryimage_by_watershed/ip_2d_split_binaryimage_by_watershed/0.0.1",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_split_binaryimage_by_watershed/ip_2d_split_binaryimage_by_watershed/0.0.1-2",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
-        ],
-        "topic_name": "imaging",
-        "topic_name_human": "Imaging",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "hela-screen-analysis",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/imaging/tutorials/hela-screen-analysis/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/hela-screen-analysis/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/hela-screen-analysis/tutorial.json"
-        },
-        "version": 9,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 167,
-        "visitors": 547,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0002-2315-9247",
-                        "name": "Till Korten",
-                        "url": "https://github.com/thawn/"
-                    }
-                ],
-                "description": "Analyse HeLa fluorescence siRNA screen",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": true
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\ninput images\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nrules\"]\n  2[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nfeature_extraction\"]\n  0 -> 2 [label=\"output\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"merge_table\"]\n  2 -> 3 [label=\"output\"]\n  k3fc2324d233b47859fb79c30b2daaef4[color=lightseagreen,label=\"Output\\noutput\"]\n  3 -> k3fc2324d233b47859fb79c30b2daaef4\n}",
-                "history": [
-                    {
-                        "hash": "d1e807a669d4a58fee5b1db2eceb8d4e4468fc21",
-                        "message": "fixed json syntax",
-                        "num": 7,
-                        "short_hash": "d1e807a66",
-                        "unix": "1699440970"
-                    },
-                    {
-                        "hash": "e34767b4ad7f4a1965ce15499e19fac5928806e0",
-                        "message": "added `creator` and `license` fields",
-                        "num": 6,
-                        "short_hash": "e34767b4a",
-                        "unix": "1699440539"
-                    },
-                    {
-                        "hash": "fab15d8bfc051c7ef280ef9aa08572543b5b24bf",
-                        "message": "updated analyze_screen.ga",
-                        "num": 5,
-                        "short_hash": "fab15d8bf",
-                        "unix": "1699376551"
-                    },
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 4,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 3,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
-                        "message": "unflatten workflows",
-                        "num": 2,
-                        "short_hash": "faf6d298a",
-                        "unix": "1576155753"
-                    },
-                    {
-                        "hash": "96462d6dcda154df6515addd109fdad1489cbe86",
-                        "message": "added second tutorial",
-                        "num": 1,
-                        "short_hash": "96462d6dc",
-                        "unix": "1565095814"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "input images"
-                            }
-                        ],
-                        "label": "input images",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 0.0,
-                            "top": 0.0
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "f021a2d0-b90b-4f1e-830c-127af3741b90",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "rules"
-                            }
-                        ],
-                        "label": "rules",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 3.140430845923717,
-                            "top": 127.71085440089814
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "8040611c-247d-4339-b8be-3858f01a0d6c",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\ninput images\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nrules\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\ud83d\udee0\ufe0f Subworkflow\\nfeature_extraction\"];\n  style 2 fill:#edd,stroke:#900,stroke-width:4px;\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"merge_table\"];\n  2 -->|output| 3;\n  3fc2324d-233b-4785-9fb7-9c30b2daaef4[\"Output\\noutput\"];\n  3 --> 3fc2324d-233b-4785-9fb7-9c30b2daaef4;\n  style 3fc2324d-233b-4785-9fb7-9c30b2daaef4 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "analyze_screen",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "input_list": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Collapse Collection",
-                                "name": "input_list"
-                            }
-                        ],
-                        "label": "merge_table",
-                        "name": "Collapse Collection",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 573.742905824752,
-                            "top": 29.554536267952393
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "90981f86000f",
-                            "name": "collapse_collections",
-                            "owner": "nml",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"filename\": {\"add_name\": false, \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"RuntimeValue\"}, \"one_header\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.1.0",
-                        "type": "tool",
-                        "uuid": "f48f5037-e4ab-4b8c-bd15-059546203e0e",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "output",
-                                "output_name": "output",
-                                "uuid": "3fc2324d-233b-4785-9fb7-9c30b2daaef4"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "imaging/hela-screen-analysis",
-                "path": "topics/imaging/tutorials/hela-screen-analysis/workflows/analyze_screen.ga",
-                "tags": [],
-                "test_results": null,
-                "tests": true,
-                "title": "analyze_screen",
-                "topic_id": "imaging",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/imaging-hela-screen-analysis/versions/analyze-screen",
-                "tutorial_id": "hela-screen-analysis",
-                "url": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/hela-screen-analysis/workflows/analyze_screen.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/hela-screen-analysis/workflows/analyze_screen.html",
-                "version": 5,
-                "wfid": "imaging-hela-screen-analysis",
-                "wfname": "analyze-screen",
-                "workflow": "analyze_screen.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.0.5",
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_filter_segmentation_by_features/ip_2d_filter_segmentation_by_features/0.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/0.0.3",
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_split_binaryimage_by_watershed/ip_2d_split_binaryimage_by_watershed/0.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
-                ],
-                "workflowhub_id": "1271"
-            },
+            "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.4",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.4-2",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5-2",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/image_info/ip_imageinfo/0.2",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.3",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.3-3",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy0"
+        ],
+        "topic_name": "imaging",
+        "topic_name_human": "Imaging",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "imaging-introduction",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/imaging/tutorials/imaging-introduction/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/imaging-introduction/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/imaging-introduction/tutorial.json"
+        },
+        "version": 11,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 99,
+        "visitors": 2029,
+        "workflows": [
             {
                 "creators": [
                     {
@@ -123622,56 +124700,63 @@
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ninput image\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nrules\"]\n  2[label=\"Filter Image\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Auto Threshold\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Split objects\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"2D Feature Extraction\"]\n  4 -> 5 [label=\"output\"]\n  6[label=\"Filter segmentation\"]\n  5 -> 6 [label=\"output\"]\n  4 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  kb90cbc9433fd460096b58cf0bcaf2e94[color=lightseagreen,label=\"Output\\noutput\"]\n  6 -> kb90cbc9433fd460096b58cf0bcaf2e94\n  7[label=\"2D Feature Extraction\"]\n  6 -> 7 [label=\"output\"]\n  0 -> 7 [label=\"output\"]\n  k3d3c037a50ef443ba6f88a37db6bfb36[color=lightseagreen,label=\"Output\\noutput\"]\n  7 -> k3d3c037a50ef443ba6f88a37db6bfb36\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ninput_image\"]\n  1[label=\"Histogram equalization\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Image Info\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Filter Image\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Filter Image\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Convert image\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Convert image\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"Auto Threshold\"]\n  3 -> 7 [label=\"output\"]\n  8[label=\"Histogram equalization\"]\n  3 -> 8 [label=\"output\"]\n  9[label=\"Binary 2 Label\"]\n  7 -> 9 [label=\"output\"]\n  10[label=\"Convert image\"]\n  8 -> 10 [label=\"output\"]\n  11[label=\"Overlay Images\"]\n  6 -> 11 [label=\"output\"]\n  9 -> 11 [label=\"output\"]\n  k85029ccbebb34a919ba3d1daefd13efc[color=lightseagreen,label=\"Output\\nout\"]\n  11 -> k85029ccbebb34a919ba3d1daefd13efc\n  12[label=\"Convert image\"]\n  9 -> 12 [label=\"output\"]\n  13[label=\"Count Objects\"]\n  9 -> 13 [label=\"output\"]\n  k1446f4bfb031405a84f088acc1a5c8a3[color=lightseagreen,label=\"Output\\noutput\"]\n  13 -> k1446f4bfb031405a84f088acc1a5c8a3\n}",
                 "history": [
                     {
-                        "hash": "d1e807a669d4a58fee5b1db2eceb8d4e4468fc21",
+                        "hash": "417cff2ccf2bd267e63d478bec4fec85b8fc04b1",
                         "message": "fixed json syntax",
-                        "num": 7,
-                        "short_hash": "d1e807a66",
-                        "unix": "1699440970"
+                        "num": 8,
+                        "short_hash": "417cff2cc",
+                        "unix": "1699440926"
                     },
                     {
-                        "hash": "e34767b4ad7f4a1965ce15499e19fac5928806e0",
+                        "hash": "9fd3cf532f4cbe3feff9ee7561ccc45fca40e4ea",
                         "message": "added `creator` and `license` fields",
-                        "num": 6,
-                        "short_hash": "e34767b4a",
-                        "unix": "1699440539"
+                        "num": 7,
+                        "short_hash": "9fd3cf532",
+                        "unix": "1699440835"
                     },
                     {
-                        "hash": "574ce45a0c0a6defc6795bb6bd67d3e2fd98d4ca",
-                        "message": "updated feature_extraction.ga",
-                        "num": 5,
-                        "short_hash": "574ce45a0",
-                        "unix": "1699376568"
+                        "hash": "f1edf310368eae3320d7cad61b45da646dcb24f8",
+                        "message": "updated ga file",
+                        "num": 6,
+                        "short_hash": "f1edf3103",
+                        "unix": "1699371738"
                     },
                     {
                         "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
                         "message": "annotation",
-                        "num": 4,
+                        "num": 5,
                         "short_hash": "667ff3de9",
                         "unix": "1579690769"
                     },
                     {
                         "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
                         "message": "Workflow renaming",
-                        "num": 3,
+                        "num": 4,
                         "short_hash": "eb4d724e0",
                         "unix": "1579084895"
                     },
                     {
                         "hash": "faf6d298afa752b6676a1533854c634efefe8075",
                         "message": "unflatten workflows",
-                        "num": 2,
+                        "num": 3,
                         "short_hash": "faf6d298a",
                         "unix": "1576155753"
                     },
                     {
-                        "hash": "96462d6dcda154df6515addd109fdad1489cbe86",
-                        "message": "added second tutorial",
+                        "hash": "5eca26d3a4b208e631bbf18232cb1a6727ec99db",
+                        "message": "update images, workflow, and final hands on box",
+                        "num": 2,
+                        "short_hash": "5eca26d3a",
+                        "unix": "1565346764"
+                    },
+                    {
+                        "hash": "2e42bf8893d877437f600ea4e849c169cbcbb263",
+                        "message": "add workflow",
                         "num": 1,
-                        "short_hash": "96462d6dc",
-                        "unix": "1565095814"
+                        "short_hash": "2e42bf889",
+                        "unix": "1565003060"
                     }
                 ],
                 "inputs": [
@@ -123684,128 +124769,93 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "input image"
-                            }
-                        ],
-                        "label": "input image",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10.46055506794869,
-                            "top": 133.99089344526203
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "15544dd3-65e5-4fdb-8648-3d8425bc77a8",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "rules"
+                                "name": "input_image"
                             }
                         ],
-                        "label": "rules",
+                        "label": "input_image",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
                             "left": 0.0,
-                            "top": 648.1594953805964
+                            "top": 184.22997472088954
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "39010bc8-dd57-4777-a325-c6d04c9f8eb6",
+                        "uuid": "3414473c-85fe-41b7-9492-61afc45dd847",
                         "when": null,
                         "workflow_outputs": []
                     }
                 ],
                 "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ninput image\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nrules\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Filter Image\"];\n  0 -->|output| 2;\n  3[\"Auto Threshold\"];\n  2 -->|output| 3;\n  4[\"Split objects\"];\n  3 -->|output| 4;\n  5[\"2D Feature Extraction\"];\n  4 -->|output| 5;\n  6[\"Filter segmentation\"];\n  5 -->|output| 6;\n  4 -->|output| 6;\n  1 -->|output| 6;\n  b90cbc94-33fd-4600-96b5-8cf0bcaf2e94[\"Output\\noutput\"];\n  6 --> b90cbc94-33fd-4600-96b5-8cf0bcaf2e94;\n  style b90cbc94-33fd-4600-96b5-8cf0bcaf2e94 stroke:#2c3143,stroke-width:4px;\n  7[\"2D Feature Extraction\"];\n  6 -->|output| 7;\n  0 -->|output| 7;\n  3d3c037a-50ef-443b-a6f8-8a37db6bfb36[\"Output\\noutput\"];\n  7 --> 3d3c037a-50ef-443b-a6f8-8a37db6bfb36;\n  style 3d3c037a-50ef-443b-a6f8-8a37db6bfb36 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "feature_extraction",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ninput_image\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Histogram equalization\"];\n  0 -->|output| 1;\n  2[\"Image Info\"];\n  0 -->|output| 2;\n  3[\"Filter Image\"];\n  0 -->|output| 3;\n  4[\"Filter Image\"];\n  0 -->|output| 4;\n  5[\"Convert image\"];\n  0 -->|output| 5;\n  6[\"Convert image\"];\n  1 -->|output| 6;\n  7[\"Auto Threshold\"];\n  3 -->|output| 7;\n  8[\"Histogram equalization\"];\n  3 -->|output| 8;\n  9[\"Binary 2 Label\"];\n  7 -->|output| 9;\n  10[\"Convert image\"];\n  8 -->|output| 10;\n  11[\"Overlay Images\"];\n  6 -->|output| 11;\n  9 -->|output| 11;\n  85029ccb-ebb3-4a91-9ba3-d1daefd13efc[\"Output\\nout\"];\n  11 --> 85029ccb-ebb3-4a91-9ba3-d1daefd13efc;\n  style 85029ccb-ebb3-4a91-9ba3-d1daefd13efc stroke:#2c3143,stroke-width:4px;\n  12[\"Convert image\"];\n  9 -->|output| 12;\n  13[\"Count Objects\"];\n  9 -->|output| 13;\n  1446f4bf-b031-405a-84f0-88acc1a5c8a3[\"Output\\noutput\"];\n  13 --> 1446f4bf-b031-405a-84f0-88acc1a5c8a3;\n  style 1446f4bf-b031-405a-84f0-88acc1a5c8a3 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "Workflow constructed from Tutorial 'Introduction to image analysis using Galaxy'",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/imgteam/2d_filter_segmentation_by_features/ip_2d_filter_segmentation_by_features/0.0.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.3",
                         "errors": null,
-                        "id": 6,
+                        "id": 11,
                         "input_connections": {
-                            "feature_file": {
-                                "id": 5,
-                                "output_name": "output"
-                            },
-                            "input": {
-                                "id": 4,
+                            "method_option|im1": {
+                                "id": 6,
                                 "output_name": "output"
                             },
-                            "rule_file": {
-                                "id": 1,
+                            "method_option|im2": {
+                                "id": 9,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Filter segmentation",
+                        "name": "Overlay Images",
                         "outputs": [
                             {
-                                "name": "output",
+                                "name": "out",
                                 "type": "tiff"
                             }
                         ],
                         "position": {
-                            "left": 934.6383840869061,
-                            "top": 550.5509793890867
+                            "left": 1103.1565029542078,
+                            "top": 4.927314536610737
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/2d_filter_segmentation_by_features/ip_2d_filter_segmentation_by_features/0.0.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "e576b73a2e2f",
-                            "name": "2d_filter_segmentation_by_features",
+                            "changeset_revision": "b74693340624",
+                            "name": "overlay_images",
                             "owner": "imgteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tiff\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"feature_file\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"rule_file\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.0.1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"method_option\": {\"method\": \"seg_contour\", \"__current_case__\": 2, \"im1\": {\"__class__\": \"ConnectedValue\"}, \"im2\": {\"__class__\": \"ConnectedValue\"}, \"thickness\": \"2\", \"color\": \"#ff0000\", \"show_label\": true, \"label_color\": \"#ffff00\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.0.3",
                         "type": "tool",
-                        "uuid": "4b253c14-4315-431e-baa2-92773c53e8ea",
+                        "uuid": "e6920848-10eb-406c-939e-6bfae3041346",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "output",
-                                "output_name": "output",
-                                "uuid": "b90cbc94-33fd-4600-96b5-8cf0bcaf2e94"
+                                "label": "out",
+                                "output_name": "out",
+                                "uuid": "85029ccb-ebb3-4a91-9ba3-d1daefd13efc"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.1.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5",
                         "errors": null,
-                        "id": 7,
+                        "id": 13,
                         "input_connections": {
-                            "input_label": {
-                                "id": 6,
-                                "output_name": "output"
-                            },
-                            "use_raw_option|input_raw": {
-                                "id": 0,
+                            "input": {
+                                "id": 9,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "2D Feature Extraction",
+                        "name": "Count Objects",
                         "outputs": [
                             {
                                 "name": "output",
@@ -123813,54 +124863,57 @@
                             }
                         ],
                         "position": {
-                            "left": 316.54453978928655,
-                            "top": 839.7316069939548
+                            "left": 1172.3462617863868,
+                            "top": 500.229868675786
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.1.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5",
                         "tool_shed_repository": {
-                            "changeset_revision": "5791a7f65275",
-                            "name": "2d_feature_extraction",
+                            "changeset_revision": "5bf8eb50b280",
+                            "name": "count_objects",
                             "owner": "imgteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tiff\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"feature_options\": {\"features\": \"select\", \"__current_case__\": 1, \"selected_features\": [\"--mean_intensity\", \"--area\", \"--major_axis_length\"]}, \"input_label\": {\"__class__\": \"ConnectedValue\"}, \"use_raw_option\": {\"use_raw\": \"raw_image\", \"__current_case__\": 1, \"input_raw\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.1",
+                        "tool_state": "{\"__input_ext\": \"tiff\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.0.5",
                         "type": "tool",
-                        "uuid": "40d50f9c-ac41-4a34-8212-6c0b67fcc409",
+                        "uuid": "3c7f2b09-2fd6-452a-983d-ca120067c1a4",
                         "when": null,
                         "workflow_outputs": [
                             {
                                 "label": "output",
                                 "output_name": "output",
-                                "uuid": "3d3c037a-50ef-443b-a6f8-8a37db6bfb36"
+                                "uuid": "1446f4bf-b031-405a-84f0-88acc1a5c8a3"
                             }
                         ]
                     }
                 ],
-                "parent_id": "imaging/hela-screen-analysis",
-                "path": "topics/imaging/tutorials/hela-screen-analysis/workflows/feature_extraction.ga",
+                "parent_id": "imaging/imaging-introduction",
+                "path": "topics/imaging/tutorials/imaging-introduction/workflows/Galaxy-Workflow-GTN_Tutorial__Introduction_to_Imaging.ga",
                 "tags": [],
                 "test_results": null,
                 "tests": true,
-                "title": "feature_extraction",
+                "title": "Workflow constructed from Tutorial 'Introduction to image analysis using Galaxy'",
                 "topic_id": "imaging",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/imaging-hela-screen-analysis/versions/feature-extraction",
-                "tutorial_id": "hela-screen-analysis",
-                "url": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/hela-screen-analysis/workflows/feature_extraction.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/hela-screen-analysis/workflows/feature_extraction.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/imaging-imaging-introduction/versions/galaxy-workflow-gtn-tutorial--introduction-to-imaging",
+                "tutorial_id": "imaging-introduction",
+                "url": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/imaging-introduction/workflows/Galaxy-Workflow-GTN_Tutorial__Introduction_to_Imaging.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/imaging-introduction/workflows/Galaxy-Workflow-GTN_Tutorial__Introduction_to_Imaging.html",
                 "version": 5,
-                "wfid": "imaging-hela-screen-analysis",
-                "wfname": "feature-extraction",
-                "workflow": "feature_extraction.ga",
+                "wfid": "imaging-imaging-introduction",
+                "wfname": "galaxy-workflow-gtn-tutorial--introduction-to-imaging",
+                "workflow": "Galaxy-Workflow-GTN_Tutorial__Introduction_to_Imaging.ga",
                 "workflow_tools": [
                     "toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.0.5",
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_filter_segmentation_by_features/ip_2d_filter_segmentation_by_features/0.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.0.1",
                     "toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/0.0.3",
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_split_binaryimage_by_watershed/ip_2d_split_binaryimage_by_watershed/0.0.1"
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.4",
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5",
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/image_info/ip_imageinfo/0.2",
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.3"
                 ],
-                "workflowhub_id": "1270"
+                "workflowhub_id": "1258"
             }
         ],
         "zenodo_link": "https://zenodo.org/record/3362976"
@@ -123870,751 +124923,238 @@
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/bioimage-metadata/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "wee-snufkin",
-                "Laura190",
-                "kkamieniecka",
-                "poterlowicz-lab"
-            ],
-            "funding": [
-                "elixir-uk-dash"
-            ]
-        },
-        "contributors": [
-            {
-                "email": "juliajot36@gmail.com",
-                "id": "wee-snufkin",
-                "joined": "2022-06",
-                "name": "Julia Jakiela",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
-            },
-            {
-                "email": "L.Cooper.5@warwick.ac.uk",
-                "id": "Laura190",
-                "joined": "2023-08",
-                "name": "Laura Cooper",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Laura190/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/Laura190.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "id": "kkamieniecka",
-                "joined": "2018-08",
-                "name": "Katarzyna Kamieniecka",
-                "orcid": "0009-0004-2454-5950",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/",
-                "twitter": "katemurat",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "id": "poterlowicz-lab",
-                "joined": "2017-09",
-                "name": "Krzysztof Poterlowicz",
-                "orcid": "0000-0001-6173-5674",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/poterlowicz-lab/",
-                "twitter": "bioinfbrad",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/poterlowicz-lab.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/dash.png",
-                "funder": true,
-                "funding_id": "MR/V038966/1",
-                "funding_statement": "This Fellowship was funded through the ELIXIR-UK DaSH project as part of the UKRI Innovation Scholars: Data Science Training in Health and Bioscience call (DaSH). (MR/V038966/1). The project aims to embed Research Data Management (RDM) know-how into UK universities and institutes by producing and delivering training in FAIR data stewardship using ELIXIR-UK knowledge and resources.",
-                "funding_system": "ukri",
-                "github": false,
-                "id": "elixir-uk-dash",
-                "joined": "2023-10",
-                "name": "DASH UK",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-uk-dash/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-uk-dash.json"
-            }
-        ],
-        "dir": "topics/imaging/tutorials/bioimage-metadata",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "fair",
-                "tutorials": [
-                    "bioimage-REMBI"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "imaging",
-                "type": "internal"
-            }
-        ],
-        "hands_on": true,
-        "id": "imaging/bioimage-metadata",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Data repositories such as BioImage Archive, Electron Microscopy Public Image Archive (EMPIAR) and Image Data Repository (IDR) are available to help make bioimaging data FAIR.",
-            "Find out what are the repository's requirements to help decide which is suitable for your data.",
-            "All repositories require some metadata, so collecting the metadata alongside data acquisition will make this process easier."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-08-18",
-        "objectives": [
-            "Locate bioimage data repositories",
-            "Compare repositories to find which are suitable for your data",
-            "Find out what the requirements are for submitting"
-        ],
-        "pageviews": 0,
-        "priority": 4,
-        "pub_date": "2024-08-18",
-        "questions": [
-            "What are the commonly used repositories for bioimaging data?",
-            "Which repositories are suitable for my data?",
-            "What are the requirements for submitting?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "fair",
-                "tutorials": [
-                    "fair-intro",
-                    "data-management"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00365",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "fair-data",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
+            "tools": [
                 {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
+                    "name": "mesmer",
+                    "owner": "goeckslab",
+                    "revisions": "187918c47051",
+                    "tool_panel_section_label": "Spatial Omics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": true,
-        "tags": [
-            "fair",
-            "data management",
-            "bioimaging"
-        ],
-        "time_estimation": "15m",
-        "title": "FAIR Bioimage Metadata",
-        "tools": [],
-        "topic_name": "imaging",
-        "topic_name_human": "Imaging",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "bioimage-metadata",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/imaging/tutorials/bioimage-metadata/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/bioimage-metadata/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/bioimage-metadata/tutorial.json"
-        },
-        "version": 0,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 0,
-        "visitors": 0,
-        "zenodo_link": ""
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/bioimage-REMBI/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "wee-snufkin",
-                "Laura190",
-                "kkamieniecka",
-                "poterlowicz-lab"
-            ],
-            "funding": [
-                "elixir-uk-dash"
-            ]
-        },
-        "contributors": [
-            {
-                "email": "juliajot36@gmail.com",
-                "id": "wee-snufkin",
-                "joined": "2022-06",
-                "name": "Julia Jakiela",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
-            },
-            {
-                "email": "L.Cooper.5@warwick.ac.uk",
-                "id": "Laura190",
-                "joined": "2023-08",
-                "name": "Laura Cooper",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Laura190/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/Laura190.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "id": "kkamieniecka",
-                "joined": "2018-08",
-                "name": "Katarzyna Kamieniecka",
-                "orcid": "0009-0004-2454-5950",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/",
-                "twitter": "katemurat",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "id": "poterlowicz-lab",
-                "joined": "2017-09",
-                "name": "Krzysztof Poterlowicz",
-                "orcid": "0000-0001-6173-5674",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/poterlowicz-lab/",
-                "twitter": "bioinfbrad",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/poterlowicz-lab.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/dash.png",
-                "funder": true,
-                "funding_id": "MR/V038966/1",
-                "funding_statement": "This Fellowship was funded through the ELIXIR-UK DaSH project as part of the UKRI Innovation Scholars: Data Science Training in Health and Bioscience call (DaSH). (MR/V038966/1). The project aims to embed Research Data Management (RDM) know-how into UK universities and institutes by producing and delivering training in FAIR data stewardship using ELIXIR-UK knowledge and resources.",
-                "funding_system": "ukri",
-                "github": false,
-                "id": "elixir-uk-dash",
-                "joined": "2023-10",
-                "name": "DASH UK",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-uk-dash/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-uk-dash.json"
-            }
-        ],
-        "dir": "topics/imaging/tutorials/bioimage-REMBI",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "imaging",
-                "type": "internal"
-            }
-        ],
-        "hands_on": true,
-        "id": "imaging/bioimage-REMBI",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "REMBI describes useful guidelines for bioimaging that can help unification and FARIfication of the data."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-08-18",
-        "objectives": [
-            "Organise bioimage metadata",
-            "Find out what REMBI is and why it is useful",
-            "Categorise what metadata belongs to each of the submodules of REMBI",
-            "Gather the metadata for an example bioimage dataset"
-        ],
-        "pageviews": 0,
-        "priority": 5,
-        "pub_date": "2024-08-18",
-        "questions": [
-            "What is REMBI and why should I use it?",
-            "What information should be included when collecting bioimage data?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "fair",
-                "tutorials": [
-                    "fair-intro",
-                    "data-management",
-                    "bioimage-metadata"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00364",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "fair-data",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "rename_tiff_channels",
+                    "owner": "goeckslab",
+                    "revisions": "09e240a12897",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
+                    "name": "scimap_mcmicro_to_anndata",
+                    "owner": "goeckslab",
+                    "revisions": "8ca435ec19be",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
+                    "name": "scimap_phenotyping",
+                    "owner": "goeckslab",
+                    "revisions": "dcfcad35e847",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": true,
-        "tags": [
-            "fair",
-            "data management",
-            "bioimaging"
-        ],
-        "time_estimation": "15m",
-        "title": "REMBI - Recommended Metadata for Biological Images \u2013 metadata guidelines for bioimaging data",
-        "tools": [],
-        "topic_name": "imaging",
-        "topic_name_human": "Imaging",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "bioimage-REMBI",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/imaging/tutorials/bioimage-REMBI/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/bioimage-REMBI/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/bioimage-REMBI/tutorial.json"
-        },
-        "version": 0,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 0,
-        "visitors": 0,
-        "zenodo_link": ""
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "vitessce_spatial",
+                    "owner": "goeckslab",
+                    "revisions": "9f60ef2d586e",
+                    "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "bfconvert",
+                    "owner": "imgteam",
+                    "revisions": "f3360fbeda64",
+                    "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "ashlar",
+                    "owner": "perssond",
+                    "revisions": "33ab2058c6d9",
+                    "tool_panel_section_label": "Spatial Omics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "column_maker",
-                    "owner": "devteam",
-                    "revisions": "6595517c2dd8",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "basic_illumination",
+                    "owner": "perssond",
+                    "revisions": "acc6f509968c",
+                    "tool_panel_section_label": "Spatial Omics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "get_flanks",
-                    "owner": "devteam",
-                    "revisions": "077f404ae1bb",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "coreograph",
+                    "owner": "perssond",
+                    "revisions": "ee92746d141a",
+                    "tool_panel_section_label": "Spatial Omics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "intersect",
-                    "owner": "devteam",
-                    "revisions": "69c10b56f46d",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "quantification",
+                    "owner": "perssond",
+                    "revisions": "3a916c4e9f5f",
+                    "tool_panel_section_label": "Spatial Omics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 6595517c2dd8\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: get_flanks\n  owner: devteam\n  revisions: 077f404ae1bb\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: intersect\n  owner: devteam\n  revisions: 69c10b56f46d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: mesmer\n  owner: goeckslab\n  revisions: 187918c47051\n  tool_panel_section_label: Spatial Omics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rename_tiff_channels\n  owner: goeckslab\n  revisions: '09e240a12897'\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scimap_mcmicro_to_anndata\n  owner: goeckslab\n  revisions: 8ca435ec19be\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scimap_phenotyping\n  owner: goeckslab\n  revisions: dcfcad35e847\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: vitessce_spatial\n  owner: goeckslab\n  revisions: 9f60ef2d586e\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bfconvert\n  owner: imgteam\n  revisions: f3360fbeda64\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ashlar\n  owner: perssond\n  revisions: 33ab2058c6d9\n  tool_panel_section_label: Spatial Omics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: basic_illumination\n  owner: perssond\n  revisions: acc6f509968c\n  tool_panel_section_label: Spatial Omics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: coreograph\n  owner: perssond\n  revisions: ee92746d141a\n  tool_panel_section_label: Spatial Omics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quantification\n  owner: perssond\n  revisions: 3a916c4e9f5f\n  tool_panel_section_label: Spatial Omics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.json",
         "contributors": [
             {
-                "id": "pajanne",
-                "joined": "2017-09",
-                "name": "Anne Pajon",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pajanne/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pajanne.json"
-            },
-            {
-                "elixir_node": "de",
-                "email": "blankclemens@gmail.com",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "blankclemens",
-                "joined": "2017-09",
-                "name": "Clemens Blank",
-                "orcid": "0000-0002-1726-2256",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankclemens/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankclemens.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
-                "fediverse_flavor": "mastodon",
-                "id": "bgruening",
-                "joined": "2017-09",
-                "linkedin": "bgruening",
-                "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
-                },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
-            },
-            {
-                "affiliations": [
-                    "earlham",
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "fediverse": "https://mstdn.science/@nsoranzo",
-                "fediverse_flavor": "mastodon",
-                "id": "nsoranzo",
-                "joined": "2017-09",
-                "linkedin": "nicola-soranzo-7884125",
-                "matrix": "nsoranzo:matrix.org",
-                "name": "Nicola Soranzo",
-                "orcid": "0000-0003-3627-5340",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
-                "twitter": "NicolaSoranzo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "id": "dyusuf",
-                "joined": "2017-09",
-                "name": "Dilmurat Yusuf",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dyusuf/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/dyusuf.json"
-            },
-            {
-                "id": "sarah-peter",
-                "joined": "2018-09",
-                "name": "Sarah Peter",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/sarah-peter/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/sarah-peter.json"
+                "email": "watsocam@ohsu.edu",
+                "id": "CameronFRWatson",
+                "joined": "2022-07",
+                "name": "Cameron Watson",
+                "orcid": "0000-0002-6942-2469",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/CameronFRWatson/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/CameronFRWatson.json"
             },
             {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+                "email": "creason@ohsu.edu",
+                "id": "alliecreason",
+                "joined": "2023-02",
+                "name": "Allison Creason",
+                "orcid": "0000-0001-5724-1276",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/alliecreason/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/alliecreason.json"
             }
         ],
-        "dir": "topics/introduction/tutorials/galaxy-intro-peaks2genes",
+        "dir": "topics/imaging/tutorials/multiplex-tissue-imaging-TMA",
         "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)"
-        ],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "introduction/galaxy-intro-peaks2genes",
-        "inexact_supported_servers": [],
+        "id": "imaging/multiplex-tissue-imaging-TMA",
+        "inexact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.no"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Galaxy provides an easy-to-use graphical user interface for often complex commandline tools",
-            "Galaxy keeps a full record of your analysis in a history",
-            "Workflows enable you to repeat your analysis on different data",
-            "Galaxy can connect to external sources for data import and visualization purposes",
-            "Galaxy provides ways to share your results and methods with others"
+            "Galaxy has tools and workflows that can be used to process and analyze multiplex tissue images",
+            "Cell feature tables produced by the Galaxy TMA workflow can be used for downstream single-cell and spatial analyses",
+            "There are powerful interactive visualization tools available in Galaxy that can combine the real images with associated data",
+            "Tissue Microarray data can be analyzed using workflows that invoke MTI tools in batch",
+            "Segmentation quality can vary significantly depending on features of the input image, tool used, and parameters"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-09",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Familiarize yourself with the basics of Galaxy",
-            "Learn how to obtain data from external sources",
-            "Learn how to run tools",
-            "Learn how histories work",
-            "Learn how to create a workflow",
-            "Learn how to share your work"
+            "Understand the tools available in Galaxy for multiplex tissue imaging analysis",
+            "Analyze and visualize publicly available TMA data using Galaxy"
         ],
-        "pageviews": 29838,
-        "pub_date": "2016-03-29",
+        "pageviews": 1069,
+        "pub_date": "2023-02-14",
         "questions": [
-            "How to use Galaxy?",
-            "How to get from peak regions to a list of gene names?"
+            "What tools are available for pre-processing multiplex tissue images in Galaxy?",
+            "What tools are available for downstream analysis of multiplex tissue images in Galaxy?",
+            "How do I pre-process and analyze Tissue Microarray data?",
+            "How can I visualize multiplex tissue images and associated data?",
+            "How can I assign phenotypes to cells in an MTI dataset?"
         ],
-        "short_id": "T00189",
+        "short_id": "T00334",
         "short_tools": [
-            "Grouping1",
-            "upload1",
-            "CONVERTER_interval_to_bed_0",
-            "get_flanks1",
-            "tp_tail_tool",
-            "Cut1",
-            "tp_sort_header_tool",
-            "Add_a_column1",
-            "gops_intersect_1",
-            "tp_replace_in_column"
+            "vitessce_spatial",
+            "rename_tiff_channels",
+            "scimap_phenotyping",
+            "scimap_mcmicro_to_anndata",
+            "ashlar",
+            "basic_illumination",
+            "mesmer",
+            "quantification",
+            "unet_coreograph",
+            "ip_convertimage"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "next-steps",
         "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
+            "exact": [],
+            "inexact": [
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
                 }
-            ],
-            "inexact": []
+            ]
         },
         "symlink": null,
         "time_estimation": "3H",
-        "title": "From peaks to genes",
+        "title": "End-to-End Tissue Microarray Image Analysis with Galaxy-ME",
         "tools": [
-            "CONVERTER_interval_to_bed_0",
-            "Cut1",
-            "Grouping1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0",
-            "upload1"
+            "toolshed.g2.bx.psu.edu/repos/goeckslab/mesmer/mesmer/0.12.3+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/goeckslab/rename_tiff_channels/rename_tiff_channels/0.0.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata/0.17.7+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_phenotyping/scimap_phenotyping/0.17.7+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/1.0.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/perssond/ashlar/ashlar/1.14.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/basic_illumination/1.0.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/perssond/coreograph/unet_coreograph/2.2.8+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/perssond/quantification/quantification/1.5.3+galaxy1"
         ],
-        "topic_name": "introduction",
-        "topic_name_human": "Introduction to Galaxy Analyses",
+        "topic_name": "imaging",
+        "topic_name_human": "Imaging",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "galaxy-intro-peaks2genes",
+        "tutorial_name": "multiplex-tissue-imaging-TMA",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/tutorial.json"
         },
-        "version": 59,
+        "version": 3,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 201,
-        "visitors": 17762,
+        "visit_duration": 115,
+        "visitors": 774,
         "workflows": [
             {
                 "creators": [],
-                "description": "Galaxy Introduction Peaks2Genes - Part 1",
+                "description": "End-to-End Tissue Microarray Analysis with Galaxy-ME",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPeaks\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenes\"]\n  2[label=\"Select last\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Replace Text\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Get flanks\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Replace Text\"]\n  3 -> 5 [label=\"outfile\"]\n  6[label=\"Replace Text\"]\n  5 -> 6 [label=\"outfile\"]\n  7[label=\"Convert Genomic Intervals To BED\"]\n  6 -> 7 [label=\"outfile\"]\n  8[label=\"Intersect\"]\n  4 -> 8 [label=\"out_file1\"]\n  7 -> 8 [label=\"output1\"]\n  9[label=\"Group\"]\n  8 -> 9 [label=\"output\"]\n  k19fb851fb203406da6d7a9e709e66459[color=lightseagreen,label=\"Output\\nchr_count\"]\n  9 -> k19fb851fb203406da6d7a9e709e66459\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmarkers.csv\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPhenotypeWorkflow\"]\n  3[label=\"BaSiC Illumination\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"ASHLAR\"]\n  3 -> 4 [label=\"output_dfp\"]\n  3 -> 4 [label=\"output_ffp\"]\n  0 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"UNetCoreograph\"]\n  4 -> 5 [label=\"output\"]\n  6[label=\"Mesmer\"]\n  5 -> 6 [label=\"tma_sections\"]\n  kee73bee359e74e1c87fd197b8eac7e15[color=lightseagreen,label=\"Output\\nMesmer on input dataset(s): Mask\"]\n  6 -> kee73bee359e74e1c87fd197b8eac7e15\n  7[label=\"Convert image\"]\n  5 -> 7 [label=\"tma_sections\"]\n  8[label=\"MCQUANT\"]\n  1 -> 8 [label=\"output\"]\n  5 -> 8 [label=\"tma_sections\"]\n  6 -> 8 [label=\"mask\"]\n  kfe28534a2b3f4ecc8ba9a106b2d1425c[color=lightseagreen,label=\"Output\\nPrimary Mask Quantification\"]\n  8 -> kfe28534a2b3f4ecc8ba9a106b2d1425c\n  9[label=\"Rename OME-TIFF Channels\"]\n  1 -> 9 [label=\"output\"]\n  7 -> 9 [label=\"output\"]\n  10[label=\"Convert McMicro Output to Anndata\"]\n  8 -> 10 [label=\"cellmask\"]\n  11[label=\"Single Cell Phenotyping\"]\n  10 -> 11 [label=\"outfile\"]\n  2 -> 11 [label=\"output\"]\n  12[label=\"Vitessce Visualization\"]\n  11 -> 12 [label=\"output\"]\n  9 -> 12 [label=\"renamed_image\"]\n  6 -> 12 [label=\"mask\"]\n}",
                 "history": [
                     {
-                        "hash": "48c2e99e6ac6b3f944b81c5725182a61c3a85d81",
-                        "message": "Add workflow test yml.",
+                        "hash": "74c571972f6c9c00bca6242b05cab50a0c947af0",
+                        "message": "update tool IDs, params to tutorial; add updated workflow; add hands-on avivator example to tutorial",
+                        "num": 3,
+                        "short_hash": "74c571972",
+                        "unix": "1675987355"
+                    },
+                    {
+                        "hash": "b0bac741569e5790eca8b5f21619220cea4ab902",
+                        "message": "update tool IDs in MTI workflow for linting",
+                        "num": 2,
+                        "short_hash": "b0bac7415",
+                        "unix": "1657213046"
+                    },
+                    {
+                        "hash": "aa2aba190643cbb000c0c2916d4c3656c1988e2d",
+                        "message": "Multiplex Imaging tutorial - initial push",
                         "num": 1,
-                        "short_hash": "48c2e99e6",
-                        "unix": "1603135863"
+                        "short_hash": "aa2aba190",
+                        "unix": "1656910720"
                     }
                 ],
                 "inputs": [
@@ -124626,124 +125166,811 @@
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Peaks",
-                                "name": "Peaks"
+                                "description": "",
+                                "name": "Input Dataset Collection"
+                            }
+                        ],
+                        "label": "Input Dataset Collection",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 371.28125,
+                            "height": 82.1953125,
+                            "left": -742,
+                            "right": -542,
+                            "top": 289.0859375,
+                            "width": 200,
+                            "x": -742,
+                            "y": 289.0859375
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "df4b5b73-b816-4362-b95b-f4571766abfe",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "markers.csv"
                             }
                         ],
-                        "label": "Peaks",
-                        "name": "Peaks",
+                        "label": "markers.csv",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 10
+                            "bottom": 760.8828125,
+                            "height": 61.796875,
+                            "left": -408,
+                            "right": -208,
+                            "top": 699.0859375,
+                            "width": 200,
+                            "x": -408,
+                            "y": 699.0859375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"Peaks\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "5827089b-d62d-47ad-bd3c-94bb09db46d2",
+                        "uuid": "8d2425da-b96c-4955-81c3-9303bec9cf9a",
                         "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Genes",
-                                "name": "Genes"
+                                "description": "",
+                                "name": "PhenotypeWorkflow"
                             }
                         ],
-                        "label": "Genes",
-                        "name": "Genes",
+                        "label": "PhenotypeWorkflow",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 130
+                            "bottom": 704.28125,
+                            "height": 82.1953125,
+                            "left": 911,
+                            "right": 1111,
+                            "top": 622.0859375,
+                            "width": 200,
+                            "x": 911,
+                            "y": 622.0859375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"Genes\"}",
+                        "tool_state": "{\"optional\": false, \"format\": [\"csv\"], \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "671479f6-42c1-4cc2-9136-90542c00b4f3",
+                        "uuid": "9748c022-951a-40b6-9371-fc35ee908110",
                         "workflow_outputs": []
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPeaks\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGenes\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Select last\"];\n  0 -->|output| 2;\n  3[\"Replace Text\"];\n  0 -->|output| 3;\n  4[\"Get flanks\"];\n  1 -->|output| 4;\n  5[\"Replace Text\"];\n  3 -->|outfile| 5;\n  6[\"Replace Text\"];\n  5 -->|outfile| 6;\n  7[\"Convert Genomic Intervals To BED\"];\n  6 -->|outfile| 7;\n  8[\"Intersect\"];\n  4 -->|out_file1| 8;\n  7 -->|output1| 8;\n  9[\"Group\"];\n  8 -->|output| 9;\n  19fb851f-b203-406d-a6d7-a9e709e66459[\"Output\\nchr_count\"];\n  9 --> 19fb851f-b203-406d-a6d7-a9e709e66459;\n  style 19fb851f-b203-406d-a6d7-a9e709e66459 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Galaxy Introduction Peaks2Genes - Part 1",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nmarkers.csv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nPhenotypeWorkflow\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"BaSiC Illumination\"];\n  0 -->|output| 3;\n  4[\"ASHLAR\"];\n  3 -->|output_dfp| 4;\n  3 -->|output_ffp| 4;\n  0 -->|output| 4;\n  1 -->|output| 4;\n  5[\"UNetCoreograph\"];\n  4 -->|output| 5;\n  6[\"Mesmer\"];\n  5 -->|tma_sections| 6;\n  ee73bee3-59e7-4e1c-87fd-197b8eac7e15[\"Output\\nMesmer on input dataset(s): Mask\"];\n  6 --> ee73bee3-59e7-4e1c-87fd-197b8eac7e15;\n  style ee73bee3-59e7-4e1c-87fd-197b8eac7e15 stroke:#2c3143,stroke-width:4px;\n  7[\"Convert image\"];\n  5 -->|tma_sections| 7;\n  8[\"MCQUANT\"];\n  1 -->|output| 8;\n  5 -->|tma_sections| 8;\n  6 -->|mask| 8;\n  fe28534a-2b3f-4ecc-8ba9-a106b2d1425c[\"Output\\nPrimary Mask Quantification\"];\n  8 --> fe28534a-2b3f-4ecc-8ba9-a106b2d1425c;\n  style fe28534a-2b3f-4ecc-8ba9-a106b2d1425c stroke:#2c3143,stroke-width:4px;\n  9[\"Rename OME-TIFF Channels\"];\n  1 -->|output| 9;\n  7 -->|output| 9;\n  10[\"Convert McMicro Output to Anndata\"];\n  8 -->|cellmask| 10;\n  11[\"Single Cell Phenotyping\"];\n  10 -->|outfile| 11;\n  2 -->|output| 11;\n  12[\"Vitessce Visualization\"];\n  11 -->|output| 12;\n  9 -->|renamed_image| 12;\n  6 -->|mask| 12;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "GTN_Exemplar_002_TMA_workflow",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "Grouping1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/basic_illumination/1.0.3+galaxy1",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "in_files": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool BaSiC Illumination",
+                                "name": "in_files"
+                            }
+                        ],
+                        "label": null,
+                        "name": "BaSiC Illumination",
+                        "outputs": [
+                            {
+                                "name": "output_dfp",
+                                "type": "tiff"
+                            },
+                            {
+                                "name": "output_ffp",
+                                "type": "tiff"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 475.875,
+                            "height": 184.7890625,
+                            "left": -430,
+                            "right": -230,
+                            "top": 291.0859375,
+                            "width": 200,
+                            "x": -430,
+                            "y": 291.0859375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/basic_illumination/1.0.3+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "acc6f509968c",
+                            "name": "basic_illumination",
+                            "owner": "perssond",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"in_files\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "d8dcb396-6420-4fd4-9ac8-8b4a86bc1767",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_dfp",
+                                "uuid": "1c6a93d0-6f2b-442a-a255-bfea77cb9c4f"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_ffp",
+                                "uuid": "b30ada0d-9d98-4cb4-aeac-570d42683135"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/perssond/ashlar/ashlar/1.14.0+galaxy1",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "ldfp": {
+                                "id": 3,
+                                "output_name": "output_dfp"
+                            },
+                            "lffp": {
+                                "id": 3,
+                                "output_name": "output_ffp"
+                            },
+                            "lraw": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "upgrade|markers_file": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool ASHLAR",
+                                "name": "ldfp"
+                            },
+                            {
+                                "description": "runtime parameter for tool ASHLAR",
+                                "name": "lffp"
+                            },
+                            {
+                                "description": "runtime parameter for tool ASHLAR",
+                                "name": "lraw"
+                            },
+                            {
+                                "description": "runtime parameter for tool ASHLAR",
+                                "name": "upgrade"
+                            }
+                        ],
+                        "label": null,
+                        "name": "ASHLAR",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "ome.tiff"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 493.875,
+                            "height": 204.7890625,
+                            "left": -168,
+                            "right": 32,
+                            "top": 289.0859375,
+                            "width": 200,
+                            "x": -168,
+                            "y": 289.0859375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/perssond/ashlar/ashlar/1.14.0+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "33ab2058c6d9",
+                            "name": "ashlar",
+                            "owner": "perssond",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv\": {\"align_channel\": \"0\", \"filter_sigma\": null, \"tile_size\": null, \"flip_mosaic_x\": \"false\", \"flip_mosaic_y\": \"false\", \"pyramid\": \"true\"}, \"flip_x\": \"false\", \"flip_y\": \"false\", \"ldfp\": {\"__class__\": \"RuntimeValue\"}, \"lffp\": {\"__class__\": \"RuntimeValue\"}, \"lraw\": {\"__class__\": \"RuntimeValue\"}, \"max_shift\": \"30\", \"upgrade\": {\"decide\": \"do_upgrade\", \"__current_case__\": 0, \"markers_file\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "01551249-f885-48f6-95de-45d12c255066",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "d86f47ed-259c-47f9-b61c-1538653c0733"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/perssond/coreograph/unet_coreograph/2.2.8+galaxy1",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "source_image": {
+                                "id": 4,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool UNetCoreograph",
+                                "name": "source_image"
+                            }
+                        ],
+                        "label": null,
+                        "name": "UNetCoreograph",
+                        "outputs": [
+                            {
+                                "name": "tma_sections",
+                                "type": "input"
+                            },
+                            {
+                                "name": "masks",
+                                "type": "input"
+                            },
+                            {
+                                "name": "TMA_MAP",
+                                "type": "tiff"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 585.8671875,
+                            "height": 296.78125,
+                            "left": 81,
+                            "right": 281,
+                            "top": 289.0859375,
+                            "width": 200,
+                            "x": 81,
+                            "y": 289.0859375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/perssond/coreograph/unet_coreograph/2.2.8+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ee92746d141a",
+                            "name": "coreograph",
+                            "owner": "perssond",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"buffer\": \"2.0\", \"channel\": \"0\", \"cluster\": \"false\", \"downsamplefactor\": \"5\", \"sensitivity\": \"0.3\", \"source_image\": {\"__class__\": \"RuntimeValue\"}, \"tissue\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "307e61ea-1b23-41dc-82c8-3df1988179c1",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "masks",
+                                "uuid": "69ca4dab-bd1f-49bc-84c5-71360be56577"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "TMA_MAP",
+                                "uuid": "e4f74e11-7d44-4cea-a065-8c15af8171df"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "tma_sections",
+                                "uuid": "b031e518-f1cc-4bef-9b90-429d36234b1b"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/mesmer/mesmer/0.12.3+galaxy2",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "image": {
+                                "id": 5,
+                                "output_name": "tma_sections"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Mesmer",
+                                "name": "image"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Mesmer",
+                        "outputs": [
+                            {
+                                "name": "mask",
+                                "type": "tiff"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 422.9921875,
+                            "height": 133.9921875,
+                            "left": 371,
+                            "right": 571,
+                            "top": 289,
+                            "width": 200,
+                            "x": 371,
+                            "y": 289
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/mesmer/mesmer/0.12.3+galaxy2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "187918c47051",
+                            "name": "mesmer",
+                            "owner": "goeckslab",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"compartment_select\": {\"compartment\": \"nuclear\", \"__current_case__\": 0, \"nuclear_options\": {\"pixel_expansion\": null, \"maxima_threshold\": \"0.1\", \"adv_options\": {\"maxima_smooth\": \"0\", \"interior_threshold\": \"0.2\", \"interior_smooth\": \"2\", \"small_objects_threshold\": \"15\", \"fill_holes_threshold\": \"15\", \"radius\": \"1\"}}}, \"image\": {\"__class__\": \"RuntimeValue\"}, \"image_mpp\": \"0.65\", \"nuclear_channels\": \"0\", \"squeeze\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "d15a2489-42d5-47f2-8da2-a4d86c293af0",
+                        "workflow_outputs": [
+                            {
+                                "label": "Mesmer on input dataset(s): Mask",
+                                "output_name": "mask",
+                                "uuid": "ee73bee3-59e7-4e1c-87fd-197b8eac7e15"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy0",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 5,
+                                "output_name": "tma_sections"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Convert image",
+                                "name": "input_file"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Convert image",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "tiff"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 729.59375,
+                            "height": 113.59375,
+                            "left": 345,
+                            "right": 545,
+                            "top": 616,
+                            "width": 200,
+                            "x": 345,
+                            "y": 616
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f3360fbeda64",
+                            "name": "bfconvert",
+                            "owner": "imgteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"bigtiff\": \"false\", \"channel_options\": {\"extract\": \"False\", \"__current_case__\": 0}, \"compression\": \"False\", \"crop_options\": {\"extract\": \"False\", \"__current_case__\": 0}, \"input_file\": {\"__class__\": \"RuntimeValue\"}, \"noflat\": \"true\", \"out_format\": \"ome.tiff\", \"pyramid_options\": {\"generate\": \"True\", \"__current_case__\": 0, \"pyramid_resolutions\": \"4\", \"pyramid_scale\": \"2\"}, \"range_options\": {\"extract\": \"False\", \"__current_case__\": 0}, \"series_options\": {\"extract\": \"False\", \"__current_case__\": 0}, \"tile_options\": {\"extract\": \"True\", \"__current_case__\": 1, \"tile_x\": \"512\", \"tile_y\": \"512\"}, \"timepoint_options\": {\"extract\": \"False\", \"__current_case__\": 0}, \"z_options\": {\"extract\": \"False\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "0bb1cbe2-35ee-4711-a37c-8ffe769a953a",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "e4bd4c1a-00b4-47f9-8e75-7968b5824e19"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/perssond/quantification/quantification/1.5.3+galaxy1",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "channel_names": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "image": {
+                                "id": 5,
+                                "output_name": "tma_sections"
+                            },
+                            "primary_mask": {
+                                "id": 6,
+                                "output_name": "mask"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool MCQUANT",
+                                "name": "channel_names"
+                            },
+                            {
+                                "description": "runtime parameter for tool MCQUANT",
+                                "name": "image"
+                            },
+                            {
+                                "description": "runtime parameter for tool MCQUANT",
+                                "name": "primary_mask"
+                            },
+                            {
+                                "description": "runtime parameter for tool MCQUANT",
+                                "name": "supp_mask"
+                            }
+                        ],
+                        "label": null,
+                        "name": "MCQUANT",
+                        "outputs": [
+                            {
+                                "name": "cellmask",
+                                "type": "csv"
+                            },
+                            {
+                                "name": "suppmask",
+                                "type": "csv"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 544.5859375,
+                            "height": 255.5859375,
+                            "left": 638,
+                            "right": 838,
+                            "top": 289,
+                            "width": 200,
+                            "x": 638,
+                            "y": 289
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionsuppmask": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "suppmask"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/perssond/quantification/quantification/1.5.3+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3a916c4e9f5f",
+                            "name": "quantification",
+                            "owner": "perssond",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"channel_names\": {\"__class__\": \"RuntimeValue\"}, \"image\": {\"__class__\": \"RuntimeValue\"}, \"intensity_props\": \"\", \"mask_props\": \"\", \"primary_mask\": {\"__class__\": \"RuntimeValue\"}, \"supp_mask\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "e743e3d4-538c-475c-95be-94af7805246c",
+                        "workflow_outputs": [
+                            {
+                                "label": "Primary Mask Quantification",
+                                "output_name": "cellmask",
+                                "uuid": "fe28534a-2b3f-4ecc-8ba9-a106b2d1425c"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/rename_tiff_channels/rename_tiff_channels/0.0.1+galaxy1",
                         "errors": null,
                         "id": 9,
                         "input_connections": {
-                            "input1": {
+                            "channel_csv": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "image": {
+                                "id": 7,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Rename OME-TIFF Channels",
+                                "name": "channel_csv"
+                            },
+                            {
+                                "description": "runtime parameter for tool Rename OME-TIFF Channels",
+                                "name": "image"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Rename OME-TIFF Channels",
+                        "outputs": [
+                            {
+                                "name": "renamed_image",
+                                "type": "ome.tiff"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 825.1875,
+                            "height": 205.1875,
+                            "left": 651,
+                            "right": 851,
+                            "top": 620,
+                            "width": 200,
+                            "x": 651,
+                            "y": 620
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/rename_tiff_channels/rename_tiff_channels/0.0.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "09e240a12897",
+                            "name": "rename_tiff_channels",
+                            "owner": "goeckslab",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"channel_csv\": {\"__class__\": \"RuntimeValue\"}, \"image\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "48533f44-e13e-4dc2-aa36-c8b2ab7fc18f",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "renamed_image",
+                                "uuid": "4d9e9fea-2636-4b36-9b8c-d8db49dedb23"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata/0.17.7+galaxy0",
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {
+                            "image_path": {
                                 "id": 8,
+                                "output_name": "cellmask"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Convert McMicro Output to Anndata",
+                                "name": "image_path"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Convert McMicro Output to Anndata",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "h5ad"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 423.9921875,
+                            "height": 133.9921875,
+                            "left": 929,
+                            "right": 1129,
+                            "top": 290,
+                            "width": 200,
+                            "x": 929,
+                            "y": 290
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata/0.17.7+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "8ca435ec19be",
+                            "name": "scimap_mcmicro_to_anndata",
+                            "owner": "goeckslab",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"drop_markers\": \"\", \"image_path\": {\"__class__\": \"RuntimeValue\"}, \"options\": {\"remove_dna\": \"false\", \"remove_string_from_name\": \"\", \"log\": \"true\", \"random_sample\": null, \"CellId\": \"CellID\", \"unique_CellId\": \"false\", \"split\": \"X_centroid\", \"custom_imageid\": \"\", \"min_cells\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "9d492127-f07a-4d1b-8e0f-f40ddcdc657a",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "f798992e-0612-4a4d-9e33-8ee4075eb74a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_phenotyping/scimap_phenotyping/0.17.7+galaxy0",
+                        "errors": null,
+                        "id": 11,
+                        "input_connections": {
+                            "anndata": {
+                                "id": 10,
+                                "output_name": "outfile"
+                            },
+                            "gating_workflow": {
+                                "id": 2,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Single Cell Phenotyping",
+                                "name": "anndata"
+                            },
+                            {
+                                "description": "runtime parameter for tool Single Cell Phenotyping",
+                                "name": "gating_workflow"
+                            },
+                            {
+                                "description": "runtime parameter for tool Single Cell Phenotyping",
+                                "name": "manual_gates"
+                            }
+                        ],
                         "label": null,
-                        "name": "Group",
+                        "name": "Single Cell Phenotyping",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "tabular"
+                                "name": "gmm_plots",
+                                "type": "input"
+                            },
+                            {
+                                "name": "output",
+                                "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 1330,
-                            "top": 10
+                            "bottom": 581.3828125,
+                            "height": 286.3828125,
+                            "left": 1192,
+                            "right": 1392,
+                            "top": 295,
+                            "width": 200,
+                            "x": 1192,
+                            "y": 295
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActiongmm_plots": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "gmm_plots"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_phenotyping/scimap_phenotyping/0.17.7+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "dcfcad35e847",
+                            "name": "scimap_phenotyping",
+                            "owner": "goeckslab",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"anndata\": {\"__class__\": \"RuntimeValue\"}, \"gating_workflow\": {\"__class__\": \"RuntimeValue\"}, \"manual_gates\": {\"__class__\": \"RuntimeValue\"}, \"rescale_plots\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "c0617ff6-1681-4ab2-a217-b61d71e50e5d",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "2e53afc6-9a31-43fd-8795-92889b92bcea"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/1.0.4+galaxy0",
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {
+                            "do_phenotyping|anndata": {
+                                "id": 11,
+                                "output_name": "output"
+                            },
+                            "image": {
+                                "id": 9,
+                                "output_name": "renamed_image"
+                            },
+                            "masks": {
+                                "id": 6,
+                                "output_name": "mask"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Vitessce Visualization",
+                                "name": "do_phenotyping"
+                            },
+                            {
+                                "description": "runtime parameter for tool Vitessce Visualization",
+                                "name": "image"
+                            },
+                            {
+                                "description": "runtime parameter for tool Vitessce Visualization",
+                                "name": "masks"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Vitessce Visualization",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "html"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 533.5859375,
+                            "height": 235.5859375,
+                            "left": 1455,
+                            "right": 1655,
+                            "top": 298,
+                            "width": 200,
+                            "x": 1455,
+                            "y": 298
                         },
                         "post_job_actions": {},
-                        "tool_id": "Grouping1",
-                        "tool_state": "{\"__input_ext\": \"bed\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/mm9.len\", \"groupcol\": \"1\", \"ignorecase\": \"false\", \"ignorelines\": null, \"input1\": null, \"operations\": [{\"__index__\": 0, \"optype\": \"length\", \"opcol\": \"1\", \"opround\": \"no\", \"opdefault\": \"\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.4",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/1.0.4+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "9f60ef2d586e",
+                            "name": "vitessce_spatial",
+                            "owner": "goeckslab",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"do_phenotyping\": {\"phenotyping_choice\": \"true\", \"__current_case__\": 0, \"anndata\": {\"__class__\": \"RuntimeValue\"}, \"scatterplot_embeddings\": {\"embedding\": \"umap\", \"__current_case__\": 0, \"options\": {\"n_neighbors\": \"30\", \"n_pcs\": \"10\", \"knn\": \"true\", \"random_state\": \"0\"}}, \"phenotype_factory\": {\"phenotype_mode\": \"choices\", \"__current_case__\": 0, \"phenotypes\": [\"phenotype\"]}}, \"image\": {\"__class__\": \"RuntimeValue\"}, \"masks\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "5e50ede1-709c-4140-a6a4-456258797b9c",
+                        "uuid": "8f4881b5-437e-4ef5-a10f-7ae2275fe758",
                         "workflow_outputs": [
                             {
-                                "label": "chr_count",
-                                "output_name": "out_file1",
-                                "uuid": "19fb851f-b203-406d-a6d7-a9e709e66459"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "8f6096d5-f5ae-4eb5-a8bd-d1f79b9b2e47"
                             }
                         ]
                     }
                 ],
-                "parent_id": "introduction/galaxy-intro-peaks2genes",
-                "path": "topics/introduction/tutorials/galaxy-intro-peaks2genes/workflows/Galaxy-Introduction-Peaks2Genes-Part-1-Workflow.ga",
+                "parent_id": "imaging/multiplex-tissue-imaging-TMA",
+                "path": "topics/imaging/tutorials/multiplex-tissue-imaging-TMA/workflows/main_workflow.ga",
                 "tags": [
-                    "introduction"
+                    "imaging"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "Galaxy Introduction Peaks2Genes - Part 1",
-                "topic_id": "introduction",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/introduction-galaxy-intro-peaks2genes/versions/galaxy-introduction-peaks2genes-part-1-workflow",
-                "tutorial_id": "galaxy-intro-peaks2genes",
-                "url": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-peaks2genes/workflows/Galaxy-Introduction-Peaks2Genes-Part-1-Workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-peaks2genes/workflows/Galaxy-Introduction-Peaks2Genes-Part-1-Workflow.html",
+                "tests": false,
+                "title": "GTN_Exemplar_002_TMA_workflow",
+                "topic_id": "imaging",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/imaging-multiplex-tissue-imaging-TMA/versions/main-workflow",
+                "tutorial_id": "multiplex-tissue-imaging-TMA",
+                "url": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/workflows/main_workflow.html",
                 "version": 1,
-                "wfid": "introduction-galaxy-intro-peaks2genes",
-                "wfname": "galaxy-introduction-peaks2genes-part-1-workflow",
-                "workflow": "Galaxy-Introduction-Peaks2Genes-Part-1-Workflow.ga",
+                "wfid": "imaging-multiplex-tissue-imaging-TMA",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "CONVERTER_interval_to_bed_0",
-                    "Grouping1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0"
+                    "toolshed.g2.bx.psu.edu/repos/goeckslab/mesmer/mesmer/0.12.3+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/goeckslab/rename_tiff_channels/rename_tiff_channels/0.0.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata/0.17.7+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_phenotyping/scimap_phenotyping/0.17.7+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/1.0.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/perssond/ashlar/ashlar/1.14.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/basic_illumination/1.0.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/perssond/coreograph/unet_coreograph/2.2.8+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/perssond/quantification/quantification/1.5.3+galaxy1"
                 ],
-                "workflowhub_id": "1102"
+                "workflowhub_id": "1267"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.1025586"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.7622545"
     },
     {
         "admin_install": {
@@ -124752,259 +125979,258 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
+                    "name": "cp_cellprofiler",
                     "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "revisions": "e917a2424690",
+                    "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bwa",
-                    "owner": "devteam",
-                    "revisions": "3fe632431b68",
-                    "tool_panel_section_label": "Mapping",
+                    "name": "cp_common",
+                    "owner": "bgruening",
+                    "revisions": "e7273daa5ae2",
+                    "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "picard",
-                    "owner": "devteam",
-                    "revisions": "a1f0b3f4b781",
-                    "tool_panel_section_label": "Picard",
+                    "name": "cp_convert_objects_to_image",
+                    "owner": "bgruening",
+                    "revisions": "df3ad3ba5c6f",
+                    "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "samtools_stats",
-                    "owner": "devteam",
-                    "revisions": "145f6d74ff5e",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "name": "cp_display_data_on_image",
+                    "owner": "bgruening",
+                    "revisions": "2484086dee41",
+                    "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fastp",
-                    "owner": "iuc",
-                    "revisions": "dbf9c561ef29",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "cp_enhance_or_suppress_features",
+                    "owner": "bgruening",
+                    "revisions": "f2ed92b011a9",
+                    "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "lofreq_call",
-                    "owner": "iuc",
-                    "revisions": "e1461b5c52a0",
-                    "tool_panel_section_label": "Variant Calling",
+                    "name": "cp_export_to_spreadsheet",
+                    "owner": "bgruening",
+                    "revisions": "f8fa0f6718a3",
+                    "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "lofreq_indelqual",
-                    "owner": "iuc",
-                    "revisions": "426d707dfc47",
-                    "tool_panel_section_label": "Variant Calling",
+                    "name": "cp_gray_to_color",
+                    "owner": "bgruening",
+                    "revisions": "31d195bedf6d",
+                    "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "lofreq_viterbi",
-                    "owner": "iuc",
-                    "revisions": "aa35ee7f3ab2",
-                    "tool_panel_section_label": "Variant Calling",
+                    "name": "cp_identify_primary_objects",
+                    "owner": "bgruening",
+                    "revisions": "993faa34333b",
+                    "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "5e33b465d8d5",
-                    "tool_panel_section_label": "Quality Control",
+                    "name": "cp_image_math",
+                    "owner": "bgruening",
+                    "revisions": "c09dcda1143f",
+                    "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "samtools_view",
-                    "owner": "iuc",
-                    "revisions": "bf328cec6a42",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "name": "cp_mask_image",
+                    "owner": "bgruening",
+                    "revisions": "3a05117669cf",
+                    "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "snpeff_sars_cov_2",
-                    "owner": "iuc",
-                    "revisions": "2a3a00c1fa0a",
-                    "tool_panel_section_label": "Variant Calling",
+                    "name": "cp_measure_granularity",
+                    "owner": "bgruening",
+                    "revisions": "a1a961c46d4b",
+                    "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "snpsift",
-                    "owner": "iuc",
-                    "revisions": "5fab4f81391d",
-                    "tool_panel_section_label": "Variant Calling",
+                    "name": "cp_measure_image_area_occupied",
+                    "owner": "bgruening",
+                    "revisions": "20dbb1f7ec7b",
+                    "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sra_tools",
-                    "owner": "iuc",
-                    "revisions": "653e89d73fc4",
-                    "tool_panel_section_label": "Get Data",
+                    "name": "cp_measure_image_intensity",
+                    "owner": "bgruening",
+                    "revisions": "5499dc6f8ac1",
+                    "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sra_tools",
-                    "owner": "iuc",
-                    "revisions": "e08a7ad4378b",
-                    "tool_panel_section_label": "Get Data",
+                    "name": "cp_measure_image_quality",
+                    "owner": "bgruening",
+                    "revisions": "e972e07c7845",
+                    "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "25136a2b0cfe",
-                    "tool_panel_section_label": "Collection Operations",
+                    "name": "cp_measure_object_intensity",
+                    "owner": "bgruening",
+                    "revisions": "980aed9e8fd5",
+                    "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "90981f86000f",
-                    "tool_panel_section_label": "Collection Operations",
+                    "name": "cp_measure_object_size_shape",
+                    "owner": "bgruening",
+                    "revisions": "79e10d12d90a",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "cp_measure_texture",
+                    "owner": "bgruening",
+                    "revisions": "035a58c7f54a",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "cp_relate_objects",
+                    "owner": "bgruening",
+                    "revisions": "8083a87d2fdf",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "cp_save_images",
+                    "owner": "bgruening",
+                    "revisions": "4ecf93628f97",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "idr_download_by_ids",
+                    "owner": "iuc",
+                    "revisions": "e08b1dc0480c",
+                    "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: 3fe632431b68\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: a1f0b3f4b781\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 145f6d74ff5e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: dbf9c561ef29\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lofreq_call\n  owner: iuc\n  revisions: e1461b5c52a0\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lofreq_indelqual\n  owner: iuc\n  revisions: 426d707dfc47\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lofreq_viterbi\n  owner: iuc\n  revisions: aa35ee7f3ab2\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 5e33b465d8d5\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: bf328cec6a42\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff_sars_cov_2\n  owner: iuc\n  revisions: 2a3a00c1fa0a\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpsift\n  owner: iuc\n  revisions: 5fab4f81391d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: 653e89d73fc4\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: e08a7ad4378b\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 25136a2b0cfe\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: cp_cellprofiler\n  owner: bgruening\n  revisions: e917a2424690\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_common\n  owner: bgruening\n  revisions: e7273daa5ae2\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_convert_objects_to_image\n  owner: bgruening\n  revisions: df3ad3ba5c6f\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_display_data_on_image\n  owner: bgruening\n  revisions: 2484086dee41\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_enhance_or_suppress_features\n  owner: bgruening\n  revisions: f2ed92b011a9\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_export_to_spreadsheet\n  owner: bgruening\n  revisions: f8fa0f6718a3\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_gray_to_color\n  owner: bgruening\n  revisions: 31d195bedf6d\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_identify_primary_objects\n  owner: bgruening\n  revisions: 993faa34333b\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_image_math\n  owner: bgruening\n  revisions: c09dcda1143f\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_mask_image\n  owner: bgruening\n  revisions: 3a05117669cf\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_measure_granularity\n  owner: bgruening\n  revisions: a1a961c46d4b\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_measure_image_area_occupied\n  owner: bgruening\n  revisions: 20dbb1f7ec7b\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_measure_image_intensity\n  owner: bgruening\n  revisions: 5499dc6f8ac1\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_measure_image_quality\n  owner: bgruening\n  revisions: e972e07c7845\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_measure_object_intensity\n  owner: bgruening\n  revisions: 980aed9e8fd5\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_measure_object_size_shape\n  owner: bgruening\n  revisions: 79e10d12d90a\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_measure_texture\n  owner: bgruening\n  revisions: 035a58c7f54a\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_relate_objects\n  owner: bgruening\n  revisions: 8083a87d2fdf\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cp_save_images\n  owner: bgruening\n  revisions: 4ecf93628f97\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: idr_download_by_ids\n  owner: iuc\n  revisions: e08b1dc0480c\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/tutorial-CP/tutorial.json",
         "contributors": [
             {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
-                "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
-            },
-            {
-                "id": "mvdbeek",
-                "joined": "2018-06",
-                "name": "Marius van den Beek",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
-            },
-            {
-                "id": "tnabtaf",
-                "joined": "2017-09",
-                "name": "Dave Clements",
-                "orcid": "0000-0002-9970-6657",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
+                "email": "beatrizserrano.galaxy@gmail.com",
+                "id": "beatrizserrano",
+                "joined": "2020-07",
+                "linkedin": "beatriz-serrano",
+                "matrix": "beatrizserrano:matrix.org",
+                "name": "Beatriz Serrano-Solano",
+                "orcid": "0000-0002-5862-6132",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/beatrizserrano/",
+                "twitter": "BSerranoSolano",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/beatrizserrano.json"
             },
             {
-                "id": "blankenberg",
-                "joined": "2018-07",
-                "name": "Daniel Blankenberg",
-                "orcid": "0000-0002-6833-9049",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankenberg/",
-                "twitter": "dblankenberg",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankenberg.json"
+                "id": "jkh1",
+                "joined": "2020-07",
+                "name": "Jean-Karim H\u00e9rich\u00e9",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jkh1/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jkh1.json"
             }
         ],
-        "dir": "topics/introduction/tutorials/galaxy-intro-ngs-data-managment",
+        "dir": "topics/imaging/tutorials/tutorial-CP",
         "edam_operation": [
-            "Sequencing quality control",
-            "Sequence contamination filtering",
-            "Genome indexing",
-            "SNP detection",
-            "Sequence alignment",
-            "Formatting",
-            "Read mapping",
-            "Generation",
-            "Data handling",
-            "Validation"
+            "Parsing",
+            "Quantification",
+            "Image analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
+            "UseGalaxy.be",
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "introduction/galaxy-intro-ngs-data-managment",
+        "id": "imaging/tutorial-CP",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
             "UseGalaxy.fr",
-            "UseGalaxy.no"
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
         ],
         "js_requirements": {
-            "mathjax": 7097,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "FASTQ Sanger version of the format is considered to be the standard form of FASTQ.",
-            "Paired end data can be provided as two files or as an interleaved one.",
-            "FastqQC is a tool allowing to check the quality of FASTQ datasets.",
-            "The most common tools for mapping are Bowtie, BWA, BWA-MEM. You can use in-built genome to map against or upload one if it is missing.",
-            "The standard format for storing aligned reads is SAM/BAM. The major toolsets to process these datasets are DeepTools, SAMtools, BAMtools and Picard.",
-            "Data can be uploaded directly from a computer, from EBI SRA and from NCBI SRA, also using FTP or URL.",
-            "One can retrieve NGS data from Sequence Read Archive",
-            "Galaxy can analyze massive amounts of data and make them suitable for secondary analysis"
+            "Galaxy workflows can download images from the IDR, selecting specific channels, time points, z-stack positions and crop the image in different ways.",
+            "CellProfiler in Galaxy can segment and extract features of any object of interest.",
+            "The features and masks can be exported for further analysis."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Understand most common types of NGS-related datatypes",
-            "Learn about how Galaxy handles NGS data using Illumina data derived from patients infected with SARS-CoV-2"
+            "How to download images from a public image repository.",
+            "How to segment cell nuclei using CellProfiler in Galaxy.",
+            "How to segment cell nucleoli using CellProfiler in Galaxy.",
+            "How to extract features for images, nuclei and nucleoli."
         ],
-        "pageviews": 28913,
-        "pub_date": "2017-02-22",
+        "pageviews": 5902177,
+        "pub_date": "2020-07-01",
         "questions": [
-            "How to manipulate and process NGS data"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "nekrut"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "15M",
-                "speakers": [
-                    "nekrut"
-                ],
-                "youtube_id": "9mIL0tIfZ_o"
-            }
+            "How do I run an image analysis pipeline on public data using CellProfiler?",
+            "How do I analyse the DNA channel of fluorescence siRNA screens?",
+            "How do I download public image data into my history?",
+            "How do I segment and label cell nuclei?",
+            "How do I segment nucleoli (as the absence of DNA)?",
+            "How do I combine nuclei and nucleoli into one segmentation mask?",
+            "How do I extract the background of an image?",
+            "How do I relate the nucleoli to their parent nucleus?",
+            "How do I measure the image and object features?",
+            "How do I measure the image quality?"
         ],
-        "short_id": "T00188",
+        "short_id": "T00183",
         "short_tools": [
-            "Grep1",
-            "picard_MarkDuplicates",
-            "samtools_stats",
-            "fastp",
-            "samtools_view",
-            "multiqc",
-            "tp_cut_tool",
-            "fasterq_dump",
-            "snpSift_extractFields",
-            "lofreq_indelqual",
-            "lofreq_call",
-            "lofreq_viterbi",
-            "bwa_mem",
-            "collapse_dataset",
-            "snpeff_sars_cov_2"
+            "cp_convert_objects_to_image",
+            "cp_common",
+            "cp_save_images",
+            "cp_identify_primary_objects",
+            "cp_mask_image",
+            "cp_export_to_spreadsheet",
+            "cp_display_data_on_image",
+            "cp_gray_to_color",
+            "cp_measure_image_intensity",
+            "cp_measure_texture",
+            "cp_cellprofiler",
+            "cp_measure_object_intensity",
+            "cp_measure_granularity",
+            "cp_measure_image_quality",
+            "cp_measure_object_size_shape",
+            "cp_image_math",
+            "idr_download_by_ids",
+            "cp_enhance_or_suppress_features",
+            "cp_measure_image_area_occupied",
+            "cp_relate_objects"
         ],
-        "slides": false,
+        "slides": true,
         "slides_recordings": false,
-        "subtopic": "next-steps",
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 }
             ],
@@ -125023,941 +126249,2439 @@
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
-        "time_estimation": "1H30M",
-        "title": "NGS data logistics",
+        "time_estimation": "4H",
+        "title": "Nucleoli segmentation and feature extraction using CellProfiler",
         "tools": [
-            "Grep1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.8+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.9+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_display_data_on_image/cp_display_data_on_image/3.1.9",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_enhance_or_suppress_features/cp_enhance_or_suppress_features/3.1.9",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_gray_to_color/cp_gray_to_color/3.1.9",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_image_math/cp_image_math/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_mask_image/cp_mask_image/3.1.9",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_granularity/cp_measure_granularity/3.1.9",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_area_occupied/cp_measure_image_area_occupied/3.1.9",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_intensity/cp_measure_image_intensity/3.1.9",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_quality/cp_measure_image_quality/3.1.9",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_texture/cp_measure_texture/3.1.9",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_relate_objects/cp_relate_objects/3.1.9",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9",
+            "toolshed.g2.bx.psu.edu/repos/iuc/idr_download_by_ids/idr_download_by_ids/0.41"
         ],
-        "topic_name": "introduction",
-        "topic_name_human": "Introduction to Galaxy Analyses",
+        "topic_name": "imaging",
+        "topic_name_human": "Imaging",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "galaxy-intro-ngs-data-managment",
+        "tutorial_name": "tutorial-CP",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/imaging/tutorials/tutorial-CP/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/tutorial-CP/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/tutorial-CP/tutorial.json"
         },
-        "version": 33,
+        "version": 8,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 198,
-        "visitors": 16208,
+        "visit_duration": 229,
+        "visitors": 2136907,
         "workflows": [
             {
                 "creators": [],
-                "description": "NGS data logistics",
+                "description": "Nucleoli segmentation and feature extraction using CellProfiler",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAccessions\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenome\"]\n  2[label=\"Faster Download and Extract Reads in FASTQ\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"fastp\"]\n  2 -> 3 [label=\"list_paired\"]\n  4[label=\"Map with BWA-MEM\"]\n  3 -> 4 [label=\"output_paired_coll\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Samtools view\"]\n  4 -> 5 [label=\"bam_output\"]\n  6[label=\"MarkDuplicates\"]\n  5 -> 6 [label=\"outputsam\"]\n  7[label=\"Samtools stats\"]\n  6 -> 7 [label=\"outFile\"]\n  8[label=\"Realign reads\"]\n  6 -> 8 [label=\"outFile\"]\n  1 -> 8 [label=\"output\"]\n  9[label=\"MultiQC\"]\n  3 -> 9 [label=\"report_json\"]\n  6 -> 9 [label=\"metrics_file\"]\n  7 -> 9 [label=\"output\"]\n  10[label=\"Insert indel qualities\"]\n  8 -> 10 [label=\"realigned\"]\n  1 -> 10 [label=\"output\"]\n  11[label=\"Call variants\"]\n  10 -> 11 [label=\"output\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"SnpEff eff:\"]\n  11 -> 12 [label=\"variants\"]\n  13[label=\"SnpSift Extract Fields\"]\n  12 -> 13 [label=\"snpeff_output\"]\n  14[label=\"Collapse Collection\"]\n  13 -> 14 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Starting modules\"]\n  1[label=\"Download images\"]\n  2[label=\"Segment complete nuclei\"]\n  0 -> 2 [label=\"output_pipeline\"]\n  3[label=\"Segmentation mask complete nuclei\"]\n  2 -> 3 [label=\"output_pipeline\"]\n  4[label=\"Label nuclei\"]\n  3 -> 4 [label=\"output_pipeline\"]\n  5[label=\"Save labelled nuclei\"]\n  4 -> 5 [label=\"output_pipeline\"]\n  6[label=\"Detect dark holes in nuclei\"]\n  5 -> 6 [label=\"output_pipeline\"]\n  7[label=\"Segment nucleoli that fall inside nuclei\"]\n  6 -> 7 [label=\"output_pipeline\"]\n  8[label=\"Segment nucleoli\"]\n  7 -> 8 [label=\"output_pipeline\"]\n  9[label=\"Convert the segmented nucleoli into an image\"]\n  8 -> 9 [label=\"output_pipeline\"]\n  10[label=\"Combine masks nuclei + nucleoli\"]\n  9 -> 10 [label=\"output_pipeline\"]\n  11[label=\"Save combined segmentation masks\"]\n  10 -> 11 [label=\"output_pipeline\"]\n  12[label=\"Segment all nuclei\"]\n  11 -> 12 [label=\"output_pipeline\"]\n  13[label=\"Segmentation mask nucleoli including cells touching borders\"]\n  12 -> 13 [label=\"output_pipeline\"]\n  14[label=\"Extract background\"]\n  13 -> 14 [label=\"output_pipeline\"]\n  15[label=\"Measure the image granularity\"]\n  14 -> 15 [label=\"output_pipeline\"]\n  16[label=\"Measure the nuclei texture\"]\n  15 -> 16 [label=\"output_pipeline\"]\n  17[label=\"Measure the nuclei intensity\"]\n  16 -> 17 [label=\"output_pipeline\"]\n  18[label=\"Measure size and shape of nuclei and nucleoli\"]\n  17 -> 18 [label=\"output_pipeline\"]\n  19[label=\"Relate nucleoli with their parent nuclei\"]\n  18 -> 19 [label=\"output_pipeline\"]\n  20[label=\"Measure the image quality\"]\n  19 -> 20 [label=\"output_pipeline\"]\n  21[label=\"Measure the area occupied by nuclei and nucleoli\"]\n  20 -> 21 [label=\"output_pipeline\"]\n  22[label=\"Measure the image intensity\"]\n  21 -> 22 [label=\"output_pipeline\"]\n  23[label=\"Export measurements\"]\n  22 -> 23 [label=\"output_pipeline\"]\n  24[label=\"Run CellProfiler\"]\n  1 -> 24 [label=\"output_tar\"]\n  23 -> 24 [label=\"output_pipeline\"]\n}",
                 "history": [
                     {
-                        "hash": "ca2265825aa1725a8d5fdc3d1c02282878db2c96",
-                        "message": "workflow changes",
+                        "hash": "bd719212c3b71090065923e9941d9f5efbb4e3e3",
+                        "message": "Update main_workflow.ga",
+                        "num": 7,
+                        "short_hash": "bd719212c",
+                        "unix": "1604492160"
+                    },
+                    {
+                        "hash": "e060051254138ba425caa5775fc10bc5ac93c33e",
+                        "message": "add missing annotation field",
+                        "num": 6,
+                        "short_hash": "e06005125",
+                        "unix": "1604488703"
+                    },
+                    {
+                        "hash": "ceef3fe076a86ac8ecc50eba9b77ff192385ab60",
+                        "message": "add tag imaging",
+                        "num": 5,
+                        "short_hash": "ceef3fe07",
+                        "unix": "1604444072"
+                    },
+                    {
+                        "hash": "28a7fb28b785ae9b4804700a389d2334dc0eeb63",
+                        "message": "Update main_workflow.ga",
+                        "num": 4,
+                        "short_hash": "28a7fb28b",
+                        "unix": "1604443613"
+                    },
+                    {
+                        "hash": "a3a14fb9052dfae1f59ddec213fe4850779b2f1e",
+                        "message": "add annotation and tags to the wf",
+                        "num": 3,
+                        "short_hash": "a3a14fb90",
+                        "unix": "1593000970"
+                    },
+                    {
+                        "hash": "8fdf6cf2d432e514ebb2fd0a79ede703f2f36efb",
+                        "message": "format wf",
                         "num": 2,
-                        "short_hash": "ca2265825",
-                        "unix": "1613070101"
+                        "short_hash": "8fdf6cf2d",
+                        "unix": "1592999030"
                     },
                     {
-                        "hash": "211e2c843aeb6d1e8aeaa48571e4ec363466f5fe",
-                        "message": "Updated NGS tutorial for GTN Sm\u00f6rg\u00e5sbord",
+                        "hash": "82051aef73313659e45e3e3fa243c84ca022dce4",
+                        "message": "training_init",
                         "num": 1,
-                        "short_hash": "211e2c843",
-                        "unix": "1613069503"
+                        "short_hash": "82051aef7",
+                        "unix": "1592558689"
                     }
                 ],
-                "inputs": [
+                "inputs": [],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"Starting modules\"];\n  1[\"Download images\"];\n  2[\"Segment complete nuclei\"];\n  0 -->|output_pipeline| 2;\n  3[\"Segmentation mask complete nuclei\"];\n  2 -->|output_pipeline| 3;\n  4[\"Label nuclei\"];\n  3 -->|output_pipeline| 4;\n  5[\"Save labelled nuclei\"];\n  4 -->|output_pipeline| 5;\n  6[\"Detect dark holes in nuclei\"];\n  5 -->|output_pipeline| 6;\n  7[\"Segment nucleoli that fall inside nuclei\"];\n  6 -->|output_pipeline| 7;\n  8[\"Segment nucleoli\"];\n  7 -->|output_pipeline| 8;\n  9[\"Convert the segmented nucleoli into an image\"];\n  8 -->|output_pipeline| 9;\n  10[\"Combine masks nuclei + nucleoli\"];\n  9 -->|output_pipeline| 10;\n  11[\"Save combined segmentation masks\"];\n  10 -->|output_pipeline| 11;\n  12[\"Segment all nuclei\"];\n  11 -->|output_pipeline| 12;\n  13[\"Segmentation mask nucleoli including cells touching borders\"];\n  12 -->|output_pipeline| 13;\n  14[\"Extract background\"];\n  13 -->|output_pipeline| 14;\n  15[\"Measure the image granularity\"];\n  14 -->|output_pipeline| 15;\n  16[\"Measure the nuclei texture\"];\n  15 -->|output_pipeline| 16;\n  17[\"Measure the nuclei intensity\"];\n  16 -->|output_pipeline| 17;\n  18[\"Measure size and shape of nuclei and nucleoli\"];\n  17 -->|output_pipeline| 18;\n  19[\"Relate nucleoli with their parent nuclei\"];\n  18 -->|output_pipeline| 19;\n  20[\"Measure the image quality\"];\n  19 -->|output_pipeline| 20;\n  21[\"Measure the area occupied by nuclei and nucleoli\"];\n  20 -->|output_pipeline| 21;\n  22[\"Measure the image intensity\"];\n  21 -->|output_pipeline| 22;\n  23[\"Export measurements\"];\n  22 -->|output_pipeline| 23;\n  24[\"Run CellProfiler\"];\n  1 -->|output_tar| 24;\n  23 -->|output_pipeline| 24;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "CP_pipeline_IDR_training",
+                "outputs": [
                     {
-                        "annotation": "",
-                        "content_id": null,
+                        "annotation": "Detail the metadata associated to the images that will be processed",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9",
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": "Starting modules",
+                        "name": "Starting Modules",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Accessions"
+                                "name": "output_pipeline",
+                                "type": "txt"
                             }
                         ],
-                        "label": "Accessions",
-                        "name": "Accessions",
-                        "outputs": [],
                         "position": {
-                            "bottom": 287.5,
-                            "height": 61,
-                            "left": -457,
-                            "right": -257,
-                            "top": 226.5,
-                            "width": 200,
-                            "x": -457,
-                            "y": 226.5
+                            "left": 200,
+                            "top": 219
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Accessions\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "66230eb7-5666-4a09-8aaa-b8881161a81b",
-                        "workflow_outputs": []
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "27396311a314",
+                            "name": "cp_common",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"groups\": {\"con_groups\": {\"group_images\": \"Yes\", \"__current_case__\": 0, \"group_category\": \"field1\"}}, \"images\": {\"filter_images\": \"Images only\"}, \"metadata\": {\"con_metadata_extraction\": {\"extract\": \"Yes\", \"__current_case__\": 0, \"extraction_method\": [{\"__index__\": 0, \"metadata_extraction_method\": \"Extract from file/folder names\", \"con_metadata_source\": {\"metadata_source\": \"File name\", \"__current_case__\": 0, \"file_name_regex\": \"(?P<field1>.*)__(?P<field2>[a-zA-Z0-9]+)__(?P<field3>[a-zA-Z0-9]+)__(?P<field4>[a-zA-Z0-9]+)__(?P<field5>[a-zA-Z0-9]+)__(?P<field6>[a-zA-Z0-9]+)\"}, \"con_metadata_extract_from\": {\"extract_metadata_from\": \"All images\", \"__current_case__\": 1}}]}}, \"nameandtypes\": {\"pixel_space\": {\"process_3d\": \"No\", \"__current_case__\": 1}, \"con_assign_a_name_to\": {\"assign_a_name_to\": \"All images\", \"__current_case__\": 0, \"name_to_assign\": \"DNA\", \"con_select_image_type\": {\"select_image_type\": \"Grayscale image\", \"__current_case__\": 0, \"con_set_intensity\": {\"set_intensity_range_from\": \"Image metadata\", \"__current_case__\": 1}}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
+                        "type": "tool",
+                        "uuid": "9cb7aa2c-b60c-4a5b-9653-fa41ab465e94",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_pipeline",
+                                "uuid": "6e8dc853-a475-401f-b276-c6ab024681fc"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/idr_download_by_ids/idr_download_by_ids/0.41",
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": "Download images",
+                        "name": "IDR Download",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Genome"
+                                "name": "out_log",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "output_tar",
+                                "type": "tar"
                             }
                         ],
-                        "label": "Genome",
-                        "name": "Genome",
-                        "outputs": [],
                         "position": {
-                            "bottom": 453.5,
-                            "height": 61,
-                            "left": -505,
-                            "right": -305,
-                            "top": 392.5,
-                            "width": 200,
-                            "x": -505,
-                            "y": 392.5
+                            "left": 200,
+                            "top": 241.25
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Genome\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "9880eb10-5648-4c94-89d3-095661f6027b",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAccessions\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGenome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Faster Download and Extract Reads in FASTQ\"];\n  0 -->|output| 2;\n  3[\"fastp\"];\n  2 -->|list_paired| 3;\n  4[\"Map with BWA-MEM\"];\n  3 -->|output_paired_coll| 4;\n  1 -->|output| 4;\n  5[\"Samtools view\"];\n  4 -->|bam_output| 5;\n  6[\"MarkDuplicates\"];\n  5 -->|outputsam| 6;\n  7[\"Samtools stats\"];\n  6 -->|outFile| 7;\n  8[\"Realign reads\"];\n  6 -->|outFile| 8;\n  1 -->|output| 8;\n  9[\"MultiQC\"];\n  3 -->|report_json| 9;\n  6 -->|metrics_file| 9;\n  7 -->|output| 9;\n  10[\"Insert indel qualities\"];\n  8 -->|realigned| 10;\n  1 -->|output| 10;\n  11[\"Call variants\"];\n  10 -->|output| 11;\n  1 -->|output| 11;\n  12[\"SnpEff eff:\"];\n  11 -->|variants| 12;\n  13[\"SnpSift Extract Fields\"];\n  12 -->|snpeff_output| 13;\n  14[\"Collapse Collection\"];\n  13 -->|output| 14;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "NGS_tutorial",
-                "outputs": [
+                        "post_job_actions": {
+                            "EmailActionout_log": {
+                                "action_arguments": {},
+                                "action_type": "EmailAction",
+                                "output_name": "out_log"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/idr_download_by_ids/idr_download_by_ids/0.41",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e08b1dc0480c",
+                            "name": "idr_download_by_ids",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"channel\": \"Cy3\", \"clip_image\": {\"select\": \"\", \"__current_case__\": 0}, \"download_tar\": \"true\", \"frame\": \"0\", \"image_ids\": {\"source\": \"link\", \"__current_case__\": 0, \"id_spec\": \"http://idr.openmicroscopy.org/webclient/?show=image-295900|image-295905|image-295910|image-295918|image-295928|image-295934\"}, \"skip_failed\": \"true\", \"z_section\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.41",
+                        "type": "tool",
+                        "uuid": "682880bc-d35f-4f77-996e-7600de735da6",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_log",
+                                "uuid": "ff013d1c-7570-4720-8b15-6689021807d5"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_tar",
+                                "uuid": "b94d5196-23db-4340-aa58-c082fc5ca449"
+                            }
+                        ]
+                    },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.8+galaxy0",
+                        "annotation": "Incomplete nuclei that are touching the borders of the image are ignored and therefore, not segmented. It doesn't include the nuclei outside the diameter range either.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9",
                         "errors": null,
                         "id": 2,
                         "input_connections": {
-                            "input|file_list": {
+                            "input_pipeline": {
                                 "id": 0,
-                                "output_name": "output"
+                                "output_name": "output_pipeline"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Faster Download and Extract Reads in FASTQ",
+                        "label": "Segment complete nuclei",
+                        "name": "IdentifyPrimaryObjects",
                         "outputs": [
                             {
-                                "name": "list_paired",
-                                "type": "input"
-                            },
+                                "name": "output_pipeline",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 272.75,
+                            "top": 219
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "52c01fb29b2a",
+                            "name": "cp_identify_primary_objects",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"con_advanced\": {\"advanced\": \"Yes\", \"__current_case__\": 1, \"input_from_nat\": \"DNA\", \"name_to_be_identified\": \"Nuclei\", \"min_diameter\": \"15\", \"max_diameter\": \"200\", \"discard_outside_border\": \"Yes\", \"discard_touching_border\": \"Yes\", \"con_threshold_strategy\": {\"threshold_strategy\": \"Global\", \"__current_case__\": 1, \"con_threshold_method\": {\"threshold_method\": \"Otsu\", \"__current_case__\": 0, \"con_threshold_class\": {\"threshold_class\": \"Two classes\", \"__current_case__\": 1}, \"threshold_smoothing_scale\": \"1.3488\", \"threshold_correction_factor\": \"0.9\", \"threshold_lower\": \"0.0\", \"threshold_upper\": \"1.0\"}}, \"con_distinguish_clumped_objects\": {\"distinguish_clumped_objects\": \"Shape\", \"__current_case__\": 0, \"con_dividing_lines\": {\"dividing_lines\": \"Shape\", \"__current_case__\": 0, \"con_smoothing_filter\": {\"smoothing_filter\": \"Yes\", \"__current_case__\": 1}, \"con_min_distance\": {\"min_distance\": \"Yes\", \"__current_case__\": 1}, \"speed_up\": \"Yes\"}}, \"fill_hole\": \"After both thresholding and declumping\", \"con_handling_excessive\": {\"excessive_handling\": \"Continue\", \"__current_case__\": 1}}, \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
+                        "type": "tool",
+                        "uuid": "1614fb83-6565-4534-9a42-03e9d5c21a75",
+                        "workflow_outputs": [
                             {
-                                "name": "output_collection",
-                                "type": "input"
-                            },
+                                "label": null,
+                                "output_name": "output_pipeline",
+                                "uuid": "efff5d2f-aa7d-406a-8927-f373feb57837"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "input_pipeline": {
+                                "id": 2,
+                                "output_name": "output_pipeline"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Segmentation mask complete nuclei",
+                        "name": "ConvertObjectsToImage",
+                        "outputs": [
                             {
-                                "name": "output_collection_other",
-                                "type": "input"
-                            },
+                                "name": "output_pipeline",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 353.5,
+                            "top": 219
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2690da374874",
+                            "name": "cp_convert_objects_to_image",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"con_color_format\": {\"color_format\": \"Binary (black & white)\", \"__current_case__\": 0}, \"input_object\": \"Nuclei\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"name_output_image\": \"MaskNuclei\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
+                        "type": "tool",
+                        "uuid": "dc500b23-6fb7-4daa-85f1-53f66b034826",
+                        "workflow_outputs": [
                             {
-                                "name": "log",
+                                "label": null,
+                                "output_name": "output_pipeline",
+                                "uuid": "3c7575e4-4094-4e19-9778-801325f82df9"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_display_data_on_image/cp_display_data_on_image/3.1.9",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "input_pipeline": {
+                                "id": 3,
+                                "output_name": "output_pipeline"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Label nuclei",
+                        "name": "DisplayDataOnImage",
+                        "outputs": [
+                            {
+                                "name": "output_pipeline",
                                 "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 412.5,
-                            "height": 262,
-                            "left": -98,
-                            "right": 102,
-                            "top": 150.5,
-                            "width": 200,
-                            "x": -98,
-                            "y": 150.5
+                            "left": 434.25,
+                            "top": 219
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.8+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_display_data_on_image/cp_display_data_on_image/3.1.9",
                         "tool_shed_repository": {
-                            "changeset_revision": "653e89d73fc4",
-                            "name": "sra_tools",
-                            "owner": "iuc",
+                            "changeset_revision": "4e12ef887a2a",
+                            "name": "cp_display_data_on_image",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adv\": {\"minlen\": null, \"split\": \"--split-3\", \"skip_technical\": \"true\"}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"input\": {\"input_select\": \"file_list\", \"__current_case__\": 2, \"file_list\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.10.8+galaxy0",
+                        "tool_state": "{\"con_display_mode\": {\"display_mode\": \"Text\", \"__current_case__\": 0, \"text_color\": \"#ff0000\", \"font_size\": \"11\", \"number_of_decimals\": \"0\", \"annotation_offset\": \"0\"}, \"con_display_obj_image\": {\"display_obj_image\": \"Object\", \"__current_case__\": 0, \"select_input_obj\": \"Nuclei\", \"con_obj_measurement_category\": {\"measurement_category\": \"Number\", \"__current_case__\": 0, \"measurement\": \"Object_Number\"}}, \"display_background_image\": \"Yes\", \"element_to_save\": \"Image\", \"image_to_display_measurements\": \"DNA\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"name_output_image\": \"ImageDisplay\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
                         "type": "tool",
-                        "uuid": "4fff5f79-2a87-48e4-a9d1-514807dbf145",
+                        "uuid": "d74959c7-b1f5-47a4-8272-b3de8adaf04a",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "list_paired",
-                                "uuid": "bfc8e1d1-aa46-44ce-ac20-203bec142d7f"
-                            },
+                                "output_name": "output_pipeline",
+                                "uuid": "113e8d23-a9e2-45a1-9d40-1e26d4f23456"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "input_pipeline": {
+                                "id": 4,
+                                "output_name": "output_pipeline"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Save labelled nuclei",
+                        "name": "SaveImages",
+                        "outputs": [
+                            {
+                                "name": "output_pipeline",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 515,
+                            "top": 219
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "a45d360ae9d9",
+                            "name": "cp_save_images",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"con_method_for_constructing\": {\"method_for_constructing\": \"From image filename\", \"__current_case__\": 0, \"name_for_file_prefix\": \"DNA\", \"con_append_suffix\": {\"append_suffix\": \"Yes\", \"__current_case__\": 0, \"text_to_append\": \"_nucleiNumbers\"}}, \"con_type_of_image\": {\"type_of_image\": \"Image\", \"__current_case__\": 0, \"con_save_file_format\": {\"file_format\": \"tiff\", \"__current_case__\": 0, \"bit_depth\": \"8-bit integer\"}}, \"image_to_save\": \"ImageDisplay\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"overwrite_without_warning\": \"Yes\", \"record_info\": \"No\", \"when_to_save\": \"Every cycle\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
+                        "type": "tool",
+                        "uuid": "32d4b134-e681-484b-a46d-6fb511358a39",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_collection",
-                                "uuid": "75c35a09-2a2c-450c-8d39-1e7b0c27643f"
-                            },
+                                "output_name": "output_pipeline",
+                                "uuid": "b1aa7814-3057-4f2f-8c8d-48aa7c1a7fa5"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_enhance_or_suppress_features/cp_enhance_or_suppress_features/3.1.9",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "input_pipeline": {
+                                "id": 5,
+                                "output_name": "output_pipeline"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Detect dark holes in nuclei",
+                        "name": "EnhanceOrSuppressFeatures",
+                        "outputs": [
+                            {
+                                "name": "output_pipeline",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 595.75,
+                            "top": 219
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_enhance_or_suppress_features/cp_enhance_or_suppress_features/3.1.9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3f9747bda8c4",
+                            "name": "cp_enhance_or_suppress_features",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"con_enhance_suppress\": {\"select_operation\": \"Enhance\", \"__current_case__\": 0, \"con_feature_type\": {\"feature_type\": \"Dark holes\", \"__current_case__\": 2, \"min_hole_size\": \"1\", \"max_hole_size\": \"15\"}}, \"input_image\": \"DNA\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"name_output_image\": \"DNAdarkholes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
+                        "type": "tool",
+                        "uuid": "2704e748-66d4-4a32-a9eb-459f65f58eb0",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_collection_other",
-                                "uuid": "02be9121-528a-451a-8db1-7e447281fd27"
-                            },
+                                "output_name": "output_pipeline",
+                                "uuid": "fd53651d-06fb-4d6a-b65b-dd686dcb0fcc"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "The dark holes enhanced in the previous step are segmented only if they are inside a nuclei",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_mask_image/cp_mask_image/3.1.9",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "input_pipeline": {
+                                "id": 6,
+                                "output_name": "output_pipeline"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Segment nucleoli that fall inside nuclei",
+                        "name": "MaskImage",
+                        "outputs": [
+                            {
+                                "name": "output_pipeline",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 677.75,
+                            "top": 219
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_mask_image/cp_mask_image/3.1.9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ca1421f7e3ed",
+                            "name": "cp_mask_image",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"con_img_obj\": {\"img_obj\": \"Objects\", \"__current_case__\": 0, \"select_obj\": \"Nuclei\"}, \"input_image\": \"DNAdarkholes\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"invert_mask\": \"No\", \"name_output_image\": \"MaskDNAdarkholes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
+                        "type": "tool",
+                        "uuid": "32492729-4cd6-419e-9429-4fdf91410591",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "log",
-                                "uuid": "56f06d1a-5221-40c3-a861-09f7cb2d0307"
+                                "output_name": "output_pipeline",
+                                "uuid": "da3978ac-fb7a-4095-80d8-df2fad05b747"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "The segmentation only affects those inside the nuclei",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "input_pipeline": {
+                                "id": 7,
+                                "output_name": "output_pipeline"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Segment nucleoli",
+                        "name": "IdentifyPrimaryObjects",
+                        "outputs": [
+                            {
+                                "name": "output_pipeline",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 758.5,
+                            "top": 219
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "52c01fb29b2a",
+                            "name": "cp_identify_primary_objects",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"con_advanced\": {\"advanced\": \"Yes\", \"__current_case__\": 1, \"input_from_nat\": \"MaskDNAdarkholes\", \"name_to_be_identified\": \"Nucleoli\", \"min_diameter\": \"2\", \"max_diameter\": \"15\", \"discard_outside_border\": \"Yes\", \"discard_touching_border\": \"No\", \"con_threshold_strategy\": {\"threshold_strategy\": \"Global\", \"__current_case__\": 1, \"con_threshold_method\": {\"threshold_method\": \"Otsu\", \"__current_case__\": 0, \"con_threshold_class\": {\"threshold_class\": \"Two classes\", \"__current_case__\": 1}, \"threshold_smoothing_scale\": \"1.3488\", \"threshold_correction_factor\": \"0.9\", \"threshold_lower\": \"0.0\", \"threshold_upper\": \"1.0\"}}, \"con_distinguish_clumped_objects\": {\"distinguish_clumped_objects\": \"Shape\", \"__current_case__\": 0, \"con_dividing_lines\": {\"dividing_lines\": \"Shape\", \"__current_case__\": 0, \"con_smoothing_filter\": {\"smoothing_filter\": \"Yes\", \"__current_case__\": 1}, \"con_min_distance\": {\"min_distance\": \"Yes\", \"__current_case__\": 1}, \"speed_up\": \"Yes\"}}, \"fill_hole\": \"After both thresholding and declumping\", \"con_handling_excessive\": {\"excessive_handling\": \"Continue\", \"__current_case__\": 1}}, \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
+                        "type": "tool",
+                        "uuid": "d9cd434a-3fca-4e45-8e73-6c8791af8304",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_pipeline",
+                                "uuid": "dbf37c30-6e43-4d38-9584-b40946194283"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9",
                         "errors": null,
-                        "id": 3,
+                        "id": 9,
                         "input_connections": {
-                            "single_paired|paired_input": {
-                                "id": 2,
-                                "output_name": "list_paired"
+                            "input_pipeline": {
+                                "id": 8,
+                                "output_name": "output_pipeline"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "fastp",
+                        "label": "Convert the segmented nucleoli into an image",
+                        "name": "ConvertObjectsToImage",
                         "outputs": [
                             {
-                                "name": "output_paired_coll",
-                                "type": "input"
-                            },
+                                "name": "output_pipeline",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 839.25,
+                            "top": 219
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2690da374874",
+                            "name": "cp_convert_objects_to_image",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"con_color_format\": {\"color_format\": \"Binary (black & white)\", \"__current_case__\": 0}, \"input_object\": \"Nucleoli\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"name_output_image\": \"MaskNucleoli\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
+                        "type": "tool",
+                        "uuid": "549c3604-1951-49d5-b170-de37f295f3ac",
+                        "workflow_outputs": [
                             {
-                                "name": "report_html",
-                                "type": "html"
-                            },
+                                "label": null,
+                                "output_name": "output_pipeline",
+                                "uuid": "9082f1cc-35ee-4993-975e-592fe84143a9"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_gray_to_color/cp_gray_to_color/3.1.9",
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {
+                            "input_pipeline": {
+                                "id": 9,
+                                "output_name": "output_pipeline"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Combine masks (nuclei + nucleoli)",
+                        "name": "GrayToColor",
+                        "outputs": [
                             {
-                                "name": "report_json",
-                                "type": "json"
+                                "name": "output_pipeline",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 893.5,
-                            "height": 212,
-                            "left": -118,
-                            "right": 82,
-                            "top": 681.5,
-                            "width": 200,
-                            "x": -118,
-                            "y": 681.5
+                            "left": 920,
+                            "top": 219
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_gray_to_color/cp_gray_to_color/3.1.9",
                         "tool_shed_repository": {
-                            "changeset_revision": "dbf9c561ef29",
-                            "name": "fastp",
-                            "owner": "iuc",
+                            "changeset_revision": "bbf1ef17c01b",
+                            "name": "cp_gray_to_color",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": \"false\", \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": \"false\", \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": \"false\", \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": \"true\", \"report_json\": \"true\"}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": \"false\", \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": \"false\", \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": \"false\", \"cut_by_quality3\": \"false\", \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": \"false\"}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 2, \"paired_input\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": \"false\", \"adapter_sequence1\": \"\", \"adapter_sequence2\": \"\"}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.20.1+galaxy0",
+                        "tool_state": "{\"con_color_scheme\": {\"color_scheme\": \"RGB\", \"__current_case__\": 0, \"rgb_red\": \"MaskNucleoli\", \"rgb_red_weight\": \"0.8\", \"rgb_green\": \"Leave this black\", \"rgb_green_weight\": \"1.0\", \"rgb_blue\": \"MaskNuclei\", \"rgb_blue_weight\": \"0.5\"}, \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"name_output_image\": \"CombinedMask\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
                         "type": "tool",
-                        "uuid": "d9327c31-29cf-4227-897d-5a2be3cf8382",
+                        "uuid": "0e09f485-e2ff-4610-bf71-31cf1168ee6d",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "report_json",
-                                "uuid": "f7f03895-44d9-40f1-9bef-7ba34c9b7c1e"
-                            },
+                                "output_name": "output_pipeline",
+                                "uuid": "1a8affd0-4d20-4335-845a-367f12879a2f"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9",
+                        "errors": null,
+                        "id": 11,
+                        "input_connections": {
+                            "input_pipeline": {
+                                "id": 10,
+                                "output_name": "output_pipeline"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Save combined segmentation masks",
+                        "name": "SaveImages",
+                        "outputs": [
+                            {
+                                "name": "output_pipeline",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 1000.75,
+                            "top": 219
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "a45d360ae9d9",
+                            "name": "cp_save_images",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"con_method_for_constructing\": {\"method_for_constructing\": \"From image filename\", \"__current_case__\": 0, \"name_for_file_prefix\": \"DNA\", \"con_append_suffix\": {\"append_suffix\": \"Yes\", \"__current_case__\": 0, \"text_to_append\": \"_combinedMask\"}}, \"con_type_of_image\": {\"type_of_image\": \"Image\", \"__current_case__\": 0, \"con_save_file_format\": {\"file_format\": \"tiff\", \"__current_case__\": 0, \"bit_depth\": \"8-bit integer\"}}, \"image_to_save\": \"CombinedMask\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"overwrite_without_warning\": \"Yes\", \"record_info\": \"No\", \"when_to_save\": \"Every cycle\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
+                        "type": "tool",
+                        "uuid": "46a80d5c-29ee-45ae-9e5b-93099e8eadc2",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_paired_coll",
-                                "uuid": "e8e2c50e-bd56-4717-9cc5-83263f63a3aa"
-                            },
+                                "output_name": "output_pipeline",
+                                "uuid": "5888c4cd-9a64-40f9-82c6-629f211fb04f"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Incomplete nuclei that are touching the borders of the image are segmented, also the nuclei outside the diameter range.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9",
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {
+                            "input_pipeline": {
+                                "id": 11,
+                                "output_name": "output_pipeline"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Segment all nuclei",
+                        "name": "IdentifyPrimaryObjects",
+                        "outputs": [
+                            {
+                                "name": "output_pipeline",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 1081.5,
+                            "top": 219
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "52c01fb29b2a",
+                            "name": "cp_identify_primary_objects",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"con_advanced\": {\"advanced\": \"Yes\", \"__current_case__\": 1, \"input_from_nat\": \"DNA\", \"name_to_be_identified\": \"NucleiIncludingTouchingBorders\", \"min_diameter\": \"15\", \"max_diameter\": \"200\", \"discard_outside_border\": \"No\", \"discard_touching_border\": \"No\", \"con_threshold_strategy\": {\"threshold_strategy\": \"Global\", \"__current_case__\": 1, \"con_threshold_method\": {\"threshold_method\": \"Otsu\", \"__current_case__\": 0, \"con_threshold_class\": {\"threshold_class\": \"Two classes\", \"__current_case__\": 1}, \"threshold_smoothing_scale\": \"1.3488\", \"threshold_correction_factor\": \"0.9\", \"threshold_lower\": \"0.0\", \"threshold_upper\": \"1.0\"}}, \"con_distinguish_clumped_objects\": {\"distinguish_clumped_objects\": \"Shape\", \"__current_case__\": 0, \"con_dividing_lines\": {\"dividing_lines\": \"Shape\", \"__current_case__\": 0, \"con_smoothing_filter\": {\"smoothing_filter\": \"Yes\", \"__current_case__\": 1}, \"con_min_distance\": {\"min_distance\": \"Yes\", \"__current_case__\": 1}, \"speed_up\": \"Yes\"}}, \"fill_hole\": \"After both thresholding and declumping\", \"con_handling_excessive\": {\"excessive_handling\": \"Continue\", \"__current_case__\": 1}}, \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
+                        "type": "tool",
+                        "uuid": "b6f8fb6c-4278-4b17-ba76-c949f87fee51",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "report_html",
-                                "uuid": "95e080c0-8cc7-406a-b470-6f8630111cd9"
+                                "output_name": "output_pipeline",
+                                "uuid": "c96b7030-c091-4961-801c-dc3e72b4a357"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9",
                         "errors": null,
-                        "id": 4,
+                        "id": 13,
                         "input_connections": {
-                            "fastq_input|fastq_input1": {
-                                "id": 3,
-                                "output_name": "output_paired_coll"
-                            },
-                            "reference_source|ref_file": {
-                                "id": 1,
-                                "output_name": "output"
+                            "input_pipeline": {
+                                "id": 12,
+                                "output_name": "output_pipeline"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Map with BWA-MEM",
+                        "label": "Segmentation mask nucleoli including cells touching borders",
+                        "name": "ConvertObjectsToImage",
                         "outputs": [
                             {
-                                "name": "bam_output",
-                                "type": "bam"
+                                "name": "output_pipeline",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 354.5,
-                            "height": 202,
-                            "left": 285,
-                            "right": 485,
-                            "top": 152.5,
-                            "width": 200,
-                            "x": 285,
-                            "y": 152.5
+                            "left": 1162.25,
+                            "top": 219
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9",
                         "tool_shed_repository": {
-                            "changeset_revision": "3fe632431b68",
-                            "name": "bwa",
-                            "owner": "devteam",
+                            "changeset_revision": "2690da374874",
+                            "name": "cp_convert_objects_to_image",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"analysis_type\": {\"analysis_type_selector\": \"illumina\", \"__current_case__\": 0}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"fastq_input\": {\"fastq_input_selector\": \"paired_collection\", \"__current_case__\": 2, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"iset_stats\": \"\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}, \"index_a\": \"auto\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.17.1",
+                        "tool_state": "{\"con_color_format\": {\"color_format\": \"Binary (black & white)\", \"__current_case__\": 0}, \"input_object\": \"NucleiIncludingTouchingBorders\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"name_output_image\": \"Image_NucleiIncludingTouchingBorders\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
+                        "type": "tool",
+                        "uuid": "adc8a062-58ee-4285-a4f2-fcf423f30bdd",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_pipeline",
+                                "uuid": "a9f1d26d-ad3d-4984-b15b-76d1e3309833"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_image_math/cp_image_math/0.1.0",
+                        "errors": null,
+                        "id": 14,
+                        "input_connections": {
+                            "input_pipeline": {
+                                "id": 13,
+                                "output_name": "output_pipeline"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Extract background",
+                        "name": "ImageMath",
+                        "outputs": [
+                            {
+                                "name": "output_pipeline",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 1243,
+                            "top": 219
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_image_math/cp_image_math/0.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "6d3851ac885f",
+                            "name": "cp_image_math",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"ignore_the_image_masks\": \"No\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"name_output_image\": \"BG\", \"operation\": {\"operation\": \"subtract\", \"__current_case__\": 1, \"first_image\": {\"image_or_measurement_first\": {\"image_or_measurement_first\": \"Image\", \"__current_case__\": 0, \"select_the_first_image\": \"DNA\"}, \"multiply_the_first_image_by\": \"1.0\"}, \"second_image\": {\"image_or_measurement_second\": {\"image_or_measurement_second\": \"Image\", \"__current_case__\": 0, \"select_the_second_image\": \"Image_NucleiIncludingTouchingBorders\"}, \"multiply_the_second_image_by\": \"1.0\"}, \"op_results\": {\"raise_the_power_of_the_result_by\": \"1.0\", \"multiply_the_result_by\": \"1.0\", \"add_to_result\": \"0.0\", \"set_values_less_than_0_equal_to_0\": \"Yes\", \"set_values_greater_than_1_equal_to_1\": \"Yes\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0",
+                        "type": "tool",
+                        "uuid": "549ce202-f817-48e7-90cb-2e3766c67e4b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_pipeline",
+                                "uuid": "b64b6fc5-593f-4755-9531-3d4b2d47cc61"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "This step measures the granularity of the original image",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_granularity/cp_measure_granularity/3.1.9",
+                        "errors": null,
+                        "id": 15,
+                        "input_connections": {
+                            "input_pipeline": {
+                                "id": 14,
+                                "output_name": "output_pipeline"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Measure the image granularity",
+                        "name": "MeasureGranularity",
+                        "outputs": [
+                            {
+                                "name": "output_pipeline",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 1323.75,
+                            "top": 219
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_granularity/cp_measure_granularity/3.1.9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "382413f8ec1d",
+                            "name": "cp_measure_granularity",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"rpt_image\": [{\"__index__\": 0, \"image_to_measure\": \"DNA\", \"subsampling_factor_granularity\": \"0.25\", \"subsampling_factor_background_reduction\": \"0.25\", \"radius\": \"10\", \"range_granular_spectrum\": \"16\", \"rpt_object\": []}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
+                        "type": "tool",
+                        "uuid": "facc511c-7f3e-48bc-8330-e9bb5b4a6b1e",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_pipeline",
+                                "uuid": "b157d712-698d-46e6-b042-913748e44f89"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "This step measures the texture of the original image and nuclei in it",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_texture/cp_measure_texture/3.1.9",
+                        "errors": null,
+                        "id": 16,
+                        "input_connections": {
+                            "input_pipeline": {
+                                "id": 15,
+                                "output_name": "output_pipeline"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Measure the nuclei texture",
+                        "name": "MeasureTexture",
+                        "outputs": [
+                            {
+                                "name": "output_pipeline",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 1404.5,
+                            "top": 219
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_texture/cp_measure_texture/3.1.9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "658a2a451aec",
+                            "name": "cp_measure_texture",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"con_img_obj\": {\"img_obj\": \"Objects\", \"__current_case__\": 0, \"rpt_obj_to_measure\": [{\"__index__\": 0, \"obj_to_measure\": \"Nuclei\"}]}, \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"rpt_image_to_measure\": [{\"__index__\": 0, \"image_to_measure\": \"DNA\"}], \"rpt_scale_to_measure\": [{\"__index__\": 0, \"scale_to_measure\": \"3\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
+                        "type": "tool",
+                        "uuid": "ae3973f7-8c6e-410e-828a-633b59839fe6",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_pipeline",
+                                "uuid": "5d4d6e55-44cf-4611-bcd8-bda8a9df7286"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "This step measures the intensity of the original image and the nuclei",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9",
+                        "errors": null,
+                        "id": 17,
+                        "input_connections": {
+                            "input_pipeline": {
+                                "id": 16,
+                                "output_name": "output_pipeline"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Measure the nuclei intensity",
+                        "name": "MeasureObjectIntensity",
+                        "outputs": [
+                            {
+                                "name": "output_pipeline",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 1485.25,
+                            "top": 219
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "b867e9317a06",
+                            "name": "cp_measure_object_intensity",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"rpt_image\": [{\"__index__\": 0, \"image_to_measure\": \"DNA\"}], \"rpt_object\": [{\"__index__\": 0, \"objects_to_measure\": \"Nuclei\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
                         "type": "tool",
-                        "uuid": "f06a5bce-2611-4eba-aaf9-d8cc063acaf7",
+                        "uuid": "0ac29831-ed29-4294-95b5-ba2400408dab",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "bam_output",
-                                "uuid": "88953a9e-a48a-4f60-8854-09b04e8c5052"
+                                "output_name": "output_pipeline",
+                                "uuid": "d26c927d-f6c3-4c53-873b-015d8fe59d0f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9",
                         "errors": null,
-                        "id": 5,
+                        "id": 18,
                         "input_connections": {
-                            "input": {
-                                "id": 4,
-                                "output_name": "bam_output"
+                            "input_pipeline": {
+                                "id": 17,
+                                "output_name": "output_pipeline"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Samtools view",
+                        "label": "Measure size and shape of nuclei and nucleoli",
+                        "name": "MeasureObjectSizeShape",
                         "outputs": [
                             {
-                                "name": "outputsam",
-                                "type": "input"
+                                "name": "output_pipeline",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 297.5,
-                            "height": 152,
-                            "left": 614,
-                            "right": 814,
-                            "top": 145.5,
-                            "width": 200,
-                            "x": 614,
-                            "y": 145.5
+                            "left": 1566,
+                            "top": 219
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9",
                         "tool_shed_repository": {
-                            "changeset_revision": "bf328cec6a42",
-                            "name": "samtools_view",
-                            "owner": "iuc",
+                            "changeset_revision": "5c9549983af8",
+                            "name": "cp_measure_object_size_shape",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"bam\", \"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"SRR12733957\", \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"quality\": \"20\", \"library\": \"\", \"cigarcons\": null, \"inclusive_filter\": [\"1\", \"2\"], \"exclusive_filter\": null, \"exclusive_filter_all\": null}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"fraction\", \"__current_case__\": 0, \"factor\": \"10.0\", \"seed\": \"1\"}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": \"false\", \"adv_output\": {\"readtags\": [], \"collapsecigar\": \"false\"}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9+galaxy2",
+                        "tool_state": "{\"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"rpt_object\": [{\"__index__\": 0, \"objects_to_measure\": \"Nuclei\"}, {\"__index__\": 1, \"objects_to_measure\": \"Nucleoli\"}], \"zernike_feature\": \"Yes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
                         "type": "tool",
-                        "uuid": "352c0b12-e4e5-409c-96ff-321de1076e56",
+                        "uuid": "580e3cc4-48f3-48d2-9d69-8bb6c3d79be9",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outputsam",
-                                "uuid": "884d1918-7037-4108-bd34-3ae703992031"
+                                "output_name": "output_pipeline",
+                                "uuid": "289985e1-f94e-4223-bc1b-64ac4eadf40e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_relate_objects/cp_relate_objects/3.1.9",
                         "errors": null,
-                        "id": 6,
+                        "id": 19,
                         "input_connections": {
-                            "inputFile": {
-                                "id": 5,
-                                "output_name": "outputsam"
+                            "input_pipeline": {
+                                "id": 18,
+                                "output_name": "output_pipeline"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "MarkDuplicates",
+                        "label": "Relate nucleoli with their parent nuclei",
+                        "name": "RelateObjects",
                         "outputs": [
                             {
-                                "name": "metrics_file",
+                                "name": "output_pipeline",
                                 "type": "txt"
-                            },
-                            {
-                                "name": "outFile",
-                                "type": "bam"
                             }
                         ],
                         "position": {
-                            "bottom": 1017.5,
-                            "height": 222,
-                            "left": 435,
-                            "right": 635,
-                            "top": 795.5,
-                            "width": 200,
-                            "x": 435,
-                            "y": 795.5
+                            "left": 1648,
+                            "top": 219
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_relate_objects/cp_relate_objects/3.1.9",
                         "tool_shed_repository": {
-                            "changeset_revision": "a1f0b3f4b781",
-                            "name": "picard",
-                            "owner": "devteam",
+                            "changeset_revision": "f3f45c42bc36",
+                            "name": "cp_relate_objects",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"bam\", \"assume_sorted\": \"true\", \"barcode_tag\": \"\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"comments\": [], \"duplicate_scoring_strategy\": \"SUM_OF_BASE_QUALITIES\", \"inputFile\": {\"__class__\": \"ConnectedValue\"}, \"inputFile|__identifier__\": \"SRR12733957\", \"optical_duplicate_pixel_distance\": \"100\", \"read_name_regex\": \"\", \"remove_duplicates\": \"true\", \"validation_stringency\": \"LENIENT\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.18.2.2",
+                        "tool_state": "{\"child_objects\": \"Nucleoli\", \"con_dist\": {\"calc_dist\": \"Both\", \"__current_case__\": 2, \"con_other_parent_dist\": {\"calc_dist_to_others\": \"No\", \"__current_case__\": 1}}, \"con_save_child\": {\"save_child_as_new\": \"Yes\", \"__current_case__\": 0, \"name_output\": \"RelateObjects\"}, \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"means_for_all\": \"Yes\", \"parent_objects\": \"Nuclei\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
                         "type": "tool",
-                        "uuid": "8073c99c-1b22-4495-aa2e-35590ea8a27a",
+                        "uuid": "d776a7aa-7154-401d-8ff5-15e986f29597",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "metrics_file",
-                                "uuid": "72b65822-0933-4ef0-af4b-7b863e79efa2"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "outFile",
-                                "uuid": "5919b29b-d3eb-4ba5-9a77-b800e27d6a7d"
+                                "output_name": "output_pipeline",
+                                "uuid": "48df535c-abd3-423e-b6c4-e3e6a2579eb7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_quality/cp_measure_image_quality/3.1.9",
                         "errors": null,
-                        "id": 7,
+                        "id": 20,
                         "input_connections": {
-                            "input": {
-                                "id": 6,
-                                "output_name": "outFile"
+                            "input_pipeline": {
+                                "id": 19,
+                                "output_name": "output_pipeline"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Samtools stats",
+                        "label": "Measure the image quality",
+                        "name": "MeasureImageQuality",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "name": "output_pipeline",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 237.5,
-                            "height": 112,
-                            "left": 957,
-                            "right": 1157,
-                            "top": 125.5,
-                            "width": 200,
-                            "x": 957,
-                            "y": 125.5
+                            "left": 1728.75,
+                            "top": 219
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_quality/cp_measure_image_quality/3.1.9",
                         "tool_shed_repository": {
-                            "changeset_revision": "145f6d74ff5e",
-                            "name": "samtools_stats",
-                            "owner": "devteam",
+                            "changeset_revision": "08a2cf887a44",
+                            "name": "cp_measure_image_quality",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"bam\", \"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cov_threshold\": null, \"coverage_cond\": {\"coverage_select\": \"no\", \"__current_case__\": 0}, \"filter_by_flags\": {\"filter_flags\": \"nofilter\", \"__current_case__\": 1}, \"gc_depth\": null, \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"SRR12733957\", \"insert_size\": null, \"most_inserts\": null, \"read_length\": null, \"remove_dups\": \"false\", \"remove_overlaps\": \"false\", \"sparse\": \"false\", \"split_output_cond\": {\"split_output_selector\": \"no\", \"__current_case__\": 0}, \"trim_quality\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy2",
+                        "tool_state": "{\"calc_for_images\": \"All loaded images\", \"calc_intensity_metrics\": \"Yes\", \"calc_saturation_metrics\": \"Yes\", \"con_calc_blur_metrics\": {\"calc_blur_metrics\": \"Yes\", \"__current_case__\": 0, \"rpt_blur_measurements\": [{\"__index__\": 0, \"blur_measurements\": \"20\"}]}, \"con_calc_threshold\": {\"calc_threshold\": \"Yes\", \"__current_case__\": 0, \"con_use_all_methods\": {\"use_all_methods\": \"No\", \"__current_case__\": 1, \"rpt_threshold_method\": [{\"__index__\": 0, \"con_threshold_methods\": {\"select_threshold_method\": \"Otsu\", \"__current_case__\": 0, \"otsu_weighted_entropy\": \"Weighted variance\", \"con_threshold_classes\": {\"threshold_classes\": \"Two classes\", \"__current_case__\": 1}}}]}}, \"include_rescaling_value\": \"Yes\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
                         "type": "tool",
-                        "uuid": "199dba34-fd3a-4a8c-9af8-96e51503689f",
+                        "uuid": "3b81db10-c6dd-4ff0-8b2d-58ab00f80260",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "d9708b0c-194c-455a-ab8a-b99f09eed498"
+                                "output_name": "output_pipeline",
+                                "uuid": "db6c90c4-44cd-405d-94f2-00f9c93a120c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_area_occupied/cp_measure_image_area_occupied/3.1.9",
                         "errors": null,
-                        "id": 8,
+                        "id": 21,
                         "input_connections": {
-                            "reads": {
-                                "id": 6,
-                                "output_name": "outFile"
-                            },
-                            "reference_source|ref": {
-                                "id": 1,
-                                "output_name": "output"
+                            "input_pipeline": {
+                                "id": 20,
+                                "output_name": "output_pipeline"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Realign reads",
+                        "label": "Measure the area occupied by nuclei and nucleoli",
+                        "name": "MeasureImageAreaOccupied",
                         "outputs": [
                             {
-                                "name": "realigned",
-                                "type": "bam"
+                                "name": "output_pipeline",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 1035.5,
-                            "height": 162,
-                            "left": 907,
-                            "right": 1107,
-                            "top": 873.5,
-                            "width": 200,
-                            "x": 907,
-                            "y": 873.5
+                            "left": 1809.5,
+                            "top": 219
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_area_occupied/cp_measure_image_area_occupied/3.1.9",
                         "tool_shed_repository": {
-                            "changeset_revision": "aa35ee7f3ab2",
-                            "name": "lofreq_viterbi",
-                            "owner": "iuc",
+                            "changeset_revision": "7a08edbc790e",
+                            "name": "cp_measure_image_area_occupied",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adv_options\": {\"keepflags\": \"false\", \"bq2_handling\": {\"replace_bq2\": \"keep\", \"__current_case__\": 0, \"defqual\": \"2\"}}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"reads|__identifier__\": \"SRR12733957\", \"reference_source\": {\"ref_selector\": \"history\", \"__current_case__\": 1, \"ref\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.5+galaxy0",
+                        "tool_state": "{\"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"rpt_area\": [{\"__index__\": 0, \"con_area\": {\"objects_or_image\": \"Objects\", \"__current_case__\": 0, \"objects_to_measure\": \"Nuclei\"}}, {\"__index__\": 1, \"con_area\": {\"objects_or_image\": \"Objects\", \"__current_case__\": 0, \"objects_to_measure\": \"Nucleoli\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
                         "type": "tool",
-                        "uuid": "53f949ab-b512-49a9-ac05-2ae2665431c2",
+                        "uuid": "3df981d5-142e-4cb5-b897-05afcb201811",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "realigned",
-                                "uuid": "7140df66-cd64-48aa-a7d4-ac916164a821"
+                                "output_name": "output_pipeline",
+                                "uuid": "58cdfb31-71f2-44ef-a385-f62188f8d2a3"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_intensity/cp_measure_image_intensity/3.1.9",
                         "errors": null,
-                        "id": 9,
+                        "id": 22,
                         "input_connections": {
-                            "results_0|software_cond|input": {
-                                "id": 3,
-                                "output_name": "report_json"
-                            },
-                            "results_1|software_cond|output_0|input": {
-                                "id": 6,
-                                "output_name": "metrics_file"
-                            },
-                            "results_2|software_cond|output_0|type|input": {
-                                "id": 7,
-                                "output_name": "output"
+                            "input_pipeline": {
+                                "id": 21,
+                                "output_name": "output_pipeline"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "MultiQC",
+                        "label": "Measure the image intensity",
+                        "name": "MeasureImageIntensity",
                         "outputs": [
                             {
-                                "name": "stats",
-                                "type": "input"
-                            },
-                            {
-                                "name": "plots",
-                                "type": "input"
-                            },
-                            {
-                                "name": "html_report",
-                                "type": "html"
+                                "name": "output_pipeline",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 973.5,
-                            "height": 312,
-                            "left": 1329,
-                            "right": 1529,
-                            "top": 661.5,
-                            "width": 200,
-                            "x": 1329,
-                            "y": 661.5
+                            "left": 1891.5,
+                            "top": 219
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_intensity/cp_measure_image_intensity/3.1.9",
                         "tool_shed_repository": {
-                            "changeset_revision": "5e33b465d8d5",
-                            "name": "multiqc",
-                            "owner": "iuc",
+                            "changeset_revision": "2681008d726f",
+                            "name": "cp_measure_image_intensity",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"json\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"comment\": \"\", \"flat\": \"false\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 23, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"stats\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8+galaxy1",
+                        "tool_state": "{\"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"rpt_intensity\": [{\"__index__\": 0, \"image_to_measure\": \"DNA\", \"con_intensity\": {\"only_from_objects\": \"No\", \"__current_case__\": 1}}, {\"__index__\": 1, \"image_to_measure\": \"DNA\", \"con_intensity\": {\"only_from_objects\": \"Yes\", \"__current_case__\": 0, \"input_objects\": \"Nuclei\"}}, {\"__index__\": 2, \"image_to_measure\": \"BG\", \"con_intensity\": {\"only_from_objects\": \"No\", \"__current_case__\": 1}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
                         "type": "tool",
-                        "uuid": "69debef6-a98f-4c07-925b-37372e8be51e",
+                        "uuid": "5aa9619d-a11a-4b22-8d13-0b39eff4f665",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "stats",
-                                "uuid": "c2a695c7-b2ee-4331-89e4-82e23045d870"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "plots",
-                                "uuid": "2f5d878b-2876-4784-822e-82b438993704"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "html_report",
-                                "uuid": "e534aca7-9f10-4060-bbb7-e2b5e8717038"
+                                "output_name": "output_pipeline",
+                                "uuid": "64333743-a286-4ecb-85be-4203f31d566c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9",
                         "errors": null,
-                        "id": 10,
+                        "id": 23,
                         "input_connections": {
-                            "reads": {
-                                "id": 8,
-                                "output_name": "realigned"
-                            },
-                            "strategy|reference_source|ref": {
-                                "id": 1,
-                                "output_name": "output"
+                            "input_pipeline": {
+                                "id": 22,
+                                "output_name": "output_pipeline"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Insert indel qualities",
+                        "label": "Export measurements",
+                        "name": "ExportToSpreadsheet",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "bam"
+                                "name": "output_pipeline",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 314.5,
-                            "height": 142,
-                            "left": 1265,
-                            "right": 1465,
-                            "top": 172.5,
-                            "width": 200,
-                            "x": 1265,
-                            "y": 172.5
+                            "left": 1972.25,
+                            "top": 219
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9",
                         "tool_shed_repository": {
-                            "changeset_revision": "426d707dfc47",
-                            "name": "lofreq_indelqual",
-                            "owner": "iuc",
+                            "changeset_revision": "72a7f23f3a79",
+                            "name": "cp_export_to_spreadsheet",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"reads|__identifier__\": \"SRR12733957\", \"strategy\": {\"selector\": \"dindel\", \"__current_case__\": 1, \"reference_source\": {\"ref_selector\": \"history\", \"__current_case__\": 1, \"ref\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.5+galaxy0",
+                        "tool_state": "{\"add_metadata_column_to_object\": \"Yes\", \"calc_mean\": \"Yes\", \"calc_median\": \"Yes\", \"calc_standard_deviation\": \"Yes\", \"con_create_gene_pattern\": {\"create_gene_pattern\": \"No\", \"__current_case__\": 1}, \"con_export_all_measurements\": {\"export_all_measurements\": \"Yes\", \"__current_case__\": 1}, \"con_prefix\": {\"add_prefix\": \"No\", \"__current_case__\": 1}, \"delimiter\": \"Tab\", \"input_pipeline\": {\"__class__\": \"ConnectedValue\"}, \"overwrite_existing_file\": \"Yes\", \"represent_nan\": \"NaN\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
                         "type": "tool",
-                        "uuid": "cd5db03f-7831-426f-b76d-c285751a9e02",
+                        "uuid": "fe3256bd-e219-48ba-9588-87ccd061ce46",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "543fdf07-db60-437c-99fe-c06bfd010081"
+                                "output_name": "output_pipeline",
+                                "uuid": "70625d77-224f-405a-ab93-3f55d644d9bd"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9",
                         "errors": null,
-                        "id": 11,
+                        "id": 24,
                         "input_connections": {
-                            "reads": {
-                                "id": 10,
-                                "output_name": "output"
-                            },
-                            "reference_source|ref": {
+                            "con_input_type|input_images": {
                                 "id": 1,
-                                "output_name": "output"
+                                "output_name": "output_tar"
+                            },
+                            "pipeline": {
+                                "id": 23,
+                                "output_name": "output_pipeline"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Call variants",
+                        "label": "Run CellProfiler",
+                        "name": "CellProfiler",
                         "outputs": [
                             {
-                                "name": "variants",
-                                "type": "vcf"
+                                "name": "pipeline_output",
+                                "type": "input"
+                            },
+                            {
+                                "name": "logs",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 462.5,
-                            "height": 122,
-                            "left": 1470,
-                            "right": 1670,
-                            "top": 340.5,
-                            "width": 200,
-                            "x": 1470,
-                            "y": 340.5
+                            "left": 2053,
+                            "top": 219
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1",
+                        "post_job_actions": {
+                            "EmailActionpipeline_output": {
+                                "action_arguments": {},
+                                "action_type": "EmailAction",
+                                "output_name": "pipeline_output"
+                            },
+                            "HideDatasetActionlogs": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "logs"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9",
                         "tool_shed_repository": {
-                            "changeset_revision": "e1461b5c52a0",
-                            "name": "lofreq_call",
-                            "owner": "iuc",
+                            "changeset_revision": "fca368c99299",
+                            "name": "cp_cellprofiler",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"call_control\": {\"set_call_options\": \"yes\", \"__current_case__\": 1, \"coverage\": {\"min_cov\": \"10\", \"max_depth\": \"1000000\"}, \"pe\": {\"use_orphan\": \"false\"}, \"bc_quals\": {\"min_bq\": \"20\", \"min_alt_bq\": \"20\", \"alt_bq\": {\"modify\": \"\", \"__current_case__\": 0}}, \"align_quals\": {\"alnqual\": {\"use_alnqual\": \"\", \"__current_case__\": 0, \"alnqual_choice\": {\"alnquals_to_use\": \"\", \"__current_case__\": 1, \"extended_baq\": \"true\"}}}, \"map_quals\": {\"min_mq\": \"20\", \"use_mq\": {\"no_mq\": \"\", \"__current_case__\": 0, \"max_mq\": \"255\"}}, \"source_qual\": {\"use_src_qual\": {\"src_qual\": \"\", \"__current_case__\": 0}}, \"joint_qual\": {\"min_jq\": \"0\", \"min_alt_jq\": \"0\", \"def_alt_jq\": \"0\"}}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"filter_control\": {\"filter_type\": \"set_lofreq_standard\", \"__current_case__\": 2, \"sig\": \"0.01\", \"bonf\": \"dynamic\", \"others\": \"\"}, \"reads\": {\"__class__\": \"ConnectedValue\"}, \"reads|__identifier__\": \"SRR12733957\", \"reference_source\": {\"ref_selector\": \"history\", \"__current_case__\": 1, \"ref\": {\"__class__\": \"ConnectedValue\"}}, \"regions\": {\"restrict_to_region\": \"genome\", \"__current_case__\": 0}, \"variant_types\": \"--call-indels\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.5+galaxy1",
+                        "tool_state": "{\"con_input_type\": {\"input_type\": \"yes\", \"__current_case__\": 1, \"input_images\": {\"__class__\": \"ConnectedValue\"}}, \"detailed_output\": \"true\", \"pipeline\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.9",
                         "type": "tool",
-                        "uuid": "d332f810-2a7c-41bf-b458-05470d3ae6b5",
+                        "uuid": "5e893441-7a89-44ce-afe8-29959465f0ee",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "variants",
-                                "uuid": "395a308b-d1ba-4c67-8b66-4e206c727a3c"
+                                "output_name": "pipeline_output",
+                                "uuid": "30778509-8776-4c05-8d4e-6823532a9c41"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "imaging/tutorial-CP",
+                "path": "topics/imaging/tutorials/tutorial-CP/workflows/main_workflow.ga",
+                "tags": [
+                    "CellProfiler",
+                    "imaging"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "CP_pipeline_IDR_training",
+                "topic_id": "imaging",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/imaging-tutorial-CP/versions/main-workflow",
+                "tutorial_id": "tutorial-CP",
+                "url": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/tutorial-CP/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/tutorial-CP/workflows/main_workflow.html",
+                "version": 3,
+                "wfid": "imaging-tutorial-CP",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_display_data_on_image/cp_display_data_on_image/3.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_enhance_or_suppress_features/cp_enhance_or_suppress_features/3.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_gray_to_color/cp_gray_to_color/3.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_image_math/cp_image_math/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_mask_image/cp_mask_image/3.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_granularity/cp_measure_granularity/3.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_area_occupied/cp_measure_image_area_occupied/3.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_intensity/cp_measure_image_intensity/3.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_quality/cp_measure_image_quality/3.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_texture/cp_measure_texture/3.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_relate_objects/cp_relate_objects/3.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/idr_download_by_ids/idr_download_by_ids/0.41"
+                ],
+                "workflowhub_id": "1262"
+            }
+        ],
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "2d_auto_threshold",
+                    "owner": "imgteam",
+                    "revisions": "0c777d708acc",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "2d_auto_threshold",
+                    "owner": "imgteam",
+                    "revisions": "3df9f0a4bf34",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "2d_feature_extraction",
+                    "owner": "imgteam",
+                    "revisions": "5791a7f65275",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "2d_feature_extraction",
+                    "owner": "imgteam",
+                    "revisions": "0a53256b48c6",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "2d_filter_segmentation_by_features",
+                    "owner": "imgteam",
+                    "revisions": "e576b73a2e2f",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "2d_simple_filter",
+                    "owner": "imgteam",
+                    "revisions": "dba87c4b32d3",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "2d_simple_filter",
+                    "owner": "imgteam",
+                    "revisions": "f70b215d155c",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "2d_split_binaryimage_by_watershed",
+                    "owner": "imgteam",
+                    "revisions": "f8f7987586b7",
+                    "tool_panel_section_label": "Imaging",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "unzip",
+                    "owner": "imgteam",
+                    "revisions": "57f0914ddb7b",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "90981f86000f",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: 2d_auto_threshold\n  owner: imgteam\n  revisions: 0c777d708acc\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_auto_threshold\n  owner: imgteam\n  revisions: 3df9f0a4bf34\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_feature_extraction\n  owner: imgteam\n  revisions: 5791a7f65275\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_feature_extraction\n  owner: imgteam\n  revisions: 0a53256b48c6\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_filter_segmentation_by_features\n  owner: imgteam\n  revisions: e576b73a2e2f\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_simple_filter\n  owner: imgteam\n  revisions: dba87c4b32d3\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_simple_filter\n  owner: imgteam\n  revisions: f70b215d155c\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_split_binaryimage_by_watershed\n  owner: imgteam\n  revisions: f8f7987586b7\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unzip\n  owner: imgteam\n  revisions: 57f0914ddb7b\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/hela-screen-analysis/tutorial.json",
+        "contributors": [
+            {
+                "former_affiliations": [
+                    "deNBI",
+                    "elixir-europe"
+                ],
+                "id": "thomaswollmann",
+                "joined": "2019-08",
+                "name": "Thomas Wollmann",
+                "orcid": "0000-0002-4741-3844",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/thomaswollmann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/thomaswollmann.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe",
+                    "deNBI"
+                ],
+                "elixir_node": "de",
+                "email": "leonid.kostrykin@bioquant.uni-heidelberg.de",
+                "id": "kostrykin",
+                "joined": "2023-08",
+                "linkedin": "kostrykin",
+                "name": "Leonid Kostrykin",
+                "orcid": "0000-0003-1323-3762",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kostrykin/",
+                "twitter": "l_kostrykin",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/kostrykin.json"
+            }
+        ],
+        "dir": "topics/imaging/tutorials/hela-screen-analysis",
+        "edam_operation": [
+            "Data handling",
+            "Visualisation",
+            "Image annotation",
+            "Image analysis"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "statistics",
+                "tutorials": [
+                    "machinelearning"
+                ],
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "imaging/hela-screen-analysis",
+        "inexact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Galaxy workflows can be used to scale image analysis pipelines to whole screens.",
+            "Segmented objects can be filtered using the **Filter label map by rules** tool.",
+            "Galaxy charts can be used to compare features extracted from screens showing cells with different treatments."
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-14",
+        "objectives": [
+            "How to segment cell nuclei in Galaxy.",
+            "How to extract features from segmentations in Galaxy.",
+            "How to filter segmentations by morphological features in Galaxy.",
+            "How to extract features from an imaging screen in Galaxy.",
+            "How to analyse extracted features from an imaging screen in Galaxy."
+        ],
+        "pageviews": 736,
+        "pub_date": "2019-08-13",
+        "questions": [
+            "How do I analyze a HeLa fluorescence siRNA screen?",
+            "How do I segment cell nuclei?",
+            "How do I extract features from segmentations?",
+            "How do I filter segmentations by morphological features?",
+            "How do I apply a feature extraction workflow to a screen?",
+            "How do I visualize feature extraction results?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "imaging",
+                "tutorials": [
+                    "imaging-introduction"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00180",
+        "short_tools": [
+            "ip_2d_split_binaryimage_by_watershed",
+            "ip_2d_feature_extraction",
+            "ip_threshold",
+            "unzip",
+            "ip_filter_standard",
+            "ip_2d_filter_segmentation_by_features",
+            "collapse_dataset"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "HeLa"
+        ],
+        "time_estimation": "1H",
+        "title": "Analyse HeLa fluorescence siRNA screen",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.0.5",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.0.5-2",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.1.1",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.1.1-2",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_filter_segmentation_by_features/ip_2d_filter_segmentation_by_features/0.0.1",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/0.0.3",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/0.0.3-3",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_split_binaryimage_by_watershed/ip_2d_split_binaryimage_by_watershed/0.0.1",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/2d_split_binaryimage_by_watershed/ip_2d_split_binaryimage_by_watershed/0.0.1-2",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
+        ],
+        "topic_name": "imaging",
+        "topic_name_human": "Imaging",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "hela-screen-analysis",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/imaging/tutorials/hela-screen-analysis/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/hela-screen-analysis/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/hela-screen-analysis/tutorial.json"
+        },
+        "version": 9,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 163,
+        "visitors": 565,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0002-2315-9247",
+                        "name": "Till Korten",
+                        "url": "https://github.com/thawn/"
+                    }
+                ],
+                "description": "Analyse HeLa fluorescence siRNA screen",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": true
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\ninput images\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nrules\"]\n  2[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nfeature_extraction\"]\n  0 -> 2 [label=\"output\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"merge_table\"]\n  2 -> 3 [label=\"output\"]\n  k3fc2324d233b47859fb79c30b2daaef4[color=lightseagreen,label=\"Output\\noutput\"]\n  3 -> k3fc2324d233b47859fb79c30b2daaef4\n}",
+                "history": [
+                    {
+                        "hash": "d1e807a669d4a58fee5b1db2eceb8d4e4468fc21",
+                        "message": "fixed json syntax",
+                        "num": 7,
+                        "short_hash": "d1e807a66",
+                        "unix": "1699440970"
+                    },
+                    {
+                        "hash": "e34767b4ad7f4a1965ce15499e19fac5928806e0",
+                        "message": "added `creator` and `license` fields",
+                        "num": 6,
+                        "short_hash": "e34767b4a",
+                        "unix": "1699440539"
+                    },
+                    {
+                        "hash": "fab15d8bfc051c7ef280ef9aa08572543b5b24bf",
+                        "message": "updated analyze_screen.ga",
+                        "num": 5,
+                        "short_hash": "fab15d8bf",
+                        "unix": "1699376551"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 4,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 3,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
+                        "message": "unflatten workflows",
+                        "num": 2,
+                        "short_hash": "faf6d298a",
+                        "unix": "1576155753"
                     },
+                    {
+                        "hash": "96462d6dcda154df6515addd109fdad1489cbe86",
+                        "message": "added second tutorial",
+                        "num": 1,
+                        "short_hash": "96462d6dc",
+                        "unix": "1565095814"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
+                        "content_id": null,
                         "errors": null,
-                        "id": 12,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "input images"
+                            }
+                        ],
+                        "label": "input images",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 0.0,
+                            "top": 0.0
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "f021a2d0-b90b-4f1e-830c-127af3741b90",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "rules"
+                            }
+                        ],
+                        "label": "rules",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 3.140430845923717,
+                            "top": 127.71085440089814
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "8040611c-247d-4339-b8be-3858f01a0d6c",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\ninput images\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nrules\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\ud83d\udee0\ufe0f Subworkflow\\nfeature_extraction\"];\n  style 2 fill:#edd,stroke:#900,stroke-width:4px;\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"merge_table\"];\n  2 -->|output| 3;\n  3fc2324d-233b-4785-9fb7-9c30b2daaef4[\"Output\\noutput\"];\n  3 --> 3fc2324d-233b-4785-9fb7-9c30b2daaef4;\n  style 3fc2324d-233b-4785-9fb7-9c30b2daaef4 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "analyze_screen",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
+                        "errors": null,
+                        "id": 3,
                         "input_connections": {
-                            "input": {
-                                "id": 11,
-                                "output_name": "variants"
+                            "input_list": {
+                                "id": 2,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "SnpEff eff:",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "snpeff_output",
-                                "type": "vcf"
-                            },
+                                "description": "runtime parameter for tool Collapse Collection",
+                                "name": "input_list"
+                            }
+                        ],
+                        "label": "merge_table",
+                        "name": "Collapse Collection",
+                        "outputs": [
                             {
-                                "name": "statsFile",
-                                "type": "html"
+                                "name": "output",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 774.5,
-                            "height": 282,
-                            "left": 1624,
-                            "right": 1824,
-                            "top": 492.5,
-                            "width": 200,
-                            "x": 1624,
-                            "y": 492.5
+                            "left": 573.742905824752,
+                            "top": 29.554536267952393
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "2a3a00c1fa0a",
-                            "name": "snpeff_sars_cov_2",
-                            "owner": "iuc",
+                            "changeset_revision": "90981f86000f",
+                            "name": "collapse_collections",
+                            "owner": "nml",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"vcf\", \"annotations\": [\"-formatEff\", \"-classic\"], \"chr\": \"\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"csvStats\": \"false\", \"filter\": {\"specificEffects\": \"no\", \"__current_case__\": 0}, \"filterOut\": null, \"generate_stats\": \"true\", \"genome_version\": \"NC_045512.2\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inputFormat\": \"vcf\", \"input|__identifier__\": \"SRR12733957\", \"intervals\": null, \"noLog\": \"true\", \"offset\": \"default\", \"outputConditional\": {\"outputFormat\": \"vcf\", \"__current_case__\": 0}, \"transcripts\": null, \"udLength\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.5covid19",
+                        "tool_state": "{\"filename\": {\"add_name\": false, \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"RuntimeValue\"}, \"one_header\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.1.0",
                         "type": "tool",
-                        "uuid": "29a0aa67-7bce-4358-a349-cc58d9824dad",
+                        "uuid": "f48f5037-e4ab-4b8c-bd15-059546203e0e",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "snpeff_output",
-                                "uuid": "69e5622c-db07-4e3c-8224-ed511d3ca7c7"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "statsFile",
-                                "uuid": "dafcfa74-d4d9-4d37-ae00-88ebce9acc14"
+                                "label": "output",
+                                "output_name": "output",
+                                "uuid": "3fc2324d-233b-4785-9fb7-9c30b2daaef4"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "imaging/hela-screen-analysis",
+                "path": "topics/imaging/tutorials/hela-screen-analysis/workflows/analyze_screen.ga",
+                "tags": [],
+                "test_results": null,
+                "tests": true,
+                "title": "analyze_screen",
+                "topic_id": "imaging",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/imaging-hela-screen-analysis/versions/analyze-screen",
+                "tutorial_id": "hela-screen-analysis",
+                "url": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/hela-screen-analysis/workflows/analyze_screen.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/hela-screen-analysis/workflows/analyze_screen.html",
+                "version": 5,
+                "wfid": "imaging-hela-screen-analysis",
+                "wfname": "analyze-screen",
+                "workflow": "analyze_screen.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.0.5",
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_filter_segmentation_by_features/ip_2d_filter_segmentation_by_features/0.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/0.0.3",
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_split_binaryimage_by_watershed/ip_2d_split_binaryimage_by_watershed/0.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
+                ],
+                "workflowhub_id": "1271"
+            },
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0002-2315-9247",
+                        "name": "Till Korten",
+                        "url": "https://github.com/thawn/"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ninput image\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nrules\"]\n  2[label=\"Filter Image\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Auto Threshold\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Split objects\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"2D Feature Extraction\"]\n  4 -> 5 [label=\"output\"]\n  6[label=\"Filter segmentation\"]\n  5 -> 6 [label=\"output\"]\n  4 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  kb90cbc9433fd460096b58cf0bcaf2e94[color=lightseagreen,label=\"Output\\noutput\"]\n  6 -> kb90cbc9433fd460096b58cf0bcaf2e94\n  7[label=\"2D Feature Extraction\"]\n  6 -> 7 [label=\"output\"]\n  0 -> 7 [label=\"output\"]\n  k3d3c037a50ef443ba6f88a37db6bfb36[color=lightseagreen,label=\"Output\\noutput\"]\n  7 -> k3d3c037a50ef443ba6f88a37db6bfb36\n}",
+                "history": [
+                    {
+                        "hash": "d1e807a669d4a58fee5b1db2eceb8d4e4468fc21",
+                        "message": "fixed json syntax",
+                        "num": 7,
+                        "short_hash": "d1e807a66",
+                        "unix": "1699440970"
+                    },
+                    {
+                        "hash": "e34767b4ad7f4a1965ce15499e19fac5928806e0",
+                        "message": "added `creator` and `license` fields",
+                        "num": 6,
+                        "short_hash": "e34767b4a",
+                        "unix": "1699440539"
+                    },
+                    {
+                        "hash": "574ce45a0c0a6defc6795bb6bd67d3e2fd98d4ca",
+                        "message": "updated feature_extraction.ga",
+                        "num": 5,
+                        "short_hash": "574ce45a0",
+                        "unix": "1699376568"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 4,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 3,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
+                        "message": "unflatten workflows",
+                        "num": 2,
+                        "short_hash": "faf6d298a",
+                        "unix": "1576155753"
+                    },
+                    {
+                        "hash": "96462d6dcda154df6515addd109fdad1489cbe86",
+                        "message": "added second tutorial",
+                        "num": 1,
+                        "short_hash": "96462d6dc",
+                        "unix": "1565095814"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "input image"
+                            }
+                        ],
+                        "label": "input image",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10.46055506794869,
+                            "top": 133.99089344526203
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "15544dd3-65e5-4fdb-8648-3d8425bc77a8",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "rules"
+                            }
+                        ],
+                        "label": "rules",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0.0,
+                            "top": 648.1594953805964
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "39010bc8-dd57-4777-a325-c6d04c9f8eb6",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ninput image\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nrules\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Filter Image\"];\n  0 -->|output| 2;\n  3[\"Auto Threshold\"];\n  2 -->|output| 3;\n  4[\"Split objects\"];\n  3 -->|output| 4;\n  5[\"2D Feature Extraction\"];\n  4 -->|output| 5;\n  6[\"Filter segmentation\"];\n  5 -->|output| 6;\n  4 -->|output| 6;\n  1 -->|output| 6;\n  b90cbc94-33fd-4600-96b5-8cf0bcaf2e94[\"Output\\noutput\"];\n  6 --> b90cbc94-33fd-4600-96b5-8cf0bcaf2e94;\n  style b90cbc94-33fd-4600-96b5-8cf0bcaf2e94 stroke:#2c3143,stroke-width:4px;\n  7[\"2D Feature Extraction\"];\n  6 -->|output| 7;\n  0 -->|output| 7;\n  3d3c037a-50ef-443b-a6f8-8a37db6bfb36[\"Output\\noutput\"];\n  7 --> 3d3c037a-50ef-443b-a6f8-8a37db6bfb36;\n  style 3d3c037a-50ef-443b-a6f8-8a37db6bfb36 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "feature_extraction",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/imgteam/2d_filter_segmentation_by_features/ip_2d_filter_segmentation_by_features/0.0.1",
                         "errors": null,
-                        "id": 13,
+                        "id": 6,
                         "input_connections": {
+                            "feature_file": {
+                                "id": 5,
+                                "output_name": "output"
+                            },
                             "input": {
-                                "id": 12,
-                                "output_name": "snpeff_output"
+                                "id": 4,
+                                "output_name": "output"
+                            },
+                            "rule_file": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "SnpSift Extract Fields",
+                        "name": "Filter segmentation",
                         "outputs": [
                             {
                                 "name": "output",
-                                "type": "tabular"
+                                "type": "tiff"
                             }
                         ],
                         "position": {
-                            "bottom": 919.5,
-                            "height": 132,
-                            "left": 1768,
-                            "right": 1968,
-                            "top": 787.5,
-                            "width": 200,
-                            "x": 1768,
-                            "y": 787.5
+                            "left": 934.6383840869061,
+                            "top": 550.5509793890867
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/2d_filter_segmentation_by_features/ip_2d_filter_segmentation_by_features/0.0.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "2e497a770bca",
-                            "name": "snpsift",
-                            "owner": "iuc",
+                            "changeset_revision": "e576b73a2e2f",
+                            "name": "2d_filter_segmentation_by_features",
+                            "owner": "imgteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"vcf\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"empty_text\": \"\", \"extract\": \"CHROM POS FILTER REF ALT QUAL DP AF SB DP4 EFF[*].IMPACT EFF[*].FUNCLASS EFF[*].EFFECT EFF[*].GENE EFF[*].CODON\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"SRR12733957\", \"one_effect_per_line\": \"true\", \"separator\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.3+t.galaxy0",
+                        "tool_state": "{\"__input_ext\": \"tiff\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"feature_file\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"rule_file\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.0.1",
                         "type": "tool",
-                        "uuid": "b4c123bb-5bf2-481b-ab0c-f23be0d7f0d3",
+                        "uuid": "4b253c14-4315-431e-baa2-92773c53e8ea",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "output",
                                 "output_name": "output",
-                                "uuid": "971988f2-f007-4394-b749-45996031dc5e"
+                                "uuid": "b90cbc94-33fd-4600-96b5-8cf0bcaf2e94"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.1.1",
                         "errors": null,
-                        "id": 14,
+                        "id": 7,
                         "input_connections": {
-                            "input_list": {
-                                "id": 13,
+                            "input_label": {
+                                "id": 6,
+                                "output_name": "output"
+                            },
+                            "use_raw_option|input_raw": {
+                                "id": 0,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Collapse Collection",
+                        "name": "2D Feature Extraction",
                         "outputs": [
                             {
                                 "name": "output",
-                                "type": "input"
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 1125.5,
-                            "height": 132,
-                            "left": 1928,
-                            "right": 2128,
-                            "top": 993.5,
-                            "width": 200,
-                            "x": 1928,
-                            "y": 993.5
+                            "left": 316.54453978928655,
+                            "top": 839.7316069939548
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.1.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "90981f86000f",
-                            "name": "collapse_collections",
-                            "owner": "nml",
+                            "changeset_revision": "5791a7f65275",
+                            "name": "2d_feature_extraction",
+                            "owner": "imgteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"filename\": {\"add_name\": \"true\", \"__current_case__\": 0, \"place_name\": \"same_multiple\"}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.1.0",
+                        "tool_state": "{\"__input_ext\": \"tiff\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"feature_options\": {\"features\": \"select\", \"__current_case__\": 1, \"selected_features\": [\"--mean_intensity\", \"--area\", \"--major_axis_length\"]}, \"input_label\": {\"__class__\": \"ConnectedValue\"}, \"use_raw_option\": {\"use_raw\": \"raw_image\", \"__current_case__\": 1, \"input_raw\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.1",
                         "type": "tool",
-                        "uuid": "be8eb89a-e88f-431c-9bd9-be2aa33b1671",
+                        "uuid": "40d50f9c-ac41-4a34-8212-6c0b67fcc409",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "output",
                                 "output_name": "output",
-                                "uuid": "756bd26f-ad93-4187-b294-358bdd455962"
+                                "uuid": "3d3c037a-50ef-443b-a6f8-8a37db6bfb36"
                             }
                         ]
                     }
                 ],
-                "parent_id": "introduction/galaxy-intro-ngs-data-managment",
-                "path": "topics/introduction/tutorials/galaxy-intro-ngs-data-managment/workflows/ngs_intro_workflow.ga",
-                "tags": [
-                    "introductions"
-                ],
+                "parent_id": "imaging/hela-screen-analysis",
+                "path": "topics/imaging/tutorials/hela-screen-analysis/workflows/feature_extraction.ga",
+                "tags": [],
                 "test_results": null,
-                "tests": false,
-                "title": "NGS_tutorial",
-                "topic_id": "introduction",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/introduction-galaxy-intro-ngs-data-managment/versions/ngs-intro-workflow",
-                "tutorial_id": "galaxy-intro-ngs-data-managment",
-                "url": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/workflows/ngs_intro_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/workflows/ngs_intro_workflow.html",
-                "version": 1,
-                "wfid": "introduction-galaxy-intro-ngs-data-managment",
-                "wfname": "ngs-intro-workflow",
-                "workflow": "ngs_intro_workflow.ga",
+                "tests": true,
+                "title": "feature_extraction",
+                "topic_id": "imaging",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/imaging-hela-screen-analysis/versions/feature-extraction",
+                "tutorial_id": "hela-screen-analysis",
+                "url": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/hela-screen-analysis/workflows/feature_extraction.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/imaging/tutorials/hela-screen-analysis/workflows/feature_extraction.html",
+                "version": 5,
+                "wfid": "imaging-hela-screen-analysis",
+                "wfname": "feature-extraction",
+                "workflow": "feature_extraction.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.8+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.0.5",
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_filter_segmentation_by_features/ip_2d_filter_segmentation_by_features/0.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/0.0.3",
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/2d_split_binaryimage_by_watershed/ip_2d_split_binaryimage_by_watershed/0.0.1"
                 ],
-                "workflowhub_id": "1115"
+                "workflowhub_id": "1270"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/3362976"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/bioimage-metadata/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "wee-snufkin",
+                "Laura190",
+                "kkamieniecka",
+                "poterlowicz-lab"
+            ],
+            "funding": [
+                "elixir-uk-dash"
+            ]
+        },
+        "contributors": [
+            {
+                "elixir_node": "uk",
+                "email": "juliajot36@gmail.com",
+                "id": "wee-snufkin",
+                "joined": "2022-06",
+                "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
+            },
+            {
+                "email": "L.Cooper.5@warwick.ac.uk",
+                "id": "Laura190",
+                "joined": "2023-08",
+                "name": "Laura Cooper",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Laura190/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Laura190.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "id": "kkamieniecka",
+                "joined": "2018-08",
+                "name": "Katarzyna Kamieniecka",
+                "orcid": "0009-0004-2454-5950",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/",
+                "twitter": "katemurat",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "id": "poterlowicz-lab",
+                "joined": "2017-09",
+                "name": "Krzysztof Poterlowicz",
+                "orcid": "0000-0001-6173-5674",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/poterlowicz-lab/",
+                "twitter": "bioinfbrad",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/poterlowicz-lab.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/dash.png",
+                "funder": true,
+                "funding_id": "MR/V038966/1",
+                "funding_statement": "This Fellowship was funded through the ELIXIR-UK DaSH project as part of the UKRI Innovation Scholars: Data Science Training in Health and Bioscience call (DaSH). (MR/V038966/1). The project aims to embed Research Data Management (RDM) know-how into UK universities and institutes by producing and delivering training in FAIR data stewardship using ELIXIR-UK knowledge and resources.",
+                "funding_system": "ukri",
+                "github": false,
+                "id": "elixir-uk-dash",
+                "joined": "2023-10",
+                "name": "DASH UK",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-uk-dash/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-uk-dash.json"
+            }
+        ],
+        "dir": "topics/imaging/tutorials/bioimage-metadata",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "fair",
+                "tutorials": [
+                    "bioimage-REMBI"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "imaging",
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "imaging/bioimage-metadata",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Data repositories such as BioImage Archive, Electron Microscopy Public Image Archive (EMPIAR) and Image Data Repository (IDR) are available to help make bioimaging data FAIR.",
+            "Find out what are the repository's requirements to help decide which is suitable for your data.",
+            "All repositories require some metadata, so collecting the metadata alongside data acquisition will make this process easier."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-10-02",
+        "objectives": [
+            "Locate bioimage data repositories",
+            "Compare repositories to find which are suitable for your data",
+            "Find out what the requirements are for submitting"
+        ],
+        "pageviews": 0,
+        "priority": 4,
+        "pub_date": "2024-10-02",
+        "questions": [
+            "What are the commonly used repositories for bioimaging data?",
+            "Which repositories are suitable for my data?",
+            "What are the requirements for submitting?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "fair",
+                "tutorials": [
+                    "fair-intro",
+                    "data-management"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00365",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "fair-data",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": true,
+        "tags": [
+            "fair",
+            "data management",
+            "bioimaging"
+        ],
+        "time_estimation": "15m",
+        "title": "FAIR Bioimage Metadata",
+        "tools": [],
+        "topic_name": "imaging",
+        "topic_name_human": "Imaging",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "bioimage-metadata",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/imaging/tutorials/bioimage-metadata/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/bioimage-metadata/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/bioimage-metadata/tutorial.json"
+        },
+        "version": 0,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 0,
+        "visitors": 0,
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/bioimage-REMBI/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "wee-snufkin",
+                "Laura190",
+                "kkamieniecka",
+                "poterlowicz-lab"
+            ],
+            "funding": [
+                "elixir-uk-dash"
+            ]
+        },
+        "contributors": [
+            {
+                "elixir_node": "uk",
+                "email": "juliajot36@gmail.com",
+                "id": "wee-snufkin",
+                "joined": "2022-06",
+                "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
+            },
+            {
+                "email": "L.Cooper.5@warwick.ac.uk",
+                "id": "Laura190",
+                "joined": "2023-08",
+                "name": "Laura Cooper",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Laura190/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Laura190.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "id": "kkamieniecka",
+                "joined": "2018-08",
+                "name": "Katarzyna Kamieniecka",
+                "orcid": "0009-0004-2454-5950",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/",
+                "twitter": "katemurat",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "id": "poterlowicz-lab",
+                "joined": "2017-09",
+                "name": "Krzysztof Poterlowicz",
+                "orcid": "0000-0001-6173-5674",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/poterlowicz-lab/",
+                "twitter": "bioinfbrad",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/poterlowicz-lab.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/dash.png",
+                "funder": true,
+                "funding_id": "MR/V038966/1",
+                "funding_statement": "This Fellowship was funded through the ELIXIR-UK DaSH project as part of the UKRI Innovation Scholars: Data Science Training in Health and Bioscience call (DaSH). (MR/V038966/1). The project aims to embed Research Data Management (RDM) know-how into UK universities and institutes by producing and delivering training in FAIR data stewardship using ELIXIR-UK knowledge and resources.",
+                "funding_system": "ukri",
+                "github": false,
+                "id": "elixir-uk-dash",
+                "joined": "2023-10",
+                "name": "DASH UK",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-uk-dash/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-uk-dash.json"
+            }
+        ],
+        "dir": "topics/imaging/tutorials/bioimage-REMBI",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "imaging",
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "imaging/bioimage-REMBI",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "REMBI describes useful guidelines for bioimaging that can help unification and FARIfication of the data."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-10-02",
+        "objectives": [
+            "Organise bioimage metadata",
+            "Find out what REMBI is and why it is useful",
+            "Categorise what metadata belongs to each of the submodules of REMBI",
+            "Gather the metadata for an example bioimage dataset"
+        ],
+        "pageviews": 0,
+        "priority": 5,
+        "pub_date": "2024-10-02",
+        "questions": [
+            "What is REMBI and why should I use it?",
+            "What information should be included when collecting bioimage data?"
+        ],
+        "recordings": [
+            {
+                "date": "2024-09-12",
+                "length": "48M14S",
+                "speakers": [
+                    "lcooper"
+                ],
+                "youtube_id": "QA82MzWle_w"
+            }
+        ],
+        "requirements": [
+            {
+                "topic_name": "fair",
+                "tutorials": [
+                    "fair-intro",
+                    "data-management",
+                    "bioimage-metadata"
+                ],
+                "type": "internal"
             }
         ],
+        "short_id": "T00364",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "fair-data",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": true,
+        "tags": [
+            "fair",
+            "data management",
+            "bioimaging"
+        ],
+        "time_estimation": "15m",
+        "title": "REMBI - Recommended Metadata for Biological Images \u2013 metadata guidelines for bioimaging data",
+        "tools": [],
+        "topic_name": "imaging",
+        "topic_name_human": "Imaging",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "bioimage-REMBI",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/imaging/tutorials/bioimage-REMBI/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/bioimage-REMBI/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/bioimage-REMBI/tutorial.json"
+        },
+        "version": 0,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 0,
+        "visitors": 0,
         "zenodo_link": ""
     },
     {
@@ -125967,9 +128691,9 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "split_file_on_column",
+                    "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "37a53100b67e",
+                    "revisions": "d698c222f354",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
@@ -125990,91 +128714,163 @@
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "d698c222f354",
+                    "revisions": "86755160afbf",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "column_maker",
                     "owner": "devteam",
-                    "revisions": "02026300aa45",
+                    "revisions": "6595517c2dd8",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "regex_find_replace",
-                    "owner": "galaxyp",
-                    "revisions": "ae8c4b2488e7",
+                    "name": "get_flanks",
+                    "owner": "devteam",
+                    "revisions": "077f404ae1bb",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "datamash_ops",
-                    "owner": "iuc",
-                    "revisions": "562f3c677828",
-                    "tool_panel_section_label": "Join, Subtract and Group",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "datamash_ops",
-                    "owner": "iuc",
-                    "revisions": "746e8e4bf929",
-                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "name": "intersect",
+                    "owner": "devteam",
+                    "revisions": "69c10b56f46d",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: split_file_on_column\n  owner: bgruening\n  revisions: 37a53100b67e\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 02026300aa45\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: ae8c4b2488e7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 562f3c677828\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 746e8e4bf929\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/data-manipulation-olympics/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 6595517c2dd8\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: get_flanks\n  owner: devteam\n  revisions: 077f404ae1bb\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: intersect\n  owner: devteam\n  revisions: 69c10b56f46d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.json",
         "contributions": {
             "authorship": [
-                "shiltemann",
-                "lybCNU"
-            ],
-            "editing": [
+                "pajanne",
+                "blankclemens",
+                "bebatut",
+                "bgruening",
+                "nsoranzo",
+                "dyusuf",
+                "sarah-peter",
                 "hexylena"
             ],
-            "funding": [
-                "gallantries"
+            "editing": [
+                "teresa-m"
             ]
         },
         "contributors": [
+            {
+                "id": "pajanne",
+                "joined": "2017-09",
+                "name": "Anne Pajon",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pajanne/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pajanne.json"
+            },
+            {
+                "elixir_node": "de",
+                "email": "blankclemens@gmail.com",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "blankclemens",
+                "joined": "2017-09",
+                "name": "Clemens Blank",
+                "orcid": "0000-0002-1726-2256",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankclemens/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankclemens.json"
+            },
             {
                 "affiliations": [
-                    "CINECA-Project",
                     "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
+                    "ifb",
+                    "elixir-europe"
                 ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
                 "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
                 "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
+                "id": "bebatut",
                 "joined": "2017-09",
-                "linkedin": "shiltemann",
+                "linkedin": "berenicebatut",
                 "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
                 },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             },
             {
-                "id": "lybCNU",
-                "joined": "2024-08",
-                "name": "Yongbin Li",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lybCNU/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/lybCNU.json"
+                "affiliations": [
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
+                "fediverse_flavor": "mastodon",
+                "id": "bgruening",
+                "joined": "2017-09",
+                "linkedin": "bgruening",
+                "location": {
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
+                },
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+            },
+            {
+                "affiliations": [
+                    "earlham",
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "fediverse": "https://mstdn.science/@nsoranzo",
+                "fediverse_flavor": "mastodon",
+                "id": "nsoranzo",
+                "joined": "2017-09",
+                "linkedin": "nicola-soranzo-7884125",
+                "matrix": "nsoranzo:matrix.org",
+                "name": "Nicola Soranzo",
+                "orcid": "0000-0003-3627-5340",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
+                "twitter": "NicolaSoranzo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "id": "dyusuf",
+                "joined": "2017-09",
+                "name": "Dilmurat Yusuf",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dyusuf/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/dyusuf.json"
+            },
+            {
+                "id": "sarah-peter",
+                "joined": "2018-09",
+                "name": "Sarah Peter",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/sarah-peter/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/sarah-peter.json"
             },
             {
                 "affiliations": [
@@ -126106,142 +128902,130 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
             {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
                 ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+                "id": "teresa-m",
+                "joined": "2022-09",
+                "name": "Teresa M\u00fcller",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json"
             }
         ],
-        "dir": "topics/introduction/tutorials/data-manipulation-olympics",
+        "dir": "topics/introduction/tutorials/galaxy-intro-peaks2genes",
         "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "introduction/data-manipulation-olympics",
-        "inexact_supported_servers": [],
+        "id": "introduction/galaxy-intro-peaks2genes",
+        "inexact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.no"
+        ],
         "js_requirements": {
-            "mathjax": 61358,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "There are a lot of tools available in Galaxy for performing basic data manipulation tasks",
-            "Basic data manipulation is often needed between steps in a larger scientific analysis in order to connect outputs from one tool to input of another.",
-            "There are often multiple ways/tools to achieve the same end result",
-            "Having a basic understanding of data manipulation tools will make it easier to do exploratory data analysis",
-            "Always read the help text of the tool before using it to get a full understanding of its workings",
-            "Always try to formulate the output you are expecting from a tool. This will make it easier to spot mistakes as soon as possible."
+            "Galaxy provides an easy-to-use graphical user interface for often complex commandline tools",
+            "Galaxy keeps a full record of your analysis in a history",
+            "Workflows enable you to repeat your analysis on different data",
+            "Galaxy can connect to external sources for data import and visualization purposes",
+            "Galaxy provides ways to share your results and methods with others"
         ],
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-07",
+        "mod_date": "2024-09-07",
         "objectives": [
-            "Familiarize yourself with data manipulation tools in Galaxy",
-            "Perform basic text manipulation tasks in Galaxy",
-            "Become comfortable converting text-based files in a variety of ways.",
-            "Reason about the expected outcome of tools"
+            "Familiarize yourself with the basics of Galaxy",
+            "Learn how to obtain data from external sources",
+            "Learn how to run tools",
+            "Learn how histories work",
+            "Learn how to create a workflow",
+            "Learn how to share your work"
         ],
-        "pageviews": 4896,
-        "pub_date": "2022-07-20",
+        "pageviews": 30397,
+        "pub_date": "2016-03-29",
         "questions": [
-            "How can I do basic data manipulation in Galaxy?",
-            "Which tools are available to convert, reformat, filter, sort etc my text-based data?"
+            "How to use Galaxy?",
+            "How to get from peak regions to a list of gene names?"
         ],
-        "short_id": "T00184",
+        "short_id": "T00189",
         "short_tools": [
-            "",
-            "Count1",
-            "Cut1",
-            "Remove beginning1",
-            "Grouping1",
-            "datamash_ops",
-            "Show beginning1",
-            "tp_sort_header_tool",
-            "tp_sorted_uniq",
-            "cat1",
-            "tp_cat",
-            "wc_gnu",
-            "Filter1",
-            "tp_split_on_column",
-            "join1",
-            "regexColumn1",
+            "CONVERTER_interval_to_bed_0",
             "upload1",
-            "tabular_to_csv",
-            "Add_a_column1"
+            "tp_sort_header_tool",
+            "Cut1",
+            "Add_a_column1",
+            "get_flanks1",
+            "gops_intersect_1",
+            "tp_tail_tool",
+            "tp_replace_in_column",
+            "Grouping1"
         ],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "next-steps",
         "supported_servers": {
-            "exact": [],
-            "inexact": []
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                }
+            ]
         },
         "symlink": null,
-        "tags": [
-            "cyoa"
-        ],
-        "time_estimation": "1h",
-        "title": "Data Manipulation Olympics",
+        "time_estimation": "3H",
+        "title": "From peaks to genes",
         "tools": [
-            "Count1",
+            "CONVERTER_interval_to_bed_0",
             "Cut1",
-            "Filter1",
             "Grouping1",
-            "Remove beginning1",
-            "Show beginning1",
-            "cat1",
-            "join1",
-            "tabular_to_csv",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
             "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2",
-            "upload1",
-            "wc_gnu",
-            "",
-            "",
-            "",
-            "",
-            "",
-            "",
-            "",
-            "",
-            "",
-            "",
-            "",
-            "",
-            "",
-            "",
-            "",
-            "",
-            "",
-            ""
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0",
+            "upload1"
         ],
         "topic_name": "introduction",
         "topic_name_human": "Introduction to Galaxy Analyses",
@@ -126251,51 +129035,37 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "data-manipulation-olympics",
+        "tutorial_name": "galaxy-intro-peaks2genes",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/data-manipulation-olympics/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/data-manipulation-olympics/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/data-manipulation-olympics/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.json"
         },
-        "version": 10,
+        "version": 61,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 211,
-        "visitors": 3135,
+        "visit_duration": 201,
+        "visitors": 18132,
         "workflows": [
             {
                 "creators": [],
-                "description": "Data Manipulation Olympics",
+                "description": "Galaxy Introduction Peaks2Genes - Part 1",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nolympics.tsv\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncountry-information.tsv\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nolympics_2022.tsv\"]\n  3[label=\"Line/Word/Character count\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"tabular-to-csv\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Sort\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Sort\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Sort\"]\n  0 -> 7 [label=\"output\"]\n  8[label=\"Sort\"]\n  0 -> 8 [label=\"output\"]\n  9[label=\"Sort\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"Sort\"]\n  0 -> 10 [label=\"output\"]\n  11[label=\"Filter\"]\n  0 -> 11 [label=\"output\"]\n  12[label=\"Filter\"]\n  0 -> 12 [label=\"output\"]\n  13[label=\"Count\"]\n  0 -> 13 [label=\"output\"]\n  14[label=\"Count\"]\n  0 -> 14 [label=\"output\"]\n  15[label=\"Count\"]\n  0 -> 15 [label=\"output\"]\n  16[label=\"Count\"]\n  0 -> 16 [label=\"output\"]\n  17[label=\"Datamash\"]\n  0 -> 17 [label=\"output\"]\n  18[label=\"Count\"]\n  0 -> 18 [label=\"output\"]\n  19[label=\"Datamash\"]\n  0 -> 19 [label=\"output\"]\n  20[label=\"Filter\"]\n  0 -> 20 [label=\"output\"]\n  21[label=\"Filter\"]\n  0 -> 21 [label=\"output\"]\n  22[label=\"Filter\"]\n  0 -> 22 [label=\"output\"]\n  23[label=\"Filter\"]\n  0 -> 23 [label=\"output\"]\n  24[label=\"Filter\"]\n  0 -> 24 [label=\"output\"]\n  25[label=\"Filter\"]\n  0 -> 25 [label=\"output\"]\n  26[label=\"Filter\"]\n  0 -> 26 [label=\"output\"]\n  27[label=\"Compute\"]\n  0 -> 27 [label=\"output\"]\n  28[label=\"Compute\"]\n  0 -> 28 [label=\"output\"]\n  29[label=\"Cut\"]\n  0 -> 29 [label=\"output\"]\n  30[label=\"Column Regex Find And Replace\"]\n  0 -> 30 [label=\"output\"]\n  31[label=\"Column Regex Find And Replace\"]\n  0 -> 31 [label=\"output\"]\n  32[label=\"Column Regex Find And Replace\"]\n  0 -> 32 [label=\"output\"]\n  33[label=\"Cut\"]\n  0 -> 33 [label=\"output\"]\n  34[label=\"Cut\"]\n  0 -> 34 [label=\"output\"]\n  35[label=\"Datamash\"]\n  0 -> 35 [label=\"output\"]\n  36[label=\"Datamash\"]\n  0 -> 36 [label=\"output\"]\n  37[label=\"Datamash\"]\n  0 -> 37 [label=\"output\"]\n  38[label=\"Datamash\"]\n  0 -> 38 [label=\"output\"]\n  39[label=\"Datamash\"]\n  0 -> 39 [label=\"output\"]\n  40[label=\"Count\"]\n  0 -> 40 [label=\"output\"]\n  41[label=\"Column Regex Find And Replace\"]\n  0 -> 41 [label=\"output\"]\n  42[label=\"Split file\"]\n  0 -> 42 [label=\"output\"]\n  43[label=\"Join two Datasets\"]\n  0 -> 43 [label=\"output\"]\n  1 -> 43 [label=\"output\"]\n  44[label=\"Remove beginning\"]\n  2 -> 44 [label=\"output\"]\n  45[label=\"Sort\"]\n  11 -> 45 [label=\"out_file1\"]\n  46[label=\"Filter\"]\n  12 -> 46 [label=\"out_file1\"]\n  47[label=\"Cut\"]\n  28 -> 47 [label=\"out_file1\"]\n  48[label=\"Unique\"]\n  29 -> 48 [label=\"out_file1\"]\n  49[label=\"Count\"]\n  41 -> 49 [label=\"out_file1\"]\n  50[label=\"Datamash\"]\n  41 -> 50 [label=\"out_file1\"]\n  51[label=\"Concatenate datasets\"]\n  0 -> 51 [label=\"output\"]\n  44 -> 51 [label=\"out_file1\"]\n  52[label=\"Filter\"]\n  45 -> 52 [label=\"outfile\"]\n  53[label=\"Sort\"]\n  46 -> 53 [label=\"out_file1\"]\n  54[label=\"Remove beginning\"]\n  47 -> 54 [label=\"out_file1\"]\n  55[label=\"Select first\"]\n  47 -> 55 [label=\"out_file1\"]\n  56[label=\"Sort\"]\n  48 -> 56 [label=\"outfile\"]\n  57[label=\"Unique\"]\n  54 -> 57 [label=\"out_file1\"]\n  58[label=\"Concatenate datasets\"]\n  55 -> 58 [label=\"out_file1\"]\n  57 -> 58 [label=\"outfile\"]\n  59[label=\"Join two Datasets\"]\n  0 -> 59 [label=\"output\"]\n  58 -> 59 [label=\"out_file1\"]\n  60[label=\"Cut\"]\n  59 -> 60 [label=\"out_file1\"]\n  61[label=\"Line/Word/Character count\"]\n  60 -> 61 [label=\"out_file1\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPeaks\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenes\"]\n  2[label=\"Select last\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Replace Text\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Get flanks\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Replace Text\"]\n  3 -> 5 [label=\"outfile\"]\n  6[label=\"Replace Text\"]\n  5 -> 6 [label=\"outfile\"]\n  7[label=\"Convert Genomic Intervals To BED\"]\n  6 -> 7 [label=\"outfile\"]\n  8[label=\"Intersect\"]\n  4 -> 8 [label=\"out_file1\"]\n  7 -> 8 [label=\"output1\"]\n  9[label=\"Group\"]\n  8 -> 9 [label=\"output\"]\n  kc5516cb081d74425b0b580c1cf1e8255[color=lightseagreen,label=\"Output\\nchr_count\"]\n  9 -> kc5516cb081d74425b0b580c1cf1e8255\n}",
                 "history": [
                     {
-                        "hash": "195fb90f3cb0f6d446d1dc200ae11795735d0bc5",
-                        "message": "update workflow",
-                        "num": 3,
-                        "short_hash": "195fb90f3",
-                        "unix": "1658327856"
-                    },
-                    {
-                        "hash": "6908a9a8092d32a2ee24f5d61463f41d83498750",
-                        "message": "add tag and annotation",
-                        "num": 2,
-                        "short_hash": "6908a9a80",
-                        "unix": "1657815002"
-                    },
-                    {
-                        "hash": "68183fdf9f2b84177b8c374291cd50b8c9a5f0b2",
-                        "message": "add workflow",
+                        "hash": "48c2e99e6ac6b3f944b81c5725182a61c3a85d81",
+                        "message": "Add workflow test yml.",
                         "num": 1,
-                        "short_hash": "68183fdf9",
-                        "unix": "1657814320"
+                        "short_hash": "48c2e99e6",
+                        "unix": "1603135863"
                     }
                 ],
                 "inputs": [
@@ -126307,22 +129077,22 @@
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "olympics.tsv"
+                                "description": "Peaks",
+                                "name": "Peaks"
                             }
                         ],
-                        "label": "olympics.tsv",
-                        "name": "Input dataset",
+                        "label": "Peaks",
+                        "name": "Peaks",
                         "outputs": [],
                         "position": {
                             "left": 10,
                             "top": 10
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"name\": \"Peaks\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "749981b6-9589-48a3-b1fe-3830a019aac3",
+                        "uuid": "5827089b-d62d-47ad-bd3c-94bb09db46d2",
                         "workflow_outputs": []
                     },
                     {
@@ -126333,96 +129103,98 @@
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "country-information.tsv"
+                                "description": "Genes",
+                                "name": "Genes"
                             }
                         ],
-                        "label": "country-information.tsv",
-                        "name": "Input dataset",
+                        "label": "Genes",
+                        "name": "Genes",
                         "outputs": [],
                         "position": {
                             "left": 10,
                             "top": 130
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"name\": \"Genes\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "4dd01f90-d214-419c-b685-187c4c7e0236",
+                        "uuid": "671479f6-42c1-4cc2-9136-90542c00b4f3",
                         "workflow_outputs": []
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPeaks\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGenes\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Select last\"];\n  0 -->|output| 2;\n  3[\"Replace Text\"];\n  0 -->|output| 3;\n  4[\"Get flanks\"];\n  1 -->|output| 4;\n  5[\"Replace Text\"];\n  3 -->|outfile| 5;\n  6[\"Replace Text\"];\n  5 -->|outfile| 6;\n  7[\"Convert Genomic Intervals To BED\"];\n  6 -->|outfile| 7;\n  8[\"Intersect\"];\n  4 -->|out_file1| 8;\n  7 -->|output1| 8;\n  9[\"Group\"];\n  8 -->|output| 9;\n  c5516cb0-81d7-4425-b0b5-80c1cf1e8255[\"Output\\nchr_count\"];\n  9 --> c5516cb0-81d7-4425-b0b5-80c1cf1e8255;\n  style c5516cb0-81d7-4425-b0b5-80c1cf1e8255 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Galaxy Introduction Peaks2Genes - Part 1",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "Grouping1",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 9,
+                        "input_connections": {
+                            "input1": {
+                                "id": 8,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Group",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "olympics_2022.tsv"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "olympics_2022.tsv",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 250
+                            "left": 1330,
+                            "top": 10
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "8caf40e8-4c72-48c5-92cb-50fef0a9da1c",
-                        "workflow_outputs": []
+                        "post_job_actions": {},
+                        "tool_id": "Grouping1",
+                        "tool_state": "{\"__input_ext\": \"bed\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/mm9.len\", \"groupcol\": \"1\", \"ignorecase\": \"false\", \"ignorelines\": null, \"input1\": null, \"operations\": [{\"__index__\": 0, \"optype\": \"length\", \"opcol\": \"1\", \"opround\": \"no\", \"opdefault\": \"\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.4",
+                        "type": "tool",
+                        "uuid": "5e50ede1-709c-4140-a6a4-456258797b9c",
+                        "workflow_outputs": [
+                            {
+                                "label": "chr_count",
+                                "output_name": "out_file1",
+                                "uuid": "c5516cb0-81d7-4425-b0b5-80c1cf1e8255"
+                            }
+                        ]
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nolympics.tsv\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ncountry-information.tsv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nolympics_2022.tsv\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Line/Word/Character count\"];\n  0 -->|output| 3;\n  4[\"tabular-to-csv\"];\n  0 -->|output| 4;\n  5[\"Sort\"];\n  0 -->|output| 5;\n  6[\"Sort\"];\n  0 -->|output| 6;\n  7[\"Sort\"];\n  0 -->|output| 7;\n  8[\"Sort\"];\n  0 -->|output| 8;\n  9[\"Sort\"];\n  0 -->|output| 9;\n  10[\"Sort\"];\n  0 -->|output| 10;\n  11[\"Filter\"];\n  0 -->|output| 11;\n  12[\"Filter\"];\n  0 -->|output| 12;\n  13[\"Count\"];\n  0 -->|output| 13;\n  14[\"Count\"];\n  0 -->|output| 14;\n  15[\"Count\"];\n  0 -->|output| 15;\n  16[\"Count\"];\n  0 -->|output| 16;\n  17[\"Datamash\"];\n  0 -->|output| 17;\n  18[\"Count\"];\n  0 -->|output| 18;\n  19[\"Datamash\"];\n  0 -->|output| 19;\n  20[\"Filter\"];\n  0 -->|output| 20;\n  21[\"Filter\"];\n  0 -->|output| 21;\n  22[\"Filter\"];\n  0 -->|output| 22;\n  23[\"Filter\"];\n  0 -->|output| 23;\n  24[\"Filter\"];\n  0 -->|output| 24;\n  25[\"Filter\"];\n  0 -->|output| 25;\n  26[\"Filter\"];\n  0 -->|output| 26;\n  27[\"Compute\"];\n  0 -->|output| 27;\n  28[\"Compute\"];\n  0 -->|output| 28;\n  29[\"Cut\"];\n  0 -->|output| 29;\n  30[\"Column Regex Find And Replace\"];\n  0 -->|output| 30;\n  31[\"Column Regex Find And Replace\"];\n  0 -->|output| 31;\n  32[\"Column Regex Find And Replace\"];\n  0 -->|output| 32;\n  33[\"Cut\"];\n  0 -->|output| 33;\n  34[\"Cut\"];\n  0 -->|output| 34;\n  35[\"Datamash\"];\n  0 -->|output| 35;\n  36[\"Datamash\"];\n  0 -->|output| 36;\n  37[\"Datamash\"];\n  0 -->|output| 37;\n  38[\"Datamash\"];\n  0 -->|output| 38;\n  39[\"Datamash\"];\n  0 -->|output| 39;\n  40[\"Count\"];\n  0 -->|output| 40;\n  41[\"Column Regex Find And Replace\"];\n  0 -->|output| 41;\n  42[\"Split file\"];\n  0 -->|output| 42;\n  43[\"Join two Datasets\"];\n  0 -->|output| 43;\n  1 -->|output| 43;\n  44[\"Remove beginning\"];\n  2 -->|output| 44;\n  45[\"Sort\"];\n  11 -->|out_file1| 45;\n  46[\"Filter\"];\n  12 -->|out_file1| 46;\n  47[\"Cut\"];\n  28 -->|out_file1| 47;\n  48[\"Unique\"];\n  29 -->|out_file1| 48;\n  49[\"Count\"];\n  41 -->|out_file1| 49;\n  50[\"Datamash\"];\n  41 -->|out_file1| 50;\n  51[\"Concatenate datasets\"];\n  0 -->|output| 51;\n  44 -->|out_file1| 51;\n  52[\"Filter\"];\n  45 -->|outfile| 52;\n  53[\"Sort\"];\n  46 -->|out_file1| 53;\n  54[\"Remove beginning\"];\n  47 -->|out_file1| 54;\n  55[\"Select first\"];\n  47 -->|out_file1| 55;\n  56[\"Sort\"];\n  48 -->|outfile| 56;\n  57[\"Unique\"];\n  54 -->|out_file1| 57;\n  58[\"Concatenate datasets\"];\n  55 -->|out_file1| 58;\n  57 -->|outfile| 58;\n  59[\"Join two Datasets\"];\n  0 -->|output| 59;\n  58 -->|out_file1| 59;\n  60[\"Cut\"];\n  59 -->|out_file1| 60;\n  61[\"Line/Word/Character count\"];\n  60 -->|out_file1| 61;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "GTN Tutorial: Data manipulation Olympics - all steps and exercises",
-                "outputs": [],
-                "parent_id": "introduction/data-manipulation-olympics",
-                "path": "topics/introduction/tutorials/data-manipulation-olympics/workflows/data_manipulation_olympics_with_exercises.ga",
+                "parent_id": "introduction/galaxy-intro-peaks2genes",
+                "path": "topics/introduction/tutorials/galaxy-intro-peaks2genes/workflows/Galaxy-Introduction-Peaks2Genes-Part-1-Workflow.ga",
                 "tags": [
                     "introduction"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "GTN Tutorial: Data manipulation Olympics - all steps and exercises",
+                "tests": true,
+                "title": "Galaxy Introduction Peaks2Genes - Part 1",
                 "topic_id": "introduction",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/introduction-data-manipulation-olympics/versions/data-manipulation-olympics-with-exercises",
-                "tutorial_id": "data-manipulation-olympics",
-                "url": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/data-manipulation-olympics/workflows/data_manipulation_olympics_with_exercises.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/data-manipulation-olympics/workflows/data_manipulation_olympics_with_exercises.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/introduction-galaxy-intro-peaks2genes/versions/galaxy-introduction-peaks2genes-part-1-workflow",
+                "tutorial_id": "galaxy-intro-peaks2genes",
+                "url": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-peaks2genes/workflows/Galaxy-Introduction-Peaks2Genes-Part-1-Workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-peaks2genes/workflows/Galaxy-Introduction-Peaks2Genes-Part-1-Workflow.html",
                 "version": 1,
-                "wfid": "introduction-data-manipulation-olympics",
-                "wfname": "data-manipulation-olympics-with-exercises",
-                "workflow": "data_manipulation_olympics_with_exercises.ga",
+                "wfid": "introduction-galaxy-intro-peaks2genes",
+                "wfname": "galaxy-introduction-peaks2genes-part-1-workflow",
+                "workflow": "Galaxy-Introduction-Peaks2Genes-Part-1-Workflow.ga",
                 "workflow_tools": [
-                    "Count1",
-                    "Cut1",
-                    "Filter1",
-                    "Remove beginning1",
-                    "Show beginning1",
-                    "cat1",
-                    "join1",
-                    "tabular_to_csv",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2",
-                    "wc_gnu"
+                    "CONVERTER_interval_to_bed_0",
+                    "Grouping1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0"
                 ],
-                "workflowhub_id": "1090"
+                "workflowhub_id": "1102"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/6803028"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.1025586"
     },
     {
         "admin_install": {
@@ -126488,6 +129260,7 @@
         "edam_topic": [],
         "exact_supported_servers": [
             "Galaxy@AuBi",
+            "UseGalaxy.be",
             "UseGalaxy.eu",
             "UseGalaxy.org (Main)"
         ],
@@ -126496,6 +129269,7 @@
         "hands_on": true,
         "id": "introduction/galaxy-reproduce",
         "inexact_supported_servers": [
+            "MISSISSIPPI",
             "UseGalaxy.cz",
             "UseGalaxy.fr",
             "UseGalaxy.no"
@@ -126519,21 +129293,21 @@
             "Learn how to run a published Galaxy workflow",
             "Learn how histories can be inspected and re-used."
         ],
-        "pageviews": 2336,
+        "pageviews": 2395,
         "pub_date": "2021-08-25",
         "questions": [
             "How to reproduce published Galaxy results (workflows and histories)"
         ],
         "short_id": "T00192",
         "short_tools": [
-            "Grouping1",
-            "datamash_ops",
+            "tp_sorted_uniq",
+            "csv_to_tabular",
+            "upload1",
             "ggplot2_point",
             "Cut1",
-            "csv_to_tabular",
             "Remove beginning1",
-            "tp_sorted_uniq",
-            "upload1"
+            "datamash_ops",
+            "Grouping1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -126545,6 +129319,11 @@
                     "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
@@ -126557,6 +129336,11 @@
                 }
             ],
             "inexact": [
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -126606,8 +129390,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 277,
-        "visitors": 1696,
+        "visit_duration": 263,
+        "visitors": 1748,
         "workflows": [
             {
                 "creators": [],
@@ -126618,7 +129402,7 @@
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\niris\"]\n  1[label=\"Convert CSV to tabular\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Datamash\"]\n  1 -> 2 [label=\"tabular\"]\n  k9745329a9e7c4e3090caa26f20bbe0b0[color=lightseagreen,label=\"Output\\ndatamash_output\"]\n  2 -> k9745329a9e7c4e3090caa26f20bbe0b0\n  3[label=\"Remove beginning\"]\n  1 -> 3 [label=\"tabular\"]\n  4[label=\"Cut\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"Group\"]\n  3 -> 5 [label=\"out_file1\"]\n  kd8fd233a5e6540ba908aa7d38b8a0755[color=lightseagreen,label=\"Output\\ngroup1\"]\n  5 -> kd8fd233a5e6540ba908aa7d38b8a0755\n  6[label=\"Group\"]\n  3 -> 6 [label=\"out_file1\"]\n  kd245986ecda741ae980538aa87a27d1f[color=lightseagreen,label=\"Output\\ngroup2\"]\n  6 -> kd245986ecda741ae980538aa87a27d1f\n  7[label=\"Scatterplot w ggplot2\"]\n  3 -> 7 [label=\"out_file1\"]\n  8[label=\"Scatterplot w ggplot2\"]\n  3 -> 8 [label=\"out_file1\"]\n  9[label=\"Unique\"]\n  4 -> 9 [label=\"out_file1\"]\n  kec39c0adeb2647d6b9a7c2e5ffa043c6[color=lightseagreen,label=\"Output\\nunique_output\"]\n  9 -> kec39c0adeb2647d6b9a7c2e5ffa043c6\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\niris\"]\n  1[label=\"Convert CSV to tabular\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Datamash\"]\n  1 -> 2 [label=\"tabular\"]\n  k3c20f940c1be4766ba5c4c12b2dcbf74[color=lightseagreen,label=\"Output\\ndatamash_output\"]\n  2 -> k3c20f940c1be4766ba5c4c12b2dcbf74\n  3[label=\"Remove beginning\"]\n  1 -> 3 [label=\"tabular\"]\n  4[label=\"Cut\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"Group\"]\n  3 -> 5 [label=\"out_file1\"]\n  kff6ea34085624177b5d001c7ac754d76[color=lightseagreen,label=\"Output\\ngroup1\"]\n  5 -> kff6ea34085624177b5d001c7ac754d76\n  6[label=\"Group\"]\n  3 -> 6 [label=\"out_file1\"]\n  ka5b275c75fb64bb4b1026e7c586badb9[color=lightseagreen,label=\"Output\\ngroup2\"]\n  6 -> ka5b275c75fb64bb4b1026e7c586badb9\n  7[label=\"Scatterplot w ggplot2\"]\n  3 -> 7 [label=\"out_file1\"]\n  8[label=\"Scatterplot w ggplot2\"]\n  3 -> 8 [label=\"out_file1\"]\n  9[label=\"Unique\"]\n  4 -> 9 [label=\"out_file1\"]\n  kec39c0adeb2647d6b9a7c2e5ffa043c6[color=lightseagreen,label=\"Output\\nunique_output\"]\n  9 -> kec39c0adeb2647d6b9a7c2e5ffa043c6\n}",
                 "history": [
                     {
                         "hash": "03bdb9f97f1f07b25cb24c182fce72381d420781",
@@ -126657,8 +129441,8 @@
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\niris\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Convert CSV to tabular\"];\n  0 -->|output| 1;\n  2[\"Datamash\"];\n  1 -->|tabular| 2;\n  9745329a-9e7c-4e30-90ca-a26f20bbe0b0[\"Output\\ndatamash_output\"];\n  2 --> 9745329a-9e7c-4e30-90ca-a26f20bbe0b0;\n  style 9745329a-9e7c-4e30-90ca-a26f20bbe0b0 stroke:#2c3143,stroke-width:4px;\n  3[\"Remove beginning\"];\n  1 -->|tabular| 3;\n  4[\"Cut\"];\n  3 -->|out_file1| 4;\n  5[\"Group\"];\n  3 -->|out_file1| 5;\n  d8fd233a-5e65-40ba-908a-a7d38b8a0755[\"Output\\ngroup1\"];\n  5 --> d8fd233a-5e65-40ba-908a-a7d38b8a0755;\n  style d8fd233a-5e65-40ba-908a-a7d38b8a0755 stroke:#2c3143,stroke-width:4px;\n  6[\"Group\"];\n  3 -->|out_file1| 6;\n  d245986e-cda7-41ae-9805-38aa87a27d1f[\"Output\\ngroup2\"];\n  6 --> d245986e-cda7-41ae-9805-38aa87a27d1f;\n  style d245986e-cda7-41ae-9805-38aa87a27d1f stroke:#2c3143,stroke-width:4px;\n  7[\"Scatterplot w ggplot2\"];\n  3 -->|out_file1| 7;\n  8[\"Scatterplot w ggplot2\"];\n  3 -->|out_file1| 8;\n  9[\"Unique\"];\n  4 -->|out_file1| 9;\n  ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6[\"Output\\nunique_output\"];\n  9 --> ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6;\n  style ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\niris\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Convert CSV to tabular\"];\n  0 -->|output| 1;\n  2[\"Datamash\"];\n  1 -->|tabular| 2;\n  3c20f940-c1be-4766-ba5c-4c12b2dcbf74[\"Output\\ndatamash_output\"];\n  2 --> 3c20f940-c1be-4766-ba5c-4c12b2dcbf74;\n  style 3c20f940-c1be-4766-ba5c-4c12b2dcbf74 stroke:#2c3143,stroke-width:4px;\n  3[\"Remove beginning\"];\n  1 -->|tabular| 3;\n  4[\"Cut\"];\n  3 -->|out_file1| 4;\n  5[\"Group\"];\n  3 -->|out_file1| 5;\n  ff6ea340-8562-4177-b5d0-01c7ac754d76[\"Output\\ngroup1\"];\n  5 --> ff6ea340-8562-4177-b5d0-01c7ac754d76;\n  style ff6ea340-8562-4177-b5d0-01c7ac754d76 stroke:#2c3143,stroke-width:4px;\n  6[\"Group\"];\n  3 -->|out_file1| 6;\n  a5b275c7-5fb6-4bb4-b102-6e7c586badb9[\"Output\\ngroup2\"];\n  6 --> a5b275c7-5fb6-4bb4-b102-6e7c586badb9;\n  style a5b275c7-5fb6-4bb4-b102-6e7c586badb9 stroke:#2c3143,stroke-width:4px;\n  7[\"Scatterplot w ggplot2\"];\n  3 -->|out_file1| 7;\n  8[\"Scatterplot w ggplot2\"];\n  3 -->|out_file1| 8;\n  9[\"Unique\"];\n  4 -->|out_file1| 9;\n  ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6[\"Output\\nunique_output\"];\n  9 --> ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6;\n  style ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
                 "name": "GTN Training: Galaxy 101 For Everyone",
                 "outputs": [
                     {
@@ -126707,7 +129491,7 @@
                             {
                                 "label": "datamash_output",
                                 "output_name": "out_file",
-                                "uuid": "9745329a-9e7c-4e30-90ca-a26f20bbe0b0"
+                                "uuid": "3c20f940-c1be-4766-ba5c-4c12b2dcbf74"
                             }
                         ]
                     },
@@ -126751,7 +129535,7 @@
                             {
                                 "label": "group1",
                                 "output_name": "out_file1",
-                                "uuid": "d8fd233a-5e65-40ba-908a-a7d38b8a0755"
+                                "uuid": "ff6ea340-8562-4177-b5d0-01c7ac754d76"
                             }
                         ]
                     },
@@ -126795,7 +129579,7 @@
                             {
                                 "label": "group2",
                                 "output_name": "out_file1",
-                                "uuid": "d245986e-cda7-41ae-9805-38aa87a27d1f"
+                                "uuid": "a5b275c7-5fb6-4bb4-b102-6e7c586badb9"
                             }
                         ]
                     },
@@ -127000,432 +129784,78 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
+                    "name": "split_file_on_column",
                     "owner": "bgruening",
-                    "revisions": "ddf54b12c295",
+                    "revisions": "37a53100b67e",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "intersect",
-                    "owner": "devteam",
-                    "revisions": "69c10b56f46d",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: ddf54b12c295\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: intersect\n  owner: devteam\n  revisions: 69c10b56f46d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-strands/tutorial.json",
-        "contributors": [
-            {
-                "id": "tnabtaf",
-                "joined": "2017-09",
-                "name": "Dave Clements",
-                "orcid": "0000-0002-9970-6657",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
-            },
-            {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "gallardoalba",
-                "joined": "2020-11",
-                "name": "Crist\u00f3bal Gallardo",
-                "orcid": "0000-0002-5752-2155",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
-            }
-        ],
-        "dir": "topics/introduction/tutorials/galaxy-intro-strands",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "introduction/galaxy-intro-strands",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Galaxy provides an easy-to-use graphical user interface for often complex command-line tools",
-            "Galaxy keeps a full record of your analysis in a history",
-            "Workflows enable you to repeat your analysis on different data",
-            "Galaxy can connect to external sources for data import and visualization purposes",
-            "Galaxy provides ways to share your results and methods with others"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Introductory",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-07-09",
-        "objectives": [
-            "Learn some of the basic concepts of genomics and bioinformatics",
-            "Familiarize yourself with the basics of Galaxy"
-        ],
-        "pageviews": 27760,
-        "pub_date": "2017-10-18",
-        "questions": [
-            "Do genes on opposite strands ever overlap?  If so, how often?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "nakucher"
-                ],
-                "date": "2023-05-18",
-                "galaxy_version": "23.01",
-                "length": "1H30M",
-                "speakers": [
-                    "nakucher"
-                ],
-                "youtube_id": "P1mEWZ_tAgQ"
-            },
-            {
-                "captioners": [
-                    "tnabtaf"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "1H30M",
-                "speakers": [
-                    "tnabtaf"
-                ],
-                "youtube_id": "1UPCrQxGwcU"
-            }
-        ],
-        "short_id": "T00191",
-        "short_tools": [
-            "cat1",
-            "tp_cat",
-            "Filter1",
-            "gene2exon1",
-            "gops_intersect_1"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "next-steps",
-        "supported_servers": {
-            "exact": [
+                },
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
+                    "name": "column_maker",
+                    "owner": "devteam",
+                    "revisions": "02026300aa45",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
+                    "name": "regex_find_replace",
+                    "owner": "galaxyp",
+                    "revisions": "ae8c4b2488e7",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
+                    "name": "datamash_ops",
+                    "owner": "iuc",
+                    "revisions": "562f3c677828",
+                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
+                    "name": "datamash_ops",
+                    "owner": "iuc",
+                    "revisions": "746e8e4bf929",
+                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
-            ],
-            "inexact": []
-        },
-        "symlink": null,
-        "time_estimation": "2H30M",
-        "title": "Introduction to Genomics and Galaxy",
-        "tools": [
-            "Filter1",
-            "cat1",
-            "gene2exon1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0"
-        ],
-        "topic_name": "introduction",
-        "topic_name_human": "Introduction to Galaxy Analyses",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "galaxy-intro-strands",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-strands/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-strands/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-strands/tutorial.json"
+            ]
         },
-        "version": 40,
-        "video": false,
-        "video_versions": 2,
-        "video_view": 0,
-        "visit_duration": 211,
-        "visitors": 17075,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Introduction to Genomics and Galaxy",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[label=\"Gene BED To Exon/Intron/Codon BED\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Filter\"]\n  1 -> 2 [label=\"out_file1\"]\n  3[label=\"Filter\"]\n  1 -> 3 [label=\"out_file1\"]\n  4[label=\"Intersect\"]\n  2 -> 4 [label=\"out_file1\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"Intersect\"]\n  3 -> 5 [label=\"out_file1\"]\n  2 -> 5 [label=\"out_file1\"]\n  6[label=\"Concatenate datasets\"]\n  5 -> 6 [label=\"output\"]\n  4 -> 6 [label=\"output\"]\n}",
-                "history": [
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 4,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 3,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
-                        "message": "Changed format of workflows",
-                        "num": 2,
-                        "short_hash": "361236c41",
-                        "unix": "1554368414"
-                    },
-                    {
-                        "hash": "8654b300bee12fde5cdb5392424e592b34757373",
-                        "message": "added workflows",
-                        "num": 1,
-                        "short_hash": "8654b300b",
-                        "unix": "1536320594"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Genes"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 10
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Genes\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "286c5925-431f-432d-a658-515befa7c6d3",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Gene BED To Exon/Intron/Codon BED\"];\n  0 -->|output| 1;\n  2[\"Filter\"];\n  1 -->|out_file1| 2;\n  3[\"Filter\"];\n  1 -->|out_file1| 3;\n  4[\"Intersect\"];\n  2 -->|out_file1| 4;\n  3 -->|out_file1| 4;\n  5[\"Intersect\"];\n  3 -->|out_file1| 5;\n  2 -->|out_file1| 5;\n  6[\"Concatenate datasets\"];\n  5 -->|output| 6;\n  4 -->|output| 6;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Galaxy Intro Strands 2",
-                "outputs": [],
-                "parent_id": "introduction/galaxy-intro-strands",
-                "path": "topics/introduction/tutorials/galaxy-intro-strands/workflows/Galaxy-Workflow-galaxy-intro-strands-2.ga",
-                "tags": [
-                    "introduction"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Galaxy Intro Strands 2",
-                "topic_id": "introduction",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/introduction-galaxy-intro-strands/versions/galaxy-workflowlaxy-intro-strands-2",
-                "tutorial_id": "galaxy-intro-strands",
-                "url": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-strands/workflows/Galaxy-Workflow-galaxy-intro-strands-2.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-strands/workflows/Galaxy-Workflow-galaxy-intro-strands-2.html",
-                "version": 4,
-                "wfid": "introduction-galaxy-intro-strands",
-                "wfname": "galaxy-workflowlaxy-intro-strands-2",
-                "workflow": "Galaxy-Workflow-galaxy-intro-strands-2.ga",
-                "workflow_tools": [
-                    "Filter1",
-                    "gene2exon1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0"
-                ],
-                "workflowhub_id": "1111"
-            },
-            {
-                "creators": [],
-                "description": "Introduction to Genomics and Galaxy",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[label=\"Filter\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Filter\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Filter\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Intersect\"]\n  2 -> 4 [label=\"out_file1\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"Intersect\"]\n  3 -> 5 [label=\"out_file1\"]\n  2 -> 5 [label=\"out_file1\"]\n  6[label=\"Concatenate datasets\"]\n  5 -> 6 [label=\"output\"]\n  4 -> 6 [label=\"output\"]\n}",
-                "history": [
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 4,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 3,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
-                        "message": "Changed format of workflows",
-                        "num": 2,
-                        "short_hash": "361236c41",
-                        "unix": "1554368414"
-                    },
-                    {
-                        "hash": "8654b300bee12fde5cdb5392424e592b34757373",
-                        "message": "added workflows",
-                        "num": 1,
-                        "short_hash": "8654b300b",
-                        "unix": "1536320594"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Genes"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 10
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Genes\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "d69a6248-140c-4b97-bc0f-ce88a4452c75",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Filter\"];\n  0 -->|output| 1;\n  2[\"Filter\"];\n  0 -->|output| 2;\n  3[\"Filter\"];\n  0 -->|output| 3;\n  4[\"Intersect\"];\n  2 -->|out_file1| 4;\n  3 -->|out_file1| 4;\n  5[\"Intersect\"];\n  3 -->|out_file1| 5;\n  2 -->|out_file1| 5;\n  6[\"Concatenate datasets\"];\n  5 -->|output| 6;\n  4 -->|output| 6;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Galaxy Intro Strands",
-                "outputs": [],
-                "parent_id": "introduction/galaxy-intro-strands",
-                "path": "topics/introduction/tutorials/galaxy-intro-strands/workflows/Galaxy-Workflow-galaxy-intro-strands.ga",
-                "tags": [
-                    "introduction"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Galaxy Intro Strands",
-                "topic_id": "introduction",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/introduction-galaxy-intro-strands/versions/galaxy-workflowlaxy-intro-strands",
-                "tutorial_id": "galaxy-intro-strands",
-                "url": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-strands/workflows/Galaxy-Workflow-galaxy-intro-strands.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-strands/workflows/Galaxy-Workflow-galaxy-intro-strands.html",
-                "version": 4,
-                "wfid": "introduction-galaxy-intro-strands",
-                "wfname": "galaxy-workflowlaxy-intro-strands",
-                "workflow": "Galaxy-Workflow-galaxy-intro-strands.ga",
-                "workflow_tools": [
-                    "Filter1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0"
-                ],
-                "workflowhub_id": "1110"
-            }
-        ],
-        "zenodo_link": ""
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: split_file_on_column\n  owner: bgruening\n  revisions: 37a53100b67e\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 02026300aa45\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: ae8c4b2488e7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 562f3c677828\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 746e8e4bf929\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/data-manipulation-olympics/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "shiltemann",
+                "lybCNU"
+            ],
+            "editing": [
+                "hexylena"
+            ],
+            "funding": [
+                "gallantries"
+            ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/introduction/tutorial.json",
         "contributors": [
-            {
-                "email": "andrea.bagnacani@gmail.com",
-                "id": "bagnacan",
-                "joined": "2017-10",
-                "name": "Andrea Bagnacani",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bagnacan/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bagnacan.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
             {
                 "affiliations": [
                     "CINECA-Project",
@@ -127457,29 +129887,11 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             },
             {
-                "id": "pajanne",
-                "joined": "2017-09",
-                "name": "Anne Pajon",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pajanne/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pajanne.json"
-            },
-            {
-                "affiliations": [
-                    "earlham",
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "fediverse": "https://mstdn.science/@nsoranzo",
-                "fediverse_flavor": "mastodon",
-                "id": "nsoranzo",
-                "joined": "2017-09",
-                "linkedin": "nicola-soranzo-7884125",
-                "matrix": "nsoranzo:matrix.org",
-                "name": "Nicola Soranzo",
-                "orcid": "0000-0003-3627-5340",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
-                "twitter": "NicolaSoranzo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
+                "id": "lybCNU",
+                "joined": "2024-08",
+                "name": "Yongbin Li",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lybCNU/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/lybCNU.json"
             },
             {
                 "affiliations": [
@@ -127511,569 +129923,143 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
             {
-                "id": "chrisbarnettster",
-                "joined": "2019-05",
-                "name": "Christopher Barnett",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/chrisbarnettster/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/chrisbarnettster.json"
-            },
-            {
-                "id": "michelemaroni89",
-                "joined": "2019-07",
-                "name": "Michele Maroni",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/michelemaroni89/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/michelemaroni89.json"
-            },
-            {
-                "elixir_node": "no",
-                "id": "annefou",
-                "joined": "2019-07",
-                "name": "Anne Fouilloux",
-                "orcid": "0000-0002-1784-2920",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annefou/",
-                "twitter": "AnneFouilloux",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/annefou.json"
-            },
-            {
-                "email": "nadia.goue@uca.fr",
-                "id": "nagoue",
-                "joined": "2019-07",
-                "name": "Nadia Gou\u00e9",
-                "orcid": "0000-0003-2750-1473",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nagoue/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nagoue.json"
-            },
-            {
-                "id": "olanag1",
-                "joined": "2019-07",
-                "name": "Olha Nahorna",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/olanag1/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/olanag1.json"
-            },
-            {
-                "id": "tnabtaf",
-                "joined": "2017-09",
-                "name": "Dave Clements",
-                "orcid": "0000-0002-9970-6657",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
-            }
-        ],
-        "dir": "topics/introduction/tutorials/introduction",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": false,
-        "id": "introduction/introduction",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "layout": "introduction_slides",
-        "license": "CC-BY-4.0",
-        "logo": "GTN",
-        "mod_date": "2024-05-07",
-        "pageviews": 5726884,
-        "priority": 1,
-        "pub_date": "2016-09-30",
-        "redirect_from": [
-            "/topics/introduction/slides/introduction",
-            "/short/introduction/introduction/slides",
-            "/short/S00073"
-        ],
-        "short_id": "S00073",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
-        "subtopic": "first",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "title": "Introduction to Galaxy",
-        "tools": [],
-        "topic_name": "introduction",
-        "topic_name_human": "Introduction to Galaxy Analyses",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "introduction",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/introduction/slides.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/introduction/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/introduction/slides.json"
-        },
-        "version": 2,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/options-for-using-galaxy/tutorial.json",
-        "contributors": [
-            {
-                "id": "tnabtaf",
-                "joined": "2017-09",
-                "name": "Dave Clements",
-                "orcid": "0000-0002-9970-6657",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "eurosciencegateway",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
-                "fediverse_flavor": "mastodon",
-                "id": "abretaud",
-                "joined": "2017-09",
-                "location": {
-                    "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
-                },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
-            },
-            {
-                "id": "pajanne",
-                "joined": "2017-09",
-                "name": "Anne Pajon",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pajanne/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pajanne.json"
-            },
-            {
-                "affiliations": [
-                    "earlham",
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "fediverse": "https://mstdn.science/@nsoranzo",
-                "fediverse_flavor": "mastodon",
-                "id": "nsoranzo",
-                "joined": "2017-09",
-                "linkedin": "nicola-soranzo-7884125",
-                "matrix": "nsoranzo:matrix.org",
-                "name": "Nicola Soranzo",
-                "orcid": "0000-0003-3627-5340",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
-                "twitter": "NicolaSoranzo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
-            },
-            {
-                "id": "alaaelghamry",
-                "joined": "2021-11",
-                "name": "Alaa Elghamry",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/alaaelghamry/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/alaaelghamry.json"
-            }
-        ],
-        "dir": "topics/introduction/tutorials/options-for-using-galaxy",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": false,
-        "id": "introduction/options-for-using-galaxy",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": null,
-        "layout": "tutorial_slides",
-        "license": "CC-BY-4.0",
-        "logo": "GTN",
-        "mod_date": "2022-09-23",
-        "objectives": null,
-        "pageviews": 5726884,
-        "pub_date": "2017-05-24",
-        "questions": [
-            "Which Galaxy instance should I use?"
-        ],
-        "short_id": "S00075",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
-        "subtopic": "next-steps",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "time_estimation": null,
-        "title": "Options for using Galaxy",
-        "tools": [],
-        "topic_name": "introduction",
-        "topic_name_human": "Introduction to Galaxy Analyses",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": true
-        },
-        "tutorial_name": "options-for-using-galaxy",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/options-for-using-galaxy/slides.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/options-for-using-galaxy/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/options-for-using-galaxy/slides.json"
-        },
-        "version": 14,
-        "video": true,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758,
-        "zenodo_link": ""
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/igv-introduction/tutorial.json",
-        "contributors": [
-            {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
-                "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
-            },
-            {
-                "elixir_node": "de",
-                "email": "wolffj@informatik.uni-freiburg.de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "joachimwolff",
-                "joined": "2017-09",
-                "name": "Joachim Wolff",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/joachimwolff.json"
-            },
-            {
-                "id": "pajanne",
-                "joined": "2017-09",
-                "name": "Anne Pajon",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pajanne/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pajanne.json"
-            }
-        ],
-        "dir": "topics/introduction/tutorials/igv-introduction",
-        "draft": true,
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "introduction/igv-introduction",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": null,
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-02-17",
-        "objectives": null,
-        "pageviews": 9960,
-        "pub_date": "2016-03-30",
-        "questions": null,
-        "short_id": "T00193",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "next-steps",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "work-in-progress"
-        ],
-        "time_estimation": "2H",
-        "title": "IGV Introduction",
-        "tools": [],
-        "topic_name": "introduction",
-        "topic_name_human": "Introduction to Galaxy Analyses",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "igv-introduction",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/igv-introduction/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/igv-introduction/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/igv-introduction/tutorial.json"
-        },
-        "version": 11,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 93,
-        "visitors": 6800,
-        "zenodo_link": ""
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/dummy/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
                 ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/introduction/tutorials/dummy",
-        "draft": true,
+        "dir": "topics/introduction/tutorials/data-manipulation-olympics",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "introduction/dummy",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
+        "id": "introduction/data-manipulation-olympics",
+        "inexact_supported_servers": [],
         "js_requirements": {
-            "mathjax": null,
+            "mathjax": 61358,
             "mermaid": false
         },
         "key_points": [
-            "There are several ways to get data into Galaxy",
-            "you can upload a file by pasting in a web address, you can upload a file from your computer, and you can import an entire history."
+            "There are a lot of tools available in Galaxy for performing basic data manipulation tasks",
+            "Basic data manipulation is often needed between steps in a larger scientific analysis in order to connect outputs from one tool to input of another.",
+            "There are often multiple ways/tools to achieve the same end result",
+            "Having a basic understanding of data manipulation tools will make it easier to do exploratory data analysis",
+            "Always read the help text of the tool before using it to get a full understanding of its workings",
+            "Always try to formulate the output you are expecting from a tool. This will make it easier to spot mistakes as soon as possible."
         ],
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-08-07",
         "objectives": [
-            "Learn how to upload a file by pasting in a URL",
-            "Learn how to import data from a shared library",
-            "Determine the best strategy to get data into Galaxy"
+            "Familiarize yourself with data manipulation tools in Galaxy",
+            "Perform basic text manipulation tasks in Galaxy",
+            "Become comfortable converting text-based files in a variety of ways.",
+            "Reason about the expected outcome of tools"
         ],
-        "pageviews": 312,
-        "pub_date": "2022-09-23",
+        "pageviews": 5158,
+        "pub_date": "2022-07-20",
         "questions": [
-            "How to upload data to Galaxy"
+            "How can I do basic data manipulation in Galaxy?",
+            "Which tools are available to convert, reformat, filter, sort etc my text-based data?"
+        ],
+        "short_id": "T00184",
+        "short_tools": [
+            "",
+            "join1",
+            "Count1",
+            "upload1",
+            "wc_gnu",
+            "datamash_ops",
+            "Grouping1",
+            "tp_sorted_uniq",
+            "tabular_to_csv",
+            "tp_cat",
+            "Filter1",
+            "tp_sort_header_tool",
+            "tp_split_on_column",
+            "Cut1",
+            "Remove beginning1",
+            "cat1",
+            "Show beginning1",
+            "Add_a_column1",
+            "regexColumn1"
         ],
-        "short_id": "T00185",
-        "short_tools": [],
         "slides": false,
         "slides_recordings": false,
+        "subtopic": "next-steps",
         "supported_servers": {
             "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
+            "inexact": []
         },
         "symlink": null,
         "tags": [
-            "work-in-progress"
+            "cyoa"
+        ],
+        "time_estimation": "1h",
+        "title": "Data Manipulation Olympics",
+        "tools": [
+            "Count1",
+            "Cut1",
+            "Filter1",
+            "Grouping1",
+            "Remove beginning1",
+            "Show beginning1",
+            "cat1",
+            "join1",
+            "tabular_to_csv",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2",
+            "upload1",
+            "wc_gnu",
+            "",
+            "",
+            "",
+            "",
+            "",
+            "",
+            "",
+            "",
+            "",
+            "",
+            "",
+            "",
+            "",
+            "",
+            "",
+            "",
+            "",
+            ""
         ],
-        "time_estimation": "40m",
-        "title": "Upload data to Galaxy",
-        "tools": [],
         "topic_name": "introduction",
         "topic_name_human": "Introduction to Galaxy Analyses",
         "tours": false,
@@ -128082,19 +130068,178 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "dummy",
+        "tutorial_name": "data-manipulation-olympics",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/dummy/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/data-manipulation-olympics/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/dummy/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/dummy/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/data-manipulation-olympics/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/data-manipulation-olympics/tutorial.json"
         },
-        "version": 5,
+        "version": 10,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 209,
-        "visitors": 265
+        "visit_duration": 210,
+        "visitors": 3366,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Data Manipulation Olympics",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nolympics.tsv\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncountry-information.tsv\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nolympics_2022.tsv\"]\n  3[label=\"Line/Word/Character count\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"tabular-to-csv\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Sort\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Sort\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Sort\"]\n  0 -> 7 [label=\"output\"]\n  8[label=\"Sort\"]\n  0 -> 8 [label=\"output\"]\n  9[label=\"Sort\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"Sort\"]\n  0 -> 10 [label=\"output\"]\n  11[label=\"Filter\"]\n  0 -> 11 [label=\"output\"]\n  12[label=\"Filter\"]\n  0 -> 12 [label=\"output\"]\n  13[label=\"Count\"]\n  0 -> 13 [label=\"output\"]\n  14[label=\"Count\"]\n  0 -> 14 [label=\"output\"]\n  15[label=\"Count\"]\n  0 -> 15 [label=\"output\"]\n  16[label=\"Count\"]\n  0 -> 16 [label=\"output\"]\n  17[label=\"Datamash\"]\n  0 -> 17 [label=\"output\"]\n  18[label=\"Count\"]\n  0 -> 18 [label=\"output\"]\n  19[label=\"Datamash\"]\n  0 -> 19 [label=\"output\"]\n  20[label=\"Filter\"]\n  0 -> 20 [label=\"output\"]\n  21[label=\"Filter\"]\n  0 -> 21 [label=\"output\"]\n  22[label=\"Filter\"]\n  0 -> 22 [label=\"output\"]\n  23[label=\"Filter\"]\n  0 -> 23 [label=\"output\"]\n  24[label=\"Filter\"]\n  0 -> 24 [label=\"output\"]\n  25[label=\"Filter\"]\n  0 -> 25 [label=\"output\"]\n  26[label=\"Filter\"]\n  0 -> 26 [label=\"output\"]\n  27[label=\"Compute\"]\n  0 -> 27 [label=\"output\"]\n  28[label=\"Compute\"]\n  0 -> 28 [label=\"output\"]\n  29[label=\"Cut\"]\n  0 -> 29 [label=\"output\"]\n  30[label=\"Column Regex Find And Replace\"]\n  0 -> 30 [label=\"output\"]\n  31[label=\"Column Regex Find And Replace\"]\n  0 -> 31 [label=\"output\"]\n  32[label=\"Column Regex Find And Replace\"]\n  0 -> 32 [label=\"output\"]\n  33[label=\"Cut\"]\n  0 -> 33 [label=\"output\"]\n  34[label=\"Cut\"]\n  0 -> 34 [label=\"output\"]\n  35[label=\"Datamash\"]\n  0 -> 35 [label=\"output\"]\n  36[label=\"Datamash\"]\n  0 -> 36 [label=\"output\"]\n  37[label=\"Datamash\"]\n  0 -> 37 [label=\"output\"]\n  38[label=\"Datamash\"]\n  0 -> 38 [label=\"output\"]\n  39[label=\"Datamash\"]\n  0 -> 39 [label=\"output\"]\n  40[label=\"Count\"]\n  0 -> 40 [label=\"output\"]\n  41[label=\"Column Regex Find And Replace\"]\n  0 -> 41 [label=\"output\"]\n  42[label=\"Split file\"]\n  0 -> 42 [label=\"output\"]\n  43[label=\"Join two Datasets\"]\n  0 -> 43 [label=\"output\"]\n  1 -> 43 [label=\"output\"]\n  44[label=\"Remove beginning\"]\n  2 -> 44 [label=\"output\"]\n  45[label=\"Sort\"]\n  11 -> 45 [label=\"out_file1\"]\n  46[label=\"Filter\"]\n  12 -> 46 [label=\"out_file1\"]\n  47[label=\"Cut\"]\n  28 -> 47 [label=\"out_file1\"]\n  48[label=\"Unique\"]\n  29 -> 48 [label=\"out_file1\"]\n  49[label=\"Count\"]\n  41 -> 49 [label=\"out_file1\"]\n  50[label=\"Datamash\"]\n  41 -> 50 [label=\"out_file1\"]\n  51[label=\"Concatenate datasets\"]\n  0 -> 51 [label=\"output\"]\n  44 -> 51 [label=\"out_file1\"]\n  52[label=\"Filter\"]\n  45 -> 52 [label=\"outfile\"]\n  53[label=\"Sort\"]\n  46 -> 53 [label=\"out_file1\"]\n  54[label=\"Remove beginning\"]\n  47 -> 54 [label=\"out_file1\"]\n  55[label=\"Select first\"]\n  47 -> 55 [label=\"out_file1\"]\n  56[label=\"Sort\"]\n  48 -> 56 [label=\"outfile\"]\n  57[label=\"Unique\"]\n  54 -> 57 [label=\"out_file1\"]\n  58[label=\"Concatenate datasets\"]\n  55 -> 58 [label=\"out_file1\"]\n  57 -> 58 [label=\"outfile\"]\n  59[label=\"Join two Datasets\"]\n  0 -> 59 [label=\"output\"]\n  58 -> 59 [label=\"out_file1\"]\n  60[label=\"Cut\"]\n  59 -> 60 [label=\"out_file1\"]\n  61[label=\"Line/Word/Character count\"]\n  60 -> 61 [label=\"out_file1\"]\n}",
+                "history": [
+                    {
+                        "hash": "195fb90f3cb0f6d446d1dc200ae11795735d0bc5",
+                        "message": "update workflow",
+                        "num": 3,
+                        "short_hash": "195fb90f3",
+                        "unix": "1658327856"
+                    },
+                    {
+                        "hash": "6908a9a8092d32a2ee24f5d61463f41d83498750",
+                        "message": "add tag and annotation",
+                        "num": 2,
+                        "short_hash": "6908a9a80",
+                        "unix": "1657815002"
+                    },
+                    {
+                        "hash": "68183fdf9f2b84177b8c374291cd50b8c9a5f0b2",
+                        "message": "add workflow",
+                        "num": 1,
+                        "short_hash": "68183fdf9",
+                        "unix": "1657814320"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "olympics.tsv"
+                            }
+                        ],
+                        "label": "olympics.tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 10
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "749981b6-9589-48a3-b1fe-3830a019aac3",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "country-information.tsv"
+                            }
+                        ],
+                        "label": "country-information.tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 130
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "4dd01f90-d214-419c-b685-187c4c7e0236",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "olympics_2022.tsv"
+                            }
+                        ],
+                        "label": "olympics_2022.tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 250
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "8caf40e8-4c72-48c5-92cb-50fef0a9da1c",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nolympics.tsv\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ncountry-information.tsv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nolympics_2022.tsv\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Line/Word/Character count\"];\n  0 -->|output| 3;\n  4[\"tabular-to-csv\"];\n  0 -->|output| 4;\n  5[\"Sort\"];\n  0 -->|output| 5;\n  6[\"Sort\"];\n  0 -->|output| 6;\n  7[\"Sort\"];\n  0 -->|output| 7;\n  8[\"Sort\"];\n  0 -->|output| 8;\n  9[\"Sort\"];\n  0 -->|output| 9;\n  10[\"Sort\"];\n  0 -->|output| 10;\n  11[\"Filter\"];\n  0 -->|output| 11;\n  12[\"Filter\"];\n  0 -->|output| 12;\n  13[\"Count\"];\n  0 -->|output| 13;\n  14[\"Count\"];\n  0 -->|output| 14;\n  15[\"Count\"];\n  0 -->|output| 15;\n  16[\"Count\"];\n  0 -->|output| 16;\n  17[\"Datamash\"];\n  0 -->|output| 17;\n  18[\"Count\"];\n  0 -->|output| 18;\n  19[\"Datamash\"];\n  0 -->|output| 19;\n  20[\"Filter\"];\n  0 -->|output| 20;\n  21[\"Filter\"];\n  0 -->|output| 21;\n  22[\"Filter\"];\n  0 -->|output| 22;\n  23[\"Filter\"];\n  0 -->|output| 23;\n  24[\"Filter\"];\n  0 -->|output| 24;\n  25[\"Filter\"];\n  0 -->|output| 25;\n  26[\"Filter\"];\n  0 -->|output| 26;\n  27[\"Compute\"];\n  0 -->|output| 27;\n  28[\"Compute\"];\n  0 -->|output| 28;\n  29[\"Cut\"];\n  0 -->|output| 29;\n  30[\"Column Regex Find And Replace\"];\n  0 -->|output| 30;\n  31[\"Column Regex Find And Replace\"];\n  0 -->|output| 31;\n  32[\"Column Regex Find And Replace\"];\n  0 -->|output| 32;\n  33[\"Cut\"];\n  0 -->|output| 33;\n  34[\"Cut\"];\n  0 -->|output| 34;\n  35[\"Datamash\"];\n  0 -->|output| 35;\n  36[\"Datamash\"];\n  0 -->|output| 36;\n  37[\"Datamash\"];\n  0 -->|output| 37;\n  38[\"Datamash\"];\n  0 -->|output| 38;\n  39[\"Datamash\"];\n  0 -->|output| 39;\n  40[\"Count\"];\n  0 -->|output| 40;\n  41[\"Column Regex Find And Replace\"];\n  0 -->|output| 41;\n  42[\"Split file\"];\n  0 -->|output| 42;\n  43[\"Join two Datasets\"];\n  0 -->|output| 43;\n  1 -->|output| 43;\n  44[\"Remove beginning\"];\n  2 -->|output| 44;\n  45[\"Sort\"];\n  11 -->|out_file1| 45;\n  46[\"Filter\"];\n  12 -->|out_file1| 46;\n  47[\"Cut\"];\n  28 -->|out_file1| 47;\n  48[\"Unique\"];\n  29 -->|out_file1| 48;\n  49[\"Count\"];\n  41 -->|out_file1| 49;\n  50[\"Datamash\"];\n  41 -->|out_file1| 50;\n  51[\"Concatenate datasets\"];\n  0 -->|output| 51;\n  44 -->|out_file1| 51;\n  52[\"Filter\"];\n  45 -->|outfile| 52;\n  53[\"Sort\"];\n  46 -->|out_file1| 53;\n  54[\"Remove beginning\"];\n  47 -->|out_file1| 54;\n  55[\"Select first\"];\n  47 -->|out_file1| 55;\n  56[\"Sort\"];\n  48 -->|outfile| 56;\n  57[\"Unique\"];\n  54 -->|out_file1| 57;\n  58[\"Concatenate datasets\"];\n  55 -->|out_file1| 58;\n  57 -->|outfile| 58;\n  59[\"Join two Datasets\"];\n  0 -->|output| 59;\n  58 -->|out_file1| 59;\n  60[\"Cut\"];\n  59 -->|out_file1| 60;\n  61[\"Line/Word/Character count\"];\n  60 -->|out_file1| 61;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "GTN Tutorial: Data manipulation Olympics - all steps and exercises",
+                "outputs": [],
+                "parent_id": "introduction/data-manipulation-olympics",
+                "path": "topics/introduction/tutorials/data-manipulation-olympics/workflows/data_manipulation_olympics_with_exercises.ga",
+                "tags": [
+                    "introduction"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "GTN Tutorial: Data manipulation Olympics - all steps and exercises",
+                "topic_id": "introduction",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/introduction-data-manipulation-olympics/versions/data-manipulation-olympics-with-exercises",
+                "tutorial_id": "data-manipulation-olympics",
+                "url": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/data-manipulation-olympics/workflows/data_manipulation_olympics_with_exercises.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/data-manipulation-olympics/workflows/data_manipulation_olympics_with_exercises.html",
+                "version": 1,
+                "wfid": "introduction-data-manipulation-olympics",
+                "wfname": "data-manipulation-olympics-with-exercises",
+                "workflow": "data_manipulation_olympics_with_exercises.ga",
+                "workflow_tools": [
+                    "Count1",
+                    "Cut1",
+                    "Filter1",
+                    "Remove beginning1",
+                    "Show beginning1",
+                    "cat1",
+                    "join1",
+                    "tabular_to_csv",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2",
+                    "wc_gnu"
+                ],
+                "workflowhub_id": "1090"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/6803028"
     },
     {
         "admin_install": {
@@ -128103,197 +130248,131 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "fastq_quality_filter",
-                    "owner": "devteam",
-                    "revisions": "43a7370aa010",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastq_quality_filter",
-                    "owner": "devteam",
-                    "revisions": "64e9a6afdd0c",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "9da02be9c6cc",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "ddf54b12c295",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fastqc",
+                    "name": "intersect",
                     "owner": "devteam",
-                    "revisions": "2c64fded1286",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "69c10b56f46d",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastq_quality_filter\n  owner: devteam\n  revisions: 43a7370aa010\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastq_quality_filter\n  owner: devteam\n  revisions: 64e9a6afdd0c\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 9da02be9c6cc\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 2c64fded1286\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-short/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "annasyme",
-                "nsoranzo"
-            ],
-            "editing": [
-                "bebatut",
-                "ahmedhamidawan"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: ddf54b12c295\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: intersect\n  owner: devteam\n  revisions: 69c10b56f46d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-strands/tutorial.json",
         "contributors": [
             {
-                "id": "annasyme",
-                "joined": "2017-09",
-                "name": "Anna Syme",
-                "orcid": "0000-0002-9906-0673",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
-            },
-            {
-                "affiliations": [
-                    "earlham",
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "fediverse": "https://mstdn.science/@nsoranzo",
-                "fediverse_flavor": "mastodon",
-                "id": "nsoranzo",
+                "id": "tnabtaf",
                 "joined": "2017-09",
-                "linkedin": "nicola-soranzo-7884125",
-                "matrix": "nsoranzo:matrix.org",
-                "name": "Nicola Soranzo",
-                "orcid": "0000-0003-3627-5340",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
-                "twitter": "NicolaSoranzo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
+                "name": "Dave Clements",
+                "orcid": "0000-0002-9970-6657",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
             },
             {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
                     "elixir-europe"
                 ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "email": "aawan7@jhu.edu",
-                "id": "ahmedhamidawan",
-                "joined": "2024-08",
-                "linkedin": "ahmed-awan-70a20919a",
-                "matrix": "ahmedhamidawan:matrix.org",
-                "name": "Ahmed Hamid Awan",
-                "orcid": "0009-0003-2600-6152",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ahmedhamidawan/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/ahmedhamidawan.json"
+                "id": "gallardoalba",
+                "joined": "2020-11",
+                "name": "Crist\u00f3bal Gallardo",
+                "orcid": "0000-0002-5752-2155",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
             }
         ],
-        "dir": "topics/introduction/tutorials/galaxy-intro-short",
-        "edam_operation": [
-            "Sequencing quality control",
-            "Sequence composition calculation",
-            "Statistical calculation"
-        ],
+        "dir": "topics/introduction/tutorials/galaxy-intro-strands",
+        "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "introduction/galaxy-intro-short",
+        "id": "introduction/galaxy-intro-strands",
         "inexact_supported_servers": [
-            "Galaxy@Pasteur",
-            "GalaxyTrakr",
-            "UseGalaxy.cz",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
+            "MISSISSIPPI"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "The Galaxy interface has an activity bar on the left, a tool (or other activated) panel next to it (if expanded), viewing pane in the middle, and a history of your data analysis on the right.",
-            "You can create a new history for each analysis. All your histories are saved.",
-            "To get data into Galaxy, you can upload a file by pasting in a web address. There are other ways to get data into Galaxy (not covered in this tutorial): you can upload a file from your computer, and you can import an entire history.",
-            "Choose a tool and change any settings for your analysis.",
-            "Run the tool. The output files will be saved at the top of your history.",
-            "View the output files by clicking on the eye icon.",
-            "View all your histories and move files between them. Switch to a different history.",
-            "Log out of your Galaxy server. When you log back in (to the same server), your histories will all be there."
+            "Galaxy provides an easy-to-use graphical user interface for often complex command-line tools",
+            "Galaxy keeps a full record of your analysis in a history",
+            "Workflows enable you to repeat your analysis on different data",
+            "Galaxy can connect to external sources for data import and visualization purposes",
+            "Galaxy provides ways to share your results and methods with others"
         ],
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-15",
+        "mod_date": "2024-07-09",
         "objectives": [
-            "Learn how to upload a file",
-            "Learn how to use a tool",
-            "Learn how to view results",
-            "Learn how to view histories",
-            "Learn how to extract and run a workflow",
-            "Learn how to share a history"
+            "Learn some of the basic concepts of genomics and bioinformatics",
+            "Familiarize yourself with the basics of Galaxy"
         ],
-        "pageviews": 5786269,
-        "priority": 2,
-        "pub_date": "2018-08-27",
+        "pageviews": 28209,
+        "pub_date": "2017-10-18",
         "questions": [
-            "How to get started in Galaxy"
+            "Do genes on opposite strands ever overlap?  If so, how often?"
         ],
-        "short_id": "T00190",
+        "recordings": [
+            {
+                "captioners": [
+                    "nakucher"
+                ],
+                "date": "2023-05-18",
+                "galaxy_version": "23.01",
+                "length": "1H30M",
+                "speakers": [
+                    "nakucher"
+                ],
+                "youtube_id": "P1mEWZ_tAgQ"
+            },
+            {
+                "captioners": [
+                    "tnabtaf"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "1H30M",
+                "speakers": [
+                    "tnabtaf"
+                ],
+                "youtube_id": "1UPCrQxGwcU"
+            }
+        ],
+        "short_id": "T00191",
         "short_tools": [
-            "fastqc",
-            "cshl_fastq_quality_filter"
+            "tp_cat",
+            "Filter1",
+            "gene2exon1",
+            "gops_intersect_1",
+            "cat1"
         ],
-        "slides": true,
+        "slides": false,
         "slides_recordings": false,
-        "subtopic": "first",
+        "subtopic": "next-steps",
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "Galaxy@Pasteur",
-                    "url": "https://galaxy.pasteur.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
                 {
@@ -128301,6 +130380,11 @@
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.fr",
                     "url": "https://usegalaxy.fr/",
@@ -128311,69 +130395,68 @@
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
                 }
+            ],
+            "inexact": [
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                }
             ]
         },
         "symlink": null,
-        "tags": [
-            "espa\u00f1ol"
-        ],
-        "time_estimation": "40m",
-        "title": "A short introduction to Galaxy",
+        "time_estimation": "2H30M",
+        "title": "Introduction to Genomics and Galaxy",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.2+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1"
+            "Filter1",
+            "cat1",
+            "gene2exon1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0"
         ],
         "topic_name": "introduction",
         "topic_name_human": "Introduction to Galaxy Analyses",
         "tours": false,
         "translations": {
-            "slides": [
-                "es"
-            ],
-            "tutorial": [
-                "es"
-            ],
-            "video": true
+            "slides": [],
+            "tutorial": [],
+            "video": false
         },
-        "tutorial_name": "galaxy-intro-short",
+        "tutorial_name": "galaxy-intro-strands",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-short/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-strands/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-short/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-short/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-strands/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-strands/tutorial.json"
         },
-        "version": 36,
-        "video": true,
-        "video_versions": 0,
+        "version": 40,
+        "video": false,
+        "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 420,
-        "visitors": 2101490,
+        "visit_duration": 211,
+        "visitors": 17424,
         "workflows": [
             {
                 "creators": [],
-                "description": "A short introduction to Galaxy",
+                "description": "Introduction to Genomics and Galaxy",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmutant_R1\"]\n  1[label=\"FastQC\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Filter by quality\"]\n  0 -> 2 [label=\"output\"]\n  k24271408b2cc4e229bf92071f41bd991[color=lightseagreen,label=\"Output\\nfilter1\"]\n  2 -> k24271408b2cc4e229bf92071f41bd991\n  3[label=\"Filter by quality\"]\n  0 -> 3 [label=\"output\"]\n  k86ed7ac57a924c1caf49eecb6baeaa9d[color=lightseagreen,label=\"Output\\nfilter2\"]\n  3 -> k86ed7ac57a924c1caf49eecb6baeaa9d\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[label=\"Gene BED To Exon/Intron/Codon BED\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Filter\"]\n  1 -> 2 [label=\"out_file1\"]\n  3[label=\"Filter\"]\n  1 -> 3 [label=\"out_file1\"]\n  4[label=\"Intersect\"]\n  2 -> 4 [label=\"out_file1\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"Intersect\"]\n  3 -> 5 [label=\"out_file1\"]\n  2 -> 5 [label=\"out_file1\"]\n  6[label=\"Concatenate datasets\"]\n  5 -> 6 [label=\"output\"]\n  4 -> 6 [label=\"output\"]\n}",
                 "history": [
-                    {
-                        "hash": "bcd92cb059319065ea797c48e5e68c47ceae2dbd",
-                        "message": "Add workflow test.",
-                        "num": 5,
-                        "short_hash": "bcd92cb05",
-                        "unix": "1603316821"
-                    },
                     {
                         "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
                         "message": "annotation",
@@ -128396,11 +130479,11 @@
                         "unix": "1554368414"
                     },
                     {
-                        "hash": "6aded48bd1b611fb111ac2818450c00dafd7d1f3",
-                        "message": "added workflow for intro-short",
+                        "hash": "8654b300bee12fde5cdb5392424e592b34757373",
+                        "message": "added workflows",
                         "num": 1,
-                        "short_hash": "6aded48bd",
-                        "unix": "1537905266"
+                        "short_hash": "8654b300b",
+                        "unix": "1536320594"
                     }
                 ],
                 "inputs": [
@@ -128413,143 +130496,153 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "mutant_R1"
+                                "name": "Genes"
                             }
                         ],
-                        "label": "mutant_R1",
-                        "name": "mutant_R1",
+                        "label": null,
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
                             "left": 10,
                             "top": 10
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"mutant_R1\"}",
+                        "tool_state": "{\"name\": \"Genes\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "e271eee4-bfb8-40b4-b691-a25cb9932327",
+                        "uuid": "286c5925-431f-432d-a658-515befa7c6d3",
                         "workflow_outputs": []
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nmutant_R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"FastQC\"];\n  0 -->|output| 1;\n  2[\"Filter by quality\"];\n  0 -->|output| 2;\n  24271408-b2cc-4e22-9bf9-2071f41bd991[\"Output\\nfilter1\"];\n  2 --> 24271408-b2cc-4e22-9bf9-2071f41bd991;\n  style 24271408-b2cc-4e22-9bf9-2071f41bd991 stroke:#2c3143,stroke-width:4px;\n  3[\"Filter by quality\"];\n  0 -->|output| 3;\n  86ed7ac5-7a92-4c1c-af49-eecb6baeaa9d[\"Output\\nfilter2\"];\n  3 --> 86ed7ac5-7a92-4c1c-af49-eecb6baeaa9d;\n  style 86ed7ac5-7a92-4c1c-af49-eecb6baeaa9d stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Galaxy Intro Short",
-                "outputs": [
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Gene BED To Exon/Intron/Codon BED\"];\n  0 -->|output| 1;\n  2[\"Filter\"];\n  1 -->|out_file1| 2;\n  3[\"Filter\"];\n  1 -->|out_file1| 3;\n  4[\"Intersect\"];\n  2 -->|out_file1| 4;\n  3 -->|out_file1| 4;\n  5[\"Intersect\"];\n  3 -->|out_file1| 5;\n  2 -->|out_file1| 5;\n  6[\"Concatenate datasets\"];\n  5 -->|output| 6;\n  4 -->|output| 6;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Galaxy Intro Strands 2",
+                "outputs": [],
+                "parent_id": "introduction/galaxy-intro-strands",
+                "path": "topics/introduction/tutorials/galaxy-intro-strands/workflows/Galaxy-Workflow-galaxy-intro-strands-2.ga",
+                "tags": [
+                    "introduction"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Galaxy Intro Strands 2",
+                "topic_id": "introduction",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/introduction-galaxy-intro-strands/versions/galaxy-workflowlaxy-intro-strands-2",
+                "tutorial_id": "galaxy-intro-strands",
+                "url": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-strands/workflows/Galaxy-Workflow-galaxy-intro-strands-2.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-strands/workflows/Galaxy-Workflow-galaxy-intro-strands-2.html",
+                "version": 4,
+                "wfid": "introduction-galaxy-intro-strands",
+                "wfname": "galaxy-workflowlaxy-intro-strands-2",
+                "workflow": "Galaxy-Workflow-galaxy-intro-strands-2.ga",
+                "workflow_tools": [
+                    "Filter1",
+                    "gene2exon1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0"
+                ],
+                "workflowhub_id": "1111"
+            },
+            {
+                "creators": [],
+                "description": "Introduction to Genomics and Galaxy",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[label=\"Filter\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Filter\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Filter\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Intersect\"]\n  2 -> 4 [label=\"out_file1\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"Intersect\"]\n  3 -> 5 [label=\"out_file1\"]\n  2 -> 5 [label=\"out_file1\"]\n  6[label=\"Concatenate datasets\"]\n  5 -> 6 [label=\"output\"]\n  4 -> 6 [label=\"output\"]\n}",
+                "history": [
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.1",
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Filter by quality",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 230,
-                            "top": 130
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "43a7370aa010",
-                            "name": "fastq_quality_filter",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__page__\": null, \"chromInfo\": \"\\\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"percent\": \"\\\"80\\\"\", \"input\": \"null\", \"quality\": \"\\\"35\\\"\"}",
-                        "tool_version": "1.0.1",
-                        "type": "tool",
-                        "uuid": "3a3ec769-355d-488a-984b-78462a794ef9",
-                        "workflow_outputs": [
-                            {
-                                "label": "filter1",
-                                "output_name": "output",
-                                "uuid": "24271408-b2cc-4e22-9bf9-2071f41bd991"
-                            }
-                        ]
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 4,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 3,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
+                        "message": "Changed format of workflows",
+                        "num": 2,
+                        "short_hash": "361236c41",
+                        "unix": "1554368414"
                     },
+                    {
+                        "hash": "8654b300bee12fde5cdb5392424e592b34757373",
+                        "message": "added workflows",
+                        "num": 1,
+                        "short_hash": "8654b300b",
+                        "unix": "1536320594"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Filter by quality",
-                        "outputs": [
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "input"
+                                "description": "",
+                                "name": "Genes"
                             }
                         ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 230,
-                            "top": 250
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "43a7370aa010",
-                            "name": "fastq_quality_filter",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 10,
+                            "top": 10
                         },
-                        "tool_state": "{\"__page__\": null, \"chromInfo\": \"\\\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"percent\": \"\\\"80\\\"\", \"input\": \"null\", \"quality\": \"\\\"36\\\"\"}",
-                        "tool_version": "1.0.1",
-                        "type": "tool",
-                        "uuid": "df2f009c-d3e5-4ccc-bf0f-10b8e44947da",
-                        "workflow_outputs": [
-                            {
-                                "label": "filter2",
-                                "output_name": "output",
-                                "uuid": "86ed7ac5-7a92-4c1c-af49-eecb6baeaa9d"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Genes\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "d69a6248-140c-4b97-bc0f-ce88a4452c75",
+                        "workflow_outputs": []
                     }
                 ],
-                "parent_id": "introduction/galaxy-intro-short",
-                "path": "topics/introduction/tutorials/galaxy-intro-short/workflows/Galaxy-Workflow-galaxy-intro-short.ga",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Filter\"];\n  0 -->|output| 1;\n  2[\"Filter\"];\n  0 -->|output| 2;\n  3[\"Filter\"];\n  0 -->|output| 3;\n  4[\"Intersect\"];\n  2 -->|out_file1| 4;\n  3 -->|out_file1| 4;\n  5[\"Intersect\"];\n  3 -->|out_file1| 5;\n  2 -->|out_file1| 5;\n  6[\"Concatenate datasets\"];\n  5 -->|output| 6;\n  4 -->|output| 6;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Galaxy Intro Strands",
+                "outputs": [],
+                "parent_id": "introduction/galaxy-intro-strands",
+                "path": "topics/introduction/tutorials/galaxy-intro-strands/workflows/Galaxy-Workflow-galaxy-intro-strands.ga",
                 "tags": [
                     "introduction"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Galaxy Intro Short",
+                "title": "Galaxy Intro Strands",
                 "topic_id": "introduction",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/introduction-galaxy-intro-short/versions/galaxy-workflowlaxy-intro-short",
-                "tutorial_id": "galaxy-intro-short",
-                "url": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-short/workflows/Galaxy-Workflow-galaxy-intro-short.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-short/workflows/Galaxy-Workflow-galaxy-intro-short.html",
-                "version": 5,
-                "wfid": "introduction-galaxy-intro-short",
-                "wfname": "galaxy-workflowlaxy-intro-short",
-                "workflow": "Galaxy-Workflow-galaxy-intro-short.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/introduction-galaxy-intro-strands/versions/galaxy-workflowlaxy-intro-strands",
+                "tutorial_id": "galaxy-intro-strands",
+                "url": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-strands/workflows/Galaxy-Workflow-galaxy-intro-strands.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-strands/workflows/Galaxy-Workflow-galaxy-intro-strands.html",
+                "version": 4,
+                "wfid": "introduction-galaxy-intro-strands",
+                "wfname": "galaxy-workflowlaxy-intro-strands",
+                "workflow": "Galaxy-Workflow-galaxy-intro-strands.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72"
+                    "Filter1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0"
                 ],
-                "workflowhub_id": "1094"
+                "workflowhub_id": "1110"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.582600"
+        "zenodo_link": ""
     },
     {
         "admin_install": {
@@ -128565,260 +130658,266 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "bwa",
+                    "owner": "devteam",
+                    "revisions": "3fe632431b68",
+                    "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bedtools",
+                    "name": "picard",
+                    "owner": "devteam",
+                    "revisions": "a1f0b3f4b781",
+                    "tool_panel_section_label": "Picard",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "samtools_stats",
+                    "owner": "devteam",
+                    "revisions": "145f6d74ff5e",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastp",
                     "owner": "iuc",
-                    "revisions": "a1a923cd89e8",
-                    "tool_panel_section_label": "BED",
+                    "revisions": "dbf9c561ef29",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "datamash_ops",
+                    "name": "lofreq_call",
                     "owner": "iuc",
-                    "revisions": "562f3c677828",
-                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "revisions": "e1461b5c52a0",
+                    "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "datamash_ops",
+                    "name": "lofreq_indelqual",
                     "owner": "iuc",
-                    "revisions": "4c07ddedc198",
-                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "revisions": "426d707dfc47",
+                    "tool_panel_section_label": "Variant Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "lofreq_viterbi",
+                    "owner": "iuc",
+                    "revisions": "aa35ee7f3ab2",
+                    "tool_panel_section_label": "Variant Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "5e33b465d8d5",
+                    "tool_panel_section_label": "Quality Control",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "samtools_view",
+                    "owner": "iuc",
+                    "revisions": "bf328cec6a42",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "snpeff_sars_cov_2",
+                    "owner": "iuc",
+                    "revisions": "2a3a00c1fa0a",
+                    "tool_panel_section_label": "Variant Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "snpsift",
+                    "owner": "iuc",
+                    "revisions": "5fab4f81391d",
+                    "tool_panel_section_label": "Variant Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sra_tools",
+                    "owner": "iuc",
+                    "revisions": "653e89d73fc4",
+                    "tool_panel_section_label": "Get Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sra_tools",
+                    "owner": "iuc",
+                    "revisions": "e08a7ad4378b",
+                    "tool_panel_section_label": "Get Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "25136a2b0cfe",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "90981f86000f",
+                    "tool_panel_section_label": "Collection Operations",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: a1a923cd89e8\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 562f3c677828\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 4c07ddedc198\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-101/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: 3fe632431b68\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: a1f0b3f4b781\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 145f6d74ff5e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: dbf9c561ef29\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lofreq_call\n  owner: iuc\n  revisions: e1461b5c52a0\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lofreq_indelqual\n  owner: iuc\n  revisions: 426d707dfc47\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lofreq_viterbi\n  owner: iuc\n  revisions: aa35ee7f3ab2\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 5e33b465d8d5\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: bf328cec6a42\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff_sars_cov_2\n  owner: iuc\n  revisions: 2a3a00c1fa0a\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpsift\n  owner: iuc\n  revisions: 5fab4f81391d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: 653e89d73fc4\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: e08a7ad4378b\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 25136a2b0cfe\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.json",
         "contributors": [
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
-            {
-                "affiliations": [
-                    "earlham",
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "fediverse": "https://mstdn.science/@nsoranzo",
-                "fediverse_flavor": "mastodon",
-                "id": "nsoranzo",
-                "joined": "2017-09",
-                "linkedin": "nicola-soranzo-7884125",
-                "matrix": "nsoranzo:matrix.org",
-                "name": "Nicola Soranzo",
-                "orcid": "0000-0003-3627-5340",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
-                "twitter": "NicolaSoranzo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
-            },
-            {
-                "elixir_node": "de",
-                "email": "blankclemens@gmail.com",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "blankclemens",
-                "joined": "2017-09",
-                "name": "Clemens Blank",
-                "orcid": "0000-0002-1726-2256",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankclemens/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankclemens.json"
-            },
             {
                 "email": "anton@nekrut.org",
                 "id": "nekrut",
                 "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
-            },
-            {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
-                "fediverse_flavor": "mastodon",
-                "id": "bgruening",
-                "joined": "2017-09",
-                "linkedin": "bgruening",
-                "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
-                },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
             },
             {
-                "id": "pajanne",
-                "joined": "2017-09",
-                "name": "Anne Pajon",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pajanne/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pajanne.json"
+                "id": "mvdbeek",
+                "joined": "2018-06",
+                "name": "Marius van den Beek",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
             },
             {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
+                "id": "tnabtaf",
                 "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+                "name": "Dave Clements",
+                "orcid": "0000-0002-9970-6657",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
+            },
+            {
+                "id": "blankenberg",
+                "joined": "2018-07",
+                "name": "Daniel Blankenberg",
+                "orcid": "0000-0002-6833-9049",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankenberg/",
+                "twitter": "dblankenberg",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankenberg.json"
             }
         ],
-        "dir": "topics/introduction/tutorials/galaxy-intro-101",
+        "dir": "topics/introduction/tutorials/galaxy-intro-ngs-data-managment",
         "edam_operation": [
-            "Mapping"
+            "Data handling",
+            "Sequence alignment",
+            "Read mapping",
+            "Sequencing quality control",
+            "Sequence contamination filtering",
+            "Generation",
+            "Validation",
+            "SNP detection",
+            "Formatting",
+            "Genome indexing"
         ],
         "edam_topic": [],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "introduction/galaxy-intro-101",
+        "id": "introduction/galaxy-intro-ngs-data-managment",
         "inexact_supported_servers": [
-            "Galaxy@AuBi",
-            "GalaxyTrakr",
+            "MISSISSIPPI",
+            "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.eu",
             "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.no"
         ],
         "js_requirements": {
-            "mathjax": null,
+            "mathjax": 7097,
             "mermaid": false
         },
         "key_points": [
-            "Galaxy provides an easy-to-use graphical user interface for often complex command-line tools",
-            "Galaxy keeps a full record of your analysis in a history",
-            "Workflows enable you to repeat your analysis on different data",
-            "Galaxy can connect to external sources for data import and visualization purposes",
-            "Galaxy provides ways to share your results and methods with others"
+            "FASTQ Sanger version of the format is considered to be the standard form of FASTQ.",
+            "Paired end data can be provided as two files or as an interleaved one.",
+            "FastqQC is a tool allowing to check the quality of FASTQ datasets.",
+            "The most common tools for mapping are Bowtie, BWA, BWA-MEM. You can use in-built genome to map against or upload one if it is missing.",
+            "The standard format for storing aligned reads is SAM/BAM. The major toolsets to process these datasets are DeepTools, SAMtools, BAMtools and Picard.",
+            "Data can be uploaded directly from a computer, from EBI SRA and from NCBI SRA, also using FTP or URL.",
+            "One can retrieve NGS data from Sequence Read Archive",
+            "Galaxy can analyze massive amounts of data and make them suitable for secondary analysis"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
         "license": "CC-BY-4.0",
         "mod_date": "2024-06-14",
         "objectives": [
-            "Familiarize yourself with the basics of Galaxy",
-            "Learn how to obtain data from external sources",
-            "Learn how to run tools",
-            "Learn how histories work",
-            "Learn how to create a workflow",
-            "Learn how to share your work"
+            "Understand most common types of NGS-related datatypes",
+            "Learn about how Galaxy handles NGS data using Illumina data derived from patients infected with SARS-CoV-2"
         ],
-        "pageviews": 52424,
-        "priority": 2,
-        "pub_date": "2016-12-19",
+        "pageviews": 29221,
+        "pub_date": "2017-02-22",
         "questions": [
-            "Which coding exon has the highest number of single nucleotide polymorphisms (SNPs) on human chromosome 22?"
+            "How to manipulate and process NGS data"
         ],
         "recordings": [
             {
                 "captioners": [
-                    "shiltemann"
+                    "nekrut"
                 ],
-                "date": "2021-07-21",
-                "length": "13M",
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "15M",
                 "speakers": [
                     "nekrut"
                 ],
-                "youtube_id": "D5HgJWdfOWw"
+                "youtube_id": "9mIL0tIfZ_o"
             }
         ],
-        "short_id": "T00186",
+        "short_id": "T00188",
         "short_tools": [
-            "bedtools_intersectbed",
-            "datamash_ops",
-            "tp_sort_header_tool",
-            "comp1",
-            "tp_head_tool",
-            "upload1"
+            "bwa_mem",
+            "samtools_stats",
+            "picard_MarkDuplicates",
+            "fastp",
+            "samtools_view",
+            "lofreq_viterbi",
+            "snpeff_sars_cov_2",
+            "multiqc",
+            "collapse_dataset",
+            "lofreq_indelqual",
+            "Grep1",
+            "fasterq_dump",
+            "lofreq_call",
+            "tp_cut_tool",
+            "snpSift_extractFields"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "core",
+        "subtopic": "next-steps",
         "supported_servers": {
-            "exact": [],
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
             "inexact": [
                 {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
                     "usegalaxy": false
                 },
                 {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
                 {
@@ -128826,11 +130925,6 @@
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
                 {
                     "name": "UseGalaxy.fr",
                     "url": "https://usegalaxy.fr/",
@@ -128840,26 +130934,30 @@
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
-        "time_estimation": "1H",
-        "title": "Galaxy Basics for genomics",
+        "time_estimation": "1H30M",
+        "title": "NGS data logistics",
         "tools": [
-            "comp1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1sort1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
-            "upload1"
+            "Grep1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.8+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.9+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
         ],
         "topic_name": "introduction",
         "topic_name_human": "Introduction to Galaxy Analyses",
@@ -128869,1286 +130967,1052 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "galaxy-intro-101",
+        "tutorial_name": "galaxy-intro-ngs-data-managment",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-101/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-101/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-101/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.json"
         },
-        "version": 63,
+        "version": 33,
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 199,
-        "visitors": 30914,
+        "visit_duration": 198,
+        "visitors": 16449,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-5987-8032",
-                        "name": "Anton Nekrutenko"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0001-9760-8992",
-                        "name": "Helena Rasche"
-                    }
-                ],
-                "description": "Galaxy 101",
+                "creators": [],
+                "description": "NGS data logistics",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nExons\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nFeatures\"]\n  2[label=\"bedtools Intersect intervals\"]\n  0 -> 2 [label=\"output\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"Datamash\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Sort\"]\n  3 -> 4 [label=\"out_file\"]\n  5[label=\"Select first\"]\n  4 -> 5 [label=\"outfile\"]\n  6[label=\"Compare two Datasets\"]\n  0 -> 6 [label=\"output\"]\n  5 -> 6 [label=\"outfile\"]\n  k565e3d7602304a5e87c19c36ce0b7df8[color=lightseagreen,label=\"Output\\ntop_5_exons\"]\n  6 -> k565e3d7602304a5e87c19c36ce0b7df8\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAccessions\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenome\"]\n  2[label=\"Faster Download and Extract Reads in FASTQ\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"fastp\"]\n  2 -> 3 [label=\"list_paired\"]\n  4[label=\"Map with BWA-MEM\"]\n  3 -> 4 [label=\"output_paired_coll\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Samtools view\"]\n  4 -> 5 [label=\"bam_output\"]\n  6[label=\"MarkDuplicates\"]\n  5 -> 6 [label=\"outputsam\"]\n  7[label=\"Samtools stats\"]\n  6 -> 7 [label=\"outFile\"]\n  8[label=\"Realign reads\"]\n  6 -> 8 [label=\"outFile\"]\n  1 -> 8 [label=\"output\"]\n  9[label=\"MultiQC\"]\n  3 -> 9 [label=\"report_json\"]\n  6 -> 9 [label=\"metrics_file\"]\n  7 -> 9 [label=\"output\"]\n  10[label=\"Insert indel qualities\"]\n  8 -> 10 [label=\"realigned\"]\n  1 -> 10 [label=\"output\"]\n  11[label=\"Call variants\"]\n  10 -> 11 [label=\"output\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"SnpEff eff:\"]\n  11 -> 12 [label=\"variants\"]\n  13[label=\"SnpSift Extract Fields\"]\n  12 -> 13 [label=\"snpeff_output\"]\n  14[label=\"Collapse Collection\"]\n  13 -> 14 [label=\"output\"]\n}",
                 "history": [
                     {
-                        "hash": "a448d335638114ae05668d8f3872a8316d8d49b0",
-                        "message": "added modified workflow",
-                        "num": 8,
-                        "short_hash": "a448d3356",
-                        "unix": "1710952427"
-                    },
-                    {
-                        "hash": "f90859e9d8100f4efa53007414e2b3849d6e1951",
-                        "message": "Fix workflow for planemo",
-                        "num": 7,
-                        "short_hash": "f90859e9d",
-                        "unix": "1684430714"
-                    },
-                    {
-                        "hash": "553ea8e510cd1e7d8a93a0a8d88dbbe0595c5619",
-                        "message": "Rename workflow",
-                        "num": 6,
-                        "short_hash": "553ea8e51",
-                        "unix": "1649867205"
-                    },
-                    {
-                        "hash": "a49d7d1a4431174af35c82ea03d9b1dd28251691",
-                        "message": "Include modifications",
-                        "num": 5,
-                        "short_hash": "a49d7d1a4",
-                        "unix": "1649867088"
-                    },
-                    {
-                        "hash": "222c554dbb9d76aaec3132c109dd701889750a94",
-                        "message": "workflow annotation wteaks",
-                        "num": 4,
-                        "short_hash": "222c554db",
-                        "unix": "1626799656"
-                    },
-                    {
-                        "hash": "43d15ed0ca2f2c0abbe58769cca667d978e48b4b",
-                        "message": "Refresh for galaxy101",
-                        "num": 3,
-                        "short_hash": "43d15ed0c",
-                        "unix": "1626797332"
-                    },
-                    {
-                        "hash": "d0f7b80091932c1f6d78357d7d4229942faf76e6",
-                        "message": "Added workflow test.",
+                        "hash": "ca2265825aa1725a8d5fdc3d1c02282878db2c96",
+                        "message": "workflow changes",
                         "num": 2,
-                        "short_hash": "d0f7b8009",
-                        "unix": "1603042314"
+                        "short_hash": "ca2265825",
+                        "unix": "1613070101"
                     },
                     {
-                        "hash": "bffe460ee012428019957f7ba57d7f5f3050a99a",
-                        "message": "Added workflow.",
+                        "hash": "211e2c843aeb6d1e8aeaa48571e4ec363466f5fe",
+                        "message": "Updated NGS tutorial for GTN Sm\u00f6rg\u00e5sbord",
                         "num": 1,
-                        "short_hash": "bffe460ee",
-                        "unix": "1603039367"
+                        "short_hash": "211e2c843",
+                        "unix": "1613069503"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "Input exons file",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Input exons file",
-                                "name": "Exons"
+                                "description": "",
+                                "name": "Accessions"
                             }
                         ],
-                        "label": "Exons",
-                        "name": "Input dataset",
+                        "label": "Accessions",
+                        "name": "Accessions",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 187.2359999999986
+                            "bottom": 287.5,
+                            "height": 61,
+                            "left": -457,
+                            "right": -257,
+                            "top": 226.5,
+                            "width": 200,
+                            "x": -457,
+                            "y": 226.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"name\": \"Accessions\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "bd3df190-bc2c-4432-a534-7b1b21cd58c9",
-                        "when": null,
+                        "uuid": "66230eb7-5666-4a09-8aaa-b8881161a81b",
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "Input features file",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Input features file",
-                                "name": "Features"
+                                "description": "",
+                                "name": "Genome"
                             }
                         ],
-                        "label": "Features",
-                        "name": "Input dataset",
+                        "label": "Genome",
+                        "name": "Genome",
                         "outputs": [],
                         "position": {
-                            "left": 49,
-                            "top": 430.2359999999986
+                            "bottom": 453.5,
+                            "height": 61,
+                            "left": -505,
+                            "right": -305,
+                            "top": 392.5,
+                            "width": 200,
+                            "x": -505,
+                            "y": 392.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"name\": \"Genome\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "b7b8e25f-8db4-4707-bfb9-9e5a527e28c3",
-                        "when": null,
+                        "uuid": "9880eb10-5648-4c94-89d3-095661f6027b",
                         "workflow_outputs": []
                     }
                 ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nExons\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nFeatures\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"bedtools Intersect intervals\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"Datamash\"];\n  2 -->|output| 3;\n  4[\"Sort\"];\n  3 -->|out_file| 4;\n  5[\"Select first\"];\n  4 -->|outfile| 5;\n  6[\"Compare two Datasets\"];\n  0 -->|output| 6;\n  5 -->|outfile| 6;\n  565e3d76-0230-4a5e-87c1-9c36ce0b7df8[\"Output\\ntop_5_exons\"];\n  6 --> 565e3d76-0230-4a5e-87c1-9c36ce0b7df8;\n  style 565e3d76-0230-4a5e-87c1-9c36ce0b7df8 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Find exons with the highest number of features",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAccessions\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGenome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Faster Download and Extract Reads in FASTQ\"];\n  0 -->|output| 2;\n  3[\"fastp\"];\n  2 -->|list_paired| 3;\n  4[\"Map with BWA-MEM\"];\n  3 -->|output_paired_coll| 4;\n  1 -->|output| 4;\n  5[\"Samtools view\"];\n  4 -->|bam_output| 5;\n  6[\"MarkDuplicates\"];\n  5 -->|outputsam| 6;\n  7[\"Samtools stats\"];\n  6 -->|outFile| 7;\n  8[\"Realign reads\"];\n  6 -->|outFile| 8;\n  1 -->|output| 8;\n  9[\"MultiQC\"];\n  3 -->|report_json| 9;\n  6 -->|metrics_file| 9;\n  7 -->|output| 9;\n  10[\"Insert indel qualities\"];\n  8 -->|realigned| 10;\n  1 -->|output| 10;\n  11[\"Call variants\"];\n  10 -->|output| 11;\n  1 -->|output| 11;\n  12[\"SnpEff eff:\"];\n  11 -->|variants| 12;\n  13[\"SnpSift Extract Fields\"];\n  12 -->|snpeff_output| 13;\n  14[\"Collapse Collection\"];\n  13 -->|output| 14;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "NGS_tutorial",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "comp1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.8+galaxy0",
                         "errors": null,
-                        "id": 6,
+                        "id": 2,
                         "input_connections": {
-                            "input1": {
+                            "input|file_list": {
                                 "id": 0,
                                 "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Faster Download and Extract Reads in FASTQ",
+                        "outputs": [
+                            {
+                                "name": "list_paired",
+                                "type": "input"
                             },
-                            "input2": {
+                            {
+                                "name": "output_collection",
+                                "type": "input"
+                            },
+                            {
+                                "name": "output_collection_other",
+                                "type": "input"
+                            },
+                            {
+                                "name": "log",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 412.5,
+                            "height": 262,
+                            "left": -98,
+                            "right": 102,
+                            "top": 150.5,
+                            "width": 200,
+                            "x": -98,
+                            "y": 150.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.8+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "653e89d73fc4",
+                            "name": "sra_tools",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"adv\": {\"minlen\": null, \"split\": \"--split-3\", \"skip_technical\": \"true\"}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"input\": {\"input_select\": \"file_list\", \"__current_case__\": 2, \"file_list\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.10.8+galaxy0",
+                        "type": "tool",
+                        "uuid": "4fff5f79-2a87-48e4-a9d1-514807dbf145",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "list_paired",
+                                "uuid": "bfc8e1d1-aa46-44ce-ac20-203bec142d7f"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_collection",
+                                "uuid": "75c35a09-2a2c-450c-8d39-1e7b0c27643f"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_collection_other",
+                                "uuid": "02be9121-528a-451a-8db1-7e447281fd27"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "log",
+                                "uuid": "56f06d1a-5221-40c3-a861-09f7cb2d0307"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "single_paired|paired_input": {
+                                "id": 2,
+                                "output_name": "list_paired"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "fastp",
+                        "outputs": [
+                            {
+                                "name": "output_paired_coll",
+                                "type": "input"
+                            },
+                            {
+                                "name": "report_html",
+                                "type": "html"
+                            },
+                            {
+                                "name": "report_json",
+                                "type": "json"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 893.5,
+                            "height": 212,
+                            "left": -118,
+                            "right": 82,
+                            "top": 681.5,
+                            "width": 200,
+                            "x": -118,
+                            "y": 681.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "dbf9c561ef29",
+                            "name": "fastp",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": \"false\", \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": \"false\", \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": \"false\", \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": \"true\", \"report_json\": \"true\"}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": \"false\", \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": \"false\", \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": \"false\", \"cut_by_quality3\": \"false\", \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": \"false\"}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 2, \"paired_input\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": \"false\", \"adapter_sequence1\": \"\", \"adapter_sequence2\": \"\"}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.20.1+galaxy0",
+                        "type": "tool",
+                        "uuid": "d9327c31-29cf-4227-897d-5a2be3cf8382",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "report_json",
+                                "uuid": "f7f03895-44d9-40f1-9bef-7ba34c9b7c1e"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_paired_coll",
+                                "uuid": "e8e2c50e-bd56-4717-9cc5-83263f63a3aa"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "report_html",
+                                "uuid": "95e080c0-8cc7-406a-b470-6f8630111cd9"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "fastq_input|fastq_input1": {
+                                "id": 3,
+                                "output_name": "output_paired_coll"
+                            },
+                            "reference_source|ref_file": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Map with BWA-MEM",
+                        "outputs": [
+                            {
+                                "name": "bam_output",
+                                "type": "bam"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 354.5,
+                            "height": 202,
+                            "left": 285,
+                            "right": 485,
+                            "top": 152.5,
+                            "width": 200,
+                            "x": 285,
+                            "y": 152.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3fe632431b68",
+                            "name": "bwa",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"analysis_type\": {\"analysis_type_selector\": \"illumina\", \"__current_case__\": 0}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"fastq_input\": {\"fastq_input_selector\": \"paired_collection\", \"__current_case__\": 2, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"iset_stats\": \"\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}, \"index_a\": \"auto\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.17.1",
+                        "type": "tool",
+                        "uuid": "f06a5bce-2611-4eba-aaf9-d8cc063acaf7",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "bam_output",
+                                "uuid": "88953a9e-a48a-4f60-8854-09b04e8c5052"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "input": {
+                                "id": 4,
+                                "output_name": "bam_output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Samtools view",
+                        "outputs": [
+                            {
+                                "name": "outputsam",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 297.5,
+                            "height": 152,
+                            "left": 614,
+                            "right": 814,
+                            "top": 145.5,
+                            "width": 200,
+                            "x": 614,
+                            "y": 145.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "bf328cec6a42",
+                            "name": "samtools_view",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"bam\", \"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"SRR12733957\", \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"quality\": \"20\", \"library\": \"\", \"cigarcons\": null, \"inclusive_filter\": [\"1\", \"2\"], \"exclusive_filter\": null, \"exclusive_filter_all\": null}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"fraction\", \"__current_case__\": 0, \"factor\": \"10.0\", \"seed\": \"1\"}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": \"false\", \"adv_output\": {\"readtags\": [], \"collapsecigar\": \"false\"}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9+galaxy2",
+                        "type": "tool",
+                        "uuid": "352c0b12-e4e5-409c-96ff-321de1076e56",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outputsam",
+                                "uuid": "884d1918-7037-4108-bd34-3ae703992031"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "inputFile": {
                                 "id": 5,
-                                "output_name": "outfile"
+                                "output_name": "outputsam"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Compare two Datasets",
+                        "name": "MarkDuplicates",
                         "outputs": [
                             {
-                                "name": "out_file1",
+                                "name": "metrics_file",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "outFile",
+                                "type": "bam"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 1017.5,
+                            "height": 222,
+                            "left": 435,
+                            "right": 635,
+                            "top": 795.5,
+                            "width": 200,
+                            "x": 435,
+                            "y": 795.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "a1f0b3f4b781",
+                            "name": "picard",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"bam\", \"assume_sorted\": \"true\", \"barcode_tag\": \"\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"comments\": [], \"duplicate_scoring_strategy\": \"SUM_OF_BASE_QUALITIES\", \"inputFile\": {\"__class__\": \"ConnectedValue\"}, \"inputFile|__identifier__\": \"SRR12733957\", \"optical_duplicate_pixel_distance\": \"100\", \"read_name_regex\": \"\", \"remove_duplicates\": \"true\", \"validation_stringency\": \"LENIENT\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.18.2.2",
+                        "type": "tool",
+                        "uuid": "8073c99c-1b22-4495-aa2e-35590ea8a27a",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "metrics_file",
+                                "uuid": "72b65822-0933-4ef0-af4b-7b863e79efa2"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outFile",
+                                "uuid": "5919b29b-d3eb-4ba5-9a77-b800e27d6a7d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "input": {
+                                "id": 6,
+                                "output_name": "outFile"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Samtools stats",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 237.5,
+                            "height": 112,
+                            "left": 957,
+                            "right": 1157,
+                            "top": 125.5,
+                            "width": 200,
+                            "x": 957,
+                            "y": 125.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "145f6d74ff5e",
+                            "name": "samtools_stats",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"bam\", \"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cov_threshold\": null, \"coverage_cond\": {\"coverage_select\": \"no\", \"__current_case__\": 0}, \"filter_by_flags\": {\"filter_flags\": \"nofilter\", \"__current_case__\": 1}, \"gc_depth\": null, \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"SRR12733957\", \"insert_size\": null, \"most_inserts\": null, \"read_length\": null, \"remove_dups\": \"false\", \"remove_overlaps\": \"false\", \"sparse\": \"false\", \"split_output_cond\": {\"split_output_selector\": \"no\", \"__current_case__\": 0}, \"trim_quality\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy2",
+                        "type": "tool",
+                        "uuid": "199dba34-fd3a-4a8c-9af8-96e51503689f",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "d9708b0c-194c-455a-ab8a-b99f09eed498"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "reads": {
+                                "id": 6,
+                                "output_name": "outFile"
+                            },
+                            "reference_source|ref": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Realign reads",
+                        "outputs": [
+                            {
+                                "name": "realigned",
+                                "type": "bam"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 1035.5,
+                            "height": 162,
+                            "left": 907,
+                            "right": 1107,
+                            "top": 873.5,
+                            "width": 200,
+                            "x": 907,
+                            "y": 873.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "aa35ee7f3ab2",
+                            "name": "lofreq_viterbi",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"adv_options\": {\"keepflags\": \"false\", \"bq2_handling\": {\"replace_bq2\": \"keep\", \"__current_case__\": 0, \"defqual\": \"2\"}}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"reads|__identifier__\": \"SRR12733957\", \"reference_source\": {\"ref_selector\": \"history\", \"__current_case__\": 1, \"ref\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.5+galaxy0",
+                        "type": "tool",
+                        "uuid": "53f949ab-b512-49a9-ac05-2ae2665431c2",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "realigned",
+                                "uuid": "7140df66-cd64-48aa-a7d4-ac916164a821"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {
+                            "results_0|software_cond|input": {
+                                "id": 3,
+                                "output_name": "report_json"
+                            },
+                            "results_1|software_cond|output_0|input": {
+                                "id": 6,
+                                "output_name": "metrics_file"
+                            },
+                            "results_2|software_cond|output_0|type|input": {
+                                "id": 7,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "MultiQC",
+                        "outputs": [
+                            {
+                                "name": "stats",
+                                "type": "input"
+                            },
+                            {
+                                "name": "plots",
                                 "type": "input"
+                            },
+                            {
+                                "name": "html_report",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 1133,
-                            "top": 208.2359999999986
+                            "bottom": 973.5,
+                            "height": 312,
+                            "left": 1329,
+                            "right": 1529,
+                            "top": 661.5,
+                            "width": 200,
+                            "x": 1329,
+                            "y": 661.5
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Top 5 exon IDs"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "5e33b465d8d5",
+                            "name": "multiqc",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"json\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"comment\": \"\", \"flat\": \"false\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 23, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"stats\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8+galaxy1",
+                        "type": "tool",
+                        "uuid": "69debef6-a98f-4c07-925b-37372e8be51e",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "stats",
+                                "uuid": "c2a695c7-b2ee-4331-89e4-82e23045d870"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "plots",
+                                "uuid": "2f5d878b-2876-4784-822e-82b438993704"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "html_report",
+                                "uuid": "e534aca7-9f10-4060-bbb7-e2b5e8717038"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {
+                            "reads": {
+                                "id": 8,
+                                "output_name": "realigned"
+                            },
+                            "strategy|reference_source|ref": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
-                        "tool_id": "comp1",
-                        "tool_state": "{\"field1\": \"4\", \"field2\": \"1\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"mode\": \"N\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Insert indel qualities",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "bam"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 314.5,
+                            "height": 142,
+                            "left": 1265,
+                            "right": 1465,
+                            "top": 172.5,
+                            "width": 200,
+                            "x": 1265,
+                            "y": 172.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "426d707dfc47",
+                            "name": "lofreq_indelqual",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"reads|__identifier__\": \"SRR12733957\", \"strategy\": {\"selector\": \"dindel\", \"__current_case__\": 1, \"reference_source\": {\"ref_selector\": \"history\", \"__current_case__\": 1, \"ref\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.5+galaxy0",
                         "type": "tool",
-                        "uuid": "52698c72-b6cc-4ca4-84b0-c84dd018e389",
-                        "when": null,
+                        "uuid": "cd5db03f-7831-426f-b76d-c285751a9e02",
                         "workflow_outputs": [
                             {
-                                "label": "top_5_exons",
-                                "output_name": "out_file1",
-                                "uuid": "565e3d76-0230-4a5e-87c1-9c36ce0b7df8"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "543fdf07-db60-437c-99fe-c06bfd010081"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "introduction/galaxy-intro-101",
-                "path": "topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow.ga",
-                "tags": [
-                    "introduction"
-                ],
-                "test_results": {
-                    "eu": {
-                        "summary": {
-                            "num_errors": 0,
-                            "num_failures": 0,
-                            "num_skips": 0,
-                            "num_tests": 1
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1",
+                        "errors": null,
+                        "id": 11,
+                        "input_connections": {
+                            "reads": {
+                                "id": 10,
+                                "output_name": "output"
+                            },
+                            "reference_source|ref": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Call variants",
+                        "outputs": [
+                            {
+                                "name": "variants",
+                                "type": "vcf"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 462.5,
+                            "height": 122,
+                            "left": 1470,
+                            "right": 1670,
+                            "top": 340.5,
+                            "width": 200,
+                            "x": 1470,
+                            "y": 340.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e1461b5c52a0",
+                            "name": "lofreq_call",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"call_control\": {\"set_call_options\": \"yes\", \"__current_case__\": 1, \"coverage\": {\"min_cov\": \"10\", \"max_depth\": \"1000000\"}, \"pe\": {\"use_orphan\": \"false\"}, \"bc_quals\": {\"min_bq\": \"20\", \"min_alt_bq\": \"20\", \"alt_bq\": {\"modify\": \"\", \"__current_case__\": 0}}, \"align_quals\": {\"alnqual\": {\"use_alnqual\": \"\", \"__current_case__\": 0, \"alnqual_choice\": {\"alnquals_to_use\": \"\", \"__current_case__\": 1, \"extended_baq\": \"true\"}}}, \"map_quals\": {\"min_mq\": \"20\", \"use_mq\": {\"no_mq\": \"\", \"__current_case__\": 0, \"max_mq\": \"255\"}}, \"source_qual\": {\"use_src_qual\": {\"src_qual\": \"\", \"__current_case__\": 0}}, \"joint_qual\": {\"min_jq\": \"0\", \"min_alt_jq\": \"0\", \"def_alt_jq\": \"0\"}}, \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"filter_control\": {\"filter_type\": \"set_lofreq_standard\", \"__current_case__\": 2, \"sig\": \"0.01\", \"bonf\": \"dynamic\", \"others\": \"\"}, \"reads\": {\"__class__\": \"ConnectedValue\"}, \"reads|__identifier__\": \"SRR12733957\", \"reference_source\": {\"ref_selector\": \"history\", \"__current_case__\": 1, \"ref\": {\"__class__\": \"ConnectedValue\"}}, \"regions\": {\"restrict_to_region\": \"genome\", \"__current_case__\": 0}, \"variant_types\": \"--call-indels\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "d332f810-2a7c-41bf-b458-05470d3ae6b5",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "variants",
+                                "uuid": "395a308b-d1ba-4c67-8b66-4e206c727a3c"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {
+                            "input": {
+                                "id": 11,
+                                "output_name": "variants"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "SnpEff eff:",
+                        "outputs": [
+                            {
+                                "name": "snpeff_output",
+                                "type": "vcf"
+                            },
+                            {
+                                "name": "statsFile",
+                                "type": "html"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 774.5,
+                            "height": 282,
+                            "left": 1624,
+                            "right": 1824,
+                            "top": 492.5,
+                            "width": 200,
+                            "x": 1624,
+                            "y": 492.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2a3a00c1fa0a",
+                            "name": "snpeff_sars_cov_2",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"vcf\", \"annotations\": [\"-formatEff\", \"-classic\"], \"chr\": \"\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"csvStats\": \"false\", \"filter\": {\"specificEffects\": \"no\", \"__current_case__\": 0}, \"filterOut\": null, \"generate_stats\": \"true\", \"genome_version\": \"NC_045512.2\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inputFormat\": \"vcf\", \"input|__identifier__\": \"SRR12733957\", \"intervals\": null, \"noLog\": \"true\", \"offset\": \"default\", \"outputConditional\": {\"outputFormat\": \"vcf\", \"__current_case__\": 0}, \"transcripts\": null, \"udLength\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.5covid19",
+                        "type": "tool",
+                        "uuid": "29a0aa67-7bce-4358-a349-cc58d9824dad",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "snpeff_output",
+                                "uuid": "69e5622c-db07-4e3c-8224-ed511d3ca7c7"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "statsFile",
+                                "uuid": "dafcfa74-d4d9-4d37-ae00-88ebce9acc14"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
+                        "errors": null,
+                        "id": 13,
+                        "input_connections": {
+                            "input": {
+                                "id": 12,
+                                "output_name": "snpeff_output"
+                            }
                         },
-                        "tests": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "SnpSift Extract Fields",
+                        "outputs": [
                             {
-                                "data": {
-                                    "end_datetime": "2023-05-18T19:40:47.480254",
-                                    "inputs": {
-                                        "Exons": {
-                                            "class": "File",
-                                            "filetype": "bed",
-                                            "location": "https://zenodo.org/record/4104428/files/UCSC-hg38-chr22-Coding-Exons.bed"
-                                        },
-                                        "Features": {
-                                            "class": "File",
-                                            "filetype": "bed",
-                                            "location": "https://zenodo.org/record/4104428/files/UCSC-hg38-chr22-dbSNP153-Whole-Gene-SNPs.bed"
-                                        }
-                                    },
-                                    "invocation_details": {
-                                        "details": {
-                                            "error_message": "",
-                                            "history_id": "a7e26bbbb0830b20",
-                                            "history_state": "ok",
-                                            "invocation_id": "4e6187ae89df9163",
-                                            "invocation_state": "scheduled",
-                                            "workflow_id": "b9fe010bdb910e56"
-                                        },
-                                        "steps": {
-                                            "0. Exons": {
-                                                "action": null,
-                                                "id": "137fffe5e92f37af",
-                                                "job_id": null,
-                                                "jobs": [],
-                                                "model_class": "WorkflowInvocationStep",
-                                                "order_index": 0,
-                                                "output_collections": {},
-                                                "outputs": {
-                                                    "output": {
-                                                        "id": "4838ba20a6d86765828ccbcc3eb28a4b",
-                                                        "src": "hda",
-                                                        "uuid": "cfb71055-95ff-4a95-9e0b-7a48161d5d0c"
-                                                    }
-                                                },
-                                                "state": "scheduled",
-                                                "subworkflow": null,
-                                                "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-18T17:34:36.117311",
-                                                "workflow_step_id": "47c79ce5a092d365",
-                                                "workflow_step_label": "Exons",
-                                                "workflow_step_uuid": "bd3df190-bc2c-4432-a534-7b1b21cd58c9"
-                                            },
-                                            "1. Features": {
-                                                "action": null,
-                                                "id": "3ea99854c46ce445",
-                                                "job_id": null,
-                                                "jobs": [],
-                                                "model_class": "WorkflowInvocationStep",
-                                                "order_index": 1,
-                                                "output_collections": {},
-                                                "outputs": {
-                                                    "output": {
-                                                        "id": "4838ba20a6d867653f5bd69298cf67f1",
-                                                        "src": "hda",
-                                                        "uuid": "f94e7844-204e-42a8-83e0-23adc4ca038b"
-                                                    }
-                                                },
-                                                "state": "scheduled",
-                                                "subworkflow": null,
-                                                "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-18T17:34:36.117314",
-                                                "workflow_step_id": "7624b0f83c340c3d",
-                                                "workflow_step_label": "Features",
-                                                "workflow_step_uuid": "b7b8e25f-8db4-4707-bfb9-9e5a527e28c3"
-                                            },
-                                            "2. Unnamed step": {
-                                                "action": null,
-                                                "id": "53d44f7f08b165d4",
-                                                "job_id": "11ac94870d0bb33a3743b59ce7fc28ea",
-                                                "jobs": [
-                                                    {
-                                                        "command_line": "bedtools intersect -a '/data/dnb08/galaxy_db/files/c/f/b/dataset_cfb71055-95ff-4a95-9e0b-7a48161d5d0c.dat'  -b '/data/dnb08/galaxy_db/files/f/9/4/dataset_f94e7844-204e-42a8-83e0-23adc4ca038b.dat'      -wb          > '/data/jwd05e/main/060/036/60036240/outputs/galaxy_dataset_1dbd5467-7362-4279-8f9f-225c450392c4.dat'",
-                                                        "command_version": "bedtools v2.30.0",
-                                                        "create_time": "2023-05-18T17:34:36.114094",
-                                                        "dependencies": [],
-                                                        "exit_code": 0,
-                                                        "external_id": "43511676",
-                                                        "galaxy_version": "23.0",
-                                                        "history_id": "a7e26bbbb0830b20",
-                                                        "id": "11ac94870d0bb33a3743b59ce7fc28ea",
-                                                        "inputs": {
-                                                            "inputA": {
-                                                                "id": "4838ba20a6d86765828ccbcc3eb28a4b",
-                                                                "src": "hda",
-                                                                "uuid": "cfb71055-95ff-4a95-9e0b-7a48161d5d0c"
-                                                            },
-                                                            "inputB": {
-                                                                "id": "4838ba20a6d867653f5bd69298cf67f1",
-                                                                "src": "hda",
-                                                                "uuid": "f94e7844-204e-42a8-83e0-23adc4ca038b"
-                                                            }
-                                                        },
-                                                        "job_messages": [],
-                                                        "job_metrics": [
-                                                            {
-                                                                "name": "hostname",
-                                                                "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c36m975-6047.novalocal",
-                                                                "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c36m975-6047.novalocal"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_slots",
-                                                                "plugin": "core",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "Cores Allocated",
-                                                                "value": "1"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_memory_mb",
-                                                                "plugin": "core",
-                                                                "raw_value": "40960.0000000",
-                                                                "title": "Memory Allocated (MB)",
-                                                                "value": "40960"
-                                                            },
-                                                            {
-                                                                "name": "start_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684431305.0000000",
-                                                                "title": "Job Start Time",
-                                                                "value": "2023-05-18 19:35:05"
-                                                            },
-                                                            {
-                                                                "name": "end_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684431327.0000000",
-                                                                "title": "Job End Time",
-                                                                "value": "2023-05-18 19:35:27"
-                                                            },
-                                                            {
-                                                                "name": "runtime_seconds",
-                                                                "plugin": "core",
-                                                                "raw_value": "22.0000000",
-                                                                "title": "Job Runtime (Wall Clock)",
-                                                                "value": "22 seconds"
-                                                            },
-                                                            {
-                                                                "name": "cpuacct.usage",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "10840959112.0000000",
-                                                                "title": "CPU Time",
-                                                                "value": "10.840959112 seconds"
-                                                            },
-                                                            {
-                                                                "name": "memory.failcnt",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Failed to allocate memory count",
-                                                                "value": 0.0
-                                                            },
-                                                            {
-                                                                "name": "memory.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "41201008640.0000000",
-                                                                "title": "Memory limit on cgroup (MEM)",
-                                                                "value": "38.4 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "200916992.0000000",
-                                                                "title": "Max memory usage (MEM)",
-                                                                "value": "191.6 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "41201012736.0000000",
-                                                                "title": "Memory limit on cgroup (MEM+SWP)",
-                                                                "value": "38.4 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "200916992.0000000",
-                                                                "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "191.6 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.oom_kill_disable",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "OOM Control enabled",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.under_oom",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Was OOM Killer active?",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.soft_limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "42949672960.0000000",
-                                                                "title": "Memory softlimit on cgroup",
-                                                                "value": "40.0 GB"
-                                                            }
-                                                        ],
-                                                        "job_stderr": "",
-                                                        "job_stdout": "",
-                                                        "model_class": "Job",
-                                                        "output_collections": {},
-                                                        "outputs": {
-                                                            "output": {
-                                                                "id": "4838ba20a6d86765192446f033baed74",
-                                                                "src": "hda",
-                                                                "uuid": "1dbd5467-7362-4279-8f9f-225c450392c4"
-                                                            }
-                                                        },
-                                                        "params": {
-                                                            "__input_ext": "\"input\"",
-                                                            "__workflow_invocation_uuid__": "\"389e354ef5a211eda9c3001e67d2ec02\"",
-                                                            "bed": "false",
-                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
-                                                            "count": "false",
-                                                            "dbkey": "\"?\"",
-                                                            "fraction_cond": "{\"__current_case__\": 0, \"fraction_select\": \"default\"}",
-                                                            "genome_file_opts": "{\"__current_case__\": 0, \"genome\": null, \"genome_file_opts_selector\": \"loc\"}",
-                                                            "header": "false",
-                                                            "invert": "false",
-                                                            "once": "false",
-                                                            "overlap_mode": "[\"-wb\"]",
-                                                            "reduce_or_iterate": "{\"__current_case__\": 0, \"inputB\": {\"values\": [{\"id\": 137365408, \"src\": \"hda\"}]}, \"reduce_or_iterate_selector\": \"iterate\"}",
-                                                            "sorted": "false",
-                                                            "split": "false",
-                                                            "strand": "\"\""
-                                                        },
-                                                        "state": "ok",
-                                                        "stderr": "",
-                                                        "stdout": "",
-                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0",
-                                                        "tool_stderr": "",
-                                                        "tool_stdout": "",
-                                                        "traceback": null,
-                                                        "update_time": "2023-05-18T17:35:28.719729",
-                                                        "user_email": "hxr@informatik.uni-freiburg.de"
-                                                    }
-                                                ],
-                                                "model_class": "WorkflowInvocationStep",
-                                                "order_index": 2,
-                                                "output_collections": {},
-                                                "outputs": {
-                                                    "output": {
-                                                        "id": "4838ba20a6d86765192446f033baed74",
-                                                        "src": "hda",
-                                                        "uuid": "1dbd5467-7362-4279-8f9f-225c450392c4"
-                                                    }
-                                                },
-                                                "state": "scheduled",
-                                                "subworkflow": null,
-                                                "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-18T17:35:28.700947",
-                                                "workflow_step_id": "0fe8e8a22ac078c9",
-                                                "workflow_step_label": null,
-                                                "workflow_step_uuid": "4fc2b17c-64d8-4c1c-a2d3-743f2ea9bcaf"
-                                            },
-                                            "3. Unnamed step": {
-                                                "action": null,
-                                                "id": "e6d3f79a3a3a71b2",
-                                                "job_id": "11ac94870d0bb33a8e9e3c167a533b1b",
-                                                "jobs": [
-                                                    {
-                                                        "command_line": "datamash      --group '4' countunique 10 < /data/dnb08/galaxy_db/files/1/d/b/dataset_1dbd5467-7362-4279-8f9f-225c450392c4.dat > '/data/jwd02f/main/060/036/60036241/outputs/galaxy_dataset_599c420f-e56b-4499-bf0e-16044fafff18.dat'",
-                                                        "command_version": null,
-                                                        "create_time": "2023-05-18T17:34:36.233576",
-                                                        "dependencies": [],
-                                                        "exit_code": 0,
-                                                        "external_id": "43511710",
-                                                        "galaxy_version": "23.0",
-                                                        "history_id": "a7e26bbbb0830b20",
-                                                        "id": "11ac94870d0bb33a8e9e3c167a533b1b",
-                                                        "inputs": {
-                                                            "in_file": {
-                                                                "id": "4838ba20a6d86765192446f033baed74",
-                                                                "src": "hda",
-                                                                "uuid": "1dbd5467-7362-4279-8f9f-225c450392c4"
-                                                            }
-                                                        },
-                                                        "job_messages": [],
-                                                        "job_metrics": [
-                                                            {
-                                                                "name": "hostname",
-                                                                "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c36m100-0658.novalocal",
-                                                                "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c36m100-0658.novalocal"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_slots",
-                                                                "plugin": "core",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "Cores Allocated",
-                                                                "value": "1"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_memory_mb",
-                                                                "plugin": "core",
-                                                                "raw_value": "3891.0000000",
-                                                                "title": "Memory Allocated (MB)",
-                                                                "value": "3891"
-                                                            },
-                                                            {
-                                                                "name": "start_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684431348.0000000",
-                                                                "title": "Job Start Time",
-                                                                "value": "2023-05-18 19:35:48"
-                                                            },
-                                                            {
-                                                                "name": "end_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684431390.0000000",
-                                                                "title": "Job End Time",
-                                                                "value": "2023-05-18 19:36:30"
-                                                            },
-                                                            {
-                                                                "name": "runtime_seconds",
-                                                                "plugin": "core",
-                                                                "raw_value": "42.0000000",
-                                                                "title": "Job Runtime (Wall Clock)",
-                                                                "value": "42 seconds"
-                                                            },
-                                                            {
-                                                                "name": "cpuacct.usage",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "9364859094.0000000",
-                                                                "title": "CPU Time",
-                                                                "value": "9.364859094 seconds"
-                                                            },
-                                                            {
-                                                                "name": "memory.failcnt",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Failed to allocate memory count",
-                                                                "value": 0.0
-                                                            },
-                                                            {
-                                                                "name": "memory.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "4160749568.0000000",
-                                                                "title": "Memory limit on cgroup (MEM)",
-                                                                "value": "3.9 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "191201280.0000000",
-                                                                "title": "Max memory usage (MEM)",
-                                                                "value": "182.3 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "4219351040.0000000",
-                                                                "title": "Memory limit on cgroup (MEM+SWP)",
-                                                                "value": "3.9 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "191201280.0000000",
-                                                                "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "182.3 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.oom_kill_disable",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "OOM Control enabled",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.under_oom",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Was OOM Killer active?",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.soft_limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Memory softlimit on cgroup",
-                                                                "value": "0 bytes"
-                                                            }
-                                                        ],
-                                                        "job_stderr": "",
-                                                        "job_stdout": "",
-                                                        "model_class": "Job",
-                                                        "output_collections": {},
-                                                        "outputs": {
-                                                            "out_file": {
-                                                                "id": "4838ba20a6d86765a402038d0b9964e3",
-                                                                "src": "hda",
-                                                                "uuid": "599c420f-e56b-4499-bf0e-16044fafff18"
-                                                            }
-                                                        },
-                                                        "params": {
-                                                            "__input_ext": "\"bed\"",
-                                                            "__workflow_invocation_uuid__": "\"389e354ef5a211eda9c3001e67d2ec02\"",
-                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
-                                                            "dbkey": "\"?\"",
-                                                            "grouping": "\"4\"",
-                                                            "header_in": "false",
-                                                            "header_out": "false",
-                                                            "ignore_case": "false",
-                                                            "need_sort": "false",
-                                                            "operations": "[{\"__index__\": 0, \"op_column\": \"10\", \"op_name\": \"countunique\"}]",
-                                                            "print_full_line": "false"
-                                                        },
-                                                        "state": "ok",
-                                                        "stderr": "",
-                                                        "stdout": "",
-                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
-                                                        "tool_stderr": "",
-                                                        "tool_stdout": "",
-                                                        "traceback": null,
-                                                        "update_time": "2023-05-18T17:36:33.513106",
-                                                        "user_email": "hxr@informatik.uni-freiburg.de"
-                                                    }
-                                                ],
-                                                "model_class": "WorkflowInvocationStep",
-                                                "order_index": 3,
-                                                "output_collections": {},
-                                                "outputs": {
-                                                    "out_file": {
-                                                        "id": "4838ba20a6d86765a402038d0b9964e3",
-                                                        "src": "hda",
-                                                        "uuid": "599c420f-e56b-4499-bf0e-16044fafff18"
-                                                    }
-                                                },
-                                                "state": "scheduled",
-                                                "subworkflow": null,
-                                                "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-18T17:36:33.486731",
-                                                "workflow_step_id": "fcac47089ebdfbc2",
-                                                "workflow_step_label": null,
-                                                "workflow_step_uuid": "d6710e24-dbfb-4aef-8a63-2836cdc831e4"
-                                            },
-                                            "4. Unnamed step": {
-                                                "action": null,
-                                                "id": "0a5ce27d3453ffc8",
-                                                "job_id": "11ac94870d0bb33aa0e24ffdcb66ba6f",
-                                                "jobs": [
-                                                    {
-                                                        "command_line": "python '/opt/galaxy/server/tools/filters/sorter.py'  --input='/data/dnb08/galaxy_db/files/5/9/9/dataset_599c420f-e56b-4499-bf0e-16044fafff18.dat' --output='/data/jwd05e/main/060/036/60036242/outputs/galaxy_dataset_c8b6796e-41f3-41de-9a94-82a3e7c388b7.dat'    --key=2,2nr   --header 0",
-                                                        "command_version": null,
-                                                        "create_time": "2023-05-18T17:34:36.326397",
-                                                        "dependencies": [],
-                                                        "exit_code": 0,
-                                                        "external_id": "43511741",
-                                                        "galaxy_version": "23.0",
-                                                        "history_id": "a7e26bbbb0830b20",
-                                                        "id": "11ac94870d0bb33aa0e24ffdcb66ba6f",
-                                                        "inputs": {
-                                                            "input": {
-                                                                "id": "4838ba20a6d86765a402038d0b9964e3",
-                                                                "src": "hda",
-                                                                "uuid": "599c420f-e56b-4499-bf0e-16044fafff18"
-                                                            }
-                                                        },
-                                                        "job_messages": [],
-                                                        "job_metrics": [
-                                                            {
-                                                                "name": "hostname",
-                                                                "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c36m100-0658.novalocal",
-                                                                "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c36m100-0658.novalocal"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_slots",
-                                                                "plugin": "core",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "Cores Allocated",
-                                                                "value": "1"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_memory_mb",
-                                                                "plugin": "core",
-                                                                "raw_value": "3891.0000000",
-                                                                "title": "Memory Allocated (MB)",
-                                                                "value": "3891"
-                                                            },
-                                                            {
-                                                                "name": "start_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684431414.0000000",
-                                                                "title": "Job Start Time",
-                                                                "value": "2023-05-18 19:36:54"
-                                                            },
-                                                            {
-                                                                "name": "end_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684431461.0000000",
-                                                                "title": "Job End Time",
-                                                                "value": "2023-05-18 19:37:41"
-                                                            },
-                                                            {
-                                                                "name": "runtime_seconds",
-                                                                "plugin": "core",
-                                                                "raw_value": "47.0000000",
-                                                                "title": "Job Runtime (Wall Clock)",
-                                                                "value": "47 seconds"
-                                                            },
-                                                            {
-                                                                "name": "cpuacct.usage",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "9815575101.0000000",
-                                                                "title": "CPU Time",
-                                                                "value": "9.815575101 seconds"
-                                                            },
-                                                            {
-                                                                "name": "memory.failcnt",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Failed to allocate memory count",
-                                                                "value": 0.0
-                                                            },
-                                                            {
-                                                                "name": "memory.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "4160749568.0000000",
-                                                                "title": "Memory limit on cgroup (MEM)",
-                                                                "value": "3.9 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "196067328.0000000",
-                                                                "title": "Max memory usage (MEM)",
-                                                                "value": "187.0 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "4219351040.0000000",
-                                                                "title": "Memory limit on cgroup (MEM+SWP)",
-                                                                "value": "3.9 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "196067328.0000000",
-                                                                "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "187.0 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.oom_kill_disable",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "OOM Control enabled",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.under_oom",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Was OOM Killer active?",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.soft_limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Memory softlimit on cgroup",
-                                                                "value": "0 bytes"
-                                                            }
-                                                        ],
-                                                        "job_stderr": "",
-                                                        "job_stdout": "",
-                                                        "model_class": "Job",
-                                                        "output_collections": {},
-                                                        "outputs": {
-                                                            "out_file1": {
-                                                                "id": "4838ba20a6d867650b679d679c1fbabd",
-                                                                "src": "hda",
-                                                                "uuid": "c8b6796e-41f3-41de-9a94-82a3e7c388b7"
-                                                            }
-                                                        },
-                                                        "params": {
-                                                            "__input_ext": "\"tabular\"",
-                                                            "__workflow_invocation_uuid__": "\"389e354ef5a211eda9c3001e67d2ec02\"",
-                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
-                                                            "column": "\"2\"",
-                                                            "column_set": "[]",
-                                                            "dbkey": "\"?\"",
-                                                            "header_lines": "\"0\"",
-                                                            "order": "\"DESC\"",
-                                                            "style": "\"num\""
-                                                        },
-                                                        "state": "ok",
-                                                        "stderr": "",
-                                                        "stdout": "",
-                                                        "tool_id": "sort1",
-                                                        "tool_stderr": "",
-                                                        "tool_stdout": "",
-                                                        "traceback": null,
-                                                        "update_time": "2023-05-18T17:37:45.740051",
-                                                        "user_email": "hxr@informatik.uni-freiburg.de"
-                                                    }
-                                                ],
-                                                "model_class": "WorkflowInvocationStep",
-                                                "order_index": 4,
-                                                "output_collections": {},
-                                                "outputs": {
-                                                    "out_file1": {
-                                                        "id": "4838ba20a6d867650b679d679c1fbabd",
-                                                        "src": "hda",
-                                                        "uuid": "c8b6796e-41f3-41de-9a94-82a3e7c388b7"
-                                                    }
-                                                },
-                                                "state": "scheduled",
-                                                "subworkflow": null,
-                                                "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-18T17:37:45.722567",
-                                                "workflow_step_id": "e42696dd961f95d2",
-                                                "workflow_step_label": null,
-                                                "workflow_step_uuid": "4dd35991-4996-4f7d-8690-bde783f6fa6a"
-                                            },
-                                            "5. Unnamed step": {
-                                                "action": null,
-                                                "id": "06226aff05ce5d1f",
-                                                "job_id": "11ac94870d0bb33ad12002ce0209213b",
-                                                "jobs": [
-                                                    {
-                                                        "command_line": "head --lines 5 '/data/dnb08/galaxy_db/files/c/8/b/dataset_c8b6796e-41f3-41de-9a94-82a3e7c388b7.dat' > '/data/jwd05e/main/060/036/60036243/outputs/galaxy_dataset_2828298d-dc7b-431b-bf03-3f6955f19dc1.dat'",
-                                                        "command_version": "head (GNU coreutils) 8.25",
-                                                        "create_time": "2023-05-18T17:34:36.414517",
-                                                        "dependencies": [],
-                                                        "exit_code": 0,
-                                                        "external_id": "43511785",
-                                                        "galaxy_version": "23.0",
-                                                        "history_id": "a7e26bbbb0830b20",
-                                                        "id": "11ac94870d0bb33ad12002ce0209213b",
-                                                        "inputs": {
-                                                            "infile": {
-                                                                "id": "4838ba20a6d867650b679d679c1fbabd",
-                                                                "src": "hda",
-                                                                "uuid": "c8b6796e-41f3-41de-9a94-82a3e7c388b7"
-                                                            }
-                                                        },
-                                                        "job_messages": [],
-                                                        "job_metrics": [
-                                                            {
-                                                                "name": "hostname",
-                                                                "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c28m475-9359.novalocal",
-                                                                "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c28m475-9359.novalocal"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_slots",
-                                                                "plugin": "core",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "Cores Allocated",
-                                                                "value": "1"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_memory_mb",
-                                                                "plugin": "core",
-                                                                "raw_value": "3891.0000000",
-                                                                "title": "Memory Allocated (MB)",
-                                                                "value": "3891"
-                                                            },
-                                                            {
-                                                                "name": "start_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684431479.0000000",
-                                                                "title": "Job Start Time",
-                                                                "value": "2023-05-18 19:37:59"
-                                                            },
-                                                            {
-                                                                "name": "end_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684431577.0000000",
-                                                                "title": "Job End Time",
-                                                                "value": "2023-05-18 19:39:37"
-                                                            },
-                                                            {
-                                                                "name": "runtime_seconds",
-                                                                "plugin": "core",
-                                                                "raw_value": "98.0000000",
-                                                                "title": "Job Runtime (Wall Clock)",
-                                                                "value": "1 minute"
-                                                            },
-                                                            {
-                                                                "name": "cpuacct.usage",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "160336864240.0000000",
-                                                                "title": "CPU Time",
-                                                                "value": "2 minutes"
-                                                            },
-                                                            {
-                                                                "name": "memory.failcnt",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "106968.0000000",
-                                                                "title": "Failed to allocate memory count",
-                                                                "value": 106968.0
-                                                            },
-                                                            {
-                                                                "name": "memory.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "4160749568.0000000",
-                                                                "title": "Memory limit on cgroup (MEM)",
-                                                                "value": "3.9 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "4160749568.0000000",
-                                                                "title": "Max memory usage (MEM)",
-                                                                "value": "3.9 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "9223372036854771712.0000000",
-                                                                "title": "Memory limit on cgroup (MEM+SWP)",
-                                                                "value": "8.0 EB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "4160880640.0000000",
-                                                                "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "3.9 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.oom_kill_disable",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "OOM Control enabled",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.under_oom",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Was OOM Killer active?",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.soft_limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Memory softlimit on cgroup",
-                                                                "value": "0 bytes"
-                                                            }
-                                                        ],
-                                                        "job_stderr": "",
-                                                        "job_stdout": "",
-                                                        "model_class": "Job",
-                                                        "output_collections": {},
-                                                        "outputs": {
-                                                            "outfile": {
-                                                                "id": "4838ba20a6d86765d96edf23a7ca38c5",
-                                                                "src": "hda",
-                                                                "uuid": "2828298d-dc7b-431b-bf03-3f6955f19dc1"
-                                                            }
-                                                        },
-                                                        "params": {
-                                                            "__input_ext": "\"tabular\"",
-                                                            "__workflow_invocation_uuid__": "\"389e354ef5a211eda9c3001e67d2ec02\"",
-                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
-                                                            "complement": "\"\"",
-                                                            "count": "\"5\"",
-                                                            "dbkey": "\"?\""
-                                                        },
-                                                        "state": "ok",
-                                                        "stderr": "",
-                                                        "stdout": "",
-                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0",
-                                                        "tool_stderr": "",
-                                                        "tool_stdout": "",
-                                                        "traceback": null,
-                                                        "update_time": "2023-05-18T17:39:41.632086",
-                                                        "user_email": "hxr@informatik.uni-freiburg.de"
-                                                    }
-                                                ],
-                                                "model_class": "WorkflowInvocationStep",
-                                                "order_index": 5,
-                                                "output_collections": {},
-                                                "outputs": {
-                                                    "outfile": {
-                                                        "id": "4838ba20a6d86765d96edf23a7ca38c5",
-                                                        "src": "hda",
-                                                        "uuid": "2828298d-dc7b-431b-bf03-3f6955f19dc1"
-                                                    }
-                                                },
-                                                "state": "scheduled",
-                                                "subworkflow": null,
-                                                "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-18T17:39:41.615934",
-                                                "workflow_step_id": "4c5e84542536cc7c",
-                                                "workflow_step_label": null,
-                                                "workflow_step_uuid": "820fd964-2460-4b50-8491-968d796500fc"
-                                            },
-                                            "6. Unnamed step": {
-                                                "action": null,
-                                                "id": "9869e0dcfb157198",
-                                                "job_id": "11ac94870d0bb33a1d0bbfc0189b52a3",
-                                                "jobs": [
-                                                    {
-                                                        "command_line": "python /opt/galaxy/server/tools/filters/joinWrapper.py /data/dnb08/galaxy_db/files/c/f/b/dataset_cfb71055-95ff-4a95-9e0b-7a48161d5d0c.dat /data/dnb08/galaxy_db/files/2/8/2/dataset_2828298d-dc7b-431b-bf03-3f6955f19dc1.dat 4 1 N /data/jwd02f/main/060/036/60036244/outputs/galaxy_dataset_1c27a522-57c3-4dd6-a98b-2978def89473.dat",
-                                                        "command_version": null,
-                                                        "create_time": "2023-05-18T17:34:36.507964",
-                                                        "dependencies": [],
-                                                        "exit_code": 0,
-                                                        "external_id": "43511832",
-                                                        "galaxy_version": "23.0",
-                                                        "history_id": "a7e26bbbb0830b20",
-                                                        "id": "11ac94870d0bb33a1d0bbfc0189b52a3",
-                                                        "inputs": {
-                                                            "input1": {
-                                                                "id": "4838ba20a6d86765828ccbcc3eb28a4b",
-                                                                "src": "hda",
-                                                                "uuid": "cfb71055-95ff-4a95-9e0b-7a48161d5d0c"
-                                                            },
-                                                            "input2": {
-                                                                "id": "4838ba20a6d86765d96edf23a7ca38c5",
-                                                                "src": "hda",
-                                                                "uuid": "2828298d-dc7b-431b-bf03-3f6955f19dc1"
-                                                            }
-                                                        },
-                                                        "job_messages": [],
-                                                        "job_metrics": [
-                                                            {
-                                                                "name": "hostname",
-                                                                "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c36m100-0658.novalocal",
-                                                                "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c36m100-0658.novalocal"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_slots",
-                                                                "plugin": "core",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "Cores Allocated",
-                                                                "value": "1"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_memory_mb",
-                                                                "plugin": "core",
-                                                                "raw_value": "3891.0000000",
-                                                                "title": "Memory Allocated (MB)",
-                                                                "value": "3891"
-                                                            },
-                                                            {
-                                                                "name": "start_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684431607.0000000",
-                                                                "title": "Job Start Time",
-                                                                "value": "2023-05-18 19:40:07"
-                                                            },
-                                                            {
-                                                                "name": "end_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684431645.0000000",
-                                                                "title": "Job End Time",
-                                                                "value": "2023-05-18 19:40:45"
-                                                            },
-                                                            {
-                                                                "name": "runtime_seconds",
-                                                                "plugin": "core",
-                                                                "raw_value": "38.0000000",
-                                                                "title": "Job Runtime (Wall Clock)",
-                                                                "value": "38 seconds"
-                                                            },
-                                                            {
-                                                                "name": "cpuacct.usage",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "9278612295.0000000",
-                                                                "title": "CPU Time",
-                                                                "value": "9.278612295 seconds"
-                                                            },
-                                                            {
-                                                                "name": "memory.failcnt",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Failed to allocate memory count",
-                                                                "value": 0.0
-                                                            },
-                                                            {
-                                                                "name": "memory.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "4160749568.0000000",
-                                                                "title": "Memory limit on cgroup (MEM)",
-                                                                "value": "3.9 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "191029248.0000000",
-                                                                "title": "Max memory usage (MEM)",
-                                                                "value": "182.2 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "4219351040.0000000",
-                                                                "title": "Memory limit on cgroup (MEM+SWP)",
-                                                                "value": "3.9 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "191029248.0000000",
-                                                                "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "182.2 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.oom_kill_disable",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "OOM Control enabled",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.under_oom",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Was OOM Killer active?",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.soft_limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Memory softlimit on cgroup",
-                                                                "value": "0 bytes"
-                                                            }
-                                                        ],
-                                                        "job_stderr": "",
-                                                        "job_stdout": "",
-                                                        "model_class": "Job",
-                                                        "output_collections": {},
-                                                        "outputs": {
-                                                            "out_file1": {
-                                                                "id": "4838ba20a6d8676569e7a7744709f3b7",
-                                                                "src": "hda",
-                                                                "uuid": "1c27a522-57c3-4dd6-a98b-2978def89473"
-                                                            }
-                                                        },
-                                                        "params": {
-                                                            "__input_ext": "\"bed\"",
-                                                            "__workflow_invocation_uuid__": "\"389e354ef5a211eda9c3001e67d2ec02\"",
-                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
-                                                            "dbkey": "\"?\"",
-                                                            "field1": "\"4\"",
-                                                            "field2": "\"1\"",
-                                                            "mode": "\"N\""
-                                                        },
-                                                        "state": "ok",
-                                                        "stderr": "",
-                                                        "stdout": "join (GNU coreutils) 8.30\nCopyright (C) 2018 Free Software Foundation, Inc.\nLicense GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.\nThis is free software: you are free to change and redistribute it.\nThere is NO WARRANTY, to the extent permitted by law.\n\nWritten by Mike Haertel.\n",
-                                                        "tool_id": "comp1",
-                                                        "tool_stderr": "",
-                                                        "tool_stdout": "join (GNU coreutils) 8.30\nCopyright (C) 2018 Free Software Foundation, Inc.\nLicense GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.\nThis is free software: you are free to change and redistribute it.\nThere is NO WARRANTY, to the extent permitted by law.\n\nWritten by Mike Haertel.\n",
-                                                        "traceback": null,
-                                                        "update_time": "2023-05-18T17:40:47.707639",
-                                                        "user_email": "hxr@informatik.uni-freiburg.de"
-                                                    }
-                                                ],
-                                                "model_class": "WorkflowInvocationStep",
-                                                "order_index": 6,
-                                                "output_collections": {},
-                                                "outputs": {
-                                                    "out_file1": {
-                                                        "id": "4838ba20a6d8676569e7a7744709f3b7",
-                                                        "src": "hda",
-                                                        "uuid": "1c27a522-57c3-4dd6-a98b-2978def89473"
-                                                    }
-                                                },
-                                                "state": "scheduled",
-                                                "subworkflow": null,
-                                                "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-18T17:40:47.686290",
-                                                "workflow_step_id": "70e011a3c2da60d6",
-                                                "workflow_step_label": null,
-                                                "workflow_step_uuid": "52698c72-b6cc-4ca4-84b0-c84dd018e389"
-                                            }
-                                        }
-                                    },
-                                    "problem_log": "No log for this engine type.",
-                                    "start_datetime": "2023-05-18T19:32:20.395205",
-                                    "status": "success"
-                                },
-                                "doc": "Test sample data for the workflow",
-                                "has_data": true,
-                                "id": "galaxy-intro-101-workflow.ga_0",
-                                "test_type": "galaxy_workflow"
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 919.5,
+                            "height": 132,
+                            "left": 1768,
+                            "right": 1968,
+                            "top": 787.5,
+                            "width": 200,
+                            "x": 1768,
+                            "y": 787.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2e497a770bca",
+                            "name": "snpsift",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"vcf\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"empty_text\": \"\", \"extract\": \"CHROM POS FILTER REF ALT QUAL DP AF SB DP4 EFF[*].IMPACT EFF[*].FUNCLASS EFF[*].EFFECT EFF[*].GENE EFF[*].CODON\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"SRR12733957\", \"one_effect_per_line\": \"true\", \"separator\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.3+t.galaxy0",
+                        "type": "tool",
+                        "uuid": "b4c123bb-5bf2-481b-ab0c-f23be0d7f0d3",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "971988f2-f007-4394-b749-45996031dc5e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
+                        "errors": null,
+                        "id": 14,
+                        "input_connections": {
+                            "input_list": {
+                                "id": 13,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Collapse Collection",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "input"
                             }
                         ],
-                        "version": "0.1"
+                        "position": {
+                            "bottom": 1125.5,
+                            "height": 132,
+                            "left": 1928,
+                            "right": 2128,
+                            "top": 993.5,
+                            "width": 200,
+                            "x": 1928,
+                            "y": 993.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "90981f86000f",
+                            "name": "collapse_collections",
+                            "owner": "nml",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"filename\": {\"add_name\": \"true\", \"__current_case__\": 0, \"place_name\": \"same_multiple\"}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.1.0",
+                        "type": "tool",
+                        "uuid": "be8eb89a-e88f-431c-9bd9-be2aa33b1671",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "756bd26f-ad93-4187-b294-358bdd455962"
+                            }
+                        ]
                     }
-                },
-                "tests": true,
-                "title": "Find exons with the highest number of features",
+                ],
+                "parent_id": "introduction/galaxy-intro-ngs-data-managment",
+                "path": "topics/introduction/tutorials/galaxy-intro-ngs-data-managment/workflows/ngs_intro_workflow.ga",
+                "tags": [
+                    "introductions"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "NGS_tutorial",
                 "topic_id": "introduction",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/introduction-galaxy-intro-101/versions/galaxy-intro-101-workflow",
-                "tutorial_id": "galaxy-intro-101",
-                "url": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow.html",
-                "version": 5,
-                "wfid": "introduction-galaxy-intro-101",
-                "wfname": "galaxy-intro-101-workflow",
-                "workflow": "galaxy-intro-101-workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/introduction-galaxy-intro-ngs-data-managment/versions/ngs-intro-workflow",
+                "tutorial_id": "galaxy-intro-ngs-data-managment",
+                "url": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/workflows/ngs_intro_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/workflows/ngs_intro_workflow.html",
+                "version": 1,
+                "wfid": "introduction-galaxy-intro-ngs-data-managment",
+                "wfname": "ngs-intro-workflow",
+                "workflow": "ngs_intro_workflow.ga",
                 "workflow_tools": [
-                    "comp1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0"
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.8+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
                 ],
-                "workflowhub_id": "1106"
+                "workflowhub_id": "1115"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.4104428"
+        "zenodo_link": ""
     },
     {
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "datamash_ops",
-                    "owner": "iuc",
-                    "revisions": "562f3c677828",
-                    "tool_panel_section_label": "Join, Subtract and Group",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ggplot2_point",
-                    "owner": "iuc",
-                    "revisions": "1acf88921176",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
+            "tools": []
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 562f3c677828\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ggplot2_point\n  owner: iuc\n  revisions: 1acf88921176\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/introduction/tutorial.json",
         "contributors": [
+            {
+                "email": "andrea.bagnacani@gmail.com",
+                "id": "bagnacan",
+                "joined": "2017-10",
+                "name": "Andrea Bagnacani",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bagnacan/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bagnacan.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
+            {
+                "id": "pajanne",
+                "joined": "2017-09",
+                "name": "Anne Pajon",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pajanne/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pajanne.json"
+            },
+            {
+                "affiliations": [
+                    "earlham",
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "fediverse": "https://mstdn.science/@nsoranzo",
+                "fediverse_flavor": "mastodon",
+                "id": "nsoranzo",
+                "joined": "2017-09",
+                "linkedin": "nicola-soranzo-7884125",
+                "matrix": "nsoranzo:matrix.org",
+                "name": "Nicola Soranzo",
+                "orcid": "0000-0003-3627-5340",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
+                "twitter": "NicolaSoranzo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "id": "chrisbarnettster",
+                "joined": "2019-05",
+                "name": "Christopher Barnett",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/chrisbarnettster/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/chrisbarnettster.json"
+            },
+            {
+                "id": "michelemaroni89",
+                "joined": "2019-07",
+                "name": "Michele Maroni",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/michelemaroni89/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/michelemaroni89.json"
+            },
             {
                 "elixir_node": "no",
                 "id": "annefou",
@@ -130168,20 +132032,6 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nagoue/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/nagoue.json"
             },
-            {
-                "id": "chrisbarnettster",
-                "joined": "2019-05",
-                "name": "Christopher Barnett",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/chrisbarnettster/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/chrisbarnettster.json"
-            },
-            {
-                "id": "michelemaroni89",
-                "joined": "2019-07",
-                "name": "Michele Maroni",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/michelemaroni89/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/michelemaroni89.json"
-            },
             {
                 "id": "olanag1",
                 "joined": "2019-07",
@@ -130189,6 +132039,118 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/olanag1/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/olanag1.json"
             },
+            {
+                "id": "tnabtaf",
+                "joined": "2017-09",
+                "name": "Dave Clements",
+                "orcid": "0000-0002-9970-6657",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
+            }
+        ],
+        "dir": "topics/introduction/tutorials/introduction",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": false,
+        "id": "introduction/introduction",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "layout": "introduction_slides",
+        "license": "CC-BY-4.0",
+        "logo": "GTN",
+        "mod_date": "2024-05-07",
+        "pageviews": 5897182,
+        "priority": 1,
+        "pub_date": "2016-09-30",
+        "redirect_from": [
+            "/topics/introduction/slides/introduction",
+            "/short/introduction/introduction/slides",
+            "/short/S00073"
+        ],
+        "short_id": "S00073",
+        "short_tools": [],
+        "slides": true,
+        "slides_recordings": false,
+        "subtopic": "first",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "title": "Introduction to Galaxy",
+        "tools": [],
+        "topic_name": "introduction",
+        "topic_name_human": "Introduction to Galaxy Analyses",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "introduction",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/introduction/slides.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/introduction/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/introduction/slides.json"
+        },
+        "version": 2,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 152,
+        "visitors": 2133582
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/options-for-using-galaxy/tutorial.json",
+        "contributors": [
             {
                 "id": "tnabtaf",
                 "joined": "2017-09",
@@ -130199,125 +132161,608 @@
             },
             {
                 "affiliations": [
-                    "CINECA-Project",
                     "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
+                    "eurosciencegateway",
+                    "elixir-europe"
                 ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
                 "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
+                "elixir_node": "fr",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
                 "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
+                "id": "abretaud",
                 "joined": "2017-09",
-                "linkedin": "shiltemann",
                 "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
+                    "country": "FR",
+                    "lat": 48.11,
+                    "lon": -1.64
                 },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+            },
+            {
+                "id": "pajanne",
+                "joined": "2017-09",
+                "name": "Anne Pajon",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pajanne/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pajanne.json"
+            },
+            {
+                "affiliations": [
+                    "earlham",
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "fediverse": "https://mstdn.science/@nsoranzo",
+                "fediverse_flavor": "mastodon",
+                "id": "nsoranzo",
+                "joined": "2017-09",
+                "linkedin": "nicola-soranzo-7884125",
+                "matrix": "nsoranzo:matrix.org",
+                "name": "Nicola Soranzo",
+                "orcid": "0000-0003-3627-5340",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
+                "twitter": "NicolaSoranzo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
+            },
+            {
+                "id": "alaaelghamry",
+                "joined": "2021-11",
+                "name": "Alaa Elghamry",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/alaaelghamry/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/alaaelghamry.json"
             }
         ],
-        "dir": "topics/introduction/tutorials/galaxy-intro-101-everyone",
-        "edam_operation": [
-            "Visualisation"
-        ],
+        "dir": "topics/introduction/tutorials/options-for-using-galaxy",
+        "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": false,
+        "id": "introduction/options-for-using-galaxy",
+        "inexact_supported_servers": [
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": null,
+        "layout": "tutorial_slides",
+        "license": "CC-BY-4.0",
+        "logo": "GTN",
+        "mod_date": "2022-09-23",
+        "objectives": null,
+        "pageviews": 5897182,
+        "pub_date": "2017-05-24",
+        "questions": [
+            "Which Galaxy instance should I use?"
+        ],
+        "short_id": "S00075",
+        "short_tools": [],
+        "slides": true,
+        "slides_recordings": false,
+        "subtopic": "next-steps",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "time_estimation": null,
+        "title": "Options for using Galaxy",
+        "tools": [],
+        "topic_name": "introduction",
+        "topic_name_human": "Introduction to Galaxy Analyses",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": true
+        },
+        "tutorial_name": "options-for-using-galaxy",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/options-for-using-galaxy/slides.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/options-for-using-galaxy/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/options-for-using-galaxy/slides.json"
+        },
+        "version": 14,
+        "video": true,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 152,
+        "visitors": 2133582,
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/dummy/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            }
         ],
+        "dir": "topics/introduction/tutorials/dummy",
+        "draft": true,
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "introduction/galaxy-intro-101-everyone",
+        "id": "introduction/dummy",
         "inexact_supported_servers": [
-            "Galaxy@AuBi",
-            "UseGalaxy.cz"
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Galaxy provides an easy-to-use graphical user interface for often complex command-line tools",
-            "Galaxy keeps a full record of your analysis in a history",
-            "Workflows enable you to repeat your analysis on different data",
-            "Galaxy can connect to external sources for data import and visualization purposes",
-            "Galaxy provides ways to share your results and methods with others"
+            "There are several ways to get data into Galaxy",
+            "you can upload a file by pasting in a web address, you can upload a file from your computer, and you can import an entire history."
         ],
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Familiarize yourself with the basics of Galaxy",
-            "Learn how to obtain data from external sources",
-            "Learn how to tag datasets",
-            "Learn how to run tools",
-            "Learn how histories work",
-            "Learn how to create a workflow",
-            "Learn how to share your work"
+            "Learn how to upload a file by pasting in a URL",
+            "Learn how to import data from a shared library",
+            "Determine the best strategy to get data into Galaxy"
         ],
-        "pageviews": 24410,
-        "priority": 2,
-        "pub_date": "2019-11-14",
+        "pageviews": 327,
+        "pub_date": "2022-09-23",
         "questions": [
-            "What are the differences between the Iris species?"
+            "How to upload data to Galaxy"
         ],
-        "recordings": [
+        "short_id": "T00185",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "work-in-progress"
+        ],
+        "time_estimation": "40m",
+        "title": "Upload data to Galaxy",
+        "tools": [],
+        "topic_name": "introduction",
+        "topic_name_human": "Introduction to Galaxy Analyses",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "dummy",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/dummy/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/dummy/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/dummy/tutorial.json"
+        },
+        "version": 5,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 205,
+        "visitors": 279
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/igv-introduction/tutorial.json",
+        "contributors": [
             {
-                "captioners": [
-                    "astrovsky01"
-                ],
-                "date": "2023-05-01",
-                "galaxy_version": "23.0",
-                "length": "20M",
-                "speakers": [
-                    "astrovsky01"
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
+                "joined": "2017-09",
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+            },
+            {
+                "elixir_node": "de",
+                "email": "wolffj@informatik.uni-freiburg.de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
                 ],
-                "youtube_id": "64oS5uXVRV0"
+                "id": "joachimwolff",
+                "joined": "2017-09",
+                "name": "Joachim Wolff",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/joachimwolff.json"
             },
             {
-                "captioners": [
-                    "tnabtaf"
+                "id": "pajanne",
+                "joined": "2017-09",
+                "name": "Anne Pajon",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pajanne/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pajanne.json"
+            }
+        ],
+        "dir": "topics/introduction/tutorials/igv-introduction",
+        "draft": true,
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "introduction/igv-introduction",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": null,
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-02-17",
+        "objectives": null,
+        "pageviews": 10111,
+        "pub_date": "2016-03-30",
+        "questions": null,
+        "short_id": "T00193",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "next-steps",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "work-in-progress"
+        ],
+        "time_estimation": "2H",
+        "title": "IGV Introduction",
+        "tools": [],
+        "topic_name": "introduction",
+        "topic_name_human": "Introduction to Galaxy Analyses",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "igv-introduction",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/igv-introduction/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/igv-introduction/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/igv-introduction/tutorial.json"
+        },
+        "version": 11,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 92,
+        "visitors": 6933,
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "fastq_quality_filter",
+                    "owner": "devteam",
+                    "revisions": "43a7370aa010",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastq_quality_filter",
+                    "owner": "devteam",
+                    "revisions": "64e9a6afdd0c",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "9da02be9c6cc",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "2c64fded1286",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastq_quality_filter\n  owner: devteam\n  revisions: 43a7370aa010\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastq_quality_filter\n  owner: devteam\n  revisions: 64e9a6afdd0c\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 9da02be9c6cc\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 2c64fded1286\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-short/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "annasyme",
+                "nsoranzo"
+            ],
+            "editing": [
+                "bebatut",
+                "ahmedhamidawan"
+            ]
+        },
+        "contributors": [
+            {
+                "id": "annasyme",
+                "joined": "2017-09",
+                "name": "Anna Syme",
+                "orcid": "0000-0002-9906-0673",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
+            },
+            {
+                "affiliations": [
+                    "earlham",
+                    "elixir-europe"
                 ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "1H15M",
-                "speakers": [
-                    "annefou",
-                    "rwinand"
+                "elixir_node": "uk",
+                "fediverse": "https://mstdn.science/@nsoranzo",
+                "fediverse_flavor": "mastodon",
+                "id": "nsoranzo",
+                "joined": "2017-09",
+                "linkedin": "nicola-soranzo-7884125",
+                "matrix": "nsoranzo:matrix.org",
+                "name": "Nicola Soranzo",
+                "orcid": "0000-0003-3627-5340",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
+                "twitter": "NicolaSoranzo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
                 ],
-                "youtube_id": "dguN6Xw2Azs"
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "email": "aawan7@jhu.edu",
+                "id": "ahmedhamidawan",
+                "joined": "2024-08",
+                "linkedin": "ahmed-awan-70a20919a",
+                "matrix": "ahmedhamidawan:matrix.org",
+                "name": "Ahmed Hamid Awan",
+                "orcid": "0009-0003-2600-6152",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ahmedhamidawan/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/ahmedhamidawan.json"
             }
         ],
-        "short_id": "T00187",
-        "short_tools": [
-            "Grouping1",
-            "datamash_ops",
-            "ggplot2_point",
-            "Cut1",
-            "csv_to_tabular",
-            "Remove beginning1",
-            "tp_sorted_uniq",
-            "upload1"
+        "dir": "topics/introduction/tutorials/galaxy-intro-short",
+        "edam_operation": [
+            "Sequencing quality control",
+            "Statistical calculation",
+            "Sequence composition calculation"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "introduction/galaxy-intro-short",
+        "inexact_supported_servers": [
+            "Galaxy@Pasteur",
+            "GalaxyTrakr",
+            "MISSISSIPPI",
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "The Galaxy interface has an activity bar on the left, a tool (or other activated) panel next to it (if expanded), viewing pane in the middle, and a history of your data analysis on the right.",
+            "You can create a new history for each analysis. All your histories are saved.",
+            "To get data into Galaxy, you can upload a file by pasting in a web address. There are other ways to get data into Galaxy (not covered in this tutorial): you can upload a file from your computer, and you can import an entire history.",
+            "Choose a tool and change any settings for your analysis.",
+            "Run the tool. The output files will be saved at the top of your history.",
+            "View the output files by clicking on the eye icon.",
+            "View all your histories and move files between them. Switch to a different history.",
+            "Log out of your Galaxy server. When you log back in (to the same server), your histories will all be there."
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-07",
+        "objectives": [
+            "Learn how to upload a file",
+            "Learn how to use a tool",
+            "Learn how to view results",
+            "Learn how to view histories",
+            "Learn how to extract and run a workflow",
+            "Learn how to share a history"
+        ],
+        "pageviews": 5958434,
+        "priority": 2,
+        "pub_date": "2018-08-27",
+        "questions": [
+            "How to get started in Galaxy"
         ],
-        "slides": false,
+        "short_id": "T00190",
+        "short_tools": [
+            "fastqc",
+            "cshl_fastq_quality_filter"
+        ],
+        "slides": true,
         "slides_recordings": false,
-        "subtopic": "core",
+        "subtopic": "first",
         "supported_servers": {
             "exact": [
                 {
@@ -130325,16 +132770,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -130343,160 +132778,130 @@
             ],
             "inexact": [
                 {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
-        "time_estimation": "1H30M",
-        "title": "Galaxy Basics for everyone",
+        "tags": [
+            "espa\u00f1ol"
+        ],
+        "time_estimation": "40m",
+        "title": "A short introduction to Galaxy",
         "tools": [
-            "Cut1",
-            "Grouping1",
-            "Remove beginning1",
-            "csv_to_tabular",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
-            "upload1"
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.2+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1"
         ],
         "topic_name": "introduction",
         "topic_name_human": "Introduction to Galaxy Analyses",
         "tours": false,
         "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
+            "slides": [
+                "es"
+            ],
+            "tutorial": [
+                "es"
+            ],
+            "video": true
         },
-        "tutorial_name": "galaxy-intro-101-everyone",
+        "tutorial_name": "galaxy-intro-short",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-short/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-short/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-short/tutorial.json"
         },
-        "version": 32,
-        "video": false,
-        "video_versions": 2,
+        "version": 36,
+        "video": true,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 252,
-        "visitors": 14550,
+        "visit_duration": 421,
+        "visitors": 2172617,
         "workflows": [
             {
                 "creators": [],
-                "description": "introduction",
+                "description": "A short introduction to Galaxy",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\niris\"]\n  1[label=\"Convert CSV to tabular\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Datamash\"]\n  1 -> 2 [label=\"tabular\"]\n  k254f1b4bd4664f0e8c460e97bbedae4d[color=lightseagreen,label=\"Output\\ndatamash_output\"]\n  2 -> k254f1b4bd4664f0e8c460e97bbedae4d\n  3[label=\"Remove beginning\"]\n  1 -> 3 [label=\"tabular\"]\n  4[label=\"Cut\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"Group\"]\n  3 -> 5 [label=\"out_file1\"]\n  ka689bddf14d04a72b1f9c34d8f50d2b3[color=lightseagreen,label=\"Output\\ngroup1\"]\n  5 -> ka689bddf14d04a72b1f9c34d8f50d2b3\n  6[label=\"Group\"]\n  3 -> 6 [label=\"out_file1\"]\n  kac7c73b258dd4c6e85ceddf49323b206[color=lightseagreen,label=\"Output\\ngroup2\"]\n  6 -> kac7c73b258dd4c6e85ceddf49323b206\n  7[label=\"Scatterplot with ggplot2\"]\n  3 -> 7 [label=\"out_file1\"]\n  8[label=\"Scatterplot with ggplot2\"]\n  3 -> 8 [label=\"out_file1\"]\n  9[label=\"Unique\"]\n  4 -> 9 [label=\"out_file1\"]\n  k8a2b5e30d42a401996744b4af00c820a[color=lightseagreen,label=\"Output\\nunique_output\"]\n  9 -> k8a2b5e30d42a401996744b4af00c820a\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmutant_R1\"]\n  1[label=\"FastQC\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Filter by quality\"]\n  0 -> 2 [label=\"output\"]\n  k4706cfda1f28494e85f01d797d3dbacc[color=lightseagreen,label=\"Output\\nfilter1\"]\n  2 -> k4706cfda1f28494e85f01d797d3dbacc\n  3[label=\"Filter by quality\"]\n  0 -> 3 [label=\"output\"]\n  k8191d6ec149a4edabd00c277f56474a8[color=lightseagreen,label=\"Output\\nfilter2\"]\n  3 -> k8191d6ec149a4edabd00c277f56474a8\n}",
                 "history": [
                     {
-                        "hash": "f5ec1c92ee0b0329a1ad5c6d52aa0e3fe82d9583",
-                        "message": "Update ggplot2 tool in galaxy101 for everyone",
-                        "num": 14,
-                        "short_hash": "f5ec1c92e",
-                        "unix": "1647276023"
-                    },
-                    {
-                        "hash": "2d1282226e93ab129a1459e45f1d26a3ba9d2411",
+                        "hash": "bcd92cb059319065ea797c48e5e68c47ceae2dbd",
                         "message": "Add workflow test.",
-                        "num": 13,
-                        "short_hash": "2d1282226",
-                        "unix": "1603313786"
-                    },
-                    {
-                        "hash": "4117bd414ffc93a9c46fe312804b63f3018d9fc4",
-                        "message": "Update tutorial workflow and data-library record",
-                        "num": 12,
-                        "short_hash": "4117bd414",
-                        "unix": "1594838956"
-                    },
-                    {
-                        "hash": "e0df2c97232b8455db1d38f63ffdfb69bb8d6389",
-                        "message": "annotation added",
-                        "num": 11,
-                        "short_hash": "e0df2c972",
-                        "unix": "1581629210"
-                    },
-                    {
-                        "hash": "232ce03723ab9acbd124828954705c1cd2679abd",
-                        "message": "removed name label bit",
-                        "num": 10,
-                        "short_hash": "232ce0372",
-                        "unix": "1581615057"
-                    },
-                    {
-                        "hash": "cccd85216e3d9baaca787eb7ae8808bd5f3fa2dc",
-                        "message": "minor tweaks and files unhidden",
-                        "num": 9,
-                        "short_hash": "cccd85216",
-                        "unix": "1581613998"
+                        "num": 5,
+                        "short_hash": "bcd92cb05",
+                        "unix": "1603316821"
                     },
                     {
                         "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
                         "message": "annotation",
-                        "num": 8,
+                        "num": 4,
                         "short_hash": "667ff3de9",
                         "unix": "1579690769"
                     },
                     {
                         "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
                         "message": "Workflow renaming",
-                        "num": 7,
+                        "num": 3,
                         "short_hash": "eb4d724e0",
                         "unix": "1579084895"
                     },
                     {
-                        "hash": "de5e2cb89a0a9f4c3ed598c448cd9cd784a706db",
-                        "message": "csv_to_tabular",
-                        "num": 6,
-                        "short_hash": "de5e2cb89",
-                        "unix": "1578923859"
-                    },
-                    {
-                        "hash": "495f4d8d3dd2309d3780edef4c3b449ae5f871f4",
-                        "message": "Workflows fix",
-                        "num": 5,
-                        "short_hash": "495f4d8d3",
-                        "unix": "1578666747"
-                    },
-                    {
-                        "hash": "a38709a415104f50fc1cbd4ac2fedccc82a0919d",
-                        "message": "workflow: update title and remove duplicate datamash step",
-                        "num": 4,
-                        "short_hash": "a38709a41",
-                        "unix": "1573571116"
-                    },
-                    {
-                        "hash": "156b6c7efa1ef3240e2118d38611650ad5a340fe",
-                        "message": "fix formatting issues, images and replace workflow",
-                        "num": 3,
-                        "short_hash": "156b6c7ef",
-                        "unix": "1568975444"
-                    },
-                    {
-                        "hash": "4fdfd40a0df85861f6b4f05762663b07b6602a87",
-                        "message": "fix format workflow in intro for everyone",
+                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
+                        "message": "Changed format of workflows",
                         "num": 2,
-                        "short_hash": "4fdfd40a0",
-                        "unix": "1568360318"
+                        "short_hash": "361236c41",
+                        "unix": "1554368414"
                     },
                     {
-                        "hash": "d90d12a047f0362c6aeb9490791f69c0aaee43b4",
-                        "message": "draft galaxy 101 for everyone with Iris dataset. - added introduction, workflow, data library.",
+                        "hash": "6aded48bd1b611fb111ac2818450c00dafd7d1f3",
+                        "message": "added workflow for intro-short",
                         "num": 1,
-                        "short_hash": "d90d12a04",
-                        "unix": "1562484318"
+                        "short_hash": "6aded48bd",
+                        "unix": "1537905266"
                     }
                 ],
                 "inputs": [
@@ -130509,374 +132914,143 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "iris"
+                                "name": "mutant_R1"
                             }
                         ],
-                        "label": "iris",
-                        "name": "Input dataset",
+                        "label": "mutant_R1",
+                        "name": "mutant_R1",
                         "outputs": [],
                         "position": {
-                            "bottom": 210.20000839233398,
-                            "height": 61.79999923706055,
-                            "left": 296.5,
-                            "right": 496.5,
-                            "top": 148.40000915527344,
-                            "width": 200,
-                            "x": 296.5,
-                            "y": 148.40000915527344
+                            "left": 10,
+                            "top": 10
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"name\": \"mutant_R1\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "6a8d8ca9-8bb9-414b-af8f-50d07721b363",
+                        "uuid": "e271eee4-bfb8-40b4-b691-a25cb9932327",
                         "workflow_outputs": []
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\niris\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Convert CSV to tabular\"];\n  0 -->|output| 1;\n  2[\"Datamash\"];\n  1 -->|tabular| 2;\n  254f1b4b-d466-4f0e-8c46-0e97bbedae4d[\"Output\\ndatamash_output\"];\n  2 --> 254f1b4b-d466-4f0e-8c46-0e97bbedae4d;\n  style 254f1b4b-d466-4f0e-8c46-0e97bbedae4d stroke:#2c3143,stroke-width:4px;\n  3[\"Remove beginning\"];\n  1 -->|tabular| 3;\n  4[\"Cut\"];\n  3 -->|out_file1| 4;\n  5[\"Group\"];\n  3 -->|out_file1| 5;\n  a689bddf-14d0-4a72-b1f9-c34d8f50d2b3[\"Output\\ngroup1\"];\n  5 --> a689bddf-14d0-4a72-b1f9-c34d8f50d2b3;\n  style a689bddf-14d0-4a72-b1f9-c34d8f50d2b3 stroke:#2c3143,stroke-width:4px;\n  6[\"Group\"];\n  3 -->|out_file1| 6;\n  ac7c73b2-58dd-4c6e-85ce-ddf49323b206[\"Output\\ngroup2\"];\n  6 --> ac7c73b2-58dd-4c6e-85ce-ddf49323b206;\n  style ac7c73b2-58dd-4c6e-85ce-ddf49323b206 stroke:#2c3143,stroke-width:4px;\n  7[\"Scatterplot with ggplot2\"];\n  3 -->|out_file1| 7;\n  8[\"Scatterplot with ggplot2\"];\n  3 -->|out_file1| 8;\n  9[\"Unique\"];\n  4 -->|out_file1| 9;\n  8a2b5e30-d42a-4019-9674-4b4af00c820a[\"Output\\nunique_output\"];\n  9 --> 8a2b5e30-d42a-4019-9674-4b4af00c820a;\n  style 8a2b5e30-d42a-4019-9674-4b4af00c820a stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "GTN Training: Galaxy 101 For Everyone",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nmutant_R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"FastQC\"];\n  0 -->|output| 1;\n  2[\"Filter by quality\"];\n  0 -->|output| 2;\n  4706cfda-1f28-494e-85f0-1d797d3dbacc[\"Output\\nfilter1\"];\n  2 --> 4706cfda-1f28-494e-85f0-1d797d3dbacc;\n  style 4706cfda-1f28-494e-85f0-1d797d3dbacc stroke:#2c3143,stroke-width:4px;\n  3[\"Filter by quality\"];\n  0 -->|output| 3;\n  8191d6ec-149a-4eda-bd00-c277f56474a8[\"Output\\nfilter2\"];\n  3 --> 8191d6ec-149a-4eda-bd00-c277f56474a8;\n  style 8191d6ec-149a-4eda-bd00-c277f56474a8 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Galaxy Intro Short",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.1",
                         "errors": null,
                         "id": 2,
                         "input_connections": {
-                            "in_file": {
-                                "id": 1,
-                                "output_name": "tabular"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Datamash",
-                        "outputs": [
-                            {
-                                "name": "out_file",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 56.99374771118164,
-                            "height": 113.5999984741211,
-                            "left": 643.5,
-                            "right": 843.5,
-                            "top": -56.60625076293945,
-                            "width": 200,
-                            "x": 643.5,
-                            "y": -56.60625076293945
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "562f3c677828",
-                            "name": "datamash_ops",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"grouping\": \"5\", \"header_in\": \"true\", \"header_out\": \"true\", \"ignore_case\": \"true\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"need_sort\": \"true\", \"operations\": [{\"__index__\": 0, \"op_name\": \"mean\", \"op_column\": \"1\"}, {\"__index__\": 1, \"op_name\": \"sstdev\", \"op_column\": \"1\"}, {\"__index__\": 2, \"op_name\": \"mean\", \"op_column\": \"2\"}, {\"__index__\": 3, \"op_name\": \"sstdev\", \"op_column\": \"2\"}, {\"__index__\": 4, \"op_name\": \"mean\", \"op_column\": \"3\"}, {\"__index__\": 5, \"op_name\": \"sstdev\", \"op_column\": \"3\"}, {\"__index__\": 6, \"op_name\": \"mean\", \"op_column\": \"4\"}, {\"__index__\": 7, \"op_name\": \"sstdev\", \"op_column\": \"4\"}], \"print_full_line\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.0",
-                        "type": "tool",
-                        "uuid": "e1a58a79-5102-450e-bfe0-200f0e64139d",
-                        "workflow_outputs": [
-                            {
-                                "label": "datamash_output",
-                                "output_name": "out_file",
-                                "uuid": "254f1b4b-d466-4f0e-8c46-0e97bbedae4d"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "Grouping1",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "input1": {
-                                "id": 3,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Group",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 500.5999984741211,
-                            "height": 93.20000457763672,
-                            "left": 1063.5,
-                            "right": 1263.5,
-                            "top": 407.3999938964844,
-                            "width": 200,
-                            "x": 1063.5,
-                            "y": 407.3999938964844
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "Grouping1",
-                        "tool_state": "{\"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"groupcol\": \"5\", \"ignorecase\": \"false\", \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.4",
-                        "type": "tool",
-                        "uuid": "dcd3ddc6-d871-45dd-94ed-3eae56dd56db",
-                        "workflow_outputs": [
-                            {
-                                "label": "group1",
-                                "output_name": "out_file1",
-                                "uuid": "a689bddf-14d0-4a72-b1f9-c34d8f50d2b3"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "Grouping1",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "input1": {
-                                "id": 3,
-                                "output_name": "out_file1"
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Group",
+                        "name": "Filter by quality",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "tabular"
+                                "name": "output",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 620.6000289916992,
-                            "height": 93.20000457763672,
-                            "left": 1063.5,
-                            "right": 1263.5,
-                            "top": 527.4000244140625,
-                            "width": 200,
-                            "x": 1063.5,
-                            "y": 527.4000244140625
+                            "left": 230,
+                            "top": 130
                         },
                         "post_job_actions": {},
-                        "tool_id": "Grouping1",
-                        "tool_state": "{\"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"groupcol\": \"5\", \"ignorecase\": \"false\", \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [{\"__index__\": 0, \"optype\": \"length\", \"opcol\": \"1\", \"opround\": \"no\", \"opdefault\": null}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.4",
-                        "type": "tool",
-                        "uuid": "285a3852-71cb-4137-be1d-b0ec0a59d9e9",
-                        "workflow_outputs": [
-                            {
-                                "label": "group2",
-                                "output_name": "out_file1",
-                                "uuid": "ac7c73b2-58dd-4c6e-85ce-ddf49323b206"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "input1": {
-                                "id": 3,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scatterplot with ggplot2",
-                        "outputs": [
-                            {
-                                "name": "output1",
-                                "type": "png"
-                            },
-                            {
-                                "name": "output2",
-                                "type": "pdf"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 873.0000305175781,
-                            "height": 225.60000610351562,
-                            "left": 1063.5,
-                            "right": 1263.5,
-                            "top": 647.4000244140625,
-                            "width": 200,
-                            "x": 1063.5,
-                            "y": 647.4000244140625
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionoutput1": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output1"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "1acf88921176",
-                            "name": "ggplot2_point",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"points\", \"__current_case__\": 0, \"points\": {\"pointoptions\": \"default\", \"__current_case__\": 0}}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"5\", \"colors\": \"Set2\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"7.0\", \"height_output_dim\": \"7.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"pdf\"}, \"title\": \"Sepal length as a function of sepal width\", \"xlab\": \"Sepal length\", \"xplot\": \"1\", \"ylab\": \"Sepal width\", \"yplot\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.3.5+galaxy0",
-                        "type": "tool",
-                        "uuid": "fa412209-5e3a-448e-8b0b-fa88870e19c1",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output2",
-                                "uuid": "08954537-18c1-4fa5-8093-b2ec90c0eb5c"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "input1": {
-                                "id": 3,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scatterplot with ggplot2",
-                        "outputs": [
-                            {
-                                "name": "output1",
-                                "type": "png"
-                            },
-                            {
-                                "name": "output2",
-                                "type": "pdf"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 993.0000305175781,
-                            "height": 225.60000610351562,
-                            "left": 1063.5,
-                            "right": 1263.5,
-                            "top": 767.4000244140625,
-                            "width": 200,
-                            "x": 1063.5,
-                            "y": 767.4000244140625
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionoutput1": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output1"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "1acf88921176",
-                            "name": "ggplot2_point",
-                            "owner": "iuc",
+                            "changeset_revision": "43a7370aa010",
+                            "name": "fastq_quality_filter",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"points\", \"__current_case__\": 0, \"points\": {\"pointoptions\": \"default\", \"__current_case__\": 0}}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"5\", \"colors\": \"Set2\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"7.0\", \"height_output_dim\": \"7.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"pdf\"}, \"title\": \"Petal length as a function of petal width\", \"xlab\": \"Petal length\", \"xplot\": \"3\", \"ylab\": \"Petal width\", \"yplot\": \"4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.3.5+galaxy0",
+                        "tool_state": "{\"__page__\": null, \"chromInfo\": \"\\\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"percent\": \"\\\"80\\\"\", \"input\": \"null\", \"quality\": \"\\\"35\\\"\"}",
+                        "tool_version": "1.0.1",
                         "type": "tool",
-                        "uuid": "8e7b3f8d-2b8b-46cb-93d4-0d74bf54441e",
+                        "uuid": "3a3ec769-355d-488a-984b-78462a794ef9",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output2",
-                                "uuid": "cc4e1426-f444-4fcd-960c-a868d98147ac"
+                                "label": "filter1",
+                                "output_name": "output",
+                                "uuid": "4706cfda-1f28-494e-85f0-1d797d3dbacc"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.1",
                         "errors": null,
-                        "id": 9,
+                        "id": 3,
                         "input_connections": {
-                            "infile": {
-                                "id": 4,
-                                "output_name": "out_file1"
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Unique",
+                        "name": "Filter by quality",
                         "outputs": [
                             {
-                                "name": "outfile",
+                                "name": "output",
                                 "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 281.00000762939453,
-                            "height": 113.5999984741211,
-                            "left": 1283.5,
-                            "right": 1483.5,
-                            "top": 167.40000915527344,
-                            "width": 200,
-                            "x": 1283.5,
-                            "y": 167.40000915527344
+                            "left": 230,
+                            "top": 250
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "43a7370aa010",
+                            "name": "fastq_quality_filter",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_numeric\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.0",
+                        "tool_state": "{\"__page__\": null, \"chromInfo\": \"\\\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"percent\": \"\\\"80\\\"\", \"input\": \"null\", \"quality\": \"\\\"36\\\"\"}",
+                        "tool_version": "1.0.1",
                         "type": "tool",
-                        "uuid": "3e2d84e9-2fff-4321-9db6-41af99367162",
+                        "uuid": "df2f009c-d3e5-4ccc-bf0f-10b8e44947da",
                         "workflow_outputs": [
                             {
-                                "label": "unique_output",
-                                "output_name": "outfile",
-                                "uuid": "8a2b5e30-d42a-4019-9674-4b4af00c820a"
+                                "label": "filter2",
+                                "output_name": "output",
+                                "uuid": "8191d6ec-149a-4eda-bd00-c277f56474a8"
                             }
                         ]
                     }
                 ],
-                "parent_id": "introduction/galaxy-intro-101-everyone",
-                "path": "topics/introduction/tutorials/galaxy-intro-101-everyone/workflows/main_workflow.ga",
+                "parent_id": "introduction/galaxy-intro-short",
+                "path": "topics/introduction/tutorials/galaxy-intro-short/workflows/Galaxy-Workflow-galaxy-intro-short.ga",
                 "tags": [
                     "introduction"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "GTN Training: Galaxy 101 For Everyone",
+                "tests": false,
+                "title": "Galaxy Intro Short",
                 "topic_id": "introduction",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/introduction-galaxy-intro-101-everyone/versions/main-workflow",
-                "tutorial_id": "galaxy-intro-101-everyone",
-                "url": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/workflows/main_workflow.html",
-                "version": 8,
-                "wfid": "introduction-galaxy-intro-101-everyone",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/introduction-galaxy-intro-short/versions/galaxy-workflowlaxy-intro-short",
+                "tutorial_id": "galaxy-intro-short",
+                "url": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-short/workflows/Galaxy-Workflow-galaxy-intro-short.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-short/workflows/Galaxy-Workflow-galaxy-intro-short.html",
+                "version": 5,
+                "wfid": "introduction-galaxy-intro-short",
+                "wfname": "galaxy-workflowlaxy-intro-short",
+                "workflow": "Galaxy-Workflow-galaxy-intro-short.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "Grouping1",
-                    "Remove beginning1",
-                    "csv_to_tabular",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0"
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72"
                 ],
-                "workflowhub_id": "1085"
+                "workflowhub_id": "1094"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/1319069/"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.582600"
     },
     {
         "admin_install": {
@@ -130885,24 +133059,107 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "fastp",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bedtools",
                     "owner": "iuc",
-                    "revisions": "65b93b623c77",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "a1a923cd89e8",
+                    "tool_panel_section_label": "BED",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "multiqc",
+                    "name": "datamash_ops",
                     "owner": "iuc",
-                    "revisions": "abfd8a6544d7",
-                    "tool_panel_section_label": "Quality Control",
+                    "revisions": "562f3c677828",
+                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "datamash_ops",
+                    "owner": "iuc",
+                    "revisions": "4c07ddedc198",
+                    "tool_panel_section_label": "Join, Subtract and Group",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: abfd8a6544d7\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/vsi_qc/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: a1a923cd89e8\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 562f3c677828\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 4c07ddedc198\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-101/tutorial.json",
         "contributors": [
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
+            {
+                "affiliations": [
+                    "earlham",
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "fediverse": "https://mstdn.science/@nsoranzo",
+                "fediverse_flavor": "mastodon",
+                "id": "nsoranzo",
+                "joined": "2017-09",
+                "linkedin": "nicola-soranzo-7884125",
+                "matrix": "nsoranzo:matrix.org",
+                "name": "Nicola Soranzo",
+                "orcid": "0000-0003-3627-5340",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
+                "twitter": "NicolaSoranzo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
+            },
+            {
+                "elixir_node": "de",
+                "email": "blankclemens@gmail.com",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "blankclemens",
+                "joined": "2017-09",
+                "name": "Clemens Blank",
+                "orcid": "0000-0002-1726-2256",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankclemens/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankclemens.json"
+            },
             {
                 "email": "anton@nekrut.org",
                 "id": "nekrut",
@@ -130910,64 +133167,166 @@
                 "name": "Anton Nekrutenko",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+            },
+            {
+                "affiliations": [
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
+                "fediverse_flavor": "mastodon",
+                "id": "bgruening",
+                "joined": "2017-09",
+                "linkedin": "bgruening",
+                "location": {
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
+                },
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+            },
+            {
+                "id": "pajanne",
+                "joined": "2017-09",
+                "name": "Anne Pajon",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pajanne/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pajanne.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/introduction/tutorials/vsi_qc",
-        "draft": true,
+        "dir": "topics/introduction/tutorials/galaxy-intro-101",
         "edam_operation": [
-            "Sequencing quality control",
-            "Sequence contamination filtering",
-            "Validation"
+            "Mapping"
         ],
         "edam_topic": [],
-        "exact_supported_servers": [
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "introduction/galaxy-intro-101",
+        "inexact_supported_servers": [
             "Galaxy@AuBi",
             "GalaxyTrakr",
-            "HyPhy HIV NGS Tools",
+            "MISSISSIPPI",
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.eu",
             "UseGalaxy.fr",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "introduction/vsi_qc",
-        "inexact_supported_servers": [
-            "UseGalaxy.no"
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)"
         ],
         "js_requirements": {
-            "mathjax": 7091,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Galaxy is an excellent tool for quickly QCing your data"
+            "Galaxy provides an easy-to-use graphical user interface for often complex command-line tools",
+            "Galaxy keeps a full record of your analysis in a history",
+            "Workflows enable you to repeat your analysis on different data",
+            "Galaxy can connect to external sources for data import and visualization purposes",
+            "Galaxy provides ways to share your results and methods with others"
         ],
         "layout": "tutorial_hands_on",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-25",
+        "mod_date": "2024-09-22",
         "objectives": [
-            "Learn about QCing Illumina and Element data",
-            "Learn about fastp",
-            "Learn about multiqc"
+            "Familiarize yourself with the basics of Galaxy",
+            "Learn how to obtain data from external sources",
+            "Learn how to run tools",
+            "Learn how histories work",
+            "Learn how to create a workflow",
+            "Learn how to share your work"
         ],
-        "pageviews": 151,
-        "priority": 10,
-        "pub_date": "2024-03-26",
+        "pageviews": 54763,
+        "priority": 2,
+        "pub_date": "2016-12-19",
         "questions": [
-            "How do I know my sequencing data is good?"
+            "Which coding exon has the highest number of single nucleotide polymorphisms (SNPs) on human chromosome 22?"
         ],
-        "short_id": "T00436",
+        "recordings": [
+            {
+                "captioners": [
+                    "shiltemann"
+                ],
+                "date": "2021-07-21",
+                "length": "13M",
+                "speakers": [
+                    "nekrut"
+                ],
+                "youtube_id": "D5HgJWdfOWw"
+            },
+            {
+                "bot-timestamp": 1726511277,
+                "captioners": [
+                    "natalie-wa"
+                ],
+                "date": "2024-09-16",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "18M",
+                "speakers": [
+                    "natalie-wa"
+                ],
+                "youtube_id": "jeRiVGJJgQA"
+            }
+        ],
+        "short_id": "T00186",
         "short_tools": [
-            "fastp",
-            "multiqc"
+            "comp1",
+            "upload1",
+            "tp_sort_header_tool",
+            "tp_head_tool",
+            "bedtools_intersectbed",
+            "datamash_ops"
         ],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "core",
         "supported_servers": {
-            "exact": [
+            "exact": [],
+            "inexact": [
                 {
                     "name": "Galaxy@AuBi",
                     "url": "https://galaxy.mesocentre.uca.fr",
@@ -130979,8 +133338,13 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "HyPhy HIV NGS Tools",
-                    "url": "https://galaxy.hyphy.org/",
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
                 {
@@ -130998,468 +133362,1286 @@
                     "url": "https://usegalaxy.fr/",
                     "usegalaxy": false
                 },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "work-in-progress"
-        ],
-        "time_estimation": "30M",
-        "title": "Very Short Introductions: QC",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1"
-        ],
-        "topic_name": "introduction",
-        "topic_name_human": "Introduction to Galaxy Analyses",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "vsi_qc",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/vsi_qc/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/vsi_qc/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/vsi_qc/tutorial.json"
-        },
-        "version": 4,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 254,
-        "visitors": 106,
-        "zenodo_link": "https://zenodo.org/records/10870107"
-    },
-    {
-        "abbreviations": {
-            "AIRSS": "Ab Initio Random Structure Search",
-            "DFT": "Density Functional Theory",
-            "UEP": "Unperturbed Electrostatic Potential"
-        },
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "pm_muairss_read",
-                    "owner": "muon-spectroscopy-computational-project",
-                    "revisions": "40071ff77285",
-                    "tool_panel_section_label": "Muon Spectroscopy",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pm_uep_opt",
-                    "owner": "muon-spectroscopy-computational-project",
-                    "revisions": "eea73e1f65cb",
-                    "tool_panel_section_label": "Muon Spectroscopy",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: pm_muairss_read\n  owner: muon-spectroscopy-computational-project\n  revisions: 40071ff77285\n  tool_panel_section_label: Muon Spectroscopy\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pm_uep_opt\n  owner: muon-spectroscopy-computational-project\n  revisions: eea73e1f65cb\n  tool_panel_section_label: Muon Spectroscopy\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "leandro-liborio",
-                "elichad",
-                "patrick-austin"
-            ],
-            "editing": [
-                "leandro-liborio"
-            ],
-            "funding": [
-                "eurosciencegateway"
-            ]
-        },
-        "contributors": [
-            {
-                "email": "leandro.liborio@stfc.ac.uk",
-                "id": "leandro-liborio",
-                "joined": "2022-11",
-                "name": "Leandro Liborio",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/leandro-liborio/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/leandro-liborio.json"
-            },
-            {
-                "email": "eli.chadwick@manchester.ac.uk",
-                "id": "elichad",
-                "joined": "2022-11",
-                "name": "Eli Chadwick",
-                "orcid": "0000-0002-0035-6475",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elichad/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/elichad.json"
-            },
-            {
-                "email": "patrick.austin@stfc.ac.uk",
-                "id": "patrick-austin",
-                "joined": "2022-11",
-                "name": "Patrick Austin",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/patrick-austin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/patrick-austin.json"
-            },
-            {
-                "email": "leandro.liborio@stfc.ac.uk",
-                "id": "leandro-liborio",
-                "joined": "2022-11",
-                "name": "Leandro Liborio",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/leandro-liborio/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/leandro-liborio.json"
-            },
-            {
-                "avatar": "/training-material/assets/images/eurosciencegateway.png",
-                "funder": true,
-                "funding_id": "101057388",
-                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "eurosciencegateway",
-                "joined": "2023-10",
-                "members": [
-                    "abretaud",
-                    "anuprulez",
-                    "bgruening",
-                    "erxleben",
-                    "pauldg",
-                    "rlibouba"
-                ],
-                "name": "EuroScienceGateway",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
-            }
-        ],
-        "dir": "topics/materials-science/tutorials/muon-stopping-sites-muairss-uep",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "materials-science/muon-stopping-sites-muairss-uep",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Galaxy supports multiple PyMuonSuite tools which can be used together to find muon stopping sites",
-            "The workflow for finding the stopping site involves three stages - structure generation, structure optimisation, and structure clustering",
-            "Within the UEP, the optimisation stage is based on analytically calculating the electrostatic forces applied to the muon, which can be performed via Galaxy.",
-            "The approach requires a CASTEP DFT calculation to be completed as a starting point"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Introductory",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
-        "objectives": [
-            "Understand why finding stopping sites is useful",
-            "Use pymuon-suite in Galaxy to find stopping sites",
-            "Understand the limitations of these tools and techniques"
-        ],
-        "pageviews": 166,
-        "priority": 2,
-        "pub_date": "2024-01-22",
-        "questions": [
-            "What are stopping sites and why is finding them important?",
-            "What computational techniques can be used to find stopping sites?",
-            "How can Galaxy help me with my analysis?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "leandro-liborio"
-                ],
-                "date": "2024-01-26",
-                "length": "22M",
-                "speakers": [
-                    "leandro-liborio"
-                ],
-                "youtube_id": "rFPtDmq7uO8"
-            }
-        ],
-        "short_id": "T00402",
-        "short_tools": [
-            "pm_muairss_read",
-            "pm_uep_opt"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "muon-spectroscopy",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 }
-            ],
-            "inexact": []
+            ]
         },
         "symlink": null,
         "time_estimation": "1H",
-        "title": "Finding the muon stopping site with pymuon-suite in Galaxy",
+        "title": "Galaxy Basics for genomics",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_muairss_read/pm_muairss_read/0.3.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_uep_opt/pm_uep_opt/0.3.0+galaxy1"
+            "comp1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1sort1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
+            "upload1"
         ],
-        "topic_name": "materials-science",
-        "topic_name_human": "Materials Science",
+        "topic_name": "introduction",
+        "topic_name_human": "Introduction to Galaxy Analyses",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "muon-stopping-sites-muairss-uep",
+        "tutorial_name": "galaxy-intro-101",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-101/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-101/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-101/tutorial.json"
         },
-        "version": 2,
+        "version": 64,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 139,
-        "visitors": 112,
+        "visit_duration": 201,
+        "visitors": 32513,
         "workflows": [
             {
                 "creators": [
                     {
-                        "class": "Organization",
-                        "name": "Muon Spectroscopy Computational Project",
-                        "url": "https://muon-spectroscopy-computational-project.github.io/"
+                        "class": "Person",
+                        "identifier": "0000-0002-5987-8032",
+                        "name": "Anton Nekrutenko"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0001-9760-8992",
+                        "name": "Helena Rasche"
                     }
                 ],
-                "description": "",
+                "description": "Galaxy 101",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCopper-out.cell\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCopper.den_fmt\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCopper.castep\"]\n  3[label=\"PyMuonSuite AIRSS UEP Optimise\"]\n  2 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  kf3be7cd2397449f2aa0e96c79b4ab34c[color=lightseagreen,label=\"Output\\nAll muons in host material\"]\n  3 -> kf3be7cd2397449f2aa0e96c79b4ab34c\n  4[label=\"PyMuonSuite AIRSS Cluster\"]\n  3 -> 4 [label=\"uep_results\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nExons\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nFeatures\"]\n  2[label=\"bedtools Intersect intervals\"]\n  0 -> 2 [label=\"output\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"Datamash\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Sort\"]\n  3 -> 4 [label=\"out_file\"]\n  5[label=\"Select first\"]\n  4 -> 5 [label=\"outfile\"]\n  6[label=\"Compare two Datasets\"]\n  0 -> 6 [label=\"output\"]\n  5 -> 6 [label=\"outfile\"]\n  k565e3d7602304a5e87c19c36ce0b7df8[color=lightseagreen,label=\"Output\\ntop_5_exons\"]\n  6 -> k565e3d7602304a5e87c19c36ce0b7df8\n}",
                 "history": [
                     {
-                        "hash": "cd4b1f827bc53928da8d0afb85d1c83590fc2638",
-                        "message": "Changes for linting and remove MuSpinSim content #1",
+                        "hash": "a448d335638114ae05668d8f3872a8316d8d49b0",
+                        "message": "added modified workflow",
+                        "num": 8,
+                        "short_hash": "a448d3356",
+                        "unix": "1710952427"
+                    },
+                    {
+                        "hash": "f90859e9d8100f4efa53007414e2b3849d6e1951",
+                        "message": "Fix workflow for planemo",
+                        "num": 7,
+                        "short_hash": "f90859e9d",
+                        "unix": "1684430714"
+                    },
+                    {
+                        "hash": "553ea8e510cd1e7d8a93a0a8d88dbbe0595c5619",
+                        "message": "Rename workflow",
+                        "num": 6,
+                        "short_hash": "553ea8e51",
+                        "unix": "1649867205"
+                    },
+                    {
+                        "hash": "a49d7d1a4431174af35c82ea03d9b1dd28251691",
+                        "message": "Include modifications",
+                        "num": 5,
+                        "short_hash": "a49d7d1a4",
+                        "unix": "1649867088"
+                    },
+                    {
+                        "hash": "222c554dbb9d76aaec3132c109dd701889750a94",
+                        "message": "workflow annotation wteaks",
+                        "num": 4,
+                        "short_hash": "222c554db",
+                        "unix": "1626799656"
+                    },
+                    {
+                        "hash": "43d15ed0ca2f2c0abbe58769cca667d978e48b4b",
+                        "message": "Refresh for galaxy101",
                         "num": 3,
-                        "short_hash": "cd4b1f827",
-                        "unix": "1702051023"
+                        "short_hash": "43d15ed0c",
+                        "unix": "1626797332"
                     },
                     {
-                        "hash": "5b3763af3729dbb2092e0757bd3aea5714960f71",
-                        "message": "Updated tutorial for finding the muon stopping site with Galaxy",
+                        "hash": "d0f7b80091932c1f6d78357d7d4229942faf76e6",
+                        "message": "Added workflow test.",
                         "num": 2,
-                        "short_hash": "5b3763af3",
-                        "unix": "1701764649"
+                        "short_hash": "d0f7b8009",
+                        "unix": "1603042314"
                     },
                     {
-                        "hash": "593f4002b4d9ecce6f6a8a91d700dea075c3662f",
-                        "message": "Address various review comments",
+                        "hash": "bffe460ee012428019957f7ba57d7f5f3050a99a",
+                        "message": "Added workflow.",
                         "num": 1,
-                        "short_hash": "593f4002b",
-                        "unix": "1673882604"
+                        "short_hash": "bffe460ee",
+                        "unix": "1603039367"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "CASTEP structural file for the relaxed host material",
+                        "annotation": "Input exons file",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "CASTEP structural file for the relaxed host material",
-                                "name": "Copper-out.cell"
+                                "description": "Input exons file",
+                                "name": "Exons"
                             }
                         ],
-                        "label": "Copper-out.cell",
+                        "label": "Exons",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 2.0965249510338584,
-                            "top": 0.08734987455441257
+                            "left": 0,
+                            "top": 187.2359999999986
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "0a1cc8d8-c2d9-48f6-9a92-9d96778249dc",
+                        "uuid": "bd3df190-bc2c-4432-a534-7b1b21cd58c9",
                         "when": null,
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "CASTEP charge density file",
+                        "annotation": "Input features file",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "CASTEP charge density file",
-                                "name": "Copper.den_fmt"
-                            }
-                        ],
-                        "label": "Copper.den_fmt",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 2.0965249510338584,
-                            "top": 86.09728918976163
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "73e18b25-ebb9-4835-933c-1b8c1feb74cb",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "main CASTEP output file ",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "main CASTEP output file ",
-                                "name": "Copper.castep"
+                                "description": "Input features file",
+                                "name": "Features"
                             }
                         ],
-                        "label": "Copper.castep",
+                        "label": "Features",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 173.59228833890583
+                            "left": 49,
+                            "top": 430.2359999999986
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "2ac4de9c-0f0a-4bdb-971a-cd471c08111e",
+                        "uuid": "b7b8e25f-8db4-4707-bfb9-9e5a527e28c3",
                         "when": null,
                         "workflow_outputs": []
                     }
                 ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nCopper-out.cell\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nCopper.den_fmt\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nCopper.castep\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"PyMuonSuite AIRSS UEP Optimise\"];\n  2 -->|output| 3;\n  1 -->|output| 3;\n  0 -->|output| 3;\n  f3be7cd2-3974-49f2-aa0e-96c79b4ab34c[\"Output\\nAll muons in host material\"];\n  3 --> f3be7cd2-3974-49f2-aa0e-96c79b4ab34c;\n  style f3be7cd2-3974-49f2-aa0e-96c79b4ab34c stroke:#2c3143,stroke-width:4px;\n  4[\"PyMuonSuite AIRSS Cluster\"];\n  3 -->|uep_results| 4;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Finding the Muon Stopping Site: pymuon-suite in Galaxy",
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nExons\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nFeatures\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"bedtools Intersect intervals\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"Datamash\"];\n  2 -->|output| 3;\n  4[\"Sort\"];\n  3 -->|out_file| 4;\n  5[\"Select first\"];\n  4 -->|outfile| 5;\n  6[\"Compare two Datasets\"];\n  0 -->|output| 6;\n  5 -->|outfile| 6;\n  565e3d76-0230-4a5e-87c1-9c36ce0b7df8[\"Output\\ntop_5_exons\"];\n  6 --> 565e3d76-0230-4a5e-87c1-9c36ce0b7df8;\n  style 565e3d76-0230-4a5e-87c1-9c36ce0b7df8 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Find exons with the highest number of features",
                 "outputs": [
                     {
-                        "annotation": "Galaxy tool used to: load the CASTEP files; complete the Generation parameters to set up the creation of randomly populated muonated structures; and complete the Optimisation parameters to set up the relaxation the electrostatic forces of the muon in each of the randomly populated muonated structures.",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_uep_opt/pm_uep_opt/0.3.0+galaxy1",
+                        "annotation": "",
+                        "content_id": "comp1",
                         "errors": null,
-                        "id": 3,
+                        "id": 6,
                         "input_connections": {
-                            "castep_log": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "charge_density": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "structure": {
+                            "input1": {
                                 "id": 0,
                                 "output_name": "output"
+                            },
+                            "input2": {
+                                "id": 5,
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
-                        "label": "PyMuonSuite AIRSS UEP Optimise",
-                        "name": "PyMuonSuite AIRSS UEP Optimise",
+                        "label": null,
+                        "name": "Compare two Datasets",
                         "outputs": [
                             {
-                                "name": "uep_results",
-                                "type": "zip"
-                            },
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1133,
+                            "top": 208.2359999999986
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Top 5 exon IDs"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "tool_id": "comp1",
+                        "tool_state": "{\"field1\": \"4\", \"field2\": \"1\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"mode\": \"N\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2",
+                        "type": "tool",
+                        "uuid": "52698c72-b6cc-4ca4-84b0-c84dd018e389",
+                        "when": null,
+                        "workflow_outputs": [
                             {
-                                "name": "allpos_file",
-                                "type": "_sniff_"
+                                "label": "top_5_exons",
+                                "output_name": "out_file1",
+                                "uuid": "565e3d76-0230-4a5e-87c1-9c36ce0b7df8"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "introduction/galaxy-intro-101",
+                "path": "topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow.ga",
+                "tags": [
+                    "introduction"
+                ],
+                "test_results": {
+                    "eu": {
+                        "summary": {
+                            "num_errors": 0,
+                            "num_failures": 0,
+                            "num_skips": 0,
+                            "num_tests": 1
+                        },
+                        "tests": [
+                            {
+                                "data": {
+                                    "end_datetime": "2023-05-18T19:40:47.480254",
+                                    "inputs": {
+                                        "Exons": {
+                                            "class": "File",
+                                            "filetype": "bed",
+                                            "location": "https://zenodo.org/record/4104428/files/UCSC-hg38-chr22-Coding-Exons.bed"
+                                        },
+                                        "Features": {
+                                            "class": "File",
+                                            "filetype": "bed",
+                                            "location": "https://zenodo.org/record/4104428/files/UCSC-hg38-chr22-dbSNP153-Whole-Gene-SNPs.bed"
+                                        }
+                                    },
+                                    "invocation_details": {
+                                        "details": {
+                                            "error_message": "",
+                                            "history_id": "a7e26bbbb0830b20",
+                                            "history_state": "ok",
+                                            "invocation_id": "4e6187ae89df9163",
+                                            "invocation_state": "scheduled",
+                                            "workflow_id": "b9fe010bdb910e56"
+                                        },
+                                        "steps": {
+                                            "0. Exons": {
+                                                "action": null,
+                                                "id": "137fffe5e92f37af",
+                                                "job_id": null,
+                                                "jobs": [],
+                                                "model_class": "WorkflowInvocationStep",
+                                                "order_index": 0,
+                                                "output_collections": {},
+                                                "outputs": {
+                                                    "output": {
+                                                        "id": "4838ba20a6d86765828ccbcc3eb28a4b",
+                                                        "src": "hda",
+                                                        "uuid": "cfb71055-95ff-4a95-9e0b-7a48161d5d0c"
+                                                    }
+                                                },
+                                                "state": "scheduled",
+                                                "subworkflow": null,
+                                                "subworkflow_invocation_id": null,
+                                                "update_time": "2023-05-18T17:34:36.117311",
+                                                "workflow_step_id": "47c79ce5a092d365",
+                                                "workflow_step_label": "Exons",
+                                                "workflow_step_uuid": "bd3df190-bc2c-4432-a534-7b1b21cd58c9"
+                                            },
+                                            "1. Features": {
+                                                "action": null,
+                                                "id": "3ea99854c46ce445",
+                                                "job_id": null,
+                                                "jobs": [],
+                                                "model_class": "WorkflowInvocationStep",
+                                                "order_index": 1,
+                                                "output_collections": {},
+                                                "outputs": {
+                                                    "output": {
+                                                        "id": "4838ba20a6d867653f5bd69298cf67f1",
+                                                        "src": "hda",
+                                                        "uuid": "f94e7844-204e-42a8-83e0-23adc4ca038b"
+                                                    }
+                                                },
+                                                "state": "scheduled",
+                                                "subworkflow": null,
+                                                "subworkflow_invocation_id": null,
+                                                "update_time": "2023-05-18T17:34:36.117314",
+                                                "workflow_step_id": "7624b0f83c340c3d",
+                                                "workflow_step_label": "Features",
+                                                "workflow_step_uuid": "b7b8e25f-8db4-4707-bfb9-9e5a527e28c3"
+                                            },
+                                            "2. Unnamed step": {
+                                                "action": null,
+                                                "id": "53d44f7f08b165d4",
+                                                "job_id": "11ac94870d0bb33a3743b59ce7fc28ea",
+                                                "jobs": [
+                                                    {
+                                                        "command_line": "bedtools intersect -a '/data/dnb08/galaxy_db/files/c/f/b/dataset_cfb71055-95ff-4a95-9e0b-7a48161d5d0c.dat'  -b '/data/dnb08/galaxy_db/files/f/9/4/dataset_f94e7844-204e-42a8-83e0-23adc4ca038b.dat'      -wb          > '/data/jwd05e/main/060/036/60036240/outputs/galaxy_dataset_1dbd5467-7362-4279-8f9f-225c450392c4.dat'",
+                                                        "command_version": "bedtools v2.30.0",
+                                                        "create_time": "2023-05-18T17:34:36.114094",
+                                                        "dependencies": [],
+                                                        "exit_code": 0,
+                                                        "external_id": "43511676",
+                                                        "galaxy_version": "23.0",
+                                                        "history_id": "a7e26bbbb0830b20",
+                                                        "id": "11ac94870d0bb33a3743b59ce7fc28ea",
+                                                        "inputs": {
+                                                            "inputA": {
+                                                                "id": "4838ba20a6d86765828ccbcc3eb28a4b",
+                                                                "src": "hda",
+                                                                "uuid": "cfb71055-95ff-4a95-9e0b-7a48161d5d0c"
+                                                            },
+                                                            "inputB": {
+                                                                "id": "4838ba20a6d867653f5bd69298cf67f1",
+                                                                "src": "hda",
+                                                                "uuid": "f94e7844-204e-42a8-83e0-23adc4ca038b"
+                                                            }
+                                                        },
+                                                        "job_messages": [],
+                                                        "job_metrics": [
+                                                            {
+                                                                "name": "hostname",
+                                                                "plugin": "hostname",
+                                                                "raw_value": "vgcnbwc-worker-c36m975-6047.novalocal",
+                                                                "title": "hostname",
+                                                                "value": "vgcnbwc-worker-c36m975-6047.novalocal"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_slots",
+                                                                "plugin": "core",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "Cores Allocated",
+                                                                "value": "1"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_memory_mb",
+                                                                "plugin": "core",
+                                                                "raw_value": "40960.0000000",
+                                                                "title": "Memory Allocated (MB)",
+                                                                "value": "40960"
+                                                            },
+                                                            {
+                                                                "name": "start_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684431305.0000000",
+                                                                "title": "Job Start Time",
+                                                                "value": "2023-05-18 19:35:05"
+                                                            },
+                                                            {
+                                                                "name": "end_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684431327.0000000",
+                                                                "title": "Job End Time",
+                                                                "value": "2023-05-18 19:35:27"
+                                                            },
+                                                            {
+                                                                "name": "runtime_seconds",
+                                                                "plugin": "core",
+                                                                "raw_value": "22.0000000",
+                                                                "title": "Job Runtime (Wall Clock)",
+                                                                "value": "22 seconds"
+                                                            },
+                                                            {
+                                                                "name": "cpuacct.usage",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "10840959112.0000000",
+                                                                "title": "CPU Time",
+                                                                "value": "10.840959112 seconds"
+                                                            },
+                                                            {
+                                                                "name": "memory.failcnt",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Failed to allocate memory count",
+                                                                "value": 0.0
+                                                            },
+                                                            {
+                                                                "name": "memory.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "41201008640.0000000",
+                                                                "title": "Memory limit on cgroup (MEM)",
+                                                                "value": "38.4 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "200916992.0000000",
+                                                                "title": "Max memory usage (MEM)",
+                                                                "value": "191.6 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "41201012736.0000000",
+                                                                "title": "Memory limit on cgroup (MEM+SWP)",
+                                                                "value": "38.4 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "200916992.0000000",
+                                                                "title": "Max memory usage (MEM+SWP)",
+                                                                "value": "191.6 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.oom_kill_disable",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "OOM Control enabled",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.under_oom",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Was OOM Killer active?",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.soft_limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "42949672960.0000000",
+                                                                "title": "Memory softlimit on cgroup",
+                                                                "value": "40.0 GB"
+                                                            }
+                                                        ],
+                                                        "job_stderr": "",
+                                                        "job_stdout": "",
+                                                        "model_class": "Job",
+                                                        "output_collections": {},
+                                                        "outputs": {
+                                                            "output": {
+                                                                "id": "4838ba20a6d86765192446f033baed74",
+                                                                "src": "hda",
+                                                                "uuid": "1dbd5467-7362-4279-8f9f-225c450392c4"
+                                                            }
+                                                        },
+                                                        "params": {
+                                                            "__input_ext": "\"input\"",
+                                                            "__workflow_invocation_uuid__": "\"389e354ef5a211eda9c3001e67d2ec02\"",
+                                                            "bed": "false",
+                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
+                                                            "count": "false",
+                                                            "dbkey": "\"?\"",
+                                                            "fraction_cond": "{\"__current_case__\": 0, \"fraction_select\": \"default\"}",
+                                                            "genome_file_opts": "{\"__current_case__\": 0, \"genome\": null, \"genome_file_opts_selector\": \"loc\"}",
+                                                            "header": "false",
+                                                            "invert": "false",
+                                                            "once": "false",
+                                                            "overlap_mode": "[\"-wb\"]",
+                                                            "reduce_or_iterate": "{\"__current_case__\": 0, \"inputB\": {\"values\": [{\"id\": 137365408, \"src\": \"hda\"}]}, \"reduce_or_iterate_selector\": \"iterate\"}",
+                                                            "sorted": "false",
+                                                            "split": "false",
+                                                            "strand": "\"\""
+                                                        },
+                                                        "state": "ok",
+                                                        "stderr": "",
+                                                        "stdout": "",
+                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0",
+                                                        "tool_stderr": "",
+                                                        "tool_stdout": "",
+                                                        "traceback": null,
+                                                        "update_time": "2023-05-18T17:35:28.719729",
+                                                        "user_email": "hxr@informatik.uni-freiburg.de"
+                                                    }
+                                                ],
+                                                "model_class": "WorkflowInvocationStep",
+                                                "order_index": 2,
+                                                "output_collections": {},
+                                                "outputs": {
+                                                    "output": {
+                                                        "id": "4838ba20a6d86765192446f033baed74",
+                                                        "src": "hda",
+                                                        "uuid": "1dbd5467-7362-4279-8f9f-225c450392c4"
+                                                    }
+                                                },
+                                                "state": "scheduled",
+                                                "subworkflow": null,
+                                                "subworkflow_invocation_id": null,
+                                                "update_time": "2023-05-18T17:35:28.700947",
+                                                "workflow_step_id": "0fe8e8a22ac078c9",
+                                                "workflow_step_label": null,
+                                                "workflow_step_uuid": "4fc2b17c-64d8-4c1c-a2d3-743f2ea9bcaf"
+                                            },
+                                            "3. Unnamed step": {
+                                                "action": null,
+                                                "id": "e6d3f79a3a3a71b2",
+                                                "job_id": "11ac94870d0bb33a8e9e3c167a533b1b",
+                                                "jobs": [
+                                                    {
+                                                        "command_line": "datamash      --group '4' countunique 10 < /data/dnb08/galaxy_db/files/1/d/b/dataset_1dbd5467-7362-4279-8f9f-225c450392c4.dat > '/data/jwd02f/main/060/036/60036241/outputs/galaxy_dataset_599c420f-e56b-4499-bf0e-16044fafff18.dat'",
+                                                        "command_version": null,
+                                                        "create_time": "2023-05-18T17:34:36.233576",
+                                                        "dependencies": [],
+                                                        "exit_code": 0,
+                                                        "external_id": "43511710",
+                                                        "galaxy_version": "23.0",
+                                                        "history_id": "a7e26bbbb0830b20",
+                                                        "id": "11ac94870d0bb33a8e9e3c167a533b1b",
+                                                        "inputs": {
+                                                            "in_file": {
+                                                                "id": "4838ba20a6d86765192446f033baed74",
+                                                                "src": "hda",
+                                                                "uuid": "1dbd5467-7362-4279-8f9f-225c450392c4"
+                                                            }
+                                                        },
+                                                        "job_messages": [],
+                                                        "job_metrics": [
+                                                            {
+                                                                "name": "hostname",
+                                                                "plugin": "hostname",
+                                                                "raw_value": "vgcnbwc-worker-c36m100-0658.novalocal",
+                                                                "title": "hostname",
+                                                                "value": "vgcnbwc-worker-c36m100-0658.novalocal"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_slots",
+                                                                "plugin": "core",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "Cores Allocated",
+                                                                "value": "1"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_memory_mb",
+                                                                "plugin": "core",
+                                                                "raw_value": "3891.0000000",
+                                                                "title": "Memory Allocated (MB)",
+                                                                "value": "3891"
+                                                            },
+                                                            {
+                                                                "name": "start_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684431348.0000000",
+                                                                "title": "Job Start Time",
+                                                                "value": "2023-05-18 19:35:48"
+                                                            },
+                                                            {
+                                                                "name": "end_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684431390.0000000",
+                                                                "title": "Job End Time",
+                                                                "value": "2023-05-18 19:36:30"
+                                                            },
+                                                            {
+                                                                "name": "runtime_seconds",
+                                                                "plugin": "core",
+                                                                "raw_value": "42.0000000",
+                                                                "title": "Job Runtime (Wall Clock)",
+                                                                "value": "42 seconds"
+                                                            },
+                                                            {
+                                                                "name": "cpuacct.usage",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "9364859094.0000000",
+                                                                "title": "CPU Time",
+                                                                "value": "9.364859094 seconds"
+                                                            },
+                                                            {
+                                                                "name": "memory.failcnt",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Failed to allocate memory count",
+                                                                "value": 0.0
+                                                            },
+                                                            {
+                                                                "name": "memory.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "4160749568.0000000",
+                                                                "title": "Memory limit on cgroup (MEM)",
+                                                                "value": "3.9 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "191201280.0000000",
+                                                                "title": "Max memory usage (MEM)",
+                                                                "value": "182.3 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "4219351040.0000000",
+                                                                "title": "Memory limit on cgroup (MEM+SWP)",
+                                                                "value": "3.9 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "191201280.0000000",
+                                                                "title": "Max memory usage (MEM+SWP)",
+                                                                "value": "182.3 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.oom_kill_disable",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "OOM Control enabled",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.under_oom",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Was OOM Killer active?",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.soft_limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Memory softlimit on cgroup",
+                                                                "value": "0 bytes"
+                                                            }
+                                                        ],
+                                                        "job_stderr": "",
+                                                        "job_stdout": "",
+                                                        "model_class": "Job",
+                                                        "output_collections": {},
+                                                        "outputs": {
+                                                            "out_file": {
+                                                                "id": "4838ba20a6d86765a402038d0b9964e3",
+                                                                "src": "hda",
+                                                                "uuid": "599c420f-e56b-4499-bf0e-16044fafff18"
+                                                            }
+                                                        },
+                                                        "params": {
+                                                            "__input_ext": "\"bed\"",
+                                                            "__workflow_invocation_uuid__": "\"389e354ef5a211eda9c3001e67d2ec02\"",
+                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
+                                                            "dbkey": "\"?\"",
+                                                            "grouping": "\"4\"",
+                                                            "header_in": "false",
+                                                            "header_out": "false",
+                                                            "ignore_case": "false",
+                                                            "need_sort": "false",
+                                                            "operations": "[{\"__index__\": 0, \"op_column\": \"10\", \"op_name\": \"countunique\"}]",
+                                                            "print_full_line": "false"
+                                                        },
+                                                        "state": "ok",
+                                                        "stderr": "",
+                                                        "stdout": "",
+                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+                                                        "tool_stderr": "",
+                                                        "tool_stdout": "",
+                                                        "traceback": null,
+                                                        "update_time": "2023-05-18T17:36:33.513106",
+                                                        "user_email": "hxr@informatik.uni-freiburg.de"
+                                                    }
+                                                ],
+                                                "model_class": "WorkflowInvocationStep",
+                                                "order_index": 3,
+                                                "output_collections": {},
+                                                "outputs": {
+                                                    "out_file": {
+                                                        "id": "4838ba20a6d86765a402038d0b9964e3",
+                                                        "src": "hda",
+                                                        "uuid": "599c420f-e56b-4499-bf0e-16044fafff18"
+                                                    }
+                                                },
+                                                "state": "scheduled",
+                                                "subworkflow": null,
+                                                "subworkflow_invocation_id": null,
+                                                "update_time": "2023-05-18T17:36:33.486731",
+                                                "workflow_step_id": "fcac47089ebdfbc2",
+                                                "workflow_step_label": null,
+                                                "workflow_step_uuid": "d6710e24-dbfb-4aef-8a63-2836cdc831e4"
+                                            },
+                                            "4. Unnamed step": {
+                                                "action": null,
+                                                "id": "0a5ce27d3453ffc8",
+                                                "job_id": "11ac94870d0bb33aa0e24ffdcb66ba6f",
+                                                "jobs": [
+                                                    {
+                                                        "command_line": "python '/opt/galaxy/server/tools/filters/sorter.py'  --input='/data/dnb08/galaxy_db/files/5/9/9/dataset_599c420f-e56b-4499-bf0e-16044fafff18.dat' --output='/data/jwd05e/main/060/036/60036242/outputs/galaxy_dataset_c8b6796e-41f3-41de-9a94-82a3e7c388b7.dat'    --key=2,2nr   --header 0",
+                                                        "command_version": null,
+                                                        "create_time": "2023-05-18T17:34:36.326397",
+                                                        "dependencies": [],
+                                                        "exit_code": 0,
+                                                        "external_id": "43511741",
+                                                        "galaxy_version": "23.0",
+                                                        "history_id": "a7e26bbbb0830b20",
+                                                        "id": "11ac94870d0bb33aa0e24ffdcb66ba6f",
+                                                        "inputs": {
+                                                            "input": {
+                                                                "id": "4838ba20a6d86765a402038d0b9964e3",
+                                                                "src": "hda",
+                                                                "uuid": "599c420f-e56b-4499-bf0e-16044fafff18"
+                                                            }
+                                                        },
+                                                        "job_messages": [],
+                                                        "job_metrics": [
+                                                            {
+                                                                "name": "hostname",
+                                                                "plugin": "hostname",
+                                                                "raw_value": "vgcnbwc-worker-c36m100-0658.novalocal",
+                                                                "title": "hostname",
+                                                                "value": "vgcnbwc-worker-c36m100-0658.novalocal"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_slots",
+                                                                "plugin": "core",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "Cores Allocated",
+                                                                "value": "1"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_memory_mb",
+                                                                "plugin": "core",
+                                                                "raw_value": "3891.0000000",
+                                                                "title": "Memory Allocated (MB)",
+                                                                "value": "3891"
+                                                            },
+                                                            {
+                                                                "name": "start_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684431414.0000000",
+                                                                "title": "Job Start Time",
+                                                                "value": "2023-05-18 19:36:54"
+                                                            },
+                                                            {
+                                                                "name": "end_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684431461.0000000",
+                                                                "title": "Job End Time",
+                                                                "value": "2023-05-18 19:37:41"
+                                                            },
+                                                            {
+                                                                "name": "runtime_seconds",
+                                                                "plugin": "core",
+                                                                "raw_value": "47.0000000",
+                                                                "title": "Job Runtime (Wall Clock)",
+                                                                "value": "47 seconds"
+                                                            },
+                                                            {
+                                                                "name": "cpuacct.usage",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "9815575101.0000000",
+                                                                "title": "CPU Time",
+                                                                "value": "9.815575101 seconds"
+                                                            },
+                                                            {
+                                                                "name": "memory.failcnt",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Failed to allocate memory count",
+                                                                "value": 0.0
+                                                            },
+                                                            {
+                                                                "name": "memory.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "4160749568.0000000",
+                                                                "title": "Memory limit on cgroup (MEM)",
+                                                                "value": "3.9 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "196067328.0000000",
+                                                                "title": "Max memory usage (MEM)",
+                                                                "value": "187.0 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "4219351040.0000000",
+                                                                "title": "Memory limit on cgroup (MEM+SWP)",
+                                                                "value": "3.9 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "196067328.0000000",
+                                                                "title": "Max memory usage (MEM+SWP)",
+                                                                "value": "187.0 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.oom_kill_disable",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "OOM Control enabled",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.under_oom",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Was OOM Killer active?",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.soft_limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Memory softlimit on cgroup",
+                                                                "value": "0 bytes"
+                                                            }
+                                                        ],
+                                                        "job_stderr": "",
+                                                        "job_stdout": "",
+                                                        "model_class": "Job",
+                                                        "output_collections": {},
+                                                        "outputs": {
+                                                            "out_file1": {
+                                                                "id": "4838ba20a6d867650b679d679c1fbabd",
+                                                                "src": "hda",
+                                                                "uuid": "c8b6796e-41f3-41de-9a94-82a3e7c388b7"
+                                                            }
+                                                        },
+                                                        "params": {
+                                                            "__input_ext": "\"tabular\"",
+                                                            "__workflow_invocation_uuid__": "\"389e354ef5a211eda9c3001e67d2ec02\"",
+                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
+                                                            "column": "\"2\"",
+                                                            "column_set": "[]",
+                                                            "dbkey": "\"?\"",
+                                                            "header_lines": "\"0\"",
+                                                            "order": "\"DESC\"",
+                                                            "style": "\"num\""
+                                                        },
+                                                        "state": "ok",
+                                                        "stderr": "",
+                                                        "stdout": "",
+                                                        "tool_id": "sort1",
+                                                        "tool_stderr": "",
+                                                        "tool_stdout": "",
+                                                        "traceback": null,
+                                                        "update_time": "2023-05-18T17:37:45.740051",
+                                                        "user_email": "hxr@informatik.uni-freiburg.de"
+                                                    }
+                                                ],
+                                                "model_class": "WorkflowInvocationStep",
+                                                "order_index": 4,
+                                                "output_collections": {},
+                                                "outputs": {
+                                                    "out_file1": {
+                                                        "id": "4838ba20a6d867650b679d679c1fbabd",
+                                                        "src": "hda",
+                                                        "uuid": "c8b6796e-41f3-41de-9a94-82a3e7c388b7"
+                                                    }
+                                                },
+                                                "state": "scheduled",
+                                                "subworkflow": null,
+                                                "subworkflow_invocation_id": null,
+                                                "update_time": "2023-05-18T17:37:45.722567",
+                                                "workflow_step_id": "e42696dd961f95d2",
+                                                "workflow_step_label": null,
+                                                "workflow_step_uuid": "4dd35991-4996-4f7d-8690-bde783f6fa6a"
+                                            },
+                                            "5. Unnamed step": {
+                                                "action": null,
+                                                "id": "06226aff05ce5d1f",
+                                                "job_id": "11ac94870d0bb33ad12002ce0209213b",
+                                                "jobs": [
+                                                    {
+                                                        "command_line": "head --lines 5 '/data/dnb08/galaxy_db/files/c/8/b/dataset_c8b6796e-41f3-41de-9a94-82a3e7c388b7.dat' > '/data/jwd05e/main/060/036/60036243/outputs/galaxy_dataset_2828298d-dc7b-431b-bf03-3f6955f19dc1.dat'",
+                                                        "command_version": "head (GNU coreutils) 8.25",
+                                                        "create_time": "2023-05-18T17:34:36.414517",
+                                                        "dependencies": [],
+                                                        "exit_code": 0,
+                                                        "external_id": "43511785",
+                                                        "galaxy_version": "23.0",
+                                                        "history_id": "a7e26bbbb0830b20",
+                                                        "id": "11ac94870d0bb33ad12002ce0209213b",
+                                                        "inputs": {
+                                                            "infile": {
+                                                                "id": "4838ba20a6d867650b679d679c1fbabd",
+                                                                "src": "hda",
+                                                                "uuid": "c8b6796e-41f3-41de-9a94-82a3e7c388b7"
+                                                            }
+                                                        },
+                                                        "job_messages": [],
+                                                        "job_metrics": [
+                                                            {
+                                                                "name": "hostname",
+                                                                "plugin": "hostname",
+                                                                "raw_value": "vgcnbwc-worker-c28m475-9359.novalocal",
+                                                                "title": "hostname",
+                                                                "value": "vgcnbwc-worker-c28m475-9359.novalocal"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_slots",
+                                                                "plugin": "core",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "Cores Allocated",
+                                                                "value": "1"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_memory_mb",
+                                                                "plugin": "core",
+                                                                "raw_value": "3891.0000000",
+                                                                "title": "Memory Allocated (MB)",
+                                                                "value": "3891"
+                                                            },
+                                                            {
+                                                                "name": "start_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684431479.0000000",
+                                                                "title": "Job Start Time",
+                                                                "value": "2023-05-18 19:37:59"
+                                                            },
+                                                            {
+                                                                "name": "end_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684431577.0000000",
+                                                                "title": "Job End Time",
+                                                                "value": "2023-05-18 19:39:37"
+                                                            },
+                                                            {
+                                                                "name": "runtime_seconds",
+                                                                "plugin": "core",
+                                                                "raw_value": "98.0000000",
+                                                                "title": "Job Runtime (Wall Clock)",
+                                                                "value": "1 minute"
+                                                            },
+                                                            {
+                                                                "name": "cpuacct.usage",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "160336864240.0000000",
+                                                                "title": "CPU Time",
+                                                                "value": "2 minutes"
+                                                            },
+                                                            {
+                                                                "name": "memory.failcnt",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "106968.0000000",
+                                                                "title": "Failed to allocate memory count",
+                                                                "value": 106968.0
+                                                            },
+                                                            {
+                                                                "name": "memory.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "4160749568.0000000",
+                                                                "title": "Memory limit on cgroup (MEM)",
+                                                                "value": "3.9 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "4160749568.0000000",
+                                                                "title": "Max memory usage (MEM)",
+                                                                "value": "3.9 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "9223372036854771712.0000000",
+                                                                "title": "Memory limit on cgroup (MEM+SWP)",
+                                                                "value": "8.0 EB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "4160880640.0000000",
+                                                                "title": "Max memory usage (MEM+SWP)",
+                                                                "value": "3.9 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.oom_kill_disable",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "OOM Control enabled",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.under_oom",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Was OOM Killer active?",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.soft_limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Memory softlimit on cgroup",
+                                                                "value": "0 bytes"
+                                                            }
+                                                        ],
+                                                        "job_stderr": "",
+                                                        "job_stdout": "",
+                                                        "model_class": "Job",
+                                                        "output_collections": {},
+                                                        "outputs": {
+                                                            "outfile": {
+                                                                "id": "4838ba20a6d86765d96edf23a7ca38c5",
+                                                                "src": "hda",
+                                                                "uuid": "2828298d-dc7b-431b-bf03-3f6955f19dc1"
+                                                            }
+                                                        },
+                                                        "params": {
+                                                            "__input_ext": "\"tabular\"",
+                                                            "__workflow_invocation_uuid__": "\"389e354ef5a211eda9c3001e67d2ec02\"",
+                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
+                                                            "complement": "\"\"",
+                                                            "count": "\"5\"",
+                                                            "dbkey": "\"?\""
+                                                        },
+                                                        "state": "ok",
+                                                        "stderr": "",
+                                                        "stdout": "",
+                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0",
+                                                        "tool_stderr": "",
+                                                        "tool_stdout": "",
+                                                        "traceback": null,
+                                                        "update_time": "2023-05-18T17:39:41.632086",
+                                                        "user_email": "hxr@informatik.uni-freiburg.de"
+                                                    }
+                                                ],
+                                                "model_class": "WorkflowInvocationStep",
+                                                "order_index": 5,
+                                                "output_collections": {},
+                                                "outputs": {
+                                                    "outfile": {
+                                                        "id": "4838ba20a6d86765d96edf23a7ca38c5",
+                                                        "src": "hda",
+                                                        "uuid": "2828298d-dc7b-431b-bf03-3f6955f19dc1"
+                                                    }
+                                                },
+                                                "state": "scheduled",
+                                                "subworkflow": null,
+                                                "subworkflow_invocation_id": null,
+                                                "update_time": "2023-05-18T17:39:41.615934",
+                                                "workflow_step_id": "4c5e84542536cc7c",
+                                                "workflow_step_label": null,
+                                                "workflow_step_uuid": "820fd964-2460-4b50-8491-968d796500fc"
+                                            },
+                                            "6. Unnamed step": {
+                                                "action": null,
+                                                "id": "9869e0dcfb157198",
+                                                "job_id": "11ac94870d0bb33a1d0bbfc0189b52a3",
+                                                "jobs": [
+                                                    {
+                                                        "command_line": "python /opt/galaxy/server/tools/filters/joinWrapper.py /data/dnb08/galaxy_db/files/c/f/b/dataset_cfb71055-95ff-4a95-9e0b-7a48161d5d0c.dat /data/dnb08/galaxy_db/files/2/8/2/dataset_2828298d-dc7b-431b-bf03-3f6955f19dc1.dat 4 1 N /data/jwd02f/main/060/036/60036244/outputs/galaxy_dataset_1c27a522-57c3-4dd6-a98b-2978def89473.dat",
+                                                        "command_version": null,
+                                                        "create_time": "2023-05-18T17:34:36.507964",
+                                                        "dependencies": [],
+                                                        "exit_code": 0,
+                                                        "external_id": "43511832",
+                                                        "galaxy_version": "23.0",
+                                                        "history_id": "a7e26bbbb0830b20",
+                                                        "id": "11ac94870d0bb33a1d0bbfc0189b52a3",
+                                                        "inputs": {
+                                                            "input1": {
+                                                                "id": "4838ba20a6d86765828ccbcc3eb28a4b",
+                                                                "src": "hda",
+                                                                "uuid": "cfb71055-95ff-4a95-9e0b-7a48161d5d0c"
+                                                            },
+                                                            "input2": {
+                                                                "id": "4838ba20a6d86765d96edf23a7ca38c5",
+                                                                "src": "hda",
+                                                                "uuid": "2828298d-dc7b-431b-bf03-3f6955f19dc1"
+                                                            }
+                                                        },
+                                                        "job_messages": [],
+                                                        "job_metrics": [
+                                                            {
+                                                                "name": "hostname",
+                                                                "plugin": "hostname",
+                                                                "raw_value": "vgcnbwc-worker-c36m100-0658.novalocal",
+                                                                "title": "hostname",
+                                                                "value": "vgcnbwc-worker-c36m100-0658.novalocal"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_slots",
+                                                                "plugin": "core",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "Cores Allocated",
+                                                                "value": "1"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_memory_mb",
+                                                                "plugin": "core",
+                                                                "raw_value": "3891.0000000",
+                                                                "title": "Memory Allocated (MB)",
+                                                                "value": "3891"
+                                                            },
+                                                            {
+                                                                "name": "start_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684431607.0000000",
+                                                                "title": "Job Start Time",
+                                                                "value": "2023-05-18 19:40:07"
+                                                            },
+                                                            {
+                                                                "name": "end_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684431645.0000000",
+                                                                "title": "Job End Time",
+                                                                "value": "2023-05-18 19:40:45"
+                                                            },
+                                                            {
+                                                                "name": "runtime_seconds",
+                                                                "plugin": "core",
+                                                                "raw_value": "38.0000000",
+                                                                "title": "Job Runtime (Wall Clock)",
+                                                                "value": "38 seconds"
+                                                            },
+                                                            {
+                                                                "name": "cpuacct.usage",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "9278612295.0000000",
+                                                                "title": "CPU Time",
+                                                                "value": "9.278612295 seconds"
+                                                            },
+                                                            {
+                                                                "name": "memory.failcnt",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Failed to allocate memory count",
+                                                                "value": 0.0
+                                                            },
+                                                            {
+                                                                "name": "memory.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "4160749568.0000000",
+                                                                "title": "Memory limit on cgroup (MEM)",
+                                                                "value": "3.9 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "191029248.0000000",
+                                                                "title": "Max memory usage (MEM)",
+                                                                "value": "182.2 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "4219351040.0000000",
+                                                                "title": "Memory limit on cgroup (MEM+SWP)",
+                                                                "value": "3.9 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "191029248.0000000",
+                                                                "title": "Max memory usage (MEM+SWP)",
+                                                                "value": "182.2 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.oom_kill_disable",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "OOM Control enabled",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.under_oom",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Was OOM Killer active?",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.soft_limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Memory softlimit on cgroup",
+                                                                "value": "0 bytes"
+                                                            }
+                                                        ],
+                                                        "job_stderr": "",
+                                                        "job_stdout": "",
+                                                        "model_class": "Job",
+                                                        "output_collections": {},
+                                                        "outputs": {
+                                                            "out_file1": {
+                                                                "id": "4838ba20a6d8676569e7a7744709f3b7",
+                                                                "src": "hda",
+                                                                "uuid": "1c27a522-57c3-4dd6-a98b-2978def89473"
+                                                            }
+                                                        },
+                                                        "params": {
+                                                            "__input_ext": "\"bed\"",
+                                                            "__workflow_invocation_uuid__": "\"389e354ef5a211eda9c3001e67d2ec02\"",
+                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
+                                                            "dbkey": "\"?\"",
+                                                            "field1": "\"4\"",
+                                                            "field2": "\"1\"",
+                                                            "mode": "\"N\""
+                                                        },
+                                                        "state": "ok",
+                                                        "stderr": "",
+                                                        "stdout": "join (GNU coreutils) 8.30\nCopyright (C) 2018 Free Software Foundation, Inc.\nLicense GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.\nThis is free software: you are free to change and redistribute it.\nThere is NO WARRANTY, to the extent permitted by law.\n\nWritten by Mike Haertel.\n",
+                                                        "tool_id": "comp1",
+                                                        "tool_stderr": "",
+                                                        "tool_stdout": "join (GNU coreutils) 8.30\nCopyright (C) 2018 Free Software Foundation, Inc.\nLicense GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.\nThis is free software: you are free to change and redistribute it.\nThere is NO WARRANTY, to the extent permitted by law.\n\nWritten by Mike Haertel.\n",
+                                                        "traceback": null,
+                                                        "update_time": "2023-05-18T17:40:47.707639",
+                                                        "user_email": "hxr@informatik.uni-freiburg.de"
+                                                    }
+                                                ],
+                                                "model_class": "WorkflowInvocationStep",
+                                                "order_index": 6,
+                                                "output_collections": {},
+                                                "outputs": {
+                                                    "out_file1": {
+                                                        "id": "4838ba20a6d8676569e7a7744709f3b7",
+                                                        "src": "hda",
+                                                        "uuid": "1c27a522-57c3-4dd6-a98b-2978def89473"
+                                                    }
+                                                },
+                                                "state": "scheduled",
+                                                "subworkflow": null,
+                                                "subworkflow_invocation_id": null,
+                                                "update_time": "2023-05-18T17:40:47.686290",
+                                                "workflow_step_id": "70e011a3c2da60d6",
+                                                "workflow_step_label": null,
+                                                "workflow_step_uuid": "52698c72-b6cc-4ca4-84b0-c84dd018e389"
+                                            }
+                                        }
+                                    },
+                                    "problem_log": "No log for this engine type.",
+                                    "start_datetime": "2023-05-18T19:32:20.395205",
+                                    "status": "success"
+                                },
+                                "doc": "Test sample data for the workflow",
+                                "has_data": true,
+                                "id": "galaxy-intro-101-workflow.ga_0",
+                                "test_type": "galaxy_workflow"
                             }
                         ],
-                        "position": {
-                            "left": 345.2278179241512,
-                            "top": 0
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_uep_opt/pm_uep_opt/0.3.0+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "eea73e1f65cb",
-                            "name": "pm_uep_opt",
-                            "owner": "muon-spectroscopy-computational-project",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"castep_log\": {\"__class__\": \"ConnectedValue\"}, \"charge_density\": {\"__class__\": \"ConnectedValue\"}, \"chromInfo\": \"/srv/galaxy/var/tool_data/shared/ucsc/chrom/?.len\", \"generation_params\": {\"poisson_r\": \"0.6\", \"vdw_scale\": \"0.5\", \"random_seed\": null, \"allpos_ext\": \"cif\"}, \"optimisation_params\": {\"geom_steps\": \"30\", \"geom_force_tol\": \"0.05\", \"uep_gw_factor\": \"5.0\"}, \"structure\": {\"__class__\": \"ConnectedValue\"}, \"testing\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3.0+galaxy1",
-                        "type": "tool",
-                        "uuid": "22131f07-c4c4-4ec0-9a45-5c8c8069600c",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "All muons in host material",
-                                "output_name": "allpos_file",
-                                "uuid": "f3be7cd2-3974-49f2-aa0e-96c79b4ab34c"
-                            }
-                        ]
+                        "version": "0.1"
                     }
-                ],
-                "parent_id": "materials-science/muon-stopping-sites-muairss-uep",
-                "path": "topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/workflows/muairss-uep.ga",
-                "tags": [],
-                "test_results": null,
+                },
                 "tests": true,
-                "title": "Finding the Muon Stopping Site: pymuon-suite in Galaxy",
-                "topic_id": "materials-science",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/materials-science-muon-stopping-sites-muairss-uep/versions/muairss-uep",
-                "tutorial_id": "muon-stopping-sites-muairss-uep",
-                "url": "https://training.galaxyproject.org/training-material/topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/workflows/muairss-uep.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/workflows/muairss-uep.html",
-                "version": 1,
-                "wfid": "materials-science-muon-stopping-sites-muairss-uep",
-                "wfname": "muairss-uep",
-                "workflow": "muairss-uep.ga",
+                "title": "Find exons with the highest number of features",
+                "topic_id": "introduction",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/introduction-galaxy-intro-101/versions/galaxy-intro-101-workflow",
+                "tutorial_id": "galaxy-intro-101",
+                "url": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow.html",
+                "version": 5,
+                "wfid": "introduction-galaxy-intro-101",
+                "wfname": "galaxy-intro-101-workflow",
+                "workflow": "galaxy-intro-101-workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_muairss_read/pm_muairss_read/0.3.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_uep_opt/pm_uep_opt/0.3.0+galaxy1"
+                    "comp1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0"
                 ],
-                "workflowhub_id": "1109"
+                "workflowhub_id": "1106"
             }
         ],
-        "zenodo_link": "https://zenodo.org/records/10219558"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.4104428"
     },
     {
         "admin_install": {
@@ -131468,171 +134650,208 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "join_files_on_column_fuzzy",
+                    "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "22ec3c1a20cd",
+                    "revisions": "d698c222f354",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cardinal_classification",
-                    "owner": "galaxyp",
-                    "revisions": "b574b84afc4d",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cardinal_combine",
-                    "owner": "galaxyp",
-                    "revisions": "48c07268f341",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cardinal_mz_images",
-                    "owner": "galaxyp",
-                    "revisions": "25b83cbd596a",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cardinal_preprocessing",
-                    "owner": "galaxyp",
-                    "revisions": "ed9ed1e6cca2",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cardinal_quality_report",
-                    "owner": "galaxyp",
-                    "revisions": "3b7a35d50ebf",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cardinal_segmentations",
-                    "owner": "galaxyp",
-                    "revisions": "82f6c2f4332d",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "maldi_quant_peak_detection",
-                    "owner": "galaxyp",
-                    "revisions": "e9300ef37403",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "datamash_ops",
+                    "owner": "iuc",
+                    "revisions": "562f3c677828",
+                    "tool_panel_section_label": "Join, Subtract and Group",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "maldi_quant_preprocessing",
-                    "owner": "galaxyp",
-                    "revisions": "71411ac28268",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "ggplot2_point",
+                    "owner": "iuc",
+                    "revisions": "1acf88921176",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: join_files_on_column_fuzzy\n  owner: bgruening\n  revisions: 22ec3c1a20cd\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_classification\n  owner: galaxyp\n  revisions: b574b84afc4d\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_combine\n  owner: galaxyp\n  revisions: 48c07268f341\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_mz_images\n  owner: galaxyp\n  revisions: 25b83cbd596a\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_preprocessing\n  owner: galaxyp\n  revisions: ed9ed1e6cca2\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_quality_report\n  owner: galaxyp\n  revisions: 3b7a35d50ebf\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_segmentations\n  owner: galaxyp\n  revisions: 82f6c2f4332d\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maldi_quant_peak_detection\n  owner: galaxyp\n  revisions: e9300ef37403\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maldi_quant_preprocessing\n  owner: galaxyp\n  revisions: 71411ac28268\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 562f3c677828\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ggplot2_point\n  owner: iuc\n  revisions: 1acf88921176\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.json",
         "contributors": [
+            {
+                "elixir_node": "no",
+                "id": "annefou",
+                "joined": "2019-07",
+                "name": "Anne Fouilloux",
+                "orcid": "0000-0002-1784-2920",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annefou/",
+                "twitter": "AnneFouilloux",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/annefou.json"
+            },
+            {
+                "email": "nadia.goue@uca.fr",
+                "id": "nagoue",
+                "joined": "2019-07",
+                "name": "Nadia Gou\u00e9",
+                "orcid": "0000-0003-2750-1473",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nagoue/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nagoue.json"
+            },
+            {
+                "id": "chrisbarnettster",
+                "joined": "2019-05",
+                "name": "Christopher Barnett",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/chrisbarnettster/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/chrisbarnettster.json"
+            },
+            {
+                "id": "michelemaroni89",
+                "joined": "2019-07",
+                "name": "Michele Maroni",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/michelemaroni89/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/michelemaroni89.json"
+            },
+            {
+                "id": "olanag1",
+                "joined": "2019-07",
+                "name": "Olha Nahorna",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/olanag1/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/olanag1.json"
+            },
+            {
+                "id": "tnabtaf",
+                "joined": "2017-09",
+                "name": "Dave Clements",
+                "orcid": "0000-0002-9970-6657",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
+            },
             {
                 "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
                     "uni-freiburg"
                 ],
-                "email": "melanie.foell@mol-med.uni-freiburg.de",
-                "id": "foellmelanie",
-                "joined": "2018-10",
-                "matrix": "foellmelanie:matrix.org",
-                "name": "Melanie F\u00f6ll",
-                "orcid": "0000-0002-1887-7543",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
-                "twitter": "MCFoell",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             }
         ],
-        "dir": "topics/metabolomics/tutorials/msi-finding-nglycans",
-        "edam_operation": [],
+        "dir": "topics/introduction/tutorials/galaxy-intro-101-everyone",
+        "edam_operation": [
+            "Visualisation"
+        ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "metabolomics/msi-finding-nglycans",
+        "id": "introduction/galaxy-intro-101-everyone",
         "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
+            "Galaxy@AuBi",
+            "MISSISSIPPI",
+            "UseGalaxy.be",
+            "UseGalaxy.cz"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Several files can be combined and the spectra used to obtain the annotation of their original file.",
-            "Preprocessing reduces the file size and can improve further analysis steps.",
-            "Unsupervised and supervised statistical analysis can reveal analytes with different abundances.",
-            "The spatial distribution of N-glycans in a tissue section can be measured by MALDI imaging.",
-            "Additional LC-MS/MS experiments enable the identification of N-glycans measured by MSI.",
-            "Some N-glycans are located to specific kidney compartments."
+            "Galaxy provides an easy-to-use graphical user interface for often complex command-line tools",
+            "Galaxy keeps a full record of your analysis in a history",
+            "Workflows enable you to repeat your analysis on different data",
+            "Galaxy can connect to external sources for data import and visualization purposes",
+            "Galaxy provides ways to share your results and methods with others"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Combining MSI datasets while using the information about each subfile in further steps.",
-            "Preprocessing raw MSI data.",
-            "Performing supervised and unsupervised statistical analysis."
+            "Familiarize yourself with the basics of Galaxy",
+            "Learn how to obtain data from external sources",
+            "Learn how to tag datasets",
+            "Learn how to run tools",
+            "Learn how histories work",
+            "Learn how to create a workflow",
+            "Learn how to share your work"
         ],
-        "pageviews": 2426,
-        "pub_date": "2019-04-13",
+        "pageviews": 25425,
+        "priority": 2,
+        "pub_date": "2019-11-14",
         "questions": [
-            "Can N-linked glycans from FFPE tissues be detected by MALDI imaging?",
-            "Can potential N-linked glycans be identified by an additional LC-MS/MS experiment?",
-            "Do specific kidney compartments have different N-linked glycan compositions?"
+            "What are the differences between the Iris species?"
         ],
-        "requirements": [
+        "recordings": [
             {
-                "topic_name": "proteomics",
-                "tutorials": [
-                    "mass-spectrometry-imaging-loading-exploring-data"
+                "captioners": [
+                    "astrovsky01"
                 ],
-                "type": "internal"
+                "date": "2023-05-01",
+                "galaxy_version": "23.0",
+                "length": "20M",
+                "speakers": [
+                    "astrovsky01"
+                ],
+                "youtube_id": "64oS5uXVRV0"
+            },
+            {
+                "captioners": [
+                    "tnabtaf"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "1H15M",
+                "speakers": [
+                    "annefou",
+                    "rwinand"
+                ],
+                "youtube_id": "dguN6Xw2Azs"
             }
         ],
-        "short_id": "T00199",
+        "short_id": "T00187",
         "short_tools": [
-            "Grep1",
-            "cardinal_combine",
-            "cardinal_mz_images",
-            "cardinal_preprocessing",
-            "join_files_on_column_fuzzy",
-            "cardinal_quality_report",
-            "cardinal_segmentations",
-            "cardinal_classification",
-            "Filter1",
-            "maldi_quant_peak_detection",
-            "maldi_quant_preprocessing",
-            "Summary_Statistics1"
+            "tp_sorted_uniq",
+            "csv_to_tabular",
+            "upload1",
+            "ggplot2_point",
+            "Cut1",
+            "Remove beginning1",
+            "datamash_ops",
+            "Grouping1"
         ],
         "slides": false,
         "slides_recordings": false,
+        "subtopic": "core",
         "supported_servers": {
             "exact": [
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.fr",
@@ -131645,89 +134864,177 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 }
+            ],
+            "inexact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
             ]
         },
         "symlink": null,
-        "time_estimation": "2H",
-        "title": "Mass spectrometry imaging: Finding differential analytes",
+        "time_estimation": "1H30M",
+        "title": "Galaxy Basics for everyone",
         "tools": [
-            "Filter1",
-            "Grep1",
-            "Summary_Statistics1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy/1.0.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/1.12.1.3",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.3",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.2",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/1.12.1.3",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.3",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.3",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.4",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.3"
+            "Cut1",
+            "Grouping1",
+            "Remove beginning1",
+            "csv_to_tabular",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
+            "upload1"
         ],
-        "topic_name": "metabolomics",
-        "topic_name_human": "Metabolomics",
+        "topic_name": "introduction",
+        "topic_name_human": "Introduction to Galaxy Analyses",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "msi-finding-nglycans",
+        "tutorial_name": "galaxy-intro-101-everyone",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.json"
         },
-        "version": 9,
+        "version": 32,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 112,
-        "visitors": 1648,
+        "visit_duration": 251,
+        "visitors": 15289,
         "workflows": [
             {
                 "creators": [],
-                "description": "Mass spectrometry imaging: Finding differential analytes",
+                "description": "introduction",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntreated\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontrol\"]\n  10[label=\"MSI classification\"]\n  9 -> 10 [label=\"outfile_imzml\"]\n  4 -> 10 [label=\"pixel_annotations\"]\n  11[label=\"MSI segmentation\"]\n  9 -> 11 [label=\"outfile_imzml\"]\n  12[label=\"Filter\"]\n  10 -> 12 [label=\"mzfeatures\"]\n  13[label=\"Join two files\"]\n  12 -> 13 [label=\"out_file1\"]\n  2 -> 13 [label=\"output\"]\n  14[label=\"Summary Statistics\"]\n  13 -> 14 [label=\"merged_file\"]\n  15[label=\"MSI mz images\"]\n  13 -> 15 [label=\"merged_file\"]\n  3 -> 15 [label=\"output\"]\n  16[label=\"Select\"]\n  13 -> 16 [label=\"merged_file\"]\n  17[label=\"MSI mz images\"]\n  16 -> 17 [label=\"out_file1\"]\n  3 -> 17 [label=\"output\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGlycan_IDs\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nall_files\"]\n  4[label=\"MSI combine\"]\n  1 -> 4 [label=\"output\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"MSI preprocessing\"]\n  4 -> 5 [label=\"outfile_imzml\"]\n  6[label=\"MSI Qualitycontrol\"]\n  4 -> 6 [label=\"outfile_imzml\"]\n  4 -> 6 [label=\"pixel_annotations\"]\n  7[label=\"MALDIquant preprocessing\"]\n  5 -> 7 [label=\"outfile_imzml\"]\n  8[label=\"MALDIquant peak detection\"]\n  7 -> 8 [label=\"outfile_imzml\"]\n  4 -> 8 [label=\"pixel_annotations\"]\n  9[label=\"MSI preprocessing\"]\n  5 -> 9 [label=\"outfile_imzml\"]\n  8 -> 9 [label=\"intensity_matrix\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\niris\"]\n  1[label=\"Convert CSV to tabular\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Datamash\"]\n  1 -> 2 [label=\"tabular\"]\n  k254f1b4bd4664f0e8c460e97bbedae4d[color=lightseagreen,label=\"Output\\ndatamash_output\"]\n  2 -> k254f1b4bd4664f0e8c460e97bbedae4d\n  3[label=\"Remove beginning\"]\n  1 -> 3 [label=\"tabular\"]\n  4[label=\"Cut\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"Group\"]\n  3 -> 5 [label=\"out_file1\"]\n  ka689bddf14d04a72b1f9c34d8f50d2b3[color=lightseagreen,label=\"Output\\ngroup1\"]\n  5 -> ka689bddf14d04a72b1f9c34d8f50d2b3\n  6[label=\"Group\"]\n  3 -> 6 [label=\"out_file1\"]\n  kac7c73b258dd4c6e85ceddf49323b206[color=lightseagreen,label=\"Output\\ngroup2\"]\n  6 -> kac7c73b258dd4c6e85ceddf49323b206\n  7[label=\"Scatterplot with ggplot2\"]\n  3 -> 7 [label=\"out_file1\"]\n  8[label=\"Scatterplot with ggplot2\"]\n  3 -> 8 [label=\"out_file1\"]\n  9[label=\"Unique\"]\n  4 -> 9 [label=\"out_file1\"]\n  k8a2b5e30d42a401996744b4af00c820a[color=lightseagreen,label=\"Output\\nunique_output\"]\n  9 -> k8a2b5e30d42a401996744b4af00c820a\n}",
                 "history": [
+                    {
+                        "hash": "f5ec1c92ee0b0329a1ad5c6d52aa0e3fe82d9583",
+                        "message": "Update ggplot2 tool in galaxy101 for everyone",
+                        "num": 14,
+                        "short_hash": "f5ec1c92e",
+                        "unix": "1647276023"
+                    },
+                    {
+                        "hash": "2d1282226e93ab129a1459e45f1d26a3ba9d2411",
+                        "message": "Add workflow test.",
+                        "num": 13,
+                        "short_hash": "2d1282226",
+                        "unix": "1603313786"
+                    },
+                    {
+                        "hash": "4117bd414ffc93a9c46fe312804b63f3018d9fc4",
+                        "message": "Update tutorial workflow and data-library record",
+                        "num": 12,
+                        "short_hash": "4117bd414",
+                        "unix": "1594838956"
+                    },
+                    {
+                        "hash": "e0df2c97232b8455db1d38f63ffdfb69bb8d6389",
+                        "message": "annotation added",
+                        "num": 11,
+                        "short_hash": "e0df2c972",
+                        "unix": "1581629210"
+                    },
+                    {
+                        "hash": "232ce03723ab9acbd124828954705c1cd2679abd",
+                        "message": "removed name label bit",
+                        "num": 10,
+                        "short_hash": "232ce0372",
+                        "unix": "1581615057"
+                    },
+                    {
+                        "hash": "cccd85216e3d9baaca787eb7ae8808bd5f3fa2dc",
+                        "message": "minor tweaks and files unhidden",
+                        "num": 9,
+                        "short_hash": "cccd85216",
+                        "unix": "1581613998"
+                    },
                     {
                         "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
                         "message": "annotation",
-                        "num": 4,
+                        "num": 8,
                         "short_hash": "667ff3de9",
                         "unix": "1579690769"
                     },
                     {
                         "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
                         "message": "Workflow renaming",
-                        "num": 3,
+                        "num": 7,
                         "short_hash": "eb4d724e0",
                         "unix": "1579084895"
                     },
                     {
-                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
-                        "message": "unflatten workflows",
+                        "hash": "de5e2cb89a0a9f4c3ed598c448cd9cd784a706db",
+                        "message": "csv_to_tabular",
+                        "num": 6,
+                        "short_hash": "de5e2cb89",
+                        "unix": "1578923859"
+                    },
+                    {
+                        "hash": "495f4d8d3dd2309d3780edef4c3b449ae5f871f4",
+                        "message": "Workflows fix",
+                        "num": 5,
+                        "short_hash": "495f4d8d3",
+                        "unix": "1578666747"
+                    },
+                    {
+                        "hash": "a38709a415104f50fc1cbd4ac2fedccc82a0919d",
+                        "message": "workflow: update title and remove duplicate datamash step",
+                        "num": 4,
+                        "short_hash": "a38709a41",
+                        "unix": "1573571116"
+                    },
+                    {
+                        "hash": "156b6c7efa1ef3240e2118d38611650ad5a340fe",
+                        "message": "fix formatting issues, images and replace workflow",
+                        "num": 3,
+                        "short_hash": "156b6c7ef",
+                        "unix": "1568975444"
+                    },
+                    {
+                        "hash": "4fdfd40a0df85861f6b4f05762663b07b6602a87",
+                        "message": "fix format workflow in intro for everyone",
                         "num": 2,
-                        "short_hash": "faf6d298a",
-                        "unix": "1576155753"
+                        "short_hash": "4fdfd40a0",
+                        "unix": "1568360318"
                     },
                     {
-                        "hash": "6b3331c232d6cad52bbb091eb603f290ffbc6b99",
-                        "message": "Adding MSI N-glycan training and small updates for the other MSI trainings (#1333)",
+                        "hash": "d90d12a047f0362c6aeb9490791f69c0aaee43b4",
+                        "message": "draft galaxy 101 for everyone with Iris dataset. - added introduction, workflow, data library.",
                         "num": 1,
-                        "short_hash": "6b3331c23",
-                        "unix": "1555170721"
+                        "short_hash": "d90d12a04",
+                        "unix": "1562484318"
                     }
                 ],
                 "inputs": [
@@ -131737,856 +135044,972 @@
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "treated",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 445.683349609375,
-                            "top": 324.8666687011719
-                        },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "337046f2-275b-4fc6-a661-16de8e6be533",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "924c77fb-2ed6-4cb2-81bc-dea777294df0"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "control",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 442.95001220703125,
-                            "top": 407.2833251953125
-                        },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "e5ee3457-2418-42ca-855e-b033b15d1eec",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "78357d0f-3571-45a2-9c8c-a06ca31a1c9f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Glycan_IDs"
+                                "name": "iris"
                             }
                         ],
-                        "label": "Glycan_IDs",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 449.91668701171875,
-                            "top": 1052.3666687011719
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Glycan_IDs\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "78e307cf-92b5-4d1b-89d7-0ebeb7c845b7",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "a028d3d6-38e3-43f7-a023-321178108dc7"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "all_files",
+                        "label": "iris",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 447,
-                            "top": 1146.7167053222656
+                            "bottom": 210.20000839233398,
+                            "height": 61.79999923706055,
+                            "left": 296.5,
+                            "right": 496.5,
+                            "top": 148.40000915527344,
+                            "width": 200,
+                            "x": 296.5,
+                            "y": 148.40000915527344
                         },
                         "tool_id": null,
-                        "tool_state": "{}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "1f30f371-a9c5-4638-a9bd-a69d7a7ee1ec",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "07af2e13-4f7d-4454-8644-4d8cda30eb70"
-                            }
-                        ]
+                        "uuid": "6a8d8ca9-8bb9-414b-af8f-50d07721b363",
+                        "workflow_outputs": []
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ntreated\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ncontrol\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"MSI classification\"];\n  9 -->|outfile_imzml| 10;\n  4 -->|pixel_annotations| 10;\n  11[\"MSI segmentation\"];\n  9 -->|outfile_imzml| 11;\n  12[\"Filter\"];\n  10 -->|mzfeatures| 12;\n  13[\"Join two files\"];\n  12 -->|out_file1| 13;\n  2 -->|output| 13;\n  14[\"Summary Statistics\"];\n  13 -->|merged_file| 14;\n  15[\"MSI mz images\"];\n  13 -->|merged_file| 15;\n  3 -->|output| 15;\n  16[\"Select\"];\n  13 -->|merged_file| 16;\n  17[\"MSI mz images\"];\n  16 -->|out_file1| 17;\n  3 -->|output| 17;\n  2[\"\u2139\ufe0f Input Dataset\\nGlycan_IDs\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nall_files\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"MSI combine\"];\n  1 -->|output| 4;\n  0 -->|output| 4;\n  5[\"MSI preprocessing\"];\n  4 -->|outfile_imzml| 5;\n  6[\"MSI Qualitycontrol\"];\n  4 -->|outfile_imzml| 6;\n  4 -->|pixel_annotations| 6;\n  7[\"MALDIquant preprocessing\"];\n  5 -->|outfile_imzml| 7;\n  8[\"MALDIquant peak detection\"];\n  7 -->|outfile_imzml| 8;\n  4 -->|pixel_annotations| 8;\n  9[\"MSI preprocessing\"];\n  5 -->|outfile_imzml| 9;\n  8 -->|intensity_matrix| 9;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "MSI Finding Diff Analytes",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\niris\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Convert CSV to tabular\"];\n  0 -->|output| 1;\n  2[\"Datamash\"];\n  1 -->|tabular| 2;\n  254f1b4b-d466-4f0e-8c46-0e97bbedae4d[\"Output\\ndatamash_output\"];\n  2 --> 254f1b4b-d466-4f0e-8c46-0e97bbedae4d;\n  style 254f1b4b-d466-4f0e-8c46-0e97bbedae4d stroke:#2c3143,stroke-width:4px;\n  3[\"Remove beginning\"];\n  1 -->|tabular| 3;\n  4[\"Cut\"];\n  3 -->|out_file1| 4;\n  5[\"Group\"];\n  3 -->|out_file1| 5;\n  a689bddf-14d0-4a72-b1f9-c34d8f50d2b3[\"Output\\ngroup1\"];\n  5 --> a689bddf-14d0-4a72-b1f9-c34d8f50d2b3;\n  style a689bddf-14d0-4a72-b1f9-c34d8f50d2b3 stroke:#2c3143,stroke-width:4px;\n  6[\"Group\"];\n  3 -->|out_file1| 6;\n  ac7c73b2-58dd-4c6e-85ce-ddf49323b206[\"Output\\ngroup2\"];\n  6 --> ac7c73b2-58dd-4c6e-85ce-ddf49323b206;\n  style ac7c73b2-58dd-4c6e-85ce-ddf49323b206 stroke:#2c3143,stroke-width:4px;\n  7[\"Scatterplot with ggplot2\"];\n  3 -->|out_file1| 7;\n  8[\"Scatterplot with ggplot2\"];\n  3 -->|out_file1| 8;\n  9[\"Unique\"];\n  4 -->|out_file1| 9;\n  8a2b5e30-d42a-4019-9674-4b4af00c820a[\"Output\\nunique_output\"];\n  9 --> 8a2b5e30-d42a-4019-9674-4b4af00c820a;\n  style 8a2b5e30-d42a-4019-9674-4b4af00c820a stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "GTN Training: Galaxy 101 For Everyone",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "treated",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 445.683349609375,
-                            "top": 324.8666687011719
-                        },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "337046f2-275b-4fc6-a661-16de8e6be533",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "924c77fb-2ed6-4cb2-81bc-dea777294df0"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "control",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 442.95001220703125,
-                            "top": 407.2833251953125
-                        },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "e5ee3457-2418-42ca-855e-b033b15d1eec",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "78357d0f-3571-45a2-9c8c-a06ca31a1c9f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/1.12.1.3",
-                        "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "infile": {
-                                "id": 9,
-                                "output_name": "outfile_imzml"
-                            },
-                            "type_cond|annotation_file": {
-                                "id": 4,
-                                "output_name": "pixel_annotations"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "MSI classification",
-                        "outputs": [
-                            {
-                                "name": "classification_images",
-                                "type": "pdf"
-                            },
-                            {
-                                "name": "mzfeatures",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "pixeloutput",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 1704.300048828125,
-                            "top": 659.8166809082031
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionpixeloutput": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "pixeloutput"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/1.12.1.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "47fc5b518ffc",
-                            "name": "cardinal_classification",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"output_rdata\": \"\\\"false\\\"\", \"__page__\": null, \"type_cond\": \"{\\\"__current_case__\\\": 0, \\\"annotation_file\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"column_fold\\\": null, \\\"column_response\\\": \\\"3\\\", \\\"column_x\\\": \\\"1\\\", \\\"column_y\\\": \\\"2\\\", \\\"method_cond\\\": {\\\"__current_case__\\\": 2, \\\"class_method\\\": \\\"spatialShrunkenCentroids\\\", \\\"ssc_analysis_cond\\\": {\\\"__current_case__\\\": 1, \\\"ssc_method\\\": \\\"ssc_analysis\\\"}, \\\"ssc_kernel_method\\\": \\\"adaptive\\\", \\\"ssc_r\\\": \\\"2\\\", \\\"ssc_s\\\": \\\"0\\\"}, \\\"tabular_header\\\": \\\"true\\\", \\\"type_method\\\": \\\"training\\\"}\", \"__rerun_remap_job_id__\": null, \"centroids\": \"\\\"true\\\"\", \"processed_cond\": \"{\\\"__current_case__\\\": 0, \\\"processed_file\\\": \\\"no_processed\\\"}\", \"chromInfo\": \"\\\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
-                        "tool_version": null,
-                        "type": "tool",
-                        "uuid": "95932b54-da4a-4625-b22e-0e0ff9bdd5bc",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "mzfeatures",
-                                "uuid": "59b45729-bf4b-44ab-8544-c8c1cb4cbcdf"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "classification_images",
-                                "uuid": "4576bca8-6d7b-4a63-a368-da7ac4982a48"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.3",
-                        "errors": null,
-                        "id": 11,
-                        "input_connections": {
-                            "infile": {
-                                "id": 9,
-                                "output_name": "outfile_imzml"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "MSI segmentation",
-                        "outputs": [
-                            {
-                                "name": "segmentationimages",
-                                "type": "pdf"
-                            },
-                            {
-                                "name": "mzfeatures",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "pixeloutput",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 1991.316650390625,
-                            "top": 255.76666259765625
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionmzfeatures": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "mzfeatures"
-                            },
-                            "HideDatasetActionpixeloutput": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "pixeloutput"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9f7d1ec01767",
-                            "name": "cardinal_segmentations",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"output_rdata\": \"\\\"false\\\"\", \"setseed\": \"\\\"1\\\"\", \"__page__\": null, \"image_type\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"svg_pixelimage\": \"\\\"false\\\"\", \"centroids\": \"\\\"true\\\"\", \"colours\": \"[{\\\"__index__\\\": 0, \\\"feature_color\\\": \\\"#4f81bd\\\"}, {\\\"__index__\\\": 1, \\\"feature_color\\\": \\\"#f79646\\\"}, {\\\"__index__\\\": 2, \\\"feature_color\\\": \\\"#92d050\\\"}, {\\\"__index__\\\": 3, \\\"feature_color\\\": \\\"#c00000\\\"}]\", \"processed_cond\": \"{\\\"__current_case__\\\": 0, \\\"processed_file\\\": \\\"no_processed\\\"}\", \"segm_cond\": \"{\\\"__current_case__\\\": 0, \\\"pca_method\\\": \\\"irlba\\\", \\\"pca_ncomp\\\": \\\"2\\\", \\\"pca_scale\\\": \\\"false\\\", \\\"segmentationtool\\\": \\\"pca\\\"}\", \"infile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
-                        "tool_version": null,
-                        "type": "tool",
-                        "uuid": "68ad8111-fad2-4642-889b-ab9c3a59f427",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "segmentationimages",
-                                "uuid": "dcc9a3e6-e63d-450b-bea1-636e9ddc091d"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy/1.0.1",
-                        "errors": null,
-                        "id": 13,
-                        "input_connections": {
-                            "f1": {
-                                "id": 12,
-                                "output_name": "out_file1"
-                            },
-                            "f2": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Join two files",
-                        "outputs": [
-                            {
-                                "name": "merged_file",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 1086.88330078125,
-                            "top": 952.0666809082031
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy/1.0.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "22ec3c1a20cd",
-                            "name": "join_files_on_column_fuzzy",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"distance\": \"\\\"300.0\\\"\", \"f2\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__page__\": null, \"f1\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"merge_mode_select\": \"\\\"closest\\\"\", \"add_distance\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"header\": \"\\\"true\\\"\", \"units\": \"\\\"ppm\\\"\", \"c2\": \"\\\"1\\\"\", \"c1\": \"\\\"1\\\"\", \"chromInfo\": \"\\\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
-                        "tool_version": null,
-                        "type": "tool",
-                        "uuid": "5b9259e3-b894-4889-8ace-b6fe932770aa",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "merged_file",
-                                "uuid": "3fd228c9-f759-4668-a883-e9f5fa11b7c0"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "Summary_Statistics1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
                         "errors": null,
-                        "id": 14,
+                        "id": 2,
                         "input_connections": {
-                            "input": {
-                                "id": 13,
-                                "output_name": "merged_file"
+                            "in_file": {
+                                "id": 1,
+                                "output_name": "tabular"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Summary Statistics",
+                        "name": "Datamash",
                         "outputs": [
                             {
-                                "name": "out_file1",
+                                "name": "out_file",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1328.0999755859375,
-                            "top": 927.6166687011719
+                            "bottom": 56.99374771118164,
+                            "height": 113.5999984741211,
+                            "left": 643.5,
+                            "right": 843.5,
+                            "top": -56.60625076293945,
+                            "width": 200,
+                            "x": 643.5,
+                            "y": -56.60625076293945
                         },
                         "post_job_actions": {},
-                        "tool_id": "Summary_Statistics1",
-                        "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c12\\\"\", \"__page__\": null}",
-                        "tool_version": null,
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "562f3c677828",
+                            "name": "datamash_ops",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"grouping\": \"5\", \"header_in\": \"true\", \"header_out\": \"true\", \"ignore_case\": \"true\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"need_sort\": \"true\", \"operations\": [{\"__index__\": 0, \"op_name\": \"mean\", \"op_column\": \"1\"}, {\"__index__\": 1, \"op_name\": \"sstdev\", \"op_column\": \"1\"}, {\"__index__\": 2, \"op_name\": \"mean\", \"op_column\": \"2\"}, {\"__index__\": 3, \"op_name\": \"sstdev\", \"op_column\": \"2\"}, {\"__index__\": 4, \"op_name\": \"mean\", \"op_column\": \"3\"}, {\"__index__\": 5, \"op_name\": \"sstdev\", \"op_column\": \"3\"}, {\"__index__\": 6, \"op_name\": \"mean\", \"op_column\": \"4\"}, {\"__index__\": 7, \"op_name\": \"sstdev\", \"op_column\": \"4\"}], \"print_full_line\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.0",
                         "type": "tool",
-                        "uuid": "510cfc59-bf52-4f8a-920f-d5437da29f78",
+                        "uuid": "e1a58a79-5102-450e-bfe0-200f0e64139d",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "c76d062a-6f36-4e88-a02a-8951f7b4c17e"
+                                "label": "datamash_output",
+                                "output_name": "out_file",
+                                "uuid": "254f1b4b-d466-4f0e-8c46-0e97bbedae4d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.2",
+                        "content_id": "Grouping1",
                         "errors": null,
-                        "id": 15,
+                        "id": 5,
                         "input_connections": {
-                            "calibrant_file": {
-                                "id": 13,
-                                "output_name": "merged_file"
-                            },
-                            "infile": {
+                            "input1": {
                                 "id": 3,
-                                "output_name": "output"
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "MSI mz images",
+                        "name": "Group",
                         "outputs": [
                             {
-                                "name": "plots",
-                                "type": "pdf"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1334.066650390625,
-                            "top": 1030.4666442871094
+                            "bottom": 500.5999984741211,
+                            "height": 93.20000457763672,
+                            "left": 1063.5,
+                            "right": 1263.5,
+                            "top": 407.3999938964844,
+                            "width": 200,
+                            "x": 1063.5,
+                            "y": 407.3999938964844
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "56b3b7d5f2b5",
-                            "name": "cardinal_mz_images",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"calibrant_header\": \"\\\"true\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"image_contrast\": \"\\\"suppression\\\"\", \"image_smoothing\": \"\\\"none\\\"\", \"image_type\": \"\\\"true\\\"\", \"name_column\": \"\\\"11\\\"\", \"__rerun_remap_job_id__\": null, \"svg_pixelimage\": \"\\\"false\\\"\", \"calibrant_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"centroids\": \"\\\"false\\\"\", \"filename\": \"\\\"\\\"\", \"colorkey\": \"\\\"true\\\"\", \"processed_cond\": \"{\\\"__current_case__\\\": 0, \\\"processed_file\\\": \\\"no_processed\\\"}\", \"strip\": \"\\\"true\\\"\", \"__page__\": null, \"overlay_cond\": \"{\\\"__current_case__\\\": 0, \\\"overlay_selection\\\": \\\"no_overlay\\\"}\", \"plusminus_dalton\": \"\\\"0.25\\\"\", \"mz_column\": \"\\\"1\\\"\"}",
-                        "tool_version": null,
+                        "tool_id": "Grouping1",
+                        "tool_state": "{\"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"groupcol\": \"5\", \"ignorecase\": \"false\", \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.4",
                         "type": "tool",
-                        "uuid": "d2ef59b6-ad5f-46ed-9342-2f49a2f98920",
+                        "uuid": "dcd3ddc6-d871-45dd-94ed-3eae56dd56db",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "svg_output",
-                                "uuid": "a3d13a98-d1d8-452d-9427-82745744f53a"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "plots",
-                                "uuid": "61a511da-3c35-45e2-a23e-d34ce4626297"
+                                "label": "group1",
+                                "output_name": "out_file1",
+                                "uuid": "a689bddf-14d0-4a72-b1f9-c34d8f50d2b3"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Grep1",
+                        "content_id": "Grouping1",
                         "errors": null,
-                        "id": 16,
+                        "id": 6,
                         "input_connections": {
-                            "input": {
-                                "id": 13,
-                                "output_name": "merged_file"
+                            "input1": {
+                                "id": 3,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Select",
+                        "name": "Group",
                         "outputs": [
                             {
                                 "name": "out_file1",
-                                "type": "input"
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1258.36669921875,
-                            "top": 1172.8166809082031
+                            "bottom": 620.6000289916992,
+                            "height": 93.20000457763672,
+                            "left": 1063.5,
+                            "right": 1263.5,
+                            "top": 527.4000244140625,
+                            "width": 200,
+                            "x": 1063.5,
+                            "y": 527.4000244140625
                         },
                         "post_job_actions": {},
-                        "tool_id": "Grep1",
-                        "tool_state": "{\"__page__\": null, \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"invert\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"pattern\": \"\\\"(1663\\\\\\\\.)|(1905\\\\\\\\.)|(2304\\\\\\\\.)\\\"\"}",
-                        "tool_version": null,
+                        "tool_id": "Grouping1",
+                        "tool_state": "{\"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"groupcol\": \"5\", \"ignorecase\": \"false\", \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [{\"__index__\": 0, \"optype\": \"length\", \"opcol\": \"1\", \"opround\": \"no\", \"opdefault\": null}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.4",
                         "type": "tool",
-                        "uuid": "28905577-0117-4139-9071-350eacf4ccfa",
+                        "uuid": "285a3852-71cb-4137-be1d-b0ec0a59d9e9",
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "group2",
                                 "output_name": "out_file1",
-                                "uuid": "783b4618-d785-43a8-a190-de80a699272f"
+                                "uuid": "ac7c73b2-58dd-4c6e-85ce-ddf49323b206"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
                         "errors": null,
-                        "id": 17,
+                        "id": 7,
                         "input_connections": {
-                            "calibrant_file": {
-                                "id": 16,
-                                "output_name": "out_file1"
-                            },
-                            "infile": {
+                            "input1": {
                                 "id": 3,
-                                "output_name": "output"
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "MSI mz images",
+                        "name": "Scatterplot with ggplot2",
                         "outputs": [
                             {
-                                "name": "plots",
+                                "name": "output1",
+                                "type": "png"
+                            },
+                            {
+                                "name": "output2",
                                 "type": "pdf"
                             }
                         ],
                         "position": {
-                            "left": 1462.9666748046875,
-                            "top": 1160.4166564941406
+                            "bottom": 873.0000305175781,
+                            "height": 225.60000610351562,
+                            "left": 1063.5,
+                            "right": 1263.5,
+                            "top": 647.4000244140625,
+                            "width": 200,
+                            "x": 1063.5,
+                            "y": 647.4000244140625
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.2",
+                        "post_job_actions": {
+                            "HideDatasetActionoutput1": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output1"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "56b3b7d5f2b5",
-                            "name": "cardinal_mz_images",
-                            "owner": "galaxyp",
+                            "changeset_revision": "1acf88921176",
+                            "name": "ggplot2_point",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"calibrant_header\": \"\\\"false\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"image_contrast\": \"\\\"suppression\\\"\", \"image_smoothing\": \"\\\"none\\\"\", \"image_type\": \"\\\"true\\\"\", \"name_column\": \"\\\"11\\\"\", \"__rerun_remap_job_id__\": null, \"svg_pixelimage\": \"\\\"false\\\"\", \"calibrant_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"centroids\": \"\\\"false\\\"\", \"filename\": \"\\\"\\\"\", \"colorkey\": \"\\\"true\\\"\", \"processed_cond\": \"{\\\"__current_case__\\\": 0, \\\"processed_file\\\": \\\"no_processed\\\"}\", \"strip\": \"\\\"true\\\"\", \"__page__\": null, \"overlay_cond\": \"{\\\"__current_case__\\\": 1, \\\"colours\\\": [{\\\"__index__\\\": 0, \\\"feature_color\\\": \\\"#1f497d\\\"}, {\\\"__index__\\\": 1, \\\"feature_color\\\": \\\"#00b050\\\"}, {\\\"__index__\\\": 2, \\\"feature_color\\\": \\\"#ff0000\\\"}], \\\"overlay_selection\\\": \\\"yes_overlay\\\"}\", \"plusminus_dalton\": \"\\\"0.25\\\"\", \"mz_column\": \"\\\"1\\\"\"}",
-                        "tool_version": null,
+                        "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"points\", \"__current_case__\": 0, \"points\": {\"pointoptions\": \"default\", \"__current_case__\": 0}}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"5\", \"colors\": \"Set2\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"7.0\", \"height_output_dim\": \"7.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"pdf\"}, \"title\": \"Sepal length as a function of sepal width\", \"xlab\": \"Sepal length\", \"xplot\": \"1\", \"ylab\": \"Sepal width\", \"yplot\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.3.5+galaxy0",
                         "type": "tool",
-                        "uuid": "16498e12-6e7a-415c-9b34-9f4b1c64131d",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "plots",
-                                "uuid": "bf27c260-9168-498e-ab18-9324b74fedad"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Glycan_IDs"
-                            }
-                        ],
-                        "label": "Glycan_IDs",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 449.91668701171875,
-                            "top": 1052.3666687011719
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Glycan_IDs\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "78e307cf-92b5-4d1b-89d7-0ebeb7c845b7",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "a028d3d6-38e3-43f7-a023-321178108dc7"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "all_files",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 447,
-                            "top": 1146.7167053222656
-                        },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "1f30f371-a9c5-4638-a9bd-a69d7a7ee1ec",
+                        "uuid": "fa412209-5e3a-448e-8b0b-fa88870e19c1",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "07af2e13-4f7d-4454-8644-4d8cda30eb70"
+                                "output_name": "output2",
+                                "uuid": "08954537-18c1-4fa5-8093-b2ec90c0eb5c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
                         "errors": null,
-                        "id": 4,
+                        "id": 8,
                         "input_connections": {
-                            "infiles": [
-                                {
-                                    "id": 1,
-                                    "output_name": "output"
-                                },
-                                {
-                                    "id": 0,
-                                    "output_name": "output"
-                                }
-                            ]
+                            "input1": {
+                                "id": 3,
+                                "output_name": "out_file1"
+                            }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "MSI combine",
+                        "name": "Scatterplot with ggplot2",
                         "outputs": [
                             {
-                                "name": "outfile_imzml",
-                                "type": "imzml"
+                                "name": "output1",
+                                "type": "png"
                             },
                             {
-                                "name": "QC_overview",
+                                "name": "output2",
                                 "type": "pdf"
-                            },
-                            {
-                                "name": "pixel_annotations",
-                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 637.4666748046875,
-                            "top": 337.5500030517578
+                            "bottom": 993.0000305175781,
+                            "height": 225.60000610351562,
+                            "left": 1063.5,
+                            "right": 1263.5,
+                            "top": 767.4000244140625,
+                            "width": 200,
+                            "x": 1063.5,
+                            "y": 767.4000244140625
                         },
                         "post_job_actions": {
-                            "HideDatasetActionQC_overview": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "QC_overview"
-                            },
-                            "HideDatasetActionpixel_annotations": {
+                            "HideDatasetActionoutput1": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "pixel_annotations"
+                                "output_name": "output1"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.3",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "48c07268f341",
-                            "name": "cardinal_combine",
-                            "owner": "galaxyp",
+                            "changeset_revision": "1acf88921176",
+                            "name": "ggplot2_point",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"infiles\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"annotation_cond\": \"{\\\"__current_case__\\\": 0, \\\"annotation_tabular\\\": \\\"no_annotation\\\"}\", \"__rerun_remap_job_id__\": null, \"combine_conditional\": \"{\\\"__current_case__\\\": 0, \\\"combine_method\\\": \\\"automatic_combine\\\"}\", \"centroids\": \"\\\"false\\\"\", \"processed_cond\": \"{\\\"__current_case__\\\": 0, \\\"processed_file\\\": \\\"no_processed\\\"}\", \"chromInfo\": \"\\\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"imzml_output\": \"\\\"imzml_format\\\"\"}",
-                        "tool_version": null,
+                        "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"points\", \"__current_case__\": 0, \"points\": {\"pointoptions\": \"default\", \"__current_case__\": 0}}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"5\", \"colors\": \"Set2\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"7.0\", \"height_output_dim\": \"7.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"pdf\"}, \"title\": \"Petal length as a function of petal width\", \"xlab\": \"Petal length\", \"xplot\": \"3\", \"ylab\": \"Petal width\", \"yplot\": \"4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.3.5+galaxy0",
                         "type": "tool",
-                        "uuid": "57b0fcdb-c511-43bf-b8af-7aafdaff0d6d",
+                        "uuid": "8e7b3f8d-2b8b-46cb-93d4-0d74bf54441e",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile_imzml",
-                                "uuid": "cdc8f02b-39b1-465b-b725-b0c2b69a5b74"
+                                "output_name": "output2",
+                                "uuid": "cc4e1426-f444-4fcd-960c-a868d98147ac"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/1.12.1.3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
                         "errors": null,
-                        "id": 5,
+                        "id": 9,
                         "input_connections": {
                             "infile": {
                                 "id": 4,
-                                "output_name": "outfile_imzml"
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "MSI preprocessing",
+                        "name": "Unique",
                         "outputs": [
                             {
-                                "name": "outfile_imzml",
-                                "type": "imzml"
-                            },
-                            {
-                                "name": "QC_overview",
-                                "type": "pdf"
+                                "name": "outfile",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 886.0499877929688,
-                            "top": 199.98333740234375
+                            "bottom": 281.00000762939453,
+                            "height": 113.5999984741211,
+                            "left": 1283.5,
+                            "right": 1483.5,
+                            "top": 167.40000915527344,
+                            "width": 200,
+                            "x": 1283.5,
+                            "y": 167.40000915527344
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/1.12.1.3",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "141a9288be9c",
-                            "name": "cardinal_preprocessing",
-                            "owner": "galaxyp",
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"methods\": \"[{\\\"__index__\\\": 0, \\\"methods_conditional\\\": {\\\"__current_case__\\\": 0, \\\"preprocessing_method\\\": \\\"Normalization\\\"}}, {\\\"__index__\\\": 1, \\\"methods_conditional\\\": {\\\"__current_case__\\\": 2, \\\"methods_for_smoothing\\\": {\\\"__current_case__\\\": 0, \\\"sd_gaussian\\\": \\\"1.0\\\", \\\"smoothing_method\\\": \\\"gaussian\\\"}, \\\"preprocessing_method\\\": \\\"Smoothing\\\", \\\"window_smoothing\\\": \\\"4.0\\\"}}, {\\\"__index__\\\": 2, \\\"methods_conditional\\\": {\\\"__current_case__\\\": 1, \\\"blocks_baseline\\\": \\\"500\\\", \\\"preprocessing_method\\\": \\\"Baseline_reduction\\\", \\\"spar_baseline\\\": \\\"1.0\\\"}}]\", \"__rerun_remap_job_id__\": null, \"centroids\": \"\\\"false\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"processed_cond\": \"{\\\"__current_case__\\\": 0, \\\"processed_file\\\": \\\"no_processed\\\"}\", \"imzml_output\": \"\\\"imzml_format\\\"\"}",
-                        "tool_version": null,
+                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"is_numeric\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.0",
                         "type": "tool",
-                        "uuid": "93149694-469a-4a76-8690-ddf691665e55",
+                        "uuid": "3e2d84e9-2fff-4321-9db6-41af99367162",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "outfile_rdata",
-                                "uuid": "613b051e-88d7-46b0-9532-a118b3adb4aa"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "outfile_imzml",
-                                "uuid": "8718b21e-a330-4a57-9548-e9257819bb45"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "QC_overview",
-                                "uuid": "3c709575-ac09-47d3-a750-2b3082805e72"
+                                "label": "unique_output",
+                                "output_name": "outfile",
+                                "uuid": "8a2b5e30-d42a-4019-9674-4b4af00c820a"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "introduction/galaxy-intro-101-everyone",
+                "path": "topics/introduction/tutorials/galaxy-intro-101-everyone/workflows/main_workflow.ga",
+                "tags": [
+                    "introduction"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "GTN Training: Galaxy 101 For Everyone",
+                "topic_id": "introduction",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/introduction-galaxy-intro-101-everyone/versions/main-workflow",
+                "tutorial_id": "galaxy-intro-101-everyone",
+                "url": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/workflows/main_workflow.html",
+                "version": 8,
+                "wfid": "introduction-galaxy-intro-101-everyone",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "Cut1",
+                    "Grouping1",
+                    "Remove beginning1",
+                    "csv_to_tabular",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0"
+                ],
+                "workflowhub_id": "1085"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/1319069/"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "fastp",
+                    "owner": "iuc",
+                    "revisions": "65b93b623c77",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "abfd8a6544d7",
+                    "tool_panel_section_label": "Quality Control",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: abfd8a6544d7\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/vsi_qc/tutorial.json",
+        "contributors": [
+            {
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
+                "joined": "2017-09",
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+            }
+        ],
+        "dir": "topics/introduction/tutorials/vsi_qc",
+        "draft": true,
+        "edam_operation": [
+            "Sequencing quality control",
+            "Validation",
+            "Sequence contamination filtering"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "Galaxy@AuBi",
+            "GalaxyTrakr",
+            "HyPhy HIV NGS Tools",
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "introduction/vsi_qc",
+        "inexact_supported_servers": [
+            "MISSISSIPPI",
+            "UseGalaxy.be",
+            "UseGalaxy.no"
+        ],
+        "js_requirements": {
+            "mathjax": 7091,
+            "mermaid": false
+        },
+        "key_points": [
+            "Galaxy is an excellent tool for quickly QCing your data"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-25",
+        "objectives": [
+            "Learn about QCing Illumina and Element data",
+            "Learn about fastp",
+            "Learn about multiqc"
+        ],
+        "pageviews": 170,
+        "priority": 10,
+        "pub_date": "2024-03-26",
+        "questions": [
+            "How do I know my sequencing data is good?"
+        ],
+        "short_id": "T00436",
+        "short_tools": [
+            "multiqc",
+            "fastp"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "core",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "work-in-progress"
+        ],
+        "time_estimation": "30M",
+        "title": "Very Short Introductions: QC",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1"
+        ],
+        "topic_name": "introduction",
+        "topic_name_human": "Introduction to Galaxy Analyses",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "vsi_qc",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/introduction/tutorials/vsi_qc/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/vsi_qc/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/introduction/tutorials/vsi_qc/tutorial.json"
+        },
+        "version": 4,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 237,
+        "visitors": 123,
+        "zenodo_link": "https://zenodo.org/records/10870107"
+    },
+    {
+        "abbreviations": {
+            "AIRSS": "Ab Initio Random Structure Search",
+            "DFT": "Density Functional Theory",
+            "UEP": "Unperturbed Electrostatic Potential"
+        },
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "pm_muairss_read",
+                    "owner": "muon-spectroscopy-computational-project",
+                    "revisions": "40071ff77285",
+                    "tool_panel_section_label": "Muon Spectroscopy",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pm_uep_opt",
+                    "owner": "muon-spectroscopy-computational-project",
+                    "revisions": "eea73e1f65cb",
+                    "tool_panel_section_label": "Muon Spectroscopy",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: pm_muairss_read\n  owner: muon-spectroscopy-computational-project\n  revisions: 40071ff77285\n  tool_panel_section_label: Muon Spectroscopy\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pm_uep_opt\n  owner: muon-spectroscopy-computational-project\n  revisions: eea73e1f65cb\n  tool_panel_section_label: Muon Spectroscopy\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "leandro-liborio",
+                "elichad",
+                "patrick-austin"
+            ],
+            "editing": [
+                "leandro-liborio"
+            ],
+            "funding": [
+                "eurosciencegateway"
+            ]
+        },
+        "contributors": [
+            {
+                "email": "leandro.liborio@stfc.ac.uk",
+                "id": "leandro-liborio",
+                "joined": "2022-11",
+                "name": "Leandro Liborio",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/leandro-liborio/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/leandro-liborio.json"
+            },
+            {
+                "email": "eli.chadwick@manchester.ac.uk",
+                "id": "elichad",
+                "joined": "2022-11",
+                "name": "Eli Chadwick",
+                "orcid": "0000-0002-0035-6475",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elichad/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/elichad.json"
+            },
+            {
+                "email": "patrick.austin@stfc.ac.uk",
+                "id": "patrick-austin",
+                "joined": "2022-11",
+                "name": "Patrick Austin",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/patrick-austin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/patrick-austin.json"
+            },
+            {
+                "email": "leandro.liborio@stfc.ac.uk",
+                "id": "leandro-liborio",
+                "joined": "2022-11",
+                "name": "Leandro Liborio",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/leandro-liborio/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/leandro-liborio.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/eurosciencegateway.png",
+                "funder": true,
+                "funding_id": "101057388",
+                "funding_statement": "EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government\u2019s Horizon Europe funding guarantee grant number 10038963.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "eurosciencegateway",
+                "joined": "2023-10",
+                "members": [
+                    "abretaud",
+                    "anuprulez",
+                    "bgruening",
+                    "erxleben",
+                    "pauldg",
+                    "rlibouba"
+                ],
+                "name": "EuroScienceGateway",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eurosciencegateway/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/eurosciencegateway.json"
+            }
+        ],
+        "dir": "topics/materials-science/tutorials/muon-stopping-sites-muairss-uep",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.eu"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "materials-science/muon-stopping-sites-muairss-uep",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Galaxy supports multiple PyMuonSuite tools which can be used together to find muon stopping sites",
+            "The workflow for finding the stopping site involves three stages - structure generation, structure optimisation, and structure clustering",
+            "Within the UEP, the optimisation stage is based on analytically calculating the electrostatic forces applied to the muon, which can be performed via Galaxy.",
+            "The approach requires a CASTEP DFT calculation to be completed as a starting point"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-14",
+        "objectives": [
+            "Understand why finding stopping sites is useful",
+            "Use pymuon-suite in Galaxy to find stopping sites",
+            "Understand the limitations of these tools and techniques"
+        ],
+        "pageviews": 179,
+        "priority": 2,
+        "pub_date": "2024-01-22",
+        "questions": [
+            "What are stopping sites and why is finding them important?",
+            "What computational techniques can be used to find stopping sites?",
+            "How can Galaxy help me with my analysis?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "leandro-liborio"
+                ],
+                "date": "2024-01-26",
+                "length": "22M",
+                "speakers": [
+                    "leandro-liborio"
+                ],
+                "youtube_id": "rFPtDmq7uO8"
+            }
+        ],
+        "short_id": "T00402",
+        "short_tools": [
+            "pm_uep_opt",
+            "pm_muairss_read"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "muon-spectroscopy",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "time_estimation": "1H",
+        "title": "Finding the muon stopping site with pymuon-suite in Galaxy",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_muairss_read/pm_muairss_read/0.3.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_uep_opt/pm_uep_opt/0.3.0+galaxy1"
+        ],
+        "topic_name": "materials-science",
+        "topic_name_human": "Materials Science",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "muon-stopping-sites-muairss-uep",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/tutorial.json"
+        },
+        "version": 2,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 135,
+        "visitors": 120,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Organization",
+                        "name": "Muon Spectroscopy Computational Project",
+                        "url": "https://muon-spectroscopy-computational-project.github.io/"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCopper-out.cell\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCopper.den_fmt\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCopper.castep\"]\n  3[label=\"PyMuonSuite AIRSS UEP Optimise\"]\n  2 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  kf3be7cd2397449f2aa0e96c79b4ab34c[color=lightseagreen,label=\"Output\\nAll muons in host material\"]\n  3 -> kf3be7cd2397449f2aa0e96c79b4ab34c\n  4[label=\"PyMuonSuite AIRSS Cluster\"]\n  3 -> 4 [label=\"uep_results\"]\n}",
+                "history": [
+                    {
+                        "hash": "cd4b1f827bc53928da8d0afb85d1c83590fc2638",
+                        "message": "Changes for linting and remove MuSpinSim content #1",
+                        "num": 3,
+                        "short_hash": "cd4b1f827",
+                        "unix": "1702051023"
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.3",
+                        "hash": "5b3763af3729dbb2092e0757bd3aea5714960f71",
+                        "message": "Updated tutorial for finding the muon stopping site with Galaxy",
+                        "num": 2,
+                        "short_hash": "5b3763af3",
+                        "unix": "1701764649"
+                    },
+                    {
+                        "hash": "593f4002b4d9ecce6f6a8a91d700dea075c3662f",
+                        "message": "Address various review comments",
+                        "num": 1,
+                        "short_hash": "593f4002b",
+                        "unix": "1673882604"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "CASTEP structural file for the relaxed host material",
+                        "content_id": null,
                         "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "infile": {
-                                "id": 4,
-                                "output_name": "outfile_imzml"
-                            },
-                            "tabular_annotation|annotation_file": {
-                                "id": 4,
-                                "output_name": "pixel_annotations"
-                            }
-                        },
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool MSI Qualitycontrol",
-                                "name": "calibrant_file"
+                                "description": "CASTEP structural file for the relaxed host material",
+                                "name": "Copper-out.cell"
                             }
                         ],
-                        "label": null,
-                        "name": "MSI Qualitycontrol",
-                        "outputs": [
+                        "label": "Copper-out.cell",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 2.0965249510338584,
+                            "top": 0.08734987455441257
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0a1cc8d8-c2d9-48f6-9a92-9d96778249dc",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "CASTEP charge density file",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "QC_report",
-                                "type": "pdf"
+                                "description": "CASTEP charge density file",
+                                "name": "Copper.den_fmt"
                             }
                         ],
+                        "label": "Copper.den_fmt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 899.6666870117188,
-                            "top": 552.4833374023438
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3b7a35d50ebf",
-                            "name": "cardinal_quality_report",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 2.0965249510338584,
+                            "top": 86.09728918976163
                         },
-                        "tool_state": "{\"calibrant_header\": \"\\\"false\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"calibrantratio\": \"[]\", \"__page__\": null, \"name_column\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"tabular_annotation\": \"{\\\"__current_case__\\\": 0, \\\"annotation_file\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"column_names\\\": \\\"3\\\", \\\"column_x\\\": \\\"1\\\", \\\"column_y\\\": \\\"2\\\", \\\"load_annotation\\\": \\\"yes_annotation\\\", \\\"tabular_header\\\": \\\"true\\\"}\", \"centroids\": \"\\\"false\\\"\", \"calibrant_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"processed_cond\": \"{\\\"__current_case__\\\": 0, \\\"processed_file\\\": \\\"no_processed\\\"}\", \"do_pca\": \"\\\"true\\\"\", \"filename\": \"\\\"\\\"\", \"plusminus_ppm\": \"\\\"200.0\\\"\", \"mz_column\": \"\\\"\\\"\"}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "238e69ed-38e9-451b-84c1-cdd050930672",
-                        "workflow_outputs": [
+                        "type": "data_input",
+                        "uuid": "73e18b25-ebb9-4835-933c-1b8c1feb74cb",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "main CASTEP output file ",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "QC_report",
-                                "uuid": "64239ff1-1dea-4482-80c7-648aa899f3ab"
+                                "description": "main CASTEP output file ",
+                                "name": "Copper.castep"
                             }
-                        ]
-                    },
+                        ],
+                        "label": "Copper.castep",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 173.59228833890583
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "2ac4de9c-0f0a-4bdb-971a-cd471c08111e",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nCopper-out.cell\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nCopper.den_fmt\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nCopper.castep\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"PyMuonSuite AIRSS UEP Optimise\"];\n  2 -->|output| 3;\n  1 -->|output| 3;\n  0 -->|output| 3;\n  f3be7cd2-3974-49f2-aa0e-96c79b4ab34c[\"Output\\nAll muons in host material\"];\n  3 --> f3be7cd2-3974-49f2-aa0e-96c79b4ab34c;\n  style f3be7cd2-3974-49f2-aa0e-96c79b4ab34c stroke:#2c3143,stroke-width:4px;\n  4[\"PyMuonSuite AIRSS Cluster\"];\n  3 -->|uep_results| 4;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Finding the Muon Stopping Site: pymuon-suite in Galaxy",
+                "outputs": [
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.3",
+                        "annotation": "Galaxy tool used to: load the CASTEP files; complete the Generation parameters to set up the creation of randomly populated muonated structures; and complete the Optimisation parameters to set up the relaxation the electrostatic forces of the muon in each of the randomly populated muonated structures.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_uep_opt/pm_uep_opt/0.3.0+galaxy1",
                         "errors": null,
-                        "id": 7,
+                        "id": 3,
                         "input_connections": {
-                            "infile": {
-                                "id": 5,
-                                "output_name": "outfile_imzml"
+                            "castep_log": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "charge_density": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "structure": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "MALDIquant preprocessing",
+                        "label": "PyMuonSuite AIRSS UEP Optimise",
+                        "name": "PyMuonSuite AIRSS UEP Optimise",
                         "outputs": [
                             {
-                                "name": "outfile_imzml",
-                                "type": "imzml"
+                                "name": "uep_results",
+                                "type": "zip"
                             },
                             {
-                                "name": "plots",
-                                "type": "pdf"
+                                "name": "allpos_file",
+                                "type": "_sniff_"
                             }
                         ],
                         "position": {
-                            "left": 1155.5999755859375,
-                            "top": 299.2833251953125
+                            "left": 345.2278179241512,
+                            "top": 0
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.3",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_uep_opt/pm_uep_opt/0.3.0+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "71411ac28268",
-                            "name": "maldi_quant_preprocessing",
-                            "owner": "galaxyp",
+                            "changeset_revision": "eea73e1f65cb",
+                            "name": "pm_uep_opt",
+                            "owner": "muon-spectroscopy-computational-project",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"methods\": \"[{\\\"__index__\\\": 0, \\\"methods_conditional\\\": {\\\"__current_case__\\\": 4, \\\"allow_nomatch\\\": \\\"true\\\", \\\"empty_nomatch\\\": \\\"true\\\", \\\"halfWindowSize\\\": \\\"4\\\", \\\"method\\\": \\\"Align\\\", \\\"peak_method\\\": \\\"MAD\\\", \\\"reference_for_alignment\\\": {\\\"__current_case__\\\": 0, \\\"align_ref\\\": \\\"no_reference\\\", \\\"min_frequency\\\": \\\"0.8\\\"}, \\\"remove_empty\\\": \\\"true\\\", \\\"snr\\\": \\\"5\\\", \\\"tolerance\\\": \\\"0.0002\\\", \\\"warping_method\\\": \\\"lowess\\\"}}]\", \"__rerun_remap_job_id__\": null, \"export_processed\": \"\\\"true\\\"\", \"restriction_conditional\": \"{\\\"__current_case__\\\": 1, \\\"restriction\\\": \\\"no_restriction\\\"}\", \"infile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
-                        "tool_version": null,
+                        "tool_state": "{\"__input_ext\": \"input\", \"castep_log\": {\"__class__\": \"ConnectedValue\"}, \"charge_density\": {\"__class__\": \"ConnectedValue\"}, \"chromInfo\": \"/srv/galaxy/var/tool_data/shared/ucsc/chrom/?.len\", \"generation_params\": {\"poisson_r\": \"0.6\", \"vdw_scale\": \"0.5\", \"random_seed\": null, \"allpos_ext\": \"cif\"}, \"optimisation_params\": {\"geom_steps\": \"30\", \"geom_force_tol\": \"0.05\", \"uep_gw_factor\": \"5.0\"}, \"structure\": {\"__class__\": \"ConnectedValue\"}, \"testing\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3.0+galaxy1",
                         "type": "tool",
-                        "uuid": "683d836c-d991-45e6-8c31-fc93ecda0e84",
+                        "uuid": "22131f07-c4c4-4ec0-9a45-5c8c8069600c",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "outfile_imzml",
-                                "uuid": "75b9894a-95d8-4f18-b65a-f4f679b0fa57"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "plots",
-                                "uuid": "eedcbadd-90f2-420c-bfcc-7aaaca296813"
+                                "label": "All muons in host material",
+                                "output_name": "allpos_file",
+                                "uuid": "f3be7cd2-3974-49f2-aa0e-96c79b4ab34c"
                             }
                         ]
                     }
                 ],
-                "parent_id": "metabolomics/msi-finding-nglycans",
-                "path": "topics/metabolomics/tutorials/msi-finding-nglycans/workflows/msi-finding-diff-analytes.ga",
-                "tags": [
-                    "metabolomics"
-                ],
+                "parent_id": "materials-science/muon-stopping-sites-muairss-uep",
+                "path": "topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/workflows/muairss-uep.ga",
+                "tags": [],
                 "test_results": null,
-                "tests": false,
-                "title": "MSI Finding Diff Analytes",
-                "topic_id": "metabolomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/metabolomics-msi-finding-nglycans/versions/msi-finding-diff-analytes",
-                "tutorial_id": "msi-finding-nglycans",
-                "url": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/msi-finding-nglycans/workflows/msi-finding-diff-analytes.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/msi-finding-nglycans/workflows/msi-finding-diff-analytes.html",
-                "version": 4,
-                "wfid": "metabolomics-msi-finding-nglycans",
-                "wfname": "msi-finding-diff-analytes",
-                "workflow": "msi-finding-diff-analytes.ga",
-                "workflow_tools": [
-                    "Filter1",
-                    "Grep1",
-                    "Summary_Statistics1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy/1.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/1.12.1.3",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.3",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/1.12.1.3",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.3",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.3",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.4",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.3"
+                "tests": true,
+                "title": "Finding the Muon Stopping Site: pymuon-suite in Galaxy",
+                "topic_id": "materials-science",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/materials-science-muon-stopping-sites-muairss-uep/versions/muairss-uep",
+                "tutorial_id": "muon-stopping-sites-muairss-uep",
+                "url": "https://training.galaxyproject.org/training-material/topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/workflows/muairss-uep.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/workflows/muairss-uep.html",
+                "version": 1,
+                "wfid": "materials-science-muon-stopping-sites-muairss-uep",
+                "wfname": "muairss-uep",
+                "workflow": "muairss-uep.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_muairss_read/pm_muairss_read/0.3.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_uep_opt/pm_uep_opt/0.3.0+galaxy1"
                 ],
-                "workflowhub_id": "1123"
+                "workflowhub_id": "1109"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/2628280"
+        "zenodo_link": "https://zenodo.org/records/10219558"
     },
     {
         "admin_install": {
@@ -132595,86 +136018,200 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "cardinal_data_exporter",
+                    "name": "msconvert",
                     "owner": "galaxyp",
-                    "revisions": "4fbffddde8cd",
-                    "tool_panel_section_label": "Proteomics",
+                    "revisions": "6153e8ada1ee",
+                    "tool_panel_section_label": "Convert Formats",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cardinal_filtering",
-                    "owner": "galaxyp",
-                    "revisions": "b8c79e70516d",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "msnbase_readmsdata",
+                    "owner": "lecorguille",
+                    "revisions": "11ab2081bd4a",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cardinal_mz_images",
-                    "owner": "galaxyp",
-                    "revisions": "daf2ee9127fd",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "xcms_fillpeaks",
+                    "owner": "lecorguille",
+                    "revisions": "26d77e9ceb49",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cardinal_mz_images",
-                    "owner": "galaxyp",
-                    "revisions": "59e85306eae5",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "xcms_group",
+                    "owner": "lecorguille",
+                    "revisions": "d45a786cbc40",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cardinal_quality_report",
-                    "owner": "galaxyp",
-                    "revisions": "5a35e3a8d013",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "xcms_merge",
+                    "owner": "lecorguille",
+                    "revisions": "5bd125a3f3b0",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cardinal_spectra_plots",
-                    "owner": "galaxyp",
-                    "revisions": "d2596e1be091",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "xcms_retcor",
+                    "owner": "lecorguille",
+                    "revisions": "aa252eec9229",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cardinal_spectra_plots",
-                    "owner": "galaxyp",
-                    "revisions": "1693b2126f30",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "xcms_xcmsset",
+                    "owner": "lecorguille",
+                    "revisions": "b02d1992a43a",
+                    "tool_panel_section_label": "Metabolomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "matchms_filtering",
+                    "owner": "recetox",
+                    "revisions": "357df6c47d92",
+                    "tool_panel_section_label": "Metabolomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "matchms_formatter",
+                    "owner": "recetox",
+                    "revisions": "1b09315a3f87",
+                    "tool_panel_section_label": "Metabolomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "matchms_similarity",
+                    "owner": "recetox",
+                    "revisions": "e5010b19d64d",
+                    "tool_panel_section_label": "Metabolomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ramclustr",
+                    "owner": "recetox",
+                    "revisions": "2ec9253a647e",
+                    "tool_panel_section_label": "Metabolomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ramclustr",
+                    "owner": "recetox",
+                    "revisions": "050cfef6ba65",
+                    "tool_panel_section_label": "Metabolomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ramclustr_define_experiment",
+                    "owner": "recetox",
+                    "revisions": "25625114618e",
+                    "tool_panel_section_label": "Metabolomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "riassigner",
+                    "owner": "recetox",
+                    "revisions": "c702620c22b1",
+                    "tool_panel_section_label": "Metabolomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "waveica",
+                    "owner": "recetox",
+                    "revisions": "b77023c41c76",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: cardinal_data_exporter\n  owner: galaxyp\n  revisions: 4fbffddde8cd\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_filtering\n  owner: galaxyp\n  revisions: b8c79e70516d\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_mz_images\n  owner: galaxyp\n  revisions: daf2ee9127fd\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_mz_images\n  owner: galaxyp\n  revisions: 59e85306eae5\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_quality_report\n  owner: galaxyp\n  revisions: 5a35e3a8d013\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_spectra_plots\n  owner: galaxyp\n  revisions: d2596e1be091\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_spectra_plots\n  owner: galaxyp\n  revisions: 1693b2126f30\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: msconvert\n  owner: galaxyp\n  revisions: 6153e8ada1ee\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msnbase_readmsdata\n  owner: lecorguille\n  revisions: 11ab2081bd4a\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_fillpeaks\n  owner: lecorguille\n  revisions: 26d77e9ceb49\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_group\n  owner: lecorguille\n  revisions: d45a786cbc40\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_merge\n  owner: lecorguille\n  revisions: 5bd125a3f3b0\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_retcor\n  owner: lecorguille\n  revisions: aa252eec9229\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_xcmsset\n  owner: lecorguille\n  revisions: b02d1992a43a\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: matchms_filtering\n  owner: recetox\n  revisions: 357df6c47d92\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: matchms_formatter\n  owner: recetox\n  revisions: 1b09315a3f87\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: matchms_similarity\n  owner: recetox\n  revisions: e5010b19d64d\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ramclustr\n  owner: recetox\n  revisions: 2ec9253a647e\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ramclustr\n  owner: recetox\n  revisions: 050cfef6ba65\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ramclustr_define_experiment\n  owner: recetox\n  revisions: 25625114618e\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: riassigner\n  owner: recetox\n  revisions: c702620c22b1\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: waveica\n  owner: recetox\n  revisions: b77023c41c76\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "xtrojak",
+                "hechth",
+                "maximskorik"
+            ],
+            "editing": [
+                "hexylena"
+            ]
+        },
         "contributors": [
             {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "email": "melanie.foell@mol-med.uni-freiburg.de",
-                "id": "foellmelanie",
-                "joined": "2018-10",
-                "matrix": "foellmelanie:matrix.org",
-                "name": "Melanie F\u00f6ll",
-                "orcid": "0000-0002-1887-7543",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
-                "twitter": "MCFoell",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
+                "email": "trojak@mail.muni.cz",
+                "id": "xtrojak",
+                "joined": "2021-06",
+                "name": "Matej Troj\u00e1k",
+                "orcid": "0000-0003-0841-2707",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/xtrojak/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/xtrojak.json"
+            },
+            {
+                "elixir_node": "cz",
+                "email": "helge.hecht@recetox.muni.cz",
+                "id": "hechth",
+                "joined": "2020-01",
+                "name": "Helge Hecht",
+                "orcid": "0000-0001-6744-996X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hechth/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hechth.json"
+            },
+            {
+                "email": "maximskoryk@gmail.com",
+                "id": "maximskorik",
+                "joined": "2023-03",
+                "name": "Maxim Skoryk",
+                "orcid": "0000-0003-2056-8018",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/maximskorik/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/maximskorik.json"
             },
             {
                 "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
                     "uni-freiburg"
                 ],
-                "id": "MarenStillger",
-                "joined": "2020-10",
-                "name": "Maren Stillger",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/MarenStillger/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/MarenStillger.json"
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/metabolomics/tutorials/msi-analyte-distribution",
-        "edam_operation": [],
+        "dir": "topics/metabolomics/tutorials/gc_ms_with_xcms",
+        "edam_operation": [
+            "Peak detection",
+            "Format validation",
+            "Standardisation and normalisation",
+            "Mass spectrum visualisation",
+            "Validation",
+            "Formatting",
+            "Chromatographic alignment",
+            "Clustering",
+            "Label-free quantification",
+            "Imputation",
+            "Correlation",
+            "Filtering",
+            "Chromatogram visualisation",
+            "Spectral library search"
+        ],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu"
@@ -132682,49 +136219,61 @@
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "metabolomics/msi-analyte-distribution",
+        "id": "metabolomics/gc_ms_with_xcms",
         "inexact_supported_servers": [
-            "HyPhy HIV NGS Tools",
             "UseGalaxy.cz",
             "UseGalaxy.fr",
-            "UseGalaxy.no",
             "UseGalaxy.org.au"
         ],
         "js_requirements": {
-            "mathjax": null,
+            "mathjax": 27731,
             "mermaid": false
         },
         "key_points": [
-            "Average and annotated mass spectra show the relevant m/z range of the dataset and different compartment-specific peaks.",
-            "MSI data can be filtered for m/z ranges of interest to speed up analysis time.",
-            "Distribution images for many analytes can be automatically generated with the MSI m/z image tool.",
-            "The MSI m/z image tools allow overlaying the distribution images for several analytes."
+            "The processing of untargeted GC-MS metabolomic data can be done using open-source tools.",
+            "This processing workflow is complementary to CAMERA and metaMS."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
         "mod_date": "2023-11-09",
         "objectives": [
-            "Plot average mass spectra and overlaid mass spectra of single spectra.",
-            "Filter MSI data for a specific m/z range.",
-            "Automatic generation of many m/z images.",
-            "Overlay the distribution of several m/z in one image."
+            "To learn about the key steps in the preprocessing and analysis of untargeted GC-MS metabolomics data.",
+            "To explore what open-source alternative tools can be used in the analysis of GC-MS data, learn about their possible parametrisations.",
+            "To analyse authentic data samples and compare them with a data library of human metabolome, composed from a collection of mostly endogenous compounds."
         ],
-        "pageviews": 3623,
-        "pub_date": "2019-02-21",
+        "pageviews": 2011,
+        "pub_date": "2023-05-08",
         "questions": [
-            "What is the typical mass range of VOCs?",
-            "In which compartments of the chilli are the measured VOCs located?",
-            "In which compartment of the chilli is the capsaicin located?"
+            "What are the main steps of gas chromatography-mass spectrometry (GC-MS) data processing for metabolomic analysis?",
+            "What similarity metrics can be used to compare a pair of mass spectra and what are the differences between them?",
+            "Do you know any alternative tools that can be used in place of the individual steps of this workflow?"
         ],
-        "short_id": "T00198",
+        "requirements": [
+            {
+                "topic_name": "metabolomics",
+                "tutorials": [
+                    "lcms-preprocessing"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00344",
         "short_tools": [
-            "cardinal_mz_images",
-            "cardinal_filtering",
-            "cardinal_spectra_plots",
-            "cardinal_data_exporter",
-            "cardinal_quality_report",
-            "Filter1"
+            "msnbase_readmsdata",
+            "riassigner",
+            "ramclustr",
+            "waveica",
+            "abims_xcms_fillPeaks",
+            "abims_xcms_xcmsSet",
+            "matchms_similarity",
+            "msconvert",
+            "xcms_merge",
+            "matchms_filtering",
+            "ramclustr_define_experiment",
+            "abims_xcms_group",
+            "matchms_formatter",
+            "abims_xcms_retcor"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -132737,11 +136286,6 @@
                 }
             ],
             "inexact": [
-                {
-                    "name": "HyPhy HIV NGS Tools",
-                    "url": "https://galaxy.hyphy.org/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -132752,11 +136296,6 @@
                     "url": "https://usegalaxy.fr/",
                     "usegalaxy": false
                 },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
@@ -132765,17 +136304,24 @@
             ]
         },
         "symlink": null,
-        "time_estimation": "1H",
-        "title": "Mass spectrometry imaging: Examining the spatial distribution of analytes",
+        "time_estimation": "2H",
+        "title": "Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)",
         "tools": [
-            "Filter1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/2.6.0.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/2.6.0.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.2",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/2.6.0.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.3"
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.12.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/recetox/matchms_filtering/matchms_filtering/0.17.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/recetox/matchms_formatter/matchms_formatter/0.20.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/recetox/matchms_similarity/matchms_similarity/0.20.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/recetox/ramclustr/ramclustr/1.2.4+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/recetox/ramclustr/ramclustr/1.3.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/recetox/ramclustr_define_experiment/ramclustr_define_experiment/1.0.2",
+            "toolshed.g2.bx.psu.edu/repos/recetox/riassigner/riassigner/0.3.4+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/recetox/waveica/waveica/0.2.0+galaxy2"
         ],
         "topic_name": "metabolomics",
         "topic_name_human": "Metabolomics",
@@ -132785,774 +136331,549 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "msi-analyte-distribution",
+        "tutorial_name": "gc_ms_with_xcms",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.json"
         },
-        "version": 17,
+        "version": 5,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 105,
-        "visitors": 2488,
+        "visit_duration": 97,
+        "visitors": 1498,
         "workflows": [
             {
-                "creators": [],
-                "description": "Mass spectrometry imaging: Examining the spatial distribution of analytes",
+                "creators": [
+                    {
+                        "class": "Organization",
+                        "email": "mailto:GalaxyToolsDevelopmentandDeployment@space.muni.cz",
+                        "name": "RECETOX"
+                    }
+                ],
+                "description": "XCMS and RAMClustR based workflow for data processing and annotation using library matching via matchms.",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nUploaded Composite Dataset imzml\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAnnotation\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nm/z features\"]\n  3[label=\"MSI Qualitycontrol\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"MSI plot spectra\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"MSI filtering\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"MSI plot spectra\"]\n  0 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"MSI data exporter\"]\n  5 -> 7 [label=\"outfile_imzml\"]\n  8[label=\"MSI mz images\"]\n  2 -> 8 [label=\"output\"]\n  5 -> 8 [label=\"outfile_imzml\"]\n  9[label=\"Filter\"]\n  7 -> 9 [label=\"feature_output\"]\n  10[label=\"MSI mz images\"]\n  9 -> 10 [label=\"out_file1\"]\n  5 -> 10 [label=\"outfile_imzml\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference compound list alkanes\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference spectra\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nsample_metadata.tsv\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  4[label=\"msconvert\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"MSnbase readMSData\"]\n  4 -> 5 [label=\"output\"]\n  6[label=\"xcms findChromPeaks xcmsSet\"]\n  5 -> 6 [label=\"xsetRData\"]\n  7[label=\"xcms findChromPeaks Merger\"]\n  6 -> 7 [label=\"xsetRData\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"xcms groupChromPeaks group\"]\n  7 -> 8 [label=\"xsetRData\"]\n  9[label=\"xcms adjustRtime retcor\"]\n  8 -> 9 [label=\"xsetRData\"]\n  10[label=\"xcms groupChromPeaks group\"]\n  9 -> 10 [label=\"xsetRData\"]\n  11[label=\"xcms fillChromPeaks fillPeaks\"]\n  10 -> 11 [label=\"xsetRData\"]\n  k940c75491bae4ddd9e9275fc7d2c8eef[color=lightseagreen,label=\"Output\\nFeature (peak) intensities\"]\n  11 -> k940c75491bae4ddd9e9275fc7d2c8eef\n  k9f910e82e7a54201b9441845ba6aa2e9[color=lightseagreen,label=\"Output\\nFeature (peak) metadata (mz, rt, ...)\"]\n  11 -> k9f910e82e7a54201b9441845ba6aa2e9\n  k5bab8f284df14397af04168546bd0e52[color=lightseagreen,label=\"Output\\nxcmsObj (XCMSnExp)\"]\n  11 -> k5bab8f284df14397af04168546bd0e52\n  12[label=\"RAMClustR\"]\n  11 -> 12 [label=\"xsetRData\"]\n  k92fac5e615784e52ac9d2982e19a5b88[color=lightseagreen,label=\"Output\\nDeconvoluted spectra\"]\n  12 -> k92fac5e615784e52ac9d2982e19a5b88\n  kf7657c1762934fbbb01428009d495de7[color=lightseagreen,label=\"Output\\nFeature (spectra) intensities\"]\n  12 -> kf7657c1762934fbbb01428009d495de7\n  13[label=\"RIAssigner\"]\n  12 -> 13 [label=\"mass_spectra_merged\"]\n  0 -> 13 [label=\"output\"]\n  k7ec6ce025d8348abba0a94976db297e5[color=lightseagreen,label=\"Output\\nRetention indexed spectra\"]\n  13 -> k7ec6ce025d8348abba0a94976db297e5\n  14[label=\"matchms similarity\"]\n  13 -> 14 [label=\"output\"]\n  1 -> 14 [label=\"output\"]\n  k024327f713b84ce987089f430d7ceedf[color=lightseagreen,label=\"Output\\nCosineGreedy scores of input dataset(s)\"]\n  14 -> k024327f713b84ce987089f430d7ceedf\n  15[label=\"matchms scores formatter\"]\n  14 -> 15 [label=\"similarity_scores\"]\n  k8a7670064b3c41babea518fd100ce930[color=lightseagreen,label=\"Output\\nmatchms_scores\"]\n  15 -> k8a7670064b3c41babea518fd100ce930\n}",
                 "history": [
                     {
-                        "hash": "a46d3c7f2d648b7c17d3daaf18cc951d5da8d5f8",
-                        "message": "small updates in figures, tutorial and workflow",
+                        "hash": "9ed3f9ed83554a79f083624b4070b85877845e17",
+                        "message": "Update test",
+                        "num": 5,
+                        "short_hash": "9ed3f9ed8",
+                        "unix": "1689330096"
+                    },
+                    {
+                        "hash": "727d0600a2d08ad3a489b57f6bf5c08807af1e47",
+                        "message": "Update workflow and tests",
+                        "num": 4,
+                        "short_hash": "727d0600a",
+                        "unix": "1688998300"
+                    },
+                    {
+                        "hash": "a726fb0c2af4a24843f6a50c6f522a629b43f6dd",
+                        "message": "Update RIAssginer tool version",
+                        "num": 3,
+                        "short_hash": "a726fb0c2",
+                        "unix": "1683106380"
+                    },
+                    {
+                        "hash": "41eb746c708ea13d1fb5aeac6ef6d7a4ccae1890",
+                        "message": "Consistency in parameter values in workflow and tutorial",
+                        "num": 2,
+                        "short_hash": "41eb746c7",
+                        "unix": "1683104559"
+                    },
+                    {
+                        "hash": "1503b9315e3fb1918a8554b3d2814fedda96e4c0",
+                        "message": "Initial commit adding GC-MS tutorial",
                         "num": 1,
-                        "short_hash": "a46d3c7f2",
-                        "unix": "1604172185"
+                        "short_hash": "1503b9315",
+                        "unix": "1677491681"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "",
+                        "annotation": "List of retention indexed reference compounds. Either a table with columns `rt` and `ri` or an MSP with retention time and index metadata.",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Uploaded Composite Dataset (imzml)"
+                                "description": "List of retention indexed reference compounds. Either a table with columns `rt` and `ri` or an MSP with retention time and index metadata.",
+                                "name": "Reference compound list (alkanes)"
                             }
                         ],
-                        "label": "Uploaded Composite Dataset (imzml)",
+                        "label": "Reference compound list (alkanes)",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 409.6999969482422,
-                            "height": 82.19999694824219,
-                            "left": 375,
-                            "right": 575,
-                            "top": 327.5,
+                            "bottom": 511.8500061035156,
+                            "height": 82.20001220703125,
+                            "left": 160.0833282470703,
+                            "right": 360.0833282470703,
+                            "top": 429.6499938964844,
                             "width": 200,
-                            "x": 375,
-                            "y": 327.5
+                            "x": 160.0833282470703,
+                            "y": 429.6499938964844
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "d6fee109-e1af-4064-b014-051fbcede1d0",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "c5922e0d-d30d-4c15-84c9-7b97bc5aa93e"
-                            }
-                        ]
+                        "uuid": "6f1c04f5-126f-4ad2-bc25-b1c4b6efce5d",
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Spectral library to use for annotation in MSP or MGF format.",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Annotation"
-                            }
-                        ],
-                        "label": "Annotation",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 522.3000030517578,
-                            "height": 61.80000305175781,
-                            "left": 377,
-                            "right": 577,
-                            "top": 460.5,
-                            "width": 200,
-                            "x": 377,
-                            "y": 460.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "d0be9936-9e28-45f6-ac65-08d037ab9dc3",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "d826e468-2c46-4a28-9a24-bff61b41b35b"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "m/z features"
-                            }
-                        ],
-                        "label": "m/z features",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 866.3000030517578,
-                            "height": 61.80000305175781,
-                            "left": 385,
-                            "right": 585,
-                            "top": 804.5,
-                            "width": 200,
-                            "x": 385,
-                            "y": 804.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "02d90f0d-2375-47a8-9a7b-5c8ee43592c3",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "2d72fda0-0ccd-46b5-9011-a62a9c4f5e8e"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nUploaded Composite Dataset imzml\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nAnnotation\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nm/z features\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"MSI Qualitycontrol\"];\n  0 -->|output| 3;\n  4[\"MSI plot spectra\"];\n  0 -->|output| 4;\n  5[\"MSI filtering\"];\n  0 -->|output| 5;\n  6[\"MSI plot spectra\"];\n  0 -->|output| 6;\n  1 -->|output| 6;\n  7[\"MSI data exporter\"];\n  5 -->|outfile_imzml| 7;\n  8[\"MSI mz images\"];\n  2 -->|output| 8;\n  5 -->|outfile_imzml| 8;\n  9[\"Filter\"];\n  7 -->|feature_output| 9;\n  10[\"MSI mz images\"];\n  9 -->|out_file1| 10;\n  5 -->|outfile_imzml| 10;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "MSI Workflow: spatial distribution",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Uploaded Composite Dataset (imzml)"
+                                "description": "Spectral library to use for annotation in MSP or MGF format.",
+                                "name": "Reference spectra"
                             }
                         ],
-                        "label": "Uploaded Composite Dataset (imzml)",
+                        "label": "Reference spectra",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 409.6999969482422,
+                            "bottom": 616.8332977294922,
                             "height": 82.19999694824219,
-                            "left": 375,
-                            "right": 575,
-                            "top": 327.5,
+                            "left": 482.1000061035156,
+                            "right": 682.1000061035156,
+                            "top": 534.63330078125,
                             "width": 200,
-                            "x": 375,
-                            "y": 327.5
+                            "x": 482.1000061035156,
+                            "y": 534.63330078125
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "d6fee109-e1af-4064-b014-051fbcede1d0",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "c5922e0d-d30d-4c15-84c9-7b97bc5aa93e"
-                            }
-                        ]
+                        "uuid": "64a5eec1-54ef-4fc2-93c5-f6ab70ce1614",
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Sample metadata sheet, containing sample name, type (QC, blank, sample, etc.), batch number and injection order.",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Annotation"
+                                "description": "Sample metadata sheet, containing sample name, type (QC, blank, sample, etc.), batch number and injection order.",
+                                "name": "sample_metadata.tsv"
                             }
                         ],
-                        "label": "Annotation",
+                        "label": "sample_metadata.tsv",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 522.3000030517578,
-                            "height": 61.80000305175781,
-                            "left": 377,
-                            "right": 577,
-                            "top": 460.5,
+                            "bottom": 489.8500061035156,
+                            "height": 82.20001220703125,
+                            "left": -1541.933349609375,
+                            "right": -1341.933349609375,
+                            "top": 407.6499938964844,
                             "width": 200,
-                            "x": 377,
-                            "y": 460.5
+                            "x": -1541.933349609375,
+                            "y": 407.6499938964844
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "d0be9936-9e28-45f6-ac65-08d037ab9dc3",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "d826e468-2c46-4a28-9a24-bff61b41b35b"
-                            }
-                        ]
+                        "uuid": "494c83fe-4407-4123-b56e-0a211f97fea2",
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Mass spectrometry data to be processed in the workflow. Please ensure the format is supported by msconvert and only use the peak picking option if the input data was acquired in profile mode.",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 3,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "m/z features"
+                                "description": "Mass spectrometry data to be processed in the workflow. Please ensure the format is supported by msconvert and only use the peak picking option if the input data was acquired in profile mode.",
+                                "name": "Input Dataset Collection"
                             }
                         ],
-                        "label": "m/z features",
-                        "name": "Input dataset",
+                        "label": "Input Dataset Collection",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "bottom": 866.3000030517578,
-                            "height": 61.80000305175781,
-                            "left": 385,
-                            "right": 585,
-                            "top": 804.5,
+                            "bottom": 105.85000610351562,
+                            "height": 82.20001220703125,
+                            "left": -2407,
+                            "right": -2207,
+                            "top": 23.649993896484375,
                             "width": 200,
-                            "x": 385,
-                            "y": 804.5
+                            "x": -2407,
+                            "y": 23.649993896484375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "02d90f0d-2375-47a8-9a7b-5c8ee43592c3",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "2d72fda0-0ccd-46b5-9011-a62a9c4f5e8e"
-                            }
-                        ]
-                    },
+                        "type": "data_collection_input",
+                        "uuid": "2e362408-24c5-46e1-861c-74b825a5feaf",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nReference compound list alkanes\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference spectra\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nsample_metadata.tsv\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"msconvert\"];\n  3 -->|output| 4;\n  5[\"MSnbase readMSData\"];\n  4 -->|output| 5;\n  6[\"xcms findChromPeaks xcmsSet\"];\n  5 -->|xsetRData| 6;\n  7[\"xcms findChromPeaks Merger\"];\n  6 -->|xsetRData| 7;\n  2 -->|output| 7;\n  8[\"xcms groupChromPeaks group\"];\n  7 -->|xsetRData| 8;\n  9[\"xcms adjustRtime retcor\"];\n  8 -->|xsetRData| 9;\n  10[\"xcms groupChromPeaks group\"];\n  9 -->|xsetRData| 10;\n  11[\"xcms fillChromPeaks fillPeaks\"];\n  10 -->|xsetRData| 11;\n  940c7549-1bae-4ddd-9e92-75fc7d2c8eef[\"Output\\nFeature (peak) intensities\"];\n  11 --> 940c7549-1bae-4ddd-9e92-75fc7d2c8eef;\n  style 940c7549-1bae-4ddd-9e92-75fc7d2c8eef stroke:#2c3143,stroke-width:4px;\n  9f910e82-e7a5-4201-b944-1845ba6aa2e9[\"Output\\nFeature (peak) metadata (mz, rt, ...)\"];\n  11 --> 9f910e82-e7a5-4201-b944-1845ba6aa2e9;\n  style 9f910e82-e7a5-4201-b944-1845ba6aa2e9 stroke:#2c3143,stroke-width:4px;\n  5bab8f28-4df1-4397-af04-168546bd0e52[\"Output\\nxcmsObj (XCMSnExp)\"];\n  11 --> 5bab8f28-4df1-4397-af04-168546bd0e52;\n  style 5bab8f28-4df1-4397-af04-168546bd0e52 stroke:#2c3143,stroke-width:4px;\n  12[\"RAMClustR\"];\n  11 -->|xsetRData| 12;\n  92fac5e6-1578-4e52-ac9d-2982e19a5b88[\"Output\\nDeconvoluted spectra\"];\n  12 --> 92fac5e6-1578-4e52-ac9d-2982e19a5b88;\n  style 92fac5e6-1578-4e52-ac9d-2982e19a5b88 stroke:#2c3143,stroke-width:4px;\n  f7657c17-6293-4fbb-b014-28009d495de7[\"Output\\nFeature (spectra) intensities\"];\n  12 --> f7657c17-6293-4fbb-b014-28009d495de7;\n  style f7657c17-6293-4fbb-b014-28009d495de7 stroke:#2c3143,stroke-width:4px;\n  13[\"RIAssigner\"];\n  12 -->|mass_spectra_merged| 13;\n  0 -->|output| 13;\n  7ec6ce02-5d83-48ab-ba0a-94976db297e5[\"Output\\nRetention indexed spectra\"];\n  13 --> 7ec6ce02-5d83-48ab-ba0a-94976db297e5;\n  style 7ec6ce02-5d83-48ab-ba0a-94976db297e5 stroke:#2c3143,stroke-width:4px;\n  14[\"matchms similarity\"];\n  13 -->|output| 14;\n  1 -->|output| 14;\n  024327f7-13b8-4ce9-8708-9f430d7ceedf[\"Output\\nCosineGreedy scores of input dataset(s)\"];\n  14 --> 024327f7-13b8-4ce9-8708-9f430d7ceedf;\n  style 024327f7-13b8-4ce9-8708-9f430d7ceedf stroke:#2c3143,stroke-width:4px;\n  15[\"matchms scores formatter\"];\n  14 -->|similarity_scores| 15;\n  8a767006-4b3c-41ba-bea5-18fd100ce930[\"Output\\nmatchms_scores\"];\n  15 --> 8a767006-4b3c-41ba-bea5-18fd100ce930;\n  style 8a767006-4b3c-41ba-bea5-18fd100ce930 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "GC MS using XCMS",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/2.6.0.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0",
                         "errors": null,
-                        "id": 3,
+                        "id": 11,
                         "input_connections": {
-                            "infile": {
-                                "id": 0,
-                                "output_name": "output"
+                            "image": {
+                                "id": 10,
+                                "output_name": "xsetRData"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "xcms fillChromPeaks (fillPeaks)",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool MSI Qualitycontrol",
-                                "name": "calibrant_file"
+                                "name": "xsetRData",
+                                "type": "rdata.xcms.fillpeaks"
                             },
                             {
-                                "description": "runtime parameter for tool MSI Qualitycontrol",
-                                "name": "infile"
-                            }
-                        ],
-                        "label": null,
-                        "name": "MSI Qualitycontrol",
-                        "outputs": [
+                                "name": "variableMetadata",
+                                "type": "tabular"
+                            },
                             {
-                                "name": "QC_report",
-                                "type": "pdf"
+                                "name": "dataMatrix",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 312.6999969482422,
-                            "height": 205.1999969482422,
-                            "left": 669,
-                            "right": 869,
-                            "top": 107.5,
+                            "bottom": 357.25,
+                            "height": 235.60000610351562,
+                            "left": -122.89999389648438,
+                            "right": 77.10000610351562,
+                            "top": 121.64999389648438,
                             "width": 200,
-                            "x": 669,
-                            "y": 107.5
+                            "x": -122.89999389648438,
+                            "y": 121.64999389648438
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/2.6.0.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "ecaebe7c7b54",
-                            "name": "cardinal_quality_report",
-                            "owner": "galaxyp",
+                            "changeset_revision": "26d77e9ceb49",
+                            "name": "xcms_fillpeaks",
+                            "owner": "lecorguille",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"calibrant_file\": {\"__class__\": \"RuntimeValue\"}, \"calibrant_header\": \"false\", \"calibrantratio\": [], \"centroids\": \"true\", \"do_pca\": \"true\", \"filename\": \"\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"mz_column\": \"\", \"name_column\": \"\", \"plusminus_ppm\": \"200.0\", \"processed_cond\": {\"processed_file\": \"processed\", \"__current_case__\": 1, \"accuracy\": \"0.2\", \"units\": \"mz\"}, \"tabular_annotation\": {\"load_annotation\": \"no_annotation\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.0.1",
+                        "tool_state": "{\"Adv\": {\"expandMz\": \"0\", \"expandRt\": \"0\", \"ppm\": \"0\"}, \"file_load_section\": {\"file_load_conditional\": {\"file_load_select\": \"no\", \"__current_case__\": 0}}, \"image\": {\"__class__\": \"ConnectedValue\"}, \"peaklist\": {\"peaklistBool\": \"True\", \"convertRTMinute\": \"true\", \"numDigitsMZ\": \"4\", \"numDigitsRT\": \"0\", \"intval\": \"into\", \"naTOzero\": \"true\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.12.0+galaxy0",
                         "type": "tool",
-                        "uuid": "2ee50695-f822-4b88-b753-04722aa2ffca",
+                        "uuid": "fae0d093-7931-4f4c-97da-09a93087d66d",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "QC_report",
-                                "uuid": "adaa90d0-760d-4605-9076-d76e35d3e03f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.0",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "infile": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool MSI plot spectra",
-                                "name": "infile"
-                            }
-                        ],
-                        "label": null,
-                        "name": "MSI plot spectra",
-                        "outputs": [
+                                "label": "Feature (peak) intensities",
+                                "output_name": "dataMatrix",
+                                "uuid": "940c7549-1bae-4ddd-9e92-75fc7d2c8eef"
+                            },
                             {
-                                "name": "plots",
-                                "type": "pdf"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 456.5,
-                            "height": 134,
-                            "left": 669,
-                            "right": 869,
-                            "top": 322.5,
-                            "width": 200,
-                            "x": 669,
-                            "y": 322.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "d2596e1be091",
-                            "name": "cardinal_spectra_plots",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"centroids\": \"true\", \"filename\": \"\", \"fullmz\": \"true\", \"grid_variable\": \"false\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"mz_range\": {\"mz_range_options\": \"manual_mz\", \"__current_case__\": 2, \"zoomed_sample\": [{\"__index__\": 0, \"xlimmin\": \"10.0\", \"xlimmax\": \"200.0\"}, {\"__index__\": 1, \"xlimmin\": \"200.0\", \"xlimmax\": \"500.0\"}, {\"__index__\": 2, \"xlimmin\": \"500.0\", \"xlimmax\": \"1000.0\"}, {\"__index__\": 3, \"xlimmin\": \"1000.0\", \"xlimmax\": \"1500.0\"}, {\"__index__\": 4, \"xlimmin\": \"1500.0\", \"xlimmax\": \"2000.0\"}]}, \"pixel_conditional\": {\"pixel_type\": \"all_pixel\", \"__current_case__\": 1}, \"processed_cond\": {\"processed_file\": \"processed\", \"__current_case__\": 1, \"accuracy\": \"0.2\", \"units\": \"mz\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.0.0",
-                        "type": "tool",
-                        "uuid": "afd04232-7e33-418c-8409-524d2331fc65",
-                        "workflow_outputs": [
+                                "label": "Feature (peak) metadata (mz, rt, ...)",
+                                "output_name": "variableMetadata",
+                                "uuid": "9f910e82-e7a5-4201-b944-1845ba6aa2e9"
+                            },
                             {
-                                "label": null,
-                                "output_name": "plots",
-                                "uuid": "9468b2d2-782c-41d9-a2f4-2ec7c838c47f"
+                                "label": "xcmsObj (XCMSnExp)",
+                                "output_name": "xsetRData",
+                                "uuid": "5bab8f28-4df1-4397-af04-168546bd0e52"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/2.6.0.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/recetox/ramclustr/ramclustr/1.2.4+galaxy2",
                         "errors": null,
-                        "id": 5,
+                        "id": 12,
                         "input_connections": {
-                            "infile": {
-                                "id": 0,
-                                "output_name": "output"
+                            "filetype|xcms|input_xcms": {
+                                "id": 11,
+                                "output_name": "xsetRData"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool MSI filtering",
-                                "name": "infile"
+                                "description": "runtime parameter for tool RAMClustR",
+                                "name": "extras"
                             }
                         ],
                         "label": null,
-                        "name": "MSI filtering",
+                        "name": "RAMClustR",
                         "outputs": [
                             {
-                                "name": "outfile_imzml",
-                                "type": "imzml"
+                                "name": "spec_abundance",
+                                "type": "csv"
                             },
                             {
-                                "name": "QC_overview",
-                                "type": "pdf"
+                                "name": "mass_spectra_merged",
+                                "type": "msp"
                             }
                         ],
                         "position": {
-                            "bottom": 824.8999938964844,
-                            "height": 164.39999389648438,
-                            "left": 672,
-                            "right": 872,
-                            "top": 660.5,
+                            "bottom": 333.8500061035156,
+                            "height": 215.20001220703125,
+                            "left": 152.10000610351562,
+                            "right": 352.1000061035156,
+                            "top": 118.64999389648438,
                             "width": 200,
-                            "x": 672,
-                            "y": 660.5
+                            "x": 152.10000610351562,
+                            "y": 118.64999389648438
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/2.6.0.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/recetox/ramclustr/ramclustr/1.2.4+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "2aefa66e48e5",
-                            "name": "cardinal_filtering",
-                            "owner": "galaxyp",
+                            "changeset_revision": "2ec9253a647e",
+                            "name": "ramclustr",
+                            "owner": "recetox",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"centroids\": \"true\", \"features_cond\": {\"features_filtering\": \"features_range\", \"__current_case__\": 2, \"min_mz\": \"15.0\", \"max_mz\": \"1000.0\"}, \"infile\": {\"__class__\": \"RuntimeValue\"}, \"pixels_cond\": {\"pixel_filtering\": \"none\", \"__current_case__\": 0}, \"processed_cond\": {\"processed_file\": \"processed\", \"__current_case__\": 1, \"accuracy\": \"0.2\", \"units\": \"mz\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.0.0",
+                        "tool_state": "{\"clustering\": {\"linkage\": \"average\", \"minModuleSize\": \"5\", \"hmax\": \"0.9\", \"deepSplit\": \"false\"}, \"extras\": {\"rt_only_low_n\": \"true\", \"replace_zeros\": \"true\", \"ExpDes\": {\"__class__\": \"RuntimeValue\"}}, \"filetype\": {\"type_choice\": \"xcms\", \"__current_case__\": 0, \"xcms\": {\"input_xcms\": {\"__class__\": \"ConnectedValue\"}, \"usePheno\": \"true\"}, \"required\": {\"st\": null, \"sr\": \"0.7\", \"cor_method\": \"pearson\", \"maxt\": \"10.0\"}}, \"msp_output_details\": {\"merge_msp\": \"true\", \"mzdec\": \"6\"}, \"normalisation\": {\"normalisation_method\": {\"normalize\": \"none\", \"__current_case__\": 3}}, \"performance\": {\"blocksize\": \"2000\", \"mult\": \"5\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.4+galaxy2",
                         "type": "tool",
-                        "uuid": "69f61159-f6e3-4dc9-a8f7-b5f1a1334fc6",
+                        "uuid": "2410e8b8-d629-4798-950d-e3d865a6aa72",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "QC_overview",
-                                "uuid": "7fc1700f-e7b5-45eb-b9d8-dd1bf6594385"
+                                "label": "Deconvoluted spectra",
+                                "output_name": "mass_spectra_merged",
+                                "uuid": "92fac5e6-1578-4e52-ac9d-2982e19a5b88"
                             },
                             {
-                                "label": null,
-                                "output_name": "outfile_imzml",
-                                "uuid": "45f6e115-e334-4ea7-9c8a-7bc36735affa"
+                                "label": "Feature (spectra) intensities",
+                                "output_name": "spec_abundance",
+                                "uuid": "f7657c17-6293-4fbb-b014-28009d495de7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/recetox/riassigner/riassigner/0.3.4+galaxy1",
                         "errors": null,
-                        "id": 6,
+                        "id": 13,
                         "input_connections": {
-                            "infile": {
-                                "id": 0,
-                                "output_name": "output"
+                            "query_section|query": {
+                                "id": 12,
+                                "output_name": "mass_spectra_merged"
                             },
-                            "pixel_conditional|pixel_file": {
-                                "id": 1,
+                            "reference_section|reference": {
+                                "id": 0,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool MSI plot spectra",
-                                "name": "infile"
-                            },
-                            {
-                                "description": "runtime parameter for tool MSI plot spectra",
-                                "name": "pixel_conditional"
-                            }
-                        ],
-                        "label": null,
-                        "name": "MSI plot spectra",
-                        "outputs": [
-                            {
-                                "name": "plots",
-                                "type": "pdf"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 649.3000030517578,
-                            "height": 184.8000030517578,
-                            "left": 669,
-                            "right": 869,
-                            "top": 464.5,
-                            "width": 200,
-                            "x": 669,
-                            "y": 464.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "d2596e1be091",
-                            "name": "cardinal_spectra_plots",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"centroids\": \"true\", \"filename\": \"\", \"fullmz\": \"true\", \"grid_variable\": \"false\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"mz_range\": {\"mz_range_options\": \"manual_mz\", \"__current_case__\": 2, \"zoomed_sample\": [{\"__index__\": 0, \"xlimmin\": \"10.0\", \"xlimmax\": \"200.0\"}, {\"__index__\": 1, \"xlimmin\": \"200.0\", \"xlimmax\": \"500.0\"}, {\"__index__\": 2, \"xlimmin\": \"500.0\", \"xlimmax\": \"1000.0\"}, {\"__index__\": 3, \"xlimmin\": \"1000.0\", \"xlimmax\": \"1500.0\"}, {\"__index__\": 4, \"xlimmin\": \"1500.0\", \"xlimmax\": \"2000.0\"}]}, \"pixel_conditional\": {\"pixel_type\": \"tabular_pixel\", \"__current_case__\": 0, \"pixel_file\": {\"__class__\": \"RuntimeValue\"}, \"column_pixel_x\": \"1\", \"column_pixel_y\": \"2\", \"column_pixel_annotation\": \"3\", \"tabular_pixel_header\": \"true\"}, \"processed_cond\": {\"processed_file\": \"processed\", \"__current_case__\": 1, \"accuracy\": \"0.2\", \"units\": \"mz\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.0.0",
-                        "type": "tool",
-                        "uuid": "27e49459-5afa-49d9-a357-811fbe90650c",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "plots",
-                                "uuid": "69cb29ad-3b9e-4c7c-b1f7-01c78525e6a6"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/2.6.0.0",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "infile": {
-                                "id": 5,
-                                "output_name": "outfile_imzml"
-                            }
-                        },
                         "inputs": [],
                         "label": null,
-                        "name": "MSI data exporter",
+                        "name": "RIAssigner",
                         "outputs": [
                             {
-                                "name": "intensity_matrix",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "feature_output",
-                                "type": "tabular"
+                                "name": "output",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 540.1000061035156,
-                            "height": 225.60000610351562,
-                            "left": 940,
-                            "right": 1140,
-                            "top": 314.5,
+                            "bottom": 466.6499938964844,
+                            "height": 144,
+                            "left": 450.08331298828125,
+                            "right": 650.0833129882812,
+                            "top": 322.6499938964844,
                             "width": 200,
-                            "x": 940,
-                            "y": 314.5
+                            "x": 450.08331298828125,
+                            "y": 322.6499938964844
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/2.6.0.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/recetox/riassigner/riassigner/0.3.4+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "137bfc63e758",
-                            "name": "cardinal_data_exporter",
-                            "owner": "galaxyp",
+                            "changeset_revision": "c702620c22b1",
+                            "name": "riassigner",
+                            "owner": "recetox",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"imzml\", \"centroids\": \"true\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"counting_calibrants\": {\"pixel_with_calibrants\": \"no_calibrants\", \"__current_case__\": 0}, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"output_options\": [\"int_matrix\", \"mz_tabular\"], \"processed_cond\": {\"processed_file\": \"no_processed\", \"__current_case__\": 0}, \"tabular_annotation\": {\"load_annotation\": \"no_annotation\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.0.0",
+                        "tool_state": "{\"method\": \"kovats\", \"query_section\": {\"query\": {\"__class__\": \"ConnectedValue\"}, \"query_rt_units\": \"seconds\"}, \"reference_section\": {\"reference\": {\"__class__\": \"ConnectedValue\"}, \"reference_rt_units\": \"seconds\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3.4+galaxy1",
                         "type": "tool",
-                        "uuid": "f1647eea-23ca-4713-ae2e-7f68e6388aa7",
+                        "uuid": "e626eac6-354c-4117-bd98-2203cb2d177b",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "intensity_matrix",
-                                "uuid": "eadf7793-dbdc-4691-b9ed-b359229b35c7"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "feature_output",
-                                "uuid": "ea4d3b0c-8b42-45c2-adaa-65fc0ce368f9"
+                                "label": "Retention indexed spectra",
+                                "output_name": "output",
+                                "uuid": "7ec6ce02-5d83-48ab-ba0a-94976db297e5"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/recetox/matchms_similarity/matchms_similarity/0.20.0+galaxy0",
                         "errors": null,
-                        "id": 8,
+                        "id": 14,
                         "input_connections": {
-                            "calibrant_file": {
-                                "id": 2,
+                            "queries": {
+                                "id": 13,
                                 "output_name": "output"
                             },
-                            "infile": {
-                                "id": 5,
-                                "output_name": "outfile_imzml"
+                            "symmetric|references": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool MSI mz images",
-                                "name": "calibrant_file"
+                                "description": "runtime parameter for tool matchms similarity",
+                                "name": "queries"
                             },
                             {
-                                "description": "runtime parameter for tool MSI mz images",
-                                "name": "infile"
+                                "description": "runtime parameter for tool matchms similarity",
+                                "name": "symmetric"
                             }
                         ],
                         "label": null,
-                        "name": "MSI mz images",
+                        "name": "matchms similarity",
                         "outputs": [
                             {
-                                "name": "plots",
-                                "type": "pdf"
+                                "name": "similarity_scores",
+                                "type": "json"
                             }
                         ],
                         "position": {
-                            "bottom": 940.3000030517578,
-                            "height": 184.8000030517578,
-                            "left": 933,
-                            "right": 1133,
-                            "top": 755.5,
+                            "bottom": 534.3999938964844,
+                            "height": 164.39999389648438,
+                            "left": 805,
+                            "right": 1005,
+                            "top": 370,
                             "width": 200,
-                            "x": 933,
-                            "y": 755.5
+                            "x": 805,
+                            "y": 370
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/recetox/matchms_similarity/matchms_similarity/0.20.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "a95a82eb4d50",
-                            "name": "cardinal_mz_images",
-                            "owner": "galaxyp",
+                            "changeset_revision": "e5010b19d64d",
+                            "name": "matchms_similarity",
+                            "owner": "recetox",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"calibrant_file\": {\"__class__\": \"RuntimeValue\"}, \"calibrant_header\": \"false\", \"centroids\": \"true\", \"colorkey\": \"true\", \"colorscale\": \"viridis\", \"filename\": \"\", \"image_contrast\": \"suppression\", \"image_smoothing\": \"none\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"mz_column\": \"1\", \"name_column\": \"1\", \"normalize_image\": \"false\", \"overlay_cond\": {\"overlay_selection\": \"yes_overlay\", \"__current_case__\": 1, \"colours\": [{\"__index__\": 0, \"feature_color\": \"#c00000\"}, {\"__index__\": 1, \"feature_color\": \"#0070c0\"}, {\"__index__\": 2, \"feature_color\": \"#92d050\"}], \"legend_position\": \"topright\"}, \"plusminus_dalton\": \"0.4\", \"processed_cond\": {\"processed_file\": \"no_processed\", \"__current_case__\": 0}, \"svg_pixelimage\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.0.1",
-                        "type": "tool",
-                        "uuid": "34143b6c-d77e-4dc8-8c5e-18cc685fdc74",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "plots",
-                                "uuid": "a8a97f8e-6bfa-4376-8c5f-a3305f8af429"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "Filter1",
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "input": {
-                                "id": 7,
-                                "output_name": "feature_output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Filter",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 570.6999969482422,
-                            "height": 93.19999694824219,
-                            "left": 1176,
-                            "right": 1376,
-                            "top": 477.5,
-                            "width": 200,
-                            "x": 1176,
-                            "y": 477.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c2>=55 and c2<=65 or c2>=75 and c2<=85\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_state": "{\"array_type\": \"numpy\", \"metric\": {\"similarity_metric\": \"CosineGreedy\", \"__current_case__\": 0, \"algorithm\": {\"tolerance\": \"0.03\", \"mz_power\": \"0.0\", \"intensity_power\": \"1.0\"}}, \"queries\": {\"__class__\": \"RuntimeValue\"}, \"ri_filtering\": {\"is_true\": \"true\", \"__current_case__\": 0, \"tolerance\": \"20.0\"}, \"symmetric\": {\"is_symmetric\": \"false\", \"__current_case__\": 0, \"references\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.20.0+galaxy0",
                         "type": "tool",
-                        "uuid": "8b864289-7691-4045-b6c2-ad191a86a6f9",
+                        "uuid": "2c42471c-f9e2-43e7-977c-2207bedbf416",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "59998a93-7244-4c6b-b2c3-be3cc5f44458"
+                                "label": "CosineGreedy scores of input dataset(s)",
+                                "output_name": "similarity_scores",
+                                "uuid": "024327f7-13b8-4ce9-8708-9f430d7ceedf"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.0",
-                        "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "calibrant_file": {
-                                "id": 9,
-                                "output_name": "out_file1"
-                            },
-                            "infile": {
-                                "id": 5,
-                                "output_name": "outfile_imzml"
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/recetox/matchms_formatter/matchms_formatter/0.20.0+galaxy0",
+                        "errors": null,
+                        "id": 15,
+                        "input_connections": {
+                            "scores": {
+                                "id": 14,
+                                "output_name": "similarity_scores"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool MSI mz images",
-                                "name": "calibrant_file"
-                            },
-                            {
-                                "description": "runtime parameter for tool MSI mz images",
-                                "name": "infile"
+                                "description": "runtime parameter for tool matchms scores formatter",
+                                "name": "scores"
                             }
                         ],
                         "label": null,
-                        "name": "MSI mz images",
+                        "name": "matchms scores formatter",
                         "outputs": [
                             {
-                                "name": "plots",
-                                "type": "pdf"
+                                "name": "output",
+                                "type": "tsv"
                             }
                         ],
                         "position": {
-                            "bottom": 791.3000030517578,
-                            "height": 184.8000030517578,
-                            "left": 1410,
-                            "right": 1610,
-                            "top": 606.5,
+                            "bottom": 506.3999938964844,
+                            "height": 154.39999389648438,
+                            "left": 1175,
+                            "right": 1375,
+                            "top": 352,
                             "width": 200,
-                            "x": 1410,
-                            "y": 606.5
+                            "x": 1175,
+                            "y": 352
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/recetox/matchms_formatter/matchms_formatter/0.20.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "a95a82eb4d50",
-                            "name": "cardinal_mz_images",
-                            "owner": "galaxyp",
+                            "changeset_revision": "1b09315a3f87",
+                            "name": "matchms_formatter",
+                            "owner": "recetox",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"calibrant_file\": {\"__class__\": \"RuntimeValue\"}, \"calibrant_header\": \"true\", \"centroids\": \"true\", \"colorkey\": \"true\", \"colorscale\": \"viridis\", \"filename\": \"\", \"image_contrast\": \"suppression\", \"image_smoothing\": \"none\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"mz_column\": \"2\", \"name_column\": \"1\", \"normalize_image\": \"false\", \"overlay_cond\": {\"overlay_selection\": \"no_overlay\", \"__current_case__\": 0}, \"plusminus_dalton\": \"0.4\", \"processed_cond\": {\"processed_file\": \"no_processed\", \"__current_case__\": 0}, \"svg_pixelimage\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.0.1",
+                        "tool_state": "{\"scores\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.20.0+galaxy0",
                         "type": "tool",
-                        "uuid": "24081ed2-7205-45c8-a3ea-9de110785398",
+                        "uuid": "64da39ef-4625-4598-978d-e38bbbc2f007",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "plots",
-                                "uuid": "095a38a2-99e1-42f1-a3d0-57c54f242c2e"
+                                "label": "matchms_scores",
+                                "output_name": "output",
+                                "uuid": "8a767006-4b3c-41ba-bea5-18fd100ce930"
                             }
                         ]
                     }
                 ],
-                "parent_id": "metabolomics/msi-analyte-distribution",
-                "path": "topics/metabolomics/tutorials/msi-analyte-distribution/workflows/wf_MSI_distribution.ga",
+                "parent_id": "metabolomics/gc_ms_with_xcms",
+                "path": "topics/metabolomics/tutorials/gc_ms_with_xcms/workflows/main_workflow.ga",
                 "tags": [
-                    "metabolomics"
+                    "GC-MS",
+                    "Metabolomics",
+                    "Expospomics"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "MSI Workflow: spatial distribution",
+                "tests": true,
+                "title": "GC MS using XCMS",
                 "topic_id": "metabolomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/metabolomics-msi-analyte-distribution/versions/wf-msi-distribution",
-                "tutorial_id": "msi-analyte-distribution",
-                "url": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/msi-analyte-distribution/workflows/wf_MSI_distribution.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/msi-analyte-distribution/workflows/wf_MSI_distribution.html",
-                "version": 1,
-                "wfid": "metabolomics-msi-analyte-distribution",
-                "wfname": "wf-msi-distribution",
-                "workflow": "wf_MSI_distribution.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/metabolomics-gc_ms_with_xcms/versions/main-workflow",
+                "tutorial_id": "gc_ms_with_xcms",
+                "url": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/gc_ms_with_xcms/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/gc_ms_with_xcms/workflows/main_workflow.html",
+                "version": 2,
+                "wfid": "metabolomics-gc_ms_with_xcms",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "Filter1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/2.6.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/2.6.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/2.6.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.0"
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2",
+                    "toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.12.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/recetox/matchms_formatter/matchms_formatter/0.20.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/recetox/matchms_similarity/matchms_similarity/0.20.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/recetox/ramclustr/ramclustr/1.2.4+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/recetox/riassigner/riassigner/0.3.4+galaxy1"
                 ],
-                "workflowhub_id": "1061"
+                "workflowhub_id": "1119"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/484496"
+        "zenodo_link": "https://zenodo.org/record/7890956"
     },
     {
         "admin_install": {
@@ -133561,266 +136882,166 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "msconvert",
-                    "owner": "galaxyp",
-                    "revisions": "6153e8ada1ee",
-                    "tool_panel_section_label": "Convert Formats",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "msnbase_readmsdata",
-                    "owner": "lecorguille",
-                    "revisions": "11ab2081bd4a",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xcms_fillpeaks",
-                    "owner": "lecorguille",
-                    "revisions": "26d77e9ceb49",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xcms_group",
-                    "owner": "lecorguille",
-                    "revisions": "d45a786cbc40",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xcms_merge",
-                    "owner": "lecorguille",
-                    "revisions": "5bd125a3f3b0",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xcms_retcor",
-                    "owner": "lecorguille",
-                    "revisions": "aa252eec9229",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xcms_xcmsset",
-                    "owner": "lecorguille",
-                    "revisions": "b02d1992a43a",
-                    "tool_panel_section_label": "Metabolomics",
+                    "name": "join_files_on_column_fuzzy",
+                    "owner": "bgruening",
+                    "revisions": "22ec3c1a20cd",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "matchms_filtering",
-                    "owner": "recetox",
-                    "revisions": "357df6c47d92",
-                    "tool_panel_section_label": "Metabolomics",
+                    "name": "cardinal_classification",
+                    "owner": "galaxyp",
+                    "revisions": "b574b84afc4d",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "matchms_formatter",
-                    "owner": "recetox",
-                    "revisions": "1b09315a3f87",
-                    "tool_panel_section_label": "Metabolomics",
+                    "name": "cardinal_combine",
+                    "owner": "galaxyp",
+                    "revisions": "48c07268f341",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "matchms_similarity",
-                    "owner": "recetox",
-                    "revisions": "e5010b19d64d",
-                    "tool_panel_section_label": "Metabolomics",
+                    "name": "cardinal_mz_images",
+                    "owner": "galaxyp",
+                    "revisions": "25b83cbd596a",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ramclustr",
-                    "owner": "recetox",
-                    "revisions": "2ec9253a647e",
-                    "tool_panel_section_label": "Metabolomics",
+                    "name": "cardinal_preprocessing",
+                    "owner": "galaxyp",
+                    "revisions": "ed9ed1e6cca2",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ramclustr",
-                    "owner": "recetox",
-                    "revisions": "050cfef6ba65",
-                    "tool_panel_section_label": "Metabolomics",
+                    "name": "cardinal_quality_report",
+                    "owner": "galaxyp",
+                    "revisions": "3b7a35d50ebf",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ramclustr_define_experiment",
-                    "owner": "recetox",
-                    "revisions": "25625114618e",
-                    "tool_panel_section_label": "Metabolomics",
+                    "name": "cardinal_segmentations",
+                    "owner": "galaxyp",
+                    "revisions": "82f6c2f4332d",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "riassigner",
-                    "owner": "recetox",
-                    "revisions": "c702620c22b1",
-                    "tool_panel_section_label": "Metabolomics",
+                    "name": "maldi_quant_peak_detection",
+                    "owner": "galaxyp",
+                    "revisions": "e9300ef37403",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "waveica",
-                    "owner": "recetox",
-                    "revisions": "b77023c41c76",
-                    "tool_panel_section_label": "Metabolomics",
+                    "name": "maldi_quant_preprocessing",
+                    "owner": "galaxyp",
+                    "revisions": "71411ac28268",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: msconvert\n  owner: galaxyp\n  revisions: 6153e8ada1ee\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msnbase_readmsdata\n  owner: lecorguille\n  revisions: 11ab2081bd4a\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_fillpeaks\n  owner: lecorguille\n  revisions: 26d77e9ceb49\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_group\n  owner: lecorguille\n  revisions: d45a786cbc40\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_merge\n  owner: lecorguille\n  revisions: 5bd125a3f3b0\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_retcor\n  owner: lecorguille\n  revisions: aa252eec9229\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_xcmsset\n  owner: lecorguille\n  revisions: b02d1992a43a\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: matchms_filtering\n  owner: recetox\n  revisions: 357df6c47d92\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: matchms_formatter\n  owner: recetox\n  revisions: 1b09315a3f87\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: matchms_similarity\n  owner: recetox\n  revisions: e5010b19d64d\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ramclustr\n  owner: recetox\n  revisions: 2ec9253a647e\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ramclustr\n  owner: recetox\n  revisions: 050cfef6ba65\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ramclustr_define_experiment\n  owner: recetox\n  revisions: 25625114618e\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: riassigner\n  owner: recetox\n  revisions: c702620c22b1\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: waveica\n  owner: recetox\n  revisions: b77023c41c76\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "xtrojak",
-                "hechth",
-                "maximskorik"
-            ],
-            "editing": [
-                "hexylena"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: join_files_on_column_fuzzy\n  owner: bgruening\n  revisions: 22ec3c1a20cd\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_classification\n  owner: galaxyp\n  revisions: b574b84afc4d\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_combine\n  owner: galaxyp\n  revisions: 48c07268f341\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_mz_images\n  owner: galaxyp\n  revisions: 25b83cbd596a\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_preprocessing\n  owner: galaxyp\n  revisions: ed9ed1e6cca2\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_quality_report\n  owner: galaxyp\n  revisions: 3b7a35d50ebf\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_segmentations\n  owner: galaxyp\n  revisions: 82f6c2f4332d\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maldi_quant_peak_detection\n  owner: galaxyp\n  revisions: e9300ef37403\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maldi_quant_preprocessing\n  owner: galaxyp\n  revisions: 71411ac28268\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.json",
         "contributors": [
-            {
-                "email": "trojak@mail.muni.cz",
-                "id": "xtrojak",
-                "joined": "2021-06",
-                "name": "Matej Troj\u00e1k",
-                "orcid": "0000-0003-0841-2707",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/xtrojak/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/xtrojak.json"
-            },
-            {
-                "email": "helge.hecht@recetox.muni.cz",
-                "id": "hechth",
-                "joined": "2020-01",
-                "name": "Helge Hecht",
-                "orcid": "0000-0001-6744-996X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hechth/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hechth.json"
-            },
-            {
-                "email": "maximskoryk@gmail.com",
-                "id": "maximskorik",
-                "joined": "2023-03",
-                "name": "Maxim Skoryk",
-                "orcid": "0000-0003-2056-8018",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/maximskorik/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/maximskorik.json"
-            },
             {
                 "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
                     "uni-freiburg"
                 ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+                "email": "melanie.foell@mol-med.uni-freiburg.de",
+                "id": "foellmelanie",
+                "joined": "2018-10",
+                "matrix": "foellmelanie:matrix.org",
+                "name": "Melanie F\u00f6ll",
+                "orcid": "0000-0002-1887-7543",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
+                "twitter": "MCFoell",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
             }
         ],
-        "dir": "topics/metabolomics/tutorials/gc_ms_with_xcms",
-        "edam_operation": [
-            "Imputation",
-            "Chromatogram visualisation",
-            "Formatting",
-            "Format validation",
-            "Validation",
-            "Filtering",
-            "Chromatographic alignment",
-            "Peak detection",
-            "Label-free quantification",
-            "Standardisation and normalisation",
-            "Clustering",
-            "Correlation",
-            "Spectral library search",
-            "Mass spectrum visualisation"
-        ],
+        "dir": "topics/metabolomics/tutorials/msi-finding-nglycans",
+        "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "metabolomics/gc_ms_with_xcms",
+        "id": "metabolomics/msi-finding-nglycans",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
             "UseGalaxy.fr",
+            "UseGalaxy.no",
             "UseGalaxy.org.au"
         ],
         "js_requirements": {
-            "mathjax": 27731,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "The processing of untargeted GC-MS metabolomic data can be done using open-source tools.",
-            "This processing workflow is complementary to CAMERA and metaMS."
+            "Several files can be combined and the spectra used to obtain the annotation of their original file.",
+            "Preprocessing reduces the file size and can improve further analysis steps.",
+            "Unsupervised and supervised statistical analysis can reveal analytes with different abundances.",
+            "The spatial distribution of N-glycans in a tissue section can be measured by MALDI imaging.",
+            "Additional LC-MS/MS experiments enable the identification of N-glycans measured by MSI.",
+            "Some N-glycans are located to specific kidney compartments."
         ],
         "layout": "tutorial_hands_on",
         "level": "Intermediate",
         "license": "CC-BY-4.0",
         "mod_date": "2023-11-09",
         "objectives": [
-            "To learn about the key steps in the preprocessing and analysis of untargeted GC-MS metabolomics data.",
-            "To explore what open-source alternative tools can be used in the analysis of GC-MS data, learn about their possible parametrisations.",
-            "To analyse authentic data samples and compare them with a data library of human metabolome, composed from a collection of mostly endogenous compounds."
+            "Combining MSI datasets while using the information about each subfile in further steps.",
+            "Preprocessing raw MSI data.",
+            "Performing supervised and unsupervised statistical analysis."
         ],
-        "pageviews": 1848,
-        "pub_date": "2023-05-08",
+        "pageviews": 2446,
+        "pub_date": "2019-04-13",
         "questions": [
-            "What are the main steps of gas chromatography-mass spectrometry (GC-MS) data processing for metabolomic analysis?",
-            "What similarity metrics can be used to compare a pair of mass spectra and what are the differences between them?",
-            "Do you know any alternative tools that can be used in place of the individual steps of this workflow?"
+            "Can N-linked glycans from FFPE tissues be detected by MALDI imaging?",
+            "Can potential N-linked glycans be identified by an additional LC-MS/MS experiment?",
+            "Do specific kidney compartments have different N-linked glycan compositions?"
         ],
         "requirements": [
             {
-                "topic_name": "metabolomics",
+                "topic_name": "proteomics",
                 "tutorials": [
-                    "lcms-preprocessing"
+                    "mass-spectrometry-imaging-loading-exploring-data"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00344",
+        "short_id": "T00199",
         "short_tools": [
-            "msconvert",
-            "matchms_filtering",
-            "abims_xcms_fillPeaks",
-            "matchms_formatter",
-            "riassigner",
-            "abims_xcms_xcmsSet",
-            "xcms_merge",
-            "abims_xcms_retcor",
-            "ramclustr_define_experiment",
-            "abims_xcms_group",
-            "waveica",
-            "matchms_similarity",
-            "msnbase_readmsdata",
-            "ramclustr"
+            "cardinal_combine",
+            "cardinal_segmentations",
+            "Summary_Statistics1",
+            "cardinal_classification",
+            "Filter1",
+            "maldi_quant_peak_detection",
+            "maldi_quant_preprocessing",
+            "cardinal_preprocessing",
+            "Grep1",
+            "cardinal_mz_images",
+            "join_files_on_column_fuzzy",
+            "cardinal_quality_report"
         ],
         "slides": false,
         "slides_recordings": false,
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
@@ -133838,6 +137059,11 @@
                     "url": "https://usegalaxy.fr/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
@@ -133847,23 +137073,20 @@
         },
         "symlink": null,
         "time_estimation": "2H",
-        "title": "Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)",
+        "title": "Mass spectrometry imaging: Finding differential analytes",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.12.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/recetox/matchms_filtering/matchms_filtering/0.17.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/recetox/matchms_formatter/matchms_formatter/0.20.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/recetox/matchms_similarity/matchms_similarity/0.20.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/recetox/ramclustr/ramclustr/1.2.4+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/recetox/ramclustr/ramclustr/1.3.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/recetox/ramclustr_define_experiment/ramclustr_define_experiment/1.0.2",
-            "toolshed.g2.bx.psu.edu/repos/recetox/riassigner/riassigner/0.3.4+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/recetox/waveica/waveica/0.2.0+galaxy2"
+            "Filter1",
+            "Grep1",
+            "Summary_Statistics1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy/1.0.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/1.12.1.3",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.3",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.2",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/1.12.1.3",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.3",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.3",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.4",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.3"
         ],
         "topic_name": "metabolomics",
         "topic_name_human": "Metabolomics",
@@ -133873,1400 +137096,1019 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "gc_ms_with_xcms",
+        "tutorial_name": "msi-finding-nglycans",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.json"
         },
-        "version": 5,
+        "version": 9,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 103,
-        "visitors": 1358,
+        "visit_duration": 111,
+        "visitors": 1667,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Organization",
-                        "email": "mailto:GalaxyToolsDevelopmentandDeployment@space.muni.cz",
-                        "name": "RECETOX"
-                    }
-                ],
-                "description": "XCMS and RAMClustR based workflow for data processing and annotation using library matching via matchms.",
+                "creators": [],
+                "description": "Mass spectrometry imaging: Finding differential analytes",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference compound list alkanes\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference spectra\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nsample_metadata.tsv\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  4[label=\"msconvert\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"MSnbase readMSData\"]\n  4 -> 5 [label=\"output\"]\n  6[label=\"xcms findChromPeaks xcmsSet\"]\n  5 -> 6 [label=\"xsetRData\"]\n  7[label=\"xcms findChromPeaks Merger\"]\n  6 -> 7 [label=\"xsetRData\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"xcms groupChromPeaks group\"]\n  7 -> 8 [label=\"xsetRData\"]\n  9[label=\"xcms adjustRtime retcor\"]\n  8 -> 9 [label=\"xsetRData\"]\n  10[label=\"xcms groupChromPeaks group\"]\n  9 -> 10 [label=\"xsetRData\"]\n  11[label=\"xcms fillChromPeaks fillPeaks\"]\n  10 -> 11 [label=\"xsetRData\"]\n  k940c75491bae4ddd9e9275fc7d2c8eef[color=lightseagreen,label=\"Output\\nFeature (peak) intensities\"]\n  11 -> k940c75491bae4ddd9e9275fc7d2c8eef\n  k9f910e82e7a54201b9441845ba6aa2e9[color=lightseagreen,label=\"Output\\nFeature (peak) metadata (mz, rt, ...)\"]\n  11 -> k9f910e82e7a54201b9441845ba6aa2e9\n  k5bab8f284df14397af04168546bd0e52[color=lightseagreen,label=\"Output\\nxcmsObj (XCMSnExp)\"]\n  11 -> k5bab8f284df14397af04168546bd0e52\n  12[label=\"RAMClustR\"]\n  11 -> 12 [label=\"xsetRData\"]\n  k92fac5e615784e52ac9d2982e19a5b88[color=lightseagreen,label=\"Output\\nDeconvoluted spectra\"]\n  12 -> k92fac5e615784e52ac9d2982e19a5b88\n  kf7657c1762934fbbb01428009d495de7[color=lightseagreen,label=\"Output\\nFeature (spectra) intensities\"]\n  12 -> kf7657c1762934fbbb01428009d495de7\n  13[label=\"RIAssigner\"]\n  12 -> 13 [label=\"mass_spectra_merged\"]\n  0 -> 13 [label=\"output\"]\n  k7ec6ce025d8348abba0a94976db297e5[color=lightseagreen,label=\"Output\\nRetention indexed spectra\"]\n  13 -> k7ec6ce025d8348abba0a94976db297e5\n  14[label=\"matchms similarity\"]\n  13 -> 14 [label=\"output\"]\n  1 -> 14 [label=\"output\"]\n  k024327f713b84ce987089f430d7ceedf[color=lightseagreen,label=\"Output\\nCosineGreedy scores of input dataset(s)\"]\n  14 -> k024327f713b84ce987089f430d7ceedf\n  15[label=\"matchms scores formatter\"]\n  14 -> 15 [label=\"similarity_scores\"]\n  k8a7670064b3c41babea518fd100ce930[color=lightseagreen,label=\"Output\\nmatchms_scores\"]\n  15 -> k8a7670064b3c41babea518fd100ce930\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntreated\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontrol\"]\n  10[label=\"MSI classification\"]\n  9 -> 10 [label=\"outfile_imzml\"]\n  4 -> 10 [label=\"pixel_annotations\"]\n  11[label=\"MSI segmentation\"]\n  9 -> 11 [label=\"outfile_imzml\"]\n  12[label=\"Filter\"]\n  10 -> 12 [label=\"mzfeatures\"]\n  13[label=\"Join two files\"]\n  12 -> 13 [label=\"out_file1\"]\n  2 -> 13 [label=\"output\"]\n  14[label=\"Summary Statistics\"]\n  13 -> 14 [label=\"merged_file\"]\n  15[label=\"MSI mz images\"]\n  13 -> 15 [label=\"merged_file\"]\n  3 -> 15 [label=\"output\"]\n  16[label=\"Select\"]\n  13 -> 16 [label=\"merged_file\"]\n  17[label=\"MSI mz images\"]\n  16 -> 17 [label=\"out_file1\"]\n  3 -> 17 [label=\"output\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGlycan_IDs\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nall_files\"]\n  4[label=\"MSI combine\"]\n  1 -> 4 [label=\"output\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"MSI preprocessing\"]\n  4 -> 5 [label=\"outfile_imzml\"]\n  6[label=\"MSI Qualitycontrol\"]\n  4 -> 6 [label=\"outfile_imzml\"]\n  4 -> 6 [label=\"pixel_annotations\"]\n  7[label=\"MALDIquant preprocessing\"]\n  5 -> 7 [label=\"outfile_imzml\"]\n  8[label=\"MALDIquant peak detection\"]\n  7 -> 8 [label=\"outfile_imzml\"]\n  4 -> 8 [label=\"pixel_annotations\"]\n  9[label=\"MSI preprocessing\"]\n  5 -> 9 [label=\"outfile_imzml\"]\n  8 -> 9 [label=\"intensity_matrix\"]\n}",
                 "history": [
                     {
-                        "hash": "9ed3f9ed83554a79f083624b4070b85877845e17",
-                        "message": "Update test",
-                        "num": 5,
-                        "short_hash": "9ed3f9ed8",
-                        "unix": "1689330096"
-                    },
-                    {
-                        "hash": "727d0600a2d08ad3a489b57f6bf5c08807af1e47",
-                        "message": "Update workflow and tests",
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
                         "num": 4,
-                        "short_hash": "727d0600a",
-                        "unix": "1688998300"
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
                     },
                     {
-                        "hash": "a726fb0c2af4a24843f6a50c6f522a629b43f6dd",
-                        "message": "Update RIAssginer tool version",
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
                         "num": 3,
-                        "short_hash": "a726fb0c2",
-                        "unix": "1683106380"
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
                     },
                     {
-                        "hash": "41eb746c708ea13d1fb5aeac6ef6d7a4ccae1890",
-                        "message": "Consistency in parameter values in workflow and tutorial",
+                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
+                        "message": "unflatten workflows",
                         "num": 2,
-                        "short_hash": "41eb746c7",
-                        "unix": "1683104559"
+                        "short_hash": "faf6d298a",
+                        "unix": "1576155753"
                     },
                     {
-                        "hash": "1503b9315e3fb1918a8554b3d2814fedda96e4c0",
-                        "message": "Initial commit adding GC-MS tutorial",
+                        "hash": "6b3331c232d6cad52bbb091eb603f290ffbc6b99",
+                        "message": "Adding MSI N-glycan training and small updates for the other MSI trainings (#1333)",
                         "num": 1,
-                        "short_hash": "1503b9315",
-                        "unix": "1677491681"
+                        "short_hash": "6b3331c23",
+                        "unix": "1555170721"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "List of retention indexed reference compounds. Either a table with columns `rt` and `ri` or an MSP with retention time and index metadata.",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "List of retention indexed reference compounds. Either a table with columns `rt` and `ri` or an MSP with retention time and index metadata.",
-                                "name": "Reference compound list (alkanes)"
-                            }
-                        ],
-                        "label": "Reference compound list (alkanes)",
+                        "inputs": [],
+                        "label": "treated",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 511.8500061035156,
-                            "height": 82.20001220703125,
-                            "left": 160.0833282470703,
-                            "right": 360.0833282470703,
-                            "top": 429.6499938964844,
-                            "width": 200,
-                            "x": 160.0833282470703,
-                            "y": 429.6499938964844
+                            "left": 445.683349609375,
+                            "top": 324.8666687011719
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "6f1c04f5-126f-4ad2-bc25-b1c4b6efce5d",
-                        "workflow_outputs": []
+                        "uuid": "337046f2-275b-4fc6-a661-16de8e6be533",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "924c77fb-2ed6-4cb2-81bc-dea777294df0"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "Spectral library to use for annotation in MSP or MGF format.",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Spectral library to use for annotation in MSP or MGF format.",
-                                "name": "Reference spectra"
-                            }
-                        ],
-                        "label": "Reference spectra",
+                        "inputs": [],
+                        "label": "control",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 616.8332977294922,
-                            "height": 82.19999694824219,
-                            "left": 482.1000061035156,
-                            "right": 682.1000061035156,
-                            "top": 534.63330078125,
-                            "width": 200,
-                            "x": 482.1000061035156,
-                            "y": 534.63330078125
+                            "left": 442.95001220703125,
+                            "top": 407.2833251953125
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "64a5eec1-54ef-4fc2-93c5-f6ab70ce1614",
-                        "workflow_outputs": []
+                        "uuid": "e5ee3457-2418-42ca-855e-b033b15d1eec",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "78357d0f-3571-45a2-9c8c-a06ca31a1c9f"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "Sample metadata sheet, containing sample name, type (QC, blank, sample, etc.), batch number and injection order.",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Sample metadata sheet, containing sample name, type (QC, blank, sample, etc.), batch number and injection order.",
-                                "name": "sample_metadata.tsv"
+                                "description": "",
+                                "name": "Glycan_IDs"
                             }
                         ],
-                        "label": "sample_metadata.tsv",
+                        "label": "Glycan_IDs",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 489.8500061035156,
-                            "height": 82.20001220703125,
-                            "left": -1541.933349609375,
-                            "right": -1341.933349609375,
-                            "top": 407.6499938964844,
-                            "width": 200,
-                            "x": -1541.933349609375,
-                            "y": 407.6499938964844
+                            "left": 449.91668701171875,
+                            "top": 1052.3666687011719
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"name\": \"Glycan_IDs\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "494c83fe-4407-4123-b56e-0a211f97fea2",
-                        "workflow_outputs": []
+                        "uuid": "78e307cf-92b5-4d1b-89d7-0ebeb7c845b7",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "a028d3d6-38e3-43f7-a023-321178108dc7"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "Mass spectrometry data to be processed in the workflow. Please ensure the format is supported by msconvert and only use the peak picking option if the input data was acquired in profile mode.",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 3,
                         "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Mass spectrometry data to be processed in the workflow. Please ensure the format is supported by msconvert and only use the peak picking option if the input data was acquired in profile mode.",
-                                "name": "Input Dataset Collection"
-                            }
-                        ],
-                        "label": "Input Dataset Collection",
-                        "name": "Input dataset collection",
+                        "inputs": [],
+                        "label": "all_files",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 105.85000610351562,
-                            "height": 82.20001220703125,
-                            "left": -2407,
-                            "right": -2207,
-                            "top": 23.649993896484375,
-                            "width": 200,
-                            "x": -2407,
-                            "y": 23.649993896484375
+                            "left": 447,
+                            "top": 1146.7167053222656
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_state": "{}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "2e362408-24c5-46e1-861c-74b825a5feaf",
-                        "workflow_outputs": []
+                        "type": "data_input",
+                        "uuid": "1f30f371-a9c5-4638-a9bd-a69d7a7ee1ec",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "07af2e13-4f7d-4454-8644-4d8cda30eb70"
+                            }
+                        ]
                     }
                 ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nReference compound list alkanes\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference spectra\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nsample_metadata.tsv\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"msconvert\"];\n  3 -->|output| 4;\n  5[\"MSnbase readMSData\"];\n  4 -->|output| 5;\n  6[\"xcms findChromPeaks xcmsSet\"];\n  5 -->|xsetRData| 6;\n  7[\"xcms findChromPeaks Merger\"];\n  6 -->|xsetRData| 7;\n  2 -->|output| 7;\n  8[\"xcms groupChromPeaks group\"];\n  7 -->|xsetRData| 8;\n  9[\"xcms adjustRtime retcor\"];\n  8 -->|xsetRData| 9;\n  10[\"xcms groupChromPeaks group\"];\n  9 -->|xsetRData| 10;\n  11[\"xcms fillChromPeaks fillPeaks\"];\n  10 -->|xsetRData| 11;\n  940c7549-1bae-4ddd-9e92-75fc7d2c8eef[\"Output\\nFeature (peak) intensities\"];\n  11 --> 940c7549-1bae-4ddd-9e92-75fc7d2c8eef;\n  style 940c7549-1bae-4ddd-9e92-75fc7d2c8eef stroke:#2c3143,stroke-width:4px;\n  9f910e82-e7a5-4201-b944-1845ba6aa2e9[\"Output\\nFeature (peak) metadata (mz, rt, ...)\"];\n  11 --> 9f910e82-e7a5-4201-b944-1845ba6aa2e9;\n  style 9f910e82-e7a5-4201-b944-1845ba6aa2e9 stroke:#2c3143,stroke-width:4px;\n  5bab8f28-4df1-4397-af04-168546bd0e52[\"Output\\nxcmsObj (XCMSnExp)\"];\n  11 --> 5bab8f28-4df1-4397-af04-168546bd0e52;\n  style 5bab8f28-4df1-4397-af04-168546bd0e52 stroke:#2c3143,stroke-width:4px;\n  12[\"RAMClustR\"];\n  11 -->|xsetRData| 12;\n  92fac5e6-1578-4e52-ac9d-2982e19a5b88[\"Output\\nDeconvoluted spectra\"];\n  12 --> 92fac5e6-1578-4e52-ac9d-2982e19a5b88;\n  style 92fac5e6-1578-4e52-ac9d-2982e19a5b88 stroke:#2c3143,stroke-width:4px;\n  f7657c17-6293-4fbb-b014-28009d495de7[\"Output\\nFeature (spectra) intensities\"];\n  12 --> f7657c17-6293-4fbb-b014-28009d495de7;\n  style f7657c17-6293-4fbb-b014-28009d495de7 stroke:#2c3143,stroke-width:4px;\n  13[\"RIAssigner\"];\n  12 -->|mass_spectra_merged| 13;\n  0 -->|output| 13;\n  7ec6ce02-5d83-48ab-ba0a-94976db297e5[\"Output\\nRetention indexed spectra\"];\n  13 --> 7ec6ce02-5d83-48ab-ba0a-94976db297e5;\n  style 7ec6ce02-5d83-48ab-ba0a-94976db297e5 stroke:#2c3143,stroke-width:4px;\n  14[\"matchms similarity\"];\n  13 -->|output| 14;\n  1 -->|output| 14;\n  024327f7-13b8-4ce9-8708-9f430d7ceedf[\"Output\\nCosineGreedy scores of input dataset(s)\"];\n  14 --> 024327f7-13b8-4ce9-8708-9f430d7ceedf;\n  style 024327f7-13b8-4ce9-8708-9f430d7ceedf stroke:#2c3143,stroke-width:4px;\n  15[\"matchms scores formatter\"];\n  14 -->|similarity_scores| 15;\n  8a767006-4b3c-41ba-bea5-18fd100ce930[\"Output\\nmatchms_scores\"];\n  15 --> 8a767006-4b3c-41ba-bea5-18fd100ce930;\n  style 8a767006-4b3c-41ba-bea5-18fd100ce930 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "GC MS using XCMS",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ntreated\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ncontrol\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"MSI classification\"];\n  9 -->|outfile_imzml| 10;\n  4 -->|pixel_annotations| 10;\n  11[\"MSI segmentation\"];\n  9 -->|outfile_imzml| 11;\n  12[\"Filter\"];\n  10 -->|mzfeatures| 12;\n  13[\"Join two files\"];\n  12 -->|out_file1| 13;\n  2 -->|output| 13;\n  14[\"Summary Statistics\"];\n  13 -->|merged_file| 14;\n  15[\"MSI mz images\"];\n  13 -->|merged_file| 15;\n  3 -->|output| 15;\n  16[\"Select\"];\n  13 -->|merged_file| 16;\n  17[\"MSI mz images\"];\n  16 -->|out_file1| 17;\n  3 -->|output| 17;\n  2[\"\u2139\ufe0f Input Dataset\\nGlycan_IDs\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nall_files\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"MSI combine\"];\n  1 -->|output| 4;\n  0 -->|output| 4;\n  5[\"MSI preprocessing\"];\n  4 -->|outfile_imzml| 5;\n  6[\"MSI Qualitycontrol\"];\n  4 -->|outfile_imzml| 6;\n  4 -->|pixel_annotations| 6;\n  7[\"MALDIquant preprocessing\"];\n  5 -->|outfile_imzml| 7;\n  8[\"MALDIquant peak detection\"];\n  7 -->|outfile_imzml| 8;\n  4 -->|pixel_annotations| 8;\n  9[\"MSI preprocessing\"];\n  5 -->|outfile_imzml| 9;\n  8 -->|intensity_matrix| 9;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "MSI Finding Diff Analytes",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "treated",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 445.683349609375,
+                            "top": 324.8666687011719
+                        },
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "337046f2-275b-4fc6-a661-16de8e6be533",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "924c77fb-2ed6-4cb2-81bc-dea777294df0"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "control",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 442.95001220703125,
+                            "top": 407.2833251953125
+                        },
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "e5ee3457-2418-42ca-855e-b033b15d1eec",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "78357d0f-3571-45a2-9c8c-a06ca31a1c9f"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/1.12.1.3",
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {
+                            "infile": {
+                                "id": 9,
+                                "output_name": "outfile_imzml"
+                            },
+                            "type_cond|annotation_file": {
+                                "id": 4,
+                                "output_name": "pixel_annotations"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "MSI classification",
+                        "outputs": [
+                            {
+                                "name": "classification_images",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "mzfeatures",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "pixeloutput",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 1704.300048828125,
+                            "top": 659.8166809082031
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionpixeloutput": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "pixeloutput"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/1.12.1.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "47fc5b518ffc",
+                            "name": "cardinal_classification",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"output_rdata\": \"\\\"false\\\"\", \"__page__\": null, \"type_cond\": \"{\\\"__current_case__\\\": 0, \\\"annotation_file\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"column_fold\\\": null, \\\"column_response\\\": \\\"3\\\", \\\"column_x\\\": \\\"1\\\", \\\"column_y\\\": \\\"2\\\", \\\"method_cond\\\": {\\\"__current_case__\\\": 2, \\\"class_method\\\": \\\"spatialShrunkenCentroids\\\", \\\"ssc_analysis_cond\\\": {\\\"__current_case__\\\": 1, \\\"ssc_method\\\": \\\"ssc_analysis\\\"}, \\\"ssc_kernel_method\\\": \\\"adaptive\\\", \\\"ssc_r\\\": \\\"2\\\", \\\"ssc_s\\\": \\\"0\\\"}, \\\"tabular_header\\\": \\\"true\\\", \\\"type_method\\\": \\\"training\\\"}\", \"__rerun_remap_job_id__\": null, \"centroids\": \"\\\"true\\\"\", \"processed_cond\": \"{\\\"__current_case__\\\": 0, \\\"processed_file\\\": \\\"no_processed\\\"}\", \"chromInfo\": \"\\\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "95932b54-da4a-4625-b22e-0e0ff9bdd5bc",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "mzfeatures",
+                                "uuid": "59b45729-bf4b-44ab-8544-c8c1cb4cbcdf"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "classification_images",
+                                "uuid": "4576bca8-6d7b-4a63-a368-da7ac4982a48"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.3",
                         "errors": null,
                         "id": 11,
                         "input_connections": {
-                            "image": {
-                                "id": 10,
-                                "output_name": "xsetRData"
+                            "infile": {
+                                "id": 9,
+                                "output_name": "outfile_imzml"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "xcms fillChromPeaks (fillPeaks)",
+                        "name": "MSI segmentation",
                         "outputs": [
                             {
-                                "name": "xsetRData",
-                                "type": "rdata.xcms.fillpeaks"
+                                "name": "segmentationimages",
+                                "type": "pdf"
                             },
                             {
-                                "name": "variableMetadata",
+                                "name": "mzfeatures",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "pixeloutput",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 1991.316650390625,
+                            "top": 255.76666259765625
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionmzfeatures": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "mzfeatures"
+                            },
+                            "HideDatasetActionpixeloutput": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "pixeloutput"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "9f7d1ec01767",
+                            "name": "cardinal_segmentations",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"output_rdata\": \"\\\"false\\\"\", \"setseed\": \"\\\"1\\\"\", \"__page__\": null, \"image_type\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"svg_pixelimage\": \"\\\"false\\\"\", \"centroids\": \"\\\"true\\\"\", \"colours\": \"[{\\\"__index__\\\": 0, \\\"feature_color\\\": \\\"#4f81bd\\\"}, {\\\"__index__\\\": 1, \\\"feature_color\\\": \\\"#f79646\\\"}, {\\\"__index__\\\": 2, \\\"feature_color\\\": \\\"#92d050\\\"}, {\\\"__index__\\\": 3, \\\"feature_color\\\": \\\"#c00000\\\"}]\", \"processed_cond\": \"{\\\"__current_case__\\\": 0, \\\"processed_file\\\": \\\"no_processed\\\"}\", \"segm_cond\": \"{\\\"__current_case__\\\": 0, \\\"pca_method\\\": \\\"irlba\\\", \\\"pca_ncomp\\\": \\\"2\\\", \\\"pca_scale\\\": \\\"false\\\", \\\"segmentationtool\\\": \\\"pca\\\"}\", \"infile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "68ad8111-fad2-4642-889b-ab9c3a59f427",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "segmentationimages",
+                                "uuid": "dcc9a3e6-e63d-450b-bea1-636e9ddc091d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy/1.0.1",
+                        "errors": null,
+                        "id": 13,
+                        "input_connections": {
+                            "f1": {
+                                "id": 12,
+                                "output_name": "out_file1"
+                            },
+                            "f2": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Join two files",
+                        "outputs": [
+                            {
+                                "name": "merged_file",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 1086.88330078125,
+                            "top": 952.0666809082031
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy/1.0.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "22ec3c1a20cd",
+                            "name": "join_files_on_column_fuzzy",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"distance\": \"\\\"300.0\\\"\", \"f2\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__page__\": null, \"f1\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"merge_mode_select\": \"\\\"closest\\\"\", \"add_distance\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"header\": \"\\\"true\\\"\", \"units\": \"\\\"ppm\\\"\", \"c2\": \"\\\"1\\\"\", \"c1\": \"\\\"1\\\"\", \"chromInfo\": \"\\\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "5b9259e3-b894-4889-8ace-b6fe932770aa",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "merged_file",
+                                "uuid": "3fd228c9-f759-4668-a883-e9f5fa11b7c0"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "Summary_Statistics1",
+                        "errors": null,
+                        "id": 14,
+                        "input_connections": {
+                            "input": {
+                                "id": 13,
+                                "output_name": "merged_file"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Summary Statistics",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
                                 "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 1328.0999755859375,
+                            "top": 927.6166687011719
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "Summary_Statistics1",
+                        "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c12\\\"\", \"__page__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "510cfc59-bf52-4f8a-920f-d5437da29f78",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "c76d062a-6f36-4e88-a02a-8951f7b4c17e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.2",
+                        "errors": null,
+                        "id": 15,
+                        "input_connections": {
+                            "calibrant_file": {
+                                "id": 13,
+                                "output_name": "merged_file"
+                            },
+                            "infile": {
+                                "id": 3,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "MSI mz images",
+                        "outputs": [
+                            {
+                                "name": "plots",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "left": 1334.066650390625,
+                            "top": 1030.4666442871094
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "56b3b7d5f2b5",
+                            "name": "cardinal_mz_images",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"calibrant_header\": \"\\\"true\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"image_contrast\": \"\\\"suppression\\\"\", \"image_smoothing\": \"\\\"none\\\"\", \"image_type\": \"\\\"true\\\"\", \"name_column\": \"\\\"11\\\"\", \"__rerun_remap_job_id__\": null, \"svg_pixelimage\": \"\\\"false\\\"\", \"calibrant_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"centroids\": \"\\\"false\\\"\", \"filename\": \"\\\"\\\"\", \"colorkey\": \"\\\"true\\\"\", \"processed_cond\": \"{\\\"__current_case__\\\": 0, \\\"processed_file\\\": \\\"no_processed\\\"}\", \"strip\": \"\\\"true\\\"\", \"__page__\": null, \"overlay_cond\": \"{\\\"__current_case__\\\": 0, \\\"overlay_selection\\\": \\\"no_overlay\\\"}\", \"plusminus_dalton\": \"\\\"0.25\\\"\", \"mz_column\": \"\\\"1\\\"\"}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "d2ef59b6-ad5f-46ed-9342-2f49a2f98920",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "svg_output",
+                                "uuid": "a3d13a98-d1d8-452d-9427-82745744f53a"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "plots",
+                                "uuid": "61a511da-3c35-45e2-a23e-d34ce4626297"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "Grep1",
+                        "errors": null,
+                        "id": 16,
+                        "input_connections": {
+                            "input": {
+                                "id": 13,
+                                "output_name": "merged_file"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Select",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1258.36669921875,
+                            "top": 1172.8166809082031
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "Grep1",
+                        "tool_state": "{\"__page__\": null, \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"invert\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"pattern\": \"\\\"(1663\\\\\\\\.)|(1905\\\\\\\\.)|(2304\\\\\\\\.)\\\"\"}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "28905577-0117-4139-9071-350eacf4ccfa",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "783b4618-d785-43a8-a190-de80a699272f"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.2",
+                        "errors": null,
+                        "id": 17,
+                        "input_connections": {
+                            "calibrant_file": {
+                                "id": 16,
+                                "output_name": "out_file1"
                             },
+                            "infile": {
+                                "id": 3,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "MSI mz images",
+                        "outputs": [
+                            {
+                                "name": "plots",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "left": 1462.9666748046875,
+                            "top": 1160.4166564941406
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "56b3b7d5f2b5",
+                            "name": "cardinal_mz_images",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"calibrant_header\": \"\\\"false\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"image_contrast\": \"\\\"suppression\\\"\", \"image_smoothing\": \"\\\"none\\\"\", \"image_type\": \"\\\"true\\\"\", \"name_column\": \"\\\"11\\\"\", \"__rerun_remap_job_id__\": null, \"svg_pixelimage\": \"\\\"false\\\"\", \"calibrant_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"centroids\": \"\\\"false\\\"\", \"filename\": \"\\\"\\\"\", \"colorkey\": \"\\\"true\\\"\", \"processed_cond\": \"{\\\"__current_case__\\\": 0, \\\"processed_file\\\": \\\"no_processed\\\"}\", \"strip\": \"\\\"true\\\"\", \"__page__\": null, \"overlay_cond\": \"{\\\"__current_case__\\\": 1, \\\"colours\\\": [{\\\"__index__\\\": 0, \\\"feature_color\\\": \\\"#1f497d\\\"}, {\\\"__index__\\\": 1, \\\"feature_color\\\": \\\"#00b050\\\"}, {\\\"__index__\\\": 2, \\\"feature_color\\\": \\\"#ff0000\\\"}], \\\"overlay_selection\\\": \\\"yes_overlay\\\"}\", \"plusminus_dalton\": \"\\\"0.25\\\"\", \"mz_column\": \"\\\"1\\\"\"}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "16498e12-6e7a-415c-9b34-9f4b1c64131d",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "plots",
+                                "uuid": "bf27c260-9168-498e-ab18-9324b74fedad"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Glycan_IDs"
+                            }
+                        ],
+                        "label": "Glycan_IDs",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 449.91668701171875,
+                            "top": 1052.3666687011719
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Glycan_IDs\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "78e307cf-92b5-4d1b-89d7-0ebeb7c845b7",
+                        "workflow_outputs": [
                             {
-                                "name": "dataMatrix",
-                                "type": "tabular"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "a028d3d6-38e3-43f7-a023-321178108dc7"
                             }
-                        ],
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "all_files",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 357.25,
-                            "height": 235.60000610351562,
-                            "left": -122.89999389648438,
-                            "right": 77.10000610351562,
-                            "top": 121.64999389648438,
-                            "width": 200,
-                            "x": -122.89999389648438,
-                            "y": 121.64999389648438
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "26d77e9ceb49",
-                            "name": "xcms_fillpeaks",
-                            "owner": "lecorguille",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 447,
+                            "top": 1146.7167053222656
                         },
-                        "tool_state": "{\"Adv\": {\"expandMz\": \"0\", \"expandRt\": \"0\", \"ppm\": \"0\"}, \"file_load_section\": {\"file_load_conditional\": {\"file_load_select\": \"no\", \"__current_case__\": 0}}, \"image\": {\"__class__\": \"ConnectedValue\"}, \"peaklist\": {\"peaklistBool\": \"True\", \"convertRTMinute\": \"true\", \"numDigitsMZ\": \"4\", \"numDigitsRT\": \"0\", \"intval\": \"into\", \"naTOzero\": \"true\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.12.0+galaxy0",
-                        "type": "tool",
-                        "uuid": "fae0d093-7931-4f4c-97da-09a93087d66d",
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "1f30f371-a9c5-4638-a9bd-a69d7a7ee1ec",
                         "workflow_outputs": [
                             {
-                                "label": "Feature (peak) intensities",
-                                "output_name": "dataMatrix",
-                                "uuid": "940c7549-1bae-4ddd-9e92-75fc7d2c8eef"
-                            },
-                            {
-                                "label": "Feature (peak) metadata (mz, rt, ...)",
-                                "output_name": "variableMetadata",
-                                "uuid": "9f910e82-e7a5-4201-b944-1845ba6aa2e9"
-                            },
-                            {
-                                "label": "xcmsObj (XCMSnExp)",
-                                "output_name": "xsetRData",
-                                "uuid": "5bab8f28-4df1-4397-af04-168546bd0e52"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "07af2e13-4f7d-4454-8644-4d8cda30eb70"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/recetox/ramclustr/ramclustr/1.2.4+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.3",
                         "errors": null,
-                        "id": 12,
+                        "id": 4,
                         "input_connections": {
-                            "filetype|xcms|input_xcms": {
-                                "id": 11,
-                                "output_name": "xsetRData"
-                            }
+                            "infiles": [
+                                {
+                                    "id": 1,
+                                    "output_name": "output"
+                                },
+                                {
+                                    "id": 0,
+                                    "output_name": "output"
+                                }
+                            ]
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool RAMClustR",
-                                "name": "extras"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "RAMClustR",
+                        "name": "MSI combine",
                         "outputs": [
                             {
-                                "name": "spec_abundance",
-                                "type": "csv"
+                                "name": "outfile_imzml",
+                                "type": "imzml"
                             },
                             {
-                                "name": "mass_spectra_merged",
-                                "type": "msp"
+                                "name": "QC_overview",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "pixel_annotations",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 333.8500061035156,
-                            "height": 215.20001220703125,
-                            "left": 152.10000610351562,
-                            "right": 352.1000061035156,
-                            "top": 118.64999389648438,
-                            "width": 200,
-                            "x": 152.10000610351562,
-                            "y": 118.64999389648438
+                            "left": 637.4666748046875,
+                            "top": 337.5500030517578
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/recetox/ramclustr/ramclustr/1.2.4+galaxy2",
+                        "post_job_actions": {
+                            "HideDatasetActionQC_overview": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "QC_overview"
+                            },
+                            "HideDatasetActionpixel_annotations": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "pixel_annotations"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "2ec9253a647e",
-                            "name": "ramclustr",
-                            "owner": "recetox",
+                            "changeset_revision": "48c07268f341",
+                            "name": "cardinal_combine",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"clustering\": {\"linkage\": \"average\", \"minModuleSize\": \"5\", \"hmax\": \"0.9\", \"deepSplit\": \"false\"}, \"extras\": {\"rt_only_low_n\": \"true\", \"replace_zeros\": \"true\", \"ExpDes\": {\"__class__\": \"RuntimeValue\"}}, \"filetype\": {\"type_choice\": \"xcms\", \"__current_case__\": 0, \"xcms\": {\"input_xcms\": {\"__class__\": \"ConnectedValue\"}, \"usePheno\": \"true\"}, \"required\": {\"st\": null, \"sr\": \"0.7\", \"cor_method\": \"pearson\", \"maxt\": \"10.0\"}}, \"msp_output_details\": {\"merge_msp\": \"true\", \"mzdec\": \"6\"}, \"normalisation\": {\"normalisation_method\": {\"normalize\": \"none\", \"__current_case__\": 3}}, \"performance\": {\"blocksize\": \"2000\", \"mult\": \"5\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.4+galaxy2",
+                        "tool_state": "{\"__page__\": null, \"infiles\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"annotation_cond\": \"{\\\"__current_case__\\\": 0, \\\"annotation_tabular\\\": \\\"no_annotation\\\"}\", \"__rerun_remap_job_id__\": null, \"combine_conditional\": \"{\\\"__current_case__\\\": 0, \\\"combine_method\\\": \\\"automatic_combine\\\"}\", \"centroids\": \"\\\"false\\\"\", \"processed_cond\": \"{\\\"__current_case__\\\": 0, \\\"processed_file\\\": \\\"no_processed\\\"}\", \"chromInfo\": \"\\\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"imzml_output\": \"\\\"imzml_format\\\"\"}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "2410e8b8-d629-4798-950d-e3d865a6aa72",
+                        "uuid": "57b0fcdb-c511-43bf-b8af-7aafdaff0d6d",
                         "workflow_outputs": [
                             {
-                                "label": "Deconvoluted spectra",
-                                "output_name": "mass_spectra_merged",
-                                "uuid": "92fac5e6-1578-4e52-ac9d-2982e19a5b88"
-                            },
-                            {
-                                "label": "Feature (spectra) intensities",
-                                "output_name": "spec_abundance",
-                                "uuid": "f7657c17-6293-4fbb-b014-28009d495de7"
+                                "label": null,
+                                "output_name": "outfile_imzml",
+                                "uuid": "cdc8f02b-39b1-465b-b725-b0c2b69a5b74"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/recetox/riassigner/riassigner/0.3.4+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/1.12.1.3",
                         "errors": null,
-                        "id": 13,
+                        "id": 5,
                         "input_connections": {
-                            "query_section|query": {
-                                "id": 12,
-                                "output_name": "mass_spectra_merged"
-                            },
-                            "reference_section|reference": {
-                                "id": 0,
-                                "output_name": "output"
+                            "infile": {
+                                "id": 4,
+                                "output_name": "outfile_imzml"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "RIAssigner",
+                        "name": "MSI preprocessing",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "input"
+                                "name": "outfile_imzml",
+                                "type": "imzml"
+                            },
+                            {
+                                "name": "QC_overview",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "bottom": 466.6499938964844,
-                            "height": 144,
-                            "left": 450.08331298828125,
-                            "right": 650.0833129882812,
-                            "top": 322.6499938964844,
-                            "width": 200,
-                            "x": 450.08331298828125,
-                            "y": 322.6499938964844
+                            "left": 886.0499877929688,
+                            "top": 199.98333740234375
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/recetox/riassigner/riassigner/0.3.4+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/1.12.1.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "c702620c22b1",
-                            "name": "riassigner",
-                            "owner": "recetox",
+                            "changeset_revision": "141a9288be9c",
+                            "name": "cardinal_preprocessing",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"method\": \"kovats\", \"query_section\": {\"query\": {\"__class__\": \"ConnectedValue\"}, \"query_rt_units\": \"seconds\"}, \"reference_section\": {\"reference\": {\"__class__\": \"ConnectedValue\"}, \"reference_rt_units\": \"seconds\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3.4+galaxy1",
+                        "tool_state": "{\"__page__\": null, \"methods\": \"[{\\\"__index__\\\": 0, \\\"methods_conditional\\\": {\\\"__current_case__\\\": 0, \\\"preprocessing_method\\\": \\\"Normalization\\\"}}, {\\\"__index__\\\": 1, \\\"methods_conditional\\\": {\\\"__current_case__\\\": 2, \\\"methods_for_smoothing\\\": {\\\"__current_case__\\\": 0, \\\"sd_gaussian\\\": \\\"1.0\\\", \\\"smoothing_method\\\": \\\"gaussian\\\"}, \\\"preprocessing_method\\\": \\\"Smoothing\\\", \\\"window_smoothing\\\": \\\"4.0\\\"}}, {\\\"__index__\\\": 2, \\\"methods_conditional\\\": {\\\"__current_case__\\\": 1, \\\"blocks_baseline\\\": \\\"500\\\", \\\"preprocessing_method\\\": \\\"Baseline_reduction\\\", \\\"spar_baseline\\\": \\\"1.0\\\"}}]\", \"__rerun_remap_job_id__\": null, \"centroids\": \"\\\"false\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"processed_cond\": \"{\\\"__current_case__\\\": 0, \\\"processed_file\\\": \\\"no_processed\\\"}\", \"imzml_output\": \"\\\"imzml_format\\\"\"}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "e626eac6-354c-4117-bd98-2203cb2d177b",
+                        "uuid": "93149694-469a-4a76-8690-ddf691665e55",
                         "workflow_outputs": [
                             {
-                                "label": "Retention indexed spectra",
-                                "output_name": "output",
-                                "uuid": "7ec6ce02-5d83-48ab-ba0a-94976db297e5"
+                                "label": null,
+                                "output_name": "outfile_rdata",
+                                "uuid": "613b051e-88d7-46b0-9532-a118b3adb4aa"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outfile_imzml",
+                                "uuid": "8718b21e-a330-4a57-9548-e9257819bb45"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "QC_overview",
+                                "uuid": "3c709575-ac09-47d3-a750-2b3082805e72"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/recetox/matchms_similarity/matchms_similarity/0.20.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.3",
                         "errors": null,
-                        "id": 14,
+                        "id": 6,
                         "input_connections": {
-                            "queries": {
-                                "id": 13,
-                                "output_name": "output"
+                            "infile": {
+                                "id": 4,
+                                "output_name": "outfile_imzml"
                             },
-                            "symmetric|references": {
-                                "id": 1,
-                                "output_name": "output"
+                            "tabular_annotation|annotation_file": {
+                                "id": 4,
+                                "output_name": "pixel_annotations"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool matchms similarity",
-                                "name": "queries"
-                            },
-                            {
-                                "description": "runtime parameter for tool matchms similarity",
-                                "name": "symmetric"
+                                "description": "runtime parameter for tool MSI Qualitycontrol",
+                                "name": "calibrant_file"
                             }
                         ],
                         "label": null,
-                        "name": "matchms similarity",
+                        "name": "MSI Qualitycontrol",
                         "outputs": [
                             {
-                                "name": "similarity_scores",
-                                "type": "json"
+                                "name": "QC_report",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "bottom": 534.3999938964844,
-                            "height": 164.39999389648438,
-                            "left": 805,
-                            "right": 1005,
-                            "top": 370,
-                            "width": 200,
-                            "x": 805,
-                            "y": 370
+                            "left": 899.6666870117188,
+                            "top": 552.4833374023438
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/recetox/matchms_similarity/matchms_similarity/0.20.0+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "e5010b19d64d",
-                            "name": "matchms_similarity",
-                            "owner": "recetox",
+                            "changeset_revision": "3b7a35d50ebf",
+                            "name": "cardinal_quality_report",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"array_type\": \"numpy\", \"metric\": {\"similarity_metric\": \"CosineGreedy\", \"__current_case__\": 0, \"algorithm\": {\"tolerance\": \"0.03\", \"mz_power\": \"0.0\", \"intensity_power\": \"1.0\"}}, \"queries\": {\"__class__\": \"RuntimeValue\"}, \"ri_filtering\": {\"is_true\": \"true\", \"__current_case__\": 0, \"tolerance\": \"20.0\"}, \"symmetric\": {\"is_symmetric\": \"false\", \"__current_case__\": 0, \"references\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.20.0+galaxy0",
+                        "tool_state": "{\"calibrant_header\": \"\\\"false\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"calibrantratio\": \"[]\", \"__page__\": null, \"name_column\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"tabular_annotation\": \"{\\\"__current_case__\\\": 0, \\\"annotation_file\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"column_names\\\": \\\"3\\\", \\\"column_x\\\": \\\"1\\\", \\\"column_y\\\": \\\"2\\\", \\\"load_annotation\\\": \\\"yes_annotation\\\", \\\"tabular_header\\\": \\\"true\\\"}\", \"centroids\": \"\\\"false\\\"\", \"calibrant_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"processed_cond\": \"{\\\"__current_case__\\\": 0, \\\"processed_file\\\": \\\"no_processed\\\"}\", \"do_pca\": \"\\\"true\\\"\", \"filename\": \"\\\"\\\"\", \"plusminus_ppm\": \"\\\"200.0\\\"\", \"mz_column\": \"\\\"\\\"\"}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "2c42471c-f9e2-43e7-977c-2207bedbf416",
+                        "uuid": "238e69ed-38e9-451b-84c1-cdd050930672",
                         "workflow_outputs": [
                             {
-                                "label": "CosineGreedy scores of input dataset(s)",
-                                "output_name": "similarity_scores",
-                                "uuid": "024327f7-13b8-4ce9-8708-9f430d7ceedf"
+                                "label": null,
+                                "output_name": "QC_report",
+                                "uuid": "64239ff1-1dea-4482-80c7-648aa899f3ab"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/recetox/matchms_formatter/matchms_formatter/0.20.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.3",
                         "errors": null,
-                        "id": 15,
+                        "id": 7,
                         "input_connections": {
-                            "scores": {
-                                "id": 14,
-                                "output_name": "similarity_scores"
+                            "infile": {
+                                "id": 5,
+                                "output_name": "outfile_imzml"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool matchms scores formatter",
-                                "name": "scores"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "matchms scores formatter",
+                        "name": "MALDIquant preprocessing",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "tsv"
+                                "name": "outfile_imzml",
+                                "type": "imzml"
+                            },
+                            {
+                                "name": "plots",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "bottom": 506.3999938964844,
-                            "height": 154.39999389648438,
-                            "left": 1175,
-                            "right": 1375,
-                            "top": 352,
-                            "width": 200,
-                            "x": 1175,
-                            "y": 352
+                            "left": 1155.5999755859375,
+                            "top": 299.2833251953125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/recetox/matchms_formatter/matchms_formatter/0.20.0+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "1b09315a3f87",
-                            "name": "matchms_formatter",
-                            "owner": "recetox",
+                            "changeset_revision": "71411ac28268",
+                            "name": "maldi_quant_preprocessing",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"scores\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.20.0+galaxy0",
+                        "tool_state": "{\"__page__\": null, \"methods\": \"[{\\\"__index__\\\": 0, \\\"methods_conditional\\\": {\\\"__current_case__\\\": 4, \\\"allow_nomatch\\\": \\\"true\\\", \\\"empty_nomatch\\\": \\\"true\\\", \\\"halfWindowSize\\\": \\\"4\\\", \\\"method\\\": \\\"Align\\\", \\\"peak_method\\\": \\\"MAD\\\", \\\"reference_for_alignment\\\": {\\\"__current_case__\\\": 0, \\\"align_ref\\\": \\\"no_reference\\\", \\\"min_frequency\\\": \\\"0.8\\\"}, \\\"remove_empty\\\": \\\"true\\\", \\\"snr\\\": \\\"5\\\", \\\"tolerance\\\": \\\"0.0002\\\", \\\"warping_method\\\": \\\"lowess\\\"}}]\", \"__rerun_remap_job_id__\": null, \"export_processed\": \"\\\"true\\\"\", \"restriction_conditional\": \"{\\\"__current_case__\\\": 1, \\\"restriction\\\": \\\"no_restriction\\\"}\", \"infile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "64da39ef-4625-4598-978d-e38bbbc2f007",
+                        "uuid": "683d836c-d991-45e6-8c31-fc93ecda0e84",
                         "workflow_outputs": [
                             {
-                                "label": "matchms_scores",
-                                "output_name": "output",
-                                "uuid": "8a767006-4b3c-41ba-bea5-18fd100ce930"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "metabolomics/gc_ms_with_xcms",
-                "path": "topics/metabolomics/tutorials/gc_ms_with_xcms/workflows/main_workflow.ga",
-                "tags": [
-                    "GC-MS",
-                    "Metabolomics",
-                    "Expospomics"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "GC MS using XCMS",
-                "topic_id": "metabolomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/metabolomics-gc_ms_with_xcms/versions/main-workflow",
-                "tutorial_id": "gc_ms_with_xcms",
-                "url": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/gc_ms_with_xcms/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/gc_ms_with_xcms/workflows/main_workflow.html",
-                "version": 2,
-                "wfid": "metabolomics-gc_ms_with_xcms",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2",
-                    "toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.12.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/recetox/matchms_formatter/matchms_formatter/0.20.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/recetox/matchms_similarity/matchms_similarity/0.20.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/recetox/ramclustr/ramclustr/1.2.4+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/recetox/riassigner/riassigner/0.3.4+galaxy1"
-                ],
-                "workflowhub_id": "1119"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/7890956"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "qualitymetrics",
-                    "owner": "ethevenot",
-                    "revisions": "acdf51018708",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "univariate",
-                    "owner": "ethevenot",
-                    "revisions": "5687435b182c",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "hmdb_ms_search",
-                    "owner": "fgiacomoni",
-                    "revisions": "49f87ddb2c78",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "camera_annotate",
-                    "owner": "lecorguille",
-                    "revisions": "73d82de36369",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "msnbase_readmsdata",
-                    "owner": "lecorguille",
-                    "revisions": "86a20118e743",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xcms_fillpeaks",
-                    "owner": "lecorguille",
-                    "revisions": "3bc94c3abb28",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xcms_group",
-                    "owner": "lecorguille",
-                    "revisions": "fe4002ac5193",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xcms_merge",
-                    "owner": "lecorguille",
-                    "revisions": "a301f001835c",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xcms_plot_chromatogram",
-                    "owner": "lecorguille",
-                    "revisions": "271c9d5f0d10",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xcms_retcor",
-                    "owner": "lecorguille",
-                    "revisions": "7faadba7c625",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xcms_xcmsset",
-                    "owner": "lecorguille",
-                    "revisions": "378ddb410225",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "batchcorrection",
-                    "owner": "melpetera",
-                    "revisions": "73892ef177e3",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "generic_filter",
-                    "owner": "melpetera",
-                    "revisions": "b1fa45bd2b44",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: qualitymetrics\n  owner: ethevenot\n  revisions: acdf51018708\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: univariate\n  owner: ethevenot\n  revisions: 5687435b182c\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: hmdb_ms_search\n  owner: fgiacomoni\n  revisions: 49f87ddb2c78\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: camera_annotate\n  owner: lecorguille\n  revisions: 73d82de36369\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msnbase_readmsdata\n  owner: lecorguille\n  revisions: 86a20118e743\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_fillpeaks\n  owner: lecorguille\n  revisions: 3bc94c3abb28\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_group\n  owner: lecorguille\n  revisions: fe4002ac5193\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_merge\n  owner: lecorguille\n  revisions: a301f001835c\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_plot_chromatogram\n  owner: lecorguille\n  revisions: 271c9d5f0d10\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_retcor\n  owner: lecorguille\n  revisions: 7faadba7c625\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_xcmsset\n  owner: lecorguille\n  revisions: 378ddb410225\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: batchcorrection\n  owner: melpetera\n  revisions: 73892ef177e3\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: generic_filter\n  owner: melpetera\n  revisions: b1fa45bd2b44\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/lcms/tutorial.json",
-        "contributors": [
-            {
-                "id": "melpetera",
-                "joined": "2019-06",
-                "name": "M\u00e9lanie Petera",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/melpetera/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/melpetera.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "fr",
-                "id": "lecorguille",
-                "joined": "2017-09",
-                "name": "Gildas Le Corguill\u00e9",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
-            },
-            {
-                "id": "jfrancoismartin",
-                "joined": "2019-06",
-                "name": "Jean-Fran\u00e7ois Martin",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jfrancoismartin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jfrancoismartin.json"
-            },
-            {
-                "id": "yguitton",
-                "joined": "2019-06",
-                "name": "Yann Guitton",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yguitton/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/yguitton.json"
-            },
-            {
-                "id": "workflow4metabolomics",
-                "joined": "2019-06",
-                "name": "Workflow4Metabolomics core team",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/workflow4metabolomics/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/workflow4metabolomics.json"
-            }
-        ],
-        "dir": "topics/metabolomics/tutorials/lcms",
-        "edam_operation": [
-            "Label-free quantification",
-            "Chromatogram visualisation",
-            "Validation",
-            "Filtering",
-            "Chromatographic alignment",
-            "Mass spectrum visualisation",
-            "Peak detection"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "metabolomics/lcms",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "To process untargeted LC-MS metabolomic data, you need a large variety of steps and tools.",
-            "Although main steps are standard, various ways to combined tools exist, depending on your data.",
-            "Resources are available in Galaxy, but do not forget that you need appropriate knowledge to perform a relevant analysis."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "To comprehend the diversity of LC-MS metabolomic data analysis.",
-            "To get familiar with the main steps constituting a metabolomic workflow for untargeted LC-MS analysis.",
-            "To evaluate the potential of a workflow approach when dealing with LC-MS metabolomic data."
-        ],
-        "pageviews": 18038,
-        "pub_date": "2019-07-02",
-        "questions": [
-            "What are the main steps of untargeted LC-MS data processing for metabolomic analysis?",
-            "How to conduct metabolomic data analysis from preprocessing to annotation using Galaxy?"
-        ],
-        "short_id": "T00195",
-        "short_tools": [
-            "wsdl_hmdb",
-            "abims_xcms_fillPeaks",
-            "quality_metrics",
-            "Univariate",
-            "abims_xcms_xcmsSet",
-            "xcms_merge",
-            "xcms_plot_chromatogram",
-            "abims_xcms_retcor",
-            "abims_CAMERA_annotateDiffreport",
-            "Batch_correction",
-            "abims_xcms_group",
-            "generic_filter",
-            "msnbase_readmsdata"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "time_estimation": "3h",
-        "title": "Mass spectrometry: LC-MS analysis",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/quality_metrics/2.2.8",
-            "toolshed.g2.bx.psu.edu/repos/ethevenot/univariate/Univariate/2.2.4",
-            "toolshed.g2.bx.psu.edu/repos/fgiacomoni/hmdb_ms_search/wsdl_hmdb/2018-10-01",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.4",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.8.2.1",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.4.4.0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.4.4.0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.4.4.0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.4.4.0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.4.4.1",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.4.4.1",
-            "toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Batch_correction/2.1.2",
-            "toolshed.g2.bx.psu.edu/repos/melpetera/generic_filter/generic_filter/2017.04"
-        ],
-        "topic_name": "metabolomics",
-        "topic_name_human": "Metabolomics",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "lcms",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/lcms/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/lcms/tutorial.json"
-        },
-        "version": 11,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 96,
-        "visitors": 10615,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Mass spectrometry: LC-MS analysis",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHU_neg_048.mzML\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  10[label=\"xcms fillChromPeaks fillPeaks\"]\n  9 -> 10 [label=\"xsetRData\"]\n  11[label=\"CAMERA.annotate\"]\n  10 -> 11 [label=\"xsetRData\"]\n  12[label=\"Batch_correction\"]\n  10 -> 12 [label=\"dataMatrix\"]\n  0 -> 12 [label=\"output\"]\n  11 -> 12 [label=\"variableMetadata\"]\n  13[label=\"Quality Metrics\"]\n  10 -> 13 [label=\"dataMatrix\"]\n  0 -> 13 [label=\"output\"]\n  11 -> 13 [label=\"variableMetadata\"]\n  14[label=\"Quality Metrics\"]\n  12 -> 14 [label=\"dataMatrix_out\"]\n  0 -> 14 [label=\"output\"]\n  12 -> 14 [label=\"variableMetadata_out\"]\n  15[label=\"Generic_Filter\"]\n  12 -> 15 [label=\"dataMatrix_out\"]\n  14 -> 15 [label=\"sampleMetadata_out\"]\n  14 -> 15 [label=\"variableMetadata_out\"]\n  16[label=\"Univariate\"]\n  15 -> 16 [label=\"dataMatrix_out\"]\n  15 -> 16 [label=\"sampleMetadata_out\"]\n  15 -> 16 [label=\"variableMetadata_out\"]\n  17[label=\"Generic_Filter\"]\n  15 -> 17 [label=\"dataMatrix_out\"]\n  15 -> 17 [label=\"sampleMetadata_out\"]\n  16 -> 17 [label=\"variableMetadata_out\"]\n  18[label=\"HMDB MS search\"]\n  17 -> 18 [label=\"variableMetadata_out\"]\n  2[label=\"MSnbase readMSData\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"xcms findChromPeaks xcmsSet\"]\n  2 -> 3 [label=\"xsetRData\"]\n  4[label=\"xcms plot chromatogram\"]\n  3 -> 4 [label=\"xsetRData\"]\n  5[label=\"xcms findChromPeaks Merger\"]\n  3 -> 5 [label=\"xsetRData\"]\n  6[label=\"xcms groupChromPeaks group\"]\n  5 -> 6 [label=\"xsetRData\"]\n  7[label=\"xcms adjustRtime retcor\"]\n  6 -> 7 [label=\"xsetRData\"]\n  8[label=\"xcms plot chromatogram\"]\n  7 -> 8 [label=\"xsetRData\"]\n  9[label=\"xcms groupChromPeaks group\"]\n  7 -> 9 [label=\"xsetRData\"]\n}",
-                "history": [
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 4,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 3,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
-                        "message": "unflatten workflows",
-                        "num": 2,
-                        "short_hash": "faf6d298a",
-                        "unix": "1576155753"
-                    },
-                    {
-                        "hash": "f03a103c9169255a7c663abd9d6823bc4fe43f55",
-                        "message": "metabo - lcms - init tutorial from workflow",
-                        "num": 1,
-                        "short_hash": "f03a103c9",
-                        "unix": "1559851449"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "HU_neg_048.mzML"
-                            }
-                        ],
-                        "label": "HU_neg_048.mzML",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 368
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"HU_neg_048.mzML\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "efe7b8e1-b3ba-4ca8-b29d-fc2c2e30be6e",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                                "label": null,
+                                "output_name": "outfile_imzml",
+                                "uuid": "75b9894a-95d8-4f18-b65a-f4f679b0fa57"
+                            },
                             {
-                                "description": "",
-                                "name": "Input Dataset Collection"
+                                "label": null,
+                                "output_name": "plots",
+                                "uuid": "eedcbadd-90f2-420c-bfcc-7aaaca296813"
                             }
-                        ],
-                        "label": null,
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 474
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "55fd4029-b619-4d84-9bc7-5e3d4e480d34",
-                        "workflow_outputs": []
+                        ]
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nHU_neg_048.mzML\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"xcms fillChromPeaks fillPeaks\"];\n  9 -->|xsetRData| 10;\n  11[\"CAMERA.annotate\"];\n  10 -->|xsetRData| 11;\n  12[\"Batch_correction\"];\n  10 -->|dataMatrix| 12;\n  0 -->|output| 12;\n  11 -->|variableMetadata| 12;\n  13[\"Quality Metrics\"];\n  10 -->|dataMatrix| 13;\n  0 -->|output| 13;\n  11 -->|variableMetadata| 13;\n  14[\"Quality Metrics\"];\n  12 -->|dataMatrix_out| 14;\n  0 -->|output| 14;\n  12 -->|variableMetadata_out| 14;\n  15[\"Generic_Filter\"];\n  12 -->|dataMatrix_out| 15;\n  14 -->|sampleMetadata_out| 15;\n  14 -->|variableMetadata_out| 15;\n  16[\"Univariate\"];\n  15 -->|dataMatrix_out| 16;\n  15 -->|sampleMetadata_out| 16;\n  15 -->|variableMetadata_out| 16;\n  17[\"Generic_Filter\"];\n  15 -->|dataMatrix_out| 17;\n  15 -->|sampleMetadata_out| 17;\n  16 -->|variableMetadata_out| 17;\n  18[\"HMDB MS search\"];\n  17 -->|variableMetadata_out| 18;\n  2[\"MSnbase readMSData\"];\n  1 -->|output| 2;\n  3[\"xcms findChromPeaks xcmsSet\"];\n  2 -->|xsetRData| 3;\n  4[\"xcms plot chromatogram\"];\n  3 -->|xsetRData| 4;\n  5[\"xcms findChromPeaks Merger\"];\n  3 -->|xsetRData| 5;\n  6[\"xcms groupChromPeaks group\"];\n  5 -->|xsetRData| 6;\n  7[\"xcms adjustRtime retcor\"];\n  6 -->|xsetRData| 7;\n  8[\"xcms plot chromatogram\"];\n  7 -->|xsetRData| 8;\n  9[\"xcms groupChromPeaks group\"];\n  7 -->|xsetRData| 9;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "Workflow Constructed From History 'imported: testpourGCC'",
-                "outputs": [],
-                "parent_id": "metabolomics/lcms",
-                "path": "topics/metabolomics/tutorials/lcms/workflows/main_workflow.ga",
+                "parent_id": "metabolomics/msi-finding-nglycans",
+                "path": "topics/metabolomics/tutorials/msi-finding-nglycans/workflows/msi-finding-diff-analytes.ga",
                 "tags": [
                     "metabolomics"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Workflow Constructed From History 'imported: testpourGCC'",
+                "title": "MSI Finding Diff Analytes",
                 "topic_id": "metabolomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/metabolomics-lcms/versions/main-workflow",
-                "tutorial_id": "lcms",
-                "url": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms/workflows/main_workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/metabolomics-msi-finding-nglycans/versions/msi-finding-diff-analytes",
+                "tutorial_id": "msi-finding-nglycans",
+                "url": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/msi-finding-nglycans/workflows/msi-finding-diff-analytes.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/msi-finding-nglycans/workflows/msi-finding-diff-analytes.html",
                 "version": 4,
-                "wfid": "metabolomics-lcms",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "wfid": "metabolomics-msi-finding-nglycans",
+                "wfname": "msi-finding-diff-analytes",
+                "workflow": "msi-finding-diff-analytes.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/quality_metrics/2.2.8",
-                    "toolshed.g2.bx.psu.edu/repos/ethevenot/univariate/Univariate/2.2.4",
-                    "toolshed.g2.bx.psu.edu/repos/fgiacomoni/hmdb_ms_search/wsdl_hmdb/2018-10-01",
-                    "toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.4",
-                    "toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.8.2.1",
-                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.4.4.0",
-                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.4.4.0",
-                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.4.4.0",
-                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.4.4.0",
-                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.4.4.1",
-                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.4.4.1",
-                    "toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Batch_correction/2.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/melpetera/generic_filter/generic_filter/2017.04"
-                ],
-                "workflowhub_id": "1065"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/3244991"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "camera_annotate",
-                    "owner": "lecorguille",
-                    "revisions": "512c2b701d96",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "msnbase_readmsdata",
-                    "owner": "lecorguille",
-                    "revisions": "11ab2081bd4a",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xcms_export_samplemetadata",
-                    "owner": "lecorguille",
-                    "revisions": "94eb263cfab4",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xcms_fillpeaks",
-                    "owner": "lecorguille",
-                    "revisions": "26d77e9ceb49",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xcms_group",
-                    "owner": "lecorguille",
-                    "revisions": "d45a786cbc40",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xcms_merge",
-                    "owner": "lecorguille",
-                    "revisions": "5bd125a3f3b0",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xcms_plot_chromatogram",
-                    "owner": "lecorguille",
-                    "revisions": "024974037c4e",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xcms_retcor",
-                    "owner": "lecorguille",
-                    "revisions": "aa252eec9229",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xcms_summary",
-                    "owner": "lecorguille",
-                    "revisions": "018a9771de28",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xcms_xcmsset",
-                    "owner": "lecorguille",
-                    "revisions": "b02d1992a43a",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "idchoice",
-                    "owner": "melpetera",
-                    "revisions": "bb19b1d15732",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "intensity_checks",
-                    "owner": "melpetera",
-                    "revisions": "a31f3f802b2b",
-                    "tool_panel_section_label": "Metabolomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: camera_annotate\n  owner: lecorguille\n  revisions: 512c2b701d96\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msnbase_readmsdata\n  owner: lecorguille\n  revisions: 11ab2081bd4a\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_export_samplemetadata\n  owner: lecorguille\n  revisions: 94eb263cfab4\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_fillpeaks\n  owner: lecorguille\n  revisions: 26d77e9ceb49\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_group\n  owner: lecorguille\n  revisions: d45a786cbc40\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_merge\n  owner: lecorguille\n  revisions: 5bd125a3f3b0\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_plot_chromatogram\n  owner: lecorguille\n  revisions: '024974037c4e'\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_retcor\n  owner: lecorguille\n  revisions: aa252eec9229\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_summary\n  owner: lecorguille\n  revisions: '018a9771de28'\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_xcmsset\n  owner: lecorguille\n  revisions: b02d1992a43a\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: idchoice\n  owner: melpetera\n  revisions: bb19b1d15732\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: intensity_checks\n  owner: melpetera\n  revisions: a31f3f802b2b\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.json",
-        "contributors": [
-            {
-                "id": "melpetera",
-                "joined": "2019-06",
-                "name": "M\u00e9lanie Petera",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/melpetera/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/melpetera.json"
-            },
-            {
-                "id": "jfrancoismartin",
-                "joined": "2019-06",
-                "name": "Jean-Fran\u00e7ois Martin",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jfrancoismartin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jfrancoismartin.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "fr",
-                "id": "lecorguille",
-                "joined": "2017-09",
-                "name": "Gildas Le Corguill\u00e9",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
-            },
-            {
-                "id": "workflow4metabolomics",
-                "joined": "2019-06",
-                "name": "Workflow4Metabolomics core team",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/workflow4metabolomics/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/workflow4metabolomics.json"
-            }
-        ],
-        "dir": "topics/metabolomics/tutorials/lcms-preprocessing",
-        "edam_operation": [
-            "Label-free quantification",
-            "Chromatogram visualisation",
-            "Validation",
-            "Filtering",
-            "Chromatographic alignment",
-            "Mass spectrum visualisation",
-            "Peak detection"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "metabolomics/lcms-preprocessing",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.no"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "To process untargeted LC-MS metabolomic data preprocessing, you need a large variety of steps and tools.",
-            "Although main steps are standard, various ways to combine and to set parameters for tools exist, depending on your data.",
-            "Resources are available in Galaxy, but do not forget that you need appropriate knowledge to perform a relevant analysis."
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "To comprehend the diversity of steps necessary to perform untargeted LC-MS metabolomic preprocessing.",
-            "To get familiar with the way to use XCMS-based Galaxy modules dedicated to LC-MS data preprocessing.",
-            "To evaluate the potential of a workflow approach when dealing with LC-MS preprocessing."
-        ],
-        "pageviews": 5734777,
-        "pub_date": "2020-02-04",
-        "questions": [
-            "What are the main steps of untargeted LC-MS data preprocessing for metabolomic analyses?",
-            "How to conduct metabolomic data preprocessing using Galaxy?"
-        ],
-        "short_id": "T00197",
-        "short_tools": [
-            "intens_check",
-            "abims_xcms_fillPeaks",
-            "msnbase_readmsdata",
-            "abims_xcms_summary",
-            "abims_xcms_xcmsSet",
-            "idchoice",
-            "xcms_merge",
-            "xcms_plot_chromatogram",
-            "abims_xcms_retcor",
-            "abims_CAMERA_annotateDiffreport",
-            "abims_xcms_group",
-            "xcms_export_samplemetadata"
-        ],
-        "slides": true,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "time_estimation": "3h",
-        "title": "Mass spectrometry: LC-MS preprocessing with XCMS",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.6+camera1.48.0-galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_export_samplemetadata/xcms_export_samplemetadata/3.12.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.12.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_summary/abims_xcms_summary/3.12.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/melpetera/idchoice/idchoice/19.12",
-            "toolshed.g2.bx.psu.edu/repos/melpetera/intensity_checks/intens_check/1.2.8"
+                    "Filter1",
+                    "Grep1",
+                    "Summary_Statistics1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/1.12.1.3",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.3",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/1.12.1.3",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.3",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.3",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.4",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.3"
+                ],
+                "workflowhub_id": "1123"
+            }
         ],
-        "topic_name": "metabolomics",
-        "topic_name_human": "Metabolomics",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "lcms-preprocessing",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.json"
-        },
-        "version": 13,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 294,
-        "visitors": 2068539,
-        "zenodo_link": "https://zenodo.org/record/3757956"
+        "zenodo_link": "https://zenodo.org/record/2628280"
     },
     {
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/introduction/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "fr",
-                "id": "lecorguille",
-                "joined": "2017-09",
-                "name": "Gildas Le Corguill\u00e9",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
-            },
-            {
-                "github": false,
-                "id": "cecilecanlet",
-                "joined": "2018-09",
-                "name": "C\u00e9cile Canlet",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cecilecanlet/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/cecilecanlet.json"
-            }
-        ],
-        "dir": "topics/metabolomics/tutorials/introduction",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": false,
-        "id": "metabolomics/introduction",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "layout": "introduction_slides",
-        "license": "CC-BY-4.0",
-        "logo": "GTN",
-        "mod_date": "2023-01-12",
-        "pageviews": 5726884,
-        "priority": 1,
-        "pub_date": "2018-11-20",
-        "redirect_from": [
-            "/topics/metabolomics/slides/introduction",
-            "/short/metabolomics/introduction/slides",
-            "/short/S00076"
-        ],
-        "short_id": "S00076",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
+            "tools": [
                 {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "qualitymetrics",
+                    "owner": "ethevenot",
+                    "revisions": "acdf51018708",
+                    "tool_panel_section_label": "Metabolomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
+                    "name": "univariate",
+                    "owner": "ethevenot",
+                    "revisions": "5687435b182c",
+                    "tool_panel_section_label": "Metabolomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
+                    "name": "hmdb_ms_search",
+                    "owner": "fgiacomoni",
+                    "revisions": "49f87ddb2c78",
+                    "tool_panel_section_label": "Metabolomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "title": "Introduction to Metabolomics",
-        "tools": [],
-        "topic_name": "metabolomics",
-        "topic_name_human": "Metabolomics",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "introduction",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/metabolomics/tutorials/introduction/slides.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/introduction/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/introduction/slides.json"
-        },
-        "version": 1,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
+                    "name": "camera_annotate",
+                    "owner": "lecorguille",
+                    "revisions": "73d82de36369",
+                    "tool_panel_section_label": "Metabolomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
-                    "name": "multivariate",
-                    "owner": "ethevenot",
-                    "revisions": "5526f8258e8a",
+                    "name": "msnbase_readmsdata",
+                    "owner": "lecorguille",
+                    "revisions": "86a20118e743",
                     "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "qualitymetrics",
-                    "owner": "ethevenot",
-                    "revisions": "acdf51018708",
+                    "name": "xcms_fillpeaks",
+                    "owner": "lecorguille",
+                    "revisions": "3bc94c3abb28",
                     "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "normalization",
-                    "owner": "marie-tremblay-metatoul",
-                    "revisions": "221cbd549c40",
+                    "name": "xcms_group",
+                    "owner": "lecorguille",
+                    "revisions": "fe4002ac5193",
                     "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "batchcorrection",
-                    "owner": "melpetera",
-                    "revisions": "23314e1192d4",
+                    "name": "xcms_merge",
+                    "owner": "lecorguille",
+                    "revisions": "a301f001835c",
                     "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "generic_filter",
+                    "name": "xcms_plot_chromatogram",
+                    "owner": "lecorguille",
+                    "revisions": "271c9d5f0d10",
+                    "tool_panel_section_label": "Metabolomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "xcms_retcor",
+                    "owner": "lecorguille",
+                    "revisions": "7faadba7c625",
+                    "tool_panel_section_label": "Metabolomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "xcms_xcmsset",
+                    "owner": "lecorguille",
+                    "revisions": "378ddb410225",
+                    "tool_panel_section_label": "Metabolomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "batchcorrection",
                     "owner": "melpetera",
-                    "revisions": "cfd7c4aa5c26",
+                    "revisions": "73892ef177e3",
                     "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "intensity_checks",
+                    "name": "generic_filter",
                     "owner": "melpetera",
-                    "revisions": "a31f3f802b2b",
+                    "revisions": "b1fa45bd2b44",
                     "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: multivariate\n  owner: ethevenot\n  revisions: 5526f8258e8a\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qualitymetrics\n  owner: ethevenot\n  revisions: acdf51018708\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: normalization\n  owner: marie-tremblay-metatoul\n  revisions: 221cbd549c40\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: batchcorrection\n  owner: melpetera\n  revisions: 23314e1192d4\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: generic_filter\n  owner: melpetera\n  revisions: cfd7c4aa5c26\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: intensity_checks\n  owner: melpetera\n  revisions: a31f3f802b2b\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: qualitymetrics\n  owner: ethevenot\n  revisions: acdf51018708\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: univariate\n  owner: ethevenot\n  revisions: 5687435b182c\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: hmdb_ms_search\n  owner: fgiacomoni\n  revisions: 49f87ddb2c78\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: camera_annotate\n  owner: lecorguille\n  revisions: 73d82de36369\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msnbase_readmsdata\n  owner: lecorguille\n  revisions: 86a20118e743\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_fillpeaks\n  owner: lecorguille\n  revisions: 3bc94c3abb28\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_group\n  owner: lecorguille\n  revisions: fe4002ac5193\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_merge\n  owner: lecorguille\n  revisions: a301f001835c\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_plot_chromatogram\n  owner: lecorguille\n  revisions: 271c9d5f0d10\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_retcor\n  owner: lecorguille\n  revisions: 7faadba7c625\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_xcmsset\n  owner: lecorguille\n  revisions: 378ddb410225\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: batchcorrection\n  owner: melpetera\n  revisions: 73892ef177e3\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: generic_filter\n  owner: melpetera\n  revisions: b1fa45bd2b44\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/lcms/tutorial.json",
         "contributors": [
             {
                 "id": "melpetera",
@@ -135275,6 +138117,31 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/melpetera/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/melpetera.json"
             },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "fr",
+                "id": "lecorguille",
+                "joined": "2017-09",
+                "name": "Gildas Le Corguill\u00e9",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
+            },
+            {
+                "id": "jfrancoismartin",
+                "joined": "2019-06",
+                "name": "Jean-Fran\u00e7ois Martin",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jfrancoismartin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jfrancoismartin.json"
+            },
+            {
+                "id": "yguitton",
+                "joined": "2019-06",
+                "name": "Yann Guitton",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yguitton/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/yguitton.json"
+            },
             {
                 "id": "workflow4metabolomics",
                 "joined": "2019-06",
@@ -135283,64 +138150,72 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/workflow4metabolomics.json"
             }
         ],
-        "dir": "topics/metabolomics/tutorials/lcms-dataprocessing",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.fr"
+        "dir": "topics/metabolomics/tutorials/lcms",
+        "edam_operation": [
+            "Peak detection",
+            "Label-free quantification",
+            "Mass spectrum visualisation",
+            "Validation",
+            "Filtering",
+            "Chromatogram visualisation",
+            "Chromatographic alignment"
         ],
+        "edam_topic": [],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "metabolomics/lcms-dataprocessing",
+        "id": "metabolomics/lcms",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.no"
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Data processing is a key step in untargeted Metabolomics analyses. The question of data filtering and correction must be addressed in all projects, even thought in some cases it may lead to the decision of no action on data. In particular, blank filtering, pool variation study and signal drift correction are common aspects to consider when dealing with LC-MS.",
-            "Although some main steps are standard, various ways to combine tools exist. Remember that depending on your context (type of samples, protocol specificities...) specific filters/normalisations may be needed, independently of standards ones.",
-            "A variety of tools is available in Galaxy, but do not forget that you need appropriate knowledge to decide what to use depending on your data."
+            "To process untargeted LC-MS metabolomic data, you need a large variety of steps and tools.",
+            "Although main steps are standard, various ways to combined tools exist, depending on your data.",
+            "Resources are available in Galaxy, but do not forget that you need appropriate knowledge to perform a relevant analysis."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
         "license": "CC-BY-4.0",
         "mod_date": "2023-11-09",
         "objectives": [
-            "To comprehend the key role of data processing.",
-            "To comprehend the diversity of steps necessary to perform untargeted LC-MS metabolomic data processing.",
-            "To be familiar with the \"identify then perform\" approach necessary to deploy relevant data processing strategies."
+            "To comprehend the diversity of LC-MS metabolomic data analysis.",
+            "To get familiar with the main steps constituting a metabolomic workflow for untargeted LC-MS analysis.",
+            "To evaluate the potential of a workflow approach when dealing with LC-MS metabolomic data."
         ],
-        "pageviews": 2652,
-        "pub_date": "2021-12-14",
+        "pageviews": 18252,
+        "pub_date": "2019-07-02",
         "questions": [
-            "Why should one consider performing data processing steps when dealing with Metabolomics data?",
-            "How to conduct LCMS-based untargeted metabolomic data processing using Galaxy?"
+            "What are the main steps of untargeted LC-MS data processing for metabolomic analysis?",
+            "How to conduct metabolomic data analysis from preprocessing to annotation using Galaxy?"
         ],
-        "short_id": "T00196",
+        "short_id": "T00195",
         "short_tools": [
-            "normalization",
-            "intens_check",
+            "msnbase_readmsdata",
+            "abims_xcms_fillPeaks",
+            "abims_xcms_xcmsSet",
+            "abims_CAMERA_annotateDiffreport",
+            "Batch_correction",
             "quality_metrics",
+            "Univariate",
+            "xcms_merge",
+            "wsdl_hmdb",
+            "xcms_plot_chromatogram",
+            "abims_xcms_group",
             "generic_filter",
-            "Batch_correction",
-            "Multivariate"
+            "abims_xcms_retcor"
         ],
         "slides": false,
         "slides_recordings": false,
         "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                }
-            ],
+            "exact": [],
             "inexact": [
                 {
                     "name": "UseGalaxy.cz",
@@ -135352,23 +138227,40 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
-        "time_estimation": "2H",
-        "title": "Mass spectrometry: LC-MS data processing",
+        "time_estimation": "3h",
+        "title": "Mass spectrometry: LC-MS analysis",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/ethevenot/multivariate/Multivariate/2.3.10",
             "toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/quality_metrics/2.2.8",
-            "toolshed.g2.bx.psu.edu/repos/marie-tremblay-metatoul/normalization/normalization/1.0.7",
-            "toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Batch_correction/3.0.0",
-            "toolshed.g2.bx.psu.edu/repos/melpetera/generic_filter/generic_filter/2020.01",
-            "toolshed.g2.bx.psu.edu/repos/melpetera/intensity_checks/intens_check/1.2.8"
+            "toolshed.g2.bx.psu.edu/repos/ethevenot/univariate/Univariate/2.2.4",
+            "toolshed.g2.bx.psu.edu/repos/fgiacomoni/hmdb_ms_search/wsdl_hmdb/2018-10-01",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.4",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.8.2.1",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.4.4.0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.4.4.0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.4.4.0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.4.4.0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.4.4.1",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.4.4.1",
+            "toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Batch_correction/2.1.2",
+            "toolshed.g2.bx.psu.edu/repos/melpetera/generic_filter/generic_filter/2017.04"
         ],
         "topic_name": "metabolomics",
         "topic_name_human": "Metabolomics",
@@ -135378,20 +138270,155 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "lcms-dataprocessing",
+        "tutorial_name": "lcms",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/lcms/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/lcms/tutorial.json"
         },
-        "version": 7,
+        "version": 11,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 115,
-        "visitors": 1918,
-        "zenodo_link": "https://zenodo.org/record/5179809"
+        "visit_duration": 95,
+        "visitors": 10803,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Mass spectrometry: LC-MS analysis",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHU_neg_048.mzML\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  10[label=\"xcms fillChromPeaks fillPeaks\"]\n  9 -> 10 [label=\"xsetRData\"]\n  11[label=\"CAMERA.annotate\"]\n  10 -> 11 [label=\"xsetRData\"]\n  12[label=\"Batch_correction\"]\n  10 -> 12 [label=\"dataMatrix\"]\n  0 -> 12 [label=\"output\"]\n  11 -> 12 [label=\"variableMetadata\"]\n  13[label=\"Quality Metrics\"]\n  10 -> 13 [label=\"dataMatrix\"]\n  0 -> 13 [label=\"output\"]\n  11 -> 13 [label=\"variableMetadata\"]\n  14[label=\"Quality Metrics\"]\n  12 -> 14 [label=\"dataMatrix_out\"]\n  0 -> 14 [label=\"output\"]\n  12 -> 14 [label=\"variableMetadata_out\"]\n  15[label=\"Generic_Filter\"]\n  12 -> 15 [label=\"dataMatrix_out\"]\n  14 -> 15 [label=\"sampleMetadata_out\"]\n  14 -> 15 [label=\"variableMetadata_out\"]\n  16[label=\"Univariate\"]\n  15 -> 16 [label=\"dataMatrix_out\"]\n  15 -> 16 [label=\"sampleMetadata_out\"]\n  15 -> 16 [label=\"variableMetadata_out\"]\n  17[label=\"Generic_Filter\"]\n  15 -> 17 [label=\"dataMatrix_out\"]\n  15 -> 17 [label=\"sampleMetadata_out\"]\n  16 -> 17 [label=\"variableMetadata_out\"]\n  18[label=\"HMDB MS search\"]\n  17 -> 18 [label=\"variableMetadata_out\"]\n  2[label=\"MSnbase readMSData\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"xcms findChromPeaks xcmsSet\"]\n  2 -> 3 [label=\"xsetRData\"]\n  4[label=\"xcms plot chromatogram\"]\n  3 -> 4 [label=\"xsetRData\"]\n  5[label=\"xcms findChromPeaks Merger\"]\n  3 -> 5 [label=\"xsetRData\"]\n  6[label=\"xcms groupChromPeaks group\"]\n  5 -> 6 [label=\"xsetRData\"]\n  7[label=\"xcms adjustRtime retcor\"]\n  6 -> 7 [label=\"xsetRData\"]\n  8[label=\"xcms plot chromatogram\"]\n  7 -> 8 [label=\"xsetRData\"]\n  9[label=\"xcms groupChromPeaks group\"]\n  7 -> 9 [label=\"xsetRData\"]\n}",
+                "history": [
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 4,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 3,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
+                        "message": "unflatten workflows",
+                        "num": 2,
+                        "short_hash": "faf6d298a",
+                        "unix": "1576155753"
+                    },
+                    {
+                        "hash": "f03a103c9169255a7c663abd9d6823bc4fe43f55",
+                        "message": "metabo - lcms - init tutorial from workflow",
+                        "num": 1,
+                        "short_hash": "f03a103c9",
+                        "unix": "1559851449"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "HU_neg_048.mzML"
+                            }
+                        ],
+                        "label": "HU_neg_048.mzML",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 368
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"HU_neg_048.mzML\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "efe7b8e1-b3ba-4ca8-b29d-fc2c2e30be6e",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Input Dataset Collection"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 474
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "55fd4029-b619-4d84-9bc7-5e3d4e480d34",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nHU_neg_048.mzML\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"xcms fillChromPeaks fillPeaks\"];\n  9 -->|xsetRData| 10;\n  11[\"CAMERA.annotate\"];\n  10 -->|xsetRData| 11;\n  12[\"Batch_correction\"];\n  10 -->|dataMatrix| 12;\n  0 -->|output| 12;\n  11 -->|variableMetadata| 12;\n  13[\"Quality Metrics\"];\n  10 -->|dataMatrix| 13;\n  0 -->|output| 13;\n  11 -->|variableMetadata| 13;\n  14[\"Quality Metrics\"];\n  12 -->|dataMatrix_out| 14;\n  0 -->|output| 14;\n  12 -->|variableMetadata_out| 14;\n  15[\"Generic_Filter\"];\n  12 -->|dataMatrix_out| 15;\n  14 -->|sampleMetadata_out| 15;\n  14 -->|variableMetadata_out| 15;\n  16[\"Univariate\"];\n  15 -->|dataMatrix_out| 16;\n  15 -->|sampleMetadata_out| 16;\n  15 -->|variableMetadata_out| 16;\n  17[\"Generic_Filter\"];\n  15 -->|dataMatrix_out| 17;\n  15 -->|sampleMetadata_out| 17;\n  16 -->|variableMetadata_out| 17;\n  18[\"HMDB MS search\"];\n  17 -->|variableMetadata_out| 18;\n  2[\"MSnbase readMSData\"];\n  1 -->|output| 2;\n  3[\"xcms findChromPeaks xcmsSet\"];\n  2 -->|xsetRData| 3;\n  4[\"xcms plot chromatogram\"];\n  3 -->|xsetRData| 4;\n  5[\"xcms findChromPeaks Merger\"];\n  3 -->|xsetRData| 5;\n  6[\"xcms groupChromPeaks group\"];\n  5 -->|xsetRData| 6;\n  7[\"xcms adjustRtime retcor\"];\n  6 -->|xsetRData| 7;\n  8[\"xcms plot chromatogram\"];\n  7 -->|xsetRData| 8;\n  9[\"xcms groupChromPeaks group\"];\n  7 -->|xsetRData| 9;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Workflow Constructed From History 'imported: testpourGCC'",
+                "outputs": [],
+                "parent_id": "metabolomics/lcms",
+                "path": "topics/metabolomics/tutorials/lcms/workflows/main_workflow.ga",
+                "tags": [
+                    "metabolomics"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Workflow Constructed From History 'imported: testpourGCC'",
+                "topic_id": "metabolomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/metabolomics-lcms/versions/main-workflow",
+                "tutorial_id": "lcms",
+                "url": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms/workflows/main_workflow.html",
+                "version": 4,
+                "wfid": "metabolomics-lcms",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/quality_metrics/2.2.8",
+                    "toolshed.g2.bx.psu.edu/repos/ethevenot/univariate/Univariate/2.2.4",
+                    "toolshed.g2.bx.psu.edu/repos/fgiacomoni/hmdb_ms_search/wsdl_hmdb/2018-10-01",
+                    "toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.4",
+                    "toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.8.2.1",
+                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.4.4.0",
+                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.4.4.0",
+                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.4.4.0",
+                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.4.4.0",
+                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.4.4.1",
+                    "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.4.4.1",
+                    "toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Batch_correction/2.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/melpetera/generic_filter/generic_filter/2017.04"
+                ],
+                "workflowhub_id": "1065"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/3244991"
     },
     {
         "admin_install": {
@@ -135400,170 +138427,204 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "msnbase_readmsdata",
-                    "owner": "lecorguille",
-                    "revisions": "11ab2081bd4a",
-                    "tool_panel_section_label": "Metabolomics",
+                    "name": "ctb_im_conformers",
+                    "owner": "bgruening",
+                    "revisions": "a4b1474efada",
+                    "tool_panel_section_label": "ChemicalToolBox",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "xcms_fillpeaks",
-                    "owner": "lecorguille",
-                    "revisions": "26d77e9ceb49",
-                    "tool_panel_section_label": "Metabolomics",
+                    "name": "openbabel_compound_convert",
+                    "owner": "bgruening",
+                    "revisions": "e2c36f62e22f",
+                    "tool_panel_section_label": "ChemicalToolBox",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "xcms_group",
-                    "owner": "lecorguille",
-                    "revisions": "d45a786cbc40",
-                    "tool_panel_section_label": "Metabolomics",
+                    "name": "split_file_to_collection",
+                    "owner": "bgruening",
+                    "revisions": "2dae863c8f42",
+                    "tool_panel_section_label": "Collection Operations",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "xcms_merge",
-                    "owner": "lecorguille",
-                    "revisions": "5bd125a3f3b0",
-                    "tool_panel_section_label": "Metabolomics",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "86755160afbf",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "xcms_xcmsset",
-                    "owner": "lecorguille",
-                    "revisions": "b02d1992a43a",
-                    "tool_panel_section_label": "Metabolomics",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "fbf99087e067",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "qcxms_getres",
+                    "owner": "recetox",
+                    "revisions": "53dce0e49af7",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "qcxms_neutral_run",
+                    "owner": "recetox",
+                    "revisions": "c1f752721827",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "qcxms_neutral_run",
+                    "owner": "recetox",
+                    "revisions": "8f465c0c3b6c",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "qcxms_production_run",
+                    "owner": "recetox",
+                    "revisions": "e97bfe7ac906",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "xtb_molecular_optimization",
+                    "owner": "recetox",
+                    "revisions": "d5633eaf3552",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "xtb_molecular_optimization",
+                    "owner": "recetox",
+                    "revisions": "6e1ef071fffc",
+                    "tool_panel_section_label": "ChemicalToolBox",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: msnbase_readmsdata\n  owner: lecorguille\n  revisions: 11ab2081bd4a\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_fillpeaks\n  owner: lecorguille\n  revisions: 26d77e9ceb49\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_group\n  owner: lecorguille\n  revisions: d45a786cbc40\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_merge\n  owner: lecorguille\n  revisions: 5bd125a3f3b0\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_xcmsset\n  owner: lecorguille\n  revisions: b02d1992a43a\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/gcms/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: ctb_im_conformers\n  owner: bgruening\n  revisions: a4b1474efada\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_compound_convert\n  owner: bgruening\n  revisions: e2c36f62e22f\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_to_collection\n  owner: bgruening\n  revisions: 2dae863c8f42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qcxms_getres\n  owner: recetox\n  revisions: 53dce0e49af7\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qcxms_neutral_run\n  owner: recetox\n  revisions: c1f752721827\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qcxms_neutral_run\n  owner: recetox\n  revisions: 8f465c0c3b6c\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qcxms_production_run\n  owner: recetox\n  revisions: e97bfe7ac906\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xtb_molecular_optimization\n  owner: recetox\n  revisions: d5633eaf3552\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xtb_molecular_optimization\n  owner: recetox\n  revisions: 6e1ef071fffc\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/qcxms-predictions/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "wee-snufkin",
+                "hechth"
+            ]
+        },
         "contributors": [
             {
-                "id": "jsaintvanne",
+                "elixir_node": "uk",
+                "email": "juliajot36@gmail.com",
+                "id": "wee-snufkin",
+                "joined": "2022-06",
+                "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
+            },
+            {
+                "elixir_node": "cz",
+                "email": "helge.hecht@recetox.muni.cz",
+                "id": "hechth",
                 "joined": "2020-01",
-                "name": "Julien Saint-Vanne",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jsaintvanne/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jsaintvanne.json"
+                "name": "Helge Hecht",
+                "orcid": "0000-0001-6744-996X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hechth/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hechth.json"
             }
         ],
-        "dir": "topics/metabolomics/tutorials/gcms",
-        "draft": true,
-        "edam_operation": [
-            "Label-free quantification",
-            "Chromatogram visualisation",
-            "Validation",
-            "Filtering",
-            "Chromatographic alignment",
-            "Mass spectrum visualisation",
-            "Peak detection"
-        ],
+        "dir": "topics/metabolomics/tutorials/qcxms-predictions",
+        "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "metabolomics/gcms",
-        "inexact_supported_servers": [
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
-        ],
+        "id": "metabolomics/qcxms-predictions",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Have a good file containing all your peaks during the first stopover",
-            "Find all your unknowns in your datas",
-            "Find your stanards if you have some"
+            "Galaxy provides access to high-performance computing (HPC) resources and hence allows the use of semi-empirical quantum mechanical (SQM) methods and *in silico* prediction of QC-based mass spectra.",
+            "The shown workflow allows to simulate mass spectra of a molecule starting from its SMILES.",
+            "The xTB package is based on a SQM method to optimise the geometry of the generated conformers.",
+            "The QCxMS tool suite performs quantum chemistry calculations to simulate mass spectra."
         ],
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-10-01",
         "objectives": [
-            "To be sure you have already comprehend the diversity of MS pre-processing analysis.",
-            "To learn the principal functions of metaMS package through Galaxy.",
-            "To evaluate the potential of this new GC-MS workflow for GC-MS metabolomic analysis."
+            "To prepare structure-data format (SDF) files for further operations analysis, starting from chemical structure descriptors in simplified molecular-input line-entry system (SMILES) format.",
+            "To generate 3D conformers and optimise them using semi-empirical quantum mechanical (SQM) methods.",
+            "To produce simulated mass spectra for a given molecule in MSP (text based) format."
         ],
-        "pageviews": 2025,
-        "pub_date": "2021-09-22",
+        "pageviews": 7612,
+        "pub_date": "2024-10-01",
         "questions": [
-            "What are the main steps of GC-MS datas processing for metabolomic analysis ?",
-            "How te be able to annotate the maximum of unknowns using Galaxy ?"
+            "Can I predict QC-based mass spectra starting from SMILES?",
+            "How can I run those computationally heavy predictions?",
+            "Can I take into account different conformers?"
         ],
         "requirements": [
             {
                 "topic_name": "metabolomics",
                 "tutorials": [
-                    "lcms"
+                    "lcms-preprocessing",
+                    "gc_ms_with_xcms"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00194",
+        "short_id": null,
         "short_tools": [
-            "abims_xcms_fillPeaks",
-            "abims_xcms_xcmsSet",
-            "xcms_merge",
-            "abims_xcms_group",
-            "msnbase_readmsdata"
+            "openbabel_compound_convert",
+            "qcxms_production_run",
+            "__FILTER_FAILED_DATASETS__",
+            "ctb_im_conformers",
+            "tp_cat",
+            "split_file_to_collection",
+            "qcxms_getres",
+            "param_value_from_file",
+            "xtb_molecular_optimization",
+            "tp_cut_tool",
+            "qcxms_neutral_run"
         ],
-        "slides": false,
+        "slides": true,
         "slides_recordings": false,
         "supported_servers": {
             "exact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
                 }
             ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
+            "inexact": []
         },
         "symlink": null,
-        "tags": [
-            "work-in-progress"
-        ],
-        "time_estimation": "2H",
-        "title": "Mass spectrometry : GC-MS analysis with metaMS package",
+        "time_estimation": "1H",
+        "title": "Predicting EI+ mass spectra with QCxMS",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy0"
+            "__FILTER_FAILED_DATASETS__",
+            "param_value_from_file",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_conformers/ctb_im_conformers/1.1.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/recetox/qcxms_getres/qcxms_getres/5.2.1+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/recetox/qcxms_neutral_run/qcxms_neutral_run/5.2.1+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/recetox/qcxms_neutral_run/qcxms_neutral_run/5.2.1+galaxy4",
+            "toolshed.g2.bx.psu.edu/repos/recetox/qcxms_production_run/qcxms_production_run/5.2.1+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/recetox/xtb_molecular_optimization/xtb_molecular_optimization/6.6.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/recetox/xtb_molecular_optimization/xtb_molecular_optimization/6.6.1+galaxy3"
         ],
         "topic_name": "metabolomics",
         "topic_name_human": "Metabolomics",
@@ -135573,223 +138634,522 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "gcms",
+        "tutorial_name": "qcxms-predictions",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/metabolomics/tutorials/gcms/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/metabolomics/tutorials/qcxms-predictions/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/gcms/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/gcms/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/qcxms-predictions/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/qcxms-predictions/tutorial.json"
         },
-        "version": 7,
+        "version": 1,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 105,
-        "visitors": 1175,
-        "zenodo_link": "https://zenodo.org/record/3244991"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/introduction/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "email": "zierep@informatik.uni-freiburg.de",
-                "id": "paulzierep",
-                "joined": "2023-02",
-                "name": "Paul Zierep",
-                "orcid": "0000-0003-2982-388X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json"
-            },
+        "visit_duration": 149,
+        "visitors": 3260,
+        "workflows": [
             {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
+                "creators": [
+                    {
+                        "class": "Organization",
+                        "email": "mailto:GalaxyToolsDevelopmentandDeployment@space.muni.cz",
+                        "name": "RECETOX SpecDat"
+                    }
                 ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
+                "description": "This workflow predict in-silico mass spectra using semi-empirical quantum physics method.",
+                "features": {
+                    "comments": true,
+                    "parameters": true,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                    },
+                    "subworkflows": false
                 },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput Molecules with SMILES and NAME without a header.\"]\n  1[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nNumber of conformers to generate\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nOptimization Levels\"]\n  3[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nQC Method\"]\n  4[label=\"Cut SMILES column\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Cut NAME column\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Split file\"]\n  4 -> 6 [label=\"output\"]\n  7[label=\"Split file\"]\n  5 -> 7 [label=\"output\"]\n  8[label=\"Parse parameter value\"]\n  7 -> 8 [label=\"list_output_tab\"]\n  9[label=\"Convert compounds from SMILES to SDF and add the name as title.\"]\n  8 -> 9 [label=\"text_param\"]\n  6 -> 9 [label=\"list_output_tab\"]\n  10[label=\"Merge the individual SDF files\"]\n  9 -> 10 [label=\"outfile\"]\n  11[label=\"Generate conformers\"]\n  10 -> 11 [label=\"out_file1\"]\n  1 -> 11 [label=\"output\"]\n  kf4f8881ecd6442ae84351288e4e473b5[color=lightseagreen,label=\"Output\\nconformer_output\"]\n  11 -> kf4f8881ecd6442ae84351288e4e473b5\n  12[label=\"Molecular format conversion \"]\n  11 -> 12 [label=\"outfile\"]\n  k5dcb6f0262c94f439810a10052b59b41[color=lightseagreen,label=\"Output\\nXYZ output\"]\n  12 -> k5dcb6f0262c94f439810a10052b59b41\n  13[label=\"xTB molecular optimization\"]\n  12 -> 13 [label=\"file_outputs\"]\n  2 -> 13 [label=\"output\"]\n  k01a9a1afe225461394f9dfdad37c93a2[color=lightseagreen,label=\"Output\\noptimized output\"]\n  13 -> k01a9a1afe225461394f9dfdad37c93a2\n  14[label=\"QCxMS neutral run\"]\n  3 -> 14 [label=\"output\"]\n  13 -> 14 [label=\"output\"]\n  ke6e6a07bd4784a87b49142abee9094b1[color=lightseagreen,label=\"Output\\n[.in] output\"]\n  14 -> ke6e6a07bd4784a87b49142abee9094b1\n  k969b3e2ffbee48f9829ac0032580e6f8[color=lightseagreen,label=\"Output\\n[.xyz] output\"]\n  14 -> k969b3e2ffbee48f9829ac0032580e6f8\n  kdc4811ad6cff42cca2f852ab585f47fe[color=lightseagreen,label=\"Output\\n[.start] output\"]\n  14 -> kdc4811ad6cff42cca2f852ab585f47fe\n  15[label=\"QCxMS production run\"]\n  14 -> 15 [label=\"coords1\"]\n  14 -> 15 [label=\"coords2\"]\n  14 -> 15 [label=\"coords3\"]\n  kfc53168a99f8441c93252d812bf03100[color=lightseagreen,label=\"Output\\nres output\"]\n  15 -> kfc53168a99f8441c93252d812bf03100\n  16[label=\"Filter failed datasets\"]\n  15 -> 16 [label=\"res_files\"]\n  17[label=\"QCxMS get results\"]\n  12 -> 17 [label=\"file_outputs\"]\n  16 -> 17 [label=\"output\"]\n  kd81bf92a604c46b986a9bf3c2281ebcb[color=lightseagreen,label=\"Output\\nMSP output\"]\n  17 -> kd81bf92a604c46b986a9bf3c2281ebcb\n}",
+                "history": [
+                    {
+                        "hash": "bfb40ba7854fa8865b8ac6ae75b772b4998780c2",
+                        "message": "workflow tests",
+                        "num": 1,
+                        "short_hash": "bfb40ba78",
+                        "unix": "1723471675"
+                    }
                 ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            }
-        ],
-        "dir": "topics/microbiome/tutorials/introduction",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": false,
-        "id": "microbiome/introduction",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "layout": "tutorial_slides",
-        "license": "CC-BY-4.0",
-        "logo": "GTN",
-        "mod_date": "2024-08-08",
-        "pageviews": 5726884,
-        "priority": 0,
-        "pub_date": "2017-06-22",
-        "recordings": [
-            {
-                "captioners": [
-                    "shiltemann"
+                "inputs": [
+                    {
+                        "annotation": "First column should containe the name of the molecule, the second should contain the SMILES code.",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "First column should containe the name of the molecule, the second should contain the SMILES code.",
+                                "name": "Input Molecules with SMILES and NAME without a header."
+                            }
+                        ],
+                        "label": "Input Molecules with SMILES and NAME without a header.",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 180
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "c77610d3-3333-4393-a5c3-8ce3037bdc9c",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "By default one conformer",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "By default one conformer",
+                                "name": "Number of conformers to generate"
+                            }
+                        ],
+                        "label": "Number of conformers to generate",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 660,
+                            "top": 70
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"default\": 1, \"parameter_type\": \"integer\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "0d45e43e-3de9-47e9-9b57-8745c433423e",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "Level of accuracy for the optimization",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Level of accuracy for the optimization",
+                                "name": "Optimization Levels"
+                            }
+                        ],
+                        "label": "Optimization Levels",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 660,
+                            "top": 190
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "597e3200-086b-49d6-b814-909c8b8ab2d4",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "Available: GFN1-xTB and GFN2-xTB",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Available: GFN1-xTB and GFN2-xTB",
+                                "name": "QC Method"
+                            }
+                        ],
+                        "label": "QC Method",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 1050,
+                            "top": 190
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "5b88e765-5c74-4348-b4db-311a2fa6fe35",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
                 ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "15M",
-                "speakers": [
-                    "shiltemann"
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput Molecules with SMILES and NAME without a header.\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nNumber of conformers to generate\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nOptimization Levels\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nQC Method\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"Cut SMILES column\"];\n  0 -->|output| 4;\n  5[\"Cut NAME column\"];\n  0 -->|output| 5;\n  6[\"Split file\"];\n  4 -->|output| 6;\n  7[\"Split file\"];\n  5 -->|output| 7;\n  8[\"Parse parameter value\"];\n  7 -->|list_output_tab| 8;\n  9[\"Convert compounds from SMILES to SDF and add the name as title.\"];\n  8 -->|text_param| 9;\n  6 -->|list_output_tab| 9;\n  10[\"Merge the individual SDF files\"];\n  9 -->|outfile| 10;\n  11[\"Generate conformers\"];\n  10 -->|out_file1| 11;\n  1 -->|output| 11;\n  f4f8881e-cd64-42ae-8435-1288e4e473b5[\"Output\\nconformer_output\"];\n  11 --> f4f8881e-cd64-42ae-8435-1288e4e473b5;\n  style f4f8881e-cd64-42ae-8435-1288e4e473b5 stroke:#2c3143,stroke-width:4px;\n  12[\"Molecular format conversion \"];\n  11 -->|outfile| 12;\n  5dcb6f02-62c9-4f43-9810-a10052b59b41[\"Output\\nXYZ output\"];\n  12 --> 5dcb6f02-62c9-4f43-9810-a10052b59b41;\n  style 5dcb6f02-62c9-4f43-9810-a10052b59b41 stroke:#2c3143,stroke-width:4px;\n  13[\"xTB molecular optimization\"];\n  12 -->|file_outputs| 13;\n  2 -->|output| 13;\n  01a9a1af-e225-4613-94f9-dfdad37c93a2[\"Output\\noptimized output\"];\n  13 --> 01a9a1af-e225-4613-94f9-dfdad37c93a2;\n  style 01a9a1af-e225-4613-94f9-dfdad37c93a2 stroke:#2c3143,stroke-width:4px;\n  14[\"QCxMS neutral run\"];\n  3 -->|output| 14;\n  13 -->|output| 14;\n  e6e6a07b-d478-4a87-b491-42abee9094b1[\"Output\\n[.in] output\"];\n  14 --> e6e6a07b-d478-4a87-b491-42abee9094b1;\n  style e6e6a07b-d478-4a87-b491-42abee9094b1 stroke:#2c3143,stroke-width:4px;\n  969b3e2f-fbee-48f9-829a-c0032580e6f8[\"Output\\n[.xyz] output\"];\n  14 --> 969b3e2f-fbee-48f9-829a-c0032580e6f8;\n  style 969b3e2f-fbee-48f9-829a-c0032580e6f8 stroke:#2c3143,stroke-width:4px;\n  dc4811ad-6cff-42cc-a2f8-52ab585f47fe[\"Output\\n[.start] output\"];\n  14 --> dc4811ad-6cff-42cc-a2f8-52ab585f47fe;\n  style dc4811ad-6cff-42cc-a2f8-52ab585f47fe stroke:#2c3143,stroke-width:4px;\n  15[\"QCxMS production run\"];\n  14 -->|coords1| 15;\n  14 -->|coords2| 15;\n  14 -->|coords3| 15;\n  fc53168a-99f8-441c-9325-2d812bf03100[\"Output\\nres output\"];\n  15 --> fc53168a-99f8-441c-9325-2d812bf03100;\n  style fc53168a-99f8-441c-9325-2d812bf03100 stroke:#2c3143,stroke-width:4px;\n  16[\"Filter failed datasets\"];\n  15 -->|res_files| 16;\n  17[\"QCxMS get results\"];\n  12 -->|file_outputs| 17;\n  16 -->|output| 17;\n  d81bf92a-604c-46b9-86a9-bf3c2281ebcb[\"Output\\nMSP output\"];\n  17 --> d81bf92a-604c-46b9-86a9-bf3c2281ebcb;\n  style d81bf92a-604c-46b9-86a9-bf3c2281ebcb stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "End-to-end EI+ mass spectra prediction workflow using QCxMS",
+                "outputs": [
+                    {
+                        "annotation": "Generate 3D conformers from SDF input for each molecule. It requires the number of conformers as an input parameter. Default parameters value is 1.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_conformers/ctb_im_conformers/1.1.4+galaxy0",
+                        "errors": null,
+                        "id": 11,
+                        "input_connections": {
+                            "infile": {
+                                "id": 10,
+                                "output_name": "out_file1"
+                            },
+                            "num": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Generate conformers",
+                        "name": "Generate conformers",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "sdf"
+                            },
+                            {
+                                "name": "logfile",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 1052.9,
+                            "top": 393.4
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionlogfile": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "logfile"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_conformers/ctb_im_conformers/1.1.4+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "a4b1474efada",
+                            "name": "ctb_im_conformers",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"attempts\": \"0\", \"conditional_cluster\": {\"cluster_method_opts\": \"none\", \"__current_case__\": 2}, \"emin\": \"0\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"num\": {\"__class__\": \"ConnectedValue\"}, \"rmsd\": \"1.0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.4+galaxy0",
+                        "type": "tool",
+                        "uuid": "2adae9dd-d0be-4873-83f3-a0268fa3f405",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "conformer_output",
+                                "output_name": "outfile",
+                                "uuid": "f4f8881e-cd64-42ae-8435-1288e4e473b5"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Convert the conformer to cartesian coordinate (XYZ) format",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0",
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {
+                            "infile": {
+                                "id": 11,
+                                "output_name": "outfile"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Molecular format conversion ",
+                        "name": "Compound conversion",
+                        "outputs": [
+                            {
+                                "name": "file_outputs",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1052.9,
+                            "top": 683.4
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e2c36f62e22f",
+                            "name": "openbabel_compound_convert",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"sdf\", \"appendtotitle\": \"\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"dative_bonds\": false, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"oformat\": {\"oformat_opts_selector\": \"xyz\", \"__current_case__\": 68}, \"ph\": \"7.0\", \"remove_h\": false, \"split\": true, \"unique\": {\"unique_opts_selector\": \"\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.1.1+galaxy0",
+                        "type": "tool",
+                        "uuid": "c847197b-8c2e-4e5e-a4ec-13890855abf1",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "XYZ output",
+                                "output_name": "file_outputs",
+                                "uuid": "5dcb6f02-62c9-4f43-9810-a10052b59b41"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Semi-empirical optimization",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/recetox/xtb_molecular_optimization/xtb_molecular_optimization/6.6.1+galaxy3",
+                        "errors": null,
+                        "id": 13,
+                        "input_connections": {
+                            "coordinates": {
+                                "id": 12,
+                                "output_name": "file_outputs"
+                            },
+                            "opt_level": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "xTB molecular optimization",
+                        "name": "xtb molecular optimization",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1052.8999933509037,
+                            "top": 883.3999791720917
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/recetox/xtb_molecular_optimization/xtb_molecular_optimization/6.6.1+galaxy3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "6e1ef071fffc",
+                            "name": "xtb_molecular_optimization",
+                            "owner": "recetox",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"coordinates\": {\"__class__\": \"ConnectedValue\"}, \"opt_level\": {\"__class__\": \"ConnectedValue\"}, \"replace_second_line\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "6.6.1+galaxy3",
+                        "type": "tool",
+                        "uuid": "4c4921af-438e-41f4-9621-bb42043bbe6f",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "optimized output",
+                                "output_name": "output",
+                                "uuid": "01a9a1af-e225-4613-94f9-dfdad37c93a2"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Produce preparation input files for production runs",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/recetox/qcxms_neutral_run/qcxms_neutral_run/5.2.1+galaxy4",
+                        "errors": null,
+                        "id": 14,
+                        "input_connections": {
+                            "QC_Level": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "mol": {
+                                "id": 13,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "QCxMS neutral run",
+                        "outputs": [
+                            {
+                                "name": "coords1",
+                                "type": "input"
+                            },
+                            {
+                                "name": "coords2",
+                                "type": "input"
+                            },
+                            {
+                                "name": "coords3",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1440,
+                            "top": 390
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/recetox/qcxms_neutral_run/qcxms_neutral_run/5.2.1+galaxy4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "8f465c0c3b6c",
+                            "name": "qcxms_neutral_run",
+                            "owner": "recetox",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"QC_Level\": {\"__class__\": \"ConnectedValue\"}, \"keywords\": {\"tmax\": \"20.0\", \"tinit\": \"500.0\", \"ieeatm\": \"0.6\", \"ntraj\": null}, \"mol\": {\"__class__\": \"ConnectedValue\"}, \"store_extended_output\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.2.1+galaxy4",
+                        "type": "tool",
+                        "uuid": "6aa75cd8-8d14-40b1-8192-f28a6b7ea6d4",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "[.in] output",
+                                "output_name": "coords1",
+                                "uuid": "e6e6a07b-d478-4a87-b491-42abee9094b1"
+                            },
+                            {
+                                "label": "[.xyz] output",
+                                "output_name": "coords3",
+                                "uuid": "969b3e2f-fbee-48f9-829a-c0032580e6f8"
+                            },
+                            {
+                                "label": "[.start] output",
+                                "output_name": "coords2",
+                                "uuid": "dc4811ad-6cff-42cc-a2f8-52ab585f47fe"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Calculate the mass spectra for a given molecule using QCxMS. It generates .res files, which are collected and converted into MSP format in the last step",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/recetox/qcxms_production_run/qcxms_production_run/5.2.1+galaxy3",
+                        "errors": null,
+                        "id": 15,
+                        "input_connections": {
+                            "in_file": {
+                                "id": 14,
+                                "output_name": "coords1"
+                            },
+                            "start_file": {
+                                "id": 14,
+                                "output_name": "coords2"
+                            },
+                            "xyz_file": {
+                                "id": 14,
+                                "output_name": "coords3"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "QCxMS production run",
+                        "outputs": [
+                            {
+                                "name": "res_files",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 1740,
+                            "top": 390
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/recetox/qcxms_production_run/qcxms_production_run/5.2.1+galaxy3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e97bfe7ac906",
+                            "name": "qcxms_production_run",
+                            "owner": "recetox",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"in_file|__identifier__\": \"TMP.100_qcxms\", \"start_file\": {\"__class__\": \"ConnectedValue\"}, \"start_file|__identifier__\": \"TMP.100_qcxms\", \"store_extended_output\": false, \"xyz_file\": {\"__class__\": \"ConnectedValue\"}, \"xyz_file|__identifier__\": \"TMP.100_start\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.2.1+galaxy3",
+                        "type": "tool",
+                        "uuid": "ad8af72d-c4e6-400f-bcd4-87b5e3ed79ac",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "res output",
+                                "output_name": "res_files",
+                                "uuid": "fc53168a-99f8-441c-9325-2d812bf03100"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Produce simulated mass spectra into MSP file format.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/recetox/qcxms_getres/qcxms_getres/5.2.1+galaxy2",
+                        "errors": null,
+                        "id": 17,
+                        "input_connections": {
+                            "mol": {
+                                "id": 12,
+                                "output_name": "file_outputs"
+                            },
+                            "res_files": {
+                                "id": 16,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "QCxMS get results",
+                        "outputs": [
+                            {
+                                "name": "msp_output",
+                                "type": "msp"
+                            }
+                        ],
+                        "position": {
+                            "left": 1740,
+                            "top": 680
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/recetox/qcxms_getres/qcxms_getres/5.2.1+galaxy2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "53dce0e49af7",
+                            "name": "qcxms_getres",
+                            "owner": "recetox",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"mol\": {\"__class__\": \"ConnectedValue\"}, \"mol|__identifier__\": \"molecule1\", \"res_files\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.2.1+galaxy2",
+                        "type": "tool",
+                        "uuid": "3b4e1353-4d54-4e6f-b1f2-ba8e7329b641",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "MSP output",
+                                "output_name": "msp_output",
+                                "uuid": "d81bf92a-604c-46b9-86a9-bf3c2281ebcb"
+                            }
+                        ]
+                    }
                 ],
-                "youtube_id": "9OY1mklWuK0"
-            }
-        ],
-        "redirect_from": [
-            "/topics/metagenomics/slides/introduction",
-            "/topics/microbiome/slides/introduction",
-            "/topics/metagenomics/tutorials/introduction/slides",
-            "/short/microbiome/introduction/slides",
-            "/short/S00078",
-            "/short/S00114"
-        ],
-        "short_id": "S00114",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": [
-            {
-                "captioners": [
-                    "shiltemann"
+                "parent_id": "metabolomics/qcxms-predictions",
+                "path": "topics/metabolomics/tutorials/qcxms-predictions/workflows/End-to-end-EI+-mass-spectra-prediction-workflow-using-QCxMS.ga",
+                "tags": [
+                    "Exposomics",
+                    "QCxMS",
+                    "GC-MS",
+                    "Metabolomics"
                 ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "15M",
-                "speakers": [
-                    "shiltemann"
+                "test_results": null,
+                "tests": true,
+                "title": "End-to-end EI+ mass spectra prediction workflow using QCxMS",
+                "topic_id": "metabolomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/metabolomics-qcxms-predictions/versions/end-to-end-ei--mass-spectra-prediction-workflow-using-qcxms",
+                "tutorial_id": "qcxms-predictions",
+                "url": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/qcxms-predictions/workflows/End-to-end-EI+-mass-spectra-prediction-workflow-using-QCxMS.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/qcxms-predictions/workflows/End-to-end-EI+-mass-spectra-prediction-workflow-using-QCxMS.html",
+                "version": 1,
+                "wfid": "metabolomics-qcxms-predictions",
+                "wfname": "end-to-end-ei--mass-spectra-prediction-workflow-using-qcxms",
+                "workflow": "End-to-end-EI+-mass-spectra-prediction-workflow-using-QCxMS.ga",
+                "workflow_tools": [
+                    "__FILTER_FAILED_DATASETS__",
+                    "param_value_from_file",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_conformers/ctb_im_conformers/1.1.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/recetox/qcxms_getres/qcxms_getres/5.2.1+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/recetox/qcxms_neutral_run/qcxms_neutral_run/5.2.1+galaxy4",
+                    "toolshed.g2.bx.psu.edu/repos/recetox/qcxms_production_run/qcxms_production_run/5.2.1+galaxy3",
+                    "toolshed.g2.bx.psu.edu/repos/recetox/xtb_molecular_optimization/xtb_molecular_optimization/6.6.1+galaxy3"
                 ],
-                "youtube_id": "9OY1mklWuK0"
+                "workflowhub_id": null
             }
         ],
-        "subtopic": "intro",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "title": "Introduction to Microbiome Analysis",
-        "tools": [],
-        "topic_name": "microbiome",
-        "topic_name_human": "Microbiome",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": true
-        },
-        "tutorial_name": "introduction",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/introduction/slides.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/introduction/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/introduction/slides.json"
-        },
-        "version": 5,
-        "video": true,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758
+        "zenodo_link": "https://zenodo.org/record/13327051"
     },
     {
         "admin_install": {
@@ -135798,243 +139158,98 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "taxonomy_krona_chart",
-                    "owner": "crs4",
-                    "revisions": "73486cc6170e",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "humann2",
-                    "owner": "iuc",
-                    "revisions": "1ab06263e083",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "humann2_regroup_table",
-                    "owner": "iuc",
-                    "revisions": "a1747df2bc21",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "humann2_renorm_table",
-                    "owner": "iuc",
-                    "revisions": "ba4dfbdc1295",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "metaphlan2",
-                    "owner": "iuc",
-                    "revisions": "8c82c4d90cc6",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "metaphlan2krona",
-                    "owner": "iuc",
-                    "revisions": "ebb74774457e",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_align_seqs",
-                    "owner": "iuc",
-                    "revisions": "2692b3107533",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_classify_otu",
-                    "owner": "iuc",
-                    "revisions": "e664787de3ab",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_classify_seqs",
-                    "owner": "iuc",
-                    "revisions": "cc9c7b550c29",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_cluster_split",
-                    "owner": "iuc",
-                    "revisions": "a29ac7993cb0",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_count_seqs",
-                    "owner": "iuc",
-                    "revisions": "ecbd9ed733e6",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_filter_seqs",
-                    "owner": "iuc",
-                    "revisions": "bf20a30c263a",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_make_biom",
-                    "owner": "iuc",
-                    "revisions": "5dc4d49a238a",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_make_group",
-                    "owner": "iuc",
-                    "revisions": "8c964d119da8",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_make_shared",
-                    "owner": "iuc",
-                    "revisions": "83dabeeadb55",
-                    "tool_panel_section_label": "Mothur",
+                    "name": "cardinal_data_exporter",
+                    "owner": "galaxyp",
+                    "revisions": "4fbffddde8cd",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_merge_files",
-                    "owner": "iuc",
-                    "revisions": "a70b25374a23",
-                    "tool_panel_section_label": "Mothur",
+                    "name": "cardinal_filtering",
+                    "owner": "galaxyp",
+                    "revisions": "b8c79e70516d",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_pre_cluster",
-                    "owner": "iuc",
-                    "revisions": "58d0fe3cc0f2",
-                    "tool_panel_section_label": "Mothur",
+                    "name": "cardinal_mz_images",
+                    "owner": "galaxyp",
+                    "revisions": "daf2ee9127fd",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_screen_seqs",
-                    "owner": "iuc",
-                    "revisions": "8743aecd26a9",
-                    "tool_panel_section_label": "Mothur",
+                    "name": "cardinal_mz_images",
+                    "owner": "galaxyp",
+                    "revisions": "59e85306eae5",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_summary_seqs",
-                    "owner": "iuc",
-                    "revisions": "e4a4cb8b6bbf",
-                    "tool_panel_section_label": "Mothur",
+                    "name": "cardinal_quality_report",
+                    "owner": "galaxyp",
+                    "revisions": "5a35e3a8d013",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_unique_seqs",
-                    "owner": "iuc",
-                    "revisions": "1f72d9a3d09f",
-                    "tool_panel_section_label": "Mothur",
+                    "name": "cardinal_spectra_plots",
+                    "owner": "galaxyp",
+                    "revisions": "d2596e1be091",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "krona_text",
-                    "owner": "saskia-hiltemann",
-                    "revisions": "b14f1444e464",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "name": "cardinal_spectra_plots",
+                    "owner": "galaxyp",
+                    "revisions": "1693b2126f30",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: taxonomy_krona_chart\n  owner: crs4\n  revisions: 73486cc6170e\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: humann2\n  owner: iuc\n  revisions: 1ab06263e083\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: humann2_regroup_table\n  owner: iuc\n  revisions: a1747df2bc21\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: humann2_renorm_table\n  owner: iuc\n  revisions: ba4dfbdc1295\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaphlan2\n  owner: iuc\n  revisions: 8c82c4d90cc6\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaphlan2krona\n  owner: iuc\n  revisions: ebb74774457e\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_align_seqs\n  owner: iuc\n  revisions: 2692b3107533\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_classify_otu\n  owner: iuc\n  revisions: e664787de3ab\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_classify_seqs\n  owner: iuc\n  revisions: cc9c7b550c29\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_cluster_split\n  owner: iuc\n  revisions: a29ac7993cb0\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_count_seqs\n  owner: iuc\n  revisions: ecbd9ed733e6\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_filter_seqs\n  owner: iuc\n  revisions: bf20a30c263a\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_make_biom\n  owner: iuc\n  revisions: 5dc4d49a238a\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_make_group\n  owner: iuc\n  revisions: 8c964d119da8\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_make_shared\n  owner: iuc\n  revisions: 83dabeeadb55\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_merge_files\n  owner: iuc\n  revisions: a70b25374a23\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_pre_cluster\n  owner: iuc\n  revisions: 58d0fe3cc0f2\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_screen_seqs\n  owner: iuc\n  revisions: 8743aecd26a9\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_summary_seqs\n  owner: iuc\n  revisions: e4a4cb8b6bbf\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_unique_seqs\n  owner: iuc\n  revisions: 1f72d9a3d09f\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: krona_text\n  owner: saskia-hiltemann\n  revisions: b14f1444e464\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/general-tutorial/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: cardinal_data_exporter\n  owner: galaxyp\n  revisions: 4fbffddde8cd\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_filtering\n  owner: galaxyp\n  revisions: b8c79e70516d\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_mz_images\n  owner: galaxyp\n  revisions: daf2ee9127fd\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_mz_images\n  owner: galaxyp\n  revisions: 59e85306eae5\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_quality_report\n  owner: galaxyp\n  revisions: 5a35e3a8d013\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_spectra_plots\n  owner: galaxyp\n  revisions: d2596e1be091\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_spectra_plots\n  owner: galaxyp\n  revisions: 1693b2126f30\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
                     "uni-freiburg"
                 ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+                "email": "melanie.foell@mol-med.uni-freiburg.de",
+                "id": "foellmelanie",
+                "joined": "2018-10",
+                "matrix": "foellmelanie:matrix.org",
+                "name": "Melanie F\u00f6ll",
+                "orcid": "0000-0002-1887-7543",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
+                "twitter": "MCFoell",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
             },
             {
                 "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
+                    "uni-freiburg"
                 ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+                "id": "MarenStillger",
+                "joined": "2020-10",
+                "name": "Maren Stillger",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/MarenStillger/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/MarenStillger.json"
             }
         ],
-        "dir": "topics/microbiome/tutorials/general-tutorial",
-        "edam_ontology": [
-            "topic_3174",
-            "topic_3697",
-            "topic_0637",
-            "topic_0080",
-            "topic_4038"
-        ],
-        "edam_operation": [
-            "Visualisation",
-            "Sequencing quality control",
-            "Phylogenetic analysis",
-            "Taxonomic classification",
-            "Sequence read processing",
-            "DNA barcoding",
-            "Sequence clustering"
-        ],
-        "edam_topic": [
-            "Metagenomics",
-            "Microbial ecology",
-            "Taxonomy",
-            "Sequence analysis"
+        "dir": "topics/metabolomics/tutorials/msi-analyte-distribution",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
         ],
-        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "microbiome/general-tutorial",
+        "id": "metabolomics/msi-analyte-distribution",
         "inexact_supported_servers": [
+            "HyPhy HIV NGS Tools",
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
             "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org.au"
@@ -136044,63 +139259,63 @@
             "mermaid": false
         },
         "key_points": [
-            "With amplicon data, we can extract information about the studied community structure",
-            "With shotgun data, we can extract information about the studied community structure and also the functions realised by the community",
-            "The tools used to analyze amplicon and shotgun data are different, except for the visualisation",
-            "Metagenomics data analyses are complex and time-consuming"
+            "Average and annotated mass spectra show the relevant m/z range of the dataset and different compartment-specific peaks.",
+            "MSI data can be filtered for m/z ranges of interest to speed up analysis time.",
+            "Distribution images for many analytes can be automatically generated with the MSI m/z image tool.",
+            "The MSI m/z image tools allow overlaying the distribution images for several analytes."
         ],
         "layout": "tutorial_hands_on",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-09",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Choosing the best approach to analyze metagenomics data",
-            "Selection of tools to analyze amplicon data or shotgun data",
-            "Visualisation of a community structure"
+            "Plot average mass spectra and overlaid mass spectra of single spectra.",
+            "Filter MSI data for a specific m/z range.",
+            "Automatic generation of many m/z images.",
+            "Overlay the distribution of several m/z in one image."
         ],
-        "pageviews": 4081,
-        "pub_date": "2017-06-22",
+        "pageviews": 3682,
+        "pub_date": "2019-02-21",
         "questions": [
-            "How to analyze metagenomics data?",
-            "What information can be extracted of metagenomics data?",
-            "What is the difference between amplicon and shotgun data?",
-            "What are the difference in the analyses of amplicon and shotgun data?"
-        ],
-        "redirect_from": [
-            "/topics/metagenomics/tutorials/general-tutorial/tutorial",
-            "/short/microbiome/general-tutorial",
-            "/short/T00201",
-            "/short/T00385"
+            "What is the typical mass range of VOCs?",
+            "In which compartments of the chilli are the measured VOCs located?",
+            "In which compartment of the chilli is the capsaicin located?"
         ],
-        "short_id": "T00385",
+        "short_id": "T00198",
         "short_tools": [
-            "mothur_cluster_split",
-            "mothur_count_seqs",
-            "mothur_classify_otu",
-            "mothur_merge_files",
-            "mothur_pre_cluster",
-            "humann2_regroup_table",
-            "mothur_make_biom",
-            "mothur_make_group",
-            "mothur_screen_seqs",
-            "mothur_unique_seqs",
-            "mothur_summary_seqs",
-            "metaphlan2",
-            "humann2",
-            "krona-text",
-            "mothur_make_shared",
-            "taxonomy_krona_chart",
-            "mothur_align_seqs",
-            "humann2_renorm_table",
-            "mothur_classify_seqs",
-            "mothur_filter_seqs",
-            "metaphlan2krona"
+            "Filter1",
+            "cardinal_data_exporter",
+            "cardinal_filtering",
+            "cardinal_mz_images",
+            "cardinal_quality_report",
+            "cardinal_spectra_plots"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "intro",
         "supported_servers": {
-            "exact": [],
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
             "inexact": [
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.fr",
                     "url": "https://usegalaxy.fr/",
@@ -136119,73 +139334,57 @@
             ]
         },
         "symlink": null,
-        "tags": [
-            "microgalaxy"
-        ],
-        "time_estimation": "2H30M",
-        "title": "Analyses of metagenomics data - The global picture",
+        "time_estimation": "1H",
+        "title": "Mass spectrometry imaging: Examining the spatial distribution of analytes",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.9.9.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/humann2_regroup_table/humann2_regroup_table/0.9.9.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/humann2_renorm_table/humann2_renorm_table/0.9.9.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.36.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.36.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.36.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.36.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.36.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.36.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.36.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_group/mothur_make_group/1.36.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.36.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.36.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.36.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.36.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.36.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.36.1.0",
-            "toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/krona-text/1"
+            "Filter1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/2.6.0.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/2.6.0.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.2",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/2.6.0.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.3"
         ],
-        "topic_name": "microbiome",
-        "topic_name_human": "Microbiome",
+        "topic_name": "metabolomics",
+        "topic_name_human": "Metabolomics",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "general-tutorial",
+        "tutorial_name": "msi-analyte-distribution",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/general-tutorial/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/general-tutorial/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.json"
         },
-        "version": 4,
+        "version": 17,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 165,
-        "visitors": 3013,
+        "visit_duration": 105,
+        "visitors": 2533,
         "workflows": [
             {
                 "creators": [],
-                "description": "Analyses of metagenomics data - The global picture",
+                "description": "Mass spectrometry imaging: Examining the spatial distribution of analytes",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSILVA Reference\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAnguil Soil Sample\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPampa Soil Sample\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTrainset PDS alignment\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTrainset PDS taxonomy\"]\n  5[label=\"Merge.files\"]\n  2 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"Make.group\"]\n  1 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"Unique.seqs\"]\n  5 -> 7 [label=\"output\"]\n  8[label=\"Count.seqs\"]\n  6 -> 8 [label=\"output\"]\n  7 -> 8 [label=\"out_names\"]\n  9[label=\"Summary.seqs\"]\n  8 -> 9 [label=\"seq_count\"]\n  7 -> 9 [label=\"out_fasta\"]\n  10[label=\"Screen.seqs\"]\n  7 -> 10 [label=\"out_fasta\"]\n  8 -> 10 [label=\"seq_count\"]\n  11[label=\"Align.seqs\"]\n  0 -> 11 [label=\"output\"]\n  10 -> 11 [label=\"fasta_out\"]\n  12[label=\"Summary.seqs\"]\n  10 -> 12 [label=\"count_out\"]\n  11 -> 12 [label=\"out_file\"]\n  13[label=\"Screen.seqs\"]\n  11 -> 13 [label=\"out_file\"]\n  10 -> 13 [label=\"count_out\"]\n  14[label=\"Filter.seqs\"]\n  13 -> 14 [label=\"fasta_out\"]\n  15[label=\"Pre.cluster\"]\n  14 -> 15 [label=\"filteredfasta\"]\n  13 -> 15 [label=\"count_out\"]\n  16[label=\"Classify.seqs\"]\n  15 -> 16 [label=\"count_out\"]\n  3 -> 16 [label=\"output\"]\n  15 -> 16 [label=\"fasta_out\"]\n  4 -> 16 [label=\"output\"]\n  17[label=\"Cluster.split\"]\n  16 -> 17 [label=\"taxonomy_out\"]\n  15 -> 17 [label=\"fasta_out\"]\n  15 -> 17 [label=\"count_out\"]\n  18[label=\"Make.shared\"]\n  15 -> 18 [label=\"count_out\"]\n  17 -> 18 [label=\"otulist\"]\n  k6ccdf4c57f914ba1ace4ad3efc649be2[color=lightseagreen,label=\"Output\\nmothur_make_shared_shared\"]\n  18 -> k6ccdf4c57f914ba1ace4ad3efc649be2\n  19[label=\"Classify.otu\"]\n  15 -> 19 [label=\"count_out\"]\n  16 -> 19 [label=\"taxonomy_out\"]\n  17 -> 19 [label=\"otulist\"]\n  20[label=\"Make.biom\"]\n  18 -> 20 [label=\"shared\"]\n  19 -> 20 [label=\"taxonomies\"]\n  21[label=\"Visualize  with Krona\"]\n  19 -> 21 [label=\"taxonomies\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nUploaded Composite Dataset imzml\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAnnotation\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nm/z features\"]\n  3[label=\"MSI Qualitycontrol\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"MSI plot spectra\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"MSI filtering\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"MSI plot spectra\"]\n  0 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"MSI data exporter\"]\n  5 -> 7 [label=\"outfile_imzml\"]\n  8[label=\"MSI mz images\"]\n  2 -> 8 [label=\"output\"]\n  5 -> 8 [label=\"outfile_imzml\"]\n  9[label=\"Filter\"]\n  7 -> 9 [label=\"feature_output\"]\n  10[label=\"MSI mz images\"]\n  9 -> 10 [label=\"out_file1\"]\n  5 -> 10 [label=\"outfile_imzml\"]\n}",
                 "history": [
                     {
-                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
-                        "message": "Rename metagenomics topic to microbiome",
+                        "hash": "a46d3c7f2d648b7c17d3daaf18cc951d5da8d5f8",
+                        "message": "small updates in figures, tutorial and workflow",
                         "num": 1,
-                        "short_hash": "0e0a2f2cc",
-                        "unix": "1704901629"
+                        "short_hash": "a46d3c7f2",
+                        "unix": "1604172185"
                     }
                 ],
                 "inputs": [
@@ -136198,22 +139397,34 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "silva"
+                                "name": "Uploaded Composite Dataset (imzml)"
                             }
                         ],
-                        "label": "SILVA Reference",
+                        "label": "Uploaded Composite Dataset (imzml)",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 463
+                            "bottom": 409.6999969482422,
+                            "height": 82.19999694824219,
+                            "left": 375,
+                            "right": 575,
+                            "top": 327.5,
+                            "width": 200,
+                            "x": 375,
+                            "y": 327.5
                         },
                         "tool_id": null,
-                        "tool_state": "{}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "372b68d9-2f00-4275-a372-ffe89cca2a63",
-                        "workflow_outputs": []
+                        "uuid": "d6fee109-e1af-4064-b014-051fbcede1d0",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "c5922e0d-d30d-4c15-84c9-7b97bc5aa93e"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
@@ -136224,294 +139435,693 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "anguil_soil_sample"
+                                "name": "Annotation"
                             }
                         ],
-                        "label": "Anguil Soil Sample",
+                        "label": "Annotation",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 209,
-                            "top": 746.5
+                            "bottom": 522.3000030517578,
+                            "height": 61.80000305175781,
+                            "left": 377,
+                            "right": 577,
+                            "top": 460.5,
+                            "width": 200,
+                            "x": 377,
+                            "y": 460.5
                         },
                         "tool_id": null,
-                        "tool_state": "{}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "3beec7e9-acbe-4c92-85b3-62d6ab3cd83d",
-                        "workflow_outputs": []
+                        "uuid": "d0be9936-9e28-45f6-ac65-08d037ab9dc3",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "d826e468-2c46-4a28-9a24-bff61b41b35b"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "m/z features"
+                            }
+                        ],
+                        "label": "m/z features",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 866.3000030517578,
+                            "height": 61.80000305175781,
+                            "left": 385,
+                            "right": 585,
+                            "top": 804.5,
+                            "width": 200,
+                            "x": 385,
+                            "y": 804.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "02d90f0d-2375-47a8-9a7b-5c8ee43592c3",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "2d72fda0-0ccd-46b5-9011-a62a9c4f5e8e"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nUploaded Composite Dataset imzml\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nAnnotation\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nm/z features\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"MSI Qualitycontrol\"];\n  0 -->|output| 3;\n  4[\"MSI plot spectra\"];\n  0 -->|output| 4;\n  5[\"MSI filtering\"];\n  0 -->|output| 5;\n  6[\"MSI plot spectra\"];\n  0 -->|output| 6;\n  1 -->|output| 6;\n  7[\"MSI data exporter\"];\n  5 -->|outfile_imzml| 7;\n  8[\"MSI mz images\"];\n  2 -->|output| 8;\n  5 -->|outfile_imzml| 8;\n  9[\"Filter\"];\n  7 -->|feature_output| 9;\n  10[\"MSI mz images\"];\n  9 -->|out_file1| 10;\n  5 -->|outfile_imzml| 10;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "MSI Workflow: spatial distribution",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Uploaded Composite Dataset (imzml)"
+                            }
+                        ],
+                        "label": "Uploaded Composite Dataset (imzml)",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 409.6999969482422,
+                            "height": 82.19999694824219,
+                            "left": 375,
+                            "right": 575,
+                            "top": 327.5,
+                            "width": 200,
+                            "x": 375,
+                            "y": 327.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "d6fee109-e1af-4064-b014-051fbcede1d0",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "c5922e0d-d30d-4c15-84c9-7b97bc5aa93e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Annotation"
+                            }
+                        ],
+                        "label": "Annotation",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 522.3000030517578,
+                            "height": 61.80000305175781,
+                            "left": 377,
+                            "right": 577,
+                            "top": 460.5,
+                            "width": 200,
+                            "x": 377,
+                            "y": 460.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "d0be9936-9e28-45f6-ac65-08d037ab9dc3",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "d826e468-2c46-4a28-9a24-bff61b41b35b"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "m/z features"
+                            }
+                        ],
+                        "label": "m/z features",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 866.3000030517578,
+                            "height": 61.80000305175781,
+                            "left": 385,
+                            "right": 585,
+                            "top": 804.5,
+                            "width": 200,
+                            "x": 385,
+                            "y": 804.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "02d90f0d-2375-47a8-9a7b-5c8ee43592c3",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "2d72fda0-0ccd-46b5-9011-a62a9c4f5e8e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/2.6.0.1",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "infile": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool MSI Qualitycontrol",
+                                "name": "calibrant_file"
+                            },
+                            {
+                                "description": "runtime parameter for tool MSI Qualitycontrol",
+                                "name": "infile"
+                            }
+                        ],
+                        "label": null,
+                        "name": "MSI Qualitycontrol",
+                        "outputs": [
+                            {
+                                "name": "QC_report",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 312.6999969482422,
+                            "height": 205.1999969482422,
+                            "left": 669,
+                            "right": 869,
+                            "top": 107.5,
+                            "width": 200,
+                            "x": 669,
+                            "y": 107.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/2.6.0.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ecaebe7c7b54",
+                            "name": "cardinal_quality_report",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"calibrant_file\": {\"__class__\": \"RuntimeValue\"}, \"calibrant_header\": \"false\", \"calibrantratio\": [], \"centroids\": \"true\", \"do_pca\": \"true\", \"filename\": \"\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"mz_column\": \"\", \"name_column\": \"\", \"plusminus_ppm\": \"200.0\", \"processed_cond\": {\"processed_file\": \"processed\", \"__current_case__\": 1, \"accuracy\": \"0.2\", \"units\": \"mz\"}, \"tabular_annotation\": {\"load_annotation\": \"no_annotation\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.0.1",
+                        "type": "tool",
+                        "uuid": "2ee50695-f822-4b88-b753-04722aa2ffca",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "QC_report",
+                                "uuid": "adaa90d0-760d-4605-9076-d76e35d3e03f"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.0",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "infile": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool MSI plot spectra",
+                                "name": "infile"
+                            }
+                        ],
+                        "label": null,
+                        "name": "MSI plot spectra",
+                        "outputs": [
+                            {
+                                "name": "plots",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 456.5,
+                            "height": 134,
+                            "left": 669,
+                            "right": 869,
+                            "top": 322.5,
+                            "width": 200,
+                            "x": 669,
+                            "y": 322.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "d2596e1be091",
+                            "name": "cardinal_spectra_plots",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"centroids\": \"true\", \"filename\": \"\", \"fullmz\": \"true\", \"grid_variable\": \"false\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"mz_range\": {\"mz_range_options\": \"manual_mz\", \"__current_case__\": 2, \"zoomed_sample\": [{\"__index__\": 0, \"xlimmin\": \"10.0\", \"xlimmax\": \"200.0\"}, {\"__index__\": 1, \"xlimmin\": \"200.0\", \"xlimmax\": \"500.0\"}, {\"__index__\": 2, \"xlimmin\": \"500.0\", \"xlimmax\": \"1000.0\"}, {\"__index__\": 3, \"xlimmin\": \"1000.0\", \"xlimmax\": \"1500.0\"}, {\"__index__\": 4, \"xlimmin\": \"1500.0\", \"xlimmax\": \"2000.0\"}]}, \"pixel_conditional\": {\"pixel_type\": \"all_pixel\", \"__current_case__\": 1}, \"processed_cond\": {\"processed_file\": \"processed\", \"__current_case__\": 1, \"accuracy\": \"0.2\", \"units\": \"mz\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.0.0",
+                        "type": "tool",
+                        "uuid": "afd04232-7e33-418c-8409-524d2331fc65",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "plots",
+                                "uuid": "9468b2d2-782c-41d9-a2f4-2ec7c838c47f"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/2.6.0.0",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "infile": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool MSI filtering",
+                                "name": "infile"
+                            }
+                        ],
+                        "label": null,
+                        "name": "MSI filtering",
+                        "outputs": [
+                            {
+                                "name": "outfile_imzml",
+                                "type": "imzml"
+                            },
+                            {
+                                "name": "QC_overview",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 824.8999938964844,
+                            "height": 164.39999389648438,
+                            "left": 672,
+                            "right": 872,
+                            "top": 660.5,
+                            "width": 200,
+                            "x": 672,
+                            "y": 660.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/2.6.0.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2aefa66e48e5",
+                            "name": "cardinal_filtering",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"centroids\": \"true\", \"features_cond\": {\"features_filtering\": \"features_range\", \"__current_case__\": 2, \"min_mz\": \"15.0\", \"max_mz\": \"1000.0\"}, \"infile\": {\"__class__\": \"RuntimeValue\"}, \"pixels_cond\": {\"pixel_filtering\": \"none\", \"__current_case__\": 0}, \"processed_cond\": {\"processed_file\": \"processed\", \"__current_case__\": 1, \"accuracy\": \"0.2\", \"units\": \"mz\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.0.0",
+                        "type": "tool",
+                        "uuid": "69f61159-f6e3-4dc9-a8f7-b5f1a1334fc6",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "QC_overview",
+                                "uuid": "7fc1700f-e7b5-45eb-b9d8-dd1bf6594385"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outfile_imzml",
+                                "uuid": "45f6e115-e334-4ea7-9c8a-7bc36735affa"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.0",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "infile": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "pixel_conditional|pixel_file": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool MSI plot spectra",
+                                "name": "infile"
+                            },
+                            {
+                                "description": "runtime parameter for tool MSI plot spectra",
+                                "name": "pixel_conditional"
+                            }
+                        ],
+                        "label": null,
+                        "name": "MSI plot spectra",
+                        "outputs": [
+                            {
+                                "name": "plots",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 649.3000030517578,
+                            "height": 184.8000030517578,
+                            "left": 669,
+                            "right": 869,
+                            "top": 464.5,
+                            "width": 200,
+                            "x": 669,
+                            "y": 464.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "d2596e1be091",
+                            "name": "cardinal_spectra_plots",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"centroids\": \"true\", \"filename\": \"\", \"fullmz\": \"true\", \"grid_variable\": \"false\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"mz_range\": {\"mz_range_options\": \"manual_mz\", \"__current_case__\": 2, \"zoomed_sample\": [{\"__index__\": 0, \"xlimmin\": \"10.0\", \"xlimmax\": \"200.0\"}, {\"__index__\": 1, \"xlimmin\": \"200.0\", \"xlimmax\": \"500.0\"}, {\"__index__\": 2, \"xlimmin\": \"500.0\", \"xlimmax\": \"1000.0\"}, {\"__index__\": 3, \"xlimmin\": \"1000.0\", \"xlimmax\": \"1500.0\"}, {\"__index__\": 4, \"xlimmin\": \"1500.0\", \"xlimmax\": \"2000.0\"}]}, \"pixel_conditional\": {\"pixel_type\": \"tabular_pixel\", \"__current_case__\": 0, \"pixel_file\": {\"__class__\": \"RuntimeValue\"}, \"column_pixel_x\": \"1\", \"column_pixel_y\": \"2\", \"column_pixel_annotation\": \"3\", \"tabular_pixel_header\": \"true\"}, \"processed_cond\": {\"processed_file\": \"processed\", \"__current_case__\": 1, \"accuracy\": \"0.2\", \"units\": \"mz\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.0.0",
+                        "type": "tool",
+                        "uuid": "27e49459-5afa-49d9-a357-811fbe90650c",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "plots",
+                                "uuid": "69cb29ad-3b9e-4c7c-b1f7-01c78525e6a6"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/2.6.0.0",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 7,
+                        "input_connections": {
+                            "infile": {
+                                "id": 5,
+                                "output_name": "outfile_imzml"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "MSI data exporter",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "pampa_soil_sample"
+                                "name": "intensity_matrix",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "feature_output",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "Pampa Soil Sample",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 212,
-                            "top": 866.5
+                            "bottom": 540.1000061035156,
+                            "height": 225.60000610351562,
+                            "left": 940,
+                            "right": 1140,
+                            "top": 314.5,
+                            "width": 200,
+                            "x": 940,
+                            "y": 314.5
                         },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "e23834b7-d5be-44b1-bbca-7bdea6884022",
-                        "workflow_outputs": []
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/2.6.0.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "137bfc63e758",
+                            "name": "cardinal_data_exporter",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"imzml\", \"centroids\": \"true\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"counting_calibrants\": {\"pixel_with_calibrants\": \"no_calibrants\", \"__current_case__\": 0}, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"output_options\": [\"int_matrix\", \"mz_tabular\"], \"processed_cond\": {\"processed_file\": \"no_processed\", \"__current_case__\": 0}, \"tabular_annotation\": {\"load_annotation\": \"no_annotation\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.0.0",
+                        "type": "tool",
+                        "uuid": "f1647eea-23ca-4713-ae2e-7f68e6388aa7",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "intensity_matrix",
+                                "uuid": "eadf7793-dbdc-4691-b9ed-b359229b35c7"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "feature_output",
+                                "uuid": "ea4d3b0c-8b42-45c2-adaa-65fc0ce368f9"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.0",
                         "errors": null,
-                        "id": 3,
-                        "input_connections": {},
+                        "id": 8,
+                        "input_connections": {
+                            "calibrant_file": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "infile": {
+                                "id": 5,
+                                "output_name": "outfile_imzml"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "trainset_alignment"
+                                "description": "runtime parameter for tool MSI mz images",
+                                "name": "calibrant_file"
+                            },
+                            {
+                                "description": "runtime parameter for tool MSI mz images",
+                                "name": "infile"
+                            }
+                        ],
+                        "label": null,
+                        "name": "MSI mz images",
+                        "outputs": [
+                            {
+                                "name": "plots",
+                                "type": "pdf"
                             }
                         ],
-                        "label": "Trainset PDS alignment",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 2468.5,
-                            "top": 280.5
+                            "bottom": 940.3000030517578,
+                            "height": 184.8000030517578,
+                            "left": 933,
+                            "right": 1133,
+                            "top": 755.5,
+                            "width": 200,
+                            "x": 933,
+                            "y": 755.5
                         },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "7368ffb8-03bd-42b4-bb81-53d147cd419b",
-                        "workflow_outputs": []
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "a95a82eb4d50",
+                            "name": "cardinal_mz_images",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"calibrant_file\": {\"__class__\": \"RuntimeValue\"}, \"calibrant_header\": \"false\", \"centroids\": \"true\", \"colorkey\": \"true\", \"colorscale\": \"viridis\", \"filename\": \"\", \"image_contrast\": \"suppression\", \"image_smoothing\": \"none\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"mz_column\": \"1\", \"name_column\": \"1\", \"normalize_image\": \"false\", \"overlay_cond\": {\"overlay_selection\": \"yes_overlay\", \"__current_case__\": 1, \"colours\": [{\"__index__\": 0, \"feature_color\": \"#c00000\"}, {\"__index__\": 1, \"feature_color\": \"#0070c0\"}, {\"__index__\": 2, \"feature_color\": \"#92d050\"}], \"legend_position\": \"topright\"}, \"plusminus_dalton\": \"0.4\", \"processed_cond\": {\"processed_file\": \"no_processed\", \"__current_case__\": 0}, \"svg_pixelimage\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.0.1",
+                        "type": "tool",
+                        "uuid": "34143b6c-d77e-4dc8-8c5e-18cc685fdc74",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "plots",
+                                "uuid": "a8a97f8e-6bfa-4376-8c5f-a3305f8af429"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "Filter1",
                         "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 9,
+                        "input_connections": {
+                            "input": {
+                                "id": 7,
+                                "output_name": "feature_output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Filter",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "trainset_taxonomy"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
-                        "label": "Trainset PDS taxonomy",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 2476.5,
-                            "top": 389.5
+                            "bottom": 570.6999969482422,
+                            "height": 93.19999694824219,
+                            "left": 1176,
+                            "right": 1376,
+                            "top": 477.5,
+                            "width": 200,
+                            "x": 1176,
+                            "y": 477.5
                         },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "31d8b02c-9ecc-4d55-ac86-8930adb5abc8",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSILVA Reference\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nAnguil Soil Sample\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nPampa Soil Sample\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nTrainset PDS alignment\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nTrainset PDS taxonomy\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Merge.files\"];\n  2 -->|output| 5;\n  1 -->|output| 5;\n  6[\"Make.group\"];\n  1 -->|output| 6;\n  2 -->|output| 6;\n  7[\"Unique.seqs\"];\n  5 -->|output| 7;\n  8[\"Count.seqs\"];\n  6 -->|output| 8;\n  7 -->|out_names| 8;\n  9[\"Summary.seqs\"];\n  8 -->|seq_count| 9;\n  7 -->|out_fasta| 9;\n  10[\"Screen.seqs\"];\n  7 -->|out_fasta| 10;\n  8 -->|seq_count| 10;\n  11[\"Align.seqs\"];\n  0 -->|output| 11;\n  10 -->|fasta_out| 11;\n  12[\"Summary.seqs\"];\n  10 -->|count_out| 12;\n  11 -->|out_file| 12;\n  13[\"Screen.seqs\"];\n  11 -->|out_file| 13;\n  10 -->|count_out| 13;\n  14[\"Filter.seqs\"];\n  13 -->|fasta_out| 14;\n  15[\"Pre.cluster\"];\n  14 -->|filteredfasta| 15;\n  13 -->|count_out| 15;\n  16[\"Classify.seqs\"];\n  15 -->|count_out| 16;\n  3 -->|output| 16;\n  15 -->|fasta_out| 16;\n  4 -->|output| 16;\n  17[\"Cluster.split\"];\n  16 -->|taxonomy_out| 17;\n  15 -->|fasta_out| 17;\n  15 -->|count_out| 17;\n  18[\"Make.shared\"];\n  15 -->|count_out| 18;\n  17 -->|otulist| 18;\n  6ccdf4c5-7f91-4ba1-ace4-ad3efc649be2[\"Output\\nmothur_make_shared_shared\"];\n  18 --> 6ccdf4c5-7f91-4ba1-ace4-ad3efc649be2;\n  style 6ccdf4c5-7f91-4ba1-ace4-ad3efc649be2 stroke:#2c3143,stroke-width:4px;\n  19[\"Classify.otu\"];\n  15 -->|count_out| 19;\n  16 -->|taxonomy_out| 19;\n  17 -->|otulist| 19;\n  20[\"Make.biom\"];\n  18 -->|shared| 20;\n  19 -->|taxonomies| 20;\n  21[\"Visualize  with Krona\"];\n  19 -->|taxonomies| 21;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Amplicon Tutorial",
-                "outputs": [
+                        "post_job_actions": {},
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c2>=55 and c2<=65 or c2>=75 and c2<=85\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
+                        "type": "tool",
+                        "uuid": "8b864289-7691-4045-b6c2-ad191a86a6f9",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "59998a93-7244-4c6b-b2c3-be3cc5f44458"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.36.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.0",
                         "errors": null,
-                        "id": 18,
+                        "id": 10,
                         "input_connections": {
-                            "intype|group": {
-                                "id": 15,
-                                "output_name": "count_out"
+                            "calibrant_file": {
+                                "id": 9,
+                                "output_name": "out_file1"
                             },
-                            "intype|otu": {
-                                "id": 17,
-                                "output_name": "otulist"
+                            "infile": {
+                                "id": 5,
+                                "output_name": "outfile_imzml"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Make.shared",
-                                "name": "intype"
+                                "description": "runtime parameter for tool MSI mz images",
+                                "name": "calibrant_file"
                             },
                             {
-                                "description": "runtime parameter for tool Make.shared",
-                                "name": "intype"
+                                "description": "runtime parameter for tool MSI mz images",
+                                "name": "infile"
                             }
                         ],
                         "label": null,
-                        "name": "Make.shared",
+                        "name": "MSI mz images",
                         "outputs": [
                             {
-                                "name": "labelshares",
-                                "type": "input"
-                            },
-                            {
-                                "name": "logfile",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "shared",
-                                "type": "mothur.shared"
-                            },
-                            {
-                                "name": "groupout",
-                                "type": "mothur.groups"
+                                "name": "plots",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "left": 3069,
-                            "top": 265
+                            "bottom": 791.3000030517578,
+                            "height": 184.8000030517578,
+                            "left": 1410,
+                            "right": 1610,
+                            "top": 606.5,
+                            "width": 200,
+                            "x": 1410,
+                            "y": 606.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.36.1.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "83dabeeadb55",
-                            "name": "mothur_make_shared",
-                            "owner": "iuc",
+                            "changeset_revision": "a95a82eb4d50",
+                            "name": "cardinal_mz_images",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"intype\": \"{\\\"group\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"label\\\": [\\\"0.03\\\"], \\\"groups\\\": null, \\\"infile\\\": \\\"otulist\\\", \\\"otu\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"chromInfo\": \"\\\"/data/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
-                        "tool_version": "1.36.1.0",
+                        "tool_state": "{\"calibrant_file\": {\"__class__\": \"RuntimeValue\"}, \"calibrant_header\": \"true\", \"centroids\": \"true\", \"colorkey\": \"true\", \"colorscale\": \"viridis\", \"filename\": \"\", \"image_contrast\": \"suppression\", \"image_smoothing\": \"none\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"mz_column\": \"2\", \"name_column\": \"1\", \"normalize_image\": \"false\", \"overlay_cond\": {\"overlay_selection\": \"no_overlay\", \"__current_case__\": 0}, \"plusminus_dalton\": \"0.4\", \"processed_cond\": {\"processed_file\": \"no_processed\", \"__current_case__\": 0}, \"svg_pixelimage\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.0.1",
                         "type": "tool",
-                        "uuid": "d554ed42-8658-47c5-952f-9dc73834f267",
+                        "uuid": "24081ed2-7205-45c8-a3ea-9de110785398",
                         "workflow_outputs": [
                             {
-                                "label": "mothur_make_shared_shared",
-                                "output_name": "shared",
-                                "uuid": "6ccdf4c5-7f91-4ba1-ace4-ad3efc649be2"
+                                "label": null,
+                                "output_name": "plots",
+                                "uuid": "095a38a2-99e1-42f1-a3d0-57c54f242c2e"
                             }
                         ]
                     }
                 ],
-                "parent_id": "microbiome/general-tutorial",
-                "path": "topics/microbiome/tutorials/general-tutorial/workflows/amplicon.ga",
-                "tags": [
-                    "microbiome"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "Amplicon Tutorial",
-                "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-general-tutorial/versions/amplicon",
-                "tutorial_id": "general-tutorial",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/general-tutorial/workflows/amplicon.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/general-tutorial/workflows/amplicon.html",
-                "version": 1,
-                "wfid": "microbiome-general-tutorial",
-                "wfname": "amplicon",
-                "workflow": "amplicon.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.36.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.36.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.36.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.36.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.36.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.36.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.36.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_group/mothur_make_group/1.36.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.36.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.36.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.36.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.36.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.36.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.36.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/krona-text/1"
-                ],
-                "workflowhub_id": "1070"
-            },
-            {
-                "creators": [],
-                "description": "Analyses of metagenomics data - The global picture",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[label=\"MetaPhlAn2\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Format MetaPhlAn2\"]\n  1 -> 2 [label=\"output_file\"]\n  3[label=\"HUMAnN2\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output_file\"]\n  4[label=\"Krona pie chart\"]\n  2 -> 4 [label=\"krona\"]\n  5[label=\"Renormalize\"]\n  3 -> 5 [label=\"gene_families_tsv\"]\n  6[label=\"Regroup\"]\n  3 -> 6 [label=\"gene_families_tsv\"]\n  7[label=\"Renormalize\"]\n  6 -> 7 [label=\"output_table\"]\n}",
-                "history": [
-                    {
-                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
-                        "message": "Rename metagenomics topic to microbiome",
-                        "num": 1,
-                        "short_hash": "0e0a2f2cc",
-                        "unix": "1704901629"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "SRR606451_pampa.fasta"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 10
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"SRR606451_pampa.fasta\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "2b9a76e9-f7fc-451a-a6f7-16d87f96547b",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"MetaPhlAn2\"];\n  0 -->|output| 1;\n  2[\"Format MetaPhlAn2\"];\n  1 -->|output_file| 2;\n  3[\"HUMAnN2\"];\n  0 -->|output| 3;\n  1 -->|output_file| 3;\n  4[\"Krona pie chart\"];\n  2 -->|krona| 4;\n  5[\"Renormalize\"];\n  3 -->|gene_families_tsv| 5;\n  6[\"Regroup\"];\n  3 -->|gene_families_tsv| 6;\n  7[\"Renormalize\"];\n  6 -->|output_table| 7;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "WGS Part In \"Analyses Of Metagenomics Data - The Global Picture\"",
-                "outputs": [],
-                "parent_id": "microbiome/general-tutorial",
-                "path": "topics/microbiome/tutorials/general-tutorial/workflows/wgs-worklow.ga",
+                "parent_id": "metabolomics/msi-analyte-distribution",
+                "path": "topics/metabolomics/tutorials/msi-analyte-distribution/workflows/wf_MSI_distribution.ga",
                 "tags": [
-                    "microbiome"
+                    "metabolomics"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "WGS Part In \"Analyses Of Metagenomics Data - The Global Picture\"",
-                "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-general-tutorial/versions/wgs-worklow",
-                "tutorial_id": "general-tutorial",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/general-tutorial/workflows/wgs-worklow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/general-tutorial/workflows/wgs-worklow.html",
+                "title": "MSI Workflow: spatial distribution",
+                "topic_id": "metabolomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/metabolomics-msi-analyte-distribution/versions/wf-msi-distribution",
+                "tutorial_id": "msi-analyte-distribution",
+                "url": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/msi-analyte-distribution/workflows/wf_MSI_distribution.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/msi-analyte-distribution/workflows/wf_MSI_distribution.html",
                 "version": 1,
-                "wfid": "microbiome-general-tutorial",
-                "wfname": "wgs-worklow",
-                "workflow": "wgs-worklow.ga",
+                "wfid": "metabolomics-msi-analyte-distribution",
+                "wfname": "wf-msi-distribution",
+                "workflow": "wf_MSI_distribution.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.9.9.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/humann2_regroup_table/humann2_regroup_table/0.9.9.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/humann2_renorm_table/humann2_renorm_table/0.9.9.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0"
+                    "Filter1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/2.6.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/2.6.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/2.6.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/2.6.0.0"
                 ],
-                "workflowhub_id": "1067"
+                "workflowhub_id": "1061"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.815875"
+        "zenodo_link": "https://zenodo.org/record/484496"
     },
     {
         "admin_install": {
@@ -136520,281 +140130,202 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "racon",
-                    "owner": "bgruening",
-                    "revisions": "aa39b19ca11e",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "racon",
-                    "owner": "bgruening",
-                    "revisions": "a199cd7ac344",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bandage",
-                    "owner": "iuc",
-                    "revisions": "067592b6b312",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bandage",
-                    "owner": "iuc",
-                    "revisions": "b2860df42e16",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gfa_to_fa",
-                    "owner": "iuc",
-                    "revisions": "49d6f8ef63b3",
-                    "tool_panel_section_label": "Convert Formats",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gfa_to_fa",
-                    "owner": "iuc",
-                    "revisions": "8e9d604e92f4",
-                    "tool_panel_section_label": "Convert Formats",
+                    "name": "camera_annotate",
+                    "owner": "lecorguille",
+                    "revisions": "512c2b701d96",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "miniasm",
-                    "owner": "iuc",
-                    "revisions": "8b6d0d85252b",
-                    "tool_panel_section_label": "Assembly",
+                    "name": "msnbase_readmsdata",
+                    "owner": "lecorguille",
+                    "revisions": "11ab2081bd4a",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "miniasm",
-                    "owner": "iuc",
-                    "revisions": "8dee0218ac7d",
-                    "tool_panel_section_label": "Assembly",
+                    "name": "xcms_export_samplemetadata",
+                    "owner": "lecorguille",
+                    "revisions": "94eb263cfab4",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "minimap2",
-                    "owner": "iuc",
-                    "revisions": "3f4d6399997b",
-                    "tool_panel_section_label": "Mapping",
+                    "name": "xcms_fillpeaks",
+                    "owner": "lecorguille",
+                    "revisions": "26d77e9ceb49",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "minimap2",
-                    "owner": "iuc",
-                    "revisions": "8c6cd2650d1f",
-                    "tool_panel_section_label": "Mapping",
+                    "name": "xcms_group",
+                    "owner": "lecorguille",
+                    "revisions": "d45a786cbc40",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "nanoplot",
-                    "owner": "iuc",
-                    "revisions": "645159bcee2d",
-                    "tool_panel_section_label": "Nanopore",
+                    "name": "xcms_merge",
+                    "owner": "lecorguille",
+                    "revisions": "5bd125a3f3b0",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "nanoplot",
-                    "owner": "iuc",
-                    "revisions": "edbb6c5028f5",
-                    "tool_panel_section_label": "Nanopore",
+                    "name": "xcms_plot_chromatogram",
+                    "owner": "lecorguille",
+                    "revisions": "024974037c4e",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "plasflow",
-                    "owner": "iuc",
-                    "revisions": "bda6012394f7",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "name": "xcms_retcor",
+                    "owner": "lecorguille",
+                    "revisions": "aa252eec9229",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "unicycler",
-                    "owner": "iuc",
-                    "revisions": "0a3a602cd1e3",
-                    "tool_panel_section_label": "Assembly",
+                    "name": "xcms_summary",
+                    "owner": "lecorguille",
+                    "revisions": "018a9771de28",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "unicycler",
-                    "owner": "iuc",
-                    "revisions": "9e3e80cc4ad4",
-                    "tool_panel_section_label": "Assembly",
+                    "name": "xcms_xcmsset",
+                    "owner": "lecorguille",
+                    "revisions": "b02d1992a43a",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "staramr",
-                    "owner": "nml",
-                    "revisions": "da787fc8b740",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "name": "idchoice",
+                    "owner": "melpetera",
+                    "revisions": "bb19b1d15732",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "staramr",
-                    "owner": "nml",
-                    "revisions": "2fd4d4c9c5c2",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "name": "intensity_checks",
+                    "owner": "melpetera",
+                    "revisions": "a31f3f802b2b",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: racon\n  owner: bgruening\n  revisions: aa39b19ca11e\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: racon\n  owner: bgruening\n  revisions: a199cd7ac344\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: '067592b6b312'\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: b2860df42e16\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfa_to_fa\n  owner: iuc\n  revisions: 49d6f8ef63b3\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfa_to_fa\n  owner: iuc\n  revisions: 8e9d604e92f4\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: miniasm\n  owner: iuc\n  revisions: 8b6d0d85252b\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: miniasm\n  owner: iuc\n  revisions: 8dee0218ac7d\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: 3f4d6399997b\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: 8c6cd2650d1f\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: 645159bcee2d\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: edbb6c5028f5\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: plasflow\n  owner: iuc\n  revisions: bda6012394f7\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unicycler\n  owner: iuc\n  revisions: 0a3a602cd1e3\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unicycler\n  owner: iuc\n  revisions: 9e3e80cc4ad4\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: staramr\n  owner: nml\n  revisions: da787fc8b740\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: staramr\n  owner: nml\n  revisions: 2fd4d4c9c5c2\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: camera_annotate\n  owner: lecorguille\n  revisions: 512c2b701d96\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msnbase_readmsdata\n  owner: lecorguille\n  revisions: 11ab2081bd4a\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_export_samplemetadata\n  owner: lecorguille\n  revisions: 94eb263cfab4\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_fillpeaks\n  owner: lecorguille\n  revisions: 26d77e9ceb49\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_group\n  owner: lecorguille\n  revisions: d45a786cbc40\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_merge\n  owner: lecorguille\n  revisions: 5bd125a3f3b0\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_plot_chromatogram\n  owner: lecorguille\n  revisions: '024974037c4e'\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_retcor\n  owner: lecorguille\n  revisions: aa252eec9229\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_summary\n  owner: lecorguille\n  revisions: '018a9771de28'\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_xcmsset\n  owner: lecorguille\n  revisions: b02d1992a43a\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: idchoice\n  owner: melpetera\n  revisions: bb19b1d15732\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: intensity_checks\n  owner: melpetera\n  revisions: a31f3f802b2b\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "nl",
-                "id": "willemdek11",
-                "joined": "2018-09",
-                "name": "Willem de Koning",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/willemdek11/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/willemdek11.json"
+                "id": "melpetera",
+                "joined": "2019-06",
+                "name": "M\u00e9lanie Petera",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/melpetera/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/melpetera.json"
+            },
+            {
+                "id": "jfrancoismartin",
+                "joined": "2019-06",
+                "name": "Jean-Fran\u00e7ois Martin",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jfrancoismartin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jfrancoismartin.json"
             },
             {
                 "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
+                    "elixir-europe"
                 ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
+                "elixir_node": "fr",
+                "id": "lecorguille",
                 "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+                "name": "Gildas Le Corguill\u00e9",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
+            },
+            {
+                "id": "workflow4metabolomics",
+                "joined": "2019-06",
+                "name": "Workflow4Metabolomics core team",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/workflow4metabolomics/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/workflow4metabolomics.json"
             }
         ],
-        "dir": "topics/microbiome/tutorials/plasmid-metagenomics-nanopore",
-        "edam_ontology": [
-            "topic_3837",
-            "topic_3305",
-            "topic_3174",
-            "topic_3301",
-            "topic_3324",
-            "topic_0080",
-            "topic_4013"
-        ],
+        "dir": "topics/metabolomics/tutorials/lcms-preprocessing",
         "edam_operation": [
-            "De-novo assembly",
-            "Sequence analysis",
-            "Box-Whisker plot plotting",
-            "Pairwise sequence alignment",
-            "Scatter plot plotting",
-            "Mapping assembly",
-            "Sequence assembly visualisation",
-            "Genome assembly",
-            "Aggregation"
-        ],
-        "edam_topic": [
-            "Metagenomic sequencing",
-            "Public health and epidemiology",
-            "Metagenomics",
-            "Microbiology",
-            "Infectious disease",
-            "Sequence analysis",
-            "Antimicrobial Resistance"
+            "Peak detection",
+            "Label-free quantification",
+            "Mass spectrum visualisation",
+            "Validation",
+            "Filtering",
+            "Chromatogram visualisation",
+            "Chromatographic alignment"
         ],
+        "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "microbiome/plasmid-metagenomics-nanopore",
+        "id": "metabolomics/lcms-preprocessing",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
+            "UseGalaxy.eu",
+            "UseGalaxy.no"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Minimap2, Miniasm, and Racon can be used for quickly assembling Nanopore data",
-            "Unicycler can be used to optimize settings of assembly tools",
-            "Nanopore sequencing is useful for reconstruction of genomes",
-            "Antimicrobial resistance genes are detectable after fast assembly",
-            "The CARD database is a useful resource describing antibiotic resistance genes"
+            "To process untargeted LC-MS metabolomic data preprocessing, you need a large variety of steps and tools.",
+            "Although main steps are standard, various ways to combine and to set parameters for tools exist, depending on your data.",
+            "Resources are available in Galaxy, but do not forget that you need appropriate knowledge to perform a relevant analysis."
         ],
         "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Perform Quality control on your reads",
-            "Assemble a genome with Minimap2/Miniasm/Racon",
-            "Determine the structure of the genome(s)",
-            "Scan for antimicrobial resistance genes with Staramr"
+            "To comprehend the diversity of steps necessary to perform untargeted LC-MS metabolomic preprocessing.",
+            "To get familiar with the way to use XCMS-based Galaxy modules dedicated to LC-MS data preprocessing.",
+            "To evaluate the potential of a workflow approach when dealing with LC-MS preprocessing."
         ],
-        "pageviews": 1752,
-        "pub_date": "2019-06-25",
+        "pageviews": 5905248,
+        "pub_date": "2020-02-04",
         "questions": [
-            "How do I assemble a genome with Nanopore data?",
-            "How do I get more information about the structure of the genomes?",
-            "How do I get more information about the antimicrobial resistance genes?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "bebatut"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "45M",
-                "speakers": [
-                    "willemdek11"
-                ],
-                "youtube_id": "ECIl8ZU1Wko"
-            }
-        ],
-        "redirect_from": [
-            "/topics/metagenomics/tutorials/plasmid-metagenomics-nanopore/tutorial",
-            "/short/microbiome/plasmid-metagenomics-nanopore",
-            "/short/T00209",
-            "/short/T00394"
+            "What are the main steps of untargeted LC-MS data preprocessing for metabolomic analyses?",
+            "How to conduct metabolomic data preprocessing using Galaxy?"
         ],
-        "short_id": "T00394",
+        "short_id": "T00197",
         "short_tools": [
-            "nanoplot",
-            "gfa_to_fa",
-            "racon",
-            "PlasFlow",
-            "miniasm",
-            "minimap2",
-            "staramr_search",
-            "bandage_image",
-            "unicycler"
+            "msnbase_readmsdata",
+            "idchoice",
+            "abims_xcms_fillPeaks",
+            "abims_xcms_xcmsSet",
+            "abims_CAMERA_annotateDiffreport",
+            "xcms_merge",
+            "xcms_plot_chromatogram",
+            "intens_check",
+            "abims_xcms_summary",
+            "xcms_export_samplemetadata",
+            "abims_xcms_group",
+            "abims_xcms_retcor"
         ],
-        "slides": false,
+        "slides": true,
         "slides_recordings": false,
-        "subtopic": "metabarcoding",
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 }
             ],
@@ -136804,153 +140335,179 @@
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "time_estimation": "3h",
+        "title": "Mass spectrometry: LC-MS preprocessing with XCMS",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.6+camera1.48.0-galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_export_samplemetadata/xcms_export_samplemetadata/3.12.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.12.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_summary/abims_xcms_summary/3.12.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/melpetera/idchoice/idchoice/19.12",
+            "toolshed.g2.bx.psu.edu/repos/melpetera/intensity_checks/intens_check/1.2.8"
+        ],
+        "topic_name": "metabolomics",
+        "topic_name_human": "Metabolomics",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "lcms-preprocessing",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.json"
+        },
+        "version": 13,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 294,
+        "visitors": 2138501,
+        "zenodo_link": "https://zenodo.org/record/3757956"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/introduction/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "fr",
+                "id": "lecorguille",
+                "joined": "2017-09",
+                "name": "Gildas Le Corguill\u00e9",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/lecorguille.json"
+            },
+            {
+                "github": false,
+                "id": "cecilecanlet",
+                "joined": "2018-09",
+                "name": "C\u00e9cile Canlet",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cecilecanlet/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/cecilecanlet.json"
+            }
+        ],
+        "dir": "topics/metabolomics/tutorials/introduction",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": false,
+        "id": "metabolomics/introduction",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "layout": "introduction_slides",
+        "license": "CC-BY-4.0",
+        "logo": "GTN",
+        "mod_date": "2023-01-12",
+        "pageviews": 5897186,
+        "priority": 1,
+        "pub_date": "2018-11-20",
+        "redirect_from": [
+            "/topics/metabolomics/slides/introduction",
+            "/short/metabolomics/introduction/slides",
+            "/short/S00076"
+        ],
+        "short_id": "S00076",
+        "short_tools": [],
+        "slides": true,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.org (Main)",
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 },
                 {
+                    "human": "Galaxy Australia",
+                    "id": "au",
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
-        "tags": [
-            "nanopore",
-            "plasmids",
-            "assembly",
-            "amr",
-            "microgalaxy"
-        ],
-        "time_estimation": "3h",
-        "title": "Antibiotic resistance detection",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.3.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17",
-            "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/plasflow/PlasFlow/1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.7.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
-            "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.5.1",
-            "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2"
-        ],
-        "topic_name": "microbiome",
-        "topic_name_human": "Microbiome",
+        "title": "Introduction to Metabolomics",
+        "tools": [],
+        "topic_name": "metabolomics",
+        "topic_name_human": "Metabolomics",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "plasmid-metagenomics-nanopore",
+        "tutorial_name": "introduction",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/metabolomics/tutorials/introduction/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/introduction/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/introduction/slides.json"
         },
-        "version": 4,
+        "version": 1,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 241,
-        "visitors": 1130,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Antibiotic resistance detection",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nPlasmids\"]\n  1[label=\"NanoPlot\"]\n  0 -> 1 [label=\"output\"]\n  10[label=\"NanoPlot\"]\n  9 -> 10 [label=\"out_fa\"]\n  11[label=\"Map with minimap2\"]\n  0 -> 11 [label=\"output\"]\n  9 -> 11 [label=\"out_fa\"]\n  12[label=\"Racon\"]\n  9 -> 12 [label=\"out_fa\"]\n  11 -> 12 [label=\"alignment_output\"]\n  0 -> 12 [label=\"output\"]\n  2[label=\"Map with minimap2\"]\n  0 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Create assemblies with Unicycler\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"miniasm\"]\n  2 -> 4 [label=\"alignment_output\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Bandage Image\"]\n  3 -> 5 [label=\"assembly_graph\"]\n  6[label=\"PlasFlow\"]\n  3 -> 6 [label=\"assembly\"]\n  7[label=\"staramr\"]\n  3 -> 7 [label=\"assembly\"]\n  8[label=\"Bandage Image\"]\n  4 -> 8 [label=\"gfa\"]\n  9[label=\"GFA to FASTA\"]\n  4 -> 9 [label=\"gfa\"]\n}",
-                "history": [
-                    {
-                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
-                        "message": "Rename metagenomics topic to microbiome",
-                        "num": 1,
-                        "short_hash": "0e0a2f2cc",
-                        "unix": "1704901629"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "Plasmids",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 173,
-                            "top": 696
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "348dcd93-2d40-4bdd-90f4-b321a1bd901d",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nPlasmids\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"NanoPlot\"];\n  0 -->|output| 1;\n  10[\"NanoPlot\"];\n  9 -->|out_fa| 10;\n  11[\"Map with minimap2\"];\n  0 -->|output| 11;\n  9 -->|out_fa| 11;\n  12[\"Racon\"];\n  9 -->|out_fa| 12;\n  11 -->|alignment_output| 12;\n  0 -->|output| 12;\n  2[\"Map with minimap2\"];\n  0 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Create assemblies with Unicycler\"];\n  0 -->|output| 3;\n  4[\"miniasm\"];\n  2 -->|alignment_output| 4;\n  0 -->|output| 4;\n  5[\"Bandage Image\"];\n  3 -->|assembly_graph| 5;\n  6[\"PlasFlow\"];\n  3 -->|assembly| 6;\n  7[\"staramr\"];\n  3 -->|assembly| 7;\n  8[\"Bandage Image\"];\n  4 -->|gfa| 8;\n  9[\"GFA to FASTA\"];\n  4 -->|gfa| 9;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Copy Of GTN Training - Antibiotic Resistance Detection",
-                "outputs": [],
-                "parent_id": "microbiome/plasmid-metagenomics-nanopore",
-                "path": "topics/microbiome/tutorials/plasmid-metagenomics-nanopore/workflows/Workflow-plasmid-metagenomics-nanopore.ga",
-                "tags": [
-                    "microbiome"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Copy Of GTN Training - Antibiotic Resistance Detection",
-                "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-plasmid-metagenomics-nanopore/versions/workflow-plasmid-metagenomics-nanopore",
-                "tutorial_id": "plasmid-metagenomics-nanopore",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/workflows/Workflow-plasmid-metagenomics-nanopore.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/workflows/Workflow-plasmid-metagenomics-nanopore.html",
-                "version": 1,
-                "wfid": "microbiome-plasmid-metagenomics-nanopore",
-                "wfname": "workflow-plasmid-metagenomics-nanopore",
-                "workflow": "Workflow-plasmid-metagenomics-nanopore.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.3.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/plasflow/PlasFlow/1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.7.0",
-                    "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.5.1"
-                ],
-                "workflowhub_id": "1107"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.3247504"
+        "visit_duration": 152,
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -136959,583 +140516,176 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "taxonomy_krona_chart",
-                    "owner": "crs4",
-                    "revisions": "1334cb4c6b68",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "taxonomy_krona_chart",
-                    "owner": "crs4",
-                    "revisions": "e9005d1f3cfd",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "name": "multivariate",
+                    "owner": "ethevenot",
+                    "revisions": "5526f8258e8a",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bracken",
-                    "owner": "iuc",
-                    "revisions": "79450f7fd718",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "name": "qualitymetrics",
+                    "owner": "ethevenot",
+                    "revisions": "acdf51018708",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "kraken2",
-                    "owner": "iuc",
-                    "revisions": "20e2f64aa1fe",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "name": "normalization",
+                    "owner": "marie-tremblay-metatoul",
+                    "revisions": "221cbd549c40",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "kraken_biom",
-                    "owner": "iuc",
-                    "revisions": "b582a159bb10",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "name": "batchcorrection",
+                    "owner": "melpetera",
+                    "revisions": "23314e1192d4",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "krakentools_kreport2krona",
-                    "owner": "iuc",
-                    "revisions": "88d274322340",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                },
+                {
+                    "name": "generic_filter",
+                    "owner": "melpetera",
+                    "revisions": "cfd7c4aa5c26",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "metaphlan",
-                    "owner": "iuc",
-                    "revisions": "1a6cdf55390f",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "name": "intensity_checks",
+                    "owner": "melpetera",
+                    "revisions": "a31f3f802b2b",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: taxonomy_krona_chart\n  owner: crs4\n  revisions: 1334cb4c6b68\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: taxonomy_krona_chart\n  owner: crs4\n  revisions: e9005d1f3cfd\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bracken\n  owner: iuc\n  revisions: 79450f7fd718\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: 20e2f64aa1fe\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken_biom\n  owner: iuc\n  revisions: b582a159bb10\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: krakentools_kreport2krona\n  owner: iuc\n  revisions: 88d274322340\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaphlan\n  owner: iuc\n  revisions: 1a6cdf55390f\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/taxonomic-profiling/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "sophia120199",
-                "bebatut",
-                "paulzierep"
-            ],
-            "funding": [
-                "gallantries"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: multivariate\n  owner: ethevenot\n  revisions: 5526f8258e8a\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qualitymetrics\n  owner: ethevenot\n  revisions: acdf51018708\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: normalization\n  owner: marie-tremblay-metatoul\n  revisions: 221cbd549c40\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: batchcorrection\n  owner: melpetera\n  revisions: 23314e1192d4\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: generic_filter\n  owner: melpetera\n  revisions: cfd7c4aa5c26\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: intensity_checks\n  owner: melpetera\n  revisions: a31f3f802b2b\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.json",
         "contributors": [
             {
-                "id": "sophia120199",
-                "joined": "2023-04",
-                "name": "Sophia Hampe",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/sophia120199/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/sophia120199.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "email": "zierep@informatik.uni-freiburg.de",
-                "id": "paulzierep",
-                "joined": "2023-02",
-                "name": "Paul Zierep",
-                "orcid": "0000-0003-2982-388X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json"
+                "id": "melpetera",
+                "joined": "2019-06",
+                "name": "M\u00e9lanie Petera",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/melpetera/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/melpetera.json"
             },
             {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+                "id": "workflow4metabolomics",
+                "joined": "2019-06",
+                "name": "Workflow4Metabolomics core team",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/workflow4metabolomics/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/workflow4metabolomics.json"
             }
         ],
-        "dir": "topics/microbiome/tutorials/taxonomic-profiling",
-        "edam_ontology": [
-            "topic_3174",
-            "topic_3697",
-            "topic_0637",
-            "topic_0080"
-        ],
-        "edam_operation": [
-            "Visualisation",
-            "Nucleic acid sequence analysis",
-            "Taxonomic classification",
-            "Phylogenetic tree analysis",
-            "Statistical calculation",
-            "Aggregation"
-        ],
-        "edam_topic": [
-            "Metagenomics",
-            "Microbial ecology",
-            "Taxonomy",
-            "Sequence analysis"
-        ],
+        "dir": "topics/metabolomics/tutorials/lcms-dataprocessing",
+        "edam_operation": [],
+        "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.fr"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "microbiome/taxonomic-profiling",
+        "id": "metabolomics/lcms-dataprocessing",
         "inexact_supported_servers": [
-            "UseGalaxy.fr",
-            "UseGalaxy.org.au"
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.no"
         ],
         "js_requirements": {
-            "mathjax": 4920,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "There are 3 different types of taxonomic assignment (genome, gene or k-mer based)",
-            "Kraken or MetaPhlAn can be used in Galaxy for taxonomic assignment",
-            "Visualization of community profiles can be done using Krona or Pavian",
-            "The taxonomic classification tool to use depends on the data"
+            "Data processing is a key step in untargeted Metabolomics analyses. The question of data filtering and correction must be addressed in all projects, even thought in some cases it may lead to the decision of no action on data. In particular, blank filtering, pool variation study and signal drift correction are common aspects to consider when dealing with LC-MS.",
+            "Although some main steps are standard, various ways to combine tools exist. Remember that depending on your context (type of samples, protocol specificities...) specific filters/normalisations may be needed, independently of standards ones.",
+            "A variety of tools is available in Galaxy, but do not forget that you need appropriate knowledge to decide what to use depending on your data."
         ],
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Explain what taxonomic assignment is",
-            "Explain how taxonomic assignment works",
-            "Apply Kraken and MetaPhlAn to assign taxonomic labels",
-            "Apply Krona and Pavian to visualize results of assignment and understand the output",
-            "Identify taxonomic classification tool that fits best depending on their data"
+            "To comprehend the key role of data processing.",
+            "To comprehend the diversity of steps necessary to perform untargeted LC-MS metabolomic data processing.",
+            "To be familiar with the \"identify then perform\" approach necessary to deploy relevant data processing strategies."
         ],
-        "pageviews": 4993,
-        "pub_date": "2023-05-03",
+        "pageviews": 2727,
+        "pub_date": "2021-12-14",
         "questions": [
-            "Which species (or genera, families, ...) are present in my sample?",
-            "What are the different approaches and tools to get the community profile of my sample?",
-            "How can we visualize and compare community profiles?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "sophia120199"
-                ],
-                "date": "2023-05-16",
-                "galaxy_version": "23.01",
-                "length": "1H15M",
-                "speakers": [
-                    "bebatut"
-                ],
-                "youtube_id": "jszMnBKm6ig"
-            }
-        ],
-        "redirect_from": [
-            "/topics/metagenomics/tutorials/taxonomic-profiling/tutorial",
-            "/short/microbiome/taxonomic-profiling",
-            "/short/T00338",
-            "/short/T00395"
+            "Why should one consider performing data processing steps when dealing with Metabolomics data?",
+            "How to conduct LCMS-based untargeted metabolomic data processing using Galaxy?"
         ],
-        "short_id": "T00395",
+        "short_id": "T00196",
         "short_tools": [
-            "est_abundance",
-            "krakentools_kreport2krona",
-            "__UNZIP_COLLECTION__",
-            "interactive_tool_phinch",
-            "taxonomy_krona_chart",
-            "interactive_tool_pavian",
-            "kraken2",
-            "metaphlan",
-            "kraken_biom"
+            "Batch_correction",
+            "quality_metrics",
+            "Multivariate",
+            "intens_check",
+            "normalization",
+            "generic_filter"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "metagenomics",
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
                 }
             ],
             "inexact": [
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
                 }
             ]
         },
         "symlink": null,
-        "tags": [
-            "metagenomics",
-            "taxonomic profiling",
-            "microgalaxy"
-        ],
         "time_estimation": "2H",
-        "title": "Taxonomic Profiling and Visualization of Metagenomic Data",
+        "title": "Mass spectrometry: LC-MS data processing",
         "tools": [
-            "__UNZIP_COLLECTION__",
-            "interactive_tool_pavian",
-            "interactive_tool_phinch",
-            "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1",
-            "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.7+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/kraken_biom/kraken_biom/1.2.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy1"
+            "toolshed.g2.bx.psu.edu/repos/ethevenot/multivariate/Multivariate/2.3.10",
+            "toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/quality_metrics/2.2.8",
+            "toolshed.g2.bx.psu.edu/repos/marie-tremblay-metatoul/normalization/normalization/1.0.7",
+            "toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Batch_correction/3.0.0",
+            "toolshed.g2.bx.psu.edu/repos/melpetera/generic_filter/generic_filter/2020.01",
+            "toolshed.g2.bx.psu.edu/repos/melpetera/intensity_checks/intens_check/1.2.8"
         ],
-        "topic_name": "microbiome",
-        "topic_name_human": "Microbiome",
+        "topic_name": "metabolomics",
+        "topic_name_human": "Metabolomics",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "taxonomic-profiling",
+        "tutorial_name": "lcms-dataprocessing",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/taxonomic-profiling/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/taxonomic-profiling/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.json"
         },
-        "version": 4,
+        "version": 7,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 117,
-        "visitors": 3655,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0001-9852-1987",
-                        "name": "B\u00e9r\u00e9nice Batut"
-                    }
-                ],
-                "description": "Taxonomic Profiling and Visualization of Metagenomic Data",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nraw-reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmetadata\"]\n  2[label=\"Unzip collection\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Kraken2\"]\n  0 -> 3 [label=\"output\"]\n  k3cc726a3208649859cf97bbbb13e18c5[color=lightseagreen,label=\"Output\\nkraken_report\"]\n  3 -> k3cc726a3208649859cf97bbbb13e18c5\n  4[label=\"MetaPhlAn\"]\n  2 -> 4 [label=\"forward\"]\n  2 -> 4 [label=\"reverse\"]\n  k97a89be1a9f647ecb5f19ccb068b4a57[color=lightseagreen,label=\"Output\\nmetaphlan_output\"]\n  4 -> k97a89be1a9f647ecb5f19ccb068b4a57\n  5[label=\"Krakentools: Convert kraken report file\"]\n  3 -> 5 [label=\"report_output\"]\n  ke610aa6c87e049a9978d2dc3ff38bb75[color=lightseagreen,label=\"Output\\nkrakentool_report\"]\n  5 -> ke610aa6c87e049a9978d2dc3ff38bb75\n  6[label=\"Kraken-biom\"]\n  3 -> 6 [label=\"report_output\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"Pavian\"]\n  3 -> 7 [label=\"report_output\"]\n  8[label=\"Estimate Abundance at Taxonomic Level\"]\n  3 -> 8 [label=\"report_output\"]\n  9[label=\"Krona pie chart\"]\n  4 -> 9 [label=\"krona_output_file\"]\n  10[label=\"Krona pie chart\"]\n  5 -> 10 [label=\"output\"]\n  11[label=\"Phinch Visualisation\"]\n  6 -> 11 [label=\"biomOutput\"]\n}",
-                "history": [
-                    {
-                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
-                        "message": "Rename metagenomics topic to microbiome",
-                        "num": 1,
-                        "short_hash": "0e0a2f2cc",
-                        "unix": "1704901629"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "raw-reads"
-                            }
-                        ],
-                        "label": "raw-reads",
-                        "name": "raw-reads",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 32
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"raw-reads\",\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "8ceaae85-1ed7-4488-b839-53d36e642378",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "metadata"
-                            }
-                        ],
-                        "label": "metadata",
-                        "name": "metadata",
-                        "outputs": [],
-                        "position": {
-                            "left": 35.48228574271107,
-                            "top": 575.2289046420843
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"metadata\", \"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "715bbeb3-cb9a-49dd-a9c5-1f184f3eb34a",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nraw-reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nmetadata\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Unzip collection\"];\n  0 -->|output| 2;\n  3[\"Kraken2\"];\n  0 -->|output| 3;\n  3cc726a3-2086-4985-9cf9-7bbbb13e18c5[\"Output\\nkraken_report\"];\n  3 --> 3cc726a3-2086-4985-9cf9-7bbbb13e18c5;\n  style 3cc726a3-2086-4985-9cf9-7bbbb13e18c5 stroke:#2c3143,stroke-width:4px;\n  4[\"MetaPhlAn\"];\n  2 -->|forward| 4;\n  2 -->|reverse| 4;\n  97a89be1-a9f6-47ec-b5f1-9ccb068b4a57[\"Output\\nmetaphlan_output\"];\n  4 --> 97a89be1-a9f6-47ec-b5f1-9ccb068b4a57;\n  style 97a89be1-a9f6-47ec-b5f1-9ccb068b4a57 stroke:#2c3143,stroke-width:4px;\n  5[\"Krakentools: Convert kraken report file\"];\n  3 -->|report_output| 5;\n  e610aa6c-87e0-49a9-978d-2dc3ff38bb75[\"Output\\nkrakentool_report\"];\n  5 --> e610aa6c-87e0-49a9-978d-2dc3ff38bb75;\n  style e610aa6c-87e0-49a9-978d-2dc3ff38bb75 stroke:#2c3143,stroke-width:4px;\n  6[\"Kraken-biom\"];\n  3 -->|report_output| 6;\n  1 -->|output| 6;\n  7[\"Pavian\"];\n  3 -->|report_output| 7;\n  8[\"Estimate Abundance at Taxonomic Level\"];\n  3 -->|report_output| 8;\n  9[\"Krona pie chart\"];\n  4 -->|krona_output_file| 9;\n  10[\"Krona pie chart\"];\n  5 -->|output| 10;\n  11[\"Phinch Visualisation\"];\n  6 -->|biomOutput| 11;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Taxonomic Profiling and Visualization of Metagenomic Data",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "single_paired|input_pair": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Kraken2",
-                        "outputs": [
-                            {
-                                "name": "report_output",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "output",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 279.9980390107984,
-                            "top": 464
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "e674066930b2",
-                            "name": "kraken2",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"confidence\": \"0.1\", \"kraken2_database\": \"2022-09-04T165121Z_standard_prebuilt_pluspf_2022-06-07\", \"min_base_quality\": \"0\", \"minimum_hit_groups\": \"2\", \"quick\": false, \"report\": {\"create_report\": true, \"use_mpa_style\": false, \"report_zero_counts\": false, \"report_minimizer_data\": false}, \"single_paired\": {\"single_paired_selector\": \"collection\", \"__current_case__\": 0, \"input_pair\": {\"__class__\": \"ConnectedValue\"}}, \"split_reads\": false, \"use_names\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.1+galaxy1",
-                        "type": "tool",
-                        "uuid": "ec3d15fe-c551-4986-b56b-6f92fe781a4e",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "kraken_report",
-                                "output_name": "report_output",
-                                "uuid": "3cc726a3-2086-4985-9cf9-7bbbb13e18c5"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy1",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "inputs|in|raw_in|in_f": {
-                                "id": 2,
-                                "output_name": "forward"
-                            },
-                            "inputs|in|raw_in|in_r": {
-                                "id": 2,
-                                "output_name": "reverse"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool MetaPhlAn",
-                                "name": "analysis"
-                            }
-                        ],
-                        "label": null,
-                        "name": "MetaPhlAn",
-                        "outputs": [
-                            {
-                                "name": "output_file",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "bowtie2out",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "sam_output_file",
-                                "type": "sam"
-                            },
-                            {
-                                "name": "biom_output_file",
-                                "type": "biom1"
-                            },
-                            {
-                                "name": "krona_output_file",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 559.9960780215968,
-                            "top": 0
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "1a6cdf55390f",
-                            "name": "metaphlan",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"analysis\": {\"analysis_type\": {\"t\": \"rel_ab\", \"__current_case__\": 0, \"tax_lev\": {\"tax_lev\": \"a\", \"__current_case__\": 0, \"split_levels\": false}}, \"min_cu_len\": \"2000\", \"min_alignment_len\": null, \"organism_profiling\": [\"add_viruses\"], \"stat\": \"tavg_g\", \"stat_q\": \"0.2\", \"perc_nonzero\": \"0.33\", \"ignore_markers\": {\"__class__\": \"RuntimeValue\"}, \"avoid_disqm\": true}, \"inputs\": {\"in\": {\"selector\": \"raw\", \"__current_case__\": 0, \"raw_in\": {\"selector\": \"paired\", \"__current_case__\": 2, \"in_f\": {\"__class__\": \"ConnectedValue\"}, \"in_r\": {\"__class__\": \"ConnectedValue\"}}, \"read_min_len\": \"70\", \"mapping\": {\"bt2_ps\": \"very-sensitive\", \"min_mapq_val\": \"5\"}}, \"db\": {\"db_selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": \"mpa_vOct22_CHOCOPhlAnSGB_202212-03042023\"}}, \"out\": {\"sample_id_key\": \"SampleID\", \"sample_id\": \"Metaphlan_Analysis\", \"use_group_representative\": false, \"legacy_output\": false, \"CAMI_format_output\": false, \"unknown_estimation\": false, \"krona_output\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.0.6+galaxy1",
-                        "type": "tool",
-                        "uuid": "12d35121-341e-46da-aa4c-c48d4318bf6d",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "metaphlan_output",
-                                "output_name": "output_file",
-                                "uuid": "97a89be1-a9f6-47ec-b5f1-9ccb068b4a57"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "report": {
-                                "id": 3,
-                                "output_name": "report_output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Krakentools: Convert kraken report file",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 559.9960852997306,
-                            "top": 459
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "88d274322340",
-                            "name": "krakentools_kreport2krona",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"intermediate_ranks\": false, \"report\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2+galaxy0",
-                        "type": "tool",
-                        "uuid": "5de62f93-4e3a-4ea6-92c6-c3afcc088bdc",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "krakentool_report",
-                                "output_name": "output",
-                                "uuid": "e610aa6c-87e0-49a9-978d-2dc3ff38bb75"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "microbiome/taxonomic-profiling",
-                "path": "topics/microbiome/tutorials/taxonomic-profiling/workflows/main-workflow.ga",
-                "tags": [
-                    "microbiome"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "Taxonomic Profiling and Visualization of Metagenomic Data",
-                "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-taxonomic-profiling/versions/main-workflow",
-                "tutorial_id": "taxonomic-profiling",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/taxonomic-profiling/workflows/main-workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/taxonomic-profiling/workflows/main-workflow.html",
-                "version": 1,
-                "wfid": "microbiome-taxonomic-profiling",
-                "wfname": "main-workflow",
-                "workflow": "main-workflow.ga",
-                "workflow_tools": [
-                    "__UNZIP_COLLECTION__",
-                    "interactive_tool_pavian",
-                    "interactive_tool_phinch",
-                    "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.7+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/kraken_biom/kraken_biom/1.2.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy1"
-                ],
-                "workflowhub_id": "1095"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/7871630"
+        "visit_duration": 113,
+        "visitors": 1987,
+        "zenodo_link": "https://zenodo.org/record/5179809"
     },
     {
         "admin_install": {
@@ -137544,143 +140694,124 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "krakentools_alpha_diversity",
-                    "owner": "iuc",
-                    "revisions": "bab112ba9d62",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "name": "msnbase_readmsdata",
+                    "owner": "lecorguille",
+                    "revisions": "11ab2081bd4a",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "krakentools_beta_diversity",
-                    "owner": "iuc",
-                    "revisions": "c254d75b8b67",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "name": "xcms_fillpeaks",
+                    "owner": "lecorguille",
+                    "revisions": "26d77e9ceb49",
+                    "tool_panel_section_label": "Metabolomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "xcms_group",
+                    "owner": "lecorguille",
+                    "revisions": "d45a786cbc40",
+                    "tool_panel_section_label": "Metabolomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "xcms_merge",
+                    "owner": "lecorguille",
+                    "revisions": "5bd125a3f3b0",
+                    "tool_panel_section_label": "Metabolomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "xcms_xcmsset",
+                    "owner": "lecorguille",
+                    "revisions": "b02d1992a43a",
+                    "tool_panel_section_label": "Metabolomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: krakentools_alpha_diversity\n  owner: iuc\n  revisions: bab112ba9d62\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: krakentools_beta_diversity\n  owner: iuc\n  revisions: c254d75b8b67\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/diversity/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "sophia120199",
-                "bebatut",
-                "paulzierep"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: msnbase_readmsdata\n  owner: lecorguille\n  revisions: 11ab2081bd4a\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_fillpeaks\n  owner: lecorguille\n  revisions: 26d77e9ceb49\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_group\n  owner: lecorguille\n  revisions: d45a786cbc40\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_merge\n  owner: lecorguille\n  revisions: 5bd125a3f3b0\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xcms_xcmsset\n  owner: lecorguille\n  revisions: b02d1992a43a\n  tool_panel_section_label: Metabolomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/gcms/tutorial.json",
         "contributors": [
             {
-                "id": "sophia120199",
-                "joined": "2023-04",
-                "name": "Sophia Hampe",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/sophia120199/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/sophia120199.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "email": "zierep@informatik.uni-freiburg.de",
-                "id": "paulzierep",
-                "joined": "2023-02",
-                "name": "Paul Zierep",
-                "orcid": "0000-0003-2982-388X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json"
+                "id": "jsaintvanne",
+                "joined": "2020-01",
+                "name": "Julien Saint-Vanne",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jsaintvanne/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jsaintvanne.json"
             }
         ],
-        "dir": "topics/microbiome/tutorials/diversity",
-        "draft": false,
+        "dir": "topics/metabolomics/tutorials/gcms",
+        "draft": true,
         "edam_operation": [
-            "Visualisation",
-            "Aggregation"
+            "Peak detection",
+            "Label-free quantification",
+            "Mass spectrum visualisation",
+            "Validation",
+            "Filtering",
+            "Chromatogram visualisation",
+            "Chromatographic alignment"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "Galaxy@Pasteur",
-            "GalaxyTrakr",
             "UseGalaxy.cz",
             "UseGalaxy.eu",
             "UseGalaxy.fr",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
+            "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "microbiome/diversity",
-        "inexact_supported_servers": [],
+        "id": "metabolomics/gcms",
+        "inexact_supported_servers": [
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
+        ],
         "js_requirements": {
-            "mathjax": 8337,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "There are 2 different types of diversity metrics (\u03b1 and \u03b2 diversity)",
-            "Krakentools can be used in Galaxy for calculating the diversity"
+            "Have a good file containing all your peaks during the first stopover",
+            "Find all your unknowns in your datas",
+            "Find your stanards if you have some"
         ],
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-06",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Explain what taxonomic diversity is",
-            "Explain different metrics to calculate \u03b1 and \u03b2 diversity",
-            "Apply Krakentools to calculate \u03b1 and \u03b2 diversity and understand the output"
+            "To be sure you have already comprehend the diversity of MS pre-processing analysis.",
+            "To learn the principal functions of metaMS package through Galaxy.",
+            "To evaluate the potential of this new GC-MS workflow for GC-MS metabolomic analysis."
         ],
-        "pageviews": 52,
-        "pub_date": "2024-08-01",
+        "pageviews": 2045,
+        "pub_date": "2021-09-22",
         "questions": [
-            "How many different taxons are present in my sample? How do I additionally take their relative abundance into account?",
-            "How similar or how dissimilar are my samples in term of taxonomic diversity?",
-            "What are the different metrics used to calculate the taxonomic diversity of my samples?"
+            "What are the main steps of GC-MS datas processing for metabolomic analysis ?",
+            "How te be able to annotate the maximum of unknowns using Galaxy ?"
         ],
-        "short_id": "T00447",
+        "requirements": [
+            {
+                "topic_name": "metabolomics",
+                "tutorials": [
+                    "lcms"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00194",
         "short_tools": [
-            "krakentools_beta_diversity",
-            "krakentools_alpha_diversity"
+            "msnbase_readmsdata",
+            "abims_xcms_group",
+            "abims_xcms_fillPeaks",
+            "xcms_merge",
+            "abims_xcms_xcmsSet"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "metagenomics",
         "supported_servers": {
             "exact": [
-                {
-                    "name": "Galaxy@Pasteur",
-                    "url": "https://galaxy.pasteur.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -137700,172 +140831,259 @@
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
                 }
-            ],
-            "inexact": []
+            ]
         },
         "symlink": null,
         "tags": [
-            "metagenomics",
-            "diversity"
+            "work-in-progress"
         ],
-        "time_estimation": "20M",
-        "title": "Calculating \u03b1 and \u03b2 diversity from microbiome taxonomic data",
+        "time_estimation": "2H",
+        "title": "Mass spectrometry : GC-MS analysis with metaMS package",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_alpha_diversity/krakentools_alpha_diversity/1.2+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_beta_diversity/krakentools_beta_diversity/1.2+galaxy1"
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy0"
         ],
-        "topic_name": "microbiome",
-        "topic_name_human": "Microbiome",
+        "topic_name": "metabolomics",
+        "topic_name_human": "Metabolomics",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "diversity",
+        "tutorial_name": "gcms",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/diversity/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/metabolomics/tutorials/gcms/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/diversity/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/diversity/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/gcms/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/metabolomics/tutorials/gcms/tutorial.json"
         },
-        "version": 4,
+        "version": 7,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 289,
-        "visitors": 40,
-        "workflows": [
+        "visit_duration": 104,
+        "visitors": 1190,
+        "zenodo_link": "https://zenodo.org/record/3244991"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/introduction/tutorial.json",
+        "contributors": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0003-2982-388X",
-                        "name": "Paul Zierep"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "NA",
-                        "name": "Sophia Hampe"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0001-9852-1987",
-                        "name": "B\u00e9r\u00e9nice Batut"
-                    }
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
                 ],
-                "description": "Calculating diversity from bracken output",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": {
-                        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
-                    },
-                    "subworkflows": false
+                "email": "zierep@informatik.uni-freiburg.de",
+                "id": "paulzierep",
+                "joined": "2023-02",
+                "name": "Paul Zierep",
+                "orcid": "0000-0003-2982-388X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  1[label=\"Krakentools: Calculates alpha diversity\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Krakentools: Calculates alpha diversity\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Krakentools: Calculates alpha diversity\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Krakentools: Calculates alpha diversity\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Krakentools: Calculates alpha diversity\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Krakentools: calculates beta diversity Bray-Curtis dissimilarity\"]\n  0 -> 6 [label=\"output\"]\n}",
-                "history": [
-                    {
-                        "hash": "e548ec8fcbcdf6978839bbd7fb0cbad8724978af",
-                        "message": "add orcid to WF",
-                        "num": 5,
-                        "short_hash": "e548ec8fc",
-                        "unix": "1722843023"
-                    },
-                    {
-                        "hash": "7e39380705c94841458f4826b03705b6aaf891e0",
-                        "message": "add license, fix alpha div formula, add subsections",
-                        "num": 4,
-                        "short_hash": "7e3938070",
-                        "unix": "1722841724"
-                    },
-                    {
-                        "hash": "d448f8052a7b897e44d2afb4a2ffe9053ab8b316",
-                        "message": "update wf creator",
-                        "num": 3,
-                        "short_hash": "d448f8052",
-                        "unix": "1722839579"
-                    },
-                    {
-                        "hash": "c0ff830e1929507fb3ad36b646990b1bcca4e748",
-                        "message": "fix workflow",
-                        "num": 2,
-                        "short_hash": "c0ff830e1",
-                        "unix": "1722519174"
-                    },
-                    {
-                        "hash": "cd4066fc9a27c98bc2f6273e8cd7d2672163a425",
-                        "message": "add workflow",
-                        "num": 1,
-                        "short_hash": "cd4066fc9",
-                        "unix": "1722518283"
-                    }
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
                 ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Input Dataset Collection"
-                            }
-                        ],
-                        "label": "Input Dataset Collection",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 340.098225676056
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "41ce4f24-4b0b-4431-bbf4-7262199838db",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            }
+        ],
+        "dir": "topics/microbiome/tutorials/introduction",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": false,
+        "id": "microbiome/introduction",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "layout": "tutorial_slides",
+        "license": "CC-BY-4.0",
+        "logo": "GTN",
+        "mod_date": "2024-08-08",
+        "pageviews": 5897186,
+        "priority": 0,
+        "pub_date": "2017-06-22",
+        "recordings": [
+            {
+                "captioners": [
+                    "shiltemann"
                 ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Krakentools: Calculates alpha diversity\"];\n  0 -->|output| 1;\n  2[\"Krakentools: Calculates alpha diversity\"];\n  0 -->|output| 2;\n  3[\"Krakentools: Calculates alpha diversity\"];\n  0 -->|output| 3;\n  4[\"Krakentools: Calculates alpha diversity\"];\n  0 -->|output| 4;\n  5[\"Krakentools: Calculates alpha diversity\"];\n  0 -->|output| 5;\n  6[\"Krakentools: calculates beta diversity Bray-Curtis dissimilarity\"];\n  0 -->|output| 6;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Calculating diversity from microbiome taxonomic data",
-                "outputs": [],
-                "parent_id": "microbiome/diversity",
-                "path": "topics/microbiome/tutorials/diversity/workflows/workflow.ga",
-                "tags": [
-                    "name:GTN"
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "15M",
+                "speakers": [
+                    "shiltemann"
                 ],
-                "test_results": null,
-                "tests": true,
-                "title": "Calculating diversity from microbiome taxonomic data",
-                "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-diversity/versions/workflow",
-                "tutorial_id": "diversity",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/diversity/workflows/workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/diversity/workflows/workflow.html",
-                "version": 1,
-                "wfid": "microbiome-diversity",
-                "wfname": "workflow",
-                "workflow": "workflow.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_alpha_diversity/krakentools_alpha_diversity/1.2+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_beta_diversity/krakentools_beta_diversity/1.2+galaxy1"
+                "youtube_id": "9OY1mklWuK0"
+            }
+        ],
+        "redirect_from": [
+            "/topics/metagenomics/slides/introduction",
+            "/topics/microbiome/slides/introduction",
+            "/topics/metagenomics/tutorials/introduction/slides",
+            "/short/microbiome/introduction/slides",
+            "/short/S00078",
+            "/short/S00114"
+        ],
+        "short_id": "S00114",
+        "short_tools": [],
+        "slides": true,
+        "slides_recordings": [
+            {
+                "captioners": [
+                    "shiltemann"
                 ],
-                "workflowhub_id": "1349"
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "15M",
+                "speakers": [
+                    "shiltemann"
+                ],
+                "youtube_id": "9OY1mklWuK0"
             }
         ],
-        "zenodo_link": "https://zenodo.org/records/13150694"
+        "subtopic": "intro",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "title": "Introduction to Microbiome Analysis",
+        "tools": [],
+        "topic_name": "microbiome",
+        "topic_name_human": "Microbiome",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": true
+        },
+        "tutorial_name": "introduction",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/introduction/slides.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/introduction/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/introduction/slides.json"
+        },
+        "version": 5,
+        "video": true,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 152,
+        "visitors": 2133582
     },
     {
         "admin_install": {
@@ -137874,162 +141092,186 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "taxonomy_krona_chart",
+                    "owner": "crs4",
+                    "revisions": "73486cc6170e",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "unique",
-                    "owner": "bgruening",
-                    "revisions": "7ce75adb93be",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "humann2",
+                    "owner": "iuc",
+                    "revisions": "1ab06263e083",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bamtools",
-                    "owner": "devteam",
-                    "revisions": "befc9dad4ca8",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "name": "humann2_regroup_table",
+                    "owner": "iuc",
+                    "revisions": "a1747df2bc21",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bowtie2",
-                    "owner": "devteam",
-                    "revisions": "f6877ad76b00",
-                    "tool_panel_section_label": "Mapping",
+                    "name": "humann2_renorm_table",
+                    "owner": "iuc",
+                    "revisions": "ba4dfbdc1295",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bowtie2",
-                    "owner": "devteam",
-                    "revisions": "03e9b2fbc005",
-                    "tool_panel_section_label": "Mapping",
+                    "name": "metaphlan2",
+                    "owner": "iuc",
+                    "revisions": "8c82c4d90cc6",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "3d0c7bdf12f5",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "metaphlan2krona",
+                    "owner": "iuc",
+                    "revisions": "ebb74774457e",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bandage",
+                    "name": "mothur_align_seqs",
                     "owner": "iuc",
-                    "revisions": "21e491ad532a",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "revisions": "2692b3107533",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bandage",
+                    "name": "mothur_classify_otu",
                     "owner": "iuc",
-                    "revisions": "21e491ad532a",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "revisions": "e664787de3ab",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "collection_column_join",
+                    "name": "mothur_classify_seqs",
                     "owner": "iuc",
-                    "revisions": "3ddd99c7efee",
-                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "revisions": "cc9c7b550c29",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "coverm_contig",
+                    "name": "mothur_cluster_split",
                     "owner": "iuc",
-                    "revisions": "6941d0d453ba",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "revisions": "a29ac7993cb0",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "filter_tabular",
+                    "name": "mothur_count_seqs",
                     "owner": "iuc",
-                    "revisions": "34d29339abab",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "revisions": "ecbd9ed733e6",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "megahit",
+                    "name": "mothur_filter_seqs",
                     "owner": "iuc",
-                    "revisions": "14ddfc8ffb93",
-                    "tool_panel_section_label": "Assembly",
+                    "revisions": "bf20a30c263a",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "megahit_contig2fastg",
+                    "name": "mothur_make_biom",
                     "owner": "iuc",
-                    "revisions": "4ec5b3777508",
-                    "tool_panel_section_label": "Proteomics",
+                    "revisions": "5dc4d49a238a",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ngsutils_bam_filter",
+                    "name": "mothur_make_group",
                     "owner": "iuc",
-                    "revisions": "2e957d4c4b95",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "revisions": "8c964d119da8",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "quast",
+                    "name": "mothur_make_shared",
                     "owner": "iuc",
-                    "revisions": "3061c8b029e5",
-                    "tool_panel_section_label": "Assembly",
+                    "revisions": "83dabeeadb55",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "quast",
+                    "name": "mothur_merge_files",
                     "owner": "iuc",
-                    "revisions": "72472698a2df",
-                    "tool_panel_section_label": "Assembly",
+                    "revisions": "a70b25374a23",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "seqtk",
+                    "name": "mothur_pre_cluster",
                     "owner": "iuc",
-                    "revisions": "3da72230c066",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "58d0fe3cc0f2",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cutadapt",
-                    "owner": "lparsons",
-                    "revisions": "5915ea1ec9b1",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "mothur_screen_seqs",
+                    "owner": "iuc",
+                    "revisions": "8743aecd26a9",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "metaspades",
-                    "owner": "nml",
-                    "revisions": "fd128c111ab0",
-                    "tool_panel_section_label": "Assembly",
+                    "name": "mothur_summary_seqs",
+                    "owner": "iuc",
+                    "revisions": "e4a4cb8b6bbf",
+                    "tool_panel_section_label": "Mothur",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mothur_unique_seqs",
+                    "owner": "iuc",
+                    "revisions": "1f72d9a3d09f",
+                    "tool_panel_section_label": "Mothur",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "krona_text",
+                    "owner": "saskia-hiltemann",
+                    "revisions": "b14f1444e464",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unique\n  owner: bgruening\n  revisions: 7ce75adb93be\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools\n  owner: devteam\n  revisions: befc9dad4ca8\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie2\n  owner: devteam\n  revisions: f6877ad76b00\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie2\n  owner: devteam\n  revisions: 03e9b2fbc005\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: 21e491ad532a\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: 21e491ad532a\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_column_join\n  owner: iuc\n  revisions: 3ddd99c7efee\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: coverm_contig\n  owner: iuc\n  revisions: 6941d0d453ba\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filter_tabular\n  owner: iuc\n  revisions: 34d29339abab\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: megahit\n  owner: iuc\n  revisions: 14ddfc8ffb93\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: megahit_contig2fastg\n  owner: iuc\n  revisions: 4ec5b3777508\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ngsutils_bam_filter\n  owner: iuc\n  revisions: 2e957d4c4b95\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 3061c8b029e5\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 72472698a2df\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 5915ea1ec9b1\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaspades\n  owner: nml\n  revisions: fd128c111ab0\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-assembly/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "plushz",
-                "bebatut"
-            ],
-            "funding": [
-                "gallantries"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: taxonomy_krona_chart\n  owner: crs4\n  revisions: 73486cc6170e\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: humann2\n  owner: iuc\n  revisions: 1ab06263e083\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: humann2_regroup_table\n  owner: iuc\n  revisions: a1747df2bc21\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: humann2_renorm_table\n  owner: iuc\n  revisions: ba4dfbdc1295\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaphlan2\n  owner: iuc\n  revisions: 8c82c4d90cc6\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaphlan2krona\n  owner: iuc\n  revisions: ebb74774457e\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_align_seqs\n  owner: iuc\n  revisions: 2692b3107533\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_classify_otu\n  owner: iuc\n  revisions: e664787de3ab\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_classify_seqs\n  owner: iuc\n  revisions: cc9c7b550c29\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_cluster_split\n  owner: iuc\n  revisions: a29ac7993cb0\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_count_seqs\n  owner: iuc\n  revisions: ecbd9ed733e6\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_filter_seqs\n  owner: iuc\n  revisions: bf20a30c263a\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_make_biom\n  owner: iuc\n  revisions: 5dc4d49a238a\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_make_group\n  owner: iuc\n  revisions: 8c964d119da8\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_make_shared\n  owner: iuc\n  revisions: 83dabeeadb55\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_merge_files\n  owner: iuc\n  revisions: a70b25374a23\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_pre_cluster\n  owner: iuc\n  revisions: 58d0fe3cc0f2\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_screen_seqs\n  owner: iuc\n  revisions: 8743aecd26a9\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_summary_seqs\n  owner: iuc\n  revisions: e4a4cb8b6bbf\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_unique_seqs\n  owner: iuc\n  revisions: 1f72d9a3d09f\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: krona_text\n  owner: saskia-hiltemann\n  revisions: b14f1444e464\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/general-tutorial/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
                     "uni-freiburg"
                 ],
-                "id": "plushz",
-                "joined": "2022-03",
-                "name": "Polina Polunina",
-                "orcid": "0000-0002-0507-4602",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/plushz/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/plushz.json"
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             },
             {
                 "affiliations": [
@@ -138056,801 +141298,189 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
                 "twitter": "bebatut",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/microbiome/tutorials/metagenomics-assembly",
+        "dir": "topics/microbiome/tutorials/general-tutorial",
         "edam_ontology": [
             "topic_3174",
-            "topic_0196"
+            "topic_3697",
+            "topic_0637",
+            "topic_0080",
+            "topic_4038"
         ],
         "edam_operation": [
+            "DNA barcoding",
             "Visualisation",
+            "Phylogenetic analysis",
             "Sequencing quality control",
-            "Primer removal",
-            "Sequence file editing",
-            "Formatting",
-            "Read mapping",
-            "Sequence assembly validation",
-            "Sequence composition calculation",
-            "Sequence assembly visualisation",
-            "Local alignment",
-            "Genome assembly",
-            "Sequence trimming",
-            "Statistical calculation",
-            "Sequence contamination filtering",
-            "Sequence alignment analysis",
-            "Read pre-processing",
-            "Data handling",
-            "Variant calling"
+            "Taxonomic classification",
+            "Sequence read processing",
+            "Sequence clustering"
         ],
         "edam_topic": [
             "Metagenomics",
-            "Sequence assembly"
+            "Microbial ecology",
+            "Taxonomy",
+            "Sequence analysis"
+        ],
+        "exact_supported_servers": [
+            "UseGalaxy.be"
         ],
-        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "microbiome/metagenomics-assembly",
+        "id": "microbiome/general-tutorial",
         "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu"
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
         ],
         "js_requirements": {
-            "mathjax": 25185,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Assembly groups reads into contigs and scafolds.",
-            "De Brujin Graphs use k-mers to assembly reads",
-            "MetaSPAdes and MEGAHIT are assemblers",
-            "Quast is the tool to assess the assembly quality"
+            "With amplicon data, we can extract information about the studied community structure",
+            "With shotgun data, we can extract information about the studied community structure and also the functions realised by the community",
+            "The tools used to analyze amplicon and shotgun data are different, except for the visualisation",
+            "Metagenomics data analyses are complex and time-consuming"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-08-09",
         "objectives": [
-            "Describe what an assembly is",
-            "Describe what de-replication is",
-            "Explain the difference between co-assembly and individual assembly",
-            "Explain the difference between reads, contigs and scaffolds",
-            "Explain how tools based on De Bruijn graph work",
-            "Apply appropriate tools for analyzing the quality of metagenomic data",
-            "Construct and apply simple assembly pipelines on short read data",
-            "Apply appropriate tools for analyzing the quality of metagenomic assembly",
-            "Evaluate the Quality of the Assembly with Quast, Bowtie2, and CoverM-Genome"
+            "Choosing the best approach to analyze metagenomics data",
+            "Selection of tools to analyze amplicon data or shotgun data",
+            "Visualisation of a community structure"
         ],
-        "pageviews": 1931,
-        "pub_date": "2022-12-05",
+        "pageviews": 4852,
+        "pub_date": "2017-06-22",
         "questions": [
-            "Why metagenomic data should be assembled?",
-            "What is the difference between co-assembly and individual assembly?",
-            "What is the difference between reads, contigs and scaffolds?",
-            "How tools based on De Bruijn graph work?",
-            "How to assess the quality of metagenomic data assembly?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "bebatut",
-                    "sophia120199"
-                ],
-                "date": "2023-05-02",
-                "galaxy_version": "23.01",
-                "length": "1H",
-                "speakers": [
-                    "bebatut"
-                ],
-                "youtube_id": "1ZYGy85Im7w"
-            }
+            "How to analyze metagenomics data?",
+            "What information can be extracted of metagenomics data?",
+            "What is the difference between amplicon and shotgun data?",
+            "What are the difference in the analyses of amplicon and shotgun data?"
         ],
         "redirect_from": [
-            "/topics/metagenomics/tutorials/metagenomics-assembly/tutorial",
-            "/short/microbiome/metagenomics-assembly",
-            "/short/T00202",
-            "/short/T00386"
+            "/topics/metagenomics/tutorials/general-tutorial/tutorial",
+            "/short/microbiome/general-tutorial",
+            "/short/T00201",
+            "/short/T00385"
         ],
-        "short_id": "T00386",
+        "short_id": "T00385",
         "short_tools": [
-            "bg_uniq",
-            "megahit_contig2fastg",
-            "ngsutils_bam_filter",
-            "megahit",
-            "bowtie2",
-            "tp_cat",
-            "quast",
-            "random_lines1",
-            "collection_column_join",
-            "filter_tabular",
-            "seqtk_subseq",
-            "fastqc",
-            "bandage_info",
-            "coverm_contig",
-            "bandage_image",
-            "bamtools",
-            "cutadapt",
-            "metaspades"
+            "humann2_regroup_table",
+            "mothur_summary_seqs",
+            "humann2_renorm_table",
+            "mothur_make_biom",
+            "mothur_count_seqs",
+            "mothur_classify_seqs",
+            "mothur_make_group",
+            "mothur_make_shared",
+            "mothur_filter_seqs",
+            "mothur_merge_files",
+            "mothur_classify_otu",
+            "mothur_align_seqs",
+            "humann2",
+            "mothur_cluster_split",
+            "mothur_screen_seqs",
+            "metaphlan2",
+            "mothur_pre_cluster",
+            "mothur_unique_seqs",
+            "taxonomy_krona_chart",
+            "krona-text",
+            "metaphlan2krona"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "metagenomics",
+        "subtopic": "intro",
         "supported_servers": {
-            "exact": [],
+            "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                }
+            ],
             "inexact": [
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "assembly",
-            "metagenomics",
-            "microgalaxy"
-        ],
-        "time_estimation": "2H",
-        "title": "Assembly of metagenomic sequencing data",
-        "tools": [
-            "random_lines1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.2.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy10",
-            "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
-            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.15.4+galaxy2"
-        ],
-        "topic_name": "microbiome",
-        "topic_name_human": "Microbiome",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "metagenomics-assembly",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-assembly/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-assembly/tutorial.json"
-        },
-        "version": 4,
-        "video": false,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 1376,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  1[label=\"metaSPAdes\"]\n  0 -> 1 [label=\"output\"]\n  k833d79ffe16f414c9c41db8dbfa8ed6b[color=lightseagreen,label=\"Output\\nmetaSPAdes on input dataset(s): Scaffolds\"]\n  1 -> k833d79ffe16f414c9c41db8dbfa8ed6b\n  k10319152d2f947d8be41f956a57e86d3[color=lightseagreen,label=\"Output\\nmetaSPAdes on input dataset(s): Assembly graph\"]\n  1 -> k10319152d2f947d8be41f956a57e86d3\n  kb1ffc3a48e394255ac57fd7cfb9c1633[color=lightseagreen,label=\"Output\\nmetaSPAdes on input dataset(s): Assembly graph with scaffolds\"]\n  1 -> kb1ffc3a48e394255ac57fd7cfb9c1633\n  kb6b74c9d5a164725a1d111c1f05ee909[color=lightseagreen,label=\"Output\\nmetaSPAdes on input dataset(s): Contigs\"]\n  1 -> kb6b74c9d5a164725a1d111c1f05ee909\n  2[label=\"MEGAHIT\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Bowtie2\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"megahit contig2fastg\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Quast\"]\n  2 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Bandage Image\"]\n  4 -> 6 [label=\"fastg\"]\n  7[label=\"Bandage Info\"]\n  4 -> 7 [label=\"fastg\"]\n  8[label=\"Column join\"]\n  7 -> 8 [label=\"outfile\"]\n}",
-                "history": [
-                    {
-                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
-                        "message": "Rename metagenomics topic to microbiome",
-                        "num": 1,
-                        "short_hash": "0e0a2f2cc",
-                        "unix": "1704901629"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Input Dataset Collection"
-                            }
-                        ],
-                        "label": "Input Dataset Collection",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 0.0,
-                            "top": 480
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "cdb65097-d956-4715-9cd4-fadc9b0c07c5",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "c8ca2f5f-b0f4-4d90-8259-9e4796c4a35f"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"metaSPAdes\"];\n  0 -->|output| 1;\n  833d79ff-e16f-414c-9c41-db8dbfa8ed6b[\"Output\\nmetaSPAdes on input dataset(s): Scaffolds\"];\n  1 --> 833d79ff-e16f-414c-9c41-db8dbfa8ed6b;\n  style 833d79ff-e16f-414c-9c41-db8dbfa8ed6b stroke:#2c3143,stroke-width:4px;\n  10319152-d2f9-47d8-be41-f956a57e86d3[\"Output\\nmetaSPAdes on input dataset(s): Assembly graph\"];\n  1 --> 10319152-d2f9-47d8-be41-f956a57e86d3;\n  style 10319152-d2f9-47d8-be41-f956a57e86d3 stroke:#2c3143,stroke-width:4px;\n  b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633[\"Output\\nmetaSPAdes on input dataset(s): Assembly graph with scaffolds\"];\n  1 --> b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633;\n  style b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633 stroke:#2c3143,stroke-width:4px;\n  b6b74c9d-5a16-4725-a1d1-11c1f05ee909[\"Output\\nmetaSPAdes on input dataset(s): Contigs\"];\n  1 --> b6b74c9d-5a16-4725-a1d1-11c1f05ee909;\n  style b6b74c9d-5a16-4725-a1d1-11c1f05ee909 stroke:#2c3143,stroke-width:4px;\n  2[\"MEGAHIT\"];\n  0 -->|output| 2;\n  3[\"Bowtie2\"];\n  0 -->|output| 3;\n  2 -->|output| 3;\n  4[\"megahit contig2fastg\"];\n  2 -->|output| 4;\n  5[\"Quast\"];\n  2 -->|output| 5;\n  0 -->|output| 5;\n  6[\"Bandage Image\"];\n  4 -->|fastg| 6;\n  7[\"Bandage Info\"];\n  4 -->|fastg| 7;\n  8[\"Column join\"];\n  7 -->|outfile| 8;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Metagenomics assembly tutorial workflow",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Input Dataset Collection"
-                            }
-                        ],
-                        "label": "Input Dataset Collection",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 0.0,
-                            "top": 480
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "cdb65097-d956-4715-9cd4-fadc9b0c07c5",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "c8ca2f5f-b0f4-4d90-8259-9e4796c4a35f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.15.4+galaxy2",
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {
-                            "singlePaired|input": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool metaSPAdes",
-                                "name": "arf"
-                            },
-                            {
-                                "description": "runtime parameter for tool metaSPAdes",
-                                "name": "arf"
-                            },
-                            {
-                                "description": "runtime parameter for tool metaSPAdes",
-                                "name": "singlePaired"
-                            }
-                        ],
-                        "label": null,
-                        "name": "metaSPAdes",
-                        "outputs": [
-                            {
-                                "name": "out_ag",
-                                "type": "fastg"
-                            },
-                            {
-                                "name": "out_ags",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "out_cn",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "out_sc",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "left": 247.0,
-                            "top": 0
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.15.4+galaxy2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "fd128c111ab0",
-                            "name": "metaspades",
-                            "owner": "nml",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"additional_reads\": {\"selector\": \"false\", \"__current_case__\": 1}, \"arf\": {\"nanopore\": {\"__class__\": \"RuntimeValue\"}, \"pacbio\": {\"__class__\": \"RuntimeValue\"}}, \"kmer_cond\": {\"kmer_sel\": \"manual\", \"__current_case__\": 1, \"manual\": \"21,33,55,77\"}, \"library_number\": \"true\", \"mode_sel\": null, \"optional_output\": [\"ag\", \"ags\", \"cn\", \"sc\"], \"phred_offset\": \"auto\", \"singlePaired\": {\"sPaired\": \"paired_collection\", \"__current_case__\": 2, \"input\": {\"__class__\": \"RuntimeValue\"}, \"type_paired\": \"pe\", \"orientation\": \"fr\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.15.4+galaxy2",
-                        "type": "tool",
-                        "uuid": "7dc08460-f398-4f1d-9f30-1736cf636a13",
-                        "workflow_outputs": [
-                            {
-                                "label": "metaSPAdes on input dataset(s): Scaffolds",
-                                "output_name": "out_sc",
-                                "uuid": "833d79ff-e16f-414c-9c41-db8dbfa8ed6b"
-                            },
-                            {
-                                "label": "metaSPAdes on input dataset(s): Assembly graph",
-                                "output_name": "out_ag",
-                                "uuid": "10319152-d2f9-47d8-be41-f956a57e86d3"
-                            },
-                            {
-                                "label": "metaSPAdes on input dataset(s): Assembly graph with scaffolds",
-                                "output_name": "out_ags",
-                                "uuid": "b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633"
-                            },
-                            {
-                                "label": "metaSPAdes on input dataset(s): Contigs",
-                                "output_name": "out_cn",
-                                "uuid": "b6b74c9d-5a16-4725-a1d1-11c1f05ee909"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "input_option|batchmode|pair_input": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "MEGAHIT",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "left": 278.0,
-                            "top": 464
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "14ddfc8ffb93",
-                            "name": "megahit",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"advanced_section\": {\"nomercy\": \"false\", \"bubble_level\": \"2\", \"merge_level\": \"20,0.95\", \"prune_level\": \"2\", \"prune_depth\": \"2\", \"disconnect_ratio\": \"0.1\", \"low_local_ratio\": \"0.2\", \"cleaning_rounds\": \"5\", \"nolocal\": \"false\", \"kmin1pass\": \"false\"}, \"basic_section\": {\"min_count\": \"2\", \"k_mer\": {\"k_mer_method\": \"klim_method\", \"__current_case__\": 1, \"k_min\": \"21\", \"k_max\": \"91\", \"k_step\": \"12\"}}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_option\": {\"choice\": \"paired_collection\", \"__current_case__\": 3, \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"pair_input\": {\"__class__\": \"ConnectedValue\"}}}, \"output_section\": {\"min_contig_len\": \"200\", \"show_intermediate_contigs\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.9+galaxy0",
-                        "type": "tool",
-                        "uuid": "ffbb16f2-580a-4832-8b6d-e67932e24b27",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "061ac8dd-de43-467d-9c15-a4f46a125103"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "library|input_1": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "reference_genome|own_file": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Bowtie2",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "bam"
-                            },
-                            {
-                                "name": "mapping_stats",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 556.0,
-                            "top": 130
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "03e9b2fbc005",
-                            "name": "bowtie2",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"no_presets\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": \"false\", \"aligned_file\": \"false\", \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"own_file|__identifier__\": \"ERR2231567\", \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 1, \"own_file\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.5.0+galaxy0",
-                        "type": "tool",
-                        "uuid": "9f445c6b-31c9-4ff0-b559-6be00fb0fc17",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "mapping_stats",
-                                "uuid": "ff350260-91cd-4f01-a82f-f64e8eddd4ed"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "2fa389b6-088a-4686-94e9-de884f86e1b7"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "contigs": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "megahit contig2fastg",
-                        "outputs": [
-                            {
-                                "name": "fastg",
-                                "type": "fastg"
-                            }
-                        ],
-                        "position": {
-                            "left": 556.0,
-                            "top": 444
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "4ec5b3777508",
-                            "name": "megahit_contig2fastg",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"contigs\": {\"__class__\": \"ConnectedValue\"}, \"contigs|__identifier__\": \"ERR2231567\", \"kmer\": \"91\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.3+galaxy1",
-                        "type": "tool",
-                        "uuid": "c839a8b8-c719-474d-957e-d94614491f13",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "fastg",
-                                "uuid": "91718981-2ae5-4cdd-8007-0ce9cc3c68f6"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "in|inputs": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "reads|input_1": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Quast",
-                        "outputs": [
-                            {
-                                "name": "metrics_tabular",
-                                "type": "input"
-                            },
-                            {
-                                "name": "metrics_pdf",
-                                "type": "input"
-                            },
-                            {
-                                "name": "report_tabular_meta",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "report_html_meta",
-                                "type": "html"
-                            },
-                            {
-                                "name": "log_meta",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "krona",
-                                "type": "html"
-                            }
-                        ],
-                        "position": {
-                            "left": 556.0,
-                            "top": 636
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3061c8b029e5",
-                            "name": "quast",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": \"false\", \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": \"true\", \"fragmented_max_indent\": null, \"report_all_metrics\": \"false\", \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": \"false\", \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": \"false\", \"upper_bound_assembly\": \"false\", \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"metagenome\", \"__current_case__\": 1, \"ref\": {\"origin\": \"none\", \"__current_case__\": 3}, \"reuse_combined_alignments\": \"false\", \"min_identity\": \"90.0\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": \"false\", \"conserved_genes_finding\": \"false\"}, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"large\": \"false\", \"min_contig\": \"500\", \"output_files\": [\"html\", \"pdf\", \"tabular\", \"log\", \"summary\", \"krona\"], \"reads\": {\"reads_option\": \"paired_collection\", \"__current_case__\": 3, \"input_1\": {\"__class__\": \"ConnectedValue\"}}, \"split_scaffolds\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.2.0+galaxy0",
-                        "type": "tool",
-                        "uuid": "12072d4c-8ad5-4de1-bbe2-3b081b8373be",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "log_meta",
-                                "uuid": "33c6424f-fceb-45d1-9462-ea3e7cda79ea"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "krona",
-                                "uuid": "44457a4b-760c-4080-b552-dc4724906b2c"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "metrics_tabular",
-                                "uuid": "9b2b72ac-a297-46a2-883f-8f1704664cf3"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "report_tabular_meta",
-                                "uuid": "1259f3a1-4952-48f1-be69-0fde3b6be9de"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "report_html_meta",
-                                "uuid": "b8f1b46c-1421-4952-9e87-1790bdd076df"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "metrics_pdf",
-                                "uuid": "ac4aa63b-5dc1-4b4c-bbb0-6afce689f0d2"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 4,
-                                "output_name": "fastg"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Bandage Image",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "jpg"
-                            }
-                        ],
-                        "position": {
-                            "left": 834.0,
-                            "top": 466
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4",
-                        "tool_shed_repository": {
-                            "changeset_revision": "21e491ad532a",
-                            "name": "bandage",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fontsize\": null, \"height\": \"1000\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"input_file|__identifier__\": \"ERR2231567\", \"lengths\": \"false\", \"names\": \"false\", \"nodewidth\": null, \"output_format\": \"jpg\", \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.8.1+galaxy4",
-                        "type": "tool",
-                        "uuid": "31b35530-ae7f-4e9c-8021-6983cf3f3401",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "e02c022d-3067-40ce-8bb6-4cc258d8523a"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 4,
-                                "output_name": "fastg"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Bandage Info",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 834.0,
-                            "top": 679
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b9e31c5c01c7",
-                            "name": "bandage",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"input_file|__identifier__\": \"ERR2231567\", \"tsv\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.8.1+galaxy2",
-                        "type": "tool",
-                        "uuid": "b63e03dc-b9be-4a72-ac81-64b63ddf99f2",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "6bd3194a-9e8c-4677-b42c-2fb3bd1116f3"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "input_tabular": {
-                                "id": 7,
-                                "output_name": "outfile"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Column join",
-                        "outputs": [
-                            {
-                                "name": "tabular_output",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 1112.0,
-                            "top": 732
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3ddd99c7efee",
-                            "name": "collection_column_join",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fill_char\": \".\", \"has_header\": \"0\", \"identifier_column\": \"1\", \"include_outputs\": null, \"input_tabular\": {\"__class__\": \"ConnectedValue\"}, \"old_col_in_header\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.0.3",
-                        "type": "tool",
-                        "uuid": "e9dc42b2-c638-4b9c-af5f-ce84f6b0d654",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "tabular_output",
-                                "uuid": "fe5b4460-6fa0-48a8-84e7-b3b8270e9b8f"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "microbiome/metagenomics-assembly",
-                "path": "topics/microbiome/tutorials/metagenomics-assembly/workflows/metagenomics_assembly_tutorial_workflow.ga",
-                "tags": [],
-                "test_results": null,
-                "tests": false,
-                "title": "Metagenomics assembly tutorial workflow",
-                "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-metagenomics-assembly/versions/metagenomics-assembly-tutorial-workflow",
-                "tutorial_id": "metagenomics-assembly",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metagenomics-assembly/workflows/metagenomics_assembly_tutorial_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metagenomics-assembly/workflows/metagenomics_assembly_tutorial_workflow.html",
-                "version": 1,
-                "wfid": "microbiome-metagenomics-assembly",
-                "wfname": "metagenomics-assembly-tutorial-workflow",
-                "workflow": "metagenomics_assembly_tutorial_workflow.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.15.4+galaxy2"
-                ],
-                "workflowhub_id": "1103"
-            },
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "microgalaxy"
+        ],
+        "time_estimation": "2H30M",
+        "title": "Analyses of metagenomics data - The global picture",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.9.9.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/humann2_regroup_table/humann2_regroup_table/0.9.9.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/humann2_renorm_table/humann2_renorm_table/0.9.9.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.36.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.36.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.36.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.36.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.36.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.36.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.36.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_group/mothur_make_group/1.36.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.36.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.36.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.36.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.36.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.36.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.36.1.0",
+            "toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/krona-text/1"
+        ],
+        "topic_name": "microbiome",
+        "topic_name_human": "Microbiome",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "general-tutorial",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/general-tutorial/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/general-tutorial/tutorial.json"
+        },
+        "version": 4,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 167,
+        "visitors": 3586,
+        "workflows": [
             {
                 "creators": [],
-                "description": "",
+                "description": "Analyses of metagenomics data - The global picture",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nERR2231567_1.fastq.gz\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nERR2231567_2.fastq.gz\"]\n  2[label=\"Cutadapt\"]\n  0 -> 2 [label=\"output\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"MEGAHIT\"]\n  2 -> 3 [label=\"out1\"]\n  2 -> 3 [label=\"out2\"]\n  4[label=\"Bowtie2\"]\n  2 -> 4 [label=\"out1\"]\n  2 -> 4 [label=\"out2\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"BAM filter\"]\n  4 -> 5 [label=\"output\"]\n  6[label=\"BAM filter\"]\n  4 -> 6 [label=\"output\"]\n  7[label=\"Convert, Merge, Randomize\"]\n  5 -> 7 [label=\"outfile\"]\n  8[label=\"Convert, Merge, Randomize\"]\n  6 -> 8 [label=\"outfile\"]\n  9[label=\"Select random lines\"]\n  7 -> 9 [label=\"out_file1\"]\n  10[label=\"Select random lines\"]\n  8 -> 10 [label=\"out_file1\"]\n  11[label=\"Filter Tabular\"]\n  9 -> 11 [label=\"out_file1\"]\n  12[label=\"Filter Tabular\"]\n  10 -> 12 [label=\"out_file1\"]\n  13[label=\"Unique\"]\n  11 -> 13 [label=\"output\"]\n  14[label=\"Unique\"]\n  12 -> 14 [label=\"output\"]\n  15[label=\"Concatenate datasets\"]\n  13 -> 15 [label=\"outfile\"]\n  14 -> 15 [label=\"outfile\"]\n  16[label=\"seqtk_subseq\"]\n  2 -> 16 [label=\"out1\"]\n  15 -> 16 [label=\"out_file1\"]\n  17[label=\"seqtk_subseq\"]\n  2 -> 17 [label=\"out2\"]\n  15 -> 17 [label=\"out_file1\"]\n  18[label=\"FastQC\"]\n  16 -> 18 [label=\"default\"]\n  19[label=\"FastQC\"]\n  17 -> 19 [label=\"default\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSILVA Reference\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAnguil Soil Sample\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPampa Soil Sample\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTrainset PDS alignment\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTrainset PDS taxonomy\"]\n  5[label=\"Merge.files\"]\n  2 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"Make.group\"]\n  1 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"Unique.seqs\"]\n  5 -> 7 [label=\"output\"]\n  8[label=\"Count.seqs\"]\n  6 -> 8 [label=\"output\"]\n  7 -> 8 [label=\"out_names\"]\n  9[label=\"Summary.seqs\"]\n  8 -> 9 [label=\"seq_count\"]\n  7 -> 9 [label=\"out_fasta\"]\n  10[label=\"Screen.seqs\"]\n  7 -> 10 [label=\"out_fasta\"]\n  8 -> 10 [label=\"seq_count\"]\n  11[label=\"Align.seqs\"]\n  0 -> 11 [label=\"output\"]\n  10 -> 11 [label=\"fasta_out\"]\n  12[label=\"Summary.seqs\"]\n  10 -> 12 [label=\"count_out\"]\n  11 -> 12 [label=\"out_file\"]\n  13[label=\"Screen.seqs\"]\n  11 -> 13 [label=\"out_file\"]\n  10 -> 13 [label=\"count_out\"]\n  14[label=\"Filter.seqs\"]\n  13 -> 14 [label=\"fasta_out\"]\n  15[label=\"Pre.cluster\"]\n  14 -> 15 [label=\"filteredfasta\"]\n  13 -> 15 [label=\"count_out\"]\n  16[label=\"Classify.seqs\"]\n  15 -> 16 [label=\"count_out\"]\n  3 -> 16 [label=\"output\"]\n  15 -> 16 [label=\"fasta_out\"]\n  4 -> 16 [label=\"output\"]\n  17[label=\"Cluster.split\"]\n  16 -> 17 [label=\"taxonomy_out\"]\n  15 -> 17 [label=\"fasta_out\"]\n  15 -> 17 [label=\"count_out\"]\n  18[label=\"Make.shared\"]\n  15 -> 18 [label=\"count_out\"]\n  17 -> 18 [label=\"otulist\"]\n  k62dd9aef795b44babfa2e63ed96c9d09[color=lightseagreen,label=\"Output\\nmothur_make_shared_shared\"]\n  18 -> k62dd9aef795b44babfa2e63ed96c9d09\n  19[label=\"Classify.otu\"]\n  15 -> 19 [label=\"count_out\"]\n  16 -> 19 [label=\"taxonomy_out\"]\n  17 -> 19 [label=\"otulist\"]\n  20[label=\"Make.biom\"]\n  18 -> 20 [label=\"shared\"]\n  19 -> 20 [label=\"taxonomies\"]\n  21[label=\"Visualize  with Krona\"]\n  19 -> 21 [label=\"taxonomies\"]\n}",
                 "history": [
                     {
                         "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
@@ -138870,21 +141500,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "ERR2231567_1.fastq.gz"
+                                "name": "silva"
                             }
                         ],
-                        "label": "ERR2231567_1.fastq.gz",
+                        "label": "SILVA Reference",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 174.98046875
+                            "left": 200,
+                            "top": 463
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ac2a7e31-6a0c-43f0-b39f-6764ae421dea",
+                        "uuid": "372b68d9-2f00-4275-a372-ffe89cca2a63",
                         "workflow_outputs": []
                     },
                     {
@@ -138896,971 +141526,294 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "ERR2231567_2.fastq.gz"
+                                "name": "anguil_soil_sample"
                             }
                         ],
-                        "label": "ERR2231567_2.fastq.gz",
+                        "label": "Anguil Soil Sample",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 1.03515625,
-                            "top": 365.0
+                            "left": 209,
+                            "top": 746.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "2e1fd5bf-3b01-49dd-a091-75c7215eb3f9",
+                        "uuid": "3beec7e9-acbe-4c92-85b3-62d6ab3cd83d",
                         "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nERR2231567_1.fastq.gz\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nERR2231567_2.fastq.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Cutadapt\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"MEGAHIT\"];\n  2 -->|out1| 3;\n  2 -->|out2| 3;\n  4[\"Bowtie2\"];\n  2 -->|out1| 4;\n  2 -->|out2| 4;\n  3 -->|output| 4;\n  5[\"BAM filter\"];\n  4 -->|output| 5;\n  6[\"BAM filter\"];\n  4 -->|output| 6;\n  7[\"Convert, Merge, Randomize\"];\n  5 -->|outfile| 7;\n  8[\"Convert, Merge, Randomize\"];\n  6 -->|outfile| 8;\n  9[\"Select random lines\"];\n  7 -->|out_file1| 9;\n  10[\"Select random lines\"];\n  8 -->|out_file1| 10;\n  11[\"Filter Tabular\"];\n  9 -->|out_file1| 11;\n  12[\"Filter Tabular\"];\n  10 -->|out_file1| 12;\n  13[\"Unique\"];\n  11 -->|output| 13;\n  14[\"Unique\"];\n  12 -->|output| 14;\n  15[\"Concatenate datasets\"];\n  13 -->|outfile| 15;\n  14 -->|outfile| 15;\n  16[\"seqtk_subseq\"];\n  2 -->|out1| 16;\n  15 -->|out_file1| 16;\n  17[\"seqtk_subseq\"];\n  2 -->|out2| 17;\n  15 -->|out_file1| 17;\n  18[\"FastQC\"];\n  16 -->|default| 18;\n  19[\"FastQC\"];\n  17 -->|default| 19;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "workflow-generate-dataset-for-assembly-tutorial",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0",
+                        "content_id": null,
                         "errors": null,
                         "id": 2,
-                        "input_connections": {
-                            "library|input_1": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "library|input_2": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cutadapt",
-                        "outputs": [
-                            {
-                                "name": "out1",
-                                "type": "fastqsanger"
-                            },
-                            {
-                                "name": "out2",
-                                "type": "fastqsanger"
-                            },
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "report",
-                                "type": "txt"
+                                "description": "",
+                                "name": "pampa_soil_sample"
                             }
                         ],
+                        "label": "Pampa Soil Sample",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 248.0078125,
-                            "top": 260.0
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "5915ea1ec9b1",
-                            "name": "cutadapt",
-                            "owner": "lparsons",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 212,
+                            "top": 866.5
                         },
-                        "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"internal\": \"\", \"error_rate\": \"0.1\", \"no_indels\": \"false\", \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"revcomp\": \"false\"}, \"filter_options\": {\"discard_trimmed\": \"false\", \"discard_untrimmed\": \"false\", \"minimum_length\": \"200\", \"maximum_length\": null, \"length_R2_options\": {\"length_R2_status\": \"False\", \"__current_case__\": 1}, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"discard_cassava\": \"false\"}, \"library\": {\"type\": \"paired\", \"__current_case__\": 1, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"input_2\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}, \"r2\": {\"adapters2\": [], \"front_adapters2\": [], \"anywhere_adapters2\": [], \"cut2\": \"0\", \"quality_cutoff2\": \"\"}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"quality_cutoff\": \"20\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"strip_suffix\": \"\", \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.0+galaxy0",
-                        "type": "tool",
-                        "uuid": "67ddef5c-cde3-462d-a189-77028682a357",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out1",
-                                "uuid": "7b3621e4-5077-4ac8-95d3-61a94a6ee664"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out2",
-                                "uuid": "f7db5a96-f4e7-4caf-8e78-093d4e6b007c"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "report",
-                                "uuid": "ff6985ad-6afe-4cf7-9def-223fdd5e5f62"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "e23834b7-d5be-44b1-bbca-7bdea6884022",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
+                        "content_id": null,
                         "errors": null,
                         "id": 3,
-                        "input_connections": {
-                            "input_option|fastq_input1": {
-                                "id": 2,
-                                "output_name": "out1"
-                            },
-                            "input_option|fastq_input2": {
-                                "id": 2,
-                                "output_name": "out2"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "MEGAHIT",
-                        "outputs": [
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "trainset_alignment"
                             }
                         ],
+                        "label": "Trainset PDS alignment",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 735.9765625,
-                            "top": 301.97265625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "14ddfc8ffb93",
-                            "name": "megahit",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 2468.5,
+                            "top": 280.5
                         },
-                        "tool_state": "{\"advanced_section\": {\"nomercy\": \"false\", \"bubble_level\": \"2\", \"merge_level\": \"20,0.95\", \"prune_level\": \"2\", \"prune_depth\": \"2\", \"disconnect_ratio\": \"0.1\", \"low_local_ratio\": \"0.2\", \"cleaning_rounds\": \"5\", \"nolocal\": \"false\", \"kmin1pass\": \"false\"}, \"basic_section\": {\"min_count\": \"2\", \"k_mer\": {\"k_mer_method\": \"klist_method\", \"__current_case__\": 0, \"k_list\": \"21,29,39,59,79,99,119,141\"}}, \"input_option\": {\"choice\": \"paired\", \"__current_case__\": 2, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"fastq_input2\": {\"__class__\": \"ConnectedValue\"}}, \"output_section\": {\"min_contig_len\": \"200\", \"show_intermediate_contigs\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.9+galaxy0",
-                        "type": "tool",
-                        "uuid": "0e1e0ffb-4536-4802-b886-5f5f391255d1",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "7a0e5487-3923-46e0-9976-d3fdc3fe7e09"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "7368ffb8-03bd-42b4-bb81-53d147cd419b",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
+                        "content_id": null,
                         "errors": null,
                         "id": 4,
-                        "input_connections": {
-                            "library|input_1": {
-                                "id": 2,
-                                "output_name": "out1"
-                            },
-                            "library|input_2": {
-                                "id": 2,
-                                "output_name": "out2"
-                            },
-                            "reference_genome|own_file": {
-                                "id": 3,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Bowtie2",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "bam"
-                            },
-                            {
-                                "name": "mapping_stats",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 979.00390625,
-                            "top": 40.9765625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f6877ad76b00",
-                            "name": "bowtie2",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"no_presets\"}, \"library\": {\"type\": \"paired\", \"__current_case__\": 1, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"input_2\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": \"false\", \"aligned_file\": \"false\", \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 1, \"own_file\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.4.5+galaxy1",
-                        "type": "tool",
-                        "uuid": "cd8574f0-da3e-4dc1-848e-6f21c57831e6",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "mapping_stats",
-                                "uuid": "cf119c49-eee7-448a-bfff-0f1053f87821"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "44b0908f-2158-4ea2-be6f-65c0dd803bcb"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "infile": {
-                                "id": 4,
-                                "output_name": "output"
-                            }
-                        },
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool BAM filter",
-                                "name": "excludebed"
-                            },
-                            {
-                                "description": "runtime parameter for tool BAM filter",
-                                "name": "includebed"
-                            }
-                        ],
-                        "label": null,
-                        "name": "BAM filter",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "bam"
+                                "description": "",
+                                "name": "trainset_taxonomy"
                             }
                         ],
+                        "label": "Trainset PDS taxonomy",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1265.01953125,
-                            "top": 0.0
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2e957d4c4b95",
-                            "name": "ngsutils_bam_filter",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 2476.5,
+                            "top": 389.5
                         },
-                        "tool_state": "{\"excludebed\": {\"__class__\": \"RuntimeValue\"}, \"excluderef\": \"\", \"ignore_strand\": \"false\", \"includebed\": {\"__class__\": \"RuntimeValue\"}, \"includeref\": \"\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mapped\": \"false\", \"mask\": \"\", \"maximum_mismatch_ratio\": null, \"maxlen\": null, \"minlen\": null, \"mismatch\": null, \"nopcrdup\": \"false\", \"noproperpair\": \"false\", \"noqcfail\": \"false\", \"nosecondary\": \"false\", \"properpair\": \"false\", \"uniq\": \"-1\", \"uniq_start\": \"false\", \"unmapped\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.5.9",
-                        "type": "tool",
-                        "uuid": "e2b45ca6-2a67-4b95-a454-5c67fa87bccb",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "c1c6c99c-c810-41f4-84f3-5998c50b1422"
-                            }
-                        ]
-                    },
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "31d8b02c-9ecc-4d55-ac86-8930adb5abc8",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSILVA Reference\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nAnguil Soil Sample\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nPampa Soil Sample\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nTrainset PDS alignment\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nTrainset PDS taxonomy\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Merge.files\"];\n  2 -->|output| 5;\n  1 -->|output| 5;\n  6[\"Make.group\"];\n  1 -->|output| 6;\n  2 -->|output| 6;\n  7[\"Unique.seqs\"];\n  5 -->|output| 7;\n  8[\"Count.seqs\"];\n  6 -->|output| 8;\n  7 -->|out_names| 8;\n  9[\"Summary.seqs\"];\n  8 -->|seq_count| 9;\n  7 -->|out_fasta| 9;\n  10[\"Screen.seqs\"];\n  7 -->|out_fasta| 10;\n  8 -->|seq_count| 10;\n  11[\"Align.seqs\"];\n  0 -->|output| 11;\n  10 -->|fasta_out| 11;\n  12[\"Summary.seqs\"];\n  10 -->|count_out| 12;\n  11 -->|out_file| 12;\n  13[\"Screen.seqs\"];\n  11 -->|out_file| 13;\n  10 -->|count_out| 13;\n  14[\"Filter.seqs\"];\n  13 -->|fasta_out| 14;\n  15[\"Pre.cluster\"];\n  14 -->|filteredfasta| 15;\n  13 -->|count_out| 15;\n  16[\"Classify.seqs\"];\n  15 -->|count_out| 16;\n  3 -->|output| 16;\n  15 -->|fasta_out| 16;\n  4 -->|output| 16;\n  17[\"Cluster.split\"];\n  16 -->|taxonomy_out| 17;\n  15 -->|fasta_out| 17;\n  15 -->|count_out| 17;\n  18[\"Make.shared\"];\n  15 -->|count_out| 18;\n  17 -->|otulist| 18;\n  62dd9aef-795b-44ba-bfa2-e63ed96c9d09[\"Output\\nmothur_make_shared_shared\"];\n  18 --> 62dd9aef-795b-44ba-bfa2-e63ed96c9d09;\n  style 62dd9aef-795b-44ba-bfa2-e63ed96c9d09 stroke:#2c3143,stroke-width:4px;\n  19[\"Classify.otu\"];\n  15 -->|count_out| 19;\n  16 -->|taxonomy_out| 19;\n  17 -->|otulist| 19;\n  20[\"Make.biom\"];\n  18 -->|shared| 20;\n  19 -->|taxonomies| 20;\n  21[\"Visualize  with Krona\"];\n  19 -->|taxonomies| 21;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Amplicon Tutorial",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.36.1.0",
                         "errors": null,
-                        "id": 6,
+                        "id": 18,
                         "input_connections": {
-                            "infile": {
-                                "id": 4,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool BAM filter",
-                                "name": "excludebed"
+                            "intype|group": {
+                                "id": 15,
+                                "output_name": "count_out"
                             },
-                            {
-                                "description": "runtime parameter for tool BAM filter",
-                                "name": "includebed"
-                            }
-                        ],
-                        "label": null,
-                        "name": "BAM filter",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "bam"
-                            }
-                        ],
-                        "position": {
-                            "left": 1268.0078125,
-                            "top": 354.00390625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2e957d4c4b95",
-                            "name": "ngsutils_bam_filter",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"excludebed\": {\"__class__\": \"RuntimeValue\"}, \"excluderef\": \"\", \"ignore_strand\": \"false\", \"includebed\": {\"__class__\": \"RuntimeValue\"}, \"includeref\": \"\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mapped\": \"true\", \"mask\": \"\", \"maximum_mismatch_ratio\": null, \"maxlen\": null, \"minlen\": null, \"mismatch\": null, \"nopcrdup\": \"false\", \"noproperpair\": \"false\", \"noqcfail\": \"false\", \"nosecondary\": \"false\", \"properpair\": \"false\", \"uniq\": \"-1\", \"uniq_start\": \"false\", \"unmapped\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.5.9",
-                        "type": "tool",
-                        "uuid": "eb538482-dcf6-4509-b4b0-3da71ac6c600",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "b7c08a3a-296d-4352-90a6-423897d8cc74"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "input_bams": {
-                                "id": 5,
-                                "output_name": "outfile"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Convert, Merge, Randomize",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 1559.00390625,
-                            "top": 110.9765625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "befc9dad4ca8",
-                            "name": "bamtools",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"convert\", \"__current_case__\": 0, \"format_type\": {\"format_type_selector\": \"sam\", \"__current_case__\": 6, \"noheader\": \"false\"}}, \"input_bams\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.5.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "8dc250e9-c89b-40be-8432-08a7330d6e27",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "8ad07a76-7793-43b2-add3-7e236a696172"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "input_bams": {
-                                "id": 6,
-                                "output_name": "outfile"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Convert, Merge, Randomize",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 1548.0078125,
-                            "top": 462.98828125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "befc9dad4ca8",
-                            "name": "bamtools",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"convert\", \"__current_case__\": 0, \"format_type\": {\"format_type_selector\": \"sam\", \"__current_case__\": 6, \"noheader\": \"false\"}}, \"input_bams\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.5.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "b5c1bcac-9624-477c-998f-a0988b110a26",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "9801f8ee-e700-4e9b-bbfc-7ccf7aa99372"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "random_lines1",
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "input": {
-                                "id": 7,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Select random lines",
-                                "name": "input"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Select random lines",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 1823.0078125,
-                            "top": 182.98828125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "random_lines1",
-                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"num_lines\": \"210000\", \"seed_source\": {\"seed_source_selector\": \"no_seed\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2",
-                        "type": "tool",
-                        "uuid": "88f4ed97-5899-48f1-a5de-256be6e58862",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "69da2900-e66d-4d95-9bdb-1d9f801097e3"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "random_lines1",
-                        "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "input": {
-                                "id": 8,
-                                "output_name": "out_file1"
+                            "intype|otu": {
+                                "id": 17,
+                                "output_name": "otulist"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Select random lines",
-                                "name": "input"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Select random lines",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 1826.9921875,
-                            "top": 535.99609375
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "random_lines1",
-                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"num_lines\": \"1000000\", \"seed_source\": {\"seed_source_selector\": \"no_seed\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2",
-                        "type": "tool",
-                        "uuid": "9064c0e8-fdc9-4347-99c2-bd6d97104fc9",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "fd4f3605-1f48-4583-b11a-91a9869e7946"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
-                        "errors": null,
-                        "id": 11,
-                        "input_connections": {
-                            "input": {
-                                "id": 9,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Filter Tabular",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 2081.015625,
-                            "top": 212.98828125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "34d29339abab",
-                            "name": "filter_tabular",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"select_columns\", \"__current_case__\": 7, \"columns\": \"1\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.0",
-                        "type": "tool",
-                        "uuid": "302a62bb-98f7-4998-b290-281bb52e3c70",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "e83fbb91-742e-448f-8592-bdf37ce3cbdf"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
-                        "errors": null,
-                        "id": 12,
-                        "input_connections": {
-                            "input": {
-                                "id": 10,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Filter Tabular",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 2085,
-                            "top": 566.97265625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "34d29339abab",
-                            "name": "filter_tabular",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"select_columns\", \"__current_case__\": 7, \"columns\": \"1\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.0",
-                        "type": "tool",
-                        "uuid": "ab1a4102-7bb2-4ba7-80d1-2a532b410201",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "2701a2bd-2ec9-433a-9f26-7f35410ec018"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
-                        "errors": null,
-                        "id": 13,
-                        "input_connections": {
-                            "input": {
-                                "id": 11,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Unique",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 2330,
-                            "top": 265.99609375
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "7ce75adb93be",
-                            "name": "unique",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"ignore_case\": \"false\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"is_numeric\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3",
-                        "type": "tool",
-                        "uuid": "2a68a6a4-4d3d-4de3-bc64-35edc63287f9",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "b2bb66d7-fe76-4ce3-bb5b-72c979a755d1"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
-                        "errors": null,
-                        "id": 14,
-                        "input_connections": {
-                            "input": {
-                                "id": 12,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Unique",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 2331.97265625,
-                            "top": 617.94921875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "7ce75adb93be",
-                            "name": "unique",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"ignore_case\": \"false\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"is_numeric\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3",
-                        "type": "tool",
-                        "uuid": "c2d1dc5c-4d14-45e5-9bb9-bdab787ea5f3",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "df0bbae1-b735-4cf4-a5a3-ef4f8b525a4e"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-                        "errors": null,
-                        "id": 15,
-                        "input_connections": {
-                            "inputs": [
-                                {
-                                    "id": 13,
-                                    "output_name": "outfile"
-                                },
-                                {
-                                    "id": 14,
-                                    "output_name": "outfile"
-                                }
-                            ]
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Concatenate datasets",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 2575,
-                            "top": 417.98828125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f46f0e4f75c4",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.1",
-                        "type": "tool",
-                        "uuid": "bf2ba224-25ae-4ec3-9a1f-7cb1afd0aef2",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "53ae320a-b570-4985-ae2a-8344e15e43f9"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-                        "errors": null,
-                        "id": 16,
-                        "input_connections": {
-                            "in_file": {
-                                "id": 2,
-                                "output_name": "out1"
+                                "description": "runtime parameter for tool Make.shared",
+                                "name": "intype"
                             },
-                            "source|name_list": {
-                                "id": 15,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "seqtk_subseq",
-                        "outputs": [
                             {
-                                "name": "default",
-                                "type": "input"
+                                "description": "runtime parameter for tool Make.shared",
+                                "name": "intype"
                             }
                         ],
-                        "position": {
-                            "left": 2847.98828125,
-                            "top": 819.98046875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3da72230c066",
-                            "name": "seqtk",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"in_file\": {\"__class__\": \"ConnectedValue\"}, \"l\": \"0\", \"source\": {\"type\": \"name\", \"__current_case__\": 1, \"name_list\": {\"__class__\": \"ConnectedValue\"}}, \"t\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3.1",
-                        "type": "tool",
-                        "uuid": "478adb2b-4910-4aed-af4e-2a66e9a1922c",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "default",
-                                "uuid": "b47e4af0-c185-4b6f-a529-6f0ef96a14ab"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-                        "errors": null,
-                        "id": 17,
-                        "input_connections": {
-                            "in_file": {
-                                "id": 2,
-                                "output_name": "out2"
-                            },
-                            "source|name_list": {
-                                "id": 15,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
                         "label": null,
-                        "name": "seqtk_subseq",
+                        "name": "Make.shared",
                         "outputs": [
                             {
-                                "name": "default",
+                                "name": "labelshares",
                                 "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 2836.97265625,
-                            "top": 1019.98046875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3da72230c066",
-                            "name": "seqtk",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"in_file\": {\"__class__\": \"ConnectedValue\"}, \"l\": \"0\", \"source\": {\"type\": \"name\", \"__current_case__\": 1, \"name_list\": {\"__class__\": \"ConnectedValue\"}}, \"t\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3.1",
-                        "type": "tool",
-                        "uuid": "81ae5423-c7d0-4ceb-a6e4-168ab1f3fd35",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "default",
-                                "uuid": "c7de5bbe-f941-4772-bb32-15aeff98678a"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-                        "errors": null,
-                        "id": 18,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 16,
-                                "output_name": "default"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "adapters"
                             },
                             {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "contaminants"
+                                "name": "logfile",
+                                "type": "txt"
                             },
                             {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "limits"
-                            }
-                        ],
-                        "label": null,
-                        "name": "FastQC",
-                        "outputs": [
-                            {
-                                "name": "html_file",
-                                "type": "html"
+                                "name": "shared",
+                                "type": "mothur.shared"
                             },
                             {
-                                "name": "text_file",
-                                "type": "txt"
+                                "name": "groupout",
+                                "type": "mothur.groups"
                             }
                         ],
                         "position": {
-                            "left": 3135.9765625,
-                            "top": 775.99609375
+                            "left": 3069,
+                            "top": 265
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.36.1.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "3d0c7bdf12f5",
-                            "name": "fastqc",
-                            "owner": "devteam",
+                            "changeset_revision": "83dabeeadb55",
+                            "name": "mothur_make_shared",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adapters\": {\"__class__\": \"RuntimeValue\"}, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"min_length\": null, \"nogroup\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.73+galaxy0",
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"intype\": \"{\\\"group\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"label\\\": [\\\"0.03\\\"], \\\"groups\\\": null, \\\"infile\\\": \\\"otulist\\\", \\\"otu\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"chromInfo\": \"\\\"/data/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
+                        "tool_version": "1.36.1.0",
                         "type": "tool",
-                        "uuid": "6d6cee2a-b879-463b-81d1-7ab4f72ca04b",
+                        "uuid": "d554ed42-8658-47c5-952f-9dc73834f267",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "text_file",
-                                "uuid": "ca3ea14a-b1cc-481d-b1a3-2b46b8d24809"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "html_file",
-                                "uuid": "6849e3f4-33bc-47a9-8ef5-b7cbbdfe0d93"
+                                "label": "mothur_make_shared_shared",
+                                "output_name": "shared",
+                                "uuid": "62dd9aef-795b-44ba-bfa2-e63ed96c9d09"
                             }
                         ]
-                    },
+                    }
+                ],
+                "parent_id": "microbiome/general-tutorial",
+                "path": "topics/microbiome/tutorials/general-tutorial/workflows/amplicon.ga",
+                "tags": [
+                    "microbiome"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "Amplicon Tutorial",
+                "topic_id": "microbiome",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-general-tutorial/versions/amplicon",
+                "tutorial_id": "general-tutorial",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/general-tutorial/workflows/amplicon.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/general-tutorial/workflows/amplicon.html",
+                "version": 1,
+                "wfid": "microbiome-general-tutorial",
+                "wfname": "amplicon",
+                "workflow": "amplicon.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.36.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.36.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.36.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.36.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.36.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.36.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.36.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_group/mothur_make_group/1.36.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.36.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.36.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.36.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.36.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.36.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.36.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/krona-text/1"
+                ],
+                "workflowhub_id": "1070"
+            },
+            {
+                "creators": [],
+                "description": "Analyses of metagenomics data - The global picture",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[label=\"MetaPhlAn2\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Format MetaPhlAn2\"]\n  1 -> 2 [label=\"output_file\"]\n  3[label=\"HUMAnN2\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output_file\"]\n  4[label=\"Krona pie chart\"]\n  2 -> 4 [label=\"krona\"]\n  5[label=\"Renormalize\"]\n  3 -> 5 [label=\"gene_families_tsv\"]\n  6[label=\"Regroup\"]\n  3 -> 6 [label=\"gene_families_tsv\"]\n  7[label=\"Renormalize\"]\n  6 -> 7 [label=\"output_table\"]\n}",
+                "history": [
+                    {
+                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
+                        "message": "Rename metagenomics topic to microbiome",
+                        "num": 1,
+                        "short_hash": "0e0a2f2cc",
+                        "unix": "1704901629"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 19,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 17,
-                                "output_name": "default"
-                            }
-                        },
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "adapters"
-                            },
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "contaminants"
-                            },
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "limits"
+                                "description": "",
+                                "name": "SRR606451_pampa.fasta"
                             }
                         ],
                         "label": null,
-                        "name": "FastQC",
-                        "outputs": [
-                            {
-                                "name": "html_file",
-                                "type": "html"
-                            },
-                            {
-                                "name": "text_file",
-                                "type": "txt"
-                            }
-                        ],
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 3133.984375,
-                            "top": 1104.98046875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3d0c7bdf12f5",
-                            "name": "fastqc",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 10,
+                            "top": 10
                         },
-                        "tool_state": "{\"adapters\": {\"__class__\": \"RuntimeValue\"}, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"min_length\": null, \"nogroup\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.73+galaxy0",
-                        "type": "tool",
-                        "uuid": "54fc20b8-5520-4b93-a7d8-ed447df19b3c",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "html_file",
-                                "uuid": "a85a4180-b2ab-4cac-9c71-76aee3df673f"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "text_file",
-                                "uuid": "65e24721-ec93-4648-9310-c3c2609b7818"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"SRR606451_pampa.fasta\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "2b9a76e9-f7fc-451a-a6f7-16d87f96547b",
+                        "workflow_outputs": []
                     }
                 ],
-                "parent_id": "microbiome/metagenomics-assembly",
-                "path": "topics/microbiome/tutorials/metagenomics-assembly/workflows/workflow-generate-dataset-for-assembly-tutorial.ga",
-                "tags": [],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"MetaPhlAn2\"];\n  0 -->|output| 1;\n  2[\"Format MetaPhlAn2\"];\n  1 -->|output_file| 2;\n  3[\"HUMAnN2\"];\n  0 -->|output| 3;\n  1 -->|output_file| 3;\n  4[\"Krona pie chart\"];\n  2 -->|krona| 4;\n  5[\"Renormalize\"];\n  3 -->|gene_families_tsv| 5;\n  6[\"Regroup\"];\n  3 -->|gene_families_tsv| 6;\n  7[\"Renormalize\"];\n  6 -->|output_table| 7;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "WGS Part In \"Analyses Of Metagenomics Data - The Global Picture\"",
+                "outputs": [],
+                "parent_id": "microbiome/general-tutorial",
+                "path": "topics/microbiome/tutorials/general-tutorial/workflows/wgs-worklow.ga",
+                "tags": [
+                    "microbiome"
+                ],
                 "test_results": null,
                 "tests": false,
-                "title": "workflow-generate-dataset-for-assembly-tutorial",
+                "title": "WGS Part In \"Analyses Of Metagenomics Data - The Global Picture\"",
                 "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-metagenomics-assembly/versions/workflow-generate-dataset-for-assembly-tutorial",
-                "tutorial_id": "metagenomics-assembly",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metagenomics-assembly/workflows/workflow-generate-dataset-for-assembly-tutorial.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metagenomics-assembly/workflows/workflow-generate-dataset-for-assembly-tutorial.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-general-tutorial/versions/wgs-worklow",
+                "tutorial_id": "general-tutorial",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/general-tutorial/workflows/wgs-worklow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/general-tutorial/workflows/wgs-worklow.html",
                 "version": 1,
-                "wfid": "microbiome-metagenomics-assembly",
-                "wfname": "workflow-generate-dataset-for-assembly-tutorial",
-                "workflow": "workflow-generate-dataset-for-assembly-tutorial.ga",
+                "wfid": "microbiome-general-tutorial",
+                "wfname": "wgs-worklow",
+                "workflow": "wgs-worklow.ga",
                 "workflow_tools": [
-                    "random_lines1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-                    "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0"
+                    "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.9.9.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/humann2_regroup_table/humann2_regroup_table/0.9.9.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/humann2_renorm_table/humann2_renorm_table/0.9.9.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0"
                 ],
-                "workflowhub_id": "1099"
+                "workflowhub_id": "1067"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/7818827"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.815875"
     },
     {
         "admin_install": {
@@ -139869,194 +141822,81 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "fbf99087e067",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "fbf99087e067",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "fbf99087e067",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "column_maker",
-                    "owner": "devteam",
-                    "revisions": "6595517c2dd8",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collection_element_identifiers",
-                    "owner": "iuc",
-                    "revisions": "d3c07d270a50",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "dada2_assigntaxonomyaddspecies",
-                    "owner": "iuc",
-                    "revisions": "7c2100246a2f",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "dada2_assigntaxonomyaddspecies",
-                    "owner": "iuc",
-                    "revisions": "65db807336bc",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "dada2_dada",
-                    "owner": "iuc",
-                    "revisions": "96336c6a2bb7",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "dada2_dada",
-                    "owner": "iuc",
-                    "revisions": "00f5005840fa",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "dada2_filterandtrim",
-                    "owner": "iuc",
-                    "revisions": "addaf9d22850",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "dada2_filterandtrim",
-                    "owner": "iuc",
-                    "revisions": "e8fba04706d3",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "dada2_learnerrors",
-                    "owner": "iuc",
-                    "revisions": "75403243703a",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "dada2_learnerrors",
-                    "owner": "iuc",
-                    "revisions": "5fe3edf19b9c",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "dada2_makesequencetable",
-                    "owner": "iuc",
-                    "revisions": "43c99742158b",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "dada2_makesequencetable",
-                    "owner": "iuc",
-                    "revisions": "75c8945b0da2",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "dada2_mergepairs",
-                    "owner": "iuc",
-                    "revisions": "5c865a382933",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "dada2_mergepairs",
-                    "owner": "iuc",
-                    "revisions": "35176674168c",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "dada2_plotqualityprofile",
-                    "owner": "iuc",
-                    "revisions": "7b8cb2b02978",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "dada2_plotqualityprofile",
-                    "owner": "iuc",
-                    "revisions": "cae017b76acb",
+                    "name": "taxonomy_krona_chart",
+                    "owner": "crs4",
+                    "revisions": "e9005d1f3cfd",
                     "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "dada2_removebimeradenovo",
-                    "owner": "iuc",
-                    "revisions": "7136e9ab70db",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "3d0c7bdf12f5",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "dada2_removebimeradenovo",
+                    "name": "fastp",
                     "owner": "iuc",
-                    "revisions": "073608a50ac3",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "revisions": "65b93b623c77",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "dada2_seqcounts",
+                    "name": "kraken2",
                     "owner": "iuc",
-                    "revisions": "19299bb1c6af",
+                    "revisions": "20e2f64aa1fe",
                     "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "dada2_seqcounts",
+                    "name": "krakentools_kreport2krona",
                     "owner": "iuc",
-                    "revisions": "a7817705348e",
+                    "revisions": "88d274322340",
                     "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "phyloseq_from_dada2",
+                    "name": "porechop",
                     "owner": "iuc",
-                    "revisions": "87064cb77a52",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "revisions": "543cbeef3949",
+                    "tool_panel_section_label": "Nanopore",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 6595517c2dd8\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_element_identifiers\n  owner: iuc\n  revisions: d3c07d270a50\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_assigntaxonomyaddspecies\n  owner: iuc\n  revisions: 7c2100246a2f\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_assigntaxonomyaddspecies\n  owner: iuc\n  revisions: 65db807336bc\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_dada\n  owner: iuc\n  revisions: 96336c6a2bb7\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_dada\n  owner: iuc\n  revisions: 00f5005840fa\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_filterandtrim\n  owner: iuc\n  revisions: addaf9d22850\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_filterandtrim\n  owner: iuc\n  revisions: e8fba04706d3\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_learnerrors\n  owner: iuc\n  revisions: 75403243703a\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_learnerrors\n  owner: iuc\n  revisions: 5fe3edf19b9c\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_makesequencetable\n  owner: iuc\n  revisions: 43c99742158b\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_makesequencetable\n  owner: iuc\n  revisions: 75c8945b0da2\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_mergepairs\n  owner: iuc\n  revisions: 5c865a382933\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_mergepairs\n  owner: iuc\n  revisions: 35176674168c\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_plotqualityprofile\n  owner: iuc\n  revisions: 7b8cb2b02978\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_plotqualityprofile\n  owner: iuc\n  revisions: cae017b76acb\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_removebimeradenovo\n  owner: iuc\n  revisions: 7136e9ab70db\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_removebimeradenovo\n  owner: iuc\n  revisions: '073608a50ac3'\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_seqcounts\n  owner: iuc\n  revisions: 19299bb1c6af\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_seqcounts\n  owner: iuc\n  revisions: a7817705348e\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: phyloseq_from_dada2\n  owner: iuc\n  revisions: 87064cb77a52\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/dada-16S/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: taxonomy_krona_chart\n  owner: crs4\n  revisions: e9005d1f3cfd\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: 20e2f64aa1fe\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: krakentools_kreport2krona\n  owner: iuc\n  revisions: 88d274322340\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: porechop\n  owner: iuc\n  revisions: 543cbeef3949\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/beer-data-analysis/tutorial.json",
         "contributions": {
             "authorship": [
-                "bebatut"
+                "plushz",
+                "chensy96",
+                "bebatut",
+                "teresa-m"
             ],
-            "editing": [
-                "bernt-matthias",
-                "clsiguret"
+            "funding": [
+                "gallantries"
             ]
         },
         "contributors": [
+            {
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "id": "plushz",
+                "joined": "2022-03",
+                "name": "Polina Polunina",
+                "orcid": "0000-0002-0507-4602",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/plushz/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/plushz.json"
+            },
+            {
+                "id": "chensy96",
+                "joined": "2022-05",
+                "name": "Siyu Chen",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/chensy96/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/chensy96.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
@@ -140083,162 +141923,187 @@
                 "twitter": "bebatut",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             },
-            {
-                "elixir_node": "de",
-                "id": "bernt-matthias",
-                "joined": "2017-09",
-                "name": "Matthias Bernt",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bernt-matthias/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bernt-matthias.json"
-            },
             {
                 "affiliations": [
-                    "ifb",
+                    "uni-freiburg",
                     "elixir-europe"
                 ],
-                "elixir_node": "fr",
-                "email": "clea.siguret@gmail.com",
-                "id": "clsiguret",
-                "joined": "2024-04",
-                "linkedin": "cl\u00e9a-siguret-58423b107",
-                "matrix": "clsiguret:matrix.org",
-                "name": "Clea Siguret",
-                "orcid": "0009-0005-6140-0379",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/clsiguret/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/clsiguret.json"
+                "id": "teresa-m",
+                "joined": "2022-09",
+                "name": "Teresa M\u00fcller",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/microbiome/tutorials/dada-16S",
+        "dir": "topics/microbiome/tutorials/beer-data-analysis",
         "edam_ontology": [
+            "topic_3174",
             "topic_3697",
             "topic_0637",
-            "topic_0080",
-            "topic_4038"
+            "topic_0080"
         ],
         "edam_operation": [
+            "Taxonomic classification",
+            "Statistical calculation",
+            "Aggregation",
             "Visualisation",
-            "Analysis",
-            "Variant calling",
-            "DNA barcoding",
-            "Deposition"
+            "Sequencing quality control",
+            "Sequence composition calculation",
+            "Sequence contamination filtering"
         ],
         "edam_topic": [
+            "Metagenomics",
             "Microbial ecology",
             "Taxonomy",
             "Sequence analysis"
         ],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "GalaxyTrakr",
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "microbiome/dada-16S",
-        "inexact_supported_servers": [],
+        "id": "microbiome/beer-data-analysis",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
+        ],
         "js_requirements": {
-            "mathjax": 14594,
+            "mathjax": 12074,
             "mermaid": false
         },
         "key_points": [
-            "DADA2 allows for the generation of precise ASV tables, providing higher resolution and more accurate representation of microbial communities compared to traditional OTU-based methods.",
-            "Key steps such as quality filtering, error rate learning, and chimera removal are essential in the DADA2 pipeline to ensure the reliability and accuracy of the resulting ASV data.",
-            "Tools like phyloseq can be effectively used to explore and visualize ASV tables, facilitating deeper ecological and evolutionary insights into microbial diversity and community structure."
+            "Data obtained by sequencing needs to be checked for quality and cleaned before further processing",
+            "Yeast species but also contamination can be identified and visualized directly from the sequences using several bioinformatics tools",
+            "With its graphical interface, Galaxy makes it easy to use the needed bioinformatics tools",
+            "Beer microbiome is not just made of yeast and can be quite complex"
         ],
         "layout": "tutorial_hands_on",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-09",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Identify the key steps in the DADA2 workflow for generating an ASV table from 16S rRNA gene sequencing data",
-            "Explain the importance of quality filtering, error rate learning, and chimera removal in ensuring accurate microbial community analysis",
-            "Execute the DADA2 pipeline to process raw 16S sequencing data and produce a high-resolution ASV table",
-            "Compare the advantages of ASV-based methods over traditional OTU-based approaches in terms of accuracy and resolution",
-            "Assess the effectiveness of using phyloseq for exploring and visualizing ASV data to gain ecological and evolutionary insights"
+            "Inspect metagenomics data",
+            "Run metagenomics tools",
+            "Identify yeast species contained in a sequenced beer sample using DNA",
+            "Visualize the microbiome community of a beer sample"
         ],
-        "pageviews": 840,
-        "pub_date": "2024-06-05",
+        "pageviews": 1942,
+        "pub_date": "2022-09-29",
         "questions": [
-            "What are the primary steps involved in generating an ASV table using DADA2 from 16S rRNA gene sequencing data?",
-            "How does DADA2 improve the accuracy of microbial community analysis compared to traditional OTU-based methods?",
-            "What is the importance of quality filtering in the DADA2 workflow, and how does it impact downstream analyses?",
-            "How does the error rate learning process contribute to the identification of true biological sequences in DADA2?",
-            "What role does chimera removal play in the DADA2 pipeline, and why is it crucial for obtaining reliable ASV data?",
-            "How can phyloseq be used to explore and visualize the ASV table generated by DADA2, and what types of ecological insights can it provide?"
+            "How can yeast strains in a beer sample be identified?",
+            "How can we process metagenomic data sequenced using Nanopore?"
         ],
-        "short_id": "T00441",
+        "recordings": [
+            {
+                "captioners": [
+                    "sophia120199"
+                ],
+                "date": "2023-05-10",
+                "galaxy_version": "23.01",
+                "length": "1H5M",
+                "speakers": [
+                    "bebatut"
+                ],
+                "youtube_id": "PJeS06yiJUM"
+            }
+        ],
+        "redirect_from": [
+            "/topics/metagenomics/tutorials/beer-data-analysis/tutorial",
+            "/short/microbiome/beer-data-analysis",
+            "/short/T00200",
+            "/short/T00384"
+        ],
+        "short_id": "T00384",
         "short_tools": [
-            "__UNZIP_COLLECTION__",
-            "phyloseq_from_dada2",
-            "interactive_tool_phyloseq",
-            "dada2_filterAndTrim",
-            "Grouping1",
-            "__SORTLIST__",
-            "dada2_learnErrors",
-            "dada2_dada",
-            "dada2_plotQualityProfile",
-            "tp_replace_in_column",
-            "dada2_removeBimeraDenovo",
-            "cat1",
-            "dada2_assignTaxonomyAddspecies",
-            "dada2_mergePairs",
-            "dada2_makeSequenceTable",
-            "collection_element_identifiers",
-            "dada2_seqCounts",
-            "tp_replace_in_line",
-            "Add_a_column1",
-            "tp_head_tool"
+            "porechop",
+            "fastp",
+            "Filter1",
+            "taxonomy_krona_chart",
+            "kraken2",
+            "krakentools_kreport2krona",
+            "fastqc"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "metabarcoding",
+        "subtopic": "metagenomics",
         "supported_servers": {
             "exact": [
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ],
-            "inexact": []
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
         },
         "symlink": null,
         "tags": [
-            "metabarcoding",
-            "16S",
+            "nanopore",
+            "beer",
+            "citizen science",
+            "metagenomics",
             "microgalaxy"
         ],
-        "time_estimation": "3H",
-        "title": "Building an amplicon sequence variant (ASV) table from 16S data using DADA2",
+        "time_estimation": "1H",
+        "title": "Identification of the micro-organisms in a beer using Nanopore sequencing",
         "tools": [
-            "Grouping1",
-            "__SORTLIST__",
-            "__UNZIP_COLLECTION__",
-            "cat1",
-            "interactive_tool_phyloseq",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/1.28+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/1.30.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/1.28+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/1.30.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim/dada2_filterAndTrim/1.28+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim/dada2_filterAndTrim/1.30.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_learnerrors/dada2_learnErrors/1.28+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_learnerrors/dada2_learnErrors/1.30.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_makesequencetable/dada2_makeSequenceTable/1.28+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_makesequencetable/dada2_makeSequenceTable/1.30.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_mergepairs/dada2_mergePairs/1.28+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_mergepairs/dada2_mergePairs/1.30.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.28+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.30.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_removebimeradenovo/dada2_removeBimeraDenovo/1.28+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_removebimeradenovo/dada2_removeBimeraDenovo/1.30.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts/dada2_seqCounts/1.28+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts/dada2_seqCounts/1.30.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/phyloseq_from_dada2/phyloseq_from_dada2/1.46.0+galaxy0"
+            "Filter1",
+            "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0"
         ],
         "topic_name": "microbiome",
         "topic_name_human": "Microbiome",
@@ -140248,242 +142113,152 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "dada-16S",
+        "tutorial_name": "beer-data-analysis",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/dada-16S/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/dada-16S/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/beer-data-analysis/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/beer-data-analysis/tutorial.json"
         },
-        "version": 7,
+        "version": 4,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 124,
-        "visitors": 614,
+        "visit_duration": 178,
+        "visitors": 1239,
         "workflows": [
             {
                 "creators": [
-                    {
-                        "class": "Organization",
-                        "isNew": true,
-                        "name": ""
-                    },
                     {
                         "class": "Person",
                         "identifier": "0000-0001-9852-1987",
                         "name": "B\u00e9r\u00e9nice Batut"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0003-1252-9684",
+                        "name": "Teresa M\u00fcller"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-0507-4602",
+                        "name": "Polina Polunina"
                     }
                 ],
-                "description": "Building an amplicon sequence variant (ASV) table from 16S data using DADA2",
+                "description": "Identification of the micro-organisms in a beer using Nanopore sequencing",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nRaw reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nheader\"]\n  2[label=\"Sort collection\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"dada2: filterAndTrim\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"dada2: plotQualityProfile\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Unzip collection\"]\n  3 -> 5 [label=\"paired_output\"]\n  6[label=\"dada2: plotQualityProfile\"]\n  3 -> 6 [label=\"paired_output\"]\n  7[label=\"dada2: learnErrors\"]\n  5 -> 7 [label=\"forward\"]\n  8[label=\"dada2: learnErrors\"]\n  5 -> 8 [label=\"reverse\"]\n  9[label=\"dada2: dada\"]\n  5 -> 9 [label=\"forward\"]\n  7 -> 9 [label=\"errors\"]\n  10[label=\"dada2: dada\"]\n  5 -> 10 [label=\"reverse\"]\n  8 -> 10 [label=\"errors\"]\n  11[label=\"dada2: mergePairs\"]\n  9 -> 11 [label=\"data_collection\"]\n  10 -> 11 [label=\"data_collection\"]\n  5 -> 11 [label=\"forward\"]\n  5 -> 11 [label=\"reverse\"]\n  12[label=\"Extract element identifiers\"]\n  11 -> 12 [label=\"merged\"]\n  13[label=\"dada2: makeSequenceTable\"]\n  11 -> 13 [label=\"merged\"]\n  k3fd2597939df4698bad1aabfccbb7bd2[color=lightseagreen,label=\"Output\\nsequence_table\"]\n  13 -> k3fd2597939df4698bad1aabfccbb7bd2\n  14[label=\"Replace Text\"]\n  12 -> 14 [label=\"output\"]\n  15[label=\"dada2: removeBimeraDenovo\"]\n  13 -> 15 [label=\"stable\"]\n  16[label=\"Select first\"]\n  14 -> 16 [label=\"outfile\"]\n  17[label=\"dada2: sequence counts\"]\n  3 -> 17 [label=\"outtab\"]\n  9 -> 17 [label=\"data_collection\"]\n  10 -> 17 [label=\"data_collection\"]\n  11 -> 17 [label=\"merged\"]\n  15 -> 17 [label=\"stable_sequencetable\"]\n  kc758f86144bc4208b1f71f5106cb678e[color=lightseagreen,label=\"Output\\nsequence_counts\"]\n  17 -> kc758f86144bc4208b1f71f5106cb678e\n  18[label=\"dada2: assignTaxonomy and addSpecies\"]\n  15 -> 18 [label=\"stable_sequencetable\"]\n  k904fe0a2832945ca8493fc688fb216c3[color=lightseagreen,label=\"Output\\ntaxons\"]\n  18 -> k904fe0a2832945ca8493fc688fb216c3\n  19[label=\"Compute\"]\n  16 -> 19 [label=\"outfile\"]\n  20[label=\"Replace Text\"]\n  19 -> 20 [label=\"out_file1\"]\n  21[label=\"Concatenate datasets\"]\n  1 -> 21 [label=\"output\"]\n  20 -> 21 [label=\"outfile\"]\n  k5479d3203e8247a9a92b6ed5959459cf[color=lightseagreen,label=\"Output\\nmetada_table\"]\n  21 -> k5479d3203e8247a9a92b6ed5959459cf\n  22[label=\"Create phyloseq object\"]\n  21 -> 22 [label=\"out_file1\"]\n  15 -> 22 [label=\"stable_sequencetable\"]\n  18 -> 22 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ninput\"]\n  1[label=\"FastQC\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Porechop\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"fastp\"]\n  2 -> 3 [label=\"outfile\"]\n  4[label=\"Kraken2\"]\n  3 -> 4 [label=\"out1\"]\n  k3a8bad46ce3e4b2384157a539ee68ebb[color=lightseagreen,label=\"Output\\nkraken_report\"]\n  4 -> k3a8bad46ce3e4b2384157a539ee68ebb\n  5[label=\"Filter\"]\n  4 -> 5 [label=\"report_output\"]\n  6[label=\"Filter\"]\n  4 -> 6 [label=\"report_output\"]\n  7[label=\"Krakentools: Convert kraken report file\"]\n  4 -> 7 [label=\"report_output\"]\n  ke24a4cb0918444a09b4c0c554f059ace[color=lightseagreen,label=\"Output\\nkrakentool_report\"]\n  7 -> ke24a4cb0918444a09b4c0c554f059ace\n  8[label=\"Krona pie chart\"]\n  7 -> 8 [label=\"output\"]\n}",
                 "history": [
                     {
-                        "hash": "97f8a3d0b5448245415db5a9d9e8ab2182f3cce8",
-                        "message": "Fix Matthias' comments",
-                        "num": 2,
-                        "short_hash": "97f8a3d0b",
-                        "unix": "1717577403"
-                    },
-                    {
-                        "hash": "c1470a165d4a76032ae6f7eec76b94a40b7930bb",
-                        "message": "Finalize tuto, add workflow+test, rename tuto folder",
+                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
+                        "message": "Rename metagenomics topic to microbiome",
                         "num": 1,
-                        "short_hash": "c1470a165",
-                        "unix": "1717074187"
+                        "short_hash": "0e0a2f2cc",
+                        "unix": "1704901629"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "raw_reads",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "raw_reads",
-                                "name": "Raw reads"
+                                "description": "",
+                                "name": "input"
                             }
                         ],
-                        "label": "Raw reads",
-                        "name": "Input dataset collection",
+                        "label": "input",
+                        "name": "input",
                         "outputs": [],
                         "position": {
                             "left": 0,
-                            "top": 72
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "2b66bb2a-4ae5-436a-9428-11ac08ab9e39",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "header",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "header",
-                                "name": "header"
-                            }
-                        ],
-                        "label": "header",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 3019,
-                            "top": 196
+                            "top": 301
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"name\": \"input\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "582c8937-b1cb-4f01-977f-93d4ccc631b8",
+                        "uuid": "31e2b384-0c1d-42fc-9379-8fb62462bffb",
                         "when": null,
                         "workflow_outputs": []
                     }
                 ],
                 "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nRaw reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nheader\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Sort collection\"];\n  0 -->|output| 2;\n  3[\"dada2: filterAndTrim\"];\n  2 -->|output| 3;\n  4[\"dada2: plotQualityProfile\"];\n  2 -->|output| 4;\n  5[\"Unzip collection\"];\n  3 -->|paired_output| 5;\n  6[\"dada2: plotQualityProfile\"];\n  3 -->|paired_output| 6;\n  7[\"dada2: learnErrors\"];\n  5 -->|forward| 7;\n  8[\"dada2: learnErrors\"];\n  5 -->|reverse| 8;\n  9[\"dada2: dada\"];\n  5 -->|forward| 9;\n  7 -->|errors| 9;\n  10[\"dada2: dada\"];\n  5 -->|reverse| 10;\n  8 -->|errors| 10;\n  11[\"dada2: mergePairs\"];\n  9 -->|data_collection| 11;\n  10 -->|data_collection| 11;\n  5 -->|forward| 11;\n  5 -->|reverse| 11;\n  12[\"Extract element identifiers\"];\n  11 -->|merged| 12;\n  13[\"dada2: makeSequenceTable\"];\n  11 -->|merged| 13;\n  3fd25979-39df-4698-bad1-aabfccbb7bd2[\"Output\\nsequence_table\"];\n  13 --> 3fd25979-39df-4698-bad1-aabfccbb7bd2;\n  style 3fd25979-39df-4698-bad1-aabfccbb7bd2 stroke:#2c3143,stroke-width:4px;\n  14[\"Replace Text\"];\n  12 -->|output| 14;\n  15[\"dada2: removeBimeraDenovo\"];\n  13 -->|stable| 15;\n  16[\"Select first\"];\n  14 -->|outfile| 16;\n  17[\"dada2: sequence counts\"];\n  3 -->|outtab| 17;\n  9 -->|data_collection| 17;\n  10 -->|data_collection| 17;\n  11 -->|merged| 17;\n  15 -->|stable_sequencetable| 17;\n  c758f861-44bc-4208-b1f7-1f5106cb678e[\"Output\\nsequence_counts\"];\n  17 --> c758f861-44bc-4208-b1f7-1f5106cb678e;\n  style c758f861-44bc-4208-b1f7-1f5106cb678e stroke:#2c3143,stroke-width:4px;\n  18[\"dada2: assignTaxonomy and addSpecies\"];\n  15 -->|stable_sequencetable| 18;\n  904fe0a2-8329-45ca-8493-fc688fb216c3[\"Output\\ntaxons\"];\n  18 --> 904fe0a2-8329-45ca-8493-fc688fb216c3;\n  style 904fe0a2-8329-45ca-8493-fc688fb216c3 stroke:#2c3143,stroke-width:4px;\n  19[\"Compute\"];\n  16 -->|outfile| 19;\n  20[\"Replace Text\"];\n  19 -->|out_file1| 20;\n  21[\"Concatenate datasets\"];\n  1 -->|output| 21;\n  20 -->|outfile| 21;\n  5479d320-3e82-47a9-a92b-6ed5959459cf[\"Output\\nmetada_table\"];\n  21 --> 5479d320-3e82-47a9-a92b-6ed5959459cf;\n  style 5479d320-3e82-47a9-a92b-6ed5959459cf stroke:#2c3143,stroke-width:4px;\n  22[\"Create phyloseq object\"];\n  21 -->|out_file1| 22;\n  15 -->|stable_sequencetable| 22;\n  18 -->|output| 22;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Building an amplicon sequence variant (ASV) table from 16S data using DADA2",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ninput\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"FastQC\"];\n  0 -->|output| 1;\n  2[\"Porechop\"];\n  0 -->|output| 2;\n  3[\"fastp\"];\n  2 -->|outfile| 3;\n  4[\"Kraken2\"];\n  3 -->|out1| 4;\n  3a8bad46-ce3e-4b23-8415-7a539ee68ebb[\"Output\\nkraken_report\"];\n  4 --> 3a8bad46-ce3e-4b23-8415-7a539ee68ebb;\n  style 3a8bad46-ce3e-4b23-8415-7a539ee68ebb stroke:#2c3143,stroke-width:4px;\n  5[\"Filter\"];\n  4 -->|report_output| 5;\n  6[\"Filter\"];\n  4 -->|report_output| 6;\n  7[\"Krakentools: Convert kraken report file\"];\n  4 -->|report_output| 7;\n  e24a4cb0-9184-44a0-9b4c-0c554f059ace[\"Output\\nkrakentool_report\"];\n  7 --> e24a4cb0-9184-44a0-9b4c-0c554f059ace;\n  style e24a4cb0-9184-44a0-9b4c-0c554f059ace stroke:#2c3143,stroke-width:4px;\n  8[\"Krona pie chart\"];\n  7 -->|output| 8;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Identification of the micro-organisms in a beer using Nanopore sequencing",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/dada2_makesequencetable/dada2_makeSequenceTable/1.30.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
                         "errors": null,
-                        "id": 13,
+                        "id": 4,
                         "input_connections": {
-                            "samples": {
-                                "id": 11,
-                                "output_name": "merged"
+                            "single_paired|input_sequences": {
+                                "id": 3,
+                                "output_name": "out1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "dada2: makeSequenceTable",
+                        "name": "Kraken2",
                         "outputs": [
                             {
-                                "name": "stable",
-                                "type": "dada2_sequencetable"
-                            },
-                            {
-                                "name": "plot_output",
-                                "type": "pdf"
-                            }
-                        ],
-                        "position": {
-                            "left": 1970.000125527473,
-                            "top": 273.99367961852937
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dada2_makesequencetable/dada2_makeSequenceTable/1.30.0+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "75c8945b0da2",
-                            "name": "dada2_makesequencetable",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"filter_cond\": {\"filter_select\": \"no\", \"__current_case__\": 0}, \"orderBy\": \"abundance\", \"plot\": true, \"samples\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.30.0+galaxy0",
-                        "type": "tool",
-                        "uuid": "609d25ec-eea3-4893-9d8f-1de0bd185664",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "sequence_table",
-                                "output_name": "stable",
-                                "uuid": "3fd25979-39df-4698-bad1-aabfccbb7bd2"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts/dada2_seqCounts/1.30.0+galaxy0",
-                        "errors": null,
-                        "id": 17,
-                        "input_connections": {
-                            "inrep_0|input": {
-                                "id": 3,
-                                "output_name": "outtab"
-                            },
-                            "inrep_1|input": {
-                                "id": 9,
-                                "output_name": "data_collection"
-                            },
-                            "inrep_2|input": {
-                                "id": 10,
-                                "output_name": "data_collection"
-                            },
-                            "inrep_3|input": {
-                                "id": 11,
-                                "output_name": "merged"
+                                "name": "report_output",
+                                "type": "tabular"
                             },
-                            "inrep_4|input": {
-                                "id": 15,
-                                "output_name": "stable_sequencetable"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "dada2: sequence counts",
-                        "outputs": [
                             {
-                                "name": "counts",
+                                "name": "output",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 2550,
-                            "top": 154
+                            "left": 840,
+                            "top": 349
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts/dada2_seqCounts/1.30.0+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "a7817705348e",
-                            "name": "dada2_seqcounts",
+                            "changeset_revision": "e674066930b2",
+                            "name": "kraken2",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"inrep\": [{\"__index__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"name\": \"FiltTrim\"}, {\"__index__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}, \"name\": \"Dada Forward\"}, {\"__index__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}, \"name\": \"Dada Reverse\"}, {\"__index__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}, \"name\": \"SeqTab\"}, {\"__index__\": 4, \"input\": {\"__class__\": \"ConnectedValue\"}, \"name\": \"Bimera\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.30.0+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"fastqsanger\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"confidence\": \"0.0\", \"kraken2_database\": \"2022-09-04T165121Z_standard_prebuilt_pluspf_2022-06-07\", \"min_base_quality\": \"0\", \"minimum_hit_groups\": \"2\", \"quick\": false, \"report\": {\"create_report\": true, \"use_mpa_style\": false, \"report_zero_counts\": false, \"report_minimizer_data\": false}, \"single_paired\": {\"single_paired_selector\": \"no\", \"__current_case__\": 2, \"input_sequences\": {\"__class__\": \"ConnectedValue\"}}, \"split_reads\": false, \"use_names\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.1+galaxy1",
                         "type": "tool",
-                        "uuid": "e749677d-de5a-4cf8-93de-e709b42b38f7",
+                        "uuid": "b0030c6f-df98-4ab9-a019-2b96fbad69e7",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "sequence_counts",
-                                "output_name": "counts",
-                                "uuid": "c758f861-44bc-4208-b1f7-1f5106cb678e"
+                                "label": "kraken_report",
+                                "output_name": "report_output",
+                                "uuid": "3a8bad46-ce3e-4b23-8415-7a539ee68ebb"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/1.30.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0",
                         "errors": null,
-                        "id": 18,
+                        "id": 7,
                         "input_connections": {
-                            "seqs": {
-                                "id": 15,
-                                "output_name": "stable_sequencetable"
+                            "report": {
+                                "id": 4,
+                                "output_name": "report_output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "dada2: assignTaxonomy and addSpecies",
+                        "name": "Krakentools: Convert kraken report file",
                         "outputs": [
                             {
                                 "name": "output",
@@ -140491,123 +142266,61 @@
                             }
                         ],
                         "position": {
-                            "left": 2830,
-                            "top": 431
+                            "left": 1120,
+                            "top": 517
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/1.30.0+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "65db807336bc",
-                            "name": "dada2_assigntaxonomyaddspecies",
+                            "changeset_revision": "88d274322340",
+                            "name": "krakentools_kreport2krona",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"addSpecies_cond\": {\"addSpecies_select\": \"TRUE\", \"__current_case__\": 1, \"speciesreference_cond\": {\"speciesreference_select\": \"builtin\", \"__current_case__\": 0, \"speciesrefFasta\": \"silva_132\"}, \"allowMultiple_cond\": {\"allowMultiple\": \"FALSE\", \"__current_case__\": 0}, \"tryRC\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"minBoot\": \"50\", \"outputBootstraps\": false, \"reference_cond\": {\"reference_select\": \"builtin\", \"__current_case__\": 0, \"refFasta\": \"silva_132\"}, \"seed\": null, \"seqs\": {\"__class__\": \"ConnectedValue\"}, \"tryRC\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.30.0+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"intermediate_ranks\": false, \"report\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2+galaxy0",
                         "type": "tool",
-                        "uuid": "984044aa-daa8-4082-9a48-623bd5e6f448",
+                        "uuid": "9c2946a8-b768-4ba1-879d-e96f1a2eda51",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "taxons",
+                                "label": "krakentool_report",
                                 "output_name": "output",
-                                "uuid": "904fe0a2-8329-45ca-8493-fc688fb216c3"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "cat1",
-                        "errors": null,
-                        "id": 21,
-                        "input_connections": {
-                            "input1": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "queries_0|input2": {
-                                "id": 20,
-                                "output_name": "outfile"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Concatenate datasets",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 3390,
-                            "top": 12
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Metadata table"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "tool_id": "cat1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [{\"__index__\": 0, \"input2\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "708b9c3c-9de6-4722-9852-39c1b82310b6",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "metada_table",
-                                "output_name": "out_file1",
-                                "uuid": "5479d320-3e82-47a9-a92b-6ed5959459cf"
+                                "uuid": "e24a4cb0-9184-44a0-9b4c-0c554f059ace"
                             }
                         ]
                     }
                 ],
-                "parent_id": "microbiome/dada-16S",
-                "path": "topics/microbiome/tutorials/dada-16S/workflows/workflow.ga",
+                "parent_id": "microbiome/beer-data-analysis",
+                "path": "topics/microbiome/tutorials/beer-data-analysis/workflows/main_workflow.ga",
                 "tags": [
-                    "microbiome"
+                    "Microbiome"
                 ],
                 "test_results": null,
                 "tests": true,
-                "title": "Building an amplicon sequence variant (ASV) table from 16S data using DADA2",
+                "title": "Identification of the micro-organisms in a beer using Nanopore sequencing",
                 "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-dada-16S/versions/workflow",
-                "tutorial_id": "dada-16S",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/dada-16S/workflows/workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/dada-16S/workflows/workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-beer-data-analysis/versions/main-workflow",
+                "tutorial_id": "beer-data-analysis",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/beer-data-analysis/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/beer-data-analysis/workflows/main_workflow.html",
                 "version": 1,
-                "wfid": "microbiome-dada-16S",
-                "wfname": "workflow",
-                "workflow": "workflow.ga",
+                "wfid": "microbiome-beer-data-analysis",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "__SORTLIST__",
-                    "__UNZIP_COLLECTION__",
-                    "cat1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/1.30.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/1.30.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim/dada2_filterAndTrim/1.30.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/dada2_learnerrors/dada2_learnErrors/1.30.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/dada2_makesequencetable/dada2_makeSequenceTable/1.30.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/dada2_mergepairs/dada2_mergePairs/1.30.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.30.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/dada2_removebimeradenovo/dada2_removeBimeraDenovo/1.30.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts/dada2_seqCounts/1.30.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/phyloseq_from_dada2/phyloseq_from_dada2/1.46.0+galaxy0"
+                    "Filter1",
+                    "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0"
                 ],
-                "workflowhub_id": "1105"
+                "workflowhub_id": "1097"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.800651"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.7093173"
     },
     {
         "admin_install": {
@@ -140667,28 +142380,28 @@
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "fbf99087e067",
+                    "revisions": "86755160afbf",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "fbf99087e067",
+                    "revisions": "86755160afbf",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "fbf99087e067",
+                    "revisions": "86755160afbf",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "fbf99087e067",
+                    "revisions": "86755160afbf",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
@@ -140793,7 +142506,7 @@
                 {
                     "name": "bcftools_consensus",
                     "owner": "iuc",
-                    "revisions": "1171446da5db",
+                    "revisions": "da0bf365652d",
                     "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
@@ -141023,7 +142736,7 @@
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: add_line_to_file\n  owner: bgruening\n  revisions: 8e251055b1a9\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: flye\n  owner: bgruening\n  revisions: 276f5d8712d5\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: flye\n  owner: bgruening\n  revisions: cb8dfd28c16f\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_on_column\n  owner: bgruening\n  revisions: ff2a81aa3f08\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_to_collection\n  owner: bgruening\n  revisions: 6cbe2f30c2d7\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: taxonomy_krona_chart\n  owner: crs4\n  revisions: e9005d1f3cfd\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clustalw\n  owner: devteam\n  revisions: 5b097fde95dd\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 6595517c2dd8\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_to_tabular\n  owner: devteam\n  revisions: e7ed3c310b74\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tabular_to_fasta\n  owner: devteam\n  revisions: 0a7799698fe5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_merge_files_and_filter_unique_sequences\n  owner: galaxyp\n  revisions: f546e7278f04\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 503bcd6ebe4b\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 503bcd6ebe4b\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: abricate\n  owner: iuc\n  revisions: c2ef298da409\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_split_mapped\n  owner: iuc\n  revisions: fa7b5520ae53\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: b2860df42e16\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_consensus\n  owner: iuc\n  revisions: 1171446da5db\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_consensus\n  owner: iuc\n  revisions: f867422772d6\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_norm\n  owner: iuc\n  revisions: da6fc9f4a367\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: a1a923cd89e8\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clair3\n  owner: iuc\n  revisions: 63e02ef6e153\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_column_join\n  owner: iuc\n  revisions: 3ddd99c7efee\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_element_identifiers\n  owner: iuc\n  revisions: d3c07d270a50\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: compose_text_param\n  owner: iuc\n  revisions: e188c9826e0f\n  tool_panel_section_label: Expression Tools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: dbf9c561ef29\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: c59d48774d03\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasttree\n  owner: iuc\n  revisions: e005e659ae21\n  tool_panel_section_label: Genome Diversity\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ggplot2_heatmap\n  owner: iuc\n  revisions: 10515715c940\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: 20e2f64aa1fe\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: krakentools_extract_kraken_reads\n  owner: iuc\n  revisions: f329328da134\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: krakentools_kreport2krona\n  owner: iuc\n  revisions: 2deaada69b14\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: medaka_consensus_pipeline\n  owner: iuc\n  revisions: 79e9a869f40e\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: 11a0d50a54e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: 5cc34c3f440d\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mlst\n  owner: iuc\n  revisions: 31812e7a1315\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 9a913cdee30e\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: abfd8a6544d7\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: edbb6c5028f5\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: a02b8b3f5a0c\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: newick_utils\n  owner: iuc\n  revisions: b4163d2f64ab\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: porechop\n  owner: iuc\n  revisions: 5f76b20953e5\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: porechop\n  owner: iuc\n  revisions: 543cbeef3949\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_coverage\n  owner: iuc\n  revisions: c4ff13d2aab3\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_depth\n  owner: iuc\n  revisions: 971dc85e9441\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_fastx\n  owner: iuc\n  revisions: 66e23b11feae\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpsift\n  owner: iuc\n  revisions: 5fab4f81391d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpsift\n  owner: iuc\n  revisions: 5fab4f81391d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: table_compute\n  owner: iuc\n  revisions: 3bf5661c0280\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: add_line_to_file\n  owner: bgruening\n  revisions: 8e251055b1a9\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: flye\n  owner: bgruening\n  revisions: 276f5d8712d5\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: flye\n  owner: bgruening\n  revisions: cb8dfd28c16f\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_on_column\n  owner: bgruening\n  revisions: ff2a81aa3f08\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_to_collection\n  owner: bgruening\n  revisions: 6cbe2f30c2d7\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: taxonomy_krona_chart\n  owner: crs4\n  revisions: e9005d1f3cfd\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clustalw\n  owner: devteam\n  revisions: 5b097fde95dd\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 6595517c2dd8\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_to_tabular\n  owner: devteam\n  revisions: e7ed3c310b74\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tabular_to_fasta\n  owner: devteam\n  revisions: 0a7799698fe5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_merge_files_and_filter_unique_sequences\n  owner: galaxyp\n  revisions: f546e7278f04\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 503bcd6ebe4b\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 503bcd6ebe4b\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: abricate\n  owner: iuc\n  revisions: c2ef298da409\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_split_mapped\n  owner: iuc\n  revisions: fa7b5520ae53\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: b2860df42e16\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_consensus\n  owner: iuc\n  revisions: da0bf365652d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_consensus\n  owner: iuc\n  revisions: f867422772d6\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_norm\n  owner: iuc\n  revisions: da6fc9f4a367\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: a1a923cd89e8\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clair3\n  owner: iuc\n  revisions: 63e02ef6e153\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_column_join\n  owner: iuc\n  revisions: 3ddd99c7efee\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_element_identifiers\n  owner: iuc\n  revisions: d3c07d270a50\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: compose_text_param\n  owner: iuc\n  revisions: e188c9826e0f\n  tool_panel_section_label: Expression Tools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: dbf9c561ef29\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: c59d48774d03\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasttree\n  owner: iuc\n  revisions: e005e659ae21\n  tool_panel_section_label: Genome Diversity\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ggplot2_heatmap\n  owner: iuc\n  revisions: 10515715c940\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: 20e2f64aa1fe\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: krakentools_extract_kraken_reads\n  owner: iuc\n  revisions: f329328da134\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: krakentools_kreport2krona\n  owner: iuc\n  revisions: 2deaada69b14\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: medaka_consensus_pipeline\n  owner: iuc\n  revisions: 79e9a869f40e\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: 11a0d50a54e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: 5cc34c3f440d\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mlst\n  owner: iuc\n  revisions: 31812e7a1315\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 9a913cdee30e\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: abfd8a6544d7\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: edbb6c5028f5\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: a02b8b3f5a0c\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: newick_utils\n  owner: iuc\n  revisions: b4163d2f64ab\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: porechop\n  owner: iuc\n  revisions: 5f76b20953e5\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: porechop\n  owner: iuc\n  revisions: 543cbeef3949\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_coverage\n  owner: iuc\n  revisions: c4ff13d2aab3\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_depth\n  owner: iuc\n  revisions: 971dc85e9441\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_fastx\n  owner: iuc\n  revisions: 66e23b11feae\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpsift\n  owner: iuc\n  revisions: 5fab4f81391d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpsift\n  owner: iuc\n  revisions: 5fab4f81391d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: table_compute\n  owner: iuc\n  revisions: 3bf5661c0280\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
         "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.json",
         "contributions": {
             "authorship": [
@@ -141189,36 +142902,36 @@
             "topic_0080"
         ],
         "edam_operation": [
+            "Scatter plot plotting",
             "Visualisation",
-            "Sequencing quality control",
-            "Sequence composition calculation",
-            "Taxonomic classification",
-            "Phylogenetic tree generation (maximum likelihood and Bayesian methods)",
-            "Phylogenetic tree generation",
-            "Phylogenetic tree generation (from molecular sequences)",
-            "Pairwise sequence alignment",
-            "Sequence assembly visualisation",
-            "Multilocus sequence typing",
             "Cross-assembly",
+            "Phylogenetic tree generation",
             "Genome assembly",
+            "Sequencing quality control",
+            "Box-Whisker plot plotting",
+            "Multiple sequence alignment",
+            "Mapping assembly",
             "Base-calling",
-            "Validation",
-            "Sequence assembly",
+            "Aggregation",
             "Statistical calculation",
-            "Phylogenetic tree reconstruction",
-            "Sequence contamination filtering",
-            "De-novo assembly",
+            "Pairwise sequence alignment",
+            "Validation",
+            "Taxonomic classification",
+            "Sequence composition calculation",
             "Mapping",
-            "Box-Whisker plot plotting",
+            "Antimicrobial resistance prediction",
             "Phylogenetic tree analysis",
-            "Sequence alignment analysis",
-            "Scatter plot plotting",
-            "Mapping assembly",
-            "Multiple sequence alignment",
             "Data handling",
+            "Multilocus sequence typing",
+            "De-novo assembly",
+            "Sequence alignment analysis",
+            "Phylogenetic tree reconstruction",
+            "Sequence contamination filtering",
+            "Sequence assembly",
             "Variant calling",
-            "Antimicrobial resistance prediction",
-            "Aggregation"
+            "Sequence assembly visualisation",
+            "Phylogenetic tree generation (from molecular sequences)",
+            "Phylogenetic tree generation (maximum likelihood and Bayesian methods)"
         ],
         "edam_topic": [
             "Metagenomics",
@@ -141235,7 +142948,9 @@
         "feedback_number": 0,
         "hands_on": true,
         "id": "microbiome/pathogen-detection-from-nanopore-foodborne-data",
-        "inexact_supported_servers": [],
+        "inexact_supported_servers": [
+            "UseGalaxy.org.au"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
@@ -141243,7 +142958,7 @@
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-26",
+        "mod_date": "2024-09-27",
         "objectives": [
             "Check quality reports generated by FastQC and NanoPlot for metagenomics Nanopore data",
             "Preprocess the sequencing data to remove adapters, poor quality base content and host/contaminating reads",
@@ -141252,7 +142967,7 @@
             "Identify pathogens via SNP calling and build the consensus gemone of the samples",
             "Relate all samples' pathogenic genes for tracking pathogens via phylogenetic trees and heatmaps"
         ],
-        "pageviews": 2521,
+        "pageviews": 2918,
         "pub_date": "2023-01-26",
         "questions": [
             "What are the preprocessing steps to prepare ONT sequencing data for further analysis?",
@@ -141271,6 +142986,19 @@
                     "EngyNasr"
                 ],
                 "youtube_id": "gQHb_jkj-Z0"
+            },
+            {
+                "bot-timestamp": 1723837296,
+                "captioners": [
+                    "EngyNasr"
+                ],
+                "date": "2024-08-16",
+                "galaxy_version": "24.1.2.dev0 ",
+                "length": "1H55M",
+                "speakers": [
+                    "EngyNasr"
+                ],
+                "youtube_id": "rGP-BKYwUbc"
             }
         ],
         "redirect_from": [
@@ -141281,67 +143009,67 @@
         ],
         "short_id": "T00393",
         "short_tools": [
-            "__BUILD_LIST__",
             "__FILTER_FAILED_DATASETS__",
-            "abricate",
-            "newick_display",
-            "krakentools_extract_kraken_reads",
             "Count1",
-            "Cut1",
-            "snpSift_extractFields",
-            "kraken2",
-            "table_compute",
-            "fasta2tab",
-            "Remove beginning1",
-            "fasttree",
-            "add_line_to_file",
-            "collapse_dataset",
-            "Grep1",
-            "Grouping1",
-            "bcftools_consensus",
+            "minimap2",
+            "snpSift_filter",
+            "compose_text_param",
+            "tab2fasta",
+            "tp_find_and_replace",
+            "tp_head_tool",
+            "tp_multijoin_tool",
+            "param_value_from_file",
+            "collection_column_join",
+            "collection_element_identifiers",
             "bcftools_norm",
+            "krakentools_kreport2krona",
+            "krakentools_extract_kraken_reads",
             "ggplot2_heatmap",
-            "collection_column_join",
-            "clair3",
-            "tp_sorted_uniq",
+            "bamtools_split_mapped",
             "fasta_merge_files_and_filter_unique_sequences",
-            "tp_replace_in_column",
-            "CONVERTER_gz_to_uncompressed",
+            "barchart_gnuplot",
+            "samtools_fastx",
+            "flye",
+            "medaka_consensus_pipeline",
+            "tp_cut_tool",
+            "fastqc",
+            "snpSift_extractFields",
             "regex1",
+            "Grouping1",
+            "tp_sorted_uniq",
             "porechop",
-            "tab2fasta",
-            "__FILTER_EMPTY_DATASETS__",
-            "taxonomy_krona_chart",
-            "tp_find_and_replace",
-            "tp_cut_tool",
-            "Paste1",
-            "flye",
-            "mlst",
-            "bedtools_getfastabed",
-            "collection_element_identifiers",
+            "table_compute",
+            "bcftools_consensus",
+            "split_file_to_collection",
             "bandage_image",
+            "abricate",
+            "Paste1",
+            "add_line_to_file",
             "tp_split_on_column",
+            "multiqc",
+            "Grep1",
+            "Cut1",
+            "collapse_dataset",
+            "Remove beginning1",
             "clustalw",
-            "regexColumn1",
-            "medaka_consensus_pipeline",
-            "samtools_coverage",
-            "krakentools_kreport2krona",
-            "barchart_gnuplot",
-            "nanoplot",
-            "param_value_from_file",
-            "compose_text_param",
+            "bedtools_getfastabed",
+            "tp_replace_in_column",
+            "fasttree",
+            "newick_display",
             "fastp",
-            "tp_multijoin_tool",
-            "multiqc",
-            "samtools_fastx",
-            "bamtools_split_mapped",
-            "snpSift_filter",
+            "samtools_coverage",
             "samtools_depth",
-            "fastqc",
-            "minimap2",
-            "split_file_to_collection",
+            "clair3",
+            "taxonomy_krona_chart",
+            "__FILTER_EMPTY_DATASETS__",
+            "kraken2",
+            "__BUILD_LIST__",
             "Add_a_column1",
-            "tp_head_tool"
+            "mlst",
+            "nanoplot",
+            "regexColumn1",
+            "CONVERTER_gz_to_uncompressed",
+            "fasta2tab"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -141354,7 +143082,13 @@
                     "usegalaxy": true
                 }
             ],
-            "inexact": []
+            "inexact": [
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
         },
         "symlink": null,
         "tags": [
@@ -141454,12 +143188,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.json"
         },
-        "version": 9,
+        "version": 11,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 181,
-        "visitors": 1680,
+        "visit_duration": 180,
+        "visitors": 1964,
         "workflows": [
             {
                 "creators": [
@@ -141585,7 +143319,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\ncollection_of_preprocessed_samples\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nsamples_profile\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nreference_genome_of_tested_strain\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Convert compressed file to uncompressed.\"];\n  2 -->|output| 3;\n  9d6bde4a-7180-4097-9ffd-6992111a617c[\"Output\\ndecompressed_rg_file\"];\n  3 --> 9d6bde4a-7180-4097-9ffd-6992111a617c;\n  style 9d6bde4a-7180-4097-9ffd-6992111a617c stroke:#2c3143,stroke-width:4px;\n  4[\"Map with minimap2\"];\n  1 -->|output| 4;\n  0 -->|output| 4;\n  3 -->|output1| 4;\n  31779c23-4f26-418e-9418-2551e883dbe7[\"Output\\nmap_with_minimap2\"];\n  4 --> 31779c23-4f26-418e-9418-2551e883dbe7;\n  style 31779c23-4f26-418e-9418-2551e883dbe7 stroke:#2c3143,stroke-width:4px;\n  5[\"Clair3\"];\n  4 -->|alignment_output| 5;\n  3 -->|output1| 5;\n  1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53[\"Output\\nclair3_pileup_vcf\"];\n  5 --> 1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53;\n  style 1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53 stroke:#2c3143,stroke-width:4px;\n  987f9145-83ab-44f1-801a-b0d527ecbce8[\"Output\\nclair3_full_alignment_vcf\"];\n  5 --> 987f9145-83ab-44f1-801a-b0d527ecbce8;\n  style 987f9145-83ab-44f1-801a-b0d527ecbce8 stroke:#2c3143,stroke-width:4px;\n  fab82215-f59a-43b1-92d7-37629a1fdb65[\"Output\\nclair3_merged_output\"];\n  5 --> fab82215-f59a-43b1-92d7-37629a1fdb65;\n  style fab82215-f59a-43b1-92d7-37629a1fdb65 stroke:#2c3143,stroke-width:4px;\n  6[\"Samtools depth\"];\n  4 -->|alignment_output| 6;\n  7[\"Samtools coverage\"];\n  4 -->|alignment_output| 7;\n  8[\"bcftools norm\"];\n  5 -->|merge_output| 8;\n  3 -->|output1| 8;\n  22553aa1-f5db-4d37-87c4-1164dbb3d2d5[\"Output\\nnormalized_vcf_output\"];\n  8 --> 22553aa1-f5db-4d37-87c4-1164dbb3d2d5;\n  style 22553aa1-f5db-4d37-87c4-1164dbb3d2d5 stroke:#2c3143,stroke-width:4px;\n  9[\"Advanced Cut\"];\n  6 -->|output| 9;\n  10[\"Remove beginning\"];\n  7 -->|output| 10;\n  11[\"SnpSift Filter\"];\n  8 -->|output_file| 11;\n  3e7981ec-2205-4571-93eb-10c0dd14b288[\"Output\\nquality_filtered_vcf_output\"];\n  11 --> 3e7981ec-2205-4571-93eb-10c0dd14b288;\n  style 3e7981ec-2205-4571-93eb-10c0dd14b288 stroke:#2c3143,stroke-width:4px;\n  12[\"Table Compute\"];\n  9 -->|output| 12;\n  13[\"Cut\"];\n  10 -->|out_file1| 13;\n  14[\"SnpSift Extract Fields\"];\n  11 -->|output| 14;\n  1b0f4f2c-4717-45be-b580-fe10cba78c35[\"Output\\nextracted_fields_from_the_vcf_output\"];\n  14 --> 1b0f4f2c-4717-45be-b580-fe10cba78c35;\n  style 1b0f4f2c-4717-45be-b580-fe10cba78c35 stroke:#2c3143,stroke-width:4px;\n  15[\"bcftools consensus\"];\n  11 -->|output| 15;\n  3 -->|output1| 15;\n  49497f3c-9332-4924-bcfd-cb71788ad2c2[\"Output\\nbcftools_consensus\"];\n  15 --> 49497f3c-9332-4924-bcfd-cb71788ad2c2;\n  style 49497f3c-9332-4924-bcfd-cb71788ad2c2 stroke:#2c3143,stroke-width:4px;\n  16[\"Select first\"];\n  13 -->|out_file1| 16;\n  17[\"Remove beginning\"];\n  14 -->|output| 17;\n  18[\"Collapse Collection\"];\n  16 -->|outfile| 18;\n  5ee1c158-1a85-45ca-9abd-b30632b3092c[\"Output\\nmapping_coverage_percentage_per_sample\"];\n  18 --> 5ee1c158-1a85-45ca-9abd-b30632b3092c;\n  style 5ee1c158-1a85-45ca-9abd-b30632b3092c stroke:#2c3143,stroke-width:4px;\n  19[\"Count\"];\n  17 -->|out_file1| 19;\n  20[\"Advanced Cut\"];\n  18 -->|output| 20;\n  21[\"Cut\"];\n  19 -->|out_file1| 21;\n  22[\"Paste\"];\n  20 -->|output| 22;\n  12 -->|table| 22;\n  25b7b87b-5ef1-487f-90cc-81351a2f81ce[\"Output\\nmapping_mean_depth_per_sample\"];\n  22 --> 25b7b87b-5ef1-487f-90cc-81351a2f81ce;\n  style 25b7b87b-5ef1-487f-90cc-81351a2f81ce stroke:#2c3143,stroke-width:4px;\n  23[\"Select first\"];\n  21 -->|out_file1| 23;\n  24[\"Collapse Collection\"];\n  23 -->|outfile| 24;\n  25[\"Column Regex Find And Replace\"];\n  24 -->|output| 25;\n  2852c4ee-24ea-4df7-b59e-54eb6e2f470b[\"Output\\nnumber_of_variants_per_sample\"];\n  25 --> 2852c4ee-24ea-4df7-b59e-54eb6e2f470b;\n  style 2852c4ee-24ea-4df7-b59e-54eb6e2f470b stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
+                "modified": "2024-10-02 12:08:09 +0000",
                 "name": "Allele-based Pathogen Identification",
                 "outputs": [
                     {
@@ -142349,7 +144083,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\ncollection_of_preprocessed_samples\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Extract element identifiers\"];\n  0 -->|output| 1;\n  d82a93c6-23a9-4f85-879c-ecd759a31087[\"Output\\nextracted_samples_IDs\"];\n  1 --> d82a93c6-23a9-4f85-879c-ecd759a31087;\n  style d82a93c6-23a9-4f85-879c-ecd759a31087 stroke:#2c3143,stroke-width:4px;\n  2[\"Build list\"];\n  0 -->|output| 2;\n  f5b5b256-8ddf-4da8-8111-b1f6d3025a0d[\"Output\\nlist_of_lists_of_preprocessed_samples\"];\n  2 --> f5b5b256-8ddf-4da8-8111-b1f6d3025a0d;\n  style f5b5b256-8ddf-4da8-8111-b1f6d3025a0d stroke:#2c3143,stroke-width:4px;\n  3[\"Split file\"];\n  1 -->|output| 3;\n  eb5317bd-4bad-4cad-9219-3ac379221d6e[\"Output\\nsplitted_extracted_samples_IDs\"];\n  3 --> eb5317bd-4bad-4cad-9219-3ac379221d6e;\n  style eb5317bd-4bad-4cad-9219-3ac379221d6e stroke:#2c3143,stroke-width:4px;\n  4[\"Flye\"];\n  2 -->|output| 4;\n  ff0d8c7b-2ac7-4c6d-a110-f71418dad938[\"Output\\nflye_consensus_fasta\"];\n  4 --> ff0d8c7b-2ac7-4c6d-a110-f71418dad938;\n  style ff0d8c7b-2ac7-4c6d-a110-f71418dad938 stroke:#2c3143,stroke-width:4px;\n  2385436f-fbe8-4d77-a40b-27a097d02941[\"Output\\nflye_assembly_graph\"];\n  4 --> 2385436f-fbe8-4d77-a40b-27a097d02941;\n  style 2385436f-fbe8-4d77-a40b-27a097d02941 stroke:#2c3143,stroke-width:4px;\n  0e42ce51-c46b-45d8-baa4-45c0e98ac712[\"Output\\nflye_assembly_gfa\"];\n  4 --> 0e42ce51-c46b-45d8-baa4-45c0e98ac712;\n  style 0e42ce51-c46b-45d8-baa4-45c0e98ac712 stroke:#2c3143,stroke-width:4px;\n  3f297aed-7cee-4999-bbf4-69d84de6b64f[\"Output\\nflye_assembly_info_tabular\"];\n  4 --> 3f297aed-7cee-4999-bbf4-69d84de6b64f;\n  style 3f297aed-7cee-4999-bbf4-69d84de6b64f stroke:#2c3143,stroke-width:4px;\n  5[\"Parse parameter value\"];\n  3 -->|list_output_txt| 5;\n  3608e170-c462-42a2-8003-f3f65baa3834[\"Output\\nparsed_extracted_samples_IDs_to_text\"];\n  5 --> 3608e170-c462-42a2-8003-f3f65baa3834;\n  style 3608e170-c462-42a2-8003-f3f65baa3834 stroke:#2c3143,stroke-width:4px;\n  6[\"medaka consensus pipeline\"];\n  4 -->|consensus| 6;\n  0 -->|output| 6;\n  9e5ad6ec-b408-4132-ba07-dec9fa626923[\"Output\\nmedaka_gaps_in_draft_bed_file\"];\n  6 --> 9e5ad6ec-b408-4132-ba07-dec9fa626923;\n  style 9e5ad6ec-b408-4132-ba07-dec9fa626923 stroke:#2c3143,stroke-width:4px;\n  fcbd3e3f-2e93-4798-b696-dad7db9f2efd[\"Output\\nmedaka_log_file\"];\n  6 --> fcbd3e3f-2e93-4798-b696-dad7db9f2efd;\n  style fcbd3e3f-2e93-4798-b696-dad7db9f2efd stroke:#2c3143,stroke-width:4px;\n  60656aac-ad2a-4c9b-9a68-b9fb18ae5595[\"Output\\nmedaka_propability_h5_file\"];\n  6 --> 60656aac-ad2a-4c9b-9a68-b9fb18ae5595;\n  style 60656aac-ad2a-4c9b-9a68-b9fb18ae5595 stroke:#2c3143,stroke-width:4px;\n  c790d434-8e78-4df0-a0d4-8f9da0692158[\"Output\\nmedaka_calls_of_draft_bam_file\"];\n  6 --> c790d434-8e78-4df0-a0d4-8f9da0692158;\n  style c790d434-8e78-4df0-a0d4-8f9da0692158 stroke:#2c3143,stroke-width:4px;\n  df361e19-b6d1-405b-96cc-b48c1ab7c604[\"Output\\nsample_all_contigs\"];\n  6 --> df361e19-b6d1-405b-96cc-b48c1ab7c604;\n  style df361e19-b6d1-405b-96cc-b48c1ab7c604 stroke:#2c3143,stroke-width:4px;\n  7[\"Bandage Image\"];\n  4 -->|assembly_gfa| 7;\n  9612a851-1f94-4d54-b001-5d082bcc9055[\"Output\\nbandage_assembly_graph_image\"];\n  7 --> 9612a851-1f94-4d54-b001-5d082bcc9055;\n  style 9612a851-1f94-4d54-b001-5d082bcc9055 stroke:#2c3143,stroke-width:4px;\n  8[\"Compose text parameter value\"];\n  5 -->|text_param| 8;\n  9[\"FASTA-to-Tabular\"];\n  6 -->|out_consensus| 9;\n  de06c362-5b0a-4c29-956e-fbf02539789a[\"Output\\nsample_specific_contigs_tabular_file_preparation\"];\n  9 --> de06c362-5b0a-4c29-956e-fbf02539789a;\n  style de06c362-5b0a-4c29-956e-fbf02539789a stroke:#2c3143,stroke-width:4px;\n  10[\"ABRicate\"];\n  6 -->|out_consensus| 10;\n  8f227fc7-2d92-4c6f-af64-e841c1315b4f[\"Output\\nabricate_with_vfdb_to_identify_genes_with_VFs\"];\n  10 --> 8f227fc7-2d92-4c6f-af64-e841c1315b4f;\n  style 8f227fc7-2d92-4c6f-af64-e841c1315b4f stroke:#2c3143,stroke-width:4px;\n  11[\"ABRicate\"];\n  6 -->|out_consensus| 11;\n  fa021d98-d885-4834-ac62-f30d5792260e[\"Output\\nabricate_report_using_ncbi_database_to_indentify_amr\"];\n  11 --> fa021d98-d885-4834-ac62-f30d5792260e;\n  style fa021d98-d885-4834-ac62-f30d5792260e stroke:#2c3143,stroke-width:4px;\n  12[\"Replace\"];\n  8 -->|out1| 12;\n  9 -->|output| 12;\n  174cb2c3-ed28-453c-8afb-85150e0b51ad[\"Output\\nsample_specific_contigs_tabular_file\"];\n  12 --> 174cb2c3-ed28-453c-8afb-85150e0b51ad;\n  style 174cb2c3-ed28-453c-8afb-85150e0b51ad stroke:#2c3143,stroke-width:4px;\n  13[\"Replace\"];\n  8 -->|out1| 13;\n  10 -->|report| 13;\n  19e56e00-6eef-4a4e-9cc6-d93dbf9420ad[\"Output\\nvfs\"];\n  13 --> 19e56e00-6eef-4a4e-9cc6-d93dbf9420ad;\n  style 19e56e00-6eef-4a4e-9cc6-d93dbf9420ad stroke:#2c3143,stroke-width:4px;\n  14[\"Replace\"];\n  8 -->|out1| 14;\n  11 -->|report| 14;\n  a8eb74a5-362b-4f0f-a944-672e27981a41[\"Output\\namrs\"];\n  14 --> a8eb74a5-362b-4f0f-a944-672e27981a41;\n  style a8eb74a5-362b-4f0f-a944-672e27981a41 stroke:#2c3143,stroke-width:4px;\n  15[\"Tabular-to-FASTA\"];\n  12 -->|outfile| 15;\n  a5bb1cbe-1bde-49a1-ad86-6d57b1319fbe[\"Output\\ncontigs\"];\n  15 --> a5bb1cbe-1bde-49a1-ad86-6d57b1319fbe;\n  style a5bb1cbe-1bde-49a1-ad86-6d57b1319fbe stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
+                "modified": "2024-10-02 12:08:09 +0000",
                 "name": "Gene-based Pathogen Identification",
                 "outputs": [
                     {
@@ -143419,7 +145153,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nsamples_profile\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\ncollection_of_all_samples\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Porechop\"];\n  1 -->|output| 2;\n  34ea26db-11cb-41ee-85c3-75af8a53a2c0[\"Output\\nporechop_output_trimmed_reads\"];\n  2 --> 34ea26db-11cb-41ee-85c3-75af8a53a2c0;\n  style 34ea26db-11cb-41ee-85c3-75af8a53a2c0 stroke:#2c3143,stroke-width:4px;\n  3[\"NanoPlot\"];\n  1 -->|output| 3;\n  15ecf5b1-e0eb-405a-ac3a-359feb66d4cd[\"Output\\nnanoplot_qc_on_reads_before_preprocessing_nanostats\"];\n  3 --> 15ecf5b1-e0eb-405a-ac3a-359feb66d4cd;\n  style 15ecf5b1-e0eb-405a-ac3a-359feb66d4cd stroke:#2c3143,stroke-width:4px;\n  304110f9-60d0-4ba2-8b3b-fae0e2a49554[\"Output\\nnanoplot_on_reads_before_preprocessing_nanostats_post_filtering\"];\n  3 --> 304110f9-60d0-4ba2-8b3b-fae0e2a49554;\n  style 304110f9-60d0-4ba2-8b3b-fae0e2a49554 stroke:#2c3143,stroke-width:4px;\n  f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e[\"Output\\nnanoplot_qc_on_reads_before_preprocessing_html_report\"];\n  3 --> f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e;\n  style f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e stroke:#2c3143,stroke-width:4px;\n  4[\"FastQC\"];\n  1 -->|output| 4;\n  d0a64624-05d0-4068-835b-a025fc011760[\"Output\\nfastqc_quality_check_before_preprocessing_html_file\"];\n  4 --> d0a64624-05d0-4068-835b-a025fc011760;\n  style d0a64624-05d0-4068-835b-a025fc011760 stroke:#2c3143,stroke-width:4px;\n  e61fef5d-1bc8-4c8e-be6a-f74e210e9920[\"Output\\nfastqc_quality_check_before_preprocessing_text_file\"];\n  4 --> e61fef5d-1bc8-4c8e-be6a-f74e210e9920;\n  style e61fef5d-1bc8-4c8e-be6a-f74e210e9920 stroke:#2c3143,stroke-width:4px;\n  5[\"fastp\"];\n  2 -->|outfile| 5;\n  a2219483-50b7-4aed-98dd-333ad2e12eb8[\"Output\\nnanopore_sequenced_reads_processed_with_fastp_after_host_removal\"];\n  5 --> a2219483-50b7-4aed-98dd-333ad2e12eb8;\n  style a2219483-50b7-4aed-98dd-333ad2e12eb8 stroke:#2c3143,stroke-width:4px;\n  2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4[\"Output\\nnanopore_sequenced_reads_processed_with_fastp_after_host_removal_html_report\"];\n  5 --> 2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4;\n  style 2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4 stroke:#2c3143,stroke-width:4px;\n  6[\"MultiQC\"];\n  4 -->|text_file| 6;\n  ebffe782-a56c-431f-8af4-c0cb8d7a02fc[\"Output\\nmultiQC_stats_before_preprocessing\"];\n  6 --> ebffe782-a56c-431f-8af4-c0cb8d7a02fc;\n  style ebffe782-a56c-431f-8af4-c0cb8d7a02fc stroke:#2c3143,stroke-width:4px;\n  0f92196d-047d-4918-819d-c0ff7cd3ae85[\"Output\\nmultiQC_html_report_before_preprocessing\"];\n  6 --> 0f92196d-047d-4918-819d-c0ff7cd3ae85;\n  style 0f92196d-047d-4918-819d-c0ff7cd3ae85 stroke:#2c3143,stroke-width:4px;\n  7[\"Map with minimap2\"];\n  0 -->|output| 7;\n  5 -->|out1| 7;\n  9d7bb3b7-09a1-401f-a132-bb35a53375ea[\"Output\\nbam_map_to_host\"];\n  7 --> 9d7bb3b7-09a1-401f-a132-bb35a53375ea;\n  style 9d7bb3b7-09a1-401f-a132-bb35a53375ea stroke:#2c3143,stroke-width:4px;\n  8[\"NanoPlot\"];\n  5 -->|out1| 8;\n  b5899290-4c57-4662-ad22-860654652ade[\"Output\\nnanoplot_qc_on_reads_after_preprocessing_html_report\"];\n  8 --> b5899290-4c57-4662-ad22-860654652ade;\n  style b5899290-4c57-4662-ad22-860654652ade stroke:#2c3143,stroke-width:4px;\n  949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf[\"Output\\nnanoplot_on_reads_after_preprocessing_nanostats_post_filtering\"];\n  8 --> 949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf;\n  style 949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf stroke:#2c3143,stroke-width:4px;\n  42db7f93-919e-4bbb-81a1-06411a9da410[\"Output\\nnanoplot_qc_on_reads_after_preprocessing_nanostats\"];\n  8 --> 42db7f93-919e-4bbb-81a1-06411a9da410;\n  style 42db7f93-919e-4bbb-81a1-06411a9da410 stroke:#2c3143,stroke-width:4px;\n  9[\"FastQC\"];\n  5 -->|out1| 9;\n  09306471-afa0-4106-9cc7-259b93dfc862[\"Output\\nfastqc_quality_check_after_preprocessing_text_file\"];\n  9 --> 09306471-afa0-4106-9cc7-259b93dfc862;\n  style 09306471-afa0-4106-9cc7-259b93dfc862 stroke:#2c3143,stroke-width:4px;\n  084f982f-20f1-457e-8012-91ebbb85633d[\"Output\\nfastqc_quality_check_after_preprocessing_html_file\"];\n  9 --> 084f982f-20f1-457e-8012-91ebbb85633d;\n  style 084f982f-20f1-457e-8012-91ebbb85633d stroke:#2c3143,stroke-width:4px;\n  10[\"Split BAM by reads mapping status\"];\n  7 -->|alignment_output| 10;\n  14a53fe2-f296-43aa-86b7-243278c1050c[\"Output\\nnon_host_sequences_bam\"];\n  10 --> 14a53fe2-f296-43aa-86b7-243278c1050c;\n  style 14a53fe2-f296-43aa-86b7-243278c1050c stroke:#2c3143,stroke-width:4px;\n  3b1e626f-6bc1-484c-be01-366534361b73[\"Output\\nhost_sequences_bam\"];\n  10 --> 3b1e626f-6bc1-484c-be01-366534361b73;\n  style 3b1e626f-6bc1-484c-be01-366534361b73 stroke:#2c3143,stroke-width:4px;\n  11[\"Select\"];\n  9 -->|text_file| 11;\n  a809853b-119f-44d2-986b-8d2006439fbe[\"Output\\ntotal_sequences_before_hosts_sequences_removal\"];\n  11 --> a809853b-119f-44d2-986b-8d2006439fbe;\n  style a809853b-119f-44d2-986b-8d2006439fbe stroke:#2c3143,stroke-width:4px;\n  12[\"Samtools fastx\"];\n  10 -->|mapped| 12;\n  10d4eaec-81d8-444e-8075-7b77a1fb6870[\"Output\\nhost_sequences_fastq\"];\n  12 --> 10d4eaec-81d8-444e-8075-7b77a1fb6870;\n  style 10d4eaec-81d8-444e-8075-7b77a1fb6870 stroke:#2c3143,stroke-width:4px;\n  13[\"Samtools fastx\"];\n  10 -->|unmapped| 13;\n  0c2dd74d-ac4f-45cf-839c-50386a7ece28[\"Output\\nnon_host_sequences_fastq\"];\n  13 --> 0c2dd74d-ac4f-45cf-839c-50386a7ece28;\n  style 0c2dd74d-ac4f-45cf-839c-50386a7ece28 stroke:#2c3143,stroke-width:4px;\n  14[\"Collapse Collection\"];\n  11 -->|out_file1| 14;\n  15[\"Filter failed datasets\"];\n  12 -->|output| 15;\n  16[\"Kraken2\"];\n  13 -->|output| 16;\n  203d303e-8f3a-4242-971f-b345842ebdb8[\"Output\\nkraken2_with_kalamri_database_output\"];\n  16 --> 203d303e-8f3a-4242-971f-b345842ebdb8;\n  style 203d303e-8f3a-4242-971f-b345842ebdb8 stroke:#2c3143,stroke-width:4px;\n  843afd4d-23a8-46e7-b945-8b67dd7ae341[\"Output\\nkraken2_with_kalamri_database_report\"];\n  16 --> 843afd4d-23a8-46e7-b945-8b67dd7ae341;\n  style 843afd4d-23a8-46e7-b945-8b67dd7ae341 stroke:#2c3143,stroke-width:4px;\n  17[\"Cut\"];\n  14 -->|output| 17;\n  d07be9f1-d250-4008-91ee-59a68521eb56[\"Output\\nquality_retained_all_reads\"];\n  17 --> d07be9f1-d250-4008-91ee-59a68521eb56;\n  style d07be9f1-d250-4008-91ee-59a68521eb56 stroke:#2c3143,stroke-width:4px;\n  18[\"FastQC\"];\n  15 -->|output| 18;\n  b0ee6e31-0eb1-437d-8c04-fc3640b9a0b7[\"Output\\nhosts_qc_text_file\"];\n  18 --> b0ee6e31-0eb1-437d-8c04-fc3640b9a0b7;\n  style b0ee6e31-0eb1-437d-8c04-fc3640b9a0b7 stroke:#2c3143,stroke-width:4px;\n  b72ff57b-0921-43bf-a817-6cd444c8f3cb[\"Output\\nhosts_qc_html\"];\n  18 --> b72ff57b-0921-43bf-a817-6cd444c8f3cb;\n  style b72ff57b-0921-43bf-a817-6cd444c8f3cb stroke:#2c3143,stroke-width:4px;\n  19[\"Krakentools: Extract Kraken Reads By ID\"];\n  5 -->|out1| 19;\n  16 -->|report_output| 19;\n  16 -->|output| 19;\n  57e3b725-8e13-40b2-9acc-31fd56ebc80a[\"Output\\ncollection_of_preprocessed_samples\"];\n  19 --> 57e3b725-8e13-40b2-9acc-31fd56ebc80a;\n  style 57e3b725-8e13-40b2-9acc-31fd56ebc80a stroke:#2c3143,stroke-width:4px;\n  20[\"Select\"];\n  18 -->|text_file| 20;\n  3ba35c71-32f0-4741-98d4-ea8522e27500[\"Output\\ntotal_sequences_after_hosts_sequences_removal\"];\n  20 --> 3ba35c71-32f0-4741-98d4-ea8522e27500;\n  style 3ba35c71-32f0-4741-98d4-ea8522e27500 stroke:#2c3143,stroke-width:4px;\n  21[\"Collapse Collection\"];\n  20 -->|out_file1| 21;\n  22[\"Cut\"];\n  21 -->|output| 22;\n  cef36c68-4549-4fd6-b7c8-71fb21df012f[\"Output\\nquality_retained_hosts_reads\"];\n  22 --> cef36c68-4549-4fd6-b7c8-71fb21df012f;\n  style cef36c68-4549-4fd6-b7c8-71fb21df012f stroke:#2c3143,stroke-width:4px;\n  23[\"Column join\"];\n  17 -->|out_file1| 23;\n  22 -->|out_file1| 23;\n  24[\"Compute\"];\n  23 -->|tabular_output| 24;\n  25[\"Column Regex Find And Replace\"];\n  24 -->|out_file1| 25;\n  470892ee-dab9-48d7-ad97-45dbd52afaa7[\"Output\\nremoved_hosts_percentage_tabular\"];\n  25 --> 470892ee-dab9-48d7-ad97-45dbd52afaa7;\n  style 470892ee-dab9-48d7-ad97-45dbd52afaa7 stroke:#2c3143,stroke-width:4px;\n  26[\"MultiQC\"];\n  9 -->|text_file| 26;\n  25 -->|out_file1| 26;\n  0b1b5a73-36ee-42a2-a220-1ced6ec7378b[\"Output\\nmultiQC_html_report_after_preprocessing\"];\n  26 --> 0b1b5a73-36ee-42a2-a220-1ced6ec7378b;\n  style 0b1b5a73-36ee-42a2-a220-1ced6ec7378b stroke:#2c3143,stroke-width:4px;\n  13cbf6c7-6954-4458-aa66-a5b020c63822[\"Output\\nmultiQC_stats_after_preprocessing\"];\n  26 --> 13cbf6c7-6954-4458-aa66-a5b020c63822;\n  style 13cbf6c7-6954-4458-aa66-a5b020c63822 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
+                "modified": "2024-10-02 12:08:09 +0000",
                 "name": "Nanopore Preprocessing",
                 "outputs": [
                     {
@@ -145190,7 +146924,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\namr_identified_by_ncbi\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nvfs_of_genes_identified_by_vfdb\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nmetadata\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nremoved_hosts_percentage_tabular\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nmapping_mean_depth_per_sample\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Collection\\namrs\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nmapping_coverage_percentage_per_sample\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nnumber_of_variants_per_sample\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Collection\\ncontigs\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"\u2139\ufe0f Input Collection\\nvfs\"];\n  style 9 stroke:#2c3143,stroke-width:4px;\n  10[\"Filter failed datasets\"];\n  0 -->|output| 10;\n  11[\"Filter failed datasets\"];\n  1 -->|output| 11;\n  12[\"Bar chart\"];\n  3 -->|output| 12;\n  0961166e-38b6-44e3-93db-100d821b0070[\"Output\\nnumber_of_reads_before_host_removal_and_number_of_host_reads_found_per_sample_fig\"];\n  12 --> 0961166e-38b6-44e3-93db-100d821b0070;\n  style 0961166e-38b6-44e3-93db-100d821b0070 stroke:#2c3143,stroke-width:4px;\n  13[\"Bar chart\"];\n  3 -->|output| 13;\n  548975e5-4619-49fc-9e95-4d7f4d761dfd[\"Output\\nremoved_host_percentage_fig\"];\n  13 --> 548975e5-4619-49fc-9e95-4d7f4d761dfd;\n  style 548975e5-4619-49fc-9e95-4d7f4d761dfd stroke:#2c3143,stroke-width:4px;\n  14[\"Bar chart\"];\n  4 -->|output| 14;\n  a71ebb67-1154-4f25-a62d-e8fa2b839e2e[\"Output\\nmapping_mean_depth_per_sample_fig\"];\n  14 --> a71ebb67-1154-4f25-a62d-e8fa2b839e2e;\n  style a71ebb67-1154-4f25-a62d-e8fa2b839e2e stroke:#2c3143,stroke-width:4px;\n  15[\"Filter failed datasets\"];\n  5 -->|output| 15;\n  16[\"Bar chart\"];\n  6 -->|output| 16;\n  2567360e-d39f-4316-84f5-77aaf8e8198c[\"Output\\nmapping_coverage_percentage_per_sample_fig\"];\n  16 --> 2567360e-d39f-4316-84f5-77aaf8e8198c;\n  style 2567360e-d39f-4316-84f5-77aaf8e8198c stroke:#2c3143,stroke-width:4px;\n  17[\"Bar chart\"];\n  7 -->|output| 17;\n  68c76f06-d2ea-4280-9e6f-a7b4f1568389[\"Output\\nnumber_of_Variants_and_SNPs_indentified_fig\"];\n  17 --> 68c76f06-d2ea-4280-9e6f-a7b4f1568389;\n  style 68c76f06-d2ea-4280-9e6f-a7b4f1568389 stroke:#2c3143,stroke-width:4px;\n  18[\"Filter failed datasets\"];\n  8 -->|output| 18;\n  19[\"Filter failed datasets\"];\n  9 -->|output| 19;\n  20[\"Remove beginning\"];\n  10 -->|output| 20;\n  21[\"Remove beginning\"];\n  11 -->|output| 21;\n  22[\"Remove beginning\"];\n  15 -->|output| 22;\n  23[\"Collapse Collection\"];\n  18 -->|output| 23;\n  86910e39-57bf-4a76-ac4c-739340fd2387[\"Output\\nall_samples_contigs_in_one_fasta_file\"];\n  23 --> 86910e39-57bf-4a76-ac4c-739340fd2387;\n  style 86910e39-57bf-4a76-ac4c-739340fd2387 stroke:#2c3143,stroke-width:4px;\n  24[\"Collapse Collection\"];\n  19 -->|output| 24;\n  02b996c6-a912-4e4e-b3ec-49601faaa452[\"Output\\nall_vfs_in_one_tabular\"];\n  24 --> 02b996c6-a912-4e4e-b3ec-49601faaa452;\n  style 02b996c6-a912-4e4e-b3ec-49601faaa452 stroke:#2c3143,stroke-width:4px;\n  25[\"Remove beginning\"];\n  19 -->|output| 25;\n  26[\"Count\"];\n  20 -->|out_file1| 26;\n  27[\"Count\"];\n  21 -->|out_file1| 27;\n  28[\"Group\"];\n  21 -->|out_file1| 28;\n  29[\"Unique\"];\n  22 -->|out_file1| 29;\n  30[\"Split by group\"];\n  24 -->|output| 30;\n  59f8cb09-424b-47b1-b94b-a612c2610cab[\"Output\\nsplit_by_group_collection\"];\n  30 --> 59f8cb09-424b-47b1-b94b-a612c2610cab;\n  style 59f8cb09-424b-47b1-b94b-a612c2610cab stroke:#2c3143,stroke-width:4px;\n  31[\"Unique\"];\n  25 -->|out_file1| 31;\n  32[\"Cut\"];\n  26 -->|out_file1| 32;\n  33[\"Cut\"];\n  27 -->|out_file1| 33;\n  34[\"Filter empty datasets\"];\n  28 -->|out_file1| 34;\n  35[\"Cut\"];\n  29 -->|outfile| 35;\n  36[\"Cut\"];\n  30 -->|split_output| 36;\n  eeb25a51-ea21-4a19-a196-55d5bd919b10[\"Output\\nadjusted_abricate_vfs_tabular_part1\"];\n  36 --> eeb25a51-ea21-4a19-a196-55d5bd919b10;\n  style eeb25a51-ea21-4a19-a196-55d5bd919b10 stroke:#2c3143,stroke-width:4px;\n  37[\"Cut\"];\n  31 -->|outfile| 37;\n  38[\"Collapse Collection\"];\n  32 -->|out_file1| 38;\n  39[\"Collapse Collection\"];\n  33 -->|out_file1| 39;\n  40[\"Column join\"];\n  34 -->|output| 40;\n  41[\"bedtools getfasta\"];\n  23 -->|output| 41;\n  35 -->|out_file1| 41;\n  42[\"Remove beginning\"];\n  36 -->|out_file1| 42;\n  aaaa4446-0817-4e5c-aa1b-9ec384f2a363[\"Output\\nadjusted_abricate_vfs_tabular_part2\"];\n  42 --> aaaa4446-0817-4e5c-aa1b-9ec384f2a363;\n  style aaaa4446-0817-4e5c-aa1b-9ec384f2a363 stroke:#2c3143,stroke-width:4px;\n  43[\"bedtools getfasta\"];\n  23 -->|output| 43;\n  37 -->|out_file1| 43;\n  44[\"Column Regex Find And Replace\"];\n  38 -->|output| 44;\n  4809c36b-31ef-4664-8e4e-47f0f72152de[\"Output\\namrs_count\"];\n  44 --> 4809c36b-31ef-4664-8e4e-47f0f72152de;\n  style 4809c36b-31ef-4664-8e4e-47f0f72152de stroke:#2c3143,stroke-width:4px;\n  45[\"Column Regex Find And Replace\"];\n  39 -->|output| 45;\n  87efc81d-4d84-4af3-831f-dfe033c59f78[\"Output\\nvfs_count\"];\n  45 --> 87efc81d-4d84-4af3-831f-dfe033c59f78;\n  style 87efc81d-4d84-4af3-831f-dfe033c59f78 stroke:#2c3143,stroke-width:4px;\n  46[\"Column Regex Find And Replace\"];\n  40 -->|tabular_output| 46;\n  f5c221e3-00ef-4834-9a5f-a94c97fd6764[\"Output\\nheatmap_table\"];\n  46 --> f5c221e3-00ef-4834-9a5f-a94c97fd6764;\n  style f5c221e3-00ef-4834-9a5f-a94c97fd6764 stroke:#2c3143,stroke-width:4px;\n  47[\"Regex Find And Replace\"];\n  41 -->|output| 47;\n  48[\"bedtools getfasta\"];\n  23 -->|output| 48;\n  42 -->|out_file1| 48;\n  82ce2107-89a3-438c-95bb-dc871b5258b7[\"Output\\nfiltered_sequences_with_vfs_fasta\"];\n  48 --> 82ce2107-89a3-438c-95bb-dc871b5258b7;\n  style 82ce2107-89a3-438c-95bb-dc871b5258b7 stroke:#2c3143,stroke-width:4px;\n  49[\"Regex Find And Replace\"];\n  43 -->|output| 49;\n  50[\"Multi-Join\"];\n  45 -->|out_file1| 50;\n  44 -->|out_file1| 50;\n  51[\"Heatmap w ggplot\"];\n  46 -->|out_file1| 51;\n  c0417c91-a513-4c6a-9a62-3aac2f1f8e85[\"Output\\nheatmap_pdf\"];\n  51 --> c0417c91-a513-4c6a-9a62-3aac2f1f8e85;\n  style c0417c91-a513-4c6a-9a62-3aac2f1f8e85 stroke:#2c3143,stroke-width:4px;\n  97816bc2-fd0c-4077-a721-8dd1470879d1[\"Output\\nheatmap_png\"];\n  51 --> 97816bc2-fd0c-4077-a721-8dd1470879d1;\n  style 97816bc2-fd0c-4077-a721-8dd1470879d1 stroke:#2c3143,stroke-width:4px;\n  52[\"Filter empty datasets\"];\n  47 -->|out_file1| 52;\n  53[\"ClustalW\"];\n  48 -->|output| 53;\n  9b7bd78c-f112-480b-a7df-c10711af254c[\"Output\\nclustalw_on_input_dnd\"];\n  53 --> 9b7bd78c-f112-480b-a7df-c10711af254c;\n  style 9b7bd78c-f112-480b-a7df-c10711af254c stroke:#2c3143,stroke-width:4px;\n  6af20322-24da-4036-80de-37bed2d25848[\"Output\\nclustalw_on_input_clustal\"];\n  53 --> 6af20322-24da-4036-80de-37bed2d25848;\n  style 6af20322-24da-4036-80de-37bed2d25848 stroke:#2c3143,stroke-width:4px;\n  54[\"Filter empty datasets\"];\n  49 -->|out_file1| 54;\n  55[\"Replace Text\"];\n  50 -->|outfile| 55;\n  91745da0-0b8d-4a7a-b927-b36107f17ec5[\"Output\\nvfs_amrs_count_table\"];\n  55 --> 91745da0-0b8d-4a7a-b927-b36107f17ec5;\n  style 91745da0-0b8d-4a7a-b927-b36107f17ec5 stroke:#2c3143,stroke-width:4px;\n  56[\"FASTA-to-Tabular\"];\n  52 -->|output| 56;\n  57[\"Filter empty datasets\"];\n  53 -->|output| 57;\n  32d00c1d-68c4-4069-8d5d-023aabdfadbe[\"Output\\nfiltered_empty_datasets\"];\n  57 --> 32d00c1d-68c4-4069-8d5d-023aabdfadbe;\n  style 32d00c1d-68c4-4069-8d5d-023aabdfadbe stroke:#2c3143,stroke-width:4px;\n  58[\"FASTA-to-Tabular\"];\n  54 -->|output| 58;\n  59[\"Cut\"];\n  56 -->|output| 59;\n  60[\"FASTTREE\"];\n  57 -->|output| 60;\n  aacdfe45-eb0c-4f6e-a479-eeb170774757[\"Output\\nfasttree_nhx\"];\n  60 --> aacdfe45-eb0c-4f6e-a479-eeb170774757;\n  style aacdfe45-eb0c-4f6e-a479-eeb170774757 stroke:#2c3143,stroke-width:4px;\n  61[\"Cut\"];\n  58 -->|output| 61;\n  62[\"Group\"];\n  59 -->|out_file1| 62;\n  63[\"Newick Display\"];\n  60 -->|output| 63;\n  0c22178c-dc85-4137-80e2-f3040b92bd20[\"Output\\nnewick_genes_tree_graphs_collection\"];\n  63 --> 0c22178c-dc85-4137-80e2-f3040b92bd20;\n  style 0c22178c-dc85-4137-80e2-f3040b92bd20 stroke:#2c3143,stroke-width:4px;\n  64[\"Group\"];\n  61 -->|out_file1| 64;\n  65[\"Tabular-to-FASTA\"];\n  62 -->|out_file1| 65;\n  66[\"Tabular-to-FASTA\"];\n  64 -->|out_file1| 66;\n  67[\"FASTA Merge Files and Filter Unique Sequences\"];\n  65 -->|output| 67;\n  68[\"FASTA Merge Files and Filter Unique Sequences\"];\n  66 -->|output| 68;\n  69[\"ClustalW\"];\n  67 -->|output| 69;\n  70[\"ClustalW\"];\n  68 -->|output| 70;\n  71[\"FASTTREE\"];\n  69 -->|output| 71;\n  72[\"FASTTREE\"];\n  70 -->|output| 72;\n  73[\"Newick Display\"];\n  71 -->|output| 73;\n  1f9cb2cf-219f-48de-8058-d6d45f3b3158[\"Output\\nall_samples_phylogenetic_tree_based_amrs\"];\n  73 --> 1f9cb2cf-219f-48de-8058-d6d45f3b3158;\n  style 1f9cb2cf-219f-48de-8058-d6d45f3b3158 stroke:#2c3143,stroke-width:4px;\n  74[\"Newick Display\"];\n  72 -->|output| 74;\n  6bb4b32b-7cca-4e04-8120-be9f64ccba39[\"Output\\nall_samples_phylogenetic_tree_based_vfs\"];\n  74 --> 6bb4b32b-7cca-4e04-8120-be9f64ccba39;\n  style 6bb4b32b-7cca-4e04-8120-be9f64ccba39 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
+                "modified": "2024-10-02 12:08:09 +0000",
                 "name": "Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation",
                 "outputs": [
                     {
@@ -146444,1101 +148178,179 @@
                 ],
                 "parent_id": "microbiome/pathogen-detection-from-nanopore-foodborne-data",
                 "path": "topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/pathogen_detection_pathoGFAIR_samples_aggregation_and_visualisation.ga",
-                "tags": [
-                    "name:Collection",
-                    "name:microGalaxy",
-                    "name:PathoGFAIR",
-                    "name:IWC"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation",
-                "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-pathogen-detection-from-nanopore-foodborne-data/versions/pathogen-detection-pathogfair-samples-aggrtion-and-visualisation",
-                "tutorial_id": "pathogen-detection-from-nanopore-foodborne-data",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/pathogen_detection_pathoGFAIR_samples_aggregation_and_visualisation.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/pathogen_detection_pathoGFAIR_samples_aggregation_and_visualisation.html",
-                "version": 2,
-                "wfid": "microbiome-pathogen-detection-from-nanopore-foodborne-data",
-                "wfname": "pathogen-detection-pathogfair-samples-aggrtion-and-visualisation",
-                "workflow": "pathogen_detection_pathoGFAIR_samples_aggregation_and_visualisation.ga",
-                "workflow_tools": [
-                    "Count1",
-                    "Cut1",
-                    "Grouping1",
-                    "Remove beginning1",
-                    "__FILTER_EMPTY_DATASETS__",
-                    "__FILTER_FAILED_DATASETS__",
-                    "barchart_gnuplot",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap/ggplot2_heatmap/3.4.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
-                ],
-                "workflowhub_id": "1077"
-            },
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0001-9047-4215",
-                        "name": "Engy Nasr",
-                        "url": "https://orcid.org/0000-0001-9047-4215"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0001-9852-1987",
-                        "name": "B\u00e9r\u00e9nice Batut",
-                        "url": "https://orcid.org/0000-0001-9852-1987"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0003-2982-388X",
-                        "name": "Paul Zierep"
-                    }
-                ],
-                "description": "Microbiome - Taxonomy Profiling",
-                "features": {
-                    "comments": true,
-                    "parameters": true,
-                    "report": {
-                        "markdown": "# Taxonomy Profiling and Visualisation with Krona Workflow Report\n\nIn this workflow you can identify your microbial community, but identifying all possible Taxon found in your samples, from the kingdom level down to the species level. In the application of the pathogen detection, this workflow gives an overview of the possible bacterial found in samples and what might be a possible suspect for pathogenicity.\n\nThe workflow uses Kraken2 tool and allow the user to choose any Kraken2 database or other added ones depending on the user application or the input samples. All Kraken2 tool databases are available in Galaxy. More description about these databases can be found [here](https://benlangmead.github.io/aws-indexes/k2). Other databases can be also added to the tool, just contact us anytime for that. We recommend using StandardPF database.\n\nVisualization is done using Krona Pie Chart, and you can replace it with any other tool. e.g. Phinch interactive tool, which is also available in Galaxy\n\n## Workflow Inputs:\n\nThe per-processing workflow main output (Collection of all samples reads after quality retaining and hosts filtering)\n\n## Workflow Outputs are:\n\n### Taxonomy Tabular Report\n\nThe report shows the abundance of every taxon from the kingdom level down to the species level\n\n```galaxy\nhistory_dataset_display(output=\"converted_kraken_report\")\n```\n\n### Taxonomy Profiling Visualization with Krona\nAn interactive Pie chart showing the different identified taxons along with their percentages, which is one of the ways to visualize the previous taxonomy tabular\n\n```galaxy\nhistory_dataset_as_image(output=\"krona_pie_chart\")\n```\n"
-                    },
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\ncollection_of_preprocessed_samples\"]\n  1[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nkraken_database\"]\n  2[label=\"Kraken2\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  k26f9041fd8a44f648a53404d5c7e2f61[color=lightseagreen,label=\"Output\\nkraken2_with_pluspf_database_output\"]\n  2 -> k26f9041fd8a44f648a53404d5c7e2f61\n  kf2ddd05b66a04cea9da6ed107eecbe1b[color=lightseagreen,label=\"Output\\nkraken2_with_pluspf_database_output_report\"]\n  2 -> kf2ddd05b66a04cea9da6ed107eecbe1b\n  3[label=\"Krakentools: Convert kraken report file\"]\n  2 -> 3 [label=\"report_output\"]\n  kc490ab8d1b1d4914aa51a62a967a4018[color=lightseagreen,label=\"Output\\nconverted_kraken_report\"]\n  3 -> kc490ab8d1b1d4914aa51a62a967a4018\n  4[label=\"Krona pie chart\"]\n  3 -> 4 [label=\"output\"]\n  kdcc857c6f5794c7484ecbb6ce3794a56[color=lightseagreen,label=\"Output\\nkrona_pie_chart\"]\n  4 -> kdcc857c6f5794c7484ecbb6ce3794a56\n}",
-                "history": [
-                    {
-                        "hash": "cdd93376adc6ce80742881c25d6810bcce85fc05",
-                        "message": "adding tags to some of the workflow outputs, updating the training with the latest PathoGFAIR  workflows updates",
-                        "num": 2,
-                        "short_hash": "cdd93376a",
-                        "unix": "1717675229"
-                    },
-                    {
-                        "hash": "c63ce23c7a7a631f1256b8e733defce3ca4e009b",
-                        "message": "updating workflows file names",
-                        "num": 1,
-                        "short_hash": "c63ce23c7",
-                        "unix": "1716726587"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "Output collection from the Nanopore Preprocessing workflow",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Output collection from the Nanopore Preprocessing workflow",
-                                "name": "collection_of_preprocessed_samples"
-                            }
-                        ],
-                        "label": "collection_of_preprocessed_samples",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 0
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "c4a14ff1-1f0c-4cb5-aefe-b56f0a84404e",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "kraken_database_for_user_to_choose",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "kraken_database_for_user_to_choose",
-                                "name": "kraken_database"
-                            }
-                        ],
-                        "label": "kraken_database",
-                        "name": "Input parameter",
-                        "outputs": [],
-                        "position": {
-                            "left": 24.79997558593749,
-                            "top": 276.7833526611328
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "cc59191c-1bc9-4007-b88c-8765ff2dfefd",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\ncollection_of_preprocessed_samples\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nkraken_database\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"Kraken2\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  26f9041f-d8a4-4f64-8a53-404d5c7e2f61[\"Output\\nkraken2_with_pluspf_database_output\"];\n  2 --> 26f9041f-d8a4-4f64-8a53-404d5c7e2f61;\n  style 26f9041f-d8a4-4f64-8a53-404d5c7e2f61 stroke:#2c3143,stroke-width:4px;\n  f2ddd05b-66a0-4cea-9da6-ed107eecbe1b[\"Output\\nkraken2_with_pluspf_database_output_report\"];\n  2 --> f2ddd05b-66a0-4cea-9da6-ed107eecbe1b;\n  style f2ddd05b-66a0-4cea-9da6-ed107eecbe1b stroke:#2c3143,stroke-width:4px;\n  3[\"Krakentools: Convert kraken report file\"];\n  2 -->|report_output| 3;\n  c490ab8d-1b1d-4914-aa51-a62a967a4018[\"Output\\nconverted_kraken_report\"];\n  3 --> c490ab8d-1b1d-4914-aa51-a62a967a4018;\n  style c490ab8d-1b1d-4914-aa51-a62a967a4018 stroke:#2c3143,stroke-width:4px;\n  4[\"Krona pie chart\"];\n  3 -->|output| 4;\n  dcc857c6-f579-4c74-84ec-bb6ce3794a56[\"Output\\nkrona_pie_chart\"];\n  4 --> dcc857c6-f579-4c74-84ec-bb6ce3794a56;\n  style dcc857c6-f579-4c74-84ec-bb6ce3794a56 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Taxonomy Profiling and Visualization with Krona",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "kraken2_database": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "single_paired|input_sequences": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Kraken2",
-                                "name": "single_paired"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Kraken2",
-                        "outputs": [
-                            {
-                                "name": "report_output",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "output",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 231.99998779296874,
-                            "top": 205.00002746582032
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "kraken2_with_pluspf_database_output"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            },
-                            "RenameDatasetActionreport_output": {
-                                "action_arguments": {
-                                    "newname": "kraken2_with_pluspf_database_output_report"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "report_output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "20e2f64aa1fe",
-                            "name": "kraken2",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"confidence\": \"0.1\", \"kraken2_database\": {\"__class__\": \"ConnectedValue\"}, \"min_base_quality\": \"0\", \"minimum_hit_groups\": \"2\", \"quick\": false, \"report\": {\"create_report\": true, \"use_mpa_style\": false, \"report_zero_counts\": false, \"report_minimizer_data\": false}, \"single_paired\": {\"single_paired_selector\": \"no\", \"__current_case__\": 2, \"input_sequences\": {\"__class__\": \"ConnectedValue\"}}, \"split_reads\": false, \"use_names\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.1+galaxy1",
-                        "type": "tool",
-                        "uuid": "ddb4e42b-6381-411e-9328-1c7959ecda47",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "kraken2_with_pluspf_database_output",
-                                "output_name": "output",
-                                "uuid": "26f9041f-d8a4-4f64-8a53-404d5c7e2f61"
-                            },
-                            {
-                                "label": "kraken2_with_pluspf_database_output_report",
-                                "output_name": "report_output",
-                                "uuid": "f2ddd05b-66a0-4cea-9da6-ed107eecbe1b"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy1",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "report": {
-                                "id": 2,
-                                "output_name": "report_output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Krakentools: Convert kraken report file",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 447.9999877929688,
-                            "top": 205.31667785644532
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "converted_kraken_report"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2deaada69b14",
-                            "name": "krakentools_kreport2krona",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"intermediate_ranks\": false, \"report\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2+galaxy1",
-                        "type": "tool",
-                        "uuid": "7464e3a0-2253-4fe5-832f-ea155a660b08",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "converted_kraken_report",
-                                "output_name": "output",
-                                "uuid": "c490ab8d-1b1d-4914-aa51-a62a967a4018"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "type_of_data|input": {
-                                "id": 3,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Krona pie chart",
-                                "name": "type_of_data"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Krona pie chart",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "html"
-                            }
-                        ],
-                        "position": {
-                            "left": 701,
-                            "top": 212.31666564941406
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "krona_pie_chart"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            },
-                            "TagDatasetActionoutput": {
-                                "action_arguments": {
-                                    "tags": "taxonomy_profiling_visualisation_krona_pie_chart"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "e9005d1f3cfd",
-                            "name": "taxonomy_krona_chart",
-                            "owner": "crs4",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"combine_inputs\": false, \"root_name\": \"Root\", \"type_of_data\": {\"type_of_data_selector\": \"text\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.7.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "8b130a6a-6fb3-4498-ac19-0d2df97c09e1",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "krona_pie_chart",
-                                "output_name": "output",
-                                "uuid": "dcc857c6-f579-4c74-84ec-bb6ce3794a56"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "microbiome/pathogen-detection-from-nanopore-foodborne-data",
-                "path": "topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/taxonomy_profiling_and_visualisation_with_krona.ga",
-                "tags": [
-                    "name:Collection",
-                    "name:microGalaxy",
-                    "name:PathoGFAIR",
-                    "name:IWC"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "Taxonomy Profiling and Visualization with Krona",
-                "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-pathogen-detection-from-nanopore-foodborne-data/versions/taxonomy-profiling-and-visualisation-with-krona",
-                "tutorial_id": "pathogen-detection-from-nanopore-foodborne-data",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/taxonomy_profiling_and_visualisation_with_krona.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/taxonomy_profiling_and_visualisation_with_krona.html",
-                "version": 2,
-                "wfid": "microbiome-pathogen-detection-from-nanopore-foodborne-data",
-                "wfname": "taxonomy-profiling-and-visualisation-with-krona",
-                "workflow": "taxonomy_profiling_and_visualisation_with_krona.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy1"
-                ],
-                "workflowhub_id": "1073"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/11222469"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "taxonomy_krona_chart",
-                    "owner": "crs4",
-                    "revisions": "1334cb4c6b68",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "e7b2202befea",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "datamash_reverse",
-                    "owner": "iuc",
-                    "revisions": "0f1724dd59d2",
-                    "tool_panel_section_label": "Join, Subtract and Group",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastp",
-                    "owner": "iuc",
-                    "revisions": "dbf9c561ef29",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "kraken2",
-                    "owner": "iuc",
-                    "revisions": "328c607150ff",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "5e33b465d8d5",
-                    "tool_panel_section_label": "Quality Control",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "porechop",
-                    "owner": "iuc",
-                    "revisions": "93d623d9979c",
-                    "tool_panel_section_label": "Nanopore",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: taxonomy_krona_chart\n  owner: crs4\n  revisions: 1334cb4c6b68\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_reverse\n  owner: iuc\n  revisions: 0f1724dd59d2\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: dbf9c561ef29\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: 328c607150ff\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 5e33b465d8d5\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: porechop\n  owner: iuc\n  revisions: 93d623d9979c\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.json",
-        "contributors": [
-            {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "gallardoalba",
-                "joined": "2020-11",
-                "name": "Crist\u00f3bal Gallardo",
-                "orcid": "0000-0002-5752-2155",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
-            }
-        ],
-        "dir": "topics/microbiome/tutorials/nanopore-16S-metagenomics",
-        "edam_ontology": [
-            "topic_3697",
-            "topic_0637",
-            "topic_0080",
-            "topic_4038"
-        ],
-        "edam_operation": [
-            "Visualisation",
-            "Sequencing quality control",
-            "Sequence contamination filtering",
-            "Validation",
-            "Sequence composition calculation",
-            "Taxonomic classification",
-            "Statistical calculation"
-        ],
-        "edam_topic": [
-            "Microbial ecology",
-            "Taxonomy",
-            "Sequence analysis"
-        ],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "microbiome/nanopore-16S-metagenomics",
-        "inexact_supported_servers": [
-            "GalaxyTrakr",
-            "UseGalaxy.cz"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "We learned to use MinION Nanopore data for analyzing the health status of the soil",
-            "We preprocessed Nanopore sequences in order to improve their quality"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-07-31",
-        "objectives": [
-            "Use Nanopore data for studying soil metagenomics",
-            "Analyze and preprocess Nanopore reads",
-            "Use Kraken2 to assign a taxonomic labels"
-        ],
-        "pageviews": 3314,
-        "pub_date": "2020-11-24",
-        "questions": [
-            "How can we analyse the health status of the soil?",
-            "How do plants modify the composition of microbial communities?"
-        ],
-        "redirect_from": [
-            "/topics/metagenomics/tutorials/nanopore-16S-metagenomics/tutorial",
-            "/short/microbiome/nanopore-16S-metagenomics",
-            "/short/T00207",
-            "/short/T00392"
-        ],
-        "short_id": "T00392",
-        "short_tools": [
-            "fastp",
-            "multiqc",
-            "taxonomy_krona_chart",
-            "fastqc",
-            "kraken2",
-            "tp_replace_in_line",
-            "Remove beginning1",
-            "datamash_reverse",
-            "porechop"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "metabarcoding",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "metabarcoding",
-            "16S",
-            "nanopore",
-            "microgalaxy",
-            "plants"
-        ],
-        "time_estimation": "2H",
-        "title": "16S Microbial analysis with Nanopore data",
-        "tools": [
-            "Remove beginning1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.0.8_beta+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3"
-        ],
-        "topic_name": "microbiome",
-        "topic_name_human": "Microbiome",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "nanopore-16S-metagenomics",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.json"
-        },
-        "version": 5,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 168,
-        "visitors": 2344,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "16S rRNA analysis with Nanopore reads",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  1[label=\"FastQC\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Porechop\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"MultiQC\"]\n  1 -> 3 [label=\"text_file\"]\n  4[label=\"fastp\"]\n  2 -> 4 [label=\"outfile\"]\n  5[label=\"FastQC\"]\n  4 -> 5 [label=\"out1\"]\n  6[label=\"Kraken2\"]\n  4 -> 6 [label=\"out1\"]\n  7[label=\"MultiQC\"]\n  5 -> 7 [label=\"text_file\"]\n  8[label=\"Reverse\"]\n  6 -> 8 [label=\"report_output\"]\n  9[label=\"Replace Text\"]\n  8 -> 9 [label=\"out_file\"]\n  10[label=\"Remove beginning\"]\n  9 -> 10 [label=\"outfile\"]\n  11[label=\"Krona pie chart\"]\n  10 -> 11 [label=\"out_file1\"]\n}",
-                "history": [
-                    {
-                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
-                        "message": "Rename metagenomics topic to microbiome",
-                        "num": 1,
-                        "short_hash": "0e0a2f2cc",
-                        "unix": "1704901629"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Input Dataset Collection"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 10
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "18fc8b44-c752-41a0-a17c-e03797a5fab1",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"FastQC\"];\n  0 -->|output| 1;\n  2[\"Porechop\"];\n  0 -->|output| 2;\n  3[\"MultiQC\"];\n  1 -->|text_file| 3;\n  4[\"fastp\"];\n  2 -->|outfile| 4;\n  5[\"FastQC\"];\n  4 -->|out1| 5;\n  6[\"Kraken2\"];\n  4 -->|out1| 6;\n  7[\"MultiQC\"];\n  5 -->|text_file| 7;\n  8[\"Reverse\"];\n  6 -->|report_output| 8;\n  9[\"Replace Text\"];\n  8 -->|out_file| 9;\n  10[\"Remove beginning\"];\n  9 -->|outfile| 10;\n  11[\"Krona pie chart\"];\n  10 -->|out_file1| 11;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Training: 16S rRNA Analysis with Nanopore Sequencing Reads",
-                "outputs": [],
-                "parent_id": "microbiome/nanopore-16S-metagenomics",
-                "path": "topics/microbiome/tutorials/nanopore-16S-metagenomics/workflows/main_workflow.ga",
-                "tags": [
-                    "microbiome"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Training: 16S rRNA Analysis with Nanopore Sequencing Reads",
-                "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-nanopore-16S-metagenomics/versions/main-workflow",
-                "tutorial_id": "nanopore-16S-metagenomics",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/nanopore-16S-metagenomics/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/nanopore-16S-metagenomics/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "microbiome-nanopore-16S-metagenomics",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "Remove beginning1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.0.8_beta+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3"
-                ],
-                "workflowhub_id": "1064"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/4274812"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "taxonomy_krona_chart",
-                    "owner": "crs4",
-                    "revisions": "e9005d1f3cfd",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "3d0c7bdf12f5",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastp",
-                    "owner": "iuc",
-                    "revisions": "65b93b623c77",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "kraken2",
-                    "owner": "iuc",
-                    "revisions": "20e2f64aa1fe",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "krakentools_kreport2krona",
-                    "owner": "iuc",
-                    "revisions": "88d274322340",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "porechop",
-                    "owner": "iuc",
-                    "revisions": "543cbeef3949",
-                    "tool_panel_section_label": "Nanopore",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: taxonomy_krona_chart\n  owner: crs4\n  revisions: e9005d1f3cfd\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: 20e2f64aa1fe\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: krakentools_kreport2krona\n  owner: iuc\n  revisions: 88d274322340\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: porechop\n  owner: iuc\n  revisions: 543cbeef3949\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/beer-data-analysis/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "plushz",
-                "chensy96",
-                "bebatut",
-                "teresa-m"
-            ],
-            "funding": [
-                "gallantries"
-            ]
-        },
-        "contributors": [
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "id": "plushz",
-                "joined": "2022-03",
-                "name": "Polina Polunina",
-                "orcid": "0000-0002-0507-4602",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/plushz/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/plushz.json"
-            },
-            {
-                "id": "chensy96",
-                "joined": "2022-05",
-                "name": "Siyu Chen",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/chensy96/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/chensy96.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "teresa-m",
-                "joined": "2022-09",
-                "name": "Teresa M\u00fcller",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/teresa-m.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
-            }
-        ],
-        "dir": "topics/microbiome/tutorials/beer-data-analysis",
-        "edam_ontology": [
-            "topic_3174",
-            "topic_3697",
-            "topic_0637",
-            "topic_0080"
-        ],
-        "edam_operation": [
-            "Visualisation",
-            "Sequencing quality control",
-            "Sequence contamination filtering",
-            "Sequence composition calculation",
-            "Taxonomic classification",
-            "Statistical calculation",
-            "Aggregation"
-        ],
-        "edam_topic": [
-            "Metagenomics",
-            "Microbial ecology",
-            "Taxonomy",
-            "Sequence analysis"
-        ],
-        "exact_supported_servers": [
-            "GalaxyTrakr",
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "microbiome/beer-data-analysis",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz"
-        ],
-        "js_requirements": {
-            "mathjax": 12074,
-            "mermaid": false
-        },
-        "key_points": [
-            "Data obtained by sequencing needs to be checked for quality and cleaned before further processing",
-            "Yeast species but also contamination can be identified and visualized directly from the sequences using several bioinformatics tools",
-            "With its graphical interface, Galaxy makes it easy to use the needed bioinformatics tools",
-            "Beer microbiome is not just made of yeast and can be quite complex"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Introductory",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
-        "objectives": [
-            "Inspect metagenomics data",
-            "Run metagenomics tools",
-            "Identify yeast species contained in a sequenced beer sample using DNA",
-            "Visualize the microbiome community of a beer sample"
-        ],
-        "pageviews": 1743,
-        "pub_date": "2022-09-29",
-        "questions": [
-            "How can yeast strains in a beer sample be identified?",
-            "How can we process metagenomic data sequenced using Nanopore?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "sophia120199"
-                ],
-                "date": "2023-05-10",
-                "galaxy_version": "23.01",
-                "length": "1H5M",
-                "speakers": [
-                    "bebatut"
-                ],
-                "youtube_id": "PJeS06yiJUM"
-            }
-        ],
-        "redirect_from": [
-            "/topics/metagenomics/tutorials/beer-data-analysis/tutorial",
-            "/short/microbiome/beer-data-analysis",
-            "/short/T00200",
-            "/short/T00384"
-        ],
-        "short_id": "T00384",
-        "short_tools": [
-            "fastp",
-            "taxonomy_krona_chart",
-            "fastqc",
-            "kraken2",
-            "Filter1",
-            "porechop",
-            "krakentools_kreport2krona"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "metagenomics",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "nanopore",
-            "beer",
-            "citizen science",
-            "metagenomics",
-            "microgalaxy"
-        ],
-        "time_estimation": "1H",
-        "title": "Identification of the micro-organisms in a beer using Nanopore sequencing",
-        "tools": [
-            "Filter1",
-            "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0"
-        ],
-        "topic_name": "microbiome",
-        "topic_name_human": "Microbiome",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "beer-data-analysis",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/beer-data-analysis/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/beer-data-analysis/tutorial.json"
-        },
-        "version": 4,
-        "video": false,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 169,
-        "visitors": 1103,
-        "workflows": [
+                "tags": [
+                    "name:Collection",
+                    "name:microGalaxy",
+                    "name:PathoGFAIR",
+                    "name:IWC"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation",
+                "topic_id": "microbiome",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-pathogen-detection-from-nanopore-foodborne-data/versions/pathogen-detection-pathogfair-samples-aggrtion-and-visualisation",
+                "tutorial_id": "pathogen-detection-from-nanopore-foodborne-data",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/pathogen_detection_pathoGFAIR_samples_aggregation_and_visualisation.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/pathogen_detection_pathoGFAIR_samples_aggregation_and_visualisation.html",
+                "version": 2,
+                "wfid": "microbiome-pathogen-detection-from-nanopore-foodborne-data",
+                "wfname": "pathogen-detection-pathogfair-samples-aggrtion-and-visualisation",
+                "workflow": "pathogen_detection_pathoGFAIR_samples_aggregation_and_visualisation.ga",
+                "workflow_tools": [
+                    "Count1",
+                    "Cut1",
+                    "Grouping1",
+                    "Remove beginning1",
+                    "__FILTER_EMPTY_DATASETS__",
+                    "__FILTER_FAILED_DATASETS__",
+                    "barchart_gnuplot",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap/ggplot2_heatmap/3.4.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
+                ],
+                "workflowhub_id": "1077"
+            },
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "0000-0001-9852-1987",
-                        "name": "B\u00e9r\u00e9nice Batut"
+                        "identifier": "0000-0001-9047-4215",
+                        "name": "Engy Nasr",
+                        "url": "https://orcid.org/0000-0001-9047-4215"
                     },
                     {
                         "class": "Person",
-                        "identifier": "0000-0003-1252-9684",
-                        "name": "Teresa M\u00fcller"
+                        "identifier": "0000-0001-9852-1987",
+                        "name": "B\u00e9r\u00e9nice Batut",
+                        "url": "https://orcid.org/0000-0001-9852-1987"
                     },
                     {
                         "class": "Person",
-                        "identifier": "0000-0002-0507-4602",
-                        "name": "Polina Polunina"
+                        "identifier": "0000-0003-2982-388X",
+                        "name": "Paul Zierep"
                     }
                 ],
-                "description": "Identification of the micro-organisms in a beer using Nanopore sequencing",
+                "description": "Microbiome - Taxonomy Profiling",
                 "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
+                    "comments": true,
+                    "parameters": true,
+                    "report": {
+                        "markdown": "# Taxonomy Profiling and Visualisation with Krona Workflow Report\n\nIn this workflow you can identify your microbial community, but identifying all possible Taxon found in your samples, from the kingdom level down to the species level. In the application of the pathogen detection, this workflow gives an overview of the possible bacterial found in samples and what might be a possible suspect for pathogenicity.\n\nThe workflow uses Kraken2 tool and allow the user to choose any Kraken2 database or other added ones depending on the user application or the input samples. All Kraken2 tool databases are available in Galaxy. More description about these databases can be found [here](https://benlangmead.github.io/aws-indexes/k2). Other databases can be also added to the tool, just contact us anytime for that. We recommend using StandardPF database.\n\nVisualization is done using Krona Pie Chart, and you can replace it with any other tool. e.g. Phinch interactive tool, which is also available in Galaxy\n\n## Workflow Inputs:\n\nThe per-processing workflow main output (Collection of all samples reads after quality retaining and hosts filtering)\n\n## Workflow Outputs are:\n\n### Taxonomy Tabular Report\n\nThe report shows the abundance of every taxon from the kingdom level down to the species level\n\n```galaxy\nhistory_dataset_display(output=\"converted_kraken_report\")\n```\n\n### Taxonomy Profiling Visualization with Krona\nAn interactive Pie chart showing the different identified taxons along with their percentages, which is one of the ways to visualize the previous taxonomy tabular\n\n```galaxy\nhistory_dataset_as_image(output=\"krona_pie_chart\")\n```\n"
+                    },
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ninput\"]\n  1[label=\"FastQC\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Porechop\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"fastp\"]\n  2 -> 3 [label=\"outfile\"]\n  4[label=\"Kraken2\"]\n  3 -> 4 [label=\"out1\"]\n  k3b674912591543d1b9dfb91648083691[color=lightseagreen,label=\"Output\\nkraken_report\"]\n  4 -> k3b674912591543d1b9dfb91648083691\n  5[label=\"Filter\"]\n  4 -> 5 [label=\"report_output\"]\n  6[label=\"Filter\"]\n  4 -> 6 [label=\"report_output\"]\n  7[label=\"Krakentools: Convert kraken report file\"]\n  4 -> 7 [label=\"report_output\"]\n  k08706a8c0f0f40c0a7b5995ca3b74c50[color=lightseagreen,label=\"Output\\nkrakentool_report\"]\n  7 -> k08706a8c0f0f40c0a7b5995ca3b74c50\n  8[label=\"Krona pie chart\"]\n  7 -> 8 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\ncollection_of_preprocessed_samples\"]\n  1[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nkraken_database\"]\n  2[label=\"Kraken2\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  k26f9041fd8a44f648a53404d5c7e2f61[color=lightseagreen,label=\"Output\\nkraken2_with_pluspf_database_output\"]\n  2 -> k26f9041fd8a44f648a53404d5c7e2f61\n  kf2ddd05b66a04cea9da6ed107eecbe1b[color=lightseagreen,label=\"Output\\nkraken2_with_pluspf_database_output_report\"]\n  2 -> kf2ddd05b66a04cea9da6ed107eecbe1b\n  3[label=\"Krakentools: Convert kraken report file\"]\n  2 -> 3 [label=\"report_output\"]\n  kc490ab8d1b1d4914aa51a62a967a4018[color=lightseagreen,label=\"Output\\nconverted_kraken_report\"]\n  3 -> kc490ab8d1b1d4914aa51a62a967a4018\n  4[label=\"Krona pie chart\"]\n  3 -> 4 [label=\"output\"]\n  kdcc857c6f5794c7484ecbb6ce3794a56[color=lightseagreen,label=\"Output\\nkrona_pie_chart\"]\n  4 -> kdcc857c6f5794c7484ecbb6ce3794a56\n}",
                 "history": [
                     {
-                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
-                        "message": "Rename metagenomics topic to microbiome",
+                        "hash": "cdd93376adc6ce80742881c25d6810bcce85fc05",
+                        "message": "adding tags to some of the workflow outputs, updating the training with the latest PathoGFAIR  workflows updates",
+                        "num": 2,
+                        "short_hash": "cdd93376a",
+                        "unix": "1717675229"
+                    },
+                    {
+                        "hash": "c63ce23c7a7a631f1256b8e733defce3ca4e009b",
+                        "message": "updating workflows file names",
                         "num": 1,
-                        "short_hash": "0e0a2f2cc",
-                        "unix": "1704901629"
+                        "short_hash": "c63ce23c7",
+                        "unix": "1716726587"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "",
+                        "annotation": "Output collection from the Nanopore Preprocessing workflow",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "input"
+                                "description": "Output collection from the Nanopore Preprocessing workflow",
+                                "name": "collection_of_preprocessed_samples"
                             }
                         ],
-                        "label": "input",
-                        "name": "input",
+                        "label": "collection_of_preprocessed_samples",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
                             "left": 0,
-                            "top": 301
+                            "top": 0
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"name\": \"input\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "31e2b384-0c1d-42fc-9379-8fb62462bffb",
+                        "type": "data_collection_input",
+                        "uuid": "c4a14ff1-1f0c-4cb5-aefe-b56f0a84404e",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "kraken_database_for_user_to_choose",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "kraken_database_for_user_to_choose",
+                                "name": "kraken_database"
+                            }
+                        ],
+                        "label": "kraken_database",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 24.79997558593749,
+                            "top": 276.7833526611328
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "cc59191c-1bc9-4007-b88c-8765ff2dfefd",
                         "when": null,
                         "workflow_outputs": []
                     }
                 ],
                 "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ninput\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"FastQC\"];\n  0 -->|output| 1;\n  2[\"Porechop\"];\n  0 -->|output| 2;\n  3[\"fastp\"];\n  2 -->|outfile| 3;\n  4[\"Kraken2\"];\n  3 -->|out1| 4;\n  3b674912-5915-43d1-b9df-b91648083691[\"Output\\nkraken_report\"];\n  4 --> 3b674912-5915-43d1-b9df-b91648083691;\n  style 3b674912-5915-43d1-b9df-b91648083691 stroke:#2c3143,stroke-width:4px;\n  5[\"Filter\"];\n  4 -->|report_output| 5;\n  6[\"Filter\"];\n  4 -->|report_output| 6;\n  7[\"Krakentools: Convert kraken report file\"];\n  4 -->|report_output| 7;\n  08706a8c-0f0f-40c0-a7b5-995ca3b74c50[\"Output\\nkrakentool_report\"];\n  7 --> 08706a8c-0f0f-40c0-a7b5-995ca3b74c50;\n  style 08706a8c-0f0f-40c0-a7b5-995ca3b74c50 stroke:#2c3143,stroke-width:4px;\n  8[\"Krona pie chart\"];\n  7 -->|output| 8;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Identification of the micro-organisms in a beer using Nanopore sequencing",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\ncollection_of_preprocessed_samples\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nkraken_database\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"Kraken2\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  26f9041f-d8a4-4f64-8a53-404d5c7e2f61[\"Output\\nkraken2_with_pluspf_database_output\"];\n  2 --> 26f9041f-d8a4-4f64-8a53-404d5c7e2f61;\n  style 26f9041f-d8a4-4f64-8a53-404d5c7e2f61 stroke:#2c3143,stroke-width:4px;\n  f2ddd05b-66a0-4cea-9da6-ed107eecbe1b[\"Output\\nkraken2_with_pluspf_database_output_report\"];\n  2 --> f2ddd05b-66a0-4cea-9da6-ed107eecbe1b;\n  style f2ddd05b-66a0-4cea-9da6-ed107eecbe1b stroke:#2c3143,stroke-width:4px;\n  3[\"Krakentools: Convert kraken report file\"];\n  2 -->|report_output| 3;\n  c490ab8d-1b1d-4914-aa51-a62a967a4018[\"Output\\nconverted_kraken_report\"];\n  3 --> c490ab8d-1b1d-4914-aa51-a62a967a4018;\n  style c490ab8d-1b1d-4914-aa51-a62a967a4018 stroke:#2c3143,stroke-width:4px;\n  4[\"Krona pie chart\"];\n  3 -->|output| 4;\n  dcc857c6-f579-4c74-84ec-bb6ce3794a56[\"Output\\nkrona_pie_chart\"];\n  4 --> dcc857c6-f579-4c74-84ec-bb6ce3794a56;\n  style dcc857c6-f579-4c74-84ec-bb6ce3794a56 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Taxonomy Profiling and Visualization with Krona",
                 "outputs": [
                     {
                         "annotation": "",
                         "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
                         "errors": null,
-                        "id": 4,
+                        "id": 2,
                         "input_connections": {
+                            "kraken2_database": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
                             "single_paired|input_sequences": {
-                                "id": 3,
-                                "output_name": "out1"
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Kraken2",
+                                "name": "single_paired"
+                            }
+                        ],
                         "label": null,
                         "name": "Kraken2",
                         "outputs": [
@@ -147552,38 +148364,58 @@
                             }
                         ],
                         "position": {
-                            "left": 840,
-                            "top": 349
+                            "left": 231.99998779296874,
+                            "top": 205.00002746582032
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "kraken2_with_pluspf_database_output"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            },
+                            "RenameDatasetActionreport_output": {
+                                "action_arguments": {
+                                    "newname": "kraken2_with_pluspf_database_output_report"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "report_output"
+                            }
                         },
-                        "post_job_actions": {},
                         "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "e674066930b2",
+                            "changeset_revision": "20e2f64aa1fe",
                             "name": "kraken2",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"fastqsanger\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"confidence\": \"0.0\", \"kraken2_database\": \"2022-09-04T165121Z_standard_prebuilt_pluspf_2022-06-07\", \"min_base_quality\": \"0\", \"minimum_hit_groups\": \"2\", \"quick\": false, \"report\": {\"create_report\": true, \"use_mpa_style\": false, \"report_zero_counts\": false, \"report_minimizer_data\": false}, \"single_paired\": {\"single_paired_selector\": \"no\", \"__current_case__\": 2, \"input_sequences\": {\"__class__\": \"ConnectedValue\"}}, \"split_reads\": false, \"use_names\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"confidence\": \"0.1\", \"kraken2_database\": {\"__class__\": \"ConnectedValue\"}, \"min_base_quality\": \"0\", \"minimum_hit_groups\": \"2\", \"quick\": false, \"report\": {\"create_report\": true, \"use_mpa_style\": false, \"report_zero_counts\": false, \"report_minimizer_data\": false}, \"single_paired\": {\"single_paired_selector\": \"no\", \"__current_case__\": 2, \"input_sequences\": {\"__class__\": \"ConnectedValue\"}}, \"split_reads\": false, \"use_names\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "2.1.1+galaxy1",
                         "type": "tool",
-                        "uuid": "b0030c6f-df98-4ab9-a019-2b96fbad69e7",
+                        "uuid": "ddb4e42b-6381-411e-9328-1c7959ecda47",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "kraken_report",
+                                "label": "kraken2_with_pluspf_database_output",
+                                "output_name": "output",
+                                "uuid": "26f9041f-d8a4-4f64-8a53-404d5c7e2f61"
+                            },
+                            {
+                                "label": "kraken2_with_pluspf_database_output_report",
                                 "output_name": "report_output",
-                                "uuid": "3b674912-5915-43d1-b9df-b91648083691"
+                                "uuid": "f2ddd05b-66a0-4cea-9da6-ed107eecbe1b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy1",
                         "errors": null,
-                        "id": 7,
+                        "id": 3,
                         "input_connections": {
                             "report": {
-                                "id": 4,
+                                "id": 2,
                                 "output_name": "report_output"
                             }
                         },
@@ -147597,61 +148429,133 @@
                             }
                         ],
                         "position": {
-                            "left": 1120,
-                            "top": 517
+                            "left": 447.9999877929688,
+                            "top": 205.31667785644532
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "converted_kraken_report"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "88d274322340",
+                            "changeset_revision": "2deaada69b14",
                             "name": "krakentools_kreport2krona",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"intermediate_ranks\": false, \"report\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2+galaxy0",
+                        "tool_state": "{\"intermediate_ranks\": false, \"report\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2+galaxy1",
                         "type": "tool",
-                        "uuid": "9c2946a8-b768-4ba1-879d-e96f1a2eda51",
+                        "uuid": "7464e3a0-2253-4fe5-832f-ea155a660b08",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "krakentool_report",
+                                "label": "converted_kraken_report",
+                                "output_name": "output",
+                                "uuid": "c490ab8d-1b1d-4914-aa51-a62a967a4018"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "type_of_data|input": {
+                                "id": 3,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Krona pie chart",
+                                "name": "type_of_data"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Krona pie chart",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "html"
+                            }
+                        ],
+                        "position": {
+                            "left": 701,
+                            "top": 212.31666564941406
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "krona_pie_chart"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            },
+                            "TagDatasetActionoutput": {
+                                "action_arguments": {
+                                    "tags": "taxonomy_profiling_visualisation_krona_pie_chart"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e9005d1f3cfd",
+                            "name": "taxonomy_krona_chart",
+                            "owner": "crs4",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"combine_inputs\": false, \"root_name\": \"Root\", \"type_of_data\": {\"type_of_data_selector\": \"text\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.7.1+galaxy0",
+                        "type": "tool",
+                        "uuid": "8b130a6a-6fb3-4498-ac19-0d2df97c09e1",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "krona_pie_chart",
                                 "output_name": "output",
-                                "uuid": "08706a8c-0f0f-40c0-a7b5-995ca3b74c50"
+                                "uuid": "dcc857c6-f579-4c74-84ec-bb6ce3794a56"
                             }
                         ]
                     }
                 ],
-                "parent_id": "microbiome/beer-data-analysis",
-                "path": "topics/microbiome/tutorials/beer-data-analysis/workflows/main_workflow.ga",
+                "parent_id": "microbiome/pathogen-detection-from-nanopore-foodborne-data",
+                "path": "topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/taxonomy_profiling_and_visualisation_with_krona.ga",
                 "tags": [
-                    "Microbiome"
+                    "name:Collection",
+                    "name:microGalaxy",
+                    "name:PathoGFAIR",
+                    "name:IWC"
                 ],
                 "test_results": null,
                 "tests": true,
-                "title": "Identification of the micro-organisms in a beer using Nanopore sequencing",
+                "title": "Taxonomy Profiling and Visualization with Krona",
                 "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-beer-data-analysis/versions/main-workflow",
-                "tutorial_id": "beer-data-analysis",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/beer-data-analysis/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/beer-data-analysis/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "microbiome-beer-data-analysis",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-pathogen-detection-from-nanopore-foodborne-data/versions/taxonomy-profiling-and-visualisation-with-krona",
+                "tutorial_id": "pathogen-detection-from-nanopore-foodborne-data",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/taxonomy_profiling_and_visualisation_with_krona.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/taxonomy_profiling_and_visualisation_with_krona.html",
+                "version": 2,
+                "wfid": "microbiome-pathogen-detection-from-nanopore-foodborne-data",
+                "wfname": "taxonomy-profiling-and-visualisation-with-krona",
+                "workflow": "taxonomy_profiling_and_visualisation_with_krona.ga",
                 "workflow_tools": [
-                    "Filter1",
                     "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
                     "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy1"
                 ],
-                "workflowhub_id": "1097"
+                "workflowhub_id": "1073"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.7093173"
+        "zenodo_link": "https://zenodo.org/record/11222469"
     },
     {
         "admin_install": {
@@ -147930,25 +148834,25 @@
         ],
         "edam_operation": [
             "Visualisation",
-            "Primer removal",
             "Sequencing quality control",
-            "Sequence similarity search",
-            "Phylogenetic analysis",
-            "Taxonomic classification",
-            "Nucleic acid sequence analysis",
-            "Sequence composition calculation",
             "Phylogenetic inference",
-            "Validation",
-            "Sequence trimming",
-            "Conversion",
-            "Statistical calculation",
-            "Species frequency estimation",
             "Phylogenetic tree editing",
+            "Statistical calculation",
+            "Taxonomic classification",
+            "Validation",
+            "Sequence composition calculation",
             "Sequence comparison",
+            "Sequence similarity search",
             "Phylogenetic tree analysis",
+            "Sequence trimming",
+            "Phylogenetic analysis",
+            "Phylogenetic tree visualisation",
             "Sequence alignment analysis",
+            "Species frequency estimation",
+            "Conversion",
+            "Nucleic acid sequence analysis",
             "Read pre-processing",
-            "Phylogenetic tree visualisation"
+            "Primer removal"
         ],
         "edam_topic": [
             "Metatranscriptomics",
@@ -147958,7 +148862,8 @@
             "Sequence analysis"
         ],
         "exact_supported_servers": [
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
@@ -147966,8 +148871,7 @@
         "id": "microbiome/metatranscriptomics",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
+            "UseGalaxy.no"
         ],
         "js_requirements": {
             "mathjax": null,
@@ -147989,7 +148893,7 @@
             "Understand where metatranscriptomics fits in 'multi-omic' analysis of microbiomes",
             "Visualise a community structure"
         ],
-        "pageviews": 5729924,
+        "pageviews": 5901051,
         "pub_date": "2019-11-21",
         "questions": [
             "How to analyze metatranscriptomics data?",
@@ -148034,26 +148938,26 @@
         ],
         "short_id": "T00388",
         "short_tools": [
-            "humann_rename_table",
-            "Cut1",
+            "fastq_paired_end_interlacer",
+            "tp_find_and_replace",
+            "metaphlan",
+            "fastqc",
+            "humann",
             "graphlan_annotate",
+            "graphlan",
+            "humann_split_stratified_table",
+            "humann_renorm_table",
             "humann_regroup_table",
-            "metaphlan",
+            "humann_rename_table",
+            "cutadapt",
+            "combine_metaphlan2_humann2",
+            "multiqc",
+            "bg_sortmerna",
             "Grep1",
+            "Cut1",
             "export2graphlan",
-            "bg_sortmerna",
-            "humann_split_stratified_table",
-            "graphlan",
-            "fastq_paired_end_interlacer",
-            "combine_metaphlan2_humann2",
-            "taxonomy_krona_chart",
-            "tp_find_and_replace",
             "humann_unpack_pathways",
-            "cutadapt",
-            "humann",
-            "multiqc",
-            "fastqc",
-            "humann_renorm_table"
+            "taxonomy_krona_chart"
         ],
         "slides": true,
         "slides_recordings": false,
@@ -148064,6 +148968,11 @@
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ],
             "inexact": [
@@ -148076,11 +148985,6 @@
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
                 }
             ]
         },
@@ -148132,8 +149036,8 @@
         "video": false,
         "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 248,
-        "visitors": 2066154,
+        "visit_duration": 256,
+        "visitors": 2136358,
         "workflows": [
             {
                 "creators": [
@@ -148250,7 +149154,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nT1A_forward\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nT1A_reverse\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\ud83d\udee0\ufe0f Subworkflow\\nWorkflow 1: Preprocessing\"];\n  style 2 fill:#edd,stroke:#900,stroke-width:4px;\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"\ud83d\udee0\ufe0f Subworkflow\\nWorkflow 2: Community Profile\"];\n  style 3 fill:#edd,stroke:#900,stroke-width:4px;\n  2 -->|Cutadapt on input datasets: Read 1 Output| 3;\n  2 -->|Cutadapt on input datasets: Read 2 Output| 3;\n  4[\"\ud83d\udee0\ufe0f Subworkflow\\nWorkflow 3: Functional Information\"];\n  style 4 fill:#edd,stroke:#900,stroke-width:4px;\n  2 -->|FASTQ interlacer pairs from input datasets| 4;\n  3 -->|MetaPhlAn on input datasets: Predicted taxon relative abundances| 4;",
-                "modified": "2024-08-18 00:06:24 +0000",
+                "modified": "2024-10-02 12:08:09 +0000",
                 "name": "Main Metatranscriptomics Analysis",
                 "outputs": [],
                 "parent_id": "microbiome/metatranscriptomics",
@@ -148295,6 +149199,591 @@
         ],
         "zenodo_link": "https://zenodo.org/record/4776250"
     },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "taxonomy_krona_chart",
+                    "owner": "crs4",
+                    "revisions": "1334cb4c6b68",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "taxonomy_krona_chart",
+                    "owner": "crs4",
+                    "revisions": "e9005d1f3cfd",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bracken",
+                    "owner": "iuc",
+                    "revisions": "79450f7fd718",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "kraken2",
+                    "owner": "iuc",
+                    "revisions": "20e2f64aa1fe",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "kraken_biom",
+                    "owner": "iuc",
+                    "revisions": "b582a159bb10",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "krakentools_kreport2krona",
+                    "owner": "iuc",
+                    "revisions": "88d274322340",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "metaphlan",
+                    "owner": "iuc",
+                    "revisions": "1a6cdf55390f",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: taxonomy_krona_chart\n  owner: crs4\n  revisions: 1334cb4c6b68\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: taxonomy_krona_chart\n  owner: crs4\n  revisions: e9005d1f3cfd\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bracken\n  owner: iuc\n  revisions: 79450f7fd718\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: 20e2f64aa1fe\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken_biom\n  owner: iuc\n  revisions: b582a159bb10\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: krakentools_kreport2krona\n  owner: iuc\n  revisions: 88d274322340\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaphlan\n  owner: iuc\n  revisions: 1a6cdf55390f\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/taxonomic-profiling/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "sophia120199",
+                "bebatut",
+                "paulzierep"
+            ],
+            "funding": [
+                "gallantries"
+            ]
+        },
+        "contributors": [
+            {
+                "id": "sophia120199",
+                "joined": "2023-04",
+                "name": "Sophia Hampe",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/sophia120199/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/sophia120199.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "email": "zierep@informatik.uni-freiburg.de",
+                "id": "paulzierep",
+                "joined": "2023-02",
+                "name": "Paul Zierep",
+                "orcid": "0000-0003-2982-388X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            }
+        ],
+        "dir": "topics/microbiome/tutorials/taxonomic-profiling",
+        "edam_ontology": [
+            "topic_3174",
+            "topic_3697",
+            "topic_0637",
+            "topic_0080"
+        ],
+        "edam_operation": [
+            "Phylogenetic tree analysis",
+            "Statistical calculation",
+            "Taxonomic classification",
+            "Aggregation",
+            "Visualisation",
+            "Nucleic acid sequence analysis"
+        ],
+        "edam_topic": [
+            "Metagenomics",
+            "Microbial ecology",
+            "Taxonomy",
+            "Sequence analysis"
+        ],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "microbiome/taxonomic-profiling",
+        "inexact_supported_servers": [
+            "UseGalaxy.fr",
+            "UseGalaxy.org.au"
+        ],
+        "js_requirements": {
+            "mathjax": 4920,
+            "mermaid": false
+        },
+        "key_points": [
+            "There are 3 different types of taxonomic assignment (genome, gene or k-mer based)",
+            "Kraken or MetaPhlAn can be used in Galaxy for taxonomic assignment",
+            "Visualization of community profiles can be done using Krona or Pavian",
+            "The taxonomic classification tool to use depends on the data"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-14",
+        "objectives": [
+            "Explain what taxonomic assignment is",
+            "Explain how taxonomic assignment works",
+            "Apply Kraken and MetaPhlAn to assign taxonomic labels",
+            "Apply Krona and Pavian to visualize results of assignment and understand the output",
+            "Identify taxonomic classification tool that fits best depending on their data"
+        ],
+        "pageviews": 6096,
+        "pub_date": "2023-05-03",
+        "questions": [
+            "Which species (or genera, families, ...) are present in my sample?",
+            "What are the different approaches and tools to get the community profile of my sample?",
+            "How can we visualize and compare community profiles?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "sophia120199"
+                ],
+                "date": "2023-05-16",
+                "galaxy_version": "23.01",
+                "length": "1H15M",
+                "speakers": [
+                    "bebatut"
+                ],
+                "youtube_id": "jszMnBKm6ig"
+            }
+        ],
+        "redirect_from": [
+            "/topics/metagenomics/tutorials/taxonomic-profiling/tutorial",
+            "/short/microbiome/taxonomic-profiling",
+            "/short/T00338",
+            "/short/T00395"
+        ],
+        "short_id": "T00395",
+        "short_tools": [
+            "interactive_tool_phinch",
+            "est_abundance",
+            "taxonomy_krona_chart",
+            "interactive_tool_pavian",
+            "kraken2",
+            "kraken_biom",
+            "__UNZIP_COLLECTION__",
+            "krakentools_kreport2krona",
+            "metaphlan"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "metagenomics",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "metagenomics",
+            "taxonomic profiling",
+            "microgalaxy"
+        ],
+        "time_estimation": "2H",
+        "title": "Taxonomic Profiling and Visualization of Metagenomic Data",
+        "tools": [
+            "__UNZIP_COLLECTION__",
+            "interactive_tool_pavian",
+            "interactive_tool_phinch",
+            "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1",
+            "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.7+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/kraken_biom/kraken_biom/1.2.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy1"
+        ],
+        "topic_name": "microbiome",
+        "topic_name_human": "Microbiome",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "taxonomic-profiling",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/taxonomic-profiling/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/taxonomic-profiling/tutorial.json"
+        },
+        "version": 4,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 118,
+        "visitors": 4443,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0001-9852-1987",
+                        "name": "B\u00e9r\u00e9nice Batut"
+                    }
+                ],
+                "description": "Taxonomic Profiling and Visualization of Metagenomic Data",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nraw-reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmetadata\"]\n  2[label=\"Unzip collection\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Kraken2\"]\n  0 -> 3 [label=\"output\"]\n  k51c22a6e07434510b4e126afc897534a[color=lightseagreen,label=\"Output\\nkraken_report\"]\n  3 -> k51c22a6e07434510b4e126afc897534a\n  4[label=\"MetaPhlAn\"]\n  2 -> 4 [label=\"forward\"]\n  2 -> 4 [label=\"reverse\"]\n  k6bcdc5a7ddf94cdf9729b359d60490fb[color=lightseagreen,label=\"Output\\nmetaphlan_output\"]\n  4 -> k6bcdc5a7ddf94cdf9729b359d60490fb\n  5[label=\"Krakentools: Convert kraken report file\"]\n  3 -> 5 [label=\"report_output\"]\n  k2cc442f840ac4c58a82ef4018ab8a0a5[color=lightseagreen,label=\"Output\\nkrakentool_report\"]\n  5 -> k2cc442f840ac4c58a82ef4018ab8a0a5\n  6[label=\"Kraken-biom\"]\n  3 -> 6 [label=\"report_output\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"Pavian\"]\n  3 -> 7 [label=\"report_output\"]\n  8[label=\"Estimate Abundance at Taxonomic Level\"]\n  3 -> 8 [label=\"report_output\"]\n  9[label=\"Krona pie chart\"]\n  4 -> 9 [label=\"krona_output_file\"]\n  10[label=\"Krona pie chart\"]\n  5 -> 10 [label=\"output\"]\n  11[label=\"Phinch Visualisation\"]\n  6 -> 11 [label=\"biomOutput\"]\n}",
+                "history": [
+                    {
+                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
+                        "message": "Rename metagenomics topic to microbiome",
+                        "num": 1,
+                        "short_hash": "0e0a2f2cc",
+                        "unix": "1704901629"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "raw-reads"
+                            }
+                        ],
+                        "label": "raw-reads",
+                        "name": "raw-reads",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 32
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"raw-reads\",\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "8ceaae85-1ed7-4488-b839-53d36e642378",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "metadata"
+                            }
+                        ],
+                        "label": "metadata",
+                        "name": "metadata",
+                        "outputs": [],
+                        "position": {
+                            "left": 35.48228574271107,
+                            "top": 575.2289046420843
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"metadata\", \"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "715bbeb3-cb9a-49dd-a9c5-1f184f3eb34a",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nraw-reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nmetadata\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Unzip collection\"];\n  0 -->|output| 2;\n  3[\"Kraken2\"];\n  0 -->|output| 3;\n  51c22a6e-0743-4510-b4e1-26afc897534a[\"Output\\nkraken_report\"];\n  3 --> 51c22a6e-0743-4510-b4e1-26afc897534a;\n  style 51c22a6e-0743-4510-b4e1-26afc897534a stroke:#2c3143,stroke-width:4px;\n  4[\"MetaPhlAn\"];\n  2 -->|forward| 4;\n  2 -->|reverse| 4;\n  6bcdc5a7-ddf9-4cdf-9729-b359d60490fb[\"Output\\nmetaphlan_output\"];\n  4 --> 6bcdc5a7-ddf9-4cdf-9729-b359d60490fb;\n  style 6bcdc5a7-ddf9-4cdf-9729-b359d60490fb stroke:#2c3143,stroke-width:4px;\n  5[\"Krakentools: Convert kraken report file\"];\n  3 -->|report_output| 5;\n  2cc442f8-40ac-4c58-a82e-f4018ab8a0a5[\"Output\\nkrakentool_report\"];\n  5 --> 2cc442f8-40ac-4c58-a82e-f4018ab8a0a5;\n  style 2cc442f8-40ac-4c58-a82e-f4018ab8a0a5 stroke:#2c3143,stroke-width:4px;\n  6[\"Kraken-biom\"];\n  3 -->|report_output| 6;\n  1 -->|output| 6;\n  7[\"Pavian\"];\n  3 -->|report_output| 7;\n  8[\"Estimate Abundance at Taxonomic Level\"];\n  3 -->|report_output| 8;\n  9[\"Krona pie chart\"];\n  4 -->|krona_output_file| 9;\n  10[\"Krona pie chart\"];\n  5 -->|output| 10;\n  11[\"Phinch Visualisation\"];\n  6 -->|biomOutput| 11;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Taxonomic Profiling and Visualization of Metagenomic Data",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "single_paired|input_pair": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Kraken2",
+                        "outputs": [
+                            {
+                                "name": "report_output",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 279.9980390107984,
+                            "top": 464
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e674066930b2",
+                            "name": "kraken2",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"confidence\": \"0.1\", \"kraken2_database\": \"2022-09-04T165121Z_standard_prebuilt_pluspf_2022-06-07\", \"min_base_quality\": \"0\", \"minimum_hit_groups\": \"2\", \"quick\": false, \"report\": {\"create_report\": true, \"use_mpa_style\": false, \"report_zero_counts\": false, \"report_minimizer_data\": false}, \"single_paired\": {\"single_paired_selector\": \"collection\", \"__current_case__\": 0, \"input_pair\": {\"__class__\": \"ConnectedValue\"}}, \"split_reads\": false, \"use_names\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.1+galaxy1",
+                        "type": "tool",
+                        "uuid": "ec3d15fe-c551-4986-b56b-6f92fe781a4e",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "kraken_report",
+                                "output_name": "report_output",
+                                "uuid": "51c22a6e-0743-4510-b4e1-26afc897534a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy1",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "inputs|in|raw_in|in_f": {
+                                "id": 2,
+                                "output_name": "forward"
+                            },
+                            "inputs|in|raw_in|in_r": {
+                                "id": 2,
+                                "output_name": "reverse"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool MetaPhlAn",
+                                "name": "analysis"
+                            }
+                        ],
+                        "label": null,
+                        "name": "MetaPhlAn",
+                        "outputs": [
+                            {
+                                "name": "output_file",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "bowtie2out",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "sam_output_file",
+                                "type": "sam"
+                            },
+                            {
+                                "name": "biom_output_file",
+                                "type": "biom1"
+                            },
+                            {
+                                "name": "krona_output_file",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 559.9960780215968,
+                            "top": 0
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "1a6cdf55390f",
+                            "name": "metaphlan",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"analysis\": {\"analysis_type\": {\"t\": \"rel_ab\", \"__current_case__\": 0, \"tax_lev\": {\"tax_lev\": \"a\", \"__current_case__\": 0, \"split_levels\": false}}, \"min_cu_len\": \"2000\", \"min_alignment_len\": null, \"organism_profiling\": [\"add_viruses\"], \"stat\": \"tavg_g\", \"stat_q\": \"0.2\", \"perc_nonzero\": \"0.33\", \"ignore_markers\": {\"__class__\": \"RuntimeValue\"}, \"avoid_disqm\": true}, \"inputs\": {\"in\": {\"selector\": \"raw\", \"__current_case__\": 0, \"raw_in\": {\"selector\": \"paired\", \"__current_case__\": 2, \"in_f\": {\"__class__\": \"ConnectedValue\"}, \"in_r\": {\"__class__\": \"ConnectedValue\"}}, \"read_min_len\": \"70\", \"mapping\": {\"bt2_ps\": \"very-sensitive\", \"min_mapq_val\": \"5\"}}, \"db\": {\"db_selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": \"mpa_vOct22_CHOCOPhlAnSGB_202212-03042023\"}}, \"out\": {\"sample_id_key\": \"SampleID\", \"sample_id\": \"Metaphlan_Analysis\", \"use_group_representative\": false, \"legacy_output\": false, \"CAMI_format_output\": false, \"unknown_estimation\": false, \"krona_output\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.0.6+galaxy1",
+                        "type": "tool",
+                        "uuid": "12d35121-341e-46da-aa4c-c48d4318bf6d",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "metaphlan_output",
+                                "output_name": "output_file",
+                                "uuid": "6bcdc5a7-ddf9-4cdf-9729-b359d60490fb"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "report": {
+                                "id": 3,
+                                "output_name": "report_output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Krakentools: Convert kraken report file",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 559.9960852997306,
+                            "top": 459
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "88d274322340",
+                            "name": "krakentools_kreport2krona",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"intermediate_ranks\": false, \"report\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2+galaxy0",
+                        "type": "tool",
+                        "uuid": "5de62f93-4e3a-4ea6-92c6-c3afcc088bdc",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "krakentool_report",
+                                "output_name": "output",
+                                "uuid": "2cc442f8-40ac-4c58-a82e-f4018ab8a0a5"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "microbiome/taxonomic-profiling",
+                "path": "topics/microbiome/tutorials/taxonomic-profiling/workflows/main-workflow.ga",
+                "tags": [
+                    "microbiome"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "Taxonomic Profiling and Visualization of Metagenomic Data",
+                "topic_id": "microbiome",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-taxonomic-profiling/versions/main-workflow",
+                "tutorial_id": "taxonomic-profiling",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/taxonomic-profiling/workflows/main-workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/taxonomic-profiling/workflows/main-workflow.html",
+                "version": 1,
+                "wfid": "microbiome-taxonomic-profiling",
+                "wfname": "main-workflow",
+                "workflow": "main-workflow.ga",
+                "workflow_tools": [
+                    "__UNZIP_COLLECTION__",
+                    "interactive_tool_pavian",
+                    "interactive_tool_phinch",
+                    "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.7+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/kraken_biom/kraken_biom/1.2.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy1"
+                ],
+                "workflowhub_id": "1095"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/7871630"
+    },
     {
         "admin_install": {
             "install_repository_dependencies": true,
@@ -148607,25 +150096,25 @@
         ],
         "edam_operation": [
             "Visualisation",
-            "Primer removal",
             "Sequencing quality control",
-            "Sequence similarity search",
-            "Phylogenetic analysis",
-            "Taxonomic classification",
-            "Nucleic acid sequence analysis",
-            "Sequence composition calculation",
             "Phylogenetic inference",
-            "Validation",
-            "Sequence trimming",
-            "Conversion",
-            "Statistical calculation",
-            "Species frequency estimation",
             "Phylogenetic tree editing",
+            "Statistical calculation",
+            "Taxonomic classification",
+            "Validation",
+            "Sequence composition calculation",
             "Sequence comparison",
+            "Sequence similarity search",
             "Phylogenetic tree analysis",
+            "Sequence trimming",
+            "Phylogenetic analysis",
+            "Phylogenetic tree visualisation",
             "Sequence alignment analysis",
+            "Species frequency estimation",
+            "Conversion",
+            "Nucleic acid sequence analysis",
             "Read pre-processing",
-            "Phylogenetic tree visualisation"
+            "Primer removal"
         ],
         "edam_topic": [
             "Metatranscriptomics",
@@ -148635,7 +150124,8 @@
             "Sequence analysis"
         ],
         "exact_supported_servers": [
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
@@ -148643,8 +150133,7 @@
         "id": "microbiome/metatranscriptomics-short",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
+            "UseGalaxy.no"
         ],
         "js_requirements": {
             "mathjax": null,
@@ -148666,7 +150155,7 @@
             "Understand where metatranscriptomics fits in 'multi-omic' analysis of microbiomes",
             "Visualise a community structure"
         ],
-        "pageviews": 297,
+        "pageviews": 351,
         "pub_date": "2020-02-13",
         "questions": [
             "How to analyze metatranscriptomics data?\"",
@@ -148711,26 +150200,26 @@
         ],
         "short_id": "T00389",
         "short_tools": [
-            "humann_rename_table",
-            "Cut1",
+            "fastq_paired_end_interlacer",
+            "tp_find_and_replace",
+            "metaphlan",
+            "fastqc",
+            "humann",
             "graphlan_annotate",
+            "graphlan",
+            "humann_split_stratified_table",
+            "humann_renorm_table",
             "humann_regroup_table",
-            "metaphlan",
+            "humann_rename_table",
+            "cutadapt",
+            "combine_metaphlan2_humann2",
+            "multiqc",
+            "bg_sortmerna",
             "Grep1",
+            "Cut1",
             "export2graphlan",
-            "bg_sortmerna",
-            "humann_split_stratified_table",
-            "graphlan",
-            "fastq_paired_end_interlacer",
-            "combine_metaphlan2_humann2",
-            "taxonomy_krona_chart",
-            "tp_find_and_replace",
             "humann_unpack_pathways",
-            "cutadapt",
-            "humann",
-            "multiqc",
-            "fastqc",
-            "humann_renorm_table"
+            "taxonomy_krona_chart"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -148741,6 +150230,11 @@
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ],
             "inexact": [
@@ -148753,11 +150247,6 @@
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
                 }
             ]
         },
@@ -148814,8 +150303,8 @@
         "video": false,
         "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 100,
-        "visitors": 234,
+        "visit_duration": 86,
+        "visitors": 274,
         "workflows": [
             {
                 "creators": [
@@ -148932,7 +150421,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nT1A_forward\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nT1A_reverse\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Quality control Forward\"];\n  0 -->|output| 2;\n  025f2766-0802-461e-afbd-a716e6f81ba8[\"Output\\nFastQC on input dataset(s): RawData\"];\n  2 --> 025f2766-0802-461e-afbd-a716e6f81ba8;\n  style 025f2766-0802-461e-afbd-a716e6f81ba8 stroke:#2c3143,stroke-width:4px;\n  a54ee2fd-7bce-439a-9f1f-f9ec9bf00efd[\"Output\\nFastQC on input dataset(s): Webpage\"];\n  2 --> a54ee2fd-7bce-439a-9f1f-f9ec9bf00efd;\n  style a54ee2fd-7bce-439a-9f1f-f9ec9bf00efd stroke:#2c3143,stroke-width:4px;\n  3[\"Quality control Reverse\"];\n  1 -->|output| 3;\n  4[\"Cutadapt\"];\n  0 -->|output| 4;\n  1 -->|output| 4;\n  4bc7c8a4-b985-41dd-b67f-a3dfecd38a67[\"Output\\nCutadapt on input dataset(s): Read 1 Output\"];\n  4 --> 4bc7c8a4-b985-41dd-b67f-a3dfecd38a67;\n  style 4bc7c8a4-b985-41dd-b67f-a3dfecd38a67 stroke:#2c3143,stroke-width:4px;\n  36ec0bba-e49a-47e2-b916-afec9b35cc3e[\"Output\\nCutadapt on input dataset(s): Read 2 Output\"];\n  4 --> 36ec0bba-e49a-47e2-b916-afec9b35cc3e;\n  style 36ec0bba-e49a-47e2-b916-afec9b35cc3e stroke:#2c3143,stroke-width:4px;\n  5[\"MultiQC\"];\n  2 -->|text_file| 5;\n  3 -->|text_file| 5;\n  b9ca2123-0ee0-40a0-b2ec-cfc94fa35849[\"Output\\nMultiQC on input dataset(s): Stats\"];\n  5 --> b9ca2123-0ee0-40a0-b2ec-cfc94fa35849;\n  style b9ca2123-0ee0-40a0-b2ec-cfc94fa35849 stroke:#2c3143,stroke-width:4px;\n  e94ceb7a-0d6b-41c8-b79d-035b315e0a06[\"Output\\nMultiQC on input dataset(s): Webpage\"];\n  5 --> e94ceb7a-0d6b-41c8-b79d-035b315e0a06;\n  style e94ceb7a-0d6b-41c8-b79d-035b315e0a06 stroke:#2c3143,stroke-width:4px;\n  6[\"rRNA/rDNA selection\"];\n  4 -->|out1| 6;\n  4 -->|out2| 6;\n  7[\"FASTQ interlacer\"];\n  6 -->|unaligned_forward| 7;\n  6 -->|unaligned_reverse| 7;\n  b060eebc-cd14-486e-806e-aae983bdf52d[\"Output\\nFASTQ interlacer singles from input dataset(s)\"];\n  7 --> b060eebc-cd14-486e-806e-aae983bdf52d;\n  style b060eebc-cd14-486e-806e-aae983bdf52d stroke:#2c3143,stroke-width:4px;\n  70b738db-5451-4eaa-91c0-eb445be297fb[\"Output\\nFASTQ interlacer pairs from input dataset(s)\"];\n  7 --> 70b738db-5451-4eaa-91c0-eb445be297fb;\n  style 70b738db-5451-4eaa-91c0-eb445be297fb stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
+                "modified": "2024-10-02 12:08:09 +0000",
                 "name": "Workflow 1: Preprocessing",
                 "outputs": [
                     {
@@ -149496,7 +150985,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQC controlled forward reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nQC controlled reverse reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Taxonomic assignation\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  b3e3198d-394e-4aeb-ba6c-9e73bfe8d049[\"Output\\nMetaPhlAn on input dataset(s): SAM file\"];\n  2 --> b3e3198d-394e-4aeb-ba6c-9e73bfe8d049;\n  style b3e3198d-394e-4aeb-ba6c-9e73bfe8d049 stroke:#2c3143,stroke-width:4px;\n  a4ecdc94-d012-413f-a9cb-6f3e9ee70d5b[\"Output\\nMetaPhlAn on input dataset(s): Predicted taxon relative abundances\"];\n  2 --> a4ecdc94-d012-413f-a9cb-6f3e9ee70d5b;\n  style a4ecdc94-d012-413f-a9cb-6f3e9ee70d5b stroke:#2c3143,stroke-width:4px;\n  30a9e692-8d31-45bd-9246-81ddead3ba03[\"Output\\nMetaPhlAn on input dataset(s): Bowtie2 output\"];\n  2 --> 30a9e692-8d31-45bd-9246-81ddead3ba03;\n  style 30a9e692-8d31-45bd-9246-81ddead3ba03 stroke:#2c3143,stroke-width:4px;\n  2465a9ab-a28e-4c58-b647-b6792f77ddf2[\"Output\\nMetaPhlAn on input dataset(s): BIOM file\"];\n  2 --> 2465a9ab-a28e-4c58-b647-b6792f77ddf2;\n  style 2465a9ab-a28e-4c58-b647-b6792f77ddf2 stroke:#2c3143,stroke-width:4px;\n  3[\"Cut\"];\n  2 -->|output_file| 3;\n  4[\"Krona pie chart\"];\n  2 -->|krona_output_file| 4;\n  5[\"Export to GraPhlAn\"];\n  3 -->|out_file1| 5;\n  f578de2e-6edd-4ee0-9bc4-9371d6fd957f[\"Output\\nExport to GraPhlAn on input dataset(s): Annotation\"];\n  5 --> f578de2e-6edd-4ee0-9bc4-9371d6fd957f;\n  style f578de2e-6edd-4ee0-9bc4-9371d6fd957f stroke:#2c3143,stroke-width:4px;\n  4e9cfae0-ee7b-4347-84db-5a3e24688e50[\"Output\\nExport to GraPhlAn on input dataset(s): Tree\"];\n  5 --> 4e9cfae0-ee7b-4347-84db-5a3e24688e50;\n  style 4e9cfae0-ee7b-4347-84db-5a3e24688e50 stroke:#2c3143,stroke-width:4px;\n  6[\"Generation, personalization and annotation of tree\"];\n  5 -->|annotation| 6;\n  5 -->|tree| 6;\n  edf4ecaf-dddd-43a3-ba4a-d683671c1815[\"Output\\nGeneration, personalization and annotation of tree on input dataset(s): Tree in PhyloXML\"];\n  6 --> edf4ecaf-dddd-43a3-ba4a-d683671c1815;\n  style edf4ecaf-dddd-43a3-ba4a-d683671c1815 stroke:#2c3143,stroke-width:4px;\n  7[\"Visualisation GraPhlAn\"];\n  6 -->|output_tree| 7;\n  b304fe87-de7e-48d2-8774-9c52d2395fa4[\"Output\\nGraPhlAn on input dataset(s): PNG\"];\n  7 --> b304fe87-de7e-48d2-8774-9c52d2395fa4;\n  style b304fe87-de7e-48d2-8774-9c52d2395fa4 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
+                "modified": "2024-10-02 12:08:09 +0000",
                 "name": "Workflow 2: Community Profile",
                 "outputs": [
                     {
@@ -149979,7 +151468,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInterlaced non-rRNA reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nPredicted taxon relative abundances\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Cut\"];\n  1 -->|output| 2;\n  3[\"Metabolic assignation\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  65797303-6f12-4ae8-9511-1af40f52e71d[\"Output\\nHUMAnN on input dataset(s): Pathways and their abundance\"];\n  3 --> 65797303-6f12-4ae8-9511-1af40f52e71d;\n  style 65797303-6f12-4ae8-9511-1af40f52e71d stroke:#2c3143,stroke-width:4px;\n  5cae6935-448b-4af9-ad78-7b17490e4d4a[\"Output\\nHUMAnN on input dataset(s): Pathways and their coverage\"];\n  3 --> 5cae6935-448b-4af9-ad78-7b17490e4d4a;\n  style 5cae6935-448b-4af9-ad78-7b17490e4d4a stroke:#2c3143,stroke-width:4px;\n  60492d72-7b3c-45c9-b32b-b6374ab08228[\"Output\\nHUMAnN on input dataset(s): Log\"];\n  3 --> 60492d72-7b3c-45c9-b32b-b6374ab08228;\n  style 60492d72-7b3c-45c9-b32b-b6374ab08228 stroke:#2c3143,stroke-width:4px;\n  ba124b0f-cbd5-4b65-b87a-84cfa578a927[\"Output\\nHUMAnN on input dataset(s): Gene families and their abundance\"];\n  3 --> ba124b0f-cbd5-4b65-b87a-84cfa578a927;\n  style ba124b0f-cbd5-4b65-b87a-84cfa578a927 stroke:#2c3143,stroke-width:4px;\n  4[\"Renormalize\"];\n  3 -->|gene_families_tsv| 4;\n  5[\"Renormalize\"];\n  3 -->|pathabundance_tsv| 5;\n  6[\"Regroup\"];\n  3 -->|gene_families_tsv| 6;\n  7[\"Replace\"];\n  4 -->|output| 7;\n  8[\"Unpack pathway abundances\"];\n  4 -->|output| 8;\n  5 -->|output| 8;\n  9[\"Rename features\"];\n  6 -->|output| 9;\n  10[\"Split a HUMAnN table\"];\n  6 -->|output| 10;\n  1ff60d0a-4a64-44c0-8b6f-bbdfa8566a0c[\"Output\\nSplit a HUMAnN table on input dataset(s): Unstratified table\"];\n  10 --> 1ff60d0a-4a64-44c0-8b6f-bbdfa8566a0c;\n  style 1ff60d0a-4a64-44c0-8b6f-bbdfa8566a0c stroke:#2c3143,stroke-width:4px;\n  6a65ee93-3a2e-4a81-94ff-35917396bdfa[\"Output\\nSplit a HUMAnN table on input dataset(s): Stratified table\"];\n  10 --> 6a65ee93-3a2e-4a81-94ff-35917396bdfa;\n  style 6a65ee93-3a2e-4a81-94ff-35917396bdfa stroke:#2c3143,stroke-width:4px;\n  11[\"Combination of taxonomic and metabolic assignations for gene families\"];\n  7 -->|outfile| 11;\n  2 -->|out_file1| 11;\n  b34cf972-ec0c-4ecc-ab77-bd0e61d8a0e2[\"Output\\nCombine MetaPhlAn2 and HUMAnN2 outputs on input dataset(s): Gene family abundances related to genus/species abundances\"];\n  11 --> b34cf972-ec0c-4ecc-ab77-bd0e61d8a0e2;\n  style b34cf972-ec0c-4ecc-ab77-bd0e61d8a0e2 stroke:#2c3143,stroke-width:4px;\n  12[\"Select\"];\n  9 -->|output| 12;\n  13[\"Select\"];\n  9 -->|output| 13;\n  14[\"Select\"];\n  9 -->|output| 14;",
-                "modified": "2024-08-18 00:06:24 +0000",
+                "modified": "2024-10-02 12:08:09 +0000",
                 "name": "Workflow 3: Functional Information",
                 "outputs": [
                     {
@@ -150740,7 +152229,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPredicted taxon relative abundances\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGene Family abundance\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nPathway abundance\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Cut\"];\n  0 -->|output| 3;\n  4[\"Renormalize\"];\n  1 -->|output| 4;\n  5[\"Regroup\"];\n  1 -->|output| 5;\n  6[\"Renormalize\"];\n  2 -->|output| 6;\n  7[\"Replace\"];\n  4 -->|output| 7;\n  8[\"Rename features\"];\n  5 -->|output| 8;\n  9[\"Split a HUMAnN table\"];\n  5 -->|output| 9;\n  7aba96f3-1648-4126-8e58-ca10cbd2e46d[\"Output\\nSplit a HUMAnN table on input dataset(s): Stratified table\"];\n  9 --> 7aba96f3-1648-4126-8e58-ca10cbd2e46d;\n  style 7aba96f3-1648-4126-8e58-ca10cbd2e46d stroke:#2c3143,stroke-width:4px;\n  2c36dc33-5981-4b2c-b615-a1677002e007[\"Output\\nSplit a HUMAnN table on input dataset(s): Unstratified table\"];\n  9 --> 2c36dc33-5981-4b2c-b615-a1677002e007;\n  style 2c36dc33-5981-4b2c-b615-a1677002e007 stroke:#2c3143,stroke-width:4px;\n  10[\"Unpack pathway abundances\"];\n  4 -->|output| 10;\n  6 -->|output| 10;\n  11[\"Combination of taxonomic and metabolic assignations for gene families\"];\n  7 -->|outfile| 11;\n  3 -->|out_file1| 11;\n  46161015-b2db-4241-846e-27dd803b0fb3[\"Output\\nCombine MetaPhlAn2 and HUMAnN2 outputs on input dataset(s): Gene family abundances related to genus/species abundances\"];\n  11 --> 46161015-b2db-4241-846e-27dd803b0fb3;\n  style 46161015-b2db-4241-846e-27dd803b0fb3 stroke:#2c3143,stroke-width:4px;\n  12[\"Select\"];\n  8 -->|output| 12;\n  13[\"Select\"];\n  8 -->|output| 13;\n  14[\"Select\"];\n  8 -->|output| 14;",
-                "modified": "2024-08-18 00:06:24 +0000",
+                "modified": "2024-10-02 12:08:09 +0000",
                 "name": "Workflow 3: Functional Information (quick)",
                 "outputs": [
                     {
@@ -151251,136 +152740,289 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "checkm_lineage_wf",
+                    "name": "racon",
+                    "owner": "bgruening",
+                    "revisions": "aa39b19ca11e",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "racon",
+                    "owner": "bgruening",
+                    "revisions": "a199cd7ac344",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bandage",
                     "owner": "iuc",
-                    "revisions": "f0107b9f2dc3",
+                    "revisions": "067592b6b312",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bandage",
+                    "owner": "iuc",
+                    "revisions": "b2860df42e16",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gfa_to_fa",
+                    "owner": "iuc",
+                    "revisions": "49d6f8ef63b3",
+                    "tool_panel_section_label": "Convert Formats",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gfa_to_fa",
+                    "owner": "iuc",
+                    "revisions": "8e9d604e92f4",
+                    "tool_panel_section_label": "Convert Formats",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "miniasm",
+                    "owner": "iuc",
+                    "revisions": "8b6d0d85252b",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "miniasm",
+                    "owner": "iuc",
+                    "revisions": "8dee0218ac7d",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "minimap2",
+                    "owner": "iuc",
+                    "revisions": "3f4d6399997b",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "minimap2",
+                    "owner": "iuc",
+                    "revisions": "8c6cd2650d1f",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "nanoplot",
+                    "owner": "iuc",
+                    "revisions": "645159bcee2d",
+                    "tool_panel_section_label": "Nanopore",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "nanoplot",
+                    "owner": "iuc",
+                    "revisions": "edbb6c5028f5",
+                    "tool_panel_section_label": "Nanopore",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "plasflow",
+                    "owner": "iuc",
+                    "revisions": "bda6012394f7",
                     "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "megahit",
+                    "name": "unicycler",
                     "owner": "iuc",
-                    "revisions": "14ddfc8ffb93",
+                    "revisions": "0a3a602cd1e3",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "unicycler",
+                    "owner": "iuc",
+                    "revisions": "9e3e80cc4ad4",
                     "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "staramr",
+                    "owner": "nml",
+                    "revisions": "da787fc8b740",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "staramr",
+                    "owner": "nml",
+                    "revisions": "2fd4d4c9c5c2",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: checkm_lineage_wf\n  owner: iuc\n  revisions: f0107b9f2dc3\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: megahit\n  owner: iuc\n  revisions: 14ddfc8ffb93\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-binning/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "npechl",
-                "fpsom"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: racon\n  owner: bgruening\n  revisions: aa39b19ca11e\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: racon\n  owner: bgruening\n  revisions: a199cd7ac344\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: '067592b6b312'\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: b2860df42e16\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfa_to_fa\n  owner: iuc\n  revisions: 49d6f8ef63b3\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfa_to_fa\n  owner: iuc\n  revisions: 8e9d604e92f4\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: miniasm\n  owner: iuc\n  revisions: 8b6d0d85252b\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: miniasm\n  owner: iuc\n  revisions: 8dee0218ac7d\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: 3f4d6399997b\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: 8c6cd2650d1f\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: 645159bcee2d\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: edbb6c5028f5\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: plasflow\n  owner: iuc\n  revisions: bda6012394f7\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unicycler\n  owner: iuc\n  revisions: 0a3a602cd1e3\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unicycler\n  owner: iuc\n  revisions: 9e3e80cc4ad4\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: staramr\n  owner: nml\n  revisions: da787fc8b740\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: staramr\n  owner: nml\n  revisions: 2fd4d4c9c5c2\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.json",
         "contributors": [
             {
-                "email": "npechlv@gmail.com",
-                "id": "npechl",
-                "joined": "2023-05",
-                "name": "Nikolaos Pechlivanis",
-                "orcid": "0000-0003-2502-612X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/npechl/",
-                "twitter": "npechl",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/npechl.json"
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "nl",
+                "id": "willemdek11",
+                "joined": "2018-09",
+                "name": "Willem de Koning",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/willemdek11/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/willemdek11.json"
             },
             {
                 "affiliations": [
+                    "CINECA-Project",
                     "gallantries",
-                    "elixir-europe"
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
                 ],
-                "elixir_node": "gr",
-                "email": "fpsom@certh.gr",
-                "id": "fpsom",
-                "joined": "2019-03",
-                "linkedin": "fpsom",
-                "matrix": "fpsom:matrix.org",
-                "name": "Fotis E. Psomopoulos",
-                "orcid": "0000-0002-0222-4273",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
-                "twitter": "fopsom",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             }
         ],
-        "dir": "topics/microbiome/tutorials/metagenomics-binning",
+        "dir": "topics/microbiome/tutorials/plasmid-metagenomics-nanopore",
         "edam_ontology": [
+            "topic_3837",
+            "topic_3305",
             "topic_3174",
-            "topic_0196"
+            "topic_3301",
+            "topic_3324",
+            "topic_0080",
+            "topic_4013"
         ],
         "edam_operation": [
-            "Sequencing quality control",
-            "Validation",
+            "Scatter plot plotting",
             "Genome assembly",
-            "Sequence assembly validation",
-            "Statistical calculation",
-            "Sequence composition calculation"
+            "Box-Whisker plot plotting",
+            "De-novo assembly",
+            "Sequence analysis",
+            "Mapping assembly",
+            "Aggregation",
+            "Sequence assembly visualisation",
+            "Pairwise sequence alignment"
         ],
         "edam_topic": [
+            "Metagenomic sequencing",
+            "Public health and epidemiology",
             "Metagenomics",
-            "Sequence assembly"
+            "Microbiology",
+            "Infectious disease",
+            "Sequence analysis",
+            "Antimicrobial Resistance"
         ],
         "exact_supported_servers": [
-            "GalaxyTrakr",
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr"
+            "UseGalaxy.eu"
         ],
-        "extra": {
-            "zenodo_link_results": "https://zenodo.org/record/7845138"
-        },
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "microbiome/metagenomics-binning",
-        "inexact_supported_servers": [],
+        "id": "microbiome/plasmid-metagenomics-nanopore",
+        "inexact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Metagenomics binning is a computational approach to grouping together DNA sequences from a mixed microbial sample into metagenome-assembled genomes (MAGs)",
-            "The metagenomics binning workflow involves several steps, including preprocessing of raw sequencing data, assembly of sequencing reads into contigs, binning of contigs into MAGs, quality assessment of MAGs, and annotation of functional genes and metabolic pathways in MAGs",
-            "The quality and completeness of MAGs can be evaluated using standard metrics, such as completeness, contamination, and genome size",
-            "Metagenomics binning can be used to gain insights into the composition, diversity, and functional potential of microbial communities, and can be applied to a range of research areas, such as human health, environmental microbiology, and biotechnology"
+            "Minimap2, Miniasm, and Racon can be used for quickly assembling Nanopore data",
+            "Unicycler can be used to optimize settings of assembly tools",
+            "Nanopore sequencing is useful for reconstruction of genomes",
+            "Antimicrobial resistance genes are detectable after fast assembly",
+            "The CARD database is a useful resource describing antibiotic resistance genes"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-14",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Describe what metagenomics binning is",
-            "Describe common problems in metagenomics binning",
-            "What software tools are available for metagenomics binning",
-            "Binning of contigs into metagenome-assembled genomes (MAGs) using MetaBAT 2 software",
-            "Evaluation of MAG quality and completeness using CheckM software"
+            "Perform Quality control on your reads",
+            "Assemble a genome with Minimap2/Miniasm/Racon",
+            "Determine the structure of the genome(s)",
+            "Scan for antimicrobial resistance genes with Staramr"
         ],
-        "pageviews": 1997,
-        "pub_date": "2023-12-05",
+        "pageviews": 1950,
+        "pub_date": "2019-06-25",
         "questions": [
-            "What is metagenomic binning refers to?",
-            "Which tools should be used for metagenomic binning?",
-            "How to assess the quality of metagenomic data binning?"
+            "How do I assemble a genome with Nanopore data?",
+            "How do I get more information about the structure of the genomes?",
+            "How do I get more information about the antimicrobial resistance genes?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "bebatut"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "45M",
+                "speakers": [
+                    "willemdek11"
+                ],
+                "youtube_id": "ECIl8ZU1Wko"
+            }
         ],
         "redirect_from": [
-            "/topics/metagenomics/tutorials/metagenomics-binning/tutorial",
-            "/short/microbiome/metagenomics-binning",
-            "/short/T00377",
-            "/short/T00387"
+            "/topics/metagenomics/tutorials/plasmid-metagenomics-nanopore/tutorial",
+            "/short/microbiome/plasmid-metagenomics-nanopore",
+            "/short/T00209",
+            "/short/T00394"
         ],
-        "short_id": "T00387",
+        "short_id": "T00394",
         "short_tools": [
-            "megahit",
-            "checkm_lineage_wf"
+            "unicycler",
+            "minimap2",
+            "bandage_image",
+            "PlasFlow",
+            "racon",
+            "nanoplot",
+            "gfa_to_fa",
+            "staramr_search",
+            "miniasm"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "metagenomics",
+        "subtopic": "metabarcoding",
         "supported_servers": {
             "exact": [
                 {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
                 {
@@ -151389,29 +153031,50 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
-            ],
-            "inexact": []
+            ]
         },
         "symlink": null,
         "tags": [
-            "binning",
-            "metagenomics",
+            "nanopore",
+            "plasmids",
+            "assembly",
+            "amr",
             "microgalaxy"
         ],
-        "time_estimation": "2H",
-        "title": "Binning of metagenomic sequencing data",
+        "time_estimation": "3h",
+        "title": "Antibiotic resistance detection",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/checkm_lineage_wf/checkm_lineage_wf/1.2.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.3.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17",
+            "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/plasflow/PlasFlow/1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.7.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0",
+            "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.5.1",
+            "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.7.1+galaxy2"
         ],
         "topic_name": "microbiome",
         "topic_name_human": "Microbiome",
@@ -151421,240 +153084,298 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "metagenomics-binning",
+        "tutorial_name": "plasmid-metagenomics-nanopore",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-binning/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-binning/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.json"
         },
-        "version": 3,
+        "version": 4,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 89,
-        "visitors": 1648,
-        "zenodo_link": "https://zenodo.org/record/7818827"
+        "visit_duration": 242,
+        "visitors": 1281,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Antibiotic resistance detection",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nPlasmids\"]\n  1[label=\"NanoPlot\"]\n  0 -> 1 [label=\"output\"]\n  10[label=\"NanoPlot\"]\n  9 -> 10 [label=\"out_fa\"]\n  11[label=\"Map with minimap2\"]\n  0 -> 11 [label=\"output\"]\n  9 -> 11 [label=\"out_fa\"]\n  12[label=\"Racon\"]\n  9 -> 12 [label=\"out_fa\"]\n  11 -> 12 [label=\"alignment_output\"]\n  0 -> 12 [label=\"output\"]\n  2[label=\"Map with minimap2\"]\n  0 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Create assemblies with Unicycler\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"miniasm\"]\n  2 -> 4 [label=\"alignment_output\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Bandage Image\"]\n  3 -> 5 [label=\"assembly_graph\"]\n  6[label=\"PlasFlow\"]\n  3 -> 6 [label=\"assembly\"]\n  7[label=\"staramr\"]\n  3 -> 7 [label=\"assembly\"]\n  8[label=\"Bandage Image\"]\n  4 -> 8 [label=\"gfa\"]\n  9[label=\"GFA to FASTA\"]\n  4 -> 9 [label=\"gfa\"]\n}",
+                "history": [
+                    {
+                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
+                        "message": "Rename metagenomics topic to microbiome",
+                        "num": 1,
+                        "short_hash": "0e0a2f2cc",
+                        "unix": "1704901629"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "Plasmids",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 173,
+                            "top": 696
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "348dcd93-2d40-4bdd-90f4-b321a1bd901d",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nPlasmids\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"NanoPlot\"];\n  0 -->|output| 1;\n  10[\"NanoPlot\"];\n  9 -->|out_fa| 10;\n  11[\"Map with minimap2\"];\n  0 -->|output| 11;\n  9 -->|out_fa| 11;\n  12[\"Racon\"];\n  9 -->|out_fa| 12;\n  11 -->|alignment_output| 12;\n  0 -->|output| 12;\n  2[\"Map with minimap2\"];\n  0 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Create assemblies with Unicycler\"];\n  0 -->|output| 3;\n  4[\"miniasm\"];\n  2 -->|alignment_output| 4;\n  0 -->|output| 4;\n  5[\"Bandage Image\"];\n  3 -->|assembly_graph| 5;\n  6[\"PlasFlow\"];\n  3 -->|assembly| 6;\n  7[\"staramr\"];\n  3 -->|assembly| 7;\n  8[\"Bandage Image\"];\n  4 -->|gfa| 8;\n  9[\"GFA to FASTA\"];\n  4 -->|gfa| 9;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Copy Of GTN Training - Antibiotic Resistance Detection",
+                "outputs": [],
+                "parent_id": "microbiome/plasmid-metagenomics-nanopore",
+                "path": "topics/microbiome/tutorials/plasmid-metagenomics-nanopore/workflows/Workflow-plasmid-metagenomics-nanopore.ga",
+                "tags": [
+                    "microbiome"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Copy Of GTN Training - Antibiotic Resistance Detection",
+                "topic_id": "microbiome",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-plasmid-metagenomics-nanopore/versions/workflow-plasmid-metagenomics-nanopore",
+                "tutorial_id": "plasmid-metagenomics-nanopore",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/workflows/Workflow-plasmid-metagenomics-nanopore.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/workflows/Workflow-plasmid-metagenomics-nanopore.html",
+                "version": 1,
+                "wfid": "microbiome-plasmid-metagenomics-nanopore",
+                "wfname": "workflow-plasmid-metagenomics-nanopore",
+                "workflow": "Workflow-plasmid-metagenomics-nanopore.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.3.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/plasflow/PlasFlow/1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.7.0",
+                    "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.5.1"
+                ],
+                "workflowhub_id": "1107"
+            }
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.3247504"
     },
     {
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "qiime2"
-            ]
-        },
-        "contributors": [
-            {
-                "avatar": "https://avatars.githubusercontent.com/u/18176583?s=200&amp;v=4",
-                "id": "qiime2",
-                "name": "QIIME2",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/qiime2/",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/qiime2.json"
-            }
-        ],
-        "dir": "topics/microbiome/tutorials/qiime2-moving-pictures",
-        "edam_ontology": [
-            "topic_3697",
-            "topic_0637",
-            "topic_0080",
-            "topic_4038"
-        ],
-        "edam_operation": [],
-        "edam_topic": [
-            "Microbial ecology",
-            "Taxonomy",
-            "Sequence analysis"
-        ],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": "external",
-        "hands_on_url": "https://docs.qiime2.org/2024.2/tutorials/moving-pictures-usage",
-        "id": "microbiome/qiime2-moving-pictures",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-03-14",
-        "pageviews": 171,
-        "pub_date": "2024-03-14",
-        "short_id": "T00427",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "metabarcoding",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
+            "tools": [
                 {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
+                    "name": "taxonomy_krona_chart",
+                    "owner": "crs4",
+                    "revisions": "1334cb4c6b68",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "e7b2202befea",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
+                    "name": "datamash_reverse",
+                    "owner": "iuc",
+                    "revisions": "0f1724dd59d2",
+                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastp",
+                    "owner": "iuc",
+                    "revisions": "dbf9c561ef29",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "kraken2",
+                    "owner": "iuc",
+                    "revisions": "328c607150ff",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "5e33b465d8d5",
+                    "tool_panel_section_label": "Quality Control",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "porechop",
+                    "owner": "iuc",
+                    "revisions": "93d623d9979c",
+                    "tool_panel_section_label": "Nanopore",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "symlink": null,
-        "tags": [
-            "metagenomics",
-            "taxonomic profiling",
-            "diversity",
-            "microgalaxy"
-        ],
-        "time_estimation": "10H",
-        "title": "QIIME 2 Moving Pictures",
-        "tools": [],
-        "topic_name": "microbiome",
-        "topic_name_human": "Microbiome",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "qiime2-moving-pictures",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.json"
-        },
-        "version": 1,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 229,
-        "visitors": 112
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "qiime2"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: taxonomy_krona_chart\n  owner: crs4\n  revisions: 1334cb4c6b68\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_reverse\n  owner: iuc\n  revisions: 0f1724dd59d2\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: dbf9c561ef29\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: 328c607150ff\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 5e33b465d8d5\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: porechop\n  owner: iuc\n  revisions: 93d623d9979c\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.json",
         "contributors": [
             {
-                "avatar": "https://avatars.githubusercontent.com/u/18176583?s=200&amp;v=4",
-                "id": "qiime2",
-                "name": "QIIME2",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/qiime2/",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/qiime2.json"
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "gallardoalba",
+                "joined": "2020-11",
+                "name": "Crist\u00f3bal Gallardo",
+                "orcid": "0000-0002-5752-2155",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
             }
         ],
-        "dir": "topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention",
+        "dir": "topics/microbiome/tutorials/nanopore-16S-metagenomics",
         "edam_ontology": [
             "topic_3697",
             "topic_0637",
             "topic_0080",
             "topic_4038"
         ],
-        "edam_operation": [],
+        "edam_operation": [
+            "Taxonomic classification",
+            "Statistical calculation",
+            "Visualisation",
+            "Validation",
+            "Sequencing quality control",
+            "Sequence composition calculation",
+            "Sequence contamination filtering"
+        ],
         "edam_topic": [
             "Microbial ecology",
             "Taxonomy",
             "Sequence analysis"
         ],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": "external",
-        "hands_on_url": "https://docs.qiime2.org/jupyterbooks/cancer-microbiome-intervention-tutorial/index.html#",
-        "id": "microbiome/qiime2-cancer-microbiome-intervention",
+        "hands_on": true,
+        "id": "microbiome/nanopore-16S-metagenomics",
         "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
+            "GalaxyTrakr",
+            "UseGalaxy.be",
+            "UseGalaxy.cz"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
+        "key_points": [
+            "We learned to use MinION Nanopore data for analyzing the health status of the soil",
+            "We preprocessed Nanopore sequences in order to improve their quality"
+        ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-14",
-        "pageviews": 220,
-        "pub_date": "2024-02-12",
-        "short_id": "T00412",
-        "short_tools": [],
+        "mod_date": "2024-07-31",
+        "objectives": [
+            "Use Nanopore data for studying soil metagenomics",
+            "Analyze and preprocess Nanopore reads",
+            "Use Kraken2 to assign a taxonomic labels"
+        ],
+        "pageviews": 3844,
+        "pub_date": "2020-11-24",
+        "questions": [
+            "How can we analyse the health status of the soil?",
+            "How do plants modify the composition of microbial communities?"
+        ],
+        "redirect_from": [
+            "/topics/metagenomics/tutorials/nanopore-16S-metagenomics/tutorial",
+            "/short/microbiome/nanopore-16S-metagenomics",
+            "/short/T00207",
+            "/short/T00392"
+        ],
+        "short_id": "T00392",
+        "short_tools": [
+            "porechop",
+            "fastp",
+            "tp_replace_in_line",
+            "taxonomy_krona_chart",
+            "multiqc",
+            "kraken2",
+            "datamash_reverse",
+            "fastqc",
+            "Remove beginning1"
+        ],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "metabarcoding",
         "supported_servers": {
-            "exact": [],
-            "inexact": [
+            "exact": [
                 {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
                 {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 },
                 {
-                    "human": "Galaxy Australia",
-                    "id": "au",
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
                 },
                 {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
                 }
             ]
         },
@@ -151662,13 +153383,23 @@
         "tags": [
             "metabarcoding",
             "16S",
-            "taxonomic profiling",
-            "diversity",
-            "microgalaxy"
+            "nanopore",
+            "microgalaxy",
+            "plants"
+        ],
+        "time_estimation": "2H",
+        "title": "16S Microbial analysis with Nanopore data",
+        "tools": [
+            "Remove beginning1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.0.8_beta+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3"
         ],
-        "time_estimation": "10H",
-        "title": "QIIME 2 Cancer Microbiome Intervention",
-        "tools": [],
         "topic_name": "microbiome",
         "topic_name_human": "Microbiome",
         "tours": false,
@@ -151677,19 +153408,104 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "qiime2-cancer-microbiome-intervention",
+        "tutorial_name": "nanopore-16S-metagenomics",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.json"
         },
-        "version": 3,
+        "version": 5,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 163,
-        "visitors": 119
+        "visitors": 2758,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "16S rRNA analysis with Nanopore reads",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  1[label=\"FastQC\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Porechop\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"MultiQC\"]\n  1 -> 3 [label=\"text_file\"]\n  4[label=\"fastp\"]\n  2 -> 4 [label=\"outfile\"]\n  5[label=\"FastQC\"]\n  4 -> 5 [label=\"out1\"]\n  6[label=\"Kraken2\"]\n  4 -> 6 [label=\"out1\"]\n  7[label=\"MultiQC\"]\n  5 -> 7 [label=\"text_file\"]\n  8[label=\"Reverse\"]\n  6 -> 8 [label=\"report_output\"]\n  9[label=\"Replace Text\"]\n  8 -> 9 [label=\"out_file\"]\n  10[label=\"Remove beginning\"]\n  9 -> 10 [label=\"outfile\"]\n  11[label=\"Krona pie chart\"]\n  10 -> 11 [label=\"out_file1\"]\n}",
+                "history": [
+                    {
+                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
+                        "message": "Rename metagenomics topic to microbiome",
+                        "num": 1,
+                        "short_hash": "0e0a2f2cc",
+                        "unix": "1704901629"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Input Dataset Collection"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 10
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "18fc8b44-c752-41a0-a17c-e03797a5fab1",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"FastQC\"];\n  0 -->|output| 1;\n  2[\"Porechop\"];\n  0 -->|output| 2;\n  3[\"MultiQC\"];\n  1 -->|text_file| 3;\n  4[\"fastp\"];\n  2 -->|outfile| 4;\n  5[\"FastQC\"];\n  4 -->|out1| 5;\n  6[\"Kraken2\"];\n  4 -->|out1| 6;\n  7[\"MultiQC\"];\n  5 -->|text_file| 7;\n  8[\"Reverse\"];\n  6 -->|report_output| 8;\n  9[\"Replace Text\"];\n  8 -->|out_file| 9;\n  10[\"Remove beginning\"];\n  9 -->|outfile| 10;\n  11[\"Krona pie chart\"];\n  10 -->|out_file1| 11;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Training: 16S rRNA Analysis with Nanopore Sequencing Reads",
+                "outputs": [],
+                "parent_id": "microbiome/nanopore-16S-metagenomics",
+                "path": "topics/microbiome/tutorials/nanopore-16S-metagenomics/workflows/main_workflow.ga",
+                "tags": [
+                    "microbiome"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Training: 16S rRNA Analysis with Nanopore Sequencing Reads",
+                "topic_id": "microbiome",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-nanopore-16S-metagenomics/versions/main-workflow",
+                "tutorial_id": "nanopore-16S-metagenomics",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/nanopore-16S-metagenomics/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/nanopore-16S-metagenomics/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "microbiome-nanopore-16S-metagenomics",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "Remove beginning1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.0.8_beta+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3"
+                ],
+                "workflowhub_id": "1064"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/4274812"
     },
     {
         "admin_install": {
@@ -151698,229 +153514,194 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "xy_plot",
-                    "owner": "devteam",
-                    "revisions": "ecb437f1d298",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_chimera_vsearch",
-                    "owner": "iuc",
-                    "revisions": "12e856482d26",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_classify_otu",
-                    "owner": "iuc",
-                    "revisions": "ff1bc0299372",
-                    "tool_panel_section_label": "Mothur",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "86755160afbf",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_classify_seqs",
-                    "owner": "iuc",
-                    "revisions": "09bf9e496c64",
-                    "tool_panel_section_label": "Mothur",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "86755160afbf",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_cluster",
-                    "owner": "iuc",
-                    "revisions": "6366f4483b35",
-                    "tool_panel_section_label": "Mothur",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_cluster_split",
-                    "owner": "iuc",
-                    "revisions": "19f45bdbffd9",
-                    "tool_panel_section_label": "Mothur",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "86755160afbf",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_count_groups",
-                    "owner": "iuc",
-                    "revisions": "dc3826bfc1ed",
-                    "tool_panel_section_label": "Mothur",
+                    "name": "column_maker",
+                    "owner": "devteam",
+                    "revisions": "6595517c2dd8",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_count_seqs",
+                    "name": "collection_element_identifiers",
                     "owner": "iuc",
-                    "revisions": "ffee46220ddd",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "d3c07d270a50",
+                    "tool_panel_section_label": "Collection Operations",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_dist_seqs",
+                    "name": "dada2_assigntaxonomyaddspecies",
                     "owner": "iuc",
-                    "revisions": "4d76fba83f24",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "7c2100246a2f",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_dist_shared",
+                    "name": "dada2_assigntaxonomyaddspecies",
                     "owner": "iuc",
-                    "revisions": "418100660ba3",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "65db807336bc",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_filter_seqs",
+                    "name": "dada2_dada",
                     "owner": "iuc",
-                    "revisions": "3524ca06478e",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "96336c6a2bb7",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_heatmap_sim",
+                    "name": "dada2_dada",
                     "owner": "iuc",
-                    "revisions": "7f5707dd6073",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "00f5005840fa",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_make_shared",
+                    "name": "dada2_filterandtrim",
                     "owner": "iuc",
-                    "revisions": "d0967ae326be",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "addaf9d22850",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_pre_cluster",
+                    "name": "dada2_filterandtrim",
                     "owner": "iuc",
-                    "revisions": "6532c3424bfe",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "e8fba04706d3",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_rarefaction_single",
+                    "name": "dada2_learnerrors",
                     "owner": "iuc",
-                    "revisions": "47264675a4ea",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "75403243703a",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_remove_groups",
+                    "name": "dada2_learnerrors",
                     "owner": "iuc",
-                    "revisions": "498dc0671d9e",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "5fe3edf19b9c",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_remove_lineage",
+                    "name": "dada2_makesequencetable",
                     "owner": "iuc",
-                    "revisions": "947faa8b3205",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "43c99742158b",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_remove_seqs",
+                    "name": "dada2_makesequencetable",
                     "owner": "iuc",
-                    "revisions": "d38f2ac5db71",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "75c8945b0da2",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_screen_seqs",
+                    "name": "dada2_mergepairs",
                     "owner": "iuc",
-                    "revisions": "63b74bfc8052",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "5c865a382933",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_sub_sample",
+                    "name": "dada2_mergepairs",
                     "owner": "iuc",
-                    "revisions": "67cb43432196",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "35176674168c",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_summary_seqs",
+                    "name": "dada2_plotqualityprofile",
                     "owner": "iuc",
-                    "revisions": "600c14c6dcc5",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "7b8cb2b02978",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_summary_single",
+                    "name": "dada2_plotqualityprofile",
                     "owner": "iuc",
-                    "revisions": "2344ed181ae6",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "cae017b76acb",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_tree_shared",
+                    "name": "dada2_removebimeradenovo",
                     "owner": "iuc",
-                    "revisions": "8bca555fbcaf",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "7136e9ab70db",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_unique_seqs",
+                    "name": "dada2_removebimeradenovo",
                     "owner": "iuc",
-                    "revisions": "a033f325ad8d",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "073608a50ac3",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_venn",
+                    "name": "dada2_seqcounts",
                     "owner": "iuc",
-                    "revisions": "4db54b1c1d83",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "19299bb1c6af",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "newick_utils",
+                    "name": "dada2_seqcounts",
                     "owner": "iuc",
-                    "revisions": "b4163d2f64ab",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "revisions": "a7817705348e",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "830961c48e42",
-                    "tool_panel_section_label": "Collection Operations",
+                    "name": "phyloseq_from_dada2",
+                    "owner": "iuc",
+                    "revisions": "87064cb77a52",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: xy_plot\n  owner: devteam\n  revisions: ecb437f1d298\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_chimera_vsearch\n  owner: iuc\n  revisions: 12e856482d26\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_classify_otu\n  owner: iuc\n  revisions: ff1bc0299372\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_classify_seqs\n  owner: iuc\n  revisions: '09bf9e496c64'\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_cluster\n  owner: iuc\n  revisions: 6366f4483b35\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_cluster_split\n  owner: iuc\n  revisions: 19f45bdbffd9\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_count_groups\n  owner: iuc\n  revisions: dc3826bfc1ed\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_count_seqs\n  owner: iuc\n  revisions: ffee46220ddd\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_dist_seqs\n  owner: iuc\n  revisions: 4d76fba83f24\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_dist_shared\n  owner: iuc\n  revisions: 418100660ba3\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_filter_seqs\n  owner: iuc\n  revisions: 3524ca06478e\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_heatmap_sim\n  owner: iuc\n  revisions: 7f5707dd6073\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_make_shared\n  owner: iuc\n  revisions: d0967ae326be\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_pre_cluster\n  owner: iuc\n  revisions: 6532c3424bfe\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_rarefaction_single\n  owner: iuc\n  revisions: 47264675a4ea\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_remove_groups\n  owner: iuc\n  revisions: 498dc0671d9e\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_remove_lineage\n  owner: iuc\n  revisions: 947faa8b3205\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_remove_seqs\n  owner: iuc\n  revisions: d38f2ac5db71\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_screen_seqs\n  owner: iuc\n  revisions: 63b74bfc8052\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_sub_sample\n  owner: iuc\n  revisions: 67cb43432196\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_summary_seqs\n  owner: iuc\n  revisions: 600c14c6dcc5\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_summary_single\n  owner: iuc\n  revisions: 2344ed181ae6\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_tree_shared\n  owner: iuc\n  revisions: 8bca555fbcaf\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_unique_seqs\n  owner: iuc\n  revisions: a033f325ad8d\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_venn\n  owner: iuc\n  revisions: 4db54b1c1d83\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: newick_utils\n  owner: iuc\n  revisions: b4163d2f64ab\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 6595517c2dd8\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_element_identifiers\n  owner: iuc\n  revisions: d3c07d270a50\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_assigntaxonomyaddspecies\n  owner: iuc\n  revisions: 7c2100246a2f\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_assigntaxonomyaddspecies\n  owner: iuc\n  revisions: 65db807336bc\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_dada\n  owner: iuc\n  revisions: 96336c6a2bb7\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_dada\n  owner: iuc\n  revisions: 00f5005840fa\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_filterandtrim\n  owner: iuc\n  revisions: addaf9d22850\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_filterandtrim\n  owner: iuc\n  revisions: e8fba04706d3\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_learnerrors\n  owner: iuc\n  revisions: 75403243703a\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_learnerrors\n  owner: iuc\n  revisions: 5fe3edf19b9c\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_makesequencetable\n  owner: iuc\n  revisions: 43c99742158b\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_makesequencetable\n  owner: iuc\n  revisions: 75c8945b0da2\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_mergepairs\n  owner: iuc\n  revisions: 5c865a382933\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_mergepairs\n  owner: iuc\n  revisions: 35176674168c\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_plotqualityprofile\n  owner: iuc\n  revisions: 7b8cb2b02978\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_plotqualityprofile\n  owner: iuc\n  revisions: cae017b76acb\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_removebimeradenovo\n  owner: iuc\n  revisions: 7136e9ab70db\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_removebimeradenovo\n  owner: iuc\n  revisions: '073608a50ac3'\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_seqcounts\n  owner: iuc\n  revisions: 19299bb1c6af\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dada2_seqcounts\n  owner: iuc\n  revisions: a7817705348e\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: phyloseq_from_dada2\n  owner: iuc\n  revisions: 87064cb77a52\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/dada-16S/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "bebatut"
+            ],
+            "editing": [
+                "bernt-matthias",
+                "clsiguret"
+            ]
+        },
         "contributors": [
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
@@ -151948,15 +153729,31 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             },
             {
-                "id": "tnabtaf",
+                "elixir_node": "de",
+                "id": "bernt-matthias",
                 "joined": "2017-09",
-                "name": "Dave Clements",
-                "orcid": "0000-0002-9970-6657",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
+                "name": "Matthias Bernt",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bernt-matthias/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bernt-matthias.json"
+            },
+            {
+                "affiliations": [
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "elixir_node": "fr",
+                "email": "clea.siguret@gmail.com",
+                "id": "clsiguret",
+                "joined": "2024-04",
+                "linkedin": "cl\u00e9a-siguret-58423b107",
+                "matrix": "clsiguret:matrix.org",
+                "name": "Clea Siguret",
+                "orcid": "0009-0005-6140-0379",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/clsiguret/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/clsiguret.json"
             }
         ],
-        "dir": "topics/microbiome/tutorials/mothur-miseq-sop-short",
+        "dir": "topics/microbiome/tutorials/dada-16S",
         "edam_ontology": [
             "topic_3697",
             "topic_0637",
@@ -151964,16 +153761,11 @@
             "topic_4038"
         ],
         "edam_operation": [
-            "Visualisation",
-            "Sequencing quality control",
-            "Phylogenetic analysis",
-            "Taxonomic classification",
-            "Phylogenetic tree analysis",
-            "Phylogenetic tree generation",
-            "Sequence read processing",
+            "Variant calling",
             "DNA barcoding",
-            "Sequence clustering",
-            "Phylogenetic tree reconstruction"
+            "Visualisation",
+            "Analysis",
+            "Deposition"
         ],
         "edam_topic": [
             "Microbial ecology",
@@ -151981,107 +153773,79 @@
             "Sequence analysis"
         ],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "microbiome/mothur-miseq-sop-short",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.fr"
-        ],
+        "id": "microbiome/dada-16S",
+        "inexact_supported_servers": [],
         "js_requirements": {
-            "mathjax": null,
+            "mathjax": 14594,
             "mermaid": false
         },
         "key_points": [
-            "16S rRNA gene sequencing analysis results depend on the many algorithms used and their settings",
-            "Quality control and cleaning of your data is a crucial step in order to obtain optimal results",
-            "Adding a mock community to serve as a control sample can help you asses the error rate of your experimental setup",
-            "We can explore alpha and beta diversities using Krona and Phinch for dynamic visualizations"
+            "DADA2 allows for the generation of precise ASV tables, providing higher resolution and more accurate representation of microbial communities compared to traditional OTU-based methods.",
+            "Key steps such as quality filtering, error rate learning, and chimera removal are essential in the DADA2 pipeline to ensure the reliability and accuracy of the resulting ASV data.",
+            "Tools like phyloseq can be effectively used to explore and visualize ASV tables, facilitating deeper ecological and evolutionary insights into microbial diversity and community structure."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-09-26",
         "objectives": [
-            "Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy",
-            "Using a mock community to assess the error rate of your sequencing experiment",
-            "Visualize sample diversity using Krona and Phinch"
+            "Identify the key steps in the DADA2 workflow for generating an ASV table from 16S rRNA gene sequencing data",
+            "Explain the importance of quality filtering, error rate learning, and chimera removal in ensuring accurate microbial community analysis",
+            "Execute the DADA2 pipeline to process raw 16S sequencing data and produce a high-resolution ASV table",
+            "Compare the advantages of ASV-based methods over traditional OTU-based approaches in terms of accuracy and resolution",
+            "Assess the effectiveness of using phyloseq for exploring and visualizing ASV data to gain ecological and evolutionary insights"
         ],
-        "pageviews": 3211,
-        "priority": 1000,
-        "pub_date": "2019-05-13",
+        "pageviews": 1460,
+        "pub_date": "2024-06-05",
         "questions": [
-            "What is the effect of normal variation in the gut microbiome on host health?"
+            "What are the primary steps involved in generating an ASV table using DADA2 from 16S rRNA gene sequencing data?",
+            "How does DADA2 improve the accuracy of microbial community analysis compared to traditional OTU-based methods?",
+            "What is the importance of quality filtering in the DADA2 workflow, and how does it impact downstream analyses?",
+            "How does the error rate learning process contribute to the identification of true biological sequences in DADA2?",
+            "What role does chimera removal play in the DADA2 pipeline, and why is it crucial for obtaining reliable ASV data?",
+            "How can phyloseq be used to explore and visualize the ASV table generated by DADA2, and what types of ecological insights can it provide?"
         ],
         "recordings": [
             {
+                "bot-timestamp": 1726830881,
                 "captioners": [
-                    "shiltemann"
-                ],
-                "date": "2023-05-19",
-                "galaxy_version": "23.01",
-                "length": "1H37M",
-                "speakers": [
-                    "shiltemann"
-                ],
-                "youtube_id": "CGSBeCW3rpA"
-            },
-            {
-                "archive-id": "smorgasbord2023",
-                "captioners": [
-                    "shiltemann"
+                    "bernt-matthias"
                 ],
-                "date": "2021-02-15",
-                "description": "This recording was created as part of the Sm\u00f6rg\u00e5sbord 2023 event.",
-                "galaxy_version": "21.01",
-                "length": "1H40M",
+                "date": "2024-09-20",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "1H36M",
                 "speakers": [
-                    "shiltemann"
+                    "bernt-matthias"
                 ],
-                "type": "Lecture & Tutorial",
-                "youtube_id": "mto4Nl-q7Kk"
+                "youtube_id": "ISocxcJZEjw"
             }
         ],
-        "redirect_from": [
-            "/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial",
-            "/short/microbiome/mothur-miseq-sop-short",
-            "/short/T00206",
-            "/short/T00391"
-        ],
-        "short_id": "T00391",
+        "short_id": "T00441",
         "short_tools": [
-            "mothur_remove_lineage",
-            "mothur_cluster_split",
-            "mothur_count_seqs",
-            "mothur_dist_shared",
-            "mothur_sub_sample",
-            "mothur_classify_otu",
-            "newick_display",
-            "mothur_chimera_vsearch",
-            "mothur_venn",
-            "mothur_pre_cluster",
-            "XY_Plot_1",
-            "mothur_rarefaction_single",
-            "collapse_dataset",
-            "mothur_screen_seqs",
-            "mothur_unique_seqs",
-            "mothur_count_groups",
-            "mothur_heatmap_sim",
-            "mothur_summary_seqs",
-            "mothur_tree_shared",
-            "mothur_remove_groups",
-            "mothur_make_shared",
-            "mothur_summary_single",
-            "mothur_cluster",
-            "mothur_classify_seqs",
-            "mothur_dist_seqs",
-            "mothur_filter_seqs",
-            "mothur_remove_seqs"
+            "tp_head_tool",
+            "collection_element_identifiers",
+            "__UNZIP_COLLECTION__",
+            "interactive_tool_phyloseq",
+            "dada2_mergePairs",
+            "dada2_removeBimeraDenovo",
+            "dada2_assignTaxonomyAddspecies",
+            "Grouping1",
+            "dada2_plotQualityProfile",
+            "dada2_filterAndTrim",
+            "cat1",
+            "tp_replace_in_column",
+            "dada2_seqCounts",
+            "dada2_makeSequenceTable",
+            "tp_replace_in_line",
+            "Add_a_column1",
+            "dada2_dada",
+            "__SORTLIST__",
+            "dada2_learnErrors",
+            "phyloseq_from_dada2"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -152092,35 +153856,9 @@
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
                 }
             ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                }
-            ]
+            "inexact": []
         },
         "symlink": null,
         "tags": [
@@ -152128,36 +153866,39 @@
             "16S",
             "microgalaxy"
         ],
-        "time_estimation": "2h",
-        "title": "16S Microbial Analysis with mothur (short)",
+        "time_estimation": "3H",
+        "title": "Building an amplicon sequence variant (ASV) table from 16S data using DADA2",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
+            "Grouping1",
+            "__SORTLIST__",
+            "__UNZIP_COLLECTION__",
+            "cat1",
+            "interactive_tool_phyloseq",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/1.28+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/1.30.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/1.28+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/1.30.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim/dada2_filterAndTrim/1.28+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim/dada2_filterAndTrim/1.30.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_learnerrors/dada2_learnErrors/1.28+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_learnerrors/dada2_learnErrors/1.30.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_makesequencetable/dada2_makeSequenceTable/1.28+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_makesequencetable/dada2_makeSequenceTable/1.30.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_mergepairs/dada2_mergePairs/1.28+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_mergepairs/dada2_mergePairs/1.30.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.28+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.30.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_removebimeradenovo/dada2_removeBimeraDenovo/1.28+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_removebimeradenovo/dada2_removeBimeraDenovo/1.30.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts/dada2_seqCounts/1.28+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts/dada2_seqCounts/1.30.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/phyloseq_from_dada2/phyloseq_from_dada2/1.46.0+galaxy0"
         ],
         "topic_name": "microbiome",
         "topic_name_human": "Microbiome",
@@ -152167,1199 +153908,1227 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "mothur-miseq-sop-short",
+        "tutorial_name": "dada-16S",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/dada-16S/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/dada-16S/tutorial.json"
         },
-        "version": 5,
+        "version": 8,
         "video": false,
-        "video_versions": 2,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 344,
-        "visitors": 1744,
+        "visit_duration": 110,
+        "visitors": 1089,
         "workflows": [
             {
                 "creators": [
                     {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0003-3803-468X",
-                        "name": "Saskia Hiltemann"
-                    }
-                ],
-                "description": "16S Microbial Analysis with mothur (short)",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nContigs\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGroups\"]\n  2[label=\"Summary.seqs\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Screen.seqs\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Summary.seqs\"]\n  3 -> 4 [label=\"fasta_out\"]\n  5[label=\"Unique.seqs\"]\n  3 -> 5 [label=\"fasta_out\"]\n  6[label=\"Count.seqs\"]\n  3 -> 6 [label=\"groups_out\"]\n  5 -> 6 [label=\"out_names\"]\n}",
-                "history": [
-                    {
-                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
-                        "message": "Rename metagenomics topic to microbiome",
-                        "num": 1,
-                        "short_hash": "0e0a2f2cc",
-                        "unix": "1704901629"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Contigs"
-                            }
-                        ],
-                        "label": "Contigs",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 239.8000030517578,
-                            "height": 61.80000305175781,
-                            "left": 313,
-                            "right": 513,
-                            "top": 178,
-                            "width": 200,
-                            "x": 313,
-                            "y": 178
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "575ac02e-83e2-4b10-88af-6016b2ad0117",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Groups"
-                            }
-                        ],
-                        "label": "Groups",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 570.8000030517578,
-                            "height": 61.80000305175781,
-                            "left": 323,
-                            "right": 523,
-                            "top": 509,
-                            "width": 200,
-                            "x": 323,
-                            "y": 509
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f6d83f4e-630a-4022-b300-e1a953c1b737",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nContigs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGroups\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Summary.seqs\"];\n  0 -->|output| 2;\n  3[\"Screen.seqs\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Summary.seqs\"];\n  3 -->|fasta_out| 4;\n  5[\"Unique.seqs\"];\n  3 -->|fasta_out| 5;\n  6[\"Count.seqs\"];\n  3 -->|groups_out| 6;\n  5 -->|out_names| 6;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur]",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "fasta": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Summary.seqs",
-                        "outputs": [
-                            {
-                                "name": "logfile",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "out_summary",
-                                "type": "mothur.summary"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 361.5,
-                            "height": 266,
-                            "left": 631,
-                            "right": 831,
-                            "top": 95.5,
-                            "width": 200,
-                            "x": 631,
-                            "y": 95.5
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionout_summary": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "out_summary"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "609770e516fa",
-                            "name": "mothur_summary_seqs",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"count\": null, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"name\": null, \"savelog\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
-                        "type": "tool",
-                        "uuid": "b289d19e-f8bd-4803-88a0-e41335c11d7a",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "logfile",
-                                "uuid": "09eb6090-e79e-44a7-bf2b-52c217a29c8f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "fasta": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "groups": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Screen.seqs",
-                        "outputs": [
-                            {
-                                "name": "fasta_out",
-                                "type": "input"
-                            },
-                            {
-                                "name": "bad_accnos",
-                                "type": "mothur.accnos"
-                            },
-                            {
-                                "name": "groups_out",
-                                "type": "mothur.groups"
-                            },
-                            {
-                                "name": "alignreport_out",
-                                "type": "mothur.align.report"
-                            },
-                            {
-                                "name": "contigsreport_out",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 1128.5,
-                            "height": 642,
-                            "left": 632,
-                            "right": 832,
-                            "top": 486.5,
-                            "width": 200,
-                            "x": 632,
-                            "y": 486.5
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionalignreport_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "alignreport_out"
-                            },
-                            "HideDatasetActioncontigsreport_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "contigsreport_out"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "63b74bfc8052",
-                            "name": "mothur_screen_seqs",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"alignrep\": {\"usealign\": \"no\", \"__current_case__\": 1}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"contigsrep\": {\"usecontigs\": \"no\", \"__current_case__\": 1}, \"count\": null, \"criteria\": \"-1\", \"end\": \"-1\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"groups\": {\"__class__\": \"ConnectedValue\"}, \"maxambig\": \"0\", \"maxhomop\": \"-1\", \"maxlength\": \"275\", \"minlength\": \"10\", \"names\": null, \"optimize\": null, \"qfile\": null, \"savelog\": \"false\", \"start\": \"-1\", \"summary\": null, \"taxonomy\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.1",
-                        "type": "tool",
-                        "uuid": "ad7d2c58-0b4d-4e3c-bb46-bfb496424b12",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "groups_out",
-                                "uuid": "3361a236-0e72-4844-9956-5200e2b01252"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "fasta_out",
-                                "uuid": "c70b5192-b093-40ff-a912-bb8deff20670"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "bad_accnos",
-                                "uuid": "71c67258-d5e3-4c63-ad49-d01e54cb56cf"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "fasta": {
-                                "id": 3,
-                                "output_name": "fasta_out"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Summary.seqs",
-                                "name": "count"
-                            },
-                            {
-                                "description": "runtime parameter for tool Summary.seqs",
-                                "name": "name"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Summary.seqs",
-                        "outputs": [
-                            {
-                                "name": "logfile",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "out_summary",
-                                "type": "mothur.summary"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 393,
-                            "height": 266,
-                            "left": 959,
-                            "right": 1159,
-                            "top": 127,
-                            "width": 200,
-                            "x": 959,
-                            "y": 127
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionout_summary": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "out_summary"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "609770e516fa",
-                            "name": "mothur_summary_seqs",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"count\": {\"__class__\": \"RuntimeValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"name\": {\"__class__\": \"RuntimeValue\"}, \"savelog\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
-                        "type": "tool",
-                        "uuid": "f7268117-2f00-48d7-aed0-cc3e149db198",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "logfile",
-                                "uuid": "b4abf87f-39ec-4d17-8e93-5a2a473dab74"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "fasta": {
-                                "id": 3,
-                                "output_name": "fasta_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Unique.seqs",
-                        "outputs": [
-                            {
-                                "name": "out_fasta",
-                                "type": "input"
-                            },
-                            {
-                                "name": "out_names",
-                                "type": "mothur.names"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 850.1000061035156,
-                            "height": 235.60000610351562,
-                            "left": 1009,
-                            "right": 1209,
-                            "top": 614.5,
-                            "width": 200,
-                            "x": 1009,
-                            "y": 614.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "d466580cd706",
-                            "name": "mothur_unique_seqs",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"format\": \"name\", \"names\": null, \"savelog\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
-                        "type": "tool",
-                        "uuid": "3256bd7b-b98f-4248-90ae-c5e73704f418",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_fasta",
-                                "uuid": "10d11427-086d-47fe-aee9-ac5d1bae3191"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_names",
-                                "uuid": "2bde74d8-08ef-4bd6-b54f-138c0d4d365f"
-                            }
-                        ]
+                        "class": "Organization",
+                        "isNew": true,
+                        "name": ""
                     },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "grouping|group": {
-                                "id": 3,
-                                "output_name": "groups_out"
-                            },
-                            "name": {
-                                "id": 5,
-                                "output_name": "out_names"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Count.seqs",
-                        "outputs": [
-                            {
-                                "name": "seq_count",
-                                "type": "mothur.count_table"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 556.6999969482422,
-                            "height": 205.1999969482422,
-                            "left": 1292,
-                            "right": 1492,
-                            "top": 351.5,
-                            "width": 200,
-                            "x": 1292,
-                            "y": 351.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "7a6f9c899221",
-                            "name": "mothur_count_seqs",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"grouping\": {\"use\": \"yes\", \"__current_case__\": 0, \"group\": {\"__class__\": \"ConnectedValue\"}, \"groups\": null}, \"name\": {\"__class__\": \"ConnectedValue\"}, \"savelog\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
-                        "type": "tool",
-                        "uuid": "51efceca-f05a-4f3f-af6b-693a14b26048",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "seq_count",
-                                "uuid": "5ffc59a1-8b3f-4b09-982d-332411f16919"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "microbiome/mothur-miseq-sop-short",
-                "path": "topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow1_quality_control.ga",
-                "tags": [
-                    "microbiome"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur]",
-                "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-mothur-miseq-sop-short/versions/workflow1-quality-control",
-                "tutorial_id": "mothur-miseq-sop-short",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow1_quality_control.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow1_quality_control.html",
-                "version": 1,
-                "wfid": "microbiome-mothur-miseq-sop-short",
-                "wfname": "workflow1-quality-control",
-                "workflow": "workflow1_quality_control.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0"
-                ],
-                "workflowhub_id": "1121"
-            },
-            {
-                "creators": [
                     {
                         "class": "Person",
-                        "identifier": "https://orcid.org/0000-0003-3803-468X",
-                        "name": "Saskia Hiltemann"
+                        "identifier": "0000-0001-9852-1987",
+                        "name": "B\u00e9r\u00e9nice Batut"
                     }
                 ],
-                "description": "16S Microbial Analysis with mothur (short)",
+                "description": "Building an amplicon sequence variant (ASV) table from 16S data using DADA2",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAligned Sequences\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCount Table\"]\n  2[label=\"Summary.seqs\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Screen.seqs\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Filter.seqs\"]\n  3 -> 4 [label=\"fasta_out\"]\n  5[label=\"Unique.seqs\"]\n  4 -> 5 [label=\"filteredfasta\"]\n  3 -> 5 [label=\"count_out\"]\n  6[label=\"Pre.cluster\"]\n  5 -> 6 [label=\"out_fasta\"]\n  5 -> 6 [label=\"out_count\"]\n  7[label=\"Summary.seqs\"]\n  6 -> 7 [label=\"count_out\"]\n  6 -> 7 [label=\"fasta_out\"]\n  ka0bbcba140f946789c478bdb4e0b7f6d[color=lightseagreen,label=\"Output\\nSummary.seqs on input dataset(s): summary\"]\n  7 -> ka0bbcba140f946789c478bdb4e0b7f6d\n  8[label=\"Chimera.vsearch\"]\n  6 -> 8 [label=\"fasta_out\"]\n  6 -> 8 [label=\"count_out\"]\n  9[label=\"Remove.seqs\"]\n  8 -> 9 [label=\"out_accnos\"]\n  8 -> 9 [label=\"out_count\"]\n  6 -> 9 [label=\"fasta_out\"]\n  10[label=\"Summary.seqs\"]\n  9 -> 10 [label=\"count_out\"]\n  9 -> 10 [label=\"fasta_out\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nRaw reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nheader\"]\n  2[label=\"Sort collection\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"dada2: filterAndTrim\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"dada2: plotQualityProfile\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Unzip collection\"]\n  3 -> 5 [label=\"paired_output\"]\n  6[label=\"dada2: plotQualityProfile\"]\n  3 -> 6 [label=\"paired_output\"]\n  7[label=\"dada2: learnErrors\"]\n  5 -> 7 [label=\"forward\"]\n  8[label=\"dada2: learnErrors\"]\n  5 -> 8 [label=\"reverse\"]\n  9[label=\"dada2: dada\"]\n  5 -> 9 [label=\"forward\"]\n  7 -> 9 [label=\"errors\"]\n  10[label=\"dada2: dada\"]\n  5 -> 10 [label=\"reverse\"]\n  8 -> 10 [label=\"errors\"]\n  11[label=\"dada2: mergePairs\"]\n  9 -> 11 [label=\"data_collection\"]\n  10 -> 11 [label=\"data_collection\"]\n  5 -> 11 [label=\"forward\"]\n  5 -> 11 [label=\"reverse\"]\n  12[label=\"Extract element identifiers\"]\n  11 -> 12 [label=\"merged\"]\n  13[label=\"dada2: makeSequenceTable\"]\n  11 -> 13 [label=\"merged\"]\n  k3fd2597939df4698bad1aabfccbb7bd2[color=lightseagreen,label=\"Output\\nsequence_table\"]\n  13 -> k3fd2597939df4698bad1aabfccbb7bd2\n  14[label=\"Replace Text\"]\n  12 -> 14 [label=\"output\"]\n  15[label=\"dada2: removeBimeraDenovo\"]\n  13 -> 15 [label=\"stable\"]\n  16[label=\"Select first\"]\n  14 -> 16 [label=\"outfile\"]\n  17[label=\"dada2: sequence counts\"]\n  3 -> 17 [label=\"outtab\"]\n  9 -> 17 [label=\"data_collection\"]\n  10 -> 17 [label=\"data_collection\"]\n  11 -> 17 [label=\"merged\"]\n  15 -> 17 [label=\"stable_sequencetable\"]\n  kc758f86144bc4208b1f71f5106cb678e[color=lightseagreen,label=\"Output\\nsequence_counts\"]\n  17 -> kc758f86144bc4208b1f71f5106cb678e\n  18[label=\"dada2: assignTaxonomy and addSpecies\"]\n  15 -> 18 [label=\"stable_sequencetable\"]\n  k904fe0a2832945ca8493fc688fb216c3[color=lightseagreen,label=\"Output\\ntaxons\"]\n  18 -> k904fe0a2832945ca8493fc688fb216c3\n  19[label=\"Compute\"]\n  16 -> 19 [label=\"outfile\"]\n  20[label=\"Replace Text\"]\n  19 -> 20 [label=\"out_file1\"]\n  21[label=\"Concatenate datasets\"]\n  1 -> 21 [label=\"output\"]\n  20 -> 21 [label=\"outfile\"]\n  k5479d3203e8247a9a92b6ed5959459cf[color=lightseagreen,label=\"Output\\nmetada_table\"]\n  21 -> k5479d3203e8247a9a92b6ed5959459cf\n  22[label=\"Create phyloseq object\"]\n  21 -> 22 [label=\"out_file1\"]\n  15 -> 22 [label=\"stable_sequencetable\"]\n  18 -> 22 [label=\"output\"]\n}",
                 "history": [
                     {
-                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
-                        "message": "Rename metagenomics topic to microbiome",
+                        "hash": "97f8a3d0b5448245415db5a9d9e8ab2182f3cce8",
+                        "message": "Fix Matthias' comments",
+                        "num": 2,
+                        "short_hash": "97f8a3d0b",
+                        "unix": "1717577403"
+                    },
+                    {
+                        "hash": "c1470a165d4a76032ae6f7eec76b94a40b7930bb",
+                        "message": "Finalize tuto, add workflow+test, rename tuto folder",
                         "num": 1,
-                        "short_hash": "0e0a2f2cc",
-                        "unix": "1704901629"
+                        "short_hash": "c1470a165",
+                        "unix": "1717074187"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "",
+                        "annotation": "raw_reads",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Aligned Sequences"
-                            }
-                        ],
-                        "label": "Aligned Sequences",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 2,
-                            "top": 262
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f08168dd-1a9a-4a0e-b1c9-006610590496",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Count Table"
-                            }
-                        ],
-                        "label": "Count Table",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 591
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "4f0b07a6-cc5f-40ed-bab5-37d7a3c6c59e",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAligned Sequences\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nCount Table\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Summary.seqs\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Screen.seqs\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  4[\"Filter.seqs\"];\n  3 -->|fasta_out| 4;\n  5[\"Unique.seqs\"];\n  4 -->|filteredfasta| 5;\n  3 -->|count_out| 5;\n  6[\"Pre.cluster\"];\n  5 -->|out_fasta| 6;\n  5 -->|out_count| 6;\n  7[\"Summary.seqs\"];\n  6 -->|count_out| 7;\n  6 -->|fasta_out| 7;\n  a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d[\"Output\\nSummary.seqs on input dataset(s): summary\"];\n  7 --> a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d;\n  style a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d stroke:#2c3143,stroke-width:4px;\n  8[\"Chimera.vsearch\"];\n  6 -->|fasta_out| 8;\n  6 -->|count_out| 8;\n  9[\"Remove.seqs\"];\n  8 -->|out_accnos| 9;\n  8 -->|out_count| 9;\n  6 -->|fasta_out| 9;\n  10[\"Summary.seqs\"];\n  9 -->|count_out| 10;\n  9 -->|fasta_out| 10;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur]",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "count": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "fasta": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Summary.seqs",
-                        "outputs": [
-                            {
-                                "name": "logfile",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "out_summary",
-                                "type": "mothur.summary"
-                            }
-                        ],
-                        "position": {
-                            "left": 301,
-                            "top": 96.5
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionout_summary": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "out_summary"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "609770e516fa",
-                            "name": "mothur_summary_seqs",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"count\": {\"__class__\": \"ConnectedValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"name\": null, \"savelog\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
-                        "type": "tool",
-                        "uuid": "0c5f9992-1de0-45bc-959e-b8965f499294",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "logfile",
-                                "uuid": "3fee996b-77af-4338-95b6-f2b53233ca79"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "count": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "fasta": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Screen.seqs",
-                        "outputs": [
-                            {
-                                "name": "fasta_out",
-                                "type": "input"
-                            },
-                            {
-                                "name": "bad_accnos",
-                                "type": "mothur.accnos"
-                            },
-                            {
-                                "name": "alignreport_out",
-                                "type": "mothur.align.report"
-                            },
-                            {
-                                "name": "contigsreport_out",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "count_out",
-                                "type": "mothur.count_table"
-                            }
-                        ],
-                        "position": {
-                            "left": 315,
-                            "top": 430.5
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionalignreport_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "alignreport_out"
-                            },
-                            "HideDatasetActioncontigsreport_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "contigsreport_out"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "63b74bfc8052",
-                            "name": "mothur_screen_seqs",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"alignrep\": {\"usealign\": \"no\", \"__current_case__\": 1}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"contigsrep\": {\"usecontigs\": \"no\", \"__current_case__\": 1}, \"count\": {\"__class__\": \"ConnectedValue\"}, \"criteria\": \"-1\", \"end\": \"11550\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"groups\": null, \"maxambig\": \"-1\", \"maxhomop\": \"8\", \"maxlength\": \"-1\", \"minlength\": \"10\", \"names\": null, \"optimize\": null, \"qfile\": null, \"savelog\": false, \"start\": \"1968\", \"summary\": null, \"taxonomy\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.1",
-                        "type": "tool",
-                        "uuid": "2663c361-5494-4eca-bd57-ffbd2dbfae03",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "count_out",
-                                "uuid": "c73cdf2e-9061-4e0b-ad9c-b88730d454f2"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "fasta_out",
-                                "uuid": "74e9d7d4-3364-4e10-bb47-9f1531657198"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "bad_accnos",
-                                "uuid": "759c0a32-df83-415e-8a9f-eee097817a6f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "fasta": {
-                                "id": 3,
-                                "output_name": "fasta_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Filter.seqs",
-                        "outputs": [
-                            {
-                                "name": "logfile",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "out_filter",
-                                "type": "mothur.filter"
-                            },
-                            {
-                                "name": "filteredfasta",
-                                "type": "fasta"
+                                "description": "raw_reads",
+                                "name": "Raw reads"
                             }
                         ],
+                        "label": "Raw reads",
+                        "name": "Input dataset collection",
+                        "outputs": [],
                         "position": {
-                            "left": 603,
-                            "top": 272.5
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionlogfile": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "logfile"
-                            },
-                            "HideDatasetActionout_filter": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "out_filter"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3524ca06478e",
-                            "name": "mothur_filter_seqs",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 72
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"hard\": null, \"inputs\": [], \"savelog\": true, \"soft\": \"0\", \"trump\": \".\", \"vertical\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
-                        "type": "tool",
-                        "uuid": "e326b83b-5d1e-447a-8971-508f72f7b8de",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "2b66bb2a-4ae5-436a-9428-11ac08ab9e39",
                         "when": null,
-                        "workflow_outputs": [
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "header",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "filteredfasta",
-                                "uuid": "c8809f97-ed35-409e-890f-ed45f534e81d"
+                                "description": "header",
+                                "name": "header"
                             }
-                        ]
-                    },
+                        ],
+                        "label": "header",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 3019,
+                            "top": 196
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "582c8937-b1cb-4f01-977f-93d4ccc631b8",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nRaw reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nheader\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Sort collection\"];\n  0 -->|output| 2;\n  3[\"dada2: filterAndTrim\"];\n  2 -->|output| 3;\n  4[\"dada2: plotQualityProfile\"];\n  2 -->|output| 4;\n  5[\"Unzip collection\"];\n  3 -->|paired_output| 5;\n  6[\"dada2: plotQualityProfile\"];\n  3 -->|paired_output| 6;\n  7[\"dada2: learnErrors\"];\n  5 -->|forward| 7;\n  8[\"dada2: learnErrors\"];\n  5 -->|reverse| 8;\n  9[\"dada2: dada\"];\n  5 -->|forward| 9;\n  7 -->|errors| 9;\n  10[\"dada2: dada\"];\n  5 -->|reverse| 10;\n  8 -->|errors| 10;\n  11[\"dada2: mergePairs\"];\n  9 -->|data_collection| 11;\n  10 -->|data_collection| 11;\n  5 -->|forward| 11;\n  5 -->|reverse| 11;\n  12[\"Extract element identifiers\"];\n  11 -->|merged| 12;\n  13[\"dada2: makeSequenceTable\"];\n  11 -->|merged| 13;\n  3fd25979-39df-4698-bad1-aabfccbb7bd2[\"Output\\nsequence_table\"];\n  13 --> 3fd25979-39df-4698-bad1-aabfccbb7bd2;\n  style 3fd25979-39df-4698-bad1-aabfccbb7bd2 stroke:#2c3143,stroke-width:4px;\n  14[\"Replace Text\"];\n  12 -->|output| 14;\n  15[\"dada2: removeBimeraDenovo\"];\n  13 -->|stable| 15;\n  16[\"Select first\"];\n  14 -->|outfile| 16;\n  17[\"dada2: sequence counts\"];\n  3 -->|outtab| 17;\n  9 -->|data_collection| 17;\n  10 -->|data_collection| 17;\n  11 -->|merged| 17;\n  15 -->|stable_sequencetable| 17;\n  c758f861-44bc-4208-b1f7-1f5106cb678e[\"Output\\nsequence_counts\"];\n  17 --> c758f861-44bc-4208-b1f7-1f5106cb678e;\n  style c758f861-44bc-4208-b1f7-1f5106cb678e stroke:#2c3143,stroke-width:4px;\n  18[\"dada2: assignTaxonomy and addSpecies\"];\n  15 -->|stable_sequencetable| 18;\n  904fe0a2-8329-45ca-8493-fc688fb216c3[\"Output\\ntaxons\"];\n  18 --> 904fe0a2-8329-45ca-8493-fc688fb216c3;\n  style 904fe0a2-8329-45ca-8493-fc688fb216c3 stroke:#2c3143,stroke-width:4px;\n  19[\"Compute\"];\n  16 -->|outfile| 19;\n  20[\"Replace Text\"];\n  19 -->|out_file1| 20;\n  21[\"Concatenate datasets\"];\n  1 -->|output| 21;\n  20 -->|outfile| 21;\n  5479d320-3e82-47a9-a92b-6ed5959459cf[\"Output\\nmetada_table\"];\n  21 --> 5479d320-3e82-47a9-a92b-6ed5959459cf;\n  style 5479d320-3e82-47a9-a92b-6ed5959459cf stroke:#2c3143,stroke-width:4px;\n  22[\"Create phyloseq object\"];\n  21 -->|out_file1| 22;\n  15 -->|stable_sequencetable| 22;\n  18 -->|output| 22;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Building an amplicon sequence variant (ASV) table from 16S data using DADA2",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/dada2_makesequencetable/dada2_makeSequenceTable/1.30.0+galaxy0",
                         "errors": null,
-                        "id": 5,
+                        "id": 13,
                         "input_connections": {
-                            "fasta": {
-                                "id": 4,
-                                "output_name": "filteredfasta"
-                            },
-                            "names": {
-                                "id": 3,
-                                "output_name": "count_out"
+                            "samples": {
+                                "id": 11,
+                                "output_name": "merged"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Unique.seqs",
+                        "name": "dada2: makeSequenceTable",
                         "outputs": [
                             {
-                                "name": "out_fasta",
-                                "type": "input"
+                                "name": "stable",
+                                "type": "dada2_sequencetable"
                             },
                             {
-                                "name": "out_count",
-                                "type": "mothur.count_table"
+                                "name": "plot_output",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "left": 882,
-                            "top": 621.5
+                            "left": 1970.000125527473,
+                            "top": 273.99367961852937
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dada2_makesequencetable/dada2_makeSequenceTable/1.30.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "d466580cd706",
-                            "name": "mothur_unique_seqs",
+                            "changeset_revision": "75c8945b0da2",
+                            "name": "dada2_makesequencetable",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"format\": \"count\", \"names\": {\"__class__\": \"ConnectedValue\"}, \"savelog\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"filter_cond\": {\"filter_select\": \"no\", \"__current_case__\": 0}, \"orderBy\": \"abundance\", \"plot\": true, \"samples\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.30.0+galaxy0",
                         "type": "tool",
-                        "uuid": "225cd752-6173-4e44-9b31-a1de097d3357",
+                        "uuid": "609d25ec-eea3-4893-9d8f-1de0bd185664",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_fasta",
-                                "uuid": "efcff963-3961-4b12-857b-9191765f5ad5"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_count",
-                                "uuid": "3e744fc6-4002-409c-b580-7a080263b39c"
+                                "label": "sequence_table",
+                                "output_name": "stable",
+                                "uuid": "3fd25979-39df-4698-bad1-aabfccbb7bd2"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts/dada2_seqCounts/1.30.0+galaxy0",
                         "errors": null,
-                        "id": 6,
+                        "id": 17,
                         "input_connections": {
-                            "fasta": {
-                                "id": 5,
-                                "output_name": "out_fasta"
+                            "inrep_0|input": {
+                                "id": 3,
+                                "output_name": "outtab"
                             },
-                            "name": {
-                                "id": 5,
-                                "output_name": "out_count"
+                            "inrep_1|input": {
+                                "id": 9,
+                                "output_name": "data_collection"
+                            },
+                            "inrep_2|input": {
+                                "id": 10,
+                                "output_name": "data_collection"
+                            },
+                            "inrep_3|input": {
+                                "id": 11,
+                                "output_name": "merged"
+                            },
+                            "inrep_4|input": {
+                                "id": 15,
+                                "output_name": "stable_sequencetable"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Pre.cluster",
+                        "name": "dada2: sequence counts",
                         "outputs": [
                             {
-                                "name": "map_out",
-                                "type": "input"
-                            },
-                            {
-                                "name": "fasta_out",
-                                "type": "input"
-                            },
-                            {
-                                "name": "names_out",
-                                "type": "mothur.names"
-                            },
-                            {
-                                "name": "count_out",
-                                "type": "mothur.count_table"
+                                "name": "counts",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1179,
-                            "top": 74.5
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionmap_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "map_out"
-                            },
-                            "HideDatasetActionnames_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "names_out"
-                            }
+                            "left": 2550,
+                            "top": 154
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts/dada2_seqCounts/1.30.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "05183ee20cf8",
-                            "name": "mothur_pre_cluster",
+                            "changeset_revision": "a7817705348e",
+                            "name": "dada2_seqcounts",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"diffs\": \"2\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gapextend\": \"-1\", \"gapopen\": \"-2\", \"group\": null, \"match\": \"1\", \"mismatch\": \"-1\", \"name\": {\"__class__\": \"ConnectedValue\"}, \"savelog\": false, \"topdown\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"inrep\": [{\"__index__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"name\": \"FiltTrim\"}, {\"__index__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}, \"name\": \"Dada Forward\"}, {\"__index__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}, \"name\": \"Dada Reverse\"}, {\"__index__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}, \"name\": \"SeqTab\"}, {\"__index__\": 4, \"input\": {\"__class__\": \"ConnectedValue\"}, \"name\": \"Bimera\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.30.0+galaxy0",
                         "type": "tool",
-                        "uuid": "6f90be44-8355-4639-a4e6-9d5cc0df50f0",
+                        "uuid": "e749677d-de5a-4cf8-93de-e709b42b38f7",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "fasta_out",
-                                "uuid": "e06f7f73-b9d6-4314-bcc6-9e0889d0f701"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "count_out",
-                                "uuid": "457b654e-4a7d-4fcd-84e2-def389e29fe6"
+                                "label": "sequence_counts",
+                                "output_name": "counts",
+                                "uuid": "c758f861-44bc-4208-b1f7-1f5106cb678e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/1.30.0+galaxy0",
                         "errors": null,
-                        "id": 7,
+                        "id": 18,
                         "input_connections": {
-                            "count": {
-                                "id": 6,
-                                "output_name": "count_out"
-                            },
-                            "fasta": {
-                                "id": 6,
-                                "output_name": "fasta_out"
+                            "seqs": {
+                                "id": 15,
+                                "output_name": "stable_sequencetable"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Summary.seqs",
-                                "name": "name"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Summary.seqs",
+                        "name": "dada2: assignTaxonomy and addSpecies",
                         "outputs": [
                             {
-                                "name": "out_summary",
-                                "type": "mothur.summary"
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1498,
-                            "top": 0
+                            "left": 2830,
+                            "top": 431
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/1.30.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "609770e516fa",
-                            "name": "mothur_summary_seqs",
+                            "changeset_revision": "65db807336bc",
+                            "name": "dada2_assigntaxonomyaddspecies",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"count\": {\"__class__\": \"ConnectedValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"name\": {\"__class__\": \"RuntimeValue\"}, \"savelog\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"addSpecies_cond\": {\"addSpecies_select\": \"TRUE\", \"__current_case__\": 1, \"speciesreference_cond\": {\"speciesreference_select\": \"builtin\", \"__current_case__\": 0, \"speciesrefFasta\": \"silva_132\"}, \"allowMultiple_cond\": {\"allowMultiple\": \"FALSE\", \"__current_case__\": 0}, \"tryRC\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"minBoot\": \"50\", \"outputBootstraps\": false, \"reference_cond\": {\"reference_select\": \"builtin\", \"__current_case__\": 0, \"refFasta\": \"silva_132\"}, \"seed\": null, \"seqs\": {\"__class__\": \"ConnectedValue\"}, \"tryRC\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.30.0+galaxy0",
                         "type": "tool",
-                        "uuid": "0ab1410f-0567-4266-9aac-9412c907da0d",
+                        "uuid": "984044aa-daa8-4082-9a48-623bd5e6f448",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Summary.seqs on input dataset(s): summary",
-                                "output_name": "out_summary",
-                                "uuid": "a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d"
+                                "label": "taxons",
+                                "output_name": "output",
+                                "uuid": "904fe0a2-8329-45ca-8493-fc688fb216c3"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1",
+                        "content_id": "cat1",
                         "errors": null,
-                        "id": 8,
+                        "id": 21,
                         "input_connections": {
-                            "fasta": {
-                                "id": 6,
-                                "output_name": "fasta_out"
+                            "input1": {
+                                "id": 1,
+                                "output_name": "output"
                             },
-                            "template|count": {
-                                "id": 6,
-                                "output_name": "count_out"
+                            "queries_0|input2": {
+                                "id": 20,
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Chimera.vsearch",
+                        "name": "Concatenate datasets",
                         "outputs": [
                             {
-                                "name": "vsearch.chimeras",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "out_accnos",
-                                "type": "mothur.accnos"
-                            },
-                            {
-                                "name": "out_count",
-                                "type": "mothur.count_table"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 1478,
-                            "top": 636.5
+                            "left": 3390,
+                            "top": 12
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "12e856482d26",
-                            "name": "mothur_chimera_vsearch",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Metadata table"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"dereplicate\": true, \"dn\": \"1.4\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"mindiffs\": \"3\", \"mindiv\": \"0.5\", \"minh\": \"0.3\", \"savelog\": false, \"template\": {\"source\": \"self\", \"__current_case__\": 2, \"abskew\": \"1.9\", \"group\": null, \"count\": {\"__class__\": \"ConnectedValue\"}}, \"xn\": \"8.0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.1",
+                        "tool_id": "cat1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [{\"__index__\": 0, \"input2\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
                         "type": "tool",
-                        "uuid": "d23b7636-fbcb-4346-992d-a79e8093d489",
+                        "uuid": "708b9c3c-9de6-4722-9852-39c1b82310b6",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_accnos",
-                                "uuid": "c975f75e-71cc-45a8-a653-df3fdd56eb9b"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_count",
-                                "uuid": "1657beb8-c142-47ca-ac8d-bf92a3b74273"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "vsearch.chimeras",
-                                "uuid": "e3cb9259-e3b1-4870-b098-eeadc7e8f4c1"
+                                "label": "metada_table",
+                                "output_name": "out_file1",
+                                "uuid": "5479d320-3e82-47a9-a92b-6ed5959459cf"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "microbiome/dada-16S",
+                "path": "topics/microbiome/tutorials/dada-16S/workflows/workflow.ga",
+                "tags": [
+                    "microbiome"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "Building an amplicon sequence variant (ASV) table from 16S data using DADA2",
+                "topic_id": "microbiome",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-dada-16S/versions/workflow",
+                "tutorial_id": "dada-16S",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/dada-16S/workflows/workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/dada-16S/workflows/workflow.html",
+                "version": 1,
+                "wfid": "microbiome-dada-16S",
+                "wfname": "workflow",
+                "workflow": "workflow.ga",
+                "workflow_tools": [
+                    "__SORTLIST__",
+                    "__UNZIP_COLLECTION__",
+                    "cat1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/1.30.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/1.30.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim/dada2_filterAndTrim/1.30.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/dada2_learnerrors/dada2_learnErrors/1.30.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/dada2_makesequencetable/dada2_makeSequenceTable/1.30.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/dada2_mergepairs/dada2_mergePairs/1.30.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.30.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/dada2_removebimeradenovo/dada2_removeBimeraDenovo/1.30.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts/dada2_seqCounts/1.30.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/phyloseq_from_dada2/phyloseq_from_dada2/1.46.0+galaxy0"
+                ],
+                "workflowhub_id": "1105"
+            }
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.800651"
+    },
+    {
+        "abbreviations": {
+            "AMF": "arbuscular mycorrhizal fungi",
+            "ASV": "Amplicon Sequence Variant",
+            "EcMF": "ectomycorrhizal fungi",
+            "ITS2": "Internal Transcribed Spacer 2",
+            "MF": "Mycorrhizal fungi",
+            "OTU": "Operating Taxonomic Unit",
+            "SPUN": "Society for the Protection of Underground Networks",
+            "SSU": "Small Subunit (RNA)",
+            "TSV": "tab-separated-values",
+            "eDNA": "environmental DNA",
+            "sdm": "simple demultiplexer"
+        },
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "lotus2",
+                    "owner": "earlhaminst",
+                    "revisions": "eb7baf1f72ca",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: lotus2\n  owner: earlhaminst\n  revisions: eb7baf1f72ca\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "answer_histories": [
+            {
+                "date": "2024-09-20",
+                "history": "https://usegalaxy.eu/u/sujai_spun_earth/h/identifying-mf-from-its2-sequencing-using-lotus2---tutorial-example-run",
+                "label": "UseGalaxy.eu"
+            }
+        ],
+        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/lotus2-identifying-fungi/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "sujaikumar"
+            ],
+            "editing": [
+                "bethanmanley"
+            ],
+            "funding": [
+                "societyprotectionundergroundnetworks"
+            ]
+        },
+        "contributors": [
+            {
+                "id": "sujaikumar",
+                "joined": "2024-09",
+                "name": "Sujai Kumar",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/sujaikumar/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/sujaikumar.json"
+            },
+            {
+                "id": "bethanmanley",
+                "joined": "2024-09",
+                "name": "Bethan Manley",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bethanmanley/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bethanmanley.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/spun-logo.png",
+                "description": "SPUN is a scientific research organization founded to map mycorrhizal fungal communities and advocate for their protection.",
+                "id": "societyprotectionundergroundnetworks",
+                "name": "Society for the Protection of Underground Networks",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/societyprotectionundergroundnetworks/",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/societyprotectionundergroundnetworks.json"
+            }
+        ],
+        "dir": "topics/microbiome/tutorials/lotus2-identifying-fungi",
+        "edam_operation": [
+            "DNA barcoding",
+            "Sequence feature detection"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "microbiome/lotus2-identifying-fungi",
+        "inexact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "LotuS is a metagenomics tool for identifying OTUs or ASVs from sequencing data",
+            "Galaxy is an easy way to run LotuS2 in the cloud for bioinformatics beginners"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-30",
+        "objectives": [
+            "Understand the files needed for running LotuS2",
+            "Learn to use datasets from Zenodo in a Galaxy tool",
+            "Learn to upload data files to Galaxy",
+            "Learn to run the Galaxy LotuS2 tool and what the parameters mean",
+            "Understand the output files from LotuS2",
+            "Understand the structure of the mapping file needed by LotuS2 to link sample metadata to a pair of FASTQ files"
+        ],
+        "pageviews": 24,
+        "pub_date": "2024-09-30",
+        "questions": [
+            "What is the fungal community composition in a given soil sample?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "introduction",
+                "tutorials": [
+                    "galaxy-intro-101-everyone"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": null,
+        "short_tools": [
+            "lotus2"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "fungi",
+            "ecology"
+        ],
+        "time_estimation": "3H",
+        "title": "Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/earlhaminst/lotus2/lotus2/2.32+galaxy0"
+        ],
+        "topic_name": "microbiome",
+        "topic_name_human": "Microbiome",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "lotus2-identifying-fungi",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/lotus2-identifying-fungi/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/lotus2-identifying-fungi/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/lotus2-identifying-fungi/tutorial.json"
+        },
+        "version": 2,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 30,
+        "visitors": 17,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Organization",
+                        "name": "Society for the Protection of Underground Networks",
+                        "url": "https://spun.earth"
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.39.5.0",
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0001-5902-6641",
+                        "name": "Sujai Kumar",
+                        "url": "https://github.com/sujaikumar"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0002-0137-6953",
+                        "name": "Bethan Manley",
+                        "url": "https://github.com/bethanmanley"
+                    }
+                ],
+                "description": "Workflow for running LotuS2 tool on fungal ITS paired-end sequencing data, to identify the fungi present in the samples",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                    },
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMapping tsv\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nsdm Options txt\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  3[label=\"LotuS2\"]\n  2 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  k7ff13687fb954b548b5c4c916500dfed[color=lightseagreen,label=\"Output\\nOTU Table\"]\n  3 -> k7ff13687fb954b548b5c4c916500dfed\n  kb341390433194fa08c172c4757af5b8c[color=lightseagreen,label=\"Output\\nOTU fasta\"]\n  3 -> kb341390433194fa08c172c4757af5b8c\n  k11ad80569572428aa3b25ceec0fa186e[color=lightseagreen,label=\"Output\\nComplete Output Zip\"]\n  3 -> k11ad80569572428aa3b25ceec0fa186e\n  k21d559708b954dca9b46e7c65340ce84[color=lightseagreen,label=\"Output\\nOTU Phylogenetic Tree\"]\n  3 -> k21d559708b954dca9b46e7c65340ce84\n}",
+                "history": [
+                    {
+                        "hash": "0cf85de6b9abbff69b43c6ac380e9a03f3a079af",
+                        "message": "Move tutorial to",
+                        "num": 1,
+                        "short_hash": "0cf85de6b",
+                        "unix": "1727445419"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "Mapping file needed by LotuS2 to link sample metadata to a pair of fastq files",
+                        "content_id": null,
                         "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "accnos": {
-                                "id": 8,
-                                "output_name": "out_accnos"
-                            },
-                            "count_in": {
-                                "id": 8,
-                                "output_name": "out_count"
-                            },
-                            "fasta_in": {
-                                "id": 6,
-                                "output_name": "fasta_out"
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Mapping file needed by LotuS2 to link sample metadata to a pair of fastq files",
+                                "name": "Mapping tsv"
                             }
+                        ],
+                        "label": "Mapping tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 0.124267578125
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Remove.seqs",
-                        "outputs": [
-                            {
-                                "name": "fasta_out",
-                                "type": "input"
-                            },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "1d2315cd-11dc-494f-9698-0749cc89bd98",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "SDM (sequence demultiplexer tool) options needed for fungal ITS illumina paired-end sequencing",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "count_out",
-                                "type": "input"
+                                "description": "SDM (sequence demultiplexer tool) options needed for fungal ITS illumina paired-end sequencing",
+                                "name": "sdm Options txt"
                             }
                         ],
+                        "label": "sdm Options txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1872,
-                            "top": 231.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.39.5.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "5097ac2cbfc3",
-                            "name": "mothur_remove_seqs",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 120.124267578125
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"accnos\": {\"__class__\": \"ConnectedValue\"}, \"alignreport_in\": null, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"count_in\": {\"__class__\": \"ConnectedValue\"}, \"dups\": true, \"fasta_in\": {\"__class__\": \"ConnectedValue\"}, \"fastq_in\": null, \"group_in\": null, \"list_in\": null, \"name_in\": null, \"qfile_in\": null, \"savelog\": false, \"taxonomy_in\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
-                        "type": "tool",
-                        "uuid": "b9b21e24-7318-474b-a145-a3be83c7d09c",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0a86f2eb-afa0-415a-9f61-496a68eb893d",
                         "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "count_out",
-                                "uuid": "8480daf7-266c-48fb-a4c7-2ff68313d6b6"
-                            },
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "List of paired fastq files needed to run LotuS2. These files MUST match the files in the Mapping File",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "fasta_out",
-                                "uuid": "51c086db-4a7e-4128-9010-01a3b6f2621e"
+                                "description": "List of paired fastq files needed to run LotuS2. These files MUST match the files in the Mapping File",
+                                "name": "Input Dataset Collection"
                             }
-                        ]
-                    },
+                        ],
+                        "label": "Input Dataset Collection",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 240.124267578125
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "4177013a-2f92-4800-9a85-517b43c45aa2",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nMapping tsv\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nsdm Options txt\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"LotuS2\"];\n  2 -->|output| 3;\n  0 -->|output| 3;\n  1 -->|output| 3;\n  7ff13687-fb95-4b54-8b5c-4c916500dfed[\"Output\\nOTU Table\"];\n  3 --> 7ff13687-fb95-4b54-8b5c-4c916500dfed;\n  style 7ff13687-fb95-4b54-8b5c-4c916500dfed stroke:#2c3143,stroke-width:4px;\n  b3413904-3319-4fa0-8c17-2c4757af5b8c[\"Output\\nOTU fasta\"];\n  3 --> b3413904-3319-4fa0-8c17-2c4757af5b8c;\n  style b3413904-3319-4fa0-8c17-2c4757af5b8c stroke:#2c3143,stroke-width:4px;\n  11ad8056-9572-428a-a3b2-5ceec0fa186e[\"Output\\nComplete Output Zip\"];\n  3 --> 11ad8056-9572-428a-a3b2-5ceec0fa186e;\n  style 11ad8056-9572-428a-a3b2-5ceec0fa186e stroke:#2c3143,stroke-width:4px;\n  21d55970-8b95-4dca-9b46-e7c65340ce84[\"Output\\nOTU Phylogenetic Tree\"];\n  3 --> 21d55970-8b95-4dca-9b46-e7c65340ce84;\n  style 21d55970-8b95-4dca-9b46-e7c65340ce84 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run'",
+                "outputs": [
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
+                        "annotation": "LotuS2 creates a large output folder which is zipped up and provided as one of the outputs. Some of the individual files within this output folder are also exposed as outputs by the Galaxy LotuS2 tool so that they can be used in subsequent downstream analyses.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/lotus2/lotus2/2.32+galaxy0",
                         "errors": null,
-                        "id": 10,
+                        "id": 3,
                         "input_connections": {
-                            "count": {
-                                "id": 9,
-                                "output_name": "count_out"
+                            "inputs|pair_input": {
+                                "id": 2,
+                                "output_name": "output"
                             },
-                            "fasta": {
-                                "id": 9,
-                                "output_name": "fasta_out"
+                            "map": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "other_opts|sdmopt": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Summary.seqs",
-                                "name": "count"
-                            },
-                            {
-                                "description": "runtime parameter for tool Summary.seqs",
-                                "name": "fasta"
+                                "description": "runtime parameter for tool LotuS2",
+                                "name": "inputs"
                             },
                             {
-                                "description": "runtime parameter for tool Summary.seqs",
-                                "name": "name"
+                                "description": "runtime parameter for tool LotuS2",
+                                "name": "other_opts"
                             }
                         ],
-                        "label": null,
-                        "name": "Summary.seqs",
+                        "label": "LotuS2",
+                        "name": "LotuS2",
                         "outputs": [
                             {
-                                "name": "logfile",
-                                "type": "txt"
+                                "name": "outputs",
+                                "type": "zip"
                             },
                             {
-                                "name": "out_summary",
-                                "type": "mothur.summary"
+                                "name": "otu",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "otu_fna",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "OTUphylo_nwk",
+                                "type": "newick"
+                            },
+                            {
+                                "name": "mapping",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "runlog",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 2298,
-                            "top": 342
+                            "left": 220,
+                            "top": 0
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
+                        "post_job_actions": {
+                            "ChangeDatatypeActionOTUphylo_nwk": {
+                                "action_arguments": {
+                                    "newtype": "newick"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "OTUphylo_nwk"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/lotus2/lotus2/2.32+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "609770e516fa",
-                            "name": "mothur_summary_seqs",
-                            "owner": "iuc",
+                            "changeset_revision": "eb7baf1f72ca",
+                            "name": "lotus2",
+                            "owner": "earlhaminst",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"count\": {\"__class__\": \"RuntimeValue\"}, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"name\": {\"__class__\": \"RuntimeValue\"}, \"savelog\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"aligner_cond\": {\"taxAligner\": \"2\", \"__current_case__\": 1, \"refDB_cond\": {\"refDB\": \"cached\", \"__current_case__\": 0, \"ref_db\": \"UNITE\", \"greengenesSpecies\": false}, \"useBestBlastHitOnly\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"clu_args\": {\"derepMin\": \"10:1,5:2,3:3\", \"deactivateChimeraCheck\": \"\", \"chim_skew\": null}, \"clu_cond\": {\"clustering\": \"8\", \"__current_case__\": 3}, \"forwardPrimer\": \"\", \"inputs\": {\"paired_or_single\": \"paired_collection\", \"__current_case__\": 1, \"pair_input\": {\"__class__\": \"ConnectedValue\"}}, \"map\": {\"__class__\": \"ConnectedValue\"}, \"other_opts\": {\"sdmopt\": {\"__class__\": \"ConnectedValue\"}, \"platform\": \"\", \"barcode\": null, \"offtarget_cond\": {\"offtargetDB\": \"no\", \"__current_case__\": 0}, \"useMini4map\": true}, \"reversePrimer\": \"\", \"tax_args\": {\"amplicon_cond\": {\"amplicon_type\": \"ITS2\", \"__current_case__\": 5, \"ITSx\": true}, \"tax_group\": \"fungi\", \"keepUnclassified\": true, \"LCA_cover\": null, \"LCA_frac\": null, \"lulu\": true, \"buildPhylo\": \"1\", \"taxExcludeGrep\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.32+galaxy0",
                         "type": "tool",
-                        "uuid": "9a018d5e-23f7-46a7-ac83-a57bc2ddd9ac",
+                        "uuid": "8d82af5f-993a-46dd-afc9-8b73170da85d",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_summary",
-                                "uuid": "f097e9a4-45a5-4168-a3bc-79ae4c0eb3d4"
+                                "label": "OTU Table",
+                                "output_name": "otu",
+                                "uuid": "7ff13687-fb95-4b54-8b5c-4c916500dfed"
+                            },
+                            {
+                                "label": "OTU fasta",
+                                "output_name": "otu_fna",
+                                "uuid": "b3413904-3319-4fa0-8c17-2c4757af5b8c"
+                            },
+                            {
+                                "label": "Complete Output Zip",
+                                "output_name": "outputs",
+                                "uuid": "11ad8056-9572-428a-a3b2-5ceec0fa186e"
+                            },
+                            {
+                                "label": "OTU Phylogenetic Tree",
+                                "output_name": "OTUphylo_nwk",
+                                "uuid": "21d55970-8b95-4dca-9b46-e7c65340ce84"
                             }
                         ]
                     }
                 ],
-                "parent_id": "microbiome/mothur-miseq-sop-short",
-                "path": "topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow2_data_cleaning.ga",
+                "parent_id": "microbiome/lotus2-identifying-fungi",
+                "path": "topics/microbiome/tutorials/lotus2-identifying-fungi/workflows/lotus2-fungi-workflow.ga",
                 "tags": [
-                    "microbiome"
+                    "lotus2",
+                    "fungi",
+                    "ecology",
+                    "metagenomics"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur]",
+                "tests": true,
+                "title": "Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run'",
                 "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-mothur-miseq-sop-short/versions/workflow2-data-cleaning",
-                "tutorial_id": "mothur-miseq-sop-short",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow2_data_cleaning.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow2_data_cleaning.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-lotus2-identifying-fungi/versions/lotus2-fungi-workflow",
+                "tutorial_id": "lotus2-identifying-fungi",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/lotus2-identifying-fungi/workflows/lotus2-fungi-workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/lotus2-identifying-fungi/workflows/lotus2-fungi-workflow.html",
                 "version": 1,
-                "wfid": "microbiome-mothur-miseq-sop-short",
-                "wfname": "workflow2-data-cleaning",
-                "workflow": "workflow2_data_cleaning.ga",
+                "wfid": "microbiome-lotus2-identifying-fungi",
+                "wfname": "lotus2-fungi-workflow",
+                "workflow": "lotus2-fungi-workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0"
+                    "toolshed.g2.bx.psu.edu/repos/earlhaminst/lotus2/lotus2/2.32+galaxy0"
                 ],
-                "workflowhub_id": "1112"
+                "workflowhub_id": null
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/records/13710591"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "unique",
+                    "owner": "bgruening",
+                    "revisions": "7ce75adb93be",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bamtools",
+                    "owner": "devteam",
+                    "revisions": "befc9dad4ca8",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bowtie2",
+                    "owner": "devteam",
+                    "revisions": "f6877ad76b00",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bowtie2",
+                    "owner": "devteam",
+                    "revisions": "03e9b2fbc005",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "3d0c7bdf12f5",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bandage",
+                    "owner": "iuc",
+                    "revisions": "21e491ad532a",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bandage",
+                    "owner": "iuc",
+                    "revisions": "21e491ad532a",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collection_column_join",
+                    "owner": "iuc",
+                    "revisions": "3ddd99c7efee",
+                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "coverm_contig",
+                    "owner": "iuc",
+                    "revisions": "6941d0d453ba",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "filter_tabular",
+                    "owner": "iuc",
+                    "revisions": "34d29339abab",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "megahit",
+                    "owner": "iuc",
+                    "revisions": "14ddfc8ffb93",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "megahit_contig2fastg",
+                    "owner": "iuc",
+                    "revisions": "4ec5b3777508",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ngsutils_bam_filter",
+                    "owner": "iuc",
+                    "revisions": "2e957d4c4b95",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "quast",
+                    "owner": "iuc",
+                    "revisions": "3061c8b029e5",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "quast",
+                    "owner": "iuc",
+                    "revisions": "72472698a2df",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seqtk",
+                    "owner": "iuc",
+                    "revisions": "3da72230c066",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "cutadapt",
+                    "owner": "lparsons",
+                    "revisions": "5915ea1ec9b1",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "metaspades",
+                    "owner": "nml",
+                    "revisions": "fd128c111ab0",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unique\n  owner: bgruening\n  revisions: 7ce75adb93be\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools\n  owner: devteam\n  revisions: befc9dad4ca8\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie2\n  owner: devteam\n  revisions: f6877ad76b00\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie2\n  owner: devteam\n  revisions: 03e9b2fbc005\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: 21e491ad532a\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: 21e491ad532a\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_column_join\n  owner: iuc\n  revisions: 3ddd99c7efee\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: coverm_contig\n  owner: iuc\n  revisions: 6941d0d453ba\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filter_tabular\n  owner: iuc\n  revisions: 34d29339abab\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: megahit\n  owner: iuc\n  revisions: 14ddfc8ffb93\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: megahit_contig2fastg\n  owner: iuc\n  revisions: 4ec5b3777508\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ngsutils_bam_filter\n  owner: iuc\n  revisions: 2e957d4c4b95\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 3061c8b029e5\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 72472698a2df\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 5915ea1ec9b1\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaspades\n  owner: nml\n  revisions: fd128c111ab0\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-assembly/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "plushz",
+                "bebatut"
+            ],
+            "funding": [
+                "gallantries"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "id": "plushz",
+                "joined": "2022-03",
+                "name": "Polina Polunina",
+                "orcid": "0000-0002-0507-4602",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/plushz/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/plushz.json"
             },
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0003-3803-468X",
-                        "name": "Saskia Hiltemann"
-                    }
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            }
+        ],
+        "dir": "topics/microbiome/tutorials/metagenomics-assembly",
+        "edam_ontology": [
+            "topic_3174",
+            "topic_0196"
+        ],
+        "edam_operation": [
+            "Data handling",
+            "Visualisation",
+            "Sequence trimming",
+            "Read mapping",
+            "Sequencing quality control",
+            "Genome assembly",
+            "Sequence alignment analysis",
+            "Sequence contamination filtering",
+            "Sequence assembly validation",
+            "Variant calling",
+            "Statistical calculation",
+            "Sequence assembly visualisation",
+            "Sequence file editing",
+            "Local alignment",
+            "Sequence composition calculation",
+            "Read pre-processing",
+            "Primer removal",
+            "Formatting"
+        ],
+        "edam_topic": [
+            "Metagenomics",
+            "Sequence assembly"
+        ],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "microbiome/metagenomics-assembly",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.eu"
+        ],
+        "js_requirements": {
+            "mathjax": 25185,
+            "mermaid": false
+        },
+        "key_points": [
+            "Assembly groups reads into contigs and scafolds.",
+            "De Brujin Graphs use k-mers to assembly reads",
+            "MetaSPAdes and MEGAHIT are assemblers",
+            "Quast is the tool to assess the assembly quality"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-14",
+        "objectives": [
+            "Describe what an assembly is",
+            "Describe what de-replication is",
+            "Explain the difference between co-assembly and individual assembly",
+            "Explain the difference between reads, contigs and scaffolds",
+            "Explain how tools based on De Bruijn graph work",
+            "Apply appropriate tools for analyzing the quality of metagenomic data",
+            "Construct and apply simple assembly pipelines on short read data",
+            "Apply appropriate tools for analyzing the quality of metagenomic assembly",
+            "Evaluate the Quality of the Assembly with Quast, Bowtie2, and CoverM-Genome"
+        ],
+        "pageviews": 2258,
+        "pub_date": "2022-12-05",
+        "questions": [
+            "Why metagenomic data should be assembled?",
+            "What is the difference between co-assembly and individual assembly?",
+            "What is the difference between reads, contigs and scaffolds?",
+            "How tools based on De Bruijn graph work?",
+            "How to assess the quality of metagenomic data assembly?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "bebatut",
+                    "sophia120199"
                 ],
-                "description": "16S Microbial Analysis with mothur (short)",
+                "date": "2023-05-02",
+                "galaxy_version": "23.01",
+                "length": "1H",
+                "speakers": [
+                    "bebatut"
+                ],
+                "youtube_id": "1ZYGy85Im7w"
+            }
+        ],
+        "redirect_from": [
+            "/topics/metagenomics/tutorials/metagenomics-assembly/tutorial",
+            "/short/microbiome/metagenomics-assembly",
+            "/short/T00202",
+            "/short/T00386"
+        ],
+        "short_id": "T00386",
+        "short_tools": [
+            "ngsutils_bam_filter",
+            "tp_cat",
+            "bamtools",
+            "bandage_image",
+            "filter_tabular",
+            "megahit_contig2fastg",
+            "bandage_info",
+            "bg_uniq",
+            "quast",
+            "seqtk_subseq",
+            "cutadapt",
+            "random_lines1",
+            "collection_column_join",
+            "megahit",
+            "coverm_contig",
+            "fastqc",
+            "metaspades",
+            "bowtie2"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "metagenomics",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "assembly",
+            "metagenomics",
+            "microgalaxy"
+        ],
+        "time_estimation": "2H",
+        "title": "Assembly of metagenomic sequencing data",
+        "tools": [
+            "random_lines1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.2.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy10",
+            "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
+            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.15.4+galaxy2"
+        ],
+        "topic_name": "microbiome",
+        "topic_name_human": "Microbiome",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "metagenomics-assembly",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-assembly/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-assembly/tutorial.json"
+        },
+        "version": 4,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 177,
+        "visitors": 1613,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCleaned Sequences\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCount Table\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTraining set FASTA\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTraining set Taxonomy\"]\n  4[label=\"Classify.seqs\"]\n  2 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  0 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"Remove.lineage\"]\n  1 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  4 -> 5 [label=\"taxonomy_out\"]\n  6[label=\"Summary.seqs\"]\n  5 -> 6 [label=\"count_out\"]\n  5 -> 6 [label=\"fasta_out\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  1[label=\"metaSPAdes\"]\n  0 -> 1 [label=\"output\"]\n  k833d79ffe16f414c9c41db8dbfa8ed6b[color=lightseagreen,label=\"Output\\nmetaSPAdes on input dataset(s): Scaffolds\"]\n  1 -> k833d79ffe16f414c9c41db8dbfa8ed6b\n  k10319152d2f947d8be41f956a57e86d3[color=lightseagreen,label=\"Output\\nmetaSPAdes on input dataset(s): Assembly graph\"]\n  1 -> k10319152d2f947d8be41f956a57e86d3\n  kb1ffc3a48e394255ac57fd7cfb9c1633[color=lightseagreen,label=\"Output\\nmetaSPAdes on input dataset(s): Assembly graph with scaffolds\"]\n  1 -> kb1ffc3a48e394255ac57fd7cfb9c1633\n  kb6b74c9d5a164725a1d111c1f05ee909[color=lightseagreen,label=\"Output\\nmetaSPAdes on input dataset(s): Contigs\"]\n  1 -> kb6b74c9d5a164725a1d111c1f05ee909\n  2[label=\"MEGAHIT\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Bowtie2\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"megahit contig2fastg\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Quast\"]\n  2 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Bandage Image\"]\n  4 -> 6 [label=\"fastg\"]\n  7[label=\"Bandage Info\"]\n  4 -> 7 [label=\"fastg\"]\n  8[label=\"Column join\"]\n  7 -> 8 [label=\"outfile\"]\n}",
                 "history": [
                     {
                         "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
@@ -153379,695 +155148,559 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Cleaned Sequences"
+                                "name": "Input Dataset Collection"
                             }
                         ],
-                        "label": "Cleaned Sequences",
-                        "name": "Input dataset",
+                        "label": "Input Dataset Collection",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 27,
-                            "top": 123.5
+                            "left": 0.0,
+                            "top": 480
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "817445c0-3b76-4949-bbed-34c88e2a0c59",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "type": "data_collection_input",
+                        "uuid": "cdb65097-d956-4715-9cd4-fadc9b0c07c5",
+                        "workflow_outputs": [
                             {
-                                "description": "",
-                                "name": "Count Table"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "c8ca2f5f-b0f4-4d90-8259-9e4796c4a35f"
                             }
-                        ],
-                        "label": "Count Table",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 304.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "7b43d972-886f-4aae-ab0e-2fd188655cbd",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"metaSPAdes\"];\n  0 -->|output| 1;\n  833d79ff-e16f-414c-9c41-db8dbfa8ed6b[\"Output\\nmetaSPAdes on input dataset(s): Scaffolds\"];\n  1 --> 833d79ff-e16f-414c-9c41-db8dbfa8ed6b;\n  style 833d79ff-e16f-414c-9c41-db8dbfa8ed6b stroke:#2c3143,stroke-width:4px;\n  10319152-d2f9-47d8-be41-f956a57e86d3[\"Output\\nmetaSPAdes on input dataset(s): Assembly graph\"];\n  1 --> 10319152-d2f9-47d8-be41-f956a57e86d3;\n  style 10319152-d2f9-47d8-be41-f956a57e86d3 stroke:#2c3143,stroke-width:4px;\n  b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633[\"Output\\nmetaSPAdes on input dataset(s): Assembly graph with scaffolds\"];\n  1 --> b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633;\n  style b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633 stroke:#2c3143,stroke-width:4px;\n  b6b74c9d-5a16-4725-a1d1-11c1f05ee909[\"Output\\nmetaSPAdes on input dataset(s): Contigs\"];\n  1 --> b6b74c9d-5a16-4725-a1d1-11c1f05ee909;\n  style b6b74c9d-5a16-4725-a1d1-11c1f05ee909 stroke:#2c3143,stroke-width:4px;\n  2[\"MEGAHIT\"];\n  0 -->|output| 2;\n  3[\"Bowtie2\"];\n  0 -->|output| 3;\n  2 -->|output| 3;\n  4[\"megahit contig2fastg\"];\n  2 -->|output| 4;\n  5[\"Quast\"];\n  2 -->|output| 5;\n  0 -->|output| 5;\n  6[\"Bandage Image\"];\n  4 -->|fastg| 6;\n  7[\"Bandage Info\"];\n  4 -->|fastg| 7;\n  8[\"Column join\"];\n  7 -->|outfile| 8;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Metagenomics assembly tutorial workflow",
+                "outputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Training set FASTA"
+                                "name": "Input Dataset Collection"
                             }
                         ],
-                        "label": "Training set FASTA",
-                        "name": "Input dataset",
+                        "label": "Input Dataset Collection",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 4,
-                            "top": 515.5
+                            "left": 0.0,
+                            "top": 480
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f2ee2034-e7ce-43b0-82c9-905c2dd0745c",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
+                        "type": "data_collection_input",
+                        "uuid": "cdb65097-d956-4715-9cd4-fadc9b0c07c5",
+                        "workflow_outputs": [
                             {
-                                "description": "",
-                                "name": "Training set Taxonomy"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "c8ca2f5f-b0f4-4d90-8259-9e4796c4a35f"
                             }
-                        ],
-                        "label": "Training set Taxonomy",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 30,
-                            "top": 694.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f1a29c9e-a70e-4d8c-b7b4-1236da5245a1",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nCleaned Sequences\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nCount Table\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nTraining set FASTA\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nTraining set Taxonomy\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Classify.seqs\"];\n  2 -->|output| 4;\n  1 -->|output| 4;\n  0 -->|output| 4;\n  3 -->|output| 4;\n  5[\"Remove.lineage\"];\n  1 -->|output| 5;\n  0 -->|output| 5;\n  4 -->|taxonomy_out| 5;\n  6[\"Summary.seqs\"];\n  5 -->|count_out| 6;\n  5 -->|fasta_out| 6;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur]",
-                "outputs": [
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.15.4+galaxy2",
                         "errors": null,
-                        "id": 4,
+                        "id": 1,
                         "input_connections": {
-                            "alignment|template": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "count": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "fasta": {
+                            "singlePaired|input": {
                                 "id": 0,
                                 "output_name": "output"
-                            },
-                            "tax|taxonomy": {
-                                "id": 3,
-                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool metaSPAdes",
+                                "name": "arf"
+                            },
+                            {
+                                "description": "runtime parameter for tool metaSPAdes",
+                                "name": "arf"
+                            },
+                            {
+                                "description": "runtime parameter for tool metaSPAdes",
+                                "name": "singlePaired"
+                            }
+                        ],
                         "label": null,
-                        "name": "Classify.seqs",
+                        "name": "metaSPAdes",
                         "outputs": [
                             {
-                                "name": "taxonomy_out",
-                                "type": "mothur.seq.taxonomy"
+                                "name": "out_ag",
+                                "type": "fastg"
                             },
                             {
-                                "name": "tax_summary",
-                                "type": "mothur.tax.summary"
+                                "name": "out_ags",
+                                "type": "txt"
                             },
                             {
-                                "name": "tree_sum",
-                                "type": "tabular"
+                                "name": "out_cn",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "out_sc",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 538,
+                            "left": 247.0,
                             "top": 0
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.15.4+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "09bf9e496c64",
-                            "name": "mothur_classify_seqs",
-                            "owner": "iuc",
+                            "changeset_revision": "fd128c111ab0",
+                            "name": "metaspades",
+                            "owner": "nml",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"alignment\": {\"source\": \"hist\", \"__current_case__\": 1, \"template\": {\"__class__\": \"ConnectedValue\"}}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"classify\": {\"method\": \"wang\", \"__current_case__\": 0, \"ksize\": \"8\", \"iters\": \"100\", \"cutoff\": \"80\", \"probs\": true}, \"count\": {\"__class__\": \"ConnectedValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"name\": null, \"output\": \"simple\", \"printlevel\": \"-1\", \"relabund\": false, \"savelog\": false, \"tax\": {\"source2\": \"hist\", \"__current_case__\": 1, \"taxonomy\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"additional_reads\": {\"selector\": \"false\", \"__current_case__\": 1}, \"arf\": {\"nanopore\": {\"__class__\": \"RuntimeValue\"}, \"pacbio\": {\"__class__\": \"RuntimeValue\"}}, \"kmer_cond\": {\"kmer_sel\": \"manual\", \"__current_case__\": 1, \"manual\": \"21,33,55,77\"}, \"library_number\": \"true\", \"mode_sel\": null, \"optional_output\": [\"ag\", \"ags\", \"cn\", \"sc\"], \"phred_offset\": \"auto\", \"singlePaired\": {\"sPaired\": \"paired_collection\", \"__current_case__\": 2, \"input\": {\"__class__\": \"RuntimeValue\"}, \"type_paired\": \"pe\", \"orientation\": \"fr\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.15.4+galaxy2",
                         "type": "tool",
-                        "uuid": "d57e48c7-34ce-4742-8545-31b9d5c4a53d",
-                        "when": null,
+                        "uuid": "7dc08460-f398-4f1d-9f30-1736cf636a13",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "taxonomy_out",
-                                "uuid": "dd10f8f4-a93e-46be-98d9-1e4d54b22fe0"
+                                "label": "metaSPAdes on input dataset(s): Scaffolds",
+                                "output_name": "out_sc",
+                                "uuid": "833d79ff-e16f-414c-9c41-db8dbfa8ed6b"
                             },
                             {
-                                "label": null,
-                                "output_name": "tree_sum",
-                                "uuid": "964cf5ca-6cb9-477f-8754-88f3bf048da9"
+                                "label": "metaSPAdes on input dataset(s): Assembly graph",
+                                "output_name": "out_ag",
+                                "uuid": "10319152-d2f9-47d8-be41-f956a57e86d3"
                             },
                             {
-                                "label": null,
-                                "output_name": "tax_summary",
-                                "uuid": "b3b100a8-87f2-4ddd-be9e-e7259399c15a"
+                                "label": "metaSPAdes on input dataset(s): Assembly graph with scaffolds",
+                                "output_name": "out_ags",
+                                "uuid": "b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633"
+                            },
+                            {
+                                "label": "metaSPAdes on input dataset(s): Contigs",
+                                "output_name": "out_cn",
+                                "uuid": "b6b74c9d-5a16-4725-a1d1-11c1f05ee909"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
                         "errors": null,
-                        "id": 5,
+                        "id": 2,
                         "input_connections": {
-                            "count": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "fasta_in": {
+                            "input_option|batchmode|pair_input": {
                                 "id": 0,
                                 "output_name": "output"
-                            },
-                            "file|taxonomy": {
-                                "id": 4,
-                                "output_name": "taxonomy_out"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Remove.lineage",
+                        "name": "MEGAHIT",
                         "outputs": [
                             {
-                                "name": "taxonomy_out",
-                                "type": "mothur.seq.taxonomy"
-                            },
-                            {
-                                "name": "fasta_out",
-                                "type": "input"
-                            },
-                            {
-                                "name": "count_out",
-                                "type": "mothur.count_table"
+                                "name": "output",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 781,
-                            "top": 593
+                            "left": 278.0,
+                            "top": 464
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "947faa8b3205",
-                            "name": "mothur_remove_lineage",
+                            "changeset_revision": "14ddfc8ffb93",
+                            "name": "megahit",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"alignreport_in\": null, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"count\": {\"__class__\": \"ConnectedValue\"}, \"dups\": true, \"fasta_in\": {\"__class__\": \"ConnectedValue\"}, \"file\": {\"filetype\": \"usetaxonomy\", \"__current_case__\": 0, \"taxonomy\": {\"__class__\": \"ConnectedValue\"}, \"taxons\": null}, \"group_in\": null, \"list_in\": null, \"name_in\": null, \"savelog\": false, \"taxon\": \"Chloroplast-Mitochondria-unknown-Archaea-Eukaryota\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"advanced_section\": {\"nomercy\": \"false\", \"bubble_level\": \"2\", \"merge_level\": \"20,0.95\", \"prune_level\": \"2\", \"prune_depth\": \"2\", \"disconnect_ratio\": \"0.1\", \"low_local_ratio\": \"0.2\", \"cleaning_rounds\": \"5\", \"nolocal\": \"false\", \"kmin1pass\": \"false\"}, \"basic_section\": {\"min_count\": \"2\", \"k_mer\": {\"k_mer_method\": \"klim_method\", \"__current_case__\": 1, \"k_min\": \"21\", \"k_max\": \"91\", \"k_step\": \"12\"}}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_option\": {\"choice\": \"paired_collection\", \"__current_case__\": 3, \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"pair_input\": {\"__class__\": \"ConnectedValue\"}}}, \"output_section\": {\"min_contig_len\": \"200\", \"show_intermediate_contigs\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.9+galaxy0",
                         "type": "tool",
-                        "uuid": "61870655-5bd1-45bc-a8fe-81b1cf8018a2",
-                        "when": null,
+                        "uuid": "ffbb16f2-580a-4832-8b6d-e67932e24b27",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "taxonomy_out",
-                                "uuid": "cdca67a9-ef60-4162-b3ba-1e502f543fde"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "fasta_out",
-                                "uuid": "7fabef22-b375-4615-8209-9e7f4685faba"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "count_out",
-                                "uuid": "452deac5-f985-4702-9028-083b62cd42c6"
+                                "output_name": "output",
+                                "uuid": "061ac8dd-de43-467d-9c15-a4f46a125103"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
                         "errors": null,
-                        "id": 6,
+                        "id": 3,
                         "input_connections": {
-                            "count": {
-                                "id": 5,
-                                "output_name": "count_out"
+                            "library|input_1": {
+                                "id": 0,
+                                "output_name": "output"
                             },
-                            "fasta": {
-                                "id": 5,
-                                "output_name": "fasta_out"
+                            "reference_genome|own_file": {
+                                "id": 2,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Summary.seqs",
-                                "name": "count"
-                            },
-                            {
-                                "description": "runtime parameter for tool Summary.seqs",
-                                "name": "fasta"
-                            },
-                            {
-                                "description": "runtime parameter for tool Summary.seqs",
-                                "name": "name"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Summary.seqs",
+                        "name": "Bowtie2",
                         "outputs": [
                             {
-                                "name": "logfile",
-                                "type": "txt"
+                                "name": "output",
+                                "type": "bam"
                             },
                             {
-                                "name": "out_summary",
-                                "type": "mothur.summary"
+                                "name": "mapping_stats",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 1128.25,
-                            "top": 788.0624885559082
+                            "left": 556.0,
+                            "top": 130
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "609770e516fa",
-                            "name": "mothur_summary_seqs",
-                            "owner": "iuc",
+                            "changeset_revision": "03e9b2fbc005",
+                            "name": "bowtie2",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"count\": {\"__class__\": \"RuntimeValue\"}, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"name\": {\"__class__\": \"RuntimeValue\"}, \"savelog\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"no_presets\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": \"false\", \"aligned_file\": \"false\", \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"own_file|__identifier__\": \"ERR2231567\", \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 1, \"own_file\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.5.0+galaxy0",
                         "type": "tool",
-                        "uuid": "c399d175-5b43-45b1-9916-f2f11f1cad25",
-                        "when": null,
+                        "uuid": "9f445c6b-31c9-4ff0-b559-6be00fb0fc17",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "logfile",
-                                "uuid": "2ba6776c-d197-4804-9654-039b997986ce"
+                                "output_name": "mapping_stats",
+                                "uuid": "ff350260-91cd-4f01-a82f-f64e8eddd4ed"
                             },
                             {
                                 "label": null,
-                                "output_name": "out_summary",
-                                "uuid": "b5e93d2a-6ff7-48bb-aa4e-5a58683910c8"
+                                "output_name": "output",
+                                "uuid": "2fa389b6-088a-4686-94e9-de884f86e1b7"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "microbiome/mothur-miseq-sop-short",
-                "path": "topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow3_classification.ga",
-                "tags": [
-                    "microbiome"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur]",
-                "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-mothur-miseq-sop-short/versions/workflow3-classification",
-                "tutorial_id": "mothur-miseq-sop-short",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow3_classification.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow3_classification.html",
-                "version": 1,
-                "wfid": "microbiome-mothur-miseq-sop-short",
-                "wfname": "workflow3-classification",
-                "workflow": "workflow3_classification.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0"
-                ],
-                "workflowhub_id": "1060"
-            },
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0003-3803-468X",
-                        "name": "Saskia Hiltemann"
-                    }
-                ],
-                "description": "16S Microbial Analysis with mothur (short)",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMock Count Table\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMock Sequences\"]\n  2[label=\"Dist.seqs\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"Cluster\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"out_dist\"]\n  4[label=\"Make.shared\"]\n  0 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"otulist\"]\n  5[label=\"Rarefaction.single\"]\n  4 -> 5 [label=\"shared\"]\n}",
-                "history": [
-                    {
-                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
-                        "message": "Rename metagenomics topic to microbiome",
-                        "num": 1,
-                        "short_hash": "0e0a2f2cc",
-                        "unix": "1704901629"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Mock Count Table"
-                            }
-                        ],
-                        "label": "Mock Count Table",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 11
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "3c149509-370a-47f2-9f6d-a0fadcd7c1b6",
-                        "when": null,
-                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Mock Sequences"
-                            }
-                        ],
-                        "label": "Mock Sequences",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 7,
-                            "top": 259
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "c020d492-fb13-43c7-85e3-faa820866965",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nMock Count Table\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nMock Sequences\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Dist.seqs\"];\n  1 -->|output| 2;\n  3[\"Cluster\"];\n  0 -->|output| 3;\n  2 -->|out_dist| 3;\n  4[\"Make.shared\"];\n  0 -->|output| 4;\n  3 -->|otulist| 4;\n  5[\"Rarefaction.single\"];\n  4 -->|shared| 5;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1",
                         "errors": null,
-                        "id": 2,
+                        "id": 4,
                         "input_connections": {
-                            "fasta": {
-                                "id": 1,
+                            "contigs": {
+                                "id": 2,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Dist.seqs",
+                        "name": "megahit contig2fastg",
                         "outputs": [
                             {
-                                "name": "out_dist",
-                                "type": "mothur.pair.dist"
+                                "name": "fastg",
+                                "type": "fastg"
                             }
                         ],
                         "position": {
-                            "left": 276,
-                            "top": 319
+                            "left": 556.0,
+                            "top": 444
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "0554c9338ca0",
-                            "name": "mothur_dist_seqs",
+                            "changeset_revision": "4ec5b3777508",
+                            "name": "megahit_contig2fastg",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"calc\": \"\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"countends\": true, \"cutoff\": \"0.2\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"output\": \"\", \"savelog\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"contigs\": {\"__class__\": \"ConnectedValue\"}, \"contigs|__identifier__\": \"ERR2231567\", \"kmer\": \"91\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.3+galaxy1",
                         "type": "tool",
-                        "uuid": "925be8d7-7355-4a1d-b375-b27826e4cd2e",
-                        "when": null,
+                        "uuid": "c839a8b8-c719-474d-957e-d94614491f13",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_dist",
-                                "uuid": "28fe4e3d-5be8-47e8-9cd3-527e8657c391"
+                                "output_name": "fastg",
+                                "uuid": "91718981-2ae5-4cdd-8007-0ce9cc3c68f6"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0",
                         "errors": null,
-                        "id": 3,
+                        "id": 5,
                         "input_connections": {
-                            "count": {
-                                "id": 0,
+                            "in|inputs": {
+                                "id": 2,
                                 "output_name": "output"
                             },
-                            "matrix|dist": {
-                                "id": 2,
-                                "output_name": "out_dist"
+                            "reads|input_1": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Cluster",
+                        "name": "Quast",
                         "outputs": [
                             {
-                                "name": "rabund",
-                                "type": "mothur.rabund"
+                                "name": "metrics_tabular",
+                                "type": "input"
                             },
                             {
-                                "name": "sabund",
-                                "type": "mothur.sabund"
+                                "name": "metrics_pdf",
+                                "type": "input"
                             },
                             {
-                                "name": "otulist",
-                                "type": "mothur.list"
+                                "name": "report_tabular_meta",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "report_html_meta",
+                                "type": "html"
+                            },
+                            {
+                                "name": "log_meta",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "krona",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 570,
-                            "top": 189
+                            "left": 556.0,
+                            "top": 636
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "528f950d1044",
-                            "name": "mothur_cluster",
+                            "changeset_revision": "3061c8b029e5",
+                            "name": "quast",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"count\": {\"__class__\": \"ConnectedValue\"}, \"cutoff\": \"0.0\", \"matrix\": {\"format\": \"column\", \"__current_case__\": 0, \"dist\": {\"__class__\": \"ConnectedValue\"}, \"name\": null}, \"precision\": \"100\", \"savelog\": false, \"select_method\": {\"method\": \"opti\", \"__current_case__\": 5, \"metric\": \"mcc\", \"initialize\": \"singleton\", \"delta\": \"0.0001\", \"iters\": \"100\"}, \"sim\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": \"false\", \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": \"true\", \"fragmented_max_indent\": null, \"report_all_metrics\": \"false\", \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": \"false\", \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": \"false\", \"upper_bound_assembly\": \"false\", \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"metagenome\", \"__current_case__\": 1, \"ref\": {\"origin\": \"none\", \"__current_case__\": 3}, \"reuse_combined_alignments\": \"false\", \"min_identity\": \"90.0\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": \"false\", \"conserved_genes_finding\": \"false\"}, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"large\": \"false\", \"min_contig\": \"500\", \"output_files\": [\"html\", \"pdf\", \"tabular\", \"log\", \"summary\", \"krona\"], \"reads\": {\"reads_option\": \"paired_collection\", \"__current_case__\": 3, \"input_1\": {\"__class__\": \"ConnectedValue\"}}, \"split_scaffolds\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.2.0+galaxy0",
                         "type": "tool",
-                        "uuid": "3f508523-34c1-420a-a0b6-2524b4d85b52",
-                        "when": null,
+                        "uuid": "12072d4c-8ad5-4de1-bbe2-3b081b8373be",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "rabund",
-                                "uuid": "5f143144-eb84-4f88-9f57-87154dc29671"
+                                "output_name": "log_meta",
+                                "uuid": "33c6424f-fceb-45d1-9462-ea3e7cda79ea"
                             },
                             {
                                 "label": null,
-                                "output_name": "otulist",
-                                "uuid": "3e79d92c-11c6-48f5-a0c2-cbf747690b2e"
+                                "output_name": "krona",
+                                "uuid": "44457a4b-760c-4080-b552-dc4724906b2c"
                             },
                             {
                                 "label": null,
-                                "output_name": "sabund",
-                                "uuid": "a698d39c-c469-4867-9450-f9d80446d99f"
+                                "output_name": "metrics_tabular",
+                                "uuid": "9b2b72ac-a297-46a2-883f-8f1704664cf3"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "report_tabular_meta",
+                                "uuid": "1259f3a1-4952-48f1-be69-0fde3b6be9de"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "report_html_meta",
+                                "uuid": "b8f1b46c-1421-4952-9e87-1790bdd076df"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "metrics_pdf",
+                                "uuid": "ac4aa63b-5dc1-4b4c-bbb0-6afce689f0d2"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4",
                         "errors": null,
-                        "id": 4,
+                        "id": 6,
                         "input_connections": {
-                            "intype|group": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "intype|otu": {
-                                "id": 3,
-                                "output_name": "otulist"
+                            "input_file": {
+                                "id": 4,
+                                "output_name": "fastg"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Make.shared",
+                        "name": "Bandage Image",
                         "outputs": [
                             {
-                                "name": "logfile",
-                                "type": "txt"
-                            },
+                                "name": "outfile",
+                                "type": "jpg"
+                            }
+                        ],
+                        "position": {
+                            "left": 834.0,
+                            "top": 466
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "21e491ad532a",
+                            "name": "bandage",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fontsize\": null, \"height\": \"1000\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"input_file|__identifier__\": \"ERR2231567\", \"lengths\": \"false\", \"names\": \"false\", \"nodewidth\": null, \"output_format\": \"jpg\", \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.8.1+galaxy4",
+                        "type": "tool",
+                        "uuid": "31b35530-ae7f-4e9c-8021-6983cf3f3401",
+                        "workflow_outputs": [
                             {
-                                "name": "shared",
-                                "type": "mothur.shared"
-                            },
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "e02c022d-3067-40ce-8bb6-4cc258d8523a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 4,
+                                "output_name": "fastg"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Bandage Info",
+                        "outputs": [
                             {
-                                "name": "groupout",
-                                "type": "mothur.groups"
+                                "name": "outfile",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 898,
-                            "top": 0
+                            "left": 834.0,
+                            "top": 679
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "0851ae17c58e",
-                            "name": "mothur_make_shared",
+                            "changeset_revision": "b9e31c5c01c7",
+                            "name": "bandage",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"intype\": {\"infile\": \"otulist\", \"__current_case__\": 0, \"otu\": {\"__class__\": \"ConnectedValue\"}, \"group\": {\"__class__\": \"ConnectedValue\"}, \"label\": [\"0.03\"], \"groups\": null}, \"savelog\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"input_file|__identifier__\": \"ERR2231567\", \"tsv\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.8.1+galaxy2",
                         "type": "tool",
-                        "uuid": "72197339-b027-4c3e-85ba-edf401b82322",
-                        "when": null,
+                        "uuid": "b63e03dc-b9be-4a72-ac81-64b63ddf99f2",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "shared",
-                                "uuid": "1d80db8c-04f6-45a0-a523-f87c7a4b87cf"
+                                "output_name": "outfile",
+                                "uuid": "6bd3194a-9e8c-4677-b42c-2fb3bd1116f3"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
                         "errors": null,
-                        "id": 5,
+                        "id": 8,
                         "input_connections": {
-                            "otu": {
-                                "id": 4,
-                                "output_name": "shared"
+                            "input_tabular": {
+                                "id": 7,
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Rarefaction.single",
+                        "name": "Column join",
                         "outputs": [
                             {
-                                "name": "rarefactioncurves",
-                                "type": "input"
+                                "name": "tabular_output",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1172,
-                            "top": 211
+                            "left": 1112.0,
+                            "top": 732
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "af521db77c56",
-                            "name": "mothur_rarefaction_single",
+                            "changeset_revision": "3ddd99c7efee",
+                            "name": "collection_column_join",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"abund\": \"10\", \"calc\": [\"sobs\"], \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"freq\": \"100.0\", \"iters\": \"1000\", \"label\": null, \"otu\": {\"__class__\": \"ConnectedValue\"}, \"savelog\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fill_char\": \".\", \"has_header\": \"0\", \"identifier_column\": \"1\", \"include_outputs\": null, \"input_tabular\": {\"__class__\": \"ConnectedValue\"}, \"old_col_in_header\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.0.3",
                         "type": "tool",
-                        "uuid": "6982780b-f8ac-4ff8-b862-29557494d9b4",
-                        "when": null,
+                        "uuid": "e9dc42b2-c638-4b9c-af5f-ce84f6b0d654",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "rarefactioncurves",
-                                "uuid": "cbf4d013-fa83-4bd9-9f97-1e3632362b36"
+                                "output_name": "tabular_output",
+                                "uuid": "fe5b4460-6fa0-48a8-84e7-b3b8270e9b8f"
                             }
                         ]
                     }
                 ],
-                "parent_id": "microbiome/mothur-miseq-sop-short",
-                "path": "topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow4_mock_otu_clustering.ga",
-                "tags": [
-                    "microbiome"
-                ],
+                "parent_id": "microbiome/metagenomics-assembly",
+                "path": "topics/microbiome/tutorials/metagenomics-assembly/workflows/metagenomics_assembly_tutorial_workflow.ga",
+                "tags": [],
                 "test_results": null,
                 "tests": false,
-                "title": "Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]",
+                "title": "Metagenomics assembly tutorial workflow",
                 "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-mothur-miseq-sop-short/versions/workflow4-mock-otu-clustering",
-                "tutorial_id": "mothur-miseq-sop-short",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow4_mock_otu_clustering.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow4_mock_otu_clustering.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-metagenomics-assembly/versions/metagenomics-assembly-tutorial-workflow",
+                "tutorial_id": "metagenomics-assembly",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metagenomics-assembly/workflows/metagenomics_assembly_tutorial_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metagenomics-assembly/workflows/metagenomics_assembly_tutorial_workflow.html",
                 "version": 1,
-                "wfid": "microbiome-mothur-miseq-sop-short",
-                "wfname": "workflow4-mock-otu-clustering",
-                "workflow": "workflow4_mock_otu_clustering.ga",
+                "wfid": "microbiome-metagenomics-assembly",
+                "wfname": "metagenomics-assembly-tutorial-workflow",
+                "workflow": "metagenomics_assembly_tutorial_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0"
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.15.4+galaxy2"
                 ],
-                "workflowhub_id": "1125"
+                "workflowhub_id": "1103"
             },
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0003-3803-468X",
-                        "name": "Saskia Hiltemann"
-                    }
-                ],
-                "description": "16S Microbial Analysis with mothur (short)",
+                "creators": [],
+                "description": "",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSequences\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCount Table\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTaxonomy\"]\n  3[label=\"Remove.groups\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Cluster.split\"]\n  3 -> 4 [label=\"fasta_out\"]\n  3 -> 4 [label=\"count_out\"]\n  3 -> 4 [label=\"taxonomy_out\"]\n  5[label=\"Make.shared\"]\n  3 -> 5 [label=\"count_out\"]\n  4 -> 5 [label=\"otulist\"]\n  6[label=\"Classify.otu\"]\n  3 -> 6 [label=\"count_out\"]\n  4 -> 6 [label=\"otulist\"]\n  3 -> 6 [label=\"taxonomy_out\"]\n  7[label=\"Count.groups\"]\n  5 -> 7 [label=\"shared\"]\n  8[label=\"Sub.sample\"]\n  5 -> 8 [label=\"shared\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nERR2231567_1.fastq.gz\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nERR2231567_2.fastq.gz\"]\n  2[label=\"Cutadapt\"]\n  0 -> 2 [label=\"output\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"MEGAHIT\"]\n  2 -> 3 [label=\"out1\"]\n  2 -> 3 [label=\"out2\"]\n  4[label=\"Bowtie2\"]\n  2 -> 4 [label=\"out1\"]\n  2 -> 4 [label=\"out2\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"BAM filter\"]\n  4 -> 5 [label=\"output\"]\n  6[label=\"BAM filter\"]\n  4 -> 6 [label=\"output\"]\n  7[label=\"Convert, Merge, Randomize\"]\n  5 -> 7 [label=\"outfile\"]\n  8[label=\"Convert, Merge, Randomize\"]\n  6 -> 8 [label=\"outfile\"]\n  9[label=\"Select random lines\"]\n  7 -> 9 [label=\"out_file1\"]\n  10[label=\"Select random lines\"]\n  8 -> 10 [label=\"out_file1\"]\n  11[label=\"Filter Tabular\"]\n  9 -> 11 [label=\"out_file1\"]\n  12[label=\"Filter Tabular\"]\n  10 -> 12 [label=\"out_file1\"]\n  13[label=\"Unique\"]\n  11 -> 13 [label=\"output\"]\n  14[label=\"Unique\"]\n  12 -> 14 [label=\"output\"]\n  15[label=\"Concatenate datasets\"]\n  13 -> 15 [label=\"outfile\"]\n  14 -> 15 [label=\"outfile\"]\n  16[label=\"seqtk_subseq\"]\n  2 -> 16 [label=\"out1\"]\n  15 -> 16 [label=\"out_file1\"]\n  17[label=\"seqtk_subseq\"]\n  2 -> 17 [label=\"out2\"]\n  15 -> 17 [label=\"out_file1\"]\n  18[label=\"FastQC\"]\n  16 -> 18 [label=\"default\"]\n  19[label=\"FastQC\"]\n  17 -> 19 [label=\"default\"]\n}",
                 "history": [
                     {
                         "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
@@ -154087,27 +155720,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Sequences"
+                                "name": "ERR2231567_1.fastq.gz"
                             }
                         ],
-                        "label": "Sequences",
+                        "label": "ERR2231567_1.fastq.gz",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 16.300003051757812,
-                            "height": 61.80000305175781,
-                            "left": 116,
-                            "right": 316,
-                            "top": -45.5,
-                            "width": 200,
-                            "x": 116,
-                            "y": -45.5
+                            "left": 0,
+                            "top": 174.98046875
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "9cdb4877-1fdf-41a7-8089-5f2ffcabbdda",
+                        "uuid": "ac2a7e31-6a0c-43f0-b39f-6764ae421dea",
                         "workflow_outputs": []
                     },
                     {
@@ -154119,1226 +155746,971 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Count Table"
-                            }
-                        ],
-                        "label": "Count Table",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 139.3000030517578,
-                            "height": 61.80000305175781,
-                            "left": 118,
-                            "right": 318,
-                            "top": 77.5,
-                            "width": 200,
-                            "x": 118,
-                            "y": 77.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "c3ebf885-3d00-4db6-828b-8c9af54f77c7",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Taxonomy"
+                                "name": "ERR2231567_2.fastq.gz"
                             }
                         ],
-                        "label": "Taxonomy",
+                        "label": "ERR2231567_2.fastq.gz",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 294.3000030517578,
-                            "height": 61.80000305175781,
-                            "left": 119,
-                            "right": 319,
-                            "top": 232.5,
-                            "width": 200,
-                            "x": 119,
-                            "y": 232.5
+                            "left": 1.03515625,
+                            "top": 365.0
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "2d1cebdc-28da-4686-8a5b-0043b34c9aac",
+                        "uuid": "2e1fd5bf-3b01-49dd-a091-75c7215eb3f9",
                         "workflow_outputs": []
                     }
                 ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSequences\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nCount Table\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nTaxonomy\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Remove.groups\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  2 -->|output| 3;\n  4[\"Cluster.split\"];\n  3 -->|fasta_out| 4;\n  3 -->|count_out| 4;\n  3 -->|taxonomy_out| 4;\n  5[\"Make.shared\"];\n  3 -->|count_out| 5;\n  4 -->|otulist| 5;\n  6[\"Classify.otu\"];\n  3 -->|count_out| 6;\n  4 -->|otulist| 6;\n  3 -->|taxonomy_out| 6;\n  7[\"Count.groups\"];\n  5 -->|shared| 7;\n  8[\"Sub.sample\"];\n  5 -->|shared| 8;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nERR2231567_1.fastq.gz\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nERR2231567_2.fastq.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Cutadapt\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"MEGAHIT\"];\n  2 -->|out1| 3;\n  2 -->|out2| 3;\n  4[\"Bowtie2\"];\n  2 -->|out1| 4;\n  2 -->|out2| 4;\n  3 -->|output| 4;\n  5[\"BAM filter\"];\n  4 -->|output| 5;\n  6[\"BAM filter\"];\n  4 -->|output| 6;\n  7[\"Convert, Merge, Randomize\"];\n  5 -->|outfile| 7;\n  8[\"Convert, Merge, Randomize\"];\n  6 -->|outfile| 8;\n  9[\"Select random lines\"];\n  7 -->|out_file1| 9;\n  10[\"Select random lines\"];\n  8 -->|out_file1| 10;\n  11[\"Filter Tabular\"];\n  9 -->|out_file1| 11;\n  12[\"Filter Tabular\"];\n  10 -->|out_file1| 12;\n  13[\"Unique\"];\n  11 -->|output| 13;\n  14[\"Unique\"];\n  12 -->|output| 14;\n  15[\"Concatenate datasets\"];\n  13 -->|outfile| 15;\n  14 -->|outfile| 15;\n  16[\"seqtk_subseq\"];\n  2 -->|out1| 16;\n  15 -->|out_file1| 16;\n  17[\"seqtk_subseq\"];\n  2 -->|out2| 17;\n  15 -->|out_file1| 17;\n  18[\"FastQC\"];\n  16 -->|default| 18;\n  19[\"FastQC\"];\n  17 -->|default| 19;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "workflow-generate-dataset-for-assembly-tutorial",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0",
                         "errors": null,
-                        "id": 3,
+                        "id": 2,
                         "input_connections": {
-                            "groupnames|fasta_in": {
+                            "library|input_1": {
                                 "id": 0,
                                 "output_name": "output"
                             },
-                            "groupnames|group_in": {
+                            "library|input_2": {
                                 "id": 1,
                                 "output_name": "output"
-                            },
-                            "groupnames|taxonomy_in": {
-                                "id": 2,
-                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Remove.groups",
-                                "name": "groupnames"
-                            },
-                            {
-                                "description": "runtime parameter for tool Remove.groups",
-                                "name": "groupnames"
-                            },
-                            {
-                                "description": "runtime parameter for tool Remove.groups",
-                                "name": "groupnames"
-                            },
-                            {
-                                "description": "runtime parameter for tool Remove.groups",
-                                "name": "groupnames"
-                            },
-                            {
-                                "description": "runtime parameter for tool Remove.groups",
-                                "name": "groupnames"
-                            },
-                            {
-                                "description": "runtime parameter for tool Remove.groups",
-                                "name": "groupnames"
-                            },
-                            {
-                                "description": "runtime parameter for tool Remove.groups",
-                                "name": "groupnames"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Remove.groups",
+                        "name": "Cutadapt",
                         "outputs": [
                             {
-                                "name": "list_out",
-                                "type": "input"
-                            },
-                            {
-                                "name": "fasta_out",
-                                "type": "input"
-                            },
-                            {
-                                "name": "group_out",
-                                "type": "mothur.groups"
-                            },
-                            {
-                                "name": "count_out",
-                                "type": "mothur.count_table"
-                            },
-                            {
-                                "name": "name_out",
-                                "type": "mothur.names"
-                            },
-                            {
-                                "name": "taxonomy_out",
-                                "type": "mothur.seq.taxonomy"
-                            },
-                            {
-                                "name": "phylip_out",
-                                "type": "input"
+                                "name": "out1",
+                                "type": "fastqsanger"
                             },
                             {
-                                "name": "column_out",
-                                "type": "mothur.pair.dist"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 1023.2999877929688,
-                            "height": 916.7999877929688,
-                            "left": 383,
-                            "right": 583,
-                            "top": 106.5,
-                            "width": 200,
-                            "x": 383,
-                            "y": 106.5
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionfasta_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "fasta_out"
-                            },
-                            "HideDatasetActionlist_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "list_out"
-                            },
-                            "HideDatasetActionname_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "name_out"
+                                "name": "out2",
+                                "type": "fastqsanger"
                             },
-                            "HideDatasetActiontaxonomy_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "taxonomy_out"
+                            {
+                                "name": "report",
+                                "type": "txt"
                             }
+                        ],
+                        "position": {
+                            "left": 248.0078125,
+                            "top": 260.0
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "498dc0671d9e",
-                            "name": "mothur_remove_groups",
-                            "owner": "iuc",
+                            "changeset_revision": "5915ea1ec9b1",
+                            "name": "cutadapt",
+                            "owner": "lparsons",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"groupnames\": {\"source\": \"other\", \"__current_case__\": 0, \"group_in\": {\"__class__\": \"RuntimeValue\"}, \"groups\": \"Mock\", \"fasta_in\": {\"__class__\": \"RuntimeValue\"}, \"name_in\": {\"__class__\": \"RuntimeValue\"}, \"list_in\": {\"__class__\": \"RuntimeValue\"}, \"taxonomy_in\": {\"__class__\": \"RuntimeValue\"}, \"phylip_in\": {\"__class__\": \"RuntimeValue\"}, \"column_in\": {\"__class__\": \"RuntimeValue\"}}, \"savelog\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"internal\": \"\", \"error_rate\": \"0.1\", \"no_indels\": \"false\", \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"revcomp\": \"false\"}, \"filter_options\": {\"discard_trimmed\": \"false\", \"discard_untrimmed\": \"false\", \"minimum_length\": \"200\", \"maximum_length\": null, \"length_R2_options\": {\"length_R2_status\": \"False\", \"__current_case__\": 1}, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"discard_cassava\": \"false\"}, \"library\": {\"type\": \"paired\", \"__current_case__\": 1, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"input_2\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}, \"r2\": {\"adapters2\": [], \"front_adapters2\": [], \"anywhere_adapters2\": [], \"cut2\": \"0\", \"quality_cutoff2\": \"\"}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"quality_cutoff\": \"20\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"strip_suffix\": \"\", \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.0+galaxy0",
                         "type": "tool",
-                        "uuid": "90df5fc1-b437-48c1-a7d3-39062fef6c0b",
+                        "uuid": "67ddef5c-cde3-462d-a189-77028682a357",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "group_out",
-                                "uuid": "3800548f-2976-4a6d-8b29-e501373719fd"
+                                "output_name": "out1",
+                                "uuid": "7b3621e4-5077-4ac8-95d3-61a94a6ee664"
                             },
                             {
                                 "label": null,
-                                "output_name": "phylip_out",
-                                "uuid": "20631d19-d683-47c6-8ae1-7e856e242e8d"
+                                "output_name": "out2",
+                                "uuid": "f7db5a96-f4e7-4caf-8e78-093d4e6b007c"
                             },
                             {
                                 "label": null,
-                                "output_name": "count_out",
-                                "uuid": "bcd6f559-2b50-4c77-bf9c-9b9de5c7159a"
+                                "output_name": "report",
+                                "uuid": "ff6985ad-6afe-4cf7-9def-223fdd5e5f62"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "input_option|fastq_input1": {
+                                "id": 2,
+                                "output_name": "out1"
                             },
+                            "input_option|fastq_input2": {
+                                "id": 2,
+                                "output_name": "out2"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "MEGAHIT",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "left": 735.9765625,
+                            "top": 301.97265625
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "14ddfc8ffb93",
+                            "name": "megahit",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"advanced_section\": {\"nomercy\": \"false\", \"bubble_level\": \"2\", \"merge_level\": \"20,0.95\", \"prune_level\": \"2\", \"prune_depth\": \"2\", \"disconnect_ratio\": \"0.1\", \"low_local_ratio\": \"0.2\", \"cleaning_rounds\": \"5\", \"nolocal\": \"false\", \"kmin1pass\": \"false\"}, \"basic_section\": {\"min_count\": \"2\", \"k_mer\": {\"k_mer_method\": \"klist_method\", \"__current_case__\": 0, \"k_list\": \"21,29,39,59,79,99,119,141\"}}, \"input_option\": {\"choice\": \"paired\", \"__current_case__\": 2, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"fastq_input2\": {\"__class__\": \"ConnectedValue\"}}, \"output_section\": {\"min_contig_len\": \"200\", \"show_intermediate_contigs\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.9+galaxy0",
+                        "type": "tool",
+                        "uuid": "0e1e0ffb-4536-4802-b886-5f5f391255d1",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "column_out",
-                                "uuid": "20bf370c-7d36-4579-b94c-ac816d789717"
+                                "output_name": "output",
+                                "uuid": "7a0e5487-3923-46e0-9976-d3fdc3fe7e09"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
                         "errors": null,
                         "id": 4,
                         "input_connections": {
-                            "splitby|fasta": {
-                                "id": 3,
-                                "output_name": "fasta_out"
+                            "library|input_1": {
+                                "id": 2,
+                                "output_name": "out1"
                             },
-                            "splitby|nameOrCount": {
-                                "id": 3,
-                                "output_name": "count_out"
+                            "library|input_2": {
+                                "id": 2,
+                                "output_name": "out2"
                             },
-                            "splitby|taxonomy": {
+                            "reference_genome|own_file": {
                                 "id": 3,
-                                "output_name": "taxonomy_out"
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Cluster.split",
+                        "name": "Bowtie2",
                         "outputs": [
                             {
-                                "name": "rabund",
-                                "type": "mothur.rabund"
-                            },
-                            {
-                                "name": "sabund",
-                                "type": "mothur.sabund"
-                            },
-                            {
-                                "name": "otulist",
-                                "type": "mothur.list"
+                                "name": "output",
+                                "type": "bam"
                             },
                             {
-                                "name": "sensspec",
+                                "name": "mapping_stats",
                                 "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 530.7000122070312,
-                            "height": 449.20001220703125,
-                            "left": 748,
-                            "right": 948,
-                            "top": 81.5,
-                            "width": 200,
-                            "x": 748,
-                            "y": 81.5
+                            "left": 979.00390625,
+                            "top": 40.9765625
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "1b7fd1678230",
-                            "name": "mothur_cluster_split",
-                            "owner": "iuc",
+                            "changeset_revision": "f6877ad76b00",
+                            "name": "bowtie2",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cluster\": \"true\", \"cutoff\": \"0.03\", \"large\": \"false\", \"precision\": \"100\", \"runsensspec\": \"true\", \"savelog\": \"false\", \"splitby\": {\"splitmethod\": \"fasta\", \"__current_case__\": 2, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"taxonomy\": {\"__class__\": \"ConnectedValue\"}, \"nameOrCount\": {\"__class__\": \"ConnectedValue\"}, \"taxlevel\": \"4\", \"classic\": \"false\", \"condmethod\": {\"method\": \"opti\", \"__current_case__\": 5, \"metric\": \"mcc\", \"initialize\": \"singleton\", \"delta\": \"0.0001\", \"iters\": \"100\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"no_presets\"}, \"library\": {\"type\": \"paired\", \"__current_case__\": 1, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"input_2\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": \"false\", \"aligned_file\": \"false\", \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 1, \"own_file\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.4.5+galaxy1",
                         "type": "tool",
-                        "uuid": "7dc5dce4-98b8-4ab3-9979-7dbe43d88b7e",
+                        "uuid": "cd8574f0-da3e-4dc1-848e-6f21c57831e6",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "otulist",
-                                "uuid": "e5100715-48a0-4ceb-a5d3-7003a43a747e"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "rabund",
-                                "uuid": "3757ba3c-d4ba-46c7-b141-23f43678e392"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "sensspec",
-                                "uuid": "f0e63d07-0f12-4ea0-b2ad-9ae6d16cd5bd"
+                                "output_name": "mapping_stats",
+                                "uuid": "cf119c49-eee7-448a-bfff-0f1053f87821"
                             },
                             {
                                 "label": null,
-                                "output_name": "sabund",
-                                "uuid": "9aecf4a0-cffa-49fd-9b5b-97d99fa7e2d2"
+                                "output_name": "output",
+                                "uuid": "44b0908f-2158-4ea2-be6f-65c0dd803bcb"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
                         "errors": null,
                         "id": 5,
                         "input_connections": {
-                            "intype|group": {
-                                "id": 3,
-                                "output_name": "count_out"
-                            },
-                            "intype|otu": {
+                            "infile": {
                                 "id": 4,
-                                "output_name": "otulist"
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Make.shared",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "shared",
-                                "type": "mothur.shared"
+                                "description": "runtime parameter for tool BAM filter",
+                                "name": "excludebed"
                             },
                             {
-                                "name": "groupout",
-                                "type": "mothur.groups"
+                                "description": "runtime parameter for tool BAM filter",
+                                "name": "includebed"
+                            }
+                        ],
+                        "label": null,
+                        "name": "BAM filter",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "bam"
                             }
                         ],
                         "position": {
-                            "bottom": 445.8999938964844,
-                            "height": 276.3999938964844,
-                            "left": 1077,
-                            "right": 1277,
-                            "top": 169.5,
-                            "width": 200,
-                            "x": 1077,
-                            "y": 169.5
+                            "left": 1265.01953125,
+                            "top": 0.0
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
                         "tool_shed_repository": {
-                            "changeset_revision": "0851ae17c58e",
-                            "name": "mothur_make_shared",
+                            "changeset_revision": "2e957d4c4b95",
+                            "name": "ngsutils_bam_filter",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"intype\": {\"infile\": \"otulist\", \"__current_case__\": 0, \"otu\": {\"__class__\": \"ConnectedValue\"}, \"group\": {\"__class__\": \"ConnectedValue\"}, \"label\": [\"0.03\"], \"groups\": null}, \"savelog\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"excludebed\": {\"__class__\": \"RuntimeValue\"}, \"excluderef\": \"\", \"ignore_strand\": \"false\", \"includebed\": {\"__class__\": \"RuntimeValue\"}, \"includeref\": \"\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mapped\": \"false\", \"mask\": \"\", \"maximum_mismatch_ratio\": null, \"maxlen\": null, \"minlen\": null, \"mismatch\": null, \"nopcrdup\": \"false\", \"noproperpair\": \"false\", \"noqcfail\": \"false\", \"nosecondary\": \"false\", \"properpair\": \"false\", \"uniq\": \"-1\", \"uniq_start\": \"false\", \"unmapped\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.5.9",
                         "type": "tool",
-                        "uuid": "57884bfc-06d6-4a1e-86cc-eb2ba23d6fe2",
+                        "uuid": "e2b45ca6-2a67-4b95-a454-5c67fa87bccb",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "shared",
-                                "uuid": "f04218ea-84e1-489e-9d92-c44ad03414db"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "groupout",
-                                "uuid": "6166859b-cc80-475b-97ff-f082289c1b56"
+                                "output_name": "outfile",
+                                "uuid": "c1c6c99c-c810-41f4-84f3-5998c50b1422"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
                         "errors": null,
                         "id": 6,
                         "input_connections": {
-                            "count": {
-                                "id": 3,
-                                "output_name": "count_out"
-                            },
-                            "otu": {
+                            "infile": {
                                 "id": 4,
-                                "output_name": "otulist"
-                            },
-                            "tax|taxonomy": {
-                                "id": 3,
-                                "output_name": "taxonomy_out"
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Classify.otu",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "taxsummaries",
-                                "type": "input"
+                                "description": "runtime parameter for tool BAM filter",
+                                "name": "excludebed"
                             },
                             {
-                                "name": "taxonomies",
-                                "type": "input"
+                                "description": "runtime parameter for tool BAM filter",
+                                "name": "includebed"
+                            }
+                        ],
+                        "label": null,
+                        "name": "BAM filter",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "bam"
                             }
                         ],
                         "position": {
-                            "bottom": 984.2999877929688,
-                            "height": 428.79998779296875,
-                            "left": 1121,
-                            "right": 1321,
-                            "top": 555.5,
-                            "width": 200,
-                            "x": 1121,
-                            "y": 555.5
+                            "left": 1268.0078125,
+                            "top": 354.00390625
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
                         "tool_shed_repository": {
-                            "changeset_revision": "02446d12c359",
-                            "name": "mothur_classify_otu",
+                            "changeset_revision": "2e957d4c4b95",
+                            "name": "ngsutils_bam_filter",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"basis\": \"otu\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"count\": {\"__class__\": \"ConnectedValue\"}, \"cutoff\": \"60\", \"group\": null, \"label\": [\"0.03\"], \"name\": null, \"otu\": {\"__class__\": \"ConnectedValue\"}, \"output\": \"simple\", \"persample\": \"false\", \"printlevel\": \"-1\", \"probs\": \"true\", \"relabund\": \"false\", \"savelog\": \"false\", \"tax\": {\"source\": \"hist\", \"__current_case__\": 1, \"taxonomy\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"excludebed\": {\"__class__\": \"RuntimeValue\"}, \"excluderef\": \"\", \"ignore_strand\": \"false\", \"includebed\": {\"__class__\": \"RuntimeValue\"}, \"includeref\": \"\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mapped\": \"true\", \"mask\": \"\", \"maximum_mismatch_ratio\": null, \"maxlen\": null, \"minlen\": null, \"mismatch\": null, \"nopcrdup\": \"false\", \"noproperpair\": \"false\", \"noqcfail\": \"false\", \"nosecondary\": \"false\", \"properpair\": \"false\", \"uniq\": \"-1\", \"uniq_start\": \"false\", \"unmapped\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.5.9",
                         "type": "tool",
-                        "uuid": "6dd79704-f3b8-4190-a7bb-34e2b4190436",
+                        "uuid": "eb538482-dcf6-4509-b4b0-3da71ac6c600",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "taxonomies",
-                                "uuid": "add9561d-239b-4236-a875-c7870d8f4aa9"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "taxsummaries",
-                                "uuid": "07f4f3ba-ee41-4f9b-aac9-ccc3262457f8"
+                                "output_name": "outfile",
+                                "uuid": "b7c08a3a-296d-4352-90a6-423897d8cc74"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
                         "errors": null,
                         "id": 7,
                         "input_connections": {
-                            "group": {
+                            "input_bams": {
                                 "id": 5,
-                                "output_name": "shared"
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Count.groups",
+                        "name": "Convert, Merge, Randomize",
                         "outputs": [
                             {
-                                "name": "grp_count",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "summary",
-                                "type": "tabular"
+                                "name": "out_file1",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 150.89999389648438,
-                            "height": 266.3999938964844,
-                            "left": 1361,
-                            "right": 1561,
-                            "top": -115.5,
-                            "width": 200,
-                            "x": 1361,
-                            "y": -115.5
+                            "left": 1559.00390625,
+                            "top": 110.9765625
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "03c86648a52e",
-                            "name": "mothur_count_groups",
-                            "owner": "iuc",
+                            "changeset_revision": "befc9dad4ca8",
+                            "name": "bamtools",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"group\": {\"__class__\": \"ConnectedValue\"}, \"groupnames\": {\"source\": \"none\", \"__current_case__\": 0}, \"savelog\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"convert\", \"__current_case__\": 0, \"format_type\": {\"format_type_selector\": \"sam\", \"__current_case__\": 6, \"noheader\": \"false\"}}, \"input_bams\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.5.1+galaxy0",
                         "type": "tool",
-                        "uuid": "5615bc17-0fdb-4610-ac78-c6aea2c08872",
+                        "uuid": "8dc250e9-c89b-40be-8432-08a7330d6e27",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "summary",
-                                "uuid": "1132f353-dc6c-4840-b8f1-91a8367af034"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "grp_count",
-                                "uuid": "19b8b29e-2970-4b2c-a8e4-ca712b257658"
+                                "output_name": "out_file1",
+                                "uuid": "8ad07a76-7793-43b2-add3-7e236a696172"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
                         "errors": null,
                         "id": 8,
                         "input_connections": {
-                            "input|otu": {
-                                "id": 5,
-                                "output_name": "shared"
+                            "input_bams": {
+                                "id": 6,
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Sub.sample",
+                        "name": "Convert, Merge, Randomize",
                         "outputs": [
                             {
-                                "name": "shared_out",
-                                "type": "input"
+                                "name": "out_file1",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 544.6999969482422,
-                            "height": 215.1999969482422,
-                            "left": 1384,
-                            "right": 1584,
-                            "top": 329.5,
-                            "width": 200,
-                            "x": 1384,
-                            "y": 329.5
+                            "left": 1548.0078125,
+                            "top": 462.98828125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "67cb43432196",
-                            "name": "mothur_sub_sample",
-                            "owner": "iuc",
+                            "changeset_revision": "befc9dad4ca8",
+                            "name": "bamtools",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"count\": null, \"input\": {\"format\": \"shared\", \"__current_case__\": 2, \"otu\": {\"__class__\": \"ConnectedValue\"}, \"groups\": null, \"label\": null}, \"savelog\": \"false\", \"size\": \"2389\", \"taxonomy\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"convert\", \"__current_case__\": 0, \"format_type\": {\"format_type_selector\": \"sam\", \"__current_case__\": 6, \"noheader\": \"false\"}}, \"input_bams\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.5.1+galaxy0",
                         "type": "tool",
-                        "uuid": "eb70e45c-1ea9-4a34-9ac0-b27a5e7018a5",
+                        "uuid": "b5c1bcac-9624-477c-998f-a0988b110a26",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "shared_out",
-                                "uuid": "a7df6943-cb20-46d7-ade1-66504b7e6eeb"
+                                "output_name": "out_file1",
+                                "uuid": "9801f8ee-e700-4e9b-bbfc-7ccf7aa99372"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "microbiome/mothur-miseq-sop-short",
-                "path": "topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow5_otu_clustering.ga",
-                "tags": [
-                    "microbiome"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]",
-                "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-mothur-miseq-sop-short/versions/workflow5-otu-clustering",
-                "tutorial_id": "mothur-miseq-sop-short",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow5_otu_clustering.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow5_otu_clustering.html",
-                "version": 1,
-                "wfid": "microbiome-mothur-miseq-sop-short",
-                "wfname": "workflow5-otu-clustering",
-                "workflow": "workflow5_otu_clustering.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0"
-                ],
-                "workflowhub_id": "1133"
-            },
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0003-3803-468X",
-                        "name": "Saskia Hiltemann"
-                    }
-                ],
-                "description": "16S Microbial Analysis with mothur (short)",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nShared file\"]\n  1[label=\"Rarefaction.single\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Summary.single\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Plotting tool\"]\n  1 -> 3 [label=\"rarefactioncurves\"]\n}",
-                "history": [
-                    {
-                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
-                        "message": "Rename metagenomics topic to microbiome",
-                        "num": 1,
-                        "short_hash": "0e0a2f2cc",
-                        "unix": "1704901629"
-                    }
-                ],
-                "inputs": [
+                    },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "random_lines1",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
+                        "id": 9,
+                        "input_connections": {
+                            "input": {
+                                "id": 7,
+                                "output_name": "out_file1"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Shared file"
+                                "description": "runtime parameter for tool Select random lines",
+                                "name": "input"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Select random lines",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
-                        "label": "Shared file",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 396.8000030517578,
-                            "height": 61.80000305175781,
-                            "left": 308,
-                            "right": 508,
-                            "top": 335,
-                            "width": 200,
-                            "x": 308,
-                            "y": 335
+                            "left": 1823.0078125,
+                            "top": 182.98828125
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "58c65102-0358-4782-b4d3-1de61937b7f7",
+                        "post_job_actions": {},
+                        "tool_id": "random_lines1",
+                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"num_lines\": \"210000\", \"seed_source\": {\"seed_source_selector\": \"no_seed\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2",
+                        "type": "tool",
+                        "uuid": "88f4ed97-5899-48f1-a5de-256be6e58862",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "43ede9d2-e2d2-46e0-a733-adea9336c50f"
+                                "output_name": "out_file1",
+                                "uuid": "69da2900-e66d-4d95-9bdb-1d9f801097e3"
                             }
                         ]
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nShared file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Rarefaction.single\"];\n  0 -->|output| 1;\n  2[\"Summary.single\"];\n  0 -->|output| 2;\n  3[\"Plotting tool\"];\n  1 -->|rarefactioncurves| 3;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "random_lines1",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
+                        "id": 10,
+                        "input_connections": {
+                            "input": {
+                                "id": 8,
+                                "output_name": "out_file1"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Shared file"
+                                "description": "runtime parameter for tool Select random lines",
+                                "name": "input"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Select random lines",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
-                        "label": "Shared file",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 396.8000030517578,
-                            "height": 61.80000305175781,
-                            "left": 308,
-                            "right": 508,
-                            "top": 335,
-                            "width": 200,
-                            "x": 308,
-                            "y": 335
+                            "left": 1826.9921875,
+                            "top": 535.99609375
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "58c65102-0358-4782-b4d3-1de61937b7f7",
+                        "post_job_actions": {},
+                        "tool_id": "random_lines1",
+                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"num_lines\": \"1000000\", \"seed_source\": {\"seed_source_selector\": \"no_seed\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2",
+                        "type": "tool",
+                        "uuid": "9064c0e8-fdc9-4347-99c2-bd6d97104fc9",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "43ede9d2-e2d2-46e0-a733-adea9336c50f"
+                                "output_name": "out_file1",
+                                "uuid": "fd4f3605-1f48-4583-b11a-91a9869e7946"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
                         "errors": null,
-                        "id": 1,
+                        "id": 11,
                         "input_connections": {
-                            "otu": {
-                                "id": 0,
-                                "output_name": "output"
+                            "input": {
+                                "id": 9,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Rarefaction.single",
+                        "name": "Filter Tabular",
                         "outputs": [
                             {
-                                "name": "rarefactioncurves",
-                                "type": "input"
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 349.8000030517578,
-                            "height": 174.8000030517578,
-                            "left": 618,
-                            "right": 818,
-                            "top": 175,
-                            "width": 200,
-                            "x": 618,
-                            "y": 175
+                            "left": 2081.015625,
+                            "top": 212.98828125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "af521db77c56",
-                            "name": "mothur_rarefaction_single",
+                            "changeset_revision": "34d29339abab",
+                            "name": "filter_tabular",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"abund\": \"10\", \"calc\": [\"sobs\"], \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"freq\": \"100.0\", \"iters\": \"1000\", \"label\": null, \"otu\": null, \"savelog\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"select_columns\", \"__current_case__\": 7, \"columns\": \"1\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.0",
                         "type": "tool",
-                        "uuid": "57642a17-6be7-4133-b573-b0175ff8cc97",
+                        "uuid": "302a62bb-98f7-4998-b290-281bb52e3c70",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "rarefactioncurves",
-                                "uuid": "955cdaca-e834-4f9b-b8d3-54d1e4e6b9cf"
+                                "output_name": "output",
+                                "uuid": "e83fbb91-742e-448f-8592-bdf37ce3cbdf"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
                         "errors": null,
-                        "id": 2,
+                        "id": 12,
                         "input_connections": {
-                            "otu": {
-                                "id": 0,
-                                "output_name": "output"
+                            "input": {
+                                "id": 10,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Summary.single",
+                        "name": "Filter Tabular",
                         "outputs": [
                             {
-                                "name": "summaryfiles",
-                                "type": "input"
-                            },
-                            {
-                                "name": "subsample_summary",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "summary",
+                                "name": "output",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 811.2000122070312,
-                            "height": 317.20001220703125,
-                            "left": 619,
-                            "right": 819,
-                            "top": 494,
-                            "width": 200,
-                            "x": 619,
-                            "y": 494
+                            "left": 2085,
+                            "top": 566.97265625
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "2344ed181ae6",
-                            "name": "mothur_summary_single",
+                            "changeset_revision": "34d29339abab",
+                            "name": "filter_tabular",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"abund\": \"10\", \"calc\": [\"sobs\", \"coverage\", \"invsimpson\", \"nseqs\"], \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"groupmode\": \"true\", \"label\": null, \"otu\": null, \"savelog\": \"false\", \"size\": \"2389\", \"subsample\": {\"use\": \"no\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.2",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"select_columns\", \"__current_case__\": 7, \"columns\": \"1\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.0",
                         "type": "tool",
-                        "uuid": "43c58fe5-5ec2-41cf-bc7a-1aed1e4ea48a",
+                        "uuid": "ab1a4102-7bb2-4ba7-80d1-2a532b410201",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "summaryfiles",
-                                "uuid": "05892980-8cd2-42f6-814b-dab57c1ebe5c"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "summary",
-                                "uuid": "8c30634d-fc8f-40d6-a5d0-93efde3874de"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "subsample_summary",
-                                "uuid": "4e8da2ff-e4f5-4109-bfbd-9a23f978227b"
+                                "output_name": "output",
+                                "uuid": "2701a2bd-2ec9-433a-9f26-7f35410ec018"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
                         "errors": null,
-                        "id": 3,
+                        "id": 13,
                         "input_connections": {
-                            "series_0|input": {
-                                "id": 1,
-                                "output_name": "rarefactioncurves"
+                            "input": {
+                                "id": 11,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Plotting tool",
+                        "name": "Unique",
                         "outputs": [
                             {
-                                "name": "out_file_png",
-                                "type": "png"
+                                "name": "outfile",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 276.1999969482422,
-                            "height": 93.19999694824219,
-                            "left": 999,
-                            "right": 1199,
-                            "top": 183,
-                            "width": 200,
-                            "x": 999,
-                            "y": 183
+                            "left": 2330,
+                            "top": 265.99609375
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "ecb437f1d298",
-                            "name": "xy_plot",
-                            "owner": "devteam",
+                            "changeset_revision": "7ce75adb93be",
+                            "name": "unique",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"main\": \"Rarefaction\", \"outftype\": \"png\", \"series\": [{\"__index__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"header\": \"true\", \"xcol\": \"1\", \"ycol\": [\"2\", \"5\", \"8\", \"11\", \"14\", \"17\", \"20\", \"23\", \"26\", \"29\", \"32\", \"35\", \"38\", \"41\", \"44\", \"47\", \"50\", \"53\", \"56\"], \"series_type\": {\"type\": \"line\", \"__current_case__\": 0, \"lty\": \"1\", \"col\": \"1\", \"lwd\": \"1.0\"}}], \"series_0|input|__identifier__\": \"sobs\", \"xlab\": \"Number of Sequences\", \"ylab\": \"Number of OTUs\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2",
+                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"ignore_case\": \"false\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"is_numeric\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3",
                         "type": "tool",
-                        "uuid": "f9ef9628-4716-49f9-bf8a-e7ec68754881",
+                        "uuid": "2a68a6a4-4d3d-4de3-bc64-35edc63287f9",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file_png",
-                                "uuid": "9f66c76d-0d54-4dda-84f5-a9671fa77740"
+                                "output_name": "outfile",
+                                "uuid": "b2bb66d7-fe76-4ce3-bb5b-72c979a755d1"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "microbiome/mothur-miseq-sop-short",
-                "path": "topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow6_alpha_diversity.ga",
-                "tags": [
-                    "microbiome"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]",
-                "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-mothur-miseq-sop-short/versions/workflow6-alpha-diversity",
-                "tutorial_id": "mothur-miseq-sop-short",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow6_alpha_diversity.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow6_alpha_diversity.html",
-                "version": 1,
-                "wfid": "microbiome-mothur-miseq-sop-short",
-                "wfname": "workflow6-alpha-diversity",
-                "workflow": "workflow6_alpha_diversity.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.2"
-                ],
-                "workflowhub_id": "1129"
-            },
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0003-3803-468X",
-                        "name": "Saskia Hiltemann"
-                    }
-                ],
-                "description": "16S Microbial Analysis with mothur (short)",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nShared file from Make.shared\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nSub.sample shared\"]\n  2[label=\"Dist.shared\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Collapse Collection\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Heatmap.sim\"]\n  2 -> 4 [label=\"distfiles\"]\n  5[label=\"Tree.shared\"]\n  2 -> 5 [label=\"distfiles\"]\n  6[label=\"Venn\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"Newick Display\"]\n  5 -> 7 [label=\"tre\"]\n}",
-                "history": [
-                    {
-                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
-                        "message": "Rename metagenomics topic to microbiome",
-                        "num": 1,
-                        "short_hash": "0e0a2f2cc",
-                        "unix": "1704901629"
-                    }
-                ],
-                "inputs": [
+                    },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Shared file from Make.shared"
+                        "id": 14,
+                        "input_connections": {
+                            "input": {
+                                "id": 12,
+                                "output_name": "output"
                             }
-                        ],
-                        "label": "Shared file from Make.shared",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 119,
-                            "top": 28
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "d0c07e4f-abd7-4af3-bda4-ab143e6859bb",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Unique",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Sub.sample shared"
+                                "name": "outfile",
+                                "type": "input"
                             }
                         ],
-                        "label": "Sub.sample shared",
-                        "name": "Input dataset collection",
-                        "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 161
+                            "left": 2331.97265625,
+                            "top": 617.94921875
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "cc9198f5-b615-4317-9837-4cbc83f4b5e7",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nShared file from Make.shared\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nSub.sample shared\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Dist.shared\"];\n  0 -->|output| 2;\n  3[\"Collapse Collection\"];\n  1 -->|output| 3;\n  4[\"Heatmap.sim\"];\n  2 -->|distfiles| 4;\n  5[\"Tree.shared\"];\n  2 -->|distfiles| 5;\n  6[\"Venn\"];\n  3 -->|output| 6;\n  7[\"Newick Display\"];\n  5 -->|tre| 7;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]",
-                "outputs": [
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "7ce75adb93be",
+                            "name": "unique",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"ignore_case\": \"false\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"is_numeric\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3",
+                        "type": "tool",
+                        "uuid": "c2d1dc5c-4d14-45e5-9bb9-bdab787ea5f3",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "df0bbae1-b735-4cf4-a5a3-ef4f8b525a4e"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
                         "errors": null,
-                        "id": 3,
+                        "id": 15,
                         "input_connections": {
-                            "input_list": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
+                            "inputs": [
+                                {
+                                    "id": 13,
+                                    "output_name": "outfile"
+                                },
+                                {
+                                    "id": 14,
+                                    "output_name": "outfile"
+                                }
+                            ]
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Collapse Collection",
+                        "name": "Concatenate datasets",
                         "outputs": [
                             {
-                                "name": "output",
+                                "name": "out_file1",
                                 "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 138,
-                            "top": 489
+                            "left": 2575,
+                            "top": 417.98828125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "830961c48e42",
-                            "name": "collapse_collections",
-                            "owner": "nml",
+                            "changeset_revision": "f46f0e4f75c4",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"filename\": {\"add_name\": false, \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.2",
+                        "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.1",
                         "type": "tool",
-                        "uuid": "aa52952a-70eb-4ed6-b6b0-28225e04091a",
-                        "when": null,
+                        "uuid": "bf2ba224-25ae-4ec3-9a1f-7cb1afd0aef2",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "01c16573-8bd5-4d62-92c0-74cd29af035a"
+                                "output_name": "out_file1",
+                                "uuid": "53ae320a-b570-4985-ae2a-8344e15e43f9"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
                         "errors": null,
-                        "id": 4,
+                        "id": 16,
                         "input_connections": {
-                            "input|dist": {
+                            "in_file": {
                                 "id": 2,
-                                "output_name": "distfiles"
+                                "output_name": "out1"
+                            },
+                            "source|name_list": {
+                                "id": 15,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Heatmap.sim",
+                        "name": "seqtk_subseq",
                         "outputs": [
                             {
-                                "name": "heatmap",
-                                "type": "svg"
+                                "name": "default",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 805,
-                            "top": 0
+                            "left": 2847.98828125,
+                            "top": 819.98046875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "7f5707dd6073",
-                            "name": "mothur_heatmap_sim",
+                            "changeset_revision": "3da72230c066",
+                            "name": "seqtk",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"count\": null, \"dist|__identifier__\": \"thetayc.0.03.lt.std\", \"fontsize\": \"24\", \"input\": {\"source\": \"phylip\", \"__current_case__\": 2, \"dist\": {\"__class__\": \"ConnectedValue\"}}, \"savelog\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"in_file\": {\"__class__\": \"ConnectedValue\"}, \"l\": \"0\", \"source\": {\"type\": \"name\", \"__current_case__\": 1, \"name_list\": {\"__class__\": \"ConnectedValue\"}}, \"t\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3.1",
                         "type": "tool",
-                        "uuid": "aa3080d1-4ec6-4c1b-8be8-532a7e12c81c",
-                        "when": null,
+                        "uuid": "478adb2b-4910-4aed-af4e-2a66e9a1922c",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "heatmap",
-                                "uuid": "6b90b099-6641-43b9-a347-5ce6e05ae67e"
+                                "output_name": "default",
+                                "uuid": "b47e4af0-c185-4b6f-a529-6f0ef96a14ab"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
                         "errors": null,
-                        "id": 5,
+                        "id": 17,
                         "input_connections": {
-                            "input|dist": {
+                            "in_file": {
                                 "id": 2,
-                                "output_name": "distfiles"
+                                "output_name": "out2"
+                            },
+                            "source|name_list": {
+                                "id": 15,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Tree.shared",
+                        "name": "seqtk_subseq",
                         "outputs": [
                             {
-                                "name": "tre",
-                                "type": "mothur.tre"
+                                "name": "default",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 763,
-                            "top": 438
+                            "left": 2836.97265625,
+                            "top": 1019.98046875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "43e2715e98c9",
-                            "name": "mothur_tree_shared",
+                            "changeset_revision": "3da72230c066",
+                            "name": "seqtk",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"calc\": [\"jclass\", \"thetayc\"], \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"dist|__identifier__\": \"thetayc.0.03.lt.std\", \"input\": {\"source\": \"phylip\", \"__current_case__\": 1, \"dist\": {\"__class__\": \"ConnectedValue\"}, \"name\": null}, \"savelog\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"in_file\": {\"__class__\": \"ConnectedValue\"}, \"l\": \"0\", \"source\": {\"type\": \"name\", \"__current_case__\": 1, \"name_list\": {\"__class__\": \"ConnectedValue\"}}, \"t\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3.1",
                         "type": "tool",
-                        "uuid": "e6bebcdf-bb0a-4b50-82a1-8c0ca2711b5e",
-                        "when": null,
+                        "uuid": "81ae5423-c7d0-4ceb-a6e4-168ab1f3fd35",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "tre",
-                                "uuid": "3a746045-e178-492c-ac40-dab92ce5189f"
+                                "output_name": "default",
+                                "uuid": "c7de5bbe-f941-4772-bb32-15aeff98678a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
                         "errors": null,
-                        "id": 6,
+                        "id": 18,
                         "input_connections": {
-                            "input|otu": {
-                                "id": 3,
-                                "output_name": "output"
+                            "input_file": {
+                                "id": 16,
+                                "output_name": "default"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Venn",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "sharedotus_out",
-                                "type": "input"
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "adapters"
                             },
                             {
-                                "name": "svgs_out",
-                                "type": "input"
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "contaminants"
                             },
                             {
-                                "name": "logfile",
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "limits"
+                            }
+                        ],
+                        "label": null,
+                        "name": "FastQC",
+                        "outputs": [
+                            {
+                                "name": "html_file",
+                                "type": "html"
+                            },
+                            {
+                                "name": "text_file",
                                 "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 419,
-                            "top": 454
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionsharedotus_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "sharedotus_out"
-                            }
+                            "left": 3135.9765625,
+                            "top": 775.99609375
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "4db54b1c1d83",
-                            "name": "mothur_venn",
-                            "owner": "iuc",
+                            "changeset_revision": "3d0c7bdf12f5",
+                            "name": "fastqc",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"fontsize\": \"24\", \"input\": {\"source\": \"shared\", \"__current_case__\": 0, \"otu\": {\"__class__\": \"ConnectedValue\"}, \"calc\": null, \"label\": null, \"groups\": [\"F3D0\", \"F3D1\", \"F3D2\", \"F3D3\"]}, \"nseqs\": false, \"permute\": \"4\", \"savelog\": true, \"sharedotus\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
+                        "tool_state": "{\"adapters\": {\"__class__\": \"RuntimeValue\"}, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"min_length\": null, \"nogroup\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.73+galaxy0",
                         "type": "tool",
-                        "uuid": "932cccf7-1743-46e2-abb9-f148ca5b617b",
-                        "when": null,
+                        "uuid": "6d6cee2a-b879-463b-81d1-7ab4f72ca04b",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "svgs_out",
-                                "uuid": "d3db2185-9a28-4bb2-abd6-6907377de73f"
+                                "output_name": "text_file",
+                                "uuid": "ca3ea14a-b1cc-481d-b1a3-2b46b8d24809"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "html_file",
+                                "uuid": "6849e3f4-33bc-47a9-8ef5-b7cbbdfe0d93"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
                         "errors": null,
-                        "id": 7,
+                        "id": 19,
                         "input_connections": {
-                            "fileNewick": {
-                                "id": 5,
-                                "output_name": "tre"
+                            "input_file": {
+                                "id": 17,
+                                "output_name": "default"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "adapters"
+                            },
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "contaminants"
+                            },
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "limits"
+                            }
+                        ],
                         "label": null,
-                        "name": "Newick Display",
+                        "name": "FastQC",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "svg"
+                                "name": "html_file",
+                                "type": "html"
+                            },
+                            {
+                                "name": "text_file",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 1141,
-                            "top": 56
+                            "left": 3133.984375,
+                            "top": 1104.98046875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "b4163d2f64ab",
-                            "name": "newick_utils",
-                            "owner": "iuc",
+                            "changeset_revision": "3d0c7bdf12f5",
+                            "name": "fastqc",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"mothur.tre\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"condbranchlength\": {\"branchlength\": \"false\", \"__current_case__\": 1}, \"condbranchsupport\": {\"branchsupport\": \"false\", \"__current_case__\": 1}, \"fileNewick\": {\"__class__\": \"ConnectedValue\"}, \"fileNewick|__identifier__\": \"thetayc.0.03.lt.std\", \"leafFont\": \"sans-serif\", \"leafSize\": \"10px\", \"legend\": \"\", \"outformat\": \"svg\", \"radial\": false, \"scalebar\": true, \"width\": \"800\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.6+galaxy1",
+                        "tool_state": "{\"adapters\": {\"__class__\": \"RuntimeValue\"}, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"min_length\": null, \"nogroup\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.73+galaxy0",
                         "type": "tool",
-                        "uuid": "8f4bff39-d764-4357-aae5-246c01ac2dcf",
-                        "when": null,
+                        "uuid": "54fc20b8-5520-4b93-a7d8-ed447df19b3c",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "544ca4c5-82b3-4bf1-9ff1-c23ebce8b098"
+                                "output_name": "html_file",
+                                "uuid": "a85a4180-b2ab-4cac-9c71-76aee3df673f"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "text_file",
+                                "uuid": "65e24721-ec93-4648-9310-c3c2609b7818"
                             }
                         ]
                     }
                 ],
-                "parent_id": "microbiome/mothur-miseq-sop-short",
-                "path": "topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow7_beta_diversity.ga",
-                "tags": [
-                    "microbiome"
-                ],
+                "parent_id": "microbiome/metagenomics-assembly",
+                "path": "topics/microbiome/tutorials/metagenomics-assembly/workflows/workflow-generate-dataset-for-assembly-tutorial.ga",
+                "tags": [],
                 "test_results": null,
                 "tests": false,
-                "title": "Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]",
+                "title": "workflow-generate-dataset-for-assembly-tutorial",
                 "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-mothur-miseq-sop-short/versions/workflow7-beta-diversity",
-                "tutorial_id": "mothur-miseq-sop-short",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow7_beta_diversity.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow7_beta_diversity.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-metagenomics-assembly/versions/workflow-generate-dataset-for-assembly-tutorial",
+                "tutorial_id": "metagenomics-assembly",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metagenomics-assembly/workflows/workflow-generate-dataset-for-assembly-tutorial.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metagenomics-assembly/workflows/workflow-generate-dataset-for-assembly-tutorial.html",
                 "version": 1,
-                "wfid": "microbiome-mothur-miseq-sop-short",
-                "wfname": "workflow7-beta-diversity",
-                "workflow": "workflow7_beta_diversity.ga",
+                "wfid": "microbiome-metagenomics-assembly",
+                "wfname": "workflow-generate-dataset-for-assembly-tutorial",
+                "workflow": "workflow-generate-dataset-for-assembly-tutorial.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
+                    "random_lines1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+                    "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0"
                 ],
-                "workflowhub_id": "1117"
+                "workflowhub_id": "1099"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.800651"
+        "zenodo_link": "https://zenodo.org/record/7818827"
     },
     {
         "admin_install": {
@@ -155347,342 +156719,565 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "taxonomy_krona_chart",
-                    "owner": "crs4",
-                    "revisions": "c9f8fef1df74",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "xy_plot",
-                    "owner": "devteam",
-                    "revisions": "ecb437f1d298",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_align_seqs",
-                    "owner": "iuc",
-                    "revisions": "abf7c15ecfef",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_chimera_vsearch",
-                    "owner": "iuc",
-                    "revisions": "12e856482d26",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_classify_otu",
-                    "owner": "iuc",
-                    "revisions": "ff1bc0299372",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_classify_seqs",
-                    "owner": "iuc",
-                    "revisions": "09bf9e496c64",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_cluster",
-                    "owner": "iuc",
-                    "revisions": "6366f4483b35",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_cluster_split",
-                    "owner": "iuc",
-                    "revisions": "19f45bdbffd9",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_count_groups",
-                    "owner": "iuc",
-                    "revisions": "dc3826bfc1ed",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_count_seqs",
-                    "owner": "iuc",
-                    "revisions": "ffee46220ddd",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_dist_seqs",
-                    "owner": "iuc",
-                    "revisions": "4d76fba83f24",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_dist_shared",
-                    "owner": "iuc",
-                    "revisions": "418100660ba3",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_filter_seqs",
-                    "owner": "iuc",
-                    "revisions": "3524ca06478e",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_get_groups",
-                    "owner": "iuc",
-                    "revisions": "03af14e245fb",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_heatmap_sim",
-                    "owner": "iuc",
-                    "revisions": "7f5707dd6073",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_make_biom",
-                    "owner": "iuc",
-                    "revisions": "0b5397a74165",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_make_contigs",
-                    "owner": "iuc",
-                    "revisions": "ab12df91b47f",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_make_shared",
-                    "owner": "iuc",
-                    "revisions": "d0967ae326be",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_pre_cluster",
+                    "name": "krakentools_alpha_diversity",
                     "owner": "iuc",
-                    "revisions": "6532c3424bfe",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "bab112ba9d62",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mothur_rarefaction_single",
+                    "name": "krakentools_beta_diversity",
                     "owner": "iuc",
-                    "revisions": "47264675a4ea",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "c254d75b8b67",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: krakentools_alpha_diversity\n  owner: iuc\n  revisions: bab112ba9d62\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: krakentools_beta_diversity\n  owner: iuc\n  revisions: c254d75b8b67\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/diversity/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "sophia120199",
+                "bebatut",
+                "paulzierep"
+            ]
+        },
+        "contributors": [
+            {
+                "id": "sophia120199",
+                "joined": "2023-04",
+                "name": "Sophia Hampe",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/sophia120199/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/sophia120199.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
                 },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "email": "zierep@informatik.uni-freiburg.de",
+                "id": "paulzierep",
+                "joined": "2023-02",
+                "name": "Paul Zierep",
+                "orcid": "0000-0003-2982-388X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/paulzierep.json"
+            }
+        ],
+        "dir": "topics/microbiome/tutorials/diversity",
+        "draft": false,
+        "edam_operation": [
+            "Aggregation",
+            "Visualisation"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "Galaxy@Pasteur",
+            "GalaxyTrakr",
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "microbiome/diversity",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": 8337,
+            "mermaid": false
+        },
+        "key_points": [
+            "There are 2 different types of diversity metrics (\u03b1 and \u03b2 diversity)",
+            "Krakentools can be used in Galaxy for calculating the diversity"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-24",
+        "objectives": [
+            "Explain what taxonomic diversity is",
+            "Explain different metrics to calculate \u03b1 and \u03b2 diversity",
+            "Apply Krakentools to calculate \u03b1 and \u03b2 diversity and understand the output"
+        ],
+        "pageviews": 370,
+        "pub_date": "2024-08-01",
+        "questions": [
+            "How many different taxons are present in my sample? How do I additionally take their relative abundance into account?",
+            "How similar or how dissimilar are my samples in term of taxonomic diversity?",
+            "What are the different metrics used to calculate the taxonomic diversity of my samples?"
+        ],
+        "recordings": [
+            {
+                "bot-timestamp": 1723117037,
+                "captioners": [
+                    "paulzierep"
+                ],
+                "date": "2024-08-08",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "23M",
+                "speakers": [
+                    "paulzierep"
+                ],
+                "youtube_id": "e4vlvMsBrhM"
+            }
+        ],
+        "short_id": "T00447",
+        "short_tools": [
+            "krakentools_beta_diversity",
+            "krakentools_alpha_diversity"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "metagenomics",
+        "supported_servers": {
+            "exact": [
                 {
-                    "name": "mothur_remove_groups",
-                    "owner": "iuc",
-                    "revisions": "498dc0671d9e",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "mothur_remove_lineage",
-                    "owner": "iuc",
-                    "revisions": "947faa8b3205",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "mothur_remove_seqs",
-                    "owner": "iuc",
-                    "revisions": "008f62670efc",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "mothur_screen_seqs",
-                    "owner": "iuc",
-                    "revisions": "f4d7d5755f01",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
                 },
                 {
-                    "name": "mothur_seq_error",
-                    "owner": "iuc",
-                    "revisions": "5a7674ac2c59",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "mothur_sub_sample",
-                    "owner": "iuc",
-                    "revisions": "67cb43432196",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 },
                 {
-                    "name": "mothur_summary_seqs",
-                    "owner": "iuc",
-                    "revisions": "600c14c6dcc5",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "metagenomics",
+            "diversity"
+        ],
+        "time_estimation": "20M",
+        "title": "Calculating \u03b1 and \u03b2 diversity from microbiome taxonomic data",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_alpha_diversity/krakentools_alpha_diversity/1.2+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_beta_diversity/krakentools_beta_diversity/1.2+galaxy1"
+        ],
+        "topic_name": "microbiome",
+        "topic_name_human": "Microbiome",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "diversity",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/diversity/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/diversity/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/diversity/tutorial.json"
+        },
+        "version": 5,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 141,
+        "visitors": 313,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0003-2982-388X",
+                        "name": "Paul Zierep"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "NA",
+                        "name": "Sophia Hampe"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0001-9852-1987",
+                        "name": "B\u00e9r\u00e9nice Batut"
+                    }
+                ],
+                "description": "Calculating diversity from bracken output",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                    },
+                    "subworkflows": false
                 },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  1[label=\"Krakentools: Calculates alpha diversity\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Krakentools: Calculates alpha diversity\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Krakentools: Calculates alpha diversity\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Krakentools: Calculates alpha diversity\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Krakentools: Calculates alpha diversity\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Krakentools: calculates beta diversity Bray-Curtis dissimilarity\"]\n  0 -> 6 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "e548ec8fcbcdf6978839bbd7fb0cbad8724978af",
+                        "message": "add orcid to WF",
+                        "num": 5,
+                        "short_hash": "e548ec8fc",
+                        "unix": "1722843023"
+                    },
+                    {
+                        "hash": "7e39380705c94841458f4826b03705b6aaf891e0",
+                        "message": "add license, fix alpha div formula, add subsections",
+                        "num": 4,
+                        "short_hash": "7e3938070",
+                        "unix": "1722841724"
+                    },
+                    {
+                        "hash": "d448f8052a7b897e44d2afb4a2ffe9053ab8b316",
+                        "message": "update wf creator",
+                        "num": 3,
+                        "short_hash": "d448f8052",
+                        "unix": "1722839579"
+                    },
+                    {
+                        "hash": "c0ff830e1929507fb3ad36b646990b1bcca4e748",
+                        "message": "fix workflow",
+                        "num": 2,
+                        "short_hash": "c0ff830e1",
+                        "unix": "1722519174"
+                    },
+                    {
+                        "hash": "cd4066fc9a27c98bc2f6273e8cd7d2672163a425",
+                        "message": "add workflow",
+                        "num": 1,
+                        "short_hash": "cd4066fc9",
+                        "unix": "1722518283"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Input Dataset Collection"
+                            }
+                        ],
+                        "label": "Input Dataset Collection",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 340.098225676056
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "41ce4f24-4b0b-4431-bbf4-7262199838db",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Krakentools: Calculates alpha diversity\"];\n  0 -->|output| 1;\n  2[\"Krakentools: Calculates alpha diversity\"];\n  0 -->|output| 2;\n  3[\"Krakentools: Calculates alpha diversity\"];\n  0 -->|output| 3;\n  4[\"Krakentools: Calculates alpha diversity\"];\n  0 -->|output| 4;\n  5[\"Krakentools: Calculates alpha diversity\"];\n  0 -->|output| 5;\n  6[\"Krakentools: calculates beta diversity Bray-Curtis dissimilarity\"];\n  0 -->|output| 6;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Calculating diversity from microbiome taxonomic data",
+                "outputs": [],
+                "parent_id": "microbiome/diversity",
+                "path": "topics/microbiome/tutorials/diversity/workflows/workflow.ga",
+                "tags": [
+                    "name:GTN"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "Calculating diversity from microbiome taxonomic data",
+                "topic_id": "microbiome",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-diversity/versions/workflow",
+                "tutorial_id": "diversity",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/diversity/workflows/workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/diversity/workflows/workflow.html",
+                "version": 1,
+                "wfid": "microbiome-diversity",
+                "wfname": "workflow",
+                "workflow": "workflow.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_alpha_diversity/krakentools_alpha_diversity/1.2+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_beta_diversity/krakentools_beta_diversity/1.2+galaxy1"
+                ],
+                "workflowhub_id": "1349"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/records/13150694"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "qiime2"
+            ]
+        },
+        "contributors": [
+            {
+                "avatar": "https://avatars.githubusercontent.com/u/18176583?s=200&amp;v=4",
+                "id": "qiime2",
+                "name": "QIIME2",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/qiime2/",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/qiime2.json"
+            }
+        ],
+        "dir": "topics/microbiome/tutorials/qiime2-moving-pictures",
+        "edam_ontology": [
+            "topic_3697",
+            "topic_0637",
+            "topic_0080",
+            "topic_4038"
+        ],
+        "edam_operation": [],
+        "edam_topic": [
+            "Microbial ecology",
+            "Taxonomy",
+            "Sequence analysis"
+        ],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": "external",
+        "hands_on_url": "https://docs.qiime2.org/2024.2/tutorials/moving-pictures-usage",
+        "id": "microbiome/qiime2-moving-pictures",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-03-14",
+        "pageviews": 195,
+        "pub_date": "2024-03-14",
+        "short_id": "T00427",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "metabarcoding",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
                 {
-                    "name": "mothur_summary_single",
-                    "owner": "iuc",
-                    "revisions": "72be09dfd803",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
                 },
                 {
-                    "name": "mothur_taxonomy_to_krona",
-                    "owner": "iuc",
-                    "revisions": "db30eb96ea23",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 },
                 {
-                    "name": "mothur_tree_shared",
-                    "owner": "iuc",
-                    "revisions": "8bca555fbcaf",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 },
                 {
-                    "name": "mothur_unique_seqs",
-                    "owner": "iuc",
-                    "revisions": "a033f325ad8d",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "metagenomics",
+            "taxonomic profiling",
+            "diversity",
+            "microgalaxy"
+        ],
+        "time_estimation": "10H",
+        "title": "QIIME 2 Moving Pictures",
+        "tools": [],
+        "topic_name": "microbiome",
+        "topic_name_human": "Microbiome",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "qiime2-moving-pictures",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.json"
+        },
+        "version": 1,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 203,
+        "visitors": 131
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
                 {
-                    "name": "mothur_venn",
+                    "name": "checkm_lineage_wf",
                     "owner": "iuc",
-                    "revisions": "4db54b1c1d83",
-                    "tool_panel_section_label": "Mothur",
+                    "revisions": "f0107b9f2dc3",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "newick_utils",
+                    "name": "megahit",
                     "owner": "iuc",
-                    "revisions": "fe4235285ee8",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "revisions": "14ddfc8ffb93",
+                    "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: taxonomy_krona_chart\n  owner: crs4\n  revisions: c9f8fef1df74\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xy_plot\n  owner: devteam\n  revisions: ecb437f1d298\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_align_seqs\n  owner: iuc\n  revisions: abf7c15ecfef\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_chimera_vsearch\n  owner: iuc\n  revisions: 12e856482d26\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_classify_otu\n  owner: iuc\n  revisions: ff1bc0299372\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_classify_seqs\n  owner: iuc\n  revisions: '09bf9e496c64'\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_cluster\n  owner: iuc\n  revisions: 6366f4483b35\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_cluster_split\n  owner: iuc\n  revisions: 19f45bdbffd9\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_count_groups\n  owner: iuc\n  revisions: dc3826bfc1ed\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_count_seqs\n  owner: iuc\n  revisions: ffee46220ddd\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_dist_seqs\n  owner: iuc\n  revisions: 4d76fba83f24\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_dist_shared\n  owner: iuc\n  revisions: 418100660ba3\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_filter_seqs\n  owner: iuc\n  revisions: 3524ca06478e\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_get_groups\n  owner: iuc\n  revisions: 03af14e245fb\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_heatmap_sim\n  owner: iuc\n  revisions: 7f5707dd6073\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_make_biom\n  owner: iuc\n  revisions: 0b5397a74165\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_make_contigs\n  owner: iuc\n  revisions: ab12df91b47f\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_make_shared\n  owner: iuc\n  revisions: d0967ae326be\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_pre_cluster\n  owner: iuc\n  revisions: 6532c3424bfe\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_rarefaction_single\n  owner: iuc\n  revisions: 47264675a4ea\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_remove_groups\n  owner: iuc\n  revisions: 498dc0671d9e\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_remove_lineage\n  owner: iuc\n  revisions: 947faa8b3205\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_remove_seqs\n  owner: iuc\n  revisions: '008f62670efc'\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_screen_seqs\n  owner: iuc\n  revisions: f4d7d5755f01\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_seq_error\n  owner: iuc\n  revisions: 5a7674ac2c59\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_sub_sample\n  owner: iuc\n  revisions: 67cb43432196\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_summary_seqs\n  owner: iuc\n  revisions: 600c14c6dcc5\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_summary_single\n  owner: iuc\n  revisions: 72be09dfd803\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_taxonomy_to_krona\n  owner: iuc\n  revisions: db30eb96ea23\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_tree_shared\n  owner: iuc\n  revisions: 8bca555fbcaf\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_unique_seqs\n  owner: iuc\n  revisions: a033f325ad8d\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_venn\n  owner: iuc\n  revisions: 4db54b1c1d83\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: newick_utils\n  owner: iuc\n  revisions: fe4235285ee8\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: checkm_lineage_wf\n  owner: iuc\n  revisions: f0107b9f2dc3\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: megahit\n  owner: iuc\n  revisions: 14ddfc8ffb93\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-binning/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "npechl",
+                "fpsom"
+            ]
+        },
         "contributors": [
             {
                 "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
+                    "inab-certh"
                 ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+                "elixir_node": "gr",
+                "id": "npechl",
+                "joined": "2023-05",
+                "linkedin": "npechl",
+                "name": "Nikos Pechlivanis",
+                "orcid": "0000-0003-2502-612X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/npechl/",
+                "twitter": "npechl",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/npechl.json"
             },
             {
                 "affiliations": [
                     "gallantries",
-                    "ifb",
                     "elixir-europe"
                 ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "id": "tnabtaf",
-                "joined": "2017-09",
-                "name": "Dave Clements",
-                "orcid": "0000-0002-9970-6657",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
+                "elixir_node": "gr",
+                "email": "fpsom@certh.gr",
+                "id": "fpsom",
+                "joined": "2019-03",
+                "linkedin": "fpsom",
+                "matrix": "fpsom:matrix.org",
+                "name": "Fotis E. Psomopoulos",
+                "orcid": "0000-0002-0222-4273",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
+                "twitter": "fopsom",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
             }
         ],
-        "dir": "topics/microbiome/tutorials/mothur-miseq-sop",
+        "dir": "topics/microbiome/tutorials/metagenomics-binning",
         "edam_ontology": [
-            "topic_3697",
-            "topic_0637",
-            "topic_0080",
-            "topic_4038"
+            "topic_3174",
+            "topic_0196"
         ],
         "edam_operation": [
-            "Visualisation",
+            "Sequence assembly validation",
+            "Statistical calculation",
             "Sequencing quality control",
-            "Phylogenetic analysis",
-            "Taxonomic classification",
-            "Phylogenetic tree analysis",
-            "Phylogenetic tree generation",
-            "Sequence read processing",
-            "DNA barcoding",
-            "Sequence clustering",
-            "Phylogenetic tree reconstruction"
+            "Validation",
+            "Genome assembly",
+            "Sequence composition calculation"
         ],
         "edam_topic": [
-            "Microbial ecology",
-            "Taxonomy",
-            "Sequence analysis"
+            "Metagenomics",
+            "Sequence assembly"
         ],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "GalaxyTrakr",
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.fr"
         ],
+        "extra": {
+            "zenodo_link_results": "https://zenodo.org/record/7845138"
+        },
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "microbiome/mothur-miseq-sop",
+        "id": "microbiome/metagenomics-binning",
         "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
         "js_requirements": {
@@ -155690,103 +157285,216 @@
             "mermaid": false
         },
         "key_points": [
-            "16S rRNA gene sequencing analysis results depend on the many algorithms used and their settings",
-            "Quality control and cleaning of your data is a crucial step in order to obtain optimal results",
-            "Adding a mock community to serve as a control sample can help you asses the error rate of your experimental setup",
-            "We can explore alpha and beta diversities using Krona and Phinch for dynamic visualizations"
+            "Metagenomics binning is a computational approach to grouping together DNA sequences from a mixed microbial sample into metagenome-assembled genomes (MAGs)",
+            "The metagenomics binning workflow involves several steps, including preprocessing of raw sequencing data, assembly of sequencing reads into contigs, binning of contigs into MAGs, quality assessment of MAGs, and annotation of functional genes and metabolic pathways in MAGs",
+            "The quality and completeness of MAGs can be evaluated using standard metrics, such as completeness, contamination, and genome size",
+            "Metagenomics binning can be used to gain insights into the composition, diversity, and functional potential of microbial communities, and can be applied to a range of research areas, such as human health, environmental microbiology, and biotechnology"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-12",
+        "objectives": [
+            "Describe what metagenomics binning is",
+            "Describe common problems in metagenomics binning",
+            "What software tools are available for metagenomics binning",
+            "Binning of contigs into metagenome-assembled genomes (MAGs) using MetaBAT 2 software",
+            "Evaluation of MAG quality and completeness using CheckM software"
+        ],
+        "pageviews": 2537,
+        "pub_date": "2023-12-05",
+        "questions": [
+            "What is metagenomic binning refers to?",
+            "Which tools should be used for metagenomic binning?",
+            "How to assess the quality of metagenomic data binning?"
+        ],
+        "recordings": [
+            {
+                "bot-timestamp": 1725013820,
+                "captioners": [
+                    "npechl"
+                ],
+                "date": "2024-08-30",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "25M",
+                "speakers": [
+                    "npechl"
+                ],
+                "youtube_id": "m8ADGsRVqYI"
+            }
+        ],
+        "redirect_from": [
+            "/topics/metagenomics/tutorials/metagenomics-binning/tutorial",
+            "/short/microbiome/metagenomics-binning",
+            "/short/T00377",
+            "/short/T00387"
+        ],
+        "short_id": "T00387",
+        "short_tools": [
+            "megahit",
+            "checkm_lineage_wf"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "metagenomics",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "binning",
+            "metagenomics",
+            "microgalaxy"
+        ],
+        "time_estimation": "2H",
+        "title": "Binning of metagenomic sequencing data",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/iuc/checkm_lineage_wf/checkm_lineage_wf/1.2.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0"
+        ],
+        "topic_name": "microbiome",
+        "topic_name_human": "Microbiome",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "metagenomics-binning",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-binning/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/metagenomics-binning/tutorial.json"
+        },
+        "version": 4,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 85,
+        "visitors": 2076,
+        "zenodo_link": "https://zenodo.org/record/7818827"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "qiime2"
+            ]
+        },
+        "contributors": [
+            {
+                "avatar": "https://avatars.githubusercontent.com/u/18176583?s=200&amp;v=4",
+                "id": "qiime2",
+                "name": "QIIME2",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/qiime2/",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/qiime2.json"
+            }
+        ],
+        "dir": "topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention",
+        "edam_ontology": [
+            "topic_3697",
+            "topic_0637",
+            "topic_0080",
+            "topic_4038"
+        ],
+        "edam_operation": [],
+        "edam_topic": [
+            "Microbial ecology",
+            "Taxonomy",
+            "Sequence analysis"
+        ],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": "external",
+        "hands_on_url": "https://docs.qiime2.org/jupyterbooks/cancer-microbiome-intervention-tutorial/index.html#",
+        "id": "microbiome/qiime2-cancer-microbiome-intervention",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
         ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2024-03-14",
-        "objectives": [
-            "Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy",
-            "Using a mock community to assess the error rate of your sequencing experiment",
-            "Visualize sample diversity using Krona and Phinch"
-        ],
-        "pageviews": 7229,
-        "priority": 1000,
-        "pub_date": "2017-02-12",
-        "questions": [
-            "What is the effect of normal variation in the gut microbiome on host health?"
-        ],
-        "redirect_from": [
-            "/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial",
-            "/short/microbiome/mothur-miseq-sop",
-            "/short/T00205",
-            "/short/T00390"
-        ],
-        "short_id": "T00390",
-        "short_tools": [
-            "mothur_remove_lineage",
-            "mothur_cluster_split",
-            "mothur_count_seqs",
-            "mothur_dist_shared",
-            "mothur_make_contigs",
-            "mothur_classify_otu",
-            "mothur_sub_sample",
-            "mothur_taxonomy_to_krona",
-            "mothur_chimera_vsearch",
-            "newick_display",
-            "mothur_venn",
-            "mothur_pre_cluster",
-            "XY_Plot_1",
-            "mothur_rarefaction_single",
-            "mothur_make_biom",
-            "mothur_screen_seqs",
-            "mothur_unique_seqs",
-            "mothur_count_groups",
-            "mothur_heatmap_sim",
-            "mothur_summary_seqs",
-            "mothur_tree_shared",
-            "mothur_remove_groups",
-            "mothur_make_shared",
-            "taxonomy_krona_chart",
-            "mothur_summary_single",
-            "mothur_cluster",
-            "mothur_seq_error",
-            "mothur_align_seqs",
-            "mothur_classify_seqs",
-            "mothur_get_groups",
-            "mothur_dist_seqs",
-            "mothur_filter_seqs",
-            "mothur_remove_seqs"
-        ],
+        "pageviews": 281,
+        "pub_date": "2024-02-12",
+        "short_id": "T00412",
+        "short_tools": [],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "metabarcoding",
         "supported_servers": {
-            "exact": [
+            "exact": [],
+            "inexact": [
                 {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.org (Main)",
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 },
                 {
+                    "human": "Galaxy Australia",
+                    "id": "au",
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
                 }
             ]
         },
@@ -155794,45 +157502,13 @@
         "tags": [
             "metabarcoding",
             "16S",
+            "taxonomic profiling",
+            "diversity",
             "microgalaxy"
         ],
-        "time_estimation": "6h",
-        "title": "16S Microbial Analysis with mothur (extended)",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_groups/mothur_get_groups/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.36.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_seq_error/mothur_seq_error/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_taxonomy_to_krona/mothur_taxonomy_to_krona/1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6"
-        ],
+        "time_estimation": "10H",
+        "title": "QIIME 2 Cancer Microbiome Intervention",
+        "tools": [],
         "topic_name": "microbiome",
         "topic_name_human": "Microbiome",
         "tours": false,
@@ -155841,228 +157517,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "mothur-miseq-sop",
+        "tutorial_name": "qiime2-cancer-microbiome-intervention",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.json"
         },
-        "version": 4,
+        "version": 3,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 179,
-        "visitors": 4695,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "16S Microbial Analysis with mothur (extended)",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput FASTQ pairs\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nsilva.v4.fasta\"]\n  10[label=\"Count.seqs\"]\n  8 -> 10 [label=\"groups_out\"]\n  9 -> 10 [label=\"out_names\"]\n  11[label=\"Align.seqs\"]\n  1 -> 11 [label=\"output\"]\n  9 -> 11 [label=\"out_fasta\"]\n  12[label=\"Summary.seqs\"]\n  10 -> 12 [label=\"seq_count\"]\n  11 -> 12 [label=\"out_align\"]\n  13[label=\"Screen.seqs\"]\n  10 -> 13 [label=\"seq_count\"]\n  11 -> 13 [label=\"out_align\"]\n  14[label=\"Filter.seqs\"]\n  13 -> 14 [label=\"fasta_out\"]\n  15[label=\"Unique.seqs\"]\n  14 -> 15 [label=\"filteredfasta\"]\n  13 -> 15 [label=\"count_out\"]\n  16[label=\"Pre.cluster\"]\n  15 -> 16 [label=\"out_fasta\"]\n  15 -> 16 [label=\"out_count\"]\n  17[label=\"Chimera.vsearch\"]\n  16 -> 17 [label=\"fasta_out\"]\n  16 -> 17 [label=\"count_out\"]\n  18[label=\"Remove.seqs\"]\n  17 -> 18 [label=\"out_accnos\"]\n  17 -> 18 [label=\"out_count\"]\n  16 -> 18 [label=\"fasta_out\"]\n  19[label=\"Classify.seqs\"]\n  2 -> 19 [label=\"output\"]\n  18 -> 19 [label=\"count_out\"]\n  18 -> 19 [label=\"fasta_out\"]\n  3 -> 19 [label=\"output\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntrainset9_032012.pds.fasta\"]\n  20[label=\"Remove.lineage\"]\n  18 -> 20 [label=\"count_out\"]\n  18 -> 20 [label=\"fasta_out\"]\n  19 -> 20 [label=\"taxonomy_out\"]\n  21[label=\"Get.groups\"]\n  20 -> 21 [label=\"fasta_out\"]\n  20 -> 21 [label=\"count_out\"]\n  22[label=\"Remove.groups\"]\n  20 -> 22 [label=\"fasta_out\"]\n  20 -> 22 [label=\"count_out\"]\n  20 -> 22 [label=\"taxonomy_out\"]\n  23[label=\"Seq.error\"]\n  4 -> 23 [label=\"output\"]\n  21 -> 23 [label=\"count_out\"]\n  21 -> 23 [label=\"fasta_out\"]\n  24[label=\"Dist.seqs\"]\n  21 -> 24 [label=\"fasta_out\"]\n  25[label=\"Cluster.split\"]\n  22 -> 25 [label=\"fasta_out\"]\n  22 -> 25 [label=\"count_out\"]\n  22 -> 25 [label=\"taxonomy_out\"]\n  26[label=\"Cluster\"]\n  21 -> 26 [label=\"count_out\"]\n  24 -> 26 [label=\"out_dist\"]\n  27[label=\"Make.shared\"]\n  22 -> 27 [label=\"count_out\"]\n  25 -> 27 [label=\"otulist\"]\n  28[label=\"Classify.otu\"]\n  22 -> 28 [label=\"count_out\"]\n  25 -> 28 [label=\"otulist\"]\n  22 -> 28 [label=\"taxonomy_out\"]\n  29[label=\"Make.shared\"]\n  21 -> 29 [label=\"count_out\"]\n  26 -> 29 [label=\"otulist\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntrainset9_032012.pds.tax\"]\n  30[label=\"Summary.single\"]\n  27 -> 30 [label=\"shared\"]\n  31[label=\"Count.groups\"]\n  27 -> 31 [label=\"shared\"]\n  32[label=\"Dist.shared\"]\n  27 -> 32 [label=\"shared\"]\n  33[label=\"Rarefaction.single\"]\n  27 -> 33 [label=\"shared\"]\n  34[label=\"Sub.sample\"]\n  27 -> 34 [label=\"shared\"]\n  35[label=\"Taxonomy-to-Krona\"]\n  28 -> 35 [label=\"taxonomies\"]\n  36[label=\"Rarefaction.single\"]\n  29 -> 36 [label=\"shared\"]\n  37[label=\"Tree.shared\"]\n  32 -> 37 [label=\"distfiles\"]\n  38[label=\"Heatmap.sim\"]\n  32 -> 38 [label=\"distfiles\"]\n  39[label=\"Plotting tool\"]\n  33 -> 39 [label=\"rarefactioncurves\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHMP_MOCK.v35.fasta\"]\n  40[label=\"Venn\"]\n  34 -> 40 [label=\"shared_out\"]\n  41[label=\"Make.biom\"]\n  28 -> 41 [label=\"taxonomies\"]\n  5 -> 41 [label=\"output\"]\n  34 -> 41 [label=\"shared_out\"]\n  42[label=\"Krona pie chart\"]\n  35 -> 42 [label=\"outputfile\"]\n  43[label=\"Newick Display\"]\n  37 -> 43 [label=\"tre\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmouse.dpw.metadata\"]\n  6[label=\"Make.contigs\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Summary.seqs\"]\n  6 -> 7 [label=\"fasta\"]\n  8[label=\"Screen.seqs\"]\n  6 -> 8 [label=\"fasta\"]\n  6 -> 8 [label=\"group\"]\n  9[label=\"Unique.seqs\"]\n  8 -> 9 [label=\"fasta_out\"]\n}",
-                "history": [
-                    {
-                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
-                        "message": "Rename metagenomics topic to microbiome",
-                        "num": 1,
-                        "short_hash": "0e0a2f2cc",
-                        "unix": "1704901629"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "Input FASTQ pairs",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 1211
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list:paired\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "a0cb222c-075e-4617-b919-5bfcf218e9b6",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "silva.v4.fasta",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 211,
-                            "top": 1316
-                        },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "074d08d3-5ea8-45ff-8ac2-f2553ccc484f",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "trainset9_032012.pds.fasta",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 203,
-                            "top": 1434
-                        },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "44b087dc-00b3-49c2-aad2-31cd468e9f2f",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "trainset9_032012.pds.tax",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 207,
-                            "top": 1581
-                        },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "986945e9-f3d2-4c0d-8eb4-8ff64517b6cd",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "HMP_MOCK.v35.fasta",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 3082,
-                            "top": 273
-                        },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "1a21d45e-6e1a-4f0b-b5f2-5d60548c3eef",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "mouse.dpw.metadata",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 4677.5,
-                            "top": 2893.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "56b633c1-dffb-4b67-8eee-c9cdb1fcdd5a",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput FASTQ pairs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nsilva.v4.fasta\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Count.seqs\"];\n  8 -->|groups_out| 10;\n  9 -->|out_names| 10;\n  11[\"Align.seqs\"];\n  1 -->|output| 11;\n  9 -->|out_fasta| 11;\n  12[\"Summary.seqs\"];\n  10 -->|seq_count| 12;\n  11 -->|out_align| 12;\n  13[\"Screen.seqs\"];\n  10 -->|seq_count| 13;\n  11 -->|out_align| 13;\n  14[\"Filter.seqs\"];\n  13 -->|fasta_out| 14;\n  15[\"Unique.seqs\"];\n  14 -->|filteredfasta| 15;\n  13 -->|count_out| 15;\n  16[\"Pre.cluster\"];\n  15 -->|out_fasta| 16;\n  15 -->|out_count| 16;\n  17[\"Chimera.vsearch\"];\n  16 -->|fasta_out| 17;\n  16 -->|count_out| 17;\n  18[\"Remove.seqs\"];\n  17 -->|out_accnos| 18;\n  17 -->|out_count| 18;\n  16 -->|fasta_out| 18;\n  19[\"Classify.seqs\"];\n  2 -->|output| 19;\n  18 -->|count_out| 19;\n  18 -->|fasta_out| 19;\n  3 -->|output| 19;\n  2[\"\u2139\ufe0f Input Dataset\\ntrainset9_032012.pds.fasta\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  20[\"Remove.lineage\"];\n  18 -->|count_out| 20;\n  18 -->|fasta_out| 20;\n  19 -->|taxonomy_out| 20;\n  21[\"Get.groups\"];\n  20 -->|fasta_out| 21;\n  20 -->|count_out| 21;\n  22[\"Remove.groups\"];\n  20 -->|fasta_out| 22;\n  20 -->|count_out| 22;\n  20 -->|taxonomy_out| 22;\n  23[\"Seq.error\"];\n  4 -->|output| 23;\n  21 -->|count_out| 23;\n  21 -->|fasta_out| 23;\n  24[\"Dist.seqs\"];\n  21 -->|fasta_out| 24;\n  25[\"Cluster.split\"];\n  22 -->|fasta_out| 25;\n  22 -->|count_out| 25;\n  22 -->|taxonomy_out| 25;\n  26[\"Cluster\"];\n  21 -->|count_out| 26;\n  24 -->|out_dist| 26;\n  27[\"Make.shared\"];\n  22 -->|count_out| 27;\n  25 -->|otulist| 27;\n  28[\"Classify.otu\"];\n  22 -->|count_out| 28;\n  25 -->|otulist| 28;\n  22 -->|taxonomy_out| 28;\n  29[\"Make.shared\"];\n  21 -->|count_out| 29;\n  26 -->|otulist| 29;\n  3[\"\u2139\ufe0f Input Dataset\\ntrainset9_032012.pds.tax\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  30[\"Summary.single\"];\n  27 -->|shared| 30;\n  31[\"Count.groups\"];\n  27 -->|shared| 31;\n  32[\"Dist.shared\"];\n  27 -->|shared| 32;\n  33[\"Rarefaction.single\"];\n  27 -->|shared| 33;\n  34[\"Sub.sample\"];\n  27 -->|shared| 34;\n  35[\"Taxonomy-to-Krona\"];\n  28 -->|taxonomies| 35;\n  36[\"Rarefaction.single\"];\n  29 -->|shared| 36;\n  37[\"Tree.shared\"];\n  32 -->|distfiles| 37;\n  38[\"Heatmap.sim\"];\n  32 -->|distfiles| 38;\n  39[\"Plotting tool\"];\n  33 -->|rarefactioncurves| 39;\n  4[\"\u2139\ufe0f Input Dataset\\nHMP_MOCK.v35.fasta\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  40[\"Venn\"];\n  34 -->|shared_out| 40;\n  41[\"Make.biom\"];\n  28 -->|taxonomies| 41;\n  5 -->|output| 41;\n  34 -->|shared_out| 41;\n  42[\"Krona pie chart\"];\n  35 -->|outputfile| 42;\n  43[\"Newick Display\"];\n  37 -->|tre| 43;\n  5[\"\u2139\ufe0f Input Dataset\\nmouse.dpw.metadata\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"Make.contigs\"];\n  0 -->|output| 6;\n  7[\"Summary.seqs\"];\n  6 -->|fasta| 7;\n  8[\"Screen.seqs\"];\n  6 -->|fasta| 8;\n  6 -->|group| 8;\n  9[\"Unique.seqs\"];\n  8 -->|fasta_out| 9;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Training: 16S rRNA Sequencing With Mothur: Main Tutorial",
-                "outputs": [],
-                "parent_id": "microbiome/mothur-miseq-sop",
-                "path": "topics/microbiome/tutorials/mothur-miseq-sop/workflows/mothur-miseq-sop.ga",
-                "tags": [
-                    "microbiome"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Training: 16S rRNA Sequencing With Mothur: Main Tutorial",
-                "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-mothur-miseq-sop/versions/mothur-miseq-sop",
-                "tutorial_id": "mothur-miseq-sop",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop/workflows/mothur-miseq-sop.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop/workflows/mothur-miseq-sop.html",
-                "version": 1,
-                "wfid": "microbiome-mothur-miseq-sop",
-                "wfname": "mothur-miseq-sop",
-                "workflow": "mothur-miseq-sop.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_groups/mothur_get_groups/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.36.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_seq_error/mothur_seq_error/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_taxonomy_to_krona/mothur_taxonomy_to_krona/1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6"
-                ],
-                "workflowhub_id": "1101"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.800651"
+        "visit_duration": 209,
+        "visitors": 153
     },
     {
         "admin_install": {
@@ -156071,810 +157538,343 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "bwa",
-                    "owner": "devteam",
-                    "revisions": "e188dc7a68e6",
-                    "tool_panel_section_label": "Mapping",
+                    "name": "taxonomy_krona_chart",
+                    "owner": "crs4",
+                    "revisions": "c9f8fef1df74",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "column_maker",
+                    "name": "xy_plot",
                     "owner": "devteam",
-                    "revisions": "6595517c2dd8",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "revisions": "ecb437f1d298",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "emboss_5",
-                    "owner": "devteam",
-                    "revisions": "63dd26468588",
-                    "tool_panel_section_label": "EMBOSS",
+                    "name": "mothur_align_seqs",
+                    "owner": "iuc",
+                    "revisions": "abf7c15ecfef",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fasta_compute_length",
-                    "owner": "devteam",
-                    "revisions": "7d37cfda8e00",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "mothur_chimera_vsearch",
+                    "owner": "iuc",
+                    "revisions": "12e856482d26",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "compose_text_param",
+                    "name": "mothur_classify_otu",
                     "owner": "iuc",
-                    "revisions": "e188c9826e0f",
-                    "tool_panel_section_label": "Expression Tools",
+                    "revisions": "ff1bc0299372",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "datamash_ops",
+                    "name": "mothur_classify_seqs",
                     "owner": "iuc",
-                    "revisions": "746e8e4bf929",
-                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "revisions": "09bf9e496c64",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fastp",
+                    "name": "mothur_cluster",
                     "owner": "iuc",
-                    "revisions": "65b93b623c77",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "6366f4483b35",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ivar_consensus",
+                    "name": "mothur_cluster_split",
                     "owner": "iuc",
-                    "revisions": "40737febe339",
-                    "tool_panel_section_label": "Virology",
+                    "revisions": "19f45bdbffd9",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ivar_trim",
+                    "name": "mothur_count_groups",
                     "owner": "iuc",
-                    "revisions": "86a20ae274fc",
-                    "tool_panel_section_label": "Virology",
+                    "revisions": "dc3826bfc1ed",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "qualimap_bamqc",
+                    "name": "mothur_count_seqs",
                     "owner": "iuc",
-                    "revisions": "19ece8afbaab",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "revisions": "ffee46220ddd",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "samtools_merge",
+                    "name": "mothur_dist_seqs",
                     "owner": "iuc",
-                    "revisions": "36677f429310",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "revisions": "4d76fba83f24",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "samtools_view",
+                    "name": "mothur_dist_shared",
                     "owner": "iuc",
-                    "revisions": "5826298f6a73",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "revisions": "418100660ba3",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ucsc_fatovcf",
+                    "name": "mothur_filter_seqs",
                     "owner": "iuc",
-                    "revisions": "78df8fc2b3ab",
-                    "tool_panel_section_label": "Variant Calling",
+                    "revisions": "3524ca06478e",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fasta_regex_finder",
-                    "owner": "mbernt",
-                    "revisions": "9a811adb714f",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "mothur_get_groups",
+                    "owner": "iuc",
+                    "revisions": "03af14e245fb",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mafft",
-                    "owner": "rnateam",
-                    "revisions": "bf28a8cff401",
-                    "tool_panel_section_label": "Multiple Alignments",
+                    "name": "mothur_heatmap_sim",
+                    "owner": "iuc",
+                    "revisions": "7f5707dd6073",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mimodd_main",
-                    "owner": "wolma",
-                    "revisions": "f0f2795de2c7",
-                    "tool_panel_section_label": "MiModD",
+                    "name": "mothur_make_biom",
+                    "owner": "iuc",
+                    "revisions": "0b5397a74165",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 6595517c2dd8\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: emboss_5\n  owner: devteam\n  revisions: 63dd26468588\n  tool_panel_section_label: EMBOSS\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_compute_length\n  owner: devteam\n  revisions: 7d37cfda8e00\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: compose_text_param\n  owner: iuc\n  revisions: e188c9826e0f\n  tool_panel_section_label: Expression Tools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 746e8e4bf929\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ivar_consensus\n  owner: iuc\n  revisions: 40737febe339\n  tool_panel_section_label: Virology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ivar_trim\n  owner: iuc\n  revisions: 86a20ae274fc\n  tool_panel_section_label: Virology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qualimap_bamqc\n  owner: iuc\n  revisions: 19ece8afbaab\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_merge\n  owner: iuc\n  revisions: 36677f429310\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: 5826298f6a73\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ucsc_fatovcf\n  owner: iuc\n  revisions: 78df8fc2b3ab\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_regex_finder\n  owner: mbernt\n  revisions: 9a811adb714f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mafft\n  owner: rnateam\n  revisions: bf28a8cff401\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mimodd_main\n  owner: wolma\n  revisions: f0f2795de2c7\n  tool_panel_section_label: MiModD\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "wm75",
-                "TKlingstrom"
-            ],
-            "funding": [
-                "by-covid",
-                "elixir-converge",
-                "h2020-defend"
-            ]
-        },
-        "contributors": [
-            {
-                "affiliations": [
-                    "by-covid",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "fediverse": "https://scholar.social/@zerodivision",
-                "fediverse_flavor": "mastodon",
-                "id": "wm75",
-                "joined": "2017-09",
-                "matrix": "wm75:matrix.org",
-                "name": "Wolfgang Maier",
-                "orcid": "0000-0002-9464-6640",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "se",
-                "email": "tomas.klingstrom@slu.se",
-                "id": "TKlingstrom",
-                "joined": "2018-11",
-                "matrix": "TKlingstrom:matrix.org",
-                "name": "Tomas Klingstr\u00f6m",
-                "orcid": "0000-0002-9504-1352",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/TKlingstrom/",
-                "twitter": "TKlingstrom",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/TKlingstrom.json"
-            },
-            {
-                "funder": true,
-                "funding_id": "101046203",
-                "funding_statement": "BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response.\n\nThis project has received funding from the European Union\u2019s Horizon Europe research and innovation programme under grant agreement \u2116 101046203 (BY-COVID)",
-                "funding_system": "cordis",
-                "id": "by-covid",
-                "joined": "2023-04",
-                "members": [
-                    "bgruening",
-                    "hexylena",
-                    "ilveroluca",
-                    "kikkomep",
-                    "mbaardwijk",
-                    "PapXis",
-                    "pauldg",
-                    "simleo",
-                    "stain",
-                    "wm75"
-                ],
-                "name": "BeYond-COVID",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/by-covid/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/by-covid.json"
-            },
-            {
-                "avatar": "https://elixir-europe.org/sites/default/files/styles/right-medium/public/images/converge_logo.png",
-                "funder": true,
-                "funding_id": "871075",
-                "funding_statement": "ELIXIR CONVERGE is connecting and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services. This project has received funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement \u2116 871075",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "elixir-converge",
-                "joined": "2023-01",
-                "members": [
-                    "bgruening",
-                    "hexylena"
-                ],
-                "name": "ELIXIR-CONVERGE",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-converge/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-converge.json"
-            },
-            {
-                "funder": true,
-                "funding_id": "773701",
-                "funding_statement": "DEFEND is Addressing the dual emerging threats of African Swine Fever and Lumpy Skin Disease in Europe.\n\nThis work has received funding from the DEFEND project (www.defend2020.eu) with funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement No 773701.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "h2020-defend",
-                "joined": "2023-05",
-                "name": "Addressing the dual emerging threats of African Swine Fever and Lumpy Skin Disease in Europe",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/h2020-defend/",
-                "short_name": "DEFEND",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/h2020-defend.json"
-            }
-        ],
-        "dir": "topics/variant-analysis/tutorials/pox-tiled-amplicon",
-        "edam_operation": [
-            "Global alignment",
-            "Sequencing quality control",
-            "Sequence contamination filtering",
-            "Genome indexing",
-            "Sequence alignment",
-            "Sequence analysis",
-            "Read mapping",
-            "Sequence alignment analysis",
-            "Multiple sequence alignment",
-            "Generation",
-            "Local alignment"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "variant-analysis/pox-tiled-amplicon",
-        "inexact_supported_servers": [
-            "UseGalaxy.org (Main)"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Compared to other viruses, analysis of sequencing data from pox viruses is complicated by the rather large genome size and by the presence of inverted terminal repeats, but well-designed wet lab and bioinformatic workflows can handle these particularities.",
-            "Galaxy and its huge set of tools are flexible enough to handle half-genome sequencing data efficiently.",
-            "A mapping-based approach can result in high-quality consensus genome reconstructions from pox virus sequencing data and appears promising even when dealing with recombinant samples."
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Advanced",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-03-20",
-        "objectives": [
-            "Learn how to deal with pox virus genomes inverted terminal repeats through a combination of wet lab protocol and tailored bioinformatics",
-            "Construct a sample consensus genome from mapped reads",
-            "Explore a recombinant pox virus genome via a multiple-sequence alignment of consensus genome and references and through lists of mutations derived from it"
-        ],
-        "pageviews": 594,
-        "pub_date": "2023-05-15",
-        "questions": [
-            "Which special challenges does one encounter during sequence data analysis of pox viruses?",
-            "How can standard workflows for viral mutation calling and consensus generation be adapted to the particularities of pox viruses?",
-            "How can viral consensus sequences, multiple-sequence alignments and mutation calls be generated from each other and used to answer questions about the data?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "collections",
-                    "upload-rules"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00347",
-        "short_tools": [
-            "samtools_view",
-            "rbc_mafft",
-            "Cut1",
-            "EMBOSS: maskseq51",
-            "ivar_consensus",
-            "Grep1",
-            "__APPLY_RULES__",
-            "datamash_ops",
-            "qualimap_bamqc",
-            "fatovcf",
-            "ivar_trim",
-            "__ZIP_COLLECTION__",
-            "fasta_regex_finder",
-            "fasta_compute_length",
-            "bwa_mem",
-            "upload1",
-            "param_value_from_file",
-            "compose_text_param",
-            "fastp",
-            "mimodd_info",
-            "Add_a_column1",
-            "samtools_merge"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "one-health",
-        "supported_servers": {
-            "exact": [
+                },
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
+                    "name": "mothur_make_contigs",
+                    "owner": "iuc",
+                    "revisions": "ab12df91b47f",
+                    "tool_panel_section_label": "Mothur",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "virology",
-            "one-health"
-        ],
-        "time_estimation": "4H",
-        "title": "Pox virus genome analysis from tiled-amplicon sequencing data",
-        "tools": [
-            "Cut1",
-            "Grep1",
-            "__APPLY_RULES__",
-            "__ZIP_COLLECTION__",
-            "param_value_from_file",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_fatovcf/fatovcf/426+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/mbernt/fasta_regex_finder/fasta_regex_finder/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.520+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_info/0.1.8_1",
-            "upload1"
-        ],
-        "topic_name": "variant-analysis",
-        "topic_name_human": "Variant Analysis",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "pox-tiled-amplicon",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.json"
-        },
-        "version": 4,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 140,
-        "visitors": 497,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0001-6897-1215",
-                        "name": "Viktoria Isabel Schwarz"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0002-9464-6640",
-                        "name": "Wolfgang Maier"
-                    }
-                ],
-                "description": "From a reference and a primer scheme generate two masked half-genome references for ITR-aware pox virus sequencing data analysis.",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
+                    "name": "mothur_make_shared",
+                    "owner": "iuc",
+                    "revisions": "d0967ae326be",
+                    "tool_panel_section_label": "Mothur",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPrimer Scheme\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference FASTA\"]\n  2[label=\"Select pool1 primers\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Select pool2 primers\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Compute sequence length\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Datamash\"]\n  2 -> 5 [label=\"out_file1\"]\n  6[label=\"Datamash\"]\n  3 -> 6 [label=\"out_file1\"]\n  7[label=\"Cut\"]\n  4 -> 7 [label=\"output\"]\n  8[label=\"Compute\"]\n  5 -> 8 [label=\"out_file\"]\n  9[label=\"Get start position of Pool2\"]\n  6 -> 9 [label=\"out_file\"]\n  10[label=\"Get end position of sequence\"]\n  7 -> 10 [label=\"out_file1\"]\n  11[label=\"Get end position of Pool1\"]\n  8 -> 11 [label=\"out_file1\"]\n  12[label=\"Compose text parameter value\"]\n  9 -> 12 [label=\"text_param\"]\n  13[label=\"Compose text parameter value\"]\n  11 -> 13 [label=\"text_param\"]\n  10 -> 13 [label=\"text_param\"]\n  14[label=\"Mask Reference for Pool2\"]\n  1 -> 14 [label=\"output\"]\n  12 -> 14 [label=\"out1\"]\n  kaf755a5e2b2049bc9d5234781f937f48[color=lightseagreen,label=\"Output\\nmasked_ref_pool2\"]\n  14 -> kaf755a5e2b2049bc9d5234781f937f48\n  15[label=\"Mask Reference for Pool1\"]\n  1 -> 15 [label=\"output\"]\n  13 -> 15 [label=\"out1\"]\n  k0c3b5b20c426428ca08bc835a82477c1[color=lightseagreen,label=\"Output\\nmasked_ref_pool1\"]\n  15 -> k0c3b5b20c426428ca08bc835a82477c1\n}",
-                "history": [
-                    {
-                        "hash": "79db81a7c1c23d9778536abaa9ca879f3b0bbda5",
-                        "message": "Update pox-virus-tiled-amplicon-ref-masking.ga",
-                        "num": 2,
-                        "short_hash": "79db81a7c",
-                        "unix": "1684740183"
-                    },
-                    {
-                        "hash": "314d08f56a2d904cbab620fa5400ed0dbfa9619a",
-                        "message": "Add some material for new pox virus tiled amplicon tutorial",
-                        "num": 1,
-                        "short_hash": "314d08f56",
-                        "unix": "1682289363"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "The workflow expects a primer scheme split into two separate sequencing pools. These pools must be denoted as pool1/pool2 in the BED score column. The pool ids may, optionally, be followed by indicators of the subpool for tiled PCR amplification (e.g., pool1a/pool1b/pool2a/pool2b)",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "The workflow expects a primer scheme split into two separate sequencing pools. These pools must be denoted as pool1/pool2 in the BED score column. The pool ids may, optionally, be followed by indicators of the subpool for tiled PCR amplification (e.g., pool1a/pool1b/pool2a/pool2b)",
-                                "name": "Primer Scheme (BED file with Pool identifiers)"
-                            }
-                        ],
-                        "label": "Primer Scheme",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 667.3406219482422
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "1829d4e0-ee74-4a94-8dc5-98a11d96b961",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "The viral reference sequence to map sequenced reads against",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "The viral reference sequence to map sequenced reads against",
-                                "name": "Reference FASTA"
-                            }
-                        ],
-                        "label": "Reference FASTA",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 251.7752034262281,
-                            "top": 650.9021921247038
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f17c7022-fc94-42b5-ae90-7b3ec3d70ffb",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPrimer Scheme\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference FASTA\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Select pool1 primers\"];\n  0 -->|output| 2;\n  3[\"Select pool2 primers\"];\n  0 -->|output| 3;\n  4[\"Compute sequence length\"];\n  1 -->|output| 4;\n  5[\"Datamash\"];\n  2 -->|out_file1| 5;\n  6[\"Datamash\"];\n  3 -->|out_file1| 6;\n  7[\"Cut\"];\n  4 -->|output| 7;\n  8[\"Compute\"];\n  5 -->|out_file| 8;\n  9[\"Get start position of Pool2\"];\n  6 -->|out_file| 9;\n  10[\"Get end position of sequence\"];\n  7 -->|out_file1| 10;\n  11[\"Get end position of Pool1\"];\n  8 -->|out_file1| 11;\n  12[\"Compose text parameter value\"];\n  9 -->|text_param| 12;\n  13[\"Compose text parameter value\"];\n  11 -->|text_param| 13;\n  10 -->|text_param| 13;\n  14[\"Mask Reference for Pool2\"];\n  1 -->|output| 14;\n  12 -->|out1| 14;\n  af755a5e-2b20-49bc-9d52-34781f937f48[\"Output\\nmasked_ref_pool2\"];\n  14 --> af755a5e-2b20-49bc-9d52-34781f937f48;\n  style af755a5e-2b20-49bc-9d52-34781f937f48 stroke:#2c3143,stroke-width:4px;\n  15[\"Mask Reference for Pool1\"];\n  1 -->|output| 15;\n  13 -->|out1| 15;\n  0c3b5b20-c426-428c-a08b-c835a82477c1[\"Output\\nmasked_ref_pool1\"];\n  15 --> 0c3b5b20-c426-428c-a08b-c835a82477c1;\n  style 0c3b5b20-c426-428c-a08b-c835a82477c1 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "pox-virus-tiled-amplicon-ref-masking",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
-                        "errors": null,
-                        "id": 14,
-                        "input_connections": {
-                            "input1": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "regions": {
-                                "id": 12,
-                                "output_name": "out1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Mask Reference for Pool2",
-                        "name": "maskseq",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "left": 1438.15352300995,
-                            "top": 648.5794855890229
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Masked reference for mapping of pool2"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ce385837c160",
-                            "name": "emboss_5",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"maskchar\": \"N\", \"out_format1\": \"fasta\", \"regions\": {\"__class__\": \"ConnectedValue\"}, \"tolower\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.0.0",
-                        "type": "tool",
-                        "uuid": "140608b3-48b3-46f2-92e3-2b9c3fb9e3b2",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "masked_ref_pool2",
-                                "output_name": "out_file1",
-                                "uuid": "af755a5e-2b20-49bc-9d52-34781f937f48"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
-                        "errors": null,
-                        "id": 15,
-                        "input_connections": {
-                            "input1": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "regions": {
-                                "id": 13,
-                                "output_name": "out1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Mask Reference for Pool1",
-                        "name": "maskseq",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "left": 1452.6333312988281,
-                            "top": 223.50729370117188
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Masked reference for mapping of pool1"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ce385837c160",
-                            "name": "emboss_5",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"maskchar\": \"N\", \"out_format1\": \"fasta\", \"regions\": {\"__class__\": \"ConnectedValue\"}, \"tolower\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.0.0",
-                        "type": "tool",
-                        "uuid": "3c8b86c1-7e53-4b72-b836-88a921a368ba",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "masked_ref_pool1",
-                                "output_name": "out_file1",
-                                "uuid": "0c3b5b20-c426-428c-a08b-c835a82477c1"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "variant-analysis/pox-tiled-amplicon",
-                "path": "topics/variant-analysis/tutorials/pox-tiled-amplicon/workflows/pox-virus-tiled-amplicon-ref-masking.ga",
-                "tags": [
-                    "GTN",
-                    "variant-analysis"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "pox-virus-tiled-amplicon-ref-masking",
-                "topic_id": "variant-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-pox-tiled-amplicon/versions/pox-virus-tiled-amplicon-ref-masking",
-                "tutorial_id": "pox-tiled-amplicon",
-                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/pox-tiled-amplicon/workflows/pox-virus-tiled-amplicon-ref-masking.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/pox-tiled-amplicon/workflows/pox-virus-tiled-amplicon-ref-masking.html",
-                "version": 2,
-                "wfid": "variant-analysis-pox-tiled-amplicon",
-                "wfname": "pox-virus-tiled-amplicon-ref-masking",
-                "workflow": "pox-virus-tiled-amplicon-ref-masking.ga",
-                "workflow_tools": [
-                    "Cut1",
-                    "Grep1",
-                    "param_value_from_file",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2"
-                ],
-                "workflowhub_id": "1078"
-            }
-        ]
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "mothur_pre_cluster",
+                    "owner": "iuc",
+                    "revisions": "6532c3424bfe",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bwa",
-                    "owner": "devteam",
-                    "revisions": "3fe632431b68",
-                    "tool_panel_section_label": "Mapping",
+                    "name": "mothur_rarefaction_single",
+                    "owner": "iuc",
+                    "revisions": "47264675a4ea",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "picard",
-                    "owner": "devteam",
-                    "revisions": "a1f0b3f4b781",
-                    "tool_panel_section_label": "Picard",
+                    "name": "mothur_remove_groups",
+                    "owner": "iuc",
+                    "revisions": "498dc0671d9e",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "samtools_stats",
-                    "owner": "devteam",
-                    "revisions": "145f6d74ff5e",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "name": "mothur_remove_lineage",
+                    "owner": "iuc",
+                    "revisions": "947faa8b3205",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fastp",
+                    "name": "mothur_remove_seqs",
+                    "owner": "iuc",
+                    "revisions": "008f62670efc",
+                    "tool_panel_section_label": "Mothur",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mothur_screen_seqs",
+                    "owner": "iuc",
+                    "revisions": "f4d7d5755f01",
+                    "tool_panel_section_label": "Mothur",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mothur_seq_error",
                     "owner": "iuc",
-                    "revisions": "dbf9c561ef29",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "5a7674ac2c59",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "lofreq_call",
+                    "name": "mothur_sub_sample",
                     "owner": "iuc",
-                    "revisions": "65432c3abf6c",
-                    "tool_panel_section_label": "Variant Calling",
+                    "revisions": "67cb43432196",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "lofreq_indelqual",
+                    "name": "mothur_summary_seqs",
                     "owner": "iuc",
-                    "revisions": "426d707dfc47",
-                    "tool_panel_section_label": "Variant Calling",
+                    "revisions": "600c14c6dcc5",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "lofreq_viterbi",
+                    "name": "mothur_summary_single",
                     "owner": "iuc",
-                    "revisions": "aa35ee7f3ab2",
-                    "tool_panel_section_label": "Variant Calling",
+                    "revisions": "72be09dfd803",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "multiqc",
+                    "name": "mothur_taxonomy_to_krona",
                     "owner": "iuc",
-                    "revisions": "bf675f34b056",
-                    "tool_panel_section_label": "Quality Control",
+                    "revisions": "db30eb96ea23",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "snpeff_sars_cov_2",
+                    "name": "mothur_tree_shared",
                     "owner": "iuc",
-                    "revisions": "2a3a00c1fa0a",
-                    "tool_panel_section_label": "Variant Calling",
+                    "revisions": "8bca555fbcaf",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "snpsift",
+                    "name": "mothur_unique_seqs",
                     "owner": "iuc",
-                    "revisions": "5fab4f81391d",
-                    "tool_panel_section_label": "Variant Calling",
+                    "revisions": "a033f325ad8d",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sra_tools",
+                    "name": "mothur_venn",
                     "owner": "iuc",
-                    "revisions": "494b2ec08162",
-                    "tool_panel_section_label": "Get Data",
+                    "revisions": "4db54b1c1d83",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sra_tools",
+                    "name": "newick_utils",
                     "owner": "iuc",
-                    "revisions": "4df8de2d0e48",
-                    "tool_panel_section_label": "Get Data",
+                    "revisions": "fe4235285ee8",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: 3fe632431b68\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: a1f0b3f4b781\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 145f6d74ff5e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: dbf9c561ef29\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lofreq_call\n  owner: iuc\n  revisions: 65432c3abf6c\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lofreq_indelqual\n  owner: iuc\n  revisions: 426d707dfc47\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lofreq_viterbi\n  owner: iuc\n  revisions: aa35ee7f3ab2\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: bf675f34b056\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff_sars_cov_2\n  owner: iuc\n  revisions: 2a3a00c1fa0a\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpsift\n  owner: iuc\n  revisions: 5fab4f81391d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: 494b2ec08162\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: 4df8de2d0e48\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "mvdbeek",
-                "tnabtaf",
-                "blankenberg",
-                "nekrut"
-            ],
-            "editing": [
-                "wm75"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: taxonomy_krona_chart\n  owner: crs4\n  revisions: c9f8fef1df74\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xy_plot\n  owner: devteam\n  revisions: ecb437f1d298\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_align_seqs\n  owner: iuc\n  revisions: abf7c15ecfef\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_chimera_vsearch\n  owner: iuc\n  revisions: 12e856482d26\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_classify_otu\n  owner: iuc\n  revisions: ff1bc0299372\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_classify_seqs\n  owner: iuc\n  revisions: '09bf9e496c64'\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_cluster\n  owner: iuc\n  revisions: 6366f4483b35\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_cluster_split\n  owner: iuc\n  revisions: 19f45bdbffd9\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_count_groups\n  owner: iuc\n  revisions: dc3826bfc1ed\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_count_seqs\n  owner: iuc\n  revisions: ffee46220ddd\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_dist_seqs\n  owner: iuc\n  revisions: 4d76fba83f24\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_dist_shared\n  owner: iuc\n  revisions: 418100660ba3\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_filter_seqs\n  owner: iuc\n  revisions: 3524ca06478e\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_get_groups\n  owner: iuc\n  revisions: 03af14e245fb\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_heatmap_sim\n  owner: iuc\n  revisions: 7f5707dd6073\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_make_biom\n  owner: iuc\n  revisions: 0b5397a74165\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_make_contigs\n  owner: iuc\n  revisions: ab12df91b47f\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_make_shared\n  owner: iuc\n  revisions: d0967ae326be\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_pre_cluster\n  owner: iuc\n  revisions: 6532c3424bfe\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_rarefaction_single\n  owner: iuc\n  revisions: 47264675a4ea\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_remove_groups\n  owner: iuc\n  revisions: 498dc0671d9e\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_remove_lineage\n  owner: iuc\n  revisions: 947faa8b3205\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_remove_seqs\n  owner: iuc\n  revisions: '008f62670efc'\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_screen_seqs\n  owner: iuc\n  revisions: f4d7d5755f01\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_seq_error\n  owner: iuc\n  revisions: 5a7674ac2c59\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_sub_sample\n  owner: iuc\n  revisions: 67cb43432196\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_summary_seqs\n  owner: iuc\n  revisions: 600c14c6dcc5\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_summary_single\n  owner: iuc\n  revisions: 72be09dfd803\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_taxonomy_to_krona\n  owner: iuc\n  revisions: db30eb96ea23\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_tree_shared\n  owner: iuc\n  revisions: 8bca555fbcaf\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_unique_seqs\n  owner: iuc\n  revisions: a033f325ad8d\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_venn\n  owner: iuc\n  revisions: 4db54b1c1d83\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: newick_utils\n  owner: iuc\n  revisions: fe4235285ee8\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.json",
         "contributors": [
             {
-                "id": "mvdbeek",
-                "joined": "2018-06",
-                "name": "Marius van den Beek",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
-            },
-            {
-                "id": "tnabtaf",
-                "joined": "2017-09",
-                "name": "Dave Clements",
-                "orcid": "0000-0002-9970-6657",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
-            },
-            {
-                "id": "blankenberg",
-                "joined": "2018-07",
-                "name": "Daniel Blankenberg",
-                "orcid": "0000-0002-6833-9049",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankenberg/",
-                "twitter": "dblankenberg",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankenberg.json"
-            },
-            {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
                 "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             },
             {
                 "affiliations": [
-                    "by-covid",
-                    "uni-freiburg",
+                    "gallantries",
+                    "ifb",
                     "elixir-europe"
                 ],
-                "elixir_node": "de",
-                "fediverse": "https://scholar.social/@zerodivision",
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
                 "fediverse_flavor": "mastodon",
-                "id": "wm75",
+                "id": "bebatut",
                 "joined": "2017-09",
-                "matrix": "wm75:matrix.org",
-                "name": "Wolfgang Maier",
-                "orcid": "0000-0002-9464-6640",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "id": "tnabtaf",
+                "joined": "2017-09",
+                "name": "Dave Clements",
+                "orcid": "0000-0002-9970-6657",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
             }
         ],
-        "dir": "topics/variant-analysis/tutorials/sars-cov-2",
+        "dir": "topics/microbiome/tutorials/mothur-miseq-sop",
+        "edam_ontology": [
+            "topic_3697",
+            "topic_0637",
+            "topic_0080",
+            "topic_4038"
+        ],
         "edam_operation": [
+            "Phylogenetic tree analysis",
+            "DNA barcoding",
+            "Visualisation",
+            "Phylogenetic analysis",
             "Sequencing quality control",
-            "Sequence contamination filtering",
-            "Genome indexing",
-            "SNP detection",
-            "Sequence alignment",
-            "Formatting",
-            "Read mapping",
-            "Generation",
-            "Data handling",
-            "Validation"
+            "Phylogenetic tree generation",
+            "Phylogenetic tree reconstruction",
+            "Taxonomic classification",
+            "Sequence read processing",
+            "Sequence clustering"
+        ],
+        "edam_topic": [
+            "Microbial ecology",
+            "Taxonomy",
+            "Sequence analysis"
         ],
-        "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.be",
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "variant-analysis/sars-cov-2",
+        "id": "microbiome/mothur-miseq-sop",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
             "UseGalaxy.fr",
             "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
         "js_requirements": {
@@ -156882,70 +157882,80 @@
             "mermaid": false
         },
         "key_points": [
-            "Sequence data in the SRA can be directly imported into Galaxy",
-            "Collections enable efficient/parallel processing of sequence data from whole batches of samples",
-            "Genomic mutations in SARS-CoV-2 viral isolates can be identified through a straightforward pipeline involving sequenced reads preprocessing, mapping to the SARS-CoV-2 reference genome, postprocessing of mapping results, and variant calling"
+            "16S rRNA gene sequencing analysis results depend on the many algorithms used and their settings",
+            "Quality control and cleaning of your data is a crucial step in order to obtain optimal results",
+            "Adding a mock community to serve as a control sample can help you asses the error rate of your experimental setup",
+            "We can explore alpha and beta diversities using Krona and Phinch for dynamic visualizations"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-03-14",
         "objectives": [
-            "Understand how Galaxy and the Sequence Read Archive interact",
-            "Be able to go from Galaxy to the Short Reach Archive, query SRA, use the SRA Run Selector to send selected metadata to Galaxy, and then import sequence data from SRA into Galaxy",
-            "Understand how collections enable processing of sequencing data in batches",
-            "Understand the analysis steps required to identify and annotate genomic mutations from sequencing data of SARS-CoV-2 samples"
+            "Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy",
+            "Using a mock community to assess the error rate of your sequencing experiment",
+            "Visualize sample diversity using Krona and Phinch"
         ],
-        "pageviews": 18450,
-        "pub_date": "2020-06-24",
+        "pageviews": 8271,
+        "priority": 1000,
+        "pub_date": "2017-02-12",
         "questions": [
-            "How can you download public sequencing data deposited in the NCBI Sequence Read Archive (SRA) into a Galaxy history for analysis?",
-            "How can you process a batch of sequencing data from several samples efficiently/in parallel with Galaxy?",
-            "Starting from raw sequenced reads of whole-genome sequenced samples of SARS-CoV-2, how can you identify mutations in the genomes of these samples?"
+            "What is the effect of normal variation in the gut microbiome on host health?"
         ],
-        "recordings": [
-            {
-                "captioners": [
-                    "nekrut"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "15M",
-                "speakers": [
-                    "nekrut"
-                ],
-                "youtube_id": "9mIL0tIfZ_o"
-            }
+        "redirect_from": [
+            "/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial",
+            "/short/microbiome/mothur-miseq-sop",
+            "/short/T00205",
+            "/short/T00390"
         ],
-        "short_id": "T00315",
+        "short_id": "T00390",
         "short_tools": [
-            "Grep1",
-            "picard_MarkDuplicates",
-            "samtools_stats",
-            "fastp",
-            "multiqc",
-            "tp_cut_tool",
-            "fasterq_dump",
-            "snpSift_extractFields",
-            "Filter1",
-            "lofreq_call",
-            "lofreq_indelqual",
-            "lofreq_viterbi",
-            "bwa_mem",
-            "snpeff_sars_cov_2"
+            "mothur_dist_shared",
+            "mothur_seq_error",
+            "mothur_summary_seqs",
+            "mothur_remove_lineage",
+            "mothur_make_biom",
+            "mothur_count_seqs",
+            "mothur_get_groups",
+            "mothur_classify_seqs",
+            "mothur_remove_groups",
+            "mothur_make_shared",
+            "mothur_filter_seqs",
+            "mothur_dist_seqs",
+            "mothur_remove_seqs",
+            "mothur_rarefaction_single",
+            "mothur_venn",
+            "mothur_classify_otu",
+            "mothur_count_groups",
+            "mothur_align_seqs",
+            "mothur_taxonomy_to_krona",
+            "mothur_heatmap_sim",
+            "mothur_chimera_vsearch",
+            "mothur_cluster_split",
+            "mothur_screen_seqs",
+            "newick_display",
+            "mothur_pre_cluster",
+            "mothur_make_contigs",
+            "mothur_unique_seqs",
+            "XY_Plot_1",
+            "taxonomy_krona_chart",
+            "mothur_cluster",
+            "mothur_tree_shared",
+            "mothur_summary_single",
+            "mothur_sub_sample"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "one-health",
+        "subtopic": "metabarcoding",
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 }
             ],
@@ -156965,6 +157975,11 @@
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
@@ -156974,144 +157989,109 @@
         },
         "symlink": null,
         "tags": [
-            "covid19",
-            "virology",
-            "one-health"
+            "metabarcoding",
+            "16S",
+            "microgalaxy"
         ],
-        "time_estimation": "1H",
-        "title": "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis",
+        "time_estimation": "6h",
+        "title": "16S Microbial Analysis with mothur (extended)",
         "tools": [
-            "Filter1",
-            "Grep1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.3+galaxy0"
+            "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_groups/mothur_get_groups/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.36.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_seq_error/mothur_seq_error/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_taxonomy_to_krona/mothur_taxonomy_to_krona/1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6"
         ],
-        "topic_name": "variant-analysis",
-        "topic_name_human": "Variant Analysis",
+        "topic_name": "microbiome",
+        "topic_name_human": "Microbiome",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "sars-cov-2",
+        "tutorial_name": "mothur-miseq-sop",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/sars-cov-2/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.json"
         },
-        "version": 16,
+        "version": 4,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 175,
-        "visitors": 12116,
+        "visit_duration": 179,
+        "visitors": 5448,
         "workflows": [
             {
                 "creators": [],
-                "description": "Analysis of variation within individual COVID-19 samples (Paired End Illumina). Does not use paured",
+                "description": "16S Microbial Analysis with mothur (extended)",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nNC_045512.2 fasta file\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSRA Manifest\"]\n  2[label=\"Faster Download and Extract Reads in FASTQ\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"fastp\"]\n  2 -> 3 [label=\"list_paired\"]\n  4[label=\"Map with BWA-MEM\"]\n  3 -> 4 [label=\"output_paired_coll\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"MarkDuplicates\"]\n  4 -> 5 [label=\"bam_output\"]\n  6[label=\"Realign reads\"]\n  5 -> 6 [label=\"outFile\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Samtools stats\"]\n  5 -> 7 [label=\"outFile\"]\n  8[label=\"Insert indel qualities\"]\n  6 -> 8 [label=\"realigned\"]\n  0 -> 8 [label=\"output\"]\n  k2ca7c89b999f41dc8037e54e25959a7e[color=lightseagreen,label=\"Output\\nRealigned Alignments with Indel Qualities\"]\n  8 -> k2ca7c89b999f41dc8037e54e25959a7e\n  9[label=\"Call variants\"]\n  8 -> 9 [label=\"output\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"SnpEff eff:\"]\n  9 -> 10 [label=\"variants\"]\n  11[label=\"SnpSift Extract Fields\"]\n  10 -> 11 [label=\"snpeff_output\"]\n  k06259137eaa5404a923c70ee5f1d89d4[color=lightseagreen,label=\"Output\\nSnpSift tabular output\"]\n  11 -> k06259137eaa5404a923c70ee5f1d89d4\n  12[label=\"MultiQC\"]\n  3 -> 12 [label=\"report_json\"]\n  7 -> 12 [label=\"output\"]\n  5 -> 12 [label=\"metrics_file\"]\n  10 -> 12 [label=\"csvFile\"]\n  k758ffde57ddd482a88b21504f8335488[color=lightseagreen,label=\"Output\\nMultiQC Report PE\"]\n  12 -> k758ffde57ddd482a88b21504f8335488\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput FASTQ pairs\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nsilva.v4.fasta\"]\n  10[label=\"Count.seqs\"]\n  8 -> 10 [label=\"groups_out\"]\n  9 -> 10 [label=\"out_names\"]\n  11[label=\"Align.seqs\"]\n  1 -> 11 [label=\"output\"]\n  9 -> 11 [label=\"out_fasta\"]\n  12[label=\"Summary.seqs\"]\n  10 -> 12 [label=\"seq_count\"]\n  11 -> 12 [label=\"out_align\"]\n  13[label=\"Screen.seqs\"]\n  10 -> 13 [label=\"seq_count\"]\n  11 -> 13 [label=\"out_align\"]\n  14[label=\"Filter.seqs\"]\n  13 -> 14 [label=\"fasta_out\"]\n  15[label=\"Unique.seqs\"]\n  14 -> 15 [label=\"filteredfasta\"]\n  13 -> 15 [label=\"count_out\"]\n  16[label=\"Pre.cluster\"]\n  15 -> 16 [label=\"out_fasta\"]\n  15 -> 16 [label=\"out_count\"]\n  17[label=\"Chimera.vsearch\"]\n  16 -> 17 [label=\"fasta_out\"]\n  16 -> 17 [label=\"count_out\"]\n  18[label=\"Remove.seqs\"]\n  17 -> 18 [label=\"out_accnos\"]\n  17 -> 18 [label=\"out_count\"]\n  16 -> 18 [label=\"fasta_out\"]\n  19[label=\"Classify.seqs\"]\n  2 -> 19 [label=\"output\"]\n  18 -> 19 [label=\"count_out\"]\n  18 -> 19 [label=\"fasta_out\"]\n  3 -> 19 [label=\"output\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntrainset9_032012.pds.fasta\"]\n  20[label=\"Remove.lineage\"]\n  18 -> 20 [label=\"count_out\"]\n  18 -> 20 [label=\"fasta_out\"]\n  19 -> 20 [label=\"taxonomy_out\"]\n  21[label=\"Get.groups\"]\n  20 -> 21 [label=\"fasta_out\"]\n  20 -> 21 [label=\"count_out\"]\n  22[label=\"Remove.groups\"]\n  20 -> 22 [label=\"fasta_out\"]\n  20 -> 22 [label=\"count_out\"]\n  20 -> 22 [label=\"taxonomy_out\"]\n  23[label=\"Seq.error\"]\n  4 -> 23 [label=\"output\"]\n  21 -> 23 [label=\"count_out\"]\n  21 -> 23 [label=\"fasta_out\"]\n  24[label=\"Dist.seqs\"]\n  21 -> 24 [label=\"fasta_out\"]\n  25[label=\"Cluster.split\"]\n  22 -> 25 [label=\"fasta_out\"]\n  22 -> 25 [label=\"count_out\"]\n  22 -> 25 [label=\"taxonomy_out\"]\n  26[label=\"Cluster\"]\n  21 -> 26 [label=\"count_out\"]\n  24 -> 26 [label=\"out_dist\"]\n  27[label=\"Make.shared\"]\n  22 -> 27 [label=\"count_out\"]\n  25 -> 27 [label=\"otulist\"]\n  28[label=\"Classify.otu\"]\n  22 -> 28 [label=\"count_out\"]\n  25 -> 28 [label=\"otulist\"]\n  22 -> 28 [label=\"taxonomy_out\"]\n  29[label=\"Make.shared\"]\n  21 -> 29 [label=\"count_out\"]\n  26 -> 29 [label=\"otulist\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntrainset9_032012.pds.tax\"]\n  30[label=\"Summary.single\"]\n  27 -> 30 [label=\"shared\"]\n  31[label=\"Count.groups\"]\n  27 -> 31 [label=\"shared\"]\n  32[label=\"Dist.shared\"]\n  27 -> 32 [label=\"shared\"]\n  33[label=\"Rarefaction.single\"]\n  27 -> 33 [label=\"shared\"]\n  34[label=\"Sub.sample\"]\n  27 -> 34 [label=\"shared\"]\n  35[label=\"Taxonomy-to-Krona\"]\n  28 -> 35 [label=\"taxonomies\"]\n  36[label=\"Rarefaction.single\"]\n  29 -> 36 [label=\"shared\"]\n  37[label=\"Tree.shared\"]\n  32 -> 37 [label=\"distfiles\"]\n  38[label=\"Heatmap.sim\"]\n  32 -> 38 [label=\"distfiles\"]\n  39[label=\"Plotting tool\"]\n  33 -> 39 [label=\"rarefactioncurves\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHMP_MOCK.v35.fasta\"]\n  40[label=\"Venn\"]\n  34 -> 40 [label=\"shared_out\"]\n  41[label=\"Make.biom\"]\n  28 -> 41 [label=\"taxonomies\"]\n  5 -> 41 [label=\"output\"]\n  34 -> 41 [label=\"shared_out\"]\n  42[label=\"Krona pie chart\"]\n  35 -> 42 [label=\"outputfile\"]\n  43[label=\"Newick Display\"]\n  37 -> 43 [label=\"tre\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmouse.dpw.metadata\"]\n  6[label=\"Make.contigs\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Summary.seqs\"]\n  6 -> 7 [label=\"fasta\"]\n  8[label=\"Screen.seqs\"]\n  6 -> 8 [label=\"fasta\"]\n  6 -> 8 [label=\"group\"]\n  9[label=\"Unique.seqs\"]\n  8 -> 9 [label=\"fasta_out\"]\n}",
                 "history": [
                     {
-                        "hash": "18338ab9a1ef29b46dc8f2e8a7f7a4b055f16e3d",
-                        "message": "Use correct fasterqdump version",
-                        "num": 7,
-                        "short_hash": "18338ab9a",
-                        "unix": "1593005231"
-                    },
-                    {
-                        "hash": "979d6cd2174d0f2ce10ad195d9d3cc4b29a1623a",
-                        "message": "Reformat workflow, bump lofreq to 2.1.5",
-                        "num": 6,
-                        "short_hash": "979d6cd21",
-                        "unix": "1593004337"
-                    },
-                    {
-                        "hash": "ced05a792b3048548fd31a9d0bde9a1bf634481f",
-                        "message": "Fix workflow connections",
-                        "num": 5,
-                        "short_hash": "ced05a792",
-                        "unix": "1592944690"
-                    },
-                    {
-                        "hash": "1c38a3ed277eb7434c02927dce89f72e8a9c0c78",
-                        "message": "Use newer, simpler output",
-                        "num": 4,
-                        "short_hash": "1c38a3ed2",
-                        "unix": "1592943019"
-                    },
-                    {
-                        "hash": "a58450027f50bbdb5e91ee3529c7deef7ee1cf4e",
-                        "message": "add topic tag to workflow",
-                        "num": 3,
-                        "short_hash": "a58450027",
-                        "unix": "1592838416"
-                    },
-                    {
-                        "hash": "e8eea07056121bf6ee287bec31c64cd69d2e6dcb",
-                        "message": "reformat workflow",
-                        "num": 2,
-                        "short_hash": "e8eea0705",
-                        "unix": "1592835884"
-                    },
-                    {
-                        "hash": "a06c40264814dc80888f2a9ce28d4f06c2c3e687",
-                        "message": "Skeleton from PE sars-cov-2 workflow",
+                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
+                        "message": "Rename metagenomics topic to microbiome",
                         "num": 1,
-                        "short_hash": "a06c40264",
-                        "unix": "1592389814"
+                        "short_hash": "0e0a2f2cc",
+                        "unix": "1704901629"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "Contains SARS-CoV-2 reference sequence",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Contains SARS-CoV-2 reference sequence",
-                                "name": "NC_045512.2 fasta file"
-                            }
-                        ],
-                        "label": "NC_045512.2 fasta file",
-                        "name": "Input dataset",
+                        "inputs": [],
+                        "label": "Input FASTQ pairs",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 199.95736694335938,
-                            "top": 317.85511016845703
+                            "left": 200,
+                            "top": 1211
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"collection_type\": \"list:paired\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "0e91bcb8-fa43-4fc5-87f9-9e65784373e6",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1dedf4c3-5fc4-4505-baa0-b13e4416d67d"
-                            }
-                        ]
+                        "type": "data_collection_input",
+                        "uuid": "a0cb222c-075e-4617-b919-5bfcf218e9b6",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
@@ -157119,475 +158099,167 @@
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "SRA Manifest"
-                            }
-                        ],
-                        "label": "SRA Manifest",
+                        "inputs": [],
+                        "label": "silva.v4.fasta",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 199.95736694335938,
-                            "top": 372.3295364379883
+                            "left": 211,
+                            "top": 1316
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "3c5adef0-7af6-435e-bb10-966361130b58",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "fa458185-44d5-4d2d-ad69-20595c8ad337"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nNC_045512.2 fasta file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSRA Manifest\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Faster Download and Extract Reads in FASTQ\"];\n  1 -->|output| 2;\n  3[\"fastp\"];\n  2 -->|list_paired| 3;\n  4[\"Map with BWA-MEM\"];\n  3 -->|output_paired_coll| 4;\n  0 -->|output| 4;\n  5[\"MarkDuplicates\"];\n  4 -->|bam_output| 5;\n  6[\"Realign reads\"];\n  5 -->|outFile| 6;\n  0 -->|output| 6;\n  7[\"Samtools stats\"];\n  5 -->|outFile| 7;\n  8[\"Insert indel qualities\"];\n  6 -->|realigned| 8;\n  0 -->|output| 8;\n  2ca7c89b-999f-41dc-8037-e54e25959a7e[\"Output\\nRealigned Alignments with Indel Qualities\"];\n  8 --> 2ca7c89b-999f-41dc-8037-e54e25959a7e;\n  style 2ca7c89b-999f-41dc-8037-e54e25959a7e stroke:#2c3143,stroke-width:4px;\n  9[\"Call variants\"];\n  8 -->|output| 9;\n  0 -->|output| 9;\n  10[\"SnpEff eff:\"];\n  9 -->|variants| 10;\n  11[\"SnpSift Extract Fields\"];\n  10 -->|snpeff_output| 11;\n  06259137-eaa5-404a-923c-70ee5f1d89d4[\"Output\\nSnpSift tabular output\"];\n  11 --> 06259137-eaa5-404a-923c-70ee5f1d89d4;\n  style 06259137-eaa5-404a-923c-70ee5f1d89d4 stroke:#2c3143,stroke-width:4px;\n  12[\"MultiQC\"];\n  3 -->|report_json| 12;\n  7 -->|output| 12;\n  5 -->|metrics_file| 12;\n  10 -->|csvFile| 12;\n  758ffde5-7ddd-482a-88b2-1504f8335488[\"Output\\nMultiQC Report PE\"];\n  12 --> 758ffde5-7ddd-482a-88b2-1504f8335488;\n  style 758ffde5-7ddd-482a-88b2-1504f8335488 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "Simple COVID-19 - PE Variation",
-                "outputs": [
+                        "uuid": "074d08d3-5ea8-45ff-8ac2-f2553ccc484f",
+                        "workflow_outputs": []
+                    },
                     {
-                        "annotation": "Contains SARS-CoV-2 reference sequence",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 2,
                         "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Contains SARS-CoV-2 reference sequence",
-                                "name": "NC_045512.2 fasta file"
-                            }
-                        ],
-                        "label": "NC_045512.2 fasta file",
+                        "inputs": [],
+                        "label": "trainset9_032012.pds.fasta",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 199.95736694335938,
-                            "top": 317.85511016845703
+                            "left": 203,
+                            "top": 1434
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "0e91bcb8-fa43-4fc5-87f9-9e65784373e6",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1dedf4c3-5fc4-4505-baa0-b13e4416d67d"
-                            }
-                        ]
+                        "uuid": "44b087dc-00b3-49c2-aad2-31cd468e9f2f",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 3,
                         "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "SRA Manifest"
-                            }
-                        ],
-                        "label": "SRA Manifest",
+                        "inputs": [],
+                        "label": "trainset9_032012.pds.tax",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 199.95736694335938,
-                            "top": 372.3295364379883
+                            "left": 207,
+                            "top": 1581
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "3c5adef0-7af6-435e-bb10-966361130b58",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "fa458185-44d5-4d2d-ad69-20595c8ad337"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1",
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "input|file_list": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Faster Download and Extract Reads in FASTQ",
-                                "name": "input"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Faster Download and Extract Reads in FASTQ",
-                        "outputs": [
-                            {
-                                "name": "list_paired",
-                                "type": "input"
-                            },
-                            {
-                                "name": "output_collection",
-                                "type": "input"
-                            },
-                            {
-                                "name": "output_collection_other",
-                                "type": "input"
-                            },
-                            {
-                                "name": "log",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 342.9971618652344,
-                            "top": 317.85511016845703
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionlog": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "log"
-                            },
-                            "HideDatasetActionoutput_collection": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_collection"
-                            },
-                            "HideDatasetActionoutput_collection_other": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_collection_other"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "248f85ff0733",
-                            "name": "sra_tools",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adv\": {\"minlen\": \"\", \"split\": \"--split-3\", \"skip_technical\": \"true\"}, \"input\": {\"input_select\": \"file_list\", \"__current_case__\": 2, \"file_list\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.10.7+galaxy1",
-                        "type": "tool",
-                        "uuid": "3ce5b504-3641-4ea9-8d24-07f9bebaec23",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "list_paired",
-                                "uuid": "9e5c0368-e97c-4def-9704-1b902fbb2ed7"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "reads": {
-                                "id": 6,
-                                "output_name": "realigned"
-                            },
-                            "strategy|reference_source|ref": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Insert indel qualities",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "bam"
-                            }
-                        ],
-                        "position": {
-                            "left": 1057.5852355957031,
-                            "top": 317.85511016845703
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Realigned Alignments with Indel Qualities"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "354b534eeab7",
-                            "name": "lofreq_indelqual",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"reads\": {\"__class__\": \"ConnectedValue\"}, \"strategy\": {\"selector\": \"dindel\", \"__current_case__\": 1, \"reference_source\": {\"ref_selector\": \"history\", \"__current_case__\": 1, \"ref\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.5+galaxy0",
-                        "type": "tool",
-                        "uuid": "cbc7ee7f-5cfa-4d45-a83e-623efbf66068",
-                        "workflow_outputs": [
-                            {
-                                "label": "Realigned Alignments with Indel Qualities",
-                                "output_name": "output",
-                                "uuid": "2ca7c89b-999f-41dc-8037-e54e25959a7e"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
-                        "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "input": {
-                                "id": 9,
-                                "output_name": "variants"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool SnpEff eff:",
-                                "name": "intervals"
-                            },
-                            {
-                                "description": "runtime parameter for tool SnpEff eff:",
-                                "name": "transcripts"
-                            }
-                        ],
-                        "label": null,
-                        "name": "SnpEff eff:",
-                        "outputs": [
-                            {
-                                "name": "snpeff_output",
-                                "type": "vcf"
-                            },
-                            {
-                                "name": "statsFile",
-                                "type": "html"
-                            },
-                            {
-                                "name": "csvFile",
-                                "type": "csv"
-                            }
-                        ],
-                        "position": {
-                            "left": 1343.0823059082031,
-                            "top": 317.85511016845703
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActioncsvFile": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "csvFile"
-                            },
-                            "HideDatasetActionstatsFile": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "statsFile"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2a3a00c1fa0a",
-                            "name": "snpeff_sars_cov_2",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"annotations\": [\"-formatEff\", \"-classic\"], \"chr\": \"\", \"csvStats\": \"true\", \"filter\": {\"specificEffects\": \"no\", \"__current_case__\": 0}, \"filterOut\": [\"-no-downstream\", \"-no-intergenic\", \"-no-upstream\", \"-no-utr\"], \"generate_stats\": \"true\", \"genome_version\": \"NC_045512.2\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inputFormat\": \"vcf\", \"intervals\": {\"__class__\": \"RuntimeValue\"}, \"noLog\": \"true\", \"offset\": \"default\", \"outputConditional\": {\"outputFormat\": \"vcf\", \"__current_case__\": 0}, \"transcripts\": {\"__class__\": \"RuntimeValue\"}, \"udLength\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.5covid19",
-                        "type": "tool",
-                        "uuid": "8fb55fb1-4986-45f5-bb6b-45c1329842b2",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "snpeff_output",
-                                "uuid": "d5bec60d-c853-4979-a191-e69f47539684"
-                            }
-                        ]
+                        "uuid": "986945e9-f3d2-4c0d-8eb4-8ff64517b6cd",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 11,
-                        "input_connections": {
-                            "input": {
-                                "id": 10,
-                                "output_name": "snpeff_output"
-                            }
-                        },
+                        "id": 4,
+                        "input_connections": {},
                         "inputs": [],
-                        "label": null,
-                        "name": "SnpSift Extract Fields",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "tabular"
-                            }
-                        ],
+                        "label": "HMP_MOCK.v35.fasta",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1486.0794982910156,
-                            "top": 317.85511016845703
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "SnpSift tabular output"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2b3e65a4252f",
-                            "name": "snpsift",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 3082,
+                            "top": 273
                         },
-                        "tool_state": "{\"empty_text\": \".\", \"extract\": \"CHROM POS REF ALT QUAL DP AF SB DP4 EFF[*].IMPACT EFF[*].FUNCLASS EFF[*].EFFECT EFF[*].GENE EFF[*].CODON\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"one_effect_per_line\": \"false\", \"separator\": \",\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.3+t.galaxy0",
-                        "type": "tool",
-                        "uuid": "33e13bce-928f-41d6-b418-bc0a9e53d83d",
-                        "workflow_outputs": [
-                            {
-                                "label": "SnpSift tabular output",
-                                "output_name": "output",
-                                "uuid": "06259137-eaa5-404a-923c-70ee5f1d89d4"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "1a21d45e-6e1a-4f0b-b5f2-5d60548c3eef",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 12,
-                        "input_connections": {
-                            "results_0|software_cond|input": {
-                                "id": 3,
-                                "output_name": "report_json"
-                            },
-                            "results_1|software_cond|output_0|type|input": {
-                                "id": 7,
-                                "output_name": "output"
-                            },
-                            "results_2|software_cond|output_0|input": {
-                                "id": 5,
-                                "output_name": "metrics_file"
-                            },
-                            "results_3|software_cond|input": {
-                                "id": 10,
-                                "output_name": "csvFile"
-                            }
-                        },
+                        "id": 5,
+                        "input_connections": {},
                         "inputs": [],
-                        "label": null,
-                        "name": "MultiQC",
-                        "outputs": [
-                            {
-                                "name": "stats",
-                                "type": "input"
-                            },
-                            {
-                                "name": "plots",
-                                "type": "input"
-                            },
-                            {
-                                "name": "html_report",
-                                "type": "html"
-                            }
-                        ],
+                        "label": "mouse.dpw.metadata",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1486.0794982910156,
-                            "top": 397.8408889770508
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionplots": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "plots"
-                            },
-                            "HideDatasetActionstats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "stats"
-                            },
-                            "RenameDatasetActionhtml_report": {
-                                "action_arguments": {
-                                    "newname": "MultiQC Report PE"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "html_report"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "bf675f34b056",
-                            "name": "multiqc",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 4677.5,
+                            "top": 2893.5
                         },
-                        "tool_state": "{\"comment\": \"\", \"flat\": \"false\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 23, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"stats\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"snpeff\", \"__current_case__\": 25, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8+galaxy0",
-                        "type": "tool",
-                        "uuid": "8c98527f-d1db-4cc4-89f1-1e75c508b8e9",
-                        "workflow_outputs": [
-                            {
-                                "label": "MultiQC Report PE",
-                                "output_name": "html_report",
-                                "uuid": "758ffde5-7ddd-482a-88b2-1504f8335488"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "56b633c1-dffb-4b67-8eee-c9cdb1fcdd5a",
+                        "workflow_outputs": []
                     }
                 ],
-                "parent_id": "variant-analysis/sars-cov-2",
-                "path": "topics/variant-analysis/tutorials/sars-cov-2/workflows/main_workflow.ga",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput FASTQ pairs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nsilva.v4.fasta\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Count.seqs\"];\n  8 -->|groups_out| 10;\n  9 -->|out_names| 10;\n  11[\"Align.seqs\"];\n  1 -->|output| 11;\n  9 -->|out_fasta| 11;\n  12[\"Summary.seqs\"];\n  10 -->|seq_count| 12;\n  11 -->|out_align| 12;\n  13[\"Screen.seqs\"];\n  10 -->|seq_count| 13;\n  11 -->|out_align| 13;\n  14[\"Filter.seqs\"];\n  13 -->|fasta_out| 14;\n  15[\"Unique.seqs\"];\n  14 -->|filteredfasta| 15;\n  13 -->|count_out| 15;\n  16[\"Pre.cluster\"];\n  15 -->|out_fasta| 16;\n  15 -->|out_count| 16;\n  17[\"Chimera.vsearch\"];\n  16 -->|fasta_out| 17;\n  16 -->|count_out| 17;\n  18[\"Remove.seqs\"];\n  17 -->|out_accnos| 18;\n  17 -->|out_count| 18;\n  16 -->|fasta_out| 18;\n  19[\"Classify.seqs\"];\n  2 -->|output| 19;\n  18 -->|count_out| 19;\n  18 -->|fasta_out| 19;\n  3 -->|output| 19;\n  2[\"\u2139\ufe0f Input Dataset\\ntrainset9_032012.pds.fasta\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  20[\"Remove.lineage\"];\n  18 -->|count_out| 20;\n  18 -->|fasta_out| 20;\n  19 -->|taxonomy_out| 20;\n  21[\"Get.groups\"];\n  20 -->|fasta_out| 21;\n  20 -->|count_out| 21;\n  22[\"Remove.groups\"];\n  20 -->|fasta_out| 22;\n  20 -->|count_out| 22;\n  20 -->|taxonomy_out| 22;\n  23[\"Seq.error\"];\n  4 -->|output| 23;\n  21 -->|count_out| 23;\n  21 -->|fasta_out| 23;\n  24[\"Dist.seqs\"];\n  21 -->|fasta_out| 24;\n  25[\"Cluster.split\"];\n  22 -->|fasta_out| 25;\n  22 -->|count_out| 25;\n  22 -->|taxonomy_out| 25;\n  26[\"Cluster\"];\n  21 -->|count_out| 26;\n  24 -->|out_dist| 26;\n  27[\"Make.shared\"];\n  22 -->|count_out| 27;\n  25 -->|otulist| 27;\n  28[\"Classify.otu\"];\n  22 -->|count_out| 28;\n  25 -->|otulist| 28;\n  22 -->|taxonomy_out| 28;\n  29[\"Make.shared\"];\n  21 -->|count_out| 29;\n  26 -->|otulist| 29;\n  3[\"\u2139\ufe0f Input Dataset\\ntrainset9_032012.pds.tax\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  30[\"Summary.single\"];\n  27 -->|shared| 30;\n  31[\"Count.groups\"];\n  27 -->|shared| 31;\n  32[\"Dist.shared\"];\n  27 -->|shared| 32;\n  33[\"Rarefaction.single\"];\n  27 -->|shared| 33;\n  34[\"Sub.sample\"];\n  27 -->|shared| 34;\n  35[\"Taxonomy-to-Krona\"];\n  28 -->|taxonomies| 35;\n  36[\"Rarefaction.single\"];\n  29 -->|shared| 36;\n  37[\"Tree.shared\"];\n  32 -->|distfiles| 37;\n  38[\"Heatmap.sim\"];\n  32 -->|distfiles| 38;\n  39[\"Plotting tool\"];\n  33 -->|rarefactioncurves| 39;\n  4[\"\u2139\ufe0f Input Dataset\\nHMP_MOCK.v35.fasta\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  40[\"Venn\"];\n  34 -->|shared_out| 40;\n  41[\"Make.biom\"];\n  28 -->|taxonomies| 41;\n  5 -->|output| 41;\n  34 -->|shared_out| 41;\n  42[\"Krona pie chart\"];\n  35 -->|outputfile| 42;\n  43[\"Newick Display\"];\n  37 -->|tre| 43;\n  5[\"\u2139\ufe0f Input Dataset\\nmouse.dpw.metadata\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"Make.contigs\"];\n  0 -->|output| 6;\n  7[\"Summary.seqs\"];\n  6 -->|fasta| 7;\n  8[\"Screen.seqs\"];\n  6 -->|fasta| 8;\n  6 -->|group| 8;\n  9[\"Unique.seqs\"];\n  8 -->|fasta_out| 9;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Training: 16S rRNA Sequencing With Mothur: Main Tutorial",
+                "outputs": [],
+                "parent_id": "microbiome/mothur-miseq-sop",
+                "path": "topics/microbiome/tutorials/mothur-miseq-sop/workflows/mothur-miseq-sop.ga",
                 "tags": [
-                    "variant-analysis"
+                    "microbiome"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Simple COVID-19 - PE Variation",
-                "topic_id": "variant-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-sars-cov-2/versions/main-workflow",
-                "tutorial_id": "sars-cov-2",
-                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2/workflows/main_workflow.html",
+                "title": "Training: 16S rRNA Sequencing With Mothur: Main Tutorial",
+                "topic_id": "microbiome",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-mothur-miseq-sop/versions/mothur-miseq-sop",
+                "tutorial_id": "mothur-miseq-sop",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop/workflows/mothur-miseq-sop.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop/workflows/mothur-miseq-sop.html",
                 "version": 1,
-                "wfid": "variant-analysis-sars-cov-2",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "wfid": "microbiome-mothur-miseq-sop",
+                "wfname": "mothur-miseq-sop",
+                "workflow": "mothur-miseq-sop.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1"
+                    "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_groups/mothur_get_groups/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.36.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_seq_error/mothur_seq_error/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_taxonomy_to_krona/mothur_taxonomy_to_krona/1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6"
                 ],
-                "workflowhub_id": "1074"
+                "workflowhub_id": "1101"
             }
-        ]
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.800651"
     },
     {
         "admin_install": {
@@ -157596,1785 +158268,1681 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "fbf99087e067",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "xy_plot",
+                    "owner": "devteam",
+                    "revisions": "ecb437f1d298",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mothur_chimera_vsearch",
+                    "owner": "iuc",
+                    "revisions": "12e856482d26",
+                    "tool_panel_section_label": "Mothur",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mothur_classify_otu",
+                    "owner": "iuc",
+                    "revisions": "ff1bc0299372",
+                    "tool_panel_section_label": "Mothur",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mothur_classify_seqs",
+                    "owner": "iuc",
+                    "revisions": "09bf9e496c64",
+                    "tool_panel_section_label": "Mothur",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mothur_cluster",
+                    "owner": "iuc",
+                    "revisions": "6366f4483b35",
+                    "tool_panel_section_label": "Mothur",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mothur_cluster_split",
+                    "owner": "iuc",
+                    "revisions": "19f45bdbffd9",
+                    "tool_panel_section_label": "Mothur",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mothur_count_groups",
+                    "owner": "iuc",
+                    "revisions": "dc3826bfc1ed",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "mothur_count_seqs",
+                    "owner": "iuc",
+                    "revisions": "ffee46220ddd",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "fbf99087e067",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "mothur_dist_seqs",
+                    "owner": "iuc",
+                    "revisions": "4d76fba83f24",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "emboss_5",
-                    "owner": "devteam",
-                    "revisions": "63dd26468588",
-                    "tool_panel_section_label": "EMBOSS",
+                    "name": "mothur_dist_shared",
+                    "owner": "iuc",
+                    "revisions": "418100660ba3",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "3d0c7bdf12f5",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "mothur_filter_seqs",
+                    "owner": "iuc",
+                    "revisions": "3524ca06478e",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "5ec9f6bceaee",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "mothur_heatmap_sim",
+                    "owner": "iuc",
+                    "revisions": "7f5707dd6073",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "samtools_stats",
-                    "owner": "devteam",
-                    "revisions": "fed4aa48ba09",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "name": "mothur_make_shared",
+                    "owner": "iuc",
+                    "revisions": "d0967ae326be",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bcftools_consensus",
+                    "name": "mothur_pre_cluster",
                     "owner": "iuc",
-                    "revisions": "1171446da5db",
-                    "tool_panel_section_label": "Variant Calling",
+                    "revisions": "6532c3424bfe",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fastp",
+                    "name": "mothur_rarefaction_single",
                     "owner": "iuc",
-                    "revisions": "c59d48774d03",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "47264675a4ea",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "jbrowse",
+                    "name": "mothur_remove_groups",
                     "owner": "iuc",
-                    "revisions": "a6e57ff585c0",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "revisions": "498dc0671d9e",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "jvarkit_wgscoverageplotter",
+                    "name": "mothur_remove_lineage",
                     "owner": "iuc",
-                    "revisions": "ac048a34cac3",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "revisions": "947faa8b3205",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "kraken2",
+                    "name": "mothur_remove_seqs",
                     "owner": "iuc",
-                    "revisions": "20e2f64aa1fe",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "revisions": "d38f2ac5db71",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mosdepth",
+                    "name": "mothur_screen_seqs",
                     "owner": "iuc",
-                    "revisions": "5854d0da92b4",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "revisions": "63b74bfc8052",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "multiqc",
+                    "name": "mothur_sub_sample",
                     "owner": "iuc",
-                    "revisions": "abfd8a6544d7",
-                    "tool_panel_section_label": "Quality Control",
+                    "revisions": "67cb43432196",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "qualimap_bamqc",
+                    "name": "mothur_summary_seqs",
                     "owner": "iuc",
-                    "revisions": "4a89c6f84425",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "revisions": "600c14c6dcc5",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "snippy",
+                    "name": "mothur_summary_single",
                     "owner": "iuc",
-                    "revisions": "d220115f882b",
-                    "tool_panel_section_label": "Variant Calling",
+                    "revisions": "2344ed181ae6",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "tb_variant_filter",
+                    "name": "mothur_tree_shared",
                     "owner": "iuc",
-                    "revisions": "32f14a2723ec",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "8bca555fbcaf",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "tbprofiler",
+                    "name": "mothur_unique_seqs",
                     "owner": "iuc",
-                    "revisions": "4839e590cb26",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "a033f325ad8d",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "tbvcfreport",
+                    "name": "mothur_venn",
                     "owner": "iuc",
-                    "revisions": "42818629ec4c",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "4db54b1c1d83",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "tbvcfreport",
+                    "name": "newick_utils",
                     "owner": "iuc",
-                    "revisions": "9793bc5d741b",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "b4163d2f64ab",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "830961c48e42",
+                    "tool_panel_section_label": "Collection Operations",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: emboss_5\n  owner: devteam\n  revisions: 63dd26468588\n  tool_panel_section_label: EMBOSS\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: fed4aa48ba09\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_consensus\n  owner: iuc\n  revisions: 1171446da5db\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: c59d48774d03\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jvarkit_wgscoverageplotter\n  owner: iuc\n  revisions: ac048a34cac3\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: 20e2f64aa1fe\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mosdepth\n  owner: iuc\n  revisions: 5854d0da92b4\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: abfd8a6544d7\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qualimap_bamqc\n  owner: iuc\n  revisions: 4a89c6f84425\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snippy\n  owner: iuc\n  revisions: d220115f882b\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tb_variant_filter\n  owner: iuc\n  revisions: 32f14a2723ec\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbprofiler\n  owner: iuc\n  revisions: 4839e590cb26\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbvcfreport\n  owner: iuc\n  revisions: 42818629ec4c\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbvcfreport\n  owner: iuc\n  revisions: 9793bc5d741b\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: xy_plot\n  owner: devteam\n  revisions: ecb437f1d298\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_chimera_vsearch\n  owner: iuc\n  revisions: 12e856482d26\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_classify_otu\n  owner: iuc\n  revisions: ff1bc0299372\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_classify_seqs\n  owner: iuc\n  revisions: '09bf9e496c64'\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_cluster\n  owner: iuc\n  revisions: 6366f4483b35\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_cluster_split\n  owner: iuc\n  revisions: 19f45bdbffd9\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_count_groups\n  owner: iuc\n  revisions: dc3826bfc1ed\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_count_seqs\n  owner: iuc\n  revisions: ffee46220ddd\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_dist_seqs\n  owner: iuc\n  revisions: 4d76fba83f24\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_dist_shared\n  owner: iuc\n  revisions: 418100660ba3\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_filter_seqs\n  owner: iuc\n  revisions: 3524ca06478e\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_heatmap_sim\n  owner: iuc\n  revisions: 7f5707dd6073\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_make_shared\n  owner: iuc\n  revisions: d0967ae326be\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_pre_cluster\n  owner: iuc\n  revisions: 6532c3424bfe\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_rarefaction_single\n  owner: iuc\n  revisions: 47264675a4ea\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_remove_groups\n  owner: iuc\n  revisions: 498dc0671d9e\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_remove_lineage\n  owner: iuc\n  revisions: 947faa8b3205\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_remove_seqs\n  owner: iuc\n  revisions: d38f2ac5db71\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_screen_seqs\n  owner: iuc\n  revisions: 63b74bfc8052\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_sub_sample\n  owner: iuc\n  revisions: 67cb43432196\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_summary_seqs\n  owner: iuc\n  revisions: 600c14c6dcc5\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_summary_single\n  owner: iuc\n  revisions: 2344ed181ae6\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_tree_shared\n  owner: iuc\n  revisions: 8bca555fbcaf\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_unique_seqs\n  owner: iuc\n  revisions: a033f325ad8d\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_venn\n  owner: iuc\n  revisions: 4db54b1c1d83\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: newick_utils\n  owner: iuc\n  revisions: b4163d2f64ab\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.json",
         "contributors": [
             {
-                "bio": "Research at the South African National Bioinformatics Institute",
-                "id": "pvanheus",
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
                 "joined": "2017-09",
-                "name": "Peter van Heusden",
-                "orcid": "0000-0001-6553-5274",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/",
-                "twitter": "pvanheus",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pvanheus.json"
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             },
             {
-                "elixir_node": "au",
-                "email": "simon.gladman@unimelb.edu.au",
-                "id": "slugger70",
-                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
                 "joined": "2017-09",
-                "name": "Simon Gladman",
-                "orcid": "0000-0002-6100-4385",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             },
             {
-                "id": "thobalose",
-                "joined": "2019-11",
-                "name": "Thoba Lose",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/thobalose/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/thobalose.json"
+                "id": "tnabtaf",
+                "joined": "2017-09",
+                "name": "Dave Clements",
+                "orcid": "0000-0002-9970-6657",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
             }
         ],
-        "dir": "topics/variant-analysis/tutorials/tb-variant-analysis",
+        "dir": "topics/microbiome/tutorials/mothur-miseq-sop-short",
         "edam_ontology": [
-            "topic_0622",
-            "topic_3301",
-            "topic_0196",
-            "topic_0199",
-            "topic_3305",
-            "topic_3324"
+            "topic_3697",
+            "topic_0637",
+            "topic_0080",
+            "topic_4038"
         ],
         "edam_operation": [
-            "Global alignment",
+            "Phylogenetic tree analysis",
+            "DNA barcoding",
+            "Visualisation",
+            "Phylogenetic analysis",
             "Sequencing quality control",
-            "Sequence contamination filtering",
-            "Sequence alignment",
-            "Sequence analysis",
-            "Sequence composition calculation",
-            "Sequence alignment analysis",
-            "Taxonomic classification",
             "Phylogenetic tree generation",
-            "Variant calling",
-            "Local alignment",
-            "Phylogenetic tree visualisation",
-            "Validation",
-            "Genome visualisation",
-            "Statistical calculation",
-            "Antimicrobial resistance prediction"
+            "Phylogenetic tree reconstruction",
+            "Taxonomic classification",
+            "Sequence read processing",
+            "Sequence clustering"
         ],
         "edam_topic": [
-            "Genomics",
-            "Microbiology",
-            "Sequence assembly",
-            "Genetic variation",
-            "Public health and epidemiology",
-            "Infectious disease"
+            "Microbial ecology",
+            "Taxonomy",
+            "Sequence analysis"
+        ],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
-        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "variant-analysis/tb-variant-analysis",
-        "inexact_supported_servers": [],
+        "id": "microbiome/mothur-miseq-sop-short",
+        "inexact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.fr"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "variants in _M. tuberculosis_ sequencing data can be discovered using common microbial bioinformatics tools",
-            "it is not enough to just call variants, variant calling involves multiple quality control steps",
-            "the choice of reference genome and some quality control procedures are species-specific, and require knowledge of the organism in question",
-            "batches of samples can be processed using Galaxy dataset collections and workflows"
+            "16S rRNA gene sequencing analysis results depend on the many algorithms used and their settings",
+            "Quality control and cleaning of your data is a crucial step in order to obtain optimal results",
+            "Adding a mock community to serve as a control sample can help you asses the error rate of your experimental setup",
+            "We can explore alpha and beta diversities using Krona and Phinch for dynamic visualizations"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-26",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "How should we filter those variants",
-            "How can we predict drug resistance from those variants",
-            "How do we annotate those variants"
+            "Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy",
+            "Using a mock community to assess the error rate of your sequencing experiment",
+            "Visualize sample diversity using Krona and Phinch"
         ],
-        "pageviews": 8997,
-        "pub_date": "2020-07-25",
+        "pageviews": 3572,
+        "priority": 1000,
+        "pub_date": "2019-05-13",
         "questions": [
-            "How do we detect differences between a set of reads from _M. tuberculosis_ (Mtb) and the Mtb reference genome"
+            "What is the effect of normal variation in the gut microbiome on host health?"
         ],
         "recordings": [
             {
                 "captioners": [
-                    "pvanheus",
-                    "nagoue",
-                    "hexylena"
+                    "shiltemann"
                 ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "40M",
+                "date": "2023-05-19",
+                "galaxy_version": "23.01",
+                "length": "1H37M",
                 "speakers": [
-                    "pvanheus"
+                    "shiltemann"
                 ],
-                "youtube_id": "G1DmquX6Wh8"
+                "youtube_id": "CGSBeCW3rpA"
             },
             {
+                "archive-id": "smorgasbord2023",
                 "captioners": [
-                    "pvanheus"
+                    "shiltemann"
                 ],
-                "date": "2024-06-11",
-                "galaxy_version": "24.0",
-                "length": "1H17M",
+                "date": "2021-02-15",
+                "description": "This recording was created as part of the Sm\u00f6rg\u00e5sbord 2023 event.",
+                "galaxy_version": "21.01",
+                "length": "1H40M",
                 "speakers": [
-                    "pvanheus"
+                    "shiltemann"
                 ],
-                "youtube_id": "-nJPngFk36c"
+                "type": "Lecture & Tutorial",
+                "youtube_id": "mto4Nl-q7Kk"
             }
         ],
-        "short_id": "T00319",
+        "redirect_from": [
+            "/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial",
+            "/short/microbiome/mothur-miseq-sop-short",
+            "/short/T00206",
+            "/short/T00391"
+        ],
+        "short_id": "T00391",
         "short_tools": [
-            "tp_awk_tool",
-            "kraken2",
-            "bcftools_consensus",
-            "mosdepth",
-            "EMBOSS: seqret84",
-            "tb_profiler_profile",
-            "qualimap_bamqc",
-            "samtools_stats",
-            "tb_variant_filter",
-            "tp_sed_tool",
-            "EMBOSS:%20seqret84",
-            "upload1",
-            "tbvcfreport",
-            "fastp",
-            "jbrowse",
-            "multiqc",
-            "jvarkit_wgscoverageplotter",
-            "snippy",
-            "fastqc",
-            "__FLATTEN__"
+            "mothur_dist_shared",
+            "mothur_summary_seqs",
+            "mothur_remove_lineage",
+            "mothur_count_seqs",
+            "mothur_classify_seqs",
+            "mothur_remove_groups",
+            "mothur_make_shared",
+            "mothur_filter_seqs",
+            "mothur_dist_seqs",
+            "mothur_remove_seqs",
+            "mothur_rarefaction_single",
+            "mothur_venn",
+            "mothur_classify_otu",
+            "mothur_count_groups",
+            "mothur_heatmap_sim",
+            "mothur_chimera_vsearch",
+            "mothur_cluster_split",
+            "mothur_screen_seqs",
+            "collapse_dataset",
+            "newick_display",
+            "mothur_pre_cluster",
+            "mothur_unique_seqs",
+            "XY_Plot_1",
+            "mothur_cluster",
+            "mothur_tree_shared",
+            "mothur_summary_single",
+            "mothur_sub_sample"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "one-health",
+        "subtopic": "metabarcoding",
         "supported_servers": {
-            "exact": [],
-            "inexact": []
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                }
+            ]
         },
         "symlink": null,
         "tags": [
-            "prokaryote",
-            "one-health",
-            "microgalaxy",
-            "tuberculosis"
+            "metabarcoding",
+            "16S",
+            "microgalaxy"
         ],
         "time_estimation": "2h",
-        "title": "M. tuberculosis Variant Analysis",
+        "title": "16S Microbial Analysis with mothur (short)",
         "tools": [
-            "__FLATTEN__",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: seqret84/5.0.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS:%20seqret84/5.0.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jvarkit_wgscoverageplotter/jvarkit_wgscoverageplotter/20201223+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mosdepth/mosdepth/0.3.8+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.4.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.2.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.1+galaxy0",
-            "upload1"
+            "toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
         ],
-        "topic_name": "variant-analysis",
-        "topic_name_human": "Variant Analysis",
+        "topic_name": "microbiome",
+        "topic_name_human": "Microbiome",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "tb-variant-analysis",
+        "tutorial_name": "mothur-miseq-sop-short",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.json"
         },
-        "version": 30,
+        "version": 5,
         "video": false,
         "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 177,
-        "visitors": 5641,
+        "visit_duration": 337,
+        "visitors": 1985,
         "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "0000-0001-6553-5274",
-                        "name": "Peter van Heusden"
+                        "identifier": "https://orcid.org/0000-0003-3803-468X",
+                        "name": "Saskia Hiltemann"
                     }
                 ],
-                "description": "Predict variants and drug resistance from M. tuberculosis sequence samples (Illumina)",
+                "description": "16S Microbial Analysis with mothur (short)",
                 "features": {
                     "comments": false,
-                    "parameters": true,
-                    "report": {
-                        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
-                    },
+                    "parameters": false,
+                    "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nReads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference Genome\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMinimum depth of coverage\"]\n  3[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMinimum variant allele frequency\"]\n  4[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nAdditional BWA-MEM options\"]\n  5[label=\"fastp\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"seqret\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"snippy\"]\n  4 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  3 -> 7 [label=\"output\"]\n  5 -> 7 [label=\"output_paired_coll\"]\n  1 -> 7 [label=\"output\"]\n  8[label=\"Kraken2\"]\n  5 -> 8 [label=\"output_paired_coll\"]\n  kc7abf2bfed4c433ea6959eca61282bb5[color=lightseagreen,label=\"Output\\nreport_output\"]\n  8 -> kc7abf2bfed4c433ea6959eca61282bb5\n  k083a0e5177804c91a071dc0e4641d060[color=lightseagreen,label=\"Output\\noutput\"]\n  8 -> k083a0e5177804c91a071dc0e4641d060\n  9[label=\"QualiMap BamQC\"]\n  7 -> 9 [label=\"snpsbam\"]\n  10[label=\"mosdepth\"]\n  2 -> 10 [label=\"output\"]\n  7 -> 10 [label=\"snpsbam\"]\n  11[label=\"TB Variant Filter\"]\n  7 -> 11 [label=\"snpvcf\"]\n  12[label=\"TB-Profiler Profile\"]\n  7 -> 12 [label=\"snpsbam\"]\n  k335635b4a4de4980ad0268f0035daeaa[color=lightseagreen,label=\"Output\\noutput_txt\"]\n  12 -> k335635b4a4de4980ad0268f0035daeaa\n  13[label=\"TB Variant Filter\"]\n  7 -> 13 [label=\"snpvcf\"]\n  14[label=\"Flatten collection\"]\n  9 -> 14 [label=\"raw_data\"]\n  15[label=\"Text reformatting\"]\n  10 -> 15 [label=\"output_quantized_bed\"]\n  16[label=\"Text transformation\"]\n  11 -> 16 [label=\"output1\"]\n  k007df8c2bd13495f8904abf31d4594d0[color=lightseagreen,label=\"Output\\nFinal annotated VCF\"]\n  16 -> k007df8c2bd13495f8904abf31d4594d0\n  17[label=\"MultiQC\"]\n  5 -> 17 [label=\"report_json\"]\n  14 -> 17 [label=\"output\"]\n  k5952823575254ef9881036f1ed0f01f6[color=lightseagreen,label=\"Output\\nhtml_report\"]\n  17 -> k5952823575254ef9881036f1ed0f01f6\n  18[label=\"bcftools consensus\"]\n  13 -> 18 [label=\"output1\"]\n  6 -> 18 [label=\"out_file1\"]\n  15 -> 18 [label=\"outfile\"]\n  kc71b135d35f944d0a20ef25528e518af[color=lightseagreen,label=\"Output\\nconsensus_genome\"]\n  18 -> kc71b135d35f944d0a20ef25528e518af\n  19[label=\"TB Variant Report\"]\n  16 -> 19 [label=\"output\"]\n  12 -> 19 [label=\"results_json\"]\n  k959528d2f8f2444099cf44fddd6c5069[color=lightseagreen,label=\"Output\\ndrug_resistance_report_html\"]\n  19 -> k959528d2f8f2444099cf44fddd6c5069\n  k4d9636eb075b4fd2a1e41a7c37a17fc0[color=lightseagreen,label=\"Output\\nvariants_report_html\"]\n  19 -> k4d9636eb075b4fd2a1e41a7c37a17fc0\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nContigs\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGroups\"]\n  2[label=\"Summary.seqs\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Screen.seqs\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Summary.seqs\"]\n  3 -> 4 [label=\"fasta_out\"]\n  5[label=\"Unique.seqs\"]\n  3 -> 5 [label=\"fasta_out\"]\n  6[label=\"Count.seqs\"]\n  3 -> 6 [label=\"groups_out\"]\n  5 -> 6 [label=\"out_names\"]\n}",
                 "history": [
                     {
-                        "hash": "c0042e7f333bb9758580a564dbf559e83396a6d3",
-                        "message": "Update to address comments from wm",
-                        "num": 14,
-                        "short_hash": "c0042e7f3",
-                        "unix": "1718025591"
-                    },
-                    {
-                        "hash": "01cf3d5e27fb411603014ca3e0729b2daacc0a0d",
-                        "message": "Add snippers for running workflow from workflowhub.eu and jbrowse vis",
-                        "num": 13,
-                        "short_hash": "01cf3d5e2",
-                        "unix": "1717788409"
-                    },
-                    {
-                        "hash": "d3db4cd3e349677c907c71a761fde1b2935928d2",
-                        "message": "Update the M. tuberculosis variant analysis tutorial * Update all tools to latest versions * Change to fastp instead of Trimmomatic * Add section on running workflow * Update workflow and workflow test",
-                        "num": 12,
-                        "short_hash": "d3db4cd3e",
-                        "unix": "1717771237"
-                    },
-                    {
-                        "hash": "d61d5645fa6b21c25cd5d09f540c4e584b35f2c2",
-                        "message": "Update tb_variant_filter to v. 0.4.0",
-                        "num": 11,
-                        "short_hash": "d61d5645f",
-                        "unix": "1695643686"
-                    },
-                    {
-                        "hash": "c89f11fe32c66c1da9f058ec3fa522e8b18cba82",
-                        "message": "Update some tools in tuberculosis variant analysis tutorial (#4070)",
-                        "num": 10,
-                        "short_hash": "c89f11fe3",
-                        "unix": "1682624753"
-                    },
-                    {
-                        "hash": "fa9e9fb000ef9d2ab91acc67c4f338c213d641e2",
-                        "message": "New variant of tb_variant_filter and tbprofiler, more detail on tb_variant_filter",
-                        "num": 9,
-                        "short_hash": "fa9e9fb00",
-                        "unix": "1672566129"
-                    },
-                    {
-                        "hash": "6e9c1860b186754249a0a90d9957dbace653e9ac",
-                        "message": "Restore workflow indentation and fix WF step order",
-                        "num": 8,
-                        "short_hash": "6e9c1860b",
-                        "unix": "1648048765"
-                    },
-                    {
-                        "hash": "354e9edf1340c37133b7d1834cea608895acebc0",
-                        "message": "Use correct snippy wrapper version everywhere",
-                        "num": 7,
-                        "short_hash": "354e9edf1",
-                        "unix": "1648028595"
-                    },
-                    {
-                        "hash": "6f476a03271eeabffcf0877e8a402f7af815deba",
-                        "message": "Update snippy to 4.6.0",
-                        "num": 6,
-                        "short_hash": "6f476a032",
-                        "unix": "1647976648"
-                    },
-                    {
-                        "hash": "946f6f60f8e068a147f03d89f369f19e552793da",
-                        "message": "Generate cleaner intermediate diff",
-                        "num": 5,
-                        "short_hash": "946f6f60f",
-                        "unix": "1647938051"
-                    },
-                    {
-                        "hash": "8e46a42b5a664cf72ea7e2aae61739348f64dfea",
-                        "message": "Autoupdate workflow, change Kraken2 test",
-                        "num": 4,
-                        "short_hash": "8e46a42b5",
-                        "unix": "1647929062"
-                    },
-                    {
-                        "hash": "f98407ff47fe6ea903372a39b09530ae075d65b3",
-                        "message": "tb-variant-analysis: label workflow outputs and add test",
-                        "num": 3,
-                        "short_hash": "f98407ff4",
-                        "unix": "1595713523"
-                    },
-                    {
-                        "hash": "392830f9b51662e8028b8984f48f827be8a10aed",
-                        "message": "Reformat tb-variant-analysis workflow",
-                        "num": 2,
-                        "short_hash": "392830f9b",
-                        "unix": "1595707349"
-                    },
-                    {
-                        "hash": "2e73bb7aa538d3fb94e7f7ca21bfc6078d35e73f",
-                        "message": "Update M. tuberculosis variant analysis tutorial with new data and workflow",
+                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
+                        "message": "Rename metagenomics topic to microbiome",
                         "num": 1,
-                        "short_hash": "2e73bb7aa",
-                        "unix": "1595705571"
+                        "short_hash": "0e0a2f2cc",
+                        "unix": "1704901629"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "List of paired Illumina reads (set format to fastqsanger or fastqsanger.gz as appropriate)",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "List of paired Illumina reads (set format to fastqsanger or fastqsanger.gz as appropriate)",
-                                "name": "Reads"
+                                "description": "",
+                                "name": "Contigs"
                             }
                         ],
-                        "label": "Reads",
-                        "name": "Input dataset collection",
+                        "label": "Contigs",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 197.65334499942068
+                            "bottom": 239.8000030517578,
+                            "height": 61.80000305175781,
+                            "left": 313,
+                            "right": 513,
+                            "top": 178,
+                            "width": 200,
+                            "x": 313,
+                            "y": 178
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "2bfdfb62-da85-4d2d-8609-8f5e6975b4b3",
-                        "when": null,
+                        "type": "data_input",
+                        "uuid": "575ac02e-83e2-4b10-88af-6016b2ad0117",
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "M. tuberculosis reference genome (must be in H37Rv coordinates. The M. tuberculosis inferred ancestral genome is recommended)",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "M. tuberculosis reference genome (must be in H37Rv coordinates. The M. tuberculosis inferred ancestral genome is recommended)",
-                                "name": "Reference Genome"
+                                "description": "",
+                                "name": "Groups"
                             }
                         ],
-                        "label": "Reference Genome",
+                        "label": "Groups",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 1.2375059369900399,
-                            "top": 468.60335731890825
+                            "bottom": 570.8000030517578,
+                            "height": 61.80000305175781,
+                            "left": 323,
+                            "right": 523,
+                            "top": 509,
+                            "width": 200,
+                            "x": 323,
+                            "y": 509
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"genbank\"], \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "023233a0-8cb1-4558-8861-cd246ab58bac",
-                        "when": null,
+                        "uuid": "f6d83f4e-630a-4022-b300-e1a953c1b737",
                         "workflow_outputs": []
-                    },
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nContigs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGroups\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Summary.seqs\"];\n  0 -->|output| 2;\n  3[\"Screen.seqs\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Summary.seqs\"];\n  3 -->|fasta_out| 4;\n  5[\"Unique.seqs\"];\n  3 -->|fasta_out| 5;\n  6[\"Count.seqs\"];\n  3 -->|groups_out| 6;\n  5 -->|out_names| 6;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur]",
+                "outputs": [
                     {
-                        "annotation": "Minimum depth of coverage for a position on the genome",
-                        "content_id": null,
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
                         "errors": null,
                         "id": 2,
-                        "input_connections": {},
+                        "input_connections": {
+                            "fasta": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Summary.seqs",
+                        "outputs": [
+                            {
+                                "name": "logfile",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "out_summary",
+                                "type": "mothur.summary"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 361.5,
+                            "height": 266,
+                            "left": 631,
+                            "right": 831,
+                            "top": 95.5,
+                            "width": 200,
+                            "x": 631,
+                            "y": 95.5
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionout_summary": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "out_summary"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "609770e516fa",
+                            "name": "mothur_summary_seqs",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"count\": null, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"name\": null, \"savelog\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
+                        "type": "tool",
+                        "uuid": "b289d19e-f8bd-4803-88a0-e41335c11d7a",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "logfile",
+                                "uuid": "09eb6090-e79e-44a7-bf2b-52c217a29c8f"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "fasta": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "groups": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Screen.seqs",
+                        "outputs": [
+                            {
+                                "name": "fasta_out",
+                                "type": "input"
+                            },
+                            {
+                                "name": "bad_accnos",
+                                "type": "mothur.accnos"
+                            },
+                            {
+                                "name": "groups_out",
+                                "type": "mothur.groups"
+                            },
+                            {
+                                "name": "alignreport_out",
+                                "type": "mothur.align.report"
+                            },
+                            {
+                                "name": "contigsreport_out",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 1128.5,
+                            "height": 642,
+                            "left": 632,
+                            "right": 832,
+                            "top": 486.5,
+                            "width": 200,
+                            "x": 632,
+                            "y": 486.5
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionalignreport_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "alignreport_out"
+                            },
+                            "HideDatasetActioncontigsreport_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "contigsreport_out"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "63b74bfc8052",
+                            "name": "mothur_screen_seqs",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"alignrep\": {\"usealign\": \"no\", \"__current_case__\": 1}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"contigsrep\": {\"usecontigs\": \"no\", \"__current_case__\": 1}, \"count\": null, \"criteria\": \"-1\", \"end\": \"-1\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"groups\": {\"__class__\": \"ConnectedValue\"}, \"maxambig\": \"0\", \"maxhomop\": \"-1\", \"maxlength\": \"275\", \"minlength\": \"10\", \"names\": null, \"optimize\": null, \"qfile\": null, \"savelog\": \"false\", \"start\": \"-1\", \"summary\": null, \"taxonomy\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.1",
+                        "type": "tool",
+                        "uuid": "ad7d2c58-0b4d-4e3c-bb46-bfb496424b12",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "groups_out",
+                                "uuid": "3361a236-0e72-4844-9956-5200e2b01252"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "fasta_out",
+                                "uuid": "c70b5192-b093-40ff-a912-bb8deff20670"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "bad_accnos",
+                                "uuid": "71c67258-d5e3-4c63-ad49-d01e54cb56cf"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "fasta": {
+                                "id": 3,
+                                "output_name": "fasta_out"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "Minimum depth of coverage for a position on the genome",
-                                "name": "Minimum depth of coverage"
+                                "description": "runtime parameter for tool Summary.seqs",
+                                "name": "count"
+                            },
+                            {
+                                "description": "runtime parameter for tool Summary.seqs",
+                                "name": "name"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Summary.seqs",
+                        "outputs": [
+                            {
+                                "name": "logfile",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "out_summary",
+                                "type": "mothur.summary"
                             }
                         ],
-                        "label": "Minimum depth of coverage",
-                        "name": "Input parameter",
-                        "outputs": [],
                         "position": {
-                            "left": 1.8793911063654463,
-                            "top": 625.941216238093
+                            "bottom": 393,
+                            "height": 266,
+                            "left": 959,
+                            "right": 1159,
+                            "top": 127,
+                            "width": 200,
+                            "x": 959,
+                            "y": 127
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": 10, \"parameter_type\": \"integer\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "e31bf396-08b6-43ce-872a-545a5e4580c6",
-                        "when": null,
-                        "workflow_outputs": []
+                        "post_job_actions": {
+                            "HideDatasetActionout_summary": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "out_summary"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "609770e516fa",
+                            "name": "mothur_summary_seqs",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"count\": {\"__class__\": \"RuntimeValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"name\": {\"__class__\": \"RuntimeValue\"}, \"savelog\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
+                        "type": "tool",
+                        "uuid": "f7268117-2f00-48d7-aed0-cc3e149db198",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "logfile",
+                                "uuid": "b4abf87f-39ec-4d17-8e93-5a2a473dab74"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "fasta": {
+                                "id": 3,
+                                "output_name": "fasta_out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Unique.seqs",
+                        "outputs": [
+                            {
+                                "name": "out_fasta",
+                                "type": "input"
+                            },
+                            {
+                                "name": "out_names",
+                                "type": "mothur.names"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 850.1000061035156,
+                            "height": 235.60000610351562,
+                            "left": 1009,
+                            "right": 1209,
+                            "top": 614.5,
+                            "width": 200,
+                            "x": 1009,
+                            "y": 614.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "d466580cd706",
+                            "name": "mothur_unique_seqs",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"format\": \"name\", \"names\": null, \"savelog\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
+                        "type": "tool",
+                        "uuid": "3256bd7b-b98f-4248-90ae-c5e73704f418",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_fasta",
+                                "uuid": "10d11427-086d-47fe-aee9-ac5d1bae3191"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_names",
+                                "uuid": "2bde74d8-08ef-4bd6-b54f-138c0d4d365f"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "Minimum proportion of reads that must support a variant for it to be called",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "grouping|group": {
+                                "id": 3,
+                                "output_name": "groups_out"
+                            },
+                            "name": {
+                                "id": 5,
+                                "output_name": "out_names"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Count.seqs",
+                        "outputs": [
+                            {
+                                "name": "seq_count",
+                                "type": "mothur.count_table"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 556.6999969482422,
+                            "height": 205.1999969482422,
+                            "left": 1292,
+                            "right": 1492,
+                            "top": 351.5,
+                            "width": 200,
+                            "x": 1292,
+                            "y": 351.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "7a6f9c899221",
+                            "name": "mothur_count_seqs",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"grouping\": {\"use\": \"yes\", \"__current_case__\": 0, \"group\": {\"__class__\": \"ConnectedValue\"}, \"groups\": null}, \"name\": {\"__class__\": \"ConnectedValue\"}, \"savelog\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
+                        "type": "tool",
+                        "uuid": "51efceca-f05a-4f3f-af6b-693a14b26048",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "seq_count",
+                                "uuid": "5ffc59a1-8b3f-4b09-982d-332411f16919"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "microbiome/mothur-miseq-sop-short",
+                "path": "topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow1_quality_control.ga",
+                "tags": [
+                    "microbiome"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur]",
+                "topic_id": "microbiome",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-mothur-miseq-sop-short/versions/workflow1-quality-control",
+                "tutorial_id": "mothur-miseq-sop-short",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow1_quality_control.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow1_quality_control.html",
+                "version": 1,
+                "wfid": "microbiome-mothur-miseq-sop-short",
+                "wfname": "workflow1-quality-control",
+                "workflow": "workflow1_quality_control.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0"
+                ],
+                "workflowhub_id": "1121"
+            },
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0003-3803-468X",
+                        "name": "Saskia Hiltemann"
+                    }
+                ],
+                "description": "16S Microbial Analysis with mothur (short)",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAligned Sequences\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCount Table\"]\n  2[label=\"Summary.seqs\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Screen.seqs\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Filter.seqs\"]\n  3 -> 4 [label=\"fasta_out\"]\n  5[label=\"Unique.seqs\"]\n  4 -> 5 [label=\"filteredfasta\"]\n  3 -> 5 [label=\"count_out\"]\n  6[label=\"Pre.cluster\"]\n  5 -> 6 [label=\"out_fasta\"]\n  5 -> 6 [label=\"out_count\"]\n  7[label=\"Summary.seqs\"]\n  6 -> 7 [label=\"count_out\"]\n  6 -> 7 [label=\"fasta_out\"]\n  ka0bbcba140f946789c478bdb4e0b7f6d[color=lightseagreen,label=\"Output\\nSummary.seqs on input dataset(s): summary\"]\n  7 -> ka0bbcba140f946789c478bdb4e0b7f6d\n  8[label=\"Chimera.vsearch\"]\n  6 -> 8 [label=\"fasta_out\"]\n  6 -> 8 [label=\"count_out\"]\n  9[label=\"Remove.seqs\"]\n  8 -> 9 [label=\"out_accnos\"]\n  8 -> 9 [label=\"out_count\"]\n  6 -> 9 [label=\"fasta_out\"]\n  10[label=\"Summary.seqs\"]\n  9 -> 10 [label=\"count_out\"]\n  9 -> 10 [label=\"fasta_out\"]\n}",
+                "history": [
+                    {
+                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
+                        "message": "Rename metagenomics topic to microbiome",
+                        "num": 1,
+                        "short_hash": "0e0a2f2cc",
+                        "unix": "1704901629"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Minimum proportion of reads that must support a variant for it to be called",
-                                "name": "Minimum variant allele frequency"
+                                "description": "",
+                                "name": "Aligned Sequences"
                             }
                         ],
-                        "label": "Minimum variant allele frequency",
-                        "name": "Input parameter",
+                        "label": "Aligned Sequences",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 1.358958473709409,
-                            "top": 769.7667492120408
+                            "left": 2,
+                            "top": 262
                         },
                         "tool_id": null,
-                        "tool_state": "{\"default\": 0.9, \"parameter_type\": \"float\", \"optional\": true}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "d1814962-a30d-463a-a081-857a5141385b",
+                        "type": "data_input",
+                        "uuid": "f08168dd-1a9a-4a0e-b1c9-006610590496",
                         "when": null,
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "Increasing the minimum seed length (-k) parameter can help eliminate matches from contaminants. If used this should be set to 2/3rds of the read length, i.e. the string \"-k 100\" should be used for 150 base pair reads",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 4,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Increasing the minimum seed length (-k) parameter can help eliminate matches from contaminants. If used this should be set to 2/3rds of the read length, i.e. the string \"-k 100\" should be used for 150 base pair reads",
-                                "name": "Additional BWA-MEM options"
+                                "description": "",
+                                "name": "Count Table"
                             }
                         ],
-                        "label": "Additional BWA-MEM options",
-                        "name": "Input parameter",
+                        "label": "Count Table",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 7.8094297093662135,
-                            "top": 931.4341211532
+                            "left": 0,
+                            "top": 591
                         },
                         "tool_id": null,
-                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "40d47253-c7c5-471b-871c-9a19fbe60bfe",
+                        "type": "data_input",
+                        "uuid": "4f0b07a6-cc5f-40ed-bab5-37d7a3c6c59e",
                         "when": null,
                         "workflow_outputs": []
                     }
                 ],
-                "license": "AGPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nReads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference Genome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nMinimum depth of coverage\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nMinimum variant allele frequency\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nAdditional BWA-MEM options\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"fastp\"];\n  0 -->|output| 5;\n  6[\"seqret\"];\n  1 -->|output| 6;\n  7[\"snippy\"];\n  4 -->|output| 7;\n  2 -->|output| 7;\n  3 -->|output| 7;\n  5 -->|output_paired_coll| 7;\n  1 -->|output| 7;\n  8[\"Kraken2\"];\n  5 -->|output_paired_coll| 8;\n  c7abf2bf-ed4c-433e-a695-9eca61282bb5[\"Output\\nreport_output\"];\n  8 --> c7abf2bf-ed4c-433e-a695-9eca61282bb5;\n  style c7abf2bf-ed4c-433e-a695-9eca61282bb5 stroke:#2c3143,stroke-width:4px;\n  083a0e51-7780-4c91-a071-dc0e4641d060[\"Output\\noutput\"];\n  8 --> 083a0e51-7780-4c91-a071-dc0e4641d060;\n  style 083a0e51-7780-4c91-a071-dc0e4641d060 stroke:#2c3143,stroke-width:4px;\n  9[\"QualiMap BamQC\"];\n  7 -->|snpsbam| 9;\n  10[\"mosdepth\"];\n  2 -->|output| 10;\n  7 -->|snpsbam| 10;\n  11[\"TB Variant Filter\"];\n  7 -->|snpvcf| 11;\n  12[\"TB-Profiler Profile\"];\n  7 -->|snpsbam| 12;\n  335635b4-a4de-4980-ad02-68f0035daeaa[\"Output\\noutput_txt\"];\n  12 --> 335635b4-a4de-4980-ad02-68f0035daeaa;\n  style 335635b4-a4de-4980-ad02-68f0035daeaa stroke:#2c3143,stroke-width:4px;\n  13[\"TB Variant Filter\"];\n  7 -->|snpvcf| 13;\n  14[\"Flatten collection\"];\n  9 -->|raw_data| 14;\n  15[\"Text reformatting\"];\n  10 -->|output_quantized_bed| 15;\n  16[\"Text transformation\"];\n  11 -->|output1| 16;\n  007df8c2-bd13-495f-8904-abf31d4594d0[\"Output\\nFinal annotated VCF\"];\n  16 --> 007df8c2-bd13-495f-8904-abf31d4594d0;\n  style 007df8c2-bd13-495f-8904-abf31d4594d0 stroke:#2c3143,stroke-width:4px;\n  17[\"MultiQC\"];\n  5 -->|report_json| 17;\n  14 -->|output| 17;\n  59528235-7525-4ef9-8810-36f1ed0f01f6[\"Output\\nhtml_report\"];\n  17 --> 59528235-7525-4ef9-8810-36f1ed0f01f6;\n  style 59528235-7525-4ef9-8810-36f1ed0f01f6 stroke:#2c3143,stroke-width:4px;\n  18[\"bcftools consensus\"];\n  13 -->|output1| 18;\n  6 -->|out_file1| 18;\n  15 -->|outfile| 18;\n  c71b135d-35f9-44d0-a20e-f25528e518af[\"Output\\nconsensus_genome\"];\n  18 --> c71b135d-35f9-44d0-a20e-f25528e518af;\n  style c71b135d-35f9-44d0-a20e-f25528e518af stroke:#2c3143,stroke-width:4px;\n  19[\"TB Variant Report\"];\n  16 -->|output| 19;\n  12 -->|results_json| 19;\n  959528d2-f8f2-4440-99cf-44fddd6c5069[\"Output\\ndrug_resistance_report_html\"];\n  19 --> 959528d2-f8f2-4440-99cf-44fddd6c5069;\n  style 959528d2-f8f2-4440-99cf-44fddd6c5069 stroke:#2c3143,stroke-width:4px;\n  4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0[\"Output\\nvariants_report_html\"];\n  19 --> 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0;\n  style 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "TB Variant Analysis v1.0",
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAligned Sequences\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nCount Table\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Summary.seqs\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Screen.seqs\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  4[\"Filter.seqs\"];\n  3 -->|fasta_out| 4;\n  5[\"Unique.seqs\"];\n  4 -->|filteredfasta| 5;\n  3 -->|count_out| 5;\n  6[\"Pre.cluster\"];\n  5 -->|out_fasta| 6;\n  5 -->|out_count| 6;\n  7[\"Summary.seqs\"];\n  6 -->|count_out| 7;\n  6 -->|fasta_out| 7;\n  a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d[\"Output\\nSummary.seqs on input dataset(s): summary\"];\n  7 --> a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d;\n  style a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d stroke:#2c3143,stroke-width:4px;\n  8[\"Chimera.vsearch\"];\n  6 -->|fasta_out| 8;\n  6 -->|count_out| 8;\n  9[\"Remove.seqs\"];\n  8 -->|out_accnos| 9;\n  8 -->|out_count| 9;\n  6 -->|fasta_out| 9;\n  10[\"Summary.seqs\"];\n  9 -->|count_out| 10;\n  9 -->|fasta_out| 10;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur]",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
                         "errors": null,
-                        "id": 8,
+                        "id": 2,
                         "input_connections": {
-                            "single_paired|input_pair": {
-                                "id": 5,
-                                "output_name": "output_paired_coll"
+                            "count": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "fasta": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Kraken2",
-                                "name": "single_paired"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Kraken2",
+                        "name": "Summary.seqs",
                         "outputs": [
                             {
-                                "name": "report_output",
-                                "type": "tabular"
+                                "name": "logfile",
+                                "type": "txt"
                             },
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "name": "out_summary",
+                                "type": "mothur.summary"
                             }
                         ],
                         "position": {
-                            "left": 1605.1346167188794,
-                            "top": 0
+                            "left": 301,
+                            "top": 96.5
                         },
                         "post_job_actions": {
-                            "HideDatasetActionoutput": {
+                            "HideDatasetActionout_summary": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "output"
-                            },
-                            "TagDatasetActionreport_output": {
-                                "action_arguments": {
-                                    "tags": "kraken_report"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "report_output"
+                                "output_name": "out_summary"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "20e2f64aa1fe",
-                            "name": "kraken2",
+                            "changeset_revision": "609770e516fa",
+                            "name": "mothur_summary_seqs",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"confidence\": \"0.0\", \"kraken2_database\": \"pluspf2021-05\", \"min_base_quality\": \"0\", \"minimum_hit_groups\": \"2\", \"quick\": false, \"report\": {\"create_report\": true, \"use_mpa_style\": false, \"report_zero_counts\": false, \"report_minimizer_data\": false}, \"single_paired\": {\"single_paired_selector\": \"collection\", \"__current_case__\": 0, \"input_pair\": {\"__class__\": \"ConnectedValue\"}}, \"split_reads\": false, \"use_names\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.1+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"count\": {\"__class__\": \"ConnectedValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"name\": null, \"savelog\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
                         "type": "tool",
-                        "uuid": "60b17d56-0ef9-4829-829e-923f66de5e2f",
+                        "uuid": "0c5f9992-1de0-45bc-959e-b8965f499294",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "report_output",
-                                "output_name": "report_output",
-                                "uuid": "c7abf2bf-ed4c-433e-a695-9eca61282bb5"
-                            },
-                            {
-                                "label": "output",
-                                "output_name": "output",
-                                "uuid": "083a0e51-7780-4c91-a071-dc0e4641d060"
+                                "label": null,
+                                "output_name": "logfile",
+                                "uuid": "3fee996b-77af-4338-95b6-f2b53233ca79"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.2.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1",
                         "errors": null,
-                        "id": 12,
+                        "id": 3,
                         "input_connections": {
-                            "fastq_or_bam|bam_input": {
-                                "id": 7,
-                                "output_name": "snpsbam"
+                            "count": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "fasta": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool TB-Profiler Profile",
-                                "name": "fastq_or_bam"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "TB-Profiler Profile",
+                        "name": "Screen.seqs",
                         "outputs": [
                             {
-                                "name": "results_json",
-                                "type": "json"
+                                "name": "fasta_out",
+                                "type": "input"
                             },
                             {
-                                "name": "output_vcf",
-                                "type": "vcf"
+                                "name": "bad_accnos",
+                                "type": "mothur.accnos"
                             },
                             {
-                                "name": "output_txt",
-                                "type": "txt"
+                                "name": "alignreport_out",
+                                "type": "mothur.align.report"
+                            },
+                            {
+                                "name": "contigsreport_out",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "count_out",
+                                "type": "mothur.count_table"
                             }
                         ],
                         "position": {
-                            "left": 1132.7778271896836,
-                            "top": 615.3961147101202
+                            "left": 315,
+                            "top": 430.5
                         },
                         "post_job_actions": {
-                            "HideDatasetActionoutput_vcf": {
+                            "HideDatasetActionalignreport_out": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "output_vcf"
+                                "output_name": "alignreport_out"
                             },
-                            "HideDatasetActionresults_json": {
+                            "HideDatasetActioncontigsreport_out": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "results_json"
-                            },
-                            "TagDatasetActionoutput_txt": {
-                                "action_arguments": {
-                                    "tags": "drug_resistance_report"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "output_txt"
+                                "output_name": "contigsreport_out"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.2.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "4839e590cb26",
-                            "name": "tbprofiler",
+                            "changeset_revision": "63b74bfc8052",
+                            "name": "mothur_screen_seqs",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced\": {\"options\": \"no\", \"__current_case__\": 0}, \"fastq_or_bam\": {\"input_select\": \"bam\", \"__current_case__\": 3, \"bam_input\": {\"__class__\": \"ConnectedValue\"}}, \"output_format\": \"txt\", \"platform\": \"illumina\", \"spoligotype\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "6.2.1+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"alignrep\": {\"usealign\": \"no\", \"__current_case__\": 1}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"contigsrep\": {\"usecontigs\": \"no\", \"__current_case__\": 1}, \"count\": {\"__class__\": \"ConnectedValue\"}, \"criteria\": \"-1\", \"end\": \"11550\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"groups\": null, \"maxambig\": \"-1\", \"maxhomop\": \"8\", \"maxlength\": \"-1\", \"minlength\": \"10\", \"names\": null, \"optimize\": null, \"qfile\": null, \"savelog\": false, \"start\": \"1968\", \"summary\": null, \"taxonomy\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.1",
                         "type": "tool",
-                        "uuid": "22d89589-70a3-4e6e-8b95-68604a287052",
+                        "uuid": "2663c361-5494-4eca-bd57-ffbd2dbfae03",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "output_txt",
-                                "output_name": "output_txt",
-                                "uuid": "335635b4-a4de-4980-ad02-68f0035daeaa"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
-                        "errors": null,
-                        "id": 16,
-                        "input_connections": {
-                            "infile": {
-                                "id": 11,
-                                "output_name": "output1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Text transformation",
-                        "outputs": [
+                                "label": null,
+                                "output_name": "count_out",
+                                "uuid": "c73cdf2e-9061-4e0b-ad9c-b88730d454f2"
+                            },
                             {
-                                "name": "output",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 1379.287563641826,
-                            "top": 248.44083584414724
-                        },
-                        "post_job_actions": {
-                            "TagDatasetActionoutput": {
-                                "action_arguments": {
-                                    "tags": "annotated_vcf"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "fbf99087e067",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"s/GENE_//g\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "9.3+galaxy1",
-                        "type": "tool",
-                        "uuid": "c45f6679-0d38-4663-a783-775b0f522bcc",
-                        "when": null,
-                        "workflow_outputs": [
+                                "label": null,
+                                "output_name": "fasta_out",
+                                "uuid": "74e9d7d4-3364-4e10-bb47-9f1531657198"
+                            },
                             {
-                                "label": "Final annotated VCF",
-                                "output_name": "output",
-                                "uuid": "007df8c2-bd13-495f-8904-abf31d4594d0"
+                                "label": null,
+                                "output_name": "bad_accnos",
+                                "uuid": "759c0a32-df83-415e-8a9f-eee097817a6f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0",
                         "errors": null,
-                        "id": 17,
+                        "id": 4,
                         "input_connections": {
-                            "results_0|software_cond|input": {
-                                "id": 5,
-                                "output_name": "report_json"
-                            },
-                            "results_1|software_cond|input": {
-                                "id": 14,
-                                "output_name": "output"
+                            "fasta": {
+                                "id": 3,
+                                "output_name": "fasta_out"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "MultiQC",
+                        "name": "Filter.seqs",
                         "outputs": [
                             {
-                                "name": "stats",
-                                "type": "input"
-                            },
-                            {
-                                "name": "html_report",
-                                "type": "html"
-                            }
-                        ],
-                        "position": {
-                            "left": 1604.2880860884582,
-                            "top": 202.3882167631859
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionstats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "stats"
-                            },
-                            "TagDatasetActionhtml_report": {
-                                "action_arguments": {
-                                    "tags": "qc_report"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "html_report"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "abfd8a6544d7",
-                            "name": "multiqc",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"qualimap\", \"__current_case__\": 20, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.11+galaxy1",
-                        "type": "tool",
-                        "uuid": "6367e2a7-c3b0-4dc4-bbc2-e861e66eaeae",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "html_report",
-                                "output_name": "html_report",
-                                "uuid": "59528235-7525-4ef9-8810-36f1ed0f01f6"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "Compute consensus genome with single nucleotide variants inserted, suitable for use in building a phylogeny",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
-                        "errors": null,
-                        "id": 18,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 13,
-                                "output_name": "output1"
-                            },
-                            "reference_source|fasta_ref": {
-                                "id": 6,
-                                "output_name": "out_file1"
+                                "name": "logfile",
+                                "type": "txt"
                             },
-                            "sec_default|mask": {
-                                "id": 15,
-                                "output_name": "outfile"
-                            }
-                        },
-                        "inputs": [
                             {
-                                "description": "runtime parameter for tool bcftools consensus",
-                                "name": "reference_source"
+                                "name": "out_filter",
+                                "type": "mothur.filter"
                             },
                             {
-                                "description": "runtime parameter for tool bcftools consensus",
-                                "name": "sec_default"
-                            }
-                        ],
-                        "label": null,
-                        "name": "bcftools consensus",
-                        "outputs": [
-                            {
-                                "name": "output_file",
+                                "name": "filteredfasta",
                                 "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 1601.1886936133394,
-                            "top": 1003.2778990479657
+                            "left": 603,
+                            "top": 272.5
                         },
                         "post_job_actions": {
-                            "TagDatasetActionoutput_file": {
-                                "action_arguments": {
-                                    "tags": "consensus_genome"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "output_file"
+                            "HideDatasetActionlogfile": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "logfile"
+                            },
+                            "HideDatasetActionout_filter": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "out_filter"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "147de996e34f",
-                            "name": "bcftools_consensus",
+                            "changeset_revision": "3524ca06478e",
+                            "name": "mothur_filter_seqs",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"absent\": \"\", \"chain\": false, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"ConnectedValue\"}}, \"rename\": false, \"sec_default\": {\"mask\": {\"__class__\": \"ConnectedValue\"}, \"iupac_codes\": false, \"sample\": null, \"select_haplotype\": null, \"mark_del\": \"\", \"mark_ins\": null, \"mark_snv\": null, \"conditional_mask\": {\"selector\": \"disabled\", \"__current_case__\": 0}}, \"sec_restrict\": {\"include\": null, \"exclude\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.15.1+galaxy3",
+                        "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"hard\": null, \"inputs\": [], \"savelog\": true, \"soft\": \"0\", \"trump\": \".\", \"vertical\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
                         "type": "tool",
-                        "uuid": "2b226e0c-8e59-472d-8bcd-6d8d84dfddab",
+                        "uuid": "e326b83b-5d1e-447a-8971-508f72f7b8de",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "consensus_genome",
-                                "output_name": "output_file",
-                                "uuid": "c71b135d-35f9-44d0-a20e-f25528e518af"
+                                "label": null,
+                                "output_name": "filteredfasta",
+                                "uuid": "c8809f97-ed35-409e-890f-ed45f534e81d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0",
                         "errors": null,
-                        "id": 19,
+                        "id": 5,
                         "input_connections": {
-                            "input_vcf": {
-                                "id": 16,
-                                "output_name": "output"
+                            "fasta": {
+                                "id": 4,
+                                "output_name": "filteredfasta"
                             },
-                            "tbprofiler_json": {
-                                "id": 12,
-                                "output_name": "results_json"
+                            "names": {
+                                "id": 3,
+                                "output_name": "count_out"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "TB Variant Report",
+                        "name": "Unique.seqs",
                         "outputs": [
                             {
-                                "name": "variants_report_html",
-                                "type": "html"
-                            },
-                            {
-                                "name": "variants_report_txt",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "drug_resistance_report_html",
-                                "type": "html"
+                                "name": "out_fasta",
+                                "type": "input"
                             },
                             {
-                                "name": "drug_resistance_report_txt",
-                                "type": "txt"
+                                "name": "out_count",
+                                "type": "mothur.count_table"
                             }
                         ],
                         "position": {
-                            "left": 1591.762535768669,
-                            "top": 427.7783435581315
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActiondrug_resistance_report_txt": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "drug_resistance_report_txt"
-                            },
-                            "HideDatasetActionvariants_report_txt": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "variants_report_txt"
-                            },
-                            "TagDatasetActiondrug_resistance_report_html": {
-                                "action_arguments": {
-                                    "tags": "variant_report"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "drug_resistance_report_html"
-                            },
-                            "TagDatasetActionvariants_report_html": {
-                                "action_arguments": {
-                                    "tags": "variant_report"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "variants_report_html"
-                            }
+                            "left": 882,
+                            "top": 621.5
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.0+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "42818629ec4c",
-                            "name": "tbvcfreport",
+                            "changeset_revision": "d466580cd706",
+                            "name": "mothur_unique_seqs",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"database_uri\": \"neodb.sanbi.ac.za\"}, \"filter_udi\": true, \"input_vcf\": {\"__class__\": \"ConnectedValue\"}, \"tbprofiler_json\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"format\": \"count\", \"names\": {\"__class__\": \"ConnectedValue\"}, \"savelog\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
                         "type": "tool",
-                        "uuid": "183d84e7-91ea-4e8f-950b-f65629b60b1b",
+                        "uuid": "225cd752-6173-4e44-9b31-a1de097d3357",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "drug_resistance_report_html",
-                                "output_name": "drug_resistance_report_html",
-                                "uuid": "959528d2-f8f2-4440-99cf-44fddd6c5069"
+                                "label": null,
+                                "output_name": "out_fasta",
+                                "uuid": "efcff963-3961-4b12-857b-9191765f5ad5"
                             },
                             {
-                                "label": "variants_report_html",
-                                "output_name": "variants_report_html",
-                                "uuid": "4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0"
+                                "label": null,
+                                "output_name": "out_count",
+                                "uuid": "3e744fc6-4002-409c-b580-7a080263b39c"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "variant-analysis/tb-variant-analysis",
-                "path": "topics/variant-analysis/tutorials/tb-variant-analysis/workflows/tb-variant-analysis.ga",
-                "tags": [
-                    "pathogen",
-                    "tuberculosis"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "TB Variant Analysis v1.0",
-                "topic_id": "variant-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-tb-variant-analysis/versions/tb-variant-analysis",
-                "tutorial_id": "tb-variant-analysis",
-                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/tb-variant-analysis/workflows/tb-variant-analysis.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/tb-variant-analysis/workflows/tb-variant-analysis.html",
-                "version": 7,
-                "wfid": "variant-analysis-tb-variant-analysis",
-                "wfname": "tb-variant-analysis",
-                "workflow": "tb-variant-analysis.ga",
-                "workflow_tools": [
-                    "__FLATTEN__",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: seqret84/5.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mosdepth/mosdepth/0.3.8+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.4.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.2.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.0+galaxy0"
-                ],
-                "workflowhub_id": "1069"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.3496437"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "datamash_ops",
-                    "owner": "iuc",
-                    "revisions": "4c07ddedc198",
-                    "tool_panel_section_label": "Join, Subtract and Group",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "nextclade",
-                    "owner": "iuc",
-                    "revisions": "4f6349228462",
-                    "tool_panel_section_label": "Phylogenetics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pangolin",
-                    "owner": "iuc",
-                    "revisions": "03ed9524dcd1",
-                    "tool_panel_section_label": "Phylogenetics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_regex_finder",
-                    "owner": "mbernt",
-                    "revisions": "9a811adb714f",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: datamash_ops\n  owner: iuc\n  revisions: 4c07ddedc198\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nextclade\n  owner: iuc\n  revisions: 4f6349228462\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pangolin\n  owner: iuc\n  revisions: 03ed9524dcd1\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_regex_finder\n  owner: mbernt\n  revisions: 9a811adb714f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "wm75",
-                "bebatut"
-            ],
-            "funding": [
-                "by-covid",
-                "elixir-converge"
-            ]
-        },
-        "contributors": [
-            {
-                "affiliations": [
-                    "by-covid",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "fediverse": "https://scholar.social/@zerodivision",
-                "fediverse_flavor": "mastodon",
-                "id": "wm75",
-                "joined": "2017-09",
-                "matrix": "wm75:matrix.org",
-                "name": "Wolfgang Maier",
-                "orcid": "0000-0002-9464-6640",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "funder": true,
-                "funding_id": "101046203",
-                "funding_statement": "BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response.\n\nThis project has received funding from the European Union\u2019s Horizon Europe research and innovation programme under grant agreement \u2116 101046203 (BY-COVID)",
-                "funding_system": "cordis",
-                "id": "by-covid",
-                "joined": "2023-04",
-                "members": [
-                    "bgruening",
-                    "hexylena",
-                    "ilveroluca",
-                    "kikkomep",
-                    "mbaardwijk",
-                    "PapXis",
-                    "pauldg",
-                    "simleo",
-                    "stain",
-                    "wm75"
-                ],
-                "name": "BeYond-COVID",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/by-covid/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/by-covid.json"
-            },
-            {
-                "avatar": "https://elixir-europe.org/sites/default/files/styles/right-medium/public/images/converge_logo.png",
-                "funder": true,
-                "funding_id": "871075",
-                "funding_statement": "ELIXIR CONVERGE is connecting and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services. This project has received funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement \u2116 871075",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "elixir-converge",
-                "joined": "2023-01",
-                "members": [
-                    "bgruening",
-                    "hexylena"
-                ],
-                "name": "ELIXIR-CONVERGE",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-converge/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-converge.json"
-            }
-        ],
-        "dir": "topics/variant-analysis/tutorials/sars-cov-2-variant-discovery",
-        "edam_operation": [
-            "Variant calling",
-            "Methylation analysis",
-            "Variant classification",
-            "Tree-based sequence alignment"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "variant-analysis/sars-cov-2-variant-discovery",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "The Galaxy Covid-19 project has developed a flexible set of workflows for SARS-CoV-2 genome surveillance, which is freely available through public workflow registries.",
-            "The workflows enable processing of whole batches of samples with rather limited user interaction.",
-            "They provide a high-throughput and flexible analysis solution without compromising on accuracy, nor on the possibility to explore intermediate steps and outputs in detail."
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
-        "objectives": [
-            "Discover and obtain recommended Galaxy workflows for SARS-CoV-2 sequence data analysis through public workflow registries",
-            "Choose and run a workflow to discover mutations in a batch of viral samples from sequencing data obtained through a range of different protocols and platforms",
-            "Run a workflow to summarize and visualize the mutation discovery results for a batch of samples",
-            "Run a workflow to construct viral consensus sequences for the samples in a batch",
-            "Know different SARS-CoV-2 lineage classification systems, and use pangolin and Nextclade to assign samples to predefined lineages",
-            "Combine information from different analysis steps to be able to draw appropriate conclusions about individual samples and batches of viral data"
-        ],
-        "pageviews": 11912,
-        "pub_date": "2021-06-30",
-        "questions": [
-            "How can a complete analysis, including viral consensus sequence reconstruction and lineage assignment be performed?",
-            "How can such an analysis be kept manageable for lots of samples, yet flexible enough to handle different types of input data?",
-            "What are key results beyond consensus genomes and lineage assignments that need to be understood to avoid inappropriate conclusions about samples?",
-            "How can the needs for high-throughput data analysis in an ongoing infectious disease outbreak/pandemic and the need for proper quality control and data inspection be balanced?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "wm75"
-                ],
-                "date": "2023-05-10",
-                "length": "55M",
-                "speakers": [
-                    "wm75"
-                ],
-                "youtube_id": "hjlmCWQhBvI"
-            },
-            {
-                "captioners": [
-                    "hexylena"
-                ],
-                "date": "2021-08-09",
-                "length": "1H30M",
-                "speakers": [
-                    "wm75"
-                ],
-                "youtube_id": "vnFQ2fR_fzw"
-            }
-        ],
-        "requirements": [
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "collections"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "variant-analysis",
-                "tutorials": [
-                    "sars-cov-2"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00316",
-        "short_tools": [
-            "nextclade",
-            "datamash_ops",
-            "fasta_regex_finder",
-            "pangolin",
-            "Filter1",
-            "upload1"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "one-health",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "covid19",
-            "virology",
-            "one-health"
-        ],
-        "time_estimation": "3H",
-        "title": "Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data",
-        "tools": [
-            "Filter1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/nextclade/nextclade/2.7.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/4.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/mbernt/fasta_regex_finder/fasta_regex_finder/0.1.0",
-            "upload1"
-        ],
-        "topic_name": "variant-analysis",
-        "topic_name_human": "Variant Analysis",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "sars-cov-2-variant-discovery",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.json"
-        },
-        "version": 15,
-        "video": false,
-        "video_versions": 2,
-        "video_view": 0,
-        "visit_duration": 207,
-        "visitors": 6391,
-        "zenodo_link": "https://zenodo.org/record/5036687"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "bowtie2",
-                    "owner": "devteam",
-                    "revisions": "03e9b2fbc005",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bakta",
-                    "owner": "iuc",
-                    "revisions": "728dacaf08a9",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "jbrowse",
-                    "owner": "iuc",
-                    "revisions": "a6e57ff585c0",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "tbl2gff3",
-                    "owner": "iuc",
-                    "revisions": "4a7f4b0cc0a3",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "staramr",
-                    "owner": "nml",
-                    "revisions": "3b22de20bd4b",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bowtie2\n  owner: devteam\n  revisions: 03e9b2fbc005\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bakta\n  owner: iuc\n  revisions: 728dacaf08a9\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbl2gff3\n  owner: iuc\n  revisions: 4a7f4b0cc0a3\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: staramr\n  owner: nml\n  revisions: 3b22de20bd4b\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "bazante1",
-                "bebatut"
-            ],
-            "editing": [
-                "hexylena",
-                "bazante1",
-                "shiltemann",
-                "miaomiaozhou88"
-            ],
-            "funding": [
-                "avans-atgm",
-                "abromics"
-            ]
-        },
-        "contributors": [
-            {
-                "affiliations": [
-                    "avans-atgm"
-                ],
-                "id": "bazante1",
-                "joined": "2020-12",
-                "name": "Bazante Sanders",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "affiliations": [
-                    "avans-atgm"
-                ],
-                "id": "bazante1",
-                "joined": "2020-12",
-                "name": "Bazante Sanders",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
-            {
-                "email": "m.zhou1@avans.nl",
-                "id": "miaomiaozhou88",
-                "joined": "2020-12",
-                "name": "Miaomiao Zhou",
-                "orcid": "0000-0003-4426-1758",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/miaomiaozhou88/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/miaomiaozhou88.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/logo-avans.png",
-                "former_members": [
-                    "dirowa",
-                    "hexylena"
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "fasta": {
+                                "id": 5,
+                                "output_name": "out_fasta"
+                            },
+                            "name": {
+                                "id": 5,
+                                "output_name": "out_count"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Pre.cluster",
+                        "outputs": [
+                            {
+                                "name": "map_out",
+                                "type": "input"
+                            },
+                            {
+                                "name": "fasta_out",
+                                "type": "input"
+                            },
+                            {
+                                "name": "names_out",
+                                "type": "mothur.names"
+                            },
+                            {
+                                "name": "count_out",
+                                "type": "mothur.count_table"
+                            }
+                        ],
+                        "position": {
+                            "left": 1179,
+                            "top": 74.5
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionmap_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "map_out"
+                            },
+                            "HideDatasetActionnames_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "names_out"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "05183ee20cf8",
+                            "name": "mothur_pre_cluster",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"diffs\": \"2\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gapextend\": \"-1\", \"gapopen\": \"-2\", \"group\": null, \"match\": \"1\", \"mismatch\": \"-1\", \"name\": {\"__class__\": \"ConnectedValue\"}, \"savelog\": false, \"topdown\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
+                        "type": "tool",
+                        "uuid": "6f90be44-8355-4639-a4e6-9d5cc0df50f0",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "fasta_out",
+                                "uuid": "e06f7f73-b9d6-4314-bcc6-9e0889d0f701"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "count_out",
+                                "uuid": "457b654e-4a7d-4fcd-84e2-def389e29fe6"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "count": {
+                                "id": 6,
+                                "output_name": "count_out"
+                            },
+                            "fasta": {
+                                "id": 6,
+                                "output_name": "fasta_out"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Summary.seqs",
+                                "name": "name"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Summary.seqs",
+                        "outputs": [
+                            {
+                                "name": "out_summary",
+                                "type": "mothur.summary"
+                            }
+                        ],
+                        "position": {
+                            "left": 1498,
+                            "top": 0
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "609770e516fa",
+                            "name": "mothur_summary_seqs",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"count\": {\"__class__\": \"ConnectedValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"name\": {\"__class__\": \"RuntimeValue\"}, \"savelog\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
+                        "type": "tool",
+                        "uuid": "0ab1410f-0567-4266-9aac-9412c907da0d",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Summary.seqs on input dataset(s): summary",
+                                "output_name": "out_summary",
+                                "uuid": "a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "fasta": {
+                                "id": 6,
+                                "output_name": "fasta_out"
+                            },
+                            "template|count": {
+                                "id": 6,
+                                "output_name": "count_out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Chimera.vsearch",
+                        "outputs": [
+                            {
+                                "name": "vsearch.chimeras",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "out_accnos",
+                                "type": "mothur.accnos"
+                            },
+                            {
+                                "name": "out_count",
+                                "type": "mothur.count_table"
+                            }
+                        ],
+                        "position": {
+                            "left": 1478,
+                            "top": 636.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "12e856482d26",
+                            "name": "mothur_chimera_vsearch",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"dereplicate\": true, \"dn\": \"1.4\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"mindiffs\": \"3\", \"mindiv\": \"0.5\", \"minh\": \"0.3\", \"savelog\": false, \"template\": {\"source\": \"self\", \"__current_case__\": 2, \"abskew\": \"1.9\", \"group\": null, \"count\": {\"__class__\": \"ConnectedValue\"}}, \"xn\": \"8.0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.1",
+                        "type": "tool",
+                        "uuid": "d23b7636-fbcb-4346-992d-a79e8093d489",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_accnos",
+                                "uuid": "c975f75e-71cc-45a8-a653-df3fdd56eb9b"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_count",
+                                "uuid": "1657beb8-c142-47ca-ac8d-bf92a3b74273"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "vsearch.chimeras",
+                                "uuid": "e3cb9259-e3b1-4870-b098-eeadc7e8f4c1"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.39.5.0",
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {
+                            "accnos": {
+                                "id": 8,
+                                "output_name": "out_accnos"
+                            },
+                            "count_in": {
+                                "id": 8,
+                                "output_name": "out_count"
+                            },
+                            "fasta_in": {
+                                "id": 6,
+                                "output_name": "fasta_out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Remove.seqs",
+                        "outputs": [
+                            {
+                                "name": "fasta_out",
+                                "type": "input"
+                            },
+                            {
+                                "name": "count_out",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1872,
+                            "top": 231.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.39.5.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "5097ac2cbfc3",
+                            "name": "mothur_remove_seqs",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"accnos\": {\"__class__\": \"ConnectedValue\"}, \"alignreport_in\": null, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"count_in\": {\"__class__\": \"ConnectedValue\"}, \"dups\": true, \"fasta_in\": {\"__class__\": \"ConnectedValue\"}, \"fastq_in\": null, \"group_in\": null, \"list_in\": null, \"name_in\": null, \"qfile_in\": null, \"savelog\": false, \"taxonomy_in\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
+                        "type": "tool",
+                        "uuid": "b9b21e24-7318-474b-a145-a3be83c7d09c",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "count_out",
+                                "uuid": "8480daf7-266c-48fb-a4c7-2ff68313d6b6"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "fasta_out",
+                                "uuid": "51c086db-4a7e-4128-9010-01a3b6f2621e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {
+                            "count": {
+                                "id": 9,
+                                "output_name": "count_out"
+                            },
+                            "fasta": {
+                                "id": 9,
+                                "output_name": "fasta_out"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Summary.seqs",
+                                "name": "count"
+                            },
+                            {
+                                "description": "runtime parameter for tool Summary.seqs",
+                                "name": "fasta"
+                            },
+                            {
+                                "description": "runtime parameter for tool Summary.seqs",
+                                "name": "name"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Summary.seqs",
+                        "outputs": [
+                            {
+                                "name": "logfile",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "out_summary",
+                                "type": "mothur.summary"
+                            }
+                        ],
+                        "position": {
+                            "left": 2298,
+                            "top": 342
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "609770e516fa",
+                            "name": "mothur_summary_seqs",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"count\": {\"__class__\": \"RuntimeValue\"}, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"name\": {\"__class__\": \"RuntimeValue\"}, \"savelog\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
+                        "type": "tool",
+                        "uuid": "9a018d5e-23f7-46a7-ac83-a57bc2ddd9ac",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_summary",
+                                "uuid": "f097e9a4-45a5-4168-a3bc-79ae4c0eb3d4"
+                            }
+                        ]
+                    }
                 ],
-                "id": "avans-atgm",
-                "joined": "2020-11",
-                "members": [
-                    "bazante1"
+                "parent_id": "microbiome/mothur-miseq-sop-short",
+                "path": "topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow2_data_cleaning.ga",
+                "tags": [
+                    "microbiome"
                 ],
-                "name": "Avans Hogeschool",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/",
-                "ror": "015d5s513",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
-            },
-            {
-                "avatar": "/training-material/assets/images/abromics.png",
-                "funder": true,
-                "github": false,
-                "id": "abromics",
-                "joined": "2024-01",
-                "name": "ABRomics",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abromics/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/abromics.json"
-            }
-        ],
-        "dir": "topics/genome-annotation/tutorials/amr-gene-detection",
-        "edam_ontology": [
-            "topic_3673",
-            "topic_3305",
-            "topic_0622",
-            "topic_3301",
-            "topic_0080",
-            "topic_3324",
-            "topic_4013"
-        ],
-        "edam_operation": [
-            "Genome visualisation",
-            "Genome annotation",
-            "Read mapping"
-        ],
-        "edam_topic": [
-            "Whole genome sequencing",
-            "Public health and epidemiology",
-            "Genomics",
-            "Microbiology",
-            "Sequence analysis",
-            "Infectious disease",
-            "Antimicrobial Resistance"
-        ],
-        "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "visualisation",
-                "tutorials": [
-                    "jbrowse"
+                "test_results": null,
+                "tests": false,
+                "title": "Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur]",
+                "topic_id": "microbiome",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-mothur-miseq-sop-short/versions/workflow2-data-cleaning",
+                "tutorial_id": "mothur-miseq-sop-short",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow2_data_cleaning.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow2_data_cleaning.html",
+                "version": 1,
+                "wfid": "microbiome-mothur-miseq-sop-short",
+                "wfname": "workflow2-data-cleaning",
+                "workflow": "workflow2_data_cleaning.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0"
                 ],
-                "type": "internal"
+                "workflowhub_id": "1112"
             },
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "history-to-workflow"
-                ],
-                "type": "internal"
-            }
-        ],
-        "hands_on": true,
-        "id": "genome-annotation/amr-gene-detection",
-        "inexact_supported_servers": [
-            "Galaxy@AuBi"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "staramr is a powerful tool to predict ARGs and plasmid genes",
-            "Visualization of the ARGs and plasmid genes in their genomic context helps to make sense of the data"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Introductory",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-03-13",
-        "objectives": [
-            "Run a series of tool to assess the presence of antimicrobial resistance genes (ARG)",
-            "Get information about ARGs",
-            "Visualize the ARGs and plasmid genes in their genomic context"
-        ],
-        "pageviews": 1368,
-        "pub_date": "2024-01-23",
-        "questions": [
-            "Which resistance genes are on a bacterial genome?",
-            "Where are the genes located on the genome?"
-        ],
-        "short_id": "T00401",
-        "short_tools": [
-            "Grep1",
-            "jbrowse",
-            "bowtie2",
-            "tbl2gff3",
-            "bakta",
-            "staramr_search",
-            "upload1"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "prokaryote",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "gmod",
-            "illumina",
-            "amr",
-            "one-health",
-            "jbrowse1",
-            "microgalaxy"
-        ],
-        "time_estimation": "2h",
-        "title": "Identification of AMR genes in an assembled bacterial genome",
-        "tools": [
-            "Grep1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2",
-            "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1",
-            "upload1"
-        ],
-        "topic_name": "genome-annotation",
-        "topic_name_human": "Genome Annotation",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "amr-gene-detection",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.json"
-        },
-        "version": 5,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 176,
-        "visitors": 967,
-        "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "https://orcid.org/0000-0003-2255-1631",
-                        "name": "Bazante Sanders"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0001-9852-1987",
-                        "name": "B\u00e9r\u00e9nice Batut"
+                        "identifier": "https://orcid.org/0000-0003-3803-468X",
+                        "name": "Saskia Hiltemann"
                     }
                 ],
-                "description": "Identification of AMR genes in an assembled bacterial genome",
+                "description": "16S Microbial Analysis with mothur (short)",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontigs\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nforward_reads\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreverse_reads\"]\n  3[label=\"staramr\"]\n  0 -> 3 [label=\"output\"]\n  k7a18df3cf28045aa92e427b79f10a005[color=lightseagreen,label=\"Output\\nstararm_detailed_summary\"]\n  3 -> k7a18df3cf28045aa92e427b79f10a005\n  4[label=\"Bakta\"]\n  0 -> 4 [label=\"output\"]\n  kead94d4086b04cf0aee2cf72a8f47933[color=lightseagreen,label=\"Output\\nbakta_annotation_summary\"]\n  4 -> kead94d4086b04cf0aee2cf72a8f47933\n  5[label=\"Bowtie2\"]\n  1 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  k0639b4672e624a52b72f35bf9f46f6a3[color=lightseagreen,label=\"Output\\nbowtie_mapping_stats\"]\n  5 -> k0639b4672e624a52b72f35bf9f46f6a3\n  6[label=\"Select\"]\n  3 -> 6 [label=\"detailed_summary\"]\n  7[label=\"Table to GFF3\"]\n  6 -> 7 [label=\"out_file1\"]\n  8[label=\"JBrowse\"]\n  4 -> 8 [label=\"annotation_gff3\"]\n  7 -> 8 [label=\"output\"]\n  5 -> 8 [label=\"output\"]\n  k910a35522a224279b15930379b31496f[color=lightseagreen,label=\"Output\\njbrowse_output\"]\n  8 -> k910a35522a224279b15930379b31496f\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCleaned Sequences\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCount Table\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTraining set FASTA\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTraining set Taxonomy\"]\n  4[label=\"Classify.seqs\"]\n  2 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  0 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"Remove.lineage\"]\n  1 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  4 -> 5 [label=\"taxonomy_out\"]\n  6[label=\"Summary.seqs\"]\n  5 -> 6 [label=\"count_out\"]\n  5 -> 6 [label=\"fasta_out\"]\n}",
                 "history": [
                     {
-                        "hash": "597f8ce954083c7cd4e43765b6c4709619637e6a",
-                        "message": "Add Bazante's ORCID",
-                        "num": 4,
-                        "short_hash": "597f8ce95",
-                        "unix": "1706018263"
-                    },
-                    {
-                        "hash": "03e4290900ade23b2dffb3f61ea2875a64f2c396",
-                        "message": "Fix workflows",
-                        "num": 3,
-                        "short_hash": "03e429090",
-                        "unix": "1706004257"
-                    },
-                    {
-                        "hash": "c88bcbb6f04ad1847e0747f7fb9256ee0ec858de",
-                        "message": "Add license and creator to workflows",
-                        "num": 2,
-                        "short_hash": "c88bcbb6f",
-                        "unix": "1705678137"
-                    },
-                    {
-                        "hash": "6d6129376b624fe20278f8df09b13cae881c5484",
-                        "message": "Expand the AMR detection tutorial",
+                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
+                        "message": "Rename metagenomics topic to microbiome",
                         "num": 1,
-                        "short_hash": "6d6129376",
-                        "unix": "1705334494"
+                        "short_hash": "0e0a2f2cc",
+                        "unix": "1704901629"
                     }
                 ],
                 "inputs": [
@@ -159387,21 +159955,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "contigs"
+                                "name": "Cleaned Sequences"
                             }
                         ],
-                        "label": "contigs",
-                        "name": "contigs",
+                        "label": "Cleaned Sequences",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 258
+                            "left": 27,
+                            "top": 123.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"name\": \"contigs\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "a18c5e52-124f-4480-80b4-ea5936618bc6",
+                        "uuid": "817445c0-3b76-4949-bbed-34c88e2a0c59",
                         "when": null,
                         "workflow_outputs": []
                     },
@@ -159414,21 +159982,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "forward_reads"
+                                "name": "Count Table"
                             }
                         ],
-                        "label": "forward_reads",
-                        "name": "forward_reads",
+                        "label": "Count Table",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0.003423507807786663,
-                            "top": 600.9912432161087
+                            "left": 0,
+                            "top": 304.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"name\": \"forward_reads\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "edd7c009-b0f1-403d-9438-f675bd61d30a",
+                        "uuid": "7b43d972-886f-4aae-ab0e-2fd188655cbd",
                         "when": null,
                         "workflow_outputs": []
                     },
@@ -159441,1319 +160009,1279 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "reverse_reads"
+                                "name": "Training set FASTA"
                             }
                         ],
-                        "label": "reverse_reads",
-                        "name": "reverse_reads",
+                        "label": "Training set FASTA",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 724
+                            "left": 4,
+                            "top": 515.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"name\": \"reverse_reads\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "595db730-f37d-4314-85a3-e10dfb11e209",
+                        "uuid": "f2ee2034-e7ce-43b0-82c9-905c2dd0745c",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Training set Taxonomy"
+                            }
+                        ],
+                        "label": "Training set Taxonomy",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 30,
+                            "top": 694.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "f1a29c9e-a70e-4d8c-b7b4-1236da5245a1",
                         "when": null,
                         "workflow_outputs": []
                     }
                 ],
                 "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nforward_reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nreverse_reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"staramr\"];\n  0 -->|output| 3;\n  7a18df3c-f280-45aa-92e4-27b79f10a005[\"Output\\nstararm_detailed_summary\"];\n  3 --> 7a18df3c-f280-45aa-92e4-27b79f10a005;\n  style 7a18df3c-f280-45aa-92e4-27b79f10a005 stroke:#2c3143,stroke-width:4px;\n  4[\"Bakta\"];\n  0 -->|output| 4;\n  ead94d40-86b0-4cf0-aee2-cf72a8f47933[\"Output\\nbakta_annotation_summary\"];\n  4 --> ead94d40-86b0-4cf0-aee2-cf72a8f47933;\n  style ead94d40-86b0-4cf0-aee2-cf72a8f47933 stroke:#2c3143,stroke-width:4px;\n  5[\"Bowtie2\"];\n  1 -->|output| 5;\n  2 -->|output| 5;\n  0 -->|output| 5;\n  0639b467-2e62-4a52-b72f-35bf9f46f6a3[\"Output\\nbowtie_mapping_stats\"];\n  5 --> 0639b467-2e62-4a52-b72f-35bf9f46f6a3;\n  style 0639b467-2e62-4a52-b72f-35bf9f46f6a3 stroke:#2c3143,stroke-width:4px;\n  6[\"Select\"];\n  3 -->|detailed_summary| 6;\n  7[\"Table to GFF3\"];\n  6 -->|out_file1| 7;\n  8[\"JBrowse\"];\n  4 -->|annotation_gff3| 8;\n  7 -->|output| 8;\n  5 -->|output| 8;\n  910a3552-2a22-4279-b159-30379b31496f[\"Output\\njbrowse_output\"];\n  8 --> 910a3552-2a22-4279-b159-30379b31496f;\n  style 910a3552-2a22-4279-b159-30379b31496f stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "mrsa AMR gene detection",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nCleaned Sequences\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nCount Table\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nTraining set FASTA\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nTraining set Taxonomy\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Classify.seqs\"];\n  2 -->|output| 4;\n  1 -->|output| 4;\n  0 -->|output| 4;\n  3 -->|output| 4;\n  5[\"Remove.lineage\"];\n  1 -->|output| 5;\n  0 -->|output| 5;\n  4 -->|taxonomy_out| 5;\n  6[\"Summary.seqs\"];\n  5 -->|count_out| 6;\n  5 -->|fasta_out| 6;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur]",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0",
                         "errors": null,
-                        "id": 3,
+                        "id": 4,
                         "input_connections": {
-                            "genomes": {
+                            "alignment|template": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "count": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "fasta": {
                                 "id": 0,
                                 "output_name": "output"
+                            },
+                            "tax|taxonomy": {
+                                "id": 3,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "staramr",
+                        "name": "Classify.seqs",
                         "outputs": [
                             {
-                                "name": "blast_hits",
-                                "type": "input"
+                                "name": "taxonomy_out",
+                                "type": "mothur.seq.taxonomy"
                             },
                             {
-                                "name": "mlst",
-                                "type": "tabular"
+                                "name": "tax_summary",
+                                "type": "mothur.tax.summary"
                             },
                             {
-                                "name": "summary",
+                                "name": "tree_sum",
                                 "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 538,
+                            "top": 0
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "09bf9e496c64",
+                            "name": "mothur_classify_seqs",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"alignment\": {\"source\": \"hist\", \"__current_case__\": 1, \"template\": {\"__class__\": \"ConnectedValue\"}}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"classify\": {\"method\": \"wang\", \"__current_case__\": 0, \"ksize\": \"8\", \"iters\": \"100\", \"cutoff\": \"80\", \"probs\": true}, \"count\": {\"__class__\": \"ConnectedValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"name\": null, \"output\": \"simple\", \"printlevel\": \"-1\", \"relabund\": false, \"savelog\": false, \"tax\": {\"source2\": \"hist\", \"__current_case__\": 1, \"taxonomy\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
+                        "type": "tool",
+                        "uuid": "d57e48c7-34ce-4742-8545-31b9d5c4a53d",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "taxonomy_out",
+                                "uuid": "dd10f8f4-a93e-46be-98d9-1e4d54b22fe0"
                             },
                             {
-                                "name": "detailed_summary",
-                                "type": "tabular"
+                                "label": null,
+                                "output_name": "tree_sum",
+                                "uuid": "964cf5ca-6cb9-477f-8754-88f3bf048da9"
                             },
                             {
-                                "name": "resfinder",
-                                "type": "tabular"
+                                "label": null,
+                                "output_name": "tax_summary",
+                                "uuid": "b3b100a8-87f2-4ddd-be9e-e7259399c15a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "count": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "fasta_in": {
+                                "id": 0,
+                                "output_name": "output"
                             },
+                            "file|taxonomy": {
+                                "id": 4,
+                                "output_name": "taxonomy_out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Remove.lineage",
+                        "outputs": [
                             {
-                                "name": "plasmidfinder",
-                                "type": "tabular"
+                                "name": "taxonomy_out",
+                                "type": "mothur.seq.taxonomy"
                             },
                             {
-                                "name": "settings",
-                                "type": "txt"
+                                "name": "fasta_out",
+                                "type": "input"
                             },
                             {
-                                "name": "excel",
-                                "type": "xlsx"
+                                "name": "count_out",
+                                "type": "mothur.count_table"
                             }
                         ],
                         "position": {
-                            "left": 290.00083115418806,
-                            "top": 261
+                            "left": 781,
+                            "top": 593
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "3b22de20bd4b",
-                            "name": "staramr",
-                            "owner": "nml",
+                            "changeset_revision": "947faa8b3205",
+                            "name": "mothur_remove_lineage",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"pid_threshold\": \"98.0\", \"plength_resfinder\": \"60.0\", \"plength_pointfinder\": \"95.0\", \"plength_plasmidfinder\": \"60.0\", \"genome_size_lower_bound\": \"4000000\", \"genome_size_upper_bound\": \"6000000\", \"minimum_N50_value\": \"10000\", \"minimum_contig_length\": \"300\", \"unacceptable_number_contigs\": \"1000\", \"report_all_blast\": false, \"exclude_negatives\": false, \"exclude_resistance_phenotypes\": false, \"mlst_scheme\": \"auto\", \"exclude_genes\": {\"exclude_genes_condition\": \"default\", \"__current_case__\": 0}, \"complex_mutations\": {\"complex_mutations_condition\": \"default\", \"__current_case__\": 0}, \"plasmidfinder_type\": \"include_all\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"genomes\": {\"__class__\": \"ConnectedValue\"}, \"pointfinder_db\": {\"use_pointfinder\": \"disabled\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.10.0+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"alignreport_in\": null, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"count\": {\"__class__\": \"ConnectedValue\"}, \"dups\": true, \"fasta_in\": {\"__class__\": \"ConnectedValue\"}, \"file\": {\"filetype\": \"usetaxonomy\", \"__current_case__\": 0, \"taxonomy\": {\"__class__\": \"ConnectedValue\"}, \"taxons\": null}, \"group_in\": null, \"list_in\": null, \"name_in\": null, \"savelog\": false, \"taxon\": \"Chloroplast-Mitochondria-unknown-Archaea-Eukaryota\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
                         "type": "tool",
-                        "uuid": "2554da56-e9f9-4e65-98b6-25b4a2861df9",
+                        "uuid": "61870655-5bd1-45bc-a8fe-81b1cf8018a2",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "stararm_detailed_summary",
-                                "output_name": "detailed_summary",
-                                "uuid": "7a18df3c-f280-45aa-92e4-27b79f10a005"
+                                "label": null,
+                                "output_name": "taxonomy_out",
+                                "uuid": "cdca67a9-ef60-4162-b3ba-1e502f543fde"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "fasta_out",
+                                "uuid": "7fabef22-b375-4615-8209-9e7f4685faba"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "count_out",
+                                "uuid": "452deac5-f985-4702-9028-083b62cd42c6"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
                         "errors": null,
-                        "id": 4,
+                        "id": 6,
                         "input_connections": {
-                            "input_option|input_file": {
-                                "id": 0,
-                                "output_name": "output"
+                            "count": {
+                                "id": 5,
+                                "output_name": "count_out"
+                            },
+                            "fasta": {
+                                "id": 5,
+                                "output_name": "fasta_out"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Bakta",
-                                "name": "annotation"
+                                "description": "runtime parameter for tool Summary.seqs",
+                                "name": "count"
                             },
                             {
-                                "description": "runtime parameter for tool Bakta",
-                                "name": "annotation"
+                                "description": "runtime parameter for tool Summary.seqs",
+                                "name": "fasta"
                             },
                             {
-                                "description": "runtime parameter for tool Bakta",
-                                "name": "annotation"
+                                "description": "runtime parameter for tool Summary.seqs",
+                                "name": "name"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Summary.seqs",
+                        "outputs": [
+                            {
+                                "name": "logfile",
+                                "type": "txt"
                             },
                             {
-                                "description": "runtime parameter for tool Bakta",
-                                "name": "input_option"
+                                "name": "out_summary",
+                                "type": "mothur.summary"
+                            }
+                        ],
+                        "position": {
+                            "left": 1128.25,
+                            "top": 788.0624885559082
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "609770e516fa",
+                            "name": "mothur_summary_seqs",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"count\": {\"__class__\": \"RuntimeValue\"}, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"name\": {\"__class__\": \"RuntimeValue\"}, \"savelog\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
+                        "type": "tool",
+                        "uuid": "c399d175-5b43-45b1-9916-f2f11f1cad25",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "logfile",
+                                "uuid": "2ba6776c-d197-4804-9654-039b997986ce"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_summary",
+                                "uuid": "b5e93d2a-6ff7-48bb-aa4e-5a58683910c8"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "microbiome/mothur-miseq-sop-short",
+                "path": "topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow3_classification.ga",
+                "tags": [
+                    "microbiome"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur]",
+                "topic_id": "microbiome",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-mothur-miseq-sop-short/versions/workflow3-classification",
+                "tutorial_id": "mothur-miseq-sop-short",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow3_classification.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow3_classification.html",
+                "version": 1,
+                "wfid": "microbiome-mothur-miseq-sop-short",
+                "wfname": "workflow3-classification",
+                "workflow": "workflow3_classification.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0"
+                ],
+                "workflowhub_id": "1060"
+            },
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0003-3803-468X",
+                        "name": "Saskia Hiltemann"
+                    }
+                ],
+                "description": "16S Microbial Analysis with mothur (short)",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMock Count Table\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMock Sequences\"]\n  2[label=\"Dist.seqs\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"Cluster\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"out_dist\"]\n  4[label=\"Make.shared\"]\n  0 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"otulist\"]\n  5[label=\"Rarefaction.single\"]\n  4 -> 5 [label=\"shared\"]\n}",
+                "history": [
+                    {
+                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
+                        "message": "Rename metagenomics topic to microbiome",
+                        "num": 1,
+                        "short_hash": "0e0a2f2cc",
+                        "unix": "1704901629"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Mock Count Table"
+                            }
+                        ],
+                        "label": "Mock Count Table",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 11
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "3c149509-370a-47f2-9f6d-a0fadcd7c1b6",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Mock Sequences"
                             }
                         ],
+                        "label": "Mock Sequences",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 7,
+                            "top": 259
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "c020d492-fb13-43c7-85e3-faa820866965",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nMock Count Table\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nMock Sequences\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Dist.seqs\"];\n  1 -->|output| 2;\n  3[\"Cluster\"];\n  0 -->|output| 3;\n  2 -->|out_dist| 3;\n  4[\"Make.shared\"];\n  0 -->|output| 4;\n  3 -->|otulist| 4;\n  5[\"Rarefaction.single\"];\n  4 -->|shared| 5;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "fasta": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
                         "label": null,
-                        "name": "Bakta",
+                        "name": "Dist.seqs",
                         "outputs": [
                             {
-                                "name": "annotation_tsv",
-                                "type": "tabular"
+                                "name": "out_dist",
+                                "type": "mothur.pair.dist"
+                            }
+                        ],
+                        "position": {
+                            "left": 276,
+                            "top": 319
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "0554c9338ca0",
+                            "name": "mothur_dist_seqs",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"calc\": \"\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"countends\": true, \"cutoff\": \"0.2\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"output\": \"\", \"savelog\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
+                        "type": "tool",
+                        "uuid": "925be8d7-7355-4a1d-b375-b27826e4cd2e",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_dist",
+                                "uuid": "28fe4e3d-5be8-47e8-9cd3-527e8657c391"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "count": {
+                                "id": 0,
+                                "output_name": "output"
                             },
+                            "matrix|dist": {
+                                "id": 2,
+                                "output_name": "out_dist"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Cluster",
+                        "outputs": [
                             {
-                                "name": "annotation_gff3",
-                                "type": "gff3"
+                                "name": "rabund",
+                                "type": "mothur.rabund"
                             },
                             {
-                                "name": "annotation_ffn",
-                                "type": "fasta"
+                                "name": "sabund",
+                                "type": "mothur.sabund"
                             },
                             {
-                                "name": "annotation_plot",
-                                "type": "svg"
+                                "name": "otulist",
+                                "type": "mothur.list"
                             }
                         ],
                         "position": {
-                            "left": 570.0016623083761,
-                            "top": 0
+                            "left": 570,
+                            "top": 189
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "728dacaf08a9",
-                            "name": "bakta",
+                            "changeset_revision": "528f950d1044",
+                            "name": "mothur_cluster",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"annotation\": {\"complete\": false, \"prodigal\": {\"__class__\": \"RuntimeValue\"}, \"translation_table\": \"11\", \"keep_contig_headers\": true, \"replicons\": {\"__class__\": \"RuntimeValue\"}, \"compliant\": false, \"proteins\": {\"__class__\": \"RuntimeValue\"}, \"meta\": false}, \"input_option\": {\"bakta_db_select\": \"V5.0_2023-02-20\", \"amrfinder_db_select\": \"amrfinderplus_V3.11_2022-12-19.1\", \"input_file\": {\"__class__\": \"RuntimeValue\"}, \"min_contig_length\": null}, \"organism\": {\"genus\": null, \"species\": null, \"strain\": null, \"plasmid\": null}, \"output_files\": {\"output_selection\": [\"file_tsv\", \"file_gff3\", \"file_ffn\", \"file_plot\"]}, \"workflow\": {\"skip_analysis\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.2+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"count\": {\"__class__\": \"ConnectedValue\"}, \"cutoff\": \"0.0\", \"matrix\": {\"format\": \"column\", \"__current_case__\": 0, \"dist\": {\"__class__\": \"ConnectedValue\"}, \"name\": null}, \"precision\": \"100\", \"savelog\": false, \"select_method\": {\"method\": \"opti\", \"__current_case__\": 5, \"metric\": \"mcc\", \"initialize\": \"singleton\", \"delta\": \"0.0001\", \"iters\": \"100\"}, \"sim\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
                         "type": "tool",
-                        "uuid": "0b92601d-5b78-438c-998d-f9f4dc61c52d",
+                        "uuid": "3f508523-34c1-420a-a0b6-2524b4d85b52",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "bakta_annotation_summary",
-                                "output_name": "annotation_tsv",
-                                "uuid": "ead94d40-86b0-4cf0-aee2-cf72a8f47933"
+                                "label": null,
+                                "output_name": "rabund",
+                                "uuid": "5f143144-eb84-4f88-9f57-87154dc29671"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "otulist",
+                                "uuid": "3e79d92c-11c6-48f5-a0c2-cbf747690b2e"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "sabund",
+                                "uuid": "a698d39c-c469-4867-9450-f9d80446d99f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0",
                         "errors": null,
-                        "id": 5,
+                        "id": 4,
                         "input_connections": {
-                            "library|input_1": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "library|input_2": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "reference_genome|own_file": {
+                            "intype|group": {
                                 "id": 0,
                                 "output_name": "output"
+                            },
+                            "intype|otu": {
+                                "id": 3,
+                                "output_name": "otulist"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Bowtie2",
+                        "name": "Make.shared",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "bam"
+                                "name": "logfile",
+                                "type": "txt"
                             },
                             {
-                                "name": "mapping_stats",
-                                "type": "txt"
+                                "name": "shared",
+                                "type": "mothur.shared"
+                            },
+                            {
+                                "name": "groupout",
+                                "type": "mothur.groups"
                             }
                         ],
                         "position": {
-                            "left": 290.00083115418806,
-                            "top": 628
+                            "left": 898,
+                            "top": 0
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "03e9b2fbc005",
-                            "name": "bowtie2",
-                            "owner": "devteam",
+                            "changeset_revision": "0851ae17c58e",
+                            "name": "mothur_make_shared",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"no_presets\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"library\": {\"type\": \"paired\", \"__current_case__\": 1, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"input_2\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": false, \"aligned_file\": false, \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 1, \"own_file\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.5.0+galaxy0",
+                        "tool_state": "{\"intype\": {\"infile\": \"otulist\", \"__current_case__\": 0, \"otu\": {\"__class__\": \"ConnectedValue\"}, \"group\": {\"__class__\": \"ConnectedValue\"}, \"label\": [\"0.03\"], \"groups\": null}, \"savelog\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
                         "type": "tool",
-                        "uuid": "7e8f9570-3d8b-4a82-b109-09bc04b82c64",
+                        "uuid": "72197339-b027-4c3e-85ba-edf401b82322",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "bowtie_mapping_stats",
-                                "output_name": "mapping_stats",
-                                "uuid": "0639b467-2e62-4a52-b72f-35bf9f46f6a3"
+                                "label": null,
+                                "output_name": "shared",
+                                "uuid": "1d80db8c-04f6-45a0-a523-f87c7a4b87cf"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0",
                         "errors": null,
-                        "id": 8,
+                        "id": 5,
                         "input_connections": {
-                            "track_groups_0|data_tracks_0|data_format|annotation": {
+                            "otu": {
                                 "id": 4,
-                                "output_name": "annotation_gff3"
-                            },
-                            "track_groups_1|data_tracks_0|data_format|annotation": {
-                                "id": 7,
-                                "output_name": "output"
-                            },
-                            "track_groups_2|data_tracks_0|data_format|annotation": {
-                                "id": 5,
-                                "output_name": "output"
+                                "output_name": "shared"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "JBrowse",
+                        "name": "Rarefaction.single",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "html"
+                                "name": "rarefactioncurves",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 1130.0033246167523,
-                            "top": 325
+                            "left": 1172,
+                            "top": 211
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "a6e57ff585c0",
-                            "name": "jbrowse",
+                            "changeset_revision": "af521db77c56",
+                            "name": "mothur_rarefaction_single",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": true, \"aboutDescription\": \"\", \"show_tracklist\": true, \"show_nav\": true, \"show_overview\": true, \"show_menu\": true, \"hideGenomeOptions\": false}, \"plugins\": {\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Bakta\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"match_part\": {\"match_part_select\": false, \"__current_case__\": 1}, \"index\": false, \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 1, \"category\": \"ARGs and plasmid genes\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"match_part\": {\"match_part_select\": false, \"__current_case__\": 1}, \"index\": false, \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 2, \"category\": \"Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"auto_snp\": false, \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16.11+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"abund\": \"10\", \"calc\": [\"sobs\"], \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"freq\": \"100.0\", \"iters\": \"1000\", \"label\": null, \"otu\": {\"__class__\": \"ConnectedValue\"}, \"savelog\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
                         "type": "tool",
-                        "uuid": "9f973678-ce81-458a-a5d0-575d93d61429",
+                        "uuid": "6982780b-f8ac-4ff8-b862-29557494d9b4",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "jbrowse_output",
-                                "output_name": "output",
-                                "uuid": "910a3552-2a22-4279-b159-30379b31496f"
+                                "label": null,
+                                "output_name": "rarefactioncurves",
+                                "uuid": "cbf4d013-fa83-4bd9-9f97-1e3632362b36"
                             }
                         ]
                     }
                 ],
-                "parent_id": "genome-annotation/amr-gene-detection",
-                "path": "topics/genome-annotation/tutorials/amr-gene-detection/workflows/main-workflow.ga",
+                "parent_id": "microbiome/mothur-miseq-sop-short",
+                "path": "topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow4_mock_otu_clustering.ga",
                 "tags": [
-                    "genome-annotation",
-                    "microgalaxy"
+                    "microbiome"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "mrsa AMR gene detection",
-                "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-amr-gene-detection/versions/main-workflow",
-                "tutorial_id": "amr-gene-detection",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/amr-gene-detection/workflows/main-workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/amr-gene-detection/workflows/main-workflow.html",
+                "tests": false,
+                "title": "Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]",
+                "topic_id": "microbiome",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-mothur-miseq-sop-short/versions/workflow4-mock-otu-clustering",
+                "tutorial_id": "mothur-miseq-sop-short",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow4_mock_otu_clustering.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow4_mock_otu_clustering.html",
                 "version": 1,
-                "wfid": "genome-annotation-amr-gene-detection",
-                "wfname": "main-workflow",
-                "workflow": "main-workflow.ga",
+                "wfid": "microbiome-mothur-miseq-sop-short",
+                "wfname": "workflow4-mock-otu-clustering",
+                "workflow": "workflow4_mock_otu_clustering.ga",
                 "workflow_tools": [
-                    "Grep1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2",
-                    "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1"
-                ],
-                "workflowhub_id": "1168"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/10572227"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bcftools_consensus",
-                    "owner": "iuc",
-                    "revisions": "1171446da5db",
-                    "tool_panel_section_label": "Variant Calling",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bcftools_consensus",
-                    "owner": "iuc",
-                    "revisions": "a87ae767b01d",
-                    "tool_panel_section_label": "Variant Calling",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_view",
-                    "owner": "iuc",
-                    "revisions": "0dbf49c414ae",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "snippy",
-                    "owner": "iuc",
-                    "revisions": "c9a8ef2aa380",
-                    "tool_panel_section_label": "Variant Calling",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "snippy",
-                    "owner": "iuc",
-                    "revisions": "d220115f882b",
-                    "tool_panel_section_label": "Variant Calling",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "snp_dists",
-                    "owner": "iuc",
-                    "revisions": "1959cc43b414",
-                    "tool_panel_section_label": "Phylogenetics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "snp_dists",
-                    "owner": "iuc",
-                    "revisions": "f78492521996",
-                    "tool_panel_section_label": "Phylogenetics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "snp_sites",
-                    "owner": "iuc",
-                    "revisions": "5804f786060d",
-                    "tool_panel_section_label": "Phylogenetics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "tb_variant_filter",
-                    "owner": "iuc",
-                    "revisions": "3b1e7c170b10",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "tb_variant_filter",
-                    "owner": "iuc",
-                    "revisions": "e7aff4a85df5",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "tb_variant_filter",
-                    "owner": "iuc",
-                    "revisions": "ee4a90760848",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "tbprofiler",
-                    "owner": "iuc",
-                    "revisions": "809dfc93d593",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "add_input_name_as_column",
-                    "owner": "mvdbeek",
-                    "revisions": "3284b72eef56",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "90981f86000f",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "trimmomatic",
-                    "owner": "pjbriggs",
-                    "revisions": "d94aff5ee623",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_consensus\n  owner: iuc\n  revisions: 1171446da5db\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_consensus\n  owner: iuc\n  revisions: a87ae767b01d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: 0dbf49c414ae\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snippy\n  owner: iuc\n  revisions: c9a8ef2aa380\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snippy\n  owner: iuc\n  revisions: d220115f882b\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snp_dists\n  owner: iuc\n  revisions: 1959cc43b414\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snp_dists\n  owner: iuc\n  revisions: f78492521996\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snp_sites\n  owner: iuc\n  revisions: 5804f786060d\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tb_variant_filter\n  owner: iuc\n  revisions: 3b1e7c170b10\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tb_variant_filter\n  owner: iuc\n  revisions: e7aff4a85df5\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tb_variant_filter\n  owner: iuc\n  revisions: ee4a90760848\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbprofiler\n  owner: iuc\n  revisions: 809dfc93d593\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: add_input_name_as_column\n  owner: mvdbeek\n  revisions: 3284b72eef56\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n  owner: pjbriggs\n  revisions: d94aff5ee623\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/evolution/tutorials/mtb_transmission/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "GaloGS",
-                "dbrites",
-                "cstritt"
-            ],
-            "editing": [
-                "wm75"
-            ]
-        },
-        "contributors": [
-            {
-                "id": "GaloGS",
-                "joined": "2022-03",
-                "name": "Galo A. Goig",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/GaloGS/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/GaloGS.json"
-            },
-            {
-                "id": "dbrites",
-                "joined": "2022-03",
-                "name": "Daniela Brites",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dbrites/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/dbrites.json"
-            },
-            {
-                "id": "cstritt",
-                "joined": "2022-03",
-                "name": "Christoph Stritt",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cstritt/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/cstritt.json"
-            },
-            {
-                "affiliations": [
-                    "by-covid",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "fediverse": "https://scholar.social/@zerodivision",
-                "fediverse_flavor": "mastodon",
-                "id": "wm75",
-                "joined": "2017-09",
-                "matrix": "wm75:matrix.org",
-                "name": "Wolfgang Maier",
-                "orcid": "0000-0002-9464-6640",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
-            }
-        ],
-        "dir": "topics/evolution/tutorials/mtb_transmission",
-        "edam_ontology": [
-            "topic_0622",
-            "topic_3301",
-            "topic_3324",
-            "topic_2885"
-        ],
-        "edam_operation": [
-            "Variant calling",
-            "Phylogenetic tree visualisation",
-            "Phylogenetic tree generation",
-            "Antimicrobial resistance prediction"
-        ],
-        "edam_topic": [
-            "Genomics",
-            "Microbiology",
-            "Infectious disease",
-            "DNA polymorphism"
-        ],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "evolution/mtb_transmission",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Clustering is a useful tool to detect transmission links between patients and oubreak investigation.",
-            "Clustering can be used to investigate the transmission of certain traits, like drug resistance.",
-            "Clustering does not provide information about particular transmission events nor their directionality (who infected whom).",
-            "Clustering is very much influenced by sampling. Lower sampling proportions and shorter sampling timeframes lead to lower clustering rates that shoud not be confounded with lack of transmission."
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-07-12",
-        "objectives": [
-            "Create a SNP alignment",
-            "Calculate pairwise SNP distances between MTB samples",
-            "Identify transmission clusters based on SNP distances",
-            "Study the emergence and spread of drug resistance based on transmission analysis."
-        ],
-        "pageviews": 2414,
-        "pub_date": "2022-03-16",
-        "requirements": [
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "collections"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0"
                 ],
-                "type": "internal"
+                "workflowhub_id": "1125"
             },
             {
-                "topic_name": "variant-analysis",
-                "tutorials": [
-                    "tb-variant-analysis"
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0003-3803-468X",
+                        "name": "Saskia Hiltemann"
+                    }
                 ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00145",
-        "short_tools": [
-            "Grep1",
-            "bcftools_consensus",
-            "tb_variant_filter",
-            "upload1",
-            "samtools_view",
-            "snp_sites",
-            "tb_profiler_profile",
-            "tp_grep_tool",
-            "tp_cat",
-            "snippy",
-            "tp_easyjoin_tool",
-            "addName",
-            "tp_sed_tool",
-            "tp_replace_in_line",
-            "snp_dists",
-            "collapse_dataset",
-            "__MERGE_COLLECTION__",
-            "trimmomatic"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "prokaryote",
-            "one-health",
-            "microgalaxy"
-        ],
-        "time_estimation": "2H",
-        "title": "Identifying tuberculosis transmission links: from SNPs to transmission clusters",
-        "tools": [
-            "Grep1",
-            "__MERGE_COLLECTION__",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.6.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.8.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.5+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/3.0.8+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
-            "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1",
-            "upload1"
-        ],
-        "topic_name": "evolution",
-        "topic_name_human": "Evolution",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "mtb_transmission",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/evolution/tutorials/mtb_transmission/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/evolution/tutorials/mtb_transmission/tutorial.json"
-        },
-        "version": 12,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 188,
-        "visitors": 1533,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Starting from the BAM files produced by snippy, generate a table that summarizes the drug-resistance profile for each sample",
+                "description": "16S Microbial Analysis with mothur (short)",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nMTB single-end BAMs\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nMTB paired-end BAMs\"]\n  2[label=\"Merge collections\"]\n  0 -> 2 [label=\"output\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"Samtools view BAM > SAM\"]\n  2 -> 3 [label=\"output\"]\n  kaa2200279d104328b2c2e4d139d5d5bd[color=lightseagreen,label=\"Output\\nSamtools view on input dataset(s): filtered alignments\"]\n  3 -> kaa2200279d104328b2c2e4d139d5d5bd\n  4[label=\"Sed MTB_anc to Chromosome\"]\n  3 -> 4 [label=\"outputsam\"]\n  5[label=\"Samtools view SAM > BAM\"]\n  4 -> 5 [label=\"output\"]\n  6[label=\"TB-profiler\"]\n  5 -> 6 [label=\"outputsam\"]\n  7[label=\"Get drug resistance profile\"]\n  6 -> 7 [label=\"output_txt\"]\n  8[label=\"Add Sample Name\"]\n  7 -> 8 [label=\"output\"]\n  9[label=\"Concatenate DR profiles in a single table\"]\n  8 -> 9 [label=\"output\"]\n  10[label=\"Cleanup the table\"]\n  9 -> 10 [label=\"out_file1\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSequences\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCount Table\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTaxonomy\"]\n  3[label=\"Remove.groups\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Cluster.split\"]\n  3 -> 4 [label=\"fasta_out\"]\n  3 -> 4 [label=\"count_out\"]\n  3 -> 4 [label=\"taxonomy_out\"]\n  5[label=\"Make.shared\"]\n  3 -> 5 [label=\"count_out\"]\n  4 -> 5 [label=\"otulist\"]\n  6[label=\"Classify.otu\"]\n  3 -> 6 [label=\"count_out\"]\n  4 -> 6 [label=\"otulist\"]\n  3 -> 6 [label=\"taxonomy_out\"]\n  7[label=\"Count.groups\"]\n  5 -> 7 [label=\"shared\"]\n  8[label=\"Sub.sample\"]\n  5 -> 8 [label=\"shared\"]\n}",
                 "history": [
                     {
-                        "hash": "103d419430b5164ef56e7de3bd3ef13e798967cd",
-                        "message": "update tag",
-                        "num": 2,
-                        "short_hash": "103d41943",
-                        "unix": "1647422971"
-                    },
-                    {
-                        "hash": "2e7ba78522415b81e10f3f5a74144f4f419b218d",
-                        "message": "tweak",
+                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
+                        "message": "Rename metagenomics topic to microbiome",
                         "num": 1,
-                        "short_hash": "2e7ba7852",
-                        "unix": "1647422653"
+                        "short_hash": "0e0a2f2cc",
+                        "unix": "1704901629"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "BAMs obtained from single-end mappings with snippy",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "BAMs obtained from single-end mappings with snippy",
-                                "name": "MTB single-end BAMs"
+                                "description": "",
+                                "name": "Sequences"
                             }
                         ],
-                        "label": "MTB single-end BAMs",
-                        "name": "Input dataset collection",
+                        "label": "Sequences",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 586.3333282470703,
-                            "height": 89.09999084472656,
-                            "left": -233.6999969482422,
-                            "right": -13.699996948242188,
-                            "top": 497.23333740234375,
-                            "width": 220,
-                            "x": -233.6999969482422,
-                            "y": 497.23333740234375
+                            "bottom": 16.300003051757812,
+                            "height": 61.80000305175781,
+                            "left": 116,
+                            "right": 316,
+                            "top": -45.5,
+                            "width": 200,
+                            "x": 116,
+                            "y": -45.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "5befe3e8-ccba-4b78-b7f1-dab039ef1011",
+                        "type": "data_input",
+                        "uuid": "9cdb4877-1fdf-41a7-8089-5f2ffcabbdda",
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "BAMs obtained from paired-end mappings with snippy",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "BAMs obtained from paired-end mappings with snippy",
-                                "name": "MTB paired-end BAMs"
+                                "description": "",
+                                "name": "Count Table"
                             }
                         ],
-                        "label": "MTB paired-end BAMs",
-                        "name": "Input dataset collection",
+                        "label": "Count Table",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 695.3333282470703,
-                            "height": 89.09999084472656,
-                            "left": -234.6999969482422,
-                            "right": -14.699996948242188,
-                            "top": 606.2333374023438,
-                            "width": 220,
-                            "x": -234.6999969482422,
-                            "y": 606.2333374023438
+                            "bottom": 139.3000030517578,
+                            "height": 61.80000305175781,
+                            "left": 118,
+                            "right": 318,
+                            "top": 77.5,
+                            "width": 200,
+                            "x": 118,
+                            "y": 77.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "d6f269d8-66e8-4baf-9b5c-de9e7313c4a0",
+                        "type": "data_input",
+                        "uuid": "c3ebf885-3d00-4db6-828b-8c9af54f77c7",
                         "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nMTB single-end BAMs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nMTB paired-end BAMs\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Merge collections\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"Samtools view BAM > SAM\"];\n  2 -->|output| 3;\n  aa220027-9d10-4328-b2c2-e4d139d5d5bd[\"Output\\nSamtools view on input dataset(s): filtered alignments\"];\n  3 --> aa220027-9d10-4328-b2c2-e4d139d5d5bd;\n  style aa220027-9d10-4328-b2c2-e4d139d5d5bd stroke:#2c3143,stroke-width:4px;\n  4[\"Sed MTB_anc to Chromosome\"];\n  3 -->|outputsam| 4;\n  5[\"Samtools view SAM > BAM\"];\n  4 -->|output| 5;\n  6[\"TB-profiler\"];\n  5 -->|outputsam| 6;\n  7[\"Get drug resistance profile\"];\n  6 -->|output_txt| 7;\n  8[\"Add Sample Name\"];\n  7 -->|output| 8;\n  9[\"Concatenate DR profiles in a single table\"];\n  8 -->|output| 9;\n  10[\"Cleanup the table\"];\n  9 -->|out_file1| 10;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "From BAMs to drug resistance prediction with TB-profiler",
-                "outputs": [
+                    },
                     {
-                        "annotation": "Merge single-end and paired-end BAMs in a single collection to be analyzed alltogether",
-                        "content_id": "__MERGE_COLLECTION__",
+                        "annotation": "",
+                        "content_id": null,
                         "errors": null,
                         "id": 2,
-                        "input_connections": {
-                            "inputs_0|input": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "inputs_1|input": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Merge collections",
-                        "name": "Merge collections",
-                        "outputs": [
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "input"
+                                "description": "",
+                                "name": "Taxonomy"
                             }
                         ],
+                        "label": "Taxonomy",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 720.5,
-                            "height": 222.26666259765625,
-                            "left": 34.80000305175781,
-                            "right": 254.8000030517578,
-                            "top": 498.23333740234375,
-                            "width": 220,
-                            "x": 34.80000305175781,
-                            "y": 498.23333740234375
+                            "bottom": 294.3000030517578,
+                            "height": 61.80000305175781,
+                            "left": 119,
+                            "right": 319,
+                            "top": 232.5,
+                            "width": 200,
+                            "x": 119,
+                            "y": 232.5
                         },
-                        "post_job_actions": {},
-                        "tool_id": "__MERGE_COLLECTION__",
-                        "tool_state": "{\"advanced\": {\"conflict\": {\"duplicate_options\": \"keep_first\", \"__current_case__\": 3}}, \"inputs\": [{\"__index__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "2142f124-4731-49fb-8e65-8e050705e001",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "180a1bdf-d552-49b7-93e9-4daf609096a6"
-                            }
-                        ]
-                    },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "2d1cebdc-28da-4686-8a5b-0043b34c9aac",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSequences\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nCount Table\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nTaxonomy\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Remove.groups\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  2 -->|output| 3;\n  4[\"Cluster.split\"];\n  3 -->|fasta_out| 4;\n  3 -->|count_out| 4;\n  3 -->|taxonomy_out| 4;\n  5[\"Make.shared\"];\n  3 -->|count_out| 5;\n  4 -->|otulist| 5;\n  6[\"Classify.otu\"];\n  3 -->|count_out| 6;\n  4 -->|otulist| 6;\n  3 -->|taxonomy_out| 6;\n  7[\"Count.groups\"];\n  5 -->|shared| 7;\n  8[\"Sub.sample\"];\n  5 -->|shared| 8;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]",
+                "outputs": [
                     {
-                        "annotation": "We want a text (SAM) file to substitute the string \"MTB_anc\" by \"Chromosome\" so it is compatible with TB-profiler",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0",
                         "errors": null,
                         "id": 3,
                         "input_connections": {
-                            "input": {
+                            "groupnames|fasta_in": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "groupnames|group_in": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "groupnames|taxonomy_in": {
                                 "id": 2,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": "Samtools view BAM > SAM",
-                        "name": "Samtools view",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "outputsam",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 951.5000152587891,
-                            "height": 189.8333282470703,
-                            "left": 277.6000061035156,
-                            "right": 497.6000061035156,
-                            "top": 761.6666870117188,
-                            "width": 220,
-                            "x": 277.6000061035156,
-                            "y": 761.6666870117188
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "0dbf49c414ae",
-                            "name": "samtools_view",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"all_reads\", \"__current_case__\": 0, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"adv_output\": {\"readtags\": [], \"collapsecigar\": \"false\"}, \"output_format\": {\"oformat\": \"sam\", \"__current_case__\": 1, \"with_header\": \"true\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.13+galaxy2",
-                        "type": "tool",
-                        "uuid": "1040a122-5729-41a4-bd45-2406231f8024",
-                        "workflow_outputs": [
+                                "description": "runtime parameter for tool Remove.groups",
+                                "name": "groupnames"
+                            },
                             {
-                                "label": "Samtools view on input dataset(s): filtered alignments",
-                                "output_name": "outputsam",
-                                "uuid": "aa220027-9d10-4328-b2c2-e4d139d5d5bd"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "Change the string MTB_anc to \"Chromosome\" so it is compatible with TB-profiler",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "infile": {
-                                "id": 3,
-                                "output_name": "outputsam"
+                                "description": "runtime parameter for tool Remove.groups",
+                                "name": "groupnames"
+                            },
+                            {
+                                "description": "runtime parameter for tool Remove.groups",
+                                "name": "groupnames"
+                            },
+                            {
+                                "description": "runtime parameter for tool Remove.groups",
+                                "name": "groupnames"
+                            },
+                            {
+                                "description": "runtime parameter for tool Remove.groups",
+                                "name": "groupnames"
+                            },
+                            {
+                                "description": "runtime parameter for tool Remove.groups",
+                                "name": "groupnames"
+                            },
+                            {
+                                "description": "runtime parameter for tool Remove.groups",
+                                "name": "groupnames"
                             }
-                        },
-                        "inputs": [],
-                        "label": "Sed (MTB_anc to Chromosome)",
-                        "name": "Text transformation",
+                        ],
+                        "label": null,
+                        "name": "Remove.groups",
                         "outputs": [
                             {
-                                "name": "output",
+                                "name": "list_out",
                                 "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 943.2000122070312,
-                            "height": 122.5333251953125,
-                            "left": 537.5999755859375,
-                            "right": 757.5999755859375,
-                            "top": 820.6666870117188,
-                            "width": 220,
-                            "x": 537.5999755859375,
-                            "y": 820.6666870117188
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"s/MTB_anc/Chromosome/g\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
-                        "type": "tool",
-                        "uuid": "95fc656b-43fc-4f1e-8850-25489e793376",
-                        "workflow_outputs": [
+                            },
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "c3b3612d-3999-4022-9d6c-49ce6756ba2a"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "input": {
-                                "id": 4,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Samtools view SAM > BAM",
-                        "name": "Samtools view",
-                        "outputs": [
+                                "name": "fasta_out",
+                                "type": "input"
+                            },
                             {
-                                "name": "outputsam",
+                                "name": "group_out",
+                                "type": "mothur.groups"
+                            },
+                            {
+                                "name": "count_out",
+                                "type": "mothur.count_table"
+                            },
+                            {
+                                "name": "name_out",
+                                "type": "mothur.names"
+                            },
+                            {
+                                "name": "taxonomy_out",
+                                "type": "mothur.seq.taxonomy"
+                            },
+                            {
+                                "name": "phylip_out",
                                 "type": "input"
+                            },
+                            {
+                                "name": "column_out",
+                                "type": "mothur.pair.dist"
                             }
                         ],
                         "position": {
-                            "bottom": 945.5000152587891,
-                            "height": 189.8333282470703,
-                            "left": 810.5999755859375,
-                            "right": 1030.5999755859375,
-                            "top": 755.6666870117188,
-                            "width": 220,
-                            "x": 810.5999755859375,
-                            "y": 755.6666870117188
+                            "bottom": 1023.2999877929688,
+                            "height": 916.7999877929688,
+                            "left": 383,
+                            "right": 583,
+                            "top": 106.5,
+                            "width": 200,
+                            "x": 383,
+                            "y": 106.5
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2",
+                        "post_job_actions": {
+                            "HideDatasetActionfasta_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "fasta_out"
+                            },
+                            "HideDatasetActionlist_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "list_out"
+                            },
+                            "HideDatasetActionname_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "name_out"
+                            },
+                            "HideDatasetActiontaxonomy_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "taxonomy_out"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "0dbf49c414ae",
-                            "name": "samtools_view",
+                            "changeset_revision": "498dc0671d9e",
+                            "name": "mothur_remove_groups",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"all_reads\", \"__current_case__\": 0, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"adv_output\": {\"readtags\": [], \"collapsecigar\": \"false\"}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.13+galaxy2",
+                        "tool_state": "{\"groupnames\": {\"source\": \"other\", \"__current_case__\": 0, \"group_in\": {\"__class__\": \"RuntimeValue\"}, \"groups\": \"Mock\", \"fasta_in\": {\"__class__\": \"RuntimeValue\"}, \"name_in\": {\"__class__\": \"RuntimeValue\"}, \"list_in\": {\"__class__\": \"RuntimeValue\"}, \"taxonomy_in\": {\"__class__\": \"RuntimeValue\"}, \"phylip_in\": {\"__class__\": \"RuntimeValue\"}, \"column_in\": {\"__class__\": \"RuntimeValue\"}}, \"savelog\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
                         "type": "tool",
-                        "uuid": "729169fd-682e-4394-8421-1cde0aa2ac37",
+                        "uuid": "90df5fc1-b437-48c1-a7d3-39062fef6c0b",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outputsam",
-                                "uuid": "67aacaf4-b657-4269-b3eb-5cf22e1e9596"
+                                "output_name": "group_out",
+                                "uuid": "3800548f-2976-4a6d-8b29-e501373719fd"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "phylip_out",
+                                "uuid": "20631d19-d683-47c6-8ae1-7e856e242e8d"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "count_out",
+                                "uuid": "bcd6f559-2b50-4c77-bf9c-9b9de5c7159a"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "column_out",
+                                "uuid": "20bf370c-7d36-4579-b94c-ac816d789717"
                             }
                         ]
                     },
                     {
-                        "annotation": "Generate TB-profiler reports with drug resistance determinants",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/3.0.8+galaxy0",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0",
                         "errors": null,
-                        "id": 6,
+                        "id": 4,
                         "input_connections": {
-                            "fastq_or_bam|bam_input": {
-                                "id": 5,
-                                "output_name": "outputsam"
+                            "splitby|fasta": {
+                                "id": 3,
+                                "output_name": "fasta_out"
+                            },
+                            "splitby|nameOrCount": {
+                                "id": 3,
+                                "output_name": "count_out"
+                            },
+                            "splitby|taxonomy": {
+                                "id": 3,
+                                "output_name": "taxonomy_out"
                             }
                         },
                         "inputs": [],
-                        "label": "TB-profiler",
-                        "name": "TB-Profiler Profile",
+                        "label": null,
+                        "name": "Cluster.split",
                         "outputs": [
                             {
-                                "name": "results_json",
-                                "type": "json"
+                                "name": "rabund",
+                                "type": "mothur.rabund"
                             },
                             {
-                                "name": "output_vcf",
-                                "type": "vcf"
+                                "name": "sabund",
+                                "type": "mothur.sabund"
                             },
                             {
-                                "name": "output_txt",
+                                "name": "otulist",
+                                "type": "mothur.list"
+                            },
+                            {
+                                "name": "sensspec",
                                 "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 724.9333343505859,
-                            "height": 254.6999969482422,
-                            "left": 1069.800048828125,
-                            "right": 1289.800048828125,
-                            "top": 470.23333740234375,
-                            "width": 220,
-                            "x": 1069.800048828125,
-                            "y": 470.23333740234375
+                            "bottom": 530.7000122070312,
+                            "height": 449.20001220703125,
+                            "left": 748,
+                            "right": 948,
+                            "top": 81.5,
+                            "width": 200,
+                            "x": 748,
+                            "y": 81.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/3.0.8+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "809dfc93d593",
-                            "name": "tbprofiler",
+                            "changeset_revision": "1b7fd1678230",
+                            "name": "mothur_cluster_split",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced\": {\"options\": \"no\", \"__current_case__\": 0}, \"fastq_or_bam\": {\"input_select\": \"bam\", \"__current_case__\": 3, \"bam_input\": {\"__class__\": \"ConnectedValue\"}}, \"output_format\": \"txt\", \"platform\": \"illumina\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.0.8+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cluster\": \"true\", \"cutoff\": \"0.03\", \"large\": \"false\", \"precision\": \"100\", \"runsensspec\": \"true\", \"savelog\": \"false\", \"splitby\": {\"splitmethod\": \"fasta\", \"__current_case__\": 2, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"taxonomy\": {\"__class__\": \"ConnectedValue\"}, \"nameOrCount\": {\"__class__\": \"ConnectedValue\"}, \"taxlevel\": \"4\", \"classic\": \"false\", \"condmethod\": {\"method\": \"opti\", \"__current_case__\": 5, \"metric\": \"mcc\", \"initialize\": \"singleton\", \"delta\": \"0.0001\", \"iters\": \"100\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
                         "type": "tool",
-                        "uuid": "07d7e2cc-9669-45b5-bc1e-27bda80752c4",
+                        "uuid": "7dc5dce4-98b8-4ab3-9979-7dbe43d88b7e",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_vcf",
-                                "uuid": "89e84a41-76ce-46eb-acec-1563e8d20ef6"
+                                "output_name": "otulist",
+                                "uuid": "e5100715-48a0-4ceb-a5d3-7003a43a747e"
                             },
                             {
                                 "label": null,
-                                "output_name": "output_txt",
-                                "uuid": "c148b074-5e6a-4846-86e7-0193a5ce38b5"
+                                "output_name": "rabund",
+                                "uuid": "3757ba3c-d4ba-46c7-b141-23f43678e392"
                             },
                             {
                                 "label": null,
-                                "output_name": "results_json",
-                                "uuid": "b22dcd19-5127-4dc3-b329-8a09ab7f5db3"
+                                "output_name": "sensspec",
+                                "uuid": "f0e63d07-0f12-4ea0-b2ad-9ae6d16cd5bd"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "sabund",
+                                "uuid": "9aecf4a0-cffa-49fd-9b5b-97d99fa7e2d2"
                             }
                         ]
                     },
                     {
-                        "annotation": "From TB profiler, search with `grep` the part of the text that describes the DR profile (e.g Drug-Resistance: MDR) ",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0",
                         "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "infile": {
-                                "id": 6,
-                                "output_name": "output_txt"
+                        "id": 5,
+                        "input_connections": {
+                            "intype|group": {
+                                "id": 3,
+                                "output_name": "count_out"
+                            },
+                            "intype|otu": {
+                                "id": 4,
+                                "output_name": "otulist"
                             }
                         },
                         "inputs": [],
-                        "label": "Get drug resistance profile",
-                        "name": "Search in textfiles",
+                        "label": null,
+                        "name": "Make.shared",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "input"
+                                "name": "shared",
+                                "type": "mothur.shared"
+                            },
+                            {
+                                "name": "groupout",
+                                "type": "mothur.groups"
                             }
                         ],
                         "position": {
-                            "bottom": 594.7666625976562,
-                            "height": 122.5333251953125,
-                            "left": 1343.800048828125,
-                            "right": 1563.800048828125,
-                            "top": 472.23333740234375,
-                            "width": 220,
-                            "x": 1343.800048828125,
-                            "y": 472.23333740234375
+                            "bottom": 445.8999938964844,
+                            "height": 276.3999938964844,
+                            "left": 1077,
+                            "right": 1277,
+                            "top": 169.5,
+                            "width": 200,
+                            "x": 1077,
+                            "y": 169.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "0851ae17c58e",
+                            "name": "mothur_make_shared",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"case_sensitive\": \"-i\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-P\", \"url_paste\": \"Drug-Resistance:\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"intype\": {\"infile\": \"otulist\", \"__current_case__\": 0, \"otu\": {\"__class__\": \"ConnectedValue\"}, \"group\": {\"__class__\": \"ConnectedValue\"}, \"label\": [\"0.03\"], \"groups\": null}, \"savelog\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
                         "type": "tool",
-                        "uuid": "9b418ac9-364d-4877-a858-b33a1e335900",
+                        "uuid": "57884bfc-06d6-4a1e-86cc-eb2ba23d6fe2",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "b876e27d-6013-4265-ae70-cffad0895db9"
+                                "output_name": "shared",
+                                "uuid": "f04218ea-84e1-489e-9d92-c44ad03414db"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "groupout",
+                                "uuid": "6166859b-cc80-475b-97ff-f082289c1b56"
                             }
                         ]
                     },
                     {
-                        "annotation": "We have generated one file per sample, that contains the DR profile (e.g Drug-Resistance: MDR) We want to prepend the name of the sample so we have: (Sample_name Drug-Resistance: MDR) ",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0",
                         "errors": null,
-                        "id": 8,
+                        "id": 6,
                         "input_connections": {
-                            "input": {
-                                "id": 7,
-                                "output_name": "output"
+                            "count": {
+                                "id": 3,
+                                "output_name": "count_out"
+                            },
+                            "otu": {
+                                "id": 4,
+                                "output_name": "otulist"
+                            },
+                            "tax|taxonomy": {
+                                "id": 3,
+                                "output_name": "taxonomy_out"
                             }
                         },
                         "inputs": [],
-                        "label": "Add Sample Name",
-                        "name": "Add input name as column",
+                        "label": null,
+                        "name": "Classify.otu",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "name": "taxsummaries",
+                                "type": "input"
+                            },
+                            {
+                                "name": "taxonomies",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 596.7666625976562,
-                            "height": 122.5333251953125,
-                            "left": 1605.800048828125,
-                            "right": 1825.800048828125,
-                            "top": 474.23333740234375,
-                            "width": 220,
-                            "x": 1605.800048828125,
-                            "y": 474.23333740234375
+                            "bottom": 984.2999877929688,
+                            "height": 428.79998779296875,
+                            "left": 1121,
+                            "right": 1321,
+                            "top": 555.5,
+                            "width": 200,
+                            "x": 1121,
+                            "y": 555.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "3284b72eef56",
-                            "name": "add_input_name_as_column",
-                            "owner": "mvdbeek",
+                            "changeset_revision": "02446d12c359",
+                            "name": "mothur_classify_otu",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"header\": {\"contains_header\": \"no\", \"__current_case__\": 1}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"prepend\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.2.0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"basis\": \"otu\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"count\": {\"__class__\": \"ConnectedValue\"}, \"cutoff\": \"60\", \"group\": null, \"label\": [\"0.03\"], \"name\": null, \"otu\": {\"__class__\": \"ConnectedValue\"}, \"output\": \"simple\", \"persample\": \"false\", \"printlevel\": \"-1\", \"probs\": \"true\", \"relabund\": \"false\", \"savelog\": \"false\", \"tax\": {\"source\": \"hist\", \"__current_case__\": 1, \"taxonomy\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
                         "type": "tool",
-                        "uuid": "d92f5d19-212d-4d8b-a7f7-f249788088ac",
+                        "uuid": "6dd79704-f3b8-4190-a7bb-34e2b4190436",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "1b9d5610-2f91-450a-a1b9-1718d8afde1a"
+                                "output_name": "taxonomies",
+                                "uuid": "add9561d-239b-4236-a875-c7870d8f4aa9"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "taxsummaries",
+                                "uuid": "07f4f3ba-ee41-4f9b-aac9-ccc3262457f8"
                             }
                         ]
                     },
                     {
-                        "annotation": "The output will be:\nSample_A  DR_profile_A\nSample_B DR_profile_B\nSample_Z DR_profile_Z",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0",
                         "errors": null,
-                        "id": 9,
+                        "id": 7,
                         "input_connections": {
-                            "inputs": {
-                                "id": 8,
-                                "output_name": "output"
+                            "group": {
+                                "id": 5,
+                                "output_name": "shared"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Concatenate datasets",
-                                "name": "inputs"
-                            }
-                        ],
-                        "label": "Concatenate DR profiles in a single table",
-                        "name": "Concatenate datasets",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Count.groups",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "grp_count",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "summary",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 596.7666625976562,
-                            "height": 122.5333251953125,
-                            "left": 1871.800048828125,
-                            "right": 2091.800048828125,
-                            "top": 474.23333740234375,
-                            "width": 220,
-                            "x": 1871.800048828125,
-                            "y": 474.23333740234375
+                            "bottom": 150.89999389648438,
+                            "height": 266.3999938964844,
+                            "left": 1361,
+                            "right": 1561,
+                            "top": -115.5,
+                            "width": 200,
+                            "x": 1361,
+                            "y": -115.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "f46f0e4f75c4",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "03c86648a52e",
+                            "name": "mothur_count_groups",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"inputs\": {\"__class__\": \"RuntimeValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"group\": {\"__class__\": \"ConnectedValue\"}, \"groupnames\": {\"source\": \"none\", \"__current_case__\": 0}, \"savelog\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
                         "type": "tool",
-                        "uuid": "44a1faa8-cd48-4a85-96f7-81dcf3041e19",
+                        "uuid": "5615bc17-0fdb-4610-ac78-c6aea2c08872",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "8bf7beae-528c-4d8b-abac-827a84a931a8"
+                                "output_name": "summary",
+                                "uuid": "1132f353-dc6c-4840-b8f1-91a8367af034"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "grp_count",
+                                "uuid": "19b8b29e-2970-4b2c-a8e4-ca712b257658"
                             }
                         ]
                     },
                     {
-                        "annotation": "Remove unnecessary text from the table like \".txt\" or \"Drug-resistance:\"",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0",
                         "errors": null,
-                        "id": 10,
+                        "id": 8,
                         "input_connections": {
-                            "infile": {
-                                "id": 9,
-                                "output_name": "out_file1"
+                            "input|otu": {
+                                "id": 5,
+                                "output_name": "shared"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Replace Text",
-                                "name": "infile"
-                            }
-                        ],
-                        "label": "Cleanup the table",
-                        "name": "Replace Text",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Sub.sample",
                         "outputs": [
                             {
-                                "name": "outfile",
+                                "name": "shared_out",
                                 "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 599.8666534423828,
-                            "height": 122.53334045410156,
-                            "left": 2136.300048828125,
-                            "right": 2356.300048828125,
-                            "top": 477.33331298828125,
-                            "width": 220,
-                            "x": 2136.300048828125,
-                            "y": 477.33331298828125
+                            "bottom": 544.6999969482422,
+                            "height": 215.1999969482422,
+                            "left": 1384,
+                            "right": 1584,
+                            "top": 329.5,
+                            "width": 200,
+                            "x": 1384,
+                            "y": 329.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "67cb43432196",
+                            "name": "mothur_sub_sample",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"infile\": {\"__class__\": \"RuntimeValue\"}, \"replacements\": [{\"__index__\": 0, \"find_pattern\": \".txt\", \"replace_pattern\": \"this is my replacement\"}, {\"__index__\": 1, \"find_pattern\": \"Drug-resistance:\", \"replace_pattern\": \"\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.2",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"count\": null, \"input\": {\"format\": \"shared\", \"__current_case__\": 2, \"otu\": {\"__class__\": \"ConnectedValue\"}, \"groups\": null, \"label\": null}, \"savelog\": \"false\", \"size\": \"2389\", \"taxonomy\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
                         "type": "tool",
-                        "uuid": "398ccbde-0309-41bb-b348-fc8ecca15cb9",
+                        "uuid": "eb70e45c-1ea9-4a34-9ac0-b27a5e7018a5",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "6b30ef89-359b-4593-a600-40d11d47138b"
+                                "output_name": "shared_out",
+                                "uuid": "a7df6943-cb20-46d7-ade1-66504b7e6eeb"
                             }
                         ]
                     }
                 ],
-                "parent_id": "evolution/mtb_transmission",
-                "path": "topics/evolution/tutorials/mtb_transmission/workflows/Galaxy-Workflow-From_BAMs_to_drug_resistance_prediction_with_TB-profiler.ga",
+                "parent_id": "microbiome/mothur-miseq-sop-short",
+                "path": "topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow5_otu_clustering.ga",
                 "tags": [
-                    "evolution"
+                    "microbiome"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "From BAMs to drug resistance prediction with TB-profiler",
-                "topic_id": "evolution",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/evolution-mtb_transmission/versions/galaxy-workflow-from-bams-to-drug-resistance-prediction-with-tb-profiler",
-                "tutorial_id": "mtb_transmission",
-                "url": "https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_transmission/workflows/Galaxy-Workflow-From_BAMs_to_drug_resistance_prediction_with_TB-profiler.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_transmission/workflows/Galaxy-Workflow-From_BAMs_to_drug_resistance_prediction_with_TB-profiler.html",
+                "title": "Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]",
+                "topic_id": "microbiome",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-mothur-miseq-sop-short/versions/workflow5-otu-clustering",
+                "tutorial_id": "mothur-miseq-sop-short",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow5_otu_clustering.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow5_otu_clustering.html",
                 "version": 1,
-                "wfid": "evolution-mtb_transmission",
-                "wfname": "galaxy-workflow-from-bams-to-drug-resistance-prediction-with-tb-profiler",
-                "workflow": "Galaxy-Workflow-From_BAMs_to_drug_resistance_prediction_with_TB-profiler.ga",
+                "wfid": "microbiome-mothur-miseq-sop-short",
+                "wfname": "workflow5-otu-clustering",
+                "workflow": "workflow5_otu_clustering.ga",
                 "workflow_tools": [
-                    "__MERGE_COLLECTION__",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/3.0.8+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0"
                 ],
-                "workflowhub_id": "1314"
+                "workflowhub_id": "1133"
             },
             {
-                "creators": [],
-                "description": "From Fastqs to VCFs and BAMs",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0003-3803-468X",
+                        "name": "Saskia Hiltemann"
+                    }
+                ],
+                "description": "16S Microbial Analysis with mothur (short)",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nSingle-End FASTQs\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nPaired-End FASTQs\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMycobacterium_tuberculosis_ancestral_reference.gbk\"]\n  3[label=\"Trimmomatic\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Trimmomatic\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Mapping and variant calling of SINGLE END FASTQs with snippy\"]\n  3 -> 5 [label=\"fastq_out\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"Mapping and variant calling of PAIRED END FASTQs with snippy\"]\n  4 -> 6 [label=\"fastq_out_paired\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"Merge PE/SE VCFs in a single collection with all samples\"]\n  5 -> 7 [label=\"snpvcf\"]\n  6 -> 7 [label=\"snpvcf\"]\n  8[label=\"Merge PE/SE BAMs in a single collection with all samples Part the workflow \u201dIdentifying DR with TB-profiler\"]\n  5 -> 8 [label=\"snpsbam\"]\n  6 -> 8 [label=\"snpsbam\"]\n  9[label=\"TB Variant Filter\"]\n  7 -> 9 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nShared file\"]\n  1[label=\"Rarefaction.single\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Summary.single\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Plotting tool\"]\n  1 -> 3 [label=\"rarefactioncurves\"]\n}",
                 "history": [
                     {
-                        "hash": "61e5383633beda63e0c40a41837ccce18db77008",
-                        "message": "update tag",
-                        "num": 2,
-                        "short_hash": "61e538363",
-                        "unix": "1647423011"
-                    },
-                    {
-                        "hash": "2e7ba78522415b81e10f3f5a74144f4f419b218d",
-                        "message": "tweak",
+                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
+                        "message": "Rename metagenomics topic to microbiome",
                         "num": 1,
-                        "short_hash": "2e7ba7852",
-                        "unix": "1647422653"
+                        "short_hash": "0e0a2f2cc",
+                        "unix": "1704901629"
                     }
                 ],
                 "inputs": [
@@ -160766,506 +161294,295 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Single-End FASTQs"
+                                "name": "Shared file"
                             }
                         ],
-                        "label": "Single-End FASTQs",
-                        "name": "Input dataset collection",
+                        "label": "Shared file",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 579.2166595458984,
-                            "height": 89.09999084472656,
-                            "left": 689.4000244140625,
-                            "right": 909.4000244140625,
-                            "top": 490.1166687011719,
-                            "width": 220,
-                            "x": 689.4000244140625,
-                            "y": 490.1166687011719
+                            "bottom": 396.8000030517578,
+                            "height": 61.80000305175781,
+                            "left": 308,
+                            "right": 508,
+                            "top": 335,
+                            "width": 200,
+                            "x": 308,
+                            "y": 335
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "30a3c256-5d21-4219-b23e-58c8f3842387",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "type": "data_input",
+                        "uuid": "58c65102-0358-4782-b4d3-1de61937b7f7",
+                        "workflow_outputs": [
                             {
-                                "description": "",
-                                "name": "Paired-End FASTQs"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "43ede9d2-e2d2-46e0-a733-adea9336c50f"
                             }
-                        ],
-                        "label": "Paired-End FASTQs",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 688.2166900634766,
-                            "height": 89.09999084472656,
-                            "left": 697.4000244140625,
-                            "right": 917.4000244140625,
-                            "top": 599.11669921875,
-                            "width": 220,
-                            "x": 697.4000244140625,
-                            "y": 599.11669921875
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list:paired\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "c04ddfda-2349-4857-8cae-b3d84dcbf9e7",
-                        "workflow_outputs": []
-                    },
+                        ]
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nShared file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Rarefaction.single\"];\n  0 -->|output| 1;\n  2[\"Summary.single\"];\n  0 -->|output| 2;\n  3[\"Plotting tool\"];\n  1 -->|rarefactioncurves| 3;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]",
+                "outputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Mycobacterium_tuberculosis_ancestral_reference.gbk"
+                                "name": "Shared file"
                             }
                         ],
-                        "label": "Mycobacterium_tuberculosis_ancestral_reference.gbk",
+                        "label": "Shared file",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 732.6500244140625,
-                            "height": 111.5333251953125,
-                            "left": 1351.4000244140625,
-                            "right": 1571.4000244140625,
-                            "top": 621.11669921875,
-                            "width": 220,
-                            "x": 1351.4000244140625,
-                            "y": 621.11669921875
+                            "bottom": 396.8000030517578,
+                            "height": 61.80000305175781,
+                            "left": 308,
+                            "right": 508,
+                            "top": 335,
+                            "width": 200,
+                            "x": 308,
+                            "y": 335
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "67484edc-af0a-4a41-8170-c78853b51319",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nSingle-End FASTQs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nPaired-End FASTQs\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nMycobacterium_tuberculosis_ancestral_reference.gbk\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Trimmomatic\"];\n  0 -->|output| 3;\n  4[\"Trimmomatic\"];\n  1 -->|output| 4;\n  5[\"Mapping and variant calling of SINGLE END FASTQs with snippy\"];\n  3 -->|fastq_out| 5;\n  2 -->|output| 5;\n  6[\"Mapping and variant calling of PAIRED END FASTQs with snippy\"];\n  4 -->|fastq_out_paired| 6;\n  2 -->|output| 6;\n  7[\"Merge PE/SE VCFs in a single collection with all samples\"];\n  5 -->|snpvcf| 7;\n  6 -->|snpvcf| 7;\n  8[\"Merge PE/SE BAMs in a single collection with all samples Part the workflow \u201dIdentifying DR with TB-profiler\"];\n  5 -->|snpsbam| 8;\n  6 -->|snpsbam| 8;\n  9[\"TB Variant Filter\"];\n  7 -->|output| 9;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "From Fastqs to VCFs and BAMs",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "readtype|fastq_in": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Trimmomatic",
-                        "outputs": [
-                            {
-                                "name": "fastq_out",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 592.2166595458984,
-                            "height": 100.09999084472656,
-                            "left": 983.4000244140625,
-                            "right": 1203.4000244140625,
-                            "top": 492.1166687011719,
-                            "width": 220,
-                            "x": 983.4000244140625,
-                            "y": 492.1166687011719
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "d94aff5ee623",
-                            "name": "trimmomatic",
-                            "owner": "pjbriggs",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"illuminaclip\": {\"do_illuminaclip\": \"false\", \"__current_case__\": 1}, \"operations\": [{\"__index__\": 0, \"operation\": {\"name\": \"SLIDINGWINDOW\", \"__current_case__\": 0, \"window_size\": \"4\", \"required_quality\": \"30\"}}, {\"__index__\": 1, \"operation\": {\"name\": \"MINLEN\", \"__current_case__\": 1, \"minlen\": \"20\"}}], \"output_err\": \"false\", \"output_logs\": \"false\", \"readtype\": {\"single_or_paired\": \"se\", \"__current_case__\": 0, \"fastq_in\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.38.1",
-                        "type": "tool",
-                        "uuid": "91899b6e-1f22-45de-a6bc-acd43adac9fb",
+                        "uuid": "58c65102-0358-4782-b4d3-1de61937b7f7",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "fastq_out",
-                                "uuid": "c206129e-10b1-4c90-8404-ee4540c7216a"
+                                "output_name": "output",
+                                "uuid": "43ede9d2-e2d2-46e0-a733-adea9336c50f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0",
                         "errors": null,
-                        "id": 4,
+                        "id": 1,
                         "input_connections": {
-                            "readtype|fastq_pair": {
-                                "id": 1,
+                            "otu": {
+                                "id": 0,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Trimmomatic",
+                        "name": "Rarefaction.single",
                         "outputs": [
                             {
-                                "name": "fastq_out_paired",
-                                "type": "input"
-                            },
-                            {
-                                "name": "fastq_out_unpaired",
+                                "name": "rarefactioncurves",
                                 "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 815.9500274658203,
-                            "height": 199.8333282470703,
-                            "left": 986.4000244140625,
-                            "right": 1206.4000244140625,
-                            "top": 616.11669921875,
-                            "width": 220,
-                            "x": 986.4000244140625,
-                            "y": 616.11669921875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "d94aff5ee623",
-                            "name": "trimmomatic",
-                            "owner": "pjbriggs",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"illuminaclip\": {\"do_illuminaclip\": \"false\", \"__current_case__\": 1}, \"operations\": [{\"__index__\": 0, \"operation\": {\"name\": \"SLIDINGWINDOW\", \"__current_case__\": 0, \"window_size\": \"4\", \"required_quality\": \"30\"}}, {\"__index__\": 1, \"operation\": {\"name\": \"MINLEN\", \"__current_case__\": 1, \"minlen\": \"20\"}}], \"output_err\": \"false\", \"output_logs\": \"false\", \"readtype\": {\"single_or_paired\": \"collection\", \"__current_case__\": 2, \"fastq_pair\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.38.1",
-                        "type": "tool",
-                        "uuid": "ee71335f-30af-4fd7-a121-bf108ffd5e0a",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "fastq_out_paired",
-                                "uuid": "11fba967-c0af-4c4d-9d25-08edfec51758"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "fastq_out_unpaired",
-                                "uuid": "b71f679d-b409-4154-9185-533fad7b45b4"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "fastq_input|fastq_input1": {
-                                "id": 3,
-                                "output_name": "fastq_out"
-                            },
-                            "ref": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Mapping and variant calling of SINGLE END FASTQs with snippy",
-                        "name": "snippy",
-                        "outputs": [
-                            {
-                                "name": "snpvcf",
-                                "type": "vcf"
-                            },
-                            {
-                                "name": "snptab",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "snpsbam",
-                                "type": "bam"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 731.1166687011719,
-                            "height": 332,
-                            "left": 1665.4000244140625,
-                            "right": 1885.4000244140625,
-                            "top": 399.1166687011719,
-                            "width": 220,
-                            "x": 1665.4000244140625,
-                            "y": 399.1166687011719
+                            "bottom": 349.8000030517578,
+                            "height": 174.8000030517578,
+                            "left": 618,
+                            "right": 818,
+                            "top": 175,
+                            "width": 200,
+                            "x": 618,
+                            "y": 175
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "c9a8ef2aa380",
-                            "name": "snippy",
+                            "changeset_revision": "af521db77c56",
+                            "name": "mothur_rarefaction_single",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"mapqual\": \"60\", \"mincov\": \"10\", \"minfrac\": \"0.1\", \"rgid\": \"\", \"bwaopt\": \"\"}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 1, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"outvcf\", \"outtab\", \"outbam\"], \"ref\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.2",
+                        "tool_state": "{\"__input_ext\": \"input\", \"abund\": \"10\", \"calc\": [\"sobs\"], \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"freq\": \"100.0\", \"iters\": \"1000\", \"label\": null, \"otu\": null, \"savelog\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
                         "type": "tool",
-                        "uuid": "e38af720-1ae1-4f32-9e9d-562d0d040a85",
+                        "uuid": "57642a17-6be7-4133-b573-b0175ff8cc97",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "snpsbam",
-                                "uuid": "4c15e214-85dd-4c43-b36a-3e482ab62879"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "snpvcf",
-                                "uuid": "60968620-b9b0-4481-a17d-33229edb91e2"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "snptab",
-                                "uuid": "128c6ded-1206-4f88-b93d-9254a37f8f25"
+                                "output_name": "rarefactioncurves",
+                                "uuid": "955cdaca-e834-4f9b-b8d3-54d1e4e6b9cf"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.2",
                         "errors": null,
-                        "id": 6,
+                        "id": 2,
                         "input_connections": {
-                            "fastq_input|fastq_input": {
-                                "id": 4,
-                                "output_name": "fastq_out_paired"
-                            },
-                            "reference_source|ref_file": {
-                                "id": 2,
+                            "otu": {
+                                "id": 0,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "Mapping and variant calling of PAIRED END FASTQs with snippy",
-                        "name": "snippy",
+                        "label": null,
+                        "name": "Summary.single",
                         "outputs": [
                             {
-                                "name": "snpvcf",
-                                "type": "vcf"
+                                "name": "summaryfiles",
+                                "type": "input"
                             },
                             {
-                                "name": "snptab",
+                                "name": "subsample_summary",
                                 "type": "tabular"
                             },
                             {
-                                "name": "snpsbam",
-                                "type": "bam"
+                                "name": "summary",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 1091.11669921875,
-                            "height": 332,
-                            "left": 1667.4000244140625,
-                            "right": 1887.4000244140625,
-                            "top": 759.11669921875,
-                            "width": 220,
-                            "x": 1667.4000244140625,
-                            "y": 759.11669921875
+                            "bottom": 811.2000122070312,
+                            "height": 317.20001220703125,
+                            "left": 619,
+                            "right": 819,
+                            "top": 494,
+                            "width": 200,
+                            "x": 619,
+                            "y": 494
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "d220115f882b",
-                            "name": "snippy",
+                            "changeset_revision": "2344ed181ae6",
+                            "name": "mothur_summary_single",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"mapqual\": \"60\", \"mincov\": \"10\", \"minfrac\": \"0.1\", \"minqual\": \"100.0\", \"rgid\": \"\", \"bwaopt\": \"\", \"rename_cons\": \"false\"}, \"fastq_input\": {\"fastq_input_selector\": \"paired_collection\", \"__current_case__\": 2, \"fastq_input\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"outvcf\", \"outtab\", \"outbam\"], \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.6.0+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"abund\": \"10\", \"calc\": [\"sobs\", \"coverage\", \"invsimpson\", \"nseqs\"], \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"groupmode\": \"true\", \"label\": null, \"otu\": null, \"savelog\": \"false\", \"size\": \"2389\", \"subsample\": {\"use\": \"no\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.2",
                         "type": "tool",
-                        "uuid": "18f42bea-16ad-4db6-9c80-26fae71d99de",
+                        "uuid": "43c58fe5-5ec2-41cf-bc7a-1aed1e4ea48a",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "snptab",
-                                "uuid": "6c7b8b74-395f-4326-bd62-e334cad878ca"
+                                "output_name": "summaryfiles",
+                                "uuid": "05892980-8cd2-42f6-814b-dab57c1ebe5c"
                             },
                             {
                                 "label": null,
-                                "output_name": "snpsbam",
-                                "uuid": "9eb3bc09-5277-48d3-a1d4-cf652d29e0d2"
+                                "output_name": "summary",
+                                "uuid": "8c30634d-fc8f-40d6-a5d0-93efde3874de"
                             },
                             {
                                 "label": null,
-                                "output_name": "snpvcf",
-                                "uuid": "7df12aa8-7a33-4985-83c4-5aeae5db29fd"
+                                "output_name": "subsample_summary",
+                                "uuid": "4e8da2ff-e4f5-4109-bfbd-9a23f978227b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "__MERGE_COLLECTION__",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2",
                         "errors": null,
-                        "id": 7,
+                        "id": 3,
                         "input_connections": {
-                            "inputs_0|input": {
-                                "id": 5,
-                                "output_name": "snpvcf"
-                            },
-                            "inputs_1|input": {
-                                "id": 6,
-                                "output_name": "snpvcf"
+                            "series_0|input": {
+                                "id": 1,
+                                "output_name": "rarefactioncurves"
                             }
                         },
                         "inputs": [],
-                        "label": "Merge PE/SE VCFs in a single collection with all samples",
-                        "name": "Merge collections",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 685.8166656494141,
-                            "height": 244.6999969482422,
-                            "left": 2111.39990234375,
-                            "right": 2331.39990234375,
-                            "top": 441.1166687011719,
-                            "width": 220,
-                            "x": 2111.39990234375,
-                            "y": 441.1166687011719
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "__MERGE_COLLECTION__",
-                        "tool_state": "{\"advanced\": {\"conflict\": {\"duplicate_options\": \"keep_first\", \"__current_case__\": 3}}, \"inputs\": [{\"__index__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "6110c068-756d-4b45-96e1-5f2334c1cf35",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "351b8679-eea7-4a76-8840-f5e34f6c4162"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.5+galaxy2",
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "input1": {
-                                "id": 7,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool TB Variant Filter",
-                                "name": "input1"
-                            }
-                        ],
                         "label": null,
-                        "name": "TB Variant Filter",
+                        "name": "Plotting tool",
                         "outputs": [
                             {
-                                "name": "output1",
-                                "type": "vcf"
+                                "name": "out_file_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": 574.6499938964844,
-                            "height": 122.5333251953125,
-                            "left": 2418.39990234375,
-                            "right": 2638.39990234375,
-                            "top": 452.1166687011719,
-                            "width": 220,
-                            "x": 2418.39990234375,
-                            "y": 452.1166687011719
+                            "bottom": 276.1999969482422,
+                            "height": 93.19999694824219,
+                            "left": 999,
+                            "right": 1199,
+                            "top": 183,
+                            "width": 200,
+                            "x": 999,
+                            "y": 183
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.5+galaxy2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "e7aff4a85df5",
-                            "name": "tb_variant_filter",
-                            "owner": "iuc",
+                            "changeset_revision": "ecb437f1d298",
+                            "name": "xy_plot",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"filter_options\": {\"show_filter_options\": \"no\", \"__current_case__\": 1}, \"filters\": [\"region_filter\", \"close_to_indel_filter\", \"min_depth_filter\"], \"input1\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3.5+galaxy2",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"main\": \"Rarefaction\", \"outftype\": \"png\", \"series\": [{\"__index__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"header\": \"true\", \"xcol\": \"1\", \"ycol\": [\"2\", \"5\", \"8\", \"11\", \"14\", \"17\", \"20\", \"23\", \"26\", \"29\", \"32\", \"35\", \"38\", \"41\", \"44\", \"47\", \"50\", \"53\", \"56\"], \"series_type\": {\"type\": \"line\", \"__current_case__\": 0, \"lty\": \"1\", \"col\": \"1\", \"lwd\": \"1.0\"}}], \"series_0|input|__identifier__\": \"sobs\", \"xlab\": \"Number of Sequences\", \"ylab\": \"Number of OTUs\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2",
                         "type": "tool",
-                        "uuid": "83df9492-d224-420e-8434-24a1a32b9da8",
+                        "uuid": "f9ef9628-4716-49f9-bf8a-e7ec68754881",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output1",
-                                "uuid": "682b8412-8ca5-42c6-bcf2-c5795629471d"
+                                "output_name": "out_file_png",
+                                "uuid": "9f66c76d-0d54-4dda-84f5-a9671fa77740"
                             }
                         ]
                     }
                 ],
-                "parent_id": "evolution/mtb_transmission",
-                "path": "topics/evolution/tutorials/mtb_transmission/workflows/Galaxy-Workflow-From_Fastqs_to_VCFs_and_BAMs.ga",
+                "parent_id": "microbiome/mothur-miseq-sop-short",
+                "path": "topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow6_alpha_diversity.ga",
                 "tags": [
-                    "evolution"
+                    "microbiome"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "From Fastqs to VCFs and BAMs",
-                "topic_id": "evolution",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/evolution-mtb_transmission/versions/galaxy-workflow-from-fastqs-to-vcfs-and-bams",
-                "tutorial_id": "mtb_transmission",
-                "url": "https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_transmission/workflows/Galaxy-Workflow-From_Fastqs_to_VCFs_and_BAMs.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_transmission/workflows/Galaxy-Workflow-From_Fastqs_to_VCFs_and_BAMs.html",
+                "title": "Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]",
+                "topic_id": "microbiome",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-mothur-miseq-sop-short/versions/workflow6-alpha-diversity",
+                "tutorial_id": "mothur-miseq-sop-short",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow6_alpha_diversity.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow6_alpha_diversity.html",
                 "version": 1,
-                "wfid": "evolution-mtb_transmission",
-                "wfname": "galaxy-workflow-from-fastqs-to-vcfs-and-bams",
-                "workflow": "Galaxy-Workflow-From_Fastqs_to_VCFs_and_BAMs.ga",
+                "wfid": "microbiome-mothur-miseq-sop-short",
+                "wfname": "workflow6-alpha-diversity",
+                "workflow": "workflow6_alpha_diversity.ga",
                 "workflow_tools": [
-                    "__MERGE_COLLECTION__",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.5+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1"
+                    "toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.2"
                 ],
-                "workflowhub_id": "1305"
+                "workflowhub_id": "1129"
             },
             {
-                "creators": [],
-                "description": "Given a set of VCF files and the reference genome used to do the mapping and SNP calling, create a multifasta file containing the genomes of all samples and calculate the matrix of pairwise SNP distances",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0003-3803-468X",
+                        "name": "Saskia Hiltemann"
+                    }
+                ],
+                "description": "16S Microbial Analysis with mothur (short)",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nCollection of VCFs to analyze\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genome of the MTBC ancestor\"]\n  2[label=\"Filter TB variants\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Generate the complete genome of each of the samples\"]\n  2 -> 3 [label=\"output1\"]\n  1 -> 3 [label=\"output\"]\n  kce5dd7a2c33d46b49f0268c2bdfcf31a[color=lightseagreen,label=\"Output\\n#{input_file}\"]\n  3 -> kce5dd7a2c33d46b49f0268c2bdfcf31a\n  4[label=\"Concatenate genomes to build a MSA\"]\n  3 -> 4 [label=\"output_file\"]\n  5[label=\"Keep only variable positions\"]\n  4 -> 5 [label=\"out_file1\"]\n  6[label=\"Calculate SNP distances\"]\n  5 -> 6 [label=\"output_fasta\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nShared file from Make.shared\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nSub.sample shared\"]\n  2[label=\"Dist.shared\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Collapse Collection\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Heatmap.sim\"]\n  2 -> 4 [label=\"distfiles\"]\n  5[label=\"Tree.shared\"]\n  2 -> 5 [label=\"distfiles\"]\n  6[label=\"Venn\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"Newick Display\"]\n  5 -> 7 [label=\"tre\"]\n}",
                 "history": [
                     {
-                        "hash": "679ca224ef8e44203f2aec12c805e0e892076d5b",
-                        "message": "update tag",
-                        "num": 2,
-                        "short_hash": "679ca224e",
-                        "unix": "1647423016"
-                    },
-                    {
-                        "hash": "2e7ba78522415b81e10f3f5a74144f4f419b218d",
-                        "message": "tweak",
+                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
+                        "message": "Rename metagenomics topic to microbiome",
                         "num": 1,
-                        "short_hash": "2e7ba7852",
-                        "unix": "1647422653"
+                        "short_hash": "0e0a2f2cc",
+                        "unix": "1704901629"
                     }
                 ],
                 "inputs": [
@@ -161278,27 +161595,22 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Collection of VCFs to analyze"
+                                "name": "Shared file from Make.shared"
                             }
                         ],
-                        "label": "Collection of VCFs to analyze",
-                        "name": "Input dataset collection",
+                        "label": "Shared file from Make.shared",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 602.3000183105469,
-                            "height": 89.10000610351562,
-                            "left": 562.0999755859375,
-                            "right": 782.0999755859375,
-                            "top": 513.2000122070312,
-                            "width": 220,
-                            "x": 562.0999755859375,
-                            "y": 513.2000122070312
+                            "left": 119,
+                            "top": 28
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "a3701b5d-9f74-46b4-ae97-51c432933230",
+                        "type": "data_input",
+                        "uuid": "d0c07e4f-abd7-4af3-bda4-ab143e6859bb",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
@@ -161310,362 +161622,299 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Reference genome of the MTBC ancestor"
+                                "name": "Sub.sample shared"
                             }
                         ],
-                        "label": "Reference genome of the MTBC ancestor",
-                        "name": "Input dataset",
+                        "label": "Sub.sample shared",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "bottom": 789.7333526611328,
-                            "height": 111.53334045410156,
-                            "left": 865.0999755859375,
-                            "right": 1085.0999755859375,
-                            "top": 678.2000122070312,
-                            "width": 220,
-                            "x": 865.0999755859375,
-                            "y": 678.2000122070312
+                            "left": 0,
+                            "top": 161
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "899dca08-73f5-4ac1-9d19-313414c90a1e",
+                        "type": "data_collection_input",
+                        "uuid": "cc9198f5-b615-4317-9837-4cbc83f4b5e7",
+                        "when": null,
                         "workflow_outputs": []
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nCollection of VCFs to analyze\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference genome of the MTBC ancestor\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Filter TB variants\"];\n  0 -->|output| 2;\n  3[\"Generate the complete genome of each of the samples\"];\n  2 -->|output1| 3;\n  1 -->|output| 3;\n  ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a[\"Output\\n#{input_file}\"];\n  3 --> ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a;\n  style ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a stroke:#2c3143,stroke-width:4px;\n  4[\"Concatenate genomes to build a MSA\"];\n  3 -->|output_file| 4;\n  5[\"Keep only variable positions\"];\n  4 -->|out_file1| 5;\n  6[\"Calculate SNP distances\"];\n  5 -->|output_fasta| 6;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "From VCFs to SNP distance matrix",
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nShared file from Make.shared\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nSub.sample shared\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Dist.shared\"];\n  0 -->|output| 2;\n  3[\"Collapse Collection\"];\n  1 -->|output| 3;\n  4[\"Heatmap.sim\"];\n  2 -->|distfiles| 4;\n  5[\"Tree.shared\"];\n  2 -->|distfiles| 5;\n  6[\"Venn\"];\n  3 -->|output| 6;\n  7[\"Newick Display\"];\n  5 -->|tre| 7;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]",
                 "outputs": [
                     {
-                        "annotation": "We will ensure at this step that variants to build the MSA are fixed variants and that we low-confidence filter repetitive regions of the MTB genome",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
                         "errors": null,
-                        "id": 2,
+                        "id": 3,
                         "input_connections": {
-                            "input1": {
-                                "id": 0,
+                            "input_list": {
+                                "id": 1,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "Filter TB variants",
-                        "name": "TB Variant Filter",
+                        "label": null,
+                        "name": "Collapse Collection",
                         "outputs": [
                             {
-                                "name": "output1",
-                                "type": "vcf"
+                                "name": "output",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 636.7333526611328,
-                            "height": 122.53334045410156,
-                            "left": 866.0999755859375,
-                            "right": 1086.0999755859375,
-                            "top": 514.2000122070312,
-                            "width": 220,
-                            "x": 866.0999755859375,
-                            "y": 514.2000122070312
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput1": {
-                                "action_arguments": {
-                                    "newname": "#{input1}.filter.vcf"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output1"
-                            }
+                            "left": 138,
+                            "top": 489
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "3b1e7c170b10",
-                            "name": "tb_variant_filter",
-                            "owner": "iuc",
+                            "changeset_revision": "830961c48e42",
+                            "name": "collapse_collections",
+                            "owner": "nml",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"filter_options\": {\"show_filter_options\": \"yes\", \"__current_case__\": 0, \"region_filter\": [\"pe_ppe\", \"uvp\"], \"indel_window_size\": \"5\", \"min_percentage_alt\": \"90.0\", \"min_depth\": \"30\"}, \"filters\": [\"region_filter\", \"close_to_indel_filter\", \"min_percentage_alt_filter\", \"snv_only_filter\"], \"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.3+galaxy0",
+                        "tool_state": "{\"filename\": {\"add_name\": false, \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.2",
                         "type": "tool",
-                        "uuid": "b6ef7486-0dc1-4f0c-ad2d-038f648670b8",
+                        "uuid": "aa52952a-70eb-4ed6-b6b0-28225e04091a",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output1",
-                                "uuid": "87f8ad83-d43e-4e44-8bed-33415b7add79"
+                                "output_name": "output",
+                                "uuid": "01c16573-8bd5-4d62-92c0-74cd29af035a"
                             }
                         ]
                     },
                     {
-                        "annotation": "The complete genome of each of the samples is generated by inserting the SNPs defined in the respective VCF in the reference genome that was used for mapping and SNP calling",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy2",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0",
                         "errors": null,
-                        "id": 3,
+                        "id": 4,
                         "input_connections": {
-                            "input_file": {
+                            "input|dist": {
                                 "id": 2,
-                                "output_name": "output1"
-                            },
-                            "reference_source|fasta_ref": {
-                                "id": 1,
-                                "output_name": "output"
+                                "output_name": "distfiles"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool bcftools consensus",
-                                "name": "input_file"
-                            },
-                            {
-                                "description": "runtime parameter for tool bcftools consensus",
-                                "name": "reference_source"
-                            },
-                            {
-                                "description": "runtime parameter for tool bcftools consensus",
-                                "name": "sec_default"
-                            }
-                        ],
-                        "label": "Generate the complete genome of each of the samples",
-                        "name": "bcftools consensus",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Heatmap.sim",
                         "outputs": [
                             {
-                                "name": "output_file",
-                                "type": "fasta"
+                                "name": "heatmap",
+                                "type": "svg"
                             }
                         ],
                         "position": {
-                            "bottom": 734.0333557128906,
-                            "height": 209.83334350585938,
-                            "left": 1144.0999755859375,
-                            "right": 1364.0999755859375,
-                            "top": 524.2000122070312,
-                            "width": 220,
-                            "x": 1144.0999755859375,
-                            "y": 524.2000122070312
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_file": {
-                                "action_arguments": {
-                                    "newname": "#{input_file}"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_file"
-                            }
+                            "left": 805,
+                            "top": 0
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy2",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "a87ae767b01d",
-                            "name": "bcftools_consensus",
+                            "changeset_revision": "7f5707dd6073",
+                            "name": "mothur_heatmap_sim",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"chain\": \"false\", \"input_file\": {\"__class__\": \"RuntimeValue\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"RuntimeValue\"}}, \"rename\": \"true\", \"sec_default\": {\"mask\": {\"__class__\": \"RuntimeValue\"}, \"iupac_codes\": \"false\", \"sample\": \"\", \"select_haplotype\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9+galaxy2",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"count\": null, \"dist|__identifier__\": \"thetayc.0.03.lt.std\", \"fontsize\": \"24\", \"input\": {\"source\": \"phylip\", \"__current_case__\": 2, \"dist\": {\"__class__\": \"ConnectedValue\"}}, \"savelog\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
                         "type": "tool",
-                        "uuid": "967af052-882a-427c-825e-e88f59ac50b3",
+                        "uuid": "aa3080d1-4ec6-4c1b-8be8-532a7e12c81c",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "#{input_file}",
-                                "output_name": "output_file",
-                                "uuid": "ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a"
+                                "label": null,
+                                "output_name": "heatmap",
+                                "uuid": "6b90b099-6641-43b9-a347-5ce6e05ae67e"
                             }
                         ]
                     },
                     {
-                        "annotation": "All genomes are concatenated in a single multifasta file. Because all o them have the same length, this may be seen as a multiple sequence alignment.",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0",
                         "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "inputs": {
-                                "id": 3,
-                                "output_name": "output_file"
+                        "id": 5,
+                        "input_connections": {
+                            "input|dist": {
+                                "id": 2,
+                                "output_name": "distfiles"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Concatenate datasets",
-                                "name": "inputs"
-                            }
-                        ],
-                        "label": "Concatenate genomes to build a MSA",
-                        "name": "Concatenate datasets",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Tree.shared",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "tre",
+                                "type": "mothur.tre"
                             }
                         ],
                         "position": {
-                            "bottom": 647.7333526611328,
-                            "height": 122.53334045410156,
-                            "left": 1519.0999755859375,
-                            "right": 1739.0999755859375,
-                            "top": 525.2000122070312,
-                            "width": 220,
-                            "x": 1519.0999755859375,
-                            "y": 525.2000122070312
+                            "left": 763,
+                            "top": 438
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "f46f0e4f75c4",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "43e2715e98c9",
+                            "name": "mothur_tree_shared",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"inputs\": {\"__class__\": \"RuntimeValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"calc\": [\"jclass\", \"thetayc\"], \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"dist|__identifier__\": \"thetayc.0.03.lt.std\", \"input\": {\"source\": \"phylip\", \"__current_case__\": 1, \"dist\": {\"__class__\": \"ConnectedValue\"}, \"name\": null}, \"savelog\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
                         "type": "tool",
-                        "uuid": "e0b536e1-c56c-41ed-9600-905d0cf58e97",
+                        "uuid": "e6bebcdf-bb0a-4b50-82a1-8c0ca2711b5e",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "c1fe096c-2693-4128-8139-4285bcd394ad"
+                                "output_name": "tre",
+                                "uuid": "3a746045-e178-492c-ac40-dab92ce5189f"
                             }
                         ]
                     },
                     {
-                        "annotation": "Discard invariant positions from the MSA to simplify the file so only contains positions with at least one SNP in at least one strain.",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0",
                         "errors": null,
-                        "id": 5,
+                        "id": 6,
                         "input_connections": {
-                            "input_fasta": {
-                                "id": 4,
-                                "output_name": "out_file1"
+                            "input|otu": {
+                                "id": 3,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Finds SNP sites",
-                                "name": "input_fasta"
-                            }
-                        ],
-                        "label": "Keep only variable positions",
-                        "name": "Finds SNP sites",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Venn",
                         "outputs": [
                             {
-                                "name": "output_fasta",
-                                "type": "fasta"
+                                "name": "sharedotus_out",
+                                "type": "input"
+                            },
+                            {
+                                "name": "svgs_out",
+                                "type": "input"
+                            },
+                            {
+                                "name": "logfile",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 647.1666870117188,
-                            "height": 144.9666748046875,
-                            "left": 1843.0999755859375,
-                            "right": 2063.0999755859375,
-                            "top": 502.20001220703125,
-                            "width": 220,
-                            "x": 1843.0999755859375,
-                            "y": 502.20001220703125
+                            "left": 419,
+                            "top": 454
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0",
+                        "post_job_actions": {
+                            "HideDatasetActionsharedotus_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "sharedotus_out"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "5804f786060d",
-                            "name": "snp_sites",
+                            "changeset_revision": "4db54b1c1d83",
+                            "name": "mothur_venn",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input_fasta\": {\"__class__\": \"RuntimeValue\"}, \"out_type\": {\"ot_select\": \"alignment\", \"__current_case__\": 0, \"formats\": [\"-m\"], \"b\": \"false\", \"c\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.5.1+galaxy0",
+                        "tool_state": "{\"fontsize\": \"24\", \"input\": {\"source\": \"shared\", \"__current_case__\": 0, \"otu\": {\"__class__\": \"ConnectedValue\"}, \"calc\": null, \"label\": null, \"groups\": [\"F3D0\", \"F3D1\", \"F3D2\", \"F3D3\"]}, \"nseqs\": false, \"permute\": \"4\", \"savelog\": true, \"sharedotus\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
                         "type": "tool",
-                        "uuid": "3718c889-5f1c-4cc7-977c-eaa564753c9b",
+                        "uuid": "932cccf7-1743-46e2-abb9-f148ca5b617b",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_fasta",
-                                "uuid": "2931ef4f-28d7-4701-bee0-292177bf0841"
+                                "output_name": "svgs_out",
+                                "uuid": "d3db2185-9a28-4bb2-abd6-6907377de73f"
                             }
                         ]
                     },
                     {
-                        "annotation": "From the MSA. Calculate pairwise SNP distances between samples. ",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.6.3+galaxy0",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1",
                         "errors": null,
-                        "id": 6,
+                        "id": 7,
                         "input_connections": {
-                            "input": {
+                            "fileNewick": {
                                 "id": 5,
-                                "output_name": "output_fasta"
+                                "output_name": "tre"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool SNP distance matrix",
-                                "name": "input"
-                            }
-                        ],
-                        "label": "Calculate SNP distances",
-                        "name": "SNP distance matrix",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Newick Display",
                         "outputs": [
                             {
                                 "name": "output",
-                                "type": "tabular"
+                                "type": "svg"
                             }
                         ],
                         "position": {
-                            "bottom": 662.6000213623047,
-                            "height": 167.40000915527344,
-                            "left": 2173.10009765625,
-                            "right": 2393.10009765625,
-                            "top": 495.20001220703125,
-                            "width": 220,
-                            "x": 2173.10009765625,
-                            "y": 495.20001220703125
+                            "left": 1141,
+                            "top": 56
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.6.3+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "1959cc43b414",
-                            "name": "snp_dists",
+                            "changeset_revision": "b4163d2f64ab",
+                            "name": "newick_utils",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"a\": \"false\", \"b\": \"false\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"k\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.6.3+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"mothur.tre\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"condbranchlength\": {\"branchlength\": \"false\", \"__current_case__\": 1}, \"condbranchsupport\": {\"branchsupport\": \"false\", \"__current_case__\": 1}, \"fileNewick\": {\"__class__\": \"ConnectedValue\"}, \"fileNewick|__identifier__\": \"thetayc.0.03.lt.std\", \"leafFont\": \"sans-serif\", \"leafSize\": \"10px\", \"legend\": \"\", \"outformat\": \"svg\", \"radial\": false, \"scalebar\": true, \"width\": \"800\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.6+galaxy1",
                         "type": "tool",
-                        "uuid": "e5f85c1b-43cc-417e-8e02-79ecc511b4ec",
+                        "uuid": "8f4bff39-d764-4357-aae5-246c01ac2dcf",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "2dff3ea9-ce2d-48eb-b9eb-90b3b6034ae6"
+                                "uuid": "544ca4c5-82b3-4bf1-9ff1-c23ebce8b098"
                             }
                         ]
                     }
                 ],
-                "parent_id": "evolution/mtb_transmission",
-                "path": "topics/evolution/tutorials/mtb_transmission/workflows/main_workflow.ga",
+                "parent_id": "microbiome/mothur-miseq-sop-short",
+                "path": "topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow7_beta_diversity.ga",
                 "tags": [
-                    "evolution"
+                    "microbiome"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "From VCFs to SNP distance matrix",
-                "topic_id": "evolution",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/evolution-mtb_transmission/versions/main-workflow",
-                "tutorial_id": "mtb_transmission",
-                "url": "https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_transmission/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_transmission/workflows/main_workflow.html",
+                "title": "Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]",
+                "topic_id": "microbiome",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-mothur-miseq-sop-short/versions/workflow7-beta-diversity",
+                "tutorial_id": "mothur-miseq-sop-short",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow7_beta_diversity.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/workflow7_beta_diversity.html",
                 "version": 1,
-                "wfid": "evolution-mtb_transmission",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "wfid": "microbiome-mothur-miseq-sop-short",
+                "wfname": "workflow7-beta-diversity",
+                "workflow": "workflow7_beta_diversity.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.6.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2"
                 ],
-                "workflowhub_id": "1309"
+                "workflowhub_id": "1117"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/6010176"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.800651"
     },
     {
         "admin_install": {
@@ -161749,8 +161998,8 @@
             "topic_3324"
         ],
         "edam_operation": [
-            "Sequence analysis",
-            "Phylogenetic tree analysis"
+            "Phylogenetic tree analysis",
+            "Sequence analysis"
         ],
         "edam_topic": [
             "Genomics",
@@ -161781,7 +162030,7 @@
             "Understand the basic concepts behind phylogenetic trees, as applied to *Mycobacterium tuberculosis*",
             "Be able to read and interrogate a phylogeny encountered in the literature"
         ],
-        "pageviews": 1983,
+        "pageviews": 2072,
         "pub_date": "2022-03-16",
         "questions": [
             "What information can I get from a phylogenetic tree?",
@@ -161805,8 +162054,8 @@
         ],
         "short_id": "T00144",
         "short_tools": [
-            "interactive_tool_rstudio",
             "upload1",
+            "interactive_tool_rstudio",
             "raxml"
         ],
         "slides": false,
@@ -161866,8 +162115,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 131,
-        "visitors": 1308,
+        "visit_duration": 133,
+        "visitors": 1374,
         "workflows": [
             {
                 "creators": [],
@@ -161938,7 +162187,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput alignment\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"RStudio\"];\n  2[\"Estimate phylogeny with RAxML\"];\n  0 -->|output| 2;\n  9f8ae577-c583-4a2d-b64d-14c25fb859d9[\"Output\\nBest-scoring ML Tree\"];\n  2 --> 9f8ae577-c583-4a2d-b64d-14c25fb859d9;\n  style 9f8ae577-c583-4a2d-b64d-14c25fb859d9 stroke:#2c3143,stroke-width:4px;\n  bdb8cf2f-b553-4a96-8b55-38b4b499ab88[\"Output\\nInfo\"];\n  2 --> bdb8cf2f-b553-4a96-8b55-38b4b499ab88;\n  style bdb8cf2f-b553-4a96-8b55-38b4b499ab88 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
+                "modified": "2024-10-02 12:08:08 +0000",
                 "name": "Mtb phylogeny",
                 "outputs": [
                     {
@@ -162072,574 +162321,26 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "ctb_frankenstein_ligand",
-                    "owner": "bgruening",
-                    "revisions": "8e214e52e461",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ctb_frankenstein_ligand",
-                    "owner": "bgruening",
-                    "revisions": "7255688c77f3",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "enumerate_charges",
-                    "owner": "bgruening",
-                    "revisions": "2a868592ebcb",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "enumerate_charges",
-                    "owner": "bgruening",
-                    "revisions": "67ee76f0e497",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openbabel_compound_convert",
-                    "owner": "bgruening",
-                    "revisions": "b59c91adeac1",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openbabel_compound_convert",
-                    "owner": "bgruening",
-                    "revisions": "e2c36f62e22f",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "rdock_rbcavity",
-                    "owner": "bgruening",
-                    "revisions": "744a777e9f90",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "rdock_rbdock",
-                    "owner": "bgruening",
-                    "revisions": "a22969b08177",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "rxdock_rbcavity",
-                    "owner": "bgruening",
-                    "revisions": "7fac8e7a12d5",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "rxdock_rbdock",
-                    "owner": "bgruening",
-                    "revisions": "6fe6b0e10ed6",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "split_file_to_collection",
-                    "owner": "bgruening",
-                    "revisions": "0046692724f9",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "split_file_to_collection",
-                    "owner": "bgruening",
-                    "revisions": "6cbe2f30c2d7",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "sucos_max_score",
+                    "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "d4c67ced6abc",
-                    "tool_panel_section_label": "ChemicalToolBox",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sucos_max_score",
+                    "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "9b48456a96fe",
-                    "tool_panel_section_label": "ChemicalToolBox",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "xchem_transfs_scoring",
+                    "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "f6f9b47d02b6",
-                    "tool_panel_section_label": "ChemicalToolBox",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "830961c48e42",
-                    "tool_panel_section_label": "Collection Operations",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: ctb_frankenstein_ligand\n  owner: bgruening\n  revisions: 8e214e52e461\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ctb_frankenstein_ligand\n  owner: bgruening\n  revisions: 7255688c77f3\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: enumerate_charges\n  owner: bgruening\n  revisions: 2a868592ebcb\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: enumerate_charges\n  owner: bgruening\n  revisions: 67ee76f0e497\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_compound_convert\n  owner: bgruening\n  revisions: b59c91adeac1\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_compound_convert\n  owner: bgruening\n  revisions: e2c36f62e22f\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rdock_rbcavity\n  owner: bgruening\n  revisions: 744a777e9f90\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rdock_rbdock\n  owner: bgruening\n  revisions: a22969b08177\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rxdock_rbcavity\n  owner: bgruening\n  revisions: 7fac8e7a12d5\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rxdock_rbdock\n  owner: bgruening\n  revisions: 6fe6b0e10ed6\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_to_collection\n  owner: bgruening\n  revisions: '0046692724f9'\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_to_collection\n  owner: bgruening\n  revisions: 6cbe2f30c2d7\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sucos_max_score\n  owner: bgruening\n  revisions: d4c67ced6abc\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sucos_max_score\n  owner: bgruening\n  revisions: 9b48456a96fe\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xchem_transfs_scoring\n  owner: bgruening\n  revisions: f6f9b47d02b6\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/covid19-docking/tutorial.json",
-        "contributors": [
-            {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "simonbray",
-                "joined": "2019-05",
-                "name": "Simon Bray",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
-            }
-        ],
-        "dir": "topics/computational-chemistry/tutorials/covid19-docking",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "computational-chemistry/covid19-docking",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Galaxy can support large, rapid studies in computational chemistry",
-            "Protein-ligand docking contributes to the discovery of new drugs"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Understand how Galaxy was used to perform docking and pose scoring on the SARS-CoV-2 main protease (MPro).",
-            "Replicate the study on a (very) small scale",
-            "Gain familiarity with the docking and scoring techniques involved."
-        ],
-        "pageviews": 4516,
-        "pub_date": "2020-03-27",
-        "questions": [
-            "How can candidate ligands be generated and docked to a protein in Galaxy?",
-            "How can the poses of the docked ligands be evaluated?",
-            "How can a workflow for drug virtual screening be constructed in Galaxy?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "computational-chemistry",
-                "tutorials": [
-                    "cheminformatics"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00049",
-        "short_tools": [
-            "enumerate_charges",
-            "xchem_transfs_scoring",
-            "rdock_rbdock",
-            "rdock_rbcavity",
-            "rxdock_rbcavity",
-            "xchem_pose_scoring",
-            "openbabel_compound_convert",
-            "split_file_to_collection",
-            "ctb_frankenstein_ligand",
-            "sucos_max_score",
-            "collapse_dataset",
-            "rxdock_rbdock"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "covid19",
-            "one-health"
-        ],
-        "time_estimation": "2H",
-        "title": "Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/2013.1-0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/0.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/2020.03.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.2.2.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbcavity/rdock_rbcavity/0.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbdock/rdock_rbdock/0.1.4",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_rbcavity/rxdock_rbcavity/0.1.5",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_rbdock/rxdock_rbdock/0.1.5",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.4.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/sucos_max_score/sucos_max_score/0.2.3",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/sucos_max_score/sucos_max_score/2020.03.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/xchem_transfs_scoring/xchem_transfs_scoring/0.4.0",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
-            "xchem_pose_scoring"
-        ],
-        "topic_name": "computational-chemistry",
-        "topic_name_human": "Computational chemistry",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "covid19-docking",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/computational-chemistry/tutorials/covid19-docking/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/covid19-docking/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/covid19-docking/tutorial.json"
-        },
-        "version": 10,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 178,
-        "visitors": 2664,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCandidates\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMpro-x0195_0_apo-desolv.pdb\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhits.sdf\"]\n  3[label=\"Enumerate changes\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Compound conversion\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Create Frankenstein ligand\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"Compound conversion\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"rDock cavity definition\"]\n  4 -> 7 [label=\"outfile\"]\n  5 -> 7 [label=\"outfile\"]\n  8[label=\"Split file\"]\n  6 -> 8 [label=\"outfile\"]\n  9[label=\"rDock docking\"]\n  4 -> 9 [label=\"outfile\"]\n  8 -> 9 [label=\"list_output_sdf\"]\n  7 -> 9 [label=\"activesite\"]\n  10[label=\"Collapse Collection\"]\n  9 -> 10 [label=\"output\"]\n  11[label=\"XChem TransFS pose scoring\"]\n  1 -> 11 [label=\"output\"]\n  10 -> 11 [label=\"output\"]\n  12[label=\"Max SuCOS score\"]\n  11 -> 12 [label=\"output\"]\n  2 -> 12 [label=\"output\"]\n}",
-                "history": [
-                    {
-                        "hash": "cf8b1cb0509e73e534c234076c8bd055379823c5",
-                        "message": "Update some workflow names for consistency",
-                        "num": 4,
-                        "short_hash": "cf8b1cb05",
-                        "unix": "1598836271"
-                    },
-                    {
-                        "hash": "60a21218780027dcf65a5f37b94148b0771303e1",
-                        "message": "update with covid19 tut with frankenstein ligand tool",
-                        "num": 3,
-                        "short_hash": "60a212187",
-                        "unix": "1591084355"
-                    },
-                    {
-                        "hash": "2bffcbdc75d8aaf32b06acc2f9f493931782546d",
-                        "message": "lint",
-                        "num": 2,
-                        "short_hash": "2bffcbdc7",
-                        "unix": "1585304017"
-                    },
-                    {
-                        "hash": "62d30105b34ea23f3280539d9880037639aa770e",
-                        "message": "linting covid19 cheminformatics tutorial",
-                        "num": 1,
-                        "short_hash": "62d30105b",
-                        "unix": "1585300158"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Candidates"
-                            }
-                        ],
-                        "label": "Candidates",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 218,
-                            "top": 200
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Candidates\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "47bf8c53-ae1e-4af6-bece-6adfd74b627c",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "cdab037e-aee1-49b8-a998-cd9fe7ddcdb7"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Mpro-x0195_0_apo-desolv.pdb"
-                            }
-                        ],
-                        "label": "Mpro-x0195_0_apo-desolv.pdb",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 218,
-                            "top": 289.76666259765625
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Mpro-x0195_0_apo-desolv.pdb\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "156f4aeb-d160-456a-974e-7884b79cb83a",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1fd1c624-37c6-4874-b863-a40eac5e4994"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "hits.sdf"
-                            }
-                        ],
-                        "label": "hits.sdf",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 218,
-                            "top": 400.5333251953125
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"hits.sdf\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "dd2d3bc0-8138-4e66-b2d9-e5e90e27b659",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1c8fb3cc-52ad-4f62-a00d-80b14b2c1d4a"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nCandidates\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nMpro-x0195_0_apo-desolv.pdb\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nhits.sdf\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Enumerate changes\"];\n  0 -->|output| 3;\n  4[\"Compound conversion\"];\n  1 -->|output| 4;\n  5[\"Create Frankenstein ligand\"];\n  2 -->|output| 5;\n  6[\"Compound conversion\"];\n  3 -->|output| 6;\n  7[\"rDock cavity definition\"];\n  4 -->|outfile| 7;\n  5 -->|outfile| 7;\n  8[\"Split file\"];\n  6 -->|outfile| 8;\n  9[\"rDock docking\"];\n  4 -->|outfile| 9;\n  8 -->|list_output_sdf| 9;\n  7 -->|activesite| 9;\n  10[\"Collapse Collection\"];\n  9 -->|output| 10;\n  11[\"XChem TransFS pose scoring\"];\n  1 -->|output| 11;\n  10 -->|output| 11;\n  12[\"Max SuCOS score\"];\n  11 -->|output| 12;\n  2 -->|output| 12;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Candidates"
-                            }
-                        ],
-                        "label": "Candidates",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 218,
-                            "top": 200
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Candidates\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "47bf8c53-ae1e-4af6-bece-6adfd74b627c",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "cdab037e-aee1-49b8-a998-cd9fe7ddcdb7"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Mpro-x0195_0_apo-desolv.pdb"
-                            }
-                        ],
-                        "label": "Mpro-x0195_0_apo-desolv.pdb",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 218,
-                            "top": 289.76666259765625
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Mpro-x0195_0_apo-desolv.pdb\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "156f4aeb-d160-456a-974e-7884b79cb83a",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1fd1c624-37c6-4874-b863-a40eac5e4994"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "hits.sdf"
-                            }
-                        ],
-                        "label": "hits.sdf",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 218,
-                            "top": 400.5333251953125
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"hits.sdf\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "dd2d3bc0-8138-4e66-b2d9-e5e90e27b659",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1c8fb3cc-52ad-4f62-a00d-80b14b2c1d4a"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "infile": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Create Frankenstein ligand",
-                                "name": "infile"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Create Frankenstein ligand",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "sdf"
-                            }
-                        ],
-                        "position": {
-                            "left": 478.76666259765625,
-                            "top": 483.5333251953125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "8e214e52e461",
-                            "name": "ctb_frankenstein_ligand",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "0.1.1",
-                        "type": "tool",
-                        "uuid": "081abe35-347a-4244-99ae-ec35329e3de0",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "53c557af-d5b9-4033-be54-7c197591e750"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "computational-chemistry/covid19-docking",
-                "path": "topics/computational-chemistry/tutorials/covid19-docking/workflows/workflow.ga",
-                "tags": [
-                    "computational-chemistry"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring",
-                "topic_id": "computational-chemistry",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/computational-chemistry-covid19-docking/versions/workflow",
-                "tutorial_id": "covid19-docking",
-                "url": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/covid19-docking/workflows/workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/covid19-docking/workflows/workflow.html",
-                "version": 3,
-                "wfid": "computational-chemistry-covid19-docking",
-                "wfname": "workflow",
-                "workflow": "workflow.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/0.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.2.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbcavity/rdock_rbcavity/0.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbdock/rdock_rbdock/0.1.4",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.4.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/sucos_max_score/sucos_max_score/0.2.3",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
-                    "xchem_pose_scoring"
-                ],
-                "workflowhub_id": "1079"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/3730474"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
@@ -162648,497 +162349,269 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bwa",
-                    "owner": "devteam",
-                    "revisions": "e188dc7a68e6",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bamtools_split_ref",
-                    "owner": "iuc",
-                    "revisions": "9b520009db81",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastp",
-                    "owner": "iuc",
-                    "revisions": "65b93b623c77",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "iqtree",
-                    "owner": "iuc",
-                    "revisions": "24d024316465",
-                    "tool_panel_section_label": "Evolution",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ivar_consensus",
-                    "owner": "iuc",
-                    "revisions": "40737febe339",
-                    "tool_panel_section_label": "Virology",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "qualimap_bamqc",
-                    "owner": "iuc",
-                    "revisions": "19ece8afbaab",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_view",
-                    "owner": "iuc",
-                    "revisions": "5826298f6a73",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "seqtk",
-                    "owner": "iuc",
-                    "revisions": "3da72230c066",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "vapor",
-                    "owner": "iuc",
-                    "revisions": "244812f5bd1f",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "90981f86000f",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mafft",
-                    "owner": "rnateam",
-                    "revisions": "bf28a8cff401",
-                    "tool_panel_section_label": "Multiple Alignments",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_split_ref\n  owner: iuc\n  revisions: 9b520009db81\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: iqtree\n  owner: iuc\n  revisions: 24d024316465\n  tool_panel_section_label: Evolution\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ivar_consensus\n  owner: iuc\n  revisions: 40737febe339\n  tool_panel_section_label: Virology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qualimap_bamqc\n  owner: iuc\n  revisions: 19ece8afbaab\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: 5826298f6a73\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: vapor\n  owner: iuc\n  revisions: 244812f5bd1f\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mafft\n  owner: rnateam\n  revisions: bf28a8cff401\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/aiv-analysis/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "by-covid",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "fediverse": "https://scholar.social/@zerodivision",
-                "fediverse_flavor": "mastodon",
-                "id": "wm75",
-                "joined": "2017-09",
-                "matrix": "wm75:matrix.org",
-                "name": "Wolfgang Maier",
-                "orcid": "0000-0002-9464-6640",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
-            }
-        ],
-        "dir": "topics/variant-analysis/tutorials/aiv-analysis",
-        "edam_operation": [
-            "Sequencing quality control",
-            "Sequence contamination filtering",
-            "Genome indexing",
-            "Sequence file editing",
-            "De-novo assembly",
-            "Sequence analysis",
-            "Read mapping",
-            "Sequence alignment analysis",
-            "Phylogenetic analysis",
-            "Sequence alignment",
-            "Data retrieval",
-            "Multiple sequence alignment",
-            "Generation",
-            "Data handling"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "variant-analysis/aiv-analysis",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Reassortment of gene segments makes reference-based mapping of influenza sequencing data challenging",
-            "An alternative to *de-novo* assembly can be mapping to a dynamically chosen reference genome",
-            "Variant calling and consensus genome construction can follow workflows used also for other viral sequence data",
-            "Standard phylogenetic tools can be used to find relationships between influenza samples but should be used on a per-segment basis"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-03-20",
-        "objectives": [
-            "Determine how reassortment impacts reference-based mapping approaches",
-            "Use a collection of per-segment reference sequences to construct a hybrid reference genome that is sufficiently close to a sequenced sample to be useful as a reference for mapping",
-            "Construct a sample consensus genome from mapped reads",
-            "Generate per-segment phylogenetic trees of AIV consensus sequences"
-        ],
-        "pageviews": 1792,
-        "pub_date": "2022-11-21",
-        "questions": [
-            "With reassortment of gene segments being a common event in avian influenza virus (AIV) evolution, does it make sense to use a reference-based mapping approach for constructing consensus genome sequences for AIV samples?",
-            "Is it possible to reuse existing tools and workflows developed for the analysis of sequencing data from other viruses?",
-            "How can we obtain meaningful phylogenetic insight from AIV consensus sequences?"
-        ],
-        "short_id": "T00308",
-        "short_tools": [
-            "Grep1",
-            "fastp",
-            "upload1",
-            "samtools_view",
-            "bamtools_split_ref",
-            "tp_find_and_replace",
-            "rbc_mafft",
-            "seqtk_subseq",
-            "qualimap_bamqc",
-            "Show beginning1",
-            "vapor",
-            "iqtree",
-            "ivar_consensus",
-            "__RELABEL_FROM_FILE__",
-            "bwa_mem",
-            "collapse_dataset"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "one-health",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "virology",
-            "one-health"
-        ],
-        "time_estimation": "4H",
-        "title": "Avian influenza viral strain analysis from gene segment sequencing data",
-        "tools": [
-            "Grep1",
-            "Show beginning1",
-            "__RELABEL_FROM_FILE__",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_ref/bamtools_split_ref/2.5.2+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.1.2+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/vapor/vapor/1.0.2+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
-            "toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.520+galaxy0",
-            "upload1"
-        ],
-        "topic_name": "variant-analysis",
-        "topic_name_human": "Variant Analysis",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "aiv-analysis",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/aiv-analysis/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/aiv-analysis/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/aiv-analysis/tutorial.json"
-        },
-        "version": 9,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 166,
-        "visitors": 1198
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "salmon",
+                    "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "e3d32471da11",
-                    "tool_panel_section_label": "RNA Analysis",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "trim_galore",
-                    "owner": "bgruening",
-                    "revisions": "949f01671246",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "bcftools_consensus",
+                    "owner": "iuc",
+                    "revisions": "da0bf365652d",
+                    "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "e7b2202befea",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "bcftools_consensus",
+                    "owner": "iuc",
+                    "revisions": "a87ae767b01d",
+                    "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "filter_by_fasta_ids",
-                    "owner": "galaxyp",
-                    "revisions": "3c623e81be77",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "samtools_view",
+                    "owner": "iuc",
+                    "revisions": "0dbf49c414ae",
+                    "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "deseq2",
+                    "name": "snippy",
                     "owner": "iuc",
-                    "revisions": "6a3a025714d3",
-                    "tool_panel_section_label": "RNA Analysis",
+                    "revisions": "c9a8ef2aa380",
+                    "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "multiqc",
+                    "name": "snippy",
                     "owner": "iuc",
-                    "revisions": "b2f1f75d49c4",
-                    "tool_panel_section_label": "Quality Control",
+                    "revisions": "d220115f882b",
+                    "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "multiqc",
+                    "name": "snp_dists",
                     "owner": "iuc",
-                    "revisions": "5e33b465d8d5",
-                    "tool_panel_section_label": "Quality Control",
+                    "revisions": "1959cc43b414",
+                    "tool_panel_section_label": "Phylogenetics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sample_seqs",
-                    "owner": "peterjc",
-                    "revisions": "7c40a1fbc82e",
-                    "tool_panel_section_label": "Filter and Sort",
+                    "name": "snp_dists",
+                    "owner": "iuc",
+                    "revisions": "f78492521996",
+                    "tool_panel_section_label": "Phylogenetics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mirdeep2_mapper",
-                    "owner": "rnateam",
-                    "revisions": "a8d24f4b6d95",
-                    "tool_panel_section_label": "RNA Analysis",
+                    "name": "snp_sites",
+                    "owner": "iuc",
+                    "revisions": "5804f786060d",
+                    "tool_panel_section_label": "Phylogenetics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mirdeep2_quantifier",
-                    "owner": "rnateam",
-                    "revisions": "d5ea61ff12eb",
-                    "tool_panel_section_label": "RNA Analysis",
+                    "name": "tb_variant_filter",
+                    "owner": "iuc",
+                    "revisions": "3b1e7c170b10",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "targetfinder",
-                    "owner": "rnateam",
-                    "revisions": "c9d56748fbde",
-                    "tool_panel_section_label": "RNA Analysis",
+                    "name": "tb_variant_filter",
+                    "owner": "iuc",
+                    "revisions": "e7aff4a85df5",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "tb_variant_filter",
+                    "owner": "iuc",
+                    "revisions": "ee4a90760848",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "tbprofiler",
+                    "owner": "iuc",
+                    "revisions": "809dfc93d593",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "add_input_name_as_column",
+                    "owner": "mvdbeek",
+                    "revisions": "3284b72eef56",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "90981f86000f",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "trimmomatic",
+                    "owner": "pjbriggs",
+                    "revisions": "d94aff5ee623",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: salmon\n  owner: bgruening\n  revisions: e3d32471da11\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trim_galore\n  owner: bgruening\n  revisions: 949f01671246\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filter_by_fasta_ids\n  owner: galaxyp\n  revisions: 3c623e81be77\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deseq2\n  owner: iuc\n  revisions: 6a3a025714d3\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: b2f1f75d49c4\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 5e33b465d8d5\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sample_seqs\n  owner: peterjc\n  revisions: 7c40a1fbc82e\n  tool_panel_section_label: Filter and Sort\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mirdeep2_mapper\n  owner: rnateam\n  revisions: a8d24f4b6d95\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mirdeep2_quantifier\n  owner: rnateam\n  revisions: d5ea61ff12eb\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: targetfinder\n  owner: rnateam\n  revisions: c9d56748fbde\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_consensus\n  owner: iuc\n  revisions: da0bf365652d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_consensus\n  owner: iuc\n  revisions: a87ae767b01d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: 0dbf49c414ae\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snippy\n  owner: iuc\n  revisions: c9a8ef2aa380\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snippy\n  owner: iuc\n  revisions: d220115f882b\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snp_dists\n  owner: iuc\n  revisions: 1959cc43b414\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snp_dists\n  owner: iuc\n  revisions: f78492521996\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snp_sites\n  owner: iuc\n  revisions: 5804f786060d\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tb_variant_filter\n  owner: iuc\n  revisions: 3b1e7c170b10\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tb_variant_filter\n  owner: iuc\n  revisions: e7aff4a85df5\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tb_variant_filter\n  owner: iuc\n  revisions: ee4a90760848\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbprofiler\n  owner: iuc\n  revisions: 809dfc93d593\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: add_input_name_as_column\n  owner: mvdbeek\n  revisions: 3284b72eef56\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n  owner: pjbriggs\n  revisions: d94aff5ee623\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/evolution/tutorials/mtb_transmission/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "GaloGS",
+                "dbrites",
+                "cstritt"
+            ],
+            "editing": [
+                "wm75"
+            ]
+        },
         "contributors": [
             {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "gallardoalba",
-                "joined": "2020-11",
-                "name": "Crist\u00f3bal Gallardo",
-                "orcid": "0000-0002-5752-2155",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
+                "id": "GaloGS",
+                "joined": "2022-03",
+                "name": "Galo A. Goig",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/GaloGS/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/GaloGS.json"
+            },
+            {
+                "id": "dbrites",
+                "joined": "2022-03",
+                "name": "Daniela Brites",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dbrites/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/dbrites.json"
+            },
+            {
+                "id": "cstritt",
+                "joined": "2022-03",
+                "name": "Christoph Stritt",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cstritt/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/cstritt.json"
             },
             {
                 "affiliations": [
+                    "by-covid",
                     "uni-freiburg",
                     "elixir-europe"
                 ],
-                "id": "pavanvidem",
+                "elixir_node": "de",
+                "fediverse": "https://scholar.social/@zerodivision",
+                "fediverse_flavor": "mastodon",
+                "id": "wm75",
                 "joined": "2017-09",
-                "name": "Pavankumar Videm",
-                "orcid": "0000-0002-5192-126X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
-            },
-            {
-                "email": "beatrizserrano.galaxy@gmail.com",
-                "id": "beatrizserrano",
-                "joined": "2020-07",
-                "linkedin": "beatriz-serrano",
-                "matrix": "beatrizserrano:matrix.org",
-                "name": "Beatriz Serrano-Solano",
-                "orcid": "0000-0002-5862-6132",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/beatrizserrano/",
-                "twitter": "BSerranoSolano",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/beatrizserrano.json"
+                "matrix": "wm75:matrix.org",
+                "name": "Wolfgang Maier",
+                "orcid": "0000-0002-9464-6640",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
             }
         ],
-        "dir": "topics/transcriptomics/tutorials/mirna-target-finder",
+        "dir": "topics/evolution/tutorials/mtb_transmission",
+        "edam_ontology": [
+            "topic_0622",
+            "topic_3301",
+            "topic_3324",
+            "topic_2885"
+        ],
         "edam_operation": [
-            "Sequencing quality control",
-            "Primer removal",
-            "Sequence composition calculation",
-            "Read pre-processing",
-            "RNA-Seq quantification",
-            "Gene expression analysis",
-            "Validation",
-            "Sequence trimming",
-            "Differential gene expression analysis",
-            "RNA-Seq analysis",
-            "Statistical calculation"
+            "Phylogenetic tree visualisation",
+            "Variant calling",
+            "Antimicrobial resistance prediction",
+            "Phylogenetic tree generation"
+        ],
+        "edam_topic": [
+            "Genomics",
+            "Microbiology",
+            "Infectious disease",
+            "DNA polymorphism"
         ],
-        "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org.au"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "transcriptomics/mirna-target-finder",
+        "id": "evolution/mtb_transmission",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.no"
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "MiRDeep2 in combination with the PmiREN database allows to quantify miRNA expression in plants",
-            "The use of the Salmon tool and the AtRTD2 transcriptome allows rapid and accurate quantification of transcripts in _Arabidopsis_",
-            "The combination of differential expression analysis and the TargetFinder tool is an effective strategy for the identification of miRNA target genes"
+            "Clustering is a useful tool to detect transmission links between patients and oubreak investigation.",
+            "Clustering can be used to investigate the transmission of certain traits, like drug resistance.",
+            "Clustering does not provide information about particular transmission events nor their directionality (who infected whom).",
+            "Clustering is very much influenced by sampling. Lower sampling proportions and shorter sampling timeframes lead to lower clustering rates that shoud not be confounded with lack of transmission."
         ],
         "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-09",
+        "mod_date": "2024-07-12",
         "objectives": [
-            "Perform miRNA differential expression analysis",
-            "Understand the quasi-mapping-based Salmon method for quantifying the expression of transcripts using RNA-Seq data",
-            "Idenfity potential miRNAs involved in brassinosteroid-mediated regulation networks"
-        ],
-        "pageviews": 5219864,
-        "pub_date": "2021-04-08",
-        "questions": [
-            "Which miRNAs are upregulated in response to brassinosteroids?",
-            "Which genes are potential target of brassinosteroid-induced miRNAs?"
+            "Create a SNP alignment",
+            "Calculate pairwise SNP distances between MTB samples",
+            "Identify transmission clusters based on SNP distances",
+            "Study the emergence and spread of drug resistance based on transmission analysis."
         ],
-        "recordings": [
+        "pageviews": 2499,
+        "pub_date": "2022-03-16",
+        "requirements": [
             {
-                "captioners": [
-                    "gallardoalba"
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "collections"
                 ],
-                "date": "2021-07-25",
-                "galaxy_version": "21.05",
-                "length": "1H10M",
-                "speakers": [
-                    "gallardoalba"
+                "type": "internal"
+            },
+            {
+                "topic_name": "variant-analysis",
+                "tutorials": [
+                    "tb-variant-analysis"
                 ],
-                "youtube_id": "wS1X_0Mgw7M"
+                "type": "internal"
             }
         ],
-        "short_id": "T00292",
+        "short_id": "T00145",
         "short_tools": [
-            "cat1",
-            "multiqc",
-            "filter_by_fasta_ids",
-            "targetfinder",
-            "sort1",
-            "sample_seqs",
-            "Cut1",
-            "fastqc",
-            "salmon",
-            "Filter1",
-            "deseq2",
-            "rbc_mirdeep2_mapper",
-            "rbc_mirdeep2_quantifier",
+            "tp_sed_tool",
+            "tp_easyjoin_tool",
+            "tp_cat",
+            "bcftools_consensus",
+            "samtools_view",
+            "upload1",
+            "snippy",
+            "tp_grep_tool",
+            "tp_replace_in_line",
+            "snp_dists",
+            "Grep1",
+            "tb_variant_filter",
+            "tb_profiler_profile",
+            "collapse_dataset",
+            "snp_sites",
+            "trimmomatic",
             "__MERGE_COLLECTION__",
-            "trim_galore"
-        ],
-        "slides": true,
-        "slides_recordings": [
-            {
-                "captioners": [
-                    "gallardoalba"
-                ],
-                "date": "2021-04-20",
-                "galaxy_version": "21.01",
-                "length": "10M",
-                "speakers": [
-                    "awspolly"
-                ],
-                "youtube_id": "FNmZoo2OXTU"
-            },
-            {
-                "captioners": [
-                    "gallardoalba"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "10M",
-                "speakers": [
-                    "awspolly"
-                ],
-                "youtube_id": "7t0Gr1Jklqs"
-            }
+            "addName"
         ],
+        "slides": false,
+        "slides_recordings": false,
         "supported_servers": {
             "exact": [
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
                 }
             ],
             "inexact": [
@@ -163151,116 +162624,696 @@
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
         "tags": [
-            "miRNA",
-            "plants",
-            "stress tolerance"
+            "prokaryote",
+            "one-health",
+            "microgalaxy"
         ],
         "time_estimation": "2H",
-        "title": "Whole transcriptome analysis of Arabidopsis thaliana",
+        "title": "Identifying tuberculosis transmission links: from SNPs to transmission clusters",
         "tools": [
-            "Cut1",
-            "Filter1",
+            "Grep1",
             "__MERGE_COLLECTION__",
-            "cat1",
-            "sort1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.14.1.2+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.2.5",
-            "toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_mapper/rbc_mirdeep2_mapper/2.0.0",
-            "toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_quantifier/rbc_mirdeep2_quantifier/2.0.0",
-            "toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.6.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.8.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.5+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/3.0.8+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
+            "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1",
+            "upload1"
         ],
-        "topic_name": "transcriptomics",
-        "topic_name_human": "Transcriptomics",
+        "topic_name": "evolution",
+        "topic_name_human": "Evolution",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": true
+            "video": false
         },
-        "tutorial_name": "mirna-target-finder",
+        "tutorial_name": "mtb_transmission",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/evolution/tutorials/mtb_transmission/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/evolution/tutorials/mtb_transmission/tutorial.json"
         },
-        "version": 17,
-        "video": true,
-        "video_versions": 1,
+        "version": 12,
+        "video": false,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 314,
-        "visitors": 1919285,
+        "visit_duration": 183,
+        "visitors": 1605,
         "workflows": [
             {
                 "creators": [],
-                "description": "Identify upregulated miRNAS and analyze potential targets in downregulated genes.",
+                "description": "Starting from the BAM files produced by snippy, generate a table that summarizes the drug-resistance profile for each sample",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nControl miRNA FASTQ collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nTreated miRNA FASTQ collection\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nTreated mRNA FASTQ collection\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPrecursor miRNA sequences\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nControl mRNA FASTQ collection\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTranscriptome FASTA\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAnnotation GTF\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMature miRNA sequences\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nStar miRNA sequenes\"]\n  9[label=\"FastQC\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"Trim Galore!\"]\n  0 -> 10 [label=\"output\"]\n  11[label=\"FastQC\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"Trim Galore!\"]\n  1 -> 12 [label=\"output\"]\n  13[label=\"FastQC\"]\n  2 -> 13 [label=\"output\"]\n  14[label=\"FastQC\"]\n  4 -> 14 [label=\"output\"]\n  15[label=\"Salmon quant\"]\n  6 -> 15 [label=\"output\"]\n  2 -> 15 [label=\"output\"]\n  5 -> 15 [label=\"output\"]\n  16[label=\"Salmon quant\"]\n  6 -> 16 [label=\"output\"]\n  4 -> 16 [label=\"output\"]\n  5 -> 16 [label=\"output\"]\n  17[label=\"FastQC\"]\n  10 -> 17 [label=\"trimmed_reads_single\"]\n  18[label=\"MiRDeep2 Mapper\"]\n  10 -> 18 [label=\"trimmed_reads_single\"]\n  19[label=\"Merge collections\"]\n  11 -> 19 [label=\"text_file\"]\n  9 -> 19 [label=\"text_file\"]\n  20[label=\"FastQC\"]\n  12 -> 20 [label=\"trimmed_reads_single\"]\n  21[label=\"MiRDeep2 Mapper\"]\n  12 -> 21 [label=\"trimmed_reads_single\"]\n  22[label=\"Merge collections\"]\n  13 -> 22 [label=\"text_file\"]\n  14 -> 22 [label=\"text_file\"]\n  23[label=\"DESeq2\"]\n  15 -> 23 [label=\"output_gene_quant\"]\n  16 -> 23 [label=\"output_gene_quant\"]\n  6 -> 23 [label=\"output\"]\n  24[label=\"MiRDeep2 Quantifier\"]\n  7 -> 24 [label=\"output\"]\n  3 -> 24 [label=\"output\"]\n  18 -> 24 [label=\"output_reads_collapsed\"]\n  8 -> 24 [label=\"output\"]\n  25[label=\"MultiQC\"]\n  19 -> 25 [label=\"output\"]\n  26[label=\"Merge collections\"]\n  20 -> 26 [label=\"text_file\"]\n  17 -> 26 [label=\"text_file\"]\n  27[label=\"MiRDeep2 Quantifier\"]\n  7 -> 27 [label=\"output\"]\n  3 -> 27 [label=\"output\"]\n  21 -> 27 [label=\"output_reads_collapsed\"]\n  8 -> 27 [label=\"output\"]\n  28[label=\"MultiQC\"]\n  22 -> 28 [label=\"output\"]\n  29[label=\"Filter\"]\n  23 -> 29 [label=\"deseq_out\"]\n  30[label=\"Cut\"]\n  24 -> 30 [label=\"miRNAsExpressed\"]\n  31[label=\"MultiQC\"]\n  26 -> 31 [label=\"output\"]\n  32[label=\"Cut\"]\n  27 -> 32 [label=\"miRNAsExpressed\"]\n  33[label=\"Filter\"]\n  29 -> 33 [label=\"out_file1\"]\n  34[label=\"Filter\"]\n  29 -> 34 [label=\"out_file1\"]\n  35[label=\"DESeq2\"]\n  32 -> 35 [label=\"out_file1\"]\n  30 -> 35 [label=\"out_file1\"]\n  36[label=\"Cut\"]\n  34 -> 36 [label=\"out_file1\"]\n  37[label=\"Filter\"]\n  35 -> 37 [label=\"deseq_out\"]\n  38[label=\"Filter FASTA\"]\n  36 -> 38 [label=\"out_file1\"]\n  5 -> 38 [label=\"output\"]\n  39[label=\"Filter\"]\n  37 -> 39 [label=\"out_file1\"]\n  40[label=\"Filter\"]\n  37 -> 40 [label=\"out_file1\"]\n  41[label=\"Cut\"]\n  40 -> 41 [label=\"out_file1\"]\n  42[label=\"Filter FASTA\"]\n  41 -> 42 [label=\"out_file1\"]\n  8 -> 42 [label=\"output\"]\n  43[label=\"Filter FASTA\"]\n  41 -> 43 [label=\"out_file1\"]\n  7 -> 43 [label=\"output\"]\n  44[label=\"Concatenate datasets\"]\n  43 -> 44 [label=\"output\"]\n  42 -> 44 [label=\"output\"]\n  45[label=\"TargetFinder\"]\n  38 -> 45 [label=\"output\"]\n  44 -> 45 [label=\"out_file1\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nMTB single-end BAMs\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nMTB paired-end BAMs\"]\n  2[label=\"Merge collections\"]\n  0 -> 2 [label=\"output\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"Samtools view BAM > SAM\"]\n  2 -> 3 [label=\"output\"]\n  kaa2200279d104328b2c2e4d139d5d5bd[color=lightseagreen,label=\"Output\\nSamtools view on input dataset(s): filtered alignments\"]\n  3 -> kaa2200279d104328b2c2e4d139d5d5bd\n  4[label=\"Sed MTB_anc to Chromosome\"]\n  3 -> 4 [label=\"outputsam\"]\n  5[label=\"Samtools view SAM > BAM\"]\n  4 -> 5 [label=\"output\"]\n  6[label=\"TB-profiler\"]\n  5 -> 6 [label=\"outputsam\"]\n  7[label=\"Get drug resistance profile\"]\n  6 -> 7 [label=\"output_txt\"]\n  8[label=\"Add Sample Name\"]\n  7 -> 8 [label=\"output\"]\n  9[label=\"Concatenate DR profiles in a single table\"]\n  8 -> 9 [label=\"output\"]\n  10[label=\"Cleanup the table\"]\n  9 -> 10 [label=\"out_file1\"]\n}",
                 "history": [
                     {
-                        "hash": "87d458cc1fd8db170670ddd5c186c98295267d9e",
-                        "message": "Undo error",
-                        "num": 7,
-                        "short_hash": "87d458cc1",
-                        "unix": "1674149735"
+                        "hash": "103d419430b5164ef56e7de3bd3ef13e798967cd",
+                        "message": "update tag",
+                        "num": 2,
+                        "short_hash": "103d41943",
+                        "unix": "1647422971"
                     },
                     {
-                        "hash": "edf36428b978d5519a494eaee576a8a17c6c948e",
-                        "message": "Fix tutorial",
-                        "num": 6,
-                        "short_hash": "edf36428b",
-                        "unix": "1669862549"
+                        "hash": "2e7ba78522415b81e10f3f5a74144f4f419b218d",
+                        "message": "tweak",
+                        "num": 1,
+                        "short_hash": "2e7ba7852",
+                        "unix": "1647422653"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "BAMs obtained from single-end mappings with snippy",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "BAMs obtained from single-end mappings with snippy",
+                                "name": "MTB single-end BAMs"
+                            }
+                        ],
+                        "label": "MTB single-end BAMs",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 586.3333282470703,
+                            "height": 89.09999084472656,
+                            "left": -233.6999969482422,
+                            "right": -13.699996948242188,
+                            "top": 497.23333740234375,
+                            "width": 220,
+                            "x": -233.6999969482422,
+                            "y": 497.23333740234375
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "5befe3e8-ccba-4b78-b7f1-dab039ef1011",
+                        "workflow_outputs": []
                     },
                     {
-                        "hash": "a6636e32469b78edc30efcc646f92e77c4bdb58b",
-                        "message": "add tags and annotation to the workflow",
-                        "num": 5,
-                        "short_hash": "a6636e324",
-                        "unix": "1617760834"
+                        "annotation": "BAMs obtained from paired-end mappings with snippy",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "BAMs obtained from paired-end mappings with snippy",
+                                "name": "MTB paired-end BAMs"
+                            }
+                        ],
+                        "label": "MTB paired-end BAMs",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 695.3333282470703,
+                            "height": 89.09999084472656,
+                            "left": -234.6999969482422,
+                            "right": -14.699996948242188,
+                            "top": 606.2333374023438,
+                            "width": 220,
+                            "x": -234.6999969482422,
+                            "y": 606.2333374023438
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "d6f269d8-66e8-4baf-9b5c-de9e7313c4a0",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nMTB single-end BAMs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nMTB paired-end BAMs\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Merge collections\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"Samtools view BAM > SAM\"];\n  2 -->|output| 3;\n  aa220027-9d10-4328-b2c2-e4d139d5d5bd[\"Output\\nSamtools view on input dataset(s): filtered alignments\"];\n  3 --> aa220027-9d10-4328-b2c2-e4d139d5d5bd;\n  style aa220027-9d10-4328-b2c2-e4d139d5d5bd stroke:#2c3143,stroke-width:4px;\n  4[\"Sed MTB_anc to Chromosome\"];\n  3 -->|outputsam| 4;\n  5[\"Samtools view SAM > BAM\"];\n  4 -->|output| 5;\n  6[\"TB-profiler\"];\n  5 -->|outputsam| 6;\n  7[\"Get drug resistance profile\"];\n  6 -->|output_txt| 7;\n  8[\"Add Sample Name\"];\n  7 -->|output| 8;\n  9[\"Concatenate DR profiles in a single table\"];\n  8 -->|output| 9;\n  10[\"Cleanup the table\"];\n  9 -->|out_file1| 10;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "From BAMs to drug resistance prediction with TB-profiler",
+                "outputs": [
+                    {
+                        "annotation": "Merge single-end and paired-end BAMs in a single collection to be analyzed alltogether",
+                        "content_id": "__MERGE_COLLECTION__",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "inputs_0|input": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "inputs_1|input": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Merge collections",
+                        "name": "Merge collections",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 720.5,
+                            "height": 222.26666259765625,
+                            "left": 34.80000305175781,
+                            "right": 254.8000030517578,
+                            "top": 498.23333740234375,
+                            "width": 220,
+                            "x": 34.80000305175781,
+                            "y": 498.23333740234375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "__MERGE_COLLECTION__",
+                        "tool_state": "{\"advanced\": {\"conflict\": {\"duplicate_options\": \"keep_first\", \"__current_case__\": 3}}, \"inputs\": [{\"__index__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "2142f124-4731-49fb-8e65-8e050705e001",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "180a1bdf-d552-49b7-93e9-4daf609096a6"
+                            }
+                        ]
                     },
                     {
-                        "hash": "a5a1a7567b95fa539b493a98f5924d2482e16997",
-                        "message": "Update workflow for miRNA target identification in Arabidopsis",
-                        "num": 4,
-                        "short_hash": "a5a1a7567",
-                        "unix": "1617760351"
+                        "annotation": "We want a text (SAM) file to substitute the string \"MTB_anc\" by \"Chromosome\" so it is compatible with TB-profiler",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "input": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Samtools view BAM > SAM",
+                        "name": "Samtools view",
+                        "outputs": [
+                            {
+                                "name": "outputsam",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 951.5000152587891,
+                            "height": 189.8333282470703,
+                            "left": 277.6000061035156,
+                            "right": 497.6000061035156,
+                            "top": 761.6666870117188,
+                            "width": 220,
+                            "x": 277.6000061035156,
+                            "y": 761.6666870117188
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "0dbf49c414ae",
+                            "name": "samtools_view",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"all_reads\", \"__current_case__\": 0, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"adv_output\": {\"readtags\": [], \"collapsecigar\": \"false\"}, \"output_format\": {\"oformat\": \"sam\", \"__current_case__\": 1, \"with_header\": \"true\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.13+galaxy2",
+                        "type": "tool",
+                        "uuid": "1040a122-5729-41a4-bd45-2406231f8024",
+                        "workflow_outputs": [
+                            {
+                                "label": "Samtools view on input dataset(s): filtered alignments",
+                                "output_name": "outputsam",
+                                "uuid": "aa220027-9d10-4328-b2c2-e4d139d5d5bd"
+                            }
+                        ]
                     },
                     {
-                        "hash": "0eacaeef42cdfef3d6f60d4ec481a3ef84b72765",
-                        "message": "Update workflow and include downregulated miRNAS",
-                        "num": 3,
-                        "short_hash": "0eacaeef4",
-                        "unix": "1617194856"
+                        "annotation": "Change the string MTB_anc to \"Chromosome\" so it is compatible with TB-profiler",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "infile": {
+                                "id": 3,
+                                "output_name": "outputsam"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Sed (MTB_anc to Chromosome)",
+                        "name": "Text transformation",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 943.2000122070312,
+                            "height": 122.5333251953125,
+                            "left": 537.5999755859375,
+                            "right": 757.5999755859375,
+                            "top": 820.6666870117188,
+                            "width": 220,
+                            "x": 537.5999755859375,
+                            "y": 820.6666870117188
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"s/MTB_anc/Chromosome/g\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
+                        "type": "tool",
+                        "uuid": "95fc656b-43fc-4f1e-8850-25489e793376",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "c3b3612d-3999-4022-9d6c-49ce6756ba2a"
+                            }
+                        ]
                     },
                     {
-                        "hash": "bdbe72dd283efbb454cf60a91384a9d130f8b342",
-                        "message": "Fix tests workflow",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "input": {
+                                "id": 4,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Samtools view SAM > BAM",
+                        "name": "Samtools view",
+                        "outputs": [
+                            {
+                                "name": "outputsam",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 945.5000152587891,
+                            "height": 189.8333282470703,
+                            "left": 810.5999755859375,
+                            "right": 1030.5999755859375,
+                            "top": 755.6666870117188,
+                            "width": 220,
+                            "x": 810.5999755859375,
+                            "y": 755.6666870117188
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "0dbf49c414ae",
+                            "name": "samtools_view",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"all_reads\", \"__current_case__\": 0, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"adv_output\": {\"readtags\": [], \"collapsecigar\": \"false\"}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.13+galaxy2",
+                        "type": "tool",
+                        "uuid": "729169fd-682e-4394-8421-1cde0aa2ac37",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outputsam",
+                                "uuid": "67aacaf4-b657-4269-b3eb-5cf22e1e9596"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Generate TB-profiler reports with drug resistance determinants",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/3.0.8+galaxy0",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "fastq_or_bam|bam_input": {
+                                "id": 5,
+                                "output_name": "outputsam"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "TB-profiler",
+                        "name": "TB-Profiler Profile",
+                        "outputs": [
+                            {
+                                "name": "results_json",
+                                "type": "json"
+                            },
+                            {
+                                "name": "output_vcf",
+                                "type": "vcf"
+                            },
+                            {
+                                "name": "output_txt",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 724.9333343505859,
+                            "height": 254.6999969482422,
+                            "left": 1069.800048828125,
+                            "right": 1289.800048828125,
+                            "top": 470.23333740234375,
+                            "width": 220,
+                            "x": 1069.800048828125,
+                            "y": 470.23333740234375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/3.0.8+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "809dfc93d593",
+                            "name": "tbprofiler",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"advanced\": {\"options\": \"no\", \"__current_case__\": 0}, \"fastq_or_bam\": {\"input_select\": \"bam\", \"__current_case__\": 3, \"bam_input\": {\"__class__\": \"ConnectedValue\"}}, \"output_format\": \"txt\", \"platform\": \"illumina\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.0.8+galaxy0",
+                        "type": "tool",
+                        "uuid": "07d7e2cc-9669-45b5-bc1e-27bda80752c4",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_vcf",
+                                "uuid": "89e84a41-76ce-46eb-acec-1563e8d20ef6"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_txt",
+                                "uuid": "c148b074-5e6a-4846-86e7-0193a5ce38b5"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "results_json",
+                                "uuid": "b22dcd19-5127-4dc3-b329-8a09ab7f5db3"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "From TB profiler, search with `grep` the part of the text that describes the DR profile (e.g Drug-Resistance: MDR) ",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "infile": {
+                                "id": 6,
+                                "output_name": "output_txt"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Get drug resistance profile",
+                        "name": "Search in textfiles",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 594.7666625976562,
+                            "height": 122.5333251953125,
+                            "left": 1343.800048828125,
+                            "right": 1563.800048828125,
+                            "top": 472.23333740234375,
+                            "width": 220,
+                            "x": 1343.800048828125,
+                            "y": 472.23333740234375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"case_sensitive\": \"-i\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-P\", \"url_paste\": \"Drug-Resistance:\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
+                        "type": "tool",
+                        "uuid": "9b418ac9-364d-4877-a858-b33a1e335900",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "b876e27d-6013-4265-ae70-cffad0895db9"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "We have generated one file per sample, that contains the DR profile (e.g Drug-Resistance: MDR) We want to prepend the name of the sample so we have: (Sample_name Drug-Resistance: MDR) ",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "input": {
+                                "id": 7,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Add Sample Name",
+                        "name": "Add input name as column",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 596.7666625976562,
+                            "height": 122.5333251953125,
+                            "left": 1605.800048828125,
+                            "right": 1825.800048828125,
+                            "top": 474.23333740234375,
+                            "width": 220,
+                            "x": 1605.800048828125,
+                            "y": 474.23333740234375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3284b72eef56",
+                            "name": "add_input_name_as_column",
+                            "owner": "mvdbeek",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"header\": {\"contains_header\": \"no\", \"__current_case__\": 1}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"prepend\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.2.0",
+                        "type": "tool",
+                        "uuid": "d92f5d19-212d-4d8b-a7f7-f249788088ac",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "1b9d5610-2f91-450a-a1b9-1718d8afde1a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "The output will be:\nSample_A  DR_profile_A\nSample_B DR_profile_B\nSample_Z DR_profile_Z",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {
+                            "inputs": {
+                                "id": 8,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Concatenate datasets",
+                                "name": "inputs"
+                            }
+                        ],
+                        "label": "Concatenate DR profiles in a single table",
+                        "name": "Concatenate datasets",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 596.7666625976562,
+                            "height": 122.5333251953125,
+                            "left": 1871.800048828125,
+                            "right": 2091.800048828125,
+                            "top": 474.23333740234375,
+                            "width": 220,
+                            "x": 1871.800048828125,
+                            "y": 474.23333740234375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f46f0e4f75c4",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"inputs\": {\"__class__\": \"RuntimeValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.1",
+                        "type": "tool",
+                        "uuid": "44a1faa8-cd48-4a85-96f7-81dcf3041e19",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "8bf7beae-528c-4d8b-abac-827a84a931a8"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Remove unnecessary text from the table like \".txt\" or \"Drug-resistance:\"",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {
+                            "infile": {
+                                "id": 9,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Replace Text",
+                                "name": "infile"
+                            }
+                        ],
+                        "label": "Cleanup the table",
+                        "name": "Replace Text",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 599.8666534423828,
+                            "height": 122.53334045410156,
+                            "left": 2136.300048828125,
+                            "right": 2356.300048828125,
+                            "top": 477.33331298828125,
+                            "width": 220,
+                            "x": 2136.300048828125,
+                            "y": 477.33331298828125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"infile\": {\"__class__\": \"RuntimeValue\"}, \"replacements\": [{\"__index__\": 0, \"find_pattern\": \".txt\", \"replace_pattern\": \"this is my replacement\"}, {\"__index__\": 1, \"find_pattern\": \"Drug-resistance:\", \"replace_pattern\": \"\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.2",
+                        "type": "tool",
+                        "uuid": "398ccbde-0309-41bb-b348-fc8ecca15cb9",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "6b30ef89-359b-4593-a600-40d11d47138b"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "evolution/mtb_transmission",
+                "path": "topics/evolution/tutorials/mtb_transmission/workflows/Galaxy-Workflow-From_BAMs_to_drug_resistance_prediction_with_TB-profiler.ga",
+                "tags": [
+                    "evolution"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "From BAMs to drug resistance prediction with TB-profiler",
+                "topic_id": "evolution",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/evolution-mtb_transmission/versions/galaxy-workflow-from-bams-to-drug-resistance-prediction-with-tb-profiler",
+                "tutorial_id": "mtb_transmission",
+                "url": "https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_transmission/workflows/Galaxy-Workflow-From_BAMs_to_drug_resistance_prediction_with_TB-profiler.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_transmission/workflows/Galaxy-Workflow-From_BAMs_to_drug_resistance_prediction_with_TB-profiler.html",
+                "version": 1,
+                "wfid": "evolution-mtb_transmission",
+                "wfname": "galaxy-workflow-from-bams-to-drug-resistance-prediction-with-tb-profiler",
+                "workflow": "Galaxy-Workflow-From_BAMs_to_drug_resistance_prediction_with_TB-profiler.ga",
+                "workflow_tools": [
+                    "__MERGE_COLLECTION__",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/3.0.8+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0"
+                ],
+                "workflowhub_id": "1314"
+            },
+            {
+                "creators": [],
+                "description": "From Fastqs to VCFs and BAMs",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nSingle-End FASTQs\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nPaired-End FASTQs\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMycobacterium_tuberculosis_ancestral_reference.gbk\"]\n  3[label=\"Trimmomatic\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Trimmomatic\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Mapping and variant calling of SINGLE END FASTQs with snippy\"]\n  3 -> 5 [label=\"fastq_out\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"Mapping and variant calling of PAIRED END FASTQs with snippy\"]\n  4 -> 6 [label=\"fastq_out_paired\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"Merge PE/SE VCFs in a single collection with all samples\"]\n  5 -> 7 [label=\"snpvcf\"]\n  6 -> 7 [label=\"snpvcf\"]\n  8[label=\"Merge PE/SE BAMs in a single collection with all samples Part the workflow \u201dIdentifying DR with TB-profiler\"]\n  5 -> 8 [label=\"snpsbam\"]\n  6 -> 8 [label=\"snpsbam\"]\n  9[label=\"TB Variant Filter\"]\n  7 -> 9 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "61e5383633beda63e0c40a41837ccce18db77008",
+                        "message": "update tag",
                         "num": 2,
-                        "short_hash": "bdbe72dd2",
-                        "unix": "1616702513"
+                        "short_hash": "61e538363",
+                        "unix": "1647423011"
                     },
                     {
-                        "hash": "4b406638ca884e2ad7b58db02d9c4cc7eff0005d",
-                        "message": "New training: miRNA target finder",
+                        "hash": "2e7ba78522415b81e10f3f5a74144f4f419b218d",
+                        "message": "tweak",
                         "num": 1,
-                        "short_hash": "4b406638c",
-                        "unix": "1616700503"
+                        "short_hash": "2e7ba7852",
+                        "unix": "1647422653"
                     }
                 ],
                 "inputs": [
@@ -163273,21 +163326,27 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Control miRNA FASTQ collection"
+                                "name": "Single-End FASTQs"
                             }
                         ],
-                        "label": "Control miRNA FASTQ collection",
+                        "label": "Single-End FASTQs",
                         "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 1.984375
+                            "bottom": 579.2166595458984,
+                            "height": 89.09999084472656,
+                            "left": 689.4000244140625,
+                            "right": 909.4000244140625,
+                            "top": 490.1166687011719,
+                            "width": 220,
+                            "x": 689.4000244140625,
+                            "y": 490.1166687011719
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
                         "tool_version": null,
                         "type": "data_collection_input",
-                        "uuid": "286f34e3-d05b-40ba-b39e-2f0c7455ff23",
+                        "uuid": "30a3c256-5d21-4219-b23e-58c8f3842387",
                         "workflow_outputs": []
                     },
                     {
@@ -163299,21 +163358,27 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Treated miRNA FASTQ collection"
+                                "name": "Paired-End FASTQs"
                             }
                         ],
-                        "label": "Treated miRNA FASTQ collection",
+                        "label": "Paired-End FASTQs",
                         "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 331.984375
+                            "bottom": 688.2166900634766,
+                            "height": 89.09999084472656,
+                            "left": 697.4000244140625,
+                            "right": 917.4000244140625,
+                            "top": 599.11669921875,
+                            "width": 220,
+                            "x": 697.4000244140625,
+                            "y": 599.11669921875
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list:paired\"}",
                         "tool_version": null,
                         "type": "data_collection_input",
-                        "uuid": "6ffd974f-fd40-4234-9bda-6edd9e65e702",
+                        "uuid": "c04ddfda-2349-4857-8cae-b3d84dcbf9e7",
                         "workflow_outputs": []
                     },
                     {
@@ -163325,620 +163390,666 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Treated mRNA FASTQ collection"
+                                "name": "Mycobacterium_tuberculosis_ancestral_reference.gbk"
                             }
                         ],
-                        "label": "Treated mRNA FASTQ collection",
-                        "name": "Input dataset collection",
+                        "label": "Mycobacterium_tuberculosis_ancestral_reference.gbk",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 1161.984375,
-                            "top": 778.984375
+                            "bottom": 732.6500244140625,
+                            "height": 111.5333251953125,
+                            "left": 1351.4000244140625,
+                            "right": 1571.4000244140625,
+                            "top": 621.11669921875,
+                            "width": 220,
+                            "x": 1351.4000244140625,
+                            "y": 621.11669921875
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "e2260dff-96ce-4345-902a-73958f9ac0cf",
+                        "type": "data_input",
+                        "uuid": "67484edc-af0a-4a41-8170-c78853b51319",
                         "workflow_outputs": []
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nSingle-End FASTQs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nPaired-End FASTQs\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nMycobacterium_tuberculosis_ancestral_reference.gbk\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Trimmomatic\"];\n  0 -->|output| 3;\n  4[\"Trimmomatic\"];\n  1 -->|output| 4;\n  5[\"Mapping and variant calling of SINGLE END FASTQs with snippy\"];\n  3 -->|fastq_out| 5;\n  2 -->|output| 5;\n  6[\"Mapping and variant calling of PAIRED END FASTQs with snippy\"];\n  4 -->|fastq_out_paired| 6;\n  2 -->|output| 6;\n  7[\"Merge PE/SE VCFs in a single collection with all samples\"];\n  5 -->|snpvcf| 7;\n  6 -->|snpvcf| 7;\n  8[\"Merge PE/SE BAMs in a single collection with all samples Part the workflow \u201dIdentifying DR with TB-profiler\"];\n  5 -->|snpsbam| 8;\n  6 -->|snpsbam| 8;\n  9[\"TB Variant Filter\"];\n  7 -->|output| 9;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "From Fastqs to VCFs and BAMs",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1",
                         "errors": null,
                         "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Precursor miRNA sequences"
+                        "input_connections": {
+                            "readtype|fastq_in": {
+                                "id": 0,
+                                "output_name": "output"
                             }
-                        ],
-                        "label": "Precursor miRNA sequences",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 575.984375,
-                            "top": 1461.984375
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "7e8825d5-8e7f-4ec4-b0b4-f0efcc70e504",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Trimmomatic",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Control mRNA FASTQ collection"
+                                "name": "fastq_out",
+                                "type": "input"
                             }
                         ],
-                        "label": "Control mRNA FASTQ collection",
-                        "name": "Input dataset collection",
-                        "outputs": [],
                         "position": {
-                            "left": 1161.984375,
-                            "top": 1101.984375
+                            "bottom": 592.2166595458984,
+                            "height": 100.09999084472656,
+                            "left": 983.4000244140625,
+                            "right": 1203.4000244140625,
+                            "top": 492.1166687011719,
+                            "width": 220,
+                            "x": 983.4000244140625,
+                            "y": 492.1166687011719
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "5f622114-e64d-4a96-9866-e519b583cd98",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "d94aff5ee623",
+                            "name": "trimmomatic",
+                            "owner": "pjbriggs",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"illuminaclip\": {\"do_illuminaclip\": \"false\", \"__current_case__\": 1}, \"operations\": [{\"__index__\": 0, \"operation\": {\"name\": \"SLIDINGWINDOW\", \"__current_case__\": 0, \"window_size\": \"4\", \"required_quality\": \"30\"}}, {\"__index__\": 1, \"operation\": {\"name\": \"MINLEN\", \"__current_case__\": 1, \"minlen\": \"20\"}}], \"output_err\": \"false\", \"output_logs\": \"false\", \"readtype\": {\"single_or_paired\": \"se\", \"__current_case__\": 0, \"fastq_in\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.38.1",
+                        "type": "tool",
+                        "uuid": "91899b6e-1f22-45de-a6bc-acd43adac9fb",
+                        "workflow_outputs": [
                             {
-                                "description": "",
-                                "name": "Transcriptome FASTA"
+                                "label": null,
+                                "output_name": "fastq_out",
+                                "uuid": "c206129e-10b1-4c90-8404-ee4540c7216a"
                             }
-                        ],
-                        "label": "Transcriptome FASTA",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 1161.984375,
-                            "top": 1220.984375
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "5bbd4e69-3b60-47e1-aecf-5d43ae6b54e5",
-                        "workflow_outputs": []
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1",
                         "errors": null,
-                        "id": 6,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Annotation GTF"
+                        "id": 4,
+                        "input_connections": {
+                            "readtype|fastq_pair": {
+                                "id": 1,
+                                "output_name": "output"
                             }
-                        ],
-                        "label": "Annotation GTF",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 1161.984375,
-                            "top": 1340
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "570e8113-930a-4567-a380-fdb93fbcc60f",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Trimmomatic",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Mature miRNA sequences"
+                                "name": "fastq_out_paired",
+                                "type": "input"
+                            },
+                            {
+                                "name": "fastq_out_unpaired",
+                                "type": "input"
                             }
                         ],
-                        "label": "Mature miRNA sequences",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 575.984375,
-                            "top": 1770.984375
+                            "bottom": 815.9500274658203,
+                            "height": 199.8333282470703,
+                            "left": 986.4000244140625,
+                            "right": 1206.4000244140625,
+                            "top": 616.11669921875,
+                            "width": 220,
+                            "x": 986.4000244140625,
+                            "y": 616.11669921875
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "5d65f949-64bf-4f17-b242-f94d342b14a8",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {},
-                        "inputs": [
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "d94aff5ee623",
+                            "name": "trimmomatic",
+                            "owner": "pjbriggs",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"illuminaclip\": {\"do_illuminaclip\": \"false\", \"__current_case__\": 1}, \"operations\": [{\"__index__\": 0, \"operation\": {\"name\": \"SLIDINGWINDOW\", \"__current_case__\": 0, \"window_size\": \"4\", \"required_quality\": \"30\"}}, {\"__index__\": 1, \"operation\": {\"name\": \"MINLEN\", \"__current_case__\": 1, \"minlen\": \"20\"}}], \"output_err\": \"false\", \"output_logs\": \"false\", \"readtype\": {\"single_or_paired\": \"collection\", \"__current_case__\": 2, \"fastq_pair\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.38.1",
+                        "type": "tool",
+                        "uuid": "ee71335f-30af-4fd7-a121-bf108ffd5e0a",
+                        "workflow_outputs": [
                             {
-                                "description": "",
-                                "name": "Star miRNA sequenes"
+                                "label": null,
+                                "output_name": "fastq_out_paired",
+                                "uuid": "11fba967-c0af-4c4d-9d25-08edfec51758"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "fastq_out_unpaired",
+                                "uuid": "b71f679d-b409-4154-9185-533fad7b45b4"
                             }
-                        ],
-                        "label": "Star miRNA sequenes",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 575.984375,
-                            "top": 1890
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "d11848be-2417-4393-b87f-5e4d9500b4ed",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nControl miRNA FASTQ collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nTreated miRNA FASTQ collection\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nTreated mRNA FASTQ collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nPrecursor miRNA sequences\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Collection\\nControl mRNA FASTQ collection\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nTranscriptome FASTA\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nAnnotation GTF\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nMature miRNA sequences\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nStar miRNA sequenes\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"FastQC\"];\n  0 -->|output| 9;\n  10[\"Trim Galore!\"];\n  0 -->|output| 10;\n  11[\"FastQC\"];\n  1 -->|output| 11;\n  12[\"Trim Galore!\"];\n  1 -->|output| 12;\n  13[\"FastQC\"];\n  2 -->|output| 13;\n  14[\"FastQC\"];\n  4 -->|output| 14;\n  15[\"Salmon quant\"];\n  6 -->|output| 15;\n  2 -->|output| 15;\n  5 -->|output| 15;\n  16[\"Salmon quant\"];\n  6 -->|output| 16;\n  4 -->|output| 16;\n  5 -->|output| 16;\n  17[\"FastQC\"];\n  10 -->|trimmed_reads_single| 17;\n  18[\"MiRDeep2 Mapper\"];\n  10 -->|trimmed_reads_single| 18;\n  19[\"Merge collections\"];\n  11 -->|text_file| 19;\n  9 -->|text_file| 19;\n  20[\"FastQC\"];\n  12 -->|trimmed_reads_single| 20;\n  21[\"MiRDeep2 Mapper\"];\n  12 -->|trimmed_reads_single| 21;\n  22[\"Merge collections\"];\n  13 -->|text_file| 22;\n  14 -->|text_file| 22;\n  23[\"DESeq2\"];\n  15 -->|output_gene_quant| 23;\n  16 -->|output_gene_quant| 23;\n  6 -->|output| 23;\n  24[\"MiRDeep2 Quantifier\"];\n  7 -->|output| 24;\n  3 -->|output| 24;\n  18 -->|output_reads_collapsed| 24;\n  8 -->|output| 24;\n  25[\"MultiQC\"];\n  19 -->|output| 25;\n  26[\"Merge collections\"];\n  20 -->|text_file| 26;\n  17 -->|text_file| 26;\n  27[\"MiRDeep2 Quantifier\"];\n  7 -->|output| 27;\n  3 -->|output| 27;\n  21 -->|output_reads_collapsed| 27;\n  8 -->|output| 27;\n  28[\"MultiQC\"];\n  22 -->|output| 28;\n  29[\"Filter\"];\n  23 -->|deseq_out| 29;\n  30[\"Cut\"];\n  24 -->|miRNAsExpressed| 30;\n  31[\"MultiQC\"];\n  26 -->|output| 31;\n  32[\"Cut\"];\n  27 -->|miRNAsExpressed| 32;\n  33[\"Filter\"];\n  29 -->|out_file1| 33;\n  34[\"Filter\"];\n  29 -->|out_file1| 34;\n  35[\"DESeq2\"];\n  32 -->|out_file1| 35;\n  30 -->|out_file1| 35;\n  36[\"Cut\"];\n  34 -->|out_file1| 36;\n  37[\"Filter\"];\n  35 -->|deseq_out| 37;\n  38[\"Filter FASTA\"];\n  36 -->|out_file1| 38;\n  5 -->|output| 38;\n  39[\"Filter\"];\n  37 -->|out_file1| 39;\n  40[\"Filter\"];\n  37 -->|out_file1| 40;\n  41[\"Cut\"];\n  40 -->|out_file1| 41;\n  42[\"Filter FASTA\"];\n  41 -->|out_file1| 42;\n  8 -->|output| 42;\n  43[\"Filter FASTA\"];\n  41 -->|out_file1| 43;\n  7 -->|output| 43;\n  44[\"Concatenate datasets\"];\n  43 -->|output| 44;\n  42 -->|output| 44;\n  45[\"TargetFinder\"];\n  38 -->|output| 45;\n  44 -->|out_file1| 45;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "Plant bulk RNA-Seq workflow",
-                "outputs": [
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2",
                         "errors": null,
-                        "id": 23,
+                        "id": 5,
                         "input_connections": {
-                            "select_data|rep_factorName_0|rep_factorLevel_0|countsFile": {
-                                "id": 15,
-                                "output_name": "output_gene_quant"
-                            },
-                            "select_data|rep_factorName_0|rep_factorLevel_1|countsFile": {
-                                "id": 16,
-                                "output_name": "output_gene_quant"
+                            "fastq_input|fastq_input1": {
+                                "id": 3,
+                                "output_name": "fastq_out"
                             },
-                            "tximport|mapping_format|gtf_file": {
-                                "id": 6,
+                            "ref": {
+                                "id": 2,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool DESeq2",
-                                "name": "batch_factors"
-                            }
-                        ],
-                        "label": null,
-                        "name": "DESeq2",
+                        "inputs": [],
+                        "label": "Mapping and variant calling of SINGLE END FASTQs with snippy",
+                        "name": "snippy",
                         "outputs": [
                             {
-                                "name": "deseq_out",
+                                "name": "snpvcf",
+                                "type": "vcf"
+                            },
+                            {
+                                "name": "snptab",
                                 "type": "tabular"
                             },
                             {
-                                "name": "plots",
-                                "type": "pdf"
+                                "name": "snpsbam",
+                                "type": "bam"
                             }
                         ],
                         "position": {
-                            "left": 1737.984375,
-                            "top": 1170.984375
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActiondeseq_out": {
-                                "action_arguments": {
-                                    "newname": "DESeq2 results mRNA"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "deseq_out"
-                            },
-                            "RenameDatasetActionplots": {
-                                "action_arguments": {
-                                    "newname": "DESeq2 plots mRNA"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "plots"
-                            }
+                            "bottom": 731.1166687011719,
+                            "height": 332,
+                            "left": 1665.4000244140625,
+                            "right": 1885.4000244140625,
+                            "top": 399.1166687011719,
+                            "width": 220,
+                            "x": 1665.4000244140625,
+                            "y": 399.1166687011719
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "6a3a025714d3",
-                            "name": "deseq2",
+                            "changeset_revision": "c9a8ef2aa380",
+                            "name": "snippy",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"auto_mean_filter_off\": \"false\", \"batch_factors\": {\"__class__\": \"RuntimeValue\"}, \"esf\": \"\", \"fit_type\": \"1\", \"header\": \"true\", \"many_contrasts\": \"false\", \"normCounts\": \"false\", \"normRLog\": \"false\", \"normVST\": \"false\", \"outlier_filter_off\": \"false\", \"outlier_replace_off\": \"false\", \"pdf\": \"true\", \"select_data\": {\"how\": \"datasets_per_level\", \"__current_case__\": 1, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": \"effects_brassinolide\", \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": \"brassinolide\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"factorLevel\": \"control\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"tximport\", \"__current_case__\": 0, \"txtype\": \"salmon\", \"mapping_format\": {\"mapping_format_selector\": \"gtf\", \"__current_case__\": 0, \"gtf_file\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.11.40.6+galaxy1",
+                        "tool_state": "{\"adv\": {\"mapqual\": \"60\", \"mincov\": \"10\", \"minfrac\": \"0.1\", \"rgid\": \"\", \"bwaopt\": \"\"}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 1, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"outvcf\", \"outtab\", \"outbam\"], \"ref\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.2",
                         "type": "tool",
-                        "uuid": "db23fb5b-af4b-4fe1-8f8d-99a3176808e7",
+                        "uuid": "e38af720-1ae1-4f32-9e9d-562d0d040a85",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "plots",
-                                "uuid": "6c720aa2-a057-45c4-a813-3065d95c6c7f"
+                                "output_name": "snpsbam",
+                                "uuid": "4c15e214-85dd-4c43-b36a-3e482ab62879"
                             },
                             {
                                 "label": null,
-                                "output_name": "deseq_out",
-                                "uuid": "77e6746d-7bf9-400f-ac1e-106db58fbbbd"
+                                "output_name": "snpvcf",
+                                "uuid": "60968620-b9b0-4481-a17d-33229edb91e2"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "snptab",
+                                "uuid": "128c6ded-1206-4f88-b93d-9254a37f8f25"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0",
                         "errors": null,
-                        "id": 25,
+                        "id": 6,
                         "input_connections": {
-                            "results_0|software_cond|output_0|input": {
-                                "id": 19,
+                            "fastq_input|fastq_input": {
+                                "id": 4,
+                                "output_name": "fastq_out_paired"
+                            },
+                            "reference_source|ref_file": {
+                                "id": 2,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "MultiQC",
+                        "label": "Mapping and variant calling of PAIRED END FASTQs with snippy",
+                        "name": "snippy",
                         "outputs": [
                             {
-                                "name": "stats",
-                                "type": "input"
+                                "name": "snpvcf",
+                                "type": "vcf"
                             },
                             {
-                                "name": "html_report",
-                                "type": "html"
+                                "name": "snptab",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "snpsbam",
+                                "type": "bam"
                             }
                         ],
                         "position": {
-                            "left": 883.984375,
-                            "top": 342.984375
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionstats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "stats"
-                            },
-                            "RenameDatasetActionhtml_report": {
-                                "action_arguments": {
-                                    "newname": "MultiQC unprocessed miRNA: Webpage"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "html_report"
-                            },
-                            "RenameDatasetActionstats": {
-                                "action_arguments": {
-                                    "newname": "MultiQC unprocessed miRNA: Stats"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "stats"
-                            }
+                            "bottom": 1091.11669921875,
+                            "height": 332,
+                            "left": 1667.4000244140625,
+                            "right": 1887.4000244140625,
+                            "top": 759.11669921875,
+                            "width": 220,
+                            "x": 1667.4000244140625,
+                            "y": 759.11669921875
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "b2f1f75d49c4",
-                            "name": "multiqc",
+                            "changeset_revision": "d220115f882b",
+                            "name": "snippy",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"comment\": \"\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": \"false\", \"title\": \"miRNA initial quality check\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7",
+                        "tool_state": "{\"adv\": {\"mapqual\": \"60\", \"mincov\": \"10\", \"minfrac\": \"0.1\", \"minqual\": \"100.0\", \"rgid\": \"\", \"bwaopt\": \"\", \"rename_cons\": \"false\"}, \"fastq_input\": {\"fastq_input_selector\": \"paired_collection\", \"__current_case__\": 2, \"fastq_input\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"outvcf\", \"outtab\", \"outbam\"], \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.6.0+galaxy0",
                         "type": "tool",
-                        "uuid": "3e845cfd-ddd1-4f60-b1cb-ac16dc2c6d10",
+                        "uuid": "18f42bea-16ad-4db6-9c80-26fae71d99de",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "html_report",
-                                "uuid": "7cd34a0f-1142-4965-afa2-5f77e9c79b9e"
+                                "output_name": "snptab",
+                                "uuid": "6c7b8b74-395f-4326-bd62-e334cad878ca"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "snpsbam",
+                                "uuid": "9eb3bc09-5277-48d3-a1d4-cf652d29e0d2"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "snpvcf",
+                                "uuid": "7df12aa8-7a33-4985-83c4-5aeae5db29fd"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "content_id": "__MERGE_COLLECTION__",
                         "errors": null,
-                        "id": 28,
+                        "id": 7,
                         "input_connections": {
-                            "results_0|software_cond|output_0|input": {
-                                "id": 22,
-                                "output_name": "output"
+                            "inputs_0|input": {
+                                "id": 5,
+                                "output_name": "snpvcf"
+                            },
+                            "inputs_1|input": {
+                                "id": 6,
+                                "output_name": "snpvcf"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "MultiQC",
+                        "label": "Merge PE/SE VCFs in a single collection with all samples",
+                        "name": "Merge collections",
                         "outputs": [
                             {
-                                "name": "stats",
+                                "name": "output",
                                 "type": "input"
-                            },
-                            {
-                                "name": "html_report",
-                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 2035.984375,
-                            "top": 1455
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionstats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "stats"
-                            },
-                            "RenameDatasetActionhtml_report": {
-                                "action_arguments": {
-                                    "newname": "MultiQC mRNA: Webpage"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "html_report"
-                            },
-                            "RenameDatasetActionstats": {
-                                "action_arguments": {
-                                    "newname": "MultiQC mRNA: Stats"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "stats"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b2f1f75d49c4",
-                            "name": "multiqc",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 685.8166656494141,
+                            "height": 244.6999969482422,
+                            "left": 2111.39990234375,
+                            "right": 2331.39990234375,
+                            "top": 441.1166687011719,
+                            "width": 220,
+                            "x": 2111.39990234375,
+                            "y": 441.1166687011719
                         },
-                        "tool_state": "{\"comment\": \"\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"RuntimeValue\"}}]}}], \"saveLog\": \"false\", \"title\": \"mRNA initial quality check\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7",
+                        "post_job_actions": {},
+                        "tool_id": "__MERGE_COLLECTION__",
+                        "tool_state": "{\"advanced\": {\"conflict\": {\"duplicate_options\": \"keep_first\", \"__current_case__\": 3}}, \"inputs\": [{\"__index__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
                         "type": "tool",
-                        "uuid": "b7ffd734-4c99-4132-814f-47b75b4b5d63",
+                        "uuid": "6110c068-756d-4b45-96e1-5f2334c1cf35",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "html_report",
-                                "uuid": "7d5b5d84-d0b0-4639-9b42-61bf9f7e014d"
+                                "output_name": "output",
+                                "uuid": "351b8679-eea7-4a76-8840-f5e34f6c4162"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.5+galaxy2",
                         "errors": null,
-                        "id": 31,
+                        "id": 9,
                         "input_connections": {
-                            "results_0|software_cond|output_0|input": {
-                                "id": 26,
+                            "input1": {
+                                "id": 7,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool TB Variant Filter",
+                                "name": "input1"
+                            }
+                        ],
                         "label": null,
-                        "name": "MultiQC",
+                        "name": "TB Variant Filter",
                         "outputs": [
                             {
-                                "name": "stats",
-                                "type": "input"
-                            },
-                            {
-                                "name": "html_report",
-                                "type": "html"
+                                "name": "output1",
+                                "type": "vcf"
                             }
                         ],
                         "position": {
-                            "left": 1161.984375,
-                            "top": 558.984375
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionstats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "stats"
-                            },
-                            "RenameDatasetActionhtml_report": {
-                                "action_arguments": {
-                                    "newname": "MultiQC processed miRNA: Webpage"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "html_report"
-                            },
-                            "RenameDatasetActionstats": {
-                                "action_arguments": {
-                                    "newname": "MultiQC processed miRNA: Stats"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "stats"
-                            }
+                            "bottom": 574.6499938964844,
+                            "height": 122.5333251953125,
+                            "left": 2418.39990234375,
+                            "right": 2638.39990234375,
+                            "top": 452.1166687011719,
+                            "width": 220,
+                            "x": 2418.39990234375,
+                            "y": 452.1166687011719
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.5+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "b2f1f75d49c4",
-                            "name": "multiqc",
+                            "changeset_revision": "e7aff4a85df5",
+                            "name": "tb_variant_filter",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"comment\": \"\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": \"false\", \"title\": \"miRNA trimmed quality check\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7",
+                        "tool_state": "{\"filter_options\": {\"show_filter_options\": \"no\", \"__current_case__\": 1}, \"filters\": [\"region_filter\", \"close_to_indel_filter\", \"min_depth_filter\"], \"input1\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3.5+galaxy2",
                         "type": "tool",
-                        "uuid": "b8e44272-be04-47ad-8b06-aa0f7d51a38c",
+                        "uuid": "83df9492-d224-420e-8434-24a1a32b9da8",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "html_report",
-                                "uuid": "45f7bd2f-aafe-471c-b41e-431cbbe28781"
+                                "output_name": "output1",
+                                "uuid": "682b8412-8ca5-42c6-bcf2-c5795629471d"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "evolution/mtb_transmission",
+                "path": "topics/evolution/tutorials/mtb_transmission/workflows/Galaxy-Workflow-From_Fastqs_to_VCFs_and_BAMs.ga",
+                "tags": [
+                    "evolution"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "From Fastqs to VCFs and BAMs",
+                "topic_id": "evolution",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/evolution-mtb_transmission/versions/galaxy-workflow-from-fastqs-to-vcfs-and-bams",
+                "tutorial_id": "mtb_transmission",
+                "url": "https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_transmission/workflows/Galaxy-Workflow-From_Fastqs_to_VCFs_and_BAMs.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_transmission/workflows/Galaxy-Workflow-From_Fastqs_to_VCFs_and_BAMs.html",
+                "version": 1,
+                "wfid": "evolution-mtb_transmission",
+                "wfname": "galaxy-workflow-from-fastqs-to-vcfs-and-bams",
+                "workflow": "Galaxy-Workflow-From_Fastqs_to_VCFs_and_BAMs.ga",
+                "workflow_tools": [
+                    "__MERGE_COLLECTION__",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.5+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1"
+                ],
+                "workflowhub_id": "1305"
+            },
+            {
+                "creators": [],
+                "description": "Given a set of VCF files and the reference genome used to do the mapping and SNP calling, create a multifasta file containing the genomes of all samples and calculate the matrix of pairwise SNP distances",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nCollection of VCFs to analyze\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genome of the MTBC ancestor\"]\n  2[label=\"Filter TB variants\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Generate the complete genome of each of the samples\"]\n  2 -> 3 [label=\"output1\"]\n  1 -> 3 [label=\"output\"]\n  kce5dd7a2c33d46b49f0268c2bdfcf31a[color=lightseagreen,label=\"Output\\n#{input_file}\"]\n  3 -> kce5dd7a2c33d46b49f0268c2bdfcf31a\n  4[label=\"Concatenate genomes to build a MSA\"]\n  3 -> 4 [label=\"output_file\"]\n  5[label=\"Keep only variable positions\"]\n  4 -> 5 [label=\"out_file1\"]\n  6[label=\"Calculate SNP distances\"]\n  5 -> 6 [label=\"output_fasta\"]\n}",
+                "history": [
+                    {
+                        "hash": "679ca224ef8e44203f2aec12c805e0e892076d5b",
+                        "message": "update tag",
+                        "num": 2,
+                        "short_hash": "679ca224e",
+                        "unix": "1647423016"
                     },
+                    {
+                        "hash": "2e7ba78522415b81e10f3f5a74144f4f419b218d",
+                        "message": "tweak",
+                        "num": 1,
+                        "short_hash": "2e7ba7852",
+                        "unix": "1647422653"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 35,
-                        "input_connections": {
-                            "select_data|rep_factorName_0|rep_factorLevel_0|countsFile": {
-                                "id": 32,
-                                "output_name": "out_file1"
-                            },
-                            "select_data|rep_factorName_0|rep_factorLevel_1|countsFile": {
-                                "id": 30,
-                                "output_name": "out_file1"
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Collection of VCFs to analyze"
                             }
+                        ],
+                        "label": "Collection of VCFs to analyze",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 602.3000183105469,
+                            "height": 89.10000610351562,
+                            "left": 562.0999755859375,
+                            "right": 782.0999755859375,
+                            "top": 513.2000122070312,
+                            "width": 220,
+                            "x": 562.0999755859375,
+                            "y": 513.2000122070312
                         },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "a3701b5d-9f74-46b4-ae97-51c432933230",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool DESeq2",
-                                "name": "batch_factors"
+                                "description": "",
+                                "name": "Reference genome of the MTBC ancestor"
                             }
                         ],
-                        "label": null,
-                        "name": "DESeq2",
+                        "label": "Reference genome of the MTBC ancestor",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 789.7333526611328,
+                            "height": 111.53334045410156,
+                            "left": 865.0999755859375,
+                            "right": 1085.0999755859375,
+                            "top": 678.2000122070312,
+                            "width": 220,
+                            "x": 865.0999755859375,
+                            "y": 678.2000122070312
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "899dca08-73f5-4ac1-9d19-313414c90a1e",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nCollection of VCFs to analyze\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference genome of the MTBC ancestor\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Filter TB variants\"];\n  0 -->|output| 2;\n  3[\"Generate the complete genome of each of the samples\"];\n  2 -->|output1| 3;\n  1 -->|output| 3;\n  ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a[\"Output\\n#{input_file}\"];\n  3 --> ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a;\n  style ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a stroke:#2c3143,stroke-width:4px;\n  4[\"Concatenate genomes to build a MSA\"];\n  3 -->|output_file| 4;\n  5[\"Keep only variable positions\"];\n  4 -->|out_file1| 5;\n  6[\"Calculate SNP distances\"];\n  5 -->|output_fasta| 6;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "From VCFs to SNP distance matrix",
+                "outputs": [
+                    {
+                        "annotation": "We will ensure at this step that variants to build the MSA are fixed variants and that we low-confidence filter repetitive regions of the MTB genome",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "input1": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Filter TB variants",
+                        "name": "TB Variant Filter",
                         "outputs": [
                             {
-                                "name": "deseq_out",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "plots",
-                                "type": "pdf"
+                                "name": "output1",
+                                "type": "vcf"
                             }
                         ],
                         "position": {
-                            "left": 1460,
-                            "top": 1445.984375
+                            "bottom": 636.7333526611328,
+                            "height": 122.53334045410156,
+                            "left": 866.0999755859375,
+                            "right": 1086.0999755859375,
+                            "top": 514.2000122070312,
+                            "width": 220,
+                            "x": 866.0999755859375,
+                            "y": 514.2000122070312
                         },
                         "post_job_actions": {
-                            "RenameDatasetActiondeseq_out": {
-                                "action_arguments": {
-                                    "newname": "DESeq2 results miRNA"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "deseq_out"
-                            },
-                            "RenameDatasetActionplots": {
+                            "RenameDatasetActionoutput1": {
                                 "action_arguments": {
-                                    "newname": "DESeq2 plots miRNA"
+                                    "newname": "#{input1}.filter.vcf"
                                 },
                                 "action_type": "RenameDatasetAction",
-                                "output_name": "plots"
+                                "output_name": "output1"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "6a3a025714d3",
-                            "name": "deseq2",
+                            "changeset_revision": "3b1e7c170b10",
+                            "name": "tb_variant_filter",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"auto_mean_filter_off\": \"false\", \"batch_factors\": {\"__class__\": \"RuntimeValue\"}, \"esf\": \"\", \"fit_type\": \"1\", \"header\": \"false\", \"many_contrasts\": \"false\", \"normCounts\": \"false\", \"normRLog\": \"false\", \"normVST\": \"false\", \"outlier_filter_off\": \"false\", \"outlier_replace_off\": \"false\", \"pdf\": \"true\", \"select_data\": {\"how\": \"datasets_per_level\", \"__current_case__\": 1, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": \"effects_brassinolide\", \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": \"brassinolide\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"factorLevel\": \"control\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"count\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.11.40.6+galaxy1",
+                        "tool_state": "{\"filter_options\": {\"show_filter_options\": \"yes\", \"__current_case__\": 0, \"region_filter\": [\"pe_ppe\", \"uvp\"], \"indel_window_size\": \"5\", \"min_percentage_alt\": \"90.0\", \"min_depth\": \"30\"}, \"filters\": [\"region_filter\", \"close_to_indel_filter\", \"min_percentage_alt_filter\", \"snv_only_filter\"], \"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.3+galaxy0",
                         "type": "tool",
-                        "uuid": "15632b70-0358-4ca6-918f-f236468dd8d5",
+                        "uuid": "b6ef7486-0dc1-4f0c-ad2d-038f648670b8",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "plots",
-                                "uuid": "b4252bda-8ee4-47f5-85e0-ccacb840c702"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "deseq_out",
-                                "uuid": "55ea0b93-52e0-4d07-a64f-4db6e39f42ab"
+                                "output_name": "output1",
+                                "uuid": "87f8ad83-d43e-4e44-8bed-33415b7add79"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1",
+                        "annotation": "The complete genome of each of the samples is generated by inserting the SNPs defined in the respective VCF in the reference genome that was used for mapping and SNP calling",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy2",
                         "errors": null,
-                        "id": 38,
+                        "id": 3,
                         "input_connections": {
-                            "header_criteria|identifiers": {
-                                "id": 36,
-                                "output_name": "out_file1"
+                            "input_file": {
+                                "id": 2,
+                                "output_name": "output1"
                             },
-                            "input": {
-                                "id": 5,
+                            "reference_source|fasta_ref": {
+                                "id": 1,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Filter FASTA",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool bcftools consensus",
+                                "name": "input_file"
+                            },
+                            {
+                                "description": "runtime parameter for tool bcftools consensus",
+                                "name": "reference_source"
+                            },
+                            {
+                                "description": "runtime parameter for tool bcftools consensus",
+                                "name": "sec_default"
+                            }
+                        ],
+                        "label": "Generate the complete genome of each of the samples",
+                        "name": "bcftools consensus",
                         "outputs": [
                             {
-                                "name": "output",
+                                "name": "output_file",
                                 "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 2880,
-                            "top": 1662.984375
+                            "bottom": 734.0333557128906,
+                            "height": 209.83334350585938,
+                            "left": 1144.0999755859375,
+                            "right": 1364.0999755859375,
+                            "top": 524.2000122070312,
+                            "width": 220,
+                            "x": 1144.0999755859375,
+                            "y": 524.2000122070312
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput": {
+                            "RenameDatasetActionoutput_file": {
                                 "action_arguments": {
-                                    "newname": "Downregulated mRNA sequences"
+                                    "newname": "#{input_file}"
                                 },
                                 "action_type": "RenameDatasetAction",
-                                "output_name": "output"
+                                "output_name": "output_file"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "3c623e81be77",
-                            "name": "filter_by_fasta_ids",
-                            "owner": "galaxyp",
+                            "changeset_revision": "a87ae767b01d",
+                            "name": "bcftools_consensus",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"dedup\": \"false\", \"header_criteria\": {\"header_criteria_select\": \"id_list\", \"__current_case__\": 1, \"identifiers\": {\"__class__\": \"ConnectedValue\"}, \"id_regex\": {\"find\": \"pattern\", \"__current_case__\": 1, \"pattern\": \"GENE=(AT.{7})\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"output_discarded\": \"false\", \"sequence_criteria\": {\"sequence_criteria_select\": \"\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1",
+                        "tool_state": "{\"chain\": \"false\", \"input_file\": {\"__class__\": \"RuntimeValue\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"RuntimeValue\"}}, \"rename\": \"true\", \"sec_default\": {\"mask\": {\"__class__\": \"RuntimeValue\"}, \"iupac_codes\": \"false\", \"sample\": \"\", \"select_haplotype\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9+galaxy2",
                         "type": "tool",
-                        "uuid": "4d1f1434-2cd7-4025-aa31-955646f26ae0",
+                        "uuid": "967af052-882a-427c-825e-e88f59ac50b3",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "e8c830ca-388d-43e9-a30a-6ce4e1db2103"
+                                "label": "#{input_file}",
+                                "output_name": "output_file",
+                                "uuid": "ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": "cat1",
+                        "annotation": "All genomes are concatenated in a single multifasta file. Because all o them have the same length, this may be seen as a multiple sequence alignment.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
                         "errors": null,
-                        "id": 44,
+                        "id": 4,
                         "input_connections": {
-                            "input1": {
-                                "id": 43,
-                                "output_name": "output"
-                            },
-                            "queries_0|input2": {
-                                "id": 42,
-                                "output_name": "output"
+                            "inputs": {
+                                "id": 3,
+                                "output_name": "output_file"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Concatenate datasets",
+                                "name": "inputs"
+                            }
+                        ],
+                        "label": "Concatenate genomes to build a MSA",
                         "name": "Concatenate datasets",
                         "outputs": [
                             {
@@ -163947,118 +164058,174 @@
                             }
                         ],
                         "position": {
-                            "left": 2880,
-                            "top": 1882.984375
+                            "bottom": 647.7333526611328,
+                            "height": 122.53334045410156,
+                            "left": 1519.0999755859375,
+                            "right": 1739.0999755859375,
+                            "top": 525.2000122070312,
+                            "width": 220,
+                            "x": 1519.0999755859375,
+                            "y": 525.2000122070312
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Upregulated miRNA sequences"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f46f0e4f75c4",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": "cat1",
-                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [{\"__index__\": 0, \"input2\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
+                        "tool_state": "{\"inputs\": {\"__class__\": \"RuntimeValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.1",
                         "type": "tool",
-                        "uuid": "97871054-6cba-4834-bc56-26a7f37be2b8",
+                        "uuid": "e0b536e1-c56c-41ed-9600-905d0cf58e97",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "out_file1",
-                                "uuid": "800ea133-2a03-469d-875e-24b0635c3cd2"
+                                "uuid": "c1fe096c-2693-4128-8139-4285bcd394ad"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1",
+                        "annotation": "Discard invariant positions from the MSA to simplify the file so only contains positions with at least one SNP in at least one strain.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0",
                         "errors": null,
-                        "id": 45,
+                        "id": 5,
                         "input_connections": {
-                            "d": {
-                                "id": 38,
-                                "output_name": "output"
-                            },
-                            "f": {
-                                "id": 44,
+                            "input_fasta": {
+                                "id": 4,
                                 "output_name": "out_file1"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "TargetFinder",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Finds SNP sites",
+                                "name": "input_fasta"
+                            }
+                        ],
+                        "label": "Keep only variable positions",
+                        "name": "Finds SNP sites",
+                        "outputs": [
+                            {
+                                "name": "output_fasta",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 647.1666870117188,
+                            "height": 144.9666748046875,
+                            "left": 1843.0999755859375,
+                            "right": 2063.0999755859375,
+                            "top": 502.20001220703125,
+                            "width": 220,
+                            "x": 1843.0999755859375,
+                            "y": 502.20001220703125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "5804f786060d",
+                            "name": "snp_sites",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input_fasta\": {\"__class__\": \"RuntimeValue\"}, \"out_type\": {\"ot_select\": \"alignment\", \"__current_case__\": 0, \"formats\": [\"-m\"], \"b\": \"false\", \"c\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.5.1+galaxy0",
+                        "type": "tool",
+                        "uuid": "3718c889-5f1c-4cc7-977c-eaa564753c9b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_fasta",
+                                "uuid": "2931ef4f-28d7-4701-bee0-292177bf0841"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "From the MSA. Calculate pairwise SNP distances between samples. ",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.6.3+galaxy0",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "input": {
+                                "id": 5,
+                                "output_name": "output_fasta"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool SNP distance matrix",
+                                "name": "input"
+                            }
+                        ],
+                        "label": "Calculate SNP distances",
+                        "name": "SNP distance matrix",
                         "outputs": [
                             {
-                                "name": "output_file",
-                                "type": "txt"
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 3157.984375,
-                            "top": 1712.984375
+                            "bottom": 662.6000213623047,
+                            "height": 167.40000915527344,
+                            "left": 2173.10009765625,
+                            "right": 2393.10009765625,
+                            "top": 495.20001220703125,
+                            "width": 220,
+                            "x": 2173.10009765625,
+                            "y": 495.20001220703125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.6.3+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "c9d56748fbde",
-                            "name": "targetfinder",
-                            "owner": "rnateam",
+                            "changeset_revision": "1959cc43b414",
+                            "name": "snp_dists",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"c\": \"4.0\", \"d\": {\"__class__\": \"ConnectedValue\"}, \"f\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"classic\", \"r\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.0+galaxy1",
+                        "tool_state": "{\"a\": \"false\", \"b\": \"false\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"k\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.6.3+galaxy0",
                         "type": "tool",
-                        "uuid": "d81d9ea9-a085-478f-a148-0c31083f16fc",
+                        "uuid": "e5f85c1b-43cc-417e-8e02-79ecc511b4ec",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_file",
-                                "uuid": "2a3de11c-addc-4e1a-a156-f760f861ce64"
+                                "output_name": "output",
+                                "uuid": "2dff3ea9-ce2d-48eb-b9eb-90b3b6034ae6"
                             }
                         ]
                     }
                 ],
-                "parent_id": "transcriptomics/mirna-target-finder",
-                "path": "topics/transcriptomics/tutorials/mirna-target-finder/workflows/main_workflow.ga",
+                "parent_id": "evolution/mtb_transmission",
+                "path": "topics/evolution/tutorials/mtb_transmission/workflows/main_workflow.ga",
                 "tags": [
-                    "transcriptomics",
-                    "mirna",
-                    "arabidopsis"
+                    "evolution"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Plant bulk RNA-Seq workflow",
-                "topic_id": "transcriptomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-mirna-target-finder/versions/main-workflow",
-                "tutorial_id": "mirna-target-finder",
-                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/mirna-target-finder/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/mirna-target-finder/workflows/main_workflow.html",
-                "version": 3,
-                "wfid": "transcriptomics-mirna-target-finder",
+                "title": "From VCFs to SNP distance matrix",
+                "topic_id": "evolution",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/evolution-mtb_transmission/versions/main-workflow",
+                "tutorial_id": "mtb_transmission",
+                "url": "https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_transmission/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_transmission/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "evolution-mtb_transmission",
                 "wfname": "main-workflow",
                 "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "Filter1",
-                    "__MERGE_COLLECTION__",
-                    "cat1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.14.1.2+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-                    "toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_mapper/rbc_mirdeep2_mapper/2.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_quantifier/rbc_mirdeep2_quantifier/2.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.6.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0"
                 ],
-                "workflowhub_id": "1318"
+                "workflowhub_id": "1309"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/4710649"
+        "zenodo_link": "https://zenodo.org/record/6010176"
     },
     {
         "admin_install": {
@@ -164067,653 +164234,428 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "taxonomy_krona_chart",
-                    "owner": "crs4",
-                    "revisions": "1334cb4c6b68",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastqc",
+                    "name": "bowtie2",
                     "owner": "devteam",
-                    "revisions": "e7b2202befea",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "datamash_reverse",
-                    "owner": "iuc",
-                    "revisions": "0f1724dd59d2",
-                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "revisions": "03e9b2fbc005",
+                    "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fastp",
+                    "name": "bakta",
                     "owner": "iuc",
-                    "revisions": "dbf9c561ef29",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "728dacaf08a9",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "kraken2",
+                    "name": "jbrowse",
                     "owner": "iuc",
-                    "revisions": "328c607150ff",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "revisions": "a6e57ff585c0",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "multiqc",
+                    "name": "tbl2gff3",
                     "owner": "iuc",
-                    "revisions": "5e33b465d8d5",
-                    "tool_panel_section_label": "Quality Control",
+                    "revisions": "4a7f4b0cc0a3",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "porechop",
-                    "owner": "iuc",
-                    "revisions": "93d623d9979c",
-                    "tool_panel_section_label": "Nanopore",
+                    "name": "staramr",
+                    "owner": "nml",
+                    "revisions": "3b22de20bd4b",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: taxonomy_krona_chart\n  owner: crs4\n  revisions: 1334cb4c6b68\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_reverse\n  owner: iuc\n  revisions: 0f1724dd59d2\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: dbf9c561ef29\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: 328c607150ff\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 5e33b465d8d5\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: porechop\n  owner: iuc\n  revisions: 93d623d9979c\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bowtie2\n  owner: devteam\n  revisions: 03e9b2fbc005\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bakta\n  owner: iuc\n  revisions: 728dacaf08a9\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbl2gff3\n  owner: iuc\n  revisions: 4a7f4b0cc0a3\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: staramr\n  owner: nml\n  revisions: 3b22de20bd4b\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "bazante1",
+                "bebatut"
+            ],
+            "editing": [
+                "hexylena",
+                "bazante1",
+                "shiltemann",
+                "miaomiaozhou88"
+            ],
+            "funding": [
+                "avans-atgm",
+                "abromics"
+            ]
+        },
         "contributors": [
             {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
+                "affiliations": [
+                    "avans-atgm"
+                ],
+                "id": "bazante1",
+                "joined": "2020-12",
+                "name": "Bazante Sanders",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
                     "elixir-europe"
                 ],
-                "id": "gallardoalba",
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "affiliations": [
+                    "avans-atgm"
+                ],
+                "id": "bazante1",
+                "joined": "2020-12",
+                "name": "Bazante Sanders",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
+            },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
+            {
+                "email": "m.zhou1@avans.nl",
+                "id": "miaomiaozhou88",
+                "joined": "2020-12",
+                "name": "Miaomiao Zhou",
+                "orcid": "0000-0003-4426-1758",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/miaomiaozhou88/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/miaomiaozhou88.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/logo-avans.png",
+                "former_members": [
+                    "dirowa",
+                    "hexylena"
+                ],
+                "id": "avans-atgm",
                 "joined": "2020-11",
-                "name": "Crist\u00f3bal Gallardo",
-                "orcid": "0000-0002-5752-2155",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
+                "members": [
+                    "bazante1"
+                ],
+                "name": "Avans Hogeschool",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/",
+                "ror": "015d5s513",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/abromics.png",
+                "funder": true,
+                "github": false,
+                "id": "abromics",
+                "joined": "2024-01",
+                "name": "ABRomics",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abromics/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/abromics.json"
             }
         ],
-        "dir": "topics/microbiome/tutorials/nanopore-16S-metagenomics",
+        "dir": "topics/genome-annotation/tutorials/amr-gene-detection",
         "edam_ontology": [
-            "topic_3697",
-            "topic_0637",
+            "topic_3673",
+            "topic_3305",
+            "topic_0622",
+            "topic_3301",
             "topic_0080",
-            "topic_4038"
+            "topic_3324",
+            "topic_4013"
         ],
         "edam_operation": [
-            "Visualisation",
-            "Sequencing quality control",
-            "Sequence contamination filtering",
-            "Validation",
-            "Sequence composition calculation",
-            "Taxonomic classification",
-            "Statistical calculation"
+            "Genome visualisation",
+            "Genome annotation",
+            "Read mapping"
         ],
         "edam_topic": [
-            "Microbial ecology",
-            "Taxonomy",
-            "Sequence analysis"
+            "Whole genome sequencing",
+            "Public health and epidemiology",
+            "Genomics",
+            "Microbiology",
+            "Sequence analysis",
+            "Infectious disease",
+            "Antimicrobial Resistance"
         ],
         "exact_supported_servers": [
+            "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
+            "UseGalaxy.fr"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": true,
-        "id": "microbiome/nanopore-16S-metagenomics",
-        "inexact_supported_servers": [
-            "GalaxyTrakr",
-            "UseGalaxy.cz"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "We learned to use MinION Nanopore data for analyzing the health status of the soil",
-            "We preprocessed Nanopore sequences in order to improve their quality"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-07-31",
-        "objectives": [
-            "Use Nanopore data for studying soil metagenomics",
-            "Analyze and preprocess Nanopore reads",
-            "Use Kraken2 to assign a taxonomic labels"
-        ],
-        "pageviews": 3314,
-        "pub_date": "2020-11-24",
-        "questions": [
-            "How can we analyse the health status of the soil?",
-            "How do plants modify the composition of microbial communities?"
-        ],
-        "redirect_from": [
-            "/topics/metagenomics/tutorials/nanopore-16S-metagenomics/tutorial",
-            "/short/microbiome/nanopore-16S-metagenomics",
-            "/short/T00207",
-            "/short/T00392"
-        ],
-        "short_id": "T00392",
-        "short_tools": [
-            "fastp",
-            "multiqc",
-            "taxonomy_krona_chart",
-            "fastqc",
-            "kraken2",
-            "tp_replace_in_line",
-            "Remove beginning1",
-            "datamash_reverse",
-            "porechop"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "metabarcoding",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "metabarcoding",
-            "16S",
-            "nanopore",
-            "microgalaxy",
-            "plants"
-        ],
-        "time_estimation": "2H",
-        "title": "16S Microbial analysis with Nanopore data",
-        "tools": [
-            "Remove beginning1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.0.8_beta+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3"
-        ],
-        "topic_name": "microbiome",
-        "topic_name_human": "Microbiome",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "nanopore-16S-metagenomics",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.json"
-        },
-        "version": 5,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 168,
-        "visitors": 2344,
-        "workflows": [
+        "follow_up_training": [
             {
-                "creators": [],
-                "description": "16S rRNA analysis with Nanopore reads",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  1[label=\"FastQC\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Porechop\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"MultiQC\"]\n  1 -> 3 [label=\"text_file\"]\n  4[label=\"fastp\"]\n  2 -> 4 [label=\"outfile\"]\n  5[label=\"FastQC\"]\n  4 -> 5 [label=\"out1\"]\n  6[label=\"Kraken2\"]\n  4 -> 6 [label=\"out1\"]\n  7[label=\"MultiQC\"]\n  5 -> 7 [label=\"text_file\"]\n  8[label=\"Reverse\"]\n  6 -> 8 [label=\"report_output\"]\n  9[label=\"Replace Text\"]\n  8 -> 9 [label=\"out_file\"]\n  10[label=\"Remove beginning\"]\n  9 -> 10 [label=\"outfile\"]\n  11[label=\"Krona pie chart\"]\n  10 -> 11 [label=\"out_file1\"]\n}",
-                "history": [
-                    {
-                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
-                        "message": "Rename metagenomics topic to microbiome",
-                        "num": 1,
-                        "short_hash": "0e0a2f2cc",
-                        "unix": "1704901629"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Input Dataset Collection"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 10
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "18fc8b44-c752-41a0-a17c-e03797a5fab1",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"FastQC\"];\n  0 -->|output| 1;\n  2[\"Porechop\"];\n  0 -->|output| 2;\n  3[\"MultiQC\"];\n  1 -->|text_file| 3;\n  4[\"fastp\"];\n  2 -->|outfile| 4;\n  5[\"FastQC\"];\n  4 -->|out1| 5;\n  6[\"Kraken2\"];\n  4 -->|out1| 6;\n  7[\"MultiQC\"];\n  5 -->|text_file| 7;\n  8[\"Reverse\"];\n  6 -->|report_output| 8;\n  9[\"Replace Text\"];\n  8 -->|out_file| 9;\n  10[\"Remove beginning\"];\n  9 -->|outfile| 10;\n  11[\"Krona pie chart\"];\n  10 -->|out_file1| 11;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Training: 16S rRNA Analysis with Nanopore Sequencing Reads",
-                "outputs": [],
-                "parent_id": "microbiome/nanopore-16S-metagenomics",
-                "path": "topics/microbiome/tutorials/nanopore-16S-metagenomics/workflows/main_workflow.ga",
-                "tags": [
-                    "microbiome"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Training: 16S rRNA Analysis with Nanopore Sequencing Reads",
-                "topic_id": "microbiome",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-nanopore-16S-metagenomics/versions/main-workflow",
-                "tutorial_id": "nanopore-16S-metagenomics",
-                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/nanopore-16S-metagenomics/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/nanopore-16S-metagenomics/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "microbiome-nanopore-16S-metagenomics",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "Remove beginning1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.0.8_beta+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3"
+                "topic_name": "visualisation",
+                "tutorials": [
+                    "jbrowse"
                 ],
-                "workflowhub_id": "1064"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/4274812"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "flye",
-                    "owner": "bgruening",
-                    "revisions": "291923e6f276",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "racon",
-                    "owner": "bgruening",
-                    "revisions": "78c533842eeb",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "5ec9f6bceaee",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bandage",
-                    "owner": "iuc",
-                    "revisions": "ddddce450736",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "busco",
-                    "owner": "iuc",
-                    "revisions": "ea8146ee148f",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_stats",
-                    "owner": "iuc",
-                    "revisions": "0dbb995c7d35",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastp",
-                    "owner": "iuc",
-                    "revisions": "c59d48774d03",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "genomescope",
-                    "owner": "iuc",
-                    "revisions": "01210c4e9144",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "medaka_consensus_pipeline",
-                    "owner": "iuc",
-                    "revisions": "fc8804320156",
-                    "tool_panel_section_label": "Nanopore",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "meryl",
-                    "owner": "iuc",
-                    "revisions": "29dabd8db6f2",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "minimap2",
-                    "owner": "iuc",
-                    "revisions": "be1d967337e4",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "abfd8a6544d7",
-                    "tool_panel_section_label": "Quality Control",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "nanoplot",
-                    "owner": "iuc",
-                    "revisions": "a02b8b3f5a0c",
-                    "tool_panel_section_label": "Nanopore",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "quast",
-                    "owner": "iuc",
-                    "revisions": "72472698a2df",
-                    "tool_panel_section_label": "Assembly",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: flye\n  owner: bgruening\n  revisions: 291923e6f276\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: racon\n  owner: bgruening\n  revisions: 78c533842eeb\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: ea8146ee148f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n  owner: iuc\n  revisions: 0dbb995c7d35\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: c59d48774d03\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: genomescope\n  owner: iuc\n  revisions: 01210c4e9144\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: medaka_consensus_pipeline\n  owner: iuc\n  revisions: fc8804320156\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n  owner: iuc\n  revisions: 29dabd8db6f2\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: be1d967337e4\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: abfd8a6544d7\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: a02b8b3f5a0c\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 72472698a2df\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/largegenome/tutorial.json",
-        "contributors": [
+                "type": "internal"
+            },
             {
-                "id": "annasyme",
-                "joined": "2017-09",
-                "name": "Anna Syme",
-                "orcid": "0000-0002-9906-0673",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "history-to-workflow"
+                ],
+                "type": "internal"
             }
         ],
-        "dir": "topics/assembly/tutorials/largegenome",
-        "edam_operation": [
-            "Visualisation",
-            "Sequencing quality control",
-            "Sequence assembly validation",
-            "Sequence composition calculation",
-            "Pairwise sequence alignment",
-            "Sequence assembly visualisation",
-            "Transcriptome assembly",
-            "Cross-assembly",
-            "Validation",
-            "Genome assembly",
-            "Base-calling",
-            "Sequence assembly",
-            "Statistical calculation",
-            "Scaffolding",
-            "Sequence contamination filtering",
-            "De-novo assembly",
-            "Box-Whisker plot plotting",
-            "Scatter plot plotting",
-            "Mapping assembly",
-            "Variant calling"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
         "hands_on": true,
-        "id": "assembly/largegenome",
+        "id": "genome-annotation/amr-gene-detection",
         "inexact_supported_servers": [
-            "UseGalaxy.cz"
+            "Galaxy@AuBi",
+            "UseGalaxy.org (Main)"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "We can assemble long reads from plant or animal species into large contigs",
-            "These contigs can be polished with both long and short reads",
-            "We can assess the quality of this assembly with various tools"
+            "staramr is a powerful tool to predict ARGs and plasmid genes",
+            "Visualization of the ARGs and plasmid genes in their genomic context helps to make sense of the data"
         ],
         "layout": "tutorial_hands_on",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-31",
+        "mod_date": "2024-09-27",
         "objectives": [
-            "Assemble a large genome from long reads",
-            "Polish the assembly",
-            "Assess the quality of the assembly"
+            "Run a series of tool to assess the presence of antimicrobial resistance genes (ARG)",
+            "Get information about ARGs",
+            "Visualize the ARGs and plasmid genes in their genomic context"
         ],
-        "pageviews": 4728,
-        "pub_date": "2023-03-06",
+        "pageviews": 1576,
+        "pub_date": "2024-01-23",
         "questions": [
-            "How can we assemble a large plant or animal genome?"
+            "Which resistance genes are on a bacterial genome?",
+            "Where are the genes located on the genome?"
         ],
         "recordings": [
             {
+                "bot-timestamp": 1727199012,
                 "captioners": [
-                    "annasyme"
+                    "SaimMomin12"
                 ],
-                "date": "2023-05-16",
-                "galaxy_version": "23.01",
-                "length": "25M",
+                "date": "2024-09-24",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "26M",
                 "speakers": [
-                    "annasyme"
+                    "SaimMomin12"
                 ],
-                "youtube_id": "BM70nvwWjOY"
+                "youtube_id": "hfiYCIcD0ww"
             }
         ],
-        "short_id": "T00331",
+        "short_id": "T00401",
         "short_tools": [
-            "barchart_gnuplot",
-            "nanoplot",
-            "fastp",
-            "multiqc",
-            "busco",
-            "racon",
-            "flye",
-            "quast",
-            "fasta-stats",
-            "fastqc",
-            "genomescope",
-            "meryl",
-            "minimap2",
-            "bandage_image",
-            "medaka_consensus_pipeline"
+            "jbrowse",
+            "tbl2gff3",
+            "upload1",
+            "Grep1",
+            "staramr_search",
+            "bakta",
+            "bowtie2"
         ],
         "slides": false,
         "slides_recordings": false,
+        "subtopic": "prokaryote",
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
                 }
             ],
             "inexact": [
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
         "tags": [
-            "assembly",
-            "polishing",
-            "nanopore",
-            "plants"
+            "gmod",
+            "illumina",
+            "amr",
+            "one-health",
+            "jbrowse1",
+            "microgalaxy"
         ],
         "time_estimation": "2h",
-        "title": "Large genome assembly and polishing",
+        "title": "Identification of AMR genes in an assembled bacterial genome",
         "tools": [
-            "barchart_gnuplot",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
-            "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
+            "Grep1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2",
+            "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1",
+            "upload1"
         ],
-        "topic_name": "assembly",
-        "topic_name_human": "Assembly",
+        "topic_name": "genome-annotation",
+        "topic_name_human": "Genome Annotation",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "largegenome",
+        "tutorial_name": "amr-gene-detection",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/largegenome/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/largegenome/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/largegenome/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.json"
         },
-        "version": 11,
+        "version": 6,
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 131,
-        "visitors": 3651,
+        "visit_duration": 165,
+        "visitors": 1138,
         "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
+                        "identifier": "https://orcid.org/0000-0003-2255-1631",
+                        "name": "Bazante Sanders"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0001-9852-1987",
+                        "name": "B\u00e9r\u00e9nice Batut"
                     }
                 ],
-                "description": "",
+                "description": "Identification of AMR genes in an assembled bacterial genome",
                 "features": {
                     "comments": false,
-                    "parameters": true,
-                    "report": {
-                        "markdown": "\n# Workflow Report for Assembly Polishing\n\n## Workflow steps\n\n```galaxy\nworkflow_display()\n```\n\n## Fasta statistics after Racon long-read polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Racon long read polish\")\n```\n\n\n## Fasta statistics after Medaka polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Medaka polish\")\n```\n\n## Fasta statistics after Racon short-read polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Racon short read polish\")\n```\n\n\n\n\n"
-                    },
-                    "subworkflows": true
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"]\n  4[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with long reads, x4 - upgraded\"]\n  0 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Medaka polish\"]\n  4 -> 5 [label=\"Assembly polished by long reads using Racon\"]\n  1 -> 5 [label=\"output\"]\n  ke3136060bce74af387c49dcbb0d1f531[color=lightseagreen,label=\"Output\\nAssembly polished by long reads using Medaka\"]\n  5 -> ke3136060bce74af387c49dcbb0d1f531\n  6[label=\"Fasta statistics after Racon long read polish\"]\n  4 -> 6 [label=\"Assembly polished by long reads using Racon\"]\n  7[label=\"Fasta statistics after Medaka polish\"]\n  5 -> 7 [label=\"out_consensus\"]\n  8[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with Illumina reads R1 only, x2 - upgraded\"]\n  5 -> 8 [label=\"out_consensus\"]\n  3 -> 8 [label=\"output\"]\n  9[label=\"Fasta statistics after Racon short read polish\"]\n  8 -> 9 [label=\"Assembly polished by short reads using Racon\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncontigs\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nforward_reads\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreverse_reads\"]\n  3[label=\"staramr\"]\n  0 -> 3 [label=\"output\"]\n  k000e2ab992db45bba0efecccf06da616[color=lightseagreen,label=\"Output\\nstararm_detailed_summary\"]\n  3 -> k000e2ab992db45bba0efecccf06da616\n  4[label=\"Bakta\"]\n  0 -> 4 [label=\"output\"]\n  kc848b1eb72624627b7a705a13b968935[color=lightseagreen,label=\"Output\\nbakta_annotation_summary\"]\n  4 -> kc848b1eb72624627b7a705a13b968935\n  5[label=\"Bowtie2\"]\n  1 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  k352e63d38aca4dff878c10497f65bb74[color=lightseagreen,label=\"Output\\nbowtie_mapping_stats\"]\n  5 -> k352e63d38aca4dff878c10497f65bb74\n  6[label=\"Select\"]\n  3 -> 6 [label=\"detailed_summary\"]\n  7[label=\"Table to GFF3\"]\n  6 -> 7 [label=\"out_file1\"]\n  8[label=\"JBrowse\"]\n  4 -> 8 [label=\"annotation_gff3\"]\n  7 -> 8 [label=\"output\"]\n  5 -> 8 [label=\"output\"]\n  k3c3bd5fd419c45b2afcdc6d02af82695[color=lightseagreen,label=\"Output\\njbrowse_output\"]\n  8 -> k3c3bd5fd419c45b2afcdc6d02af82695\n}",
                 "history": [
                     {
-                        "hash": "091a0834c77e69841f4d07570420c632c6c5043c",
-                        "message": "Update Galaxy-Workflow-Assembly_polishing.ga",
-                        "num": 5,
-                        "short_hash": "091a0834c",
-                        "unix": "1715074278"
-                    },
-                    {
-                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
-                        "message": "new versions of workflows",
+                        "hash": "597f8ce954083c7cd4e43765b6c4709619637e6a",
+                        "message": "Add Bazante's ORCID",
                         "num": 4,
-                        "short_hash": "e8ddbcdd5",
-                        "unix": "1714537936"
+                        "short_hash": "597f8ce95",
+                        "unix": "1706018263"
                     },
                     {
-                        "hash": "f294a05b57afbe9ec436008d1d2571f6d42fb977",
-                        "message": "Rename Galaxy-Workflow-Assembly_polishing.ga to Galaxy-Workflow-Assembly_polishing_old.ga",
+                        "hash": "03e4290900ade23b2dffb3f61ea2875a64f2c396",
+                        "message": "Fix workflows",
                         "num": 3,
-                        "short_hash": "f294a05b5",
-                        "unix": "1714537220"
+                        "short_hash": "03e429090",
+                        "unix": "1706004257"
                     },
                     {
-                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
-                        "message": "add/complete creator info on workflows",
+                        "hash": "c88bcbb6f04ad1847e0747f7fb9256ee0ec858de",
+                        "message": "Add license and creator to workflows",
                         "num": 2,
-                        "short_hash": "62e77944b",
-                        "unix": "1676627603"
+                        "short_hash": "c88bcbb6f",
+                        "unix": "1705678137"
                     },
                     {
-                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
-                        "message": "large genome tutorial",
+                        "hash": "6d6129376b624fe20278f8df09b13cae881c5484",
+                        "message": "Expand the AMR detection tutorial",
                         "num": 1,
-                        "short_hash": "9fcb3aeec",
-                        "unix": "1665123856"
+                        "short_hash": "6d6129376",
+                        "unix": "1705334494"
                     }
                 ],
                 "inputs": [
@@ -164726,21 +164668,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Assembly to be polished"
+                                "name": "contigs"
                             }
                         ],
-                        "label": "Assembly to be polished",
-                        "name": "Input dataset",
+                        "label": "contigs",
+                        "name": "contigs",
                         "outputs": [],
                         "position": {
-                            "left": 19.464939294568495,
-                            "top": 0.0
+                            "left": 0,
+                            "top": 258
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"name\": \"contigs\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "52bc9ac4-ac3c-48eb-aead-94a0a14417fc",
+                        "uuid": "a18c5e52-124f-4480-80b4-ea5936618bc6",
                         "when": null,
                         "workflow_outputs": []
                     },
@@ -164753,21 +164695,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "long reads"
+                                "name": "forward_reads"
                             }
                         ],
-                        "label": "long reads",
-                        "name": "Input dataset",
+                        "label": "forward_reads",
+                        "name": "forward_reads",
                         "outputs": [],
                         "position": {
-                            "left": 0.0,
-                            "top": 142.48340578478533
+                            "left": 0.003423507807786663,
+                            "top": 600.9912432161087
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"name\": \"forward_reads\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "688866c4-de9b-4b78-8df3-b169d28b1617",
+                        "uuid": "edd7c009-b0f1-403d-9438-f675bd61d30a",
                         "when": null,
                         "workflow_outputs": []
                     },
@@ -164780,865 +164722,604 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "minimap setting (for long reads)"
+                                "name": "reverse_reads"
                             }
                         ],
-                        "label": "minimap setting (for long reads)",
-                        "name": "Input parameter",
+                        "label": "reverse_reads",
+                        "name": "reverse_reads",
                         "outputs": [],
                         "position": {
-                            "left": 13.133522093825794,
-                            "top": 247.1519749531627
+                            "left": 0,
+                            "top": 724
                         },
                         "tool_id": null,
-                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"name\": \"reverse_reads\"}",
                         "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "c1f18b5c-e8db-4046-b876-9b28a77cf66e",
+                        "type": "data_input",
+                        "uuid": "595db730-f37d-4314-85a3-e10dfb11e209",
                         "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "ce393bcf-42e3-43ee-9056-a99e8c077a29"
-                            }
-                        ]
-                    },
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nforward_reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nreverse_reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"staramr\"];\n  0 -->|output| 3;\n  000e2ab9-92db-45bb-a0ef-ecccf06da616[\"Output\\nstararm_detailed_summary\"];\n  3 --> 000e2ab9-92db-45bb-a0ef-ecccf06da616;\n  style 000e2ab9-92db-45bb-a0ef-ecccf06da616 stroke:#2c3143,stroke-width:4px;\n  4[\"Bakta\"];\n  0 -->|output| 4;\n  c848b1eb-7262-4627-b7a7-05a13b968935[\"Output\\nbakta_annotation_summary\"];\n  4 --> c848b1eb-7262-4627-b7a7-05a13b968935;\n  style c848b1eb-7262-4627-b7a7-05a13b968935 stroke:#2c3143,stroke-width:4px;\n  5[\"Bowtie2\"];\n  1 -->|output| 5;\n  2 -->|output| 5;\n  0 -->|output| 5;\n  352e63d3-8aca-4dff-878c-10497f65bb74[\"Output\\nbowtie_mapping_stats\"];\n  5 --> 352e63d3-8aca-4dff-878c-10497f65bb74;\n  style 352e63d3-8aca-4dff-878c-10497f65bb74 stroke:#2c3143,stroke-width:4px;\n  6[\"Select\"];\n  3 -->|detailed_summary| 6;\n  7[\"Table to GFF3\"];\n  6 -->|out_file1| 7;\n  8[\"JBrowse\"];\n  4 -->|annotation_gff3| 8;\n  7 -->|output| 8;\n  5 -->|output| 8;\n  3c3bd5fd-419c-45b2-afcd-c6d02af82695[\"Output\\njbrowse_output\"];\n  8 --> 3c3bd5fd-419c-45b2-afcd-c6d02af82695;\n  style 3c3bd5fd-419c-45b2-afcd-c6d02af82695 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "mrsa AMR gene detection",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1",
                         "errors": null,
                         "id": 3,
-                        "input_connections": {},
-                        "inputs": [
+                        "input_connections": {
+                            "genomes": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "staramr",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Illumina reads R1"
+                                "name": "blast_hits",
+                                "type": "input"
+                            },
+                            {
+                                "name": "mlst",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "summary",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "detailed_summary",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "resfinder",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "plasmidfinder",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "settings",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "excel",
+                                "type": "xlsx"
                             }
                         ],
-                        "label": "Illumina reads R1",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 617.719019724734,
-                            "top": 600.0866464299372
+                            "left": 290.00083115418806,
+                            "top": 261
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ea859a58-c81a-4ef6-9bd2-4ef2f17bb5a9",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3b22de20bd4b",
+                            "name": "staramr",
+                            "owner": "nml",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"pid_threshold\": \"98.0\", \"plength_resfinder\": \"60.0\", \"plength_pointfinder\": \"95.0\", \"plength_plasmidfinder\": \"60.0\", \"genome_size_lower_bound\": \"4000000\", \"genome_size_upper_bound\": \"6000000\", \"minimum_N50_value\": \"10000\", \"minimum_contig_length\": \"300\", \"unacceptable_number_contigs\": \"1000\", \"report_all_blast\": false, \"exclude_negatives\": false, \"exclude_resistance_phenotypes\": false, \"mlst_scheme\": \"auto\", \"exclude_genes\": {\"exclude_genes_condition\": \"default\", \"__current_case__\": 0}, \"complex_mutations\": {\"complex_mutations_condition\": \"default\", \"__current_case__\": 0}, \"plasmidfinder_type\": \"include_all\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"genomes\": {\"__class__\": \"ConnectedValue\"}, \"pointfinder_db\": {\"use_pointfinder\": \"disabled\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.10.0+galaxy1",
+                        "type": "tool",
+                        "uuid": "2554da56-e9f9-4e65-98b6-25b4a2861df9",
                         "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with long reads, x4 - upgraded\"];\n  style 4 fill:#edd,stroke:#900,stroke-width:4px;\n  0 -->|output| 4;\n  1 -->|output| 4;\n  2 -->|output| 4;\n  5[\"Medaka polish\"];\n  4 -->|Assembly polished by long reads using Racon| 5;\n  1 -->|output| 5;\n  e3136060-bce7-4af3-87c4-9dcbb0d1f531[\"Output\\nAssembly polished by long reads using Medaka\"];\n  5 --> e3136060-bce7-4af3-87c4-9dcbb0d1f531;\n  style e3136060-bce7-4af3-87c4-9dcbb0d1f531 stroke:#2c3143,stroke-width:4px;\n  6[\"Fasta statistics after Racon long read polish\"];\n  4 -->|Assembly polished by long reads using Racon| 6;\n  7[\"Fasta statistics after Medaka polish\"];\n  5 -->|out_consensus| 7;\n  8[\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with Illumina reads R1 only, x2 - upgraded\"];\n  style 8 fill:#edd,stroke:#900,stroke-width:4px;\n  5 -->|out_consensus| 8;\n  3 -->|output| 8;\n  9[\"Fasta statistics after Racon short read polish\"];\n  8 -->|Assembly polished by short reads using Racon| 9;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Assembly polishing - upgraded",
-                "outputs": [
+                        "workflow_outputs": [
+                            {
+                                "label": "stararm_detailed_summary",
+                                "output_name": "detailed_summary",
+                                "uuid": "000e2ab9-92db-45bb-a0ef-ecccf06da616"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
+                        "id": 4,
+                        "input_connections": {
+                            "input_option|input_file": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "minimap setting (for long reads)"
+                                "description": "runtime parameter for tool Bakta",
+                                "name": "annotation"
+                            },
+                            {
+                                "description": "runtime parameter for tool Bakta",
+                                "name": "annotation"
+                            },
+                            {
+                                "description": "runtime parameter for tool Bakta",
+                                "name": "annotation"
+                            },
+                            {
+                                "description": "runtime parameter for tool Bakta",
+                                "name": "input_option"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Bakta",
+                        "outputs": [
+                            {
+                                "name": "annotation_tsv",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "annotation_gff3",
+                                "type": "gff3"
+                            },
+                            {
+                                "name": "annotation_ffn",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "annotation_plot",
+                                "type": "svg"
                             }
                         ],
-                        "label": "minimap setting (for long reads)",
-                        "name": "Input parameter",
-                        "outputs": [],
                         "position": {
-                            "left": 13.133522093825794,
-                            "top": 247.1519749531627
+                            "left": 570.0016623083761,
+                            "top": 0
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "c1f18b5c-e8db-4046-b876-9b28a77cf66e",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "728dacaf08a9",
+                            "name": "bakta",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"annotation\": {\"complete\": false, \"prodigal\": {\"__class__\": \"RuntimeValue\"}, \"translation_table\": \"11\", \"keep_contig_headers\": true, \"replicons\": {\"__class__\": \"RuntimeValue\"}, \"compliant\": false, \"proteins\": {\"__class__\": \"RuntimeValue\"}, \"meta\": false}, \"input_option\": {\"bakta_db_select\": \"V5.0_2023-02-20\", \"amrfinder_db_select\": \"amrfinderplus_V3.11_2022-12-19.1\", \"input_file\": {\"__class__\": \"RuntimeValue\"}, \"min_contig_length\": null}, \"organism\": {\"genus\": null, \"species\": null, \"strain\": null, \"plasmid\": null}, \"output_files\": {\"output_selection\": [\"file_tsv\", \"file_gff3\", \"file_ffn\", \"file_plot\"]}, \"workflow\": {\"skip_analysis\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.2+galaxy0",
+                        "type": "tool",
+                        "uuid": "0b92601d-5b78-438c-998d-f9f4dc61c52d",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "ce393bcf-42e3-43ee-9056-a99e8c077a29"
+                                "label": "bakta_annotation_summary",
+                                "output_name": "annotation_tsv",
+                                "uuid": "c848b1eb-7262-4627-b7a7-05a13b968935"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "id": 4,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
+                        "errors": null,
+                        "id": 5,
                         "input_connections": {
-                            "Assembly to be polished": {
-                                "id": 0,
-                                "input_subworkflow_step_id": 0,
-                                "output_name": "output"
-                            },
-                            "long reads": {
+                            "library|input_1": {
                                 "id": 1,
-                                "input_subworkflow_step_id": 1,
                                 "output_name": "output"
                             },
-                            "minimap setting (for long reads) ": {
+                            "library|input_2": {
                                 "id": 2,
-                                "input_subworkflow_step_id": 2,
+                                "output_name": "output"
+                            },
+                            "reference_genome|own_file": {
+                                "id": 0,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Racon polish with long reads, x4 - upgraded",
-                        "outputs": [],
+                        "name": "Bowtie2",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "bam"
+                            },
+                            {
+                                "name": "mapping_stats",
+                                "type": "txt"
+                            }
+                        ],
                         "position": {
-                            "left": 299.6429464825318,
-                            "top": 72.0364210406818
+                            "left": 290.00083115418806,
+                            "top": 628
                         },
-                        "subworkflow": {
-                            "a_galaxy_workflow": "true",
-                            "annotation": "",
-                            "comments": [],
-                            "creator": [
-                                {
-                                    "class": "Person",
-                                    "identifier": "0000-0002-9906-0673",
-                                    "name": "Anna Syme"
-                                }
-                            ],
-                            "format-version": "0.1",
-                            "name": "Racon polish with long reads, x4 - upgraded",
-                            "report": {
-                                "markdown": "\n# Workflow Execution Report\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
-                            },
-                            "steps": {
-                                "0": {
-                                    "annotation": "",
-                                    "content_id": null,
-                                    "errors": null,
-                                    "id": 0,
-                                    "input_connections": {},
-                                    "inputs": [
-                                        {
-                                            "description": "",
-                                            "name": "Assembly to be polished"
-                                        }
-                                    ],
-                                    "label": "Assembly to be polished",
-                                    "name": "Input dataset",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 0,
-                                        "top": 216.625
-                                    },
-                                    "tool_id": null,
-                                    "tool_state": "{\"optional\": false, \"tag\": null}",
-                                    "tool_version": null,
-                                    "type": "data_input",
-                                    "uuid": "c7796c36-adf8-49e4-a8e4-66e606d70311",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "1": {
-                                    "annotation": "",
-                                    "content_id": null,
-                                    "errors": null,
-                                    "id": 1,
-                                    "input_connections": {},
-                                    "inputs": [
-                                        {
-                                            "description": "",
-                                            "name": "long reads"
-                                        }
-                                    ],
-                                    "label": "long reads",
-                                    "name": "Input dataset",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 4.5,
-                                        "top": 360.234375
-                                    },
-                                    "tool_id": null,
-                                    "tool_state": "{\"optional\": false, \"tag\": null}",
-                                    "tool_version": null,
-                                    "type": "data_input",
-                                    "uuid": "e2e4a70b-6e36-4b8b-bdf6-12b97189a6bd",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "10": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                    "errors": null,
-                                    "id": 10,
-                                    "input_connections": {
-                                        "corrected_reads": {
-                                            "id": 8,
-                                            "output_name": "consensus"
-                                        },
-                                        "overlaps": {
-                                            "id": 9,
-                                            "output_name": "alignment_output"
-                                        },
-                                        "reads": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Racon: polish 4",
-                                    "name": "Racon",
-                                    "outputs": [
-                                        {
-                                            "name": "consensus",
-                                            "type": "fasta"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 1496.078125,
-                                        "top": 431.1875
-                                    },
-                                    "post_job_actions": {
-                                        "RenameDatasetActionconsensus": {
-                                            "action_arguments": {
-                                                "newname": "Racon_long_reads_polished_assembly.fasta"
-                                            },
-                                            "action_type": "RenameDatasetAction",
-                                            "output_name": "consensus"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "78c533842eeb",
-                                        "name": "racon",
-                                        "owner": "bgruening",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "1.5.0+galaxy1",
-                                    "type": "tool",
-                                    "uuid": "53f4572e-3a4a-4585-89ab-9459f8a61720",
-                                    "when": null,
-                                    "workflow_outputs": [
-                                        {
-                                            "label": "Assembly polished by long reads using Racon",
-                                            "output_name": "consensus",
-                                            "uuid": "bcf0f03c-5951-46a7-aa38-545aed9bc183"
-                                        }
-                                    ]
-                                },
-                                "2": {
-                                    "annotation": "",
-                                    "content_id": null,
-                                    "errors": null,
-                                    "id": 2,
-                                    "input_connections": {},
-                                    "inputs": [
-                                        {
-                                            "description": "",
-                                            "name": "minimap setting (for long reads) "
-                                        }
-                                    ],
-                                    "label": "minimap setting (for long reads) ",
-                                    "name": "Input parameter",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 0.578125,
-                                        "top": 495.859375
-                                    },
-                                    "tool_id": null,
-                                    "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
-                                    "tool_version": null,
-                                    "type": "parameter_input",
-                                    "uuid": "fb80c05c-08d4-4ac2-b4bf-81ed906e4d72",
-                                    "when": null,
-                                    "workflow_outputs": [
-                                        {
-                                            "label": null,
-                                            "output_name": "output",
-                                            "uuid": "3983ef22-5f05-4384-8f34-6ac8c4b2cc83"
-                                        }
-                                    ]
-                                },
-                                "3": {
-                                    "annotation": "Map raw reads to assembly; output paf",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                    "errors": null,
-                                    "id": 3,
-                                    "input_connections": {
-                                        "fastq_input|analysis_type_selector": {
-                                            "id": 2,
-                                            "output_name": "output"
-                                        },
-                                        "fastq_input|fastq_input1": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        },
-                                        "reference_source|ref_file": {
-                                            "id": 0,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "fastq_input"
-                                        },
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "fastq_input"
-                                        },
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "reference_source"
-                                        }
-                                    ],
-                                    "label": "Minimap2: map long reads to assembly",
-                                    "name": "Map with minimap2",
-                                    "outputs": [
-                                        {
-                                            "name": "alignment_output",
-                                            "type": "bam"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 377.640625,
-                                        "top": 0
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionalignment_output": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "alignment_output"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "be1d967337e4",
-                                        "name": "minimap2",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "2.26+galaxy0",
-                                    "type": "tool",
-                                    "uuid": "0c06144f-d1ac-4b45-9669-1ddf11fcb06b",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "4": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                    "errors": null,
-                                    "id": 4,
-                                    "input_connections": {
-                                        "corrected_reads": {
-                                            "id": 0,
-                                            "output_name": "output"
-                                        },
-                                        "overlaps": {
-                                            "id": 3,
-                                            "output_name": "alignment_output"
-                                        },
-                                        "reads": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Racon: polish 1",
-                                    "name": "Racon",
-                                    "outputs": [
-                                        {
-                                            "name": "consensus",
-                                            "type": "fasta"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 458.640625,
-                                        "top": 518.875
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionconsensus": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "consensus"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "78c533842eeb",
-                                        "name": "racon",
-                                        "owner": "bgruening",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "1.5.0+galaxy1",
-                                    "type": "tool",
-                                    "uuid": "6c144354-91f2-49dd-a1f5-7c4119859730",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "5": {
-                                    "annotation": "Map raw reads to assembly; output paf",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                    "errors": null,
-                                    "id": 5,
-                                    "input_connections": {
-                                        "fastq_input|analysis_type_selector": {
-                                            "id": 2,
-                                            "output_name": "output"
-                                        },
-                                        "fastq_input|fastq_input1": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        },
-                                        "reference_source|ref_file": {
-                                            "id": 4,
-                                            "output_name": "consensus"
-                                        }
-                                    },
-                                    "inputs": [
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "fastq_input"
-                                        },
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "fastq_input"
-                                        },
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "reference_source"
-                                        }
-                                    ],
-                                    "label": "Minimap2: map long reads to polished assembly 1",
-                                    "name": "Map with minimap2",
-                                    "outputs": [
-                                        {
-                                            "name": "alignment_output",
-                                            "type": "bam"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 698.859375,
-                                        "top": 13.390625
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionalignment_output": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "alignment_output"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "be1d967337e4",
-                                        "name": "minimap2",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "2.26+galaxy0",
-                                    "type": "tool",
-                                    "uuid": "c1b83dad-a8ed-42cb-951f-73f59f2dfa92",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "6": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                    "errors": null,
-                                    "id": 6,
-                                    "input_connections": {
-                                        "corrected_reads": {
-                                            "id": 4,
-                                            "output_name": "consensus"
-                                        },
-                                        "overlaps": {
-                                            "id": 5,
-                                            "output_name": "alignment_output"
-                                        },
-                                        "reads": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Racon: polish 2",
-                                    "name": "Racon",
-                                    "outputs": [
-                                        {
-                                            "name": "consensus",
-                                            "type": "fasta"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 759.9375,
-                                        "top": 485.71875
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionconsensus": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "consensus"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "78c533842eeb",
-                                        "name": "racon",
-                                        "owner": "bgruening",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "1.5.0+galaxy1",
-                                    "type": "tool",
-                                    "uuid": "3208491e-b831-4238-957e-5b7388d7ff8d",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "7": {
-                                    "annotation": "Map raw reads to assembly; output paf",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                    "errors": null,
-                                    "id": 7,
-                                    "input_connections": {
-                                        "fastq_input|analysis_type_selector": {
-                                            "id": 2,
-                                            "output_name": "output"
-                                        },
-                                        "fastq_input|fastq_input1": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        },
-                                        "reference_source|ref_file": {
-                                            "id": 6,
-                                            "output_name": "consensus"
-                                        }
-                                    },
-                                    "inputs": [
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "fastq_input"
-                                        },
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "fastq_input"
-                                        },
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "reference_source"
-                                        }
-                                    ],
-                                    "label": "Minimap2: map long reads to polished assembly 2",
-                                    "name": "Map with minimap2",
-                                    "outputs": [
-                                        {
-                                            "name": "alignment_output",
-                                            "type": "bam"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 998.75,
-                                        "top": 27.9375
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionalignment_output": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "alignment_output"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "be1d967337e4",
-                                        "name": "minimap2",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "2.26+galaxy0",
-                                    "type": "tool",
-                                    "uuid": "42af524b-7f74-4c75-8d78-f6888078dd2e",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "8": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                    "errors": null,
-                                    "id": 8,
-                                    "input_connections": {
-                                        "corrected_reads": {
-                                            "id": 6,
-                                            "output_name": "consensus"
-                                        },
-                                        "overlaps": {
-                                            "id": 7,
-                                            "output_name": "alignment_output"
-                                        },
-                                        "reads": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Racon: polish 3",
-                                    "name": "Racon",
-                                    "outputs": [
-                                        {
-                                            "name": "consensus",
-                                            "type": "fasta"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 1089.71875,
-                                        "top": 455.53125
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionconsensus": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "consensus"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "78c533842eeb",
-                                        "name": "racon",
-                                        "owner": "bgruening",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "1.5.0+galaxy1",
-                                    "type": "tool",
-                                    "uuid": "21f339bd-ebc1-4c73-a976-5d0b9ab2127a",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "9": {
-                                    "annotation": "Map raw reads to assembly; output paf",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                    "errors": null,
-                                    "id": 9,
-                                    "input_connections": {
-                                        "fastq_input|analysis_type_selector": {
-                                            "id": 2,
-                                            "output_name": "output"
-                                        },
-                                        "fastq_input|fastq_input1": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        },
-                                        "reference_source|ref_file": {
-                                            "id": 8,
-                                            "output_name": "consensus"
-                                        }
-                                    },
-                                    "inputs": [
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "fastq_input"
-                                        },
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "fastq_input"
-                                        },
-                                        {
-                                            "description": "runtime parameter for tool Map with minimap2",
-                                            "name": "reference_source"
-                                        }
-                                    ],
-                                    "label": "Minimap2: map long reads to polished assembly 3",
-                                    "name": "Map with minimap2",
-                                    "outputs": [
-                                        {
-                                            "name": "alignment_output",
-                                            "type": "bam"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 1316.53125,
-                                        "top": 38.046875
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionalignment_output": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "alignment_output"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "be1d967337e4",
-                                        "name": "minimap2",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "2.26+galaxy0",
-                                    "type": "tool",
-                                    "uuid": "7d36291e-aa76-4312-9943-b5e56d0e90c5",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                }
-                            },
-                            "tags": "",
-                            "uuid": "c57efd37-4cf6-4cc7-abf4-2bab22a2e9a0"
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "03e9b2fbc005",
+                            "name": "bowtie2",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": null,
-                        "type": "subworkflow",
-                        "uuid": "58c99e4b-fd6a-401d-b9c7-cdf7e6d1757d",
+                        "tool_state": "{\"__input_ext\": \"input\", \"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"no_presets\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"library\": {\"type\": \"paired\", \"__current_case__\": 1, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"input_2\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": false, \"aligned_file\": false, \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 1, \"own_file\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.5.0+galaxy0",
+                        "type": "tool",
+                        "uuid": "7e8f9570-3d8b-4a82-b109-09bc04b82c64",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "2:output",
-                                "uuid": "50fa1032-8037-454e-8192-b95405bcd5d4"
+                                "label": "bowtie_mapping_stats",
+                                "output_name": "mapping_stats",
+                                "uuid": "352e63d3-8aca-4dff-878c-10497f65bb74"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
                         "errors": null,
-                        "id": 5,
+                        "id": 8,
                         "input_connections": {
-                            "d": {
+                            "track_groups_0|data_tracks_0|data_format|annotation": {
                                 "id": 4,
-                                "output_name": "Assembly polished by long reads using Racon"
+                                "output_name": "annotation_gff3"
                             },
-                            "i": {
-                                "id": 1,
+                            "track_groups_1|data_tracks_0|data_format|annotation": {
+                                "id": 7,
+                                "output_name": "output"
+                            },
+                            "track_groups_2|data_tracks_0|data_format|annotation": {
+                                "id": 5,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "Medaka polish",
-                        "name": "medaka consensus pipeline",
+                        "label": null,
+                        "name": "JBrowse",
                         "outputs": [
                             {
-                                "name": "out_consensus",
-                                "type": "fasta"
+                                "name": "output",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 515.5164024294684,
-                            "top": 305.08460859328346
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_consensus": {
-                                "action_arguments": {
-                                    "newname": "Medaka_long_reads_polished_assembly.fasta"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_consensus"
-                            }
+                            "left": 1130.0033246167523,
+                            "top": 325
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "fc8804320156",
-                            "name": "medaka_consensus_pipeline",
+                            "changeset_revision": "a6e57ff585c0",
+                            "name": "jbrowse",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"b\": \"100\", \"d\": {\"__class__\": \"ConnectedValue\"}, \"g\": false, \"i\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"r941_min_high_g360\", \"out\": [\"consensus\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.2+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": true, \"aboutDescription\": \"\", \"show_tracklist\": true, \"show_nav\": true, \"show_overview\": true, \"show_menu\": true, \"hideGenomeOptions\": false}, \"plugins\": {\"BlastView\": true, \"ComboTrackSelector\": false, \"GCContent\": false}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Bakta\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"match_part\": {\"match_part_select\": false, \"__current_case__\": 1}, \"index\": false, \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 1, \"category\": \"ARGs and plasmid genes\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"match_part\": {\"match_part_select\": false, \"__current_case__\": 1}, \"index\": false, \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": null}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}, {\"__index__\": 2, \"category\": \"Coverage\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"auto_snp\": false, \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.11+galaxy1",
                         "type": "tool",
-                        "uuid": "14c5ce9c-df92-4e20-85da-7a161eaa759d",
+                        "uuid": "9f973678-ce81-458a-a5d0-575d93d61429",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Assembly polished by long reads using Medaka",
-                                "output_name": "out_consensus",
-                                "uuid": "e3136060-bce7-4af3-87c4-9dcbb0d1f531"
+                                "label": "jbrowse_output",
+                                "output_name": "output",
+                                "uuid": "3c3bd5fd-419c-45b2-afcd-c6d02af82695"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/largegenome",
-                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_polishing.ga",
+                "parent_id": "genome-annotation/amr-gene-detection",
+                "path": "topics/genome-annotation/tutorials/amr-gene-detection/workflows/main-workflow.ga",
                 "tags": [
-                    "LG-WF",
-                    "GTN"
+                    "genome-annotation",
+                    "microgalaxy"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "Assembly polishing - upgraded",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-assembly-polishing",
-                "tutorial_id": "largegenome",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_polishing.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_polishing.html",
-                "version": 2,
-                "wfid": "assembly-largegenome",
-                "wfname": "galaxy-workflow-assembly-polishing",
-                "workflow": "Galaxy-Workflow-Assembly_polishing.ga",
+                "tests": true,
+                "title": "mrsa AMR gene detection",
+                "topic_id": "genome-annotation",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-amr-gene-detection/versions/main-workflow",
+                "tutorial_id": "amr-gene-detection",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/amr-gene-detection/workflows/main-workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/amr-gene-detection/workflows/main-workflow.html",
+                "version": 1,
+                "wfid": "genome-annotation-amr-gene-detection",
+                "wfname": "main-workflow",
+                "workflow": "main-workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0"
+                    "Grep1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta/1.8.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/tbl2gff3/tbl2gff3/1.2",
+                    "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1"
                 ],
-                "workflowhub_id": "1174"
-            },
+                "workflowhub_id": "1168"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/10572227"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "ctb_frankenstein_ligand",
+                    "owner": "bgruening",
+                    "revisions": "8e214e52e461",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ctb_frankenstein_ligand",
+                    "owner": "bgruening",
+                    "revisions": "7255688c77f3",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "enumerate_charges",
+                    "owner": "bgruening",
+                    "revisions": "2a868592ebcb",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "enumerate_charges",
+                    "owner": "bgruening",
+                    "revisions": "67ee76f0e497",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openbabel_compound_convert",
+                    "owner": "bgruening",
+                    "revisions": "b59c91adeac1",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openbabel_compound_convert",
+                    "owner": "bgruening",
+                    "revisions": "e2c36f62e22f",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rdock_rbcavity",
+                    "owner": "bgruening",
+                    "revisions": "744a777e9f90",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rdock_rbdock",
+                    "owner": "bgruening",
+                    "revisions": "a22969b08177",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rxdock_rbcavity",
+                    "owner": "bgruening",
+                    "revisions": "7fac8e7a12d5",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rxdock_rbdock",
+                    "owner": "bgruening",
+                    "revisions": "6fe6b0e10ed6",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "split_file_to_collection",
+                    "owner": "bgruening",
+                    "revisions": "0046692724f9",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "split_file_to_collection",
+                    "owner": "bgruening",
+                    "revisions": "6cbe2f30c2d7",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sucos_max_score",
+                    "owner": "bgruening",
+                    "revisions": "d4c67ced6abc",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sucos_max_score",
+                    "owner": "bgruening",
+                    "revisions": "9b48456a96fe",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "xchem_transfs_scoring",
+                    "owner": "bgruening",
+                    "revisions": "f6f9b47d02b6",
+                    "tool_panel_section_label": "ChemicalToolBox",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "830961c48e42",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: ctb_frankenstein_ligand\n  owner: bgruening\n  revisions: 8e214e52e461\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ctb_frankenstein_ligand\n  owner: bgruening\n  revisions: 7255688c77f3\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: enumerate_charges\n  owner: bgruening\n  revisions: 2a868592ebcb\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: enumerate_charges\n  owner: bgruening\n  revisions: 67ee76f0e497\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_compound_convert\n  owner: bgruening\n  revisions: b59c91adeac1\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openbabel_compound_convert\n  owner: bgruening\n  revisions: e2c36f62e22f\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rdock_rbcavity\n  owner: bgruening\n  revisions: 744a777e9f90\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rdock_rbdock\n  owner: bgruening\n  revisions: a22969b08177\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rxdock_rbcavity\n  owner: bgruening\n  revisions: 7fac8e7a12d5\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rxdock_rbdock\n  owner: bgruening\n  revisions: 6fe6b0e10ed6\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_to_collection\n  owner: bgruening\n  revisions: '0046692724f9'\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: split_file_to_collection\n  owner: bgruening\n  revisions: 6cbe2f30c2d7\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sucos_max_score\n  owner: bgruening\n  revisions: d4c67ced6abc\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sucos_max_score\n  owner: bgruening\n  revisions: 9b48456a96fe\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: xchem_transfs_scoring\n  owner: bgruening\n  revisions: f6f9b47d02b6\n  tool_panel_section_label: ChemicalToolBox\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 830961c48e42\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/covid19-docking/tutorial.json",
+        "contributors": [
+            {
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "simonbray",
+                "joined": "2019-05",
+                "name": "Simon Bray",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
+            }
+        ],
+        "dir": "topics/computational-chemistry/tutorials/covid19-docking",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "computational-chemistry/covid19-docking",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Galaxy can support large, rapid studies in computational chemistry",
+            "Protein-ligand docking contributes to the discovery of new drugs"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": [
+            "Understand how Galaxy was used to perform docking and pose scoring on the SARS-CoV-2 main protease (MPro).",
+            "Replicate the study on a (very) small scale",
+            "Gain familiarity with the docking and scoring techniques involved."
+        ],
+        "pageviews": 4569,
+        "pub_date": "2020-03-27",
+        "questions": [
+            "How can candidate ligands be generated and docked to a protein in Galaxy?",
+            "How can the poses of the docked ligands be evaluated?",
+            "How can a workflow for drug virtual screening be constructed in Galaxy?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "computational-chemistry",
+                "tutorials": [
+                    "cheminformatics"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00049",
+        "short_tools": [
+            "openbabel_compound_convert",
+            "split_file_to_collection",
+            "enumerate_charges",
+            "rxdock_rbcavity",
+            "sucos_max_score",
+            "collapse_dataset",
+            "xchem_pose_scoring",
+            "rxdock_rbdock",
+            "ctb_frankenstein_ligand",
+            "rdock_rbdock",
+            "rdock_rbcavity",
+            "xchem_transfs_scoring"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "covid19",
+            "one-health"
+        ],
+        "time_estimation": "2H",
+        "title": "Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/2013.1-0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/0.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/2020.03.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.2.2.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbcavity/rdock_rbcavity/0.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbdock/rdock_rbdock/0.1.4",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_rbcavity/rxdock_rbcavity/0.1.5",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_rbdock/rxdock_rbdock/0.1.5",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.4.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/sucos_max_score/sucos_max_score/0.2.3",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/sucos_max_score/sucos_max_score/2020.03.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/xchem_transfs_scoring/xchem_transfs_scoring/0.4.0",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
+            "xchem_pose_scoring"
+        ],
+        "topic_name": "computational-chemistry",
+        "topic_name_human": "Computational chemistry",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "covid19-docking",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/computational-chemistry/tutorials/covid19-docking/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/covid19-docking/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/covid19-docking/tutorial.json"
+        },
+        "version": 10,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 179,
+        "visitors": 2707,
+        "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
-                    }
-                ],
-                "description": "",
+                "creators": [],
+                "description": "Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring",
                 "features": {
                     "comments": false,
                     "parameters": false,
-                    "report": {
-                        "markdown": "# Workflow Report for Assembly with Flye\n\n\n## Workflow steps\n\n```galaxy\nworkflow_display()\n```\n\n## Dataset - fasta stats. \n\n```galaxy\nhistory_dataset_display(output=\"Fasta Statistics on input dataset(s): Fasta summary stats\")\n```\n\n## Contig sizes\n\n```galaxy\nhistory_dataset_as_image(output=\"Bar chart showing contig sizes\")\n```\n\n\n## Bandage image\n\n```galaxy\nhistory_dataset_as_image(output=\"Bandage Image on input dataset(s): Assembly Graph Image\")\n```\n\n## Quast report\n\n\r\n```galaxy\nhistory_dataset_display(output=\"Quast on input dataset(s):  PDF report\")\n```\r\n\n\n\n"
-                    },
+                    "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  1[label=\"Flye: assembly\"]\n  0 -> 1 [label=\"output\"]\n  k3960e31d7a9e400cbb21f6e47b75e649[color=lightseagreen,label=\"Output\\nFlye assembly on input dataset(s) (consensus)\"]\n  1 -> k3960e31d7a9e400cbb21f6e47b75e649\n  ke524f295a9574c91838cf8e98e809b6c[color=lightseagreen,label=\"Output\\nFlye assembly on input dataset(s) (assembly_graph)\"]\n  1 -> ke524f295a9574c91838cf8e98e809b6c\n  k48b854e2dd6e43458d0509abca6659da[color=lightseagreen,label=\"Output\\nFlye assembly on input dataset(s) (Graphical Fragment Assembly)\"]\n  1 -> k48b854e2dd6e43458d0509abca6659da\n  k8672c17271a7432c9679a8e37f36cf53[color=lightseagreen,label=\"Output\\nFlye assembly on input dataset(s) (assembly_info)\"]\n  1 -> k8672c17271a7432c9679a8e37f36cf53\n  2[label=\"Fasta statistics\"]\n  1 -> 2 [label=\"consensus\"]\n  3[label=\"Quast genome report\"]\n  1 -> 3 [label=\"consensus\"]\n  k17cdf8e08ad44570afae1861934fc678[color=lightseagreen,label=\"Output\\nQuast on input dataset(s):  HTML report\"]\n  3 -> k17cdf8e08ad44570afae1861934fc678\n  4[label=\"Bandage image: Flye assembly\"]\n  1 -> 4 [label=\"assembly_gfa\"]\n  ke66bd129146f48dc95b839a2a1ffb68d[color=lightseagreen,label=\"Output\\nBandage Image on input dataset(s): Assembly Graph Image\"]\n  4 -> ke66bd129146f48dc95b839a2a1ffb68d\n  5[label=\"Bar chart: show contig sizes\"]\n  1 -> 5 [label=\"assembly_info\"]\n  k6d0a4e23d6314e3789303d22fc91369b[color=lightseagreen,label=\"Output\\nBar chart showing contig sizes\"]\n  5 -> k6d0a4e23d6314e3789303d22fc91369b\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCandidates\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMpro-x0195_0_apo-desolv.pdb\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhits.sdf\"]\n  3[label=\"Enumerate changes\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Compound conversion\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Create Frankenstein ligand\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"Compound conversion\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"rDock cavity definition\"]\n  4 -> 7 [label=\"outfile\"]\n  5 -> 7 [label=\"outfile\"]\n  8[label=\"Split file\"]\n  6 -> 8 [label=\"outfile\"]\n  9[label=\"rDock docking\"]\n  4 -> 9 [label=\"outfile\"]\n  8 -> 9 [label=\"list_output_sdf\"]\n  7 -> 9 [label=\"activesite\"]\n  10[label=\"Collapse Collection\"]\n  9 -> 10 [label=\"output\"]\n  11[label=\"XChem TransFS pose scoring\"]\n  1 -> 11 [label=\"output\"]\n  10 -> 11 [label=\"output\"]\n  12[label=\"Max SuCOS score\"]\n  11 -> 12 [label=\"output\"]\n  2 -> 12 [label=\"output\"]\n}",
                 "history": [
                     {
-                        "hash": "f3dd8377556ae73d56d73612a37a5a7e20c98093",
-                        "message": "Update Galaxy-Workflow-Assembly_with_Flye.ga",
-                        "num": 5,
-                        "short_hash": "f3dd83775",
-                        "unix": "1715074300"
-                    },
-                    {
-                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
-                        "message": "new versions of workflows",
+                        "hash": "cf8b1cb0509e73e534c234076c8bd055379823c5",
+                        "message": "Update some workflow names for consistency",
                         "num": 4,
-                        "short_hash": "e8ddbcdd5",
-                        "unix": "1714537936"
+                        "short_hash": "cf8b1cb05",
+                        "unix": "1598836271"
                     },
                     {
-                        "hash": "43baea079b7b412f3f272ac1ac887cd67aef6c49",
-                        "message": "Rename Galaxy-Workflow-Assembly_with_Flye.ga to Galaxy-Workflow-Assembly_with_Flye_old.ga",
+                        "hash": "60a21218780027dcf65a5f37b94148b0771303e1",
+                        "message": "update with covid19 tut with frankenstein ligand tool",
                         "num": 3,
-                        "short_hash": "43baea079",
-                        "unix": "1714537239"
+                        "short_hash": "60a212187",
+                        "unix": "1591084355"
                     },
                     {
-                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
-                        "message": "add/complete creator info on workflows",
+                        "hash": "2bffcbdc75d8aaf32b06acc2f9f493931782546d",
+                        "message": "lint",
                         "num": 2,
-                        "short_hash": "62e77944b",
-                        "unix": "1676627603"
+                        "short_hash": "2bffcbdc7",
+                        "unix": "1585304017"
                     },
                     {
-                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
-                        "message": "large genome tutorial",
+                        "hash": "62d30105b34ea23f3280539d9880037639aa770e",
+                        "message": "linting covid19 cheminformatics tutorial",
                         "num": 1,
-                        "short_hash": "9fcb3aeec",
-                        "unix": "1665123856"
+                        "short_hash": "62d30105b",
+                        "unix": "1585300158"
                     }
                 ],
                 "inputs": [
@@ -165651,315 +165332,99 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "long reads"
+                                "name": "Candidates"
                             }
                         ],
-                        "label": "long reads",
+                        "label": "Candidates",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 398.40625
+                            "left": 218,
+                            "top": 200
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"name\": \"Candidates\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "501d7387-3bed-4510-891f-a4571a48d9ab",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Flye: assembly\"];\n  0 -->|output| 1;\n  3960e31d-7a9e-400c-bb21-f6e47b75e649[\"Output\\nFlye assembly on input dataset(s) (consensus)\"];\n  1 --> 3960e31d-7a9e-400c-bb21-f6e47b75e649;\n  style 3960e31d-7a9e-400c-bb21-f6e47b75e649 stroke:#2c3143,stroke-width:4px;\n  e524f295-a957-4c91-838c-f8e98e809b6c[\"Output\\nFlye assembly on input dataset(s) (assembly_graph)\"];\n  1 --> e524f295-a957-4c91-838c-f8e98e809b6c;\n  style e524f295-a957-4c91-838c-f8e98e809b6c stroke:#2c3143,stroke-width:4px;\n  48b854e2-dd6e-4345-8d05-09abca6659da[\"Output\\nFlye assembly on input dataset(s) (Graphical Fragment Assembly)\"];\n  1 --> 48b854e2-dd6e-4345-8d05-09abca6659da;\n  style 48b854e2-dd6e-4345-8d05-09abca6659da stroke:#2c3143,stroke-width:4px;\n  8672c172-71a7-432c-9679-a8e37f36cf53[\"Output\\nFlye assembly on input dataset(s) (assembly_info)\"];\n  1 --> 8672c172-71a7-432c-9679-a8e37f36cf53;\n  style 8672c172-71a7-432c-9679-a8e37f36cf53 stroke:#2c3143,stroke-width:4px;\n  2[\"Fasta statistics\"];\n  1 -->|consensus| 2;\n  3[\"Quast genome report\"];\n  1 -->|consensus| 3;\n  17cdf8e0-8ad4-4570-afae-1861934fc678[\"Output\\nQuast on input dataset(s):  HTML report\"];\n  3 --> 17cdf8e0-8ad4-4570-afae-1861934fc678;\n  style 17cdf8e0-8ad4-4570-afae-1861934fc678 stroke:#2c3143,stroke-width:4px;\n  4[\"Bandage image: Flye assembly\"];\n  1 -->|assembly_gfa| 4;\n  e66bd129-146f-48dc-95b8-39a2a1ffb68d[\"Output\\nBandage Image on input dataset(s): Assembly Graph Image\"];\n  4 --> e66bd129-146f-48dc-95b8-39a2a1ffb68d;\n  style e66bd129-146f-48dc-95b8-39a2a1ffb68d stroke:#2c3143,stroke-width:4px;\n  5[\"Bar chart: show contig sizes\"];\n  1 -->|assembly_info| 5;\n  6d0a4e23-d631-4e37-8930-3d22fc91369b[\"Output\\nBar chart showing contig sizes\"];\n  5 --> 6d0a4e23-d631-4e37-8930-3d22fc91369b;\n  style 6d0a4e23-d631-4e37-8930-3d22fc91369b stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Assembly with Flye - upgraded",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {
-                            "inputs": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Flye: assembly",
-                        "name": "Flye",
-                        "outputs": [
-                            {
-                                "name": "consensus",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "assembly_graph",
-                                "type": "graph_dot"
-                            },
-                            {
-                                "name": "assembly_gfa",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "assembly_info",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 260.57143695759436,
-                            "top": 248.74363091133793
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "291923e6f276",
-                            "name": "flye",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"asm\": {\"asm_select\": \"false\", \"__current_case__\": 1}, \"generate_log\": false, \"i\": \"1\", \"inputs\": {\"__class__\": \"ConnectedValue\"}, \"iterations\": \"1\", \"keep_haplotypes\": false, \"m\": null, \"meta\": false, \"min_overlap\": null, \"mode\": \"--nano-raw\", \"mode_conditional\": {\"mode\": \"--nano-raw\", \"__current_case__\": 0}, \"no_alt_contigs\": false, \"no_trestle\": \"false\", \"plasmids\": \"false\", \"scaffold\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.9.3+galaxy0",
-                        "type": "tool",
-                        "uuid": "8bed3591-266a-41f1-91d3-11b3456e8609",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Flye assembly on input dataset(s) (consensus)",
-                                "output_name": "consensus",
-                                "uuid": "3960e31d-7a9e-400c-bb21-f6e47b75e649"
-                            },
-                            {
-                                "label": "Flye assembly on input dataset(s) (assembly_graph)",
-                                "output_name": "assembly_graph",
-                                "uuid": "e524f295-a957-4c91-838c-f8e98e809b6c"
-                            },
-                            {
-                                "label": "Flye assembly on input dataset(s) (Graphical Fragment Assembly)",
-                                "output_name": "assembly_gfa",
-                                "uuid": "48b854e2-dd6e-4345-8d05-09abca6659da"
-                            },
-                            {
-                                "label": "Flye assembly on input dataset(s) (assembly_info)",
-                                "output_name": "assembly_info",
-                                "uuid": "8672c172-71a7-432c-9679-a8e37f36cf53"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "mode|in|inputs": {
-                                "id": 1,
-                                "output_name": "consensus"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Quast genome report",
-                        "name": "Quast",
-                        "outputs": [
-                            {
-                                "name": "report_html",
-                                "type": "html"
-                            }
-                        ],
-                        "position": {
-                            "left": 697.3759752425051,
-                            "top": 194.46891558901518
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "72472698a2df",
-                            "name": "quast",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"al\": {\"ambiguity_score\": \"0.99\", \"ambiguity_usage\": \"one\", \"fragmented\": false, \"fragmented_max_indent\": \"50\", \"min_alignment\": \"65\", \"min_identity\": \"95.0\", \"upper_bound_assembly\": false, \"upper_bound_min_con\": \"2\", \"use_all_alignments\": false}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"false\", \"__current_case__\": 1, \"est_ref_size\": null}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"circos\": \"false\", \"contig_thresholds\": \"0,1000\", \"extensive_mis_size\": \"1000\", \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": false}, \"in\": {\"__current_case__\": 1, \"custom\": \"false\", \"inputs\": {\"__class__\": \"RuntimeValue\"}}, \"k_mer\": {\"__current_case__\": 1, \"k_mer_stats\": \"\"}, \"large\": true, \"min_contig\": \"500\", \"mode\": {\"mode\": \"co\", \"__current_case__\": 1, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": \"html\", \"scaffold_gap_max_size\": \"1000\", \"skip_unaligned_mis_contigs\": \"false\", \"split_scaffolds\": false, \"strict_NA\": \"false\", \"unaligned_part_size\": \"500\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.2.0+galaxy1",
-                        "type": "tool",
-                        "uuid": "5bc29646-ec4c-4eb3-af01-73d82fc690a2",
-                        "when": null,
+                        "uuid": "47bf8c53-ae1e-4af6-bece-6adfd74b627c",
                         "workflow_outputs": [
                             {
-                                "label": "Quast on input dataset(s):  HTML report",
-                                "output_name": "report_html",
-                                "uuid": "17cdf8e0-8ad4-4570-afae-1861934fc678"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "cdab037e-aee1-49b8-a998-cd9fe7ddcdb7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                        "content_id": null,
                         "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 1,
-                                "output_name": "assembly_gfa"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Bandage image: Flye assembly",
-                        "name": "Bandage Image",
-                        "outputs": [
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "outfile",
-                                "type": "jpg"
+                                "description": "",
+                                "name": "Mpro-x0195_0_apo-desolv.pdb"
                             }
                         ],
+                        "label": "Mpro-x0195_0_apo-desolv.pdb",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 583.546875,
-                            "top": 446.40625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ddddce450736",
-                            "name": "bandage",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 218,
+                            "top": 289.76666259765625
                         },
-                        "tool_state": "{\"fontsize\": null, \"height\": \"1000\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"lengths\": false, \"names\": false, \"nodewidth\": null, \"output_format\": \"jpg\", \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2022.09+galaxy4",
-                        "type": "tool",
-                        "uuid": "395f2dfe-3fa5-4684-bf97-7dd12e970f78",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Mpro-x0195_0_apo-desolv.pdb\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "156f4aeb-d160-456a-974e-7884b79cb83a",
                         "workflow_outputs": [
                             {
-                                "label": "Bandage Image on input dataset(s): Assembly Graph Image",
-                                "output_name": "outfile",
-                                "uuid": "e66bd129-146f-48dc-95b8-39a2a1ffb68d"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "1fd1c624-37c6-4874-b863-a40eac5e4994"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "barchart_gnuplot",
+                        "content_id": null,
                         "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "input": {
-                                "id": 1,
-                                "output_name": "assembly_info"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Bar chart: show contig sizes",
-                        "name": "Bar chart",
-                        "outputs": [
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "png"
+                                "description": "",
+                                "name": "hits.sdf"
                             }
                         ],
+                        "label": "hits.sdf",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 595.421875,
-                            "top": 688.984375
+                            "left": 218,
+                            "top": 400.5333251953125
                         },
-                        "post_job_actions": {},
-                        "tool_id": "barchart_gnuplot",
-                        "tool_state": "{\"colList\": \"2\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"pdf_size\": \"800,600\", \"title\": \"Assembly contig sizes\", \"xtic\": {\"userSpecified\": \"No\", \"__current_case__\": 1}, \"ylabel\": \"lengths\", \"ymax\": \"0\", \"ymin\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "cb9d5059-bf42-4a0e-8150-f5089e0d5b1b",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"hits.sdf\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "dd2d3bc0-8138-4e66-b2d9-e5e90e27b659",
                         "workflow_outputs": [
                             {
-                                "label": "Bar chart showing contig sizes",
-                                "output_name": "out_file1",
-                                "uuid": "6d0a4e23-d631-4e37-8930-3d22fc91369b"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "1c8fb3cc-52ad-4f62-a00d-80b14b2c1d4a"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/largegenome",
-                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_with_Flye.ga",
-                "tags": [
-                    "LG-WF",
-                    "GTN"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Assembly with Flye - upgraded",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-assembly-with-flye",
-                "tutorial_id": "largegenome",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_with_Flye.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_with_Flye.html",
-                "version": 2,
-                "wfid": "assembly-largegenome",
-                "wfname": "galaxy-workflow-assembly-with-flye",
-                "workflow": "Galaxy-Workflow-Assembly_with_Flye.ga",
-                "workflow_tools": [
-                    "barchart_gnuplot",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
-                ],
-                "workflowhub_id": "1170"
-            },
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
-                    }
-                ],
-                "description": "",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": {
-                        "markdown": "\n# Workflow Execution Report\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n\n## Busco results\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco short summary\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco summary image\")\n```\n\n## Quast results\n\n\n```galaxy\nhistory_dataset_display(output=\"Quast on input dataset(s): tabular report\")\n```\n\n\n"
-                    },
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPolished assembly\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genome\"]\n  2[label=\"Busco: assess assembly\"]\n  0 -> 2 [label=\"output\"]\n  k219e495236e04b01a407e774b5b02dca[color=lightseagreen,label=\"Output\\nBusco short summary\"]\n  2 -> k219e495236e04b01a407e774b5b02dca\n  3[label=\"Quast: assess assembly\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  k77ab01864cfd460fb71e39a923414ef4[color=lightseagreen,label=\"Output\\nQuast on input dataset(s):  HTML report\"]\n  3 -> k77ab01864cfd460fb71e39a923414ef4\n}",
-                "history": [
-                    {
-                        "hash": "1b47a1ad8d46b114394c0579436c448e6bb7efcf",
-                        "message": "Update Galaxy-Workflow-Assess_genome_quality.ga",
-                        "num": 5,
-                        "short_hash": "1b47a1ad8",
-                        "unix": "1715074319"
-                    },
-                    {
-                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
-                        "message": "new versions of workflows",
-                        "num": 4,
-                        "short_hash": "e8ddbcdd5",
-                        "unix": "1714537936"
-                    },
-                    {
-                        "hash": "fc05e79f01c6b59c4dfc6aa59ebf592ae615641f",
-                        "message": "Rename Galaxy-Workflow-Assess_genome_quality.ga to Galaxy-Workflow-Assess_genome_quality_old.ga",
-                        "num": 3,
-                        "short_hash": "fc05e79f0",
-                        "unix": "1714537255"
-                    },
-                    {
-                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
-                        "message": "add/complete creator info on workflows",
-                        "num": 2,
-                        "short_hash": "62e77944b",
-                        "unix": "1676627603"
-                    },
-                    {
-                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
-                        "message": "large genome tutorial",
-                        "num": 1,
-                        "short_hash": "9fcb3aeec",
-                        "unix": "1665123856"
-                    }
-                ],
-                "inputs": [
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nCandidates\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nMpro-x0195_0_apo-desolv.pdb\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nhits.sdf\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Enumerate changes\"];\n  0 -->|output| 3;\n  4[\"Compound conversion\"];\n  1 -->|output| 4;\n  5[\"Create Frankenstein ligand\"];\n  2 -->|output| 5;\n  6[\"Compound conversion\"];\n  3 -->|output| 6;\n  7[\"rDock cavity definition\"];\n  4 -->|outfile| 7;\n  5 -->|outfile| 7;\n  8[\"Split file\"];\n  6 -->|outfile| 8;\n  9[\"rDock docking\"];\n  4 -->|outfile| 9;\n  8 -->|list_output_sdf| 9;\n  7 -->|activesite| 9;\n  10[\"Collapse Collection\"];\n  9 -->|output| 10;\n  11[\"XChem TransFS pose scoring\"];\n  1 -->|output| 11;\n  10 -->|output| 11;\n  12[\"Max SuCOS score\"];\n  11 -->|output| 12;\n  2 -->|output| 12;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring",
+                "outputs": [
                     {
                         "annotation": "",
                         "content_id": null,
@@ -165969,23 +165434,28 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Polished assembly"
+                                "name": "Candidates"
                             }
                         ],
-                        "label": "Polished assembly",
+                        "label": "Candidates",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 101.09375
+                            "left": 218,
+                            "top": 200
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"name\": \"Candidates\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "2ed19084-9eaf-4efb-acdc-b81536e7c024",
-                        "when": null,
-                        "workflow_outputs": []
+                        "uuid": "47bf8c53-ae1e-4af6-bece-6adfd74b627c",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "cdab037e-aee1-49b8-a998-cd9fe7ddcdb7"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
@@ -165996,2107 +165466,3524 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Reference genome"
+                                "name": "Mpro-x0195_0_apo-desolv.pdb"
                             }
                         ],
-                        "label": "Reference genome",
+                        "label": "Mpro-x0195_0_apo-desolv.pdb",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 246.765625,
-                            "top": 0.0
+                            "left": 218,
+                            "top": 289.76666259765625
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"name\": \"Mpro-x0195_0_apo-desolv.pdb\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "5b12a6af-13c3-4520-a549-280de6a3df17",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPolished assembly\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Busco: assess assembly\"];\n  0 -->|output| 2;\n  219e4952-36e0-4b01-a407-e774b5b02dca[\"Output\\nBusco short summary\"];\n  2 --> 219e4952-36e0-4b01-a407-e774b5b02dca;\n  style 219e4952-36e0-4b01-a407-e774b5b02dca stroke:#2c3143,stroke-width:4px;\n  3[\"Quast: assess assembly\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  77ab0186-4cfd-460f-b71e-39a923414ef4[\"Output\\nQuast on input dataset(s):  HTML report\"];\n  3 --> 77ab0186-4cfd-460f-b71e-39a923414ef4;\n  style 77ab0186-4cfd-460f-b71e-39a923414ef4 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Assess genome quality - upgraded",
-                "outputs": [
+                        "uuid": "156f4aeb-d160-456a-974e-7884b79cb83a",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "1fd1c624-37c6-4874-b863-a40eac5e4994"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
+                        "content_id": null,
                         "errors": null,
                         "id": 2,
-                        "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Busco: assess assembly",
-                        "name": "Busco",
-                        "outputs": [
-                            {
-                                "name": "busco_sum",
-                                "type": "txt"
-                            },
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "busco_table",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "hits.sdf"
                             }
                         ],
+                        "label": "hits.sdf",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 294.42303466796875,
-                            "top": 200.68505859375
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ea8146ee148f",
-                            "name": "busco",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 218,
+                            "top": 400.5333251953125
                         },
-                        "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"auto_detect\", \"__current_case__\": 0, \"auto_lineage\": \"--auto-lineage\"}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"lineage_dataset\": \"eukaryota_odb10\", \"outputs\": \"short_summary\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.5.0+galaxy0",
-                        "type": "tool",
-                        "uuid": "8f5f17de-a21e-49f4-b55c-6eff5f4fa213",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"hits.sdf\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "dd2d3bc0-8138-4e66-b2d9-e5e90e27b659",
                         "workflow_outputs": [
-                            {
-                                "label": "Busco short summary",
-                                "output_name": "busco_sum",
-                                "uuid": "219e4952-36e0-4b01-a407-e774b5b02dca"
-                            },
                             {
                                 "label": null,
-                                "output_name": "busco_table",
-                                "uuid": "fc06df63-3453-4303-80d1-c76823ba384a"
+                                "output_name": "output",
+                                "uuid": "1c8fb3cc-52ad-4f62-a00d-80b14b2c1d4a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1",
                         "errors": null,
-                        "id": 3,
+                        "id": 5,
                         "input_connections": {
-                            "assembly|ref|r": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "mode|in|inputs": {
-                                "id": 0,
+                            "infile": {
+                                "id": 2,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": "Quast: assess assembly",
-                        "name": "Quast",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Create Frankenstein ligand",
+                                "name": "infile"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Create Frankenstein ligand",
                         "outputs": [
                             {
-                                "name": "report_html",
-                                "type": "html"
+                                "name": "outfile",
+                                "type": "sdf"
                             }
                         ],
                         "position": {
-                            "left": 564.8660278320312,
-                            "top": 56.71406029052495
+                            "left": 478.76666259765625,
+                            "top": 483.5333251953125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "72472698a2df",
-                            "name": "quast",
-                            "owner": "iuc",
+                            "changeset_revision": "8e214e52e461",
+                            "name": "ctb_frankenstein_ligand",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"true\", \"__current_case__\": 0, \"r\": {\"__class__\": \"RuntimeValue\"}, \"features\": {\"__class__\": \"RuntimeValue\"}, \"operons\": {\"__class__\": \"RuntimeValue\"}, \"k_mer\": {\"k_mer_stats\": \"\", \"__current_case__\": 1}, \"circos\": false}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": false}, \"large\": true, \"min_contig\": \"0\", \"mode\": {\"mode\": \"individual\", \"__current_case__\": 0, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"RuntimeValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": \"html\", \"split_scaffolds\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.2.0+galaxy1",
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "0.1.1",
                         "type": "tool",
-                        "uuid": "6caef18b-b257-472d-b8d0-fac523a72d37",
-                        "when": null,
+                        "uuid": "081abe35-347a-4244-99ae-ec35329e3de0",
                         "workflow_outputs": [
                             {
-                                "label": "Quast on input dataset(s):  HTML report",
-                                "output_name": "report_html",
-                                "uuid": "77ab0186-4cfd-460f-b71e-39a923414ef4"
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "53c557af-d5b9-4033-be54-7c197591e750"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/largegenome",
-                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assess_genome_quality.ga",
+                "parent_id": "computational-chemistry/covid19-docking",
+                "path": "topics/computational-chemistry/tutorials/covid19-docking/workflows/workflow.ga",
                 "tags": [
-                    "LG-WF",
-                    "GTN"
+                    "computational-chemistry"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Assess genome quality - upgraded",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-assess-genome-quality",
-                "tutorial_id": "largegenome",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assess_genome_quality.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assess_genome_quality.html",
-                "version": 2,
-                "wfid": "assembly-largegenome",
-                "wfname": "galaxy-workflow-assess-genome-quality",
-                "workflow": "Galaxy-Workflow-Assess_genome_quality.ga",
+                "title": "Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring",
+                "topic_id": "computational-chemistry",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/computational-chemistry-covid19-docking/versions/workflow",
+                "tutorial_id": "covid19-docking",
+                "url": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/covid19-docking/workflows/workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/covid19-docking/workflows/workflow.html",
+                "version": 3,
+                "wfid": "computational-chemistry-covid19-docking",
+                "wfname": "workflow",
+                "workflow": "workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/0.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.2.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbcavity/rdock_rbcavity/0.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbdock/rdock_rbdock/0.1.4",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.4.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/sucos_max_score/sucos_max_score/0.2.3",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
+                    "xchem_pose_scoring"
                 ],
-                "workflowhub_id": "1158"
+                "workflowhub_id": "1079"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/3730474"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "86755160afbf",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "86755160afbf",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "emboss_5",
+                    "owner": "devteam",
+                    "revisions": "63dd26468588",
+                    "tool_panel_section_label": "EMBOSS",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "3d0c7bdf12f5",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "5ec9f6bceaee",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "samtools_stats",
+                    "owner": "devteam",
+                    "revisions": "541082d03bef",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bcftools_consensus",
+                    "owner": "iuc",
+                    "revisions": "da0bf365652d",
+                    "tool_panel_section_label": "Variant Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastp",
+                    "owner": "iuc",
+                    "revisions": "c59d48774d03",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "jbrowse",
+                    "owner": "iuc",
+                    "revisions": "a6e57ff585c0",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "jvarkit_wgscoverageplotter",
+                    "owner": "iuc",
+                    "revisions": "ac048a34cac3",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "kraken2",
+                    "owner": "iuc",
+                    "revisions": "20e2f64aa1fe",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mosdepth",
+                    "owner": "iuc",
+                    "revisions": "5854d0da92b4",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "abfd8a6544d7",
+                    "tool_panel_section_label": "Quality Control",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "qualimap_bamqc",
+                    "owner": "iuc",
+                    "revisions": "4a89c6f84425",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "snippy",
+                    "owner": "iuc",
+                    "revisions": "d220115f882b",
+                    "tool_panel_section_label": "Variant Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "tb_variant_filter",
+                    "owner": "iuc",
+                    "revisions": "32f14a2723ec",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "tbprofiler",
+                    "owner": "iuc",
+                    "revisions": "4839e590cb26",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "tbvcfreport",
+                    "owner": "iuc",
+                    "revisions": "42818629ec4c",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "tbvcfreport",
+                    "owner": "iuc",
+                    "revisions": "9793bc5d741b",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: emboss_5\n  owner: devteam\n  revisions: 63dd26468588\n  tool_panel_section_label: EMBOSS\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 541082d03bef\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_consensus\n  owner: iuc\n  revisions: da0bf365652d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: c59d48774d03\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jvarkit_wgscoverageplotter\n  owner: iuc\n  revisions: ac048a34cac3\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: 20e2f64aa1fe\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mosdepth\n  owner: iuc\n  revisions: 5854d0da92b4\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: abfd8a6544d7\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qualimap_bamqc\n  owner: iuc\n  revisions: 4a89c6f84425\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snippy\n  owner: iuc\n  revisions: d220115f882b\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tb_variant_filter\n  owner: iuc\n  revisions: 32f14a2723ec\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbprofiler\n  owner: iuc\n  revisions: 4839e590cb26\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbvcfreport\n  owner: iuc\n  revisions: 42818629ec4c\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbvcfreport\n  owner: iuc\n  revisions: 9793bc5d741b\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.json",
+        "contributors": [
+            {
+                "bio": "Research at the South African National Bioinformatics Institute",
+                "id": "pvanheus",
+                "joined": "2017-09",
+                "name": "Peter van Heusden",
+                "orcid": "0000-0001-6553-5274",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/",
+                "twitter": "pvanheus",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pvanheus.json"
+            },
+            {
+                "elixir_node": "au",
+                "email": "simon.gladman@unimelb.edu.au",
+                "id": "slugger70",
+                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
+                "joined": "2017-09",
+                "name": "Simon Gladman",
+                "orcid": "0000-0002-6100-4385",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
+            },
+            {
+                "id": "thobalose",
+                "joined": "2019-11",
+                "name": "Thoba Lose",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/thobalose/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/thobalose.json"
+            }
+        ],
+        "dir": "topics/variant-analysis/tutorials/tb-variant-analysis",
+        "edam_ontology": [
+            "topic_0622",
+            "topic_3301",
+            "topic_0196",
+            "topic_0199",
+            "topic_3305",
+            "topic_3324"
+        ],
+        "edam_operation": [
+            "Sequence alignment",
+            "Phylogenetic tree generation",
+            "Phylogenetic tree visualisation",
+            "Sequencing quality control",
+            "Sequence alignment analysis",
+            "Genome visualisation",
+            "Sequence analysis",
+            "Sequence contamination filtering",
+            "Variant calling",
+            "Global alignment",
+            "Statistical calculation",
+            "Taxonomic classification",
+            "Validation",
+            "Local alignment",
+            "Sequence composition calculation",
+            "Antimicrobial resistance prediction"
+        ],
+        "edam_topic": [
+            "Genomics",
+            "Microbiology",
+            "Sequence assembly",
+            "Genetic variation",
+            "Public health and epidemiology",
+            "Infectious disease"
+        ],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "variant-analysis/tb-variant-analysis",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "variants in _M. tuberculosis_ sequencing data can be discovered using common microbial bioinformatics tools",
+            "it is not enough to just call variants, variant calling involves multiple quality control steps",
+            "the choice of reference genome and some quality control procedures are species-specific, and require knowledge of the organism in question",
+            "batches of samples can be processed using Galaxy dataset collections and workflows"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-07-26",
+        "objectives": [
+            "How should we filter those variants",
+            "How can we predict drug resistance from those variants",
+            "How do we annotate those variants"
+        ],
+        "pageviews": 9172,
+        "pub_date": "2020-07-25",
+        "questions": [
+            "How do we detect differences between a set of reads from _M. tuberculosis_ (Mtb) and the Mtb reference genome"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "pvanheus",
+                    "nagoue",
+                    "hexylena"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "40M",
+                "speakers": [
+                    "pvanheus"
+                ],
+                "youtube_id": "G1DmquX6Wh8"
             },
+            {
+                "captioners": [
+                    "pvanheus"
+                ],
+                "date": "2024-06-11",
+                "galaxy_version": "24.0",
+                "length": "1H17M",
+                "speakers": [
+                    "pvanheus"
+                ],
+                "youtube_id": "-nJPngFk36c"
+            }
+        ],
+        "short_id": "T00319",
+        "short_tools": [
+            "tp_sed_tool",
+            "upload1",
+            "snippy",
+            "qualimap_bamqc",
+            "tb_variant_filter",
+            "EMBOSS: seqret84",
+            "tb_profiler_profile",
+            "mosdepth",
+            "jvarkit_wgscoverageplotter",
+            "tbvcfreport",
+            "tp_awk_tool",
+            "fastqc",
+            "jbrowse",
+            "samtools_stats",
+            "bcftools_consensus",
+            "multiqc",
+            "fastp",
+            "kraken2",
+            "EMBOSS:%20seqret84",
+            "__FLATTEN__"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "one-health",
+        "supported_servers": {
+            "exact": [],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "prokaryote",
+            "one-health",
+            "microgalaxy",
+            "tuberculosis"
+        ],
+        "time_estimation": "2h",
+        "title": "M. tuberculosis Variant Analysis",
+        "tools": [
+            "__FLATTEN__",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: seqret84/5.0.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS:%20seqret84/5.0.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jvarkit_wgscoverageplotter/jvarkit_wgscoverageplotter/20201223+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mosdepth/mosdepth/0.3.8+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.4.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.2.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.1+galaxy0",
+            "upload1"
+        ],
+        "topic_name": "variant-analysis",
+        "topic_name_human": "Variant Analysis",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "tb-variant-analysis",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.json"
+        },
+        "version": 30,
+        "video": false,
+        "video_versions": 2,
+        "video_view": 0,
+        "visit_duration": 177,
+        "visitors": 5788,
+        "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
+                        "identifier": "0000-0001-6553-5274",
+                        "name": "Peter van Heusden"
                     }
                 ],
-                "description": "",
+                "description": "Predict variants and drug resistance from M. tuberculosis sequence samples (Illumina)",
                 "features": {
                     "comments": false,
                     "parameters": true,
                     "report": {
-                        "markdown": "\n# Workflow Execution Report\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                    },
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nReads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference Genome\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMinimum depth of coverage\"]\n  3[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMinimum variant allele frequency\"]\n  4[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nAdditional BWA-MEM options\"]\n  5[label=\"fastp\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"seqret\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"snippy\"]\n  4 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  3 -> 7 [label=\"output\"]\n  5 -> 7 [label=\"output_paired_coll\"]\n  1 -> 7 [label=\"output\"]\n  8[label=\"Kraken2\"]\n  5 -> 8 [label=\"output_paired_coll\"]\n  kc7abf2bfed4c433ea6959eca61282bb5[color=lightseagreen,label=\"Output\\nreport_output\"]\n  8 -> kc7abf2bfed4c433ea6959eca61282bb5\n  k083a0e5177804c91a071dc0e4641d060[color=lightseagreen,label=\"Output\\noutput\"]\n  8 -> k083a0e5177804c91a071dc0e4641d060\n  9[label=\"QualiMap BamQC\"]\n  7 -> 9 [label=\"snpsbam\"]\n  10[label=\"mosdepth\"]\n  2 -> 10 [label=\"output\"]\n  7 -> 10 [label=\"snpsbam\"]\n  11[label=\"TB Variant Filter\"]\n  7 -> 11 [label=\"snpvcf\"]\n  12[label=\"TB-Profiler Profile\"]\n  7 -> 12 [label=\"snpsbam\"]\n  k335635b4a4de4980ad0268f0035daeaa[color=lightseagreen,label=\"Output\\noutput_txt\"]\n  12 -> k335635b4a4de4980ad0268f0035daeaa\n  13[label=\"TB Variant Filter\"]\n  7 -> 13 [label=\"snpvcf\"]\n  14[label=\"Flatten collection\"]\n  9 -> 14 [label=\"raw_data\"]\n  15[label=\"Text reformatting\"]\n  10 -> 15 [label=\"output_quantized_bed\"]\n  16[label=\"Text transformation\"]\n  11 -> 16 [label=\"output1\"]\n  k007df8c2bd13495f8904abf31d4594d0[color=lightseagreen,label=\"Output\\nFinal annotated VCF\"]\n  16 -> k007df8c2bd13495f8904abf31d4594d0\n  17[label=\"MultiQC\"]\n  5 -> 17 [label=\"report_json\"]\n  14 -> 17 [label=\"output\"]\n  k5952823575254ef9881036f1ed0f01f6[color=lightseagreen,label=\"Output\\nhtml_report\"]\n  17 -> k5952823575254ef9881036f1ed0f01f6\n  18[label=\"bcftools consensus\"]\n  13 -> 18 [label=\"output1\"]\n  6 -> 18 [label=\"out_file1\"]\n  15 -> 18 [label=\"outfile\"]\n  kc71b135d35f944d0a20ef25528e518af[color=lightseagreen,label=\"Output\\nconsensus_genome\"]\n  18 -> kc71b135d35f944d0a20ef25528e518af\n  19[label=\"TB Variant Report\"]\n  16 -> 19 [label=\"output\"]\n  12 -> 19 [label=\"results_json\"]\n  k959528d2f8f2444099cf44fddd6c5069[color=lightseagreen,label=\"Output\\ndrug_resistance_report_html\"]\n  19 -> k959528d2f8f2444099cf44fddd6c5069\n  k4d9636eb075b4fd2a1e41a7c37a17fc0[color=lightseagreen,label=\"Output\\nvariants_report_html\"]\n  19 -> k4d9636eb075b4fd2a1e41a7c37a17fc0\n}",
+                "history": [
+                    {
+                        "hash": "c0042e7f333bb9758580a564dbf559e83396a6d3",
+                        "message": "Update to address comments from wm",
+                        "num": 14,
+                        "short_hash": "c0042e7f3",
+                        "unix": "1718025591"
+                    },
+                    {
+                        "hash": "01cf3d5e27fb411603014ca3e0729b2daacc0a0d",
+                        "message": "Add snippers for running workflow from workflowhub.eu and jbrowse vis",
+                        "num": 13,
+                        "short_hash": "01cf3d5e2",
+                        "unix": "1717788409"
+                    },
+                    {
+                        "hash": "d3db4cd3e349677c907c71a761fde1b2935928d2",
+                        "message": "Update the M. tuberculosis variant analysis tutorial * Update all tools to latest versions * Change to fastp instead of Trimmomatic * Add section on running workflow * Update workflow and workflow test",
+                        "num": 12,
+                        "short_hash": "d3db4cd3e",
+                        "unix": "1717771237"
+                    },
+                    {
+                        "hash": "d61d5645fa6b21c25cd5d09f540c4e584b35f2c2",
+                        "message": "Update tb_variant_filter to v. 0.4.0",
+                        "num": 11,
+                        "short_hash": "d61d5645f",
+                        "unix": "1695643686"
+                    },
+                    {
+                        "hash": "c89f11fe32c66c1da9f058ec3fa522e8b18cba82",
+                        "message": "Update some tools in tuberculosis variant analysis tutorial (#4070)",
+                        "num": 10,
+                        "short_hash": "c89f11fe3",
+                        "unix": "1682624753"
+                    },
+                    {
+                        "hash": "fa9e9fb000ef9d2ab91acc67c4f338c213d641e2",
+                        "message": "New variant of tb_variant_filter and tbprofiler, more detail on tb_variant_filter",
+                        "num": 9,
+                        "short_hash": "fa9e9fb00",
+                        "unix": "1672566129"
+                    },
+                    {
+                        "hash": "6e9c1860b186754249a0a90d9957dbace653e9ac",
+                        "message": "Restore workflow indentation and fix WF step order",
+                        "num": 8,
+                        "short_hash": "6e9c1860b",
+                        "unix": "1648048765"
+                    },
+                    {
+                        "hash": "354e9edf1340c37133b7d1834cea608895acebc0",
+                        "message": "Use correct snippy wrapper version everywhere",
+                        "num": 7,
+                        "short_hash": "354e9edf1",
+                        "unix": "1648028595"
                     },
-                    "subworkflows": true
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR1\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR2\"]\n  3[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nminimap settings for long reads\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genome for Quast\"]\n  5[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nkmer counting - meryl - upgraded\"]\n  1 -> 5 [label=\"output\"]\n  6[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nData QC - upgraded\"]\n  1 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  0 -> 6 [label=\"output\"]\n  7[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nTrim and filter reads - fastp - upgraded \"]\n  1 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  0 -> 7 [label=\"output\"]\n  8[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly with Flye - upgraded\"]\n  7 -> 8 [label=\"fastp filtered long reads\"]\n  9[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly polishing - upgraded\"]\n  8 -> 9 [label=\"Flye assembly on input datasets consensus\"]\n  7 -> 9 [label=\"fastp filtered R1 reads\"]\n  7 -> 9 [label=\"fastp filtered long reads\"]\n  3 -> 9 [label=\"output\"]\n  10[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nAssess genome quality - upgraded\"]\n  9 -> 10 [label=\"Assembly polished by long reads using Medaka\"]\n  4 -> 10 [label=\"output\"]\n}",
-                "history": [
                     {
-                        "hash": "01cffeed0413d12d37753e72aa81c95fb47e2179",
-                        "message": "Update Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga",
+                        "hash": "6f476a03271eeabffcf0877e8a402f7af815deba",
+                        "message": "Update snippy to 4.6.0",
+                        "num": 6,
+                        "short_hash": "6f476a032",
+                        "unix": "1647976648"
+                    },
+                    {
+                        "hash": "946f6f60f8e068a147f03d89f369f19e552793da",
+                        "message": "Generate cleaner intermediate diff",
                         "num": 5,
-                        "short_hash": "01cffeed0",
-                        "unix": "1715074366"
+                        "short_hash": "946f6f60f",
+                        "unix": "1647938051"
                     },
                     {
-                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
-                        "message": "new versions of workflows",
+                        "hash": "8e46a42b5a664cf72ea7e2aae61739348f64dfea",
+                        "message": "Autoupdate workflow, change Kraken2 test",
                         "num": 4,
-                        "short_hash": "e8ddbcdd5",
-                        "unix": "1714537936"
+                        "short_hash": "8e46a42b5",
+                        "unix": "1647929062"
                     },
                     {
-                        "hash": "bd0db2c9632aca4fc5faba5e811b23e9f98817f0",
-                        "message": "Rename Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga to Galaxy-Workflow-Combined_workflows_for_large_genome_assembly_old.ga",
+                        "hash": "f98407ff47fe6ea903372a39b09530ae075d65b3",
+                        "message": "tb-variant-analysis: label workflow outputs and add test",
                         "num": 3,
-                        "short_hash": "bd0db2c96",
-                        "unix": "1714537274"
+                        "short_hash": "f98407ff4",
+                        "unix": "1595713523"
                     },
                     {
-                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
-                        "message": "add/complete creator info on workflows",
+                        "hash": "392830f9b51662e8028b8984f48f827be8a10aed",
+                        "message": "Reformat tb-variant-analysis workflow",
                         "num": 2,
-                        "short_hash": "62e77944b",
-                        "unix": "1676627603"
+                        "short_hash": "392830f9b",
+                        "unix": "1595707349"
                     },
                     {
-                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
-                        "message": "large genome tutorial",
+                        "hash": "2e73bb7aa538d3fb94e7f7ca21bfc6078d35e73f",
+                        "message": "Update M. tuberculosis variant analysis tutorial with new data and workflow",
                         "num": 1,
-                        "short_hash": "9fcb3aeec",
-                        "unix": "1665123856"
+                        "short_hash": "2e73bb7aa",
+                        "unix": "1595705571"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "",
+                        "annotation": "List of paired Illumina reads (set format to fastqsanger or fastqsanger.gz as appropriate)",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "long reads"
-                            }
-                        ],
-                        "label": "long reads",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 37.09056155334109,
-                            "top": 117.80110422489305
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f9154ba8-6c56-4b8c-b3a6-79bf72638963",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "R1"
-                            }
-                        ],
-                        "label": "R1",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 296.6915657131622
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "2152a89a-64b2-4e77-897e-97c2e951f0d4",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "R2"
-                            }
-                        ],
-                        "label": "R2",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 18.331891780359495,
-                            "top": 404.60599487314124
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "04ed4838-38d0-47c6-9692-af43b305750c",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "minimap settings (for long reads)"
-                            }
-                        ],
-                        "label": "minimap settings (for long reads)",
-                        "name": "Input parameter",
-                        "outputs": [],
-                        "position": {
-                            "left": 953.979654343896,
-                            "top": 53.88085686443145
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "925fcb63-babc-42b5-9510-c82277158288",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "3643a598-963e-42d9-b625-41f5256dee4a"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Reference genome for Quast"
-                            }
-                        ],
-                        "label": "Reference genome for Quast",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 1271.7306972391564,
-                            "top": 75.04279962197629
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "5bd59f90-9351-4b1e-bc0d-11fee8b4a435",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nR1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nR2\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nminimap settings for long reads\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nReference genome for Quast\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\ud83d\udee0\ufe0f Subworkflow\\nkmer counting - meryl - upgraded\"];\n  style 5 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 5;\n  6[\"\ud83d\udee0\ufe0f Subworkflow\\nData QC - upgraded\"];\n  style 6 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 6;\n  2 -->|output| 6;\n  0 -->|output| 6;\n  7[\"\ud83d\udee0\ufe0f Subworkflow\\nTrim and filter reads - fastp - upgraded \"];\n  style 7 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 7;\n  2 -->|output| 7;\n  0 -->|output| 7;\n  8[\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly with Flye - upgraded\"];\n  style 8 fill:#edd,stroke:#900,stroke-width:4px;\n  7 -->|fastp filtered long reads| 8;\n  9[\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly polishing - upgraded\"];\n  style 9 fill:#edd,stroke:#900,stroke-width:4px;\n  8 -->|Flye assembly on input datasets consensus| 9;\n  7 -->|fastp filtered R1 reads| 9;\n  7 -->|fastp filtered long reads| 9;\n  3 -->|output| 9;\n  10[\"\ud83d\udee0\ufe0f Subworkflow\\nAssess genome quality - upgraded\"];\n  style 10 fill:#edd,stroke:#900,stroke-width:4px;\n  9 -->|Assembly polished by long reads using Medaka| 10;\n  4 -->|output| 10;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Combined workflows for large genome assembly - upgraded ",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "minimap settings (for long reads)"
+                                "description": "List of paired Illumina reads (set format to fastqsanger or fastqsanger.gz as appropriate)",
+                                "name": "Reads"
                             }
                         ],
-                        "label": "minimap settings (for long reads)",
-                        "name": "Input parameter",
-                        "outputs": [],
-                        "position": {
-                            "left": 953.979654343896,
-                            "top": 53.88085686443145
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "925fcb63-babc-42b5-9510-c82277158288",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "3643a598-963e-42d9-b625-41f5256dee4a"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "id": 9,
-                        "input_connections": {
-                            "Assembly to be polished": {
-                                "id": 8,
-                                "input_subworkflow_step_id": 0,
-                                "output_name": "Flye assembly on input dataset(s) (consensus)"
-                            },
-                            "Illumina reads R1": {
-                                "id": 7,
-                                "input_subworkflow_step_id": 3,
-                                "output_name": "fastp filtered R1 reads"
-                            },
-                            "long reads": {
-                                "id": 7,
-                                "input_subworkflow_step_id": 1,
-                                "output_name": "fastp filtered long reads"
-                            },
-                            "minimap setting (for long reads)": {
-                                "id": 3,
-                                "input_subworkflow_step_id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Assembly polishing - upgraded",
-                        "outputs": [],
-                        "position": {
-                            "left": 1260.7587450660599,
-                            "top": 269.3075732043599
-                        },
-                        "subworkflow": {
-                            "a_galaxy_workflow": "true",
-                            "annotation": "",
-                            "comments": [],
-                            "creator": [
-                                {
-                                    "class": "Person",
-                                    "identifier": "0000-0002-9906-0673",
-                                    "name": "Anna Syme"
-                                }
-                            ],
-                            "format-version": "0.1",
-                            "name": "Assembly polishing - upgraded",
-                            "report": {
-                                "markdown": "\n# Workflow Report for Assembly Polishing\n\n## Workflow steps\n\n```galaxy\nworkflow_display()\n```\n\n## Fasta statistics after Racon long-read polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Racon long read polish\")\n```\n\n\n## Fasta statistics after Medaka polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Medaka polish\")\n```\n\n## Fasta statistics after Racon short-read polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Racon short read polish\")\n```\n\n\n\n\n"
-                            },
-                            "steps": {
-                                "0": {
-                                    "annotation": "",
-                                    "content_id": null,
-                                    "errors": null,
-                                    "id": 0,
-                                    "input_connections": {},
-                                    "inputs": [
-                                        {
-                                            "description": "",
-                                            "name": "Assembly to be polished"
-                                        }
-                                    ],
-                                    "label": "Assembly to be polished",
-                                    "name": "Input dataset",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 19.464939294568495,
-                                        "top": 0.0
-                                    },
-                                    "tool_id": null,
-                                    "tool_state": "{\"optional\": false, \"tag\": null}",
-                                    "tool_version": null,
-                                    "type": "data_input",
-                                    "uuid": "52bc9ac4-ac3c-48eb-aead-94a0a14417fc",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "1": {
-                                    "annotation": "",
-                                    "content_id": null,
-                                    "errors": null,
-                                    "id": 1,
-                                    "input_connections": {},
-                                    "inputs": [
-                                        {
-                                            "description": "",
-                                            "name": "long reads"
-                                        }
-                                    ],
-                                    "label": "long reads",
-                                    "name": "Input dataset",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 0.0,
-                                        "top": 142.48340578478533
-                                    },
-                                    "tool_id": null,
-                                    "tool_state": "{\"optional\": false, \"tag\": null}",
-                                    "tool_version": null,
-                                    "type": "data_input",
-                                    "uuid": "688866c4-de9b-4b78-8df3-b169d28b1617",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "2": {
-                                    "annotation": "",
-                                    "content_id": null,
-                                    "errors": null,
-                                    "id": 2,
-                                    "input_connections": {},
-                                    "inputs": [
-                                        {
-                                            "description": "",
-                                            "name": "minimap setting (for long reads)"
-                                        }
-                                    ],
-                                    "label": "minimap setting (for long reads)",
-                                    "name": "Input parameter",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 13.133522093825794,
-                                        "top": 247.1519749531627
-                                    },
-                                    "tool_id": null,
-                                    "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
-                                    "tool_version": null,
-                                    "type": "parameter_input",
-                                    "uuid": "c1f18b5c-e8db-4046-b876-9b28a77cf66e",
-                                    "when": null,
-                                    "workflow_outputs": [
-                                        {
-                                            "label": null,
-                                            "output_name": "output",
-                                            "uuid": "ce393bcf-42e3-43ee-9056-a99e8c077a29"
-                                        }
-                                    ]
-                                },
-                                "3": {
-                                    "annotation": "",
-                                    "content_id": null,
-                                    "errors": null,
-                                    "id": 3,
-                                    "input_connections": {},
-                                    "inputs": [
-                                        {
-                                            "description": "",
-                                            "name": "Illumina reads R1"
-                                        }
-                                    ],
-                                    "label": "Illumina reads R1",
-                                    "name": "Input dataset",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 617.719019724734,
-                                        "top": 600.0866464299372
-                                    },
-                                    "tool_id": null,
-                                    "tool_state": "{\"optional\": false, \"tag\": null}",
-                                    "tool_version": null,
-                                    "type": "data_input",
-                                    "uuid": "ea859a58-c81a-4ef6-9bd2-4ef2f17bb5a9",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                },
-                                "4": {
-                                    "annotation": "",
-                                    "id": 4,
-                                    "input_connections": {
-                                        "Assembly to be polished": {
-                                            "id": 0,
-                                            "input_subworkflow_step_id": 0,
-                                            "output_name": "output"
-                                        },
-                                        "long reads": {
-                                            "id": 1,
-                                            "input_subworkflow_step_id": 1,
-                                            "output_name": "output"
-                                        },
-                                        "minimap setting (for long reads) ": {
-                                            "id": 2,
-                                            "input_subworkflow_step_id": 2,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": null,
-                                    "name": "Racon polish with long reads, x4 - upgraded",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 299.6429464825318,
-                                        "top": 72.0364210406818
-                                    },
-                                    "subworkflow": {
-                                        "a_galaxy_workflow": "true",
-                                        "annotation": "",
-                                        "comments": [],
-                                        "creator": [
-                                            {
-                                                "class": "Person",
-                                                "identifier": "0000-0002-9906-0673",
-                                                "name": "Anna Syme"
-                                            }
-                                        ],
-                                        "format-version": "0.1",
-                                        "name": "Racon polish with long reads, x4 - upgraded",
-                                        "report": {
-                                            "markdown": "\n# Workflow Execution Report\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
-                                        },
-                                        "steps": {
-                                            "0": {
-                                                "annotation": "",
-                                                "content_id": null,
-                                                "errors": null,
-                                                "id": 0,
-                                                "input_connections": {},
-                                                "inputs": [
-                                                    {
-                                                        "description": "",
-                                                        "name": "Assembly to be polished"
-                                                    }
-                                                ],
-                                                "label": "Assembly to be polished",
-                                                "name": "Input dataset",
-                                                "outputs": [],
-                                                "position": {
-                                                    "left": 0,
-                                                    "top": 216.625
-                                                },
-                                                "tool_id": null,
-                                                "tool_state": "{\"optional\": false, \"tag\": null}",
-                                                "tool_version": null,
-                                                "type": "data_input",
-                                                "uuid": "c7796c36-adf8-49e4-a8e4-66e606d70311",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "1": {
-                                                "annotation": "",
-                                                "content_id": null,
-                                                "errors": null,
-                                                "id": 1,
-                                                "input_connections": {},
-                                                "inputs": [
-                                                    {
-                                                        "description": "",
-                                                        "name": "long reads"
-                                                    }
-                                                ],
-                                                "label": "long reads",
-                                                "name": "Input dataset",
-                                                "outputs": [],
-                                                "position": {
-                                                    "left": 4.5,
-                                                    "top": 360.234375
-                                                },
-                                                "tool_id": null,
-                                                "tool_state": "{\"optional\": false, \"tag\": null}",
-                                                "tool_version": null,
-                                                "type": "data_input",
-                                                "uuid": "e2e4a70b-6e36-4b8b-bdf6-12b97189a6bd",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "10": {
-                                                "annotation": "",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "errors": null,
-                                                "id": 10,
-                                                "input_connections": {
-                                                    "corrected_reads": {
-                                                        "id": 8,
-                                                        "output_name": "consensus"
-                                                    },
-                                                    "overlaps": {
-                                                        "id": 9,
-                                                        "output_name": "alignment_output"
-                                                    },
-                                                    "reads": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    }
-                                                },
-                                                "inputs": [],
-                                                "label": "Racon: polish 4",
-                                                "name": "Racon",
-                                                "outputs": [
-                                                    {
-                                                        "name": "consensus",
-                                                        "type": "fasta"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 1496.078125,
-                                                    "top": 431.1875
-                                                },
-                                                "post_job_actions": {
-                                                    "RenameDatasetActionconsensus": {
-                                                        "action_arguments": {
-                                                            "newname": "Racon_long_reads_polished_assembly.fasta"
-                                                        },
-                                                        "action_type": "RenameDatasetAction",
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "78c533842eeb",
-                                                    "name": "racon",
-                                                    "owner": "bgruening",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "1.5.0+galaxy1",
-                                                "type": "tool",
-                                                "uuid": "53f4572e-3a4a-4585-89ab-9459f8a61720",
-                                                "when": null,
-                                                "workflow_outputs": [
-                                                    {
-                                                        "label": "Assembly polished by long reads using Racon",
-                                                        "output_name": "consensus",
-                                                        "uuid": "bcf0f03c-5951-46a7-aa38-545aed9bc183"
-                                                    }
-                                                ]
-                                            },
-                                            "2": {
-                                                "annotation": "",
-                                                "content_id": null,
-                                                "errors": null,
-                                                "id": 2,
-                                                "input_connections": {},
-                                                "inputs": [
-                                                    {
-                                                        "description": "",
-                                                        "name": "minimap setting (for long reads) "
-                                                    }
-                                                ],
-                                                "label": "minimap setting (for long reads) ",
-                                                "name": "Input parameter",
-                                                "outputs": [],
-                                                "position": {
-                                                    "left": 0.578125,
-                                                    "top": 495.859375
-                                                },
-                                                "tool_id": null,
-                                                "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
-                                                "tool_version": null,
-                                                "type": "parameter_input",
-                                                "uuid": "fb80c05c-08d4-4ac2-b4bf-81ed906e4d72",
-                                                "when": null,
-                                                "workflow_outputs": [
-                                                    {
-                                                        "label": null,
-                                                        "output_name": "output",
-                                                        "uuid": "3983ef22-5f05-4384-8f34-6ac8c4b2cc83"
-                                                    }
-                                                ]
-                                            },
-                                            "3": {
-                                                "annotation": "Map raw reads to assembly; output paf",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "errors": null,
-                                                "id": 3,
-                                                "input_connections": {
-                                                    "fastq_input|analysis_type_selector": {
-                                                        "id": 2,
-                                                        "output_name": "output"
-                                                    },
-                                                    "fastq_input|fastq_input1": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    },
-                                                    "reference_source|ref_file": {
-                                                        "id": 0,
-                                                        "output_name": "output"
-                                                    }
-                                                },
-                                                "inputs": [
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "reference_source"
-                                                    }
-                                                ],
-                                                "label": "Minimap2: map long reads to assembly",
-                                                "name": "Map with minimap2",
-                                                "outputs": [
-                                                    {
-                                                        "name": "alignment_output",
-                                                        "type": "bam"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 377.640625,
-                                                    "top": 0
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionalignment_output": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "alignment_output"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "be1d967337e4",
-                                                    "name": "minimap2",
-                                                    "owner": "iuc",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "2.26+galaxy0",
-                                                "type": "tool",
-                                                "uuid": "0c06144f-d1ac-4b45-9669-1ddf11fcb06b",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "4": {
-                                                "annotation": "",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "errors": null,
-                                                "id": 4,
-                                                "input_connections": {
-                                                    "corrected_reads": {
-                                                        "id": 0,
-                                                        "output_name": "output"
-                                                    },
-                                                    "overlaps": {
-                                                        "id": 3,
-                                                        "output_name": "alignment_output"
-                                                    },
-                                                    "reads": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    }
-                                                },
-                                                "inputs": [],
-                                                "label": "Racon: polish 1",
-                                                "name": "Racon",
-                                                "outputs": [
-                                                    {
-                                                        "name": "consensus",
-                                                        "type": "fasta"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 458.640625,
-                                                    "top": 518.875
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionconsensus": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "78c533842eeb",
-                                                    "name": "racon",
-                                                    "owner": "bgruening",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "1.5.0+galaxy1",
-                                                "type": "tool",
-                                                "uuid": "6c144354-91f2-49dd-a1f5-7c4119859730",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "5": {
-                                                "annotation": "Map raw reads to assembly; output paf",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "errors": null,
-                                                "id": 5,
-                                                "input_connections": {
-                                                    "fastq_input|analysis_type_selector": {
-                                                        "id": 2,
-                                                        "output_name": "output"
-                                                    },
-                                                    "fastq_input|fastq_input1": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    },
-                                                    "reference_source|ref_file": {
-                                                        "id": 4,
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "inputs": [
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "reference_source"
-                                                    }
-                                                ],
-                                                "label": "Minimap2: map long reads to polished assembly 1",
-                                                "name": "Map with minimap2",
-                                                "outputs": [
-                                                    {
-                                                        "name": "alignment_output",
-                                                        "type": "bam"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 698.859375,
-                                                    "top": 13.390625
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionalignment_output": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "alignment_output"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "be1d967337e4",
-                                                    "name": "minimap2",
-                                                    "owner": "iuc",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "2.26+galaxy0",
-                                                "type": "tool",
-                                                "uuid": "c1b83dad-a8ed-42cb-951f-73f59f2dfa92",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "6": {
-                                                "annotation": "",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "errors": null,
-                                                "id": 6,
-                                                "input_connections": {
-                                                    "corrected_reads": {
-                                                        "id": 4,
-                                                        "output_name": "consensus"
-                                                    },
-                                                    "overlaps": {
-                                                        "id": 5,
-                                                        "output_name": "alignment_output"
-                                                    },
-                                                    "reads": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    }
-                                                },
-                                                "inputs": [],
-                                                "label": "Racon: polish 2",
-                                                "name": "Racon",
-                                                "outputs": [
-                                                    {
-                                                        "name": "consensus",
-                                                        "type": "fasta"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 759.9375,
-                                                    "top": 485.71875
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionconsensus": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "78c533842eeb",
-                                                    "name": "racon",
-                                                    "owner": "bgruening",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "1.5.0+galaxy1",
-                                                "type": "tool",
-                                                "uuid": "3208491e-b831-4238-957e-5b7388d7ff8d",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "7": {
-                                                "annotation": "Map raw reads to assembly; output paf",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "errors": null,
-                                                "id": 7,
-                                                "input_connections": {
-                                                    "fastq_input|analysis_type_selector": {
-                                                        "id": 2,
-                                                        "output_name": "output"
-                                                    },
-                                                    "fastq_input|fastq_input1": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    },
-                                                    "reference_source|ref_file": {
-                                                        "id": 6,
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "inputs": [
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "reference_source"
-                                                    }
-                                                ],
-                                                "label": "Minimap2: map long reads to polished assembly 2",
-                                                "name": "Map with minimap2",
-                                                "outputs": [
-                                                    {
-                                                        "name": "alignment_output",
-                                                        "type": "bam"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 998.75,
-                                                    "top": 27.9375
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionalignment_output": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "alignment_output"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "be1d967337e4",
-                                                    "name": "minimap2",
-                                                    "owner": "iuc",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "2.26+galaxy0",
-                                                "type": "tool",
-                                                "uuid": "42af524b-7f74-4c75-8d78-f6888078dd2e",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "8": {
-                                                "annotation": "",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "errors": null,
-                                                "id": 8,
-                                                "input_connections": {
-                                                    "corrected_reads": {
-                                                        "id": 6,
-                                                        "output_name": "consensus"
-                                                    },
-                                                    "overlaps": {
-                                                        "id": 7,
-                                                        "output_name": "alignment_output"
-                                                    },
-                                                    "reads": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    }
-                                                },
-                                                "inputs": [],
-                                                "label": "Racon: polish 3",
-                                                "name": "Racon",
-                                                "outputs": [
-                                                    {
-                                                        "name": "consensus",
-                                                        "type": "fasta"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 1089.71875,
-                                                    "top": 455.53125
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionconsensus": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "78c533842eeb",
-                                                    "name": "racon",
-                                                    "owner": "bgruening",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "1.5.0+galaxy1",
-                                                "type": "tool",
-                                                "uuid": "21f339bd-ebc1-4c73-a976-5d0b9ab2127a",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "9": {
-                                                "annotation": "Map raw reads to assembly; output paf",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "errors": null,
-                                                "id": 9,
-                                                "input_connections": {
-                                                    "fastq_input|analysis_type_selector": {
-                                                        "id": 2,
-                                                        "output_name": "output"
-                                                    },
-                                                    "fastq_input|fastq_input1": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    },
-                                                    "reference_source|ref_file": {
-                                                        "id": 8,
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "inputs": [
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "reference_source"
-                                                    }
-                                                ],
-                                                "label": "Minimap2: map long reads to polished assembly 3",
-                                                "name": "Map with minimap2",
-                                                "outputs": [
-                                                    {
-                                                        "name": "alignment_output",
-                                                        "type": "bam"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 1316.53125,
-                                                    "top": 38.046875
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionalignment_output": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "alignment_output"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "be1d967337e4",
-                                                    "name": "minimap2",
-                                                    "owner": "iuc",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "2.26+galaxy0",
-                                                "type": "tool",
-                                                "uuid": "7d36291e-aa76-4312-9943-b5e56d0e90c5",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            }
-                                        },
-                                        "tags": "",
-                                        "uuid": "c57efd37-4cf6-4cc7-abf4-2bab22a2e9a0"
-                                    },
-                                    "tool_id": null,
-                                    "type": "subworkflow",
-                                    "uuid": "58c99e4b-fd6a-401d-b9c7-cdf7e6d1757d",
-                                    "when": null,
-                                    "workflow_outputs": [
-                                        {
-                                            "label": null,
-                                            "output_name": "2:output",
-                                            "uuid": "50fa1032-8037-454e-8192-b95405bcd5d4"
-                                        }
-                                    ]
+                        "label": "Reads",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 197.65334499942068
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "2bfdfb62-da85-4d2d-8609-8f5e6975b4b3",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "M. tuberculosis reference genome (must be in H37Rv coordinates. The M. tuberculosis inferred ancestral genome is recommended)",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "M. tuberculosis reference genome (must be in H37Rv coordinates. The M. tuberculosis inferred ancestral genome is recommended)",
+                                "name": "Reference Genome"
+                            }
+                        ],
+                        "label": "Reference Genome",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 1.2375059369900399,
+                            "top": 468.60335731890825
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"genbank\"], \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "023233a0-8cb1-4558-8861-cd246ab58bac",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "Minimum depth of coverage for a position on the genome",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Minimum depth of coverage for a position on the genome",
+                                "name": "Minimum depth of coverage"
+                            }
+                        ],
+                        "label": "Minimum depth of coverage",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 1.8793911063654463,
+                            "top": 625.941216238093
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"default\": 10, \"parameter_type\": \"integer\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "e31bf396-08b6-43ce-872a-545a5e4580c6",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "Minimum proportion of reads that must support a variant for it to be called",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Minimum proportion of reads that must support a variant for it to be called",
+                                "name": "Minimum variant allele frequency"
+                            }
+                        ],
+                        "label": "Minimum variant allele frequency",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 1.358958473709409,
+                            "top": 769.7667492120408
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"default\": 0.9, \"parameter_type\": \"float\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "d1814962-a30d-463a-a081-857a5141385b",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "Increasing the minimum seed length (-k) parameter can help eliminate matches from contaminants. If used this should be set to 2/3rds of the read length, i.e. the string \"-k 100\" should be used for 150 base pair reads",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Increasing the minimum seed length (-k) parameter can help eliminate matches from contaminants. If used this should be set to 2/3rds of the read length, i.e. the string \"-k 100\" should be used for 150 base pair reads",
+                                "name": "Additional BWA-MEM options"
+                            }
+                        ],
+                        "label": "Additional BWA-MEM options",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 7.8094297093662135,
+                            "top": 931.4341211532
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "40d47253-c7c5-471b-871c-9a19fbe60bfe",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "AGPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nReads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference Genome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nMinimum depth of coverage\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nMinimum variant allele frequency\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nAdditional BWA-MEM options\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"fastp\"];\n  0 -->|output| 5;\n  6[\"seqret\"];\n  1 -->|output| 6;\n  7[\"snippy\"];\n  4 -->|output| 7;\n  2 -->|output| 7;\n  3 -->|output| 7;\n  5 -->|output_paired_coll| 7;\n  1 -->|output| 7;\n  8[\"Kraken2\"];\n  5 -->|output_paired_coll| 8;\n  c7abf2bf-ed4c-433e-a695-9eca61282bb5[\"Output\\nreport_output\"];\n  8 --> c7abf2bf-ed4c-433e-a695-9eca61282bb5;\n  style c7abf2bf-ed4c-433e-a695-9eca61282bb5 stroke:#2c3143,stroke-width:4px;\n  083a0e51-7780-4c91-a071-dc0e4641d060[\"Output\\noutput\"];\n  8 --> 083a0e51-7780-4c91-a071-dc0e4641d060;\n  style 083a0e51-7780-4c91-a071-dc0e4641d060 stroke:#2c3143,stroke-width:4px;\n  9[\"QualiMap BamQC\"];\n  7 -->|snpsbam| 9;\n  10[\"mosdepth\"];\n  2 -->|output| 10;\n  7 -->|snpsbam| 10;\n  11[\"TB Variant Filter\"];\n  7 -->|snpvcf| 11;\n  12[\"TB-Profiler Profile\"];\n  7 -->|snpsbam| 12;\n  335635b4-a4de-4980-ad02-68f0035daeaa[\"Output\\noutput_txt\"];\n  12 --> 335635b4-a4de-4980-ad02-68f0035daeaa;\n  style 335635b4-a4de-4980-ad02-68f0035daeaa stroke:#2c3143,stroke-width:4px;\n  13[\"TB Variant Filter\"];\n  7 -->|snpvcf| 13;\n  14[\"Flatten collection\"];\n  9 -->|raw_data| 14;\n  15[\"Text reformatting\"];\n  10 -->|output_quantized_bed| 15;\n  16[\"Text transformation\"];\n  11 -->|output1| 16;\n  007df8c2-bd13-495f-8904-abf31d4594d0[\"Output\\nFinal annotated VCF\"];\n  16 --> 007df8c2-bd13-495f-8904-abf31d4594d0;\n  style 007df8c2-bd13-495f-8904-abf31d4594d0 stroke:#2c3143,stroke-width:4px;\n  17[\"MultiQC\"];\n  5 -->|report_json| 17;\n  14 -->|output| 17;\n  59528235-7525-4ef9-8810-36f1ed0f01f6[\"Output\\nhtml_report\"];\n  17 --> 59528235-7525-4ef9-8810-36f1ed0f01f6;\n  style 59528235-7525-4ef9-8810-36f1ed0f01f6 stroke:#2c3143,stroke-width:4px;\n  18[\"bcftools consensus\"];\n  13 -->|output1| 18;\n  6 -->|out_file1| 18;\n  15 -->|outfile| 18;\n  c71b135d-35f9-44d0-a20e-f25528e518af[\"Output\\nconsensus_genome\"];\n  18 --> c71b135d-35f9-44d0-a20e-f25528e518af;\n  style c71b135d-35f9-44d0-a20e-f25528e518af stroke:#2c3143,stroke-width:4px;\n  19[\"TB Variant Report\"];\n  16 -->|output| 19;\n  12 -->|results_json| 19;\n  959528d2-f8f2-4440-99cf-44fddd6c5069[\"Output\\ndrug_resistance_report_html\"];\n  19 --> 959528d2-f8f2-4440-99cf-44fddd6c5069;\n  style 959528d2-f8f2-4440-99cf-44fddd6c5069 stroke:#2c3143,stroke-width:4px;\n  4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0[\"Output\\nvariants_report_html\"];\n  19 --> 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0;\n  style 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "TB Variant Analysis v1.0",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "single_paired|input_pair": {
+                                "id": 5,
+                                "output_name": "output_paired_coll"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Kraken2",
+                                "name": "single_paired"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Kraken2",
+                        "outputs": [
+                            {
+                                "name": "report_output",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 1605.1346167188794,
+                            "top": 0
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionoutput": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output"
+                            },
+                            "TagDatasetActionreport_output": {
+                                "action_arguments": {
+                                    "tags": "kraken_report"
                                 },
-                                "5": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
-                                    "errors": null,
-                                    "id": 5,
-                                    "input_connections": {
-                                        "d": {
-                                            "id": 4,
-                                            "output_name": "Assembly polished by long reads using Racon"
-                                        },
-                                        "i": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Medaka polish",
-                                    "name": "medaka consensus pipeline",
-                                    "outputs": [
-                                        {
-                                            "name": "out_consensus",
-                                            "type": "fasta"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 515.5164024294684,
-                                        "top": 305.08460859328346
-                                    },
-                                    "post_job_actions": {
-                                        "RenameDatasetActionout_consensus": {
-                                            "action_arguments": {
-                                                "newname": "Medaka_long_reads_polished_assembly.fasta"
-                                            },
-                                            "action_type": "RenameDatasetAction",
-                                            "output_name": "out_consensus"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "fc8804320156",
-                                        "name": "medaka_consensus_pipeline",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"b\": \"100\", \"d\": {\"__class__\": \"ConnectedValue\"}, \"g\": false, \"i\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"r941_min_high_g360\", \"out\": [\"consensus\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "1.7.2+galaxy1",
-                                    "type": "tool",
-                                    "uuid": "14c5ce9c-df92-4e20-85da-7a161eaa759d",
-                                    "when": null,
-                                    "workflow_outputs": [
-                                        {
-                                            "label": "Assembly polished by long reads using Medaka",
-                                            "output_name": "out_consensus",
-                                            "uuid": "e3136060-bce7-4af3-87c4-9dcbb0d1f531"
-                                        }
-                                    ]
+                                "action_type": "TagDatasetAction",
+                                "output_name": "report_output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "20e2f64aa1fe",
+                            "name": "kraken2",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"confidence\": \"0.0\", \"kraken2_database\": \"pluspf2021-05\", \"min_base_quality\": \"0\", \"minimum_hit_groups\": \"2\", \"quick\": false, \"report\": {\"create_report\": true, \"use_mpa_style\": false, \"report_zero_counts\": false, \"report_minimizer_data\": false}, \"single_paired\": {\"single_paired_selector\": \"collection\", \"__current_case__\": 0, \"input_pair\": {\"__class__\": \"ConnectedValue\"}}, \"split_reads\": false, \"use_names\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.1+galaxy1",
+                        "type": "tool",
+                        "uuid": "60b17d56-0ef9-4829-829e-923f66de5e2f",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "report_output",
+                                "output_name": "report_output",
+                                "uuid": "c7abf2bf-ed4c-433e-a695-9eca61282bb5"
+                            },
+                            {
+                                "label": "output",
+                                "output_name": "output",
+                                "uuid": "083a0e51-7780-4c91-a071-dc0e4641d060"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.2.1+galaxy0",
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {
+                            "fastq_or_bam|bam_input": {
+                                "id": 7,
+                                "output_name": "snpsbam"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool TB-Profiler Profile",
+                                "name": "fastq_or_bam"
+                            }
+                        ],
+                        "label": null,
+                        "name": "TB-Profiler Profile",
+                        "outputs": [
+                            {
+                                "name": "results_json",
+                                "type": "json"
+                            },
+                            {
+                                "name": "output_vcf",
+                                "type": "vcf"
+                            },
+                            {
+                                "name": "output_txt",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 1132.7778271896836,
+                            "top": 615.3961147101202
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionoutput_vcf": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_vcf"
+                            },
+                            "HideDatasetActionresults_json": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "results_json"
+                            },
+                            "TagDatasetActionoutput_txt": {
+                                "action_arguments": {
+                                    "tags": "drug_resistance_report"
                                 },
-                                "6": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                                    "errors": null,
-                                    "id": 6,
-                                    "input_connections": {
-                                        "fasta": {
-                                            "id": 4,
-                                            "output_name": "Assembly polished by long reads using Racon"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Fasta statistics after Racon long read polish",
-                                    "name": "Fasta Statistics",
-                                    "outputs": [
-                                        {
-                                            "name": "stats_output",
-                                            "type": "tabular"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 611.8186129984722,
-                                        "top": 131.47863560473016
-                                    },
-                                    "post_job_actions": {},
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "0dbb995c7d35",
-                                        "name": "fasta_stats",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gaps_option\": false, \"genome_size\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "2.0",
-                                    "type": "tool",
-                                    "uuid": "e78db141-a6d2-42b1-b2b6-aee5e900d3f4",
-                                    "when": null,
-                                    "workflow_outputs": []
+                                "action_type": "TagDatasetAction",
+                                "output_name": "output_txt"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.2.1+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "4839e590cb26",
+                            "name": "tbprofiler",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"advanced\": {\"options\": \"no\", \"__current_case__\": 0}, \"fastq_or_bam\": {\"input_select\": \"bam\", \"__current_case__\": 3, \"bam_input\": {\"__class__\": \"ConnectedValue\"}}, \"output_format\": \"txt\", \"platform\": \"illumina\", \"spoligotype\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "6.2.1+galaxy0",
+                        "type": "tool",
+                        "uuid": "22d89589-70a3-4e6e-8b95-68604a287052",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "output_txt",
+                                "output_name": "output_txt",
+                                "uuid": "335635b4-a4de-4980-ad02-68f0035daeaa"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
+                        "errors": null,
+                        "id": 16,
+                        "input_connections": {
+                            "infile": {
+                                "id": 11,
+                                "output_name": "output1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Text transformation",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1379.287563641826,
+                            "top": 248.44083584414724
+                        },
+                        "post_job_actions": {
+                            "TagDatasetActionoutput": {
+                                "action_arguments": {
+                                    "tags": "annotated_vcf"
                                 },
-                                "7": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                                    "errors": null,
-                                    "id": 7,
-                                    "input_connections": {
-                                        "fasta": {
-                                            "id": 5,
-                                            "output_name": "out_consensus"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Fasta statistics after Medaka polish",
-                                    "name": "Fasta Statistics",
-                                    "outputs": [
-                                        {
-                                            "name": "stats_output",
-                                            "type": "tabular"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 816.9504695700908,
-                                        "top": 343.05724959525315
-                                    },
-                                    "post_job_actions": {},
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "0dbb995c7d35",
-                                        "name": "fasta_stats",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gaps_option\": false, \"genome_size\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "2.0",
-                                    "type": "tool",
-                                    "uuid": "96f313ee-4a6a-4ba9-86f8-3dedc1d5d30d",
-                                    "when": null,
-                                    "workflow_outputs": []
+                                "action_type": "TagDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "fbf99087e067",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"s/GENE_//g\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "9.3+galaxy1",
+                        "type": "tool",
+                        "uuid": "c45f6679-0d38-4663-a783-775b0f522bcc",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Final annotated VCF",
+                                "output_name": "output",
+                                "uuid": "007df8c2-bd13-495f-8904-abf31d4594d0"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+                        "errors": null,
+                        "id": 17,
+                        "input_connections": {
+                            "results_0|software_cond|input": {
+                                "id": 5,
+                                "output_name": "report_json"
+                            },
+                            "results_1|software_cond|input": {
+                                "id": 14,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "MultiQC",
+                        "outputs": [
+                            {
+                                "name": "stats",
+                                "type": "input"
+                            },
+                            {
+                                "name": "html_report",
+                                "type": "html"
+                            }
+                        ],
+                        "position": {
+                            "left": 1604.2880860884582,
+                            "top": 202.3882167631859
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "TagDatasetActionhtml_report": {
+                                "action_arguments": {
+                                    "tags": "qc_report"
                                 },
-                                "8": {
-                                    "annotation": "",
-                                    "id": 8,
-                                    "input_connections": {
-                                        "Assembly to be polished": {
-                                            "id": 5,
-                                            "input_subworkflow_step_id": 0,
-                                            "output_name": "out_consensus"
-                                        },
-                                        "Illumina reads, R1, in fastq.gz format": {
-                                            "id": 3,
-                                            "input_subworkflow_step_id": 1,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": null,
-                                    "name": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 915.3758175639219,
-                                        "top": 512.306732089216
-                                    },
-                                    "subworkflow": {
-                                        "a_galaxy_workflow": "true",
-                                        "annotation": "",
-                                        "comments": [],
-                                        "creator": [
-                                            {
-                                                "class": "Person",
-                                                "identifier": "0000-0002-9906-0673",
-                                                "name": "Anna Syme"
-                                            }
-                                        ],
-                                        "format-version": "0.1",
-                                        "name": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
-                                        "steps": {
-                                            "0": {
-                                                "annotation": "",
-                                                "content_id": null,
-                                                "errors": null,
-                                                "id": 0,
-                                                "input_connections": {},
-                                                "inputs": [
-                                                    {
-                                                        "description": "",
-                                                        "name": "Assembly to be polished"
-                                                    }
-                                                ],
-                                                "label": "Assembly to be polished",
-                                                "name": "Input dataset",
-                                                "outputs": [],
-                                                "position": {
-                                                    "left": 0,
-                                                    "top": 72.5176329833982
-                                                },
-                                                "tool_id": null,
-                                                "tool_state": "{\"optional\": false, \"tag\": null}",
-                                                "tool_version": null,
-                                                "type": "data_input",
-                                                "uuid": "28669894-74e2-4ba1-9d49-6e3209b5a1de",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "1": {
-                                                "annotation": "",
-                                                "content_id": null,
-                                                "errors": null,
-                                                "id": 1,
-                                                "input_connections": {},
-                                                "inputs": [
-                                                    {
-                                                        "description": "",
-                                                        "name": "Illumina reads, R1, in fastq.gz format"
-                                                    }
-                                                ],
-                                                "label": "Illumina reads, R1, in fastq.gz format",
-                                                "name": "Input dataset",
-                                                "outputs": [],
-                                                "position": {
-                                                    "left": 8.5,
-                                                    "top": 341.2832579833982
-                                                },
-                                                "tool_id": null,
-                                                "tool_state": "{\"optional\": false, \"tag\": null}",
-                                                "tool_version": null,
-                                                "type": "data_input",
-                                                "uuid": "bc936fdc-22a9-4507-aa47-4a70a3f93923",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "2": {
-                                                "annotation": "",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "errors": null,
-                                                "id": 2,
-                                                "input_connections": {
-                                                    "fastq_input|fastq_input1": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    },
-                                                    "reference_source|ref_file": {
-                                                        "id": 0,
-                                                        "output_name": "output"
-                                                    }
-                                                },
-                                                "inputs": [
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "reference_source"
-                                                    }
-                                                ],
-                                                "label": "Minimap2 round 1: map reads to assembly",
-                                                "name": "Map with minimap2",
-                                                "outputs": [
-                                                    {
-                                                        "name": "alignment_output",
-                                                        "type": "bam"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 399.936279296875,
-                                                    "top": 0
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionalignment_output": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "alignment_output"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "be1d967337e4",
-                                                    "name": "minimap2",
-                                                    "owner": "iuc",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": \"sr\"}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "2.26+galaxy0",
-                                                "type": "tool",
-                                                "uuid": "b01b8c3d-c33b-47b2-9a83-297c19d63ab7",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "3": {
-                                                "annotation": "",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "errors": null,
-                                                "id": 3,
-                                                "input_connections": {
-                                                    "corrected_reads": {
-                                                        "id": 0,
-                                                        "output_name": "output"
-                                                    },
-                                                    "overlaps": {
-                                                        "id": 2,
-                                                        "output_name": "alignment_output"
-                                                    },
-                                                    "reads": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    }
-                                                },
-                                                "inputs": [],
-                                                "label": "Racon round 1: polish assembly",
-                                                "name": "Racon",
-                                                "outputs": [
-                                                    {
-                                                        "name": "consensus",
-                                                        "type": "fasta"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 635.5625200274146,
-                                                    "top": 432.13610641498093
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionconsensus": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "78c533842eeb",
-                                                    "name": "racon",
-                                                    "owner": "bgruening",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"error_threshold\": \"0.3\", \"fragment_correction\": false, \"gap\": \"-4\", \"include_unpolished\": false, \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"window_length\": \"500\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "1.5.0+galaxy1",
-                                                "type": "tool",
-                                                "uuid": "fe32d046-4ff2-485e-84e8-191b04803afc",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "4": {
-                                                "annotation": "",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "errors": null,
-                                                "id": 4,
-                                                "input_connections": {
-                                                    "fastq_input|fastq_input1": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    },
-                                                    "reference_source|ref_file": {
-                                                        "id": 3,
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "inputs": [
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "fastq_input"
-                                                    },
-                                                    {
-                                                        "description": "runtime parameter for tool Map with minimap2",
-                                                        "name": "reference_source"
-                                                    }
-                                                ],
-                                                "label": "Minimap2 round 2: map reads to assembly",
-                                                "name": "Map with minimap2",
-                                                "outputs": [
-                                                    {
-                                                        "name": "alignment_output",
-                                                        "type": "bam"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 859.5,
-                                                    "top": 23.955132983398205
-                                                },
-                                                "post_job_actions": {
-                                                    "HideDatasetActionalignment_output": {
-                                                        "action_arguments": {},
-                                                        "action_type": "HideDatasetAction",
-                                                        "output_name": "alignment_output"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "be1d967337e4",
-                                                    "name": "minimap2",
-                                                    "owner": "iuc",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": \"sr\"}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "2.26+galaxy0",
-                                                "type": "tool",
-                                                "uuid": "ee834cad-027a-4a84-963b-141b22eaa70a",
-                                                "when": null,
-                                                "workflow_outputs": []
-                                            },
-                                            "5": {
-                                                "annotation": "",
-                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "errors": null,
-                                                "id": 5,
-                                                "input_connections": {
-                                                    "corrected_reads": {
-                                                        "id": 3,
-                                                        "output_name": "consensus"
-                                                    },
-                                                    "overlaps": {
-                                                        "id": 4,
-                                                        "output_name": "alignment_output"
-                                                    },
-                                                    "reads": {
-                                                        "id": 1,
-                                                        "output_name": "output"
-                                                    }
-                                                },
-                                                "inputs": [],
-                                                "label": "Racon round 2: polish assembly",
-                                                "name": "Racon",
-                                                "outputs": [
-                                                    {
-                                                        "name": "consensus",
-                                                        "type": "fasta"
-                                                    }
-                                                ],
-                                                "position": {
-                                                    "left": 1198.765625,
-                                                    "top": 332.4707579833982
-                                                },
-                                                "post_job_actions": {
-                                                    "RenameDatasetActionconsensus": {
-                                                        "action_arguments": {
-                                                            "newname": "Racon_short_reads_polished_assembly.fasta"
-                                                        },
-                                                        "action_type": "RenameDatasetAction",
-                                                        "output_name": "consensus"
-                                                    }
-                                                },
-                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                                                "tool_shed_repository": {
-                                                    "changeset_revision": "78c533842eeb",
-                                                    "name": "racon",
-                                                    "owner": "bgruening",
-                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
-                                                },
-                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                                "tool_version": "1.5.0+galaxy1",
-                                                "type": "tool",
-                                                "uuid": "b3c89c40-3ad0-454c-a4d4-dfa34fb09f24",
-                                                "when": null,
-                                                "workflow_outputs": [
-                                                    {
-                                                        "label": "Assembly polished by short reads using Racon",
-                                                        "output_name": "consensus",
-                                                        "uuid": "594819c3-668e-4575-b9a6-4459ffacf952"
-                                                    }
-                                                ]
-                                            }
-                                        },
-                                        "tags": "",
-                                        "uuid": "1b96b1cf-dbd4-46b1-8a59-aebfe80135c2"
-                                    },
-                                    "tool_id": null,
-                                    "type": "subworkflow",
-                                    "uuid": "46288abb-a2bc-43d5-822a-a93af0d346cf",
-                                    "when": null,
-                                    "workflow_outputs": []
+                                "action_type": "TagDatasetAction",
+                                "output_name": "html_report"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "abfd8a6544d7",
+                            "name": "multiqc",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"qualimap\", \"__current_case__\": 20, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.11+galaxy1",
+                        "type": "tool",
+                        "uuid": "6367e2a7-c3b0-4dc4-bbc2-e861e66eaeae",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "html_report",
+                                "output_name": "html_report",
+                                "uuid": "59528235-7525-4ef9-8810-36f1ed0f01f6"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Compute consensus genome with single nucleotide variants inserted, suitable for use in building a phylogeny",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
+                        "errors": null,
+                        "id": 18,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 13,
+                                "output_name": "output1"
+                            },
+                            "reference_source|fasta_ref": {
+                                "id": 6,
+                                "output_name": "out_file1"
+                            },
+                            "sec_default|mask": {
+                                "id": 15,
+                                "output_name": "outfile"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool bcftools consensus",
+                                "name": "reference_source"
+                            },
+                            {
+                                "description": "runtime parameter for tool bcftools consensus",
+                                "name": "sec_default"
+                            }
+                        ],
+                        "label": null,
+                        "name": "bcftools consensus",
+                        "outputs": [
+                            {
+                                "name": "output_file",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "left": 1601.1886936133394,
+                            "top": 1003.2778990479657
+                        },
+                        "post_job_actions": {
+                            "TagDatasetActionoutput_file": {
+                                "action_arguments": {
+                                    "tags": "consensus_genome"
                                 },
-                                "9": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                                    "errors": null,
-                                    "id": 9,
-                                    "input_connections": {
-                                        "fasta": {
-                                            "id": 8,
-                                            "output_name": "Assembly polished by short reads using Racon"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Fasta statistics after Racon short read polish",
-                                    "name": "Fasta Statistics",
-                                    "outputs": [
-                                        {
-                                            "name": "stats_output",
-                                            "type": "tabular"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 1179.1223817823236,
-                                        "top": 547.060000097866
-                                    },
-                                    "post_job_actions": {},
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "0dbb995c7d35",
-                                        "name": "fasta_stats",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gaps_option\": false, \"genome_size\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": "2.0",
-                                    "type": "tool",
-                                    "uuid": "3c06b177-02b5-4068-8056-56b653d95379",
-                                    "when": null,
-                                    "workflow_outputs": []
-                                }
+                                "action_type": "TagDatasetAction",
+                                "output_name": "output_file"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "147de996e34f",
+                            "name": "bcftools_consensus",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"absent\": \"\", \"chain\": false, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"ConnectedValue\"}}, \"rename\": false, \"sec_default\": {\"mask\": {\"__class__\": \"ConnectedValue\"}, \"iupac_codes\": false, \"sample\": null, \"select_haplotype\": null, \"mark_del\": \"\", \"mark_ins\": null, \"mark_snv\": null, \"conditional_mask\": {\"selector\": \"disabled\", \"__current_case__\": 0}}, \"sec_restrict\": {\"include\": null, \"exclude\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.15.1+galaxy3",
+                        "type": "tool",
+                        "uuid": "2b226e0c-8e59-472d-8bcd-6d8d84dfddab",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "consensus_genome",
+                                "output_name": "output_file",
+                                "uuid": "c71b135d-35f9-44d0-a20e-f25528e518af"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.0+galaxy0",
+                        "errors": null,
+                        "id": 19,
+                        "input_connections": {
+                            "input_vcf": {
+                                "id": 16,
+                                "output_name": "output"
+                            },
+                            "tbprofiler_json": {
+                                "id": 12,
+                                "output_name": "results_json"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "TB Variant Report",
+                        "outputs": [
+                            {
+                                "name": "variants_report_html",
+                                "type": "html"
+                            },
+                            {
+                                "name": "variants_report_txt",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "drug_resistance_report_html",
+                                "type": "html"
+                            },
+                            {
+                                "name": "drug_resistance_report_txt",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 1591.762535768669,
+                            "top": 427.7783435581315
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActiondrug_resistance_report_txt": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "drug_resistance_report_txt"
+                            },
+                            "HideDatasetActionvariants_report_txt": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "variants_report_txt"
+                            },
+                            "TagDatasetActiondrug_resistance_report_html": {
+                                "action_arguments": {
+                                    "tags": "variant_report"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "drug_resistance_report_html"
+                            },
+                            "TagDatasetActionvariants_report_html": {
+                                "action_arguments": {
+                                    "tags": "variant_report"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "variants_report_html"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.0+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "42818629ec4c",
+                            "name": "tbvcfreport",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv\": {\"database_uri\": \"neodb.sanbi.ac.za\"}, \"filter_udi\": true, \"input_vcf\": {\"__class__\": \"ConnectedValue\"}, \"tbprofiler_json\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0+galaxy0",
+                        "type": "tool",
+                        "uuid": "183d84e7-91ea-4e8f-950b-f65629b60b1b",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "drug_resistance_report_html",
+                                "output_name": "drug_resistance_report_html",
+                                "uuid": "959528d2-f8f2-4440-99cf-44fddd6c5069"
                             },
-                            "tags": "",
-                            "uuid": "af8b99cb-cfc5-4f96-ba6c-6a178826ca98"
+                            {
+                                "label": "variants_report_html",
+                                "output_name": "variants_report_html",
+                                "uuid": "4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "variant-analysis/tb-variant-analysis",
+                "path": "topics/variant-analysis/tutorials/tb-variant-analysis/workflows/tb-variant-analysis.ga",
+                "tags": [
+                    "pathogen",
+                    "tuberculosis"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "TB Variant Analysis v1.0",
+                "topic_id": "variant-analysis",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-tb-variant-analysis/versions/tb-variant-analysis",
+                "tutorial_id": "tb-variant-analysis",
+                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/tb-variant-analysis/workflows/tb-variant-analysis.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/tb-variant-analysis/workflows/tb-variant-analysis.html",
+                "version": 7,
+                "wfid": "variant-analysis-tb-variant-analysis",
+                "wfname": "tb-variant-analysis",
+                "workflow": "tb-variant-analysis.ga",
+                "workflow_tools": [
+                    "__FLATTEN__",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: seqret84/5.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mosdepth/mosdepth/0.3.8+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.4.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.2.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.0+galaxy0"
+                ],
+                "workflowhub_id": "1069"
+            }
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.3496437"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bwa",
+                    "owner": "devteam",
+                    "revisions": "3fe632431b68",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "picard",
+                    "owner": "devteam",
+                    "revisions": "a1f0b3f4b781",
+                    "tool_panel_section_label": "Picard",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "samtools_stats",
+                    "owner": "devteam",
+                    "revisions": "145f6d74ff5e",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastp",
+                    "owner": "iuc",
+                    "revisions": "dbf9c561ef29",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "lofreq_call",
+                    "owner": "iuc",
+                    "revisions": "65432c3abf6c",
+                    "tool_panel_section_label": "Variant Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "lofreq_indelqual",
+                    "owner": "iuc",
+                    "revisions": "426d707dfc47",
+                    "tool_panel_section_label": "Variant Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "lofreq_viterbi",
+                    "owner": "iuc",
+                    "revisions": "aa35ee7f3ab2",
+                    "tool_panel_section_label": "Variant Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "bf675f34b056",
+                    "tool_panel_section_label": "Quality Control",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "snpeff_sars_cov_2",
+                    "owner": "iuc",
+                    "revisions": "2a3a00c1fa0a",
+                    "tool_panel_section_label": "Variant Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "snpsift",
+                    "owner": "iuc",
+                    "revisions": "5fab4f81391d",
+                    "tool_panel_section_label": "Variant Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sra_tools",
+                    "owner": "iuc",
+                    "revisions": "494b2ec08162",
+                    "tool_panel_section_label": "Get Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sra_tools",
+                    "owner": "iuc",
+                    "revisions": "4df8de2d0e48",
+                    "tool_panel_section_label": "Get Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: 3fe632431b68\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: a1f0b3f4b781\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 145f6d74ff5e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: dbf9c561ef29\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lofreq_call\n  owner: iuc\n  revisions: 65432c3abf6c\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lofreq_indelqual\n  owner: iuc\n  revisions: 426d707dfc47\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lofreq_viterbi\n  owner: iuc\n  revisions: aa35ee7f3ab2\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: bf675f34b056\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff_sars_cov_2\n  owner: iuc\n  revisions: 2a3a00c1fa0a\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpsift\n  owner: iuc\n  revisions: 5fab4f81391d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: 494b2ec08162\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: 4df8de2d0e48\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "mvdbeek",
+                "tnabtaf",
+                "blankenberg",
+                "nekrut"
+            ],
+            "editing": [
+                "wm75"
+            ]
+        },
+        "contributors": [
+            {
+                "id": "mvdbeek",
+                "joined": "2018-06",
+                "name": "Marius van den Beek",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
+            },
+            {
+                "id": "tnabtaf",
+                "joined": "2017-09",
+                "name": "Dave Clements",
+                "orcid": "0000-0002-9970-6657",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
+            },
+            {
+                "id": "blankenberg",
+                "joined": "2018-07",
+                "name": "Daniel Blankenberg",
+                "orcid": "0000-0002-6833-9049",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankenberg/",
+                "twitter": "dblankenberg",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankenberg.json"
+            },
+            {
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
+                "joined": "2017-09",
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+            },
+            {
+                "affiliations": [
+                    "by-covid",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "elixir_node": "de",
+                "fediverse": "https://scholar.social/@zerodivision",
+                "fediverse_flavor": "mastodon",
+                "id": "wm75",
+                "joined": "2017-09",
+                "matrix": "wm75:matrix.org",
+                "name": "Wolfgang Maier",
+                "orcid": "0000-0002-9464-6640",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
+            }
+        ],
+        "dir": "topics/variant-analysis/tutorials/sars-cov-2",
+        "edam_operation": [
+            "Data handling",
+            "Sequence alignment",
+            "Read mapping",
+            "Sequencing quality control",
+            "Sequence contamination filtering",
+            "Generation",
+            "Validation",
+            "SNP detection",
+            "Formatting",
+            "Genome indexing"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "variant-analysis/sars-cov-2",
+        "inexact_supported_servers": [
+            "MISSISSIPPI",
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Sequence data in the SRA can be directly imported into Galaxy",
+            "Collections enable efficient/parallel processing of sequence data from whole batches of samples",
+            "Genomic mutations in SARS-CoV-2 viral isolates can be identified through a straightforward pipeline involving sequenced reads preprocessing, mapping to the SARS-CoV-2 reference genome, postprocessing of mapping results, and variant calling"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-14",
+        "objectives": [
+            "Understand how Galaxy and the Sequence Read Archive interact",
+            "Be able to go from Galaxy to the Short Reach Archive, query SRA, use the SRA Run Selector to send selected metadata to Galaxy, and then import sequence data from SRA into Galaxy",
+            "Understand how collections enable processing of sequencing data in batches",
+            "Understand the analysis steps required to identify and annotate genomic mutations from sequencing data of SARS-CoV-2 samples"
+        ],
+        "pageviews": 18702,
+        "pub_date": "2020-06-24",
+        "questions": [
+            "How can you download public sequencing data deposited in the NCBI Sequence Read Archive (SRA) into a Galaxy history for analysis?",
+            "How can you process a batch of sequencing data from several samples efficiently/in parallel with Galaxy?",
+            "Starting from raw sequenced reads of whole-genome sequenced samples of SARS-CoV-2, how can you identify mutations in the genomes of these samples?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "nekrut"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "15M",
+                "speakers": [
+                    "nekrut"
+                ],
+                "youtube_id": "9mIL0tIfZ_o"
+            }
+        ],
+        "short_id": "T00315",
+        "short_tools": [
+            "bwa_mem",
+            "samtools_stats",
+            "picard_MarkDuplicates",
+            "fastp",
+            "Filter1",
+            "lofreq_viterbi",
+            "snpeff_sars_cov_2",
+            "multiqc",
+            "lofreq_indelqual",
+            "Grep1",
+            "fasterq_dump",
+            "lofreq_call",
+            "tp_cut_tool",
+            "snpSift_extractFields"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "one-health",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "covid19",
+            "virology",
+            "one-health"
+        ],
+        "time_estimation": "1H",
+        "title": "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis",
+        "tools": [
+            "Filter1",
+            "Grep1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.3+galaxy0"
+        ],
+        "topic_name": "variant-analysis",
+        "topic_name_human": "Variant Analysis",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "sars-cov-2",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/sars-cov-2/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2/tutorial.json"
+        },
+        "version": 16,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 174,
+        "visitors": 12312,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Analysis of variation within individual COVID-19 samples (Paired End Illumina). Does not use paured",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nNC_045512.2 fasta file\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSRA Manifest\"]\n  2[label=\"Faster Download and Extract Reads in FASTQ\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"fastp\"]\n  2 -> 3 [label=\"list_paired\"]\n  4[label=\"Map with BWA-MEM\"]\n  3 -> 4 [label=\"output_paired_coll\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"MarkDuplicates\"]\n  4 -> 5 [label=\"bam_output\"]\n  6[label=\"Realign reads\"]\n  5 -> 6 [label=\"outFile\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Samtools stats\"]\n  5 -> 7 [label=\"outFile\"]\n  8[label=\"Insert indel qualities\"]\n  6 -> 8 [label=\"realigned\"]\n  0 -> 8 [label=\"output\"]\n  k2ca7c89b999f41dc8037e54e25959a7e[color=lightseagreen,label=\"Output\\nRealigned Alignments with Indel Qualities\"]\n  8 -> k2ca7c89b999f41dc8037e54e25959a7e\n  9[label=\"Call variants\"]\n  8 -> 9 [label=\"output\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"SnpEff eff:\"]\n  9 -> 10 [label=\"variants\"]\n  11[label=\"SnpSift Extract Fields\"]\n  10 -> 11 [label=\"snpeff_output\"]\n  k06259137eaa5404a923c70ee5f1d89d4[color=lightseagreen,label=\"Output\\nSnpSift tabular output\"]\n  11 -> k06259137eaa5404a923c70ee5f1d89d4\n  12[label=\"MultiQC\"]\n  3 -> 12 [label=\"report_json\"]\n  7 -> 12 [label=\"output\"]\n  5 -> 12 [label=\"metrics_file\"]\n  10 -> 12 [label=\"csvFile\"]\n  k758ffde57ddd482a88b21504f8335488[color=lightseagreen,label=\"Output\\nMultiQC Report PE\"]\n  12 -> k758ffde57ddd482a88b21504f8335488\n}",
+                "history": [
+                    {
+                        "hash": "18338ab9a1ef29b46dc8f2e8a7f7a4b055f16e3d",
+                        "message": "Use correct fasterqdump version",
+                        "num": 7,
+                        "short_hash": "18338ab9a",
+                        "unix": "1593005231"
+                    },
+                    {
+                        "hash": "979d6cd2174d0f2ce10ad195d9d3cc4b29a1623a",
+                        "message": "Reformat workflow, bump lofreq to 2.1.5",
+                        "num": 6,
+                        "short_hash": "979d6cd21",
+                        "unix": "1593004337"
+                    },
+                    {
+                        "hash": "ced05a792b3048548fd31a9d0bde9a1bf634481f",
+                        "message": "Fix workflow connections",
+                        "num": 5,
+                        "short_hash": "ced05a792",
+                        "unix": "1592944690"
+                    },
+                    {
+                        "hash": "1c38a3ed277eb7434c02927dce89f72e8a9c0c78",
+                        "message": "Use newer, simpler output",
+                        "num": 4,
+                        "short_hash": "1c38a3ed2",
+                        "unix": "1592943019"
+                    },
+                    {
+                        "hash": "a58450027f50bbdb5e91ee3529c7deef7ee1cf4e",
+                        "message": "add topic tag to workflow",
+                        "num": 3,
+                        "short_hash": "a58450027",
+                        "unix": "1592838416"
+                    },
+                    {
+                        "hash": "e8eea07056121bf6ee287bec31c64cd69d2e6dcb",
+                        "message": "reformat workflow",
+                        "num": 2,
+                        "short_hash": "e8eea0705",
+                        "unix": "1592835884"
+                    },
+                    {
+                        "hash": "a06c40264814dc80888f2a9ce28d4f06c2c3e687",
+                        "message": "Skeleton from PE sars-cov-2 workflow",
+                        "num": 1,
+                        "short_hash": "a06c40264",
+                        "unix": "1592389814"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "Contains SARS-CoV-2 reference sequence",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Contains SARS-CoV-2 reference sequence",
+                                "name": "NC_045512.2 fasta file"
+                            }
+                        ],
+                        "label": "NC_045512.2 fasta file",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 199.95736694335938,
+                            "top": 317.85511016845703
                         },
                         "tool_id": null,
-                        "type": "subworkflow",
-                        "uuid": "6b6668c9-25b7-4135-ac9b-140a6d1593b0",
-                        "when": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0e91bcb8-fa43-4fc5-87f9-9e65784373e6",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "2:output",
-                                "uuid": "f740de36-9921-4f0c-924e-3902bc2083b7"
+                                "output_name": "output",
+                                "uuid": "1dedf4c3-5fc4-4505-baa0-b13e4416d67d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "SRA Manifest"
+                            }
+                        ],
+                        "label": "SRA Manifest",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 199.95736694335938,
+                            "top": 372.3295364379883
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "3c5adef0-7af6-435e-bb10-966361130b58",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "fa458185-44d5-4d2d-ad69-20595c8ad337"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nNC_045512.2 fasta file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSRA Manifest\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Faster Download and Extract Reads in FASTQ\"];\n  1 -->|output| 2;\n  3[\"fastp\"];\n  2 -->|list_paired| 3;\n  4[\"Map with BWA-MEM\"];\n  3 -->|output_paired_coll| 4;\n  0 -->|output| 4;\n  5[\"MarkDuplicates\"];\n  4 -->|bam_output| 5;\n  6[\"Realign reads\"];\n  5 -->|outFile| 6;\n  0 -->|output| 6;\n  7[\"Samtools stats\"];\n  5 -->|outFile| 7;\n  8[\"Insert indel qualities\"];\n  6 -->|realigned| 8;\n  0 -->|output| 8;\n  2ca7c89b-999f-41dc-8037-e54e25959a7e[\"Output\\nRealigned Alignments with Indel Qualities\"];\n  8 --> 2ca7c89b-999f-41dc-8037-e54e25959a7e;\n  style 2ca7c89b-999f-41dc-8037-e54e25959a7e stroke:#2c3143,stroke-width:4px;\n  9[\"Call variants\"];\n  8 -->|output| 9;\n  0 -->|output| 9;\n  10[\"SnpEff eff:\"];\n  9 -->|variants| 10;\n  11[\"SnpSift Extract Fields\"];\n  10 -->|snpeff_output| 11;\n  06259137-eaa5-404a-923c-70ee5f1d89d4[\"Output\\nSnpSift tabular output\"];\n  11 --> 06259137-eaa5-404a-923c-70ee5f1d89d4;\n  style 06259137-eaa5-404a-923c-70ee5f1d89d4 stroke:#2c3143,stroke-width:4px;\n  12[\"MultiQC\"];\n  3 -->|report_json| 12;\n  7 -->|output| 12;\n  5 -->|metrics_file| 12;\n  10 -->|csvFile| 12;\n  758ffde5-7ddd-482a-88b2-1504f8335488[\"Output\\nMultiQC Report PE\"];\n  12 --> 758ffde5-7ddd-482a-88b2-1504f8335488;\n  style 758ffde5-7ddd-482a-88b2-1504f8335488 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "Simple COVID-19 - PE Variation",
+                "outputs": [
+                    {
+                        "annotation": "Contains SARS-CoV-2 reference sequence",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Contains SARS-CoV-2 reference sequence",
+                                "name": "NC_045512.2 fasta file"
+                            }
+                        ],
+                        "label": "NC_045512.2 fasta file",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 199.95736694335938,
+                            "top": 317.85511016845703
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0e91bcb8-fa43-4fc5-87f9-9e65784373e6",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "1dedf4c3-5fc4-4505-baa0-b13e4416d67d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "SRA Manifest"
+                            }
+                        ],
+                        "label": "SRA Manifest",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 199.95736694335938,
+                            "top": 372.3295364379883
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "3c5adef0-7af6-435e-bb10-966361130b58",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "fa458185-44d5-4d2d-ad69-20595c8ad337"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "input|file_list": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Faster Download and Extract Reads in FASTQ",
+                                "name": "input"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Faster Download and Extract Reads in FASTQ",
+                        "outputs": [
+                            {
+                                "name": "list_paired",
+                                "type": "input"
+                            },
+                            {
+                                "name": "output_collection",
+                                "type": "input"
+                            },
+                            {
+                                "name": "output_collection_other",
+                                "type": "input"
+                            },
+                            {
+                                "name": "log",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 342.9971618652344,
+                            "top": 317.85511016845703
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionlog": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "log"
+                            },
+                            "HideDatasetActionoutput_collection": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_collection"
                             },
+                            "HideDatasetActionoutput_collection_other": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_collection_other"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "248f85ff0733",
+                            "name": "sra_tools",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv\": {\"minlen\": \"\", \"split\": \"--split-3\", \"skip_technical\": \"true\"}, \"input\": {\"input_select\": \"file_list\", \"__current_case__\": 2, \"file_list\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.10.7+galaxy1",
+                        "type": "tool",
+                        "uuid": "3ce5b504-3641-4ea9-8d24-07f9bebaec23",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "4:2:output",
-                                "uuid": "2b5d309e-c47e-4a79-a69c-4d4fd6a93d8b"
+                                "output_name": "list_paired",
+                                "uuid": "9e5c0368-e97c-4def-9704-1b902fbb2ed7"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "reads": {
+                                "id": 6,
+                                "output_name": "realigned"
+                            },
+                            "strategy|reference_source|ref": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Insert indel qualities",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "bam"
+                            }
+                        ],
+                        "position": {
+                            "left": 1057.5852355957031,
+                            "top": 317.85511016845703
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Realigned Alignments with Indel Qualities"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "354b534eeab7",
+                            "name": "lofreq_indelqual",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"reads\": {\"__class__\": \"ConnectedValue\"}, \"strategy\": {\"selector\": \"dindel\", \"__current_case__\": 1, \"reference_source\": {\"ref_selector\": \"history\", \"__current_case__\": 1, \"ref\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.5+galaxy0",
+                        "type": "tool",
+                        "uuid": "cbc7ee7f-5cfa-4d45-a83e-623efbf66068",
+                        "workflow_outputs": [
+                            {
+                                "label": "Realigned Alignments with Indel Qualities",
+                                "output_name": "output",
+                                "uuid": "2ca7c89b-999f-41dc-8037-e54e25959a7e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {
+                            "input": {
+                                "id": 9,
+                                "output_name": "variants"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool SnpEff eff:",
+                                "name": "intervals"
+                            },
+                            {
+                                "description": "runtime parameter for tool SnpEff eff:",
+                                "name": "transcripts"
+                            }
+                        ],
+                        "label": null,
+                        "name": "SnpEff eff:",
+                        "outputs": [
+                            {
+                                "name": "snpeff_output",
+                                "type": "vcf"
+                            },
+                            {
+                                "name": "statsFile",
+                                "type": "html"
+                            },
+                            {
+                                "name": "csvFile",
+                                "type": "csv"
+                            }
+                        ],
+                        "position": {
+                            "left": 1343.0823059082031,
+                            "top": 317.85511016845703
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActioncsvFile": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "csvFile"
+                            },
+                            "HideDatasetActionstatsFile": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "statsFile"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2a3a00c1fa0a",
+                            "name": "snpeff_sars_cov_2",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"annotations\": [\"-formatEff\", \"-classic\"], \"chr\": \"\", \"csvStats\": \"true\", \"filter\": {\"specificEffects\": \"no\", \"__current_case__\": 0}, \"filterOut\": [\"-no-downstream\", \"-no-intergenic\", \"-no-upstream\", \"-no-utr\"], \"generate_stats\": \"true\", \"genome_version\": \"NC_045512.2\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inputFormat\": \"vcf\", \"intervals\": {\"__class__\": \"RuntimeValue\"}, \"noLog\": \"true\", \"offset\": \"default\", \"outputConditional\": {\"outputFormat\": \"vcf\", \"__current_case__\": 0}, \"transcripts\": {\"__class__\": \"RuntimeValue\"}, \"udLength\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.5covid19",
+                        "type": "tool",
+                        "uuid": "8fb55fb1-4986-45f5-bb6b-45c1329842b2",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "snpeff_output",
+                                "uuid": "d5bec60d-c853-4979-a191-e69f47539684"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
+                        "errors": null,
+                        "id": 11,
+                        "input_connections": {
+                            "input": {
+                                "id": 10,
+                                "output_name": "snpeff_output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "SnpSift Extract Fields",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 1486.0794982910156,
+                            "top": 317.85511016845703
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "SnpSift tabular output"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2b3e65a4252f",
+                            "name": "snpsift",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"empty_text\": \".\", \"extract\": \"CHROM POS REF ALT QUAL DP AF SB DP4 EFF[*].IMPACT EFF[*].FUNCLASS EFF[*].EFFECT EFF[*].GENE EFF[*].CODON\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"one_effect_per_line\": \"false\", \"separator\": \",\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.3+t.galaxy0",
+                        "type": "tool",
+                        "uuid": "33e13bce-928f-41d6-b418-bc0a9e53d83d",
+                        "workflow_outputs": [
+                            {
+                                "label": "SnpSift tabular output",
+                                "output_name": "output",
+                                "uuid": "06259137-eaa5-404a-923c-70ee5f1d89d4"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {
+                            "results_0|software_cond|input": {
+                                "id": 3,
+                                "output_name": "report_json"
+                            },
+                            "results_1|software_cond|output_0|type|input": {
+                                "id": 7,
+                                "output_name": "output"
+                            },
+                            "results_2|software_cond|output_0|input": {
+                                "id": 5,
+                                "output_name": "metrics_file"
+                            },
+                            "results_3|software_cond|input": {
+                                "id": 10,
+                                "output_name": "csvFile"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "MultiQC",
+                        "outputs": [
+                            {
+                                "name": "stats",
+                                "type": "input"
+                            },
+                            {
+                                "name": "plots",
+                                "type": "input"
+                            },
+                            {
+                                "name": "html_report",
+                                "type": "html"
+                            }
+                        ],
+                        "position": {
+                            "left": 1486.0794982910156,
+                            "top": 397.8408889770508
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionplots": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "plots"
+                            },
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "RenameDatasetActionhtml_report": {
+                                "action_arguments": {
+                                    "newname": "MultiQC Report PE"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "html_report"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "bf675f34b056",
+                            "name": "multiqc",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"comment\": \"\", \"flat\": \"false\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 23, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"stats\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"snpeff\", \"__current_case__\": 25, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8+galaxy0",
+                        "type": "tool",
+                        "uuid": "8c98527f-d1db-4cc4-89f1-1e75c508b8e9",
+                        "workflow_outputs": [
+                            {
+                                "label": "MultiQC Report PE",
+                                "output_name": "html_report",
+                                "uuid": "758ffde5-7ddd-482a-88b2-1504f8335488"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/largegenome",
-                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga",
-                "tags": [
-                    "LG-WF",
-                    "GTN"
+                "parent_id": "variant-analysis/sars-cov-2",
+                "path": "topics/variant-analysis/tutorials/sars-cov-2/workflows/main_workflow.ga",
+                "tags": [
+                    "variant-analysis"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Simple COVID-19 - PE Variation",
+                "topic_id": "variant-analysis",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-sars-cov-2/versions/main-workflow",
+                "tutorial_id": "sars-cov-2",
+                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "variant-analysis-sars-cov-2",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1"
+                ],
+                "workflowhub_id": "1074"
+            }
+        ]
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "bwa",
+                    "owner": "devteam",
+                    "revisions": "e188dc7a68e6",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "column_maker",
+                    "owner": "devteam",
+                    "revisions": "6595517c2dd8",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "emboss_5",
+                    "owner": "devteam",
+                    "revisions": "63dd26468588",
+                    "tool_panel_section_label": "EMBOSS",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_compute_length",
+                    "owner": "devteam",
+                    "revisions": "7d37cfda8e00",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "compose_text_param",
+                    "owner": "iuc",
+                    "revisions": "e188c9826e0f",
+                    "tool_panel_section_label": "Expression Tools",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "datamash_ops",
+                    "owner": "iuc",
+                    "revisions": "746e8e4bf929",
+                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastp",
+                    "owner": "iuc",
+                    "revisions": "65b93b623c77",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ivar_consensus",
+                    "owner": "iuc",
+                    "revisions": "40737febe339",
+                    "tool_panel_section_label": "Virology",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ivar_trim",
+                    "owner": "iuc",
+                    "revisions": "86a20ae274fc",
+                    "tool_panel_section_label": "Virology",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "qualimap_bamqc",
+                    "owner": "iuc",
+                    "revisions": "19ece8afbaab",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "samtools_merge",
+                    "owner": "iuc",
+                    "revisions": "36677f429310",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "samtools_view",
+                    "owner": "iuc",
+                    "revisions": "5826298f6a73",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ucsc_fatovcf",
+                    "owner": "iuc",
+                    "revisions": "78df8fc2b3ab",
+                    "tool_panel_section_label": "Variant Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_regex_finder",
+                    "owner": "mbernt",
+                    "revisions": "9a811adb714f",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mafft",
+                    "owner": "rnateam",
+                    "revisions": "bf28a8cff401",
+                    "tool_panel_section_label": "Multiple Alignments",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mimodd_main",
+                    "owner": "wolma",
+                    "revisions": "f0f2795de2c7",
+                    "tool_panel_section_label": "MiModD",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 6595517c2dd8\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: emboss_5\n  owner: devteam\n  revisions: 63dd26468588\n  tool_panel_section_label: EMBOSS\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_compute_length\n  owner: devteam\n  revisions: 7d37cfda8e00\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: compose_text_param\n  owner: iuc\n  revisions: e188c9826e0f\n  tool_panel_section_label: Expression Tools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 746e8e4bf929\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ivar_consensus\n  owner: iuc\n  revisions: 40737febe339\n  tool_panel_section_label: Virology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ivar_trim\n  owner: iuc\n  revisions: 86a20ae274fc\n  tool_panel_section_label: Virology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qualimap_bamqc\n  owner: iuc\n  revisions: 19ece8afbaab\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_merge\n  owner: iuc\n  revisions: 36677f429310\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: 5826298f6a73\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ucsc_fatovcf\n  owner: iuc\n  revisions: 78df8fc2b3ab\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_regex_finder\n  owner: mbernt\n  revisions: 9a811adb714f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mafft\n  owner: rnateam\n  revisions: bf28a8cff401\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mimodd_main\n  owner: wolma\n  revisions: f0f2795de2c7\n  tool_panel_section_label: MiModD\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "wm75",
+                "TKlingstrom"
+            ],
+            "funding": [
+                "by-covid",
+                "elixir-converge",
+                "h2020-defend"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "by-covid",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "elixir_node": "de",
+                "fediverse": "https://scholar.social/@zerodivision",
+                "fediverse_flavor": "mastodon",
+                "id": "wm75",
+                "joined": "2017-09",
+                "matrix": "wm75:matrix.org",
+                "name": "Wolfgang Maier",
+                "orcid": "0000-0002-9464-6640",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
                 ],
-                "test_results": null,
-                "tests": false,
-                "title": "Combined workflows for large genome assembly - upgraded ",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-combined-workflows-for-large-genome-assembly",
-                "tutorial_id": "largegenome",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.html",
-                "version": 2,
-                "wfid": "assembly-largegenome",
-                "wfname": "galaxy-workflow-combined-workflows-for-large-genome-assembly",
-                "workflow": "Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga",
-                "workflow_tools": [
-                    "barchart_gnuplot",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
+                "elixir_node": "se",
+                "email": "tomas.klingstrom@slu.se",
+                "id": "TKlingstrom",
+                "joined": "2018-11",
+                "matrix": "TKlingstrom:matrix.org",
+                "name": "Tomas Klingstr\u00f6m",
+                "orcid": "0000-0002-9504-1352",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/TKlingstrom/",
+                "twitter": "TKlingstrom",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/TKlingstrom.json"
+            },
+            {
+                "funder": true,
+                "funding_id": "101046203",
+                "funding_statement": "BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response.\n\nThis project has received funding from the European Union\u2019s Horizon Europe research and innovation programme under grant agreement \u2116 101046203 (BY-COVID)",
+                "funding_system": "cordis",
+                "id": "by-covid",
+                "joined": "2023-04",
+                "members": [
+                    "bgruening",
+                    "hexylena",
+                    "ilveroluca",
+                    "kikkomep",
+                    "mbaardwijk",
+                    "PapXis",
+                    "pauldg",
+                    "simleo",
+                    "stain",
+                    "wm75"
                 ],
-                "workflowhub_id": "1176"
+                "name": "BeYond-COVID",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/by-covid/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/by-covid.json"
+            },
+            {
+                "avatar": "https://elixir-europe.org/sites/default/files/styles/right-medium/public/images/converge_logo.png",
+                "funder": true,
+                "funding_id": "871075",
+                "funding_statement": "ELIXIR CONVERGE is connecting and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services. This project has received funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement \u2116 871075",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "elixir-converge",
+                "joined": "2023-01",
+                "members": [
+                    "bgruening",
+                    "hexylena"
+                ],
+                "name": "ELIXIR-CONVERGE",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-converge/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-converge.json"
             },
+            {
+                "funder": true,
+                "funding_id": "773701",
+                "funding_statement": "DEFEND is Addressing the dual emerging threats of African Swine Fever and Lumpy Skin Disease in Europe.\n\nThis work has received funding from the DEFEND project (www.defend2020.eu) with funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement No 773701.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "h2020-defend",
+                "joined": "2023-05",
+                "name": "Addressing the dual emerging threats of African Swine Fever and Lumpy Skin Disease in Europe",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/h2020-defend/",
+                "short_name": "DEFEND",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/h2020-defend.json"
+            }
+        ],
+        "dir": "topics/variant-analysis/tutorials/pox-tiled-amplicon",
+        "edam_operation": [
+            "Sequence alignment",
+            "Read mapping",
+            "Sequencing quality control",
+            "Sequence alignment analysis",
+            "Sequence analysis",
+            "Multiple sequence alignment",
+            "Sequence contamination filtering",
+            "Generation",
+            "Global alignment",
+            "Local alignment",
+            "Genome indexing"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "variant-analysis/pox-tiled-amplicon",
+        "inexact_supported_servers": [
+            "UseGalaxy.org (Main)"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Compared to other viruses, analysis of sequencing data from pox viruses is complicated by the rather large genome size and by the presence of inverted terminal repeats, but well-designed wet lab and bioinformatic workflows can handle these particularities.",
+            "Galaxy and its huge set of tools are flexible enough to handle half-genome sequencing data efficiently.",
+            "A mapping-based approach can result in high-quality consensus genome reconstructions from pox virus sequencing data and appears promising even when dealing with recombinant samples."
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Advanced",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-03-20",
+        "objectives": [
+            "Learn how to deal with pox virus genomes inverted terminal repeats through a combination of wet lab protocol and tailored bioinformatics",
+            "Construct a sample consensus genome from mapped reads",
+            "Explore a recombinant pox virus genome via a multiple-sequence alignment of consensus genome and references and through lists of mutations derived from it"
+        ],
+        "pageviews": 670,
+        "pub_date": "2023-05-15",
+        "questions": [
+            "Which special challenges does one encounter during sequence data analysis of pox viruses?",
+            "How can standard workflows for viral mutation calling and consensus generation be adapted to the particularities of pox viruses?",
+            "How can viral consensus sequences, multiple-sequence alignments and mutation calls be generated from each other and used to answer questions about the data?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "collections",
+                    "upload-rules"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00347",
+        "short_tools": [
+            "ivar_trim",
+            "upload1",
+            "compose_text_param",
+            "qualimap_bamqc",
+            "param_value_from_file",
+            "__ZIP_COLLECTION__",
+            "mimodd_info",
+            "datamash_ops",
+            "bwa_mem",
+            "ivar_consensus",
+            "fatovcf",
+            "EMBOSS: maskseq51",
+            "__APPLY_RULES__",
+            "samtools_view",
+            "rbc_mafft",
+            "Grep1",
+            "Cut1",
+            "fasta_regex_finder",
+            "samtools_merge",
+            "fastp",
+            "fasta_compute_length",
+            "Add_a_column1"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "one-health",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "virology",
+            "one-health"
+        ],
+        "time_estimation": "4H",
+        "title": "Pox virus genome analysis from tiled-amplicon sequencing data",
+        "tools": [
+            "Cut1",
+            "Grep1",
+            "__APPLY_RULES__",
+            "__ZIP_COLLECTION__",
+            "param_value_from_file",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_fatovcf/fatovcf/426+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/mbernt/fasta_regex_finder/fasta_regex_finder/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.520+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_info/0.1.8_1",
+            "upload1"
+        ],
+        "topic_name": "variant-analysis",
+        "topic_name_human": "Variant Analysis",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "pox-tiled-amplicon",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.json"
+        },
+        "version": 4,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 145,
+        "visitors": 562,
+        "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
+                        "identifier": "https://orcid.org/0000-0001-6897-1215",
+                        "name": "Viktoria Isabel Schwarz"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0002-9464-6640",
+                        "name": "Wolfgang Maier"
                     }
                 ],
-                "description": "",
+                "description": "From a reference and a primer scheme generate two masked half-genome references for ITR-aware pox virus sequencing data analysis.",
                 "features": {
                     "comments": false,
                     "parameters": false,
-                    "report": {
-                        "markdown": "\n# Workflow Report for Data QC\n\n## Workflow steps\n\n```galaxy\nworkflow_display()\n```\n\n"
-                    },
+                    "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput file: long reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R1\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R2\"]\n  3[label=\"Nanoplot: long reads\"]\n  0 -> 3 [label=\"output\"]\n  k73d0e4cf366e41c1810ab269638826b3[color=lightseagreen,label=\"Output\\nNanoPlot on input dataset(s): HTML report\"]\n  3 -> k73d0e4cf366e41c1810ab269638826b3\n  4[label=\"FastQC on R1\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"FastQC on R2\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"MultiQC: combine fastQC reports\"]\n  4 -> 6 [label=\"text_file\"]\n  5 -> 6 [label=\"text_file\"]\n  k8baf8700876e4a74ad996e656f3ba618[color=lightseagreen,label=\"Output\\nMultiQC on input dataset(s): Webpage\"]\n  6 -> k8baf8700876e4a74ad996e656f3ba618\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPrimer Scheme\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference FASTA\"]\n  2[label=\"Select pool1 primers\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Select pool2 primers\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Compute sequence length\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Datamash\"]\n  2 -> 5 [label=\"out_file1\"]\n  6[label=\"Datamash\"]\n  3 -> 6 [label=\"out_file1\"]\n  7[label=\"Cut\"]\n  4 -> 7 [label=\"output\"]\n  8[label=\"Compute\"]\n  5 -> 8 [label=\"out_file\"]\n  9[label=\"Get start position of Pool2\"]\n  6 -> 9 [label=\"out_file\"]\n  10[label=\"Get end position of sequence\"]\n  7 -> 10 [label=\"out_file1\"]\n  11[label=\"Get end position of Pool1\"]\n  8 -> 11 [label=\"out_file1\"]\n  12[label=\"Compose text parameter value\"]\n  9 -> 12 [label=\"text_param\"]\n  13[label=\"Compose text parameter value\"]\n  11 -> 13 [label=\"text_param\"]\n  10 -> 13 [label=\"text_param\"]\n  14[label=\"Mask Reference for Pool2\"]\n  1 -> 14 [label=\"output\"]\n  12 -> 14 [label=\"out1\"]\n  kaf755a5e2b2049bc9d5234781f937f48[color=lightseagreen,label=\"Output\\nmasked_ref_pool2\"]\n  14 -> kaf755a5e2b2049bc9d5234781f937f48\n  15[label=\"Mask Reference for Pool1\"]\n  1 -> 15 [label=\"output\"]\n  13 -> 15 [label=\"out1\"]\n  k0c3b5b20c426428ca08bc835a82477c1[color=lightseagreen,label=\"Output\\nmasked_ref_pool1\"]\n  15 -> k0c3b5b20c426428ca08bc835a82477c1\n}",
                 "history": [
                     {
-                        "hash": "d35221f6506e7b95e8b3ff679a2ad01edf1a560a",
-                        "message": "Update Galaxy-Workflow-Data_QC.ga",
-                        "num": 5,
-                        "short_hash": "d35221f65",
-                        "unix": "1715074384"
-                    },
-                    {
-                        "hash": "a737e5f1b936379382f4d568b0caeb664d81c392",
-                        "message": "Rename Galaxy-Workflow-Data_QC_-_upgraded.ga to Galaxy-Workflow-Data_QC.ga",
-                        "num": 4,
-                        "short_hash": "a737e5f1b",
-                        "unix": "1714537191"
-                    },
-                    {
-                        "hash": "9ca497557dddc43b116a61592a953f455046bc86",
-                        "message": "Rename Galaxy-Workflow-Data_QC.ga to Galaxy-Workflow-Data_QC_old.ga",
-                        "num": 3,
-                        "short_hash": "9ca497557",
-                        "unix": "1714537118"
-                    },
-                    {
-                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
-                        "message": "add/complete creator info on workflows",
+                        "hash": "79db81a7c1c23d9778536abaa9ca879f3b0bbda5",
+                        "message": "Update pox-virus-tiled-amplicon-ref-masking.ga",
                         "num": 2,
-                        "short_hash": "62e77944b",
-                        "unix": "1676627603"
+                        "short_hash": "79db81a7c",
+                        "unix": "1684740183"
                     },
                     {
-                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
-                        "message": "large genome tutorial",
+                        "hash": "314d08f56a2d904cbab620fa5400ed0dbfa9619a",
+                        "message": "Add some material for new pox virus tiled amplicon tutorial",
                         "num": 1,
-                        "short_hash": "9fcb3aeec",
-                        "unix": "1665123856"
+                        "short_hash": "314d08f56",
+                        "unix": "1682289363"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "",
+                        "annotation": "The workflow expects a primer scheme split into two separate sequencing pools. These pools must be denoted as pool1/pool2 in the BED score column. The pool ids may, optionally, be followed by indicators of the subpool for tiled PCR amplification (e.g., pool1a/pool1b/pool2a/pool2b)",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Input file: long reads"
+                                "description": "The workflow expects a primer scheme split into two separate sequencing pools. These pools must be denoted as pool1/pool2 in the BED score column. The pool ids may, optionally, be followed by indicators of the subpool for tiled PCR amplification (e.g., pool1a/pool1b/pool2a/pool2b)",
+                                "name": "Primer Scheme (BED file with Pool identifiers)"
                             }
                         ],
-                        "label": "Input file: long reads",
+                        "label": "Primer Scheme",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
                             "left": 0,
-                            "top": 0.0
+                            "top": 667.3406219482422
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "e2e4a70b-6e36-4b8b-bdf6-12b97189a6bd",
+                        "uuid": "1829d4e0-ee74-4a94-8dc5-98a11d96b961",
                         "when": null,
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "The viral reference sequence to map sequenced reads against",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Input file: Illumina reads R1"
-                            }
-                        ],
-                        "label": "Input file: Illumina reads R1",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 535.703125,
-                            "top": 21.0
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ea859a58-c81a-4ef6-9bd2-4ef2f17bb5a9",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Input file: Illumina reads R2"
+                                "description": "The viral reference sequence to map sequenced reads against",
+                                "name": "Reference FASTA"
                             }
                         ],
-                        "label": "Input file: Illumina reads R2",
+                        "label": "Reference FASTA",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 530.703125,
-                            "top": 379.984375
+                            "left": 251.7752034262281,
+                            "top": 650.9021921247038
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "472adc05-88a5-4955-9e43-e82e9550ad08",
+                        "uuid": "f17c7022-fc94-42b5-ae90-7b3ec3d70ffb",
                         "when": null,
                         "workflow_outputs": []
                     }
                 ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput file: long reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R2\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Nanoplot: long reads\"];\n  0 -->|output| 3;\n  73d0e4cf-366e-41c1-810a-b269638826b3[\"Output\\nNanoPlot on input dataset(s): HTML report\"];\n  3 --> 73d0e4cf-366e-41c1-810a-b269638826b3;\n  style 73d0e4cf-366e-41c1-810a-b269638826b3 stroke:#2c3143,stroke-width:4px;\n  4[\"FastQC on R1\"];\n  1 -->|output| 4;\n  5[\"FastQC on R2\"];\n  2 -->|output| 5;\n  6[\"MultiQC: combine fastQC reports\"];\n  4 -->|text_file| 6;\n  5 -->|text_file| 6;\n  8baf8700-876e-4a74-ad99-6e656f3ba618[\"Output\\nMultiQC on input dataset(s): Webpage\"];\n  6 --> 8baf8700-876e-4a74-ad99-6e656f3ba618;\n  style 8baf8700-876e-4a74-ad99-6e656f3ba618 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Data QC - upgraded",
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPrimer Scheme\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference FASTA\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Select pool1 primers\"];\n  0 -->|output| 2;\n  3[\"Select pool2 primers\"];\n  0 -->|output| 3;\n  4[\"Compute sequence length\"];\n  1 -->|output| 4;\n  5[\"Datamash\"];\n  2 -->|out_file1| 5;\n  6[\"Datamash\"];\n  3 -->|out_file1| 6;\n  7[\"Cut\"];\n  4 -->|output| 7;\n  8[\"Compute\"];\n  5 -->|out_file| 8;\n  9[\"Get start position of Pool2\"];\n  6 -->|out_file| 9;\n  10[\"Get end position of sequence\"];\n  7 -->|out_file1| 10;\n  11[\"Get end position of Pool1\"];\n  8 -->|out_file1| 11;\n  12[\"Compose text parameter value\"];\n  9 -->|text_param| 12;\n  13[\"Compose text parameter value\"];\n  11 -->|text_param| 13;\n  10 -->|text_param| 13;\n  14[\"Mask Reference for Pool2\"];\n  1 -->|output| 14;\n  12 -->|out1| 14;\n  af755a5e-2b20-49bc-9d52-34781f937f48[\"Output\\nmasked_ref_pool2\"];\n  14 --> af755a5e-2b20-49bc-9d52-34781f937f48;\n  style af755a5e-2b20-49bc-9d52-34781f937f48 stroke:#2c3143,stroke-width:4px;\n  15[\"Mask Reference for Pool1\"];\n  1 -->|output| 15;\n  13 -->|out1| 15;\n  0c3b5b20-c426-428c-a08b-c835a82477c1[\"Output\\nmasked_ref_pool1\"];\n  15 --> 0c3b5b20-c426-428c-a08b-c835a82477c1;\n  style 0c3b5b20-c426-428c-a08b-c835a82477c1 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "pox-virus-tiled-amplicon-ref-masking",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
                         "errors": null,
-                        "id": 3,
+                        "id": 14,
                         "input_connections": {
-                            "mode|reads|files": {
-                                "id": 0,
+                            "input1": {
+                                "id": 1,
                                 "output_name": "output"
+                            },
+                            "regions": {
+                                "id": 12,
+                                "output_name": "out1"
                             }
                         },
                         "inputs": [],
-                        "label": "Nanoplot: long reads",
-                        "name": "NanoPlot",
+                        "label": "Mask Reference for Pool2",
+                        "name": "maskseq",
                         "outputs": [
                             {
-                                "name": "output_html",
-                                "type": "html"
-                            },
-                            {
-                                "name": "nanostats",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "nanostats_post_filtering",
-                                "type": "tabular"
+                                "name": "out_file1",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 240.84375,
-                            "top": 104.359375
+                            "left": 1438.15352300995,
+                            "top": 648.5794855890229
                         },
                         "post_job_actions": {
-                            "HideDatasetActionlog_read_length": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "log_read_length"
-                            },
-                            "HideDatasetActionnanostats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "nanostats"
-                            },
-                            "HideDatasetActionnanostats_post_filtering": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "nanostats_post_filtering"
-                            },
-                            "HideDatasetActionread_length": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "read_length"
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Masked reference for mapping of pool2"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "a02b8b3f5a0c",
-                            "name": "nanoplot",
-                            "owner": "iuc",
+                            "changeset_revision": "ce385837c160",
+                            "name": "emboss_5",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"customization\": {\"color\": null, \"plots\": null, \"N50\": false}, \"filter\": {\"maxlength\": null, \"minlength\": null, \"drop_outliers\": false, \"downsample\": null, \"loglength\": false, \"percentqual\": false, \"alength\": false, \"minqual\": null, \"runtime_until\": null, \"readtype\": null, \"barcoded\": false, \"no_supplementary\": false}, \"mode\": {\"choice\": \"batch\", \"__current_case__\": 0, \"reads\": {\"type\": \"fastq\", \"__current_case__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.42.0+galaxy1",
+                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"maskchar\": \"N\", \"out_format1\": \"fasta\", \"regions\": {\"__class__\": \"ConnectedValue\"}, \"tolower\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.0.0",
                         "type": "tool",
-                        "uuid": "3b8a87fe-1506-48d2-a4d9-f4dca8b6065d",
+                        "uuid": "140608b3-48b3-46f2-92e3-2b9c3fb9e3b2",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "NanoPlot on input dataset(s): HTML report",
-                                "output_name": "output_html",
-                                "uuid": "73d0e4cf-366e-41c1-810a-b269638826b3"
+                                "label": "masked_ref_pool2",
+                                "output_name": "out_file1",
+                                "uuid": "af755a5e-2b20-49bc-9d52-34781f937f48"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
                         "errors": null,
-                        "id": 6,
+                        "id": 15,
                         "input_connections": {
-                            "results_0|software_cond|output_0|input": {
-                                "id": 4,
-                                "output_name": "text_file"
+                            "input1": {
+                                "id": 1,
+                                "output_name": "output"
                             },
-                            "results_0|software_cond|output_1|input": {
-                                "id": 5,
-                                "output_name": "text_file"
+                            "regions": {
+                                "id": 13,
+                                "output_name": "out1"
                             }
                         },
                         "inputs": [],
-                        "label": "MultiQC: combine fastQC reports",
-                        "name": "MultiQC",
+                        "label": "Mask Reference for Pool1",
+                        "name": "maskseq",
                         "outputs": [
                             {
-                                "name": "stats",
-                                "type": "input"
-                            },
-                            {
-                                "name": "html_report",
-                                "type": "html"
+                                "name": "out_file1",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 1233.5,
-                            "top": 230.844970703125
+                            "left": 1452.6333312988281,
+                            "top": 223.50729370117188
                         },
                         "post_job_actions": {
-                            "HideDatasetActionstats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "stats"
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Masked reference for mapping of pool1"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "abfd8a6544d7",
-                            "name": "multiqc",
-                            "owner": "iuc",
+                            "changeset_revision": "ce385837c160",
+                            "name": "emboss_5",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.11+galaxy1",
+                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"maskchar\": \"N\", \"out_format1\": \"fasta\", \"regions\": {\"__class__\": \"ConnectedValue\"}, \"tolower\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.0.0",
                         "type": "tool",
-                        "uuid": "3e29a59b-dca0-4993-b20d-495a3f17e291",
+                        "uuid": "3c8b86c1-7e53-4b72-b836-88a921a368ba",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "MultiQC on input dataset(s): Webpage",
-                                "output_name": "html_report",
-                                "uuid": "8baf8700-876e-4a74-ad99-6e656f3ba618"
+                                "label": "masked_ref_pool1",
+                                "output_name": "out_file1",
+                                "uuid": "0c3b5b20-c426-428c-a08b-c835a82477c1"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/largegenome",
-                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Data_QC.ga",
+                "parent_id": "variant-analysis/pox-tiled-amplicon",
+                "path": "topics/variant-analysis/tutorials/pox-tiled-amplicon/workflows/pox-virus-tiled-amplicon-ref-masking.ga",
                 "tags": [
-                    "LG-WF",
-                    "GTN"
+                    "GTN",
+                    "variant-analysis"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "Data QC - upgraded",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-data-qc",
-                "tutorial_id": "largegenome",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Data_QC.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Data_QC.html",
+                "tests": true,
+                "title": "pox-virus-tiled-amplicon-ref-masking",
+                "topic_id": "variant-analysis",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-pox-tiled-amplicon/versions/pox-virus-tiled-amplicon-ref-masking",
+                "tutorial_id": "pox-tiled-amplicon",
+                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/pox-tiled-amplicon/workflows/pox-virus-tiled-amplicon-ref-masking.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/pox-tiled-amplicon/workflows/pox-virus-tiled-amplicon-ref-masking.html",
                 "version": 2,
-                "wfid": "assembly-largegenome",
-                "wfname": "galaxy-workflow-data-qc",
-                "workflow": "Galaxy-Workflow-Data_QC.ga",
+                "wfid": "variant-analysis-pox-tiled-amplicon",
+                "wfname": "pox-virus-tiled-amplicon-ref-masking",
+                "workflow": "pox-virus-tiled-amplicon-ref-masking.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1"
+                    "Cut1",
+                    "Grep1",
+                    "param_value_from_file",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2"
+                ],
+                "workflowhub_id": "1078"
+            }
+        ]
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "datamash_ops",
+                    "owner": "iuc",
+                    "revisions": "4c07ddedc198",
+                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "nextclade",
+                    "owner": "iuc",
+                    "revisions": "4f6349228462",
+                    "tool_panel_section_label": "Phylogenetics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pangolin",
+                    "owner": "iuc",
+                    "revisions": "8ad84c5753ea",
+                    "tool_panel_section_label": "Phylogenetics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_regex_finder",
+                    "owner": "mbernt",
+                    "revisions": "9a811adb714f",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: datamash_ops\n  owner: iuc\n  revisions: 4c07ddedc198\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nextclade\n  owner: iuc\n  revisions: 4f6349228462\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pangolin\n  owner: iuc\n  revisions: 8ad84c5753ea\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_regex_finder\n  owner: mbernt\n  revisions: 9a811adb714f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "wm75",
+                "bebatut"
+            ],
+            "funding": [
+                "by-covid",
+                "elixir-converge"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "by-covid",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "elixir_node": "de",
+                "fediverse": "https://scholar.social/@zerodivision",
+                "fediverse_flavor": "mastodon",
+                "id": "wm75",
+                "joined": "2017-09",
+                "matrix": "wm75:matrix.org",
+                "name": "Wolfgang Maier",
+                "orcid": "0000-0002-9464-6640",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "funder": true,
+                "funding_id": "101046203",
+                "funding_statement": "BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response.\n\nThis project has received funding from the European Union\u2019s Horizon Europe research and innovation programme under grant agreement \u2116 101046203 (BY-COVID)",
+                "funding_system": "cordis",
+                "id": "by-covid",
+                "joined": "2023-04",
+                "members": [
+                    "bgruening",
+                    "hexylena",
+                    "ilveroluca",
+                    "kikkomep",
+                    "mbaardwijk",
+                    "PapXis",
+                    "pauldg",
+                    "simleo",
+                    "stain",
+                    "wm75"
+                ],
+                "name": "BeYond-COVID",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/by-covid/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/by-covid.json"
+            },
+            {
+                "avatar": "https://elixir-europe.org/sites/default/files/styles/right-medium/public/images/converge_logo.png",
+                "funder": true,
+                "funding_id": "871075",
+                "funding_statement": "ELIXIR CONVERGE is connecting and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services. This project has received funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement \u2116 871075",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "elixir-converge",
+                "joined": "2023-01",
+                "members": [
+                    "bgruening",
+                    "hexylena"
+                ],
+                "name": "ELIXIR-CONVERGE",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-converge/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-converge.json"
+            }
+        ],
+        "dir": "topics/variant-analysis/tutorials/sars-cov-2-variant-discovery",
+        "edam_operation": [
+            "Tree-based sequence alignment",
+            "Variant calling",
+            "Variant classification",
+            "Methylation analysis"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "variant-analysis/sars-cov-2-variant-discovery",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "The Galaxy Covid-19 project has developed a flexible set of workflows for SARS-CoV-2 genome surveillance, which is freely available through public workflow registries.",
+            "The workflows enable processing of whole batches of samples with rather limited user interaction.",
+            "They provide a high-throughput and flexible analysis solution without compromising on accuracy, nor on the possibility to explore intermediate steps and outputs in detail."
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-10-01",
+        "objectives": [
+            "Discover and obtain recommended Galaxy workflows for SARS-CoV-2 sequence data analysis through public workflow registries",
+            "Choose and run a workflow to discover mutations in a batch of viral samples from sequencing data obtained through a range of different protocols and platforms",
+            "Run a workflow to summarize and visualize the mutation discovery results for a batch of samples",
+            "Run a workflow to construct viral consensus sequences for the samples in a batch",
+            "Know different SARS-CoV-2 lineage classification systems, and use pangolin and Nextclade to assign samples to predefined lineages",
+            "Combine information from different analysis steps to be able to draw appropriate conclusions about individual samples and batches of viral data"
+        ],
+        "pageviews": 12061,
+        "pub_date": "2021-06-30",
+        "questions": [
+            "How can a complete analysis, including viral consensus sequence reconstruction and lineage assignment be performed?",
+            "How can such an analysis be kept manageable for lots of samples, yet flexible enough to handle different types of input data?",
+            "What are key results beyond consensus genomes and lineage assignments that need to be understood to avoid inappropriate conclusions about samples?",
+            "How can the needs for high-throughput data analysis in an ongoing infectious disease outbreak/pandemic and the need for proper quality control and data inspection be balanced?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "wm75"
+                ],
+                "date": "2023-05-10",
+                "length": "55M",
+                "speakers": [
+                    "wm75"
+                ],
+                "youtube_id": "hjlmCWQhBvI"
+            },
+            {
+                "captioners": [
+                    "hexylena"
+                ],
+                "date": "2021-08-09",
+                "length": "1H30M",
+                "speakers": [
+                    "wm75"
+                ],
+                "youtube_id": "vnFQ2fR_fzw"
+            },
+            {
+                "bot-timestamp": 1727459029,
+                "captioners": [
+                    "wm75"
+                ],
+                "date": "2024-09-27",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "55M",
+                "speakers": [
+                    "wm75"
+                ],
+                "youtube_id": "-HQB1zyWWXM"
+            }
+        ],
+        "requirements": [
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "collections"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "variant-analysis",
+                "tutorials": [
+                    "sars-cov-2"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00316",
+        "short_tools": [
+            "pangolin",
+            "Filter1",
+            "upload1",
+            "fasta_regex_finder",
+            "nextclade",
+            "datamash_ops"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "one-health",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "covid19",
+            "virology",
+            "one-health"
+        ],
+        "time_estimation": "3H",
+        "title": "Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data",
+        "tools": [
+            "Filter1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/nextclade/nextclade/2.7.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/4.3+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/mbernt/fasta_regex_finder/fasta_regex_finder/0.1.0",
+            "upload1"
+        ],
+        "topic_name": "variant-analysis",
+        "topic_name_human": "Variant Analysis",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "sars-cov-2-variant-discovery",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.json"
+        },
+        "version": 17,
+        "video": false,
+        "video_versions": 3,
+        "video_view": 0,
+        "visit_duration": 208,
+        "visitors": 6502
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bwa",
+                    "owner": "devteam",
+                    "revisions": "e188dc7a68e6",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bamtools_split_ref",
+                    "owner": "iuc",
+                    "revisions": "9b520009db81",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastp",
+                    "owner": "iuc",
+                    "revisions": "65b93b623c77",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "iqtree",
+                    "owner": "iuc",
+                    "revisions": "24d024316465",
+                    "tool_panel_section_label": "Evolution",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ivar_consensus",
+                    "owner": "iuc",
+                    "revisions": "40737febe339",
+                    "tool_panel_section_label": "Virology",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "qualimap_bamqc",
+                    "owner": "iuc",
+                    "revisions": "19ece8afbaab",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "samtools_view",
+                    "owner": "iuc",
+                    "revisions": "5826298f6a73",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seqtk",
+                    "owner": "iuc",
+                    "revisions": "3da72230c066",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "vapor",
+                    "owner": "iuc",
+                    "revisions": "244812f5bd1f",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "90981f86000f",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mafft",
+                    "owner": "rnateam",
+                    "revisions": "bf28a8cff401",
+                    "tool_panel_section_label": "Multiple Alignments",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_split_ref\n  owner: iuc\n  revisions: 9b520009db81\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: iqtree\n  owner: iuc\n  revisions: 24d024316465\n  tool_panel_section_label: Evolution\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ivar_consensus\n  owner: iuc\n  revisions: 40737febe339\n  tool_panel_section_label: Virology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qualimap_bamqc\n  owner: iuc\n  revisions: 19ece8afbaab\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: 5826298f6a73\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: vapor\n  owner: iuc\n  revisions: 244812f5bd1f\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mafft\n  owner: rnateam\n  revisions: bf28a8cff401\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/aiv-analysis/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "by-covid",
+                    "uni-freiburg",
+                    "elixir-europe"
                 ],
-                "workflowhub_id": "1162"
-            },
+                "elixir_node": "de",
+                "fediverse": "https://scholar.social/@zerodivision",
+                "fediverse_flavor": "mastodon",
+                "id": "wm75",
+                "joined": "2017-09",
+                "matrix": "wm75:matrix.org",
+                "name": "Wolfgang Maier",
+                "orcid": "0000-0002-9464-6640",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
+            }
+        ],
+        "dir": "topics/variant-analysis/tutorials/aiv-analysis",
+        "edam_operation": [
+            "Data handling",
+            "Sequence alignment",
+            "Read mapping",
+            "Sequencing quality control",
+            "De-novo assembly",
+            "Sequence alignment analysis",
+            "Phylogenetic analysis",
+            "Sequence contamination filtering",
+            "Sequence analysis",
+            "Multiple sequence alignment",
+            "Generation",
+            "Sequence file editing",
+            "Data retrieval",
+            "Genome indexing"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "variant-analysis/aiv-analysis",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Reassortment of gene segments makes reference-based mapping of influenza sequencing data challenging",
+            "An alternative to *de-novo* assembly can be mapping to a dynamically chosen reference genome",
+            "Variant calling and consensus genome construction can follow workflows used also for other viral sequence data",
+            "Standard phylogenetic tools can be used to find relationships between influenza samples but should be used on a per-segment basis"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-03-20",
+        "objectives": [
+            "Determine how reassortment impacts reference-based mapping approaches",
+            "Use a collection of per-segment reference sequences to construct a hybrid reference genome that is sufficiently close to a sequenced sample to be useful as a reference for mapping",
+            "Construct a sample consensus genome from mapped reads",
+            "Generate per-segment phylogenetic trees of AIV consensus sequences"
+        ],
+        "pageviews": 1887,
+        "pub_date": "2022-11-21",
+        "questions": [
+            "With reassortment of gene segments being a common event in avian influenza virus (AIV) evolution, does it make sense to use a reference-based mapping approach for constructing consensus genome sequences for AIV samples?",
+            "Is it possible to reuse existing tools and workflows developed for the analysis of sequencing data from other viruses?",
+            "How can we obtain meaningful phylogenetic insight from AIV consensus sequences?"
+        ],
+        "short_id": "T00308",
+        "short_tools": [
+            "bwa_mem",
+            "fastp",
+            "samtools_view",
+            "vapor",
+            "upload1",
+            "Show beginning1",
+            "__RELABEL_FROM_FILE__",
+            "tp_find_and_replace",
+            "ivar_consensus",
+            "qualimap_bamqc",
+            "seqtk_subseq",
+            "Grep1",
+            "bamtools_split_ref",
+            "iqtree",
+            "rbc_mafft",
+            "collapse_dataset"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "one-health",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "virology",
+            "one-health"
+        ],
+        "time_estimation": "4H",
+        "title": "Avian influenza viral strain analysis from gene segment sequencing data",
+        "tools": [
+            "Grep1",
+            "Show beginning1",
+            "__RELABEL_FROM_FILE__",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_ref/bamtools_split_ref/2.5.2+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.1.2+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/vapor/vapor/1.0.2+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
+            "toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.520+galaxy0",
+            "upload1"
+        ],
+        "topic_name": "variant-analysis",
+        "topic_name_human": "Variant Analysis",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "aiv-analysis",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/aiv-analysis/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/aiv-analysis/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/aiv-analysis/tutorial.json"
+        },
+        "version": 9,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 163,
+        "visitors": 1279
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "clustalw",
+                    "owner": "devteam",
+                    "revisions": "d6694932c5e0",
+                    "tool_panel_section_label": "Multiple Alignments",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "chromeister",
+                    "owner": "iuc",
+                    "revisions": "e483be1014b6",
+                    "tool_panel_section_label": "Multiple Alignments",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gecko",
+                    "owner": "iuc",
+                    "revisions": "5efbd15675ca",
+                    "tool_panel_section_label": "Multiple Alignments",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clustalw\n  owner: devteam\n  revisions: d6694932c5e0\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chromeister\n  owner: iuc\n  revisions: e483be1014b6\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gecko\n  owner: iuc\n  revisions: 5efbd15675ca\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.json",
+        "contributors": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
-                    }
+                "elixir_node": "es",
+                "email": "estebanpw@uma.es",
+                "id": "estebanpw",
+                "joined": "2020-11",
+                "name": "Esteban Perez-Wohlfeil",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/estebanpw/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/estebanpw.json"
+            }
+        ],
+        "dir": "topics/genome-annotation/tutorials/hpc-for-lsgc",
+        "edam_operation": [
+            "Multiple sequence alignment"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.eu",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "genome-annotation/hpc-for-lsgc",
+        "inexact_supported_servers": [
+            "GalaxyTrakr",
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": 10229,
+            "mermaid": false
+        },
+        "key_points": [
+            "We learnt that sequence comparison is a demanding problem and that there are several ways to approach it",
+            "We learnt how to run sequence comparisons in Galaxy with different levels of precision, particularly fine-grained and coarse-grained sequence comparison using GECKO and CHROMEISTER for smaller and larger sequences, respectively",
+            "We learnt how to post-process our comparison by extracting alignments, fine-tuning with multiple sequence alignment, detecting rearrangements, etc."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-07-31",
+        "objectives": [
+            "Learn the basics of pairwise sequence comparison",
+            "Learn how to run different tools in Galaxy to perform sequence comparison at fine and coarse-grained levels",
+            "Learn how to post-process your sequence comparisons"
+        ],
+        "pageviews": 5735970,
+        "pub_date": "2021-02-08",
+        "questions": [
+            "How can we run pairwise genome comparisons using Galaxy?",
+            "How can we run massive chromosome comparisons in Galaxy?",
+            "How can we quickly visualize genome comparisons in Galaxy?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "introduction",
+                "tutorials": [
+                    "galaxy-intro-101"
                 ],
-                "description": "",
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00176",
+        "short_tools": [
+            "tp_awk_tool",
+            "gecko",
+            "clustalw",
+            "chromeister"
+        ],
+        "slides": true,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "plants",
+            "prokaryote"
+        ],
+        "time_estimation": "2H",
+        "title": "From small to large-scale genome comparison",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a",
+            "toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2"
+        ],
+        "topic_name": "genome-annotation",
+        "topic_name_human": "Genome Annotation",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "hpc-for-lsgc",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.json"
+        },
+        "version": 8,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 283,
+        "visitors": 2085817,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "A workflow designed to compare chromosomes and study large-scale rearrangements using CHROMEISTER",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads, R1, in fastq.gz format\"]\n  2[label=\"Minimap2 round 1: map reads to assembly\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Racon round 1: polish assembly\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"alignment_output\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Minimap2 round 2: map reads to assembly\"]\n  1 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"consensus\"]\n  5[label=\"Racon round 2: polish assembly\"]\n  3 -> 5 [label=\"consensus\"]\n  4 -> 5 [label=\"alignment_output\"]\n  1 -> 5 [label=\"output\"]\n  k594819c3668e4575b9a64459ffacf952[color=lightseagreen,label=\"Output\\nAssembly polished by short reads using Racon\"]\n  5 -> k594819c3668e4575b9a64459ffacf952\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nQuery chromosome\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference chromosome\"]\n  2[label=\"Chromeister\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  k58cf0c0c92004ba497276d908ccdfa9a[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Detected events\"]\n  2 -> k58cf0c0c92004ba497276d908ccdfa9a\n  k2afd0e7cd1cf4bfdbec66cc237ff3e2c[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Comparison metainformation\"]\n  2 -> k2afd0e7cd1cf4bfdbec66cc237ff3e2c\n  kc248576c1c39416c99d040c520e3da67[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Comparison dotplot\"]\n  2 -> kc248576c1c39416c99d040c520e3da67\n  k5f9aad77f9ee4932ab22bb5fd83f416c[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Comparison matrix\"]\n  2 -> k5f9aad77f9ee4932ab22bb5fd83f416c\n  kdea450c2712643dcaf7a9f2b704c76dd[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Comparison score\"]\n  2 -> kdea450c2712643dcaf7a9f2b704c76dd\n  k9a03f72255884a3fb70e0ec9979c16dd[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Detected events plot\"]\n  2 -> k9a03f72255884a3fb70e0ec9979c16dd\n}",
                 "history": [
                     {
-                        "hash": "3be0312ca5a2e27bc1f8573e28943833be988894",
-                        "message": "Update Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga",
-                        "num": 5,
-                        "short_hash": "3be0312ca",
-                        "unix": "1715074403"
-                    },
-                    {
-                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
-                        "message": "new versions of workflows",
-                        "num": 4,
-                        "short_hash": "e8ddbcdd5",
-                        "unix": "1714537936"
-                    },
-                    {
-                        "hash": "7d222309ffbec070126e3e749ba6f3d4e510cc6e",
-                        "message": "Rename Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga to Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2_old.ga",
-                        "num": 3,
-                        "short_hash": "7d222309f",
-                        "unix": "1714537293"
-                    },
-                    {
-                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
-                        "message": "add/complete creator info on workflows",
-                        "num": 2,
-                        "short_hash": "62e77944b",
-                        "unix": "1676627603"
-                    },
-                    {
-                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
-                        "message": "large genome tutorial",
+                        "hash": "ae7dbf55cc79f67b32661f650f26d5baad4779b3",
+                        "message": "added workflow for chromeister",
                         "num": 1,
-                        "short_hash": "9fcb3aeec",
-                        "unix": "1665123856"
+                        "short_hash": "ae7dbf55c",
+                        "unix": "1612266607"
                     }
                 ],
                 "inputs": [
@@ -168109,225 +168996,34 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Assembly to be polished"
-                            }
-                        ],
-                        "label": "Assembly to be polished",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 72.5176329833982
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "28669894-74e2-4ba1-9d49-6e3209b5a1de",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Illumina reads, R1, in fastq.gz format"
+                                "name": "Query chromosome"
                             }
                         ],
-                        "label": "Illumina reads, R1, in fastq.gz format",
+                        "label": "Query chromosome",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 8.5,
-                            "top": 341.2832579833982
+                            "bottom": 345.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 446,
+                            "right": 646,
+                            "top": 263,
+                            "width": 200,
+                            "x": 446,
+                            "y": 263
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "bc936fdc-22a9-4507-aa47-4a70a3f93923",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nIllumina reads, R1, in fastq.gz format\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Minimap2 round 1: map reads to assembly\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Racon round 1: polish assembly\"];\n  0 -->|output| 3;\n  2 -->|alignment_output| 3;\n  1 -->|output| 3;\n  4[\"Minimap2 round 2: map reads to assembly\"];\n  1 -->|output| 4;\n  3 -->|consensus| 4;\n  5[\"Racon round 2: polish assembly\"];\n  3 -->|consensus| 5;\n  4 -->|alignment_output| 5;\n  1 -->|output| 5;\n  594819c3-668e-4575-b9a6-4459ffacf952[\"Output\\nAssembly polished by short reads using Racon\"];\n  5 --> 594819c3-668e-4575-b9a6-4459ffacf952;\n  style 594819c3-668e-4575-b9a6-4459ffacf952 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "corrected_reads": {
-                                "id": 3,
-                                "output_name": "consensus"
-                            },
-                            "overlaps": {
-                                "id": 4,
-                                "output_name": "alignment_output"
-                            },
-                            "reads": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Racon round 2: polish assembly",
-                        "name": "Racon",
-                        "outputs": [
-                            {
-                                "name": "consensus",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "left": 1198.765625,
-                            "top": 332.4707579833982
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionconsensus": {
-                                "action_arguments": {
-                                    "newname": "Racon_short_reads_polished_assembly.fasta"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "consensus"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "78c533842eeb",
-                            "name": "racon",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.5.0+galaxy1",
-                        "type": "tool",
-                        "uuid": "b3c89c40-3ad0-454c-a4d4-dfa34fb09f24",
-                        "when": null,
+                        "uuid": "fdde703b-e59f-403b-be56-28b4fde66d17",
                         "workflow_outputs": [
                             {
-                                "label": "Assembly polished by short reads using Racon",
-                                "output_name": "consensus",
-                                "uuid": "594819c3-668e-4575-b9a6-4459ffacf952"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "e6b6ae7f-73c3-450e-a997-103138788bc6"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "assembly/largegenome",
-                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga",
-                "tags": [
-                    "LG-WF",
-                    "GTN"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-racon-polish-with-illumina-reads-x2",
-                "tutorial_id": "largegenome",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.html",
-                "version": 2,
-                "wfid": "assembly-largegenome",
-                "wfname": "galaxy-workflow-racon-polish-with-illumina-reads-x2",
-                "workflow": "Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0"
-                ],
-                "workflowhub_id": "1148"
-            },
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
-                    }
-                ],
-                "description": "",
-                "features": {
-                    "comments": false,
-                    "parameters": true,
-                    "report": {
-                        "markdown": "\n# Workflow Execution Report\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
-                    },
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads \"]\n  3[label=\"Minimap2: map long reads to assembly\"]\n  2 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Racon: polish 1\"]\n  0 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"alignment_output\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Minimap2: map long reads to polished assembly 1\"]\n  2 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  4 -> 5 [label=\"consensus\"]\n  6[label=\"Racon: polish 2\"]\n  4 -> 6 [label=\"consensus\"]\n  5 -> 6 [label=\"alignment_output\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"Minimap2: map long reads to polished assembly 2\"]\n  2 -> 7 [label=\"output\"]\n  1 -> 7 [label=\"output\"]\n  6 -> 7 [label=\"consensus\"]\n  8[label=\"Racon: polish 3\"]\n  6 -> 8 [label=\"consensus\"]\n  7 -> 8 [label=\"alignment_output\"]\n  1 -> 8 [label=\"output\"]\n  9[label=\"Minimap2: map long reads to polished assembly 3\"]\n  2 -> 9 [label=\"output\"]\n  1 -> 9 [label=\"output\"]\n  8 -> 9 [label=\"consensus\"]\n  10[label=\"Racon: polish 4\"]\n  8 -> 10 [label=\"consensus\"]\n  9 -> 10 [label=\"alignment_output\"]\n  1 -> 10 [label=\"output\"]\n  kbcf0f03c595146a7aa38545aed9bc183[color=lightseagreen,label=\"Output\\nAssembly polished by long reads using Racon\"]\n  10 -> kbcf0f03c595146a7aa38545aed9bc183\n}",
-                "history": [
-                    {
-                        "hash": "ea8cb9df4cc68241e9b406bde825b4c16647280b",
-                        "message": "Update Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga",
-                        "num": 5,
-                        "short_hash": "ea8cb9df4",
-                        "unix": "1715074423"
-                    },
-                    {
-                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
-                        "message": "new versions of workflows",
-                        "num": 4,
-                        "short_hash": "e8ddbcdd5",
-                        "unix": "1714537936"
-                    },
-                    {
-                        "hash": "7bd7c55df24dd71009cbde6408fb87d49901a84a",
-                        "message": "Rename Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga to Galaxy-Workflow-Racon_polish_with_long_reads_x4_old.ga",
-                        "num": 3,
-                        "short_hash": "7bd7c55df",
-                        "unix": "1714537311"
-                    },
-                    {
-                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
-                        "message": "add/complete creator info on workflows",
-                        "num": 2,
-                        "short_hash": "62e77944b",
-                        "unix": "1676627603"
-                    },
-                    {
-                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
-                        "message": "large genome tutorial",
-                        "num": 1,
-                        "short_hash": "9fcb3aeec",
-                        "unix": "1665123856"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Assembly to be polished"
-                            }
-                        ],
-                        "label": "Assembly to be polished",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 216.625
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "c7796c36-adf8-49e4-a8e4-66e606d70311",
-                        "when": null,
-                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
@@ -168338,264 +169034,78 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "long reads"
+                                "name": "Reference chromosome"
                             }
                         ],
-                        "label": "long reads",
+                        "label": "Reference chromosome",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 4.5,
-                            "top": 360.234375
+                            "bottom": 445.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 448,
+                            "right": 648,
+                            "top": 363,
+                            "width": 200,
+                            "x": 448,
+                            "y": 363
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "e2e4a70b-6e36-4b8b-bdf6-12b97189a6bd",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "minimap setting (for long reads) "
-                            }
-                        ],
-                        "label": "minimap setting (for long reads) ",
-                        "name": "Input parameter",
-                        "outputs": [],
-                        "position": {
-                            "left": 0.578125,
-                            "top": 495.859375
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "fb80c05c-08d4-4ac2-b4bf-81ed906e4d72",
-                        "when": null,
+                        "uuid": "43a48ede-1c2e-4b0d-bf74-da212443a7de",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "3983ef22-5f05-4384-8f34-6ac8c4b2cc83"
+                                "uuid": "1007eb1e-be5f-4f22-9d42-046f5e695dc4"
                             }
                         ]
                     }
                 ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads \"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"Minimap2: map long reads to assembly\"];\n  2 -->|output| 3;\n  1 -->|output| 3;\n  0 -->|output| 3;\n  4[\"Racon: polish 1\"];\n  0 -->|output| 4;\n  3 -->|alignment_output| 4;\n  1 -->|output| 4;\n  5[\"Minimap2: map long reads to polished assembly 1\"];\n  2 -->|output| 5;\n  1 -->|output| 5;\n  4 -->|consensus| 5;\n  6[\"Racon: polish 2\"];\n  4 -->|consensus| 6;\n  5 -->|alignment_output| 6;\n  1 -->|output| 6;\n  7[\"Minimap2: map long reads to polished assembly 2\"];\n  2 -->|output| 7;\n  1 -->|output| 7;\n  6 -->|consensus| 7;\n  8[\"Racon: polish 3\"];\n  6 -->|consensus| 8;\n  7 -->|alignment_output| 8;\n  1 -->|output| 8;\n  9[\"Minimap2: map long reads to polished assembly 3\"];\n  2 -->|output| 9;\n  1 -->|output| 9;\n  8 -->|consensus| 9;\n  10[\"Racon: polish 4\"];\n  8 -->|consensus| 10;\n  9 -->|alignment_output| 10;\n  1 -->|output| 10;\n  bcf0f03c-5951-46a7-aa38-545aed9bc183[\"Output\\nAssembly polished by long reads using Racon\"];\n  10 --> bcf0f03c-5951-46a7-aa38-545aed9bc183;\n  style bcf0f03c-5951-46a7-aa38-545aed9bc183 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Racon polish with long reads, x4 - upgraded",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQuery chromosome\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference chromosome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Chromeister\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  58cf0c0c-9200-4ba4-9727-6d908ccdfa9a[\"Output\\nChromeister on input dataset(s): Detected events\"];\n  2 --> 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a;\n  style 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a stroke:#2c3143,stroke-width:4px;\n  2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c[\"Output\\nChromeister on input dataset(s): Comparison metainformation\"];\n  2 --> 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c;\n  style 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c stroke:#2c3143,stroke-width:4px;\n  c248576c-1c39-416c-99d0-40c520e3da67[\"Output\\nChromeister on input dataset(s): Comparison dotplot\"];\n  2 --> c248576c-1c39-416c-99d0-40c520e3da67;\n  style c248576c-1c39-416c-99d0-40c520e3da67 stroke:#2c3143,stroke-width:4px;\n  5f9aad77-f9ee-4932-ab22-bb5fd83f416c[\"Output\\nChromeister on input dataset(s): Comparison matrix\"];\n  2 --> 5f9aad77-f9ee-4932-ab22-bb5fd83f416c;\n  style 5f9aad77-f9ee-4932-ab22-bb5fd83f416c stroke:#2c3143,stroke-width:4px;\n  dea450c2-7126-43dc-af7a-9f2b704c76dd[\"Output\\nChromeister on input dataset(s): Comparison score\"];\n  2 --> dea450c2-7126-43dc-af7a-9f2b704c76dd;\n  style dea450c2-7126-43dc-af7a-9f2b704c76dd stroke:#2c3143,stroke-width:4px;\n  9a03f722-5588-4a3f-b70e-0ec9979c16dd[\"Output\\nChromeister on input dataset(s): Detected events plot\"];\n  2 --> 9a03f722-5588-4a3f-b70e-0ec9979c16dd;\n  style 9a03f722-5588-4a3f-b70e-0ec9979c16dd stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "CHROMEISTER chromosome comparison",
                 "outputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "minimap setting (for long reads) "
+                                "name": "Query chromosome"
                             }
                         ],
-                        "label": "minimap setting (for long reads) ",
-                        "name": "Input parameter",
+                        "label": "Query chromosome",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0.578125,
-                            "top": 495.859375
+                            "bottom": 345.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 446,
+                            "right": 646,
+                            "top": 263,
+                            "width": 200,
+                            "x": 446,
+                            "y": 263
                         },
                         "tool_id": null,
-                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
                         "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "fb80c05c-08d4-4ac2-b4bf-81ed906e4d72",
-                        "when": null,
+                        "type": "data_input",
+                        "uuid": "fdde703b-e59f-403b-be56-28b4fde66d17",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "3983ef22-5f05-4384-8f34-6ac8c4b2cc83"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                        "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "corrected_reads": {
-                                "id": 8,
-                                "output_name": "consensus"
-                            },
-                            "overlaps": {
-                                "id": 9,
-                                "output_name": "alignment_output"
-                            },
-                            "reads": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Racon: polish 4",
-                        "name": "Racon",
-                        "outputs": [
-                            {
-                                "name": "consensus",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "left": 1496.078125,
-                            "top": 431.1875
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionconsensus": {
-                                "action_arguments": {
-                                    "newname": "Racon_long_reads_polished_assembly.fasta"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "consensus"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "78c533842eeb",
-                            "name": "racon",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.5.0+galaxy1",
-                        "type": "tool",
-                        "uuid": "53f4572e-3a4a-4585-89ab-9459f8a61720",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Assembly polished by long reads using Racon",
-                                "output_name": "consensus",
-                                "uuid": "bcf0f03c-5951-46a7-aa38-545aed9bc183"
+                                "uuid": "e6b6ae7f-73c3-450e-a997-103138788bc6"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "assembly/largegenome",
-                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga",
-                "tags": [
-                    "LG-WF",
-                    "GTN"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Racon polish with long reads, x4 - upgraded",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-racon-polish-with-long-reads-x4",
-                "tutorial_id": "largegenome",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_long_reads_x4.html",
-                "version": 2,
-                "wfid": "assembly-largegenome",
-                "wfname": "galaxy-workflow-racon-polish-with-long-reads-x4",
-                "workflow": "Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0"
-                ],
-                "workflowhub_id": "1154"
-            },
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
-                    }
-                ],
-                "description": "",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": {
-                        "markdown": "\n# Workflow for Trim and Filter Reads\n\n## Workflow steps\n```galaxy\nworkflow_display()\n```\n\n\n\n\n"
-                    },
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads R2\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  3[label=\"fastp on short reads\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  k656e413841ab4561898933de9ac9a2f3[color=lightseagreen,label=\"Output\\nfastp report on short reads html\"]\n  3 -> k656e413841ab4561898933de9ac9a2f3\n  k0d53f347036847cb953a2e4dac57e013[color=lightseagreen,label=\"Output\\nfastp filtered R1 reads\"]\n  3 -> k0d53f347036847cb953a2e4dac57e013\n  k10fbe1e5400c4ffe87949b776b0d7322[color=lightseagreen,label=\"Output\\nfastp report on short reads json\"]\n  3 -> k10fbe1e5400c4ffe87949b776b0d7322\n  k639ed3f70e514e5db6f8081378962109[color=lightseagreen,label=\"Output\\nfastp filtered R2 reads\"]\n  3 -> k639ed3f70e514e5db6f8081378962109\n  4[label=\"fastp on long reads\"]\n  2 -> 4 [label=\"output\"]\n  k5e0d2c3d41a44823ae9cb1e4d2826541[color=lightseagreen,label=\"Output\\nfastp report on long reads html\"]\n  4 -> k5e0d2c3d41a44823ae9cb1e4d2826541\n  ke6018ad686f44e788cf2ccc8b97022fe[color=lightseagreen,label=\"Output\\nfastp filtered long reads\"]\n  4 -> ke6018ad686f44e788cf2ccc8b97022fe\n  k69f8383ba1be4a7495f43dba35e01426[color=lightseagreen,label=\"Output\\nfastp report on long reads json\"]\n  4 -> k69f8383ba1be4a7495f43dba35e01426\n}",
-                "history": [
-                    {
-                        "hash": "1fe24b92fd7cf3bf693a850751a6215f7b9273bd",
-                        "message": "Update Galaxy-Workflow-Trim_and_filter_reads.ga",
-                        "num": 5,
-                        "short_hash": "1fe24b92f",
-                        "unix": "1715074442"
-                    },
-                    {
-                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
-                        "message": "new versions of workflows",
-                        "num": 4,
-                        "short_hash": "e8ddbcdd5",
-                        "unix": "1714537936"
-                    },
-                    {
-                        "hash": "12f721099e26ef4bd152c1c2b56ccb51e6bd31ab",
-                        "message": "Rename Galaxy-Workflow-Trim_and_filter_reads.ga to Galaxy-Workflow-Trim_and_filter_reads_old.ga",
-                        "num": 3,
-                        "short_hash": "12f721099",
-                        "unix": "1714537350"
-                    },
-                    {
-                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
-                        "message": "add/complete creator info on workflows",
-                        "num": 2,
-                        "short_hash": "62e77944b",
-                        "unix": "1676627603"
-                    },
-                    {
-                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
-                        "message": "large genome tutorial",
-                        "num": 1,
-                        "short_hash": "9fcb3aeec",
-                        "unix": "1665123856"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Illumina reads R1"
-                            }
-                        ],
-                        "label": "Illumina reads R1",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 29.045160466974437
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "00a54054-e3f7-4e4f-9195-563e54df899a",
-                        "when": null,
-                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
@@ -168606,348 +169116,190 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Illumina reads R2"
-                            }
-                        ],
-                        "label": "Illumina reads R2",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 145.03474842418325
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "14062fd8-1aa9-4a18-94d8-bbbb0e1a9262",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "long reads"
+                                "name": "Reference chromosome"
                             }
                         ],
-                        "label": "long reads",
+                        "label": "Reference chromosome",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 576.5103981711648,
-                            "top": 35.50348455255681
+                            "bottom": 445.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 448,
+                            "right": 648,
+                            "top": 363,
+                            "width": 200,
+                            "x": 448,
+                            "y": 363
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "08eeb0d3-6ad6-4e7f-ac6a-d00c8e87fd08",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nIllumina reads R2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"fastp on short reads\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  656e4138-41ab-4561-8989-33de9ac9a2f3[\"Output\\nfastp report on short reads html\"];\n  3 --> 656e4138-41ab-4561-8989-33de9ac9a2f3;\n  style 656e4138-41ab-4561-8989-33de9ac9a2f3 stroke:#2c3143,stroke-width:4px;\n  0d53f347-0368-47cb-953a-2e4dac57e013[\"Output\\nfastp filtered R1 reads\"];\n  3 --> 0d53f347-0368-47cb-953a-2e4dac57e013;\n  style 0d53f347-0368-47cb-953a-2e4dac57e013 stroke:#2c3143,stroke-width:4px;\n  10fbe1e5-400c-4ffe-8794-9b776b0d7322[\"Output\\nfastp report on short reads json\"];\n  3 --> 10fbe1e5-400c-4ffe-8794-9b776b0d7322;\n  style 10fbe1e5-400c-4ffe-8794-9b776b0d7322 stroke:#2c3143,stroke-width:4px;\n  639ed3f7-0e51-4e5d-b6f8-081378962109[\"Output\\nfastp filtered R2 reads\"];\n  3 --> 639ed3f7-0e51-4e5d-b6f8-081378962109;\n  style 639ed3f7-0e51-4e5d-b6f8-081378962109 stroke:#2c3143,stroke-width:4px;\n  4[\"fastp on long reads\"];\n  2 -->|output| 4;\n  5e0d2c3d-41a4-4823-ae9c-b1e4d2826541[\"Output\\nfastp report on long reads html\"];\n  4 --> 5e0d2c3d-41a4-4823-ae9c-b1e4d2826541;\n  style 5e0d2c3d-41a4-4823-ae9c-b1e4d2826541 stroke:#2c3143,stroke-width:4px;\n  e6018ad6-86f4-4e78-8cf2-ccc8b97022fe[\"Output\\nfastp filtered long reads\"];\n  4 --> e6018ad6-86f4-4e78-8cf2-ccc8b97022fe;\n  style e6018ad6-86f4-4e78-8cf2-ccc8b97022fe stroke:#2c3143,stroke-width:4px;\n  69f8383b-a1be-4a74-95f4-3dba35e01426[\"Output\\nfastp report on long reads json\"];\n  4 --> 69f8383b-a1be-4a74-95f4-3dba35e01426;\n  style 69f8383b-a1be-4a74-95f4-3dba35e01426 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "Trim and filter reads - fastp - upgraded ",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "single_paired|in1": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "single_paired|in2": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool fastp",
-                                "name": "single_paired"
-                            },
-                            {
-                                "description": "runtime parameter for tool fastp",
-                                "name": "single_paired"
-                            }
-                        ],
-                        "label": "fastp on short reads",
-                        "name": "fastp",
-                        "outputs": [
-                            {
-                                "name": "out1",
-                                "type": "input"
-                            },
-                            {
-                                "name": "out2",
-                                "type": "input"
-                            },
-                            {
-                                "name": "report_html",
-                                "type": "html"
-                            },
-                            {
-                                "name": "report_json",
-                                "type": "json"
-                            }
-                        ],
-                        "position": {
-                            "left": 290.5382191051136,
-                            "top": 0
-                        },
-                        "post_job_actions": {
-                            "DeleteIntermediatesActionout1": {
-                                "action_arguments": {},
-                                "action_type": "DeleteIntermediatesAction",
-                                "output_name": "out1"
-                            },
-                            "RenameDatasetActionout1": {
-                                "action_arguments": {
-                                    "newname": "fastp_filtered_R1.fastq.gz"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out1"
-                            },
-                            "RenameDatasetActionout2": {
-                                "action_arguments": {
-                                    "newname": "fastp_filtered_R2.fastq.gz"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out2"
-                            },
-                            "RenameDatasetActionreport_html": {
-                                "action_arguments": {
-                                    "newname": "fastp_illumina.html"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "report_html"
-                            },
-                            "RenameDatasetActionreport_json": {
-                                "action_arguments": {
-                                    "newname": "fastp_illumina.json"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "report_json"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "c59d48774d03",
-                            "name": "fastp",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired\", \"__current_case__\": 1, \"in1\": {\"__class__\": \"ConnectedValue\"}, \"in2\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": \"\", \"adapter_sequence2\": \"\"}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.23.4+galaxy0",
-                        "type": "tool",
-                        "uuid": "c38e84b3-771c-428e-9d2d-ce84d5e1153c",
-                        "when": null,
+                        "uuid": "43a48ede-1c2e-4b0d-bf74-da212443a7de",
                         "workflow_outputs": [
                             {
-                                "label": "fastp report on short reads html",
-                                "output_name": "report_html",
-                                "uuid": "656e4138-41ab-4561-8989-33de9ac9a2f3"
-                            },
-                            {
-                                "label": "fastp filtered R1 reads",
-                                "output_name": "out1",
-                                "uuid": "0d53f347-0368-47cb-953a-2e4dac57e013"
-                            },
-                            {
-                                "label": "fastp report on short reads json",
-                                "output_name": "report_json",
-                                "uuid": "10fbe1e5-400c-4ffe-8794-9b776b0d7322"
-                            },
-                            {
-                                "label": "fastp filtered R2 reads",
-                                "output_name": "out2",
-                                "uuid": "639ed3f7-0e51-4e5d-b6f8-081378962109"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "1007eb1e-be5f-4f22-9d42-046f5e695dc4"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a",
                         "errors": null,
-                        "id": 4,
+                        "id": 2,
                         "input_connections": {
-                            "single_paired|in1": {
-                                "id": 2,
+                            "db": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "query": {
+                                "id": 0,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool fastp",
-                                "name": "single_paired"
+                                "description": "runtime parameter for tool Chromeister",
+                                "name": "db"
+                            },
+                            {
+                                "description": "runtime parameter for tool Chromeister",
+                                "name": "query"
                             }
                         ],
-                        "label": "fastp on long reads",
-                        "name": "fastp",
+                        "label": null,
+                        "name": "Chromeister",
                         "outputs": [
                             {
-                                "name": "out1",
-                                "type": "input"
+                                "name": "output",
+                                "type": "txt"
                             },
                             {
-                                "name": "report_html",
-                                "type": "html"
+                                "name": "output_imagen",
+                                "type": "png"
                             },
                             {
-                                "name": "report_json",
-                                "type": "json"
-                            }
-                        ],
-                        "position": {
-                            "left": 804.010509144176,
-                            "top": 22.482646595348
-                        },
-                        "post_job_actions": {
-                            "DeleteIntermediatesActionout1": {
-                                "action_arguments": {},
-                                "action_type": "DeleteIntermediatesAction",
-                                "output_name": "out1"
+                                "name": "output_csv",
+                                "type": "csv"
                             },
-                            "RenameDatasetActionout1": {
-                                "action_arguments": {
-                                    "newname": "fastp_filtered_long_reads.fastq.gz"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out1"
+                            {
+                                "name": "output_events",
+                                "type": "txt"
                             },
-                            "RenameDatasetActionreport_html": {
-                                "action_arguments": {
-                                    "newname": "fastp_longreads.html"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "report_html"
+                            {
+                                "name": "output_events_png",
+                                "type": "png"
                             },
-                            "RenameDatasetActionreport_json": {
-                                "action_arguments": {
-                                    "newname": "fastp_longreads.json"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "report_json"
+                            {
+                                "name": "output_score",
+                                "type": "txt"
                             }
+                        ],
+                        "position": {
+                            "bottom": 793.4000244140625,
+                            "height": 520.4000244140625,
+                            "left": 851,
+                            "right": 1051,
+                            "top": 273,
+                            "width": 200,
+                            "x": 851,
+                            "y": 273
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a",
                         "tool_shed_repository": {
-                            "changeset_revision": "c59d48774d03",
-                            "name": "fastp",
+                            "changeset_revision": "a6d1f83c46b4",
+                            "name": "chromeister",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": true, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": true, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"-G\", \"__current_case__\": 2}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"single\", \"__current_case__\": 0, \"in1\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": true, \"adapter_sequence1\": \"\"}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.23.4+galaxy0",
+                        "tool_state": "{\"db\": {\"__class__\": \"RuntimeValue\"}, \"diffuse\": \"4\", \"dimension\": \"1000\", \"grid\": \"true\", \"kmer\": \"32\", \"pngevents\": \"true\", \"query\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.5.a",
                         "type": "tool",
-                        "uuid": "93602736-2d22-43e4-a53a-803326ccab9e",
-                        "when": null,
+                        "uuid": "79507815-b059-4f21-b74e-8e390fbb4bf2",
                         "workflow_outputs": [
                             {
-                                "label": "fastp report on long reads html",
-                                "output_name": "report_html",
-                                "uuid": "5e0d2c3d-41a4-4823-ae9c-b1e4d2826541"
+                                "label": "Chromeister on input dataset(s): Detected events",
+                                "output_name": "output_events",
+                                "uuid": "58cf0c0c-9200-4ba4-9727-6d908ccdfa9a"
                             },
                             {
-                                "label": "fastp filtered long reads",
-                                "output_name": "out1",
-                                "uuid": "e6018ad6-86f4-4e78-8cf2-ccc8b97022fe"
+                                "label": "Chromeister on input dataset(s): Comparison metainformation",
+                                "output_name": "output_csv",
+                                "uuid": "2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c"
                             },
                             {
-                                "label": "fastp report on long reads json",
-                                "output_name": "report_json",
-                                "uuid": "69f8383b-a1be-4a74-95f4-3dba35e01426"
+                                "label": "Chromeister on input dataset(s): Comparison dotplot",
+                                "output_name": "output_imagen",
+                                "uuid": "c248576c-1c39-416c-99d0-40c520e3da67"
+                            },
+                            {
+                                "label": "Chromeister on input dataset(s): Comparison matrix",
+                                "output_name": "output",
+                                "uuid": "5f9aad77-f9ee-4932-ab22-bb5fd83f416c"
+                            },
+                            {
+                                "label": "Chromeister on input dataset(s): Comparison score",
+                                "output_name": "output_score",
+                                "uuid": "dea450c2-7126-43dc-af7a-9f2b704c76dd"
+                            },
+                            {
+                                "label": "Chromeister on input dataset(s): Detected events plot",
+                                "output_name": "output_events_png",
+                                "uuid": "9a03f722-5588-4a3f-b70e-0ec9979c16dd"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/largegenome",
-                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Trim_and_filter_reads.ga",
+                "parent_id": "genome-annotation/hpc-for-lsgc",
+                "path": "topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/CHROMEISTER_chromosome_comparison.ga",
                 "tags": [
-                    "LG-WF",
-                    "GTN"
+                    "genome-annotation"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Trim and filter reads - fastp - upgraded ",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-trim-and-filter-reads",
-                "tutorial_id": "largegenome",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Trim_and_filter_reads.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Trim_and_filter_reads.html",
-                "version": 2,
-                "wfid": "assembly-largegenome",
-                "wfname": "galaxy-workflow-trim-and-filter-reads",
-                "workflow": "Galaxy-Workflow-Trim_and_filter_reads.ga",
+                "title": "CHROMEISTER chromosome comparison",
+                "topic_id": "genome-annotation",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-hpc-for-lsgc/versions/chromeister-chromosome-comparison",
+                "tutorial_id": "hpc-for-lsgc",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/CHROMEISTER_chromosome_comparison.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/CHROMEISTER_chromosome_comparison.html",
+                "version": 1,
+                "wfid": "genome-annotation-hpc-for-lsgc",
+                "wfname": "chromeister-chromosome-comparison",
+                "workflow": "CHROMEISTER_chromosome_comparison.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a"
                 ],
-                "workflowhub_id": "1144"
+                "workflowhub_id": "1156"
             },
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-9906-0673",
-                        "name": "Anna Syme"
-                    }
-                ],
-                "description": "",
+                "creators": [],
+                "description": "A workflow designed to compare two sequences using GECKO, extract repeats and perform multiple sequence alignment",
                 "features": {
                     "comments": false,
                     "parameters": false,
-                    "report": {
-                        "markdown": "\n# Workflow Execution Report\n\n\r\n```galaxy\nworkflow_display()\n```\r\n"
-                    },
+                    "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"]\n  1[label=\"Meryl - count kmers\"]\n  0 -> 1 [label=\"output\"]\n  k899ddd934c0f4f81a9738120494ed983[color=lightseagreen,label=\"Output\\nMeryl on input dataset(s): read-db.meryldb\"]\n  1 -> k899ddd934c0f4f81a9738120494ed983\n  2[label=\"Meryl - generate histogram\"]\n  1 -> 2 [label=\"read_db\"]\n  3[label=\"Genomescope\"]\n  2 -> 3 [label=\"read_db_hist\"]\n  kefc727b61ef44c4c8cce35c7d3cc8aac[color=lightseagreen,label=\"Output\\nGenomeScope on input dataset(s) Transformed log plot\"]\n  3 -> kefc727b61ef44c4c8cce35c7d3cc8aac\n  k701df341576744bcade26af498ab7467[color=lightseagreen,label=\"Output\\nGenomeScope on input dataset(s) Transformed linear plot\"]\n  3 -> k701df341576744bcade26af498ab7467\n  k85fa4004b35147b384aa6788d338037a[color=lightseagreen,label=\"Output\\nGenomeScope on input dataset(s) Log plot\"]\n  3 -> k85fa4004b35147b384aa6788d338037a\n  kc71ce05598f0435493972f8833b90cc4[color=lightseagreen,label=\"Output\\nGenomeScope on input dataset(s) Linear plot\"]\n  3 -> kc71ce05598f0435493972f8833b90cc4\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nQuery sequence\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference sequence\"]\n  2[label=\"Gecko\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  k6275abc1d74e45a7b8ab3c88426cc488[color=lightseagreen,label=\"Output\\nGecko on input dataset(s): CSV\"]\n  2 -> k6275abc1d74e45a7b8ab3c88426cc488\n  3[label=\"Text reformatting\"]\n  2 -> 3 [label=\"alignments2\"]\n  4[label=\"ClustalW\"]\n  3 -> 4 [label=\"outfile\"]\n  kd63c1172a5914bf6b307052ca19e7098[color=lightseagreen,label=\"Output\\nClustalW on input dataset(s): clustal\"]\n  4 -> kd63c1172a5914bf6b307052ca19e7098\n  kd7758e3a522d44398c9a03f784284ebd[color=lightseagreen,label=\"Output\\nClustalW on input dataset(s): dnd\"]\n  4 -> kd7758e3a522d44398c9a03f784284ebd\n}",
                 "history": [
                     {
-                        "hash": "b74cf5a09d0d563d658d374ed6d287db85df3a8a",
-                        "message": "Update Galaxy-Workflow-kmer_counting.ga",
-                        "num": 5,
-                        "short_hash": "b74cf5a09",
-                        "unix": "1715074461"
-                    },
-                    {
-                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
-                        "message": "new versions of workflows",
-                        "num": 4,
-                        "short_hash": "e8ddbcdd5",
-                        "unix": "1714537936"
-                    },
-                    {
-                        "hash": "0be0483e2cbaa0ab18026da1f19f4b124d78e1c4",
-                        "message": "Rename Galaxy-Workflow-kmer_counting.ga to Galaxy-Workflow-kmer_counting_old.ga",
-                        "num": 3,
-                        "short_hash": "0be0483e2",
-                        "unix": "1714537366"
-                    },
-                    {
-                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
-                        "message": "add/complete creator info on workflows",
+                        "hash": "ae7dbf55cc79f67b32661f650f26d5baad4779b3",
+                        "message": "added workflow for chromeister",
                         "num": 2,
-                        "short_hash": "62e77944b",
-                        "unix": "1676627603"
+                        "short_hash": "ae7dbf55c",
+                        "unix": "1612266607"
                     },
                     {
-                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
-                        "message": "large genome tutorial",
+                        "hash": "42c257d5c78780b24fb384627c26488a90eeda4f",
+                        "message": "changed topic to genome-annotation",
                         "num": 1,
-                        "short_hash": "9fcb3aeec",
-                        "unix": "1665123856"
+                        "short_hash": "42c257d5c",
+                        "unix": "1612264525"
                     }
                 ],
                 "inputs": [
@@ -168960,261 +169312,362 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Illumina reads R1"
+                                "name": "Query sequence"
                             }
                         ],
-                        "label": "Illumina reads R1",
+                        "label": "Query sequence",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 31.5
+                            "bottom": 473.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 481,
+                            "right": 681,
+                            "top": 391,
+                            "width": 200,
+                            "x": 481,
+                            "y": 391
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "3daa3f25-6fff-4766-9d45-b991fd6751a5",
-                        "when": null,
-                        "workflow_outputs": []
+                        "uuid": "63490a28-7edf-4e4f-8697-5cbf621b0768",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "f1c8c4bf-126f-4c4b-8e5a-512cd0d270cd"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Reference sequence"
+                            }
+                        ],
+                        "label": "Reference sequence",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 598.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 482,
+                            "right": 682,
+                            "top": 516,
+                            "width": 200,
+                            "x": 482,
+                            "y": 516
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "f49e63f9-977e-4a1f-bf43-9a50cfa14ee3",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "0867afff-2445-4a26-b21c-2476606adb88"
+                            }
+                        ]
                     }
                 ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Meryl - count kmers\"];\n  0 -->|output| 1;\n  899ddd93-4c0f-4f81-a973-8120494ed983[\"Output\\nMeryl on input dataset(s): read-db.meryldb\"];\n  1 --> 899ddd93-4c0f-4f81-a973-8120494ed983;\n  style 899ddd93-4c0f-4f81-a973-8120494ed983 stroke:#2c3143,stroke-width:4px;\n  2[\"Meryl - generate histogram\"];\n  1 -->|read_db| 2;\n  3[\"Genomescope\"];\n  2 -->|read_db_hist| 3;\n  efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac[\"Output\\nGenomeScope on input dataset(s) Transformed log plot\"];\n  3 --> efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac;\n  style efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac stroke:#2c3143,stroke-width:4px;\n  701df341-5767-44bc-ade2-6af498ab7467[\"Output\\nGenomeScope on input dataset(s) Transformed linear plot\"];\n  3 --> 701df341-5767-44bc-ade2-6af498ab7467;\n  style 701df341-5767-44bc-ade2-6af498ab7467 stroke:#2c3143,stroke-width:4px;\n  85fa4004-b351-47b3-84aa-6788d338037a[\"Output\\nGenomeScope on input dataset(s) Log plot\"];\n  3 --> 85fa4004-b351-47b3-84aa-6788d338037a;\n  style 85fa4004-b351-47b3-84aa-6788d338037a stroke:#2c3143,stroke-width:4px;\n  c71ce055-98f0-4354-9397-2f8833b90cc4[\"Output\\nGenomeScope on input dataset(s) Linear plot\"];\n  3 --> c71ce055-98f0-4354-9397-2f8833b90cc4;\n  style c71ce055-98f0-4354-9397-2f8833b90cc4 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:21 +0000",
-                "name": "kmer counting - meryl - upgraded",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQuery sequence\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference sequence\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Gecko\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  6275abc1-d74e-45a7-b8ab-3c88426cc488[\"Output\\nGecko on input dataset(s): CSV\"];\n  2 --> 6275abc1-d74e-45a7-b8ab-3c88426cc488;\n  style 6275abc1-d74e-45a7-b8ab-3c88426cc488 stroke:#2c3143,stroke-width:4px;\n  3[\"Text reformatting\"];\n  2 -->|alignments2| 3;\n  4[\"ClustalW\"];\n  3 -->|outfile| 4;\n  d63c1172-a591-4bf6-b307-052ca19e7098[\"Output\\nClustalW on input dataset(s): clustal\"];\n  4 --> d63c1172-a591-4bf6-b307-052ca19e7098;\n  style d63c1172-a591-4bf6-b307-052ca19e7098 stroke:#2c3143,stroke-width:4px;\n  d7758e3a-522d-4439-8c9a-03f784284ebd[\"Output\\nClustalW on input dataset(s): dnd\"];\n  4 --> d7758e3a-522d-4439-8c9a-03f784284ebd;\n  style d7758e3a-522d-4439-8c9a-03f784284ebd stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:08 +0000",
+                "name": "GECKO pairwise comparison",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+                        "content_id": null,
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {
-                            "operation_type|input_reads": {
-                                "id": 0,
-                                "output_name": "output"
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Query sequence"
                             }
+                        ],
+                        "label": "Query sequence",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 473.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 481,
+                            "right": 681,
+                            "top": 391,
+                            "width": 200,
+                            "x": 481,
+                            "y": 391
                         },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "63490a28-7edf-4e4f-8697-5cbf621b0768",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "f1c8c4bf-126f-4c4b-8e5a-512cd0d270cd"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Meryl",
-                                "name": "operation_type"
+                                "description": "",
+                                "name": "Reference sequence"
                             }
                         ],
-                        "label": "Meryl - count kmers",
-                        "name": "Meryl",
+                        "label": "Reference sequence",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 598.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 482,
+                            "right": 682,
+                            "top": 516,
+                            "width": 200,
+                            "x": 482,
+                            "y": 516
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "f49e63f9-977e-4a1f-bf43-9a50cfa14ee3",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "0867afff-2445-4a26-b21c-2476606adb88"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "db": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "query": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Gecko",
                         "outputs": [
                             {
-                                "name": "read_db",
-                                "type": "meryldb"
+                                "name": "csv_output1",
+                                "type": "csv"
+                            },
+                            {
+                                "name": "alignments2",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 228,
-                            "top": 103.5
+                            "bottom": 709.8000030517578,
+                            "height": 194.8000030517578,
+                            "left": 841,
+                            "right": 1041,
+                            "top": 515,
+                            "width": 200,
+                            "x": 841,
+                            "y": 515
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "29dabd8db6f2",
-                            "name": "meryl",
+                            "changeset_revision": "5efbd15675ca",
+                            "name": "gecko",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"operation_type\": {\"command_type\": \"count-kmers\", \"__current_case__\": 0, \"count_operations\": \"count\", \"input_reads\": {\"__class__\": \"RuntimeValue\"}, \"options_kmer_size\": {\"kmer_size\": \"provide\", \"__current_case__\": 0, \"input_kmer_size\": \"21\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3+galaxy6",
+                        "tool_state": "{\"db\": {\"__class__\": \"ConnectedValue\"}, \"kmer\": \"16\", \"minlen\": \"50\", \"options\": {\"selection_mode\": \"alignments\", \"__current_case__\": 0}, \"query\": {\"__class__\": \"ConnectedValue\"}, \"similarity\": \"60\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2",
                         "type": "tool",
-                        "uuid": "0a85d93b-8f53-4bc8-b89b-4be6f306f2c6",
-                        "when": null,
+                        "uuid": "217b825b-dfa8-4443-95cb-ea55dd499397",
                         "workflow_outputs": [
                             {
-                                "label": "Meryl on input dataset(s): read-db.meryldb",
-                                "output_name": "read_db",
-                                "uuid": "899ddd93-4c0f-4f81-a973-8120494ed983"
+                                "label": "Gecko on input dataset(s): CSV",
+                                "output_name": "csv_output1",
+                                "uuid": "6275abc1-d74e-45a7-b8ab-3c88426cc488"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "alignments2",
+                                "uuid": "643f73a5-9648-4b78-8b39-4643a0f4438a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
                         "errors": null,
-                        "id": 2,
+                        "id": 3,
                         "input_connections": {
-                            "operation_type|input_meryldb_02": {
-                                "id": 1,
-                                "output_name": "read_db"
+                            "infile": {
+                                "id": 2,
+                                "output_name": "alignments2"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Meryl",
-                                "name": "operation_type"
-                            }
-                        ],
-                        "label": "Meryl - generate histogram",
-                        "name": "Meryl",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Text reformatting",
                         "outputs": [
                             {
-                                "name": "read_db_hist",
-                                "type": "tabular"
+                                "name": "outfile",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 465.5,
-                            "top": 110
+                            "bottom": 740.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": 1162,
+                            "right": 1362,
+                            "top": 627,
+                            "width": 200,
+                            "x": 1162,
+                            "y": 627
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+                        "post_job_actions": {
+                            "ChangeDatatypeActionoutfile": {
+                                "action_arguments": {
+                                    "newtype": "fasta"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "outfile"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "29dabd8db6f2",
-                            "name": "meryl",
-                            "owner": "iuc",
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"operation_type\": {\"command_type\": \"histogram-kmers\", \"__current_case__\": 4, \"input_meryldb_02\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3+galaxy6",
+                        "tool_state": "{\"code\": \"BEGIN{FS=\\\" \\\"} /@\\\\(196[0-9][0-9]/ { printf(\\\">sequence%s%s\\\\n\\\", $(NF-1), $NF); getline; while(substr($0,1,1) != \\\">\\\"){ if(substr($0,1,1) ==\\\"Y\\\"){ print $2; } getline; } } \", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.2",
                         "type": "tool",
-                        "uuid": "80dbb867-84f7-4349-ae1d-1c7b87d0dce7",
-                        "when": null,
+                        "uuid": "ac13faf0-b6dc-48fa-b5b4-31fec9a4733f",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "read_db_hist",
-                                "uuid": "bf11e7cb-61a2-4c27-9aa1-4c7a42028330"
+                                "output_name": "outfile",
+                                "uuid": "789a050e-0ab3-4296-b64d-9b7ad67af768"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
                         "errors": null,
-                        "id": 3,
+                        "id": 4,
                         "input_connections": {
                             "input": {
-                                "id": 2,
-                                "output_name": "read_db_hist"
+                                "id": 3,
+                                "output_name": "outfile"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool GenomeScope",
-                                "name": "input"
-                            }
-                        ],
-                        "label": "Genomescope",
-                        "name": "GenomeScope",
+                        "inputs": [],
+                        "label": null,
+                        "name": "ClustalW",
                         "outputs": [
                             {
-                                "name": "linear_plot",
-                                "type": "png"
-                            },
-                            {
-                                "name": "log_plot",
-                                "type": "png"
-                            },
-                            {
-                                "name": "transformed_linear_plot",
-                                "type": "png"
-                            },
-                            {
-                                "name": "transformed_log_plot",
-                                "type": "png"
-                            },
-                            {
-                                "name": "model",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "summary",
-                                "type": "txt"
+                                "name": "output",
+                                "type": "clustal"
                             },
                             {
-                                "name": "progress",
-                                "type": "txt"
+                                "name": "dnd",
+                                "type": "nhx"
                             }
                         ],
                         "position": {
-                            "left": 699.204345703125,
-                            "top": 0
+                            "bottom": 864.8000030517578,
+                            "height": 184.8000030517578,
+                            "left": 1536,
+                            "right": 1736,
+                            "top": 680,
+                            "width": 200,
+                            "x": 1536,
+                            "y": 680
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "01210c4e9144",
-                            "name": "genomescope",
-                            "owner": "iuc",
+                            "changeset_revision": "d6694932c5e0",
+                            "name": "clustalw",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_options\": {\"topology\": null, \"initial_repetitiveness\": null, \"initial_heterozygosities\": \"\", \"transform_exp\": null, \"testing\": false, \"true_params\": \"\", \"trace_flag\": false, \"num_rounds\": null}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"kmer_length\": \"21\", \"lambda\": null, \"max_kmercov\": null, \"output_options\": {\"output_files\": [\"model_output\", \"summary_output\", \"progress_output\"], \"no_unique_sequence\": false}, \"ploidy\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0+galaxy2",
+                        "tool_state": "{\"dnarna\": \"DNA\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"out_order\": \"ALIGNED\", \"outcontrol\": {\"outform\": \"clustal\", \"__current_case__\": 2, \"out_seqnos\": \"false\"}, \"range\": {\"mode\": \"complete\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1",
                         "type": "tool",
-                        "uuid": "fa7a5012-8bd0-4b35-b337-249245e0932b",
-                        "when": null,
+                        "uuid": "b95c1c44-a967-47fd-a85c-3a3121163486",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "progress",
-                                "uuid": "fedca588-8be6-4e13-9ff5-62387a5a90af"
-                            },
-                            {
-                                "label": "GenomeScope on input dataset(s) Transformed log plot",
-                                "output_name": "transformed_log_plot",
-                                "uuid": "efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "summary",
-                                "uuid": "fd17af72-7c2a-4167-9880-7fbda525ccbb"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "model",
-                                "uuid": "ede2b1a5-4017-4aef-a6d2-bac5d17bc7b5"
-                            },
-                            {
-                                "label": "GenomeScope on input dataset(s) Transformed linear plot",
-                                "output_name": "transformed_linear_plot",
-                                "uuid": "701df341-5767-44bc-ade2-6af498ab7467"
-                            },
-                            {
-                                "label": "GenomeScope on input dataset(s) Log plot",
-                                "output_name": "log_plot",
-                                "uuid": "85fa4004-b351-47b3-84aa-6788d338037a"
+                                "label": "ClustalW on input dataset(s): clustal",
+                                "output_name": "output",
+                                "uuid": "d63c1172-a591-4bf6-b307-052ca19e7098"
                             },
                             {
-                                "label": "GenomeScope on input dataset(s) Linear plot",
-                                "output_name": "linear_plot",
-                                "uuid": "c71ce055-98f0-4354-9397-2f8833b90cc4"
+                                "label": "ClustalW on input dataset(s): dnd",
+                                "output_name": "dnd",
+                                "uuid": "d7758e3a-522d-4439-8c9a-03f784284ebd"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/largegenome",
-                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-kmer_counting.ga",
+                "parent_id": "genome-annotation/hpc-for-lsgc",
+                "path": "topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/GECKO_pairwise_comparison.ga",
                 "tags": [
-                    "GTN",
-                    "LG-WF"
+                    "genome-annotation"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "kmer counting - meryl - upgraded",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-kmer-counting",
-                "tutorial_id": "largegenome",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-kmer_counting.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-kmer_counting.html",
-                "version": 2,
-                "wfid": "assembly-largegenome",
-                "wfname": "galaxy-workflow-kmer-counting",
-                "workflow": "Galaxy-Workflow-kmer_counting.ga",
+                "title": "GECKO pairwise comparison",
+                "topic_id": "genome-annotation",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-hpc-for-lsgc/versions/gecko-pairwise-comparison",
+                "tutorial_id": "hpc-for-lsgc",
+                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/GECKO_pairwise_comparison.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/GECKO_pairwise_comparison.html",
+                "version": 1,
+                "wfid": "genome-annotation-hpc-for-lsgc",
+                "wfname": "gecko-pairwise-comparison",
+                "workflow": "GECKO_pairwise_comparison.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2"
                 ],
-                "workflowhub_id": "1166"
+                "workflowhub_id": "1160"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.7055935"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.4485547"
     },
     {
         "admin_install": {
@@ -169223,150 +169676,416 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "blobtoolkit",
+                    "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "7d9ee8cd14b8",
-                    "tool_panel_section_label": "Assembly",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "blobtoolkit",
-                    "owner": "bgruening",
-                    "revisions": "53dd00a4ab68",
-                    "tool_panel_section_label": "Assembly",
+                    "name": "taxonomy_krona_chart",
+                    "owner": "crs4",
+                    "revisions": "1334cb4c6b68",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "diamond",
-                    "owner": "bgruening",
-                    "revisions": "e8ac2b53f262",
-                    "tool_panel_section_label": "NCBI Blast",
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "e7b2202befea",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "gfastats",
-                    "owner": "bgruening",
-                    "revisions": "5799092ffdff",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "datamash_reverse",
+                    "owner": "iuc",
+                    "revisions": "0f1724dd59d2",
+                    "tool_panel_section_label": "Join, Subtract and Group",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "gfastats",
-                    "owner": "bgruening",
-                    "revisions": "3ef480892a9f",
+                    "name": "fastp",
+                    "owner": "iuc",
+                    "revisions": "dbf9c561ef29",
                     "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "kraken2",
+                    "owner": "iuc",
+                    "revisions": "328c607150ff",
+                    "tool_panel_section_label": "Metagenomic Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "samtools_stats",
-                    "owner": "devteam",
-                    "revisions": "3a0efe14891f",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "5e33b465d8d5",
+                    "tool_panel_section_label": "Quality Control",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "smudgeplot",
-                    "owner": "galaxy-australia",
-                    "revisions": "5e0825476fb7",
-                    "tool_panel_section_label": "Assembly",
+                    "name": "porechop",
+                    "owner": "iuc",
+                    "revisions": "93d623d9979c",
+                    "tool_panel_section_label": "Nanopore",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: taxonomy_krona_chart\n  owner: crs4\n  revisions: 1334cb4c6b68\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_reverse\n  owner: iuc\n  revisions: 0f1724dd59d2\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: dbf9c561ef29\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: 328c607150ff\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 5e33b465d8d5\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: porechop\n  owner: iuc\n  revisions: 93d623d9979c\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.json",
+        "contributors": [
+            {
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "gallardoalba",
+                "joined": "2020-11",
+                "name": "Crist\u00f3bal Gallardo",
+                "orcid": "0000-0002-5752-2155",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
+            }
+        ],
+        "dir": "topics/microbiome/tutorials/nanopore-16S-metagenomics",
+        "edam_ontology": [
+            "topic_3697",
+            "topic_0637",
+            "topic_0080",
+            "topic_4038"
+        ],
+        "edam_operation": [
+            "Taxonomic classification",
+            "Statistical calculation",
+            "Visualisation",
+            "Validation",
+            "Sequencing quality control",
+            "Sequence composition calculation",
+            "Sequence contamination filtering"
+        ],
+        "edam_topic": [
+            "Microbial ecology",
+            "Taxonomy",
+            "Sequence analysis"
+        ],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "microbiome/nanopore-16S-metagenomics",
+        "inexact_supported_servers": [
+            "GalaxyTrakr",
+            "UseGalaxy.be",
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "We learned to use MinION Nanopore data for analyzing the health status of the soil",
+            "We preprocessed Nanopore sequences in order to improve their quality"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-07-31",
+        "objectives": [
+            "Use Nanopore data for studying soil metagenomics",
+            "Analyze and preprocess Nanopore reads",
+            "Use Kraken2 to assign a taxonomic labels"
+        ],
+        "pageviews": 3844,
+        "pub_date": "2020-11-24",
+        "questions": [
+            "How can we analyse the health status of the soil?",
+            "How do plants modify the composition of microbial communities?"
+        ],
+        "redirect_from": [
+            "/topics/metagenomics/tutorials/nanopore-16S-metagenomics/tutorial",
+            "/short/microbiome/nanopore-16S-metagenomics",
+            "/short/T00207",
+            "/short/T00392"
+        ],
+        "short_id": "T00392",
+        "short_tools": [
+            "porechop",
+            "fastp",
+            "tp_replace_in_line",
+            "taxonomy_krona_chart",
+            "multiqc",
+            "kraken2",
+            "datamash_reverse",
+            "fastqc",
+            "Remove beginning1"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "metabarcoding",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
                 },
                 {
-                    "name": "bandage",
-                    "owner": "iuc",
-                    "revisions": "ddddce450736",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "metabarcoding",
+            "16S",
+            "nanopore",
+            "microgalaxy",
+            "plants"
+        ],
+        "time_estimation": "2H",
+        "title": "16S Microbial analysis with Nanopore data",
+        "tools": [
+            "Remove beginning1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.0.8_beta+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3"
+        ],
+        "topic_name": "microbiome",
+        "topic_name_human": "Microbiome",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "nanopore-16S-metagenomics",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.json"
+        },
+        "version": 5,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 163,
+        "visitors": 2758,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "16S rRNA analysis with Nanopore reads",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  1[label=\"FastQC\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Porechop\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"MultiQC\"]\n  1 -> 3 [label=\"text_file\"]\n  4[label=\"fastp\"]\n  2 -> 4 [label=\"outfile\"]\n  5[label=\"FastQC\"]\n  4 -> 5 [label=\"out1\"]\n  6[label=\"Kraken2\"]\n  4 -> 6 [label=\"out1\"]\n  7[label=\"MultiQC\"]\n  5 -> 7 [label=\"text_file\"]\n  8[label=\"Reverse\"]\n  6 -> 8 [label=\"report_output\"]\n  9[label=\"Replace Text\"]\n  8 -> 9 [label=\"out_file\"]\n  10[label=\"Remove beginning\"]\n  9 -> 10 [label=\"outfile\"]\n  11[label=\"Krona pie chart\"]\n  10 -> 11 [label=\"out_file1\"]\n}",
+                "history": [
+                    {
+                        "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
+                        "message": "Rename metagenomics topic to microbiome",
+                        "num": 1,
+                        "short_hash": "0e0a2f2cc",
+                        "unix": "1704901629"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Input Dataset Collection"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 10
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "18fc8b44-c752-41a0-a17c-e03797a5fab1",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"FastQC\"];\n  0 -->|output| 1;\n  2[\"Porechop\"];\n  0 -->|output| 2;\n  3[\"MultiQC\"];\n  1 -->|text_file| 3;\n  4[\"fastp\"];\n  2 -->|outfile| 4;\n  5[\"FastQC\"];\n  4 -->|out1| 5;\n  6[\"Kraken2\"];\n  4 -->|out1| 6;\n  7[\"MultiQC\"];\n  5 -->|text_file| 7;\n  8[\"Reverse\"];\n  6 -->|report_output| 8;\n  9[\"Replace Text\"];\n  8 -->|out_file| 9;\n  10[\"Remove beginning\"];\n  9 -->|outfile| 10;\n  11[\"Krona pie chart\"];\n  10 -->|out_file1| 11;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Training: 16S rRNA Analysis with Nanopore Sequencing Reads",
+                "outputs": [],
+                "parent_id": "microbiome/nanopore-16S-metagenomics",
+                "path": "topics/microbiome/tutorials/nanopore-16S-metagenomics/workflows/main_workflow.ga",
+                "tags": [
+                    "microbiome"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Training: 16S rRNA Analysis with Nanopore Sequencing Reads",
+                "topic_id": "microbiome",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/microbiome-nanopore-16S-metagenomics/versions/main-workflow",
+                "tutorial_id": "nanopore-16S-metagenomics",
+                "url": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/nanopore-16S-metagenomics/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/nanopore-16S-metagenomics/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "microbiome-nanopore-16S-metagenomics",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "Remove beginning1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.0.8_beta+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3"
+                ],
+                "workflowhub_id": "1064"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/4274812"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "salmon",
+                    "owner": "bgruening",
+                    "revisions": "e3d32471da11",
+                    "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bellerophon",
-                    "owner": "iuc",
-                    "revisions": "25ca5d73aedf",
-                    "tool_panel_section_label": "Assembly",
+                    "name": "trim_galore",
+                    "owner": "bgruening",
+                    "revisions": "949f01671246",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "busco",
-                    "owner": "iuc",
-                    "revisions": "bb935709506a",
-                    "tool_panel_section_label": "Annotation",
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "e7b2202befea",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bwa_mem2",
-                    "owner": "iuc",
-                    "revisions": "b4a22d90cce9",
-                    "tool_panel_section_label": "Mapping",
+                    "name": "filter_by_fasta_ids",
+                    "owner": "galaxyp",
+                    "revisions": "3c623e81be77",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "genomescope",
+                    "name": "deseq2",
                     "owner": "iuc",
-                    "revisions": "01210c4e9144",
-                    "tool_panel_section_label": "Assembly",
+                    "revisions": "6a3a025714d3",
+                    "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "hisat2",
+                    "name": "multiqc",
                     "owner": "iuc",
-                    "revisions": "f4af63aaf57a",
-                    "tool_panel_section_label": "Mapping",
+                    "revisions": "b2f1f75d49c4",
+                    "tool_panel_section_label": "Quality Control",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "merqury",
+                    "name": "multiqc",
                     "owner": "iuc",
-                    "revisions": "f8113c25bc6b",
-                    "tool_panel_section_label": "Assembly",
+                    "revisions": "5e33b465d8d5",
+                    "tool_panel_section_label": "Quality Control",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "meryl",
-                    "owner": "iuc",
-                    "revisions": "29dabd8db6f2",
-                    "tool_panel_section_label": "Assembly",
+                    "name": "sample_seqs",
+                    "owner": "peterjc",
+                    "revisions": "7c40a1fbc82e",
+                    "tool_panel_section_label": "Filter and Sort",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pretext_map",
-                    "owner": "iuc",
-                    "revisions": "dfb8a4497339",
-                    "tool_panel_section_label": "Assembly",
+                    "name": "mirdeep2_mapper",
+                    "owner": "rnateam",
+                    "revisions": "a8d24f4b6d95",
+                    "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pretext_snapshot",
-                    "owner": "iuc",
-                    "revisions": "44c66e8d21e6",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "name": "mirdeep2_quantifier",
+                    "owner": "rnateam",
+                    "revisions": "d5ea61ff12eb",
+                    "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "90981f86000f",
-                    "tool_panel_section_label": "Collection Operations",
+                    "name": "targetfinder",
+                    "owner": "rnateam",
+                    "revisions": "c9d56748fbde",
+                    "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: blobtoolkit\n  owner: bgruening\n  revisions: 7d9ee8cd14b8\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: blobtoolkit\n  owner: bgruening\n  revisions: 53dd00a4ab68\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: diamond\n  owner: bgruening\n  revisions: e8ac2b53f262\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n  owner: bgruening\n  revisions: 5799092ffdff\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n  owner: bgruening\n  revisions: 3ef480892a9f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 3a0efe14891f\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: smudgeplot\n  owner: galaxy-australia\n  revisions: 5e0825476fb7\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bellerophon\n  owner: iuc\n  revisions: 25ca5d73aedf\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: bb935709506a\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_mem2\n  owner: iuc\n  revisions: b4a22d90cce9\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: genomescope\n  owner: iuc\n  revisions: 01210c4e9144\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: hisat2\n  owner: iuc\n  revisions: f4af63aaf57a\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merqury\n  owner: iuc\n  revisions: f8113c25bc6b\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n  owner: iuc\n  revisions: 29dabd8db6f2\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_map\n  owner: iuc\n  revisions: dfb8a4497339\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_snapshot\n  owner: iuc\n  revisions: 44c66e8d21e6\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: salmon\n  owner: bgruening\n  revisions: e3d32471da11\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trim_galore\n  owner: bgruening\n  revisions: 949f01671246\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filter_by_fasta_ids\n  owner: galaxyp\n  revisions: 3c623e81be77\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deseq2\n  owner: iuc\n  revisions: 6a3a025714d3\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: b2f1f75d49c4\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 5e33b465d8d5\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sample_seqs\n  owner: peterjc\n  revisions: 7c40a1fbc82e\n  tool_panel_section_label: Filter and Sort\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mirdeep2_mapper\n  owner: rnateam\n  revisions: a8d24f4b6d95\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mirdeep2_quantifier\n  owner: rnateam\n  revisions: d5ea61ff12eb\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: targetfinder\n  owner: rnateam\n  revisions: c9d56748fbde\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.json",
         "contributors": [
-            {
-                "id": "GitFab93",
-                "joined": "2023-03",
-                "name": "Fabian Recktenwald",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/GitFab93/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/GitFab93.json"
-            },
             {
                 "elixir_node": "de",
                 "former_affiliations": [
@@ -169379,187 +170098,274 @@
                 "orcid": "0000-0002-5752-2155",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "pavanvidem",
+                "joined": "2017-09",
+                "name": "Pavankumar Videm",
+                "orcid": "0000-0002-5192-126X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
+            },
+            {
+                "email": "beatrizserrano.galaxy@gmail.com",
+                "id": "beatrizserrano",
+                "joined": "2020-07",
+                "linkedin": "beatriz-serrano",
+                "matrix": "beatrizserrano:matrix.org",
+                "name": "Beatriz Serrano-Solano",
+                "orcid": "0000-0002-5862-6132",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/beatrizserrano/",
+                "twitter": "BSerranoSolano",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/beatrizserrano.json"
             }
         ],
-        "dir": "topics/assembly/tutorials/ERGA-post-assembly-QC",
+        "dir": "topics/transcriptomics/tutorials/mirna-target-finder",
         "edam_operation": [
-            "Phasing",
-            "De-novo assembly",
-            "Sequence alignment",
-            "Genotyping",
-            "Sequence assembly validation",
-            "Sequence alignment analysis",
-            "Sequence assembly visualisation",
-            "Transcriptome assembly",
-            "Data handling",
-            "Genome assembly",
             "Sequence trimming",
-            "k-mer counting",
-            "Scaffolding"
+            "Differential gene expression analysis",
+            "Sequencing quality control",
+            "RNA-Seq analysis",
+            "Statistical calculation",
+            "Gene expression analysis",
+            "RNA-Seq quantification",
+            "Validation",
+            "Sequence composition calculation",
+            "Read pre-processing",
+            "Primer removal"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.eu",
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "assembly/ERGA-post-assembly-QC",
+        "id": "transcriptomics/mirna-target-finder",
         "inexact_supported_servers": [
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.cz",
+            "UseGalaxy.no"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "The ERGA post-assembly pipeline allows to assess and improve the quality of genome assemblies",
-            "The ERGA post-assembly pipeline contains of three main steps: Genome assembly decontamination and overview with BlobToolKit, providing analysis information and statistics and Hi-C scaffolding."
+            "MiRDeep2 in combination with the PmiREN database allows to quantify miRNA expression in plants",
+            "The use of the Salmon tool and the AtRTD2 transcriptome allows rapid and accurate quantification of transcripts in _Arabidopsis_",
+            "The combination of differential expression analysis and the TargetFinder tool is an effective strategy for the identification of miRNA target genes"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-31",
+        "mod_date": "2024-08-09",
         "objectives": [
-            "apply the post-assembly-QC-workflow using the necessary tools",
-            "analyse and evaluate the results of the workflow"
+            "Perform miRNA differential expression analysis",
+            "Understand the quasi-mapping-based Salmon method for quantifying the expression of transcripts using RNA-Seq data",
+            "Idenfity potential miRNAs involved in brassinosteroid-mediated regulation networks"
         ],
-        "pageviews": 1088,
-        "pub_date": "2023-06-23",
+        "pageviews": 5390921,
+        "pub_date": "2021-04-08",
         "questions": [
-            "what combination of tools can assess the quality of an post-assembly?",
-            "what metrics can help to analyse the quality?",
-            "how to evaluate the outputs?"
+            "Which miRNAs are upregulated in response to brassinosteroids?",
+            "Which genes are potential target of brassinosteroid-induced miRNAs?"
         ],
-        "short_id": "T00355",
+        "recordings": [
+            {
+                "captioners": [
+                    "gallardoalba"
+                ],
+                "date": "2021-07-25",
+                "galaxy_version": "21.05",
+                "length": "1H10M",
+                "speakers": [
+                    "gallardoalba"
+                ],
+                "youtube_id": "wS1X_0Mgw7M"
+            }
+        ],
+        "short_id": "T00292",
         "short_tools": [
-            "bellerophon",
-            "meryl",
-            "collapse_dataset",
-            "__EXTRACT_DATASET__",
-            "hisat2",
-            "busco",
-            "genomescope",
-            "blobtoolkit",
-            "pretext_map",
-            "CONVERTER_gz_to_uncompressed",
-            "samtools_stats",
-            "interactive_tool_blobtoolkit",
-            "tp_find_and_replace",
-            "smudgeplot",
-            "gfastats",
-            "bg_diamond",
-            "bandage_image",
-            "merqury",
-            "pretext_snapshot",
-            "bwa_mem2"
+            "filter_by_fasta_ids",
+            "targetfinder",
+            "sample_seqs",
+            "sort1",
+            "rbc_mirdeep2_mapper",
+            "Filter1",
+            "multiqc",
+            "rbc_mirdeep2_quantifier",
+            "Cut1",
+            "deseq2",
+            "fastqc",
+            "salmon",
+            "__MERGE_COLLECTION__",
+            "cat1",
+            "trim_galore"
+        ],
+        "slides": true,
+        "slides_recordings": [
+            {
+                "captioners": [
+                    "gallardoalba"
+                ],
+                "date": "2021-04-20",
+                "galaxy_version": "21.01",
+                "length": "10M",
+                "speakers": [
+                    "awspolly"
+                ],
+                "youtube_id": "FNmZoo2OXTU"
+            },
+            {
+                "captioners": [
+                    "gallardoalba"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "10M",
+                "speakers": [
+                    "awspolly"
+                ],
+                "youtube_id": "7t0Gr1Jklqs"
+            }
         ],
-        "slides": false,
-        "slides_recordings": false,
         "supported_servers": {
             "exact": [
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ],
             "inexact": [
                 {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
                 }
             ]
         },
         "symlink": null,
         "tags": [
-            "plants"
+            "miRNA",
+            "plants",
+            "stress tolerance"
         ],
-        "time_estimation": "3H",
-        "title": "ERGA post-assembly QC",
+        "time_estimation": "2H",
+        "title": "Whole transcriptome analysis of Arabidopsis thaliana",
         "tools": [
-            "CONVERTER_gz_to_uncompressed",
-            "__EXTRACT_DATASET__",
-            "interactive_tool_blobtoolkit",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/3.4.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.0.7+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.2.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4",
-            "toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy+2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
-            "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
+            "Cut1",
+            "Filter1",
+            "__MERGE_COLLECTION__",
+            "cat1",
+            "sort1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.14.1.2+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.2.5",
+            "toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_mapper/rbc_mirdeep2_mapper/2.0.0",
+            "toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_quantifier/rbc_mirdeep2_quantifier/2.0.0",
+            "toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1"
         ],
-        "topic_name": "assembly",
-        "topic_name_human": "Assembly",
+        "topic_name": "transcriptomics",
+        "topic_name_human": "Transcriptomics",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": false
+            "video": true
         },
-        "tutorial_name": "ERGA-post-assembly-QC",
+        "tutorial_name": "mirna-target-finder",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.json"
         },
-        "version": 3,
-        "video": false,
-        "video_versions": 0,
+        "version": 17,
+        "video": true,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 98,
-        "visitors": 820,
+        "visit_duration": 313,
+        "visitors": 1988915,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-5752-2155",
-                        "name": "Crist\u00f3bal Gallardo Alba"
-                    }
-                ],
-                "description": "ERGA post-assembly QC",
+                "creators": [],
+                "description": "Identify upregulated miRNAS and analyze potential targets in downregulated genes.",
                 "features": {
                     "comments": false,
-                    "parameters": true,
+                    "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMetadata file\"]\n  1[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nNCBI taxonomic ID\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nNCBI taxdump directory\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nFASTQ files\"]\n  4[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nPloidy for model to use\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPrimary genome assembly file fasta\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDIAMOND database\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nHi-C reverse\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nHi-C forward\"]\n  9[label=\"Meryl\"]\n  3 -> 9 [label=\"output\"]\n  10[label=\"Collapse Collection\"]\n  3 -> 10 [label=\"output\"]\n  11[label=\"Create BlobtoolKit\"]\n  5 -> 11 [label=\"output\"]\n  0 -> 11 [label=\"output\"]\n  2 -> 11 [label=\"output\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"gfastats\"]\n  5 -> 12 [label=\"output\"]\n  13[label=\"Convert compressed file to uncompressed.\"]\n  5 -> 13 [label=\"output\"]\n  14[label=\"gfastats\"]\n  5 -> 14 [label=\"output\"]\n  15[label=\"Diamond\"]\n  5 -> 15 [label=\"output\"]\n  6 -> 15 [label=\"output\"]\n  16[label=\"Collapse Collection\"]\n  7 -> 16 [label=\"output\"]\n  17[label=\"Collapse Collection\"]\n  8 -> 17 [label=\"output\"]\n  18[label=\"Meryl\"]\n  9 -> 18 [label=\"read_db\"]\n  19[label=\"HISAT2\"]\n  10 -> 19 [label=\"output\"]\n  5 -> 19 [label=\"output\"]\n  20[label=\"Smudgeplot\"]\n  10 -> 20 [label=\"output\"]\n  21[label=\"Replace\"]\n  13 -> 21 [label=\"output1\"]\n  22[label=\"Bandage Image\"]\n  14 -> 22 [label=\"output\"]\n  23[label=\"BWA-MEM2\"]\n  16 -> 23 [label=\"output\"]\n  5 -> 23 [label=\"output\"]\n  24[label=\"BWA-MEM2\"]\n  17 -> 24 [label=\"output\"]\n  5 -> 24 [label=\"output\"]\n  25[label=\"Merqury\"]\n  5 -> 25 [label=\"output\"]\n  18 -> 25 [label=\"read_db\"]\n  kc2fe83a3754a4544bb87df16f3537ab4[color=lightseagreen,label=\"Output\\nMerqury on input dataset(s): stats\"]\n  25 -> kc2fe83a3754a4544bb87df16f3537ab4\n  k8f08d8f67615420c8a15201a61b5d3bb[color=lightseagreen,label=\"Output\\nMerqury on input dataset(s): plots\"]\n  25 -> k8f08d8f67615420c8a15201a61b5d3bb\n  k7a8d951a6a314b02aeba0eb3061f85ce[color=lightseagreen,label=\"Output\\nMerqury on input dataset(s): QV stats\"]\n  25 -> k7a8d951a6a314b02aeba0eb3061f85ce\n  26[label=\"Meryl\"]\n  18 -> 26 [label=\"read_db\"]\n  27[label=\"Samtools stats\"]\n  19 -> 27 [label=\"output_alignments\"]\n  28[label=\"Busco\"]\n  21 -> 28 [label=\"outfile\"]\n  k1d4e45428bf14e32890b2e18df95a0de[color=lightseagreen,label=\"Output\\nBusco on input dataset(s): full table\"]\n  28 -> k1d4e45428bf14e32890b2e18df95a0de\n  k680b817736534630ab99c1d2304dc485[color=lightseagreen,label=\"Output\\nBusco on input dataset(s): short summary\"]\n  28 -> k680b817736534630ab99c1d2304dc485\n  29[label=\"Filter and merge\"]\n  24 -> 29 [label=\"bam_output\"]\n  23 -> 29 [label=\"bam_output\"]\n  30[label=\"Merqury plot 2\"]\n  25 -> 30 [label=\"png_files\"]\n  31[label=\"Merqury plot 1\"]\n  25 -> 31 [label=\"png_files\"]\n  32[label=\"Merqury plot 3\"]\n  25 -> 32 [label=\"png_files\"]\n  33[label=\"Merqury plot 5\"]\n  25 -> 33 [label=\"png_files\"]\n  34[label=\"Merqury plot 4\"]\n  25 -> 34 [label=\"png_files\"]\n  35[label=\"GenomeScope\"]\n  26 -> 35 [label=\"read_db_hist\"]\n  4 -> 35 [label=\"output\"]\n  36[label=\"BlobToolKit\"]\n  15 -> 36 [label=\"blast_tabular\"]\n  11 -> 36 [label=\"blobdir\"]\n  28 -> 36 [label=\"busco_table\"]\n  19 -> 36 [label=\"output_alignments\"]\n  37[label=\"PretextMap\"]\n  29 -> 37 [label=\"outfile\"]\n  38[label=\"Interactive BlobToolKit\"]\n  36 -> 38 [label=\"blobdir\"]\n  39[label=\"Pretext Snapshot\"]\n  37 -> 39 [label=\"pretext_map_out\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nControl miRNA FASTQ collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nTreated miRNA FASTQ collection\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nTreated mRNA FASTQ collection\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPrecursor miRNA sequences\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nControl mRNA FASTQ collection\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTranscriptome FASTA\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAnnotation GTF\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMature miRNA sequences\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nStar miRNA sequenes\"]\n  9[label=\"FastQC\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"Trim Galore!\"]\n  0 -> 10 [label=\"output\"]\n  11[label=\"FastQC\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"Trim Galore!\"]\n  1 -> 12 [label=\"output\"]\n  13[label=\"FastQC\"]\n  2 -> 13 [label=\"output\"]\n  14[label=\"FastQC\"]\n  4 -> 14 [label=\"output\"]\n  15[label=\"Salmon quant\"]\n  6 -> 15 [label=\"output\"]\n  2 -> 15 [label=\"output\"]\n  5 -> 15 [label=\"output\"]\n  16[label=\"Salmon quant\"]\n  6 -> 16 [label=\"output\"]\n  4 -> 16 [label=\"output\"]\n  5 -> 16 [label=\"output\"]\n  17[label=\"FastQC\"]\n  10 -> 17 [label=\"trimmed_reads_single\"]\n  18[label=\"MiRDeep2 Mapper\"]\n  10 -> 18 [label=\"trimmed_reads_single\"]\n  19[label=\"Merge collections\"]\n  11 -> 19 [label=\"text_file\"]\n  9 -> 19 [label=\"text_file\"]\n  20[label=\"FastQC\"]\n  12 -> 20 [label=\"trimmed_reads_single\"]\n  21[label=\"MiRDeep2 Mapper\"]\n  12 -> 21 [label=\"trimmed_reads_single\"]\n  22[label=\"Merge collections\"]\n  13 -> 22 [label=\"text_file\"]\n  14 -> 22 [label=\"text_file\"]\n  23[label=\"DESeq2\"]\n  15 -> 23 [label=\"output_gene_quant\"]\n  16 -> 23 [label=\"output_gene_quant\"]\n  6 -> 23 [label=\"output\"]\n  24[label=\"MiRDeep2 Quantifier\"]\n  7 -> 24 [label=\"output\"]\n  3 -> 24 [label=\"output\"]\n  18 -> 24 [label=\"output_reads_collapsed\"]\n  8 -> 24 [label=\"output\"]\n  25[label=\"MultiQC\"]\n  19 -> 25 [label=\"output\"]\n  26[label=\"Merge collections\"]\n  20 -> 26 [label=\"text_file\"]\n  17 -> 26 [label=\"text_file\"]\n  27[label=\"MiRDeep2 Quantifier\"]\n  7 -> 27 [label=\"output\"]\n  3 -> 27 [label=\"output\"]\n  21 -> 27 [label=\"output_reads_collapsed\"]\n  8 -> 27 [label=\"output\"]\n  28[label=\"MultiQC\"]\n  22 -> 28 [label=\"output\"]\n  29[label=\"Filter\"]\n  23 -> 29 [label=\"deseq_out\"]\n  30[label=\"Cut\"]\n  24 -> 30 [label=\"miRNAsExpressed\"]\n  31[label=\"MultiQC\"]\n  26 -> 31 [label=\"output\"]\n  32[label=\"Cut\"]\n  27 -> 32 [label=\"miRNAsExpressed\"]\n  33[label=\"Filter\"]\n  29 -> 33 [label=\"out_file1\"]\n  34[label=\"Filter\"]\n  29 -> 34 [label=\"out_file1\"]\n  35[label=\"DESeq2\"]\n  32 -> 35 [label=\"out_file1\"]\n  30 -> 35 [label=\"out_file1\"]\n  36[label=\"Cut\"]\n  34 -> 36 [label=\"out_file1\"]\n  37[label=\"Filter\"]\n  35 -> 37 [label=\"deseq_out\"]\n  38[label=\"Filter FASTA\"]\n  36 -> 38 [label=\"out_file1\"]\n  5 -> 38 [label=\"output\"]\n  39[label=\"Filter\"]\n  37 -> 39 [label=\"out_file1\"]\n  40[label=\"Filter\"]\n  37 -> 40 [label=\"out_file1\"]\n  41[label=\"Cut\"]\n  40 -> 41 [label=\"out_file1\"]\n  42[label=\"Filter FASTA\"]\n  41 -> 42 [label=\"out_file1\"]\n  8 -> 42 [label=\"output\"]\n  43[label=\"Filter FASTA\"]\n  41 -> 43 [label=\"out_file1\"]\n  7 -> 43 [label=\"output\"]\n  44[label=\"Concatenate datasets\"]\n  43 -> 44 [label=\"output\"]\n  42 -> 44 [label=\"output\"]\n  45[label=\"TargetFinder\"]\n  38 -> 45 [label=\"output\"]\n  44 -> 45 [label=\"out_file1\"]\n}",
                 "history": [
                     {
-                        "hash": "807026b8414e9d8e35cb6805104338150b1131f0",
-                        "message": "Update topics/assembly/tutorials/ERGA-post-assembly-QC/workflows/main_workflow.ga",
+                        "hash": "87d458cc1fd8db170670ddd5c186c98295267d9e",
+                        "message": "Undo error",
+                        "num": 7,
+                        "short_hash": "87d458cc1",
+                        "unix": "1674149735"
+                    },
+                    {
+                        "hash": "edf36428b978d5519a494eaee576a8a17c6c948e",
+                        "message": "Fix tutorial",
+                        "num": 6,
+                        "short_hash": "edf36428b",
+                        "unix": "1669862549"
+                    },
+                    {
+                        "hash": "a6636e32469b78edc30efcc646f92e77c4bdb58b",
+                        "message": "add tags and annotation to the workflow",
+                        "num": 5,
+                        "short_hash": "a6636e324",
+                        "unix": "1617760834"
+                    },
+                    {
+                        "hash": "a5a1a7567b95fa539b493a98f5924d2482e16997",
+                        "message": "Update workflow for miRNA target identification in Arabidopsis",
+                        "num": 4,
+                        "short_hash": "a5a1a7567",
+                        "unix": "1617760351"
+                    },
+                    {
+                        "hash": "0eacaeef42cdfef3d6f60d4ec481a3ef84b72765",
+                        "message": "Update workflow and include downregulated miRNAS",
                         "num": 3,
-                        "short_hash": "807026b84",
-                        "unix": "1687524556"
+                        "short_hash": "0eacaeef4",
+                        "unix": "1617194856"
                     },
                     {
-                        "hash": "c5bb8031a5b03030e4fdc5c0a478a87e7c1e3c13",
-                        "message": "Fix testes",
+                        "hash": "bdbe72dd283efbb454cf60a91384a9d130f8b342",
+                        "message": "Fix tests workflow",
                         "num": 2,
-                        "short_hash": "c5bb8031a",
-                        "unix": "1687511093"
+                        "short_hash": "bdbe72dd2",
+                        "unix": "1616702513"
                     },
                     {
-                        "hash": "893cd527b9bd282e7f98475f5c3cd3e2f3ea89b0",
-                        "message": "Add images and rename tutorial",
+                        "hash": "4b406638ca884e2ad7b58db02d9c4cc7eff0005d",
+                        "message": "New training: miRNA target finder",
                         "num": 1,
-                        "short_hash": "893cd527b",
-                        "unix": "1682673537"
+                        "short_hash": "4b406638c",
+                        "unix": "1616700503"
                     }
                 ],
                 "inputs": [
@@ -169572,22 +170378,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Metadata file"
+                                "name": "Control miRNA FASTQ collection"
                             }
                         ],
-                        "label": "Metadata file",
-                        "name": "Input dataset",
+                        "label": "Control miRNA FASTQ collection",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 280,
-                            "top": 0
+                            "left": 0,
+                            "top": 1.984375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": true, \"tag\": \"\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "4e2925a6-af6c-4a48-95e1-334ee4cebee4",
-                        "when": null,
+                        "type": "data_collection_input",
+                        "uuid": "286f34e3-d05b-40ba-b39e-2f0c7455ff23",
                         "workflow_outputs": []
                     },
                     {
@@ -169599,22 +170404,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "NCBI taxonomic ID"
+                                "name": "Treated miRNA FASTQ collection"
                             }
                         ],
-                        "label": "NCBI taxonomic ID",
-                        "name": "Input parameter",
+                        "label": "Treated miRNA FASTQ collection",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 280,
-                            "top": 123
+                            "left": 0,
+                            "top": 331.984375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "ffe0dbe7-597d-45ed-a356-f036d807b80a",
-                        "when": null,
+                        "type": "data_collection_input",
+                        "uuid": "6ffd974f-fd40-4234-9bda-6edd9e65e702",
                         "workflow_outputs": []
                     },
                     {
@@ -169626,22 +170430,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "NCBI taxdump directory"
+                                "name": "Treated mRNA FASTQ collection"
                             }
                         ],
-                        "label": "NCBI taxdump directory",
-                        "name": "Input dataset",
+                        "label": "Treated mRNA FASTQ collection",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 280,
-                            "top": 246
+                            "left": 1161.984375,
+                            "top": 778.984375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "a04c5335-88b6-4d11-9924-5752df4204e1",
-                        "when": null,
+                        "type": "data_collection_input",
+                        "uuid": "e2260dff-96ce-4345-902a-73958f9ac0cf",
                         "workflow_outputs": []
                     },
                     {
@@ -169653,22 +170456,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "FASTQ files"
+                                "name": "Precursor miRNA sequences"
                             }
                         ],
-                        "label": "FASTQ files",
-                        "name": "Input dataset collection",
+                        "label": "Precursor miRNA sequences",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 1182
+                            "left": 575.984375,
+                            "top": 1461.984375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "7cb038c5-3dd4-4313-b178-dd05cdc96721",
-                        "when": null,
+                        "type": "data_input",
+                        "uuid": "7e8825d5-8e7f-4ec4-b0b4-f0efcc70e504",
                         "workflow_outputs": []
                     },
                     {
@@ -169680,22 +170482,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Ploidy for model to use"
+                                "name": "Control mRNA FASTQ collection"
                             }
                         ],
-                        "label": "Ploidy for model to use",
-                        "name": "Input parameter",
+                        "label": "Control mRNA FASTQ collection",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 860,
-                            "top": 1011
+                            "left": 1161.984375,
+                            "top": 1101.984375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"default\": 2, \"parameter_type\": \"integer\", \"optional\": true}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "e586fc91-192f-45c1-bccb-b3a017ff5b26",
-                        "when": null,
+                        "type": "data_collection_input",
+                        "uuid": "5f622114-e64d-4a96-9866-e519b583cd98",
                         "workflow_outputs": []
                     },
                     {
@@ -169707,22 +170508,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Primary genome assembly file (fasta)"
+                                "name": "Transcriptome FASTA"
                             }
                         ],
-                        "label": "Primary genome assembly file (fasta)",
+                        "label": "Transcriptome FASTA",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 280,
-                            "top": 1310
+                            "left": 1161.984375,
+                            "top": 1220.984375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "1b4475cb-0cc2-4371-ac68-c1bd2f868e50",
-                        "when": null,
+                        "uuid": "5bbd4e69-3b60-47e1-aecf-5d43ae6b54e5",
                         "workflow_outputs": []
                     },
                     {
@@ -169734,22 +170534,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "DIAMOND database"
+                                "name": "Annotation GTF"
                             }
                         ],
-                        "label": "DIAMOND database",
+                        "label": "Annotation GTF",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 280,
-                            "top": 1735
+                            "left": 1161.984375,
+                            "top": 1340
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "68be0d0c-35a9-4c73-a61e-56c1486e3548",
-                        "when": null,
+                        "uuid": "570e8113-930a-4567-a380-fdb93fbcc60f",
                         "workflow_outputs": []
                     },
                     {
@@ -169761,22 +170560,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Hi-C reverse"
+                                "name": "Mature miRNA sequences"
                             }
                         ],
-                        "label": "Hi-C reverse",
-                        "name": "Input dataset collection",
+                        "label": "Mature miRNA sequences",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 2172
+                            "left": 575.984375,
+                            "top": 1770.984375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "8e598f70-ebee-4264-84a4-5d40642004a4",
-                        "when": null,
+                        "type": "data_input",
+                        "uuid": "5d65f949-64bf-4f17-b242-f94d342b14a8",
                         "workflow_outputs": []
                     },
                     {
@@ -169788,503 +170586,584 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Hi-C forward"
+                                "name": "Star miRNA sequenes"
                             }
                         ],
-                        "label": "Hi-C forward",
-                        "name": "Input dataset collection",
+                        "label": "Star miRNA sequenes",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 2602
+                            "left": 575.984375,
+                            "top": 1890
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "b1a0825d-054b-4d34-a735-4f8b2f57df4c",
-                        "when": null,
+                        "type": "data_input",
+                        "uuid": "d11848be-2417-4393-b87f-5e4d9500b4ed",
                         "workflow_outputs": []
                     }
                 ],
-                "license": "AGPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nMetadata file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nNCBI taxonomic ID\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nNCBI taxdump directory\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Collection\\nFASTQ files\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nPloidy for model to use\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nPrimary genome assembly file fasta\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nDIAMOND database\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Collection\\nHi-C reverse\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Collection\\nHi-C forward\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"Meryl\"];\n  3 -->|output| 9;\n  10[\"Collapse Collection\"];\n  3 -->|output| 10;\n  11[\"Create BlobtoolKit\"];\n  5 -->|output| 11;\n  0 -->|output| 11;\n  2 -->|output| 11;\n  1 -->|output| 11;\n  12[\"gfastats\"];\n  5 -->|output| 12;\n  13[\"Convert compressed file to uncompressed.\"];\n  5 -->|output| 13;\n  14[\"gfastats\"];\n  5 -->|output| 14;\n  15[\"Diamond\"];\n  5 -->|output| 15;\n  6 -->|output| 15;\n  16[\"Collapse Collection\"];\n  7 -->|output| 16;\n  17[\"Collapse Collection\"];\n  8 -->|output| 17;\n  18[\"Meryl\"];\n  9 -->|read_db| 18;\n  19[\"HISAT2\"];\n  10 -->|output| 19;\n  5 -->|output| 19;\n  20[\"Smudgeplot\"];\n  10 -->|output| 20;\n  21[\"Replace\"];\n  13 -->|output1| 21;\n  22[\"Bandage Image\"];\n  14 -->|output| 22;\n  23[\"BWA-MEM2\"];\n  16 -->|output| 23;\n  5 -->|output| 23;\n  24[\"BWA-MEM2\"];\n  17 -->|output| 24;\n  5 -->|output| 24;\n  25[\"Merqury\"];\n  5 -->|output| 25;\n  18 -->|read_db| 25;\n  c2fe83a3-754a-4544-bb87-df16f3537ab4[\"Output\\nMerqury on input dataset(s): stats\"];\n  25 --> c2fe83a3-754a-4544-bb87-df16f3537ab4;\n  style c2fe83a3-754a-4544-bb87-df16f3537ab4 stroke:#2c3143,stroke-width:4px;\n  8f08d8f6-7615-420c-8a15-201a61b5d3bb[\"Output\\nMerqury on input dataset(s): plots\"];\n  25 --> 8f08d8f6-7615-420c-8a15-201a61b5d3bb;\n  style 8f08d8f6-7615-420c-8a15-201a61b5d3bb stroke:#2c3143,stroke-width:4px;\n  7a8d951a-6a31-4b02-aeba-0eb3061f85ce[\"Output\\nMerqury on input dataset(s): QV stats\"];\n  25 --> 7a8d951a-6a31-4b02-aeba-0eb3061f85ce;\n  style 7a8d951a-6a31-4b02-aeba-0eb3061f85ce stroke:#2c3143,stroke-width:4px;\n  26[\"Meryl\"];\n  18 -->|read_db| 26;\n  27[\"Samtools stats\"];\n  19 -->|output_alignments| 27;\n  28[\"Busco\"];\n  21 -->|outfile| 28;\n  1d4e4542-8bf1-4e32-890b-2e18df95a0de[\"Output\\nBusco on input dataset(s): full table\"];\n  28 --> 1d4e4542-8bf1-4e32-890b-2e18df95a0de;\n  style 1d4e4542-8bf1-4e32-890b-2e18df95a0de stroke:#2c3143,stroke-width:4px;\n  680b8177-3653-4630-ab99-c1d2304dc485[\"Output\\nBusco on input dataset(s): short summary\"];\n  28 --> 680b8177-3653-4630-ab99-c1d2304dc485;\n  style 680b8177-3653-4630-ab99-c1d2304dc485 stroke:#2c3143,stroke-width:4px;\n  29[\"Filter and merge\"];\n  24 -->|bam_output| 29;\n  23 -->|bam_output| 29;\n  30[\"Merqury plot 2\"];\n  25 -->|png_files| 30;\n  31[\"Merqury plot 1\"];\n  25 -->|png_files| 31;\n  32[\"Merqury plot 3\"];\n  25 -->|png_files| 32;\n  33[\"Merqury plot 5\"];\n  25 -->|png_files| 33;\n  34[\"Merqury plot 4\"];\n  25 -->|png_files| 34;\n  35[\"GenomeScope\"];\n  26 -->|read_db_hist| 35;\n  4 -->|output| 35;\n  36[\"BlobToolKit\"];\n  15 -->|blast_tabular| 36;\n  11 -->|blobdir| 36;\n  28 -->|busco_table| 36;\n  19 -->|output_alignments| 36;\n  37[\"PretextMap\"];\n  29 -->|outfile| 37;\n  38[\"Interactive BlobToolKit\"];\n  36 -->|blobdir| 38;\n  39[\"Pretext Snapshot\"];\n  37 -->|pretext_map_out| 39;",
-                "modified": "2024-08-18 00:06:20 +0000",
-                "name": "Post-assembly workflow",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nControl miRNA FASTQ collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nTreated miRNA FASTQ collection\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nTreated mRNA FASTQ collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nPrecursor miRNA sequences\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Collection\\nControl mRNA FASTQ collection\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nTranscriptome FASTA\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nAnnotation GTF\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nMature miRNA sequences\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nStar miRNA sequenes\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"FastQC\"];\n  0 -->|output| 9;\n  10[\"Trim Galore!\"];\n  0 -->|output| 10;\n  11[\"FastQC\"];\n  1 -->|output| 11;\n  12[\"Trim Galore!\"];\n  1 -->|output| 12;\n  13[\"FastQC\"];\n  2 -->|output| 13;\n  14[\"FastQC\"];\n  4 -->|output| 14;\n  15[\"Salmon quant\"];\n  6 -->|output| 15;\n  2 -->|output| 15;\n  5 -->|output| 15;\n  16[\"Salmon quant\"];\n  6 -->|output| 16;\n  4 -->|output| 16;\n  5 -->|output| 16;\n  17[\"FastQC\"];\n  10 -->|trimmed_reads_single| 17;\n  18[\"MiRDeep2 Mapper\"];\n  10 -->|trimmed_reads_single| 18;\n  19[\"Merge collections\"];\n  11 -->|text_file| 19;\n  9 -->|text_file| 19;\n  20[\"FastQC\"];\n  12 -->|trimmed_reads_single| 20;\n  21[\"MiRDeep2 Mapper\"];\n  12 -->|trimmed_reads_single| 21;\n  22[\"Merge collections\"];\n  13 -->|text_file| 22;\n  14 -->|text_file| 22;\n  23[\"DESeq2\"];\n  15 -->|output_gene_quant| 23;\n  16 -->|output_gene_quant| 23;\n  6 -->|output| 23;\n  24[\"MiRDeep2 Quantifier\"];\n  7 -->|output| 24;\n  3 -->|output| 24;\n  18 -->|output_reads_collapsed| 24;\n  8 -->|output| 24;\n  25[\"MultiQC\"];\n  19 -->|output| 25;\n  26[\"Merge collections\"];\n  20 -->|text_file| 26;\n  17 -->|text_file| 26;\n  27[\"MiRDeep2 Quantifier\"];\n  7 -->|output| 27;\n  3 -->|output| 27;\n  21 -->|output_reads_collapsed| 27;\n  8 -->|output| 27;\n  28[\"MultiQC\"];\n  22 -->|output| 28;\n  29[\"Filter\"];\n  23 -->|deseq_out| 29;\n  30[\"Cut\"];\n  24 -->|miRNAsExpressed| 30;\n  31[\"MultiQC\"];\n  26 -->|output| 31;\n  32[\"Cut\"];\n  27 -->|miRNAsExpressed| 32;\n  33[\"Filter\"];\n  29 -->|out_file1| 33;\n  34[\"Filter\"];\n  29 -->|out_file1| 34;\n  35[\"DESeq2\"];\n  32 -->|out_file1| 35;\n  30 -->|out_file1| 35;\n  36[\"Cut\"];\n  34 -->|out_file1| 36;\n  37[\"Filter\"];\n  35 -->|deseq_out| 37;\n  38[\"Filter FASTA\"];\n  36 -->|out_file1| 38;\n  5 -->|output| 38;\n  39[\"Filter\"];\n  37 -->|out_file1| 39;\n  40[\"Filter\"];\n  37 -->|out_file1| 40;\n  41[\"Cut\"];\n  40 -->|out_file1| 41;\n  42[\"Filter FASTA\"];\n  41 -->|out_file1| 42;\n  8 -->|output| 42;\n  43[\"Filter FASTA\"];\n  41 -->|out_file1| 43;\n  7 -->|output| 43;\n  44[\"Concatenate datasets\"];\n  43 -->|output| 44;\n  42 -->|output| 44;\n  45[\"TargetFinder\"];\n  38 -->|output| 45;\n  44 -->|out_file1| 45;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "Plant bulk RNA-Seq workflow",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.2.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
                         "errors": null,
-                        "id": 12,
+                        "id": 23,
                         "input_connections": {
-                            "input_file": {
-                                "id": 5,
+                            "select_data|rep_factorName_0|rep_factorLevel_0|countsFile": {
+                                "id": 15,
+                                "output_name": "output_gene_quant"
+                            },
+                            "select_data|rep_factorName_0|rep_factorLevel_1|countsFile": {
+                                "id": 16,
+                                "output_name": "output_gene_quant"
+                            },
+                            "tximport|mapping_format|gtf_file": {
+                                "id": 6,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool DESeq2",
+                                "name": "batch_factors"
+                            }
+                        ],
                         "label": null,
-                        "name": "gfastats",
+                        "name": "DESeq2",
                         "outputs": [
                             {
-                                "name": "stats",
+                                "name": "deseq_out",
                                 "type": "tabular"
+                            },
+                            {
+                                "name": "plots",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "left": 570,
-                            "top": 1150
+                            "left": 1737.984375,
+                            "top": 1170.984375
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.2.0+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActiondeseq_out": {
+                                "action_arguments": {
+                                    "newname": "DESeq2 results mRNA"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "deseq_out"
+                            },
+                            "RenameDatasetActionplots": {
+                                "action_arguments": {
+                                    "newname": "DESeq2 plots mRNA"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "plots"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "5799092ffdff",
-                            "name": "gfastats",
-                            "owner": "bgruening",
+                            "changeset_revision": "6a3a025714d3",
+                            "name": "deseq2",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"assembly\", \"__current_case__\": 2, \"expected_genomesize\": null}, \"tabular\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.0+galaxy0",
+                        "tool_state": "{\"auto_mean_filter_off\": \"false\", \"batch_factors\": {\"__class__\": \"RuntimeValue\"}, \"esf\": \"\", \"fit_type\": \"1\", \"header\": \"true\", \"many_contrasts\": \"false\", \"normCounts\": \"false\", \"normRLog\": \"false\", \"normVST\": \"false\", \"outlier_filter_off\": \"false\", \"outlier_replace_off\": \"false\", \"pdf\": \"true\", \"select_data\": {\"how\": \"datasets_per_level\", \"__current_case__\": 1, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": \"effects_brassinolide\", \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": \"brassinolide\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"factorLevel\": \"control\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"tximport\", \"__current_case__\": 0, \"txtype\": \"salmon\", \"mapping_format\": {\"mapping_format_selector\": \"gtf\", \"__current_case__\": 0, \"gtf_file\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.11.40.6+galaxy1",
                         "type": "tool",
-                        "uuid": "7b6264cf-7b3e-4df7-8091-4fe9db70ba0b",
-                        "when": null,
+                        "uuid": "db23fb5b-af4b-4fe1-8f8d-99a3176808e7",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "stats",
-                                "uuid": "6c86bd99-c6d3-49a5-9ffe-5d86d045128d"
+                                "output_name": "plots",
+                                "uuid": "6c720aa2-a057-45c4-a813-3065d95c6c7f"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "deseq_out",
+                                "uuid": "77e6746d-7bf9-400f-ac1e-106db58fbbbd"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy+2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
                         "errors": null,
-                        "id": 20,
+                        "id": 25,
                         "input_connections": {
-                            "file|input|reads": {
-                                "id": 10,
+                            "results_0|software_cond|output_0|input": {
+                                "id": 19,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Smudgeplot",
+                        "name": "MultiQC",
                         "outputs": [
                             {
-                                "name": "smudgeplot",
-                                "type": "png"
+                                "name": "stats",
+                                "type": "input"
                             },
                             {
-                                "name": "smudgeplot_log",
-                                "type": "png"
+                                "name": "html_report",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 570,
-                            "top": 2319
+                            "left": 883.984375,
+                            "top": 342.984375
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy+2",
+                        "post_job_actions": {
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "RenameDatasetActionhtml_report": {
+                                "action_arguments": {
+                                    "newname": "MultiQC unprocessed miRNA: Webpage"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "html_report"
+                            },
+                            "RenameDatasetActionstats": {
+                                "action_arguments": {
+                                    "newname": "MultiQC unprocessed miRNA: Stats"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "stats"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
                         "tool_shed_repository": {
-                            "changeset_revision": "5e0825476fb7",
-                            "name": "smudgeplot",
-                            "owner": "galaxy-australia",
+                            "changeset_revision": "b2f1f75d49c4",
+                            "name": "multiqc",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"file\": {\"input\": {\"input_select\": \"reads\", \"__current_case__\": 0, \"reads\": {\"__class__\": \"ConnectedValue\"}, \"mer_len\": \"21\", \"lower_cutoff\": null, \"upper_cutoff\": null}}, \"homozygous\": false, \"table_output\": false, \"verbose_output\": false, \"warnings_output\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.2.5+galaxy+2",
+                        "tool_state": "{\"comment\": \"\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": \"false\", \"title\": \"miRNA initial quality check\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7",
                         "type": "tool",
-                        "uuid": "2b550197-cc54-44e7-be71-8d15a093fda6",
-                        "when": null,
+                        "uuid": "3e845cfd-ddd1-4f60-b1cb-ac16dc2c6d10",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "smudgeplot_log",
-                                "uuid": "7573ecef-1ef1-4879-b602-f4dcc92e0bfb"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "smudgeplot",
-                                "uuid": "ab18b562-de82-40f4-8c30-3f730479d97c"
+                                "output_name": "html_report",
+                                "uuid": "7cd34a0f-1142-4965-afa2-5f77e9c79b9e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
                         "errors": null,
-                        "id": 22,
+                        "id": 28,
                         "input_connections": {
-                            "input_file": {
-                                "id": 14,
+                            "results_0|software_cond|output_0|input": {
+                                "id": 22,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Bandage Image",
+                        "name": "MultiQC",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "jpg"
+                                "name": "stats",
+                                "type": "input"
+                            },
+                            {
+                                "name": "html_report",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 860,
-                            "top": 1499
+                            "left": 2035.984375,
+                            "top": 1455
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                        "post_job_actions": {
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "RenameDatasetActionhtml_report": {
+                                "action_arguments": {
+                                    "newname": "MultiQC mRNA: Webpage"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "html_report"
+                            },
+                            "RenameDatasetActionstats": {
+                                "action_arguments": {
+                                    "newname": "MultiQC mRNA: Stats"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "stats"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
                         "tool_shed_repository": {
-                            "changeset_revision": "ddddce450736",
-                            "name": "bandage",
+                            "changeset_revision": "b2f1f75d49c4",
+                            "name": "multiqc",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"fontsize\": null, \"height\": \"1000\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"lengths\": false, \"names\": false, \"nodewidth\": null, \"output_format\": \"jpg\", \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2022.09+galaxy4",
+                        "tool_state": "{\"comment\": \"\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"RuntimeValue\"}}]}}], \"saveLog\": \"false\", \"title\": \"mRNA initial quality check\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7",
                         "type": "tool",
-                        "uuid": "17e86ff6-8432-4125-aee6-63630ea662cc",
-                        "when": null,
+                        "uuid": "b7ffd734-4c99-4132-814f-47b75b4b5d63",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "25323480-dacf-41b4-a7e9-c02f557737de"
+                                "output_name": "html_report",
+                                "uuid": "7d5b5d84-d0b0-4639-9b42-61bf9f7e014d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
                         "errors": null,
-                        "id": 25,
+                        "id": 31,
                         "input_connections": {
-                            "mode|assembly_options|assembly_01": {
-                                "id": 5,
+                            "results_0|software_cond|output_0|input": {
+                                "id": 26,
                                 "output_name": "output"
-                            },
-                            "mode|meryldb_F1": {
-                                "id": 18,
-                                "output_name": "read_db"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Merqury",
+                        "name": "MultiQC",
                         "outputs": [
                             {
-                                "name": "qv_files",
-                                "type": "input"
-                            },
-                            {
-                                "name": "png_files",
+                                "name": "stats",
                                 "type": "input"
                             },
                             {
-                                "name": "stats_files",
-                                "type": "input"
+                                "name": "html_report",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 860,
-                            "top": 581
+                            "left": 1161.984375,
+                            "top": 558.984375
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
+                        "post_job_actions": {
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "RenameDatasetActionhtml_report": {
+                                "action_arguments": {
+                                    "newname": "MultiQC processed miRNA: Webpage"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "html_report"
+                            },
+                            "RenameDatasetActionstats": {
+                                "action_arguments": {
+                                    "newname": "MultiQC processed miRNA: Stats"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "stats"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
                         "tool_shed_repository": {
-                            "changeset_revision": "f8113c25bc6b",
-                            "name": "merqury",
+                            "changeset_revision": "b2f1f75d49c4",
+                            "name": "multiqc",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"label\": \"output_merqury\", \"mode\": {\"options\": \"default\", \"__current_case__\": 0, \"meryldb_F1\": {\"__class__\": \"ConnectedValue\"}, \"assembly_options\": {\"number_assemblies\": \"one\", \"__current_case__\": 0, \"assembly_01\": {\"__class__\": \"ConnectedValue\"}}}, \"output_add_headers\": false, \"output_selector\": [\"qv\", \"plots\", \"stats\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3+galaxy2",
+                        "tool_state": "{\"comment\": \"\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": \"false\", \"title\": \"miRNA trimmed quality check\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7",
                         "type": "tool",
-                        "uuid": "60379717-8086-422d-8300-9d1b459a473a",
-                        "when": null,
+                        "uuid": "b8e44272-be04-47ad-8b06-aa0f7d51a38c",
                         "workflow_outputs": [
                             {
-                                "label": "Merqury on input dataset(s): stats",
-                                "output_name": "stats_files",
-                                "uuid": "c2fe83a3-754a-4544-bb87-df16f3537ab4"
-                            },
-                            {
-                                "label": "Merqury on input dataset(s): plots",
-                                "output_name": "png_files",
-                                "uuid": "8f08d8f6-7615-420c-8a15-201a61b5d3bb"
-                            },
-                            {
-                                "label": "Merqury on input dataset(s): QV stats",
-                                "output_name": "qv_files",
-                                "uuid": "7a8d951a-6a31-4b02-aeba-0eb3061f85ce"
+                                "label": null,
+                                "output_name": "html_report",
+                                "uuid": "45f7bd2f-aafe-471c-b41e-431cbbe28781"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
                         "errors": null,
-                        "id": 27,
+                        "id": 35,
                         "input_connections": {
-                            "input": {
-                                "id": 19,
-                                "output_name": "output_alignments"
+                            "select_data|rep_factorName_0|rep_factorLevel_0|countsFile": {
+                                "id": 32,
+                                "output_name": "out_file1"
+                            },
+                            "select_data|rep_factorName_0|rep_factorLevel_1|countsFile": {
+                                "id": 30,
+                                "output_name": "out_file1"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool DESeq2",
+                                "name": "batch_factors"
+                            }
+                        ],
                         "label": null,
-                        "name": "Samtools stats",
+                        "name": "DESeq2",
                         "outputs": [
                             {
-                                "name": "output",
+                                "name": "deseq_out",
                                 "type": "tabular"
+                            },
+                            {
+                                "name": "plots",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "left": 860,
-                            "top": 1816
+                            "left": 1460,
+                            "top": 1445.984375
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4",
+                        "post_job_actions": {
+                            "RenameDatasetActiondeseq_out": {
+                                "action_arguments": {
+                                    "newname": "DESeq2 results miRNA"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "deseq_out"
+                            },
+                            "RenameDatasetActionplots": {
+                                "action_arguments": {
+                                    "newname": "DESeq2 plots miRNA"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "plots"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "3a0efe14891f",
-                            "name": "samtools_stats",
-                            "owner": "devteam",
+                            "changeset_revision": "6a3a025714d3",
+                            "name": "deseq2",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cov_threshold\": null, \"coverage_cond\": {\"coverage_select\": \"no\", \"__current_case__\": 0}, \"filter_by_flags\": {\"filter_flags\": \"nofilter\", \"__current_case__\": 1}, \"gc_depth\": null, \"input\": {\"__class__\": \"ConnectedValue\"}, \"insert_size\": null, \"most_inserts\": null, \"read_group\": null, \"read_length\": null, \"remove_dups\": false, \"remove_overlaps\": false, \"sparse\": false, \"split_output_cond\": {\"split_output_selector\": \"no\", \"__current_case__\": 0}, \"trim_quality\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.4",
+                        "tool_state": "{\"auto_mean_filter_off\": \"false\", \"batch_factors\": {\"__class__\": \"RuntimeValue\"}, \"esf\": \"\", \"fit_type\": \"1\", \"header\": \"false\", \"many_contrasts\": \"false\", \"normCounts\": \"false\", \"normRLog\": \"false\", \"normVST\": \"false\", \"outlier_filter_off\": \"false\", \"outlier_replace_off\": \"false\", \"pdf\": \"true\", \"select_data\": {\"how\": \"datasets_per_level\", \"__current_case__\": 1, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": \"effects_brassinolide\", \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": \"brassinolide\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"factorLevel\": \"control\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"count\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.11.40.6+galaxy1",
                         "type": "tool",
-                        "uuid": "d6f1f5fe-736a-4e1f-87d5-0ae8bba7ad11",
-                        "when": null,
+                        "uuid": "15632b70-0358-4ca6-918f-f236468dd8d5",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "c26fc7dd-b185-42fc-b831-e3e9a5e6d741"
+                                "output_name": "plots",
+                                "uuid": "b4252bda-8ee4-47f5-85e0-ccacb840c702"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "deseq_out",
+                                "uuid": "55ea0b93-52e0-4d07-a64f-4db6e39f42ab"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.4+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1",
                         "errors": null,
-                        "id": 28,
+                        "id": 38,
                         "input_connections": {
+                            "header_criteria|identifiers": {
+                                "id": 36,
+                                "output_name": "out_file1"
+                            },
                             "input": {
-                                "id": 21,
-                                "output_name": "outfile"
+                                "id": 5,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Busco",
+                        "name": "Filter FASTA",
                         "outputs": [
                             {
-                                "name": "busco_sum",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "busco_table",
-                                "type": "tabular"
+                                "name": "output",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 1140,
-                            "top": 1293
+                            "left": 2880,
+                            "top": 1662.984375
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.4+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Downregulated mRNA sequences"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "bb935709506a",
-                            "name": "busco",
-                            "owner": "iuc",
+                            "changeset_revision": "3c623e81be77",
+                            "name": "filter_by_fasta_ids",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"auto_detect\", \"__current_case__\": 0, \"auto_lineage\": \"--auto-lineage\"}, \"outputs\": [\"short_summary\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.4.4+galaxy0",
+                        "tool_state": "{\"dedup\": \"false\", \"header_criteria\": {\"header_criteria_select\": \"id_list\", \"__current_case__\": 1, \"identifiers\": {\"__class__\": \"ConnectedValue\"}, \"id_regex\": {\"find\": \"pattern\", \"__current_case__\": 1, \"pattern\": \"GENE=(AT.{7})\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"output_discarded\": \"false\", \"sequence_criteria\": {\"sequence_criteria_select\": \"\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1",
                         "type": "tool",
-                        "uuid": "3a41b74c-9ed5-4a4c-a92d-f48cf6d5f35d",
-                        "when": null,
+                        "uuid": "4d1f1434-2cd7-4025-aa31-955646f26ae0",
                         "workflow_outputs": [
                             {
-                                "label": "Busco on input dataset(s): full table",
-                                "output_name": "busco_table",
-                                "uuid": "1d4e4542-8bf1-4e32-890b-2e18df95a0de"
-                            },
-                            {
-                                "label": "Busco on input dataset(s): short summary",
-                                "output_name": "busco_sum",
-                                "uuid": "680b8177-3653-4630-ab99-c1d2304dc485"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "e8c830ca-388d-43e9-a30a-6ce4e1db2103"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
+                        "content_id": "cat1",
                         "errors": null,
-                        "id": 35,
+                        "id": 44,
                         "input_connections": {
-                            "input": {
-                                "id": 26,
-                                "output_name": "read_db_hist"
+                            "input1": {
+                                "id": 43,
+                                "output_name": "output"
                             },
-                            "ploidy": {
-                                "id": 4,
+                            "queries_0|input2": {
+                                "id": 42,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "GenomeScope",
+                        "name": "Concatenate datasets",
                         "outputs": [
                             {
-                                "name": "linear_plot",
-                                "type": "png"
-                            },
-                            {
-                                "name": "log_plot",
-                                "type": "png"
-                            },
-                            {
-                                "name": "transformed_linear_plot",
-                                "type": "png"
-                            },
-                            {
-                                "name": "transformed_log_plot",
-                                "type": "png"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 1140,
-                            "top": 977
+                            "left": 2880,
+                            "top": 1882.984375
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "01210c4e9144",
-                            "name": "genomescope",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Upregulated miRNA sequences"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
                         },
-                        "tool_state": "{\"advanced_options\": {\"topology\": null, \"initial_repetitiveness\": null, \"initial_heterozygosities\": \"\", \"transform_exp\": null, \"testing\": false, \"true_params\": \"\", \"trace_flag\": false, \"num_rounds\": null}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"kmer_length\": \"21\", \"lambda\": null, \"max_kmercov\": null, \"output_options\": {\"output_files\": null, \"no_unique_sequence\": false}, \"ploidy\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0+galaxy2",
+                        "tool_id": "cat1",
+                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [{\"__index__\": 0, \"input2\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
                         "type": "tool",
-                        "uuid": "123fa27b-c25d-422f-ab18-5996179a50a0",
-                        "when": null,
+                        "uuid": "97871054-6cba-4834-bc56-26a7f37be2b8",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "transformed_linear_plot",
-                                "uuid": "a7482d1b-bc8b-4d99-9095-14008f64ca7e"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "log_plot",
-                                "uuid": "2fd6f906-f4ec-4d9a-8043-2185ffde267d"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "linear_plot",
-                                "uuid": "ed2a9a05-d98f-4edd-b033-2312990b215b"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "transformed_log_plot",
-                                "uuid": "3e5db883-c25e-470e-bb18-be0da5dcd4f0"
+                                "output_name": "out_file1",
+                                "uuid": "800ea133-2a03-469d-875e-24b0635c3cd2"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1",
                         "errors": null,
-                        "id": 39,
+                        "id": 45,
                         "input_connections": {
-                            "input": {
-                                "id": 37,
-                                "output_name": "pretext_map_out"
+                            "d": {
+                                "id": 38,
+                                "output_name": "output"
+                            },
+                            "f": {
+                                "id": 44,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Pretext Snapshot",
+                        "name": "TargetFinder",
                         "outputs": [
                             {
-                                "name": "pretext_snap_out",
-                                "type": "input"
+                                "name": "output_file",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 1430,
-                            "top": 2162
+                            "left": 3157.984375,
+                            "top": 1712.984375
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "44c66e8d21e6",
-                            "name": "pretext_snapshot",
-                            "owner": "iuc",
+                            "changeset_revision": "c9d56748fbde",
+                            "name": "targetfinder",
+                            "owner": "rnateam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"colormap\": \"5\", \"formats\": {\"outformat\": \"png\", \"__current_case__\": 0}, \"grid\": {\"showGrid\": true, \"__current_case__\": 0, \"gridsize\": \"1\", \"gridcolor\": \"black\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mintexels\": \"64\", \"resolution\": \"1000\", \"sequencenames\": false, \"sequences\": \"=full, =all\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.0.3+galaxy1",
+                        "tool_state": "{\"c\": \"4.0\", \"d\": {\"__class__\": \"ConnectedValue\"}, \"f\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"classic\", \"r\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.0+galaxy1",
                         "type": "tool",
-                        "uuid": "576bcaf5-7b61-494c-b6cd-e10084628f08",
-                        "when": null,
+                        "uuid": "d81d9ea9-a085-478f-a148-0c31083f16fc",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "pretext_snap_out",
-                                "uuid": "ac2cda6a-0fdd-476b-b6ba-7e5312d9f409"
+                                "output_name": "output_file",
+                                "uuid": "2a3de11c-addc-4e1a-a156-f760f861ce64"
                             }
                         ]
                     }
                 ],
-                "parent_id": "assembly/ERGA-post-assembly-QC",
-                "path": "topics/assembly/tutorials/ERGA-post-assembly-QC/workflows/main_workflow.ga",
-                "tags": [],
+                "parent_id": "transcriptomics/mirna-target-finder",
+                "path": "topics/transcriptomics/tutorials/mirna-target-finder/workflows/main_workflow.ga",
+                "tags": [
+                    "transcriptomics",
+                    "mirna",
+                    "arabidopsis"
+                ],
                 "test_results": null,
-                "tests": true,
-                "title": "Post-assembly workflow",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-ERGA-post-assembly-QC/versions/main-workflow",
-                "tutorial_id": "ERGA-post-assembly-QC",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/ERGA-post-assembly-QC/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/ERGA-post-assembly-QC/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "assembly-ERGA-post-assembly-QC",
+                "tests": false,
+                "title": "Plant bulk RNA-Seq workflow",
+                "topic_id": "transcriptomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-mirna-target-finder/versions/main-workflow",
+                "tutorial_id": "mirna-target-finder",
+                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/mirna-target-finder/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/mirna-target-finder/workflows/main_workflow.html",
+                "version": 3,
+                "wfid": "transcriptomics-mirna-target-finder",
                 "wfname": "main-workflow",
                 "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "CONVERTER_gz_to_uncompressed",
-                    "__EXTRACT_DATASET__",
-                    "interactive_tool_blobtoolkit",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.0.7+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.2.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4",
-                    "toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy+2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.4+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
+                    "Cut1",
+                    "Filter1",
+                    "__MERGE_COLLECTION__",
+                    "cat1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.14.1.2+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                    "toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_mapper/rbc_mirdeep2_mapper/2.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_quantifier/rbc_mirdeep2_quantifier/2.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1"
                 ],
-                "workflowhub_id": "1127"
+                "workflowhub_id": "1318"
             }
-        ]
+        ],
+        "zenodo_link": "https://zenodo.org/record/4710649"
     },
     {
         "admin_install": {
@@ -170392,24 +171271,24 @@
         ],
         "dir": "topics/assembly/tutorials/chloroplast-assembly",
         "edam_operation": [
-            "Genome indexing",
-            "De-novo assembly",
-            "Sequence alignment",
-            "Box-Whisker plot plotting",
+            "Scatter plot plotting",
             "Genome annotation",
+            "Sequence alignment",
+            "Cross-assembly",
             "Read mapping",
-            "Scatter plot plotting",
-            "Mapping assembly",
             "Genome visualisation",
-            "Sequence assembly visualisation",
-            "Generation",
-            "Analysis",
-            "Coding region prediction",
-            "Cross-assembly",
             "Genome assembly",
+            "De-novo assembly",
+            "Box-Whisker plot plotting",
+            "Analysis",
             "Sequence assembly",
+            "Generation",
             "Gene prediction",
-            "Read alignment"
+            "Mapping assembly",
+            "Sequence assembly visualisation",
+            "Read alignment",
+            "Genome indexing",
+            "Coding region prediction"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -170421,6 +171300,7 @@
         "id": "assembly/chloroplast-assembly",
         "inexact_supported_servers": [
             "GalaxyTrakr",
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.fr",
             "UseGalaxy.no",
@@ -170438,14 +171318,14 @@
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-09-18",
         "objectives": [
             "Assemble a chloroplast genome from long reads",
             "Polish the assembly with short reads",
             "Annotate the assembly and view",
             "Map reads to the assembly and view"
         ],
-        "pageviews": 9428,
+        "pageviews": 9815,
         "pub_date": "2020-12-04",
         "questions": [
             "How can we assemble a chloroplast genome?"
@@ -170462,19 +171342,32 @@
                     "annasyme"
                 ],
                 "youtube_id": "eyfCyINTD_E"
+            },
+            {
+                "bot-timestamp": 1726113532,
+                "captioners": [
+                    "hannahkimincompbio"
+                ],
+                "date": "2024-09-12",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "16M",
+                "speakers": [
+                    "hannahkimincompbio"
+                ],
+                "youtube_id": "gIcbY9kXdTo"
             }
         ],
         "short_id": "T00030",
         "short_tools": [
-            "nanoplot",
-            "jbrowse",
-            "flye",
-            "fasta-stats",
+            "bwa_mem",
             "prokka",
-            "bandage_info",
+            "jbrowse",
             "bandage_image",
-            "bwa_mem",
             "upload1",
+            "bandage_info",
+            "fasta-stats",
+            "flye",
+            "nanoplot",
             "pilon"
         ],
         "slides": false,
@@ -170493,6 +171386,11 @@
                     "url": "https://galaxytrakr.org/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -170554,12 +171452,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/chloroplast-assembly/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/chloroplast-assembly/tutorial.json"
         },
-        "version": 17,
+        "version": 19,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 170,
-        "visitors": 5895,
+        "visit_duration": 172,
+        "visitors": 6134,
         "workflows": [
             {
                 "creators": [],
@@ -170702,7 +171600,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIllumina_reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nNanopore_reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nTiny_set_illumina_read\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nTiny_set_nanopore_reads\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Flye assembly\"];\n  1 -->|output| 4;\n  5[\"NanoPlot\"];\n  1 -->|output| 5;\n  6[\"Map with BWA-MEM\"];\n  0 -->|output| 6;\n  4 -->|consensus| 6;\n  7[\"Fasta Statistics\"];\n  4 -->|consensus| 7;\n  8[\"Bandage Info\"];\n  4 -->|assembly_gfa| 8;\n  9[\"Bandage Image\"];\n  4 -->|assembly_gfa| 9;\n  10[\"pilon\"];\n  6 -->|bam_output| 10;\n  4 -->|consensus| 10;\n  11[\"Fasta Statistics\"];\n  10 -->|output_fasta| 11;\n  12[\"Map with BWA-MEM\"];\n  2 -->|output| 12;\n  10 -->|output_fasta| 12;\n  13[\"Map with BWA-MEM\"];\n  3 -->|output| 13;\n  10 -->|output_fasta| 13;\n  14[\"Prokka\"];\n  10 -->|output_fasta| 14;\n  15[\"JBrowse\"];\n  10 -->|output_fasta| 15;\n  12 -->|bam_output| 15;\n  13 -->|bam_output| 15;\n  16[\"JBrowse\"];\n  10 -->|output_fasta| 16;\n  14 -->|out_gff| 16;",
-                "modified": "2024-08-18 00:06:20 +0000",
+                "modified": "2024-10-02 12:08:06 +0000",
                 "name": "Chloroplast-genome-assembly-and-annotation",
                 "outputs": [
                     {
@@ -171291,1195 +172189,324 @@
                                 },
                                 "action_type": "RenameDatasetAction",
                                 "output_name": "bam_output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "dfd8b7f78c37",
-                            "name": "bwa",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"ont2d\", \"__current_case__\": 2}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 1, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}, \"index_a\": \"auto\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.17.1",
-                        "type": "tool",
-                        "uuid": "c91315b3-c7f8-458c-a182-2b561d825837",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "bam_output",
-                                "uuid": "bebb5b25-00c2-456a-92a0-cd133a169e0e"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
-                        "errors": null,
-                        "id": 14,
-                        "input_connections": {
-                            "input": {
-                                "id": 10,
-                                "output_name": "output_fasta"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Prokka",
-                                "name": "proteins"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Prokka",
-                        "outputs": [
-                            {
-                                "name": "out_gff",
-                                "type": "gff"
-                            },
-                            {
-                                "name": "out_gbk",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "out_fna",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "out_faa",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "out_ffn",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "out_sqn",
-                                "type": "asn1"
-                            },
-                            {
-                                "name": "out_fsa",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "out_tbl",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "out_tsv",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "out_err",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "out_txt",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "out_log",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 1704.984375,
-                            "top": 350.234375
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
-                        "tool_shed_repository": {
-                            "changeset_revision": "bf68eb663bc3",
-                            "name": "prokka",
-                            "owner": "crs4",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"centre\": \"\", \"compliant\": {\"compliant_select\": \"no\", \"__current_case__\": 0, \"addgenes\": \"false\", \"mincontig\": \"200\"}, \"evalue\": \"1e-06\", \"fast\": \"false\", \"genus\": \"\", \"gffver\": \"3\", \"increment\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"kingdom\": {\"kingdom_select\": \"Bacteria\", \"__current_case__\": 1, \"gcode\": \"11\"}, \"locustag\": \"\", \"metagenome\": \"false\", \"norrna\": \"false\", \"notrna\": \"false\", \"outputs\": [\"gff\", \"gbk\", \"fna\", \"faa\", \"ffn\", \"sqn\", \"fsa\", \"tbl\", \"tsv\", \"err\", \"txt\"], \"plasmid\": \"\", \"proteins\": {\"__class__\": \"RuntimeValue\"}, \"rfam\": \"false\", \"species\": \"\", \"strain\": \"\", \"usegenus\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.14.5",
-                        "type": "tool",
-                        "uuid": "489e19de-1324-472c-8c8e-77e95572b6c3",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_err",
-                                "uuid": "a5f8d2e3-b2ca-46c3-83c5-36bc15507046"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_fna",
-                                "uuid": "1d83fde1-6207-46cc-b65e-a71815c578d8"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_faa",
-                                "uuid": "8e49b1a0-fd5b-4a80-8714-5fe51e7e6096"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_tbl",
-                                "uuid": "638f81aa-0004-4497-aeb9-6c1964cb27a7"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_fsa",
-                                "uuid": "773f3ba6-43ff-41aa-b498-ee509d71a58a"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_ffn",
-                                "uuid": "fd75d3c5-5cff-448e-9fd6-92b8af36e5cf"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_tsv",
-                                "uuid": "0efb82cf-84b6-49dd-bab4-d64d7356e0c7"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_txt",
-                                "uuid": "da1cc1bc-e00c-4f65-afbc-1a118b23274a"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_sqn",
-                                "uuid": "a5a04271-fc67-4ce3-95dc-9f01ee77775c"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_log",
-                                "uuid": "ca98afab-a3d2-4beb-b3f0-de7f38bf5c6b"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_gff",
-                                "uuid": "bae78be6-7c70-42bf-95c1-cae45c51871d"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_gbk",
-                                "uuid": "9a2a7aab-fde6-4a9c-b098-17b958ff2f20"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
-                        "errors": null,
-                        "id": 15,
-                        "input_connections": {
-                            "reference_genome|genome": {
-                                "id": 10,
-                                "output_name": "output_fasta"
-                            },
-                            "track_groups_0|data_tracks_0|data_format|annotation": {
-                                "id": 12,
-                                "output_name": "bam_output"
-                            },
-                            "track_groups_0|data_tracks_1|data_format|annotation": {
-                                "id": 13,
-                                "output_name": "bam_output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "JBrowse",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "html"
-                            }
-                        ],
-                        "position": {
-                            "left": 1469.125,
-                            "top": 558.828125
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "JBrowse-view-assembly-and-reads"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "17359b808b01",
-                            "name": "jbrowse",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"11\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Default\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"auto_snp\": \"false\", \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"force\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"auto_snp\": \"false\", \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"force\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16.9+galaxy0",
-                        "type": "tool",
-                        "uuid": "9ae0aa01-72e9-4481-b992-248f3ec20a07",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "b5c7a4ed-bb41-4486-b01f-270071e23e52"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
-                        "errors": null,
-                        "id": 16,
-                        "input_connections": {
-                            "reference_genome|genome": {
-                                "id": 10,
-                                "output_name": "output_fasta"
-                            },
-                            "track_groups_0|data_tracks_0|data_format|annotation": {
-                                "id": 14,
-                                "output_name": "out_gff"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "JBrowse",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "html"
-                            }
-                        ],
-                        "position": {
-                            "left": 1981.40625,
-                            "top": 224.328125
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "JBrowse-view-annotations"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "17359b808b01",
-                            "name": "jbrowse",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"11\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Default\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"force\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16.9+galaxy0",
-                        "type": "tool",
-                        "uuid": "7e5c8b63-2538-4898-9644-71453e17c0ba",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "5ad68433-82c3-47aa-b3e4-ef1b07ed790e"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "assembly/chloroplast-assembly",
-                "path": "topics/assembly/tutorials/chloroplast-assembly/workflows/Galaxy-Workflow-Chloroplast-genome-assembly-and-annotation.ga",
-                "tags": [
-                    "assembly"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Chloroplast-genome-assembly-and-annotation",
-                "topic_id": "assembly",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-chloroplast-assembly/versions/galaxy-workflow-chloroplast-genome-assembly-and-annotation",
-                "tutorial_id": "chloroplast-assembly",
-                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/chloroplast-assembly/workflows/Galaxy-Workflow-Chloroplast-genome-assembly-and-annotation.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/chloroplast-assembly/workflows/Galaxy-Workflow-Chloroplast-genome-assembly-and-annotation.html",
-                "version": 3,
-                "wfid": "assembly-chloroplast-assembly",
-                "wfname": "galaxy-workflow-chloroplast-genome-assembly-and-annotation",
-                "workflow": "Galaxy-Workflow-Chloroplast-genome-assembly-and-annotation.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6",
-                    "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1"
-                ],
-                "workflowhub_id": "1139"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.3567224"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "clustalw",
-                    "owner": "devteam",
-                    "revisions": "d6694932c5e0",
-                    "tool_panel_section_label": "Multiple Alignments",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "chromeister",
-                    "owner": "iuc",
-                    "revisions": "e483be1014b6",
-                    "tool_panel_section_label": "Multiple Alignments",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gecko",
-                    "owner": "iuc",
-                    "revisions": "5efbd15675ca",
-                    "tool_panel_section_label": "Multiple Alignments",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: clustalw\n  owner: devteam\n  revisions: d6694932c5e0\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chromeister\n  owner: iuc\n  revisions: e483be1014b6\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gecko\n  owner: iuc\n  revisions: 5efbd15675ca\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.json",
-        "contributors": [
-            {
-                "elixir_node": "es",
-                "email": "estebanpw@uma.es",
-                "id": "estebanpw",
-                "joined": "2020-11",
-                "name": "Esteban Perez-Wohlfeil",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/estebanpw/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/estebanpw.json"
-            }
-        ],
-        "dir": "topics/genome-annotation/tutorials/hpc-for-lsgc",
-        "edam_operation": [
-            "Multiple sequence alignment"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "genome-annotation/hpc-for-lsgc",
-        "inexact_supported_servers": [
-            "GalaxyTrakr",
-            "UseGalaxy.cz"
-        ],
-        "js_requirements": {
-            "mathjax": 10229,
-            "mermaid": false
-        },
-        "key_points": [
-            "We learnt that sequence comparison is a demanding problem and that there are several ways to approach it",
-            "We learnt how to run sequence comparisons in Galaxy with different levels of precision, particularly fine-grained and coarse-grained sequence comparison using GECKO and CHROMEISTER for smaller and larger sequences, respectively",
-            "We learnt how to post-process our comparison by extracting alignments, fine-tuning with multiple sequence alignment, detecting rearrangements, etc."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-07-31",
-        "objectives": [
-            "Learn the basics of pairwise sequence comparison",
-            "Learn how to run different tools in Galaxy to perform sequence comparison at fine and coarse-grained levels",
-            "Learn how to post-process your sequence comparisons"
-        ],
-        "pageviews": 5565092,
-        "pub_date": "2021-02-08",
-        "questions": [
-            "How can we run pairwise genome comparisons using Galaxy?",
-            "How can we run massive chromosome comparisons in Galaxy?",
-            "How can we quickly visualize genome comparisons in Galaxy?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "introduction",
-                "tutorials": [
-                    "galaxy-intro-101"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00176",
-        "short_tools": [
-            "clustalw",
-            "gecko",
-            "tp_awk_tool",
-            "chromeister"
-        ],
-        "slides": true,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "plants",
-            "prokaryote"
-        ],
-        "time_estimation": "2H",
-        "title": "From small to large-scale genome comparison",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a",
-            "toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2"
-        ],
-        "topic_name": "genome-annotation",
-        "topic_name_human": "Genome Annotation",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "hpc-for-lsgc",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/hpc-for-lsgc/tutorial.json"
-        },
-        "version": 8,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 282,
-        "visitors": 2016344,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "A workflow designed to compare chromosomes and study large-scale rearrangements using CHROMEISTER",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nQuery chromosome\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference chromosome\"]\n  2[label=\"Chromeister\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  k58cf0c0c92004ba497276d908ccdfa9a[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Detected events\"]\n  2 -> k58cf0c0c92004ba497276d908ccdfa9a\n  k2afd0e7cd1cf4bfdbec66cc237ff3e2c[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Comparison metainformation\"]\n  2 -> k2afd0e7cd1cf4bfdbec66cc237ff3e2c\n  kc248576c1c39416c99d040c520e3da67[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Comparison dotplot\"]\n  2 -> kc248576c1c39416c99d040c520e3da67\n  k5f9aad77f9ee4932ab22bb5fd83f416c[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Comparison matrix\"]\n  2 -> k5f9aad77f9ee4932ab22bb5fd83f416c\n  kdea450c2712643dcaf7a9f2b704c76dd[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Comparison score\"]\n  2 -> kdea450c2712643dcaf7a9f2b704c76dd\n  k9a03f72255884a3fb70e0ec9979c16dd[color=lightseagreen,label=\"Output\\nChromeister on input dataset(s): Detected events plot\"]\n  2 -> k9a03f72255884a3fb70e0ec9979c16dd\n}",
-                "history": [
-                    {
-                        "hash": "ae7dbf55cc79f67b32661f650f26d5baad4779b3",
-                        "message": "added workflow for chromeister",
-                        "num": 1,
-                        "short_hash": "ae7dbf55c",
-                        "unix": "1612266607"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Query chromosome"
-                            }
-                        ],
-                        "label": "Query chromosome",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 345.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 446,
-                            "right": 646,
-                            "top": 263,
-                            "width": 200,
-                            "x": 446,
-                            "y": 263
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "fdde703b-e59f-403b-be56-28b4fde66d17",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "e6b6ae7f-73c3-450e-a997-103138788bc6"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Reference chromosome"
-                            }
-                        ],
-                        "label": "Reference chromosome",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 445.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 448,
-                            "right": 648,
-                            "top": 363,
-                            "width": 200,
-                            "x": 448,
-                            "y": 363
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "43a48ede-1c2e-4b0d-bf74-da212443a7de",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1007eb1e-be5f-4f22-9d42-046f5e695dc4"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQuery chromosome\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference chromosome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Chromeister\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  58cf0c0c-9200-4ba4-9727-6d908ccdfa9a[\"Output\\nChromeister on input dataset(s): Detected events\"];\n  2 --> 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a;\n  style 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a stroke:#2c3143,stroke-width:4px;\n  2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c[\"Output\\nChromeister on input dataset(s): Comparison metainformation\"];\n  2 --> 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c;\n  style 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c stroke:#2c3143,stroke-width:4px;\n  c248576c-1c39-416c-99d0-40c520e3da67[\"Output\\nChromeister on input dataset(s): Comparison dotplot\"];\n  2 --> c248576c-1c39-416c-99d0-40c520e3da67;\n  style c248576c-1c39-416c-99d0-40c520e3da67 stroke:#2c3143,stroke-width:4px;\n  5f9aad77-f9ee-4932-ab22-bb5fd83f416c[\"Output\\nChromeister on input dataset(s): Comparison matrix\"];\n  2 --> 5f9aad77-f9ee-4932-ab22-bb5fd83f416c;\n  style 5f9aad77-f9ee-4932-ab22-bb5fd83f416c stroke:#2c3143,stroke-width:4px;\n  dea450c2-7126-43dc-af7a-9f2b704c76dd[\"Output\\nChromeister on input dataset(s): Comparison score\"];\n  2 --> dea450c2-7126-43dc-af7a-9f2b704c76dd;\n  style dea450c2-7126-43dc-af7a-9f2b704c76dd stroke:#2c3143,stroke-width:4px;\n  9a03f722-5588-4a3f-b70e-0ec9979c16dd[\"Output\\nChromeister on input dataset(s): Detected events plot\"];\n  2 --> 9a03f722-5588-4a3f-b70e-0ec9979c16dd;\n  style 9a03f722-5588-4a3f-b70e-0ec9979c16dd stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "CHROMEISTER chromosome comparison",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Query chromosome"
-                            }
-                        ],
-                        "label": "Query chromosome",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 345.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 446,
-                            "right": 646,
-                            "top": 263,
-                            "width": 200,
-                            "x": 446,
-                            "y": 263
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "fdde703b-e59f-403b-be56-28b4fde66d17",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "e6b6ae7f-73c3-450e-a997-103138788bc6"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Reference chromosome"
-                            }
-                        ],
-                        "label": "Reference chromosome",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 445.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 448,
-                            "right": 648,
-                            "top": 363,
-                            "width": 200,
-                            "x": 448,
-                            "y": 363
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "43a48ede-1c2e-4b0d-bf74-da212443a7de",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1007eb1e-be5f-4f22-9d42-046f5e695dc4"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a",
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "db": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "query": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Chromeister",
-                                "name": "db"
-                            },
-                            {
-                                "description": "runtime parameter for tool Chromeister",
-                                "name": "query"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Chromeister",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "output_imagen",
-                                "type": "png"
-                            },
-                            {
-                                "name": "output_csv",
-                                "type": "csv"
-                            },
-                            {
-                                "name": "output_events",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "output_events_png",
-                                "type": "png"
-                            },
-                            {
-                                "name": "output_score",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 793.4000244140625,
-                            "height": 520.4000244140625,
-                            "left": 851,
-                            "right": 1051,
-                            "top": 273,
-                            "width": 200,
-                            "x": 851,
-                            "y": 273
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a",
-                        "tool_shed_repository": {
-                            "changeset_revision": "a6d1f83c46b4",
-                            "name": "chromeister",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"db\": {\"__class__\": \"RuntimeValue\"}, \"diffuse\": \"4\", \"dimension\": \"1000\", \"grid\": \"true\", \"kmer\": \"32\", \"pngevents\": \"true\", \"query\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.5.a",
-                        "type": "tool",
-                        "uuid": "79507815-b059-4f21-b74e-8e390fbb4bf2",
-                        "workflow_outputs": [
-                            {
-                                "label": "Chromeister on input dataset(s): Detected events",
-                                "output_name": "output_events",
-                                "uuid": "58cf0c0c-9200-4ba4-9727-6d908ccdfa9a"
-                            },
-                            {
-                                "label": "Chromeister on input dataset(s): Comparison metainformation",
-                                "output_name": "output_csv",
-                                "uuid": "2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c"
-                            },
-                            {
-                                "label": "Chromeister on input dataset(s): Comparison dotplot",
-                                "output_name": "output_imagen",
-                                "uuid": "c248576c-1c39-416c-99d0-40c520e3da67"
-                            },
-                            {
-                                "label": "Chromeister on input dataset(s): Comparison matrix",
-                                "output_name": "output",
-                                "uuid": "5f9aad77-f9ee-4932-ab22-bb5fd83f416c"
-                            },
-                            {
-                                "label": "Chromeister on input dataset(s): Comparison score",
-                                "output_name": "output_score",
-                                "uuid": "dea450c2-7126-43dc-af7a-9f2b704c76dd"
-                            },
-                            {
-                                "label": "Chromeister on input dataset(s): Detected events plot",
-                                "output_name": "output_events_png",
-                                "uuid": "9a03f722-5588-4a3f-b70e-0ec9979c16dd"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "genome-annotation/hpc-for-lsgc",
-                "path": "topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/CHROMEISTER_chromosome_comparison.ga",
-                "tags": [
-                    "genome-annotation"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "CHROMEISTER chromosome comparison",
-                "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-hpc-for-lsgc/versions/chromeister-chromosome-comparison",
-                "tutorial_id": "hpc-for-lsgc",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/CHROMEISTER_chromosome_comparison.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/CHROMEISTER_chromosome_comparison.html",
-                "version": 1,
-                "wfid": "genome-annotation-hpc-for-lsgc",
-                "wfname": "chromeister-chromosome-comparison",
-                "workflow": "CHROMEISTER_chromosome_comparison.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/chromeister/chromeister/1.5.a"
-                ],
-                "workflowhub_id": "1156"
-            },
-            {
-                "creators": [],
-                "description": "A workflow designed to compare two sequences using GECKO, extract repeats and perform multiple sequence alignment",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nQuery sequence\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference sequence\"]\n  2[label=\"Gecko\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  k6275abc1d74e45a7b8ab3c88426cc488[color=lightseagreen,label=\"Output\\nGecko on input dataset(s): CSV\"]\n  2 -> k6275abc1d74e45a7b8ab3c88426cc488\n  3[label=\"Text reformatting\"]\n  2 -> 3 [label=\"alignments2\"]\n  4[label=\"ClustalW\"]\n  3 -> 4 [label=\"outfile\"]\n  kd63c1172a5914bf6b307052ca19e7098[color=lightseagreen,label=\"Output\\nClustalW on input dataset(s): clustal\"]\n  4 -> kd63c1172a5914bf6b307052ca19e7098\n  kd7758e3a522d44398c9a03f784284ebd[color=lightseagreen,label=\"Output\\nClustalW on input dataset(s): dnd\"]\n  4 -> kd7758e3a522d44398c9a03f784284ebd\n}",
-                "history": [
-                    {
-                        "hash": "ae7dbf55cc79f67b32661f650f26d5baad4779b3",
-                        "message": "added workflow for chromeister",
-                        "num": 2,
-                        "short_hash": "ae7dbf55c",
-                        "unix": "1612266607"
-                    },
-                    {
-                        "hash": "42c257d5c78780b24fb384627c26488a90eeda4f",
-                        "message": "changed topic to genome-annotation",
-                        "num": 1,
-                        "short_hash": "42c257d5c",
-                        "unix": "1612264525"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Query sequence"
-                            }
-                        ],
-                        "label": "Query sequence",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 473.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 481,
-                            "right": 681,
-                            "top": 391,
-                            "width": 200,
-                            "x": 481,
-                            "y": 391
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "63490a28-7edf-4e4f-8697-5cbf621b0768",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "f1c8c4bf-126f-4c4b-8e5a-512cd0d270cd"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Reference sequence"
-                            }
-                        ],
-                        "label": "Reference sequence",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 598.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 482,
-                            "right": 682,
-                            "top": 516,
-                            "width": 200,
-                            "x": 482,
-                            "y": 516
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f49e63f9-977e-4a1f-bf43-9a50cfa14ee3",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "0867afff-2445-4a26-b21c-2476606adb88"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQuery sequence\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference sequence\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Gecko\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  6275abc1-d74e-45a7-b8ab-3c88426cc488[\"Output\\nGecko on input dataset(s): CSV\"];\n  2 --> 6275abc1-d74e-45a7-b8ab-3c88426cc488;\n  style 6275abc1-d74e-45a7-b8ab-3c88426cc488 stroke:#2c3143,stroke-width:4px;\n  3[\"Text reformatting\"];\n  2 -->|alignments2| 3;\n  4[\"ClustalW\"];\n  3 -->|outfile| 4;\n  d63c1172-a591-4bf6-b307-052ca19e7098[\"Output\\nClustalW on input dataset(s): clustal\"];\n  4 --> d63c1172-a591-4bf6-b307-052ca19e7098;\n  style d63c1172-a591-4bf6-b307-052ca19e7098 stroke:#2c3143,stroke-width:4px;\n  d7758e3a-522d-4439-8c9a-03f784284ebd[\"Output\\nClustalW on input dataset(s): dnd\"];\n  4 --> d7758e3a-522d-4439-8c9a-03f784284ebd;\n  style d7758e3a-522d-4439-8c9a-03f784284ebd stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:23 +0000",
-                "name": "GECKO pairwise comparison",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Query sequence"
-                            }
-                        ],
-                        "label": "Query sequence",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 473.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 481,
-                            "right": 681,
-                            "top": 391,
-                            "width": 200,
-                            "x": 481,
-                            "y": 391
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "63490a28-7edf-4e4f-8697-5cbf621b0768",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "f1c8c4bf-126f-4c4b-8e5a-512cd0d270cd"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Reference sequence"
-                            }
-                        ],
-                        "label": "Reference sequence",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 598.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 482,
-                            "right": 682,
-                            "top": 516,
-                            "width": 200,
-                            "x": 482,
-                            "y": 516
+                            }
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"]}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f49e63f9-977e-4a1f-bf43-9a50cfa14ee3",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "dfd8b7f78c37",
+                            "name": "bwa",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"ont2d\", \"__current_case__\": 2}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 1, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}, \"index_a\": \"auto\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.17.1",
+                        "type": "tool",
+                        "uuid": "c91315b3-c7f8-458c-a182-2b561d825837",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "0867afff-2445-4a26-b21c-2476606adb88"
+                                "output_name": "bam_output",
+                                "uuid": "bebb5b25-00c2-456a-92a0-cd133a169e0e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
                         "errors": null,
-                        "id": 2,
+                        "id": 14,
                         "input_connections": {
-                            "db": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "query": {
-                                "id": 0,
-                                "output_name": "output"
+                            "input": {
+                                "id": 10,
+                                "output_name": "output_fasta"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Prokka",
+                                "name": "proteins"
+                            }
+                        ],
                         "label": null,
-                        "name": "Gecko",
+                        "name": "Prokka",
                         "outputs": [
                             {
-                                "name": "csv_output1",
-                                "type": "csv"
+                                "name": "out_gff",
+                                "type": "gff"
                             },
                             {
-                                "name": "alignments2",
+                                "name": "out_gbk",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "out_fna",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "out_faa",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "out_ffn",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "out_sqn",
+                                "type": "asn1"
+                            },
+                            {
+                                "name": "out_fsa",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "out_tbl",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "out_tsv",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "out_err",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "out_txt",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "out_log",
                                 "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 709.8000030517578,
-                            "height": 194.8000030517578,
-                            "left": 841,
-                            "right": 1041,
-                            "top": 515,
-                            "width": 200,
-                            "x": 841,
-                            "y": 515
+                            "left": 1704.984375,
+                            "top": 350.234375
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
                         "tool_shed_repository": {
-                            "changeset_revision": "5efbd15675ca",
-                            "name": "gecko",
-                            "owner": "iuc",
+                            "changeset_revision": "bf68eb663bc3",
+                            "name": "prokka",
+                            "owner": "crs4",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"db\": {\"__class__\": \"ConnectedValue\"}, \"kmer\": \"16\", \"minlen\": \"50\", \"options\": {\"selection_mode\": \"alignments\", \"__current_case__\": 0}, \"query\": {\"__class__\": \"ConnectedValue\"}, \"similarity\": \"60\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2",
+                        "tool_state": "{\"centre\": \"\", \"compliant\": {\"compliant_select\": \"no\", \"__current_case__\": 0, \"addgenes\": \"false\", \"mincontig\": \"200\"}, \"evalue\": \"1e-06\", \"fast\": \"false\", \"genus\": \"\", \"gffver\": \"3\", \"increment\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"kingdom\": {\"kingdom_select\": \"Bacteria\", \"__current_case__\": 1, \"gcode\": \"11\"}, \"locustag\": \"\", \"metagenome\": \"false\", \"norrna\": \"false\", \"notrna\": \"false\", \"outputs\": [\"gff\", \"gbk\", \"fna\", \"faa\", \"ffn\", \"sqn\", \"fsa\", \"tbl\", \"tsv\", \"err\", \"txt\"], \"plasmid\": \"\", \"proteins\": {\"__class__\": \"RuntimeValue\"}, \"rfam\": \"false\", \"species\": \"\", \"strain\": \"\", \"usegenus\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.14.5",
                         "type": "tool",
-                        "uuid": "217b825b-dfa8-4443-95cb-ea55dd499397",
+                        "uuid": "489e19de-1324-472c-8c8e-77e95572b6c3",
                         "workflow_outputs": [
                             {
-                                "label": "Gecko on input dataset(s): CSV",
-                                "output_name": "csv_output1",
-                                "uuid": "6275abc1-d74e-45a7-b8ab-3c88426cc488"
+                                "label": null,
+                                "output_name": "out_err",
+                                "uuid": "a5f8d2e3-b2ca-46c3-83c5-36bc15507046"
                             },
                             {
                                 "label": null,
-                                "output_name": "alignments2",
-                                "uuid": "643f73a5-9648-4b78-8b39-4643a0f4438a"
+                                "output_name": "out_fna",
+                                "uuid": "1d83fde1-6207-46cc-b65e-a71815c578d8"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_faa",
+                                "uuid": "8e49b1a0-fd5b-4a80-8714-5fe51e7e6096"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_tbl",
+                                "uuid": "638f81aa-0004-4497-aeb9-6c1964cb27a7"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_fsa",
+                                "uuid": "773f3ba6-43ff-41aa-b498-ee509d71a58a"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_ffn",
+                                "uuid": "fd75d3c5-5cff-448e-9fd6-92b8af36e5cf"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_tsv",
+                                "uuid": "0efb82cf-84b6-49dd-bab4-d64d7356e0c7"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_txt",
+                                "uuid": "da1cc1bc-e00c-4f65-afbc-1a118b23274a"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_sqn",
+                                "uuid": "a5a04271-fc67-4ce3-95dc-9f01ee77775c"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_log",
+                                "uuid": "ca98afab-a3d2-4beb-b3f0-de7f38bf5c6b"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_gff",
+                                "uuid": "bae78be6-7c70-42bf-95c1-cae45c51871d"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_gbk",
+                                "uuid": "9a2a7aab-fde6-4a9c-b098-17b958ff2f20"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
                         "errors": null,
-                        "id": 3,
+                        "id": 15,
                         "input_connections": {
-                            "infile": {
-                                "id": 2,
-                                "output_name": "alignments2"
+                            "reference_genome|genome": {
+                                "id": 10,
+                                "output_name": "output_fasta"
+                            },
+                            "track_groups_0|data_tracks_0|data_format|annotation": {
+                                "id": 12,
+                                "output_name": "bam_output"
+                            },
+                            "track_groups_0|data_tracks_1|data_format|annotation": {
+                                "id": 13,
+                                "output_name": "bam_output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Text reformatting",
+                        "name": "JBrowse",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "input"
+                                "name": "output",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "bottom": 740.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": 1162,
-                            "right": 1362,
-                            "top": 627,
-                            "width": 200,
-                            "x": 1162,
-                            "y": 627
+                            "left": 1469.125,
+                            "top": 558.828125
                         },
                         "post_job_actions": {
-                            "ChangeDatatypeActionoutfile": {
+                            "RenameDatasetActionoutput": {
                                 "action_arguments": {
-                                    "newtype": "fasta"
+                                    "newname": "JBrowse-view-assembly-and-reads"
                                 },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "outfile"
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "17359b808b01",
+                            "name": "jbrowse",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"code\": \"BEGIN{FS=\\\" \\\"} /@\\\\(196[0-9][0-9]/ { printf(\\\">sequence%s%s\\\\n\\\", $(NF-1), $NF); getline; while(substr($0,1,1) != \\\">\\\"){ if(substr($0,1,1) ==\\\"Y\\\"){ print $2; } getline; } } \", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.2",
+                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"11\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Default\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"auto_snp\": \"false\", \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"force\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}, {\"__index__\": 1, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"auto_snp\": \"false\", \"chunkSizeLimit\": \"5000000\", \"jb_custom_config\": {\"option\": []}, \"track_visibility\": \"force\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.9+galaxy0",
                         "type": "tool",
-                        "uuid": "ac13faf0-b6dc-48fa-b5b4-31fec9a4733f",
+                        "uuid": "9ae0aa01-72e9-4481-b992-248f3ec20a07",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "789a050e-0ab3-4296-b64d-9b7ad67af768"
+                                "output_name": "output",
+                                "uuid": "b5c7a4ed-bb41-4486-b01f-270071e23e52"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
                         "errors": null,
-                        "id": 4,
+                        "id": 16,
                         "input_connections": {
-                            "input": {
-                                "id": 3,
-                                "output_name": "outfile"
+                            "reference_genome|genome": {
+                                "id": 10,
+                                "output_name": "output_fasta"
+                            },
+                            "track_groups_0|data_tracks_0|data_format|annotation": {
+                                "id": 14,
+                                "output_name": "out_gff"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "ClustalW",
+                        "name": "JBrowse",
                         "outputs": [
                             {
                                 "name": "output",
-                                "type": "clustal"
-                            },
-                            {
-                                "name": "dnd",
-                                "type": "nhx"
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "bottom": 864.8000030517578,
-                            "height": 184.8000030517578,
-                            "left": 1536,
-                            "right": 1736,
-                            "top": 680,
-                            "width": 200,
-                            "x": 1536,
-                            "y": 680
+                            "left": 1981.40625,
+                            "top": 224.328125
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "JBrowse-view-annotations"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "d6694932c5e0",
-                            "name": "clustalw",
-                            "owner": "devteam",
+                            "changeset_revision": "17359b808b01",
+                            "name": "jbrowse",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"dnarna\": \"DNA\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"out_order\": \"ALIGNED\", \"outcontrol\": {\"outform\": \"clustal\", \"__current_case__\": 2, \"out_seqnos\": \"false\"}, \"range\": {\"mode\": \"complete\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1",
+                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"11\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"ConnectedValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Default\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"feature\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": []}, \"track_visibility\": \"force\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.9+galaxy0",
                         "type": "tool",
-                        "uuid": "b95c1c44-a967-47fd-a85c-3a3121163486",
+                        "uuid": "7e5c8b63-2538-4898-9644-71453e17c0ba",
                         "workflow_outputs": [
                             {
-                                "label": "ClustalW on input dataset(s): clustal",
+                                "label": null,
                                 "output_name": "output",
-                                "uuid": "d63c1172-a591-4bf6-b307-052ca19e7098"
-                            },
-                            {
-                                "label": "ClustalW on input dataset(s): dnd",
-                                "output_name": "dnd",
-                                "uuid": "d7758e3a-522d-4439-8c9a-03f784284ebd"
+                                "uuid": "5ad68433-82c3-47aa-b3e4-ef1b07ed790e"
                             }
                         ]
                     }
                 ],
-                "parent_id": "genome-annotation/hpc-for-lsgc",
-                "path": "topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/GECKO_pairwise_comparison.ga",
+                "parent_id": "assembly/chloroplast-assembly",
+                "path": "topics/assembly/tutorials/chloroplast-assembly/workflows/Galaxy-Workflow-Chloroplast-genome-assembly-and-annotation.ga",
                 "tags": [
-                    "genome-annotation"
+                    "assembly"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "GECKO pairwise comparison",
-                "topic_id": "genome-annotation",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/genome-annotation-hpc-for-lsgc/versions/gecko-pairwise-comparison",
-                "tutorial_id": "hpc-for-lsgc",
-                "url": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/GECKO_pairwise_comparison.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/hpc-for-lsgc/workflows/GECKO_pairwise_comparison.html",
-                "version": 1,
-                "wfid": "genome-annotation-hpc-for-lsgc",
-                "wfname": "gecko-pairwise-comparison",
-                "workflow": "GECKO_pairwise_comparison.ga",
+                "title": "Chloroplast-genome-assembly-and-annotation",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-chloroplast-assembly/versions/galaxy-workflow-chloroplast-genome-assembly-and-annotation",
+                "tutorial_id": "chloroplast-assembly",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/chloroplast-assembly/workflows/Galaxy-Workflow-Chloroplast-genome-assembly-and-annotation.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/chloroplast-assembly/workflows/Galaxy-Workflow-Chloroplast-genome-assembly-and-annotation.html",
+                "version": 3,
+                "wfid": "assembly-chloroplast-assembly",
+                "wfname": "galaxy-workflow-chloroplast-genome-assembly-and-annotation",
+                "workflow": "Galaxy-Workflow-Chloroplast-genome-assembly-and-annotation.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6",
+                    "toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1"
                 ],
-                "workflowhub_id": "1160"
+                "workflowhub_id": "1139"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.4485547"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.3567224"
     },
     {
         "admin_install": {
@@ -172488,301 +172515,149 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "diamond",
+                    "name": "blobtoolkit",
                     "owner": "bgruening",
-                    "revisions": "e8ac2b53f262",
-                    "tool_panel_section_label": "NCBI Blast",
+                    "revisions": "7d9ee8cd14b8",
+                    "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ncbi_blast_plus",
-                    "owner": "devteam",
-                    "revisions": "0e3cf9594bb7",
-                    "tool_panel_section_label": "NCBI Blast",
+                    "name": "blobtoolkit",
+                    "owner": "bgruening",
+                    "revisions": "8c2167481e72",
+                    "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ncbi_blast_plus",
-                    "owner": "devteam",
-                    "revisions": "0e3cf9594bb7",
+                    "name": "diamond",
+                    "owner": "bgruening",
+                    "revisions": "e8ac2b53f262",
                     "tool_panel_section_label": "NCBI Blast",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: diamond\n  owner: bgruening\n  revisions: e8ac2b53f262\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: 0e3cf9594bb7\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: 0e3cf9594bb7\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "deeptivarshney"
-            ],
-            "funding": [
-                "madland",
-                "nfdi4plants"
-            ]
-        },
-        "contributors": [
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "deeptivarshney",
-                "joined": "2022-12",
-                "name": "Deepti Varshney",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/deeptivarshney.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/logo-madland.jpg",
-                "funder": true,
-                "github": false,
-                "id": "madland",
-                "joined": "2024-07",
-                "name": "MAdLand",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/madland/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/madland.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/logo-dataplant.svg",
-                "funder": true,
-                "id": "nfdi4plants",
-                "joined": "2024-07",
-                "name": "DataPLANT",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nfdi4plants/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/nfdi4plants.json"
-            }
-        ],
-        "dir": "topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland",
-        "edam_operation": [
-            "Sequence alignment analysis"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "sequence-analysis/ncbi-blast-against-the-madland",
-        "inexact_supported_servers": [
-            "Center for Phage Technology (CPT)",
-            "Galaxy@AuBi",
-            "GalaxyTrakr",
-            "UseGalaxy.no"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Blast tool searches a database of sequences for similar sequences to a query sequence.",
-            "Diamond  quickly aligns large-scale data sets using a compressed version of the reference sequences called a \"database diamond\".",
-            "MAdLand is a database of fully sequenced plant and algal genomes, with an emphasis on non-seed plants and streptophyte algae that can be use for sequence similarity search."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-07-31",
-        "objectives": [
-            "Load FASTA sequence into Galaxy",
-            "Perform NCBI-Blast+ analysis against MAdLandDB"
-        ],
-        "pageviews": 1348,
-        "pub_date": "2023-01-16",
-        "questions": [
-            "What is MAdLand DB?",
-            "How can we perform Blast analysis on Galaxy?"
-        ],
-        "short_id": "T00238",
-        "short_tools": [
-            "ncbi_blastx_wrapper",
-            "ncbi_blastp_wrapper",
-            "bg_diamond"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "gfastats",
+                    "owner": "bgruening",
+                    "revisions": "5799092ffdff",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
+                    "name": "gfastats",
+                    "owner": "bgruening",
+                    "revisions": "3ef480892a9f",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "Center for Phage Technology (CPT)",
-                    "url": "https://cpt.tamu.edu/galaxy-public/",
-                    "usegalaxy": false
+                    "name": "samtools_stats",
+                    "owner": "devteam",
+                    "revisions": "3a0efe14891f",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
+                    "name": "smudgeplot",
+                    "owner": "galaxy-australia",
+                    "revisions": "5e0825476fb7",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
+                    "name": "bandage",
+                    "owner": "iuc",
+                    "revisions": "ddddce450736",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "plants"
-        ],
-        "time_estimation": "15m",
-        "title": "NCBI BLAST+ against the MAdLand",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/2.10.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/2.10.1+galaxy2"
-        ],
-        "topic_name": "sequence-analysis",
-        "topic_name_human": "Sequence analysis",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "ncbi-blast-against-the-madland",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.json"
-        },
-        "version": 9,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 166,
-        "visitors": 1042,
-        "zenodo_link": "https://zenodo.org/records/7524427"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
+                    "name": "bellerophon",
+                    "owner": "iuc",
+                    "revisions": "25ca5d73aedf",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
-                    "name": "anndata_import",
+                    "name": "busco",
                     "owner": "iuc",
-                    "revisions": "55e35e9203cf",
-                    "tool_panel_section_label": "Single-cell",
+                    "revisions": "bb935709506a",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "anndata_manipulate",
+                    "name": "bwa_mem2",
                     "owner": "iuc",
-                    "revisions": "9bd945a03d7b",
-                    "tool_panel_section_label": "Single-cell",
+                    "revisions": "b4a22d90cce9",
+                    "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_cluster_reduce_dimension",
+                    "name": "genomescope",
                     "owner": "iuc",
-                    "revisions": "aaa5da8e73a9",
-                    "tool_panel_section_label": "Single-cell",
+                    "revisions": "01210c4e9144",
+                    "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_filter",
+                    "name": "merqury",
                     "owner": "iuc",
-                    "revisions": "b409c2486353",
-                    "tool_panel_section_label": "Single-cell",
+                    "revisions": "f8113c25bc6b",
+                    "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_inspect",
+                    "name": "meryl",
                     "owner": "iuc",
-                    "revisions": "c5d3684f7c4c",
-                    "tool_panel_section_label": "Single-cell",
+                    "revisions": "29dabd8db6f2",
+                    "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_normalize",
+                    "name": "minimap2",
                     "owner": "iuc",
-                    "revisions": "ab55fe8030b6",
-                    "tool_panel_section_label": "Single-cell",
+                    "revisions": "5cc34c3f440d",
+                    "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_plot",
+                    "name": "pretext_map",
                     "owner": "iuc",
-                    "revisions": "6adf98e782f3",
-                    "tool_panel_section_label": "Single-cell",
+                    "revisions": "dfb8a4497339",
+                    "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_remove_confounders",
+                    "name": "pretext_snapshot",
                     "owner": "iuc",
-                    "revisions": "bf2017df9837",
-                    "tool_panel_section_label": "Single-cell",
+                    "revisions": "44c66e8d21e6",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "90981f86000f",
+                    "tool_panel_section_label": "Collection Operations",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: anndata_import\n  owner: iuc\n  revisions: 55e35e9203cf\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n  owner: iuc\n  revisions: 9bd945a03d7b\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_cluster_reduce_dimension\n  owner: iuc\n  revisions: aaa5da8e73a9\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter\n  owner: iuc\n  revisions: b409c2486353\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_inspect\n  owner: iuc\n  revisions: c5d3684f7c4c\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_normalize\n  owner: iuc\n  revisions: ab55fe8030b6\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot\n  owner: iuc\n  revisions: 6adf98e782f3\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_remove_confounders\n  owner: iuc\n  revisions: bf2017df9837\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plant/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: blobtoolkit\n  owner: bgruening\n  revisions: 7d9ee8cd14b8\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: blobtoolkit\n  owner: bgruening\n  revisions: 8c2167481e72\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: diamond\n  owner: bgruening\n  revisions: e8ac2b53f262\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n  owner: bgruening\n  revisions: 5799092ffdff\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n  owner: bgruening\n  revisions: 3ef480892a9f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 3a0efe14891f\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: smudgeplot\n  owner: galaxy-australia\n  revisions: 5e0825476fb7\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bellerophon\n  owner: iuc\n  revisions: 25ca5d73aedf\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: bb935709506a\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_mem2\n  owner: iuc\n  revisions: b4a22d90cce9\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: genomescope\n  owner: iuc\n  revisions: 01210c4e9144\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merqury\n  owner: iuc\n  revisions: f8113c25bc6b\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n  owner: iuc\n  revisions: 29dabd8db6f2\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: 5cc34c3f440d\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_map\n  owner: iuc\n  revisions: dfb8a4497339\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_snapshot\n  owner: iuc\n  revisions: 44c66e8d21e6\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "elixir_node": "de",
-                "email": "mtekman89@gmail.com",
-                "former_affiliations": [
-                    "elixir-europe"
-                ],
-                "id": "mtekman",
-                "joined": "2018-11",
-                "name": "Mehmet Tekman",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
-            },
-            {
-                "email": "beatrizserrano.galaxy@gmail.com",
-                "id": "beatrizserrano",
-                "joined": "2020-07",
-                "linkedin": "beatriz-serrano",
-                "matrix": "beatrizserrano:matrix.org",
-                "name": "Beatriz Serrano-Solano",
-                "orcid": "0000-0002-5862-6132",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/beatrizserrano/",
-                "twitter": "BSerranoSolano",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/beatrizserrano.json"
+                "id": "GitFab93",
+                "joined": "2023-03",
+                "name": "Fabian Recktenwald",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/GitFab93/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/GitFab93.json"
             },
             {
                 "elixir_node": "de",
@@ -172798,109 +172673,100 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
             },
             {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "pavanvidem",
-                "joined": "2017-09",
-                "name": "Pavankumar Videm",
-                "orcid": "0000-0002-5192-126X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
+                "email": "brown@izw-berlin.de",
+                "id": "tbrown91",
+                "joined": "2024-08",
+                "name": "Tom Brown",
+                "orcid": "0000-0001-8293-4816",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tbrown91/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tbrown91.json"
             }
         ],
-        "dir": "topics/single-cell/tutorials/scrna-plant",
+        "dir": "topics/assembly/tutorials/ERGA-post-assembly-QC",
         "edam_operation": [
-            "Differential gene expression analysis"
+            "Data handling",
+            "Sequence alignment",
+            "Sequence trimming",
+            "Genome assembly",
+            "De-novo assembly",
+            "Sequence alignment analysis",
+            "Phasing",
+            "Sequence assembly validation",
+            "Scaffolding",
+            "Sequence assembly visualisation",
+            "Pairwise sequence alignment",
+            "k-mer counting",
+            "Transcriptome assembly",
+            "Genotyping"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "gitter": "Galaxy-Training-Network/galaxy-single-cell",
         "hands_on": true,
-        "id": "single-cell/scrna-plant",
+        "id": "assembly/ERGA-post-assembly-QC",
         "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.no"
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Filtering parameters are dependent on the dataset, and should be explored using scatter or violin plots",
-            "A DotPlot is a fantastic way to validate clusters across different analyses"
+            "The ERGA post-assembly pipeline allows users to assess and improve the quality of genome assemblies",
+            "The ERGA post-assembly pipeline consists of three main steps: Genome assembly decontamination and overview with BlobToolKit, providing analysis information and statistics, and Hi-C scaffolding."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-09-06",
         "objectives": [
-            "Perform filtering, dimensionality reduction, and clustering",
-            "Generate a DotPlot emulating the original paper using a different analysis tool",
-            "Determine robust clusters across scRNA-seq pipelines"
+            "Apply the post-assembly-QC-workflow using the necessary tools",
+            "Analyse and evaluate the results of the workflow"
         ],
-        "pageviews": 2387,
-        "priority": 3,
-        "pub_date": "2021-04-08",
+        "pageviews": 1211,
+        "pub_date": "2023-06-23",
         "questions": [
-            "Can we reclaim cell markers using a different analysis method?",
-            "Are highly variable genes paramount to the analysis?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "mtekman"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "55M",
-                "speakers": [
-                    "mtekman"
-                ],
-                "youtube_id": "yKlJ5ESri7o"
-            }
-        ],
-        "redirect_from": [
-            "/topics/transcriptomics/tutorials/scrna-plant/tutorial",
-            "/short/single-cell/scrna-plant",
-            "/short/T00250"
-        ],
-        "requirements": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-scanpy-pbmc3k"
-                ],
-                "type": "internal"
-            }
+            "What combination of tools can assess the quality of a genome assembly?",
+            "What metrics can help to analyse the quality of an asembly?",
+            "How do we evaluate the outputs?"
         ],
-        "short_id": "T00250",
+        "short_id": "T00355",
         "short_tools": [
-            "anndata_manipulate",
-            "scanpy_inspect",
-            "scanpy_plot",
-            "scanpy_normalize",
-            "scanpy_cluster_reduce_dimension",
-            "anndata_import",
-            "scanpy_filter",
-            "scanpy_remove_confounders"
+            "merqury",
+            "minimap2",
+            "busco",
+            "tp_find_and_replace",
+            "pretext_snapshot",
+            "bwa_mem2",
+            "gfastats",
+            "bg_diamond",
+            "pretext_map",
+            "__EXTRACT_DATASET__",
+            "samtools_stats",
+            "genomescope",
+            "bandage_image",
+            "blobtoolkit",
+            "interactive_tool_blobtoolkit",
+            "bellerophon",
+            "collapse_dataset",
+            "meryl",
+            "smudgeplot",
+            "CONVERTER_gz_to_uncompressed"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "end-to-end",
         "supported_servers": {
             "exact": [
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                },
+                }
+            ],
+            "inexact": [
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -172911,76 +172777,124 @@
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
                 }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                }
             ]
         },
         "symlink": null,
         "tags": [
             "plants",
-            "paper-replication"
+            "animals",
+            "genome",
+            "assembly",
+            "QC"
         ],
-        "time_estimation": "2H",
-        "title": "Analysis of plant scRNA-Seq Data with Scanpy",
+        "time_estimation": "3H",
+        "title": "ERGA post-assembly QC",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0"
+            "CONVERTER_gz_to_uncompressed",
+            "__EXTRACT_DATASET__",
+            "interactive_tool_blobtoolkit",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/3.4.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.0.7+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.2.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4",
+            "toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy+2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+            "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
         ],
-        "topic_name": "single-cell",
-        "topic_name_human": "Single Cell",
+        "topic_name": "assembly",
+        "topic_name_human": "Assembly",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "scrna-plant",
+        "tutorial_name": "ERGA-post-assembly-QC",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-plant/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plant/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plant/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json"
         },
-        "version": 5,
+        "version": 4,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 85,
-        "visitors": 1878,
+        "visit_duration": 97,
+        "visitors": 918,
         "workflows": [
             {
-                "creators": [],
-                "description": "Downstream Single-cell RNA Plant analysis with ScanPy",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-5752-2155",
+                        "name": "Crist\u00f3bal Gallardo Alba"
+                    }
+                ],
+                "description": "ERGA post-assembly QC",
                 "features": {
                     "comments": false,
                     "parameters": true,
-                    "report": null,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                    },
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nLeiden Resolution\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSHR CSV.gz\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nWT CSV.gz\"]\n  3[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMin Genes\"]\n  4[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMin Cells\"]\n  5[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMax Features\"]\n  6[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMax Lib Size\"]\n  7[label=\"Import Anndata and loom\"]\n  1 -> 7 [label=\"output\"]\n  8[label=\"Import Anndata and loom\"]\n  2 -> 8 [label=\"output\"]\n  9[label=\"Manipulate AnnData\"]\n  7 -> 9 [label=\"anndata\"]\n  8 -> 9 [label=\"anndata\"]\n  10[label=\"Rename Batches\"]\n  9 -> 10 [label=\"anndata\"]\n  k680180f6edfc4f66b2657a63aaa22b39[color=lightseagreen,label=\"Output\\nscRNA Concatenated Datasets\"]\n  10 -> k680180f6edfc4f66b2657a63aaa22b39\n  11[label=\"QC metrics\"]\n  10 -> 11 [label=\"anndata\"]\n  12[label=\"Filter genes\"]\n  11 -> 12 [label=\"anndata_out\"]\n  3 -> 12 [label=\"output\"]\n  13[label=\"Plot Violin\"]\n  11 -> 13 [label=\"anndata_out\"]\n  14[label=\"Filter Cells\"]\n  12 -> 14 [label=\"anndata_out\"]\n  4 -> 14 [label=\"output\"]\n  15[label=\"Filter Max Features\"]\n  14 -> 15 [label=\"anndata_out\"]\n  5 -> 15 [label=\"output\"]\n  16[label=\"Filter Max Library Size\"]\n  15 -> 16 [label=\"anndata\"]\n  6 -> 16 [label=\"output\"]\n  17[label=\"Save RAW\"]\n  16 -> 17 [label=\"anndata\"]\n  18[label=\"Norm to 1e4\"]\n  17 -> 18 [label=\"anndata\"]\n  19[label=\"Log1p\"]\n  18 -> 19 [label=\"anndata_out\"]\n  20[label=\"Regress total counts\"]\n  19 -> 20 [label=\"anndata_out\"]\n  21[label=\"Scale\"]\n  20 -> 21 [label=\"anndata_out\"]\n  22[label=\"PCA\"]\n  21 -> 22 [label=\"anndata_out\"]\n  23[label=\"Neighborhod\"]\n  22 -> 23 [label=\"anndata_out\"]\n  24[label=\"UMAP\"]\n  23 -> 24 [label=\"anndata_out\"]\n  25[label=\"Leiden\"]\n  24 -> 25 [label=\"anndata_out\"]\n  0 -> 25 [label=\"output\"]\n  k48cf046584ba461abdb961625626de42[color=lightseagreen,label=\"Output\\nscRNA with clusters Dataset\"]\n  25 -> k48cf046584ba461abdb961625626de42\n  26[label=\"Plot PCA batch\"]\n  24 -> 26 [label=\"anndata_out\"]\n  27[label=\"Plot UMAP batch\"]\n  24 -> 27 [label=\"anndata_out\"]\n  28[label=\"Plot UMAP leiden, batch\"]\n  25 -> 28 [label=\"anndata_out\"]\n  29[label=\"Rename Clusters\"]\n  25 -> 29 [label=\"anndata_out\"]\n  30[label=\"Complex DotPlot\"]\n  25 -> 30 [label=\"anndata_out\"]\n  31[label=\"Complex DotPlot with new labels\"]\n  29 -> 31 [label=\"anndata\"]\n  32[label=\"Plot UMAP with new labels\"]\n  29 -> 32 [label=\"anndata\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMetadata file\"]\n  1[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nNCBI taxonomic ID\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nNCBI taxdump directory\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nLong-read FASTQ files\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPrimary genome assembly file fasta\"]\n  5[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nPloidy for model to use\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDIAMOND database\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nHi-C reverse\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nHi-C forward\"]\n  9[label=\"Meryl\"]\n  3 -> 9 [label=\"output\"]\n  10[label=\"Collapse Collection\"]\n  3 -> 10 [label=\"output\"]\n  11[label=\"Create BlobtoolKit\"]\n  4 -> 11 [label=\"output\"]\n  0 -> 11 [label=\"output\"]\n  2 -> 11 [label=\"output\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"gfastats\"]\n  4 -> 12 [label=\"output\"]\n  13[label=\"Convert compressed file to uncompressed.\"]\n  4 -> 13 [label=\"output\"]\n  14[label=\"gfastats\"]\n  4 -> 14 [label=\"output\"]\n  15[label=\"Diamond\"]\n  4 -> 15 [label=\"output\"]\n  6 -> 15 [label=\"output\"]\n  16[label=\"Collapse Collection\"]\n  7 -> 16 [label=\"output\"]\n  17[label=\"Collapse Collection\"]\n  8 -> 17 [label=\"output\"]\n  18[label=\"Meryl\"]\n  9 -> 18 [label=\"read_db\"]\n  19[label=\"Map with minimap2\"]\n  10 -> 19 [label=\"output\"]\n  4 -> 19 [label=\"output\"]\n  20[label=\"Smudgeplot\"]\n  10 -> 20 [label=\"output\"]\n  21[label=\"Replace\"]\n  13 -> 21 [label=\"output1\"]\n  22[label=\"Bandage Image\"]\n  14 -> 22 [label=\"output\"]\n  23[label=\"BWA-MEM2\"]\n  16 -> 23 [label=\"output\"]\n  4 -> 23 [label=\"output\"]\n  24[label=\"BWA-MEM2\"]\n  17 -> 24 [label=\"output\"]\n  4 -> 24 [label=\"output\"]\n  25[label=\"Merqury\"]\n  4 -> 25 [label=\"output\"]\n  18 -> 25 [label=\"read_db\"]\n  kd2dbf498515543b2bf2affed5c45100d[color=lightseagreen,label=\"Output\\nMerqury on input dataset(s): stats\"]\n  25 -> kd2dbf498515543b2bf2affed5c45100d\n  k0b43d206253f4c0ba1f4971402851c6d[color=lightseagreen,label=\"Output\\nMerqury on input dataset(s): plots\"]\n  25 -> k0b43d206253f4c0ba1f4971402851c6d\n  k811a77e8eb994dc79295f0000fcb9fe5[color=lightseagreen,label=\"Output\\nMerqury on input dataset(s): QV stats\"]\n  25 -> k811a77e8eb994dc79295f0000fcb9fe5\n  26[label=\"Meryl\"]\n  18 -> 26 [label=\"read_db\"]\n  27[label=\"Samtools stats\"]\n  19 -> 27 [label=\"alignment_output\"]\n  28[label=\"Busco\"]\n  21 -> 28 [label=\"outfile\"]\n  kaf98aae6f1a3493c9cef08e0926210d3[color=lightseagreen,label=\"Output\\nBusco on input dataset(s): full table\"]\n  28 -> kaf98aae6f1a3493c9cef08e0926210d3\n  k929439b7c68845ea848a97c13d3e0028[color=lightseagreen,label=\"Output\\nBusco on input dataset(s): short summary\"]\n  28 -> k929439b7c68845ea848a97c13d3e0028\n  29[label=\"Filter and merge\"]\n  24 -> 29 [label=\"bam_output\"]\n  23 -> 29 [label=\"bam_output\"]\n  30[label=\"Merqury plot 2\"]\n  25 -> 30 [label=\"png_files\"]\n  31[label=\"Merqury plot 1\"]\n  25 -> 31 [label=\"png_files\"]\n  32[label=\"Merqury plot 3\"]\n  25 -> 32 [label=\"png_files\"]\n  33[label=\"Merqury plot 5\"]\n  25 -> 33 [label=\"png_files\"]\n  34[label=\"Merqury plot 4\"]\n  25 -> 34 [label=\"png_files\"]\n  35[label=\"GenomeScope\"]\n  26 -> 35 [label=\"read_db_hist\"]\n  5 -> 35 [label=\"output\"]\n  36[label=\"BlobToolKit\"]\n  15 -> 36 [label=\"blast_tabular\"]\n  11 -> 36 [label=\"blobdir\"]\n  28 -> 36 [label=\"busco_table\"]\n  19 -> 36 [label=\"alignment_output\"]\n  37[label=\"PretextMap\"]\n  29 -> 37 [label=\"outfile\"]\n  38[label=\"BlobToolKit\"]\n  36 -> 38 [label=\"blobdir\"]\n  39[label=\"BlobToolKit\"]\n  36 -> 39 [label=\"blobdir\"]\n  40[label=\"BlobToolKit\"]\n  36 -> 40 [label=\"blobdir\"]\n  41[label=\"Pretext Snapshot\"]\n  37 -> 41 [label=\"pretext_map_out\"]\n}",
                 "history": [
                     {
-                        "hash": "327fd2b842f45de3dc2a30067714352675ad69ae",
-                        "message": "Making a single cell topics",
+                        "hash": "49cec9ea83fb11ba5bbf653257a0723f4ce541fc",
+                        "message": "Rename post-assembly-workflow.ga to main_workflow.ga",
+                        "num": 6,
+                        "short_hash": "49cec9ea8",
+                        "unix": "1725444408"
+                    },
+                    {
+                        "hash": "cf8e17d6d77d0ae7c26ffe5f83eecab712ed5a94",
+                        "message": "Add workflow test",
+                        "num": 5,
+                        "short_hash": "cf8e17d6d",
+                        "unix": "1724836602"
+                    },
+                    {
+                        "hash": "93e0f85071edf315b8b1e58830a40fdd0e32b858",
+                        "message": "Change mapping tool to minimap and add more details about the downloaded databases",
+                        "num": 4,
+                        "short_hash": "93e0f8507",
+                        "unix": "1719568805"
+                    },
+                    {
+                        "hash": "807026b8414e9d8e35cb6805104338150b1131f0",
+                        "message": "Update topics/assembly/tutorials/ERGA-post-assembly-QC/workflows/main_workflow.ga",
+                        "num": 3,
+                        "short_hash": "807026b84",
+                        "unix": "1687524556"
+                    },
+                    {
+                        "hash": "c5bb8031a5b03030e4fdc5c0a478a87e7c1e3c13",
+                        "message": "Fix testes",
+                        "num": 2,
+                        "short_hash": "c5bb8031a",
+                        "unix": "1687511093"
+                    },
+                    {
+                        "hash": "893cd527b9bd282e7f98475f5c3cd3e2f3ea89b0",
+                        "message": "Add images and rename tutorial",
                         "num": 1,
-                        "short_hash": "327fd2b84",
-                        "unix": "1668273265"
+                        "short_hash": "893cd527b",
+                        "unix": "1682673537"
                     }
                 ],
                 "inputs": [
@@ -172993,156 +172907,290 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Leiden Resolution"
+                                "name": "Metadata file"
                             }
                         ],
-                        "label": "Leiden Resolution",
+                        "label": "Metadata file",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 707.9000006004667,
+                            "top": 0
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": true, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "7ffa45d8-0b67-457d-bb1c-25c83c87ad8c",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "NCBI taxonomic ID"
+                            }
+                        ],
+                        "label": "NCBI taxonomic ID",
                         "name": "Input parameter",
                         "outputs": [],
                         "position": {
-                            "bottom": 195.5,
-                            "height": 84,
-                            "left": 121.5,
-                            "right": 321.5,
-                            "top": 111.5,
-                            "width": 200,
-                            "x": 121.5,
-                            "y": 111.5
+                            "left": 707.9000006004667,
+                            "top": 123
                         },
                         "tool_id": null,
-                        "tool_state": "{\"default\": 0.35, \"parameter_type\": \"float\", \"optional\": true}",
+                        "tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}",
                         "tool_version": null,
                         "type": "parameter_input",
-                        "uuid": "eddf8108-6913-40d2-819d-a84677dee3f4",
+                        "uuid": "2ecb111b-eba8-497c-960c-4ba9c3717606",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "55a176c7-cffb-4f80-9ac4-e396051e30d7"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "NCBI taxdump directory"
+                            }
+                        ],
+                        "label": "NCBI taxdump directory",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 707.9000006004667,
+                            "top": 246
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "f5be1515-252f-4f5d-87ec-d0a8c3c29802",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Long-read FASTQ files"
+                            }
+                        ],
+                        "label": "Long-read FASTQ files",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 1252.495997073411
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fastq.gz\"], \"tag\": \"\", \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "ecf4c98a-b500-4c53-a953-6588d99a669a",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Primary genome assembly file (fasta)"
+                            }
+                        ],
+                        "label": "Primary genome assembly file (fasta)",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 707.9000006004667,
+                            "top": 1310
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "6baf378a-2cb5-4e3d-8d52-f129b3f86ff8",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 5,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Ploidy for model to use"
+                            }
+                        ],
+                        "label": "Ploidy for model to use",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 1287.9000006004667,
+                            "top": 1011
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"default\": 2, \"parameter_type\": \"integer\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "bed1e2ca-2039-4f88-bd25-2646c6b5887d",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "8c56cbc1-c86f-4aef-b0b9-8ef1cde9c5b7"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 6,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "SHR (CSV.gz)"
+                                "name": "DIAMOND database"
                             }
                         ],
-                        "label": "SHR (CSV.gz)",
+                        "label": "DIAMOND database",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 302,
-                            "height": 84,
-                            "left": 116,
-                            "right": 316,
-                            "top": 218,
-                            "width": 200,
-                            "x": 116,
-                            "y": 218
+                            "left": 707.9000006004667,
+                            "top": 1735
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "4cf4f111-d63b-47ad-bcbf-8ebb290b3431",
+                        "uuid": "7d4e2fa7-0b60-47ce-bbc3-a4bcb4443ccc",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 7,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "WT (CSV.gz)"
+                                "name": "Hi-C reverse"
                             }
                         ],
-                        "label": "WT (CSV.gz)",
-                        "name": "Input dataset",
+                        "label": "Hi-C reverse",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "bottom": 403,
-                            "height": 84,
-                            "left": 114,
-                            "right": 314,
-                            "top": 319,
-                            "width": 200,
-                            "x": 114,
-                            "y": 319
+                            "left": 427.9000006004666,
+                            "top": 2172
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"format\": [\"fastq.gz\"], \"tag\": null, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "94fba59a-ba9d-452d-b325-cb558201f674",
+                        "type": "data_collection_input",
+                        "uuid": "26e380fd-6706-4c6a-8915-e6a11fd442fc",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 8,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Min Genes"
+                                "name": "Hi-C forward"
                             }
                         ],
-                        "label": "Min Genes",
-                        "name": "Input parameter",
+                        "label": "Hi-C forward",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "bottom": 503.75,
-                            "height": 64.25,
-                            "left": 16,
-                            "right": 216,
-                            "top": 439.5,
-                            "width": 200,
-                            "x": 16,
-                            "y": 439.5
+                            "left": 430,
+                            "top": 2600
                         },
                         "tool_id": null,
-                        "tool_state": "{\"default\": 100, \"parameter_type\": \"integer\", \"optional\": true}",
+                        "tool_state": "{\"optional\": false, \"format\": [\"fastq.gz\"], \"tag\": null, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "c9a62328-f049-43b6-92fb-df5c42982573",
+                        "type": "data_collection_input",
+                        "uuid": "2a65547b-b40d-4d99-9bd1-388460eb3faa",
+                        "when": null,
                         "workflow_outputs": []
-                    },
+                    }
+                ],
+                "license": "AGPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nMetadata file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nNCBI taxonomic ID\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nNCBI taxdump directory\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Collection\\nLong-read FASTQ files\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nPrimary genome assembly file fasta\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Parameter\\nPloidy for model to use\"];\n  style 5 fill:#ded,stroke:#393,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nDIAMOND database\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Collection\\nHi-C reverse\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Collection\\nHi-C forward\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"Meryl\"];\n  3 -->|output| 9;\n  10[\"Collapse Collection\"];\n  3 -->|output| 10;\n  11[\"Create BlobtoolKit\"];\n  4 -->|output| 11;\n  0 -->|output| 11;\n  2 -->|output| 11;\n  1 -->|output| 11;\n  12[\"gfastats\"];\n  4 -->|output| 12;\n  13[\"Convert compressed file to uncompressed.\"];\n  4 -->|output| 13;\n  14[\"gfastats\"];\n  4 -->|output| 14;\n  15[\"Diamond\"];\n  4 -->|output| 15;\n  6 -->|output| 15;\n  16[\"Collapse Collection\"];\n  7 -->|output| 16;\n  17[\"Collapse Collection\"];\n  8 -->|output| 17;\n  18[\"Meryl\"];\n  9 -->|read_db| 18;\n  19[\"Map with minimap2\"];\n  10 -->|output| 19;\n  4 -->|output| 19;\n  20[\"Smudgeplot\"];\n  10 -->|output| 20;\n  21[\"Replace\"];\n  13 -->|output1| 21;\n  22[\"Bandage Image\"];\n  14 -->|output| 22;\n  23[\"BWA-MEM2\"];\n  16 -->|output| 23;\n  4 -->|output| 23;\n  24[\"BWA-MEM2\"];\n  17 -->|output| 24;\n  4 -->|output| 24;\n  25[\"Merqury\"];\n  4 -->|output| 25;\n  18 -->|read_db| 25;\n  d2dbf498-5155-43b2-bf2a-ffed5c45100d[\"Output\\nMerqury on input dataset(s): stats\"];\n  25 --> d2dbf498-5155-43b2-bf2a-ffed5c45100d;\n  style d2dbf498-5155-43b2-bf2a-ffed5c45100d stroke:#2c3143,stroke-width:4px;\n  0b43d206-253f-4c0b-a1f4-971402851c6d[\"Output\\nMerqury on input dataset(s): plots\"];\n  25 --> 0b43d206-253f-4c0b-a1f4-971402851c6d;\n  style 0b43d206-253f-4c0b-a1f4-971402851c6d stroke:#2c3143,stroke-width:4px;\n  811a77e8-eb99-4dc7-9295-f0000fcb9fe5[\"Output\\nMerqury on input dataset(s): QV stats\"];\n  25 --> 811a77e8-eb99-4dc7-9295-f0000fcb9fe5;\n  style 811a77e8-eb99-4dc7-9295-f0000fcb9fe5 stroke:#2c3143,stroke-width:4px;\n  26[\"Meryl\"];\n  18 -->|read_db| 26;\n  27[\"Samtools stats\"];\n  19 -->|alignment_output| 27;\n  28[\"Busco\"];\n  21 -->|outfile| 28;\n  af98aae6-f1a3-493c-9cef-08e0926210d3[\"Output\\nBusco on input dataset(s): full table\"];\n  28 --> af98aae6-f1a3-493c-9cef-08e0926210d3;\n  style af98aae6-f1a3-493c-9cef-08e0926210d3 stroke:#2c3143,stroke-width:4px;\n  929439b7-c688-45ea-848a-97c13d3e0028[\"Output\\nBusco on input dataset(s): short summary\"];\n  28 --> 929439b7-c688-45ea-848a-97c13d3e0028;\n  style 929439b7-c688-45ea-848a-97c13d3e0028 stroke:#2c3143,stroke-width:4px;\n  29[\"Filter and merge\"];\n  24 -->|bam_output| 29;\n  23 -->|bam_output| 29;\n  30[\"Merqury plot 2\"];\n  25 -->|png_files| 30;\n  31[\"Merqury plot 1\"];\n  25 -->|png_files| 31;\n  32[\"Merqury plot 3\"];\n  25 -->|png_files| 32;\n  33[\"Merqury plot 5\"];\n  25 -->|png_files| 33;\n  34[\"Merqury plot 4\"];\n  25 -->|png_files| 34;\n  35[\"GenomeScope\"];\n  26 -->|read_db_hist| 35;\n  5 -->|output| 35;\n  36[\"BlobToolKit\"];\n  15 -->|blast_tabular| 36;\n  11 -->|blobdir| 36;\n  28 -->|busco_table| 36;\n  19 -->|alignment_output| 36;\n  37[\"PretextMap\"];\n  29 -->|outfile| 37;\n  38[\"BlobToolKit\"];\n  36 -->|blobdir| 38;\n  39[\"BlobToolKit\"];\n  36 -->|blobdir| 39;\n  40[\"BlobToolKit\"];\n  36 -->|blobdir| 40;\n  41[\"Pretext Snapshot\"];\n  37 -->|pretext_map_out| 41;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Post-assembly workflow",
+                "outputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 4,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Min Cells"
+                                "name": "NCBI taxonomic ID"
                             }
                         ],
-                        "label": "Min Cells",
+                        "label": "NCBI taxonomic ID",
                         "name": "Input parameter",
                         "outputs": [],
                         "position": {
-                            "bottom": 578.75,
-                            "height": 64.25,
-                            "left": 17,
-                            "right": 217,
-                            "top": 514.5,
-                            "width": 200,
-                            "x": 17,
-                            "y": 514.5
+                            "left": 707.9000006004667,
+                            "top": 123
                         },
                         "tool_id": null,
-                        "tool_state": "{\"default\": 2, \"parameter_type\": \"integer\", \"optional\": true}",
+                        "tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}",
                         "tool_version": null,
                         "type": "parameter_input",
-                        "uuid": "7bf5f0e1-b482-45c3-9bcb-10ca93e6b7dc",
-                        "workflow_outputs": []
+                        "uuid": "2ecb111b-eba8-497c-960c-4ba9c3717606",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "55a176c7-cffb-4f80-9ac4-e396051e30d7"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
@@ -173153,767 +173201,1767 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Max Features"
+                                "name": "Ploidy for model to use"
                             }
                         ],
-                        "label": "Max Features",
+                        "label": "Ploidy for model to use",
                         "name": "Input parameter",
                         "outputs": [],
                         "position": {
-                            "bottom": 671.5,
-                            "height": 84,
-                            "left": 23,
-                            "right": 223,
-                            "top": 587.5,
-                            "width": 200,
-                            "x": 23,
-                            "y": 587.5
+                            "left": 1287.9000006004667,
+                            "top": 1011
                         },
                         "tool_id": null,
-                        "tool_state": "{\"default\": 12000.0, \"parameter_type\": \"float\", \"optional\": true}",
+                        "tool_state": "{\"default\": 2, \"parameter_type\": \"integer\", \"optional\": true}",
                         "tool_version": null,
                         "type": "parameter_input",
-                        "uuid": "8902a917-75fb-49c6-9e5d-15f87bd91d46",
-                        "workflow_outputs": []
+                        "uuid": "bed1e2ca-2039-4f88-bd25-2646c6b5887d",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "8c56cbc1-c86f-4aef-b0b9-8ef1cde9c5b7"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.2.0+galaxy0",
                         "errors": null,
-                        "id": 6,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 12,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 4,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "gfastats",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Max Lib Size"
+                                "name": "stats",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "Max Lib Size",
-                        "name": "Input parameter",
-                        "outputs": [],
                         "position": {
-                            "bottom": 764.5,
-                            "height": 84,
-                            "left": 15,
-                            "right": 215,
-                            "top": 680.5,
-                            "width": 200,
-                            "x": 15,
-                            "y": 680.5
+                            "left": 997.9000006004667,
+                            "top": 1150
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": 120000.0, \"parameter_type\": \"float\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "db068cdb-53c4-48a3-95c2-141fa83c271b",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nLeiden Resolution\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSHR CSV.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nWT CSV.gz\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nMin Genes\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nMin Cells\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Parameter\\nMax Features\"];\n  style 5 fill:#ded,stroke:#393,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Parameter\\nMax Lib Size\"];\n  style 6 fill:#ded,stroke:#393,stroke-width:4px;\n  7[\"Import Anndata and loom\"];\n  1 -->|output| 7;\n  8[\"Import Anndata and loom\"];\n  2 -->|output| 8;\n  9[\"Manipulate AnnData\"];\n  7 -->|anndata| 9;\n  8 -->|anndata| 9;\n  10[\"Rename Batches\"];\n  9 -->|anndata| 10;\n  680180f6-edfc-4f66-b265-7a63aaa22b39[\"Output\\nscRNA Concatenated Datasets\"];\n  10 --> 680180f6-edfc-4f66-b265-7a63aaa22b39;\n  style 680180f6-edfc-4f66-b265-7a63aaa22b39 stroke:#2c3143,stroke-width:4px;\n  11[\"QC metrics\"];\n  10 -->|anndata| 11;\n  12[\"Filter genes\"];\n  11 -->|anndata_out| 12;\n  3 -->|output| 12;\n  13[\"Plot Violin\"];\n  11 -->|anndata_out| 13;\n  14[\"Filter Cells\"];\n  12 -->|anndata_out| 14;\n  4 -->|output| 14;\n  15[\"Filter Max Features\"];\n  14 -->|anndata_out| 15;\n  5 -->|output| 15;\n  16[\"Filter Max Library Size\"];\n  15 -->|anndata| 16;\n  6 -->|output| 16;\n  17[\"Save RAW\"];\n  16 -->|anndata| 17;\n  18[\"Norm to 1e4\"];\n  17 -->|anndata| 18;\n  19[\"Log1p\"];\n  18 -->|anndata_out| 19;\n  20[\"Regress total counts\"];\n  19 -->|anndata_out| 20;\n  21[\"Scale\"];\n  20 -->|anndata_out| 21;\n  22[\"PCA\"];\n  21 -->|anndata_out| 22;\n  23[\"Neighborhod\"];\n  22 -->|anndata_out| 23;\n  24[\"UMAP\"];\n  23 -->|anndata_out| 24;\n  25[\"Leiden\"];\n  24 -->|anndata_out| 25;\n  0 -->|output| 25;\n  48cf0465-84ba-461a-bdb9-61625626de42[\"Output\\nscRNA with clusters Dataset\"];\n  25 --> 48cf0465-84ba-461a-bdb9-61625626de42;\n  style 48cf0465-84ba-461a-bdb9-61625626de42 stroke:#2c3143,stroke-width:4px;\n  26[\"Plot PCA batch\"];\n  24 -->|anndata_out| 26;\n  27[\"Plot UMAP batch\"];\n  24 -->|anndata_out| 27;\n  28[\"Plot UMAP leiden, batch\"];\n  25 -->|anndata_out| 28;\n  29[\"Rename Clusters\"];\n  25 -->|anndata_out| 29;\n  30[\"Complex DotPlot\"];\n  25 -->|anndata_out| 30;\n  31[\"Complex DotPlot with new labels\"];\n  29 -->|anndata| 31;\n  32[\"Plot UMAP with new labels\"];\n  29 -->|anndata| 32;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "scRNA Plant Analysis",
-                "outputs": [
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.2.0+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "5799092ffdff",
+                            "name": "gfastats",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"assembly\", \"__current_case__\": 2, \"expected_genomesize\": null}, \"tabular\": true}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.0+galaxy0",
+                        "type": "tool",
+                        "uuid": "94888424-570c-4bd8-8fd0-32691fec5ceb",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "stats",
+                                "uuid": "e0521266-b734-41e6-98a4-bb89b12f6220"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy+2",
                         "errors": null,
-                        "id": 10,
+                        "id": 20,
                         "input_connections": {
-                            "input": {
-                                "id": 9,
-                                "output_name": "anndata"
+                            "file|input|reads": {
+                                "id": 10,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "Rename Batches",
-                        "name": "Manipulate AnnData",
+                        "label": null,
+                        "name": "Smudgeplot",
                         "outputs": [
                             {
-                                "name": "anndata",
-                                "type": "h5ad"
+                                "name": "smudgeplot",
+                                "type": "png"
+                            },
+                            {
+                                "name": "smudgeplot_log",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": 354.3999938964844,
-                            "height": 136.39999389648438,
-                            "left": 955,
-                            "right": 1155,
-                            "top": 218,
-                            "width": 200,
-                            "x": 955,
-                            "y": 218
+                            "left": 997.9000006004667,
+                            "top": 2319
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy+2",
                         "tool_shed_repository": {
-                            "changeset_revision": "8db95f488f0f",
-                            "name": "anndata_manipulate",
-                            "owner": "iuc",
+                            "changeset_revision": "5e0825476fb7",
+                            "name": "smudgeplot",
+                            "owner": "galaxy-australia",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"rename_categories\", \"__current_case__\": 3, \"key\": \"batch\", \"categories\": \"shr, wt\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.5+galaxy0",
+                        "tool_state": "{\"file\": {\"input\": {\"input_select\": \"reads\", \"__current_case__\": 0, \"reads\": {\"__class__\": \"ConnectedValue\"}, \"mer_len\": \"21\", \"lower_cutoff\": null, \"upper_cutoff\": null}}, \"homozygous\": false, \"table_output\": false, \"verbose_output\": false, \"warnings_output\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.2.5+galaxy+2",
                         "type": "tool",
-                        "uuid": "0a25ffc3-ac58-4c17-9f22-b4127952027a",
+                        "uuid": "2de39e7c-bdfd-4918-8d52-baf5f67f5522",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "scRNA Concatenated Datasets",
-                                "output_name": "anndata",
-                                "uuid": "680180f6-edfc-4f66-b265-7a63aaa22b39"
+                                "label": null,
+                                "output_name": "smudgeplot_log",
+                                "uuid": "a6e4bae9-63de-4258-b429-6a6b9a46d7cf"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "smudgeplot",
+                                "uuid": "150d5e72-b06c-4556-915a-d23d410f5aa0"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
                         "errors": null,
-                        "id": 13,
+                        "id": 22,
                         "input_connections": {
-                            "adata": {
-                                "id": 11,
-                                "output_name": "anndata_out"
+                            "input_file": {
+                                "id": 14,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "Plot Violin",
-                        "name": "Plot",
+                        "label": null,
+                        "name": "Bandage Image",
                         "outputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "name": "outfile",
+                                "type": "jpg"
                             }
                         ],
                         "position": {
-                            "bottom": 259.8000030517578,
-                            "height": 116.65000915527344,
-                            "left": 1867.2833251953125,
-                            "right": 2067.2833251953125,
-                            "top": 143.14999389648438,
-                            "width": 200,
-                            "x": 1867.2833251953125,
-                            "y": 143.14999389648438
+                            "left": 1287.9000006004667,
+                            "top": 1499
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
                         "tool_shed_repository": {
-                            "changeset_revision": "6adf98e782f3",
-                            "name": "scanpy_plot",
+                            "changeset_revision": "ddddce450736",
+                            "name": "bandage",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"n_genes_by_counts, total_counts\"}, \"groupby\": \"batch\", \"log\": \"false\", \"use_raw\": \"false\", \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"0.4\"}}, \"multi_panel\": {\"multi_panel\": \"True\", \"__current_case__\": 0, \"width\": null, \"height\": null}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy0",
+                        "tool_state": "{\"fontsize\": null, \"height\": \"1000\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"lengths\": false, \"names\": false, \"nodewidth\": null, \"output_format\": \"jpg\", \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2022.09+galaxy4",
                         "type": "tool",
-                        "uuid": "9dfc1e59-71aa-40b8-b504-2498a8dc5409",
+                        "uuid": "255d0a7d-e006-4392-99db-c313b0154572",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_png",
-                                "uuid": "2fb1d919-0e60-4c81-92d2-83c28b1ef654"
+                                "output_name": "outfile",
+                                "uuid": "1483321a-d6af-498f-9873-6280c6057cb3"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
                         "errors": null,
                         "id": 25,
                         "input_connections": {
-                            "adata": {
-                                "id": 24,
-                                "output_name": "anndata_out"
-                            },
-                            "method|resolution": {
-                                "id": 0,
+                            "mode|assembly_options|assembly_01": {
+                                "id": 4,
                                 "output_name": "output"
+                            },
+                            "mode|meryldb_F1": {
+                                "id": 18,
+                                "output_name": "read_db"
                             }
                         },
-                        "inputs": [],
-                        "label": "Leiden",
-                        "name": "Cluster, infer trajectories and embed",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Merqury",
+                                "name": "mode"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Merqury",
                         "outputs": [
                             {
-                                "name": "anndata_out",
-                                "type": "h5ad"
+                                "name": "qv_files",
+                                "type": "input"
+                            },
+                            {
+                                "name": "png_files",
+                                "type": "input"
+                            },
+                            {
+                                "name": "stats_files",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 562.0500030517578,
-                            "height": 147.0500030517578,
-                            "left": 1389,
-                            "right": 1589,
-                            "top": 415,
-                            "width": 200,
-                            "x": 1389,
-                            "y": 415
+                            "left": 1287.9000006004667,
+                            "top": 581
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "35bc2eb568ed",
-                            "name": "scanpy_cluster_reduce_dimension",
+                            "changeset_revision": "f8113c25bc6b",
+                            "name": "merqury",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"method\": {\"method\": \"tl.leiden\", \"__current_case__\": 1, \"resolution\": {\"__class__\": \"ConnectedValue\"}, \"random_state\": \"0\", \"key_added\": \"leiden\", \"use_weights\": \"false\", \"n_iterations\": \"-1\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy0",
+                        "tool_state": "{\"label\": \"output_merqury\", \"mode\": {\"options\": \"default\", \"__current_case__\": 0, \"meryldb_F1\": {\"__class__\": \"ConnectedValue\"}, \"assembly_options\": {\"number_assemblies\": \"one\", \"__current_case__\": 0, \"assembly_01\": {\"__class__\": \"ConnectedValue\"}}}, \"output_add_headers\": false, \"output_selector\": [\"qv\", \"plots\", \"stats\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3+galaxy2",
                         "type": "tool",
-                        "uuid": "99494ea7-377c-4f3d-a45a-18bfd81b7888",
+                        "uuid": "72f5cbe8-5d1c-4d0b-942e-ed18718ca39a",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "scRNA with clusters Dataset",
-                                "output_name": "anndata_out",
-                                "uuid": "48cf0465-84ba-461a-bdb9-61625626de42"
+                                "label": "Merqury on input dataset(s): stats",
+                                "output_name": "stats_files",
+                                "uuid": "d2dbf498-5155-43b2-bf2a-ffed5c45100d"
+                            },
+                            {
+                                "label": "Merqury on input dataset(s): plots",
+                                "output_name": "png_files",
+                                "uuid": "0b43d206-253f-4c0b-a1f4-971402851c6d"
+                            },
+                            {
+                                "label": "Merqury on input dataset(s): QV stats",
+                                "output_name": "qv_files",
+                                "uuid": "811a77e8-eb99-4dc7-9295-f0000fcb9fe5"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4",
                         "errors": null,
-                        "id": 26,
+                        "id": 27,
                         "input_connections": {
-                            "adata": {
-                                "id": 24,
-                                "output_name": "anndata_out"
+                            "input": {
+                                "id": 19,
+                                "output_name": "alignment_output"
                             }
                         },
                         "inputs": [],
-                        "label": "Plot PCA (batch)",
-                        "name": "Plot",
+                        "label": null,
+                        "name": "Samtools stats",
                         "outputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 277.5500030517578,
-                            "height": 136.40000915527344,
-                            "left": 1629.433349609375,
-                            "right": 1829.433349609375,
-                            "top": 141.14999389648438,
-                            "width": 200,
-                            "x": 1629.433349609375,
-                            "y": 141.14999389648438
+                            "left": 1507.0317775869937,
+                            "top": 1886.4967353214358
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4",
                         "tool_shed_repository": {
-                            "changeset_revision": "6adf98e782f3",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
+                            "changeset_revision": "3a0efe14891f",
+                            "name": "samtools_stats",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.pca\", \"__current_case__\": 9, \"color\": \"batch\", \"use_raw\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy0",
+                        "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cov_threshold\": null, \"coverage_cond\": {\"coverage_select\": \"no\", \"__current_case__\": 0}, \"filter_by_flags\": {\"filter_flags\": \"nofilter\", \"__current_case__\": 1}, \"gc_depth\": null, \"input\": {\"__class__\": \"ConnectedValue\"}, \"insert_size\": null, \"most_inserts\": null, \"read_group\": null, \"read_length\": null, \"remove_dups\": false, \"remove_overlaps\": false, \"sparse\": false, \"split_output_cond\": {\"split_output_selector\": \"no\", \"__current_case__\": 0}, \"trim_quality\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.4",
                         "type": "tool",
-                        "uuid": "e2daa4c6-9a39-4c42-852e-4f61b65202c2",
+                        "uuid": "c5d1a111-ba0d-4299-8d29-643377acfe3e",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_png",
-                                "uuid": "72d1a264-3ace-4d2e-910a-5e2a0fa6721f"
+                                "output_name": "output",
+                                "uuid": "fbad75d5-c42f-4368-a8dd-45eafcc2f42e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.4+galaxy0",
                         "errors": null,
-                        "id": 27,
+                        "id": 28,
                         "input_connections": {
-                            "adata": {
-                                "id": 24,
-                                "output_name": "anndata_out"
+                            "input": {
+                                "id": 21,
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
-                        "label": "Plot UMAP (batch)",
-                        "name": "Plot",
+                        "label": null,
+                        "name": "Busco",
                         "outputs": [
                             {
-                                "name": "out_png",
+                                "name": "busco_sum",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "busco_table",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 1567.9000006004667,
+                            "top": 1293
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.4+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "bb935709506a",
+                            "name": "busco",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"auto_detect\", \"__current_case__\": 0, \"auto_lineage\": \"--auto-lineage\"}, \"outputs\": [\"short_summary\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.4.4+galaxy0",
+                        "type": "tool",
+                        "uuid": "8f354503-9332-4dc2-8e7e-2ec42adab839",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Busco on input dataset(s): full table",
+                                "output_name": "busco_table",
+                                "uuid": "af98aae6-f1a3-493c-9cef-08e0926210d3"
+                            },
+                            {
+                                "label": "Busco on input dataset(s): short summary",
+                                "output_name": "busco_sum",
+                                "uuid": "929439b7-c688-45ea-848a-97c13d3e0028"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
+                        "errors": null,
+                        "id": 35,
+                        "input_connections": {
+                            "input": {
+                                "id": 26,
+                                "output_name": "read_db_hist"
+                            },
+                            "ploidy": {
+                                "id": 5,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "GenomeScope",
+                        "outputs": [
+                            {
+                                "name": "linear_plot",
+                                "type": "png"
+                            },
+                            {
+                                "name": "log_plot",
+                                "type": "png"
+                            },
+                            {
+                                "name": "transformed_linear_plot",
+                                "type": "png"
+                            },
+                            {
+                                "name": "transformed_log_plot",
                                 "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": 406.3999938964844,
-                            "height": 136.39999389648438,
-                            "left": 1862,
-                            "right": 2062,
-                            "top": 270,
-                            "width": 200,
-                            "x": 1862,
-                            "y": 270
+                            "left": 1567.9000006004667,
+                            "top": 977
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "6adf98e782f3",
-                            "name": "scanpy_plot",
+                            "changeset_revision": "01210c4e9144",
+                            "name": "genomescope",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"batch\", \"use_raw\": \"false\", \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": \"14\", \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy0",
+                        "tool_state": "{\"advanced_options\": {\"topology\": null, \"initial_repetitiveness\": null, \"initial_heterozygosities\": \"\", \"transform_exp\": null, \"testing\": false, \"true_params\": \"\", \"trace_flag\": false, \"num_rounds\": null}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"kmer_length\": \"21\", \"lambda\": null, \"max_kmercov\": null, \"output_options\": {\"output_files\": null, \"no_unique_sequence\": false}, \"ploidy\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0+galaxy2",
                         "type": "tool",
-                        "uuid": "e70d8e14-1983-4381-8feb-bba7d5dbb4d6",
+                        "uuid": "fc99955a-fa06-415a-9073-973432021b09",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_png",
-                                "uuid": "c223e762-7e90-41e1-b354-bbe6e278b5c0"
+                                "output_name": "transformed_linear_plot",
+                                "uuid": "e90780ce-d82c-4cd5-8d10-c8702c7fa312"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "log_plot",
+                                "uuid": "deebd887-e5f3-434b-80c8-b3978c7e5c47"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "linear_plot",
+                                "uuid": "0f6ee759-0f6e-4d66-9426-dc0b6349d16d"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "transformed_log_plot",
+                                "uuid": "b6ba52b5-bbd0-4764-abf9-e8c11b3ce327"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
                         "errors": null,
-                        "id": 28,
+                        "id": 41,
                         "input_connections": {
-                            "adata": {
-                                "id": 25,
-                                "output_name": "anndata_out"
+                            "input": {
+                                "id": 37,
+                                "output_name": "pretext_map_out"
                             }
                         },
                         "inputs": [],
-                        "label": "Plot UMAP (leiden, batch)",
-                        "name": "Plot",
+                        "label": null,
+                        "name": "Pretext Snapshot",
                         "outputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "name": "pretext_snap_out",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 442.5500030517578,
-                            "height": 136.40000915527344,
-                            "left": 1630.433349609375,
-                            "right": 1830.433349609375,
-                            "top": 306.1499938964844,
-                            "width": 200,
-                            "x": 1630.433349609375,
-                            "y": 306.1499938964844
+                            "left": 1857.9000006004667,
+                            "top": 2162
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "6adf98e782f3",
-                            "name": "scanpy_plot",
+                            "changeset_revision": "44c66e8d21e6",
+                            "name": "pretext_snapshot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"leiden, batch\", \"use_raw\": \"false\", \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": \"14\", \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy0",
+                        "tool_state": "{\"colormap\": \"5\", \"formats\": {\"outformat\": \"png\", \"__current_case__\": 0}, \"grid\": {\"showGrid\": true, \"__current_case__\": 0, \"gridsize\": \"1\", \"gridcolor\": \"black\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mintexels\": \"64\", \"resolution\": \"1000\", \"sequencenames\": false, \"sequences\": \"=full, =all\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.0.3+galaxy1",
                         "type": "tool",
-                        "uuid": "b88358ff-0dda-4c2e-bce6-124a0ab8fa28",
+                        "uuid": "414d726e-7a86-4c9e-a8b0-3d6afc9ec374",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_png",
-                                "uuid": "26c65cd9-74aa-4574-a5f3-ac10caced4da"
+                                "output_name": "pretext_snap_out",
+                                "uuid": "16969c99-f550-4bff-8df6-98b1fecd3b00"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "assembly/ERGA-post-assembly-QC",
+                "path": "topics/assembly/tutorials/ERGA-post-assembly-QC/workflows/main_workflow.ga",
+                "tags": [
+                    "ReferenceGenome",
+                    "name:ERGA"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "Post-assembly workflow",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-ERGA-post-assembly-QC/versions/main-workflow",
+                "tutorial_id": "ERGA-post-assembly-QC",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/ERGA-post-assembly-QC/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/ERGA-post-assembly-QC/workflows/main_workflow.html",
+                "version": 2,
+                "wfid": "assembly-ERGA-post-assembly-QC",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "CONVERTER_gz_to_uncompressed",
+                    "__EXTRACT_DATASET__",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/blobtoolkit/blobtoolkit/4.0.7+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.2.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.4",
+                    "toolshed.g2.bx.psu.edu/repos/galaxy-australia/smudgeplot/smudgeplot/0.2.5+galaxy+2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
+                ],
+                "workflowhub_id": "1127"
+            }
+        ]
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "flye",
+                    "owner": "bgruening",
+                    "revisions": "291923e6f276",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "racon",
+                    "owner": "bgruening",
+                    "revisions": "78c533842eeb",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "5ec9f6bceaee",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bandage",
+                    "owner": "iuc",
+                    "revisions": "ddddce450736",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "busco",
+                    "owner": "iuc",
+                    "revisions": "ea8146ee148f",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_stats",
+                    "owner": "iuc",
+                    "revisions": "0dbb995c7d35",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastp",
+                    "owner": "iuc",
+                    "revisions": "c59d48774d03",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "genomescope",
+                    "owner": "iuc",
+                    "revisions": "01210c4e9144",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "medaka_consensus_pipeline",
+                    "owner": "iuc",
+                    "revisions": "fc8804320156",
+                    "tool_panel_section_label": "Nanopore",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "meryl",
+                    "owner": "iuc",
+                    "revisions": "29dabd8db6f2",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "minimap2",
+                    "owner": "iuc",
+                    "revisions": "be1d967337e4",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "abfd8a6544d7",
+                    "tool_panel_section_label": "Quality Control",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "nanoplot",
+                    "owner": "iuc",
+                    "revisions": "a02b8b3f5a0c",
+                    "tool_panel_section_label": "Nanopore",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "quast",
+                    "owner": "iuc",
+                    "revisions": "72472698a2df",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: flye\n  owner: bgruening\n  revisions: 291923e6f276\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: racon\n  owner: bgruening\n  revisions: 78c533842eeb\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: ea8146ee148f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_stats\n  owner: iuc\n  revisions: 0dbb995c7d35\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: c59d48774d03\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: genomescope\n  owner: iuc\n  revisions: 01210c4e9144\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: medaka_consensus_pipeline\n  owner: iuc\n  revisions: fc8804320156\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n  owner: iuc\n  revisions: 29dabd8db6f2\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: be1d967337e4\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: abfd8a6544d7\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: a02b8b3f5a0c\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: quast\n  owner: iuc\n  revisions: 72472698a2df\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/largegenome/tutorial.json",
+        "contributors": [
+            {
+                "id": "annasyme",
+                "joined": "2017-09",
+                "name": "Anna Syme",
+                "orcid": "0000-0002-9906-0673",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annasyme/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/annasyme.json"
+            }
+        ],
+        "dir": "topics/assembly/tutorials/largegenome",
+        "edam_operation": [
+            "Scatter plot plotting",
+            "Visualisation",
+            "Cross-assembly",
+            "Sequencing quality control",
+            "Genome assembly",
+            "Box-Whisker plot plotting",
+            "Sequence assembly validation",
+            "Mapping assembly",
+            "Base-calling",
+            "Statistical calculation",
+            "Pairwise sequence alignment",
+            "Validation",
+            "Sequence composition calculation",
+            "De-novo assembly",
+            "Sequence contamination filtering",
+            "Sequence assembly",
+            "Variant calling",
+            "Scaffolding",
+            "Sequence assembly visualisation",
+            "Transcriptome assembly"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "assembly/largegenome",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "We can assemble long reads from plant or animal species into large contigs",
+            "These contigs can be polished with both long and short reads",
+            "We can assess the quality of this assembly with various tools"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-07-31",
+        "objectives": [
+            "Assemble a large genome from long reads",
+            "Polish the assembly",
+            "Assess the quality of the assembly"
+        ],
+        "pageviews": 5225,
+        "pub_date": "2023-03-06",
+        "questions": [
+            "How can we assemble a large plant or animal genome?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "annasyme"
+                ],
+                "date": "2023-05-16",
+                "galaxy_version": "23.01",
+                "length": "25M",
+                "speakers": [
+                    "annasyme"
+                ],
+                "youtube_id": "BM70nvwWjOY"
+            }
+        ],
+        "short_id": "T00331",
+        "short_tools": [
+            "genomescope",
+            "fastp",
+            "minimap2",
+            "bandage_image",
+            "barchart_gnuplot",
+            "busco",
+            "racon",
+            "fasta-stats",
+            "quast",
+            "multiqc",
+            "flye",
+            "nanoplot",
+            "medaka_consensus_pipeline",
+            "fastqc",
+            "meryl"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "assembly",
+            "polishing",
+            "nanopore",
+            "plants"
+        ],
+        "time_estimation": "2h",
+        "title": "Large genome assembly and polishing",
+        "tools": [
+            "barchart_gnuplot",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+            "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
+        ],
+        "topic_name": "assembly",
+        "topic_name_human": "Assembly",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "largegenome",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/assembly/tutorials/largegenome/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/largegenome/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/largegenome/tutorial.json"
+        },
+        "version": 11,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 127,
+        "visitors": 4015,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": true,
+                    "report": {
+                        "markdown": "\n# Workflow Report for Assembly Polishing\n\n## Workflow steps\n\n```galaxy\nworkflow_display()\n```\n\n## Fasta statistics after Racon long-read polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Racon long read polish\")\n```\n\n\n## Fasta statistics after Medaka polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Medaka polish\")\n```\n\n## Fasta statistics after Racon short-read polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Racon short read polish\")\n```\n\n\n\n\n"
+                    },
+                    "subworkflows": true
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"]\n  4[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with long reads, x4 - upgraded\"]\n  0 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Medaka polish\"]\n  4 -> 5 [label=\"Assembly polished by long reads using Racon\"]\n  1 -> 5 [label=\"output\"]\n  ke3136060bce74af387c49dcbb0d1f531[color=lightseagreen,label=\"Output\\nAssembly polished by long reads using Medaka\"]\n  5 -> ke3136060bce74af387c49dcbb0d1f531\n  6[label=\"Fasta statistics after Racon long read polish\"]\n  4 -> 6 [label=\"Assembly polished by long reads using Racon\"]\n  7[label=\"Fasta statistics after Medaka polish\"]\n  5 -> 7 [label=\"out_consensus\"]\n  8[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with Illumina reads R1 only, x2 - upgraded\"]\n  5 -> 8 [label=\"out_consensus\"]\n  3 -> 8 [label=\"output\"]\n  9[label=\"Fasta statistics after Racon short read polish\"]\n  8 -> 9 [label=\"Assembly polished by short reads using Racon\"]\n}",
+                "history": [
+                    {
+                        "hash": "091a0834c77e69841f4d07570420c632c6c5043c",
+                        "message": "Update Galaxy-Workflow-Assembly_polishing.ga",
+                        "num": 5,
+                        "short_hash": "091a0834c",
+                        "unix": "1715074278"
+                    },
+                    {
+                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
+                        "message": "new versions of workflows",
+                        "num": 4,
+                        "short_hash": "e8ddbcdd5",
+                        "unix": "1714537936"
+                    },
+                    {
+                        "hash": "f294a05b57afbe9ec436008d1d2571f6d42fb977",
+                        "message": "Rename Galaxy-Workflow-Assembly_polishing.ga to Galaxy-Workflow-Assembly_polishing_old.ga",
+                        "num": 3,
+                        "short_hash": "f294a05b5",
+                        "unix": "1714537220"
+                    },
+                    {
+                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
+                        "message": "add/complete creator info on workflows",
+                        "num": 2,
+                        "short_hash": "62e77944b",
+                        "unix": "1676627603"
+                    },
+                    {
+                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
+                        "message": "large genome tutorial",
+                        "num": 1,
+                        "short_hash": "9fcb3aeec",
+                        "unix": "1665123856"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Assembly to be polished"
+                            }
+                        ],
+                        "label": "Assembly to be polished",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 19.464939294568495,
+                            "top": 0.0
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "52bc9ac4-ac3c-48eb-aead-94a0a14417fc",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "long reads"
+                            }
+                        ],
+                        "label": "long reads",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0.0,
+                            "top": 142.48340578478533
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "688866c4-de9b-4b78-8df3-b169d28b1617",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "minimap setting (for long reads)"
+                            }
+                        ],
+                        "label": "minimap setting (for long reads)",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 13.133522093825794,
+                            "top": 247.1519749531627
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "c1f18b5c-e8db-4046-b876-9b28a77cf66e",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "ce393bcf-42e3-43ee-9056-a99e8c077a29"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Illumina reads R1"
+                            }
+                        ],
+                        "label": "Illumina reads R1",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 617.719019724734,
+                            "top": 600.0866464299372
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ea859a58-c81a-4ef6-9bd2-4ef2f17bb5a9",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with long reads, x4 - upgraded\"];\n  style 4 fill:#edd,stroke:#900,stroke-width:4px;\n  0 -->|output| 4;\n  1 -->|output| 4;\n  2 -->|output| 4;\n  5[\"Medaka polish\"];\n  4 -->|Assembly polished by long reads using Racon| 5;\n  1 -->|output| 5;\n  e3136060-bce7-4af3-87c4-9dcbb0d1f531[\"Output\\nAssembly polished by long reads using Medaka\"];\n  5 --> e3136060-bce7-4af3-87c4-9dcbb0d1f531;\n  style e3136060-bce7-4af3-87c4-9dcbb0d1f531 stroke:#2c3143,stroke-width:4px;\n  6[\"Fasta statistics after Racon long read polish\"];\n  4 -->|Assembly polished by long reads using Racon| 6;\n  7[\"Fasta statistics after Medaka polish\"];\n  5 -->|out_consensus| 7;\n  8[\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with Illumina reads R1 only, x2 - upgraded\"];\n  style 8 fill:#edd,stroke:#900,stroke-width:4px;\n  5 -->|out_consensus| 8;\n  3 -->|output| 8;\n  9[\"Fasta statistics after Racon short read polish\"];\n  8 -->|Assembly polished by short reads using Racon| 9;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Assembly polishing - upgraded",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
                         "errors": null,
-                        "id": 30,
-                        "input_connections": {
-                            "adata": {
-                                "id": 25,
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Complex DotPlot",
-                        "name": "Plot",
-                        "outputs": [
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "description": "",
+                                "name": "minimap setting (for long reads)"
                             }
                         ],
+                        "label": "minimap setting (for long reads)",
+                        "name": "Input parameter",
+                        "outputs": [],
                         "position": {
-                            "bottom": 557.3999938964844,
-                            "height": 136.39999389648438,
-                            "left": 1861,
-                            "right": 2061,
-                            "top": 421,
-                            "width": 200,
-                            "x": 1861,
-                            "y": 421
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6adf98e782f3",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 13.133522093825794,
+                            "top": 247.1519749531627
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.dotplot\", \"__current_case__\": 2, \"var_names\": {\"type\": \"custom\", \"__current_case__\": 1, \"var_names\": \"AT1G26680,COBL2,AT3G55180,NCED2,AT5G22550,ATL63,RGF8,TEL1,DUF9,AGL42,PLT1,PLT2,PER3,PER9,PBL15,TBL30,AT2G48130,AT3G22620,AED3,T3P18-7,MBK21-8,NPF6-4,CYP71B34,IAMT1,AT1G31950,F14G6-22,GL2,ANL2,PMEI4,MUD21-4,EXPA7,MES15,ADF8,COBL9,TPR14,BHLH144,MYB83,SCPL35,MYB46,COBL4,PIN7,PIN3   \"}, \"groupby\": \"leiden\", \"num_categories\": \"9\", \"log\": \"false\", \"use_raw\": \"true\", \"dendrogram\": \"false\", \"var_group_positions\": [{\"__index__\": 0, \"start\": \"0\", \"end\": \"5\", \"label\": \"Columella\"}, {\"__index__\": 1, \"start\": \"6\", \"end\": \"9\", \"label\": \"QC\"}, {\"__index__\": 2, \"start\": \"10\", \"end\": \"11\", \"label\": \"NC\"}, {\"__index__\": 3, \"start\": \"12\", \"end\": \"17\", \"label\": \"Endodermis\"}, {\"__index__\": 4, \"start\": \"18\", \"end\": \"23\", \"label\": \"Cortex\"}, {\"__index__\": 5, \"start\": \"24\", \"end\": \"29\", \"label\": \"Atrichoblast\"}, {\"__index__\": 6, \"start\": \"30\", \"end\": \"34\", \"label\": \"Trichoblast\"}, {\"__index__\": 7, \"start\": \"35\", \"end\": \"39\", \"label\": \"Xylem\"}, {\"__index__\": 8, \"start\": \"40\", \"end\": \"41\", \"label\": \"VC\"}], \"var_group_rotation\": null, \"figsize\": {\"test\": \"no\", \"__current_case__\": 1}, \"layer\": \"\", \"color_map\": \"viridis\", \"dot_max\": null, \"dot_min\": null, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "625a157f-f08f-4137-a27b-721bee0feb59",
+                        "tool_id": null,
+                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "c1f18b5c-e8db-4046-b876-9b28a77cf66e",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_png",
-                                "uuid": "b35ffb5a-5f29-4105-a016-c02ceee0d9da"
+                                "output_name": "output",
+                                "uuid": "ce393bcf-42e3-43ee-9056-a99e8c077a29"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
-                        "errors": null,
-                        "id": 31,
+                        "id": 4,
                         "input_connections": {
-                            "adata": {
-                                "id": 29,
-                                "output_name": "anndata"
+                            "Assembly to be polished": {
+                                "id": 0,
+                                "input_subworkflow_step_id": 0,
+                                "output_name": "output"
+                            },
+                            "long reads": {
+                                "id": 1,
+                                "input_subworkflow_step_id": 1,
+                                "output_name": "output"
+                            },
+                            "minimap setting (for long reads) ": {
+                                "id": 2,
+                                "input_subworkflow_step_id": 2,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "Complex DotPlot with new labels",
-                        "name": "Plot",
-                        "outputs": [
-                            {
-                                "name": "out_png",
-                                "type": "png"
-                            }
-                        ],
+                        "label": null,
+                        "name": "Racon polish with long reads, x4 - upgraded",
+                        "outputs": [],
                         "position": {
-                            "bottom": 733.4666748046875,
-                            "height": 156.79998779296875,
-                            "left": 1860.449951171875,
-                            "right": 2060.449951171875,
-                            "top": 576.6666870117188,
-                            "width": 200,
-                            "x": 1860.449951171875,
-                            "y": 576.6666870117188
+                            "left": 299.6429464825318,
+                            "top": 72.0364210406818
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6adf98e782f3",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        "subworkflow": {
+                            "a_galaxy_workflow": "true",
+                            "annotation": "",
+                            "comments": [],
+                            "creator": [
+                                {
+                                    "class": "Person",
+                                    "identifier": "0000-0002-9906-0673",
+                                    "name": "Anna Syme"
+                                }
+                            ],
+                            "format-version": "0.1",
+                            "name": "Racon polish with long reads, x4 - upgraded",
+                            "report": {
+                                "markdown": "\n# Workflow Execution Report\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                            },
+                            "steps": {
+                                "0": {
+                                    "annotation": "",
+                                    "content_id": null,
+                                    "errors": null,
+                                    "id": 0,
+                                    "input_connections": {},
+                                    "inputs": [
+                                        {
+                                            "description": "",
+                                            "name": "Assembly to be polished"
+                                        }
+                                    ],
+                                    "label": "Assembly to be polished",
+                                    "name": "Input dataset",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 0,
+                                        "top": 216.625
+                                    },
+                                    "tool_id": null,
+                                    "tool_state": "{\"optional\": false, \"tag\": null}",
+                                    "tool_version": null,
+                                    "type": "data_input",
+                                    "uuid": "c7796c36-adf8-49e4-a8e4-66e606d70311",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "1": {
+                                    "annotation": "",
+                                    "content_id": null,
+                                    "errors": null,
+                                    "id": 1,
+                                    "input_connections": {},
+                                    "inputs": [
+                                        {
+                                            "description": "",
+                                            "name": "long reads"
+                                        }
+                                    ],
+                                    "label": "long reads",
+                                    "name": "Input dataset",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 4.5,
+                                        "top": 360.234375
+                                    },
+                                    "tool_id": null,
+                                    "tool_state": "{\"optional\": false, \"tag\": null}",
+                                    "tool_version": null,
+                                    "type": "data_input",
+                                    "uuid": "e2e4a70b-6e36-4b8b-bdf6-12b97189a6bd",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "10": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                    "errors": null,
+                                    "id": 10,
+                                    "input_connections": {
+                                        "corrected_reads": {
+                                            "id": 8,
+                                            "output_name": "consensus"
+                                        },
+                                        "overlaps": {
+                                            "id": 9,
+                                            "output_name": "alignment_output"
+                                        },
+                                        "reads": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Racon: polish 4",
+                                    "name": "Racon",
+                                    "outputs": [
+                                        {
+                                            "name": "consensus",
+                                            "type": "fasta"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 1496.078125,
+                                        "top": 431.1875
+                                    },
+                                    "post_job_actions": {
+                                        "RenameDatasetActionconsensus": {
+                                            "action_arguments": {
+                                                "newname": "Racon_long_reads_polished_assembly.fasta"
+                                            },
+                                            "action_type": "RenameDatasetAction",
+                                            "output_name": "consensus"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "78c533842eeb",
+                                        "name": "racon",
+                                        "owner": "bgruening",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "1.5.0+galaxy1",
+                                    "type": "tool",
+                                    "uuid": "53f4572e-3a4a-4585-89ab-9459f8a61720",
+                                    "when": null,
+                                    "workflow_outputs": [
+                                        {
+                                            "label": "Assembly polished by long reads using Racon",
+                                            "output_name": "consensus",
+                                            "uuid": "bcf0f03c-5951-46a7-aa38-545aed9bc183"
+                                        }
+                                    ]
+                                },
+                                "2": {
+                                    "annotation": "",
+                                    "content_id": null,
+                                    "errors": null,
+                                    "id": 2,
+                                    "input_connections": {},
+                                    "inputs": [
+                                        {
+                                            "description": "",
+                                            "name": "minimap setting (for long reads) "
+                                        }
+                                    ],
+                                    "label": "minimap setting (for long reads) ",
+                                    "name": "Input parameter",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 0.578125,
+                                        "top": 495.859375
+                                    },
+                                    "tool_id": null,
+                                    "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                                    "tool_version": null,
+                                    "type": "parameter_input",
+                                    "uuid": "fb80c05c-08d4-4ac2-b4bf-81ed906e4d72",
+                                    "when": null,
+                                    "workflow_outputs": [
+                                        {
+                                            "label": null,
+                                            "output_name": "output",
+                                            "uuid": "3983ef22-5f05-4384-8f34-6ac8c4b2cc83"
+                                        }
+                                    ]
+                                },
+                                "3": {
+                                    "annotation": "Map raw reads to assembly; output paf",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                    "errors": null,
+                                    "id": 3,
+                                    "input_connections": {
+                                        "fastq_input|analysis_type_selector": {
+                                            "id": 2,
+                                            "output_name": "output"
+                                        },
+                                        "fastq_input|fastq_input1": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        },
+                                        "reference_source|ref_file": {
+                                            "id": 0,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "fastq_input"
+                                        },
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "fastq_input"
+                                        },
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "reference_source"
+                                        }
+                                    ],
+                                    "label": "Minimap2: map long reads to assembly",
+                                    "name": "Map with minimap2",
+                                    "outputs": [
+                                        {
+                                            "name": "alignment_output",
+                                            "type": "bam"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 377.640625,
+                                        "top": 0
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionalignment_output": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "alignment_output"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "be1d967337e4",
+                                        "name": "minimap2",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "2.26+galaxy0",
+                                    "type": "tool",
+                                    "uuid": "0c06144f-d1ac-4b45-9669-1ddf11fcb06b",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "4": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                    "errors": null,
+                                    "id": 4,
+                                    "input_connections": {
+                                        "corrected_reads": {
+                                            "id": 0,
+                                            "output_name": "output"
+                                        },
+                                        "overlaps": {
+                                            "id": 3,
+                                            "output_name": "alignment_output"
+                                        },
+                                        "reads": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Racon: polish 1",
+                                    "name": "Racon",
+                                    "outputs": [
+                                        {
+                                            "name": "consensus",
+                                            "type": "fasta"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 458.640625,
+                                        "top": 518.875
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionconsensus": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "consensus"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "78c533842eeb",
+                                        "name": "racon",
+                                        "owner": "bgruening",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "1.5.0+galaxy1",
+                                    "type": "tool",
+                                    "uuid": "6c144354-91f2-49dd-a1f5-7c4119859730",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "5": {
+                                    "annotation": "Map raw reads to assembly; output paf",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                    "errors": null,
+                                    "id": 5,
+                                    "input_connections": {
+                                        "fastq_input|analysis_type_selector": {
+                                            "id": 2,
+                                            "output_name": "output"
+                                        },
+                                        "fastq_input|fastq_input1": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        },
+                                        "reference_source|ref_file": {
+                                            "id": 4,
+                                            "output_name": "consensus"
+                                        }
+                                    },
+                                    "inputs": [
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "fastq_input"
+                                        },
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "fastq_input"
+                                        },
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "reference_source"
+                                        }
+                                    ],
+                                    "label": "Minimap2: map long reads to polished assembly 1",
+                                    "name": "Map with minimap2",
+                                    "outputs": [
+                                        {
+                                            "name": "alignment_output",
+                                            "type": "bam"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 698.859375,
+                                        "top": 13.390625
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionalignment_output": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "alignment_output"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "be1d967337e4",
+                                        "name": "minimap2",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "2.26+galaxy0",
+                                    "type": "tool",
+                                    "uuid": "c1b83dad-a8ed-42cb-951f-73f59f2dfa92",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "6": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                    "errors": null,
+                                    "id": 6,
+                                    "input_connections": {
+                                        "corrected_reads": {
+                                            "id": 4,
+                                            "output_name": "consensus"
+                                        },
+                                        "overlaps": {
+                                            "id": 5,
+                                            "output_name": "alignment_output"
+                                        },
+                                        "reads": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Racon: polish 2",
+                                    "name": "Racon",
+                                    "outputs": [
+                                        {
+                                            "name": "consensus",
+                                            "type": "fasta"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 759.9375,
+                                        "top": 485.71875
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionconsensus": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "consensus"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "78c533842eeb",
+                                        "name": "racon",
+                                        "owner": "bgruening",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "1.5.0+galaxy1",
+                                    "type": "tool",
+                                    "uuid": "3208491e-b831-4238-957e-5b7388d7ff8d",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "7": {
+                                    "annotation": "Map raw reads to assembly; output paf",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                    "errors": null,
+                                    "id": 7,
+                                    "input_connections": {
+                                        "fastq_input|analysis_type_selector": {
+                                            "id": 2,
+                                            "output_name": "output"
+                                        },
+                                        "fastq_input|fastq_input1": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        },
+                                        "reference_source|ref_file": {
+                                            "id": 6,
+                                            "output_name": "consensus"
+                                        }
+                                    },
+                                    "inputs": [
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "fastq_input"
+                                        },
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "fastq_input"
+                                        },
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "reference_source"
+                                        }
+                                    ],
+                                    "label": "Minimap2: map long reads to polished assembly 2",
+                                    "name": "Map with minimap2",
+                                    "outputs": [
+                                        {
+                                            "name": "alignment_output",
+                                            "type": "bam"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 998.75,
+                                        "top": 27.9375
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionalignment_output": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "alignment_output"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "be1d967337e4",
+                                        "name": "minimap2",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "2.26+galaxy0",
+                                    "type": "tool",
+                                    "uuid": "42af524b-7f74-4c75-8d78-f6888078dd2e",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "8": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                    "errors": null,
+                                    "id": 8,
+                                    "input_connections": {
+                                        "corrected_reads": {
+                                            "id": 6,
+                                            "output_name": "consensus"
+                                        },
+                                        "overlaps": {
+                                            "id": 7,
+                                            "output_name": "alignment_output"
+                                        },
+                                        "reads": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Racon: polish 3",
+                                    "name": "Racon",
+                                    "outputs": [
+                                        {
+                                            "name": "consensus",
+                                            "type": "fasta"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 1089.71875,
+                                        "top": 455.53125
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionconsensus": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "consensus"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "78c533842eeb",
+                                        "name": "racon",
+                                        "owner": "bgruening",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "1.5.0+galaxy1",
+                                    "type": "tool",
+                                    "uuid": "21f339bd-ebc1-4c73-a976-5d0b9ab2127a",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "9": {
+                                    "annotation": "Map raw reads to assembly; output paf",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                    "errors": null,
+                                    "id": 9,
+                                    "input_connections": {
+                                        "fastq_input|analysis_type_selector": {
+                                            "id": 2,
+                                            "output_name": "output"
+                                        },
+                                        "fastq_input|fastq_input1": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        },
+                                        "reference_source|ref_file": {
+                                            "id": 8,
+                                            "output_name": "consensus"
+                                        }
+                                    },
+                                    "inputs": [
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "fastq_input"
+                                        },
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "fastq_input"
+                                        },
+                                        {
+                                            "description": "runtime parameter for tool Map with minimap2",
+                                            "name": "reference_source"
+                                        }
+                                    ],
+                                    "label": "Minimap2: map long reads to polished assembly 3",
+                                    "name": "Map with minimap2",
+                                    "outputs": [
+                                        {
+                                            "name": "alignment_output",
+                                            "type": "bam"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 1316.53125,
+                                        "top": 38.046875
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionalignment_output": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "alignment_output"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "be1d967337e4",
+                                        "name": "minimap2",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "2.26+galaxy0",
+                                    "type": "tool",
+                                    "uuid": "7d36291e-aa76-4312-9943-b5e56d0e90c5",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                }
+                            },
+                            "tags": "",
+                            "uuid": "c57efd37-4cf6-4cc7-abf4-2bab22a2e9a0"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.dotplot\", \"__current_case__\": 2, \"var_names\": {\"type\": \"custom\", \"__current_case__\": 1, \"var_names\": \"AT1G26680,COBL2,AT3G55180,NCED2,AT5G22550,ATL63,RGF8,TEL1,DUF9,AGL42,PLT1,PLT2,PER3,PER9,PBL15,TBL30,AT2G48130,AT3G22620,AED3,T3P18-7,MBK21-8,NPF6-4,CYP71B34,IAMT1,AT1G31950,F14G6-22,GL2,ANL2,PMEI4,MUD21-4,EXPA7,MES15,ADF8,COBL9,TPR14,BHLH144,MYB83,SCPL35,MYB46,COBL4,PIN7,PIN3   \"}, \"groupby\": \"leiden\", \"num_categories\": \"9\", \"log\": \"false\", \"use_raw\": \"true\", \"dendrogram\": \"false\", \"var_group_positions\": [{\"__index__\": 0, \"start\": \"0\", \"end\": \"5\", \"label\": \"Columella\"}, {\"__index__\": 1, \"start\": \"6\", \"end\": \"9\", \"label\": \"QC\"}, {\"__index__\": 2, \"start\": \"10\", \"end\": \"11\", \"label\": \"NC\"}, {\"__index__\": 3, \"start\": \"12\", \"end\": \"17\", \"label\": \"Endodermis\"}, {\"__index__\": 4, \"start\": \"18\", \"end\": \"23\", \"label\": \"Cortex\"}, {\"__index__\": 5, \"start\": \"24\", \"end\": \"29\", \"label\": \"Atrichoblast\"}, {\"__index__\": 6, \"start\": \"30\", \"end\": \"34\", \"label\": \"Trichoblast\"}, {\"__index__\": 7, \"start\": \"35\", \"end\": \"39\", \"label\": \"Xylem\"}, {\"__index__\": 8, \"start\": \"40\", \"end\": \"41\", \"label\": \"VC\"}], \"var_group_rotation\": null, \"figsize\": {\"test\": \"no\", \"__current_case__\": 1}, \"layer\": \"\", \"color_map\": \"viridis\", \"dot_max\": null, \"dot_min\": null, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "a2f04375-1e67-4764-ae78-2678dcf2c03a",
+                        "tool_id": null,
+                        "type": "subworkflow",
+                        "uuid": "58c99e4b-fd6a-401d-b9c7-cdf7e6d1757d",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_png",
-                                "uuid": "329e95de-cf53-4c0b-9a9b-ad30632ceeb8"
+                                "output_name": "2:output",
+                                "uuid": "50fa1032-8037-454e-8192-b95405bcd5d4"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
                         "errors": null,
-                        "id": 32,
+                        "id": 5,
                         "input_connections": {
-                            "adata": {
-                                "id": 29,
-                                "output_name": "anndata"
+                            "d": {
+                                "id": 4,
+                                "output_name": "Assembly polished by long reads using Racon"
+                            },
+                            "i": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "Plot UMAP with new labels",
-                        "name": "Plot",
+                        "label": "Medaka polish",
+                        "name": "medaka consensus pipeline",
                         "outputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "name": "out_consensus",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "bottom": 885.3999938964844,
-                            "height": 136.39999389648438,
-                            "left": 1863,
-                            "right": 2063,
-                            "top": 749,
-                            "width": 200,
-                            "x": 1863,
-                            "y": 749
+                            "left": 515.5164024294684,
+                            "top": 305.08460859328346
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActionout_consensus": {
+                                "action_arguments": {
+                                    "newname": "Medaka_long_reads_polished_assembly.fasta"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_consensus"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "6adf98e782f3",
-                            "name": "scanpy_plot",
+                            "changeset_revision": "fc8804320156",
+                            "name": "medaka_consensus_pipeline",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"leiden, batch\", \"use_raw\": \"false\", \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"on data\", \"legend_fontsize\": \"14\", \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy0",
+                        "tool_state": "{\"b\": \"100\", \"d\": {\"__class__\": \"ConnectedValue\"}, \"g\": false, \"i\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"r941_min_high_g360\", \"out\": [\"consensus\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.2+galaxy1",
                         "type": "tool",
-                        "uuid": "c83c81b0-cd9e-41c5-8b72-4b024b7260dc",
+                        "uuid": "14c5ce9c-df92-4e20-85da-7a161eaa759d",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_png",
-                                "uuid": "579d19d3-a98c-4e3a-92aa-0b65e2ffcefd"
+                                "label": "Assembly polished by long reads using Medaka",
+                                "output_name": "out_consensus",
+                                "uuid": "e3136060-bce7-4af3-87c4-9dcbb0d1f531"
                             }
                         ]
                     }
                 ],
-                "parent_id": "single-cell/scrna-plant",
-                "path": "topics/single-cell/tutorials/scrna-plant/workflows/main_workflow.ga",
+                "parent_id": "assembly/largegenome",
+                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_polishing.ga",
                 "tags": [
-                    "transcriptomics",
-                    "single-cell"
+                    "LG-WF",
+                    "GTN"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "scRNA Plant Analysis",
-                "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-plant/versions/main-workflow",
-                "tutorial_id": "scrna-plant",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-plant/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-plant/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "single-cell-scrna-plant",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "title": "Assembly polishing - upgraded",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-assembly-polishing",
+                "tutorial_id": "largegenome",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_polishing.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_polishing.html",
+                "version": 2,
+                "wfid": "assembly-largegenome",
+                "wfname": "galaxy-workflow-assembly-polishing",
+                "workflow": "Galaxy-Workflow-Assembly_polishing.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0"
-                ],
-                "workflowhub_id": "1266"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/4597857"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "histogram",
-                    "owner": "devteam",
-                    "revisions": "6f134426c2b0",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "msstats",
-                    "owner": "galaxyp",
-                    "revisions": "52ac6fde9a5b",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: histogram\n  owner: devteam\n  revisions: 6f134426c2b0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msstats\n  owner: galaxyp\n  revisions: 52ac6fde9a5b\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "uni-freiburg"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0"
                 ],
-                "email": "matthias.fahrner@uniklinik-freiburg.de",
-                "id": "matthias313",
-                "joined": "2019-03",
-                "name": "Matthias Fahrner",
-                "orcid": "0000-0001-7955-2518",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/matthias313/",
-                "twitter": "mfahrner313",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/matthias313.json"
+                "workflowhub_id": "1174"
             },
             {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "email": "melanie.foell@mol-med.uni-freiburg.de",
-                "id": "foellmelanie",
-                "joined": "2018-10",
-                "matrix": "foellmelanie:matrix.org",
-                "name": "Melanie F\u00f6ll",
-                "orcid": "0000-0002-1887-7543",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
-                "twitter": "MCFoell",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
-            }
-        ],
-        "dir": "topics/proteomics/tutorials/DIA_Analysis_MSstats",
-        "edam_operation": [
-            "Differential protein expression profiling",
-            "Spectrum calculation",
-            "Tag-based peptide identification"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "proteomics/DIA_Analysis_MSstats",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.org.au"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Statistical analyses are crucial for meaningful conclusion in proteomic studies",
-            "MSstats enables statistical analysis of data independent acquisition mass spectrometry data"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Statistical analysis of a HEK-Ecoli Benchmark DIA dataset",
-            "Understanding statistical approaches in proteomic analysis",
-            "Using MSstats to find significantly dysregulated proteins in a Spike-in dataset"
-        ],
-        "pageviews": 1354,
-        "pub_date": "2020-12-02",
-        "questions": [
-            "How to perform statistical analysis on DIA mass spectrometry data?",
-            "How to detect and quantify differentially abundant proteins in a HEK-Ecoli Benchmark DIA datatset?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "proteomics",
-                "tutorials": [
-                    "DIA_lib_OSW",
-                    "DIA_Analysis_OSW"
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
+                    }
                 ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00210",
-        "short_tools": [
-            "Grep1",
-            "histogram_rpy",
-            "msstats",
-            "Filter1"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "post-process",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "DIA"
-        ],
-        "time_estimation": "1H",
-        "title": "Statistical analysis of DIA data",
-        "tools": [
-            "Filter1",
-            "Grep1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0"
-        ],
-        "topic_name": "proteomics",
-        "topic_name_human": "Proteomics",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "DIA_Analysis_MSstats",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.json"
-        },
-        "version": 9,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 97,
-        "visitors": 1001,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "DIA MSstats Training export tabular",
+                "description": "",
                 "features": {
                     "comments": false,
                     "parameters": false,
-                    "report": null,
+                    "report": {
+                        "markdown": "# Workflow Report for Assembly with Flye\n\n\n## Workflow steps\n\n```galaxy\nworkflow_display()\n```\n\n## Dataset - fasta stats. \n\n```galaxy\nhistory_dataset_display(output=\"Fasta Statistics on input dataset(s): Fasta summary stats\")\n```\n\n## Contig sizes\n\n```galaxy\nhistory_dataset_as_image(output=\"Bar chart showing contig sizes\")\n```\n\n\n## Bandage image\n\n```galaxy\nhistory_dataset_as_image(output=\"Bandage Image on input dataset(s): Assembly Graph Image\")\n```\n\n## Quast report\n\n\r\n```galaxy\nhistory_dataset_display(output=\"Quast on input dataset(s):  PDF report\")\n```\r\n\n\n\n"
+                    },
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPyProphet export tabular\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nComparison matrix\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSample annot MSstats\"]\n  3[label=\"MSstats\"]\n  1 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Select\"]\n  3 -> 4 [label=\"comparison_result\"]\n  k0de65b2cf62c40688ac0466e419d495b[color=lightseagreen,label=\"Output\\nSelect_Ecoli\"]\n  4 -> k0de65b2cf62c40688ac0466e419d495b\n  5[label=\"Filter\"]\n  4 -> 5 [label=\"out_file1\"]\n  k197e8a45392f498186842c8326af4528[color=lightseagreen,label=\"Output\\nFilter_Ecoli\"]\n  5 -> k197e8a45392f498186842c8326af4528\n  6[label=\"Histogram\"]\n  5 -> 6 [label=\"out_file1\"]\n  k04c6287dfd0d478099b6cf52ee18e06f[color=lightseagreen,label=\"Output\\nHistogram_Ecoli\"]\n  6 -> k04c6287dfd0d478099b6cf52ee18e06f\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  1[label=\"Flye: assembly\"]\n  0 -> 1 [label=\"output\"]\n  k3960e31d7a9e400cbb21f6e47b75e649[color=lightseagreen,label=\"Output\\nFlye assembly on input dataset(s) (consensus)\"]\n  1 -> k3960e31d7a9e400cbb21f6e47b75e649\n  ke524f295a9574c91838cf8e98e809b6c[color=lightseagreen,label=\"Output\\nFlye assembly on input dataset(s) (assembly_graph)\"]\n  1 -> ke524f295a9574c91838cf8e98e809b6c\n  k48b854e2dd6e43458d0509abca6659da[color=lightseagreen,label=\"Output\\nFlye assembly on input dataset(s) (Graphical Fragment Assembly)\"]\n  1 -> k48b854e2dd6e43458d0509abca6659da\n  k8672c17271a7432c9679a8e37f36cf53[color=lightseagreen,label=\"Output\\nFlye assembly on input dataset(s) (assembly_info)\"]\n  1 -> k8672c17271a7432c9679a8e37f36cf53\n  2[label=\"Fasta statistics\"]\n  1 -> 2 [label=\"consensus\"]\n  3[label=\"Quast genome report\"]\n  1 -> 3 [label=\"consensus\"]\n  k17cdf8e08ad44570afae1861934fc678[color=lightseagreen,label=\"Output\\nQuast on input dataset(s):  HTML report\"]\n  3 -> k17cdf8e08ad44570afae1861934fc678\n  4[label=\"Bandage image: Flye assembly\"]\n  1 -> 4 [label=\"assembly_gfa\"]\n  ke66bd129146f48dc95b839a2a1ffb68d[color=lightseagreen,label=\"Output\\nBandage Image on input dataset(s): Assembly Graph Image\"]\n  4 -> ke66bd129146f48dc95b839a2a1ffb68d\n  5[label=\"Bar chart: show contig sizes\"]\n  1 -> 5 [label=\"assembly_info\"]\n  k6d0a4e23d6314e3789303d22fc91369b[color=lightseagreen,label=\"Output\\nBar chart showing contig sizes\"]\n  5 -> k6d0a4e23d6314e3789303d22fc91369b\n}",
                 "history": [
                     {
-                        "hash": "bef209fa8b13cca27b8deae81ff1675433201d9f",
-                        "message": "Add workflow tests to DIA_MSstats_Training tutorial",
+                        "hash": "f3dd8377556ae73d56d73612a37a5a7e20c98093",
+                        "message": "Update Galaxy-Workflow-Assembly_with_Flye.ga",
+                        "num": 5,
+                        "short_hash": "f3dd83775",
+                        "unix": "1715074300"
+                    },
+                    {
+                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
+                        "message": "new versions of workflows",
+                        "num": 4,
+                        "short_hash": "e8ddbcdd5",
+                        "unix": "1714537936"
+                    },
+                    {
+                        "hash": "43baea079b7b412f3f272ac1ac887cd67aef6c49",
+                        "message": "Rename Galaxy-Workflow-Assembly_with_Flye.ga to Galaxy-Workflow-Assembly_with_Flye_old.ga",
                         "num": 3,
-                        "short_hash": "bef209fa8",
-                        "unix": "1642736930"
+                        "short_hash": "43baea079",
+                        "unix": "1714537239"
                     },
                     {
-                        "hash": "15a13c3667af0db6a6ca380ca1b998c9faf625d3",
-                        "message": "updated workflow annotation and name",
+                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
+                        "message": "add/complete creator info on workflows",
                         "num": 2,
-                        "short_hash": "15a13c366",
-                        "unix": "1606931443"
+                        "short_hash": "62e77944b",
+                        "unix": "1676627603"
                     },
                     {
-                        "hash": "e8f20c190bc7a0d319835969a36114d939bd4dce",
-                        "message": "generated three tutorials on DIA data analysis in galaxy",
+                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
+                        "message": "large genome tutorial",
                         "num": 1,
-                        "short_hash": "e8f20c190",
-                        "unix": "1606930318"
+                        "short_hash": "9fcb3aeec",
+                        "unix": "1665123856"
                     }
                 ],
                 "inputs": [
@@ -173926,553 +174974,556 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "PyProphet export tabular"
+                                "name": "long reads"
                             }
                         ],
-                        "label": "PyProphet export tabular",
+                        "label": "long reads",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 298.94485783397704,
-                            "height": 109.33332824707031,
-                            "left": 94.64912127731438,
-                            "right": 360.6491212773144,
-                            "top": 189.6115295869067,
-                            "width": 266,
-                            "x": 94.64912127731438,
-                            "y": 189.6115295869067
+                            "left": 0,
+                            "top": 398.40625
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ccdce674-490b-493c-a03b-786c9e9ec472",
+                        "uuid": "501d7387-3bed-4510-891f-a4571a48d9ab",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Flye: assembly\"];\n  0 -->|output| 1;\n  3960e31d-7a9e-400c-bb21-f6e47b75e649[\"Output\\nFlye assembly on input dataset(s) (consensus)\"];\n  1 --> 3960e31d-7a9e-400c-bb21-f6e47b75e649;\n  style 3960e31d-7a9e-400c-bb21-f6e47b75e649 stroke:#2c3143,stroke-width:4px;\n  e524f295-a957-4c91-838c-f8e98e809b6c[\"Output\\nFlye assembly on input dataset(s) (assembly_graph)\"];\n  1 --> e524f295-a957-4c91-838c-f8e98e809b6c;\n  style e524f295-a957-4c91-838c-f8e98e809b6c stroke:#2c3143,stroke-width:4px;\n  48b854e2-dd6e-4345-8d05-09abca6659da[\"Output\\nFlye assembly on input dataset(s) (Graphical Fragment Assembly)\"];\n  1 --> 48b854e2-dd6e-4345-8d05-09abca6659da;\n  style 48b854e2-dd6e-4345-8d05-09abca6659da stroke:#2c3143,stroke-width:4px;\n  8672c172-71a7-432c-9679-a8e37f36cf53[\"Output\\nFlye assembly on input dataset(s) (assembly_info)\"];\n  1 --> 8672c172-71a7-432c-9679-a8e37f36cf53;\n  style 8672c172-71a7-432c-9679-a8e37f36cf53 stroke:#2c3143,stroke-width:4px;\n  2[\"Fasta statistics\"];\n  1 -->|consensus| 2;\n  3[\"Quast genome report\"];\n  1 -->|consensus| 3;\n  17cdf8e0-8ad4-4570-afae-1861934fc678[\"Output\\nQuast on input dataset(s):  HTML report\"];\n  3 --> 17cdf8e0-8ad4-4570-afae-1861934fc678;\n  style 17cdf8e0-8ad4-4570-afae-1861934fc678 stroke:#2c3143,stroke-width:4px;\n  4[\"Bandage image: Flye assembly\"];\n  1 -->|assembly_gfa| 4;\n  e66bd129-146f-48dc-95b8-39a2a1ffb68d[\"Output\\nBandage Image on input dataset(s): Assembly Graph Image\"];\n  4 --> e66bd129-146f-48dc-95b8-39a2a1ffb68d;\n  style e66bd129-146f-48dc-95b8-39a2a1ffb68d stroke:#2c3143,stroke-width:4px;\n  5[\"Bar chart: show contig sizes\"];\n  1 -->|assembly_info| 5;\n  6d0a4e23-d631-4e37-8930-3d22fc91369b[\"Output\\nBar chart showing contig sizes\"];\n  5 --> 6d0a4e23-d631-4e37-8930-3d22fc91369b;\n  style 6d0a4e23-d631-4e37-8930-3d22fc91369b stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Assembly with Flye - upgraded",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {
+                            "inputs": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Flye: assembly",
+                        "name": "Flye",
+                        "outputs": [
+                            {
+                                "name": "consensus",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "assembly_graph",
+                                "type": "graph_dot"
+                            },
+                            {
+                                "name": "assembly_gfa",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "assembly_info",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 260.57143695759436,
+                            "top": 248.74363091133793
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "291923e6f276",
+                            "name": "flye",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"asm\": {\"asm_select\": \"false\", \"__current_case__\": 1}, \"generate_log\": false, \"i\": \"1\", \"inputs\": {\"__class__\": \"ConnectedValue\"}, \"iterations\": \"1\", \"keep_haplotypes\": false, \"m\": null, \"meta\": false, \"min_overlap\": null, \"mode\": \"--nano-raw\", \"mode_conditional\": {\"mode\": \"--nano-raw\", \"__current_case__\": 0}, \"no_alt_contigs\": false, \"no_trestle\": \"false\", \"plasmids\": \"false\", \"scaffold\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.9.3+galaxy0",
+                        "type": "tool",
+                        "uuid": "8bed3591-266a-41f1-91d3-11b3456e8609",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "771735fa-1a49-429d-b602-b5cd4b90a78b"
+                                "label": "Flye assembly on input dataset(s) (consensus)",
+                                "output_name": "consensus",
+                                "uuid": "3960e31d-7a9e-400c-bb21-f6e47b75e649"
+                            },
+                            {
+                                "label": "Flye assembly on input dataset(s) (assembly_graph)",
+                                "output_name": "assembly_graph",
+                                "uuid": "e524f295-a957-4c91-838c-f8e98e809b6c"
+                            },
+                            {
+                                "label": "Flye assembly on input dataset(s) (Graphical Fragment Assembly)",
+                                "output_name": "assembly_gfa",
+                                "uuid": "48b854e2-dd6e-4345-8d05-09abca6659da"
+                            },
+                            {
+                                "label": "Flye assembly on input dataset(s) (assembly_info)",
+                                "output_name": "assembly_info",
+                                "uuid": "8672c172-71a7-432c-9679-a8e37f36cf53"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 3,
+                        "input_connections": {
+                            "mode|in|inputs": {
+                                "id": 1,
+                                "output_name": "consensus"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Quast genome report",
+                        "name": "Quast",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Comparison matrix"
+                                "name": "report_html",
+                                "type": "html"
                             }
                         ],
-                        "label": "Comparison matrix",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 400.3483566628363,
-                            "height": 109.33332824707031,
-                            "left": 97.53132296684093,
-                            "right": 363.53132296684095,
-                            "top": 291.015028415766,
-                            "width": 266,
-                            "x": 97.53132296684093,
-                            "y": 291.015028415766
+                            "left": 697.3759752425051,
+                            "top": 194.46891558901518
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "9773176c-aeef-4430-9c9d-5c276bfd13bb",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "72472698a2df",
+                            "name": "quast",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"al\": {\"ambiguity_score\": \"0.99\", \"ambiguity_usage\": \"one\", \"fragmented\": false, \"fragmented_max_indent\": \"50\", \"min_alignment\": \"65\", \"min_identity\": \"95.0\", \"upper_bound_assembly\": false, \"upper_bound_min_con\": \"2\", \"use_all_alignments\": false}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"false\", \"__current_case__\": 1, \"est_ref_size\": null}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"circos\": \"false\", \"contig_thresholds\": \"0,1000\", \"extensive_mis_size\": \"1000\", \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": false}, \"in\": {\"__current_case__\": 1, \"custom\": \"false\", \"inputs\": {\"__class__\": \"RuntimeValue\"}}, \"k_mer\": {\"__current_case__\": 1, \"k_mer_stats\": \"\"}, \"large\": true, \"min_contig\": \"500\", \"mode\": {\"mode\": \"co\", \"__current_case__\": 1, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": \"html\", \"scaffold_gap_max_size\": \"1000\", \"skip_unaligned_mis_contigs\": \"false\", \"split_scaffolds\": false, \"strict_NA\": \"false\", \"unaligned_part_size\": \"500\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.2.0+galaxy1",
+                        "type": "tool",
+                        "uuid": "5bc29646-ec4c-4eb3-af01-73d82fc690a2",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "dcc7e278-b396-463e-9275-b669bb71ae30"
+                                "label": "Quast on input dataset(s):  HTML report",
+                                "output_name": "report_html",
+                                "uuid": "17cdf8e0-8ad4-4570-afae-1861934fc678"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 4,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 1,
+                                "output_name": "assembly_gfa"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Bandage image: Flye assembly",
+                        "name": "Bandage Image",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Sample annot MSstats"
+                                "name": "outfile",
+                                "type": "jpg"
                             }
                         ],
-                        "label": "Sample annot MSstats",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 501.86464433024696,
-                            "height": 109.33332824707031,
-                            "left": 98.42104804246945,
-                            "right": 364.42104804246947,
-                            "top": 392.53131608317665,
-                            "width": 266,
-                            "x": 98.42104804246945,
-                            "y": 392.53131608317665
+                            "left": 583.546875,
+                            "top": 446.40625
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "b0cf95a5-fca3-45ea-88df-37b06948099c",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ddddce450736",
+                            "name": "bandage",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"fontsize\": null, \"height\": \"1000\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"lengths\": false, \"names\": false, \"nodewidth\": null, \"output_format\": \"jpg\", \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2022.09+galaxy4",
+                        "type": "tool",
+                        "uuid": "395f2dfe-3fa5-4684-bf97-7dd12e970f78",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "489e9abe-be00-44c1-89e8-643eaecb75dd"
+                                "label": "Bandage Image on input dataset(s): Assembly Graph Image",
+                                "output_name": "outfile",
+                                "uuid": "e66bd129-146f-48dc-95b8-39a2a1ffb68d"
                             }
                         ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPyProphet export tabular\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nComparison matrix\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nSample annot MSstats\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"MSstats\"];\n  1 -->|output| 3;\n  2 -->|output| 3;\n  0 -->|output| 3;\n  4[\"Select\"];\n  3 -->|comparison_result| 4;\n  0de65b2c-f62c-4068-8ac0-466e419d495b[\"Output\\nSelect_Ecoli\"];\n  4 --> 0de65b2c-f62c-4068-8ac0-466e419d495b;\n  style 0de65b2c-f62c-4068-8ac0-466e419d495b stroke:#2c3143,stroke-width:4px;\n  5[\"Filter\"];\n  4 -->|out_file1| 5;\n  197e8a45-392f-4981-8684-2c8326af4528[\"Output\\nFilter_Ecoli\"];\n  5 --> 197e8a45-392f-4981-8684-2c8326af4528;\n  style 197e8a45-392f-4981-8684-2c8326af4528 stroke:#2c3143,stroke-width:4px;\n  6[\"Histogram\"];\n  5 -->|out_file1| 6;\n  04c6287d-fd0d-4780-99b6-cf52ee18e06f[\"Output\\nHistogram_Ecoli\"];\n  6 --> 04c6287d-fd0d-4780-99b6-cf52ee18e06f;\n  style 04c6287d-fd0d-4780-99b6-cf52ee18e06f stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "DIA_analysis_MSstats",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "barchart_gnuplot",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 5,
+                        "input_connections": {
+                            "input": {
+                                "id": 1,
+                                "output_name": "assembly_info"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Bar chart: show contig sizes",
+                        "name": "Bar chart",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "PyProphet export tabular"
+                                "name": "out_file1",
+                                "type": "png"
                             }
                         ],
-                        "label": "PyProphet export tabular",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 298.94485783397704,
-                            "height": 109.33332824707031,
-                            "left": 94.64912127731438,
-                            "right": 360.6491212773144,
-                            "top": 189.6115295869067,
-                            "width": 266,
-                            "x": 94.64912127731438,
-                            "y": 189.6115295869067
+                            "left": 595.421875,
+                            "top": 688.984375
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ccdce674-490b-493c-a03b-786c9e9ec472",
+                        "post_job_actions": {},
+                        "tool_id": "barchart_gnuplot",
+                        "tool_state": "{\"colList\": \"2\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"pdf_size\": \"800,600\", \"title\": \"Assembly contig sizes\", \"xtic\": {\"userSpecified\": \"No\", \"__current_case__\": 1}, \"ylabel\": \"lengths\", \"ymax\": \"0\", \"ymin\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "cb9d5059-bf42-4a0e-8150-f5089e0d5b1b",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "771735fa-1a49-429d-b602-b5cd4b90a78b"
+                                "label": "Bar chart showing contig sizes",
+                                "output_name": "out_file1",
+                                "uuid": "6d0a4e23-d631-4e37-8930-3d22fc91369b"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "assembly/largegenome",
+                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_with_Flye.ga",
+                "tags": [
+                    "LG-WF",
+                    "GTN"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Assembly with Flye - upgraded",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-assembly-with-flye",
+                "tutorial_id": "largegenome",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_with_Flye.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assembly_with_Flye.html",
+                "version": 2,
+                "wfid": "assembly-largegenome",
+                "wfname": "galaxy-workflow-assembly-with-flye",
+                "workflow": "Galaxy-Workflow-Assembly_with_Flye.ga",
+                "workflow_tools": [
+                    "barchart_gnuplot",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
+                ],
+                "workflowhub_id": "1170"
+            },
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n\n## Busco results\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco short summary\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco summary image\")\n```\n\n## Quast results\n\n\n```galaxy\nhistory_dataset_display(output=\"Quast on input dataset(s): tabular report\")\n```\n\n\n"
+                    },
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPolished assembly\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genome\"]\n  2[label=\"Busco: assess assembly\"]\n  0 -> 2 [label=\"output\"]\n  k219e495236e04b01a407e774b5b02dca[color=lightseagreen,label=\"Output\\nBusco short summary\"]\n  2 -> k219e495236e04b01a407e774b5b02dca\n  3[label=\"Quast: assess assembly\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  k77ab01864cfd460fb71e39a923414ef4[color=lightseagreen,label=\"Output\\nQuast on input dataset(s):  HTML report\"]\n  3 -> k77ab01864cfd460fb71e39a923414ef4\n}",
+                "history": [
+                    {
+                        "hash": "1b47a1ad8d46b114394c0579436c448e6bb7efcf",
+                        "message": "Update Galaxy-Workflow-Assess_genome_quality.ga",
+                        "num": 5,
+                        "short_hash": "1b47a1ad8",
+                        "unix": "1715074319"
+                    },
+                    {
+                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
+                        "message": "new versions of workflows",
+                        "num": 4,
+                        "short_hash": "e8ddbcdd5",
+                        "unix": "1714537936"
+                    },
+                    {
+                        "hash": "fc05e79f01c6b59c4dfc6aa59ebf592ae615641f",
+                        "message": "Rename Galaxy-Workflow-Assess_genome_quality.ga to Galaxy-Workflow-Assess_genome_quality_old.ga",
+                        "num": 3,
+                        "short_hash": "fc05e79f0",
+                        "unix": "1714537255"
+                    },
+                    {
+                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
+                        "message": "add/complete creator info on workflows",
+                        "num": 2,
+                        "short_hash": "62e77944b",
+                        "unix": "1676627603"
                     },
+                    {
+                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
+                        "message": "large genome tutorial",
+                        "num": 1,
+                        "short_hash": "9fcb3aeec",
+                        "unix": "1665123856"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Comparison matrix"
+                                "name": "Polished assembly"
                             }
                         ],
-                        "label": "Comparison matrix",
+                        "label": "Polished assembly",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 400.3483566628363,
-                            "height": 109.33332824707031,
-                            "left": 97.53132296684093,
-                            "right": 363.53132296684095,
-                            "top": 291.015028415766,
-                            "width": 266,
-                            "x": 97.53132296684093,
-                            "y": 291.015028415766
+                            "left": 0,
+                            "top": 101.09375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "9773176c-aeef-4430-9c9d-5c276bfd13bb",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "dcc7e278-b396-463e-9275-b669bb71ae30"
-                            }
-                        ]
+                        "uuid": "2ed19084-9eaf-4efb-acdc-b81536e7c024",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Sample annot MSstats"
+                                "name": "Reference genome"
                             }
                         ],
-                        "label": "Sample annot MSstats",
+                        "label": "Reference genome",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 501.86464433024696,
-                            "height": 109.33332824707031,
-                            "left": 98.42104804246945,
-                            "right": 364.42104804246947,
-                            "top": 392.53131608317665,
-                            "width": 266,
-                            "x": 98.42104804246945,
-                            "y": 392.53131608317665
+                            "left": 246.765625,
+                            "top": 0.0
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "b0cf95a5-fca3-45ea-88df-37b06948099c",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "489e9abe-be00-44c1-89e8-643eaecb75dd"
-                            }
-                        ]
-                    },
+                        "uuid": "5b12a6af-13c3-4520-a549-280de6a3df17",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPolished assembly\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Busco: assess assembly\"];\n  0 -->|output| 2;\n  219e4952-36e0-4b01-a407-e774b5b02dca[\"Output\\nBusco short summary\"];\n  2 --> 219e4952-36e0-4b01-a407-e774b5b02dca;\n  style 219e4952-36e0-4b01-a407-e774b5b02dca stroke:#2c3143,stroke-width:4px;\n  3[\"Quast: assess assembly\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  77ab0186-4cfd-460f-b71e-39a923414ef4[\"Output\\nQuast on input dataset(s):  HTML report\"];\n  3 --> 77ab0186-4cfd-460f-b71e-39a923414ef4;\n  style 77ab0186-4cfd-460f-b71e-39a923414ef4 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Assess genome quality - upgraded",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
                         "errors": null,
-                        "id": 3,
+                        "id": 2,
                         "input_connections": {
-                            "group|comparison_matrix": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "input|annotation": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "input|evidence": {
+                            "input": {
                                 "id": 0,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "MSstats",
+                        "label": "Busco: assess assembly",
+                        "name": "Busco",
                         "outputs": [
                             {
-                                "name": "log",
+                                "name": "busco_sum",
                                 "type": "txt"
                             },
                             {
-                                "name": "processed_data",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "qcplot",
-                                "type": "pdf"
-                            },
-                            {
-                                "name": "quant_group_matrix",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "comparison_result",
+                                "name": "busco_table",
                                 "type": "tabular"
-                            },
-                            {
-                                "name": "fittedmodel",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "volcanoplot",
-                                "type": "pdf"
-                            },
-                            {
-                                "name": "comparisonplot",
-                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "bottom": 803.8629044841107,
-                            "height": 732.0333251953125,
-                            "left": 406.11526374530075,
-                            "right": 672.1152637453008,
-                            "top": 71.82957928879816,
-                            "width": 266,
-                            "x": 406.11526374530075,
-                            "y": 71.82957928879816
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionfittedmodel": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "fittedmodel"
-                            },
-                            "HideDatasetActionlog": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "log"
-                            },
-                            "HideDatasetActionquant_group_matrix": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "quant_group_matrix"
-                            }
+                            "left": 294.42303466796875,
+                            "top": 200.68505859375
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "52ac6fde9a5b",
-                            "name": "msstats",
-                            "owner": "galaxyp",
+                            "changeset_revision": "ea8146ee148f",
+                            "name": "busco",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"dp_options\": {\"logTrans\": \"2\", \"norm\": {\"normalization\": \"equalizeMedians\", \"__current_case__\": 0}, \"fillIncompleteRows\": \"true\", \"features\": {\"featureSubset\": \"all\", \"__current_case__\": 0}, \"summarize\": {\"summaryMethod\": \"TMP\", \"__current_case__\": 0, \"MBimpute\": \"true\", \"remove50missing\": \"false\"}, \"censoredInt\": \"NA\", \"cutoffCensored\": \"minFeature\", \"maxQuantileforCensored\": \"0.999\"}, \"group\": {\"group_comparison\": \"yes\", \"__current_case__\": 1, \"comparison_matrix\": {\"__class__\": \"ConnectedValue\"}, \"select_outputs\": [\"fittedmodel\", \"comparison_result\", \"volcanoplot\", \"comparisonplot\"]}, \"input\": {\"input_src\": \"OpenSWATH\", \"__current_case__\": 2, \"evidence\": {\"__class__\": \"ConnectedValue\"}, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"input_options\": {\"filter_with_mscore\": \"true\", \"mscore_cutoff\": \"0.01\", \"useUniquePeptide\": \"true\", \"fewMeasurements\": \"remove\", \"summaryforMultipleRows\": \"max\", \"removeProtein_with1Feature\": \"false\"}}, \"selected_outputs\": [\"log\", \"processed_data\", \"qcplot\", \"quant_group_matrix\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.20.1.0",
+                        "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"auto_detect\", \"__current_case__\": 0, \"auto_lineage\": \"--auto-lineage\"}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"lineage_dataset\": \"eukaryota_odb10\", \"outputs\": \"short_summary\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.5.0+galaxy0",
                         "type": "tool",
-                        "uuid": "810a6c7a-a171-44db-aadf-917c32e31d78",
+                        "uuid": "8f5f17de-a21e-49f4-b55c-6eff5f4fa213",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "processed_data",
-                                "uuid": "15fd08bb-7103-4f19-9998-38709822e2d2"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "comparisonplot",
-                                "uuid": "dfeb77e1-05b5-4236-96e9-694a7a969b70"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "volcanoplot",
-                                "uuid": "a369af4d-082b-4549-9417-1af61291e166"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "comparison_result",
-                                "uuid": "1b702487-ba66-4987-8f7d-5e624f90efac"
+                                "label": "Busco short summary",
+                                "output_name": "busco_sum",
+                                "uuid": "219e4952-36e0-4b01-a407-e774b5b02dca"
                             },
                             {
                                 "label": null,
-                                "output_name": "qcplot",
-                                "uuid": "5ddda783-dfb8-4c06-ae95-2f26df51ac64"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "Grep1",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "input": {
-                                "id": 3,
-                                "output_name": "comparison_result"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Select",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 329.3259474675458,
-                            "height": 123.95001220703125,
-                            "left": 664.0476312852443,
-                            "right": 930.0476312852443,
-                            "top": 205.37593526051455,
-                            "width": 266,
-                            "x": 664.0476312852443,
-                            "y": 205.37593526051455
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "Grep1",
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"false\", \"pattern\": \"(ECOLI)|(logFC)\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.1",
-                        "type": "tool",
-                        "uuid": "0d3aefe9-d49e-4a5e-96b0-d2a93c164b5a",
-                        "workflow_outputs": [
-                            {
-                                "label": "Select_Ecoli",
-                                "output_name": "out_file1",
-                                "uuid": "0de65b2c-f62c-4068-8ac0-466e419d495b"
+                                "output_name": "busco_table",
+                                "uuid": "fc06df63-3453-4303-80d1-c76823ba384a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Filter1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
                         "errors": null,
-                        "id": 5,
+                        "id": 3,
                         "input_connections": {
-                            "input": {
-                                "id": 4,
-                                "output_name": "out_file1"
+                            "assembly|ref|r": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "mode|in|inputs": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Filter",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 458.83722566303453,
-                            "height": 123.95001220703125,
-                            "left": 888.0450944255168,
-                            "right": 1154.0450944255167,
-                            "top": 334.8872134560033,
-                            "width": 266,
-                            "x": 888.0450944255168,
-                            "y": 334.8872134560033
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"cond\": \"c7!='NA'\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
-                        "type": "tool",
-                        "uuid": "22227f86-1d56-4e67-b76e-9fcdb409741e",
-                        "workflow_outputs": [
-                            {
-                                "label": "Filter_Ecoli",
-                                "output_name": "out_file1",
-                                "uuid": "197e8a45-392f-4981-8684-2c8326af4528"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "input": {
-                                "id": 5,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Histogram",
-                                "name": "input"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Histogram",
+                        "label": "Quast: assess assembly",
+                        "name": "Quast",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "pdf"
+                                "name": "report_html",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "bottom": 382.0702885219029,
-                            "height": 123.94999694824219,
-                            "left": 1130.7142673578476,
-                            "right": 1396.7142673578476,
-                            "top": 258.1202915736607,
-                            "width": 266,
-                            "x": 1130.7142673578476,
-                            "y": 258.1202915736607
+                            "left": 564.8660278320312,
+                            "top": 56.71406029052495
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "6f134426c2b0",
-                            "name": "histogram",
-                            "owner": "devteam",
+                            "changeset_revision": "72472698a2df",
+                            "name": "quast",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"breaks\": \"25\", \"density\": \"true\", \"frequency\": \"false\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"numerical_column\": \"3\", \"title\": \"Distribution of Ecoli Protein log FC values\", \"xlab\": \"log2 Fold Change\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.3",
+                        "tool_state": "{\"advanced\": {\"contig_thresholds\": \"0,1000\", \"strict_NA\": false, \"extensive_mis_size\": \"1000\", \"scaffold_gap_max_size\": \"1000\", \"unaligned_part_size\": \"500\", \"skip_unaligned_mis_contigs\": true, \"fragmented_max_indent\": null, \"report_all_metrics\": false, \"x_for_Nx\": \"90\"}, \"alignments\": {\"use_all_alignments\": false, \"min_alignment\": \"65\", \"ambiguity_usage\": \"one\", \"ambiguity_score\": \"0.99\", \"fragmented\": false, \"upper_bound_assembly\": false, \"upper_bound_min_con\": null, \"local_mis_size\": \"200\"}, \"assembly\": {\"type\": \"genome\", \"__current_case__\": 0, \"ref\": {\"use_ref\": \"true\", \"__current_case__\": 0, \"r\": {\"__class__\": \"RuntimeValue\"}, \"features\": {\"__class__\": \"RuntimeValue\"}, \"operons\": {\"__class__\": \"RuntimeValue\"}, \"k_mer\": {\"k_mer_stats\": \"\", \"__current_case__\": 1}, \"circos\": false}, \"orga_type\": \"\", \"min_identity\": \"95.0\"}, \"genes\": {\"gene_finding\": {\"tool\": \"none\", \"__current_case__\": 0}, \"rna_finding\": false, \"conserved_genes_finding\": false}, \"large\": true, \"min_contig\": \"0\", \"mode\": {\"mode\": \"individual\", \"__current_case__\": 0, \"in\": {\"custom\": \"false\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"RuntimeValue\"}}, \"reads\": {\"reads_option\": \"disabled\", \"__current_case__\": 0}}, \"output_files\": \"html\", \"split_scaffolds\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.2.0+galaxy1",
                         "type": "tool",
-                        "uuid": "dc481c56-b123-48ec-bc5c-81411c3a7a9f",
+                        "uuid": "6caef18b-b257-472d-b8d0-fac523a72d37",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Histogram_Ecoli",
-                                "output_name": "out_file1",
-                                "uuid": "04c6287d-fd0d-4780-99b6-cf52ee18e06f"
+                                "label": "Quast on input dataset(s):  HTML report",
+                                "output_name": "report_html",
+                                "uuid": "77ab0186-4cfd-460f-b71e-39a923414ef4"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/DIA_Analysis_MSstats",
-                "path": "topics/proteomics/tutorials/DIA_Analysis_MSstats/workflows/Galaxy-Workflow-DIA_MSstats_Training_export_tabular.ga",
+                "parent_id": "assembly/largegenome",
+                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assess_genome_quality.ga",
                 "tags": [
-                    "proteomics"
+                    "LG-WF",
+                    "GTN"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "DIA_analysis_MSstats",
-                "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-DIA_Analysis_MSstats/versions/galaxy-workflow-dia-msstats-training-export-tabular",
-                "tutorial_id": "DIA_Analysis_MSstats",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/DIA_Analysis_MSstats/workflows/Galaxy-Workflow-DIA_MSstats_Training_export_tabular.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/DIA_Analysis_MSstats/workflows/Galaxy-Workflow-DIA_MSstats_Training_export_tabular.html",
+                "tests": false,
+                "title": "Assess genome quality - upgraded",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-assess-genome-quality",
+                "tutorial_id": "largegenome",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assess_genome_quality.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Assess_genome_quality.html",
                 "version": 2,
-                "wfid": "proteomics-DIA_Analysis_MSstats",
-                "wfname": "galaxy-workflow-dia-msstats-training-export-tabular",
-                "workflow": "Galaxy-Workflow-DIA_MSstats_Training_export_tabular.ga",
+                "wfid": "assembly-largegenome",
+                "wfname": "galaxy-workflow-assess-genome-quality",
+                "workflow": "Galaxy-Workflow-Assess_genome_quality.ga",
                 "workflow_tools": [
-                    "Filter1",
-                    "Grep1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
                 ],
-                "workflowhub_id": "1167"
+                "workflowhub_id": "1158"
             },
             {
-                "creators": [],
-                "description": "DIA MSstats Training msstats input tabular",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
+                    }
+                ],
+                "description": "",
                 "features": {
                     "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
+                    "parameters": true,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                    },
+                    "subworkflows": true
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPyProphet MSstats input\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nComparison matrix\"]\n  2[label=\"MSstats\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Select\"]\n  2 -> 3 [label=\"comparison_result\"]\n  k6e8589bd13fd4a97a9c3ea0a5a0e2326[color=lightseagreen,label=\"Output\\nSelect_Ecoli\"]\n  3 -> k6e8589bd13fd4a97a9c3ea0a5a0e2326\n  4[label=\"Filter\"]\n  3 -> 4 [label=\"out_file1\"]\n  k6997a43aa17b418bbb6d7d32a6c277ae[color=lightseagreen,label=\"Output\\nFilter_Ecoli\"]\n  4 -> k6997a43aa17b418bbb6d7d32a6c277ae\n  5[label=\"Histogram\"]\n  4 -> 5 [label=\"out_file1\"]\n  kcf3abac382274af8a5516aeae154a0e4[color=lightseagreen,label=\"Output\\nHistogram_Ecoli\"]\n  5 -> kcf3abac382274af8a5516aeae154a0e4\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR1\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nR2\"]\n  3[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nminimap settings for long reads\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genome for Quast\"]\n  5[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nkmer counting - meryl - upgraded\"]\n  1 -> 5 [label=\"output\"]\n  6[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nData QC - upgraded\"]\n  1 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  0 -> 6 [label=\"output\"]\n  7[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nTrim and filter reads - fastp - upgraded \"]\n  1 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  0 -> 7 [label=\"output\"]\n  8[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly with Flye - upgraded\"]\n  7 -> 8 [label=\"fastp filtered long reads\"]\n  9[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly polishing - upgraded\"]\n  8 -> 9 [label=\"Flye assembly on input datasets consensus\"]\n  7 -> 9 [label=\"fastp filtered R1 reads\"]\n  7 -> 9 [label=\"fastp filtered long reads\"]\n  3 -> 9 [label=\"output\"]\n  10[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nAssess genome quality - upgraded\"]\n  9 -> 10 [label=\"Assembly polished by long reads using Medaka\"]\n  4 -> 10 [label=\"output\"]\n}",
                 "history": [
                     {
-                        "hash": "bef209fa8b13cca27b8deae81ff1675433201d9f",
-                        "message": "Add workflow tests to DIA_MSstats_Training tutorial",
+                        "hash": "01cffeed0413d12d37753e72aa81c95fb47e2179",
+                        "message": "Update Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga",
+                        "num": 5,
+                        "short_hash": "01cffeed0",
+                        "unix": "1715074366"
+                    },
+                    {
+                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
+                        "message": "new versions of workflows",
+                        "num": 4,
+                        "short_hash": "e8ddbcdd5",
+                        "unix": "1714537936"
+                    },
+                    {
+                        "hash": "bd0db2c9632aca4fc5faba5e811b23e9f98817f0",
+                        "message": "Rename Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga to Galaxy-Workflow-Combined_workflows_for_large_genome_assembly_old.ga",
                         "num": 3,
-                        "short_hash": "bef209fa8",
-                        "unix": "1642736930"
+                        "short_hash": "bd0db2c96",
+                        "unix": "1714537274"
                     },
                     {
-                        "hash": "15a13c3667af0db6a6ca380ca1b998c9faf625d3",
-                        "message": "updated workflow annotation and name",
+                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
+                        "message": "add/complete creator info on workflows",
                         "num": 2,
-                        "short_hash": "15a13c366",
-                        "unix": "1606931443"
+                        "short_hash": "62e77944b",
+                        "unix": "1676627603"
                     },
                     {
-                        "hash": "e8f20c190bc7a0d319835969a36114d939bd4dce",
-                        "message": "generated three tutorials on DIA data analysis in galaxy",
+                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
+                        "message": "large genome tutorial",
                         "num": 1,
-                        "short_hash": "e8f20c190",
-                        "unix": "1606930318"
+                        "short_hash": "9fcb3aeec",
+                        "unix": "1665123856"
                     }
                 ],
                 "inputs": [
@@ -174485,34 +175536,23 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "PyProphet MSstats input"
+                                "name": "long reads"
                             }
                         ],
-                        "label": "PyProphet MSstats input",
+                        "label": "long reads",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 524.5333251953125,
-                            "height": 82.20001220703125,
-                            "left": 127.5,
-                            "right": 327.5,
-                            "top": 442.33331298828125,
-                            "width": 200,
-                            "x": 127.5,
-                            "y": 442.33331298828125
+                            "left": 37.09056155334109,
+                            "top": 117.80110422489305
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "970f9184-0af8-46ef-84c6-8ce933204ab8",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "bfbca2d5-0d5d-4860-a4c2-bd0c97113322"
-                            }
-                        ]
+                        "uuid": "f9154ba8-6c56-4b8c-b3a6-79bf72638963",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
@@ -174523,76 +175563,81 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Comparison matrix"
+                                "name": "R1"
                             }
                         ],
-                        "label": "Comparison matrix",
+                        "label": "R1",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 641.1000366210938,
-                            "height": 82.20001220703125,
-                            "left": 128.63333129882812,
-                            "right": 328.6333312988281,
-                            "top": 558.9000244140625,
-                            "width": 200,
-                            "x": 128.63333129882812,
-                            "y": 558.9000244140625
+                            "left": 0,
+                            "top": 296.6915657131622
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "9773176c-aeef-4430-9c9d-5c276bfd13bb",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "e84e8bf5-5e49-4783-bbff-0b6534bcf60a"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPyProphet MSstats input\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nComparison matrix\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"MSstats\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Select\"];\n  2 -->|comparison_result| 3;\n  6e8589bd-13fd-4a97-a9c3-ea0a5a0e2326[\"Output\\nSelect_Ecoli\"];\n  3 --> 6e8589bd-13fd-4a97-a9c3-ea0a5a0e2326;\n  style 6e8589bd-13fd-4a97-a9c3-ea0a5a0e2326 stroke:#2c3143,stroke-width:4px;\n  4[\"Filter\"];\n  3 -->|out_file1| 4;\n  6997a43a-a17b-418b-bb6d-7d32a6c277ae[\"Output\\nFilter_Ecoli\"];\n  4 --> 6997a43a-a17b-418b-bb6d-7d32a6c277ae;\n  style 6997a43a-a17b-418b-bb6d-7d32a6c277ae stroke:#2c3143,stroke-width:4px;\n  5[\"Histogram\"];\n  4 -->|out_file1| 5;\n  cf3abac3-8227-4af8-a551-6aeae154a0e4[\"Output\\nHistogram_Ecoli\"];\n  5 --> cf3abac3-8227-4af8-a551-6aeae154a0e4;\n  style cf3abac3-8227-4af8-a551-6aeae154a0e4 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "DIA_analysis_MSstats",
-                "outputs": [
+                        "uuid": "2152a89a-64b2-4e77-897e-97c2e951f0d4",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "PyProphet MSstats input"
+                                "name": "R2"
                             }
                         ],
-                        "label": "PyProphet MSstats input",
+                        "label": "R2",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 524.5333251953125,
-                            "height": 82.20001220703125,
-                            "left": 127.5,
-                            "right": 327.5,
-                            "top": 442.33331298828125,
-                            "width": 200,
-                            "x": 127.5,
-                            "y": 442.33331298828125
+                            "left": 18.331891780359495,
+                            "top": 404.60599487314124
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "970f9184-0af8-46ef-84c6-8ce933204ab8",
+                        "uuid": "04ed4838-38d0-47c6-9692-af43b305750c",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "minimap settings (for long reads)"
+                            }
+                        ],
+                        "label": "minimap settings (for long reads)",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 953.979654343896,
+                            "top": 53.88085686443145
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "925fcb63-babc-42b5-9510-c82277158288",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "bfbca2d5-0d5d-4860-a4c2-bd0c97113322"
+                                "uuid": "3643a598-963e-42d9-b625-41f5256dee4a"
                             }
                         ]
                     },
@@ -174600,646 +175645,1481 @@
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 4,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Comparison matrix"
+                                "name": "Reference genome for Quast"
                             }
                         ],
-                        "label": "Comparison matrix",
+                        "label": "Reference genome for Quast",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 641.1000366210938,
-                            "height": 82.20001220703125,
-                            "left": 128.63333129882812,
-                            "right": 328.6333312988281,
-                            "top": 558.9000244140625,
-                            "width": 200,
-                            "x": 128.63333129882812,
-                            "y": 558.9000244140625
+                            "left": 1271.7306972391564,
+                            "top": 75.04279962197629
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "9773176c-aeef-4430-9c9d-5c276bfd13bb",
+                        "uuid": "5bd59f90-9351-4b1e-bc0d-11fee8b4a435",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nR1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nR2\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nminimap settings for long reads\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nReference genome for Quast\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\ud83d\udee0\ufe0f Subworkflow\\nkmer counting - meryl - upgraded\"];\n  style 5 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 5;\n  6[\"\ud83d\udee0\ufe0f Subworkflow\\nData QC - upgraded\"];\n  style 6 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 6;\n  2 -->|output| 6;\n  0 -->|output| 6;\n  7[\"\ud83d\udee0\ufe0f Subworkflow\\nTrim and filter reads - fastp - upgraded \"];\n  style 7 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 7;\n  2 -->|output| 7;\n  0 -->|output| 7;\n  8[\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly with Flye - upgraded\"];\n  style 8 fill:#edd,stroke:#900,stroke-width:4px;\n  7 -->|fastp filtered long reads| 8;\n  9[\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly polishing - upgraded\"];\n  style 9 fill:#edd,stroke:#900,stroke-width:4px;\n  8 -->|Flye assembly on input datasets consensus| 9;\n  7 -->|fastp filtered R1 reads| 9;\n  7 -->|fastp filtered long reads| 9;\n  3 -->|output| 9;\n  10[\"\ud83d\udee0\ufe0f Subworkflow\\nAssess genome quality - upgraded\"];\n  style 10 fill:#edd,stroke:#900,stroke-width:4px;\n  9 -->|Assembly polished by long reads using Medaka| 10;\n  4 -->|output| 10;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Combined workflows for large genome assembly - upgraded ",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "minimap settings (for long reads)"
+                            }
+                        ],
+                        "label": "minimap settings (for long reads)",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 953.979654343896,
+                            "top": 53.88085686443145
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "925fcb63-babc-42b5-9510-c82277158288",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "e84e8bf5-5e49-4783-bbff-0b6534bcf60a"
+                                "uuid": "3643a598-963e-42d9-b625-41f5256dee4a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0",
-                        "errors": null,
-                        "id": 2,
+                        "id": 9,
                         "input_connections": {
-                            "group|comparison_matrix": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "input|msstats_input": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "MSstats",
-                        "outputs": [
-                            {
-                                "name": "log",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "processed_data",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "qcplot",
-                                "type": "pdf"
-                            },
-                            {
-                                "name": "quant_group_matrix",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "comparison_result",
-                                "type": "tabular"
+                            "Assembly to be polished": {
+                                "id": 8,
+                                "input_subworkflow_step_id": 0,
+                                "output_name": "Flye assembly on input dataset(s) (consensus)"
                             },
-                            {
-                                "name": "fittedmodel",
-                                "type": "txt"
+                            "Illumina reads R1": {
+                                "id": 7,
+                                "input_subworkflow_step_id": 3,
+                                "output_name": "fastp filtered R1 reads"
                             },
-                            {
-                                "name": "volcanoplot",
-                                "type": "pdf"
+                            "long reads": {
+                                "id": 7,
+                                "input_subworkflow_step_id": 1,
+                                "output_name": "fastp filtered long reads"
                             },
-                            {
-                                "name": "comparisonplot",
-                                "type": "pdf"
+                            "minimap setting (for long reads)": {
+                                "id": 3,
+                                "input_subworkflow_step_id": 2,
+                                "output_name": "output"
                             }
-                        ],
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Assembly polishing - upgraded",
+                        "outputs": [],
                         "position": {
-                            "bottom": 785.5,
-                            "height": 520,
-                            "left": 424.5333251953125,
-                            "right": 624.5333251953125,
-                            "top": 265.5,
-                            "width": 200,
-                            "x": 424.5333251953125,
-                            "y": 265.5
+                            "left": 1260.7587450660599,
+                            "top": 269.3075732043599
                         },
-                        "post_job_actions": {
-                            "HideDatasetActionfittedmodel": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "fittedmodel"
+                        "subworkflow": {
+                            "a_galaxy_workflow": "true",
+                            "annotation": "",
+                            "comments": [],
+                            "creator": [
+                                {
+                                    "class": "Person",
+                                    "identifier": "0000-0002-9906-0673",
+                                    "name": "Anna Syme"
+                                }
+                            ],
+                            "format-version": "0.1",
+                            "name": "Assembly polishing - upgraded",
+                            "report": {
+                                "markdown": "\n# Workflow Report for Assembly Polishing\n\n## Workflow steps\n\n```galaxy\nworkflow_display()\n```\n\n## Fasta statistics after Racon long-read polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Racon long read polish\")\n```\n\n\n## Fasta statistics after Medaka polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Medaka polish\")\n```\n\n## Fasta statistics after Racon short-read polish\n\n```galaxy\nhistory_dataset_display(output=\"Fasta statistics after Racon short read polish\")\n```\n\n\n\n\n"
                             },
-                            "HideDatasetActionlog": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "log"
+                            "steps": {
+                                "0": {
+                                    "annotation": "",
+                                    "content_id": null,
+                                    "errors": null,
+                                    "id": 0,
+                                    "input_connections": {},
+                                    "inputs": [
+                                        {
+                                            "description": "",
+                                            "name": "Assembly to be polished"
+                                        }
+                                    ],
+                                    "label": "Assembly to be polished",
+                                    "name": "Input dataset",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 19.464939294568495,
+                                        "top": 0.0
+                                    },
+                                    "tool_id": null,
+                                    "tool_state": "{\"optional\": false, \"tag\": null}",
+                                    "tool_version": null,
+                                    "type": "data_input",
+                                    "uuid": "52bc9ac4-ac3c-48eb-aead-94a0a14417fc",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "1": {
+                                    "annotation": "",
+                                    "content_id": null,
+                                    "errors": null,
+                                    "id": 1,
+                                    "input_connections": {},
+                                    "inputs": [
+                                        {
+                                            "description": "",
+                                            "name": "long reads"
+                                        }
+                                    ],
+                                    "label": "long reads",
+                                    "name": "Input dataset",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 0.0,
+                                        "top": 142.48340578478533
+                                    },
+                                    "tool_id": null,
+                                    "tool_state": "{\"optional\": false, \"tag\": null}",
+                                    "tool_version": null,
+                                    "type": "data_input",
+                                    "uuid": "688866c4-de9b-4b78-8df3-b169d28b1617",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "2": {
+                                    "annotation": "",
+                                    "content_id": null,
+                                    "errors": null,
+                                    "id": 2,
+                                    "input_connections": {},
+                                    "inputs": [
+                                        {
+                                            "description": "",
+                                            "name": "minimap setting (for long reads)"
+                                        }
+                                    ],
+                                    "label": "minimap setting (for long reads)",
+                                    "name": "Input parameter",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 13.133522093825794,
+                                        "top": 247.1519749531627
+                                    },
+                                    "tool_id": null,
+                                    "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                                    "tool_version": null,
+                                    "type": "parameter_input",
+                                    "uuid": "c1f18b5c-e8db-4046-b876-9b28a77cf66e",
+                                    "when": null,
+                                    "workflow_outputs": [
+                                        {
+                                            "label": null,
+                                            "output_name": "output",
+                                            "uuid": "ce393bcf-42e3-43ee-9056-a99e8c077a29"
+                                        }
+                                    ]
+                                },
+                                "3": {
+                                    "annotation": "",
+                                    "content_id": null,
+                                    "errors": null,
+                                    "id": 3,
+                                    "input_connections": {},
+                                    "inputs": [
+                                        {
+                                            "description": "",
+                                            "name": "Illumina reads R1"
+                                        }
+                                    ],
+                                    "label": "Illumina reads R1",
+                                    "name": "Input dataset",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 617.719019724734,
+                                        "top": 600.0866464299372
+                                    },
+                                    "tool_id": null,
+                                    "tool_state": "{\"optional\": false, \"tag\": null}",
+                                    "tool_version": null,
+                                    "type": "data_input",
+                                    "uuid": "ea859a58-c81a-4ef6-9bd2-4ef2f17bb5a9",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "4": {
+                                    "annotation": "",
+                                    "id": 4,
+                                    "input_connections": {
+                                        "Assembly to be polished": {
+                                            "id": 0,
+                                            "input_subworkflow_step_id": 0,
+                                            "output_name": "output"
+                                        },
+                                        "long reads": {
+                                            "id": 1,
+                                            "input_subworkflow_step_id": 1,
+                                            "output_name": "output"
+                                        },
+                                        "minimap setting (for long reads) ": {
+                                            "id": 2,
+                                            "input_subworkflow_step_id": 2,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": null,
+                                    "name": "Racon polish with long reads, x4 - upgraded",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 299.6429464825318,
+                                        "top": 72.0364210406818
+                                    },
+                                    "subworkflow": {
+                                        "a_galaxy_workflow": "true",
+                                        "annotation": "",
+                                        "comments": [],
+                                        "creator": [
+                                            {
+                                                "class": "Person",
+                                                "identifier": "0000-0002-9906-0673",
+                                                "name": "Anna Syme"
+                                            }
+                                        ],
+                                        "format-version": "0.1",
+                                        "name": "Racon polish with long reads, x4 - upgraded",
+                                        "report": {
+                                            "markdown": "\n# Workflow Execution Report\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                                        },
+                                        "steps": {
+                                            "0": {
+                                                "annotation": "",
+                                                "content_id": null,
+                                                "errors": null,
+                                                "id": 0,
+                                                "input_connections": {},
+                                                "inputs": [
+                                                    {
+                                                        "description": "",
+                                                        "name": "Assembly to be polished"
+                                                    }
+                                                ],
+                                                "label": "Assembly to be polished",
+                                                "name": "Input dataset",
+                                                "outputs": [],
+                                                "position": {
+                                                    "left": 0,
+                                                    "top": 216.625
+                                                },
+                                                "tool_id": null,
+                                                "tool_state": "{\"optional\": false, \"tag\": null}",
+                                                "tool_version": null,
+                                                "type": "data_input",
+                                                "uuid": "c7796c36-adf8-49e4-a8e4-66e606d70311",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "1": {
+                                                "annotation": "",
+                                                "content_id": null,
+                                                "errors": null,
+                                                "id": 1,
+                                                "input_connections": {},
+                                                "inputs": [
+                                                    {
+                                                        "description": "",
+                                                        "name": "long reads"
+                                                    }
+                                                ],
+                                                "label": "long reads",
+                                                "name": "Input dataset",
+                                                "outputs": [],
+                                                "position": {
+                                                    "left": 4.5,
+                                                    "top": 360.234375
+                                                },
+                                                "tool_id": null,
+                                                "tool_state": "{\"optional\": false, \"tag\": null}",
+                                                "tool_version": null,
+                                                "type": "data_input",
+                                                "uuid": "e2e4a70b-6e36-4b8b-bdf6-12b97189a6bd",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "10": {
+                                                "annotation": "",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "errors": null,
+                                                "id": 10,
+                                                "input_connections": {
+                                                    "corrected_reads": {
+                                                        "id": 8,
+                                                        "output_name": "consensus"
+                                                    },
+                                                    "overlaps": {
+                                                        "id": 9,
+                                                        "output_name": "alignment_output"
+                                                    },
+                                                    "reads": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    }
+                                                },
+                                                "inputs": [],
+                                                "label": "Racon: polish 4",
+                                                "name": "Racon",
+                                                "outputs": [
+                                                    {
+                                                        "name": "consensus",
+                                                        "type": "fasta"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 1496.078125,
+                                                    "top": 431.1875
+                                                },
+                                                "post_job_actions": {
+                                                    "RenameDatasetActionconsensus": {
+                                                        "action_arguments": {
+                                                            "newname": "Racon_long_reads_polished_assembly.fasta"
+                                                        },
+                                                        "action_type": "RenameDatasetAction",
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "78c533842eeb",
+                                                    "name": "racon",
+                                                    "owner": "bgruening",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "1.5.0+galaxy1",
+                                                "type": "tool",
+                                                "uuid": "53f4572e-3a4a-4585-89ab-9459f8a61720",
+                                                "when": null,
+                                                "workflow_outputs": [
+                                                    {
+                                                        "label": "Assembly polished by long reads using Racon",
+                                                        "output_name": "consensus",
+                                                        "uuid": "bcf0f03c-5951-46a7-aa38-545aed9bc183"
+                                                    }
+                                                ]
+                                            },
+                                            "2": {
+                                                "annotation": "",
+                                                "content_id": null,
+                                                "errors": null,
+                                                "id": 2,
+                                                "input_connections": {},
+                                                "inputs": [
+                                                    {
+                                                        "description": "",
+                                                        "name": "minimap setting (for long reads) "
+                                                    }
+                                                ],
+                                                "label": "minimap setting (for long reads) ",
+                                                "name": "Input parameter",
+                                                "outputs": [],
+                                                "position": {
+                                                    "left": 0.578125,
+                                                    "top": 495.859375
+                                                },
+                                                "tool_id": null,
+                                                "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                                                "tool_version": null,
+                                                "type": "parameter_input",
+                                                "uuid": "fb80c05c-08d4-4ac2-b4bf-81ed906e4d72",
+                                                "when": null,
+                                                "workflow_outputs": [
+                                                    {
+                                                        "label": null,
+                                                        "output_name": "output",
+                                                        "uuid": "3983ef22-5f05-4384-8f34-6ac8c4b2cc83"
+                                                    }
+                                                ]
+                                            },
+                                            "3": {
+                                                "annotation": "Map raw reads to assembly; output paf",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "errors": null,
+                                                "id": 3,
+                                                "input_connections": {
+                                                    "fastq_input|analysis_type_selector": {
+                                                        "id": 2,
+                                                        "output_name": "output"
+                                                    },
+                                                    "fastq_input|fastq_input1": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    },
+                                                    "reference_source|ref_file": {
+                                                        "id": 0,
+                                                        "output_name": "output"
+                                                    }
+                                                },
+                                                "inputs": [
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "reference_source"
+                                                    }
+                                                ],
+                                                "label": "Minimap2: map long reads to assembly",
+                                                "name": "Map with minimap2",
+                                                "outputs": [
+                                                    {
+                                                        "name": "alignment_output",
+                                                        "type": "bam"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 377.640625,
+                                                    "top": 0
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionalignment_output": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "alignment_output"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "be1d967337e4",
+                                                    "name": "minimap2",
+                                                    "owner": "iuc",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "2.26+galaxy0",
+                                                "type": "tool",
+                                                "uuid": "0c06144f-d1ac-4b45-9669-1ddf11fcb06b",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "4": {
+                                                "annotation": "",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "errors": null,
+                                                "id": 4,
+                                                "input_connections": {
+                                                    "corrected_reads": {
+                                                        "id": 0,
+                                                        "output_name": "output"
+                                                    },
+                                                    "overlaps": {
+                                                        "id": 3,
+                                                        "output_name": "alignment_output"
+                                                    },
+                                                    "reads": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    }
+                                                },
+                                                "inputs": [],
+                                                "label": "Racon: polish 1",
+                                                "name": "Racon",
+                                                "outputs": [
+                                                    {
+                                                        "name": "consensus",
+                                                        "type": "fasta"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 458.640625,
+                                                    "top": 518.875
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionconsensus": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "78c533842eeb",
+                                                    "name": "racon",
+                                                    "owner": "bgruening",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "1.5.0+galaxy1",
+                                                "type": "tool",
+                                                "uuid": "6c144354-91f2-49dd-a1f5-7c4119859730",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "5": {
+                                                "annotation": "Map raw reads to assembly; output paf",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "errors": null,
+                                                "id": 5,
+                                                "input_connections": {
+                                                    "fastq_input|analysis_type_selector": {
+                                                        "id": 2,
+                                                        "output_name": "output"
+                                                    },
+                                                    "fastq_input|fastq_input1": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    },
+                                                    "reference_source|ref_file": {
+                                                        "id": 4,
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "inputs": [
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "reference_source"
+                                                    }
+                                                ],
+                                                "label": "Minimap2: map long reads to polished assembly 1",
+                                                "name": "Map with minimap2",
+                                                "outputs": [
+                                                    {
+                                                        "name": "alignment_output",
+                                                        "type": "bam"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 698.859375,
+                                                    "top": 13.390625
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionalignment_output": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "alignment_output"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "be1d967337e4",
+                                                    "name": "minimap2",
+                                                    "owner": "iuc",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "2.26+galaxy0",
+                                                "type": "tool",
+                                                "uuid": "c1b83dad-a8ed-42cb-951f-73f59f2dfa92",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "6": {
+                                                "annotation": "",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "errors": null,
+                                                "id": 6,
+                                                "input_connections": {
+                                                    "corrected_reads": {
+                                                        "id": 4,
+                                                        "output_name": "consensus"
+                                                    },
+                                                    "overlaps": {
+                                                        "id": 5,
+                                                        "output_name": "alignment_output"
+                                                    },
+                                                    "reads": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    }
+                                                },
+                                                "inputs": [],
+                                                "label": "Racon: polish 2",
+                                                "name": "Racon",
+                                                "outputs": [
+                                                    {
+                                                        "name": "consensus",
+                                                        "type": "fasta"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 759.9375,
+                                                    "top": 485.71875
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionconsensus": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "78c533842eeb",
+                                                    "name": "racon",
+                                                    "owner": "bgruening",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "1.5.0+galaxy1",
+                                                "type": "tool",
+                                                "uuid": "3208491e-b831-4238-957e-5b7388d7ff8d",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "7": {
+                                                "annotation": "Map raw reads to assembly; output paf",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "errors": null,
+                                                "id": 7,
+                                                "input_connections": {
+                                                    "fastq_input|analysis_type_selector": {
+                                                        "id": 2,
+                                                        "output_name": "output"
+                                                    },
+                                                    "fastq_input|fastq_input1": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    },
+                                                    "reference_source|ref_file": {
+                                                        "id": 6,
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "inputs": [
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "reference_source"
+                                                    }
+                                                ],
+                                                "label": "Minimap2: map long reads to polished assembly 2",
+                                                "name": "Map with minimap2",
+                                                "outputs": [
+                                                    {
+                                                        "name": "alignment_output",
+                                                        "type": "bam"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 998.75,
+                                                    "top": 27.9375
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionalignment_output": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "alignment_output"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "be1d967337e4",
+                                                    "name": "minimap2",
+                                                    "owner": "iuc",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "2.26+galaxy0",
+                                                "type": "tool",
+                                                "uuid": "42af524b-7f74-4c75-8d78-f6888078dd2e",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "8": {
+                                                "annotation": "",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "errors": null,
+                                                "id": 8,
+                                                "input_connections": {
+                                                    "corrected_reads": {
+                                                        "id": 6,
+                                                        "output_name": "consensus"
+                                                    },
+                                                    "overlaps": {
+                                                        "id": 7,
+                                                        "output_name": "alignment_output"
+                                                    },
+                                                    "reads": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    }
+                                                },
+                                                "inputs": [],
+                                                "label": "Racon: polish 3",
+                                                "name": "Racon",
+                                                "outputs": [
+                                                    {
+                                                        "name": "consensus",
+                                                        "type": "fasta"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 1089.71875,
+                                                    "top": 455.53125
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionconsensus": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "78c533842eeb",
+                                                    "name": "racon",
+                                                    "owner": "bgruening",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "1.5.0+galaxy1",
+                                                "type": "tool",
+                                                "uuid": "21f339bd-ebc1-4c73-a976-5d0b9ab2127a",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "9": {
+                                                "annotation": "Map raw reads to assembly; output paf",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "errors": null,
+                                                "id": 9,
+                                                "input_connections": {
+                                                    "fastq_input|analysis_type_selector": {
+                                                        "id": 2,
+                                                        "output_name": "output"
+                                                    },
+                                                    "fastq_input|fastq_input1": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    },
+                                                    "reference_source|ref_file": {
+                                                        "id": 8,
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "inputs": [
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "reference_source"
+                                                    }
+                                                ],
+                                                "label": "Minimap2: map long reads to polished assembly 3",
+                                                "name": "Map with minimap2",
+                                                "outputs": [
+                                                    {
+                                                        "name": "alignment_output",
+                                                        "type": "bam"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 1316.53125,
+                                                    "top": 38.046875
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionalignment_output": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "alignment_output"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "be1d967337e4",
+                                                    "name": "minimap2",
+                                                    "owner": "iuc",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "2.26+galaxy0",
+                                                "type": "tool",
+                                                "uuid": "7d36291e-aa76-4312-9943-b5e56d0e90c5",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            }
+                                        },
+                                        "tags": "",
+                                        "uuid": "c57efd37-4cf6-4cc7-abf4-2bab22a2e9a0"
+                                    },
+                                    "tool_id": null,
+                                    "type": "subworkflow",
+                                    "uuid": "58c99e4b-fd6a-401d-b9c7-cdf7e6d1757d",
+                                    "when": null,
+                                    "workflow_outputs": [
+                                        {
+                                            "label": null,
+                                            "output_name": "2:output",
+                                            "uuid": "50fa1032-8037-454e-8192-b95405bcd5d4"
+                                        }
+                                    ]
+                                },
+                                "5": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
+                                    "errors": null,
+                                    "id": 5,
+                                    "input_connections": {
+                                        "d": {
+                                            "id": 4,
+                                            "output_name": "Assembly polished by long reads using Racon"
+                                        },
+                                        "i": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Medaka polish",
+                                    "name": "medaka consensus pipeline",
+                                    "outputs": [
+                                        {
+                                            "name": "out_consensus",
+                                            "type": "fasta"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 515.5164024294684,
+                                        "top": 305.08460859328346
+                                    },
+                                    "post_job_actions": {
+                                        "RenameDatasetActionout_consensus": {
+                                            "action_arguments": {
+                                                "newname": "Medaka_long_reads_polished_assembly.fasta"
+                                            },
+                                            "action_type": "RenameDatasetAction",
+                                            "output_name": "out_consensus"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "fc8804320156",
+                                        "name": "medaka_consensus_pipeline",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"b\": \"100\", \"d\": {\"__class__\": \"ConnectedValue\"}, \"g\": false, \"i\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"r941_min_high_g360\", \"out\": [\"consensus\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "1.7.2+galaxy1",
+                                    "type": "tool",
+                                    "uuid": "14c5ce9c-df92-4e20-85da-7a161eaa759d",
+                                    "when": null,
+                                    "workflow_outputs": [
+                                        {
+                                            "label": "Assembly polished by long reads using Medaka",
+                                            "output_name": "out_consensus",
+                                            "uuid": "e3136060-bce7-4af3-87c4-9dcbb0d1f531"
+                                        }
+                                    ]
+                                },
+                                "6": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                                    "errors": null,
+                                    "id": 6,
+                                    "input_connections": {
+                                        "fasta": {
+                                            "id": 4,
+                                            "output_name": "Assembly polished by long reads using Racon"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Fasta statistics after Racon long read polish",
+                                    "name": "Fasta Statistics",
+                                    "outputs": [
+                                        {
+                                            "name": "stats_output",
+                                            "type": "tabular"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 611.8186129984722,
+                                        "top": 131.47863560473016
+                                    },
+                                    "post_job_actions": {},
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "0dbb995c7d35",
+                                        "name": "fasta_stats",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gaps_option\": false, \"genome_size\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "2.0",
+                                    "type": "tool",
+                                    "uuid": "e78db141-a6d2-42b1-b2b6-aee5e900d3f4",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "7": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                                    "errors": null,
+                                    "id": 7,
+                                    "input_connections": {
+                                        "fasta": {
+                                            "id": 5,
+                                            "output_name": "out_consensus"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Fasta statistics after Medaka polish",
+                                    "name": "Fasta Statistics",
+                                    "outputs": [
+                                        {
+                                            "name": "stats_output",
+                                            "type": "tabular"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 816.9504695700908,
+                                        "top": 343.05724959525315
+                                    },
+                                    "post_job_actions": {},
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "0dbb995c7d35",
+                                        "name": "fasta_stats",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gaps_option\": false, \"genome_size\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "2.0",
+                                    "type": "tool",
+                                    "uuid": "96f313ee-4a6a-4ba9-86f8-3dedc1d5d30d",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "8": {
+                                    "annotation": "",
+                                    "id": 8,
+                                    "input_connections": {
+                                        "Assembly to be polished": {
+                                            "id": 5,
+                                            "input_subworkflow_step_id": 0,
+                                            "output_name": "out_consensus"
+                                        },
+                                        "Illumina reads, R1, in fastq.gz format": {
+                                            "id": 3,
+                                            "input_subworkflow_step_id": 1,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": null,
+                                    "name": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 915.3758175639219,
+                                        "top": 512.306732089216
+                                    },
+                                    "subworkflow": {
+                                        "a_galaxy_workflow": "true",
+                                        "annotation": "",
+                                        "comments": [],
+                                        "creator": [
+                                            {
+                                                "class": "Person",
+                                                "identifier": "0000-0002-9906-0673",
+                                                "name": "Anna Syme"
+                                            }
+                                        ],
+                                        "format-version": "0.1",
+                                        "name": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
+                                        "steps": {
+                                            "0": {
+                                                "annotation": "",
+                                                "content_id": null,
+                                                "errors": null,
+                                                "id": 0,
+                                                "input_connections": {},
+                                                "inputs": [
+                                                    {
+                                                        "description": "",
+                                                        "name": "Assembly to be polished"
+                                                    }
+                                                ],
+                                                "label": "Assembly to be polished",
+                                                "name": "Input dataset",
+                                                "outputs": [],
+                                                "position": {
+                                                    "left": 0,
+                                                    "top": 72.5176329833982
+                                                },
+                                                "tool_id": null,
+                                                "tool_state": "{\"optional\": false, \"tag\": null}",
+                                                "tool_version": null,
+                                                "type": "data_input",
+                                                "uuid": "28669894-74e2-4ba1-9d49-6e3209b5a1de",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "1": {
+                                                "annotation": "",
+                                                "content_id": null,
+                                                "errors": null,
+                                                "id": 1,
+                                                "input_connections": {},
+                                                "inputs": [
+                                                    {
+                                                        "description": "",
+                                                        "name": "Illumina reads, R1, in fastq.gz format"
+                                                    }
+                                                ],
+                                                "label": "Illumina reads, R1, in fastq.gz format",
+                                                "name": "Input dataset",
+                                                "outputs": [],
+                                                "position": {
+                                                    "left": 8.5,
+                                                    "top": 341.2832579833982
+                                                },
+                                                "tool_id": null,
+                                                "tool_state": "{\"optional\": false, \"tag\": null}",
+                                                "tool_version": null,
+                                                "type": "data_input",
+                                                "uuid": "bc936fdc-22a9-4507-aa47-4a70a3f93923",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "2": {
+                                                "annotation": "",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "errors": null,
+                                                "id": 2,
+                                                "input_connections": {
+                                                    "fastq_input|fastq_input1": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    },
+                                                    "reference_source|ref_file": {
+                                                        "id": 0,
+                                                        "output_name": "output"
+                                                    }
+                                                },
+                                                "inputs": [
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "reference_source"
+                                                    }
+                                                ],
+                                                "label": "Minimap2 round 1: map reads to assembly",
+                                                "name": "Map with minimap2",
+                                                "outputs": [
+                                                    {
+                                                        "name": "alignment_output",
+                                                        "type": "bam"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 399.936279296875,
+                                                    "top": 0
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionalignment_output": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "alignment_output"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "be1d967337e4",
+                                                    "name": "minimap2",
+                                                    "owner": "iuc",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": \"sr\"}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "2.26+galaxy0",
+                                                "type": "tool",
+                                                "uuid": "b01b8c3d-c33b-47b2-9a83-297c19d63ab7",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "3": {
+                                                "annotation": "",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "errors": null,
+                                                "id": 3,
+                                                "input_connections": {
+                                                    "corrected_reads": {
+                                                        "id": 0,
+                                                        "output_name": "output"
+                                                    },
+                                                    "overlaps": {
+                                                        "id": 2,
+                                                        "output_name": "alignment_output"
+                                                    },
+                                                    "reads": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    }
+                                                },
+                                                "inputs": [],
+                                                "label": "Racon round 1: polish assembly",
+                                                "name": "Racon",
+                                                "outputs": [
+                                                    {
+                                                        "name": "consensus",
+                                                        "type": "fasta"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 635.5625200274146,
+                                                    "top": 432.13610641498093
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionconsensus": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "78c533842eeb",
+                                                    "name": "racon",
+                                                    "owner": "bgruening",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"error_threshold\": \"0.3\", \"fragment_correction\": false, \"gap\": \"-4\", \"include_unpolished\": false, \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"window_length\": \"500\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "1.5.0+galaxy1",
+                                                "type": "tool",
+                                                "uuid": "fe32d046-4ff2-485e-84e8-191b04803afc",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "4": {
+                                                "annotation": "",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "errors": null,
+                                                "id": 4,
+                                                "input_connections": {
+                                                    "fastq_input|fastq_input1": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    },
+                                                    "reference_source|ref_file": {
+                                                        "id": 3,
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "inputs": [
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "fastq_input"
+                                                    },
+                                                    {
+                                                        "description": "runtime parameter for tool Map with minimap2",
+                                                        "name": "reference_source"
+                                                    }
+                                                ],
+                                                "label": "Minimap2 round 2: map reads to assembly",
+                                                "name": "Map with minimap2",
+                                                "outputs": [
+                                                    {
+                                                        "name": "alignment_output",
+                                                        "type": "bam"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 859.5,
+                                                    "top": 23.955132983398205
+                                                },
+                                                "post_job_actions": {
+                                                    "HideDatasetActionalignment_output": {
+                                                        "action_arguments": {},
+                                                        "action_type": "HideDatasetAction",
+                                                        "output_name": "alignment_output"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "be1d967337e4",
+                                                    "name": "minimap2",
+                                                    "owner": "iuc",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": \"sr\"}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "2.26+galaxy0",
+                                                "type": "tool",
+                                                "uuid": "ee834cad-027a-4a84-963b-141b22eaa70a",
+                                                "when": null,
+                                                "workflow_outputs": []
+                                            },
+                                            "5": {
+                                                "annotation": "",
+                                                "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "errors": null,
+                                                "id": 5,
+                                                "input_connections": {
+                                                    "corrected_reads": {
+                                                        "id": 3,
+                                                        "output_name": "consensus"
+                                                    },
+                                                    "overlaps": {
+                                                        "id": 4,
+                                                        "output_name": "alignment_output"
+                                                    },
+                                                    "reads": {
+                                                        "id": 1,
+                                                        "output_name": "output"
+                                                    }
+                                                },
+                                                "inputs": [],
+                                                "label": "Racon round 2: polish assembly",
+                                                "name": "Racon",
+                                                "outputs": [
+                                                    {
+                                                        "name": "consensus",
+                                                        "type": "fasta"
+                                                    }
+                                                ],
+                                                "position": {
+                                                    "left": 1198.765625,
+                                                    "top": 332.4707579833982
+                                                },
+                                                "post_job_actions": {
+                                                    "RenameDatasetActionconsensus": {
+                                                        "action_arguments": {
+                                                            "newname": "Racon_short_reads_polished_assembly.fasta"
+                                                        },
+                                                        "action_type": "RenameDatasetAction",
+                                                        "output_name": "consensus"
+                                                    }
+                                                },
+                                                "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                                                "tool_shed_repository": {
+                                                    "changeset_revision": "78c533842eeb",
+                                                    "name": "racon",
+                                                    "owner": "bgruening",
+                                                    "tool_shed": "toolshed.g2.bx.psu.edu"
+                                                },
+                                                "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                                "tool_version": "1.5.0+galaxy1",
+                                                "type": "tool",
+                                                "uuid": "b3c89c40-3ad0-454c-a4d4-dfa34fb09f24",
+                                                "when": null,
+                                                "workflow_outputs": [
+                                                    {
+                                                        "label": "Assembly polished by short reads using Racon",
+                                                        "output_name": "consensus",
+                                                        "uuid": "594819c3-668e-4575-b9a6-4459ffacf952"
+                                                    }
+                                                ]
+                                            }
+                                        },
+                                        "tags": "",
+                                        "uuid": "1b96b1cf-dbd4-46b1-8a59-aebfe80135c2"
+                                    },
+                                    "tool_id": null,
+                                    "type": "subworkflow",
+                                    "uuid": "46288abb-a2bc-43d5-822a-a93af0d346cf",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                },
+                                "9": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                                    "errors": null,
+                                    "id": 9,
+                                    "input_connections": {
+                                        "fasta": {
+                                            "id": 8,
+                                            "output_name": "Assembly polished by short reads using Racon"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Fasta statistics after Racon short read polish",
+                                    "name": "Fasta Statistics",
+                                    "outputs": [
+                                        {
+                                            "name": "stats_output",
+                                            "type": "tabular"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 1179.1223817823236,
+                                        "top": 547.060000097866
+                                    },
+                                    "post_job_actions": {},
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "0dbb995c7d35",
+                                        "name": "fasta_stats",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"dataset\": {\"__class__\": \"ConnectedValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gaps_option\": false, \"genome_size\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": "2.0",
+                                    "type": "tool",
+                                    "uuid": "3c06b177-02b5-4068-8056-56b653d95379",
+                                    "when": null,
+                                    "workflow_outputs": []
+                                }
                             },
-                            "HideDatasetActionquant_group_matrix": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "quant_group_matrix"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "52ac6fde9a5b",
-                            "name": "msstats",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "tags": "",
+                            "uuid": "af8b99cb-cfc5-4f96-ba6c-6a178826ca98"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"dp_options\": {\"logTrans\": \"2\", \"norm\": {\"normalization\": \"equalizeMedians\", \"__current_case__\": 0}, \"fillIncompleteRows\": \"true\", \"features\": {\"featureSubset\": \"all\", \"__current_case__\": 0}, \"summarize\": {\"summaryMethod\": \"TMP\", \"__current_case__\": 0, \"MBimpute\": \"true\", \"remove50missing\": \"false\"}, \"censoredInt\": \"NA\", \"cutoffCensored\": \"minFeature\", \"maxQuantileforCensored\": \"0.999\"}, \"group\": {\"group_comparison\": \"yes\", \"__current_case__\": 1, \"comparison_matrix\": {\"__class__\": \"ConnectedValue\"}, \"select_outputs\": [\"fittedmodel\", \"comparison_result\", \"volcanoplot\", \"comparisonplot\"]}, \"input\": {\"input_src\": \"MSstats\", \"__current_case__\": 0, \"msstats_input\": {\"__class__\": \"ConnectedValue\"}}, \"selected_outputs\": [\"log\", \"processed_data\", \"qcplot\", \"quant_group_matrix\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.20.1.0",
-                        "type": "tool",
-                        "uuid": "cb3da2fb-604c-43e7-8540-84de6d00ff0f",
+                        "tool_id": null,
+                        "type": "subworkflow",
+                        "uuid": "6b6668c9-25b7-4135-ac9b-140a6d1593b0",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "volcanoplot",
-                                "uuid": "4dabaa14-50b0-4225-aa6c-72470f1df31e"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "comparisonplot",
-                                "uuid": "f3a3175f-a995-406a-a3d2-287b38d0e8ff"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "processed_data",
-                                "uuid": "bf41d447-8dbd-4554-b684-8cf5965d2c7b"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "comparison_result",
-                                "uuid": "3b09f94d-6c38-49da-9938-e99e5e79fd77"
+                                "output_name": "2:output",
+                                "uuid": "f740de36-9921-4f0c-924e-3902bc2083b7"
                             },
                             {
                                 "label": null,
-                                "output_name": "qcplot",
-                                "uuid": "a09e7723-369d-4c2d-b209-eb82e3c2404d"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "Grep1",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "input": {
-                                "id": 2,
-                                "output_name": "comparison_result"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Select",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 523.4666595458984,
-                            "height": 93.19999694824219,
-                            "left": 674.13330078125,
-                            "right": 874.13330078125,
-                            "top": 430.26666259765625,
-                            "width": 200,
-                            "x": 674.13330078125,
-                            "y": 430.26666259765625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "Grep1",
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"false\", \"pattern\": \"(ECOLI)|(logFC)\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.1",
-                        "type": "tool",
-                        "uuid": "7086c065-874a-4fe2-a084-c55b39febd65",
-                        "workflow_outputs": [
-                            {
-                                "label": "Select_Ecoli",
-                                "output_name": "out_file1",
-                                "uuid": "6e8589bd-13fd-4a97-a9c3-ea0a5a0e2326"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "Filter1",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "input": {
-                                "id": 3,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Filter",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 663.9666595458984,
-                            "height": 93.19999694824219,
-                            "left": 900.63330078125,
-                            "right": 1100.63330078125,
-                            "top": 570.7666625976562,
-                            "width": 200,
-                            "x": 900.63330078125,
-                            "y": 570.7666625976562
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"cond\": \"c7!='NA'\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
-                        "type": "tool",
-                        "uuid": "3f136bb5-3387-4f1a-abf2-07b7ce58d577",
-                        "workflow_outputs": [
-                            {
-                                "label": "Filter_Ecoli",
-                                "output_name": "out_file1",
-                                "uuid": "6997a43a-a17b-418b-bb6d-7d32a6c277ae"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "input": {
-                                "id": 4,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Histogram",
-                                "name": "input"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Histogram",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "pdf"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 536.1999969482422,
-                            "height": 93.19999694824219,
-                            "left": 1081.36669921875,
-                            "right": 1281.36669921875,
-                            "top": 443,
-                            "width": 200,
-                            "x": 1081.36669921875,
-                            "y": 443
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6f134426c2b0",
-                            "name": "histogram",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"breaks\": \"25\", \"density\": \"true\", \"frequency\": \"false\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"numerical_column\": \"3\", \"title\": \"Distribution of Ecoli Protein log FC values\", \"xlab\": \"log2 Fold Change\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.3",
-                        "type": "tool",
-                        "uuid": "65080a30-a49c-4414-a9b7-d72390001eab",
-                        "workflow_outputs": [
-                            {
-                                "label": "Histogram_Ecoli",
-                                "output_name": "out_file1",
-                                "uuid": "cf3abac3-8227-4af8-a551-6aeae154a0e4"
+                                "output_name": "4:2:output",
+                                "uuid": "2b5d309e-c47e-4a79-a69c-4d4fd6a93d8b"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/DIA_Analysis_MSstats",
-                "path": "topics/proteomics/tutorials/DIA_Analysis_MSstats/workflows/Galaxy-Workflow-DIA_MSstats_Training_msstats_input_tabular.ga",
+                "parent_id": "assembly/largegenome",
+                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga",
                 "tags": [
-                    "proteomics"
+                    "LG-WF",
+                    "GTN"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "DIA_analysis_MSstats",
-                "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-DIA_Analysis_MSstats/versions/galaxy-workflow-dia-msstats-training-msstats-input-tabular",
-                "tutorial_id": "DIA_Analysis_MSstats",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/DIA_Analysis_MSstats/workflows/Galaxy-Workflow-DIA_MSstats_Training_msstats_input_tabular.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/DIA_Analysis_MSstats/workflows/Galaxy-Workflow-DIA_MSstats_Training_msstats_input_tabular.html",
+                "tests": false,
+                "title": "Combined workflows for large genome assembly - upgraded ",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-combined-workflows-for-large-genome-assembly",
+                "tutorial_id": "largegenome",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.html",
                 "version": 2,
-                "wfid": "proteomics-DIA_Analysis_MSstats",
-                "wfname": "galaxy-workflow-dia-msstats-training-msstats-input-tabular",
-                "workflow": "Galaxy-Workflow-DIA_MSstats_Training_msstats_input_tabular.ga",
+                "wfid": "assembly-largegenome",
+                "wfname": "galaxy-workflow-combined-workflows-for-large-genome-assembly",
+                "workflow": "Galaxy-Workflow-Combined_workflows_for_large_genome_assembly.ga",
                 "workflow_tools": [
-                    "Filter1",
-                    "Grep1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0"
+                    "barchart_gnuplot",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1"
                 ],
-                "workflowhub_id": "1163"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/4307758"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "tabular_to_fasta",
-                    "owner": "devteam",
-                    "revisions": "0a7799698fe5",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mz_to_sqlite",
-                    "owner": "galaxyp",
-                    "revisions": "f5c632894818",
-                    "tool_panel_section_label": "Convert Formats",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "peptideshaker",
-                    "owner": "galaxyp",
-                    "revisions": "7fdd9119cc4f",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "peptideshaker",
-                    "owner": "galaxyp",
-                    "revisions": "7fdd9119cc4f",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "query_tabular",
-                    "owner": "iuc",
-                    "revisions": "33d61c89fb8d",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: tabular_to_fasta\n  owner: devteam\n  revisions: 0a7799698fe5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mz_to_sqlite\n  owner: galaxyp\n  revisions: f5c632894818\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 7fdd9119cc4f\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 7fdd9119cc4f\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n  owner: iuc\n  revisions: 33d61c89fb8d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.json",
-        "contributors": [
-            {
-                "email": "subinamehta@gmail.com",
-                "id": "subinamehta",
-                "joined": "2018-06",
-                "linkedin": "subinamehta",
-                "matrix": "subinamehta:matrix.org",
-                "name": "Subina Mehta",
-                "orcid": "0000-0001-9818-0537",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
-                "twitter": "Subina_Mehta",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
-            },
-            {
-                "email": "tgriffin@umn.edu",
-                "github": false,
-                "id": "timothygriffin",
-                "joined": "2017-09",
-                "name": "Timothy J. Griffin",
-                "orcid": "0000-0001-6801-2559",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
-            },
-            {
-                "email": "pjagtap@umn.edu",
-                "id": "pratikdjagtap",
-                "joined": "2017-09",
-                "name": "Pratik Jagtap",
-                "orcid": "0000-0003-0984-0973",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
-            },
-            {
-                "email": "rsajulga@umn.edu",
-                "id": "jraysajulga",
-                "joined": "2018-11",
-                "name": "Ray Sajulga",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jraysajulga/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jraysajulga.json"
-            },
-            {
-                "email": "jj@umn.edu",
-                "id": "jj-umn",
-                "in_memoriam": "<a href=\"https://galaxyproject.org/news/2024-03-19-remembrances-of-jj/\">James \u2018JJ\u2019 Johnson, was a Galaxy community rock star most known for his indispensable contributions to the Galaxy Proteomics community.</a>\n\nJJ\u2019s works will live on in so many Galaxy tools and workflows for years to come.",
-                "joined": "2017-09",
-                "name": "James Johnson",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jj-umn/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jj-umn.json"
+                "workflowhub_id": "1176"
             },
             {
-                "email": "kumar207@umn.edu",
-                "id": "pravs3683",
-                "joined": "2019-04",
-                "name": "Praveen Kumar",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pravs3683/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pravs3683.json"
-            }
-        ],
-        "dir": "topics/proteomics/tutorials/proteogenomics-dbsearch",
-        "edam_operation": [
-            "Conversion",
-            "Peptide database search"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "proteomics",
-                "tutorials": [
-                    "proteogenomics-novel-peptide-analysis"
-                ],
-                "type": "internal"
-            }
-        ],
-        "hands_on": true,
-        "id": "proteomics/proteogenomics-dbsearch",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "With SearchGUI and PeptideShaker you can gain access to multiple search engines"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-08-09",
-        "objectives": [
-            "A proteogenomic data analysis of mass spectrometry data to identify and visualize variant peptides."
-        ],
-        "pageviews": 1897,
-        "pub_date": "2018-11-20",
-        "questions": [
-            "How to identify variant proteoforms in MS data by searching with the customized Protein database?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "emmaleith"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "30M",
-                "speakers": [
-                    "andrewr"
-                ],
-                "youtube_id": "q1OjmTcbvBA"
-            }
-        ],
-        "requirements": [
-            {
-                "topic_name": "proteomics",
-                "tutorials": [
-                    "proteogenomics-dbcreation"
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
+                    }
                 ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00232",
-        "short_tools": [
-            "tab2fasta",
-            "peptide_shaker",
-            "search_gui",
-            "query_tabular",
-            "mz_to_sqlite"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "multi-omics",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "proteogenomics"
-        ],
-        "time_estimation": "15m",
-        "title": "Proteogenomics 2: Database Search",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite/mz_to_sqlite/2.0.4+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0"
-        ],
-        "topic_name": "proteomics",
-        "topic_name_human": "Proteomics",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "proteogenomics-dbsearch",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.json"
-        },
-        "version": 23,
-        "video": false,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 301,
-        "visitors": 1217,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Proteogenomics 2: Database Search",
+                "description": "",
                 "features": {
                     "comments": false,
                     "parameters": false,
-                    "report": null,
+                    "report": {
+                        "markdown": "\n# Workflow Report for Data QC\n\n## Workflow steps\n\n```galaxy\nworkflow_display()\n```\n\n"
+                    },
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nUniprot_cRAP_SAV_indel_translatedbed.FASTA\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nMGF Collection\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference Protein Accessions\"]\n  3[label=\"Search GUI\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  kd14f948180db4c158afc6fa38ef61deb[color=lightseagreen,label=\"Output\\nSearch GUI on input dataset(s)\"]\n  3 -> kd14f948180db4c158afc6fa38ef61deb\n  4[label=\"Peptide Shaker\"]\n  3 -> 4 [label=\"searchgui_results\"]\n  kafe0f1a528bb44bdb32bc634aa2154f3[color=lightseagreen,label=\"Output\\nPeptide Shaker on input dataset(s): mzidentML file\"]\n  4 -> kafe0f1a528bb44bdb32bc634aa2154f3\n  5[label=\"mz to sqlite\"]\n  4 -> 5 [label=\"mzidentML\"]\n  1 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  kb43a2136cf594fb0bb2b0d5b446c8ba9[color=lightseagreen,label=\"Output\\nmz to sqlite on input dataset(s)\"]\n  5 -> kb43a2136cf594fb0bb2b0d5b446c8ba9\n  6[label=\"Removing reference proteins\"]\n  4 -> 6 [label=\"output_psm\"]\n  4 -> 6 [label=\"output_psm\"]\n  2 -> 6 [label=\"output\"]\n  ka06ad5fa9a004867b9763745c5e59c80[color=lightseagreen,label=\"Output\\nRemoving reference proteins\"]\n  6 -> ka06ad5fa9a004867b9763745c5e59c80\n  7[label=\"Selecting sequence with length >6 and <30\"]\n  6 -> 7 [label=\"output\"]\n  kb71e541728644712b5c1c90725976baf[color=lightseagreen,label=\"Output\\nSelecting sequence with length >6 and <30\"]\n  7 -> kb71e541728644712b5c1c90725976baf\n  8[label=\"Peptides for BlastP analysis\"]\n  7 -> 8 [label=\"output\"]\n  k1ac3c77680954db185183643dc081006[color=lightseagreen,label=\"Output\\nPeptides_for_BlastP_analysis\"]\n  8 -> k1ac3c77680954db185183643dc081006\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput file: long reads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R1\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R2\"]\n  3[label=\"Nanoplot: long reads\"]\n  0 -> 3 [label=\"output\"]\n  k73d0e4cf366e41c1810ab269638826b3[color=lightseagreen,label=\"Output\\nNanoPlot on input dataset(s): HTML report\"]\n  3 -> k73d0e4cf366e41c1810ab269638826b3\n  4[label=\"FastQC on R1\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"FastQC on R2\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"MultiQC: combine fastQC reports\"]\n  4 -> 6 [label=\"text_file\"]\n  5 -> 6 [label=\"text_file\"]\n  k8baf8700876e4a74ad996e656f3ba618[color=lightseagreen,label=\"Output\\nMultiQC on input dataset(s): Webpage\"]\n  6 -> k8baf8700876e4a74ad996e656f3ba618\n}",
                 "history": [
                     {
-                        "hash": "6474a188df5601dc13cccb8fcfcd99cab9c6d1f4",
-                        "message": "Update galaxy-workflow-mouse_rnaseq_dbsearch.ga",
-                        "num": 8,
-                        "short_hash": "6474a188d",
-                        "unix": "1612811785"
-                    },
-                    {
-                        "hash": "42e6b15fc35a261ef9aed129c2d28385e747e1d1",
-                        "message": "Update galaxy-workflow-mouse_rnaseq_dbsearch.ga",
-                        "num": 7,
-                        "short_hash": "42e6b15fc",
-                        "unix": "1611782271"
-                    },
-                    {
-                        "hash": "8011373088f966876016f1afc71237d842ba13d7",
-                        "message": "Update galaxy-workflow-mouse_rnaseq_dbsearch.ga",
-                        "num": 6,
-                        "short_hash": "801137308",
-                        "unix": "1611781407"
-                    },
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
+                        "hash": "d35221f6506e7b95e8b3ff679a2ad01edf1a560a",
+                        "message": "Update Galaxy-Workflow-Data_QC.ga",
                         "num": 5,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
+                        "short_hash": "d35221f65",
+                        "unix": "1715074384"
                     },
                     {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
+                        "hash": "a737e5f1b936379382f4d568b0caeb664d81c392",
+                        "message": "Rename Galaxy-Workflow-Data_QC_-_upgraded.ga to Galaxy-Workflow-Data_QC.ga",
                         "num": 4,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
+                        "short_hash": "a737e5f1b",
+                        "unix": "1714537191"
                     },
                     {
-                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
-                        "message": "Changed format of workflows",
+                        "hash": "9ca497557dddc43b116a61592a953f455046bc86",
+                        "message": "Rename Galaxy-Workflow-Data_QC.ga to Galaxy-Workflow-Data_QC_old.ga",
                         "num": 3,
-                        "short_hash": "361236c41",
-                        "unix": "1554368414"
+                        "short_hash": "9ca497557",
+                        "unix": "1714537118"
                     },
                     {
-                        "hash": "6eef55b7e8306d8ce46ac08e7799f6f65ae106aa",
-                        "message": "Updated install_tutorial_requirements.sh + minor fixes (#1275)",
+                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
+                        "message": "add/complete creator info on workflows",
                         "num": 2,
-                        "short_hash": "6eef55b7e",
-                        "unix": "1551293676"
+                        "short_hash": "62e77944b",
+                        "unix": "1676627603"
                     },
                     {
-                        "hash": "715d5f2ee1d9cfa74c5230a0a4bf746df8758e87",
-                        "message": "fix folder names",
+                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
+                        "message": "large genome tutorial",
                         "num": 1,
-                        "short_hash": "715d5f2ee",
-                        "unix": "1542746779"
+                        "short_hash": "9fcb3aeec",
+                        "unix": "1665123856"
                     }
                 ],
                 "inputs": [
@@ -175252,2178 +177132,1412 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Uniprot_cRAP_SAV_indel_translatedbed.FASTA"
-                            }
-                        ],
-                        "label": "Uniprot_cRAP_SAV_indel_translatedbed.FASTA",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 290,
-                            "height": 105,
-                            "left": -277.5,
-                            "right": -77.5,
-                            "top": 185,
-                            "width": 200,
-                            "x": -277.5,
-                            "y": 185
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "eb7142ae-40cc-4c61-b744-bf7f3c8ed096",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "a125ba5f-316b-4f95-a8f2-978e9a9affda"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "MGF Collection"
-                            }
-                        ],
-                        "label": "MGF Collection",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 433.984375,
-                            "height": 84,
-                            "left": -277.46875,
-                            "right": -77.46875,
-                            "top": 349.984375,
-                            "width": 200,
-                            "x": -277.46875,
-                            "y": 349.984375
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "d7429ce1-2fc7-4ffa-87dd-4c4c343f8496",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "f0af224e-c8cd-412b-803b-ee636c1b924c"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Reference Protein Accessions"
-                            }
-                        ],
-                        "label": "Reference Protein Accessions",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 592.625,
-                            "height": 84,
-                            "left": -264.5,
-                            "right": -64.5,
-                            "top": 508.625,
-                            "width": 200,
-                            "x": -264.5,
-                            "y": 508.625
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "99f0374c-ea36-4def-822a-2feb64aee67b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "4a838c43-d3ba-4037-9ce1-0a47f919ac94"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nUniprot_cRAP_SAV_indel_translatedbed.FASTA\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nMGF Collection\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nReference Protein Accessions\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Search GUI\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  d14f9481-80db-4c15-8afc-6fa38ef61deb[\"Output\\nSearch GUI on input dataset(s)\"];\n  3 --> d14f9481-80db-4c15-8afc-6fa38ef61deb;\n  style d14f9481-80db-4c15-8afc-6fa38ef61deb stroke:#2c3143,stroke-width:4px;\n  4[\"Peptide Shaker\"];\n  3 -->|searchgui_results| 4;\n  afe0f1a5-28bb-44bd-b32b-c634aa2154f3[\"Output\\nPeptide Shaker on input dataset(s): mzidentML file\"];\n  4 --> afe0f1a5-28bb-44bd-b32b-c634aa2154f3;\n  style afe0f1a5-28bb-44bd-b32b-c634aa2154f3 stroke:#2c3143,stroke-width:4px;\n  5[\"mz to sqlite\"];\n  4 -->|mzidentML| 5;\n  1 -->|output| 5;\n  0 -->|output| 5;\n  b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9[\"Output\\nmz to sqlite on input dataset(s)\"];\n  5 --> b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9;\n  style b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9 stroke:#2c3143,stroke-width:4px;\n  6[\"Removing reference proteins\"];\n  4 -->|output_psm| 6;\n  4 -->|output_psm| 6;\n  2 -->|output| 6;\n  a06ad5fa-9a00-4867-b976-3745c5e59c80[\"Output\\nRemoving reference proteins\"];\n  6 --> a06ad5fa-9a00-4867-b976-3745c5e59c80;\n  style a06ad5fa-9a00-4867-b976-3745c5e59c80 stroke:#2c3143,stroke-width:4px;\n  7[\"Selecting sequence with length >6 and <30\"];\n  6 -->|output| 7;\n  b71e5417-2864-4712-b5c1-c90725976baf[\"Output\\nSelecting sequence with length >6 and <30\"];\n  7 --> b71e5417-2864-4712-b5c1-c90725976baf;\n  style b71e5417-2864-4712-b5c1-c90725976baf stroke:#2c3143,stroke-width:4px;\n  8[\"Peptides for BlastP analysis\"];\n  7 -->|output| 8;\n  1ac3c776-8095-4db1-8518-3643dc081006[\"Output\\nPeptides_for_BlastP_analysis\"];\n  8 --> 1ac3c776-8095-4db1-8518-3643dc081006;\n  style 1ac3c776-8095-4db1-8518-3643dc081006 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "GTN Proteogemics2 Database Search",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Uniprot_cRAP_SAV_indel_translatedbed.FASTA"
+                                "name": "Input file: long reads"
                             }
                         ],
-                        "label": "Uniprot_cRAP_SAV_indel_translatedbed.FASTA",
+                        "label": "Input file: long reads",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 290,
-                            "height": 105,
-                            "left": -277.5,
-                            "right": -77.5,
-                            "top": 185,
-                            "width": 200,
-                            "x": -277.5,
-                            "y": 185
+                            "left": 0,
+                            "top": 0.0
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "eb7142ae-40cc-4c61-b744-bf7f3c8ed096",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "a125ba5f-316b-4f95-a8f2-978e9a9affda"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "MGF Collection"
-                            }
-                        ],
-                        "label": "MGF Collection",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 433.984375,
-                            "height": 84,
-                            "left": -277.46875,
-                            "right": -77.46875,
-                            "top": 349.984375,
-                            "width": 200,
-                            "x": -277.46875,
-                            "y": 349.984375
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "d7429ce1-2fc7-4ffa-87dd-4c4c343f8496",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "f0af224e-c8cd-412b-803b-ee636c1b924c"
-                            }
-                        ]
+                        "uuid": "e2e4a70b-6e36-4b8b-bdf6-12b97189a6bd",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Reference Protein Accessions"
+                                "name": "Input file: Illumina reads R1"
                             }
                         ],
-                        "label": "Reference Protein Accessions",
+                        "label": "Input file: Illumina reads R1",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 592.625,
-                            "height": 84,
-                            "left": -264.5,
-                            "right": -64.5,
-                            "top": 508.625,
-                            "width": 200,
-                            "x": -264.5,
-                            "y": 508.625
+                            "left": 535.703125,
+                            "top": 21.0
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "99f0374c-ea36-4def-822a-2feb64aee67b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "4a838c43-d3ba-4037-9ce1-0a47f919ac94"
-                            }
-                        ]
+                        "uuid": "ea859a58-c81a-4ef6-9bd2-4ef2f17bb5a9",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "input_database": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "peak_lists": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Search GUI",
-                        "outputs": [
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "searchgui_results",
-                                "type": "searchgui_archive"
+                                "description": "",
+                                "name": "Input file: Illumina reads R2"
                             }
                         ],
+                        "label": "Input file: Illumina reads R2",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 514,
-                            "height": 168,
-                            "left": 22.53125,
-                            "right": 222.53125,
-                            "top": 346,
-                            "width": 200,
-                            "x": 22.53125,
-                            "y": 346
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "7fdd9119cc4f",
-                            "name": "peptideshaker",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 530.703125,
+                            "top": 379.984375
                         },
-                        "tool_state": "{\"advanced_options\": {\"searchgui_advanced\": {\"searchgui_advanced_selector\": \"basic\", \"__current_case__\": 0}, \"xtandem\": {\"xtandem_advanced\": \"no\", \"__current_case__\": 0}, \"omssa\": {\"omssa_advanced\": \"no\", \"__current_case__\": 0}, \"msgf\": {\"msgf_advanced\": \"no\", \"__current_case__\": 0}, \"ms_amanda\": {\"ms_amanda_advanced\": \"no\", \"__current_case__\": 0}, \"tide\": {\"tide_advanced\": \"no\", \"__current_case__\": 0}, \"myrimatch\": {\"myrimatch_advanced\": \"no\", \"__current_case__\": 0}, \"comet\": {\"comet_advanced\": \"no\", \"__current_case__\": 0}, \"directtag\": {\"directtag_advanced\": \"no\", \"__current_case__\": 0}, \"novor\": {\"novor_advanced\": \"no\", \"__current_case__\": 0}}, \"input_database\": {\"__class__\": \"ConnectedValue\"}, \"peak_lists\": {\"__class__\": \"ConnectedValue\"}, \"precursor_options\": {\"precursor_ion_tol_units\": \"1\", \"precursor_ion_tol\": \"10.0\", \"fragment_tol_units\": \"0\", \"fragment_tol\": \"0.5\", \"min_charge\": \"2\", \"max_charge\": \"6\", \"forward_ion\": \"b\", \"reverse_ion\": \"y\", \"min_isotope\": \"0\", \"max_isotope\": \"1\"}, \"protein_database_options\": {\"create_decoy\": \"true\", \"use_gene_mapping\": \"false\", \"update_gene_mapping\": \"false\"}, \"protein_digest_options\": {\"digestion\": {\"cleavage\": \"0\", \"__current_case__\": 0, \"digests\": [{\"__index__\": 0, \"enzyme\": \"Trypsin\", \"missed_cleavages\": \"2\"}]}}, \"protein_modification_options\": {\"fixed_modifications\": [\"Carbamidomethylation of C\", \"iTRAQ 4-plex of K\", \"iTRAQ 4-plex of peptide N-term\"], \"variable_modifications\": [\"Oxidation of M\", \"iTRAQ 4-plex of Y\"]}, \"search_engines_options\": {\"engines\": [\"X!Tandem\"]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.3.10.1",
-                        "type": "tool",
-                        "uuid": "41bfe37f-62de-44cd-9a2c-26f007258c61",
-                        "workflow_outputs": [
-                            {
-                                "label": "Search GUI on input dataset(s)",
-                                "output_name": "searchgui_results",
-                                "uuid": "d14f9481-80db-4c15-8afc-6fa38ef61deb"
-                            }
-                        ]
-                    },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "472adc05-88a5-4955-9e43-e82e9550ad08",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput file: long reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R2\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Nanoplot: long reads\"];\n  0 -->|output| 3;\n  73d0e4cf-366e-41c1-810a-b269638826b3[\"Output\\nNanoPlot on input dataset(s): HTML report\"];\n  3 --> 73d0e4cf-366e-41c1-810a-b269638826b3;\n  style 73d0e4cf-366e-41c1-810a-b269638826b3 stroke:#2c3143,stroke-width:4px;\n  4[\"FastQC on R1\"];\n  1 -->|output| 4;\n  5[\"FastQC on R2\"];\n  2 -->|output| 5;\n  6[\"MultiQC: combine fastQC reports\"];\n  4 -->|text_file| 6;\n  5 -->|text_file| 6;\n  8baf8700-876e-4a74-ad99-6e656f3ba618[\"Output\\nMultiQC on input dataset(s): Webpage\"];\n  6 --> 8baf8700-876e-4a74-ad99-6e656f3ba618;\n  style 8baf8700-876e-4a74-ad99-6e656f3ba618 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Data QC - upgraded",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1",
                         "errors": null,
-                        "id": 4,
+                        "id": 3,
                         "input_connections": {
-                            "searchgui_input": {
-                                "id": 3,
-                                "output_name": "searchgui_results"
+                            "mode|reads|files": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Peptide Shaker",
+                        "label": "Nanoplot: long reads",
+                        "name": "NanoPlot",
                         "outputs": [
                             {
-                                "name": "mzidentML",
-                                "type": "mzid"
-                            },
-                            {
-                                "name": "output_certificate",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "output_psm",
-                                "type": "tabular"
+                                "name": "output_html",
+                                "type": "html"
                             },
                             {
-                                "name": "output_peptides",
+                                "name": "nanostats",
                                 "type": "tabular"
                             },
                             {
-                                "name": "output_proteins",
+                                "name": "nanostats_post_filtering",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 704.125,
-                            "height": 471,
-                            "left": 309.53125,
-                            "right": 509.53125,
-                            "top": 233.125,
-                            "width": 200,
-                            "x": 309.53125,
-                            "y": 233.125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "7fdd9119cc4f",
-                            "name": "peptideshaker",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 240.84375,
+                            "top": 104.359375
                         },
-                        "tool_state": "{\"contact_options\": {\"contact_options_selector\": \"no\", \"__current_case__\": 0}, \"exporting_options\": {\"mzidentml_conditional\": {\"mzidentml_creation\": \"true\", \"__current_case__\": 0, \"include_sequences\": \"false\"}, \"zip_conditional\": {\"zip_output_boolean\": \"false\", \"__current_case__\": 0, \"export_cps\": \"false\"}, \"output_reports\": [\"3\", \"6\", \"9\", \"0\"]}, \"filtering_options\": {\"filtering_options_selector\": \"no\", \"__current_case__\": 0}, \"processing_options\": {\"processing_options_selector\": \"no\", \"__current_case__\": 0}, \"searchgui_input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16.36.3",
-                        "type": "tool",
-                        "uuid": "3d435aa3-cc94-4320-94a4-a49503f7e82e",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_certificate",
-                                "uuid": "1c33ea40-12f5-4e28-b4da-5b7975f2c13f"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_psm",
-                                "uuid": "6425fbc7-08cf-4633-ac15-74993be5851f"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_proteins",
-                                "uuid": "a52e58b1-de72-4bd6-a434-674f20c5d19d"
-                            },
-                            {
-                                "label": "Peptide Shaker on input dataset(s): mzidentML file",
-                                "output_name": "mzidentML",
-                                "uuid": "afe0f1a5-28bb-44bd-b32b-c634aa2154f3"
+                        "post_job_actions": {
+                            "HideDatasetActionlog_read_length": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "log_read_length"
                             },
-                            {
-                                "label": null,
-                                "output_name": "output_peptides",
-                                "uuid": "75e03205-eb1a-4cfd-847f-c70dd5c3209a"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite/mz_to_sqlite/2.0.4+galaxy1",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "mzinput": {
-                                "id": 4,
-                                "output_name": "mzidentML"
+                            "HideDatasetActionnanostats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "nanostats"
                             },
-                            "scanfiles": {
-                                "id": 1,
-                                "output_name": "output"
+                            "HideDatasetActionnanostats_post_filtering": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "nanostats_post_filtering"
                             },
-                            "searchdbs": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "mz to sqlite",
-                        "outputs": [
-                            {
-                                "name": "sqlite_db",
-                                "type": "mz.sqlite"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 411.484375,
-                            "height": 220,
-                            "left": 651.546875,
-                            "right": 851.546875,
-                            "top": 191.484375,
-                            "width": 200,
-                            "x": 651.546875,
-                            "y": 191.484375
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionsqlite_db": {
-                                "action_arguments": {
-                                    "newname": "Mz to sqlite"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "sqlite_db"
+                            "HideDatasetActionread_length": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "read_length"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite/mz_to_sqlite/2.0.4+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "f5c632894818",
-                            "name": "mz_to_sqlite",
-                            "owner": "galaxyp",
+                            "changeset_revision": "a02b8b3f5a0c",
+                            "name": "nanoplot",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"mzinput\": {\"__class__\": \"ConnectedValue\"}, \"scanfiles\": {\"__class__\": \"ConnectedValue\"}, \"searchdbs\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.4+galaxy1",
+                        "tool_state": "{\"customization\": {\"color\": null, \"plots\": null, \"N50\": false}, \"filter\": {\"maxlength\": null, \"minlength\": null, \"drop_outliers\": false, \"downsample\": null, \"loglength\": false, \"percentqual\": false, \"alength\": false, \"minqual\": null, \"runtime_until\": null, \"readtype\": null, \"barcoded\": false, \"no_supplementary\": false}, \"mode\": {\"choice\": \"batch\", \"__current_case__\": 0, \"reads\": {\"type\": \"fastq\", \"__current_case__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.42.0+galaxy1",
                         "type": "tool",
-                        "uuid": "1985019a-af9a-4ebc-82c6-448a6ae62166",
+                        "uuid": "3b8a87fe-1506-48d2-a4d9-f4dca8b6065d",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "mz to sqlite on input dataset(s)",
-                                "output_name": "sqlite_db",
-                                "uuid": "b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9"
+                                "label": "NanoPlot on input dataset(s): HTML report",
+                                "output_name": "output_html",
+                                "uuid": "73d0e4cf-366e-41c1-810a-b269638826b3"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
                         "errors": null,
                         "id": 6,
                         "input_connections": {
-                            "tables_0|table": {
-                                "id": 4,
-                                "output_name": "output_psm"
-                            },
-                            "tables_1|table": {
+                            "results_0|software_cond|output_0|input": {
                                 "id": 4,
-                                "output_name": "output_psm"
+                                "output_name": "text_file"
                             },
-                            "tables_2|table": {
-                                "id": 2,
-                                "output_name": "output"
+                            "results_0|software_cond|output_1|input": {
+                                "id": 5,
+                                "output_name": "text_file"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Query Tabular",
-                                "name": "add_to_database"
-                            }
-                        ],
-                        "label": "Removing reference proteins",
-                        "name": "Query Tabular",
+                        "inputs": [],
+                        "label": "MultiQC: combine fastQC reports",
+                        "name": "MultiQC",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 821.640625,
-                            "height": 314,
-                            "left": 609.546875,
-                            "right": 809.546875,
-                            "top": 507.640625,
-                            "width": 200,
-                            "x": 609.546875,
-                            "y": 507.640625
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Removing reference proteins"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "33d61c89fb8d",
-                            "name": "query_tabular",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"save_db\": \"false\", \"sqlquery\": \"SELECT psms.*\\nFROM psms\\nWHERE psms.id NOT IN\\n(SELECT distinct prots.id\\nFROM prots JOIN uniprot ON prots.prot = uniprot.prot)\\nORDER BY psms.id\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"skip\", \"__current_case__\": 0, \"skip_lines\": \"1\"}}]}, \"tbl_opts\": {\"table_name\": \"psms\", \"column_names_from_first_line\": \"false\", \"col_names\": \"id,Proteins,Sequence\", \"load_named_columns\": \"true\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"id\"}]}}, {\"__index__\": 1, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"skip\", \"__current_case__\": 0, \"skip_lines\": \"1\"}}, {\"__index__\": 1, \"filter\": {\"filter_type\": \"select_columns\", \"__current_case__\": 7, \"columns\": \"1,2\"}}, {\"__index__\": 2, \"filter\": {\"filter_type\": \"normalize\", \"__current_case__\": 9, \"columns\": \"2\", \"separator\": \",\"}}]}, \"tbl_opts\": {\"table_name\": \"prots\", \"column_names_from_first_line\": \"false\", \"col_names\": \"id,prot\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"prot,id\"}]}}, {\"__index__\": 2, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"Uniprot\", \"column_names_from_first_line\": \"false\", \"col_names\": \"prot\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"prot\"}]}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.0.0",
-                        "type": "tool",
-                        "uuid": "90f1b13e-0ba1-4373-92c5-8b31adbdcdbb",
-                        "workflow_outputs": [
-                            {
-                                "label": "Removing reference proteins",
-                                "output_name": "output",
-                                "uuid": "a06ad5fa-9a00-4867-b976-3745c5e59c80"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "tables_0|table": {
-                                "id": 6,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Query Tabular",
-                                "name": "add_to_database"
-                            }
-                        ],
-                        "label": "Selecting sequence with length >6 and <30",
-                        "name": "Query Tabular",
-                        "outputs": [
+                                "name": "stats",
+                                "type": "input"
+                            },
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "name": "html_report",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "bottom": 767.140625,
-                            "height": 252,
-                            "left": 836.546875,
-                            "right": 1036.546875,
-                            "top": 515.140625,
-                            "width": 200,
-                            "x": 836.546875,
-                            "y": 515.140625
+                            "left": 1233.5,
+                            "top": 230.844970703125
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Selecting sequence with length >6 and <30"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "33d61c89fb8d",
-                            "name": "query_tabular",
+                            "changeset_revision": "abfd8a6544d7",
+                            "name": "multiqc",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"save_db\": \"false\", \"sqlquery\": \"SELECT Sequence || ' PSM=' || group_concat(id,',') || ' length='\\n|| length(Sequence) as \\\"ID\\\",Sequence\\nFROM  psm\\nWHERE length(Sequence) >6\\nAND length(Sequence) <= 30\\nGROUP BY Sequence\\nORDER BY length(Sequence),Sequence\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"skip\", \"__current_case__\": 0, \"skip_lines\": \"1\"}}]}, \"tbl_opts\": {\"table_name\": \"psm\", \"column_names_from_first_line\": \"false\", \"col_names\": \"id,Proteins,Sequence\", \"load_named_columns\": \"true\", \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.0.0",
-                        "type": "tool",
-                        "uuid": "7a40e039-01e2-4b13-b72f-7bb91061c50a",
-                        "workflow_outputs": [
-                            {
-                                "label": "Selecting sequence with length >6 and <30",
-                                "output_name": "output",
-                                "uuid": "b71e5417-2864-4712-b5c1-c90725976baf"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "input": {
-                                "id": 7,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Tabular-to-FASTA",
-                                "name": "input"
-                            }
-                        ],
-                        "label": "Peptides for BlastP analysis",
-                        "name": "Tabular-to-FASTA",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 724.9375,
-                            "height": 158,
-                            "left": 1066.546875,
-                            "right": 1266.546875,
-                            "top": 566.9375,
-                            "width": 200,
-                            "x": 1066.546875,
-                            "y": 566.9375
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Peptides for BlastP analysis"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "0a7799698fe5",
-                            "name": "tabular_to_fasta",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"seq_col\": \"2\", \"title_col\": \"1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.11+galaxy1",
                         "type": "tool",
-                        "uuid": "135caaf1-ceda-47b6-9f1a-8b0659d8e6a2",
+                        "uuid": "3e29a59b-dca0-4993-b20d-495a3f17e291",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Peptides_for_BlastP_analysis",
-                                "output_name": "output",
-                                "uuid": "1ac3c776-8095-4db1-8518-3643dc081006"
+                                "label": "MultiQC on input dataset(s): Webpage",
+                                "output_name": "html_report",
+                                "uuid": "8baf8700-876e-4a74-ad99-6e656f3ba618"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/proteogenomics-dbsearch",
-                "path": "topics/proteomics/tutorials/proteogenomics-dbsearch/workflows/galaxy-workflow-mouse_rnaseq_dbsearch.ga",
+                "parent_id": "assembly/largegenome",
+                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Data_QC.ga",
                 "tags": [
-                    "proteomics"
+                    "LG-WF",
+                    "GTN"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "GTN Proteogemics2 Database Search",
-                "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-proteogenomics-dbsearch/versions/galaxy-workflow-mouse-rnaseq-dbsearch",
-                "tutorial_id": "proteogenomics-dbsearch",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteogenomics-dbsearch/workflows/galaxy-workflow-mouse_rnaseq_dbsearch.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteogenomics-dbsearch/workflows/galaxy-workflow-mouse_rnaseq_dbsearch.html",
-                "version": 7,
-                "wfid": "proteomics-proteogenomics-dbsearch",
-                "wfname": "galaxy-workflow-mouse-rnaseq-dbsearch",
-                "workflow": "galaxy-workflow-mouse_rnaseq_dbsearch.ga",
+                "title": "Data QC - upgraded",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-data-qc",
+                "tutorial_id": "largegenome",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Data_QC.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Data_QC.html",
+                "version": 2,
+                "wfid": "assembly-largegenome",
+                "wfname": "galaxy-workflow-data-qc",
+                "workflow": "Galaxy-Workflow-Data_QC.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite/mz_to_sqlite/2.0.4+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0"
-                ],
-                "workflowhub_id": "1151"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.1489208"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "fasta_to_tabular",
-                    "owner": "devteam",
-                    "revisions": "e7ed3c310b74",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "tabular_to_fasta",
-                    "owner": "devteam",
-                    "revisions": "0a7799698fe5",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "dbbuilder",
-                    "owner": "galaxyp",
-                    "revisions": "c1b437242fee",
-                    "tool_panel_section_label": "Get Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_merge_files_and_filter_unique_sequences",
-                    "owner": "galaxyp",
-                    "revisions": "f546e7278f04",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_decoydatabase",
-                    "owner": "galaxyp",
-                    "revisions": "370141bc0da3",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fasta_to_tabular\n  owner: devteam\n  revisions: e7ed3c310b74\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tabular_to_fasta\n  owner: devteam\n  revisions: 0a7799698fe5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dbbuilder\n  owner: galaxyp\n  revisions: c1b437242fee\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_merge_files_and_filter_unique_sequences\n  owner: galaxyp\n  revisions: f546e7278f04\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_decoydatabase\n  owner: galaxyp\n  revisions: 370141bc0da3\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/database-handling/tutorial.json",
-        "contributors": [
-            {
-                "email": "sigloch+github@mailbox.org",
-                "former_affiliations": [
-                    "uni-freiburg"
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1"
                 ],
-                "id": "stortebecker",
-                "joined": "2017-09",
-                "name": "Florian Christoph Sigloch",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stortebecker/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/stortebecker.json"
+                "workflowhub_id": "1162"
             },
             {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
-                    "elixir-europe"
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
+                    }
                 ],
-                "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
-                "fediverse_flavor": "mastodon",
-                "id": "bgruening",
-                "joined": "2017-09",
-                "linkedin": "bgruening",
-                "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
-                },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
-            }
-        ],
-        "dir": "topics/proteomics/tutorials/database-handling",
-        "edam_ontology": [
-            "topic_0121"
-        ],
-        "edam_operation": [],
-        "edam_topic": [
-            "Proteomics"
-        ],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "proteomics/database-handling",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.no"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "There are several types of Uniprot databases.",
-            "Search databases should always include possible contaminants.",
-            "For analyzing cell culture or organic samples, search databases should include mycoplasma databases.",
-            "Some peptide search engines depend on decoys to calculate the FDR."
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Introductory",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Creation of a protein FASTA database ready for use with database search algorithms."
-        ],
-        "pageviews": 6389,
-        "pub_date": "2017-02-14",
-        "questions": [
-            "How to download protein FASTA databases of a certain organism?",
-            "How to download a contaminant database?",
-            "How to create a decoy database?",
-            "How to combine databases?"
-        ],
-        "short_id": "T00214",
-        "short_tools": [
-            "tab2fasta",
-            "dbbuilder",
-            "DecoyDatabase",
-            "fasta2tab",
-            "fasta_merge_files_and_filter_unique_sequences",
-            "addValue"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "id-quant",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "DDA"
-        ],
-        "time_estimation": "30m",
-        "title": "Protein FASTA Database Handling",
-        "tools": [
-            "addValue",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.6+galaxy0"
-        ],
-        "topic_name": "proteomics",
-        "topic_name_human": "Proteomics",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "database-handling",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/database-handling/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/database-handling/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/database-handling/tutorial.json"
-        },
-        "version": 29,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 118,
-        "visitors": 3847,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Protein FASTA Database Handling",
+                "description": "",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Protein Database Downloader\"]\n  1[label=\"Protein Database Downloader\"]\n  2[label=\"FASTA-to-Tabular\"]\n  0 -> 2 [label=\"output_database\"]\n  3[label=\"Add column\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Tabular-to-FASTA\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"FASTA Merge Files and Filter Unique Sequences\"]\n  4 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output_database\"]\n  6[label=\"DecoyDatabase\"]\n  5 -> 6 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads, R1, in fastq.gz format\"]\n  2[label=\"Minimap2 round 1: map reads to assembly\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Racon round 1: polish assembly\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"alignment_output\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Minimap2 round 2: map reads to assembly\"]\n  1 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"consensus\"]\n  5[label=\"Racon round 2: polish assembly\"]\n  3 -> 5 [label=\"consensus\"]\n  4 -> 5 [label=\"alignment_output\"]\n  1 -> 5 [label=\"output\"]\n  k594819c3668e4575b9a64459ffacf952[color=lightseagreen,label=\"Output\\nAssembly polished by short reads using Racon\"]\n  5 -> k594819c3668e4575b9a64459ffacf952\n}",
                 "history": [
                     {
-                        "hash": "54b4d9fcc78b1394f71f7affd51ca15e83b211d5",
-                        "message": "Adding tags to workflows",
-                        "num": 6,
-                        "short_hash": "54b4d9fcc",
-                        "unix": "1604224600"
-                    },
-                    {
-                        "hash": "ca84d739509bdb1ef8f3cfc64c15242ef0363407",
-                        "message": "Updating Tutorials to OpenMS 2.6, adjusting of parameters and tools, adding tool versions",
+                        "hash": "3be0312ca5a2e27bc1f8573e28943833be988894",
+                        "message": "Update Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga",
                         "num": 5,
-                        "short_hash": "ca84d7395",
-                        "unix": "1604176914"
+                        "short_hash": "3be0312ca",
+                        "unix": "1715074403"
                     },
                     {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
+                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
+                        "message": "new versions of workflows",
                         "num": 4,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
+                        "short_hash": "e8ddbcdd5",
+                        "unix": "1714537936"
                     },
                     {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
+                        "hash": "7d222309ffbec070126e3e749ba6f3d4e510cc6e",
+                        "message": "Rename Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga to Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2_old.ga",
                         "num": 3,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
+                        "short_hash": "7d222309f",
+                        "unix": "1714537293"
                     },
                     {
-                        "hash": "7da80b34185f4165852feb3bfe80d692609685db",
-                        "message": "Workflows fix",
+                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
+                        "message": "add/complete creator info on workflows",
                         "num": 2,
-                        "short_hash": "7da80b341",
-                        "unix": "1578668175"
+                        "short_hash": "62e77944b",
+                        "unix": "1676627603"
                     },
                     {
-                        "hash": "2c1271b670d336517fb123fb632ce13c93c40465",
-                        "message": "Restructure proteomics",
+                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
+                        "message": "large genome tutorial",
                         "num": 1,
-                        "short_hash": "2c1271b67",
-                        "unix": "1495544862"
+                        "short_hash": "9fcb3aeec",
+                        "unix": "1665123856"
                     }
                 ],
-                "inputs": [],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"Protein Database Downloader\"];\n  1[\"Protein Database Downloader\"];\n  2[\"FASTA-to-Tabular\"];\n  0 -->|output_database| 2;\n  3[\"Add column\"];\n  2 -->|output| 3;\n  4[\"Tabular-to-FASTA\"];\n  3 -->|out_file1| 4;\n  5[\"FASTA Merge Files and Filter Unique Sequences\"];\n  4 -->|output| 5;\n  1 -->|output_database| 5;\n  6[\"DecoyDatabase\"];\n  5 -->|output| 6;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Proteomics: database handling",
-                "outputs": [
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "Protein Database Downloader",
-                        "outputs": [
-                            {
-                                "name": "output_database",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 380.6000061035156,
-                            "height": 102.60000610351562,
-                            "left": -110,
-                            "right": 90,
-                            "top": 278,
-                            "width": 200,
-                            "x": -110,
-                            "y": 278
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "c1b437242fee",
-                            "name": "dbbuilder",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"cRAP\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3.1",
-                        "type": "tool",
-                        "uuid": "6613b72c-2bab-423c-88fc-05edfe9ea8ec",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_database",
-                                "uuid": "2d289b03-c396-46a2-a725-987b6c75ada9"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "Protein Database Downloader",
-                        "outputs": [
-                            {
-                                "name": "output_database",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 632.6000061035156,
-                            "height": 102.60000610351562,
-                            "left": -83,
-                            "right": 117,
-                            "top": 530,
-                            "width": 200,
-                            "x": -83,
-                            "y": 530
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "c1b437242fee",
-                            "name": "dbbuilder",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"9606\", \"reviewed\": \"+reviewed%3Ayes\", \"set\": \"+keyword%3a1185\", \"include_isoform\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3.1",
-                        "type": "tool",
-                        "uuid": "ee46d245-5fdd-4d02-9148-49a26c98ed81",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_database",
-                                "uuid": "8b345bac-fbae-4fee-aced-a3f56e72aa21"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "output_database"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "FASTA-to-Tabular",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 383.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": 146,
-                            "right": 346,
-                            "top": 270,
-                            "width": 200,
-                            "x": 146,
-                            "y": 270
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "e7ed3c310b74",
-                            "name": "fasta_to_tabular",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"descr_columns\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
-                        "type": "tool",
-                        "uuid": "c7bafec5-de51-4a49-80f8-402e443fa3fb",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "d320cd9d-fa50-41ab-96f9-0715e2467d55"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "addValue",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "input": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Add column",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 363.1999969482422,
-                            "height": 93.19999694824219,
-                            "left": 366,
-                            "right": 566,
-                            "top": 270,
-                            "width": 200,
-                            "x": 366,
-                            "y": 270
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "addValue",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"exp\": \"CONTAMINANT\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "27172bb3-7f15-49d9-961e-4a87401812c7",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "12d78b53-8f63-4349-89b5-4f5770d3ac4d"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "input": {
-                                "id": 3,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Tabular-to-FASTA",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "Assembly to be polished"
                             }
                         ],
+                        "label": "Assembly to be polished",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 383.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": 586,
-                            "right": 786,
-                            "top": 270,
-                            "width": 200,
-                            "x": 586,
-                            "y": 270
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "0a7799698fe5",
-                            "name": "tabular_to_fasta",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 72.5176329833982
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"seq_col\": \"2\", \"title_col\": [\"1\", \"3\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
-                        "type": "tool",
-                        "uuid": "d8a59abc-1be6-41e9-8df0-c8b06d8430c7",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "a1dccdc6-a13f-4326-bb33-a75581b22d9b"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "28669894-74e2-4ba1-9d49-6e3209b5a1de",
+                        "when": null,
+                        "workflow_outputs": []
                     },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "batchmode|input_fastas_0|input_fasta": {
-                                "id": 4,
-                                "output_name": "output"
-                            },
-                            "batchmode|input_fastas_1|input_fasta": {
-                                "id": 1,
-                                "output_name": "output_database"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "FASTA Merge Files and Filter Unique Sequences",
-                        "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "Illumina reads, R1, in fastq.gz format"
                             }
                         ],
+                        "label": "Illumina reads, R1, in fastq.gz format",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 516,
-                            "height": 246,
-                            "left": 806,
-                            "right": 1006,
-                            "top": 270,
-                            "width": 200,
-                            "x": 806,
-                            "y": 270
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "650d553c1fda",
-                            "name": "fasta_merge_files_and_filter_unique_sequences",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 8.5,
+                            "top": 341.2832579833982
                         },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"accession_parser\": \"^>([^ ]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"uniqueness_criterion\": \"accession\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.0",
-                        "type": "tool",
-                        "uuid": "609ed0b7-37b3-459b-ab69-e10ff898b372",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "b7b9b10b-9f63-4e66-b25a-da521756b75d"
-                            }
-                        ]
-                    },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "bc936fdc-22a9-4507-aa47-4a70a3f93923",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nIllumina reads, R1, in fastq.gz format\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Minimap2 round 1: map reads to assembly\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Racon round 1: polish assembly\"];\n  0 -->|output| 3;\n  2 -->|alignment_output| 3;\n  1 -->|output| 3;\n  4[\"Minimap2 round 2: map reads to assembly\"];\n  1 -->|output| 4;\n  3 -->|consensus| 4;\n  5[\"Racon round 2: polish assembly\"];\n  3 -->|consensus| 5;\n  4 -->|alignment_output| 5;\n  1 -->|output| 5;\n  594819c3-668e-4575-b9a6-4459ffacf952[\"Output\\nAssembly polished by short reads using Racon\"];\n  5 --> 594819c3-668e-4575-b9a6-4459ffacf952;\n  style 594819c3-668e-4575-b9a6-4459ffacf952 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.6+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
                         "errors": null,
-                        "id": 6,
+                        "id": 5,
                         "input_connections": {
-                            "in": {
-                                "id": 5,
+                            "corrected_reads": {
+                                "id": 3,
+                                "output_name": "consensus"
+                            },
+                            "overlaps": {
+                                "id": 4,
+                                "output_name": "alignment_output"
+                            },
+                            "reads": {
+                                "id": 1,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "DecoyDatabase",
+                        "label": "Racon round 2: polish assembly",
+                        "name": "Racon",
                         "outputs": [
                             {
-                                "name": "out",
+                                "name": "consensus",
                                 "type": "fasta"
                             }
                         ],
                         "position": {
-                            "bottom": 428.3999938964844,
-                            "height": 154.39999389648438,
-                            "left": 1137,
-                            "right": 1337,
-                            "top": 274,
-                            "width": 200,
-                            "x": 1137,
-                            "y": 274
+                            "left": 1198.765625,
+                            "top": 332.4707579833982
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.6+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActionconsensus": {
+                                "action_arguments": {
+                                    "newname": "Racon_short_reads_polished_assembly.fasta"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "consensus"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "71a6c870aa48",
-                            "name": "openms_decoydatabase",
-                            "owner": "galaxyp",
+                            "changeset_revision": "78c533842eeb",
+                            "name": "racon",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"Decoy\": {\"non_shuffle_pattern\": \"\", \"keepPeptideNTerm\": \"true\", \"keepPeptideCTerm\": \"true\"}, \"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"decoy_string\": \"DECOY_\", \"decoy_string_position\": \"prefix\", \"enzyme\": \"Trypsin\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"method\": \"reverse\", \"only_decoy\": \"false\", \"type\": \"protein\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.5.0+galaxy1",
                         "type": "tool",
-                        "uuid": "053fc094-7146-4bf7-91bd-df3f8fdc3f05",
+                        "uuid": "b3c89c40-3ad0-454c-a4d4-dfa34fb09f24",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out",
-                                "uuid": "54465c5a-911c-46a7-91d2-78e40ba9e92f"
+                                "label": "Assembly polished by short reads using Racon",
+                                "output_name": "consensus",
+                                "uuid": "594819c3-668e-4575-b9a6-4459ffacf952"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/database-handling",
-                "path": "topics/proteomics/tutorials/database-handling/workflows/wf_database-handling.ga",
+                "parent_id": "assembly/largegenome",
+                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga",
                 "tags": [
-                    "proteomics"
+                    "LG-WF",
+                    "GTN"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Proteomics: database handling",
-                "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-database-handling/versions/wf-database-handling",
-                "tutorial_id": "database-handling",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/database-handling/workflows/wf_database-handling.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/database-handling/workflows/wf_database-handling.html",
-                "version": 5,
-                "wfid": "proteomics-database-handling",
-                "wfname": "wf-database-handling",
-                "workflow": "wf_database-handling.ga",
+                "title": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-racon-polish-with-illumina-reads-x2",
+                "tutorial_id": "largegenome",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.html",
+                "version": 2,
+                "wfid": "assembly-largegenome",
+                "wfname": "galaxy-workflow-racon-polish-with-illumina-reads-x2",
+                "workflow": "Galaxy-Workflow-Racon_polish_with_Illumina_reads_x2.ga",
                 "workflow_tools": [
-                    "addValue",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.6+galaxy0"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0"
                 ],
-                "workflowhub_id": "1204"
+                "workflowhub_id": "1148"
             },
             {
-                "creators": [],
-                "description": "Protein FASTA Database Handling",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
+                    }
+                ],
+                "description": "",
                 "features": {
                     "comments": false,
-                    "parameters": false,
-                    "report": null,
+                    "parameters": true,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                    },
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Protein Database Downloader\"]\n  1[label=\"Protein Database Downloader\"]\n  2[label=\"Protein Database Downloader\"]\n  3[label=\"Protein Database Downloader\"]\n  4[label=\"Protein Database Downloader\"]\n  5[label=\"Protein Database Downloader\"]\n  6[label=\"Protein Database Downloader\"]\n  7[label=\"Protein Database Downloader\"]\n  8[label=\"FASTA-to-Tabular\"]\n  2 -> 8 [label=\"output_database\"]\n  9[label=\"FASTA Merge Files and Filter Unique Sequences\"]\n  5 -> 9 [label=\"output_database\"]\n  4 -> 9 [label=\"output_database\"]\n  3 -> 9 [label=\"output_database\"]\n  1 -> 9 [label=\"output_database\"]\n  0 -> 9 [label=\"output_database\"]\n  6 -> 9 [label=\"output_database\"]\n  10[label=\"Add column\"]\n  8 -> 10 [label=\"output\"]\n  11[label=\"FASTA-to-Tabular\"]\n  9 -> 11 [label=\"output\"]\n  12[label=\"Tabular-to-FASTA\"]\n  10 -> 12 [label=\"out_file1\"]\n  13[label=\"Add column\"]\n  11 -> 13 [label=\"output\"]\n  14[label=\"Tabular-to-FASTA\"]\n  13 -> 14 [label=\"out_file1\"]\n  15[label=\"FASTA Merge Files and Filter Unique Sequences\"]\n  12 -> 15 [label=\"output\"]\n  7 -> 15 [label=\"output_database\"]\n  14 -> 15 [label=\"output\"]\n  16[label=\"DecoyDatabase\"]\n  15 -> 16 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads \"]\n  3[label=\"Minimap2: map long reads to assembly\"]\n  2 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Racon: polish 1\"]\n  0 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"alignment_output\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Minimap2: map long reads to polished assembly 1\"]\n  2 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  4 -> 5 [label=\"consensus\"]\n  6[label=\"Racon: polish 2\"]\n  4 -> 6 [label=\"consensus\"]\n  5 -> 6 [label=\"alignment_output\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"Minimap2: map long reads to polished assembly 2\"]\n  2 -> 7 [label=\"output\"]\n  1 -> 7 [label=\"output\"]\n  6 -> 7 [label=\"consensus\"]\n  8[label=\"Racon: polish 3\"]\n  6 -> 8 [label=\"consensus\"]\n  7 -> 8 [label=\"alignment_output\"]\n  1 -> 8 [label=\"output\"]\n  9[label=\"Minimap2: map long reads to polished assembly 3\"]\n  2 -> 9 [label=\"output\"]\n  1 -> 9 [label=\"output\"]\n  8 -> 9 [label=\"consensus\"]\n  10[label=\"Racon: polish 4\"]\n  8 -> 10 [label=\"consensus\"]\n  9 -> 10 [label=\"alignment_output\"]\n  1 -> 10 [label=\"output\"]\n  kbcf0f03c595146a7aa38545aed9bc183[color=lightseagreen,label=\"Output\\nAssembly polished by long reads using Racon\"]\n  10 -> kbcf0f03c595146a7aa38545aed9bc183\n}",
                 "history": [
                     {
-                        "hash": "30b5abb36b9cfef5ca43d0f8c6fc504dd9bc459a",
-                        "message": "Update wf_database-handling_mycoplasma.ga",
-                        "num": 8,
-                        "short_hash": "30b5abb36",
-                        "unix": "1608207012"
-                    },
-                    {
-                        "hash": "30e6e1ac18f3e4e93c1f1d322d8423070cf3a4a5",
-                        "message": "Update wf_database-handling_mycoplasma.ga workflow",
-                        "num": 7,
-                        "short_hash": "30e6e1ac1",
-                        "unix": "1608205362"
-                    },
-                    {
-                        "hash": "54b4d9fcc78b1394f71f7affd51ca15e83b211d5",
-                        "message": "Adding tags to workflows",
-                        "num": 6,
-                        "short_hash": "54b4d9fcc",
-                        "unix": "1604224600"
-                    },
-                    {
-                        "hash": "ca84d739509bdb1ef8f3cfc64c15242ef0363407",
-                        "message": "Updating Tutorials to OpenMS 2.6, adjusting of parameters and tools, adding tool versions",
+                        "hash": "ea8cb9df4cc68241e9b406bde825b4c16647280b",
+                        "message": "Update Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga",
                         "num": 5,
-                        "short_hash": "ca84d7395",
-                        "unix": "1604176914"
+                        "short_hash": "ea8cb9df4",
+                        "unix": "1715074423"
                     },
                     {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
+                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
+                        "message": "new versions of workflows",
                         "num": 4,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
+                        "short_hash": "e8ddbcdd5",
+                        "unix": "1714537936"
                     },
                     {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
+                        "hash": "7bd7c55df24dd71009cbde6408fb87d49901a84a",
+                        "message": "Rename Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga to Galaxy-Workflow-Racon_polish_with_long_reads_x4_old.ga",
                         "num": 3,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
+                        "short_hash": "7bd7c55df",
+                        "unix": "1714537311"
                     },
                     {
-                        "hash": "7da80b34185f4165852feb3bfe80d692609685db",
-                        "message": "Workflows fix",
+                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
+                        "message": "add/complete creator info on workflows",
                         "num": 2,
-                        "short_hash": "7da80b341",
-                        "unix": "1578668175"
+                        "short_hash": "62e77944b",
+                        "unix": "1676627603"
                     },
                     {
-                        "hash": "2c1271b670d336517fb123fb632ce13c93c40465",
-                        "message": "Restructure proteomics",
+                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
+                        "message": "large genome tutorial",
                         "num": 1,
-                        "short_hash": "2c1271b67",
-                        "unix": "1495544862"
+                        "short_hash": "9fcb3aeec",
+                        "unix": "1665123856"
                     }
                 ],
-                "inputs": [],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"Protein Database Downloader\"];\n  1[\"Protein Database Downloader\"];\n  2[\"Protein Database Downloader\"];\n  3[\"Protein Database Downloader\"];\n  4[\"Protein Database Downloader\"];\n  5[\"Protein Database Downloader\"];\n  6[\"Protein Database Downloader\"];\n  7[\"Protein Database Downloader\"];\n  8[\"FASTA-to-Tabular\"];\n  2 -->|output_database| 8;\n  9[\"FASTA Merge Files and Filter Unique Sequences\"];\n  5 -->|output_database| 9;\n  4 -->|output_database| 9;\n  3 -->|output_database| 9;\n  1 -->|output_database| 9;\n  0 -->|output_database| 9;\n  6 -->|output_database| 9;\n  10[\"Add column\"];\n  8 -->|output| 10;\n  11[\"FASTA-to-Tabular\"];\n  9 -->|output| 11;\n  12[\"Tabular-to-FASTA\"];\n  10 -->|out_file1| 12;\n  13[\"Add column\"];\n  11 -->|output| 13;\n  14[\"Tabular-to-FASTA\"];\n  13 -->|out_file1| 14;\n  15[\"FASTA Merge Files and Filter Unique Sequences\"];\n  12 -->|output| 15;\n  7 -->|output_database| 15;\n  14 -->|output| 15;\n  16[\"DecoyDatabase\"];\n  15 -->|output| 16;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Proteomics: database handling including mycoplasma",
-                "outputs": [
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "Protein Database Downloader",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "output_database",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "Assembly to be polished"
                             }
                         ],
+                        "label": "Assembly to be polished",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 186.171875,
-                            "height": 101,
-                            "left": 489.96875,
-                            "right": 689.96875,
-                            "top": 85.171875,
-                            "width": 200,
-                            "x": 489.96875,
-                            "y": 85.171875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "c1b437242fee",
-                            "name": "dbbuilder",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 216.625
                         },
-                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"2121\", \"reviewed\": \"+\", \"set\": \"+keyword%3a1185\", \"include_isoform\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3.1",
-                        "type": "tool",
-                        "uuid": "4114a759-55b3-41e4-866d-b4ce95b7064a",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_database",
-                                "uuid": "7139701a-2418-4a54-8708-69e50cdf64b1"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "c7796c36-adf8-49e4-a8e4-66e606d70311",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "Protein Database Downloader",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "output_database",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "long reads"
                             }
                         ],
+                        "label": "long reads",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 293.171875,
-                            "height": 101,
-                            "left": 508.96875,
-                            "right": 708.96875,
-                            "top": 192.171875,
-                            "width": 200,
-                            "x": 508.96875,
-                            "y": 192.171875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "c1b437242fee",
-                            "name": "dbbuilder",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 4.5,
+                            "top": 360.234375
                         },
-                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"2100\", \"reviewed\": \"+\", \"set\": \"+keyword%3a1185\", \"include_isoform\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3.1",
-                        "type": "tool",
-                        "uuid": "9d6509a8-45b2-463c-a37c-5330280a2302",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_database",
-                                "uuid": "02415048-af7f-482d-bc30-af3315ae63b2"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "e2e4a70b-6e36-4b8b-bdf6-12b97189a6bd",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "content_id": null,
                         "errors": null,
                         "id": 2,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "Protein Database Downloader",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "output_database",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "minimap setting (for long reads) "
                             }
                         ],
+                        "label": "minimap setting (for long reads) ",
+                        "name": "Input parameter",
+                        "outputs": [],
                         "position": {
-                            "bottom": -196.828125,
-                            "height": 101,
-                            "left": 471.96875,
-                            "right": 671.96875,
-                            "top": -297.828125,
-                            "width": 200,
-                            "x": 471.96875,
-                            "y": -297.828125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "c1b437242fee",
-                            "name": "dbbuilder",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0.578125,
+                            "top": 495.859375
                         },
-                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"cRAP\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3.1",
-                        "type": "tool",
-                        "uuid": "357e8c0f-93cd-4ebc-81ac-6ece5de019e5",
+                        "tool_id": null,
+                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "fb80c05c-08d4-4ac2-b4bf-81ed906e4d72",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_database",
-                                "uuid": "1605ec3f-5755-43d4-813d-a865518bda07"
+                                "output_name": "output",
+                                "uuid": "3983ef22-5f05-4384-8f34-6ac8c4b2cc83"
                             }
                         ]
-                    },
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads \"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"Minimap2: map long reads to assembly\"];\n  2 -->|output| 3;\n  1 -->|output| 3;\n  0 -->|output| 3;\n  4[\"Racon: polish 1\"];\n  0 -->|output| 4;\n  3 -->|alignment_output| 4;\n  1 -->|output| 4;\n  5[\"Minimap2: map long reads to polished assembly 1\"];\n  2 -->|output| 5;\n  1 -->|output| 5;\n  4 -->|consensus| 5;\n  6[\"Racon: polish 2\"];\n  4 -->|consensus| 6;\n  5 -->|alignment_output| 6;\n  1 -->|output| 6;\n  7[\"Minimap2: map long reads to polished assembly 2\"];\n  2 -->|output| 7;\n  1 -->|output| 7;\n  6 -->|consensus| 7;\n  8[\"Racon: polish 3\"];\n  6 -->|consensus| 8;\n  7 -->|alignment_output| 8;\n  1 -->|output| 8;\n  9[\"Minimap2: map long reads to polished assembly 3\"];\n  2 -->|output| 9;\n  1 -->|output| 9;\n  8 -->|consensus| 9;\n  10[\"Racon: polish 4\"];\n  8 -->|consensus| 10;\n  9 -->|alignment_output| 10;\n  1 -->|output| 10;\n  bcf0f03c-5951-46a7-aa38-545aed9bc183[\"Output\\nAssembly polished by long reads using Racon\"];\n  10 --> bcf0f03c-5951-46a7-aa38-545aed9bc183;\n  style bcf0f03c-5951-46a7-aa38-545aed9bc183 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Racon polish with long reads, x4 - upgraded",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 2,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "Protein Database Downloader",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "output_database",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "minimap setting (for long reads) "
                             }
                         ],
+                        "label": "minimap setting (for long reads) ",
+                        "name": "Input parameter",
+                        "outputs": [],
                         "position": {
-                            "bottom": 413.171875,
-                            "height": 101,
-                            "left": 508.96875,
-                            "right": 708.96875,
-                            "top": 312.171875,
-                            "width": 200,
-                            "x": 508.96875,
-                            "y": 312.171875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "c1b437242fee",
-                            "name": "dbbuilder",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0.578125,
+                            "top": 495.859375
                         },
-                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"2094\", \"reviewed\": \"+\", \"set\": \"+keyword%3a1185\", \"include_isoform\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3.1",
-                        "type": "tool",
-                        "uuid": "6124a009-45b4-44f3-a143-61d47fbe17a9",
+                        "tool_id": null,
+                        "tool_state": "{\"default\": \"map-ont\", \"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "fb80c05c-08d4-4ac2-b4bf-81ed906e4d72",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_database",
-                                "uuid": "55cd7e71-a1f9-4dea-8355-462fefce371a"
+                                "output_name": "output",
+                                "uuid": "3983ef22-5f05-4384-8f34-6ac8c4b2cc83"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
                         "errors": null,
-                        "id": 4,
-                        "input_connections": {},
+                        "id": 10,
+                        "input_connections": {
+                            "corrected_reads": {
+                                "id": 8,
+                                "output_name": "consensus"
+                            },
+                            "overlaps": {
+                                "id": 9,
+                                "output_name": "alignment_output"
+                            },
+                            "reads": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
                         "inputs": [],
-                        "label": null,
-                        "name": "Protein Database Downloader",
+                        "label": "Racon: polish 4",
+                        "name": "Racon",
                         "outputs": [
                             {
-                                "name": "output_database",
+                                "name": "consensus",
                                 "type": "fasta"
                             }
                         ],
                         "position": {
-                            "bottom": 533.171875,
-                            "height": 101,
-                            "left": 508.96875,
-                            "right": 708.96875,
-                            "top": 432.171875,
-                            "width": 200,
-                            "x": 508.96875,
-                            "y": 432.171875
+                            "left": 1496.078125,
+                            "top": 431.1875
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "post_job_actions": {
+                            "RenameDatasetActionconsensus": {
+                                "action_arguments": {
+                                    "newname": "Racon_long_reads_polished_assembly.fasta"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "consensus"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "c1b437242fee",
-                            "name": "dbbuilder",
-                            "owner": "galaxyp",
+                            "changeset_revision": "78c533842eeb",
+                            "name": "racon",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"2115\", \"reviewed\": \"+\", \"set\": \"+keyword%3a1185\", \"include_isoform\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3.1",
+                        "tool_state": "{\"corrected_reads\": {\"__class__\": \"ConnectedValue\"}, \"e\": \"0.3\", \"error_threshold\": \"0.3\", \"f\": \"false\", \"fragment_correction\": false, \"g\": \"-8\", \"gap\": \"-4\", \"include_unpolished\": false, \"m\": \"5\", \"match\": \"3\", \"mismatch\": \"-5\", \"no_trimming\": false, \"overlaps\": {\"__class__\": \"ConnectedValue\"}, \"q\": \"10.0\", \"quality_threshold\": \"10.0\", \"reads\": {\"__class__\": \"ConnectedValue\"}, \"u\": \"true\", \"w\": \"500\", \"window_length\": \"500\", \"x\": \"-4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.5.0+galaxy1",
                         "type": "tool",
-                        "uuid": "f01d73bd-e427-40f1-94d0-732836dc3c32",
+                        "uuid": "53f4572e-3a4a-4585-89ab-9459f8a61720",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_database",
-                                "uuid": "180b1779-a0dc-4a20-aeb8-c451b67e589f"
+                                "label": "Assembly polished by long reads using Racon",
+                                "output_name": "consensus",
+                                "uuid": "bcf0f03c-5951-46a7-aa38-545aed9bc183"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "assembly/largegenome",
+                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga",
+                "tags": [
+                    "LG-WF",
+                    "GTN"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Racon polish with long reads, x4 - upgraded",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-racon-polish-with-long-reads-x4",
+                "tutorial_id": "largegenome",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Racon_polish_with_long_reads_x4.html",
+                "version": 2,
+                "wfid": "assembly-largegenome",
+                "wfname": "galaxy-workflow-racon-polish-with-long-reads-x4",
+                "workflow": "Galaxy-Workflow-Racon_polish_with_long_reads_x4.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.5.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0"
+                ],
+                "workflowhub_id": "1154"
+            },
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": {
+                        "markdown": "\n# Workflow for Trim and Filter Reads\n\n## Workflow steps\n```galaxy\nworkflow_display()\n```\n\n\n\n\n"
+                    },
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads R2\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlong reads\"]\n  3[label=\"fastp on short reads\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  k656e413841ab4561898933de9ac9a2f3[color=lightseagreen,label=\"Output\\nfastp report on short reads html\"]\n  3 -> k656e413841ab4561898933de9ac9a2f3\n  k0d53f347036847cb953a2e4dac57e013[color=lightseagreen,label=\"Output\\nfastp filtered R1 reads\"]\n  3 -> k0d53f347036847cb953a2e4dac57e013\n  k10fbe1e5400c4ffe87949b776b0d7322[color=lightseagreen,label=\"Output\\nfastp report on short reads json\"]\n  3 -> k10fbe1e5400c4ffe87949b776b0d7322\n  k639ed3f70e514e5db6f8081378962109[color=lightseagreen,label=\"Output\\nfastp filtered R2 reads\"]\n  3 -> k639ed3f70e514e5db6f8081378962109\n  4[label=\"fastp on long reads\"]\n  2 -> 4 [label=\"output\"]\n  k5e0d2c3d41a44823ae9cb1e4d2826541[color=lightseagreen,label=\"Output\\nfastp report on long reads html\"]\n  4 -> k5e0d2c3d41a44823ae9cb1e4d2826541\n  ke6018ad686f44e788cf2ccc8b97022fe[color=lightseagreen,label=\"Output\\nfastp filtered long reads\"]\n  4 -> ke6018ad686f44e788cf2ccc8b97022fe\n  k69f8383ba1be4a7495f43dba35e01426[color=lightseagreen,label=\"Output\\nfastp report on long reads json\"]\n  4 -> k69f8383ba1be4a7495f43dba35e01426\n}",
+                "history": [
+                    {
+                        "hash": "1fe24b92fd7cf3bf693a850751a6215f7b9273bd",
+                        "message": "Update Galaxy-Workflow-Trim_and_filter_reads.ga",
+                        "num": 5,
+                        "short_hash": "1fe24b92f",
+                        "unix": "1715074442"
+                    },
+                    {
+                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
+                        "message": "new versions of workflows",
+                        "num": 4,
+                        "short_hash": "e8ddbcdd5",
+                        "unix": "1714537936"
+                    },
+                    {
+                        "hash": "12f721099e26ef4bd152c1c2b56ccb51e6bd31ab",
+                        "message": "Rename Galaxy-Workflow-Trim_and_filter_reads.ga to Galaxy-Workflow-Trim_and_filter_reads_old.ga",
+                        "num": 3,
+                        "short_hash": "12f721099",
+                        "unix": "1714537350"
+                    },
+                    {
+                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
+                        "message": "add/complete creator info on workflows",
+                        "num": 2,
+                        "short_hash": "62e77944b",
+                        "unix": "1676627603"
                     },
+                    {
+                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
+                        "message": "large genome tutorial",
+                        "num": 1,
+                        "short_hash": "9fcb3aeec",
+                        "unix": "1665123856"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 5,
+                        "id": 0,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "Protein Database Downloader",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "output_database",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "Illumina reads R1"
                             }
                         ],
+                        "label": "Illumina reads R1",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 653.171875,
-                            "height": 101,
-                            "left": 508.96875,
-                            "right": 708.96875,
-                            "top": 552.171875,
-                            "width": 200,
-                            "x": 508.96875,
-                            "y": 552.171875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "c1b437242fee",
-                            "name": "dbbuilder",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 29.045160466974437
                         },
-                        "tool_state": "{\"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"2098\", \"reviewed\": \"+\", \"set\": \"+keyword%3a1185\", \"include_isoform\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3.1",
-                        "type": "tool",
-                        "uuid": "b725bbfe-011f-4ebf-b94d-235db3811db5",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_database",
-                                "uuid": "8458bb43-85bd-4b58-810b-d87277b0fa51"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "00a54054-e3f7-4e4f-9195-563e54df899a",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 6,
+                        "id": 1,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "Protein Database Downloader",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "output_database",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "Illumina reads R2"
                             }
                         ],
+                        "label": "Illumina reads R2",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 770.171875,
-                            "height": 101,
-                            "left": 512.5625,
-                            "right": 712.5625,
-                            "top": 669.171875,
-                            "width": 200,
-                            "x": 512.5625,
-                            "y": 669.171875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "c1b437242fee",
-                            "name": "dbbuilder",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 145.03474842418325
                         },
-                        "tool_state": "{\"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"2148\", \"reviewed\": \"+\", \"set\": \"+keyword%3a1185\", \"include_isoform\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3.1",
-                        "type": "tool",
-                        "uuid": "0b7814d9-5511-4278-9ca3-19748a1f9ece",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_database",
-                                "uuid": "cc6b866c-4912-421d-a342-23baef5d2c95"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "14062fd8-1aa9-4a18-94d8-bbbb0e1a9262",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 7,
+                        "id": 2,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "Protein Database Downloader",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "long reads"
+                            }
+                        ],
+                        "label": "long reads",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 576.5103981711648,
+                            "top": 35.50348455255681
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "08eeb0d3-6ad6-4e7f-ac6a-d00c8e87fd08",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nIllumina reads R2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"fastp on short reads\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  656e4138-41ab-4561-8989-33de9ac9a2f3[\"Output\\nfastp report on short reads html\"];\n  3 --> 656e4138-41ab-4561-8989-33de9ac9a2f3;\n  style 656e4138-41ab-4561-8989-33de9ac9a2f3 stroke:#2c3143,stroke-width:4px;\n  0d53f347-0368-47cb-953a-2e4dac57e013[\"Output\\nfastp filtered R1 reads\"];\n  3 --> 0d53f347-0368-47cb-953a-2e4dac57e013;\n  style 0d53f347-0368-47cb-953a-2e4dac57e013 stroke:#2c3143,stroke-width:4px;\n  10fbe1e5-400c-4ffe-8794-9b776b0d7322[\"Output\\nfastp report on short reads json\"];\n  3 --> 10fbe1e5-400c-4ffe-8794-9b776b0d7322;\n  style 10fbe1e5-400c-4ffe-8794-9b776b0d7322 stroke:#2c3143,stroke-width:4px;\n  639ed3f7-0e51-4e5d-b6f8-081378962109[\"Output\\nfastp filtered R2 reads\"];\n  3 --> 639ed3f7-0e51-4e5d-b6f8-081378962109;\n  style 639ed3f7-0e51-4e5d-b6f8-081378962109 stroke:#2c3143,stroke-width:4px;\n  4[\"fastp on long reads\"];\n  2 -->|output| 4;\n  5e0d2c3d-41a4-4823-ae9c-b1e4d2826541[\"Output\\nfastp report on long reads html\"];\n  4 --> 5e0d2c3d-41a4-4823-ae9c-b1e4d2826541;\n  style 5e0d2c3d-41a4-4823-ae9c-b1e4d2826541 stroke:#2c3143,stroke-width:4px;\n  e6018ad6-86f4-4e78-8cf2-ccc8b97022fe[\"Output\\nfastp filtered long reads\"];\n  4 --> e6018ad6-86f4-4e78-8cf2-ccc8b97022fe;\n  style e6018ad6-86f4-4e78-8cf2-ccc8b97022fe stroke:#2c3143,stroke-width:4px;\n  69f8383b-a1be-4a74-95f4-3dba35e01426[\"Output\\nfastp report on long reads json\"];\n  4 --> 69f8383b-a1be-4a74-95f4-3dba35e01426;\n  style 69f8383b-a1be-4a74-95f4-3dba35e01426 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "Trim and filter reads - fastp - upgraded ",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "single_paired|in1": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "single_paired|in2": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool fastp",
+                                "name": "single_paired"
+                            },
+                            {
+                                "description": "runtime parameter for tool fastp",
+                                "name": "single_paired"
+                            }
+                        ],
+                        "label": "fastp on short reads",
+                        "name": "fastp",
                         "outputs": [
                             {
-                                "name": "output_database",
-                                "type": "fasta"
+                                "name": "out1",
+                                "type": "input"
+                            },
+                            {
+                                "name": "out2",
+                                "type": "input"
+                            },
+                            {
+                                "name": "report_html",
+                                "type": "html"
+                            },
+                            {
+                                "name": "report_json",
+                                "type": "json"
                             }
                         ],
                         "position": {
-                            "bottom": 358.171875,
-                            "height": 101,
-                            "left": 1149.96875,
-                            "right": 1349.96875,
-                            "top": 257.171875,
-                            "width": 200,
-                            "x": 1149.96875,
-                            "y": 257.171875
+                            "left": 290.5382191051136,
+                            "top": 0
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "post_job_actions": {
+                            "DeleteIntermediatesActionout1": {
+                                "action_arguments": {},
+                                "action_type": "DeleteIntermediatesAction",
+                                "output_name": "out1"
+                            },
+                            "RenameDatasetActionout1": {
+                                "action_arguments": {
+                                    "newname": "fastp_filtered_R1.fastq.gz"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out1"
+                            },
+                            "RenameDatasetActionout2": {
+                                "action_arguments": {
+                                    "newname": "fastp_filtered_R2.fastq.gz"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out2"
+                            },
+                            "RenameDatasetActionreport_html": {
+                                "action_arguments": {
+                                    "newname": "fastp_illumina.html"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "report_html"
+                            },
+                            "RenameDatasetActionreport_json": {
+                                "action_arguments": {
+                                    "newname": "fastp_illumina.json"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "report_json"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "c1b437242fee",
-                            "name": "dbbuilder",
-                            "owner": "galaxyp",
+                            "changeset_revision": "c59d48774d03",
+                            "name": "fastp",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"9606\", \"reviewed\": \"+reviewed%3Ayes\", \"set\": \"+keyword%3a1185\", \"include_isoform\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3.1",
+                        "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired\", \"__current_case__\": 1, \"in1\": {\"__class__\": \"ConnectedValue\"}, \"in2\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": \"\", \"adapter_sequence2\": \"\"}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.23.4+galaxy0",
                         "type": "tool",
-                        "uuid": "8edafc35-59c1-4043-adf2-9413a5959ffe",
+                        "uuid": "c38e84b3-771c-428e-9d2d-ce84d5e1153c",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_database",
-                                "uuid": "9b9e1bc5-f179-47e7-bb74-0979ca293e8a"
+                                "label": "fastp report on short reads html",
+                                "output_name": "report_html",
+                                "uuid": "656e4138-41ab-4561-8989-33de9ac9a2f3"
+                            },
+                            {
+                                "label": "fastp filtered R1 reads",
+                                "output_name": "out1",
+                                "uuid": "0d53f347-0368-47cb-953a-2e4dac57e013"
+                            },
+                            {
+                                "label": "fastp report on short reads json",
+                                "output_name": "report_json",
+                                "uuid": "10fbe1e5-400c-4ffe-8794-9b776b0d7322"
+                            },
+                            {
+                                "label": "fastp filtered R2 reads",
+                                "output_name": "out2",
+                                "uuid": "639ed3f7-0e51-4e5d-b6f8-081378962109"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
                         "errors": null,
-                        "id": 8,
+                        "id": 4,
                         "input_connections": {
-                            "input": {
+                            "single_paired|in1": {
                                 "id": 2,
-                                "output_name": "output_database"
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "FASTA-to-Tabular",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool fastp",
+                                "name": "single_paired"
+                            }
+                        ],
+                        "label": "fastp on long reads",
+                        "name": "fastp",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "name": "out1",
+                                "type": "input"
+                            },
+                            {
+                                "name": "report_html",
+                                "type": "html"
+                            },
+                            {
+                                "name": "report_json",
+                                "type": "json"
                             }
                         ],
                         "position": {
-                            "bottom": -55.828125,
-                            "height": 112,
-                            "left": 728.96875,
-                            "right": 928.96875,
-                            "top": -167.828125,
-                            "width": 200,
-                            "x": 728.96875,
-                            "y": -167.828125
+                            "left": 804.010509144176,
+                            "top": 22.482646595348
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                        "post_job_actions": {
+                            "DeleteIntermediatesActionout1": {
+                                "action_arguments": {},
+                                "action_type": "DeleteIntermediatesAction",
+                                "output_name": "out1"
+                            },
+                            "RenameDatasetActionout1": {
+                                "action_arguments": {
+                                    "newname": "fastp_filtered_long_reads.fastq.gz"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out1"
+                            },
+                            "RenameDatasetActionreport_html": {
+                                "action_arguments": {
+                                    "newname": "fastp_longreads.html"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "report_html"
+                            },
+                            "RenameDatasetActionreport_json": {
+                                "action_arguments": {
+                                    "newname": "fastp_longreads.json"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "report_json"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "e7ed3c310b74",
-                            "name": "fasta_to_tabular",
-                            "owner": "devteam",
+                            "changeset_revision": "c59d48774d03",
+                            "name": "fastp",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"descr_columns\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": true, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": true, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"-G\", \"__current_case__\": 2}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"single\", \"__current_case__\": 0, \"in1\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": true, \"adapter_sequence1\": \"\"}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.23.4+galaxy0",
                         "type": "tool",
-                        "uuid": "43204d4a-03b7-46c1-b96f-d9cce74ad707",
+                        "uuid": "93602736-2d22-43e4-a53a-803326ccab9e",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "28ec9532-c442-4b0a-889e-5809098b1b7f"
+                                "label": "fastp report on long reads html",
+                                "output_name": "report_html",
+                                "uuid": "5e0d2c3d-41a4-4823-ae9c-b1e4d2826541"
+                            },
+                            {
+                                "label": "fastp filtered long reads",
+                                "output_name": "out1",
+                                "uuid": "e6018ad6-86f4-4e78-8cf2-ccc8b97022fe"
+                            },
+                            {
+                                "label": "fastp report on long reads json",
+                                "output_name": "report_json",
+                                "uuid": "69f8383b-a1be-4a74-95f4-3dba35e01426"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "assembly/largegenome",
+                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Trim_and_filter_reads.ga",
+                "tags": [
+                    "LG-WF",
+                    "GTN"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Trim and filter reads - fastp - upgraded ",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-trim-and-filter-reads",
+                "tutorial_id": "largegenome",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Trim_and_filter_reads.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Trim_and_filter_reads.html",
+                "version": 2,
+                "wfid": "assembly-largegenome",
+                "wfname": "galaxy-workflow-trim-and-filter-reads",
+                "workflow": "Galaxy-Workflow-Trim_and_filter_reads.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0"
+                ],
+                "workflowhub_id": "1144"
+            },
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-9906-0673",
+                        "name": "Anna Syme"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n\r\n```galaxy\nworkflow_display()\n```\r\n"
+                    },
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"]\n  1[label=\"Meryl - count kmers\"]\n  0 -> 1 [label=\"output\"]\n  k899ddd934c0f4f81a9738120494ed983[color=lightseagreen,label=\"Output\\nMeryl on input dataset(s): read-db.meryldb\"]\n  1 -> k899ddd934c0f4f81a9738120494ed983\n  2[label=\"Meryl - generate histogram\"]\n  1 -> 2 [label=\"read_db\"]\n  3[label=\"Genomescope\"]\n  2 -> 3 [label=\"read_db_hist\"]\n  kefc727b61ef44c4c8cce35c7d3cc8aac[color=lightseagreen,label=\"Output\\nGenomeScope on input dataset(s) Transformed log plot\"]\n  3 -> kefc727b61ef44c4c8cce35c7d3cc8aac\n  k701df341576744bcade26af498ab7467[color=lightseagreen,label=\"Output\\nGenomeScope on input dataset(s) Transformed linear plot\"]\n  3 -> k701df341576744bcade26af498ab7467\n  k85fa4004b35147b384aa6788d338037a[color=lightseagreen,label=\"Output\\nGenomeScope on input dataset(s) Log plot\"]\n  3 -> k85fa4004b35147b384aa6788d338037a\n  kc71ce05598f0435493972f8833b90cc4[color=lightseagreen,label=\"Output\\nGenomeScope on input dataset(s) Linear plot\"]\n  3 -> kc71ce05598f0435493972f8833b90cc4\n}",
+                "history": [
+                    {
+                        "hash": "b74cf5a09d0d563d658d374ed6d287db85df3a8a",
+                        "message": "Update Galaxy-Workflow-kmer_counting.ga",
+                        "num": 5,
+                        "short_hash": "b74cf5a09",
+                        "unix": "1715074461"
+                    },
+                    {
+                        "hash": "e8ddbcdd5e3fb5b0caac0dac60dc6abce06e1792",
+                        "message": "new versions of workflows",
+                        "num": 4,
+                        "short_hash": "e8ddbcdd5",
+                        "unix": "1714537936"
+                    },
+                    {
+                        "hash": "0be0483e2cbaa0ab18026da1f19f4b124d78e1c4",
+                        "message": "Rename Galaxy-Workflow-kmer_counting.ga to Galaxy-Workflow-kmer_counting_old.ga",
+                        "num": 3,
+                        "short_hash": "0be0483e2",
+                        "unix": "1714537366"
+                    },
+                    {
+                        "hash": "62e77944bdfffa3045148d04ebc741853c6d7d05",
+                        "message": "add/complete creator info on workflows",
+                        "num": 2,
+                        "short_hash": "62e77944b",
+                        "unix": "1676627603"
                     },
+                    {
+                        "hash": "9fcb3aeec26986b2e348d7a1694668a2414e7156",
+                        "message": "large genome tutorial",
+                        "num": 1,
+                        "short_hash": "9fcb3aeec",
+                        "unix": "1665123856"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "batchmode|input_fastas_0|input_fasta": {
-                                "id": 5,
-                                "output_name": "output_database"
-                            },
-                            "batchmode|input_fastas_1|input_fasta": {
-                                "id": 4,
-                                "output_name": "output_database"
-                            },
-                            "batchmode|input_fastas_2|input_fasta": {
-                                "id": 3,
-                                "output_name": "output_database"
-                            },
-                            "batchmode|input_fastas_3|input_fasta": {
-                                "id": 1,
-                                "output_name": "output_database"
-                            },
-                            "batchmode|input_fastas_4|input_fasta": {
-                                "id": 0,
-                                "output_name": "output_database"
-                            },
-                            "batchmode|input_fastas_5|input_fasta": {
-                                "id": 6,
-                                "output_name": "output_database"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "FASTA Merge Files and Filter Unique Sequences",
-                        "outputs": [
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "Illumina reads R1"
                             }
                         ],
+                        "label": "Illumina reads R1",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 394.171875,
-                            "height": 442,
-                            "left": 728.96875,
-                            "right": 928.96875,
-                            "top": -47.828125,
-                            "width": 200,
-                            "x": 728.96875,
-                            "y": -47.828125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f546e7278f04",
-                            "name": "fasta_merge_files_and_filter_unique_sequences",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 31.5
                         },
-                        "tool_state": "{\"accession_parser\": \"^>([^ ]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 3, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 4, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 5, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"uniqueness_criterion\": \"sequence\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.0",
-                        "type": "tool",
-                        "uuid": "2f3e5008-14dc-4078-ab3d-72faf16b21ce",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "0a40b18e-1b8a-4f70-a134-44a449069a6b"
-                            }
-                        ]
-                    },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "3daa3f25-6fff-4766-9d45-b991fd6751a5",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Meryl - count kmers\"];\n  0 -->|output| 1;\n  899ddd93-4c0f-4f81-a973-8120494ed983[\"Output\\nMeryl on input dataset(s): read-db.meryldb\"];\n  1 --> 899ddd93-4c0f-4f81-a973-8120494ed983;\n  style 899ddd93-4c0f-4f81-a973-8120494ed983 stroke:#2c3143,stroke-width:4px;\n  2[\"Meryl - generate histogram\"];\n  1 -->|read_db| 2;\n  3[\"Genomescope\"];\n  2 -->|read_db_hist| 3;\n  efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac[\"Output\\nGenomeScope on input dataset(s) Transformed log plot\"];\n  3 --> efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac;\n  style efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac stroke:#2c3143,stroke-width:4px;\n  701df341-5767-44bc-ade2-6af498ab7467[\"Output\\nGenomeScope on input dataset(s) Transformed linear plot\"];\n  3 --> 701df341-5767-44bc-ade2-6af498ab7467;\n  style 701df341-5767-44bc-ade2-6af498ab7467 stroke:#2c3143,stroke-width:4px;\n  85fa4004-b351-47b3-84aa-6788d338037a[\"Output\\nGenomeScope on input dataset(s) Log plot\"];\n  3 --> 85fa4004-b351-47b3-84aa-6788d338037a;\n  style 85fa4004-b351-47b3-84aa-6788d338037a stroke:#2c3143,stroke-width:4px;\n  c71ce055-98f0-4354-9397-2f8833b90cc4[\"Output\\nGenomeScope on input dataset(s) Linear plot\"];\n  3 --> c71ce055-98f0-4354-9397-2f8833b90cc4;\n  style c71ce055-98f0-4354-9397-2f8833b90cc4 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:06 +0000",
+                "name": "kmer counting - meryl - upgraded",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "addValue",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
                         "errors": null,
-                        "id": 10,
+                        "id": 1,
                         "input_connections": {
-                            "input": {
-                                "id": 8,
+                            "operation_type|input_reads": {
+                                "id": 0,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Add column",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "description": "runtime parameter for tool Meryl",
+                                "name": "operation_type"
                             }
                         ],
-                        "position": {
-                            "bottom": -75.828125,
-                            "height": 92,
-                            "left": 948.96875,
-                            "right": 1148.96875,
-                            "top": -167.828125,
-                            "width": 200,
-                            "x": 948.96875,
-                            "y": -167.828125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "addValue",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"exp\": \"CONTAMINANT\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "74c42033-1c6c-4647-b99b-d50eeba95063",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "1d442a40-1bcf-4d3b-979f-0ef7233c7db9"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
-                        "errors": null,
-                        "id": 11,
-                        "input_connections": {
-                            "input": {
-                                "id": 9,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "FASTA-to-Tabular",
+                        "label": "Meryl - count kmers",
+                        "name": "Meryl",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "name": "read_db",
+                                "type": "meryldb"
                             }
                         ],
                         "position": {
-                            "bottom": 64.171875,
-                            "height": 112,
-                            "left": 948.96875,
-                            "right": 1148.96875,
-                            "top": -47.828125,
-                            "width": 200,
-                            "x": 948.96875,
-                            "y": -47.828125
+                            "left": 228,
+                            "top": 103.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
                         "tool_shed_repository": {
-                            "changeset_revision": "e7ed3c310b74",
-                            "name": "fasta_to_tabular",
-                            "owner": "devteam",
+                            "changeset_revision": "29dabd8db6f2",
+                            "name": "meryl",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"descr_columns\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_state": "{\"operation_type\": {\"command_type\": \"count-kmers\", \"__current_case__\": 0, \"count_operations\": \"count\", \"input_reads\": {\"__class__\": \"RuntimeValue\"}, \"options_kmer_size\": {\"kmer_size\": \"provide\", \"__current_case__\": 0, \"input_kmer_size\": \"21\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3+galaxy6",
                         "type": "tool",
-                        "uuid": "c9832b4a-7f75-4763-bd5e-d7de8a80ed3a",
+                        "uuid": "0a85d93b-8f53-4bc8-b89b-4be6f306f2c6",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "b549c26c-0f66-438f-9c44-e45372fe4cd1"
+                                "label": "Meryl on input dataset(s): read-db.meryldb",
+                                "output_name": "read_db",
+                                "uuid": "899ddd93-4c0f-4f81-a973-8120494ed983"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
                         "errors": null,
-                        "id": 12,
+                        "id": 2,
                         "input_connections": {
-                            "input": {
-                                "id": 10,
-                                "output_name": "out_file1"
+                            "operation_type|input_meryldb_02": {
+                                "id": 1,
+                                "output_name": "read_db"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Tabular-to-FASTA",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Meryl",
+                                "name": "operation_type"
+                            }
+                        ],
+                        "label": "Meryl - generate histogram",
+                        "name": "Meryl",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "fasta"
+                                "name": "read_db_hist",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": -55.828125,
-                            "height": 112,
-                            "left": 1168.96875,
-                            "right": 1368.96875,
-                            "top": -167.828125,
-                            "width": 200,
-                            "x": 1168.96875,
-                            "y": -167.828125
+                            "left": 465.5,
+                            "top": 110
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
                         "tool_shed_repository": {
-                            "changeset_revision": "0a7799698fe5",
-                            "name": "tabular_to_fasta",
-                            "owner": "devteam",
+                            "changeset_revision": "29dabd8db6f2",
+                            "name": "meryl",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"seq_col\": \"2\", \"title_col\": [\"1\", \"3\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_state": "{\"operation_type\": {\"command_type\": \"histogram-kmers\", \"__current_case__\": 4, \"input_meryldb_02\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3+galaxy6",
                         "type": "tool",
-                        "uuid": "396df67c-421c-4a4a-9965-d5eee8d20982",
+                        "uuid": "80dbb867-84f7-4349-ae1d-1c7b87d0dce7",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "d27e6997-b84e-4671-806b-ec8ac62e8fb5"
+                                "output_name": "read_db_hist",
+                                "uuid": "bf11e7cb-61a2-4c27-9aa1-4c7a42028330"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "addValue",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
                         "errors": null,
-                        "id": 13,
+                        "id": 3,
                         "input_connections": {
                             "input": {
-                                "id": 11,
-                                "output_name": "output"
+                                "id": 2,
+                                "output_name": "read_db_hist"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Add column",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "description": "runtime parameter for tool GenomeScope",
+                                "name": "input"
                             }
                         ],
-                        "position": {
-                            "bottom": 44.171875,
-                            "height": 92,
-                            "left": 1168.96875,
-                            "right": 1368.96875,
-                            "top": -47.828125,
-                            "width": 200,
-                            "x": 1168.96875,
-                            "y": -47.828125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "addValue",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"exp\": \"MYCOPLASMA_CONTAMINANT\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "5a462916-3e19-4344-80b4-e1b1f0d3fb9d",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "36488f81-9674-4e5c-ab0a-73c91d2b71fd"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
-                        "errors": null,
-                        "id": 14,
-                        "input_connections": {
-                            "input": {
-                                "id": 13,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Tabular-to-FASTA",
+                        "label": "Genomescope",
+                        "name": "GenomeScope",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "fasta"
+                                "name": "linear_plot",
+                                "type": "png"
+                            },
+                            {
+                                "name": "log_plot",
+                                "type": "png"
+                            },
+                            {
+                                "name": "transformed_linear_plot",
+                                "type": "png"
+                            },
+                            {
+                                "name": "transformed_log_plot",
+                                "type": "png"
+                            },
+                            {
+                                "name": "model",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "summary",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "progress",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 125.171875,
-                            "height": 112,
-                            "left": 1379.96875,
-                            "right": 1579.96875,
-                            "top": 13.171875,
-                            "width": 200,
-                            "x": 1379.96875,
-                            "y": 13.171875
+                            "left": 699.204345703125,
+                            "top": 0
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "0a7799698fe5",
-                            "name": "tabular_to_fasta",
-                            "owner": "devteam",
+                            "changeset_revision": "01210c4e9144",
+                            "name": "genomescope",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"seq_col\": \"2\", \"title_col\": [\"1\", \"3\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_state": "{\"advanced_options\": {\"topology\": null, \"initial_repetitiveness\": null, \"initial_heterozygosities\": \"\", \"transform_exp\": null, \"testing\": false, \"true_params\": \"\", \"trace_flag\": false, \"num_rounds\": null}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"kmer_length\": \"21\", \"lambda\": null, \"max_kmercov\": null, \"output_options\": {\"output_files\": [\"model_output\", \"summary_output\", \"progress_output\"], \"no_unique_sequence\": false}, \"ploidy\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0+galaxy2",
                         "type": "tool",
-                        "uuid": "688b1790-2b96-46cc-849f-7c981b8d6e8c",
+                        "uuid": "fa7a5012-8bd0-4b35-b337-249245e0932b",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "c7b7f6bf-b83f-424d-b1ca-63161427c7ab"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-                        "errors": null,
-                        "id": 15,
-                        "input_connections": {
-                            "batchmode|input_fastas_0|input_fasta": {
-                                "id": 12,
-                                "output_name": "output"
+                                "output_name": "progress",
+                                "uuid": "fedca588-8be6-4e13-9ff5-62387a5a90af"
                             },
-                            "batchmode|input_fastas_1|input_fasta": {
-                                "id": 7,
-                                "output_name": "output_database"
+                            {
+                                "label": "GenomeScope on input dataset(s) Transformed log plot",
+                                "output_name": "transformed_log_plot",
+                                "uuid": "efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac"
                             },
-                            "batchmode|input_fastas_2|input_fasta": {
-                                "id": 14,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "FASTA Merge Files and Filter Unique Sequences",
-                        "outputs": [
                             {
-                                "name": "output",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 533.171875,
-                            "height": 292,
-                            "left": 1521.96875,
-                            "right": 1721.96875,
-                            "top": 241.171875,
-                            "width": 200,
-                            "x": 1521.96875,
-                            "y": 241.171875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f546e7278f04",
-                            "name": "fasta_merge_files_and_filter_unique_sequences",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"accession_parser\": \"^>([^ ]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"uniqueness_criterion\": \"accession\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.0",
-                        "type": "tool",
-                        "uuid": "a6d6aafa-1474-44ee-812a-3d700643e350",
-                        "workflow_outputs": [
+                                "label": null,
+                                "output_name": "summary",
+                                "uuid": "fd17af72-7c2a-4167-9880-7fbda525ccbb"
+                            },
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "7571d011-cfdf-4c97-bd1b-65a13f26b044"
+                                "output_name": "model",
+                                "uuid": "ede2b1a5-4017-4aef-a6d2-bac5d17bc7b5"
+                            },
+                            {
+                                "label": "GenomeScope on input dataset(s) Transformed linear plot",
+                                "output_name": "transformed_linear_plot",
+                                "uuid": "701df341-5767-44bc-ade2-6af498ab7467"
+                            },
+                            {
+                                "label": "GenomeScope on input dataset(s) Log plot",
+                                "output_name": "log_plot",
+                                "uuid": "85fa4004-b351-47b3-84aa-6788d338037a"
+                            },
+                            {
+                                "label": "GenomeScope on input dataset(s) Linear plot",
+                                "output_name": "linear_plot",
+                                "uuid": "c71ce055-98f0-4354-9397-2f8833b90cc4"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/database-handling",
-                "path": "topics/proteomics/tutorials/database-handling/workflows/wf_database-handling_mycoplasma.ga",
+                "parent_id": "assembly/largegenome",
+                "path": "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-kmer_counting.ga",
                 "tags": [
-                    "proteomics"
+                    "GTN",
+                    "LG-WF"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Proteomics: database handling including mycoplasma",
-                "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-database-handling/versions/wf-database-handling-mycoplasma",
-                "tutorial_id": "database-handling",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/database-handling/workflows/wf_database-handling_mycoplasma.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/database-handling/workflows/wf_database-handling_mycoplasma.html",
-                "version": 6,
-                "wfid": "proteomics-database-handling",
-                "wfname": "wf-database-handling-mycoplasma",
-                "workflow": "wf_database-handling_mycoplasma.ga",
+                "title": "kmer counting - meryl - upgraded",
+                "topic_id": "assembly",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/assembly-largegenome/versions/galaxy-workflow-kmer-counting",
+                "tutorial_id": "largegenome",
+                "url": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-kmer_counting.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-kmer_counting.html",
+                "version": 2,
+                "wfid": "assembly-largegenome",
+                "wfname": "galaxy-workflow-kmer-counting",
+                "workflow": "Galaxy-Workflow-kmer_counting.ga",
                 "workflow_tools": [
-                    "addValue",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.6+galaxy0"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6"
                 ],
-                "workflowhub_id": "1199"
+                "workflowhub_id": "1166"
             }
         ],
-        "zenodo_link": ""
+        "zenodo_link": "https://doi.org/10.5281/zenodo.7055935"
     },
     {
         "admin_install": {
@@ -177432,351 +178546,201 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "pdaug_addclasslabel",
-                    "owner": "jay",
-                    "revisions": "7160bfd77aef",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pdaug_basic_plots",
-                    "owner": "jay",
-                    "revisions": "15b6eec94c40",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pdaug_fishers_plot",
-                    "owner": "jay",
-                    "revisions": "2fe62dfbdc9d",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pdaug_merge_dataframes",
-                    "owner": "jay",
-                    "revisions": "2dbfb42d34bc",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pdaug_peptide_data_access",
-                    "owner": "jay",
-                    "revisions": "7cf1e907c31d",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pdaug_peptide_sequence_analysis",
-                    "owner": "jay",
-                    "revisions": "90e3b1968ae6",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "diamond",
+                    "owner": "bgruening",
+                    "revisions": "e8ac2b53f262",
+                    "tool_panel_section_label": "NCBI Blast",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pdaug_sequence_property_based_descriptors",
-                    "owner": "jay",
-                    "revisions": "187c6f2d3b55",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "ncbi_blast_plus",
+                    "owner": "devteam",
+                    "revisions": "0e3cf9594bb7",
+                    "tool_panel_section_label": "NCBI Blast",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pdaug_tsvtofasta",
-                    "owner": "jay",
-                    "revisions": "03f954dd8360",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "ncbi_blast_plus",
+                    "owner": "devteam",
+                    "revisions": "0e3cf9594bb7",
+                    "tool_panel_section_label": "NCBI Blast",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: pdaug_addclasslabel\n  owner: jay\n  revisions: 7160bfd77aef\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_basic_plots\n  owner: jay\n  revisions: 15b6eec94c40\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_fishers_plot\n  owner: jay\n  revisions: 2fe62dfbdc9d\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_merge_dataframes\n  owner: jay\n  revisions: 2dbfb42d34bc\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_peptide_data_access\n  owner: jay\n  revisions: 7cf1e907c31d\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_peptide_sequence_analysis\n  owner: jay\n  revisions: 90e3b1968ae6\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_sequence_property_based_descriptors\n  owner: jay\n  revisions: 187c6f2d3b55\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_tsvtofasta\n  owner: jay\n  revisions: 03f954dd8360\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/peptide-library-data-analysis/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: diamond\n  owner: bgruening\n  revisions: e8ac2b53f262\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: 0e3cf9594bb7\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: 0e3cf9594bb7\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "deeptivarshney"
+            ],
+            "funding": [
+                "madland",
+                "nfdi4plants"
+            ]
+        },
         "contributors": [
             {
-                "id": "jaidevjoshi83",
-                "joined": "2020-11",
-                "name": "Jayadev Joshi",
-                "orcid": "0000-0001-7589-5230",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jaidevjoshi83/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jaidevjoshi83.json"
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "deeptivarshney",
+                "joined": "2022-12",
+                "name": "Deepti Varshney",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/deeptivarshney.json"
             },
             {
-                "id": "blankenberg",
-                "joined": "2018-07",
-                "name": "Daniel Blankenberg",
-                "orcid": "0000-0002-6833-9049",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankenberg/",
-                "twitter": "dblankenberg",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankenberg.json"
+                "avatar": "/training-material/shared/images/logo-madland.jpg",
+                "funder": true,
+                "github": false,
+                "id": "madland",
+                "joined": "2024-07",
+                "name": "MAdLand",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/madland/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/madland.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/logo-dataplant.svg",
+                "funder": true,
+                "id": "nfdi4plants",
+                "joined": "2024-07",
+                "name": "DataPLANT",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nfdi4plants/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/nfdi4plants.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/peptide-library-data-analysis",
-        "edam_operation": [],
+        "dir": "topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland",
+        "edam_operation": [
+            "Sequence alignment analysis"
+        ],
         "edam_topic": [],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "proteomics/peptide-library-data-analysis",
-        "inexact_supported_servers": [],
+        "id": "sequence-analysis/ncbi-blast-against-the-madland",
+        "inexact_supported_servers": [
+            "Galaxy@AuBi",
+            "GalaxyTrakr",
+            "UseGalaxy.no"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
+        "key_points": [
+            "Blast tool searches a database of sequences for similar sequences to a query sequence.",
+            "Diamond  quickly aligns large-scale data sets using a compressed version of the reference sequences called a \"database diamond\".",
+            "MAdLand is a database of fully sequenced plant and algal genomes, with an emphasis on non-seed plants and streptophyte algae that can be use for sequence similarity search."
+        ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-07-31",
         "objectives": [
-            "Calculate descriptors",
-            "Quantitative analysis of peptide sequence properties"
+            "Load FASTA sequence into Galaxy",
+            "Perform NCBI-Blast+ analysis against MAdLandDB"
         ],
-        "pageviews": 790,
-        "pub_date": "2021-01-22",
+        "pageviews": 1414,
+        "pub_date": "2023-01-16",
         "questions": [
-            "How to utilize quantitative properties of amino acids and peptide sequence to analyse peptide data?"
+            "What is MAdLand DB?",
+            "How can we perform Blast analysis on Galaxy?"
         ],
-        "short_id": "T00227",
+        "short_id": "T00238",
         "short_tools": [
-            "pdaug_basic_plots",
-            "pdaug_sequence_property_based_descriptors",
-            "pdaug_tsvtofasta",
-            "pdaug_fishers_plot",
-            "pdaug_peptide_sequence_analysis",
-            "pdaug_merge_dataframes",
-            "pdaug_peptide_data_access",
-            "pdaug_addclasslabel"
+            "ncbi_blastp_wrapper",
+            "ncbi_blastx_wrapper",
+            "bg_diamond"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "property-prediction",
         "supported_servers": {
-            "exact": [],
-            "inexact": []
+            "exact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                }
+            ]
         },
         "symlink": null,
-        "tags": [],
-        "time_estimation": "20m",
-        "title": "Peptide Library Data Analysis",
+        "tags": [
+            "plants"
+        ],
+        "time_estimation": "15m",
+        "title": "NCBI BLAST+ against the MAdLand",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_addclasslabel/pdaug_addclasslabel/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_basic_plots/pdaug_basic_plots/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_fishers_plot/pdaug_fishers_plot/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_merge_dataframes/pdaug_merge_dataframes/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_peptide_data_access/pdaug_peptide_data_access/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_peptide_sequence_analysis/pdaug_peptide_sequence_analysis/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_sequence_property_based_descriptors/pdaug_sequence_property_based_descriptors/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_tsvtofasta/pdaug_tsvtofasta/0.1.0"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/2.10.1+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/2.10.1+galaxy2"
         ],
-        "topic_name": "proteomics",
-        "topic_name_human": "Proteomics",
+        "topic_name": "sequence-analysis",
+        "topic_name_human": "Sequence analysis",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "peptide-library-data-analysis",
+        "tutorial_name": "ncbi-blast-against-the-madland",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/peptide-library-data-analysis/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/peptide-library-data-analysis/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/peptide-library-data-analysis/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.json"
         },
-        "version": 5,
+        "version": 9,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 160,
-        "visitors": 564,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Peptide Library Data Analysis",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"PDAUG Peptide Data Access\"]\n  1[label=\"PDAUG TSVtoFASTA\"]\n  0 -> 1 [label=\"output1\"]\n  2[label=\"PDAUG Peptide Sequence Analysis\"]\n  1 -> 2 [label=\"output3\"]\n  1 -> 2 [label=\"output2\"]\n  3[label=\"PDAUG Sequence Property Based Descriptors\"]\n  1 -> 3 [label=\"output2\"]\n  4[label=\"PDAUG Sequence Property Based Descriptors\"]\n  1 -> 4 [label=\"output3\"]\n  5[label=\"PDAUG Fisher\u2019s Plot\"]\n  1 -> 5 [label=\"output3\"]\n  1 -> 5 [label=\"output2\"]\n  6[label=\"AMP\"]\n  3 -> 6 [label=\"output1\"]\n  7[label=\"TMP\"]\n  4 -> 7 [label=\"output1\"]\n  8[label=\"PDAUG Merge Dataframes\"]\n  6 -> 8 [label=\"OutFile1\"]\n  7 -> 8 [label=\"OutFile1\"]\n  9[label=\"PDAUG Basic Plots\"]\n  8 -> 9 [label=\"output1\"]\n}",
-                "history": [
-                    {
-                        "hash": "c6cb67762f0c2d329bb52c6e6fb805df376f9ea0",
-                        "message": "Tutorials for PDAUG tool suite (#2150)",
-                        "num": 1,
-                        "short_hash": "c6cb67762",
-                        "unix": "1611340147"
-                    }
-                ],
-                "inputs": [],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"PDAUG Peptide Data Access\"];\n  1[\"PDAUG TSVtoFASTA\"];\n  0 -->|output1| 1;\n  2[\"PDAUG Peptide Sequence Analysis\"];\n  1 -->|output3| 2;\n  1 -->|output2| 2;\n  3[\"PDAUG Sequence Property Based Descriptors\"];\n  1 -->|output2| 3;\n  4[\"PDAUG Sequence Property Based Descriptors\"];\n  1 -->|output3| 4;\n  5[\"PDAUG Fisher\u2019s Plot\"];\n  1 -->|output3| 5;\n  1 -->|output2| 5;\n  6[\"AMP\"];\n  3 -->|output1| 6;\n  7[\"TMP\"];\n  4 -->|output1| 7;\n  8[\"PDAUG Merge Dataframes\"];\n  6 -->|OutFile1| 8;\n  7 -->|OutFile1| 8;\n  9[\"PDAUG Basic Plots\"];\n  8 -->|output1| 9;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Copy of PeptideDataAnalysis (imported from uploaded file)",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_peptide_data_access/pdaug_peptide_data_access/0.1.0",
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "PDAUG Peptide Data Access",
-                        "outputs": [
-                            {
-                                "name": "output1",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 200,
-                            "top": 200
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_peptide_data_access/pdaug_peptide_data_access/0.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3eb014f169cf",
-                            "name": "pdaug_peptide_data_access",
-                            "owner": "jay",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"SelectDatasets\": {\"DataBaseType\": \"AMPvsTMP\", \"__current_case__\": 4}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.0",
-                        "type": "tool",
-                        "uuid": "cc540442-0f77-4623-acac-962820250573",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output1",
-                                "uuid": "18bdb5f0-767f-4f38-a49d-daaf38287b79"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_fishers_plot/pdaug_fishers_plot/0.1.0",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "Fasta1": {
-                                "id": 1,
-                                "output_name": "output3"
-                            },
-                            "Fasta2": {
-                                "id": 1,
-                                "output_name": "output2"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "PDAUG Fisher's Plot",
-                        "outputs": [
-                            {
-                                "name": "output2",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 770.99609375,
-                            "top": 912.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_fishers_plot/pdaug_fishers_plot/0.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "7a9f6ac448bc",
-                            "name": "pdaug_fishers_plot",
-                            "owner": "jay",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"Fasta1\": {\"__class__\": \"ConnectedValue\"}, \"Fasta2\": {\"__class__\": \"ConnectedValue\"}, \"overlap_factor\": \"5\", \"pop1_label\": \"TMPs\", \"pop2_label\": \"AMPs\", \"windows_per_frame\": \"5\", \"xlabel\": \"Mean volume\", \"ylabel\": \"Mean hydropathy\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.0",
-                        "type": "tool",
-                        "uuid": "61d70923-d629-49a4-be01-0ead9c18bdb8",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output2",
-                                "uuid": "c5869465-89c0-4183-9834-04d34f90233f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_basic_plots/pdaug_basic_plots/0.1.0",
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "SelPlotting|InFile": {
-                                "id": 8,
-                                "output_name": "output1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "PDAUG Basic Plots",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "html"
-                            }
-                        ],
-                        "position": {
-                            "left": 1627.5,
-                            "top": 200
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_basic_plots/pdaug_basic_plots/0.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "080b372fe513",
-                            "name": "pdaug_basic_plots",
-                            "owner": "jay",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"SelPlotting\": {\"Plot\": \"ScatterPlot\", \"__current_case__\": 2, \"InFile\": {\"__class__\": \"ConnectedValue\"}, \"PlotType\": {\"SelectPlot\": \"3D\", \"__current_case__\": 1, \"Features1\": \"_SecondaryStrD1100\", \"Features2\": \"_SolventAccessibilityD2001\", \"Features3\": \"_NormalizedVDWVD3050\"}, \"Label\": \"Class_label\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.0",
-                        "type": "tool",
-                        "uuid": "457cfde2-d691-4e9c-af64-5416ae609770",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "269a24c3-8cf7-4ab6-b08d-f91fd9996756"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "proteomics/peptide-library-data-analysis",
-                "path": "topics/proteomics/tutorials/peptide-library-data-analysis/workflows/PeptideDataAnalysis.ga",
-                "tags": [
-                    "proteomics"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Copy of PeptideDataAnalysis (imported from uploaded file)",
-                "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-peptide-library-data-analysis/versions/peptidedataanalysis",
-                "tutorial_id": "peptide-library-data-analysis",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/peptide-library-data-analysis/workflows/PeptideDataAnalysis.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/peptide-library-data-analysis/workflows/PeptideDataAnalysis.html",
-                "version": 1,
-                "wfid": "proteomics-peptide-library-data-analysis",
-                "wfname": "peptidedataanalysis",
-                "workflow": "PeptideDataAnalysis.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_addclasslabel/pdaug_addclasslabel/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_basic_plots/pdaug_basic_plots/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_fishers_plot/pdaug_fishers_plot/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_merge_dataframes/pdaug_merge_dataframes/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_peptide_data_access/pdaug_peptide_data_access/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_peptide_sequence_analysis/pdaug_peptide_sequence_analysis/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_sequence_property_based_descriptors/pdaug_sequence_property_based_descriptors/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_tsvtofasta/pdaug_tsvtofasta/0.1.0"
-                ],
-                "workflowhub_id": "1244"
-            }
-        ]
+        "visit_duration": 158,
+        "visitors": 1103,
+        "zenodo_link": "https://zenodo.org/records/7524427"
     },
     {
         "admin_install": {
@@ -177785,258 +178749,228 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "metaquantome_db",
-                    "owner": "galaxyp",
-                    "revisions": "7c45aa1c9464",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "metaquantome_db",
-                    "owner": "galaxyp",
-                    "revisions": "e63db1aa82ee",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "metaquantome_expand",
-                    "owner": "galaxyp",
-                    "revisions": "eb65ab160a10",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "metaquantome_expand",
-                    "owner": "galaxyp",
-                    "revisions": "767c1d761aaf",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "metaquantome_filter",
-                    "owner": "galaxyp",
-                    "revisions": "7d1c20b315ff",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "metaquantome_filter",
-                    "owner": "galaxyp",
-                    "revisions": "35cc7ca0bdc7",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "anndata_import",
+                    "owner": "iuc",
+                    "revisions": "55e35e9203cf",
+                    "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "metaquantome_sample",
-                    "owner": "galaxyp",
-                    "revisions": "49a957fb353a",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "anndata_manipulate",
+                    "owner": "iuc",
+                    "revisions": "9bd945a03d7b",
+                    "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "metaquantome_sample",
-                    "owner": "galaxyp",
-                    "revisions": "06f6826d380c",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "scanpy_cluster_reduce_dimension",
+                    "owner": "iuc",
+                    "revisions": "aaa5da8e73a9",
+                    "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "metaquantome_stat",
-                    "owner": "galaxyp",
-                    "revisions": "982a442a98dd",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "scanpy_filter",
+                    "owner": "iuc",
+                    "revisions": "b409c2486353",
+                    "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "metaquantome_stat",
-                    "owner": "galaxyp",
-                    "revisions": "b9d453dca8d3",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "scanpy_inspect",
+                    "owner": "iuc",
+                    "revisions": "c5d3684f7c4c",
+                    "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "metaquantome_viz",
-                    "owner": "galaxyp",
-                    "revisions": "02da24eac445",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "scanpy_normalize",
+                    "owner": "iuc",
+                    "revisions": "ab55fe8030b6",
+                    "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "metaquantome_viz",
-                    "owner": "galaxyp",
-                    "revisions": "8bd7734309f6",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: metaquantome_db\n  owner: galaxyp\n  revisions: 7c45aa1c9464\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_db\n  owner: galaxyp\n  revisions: e63db1aa82ee\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_expand\n  owner: galaxyp\n  revisions: eb65ab160a10\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_expand\n  owner: galaxyp\n  revisions: 767c1d761aaf\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_filter\n  owner: galaxyp\n  revisions: 7d1c20b315ff\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_filter\n  owner: galaxyp\n  revisions: 35cc7ca0bdc7\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_sample\n  owner: galaxyp\n  revisions: 49a957fb353a\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_sample\n  owner: galaxyp\n  revisions: 06f6826d380c\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_stat\n  owner: galaxyp\n  revisions: 982a442a98dd\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_stat\n  owner: galaxyp\n  revisions: b9d453dca8d3\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_viz\n  owner: galaxyp\n  revisions: 02da24eac445\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_viz\n  owner: galaxyp\n  revisions: 8bd7734309f6\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-function/tutorial.json",
-        "contributors": [
-            {
-                "email": "subinamehta@gmail.com",
-                "id": "subinamehta",
-                "joined": "2018-06",
-                "linkedin": "subinamehta",
-                "matrix": "subinamehta:matrix.org",
-                "name": "Subina Mehta",
-                "orcid": "0000-0001-9818-0537",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
-                "twitter": "Subina_Mehta",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
-            },
-            {
-                "email": "tgriffin@umn.edu",
-                "github": false,
-                "id": "timothygriffin",
-                "joined": "2017-09",
-                "name": "Timothy J. Griffin",
-                "orcid": "0000-0001-6801-2559",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
-            },
+                    "name": "scanpy_plot",
+                    "owner": "iuc",
+                    "revisions": "6adf98e782f3",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_remove_confounders",
+                    "owner": "iuc",
+                    "revisions": "bf2017df9837",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: anndata_import\n  owner: iuc\n  revisions: 55e35e9203cf\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n  owner: iuc\n  revisions: 9bd945a03d7b\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_cluster_reduce_dimension\n  owner: iuc\n  revisions: aaa5da8e73a9\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter\n  owner: iuc\n  revisions: b409c2486353\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_inspect\n  owner: iuc\n  revisions: c5d3684f7c4c\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_normalize\n  owner: iuc\n  revisions: ab55fe8030b6\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot\n  owner: iuc\n  revisions: 6adf98e782f3\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_remove_confounders\n  owner: iuc\n  revisions: bf2017df9837\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plant/tutorial.json",
+        "contributors": [
             {
-                "email": "pjagtap@umn.edu",
-                "id": "pratikdjagtap",
-                "joined": "2017-09",
-                "name": "Pratik Jagtap",
-                "orcid": "0000-0003-0984-0973",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "elixir_node": "de",
+                "email": "mtekman89@gmail.com",
+                "former_affiliations": [
+                    "elixir-europe"
+                ],
+                "id": "mtekman",
+                "joined": "2018-11",
+                "name": "Mehmet Tekman",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
             },
             {
-                "email": "leith023@umn.edu",
-                "id": "emmaleith",
-                "joined": "2019-07",
-                "name": "Emma Leith",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/emmaleith/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/emmaleith.json"
+                "email": "beatrizserrano.galaxy@gmail.com",
+                "id": "beatrizserrano",
+                "joined": "2020-07",
+                "linkedin": "beatriz-serrano",
+                "matrix": "beatrizserrano:matrix.org",
+                "name": "Beatriz Serrano-Solano",
+                "orcid": "0000-0002-5862-6132",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/beatrizserrano/",
+                "twitter": "BSerranoSolano",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/beatrizserrano.json"
             },
             {
-                "email": "crane136@umn.edu",
-                "id": "mariecrane",
-                "joined": "2019-05",
-                "name": "Marie Crane",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mariecrane/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mariecrane.json"
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "gallardoalba",
+                "joined": "2020-11",
+                "name": "Crist\u00f3bal Gallardo",
+                "orcid": "0000-0002-5752-2155",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
             },
             {
-                "email": "kumar207@umn.edu",
-                "id": "pravs3683",
-                "joined": "2019-04",
-                "name": "Praveen Kumar",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pravs3683/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pravs3683.json"
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "pavanvidem",
+                "joined": "2017-09",
+                "name": "Pavankumar Videm",
+                "orcid": "0000-0002-5192-126X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/metaquantome-function",
-        "edam_ontology": [
-            "topic_0121",
-            "topic_3922",
-            "topic_3941",
-            "topic_3697",
-            "topic_3174"
-        ],
+        "dir": "topics/single-cell/tutorials/scrna-plant",
         "edam_operation": [
-            "Visualisation",
-            "Differential protein expression analysis",
-            "Functional clustering",
-            "Query and retrieval",
-            "Indexing",
-            "Filtering",
-            "Heat map generation",
-            "Statistical inference",
-            "Principal component visualisation",
-            "Quantification"
-        ],
-        "edam_topic": [
-            "Proteomics",
-            "Proteogenomics",
-            "Metatranscriptomics",
-            "Microbial ecology",
-            "Metagenomics"
+            "Differential gene expression analysis"
         ],
+        "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "proteomics",
-                "tutorials": [
-                    "metaproteomics"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "proteomics",
-                "tutorials": [
-                    "metaquantome-taxonomy"
-                ],
-                "type": "internal"
-            }
-        ],
+        "gitter": "Galaxy-Training-Network/galaxy-single-cell",
         "hands_on": true,
-        "id": "proteomics/metaquantome-function",
+        "id": "single-cell/scrna-plant",
         "inexact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
+            "UseGalaxy.no"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "All the inputs should have one column in common i.e. peptides.",
-            "Functional annotation can be performed using GO terms and EC numbers",
-            "Having basic knowledge regarding tools that can perform functional annotation can come in handy"
+            "Filtering parameters are dependent on the dataset, and should be explored using scatter or violin plots",
+            "A DotPlot is a fantastic way to validate clusters across different analyses"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-15",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "A functional and quantitational analysis of metaproteomic mass spectrometry data."
+            "Perform filtering, dimensionality reduction, and clustering",
+            "Generate a DotPlot emulating the original paper using a different analysis tool",
+            "Determine robust clusters across scRNA-seq pipelines"
         ],
-        "pageviews": 504,
-        "pub_date": "2020-10-29",
+        "pageviews": 2483,
+        "priority": 3,
+        "pub_date": "2021-04-08",
         "questions": [
-            "How do I look at differentially expressed proteins?",
-            "How do I get top 5 or 10 function present in the sample?",
-            "How can I visualize my results?"
+            "Can we reclaim cell markers using a different analysis method?",
+            "Are highly variable genes paramount to the analysis?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "mtekman"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "55M",
+                "speakers": [
+                    "mtekman"
+                ],
+                "youtube_id": "yKlJ5ESri7o"
+            }
+        ],
+        "redirect_from": [
+            "/topics/transcriptomics/tutorials/scrna-plant/tutorial",
+            "/short/single-cell/scrna-plant",
+            "/short/T00250"
         ],
         "requirements": [
             {
-                "topic_name": "proteomics",
+                "topic_name": "single-cell",
                 "tutorials": [
-                    "metaquantome-data-creation"
+                    "scrna-scanpy-pbmc3k"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00223",
+        "short_id": "T00250",
         "short_tools": [
-            "metaquantome_db",
-            "metaquantome_sample",
-            "metaquantome_stat",
-            "metaquantome_expand",
-            "metaquantome_filter",
-            "metaquantome_viz"
+            "scanpy_remove_confounders",
+            "anndata_import",
+            "scanpy_plot",
+            "scanpy_cluster_reduce_dimension",
+            "anndata_manipulate",
+            "scanpy_filter",
+            "scanpy_inspect",
+            "scanpy_normalize"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "multi-omics",
+        "subtopic": "end-to-end",
         "supported_servers": {
             "exact": [
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ],
             "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -178046,94 +178980,65 @@
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
         "tags": [
-            "microgalaxy"
+            "plants",
+            "paper-replication"
         ],
-        "time_estimation": "1h",
-        "title": "metaQuantome 2: Function",
+        "time_estimation": "2H",
+        "title": "Analysis of plant scRNA-Seq Data with Scanpy",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.0-0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.0-0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.0-0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.0-0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.0-0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0"
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0"
         ],
-        "topic_name": "proteomics",
-        "topic_name_human": "Proteomics",
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "metaquantome-function",
+        "tutorial_name": "scrna-plant",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-plant/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-function/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-function/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plant/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plant/tutorial.json"
         },
-        "version": 14,
+        "version": 5,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 228,
-        "visitors": 348,
+        "visit_duration": 83,
+        "visitors": 1962,
         "workflows": [
             {
                 "creators": [],
-                "description": "metaquantome-function",
+                "description": "Downstream Single-cell RNA Plant analysis with ScanPy",
                 "features": {
                     "comments": false,
-                    "parameters": false,
+                    "parameters": true,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"metaQuantome: database\"]\n  1[label=\"metaQuantome: create samples file\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nFunctional file\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIntensity file\"]\n  4[label=\"metaQuantome: expand\"]\n  0 -> 4 [label=\"outfile\"]\n  3 -> 4 [label=\"output\"]\n  2 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"samples_file\"]\n  5[label=\"metaQuantome: filter\"]\n  4 -> 5 [label=\"outfile\"]\n  1 -> 5 [label=\"samples_file\"]\n  6[label=\"metaQuantome: stat\"]\n  5 -> 6 [label=\"outfile\"]\n  1 -> 6 [label=\"samples_file\"]\n  7[label=\"T2-Bar-Plot\"]\n  6 -> 7 [label=\"outfile\"]\n  6 -> 7 [label=\"outfile\"]\n  8[label=\"T4-Bar-Plot\"]\n  6 -> 8 [label=\"outfile\"]\n  1 -> 8 [label=\"samples_file\"]\n  9[label=\"T7-Bar-Plot\"]\n  6 -> 9 [label=\"outfile\"]\n  1 -> 9 [label=\"samples_file\"]\n  10[label=\"T7-T2-Volcano-Plot\"]\n  6 -> 10 [label=\"outfile\"]\n  1 -> 10 [label=\"samples_file\"]\n  11[label=\"T4-T2-Volcano-Plot\"]\n  6 -> 11 [label=\"outfile\"]\n  1 -> 11 [label=\"samples_file\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nLeiden Resolution\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSHR CSV.gz\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nWT CSV.gz\"]\n  3[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMin Genes\"]\n  4[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMin Cells\"]\n  5[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMax Features\"]\n  6[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMax Lib Size\"]\n  7[label=\"Import Anndata and loom\"]\n  1 -> 7 [label=\"output\"]\n  8[label=\"Import Anndata and loom\"]\n  2 -> 8 [label=\"output\"]\n  9[label=\"Manipulate AnnData\"]\n  7 -> 9 [label=\"anndata\"]\n  8 -> 9 [label=\"anndata\"]\n  10[label=\"Rename Batches\"]\n  9 -> 10 [label=\"anndata\"]\n  k680180f6edfc4f66b2657a63aaa22b39[color=lightseagreen,label=\"Output\\nscRNA Concatenated Datasets\"]\n  10 -> k680180f6edfc4f66b2657a63aaa22b39\n  11[label=\"QC metrics\"]\n  10 -> 11 [label=\"anndata\"]\n  12[label=\"Filter genes\"]\n  11 -> 12 [label=\"anndata_out\"]\n  3 -> 12 [label=\"output\"]\n  13[label=\"Plot Violin\"]\n  11 -> 13 [label=\"anndata_out\"]\n  14[label=\"Filter Cells\"]\n  12 -> 14 [label=\"anndata_out\"]\n  4 -> 14 [label=\"output\"]\n  15[label=\"Filter Max Features\"]\n  14 -> 15 [label=\"anndata_out\"]\n  5 -> 15 [label=\"output\"]\n  16[label=\"Filter Max Library Size\"]\n  15 -> 16 [label=\"anndata\"]\n  6 -> 16 [label=\"output\"]\n  17[label=\"Save RAW\"]\n  16 -> 17 [label=\"anndata\"]\n  18[label=\"Norm to 1e4\"]\n  17 -> 18 [label=\"anndata\"]\n  19[label=\"Log1p\"]\n  18 -> 19 [label=\"anndata_out\"]\n  20[label=\"Regress total counts\"]\n  19 -> 20 [label=\"anndata_out\"]\n  21[label=\"Scale\"]\n  20 -> 21 [label=\"anndata_out\"]\n  22[label=\"PCA\"]\n  21 -> 22 [label=\"anndata_out\"]\n  23[label=\"Neighborhod\"]\n  22 -> 23 [label=\"anndata_out\"]\n  24[label=\"UMAP\"]\n  23 -> 24 [label=\"anndata_out\"]\n  25[label=\"Leiden\"]\n  24 -> 25 [label=\"anndata_out\"]\n  0 -> 25 [label=\"output\"]\n  k48cf046584ba461abdb961625626de42[color=lightseagreen,label=\"Output\\nscRNA with clusters Dataset\"]\n  25 -> k48cf046584ba461abdb961625626de42\n  26[label=\"Plot PCA batch\"]\n  24 -> 26 [label=\"anndata_out\"]\n  27[label=\"Plot UMAP batch\"]\n  24 -> 27 [label=\"anndata_out\"]\n  28[label=\"Plot UMAP leiden, batch\"]\n  25 -> 28 [label=\"anndata_out\"]\n  29[label=\"Rename Clusters\"]\n  25 -> 29 [label=\"anndata_out\"]\n  30[label=\"Complex DotPlot\"]\n  25 -> 30 [label=\"anndata_out\"]\n  31[label=\"Complex DotPlot with new labels\"]\n  29 -> 31 [label=\"anndata\"]\n  32[label=\"Plot UMAP with new labels\"]\n  29 -> 32 [label=\"anndata\"]\n}",
                 "history": [
                     {
-                        "hash": "9d12ea3f6c949d0485659fb58ac0eda7c8814a74",
-                        "message": "Update main_workflow.ga",
-                        "num": 4,
-                        "short_hash": "9d12ea3f6",
-                        "unix": "1636475724"
-                    },
-                    {
-                        "hash": "b44e7f7c70e9638f17ca09238d425e0d8542d2a9",
-                        "message": "Update main_workflow.ga",
-                        "num": 3,
-                        "short_hash": "b44e7f7c7",
-                        "unix": "1603726491"
-                    },
-                    {
-                        "hash": "619a94b389406eacd755598aa6ce4fab95f867f6",
-                        "message": "Update main_workflow.ga",
-                        "num": 2,
-                        "short_hash": "619a94b38",
-                        "unix": "1603158677"
-                    },
-                    {
-                        "hash": "426a2746eee3945edd669f81b15b222493c46c82",
-                        "message": "tutorial skeletons generated by planemo",
+                        "hash": "327fd2b842f45de3dc2a30067714352675ad69ae",
+                        "message": "Making a single cell topics",
                         "num": 1,
-                        "short_hash": "426a2746e",
-                        "unix": "1602853461"
+                        "short_hash": "327fd2b84",
+                        "unix": "1668273265"
                     }
                 ],
                 "inputs": [
@@ -178141,677 +179046,719 @@
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Functional file"
+                                "name": "Leiden Resolution"
                             }
                         ],
-                        "label": "Functional file",
+                        "label": "Leiden Resolution",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 195.5,
+                            "height": 84,
+                            "left": 121.5,
+                            "right": 321.5,
+                            "top": 111.5,
+                            "width": 200,
+                            "x": 121.5,
+                            "y": 111.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"default\": 0.35, \"parameter_type\": \"float\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "eddf8108-6913-40d2-819d-a84677dee3f4",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "SHR (CSV.gz)"
+                            }
+                        ],
+                        "label": "SHR (CSV.gz)",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 856.578125,
-                            "height": 81,
-                            "left": 397.546875,
-                            "right": 597.546875,
-                            "top": 775.578125,
+                            "bottom": 302,
+                            "height": 84,
+                            "left": 116,
+                            "right": 316,
+                            "top": 218,
                             "width": 200,
-                            "x": 397.546875,
-                            "y": 775.578125
+                            "x": 116,
+                            "y": 218
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "7d436bc0-0e63-4445-93d5-5600c9a5c383",
+                        "uuid": "4cf4f111-d63b-47ad-bcbf-8ebb290b3431",
                         "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Intensity file"
+                                "name": "WT (CSV.gz)"
                             }
                         ],
-                        "label": "Intensity file",
+                        "label": "WT (CSV.gz)",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 953.578125,
-                            "height": 61,
-                            "left": 391.5625,
-                            "right": 591.5625,
-                            "top": 892.578125,
+                            "bottom": 403,
+                            "height": 84,
+                            "left": 114,
+                            "right": 314,
+                            "top": 319,
                             "width": 200,
-                            "x": 391.5625,
-                            "y": 892.578125
+                            "x": 114,
+                            "y": 319
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "1e20e3c4-3b6f-4e0c-a5b6-8f8f3d220441",
+                        "uuid": "94fba59a-ba9d-452d-b325-cb558201f674",
                         "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"metaQuantome: database\"];\n  1[\"metaQuantome: create samples file\"];\n  2[\"\u2139\ufe0f Input Dataset\\nFunctional file\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nIntensity file\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"metaQuantome: expand\"];\n  0 -->|outfile| 4;\n  3 -->|output| 4;\n  2 -->|output| 4;\n  1 -->|samples_file| 4;\n  5[\"metaQuantome: filter\"];\n  4 -->|outfile| 5;\n  1 -->|samples_file| 5;\n  6[\"metaQuantome: stat\"];\n  5 -->|outfile| 6;\n  1 -->|samples_file| 6;\n  7[\"T2-Bar-Plot\"];\n  6 -->|outfile| 7;\n  6 -->|outfile| 7;\n  8[\"T4-Bar-Plot\"];\n  6 -->|outfile| 8;\n  1 -->|samples_file| 8;\n  9[\"T7-Bar-Plot\"];\n  6 -->|outfile| 9;\n  1 -->|samples_file| 9;\n  10[\"T7-T2-Volcano-Plot\"];\n  6 -->|outfile| 10;\n  1 -->|samples_file| 10;\n  11[\"T4-T2-Volcano-Plot\"];\n  6 -->|outfile| 11;\n  1 -->|samples_file| 11;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "metaquantome-function-worklow",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.2+galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 3,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "metaQuantome: database",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "outfile",
-                                "type": "tar"
+                                "description": "",
+                                "name": "Min Genes"
                             }
                         ],
+                        "label": "Min Genes",
+                        "name": "Input parameter",
+                        "outputs": [],
                         "position": {
-                            "bottom": 555.953125,
-                            "height": 101,
-                            "left": 380.078125,
-                            "right": 580.078125,
-                            "top": 454.953125,
+                            "bottom": 503.75,
+                            "height": 64.25,
+                            "left": 16,
+                            "right": 216,
+                            "top": 439.5,
                             "width": 200,
-                            "x": 380.078125,
-                            "y": 454.953125
+                            "x": 16,
+                            "y": 439.5
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.2+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "860429737408",
-                            "name": "metaquantome_db",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        "tool_id": null,
+                        "tool_state": "{\"default\": 100, \"parameter_type\": \"integer\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "c9a62328-f049-43b6-92fb-df5c42982573",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Min Cells"
+                            }
+                        ],
+                        "label": "Min Cells",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 578.75,
+                            "height": 64.25,
+                            "left": 17,
+                            "right": 217,
+                            "top": 514.5,
+                            "width": 200,
+                            "x": 17,
+                            "y": 514.5
                         },
-                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"databases\": [\"ncbi\", \"go\", \"ec\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
-                        "type": "tool",
-                        "uuid": "8d2913b3-9c27-4a7e-989b-3e99642caa7e",
-                        "workflow_outputs": [
+                        "tool_id": null,
+                        "tool_state": "{\"default\": 2, \"parameter_type\": \"integer\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "7bf5f0e1-b482-45c3-9bcb-10ca93e6b7dc",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "f0040af5-b737-40da-8965-4c1ff91aa3ed"
+                                "description": "",
+                                "name": "Max Features"
                             }
-                        ]
+                        ],
+                        "label": "Max Features",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 671.5,
+                            "height": 84,
+                            "left": 23,
+                            "right": 223,
+                            "top": 587.5,
+                            "width": 200,
+                            "x": 23,
+                            "y": 587.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"default\": 12000.0, \"parameter_type\": \"float\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "8902a917-75fb-49c6-9e5d-15f87bd91d46",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.2+galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 6,
                         "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Max Lib Size"
+                            }
+                        ],
+                        "label": "Max Lib Size",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 764.5,
+                            "height": 84,
+                            "left": 15,
+                            "right": 215,
+                            "top": 680.5,
+                            "width": 200,
+                            "x": 15,
+                            "y": 680.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"default\": 120000.0, \"parameter_type\": \"float\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "db068cdb-53c4-48a3-95c2-141fa83c271b",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nLeiden Resolution\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSHR CSV.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nWT CSV.gz\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nMin Genes\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nMin Cells\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Parameter\\nMax Features\"];\n  style 5 fill:#ded,stroke:#393,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Parameter\\nMax Lib Size\"];\n  style 6 fill:#ded,stroke:#393,stroke-width:4px;\n  7[\"Import Anndata and loom\"];\n  1 -->|output| 7;\n  8[\"Import Anndata and loom\"];\n  2 -->|output| 8;\n  9[\"Manipulate AnnData\"];\n  7 -->|anndata| 9;\n  8 -->|anndata| 9;\n  10[\"Rename Batches\"];\n  9 -->|anndata| 10;\n  680180f6-edfc-4f66-b265-7a63aaa22b39[\"Output\\nscRNA Concatenated Datasets\"];\n  10 --> 680180f6-edfc-4f66-b265-7a63aaa22b39;\n  style 680180f6-edfc-4f66-b265-7a63aaa22b39 stroke:#2c3143,stroke-width:4px;\n  11[\"QC metrics\"];\n  10 -->|anndata| 11;\n  12[\"Filter genes\"];\n  11 -->|anndata_out| 12;\n  3 -->|output| 12;\n  13[\"Plot Violin\"];\n  11 -->|anndata_out| 13;\n  14[\"Filter Cells\"];\n  12 -->|anndata_out| 14;\n  4 -->|output| 14;\n  15[\"Filter Max Features\"];\n  14 -->|anndata_out| 15;\n  5 -->|output| 15;\n  16[\"Filter Max Library Size\"];\n  15 -->|anndata| 16;\n  6 -->|output| 16;\n  17[\"Save RAW\"];\n  16 -->|anndata| 17;\n  18[\"Norm to 1e4\"];\n  17 -->|anndata| 18;\n  19[\"Log1p\"];\n  18 -->|anndata_out| 19;\n  20[\"Regress total counts\"];\n  19 -->|anndata_out| 20;\n  21[\"Scale\"];\n  20 -->|anndata_out| 21;\n  22[\"PCA\"];\n  21 -->|anndata_out| 22;\n  23[\"Neighborhod\"];\n  22 -->|anndata_out| 23;\n  24[\"UMAP\"];\n  23 -->|anndata_out| 24;\n  25[\"Leiden\"];\n  24 -->|anndata_out| 25;\n  0 -->|output| 25;\n  48cf0465-84ba-461a-bdb9-61625626de42[\"Output\\nscRNA with clusters Dataset\"];\n  25 --> 48cf0465-84ba-461a-bdb9-61625626de42;\n  style 48cf0465-84ba-461a-bdb9-61625626de42 stroke:#2c3143,stroke-width:4px;\n  26[\"Plot PCA batch\"];\n  24 -->|anndata_out| 26;\n  27[\"Plot UMAP batch\"];\n  24 -->|anndata_out| 27;\n  28[\"Plot UMAP leiden, batch\"];\n  25 -->|anndata_out| 28;\n  29[\"Rename Clusters\"];\n  25 -->|anndata_out| 29;\n  30[\"Complex DotPlot\"];\n  25 -->|anndata_out| 30;\n  31[\"Complex DotPlot with new labels\"];\n  29 -->|anndata| 31;\n  32[\"Plot UMAP with new labels\"];\n  29 -->|anndata| 32;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "scRNA Plant Analysis",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0",
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {
+                            "input": {
+                                "id": 9,
+                                "output_name": "anndata"
+                            }
+                        },
                         "inputs": [],
-                        "label": null,
-                        "name": "metaQuantome: create samples file",
+                        "label": "Rename Batches",
+                        "name": "Manipulate AnnData",
                         "outputs": [
                             {
-                                "name": "samples_file",
-                                "type": "tabular"
+                                "name": "anndata",
+                                "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "bottom": 742,
-                            "height": 141,
-                            "left": 386.09375,
-                            "right": 586.09375,
-                            "top": 601,
+                            "bottom": 354.3999938964844,
+                            "height": 136.39999389648438,
+                            "left": 955,
+                            "right": 1155,
+                            "top": 218,
                             "width": 200,
-                            "x": 386.09375,
-                            "y": 601
+                            "x": 955,
+                            "y": 218
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.2+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "40ca115438d2",
-                            "name": "metaquantome_sample",
-                            "owner": "galaxyp",
+                            "changeset_revision": "8db95f488f0f",
+                            "name": "anndata_manipulate",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"samps_args\": {\"samps_src\": \"build\", \"__current_case__\": 0, \"samps\": [{\"__index__\": 0, \"group_name\": \"T2\", \"col_names\": \"T2_A1,T2_B1\"}, {\"__index__\": 1, \"group_name\": \"T4\", \"col_names\": \"T4A_1,T4B_1\"}, {\"__index__\": 2, \"group_name\": \"T7\", \"col_names\": \"T7A_1,T7B_1\"}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"rename_categories\", \"__current_case__\": 3, \"key\": \"batch\", \"categories\": \"shr, wt\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.5+galaxy0",
                         "type": "tool",
-                        "uuid": "9f37b361-1999-45f1-bdff-91e40d1b7783",
+                        "uuid": "0a25ffc3-ac58-4c17-9f22-b4127952027a",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "samples_file",
-                                "uuid": "729e43a9-27eb-4ab8-b89d-af815d52defd"
+                                "label": "scRNA Concatenated Datasets",
+                                "output_name": "anndata",
+                                "uuid": "680180f6-edfc-4f66-b265-7a63aaa22b39"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.2+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "errors": null,
-                        "id": 4,
+                        "id": 13,
                         "input_connections": {
-                            "db_tar": {
-                                "id": 0,
-                                "output_name": "outfile"
-                            },
-                            "int_file": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "mode_args|func_file": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "samps": {
-                                "id": 1,
-                                "output_name": "samples_file"
+                            "adata": {
+                                "id": 11,
+                                "output_name": "anndata_out"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "metaQuantome: expand",
+                        "label": "Plot Violin",
+                        "name": "Plot",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "tabular"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": 552.96875,
-                            "height": 242,
-                            "left": 713.109375,
-                            "right": 913.109375,
-                            "top": 310.96875,
+                            "bottom": 259.8000030517578,
+                            "height": 116.65000915527344,
+                            "left": 1867.2833251953125,
+                            "right": 2067.2833251953125,
+                            "top": 143.14999389648438,
                             "width": 200,
-                            "x": 713.109375,
-                            "y": 310.96875
+                            "x": 1867.2833251953125,
+                            "y": 143.14999389648438
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.2+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "4187b6df1a40",
-                            "name": "metaquantome_expand",
-                            "owner": "galaxyp",
+                            "changeset_revision": "6adf98e782f3",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"db_tar\": {\"__class__\": \"ConnectedValue\"}, \"int_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"f\", \"__current_case__\": 0, \"func_file\": {\"__class__\": \"ConnectedValue\"}, \"pep_colname_func\": \"peptide\", \"ontology_args\": {\"ontology\": \"go\", \"__current_case__\": 0, \"slim_down\": \"false\"}, \"func_colname\": \"go_term\"}, \"pep_colname_int\": \"peptide\", \"samps\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"n_genes_by_counts, total_counts\"}, \"groupby\": \"batch\", \"log\": \"false\", \"use_raw\": \"false\", \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"0.4\"}}, \"multi_panel\": {\"multi_panel\": \"True\", \"__current_case__\": 0, \"width\": null, \"height\": null}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy0",
                         "type": "tool",
-                        "uuid": "6ba916f3-e8d2-4efb-bee8-d190d4497e99",
+                        "uuid": "9dfc1e59-71aa-40b8-b504-2498a8dc5409",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "a695a223-52de-4b99-a457-fc002123d7f4"
+                                "output_name": "out_png",
+                                "uuid": "2fb1d919-0e60-4c81-92d2-83c28b1ef654"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.2+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
                         "errors": null,
-                        "id": 5,
+                        "id": 25,
                         "input_connections": {
-                            "expand_file": {
-                                "id": 4,
-                                "output_name": "outfile"
+                            "adata": {
+                                "id": 24,
+                                "output_name": "anndata_out"
                             },
-                            "samps": {
-                                "id": 1,
-                                "output_name": "samples_file"
+                            "method|resolution": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "metaQuantome: filter",
+                        "label": "Leiden",
+                        "name": "Cluster, infer trajectories and embed",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "tabular"
+                                "name": "anndata_out",
+                                "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "bottom": 986.984375,
-                            "height": 182,
-                            "left": 712.109375,
-                            "right": 912.109375,
-                            "top": 804.984375,
+                            "bottom": 562.0500030517578,
+                            "height": 147.0500030517578,
+                            "left": 1389,
+                            "right": 1589,
+                            "top": 415,
                             "width": 200,
-                            "x": 712.109375,
-                            "y": 804.984375
+                            "x": 1389,
+                            "y": 415
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.2+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "a1daafbf5233",
-                            "name": "metaquantome_filter",
-                            "owner": "galaxyp",
+                            "changeset_revision": "35bc2eb568ed",
+                            "name": "scanpy_cluster_reduce_dimension",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"expand_file\": {\"__class__\": \"ConnectedValue\"}, \"min_child_nsamp\": \"1\", \"min_children_non_leaf\": \"2\", \"min_pep_nsamp\": \"1\", \"min_peptides\": \"1\", \"mode_args\": {\"mode\": \"f\", \"__current_case__\": 0, \"ontology_args\": {\"ontology\": \"go\", \"__current_case__\": 0, \"slim_down\": \"false\"}}, \"qthreshold\": \"2\", \"samps\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"method\": {\"method\": \"tl.leiden\", \"__current_case__\": 1, \"resolution\": {\"__class__\": \"ConnectedValue\"}, \"random_state\": \"0\", \"key_added\": \"leiden\", \"use_weights\": \"false\", \"n_iterations\": \"-1\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy0",
                         "type": "tool",
-                        "uuid": "4d85cd84-63b6-4822-a1c1-b4555317fc92",
+                        "uuid": "99494ea7-377c-4f3d-a45a-18bfd81b7888",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "1fcbebef-7f9d-4c46-90e4-ecce3dc87c3c"
+                                "label": "scRNA with clusters Dataset",
+                                "output_name": "anndata_out",
+                                "uuid": "48cf0465-84ba-461a-bdb9-61625626de42"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.2+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "errors": null,
-                        "id": 6,
+                        "id": 26,
                         "input_connections": {
-                            "file": {
-                                "id": 5,
-                                "output_name": "outfile"
-                            },
-                            "samps": {
-                                "id": 1,
-                                "output_name": "samples_file"
+                            "adata": {
+                                "id": 24,
+                                "output_name": "anndata_out"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "metaQuantome: stat",
+                        "label": "Plot PCA (batch)",
+                        "name": "Plot",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "tabular"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": 683,
-                            "height": 202,
-                            "left": 1001.109375,
-                            "right": 1201.109375,
-                            "top": 481,
+                            "bottom": 277.5500030517578,
+                            "height": 136.40000915527344,
+                            "left": 1629.433349609375,
+                            "right": 1829.433349609375,
+                            "top": 141.14999389648438,
                             "width": 200,
-                            "x": 1001.109375,
-                            "y": 481
+                            "x": 1629.433349609375,
+                            "y": 141.14999389648438
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.2+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "b648e45fd3cf",
-                            "name": "metaquantome_stat",
-                            "owner": "galaxyp",
+                            "changeset_revision": "6adf98e782f3",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"control_group\": \"T2\", \"file\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"f\", \"__current_case__\": 0, \"ontology_args\": {\"ontology\": \"go\", \"__current_case__\": 0, \"slim_down\": \"false\"}}, \"paired\": \"true\", \"parametric\": \"True\", \"samps\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.pca\", \"__current_case__\": 9, \"color\": \"batch\", \"use_raw\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy0",
                         "type": "tool",
-                        "uuid": "53c9d15f-ef26-4bed-a07c-e5aae09c6ec2",
+                        "uuid": "e2daa4c6-9a39-4c42-852e-4f61b65202c2",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "114546bc-4c2f-484d-9f4f-e6af605f30a4"
+                                "output_name": "out_png",
+                                "uuid": "72d1a264-3ace-4d2e-910a-5e2a0fa6721f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "errors": null,
-                        "id": 7,
+                        "id": 27,
                         "input_connections": {
-                            "infile": {
-                                "id": 6,
-                                "output_name": "outfile"
-                            },
-                            "samps": {
-                                "id": 6,
-                                "output_name": "outfile"
+                            "adata": {
+                                "id": 24,
+                                "output_name": "anndata_out"
                             }
                         },
                         "inputs": [],
-                        "label": "T2-Bar-Plot",
-                        "name": "metaQuantome: visualize",
+                        "label": "Plot UMAP (batch)",
+                        "name": "Plot",
                         "outputs": [
                             {
-                                "name": "wrapped_outfile",
-                                "type": "html"
-                            },
-                            {
-                                "name": "plotdata",
-                                "type": "tabular"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": 683,
-                            "height": 292,
-                            "left": 1344.078125,
-                            "right": 1544.078125,
-                            "top": 391,
+                            "bottom": 406.3999938964844,
+                            "height": 136.39999389648438,
+                            "left": 1862,
+                            "right": 2062,
+                            "top": 270,
                             "width": 200,
-                            "x": 1344.078125,
-                            "y": 391
+                            "x": 1862,
+                            "y": 270
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "eb811f3018ea",
-                            "name": "metaquantome_viz",
-                            "owner": "galaxyp",
+                            "changeset_revision": "6adf98e782f3",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"f\", \"__current_case__\": 0, \"ontology\": \"go\", \"plot\": {\"plottype\": \"bar\", \"__current_case__\": 0, \"meancol\": \"T2_mean\", \"nterms\": \"5\", \"target_onto\": \"mf\", \"barcol\": \"2\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"batch\", \"use_raw\": \"false\", \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": \"14\", \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy0",
                         "type": "tool",
-                        "uuid": "22e19420-d346-4080-a941-d7f6eeb34bf1",
+                        "uuid": "e70d8e14-1983-4381-8feb-bba7d5dbb4d6",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "plotdata",
-                                "uuid": "f5f8721f-3fee-4164-b155-565ecba9c15f"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "wrapped_outfile",
-                                "uuid": "3a1f5a00-68cd-4b78-a231-377f15278758"
+                                "output_name": "out_png",
+                                "uuid": "c223e762-7e90-41e1-b354-bbe6e278b5c0"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "errors": null,
-                        "id": 8,
+                        "id": 28,
                         "input_connections": {
-                            "infile": {
-                                "id": 6,
-                                "output_name": "outfile"
-                            },
-                            "samps": {
-                                "id": 1,
-                                "output_name": "samples_file"
+                            "adata": {
+                                "id": 25,
+                                "output_name": "anndata_out"
                             }
                         },
                         "inputs": [],
-                        "label": "T4-Bar-Plot",
-                        "name": "metaQuantome: visualize",
+                        "label": "Plot UMAP (leiden, batch)",
+                        "name": "Plot",
                         "outputs": [
                             {
-                                "name": "wrapped_outfile",
-                                "type": "html"
-                            },
-                            {
-                                "name": "plotdata",
-                                "type": "tabular"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": 985.578125,
-                            "height": 292,
-                            "left": 1358.5625,
-                            "right": 1558.5625,
-                            "top": 693.578125,
+                            "bottom": 442.5500030517578,
+                            "height": 136.40000915527344,
+                            "left": 1630.433349609375,
+                            "right": 1830.433349609375,
+                            "top": 306.1499938964844,
                             "width": 200,
-                            "x": 1358.5625,
-                            "y": 693.578125
+                            "x": 1630.433349609375,
+                            "y": 306.1499938964844
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "eb811f3018ea",
-                            "name": "metaquantome_viz",
-                            "owner": "galaxyp",
+                            "changeset_revision": "6adf98e782f3",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"f\", \"__current_case__\": 0, \"ontology\": \"go\", \"plot\": {\"plottype\": \"bar\", \"__current_case__\": 0, \"meancol\": \"T4_mean\", \"nterms\": \"5\", \"target_onto\": \"mf\", \"barcol\": \"2\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"leiden, batch\", \"use_raw\": \"false\", \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": \"14\", \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy0",
                         "type": "tool",
-                        "uuid": "be87379d-46ef-458e-941d-6b74d95056b2",
+                        "uuid": "b88358ff-0dda-4c2e-bce6-124a0ab8fa28",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "plotdata",
-                                "uuid": "3690aff1-2671-4667-8b30-82e69cd93ae4"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "wrapped_outfile",
-                                "uuid": "46b92417-58a7-47f1-b144-21b4ec612962"
+                                "output_name": "out_png",
+                                "uuid": "26c65cd9-74aa-4574-a5f3-ac10caced4da"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "errors": null,
-                        "id": 9,
+                        "id": 30,
                         "input_connections": {
-                            "infile": {
-                                "id": 6,
-                                "output_name": "outfile"
-                            },
-                            "samps": {
-                                "id": 1,
-                                "output_name": "samples_file"
+                            "adata": {
+                                "id": 25,
+                                "output_name": "anndata_out"
                             }
                         },
                         "inputs": [],
-                        "label": "T7-Bar-Plot",
-                        "name": "metaQuantome: visualize",
+                        "label": "Complex DotPlot",
+                        "name": "Plot",
                         "outputs": [
                             {
-                                "name": "wrapped_outfile",
-                                "type": "html"
-                            },
-                            {
-                                "name": "plotdata",
-                                "type": "tabular"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": 1273.5625,
-                            "height": 292,
-                            "left": 1358.484375,
-                            "right": 1558.484375,
-                            "top": 981.5625,
+                            "bottom": 557.3999938964844,
+                            "height": 136.39999389648438,
+                            "left": 1861,
+                            "right": 2061,
+                            "top": 421,
                             "width": 200,
-                            "x": 1358.484375,
-                            "y": 981.5625
+                            "x": 1861,
+                            "y": 421
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "eb811f3018ea",
-                            "name": "metaquantome_viz",
-                            "owner": "galaxyp",
+                            "changeset_revision": "6adf98e782f3",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"f\", \"__current_case__\": 0, \"ontology\": \"go\", \"plot\": {\"plottype\": \"bar\", \"__current_case__\": 0, \"meancol\": \"T7_mean\", \"nterms\": \"5\", \"target_onto\": \"mf\", \"barcol\": \"2\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.dotplot\", \"__current_case__\": 2, \"var_names\": {\"type\": \"custom\", \"__current_case__\": 1, \"var_names\": \"AT1G26680,COBL2,AT3G55180,NCED2,AT5G22550,ATL63,RGF8,TEL1,DUF9,AGL42,PLT1,PLT2,PER3,PER9,PBL15,TBL30,AT2G48130,AT3G22620,AED3,T3P18-7,MBK21-8,NPF6-4,CYP71B34,IAMT1,AT1G31950,F14G6-22,GL2,ANL2,PMEI4,MUD21-4,EXPA7,MES15,ADF8,COBL9,TPR14,BHLH144,MYB83,SCPL35,MYB46,COBL4,PIN7,PIN3   \"}, \"groupby\": \"leiden\", \"num_categories\": \"9\", \"log\": \"false\", \"use_raw\": \"true\", \"dendrogram\": \"false\", \"var_group_positions\": [{\"__index__\": 0, \"start\": \"0\", \"end\": \"5\", \"label\": \"Columella\"}, {\"__index__\": 1, \"start\": \"6\", \"end\": \"9\", \"label\": \"QC\"}, {\"__index__\": 2, \"start\": \"10\", \"end\": \"11\", \"label\": \"NC\"}, {\"__index__\": 3, \"start\": \"12\", \"end\": \"17\", \"label\": \"Endodermis\"}, {\"__index__\": 4, \"start\": \"18\", \"end\": \"23\", \"label\": \"Cortex\"}, {\"__index__\": 5, \"start\": \"24\", \"end\": \"29\", \"label\": \"Atrichoblast\"}, {\"__index__\": 6, \"start\": \"30\", \"end\": \"34\", \"label\": \"Trichoblast\"}, {\"__index__\": 7, \"start\": \"35\", \"end\": \"39\", \"label\": \"Xylem\"}, {\"__index__\": 8, \"start\": \"40\", \"end\": \"41\", \"label\": \"VC\"}], \"var_group_rotation\": null, \"figsize\": {\"test\": \"no\", \"__current_case__\": 1}, \"layer\": \"\", \"color_map\": \"viridis\", \"dot_max\": null, \"dot_min\": null, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy0",
                         "type": "tool",
-                        "uuid": "d9b6f1d7-671d-4d7a-915f-2cb12a2e1d7f",
+                        "uuid": "625a157f-f08f-4137-a27b-721bee0feb59",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "plotdata",
-                                "uuid": "48d40170-76bb-4b9e-a014-9b7f16d4212b"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "wrapped_outfile",
-                                "uuid": "51f1a1c6-960d-4f74-9cce-bf7d03f57297"
+                                "output_name": "out_png",
+                                "uuid": "b35ffb5a-5f29-4105-a016-c02ceee0d9da"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "errors": null,
-                        "id": 10,
+                        "id": 31,
                         "input_connections": {
-                            "infile": {
-                                "id": 6,
-                                "output_name": "outfile"
-                            },
-                            "samps": {
-                                "id": 1,
-                                "output_name": "samples_file"
+                            "adata": {
+                                "id": 29,
+                                "output_name": "anndata"
                             }
                         },
                         "inputs": [],
-                        "label": "T7-T2-Volcano-Plot",
-                        "name": "metaQuantome: visualize",
+                        "label": "Complex DotPlot with new labels",
+                        "name": "Plot",
                         "outputs": [
                             {
-                                "name": "wrapped_outfile",
-                                "type": "html"
-                            },
-                            {
-                                "name": "plotdata",
-                                "type": "tabular"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": 783.9375,
-                            "height": 332,
-                            "left": 1647.078125,
-                            "right": 1847.078125,
-                            "top": 451.9375,
+                            "bottom": 733.4666748046875,
+                            "height": 156.79998779296875,
+                            "left": 1860.449951171875,
+                            "right": 2060.449951171875,
+                            "top": 576.6666870117188,
                             "width": 200,
-                            "x": 1647.078125,
-                            "y": 451.9375
+                            "x": 1860.449951171875,
+                            "y": 576.6666870117188
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "eb811f3018ea",
-                            "name": "metaquantome_viz",
-                            "owner": "galaxyp",
+                            "changeset_revision": "6adf98e782f3",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"f\", \"__current_case__\": 0, \"ontology\": \"go\", \"plot\": {\"plottype\": \"volcano\", \"__current_case__\": 1, \"fc_name\": \"log2fc_T7_over_T2\", \"fc_corr_p\": \"corrected_p_T7_over_T2\", \"textannot\": \"id\", \"flip_fc\": \"false\", \"gosplit\": \"true\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.dotplot\", \"__current_case__\": 2, \"var_names\": {\"type\": \"custom\", \"__current_case__\": 1, \"var_names\": \"AT1G26680,COBL2,AT3G55180,NCED2,AT5G22550,ATL63,RGF8,TEL1,DUF9,AGL42,PLT1,PLT2,PER3,PER9,PBL15,TBL30,AT2G48130,AT3G22620,AED3,T3P18-7,MBK21-8,NPF6-4,CYP71B34,IAMT1,AT1G31950,F14G6-22,GL2,ANL2,PMEI4,MUD21-4,EXPA7,MES15,ADF8,COBL9,TPR14,BHLH144,MYB83,SCPL35,MYB46,COBL4,PIN7,PIN3   \"}, \"groupby\": \"leiden\", \"num_categories\": \"9\", \"log\": \"false\", \"use_raw\": \"true\", \"dendrogram\": \"false\", \"var_group_positions\": [{\"__index__\": 0, \"start\": \"0\", \"end\": \"5\", \"label\": \"Columella\"}, {\"__index__\": 1, \"start\": \"6\", \"end\": \"9\", \"label\": \"QC\"}, {\"__index__\": 2, \"start\": \"10\", \"end\": \"11\", \"label\": \"NC\"}, {\"__index__\": 3, \"start\": \"12\", \"end\": \"17\", \"label\": \"Endodermis\"}, {\"__index__\": 4, \"start\": \"18\", \"end\": \"23\", \"label\": \"Cortex\"}, {\"__index__\": 5, \"start\": \"24\", \"end\": \"29\", \"label\": \"Atrichoblast\"}, {\"__index__\": 6, \"start\": \"30\", \"end\": \"34\", \"label\": \"Trichoblast\"}, {\"__index__\": 7, \"start\": \"35\", \"end\": \"39\", \"label\": \"Xylem\"}, {\"__index__\": 8, \"start\": \"40\", \"end\": \"41\", \"label\": \"VC\"}], \"var_group_rotation\": null, \"figsize\": {\"test\": \"no\", \"__current_case__\": 1}, \"layer\": \"\", \"color_map\": \"viridis\", \"dot_max\": null, \"dot_min\": null, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy0",
                         "type": "tool",
-                        "uuid": "19539885-0990-4eda-8f07-deb39f11343f",
+                        "uuid": "a2f04375-1e67-4764-ae78-2678dcf2c03a",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "plotdata",
-                                "uuid": "f78ca1ea-8601-49a4-b816-7c1b9f97b06a"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "wrapped_outfile",
-                                "uuid": "48985efc-d6ef-4560-bc06-be28aec7e6d8"
+                                "output_name": "out_png",
+                                "uuid": "329e95de-cf53-4c0b-9a9b-ad30632ceeb8"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "errors": null,
-                        "id": 11,
+                        "id": 32,
                         "input_connections": {
-                            "infile": {
-                                "id": 6,
-                                "output_name": "outfile"
-                            },
-                            "samps": {
-                                "id": 1,
-                                "output_name": "samples_file"
+                            "adata": {
+                                "id": 29,
+                                "output_name": "anndata"
                             }
                         },
                         "inputs": [],
-                        "label": "T4-T2-Volcano-Plot",
-                        "name": "metaQuantome: visualize",
-                        "outputs": [
-                            {
-                                "name": "wrapped_outfile",
-                                "type": "html"
-                            },
+                        "label": "Plot UMAP with new labels",
+                        "name": "Plot",
+                        "outputs": [
                             {
-                                "name": "plotdata",
-                                "type": "tabular"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": 1148.53125,
-                            "height": 332,
-                            "left": 1644.46875,
-                            "right": 1844.46875,
-                            "top": 816.53125,
+                            "bottom": 885.3999938964844,
+                            "height": 136.39999389648438,
+                            "left": 1863,
+                            "right": 2063,
+                            "top": 749,
                             "width": 200,
-                            "x": 1644.46875,
-                            "y": 816.53125
+                            "x": 1863,
+                            "y": 749
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "eb811f3018ea",
-                            "name": "metaquantome_viz",
-                            "owner": "galaxyp",
+                            "changeset_revision": "6adf98e782f3",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"f\", \"__current_case__\": 0, \"ontology\": \"go\", \"plot\": {\"plottype\": \"volcano\", \"__current_case__\": 1, \"fc_name\": \"log2fc_T4_over_T2\", \"fc_corr_p\": \"corrected_p_T4_over_T2\", \"textannot\": \"id\", \"flip_fc\": \"false\", \"gosplit\": \"true\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"leiden, batch\", \"use_raw\": \"false\", \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"on data\", \"legend_fontsize\": \"14\", \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy0",
                         "type": "tool",
-                        "uuid": "80ea05c8-f9c1-46f1-a0d0-a66c494d22fd",
+                        "uuid": "c83c81b0-cd9e-41c5-8b72-4b024b7260dc",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "plotdata",
-                                "uuid": "2fbd499f-b9e7-403e-bbc9-e13670cacd52"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "wrapped_outfile",
-                                "uuid": "4be072a7-8373-4d49-a71a-ffdc1ac318de"
+                                "output_name": "out_png",
+                                "uuid": "579d19d3-a98c-4e3a-92aa-0b65e2ffcefd"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/metaquantome-function",
-                "path": "topics/proteomics/tutorials/metaquantome-function/workflows/main_workflow.ga",
+                "parent_id": "single-cell/scrna-plant",
+                "path": "topics/single-cell/tutorials/scrna-plant/workflows/main_workflow.ga",
                 "tags": [
-                    "proteomics"
+                    "transcriptomics",
+                    "single-cell"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "metaquantome-function-worklow",
-                "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-metaquantome-function/versions/main-workflow",
-                "tutorial_id": "metaquantome-function",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaquantome-function/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaquantome-function/workflows/main_workflow.html",
-                "version": 2,
-                "wfid": "proteomics-metaquantome-function",
+                "title": "scRNA Plant Analysis",
+                "topic_id": "single-cell",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-plant/versions/main-workflow",
+                "tutorial_id": "scrna-plant",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-plant/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-plant/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "single-cell-scrna-plant",
                 "wfname": "main-workflow",
                 "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0"
                 ],
-                "workflowhub_id": "1221"
+                "workflowhub_id": "1266"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.4110725"
+        "zenodo_link": "https://zenodo.org/record/4597857"
     },
     {
         "admin_install": {
@@ -178820,204 +179767,163 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "dbbuilder",
-                    "owner": "galaxyp",
-                    "revisions": "983bf725dfc2",
-                    "tool_panel_section_label": "Get Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_merge_files_and_filter_unique_sequences",
-                    "owner": "galaxyp",
-                    "revisions": "f546e7278f04",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "histogram",
+                    "owner": "devteam",
+                    "revisions": "6f134426c2b0",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "metanovo",
+                    "name": "msstats",
                     "owner": "galaxyp",
-                    "revisions": "d6dcd3173bdf",
+                    "revisions": "52ac6fde9a5b",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "uniprotxml_downloader",
-                    "owner": "galaxyp",
-                    "revisions": "265c35540faa",
-                    "tool_panel_section_label": "Get Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: dbbuilder\n  owner: galaxyp\n  revisions: 983bf725dfc2\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_merge_files_and_filter_unique_sequences\n  owner: galaxyp\n  revisions: f546e7278f04\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metanovo\n  owner: galaxyp\n  revisions: d6dcd3173bdf\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: uniprotxml_downloader\n  owner: galaxyp\n  revisions: 265c35540faa\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "subinamehta",
-                "katherine-d21",
-                "dechendb"
-            ],
-            "editing": [
-                "pratikdjagtap",
-                "timothygriffin"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: histogram\n  owner: devteam\n  revisions: 6f134426c2b0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msstats\n  owner: galaxyp\n  revisions: 52ac6fde9a5b\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.json",
         "contributors": [
             {
-                "email": "subinamehta@gmail.com",
-                "id": "subinamehta",
-                "joined": "2018-06",
-                "linkedin": "subinamehta",
-                "matrix": "subinamehta:matrix.org",
-                "name": "Subina Mehta",
-                "orcid": "0000-0001-9818-0537",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
-                "twitter": "Subina_Mehta",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
-            },
-            {
-                "id": "katherine-d21",
-                "joined": "2023-08",
-                "name": "Katherine Do",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/katherine-d21/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/katherine-d21.json"
-            },
-            {
-                "id": "dechendb",
-                "joined": "2023-06",
-                "name": "Dechen Bhuming",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dechendb/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/dechendb.json"
-            },
-            {
-                "email": "pjagtap@umn.edu",
-                "id": "pratikdjagtap",
-                "joined": "2017-09",
-                "name": "Pratik Jagtap",
-                "orcid": "0000-0003-0984-0973",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "email": "matthias.fahrner@uniklinik-freiburg.de",
+                "id": "matthias313",
+                "joined": "2019-03",
+                "name": "Matthias Fahrner",
+                "orcid": "0000-0001-7955-2518",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/matthias313/",
+                "twitter": "mfahrner313",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/matthias313.json"
             },
             {
-                "email": "tgriffin@umn.edu",
-                "github": false,
-                "id": "timothygriffin",
-                "joined": "2017-09",
-                "name": "Timothy J. Griffin",
-                "orcid": "0000-0001-6801-2559",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "email": "melanie.foell@mol-med.uni-freiburg.de",
+                "id": "foellmelanie",
+                "joined": "2018-10",
+                "matrix": "foellmelanie:matrix.org",
+                "name": "Melanie F\u00f6ll",
+                "orcid": "0000-0002-1887-7543",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
+                "twitter": "MCFoell",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/clinical-mp-1-database-generation",
+        "dir": "topics/proteomics/tutorials/DIA_Analysis_MSstats",
         "edam_operation": [
-            "Expression analysis",
-            "Tag-based peptide identification",
-            "Target-Decoy",
-            "Protein identification",
-            "de Novo sequencing"
+            "Differential protein expression profiling",
+            "Spectrum calculation",
+            "Tag-based peptide identification"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu"
+            "UseGalaxy.be",
+            "UseGalaxy.eu",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "proteomics",
-                "tutorials": [
-                    "clinical-mp-2-discovery"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "proteomics/clinical-mp-1-database-generation",
-        "inexact_supported_servers": [],
+        "id": "proteomics/DIA_Analysis_MSstats",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.org.au"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Create a customized proteomics database from 16SrRNA results."
+            "Statistical analyses are crucial for meaningful conclusion in proteomic studies",
+            "MSstats enables statistical analysis of data independent acquisition mass spectrometry data"
         ],
         "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-08",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Downloading databases related to 16SrRNA data",
-            "For better identification results, combine host and microbial proteins.",
-            "Reduced database provides better FDR stats."
+            "Statistical analysis of a HEK-Ecoli Benchmark DIA dataset",
+            "Understanding statistical approaches in proteomic analysis",
+            "Using MSstats to find significantly dysregulated proteins in a Spike-in dataset"
         ],
-        "pageviews": 301,
-        "pub_date": "2024-02-06",
+        "pageviews": 1383,
+        "pub_date": "2020-12-02",
         "questions": [
-            "Why do we need to generate a customized database for metaproteomics research?",
-            "How do we reduce the size of the database?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "katherine-d21"
-                ],
-                "date": "2024-06-21",
-                "galaxy_version": "23.1",
-                "length": "15M",
-                "speakers": [
-                    "katherine-d21"
-                ],
-                "youtube_id": "FEAEyqcjxkE"
-            }
-        ],
-        "redirect_from": [
-            "/topics/proteomics/tutorials/clinical-mp-database-generation/tutorial",
-            "/short/proteomics/clinical-mp-1-database-generation",
-            "/short/T00413"
+            "How to perform statistical analysis on DIA mass spectrometry data?",
+            "How to detect and quantify differentially abundant proteins in a HEK-Ecoli Benchmark DIA datatset?"
         ],
         "requirements": [
             {
                 "topic_name": "proteomics",
+                "tutorials": [
+                    "DIA_lib_OSW",
+                    "DIA_Analysis_OSW"
+                ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00413",
+        "short_id": "T00210",
         "short_tools": [
-            "uniprotxml_downloader",
-            "dbbuilder",
-            "fasta_merge_files_and_filter_unique_sequences",
-            "metanovo"
+            "Filter1",
+            "Grep1",
+            "histogram_rpy",
+            "msstats"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "clinical-metaproteomics",
+        "subtopic": "post-process",
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 }
             ],
-            "inexact": []
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
         },
         "symlink": null,
         "tags": [
-            "label-TMT11"
+            "DIA"
         ],
-        "time_estimation": "3H",
-        "title": "Clinical Metaproteiomics 1: Database-Generation",
+        "time_estimation": "1H",
+        "title": "Statistical analysis of DIA data",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/metanovo/metanovo/1.9.4+galaxy4",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.3.0"
+            "Filter1",
+            "Grep1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0"
         ],
         "topic_name": "proteomics",
         "topic_name_human": "Proteomics",
@@ -179027,43 +179933,51 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "clinical-mp-1-database-generation",
+        "tutorial_name": "DIA_Analysis_MSstats",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/DIA_Analysis_MSstats/tutorial.json"
         },
-        "version": 2,
+        "version": 9,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 237,
-        "visitors": 171,
+        "visit_duration": 103,
+        "visitors": 1022,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Organization",
-                        "identifier": "0000-0001-9818-0537",
-                        "name": "Subina Mehta"
-                    }
-                ],
-                "description": "Generating a large database and then reducing it to a compact database using Metanovo",
+                "creators": [],
+                "description": "DIA MSstats Training export tabular",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHUMAN SwissProt Protein Database\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput MGF files Dataset Collection\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSpecies_UniProt_FASTA\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nContaminants cRAP Protein Database \"]\n  4[label=\"Human UniProt Microbial Proteins cRAP for MetaNovo\"]\n  0 -> 4 [label=\"output\"]\n  2 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  k286f5bd4fb0d46498dacf191acc72722[color=lightseagreen,label=\"Output\\nHuman UniProt Microbial Proteins cRAP for MetaNovo\"]\n  4 -> k286f5bd4fb0d46498dacf191acc72722\n  5[label=\"MetaNovo\"]\n  4 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"FASTA Merge Files and Filter Unique Sequences\"]\n  0 -> 6 [label=\"output\"]\n  5 -> 6 [label=\"output_fasta\"]\n  3 -> 6 [label=\"output\"]\n  kde57cd9dac0543979d44e65620913447[color=lightseagreen,label=\"Output\\nHuman UniProt Microbial Proteins (from MetaNovo) and cRAP \"]\n  6 -> kde57cd9dac0543979d44e65620913447\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPyProphet export tabular\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nComparison matrix\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSample annot MSstats\"]\n  3[label=\"MSstats\"]\n  1 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Select\"]\n  3 -> 4 [label=\"comparison_result\"]\n  k0de65b2cf62c40688ac0466e419d495b[color=lightseagreen,label=\"Output\\nSelect_Ecoli\"]\n  4 -> k0de65b2cf62c40688ac0466e419d495b\n  5[label=\"Filter\"]\n  4 -> 5 [label=\"out_file1\"]\n  k197e8a45392f498186842c8326af4528[color=lightseagreen,label=\"Output\\nFilter_Ecoli\"]\n  5 -> k197e8a45392f498186842c8326af4528\n  6[label=\"Histogram\"]\n  5 -> 6 [label=\"out_file1\"]\n  k04c6287dfd0d478099b6cf52ee18e06f[color=lightseagreen,label=\"Output\\nHistogram_Ecoli\"]\n  6 -> k04c6287dfd0d478099b6cf52ee18e06f\n}",
                 "history": [
                     {
-                        "hash": "9a94b97ceccea577f680e7b454b6b8b7995801de",
-                        "message": "add workflow",
+                        "hash": "bef209fa8b13cca27b8deae81ff1675433201d9f",
+                        "message": "Add workflow tests to DIA_MSstats_Training tutorial",
+                        "num": 3,
+                        "short_hash": "bef209fa8",
+                        "unix": "1642736930"
+                    },
+                    {
+                        "hash": "15a13c3667af0db6a6ca380ca1b998c9faf625d3",
+                        "message": "updated workflow annotation and name",
+                        "num": 2,
+                        "short_hash": "15a13c366",
+                        "unix": "1606931443"
+                    },
+                    {
+                        "hash": "e8f20c190bc7a0d319835969a36114d939bd4dce",
+                        "message": "generated three tutorials on DIA data analysis in galaxy",
                         "num": 1,
-                        "short_hash": "9a94b97ce",
-                        "unix": "1723116168"
+                        "short_hash": "e8f20c190",
+                        "unix": "1606930318"
                     }
                 ],
                 "inputs": [
@@ -179076,23 +179990,34 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "HUMAN SwissProt Protein Database"
+                                "name": "PyProphet export tabular"
                             }
                         ],
-                        "label": "HUMAN SwissProt Protein Database",
+                        "label": "PyProphet export tabular",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 204.86580898284382
+                            "bottom": 298.94485783397704,
+                            "height": 109.33332824707031,
+                            "left": 94.64912127731438,
+                            "right": 360.6491212773144,
+                            "top": 189.6115295869067,
+                            "width": 266,
+                            "x": 94.64912127731438,
+                            "y": 189.6115295869067
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "bb037df4-ef56-42ad-8b3e-93425bc7bdfa",
-                        "when": null,
-                        "workflow_outputs": []
+                        "uuid": "ccdce674-490b-493c-a03b-786c9e9ec472",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "771735fa-1a49-429d-b602-b5cd4b90a78b"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
@@ -179103,23 +180028,34 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Input MGF files (Dataset Collection)"
+                                "name": "Comparison matrix"
                             }
                         ],
-                        "label": "Input MGF files (Dataset Collection)",
-                        "name": "Input dataset collection",
+                        "label": "Comparison matrix",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 260.9789733886719,
-                            "top": 0
+                            "bottom": 400.3483566628363,
+                            "height": 109.33332824707031,
+                            "left": 97.53132296684093,
+                            "right": 363.53132296684095,
+                            "top": 291.015028415766,
+                            "width": 266,
+                            "x": 97.53132296684093,
+                            "y": 291.015028415766
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "d6bb6e3e-ebf6-4c65-bcf7-ea9527cf8653",
-                        "when": null,
-                        "workflow_outputs": []
+                        "type": "data_input",
+                        "uuid": "9773176c-aeef-4430-9c9d-5c276bfd13bb",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "dcc7e278-b396-463e-9275-b669bb71ae30"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
@@ -179130,562 +180066,482 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Species_UniProt_FASTA"
+                                "name": "Sample annot MSstats"
                             }
                         ],
-                        "label": "Species_UniProt_FASTA",
+                        "label": "Sample annot MSstats",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 2.443389892578125,
-                            "top": 369.4779610824532
+                            "bottom": 501.86464433024696,
+                            "height": 109.33332824707031,
+                            "left": 98.42104804246945,
+                            "right": 364.42104804246947,
+                            "top": 392.53131608317665,
+                            "width": 266,
+                            "x": 98.42104804246945,
+                            "y": 392.53131608317665
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "b4b90dcd-9228-4aad-b51d-2f08b2d4cc0d",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
+                        "uuid": "b0cf95a5-fca3-45ea-88df-37b06948099c",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "489e9abe-be00-44c1-89e8-643eaecb75dd"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPyProphet export tabular\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nComparison matrix\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nSample annot MSstats\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"MSstats\"];\n  1 -->|output| 3;\n  2 -->|output| 3;\n  0 -->|output| 3;\n  4[\"Select\"];\n  3 -->|comparison_result| 4;\n  0de65b2c-f62c-4068-8ac0-466e419d495b[\"Output\\nSelect_Ecoli\"];\n  4 --> 0de65b2c-f62c-4068-8ac0-466e419d495b;\n  style 0de65b2c-f62c-4068-8ac0-466e419d495b stroke:#2c3143,stroke-width:4px;\n  5[\"Filter\"];\n  4 -->|out_file1| 5;\n  197e8a45-392f-4981-8684-2c8326af4528[\"Output\\nFilter_Ecoli\"];\n  5 --> 197e8a45-392f-4981-8684-2c8326af4528;\n  style 197e8a45-392f-4981-8684-2c8326af4528 stroke:#2c3143,stroke-width:4px;\n  6[\"Histogram\"];\n  5 -->|out_file1| 6;\n  04c6287d-fd0d-4780-99b6-cf52ee18e06f[\"Output\\nHistogram_Ecoli\"];\n  6 --> 04c6287d-fd0d-4780-99b6-cf52ee18e06f;\n  style 04c6287d-fd0d-4780-99b6-cf52ee18e06f stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "DIA_analysis_MSstats",
+                "outputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Contaminants (cRAP) Protein Database "
+                                "name": "PyProphet export tabular"
                             }
                         ],
-                        "label": "Contaminants (cRAP) Protein Database ",
+                        "label": "PyProphet export tabular",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 14.413701296714208,
-                            "top": 468.23383463562413
+                            "bottom": 298.94485783397704,
+                            "height": 109.33332824707031,
+                            "left": 94.64912127731438,
+                            "right": 360.6491212773144,
+                            "top": 189.6115295869067,
+                            "width": 266,
+                            "x": 94.64912127731438,
+                            "y": 189.6115295869067
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ca7de659-6e60-4bd5-aa4c-a88f2860e8c9",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nHUMAN SwissProt Protein Database\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nInput MGF files Dataset Collection\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nSpecies_UniProt_FASTA\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nContaminants cRAP Protein Database \"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Human UniProt Microbial Proteins cRAP for MetaNovo\"];\n  0 -->|output| 4;\n  2 -->|output| 4;\n  3 -->|output| 4;\n  286f5bd4-fb0d-4649-8dac-f191acc72722[\"Output\\nHuman UniProt Microbial Proteins cRAP for MetaNovo\"];\n  4 --> 286f5bd4-fb0d-4649-8dac-f191acc72722;\n  style 286f5bd4-fb0d-4649-8dac-f191acc72722 stroke:#2c3143,stroke-width:4px;\n  5[\"MetaNovo\"];\n  4 -->|output| 5;\n  1 -->|output| 5;\n  6[\"FASTA Merge Files and Filter Unique Sequences\"];\n  0 -->|output| 6;\n  5 -->|output_fasta| 6;\n  3 -->|output| 6;\n  de57cd9d-ac05-4397-9d44-e65620913447[\"Output\\nHuman UniProt Microbial Proteins (from MetaNovo) and cRAP \"];\n  6 --> de57cd9d-ac05-4397-9d44-e65620913447;\n  style de57cd9d-ac05-4397-9d44-e65620913447 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "WF1_Database_Generation_Workflow",
-                "outputs": [
+                        "uuid": "ccdce674-490b-493c-a03b-786c9e9ec472",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "771735fa-1a49-429d-b602-b5cd4b90a78b"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "batchmode|input_fastas_0|input_fasta": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "batchmode|input_fastas_1|input_fasta": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "batchmode|input_fastas_2|input_fasta": {
-                                "id": 3,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Human UniProt Microbial Proteins cRAP for MetaNovo",
-                        "name": "FASTA Merge Files and Filter Unique Sequences",
-                        "outputs": [
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "Comparison matrix"
                             }
                         ],
+                        "label": "Comparison matrix",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 332.14166641631607,
-                            "top": 272.4446413680965
+                            "bottom": 400.3483566628363,
+                            "height": 109.33332824707031,
+                            "left": 97.53132296684093,
+                            "right": 363.53132296684095,
+                            "top": 291.015028415766,
+                            "width": 266,
+                            "x": 97.53132296684093,
+                            "y": 291.015028415766
                         },
-                        "post_job_actions": {
-                            "EmailActionoutput": {
-                                "action_arguments": {
-                                    "host": "usegalaxy.eu"
-                                },
-                                "action_type": "EmailAction",
-                                "output_name": "output"
-                            },
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Human UniProt Microbial Proteins cRAP for MetaNovo"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "9773176c-aeef-4430-9c9d-5c276bfd13bb",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "dcc7e278-b396-463e-9275-b669bb71ae30"
                             }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Sample annot MSstats"
+                            }
+                        ],
+                        "label": "Sample annot MSstats",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 501.86464433024696,
+                            "height": 109.33332824707031,
+                            "left": 98.42104804246945,
+                            "right": 364.42104804246947,
+                            "top": 392.53131608317665,
+                            "width": 266,
+                            "x": 98.42104804246945,
+                            "y": 392.53131608317665
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f546e7278f04",
-                            "name": "fasta_merge_files_and_filter_unique_sequences",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"accession_parser\": \"^>([^ ]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"uniqueness_criterion\": \"sequence\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.0",
-                        "type": "tool",
-                        "uuid": "4c1b21ac-9ceb-49be-9c48-771a3fda8db4",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "b0cf95a5-fca3-45ea-88df-37b06948099c",
                         "workflow_outputs": [
                             {
-                                "label": "Human UniProt Microbial Proteins cRAP for MetaNovo",
+                                "label": null,
                                 "output_name": "output",
-                                "uuid": "286f5bd4-fb0d-4649-8dac-f191acc72722"
+                                "uuid": "489e9abe-be00-44c1-89e8-643eaecb75dd"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metanovo/metanovo/1.9.4+galaxy4",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0",
                         "errors": null,
-                        "id": 5,
+                        "id": 3,
                         "input_connections": {
-                            "input_fasta": {
-                                "id": 4,
+                            "group|comparison_matrix": {
+                                "id": 1,
                                 "output_name": "output"
                             },
-                            "input_type|input_mgf_collection": {
-                                "id": 1,
+                            "input|annotation": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "input|evidence": {
+                                "id": 0,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool MetaNovo",
-                                "name": "input_type"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "MetaNovo",
+                        "name": "MSstats",
                         "outputs": [
                             {
-                                "name": "output_fasta",
-                                "type": "fasta"
+                                "name": "log",
+                                "type": "txt"
                             },
                             {
-                                "name": "output_csv",
-                                "type": "csv"
+                                "name": "processed_data",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "qcplot",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "quant_group_matrix",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "comparison_result",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "fittedmodel",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "volcanoplot",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "comparisonplot",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "left": 641.8293151855469,
-                            "top": 171.08148193359375
+                            "bottom": 803.8629044841107,
+                            "height": 732.0333251953125,
+                            "left": 406.11526374530075,
+                            "right": 672.1152637453008,
+                            "top": 71.82957928879816,
+                            "width": 266,
+                            "x": 406.11526374530075,
+                            "y": 71.82957928879816
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput_fasta": {
-                                "action_arguments": {
-                                    "newname": "Metanovo Compact database"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_fasta"
+                            "HideDatasetActionfittedmodel": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "fittedmodel"
+                            },
+                            "HideDatasetActionlog": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "log"
+                            },
+                            "HideDatasetActionquant_group_matrix": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "quant_group_matrix"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metanovo/metanovo/1.9.4+galaxy4",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "d6dcd3173bdf",
-                            "name": "metanovo",
+                            "changeset_revision": "52ac6fde9a5b",
+                            "name": "msstats",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"directag\": {\"directag_tic_cutoff\": \"85\", \"directag_max_peak_count\": \"400\", \"directag_intensity_classes\": \"3\", \"directag_adjust_precursor\": false, \"directag_min_adjustment\": \"-2.5\", \"directag_max_adjustment\": \"2.5\", \"directag_adjustment_step\": \"0.1\", \"directag_charge_states\": \"3\", \"directag_ms_charge_state\": false, \"directag_duplicate_spectra\": true, \"directag_deisotoping\": \"0\", \"directag_isotope_tolerance\": \"0.25\", \"directag_complement_tolerance\": \"0.5\", \"directag_tag_length\": \"4\", \"directag_max_var_mods\": \"2\", \"directag_max_tag_count\": \"5\", \"directag_intensity_weight\": \"1.0\", \"directag_fidelity_weight\": \"1.0\", \"directag_complement_weight\": \"1.0\"}, \"fraction_analysis\": {\"protein_fraction_mw_confidence\": \"95.0\"}, \"gene_annotation\": {\"useGeneMapping\": true, \"updateGeneMapping\": true}, \"import_filters\": {\"import_peptide_length_min\": \"8\", \"import_peptide_length_max\": \"50\", \"import_precursor_mz_ppm\": \"0\", \"exclude_unknown_ptms\": true}, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}, \"input_type\": {\"type\": \"collection\", \"__current_case__\": 1, \"input_mgf_collection\": {\"__class__\": \"ConnectedValue\"}}, \"metanovo_parameters\": {\"mn_specificity\": \"specific\", \"mn_enzymes\": \"Trypsin, no P rule\", \"mn_max_missed_cleavages\": \"2\"}, \"processing_control\": {\"CHUNKSIZE\": \"100000\"}, \"protein_inference\": {\"simplify_groups\": true, \"simplify_score\": true, \"simplify_enzymaticity\": true, \"simplify_evidence\": true, \"simplify_uncharacterized\": true}, \"ptm_localization\": {\"ptm_score\": \"1\", \"score_neutral_losses\": false, \"ptm_sequence_matching_type\": \"1\", \"ptm_alignment\": true}, \"sequence_matching\": {\"sequence_index_type\": \"0\", \"sequence_matching_type\": \"2\", \"sequence_matching_x\": \"0.25\"}, \"spectrum_annotation\": {\"annotation_level\": \"0.75\", \"annotation_high_resolution\": true}, \"spectrum_matching_parameters\": {\"prec_tol\": \"10.0\", \"prec_ppm\": \"1\", \"frag_tol\": \"0.01\", \"frag_ppm\": \"0\", \"digestion\": \"0\", \"enzyme\": [\"Trypsin (no P rule)\"], \"specificity\": \"0\", \"mc\": \"2\", \"fixed_mods\": [\"Carbamidomethylation of C\", \"TMT 10-plex of K\", \"TMT 10-plex of peptide N-term\"], \"variable_mods\": [\"Oxidation of M\"], \"min_charge\": \"2\", \"max_charge\": \"5\", \"fi\": \"b\", \"ri\": \"y\", \"min_isotope\": \"0\", \"max_isotope\": \"1\"}, \"validation_levels\": {\"psm_fdr\": \"1\", \"peptide_fdr\": \"1\", \"protein_fdr\": \"1\", \"group_psms\": true, \"group_peptides\": true, \"merge_subgroups\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.4+galaxy4",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"dp_options\": {\"logTrans\": \"2\", \"norm\": {\"normalization\": \"equalizeMedians\", \"__current_case__\": 0}, \"fillIncompleteRows\": \"true\", \"features\": {\"featureSubset\": \"all\", \"__current_case__\": 0}, \"summarize\": {\"summaryMethod\": \"TMP\", \"__current_case__\": 0, \"MBimpute\": \"true\", \"remove50missing\": \"false\"}, \"censoredInt\": \"NA\", \"cutoffCensored\": \"minFeature\", \"maxQuantileforCensored\": \"0.999\"}, \"group\": {\"group_comparison\": \"yes\", \"__current_case__\": 1, \"comparison_matrix\": {\"__class__\": \"ConnectedValue\"}, \"select_outputs\": [\"fittedmodel\", \"comparison_result\", \"volcanoplot\", \"comparisonplot\"]}, \"input\": {\"input_src\": \"OpenSWATH\", \"__current_case__\": 2, \"evidence\": {\"__class__\": \"ConnectedValue\"}, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"input_options\": {\"filter_with_mscore\": \"true\", \"mscore_cutoff\": \"0.01\", \"useUniquePeptide\": \"true\", \"fewMeasurements\": \"remove\", \"summaryforMultipleRows\": \"max\", \"removeProtein_with1Feature\": \"false\"}}, \"selected_outputs\": [\"log\", \"processed_data\", \"qcplot\", \"quant_group_matrix\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.20.1.0",
                         "type": "tool",
-                        "uuid": "07d51088-eb68-4ffd-b505-7228a21de93c",
-                        "when": null,
+                        "uuid": "810a6c7a-a171-44db-aadf-917c32e31d78",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_fasta",
-                                "uuid": "7d35c0ce-359a-4b99-bc50-7898bbb9f6c7"
+                                "output_name": "processed_data",
+                                "uuid": "15fd08bb-7103-4f19-9998-38709822e2d2"
                             },
                             {
                                 "label": null,
-                                "output_name": "output_csv",
-                                "uuid": "a37b2a24-df14-4ce0-9bec-38cc327a044d"
+                                "output_name": "comparisonplot",
+                                "uuid": "dfeb77e1-05b5-4236-96e9-694a7a969b70"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "volcanoplot",
+                                "uuid": "a369af4d-082b-4549-9417-1af61291e166"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "comparison_result",
+                                "uuid": "1b702487-ba66-4987-8f7d-5e624f90efac"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "qcplot",
+                                "uuid": "5ddda783-dfb8-4c06-ae95-2f26df51ac64"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+                        "content_id": "Grep1",
                         "errors": null,
-                        "id": 6,
+                        "id": 4,
                         "input_connections": {
-                            "batchmode|input_fastas_0|input_fasta": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "batchmode|input_fastas_1|input_fasta": {
-                                "id": 5,
-                                "output_name": "output_fasta"
-                            },
-                            "batchmode|input_fastas_2|input_fasta": {
+                            "input": {
                                 "id": 3,
-                                "output_name": "output"
+                                "output_name": "comparison_result"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "FASTA Merge Files and Filter Unique Sequences",
+                        "name": "Select",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "fasta"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 924.9069441945012,
-                            "top": 319.6465149119742
+                            "bottom": 329.3259474675458,
+                            "height": 123.95001220703125,
+                            "left": 664.0476312852443,
+                            "right": 930.0476312852443,
+                            "top": 205.37593526051455,
+                            "width": 266,
+                            "x": 664.0476312852443,
+                            "y": 205.37593526051455
                         },
-                        "post_job_actions": {
-                            "EmailActionoutput": {
-                                "action_arguments": {
-                                    "host": "usegalaxy.eu"
-                                },
-                                "action_type": "EmailAction",
-                                "output_name": "output"
-                            },
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Human UniProt Microbial Proteins (from MetaNovo) and cRAP "
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
+                        "post_job_actions": {},
+                        "tool_id": "Grep1",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"false\", \"pattern\": \"(ECOLI)|(logFC)\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.1",
+                        "type": "tool",
+                        "uuid": "0d3aefe9-d49e-4a5e-96b0-d2a93c164b5a",
+                        "workflow_outputs": [
+                            {
+                                "label": "Select_Ecoli",
+                                "output_name": "out_file1",
+                                "uuid": "0de65b2c-f62c-4068-8ac0-466e419d495b"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "Filter1",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "input": {
+                                "id": 4,
+                                "output_name": "out_file1"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f546e7278f04",
-                            "name": "fasta_merge_files_and_filter_unique_sequences",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        "inputs": [],
+                        "label": null,
+                        "name": "Filter",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 458.83722566303453,
+                            "height": 123.95001220703125,
+                            "left": 888.0450944255168,
+                            "right": 1154.0450944255167,
+                            "top": 334.8872134560033,
+                            "width": 266,
+                            "x": 888.0450944255168,
+                            "y": 334.8872134560033
                         },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"accession_parser\": \"^>([^ ]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"uniqueness_criterion\": \"sequence\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.0",
+                        "post_job_actions": {},
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"cond\": \"c7!='NA'\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
                         "type": "tool",
-                        "uuid": "3880c712-4f3c-4edc-bda0-ee348ab1a2c4",
-                        "when": null,
+                        "uuid": "22227f86-1d56-4e67-b76e-9fcdb409741e",
                         "workflow_outputs": [
                             {
-                                "label": "Human UniProt Microbial Proteins (from MetaNovo) and cRAP ",
-                                "output_name": "output",
-                                "uuid": "de57cd9d-ac05-4397-9d44-e65620913447"
+                                "label": "Filter_Ecoli",
+                                "output_name": "out_file1",
+                                "uuid": "197e8a45-392f-4981-8684-2c8326af4528"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "proteomics/clinical-mp-1-database-generation",
-                "path": "topics/proteomics/tutorials/clinical-mp-1-database-generation/workflows/WF1_Database_Generation_Workflow.ga",
-                "tags": [
-                    "name:clinicalMP"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "WF1_Database_Generation_Workflow",
-                "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-clinical-mp-1-database-generation/versions/wf1-database-generation-workflow",
-                "tutorial_id": "clinical-mp-1-database-generation",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-1-database-generation/workflows/WF1_Database_Generation_Workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-1-database-generation/workflows/WF1_Database_Generation_Workflow.html",
-                "version": 1,
-                "wfid": "proteomics-clinical-mp-1-database-generation",
-                "wfname": "wf1-database-generation-workflow",
-                "workflow": "WF1_Database_Generation_Workflow.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metanovo/metanovo/1.9.4+galaxy4"
-                ],
-                "workflowhub_id": "1350"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.10105821"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "encyclopedia_quantify",
-                    "owner": "galaxyp",
-                    "revisions": "4081e4faa4ab",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "encyclopedia_quantify",
-                    "owner": "galaxyp",
-                    "revisions": "1c5cbf8f79ce",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "encyclopedia_searchtolib",
-                    "owner": "galaxyp",
-                    "revisions": "62a718b76f62",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "encyclopedia_searchtolib",
-                    "owner": "galaxyp",
-                    "revisions": "36880dfd9fa7",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "msconvert",
-                    "owner": "galaxyp",
-                    "revisions": "3cf310697624",
-                    "tool_panel_section_label": "Convert Formats",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "msconvert",
-                    "owner": "galaxyp",
-                    "revisions": "6153e8ada1ee",
-                    "tool_panel_section_label": "Convert Formats",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: encyclopedia_quantify\n  owner: galaxyp\n  revisions: 4081e4faa4ab\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: encyclopedia_quantify\n  owner: galaxyp\n  revisions: 1c5cbf8f79ce\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: encyclopedia_searchtolib\n  owner: galaxyp\n  revisions: 62a718b76f62\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: encyclopedia_searchtolib\n  owner: galaxyp\n  revisions: 36880dfd9fa7\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msconvert\n  owner: galaxyp\n  revisions: 3cf310697624\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msconvert\n  owner: galaxyp\n  revisions: 6153e8ada1ee\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/encyclopedia/tutorial.json",
-        "contributors": [
-            {
-                "email": "leith023@umn.edu",
-                "id": "emmaleith",
-                "joined": "2019-07",
-                "name": "Emma Leith",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/emmaleith/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/emmaleith.json"
-            },
-            {
-                "email": "subinamehta@gmail.com",
-                "id": "subinamehta",
-                "joined": "2018-06",
-                "linkedin": "subinamehta",
-                "matrix": "subinamehta:matrix.org",
-                "name": "Subina Mehta",
-                "orcid": "0000-0001-9818-0537",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
-                "twitter": "Subina_Mehta",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
-            },
-            {
-                "email": "jj@umn.edu",
-                "id": "jj-umn",
-                "in_memoriam": "<a href=\"https://galaxyproject.org/news/2024-03-19-remembrances-of-jj/\">James \u2018JJ\u2019 Johnson, was a Galaxy community rock star most known for his indispensable contributions to the Galaxy Proteomics community.</a>\n\nJJ\u2019s works will live on in so many Galaxy tools and workflows for years to come.",
-                "joined": "2017-09",
-                "name": "James Johnson",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jj-umn/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jj-umn.json"
-            },
-            {
-                "email": "pjagtap@umn.edu",
-                "id": "pratikdjagtap",
-                "joined": "2017-09",
-                "name": "Pratik Jagtap",
-                "orcid": "0000-0003-0984-0973",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
-            },
-            {
-                "email": "tgriffin@umn.edu",
-                "github": false,
-                "id": "timothygriffin",
-                "joined": "2017-09",
-                "name": "Timothy J. Griffin",
-                "orcid": "0000-0001-6801-2559",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
-            }
-        ],
-        "dir": "topics/proteomics/tutorials/encyclopedia",
-        "edam_operation": [
-            "Filtering",
-            "Formatting"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "proteomics/encyclopedia",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.org.au"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "With SearchToLib, Chromatogram Libraries can be created",
-            "Learning conversion of file types using msconvert"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
-        "objectives": [
-            "Understand the difference between DDA and DIA methods",
-            "Performing quantitative analysis using DIA data",
-            "Understand the purpose and benefits of using a Chromatogram Library for detection of peptides",
-            "You can use Bloom's Taxonomy to write effective learning objectives"
-        ],
-        "pageviews": 1973,
-        "pub_date": "2021-06-21",
-        "questions": [
-            "How to perform quantitative analysis using DIA data with the help of EncyclopeDIA?",
-            "How to perform quantitation with or without Chromatogram Libraries?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "mtekman"
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "input": {
+                                "id": 5,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Histogram",
+                                "name": "input"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Histogram",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 382.0702885219029,
+                            "height": 123.94999694824219,
+                            "left": 1130.7142673578476,
+                            "right": 1396.7142673578476,
+                            "top": 258.1202915736607,
+                            "width": 266,
+                            "x": 1130.7142673578476,
+                            "y": 258.1202915736607
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "6f134426c2b0",
+                            "name": "histogram",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"breaks\": \"25\", \"density\": \"true\", \"frequency\": \"false\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"numerical_column\": \"3\", \"title\": \"Distribution of Ecoli Protein log FC values\", \"xlab\": \"log2 Fold Change\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.3",
+                        "type": "tool",
+                        "uuid": "dc481c56-b123-48ec-bc5c-81411c3a7a9f",
+                        "workflow_outputs": [
+                            {
+                                "label": "Histogram_Ecoli",
+                                "output_name": "out_file1",
+                                "uuid": "04c6287d-fd0d-4780-99b6-cf52ee18e06f"
+                            }
+                        ]
+                    }
                 ],
-                "date": "2021-06-25",
-                "galaxy_version": "21.01",
-                "length": "30M",
-                "speakers": [
-                    "emmaleith"
+                "parent_id": "proteomics/DIA_Analysis_MSstats",
+                "path": "topics/proteomics/tutorials/DIA_Analysis_MSstats/workflows/Galaxy-Workflow-DIA_MSstats_Training_export_tabular.ga",
+                "tags": [
+                    "proteomics"
                 ],
-                "youtube_id": "eCEjHtbZLVg"
-            }
-        ],
-        "short_id": "T00215",
-        "short_tools": [
-            "encyclopedia_quantify",
-            "encyclopedia_searchtolib",
-            "msconvert"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "id-quant",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "DIA"
-        ],
-        "time_estimation": "6H",
-        "title": "EncyclopeDIA",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_quantify/encyclopedia_quantify/0.9.5.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_quantify/encyclopedia_quantify/1.2.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_searchtolib/encyclopedia_searchtolib/0.9.5.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_searchtolib/encyclopedia_searchtolib/1.2.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2"
-        ],
-        "topic_name": "proteomics",
-        "topic_name_human": "Proteomics",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "encyclopedia",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/encyclopedia/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/encyclopedia/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/encyclopedia/tutorial.json"
-        },
-        "version": 7,
-        "video": false,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 114,
-        "visitors": 1371,
-        "workflows": [
+                "test_results": null,
+                "tests": true,
+                "title": "DIA_analysis_MSstats",
+                "topic_id": "proteomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-DIA_Analysis_MSstats/versions/galaxy-workflow-dia-msstats-training-export-tabular",
+                "tutorial_id": "DIA_Analysis_MSstats",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/DIA_Analysis_MSstats/workflows/Galaxy-Workflow-DIA_MSstats_Training_export_tabular.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/DIA_Analysis_MSstats/workflows/Galaxy-Workflow-DIA_MSstats_Training_export_tabular.html",
+                "version": 2,
+                "wfid": "proteomics-DIA_Analysis_MSstats",
+                "wfname": "galaxy-workflow-dia-msstats-training-export-tabular",
+                "workflow": "Galaxy-Workflow-DIA_MSstats_Training_export_tabular.ga",
+                "workflow_tools": [
+                    "Filter1",
+                    "Grep1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0"
+                ],
+                "workflowhub_id": "1167"
+            },
             {
                 "creators": [],
-                "description": "encyclopedia",
+                "description": "DIA MSstats Training msstats input tabular",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nGPF DIA mzML Files Dataset collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSPECTRAL OR PROSIT LIBRARY\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nEXPERIMENTAL DIA mzML FILES WIDE\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBACKGROUND PROTEIN FASTA FILE\"]\n  4[label=\"msconvert\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"msconvert\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"SearchToLib\"]\n  3 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  4 -> 6 [label=\"output\"]\n  7[label=\"EncyclopeDIA Quantify\"]\n  3 -> 7 [label=\"output\"]\n  6 -> 7 [label=\"elib\"]\n  5 -> 7 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPyProphet MSstats input\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nComparison matrix\"]\n  2[label=\"MSstats\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Select\"]\n  2 -> 3 [label=\"comparison_result\"]\n  k6e8589bd13fd4a97a9c3ea0a5a0e2326[color=lightseagreen,label=\"Output\\nSelect_Ecoli\"]\n  3 -> k6e8589bd13fd4a97a9c3ea0a5a0e2326\n  4[label=\"Filter\"]\n  3 -> 4 [label=\"out_file1\"]\n  k6997a43aa17b418bbb6d7d32a6c277ae[color=lightseagreen,label=\"Output\\nFilter_Ecoli\"]\n  4 -> k6997a43aa17b418bbb6d7d32a6c277ae\n  5[label=\"Histogram\"]\n  4 -> 5 [label=\"out_file1\"]\n  kcf3abac382274af8a5516aeae154a0e4[color=lightseagreen,label=\"Output\\nHistogram_Ecoli\"]\n  5 -> kcf3abac382274af8a5516aeae154a0e4\n}",
                 "history": [
                     {
-                        "hash": "9126f68f0d5565a9630e9f3e92784308a4a24662",
-                        "message": "Update main_workflow.ga",
-                        "num": 4,
-                        "short_hash": "9126f68f0",
-                        "unix": "1623859793"
-                    },
-                    {
-                        "hash": "0a1ee8353f1a3c919f53904b61c778db04495f6b",
-                        "message": "Rename Workflow-May19_EncyclopeDIA_raw_inputs.ga to main_workflow.ga",
+                        "hash": "bef209fa8b13cca27b8deae81ff1675433201d9f",
+                        "message": "Add workflow tests to DIA_MSstats_Training tutorial",
                         "num": 3,
-                        "short_hash": "0a1ee8353",
-                        "unix": "1623859630"
+                        "short_hash": "bef209fa8",
+                        "unix": "1642736930"
                     },
                     {
-                        "hash": "c07e80f5e0a299c6c0abc2abc70fac0baa4a99f0",
-                        "message": "Delete main_workflow.ga",
+                        "hash": "15a13c3667af0db6a6ca380ca1b998c9faf625d3",
+                        "message": "updated workflow annotation and name",
                         "num": 2,
-                        "short_hash": "c07e80f5e",
-                        "unix": "1623859613"
+                        "short_hash": "15a13c366",
+                        "unix": "1606931443"
                     },
                     {
-                        "hash": "34e20aef08d95022e0a31d81ca9b28f3627d975d",
-                        "message": "add tutorial skeleton",
+                        "hash": "e8f20c190bc7a0d319835969a36114d939bd4dce",
+                        "message": "generated three tutorials on DIA data analysis in galaxy",
                         "num": 1,
-                        "short_hash": "34e20aef0",
-                        "unix": "1607964775"
+                        "short_hash": "e8f20c190",
+                        "unix": "1606930318"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "encyclopedia",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
@@ -179693,28 +180549,34 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "GPF DIA mzML Files (Dataset collection)"
+                                "name": "PyProphet MSstats input"
                             }
                         ],
-                        "label": "GPF DIA mzML Files (Dataset collection)",
-                        "name": "Input dataset collection",
+                        "label": "PyProphet MSstats input",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 434,
-                            "height": 105,
-                            "left": 450.46875,
-                            "right": 650.46875,
-                            "top": 329,
+                            "bottom": 524.5333251953125,
+                            "height": 82.20001220703125,
+                            "left": 127.5,
+                            "right": 327.5,
+                            "top": 442.33331298828125,
                             "width": 200,
-                            "x": 450.46875,
-                            "y": 329
+                            "x": 127.5,
+                            "y": 442.33331298828125
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "ba253b0a-c081-4dcb-9d3d-2c3b4b36f10d",
-                        "workflow_outputs": []
+                        "type": "data_input",
+                        "uuid": "970f9184-0af8-46ef-84c6-8ce933204ab8",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "bfbca2d5-0d5d-4860-a4c2-bd0c97113322"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
@@ -179725,430 +180587,406 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "SPECTRAL OR PROSIT LIBRARY"
+                                "name": "Comparison matrix"
                             }
                         ],
-                        "label": "SPECTRAL OR PROSIT LIBRARY",
+                        "label": "Comparison matrix",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 628,
-                            "height": 84,
-                            "left": 460.703125,
-                            "right": 660.703125,
-                            "top": 544,
+                            "bottom": 641.1000366210938,
+                            "height": 82.20001220703125,
+                            "left": 128.63333129882812,
+                            "right": 328.6333312988281,
+                            "top": 558.9000244140625,
                             "width": 200,
-                            "x": 460.703125,
-                            "y": 544
+                            "x": 128.63333129882812,
+                            "y": 558.9000244140625
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "417bc894-7c88-4633-80ce-ba418dd4179a",
-                        "workflow_outputs": []
-                    },
+                        "uuid": "9773176c-aeef-4430-9c9d-5c276bfd13bb",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "e84e8bf5-5e49-4783-bbff-0b6534bcf60a"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPyProphet MSstats input\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nComparison matrix\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"MSstats\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Select\"];\n  2 -->|comparison_result| 3;\n  6e8589bd-13fd-4a97-a9c3-ea0a5a0e2326[\"Output\\nSelect_Ecoli\"];\n  3 --> 6e8589bd-13fd-4a97-a9c3-ea0a5a0e2326;\n  style 6e8589bd-13fd-4a97-a9c3-ea0a5a0e2326 stroke:#2c3143,stroke-width:4px;\n  4[\"Filter\"];\n  3 -->|out_file1| 4;\n  6997a43a-a17b-418b-bb6d-7d32a6c277ae[\"Output\\nFilter_Ecoli\"];\n  4 --> 6997a43a-a17b-418b-bb6d-7d32a6c277ae;\n  style 6997a43a-a17b-418b-bb6d-7d32a6c277ae stroke:#2c3143,stroke-width:4px;\n  5[\"Histogram\"];\n  4 -->|out_file1| 5;\n  cf3abac3-8227-4af8-a551-6aeae154a0e4[\"Output\\nHistogram_Ecoli\"];\n  5 --> cf3abac3-8227-4af8-a551-6aeae154a0e4;\n  style cf3abac3-8227-4af8-a551-6aeae154a0e4 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "DIA_analysis_MSstats",
+                "outputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "EXPERIMENTAL DIA mzML FILES (WIDE)"
+                                "name": "PyProphet MSstats input"
                             }
                         ],
-                        "label": "EXPERIMENTAL DIA mzML FILES (WIDE)",
-                        "name": "Input dataset collection",
+                        "label": "PyProphet MSstats input",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 317,
-                            "height": 105,
-                            "left": 709.578125,
-                            "right": 909.578125,
-                            "top": 212,
+                            "bottom": 524.5333251953125,
+                            "height": 82.20001220703125,
+                            "left": 127.5,
+                            "right": 327.5,
+                            "top": 442.33331298828125,
                             "width": 200,
-                            "x": 709.578125,
-                            "y": 212
+                            "x": 127.5,
+                            "y": 442.33331298828125
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "9f96077e-d7b3-47d4-bc71-d42c9db72b59",
-                        "workflow_outputs": []
+                        "type": "data_input",
+                        "uuid": "970f9184-0af8-46ef-84c6-8ce933204ab8",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "bfbca2d5-0d5d-4860-a4c2-bd0c97113322"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "BACKGROUND PROTEIN FASTA FILE"
+                                "name": "Comparison matrix"
                             }
                         ],
-                        "label": "BACKGROUND PROTEIN FASTA FILE",
+                        "label": "Comparison matrix",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 839,
-                            "height": 105,
-                            "left": 440.703125,
-                            "right": 640.703125,
-                            "top": 734,
+                            "bottom": 641.1000366210938,
+                            "height": 82.20001220703125,
+                            "left": 128.63333129882812,
+                            "right": 328.6333312988281,
+                            "top": 558.9000244140625,
                             "width": 200,
-                            "x": 440.703125,
-                            "y": 734
+                            "x": 128.63333129882812,
+                            "y": 558.9000244140625
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "b45f41c6-0b3b-48ad-8a1f-73c355c22d61",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nGPF DIA mzML Files Dataset collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSPECTRAL OR PROSIT LIBRARY\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nEXPERIMENTAL DIA mzML FILES WIDE\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nBACKGROUND PROTEIN FASTA FILE\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"msconvert\"];\n  0 -->|output| 4;\n  5[\"msconvert\"];\n  2 -->|output| 5;\n  6[\"SearchToLib\"];\n  3 -->|output| 6;\n  1 -->|output| 6;\n  4 -->|output| 6;\n  7[\"EncyclopeDIA Quantify\"];\n  3 -->|output| 7;\n  6 -->|elib| 7;\n  5 -->|output| 7;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "May19 EncyclopeDIA raw inputs",
-                "outputs": [
+                        "uuid": "9773176c-aeef-4430-9c9d-5c276bfd13bb",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "e84e8bf5-5e49-4783-bbff-0b6534bcf60a"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0",
                         "errors": null,
-                        "id": 4,
+                        "id": 2,
                         "input_connections": {
-                            "input": {
+                            "group|comparison_matrix": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "input|msstats_input": {
                                 "id": 0,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool msconvert",
-                                "name": "input"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "msconvert",
+                        "name": "MSstats",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "mzml"
+                                "name": "log",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "processed_data",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "qcplot",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "quant_group_matrix",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "comparison_result",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "fittedmodel",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "volcanoplot",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "comparisonplot",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "bottom": 562.5,
-                            "height": 116,
-                            "left": 739.703125,
-                            "right": 939.703125,
-                            "top": 446.5,
+                            "bottom": 785.5,
+                            "height": 520,
+                            "left": 424.5333251953125,
+                            "right": 624.5333251953125,
+                            "top": 265.5,
                             "width": 200,
-                            "x": 739.703125,
-                            "y": 446.5
+                            "x": 424.5333251953125,
+                            "y": 265.5
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2",
+                        "post_job_actions": {
+                            "HideDatasetActionfittedmodel": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "fittedmodel"
+                            },
+                            "HideDatasetActionlog": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "log"
+                            },
+                            "HideDatasetActionquant_group_matrix": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "quant_group_matrix"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "6153e8ada1ee",
-                            "name": "msconvert",
+                            "changeset_revision": "52ac6fde9a5b",
+                            "name": "msstats",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"data_processing\": {\"peak_picking\": {\"pick_peaks\": \"false\", \"__current_case__\": 0}, \"precursor_refinement\": {\"use_mzrefinement\": \"false\", \"__current_case__\": 0}, \"charge_state_calculation\": {\"charge_state_calculation_method\": \"false\", \"__current_case__\": 0}, \"thresholds\": [], \"filter_mz_windows\": {\"do_mzwindow_filter\": \"false\", \"__current_case__\": 0}, \"etd_filtering\": {\"do_etd_filtering\": \"false\", \"__current_case__\": 0}, \"ms2denoise\": {\"denoise\": \"false\", \"__current_case__\": 1}, \"ms2deisotope\": \"false\", \"demultiplex\": {\"demultiplex_on\": \"false\", \"__current_case__\": 1}}, \"filtering\": {\"activation\": \"false\", \"indices\": [], \"scan_numbers\": [], \"strip_it\": \"false\", \"filter_ms_levels\": {\"do_ms_level_filter\": \"false\", \"__current_case__\": 0}, \"polarity\": \"false\", \"analyzer\": \"false\"}, \"general_options\": {\"combineIonMobilitySpectra\": \"false\", \"scan_summing\": {\"do_scan_summing\": \"false\", \"__current_case__\": 0}, \"simAsSpectra\": \"false\", \"srmAsSpectra\": \"false\", \"acceptZeroLengthSpectra\": \"false\", \"ignoreUnknownInstrumentError\": \"false\", \"multi_run_output\": {\"do_multi_run_output\": \"false\", \"__current_case__\": 0, \"runIndexSet\": \"0\"}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"license_agreement\": \"true\", \"output_type\": \"mzML\", \"settings\": {\"mz_encoding\": \"64\", \"intensity_encoding\": \"32\", \"binary_compression\": \"zlib\", \"gzip_compression\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.0.20287.2",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"dp_options\": {\"logTrans\": \"2\", \"norm\": {\"normalization\": \"equalizeMedians\", \"__current_case__\": 0}, \"fillIncompleteRows\": \"true\", \"features\": {\"featureSubset\": \"all\", \"__current_case__\": 0}, \"summarize\": {\"summaryMethod\": \"TMP\", \"__current_case__\": 0, \"MBimpute\": \"true\", \"remove50missing\": \"false\"}, \"censoredInt\": \"NA\", \"cutoffCensored\": \"minFeature\", \"maxQuantileforCensored\": \"0.999\"}, \"group\": {\"group_comparison\": \"yes\", \"__current_case__\": 1, \"comparison_matrix\": {\"__class__\": \"ConnectedValue\"}, \"select_outputs\": [\"fittedmodel\", \"comparison_result\", \"volcanoplot\", \"comparisonplot\"]}, \"input\": {\"input_src\": \"MSstats\", \"__current_case__\": 0, \"msstats_input\": {\"__class__\": \"ConnectedValue\"}}, \"selected_outputs\": [\"log\", \"processed_data\", \"qcplot\", \"quant_group_matrix\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.20.1.0",
                         "type": "tool",
-                        "uuid": "e4cfea9c-2d49-4c2d-af72-a1d352303432",
+                        "uuid": "cb3da2fb-604c-43e7-8540-84de6d00ff0f",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "4ec33042-9998-40ac-8c44-5005ee2e5cef"
+                                "output_name": "volcanoplot",
+                                "uuid": "4dabaa14-50b0-4225-aa6c-72470f1df31e"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "comparisonplot",
+                                "uuid": "f3a3175f-a995-406a-a3d2-287b38d0e8ff"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "processed_data",
+                                "uuid": "bf41d447-8dbd-4554-b684-8cf5965d2c7b"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "comparison_result",
+                                "uuid": "3b09f94d-6c38-49da-9938-e99e5e79fd77"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "qcplot",
+                                "uuid": "a09e7723-369d-4c2d-b209-eb82e3c2404d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2",
+                        "content_id": "Grep1",
                         "errors": null,
-                        "id": 5,
+                        "id": 3,
                         "input_connections": {
                             "input": {
                                 "id": 2,
-                                "output_name": "output"
+                                "output_name": "comparison_result"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool msconvert",
-                                "name": "input"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "msconvert",
+                        "name": "Select",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "mzml"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 403.5,
-                            "height": 116,
-                            "left": 1009.703125,
-                            "right": 1209.703125,
-                            "top": 287.5,
+                            "bottom": 523.4666595458984,
+                            "height": 93.19999694824219,
+                            "left": 674.13330078125,
+                            "right": 874.13330078125,
+                            "top": 430.26666259765625,
                             "width": 200,
-                            "x": 1009.703125,
-                            "y": 287.5
+                            "x": 674.13330078125,
+                            "y": 430.26666259765625
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6153e8ada1ee",
-                            "name": "msconvert",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"data_processing\": {\"peak_picking\": {\"pick_peaks\": \"false\", \"__current_case__\": 0}, \"precursor_refinement\": {\"use_mzrefinement\": \"false\", \"__current_case__\": 0}, \"charge_state_calculation\": {\"charge_state_calculation_method\": \"false\", \"__current_case__\": 0}, \"thresholds\": [], \"filter_mz_windows\": {\"do_mzwindow_filter\": \"false\", \"__current_case__\": 0}, \"etd_filtering\": {\"do_etd_filtering\": \"false\", \"__current_case__\": 0}, \"ms2denoise\": {\"denoise\": \"false\", \"__current_case__\": 1}, \"ms2deisotope\": \"false\", \"demultiplex\": {\"demultiplex_on\": \"false\", \"__current_case__\": 1}}, \"filtering\": {\"activation\": \"false\", \"indices\": [], \"scan_numbers\": [], \"strip_it\": \"false\", \"filter_ms_levels\": {\"do_ms_level_filter\": \"false\", \"__current_case__\": 0}, \"polarity\": \"false\", \"analyzer\": \"false\"}, \"general_options\": {\"combineIonMobilitySpectra\": \"false\", \"scan_summing\": {\"do_scan_summing\": \"false\", \"__current_case__\": 0}, \"simAsSpectra\": \"false\", \"srmAsSpectra\": \"false\", \"acceptZeroLengthSpectra\": \"false\", \"ignoreUnknownInstrumentError\": \"false\", \"multi_run_output\": {\"do_multi_run_output\": \"false\", \"__current_case__\": 0, \"runIndexSet\": \"0\"}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"license_agreement\": \"true\", \"output_type\": \"mzML\", \"settings\": {\"mz_encoding\": \"64\", \"intensity_encoding\": \"32\", \"binary_compression\": \"zlib\", \"gzip_compression\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.0.20287.2",
+                        "tool_id": "Grep1",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"false\", \"pattern\": \"(ECOLI)|(logFC)\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.1",
                         "type": "tool",
-                        "uuid": "8dcbc065-269f-47cf-aea0-dba0b283082b",
+                        "uuid": "7086c065-874a-4fe2-a084-c55b39febd65",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "9bc6c507-ff1a-4422-812a-662611e45369"
+                                "label": "Select_Ecoli",
+                                "output_name": "out_file1",
+                                "uuid": "6e8589bd-13fd-4a97-a9c3-ea0a5a0e2326"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_searchtolib/encyclopedia_searchtolib/1.2.2+galaxy0",
+                        "content_id": "Filter1",
                         "errors": null,
-                        "id": 6,
+                        "id": 4,
                         "input_connections": {
-                            "fasta": {
+                            "input": {
                                 "id": 3,
-                                "output_name": "output"
-                            },
-                            "library": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "scan_inputs": {
-                                "id": 4,
-                                "output_name": "output"
+                                "output_name": "out_file1"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool SearchToLib",
-                                "name": "target_fasta"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "SearchToLib",
+                        "name": "Filter",
                         "outputs": [
                             {
-                                "name": "log",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "elib",
-                                "type": "elib"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 956.5,
-                            "height": 324,
-                            "left": 909.703125,
-                            "right": 1109.703125,
-                            "top": 632.5,
+                            "bottom": 663.9666595458984,
+                            "height": 93.19999694824219,
+                            "left": 900.63330078125,
+                            "right": 1100.63330078125,
+                            "top": 570.7666625976562,
                             "width": 200,
-                            "x": 909.703125,
-                            "y": 632.5
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionelib": {
-                                "action_arguments": {
-                                    "newname": "CHROMATOGRAM LIBRARY"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "elib"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_searchtolib/encyclopedia_searchtolib/1.2.2+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "36880dfd9fa7",
-                            "name": "encyclopedia_searchtolib",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "x": 900.63330078125,
+                            "y": 570.7666625976562
                         },
-                        "tool_state": "{\"a\": \"false\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"library\": {\"__class__\": \"ConnectedValue\"}, \"options\": {\"acquisition\": {\"set_acquisition\": \"no\", \"__current_case__\": 0}, \"tolerance\": {\"set_tolerance\": \"no\", \"__current_case__\": 0}, \"percolator\": {\"set_percolator\": \"no\", \"__current_case__\": 0}, \"peak\": {\"set_peak\": \"no\", \"__current_case__\": 0}, \"window\": {\"set_window\": \"no\", \"__current_case__\": 0}, \"modifications\": {\"set_modifications\": \"no\", \"__current_case__\": 0}, \"search\": {\"set_search\": \"no\", \"__current_case__\": 0}}, \"scan_inputs\": {\"__class__\": \"ConnectedValue\"}, \"select_outputs\": [\"log\", \"elib\"], \"target_fasta\": {\"__class__\": \"RuntimeValue\"}, \"tp\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.2+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"cond\": \"c7!='NA'\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
                         "type": "tool",
-                        "uuid": "128970ae-d036-4960-b88c-b4f90e2c9c5f",
+                        "uuid": "3f136bb5-3387-4f1a-abf2-07b7ce58d577",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "elib",
-                                "uuid": "4c03ecb4-1a34-45aa-bdec-7248a773d28f"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "log",
-                                "uuid": "5da7e8b9-5220-47de-b253-74d01d1bc998"
+                                "label": "Filter_Ecoli",
+                                "output_name": "out_file1",
+                                "uuid": "6997a43a-a17b-418b-bb6d-7d32a6c277ae"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_quantify/encyclopedia_quantify/1.2.2+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
                         "errors": null,
-                        "id": 7,
+                        "id": 5,
                         "input_connections": {
-                            "fasta": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "library": {
-                                "id": 6,
-                                "output_name": "elib"
-                            },
-                            "scan_inputs": {
-                                "id": 5,
-                                "output_name": "output"
+                            "input": {
+                                "id": 4,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool EncyclopeDIA Quantify",
-                                "name": "target_fasta"
+                                "description": "runtime parameter for tool Histogram",
+                                "name": "input"
                             }
                         ],
                         "label": null,
-                        "name": "EncyclopeDIA Quantify",
+                        "name": "Histogram",
                         "outputs": [
                             {
-                                "name": "log",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "elib",
-                                "type": "elib"
-                            },
-                            {
-                                "name": "results",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "peptides",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "proteins",
-                                "type": "tabular"
+                                "name": "out_file1",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "bottom": 1093,
-                            "height": 585,
-                            "left": 1180.15625,
-                            "right": 1380.15625,
-                            "top": 508,
+                            "bottom": 536.1999969482422,
+                            "height": 93.19999694824219,
+                            "left": 1081.36669921875,
+                            "right": 1281.36669921875,
+                            "top": 443,
                             "width": 200,
-                            "x": 1180.15625,
-                            "y": 508
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionelib": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "elib"
-                            },
-                            "HideDatasetActionresults": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "results"
-                            },
-                            "RenameDatasetActionpeptides": {
-                                "action_arguments": {
-                                    "newname": "PEPTIDE QUANTITATION OUTPUT"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "peptides"
-                            },
-                            "RenameDatasetActionproteins": {
-                                "action_arguments": {
-                                    "newname": "PROTEIN QUANTITATION OUTPUT"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "proteins"
-                            }
+                            "x": 1081.36669921875,
+                            "y": 443
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_quantify/encyclopedia_quantify/1.2.2+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
                         "tool_shed_repository": {
-                            "changeset_revision": "1c5cbf8f79ce",
-                            "name": "encyclopedia_quantify",
-                            "owner": "galaxyp",
+                            "changeset_revision": "6f134426c2b0",
+                            "name": "histogram",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"a\": \"true\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"library\": {\"__class__\": \"ConnectedValue\"}, \"options\": {\"acquisition\": {\"set_acquisition\": \"no\", \"__current_case__\": 0}, \"tolerance\": {\"set_tolerance\": \"no\", \"__current_case__\": 0}, \"percolator\": {\"set_percolator\": \"no\", \"__current_case__\": 0}, \"peak\": {\"set_peak\": \"no\", \"__current_case__\": 0}, \"window\": {\"set_window\": \"no\", \"__current_case__\": 0}, \"modifications\": {\"set_modifications\": \"no\", \"__current_case__\": 0}, \"search\": {\"set_search\": \"no\", \"__current_case__\": 0}}, \"scan_inputs\": {\"__class__\": \"ConnectedValue\"}, \"select_outputs\": [\"log\", \"elib\", \"results\", \"peptides\", \"proteins\"], \"target_fasta\": {\"__class__\": \"RuntimeValue\"}, \"tp\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.2+galaxy0",
+                        "tool_state": "{\"breaks\": \"25\", \"density\": \"true\", \"frequency\": \"false\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"numerical_column\": \"3\", \"title\": \"Distribution of Ecoli Protein log FC values\", \"xlab\": \"log2 Fold Change\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.3",
                         "type": "tool",
-                        "uuid": "f8f64f5a-cf05-4529-a354-c8171e8537c6",
+                        "uuid": "65080a30-a49c-4414-a9b7-d72390001eab",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "peptides",
-                                "uuid": "1e7fbdde-967c-49f3-9e01-32fdffbf0e06"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "proteins",
-                                "uuid": "d7d6276c-44bc-452e-8a36-51fcb9817f4c"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "log",
-                                "uuid": "d4691eee-fb32-4278-8c8a-6e12c7cf7d3f"
+                                "label": "Histogram_Ecoli",
+                                "output_name": "out_file1",
+                                "uuid": "cf3abac3-8227-4af8-a551-6aeae154a0e4"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/encyclopedia",
-                "path": "topics/proteomics/tutorials/encyclopedia/workflows/main_workflow.ga",
+                "parent_id": "proteomics/DIA_Analysis_MSstats",
+                "path": "topics/proteomics/tutorials/DIA_Analysis_MSstats/workflows/Galaxy-Workflow-DIA_MSstats_Training_msstats_input_tabular.ga",
                 "tags": [
                     "proteomics"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "May19 EncyclopeDIA raw inputs",
+                "tests": true,
+                "title": "DIA_analysis_MSstats",
                 "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-encyclopedia/versions/main-workflow",
-                "tutorial_id": "encyclopedia",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/encyclopedia/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/encyclopedia/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "proteomics-encyclopedia",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-DIA_Analysis_MSstats/versions/galaxy-workflow-dia-msstats-training-msstats-input-tabular",
+                "tutorial_id": "DIA_Analysis_MSstats",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/DIA_Analysis_MSstats/workflows/Galaxy-Workflow-DIA_MSstats_Training_msstats_input_tabular.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/DIA_Analysis_MSstats/workflows/Galaxy-Workflow-DIA_MSstats_Training_msstats_input_tabular.html",
+                "version": 2,
+                "wfid": "proteomics-DIA_Analysis_MSstats",
+                "wfname": "galaxy-workflow-dia-msstats-training-msstats-input-tabular",
+                "workflow": "Galaxy-Workflow-DIA_MSstats_Training_msstats_input_tabular.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_quantify/encyclopedia_quantify/1.2.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_searchtolib/encyclopedia_searchtolib/1.2.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2"
+                    "Filter1",
+                    "Grep1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0"
                 ],
-                "workflowhub_id": "1146"
+                "workflowhub_id": "1163"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.4926594"
+        "zenodo_link": "https://zenodo.org/record/4307758"
     },
     {
         "admin_install": {
@@ -180157,66 +180995,157 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "diapysef",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "histogram",
+                    "owner": "devteam",
+                    "revisions": "6f134426c2b0",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_falsediscoveryrate",
                     "owner": "galaxyp",
-                    "revisions": "8eed818f5d48",
+                    "revisions": "c9eff69a7c62",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "maxquant",
+                    "name": "openms_featurefindermultiplex",
                     "owner": "galaxyp",
-                    "revisions": "37d669de2828",
+                    "revisions": "5e948629bc73",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "openms_openswathassaygenerator",
+                    "name": "openms_fidoadapter",
                     "owner": "galaxyp",
-                    "revisions": "df72ca515420",
+                    "revisions": "658494a2cb00",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "openms_openswathassaygenerator",
+                    "name": "openms_fileinfo",
                     "owner": "galaxyp",
-                    "revisions": "2a9ff56cb279",
+                    "revisions": "52ba9695e752",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "openms_openswathdecoygenerator",
+                    "name": "openms_idconflictresolver",
                     "owner": "galaxyp",
-                    "revisions": "965413f29bf5",
+                    "revisions": "c28f13cab67a",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "openms_openswathdecoygenerator",
+                    "name": "openms_idmapper",
                     "owner": "galaxyp",
-                    "revisions": "f861ec9fbe59",
+                    "revisions": "39caaa778d2e",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "openms_targetedfileconverter",
+                    "name": "openms_idposteriorerrorprobability",
                     "owner": "galaxyp",
-                    "revisions": "aa62f8f48dd4",
+                    "revisions": "111c3a00136d",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "openms_targetedfileconverter",
+                    "name": "openms_idscoreswitcher",
                     "owner": "galaxyp",
-                    "revisions": "dd71e020e2aa",
+                    "revisions": "be74a8cd7d66",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_multiplexresolver",
+                    "owner": "galaxyp",
+                    "revisions": "fb647b7cf2c1",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_peptideindexer",
+                    "owner": "galaxyp",
+                    "revisions": "dd173849c3d8",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_proteinquantifier",
+                    "owner": "galaxyp",
+                    "revisions": "16026cdb1330",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_textexporter",
+                    "owner": "galaxyp",
+                    "revisions": "9020199dba0a",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_xtandemadapter",
+                    "owner": "galaxyp",
+                    "revisions": "7f6a1f27553e",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: diapysef\n  owner: galaxyp\n  revisions: 8eed818f5d48\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maxquant\n  owner: galaxyp\n  revisions: 37d669de2828\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_openswathassaygenerator\n  owner: galaxyp\n  revisions: df72ca515420\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_openswathassaygenerator\n  owner: galaxyp\n  revisions: 2a9ff56cb279\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_openswathdecoygenerator\n  owner: galaxyp\n  revisions: 965413f29bf5\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_openswathdecoygenerator\n  owner: galaxyp\n  revisions: f861ec9fbe59\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_targetedfileconverter\n  owner: galaxyp\n  revisions: aa62f8f48dd4\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_targetedfileconverter\n  owner: galaxyp\n  revisions: dd71e020e2aa\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/DIA_lib_OSW/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: histogram\n  owner: devteam\n  revisions: 6f134426c2b0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_falsediscoveryrate\n  owner: galaxyp\n  revisions: c9eff69a7c62\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_featurefindermultiplex\n  owner: galaxyp\n  revisions: 5e948629bc73\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_fidoadapter\n  owner: galaxyp\n  revisions: 658494a2cb00\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_fileinfo\n  owner: galaxyp\n  revisions: 52ba9695e752\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idconflictresolver\n  owner: galaxyp\n  revisions: c28f13cab67a\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idmapper\n  owner: galaxyp\n  revisions: 39caaa778d2e\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idposteriorerrorprobability\n  owner: galaxyp\n  revisions: 111c3a00136d\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idscoreswitcher\n  owner: galaxyp\n  revisions: be74a8cd7d66\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_multiplexresolver\n  owner: galaxyp\n  revisions: fb647b7cf2c1\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_peptideindexer\n  owner: galaxyp\n  revisions: dd173849c3d8\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_proteinquantifier\n  owner: galaxyp\n  revisions: 16026cdb1330\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_textexporter\n  owner: galaxyp\n  revisions: 9020199dba0a\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_xtandemadapter\n  owner: galaxyp\n  revisions: 7f6a1f27553e\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/protein-quant-sil/tutorial.json",
         "contributors": [
+            {
+                "email": "sigloch+github@mailbox.org",
+                "former_affiliations": [
+                    "uni-freiburg"
+                ],
+                "id": "stortebecker",
+                "joined": "2017-09",
+                "name": "Florian Christoph Sigloch",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stortebecker/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/stortebecker.json"
+            },
+            {
+                "affiliations": [
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
+                "fediverse_flavor": "mastodon",
+                "id": "bgruening",
+                "joined": "2017-09",
+                "linkedin": "bgruening",
+                "location": {
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
+                },
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+            },
             {
                 "affiliations": [
                     "uni-freiburg"
@@ -180229,33 +181158,10 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/matthias313/",
                 "twitter": "mfahrner313",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/matthias313.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "email": "melanie.foell@mol-med.uni-freiburg.de",
-                "id": "foellmelanie",
-                "joined": "2018-10",
-                "matrix": "foellmelanie:matrix.org",
-                "name": "Melanie F\u00f6ll",
-                "orcid": "0000-0002-1887-7543",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
-                "twitter": "MCFoell",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/DIA_lib_OSW",
-        "edam_operation": [
-            "Visualisation",
-            "Imputation",
-            "Heat map generation",
-            "Standardisation and normalisation",
-            "Principal component plotting",
-            "Protein quantification",
-            "Clustering",
-            "Statistical calculation"
-        ],
+        "dir": "topics/proteomics/tutorials/protein-quant-sil",
+        "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu"
@@ -180263,43 +181169,67 @@
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "proteomics/DIA_lib_OSW",
+        "id": "proteomics/protein-quant-sil",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
             "UseGalaxy.no",
             "UseGalaxy.org.au"
         ],
         "js_requirements": {
-            "mathjax": null,
+            "mathjax": 8638,
             "mermaid": false
         },
         "key_points": [
-            "MaxQuant, diapysef and OpenSwath tools enable the generation of spectral libraries from DDA data",
-            "Generated spectral libraries can be used for the analysis of DIA data"
+            "Peptides labelled with stable isotopes result in multiple parallel MS1 ion traces.",
+            "MS1 features can be used for relative protein quantitation.",
+            "Quantitations have to be mapped to PSMs.",
+            "PSM quantitations can be used to calculate protein quantitations.",
+            "Proper quantitation and mapping needs careful evaluation and optimization."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
+        "level": "Advanced",
         "license": "CC-BY-4.0",
         "mod_date": "2023-11-09",
         "objectives": [
-            "Generating a spectral library from data dependent acquisition (DDA) MS data",
-            "Understanding DIA data principles and characteristics",
-            "Optimizing and refining a spectral library for the analysis of DIA data"
+            "MS1 feature quantitation and mapping of quantitations to peptide and protein IDs."
         ],
-        "pageviews": 4900,
-        "pub_date": "2020-12-02",
+        "pageviews": 1650,
+        "pub_date": "2017-03-17",
         "questions": [
-            "How does the peptide identification work in data independent acquisition (DIA) mass spectrometry (MS) data?",
-            "What is a spectral library and how to generate a spectral library using Maxquant, diapysef and OpenSwath tools?"
+            "What are MS1 features?",
+            "How to quantify based on MS1 features?",
+            "How to map MS1 features to MS2 identifications?",
+            "How to evaluate and optimize the results?"
         ],
-        "short_id": "T00212",
+        "requirements": [
+            {
+                "topic_name": "proteomics",
+                "tutorials": [
+                    "database-handling",
+                    "protein-id-oms"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00230",
         "short_tools": [
-            "OpenSwathAssayGenerator",
-            "OpenSwathDecoyGenerator",
-            "maxquant",
-            "TargetedFileConverter",
-            "Filter1",
-            "diapysef"
+            "ProteinQuantifier",
+            "IDMapper",
+            "FalseDiscoveryRate",
+            "Summary_Statistics1",
+            "MultiplexResolver",
+            "IDScoreSwitcher",
+            "TextExporter",
+            "FileInfo",
+            "histogram_rpy",
+            "XTandemAdapter",
+            "IDConflictResolver",
+            "Grep1",
+            "FeatureFinderMultiplex",
+            "PeptideIndexer",
+            "IDPosteriorErrorProbability",
+            "tp_tail_tool",
+            "FidoAdapter"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -180332,20 +181262,29 @@
         },
         "symlink": null,
         "tags": [
-            "DIA"
+            "DDA",
+            "SILAC"
         ],
-        "time_estimation": "1H",
-        "title": "Library Generation for DIA Analysis",
+        "time_estimation": "1h",
+        "title": "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)",
         "tools": [
-            "Filter1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/diapysef/diapysef/0.3.5.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathassaygenerator/OpenSwathAssayGenerator/2.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathassaygenerator/OpenSwathAssayGenerator/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator/2.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_targetedfileconverter/TargetedFileConverter/2.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_targetedfileconverter/TargetedFileConverter/2.6+galaxy0"
+            "Grep1",
+            "Summary_Statistics1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_multiplexresolver/MultiplexResolver/2.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0"
         ],
         "topic_name": "proteomics",
         "topic_name_human": "Proteomics",
@@ -180355,47 +181294,192 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "DIA_lib_OSW",
+        "tutorial_name": "protein-quant-sil",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_lib_OSW/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/protein-quant-sil/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/DIA_lib_OSW/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/DIA_lib_OSW/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/protein-quant-sil/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/protein-quant-sil/tutorial.json"
         },
-        "version": 10,
+        "version": 31,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 84,
-        "visitors": 3696,
+        "visit_duration": 101,
+        "visitors": 1141,
         "workflows": [
             {
                 "creators": [],
-                "description": "DIA library Training HEK Ecoli data",
+                "description": "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHEK_Ecoli_exp_design.txt\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\niRTassays.tsv\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nFASTA collection\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nDDA_data collection\"]\n  4[label=\"MaxQuant\"]\n  2 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Filter\"]\n  4 -> 5 [label=\"evidence\"]\n  6[label=\"Filter\"]\n  4 -> 6 [label=\"msms\"]\n  7[label=\"diapysef library generation\"]\n  5 -> 7 [label=\"out_file1\"]\n  1 -> 7 [label=\"output\"]\n  6 -> 7 [label=\"out_file1\"]\n  8[label=\"OpenSwathAssayGenerator\"]\n  7 -> 8 [label=\"output_tabular\"]\n  9[label=\"OpenSwathDecoyGenerator\"]\n  8 -> 9 [label=\"out\"]\n  10[label=\"TargetedFileConverter\"]\n  9 -> 10 [label=\"out\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmzml raw file\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nfasta file\"]\n  2[label=\"FeatureFinderMultiplex\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"XTandemAdapter\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"FileInfo\"]\n  3 -> 4 [label=\"out\"]\n  5[label=\"PeptideIndexer\"]\n  1 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"out\"]\n  6[label=\"IDPosteriorErrorProbability\"]\n  5 -> 6 [label=\"out\"]\n  7[label=\"FalseDiscoveryRate\"]\n  6 -> 7 [label=\"out\"]\n  8[label=\"IDScoreSwitcher\"]\n  7 -> 8 [label=\"out\"]\n  9[label=\"FileInfo\"]\n  8 -> 9 [label=\"out\"]\n  10[label=\"FidoAdapter\"]\n  8 -> 10 [label=\"out\"]\n  11[label=\"FalseDiscoveryRate\"]\n  10 -> 11 [label=\"out\"]\n  12[label=\"FileInfo\"]\n  11 -> 12 [label=\"out\"]\n  13[label=\"TextExporter\"]\n  11 -> 13 [label=\"out\"]\n  14[label=\"IDMapper\"]\n  11 -> 14 [label=\"out\"]\n  2 -> 14 [label=\"out_multiplets\"]\n  15[label=\"Select\"]\n  13 -> 15 [label=\"out\"]\n  16[label=\"Select\"]\n  13 -> 16 [label=\"out\"]\n  17[label=\"IDConflictResolver\"]\n  14 -> 17 [label=\"out\"]\n  18[label=\"MultiplexResolver\"]\n  17 -> 18 [label=\"out\"]\n  19[label=\"ProteinQuantifier\"]\n  18 -> 19 [label=\"out\"]\n  11 -> 19 [label=\"out\"]\n  20[label=\"Summary Statistics\"]\n  19 -> 20 [label=\"out\"]\n  21[label=\"Select last\"]\n  19 -> 21 [label=\"out\"]\n  22[label=\"Histogram\"]\n  21 -> 22 [label=\"outfile\"]\n}",
                 "history": [
                     {
-                        "hash": "15a13c3667af0db6a6ca380ca1b998c9faf625d3",
-                        "message": "updated workflow annotation and name",
+                        "hash": "54b4d9fcc78b1394f71f7affd51ca15e83b211d5",
+                        "message": "Adding tags to workflows",
+                        "num": 11,
+                        "short_hash": "54b4d9fcc",
+                        "unix": "1604224600"
+                    },
+                    {
+                        "hash": "ca84d739509bdb1ef8f3cfc64c15242ef0363407",
+                        "message": "Updating Tutorials to OpenMS 2.6, adjusting of parameters and tools, adding tool versions",
+                        "num": 10,
+                        "short_hash": "ca84d7395",
+                        "unix": "1604176914"
+                    },
+                    {
+                        "hash": "c5002c655c4206fb1d6712d1c1543f9b7ea2e3cb",
+                        "message": "protein-quant-sil",
+                        "num": 9,
+                        "short_hash": "c5002c655",
+                        "unix": "1601688681"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 8,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 7,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "e42145c47e6b093c441a431ec3c5671b7ddfc176",
+                        "message": "Updated workflow",
+                        "num": 6,
+                        "short_hash": "e42145c47",
+                        "unix": "1553096121"
+                    },
+                    {
+                        "hash": "3a0757df3e7b39d74c5e9e124018710702ca0ab0",
+                        "message": "Enabled FFMult advanced options without changing any parameter",
+                        "num": 5,
+                        "short_hash": "3a0757df3",
+                        "unix": "1511966670"
+                    },
+                    {
+                        "hash": "66e504fe259577c3473db9b51c320674d62eb504",
+                        "message": "Workaround for ProteinQuantifier bug: changed '-include_all' to TRUE",
+                        "num": 4,
+                        "short_hash": "66e504fe2",
+                        "unix": "1511867833"
+                    },
+                    {
+                        "hash": "ed8674c45632a609171092f22c9e16fbb69e1342",
+                        "message": "Updated workflow parameters",
+                        "num": 3,
+                        "short_hash": "ed8674c45",
+                        "unix": "1511865952"
+                    },
+                    {
+                        "hash": "c7d698525c66e52498ec708408d5045883619da2",
+                        "message": "Fill workflow file with an empty workflow",
                         "num": 2,
-                        "short_hash": "15a13c366",
-                        "unix": "1606931443"
+                        "short_hash": "c7d698525",
+                        "unix": "1496938362"
                     },
                     {
-                        "hash": "e8f20c190bc7a0d319835969a36114d939bd4dce",
-                        "message": "generated three tutorials on DIA data analysis in galaxy",
+                        "hash": "2c1271b670d336517fb123fb632ce13c93c40465",
+                        "message": "Restructure proteomics",
                         "num": 1,
-                        "short_hash": "e8f20c190",
-                        "unix": "1606930318"
+                        "short_hash": "2c1271b67",
+                        "unix": "1495544862"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "mzml raw file"
+                            }
+                        ],
+                        "label": "mzml raw file",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 307.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": -1679,
+                            "right": -1479,
+                            "top": 225,
+                            "width": 200,
+                            "x": -1679,
+                            "y": 225
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "a2382c96-bff3-4807-bbb7-20f74d014134",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "da762be8-3c8c-42a9-b749-8a38a004b944"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "fasta file"
+                            }
+                        ],
+                        "label": "fasta file",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 466.8000030517578,
+                            "height": 61.80000305175781,
+                            "left": -1680,
+                            "right": -1480,
+                            "top": 405,
+                            "width": 200,
+                            "x": -1680,
+                            "y": 405
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "94c0bbb8-89a2-43a2-980b-65f44c21aa51",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "c9862313-9f50-4042-a35a-7db1f3af9a4d"
+                            }
+                        ]
                     }
                 ],
-                "inputs": [
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nmzml raw file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nfasta file\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"FeatureFinderMultiplex\"];\n  0 -->|output| 2;\n  3[\"XTandemAdapter\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  4[\"FileInfo\"];\n  3 -->|out| 4;\n  5[\"PeptideIndexer\"];\n  1 -->|output| 5;\n  3 -->|out| 5;\n  6[\"IDPosteriorErrorProbability\"];\n  5 -->|out| 6;\n  7[\"FalseDiscoveryRate\"];\n  6 -->|out| 7;\n  8[\"IDScoreSwitcher\"];\n  7 -->|out| 8;\n  9[\"FileInfo\"];\n  8 -->|out| 9;\n  10[\"FidoAdapter\"];\n  8 -->|out| 10;\n  11[\"FalseDiscoveryRate\"];\n  10 -->|out| 11;\n  12[\"FileInfo\"];\n  11 -->|out| 12;\n  13[\"TextExporter\"];\n  11 -->|out| 13;\n  14[\"IDMapper\"];\n  11 -->|out| 14;\n  2 -->|out_multiplets| 14;\n  15[\"Select\"];\n  13 -->|out| 15;\n  16[\"Select\"];\n  13 -->|out| 16;\n  17[\"IDConflictResolver\"];\n  14 -->|out| 17;\n  18[\"MultiplexResolver\"];\n  17 -->|out| 18;\n  19[\"ProteinQuantifier\"];\n  18 -->|out| 19;\n  11 -->|out| 19;\n  20[\"Summary Statistics\"];\n  19 -->|out| 20;\n  21[\"Select last\"];\n  19 -->|out| 21;\n  22[\"Histogram\"];\n  21 -->|outfile| 22;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Proteomics: Peptide and Protein Quantification via stable istobe labeling",
+                "outputs": [
                     {
                         "annotation": "",
                         "content_id": null,
@@ -180405,32 +181489,32 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "HEK_Ecoli_exp_design.txt"
+                                "name": "mzml raw file"
                             }
                         ],
-                        "label": "HEK_Ecoli_exp_design.txt",
+                        "label": "mzml raw file",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 253.1999969482422,
+                            "bottom": 307.1999969482422,
                             "height": 82.19999694824219,
-                            "left": -302.5,
-                            "right": -102.5,
-                            "top": 171,
+                            "left": -1679,
+                            "right": -1479,
+                            "top": 225,
                             "width": 200,
-                            "x": -302.5,
-                            "y": 171
+                            "x": -1679,
+                            "y": 225
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "b7a2d992-bc43-4699-8914-4315558acf72",
+                        "uuid": "a2382c96-bff3-4807-bbb7-20f74d014134",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "be397353-5730-4e2d-a975-5342da357935"
+                                "uuid": "da762be8-3c8c-42a9-b749-8a38a004b944"
                             }
                         ]
                     },
@@ -180443,386 +181527,711 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "iRTassays.tsv"
+                                "name": "fasta file"
                             }
                         ],
-                        "label": "iRTassays.tsv",
+                        "label": "fasta file",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 369.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": -347.5,
-                            "right": -147.5,
-                            "top": 287,
+                            "bottom": 466.8000030517578,
+                            "height": 61.80000305175781,
+                            "left": -1680,
+                            "right": -1480,
+                            "top": 405,
                             "width": 200,
-                            "x": -347.5,
-                            "y": 287
+                            "x": -1680,
+                            "y": 405
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "2020e579-6339-4c24-baf0-556c6e07d94e",
+                        "uuid": "94c0bbb8-89a2-43a2-980b-65f44c21aa51",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "facf90b8-ddac-410e-a894-c966b56f21a2"
+                                "uuid": "c9862313-9f50-4042-a35a-7db1f3af9a4d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.6+galaxy0",
                         "errors": null,
                         "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "input_connections": {
+                            "in": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FeatureFinderMultiplex",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "FASTA collection"
+                                "name": "out_multiplets",
+                                "type": "consensusxml"
                             }
                         ],
-                        "label": "FASTA collection",
-                        "name": "Input dataset collection",
-                        "outputs": [],
                         "position": {
-                            "bottom": 478.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": -337.5,
-                            "right": -137.5,
-                            "top": 396,
+                            "bottom": 587.1999969482422,
+                            "height": 195.1999969482422,
+                            "left": -1373,
+                            "right": -1173,
+                            "top": 392,
                             "width": 200,
-                            "x": -337.5,
-                            "y": 396
+                            "x": -1373,
+                            "y": 392
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "b990e20a-52da-44de-9a00-22ae2e400e5e",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "5e5771b511a3",
+                            "name": "openms_featurefindermultiplex",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": [\"out_multiplets_FLAG\"], \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"algorithm\": {\"labels\": \"[ ][Arg6,Lys6]\", \"charge\": \"1:4\", \"isotopes_per_peptide\": \"3:6\", \"rt_typical\": \"40.0\", \"rt_band\": \"0.0\", \"rt_min\": \"2.0\", \"mz_tolerance\": \"10.0\", \"mz_unit\": \"ppm\", \"intensity_cutoff\": \"1000.0\", \"peptide_similarity\": \"0.5\", \"averagine_similarity\": \"0.4\", \"averagine_similarity_scaling\": \"0.95\", \"missed_cleavages\": \"1\", \"spectrum_type\": \"automatic\", \"averagine_type\": \"peptide\", \"knock_out\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"labels\": {\"Arg6\": \"6.0201290268\", \"Arg10\": \"10.0082686\", \"Lys4\": \"4.0251069836\", \"Lys6\": \"6.0201290268\", \"Lys8\": \"8.0141988132\", \"Leu3\": \"3.01883\", \"Dimethyl0\": \"28.0313\", \"Dimethyl4\": \"32.056407\", \"Dimethyl6\": \"34.063117\", \"Dimethyl8\": \"36.07567\", \"ICPL0\": \"105.021464\", \"ICPL4\": \"109.046571\", \"ICPL6\": \"111.041593\", \"ICPL10\": \"115.0667\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "eaa992c7-823d-46df-8e6c-161733ed043c",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "7867b0df-a52a-4c04-a488-c03e1db17631"
+                                "output_name": "out_multiplets",
+                                "uuid": "c4519437-723f-4033-884e-90686600a9cd"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0",
                         "errors": null,
                         "id": 3,
-                        "input_connections": {},
-                        "inputs": [
+                        "input_connections": {
+                            "database": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "in": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "XTandemAdapter",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "DDA_data collection"
+                                "name": "out",
+                                "type": "idxml"
                             }
                         ],
-                        "label": "DDA_data collection",
-                        "name": "Input dataset collection",
-                        "outputs": [],
                         "position": {
-                            "bottom": 608.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": -344.5,
-                            "right": -144.5,
-                            "top": 526,
+                            "bottom": 317.1999969482422,
+                            "height": 215.1999969482422,
+                            "left": -1381,
+                            "right": -1181,
+                            "top": 102,
                             "width": 200,
-                            "x": -344.5,
-                            "y": 526
+                            "x": -1381,
+                            "y": 102
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "2a32fc5d-36c4-46ee-a2cd-b80be12da5e3",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "1add9bacdccd",
+                            "name": "openms_xtandemadapter",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": [\"out_FLAG\"], \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"database\": {\"__class__\": \"ConnectedValue\"}, \"default_config_file\": null, \"enzyme\": \"Trypsin\", \"fixed_modifications\": [\"Carbamidomethyl (C)\"], \"fragment_error_units\": \"ppm\", \"fragment_mass_tolerance\": \"10.0\", \"ignore_adapter_param\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"max_precursor_charge\": \"4\", \"max_valid_expect\": \"0.1\", \"minimum_fragment_mz\": \"150.0\", \"missed_cleavages\": \"1\", \"no_isotope_error\": \"false\", \"output_results\": \"all\", \"precursor_error_units\": \"ppm\", \"precursor_mass_tolerance\": \"10.0\", \"semi_cleavage\": \"false\", \"variable_modifications\": [\"Label:13C(6) (K)\", \"Label:13C(6) (R)\", \"Oxidation (M)\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "0118ed37-ce01-4abd-9551-e84807f0b008",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "14a26fc5-5e3e-4bca-84fc-057c6f828155"
+                                "output_name": "out",
+                                "uuid": "2c114d65-1bd5-451a-9cd3-eaa334d3000b"
                             }
                         ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nHEK_Ecoli_exp_design.txt\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\niRTassays.tsv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nFASTA collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Collection\\nDDA_data collection\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"MaxQuant\"];\n  2 -->|output| 4;\n  3 -->|output| 4;\n  0 -->|output| 4;\n  5[\"Filter\"];\n  4 -->|evidence| 5;\n  6[\"Filter\"];\n  4 -->|msms| 6;\n  7[\"diapysef library generation\"];\n  5 -->|out_file1| 7;\n  1 -->|output| 7;\n  6 -->|out_file1| 7;\n  8[\"OpenSwathAssayGenerator\"];\n  7 -->|output_tabular| 8;\n  9[\"OpenSwathDecoyGenerator\"];\n  8 -->|out| 9;\n  10[\"TargetedFileConverter\"];\n  9 -->|out| 10;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "DIA_lib_OSW",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 4,
+                        "input_connections": {
+                            "in": {
+                                "id": 3,
+                                "output_name": "out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FileInfo",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "HEK_Ecoli_exp_design.txt"
+                                "name": "out",
+                                "type": "txt"
                             }
                         ],
-                        "label": "HEK_Ecoli_exp_design.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 253.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": -302.5,
-                            "right": -102.5,
-                            "top": 171,
+                            "bottom": 385.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": -1153,
+                            "right": -953,
+                            "top": 272,
                             "width": 200,
-                            "x": -302.5,
-                            "y": 171
+                            "x": -1153,
+                            "y": 272
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "b7a2d992-bc43-4699-8914-4315558acf72",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e8dce5e07fa5",
+                            "name": "openms_fileinfo",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"c\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"d\": \"false\", \"i\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"false\", \"p\": \"false\", \"s\": \"false\", \"v\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "a2a5218c-cdd7-4d84-904a-4fe5d9763927",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "be397353-5730-4e2d-a975-5342da357935"
+                                "output_name": "out",
+                                "uuid": "4d3e6847-d51d-410f-9bbf-168ab598b108"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 5,
+                        "input_connections": {
+                            "fasta": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "in": {
+                                "id": 3,
+                                "output_name": "out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "PeptideIndexer",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "iRTassays.tsv"
+                                "name": "out",
+                                "type": "idxml"
                             }
                         ],
-                        "label": "iRTassays.tsv",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 369.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": -347.5,
-                            "right": -147.5,
-                            "top": 287,
+                            "bottom": 597.1999969482422,
+                            "height": 205.1999969482422,
+                            "left": -1153,
+                            "right": -953,
+                            "top": 392,
                             "width": 200,
-                            "x": -347.5,
-                            "y": 287
+                            "x": -1153,
+                            "y": 392
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "2020e579-6339-4c24-baf0-556c6e07d94e",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "d8ee5700c66b",
+                            "name": "openms_peptideindexer",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"IL_equivalent\": \"false\", \"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"aaa_max\": \"3\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"decoy_string\": \"\", \"decoy_string_position\": \"prefix\", \"enzyme\": {\"name\": \"auto\", \"specificity\": \"none\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"in\": {\"__class__\": \"ConnectedValue\"}, \"keep_unreferenced_proteins\": \"false\", \"mismatches_max\": \"0\", \"missing_decoy_action\": \"error\", \"unmatched_action\": \"error\", \"write_protein_description\": \"true\", \"write_protein_sequence\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "d7e47129-c738-4174-b7e4-4d387a5b24f1",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "facf90b8-ddac-410e-a894-c966b56f21a2"
+                                "output_name": "out",
+                                "uuid": "dc35fedb-9094-4984-9936-0aeb83d98e72"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy0",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 6,
+                        "input_connections": {
+                            "in": {
+                                "id": 5,
+                                "output_name": "out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "IDPosteriorErrorProbability",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "FASTA collection"
+                                "name": "out",
+                                "type": "idxml"
                             }
                         ],
-                        "label": "FASTA collection",
-                        "name": "Input dataset collection",
-                        "outputs": [],
                         "position": {
-                            "bottom": 478.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": -337.5,
-                            "right": -137.5,
-                            "top": 396,
+                            "bottom": 446.8000030517578,
+                            "height": 174.8000030517578,
+                            "left": -933,
+                            "right": -733,
+                            "top": 272,
                             "width": 200,
-                            "x": -337.5,
-                            "y": 396
+                            "x": -933,
+                            "y": 272
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "b990e20a-52da-44de-9a00-22ae2e400e5e",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "711a081d80ba",
+                            "name": "openms_idposteriorerrorprobability",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fit_algorithm\": {\"number_of_bins\": \"100\", \"incorrectly_assigned\": \"Gumbel\", \"max_nr_iterations\": \"1000\", \"neg_log_delta\": \"6\", \"outlier_handling\": \"ignore_iqr_outliers\"}, \"ignore_bad_data\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"prob_correct\": \"true\", \"split_charge\": \"false\", \"top_hits_only\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "3d87b974-366d-4ffa-b626-bb0c63bef28e",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "7867b0df-a52a-4c04-a488-c03e1db17631"
+                                "output_name": "out",
+                                "uuid": "c24e8bab-c848-46d1-b469-2537f21d4b69"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
                         "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 7,
+                        "input_connections": {
+                            "in": {
+                                "id": 6,
+                                "output_name": "out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FalseDiscoveryRate",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "DDA_data collection"
+                                "name": "out",
+                                "type": "idxml"
                             }
                         ],
-                        "label": "DDA_data collection",
-                        "name": "Input dataset collection",
-                        "outputs": [],
                         "position": {
-                            "bottom": 608.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": -344.5,
-                            "right": -144.5,
-                            "top": 526,
+                            "bottom": 446.8000030517578,
+                            "height": 174.8000030517578,
+                            "left": -713,
+                            "right": -513,
+                            "top": 272,
                             "width": 200,
-                            "x": -344.5,
-                            "y": 526
+                            "x": -713,
+                            "y": 272
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "2a32fc5d-36c4-46ee-a2cd-b80be12da5e3",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "469690558892",
+                            "name": "openms_falsediscoveryrate",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"FDR\": {\"PSM\": \"0.01\", \"protein\": \"1.0\", \"cleanup\": {\"remove_proteins_without_psms\": \"true\", \"remove_psms_without_proteins\": \"true\", \"remove_spectra_without_psms\": \"true\"}}, \"OPTIONAL_OUTPUTS\": null, \"PSM\": \"true\", \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"algorithm\": {\"no_qvalues\": \"false\", \"use_all_hits\": \"false\", \"split_charge_variants\": \"false\", \"treat_runs_separately\": \"false\", \"add_decoy_peptides\": \"true\", \"add_decoy_proteins\": \"false\", \"conservative\": \"true\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"protein\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "b9a62ef4-7758-41ed-a57f-07a761f34ea7",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "14a26fc5-5e3e-4bca-84fc-057c6f828155"
+                                "output_name": "out",
+                                "uuid": "13259070-1f50-4f87-84b0-c1d3640db605"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.6+galaxy0",
                         "errors": null,
-                        "id": 4,
+                        "id": 8,
                         "input_connections": {
-                            "input_opts|fasta_files": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "paramGroups_0|files": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "search_opts|template": {
-                                "id": 0,
-                                "output_name": "output"
+                            "in": {
+                                "id": 7,
+                                "output_name": "out"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "MaxQuant",
+                        "name": "IDScoreSwitcher",
                         "outputs": [
                             {
-                                "name": "proteinGroups",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "mqpar",
-                                "type": "xml"
-                            },
+                                "name": "out",
+                                "type": "idxml"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 406,
+                            "height": 134,
+                            "left": -493,
+                            "right": -293,
+                            "top": 272,
+                            "width": 200,
+                            "x": -493,
+                            "y": 272
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ec0d05b20eed",
+                            "name": "openms_idscoreswitcher",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"new_score\": \"Posterior Probability_score\", \"new_score_orientation\": \"higher_better\", \"new_score_type\": \"\", \"old_score\": \"\", \"proteins\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "659bd32d-fbc8-4c81-a48e-6f1c118b9416",
+                        "workflow_outputs": [
                             {
-                                "name": "peptides",
-                                "type": "tabular"
-                            },
+                                "label": null,
+                                "output_name": "out",
+                                "uuid": "01759e5a-51ec-4358-89bf-040a35560402"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {
+                            "in": {
+                                "id": 8,
+                                "output_name": "out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FileInfo",
+                        "outputs": [
                             {
-                                "name": "evidence",
-                                "type": "tabular"
-                            },
+                                "name": "out",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 385.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": -273,
+                            "right": -73,
+                            "top": 272,
+                            "width": 200,
+                            "x": -273,
+                            "y": 272
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e8dce5e07fa5",
+                            "name": "openms_fileinfo",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"c\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"d\": \"false\", \"i\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"false\", \"p\": \"false\", \"s\": \"false\", \"v\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "a871c553-362d-4e80-bbdb-9cb7b866e370",
+                        "workflow_outputs": [
                             {
-                                "name": "msms",
-                                "type": "tabular"
-                            },
+                                "label": null,
+                                "output_name": "out",
+                                "uuid": "21b6c69b-b138-4db8-9950-de68dac93a05"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0",
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {
+                            "in": {
+                                "id": 8,
+                                "output_name": "out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FidoAdapter",
+                        "outputs": [
                             {
-                                "name": "ptxqc_report",
-                                "type": "pdf"
+                                "name": "out",
+                                "type": "idxml"
                             }
                         ],
                         "position": {
-                            "bottom": 681,
-                            "height": 510,
-                            "left": -82.5,
-                            "right": 117.5,
-                            "top": 171,
+                            "bottom": 505.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": -273,
+                            "right": -73,
+                            "top": 392,
                             "width": 200,
-                            "x": -82.5,
-                            "y": 171
+                            "x": -273,
+                            "y": 392
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "ea0a1d50c83f",
-                            "name": "maxquant",
+                            "changeset_revision": "c3a5cd016963",
+                            "name": "openms_fidoadapter",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_opts\": {\"ftype\": \".thermo.raw\", \"fasta_files\": {\"__class__\": \"ConnectedValue\"}, \"identifier_parse_rule\": \">([^ ]*)\", \"description_parse_rule\": \"^>.*\\\\|.*\\\\|[^ ]+ (.*) OS.*$\"}, \"output_opts\": {\"dry_run\": \"false\", \"output\": [\"proteinGroups\", \"mqpar\", \"peptides\", \"evidence\", \"msms\"]}, \"paramGroups\": [{\"__index__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}, \"maxMissedCleavages\": \"1\", \"fixedModifications\": [\"Carbamidomethyl (C)\"], \"variableModifications\": [\"Oxidation (M)\"], \"enzymes\": [\"Trypsin/P\"], \"digestion_mode\": \"0\", \"quant_method\": {\"select_quant_method\": \"\", \"__current_case__\": 0}}], \"protein_quant\": {\"peptides_for_quantification\": \"1\", \"only_unmod_prot\": {\"unmod_prot\": \"False\", \"__current_case__\": 1}, \"lfq_opts\": {\"separateLfq\": \"false\", \"lfqStabilizeLargeRatios\": \"true\", \"lfqRequireMsms\": \"true\", \"do_ibaq\": {\"ibaq\": \"False\", \"__current_case__\": 1}, \"advancedSiteIntensities\": \"true\"}}, \"qc\": {\"do_it\": \"true\", \"__current_case__\": 0, \"parameters\": \"true\", \"summary\": \"true\", \"proteingroups\": \"true\", \"evidence\": \"true\", \"msms\": \"true\", \"msmsscans\": \"true\"}, \"search_opts\": {\"template\": {\"__class__\": \"ConnectedValue\"}, \"min_peptide_len\": \"7\", \"max_peptide_mass\": \"4600\", \"min_unique_pep\": \"1\", \"calc_peak_properties\": \"false\", \"match_between_runs\": \"true\", \"incl_contaminants\": \"true\", \"decoy_mode\": \"revert\", \"psm_fdr\": \"0.01\", \"protein_fdr\": \"0.01\", \"min_pep_length\": \"8\", \"max_pep_length\": \"25\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.6.10.43+galaxy3",
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"all_PSMs\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"greedy_group_resolution\": \"true\", \"group_level\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"log2_states\": \"0\", \"no_cleanup\": \"false\", \"prob\": {\"protein\": \"0.0\", \"peptide\": \"0.0\", \"spurious\": \"0.0\"}, \"separate_runs\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
                         "type": "tool",
-                        "uuid": "0ee17766-fdba-4ff9-b274-5a3c6a7f1e3d",
+                        "uuid": "404e63ae-e855-4cef-9352-8fcb43de3f13",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "proteinGroups",
-                                "uuid": "59c88bb8-68af-43df-991b-0a012cc639be"
-                            },
+                                "output_name": "out",
+                                "uuid": "e1a8b9e2-3fe9-4c6d-b8c7-b292ce47374f"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
+                        "errors": null,
+                        "id": 11,
+                        "input_connections": {
+                            "in": {
+                                "id": 10,
+                                "output_name": "out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FalseDiscoveryRate",
+                        "outputs": [
                             {
-                                "label": null,
-                                "output_name": "msms",
-                                "uuid": "e1310278-385d-404f-b9ba-68d2fbd2dd25"
-                            },
+                                "name": "out",
+                                "type": "idxml"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 446.8000030517578,
+                            "height": 174.8000030517578,
+                            "left": -53,
+                            "right": 147,
+                            "top": 272,
+                            "width": 200,
+                            "x": -53,
+                            "y": 272
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "469690558892",
+                            "name": "openms_falsediscoveryrate",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"FDR\": {\"PSM\": \"1.0\", \"protein\": \"0.01\", \"cleanup\": {\"remove_proteins_without_psms\": \"true\", \"remove_psms_without_proteins\": \"true\", \"remove_spectra_without_psms\": \"true\"}}, \"OPTIONAL_OUTPUTS\": null, \"PSM\": \"false\", \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"algorithm\": {\"no_qvalues\": \"false\", \"use_all_hits\": \"false\", \"split_charge_variants\": \"false\", \"treat_runs_separately\": \"false\", \"add_decoy_peptides\": \"false\", \"add_decoy_proteins\": \"false\", \"conservative\": \"true\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"protein\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "886f5485-8805-494f-99aa-f50c7c84e156",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "evidence",
-                                "uuid": "a9bef4a5-cdb4-4b74-a46e-fe7249f1e771"
-                            },
+                                "output_name": "out",
+                                "uuid": "a047eec1-fc49-4adb-a48b-eebfcf86b4ba"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {
+                            "in": {
+                                "id": 11,
+                                "output_name": "out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FileInfo",
+                        "outputs": [
+                            {
+                                "name": "out",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 385.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": 167,
+                            "right": 367,
+                            "top": 272,
+                            "width": 200,
+                            "x": 167,
+                            "y": 272
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e8dce5e07fa5",
+                            "name": "openms_fileinfo",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"c\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"d\": \"false\", \"i\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"false\", \"p\": \"false\", \"s\": \"false\", \"v\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "d13e8538-3432-4a00-9cca-7e8280947bb9",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "peptides",
-                                "uuid": "c1a3b7df-3441-458c-9fef-8fdab2f19576"
-                            },
+                                "output_name": "out",
+                                "uuid": "28b66dcf-19db-4d93-959d-ec6af66ed496"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.6+galaxy0",
+                        "errors": null,
+                        "id": 13,
+                        "input_connections": {
+                            "in": {
+                                "id": 11,
+                                "output_name": "out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "TextExporter",
+                        "outputs": [
+                            {
+                                "name": "out",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 505.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": 167,
+                            "right": 367,
+                            "top": 392,
+                            "width": 200,
+                            "x": 167,
+                            "y": 392
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "1c596fdaf34a",
+                            "name": "openms_textexporter",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"consensus\": {\"sorting_method\": \"none\", \"sort_by_maps\": \"false\", \"sort_by_size\": \"false\"}, \"feature\": {\"minimal\": \"false\", \"add_metavalues\": \"-1\"}, \"id\": {\"proteins_only\": \"false\", \"peptides_only\": \"false\", \"protein_groups\": \"false\", \"first_dim_rt\": \"false\", \"add_metavalues\": \"-1\", \"add_hit_metavalues\": \"-1\", \"add_protein_hit_metavalues\": \"-1\"}, \"in\": {\"__class__\": \"ConnectedValue\"}, \"no_ids\": \"false\", \"quoting\": \"none\", \"replacement\": \"_\", \"separator\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "e206c716-a374-4810-a560-e57e6761aa2c",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "mqpar",
-                                "uuid": "65605a07-5a17-4d31-b92b-afaf5dcb8837"
+                                "output_name": "out",
+                                "uuid": "b9156da0-a6b3-47d9-a352-836aee0451bc"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.6+galaxy0",
+                        "errors": null,
+                        "id": 14,
+                        "input_connections": {
+                            "id": {
+                                "id": 11,
+                                "output_name": "out"
                             },
+                            "in": {
+                                "id": 2,
+                                "output_name": "out_multiplets"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "IDMapper",
+                        "outputs": [
+                            {
+                                "name": "out",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 788.3999938964844,
+                            "height": 276.3999938964844,
+                            "left": 167,
+                            "right": 367,
+                            "top": 512,
+                            "width": 200,
+                            "x": 167,
+                            "y": 512
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2517c03f5cd3",
+                            "name": "openms_idmapper",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"consensus\": {\"use_subelements\": \"true\", \"annotate_ids_with_subelements\": \"true\"}, \"feature\": {\"use_centroid_rt\": \"false\", \"use_centroid_mz\": \"true\"}, \"id\": {\"__class__\": \"ConnectedValue\"}, \"in\": {\"__class__\": \"ConnectedValue\"}, \"mz_measure\": \"ppm\", \"mz_reference\": \"peptide\", \"mz_tolerance\": \"10.0\", \"rt_tolerance\": \"20.0\", \"spectra\": {\"_in\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "f368bcfb-dcd6-4006-b0fb-54684f73f36c",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "ptxqc_report",
-                                "uuid": "0b1667be-be49-4ea7-a3b2-48d099a44103"
+                                "output_name": "out",
+                                "uuid": "2385a34d-3bf9-4b1e-8c09-ececeec35479"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Filter1",
+                        "content_id": "Grep1",
                         "errors": null,
-                        "id": 5,
+                        "id": 15,
                         "input_connections": {
                             "input": {
-                                "id": 4,
-                                "output_name": "evidence"
+                                "id": 13,
+                                "output_name": "out"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Filter",
+                        "name": "Select",
                         "outputs": [
                             {
                                 "name": "out_file1",
@@ -180830,43 +182239,43 @@
                             }
                         ],
                         "position": {
-                            "bottom": 264.1999969482422,
+                            "bottom": 365.1999969482422,
                             "height": 93.19999694824219,
-                            "left": 137.5,
-                            "right": 337.5,
-                            "top": 171,
+                            "left": 387,
+                            "right": 587,
+                            "top": 272,
                             "width": 200,
-                            "x": 137.5,
-                            "y": 171
+                            "x": 387,
+                            "y": 272
                         },
                         "post_job_actions": {},
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"len(c9.split(';')) < 2\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_id": "Grep1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"false\", \"pattern\": \"CONTAMINANT\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.1",
                         "type": "tool",
-                        "uuid": "22368d26-e6a2-41f8-99d2-321bddd04840",
+                        "uuid": "bd3098ce-6f2f-4c3d-8580-35a559c5a07b",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "out_file1",
-                                "uuid": "44b9a121-c925-41a9-945f-52c7c8aeceb9"
+                                "uuid": "57f19087-b67a-40f4-9fcd-ab338a853e59"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Filter1",
+                        "content_id": "Grep1",
                         "errors": null,
-                        "id": 6,
+                        "id": 16,
                         "input_connections": {
                             "input": {
-                                "id": 4,
-                                "output_name": "msms"
+                                "id": 13,
+                                "output_name": "out"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Filter",
+                        "name": "Select",
                         "outputs": [
                             {
                                 "name": "out_file1",
@@ -180874,299 +182283,758 @@
                             }
                         ],
                         "position": {
-                            "bottom": 384.1999969482422,
+                            "bottom": 485.1999969482422,
                             "height": 93.19999694824219,
-                            "left": 137.5,
-                            "right": 337.5,
-                            "top": 291,
+                            "left": 387,
+                            "right": 587,
+                            "top": 392,
                             "width": 200,
-                            "x": 137.5,
-                            "y": 291
+                            "x": 387,
+                            "y": 392
                         },
                         "post_job_actions": {},
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"len(c12.split(';')) < 2\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_id": "Grep1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"false\", \"pattern\": \"HUMAN\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.1",
                         "type": "tool",
-                        "uuid": "eb4fa570-9fdd-40a3-a980-f494cde96317",
+                        "uuid": "24029aca-9eb6-423a-9474-b05961073a01",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "out_file1",
-                                "uuid": "95eda6f0-e8b5-4cdc-8cf6-d6ed53933077"
+                                "uuid": "19884cc2-1a3c-4f84-ab1d-192c8238ecd1"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/diapysef/diapysef/0.3.5.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.6+galaxy0",
                         "errors": null,
-                        "id": 7,
+                        "id": 17,
                         "input_connections": {
-                            "input_evidence": {
-                                "id": 5,
-                                "output_name": "out_file1"
-                            },
-                            "input_irtassays": {
-                                "id": 1,
-                                "output_name": "output"
+                            "in": {
+                                "id": 14,
+                                "output_name": "out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "IDConflictResolver",
+                        "outputs": [
+                            {
+                                "name": "out",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 666.3999938964844,
+                            "height": 154.39999389648438,
+                            "left": 387,
+                            "right": 587,
+                            "top": 512,
+                            "width": 200,
+                            "x": 387,
+                            "y": 512
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "fb0e6f70a1df",
+                            "name": "openms_idconflictresolver",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"resolve_between_features\": \"off\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "29e2c398-4df7-40c8-8fa7-b03eaeb86eb7",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out",
+                                "uuid": "b261502d-5f97-4263-b79e-575000d63c07"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_multiplexresolver/MultiplexResolver/2.5+galaxy0",
+                        "errors": null,
+                        "id": 18,
+                        "input_connections": {
+                            "in": {
+                                "id": 17,
+                                "output_name": "out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "MultiplexResolver",
+                        "outputs": [
+                            {
+                                "name": "out",
+                                "type": "consensusxml"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 538.3999938964844,
+                            "height": 266.3999938964844,
+                            "left": 607,
+                            "right": 807,
+                            "top": 272,
+                            "width": 200,
+                            "x": 607,
+                            "y": 272
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_multiplexresolver/MultiplexResolver/2.5+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "fb647b7cf2c1",
+                            "name": "openms_multiplexresolver",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"algorithm\": {\"labels\": \"[ ][Arg6,Lys6]\", \"missed_cleavages\": \"1\", \"mass_tolerance\": \"0.1\", \"mz_tolerance\": \"10\", \"rt_tolerance\": \"5\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"in_blacklist\": null, \"labels\": {\"Arg6\": \"6.0201290268\", \"Arg10\": \"10.0082686\", \"Lys4\": \"4.0251069836\", \"Lys6\": \"6.0201290268\", \"Lys8\": \"8.0141988132\", \"Leu3\": \"3.01883\", \"Dimethyl0\": \"28.0313\", \"Dimethyl4\": \"32.056407\", \"Dimethyl6\": \"34.063117\", \"Dimethyl8\": \"36.07567\", \"ICPL0\": \"105.021464\", \"ICPL4\": \"109.046571\", \"ICPL6\": \"111.041593\", \"ICPL10\": \"115.0667\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.5+galaxy0",
+                        "type": "tool",
+                        "uuid": "c8cead64-a291-4bbc-b400-df3b0c87cb05",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out",
+                                "uuid": "2d191fe3-d682-4bc1-ac64-f5a5a2cdc04a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.6+galaxy0",
+                        "errors": null,
+                        "id": 19,
+                        "input_connections": {
+                            "in": {
+                                "id": 18,
+                                "output_name": "out"
                             },
-                            "input_msms": {
-                                "id": 6,
-                                "output_name": "out_file1"
+                            "protein_groups": {
+                                "id": 11,
+                                "output_name": "out"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "diapysef library generation",
+                        "name": "ProteinQuantifier",
                         "outputs": [
                             {
-                                "name": "output_tabular",
-                                "type": "tabular"
+                                "name": "out",
+                                "type": "csv"
                             },
                             {
-                                "name": "output_pdf",
-                                "type": "pdf"
+                                "name": "peptide_out",
+                                "type": "csv"
                             }
                         ],
                         "position": {
-                            "bottom": 559.3999938964844,
-                            "height": 388.3999938964844,
-                            "left": 357.5,
-                            "right": 557.5,
-                            "top": 171,
+                            "bottom": 619.6000061035156,
+                            "height": 347.6000061035156,
+                            "left": 827,
+                            "right": 1027,
+                            "top": 272,
                             "width": 200,
-                            "x": 357.5,
-                            "y": 171
+                            "x": 827,
+                            "y": 272
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/diapysef/diapysef/0.3.5.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.6+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "8eed818f5d48",
-                            "name": "diapysef",
+                            "changeset_revision": "bb1e75938909",
+                            "name": "openms_proteinquantifier",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"alignment\": \"linear\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_evidence\": {\"__class__\": \"ConnectedValue\"}, \"input_irtassays\": {\"__class__\": \"ConnectedValue\"}, \"input_msms\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3.5.0",
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": [\"out_FLAG\", \"peptide_out_FLAG\"], \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"average\": \"sum\", \"best_charge_and_fraction\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"consensus\": {\"normalize\": \"false\", \"fix_peptides\": \"false\"}, \"design\": null, \"format\": {\"separator\": \"\", \"quoting\": \"double\", \"replacement\": \"_\"}, \"greedy_group_resolution\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"include_all\": \"false\", \"protein_groups\": {\"__class__\": \"ConnectedValue\"}, \"ratios\": \"true\", \"ratiosSILAC\": \"false\", \"top\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
                         "type": "tool",
-                        "uuid": "50c157a3-ceb5-4d34-aadf-a635f2d9c62c",
+                        "uuid": "f45eb629-cead-420b-b277-a1d9dd781c70",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_pdf",
-                                "uuid": "3dde2b97-a71d-40e6-bfd5-a818577596c7"
+                                "output_name": "out",
+                                "uuid": "69c464ef-cf41-4bd2-b8ea-e10560b8d6fd"
                             },
                             {
                                 "label": null,
-                                "output_name": "output_tabular",
-                                "uuid": "9db078b5-7289-4de8-80e0-3af5466d5f4b"
+                                "output_name": "peptide_out",
+                                "uuid": "a9eeea33-4858-402a-a526-4ce950474f6f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathassaygenerator/OpenSwathAssayGenerator/2.5+galaxy0",
+                        "content_id": "Summary_Statistics1",
                         "errors": null,
-                        "id": 8,
+                        "id": 20,
                         "input_connections": {
-                            "in": {
-                                "id": 7,
-                                "output_name": "output_tabular"
+                            "input": {
+                                "id": 19,
+                                "output_name": "out"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool OpenSwathAssayGenerator",
-                                "name": "in"
-                            },
-                            {
-                                "description": "runtime parameter for tool OpenSwathAssayGenerator",
-                                "name": "swath_windows_file"
-                            },
-                            {
-                                "description": "runtime parameter for tool OpenSwathAssayGenerator",
-                                "name": "unimod_file"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "OpenSwathAssayGenerator",
+                        "name": "Summary Statistics",
                         "outputs": [
                             {
-                                "name": "out",
-                                "type": "data"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 590.2000122070312,
-                            "height": 419.20001220703125,
-                            "left": 577.5,
-                            "right": 777.5,
-                            "top": 171,
+                            "bottom": 385.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": 1047,
+                            "right": 1247,
+                            "top": 272,
                             "width": 200,
-                            "x": 577.5,
-                            "y": 171
+                            "x": 1047,
+                            "y": 272
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathassaygenerator/OpenSwathAssayGenerator/2.5+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2a9ff56cb279",
-                            "name": "openms_openswathassaygenerator",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"adv_opts_cond\": {\"adv_opts_selector\": \"advanced\", \"__current_case__\": 1, \"max_num_alternative_localizations\": \"10000\", \"disable_identification_ms2_precursors\": \"false\", \"disable_identification_specific_losses\": \"false\", \"enable_identification_unspecific_losses\": \"false\", \"enable_swath_specifity\": \"false\", \"force\": \"false\", \"test\": \"False\"}, \"allowed_fragment_charges\": \"1,2,3,4\", \"allowed_fragment_types\": \"b,y\", \"enable_detection_specific_losses\": \"false\", \"enable_detection_unspecific_losses\": \"false\", \"enable_ipf\": \"false\", \"in\": {\"__class__\": \"RuntimeValue\"}, \"max_transitions\": \"6\", \"min_transitions\": \"6\", \"out_type\": \"tsv\", \"precursor_lower_mz_limit\": \"400.0\", \"precursor_mz_threshold\": \"0.015\", \"precursor_upper_mz_limit\": \"1000.0\", \"product_lower_mz_limit\": \"350.0\", \"product_mz_threshold\": \"0.015\", \"product_upper_mz_limit\": \"2000.0\", \"swath_windows_file\": {\"__class__\": \"RuntimeValue\"}, \"unimod_file\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_id": "Summary_Statistics1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c8\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.2",
                         "type": "tool",
-                        "uuid": "ed923bff-cb4e-4d69-9b95-90c85e709fa2",
+                        "uuid": "2271282e-d599-4d40-9b0c-42adb142874f",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "b759b71c-1b1a-4240-9ee5-8294990dc07d"
+                                "output_name": "out_file1",
+                                "uuid": "ed52356c-4179-444a-9761-f7c0edf4c642"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator/2.5+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
                         "errors": null,
-                        "id": 9,
+                        "id": 21,
                         "input_connections": {
-                            "in": {
-                                "id": 8,
+                            "infile": {
+                                "id": 19,
                                 "output_name": "out"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool OpenSwathDecoyGenerator",
-                                "name": "in"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "OpenSwathDecoyGenerator",
+                        "name": "Select last",
                         "outputs": [
                             {
-                                "name": "out",
-                                "type": "data"
+                                "name": "outfile",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 345.8000030517578,
-                            "height": 174.8000030517578,
-                            "left": 797.5,
-                            "right": 997.5,
-                            "top": 171,
+                            "bottom": 485.1999969482422,
+                            "height": 93.19999694824219,
+                            "left": 1047,
+                            "right": 1247,
+                            "top": 392,
                             "width": 200,
-                            "x": 797.5,
-                            "y": 171
+                            "x": 1047,
+                            "y": 392
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator/2.5+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "f861ec9fbe59",
-                            "name": "openms_openswathdecoygenerator",
-                            "owner": "galaxyp",
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"adv_opts_cond\": {\"adv_opts_selector\": \"advanced\", \"__current_case__\": 1, \"min_decoy_fraction\": \"0.8\", \"aim_decoy_fraction\": \"1.0\", \"shuffle_max_attempts\": \"30\", \"shuffle_sequence_identity_threshold\": \"0.5\", \"shift_precursor_mz_shift\": \"0.0\", \"shift_product_mz_shift\": \"20.0\", \"product_mz_threshold\": \"0.015\", \"allowed_fragment_types\": \"b,y\", \"allowed_fragment_charges\": \"1,2,3,4\", \"enable_detection_specific_losses\": \"false\", \"enable_detection_unspecific_losses\": \"false\", \"separate\": \"false\", \"force\": \"false\", \"test\": \"False\"}, \"decoy_tag\": \"DECOY_\", \"in\": {\"__class__\": \"RuntimeValue\"}, \"method\": \"shuffle\", \"out_type\": \"tsv\", \"switchKR\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"csv\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"complement\": \"+\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"num_lines\": \"4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.0",
                         "type": "tool",
-                        "uuid": "fb0b6f0e-4a95-4fa0-80d3-8a6dfa0edf25",
+                        "uuid": "522bc5dc-d39a-4448-b887-848bb5cf5c55",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "c068a0cc-c6e9-44ac-bc64-9714b89841f7"
+                                "output_name": "outfile",
+                                "uuid": "52919249-1fb8-4481-95fc-ba6c40d4399c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_targetedfileconverter/TargetedFileConverter/2.5+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
                         "errors": null,
-                        "id": 10,
+                        "id": 22,
                         "input_connections": {
-                            "in": {
-                                "id": 9,
-                                "output_name": "out"
+                            "input": {
+                                "id": 21,
+                                "output_name": "outfile"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool TargetedFileConverter",
-                                "name": "in"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "TargetedFileConverter",
+                        "name": "Histogram",
                         "outputs": [
                             {
-                                "name": "out",
-                                "type": "data"
+                                "name": "out_file1",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "bottom": 325.3999938964844,
-                            "height": 154.39999389648438,
-                            "left": 1017.5,
-                            "right": 1217.5,
-                            "top": 171,
+                            "bottom": 365.1999969482422,
+                            "height": 93.19999694824219,
+                            "left": 1267,
+                            "right": 1467,
+                            "top": 272,
                             "width": 200,
-                            "x": 1017.5,
-                            "y": 171
+                            "x": 1267,
+                            "y": 272
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_targetedfileconverter/TargetedFileConverter/2.5+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
                         "tool_shed_repository": {
-                            "changeset_revision": "dd71e020e2aa",
-                            "name": "openms_targetedfileconverter",
-                            "owner": "galaxyp",
+                            "changeset_revision": "6f134426c2b0",
+                            "name": "histogram",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"adv_opts_cond\": {\"adv_opts_selector\": \"advanced\", \"__current_case__\": 1, \"legacy_traml_id\": \"false\", \"force\": \"false\", \"test\": \"False\"}, \"algorithm\": {\"retentionTimeInterpretation\": \"iRT\", \"override_group_label_check\": \"false\", \"force_invalid_mods\": \"false\"}, \"in\": {\"__class__\": \"RuntimeValue\"}, \"out_type\": \"pqp\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"breaks\": \"20\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"density\": \"true\", \"frequency\": \"false\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"numerical_column\": \"8\", \"title\": \"Histogram\", \"xlab\": \"V1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.4",
                         "type": "tool",
-                        "uuid": "c91c0e6d-282a-46ae-bb47-1425f1b0f1f3",
+                        "uuid": "67a0985f-236d-4b84-a51e-86c4cbf657b4",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "5721be8a-32ce-4d4d-8d50-6deeae3b61d2"
+                                "output_name": "out_file1",
+                                "uuid": "11f0da6d-4f57-487a-ae21-042b1d8badf6"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/DIA_lib_OSW",
-                "path": "topics/proteomics/tutorials/DIA_lib_OSW/workflows/Galaxy-Workflow-DIA_lib_Training_HEK_Ecoli_3_EG_data.ga",
+                "parent_id": "proteomics/protein-quant-sil",
+                "path": "topics/proteomics/tutorials/protein-quant-sil/workflows/workflow.ga",
                 "tags": [
                     "proteomics"
                 ],
                 "test_results": null,
+                "tests": true,
+                "title": "Proteomics: Peptide and Protein Quantification via stable istobe labeling",
+                "topic_id": "proteomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-protein-quant-sil/versions/workflow",
+                "tutorial_id": "protein-quant-sil",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/protein-quant-sil/workflows/workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/protein-quant-sil/workflows/workflow.html",
+                "version": 7,
+                "wfid": "proteomics-protein-quant-sil",
+                "wfname": "workflow",
+                "workflow": "workflow.ga",
+                "workflow_tools": [
+                    "Grep1",
+                    "Summary_Statistics1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_multiplexresolver/MultiplexResolver/2.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0"
+                ],
+                "workflowhub_id": "1215"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/1051552"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "maxquant",
+                    "owner": "galaxyp",
+                    "revisions": "1f39c833f65f",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: maxquant\n  owner: galaxyp\n  revisions: 1f39c833f65f\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "subinamehta",
+                "katherine-d21",
+                "dechendb"
+            ],
+            "editing": [
+                "pratikdjagtap",
+                "timothygriffin"
+            ]
+        },
+        "contributors": [
+            {
+                "email": "subinamehta@gmail.com",
+                "id": "subinamehta",
+                "joined": "2018-06",
+                "linkedin": "subinamehta",
+                "matrix": "subinamehta:matrix.org",
+                "name": "Subina Mehta",
+                "orcid": "0000-0001-9818-0537",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
+                "twitter": "Subina_Mehta",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
+            },
+            {
+                "id": "katherine-d21",
+                "joined": "2023-08",
+                "name": "Katherine Do",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/katherine-d21/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/katherine-d21.json"
+            },
+            {
+                "id": "dechendb",
+                "joined": "2023-06",
+                "name": "Dechen Bhuming",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dechendb/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/dechendb.json"
+            },
+            {
+                "email": "pjagtap@umn.edu",
+                "id": "pratikdjagtap",
+                "joined": "2017-09",
+                "name": "Pratik Jagtap",
+                "orcid": "0000-0003-0984-0973",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
+            },
+            {
+                "email": "tgriffin@umn.edu",
+                "github": false,
+                "id": "timothygriffin",
+                "joined": "2017-09",
+                "name": "Timothy J. Griffin",
+                "orcid": "0000-0001-6801-2559",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
+            }
+        ],
+        "dir": "topics/proteomics/tutorials/clinical-mp-4-quantitation",
+        "edam_operation": [
+            "Principal component plotting",
+            "Visualisation",
+            "Clustering",
+            "Protein quantification",
+            "Standardisation and normalisation",
+            "Imputation",
+            "Statistical calculation",
+            "Heat map generation"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "proteomics",
+                "tutorials": [
+                    "clinical-mp-5-data-interpretation"
+                ],
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "proteomics/clinical-mp-4-quantitation",
+        "inexact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.no"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Quantified Microbial and Human peptides/proteins can be analyzed separately so that the results are more comparative."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-08-08",
+        "objectives": [
+            "Perform quantitation using MaxQuant and extract microbial and human proteins and peptides."
+        ],
+        "pageviews": 74,
+        "pub_date": "2024-02-06",
+        "questions": [
+            "How to perform quantitation?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "katherine-d21"
+                ],
+                "date": "2024-06-21",
+                "galaxy_version": "23.1",
+                "length": "8M",
+                "speakers": [
+                    "katherine-d21"
+                ],
+                "youtube_id": "_e0l1AtfZ4Y"
+            }
+        ],
+        "redirect_from": [
+            "/topics/proteomics/tutorials/clinical-mp-quantitation/tutorial",
+            "/short/proteomics/clinical-mp-4-quantitation",
+            "/short/T00416"
+        ],
+        "requirements": [
+            {
+                "topic_name": "proteomics",
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00416",
+        "short_tools": [
+            "Grep1",
+            "Cut1",
+            "maxquant",
+            "Grouping1"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "clinical-metaproteomics",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "label-TMT11"
+        ],
+        "time_estimation": "3H",
+        "title": "Clinical Metaproteomics 4: Quantitation",
+        "tools": [
+            "Cut1",
+            "Grep1",
+            "Grouping1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.17.0+galaxy4"
+        ],
+        "topic_name": "proteomics",
+        "topic_name_human": "Proteomics",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "clinical-mp-4-quantitation",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.json"
+        },
+        "version": 2,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 317,
+        "visitors": 47,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Organization",
+                        "identifier": "0000-0001-9818-0537",
+                        "name": "Subina Mehta"
+                    }
+                ],
+                "description": "Quantification using the MaxQuant tool",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nQuantitation_Database-For-MaxQuant\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nExperimental-Design Discovery MaxQuant\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Raw-files\"]\n  3[label=\"MaxQuant\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Select\"]\n  3 -> 4 [label=\"proteinGroups\"]\n  5[label=\"Select\"]\n  3 -> 5 [label=\"peptides\"]\n  6[label=\"Cut\"]\n  4 -> 6 [label=\"out_file1\"]\n  7[label=\"Cut\"]\n  5 -> 7 [label=\"out_file1\"]\n  8[label=\"Group\"]\n  6 -> 8 [label=\"out_file1\"]\n  9[label=\"Group\"]\n  7 -> 9 [label=\"out_file1\"]\n}",
+                "history": [
+                    {
+                        "hash": "40391e78410baebc3f2ffd02ffbd1a3642903251",
+                        "message": "add missing metadata",
+                        "num": 2,
+                        "short_hash": "40391e784",
+                        "unix": "1723120010"
+                    },
+                    {
+                        "hash": "e0464fd1787b4ca7dea72ca77b7ab2ad03a8292a",
+                        "message": "add workflows",
+                        "num": 1,
+                        "short_hash": "e0464fd17",
+                        "unix": "1723118192"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Quantitation_Database-For-MaxQuant"
+                            }
+                        ],
+                        "label": "Quantitation_Database-For-MaxQuant",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0.0,
+                            "top": 0.0
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "c2311b55-b0c7-4237-bed1-4b25bf1a1655",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Experimental-Design Discovery MaxQuant"
+                            }
+                        ],
+                        "label": "Experimental-Design Discovery MaxQuant",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 69.76104736328125,
+                            "top": 268.9728088378906
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "d957f00d-79a9-4e2e-8e15-088444ca5605",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Input Raw-files"
+                            }
+                        ],
+                        "label": "Input Raw-files",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 41.42888775537051,
+                            "top": 531.8779602050781
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "2864b493-6d12-4313-ad29-f3b1e2564aba",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQuantitation_Database-For-MaxQuant\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nExperimental-Design Discovery MaxQuant\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nInput Raw-files\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"MaxQuant\"];\n  0 -->|output| 3;\n  2 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Select\"];\n  3 -->|proteinGroups| 4;\n  5[\"Select\"];\n  3 -->|peptides| 5;\n  6[\"Cut\"];\n  4 -->|out_file1| 6;\n  7[\"Cut\"];\n  5 -->|out_file1| 7;\n  8[\"Group\"];\n  6 -->|out_file1| 8;\n  9[\"Group\"];\n  7 -->|out_file1| 9;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "WF4_Quantitation_Workflow",
+                "outputs": [],
+                "parent_id": "proteomics/clinical-mp-4-quantitation",
+                "path": "topics/proteomics/tutorials/clinical-mp-4-quantitation/workflows/WF4_Quantitation_Workflow.ga",
+                "tags": [
+                    "name:clinicalMP"
+                ],
+                "test_results": null,
                 "tests": false,
-                "title": "DIA_lib_OSW",
+                "title": "WF4_Quantitation_Workflow",
                 "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-DIA_lib_OSW/versions/galaxy-workflow-dia-lib-training-hek-ecoli-3-eg-data",
-                "tutorial_id": "DIA_lib_OSW",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/DIA_lib_OSW/workflows/Galaxy-Workflow-DIA_lib_Training_HEK_Ecoli_3_EG_data.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/DIA_lib_OSW/workflows/Galaxy-Workflow-DIA_lib_Training_HEK_Ecoli_3_EG_data.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-clinical-mp-4-quantitation/versions/wf4-quantitation-workflow",
+                "tutorial_id": "clinical-mp-4-quantitation",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-4-quantitation/workflows/WF4_Quantitation_Workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-4-quantitation/workflows/WF4_Quantitation_Workflow.html",
                 "version": 1,
-                "wfid": "proteomics-DIA_lib_OSW",
-                "wfname": "galaxy-workflow-dia-lib-training-hek-ecoli-3-eg-data",
-                "workflow": "Galaxy-Workflow-DIA_lib_Training_HEK_Ecoli_3_EG_data.ga",
+                "wfid": "proteomics-clinical-mp-4-quantitation",
+                "wfname": "wf4-quantitation-workflow",
+                "workflow": "WF4_Quantitation_Workflow.ga",
                 "workflow_tools": [
-                    "Filter1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/diapysef/diapysef/0.3.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathassaygenerator/OpenSwathAssayGenerator/2.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator/2.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_targetedfileconverter/TargetedFileConverter/2.5+galaxy0"
+                    "Cut1",
+                    "Grep1",
+                    "Grouping1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.17.0+galaxy4"
                 ],
-                "workflowhub_id": "1224"
+                "workflowhub_id": "1353"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/4293493"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.10105821"
     },
     {
         "admin_install": {
@@ -181175,118 +183043,257 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "pdaug_addclasslabel",
-                    "owner": "jay",
-                    "revisions": "7160bfd77aef",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pdaug_basic_plots",
-                    "owner": "jay",
-                    "revisions": "15b6eec94c40",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "uniprot_rest_interface",
+                    "owner": "bgruening",
+                    "revisions": "054483e27a35",
+                    "tool_panel_section_label": "Convert Formats",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "uniprot_rest_interface",
+                    "owner": "bgruening",
+                    "revisions": "468c71dac78a",
+                    "tool_panel_section_label": "Convert Formats",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_to_tabular",
+                    "owner": "devteam",
+                    "revisions": "e7ed3c310b74",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "maxquant",
+                    "owner": "galaxyp",
+                    "revisions": "37d669de2828",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pdaug_merge_dataframes",
-                    "owner": "jay",
-                    "revisions": "2dbfb42d34bc",
+                    "name": "maxquant",
+                    "owner": "galaxyp",
+                    "revisions": "f522c08e900c",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pdaug_ml_models",
-                    "owner": "jay",
-                    "revisions": "aa0b1cb1260c",
+                    "name": "msstats",
+                    "owner": "galaxyp",
+                    "revisions": "593839e1f2c3",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pdaug_sequence_property_based_descriptors",
-                    "owner": "jay",
-                    "revisions": "187c6f2d3b55",
+                    "name": "msstats",
+                    "owner": "galaxyp",
+                    "revisions": "28434abe6c5c",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ggplot2_heatmap2",
+                    "owner": "iuc",
+                    "revisions": "ca7cb0eaad62",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: pdaug_addclasslabel\n  owner: jay\n  revisions: 7160bfd77aef\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_basic_plots\n  owner: jay\n  revisions: 15b6eec94c40\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_merge_dataframes\n  owner: jay\n  revisions: 2dbfb42d34bc\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_ml_models\n  owner: jay\n  revisions: aa0b1cb1260c\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_sequence_property_based_descriptors\n  owner: jay\n  revisions: 187c6f2d3b55\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: uniprot_rest_interface\n  owner: bgruening\n  revisions: '054483e27a35'\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: uniprot_rest_interface\n  owner: bgruening\n  revisions: 468c71dac78a\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_to_tabular\n  owner: devteam\n  revisions: e7ed3c310b74\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maxquant\n  owner: galaxyp\n  revisions: 37d669de2828\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maxquant\n  owner: galaxyp\n  revisions: f522c08e900c\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msstats\n  owner: galaxyp\n  revisions: 593839e1f2c3\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msstats\n  owner: galaxyp\n  revisions: 28434abe6c5c\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ggplot2_heatmap2\n  owner: iuc\n  revisions: ca7cb0eaad62\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.json",
         "contributors": [
             {
-                "id": "jaidevjoshi83",
-                "joined": "2020-11",
-                "name": "Jayadev Joshi",
-                "orcid": "0000-0001-7589-5230",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jaidevjoshi83/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jaidevjoshi83.json"
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "email": "melanie.foell@mol-med.uni-freiburg.de",
+                "id": "foellmelanie",
+                "joined": "2018-10",
+                "matrix": "foellmelanie:matrix.org",
+                "name": "Melanie F\u00f6ll",
+                "orcid": "0000-0002-1887-7543",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
+                "twitter": "MCFoell",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
             },
             {
-                "id": "blankenberg",
-                "joined": "2018-07",
-                "name": "Daniel Blankenberg",
-                "orcid": "0000-0002-6833-9049",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankenberg/",
-                "twitter": "dblankenberg",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankenberg.json"
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "email": "matthias.fahrner@uniklinik-freiburg.de",
+                "id": "matthias313",
+                "joined": "2019-03",
+                "name": "Matthias Fahrner",
+                "orcid": "0000-0001-7955-2518",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/matthias313/",
+                "twitter": "mfahrner313",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/matthias313.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides",
-        "edam_operation": [],
+        "dir": "topics/proteomics/tutorials/maxquant-msstats-dda-lfq",
+        "edam_operation": [
+            "Principal component plotting",
+            "Visualisation",
+            "Clustering",
+            "Protein quantification",
+            "Standardisation and normalisation",
+            "Imputation",
+            "Spectrum calculation",
+            "Differential protein expression profiling",
+            "Statistical calculation",
+            "Heat map generation",
+            "Tag-based peptide identification"
+        ],
         "edam_topic": [],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "proteomics/ml-modeling-of-anti-cancer-peptides",
-        "inexact_supported_servers": [],
+        "id": "proteomics/maxquant-msstats-dda-lfq",
+        "inexact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
+        "key_points": [
+            "MaxQuant offers a single tool solution for protein identification and quantification.",
+            "Label-free quantitation reveals the most abundant proteins in serum samples."
+        ],
         "layout": "tutorial_hands_on",
         "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-09-03",
         "objectives": [
-            "Learn, how to calculate peptide descriptor",
-            "Learn, how to create training data set from features?",
-            "Assessment of best ML algorithm in predicting anticancer peptide"
+            "Learn how to use MaxQuant and MSstats for the analysis of label-free shotgun (DDA) data"
         ],
-        "pageviews": 1295,
-        "pub_date": "2021-01-22",
+        "pageviews": 10703,
+        "pub_date": "2021-02-17",
         "questions": [
-            "Which machine learning (ML) algorithm is superior in classifying anticancer peptides (ACPs) and non-anticancer peptides (non-ACPs)?"
+            "How to perform label-free shotgun (DDA) data analysis in MaxQuant and MSstats?",
+            "Which proteins are differentially abundant in the two types of cutaneous squamous cell carcinomas?"
         ],
-        "short_id": "T00225",
+        "recordings": [
+            {
+                "captioners": [
+                    "foellmelanie"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "1H",
+                "speakers": [
+                    "foellmelanie"
+                ],
+                "youtube_id": "IXdLAt2PAT4"
+            }
+        ],
+        "requirements": [
+            {
+                "topic_name": "proteomics",
+                "tutorials": [
+                    "maxquant-label-free"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00219",
         "short_tools": [
-            "pdaug_sequence_property_based_descriptors",
-            "pdaug_basic_plots",
-            "pdaug_ml_models",
-            "pdaug_merge_dataframes",
-            "pdaug_addclasslabel"
+            "Summary_Statistics1",
+            "tp_easyjoin_tool",
+            "Filter1",
+            "ggplot2_heatmap2",
+            "Grep1",
+            "Cut1",
+            "maxquant",
+            "msstats",
+            "uniprot",
+            "fasta2tab",
+            "datamash_ops",
+            "tp_replace_in_column"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "property-prediction",
+        "subtopic": "id-quant",
         "supported_servers": {
-            "exact": [],
-            "inexact": []
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
         },
         "symlink": null,
         "tags": [
-            "ML",
-            "cancer"
+            "label-free"
         ],
-        "time_estimation": "30m",
-        "title": "Machine Learning Modeling of Anticancer Peptides",
+        "time_estimation": "2H",
+        "title": "MaxQuant and MSstats for the analysis of label-free data",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_addclasslabel/pdaug_addclasslabel/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_basic_plots/pdaug_basic_plots/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_merge_dataframes/pdaug_merge_dataframes/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_ml_models/pdaug_ml_models/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_sequence_property_based_descriptors/pdaug_sequence_property_based_descriptors/0.1.0"
+            "Cut1",
+            "Filter1",
+            "Grep1",
+            "Summary_Statistics1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.5",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy4",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.22.0.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/4.0.0.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/datamash_ops/1.0.6",
+            "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1"
         ],
         "topic_name": "proteomics",
         "topic_name_human": "Proteomics",
@@ -181296,37 +183303,51 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "ml-modeling-of-anti-cancer-peptides",
+        "tutorial_name": "maxquant-msstats-dda-lfq",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.json"
         },
-        "version": 8,
+        "version": 14,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 118,
-        "visitors": 845,
+        "visit_duration": 159,
+        "visitors": 6339,
         "workflows": [
             {
                 "creators": [],
-                "description": "ML Modeling of Anti-cancer Peptides",
+                "description": "MaxQuant and MSstats for the analysis of label-free data",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nACPs\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nnon-ACPs\"]\n  2[label=\"PDAUG Sequence Property Based Descriptors\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"PDAUG Sequence Property Based Descriptors\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"PDAUG Add Class Label\"]\n  2 -> 4 [label=\"output1\"]\n  5[label=\"PDAUG Add Class Label\"]\n  3 -> 5 [label=\"output1\"]\n  6[label=\"PDAUG Merge Dataframes\"]\n  4 -> 6 [label=\"OutFile1\"]\n  5 -> 6 [label=\"OutFile1\"]\n  7[label=\"PDAUG ML Models\"]\n  6 -> 7 [label=\"output1\"]\n  8[label=\"PDAUG ML Models\"]\n  6 -> 8 [label=\"output1\"]\n  9[label=\"PDAUG ML Models\"]\n  6 -> 9 [label=\"output1\"]\n  10[label=\"PDAUG ML Models\"]\n  6 -> 10 [label=\"output1\"]\n  11[label=\"PDAUG ML Models\"]\n  6 -> 11 [label=\"output1\"]\n  12[label=\"PDAUG ML Models\"]\n  6 -> 12 [label=\"output1\"]\n  13[label=\"PDAUG Merge Dataframes\"]\n  7 -> 13 [label=\"output1\"]\n  9 -> 13 [label=\"output1\"]\n  8 -> 13 [label=\"output1\"]\n  10 -> 13 [label=\"output1\"]\n  11 -> 13 [label=\"output1\"]\n  12 -> 13 [label=\"output1\"]\n  14[label=\"PDAUG Basic Plots\"]\n  13 -> 14 [label=\"output1\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nannotation file\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncomparison matrix\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nfasta protein database\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nraw files\"]\n  4[label=\"MaxQuant\"]\n  2 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"Select\"]\n  4 -> 5 [label=\"proteinGroups\"]\n  6[label=\"Select\"]\n  4 -> 6 [label=\"evidence\"]\n  7[label=\"Replace Text\"]\n  5 -> 7 [label=\"out_file1\"]\n  8[label=\"Replace Text\"]\n  6 -> 8 [label=\"out_file1\"]\n  9[label=\"MSstats\"]\n  1 -> 9 [label=\"output\"]\n  0 -> 9 [label=\"output\"]\n  8 -> 9 [label=\"outfile\"]\n  7 -> 9 [label=\"outfile\"]\n  10[label=\"Datamash\"]\n  9 -> 10 [label=\"runlevel_data\"]\n  11[label=\"Summary Statistics\"]\n  9 -> 11 [label=\"runlevel_data\"]\n  12[label=\"Replace Text\"]\n  9 -> 12 [label=\"comparison_result\"]\n  13[label=\"Replace Text\"]\n  9 -> 13 [label=\"quant_sample_matrix\"]\n  14[label=\"Filter\"]\n  12 -> 14 [label=\"outfile\"]\n  15[label=\"Filter\"]\n  14 -> 15 [label=\"out_file1\"]\n  16[label=\"Filter\"]\n  14 -> 16 [label=\"out_file1\"]\n  17[label=\"Filter\"]\n  15 -> 17 [label=\"out_file1\"]\n  18[label=\"Filter\"]\n  16 -> 18 [label=\"out_file1\"]\n  19[label=\"Cut\"]\n  17 -> 19 [label=\"out_file1\"]\n  20[label=\"Cut\"]\n  18 -> 20 [label=\"out_file1\"]\n  21[label=\"Join\"]\n  13 -> 21 [label=\"outfile\"]\n  19 -> 21 [label=\"out_file1\"]\n  22[label=\"Join\"]\n  13 -> 22 [label=\"outfile\"]\n  20 -> 22 [label=\"out_file1\"]\n  23[label=\"heatmap2\"]\n  21 -> 23 [label=\"output\"]\n  24[label=\"UniProt\"]\n  21 -> 24 [label=\"output\"]\n  25[label=\"heatmap2\"]\n  22 -> 25 [label=\"output\"]\n  26[label=\"UniProt\"]\n  22 -> 26 [label=\"output\"]\n  27[label=\"FASTA-to-Tabular\"]\n  24 -> 27 [label=\"outfile_retrieve_fasta\"]\n  28[label=\"FASTA-to-Tabular\"]\n  26 -> 28 [label=\"outfile_retrieve_fasta\"]\n}",
                 "history": [
                     {
-                        "hash": "c6cb67762f0c2d329bb52c6e6fb805df376f9ea0",
-                        "message": "Tutorials for PDAUG tool suite (#2150)",
+                        "hash": "e1daddc515c5b61f6c9170e1415a3ea9a43ea096",
+                        "message": "fixing broken boxes, adjusting results for actual set MSstats parameters",
+                        "num": 3,
+                        "short_hash": "e1daddc51",
+                        "unix": "1622784375"
+                    },
+                    {
+                        "hash": "0463f30a6b57a55c89db3bffafeef808eb170a51",
+                        "message": "changed Maxquant parameters and removed middle part of training",
+                        "num": 2,
+                        "short_hash": "0463f30a6",
+                        "unix": "1622722954"
+                    },
+                    {
+                        "hash": "ae8154eef553947defbdf59c7ae4460dffbb33d9",
+                        "message": "Adding new maxquant msstats tutorial",
                         "num": 1,
-                        "short_hash": "c6cb67762",
-                        "unix": "1611340147"
+                        "short_hash": "ae8154eef",
+                        "unix": "1613563165"
                     }
                 ],
                 "inputs": [
@@ -181339,1786 +183360,1476 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "ACPs"
+                                "name": "annotation file"
                             }
                         ],
-                        "label": "ACPs",
+                        "label": "annotation file",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 136.59375,
-                            "top": 125.359375
+                            "bottom": 315.78334045410156,
+                            "height": 81.95001220703125,
+                            "left": -341.33331298828125,
+                            "right": -141.33331298828125,
+                            "top": 233.8333282470703,
+                            "width": 200,
+                            "x": -341.33331298828125,
+                            "y": 233.8333282470703
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "471cb99c-89a3-4e6e-930a-b344d2b44b14",
-                        "workflow_outputs": [
+                        "uuid": "1884c487-3263-45f5-a735-61c3a466b830",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "6b2eaf3c-5598-44ce-a7e8-5f6e262c92b0"
+                                "description": "",
+                                "name": "comparison matrix"
                             }
-                        ]
+                        ],
+                        "label": "comparison matrix",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 491.7833251953125,
+                            "height": 81.95001220703125,
+                            "left": -341.33331298828125,
+                            "right": -141.33331298828125,
+                            "top": 409.83331298828125,
+                            "width": 200,
+                            "x": -341.33331298828125,
+                            "y": 409.83331298828125
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ba82de42-628d-44c4-9795-33d8924a37b1",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "non-ACPs"
+                                "name": "fasta protein database"
                             }
                         ],
-                        "label": "non-ACPs",
+                        "label": "fasta protein database",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 134,
-                            "top": 202.328125
+                            "bottom": 633.7833251953125,
+                            "height": 81.95001220703125,
+                            "left": -264.48333740234375,
+                            "right": -64.48333740234375,
+                            "top": 551.8333129882812,
+                            "width": 200,
+                            "x": -264.48333740234375,
+                            "y": 551.8333129882812
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "1690c4bb-afa2-47cf-9a34-381d59ac348d",
-                        "workflow_outputs": [
+                        "uuid": "740e4036-bc46-44cc-b270-1b3962760293",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "raw files"
+                            }
+                        ],
+                        "label": "raw files",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 737.3833160400391,
+                            "height": 61.55000305175781,
+                            "left": -273.816650390625,
+                            "right": -73.816650390625,
+                            "top": 675.8333129882812,
+                            "width": 200,
+                            "x": -273.816650390625,
+                            "y": 675.8333129882812
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "20726c07-2b97-4f61-8ece-02d09df86a21",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nannotation file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ncomparison matrix\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nfasta protein database\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Collection\\nraw files\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"MaxQuant\"];\n  2 -->|output| 4;\n  3 -->|output| 4;\n  5[\"Select\"];\n  4 -->|proteinGroups| 5;\n  6[\"Select\"];\n  4 -->|evidence| 6;\n  7[\"Replace Text\"];\n  5 -->|out_file1| 7;\n  8[\"Replace Text\"];\n  6 -->|out_file1| 8;\n  9[\"MSstats\"];\n  1 -->|output| 9;\n  0 -->|output| 9;\n  8 -->|outfile| 9;\n  7 -->|outfile| 9;\n  10[\"Datamash\"];\n  9 -->|runlevel_data| 10;\n  11[\"Summary Statistics\"];\n  9 -->|runlevel_data| 11;\n  12[\"Replace Text\"];\n  9 -->|comparison_result| 12;\n  13[\"Replace Text\"];\n  9 -->|quant_sample_matrix| 13;\n  14[\"Filter\"];\n  12 -->|outfile| 14;\n  15[\"Filter\"];\n  14 -->|out_file1| 15;\n  16[\"Filter\"];\n  14 -->|out_file1| 16;\n  17[\"Filter\"];\n  15 -->|out_file1| 17;\n  18[\"Filter\"];\n  16 -->|out_file1| 18;\n  19[\"Cut\"];\n  17 -->|out_file1| 19;\n  20[\"Cut\"];\n  18 -->|out_file1| 20;\n  21[\"Join\"];\n  13 -->|outfile| 21;\n  19 -->|out_file1| 21;\n  22[\"Join\"];\n  13 -->|outfile| 22;\n  20 -->|out_file1| 22;\n  23[\"heatmap2\"];\n  21 -->|output| 23;\n  24[\"UniProt\"];\n  21 -->|output| 24;\n  25[\"heatmap2\"];\n  22 -->|output| 25;\n  26[\"UniProt\"];\n  22 -->|output| 26;\n  27[\"FASTA-to-Tabular\"];\n  24 -->|outfile_retrieve_fasta| 27;\n  28[\"FASTA-to-Tabular\"];\n  26 -->|outfile_retrieve_fasta| 28;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Proteomics: MaxQuant and MSstats LFQ workflow",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy4",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "input_opts|fasta_files": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "paramGroups_0|files": {
+                                "id": 3,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "MaxQuant",
+                        "outputs": [
+                            {
+                                "name": "proteinGroups",
+                                "type": "tabular"
+                            },
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "6449070c-3e6b-4088-98a4-dcb7449bf279"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nACPs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nnon-ACPs\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"PDAUG Sequence Property Based Descriptors\"];\n  0 -->|output| 2;\n  3[\"PDAUG Sequence Property Based Descriptors\"];\n  1 -->|output| 3;\n  4[\"PDAUG Add Class Label\"];\n  2 -->|output1| 4;\n  5[\"PDAUG Add Class Label\"];\n  3 -->|output1| 5;\n  6[\"PDAUG Merge Dataframes\"];\n  4 -->|OutFile1| 6;\n  5 -->|OutFile1| 6;\n  7[\"PDAUG ML Models\"];\n  6 -->|output1| 7;\n  8[\"PDAUG ML Models\"];\n  6 -->|output1| 8;\n  9[\"PDAUG ML Models\"];\n  6 -->|output1| 9;\n  10[\"PDAUG ML Models\"];\n  6 -->|output1| 10;\n  11[\"PDAUG ML Models\"];\n  6 -->|output1| 11;\n  12[\"PDAUG ML Models\"];\n  6 -->|output1| 12;\n  13[\"PDAUG Merge Dataframes\"];\n  7 -->|output1| 13;\n  9 -->|output1| 13;\n  8 -->|output1| 13;\n  10 -->|output1| 13;\n  11 -->|output1| 13;\n  12 -->|output1| 13;\n  14[\"PDAUG Basic Plots\"];\n  13 -->|output1| 14;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "PeptideML",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                                "name": "evidence",
+                                "type": "tabular"
+                            },
                             {
-                                "description": "",
-                                "name": "ACPs"
+                                "name": "ptxqc_report",
+                                "type": "pdf"
                             }
                         ],
-                        "label": "ACPs",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 136.59375,
-                            "top": 125.359375
+                            "bottom": 825.7666625976562,
+                            "height": 357.26666259765625,
+                            "left": 61.33332824707031,
+                            "right": 261.3333282470703,
+                            "top": 468.5,
+                            "width": 200,
+                            "x": 61.33332824707031,
+                            "y": 468.5
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "471cb99c-89a3-4e6e-930a-b344d2b44b14",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f522c08e900c",
+                            "name": "maxquant",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"__workflow_invocation_uuid__\": \"a5b196c8c2c611eb9ee3001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_opts\": {\"ftype\": \".thermo.raw\", \"fasta_files\": {\"__class__\": \"ConnectedValue\"}, \"identifier_parse_rule\": \">([^\\\\s]*)\", \"description_parse_rule\": \">(.*)\"}, \"output_opts\": {\"dry_run\": \"false\", \"output\": [\"proteinGroups\", \"evidence\"]}, \"paramGroups\": [{\"__index__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}, \"maxMissedCleavages\": \"2\", \"fixedModifications\": [\"Carbamidomethyl (C)\"], \"variableModifications\": [\"Acetyl (Protein N-term)\", \"Oxidation (M)\"], \"enzymes\": [\"Trypsin/P\"], \"digestion_mode\": \"0\", \"quant_method\": {\"select_quant_method\": \"lfq\", \"__current_case__\": 2, \"lfqMinRatioCount\": \"2\", \"lfqMinEdgesPerNode\": \"3\", \"lfqAvEdgesPerNode\": \"6\", \"lfqSkipNorm\": \"true\"}}], \"protein_quant\": {\"peptides_for_quantification\": \"1\", \"only_unmod_prot\": {\"unmod_prot\": \"True\", \"__current_case__\": 0, \"mods_used_prot_quant\": [\"Acetyl (Protein N-term)\", \"Oxidation (M)\"], \"discard_unmod_cpart_peptides\": \"true\"}, \"lfq_opts\": {\"separateLfq\": \"false\", \"lfqStabilizeLargeRatios\": \"true\", \"lfqRequireMsms\": \"true\", \"do_ibaq\": {\"ibaq\": \"False\", \"__current_case__\": 1}, \"advancedSiteIntensities\": \"true\"}}, \"qc\": {\"do_it\": \"true\", \"__current_case__\": 0, \"parameters\": \"true\", \"summary\": \"true\", \"proteingroups\": \"true\", \"evidence\": \"true\", \"msms\": \"true\", \"msmsscans\": \"true\"}, \"search_opts\": {\"template\": null, \"min_peptide_len\": \"7\", \"max_peptide_mass\": \"4600\", \"min_unique_pep\": \"1\", \"calc_peak_properties\": \"false\", \"mbr\": {\"match_between_runs\": \"True\", \"__current_case__\": 1, \"matching_time_window\": \"0.7\", \"matching_ion_mobility_window\": \"0.05\", \"alignment_time_window\": \"20\", \"alignment_ion_mobility_window\": \"1\", \"match_unidentified_features\": \"false\"}, \"incl_contaminants\": \"true\", \"decoy_mode\": \"revert\", \"psm_fdr\": \"0.01\", \"protein_fdr\": \"0.01\", \"min_pep_length\": \"8\", \"max_pep_length\": \"25\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.6.10.43+galaxy4",
+                        "type": "tool",
+                        "uuid": "8eb1e949-4cfc-402e-971a-1ab02dd124db",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "6b2eaf3c-5598-44ce-a7e8-5f6e262c92b0"
+                                "output_name": "ptxqc_report",
+                                "uuid": "934770a0-48e9-4901-b9a5-8c9dd97f6ef1"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "proteinGroups",
+                                "uuid": "f6a17442-5d9b-4972-9b94-2ff2f55c02ff"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "evidence",
+                                "uuid": "51525532-28c7-4e01-951f-8886fc19dedf"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "Grep1",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 5,
+                        "input_connections": {
+                            "input": {
+                                "id": 4,
+                                "output_name": "proteinGroups"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Select",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "non-ACPs"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
-                        "label": "non-ACPs",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 134,
-                            "top": 202.328125
+                            "bottom": 268.03334045410156,
+                            "height": 92.86666870117188,
+                            "left": 76,
+                            "right": 276,
+                            "top": 175.1666717529297,
+                            "width": 200,
+                            "x": 76,
+                            "y": 175.1666717529297
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "1690c4bb-afa2-47cf-9a34-381d59ac348d",
+                        "post_job_actions": {},
+                        "tool_id": "Grep1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"false\", \"pattern\": \"(HUMAN)|(Majority)\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.1",
+                        "type": "tool",
+                        "uuid": "955e509e-f02c-4b30-ac4f-b2dd66a23468",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "6449070c-3e6b-4088-98a4-dcb7449bf279"
+                                "output_name": "out_file1",
+                                "uuid": "e36fbdbe-c076-4efd-b792-1c6e3f190b14"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_sequence_property_based_descriptors/pdaug_sequence_property_based_descriptors/0.1.0",
+                        "content_id": "Grep1",
                         "errors": null,
-                        "id": 2,
+                        "id": 6,
                         "input_connections": {
-                            "input1": {
-                                "id": 0,
-                                "output_name": "output"
+                            "input": {
+                                "id": 4,
+                                "output_name": "evidence"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "PDAUG Sequence Property Based Descriptors",
+                        "name": "Select",
                         "outputs": [
                             {
-                                "name": "output1",
-                                "type": "tabular"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 325.609375,
-                            "top": 142.703125
+                            "bottom": 388.0333557128906,
+                            "height": 92.86666870117188,
+                            "left": 76,
+                            "right": 276,
+                            "top": 295.16668701171875,
+                            "width": 200,
+                            "x": 76,
+                            "y": 295.16668701171875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_sequence_property_based_descriptors/pdaug_sequence_property_based_descriptors/0.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6b6aec52638d",
-                            "name": "pdaug_sequence_property_based_descriptors",
-                            "owner": "jay",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"SelectDiscriptor\": {\"DesType\": \"CTD\", \"__current_case__\": 9}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.0",
+                        "tool_id": "Grep1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"false\", \"pattern\": \"(HUMAN)|(Sequence)\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.1",
                         "type": "tool",
-                        "uuid": "d751bc15-62a7-4c2b-959d-ec32b7bf9929",
+                        "uuid": "5e5ab4af-2096-4cd6-a93d-adec152e4bdd",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output1",
-                                "uuid": "4ce6e57c-1fb3-4ccb-857a-13f1a50e3fe7"
+                                "output_name": "out_file1",
+                                "uuid": "d5069d61-91f6-4580-9574-a80962e19a43"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_addclasslabel/pdaug_addclasslabel/0.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
                         "errors": null,
-                        "id": 4,
+                        "id": 7,
                         "input_connections": {
-                            "input1": {
-                                "id": 2,
-                                "output_name": "output1"
+                            "infile": {
+                                "id": 5,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "PDAUG Add Class Label",
+                        "name": "Replace Text",
                         "outputs": [
                             {
-                                "name": "OutFile1",
-                                "type": "tabular"
+                                "name": "outfile",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 517.234375,
-                            "top": 142.703125
+                            "bottom": 268.03334045410156,
+                            "height": 92.86666870117188,
+                            "left": 296,
+                            "right": 496,
+                            "top": 175.1666717529297,
+                            "width": 200,
+                            "x": 296,
+                            "y": 175.1666717529297
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_addclasslabel/pdaug_addclasslabel/0.1.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "2df11ea23f10",
-                            "name": "pdaug_addclasslabel",
-                            "owner": "jay",
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"ClassLabel\": \"0\", \"ClassLabelTitle\": \"Class_label\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.0",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"column\": \"118\", \"find_pattern\": \"+\", \"replace_pattern\": \"\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.3",
                         "type": "tool",
-                        "uuid": "37498ada-bad4-456d-91e6-f21a6fe98c5d",
+                        "uuid": "fdeab669-5c90-4169-9b10-969ed89bbdc7",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "OutFile1",
-                                "uuid": "47d6dd33-c08f-4818-87f5-02eb73dc97b5"
+                                "output_name": "outfile",
+                                "uuid": "0e37dd18-2246-456e-b03b-9da9f7b11ebd"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_merge_dataframes/pdaug_merge_dataframes/0.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
                         "errors": null,
-                        "id": 6,
+                        "id": 8,
                         "input_connections": {
-                            "input1": [
-                                {
-                                    "id": 4,
-                                    "output_name": "OutFile1"
-                                },
-                                {
-                                    "id": 5,
-                                    "output_name": "OutFile1"
-                                }
-                            ]
+                            "infile": {
+                                "id": 6,
+                                "output_name": "out_file1"
+                            }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "PDAUG Merge Dataframes",
+                        "name": "Replace Text",
                         "outputs": [
                             {
-                                "name": "output1",
-                                "type": "tabular"
+                                "name": "outfile",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 708.859375,
-                            "top": 142.703125
+                            "bottom": 388.0333557128906,
+                            "height": 92.86666870117188,
+                            "left": 296,
+                            "right": 496,
+                            "top": 295.16668701171875,
+                            "width": 200,
+                            "x": 296,
+                            "y": 295.16668701171875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_merge_dataframes/pdaug_merge_dataframes/0.1.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "5bb52d4bf172",
-                            "name": "pdaug_merge_dataframes",
-                            "owner": "jay",
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.0",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"column\": \"54\", \"find_pattern\": \"+\", \"replace_pattern\": \"\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.3",
                         "type": "tool",
-                        "uuid": "f8d1b048-a859-40d0-9572-f3a21230229d",
+                        "uuid": "3e0d0a18-3cfb-4c90-a9e2-9fdc3af29786",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output1",
-                                "uuid": "98bb1ac8-f0a1-48fa-9e77-55f0df88c35f"
+                                "output_name": "outfile",
+                                "uuid": "00a0fa1a-91e7-4034-9484-cb788ccf6b16"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_ml_models/pdaug_ml_models/0.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.22.0.1",
                         "errors": null,
-                        "id": 7,
+                        "id": 9,
                         "input_connections": {
-                            "input1": {
-                                "id": 6,
-                                "output_name": "output1"
+                            "group|comparison_matrix": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "input|annotation": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "input|evidence": {
+                                "id": 8,
+                                "output_name": "outfile"
+                            },
+                            "input|proteinGroups": {
+                                "id": 7,
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool PDAUG ML Models",
-                                "name": "input1"
+                                "description": "runtime parameter for tool MSstats",
+                                "name": "group"
+                            },
+                            {
+                                "description": "runtime parameter for tool MSstats",
+                                "name": "input"
+                            },
+                            {
+                                "description": "runtime parameter for tool MSstats",
+                                "name": "input"
+                            },
+                            {
+                                "description": "runtime parameter for tool MSstats",
+                                "name": "input"
                             }
                         ],
                         "label": null,
-                        "name": "PDAUG ML Models",
+                        "name": "MSstats",
                         "outputs": [
                             {
-                                "name": "output1",
+                                "name": "log",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "processed_data",
                                 "type": "tabular"
                             },
                             {
-                                "name": "output2",
-                                "type": "html"
+                                "name": "runlevel_data",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "QCPlot",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "quant_sample_matrix",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "quant_group_matrix",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "comparison_result",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "VolcanoPlot",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "left": 900.46875,
-                            "top": 142.703125
+                            "bottom": 918.8332977294922,
+                            "height": 743.6666259765625,
+                            "left": 516,
+                            "right": 716,
+                            "top": 175.1666717529297,
+                            "width": 200,
+                            "x": 516,
+                            "y": 175.1666717529297
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_ml_models/pdaug_ml_models/0.1.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.22.0.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "0973f093d98f",
-                            "name": "pdaug_ml_models",
-                            "owner": "jay",
+                            "changeset_revision": "593839e1f2c3",
+                            "name": "msstats",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"SelMLAlgo\": {\"MLAlgo\": \"SVMC\", \"__current_case__\": 0, \"settings\": {\"advanced\": \"simple\", \"__current_case__\": 0}}, \"TestMethods\": {\"SelTestMethods\": \"Internal\", \"__current_case__\": 0, \"nFolds\": \"10\"}, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"scalling\": \"Min_Max\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.0",
+                        "tool_state": "{\"dp_options\": {\"selected_outputs\": [\"log\", \"processed_data\", \"runlevel_data\", \"quant_sample_matrix\", \"quant_group_matrix\"], \"logTrans\": \"2\", \"norm\": {\"normalization\": \"equalizeMedians\", \"__current_case__\": 0}, \"fillIncompleteRows\": \"true\", \"features\": {\"featureSubset\": \"all\", \"__current_case__\": 0}, \"summarize\": {\"summaryMethod\": \"TMP\", \"__current_case__\": 0, \"MBimpute\": \"true\", \"remove50missing\": \"false\"}, \"censoredInt\": \"NA\", \"cutoffCensored\": \"minFeature\", \"maxQuantileforCensored\": \"0.999\", \"out_plots_opt\": {\"selected_vis_outputs\": [\"QCPlot\"], \"which_Protein\": {\"select\": \"allonly\", \"__current_case__\": 1}, \"width\": \"8\", \"height\": \"5\", \"proc_plots_advanced\": {\"featureName\": \"Transition\", \"ylimUp\": null, \"ylimDown\": null, \"scale\": \"false\", \"interval\": \"CI\", \"x_axis_size\": \"10\", \"y_axis_size\": \"10\", \"text_size\": \"4\", \"text_angle\": \"0\", \"legend_size\": \"7\", \"dot_size_profile\": \"2\", \"dot_size_condition\": \"3\", \"remove_uninformative_feature_outlier\": \"false\"}}}, \"group\": {\"group_comparison\": \"yes\", \"__current_case__\": 1, \"comparison_matrix\": {\"__class__\": \"RuntimeValue\"}, \"select_outputs\": [\"comparison_result\"], \"comparison_plots_opt\": {\"select_comparison_plots\": [\"VolcanoPlot\"], \"width\": \"8\", \"height\": \"5\", \"which_Protein\": {\"select\": \"all\", \"__current_case__\": 0}, \"comparison_vis_options\": {\"sig\": \"0.05\", \"FCcutoff\": \"1.5\", \"logBase_pvalue\": \"10\", \"ylimUp\": null, \"ylimDown\": null, \"xlimUp\": null, \"axis_size\": \"10\", \"x_axis_size\": \"10\", \"y_axis_size\": \"10\", \"dot_size\": \"3\", \"text_size\": \"4\", \"text_angle\": \"90\", \"legend_size\": \"7\", \"ProteinName\": \"false\", \"colorkey\": \"true\", \"numProtein\": \"100\", \"clustering\": \"protein\", \"which_Comparison\": {\"select\": \"all\", \"__current_case__\": 0}}}}, \"input\": {\"input_src\": \"MaxQuant\", \"__current_case__\": 1, \"evidence\": {\"__class__\": \"RuntimeValue\"}, \"proteinGroups\": {\"__class__\": \"RuntimeValue\"}, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"proteinID\": \"Leading.razor.protein\", \"input_options\": {\"useUniquePeptide\": \"true\", \"summaryforMultipleRows\": \"max\", \"fewMeasurements\": \"remove\", \"removeMpeptides\": \"false\", \"removeOxidationMpeptides\": \"false\", \"removeProtein_with1Peptide\": \"true\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.22.0.1",
                         "type": "tool",
-                        "uuid": "670d3053-75fe-4e1f-80a3-ca5a8d46448c",
+                        "uuid": "b3968b97-c518-4333-be78-a10676d0c260",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output1",
-                                "uuid": "bf8f300a-b4d8-448b-9b6a-ce55bb5cb1a1"
+                                "output_name": "comparison_result",
+                                "uuid": "5d3ee1c6-32bb-4899-b7e7-e84477cc2127"
                             },
                             {
                                 "label": null,
-                                "output_name": "output2",
-                                "uuid": "18a6b311-3cf4-4d6e-9fea-62b9633a9953"
+                                "output_name": "log",
+                                "uuid": "1dd1ac5c-eb19-4b9c-8786-b72776ebb1a4"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "processed_data",
+                                "uuid": "7549686d-4219-4c17-9f4d-5d1ed7bb92cf"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "QCPlot",
+                                "uuid": "44092c24-df36-4d05-91ae-5fca98f4bc36"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "quant_sample_matrix",
+                                "uuid": "6aa35c51-4144-4aec-a597-4591386279b1"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "quant_group_matrix",
+                                "uuid": "0c980fd2-d34a-4fb0-8adb-2e974c8261f0"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "runlevel_data",
+                                "uuid": "14636105-8e4d-4f00-8da1-5468aa830132"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "VolcanoPlot",
+                                "uuid": "91943356-70a8-4598-a24e-4ac6f6354e1c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_merge_dataframes/pdaug_merge_dataframes/0.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/datamash_ops/1.0.6",
                         "errors": null,
-                        "id": 13,
+                        "id": 10,
                         "input_connections": {
-                            "input1": [
-                                {
-                                    "id": 7,
-                                    "output_name": "output1"
-                                },
-                                {
-                                    "id": 9,
-                                    "output_name": "output1"
-                                },
-                                {
-                                    "id": 8,
-                                    "output_name": "output1"
-                                },
-                                {
-                                    "id": 10,
-                                    "output_name": "output1"
-                                },
-                                {
-                                    "id": 11,
-                                    "output_name": "output1"
-                                },
-                                {
-                                    "id": 12,
-                                    "output_name": "output1"
-                                }
-                            ]
+                            "in_file": {
+                                "id": 9,
+                                "output_name": "runlevel_data"
+                            }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "PDAUG Merge Dataframes",
+                        "name": "Datamash",
                         "outputs": [
                             {
-                                "name": "output1",
+                                "name": "out_file",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1092.09375,
-                            "top": 142.703125
+                            "bottom": 288.43333435058594,
+                            "height": 113.26666259765625,
+                            "left": 736,
+                            "right": 936,
+                            "top": 175.1666717529297,
+                            "width": 200,
+                            "x": 736,
+                            "y": 175.1666717529297
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_merge_dataframes/pdaug_merge_dataframes/0.1.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/datamash_ops/1.0.6",
                         "tool_shed_repository": {
-                            "changeset_revision": "5bb52d4bf172",
-                            "name": "pdaug_merge_dataframes",
-                            "owner": "jay",
+                            "changeset_revision": "2f3c6f2dcf39",
+                            "name": "datamash_ops",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.0",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"grouping\": \"8\", \"header_in\": \"true\", \"header_out\": \"true\", \"ignore_case\": \"false\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"need_sort\": \"true\", \"operations\": [{\"__index__\": 0, \"op_name\": \"count\", \"op_column\": \"1\"}], \"print_full_line\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.6",
                         "type": "tool",
-                        "uuid": "c5de6791-d223-450d-af1b-df0334d30290",
+                        "uuid": "4c334a37-a534-46b0-9d1c-9d0c1e91b8e7",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output1",
-                                "uuid": "1261809f-eb67-4012-84bb-24770f3177a2"
+                                "output_name": "out_file",
+                                "uuid": "9897b924-bd51-46f3-8e86-2282f96be68b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_basic_plots/pdaug_basic_plots/0.1.0",
+                        "content_id": "Summary_Statistics1",
                         "errors": null,
-                        "id": 14,
+                        "id": 11,
                         "input_connections": {
-                            "SelPlotting|InFile": {
-                                "id": 13,
-                                "output_name": "output1"
+                            "input": {
+                                "id": 9,
+                                "output_name": "runlevel_data"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "PDAUG Basic Plots",
+                        "name": "Summary Statistics",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "html"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1283.6875,
-                            "top": 142.703125
+                            "bottom": 408.433349609375,
+                            "height": 113.26666259765625,
+                            "left": 736,
+                            "right": 936,
+                            "top": 295.16668701171875,
+                            "width": 200,
+                            "x": 736,
+                            "y": 295.16668701171875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_basic_plots/pdaug_basic_plots/0.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "7d247e27ff11",
-                            "name": "pdaug_basic_plots",
-                            "owner": "jay",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"SelPlotting\": {\"Plot\": \"HeatMap\", \"__current_case__\": 0, \"InFile\": {\"__class__\": \"ConnectedValue\"}, \"IndexColumn\": \"Algo\", \"x_label\": \"Performance measures\", \"y_label\": \"ML algorithms \"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.0",
+                        "tool_id": "Summary_Statistics1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c4\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.2",
                         "type": "tool",
-                        "uuid": "dad0ec0d-cef5-49f9-8592-f83bb8cb03e5",
+                        "uuid": "14d4f8b8-2729-41b1-9f10-58eafdb43d5f",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "8e28f651-ba58-43dc-b894-074fe90aa50a"
+                                "output_name": "out_file1",
+                                "uuid": "105467da-afe7-470f-b3d3-1868ab1e2e50"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "proteomics/ml-modeling-of-anti-cancer-peptides",
-                "path": "topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/workflows/PeptideML.ga",
-                "tags": [
-                    "proteomics"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "PeptideML",
-                "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-ml-modeling-of-anti-cancer-peptides/versions/peptideml",
-                "tutorial_id": "ml-modeling-of-anti-cancer-peptides",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/workflows/PeptideML.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/workflows/PeptideML.html",
-                "version": 1,
-                "wfid": "proteomics-ml-modeling-of-anti-cancer-peptides",
-                "wfname": "peptideml",
-                "workflow": "PeptideML.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_addclasslabel/pdaug_addclasslabel/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_basic_plots/pdaug_basic_plots/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_merge_dataframes/pdaug_merge_dataframes/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_ml_models/pdaug_ml_models/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_sequence_property_based_descriptors/pdaug_sequence_property_based_descriptors/0.1.0"
-                ],
-                "workflowhub_id": "1196"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.4111092"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/ntails/tutorial.json",
-        "contributors": [
-            {
-                "email": "sigloch+github@mailbox.org",
-                "former_affiliations": [
-                    "uni-freiburg"
-                ],
-                "id": "stortebecker",
-                "joined": "2017-09",
-                "name": "Florian Christoph Sigloch",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stortebecker/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/stortebecker.json"
-            },
-            {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
-                "fediverse_flavor": "mastodon",
-                "id": "bgruening",
-                "joined": "2017-09",
-                "linkedin": "bgruening",
-                "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
-                },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
-            }
-        ],
-        "dir": "topics/proteomics/tutorials/ntails",
-        "edam_ontology": [
-            "topic_0121"
-        ],
-        "edam_operation": [],
-        "edam_topic": [
-            "Proteomics"
-        ],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "proteomics/ntails",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "N-TAILS enriches natural protein N-termini and neo-N-termini.",
-            "neo-N-termini are typically generated by protease cleavage.",
-            "N-TAILS can be used for analysis of protease cleavage."
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-05-16",
-        "objectives": [
-            "Run an N-TAILS data analysis."
-        ],
-        "pageviews": 972,
-        "pub_date": "2017-02-14",
-        "questions": [
-            "How can protein N-termini be enriched for LC-MS/MS?",
-            "How to analyze the LC-MS/MS data?"
-        ],
-        "short_id": "T00226",
-        "short_tools": [
-            "MzTabExporter",
-            "FileMerger",
-            "FalseDiscoveryRate",
-            "IDConflictResolver",
-            "MSGFPlusAdapter",
-            "FeatureFinderMultiplex",
-            "PeptideIndexer",
-            "ConsensusID",
-            "HighResPrecursorMassCorrector",
-            "FileFilter",
-            "IDFilter",
-            "IDMerger",
-            "IDMapper"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "special",
-        "supported_servers": {
-            "exact": [],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [],
-        "time_estimation": "1h",
-        "title": "Detection and quantitation of N-termini (degradomics) via N-TAILS",
-        "tools": [
-            "ConsensusID",
-            "FalseDiscoveryRate",
-            "FeatureFinderMultiplex",
-            "FileFilter",
-            "FileMerger",
-            "HighResPrecursorMassCorrector",
-            "IDConflictResolver",
-            "IDFilter",
-            "IDMapper",
-            "IDMerger",
-            "MSGFPlusAdapter",
-            "MzTabExporter",
-            "PeptideIndexer"
-        ],
-        "topic_name": "proteomics",
-        "topic_name_human": "Proteomics",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "ntails",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/ntails/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/ntails/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/ntails/tutorial.json"
-        },
-        "version": 15,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 86,
-        "visitors": 664,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Detection and quantitation of N-termini (degradomics) via N-TAILS",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[label=\"FeatureFinderMultiplex\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"HighResPrecursorMassCorrector\"]\n  2 -> 3 [label=\"param_out_features\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"MSGFPlusAdapter\"]\n  1 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"param_out\"]\n  5[label=\"MSGFPlusAdapter\"]\n  1 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"param_out\"]\n  6[label=\"MSGFPlusAdapter\"]\n  3 -> 6 [label=\"param_out\"]\n  7[label=\"PeptideIndexer\"]\n  1 -> 7 [label=\"output\"]\n  4 -> 7 [label=\"param_out\"]\n  8[label=\"PeptideIndexer\"]\n  1 -> 8 [label=\"output\"]\n  5 -> 8 [label=\"param_out\"]\n  9[label=\"PeptideIndexer\"]\n  1 -> 9 [label=\"output\"]\n  6 -> 9 [label=\"param_out\"]\n  10[label=\"IDMerger\"]\n  7 -> 10 [label=\"param_out\"]\n  8 -> 10 [label=\"param_out\"]\n  9 -> 10 [label=\"param_out\"]\n  11[label=\"ConsensusID\"]\n  10 -> 11 [label=\"param_out\"]\n  12[label=\"PeptideIndexer\"]\n  1 -> 12 [label=\"output\"]\n  11 -> 12 [label=\"param_out\"]\n  13[label=\"FalseDiscoveryRate\"]\n  12 -> 13 [label=\"param_out\"]\n  14[label=\"IDFilter\"]\n  13 -> 14 [label=\"param_out\"]\n  15[label=\"IDMapper\"]\n  14 -> 15 [label=\"param_out\"]\n  2 -> 15 [label=\"param_out\"]\n  16[label=\"IDConflictResolver\"]\n  15 -> 16 [label=\"param_out\"]\n  17[label=\"FileFilter\"]\n  16 -> 17 [label=\"param_out\"]\n  18[label=\"FileMerger\"]\n  17 -> 18 [label=\"param_out\"]\n  19[label=\"MzTabExporter\"]\n  18 -> 19 [label=\"param_out\"]\n}",
-                "history": [
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 4,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 3,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "7da80b34185f4165852feb3bfe80d692609685db",
-                        "message": "Workflows fix",
-                        "num": 2,
-                        "short_hash": "7da80b341",
-                        "unix": "1578668175"
                     },
-                    {
-                        "hash": "2c1271b670d336517fb123fb632ce13c93c40465",
-                        "message": "Restructure proteomics",
-                        "num": 1,
-                        "short_hash": "2c1271b67",
-                        "unix": "1495544862"
-                    }
-                ],
-                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Input Dataset Collection (mzML files)"
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {
+                            "infile": {
+                                "id": 9,
+                                "output_name": "comparison_result"
                             }
-                        ],
-                        "label": null,
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 199.9666748046875,
-                            "top": 435.20001220703125
                         },
-                        "tool_errors": null,
-                        "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection (mzML files)\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "7bf13771-4620-4563-b972-efaf74887ce5",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "11ba0e33-3924-43e2-a8f9-85e0e6c12cfe"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "UniProt database (FASTA file)"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 241,
-                            "top": 603.2166748046875
-                        },
-                        "tool_errors": null,
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"UniProt database (FASTA file)\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "05f5cbd8-8459-47a0-8faf-95c0821f25fc",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "3d25e478-d053-4d4e-9c7f-92fec2d6b09c"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"FeatureFinderMultiplex\"];\n  0 -->|output| 2;\n  3[\"HighResPrecursorMassCorrector\"];\n  2 -->|param_out_features| 3;\n  0 -->|output| 3;\n  4[\"MSGFPlusAdapter\"];\n  1 -->|output| 4;\n  3 -->|param_out| 4;\n  5[\"MSGFPlusAdapter\"];\n  1 -->|output| 5;\n  3 -->|param_out| 5;\n  6[\"MSGFPlusAdapter\"];\n  3 -->|param_out| 6;\n  7[\"PeptideIndexer\"];\n  1 -->|output| 7;\n  4 -->|param_out| 7;\n  8[\"PeptideIndexer\"];\n  1 -->|output| 8;\n  5 -->|param_out| 8;\n  9[\"PeptideIndexer\"];\n  1 -->|output| 9;\n  6 -->|param_out| 9;\n  10[\"IDMerger\"];\n  7 -->|param_out| 10;\n  8 -->|param_out| 10;\n  9 -->|param_out| 10;\n  11[\"ConsensusID\"];\n  10 -->|param_out| 11;\n  12[\"PeptideIndexer\"];\n  1 -->|output| 12;\n  11 -->|param_out| 12;\n  13[\"FalseDiscoveryRate\"];\n  12 -->|param_out| 13;\n  14[\"IDFilter\"];\n  13 -->|param_out| 14;\n  15[\"IDMapper\"];\n  14 -->|param_out| 15;\n  2 -->|param_out| 15;\n  16[\"IDConflictResolver\"];\n  15 -->|param_out| 16;\n  17[\"FileFilter\"];\n  16 -->|param_out| 17;\n  18[\"FileMerger\"];\n  17 -->|param_out| 18;\n  19[\"MzTabExporter\"];\n  18 -->|param_out| 19;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Tails Triple Dimethyl OpenMS2.1",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                        "name": "Replace Text",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Input Dataset Collection (mzML files)"
+                                "name": "outfile",
+                                "type": "input"
                             }
                         ],
-                        "label": null,
-                        "name": "Input dataset collection",
-                        "outputs": [],
                         "position": {
-                            "left": 199.9666748046875,
-                            "top": 435.20001220703125
+                            "bottom": 508.0333557128906,
+                            "height": 92.86666870117188,
+                            "left": 736,
+                            "right": 936,
+                            "top": 415.16668701171875,
+                            "width": 200,
+                            "x": 736,
+                            "y": 415.16668701171875
                         },
-                        "tool_errors": null,
-                        "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection (mzML files)\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "7bf13771-4620-4563-b972-efaf74887ce5",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "11ba0e33-3924-43e2-a8f9-85e0e6c12cfe"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "UniProt database (FASTA file)"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 241,
-                            "top": 603.2166748046875
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_errors": null,
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"UniProt database (FASTA file)\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "05f5cbd8-8459-47a0-8faf-95c0821f25fc",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"column\": \"1\", \"find_pattern\": \"sp\\\\|\", \"replace_pattern\": \"\"}, {\"__index__\": 1, \"column\": \"1\", \"find_pattern\": \"\\\\|.*\", \"replace_pattern\": \"\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.3",
+                        "type": "tool",
+                        "uuid": "d79c82bc-9b4d-43b9-bb39-42b4cdf81bdb",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "3d25e478-d053-4d4e-9c7f-92fec2d6b09c"
+                                "output_name": "outfile",
+                                "uuid": "851024bd-132d-4bd6-87c6-5249211d6666"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "FeatureFinderMultiplex",
-                        "id": 2,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+                        "errors": null,
+                        "id": 13,
                         "input_connections": {
-                            "param_in": {
-                                "id": 0,
-                                "output_name": "output"
+                            "infile": {
+                                "id": 9,
+                                "output_name": "quant_sample_matrix"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool FeatureFinderMultiplex",
-                                "name": "param_in"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "FeatureFinderMultiplex",
+                        "name": "Replace Text",
                         "outputs": [
                             {
-                                "name": "param_out",
-                                "type": "consensusxml"
-                            },
-                            {
-                                "name": "param_out_features",
-                                "type": "featurexml"
-                            },
-                            {
-                                "name": "param_out_mzq",
-                                "type": "mzq"
+                                "name": "outfile",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 1228.9666748046875,
-                            "top": 1174.88330078125
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionparam_out_mzq": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "param_out_mzq"
-                            }
+                            "bottom": 628.0333557128906,
+                            "height": 92.86666870117188,
+                            "left": 736,
+                            "right": 936,
+                            "top": 535.1666870117188,
+                            "width": 200,
+                            "x": 736,
+                            "y": 535.1666870117188
                         },
-                        "tool_errors": null,
-                        "tool_id": "FeatureFinderMultiplex",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "ca88bd28f116",
-                            "name": "openms_featurefindermultiplex",
-                            "owner": "galaxyp",
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"param_algorithm_averagine_similarity\": \"\\\"0.6\\\"\", \"param_algorithm_rt_min\": \"\\\"3.0\\\"\", \"__page__\": 0, \"param_algorithm_missed_cleavages\": \"\\\"2\\\"\", \"param_algorithm_peptide_similarity\": \"\\\"0.7\\\"\", \"adv_opts\": \"{\\\"param_algorithm_knock_out\\\": \\\"true\\\", \\\"param_labels_Dimethyl4\\\": \\\"32.056407\\\", \\\"param_algorithm_isotopes_per_peptide\\\": \\\"3:6\\\", \\\"param_labels_Lys4\\\": \\\"4.0251069836\\\", \\\"param_labels_Dimethyl0\\\": \\\"28.0313\\\", \\\"param_labels_Lys8\\\": \\\"8.0141988132\\\", \\\"param_labels_ICPL10\\\": \\\"115.0667\\\", \\\"param_labels_Lys6\\\": \\\"6.0201290268\\\", \\\"param_labels_Arg10\\\": \\\"10.0082686\\\", \\\"param_labels_Dimethyl8\\\": \\\"36.07567\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"param_labels_ICPL6\\\": \\\"111.041593\\\", \\\"param_force\\\": \\\"false\\\", \\\"param_labels_Dimethyl6\\\": \\\"34.063117\\\", \\\"param_labels_Arg6\\\": \\\"6.0201290268\\\", \\\"__current_case__\\\": 1, \\\"param_algorithm_averagine_type\\\": \\\"peptide\\\", \\\"param_labels_ICPL0\\\": \\\"105.021464\\\", \\\"param_labels_Leu3\\\": \\\"3.01883\\\", \\\"param_labels_ICPL4\\\": \\\"109.046571\\\", \\\"param_algorithm_averagine_similarity_scaling\\\": \\\"0.6\\\"}\", \"param_algorithm_mz_tolerance\": \"\\\"15.0\\\"\", \"param_algorithm_charge\": \"\\\"1:5\\\"\", \"param_algorithm_mz_unit\": \"\\\"ppm\\\"\", \"param_algorithm_labels\": \"\\\"[Dimethyl0][Dimethyl4][Dimethyl8]\\\"\", \"param_algorithm_intensity_cutoff\": \"\\\"10.0\\\"\", \"param_algorithm_rt_typical\": \"\\\"50.0\\\"\", \"__rerun_remap_job_id__\": null, \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "2.1.0",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"column\": \"1\", \"find_pattern\": \"sp\\\\|\", \"replace_pattern\": \"\"}, {\"__index__\": 1, \"column\": \"1\", \"find_pattern\": \"\\\\|.*\", \"replace_pattern\": \"\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.3",
                         "type": "tool",
-                        "uuid": "627672fc-feef-4e31-9208-182a27df2533",
+                        "uuid": "e3f8c7ce-c2cf-488a-bf80-eb18d677d8a7",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "param_out",
-                                "uuid": "6e1e9231-52a0-4d05-9491-31f4b162d405"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "param_out_features",
-                                "uuid": "a8b8b589-661b-49ca-9832-556069bf98bc"
+                                "output_name": "outfile",
+                                "uuid": "02878b52-bd9d-4e3d-914a-3925430524d9"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "HighResPrecursorMassCorrector",
-                        "id": 3,
+                        "content_id": "Filter1",
+                        "errors": null,
+                        "id": 14,
                         "input_connections": {
-                            "param_feature_in": {
-                                "id": 2,
-                                "output_name": "param_out_features"
-                            },
-                            "param_in": {
-                                "id": 0,
-                                "output_name": "output"
+                            "input": {
+                                "id": 12,
+                                "output_name": "outfile"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool HighResPrecursorMassCorrector",
-                                "name": "param_feature_in"
-                            },
-                            {
-                                "description": "runtime parameter for tool HighResPrecursorMassCorrector",
-                                "name": "param_in"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "HighResPrecursorMassCorrector",
+                        "name": "Filter",
                         "outputs": [
                             {
-                                "name": "param_out",
-                                "type": "mzml"
-                            },
-                            {
-                                "name": "param_out_csv",
-                                "type": "tabular"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 484.54998779296875,
-                            "top": 151.1999969482422
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionparam_out_csv": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "param_out_csv"
-                            },
-                            "RenameDatasetActionparam_out": {
-                                "action_arguments": {
-                                    "newname": "HighRes_out"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "param_out"
-                            }
-                        },
-                        "tool_errors": null,
-                        "tool_id": "HighResPrecursorMassCorrector",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9e26f5c770f8",
-                            "name": "openms_highresprecursormasscorrector",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 268.03334045410156,
+                            "height": 92.86666870117188,
+                            "left": 956,
+                            "right": 1156,
+                            "top": 175.1666717529297,
+                            "width": 200,
+                            "x": 956,
+                            "y": 175.1666717529297
                         },
-                        "tool_state": "{\"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_feature_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_feature_rt_tolerance\": \"\\\"15.0\\\"\", \"param_nearest_peak_mz_tolerance_unit\": \"\\\"ppm\\\"\", \"param_feature_mz_tolerance_unit\": \"\\\"ppm\\\"\", \"param_feature_mz_tolerance\": \"\\\"40.0\\\"\", \"param_feature_keep_original\": \"\\\"false\\\"\", \"param_feature_assign_all_matching\": \"\\\"false\\\"\", \"param_feature_believe_charge\": \"\\\"false\\\"\", \"param_nearest_peak_mz_tolerance\": \"\\\"0.0\\\"\"}",
-                        "tool_version": "2.1.0",
+                        "post_job_actions": {},
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c8<0.05\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
                         "type": "tool",
-                        "uuid": "3d7f4c8b-1896-4365-b41a-77b152ec84b4",
+                        "uuid": "a8c17ba0-9fd9-45cb-a195-bd3f6af256e8",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "param_out",
-                                "uuid": "be0344fb-dccf-4d28-a45e-9d1aded44e41"
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "3c3a85e8-3934-4439-9836-cfff976035e7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "MSGFPlusAdapter",
-                        "id": 4,
+                        "content_id": "Filter1",
+                        "errors": null,
+                        "id": 15,
                         "input_connections": {
-                            "param_database": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "param_in": {
-                                "id": 3,
-                                "output_name": "param_out"
+                            "input": {
+                                "id": 14,
+                                "output_name": "out_file1"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool MSGFPlusAdapter",
-                                "name": "param_in"
-                            },
-                            {
-                                "description": "runtime parameter for tool MSGFPlusAdapter",
-                                "name": "param_database"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "MSGFPlusAdapter",
+                        "name": "Filter",
                         "outputs": [
                             {
-                                "name": "param_out",
-                                "type": "idxml"
-                            },
-                            {
-                                "name": "param_mzid_out",
-                                "type": "mzid"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 849.0500030517578,
-                            "top": 186.21665954589844
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionparam_mzid_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "param_mzid_out"
-                            }
-                        },
-                        "tool_errors": null,
-                        "tool_id": "MSGFPlusAdapter",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2b2a7551a857",
-                            "name": "openms_msgfplusadapter",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 268.03334045410156,
+                            "height": 92.86666870117188,
+                            "left": 1176,
+                            "right": 1376,
+                            "top": 175.1666717529297,
+                            "width": 200,
+                            "x": 1176,
+                            "y": 175.1666717529297
                         },
-                        "tool_state": "{\"param_java_executable\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_max_precursor_charge\": \"\\\"4\\\"\", \"param_min_precursor_charge\": \"\\\"2\\\"\", \"param_min_peptide_length\": \"\\\"7\\\"\", \"param_precursor_error_units\": \"\\\"ppm\\\"\", \"param_protocol\": \"\\\"none\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"param_tryptic\": \"\\\"semi\\\"\", \"param_max_mods\": \"\\\"3\\\"\", \"rep_param_fixed_modifications\": \"[{\\\"__index__\\\": 0, \\\"param_fixed_modifications\\\": \\\"Carbamidomethyl (C)\\\"}, {\\\"__index__\\\": 1, \\\"param_fixed_modifications\\\": \\\"Dimethyl (K)\\\"}, {\\\"__index__\\\": 2, \\\"param_fixed_modifications\\\": \\\"Dimethyl (N-term)\\\"}]\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_add_decoys\": \"\\\"false\\\"\", \"param_matches_per_spec\": \"\\\"1\\\"\", \"param_max_peptide_length\": \"\\\"40\\\"\", \"param_instrument\": \"\\\"Q_Exactive\\\"\", \"param_precursor_mass_tolerance\": \"\\\"20.0\\\"\", \"rep_param_variable_modifications\": \"[]\", \"param_add_features\": \"\\\"true\\\"\", \"param_enzyme\": \"\\\"ArgC\\\"\", \"param_database\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_fragment_method\": \"\\\"from_spectrum\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"param_java_memory\": \"\\\"3500\\\"\", \"param_isotope_error_range\": \"\\\"0,0\\\"\"}",
-                        "tool_version": "2.1.0",
+                        "post_job_actions": {},
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c3>0.58\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
                         "type": "tool",
-                        "uuid": "cc98863a-5f1a-42ef-bd30-a7c6002f3efa",
+                        "uuid": "d27bb3b9-ff30-4004-8cc1-60b0085bbeea",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "param_out",
-                                "uuid": "7066dfd9-e896-462b-8877-68580da0cc08"
+                                "output_name": "out_file1",
+                                "uuid": "01a2b15e-f55e-4485-acf6-b24063e79b7c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "MSGFPlusAdapter",
-                        "id": 5,
+                        "content_id": "Filter1",
+                        "errors": null,
+                        "id": 16,
                         "input_connections": {
-                            "param_database": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "param_in": {
-                                "id": 3,
-                                "output_name": "param_out"
+                            "input": {
+                                "id": 14,
+                                "output_name": "out_file1"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool MSGFPlusAdapter",
-                                "name": "param_in"
-                            },
-                            {
-                                "description": "runtime parameter for tool MSGFPlusAdapter",
-                                "name": "param_database"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "MSGFPlusAdapter",
+                        "name": "Filter",
                         "outputs": [
                             {
-                                "name": "param_out",
-                                "type": "idxml"
-                            },
-                            {
-                                "name": "param_mzid_out",
-                                "type": "mzid"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 887,
-                            "top": 394.20001220703125
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionparam_mzid_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "param_mzid_out"
-                            }
-                        },
-                        "tool_errors": null,
-                        "tool_id": "MSGFPlusAdapter",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2b2a7551a857",
-                            "name": "openms_msgfplusadapter",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 388.0333557128906,
+                            "height": 92.86666870117188,
+                            "left": 1176,
+                            "right": 1376,
+                            "top": 295.16668701171875,
+                            "width": 200,
+                            "x": 1176,
+                            "y": 295.16668701171875
                         },
-                        "tool_state": "{\"param_java_executable\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_max_precursor_charge\": \"\\\"4\\\"\", \"param_min_precursor_charge\": \"\\\"2\\\"\", \"param_min_peptide_length\": \"\\\"7\\\"\", \"param_precursor_error_units\": \"\\\"ppm\\\"\", \"param_protocol\": \"\\\"none\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"param_tryptic\": \"\\\"semi\\\"\", \"param_max_mods\": \"\\\"3\\\"\", \"rep_param_fixed_modifications\": \"[{\\\"__index__\\\": 0, \\\"param_fixed_modifications\\\": \\\"Carbamidomethyl (C)\\\"}, {\\\"__index__\\\": 1, \\\"param_fixed_modifications\\\": \\\"Dimethyl:2H(4) (K)\\\"}, {\\\"__index__\\\": 2, \\\"param_fixed_modifications\\\": \\\"Dimethyl:2H(4) (N-term)\\\"}]\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_add_decoys\": \"\\\"false\\\"\", \"param_matches_per_spec\": \"\\\"1\\\"\", \"param_max_peptide_length\": \"\\\"40\\\"\", \"param_instrument\": \"\\\"Q_Exactive\\\"\", \"param_precursor_mass_tolerance\": \"\\\"20.0\\\"\", \"rep_param_variable_modifications\": \"[]\", \"param_add_features\": \"\\\"true\\\"\", \"param_enzyme\": \"\\\"ArgC\\\"\", \"param_database\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_fragment_method\": \"\\\"from_spectrum\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"param_java_memory\": \"\\\"3500\\\"\", \"param_isotope_error_range\": \"\\\"0,0\\\"\"}",
-                        "tool_version": "2.1.0",
+                        "post_job_actions": {},
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c3<-0.58\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
                         "type": "tool",
-                        "uuid": "3a2ce94c-c7c0-43e8-a95a-29773f41ff83",
+                        "uuid": "8cd26d6e-9eab-4329-aa4f-4baeb79cba8e",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "param_out",
-                                "uuid": "7d1226d5-80ff-4f81-b2f8-1298517f98f8"
+                                "output_name": "out_file1",
+                                "uuid": "9878106d-9970-49e2-9498-12786bf87859"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "MSGFPlusAdapter",
-                        "id": 6,
+                        "content_id": "Filter1",
+                        "errors": null,
+                        "id": 17,
                         "input_connections": {
-                            "param_in": {
-                                "id": 3,
-                                "output_name": "param_out"
+                            "input": {
+                                "id": 15,
+                                "output_name": "out_file1"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool MSGFPlusAdapter",
-                                "name": "param_in"
-                            },
-                            {
-                                "description": "runtime parameter for tool MSGFPlusAdapter",
-                                "name": "param_database"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "MSGFPlusAdapter",
+                        "name": "Filter",
                         "outputs": [
                             {
-                                "name": "param_out",
-                                "type": "idxml"
-                            },
-                            {
-                                "name": "param_mzid_out",
-                                "type": "mzid"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 892.5,
-                            "top": 590
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionparam_mzid_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "param_mzid_out"
-                            }
-                        },
-                        "tool_errors": null,
-                        "tool_id": "MSGFPlusAdapter",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2b2a7551a857",
-                            "name": "openms_msgfplusadapter",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 268.03334045410156,
+                            "height": 92.86666870117188,
+                            "left": 1396,
+                            "right": 1596,
+                            "top": 175.1666717529297,
+                            "width": 200,
+                            "x": 1396,
+                            "y": 175.1666717529297
                         },
-                        "tool_state": "{\"param_java_executable\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_max_precursor_charge\": \"\\\"4\\\"\", \"param_min_precursor_charge\": \"\\\"2\\\"\", \"param_min_peptide_length\": \"\\\"7\\\"\", \"param_precursor_error_units\": \"\\\"ppm\\\"\", \"param_protocol\": \"\\\"none\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"param_tryptic\": \"\\\"semi\\\"\", \"param_max_mods\": \"\\\"3\\\"\", \"rep_param_fixed_modifications\": \"[{\\\"__index__\\\": 0, \\\"param_fixed_modifications\\\": \\\"Carbamidomethyl (C)\\\"}, {\\\"__index__\\\": 1, \\\"param_fixed_modifications\\\": \\\"Dimethyl:2H(6)13C(2) (K)\\\"}, {\\\"__index__\\\": 2, \\\"param_fixed_modifications\\\": \\\"Dimethyl:2H(6)13C(2) (N-term)\\\"}]\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_add_decoys\": \"\\\"false\\\"\", \"param_matches_per_spec\": \"\\\"1\\\"\", \"param_max_peptide_length\": \"\\\"40\\\"\", \"param_instrument\": \"\\\"Q_Exactive\\\"\", \"param_precursor_mass_tolerance\": \"\\\"20.0\\\"\", \"rep_param_variable_modifications\": \"[]\", \"param_add_features\": \"\\\"true\\\"\", \"param_enzyme\": \"\\\"ArgC\\\"\", \"param_database\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_fragment_method\": \"\\\"from_spectrum\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"param_java_memory\": \"\\\"3500\\\"\", \"param_isotope_error_range\": \"\\\"0,0\\\"\"}",
-                        "tool_version": "2.1.0",
+                        "post_job_actions": {},
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c8>0\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
                         "type": "tool",
-                        "uuid": "05593ca7-2056-4201-9ce7-60b4abc82ff5",
+                        "uuid": "d748fc5d-a609-472d-b6cb-0b6ec18affe0",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "param_out",
-                                "uuid": "22b3fa5a-a162-4ce1-8c07-8c3f84fc0551"
+                                "output_name": "out_file1",
+                                "uuid": "6c12e078-7e56-47c5-9524-462cc9e285c7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "PeptideIndexer",
-                        "id": 7,
+                        "content_id": "Filter1",
+                        "errors": null,
+                        "id": 18,
                         "input_connections": {
-                            "param_fasta": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "param_in": {
-                                "id": 4,
-                                "output_name": "param_out"
+                            "input": {
+                                "id": 16,
+                                "output_name": "out_file1"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool PeptideIndexer",
-                                "name": "param_fasta"
-                            },
-                            {
-                                "description": "runtime parameter for tool PeptideIndexer",
-                                "name": "param_in"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "PeptideIndexer",
+                        "name": "Filter",
                         "outputs": [
                             {
-                                "name": "param_out",
-                                "type": "idxml"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 1191,
-                            "top": 181.1999969482422
+                            "bottom": 388.0333557128906,
+                            "height": 92.86666870117188,
+                            "left": 1396,
+                            "right": 1596,
+                            "top": 295.16668701171875,
+                            "width": 200,
+                            "x": 1396,
+                            "y": 295.16668701171875
                         },
                         "post_job_actions": {},
-                        "tool_errors": null,
-                        "tool_id": "PeptideIndexer",
-                        "tool_shed_repository": {
-                            "changeset_revision": "539a3a4dcc9e",
-                            "name": "openms_peptideindexer",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"param_write_protein_sequence\": \"\\\"true\\\"\", \"param_missing_decoy_action\": \"\\\"error\\\"\", \"param_filter_aaa_proteins\": \"\\\"false\\\"\", \"param_prefix\": \"\\\"true\\\"\", \"param_keep_unreferenced_proteins\": \"\\\"false\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"param_allow_unmatched\": \"\\\"true\\\"\", \"param_decoy_string_position\": \"\\\"prefix\\\"\", \"param_mismatches_max\": \"\\\"0\\\"\", \"param_enzyme_name\": \"\\\"Trypsin/P\\\"\", \"param_enzyme_specificity\": \"\\\"semi\\\"\", \"param_decoy_string\": \"\\\"dec_\\\"\", \"__rerun_remap_job_id__\": null, \"param_write_protein_description\": \"\\\"true\\\"\", \"param_full_tolerant_search\": \"\\\"false\\\"\", \"param_fasta\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_aaa_max\": \"\\\"4\\\"\", \"param_annotate_proteins\": \"\\\"True\\\"\", \"param_IL_equivalent\": \"\\\"false\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "2.1.0",
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c8>0\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
                         "type": "tool",
-                        "uuid": "6d75c013-51d3-49f5-8b26-876a8b1c06d5",
+                        "uuid": "fc4b67ba-8f8d-41b4-a797-20221cc7bcbd",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "param_out",
-                                "uuid": "92afc5d3-a20f-4f89-8b80-f6618ba430d0"
+                                "output_name": "out_file1",
+                                "uuid": "de5996ce-55a9-45dc-876b-3877fa1b778b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "PeptideIndexer",
-                        "id": 8,
+                        "content_id": "Cut1",
+                        "errors": null,
+                        "id": 19,
                         "input_connections": {
-                            "param_fasta": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "param_in": {
-                                "id": 5,
-                                "output_name": "param_out"
+                            "input": {
+                                "id": 17,
+                                "output_name": "out_file1"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool PeptideIndexer",
-                                "name": "param_fasta"
-                            },
-                            {
-                                "description": "runtime parameter for tool PeptideIndexer",
-                                "name": "param_in"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "PeptideIndexer",
+                        "name": "Cut",
                         "outputs": [
                             {
-                                "name": "param_out",
-                                "type": "idxml"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1155,
-                            "top": 398.2166748046875
+                            "bottom": 268.03334045410156,
+                            "height": 92.86666870117188,
+                            "left": 1616,
+                            "right": 1816,
+                            "top": 175.1666717529297,
+                            "width": 200,
+                            "x": 1616,
+                            "y": 175.1666717529297
                         },
                         "post_job_actions": {},
-                        "tool_errors": null,
-                        "tool_id": "PeptideIndexer",
-                        "tool_shed_repository": {
-                            "changeset_revision": "539a3a4dcc9e",
-                            "name": "openms_peptideindexer",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"param_write_protein_sequence\": \"\\\"true\\\"\", \"param_missing_decoy_action\": \"\\\"error\\\"\", \"param_filter_aaa_proteins\": \"\\\"false\\\"\", \"param_prefix\": \"\\\"true\\\"\", \"param_keep_unreferenced_proteins\": \"\\\"false\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"param_allow_unmatched\": \"\\\"true\\\"\", \"param_decoy_string_position\": \"\\\"prefix\\\"\", \"param_mismatches_max\": \"\\\"0\\\"\", \"param_enzyme_name\": \"\\\"Trypsin/P\\\"\", \"param_enzyme_specificity\": \"\\\"semi\\\"\", \"param_decoy_string\": \"\\\"dec_\\\"\", \"__rerun_remap_job_id__\": null, \"param_write_protein_description\": \"\\\"true\\\"\", \"param_full_tolerant_search\": \"\\\"false\\\"\", \"param_fasta\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_aaa_max\": \"\\\"4\\\"\", \"param_annotate_proteins\": \"\\\"True\\\"\", \"param_IL_equivalent\": \"\\\"false\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "2.1.0",
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c1\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2",
                         "type": "tool",
-                        "uuid": "8cd335cb-9d51-4c04-99b3-38fed4f3c3b6",
+                        "uuid": "85e52e8f-4bc9-4c0f-9ea3-99e2f5939a83",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "param_out",
-                                "uuid": "9774a600-1f91-4927-932a-b887a1b6f73a"
+                                "output_name": "out_file1",
+                                "uuid": "466eb4ff-3685-425d-b1aa-4f6fb834dd70"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "IDMerger",
-                        "id": 10,
+                        "content_id": "Cut1",
+                        "errors": null,
+                        "id": 20,
                         "input_connections": {
-                            "param_in": [
-                                {
-                                    "id": 7,
-                                    "output_name": "param_out"
-                                },
-                                {
-                                    "id": 8,
-                                    "output_name": "param_out"
-                                },
-                                {
-                                    "id": 9,
-                                    "output_name": "param_out"
-                                }
-                            ]
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool IDMerger",
-                                "name": "param_add_to"
-                            },
-                            {
-                                "description": "runtime parameter for tool IDMerger",
-                                "name": "param_in"
+                            "input": {
+                                "id": 18,
+                                "output_name": "out_file1"
                             }
-                        ],
+                        },
+                        "inputs": [],
                         "label": null,
-                        "name": "IDMerger",
+                        "name": "Cut",
                         "outputs": [
                             {
-                                "name": "param_out",
-                                "type": "idxml"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1441,
-                            "top": 352.20001220703125
+                            "bottom": 388.0333557128906,
+                            "height": 92.86666870117188,
+                            "left": 1616,
+                            "right": 1816,
+                            "top": 295.16668701171875,
+                            "width": 200,
+                            "x": 1616,
+                            "y": 295.16668701171875
                         },
                         "post_job_actions": {},
-                        "tool_errors": null,
-                        "tool_id": "IDMerger",
-                        "tool_shed_repository": {
-                            "changeset_revision": "18f93351f8b6",
-                            "name": "openms_idmerger",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"inputs\": \"[{\\\"__index__\\\": 0, \\\"param_in\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"__index__\\\": 1, \\\"param_in\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}]\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"param_annotate_file_origin\": \"\\\"false\\\"\", \"param_pepxml_protxml\": \"\\\"false\\\"\", \"param_add_to\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_in1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "2.1.0",
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c1\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2",
                         "type": "tool",
-                        "uuid": "3616471f-09c7-4c6a-8118-e92619874f09",
+                        "uuid": "bf3841cb-6e7f-4a3d-988f-df196aca874a",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "param_out",
-                                "uuid": "f78b508e-7e25-4d72-a870-9f12371c95ea"
+                                "output_name": "out_file1",
+                                "uuid": "9d0a535d-ed5b-448f-bbc4-795ec0b7ae4b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "ConsensusID",
-                        "id": 11,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "errors": null,
+                        "id": 21,
                         "input_connections": {
-                            "param_in": {
-                                "id": 10,
-                                "output_name": "param_out"
+                            "infile1": {
+                                "id": 13,
+                                "output_name": "outfile"
+                            },
+                            "infile2": {
+                                "id": 19,
+                                "output_name": "out_file1"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool ConsensusID",
-                                "name": "param_in"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "ConsensusID",
+                        "name": "Join",
                         "outputs": [
                             {
-                                "name": "param_out",
+                                "name": "output",
                                 "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 1609,
-                            "top": 470.20001220703125
+                            "bottom": 298.43333435058594,
+                            "height": 123.26666259765625,
+                            "left": 1836,
+                            "right": 2036,
+                            "top": 175.1666717529297,
+                            "width": 200,
+                            "x": 1836,
+                            "y": 175.1666717529297
                         },
                         "post_job_actions": {},
-                        "tool_errors": null,
-                        "tool_id": "ConsensusID",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "8960fb791701",
-                            "name": "openms_consensusid",
-                            "owner": "galaxyp",
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": 0, \"param_algorithm\": \"\\\"best\\\"\", \"param_filter_considered_hits\": \"\\\"0\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"param_filter_count_empty\": \"\\\"false\\\"\", \"param_PEPIons_mass_tolerance\": \"\\\"0.5\\\"\", \"param_PEPIons_min_shared\": \"\\\"2\\\"\", \"param_PEPMatrix_penalty\": \"\\\"5\\\"\", \"param_filter_min_support\": \"\\\"0.0\\\"\", \"param_rt_delta\": \"\\\"0.1\\\"\", \"param_PEPMatrix_matrix\": \"\\\"identity\\\"\", \"param_mz_delta\": \"\\\"0.1\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "2.1.0",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": \"true\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.2",
                         "type": "tool",
-                        "uuid": "a397db69-017e-4988-9f94-7ecbc119e3f3",
+                        "uuid": "a006f45e-d6ee-457f-b9af-84d5d86c24b7",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "param_out",
-                                "uuid": "b05c7e3e-e094-4366-9163-e0c1984974b9"
+                                "output_name": "output",
+                                "uuid": "f24e4056-f3ba-40bd-ac6e-0421584ff7b9"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "PeptideIndexer",
-                        "id": 12,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "errors": null,
+                        "id": 22,
                         "input_connections": {
-                            "param_fasta": {
-                                "id": 1,
-                                "output_name": "output"
+                            "infile1": {
+                                "id": 13,
+                                "output_name": "outfile"
                             },
-                            "param_in": {
-                                "id": 11,
-                                "output_name": "param_out"
+                            "infile2": {
+                                "id": 20,
+                                "output_name": "out_file1"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool PeptideIndexer",
-                                "name": "param_fasta"
-                            },
-                            {
-                                "description": "runtime parameter for tool PeptideIndexer",
-                                "name": "param_in"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "PeptideIndexer",
+                        "name": "Join",
                         "outputs": [
                             {
-                                "name": "param_out",
-                                "type": "idxml"
+                                "name": "output",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 1003,
-                            "top": 820.2000122070312
+                            "bottom": 418.433349609375,
+                            "height": 123.26666259765625,
+                            "left": 1836,
+                            "right": 2036,
+                            "top": 295.16668701171875,
+                            "width": 200,
+                            "x": 1836,
+                            "y": 295.16668701171875
                         },
                         "post_job_actions": {},
-                        "tool_errors": null,
-                        "tool_id": "PeptideIndexer",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "539a3a4dcc9e",
-                            "name": "openms_peptideindexer",
-                            "owner": "galaxyp",
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"param_write_protein_sequence\": \"\\\"true\\\"\", \"param_missing_decoy_action\": \"\\\"error\\\"\", \"param_filter_aaa_proteins\": \"\\\"false\\\"\", \"param_prefix\": \"\\\"true\\\"\", \"param_keep_unreferenced_proteins\": \"\\\"false\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"param_allow_unmatched\": \"\\\"true\\\"\", \"param_decoy_string_position\": \"\\\"prefix\\\"\", \"param_mismatches_max\": \"\\\"0\\\"\", \"param_enzyme_name\": \"\\\"Trypsin/P\\\"\", \"param_enzyme_specificity\": \"\\\"none\\\"\", \"param_decoy_string\": \"\\\"dec_\\\"\", \"__rerun_remap_job_id__\": null, \"param_write_protein_description\": \"\\\"true\\\"\", \"param_full_tolerant_search\": \"\\\"false\\\"\", \"param_fasta\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_aaa_max\": \"\\\"4\\\"\", \"param_annotate_proteins\": \"\\\"True\\\"\", \"param_IL_equivalent\": \"\\\"false\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "2.1.0",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": \"true\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.2",
                         "type": "tool",
-                        "uuid": "868442d2-bb81-4d9a-b783-448377dce6d7",
+                        "uuid": "33d235ba-6450-4f5a-8f41-8611e2153ed9",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "param_out",
-                                "uuid": "f026ce76-91ea-40df-99bb-00ae4bacf3f6"
+                                "output_name": "output",
+                                "uuid": "9a2e9e3a-6e50-4ee8-b599-b6186975f1fc"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "IDFilter",
-                        "id": 14,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1",
+                        "errors": null,
+                        "id": 23,
                         "input_connections": {
-                            "param_in": {
-                                "id": 13,
-                                "output_name": "param_out"
+                            "input1": {
+                                "id": 21,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool IDFilter",
-                                "name": "param_whitelist_peptides"
-                            },
-                            {
-                                "description": "runtime parameter for tool IDFilter",
-                                "name": "param_whitelist_proteins"
-                            },
-                            {
-                                "description": "runtime parameter for tool IDFilter",
-                                "name": "param_blacklist_proteins"
-                            },
-                            {
-                                "description": "runtime parameter for tool IDFilter",
-                                "name": "param_in"
-                            },
-                            {
-                                "description": "runtime parameter for tool IDFilter",
-                                "name": "param_blacklist_peptides"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "IDFilter",
+                        "name": "heatmap2",
                         "outputs": [
                             {
-                                "name": "param_out",
-                                "type": "idxml"
+                                "name": "output1",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "left": 1647.9666748046875,
-                            "top": 808.88330078125
+                            "bottom": 308.8333282470703,
+                            "height": 133.66665649414062,
+                            "left": 2056,
+                            "right": 2256,
+                            "top": 175.1666717529297,
+                            "width": 200,
+                            "x": 2056,
+                            "y": 175.1666717529297
                         },
                         "post_job_actions": {},
-                        "tool_errors": null,
-                        "tool_id": "IDFilter",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "c427a8628cbe",
-                            "name": "openms_idfilter",
-                            "owner": "galaxyp",
+                            "changeset_revision": "ca7cb0eaad62",
+                            "name": "ggplot2_heatmap2",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"param_whitelist_peptides\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_length\": \"\\\":\\\"\", \"param_keep_unreferenced_protein_hits\": \"\\\"false\\\"\", \"param_unique\": \"\\\"false\\\"\", \"param_whitelist_proteins\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_unique_per_protein\": \"\\\"false\\\"\", \"param_remove_decoys\": \"\\\"false\\\"\", \"param_score_prot\": \"\\\"0.0\\\"\", \"param_rt_p_value_1st_dim\": \"\\\"0.0\\\"\", \"param_best_n_protein_hits\": \"\\\"0\\\"\", \"param_min_length\": \"\\\"0\\\"\", \"__rerun_remap_job_id__\": null, \"param_precursor_mz\": \"\\\":\\\"\", \"param_mz_error\": \"\\\"-1.0\\\"\", \"rep_param_blacklist_modifications\": \"[]\", \"param_precursor_allow_missing\": \"\\\"false\\\"\", \"param_blacklist_proteins\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_delete_unreferenced_peptide_hits\": \"\\\"false\\\"\", \"param_precursor_rt\": \"\\\":\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0, \"param_charge\": \"\\\":\\\"\", \"param_var_mods\": \"\\\"false\\\"\", \"param_max_length\": \"\\\"0\\\"\", \"param_best_strict\": \"\\\"false\\\"\", \"rep_param_whitelist_protein_accessions\": \"[]\", \"rep_param_whitelist_modifications\": \"[]\", \"param_thresh_pep\": \"\\\"0.0\\\"\", \"param_mz_unit\": \"\\\"ppm\\\"\", \"param_best_n_peptide_hits\": \"\\\"0\\\"\", \"param_whitelist_by_seq_only\": \"\\\"false\\\"\", \"param_blacklist_peptides\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"param_score_pep\": \"\\\"0.05\\\"\", \"param_rt_p_value\": \"\\\"0.0\\\"\", \"param_min_charge\": \"\\\"1\\\"\", \"param_blacklist_ignore_modifications\": \"\\\"false\\\"\", \"rep_param_blacklist_protein_accessions\": \"[]\", \"param_whitelist_ignore_modifications\": \"\\\"false\\\"\", \"param_thresh_prot\": \"\\\"0.0\\\"\"}",
-                        "tool_version": "2.1.0",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cluster_cond\": {\"cluster\": \"\", \"__current_case__\": 1}, \"colorscheme\": \"whrd\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"key\": \"\", \"labels\": \"both\", \"scale\": \"row\", \"title\": \"Upregulated proteins in metastasized cSCC\", \"transform\": \"none\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.0.1",
                         "type": "tool",
-                        "uuid": "458f5b98-62dd-4650-86dc-f3fc3da4584e",
+                        "uuid": "bee1e0b5-2251-4f85-8737-243dacef01a7",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "param_out",
-                                "uuid": "ac38c879-b0a6-4260-a659-32bc6f531232"
+                                "output_name": "output1",
+                                "uuid": "cf47dbb9-afc4-4d9b-985b-0a18bd95ebfe"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "IDMapper",
-                        "id": 15,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2",
+                        "errors": null,
+                        "id": 24,
                         "input_connections": {
-                            "param_id": {
-                                "id": 14,
-                                "output_name": "param_out"
-                            },
-                            "param_in": {
-                                "id": 2,
-                                "output_name": "param_out"
+                            "infile": {
+                                "id": 21,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool IDMapper",
-                                "name": "param_id"
-                            },
-                            {
-                                "description": "runtime parameter for tool IDMapper",
-                                "name": "param_in"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "IDMapper",
+                        "name": "UniProt",
                         "outputs": [
                             {
-                                "name": "param_out",
-                                "type": "input"
+                                "name": "outfile_retrieve_fasta",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 1979.9666748046875,
-                            "top": 843.88330078125
+                            "bottom": 548.8333435058594,
+                            "height": 133.66665649414062,
+                            "left": 2056,
+                            "right": 2256,
+                            "top": 415.16668701171875,
+                            "width": 200,
+                            "x": 2056,
+                            "y": 415.16668701171875
                         },
                         "post_job_actions": {},
-                        "tool_errors": null,
-                        "tool_id": "IDMapper",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "b5d0905419da",
-                            "name": "openms_idmapper",
-                            "owner": "galaxyp",
+                            "changeset_revision": "054483e27a35",
+                            "name": "uniprot_rest_interface",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"param_mz_tolerance\": \"\\\"30.0\\\"\", \"param_ignore_charge\": \"\\\"true\\\"\", \"param_feature_use_centroid_rt\": \"\\\"false\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"param_mz_measure\": \"\\\"ppm\\\"\", \"param_mz_reference\": \"\\\"precursor\\\"\", \"param_id\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_rt_tolerance\": \"\\\"50.0\\\"\", \"param_consensus_use_subelements\": \"\\\"true\\\"\", \"param_feature_use_centroid_mz\": \"\\\"false\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "2.1.0",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"id_column\": \"1\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"tool\": {\"tool_choice\": \"retrieve\", \"__current_case__\": 1, \"format\": \"fasta\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.2",
                         "type": "tool",
-                        "uuid": "f199e8c6-c243-4fce-8dac-a62d504c9cdd",
+                        "uuid": "5f1dd559-3d47-464d-ac73-72684267aaf4",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "param_out",
-                                "uuid": "84923098-0cc0-4c3b-ac19-aa12ef6a5244"
+                                "output_name": "outfile_retrieve_fasta",
+                                "uuid": "141b0dcd-080b-440d-81d0-85f7297d8054"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "IDConflictResolver",
-                        "id": 16,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1",
+                        "errors": null,
+                        "id": 25,
                         "input_connections": {
-                            "param_in": {
-                                "id": 15,
-                                "output_name": "param_out"
+                            "input1": {
+                                "id": 22,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool IDConflictResolver",
-                                "name": "param_in"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "IDConflictResolver",
+                        "name": "heatmap2",
                         "outputs": [
                             {
-                                "name": "param_out",
-                                "type": "input"
+                                "name": "output1",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "left": 2220.449951171875,
-                            "top": 881.88330078125
+                            "bottom": 428.8333435058594,
+                            "height": 133.66665649414062,
+                            "left": 2056,
+                            "right": 2256,
+                            "top": 295.16668701171875,
+                            "width": 200,
+                            "x": 2056,
+                            "y": 295.16668701171875
                         },
                         "post_job_actions": {},
-                        "tool_errors": null,
-                        "tool_id": "IDConflictResolver",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "8a04ed1c1d1b",
-                            "name": "openms_idconflictresolver",
-                            "owner": "galaxyp",
+                            "changeset_revision": "ca7cb0eaad62",
+                            "name": "ggplot2_heatmap2",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv_opts\": \"{\\\"param_force\\\": \\\"false\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "2.1.0",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cluster_cond\": {\"cluster\": \"\", \"__current_case__\": 1}, \"colorscheme\": \"whrd\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"key\": \"\", \"labels\": \"both\", \"scale\": \"row\", \"title\": \"Upregulated proteins in RDEB cSCC\", \"transform\": \"none\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.0.1",
                         "type": "tool",
-                        "uuid": "6f4dc17d-b0fd-4b66-9487-3fda71316199",
+                        "uuid": "df17ae43-0885-4132-b75a-6917049e573c",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "param_out",
-                                "uuid": "485d4684-835d-4ff0-9ca5-3400a0b8fa22"
+                                "output_name": "output1",
+                                "uuid": "1dd011a1-b91e-4b39-8fa6-c9585946df63"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "FileFilter",
-                        "id": 17,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2",
+                        "errors": null,
+                        "id": 26,
                         "input_connections": {
-                            "param_in": {
-                                "id": 16,
-                                "output_name": "param_out"
+                            "infile": {
+                                "id": 22,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool FileFilter",
-                                "name": "param_in"
-                            },
-                            {
-                                "description": "runtime parameter for tool FileFilter",
-                                "name": "param_id_blacklist"
-                            },
-                            {
-                                "description": "runtime parameter for tool FileFilter",
-                                "name": "param_consensus_blackorwhitelist_file"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "FileFilter",
+                        "name": "UniProt",
                         "outputs": [
                             {
-                                "name": "param_out",
-                                "type": "input"
+                                "name": "outfile_retrieve_fasta",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 2531,
-                            "top": 786.88330078125
+                            "bottom": 668.8333435058594,
+                            "height": 133.66665649414062,
+                            "left": 2056,
+                            "right": 2256,
+                            "top": 535.1666870117188,
+                            "width": 200,
+                            "x": 2056,
+                            "y": 535.1666870117188
                         },
                         "post_job_actions": {},
-                        "tool_errors": null,
-                        "tool_id": "FileFilter",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "d6878d27f051",
-                            "name": "openms_filefilter",
-                            "owner": "galaxyp",
+                            "changeset_revision": "054483e27a35",
+                            "name": "uniprot_rest_interface",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"rep_param_id_sequences_whitelist\": \"[]\", \"param_algorithm_SignalToNoise_win_len\": \"\\\"200.0\\\"\", \"param_algorithm_SignalToNoise_bin_count\": \"\\\"30\\\"\", \"param_peak_options_sn\": \"\\\"0.0\\\"\", \"param_id_mz\": \"\\\"0.001\\\"\", \"param_spectra_select_polarity\": \"null\", \"param_spectra_remove_collision_energy\": \"\\\":\\\"\", \"param_id_blacklist_imperfect\": \"\\\"false\\\"\", \"param_mz\": \"\\\":\\\"\", \"param_int\": \"\\\":\\\"\", \"param_spectra_select_isolation_window_width\": \"\\\":\\\"\", \"param_peak_options_indexed_file\": \"\\\"false\\\"\", \"param_spectra_select_activation\": \"null\", \"param_id_remove_annotated_features\": \"\\\"false\\\"\", \"__page__\": 0, \"param_peak_options_no_chromatograms\": \"\\\"false\\\"\", \"rep_param_peak_options_pc_mz_list\": \"[]\", \"param_peak_options_numpress_masstime\": \"\\\"none\\\"\", \"param_peak_options_remove_chromatograms\": \"\\\"false\\\"\", \"rep_param_consensus_map\": \"[]\", \"param_peak_options_numpress_intensity\": \"\\\"none\\\"\", \"param_pc_mz\": \"\\\":\\\"\", \"__rerun_remap_job_id__\": null, \"param_spectra_select_mode\": \"null\", \"param_rt\": \"\\\":\\\"\", \"param_algorithm_SignalToNoise_write_log_messages\": \"\\\"true\\\"\", \"param_consensus_blackorwhitelist_use_ppm_tolerance\": \"\\\"false\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_id_remove_unannotated_features\": \"\\\"true\\\"\", \"param_peak_options_sort_peaks\": \"\\\"false\\\"\", \"param_peak_options_int_precision\": \"\\\"32\\\"\", \"rep_param_id_accessions_whitelist\": \"[]\", \"param_peak_options_pc_mz_range\": \"\\\":\\\"\", \"param_out_type\": \"\\\"consensusXML\\\"\", \"param_spectra_remove_mode\": \"null\", \"param_consensus_blackorwhitelist_blacklist\": \"\\\"true\\\"\", \"rep_param_peak_options_level\": \"[{\\\"__index__\\\": 0, \\\"param_peak_options_level\\\": \\\"1 2 3\\\"}]\", \"rep_param_f_and_c_remove_meta\": \"[]\", \"param_f_and_c_size\": \"\\\":\\\"\", \"param_id_remove_unassigned_ids\": \"\\\"true\\\"\", \"param_spectra_remove_zoom\": \"\\\"false\\\"\", \"param_peak_options_mz_precision\": \"\\\"64\\\"\", \"param_sort\": \"\\\"false\\\"\", \"param_algorithm_SignalToNoise_min_required_elements\": \"\\\"10\\\"\", \"param_consensus_blackorwhitelist_rt\": \"\\\"60.0\\\"\", \"rep_param_peak_options_rm_pc_charge\": \"[]\", \"param_peak_options_numpress_intensity_error\": \"\\\"0.0001\\\"\", \"param_id_rt\": \"\\\"0.1\\\"\", \"param_id_keep_best_score_id\": \"\\\"false\\\"\", \"param_id_blacklist\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_spectra_select_collision_energy\": \"\\\":\\\"\", \"param_feature_q\": \"\\\":\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"param_f_and_c_charge\": \"\\\":\\\"\", \"param_consensus_map_and\": \"\\\"false\\\"\", \"param_spectra_select_zoom\": \"\\\"false\\\"\", \"param_consensus_blackorwhitelist_mz\": \"\\\"0.01\\\"\", \"param_consensus_blackorwhitelist_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"rep_param_consensus_blackorwhitelist_maps\": \"[]\", \"param_spectra_remove_activation\": \"null\", \"param_peak_options_numpress_masstime_error\": \"\\\"0.0001\\\"\", \"param_spectra_remove_isolation_window_width\": \"\\\":\\\"\"}",
-                        "tool_version": "2.1.0",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"id_column\": \"1\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"tool\": {\"tool_choice\": \"retrieve\", \"__current_case__\": 1, \"format\": \"fasta\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.2",
                         "type": "tool",
-                        "uuid": "77e6a295-f6e2-4d72-a7e3-94f682d916a7",
+                        "uuid": "c8c7914e-7c65-40b3-931b-c64b3848d383",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "param_out",
-                                "uuid": "55dc6d2b-f473-4496-abaf-86630ad0151b"
+                                "output_name": "outfile_retrieve_fasta",
+                                "uuid": "ce31b047-1193-4937-9d7b-2a5c5d2c9d6d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "FileMerger",
-                        "id": 18,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                        "errors": null,
+                        "id": 27,
                         "input_connections": {
-                            "param_in": {
-                                "id": 17,
-                                "output_name": "param_out"
+                            "input": {
+                                "id": 24,
+                                "output_name": "outfile_retrieve_fasta"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool FileMerger",
-                                "name": "param_in"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "FileMerger",
+                        "name": "FASTA-to-Tabular",
                         "outputs": [
                             {
-                                "name": "param_out",
-                                "type": "featurexml"
-                            },
-                            {
-                                "name": "param_rt_concat_trafo_out",
-                                "type": "trafoxml"
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 2832.966552734375,
-                            "top": 1062.9000244140625
+                            "bottom": 288.43333435058594,
+                            "height": 113.26666259765625,
+                            "left": 2276,
+                            "right": 2476,
+                            "top": 175.1666717529297,
+                            "width": 200,
+                            "x": 2276,
+                            "y": 175.1666717529297
                         },
                         "post_job_actions": {},
-                        "tool_errors": null,
-                        "tool_id": "FileMerger",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "39e8fde08881",
-                            "name": "openms_filemerger",
-                            "owner": "galaxyp",
+                            "changeset_revision": "e7ed3c310b74",
+                            "name": "fasta_to_tabular",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"param_raw_user_ms_level\": \"\\\"False\\\"\", \"param_raw_rt_auto\": \"\\\"false\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"param_raw_rt_filename\": \"\\\"false\\\"\", \"param_rt_concat_gap\": \"\\\"0.0\\\"\", \"param_annotate_file_origin\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"param_raw_ms_level\": \"\\\"2\\\"\", \"rep_param_raw_rt_custom\": \"[]\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "2.1.0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"descr_columns\": \"2\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
                         "type": "tool",
-                        "uuid": "d82505c8-6f1c-43a9-a9c7-c572ad2aa3c8",
+                        "uuid": "da7d791d-50c8-4c98-80dd-dc5fdee242d4",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "param_out",
-                                "uuid": "db9ffdb1-ef2f-4d53-9808-bef6de3d85b4"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "param_rt_concat_trafo_out",
-                                "uuid": "47af80c0-5efb-43b3-a830-c3df9fc0528d"
+                                "output_name": "output",
+                                "uuid": "bff31e15-ee6c-4972-9795-b478d0a0e9e7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "MzTabExporter",
-                        "id": 19,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                        "errors": null,
+                        "id": 28,
                         "input_connections": {
-                            "param_in": {
-                                "id": 18,
-                                "output_name": "param_out"
+                            "input": {
+                                "id": 26,
+                                "output_name": "outfile_retrieve_fasta"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool MzTabExporter",
-                                "name": "param_in"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "MzTabExporter",
+                        "name": "FASTA-to-Tabular",
                         "outputs": [
                             {
-                                "name": "param_out",
+                                "name": "output",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 3076.5,
-                            "top": 1061.88330078125
+                            "bottom": 408.433349609375,
+                            "height": 113.26666259765625,
+                            "left": 2276,
+                            "right": 2476,
+                            "top": 295.16668701171875,
+                            "width": 200,
+                            "x": 2276,
+                            "y": 295.16668701171875
                         },
                         "post_job_actions": {},
-                        "tool_errors": null,
-                        "tool_id": "MzTabExporter",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "bf32e0bcf554",
-                            "name": "openms_mztabexporter",
-                            "owner": "galaxyp",
+                            "changeset_revision": "e7ed3c310b74",
+                            "name": "fasta_to_tabular",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "2.1.0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"descr_columns\": \"2\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
                         "type": "tool",
-                        "uuid": "3f6cb69e-8629-4fea-ab74-dec388ed0fd4",
+                        "uuid": "6df99dbd-ac3d-4574-90dd-11f93c65d4c4",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "param_out",
-                                "uuid": "a6361de3-6865-4c6b-9920-d7a8c6a27645"
+                                "output_name": "output",
+                                "uuid": "f661462b-ca82-4621-9f2a-1c7892b89918"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/ntails",
-                "path": "topics/proteomics/tutorials/ntails/workflows/WF_ntails.ga",
+                "parent_id": "proteomics/maxquant-msstats-dda-lfq",
+                "path": "topics/proteomics/tutorials/maxquant-msstats-dda-lfq/workflows/main_workflow.ga",
                 "tags": [
                     "proteomics"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Tails Triple Dimethyl OpenMS2.1",
+                "title": "Proteomics: MaxQuant and MSstats LFQ workflow",
                 "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-ntails/versions/wf-ntails",
-                "tutorial_id": "ntails",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/ntails/workflows/WF_ntails.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/ntails/workflows/WF_ntails.html",
-                "version": 4,
-                "wfid": "proteomics-ntails",
-                "wfname": "wf-ntails",
-                "workflow": "WF_ntails.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-maxquant-msstats-dda-lfq/versions/main-workflow",
+                "tutorial_id": "maxquant-msstats-dda-lfq",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/workflows/main_workflow.html",
+                "version": 3,
+                "wfid": "proteomics-maxquant-msstats-dda-lfq",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "ConsensusID",
-                    "FalseDiscoveryRate",
-                    "FeatureFinderMultiplex",
-                    "FileFilter",
-                    "FileMerger",
-                    "HighResPrecursorMassCorrector",
-                    "IDConflictResolver",
-                    "IDFilter",
-                    "IDMapper",
-                    "IDMerger",
-                    "MSGFPlusAdapter",
-                    "MzTabExporter",
-                    "PeptideIndexer"
+                    "Cut1",
+                    "Filter1",
+                    "Grep1",
+                    "Summary_Statistics1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy4",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.22.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/datamash_ops/1.0.6",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1"
                 ],
-                "workflowhub_id": "1213"
+                "workflowhub_id": "1240"
             }
         ],
         "zenodo_link": ""
@@ -183130,163 +184841,293 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "msconvert",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "ddf54b12c295",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_to_tabular",
+                    "owner": "devteam",
+                    "revisions": "e7ed3c310b74",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "freebayes",
+                    "owner": "devteam",
+                    "revisions": "ef2c525bd8cd",
+                    "tool_panel_section_label": "Variant Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "tabular_to_fasta",
+                    "owner": "devteam",
+                    "revisions": "0a7799698fe5",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bed_to_protein_map",
                     "owner": "galaxyp",
-                    "revisions": "3cf310697624",
+                    "revisions": "a7c58b43cbaa",
                     "tool_panel_section_label": "Convert Formats",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "openms_openswathworkflow",
+                    "name": "custom_pro_db",
                     "owner": "galaxyp",
-                    "revisions": "887be35bc42e",
+                    "revisions": "2c7df0077d28",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "openms_openswathworkflow",
+                    "name": "fasta_merge_files_and_filter_unique_sequences",
                     "owner": "galaxyp",
-                    "revisions": "2aebe58de46e",
-                    "tool_panel_section_label": "Proteomics",
+                    "revisions": "f546e7278f04",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pyprophet_export",
+                    "name": "gffcompare_to_bed",
                     "owner": "galaxyp",
-                    "revisions": "3cf580bf28e2",
-                    "tool_panel_section_label": "Proteomics",
+                    "revisions": "ba5368c19dbd",
+                    "tool_panel_section_label": "Convert Formats",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pyprophet_merge",
+                    "name": "regex_find_replace",
                     "owner": "galaxyp",
-                    "revisions": "a67b508b1dc5",
-                    "tool_panel_section_label": "Proteomics",
+                    "revisions": "209b7c5ee9d7",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pyprophet_peptide",
+                    "name": "translate_bed",
                     "owner": "galaxyp",
-                    "revisions": "4504b3bc1eed",
-                    "tool_panel_section_label": "Proteomics",
+                    "revisions": "038ecf54cbec",
+                    "tool_panel_section_label": "Operate on Genomic Intervals",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "filter_tabular",
+                    "owner": "iuc",
+                    "revisions": "34d29339abab",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gffcompare",
+                    "owner": "iuc",
+                    "revisions": "0f710191a66d",
+                    "tool_panel_section_label": "Filter and Sort",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "hisat2",
+                    "owner": "iuc",
+                    "revisions": "a86e80d3c09c",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "query_tabular",
+                    "owner": "iuc",
+                    "revisions": "33d61c89fb8d",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pyprophet_protein",
-                    "owner": "galaxyp",
-                    "revisions": "2320f48209fc",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "sqlite_to_tabular",
+                    "owner": "iuc",
+                    "revisions": "b722161a845a",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pyprophet_score",
-                    "owner": "galaxyp",
-                    "revisions": "77f068ba47dd",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "stringtie",
+                    "owner": "iuc",
+                    "revisions": "1ebd14235b92",
+                    "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: msconvert\n  owner: galaxyp\n  revisions: 3cf310697624\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_openswathworkflow\n  owner: galaxyp\n  revisions: 887be35bc42e\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_openswathworkflow\n  owner: galaxyp\n  revisions: 2aebe58de46e\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pyprophet_export\n  owner: galaxyp\n  revisions: 3cf580bf28e2\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pyprophet_merge\n  owner: galaxyp\n  revisions: a67b508b1dc5\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pyprophet_peptide\n  owner: galaxyp\n  revisions: 4504b3bc1eed\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pyprophet_protein\n  owner: galaxyp\n  revisions: 2320f48209fc\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pyprophet_score\n  owner: galaxyp\n  revisions: 77f068ba47dd\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: ddf54b12c295\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_to_tabular\n  owner: devteam\n  revisions: e7ed3c310b74\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: freebayes\n  owner: devteam\n  revisions: ef2c525bd8cd\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tabular_to_fasta\n  owner: devteam\n  revisions: 0a7799698fe5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bed_to_protein_map\n  owner: galaxyp\n  revisions: a7c58b43cbaa\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: custom_pro_db\n  owner: galaxyp\n  revisions: 2c7df0077d28\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_merge_files_and_filter_unique_sequences\n  owner: galaxyp\n  revisions: f546e7278f04\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gffcompare_to_bed\n  owner: galaxyp\n  revisions: ba5368c19dbd\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 209b7c5ee9d7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: translate_bed\n  owner: galaxyp\n  revisions: '038ecf54cbec'\n  tool_panel_section_label: Operate on Genomic Intervals\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filter_tabular\n  owner: iuc\n  revisions: 34d29339abab\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gffcompare\n  owner: iuc\n  revisions: 0f710191a66d\n  tool_panel_section_label: Filter and Sort\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: hisat2\n  owner: iuc\n  revisions: a86e80d3c09c\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n  owner: iuc\n  revisions: 33d61c89fb8d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sqlite_to_tabular\n  owner: iuc\n  revisions: b722161a845a\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stringtie\n  owner: iuc\n  revisions: 1ebd14235b92\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "email": "matthias.fahrner@uniklinik-freiburg.de",
-                "id": "matthias313",
-                "joined": "2019-03",
-                "name": "Matthias Fahrner",
-                "orcid": "0000-0001-7955-2518",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/matthias313/",
-                "twitter": "mfahrner313",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/matthias313.json"
+                "email": "subinamehta@gmail.com",
+                "id": "subinamehta",
+                "joined": "2018-06",
+                "linkedin": "subinamehta",
+                "matrix": "subinamehta:matrix.org",
+                "name": "Subina Mehta",
+                "orcid": "0000-0001-9818-0537",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
+                "twitter": "Subina_Mehta",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
             },
             {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "email": "melanie.foell@mol-med.uni-freiburg.de",
-                "id": "foellmelanie",
-                "joined": "2018-10",
-                "matrix": "foellmelanie:matrix.org",
-                "name": "Melanie F\u00f6ll",
-                "orcid": "0000-0002-1887-7543",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
-                "twitter": "MCFoell",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
+                "email": "tgriffin@umn.edu",
+                "github": false,
+                "id": "timothygriffin",
+                "joined": "2017-09",
+                "name": "Timothy J. Griffin",
+                "orcid": "0000-0001-6801-2559",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
+            },
+            {
+                "email": "pjagtap@umn.edu",
+                "id": "pratikdjagtap",
+                "joined": "2017-09",
+                "name": "Pratik Jagtap",
+                "orcid": "0000-0003-0984-0973",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
+            },
+            {
+                "email": "rsajulga@umn.edu",
+                "id": "jraysajulga",
+                "joined": "2018-11",
+                "name": "Ray Sajulga",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jraysajulga/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jraysajulga.json"
+            },
+            {
+                "email": "jj@umn.edu",
+                "id": "jj-umn",
+                "in_memoriam": "<a href=\"https://galaxyproject.org/news/2024-03-19-remembrances-of-jj/\">James \u2018JJ\u2019 Johnson, was a Galaxy community rock star most known for his indispensable contributions to the Galaxy Proteomics community.</a>\n\nJJ\u2019s works will live on in so many Galaxy tools and workflows for years to come.",
+                "joined": "2017-09",
+                "name": "James Johnson",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jj-umn/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jj-umn.json"
+            },
+            {
+                "email": "kumar207@umn.edu",
+                "id": "pravs3683",
+                "joined": "2019-04",
+                "name": "Praveen Kumar",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pravs3683/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pravs3683.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/DIA_Analysis_OSW",
+        "dir": "topics/proteomics/tutorials/proteogenomics-dbcreation",
         "edam_operation": [
-            "Filtering",
-            "Formatting"
+            "Statistical calculation",
+            "Variant calling",
+            "Sequence annotation",
+            "Sequence alignment",
+            "Transcriptome assembly",
+            "RNA-Seq analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.be",
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "proteomics",
+                "tutorials": [
+                    "proteogenomics-dbsearch",
+                    "proteogenomics-novel-peptide-analysis"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "proteomics/DIA_Analysis_OSW",
+        "id": "proteomics/proteogenomics-dbcreation",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.no"
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "OpenSwathWorkflow enables analysis of data independent acquisition mass spectrometry data",
-            "DIA data analysis of HEK-Ecoli Spike-in dataset"
+            "Generating variant protein database",
+            "Generating genomic and variant mapping files for visualization"
         ],
         "layout": "tutorial_hands_on",
         "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-08-09",
         "objectives": [
-            "Analysis of HEK-Ecoli Spike-in DIA data in Galaxy",
-            "Understanding DIA data principles and characteristics",
-            "Using OpenSwathworkflow to analyze HEK-Ecoli Spike-in DIA data"
+            "Generating a customized Protein sequence database with variants, indels, splice junctions and known sequences."
         ],
-        "pageviews": 3284,
-        "pub_date": "2020-12-02",
+        "pageviews": 7973,
+        "pub_date": "2018-11-20",
         "questions": [
-            "How to analyze data independent acquisition (DIA) mass spectrometry (MS) data using OpenSwathWorkflow?",
-            "How to detect different Spike-in amounts of Ecoli in a HEK-Ecoli Benchmark DIA dataset?"
+            "How to create a customized Protein Database from RNAseq data?"
         ],
-        "requirements": [
+        "recordings": [
             {
-                "topic_name": "proteomics",
-                "tutorials": [
-                    "DIA_lib_OSW"
+                "captioners": [
+                    "emmaleith"
                 ],
-                "type": "internal"
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "40M",
+                "speakers": [
+                    "jj-umn"
+                ],
+                "youtube_id": "b_kZf8mXHdo"
             }
         ],
-        "short_id": "T00211",
+        "short_id": "T00231",
         "short_tools": [
-            "Grep1",
-            "msconvert",
-            "pyprophet_peptide",
-            "pyprophet_merge",
-            "pyprophet_protein",
-            "pyprophet_score",
-            "OpenSwathWorkflow",
-            "pyprophet_export"
+            "hisat2",
+            "query_tabular",
+            "tp_cat",
+            "custom_pro_db",
+            "fasta_merge_files_and_filter_unique_sequences",
+            "filter_tabular",
+            "gffcompare",
+            "sqlite_to_tabular",
+            "tab2fasta",
+            "bed_to_protein_map",
+            "stringtie",
+            "translate_bed",
+            "gffcompare_to_bed",
+            "regexColumn1",
+            "fasta2tab",
+            "freebayes",
+            "tp_replace_in_column"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "id-quant",
+        "subtopic": "multi-omics",
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 }
             ],
             "inexact": [
@@ -183299,25 +185140,38 @@
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
         "tags": [
-            "DIA"
+            "proteogenomics"
         ],
-        "time_estimation": "2H",
-        "title": "DIA Analysis using OpenSwathWorkflow",
+        "time_estimation": "30m",
+        "title": "Proteogenomics 1: Database Creation",
         "tools": [
-            "Grep1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/2.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_export/pyprophet_export/2.1.4.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_merge/pyprophet_merge/2.1.4.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_peptide/pyprophet_peptide/2.1.4.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_protein/pyprophet_protein/2.1.4.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_score/pyprophet_score/2.1.4.2"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/bed_to_protein_map/bed_to_protein_map/0.2.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.22.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/gffcompare_to_bed/gffcompare_to_bed/0.2.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed/translate_bed/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.11.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5",
+            "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1"
         ],
         "topic_name": "proteomics",
         "topic_name_human": "Proteomics",
@@ -183327,44 +185181,114 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "DIA_Analysis_OSW",
+        "tutorial_name": "proteogenomics-dbcreation",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.json"
         },
-        "version": 10,
+        "version": 27,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 134,
-        "visitors": 2259,
+        "visit_duration": 156,
+        "visitors": 4619,
         "workflows": [
             {
                 "creators": [],
-                "description": "DIA Analysis Training using HEK Ecoli data in OSW",
+                "description": "Proteogenomics Galaxy Training Network Database Creation",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput exp. design annotation\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\niRTassays.tsv\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSpectral library\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Collection\\n\u201dInput Dataset Collection\u201d\"]\n  4[label=\"msconvert\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"OpenSwathWorkflow\"]\n  4 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"PyProphet merge\"]\n  5 -> 6 [label=\"out_osw\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"PyProphet score\"]\n  6 -> 7 [label=\"output\"]\n  8[label=\"PyProphet peptide\"]\n  7 -> 8 [label=\"output\"]\n  9[label=\"PyProphet peptide\"]\n  8 -> 9 [label=\"output\"]\n  10[label=\"PyProphet protein\"]\n  9 -> 10 [label=\"output\"]\n  11[label=\"PyProphet protein\"]\n  10 -> 11 [label=\"output\"]\n  12[label=\"PyProphet export\"]\n  0 -> 12 [label=\"output\"]\n  11 -> 12 [label=\"output\"]\n  13[label=\"Ecoli protein expression matrix\"]\n  12 -> 13 [label=\"protein_signal\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nFASTQ_ProB_22LIST.fastqsanger\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMus_musculus.GRCm38.86.gtf\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTrimmed_ref_5000_uniprot_cRAP.fasta\"]\n  3[label=\"HISAT2\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Editing GTF File\"]\n  1 -> 4 [label=\"output\"]\n  k70b6f719803f4fa98394a3b64b71ec01[color=lightseagreen,label=\"Output\\nchr_corrected_gtf\"]\n  4 -> k70b6f719803f4fa98394a3b64b71ec01\n  5[label=\"FASTA-to-Tabular\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"FreeBayes\"]\n  3 -> 6 [label=\"output_alignments\"]\n  7[label=\"StringTie\"]\n  4 -> 7 [label=\"outfile\"]\n  3 -> 7 [label=\"output_alignments\"]\n  8[label=\"Filter Tabular\"]\n  5 -> 8 [label=\"output\"]\n  9[label=\"CustomProDB\"]\n  3 -> 9 [label=\"output_alignments\"]\n  6 -> 9 [label=\"output_vcf\"]\n  10[label=\"GffCompare\"]\n  4 -> 10 [label=\"outfile\"]\n  7 -> 10 [label=\"output_gtf\"]\n  11[label=\"SQLite to tabular\"]\n  9 -> 11 [label=\"output_genomic_mapping_sqlite\"]\n  12[label=\"SQLite to tabular\"]\n  9 -> 12 [label=\"output_variant_annotation_sqlite\"]\n  13[label=\"FASTA Merge Files and Filter Unique Sequences\"]\n  9 -> 13 [label=\"output_rpkm\"]\n  9 -> 13 [label=\"output_snv\"]\n  9 -> 13 [label=\"output_indel\"]\n  ka5054be9dd744d60a4c6494fdbcb97a1[color=lightseagreen,label=\"Output\\nCustomProDB_FASTA\"]\n  13 -> ka5054be9dd744d60a4c6494fdbcb97a1\n  14[label=\"FASTA-to-Tabular\"]\n  9 -> 14 [label=\"output_rpkm\"]\n  15[label=\"Convert gffCompare annotated GTF to BED\"]\n  10 -> 15 [label=\"transcripts_annotated\"]\n  16[label=\"Column Regex Find And Replace\"]\n  11 -> 16 [label=\"query_results\"]\n  17[label=\"Column Regex Find And Replace\"]\n  12 -> 17 [label=\"query_results\"]\n  18[label=\"FASTA-to-Tabular\"]\n  13 -> 18 [label=\"output\"]\n  19[label=\"Filter Tabular\"]\n  14 -> 19 [label=\"output\"]\n  20[label=\"Translate BED transcripts\"]\n  15 -> 20 [label=\"output\"]\n  21[label=\"Query Tabular\"]\n  17 -> 21 [label=\"out_file1\"]\n  ke94684794ebd4ced8086c10e916b97c5[color=lightseagreen,label=\"Output\\nvariant_annoation_sqlite\"]\n  21 -> ke94684794ebd4ced8086c10e916b97c5\n  22[label=\"Column Regex Find And Replace\"]\n  18 -> 22 [label=\"output\"]\n  23[label=\"Reference Protein Accessions\"]\n  19 -> 23 [label=\"output\"]\n  8 -> 23 [label=\"output\"]\n  k19aa5a8559334ab5ae76e4b1ec5b2f85[color=lightseagreen,label=\"Output\\nReference_Protein_Accessions\"]\n  23 -> k19aa5a8559334ab5ae76e4b1ec5b2f85\n  24[label=\"bed to protein map\"]\n  20 -> 24 [label=\"translation_bed\"]\n  25[label=\"Tabular-to-FASTA\"]\n  22 -> 25 [label=\"out_file1\"]\n  26[label=\"Concatenate datasets\"]\n  24 -> 26 [label=\"output\"]\n  16 -> 26 [label=\"out_file1\"]\n  27[label=\"FASTA Merge Files and Filter Unique Sequences\"]\n  2 -> 27 [label=\"output\"]\n  25 -> 27 [label=\"output\"]\n  20 -> 27 [label=\"translation_fasta\"]\n  k924bce7c5c6a4cb3a45918784a55ae01[color=lightseagreen,label=\"Output\\nUniprot_cRAP_SAV_indel_translatedbed_FASTA\"]\n  27 -> k924bce7c5c6a4cb3a45918784a55ae01\n  28[label=\"Genomic_mapping_sqlite\"]\n  26 -> 28 [label=\"out_file1\"]\n  k6542c4e5289a4be49b427a4e170ba198[color=lightseagreen,label=\"Output\\ngenomic_mapping_sqlite\"]\n  28 -> k6542c4e5289a4be49b427a4e170ba198\n}",
                 "history": [
                     {
-                        "hash": "15a13c3667af0db6a6ca380ca1b998c9faf625d3",
-                        "message": "updated workflow annotation and name",
+                        "hash": "28fc28c45aa8516e99a6f1f975814904be546a3a",
+                        "message": "Update galaxy-workflow-mouse_rnaseq_dbcreation.ga",
+                        "num": 12,
+                        "short_hash": "28fc28c45",
+                        "unix": "1612811929"
+                    },
+                    {
+                        "hash": "1eca54ca9d40ba883df90c41f9e671ffd4e45d59",
+                        "message": "Update galaxy-workflow-mouse_rnaseq_dbcreation.ga",
+                        "num": 11,
+                        "short_hash": "1eca54ca9",
+                        "unix": "1611784076"
+                    },
+                    {
+                        "hash": "0db38ae94eb41e0f3a8af428a741559473c8543f",
+                        "message": "Update galaxy-workflow-mouse_rnaseq_dbcreation.ga",
+                        "num": 10,
+                        "short_hash": "0db38ae94",
+                        "unix": "1611783698"
+                    },
+                    {
+                        "hash": "13e2ffc4d065eb5e76df61af4d1627e1e74ad103",
+                        "message": "Update galaxy-workflow-mouse_rnaseq_dbcreation.ga",
+                        "num": 9,
+                        "short_hash": "13e2ffc4d",
+                        "unix": "1611782854"
+                    },
+                    {
+                        "hash": "2c4b4646c61b3da411901fd4edc3e7f2270cd8bf",
+                        "message": "Update galaxy-workflow-mouse_rnaseq_dbcreation.ga",
+                        "num": 8,
+                        "short_hash": "2c4b4646c",
+                        "unix": "1611782235"
+                    },
+                    {
+                        "hash": "f99b54e3c22e74a3572ee864041f4726f4838727",
+                        "message": "Update galaxy-workflow-mouse_rnaseq_dbcreation.ga",
+                        "num": 7,
+                        "short_hash": "f99b54e3c",
+                        "unix": "1611781308"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 6,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 5,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "55fe079b2828d71aabb21fa0700f6f77ac76052c",
+                        "message": "WoLF PSORT WF",
+                        "num": 4,
+                        "short_hash": "55fe079b2",
+                        "unix": "1578933056"
+                    },
+                    {
+                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
+                        "message": "Changed format of workflows",
+                        "num": 3,
+                        "short_hash": "361236c41",
+                        "unix": "1554368414"
+                    },
+                    {
+                        "hash": "6eef55b7e8306d8ce46ac08e7799f6f65ae106aa",
+                        "message": "Updated install_tutorial_requirements.sh + minor fixes (#1275)",
                         "num": 2,
-                        "short_hash": "15a13c366",
-                        "unix": "1606931443"
+                        "short_hash": "6eef55b7e",
+                        "unix": "1551293676"
                     },
                     {
-                        "hash": "e8f20c190bc7a0d319835969a36114d939bd4dce",
-                        "message": "generated three tutorials on DIA data analysis in galaxy",
+                        "hash": "a928824de1a4881491bd2c63f7b60ba800319437",
+                        "message": "add protegenomics dbcreation tutorial",
                         "num": 1,
-                        "short_hash": "e8f20c190",
-                        "unix": "1606930318"
+                        "short_hash": "a928824de",
+                        "unix": "1535188370"
                     }
                 ],
                 "inputs": [
@@ -183377,32 +185301,32 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Input exp. design annotation"
+                                "name": "FASTQ_ProB_22LIST.fastqsanger"
                             }
                         ],
-                        "label": "Input exp. design annotation",
+                        "label": "FASTQ_ProB_22LIST.fastqsanger",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 646.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 490.5,
-                            "right": 690.5,
-                            "top": 564,
-                            "width": 200,
-                            "x": 490.5,
-                            "y": 564
+                            "bottom": 479.57811737060547,
+                            "height": 84,
+                            "left": 465.49999237060547,
+                            "right": 625.5000228881836,
+                            "top": 395.57811737060547,
+                            "width": 160.00003051757812,
+                            "x": 465.49999237060547,
+                            "y": 395.57811737060547
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "a5d35883-fba0-4de7-a883-8bb6b2be333d",
+                        "uuid": "a4deaec6-bac9-4c6d-9b55-1db09bd68be5",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "c5372600-b105-4692-8d32-60b4e882c235"
+                                "uuid": "8ce4f9b5-2fc0-4a8b-977c-0042f2f4bc60"
                             }
                         ]
                     },
@@ -183415,32 +185339,32 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "iRTassays.tsv"
+                                "name": "Mus_musculus.GRCm38.86.gtf"
                             }
                         ],
-                        "label": "iRTassays.tsv",
+                        "label": "Mus_musculus.GRCm38.86.gtf",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 184.8000030517578,
-                            "height": 61.80000305175781,
-                            "left": -1122.5,
-                            "right": -922.5,
-                            "top": 123,
-                            "width": 200,
-                            "x": -1122.5,
-                            "y": 123
+                            "bottom": 717.5468978881836,
+                            "height": 84.00003051757812,
+                            "left": 448.46874237060547,
+                            "right": 608.4687728881836,
+                            "top": 633.5468673706055,
+                            "width": 160.00003051757812,
+                            "x": 448.46874237060547,
+                            "y": 633.5468673706055
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "03ffba1e-879b-47ae-995d-ceb262b4ff4e",
+                        "uuid": "39d9897f-14c7-476a-a85d-08425745e5a3",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "8307748d-8fe6-4cee-8ac8-4d65bb598b0a"
+                                "uuid": "66e6bfc3-7f7f-415b-91be-a8d5deabe21f"
                             }
                         ]
                     },
@@ -183453,114 +185377,114 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Spectral library"
+                                "name": "Trimmed_ref_5000_uniprot_cRAP.fasta"
                             }
                         ],
-                        "label": "Spectral library",
+                        "label": "Trimmed_ref_5000_uniprot_cRAP.fasta",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 426.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": -1117.5,
-                            "right": -917.5,
-                            "top": 344,
-                            "width": 200,
-                            "x": -1117.5,
-                            "y": 344
+                            "bottom": 186.8125,
+                            "height": 84,
+                            "left": 2539.6719360351562,
+                            "right": 2699.6719360351562,
+                            "top": 102.8125,
+                            "width": 160,
+                            "x": 2539.6719360351562,
+                            "y": 102.8125
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "a2c7f825-ad7c-4966-ad08-a1634f7b5453",
+                        "uuid": "4ae4a7cf-adbd-4529-b4a5-e3a37d7c0120",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "1caaf3b7-2710-4835-89da-816d079a9e8a"
+                                "uuid": "f8446100-0e31-437c-a642-27c70ec4d7ef"
                             }
                         ]
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nFASTQ_ProB_22LIST.fastqsanger\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nMus_musculus.GRCm38.86.gtf\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nTrimmed_ref_5000_uniprot_cRAP.fasta\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"HISAT2\"];\n  0 -->|output| 3;\n  4[\"Editing GTF File\"];\n  1 -->|output| 4;\n  70b6f719-803f-4fa9-8394-a3b64b71ec01[\"Output\\nchr_corrected_gtf\"];\n  4 --> 70b6f719-803f-4fa9-8394-a3b64b71ec01;\n  style 70b6f719-803f-4fa9-8394-a3b64b71ec01 stroke:#2c3143,stroke-width:4px;\n  5[\"FASTA-to-Tabular\"];\n  2 -->|output| 5;\n  6[\"FreeBayes\"];\n  3 -->|output_alignments| 6;\n  7[\"StringTie\"];\n  4 -->|outfile| 7;\n  3 -->|output_alignments| 7;\n  8[\"Filter Tabular\"];\n  5 -->|output| 8;\n  9[\"CustomProDB\"];\n  3 -->|output_alignments| 9;\n  6 -->|output_vcf| 9;\n  10[\"GffCompare\"];\n  4 -->|outfile| 10;\n  7 -->|output_gtf| 10;\n  11[\"SQLite to tabular\"];\n  9 -->|output_genomic_mapping_sqlite| 11;\n  12[\"SQLite to tabular\"];\n  9 -->|output_variant_annotation_sqlite| 12;\n  13[\"FASTA Merge Files and Filter Unique Sequences\"];\n  9 -->|output_rpkm| 13;\n  9 -->|output_snv| 13;\n  9 -->|output_indel| 13;\n  a5054be9-dd74-4d60-a4c6-494fdbcb97a1[\"Output\\nCustomProDB_FASTA\"];\n  13 --> a5054be9-dd74-4d60-a4c6-494fdbcb97a1;\n  style a5054be9-dd74-4d60-a4c6-494fdbcb97a1 stroke:#2c3143,stroke-width:4px;\n  14[\"FASTA-to-Tabular\"];\n  9 -->|output_rpkm| 14;\n  15[\"Convert gffCompare annotated GTF to BED\"];\n  10 -->|transcripts_annotated| 15;\n  16[\"Column Regex Find And Replace\"];\n  11 -->|query_results| 16;\n  17[\"Column Regex Find And Replace\"];\n  12 -->|query_results| 17;\n  18[\"FASTA-to-Tabular\"];\n  13 -->|output| 18;\n  19[\"Filter Tabular\"];\n  14 -->|output| 19;\n  20[\"Translate BED transcripts\"];\n  15 -->|output| 20;\n  21[\"Query Tabular\"];\n  17 -->|out_file1| 21;\n  e9468479-4ebd-4ced-8086-c10e916b97c5[\"Output\\nvariant_annoation_sqlite\"];\n  21 --> e9468479-4ebd-4ced-8086-c10e916b97c5;\n  style e9468479-4ebd-4ced-8086-c10e916b97c5 stroke:#2c3143,stroke-width:4px;\n  22[\"Column Regex Find And Replace\"];\n  18 -->|output| 22;\n  23[\"Reference Protein Accessions\"];\n  19 -->|output| 23;\n  8 -->|output| 23;\n  19aa5a85-5933-4ab5-ae76-e4b1ec5b2f85[\"Output\\nReference_Protein_Accessions\"];\n  23 --> 19aa5a85-5933-4ab5-ae76-e4b1ec5b2f85;\n  style 19aa5a85-5933-4ab5-ae76-e4b1ec5b2f85 stroke:#2c3143,stroke-width:4px;\n  24[\"bed to protein map\"];\n  20 -->|translation_bed| 24;\n  25[\"Tabular-to-FASTA\"];\n  22 -->|out_file1| 25;\n  26[\"Concatenate datasets\"];\n  24 -->|output| 26;\n  16 -->|out_file1| 26;\n  27[\"FASTA Merge Files and Filter Unique Sequences\"];\n  2 -->|output| 27;\n  25 -->|output| 27;\n  20 -->|translation_fasta| 27;\n  924bce7c-5c6a-4cb3-a459-18784a55ae01[\"Output\\nUniprot_cRAP_SAV_indel_translatedbed_FASTA\"];\n  27 --> 924bce7c-5c6a-4cb3-a459-18784a55ae01;\n  style 924bce7c-5c6a-4cb3-a459-18784a55ae01 stroke:#2c3143,stroke-width:4px;\n  28[\"Genomic_mapping_sqlite\"];\n  26 -->|out_file1| 28;\n  6542c4e5-289a-4be4-9b42-7a4e170ba198[\"Output\\ngenomic_mapping_sqlite\"];\n  28 --> 6542c4e5-289a-4be4-9b42-7a4e170ba198;\n  style 6542c4e5-289a-4be4-9b42-7a4e170ba198 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "GTN Proteogenomics1 Database Creation",
+                "outputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "\"Input Dataset Collection\""
+                                "name": "FASTQ_ProB_22LIST.fastqsanger"
                             }
                         ],
-                        "label": "\"Input Dataset Collection\"",
-                        "name": "Input dataset collection",
+                        "label": "FASTQ_ProB_22LIST.fastqsanger",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 469.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": -1330.5,
-                            "right": -1130.5,
-                            "top": 387,
-                            "width": 200,
-                            "x": -1330.5,
-                            "y": 387
+                            "bottom": 479.57811737060547,
+                            "height": 84,
+                            "left": 465.49999237060547,
+                            "right": 625.5000228881836,
+                            "top": 395.57811737060547,
+                            "width": 160.00003051757812,
+                            "x": 465.49999237060547,
+                            "y": 395.57811737060547
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "e5b0dbc4-3478-4d5b-a220-ca720f06c787",
+                        "type": "data_input",
+                        "uuid": "a4deaec6-bac9-4c6d-9b55-1db09bd68be5",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "dee72339-437a-4b71-8aab-85fce61e7369"
+                                "uuid": "8ce4f9b5-2fc0-4a8b-977c-0042f2f4bc60"
                             }
                         ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput exp. design annotation\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\niRTassays.tsv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nSpectral library\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Collection\\n\u201dInput Dataset Collection\u201d\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"msconvert\"];\n  3 -->|output| 4;\n  5[\"OpenSwathWorkflow\"];\n  4 -->|output| 5;\n  2 -->|output| 5;\n  1 -->|output| 5;\n  6[\"PyProphet merge\"];\n  5 -->|out_osw| 6;\n  2 -->|output| 6;\n  7[\"PyProphet score\"];\n  6 -->|output| 7;\n  8[\"PyProphet peptide\"];\n  7 -->|output| 8;\n  9[\"PyProphet peptide\"];\n  8 -->|output| 9;\n  10[\"PyProphet protein\"];\n  9 -->|output| 10;\n  11[\"PyProphet protein\"];\n  10 -->|output| 11;\n  12[\"PyProphet export\"];\n  0 -->|output| 12;\n  11 -->|output| 12;\n  13[\"Ecoli protein expression matrix\"];\n  12 -->|protein_signal| 13;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "DIA_Analysis_OSW",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Input exp. design annotation"
+                                "name": "Mus_musculus.GRCm38.86.gtf"
                             }
                         ],
-                        "label": "Input exp. design annotation",
+                        "label": "Mus_musculus.GRCm38.86.gtf",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 646.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 490.5,
-                            "right": 690.5,
-                            "top": 564,
-                            "width": 200,
-                            "x": 490.5,
-                            "y": 564
+                            "bottom": 717.5468978881836,
+                            "height": 84.00003051757812,
+                            "left": 448.46874237060547,
+                            "right": 608.4687728881836,
+                            "top": 633.5468673706055,
+                            "width": 160.00003051757812,
+                            "x": 448.46874237060547,
+                            "y": 633.5468673706055
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "a5d35883-fba0-4de7-a883-8bb6b2be333d",
+                        "uuid": "39d9897f-14c7-476a-a85d-08425745e5a3",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "c5372600-b105-4692-8d32-60b4e882c235"
+                                "uuid": "66e6bfc3-7f7f-415b-91be-a8d5deabe21f"
                             }
                         ]
                     },
@@ -183568,704 +185492,885 @@
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "iRTassays.tsv"
+                                "name": "Trimmed_ref_5000_uniprot_cRAP.fasta"
                             }
                         ],
-                        "label": "iRTassays.tsv",
+                        "label": "Trimmed_ref_5000_uniprot_cRAP.fasta",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 184.8000030517578,
-                            "height": 61.80000305175781,
-                            "left": -1122.5,
-                            "right": -922.5,
-                            "top": 123,
-                            "width": 200,
-                            "x": -1122.5,
-                            "y": 123
+                            "bottom": 186.8125,
+                            "height": 84,
+                            "left": 2539.6719360351562,
+                            "right": 2699.6719360351562,
+                            "top": 102.8125,
+                            "width": 160,
+                            "x": 2539.6719360351562,
+                            "y": 102.8125
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "03ffba1e-879b-47ae-995d-ceb262b4ff4e",
+                        "uuid": "4ae4a7cf-adbd-4529-b4a5-e3a37d7c0120",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "8307748d-8fe6-4cee-8ac8-4d65bb598b0a"
+                                "uuid": "f8446100-0e31-437c-a642-27c70ec4d7ef"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 3,
+                        "input_connections": {
+                            "library|input_1": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "HISAT2",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Spectral library"
+                                "name": "output_alignments",
+                                "type": "bam"
                             }
                         ],
-                        "label": "Spectral library",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 426.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": -1117.5,
-                            "right": -917.5,
-                            "top": 344,
-                            "width": 200,
-                            "x": -1117.5,
-                            "y": 344
+                            "bottom": 504.17813873291016,
+                            "height": 109.60000610351562,
+                            "left": 716.5000152587891,
+                            "right": 876.5000152587891,
+                            "top": 394.57813262939453,
+                            "width": 160,
+                            "x": 716.5000152587891,
+                            "y": 394.57813262939453
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5",
+                        "tool_shed_repository": {
+                            "changeset_revision": "a86e80d3c09c",
+                            "name": "hisat2",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv\": {\"input_options\": {\"input_options_selector\": \"defaults\", \"__current_case__\": 0}, \"alignment_options\": {\"alignment_options_selector\": \"defaults\", \"__current_case__\": 0}, \"scoring_options\": {\"scoring_options_selector\": \"defaults\", \"__current_case__\": 0}, \"spliced_options\": {\"spliced_options_selector\": \"defaults\", \"__current_case__\": 0}, \"reporting_options\": {\"reporting_options_selector\": \"defaults\", \"__current_case__\": 0}, \"output_options\": {\"output_options_selector\": \"defaults\", \"__current_case__\": 0}, \"other_options\": {\"other_options_selector\": \"defaults\", \"__current_case__\": 0}}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"rna_strandness\": \"\"}, \"reference_genome\": {\"source\": \"indexed\", \"__current_case__\": 0, \"index\": \"mm10\"}, \"sum\": {\"new_summary\": \"false\", \"summary_file\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "a2c7f825-ad7c-4966-ad08-a1634f7b5453",
+                        "type": "tool",
+                        "uuid": "6ebfb19c-ad93-4506-96f8-8c6ecbff76d0",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "1caaf3b7-2710-4835-89da-816d079a9e8a"
+                                "output_name": "output_alignments",
+                                "uuid": "e3257606-a1f4-4a0e-9cfa-f2a5a5aee993"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
                         "errors": null,
-                        "id": 3,
-                        "input_connections": {},
+                        "id": 4,
+                        "input_connections": {
+                            "infile": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "\"Input Dataset Collection\""
+                                "description": "runtime parameter for tool Replace Text",
+                                "name": "infile"
+                            }
+                        ],
+                        "label": "Editing GTF File",
+                        "name": "Replace Text",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "input"
                             }
                         ],
-                        "label": "\"Input Dataset Collection\"",
-                        "name": "Input dataset collection",
-                        "outputs": [],
                         "position": {
-                            "bottom": 469.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": -1330.5,
-                            "right": -1130.5,
-                            "top": 387,
-                            "width": 200,
-                            "x": -1330.5,
-                            "y": 387
+                            "bottom": 949.1468658447266,
+                            "height": 109.5999755859375,
+                            "left": 715.5625152587891,
+                            "right": 875.5625152587891,
+                            "top": 839.5468902587891,
+                            "width": 160,
+                            "x": 715.5625152587891,
+                            "y": 839.5468902587891
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutfile": {
+                                "action_arguments": {
+                                    "newname": "Edited_Mus_Musculus.GRCm38.86"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "outfile"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "a6f147a050a2",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"infile\": {\"__class__\": \"RuntimeValue\"}, \"replacements\": [{\"__index__\": 0, \"column\": \"1\", \"find_pattern\": \"^([1-9][0-9]*)$\", \"replace_pattern\": \"chr\\\\\\\\1\"}, {\"__index__\": 1, \"column\": \"1\", \"find_pattern\": \"^([XY])$\", \"replace_pattern\": \"chr\\\\\\\\1\"}, {\"__index__\": 2, \"column\": \"1\", \"find_pattern\": \"^MT$\", \"replace_pattern\": \"chrM\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "e5b0dbc4-3478-4d5b-a220-ca720f06c787",
+                        "type": "tool",
+                        "uuid": "1771bf89-9c60-4d45-bbf9-15c937b5aa3a",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "dee72339-437a-4b71-8aab-85fce61e7369"
+                                "label": "chr_corrected_gtf",
+                                "output_name": "outfile",
+                                "uuid": "70b6f719-803f-4fa9-8394-a3b64b71ec01"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
                         "errors": null,
-                        "id": 4,
+                        "id": 5,
                         "input_connections": {
                             "input": {
-                                "id": 3,
+                                "id": 2,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "msconvert",
+                        "name": "FASTA-to-Tabular",
                         "outputs": [
                             {
                                 "name": "output",
-                                "type": "mzml"
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 596.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": -1122.5,
-                            "right": -922.5,
-                            "top": 483,
-                            "width": 200,
-                            "x": -1122.5,
-                            "y": 483
+                            "bottom": 209.8312530517578,
+                            "height": 92.80000305175781,
+                            "left": 2793.7655639648438,
+                            "right": 2953.7655639648438,
+                            "top": 117.03125,
+                            "width": 160,
+                            "x": 2793.7655639648438,
+                            "y": 117.03125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "3cf310697624",
-                            "name": "msconvert",
-                            "owner": "galaxyp",
+                            "changeset_revision": "7e801ab2b70e",
+                            "name": "fasta_to_tabular",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"data_processing\": {\"peak_picking\": {\"pick_peaks\": \"true\", \"__current_case__\": 1, \"pick_peaks_ms_levels\": \"1-\", \"pick_peaks_algorithm\": \"vendor\"}, \"precursor_refinement\": {\"use_mzrefinement\": \"false\", \"__current_case__\": 0}, \"charge_state_calculation\": {\"charge_state_calculation_method\": \"false\", \"__current_case__\": 0}, \"thresholds\": [], \"filter_mz_windows\": {\"do_mzwindow_filter\": \"false\", \"__current_case__\": 0}, \"etd_filtering\": {\"do_etd_filtering\": \"false\", \"__current_case__\": 0}, \"ms2denoise\": {\"denoise\": \"false\", \"__current_case__\": 1}, \"ms2deisotope\": \"false\", \"demultiplex\": {\"demultiplex_on\": \"true\", \"__current_case__\": 0, \"massError\": \"10.0\", \"massErrorUnits\": \"PPM\", \"nnlsMaxIter\": \"50\", \"nnlsEps\": \"1e-10\", \"demuxBlockExtra\": \"0.0\", \"variableFill\": \"false\", \"noSumNormalize\": \"true\", \"optimization\": \"overlap_only\", \"interpolateRT\": \"true\", \"noWeighting\": \"true\", \"minWindowSize\": \"0.2\"}}, \"filtering\": {\"activation\": \"false\", \"indices\": [], \"scan_numbers\": [], \"strip_it\": \"false\", \"filter_ms_levels\": {\"do_ms_level_filter\": \"false\", \"__current_case__\": 0}, \"polarity\": \"false\", \"analyzer\": \"false\"}, \"general_options\": {\"combineIonMobilitySpectra\": \"false\", \"scan_summing\": {\"do_scan_summing\": \"false\", \"__current_case__\": 0}, \"simAsSpectra\": \"true\", \"srmAsSpectra\": \"false\", \"acceptZeroLengthSpectra\": \"false\", \"ignoreUnknownInstrumentError\": \"true\", \"multi_run_output\": {\"do_multi_run_output\": \"false\", \"__current_case__\": 0, \"runIndexSet\": \"0\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"license_agreement\": \"true\", \"output_type\": \"mzML\", \"settings\": {\"mz_encoding\": \"64\", \"intensity_encoding\": \"64\", \"binary_compression\": \"zlib\", \"gzip_compression\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.0.19052.1",
+                        "tool_state": "{\"descr_columns\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "e83c6a83-748d-478f-a2cb-0992b2e8b780",
+                        "uuid": "1c90c734-44df-433a-8431-da0dae1e46d0",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "0fd858b9-4bca-44c8-baa3-e0e50e45ac1d"
+                                "uuid": "55a4c3db-64ee-4631-aecd-11e9dc0d8bac"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/2.5+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1",
                         "errors": null,
-                        "id": 5,
+                        "id": 6,
                         "input_connections": {
-                            "in": {
+                            "reference_source|batchmode|input_bams": {
+                                "id": 3,
+                                "output_name": "output_alignments"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FreeBayes",
+                        "outputs": [
+                            {
+                                "name": "output_vcf",
+                                "type": "vcf"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 534.3468780517578,
+                            "height": 92.80001831054688,
+                            "left": 1046.5625,
+                            "right": 1206.5625,
+                            "top": 441.54685974121094,
+                            "width": 160,
+                            "x": 1046.5625,
+                            "y": 441.54685974121094
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ef2c525bd8cd",
+                            "name": "freebayes",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"coverage_options\": {\"coverage_options_selector\": \"do_not_set\", \"__current_case__\": 1}, \"options_type\": {\"options_type_selector\": \"simple\", \"__current_case__\": 1}, \"reference_source\": {\"reference_source_selector\": \"cached\", \"__current_case__\": 0, \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_bams\": {\"__class__\": \"ConnectedValue\"}}, \"ref_file\": \"mm10full\"}, \"target_limit_type\": {\"target_limit_type_selector\": \"do_not_limit\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "c02258e7-9b87-4a32-9a49-a4edb44a293f",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_vcf",
+                                "uuid": "3ce080ca-cae9-457f-8606-4357fd9c5736"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "guide|guide_source|ref_hist": {
                                 "id": 4,
-                                "output_name": "output"
-                            },
-                            "tr": {
-                                "id": 2,
-                                "output_name": "output"
+                                "output_name": "outfile"
                             },
-                            "tr_irt": {
-                                "id": 1,
-                                "output_name": "output"
+                            "input_bam": {
+                                "id": 3,
+                                "output_name": "output_alignments"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "StringTie",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool OpenSwathWorkflow",
-                                "name": "adv_opts_cond"
-                            },
+                                "name": "output_gtf",
+                                "type": "gtf"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 808.7781372070312,
+                            "height": 151.20001220703125,
+                            "left": 1039.53125,
+                            "right": 1199.53125,
+                            "top": 657.578125,
+                            "width": 160,
+                            "x": 1039.53125,
+                            "y": 657.578125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "1ebd14235b92",
+                            "name": "stringtie",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"bam\", \"adv\": {\"abundance_estimation\": \"false\", \"omit_sequences\": \"\", \"name_prefix\": \"\", \"fraction\": \"0.15\", \"min_tlen\": \"200\", \"min_anchor_len\": \"10\", \"min_anchor_cov\": \"1\", \"min_bundle_cov\": \"2\", \"bdist\": \"50\", \"bundle_fraction\": \"0.95\", \"disable_trimming\": \"false\", \"multi_mapping\": \"false\"}, \"chromInfo\": \"/panfs/roc/website/galaxyp.msi.umn.edu/galaxy/tool-data/shared/ucsc/chrom/mm10.len\", \"guide\": {\"use_guide\": \"yes\", \"__current_case__\": 1, \"guide_source\": {\"guide_gff_select\": \"history\", \"__current_case__\": 1, \"ref_hist\": {\"__class__\": \"ConnectedValue\"}}, \"input_estimation\": \"false\", \"special_outputs\": {\"special_outputs_select\": \"no\", \"__current_case__\": 2}, \"coverage_file\": \"false\"}, \"input_bam\": {\"__class__\": \"ConnectedValue\"}, \"long_reads\": \"false\", \"rna_strandness\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "fad69441-c09f-410c-8c49-34832d8e297d",
+                        "workflow_outputs": [
                             {
-                                "description": "runtime parameter for tool OpenSwathWorkflow",
-                                "name": "swath_windows_file"
-                            },
+                                "label": null,
+                                "output_name": "output_gtf",
+                                "uuid": "12837520-843e-49c1-be1e-06a44985c2b9"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "input": {
+                                "id": 5,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Filter Tabular",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool OpenSwathWorkflow",
-                                "name": "tr_irt_nonlinear"
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
+                        "position": {
+                            "bottom": 252.8000030517578,
+                            "height": 92.80000305175781,
+                            "left": 3066.40625,
+                            "right": 3226.40625,
+                            "top": 160,
+                            "width": 160,
+                            "x": 3066.40625,
+                            "y": 160
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "34d29339abab",
+                            "name": "filter_tabular",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"select_columns\", \"__current_case__\": 7, \"columns\": \"1\"}}, {\"__index__\": 1, \"filter\": {\"filter_type\": \"replace\", \"__current_case__\": 8, \"column\": \"1\", \"regex_pattern\": \"^[^|]+[|]([^| ]+).*$\", \"regex_replace\": \"\\\\1\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "067ce402-0494-4d31-860f-50097b76449d",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "adbd3988-0a8e-409c-b1b2-4939fe9611a4"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.22.0",
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {
+                            "genome_annotation|bamInput": {
+                                "id": 3,
+                                "output_name": "output_alignments"
+                            },
+                            "genome_annotation|vcfInput": {
+                                "id": 6,
+                                "output_name": "output_vcf"
+                            }
+                        },
+                        "inputs": [],
                         "label": null,
-                        "name": "OpenSwathWorkflow",
+                        "name": "CustomProDB",
                         "outputs": [
                             {
-                                "name": "out_osw",
-                                "type": "osw"
+                                "name": "output_rpkm",
+                                "type": "fasta"
                             },
                             {
-                                "name": "ctd_out",
-                                "type": "xml"
+                                "name": "output_snv",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "output_indel",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "output_variant_annotation_rdata",
+                                "type": "rdata"
+                            },
+                            {
+                                "name": "output_genomic_mapping_sqlite",
+                                "type": "sqlite"
+                            },
+                            {
+                                "name": "output_variant_annotation_sqlite",
+                                "type": "sqlite"
                             }
                         ],
                         "position": {
-                            "bottom": 903.7999877929688,
-                            "height": 540.7999877929688,
-                            "left": -839.5,
-                            "right": -639.5,
-                            "top": 363,
-                            "width": 200,
-                            "x": -839.5,
-                            "y": 363
+                            "bottom": 391.89999198913574,
+                            "height": 342.3999938964844,
+                            "left": 1294.6719360351562,
+                            "right": 1454.6719360351562,
+                            "top": 49.49999809265137,
+                            "width": 160,
+                            "x": 1294.6719360351562,
+                            "y": 49.49999809265137
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/2.5+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.22.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "2aebe58de46e",
-                            "name": "openms_openswathworkflow",
+                            "changeset_revision": "2c7df0077d28",
+                            "name": "custom_pro_db",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"Calibration\": {\"ms1_im_calibration\": \"false\", \"im_correction_function\": \"linear\", \"debug_im_file\": \"\", \"debug_mz_file\": \"\"}, \"Library\": {\"retentionTimeInterpretation\": \"iRT\", \"override_group_label_check\": \"false\", \"force_invalid_mods\": \"false\"}, \"OPTIONAL_OUTPUTS\": [\"out_osw_FLAG\", \"ctd_out_FLAG\"], \"RTNormalization\": {\"alignmentMethod\": \"linear\", \"outlierMethod\": \"none\", \"useIterativeChauvenet\": \"false\", \"RANSACMaxIterations\": \"1000\", \"RANSACMaxPercentRTThreshold\": \"3\", \"RANSACSamplingSize\": \"10\", \"estimateBestPeptides\": \"true\", \"InitialQualityCutoff\": \"0.5\", \"OverallQualityCutoff\": \"5.5\", \"NrRTBins\": \"10\", \"MinPeptidesPerBin\": \"1\", \"MinBinsFilled\": \"7\", \"lowess\": {\"span\": \"0.666666666666667\"}, \"b_spline\": {\"num_nodes\": \"5\"}}, \"Scoring\": {\"stop_report_after_feature\": \"5\", \"rt_normalization_factor\": \"100.0\", \"quantification_cutoff\": \"0.0\", \"write_convex_hull\": \"false\", \"spectrum_addition_method\": \"simple\", \"add_up_spectra\": \"1\", \"spacing_for_spectra_resampling\": \"0.005\", \"uis_threshold_sn\": \"0\", \"uis_threshold_peak_area\": \"0\", \"scoring_model\": \"default\", \"im_extra_drift\": \"0.0\", \"strict\": \"true\", \"TransitionGroupPicker\": {\"stop_after_feature\": \"-1\", \"min_peak_width\": \"5.0\", \"peak_integration\": \"original\", \"background_subtraction\": \"none\", \"recalculate_peaks\": \"true\", \"use_precursors\": \"false\", \"use_consensus\": \"true\", \"recalculate_peaks_max_z\": \"0.75\", \"minimal_quality\": \"-1.5\", \"resample_boundary\": \"15.0\", \"compute_peak_quality\": \"false\", \"compute_peak_shape_metrics\": \"false\", \"compute_total_mi\": \"false\", \"boundary_selection_method\": \"largest\", \"PeakPickerMRM\": {\"sgolay_frame_length\": \"11\", \"sgolay_polynomial_order\": \"3\", \"gauss_width\": \"30.0\", \"use_gauss\": \"false\", \"peak_width\": \"-1.0\", \"signal_to_noise\": \"0.1\", \"write_sn_log_messages\": \"false\", \"remove_overlapping_peaks\": \"true\", \"method\": \"corrected\"}, \"PeakIntegrator\": {\"integration_type\": \"intensity_sum\", \"baseline_type\": \"base_to_base\", \"fit_EMG\": \"false\"}}, \"DIAScoring\": {\"dia_extraction_window\": \"0.05\", \"dia_extraction_unit\": \"Th\", \"dia_centroided\": \"false\", \"dia_byseries_intensity_min\": \"300.0\", \"dia_byseries_ppm_diff\": \"10.0\", \"dia_nr_isotopes\": \"4\", \"dia_nr_charges\": \"4\", \"peak_before_mono_max_ppm_diff\": \"20.0\"}, \"EMGScoring\": {\"max_iteration\": \"10\"}, \"Scores\": {\"use_shape_score\": \"true\", \"use_coelution_score\": \"true\", \"use_rt_score\": \"true\", \"use_library_score\": \"true\", \"use_intensity_score\": \"true\", \"use_nr_peaks_score\": \"true\", \"use_total_xic_score\": \"true\", \"use_total_mi_score\": \"false\", \"use_sn_score\": \"true\", \"use_mi_score\": \"false\", \"use_dia_scores\": \"true\", \"use_ms1_correlation\": \"false\", \"use_sonar_scores\": \"false\", \"use_ion_mobility_scores\": \"false\", \"use_ms1_fullscan\": \"false\", \"use_ms1_mi\": \"true\", \"use_uis_scores\": \"false\"}}, \"adv_opts_cond\": {\"adv_opts_selector\": \"advanced\", \"__current_case__\": 1, \"rt_norm\": {\"__class__\": \"RuntimeValue\"}, \"sort_swath_maps\": \"false\", \"enable_ms1\": \"true\", \"enable_ipf\": \"true\", \"out_chrom_type\": \"mzML\", \"min_upper_edge_dist\": \"0.0\", \"extra_rt_extraction_window\": \"100.0\", \"mz_extraction_window_unit\": \"ppm\", \"mz_extraction_window_ms1_unit\": \"ppm\", \"use_ms1_ion_mobility\": \"false\", \"matching_window_only\": \"false\", \"irt_mz_extraction_window\": \"10.0\", \"irt_mz_extraction_window_unit\": \"ppm\", \"irt_im_extraction_window\": \"-1.0\", \"min_rsq\": \"0.95\", \"min_coverage\": \"0.6\", \"split_file_input\": \"false\", \"use_elution_model_score\": \"false\", \"readOptions\": \"cacheWorkingInMemory\", \"mz_correction_function\": \"regression_delta_ppm\", \"extraction_function\": \"tophat\", \"batchSize\": \"1000\", \"ms1_isotopes\": \"3\", \"force\": \"false\", \"test\": \"False\"}, \"im_extraction_window_ms1\": \"-1.0\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"ion_mobility_window\": \"-1.0\", \"mz_extraction_window\": \"10.0\", \"mz_extraction_window_ms1\": \"10.0\", \"rt_extraction_window\": \"600.0\", \"sonar\": \"false\", \"swath_windows_file\": {\"__class__\": \"RuntimeValue\"}, \"tr\": {\"__class__\": \"ConnectedValue\"}, \"tr_irt\": {\"__class__\": \"ConnectedValue\"}, \"tr_irt_nonlinear\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"genome_annotation\": {\"source\": \"builtin\", \"__current_case__\": 0, \"builtin\": \"mm10_GRCm38.p5\", \"bamInput\": {\"__class__\": \"ConnectedValue\"}, \"vcfInput\": {\"__class__\": \"ConnectedValue\"}, \"dbsnpInCoding\": \"false\", \"cosmic\": \"false\"}, \"outputIndels\": \"true\", \"outputRData\": \"true\", \"outputSQLite\": \"true\", \"rpkmCutoff\": \"1.0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "77259b26-ee12-4fff-a26b-4233bd95bf2c",
+                        "uuid": "3268fd0d-0aa0-45d2-ad2d-2ba443d94a2b",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_osw",
-                                "uuid": "263858ee-f576-4b39-9f4b-1487bf60212e"
+                                "output_name": "output_rpkm",
+                                "uuid": "2e2725cd-de12-4fa3-ae65-dfc52dbe45bf"
                             },
                             {
                                 "label": null,
-                                "output_name": "ctd_out",
-                                "uuid": "7a6e422b-1246-4ed9-945e-fa215225e53a"
+                                "output_name": "output_snv",
+                                "uuid": "9dddcd8b-25bc-4bc0-9240-fd3157340cbd"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_indel",
+                                "uuid": "d8ba561c-2dc7-4668-ab3c-8d11a0bbc8db"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_variant_annotation_rdata",
+                                "uuid": "951816e4-4410-4bf9-982c-0604ecfc5a4b"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_genomic_mapping_sqlite",
+                                "uuid": "a856b8cf-185e-435a-8c5c-0e87fa5fb7ac"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_variant_annotation_sqlite",
+                                "uuid": "045869cc-5493-439c-b870-b2be30170137"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_merge/pyprophet_merge/2.1.4.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.11.2",
                         "errors": null,
-                        "id": 6,
+                        "id": 10,
                         "input_connections": {
-                            "inputs": {
-                                "id": 5,
-                                "output_name": "out_osw"
+                            "annotation|ref_source|reference_annotation": {
+                                "id": 4,
+                                "output_name": "outfile"
                             },
-                            "template": {
-                                "id": 2,
-                                "output_name": "output"
+                            "gffinputs": {
+                                "id": 7,
+                                "output_name": "output_gtf"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "PyProphet merge",
+                        "name": "GffCompare",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "osw"
+                                "name": "refmap_output",
+                                "type": "input"
+                            },
+                            {
+                                "name": "tmap_output",
+                                "type": "input"
+                            },
+                            {
+                                "name": "transcripts_stats",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "transcripts_loci",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "transcripts_tracking",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "transcripts_annotated",
+                                "type": "gtf"
                             }
                         ],
                         "position": {
-                            "bottom": 307.8000030517578,
-                            "height": 184.8000030517578,
-                            "left": -682.5,
-                            "right": -482.5,
-                            "top": 123,
-                            "width": 200,
-                            "x": -682.5,
-                            "y": 123
+                            "bottom": 1232.715576171875,
+                            "height": 359.199951171875,
+                            "left": 1283.6563110351562,
+                            "right": 1443.6563110351562,
+                            "top": 873.515625,
+                            "width": 160,
+                            "x": 1283.6563110351562,
+                            "y": 873.515625
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_merge/pyprophet_merge/2.1.4.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.11.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "a67b508b1dc5",
-                            "name": "pyprophet_merge",
-                            "owner": "galaxyp",
+                            "changeset_revision": "0f710191a66d",
+                            "name": "gffcompare",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"osw\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"inputs\": {\"__class__\": \"ConnectedValue\"}, \"same_run\": \"false\", \"template\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.4.0",
+                        "tool_state": "{\"__input_ext\": \"gtf\", \"adv_output\": {\"p\": \"TCONS\", \"C\": \"false\", \"A\": \"false\", \"X\": \"false\", \"K\": \"false\"}, \"annotation\": {\"use_ref_annotation\": \"Yes\", \"__current_case__\": 0, \"ref_source\": {\"ref_source_sel\": \"history\", \"__current_case__\": 1, \"reference_annotation\": {\"__class__\": \"ConnectedValue\"}}, \"ignore_nonoverlapping_reference\": \"false\", \"ignore_nonoverlapping_transfrags\": \"false\", \"strict_match\": \"false\", \"refmap_tmap\": [\"refmap\", \"tmap\"]}, \"chr_stats\": \"false\", \"chromInfo\": \"/panfs/roc/website/galaxyp.msi.umn.edu/galaxy/tool-data/shared/ucsc/chrom/mm10.len\", \"discard_duplicates\": \"\", \"discard_single_exon\": \"\", \"gffinputs\": {\"__class__\": \"ConnectedValue\"}, \"max_dist_exon\": \"100\", \"max_dist_group\": \"100\", \"no_merge\": \"false\", \"seq_data\": {\"use_seq_data\": \"No\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "cfe13aec-2644-4a6e-8a2b-d3dc6cd0aec8",
+                        "uuid": "6b917971-f710-4e39-b795-edda6bb0042e",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "61dd81a7-9a2d-4e9b-b8cb-a93245e9dbbb"
+                                "output_name": "transcripts_annotated",
+                                "uuid": "94d389ff-4147-4d17-9a88-ee40b51b1385"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "transcripts_loci",
+                                "uuid": "6572f472-1780-465a-94b1-194bc90100f5"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "transcripts_tracking",
+                                "uuid": "b98508c8-733f-4a08-ad97-4878dea87ec7"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "transcripts_stats",
+                                "uuid": "9b35be89-e7d9-4e01-b410-b5c3006879c8"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "refmap_output",
+                                "uuid": "e9e58252-6620-43f7-88aa-be97ca06eda2"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "tmap_output",
+                                "uuid": "48258492-2e3d-4e61-9789-b2e347306a17"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_score/pyprophet_score/2.1.4.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
                         "errors": null,
-                        "id": 7,
+                        "id": 11,
                         "input_connections": {
-                            "input": {
-                                "id": 6,
-                                "output_name": "output"
+                            "sqlitedb": {
+                                "id": 9,
+                                "output_name": "output_genomic_mapping_sqlite"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "PyProphet score",
+                        "name": "SQLite to tabular",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "osw"
-                            },
-                            {
-                                "name": "score_report",
-                                "type": "pdf"
+                                "name": "query_results",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 399.3999938964844,
-                            "height": 276.3999938964844,
-                            "left": -462.5,
-                            "right": -262.5,
-                            "top": 123,
-                            "width": 200,
-                            "x": -462.5,
-                            "y": 123
+                            "bottom": 637.3312377929688,
+                            "height": 92.79998779296875,
+                            "left": 1521.1563110351562,
+                            "right": 1681.1563110351562,
+                            "top": 544.53125,
+                            "width": 160,
+                            "x": 1521.1563110351562,
+                            "y": 544.53125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_score/pyprophet_score/2.1.4.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "77f068ba47dd",
-                            "name": "pyprophet_score",
-                            "owner": "galaxyp",
+                            "changeset_revision": "b722161a845a",
+                            "name": "sqlite_to_tabular",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"osw\", \"apply_weights\": null, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"conditional_classifier\": {\"classifier\": \"XGBoost\", \"__current_case__\": 1, \"xgb_autotune\": \"false\"}, \"group_id\": \"group_id\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"ipf_max_peakgroup_pep\": \"0.7\", \"ipf_max_peakgroup_rank\": \"1\", \"ipf_max_transition_isotope_overlap\": \"0.5\", \"ipf_min_transition_sn\": \"0.0\", \"level\": \"ms1ms2\", \"lfdr_adj\": \"1.5\", \"lfdr_eps\": \"1e-08\", \"lfdr_monotone\": \"true\", \"lfdr_transformation\": \"probit\", \"lfdr_truncate\": \"true\", \"parametric\": \"false\", \"pfdr\": \"false\", \"pi0_lambda_end\": \"0.5\", \"pi0_lambda_start\": \"0.1\", \"pi0_lambda_steps\": \"0.05\", \"pi0_method\": \"bootstrap\", \"pi0_smooth_df\": \"3\", \"pi0_smooth_log\": \"false\", \"ss_initial_fdr\": \"0.15\", \"ss_iteration_fdr\": \"0.05\", \"ss_main_score\": \"var_xcorr_shape\", \"ss_num_iter\": \"10\", \"test_mode\": \"false\", \"tric_chromprob\": \"false\", \"xeval_fraction\": \"0.5\", \"xeval_num_iter\": \"10\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.4.2",
+                        "tool_state": "{\"__input_ext\": \"sqlite\", \"chromInfo\": \"/panfs/roc/website/galaxyp.msi.umn.edu/galaxy/tool-data/shared/ucsc/chrom/mm10.len\", \"query_result\": {\"header\": \"no\", \"__current_case__\": 1}, \"sqlitedb\": {\"__class__\": \"ConnectedValue\"}, \"sqlquery\": \"SELECT pro_name, chr_name, cds_chr_start - 1, cds_chr_end,strand,cds_start - 1, cds_end\\n  FROM genomic_mapping\\n  ORDER BY pro_name, cds_start, cds_end\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "40fc02c5-56f8-4e65-9e52-cd59ed321f5b",
+                        "uuid": "235f73d3-b7b1-4c7b-956b-e4942ccd8a96",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "score_report",
-                                "uuid": "78b03dbb-9561-4ccb-aa47-5ab90bf063ef"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "70ab8388-f777-4fd3-8b5b-e34ef9b351f3"
+                                "output_name": "query_results",
+                                "uuid": "78c872b0-6405-4398-a4ce-217b5aea935d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_peptide/pyprophet_peptide/2.1.4.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
                         "errors": null,
-                        "id": 8,
+                        "id": 12,
                         "input_connections": {
-                            "input": {
-                                "id": 7,
-                                "output_name": "output"
+                            "sqlitedb": {
+                                "id": 9,
+                                "output_name": "output_variant_annotation_sqlite"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "PyProphet peptide",
+                        "name": "SQLite to tabular",
                         "outputs": [
                             {
-                                "name": "peptide_plots",
-                                "type": "pdf"
-                            },
-                            {
-                                "name": "output",
-                                "type": "osw"
+                                "name": "query_results",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 348.6000061035156,
-                            "height": 225.60000610351562,
-                            "left": -242.5,
-                            "right": -42.5,
-                            "top": 123,
-                            "width": 200,
-                            "x": -242.5,
-                            "y": 123
+                            "bottom": 774.7062683105469,
+                            "height": 92.79998779296875,
+                            "left": 1518.1562805175781,
+                            "right": 1678.1562805175781,
+                            "top": 681.9062805175781,
+                            "width": 160,
+                            "x": 1518.1562805175781,
+                            "y": 681.9062805175781
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_peptide/pyprophet_peptide/2.1.4.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "4504b3bc1eed",
-                            "name": "pyprophet_peptide",
-                            "owner": "galaxyp",
+                            "changeset_revision": "b722161a845a",
+                            "name": "sqlite_to_tabular",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"osw\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"context\": \"experiment-wide\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"lfdr_adj\": \"1.5\", \"lfdr_eps\": \"1e-08\", \"lfdr_monotone\": \"true\", \"lfdr_transformation\": \"probit\", \"lfdr_truncate\": \"true\", \"parametric\": \"false\", \"pfdr\": \"false\", \"pi0_lambda_end\": \"0.5\", \"pi0_lambda_start\": \"0.1\", \"pi0_lambda_steps\": \"0.05\", \"pi0_method\": \"bootstrap\", \"pi0_smooth_df\": \"3\", \"pi0_smooth_log\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.4.0",
+                        "tool_state": "{\"__input_ext\": \"sqlite\", \"chromInfo\": \"/panfs/roc/website/galaxyp.msi.umn.edu/galaxy/tool-data/shared/ucsc/chrom/mm10.len\", \"query_result\": {\"header\": \"no\", \"__current_case__\": 1}, \"sqlitedb\": {\"__class__\": \"ConnectedValue\"}, \"sqlquery\": \"SELECT var_pro_name,pro_name,cigar,annotation\\nFROM variant_annotation\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "e1f109cb-bc55-4b81-9f74-d9d02553a91b",
+                        "uuid": "0f9a44cc-2215-4576-96b1-0d58c71972ae",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "a4dc51f3-11f6-457b-aff8-0ea597114b92"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "peptide_plots",
-                                "uuid": "f998ff80-a2ab-4b82-8b76-bb13ed2d207b"
+                                "output_name": "query_results",
+                                "uuid": "a43002ec-42c3-4796-9c37-5fd478a16534"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_peptide/pyprophet_peptide/2.1.4.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
                         "errors": null,
-                        "id": 9,
+                        "id": 13,
                         "input_connections": {
-                            "input": {
-                                "id": 8,
-                                "output_name": "output"
+                            "batchmode|input_fastas_0|input_fasta": {
+                                "id": 9,
+                                "output_name": "output_rpkm"
+                            },
+                            "batchmode|input_fastas_1|input_fasta": {
+                                "id": 9,
+                                "output_name": "output_snv"
+                            },
+                            "batchmode|input_fastas_2|input_fasta": {
+                                "id": 9,
+                                "output_name": "output_indel"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "PyProphet peptide",
+                        "name": "FASTA Merge Files and Filter Unique Sequences",
                         "outputs": [
-                            {
-                                "name": "peptide_plots",
-                                "type": "pdf"
-                            },
                             {
                                 "name": "output",
-                                "type": "osw"
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "bottom": 348.6000061035156,
-                            "height": 225.60000610351562,
-                            "left": -22.5,
-                            "right": 177.5,
-                            "top": 123,
-                            "width": 200,
-                            "x": -22.5,
-                            "y": 123
+                            "bottom": 432.9000053405762,
+                            "height": 226.40000915527344,
+                            "left": 1772.6718139648438,
+                            "right": 1932.6718139648438,
+                            "top": 206.49999618530273,
+                            "width": 160,
+                            "x": 1772.6718139648438,
+                            "y": 206.49999618530273
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_peptide/pyprophet_peptide/2.1.4.0",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "CustomProDB_FASTA"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "4504b3bc1eed",
-                            "name": "pyprophet_peptide",
+                            "changeset_revision": "f546e7278f04",
+                            "name": "fasta_merge_files_and_filter_unique_sequences",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"osw\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"context\": \"global\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"lfdr_adj\": \"1.5\", \"lfdr_eps\": \"1e-08\", \"lfdr_monotone\": \"true\", \"lfdr_transformation\": \"probit\", \"lfdr_truncate\": \"true\", \"parametric\": \"false\", \"pfdr\": \"false\", \"pi0_lambda_end\": \"0.5\", \"pi0_lambda_start\": \"0.1\", \"pi0_lambda_steps\": \"0.05\", \"pi0_method\": \"bootstrap\", \"pi0_smooth_df\": \"3\", \"pi0_smooth_log\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.4.0",
+                        "tool_state": "{\"accession_parser\": \"^>([^ |]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"uniqueness_criterion\": \"sequence\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "68693bad-fc8d-4e7a-94aa-137d8dcb3d98",
+                        "uuid": "5f8e4568-d12e-4a43-86d1-f68fbb3b9da0",
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "CustomProDB_FASTA",
                                 "output_name": "output",
-                                "uuid": "d1fb3ae7-3b84-4be6-8bb1-126a181c9269"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "peptide_plots",
-                                "uuid": "bc401b01-b1a5-420a-a455-8fdd9cbc2b5c"
+                                "uuid": "a5054be9-dd74-4d60-a4c6-494fdbcb97a1"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_protein/pyprophet_protein/2.1.4.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
                         "errors": null,
-                        "id": 10,
+                        "id": 14,
                         "input_connections": {
                             "input": {
                                 "id": 9,
-                                "output_name": "output"
+                                "output_name": "output_rpkm"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "PyProphet protein",
+                        "name": "FASTA-to-Tabular",
                         "outputs": [
                             {
                                 "name": "output",
-                                "type": "osw"
-                            },
-                            {
-                                "name": "protein_plots",
-                                "type": "pdf"
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 348.6000061035156,
-                            "height": 225.60000610351562,
-                            "left": 197.5,
-                            "right": 397.5,
-                            "top": 123,
-                            "width": 200,
-                            "x": 197.5,
-                            "y": 123
+                            "bottom": 75.04999923706055,
+                            "height": 92.79999542236328,
+                            "left": 2794.2657470703125,
+                            "right": 2954.2657470703125,
+                            "top": -17.749996185302734,
+                            "width": 160,
+                            "x": 2794.2657470703125,
+                            "y": -17.749996185302734
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_protein/pyprophet_protein/2.1.4.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "2320f48209fc",
-                            "name": "pyprophet_protein",
-                            "owner": "galaxyp",
+                            "changeset_revision": "7e801ab2b70e",
+                            "name": "fasta_to_tabular",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"osw\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"context\": \"experiment-wide\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"lfdr_adj\": \"1.5\", \"lfdr_eps\": \"1e-08\", \"lfdr_monotone\": \"true\", \"lfdr_transformation\": \"probit\", \"lfdr_truncate\": \"true\", \"parametric\": \"false\", \"pfdr\": \"false\", \"pi0_lambda_end\": \"0.5\", \"pi0_lambda_start\": \"0.1\", \"pi0_lambda_steps\": \"0.05\", \"pi0_method\": \"bootstrap\", \"pi0_smooth_df\": \"3\", \"pi0_smooth_log\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.4.0",
+                        "tool_state": "{\"descr_columns\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "e8bc07ea-ba5d-4e3d-b439-894a786d7a63",
+                        "uuid": "3b77287d-b9c2-4bc9-968d-c98db680292f",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "c2b6fd5f-add6-477f-892f-e282df6345d0"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "protein_plots",
-                                "uuid": "699f4df0-df42-4acb-bd74-74aad82f3040"
+                                "uuid": "5ec3c54b-c7a8-45b5-99c2-b9768bd8c037"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_protein/pyprophet_protein/2.1.4.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/gffcompare_to_bed/gffcompare_to_bed/0.2.1",
                         "errors": null,
-                        "id": 11,
+                        "id": 15,
                         "input_connections": {
                             "input": {
                                 "id": 10,
-                                "output_name": "output"
+                                "output_name": "transcripts_annotated"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "PyProphet protein",
+                        "name": "Convert gffCompare annotated GTF to BED",
                         "outputs": [
                             {
                                 "name": "output",
-                                "type": "osw"
-                            },
-                            {
-                                "name": "protein_plots",
-                                "type": "pdf"
+                                "type": "bed"
                             }
                         ],
                         "position": {
-                            "bottom": 348.6000061035156,
-                            "height": 225.60000610351562,
-                            "left": 417.5,
-                            "right": 617.5,
-                            "top": 123,
-                            "width": 200,
-                            "x": 417.5,
-                            "y": 123
+                            "bottom": 1182.9781036376953,
+                            "height": 126.39996337890625,
+                            "left": 1517.6406860351562,
+                            "right": 1677.6406860351562,
+                            "top": 1056.578140258789,
+                            "width": 160,
+                            "x": 1517.6406860351562,
+                            "y": 1056.578140258789
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_protein/pyprophet_protein/2.1.4.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/gffcompare_to_bed/gffcompare_to_bed/0.2.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "2320f48209fc",
-                            "name": "pyprophet_protein",
+                            "changeset_revision": "ba5368c19dbd",
+                            "name": "gffcompare_to_bed",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"osw\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"context\": \"global\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"lfdr_adj\": \"1.5\", \"lfdr_eps\": \"1e-08\", \"lfdr_monotone\": \"true\", \"lfdr_transformation\": \"probit\", \"lfdr_truncate\": \"true\", \"parametric\": \"false\", \"pfdr\": \"false\", \"pi0_lambda_end\": \"0.5\", \"pi0_lambda_start\": \"0.1\", \"pi0_lambda_steps\": \"0.05\", \"pi0_method\": \"bootstrap\", \"pi0_smooth_df\": \"3\", \"pi0_smooth_log\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.4.0",
+                        "tool_state": "{\"__input_ext\": \"gtf\", \"chromInfo\": \"/panfs/roc/website/galaxyp.msi.umn.edu/galaxy/tool-data/shared/ucsc/chrom/mm10.len\", \"class_codes\": [\"j\", \"e\", \"i\", \"p\", \"u\"], \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "3d0fc6f5-1027-4074-bcd1-5f73b1493f5b",
+                        "uuid": "397b735d-cfc5-4a63-8d8c-3cbda7dcf0ad",
                         "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "protein_plots",
-                                "uuid": "168a4e50-79f9-458c-876a-79cb5cad5198"
-                            },
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "ec047143-40ef-4061-8c1a-2fb6e81a6e62"
+                                "uuid": "a294134b-17fd-4590-affe-f1363a292ff1"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_export/pyprophet_export/2.1.4.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
                         "errors": null,
-                        "id": 12,
+                        "id": 16,
                         "input_connections": {
-                            "conditional_swath2stats|study_design": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
                             "input": {
                                 "id": 11,
-                                "output_name": "output"
+                                "output_name": "query_results"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "PyProphet export",
+                        "name": "Column Regex Find And Replace",
                         "outputs": [
                             {
-                                "name": "export_file",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "summary",
-                                "type": "pdf"
-                            },
-                            {
-                                "name": "peptide_signal",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "protein_signal",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "msstats_input",
-                                "type": "tabular"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 666.7999877929688,
-                            "height": 530.7999877929688,
-                            "left": 754.5,
-                            "right": 954.5,
-                            "top": 136,
-                            "width": 200,
-                            "x": 754.5,
-                            "y": 136
+                            "bottom": 636.8468475341797,
+                            "height": 92.79998779296875,
+                            "left": 1767.96875,
+                            "right": 1927.96875,
+                            "top": 544.0468597412109,
+                            "width": 160,
+                            "x": 1767.96875,
+                            "y": 544.0468597412109
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_export/pyprophet_export/2.1.4.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "3cf580bf28e2",
-                            "name": "pyprophet_export",
+                            "changeset_revision": "209b7c5ee9d7",
+                            "name": "regex_find_replace",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"osw\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"conditional_output\": {\"format\": \"legacy_merged\", \"__current_case__\": 1, \"transition_quant\": \"true\", \"max_transition_pep\": \"0.7\", \"ipf\": \"peptidoform\", \"ipf_max_peptidoform_pep\": \"0.4\", \"max_rs_peakgroup_qvalue\": \"0.05\", \"max_global_peptide_qvalue\": \"0.01\", \"max_global_protein_qvalue\": \"0.01\"}, \"conditional_swath2stats\": {\"swath2stats\": \"yes_swath2stats\", \"__current_case__\": 0, \"study_design\": {\"__class__\": \"ConnectedValue\"}, \"conditional_fdr_replica\": {\"calc_fdr_replica\": \"calc_fdr_replica_yes\", \"__current_case__\": 0, \"fft\": \"0.5\", \"n_range\": \"10.0\", \"fdr_target\": \"0.05\", \"n_replica\": \"2\"}, \"conditional_max_pep\": {\"filter_max_pep\": \"filter_max_pep_yes\", \"__current_case__\": 0, \"n_peptides_max\": \"10\"}, \"conditional_min_pep\": {\"filter_min_pep\": \"filter_min_pep_yes\", \"__current_case__\": 0, \"n_peptides_min\": \"2\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"peptide_error\": \"true\", \"protein_error\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.4.1",
+                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \"^(ENS[^_]+_\\\\d+:)([ACGTacgt]+)>([ACGTacgt]+)\\\\s*\", \"replacement\": \"\\\\1\\\\2_\\\\3\"}, {\"__index__\": 1, \"pattern\": \",([A-Y]\\\\d+[A-Y]?)\\\\s*\", \"replacement\": \".\\\\1\"}, {\"__index__\": 2, \"pattern\": \"^(ENS[^ |]*)\\\\s*\", \"replacement\": \"\\\\1\"}], \"field\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "48d5be06-8816-4da4-a70d-12b5a219f07b",
+                        "uuid": "286d169c-079e-42a3-beb5-7515c2109f3c",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "msstats_input",
-                                "uuid": "e287c3d3-cb72-4d70-809b-acb86932a2db"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "summary",
-                                "uuid": "f5be16a2-f5a0-4abb-807c-079bddfaeb5c"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "export_file",
-                                "uuid": "6d808fed-9f94-4a95-a0ad-ce0f41170e69"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "peptide_signal",
-                                "uuid": "d044b25c-c339-4bdf-8c18-422a88f029b0"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "protein_signal",
-                                "uuid": "d45a777c-0af4-4569-a427-8ae99e0314ff"
+                                "output_name": "out_file1",
+                                "uuid": "4ade9d67-ccc6-481c-b749-b3363871ea56"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Grep1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
                         "errors": null,
-                        "id": 13,
+                        "id": 17,
                         "input_connections": {
                             "input": {
                                 "id": 12,
-                                "output_name": "protein_signal"
+                                "output_name": "query_results"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Select",
-                                "name": "input"
-                            }
-                        ],
-                        "label": "Ecoli protein expression matrix",
-                        "name": "Select",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Column Regex Find And Replace",
                         "outputs": [
                             {
                                 "name": "out_file1",
@@ -184273,1040 +186378,697 @@
                             }
                         ],
                         "position": {
-                            "bottom": 483.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": 1058.5,
-                            "right": 1258.5,
-                            "top": 370,
-                            "width": 200,
-                            "x": 1058.5,
-                            "y": 370
+                            "bottom": 807.5812530517578,
+                            "height": 92.79998779296875,
+                            "left": 1745.5781555175781,
+                            "right": 1905.5781555175781,
+                            "top": 714.7812652587891,
+                            "width": 160,
+                            "x": 1745.5781555175781,
+                            "y": 714.7812652587891
                         },
                         "post_job_actions": {},
-                        "tool_id": "Grep1",
-                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"invert\": \"false\", \"pattern\": \"(ECOLI)|(Spike-in)\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "209b7c5ee9d7",
+                            "name": "regex_find_replace",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \"^(ENS[^_]+_\\\\d+:)([ACGTacgt]+)>([ACGTacgt]+)\\\\s*\", \"replacement\": \"\\\\1\\\\2_\\\\3\"}, {\"__index__\": 1, \"pattern\": \",([A-Y]\\\\d+[A-Y]?)\\\\s*\", \"replacement\": \".\\\\1\"}, {\"__index__\": 2, \"pattern\": \"^(ENS[^ |]*)\\\\s*\", \"replacement\": \"\\\\1\"}], \"field\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "5282f24d-8985-472e-9669-f5484a9a2594",
+                        "uuid": "3c96276e-032e-43cb-a7d0-8045941b9674",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "out_file1",
-                                "uuid": "26ace007-a011-453e-b37e-1a2056a6184b"
+                                "uuid": "f6507937-030f-40b0-aff6-828d6e28aeae"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "proteomics/DIA_Analysis_OSW",
-                "path": "topics/proteomics/tutorials/DIA_Analysis_OSW/workflows/Galaxy-Workflow-_DIA_Training_using_HEK_Ecoli_3_EG_data_.ga",
-                "tags": [
-                    "proteomics"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "DIA_Analysis_OSW",
-                "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-DIA_Analysis_OSW/versions/galaxy-workflow--dia-training-using-hek-ecoli-3-eg-data-",
-                "tutorial_id": "DIA_Analysis_OSW",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/DIA_Analysis_OSW/workflows/Galaxy-Workflow-_DIA_Training_using_HEK_Ecoli_3_EG_data_.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/DIA_Analysis_OSW/workflows/Galaxy-Workflow-_DIA_Training_using_HEK_Ecoli_3_EG_data_.html",
-                "version": 1,
-                "wfid": "proteomics-DIA_Analysis_OSW",
-                "wfname": "galaxy-workflow--dia-training-using-hek-ecoli-3-eg-data-",
-                "workflow": "Galaxy-Workflow-_DIA_Training_using_HEK_Ecoli_3_EG_data_.ga",
-                "workflow_tools": [
-                    "Grep1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/2.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_export/pyprophet_export/2.1.4.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_merge/pyprophet_merge/2.1.4.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_peptide/pyprophet_peptide/2.1.4.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_protein/pyprophet_protein/2.1.4.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_score/pyprophet_score/2.1.4.2"
-                ],
-                "workflowhub_id": "1180"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/4307762"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "metaquantome_db",
-                    "owner": "galaxyp",
-                    "revisions": "7c45aa1c9464",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "metaquantome_expand",
-                    "owner": "galaxyp",
-                    "revisions": "eb65ab160a10",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "metaquantome_filter",
-                    "owner": "galaxyp",
-                    "revisions": "7d1c20b315ff",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "metaquantome_sample",
-                    "owner": "galaxyp",
-                    "revisions": "49a957fb353a",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "metaquantome_stat",
-                    "owner": "galaxyp",
-                    "revisions": "982a442a98dd",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "metaquantome_viz",
-                    "owner": "galaxyp",
-                    "revisions": "02da24eac445",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: metaquantome_db\n  owner: galaxyp\n  revisions: 7c45aa1c9464\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_expand\n  owner: galaxyp\n  revisions: eb65ab160a10\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_filter\n  owner: galaxyp\n  revisions: 7d1c20b315ff\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_sample\n  owner: galaxyp\n  revisions: 49a957fb353a\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_stat\n  owner: galaxyp\n  revisions: 982a442a98dd\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_viz\n  owner: galaxyp\n  revisions: 02da24eac445\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.json",
-        "contributors": [
-            {
-                "email": "subinamehta@gmail.com",
-                "id": "subinamehta",
-                "joined": "2018-06",
-                "linkedin": "subinamehta",
-                "matrix": "subinamehta:matrix.org",
-                "name": "Subina Mehta",
-                "orcid": "0000-0001-9818-0537",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
-                "twitter": "Subina_Mehta",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
-            },
-            {
-                "email": "tgriffin@umn.edu",
-                "github": false,
-                "id": "timothygriffin",
-                "joined": "2017-09",
-                "name": "Timothy J. Griffin",
-                "orcid": "0000-0001-6801-2559",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
-            },
-            {
-                "email": "pjagtap@umn.edu",
-                "id": "pratikdjagtap",
-                "joined": "2017-09",
-                "name": "Pratik Jagtap",
-                "orcid": "0000-0003-0984-0973",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
-            },
-            {
-                "email": "leith023@umn.edu",
-                "id": "emmaleith",
-                "joined": "2019-07",
-                "name": "Emma Leith",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/emmaleith/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/emmaleith.json"
-            },
-            {
-                "email": "crane136@umn.edu",
-                "id": "mariecrane",
-                "joined": "2019-05",
-                "name": "Marie Crane",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mariecrane/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mariecrane.json"
-            },
-            {
-                "email": "kumar207@umn.edu",
-                "id": "pravs3683",
-                "joined": "2019-04",
-                "name": "Praveen Kumar",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pravs3683/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pravs3683.json"
-            }
-        ],
-        "dir": "topics/proteomics/tutorials/metaquantome-taxonomy",
-        "edam_ontology": [
-            "topic_0121",
-            "topic_3922",
-            "topic_3941",
-            "topic_3697",
-            "topic_3174",
-            "topic_0637"
-        ],
-        "edam_operation": [
-            "Visualisation",
-            "Differential protein expression analysis",
-            "Functional clustering",
-            "Query and retrieval",
-            "Indexing",
-            "Filtering",
-            "Heat map generation",
-            "Statistical inference",
-            "Principal component visualisation",
-            "Quantification"
-        ],
-        "edam_topic": [
-            "Proteomics",
-            "Proteogenomics",
-            "Metatranscriptomics",
-            "Microbial ecology",
-            "Metagenomics",
-            "Taxonomy"
-        ],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "proteomics",
-                "tutorials": [
-                    "metaproteomics",
-                    "metaquantome-function"
-                ],
-                "type": "internal"
-            }
-        ],
-        "hands_on": true,
-        "id": "proteomics/metaquantome-taxonomy",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "All the inputs should have one column in common i.e. peptides.",
-            "Learning different tools such as Unipept, MEGAN, MetaGOmics etc. for taxonomic annotation of peptides will benefit."
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-03-15",
-        "objectives": [
-            "A taxonomy and quantitational analysis of metaproteomic mass spectrometry data."
-        ],
-        "pageviews": 502,
-        "pub_date": "2020-10-29",
-        "questions": [
-            "How do I look at differentially expressed taxa?",
-            "Can we get top 5 or 10 taxa present in the sample?",
-            "How can I visualize my results?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "proteomics",
-                "tutorials": [
-                    "metaquantome-data-creation"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00224",
-        "short_tools": [
-            "metaquantome_db",
-            "metaquantome_sample",
-            "metaquantome_stat",
-            "metaquantome_expand",
-            "metaquantome_filter",
-            "metaquantome_viz"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "multi-omics",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "microgalaxy"
-        ],
-        "time_estimation": "1h",
-        "title": "metaQuantome 3: Taxonomy",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.0-0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.0-0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.0-0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.0-0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.0-0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0"
-        ],
-        "topic_name": "proteomics",
-        "topic_name_human": "Proteomics",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "metaquantome-taxonomy",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.json"
-        },
-        "version": 14,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 158,
-        "visitors": 371,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "metaquantome-taxonomy",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"metaQuantome: create samples file\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTaxa\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIntensity\"]\n  3[label=\"metaQuantome: database\"]\n  4[label=\"metaQuantome: expand\"]\n  3 -> 4 [label=\"outfile\"]\n  2 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  0 -> 4 [label=\"samples_file\"]\n  5[label=\"metaQuantome: filter\"]\n  4 -> 5 [label=\"outfile\"]\n  0 -> 5 [label=\"samples_file\"]\n  6[label=\"metaQuantome: stat\"]\n  5 -> 6 [label=\"outfile\"]\n  0 -> 6 [label=\"samples_file\"]\n  7[label=\"T2-Bar-Plot\"]\n  6 -> 7 [label=\"outfile\"]\n  0 -> 7 [label=\"samples_file\"]\n  8[label=\"T7-T2_volcano-plot\"]\n  6 -> 8 [label=\"outfile\"]\n  0 -> 8 [label=\"samples_file\"]\n  9[label=\"T4-Bar-Plot\"]\n  6 -> 9 [label=\"outfile\"]\n  0 -> 9 [label=\"samples_file\"]\n  10[label=\"T7-Bar-Plot\"]\n  6 -> 10 [label=\"outfile\"]\n  0 -> 10 [label=\"samples_file\"]\n  11[label=\"T4-T2_volcano-plot\"]\n  6 -> 11 [label=\"outfile\"]\n  0 -> 11 [label=\"samples_file\"]\n}",
-                "history": [
-                    {
-                        "hash": "23fe00a8ab231d19aad201787b67446f76d72128",
-                        "message": "Update main_workflow.ga",
-                        "num": 3,
-                        "short_hash": "23fe00a8a",
-                        "unix": "1636494825"
-                    },
-                    {
-                        "hash": "6508b46449968fac766df69a5fee4295fa7e362f",
-                        "message": "Update main_workflow.ga",
-                        "num": 2,
-                        "short_hash": "6508b4644",
-                        "unix": "1603158930"
                     },
-                    {
-                        "hash": "426a2746eee3945edd669f81b15b222493c46c82",
-                        "message": "tutorial skeletons generated by planemo",
-                        "num": 1,
-                        "short_hash": "426a2746e",
-                        "unix": "1602853461"
-                    }
-                ],
-                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 18,
+                        "input_connections": {
+                            "input": {
+                                "id": 13,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FASTA-to-Tabular",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Taxa"
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "Taxa",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 306.6493225097656,
-                            "top": 535.6250152587891
+                            "bottom": 416.9874954223633,
+                            "height": 92.79998779296875,
+                            "left": 2049.640655517578,
+                            "right": 2209.640655517578,
+                            "top": 324.18750762939453,
+                            "width": 160,
+                            "x": 2049.640655517578,
+                            "y": 324.18750762939453
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "7e801ab2b70e",
+                            "name": "fasta_to_tabular",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"descr_columns\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "dea4289e-33b0-4215-8768-da6c65f8cd83",
+                        "type": "tool",
+                        "uuid": "f77ceead-9781-4122-a033-e5e675d1d0af",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "fbf383a9-1774-483c-a1f1-1aa4d0a5659f"
+                                "uuid": "6f986155-b096-40f3-981b-edf3f3b75617"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Intensity"
+                        "id": 19,
+                        "input_connections": {
+                            "input": {
+                                "id": 14,
+                                "output_name": "output"
                             }
-                        ],
-                        "label": "Intensity",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 304.6180725097656,
-                            "top": 659.6180877685547
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "be000472-cc47-456f-8791-b62c1a6308ec",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "42e60127-395b-451f-a31c-191f6f82f2e0"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"metaQuantome: create samples file\"];\n  1[\"\u2139\ufe0f Input Dataset\\nTaxa\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nIntensity\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"metaQuantome: database\"];\n  4[\"metaQuantome: expand\"];\n  3 -->|outfile| 4;\n  2 -->|output| 4;\n  1 -->|output| 4;\n  0 -->|samples_file| 4;\n  5[\"metaQuantome: filter\"];\n  4 -->|outfile| 5;\n  0 -->|samples_file| 5;\n  6[\"metaQuantome: stat\"];\n  5 -->|outfile| 6;\n  0 -->|samples_file| 6;\n  7[\"T2-Bar-Plot\"];\n  6 -->|outfile| 7;\n  0 -->|samples_file| 7;\n  8[\"T7-T2_volcano-plot\"];\n  6 -->|outfile| 8;\n  0 -->|samples_file| 8;\n  9[\"T4-Bar-Plot\"];\n  6 -->|outfile| 9;\n  0 -->|samples_file| 9;\n  10[\"T7-Bar-Plot\"];\n  6 -->|outfile| 10;\n  0 -->|samples_file| 10;\n  11[\"T4-T2_volcano-plot\"];\n  6 -->|outfile| 11;\n  0 -->|samples_file| 11;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "metaquantome-taxonomy-workflow",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.0-0",
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
                         "inputs": [],
                         "label": null,
-                        "name": "metaQuantome: create samples file",
+                        "name": "Filter Tabular",
                         "outputs": [
                             {
-                                "name": "samples_file",
+                                "name": "output",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 324.2882385253906,
-                            "top": 367.9861297607422
+                            "bottom": 105.04999923706055,
+                            "height": 92.79999542236328,
+                            "left": 3064.4061279296875,
+                            "right": 3224.4061279296875,
+                            "top": 12.250003814697266,
+                            "width": 160,
+                            "x": 3064.4061279296875,
+                            "y": 12.250003814697266
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.0-0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "40ca115438d2",
-                            "name": "metaquantome_sample",
-                            "owner": "galaxyp",
+                            "changeset_revision": "34d29339abab",
+                            "name": "filter_tabular",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"samps_args\": {\"samps_src\": \"build\", \"__current_case__\": 0, \"samps\": [{\"__index__\": 0, \"group_name\": \"T2\", \"col_names\": \"T2_A1,T2_B1\"}, {\"__index__\": 1, \"group_name\": \"T4\", \"col_names\": \"T4A_1,T4B_1\"}, {\"__index__\": 2, \"group_name\": \"T7\", \"col_names\": \"T7A_1,T7B_1\"}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
-                        "type": "tool",
-                        "uuid": "8f8b3a5c-1ada-4b83-988b-46ff7e2e9468",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "samples_file",
-                                "uuid": "d0b1aed8-8212-4e20-b1b4-b10bf76a394d"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Taxa"
-                            }
-                        ],
-                        "label": "Taxa",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 306.6493225097656,
-                            "top": 535.6250152587891
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"select_columns\", \"__current_case__\": 7, \"columns\": \"1\"}}, {\"__index__\": 1, \"filter\": {\"filter_type\": \"replace\", \"__current_case__\": 8, \"column\": \"1\", \"regex_pattern\": \"^([^ |]+).*$\", \"regex_replace\": \"\\\\1\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "dea4289e-33b0-4215-8768-da6c65f8cd83",
+                        "type": "tool",
+                        "uuid": "c5a70a7c-b161-4468-8fe6-c5aa7a62ea97",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "fbf383a9-1774-483c-a1f1-1aa4d0a5659f"
+                                "uuid": "02d27417-7639-4052-8f09-4d97225efb7b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed/translate_bed/0.1.0",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Intensity"
+                        "id": 20,
+                        "input_connections": {
+                            "input": {
+                                "id": 15,
+                                "output_name": "output"
                             }
-                        ],
-                        "label": "Intensity",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 304.6180725097656,
-                            "top": 659.6180877685547
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "be000472-cc47-456f-8791-b62c1a6308ec",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "42e60127-395b-451f-a31c-191f6f82f2e0"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.0-0",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
                         "inputs": [],
                         "label": null,
-                        "name": "metaQuantome: database",
+                        "name": "Translate BED transcripts",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "tar"
+                                "name": "translation_bed",
+                                "type": "bed"
+                            },
+                            {
+                                "name": "translation_fasta",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 293.2986145019531,
-                            "top": 780.0000152587891
+                            "bottom": 1166.1468811035156,
+                            "height": 117.5999755859375,
+                            "left": 1742.6094055175781,
+                            "right": 1902.6094055175781,
+                            "top": 1048.5469055175781,
+                            "width": 160,
+                            "x": 1742.6094055175781,
+                            "y": 1048.5469055175781
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.0-0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed/translate_bed/0.1.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "860429737408",
-                            "name": "metaquantome_db",
+                            "changeset_revision": "038ecf54cbec",
+                            "name": "translate_bed",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"databases\": [\"ncbi\", \"go\", \"ec\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"bed\", \"bed_filters\": {\"regions\": \"\", \"biotypes\": \"\"}, \"chromInfo\": \"/panfs/roc/website/galaxyp.msi.umn.edu/galaxy/tool-data/shared/ucsc/chrom/mm10.len\", \"fa_id\": {\"reference\": \"\", \"fa_db\": \"generic\", \"fa_sep\": \"\", \"id_prefix\": \"\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ref\": {\"ref_source\": \"cached\", \"__current_case__\": 0, \"ref_loc\": \"mm10\"}, \"translations\": {\"translate\": \"cDNA_minus_CDS\", \"min_length\": \"10\", \"start_codon\": \"false\", \"enzyme\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "25b0969d-52fb-4942-b37f-d9bfb88d048b",
+                        "uuid": "23639fe3-f5d9-40e7-9377-f0a9657a70df",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "4136ae07-b54f-4dea-bb43-b79259ea1df2"
+                                "output_name": "translation_fasta",
+                                "uuid": "9de63997-d103-4efa-a7ec-0720d7b35b5e"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "translation_bed",
+                                "uuid": "5512409b-e1d2-4722-9398-4af66e2df909"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.0-0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "errors": null,
-                        "id": 4,
+                        "id": 21,
                         "input_connections": {
-                            "db_tar": {
-                                "id": 3,
-                                "output_name": "outfile"
-                            },
-                            "int_file": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "mode_args|tax_file": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "samps": {
-                                "id": 0,
-                                "output_name": "samples_file"
+                            "tables_0|table": {
+                                "id": 17,
+                                "output_name": "out_file1"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Query Tabular",
+                                "name": "add_to_database"
+                            }
+                        ],
                         "label": null,
-                        "name": "metaQuantome: expand",
+                        "name": "Query Tabular",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "tabular"
+                                "name": "sqlitedb",
+                                "type": "sqlite"
                             }
                         ],
                         "position": {
-                            "left": 595.2430725097656,
-                            "top": 528.0034942626953
+                            "bottom": 831.2187652587891,
+                            "height": 168,
+                            "left": 1982.6406860351562,
+                            "right": 2142.6406860351562,
+                            "top": 663.2187652587891,
+                            "width": 160,
+                            "x": 1982.6406860351562,
+                            "y": 663.2187652587891
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.0-0",
+                        "post_job_actions": {
+                            "RenameDatasetActionsqlitedb": {
+                                "action_arguments": {
+                                    "newname": "variant_annoation.sqlite"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "sqlitedb"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "4187b6df1a40",
-                            "name": "metaquantome_expand",
-                            "owner": "galaxyp",
+                            "changeset_revision": "33d61c89fb8d",
+                            "name": "query_tabular",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tar\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"db_tar\": {\"__class__\": \"ConnectedValue\"}, \"int_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"t\", \"__current_case__\": 1, \"tax_file\": {\"__class__\": \"ConnectedValue\"}, \"pep_colname_tax\": \"peptide\", \"tax_colname\": \"taxon_id\"}, \"pep_colname_int\": \"peptide\", \"samps\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
+                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"save_db\": \"true\", \"sqlquery\": \"\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"variant_annotation\", \"column_names_from_first_line\": \"false\", \"col_names\": \"name,reference,cigar,annotation\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"name,cigar\"}]}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "6d9549b9-849e-4412-8a51-1aa88f34eb8c",
+                        "uuid": "81d10709-f407-43c9-b867-b23d52759775",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "8cc0c4b0-53d3-40b0-aae4-609a33c3de73"
+                                "label": "variant_annoation_sqlite",
+                                "output_name": "sqlitedb",
+                                "uuid": "e9468479-4ebd-4ced-8086-c10e916b97c5"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.0-0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
                         "errors": null,
-                        "id": 5,
+                        "id": 22,
                         "input_connections": {
-                            "expand_file": {
-                                "id": 4,
-                                "output_name": "outfile"
-                            },
-                            "samps": {
-                                "id": 0,
-                                "output_name": "samples_file"
+                            "input": {
+                                "id": 18,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "metaQuantome: filter",
+                        "name": "Column Regex Find And Replace",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "tabular"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 626.2674255371094,
-                            "top": 899.0104522705078
+                            "bottom": 427.9718780517578,
+                            "height": 92.79998779296875,
+                            "left": 2311.671905517578,
+                            "right": 2471.671905517578,
+                            "top": 335.17189025878906,
+                            "width": 160,
+                            "x": 2311.671905517578,
+                            "y": 335.17189025878906
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.0-0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "a1daafbf5233",
-                            "name": "metaquantome_filter",
+                            "changeset_revision": "209b7c5ee9d7",
+                            "name": "regex_find_replace",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"expand_file\": {\"__class__\": \"ConnectedValue\"}, \"min_child_nsamp\": \"1\", \"min_children_non_leaf\": \"2\", \"min_pep_nsamp\": \"1\", \"min_peptides\": \"1\", \"mode_args\": {\"mode\": \"t\", \"__current_case__\": 1}, \"qthreshold\": \"2\", \"samps\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
+                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \"^(ENS[^_]+_\\\\d+:)([ACGTacgt]+)>([ACGTacgt]+)\\\\s*\", \"replacement\": \"\\\\1\\\\2_\\\\3\"}, {\"__index__\": 1, \"pattern\": \",([A-Y]\\\\d+[A-Y]?)\\\\s*\", \"replacement\": \".\\\\1\"}, {\"__index__\": 2, \"pattern\": \"^(ENS[^ |]*)\\\\s*\", \"replacement\": \"\\\\1\"}, {\"__index__\": 3, \"pattern\": \"^(.*)$\", \"replacement\": \"generic|\\\\1\"}], \"field\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "afab6ea9-b83d-426f-badc-14ca1e4596d9",
+                        "uuid": "4fe7754b-ecb7-4447-b66d-5f8ab520c6ea",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "6d31b51a-5045-4a68-ba38-507d06331904"
+                                "output_name": "out_file1",
+                                "uuid": "1c721b4b-9acf-4f5c-b5e6-4a5bad5aa3f7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.0-0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
                         "errors": null,
-                        "id": 6,
+                        "id": 23,
                         "input_connections": {
-                            "file": {
-                                "id": 5,
-                                "output_name": "outfile"
-                            },
-                            "samps": {
-                                "id": 0,
-                                "output_name": "samples_file"
-                            }
+                            "inputs": [
+                                {
+                                    "id": 19,
+                                    "output_name": "output"
+                                },
+                                {
+                                    "id": 8,
+                                    "output_name": "output"
+                                }
+                            ]
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "metaQuantome: stat",
+                        "label": "Reference Protein Accessions",
+                        "name": "Concatenate datasets",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "tabular"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 890.2951354980469,
-                            "top": 523.9930877685547
+                            "bottom": 209.64999961853027,
+                            "height": 126.4000015258789,
+                            "left": 3312.6251220703125,
+                            "right": 3472.6251220703125,
+                            "top": 83.24999809265137,
+                            "width": 160,
+                            "x": 3312.6251220703125,
+                            "y": 83.24999809265137
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.0-0",
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Reference_Protein_Accessions"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "b648e45fd3cf",
-                            "name": "metaquantome_stat",
-                            "owner": "galaxyp",
+                            "changeset_revision": "20344ce0c811",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"control_group\": \"T2\", \"file\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"t\", \"__current_case__\": 1}, \"paired\": \"true\", \"parametric\": \"True\", \"samps\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
+                        "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "06bf363c-be87-4342-b803-38e5b0b9b1e0",
+                        "uuid": "815c5137-f521-4c1c-9d38-e959ac23bfa6",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "b66b5425-b16e-4034-899e-033f15f94bbf"
+                                "label": "Reference_Protein_Accessions",
+                                "output_name": "out_file1",
+                                "uuid": "19aa5a85-5933-4ab5-ae76-e4b1ec5b2f85"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/bed_to_protein_map/bed_to_protein_map/0.2.0",
                         "errors": null,
-                        "id": 7,
+                        "id": 24,
                         "input_connections": {
-                            "infile": {
-                                "id": 6,
-                                "output_name": "outfile"
-                            },
-                            "samps": {
-                                "id": 0,
-                                "output_name": "samples_file"
+                            "input": {
+                                "id": 20,
+                                "output_name": "translation_bed"
                             }
                         },
                         "inputs": [],
-                        "label": "T2-Bar-Plot",
-                        "name": "metaQuantome: visualize",
+                        "label": null,
+                        "name": "bed to protein map",
                         "outputs": [
                             {
-                                "name": "wrapped_outfile",
-                                "type": "html"
-                            },
-                            {
-                                "name": "plotdata",
+                                "name": "output",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1236.3020935058594,
-                            "top": 200.00000762939453
+                            "bottom": 1037.8718719482422,
+                            "height": 143.20001220703125,
+                            "left": 1954.1719055175781,
+                            "right": 2114.171905517578,
+                            "top": 894.6718597412109,
+                            "width": 160,
+                            "x": 1954.1719055175781,
+                            "y": 894.6718597412109
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/bed_to_protein_map/bed_to_protein_map/0.2.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "eb811f3018ea",
-                            "name": "metaquantome_viz",
+                            "changeset_revision": "a7c58b43cbaa",
+                            "name": "bed_to_protein_map",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"t\", \"__current_case__\": 1, \"plot\": {\"plottype\": \"bar\", \"__current_case__\": 0, \"target_rank\": \"genus\", \"meancol\": \"T2_mean\", \"nterms\": \"5\", \"barcol\": \"1\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "403554ac-e02a-423c-8342-a2813b4f160a",
+                        "uuid": "f32d0b6f-c434-47ea-88b1-391147c88f92",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "plotdata",
-                                "uuid": "0f00b678-12ee-40a4-919a-736998f1da10"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "wrapped_outfile",
-                                "uuid": "5ce4440c-d524-47a1-a990-069824a9c20e"
+                                "output_name": "output",
+                                "uuid": "ec2b95fe-e600-490e-abde-a8b0d80d1ac9"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
                         "errors": null,
-                        "id": 8,
+                        "id": 25,
                         "input_connections": {
-                            "infile": {
-                                "id": 6,
-                                "output_name": "outfile"
-                            },
-                            "samps": {
-                                "id": 0,
-                                "output_name": "samples_file"
+                            "input": {
+                                "id": 22,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
-                        "label": "T7-T2_volcano-plot",
-                        "name": "metaQuantome: visualize",
+                        "label": null,
+                        "name": "Tabular-to-FASTA",
                         "outputs": [
                             {
-                                "name": "wrapped_outfile",
-                                "type": "html"
-                            },
-                            {
-                                "name": "plotdata",
-                                "type": "tabular"
+                                "name": "output",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 931.5625915527344,
-                            "top": 947.6042022705078
+                            "bottom": 478.0031204223633,
+                            "height": 92.79998779296875,
+                            "left": 2557.6718139648438,
+                            "right": 2717.6718139648438,
+                            "top": 385.20313262939453,
+                            "width": 160,
+                            "x": 2557.6718139648438,
+                            "y": 385.20313262939453
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "eb811f3018ea",
-                            "name": "metaquantome_viz",
-                            "owner": "galaxyp",
+                            "changeset_revision": "0b4e36026794",
+                            "name": "tabular_to_fasta",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"t\", \"__current_case__\": 1, \"plot\": {\"plottype\": \"volcano\", \"__current_case__\": 1, \"fc_name\": \"log2fc_T7_over_T2\", \"fc_corr_p\": \"corrected_p_T7_over_T2\", \"textannot\": \"\", \"flip_fc\": \"false\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"seq_col\": \"2\", \"title_col\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "56b5e0c8-654f-48a1-80f2-5dee80f2ea28",
+                        "uuid": "10d46847-b9e3-43b5-868c-bc34ab8e16b5",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "plotdata",
-                                "uuid": "8a5b5357-fdf6-4a08-80fc-ccc961e197d3"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "wrapped_outfile",
-                                "uuid": "1885e756-240c-4c52-9a92-3031c86fa28b"
+                                "output_name": "output",
+                                "uuid": "a20fd7ce-326c-4fb2-845b-ba93bc2d24a5"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
                         "errors": null,
-                        "id": 9,
+                        "id": 26,
                         "input_connections": {
-                            "infile": {
-                                "id": 6,
-                                "output_name": "outfile"
-                            },
-                            "samps": {
-                                "id": 0,
-                                "output_name": "samples_file"
-                            }
+                            "inputs": [
+                                {
+                                    "id": 24,
+                                    "output_name": "output"
+                                },
+                                {
+                                    "id": 16,
+                                    "output_name": "out_file1"
+                                }
+                            ]
                         },
                         "inputs": [],
-                        "label": "T4-Bar-Plot",
-                        "name": "metaQuantome: visualize",
+                        "label": null,
+                        "name": "Concatenate datasets",
                         "outputs": [
                             {
-                                "name": "wrapped_outfile",
-                                "type": "html"
-                            },
-                            {
-                                "name": "plotdata",
-                                "type": "tabular"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 1236.3020935058594,
-                            "top": 540.0000152587891
+                            "bottom": 662.2062606811523,
+                            "height": 92.80001831054688,
+                            "left": 2288.093719482422,
+                            "right": 2448.093719482422,
+                            "top": 569.4062423706055,
+                            "width": 160,
+                            "x": 2288.093719482422,
+                            "y": 569.4062423706055
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "eb811f3018ea",
-                            "name": "metaquantome_viz",
-                            "owner": "galaxyp",
+                            "changeset_revision": "20344ce0c811",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"t\", \"__current_case__\": 1, \"plot\": {\"plottype\": \"bar\", \"__current_case__\": 0, \"target_rank\": \"genus\", \"meancol\": \"T4_mean\", \"nterms\": \"5\", \"barcol\": \"1\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
+                        "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "a4d4199a-6fac-4027-9403-317561ea3ca0",
+                        "uuid": "943dd8be-c5e3-45cf-9b22-8b6d92e2fe4f",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "wrapped_outfile",
-                                "uuid": "5db21144-afd7-486a-ad2e-e2186ccb2759"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "plotdata",
-                                "uuid": "a6fb4b9a-b0fb-4a0e-af13-6cd78d2a804b"
+                                "output_name": "out_file1",
+                                "uuid": "e24d9b68-120f-43da-91a1-34f0daaceb7f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
                         "errors": null,
-                        "id": 10,
+                        "id": 27,
                         "input_connections": {
-                            "infile": {
-                                "id": 6,
-                                "output_name": "outfile"
+                            "batchmode|input_fastas_0|input_fasta": {
+                                "id": 2,
+                                "output_name": "output"
                             },
-                            "samps": {
-                                "id": 0,
-                                "output_name": "samples_file"
+                            "batchmode|input_fastas_1|input_fasta": {
+                                "id": 25,
+                                "output_name": "output"
+                            },
+                            "batchmode|input_fastas_2|input_fasta": {
+                                "id": 20,
+                                "output_name": "translation_fasta"
                             }
                         },
                         "inputs": [],
-                        "label": "T7-Bar-Plot",
-                        "name": "metaQuantome: visualize",
+                        "label": null,
+                        "name": "FASTA Merge Files and Filter Unique Sequences",
                         "outputs": [
                             {
-                                "name": "wrapped_outfile",
-                                "type": "html"
-                            },
-                            {
-                                "name": "plotdata",
-                                "type": "tabular"
+                                "name": "output",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 1244.3056335449219,
-                            "top": 834.0104522705078
+                            "bottom": 801.796875,
+                            "height": 260,
+                            "left": 2996.5780639648438,
+                            "right": 3156.5780639648438,
+                            "top": 541.796875,
+                            "width": 160,
+                            "x": 2996.5780639648438,
+                            "y": 541.796875
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Uniprot_cRAP_SAV_indel_translatedbed.FASTA"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "eb811f3018ea",
-                            "name": "metaquantome_viz",
+                            "changeset_revision": "f546e7278f04",
+                            "name": "fasta_merge_files_and_filter_unique_sequences",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"t\", \"__current_case__\": 1, \"plot\": {\"plottype\": \"bar\", \"__current_case__\": 0, \"target_rank\": \"genus\", \"meancol\": \"T7_mean\", \"nterms\": \"5\", \"barcol\": \"1\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
+                        "tool_state": "{\"accession_parser\": \"^>([^ ]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"uniqueness_criterion\": \"sequence\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "3e71e1e5-5f29-4e02-87d4-431a93d72eb0",
+                        "uuid": "ee552030-2599-41c9-9bd1-0c6e3d311cae",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "wrapped_outfile",
-                                "uuid": "c49669b7-f4c9-4e84-89bf-86484a3e11d0"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "plotdata",
-                                "uuid": "b17119dd-9b47-40ba-9610-53f1fbffab04"
+                                "label": "Uniprot_cRAP_SAV_indel_translatedbed_FASTA",
+                                "output_name": "output",
+                                "uuid": "924bce7c-5c6a-4cb3-a459-18784a55ae01"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "errors": null,
-                        "id": 11,
+                        "id": 28,
                         "input_connections": {
-                            "infile": {
-                                "id": 6,
-                                "output_name": "outfile"
-                            },
-                            "samps": {
-                                "id": 0,
-                                "output_name": "samples_file"
+                            "tables_0|table": {
+                                "id": 26,
+                                "output_name": "out_file1"
                             }
                         },
-                        "inputs": [],
-                        "label": "T4-T2_volcano-plot",
-                        "name": "metaQuantome: visualize",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "wrapped_outfile",
-                                "type": "html"
-                            },
+                                "description": "runtime parameter for tool Query Tabular",
+                                "name": "add_to_database"
+                            }
+                        ],
+                        "label": "Genomic_mapping_sqlite",
+                        "name": "Query Tabular",
+                        "outputs": [
                             {
-                                "name": "plotdata",
-                                "type": "tabular"
+                                "name": "sqlitedb",
+                                "type": "sqlite"
                             }
                         ],
                         "position": {
-                            "left": 1275.2778015136719,
-                            "top": 1161.0069732666016
+                            "bottom": 735.6281509399414,
+                            "height": 184.80001831054688,
+                            "left": 2532.6718139648438,
+                            "right": 2692.6718139648438,
+                            "top": 550.8281326293945,
+                            "width": 160,
+                            "x": 2532.6718139648438,
+                            "y": 550.8281326293945
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
+                        "post_job_actions": {
+                            "RenameDatasetActionsqlitedb": {
+                                "action_arguments": {
+                                    "newname": "genomic_mapping.sqlite"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "sqlitedb"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "eb811f3018ea",
-                            "name": "metaquantome_viz",
-                            "owner": "galaxyp",
+                            "changeset_revision": "33d61c89fb8d",
+                            "name": "query_tabular",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"t\", \"__current_case__\": 1, \"plot\": {\"plottype\": \"volcano\", \"__current_case__\": 1, \"fc_name\": \"log2fc_T4_over_T2\", \"fc_corr_p\": \"corrected_p_T4_over_T2\", \"textannot\": \"\", \"flip_fc\": \"false\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy0",
+                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"save_db\": \"true\", \"sqlquery\": \"\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"feature_cds_map\", \"column_names_from_first_line\": \"false\", \"col_names\": \"name,chrom,start,end,strand,cds_start,cds_end\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"name,cds_start,cds_end\"}]}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "6d7fa5d9-4ece-4f7c-9a5c-21366e78b7de",
+                        "uuid": "0af1f230-f319-41ab-946a-98ada6900f17",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "wrapped_outfile",
-                                "uuid": "c06ba8b9-d6ae-409a-8418-01a21e80c209"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "plotdata",
-                                "uuid": "f18da0f4-0758-472d-94fa-737119726861"
+                                "label": "genomic_mapping_sqlite",
+                                "output_name": "sqlitedb",
+                                "uuid": "6542c4e5-289a-4be4-9b42-7a4e170ba198"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/metaquantome-taxonomy",
-                "path": "topics/proteomics/tutorials/metaquantome-taxonomy/workflows/main_workflow.ga",
+                "parent_id": "proteomics/proteogenomics-dbcreation",
+                "path": "topics/proteomics/tutorials/proteogenomics-dbcreation/workflows/galaxy-workflow-mouse_rnaseq_dbcreation.ga",
                 "tags": [
                     "proteomics"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "metaquantome-taxonomy-workflow",
+                "title": "GTN Proteogenomics1 Database Creation",
                 "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-metaquantome-taxonomy/versions/main-workflow",
-                "tutorial_id": "metaquantome-taxonomy",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaquantome-taxonomy/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaquantome-taxonomy/workflows/main_workflow.html",
-                "version": 2,
-                "wfid": "proteomics-metaquantome-taxonomy",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-proteogenomics-dbcreation/versions/galaxy-workflow-mouse-rnaseq-dbcreation",
+                "tutorial_id": "proteogenomics-dbcreation",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteogenomics-dbcreation/workflows/galaxy-workflow-mouse_rnaseq_dbcreation.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteogenomics-dbcreation/workflows/galaxy-workflow-mouse_rnaseq_dbcreation.html",
+                "version": 8,
+                "wfid": "proteomics-proteogenomics-dbcreation",
+                "wfname": "galaxy-workflow-mouse-rnaseq-dbcreation",
+                "workflow": "galaxy-workflow-mouse_rnaseq_dbcreation.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.0-0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.0-0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.0-0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.0-0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.0-0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/bed_to_protein_map/bed_to_protein_map/0.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.22.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/gffcompare_to_bed/gffcompare_to_bed/0.2.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed/translate_bed/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.11.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1"
                 ],
-                "workflowhub_id": "1155"
+                "workflowhub_id": "1201"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.4110725"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.1489208"
     },
     {
         "admin_install": {
@@ -185317,430 +187079,141 @@
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "288462ec2630",
+                    "revisions": "d698c222f354",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "proteore_expression_rnaseq_abbased",
-                    "owner": "proteore",
-                    "revisions": "dbeabf9bf091",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "proteore_filter_keywords_values",
-                    "owner": "proteore",
-                    "revisions": "33ca9ba2495a",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "proteore_id_converter",
-                    "owner": "proteore",
-                    "revisions": "b6607b7e683f",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "proteore_ms_observation_pepatlas",
-                    "owner": "proteore",
-                    "revisions": "299eb4a62e0c",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "column_maker",
+                    "owner": "devteam",
+                    "revisions": "be25c075ed54",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "proteore_prot_features",
-                    "owner": "proteore",
-                    "revisions": "8df559ad14a7",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "histogram",
+                    "owner": "devteam",
+                    "revisions": "6f134426c2b0",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "proteore_tissue_specific_expression_data",
-                    "owner": "proteore",
-                    "revisions": "3e65e0249976",
+                    "name": "maxquant",
+                    "owner": "galaxyp",
+                    "revisions": "37d669de2828",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "proteore_venn_diagram",
-                    "owner": "proteore",
-                    "revisions": "d1fd04dcb13a",
+                    "name": "msstats",
+                    "owner": "galaxyp",
+                    "revisions": "52ac6fde9a5b",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: 288462ec2630\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_expression_rnaseq_abbased\n  owner: proteore\n  revisions: dbeabf9bf091\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_filter_keywords_values\n  owner: proteore\n  revisions: 33ca9ba2495a\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_id_converter\n  owner: proteore\n  revisions: b6607b7e683f\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_ms_observation_pepatlas\n  owner: proteore\n  revisions: 299eb4a62e0c\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_prot_features\n  owner: proteore\n  revisions: 8df559ad14a7\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_tissue_specific_expression_data\n  owner: proteore\n  revisions: 3e65e0249976\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_venn_diagram\n  owner: proteore\n  revisions: d1fd04dcb13a\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/biomarker_selection/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: be25c075ed54\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: histogram\n  owner: devteam\n  revisions: 6f134426c2b0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maxquant\n  owner: galaxyp\n  revisions: 37d669de2828\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msstats\n  owner: galaxyp\n  revisions: 52ac6fde9a5b\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/maxquant-label-free/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
-                    "elixir-europe"
+                    "uni-freiburg"
                 ],
-                "elixir_node": "fr",
-                "email": "florence.combes@cea.fr",
-                "id": "combesf",
-                "joined": "2019-04",
-                "name": "Florence Combes",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/combesf/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/combesf.json"
-            },
-            {
-                "id": "davidchristiany",
-                "joined": "2019-04",
-                "name": "David Christiany",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/davidchristiany/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/davidchristiany.json"
-            },
-            {
-                "id": "vloux",
-                "joined": "2019-04",
-                "name": "Valentin Loux",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/vloux/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/vloux.json"
+                "email": "melanie.foell@mol-med.uni-freiburg.de",
+                "id": "foellmelanie",
+                "joined": "2018-10",
+                "matrix": "foellmelanie:matrix.org",
+                "name": "Melanie F\u00f6ll",
+                "orcid": "0000-0002-1887-7543",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
+                "twitter": "MCFoell",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
             },
             {
-                "id": "yvandenb",
-                "joined": "2019-04",
-                "name": "Yves Vandenbrouck",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvandenb/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/yvandenb.json"
-            }
-        ],
-        "dir": "topics/proteomics/tutorials/biomarker_selection",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "proteomics/biomarker_selection",
-        "inexact_supported_servers": [
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Public proteomics databases are useful resources for annotation of biomarker candidates"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Build a workflow implementing a strategy for the selection of tissue-leakage biomarkers using ProteoRE"
-        ],
-        "pageviews": 1899,
-        "pub_date": "2019-06-13",
-        "questions": [
-            "How to mine public databases to retrieve info?",
-            "How to build a selection strategy by applying successive biochemical/cellular criteria to a list of gene/protein?",
-            "How to select biomarkers candidates using experimental information (transcriptomics & proteomics) and annotation from public databases?"
-        ],
-        "short_id": "T00213",
-        "short_tools": [
-            "IDconverter",
-            "MQoutputfilter",
-            "prot_features",
-            "retr_pepatlas1",
-            "tp_cut_tool",
-            "retrieve_from_hpa",
-            "rna_abbased_data",
-            "Jvenn"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "post-process",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "DDA",
-            "human"
-        ],
-        "time_estimation": "3H",
-        "title": "Biomarker candidate identification",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.0.0",
-            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_expression_rnaseq_abbased/rna_abbased_data/2019.03.07",
-            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_filter_keywords_values/MQoutputfilter/2019.03.05",
-            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_id_converter/IDconverter/2019.01.28",
-            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_ms_observation_pepatlas/retr_pepatlas1/2019.02.01.1",
-            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_prot_features/prot_features/2019.01.18",
-            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_tissue_specific_expression_data/retrieve_from_hpa/2019.02.27",
-            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/Jvenn/2018.12.18"
-        ],
-        "topic_name": "proteomics",
-        "topic_name_human": "Proteomics",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "biomarker_selection",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/biomarker_selection/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/biomarker_selection/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/biomarker_selection/tutorial.json"
-        },
-        "version": 9,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 159,
-        "visitors": 1369,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Biomarker candidate identification",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Build tissue-specific expression dataset\"]\n  1[label=\"Build tissue-specific expression dataset\"]\n  2[label=\"Filter by keywords and/or numerical value\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"Venn diagram\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"kept_lines\"]\n  4[label=\"Cut\"]\n  3 -> 4 [label=\"output_text\"]\n  5[label=\"Filter by keywords and/or numerical value\"]\n  4 -> 5 [label=\"output\"]\n  6[label=\"Add expression data\"]\n  5 -> 6 [label=\"kept_lines\"]\n  7[label=\"Filter by keywords and/or numerical value\"]\n  6 -> 7 [label=\"output\"]\n  8[label=\"ID Converter\"]\n  7 -> 8 [label=\"kept_lines\"]\n  9[label=\"Add protein features\"]\n  8 -> 9 [label=\"output\"]\n  10[label=\"Filter by keywords and/or numerical value\"]\n  9 -> 10 [label=\"output\"]\n  11[label=\"Get MS/MS observations in tissue/fluid\"]\n  10 -> 11 [label=\"kept_lines\"]\n  12[label=\"Filter by keywords and/or numerical value\"]\n  11 -> 12 [label=\"output\"]\n}",
-                "history": [
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 3,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 2,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "efe1128541cbed0185333343ba7bd94fb3bab869",
-                        "message": "Add first version of biomarker selection tutorial",
-                        "num": 1,
-                        "short_hash": "efe112854",
-                        "unix": "1556267888"
-                    }
-                ],
-                "inputs": [],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"Build tissue-specific expression dataset\"];\n  1[\"Build tissue-specific expression dataset\"];\n  2[\"Filter by keywords and/or numerical value\"];\n  1 -->|output| 2;\n  3[\"Venn diagram\"];\n  0 -->|output| 3;\n  2 -->|kept_lines| 3;\n  4[\"Cut\"];\n  3 -->|output_text| 4;\n  5[\"Filter by keywords and/or numerical value\"];\n  4 -->|output| 5;\n  6[\"Add expression data\"];\n  5 -->|kept_lines| 6;\n  7[\"Filter by keywords and/or numerical value\"];\n  6 -->|output| 7;\n  8[\"ID Converter\"];\n  7 -->|kept_lines| 8;\n  9[\"Add protein features\"];\n  8 -->|output| 9;\n  10[\"Filter by keywords and/or numerical value\"];\n  9 -->|output| 10;\n  11[\"Get MS/MS observations in tissue/fluid\"];\n  10 -->|kept_lines| 11;\n  12[\"Filter by keywords and/or numerical value\"];\n  11 -->|output| 12;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "'Biomarkers4Paris' Workflow",
-                "outputs": [],
-                "parent_id": "proteomics/biomarker_selection",
-                "path": "topics/proteomics/tutorials/biomarker_selection/workflows/main_workflow.ga",
-                "tags": [
-                    "proteomics"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "'Biomarkers4Paris' Workflow",
-                "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-biomarker_selection/versions/main-workflow",
-                "tutorial_id": "biomarker_selection",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/biomarker_selection/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/biomarker_selection/workflows/main_workflow.html",
-                "version": 3,
-                "wfid": "proteomics-biomarker_selection",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_expression_rnaseq_abbased/rna_abbased_data/2019.03.07",
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_filter_keywords_values/MQoutputfilter/2019.03.05",
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_id_converter/IDconverter/2019.01.28",
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_ms_observation_pepatlas/retr_pepatlas1/2019.02.01.1",
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_prot_features/prot_features/2019.01.18",
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_tissue_specific_expression_data/retrieve_from_hpa/2019.02.27",
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/Jvenn/2018.12.18"
+                "affiliations": [
+                    "uni-freiburg"
                 ],
-                "workflowhub_id": "1232"
-            }
-        ],
-        "zenodo_link": ""
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "msstatstmt",
-                    "owner": "galaxyp",
-                    "revisions": "bd1535813cfe",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "unipept",
-                    "owner": "galaxyp",
-                    "revisions": "21a560af5913",
-                    "tool_panel_section_label": "Get Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: msstatstmt\n  owner: galaxyp\n  revisions: bd1535813cfe\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unipept\n  owner: galaxyp\n  revisions: 21a560af5913\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-5-data-interpretation/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "subinamehta",
-                "katherine-d21",
-                "dechendb"
-            ],
-            "editing": [
-                "pratikdjagtap",
-                "timothygriffin"
-            ]
-        },
-        "contributors": [
-            {
-                "email": "subinamehta@gmail.com",
-                "id": "subinamehta",
-                "joined": "2018-06",
-                "linkedin": "subinamehta",
-                "matrix": "subinamehta:matrix.org",
-                "name": "Subina Mehta",
-                "orcid": "0000-0001-9818-0537",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
-                "twitter": "Subina_Mehta",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
-            },
-            {
-                "id": "katherine-d21",
-                "joined": "2023-08",
-                "name": "Katherine Do",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/katherine-d21/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/katherine-d21.json"
-            },
-            {
-                "id": "dechendb",
-                "joined": "2023-06",
-                "name": "Dechen Bhuming",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dechendb/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/dechendb.json"
-            },
-            {
-                "email": "pjagtap@umn.edu",
-                "id": "pratikdjagtap",
-                "joined": "2017-09",
-                "name": "Pratik Jagtap",
-                "orcid": "0000-0003-0984-0973",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
-            },
-            {
-                "email": "tgriffin@umn.edu",
-                "github": false,
-                "id": "timothygriffin",
-                "joined": "2017-09",
-                "name": "Timothy J. Griffin",
-                "orcid": "0000-0001-6801-2559",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
+                "email": "matthias.fahrner@uniklinik-freiburg.de",
+                "id": "matthias313",
+                "joined": "2019-03",
+                "name": "Matthias Fahrner",
+                "orcid": "0000-0001-7955-2518",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/matthias313/",
+                "twitter": "mfahrner313",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/matthias313.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/clinical-mp-5-data-interpretation",
+        "dir": "topics/proteomics/tutorials/maxquant-label-free",
         "edam_operation": [
+            "Principal component plotting",
             "Visualisation",
-            "Prediction and recognition"
+            "Clustering",
+            "Protein quantification",
+            "Standardisation and normalisation",
+            "Imputation",
+            "Spectrum calculation",
+            "Differential protein expression profiling",
+            "Statistical calculation",
+            "Heat map generation",
+            "Tag-based peptide identification"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.cz",
+            "UseGalaxy.be",
             "UseGalaxy.eu",
-            "UseGalaxy.org.au"
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "proteomics",
-                "tutorials": [
-                    "metaproteomics"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "proteomics/clinical-mp-5-data-interpretation",
-        "inexact_supported_servers": [],
+        "id": "proteomics/maxquant-label-free",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.org.au"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Data interpretation and visualization of clinical samples."
+            "MaxQuant offers a single tool solution for protein identification and quantification.",
+            "Label-free quantitation reveals the most abundant proteins in serum samples."
         ],
         "layout": "tutorial_hands_on",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-08",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Perform group comparison analysis.",
-            "Analyze significant proteins",
-            "Look at the taxonomic distribution of the quantified peptides"
+            "Analysis of human serum proteome samples with label-free quantification in MaxQuant"
         ],
-        "pageviews": 73,
-        "pub_date": "2024-02-06",
+        "pageviews": 24393,
+        "pub_date": "2020-04-29",
         "questions": [
-            "Why do we need to interpret the data?",
-            "Can we visualize the data?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "katherine-d21"
-                ],
-                "date": "2024-06-21",
-                "galaxy_version": "23.1",
-                "length": "20M",
-                "speakers": [
-                    "katherine-d21"
-                ],
-                "youtube_id": "uDs9bXAwCHo"
-            }
-        ],
-        "redirect_from": [
-            "/topics/proteomics/tutorials/clinical-mp-data-interpretation/tutorial",
-            "/short/proteomics/clinical-mp-5-data-interpretation",
-            "/short/T00417"
-        ],
-        "requirements": [
-            {
-                "topic_name": "proteomics",
-                "type": "internal"
-            }
+            "How to perform label-free analysis in Maxquant?",
+            "Which are the most abundant proteins in serum?",
+            "How successful was the depletion of those in our experiment?"
         ],
-        "short_id": "T00417",
+        "short_id": "T00218",
         "short_tools": [
+            "Filter1",
+            "tp_sort_header_tool",
+            "histogram_rpy",
             "Grep1",
-            "unipept",
-            "msstatstmt"
+            "Add_a_column1",
+            "Cut1",
+            "maxquant",
+            "msstats"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "clinical-metaproteomics",
+        "subtopic": "id-quant",
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
                 {
@@ -185748,24 +187221,46 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
                 }
-            ],
-            "inexact": []
+            ]
         },
         "symlink": null,
         "tags": [
-            "label-TMT11"
+            "DDA",
+            "label-free"
         ],
-        "time_estimation": "3H",
-        "title": "Clinical Metaproteomics 5: Data Interpretation",
+        "time_estimation": "1H",
+        "title": "Label-free data analysis using MaxQuant",
         "tools": [
+            "Cut1",
+            "Filter1",
             "Grep1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/msstatstmt/msstatstmt/2.0.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.5.1"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0"
         ],
         "topic_name": "proteomics",
         "topic_name_human": "Proteomics",
@@ -185775,50 +187270,86 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "clinical-mp-5-data-interpretation",
+        "tutorial_name": "maxquant-label-free",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-5-data-interpretation/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-label-free/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-5-data-interpretation/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-5-data-interpretation/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/maxquant-label-free/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/maxquant-label-free/tutorial.json"
         },
-        "version": 2,
+        "version": 12,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 558,
-        "visitors": 49,
+        "visit_duration": 101,
+        "visitors": 16500,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Organization",
-                        "identifier": "0000-0001-9818-0537",
-                        "name": "Subina Mehta"
-                    }
-                ],
-                "description": "Interpreting MaxQuant data using MSstats involves applying a rigorous statistical framework to glean meaningful insights from quantitative proteomic datasets",
+                "creators": [],
+                "description": "Label-free data analysis using MaxQuant",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nQuantified Peptides\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMaxQuant Protein Groups\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMaxQuant Evidence\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAnnotation.txt\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nComparison Matrix\"]\n  5[label=\"Unipept\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Microbial Proteins\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"Select\"]\n  1 -> 7 [label=\"output\"]\n  8[label=\"MSstatsTMT\"]\n  4 -> 8 [label=\"output\"]\n  3 -> 8 [label=\"output\"]\n  2 -> 8 [label=\"output\"]\n  6 -> 8 [label=\"out_file1\"]\n  9[label=\"HUMAN-Proteins\"]\n  7 -> 9 [label=\"out_file1\"]\n  10[label=\"MSstatsTMT\"]\n  4 -> 10 [label=\"output\"]\n  3 -> 10 [label=\"output\"]\n  2 -> 10 [label=\"output\"]\n  9 -> 10 [label=\"out_file1\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nProtein_database\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSample1\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSample2\"]\n  3[label=\"MaxQuant\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Filter\"]\n  3 -> 4 [label=\"proteinGroups\"]\n  5[label=\"Select\"]\n  4 -> 5 [label=\"out_file1\"]\n  6[label=\"Cut\"]\n  5 -> 6 [label=\"out_file1\"]\n  7[label=\"Sort\"]\n  6 -> 7 [label=\"out_file1\"]\n  8[label=\"Compute\"]\n  6 -> 8 [label=\"out_file1\"]\n  9[label=\"Sort\"]\n  7 -> 9 [label=\"outfile\"]\n  10[label=\"Compute\"]\n  8 -> 10 [label=\"out_file1\"]\n  11[label=\"Cut\"]\n  10 -> 11 [label=\"out_file1\"]\n  12[label=\"Compute\"]\n  10 -> 12 [label=\"out_file1\"]\n  13[label=\"Histogram\"]\n  12 -> 13 [label=\"out_file1\"]\n}",
                 "history": [
                     {
-                        "hash": "e8db145f1d7e42048e01ecc851e6c2bf5caf0f1a",
-                        "message": "add missing metadata",
+                        "hash": "1a316efffa5d21398409e859952e3f99ae0aac9a",
+                        "message": "update wf parameter",
+                        "num": 8,
+                        "short_hash": "1a316efff",
+                        "unix": "1605483358"
+                    },
+                    {
+                        "hash": "dffe67cc1cd22e5f34204ccd105a156188c88fc8",
+                        "message": "Updating figure and workflow",
+                        "num": 7,
+                        "short_hash": "dffe67cc1",
+                        "unix": "1604174052"
+                    },
+                    {
+                        "hash": "3fd8e24d19128f02d08c3dd8d44ca034fd0bba9d",
+                        "message": "Adding steps to workflow",
+                        "num": 6,
+                        "short_hash": "3fd8e24d1",
+                        "unix": "1603366973"
+                    },
+                    {
+                        "hash": "cf8b1cb0509e73e534c234076c8bd055379823c5",
+                        "message": "Update some workflow names for consistency",
+                        "num": 5,
+                        "short_hash": "cf8b1cb05",
+                        "unix": "1598836271"
+                    },
+                    {
+                        "hash": "cdab43efb540f8228bce6af36097b4ce2f7b8019",
+                        "message": "update maxquant workflow histogram version to 1.0.4, add test",
+                        "num": 4,
+                        "short_hash": "cdab43efb",
+                        "unix": "1596427673"
+                    },
+                    {
+                        "hash": "ba67a0dfefa95ef6538d0c229146b475ba806f0a",
+                        "message": "Adding a few more follow up steps and improving some older training content",
+                        "num": 3,
+                        "short_hash": "ba67a0dfe",
+                        "unix": "1591567276"
+                    },
+                    {
+                        "hash": "5d041fcf71bb9e8c35d11b00a7531b32de608ce2",
+                        "message": "adding more stuff to the workflow",
                         "num": 2,
-                        "short_hash": "e8db145f1",
-                        "unix": "1723120021"
+                        "short_hash": "5d041fcf7",
+                        "unix": "1588178974"
                     },
                     {
-                        "hash": "e0464fd1787b4ca7dea72ca77b7ab2ad03a8292a",
-                        "message": "add workflows",
+                        "hash": "83de9bde8bfd5f709f0e1347841e30664057b6c2",
+                        "message": "Adding MaxQuant training and levels for other proteomics tutorials",
                         "num": 1,
-                        "short_hash": "e0464fd17",
-                        "unix": "1723118192"
+                        "short_hash": "83de9bde8",
+                        "unix": "1588175696"
                     }
                 ],
                 "inputs": [
@@ -185831,23 +187362,34 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Quantified Peptides"
+                                "name": "Protein_database"
                             }
                         ],
-                        "label": "Quantified Peptides",
+                        "label": "Protein_database",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 189.871337890625,
-                            "top": 0
+                            "bottom": 525.6999969482422,
+                            "height": 82.19999694824219,
+                            "left": -15,
+                            "right": 185,
+                            "top": 443.5,
+                            "width": 200,
+                            "x": -15,
+                            "y": 443.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "cd669a99-182a-48db-a2c6-f8d24323e353",
-                        "when": null,
-                        "workflow_outputs": []
+                        "uuid": "90cc78f2-681e-4855-8e66-e4884558be47",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "bc660f8d-110e-4c33-909b-66c0c29748c9"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
@@ -185858,23 +187400,34 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "MaxQuant Protein Groups"
+                                "name": "Sample1"
                             }
                         ],
-                        "label": "MaxQuant Protein Groups",
+                        "label": "Sample1",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 289.65196228027344
+                            "bottom": 637.3000030517578,
+                            "height": 61.80000305175781,
+                            "left": -49,
+                            "right": 151,
+                            "top": 575.5,
+                            "width": 200,
+                            "x": -49,
+                            "y": 575.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "2ecd2d61-5e94-4dbd-a0cc-c30c343b38b4",
-                        "when": null,
-                        "workflow_outputs": []
+                        "uuid": "eb754bfe-49b1-406d-8eb9-842b8f1fab22",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "9a0693dc-6c4d-4fe8-8c8d-4846938278c3"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
@@ -185885,110 +187438,749 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "MaxQuant Evidence"
+                                "name": "Sample2"
                             }
                         ],
-                        "label": "MaxQuant Evidence",
+                        "label": "Sample2",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 221.97045898437503,
-                            "top": 568.7156335895269
+                            "bottom": 766.3000030517578,
+                            "height": 61.80000305175781,
+                            "left": -42,
+                            "right": 158,
+                            "top": 704.5,
+                            "width": 200,
+                            "x": -42,
+                            "y": 704.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "11afae12-7cc4-402b-a0e3-cf6e53276674",
-                        "when": null,
-                        "workflow_outputs": []
+                        "uuid": "321c3baa-dd58-45ce-9a28-ee1eb7332f0f",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "0a8fcb2d-5b66-4e0f-bb8c-46017c426cf2"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nProtein_database\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSample1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nSample2\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"MaxQuant\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  2 -->|output| 3;\n  4[\"Filter\"];\n  3 -->|proteinGroups| 4;\n  5[\"Select\"];\n  4 -->|out_file1| 5;\n  6[\"Cut\"];\n  5 -->|out_file1| 6;\n  7[\"Sort\"];\n  6 -->|out_file1| 7;\n  8[\"Compute\"];\n  6 -->|out_file1| 8;\n  9[\"Sort\"];\n  7 -->|outfile| 9;\n  10[\"Compute\"];\n  8 -->|out_file1| 10;\n  11[\"Cut\"];\n  10 -->|out_file1| 11;\n  12[\"Compute\"];\n  10 -->|out_file1| 12;\n  13[\"Histogram\"];\n  12 -->|out_file1| 13;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Proteomics: MaxQuant workflow",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Protein_database"
+                            }
+                        ],
+                        "label": "Protein_database",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 525.6999969482422,
+                            "height": 82.19999694824219,
+                            "left": -15,
+                            "right": 185,
+                            "top": 443.5,
+                            "width": 200,
+                            "x": -15,
+                            "y": 443.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "90cc78f2-681e-4855-8e66-e4884558be47",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "bc660f8d-110e-4c33-909b-66c0c29748c9"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Annotation.txt"
+                                "name": "Sample1"
                             }
                         ],
-                        "label": "Annotation.txt",
+                        "label": "Sample1",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 293.3940978424075,
-                            "top": 851.982536255788
+                            "bottom": 637.3000030517578,
+                            "height": 61.80000305175781,
+                            "left": -49,
+                            "right": 151,
+                            "top": 575.5,
+                            "width": 200,
+                            "x": -49,
+                            "y": 575.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "4ed9cd3d-2473-4b69-8ac8-3404e5628f85",
-                        "when": null,
-                        "workflow_outputs": []
+                        "uuid": "eb754bfe-49b1-406d-8eb9-842b8f1fab22",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "9a0693dc-6c4d-4fe8-8c8d-4846938278c3"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 4,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Comparison Matrix"
+                                "name": "Sample2"
                             }
                         ],
-                        "label": "Comparison Matrix",
+                        "label": "Sample2",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 307.5031433105469,
-                            "top": 973.9487421100347
+                            "bottom": 766.3000030517578,
+                            "height": 61.80000305175781,
+                            "left": -42,
+                            "right": 158,
+                            "top": 704.5,
+                            "width": 200,
+                            "x": -42,
+                            "y": 704.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "6c47825f-c68c-4f0e-a99b-a961f27c7719",
-                        "when": null,
-                        "workflow_outputs": []
+                        "uuid": "321c3baa-dd58-45ce-9a28-ee1eb7332f0f",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "0a8fcb2d-5b66-4e0f-bb8c-46017c426cf2"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "input_opts|fasta_files": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "paramGroups_0|files": [
+                                {
+                                    "id": 1,
+                                    "output_name": "output"
+                                },
+                                {
+                                    "id": 2,
+                                    "output_name": "output"
+                                }
+                            ]
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "MaxQuant",
+                        "outputs": [
+                            {
+                                "name": "proteinGroups",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "mqpar",
+                                "type": "xml"
+                            },
+                            {
+                                "name": "peptides",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "ptxqc_report",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 780.8999938964844,
+                            "height": 408.3999938964844,
+                            "left": 310,
+                            "right": 510,
+                            "top": 372.5,
+                            "width": 200,
+                            "x": 310,
+                            "y": 372.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ea0a1d50c83f",
+                            "name": "maxquant",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_opts\": {\"ftype\": \".thermo.raw\", \"fasta_files\": {\"__class__\": \"ConnectedValue\"}, \"identifier_parse_rule\": \">.*\\\\|(.*)\\\\|\", \"description_parse_rule\": \">(.*) OS\"}, \"output_opts\": {\"dry_run\": \"false\", \"output\": [\"proteinGroups\", \"mqpar\", \"peptides\"]}, \"paramGroups\": [{\"__index__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}, \"maxMissedCleavages\": \"1\", \"fixedModifications\": [\"Carbamidomethyl (C)\"], \"variableModifications\": null, \"enzymes\": [\"Trypsin/P\"], \"digestion_mode\": \"0\", \"quant_method\": {\"select_quant_method\": \"lfq\", \"__current_case__\": 2, \"lfqMinRatioCount\": \"2\", \"lfqMinEdgesPerNode\": \"3\", \"lfqAvEdgesPerNode\": \"6\", \"lfqSkipNorm\": \"true\"}}], \"protein_quant\": {\"peptides_for_quantification\": \"1\", \"only_unmod_prot\": {\"unmod_prot\": \"True\", \"__current_case__\": 0, \"mods_used_prot_quant\": [\"Acetyl (Protein N-term)\", \"Oxidation (M)\"], \"discard_unmod_cpart_peptides\": \"true\"}, \"lfq_opts\": {\"separateLfq\": \"false\", \"lfqStabilizeLargeRatios\": \"true\", \"lfqRequireMsms\": \"true\", \"do_ibaq\": {\"ibaq\": \"False\", \"__current_case__\": 1}, \"advancedSiteIntensities\": \"true\"}}, \"qc\": {\"do_it\": \"true\", \"__current_case__\": 0, \"parameters\": \"true\", \"summary\": \"true\", \"proteingroups\": \"true\", \"evidence\": \"true\", \"msms\": \"true\", \"msmsscans\": \"true\"}, \"search_opts\": {\"template\": null, \"min_peptide_len\": \"7\", \"max_peptide_mass\": \"4600\", \"min_unique_pep\": \"1\", \"calc_peak_properties\": \"false\", \"match_between_runs\": \"false\", \"incl_contaminants\": \"true\", \"decoy_mode\": \"revert\", \"psm_fdr\": \"0.01\", \"protein_fdr\": \"0.01\", \"min_pep_length\": \"8\", \"max_pep_length\": \"25\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.6.10.43+galaxy3",
+                        "type": "tool",
+                        "uuid": "ae1d3f39-d1a8-4cd3-9534-64cc69f175a9",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "peptides",
+                                "uuid": "fe9cec5c-de9c-4c39-bddd-e7dd199f2564"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "ptxqc_report",
+                                "uuid": "360aa96f-bebf-46b6-9b30-1d6940779216"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "proteinGroups",
+                                "uuid": "c155ddc4-7084-4830-836d-b71f7557a86e"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "mqpar",
+                                "uuid": "23b1a6e3-3da7-4c60-951b-71b1f4da33ba"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "Filter1",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "input": {
+                                "id": 3,
+                                "output_name": "proteinGroups"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Filter",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 465.6999969482422,
+                            "height": 93.19999694824219,
+                            "left": 530,
+                            "right": 730,
+                            "top": 372.5,
+                            "width": 200,
+                            "x": 530,
+                            "y": 372.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c38!=\\\"+\\\"\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
+                        "type": "tool",
+                        "uuid": "295e41a6-0642-414e-a939-8179f8b5f47d",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "7d51c925-9c11-4125-98f3-abe19bc22825"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "Grep1",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "input": {
+                                "id": 4,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Select",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 470.6999969482422,
+                            "height": 93.19999694824219,
+                            "left": 745,
+                            "right": 945,
+                            "top": 377.5,
+                            "width": 200,
+                            "x": 745,
+                            "y": 377.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "Grep1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"false\", \"pattern\": \"(HUMAN)|(Majority)\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.1",
+                        "type": "tool",
+                        "uuid": "f582f3e8-8308-49c3-a1ee-3ba9051f5a85",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "e88a2cae-98f1-471d-9131-338a6e1169fd"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "Cut1",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "input": {
+                                "id": 5,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Cut",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 465.6999969482422,
+                            "height": 93.19999694824219,
+                            "left": 970,
+                            "right": 1170,
+                            "top": 372.5,
+                            "width": 200,
+                            "x": 970,
+                            "y": 372.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c8,c32,c33\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2",
+                        "type": "tool",
+                        "uuid": "99557c29-6927-4736-afff-9a2be53e967e",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "a97baff1-6f76-4400-98c7-138666974448"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "infile": {
+                                "id": 6,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Sort",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 344.6999969482422,
+                            "height": 93.19999694824219,
+                            "left": 1162,
+                            "right": 1362,
+                            "top": 251.5,
+                            "width": 200,
+                            "x": 1162,
+                            "y": 251.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"header\": \"1\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"2\", \"order\": \"r\", \"style\": \"g\"}], \"unique\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
+                        "type": "tool",
+                        "uuid": "c6da37e8-98fc-4ab2-8ec1-9a55510b09c5",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "44df6e3d-01b3-4136-b18b-694f4d153b32"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "input": {
+                                "id": 6,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Compute",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 585.6999969482422,
+                            "height": 93.19999694824219,
+                            "left": 1190,
+                            "right": 1390,
+                            "top": 492.5,
+                            "width": 200,
+                            "x": 1190,
+                            "y": 492.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "be25c075ed54",
+                            "name": "column_maker",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"avoid_scientific_notation\": \"no\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"log(c2,2)\", \"header_lines_conditional\": {\"header_lines_select\": \"yes\", \"__current_case__\": 1, \"header_new_column_name\": \"log2 intensity sample1\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"round\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3.0",
+                        "type": "tool",
+                        "uuid": "a73294a5-050b-436a-95c2-7042aa30bab3",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "ec3d0fb2-8ce0-48d9-92d5-590c2644e326"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {
+                            "infile": {
+                                "id": 7,
+                                "output_name": "outfile"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Sort",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 339.6999969482422,
+                            "height": 93.19999694824219,
+                            "left": 1410,
+                            "right": 1610,
+                            "top": 246.5,
+                            "width": 200,
+                            "x": 1410,
+                            "y": 246.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"header\": \"1\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"3\", \"order\": \"r\", \"style\": \"g\"}], \"unique\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
+                        "type": "tool",
+                        "uuid": "3f46dbc8-6684-4e43-bfca-114671eff459",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "9ea6d4d3-05a4-4b64-a36c-eb4417be546d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {
+                            "input": {
+                                "id": 8,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Compute",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 585.6999969482422,
+                            "height": 93.19999694824219,
+                            "left": 1410,
+                            "right": 1610,
+                            "top": 492.5,
+                            "width": 200,
+                            "x": 1410,
+                            "y": 492.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "be25c075ed54",
+                            "name": "column_maker",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"avoid_scientific_notation\": \"no\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"log(c3,2)\", \"header_lines_conditional\": {\"header_lines_select\": \"yes\", \"__current_case__\": 1, \"header_new_column_name\": \"log2 intensity sample2\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"round\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3.0",
+                        "type": "tool",
+                        "uuid": "f164eec0-10d2-446d-ada7-db67303384f9",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "1905e349-23d8-4b81-a156-7e22977d3593"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "Cut1",
+                        "errors": null,
+                        "id": 11,
+                        "input_connections": {
+                            "input": {
+                                "id": 10,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Cut",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 766.6999969482422,
+                            "height": 93.19999694824219,
+                            "left": 1568,
+                            "right": 1768,
+                            "top": 673.5,
+                            "width": 200,
+                            "x": 1568,
+                            "y": 673.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c4,c5\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2",
+                        "type": "tool",
+                        "uuid": "7e308945-aa0f-494a-a59f-b960614e0a03",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "70c5c495-69e5-41e2-aefa-2bcc18aa5fd4"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {
+                            "input": {
+                                "id": 10,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Compute",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 598.6999969482422,
+                            "height": 93.19999694824219,
+                            "left": 1707,
+                            "right": 1907,
+                            "top": 505.5,
+                            "width": 200,
+                            "x": 1707,
+                            "y": 505.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "be25c075ed54",
+                            "name": "column_maker",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"avoid_scientific_notation\": \"no\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c4-c5\", \"header_lines_conditional\": {\"header_lines_select\": \"yes\", \"__current_case__\": 1, \"header_new_column_name\": \"log2 Fold Change\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"round\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3.0",
+                        "type": "tool",
+                        "uuid": "55d7d873-c11c-47ce-8c53-022ab234f8e1",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "f61c7a19-b543-4f5a-afe0-44c06bb28cd4"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
+                        "errors": null,
+                        "id": 13,
+                        "input_connections": {
+                            "input": {
+                                "id": 12,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Histogram",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 465.6999969482422,
+                            "height": 93.19999694824219,
+                            "left": 1850,
+                            "right": 2050,
+                            "top": 372.5,
+                            "width": 200,
+                            "x": 1850,
+                            "y": 372.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "6f134426c2b0",
+                            "name": "histogram",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"breaks\": \"0\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"density\": \"true\", \"frequency\": \"false\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"numerical_column\": \"6\", \"title\": \"log2 Fold Change\", \"xlab\": \"V1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.4",
+                        "type": "tool",
+                        "uuid": "0cffa4b8-d1df-4339-a6f8-18041a18c7e2",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "8b6f54e6-bea6-4dac-9226-f5468661fcd5"
+                            }
+                        ]
                     }
                 ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQuantified Peptides\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nMaxQuant Protein Groups\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nMaxQuant Evidence\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nAnnotation.txt\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nComparison Matrix\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Unipept\"];\n  0 -->|output| 5;\n  6[\"Microbial Proteins\"];\n  1 -->|output| 6;\n  7[\"Select\"];\n  1 -->|output| 7;\n  8[\"MSstatsTMT\"];\n  4 -->|output| 8;\n  3 -->|output| 8;\n  2 -->|output| 8;\n  6 -->|out_file1| 8;\n  9[\"HUMAN-Proteins\"];\n  7 -->|out_file1| 9;\n  10[\"MSstatsTMT\"];\n  4 -->|output| 10;\n  3 -->|output| 10;\n  2 -->|output| 10;\n  9 -->|out_file1| 10;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "WF5_Data_Interpretation_Worklow",
-                "outputs": [],
-                "parent_id": "proteomics/clinical-mp-5-data-interpretation",
-                "path": "topics/proteomics/tutorials/clinical-mp-5-data-interpretation/workflows/WF5_Data_Interpretation_Worklow.ga",
+                "parent_id": "proteomics/maxquant-label-free",
+                "path": "topics/proteomics/tutorials/maxquant-label-free/workflows/maxquant_label_free.ga",
                 "tags": [
-                    "name:clinicalMP"
+                    "proteomics"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "WF5_Data_Interpretation_Worklow",
+                "tests": true,
+                "title": "Proteomics: MaxQuant workflow",
                 "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-clinical-mp-5-data-interpretation/versions/wf5-data-interpretation-worklow",
-                "tutorial_id": "clinical-mp-5-data-interpretation",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-5-data-interpretation/workflows/WF5_Data_Interpretation_Worklow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-5-data-interpretation/workflows/WF5_Data_Interpretation_Worklow.html",
-                "version": 1,
-                "wfid": "proteomics-clinical-mp-5-data-interpretation",
-                "wfname": "wf5-data-interpretation-worklow",
-                "workflow": "WF5_Data_Interpretation_Worklow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-maxquant-label-free/versions/maxquant-label-free",
+                "tutorial_id": "maxquant-label-free",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/maxquant-label-free/workflows/maxquant_label_free.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/maxquant-label-free/workflows/maxquant_label_free.html",
+                "version": 6,
+                "wfid": "proteomics-maxquant-label-free",
+                "wfname": "maxquant-label-free",
+                "workflow": "maxquant_label_free.ga",
                 "workflow_tools": [
+                    "Cut1",
+                    "Filter1",
                     "Grep1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msstatstmt/msstatstmt/2.0.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.5.1"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3"
                 ],
-                "workflowhub_id": "1352"
+                "workflowhub_id": "1140"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.10105821"
+        "zenodo_link": "https://zenodo.org/record/3774452"
     },
     {
         "admin_install": {
@@ -185996,172 +188188,108 @@
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
             "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "flashlfq",
-                    "owner": "galaxyp",
-                    "revisions": "878f6725c4f3",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
                 {
                     "name": "msconvert",
                     "owner": "galaxyp",
-                    "revisions": "9ec469ff191a",
+                    "revisions": "3cf310697624",
                     "tool_panel_section_label": "Convert Formats",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "peptideshaker",
+                    "name": "openms_openswathworkflow",
                     "owner": "galaxyp",
-                    "revisions": "7fdd9119cc4f",
+                    "revisions": "887be35bc42e",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "peptideshaker",
+                    "name": "openms_openswathworkflow",
                     "owner": "galaxyp",
-                    "revisions": "7fdd9119cc4f",
+                    "revisions": "2aebe58de46e",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "regex_find_replace",
+                    "name": "pyprophet_export",
                     "owner": "galaxyp",
-                    "revisions": "209b7c5ee9d7",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "revisions": "3cf580bf28e2",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "unipept",
+                    "name": "pyprophet_merge",
                     "owner": "galaxyp",
-                    "revisions": "4953dcd7dd39",
-                    "tool_panel_section_label": "Get Data",
+                    "revisions": "a67b508b1dc5",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "unipept",
+                    "name": "pyprophet_peptide",
                     "owner": "galaxyp",
-                    "revisions": "9aaa46d45472",
-                    "tool_panel_section_label": "Get Data",
+                    "revisions": "4504b3bc1eed",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "unipept",
+                    "name": "pyprophet_protein",
                     "owner": "galaxyp",
-                    "revisions": "75b3b3d0adbf",
-                    "tool_panel_section_label": "Get Data",
+                    "revisions": "2320f48209fc",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "query_tabular",
-                    "owner": "iuc",
-                    "revisions": "33d61c89fb8d",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "pyprophet_score",
+                    "owner": "galaxyp",
+                    "revisions": "77f068ba47dd",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: flashlfq\n  owner: galaxyp\n  revisions: 878f6725c4f3\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msconvert\n  owner: galaxyp\n  revisions: 9ec469ff191a\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 7fdd9119cc4f\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 7fdd9119cc4f\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 209b7c5ee9d7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unipept\n  owner: galaxyp\n  revisions: 4953dcd7dd39\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unipept\n  owner: galaxyp\n  revisions: 9aaa46d45472\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unipept\n  owner: galaxyp\n  revisions: 75b3b3d0adbf\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n  owner: iuc\n  revisions: 33d61c89fb8d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: msconvert\n  owner: galaxyp\n  revisions: 3cf310697624\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_openswathworkflow\n  owner: galaxyp\n  revisions: 887be35bc42e\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_openswathworkflow\n  owner: galaxyp\n  revisions: 2aebe58de46e\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pyprophet_export\n  owner: galaxyp\n  revisions: 3cf580bf28e2\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pyprophet_merge\n  owner: galaxyp\n  revisions: a67b508b1dc5\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pyprophet_peptide\n  owner: galaxyp\n  revisions: 4504b3bc1eed\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pyprophet_protein\n  owner: galaxyp\n  revisions: 2320f48209fc\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pyprophet_score\n  owner: galaxyp\n  revisions: 77f068ba47dd\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.json",
         "contributors": [
             {
-                "email": "subinamehta@gmail.com",
-                "id": "subinamehta",
-                "joined": "2018-06",
-                "linkedin": "subinamehta",
-                "matrix": "subinamehta:matrix.org",
-                "name": "Subina Mehta",
-                "orcid": "0000-0001-9818-0537",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
-                "twitter": "Subina_Mehta",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
-            },
-            {
-                "email": "tgriffin@umn.edu",
-                "github": false,
-                "id": "timothygriffin",
-                "joined": "2017-09",
-                "name": "Timothy J. Griffin",
-                "orcid": "0000-0001-6801-2559",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
-            },
-            {
-                "email": "pjagtap@umn.edu",
-                "id": "pratikdjagtap",
-                "joined": "2017-09",
-                "name": "Pratik Jagtap",
-                "orcid": "0000-0003-0984-0973",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
-            },
-            {
-                "email": "leith023@umn.edu",
-                "id": "emmaleith",
-                "joined": "2019-07",
-                "name": "Emma Leith",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/emmaleith/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/emmaleith.json"
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "email": "matthias.fahrner@uniklinik-freiburg.de",
+                "id": "matthias313",
+                "joined": "2019-03",
+                "name": "Matthias Fahrner",
+                "orcid": "0000-0001-7955-2518",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/matthias313/",
+                "twitter": "mfahrner313",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/matthias313.json"
             },
             {
-                "email": "crane136@umn.edu",
-                "id": "mariecrane",
-                "joined": "2019-05",
-                "name": "Marie Crane",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mariecrane/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mariecrane.json"
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "email": "melanie.foell@mol-med.uni-freiburg.de",
+                "id": "foellmelanie",
+                "joined": "2018-10",
+                "matrix": "foellmelanie:matrix.org",
+                "name": "Melanie F\u00f6ll",
+                "orcid": "0000-0002-1887-7543",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
+                "twitter": "MCFoell",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/metaquantome-data-creation",
-        "edam_ontology": [
-            "topic_0121",
-            "topic_3922",
-            "topic_3050",
-            "topic_0637"
-        ],
+        "dir": "topics/proteomics/tutorials/DIA_Analysis_OSW",
         "edam_operation": [
-            "Visualisation",
-            "Label-free quantification",
             "Filtering",
-            "Formatting",
-            "Prediction and recognition"
-        ],
-        "edam_topic": [
-            "Proteomics",
-            "Proteogenomics",
-            "Biodiversity",
-            "Taxonomy"
-        ],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "proteomics",
-                "tutorials": [
-                    "metaproteomics"
-                ],
-                "type": "internal"
-            }
+            "Formatting"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
         ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
         "hands_on": true,
-        "id": "proteomics/metaquantome-data-creation",
+        "id": "proteomics/DIA_Analysis_OSW",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
             "UseGalaxy.no",
@@ -186172,43 +188300,47 @@
             "mermaid": false
         },
         "key_points": [
-            "Use dataset collections",
-            "With SearchGUI and PeptideShaker you can gain access to multiple search engines",
-            "Learning the basics of SQL queries can pay off"
+            "OpenSwathWorkflow enables analysis of data independent acquisition mass spectrometry data",
+            "DIA data analysis of HEK-Ecoli Spike-in dataset"
         ],
         "layout": "tutorial_hands_on",
         "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-14",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "A taxonomy, functional and quantitational analysis of metaproteomic mass spectrometry data."
+            "Analysis of HEK-Ecoli Spike-in DIA data in Galaxy",
+            "Understanding DIA data principles and characteristics",
+            "Using OpenSwathworkflow to analyze HEK-Ecoli Spike-in DIA data"
         ],
-        "pageviews": 1343,
-        "pub_date": "2020-10-16",
+        "pageviews": 3351,
+        "pub_date": "2020-12-02",
         "questions": [
-            "How do I perform functional and taxonomy analysis on metaproteomics data?",
-            "How can I perform quantitation on metaproteomics data?",
-            "How do I create inputs that can be used in metaquantome to examine differentially expressed proteins?"
+            "How to analyze data independent acquisition (DIA) mass spectrometry (MS) data using OpenSwathWorkflow?",
+            "How to detect different Spike-in amounts of Ecoli in a HEK-Ecoli Benchmark DIA dataset?"
         ],
-        "short_id": "T00222",
+        "requirements": [
+            {
+                "topic_name": "proteomics",
+                "tutorials": [
+                    "DIA_lib_OSW"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00211",
         "short_tools": [
-            "Grep1",
+            "pyprophet_protein",
             "msconvert",
-            "peptide_shaker",
-            "search_gui",
-            "Cut1",
-            "unipept",
-            "Filter1",
-            "query_tabular",
-            "tp_replace_in_line",
-            "Remove beginning1",
-            "regex1",
-            "flashlfq",
-            "tp_replace_in_column"
+            "OpenSwathWorkflow",
+            "pyprophet_peptide",
+            "Grep1",
+            "pyprophet_merge",
+            "pyprophet_export",
+            "pyprophet_score"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "multi-omics",
+        "subtopic": "id-quant",
         "supported_servers": {
             "exact": [
                 {
@@ -186237,26 +188369,20 @@
         },
         "symlink": null,
         "tags": [
-            "microgalaxy"
+            "DIA"
         ],
-        "time_estimation": "1h",
-        "title": "metaQuantome 1: Data creation",
+        "time_estimation": "2H",
+        "title": "DIA Analysis using OpenSwathWorkflow",
         "tools": [
-            "Cut1",
-            "Filter1",
             "Grep1",
-            "Remove beginning1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/flashlfq/flashlfq/1.0.3.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.0.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0"
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/2.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_export/pyprophet_export/2.1.4.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_merge/pyprophet_merge/2.1.4.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_peptide/pyprophet_peptide/2.1.4.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_protein/pyprophet_protein/2.1.4.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_score/pyprophet_score/2.1.4.2"
         ],
         "topic_name": "proteomics",
         "topic_name_human": "Proteomics",
@@ -186266,157 +188392,84 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "metaquantome-data-creation",
+        "tutorial_name": "DIA_Analysis_OSW",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.json"
         },
-        "version": 20,
+        "version": 10,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 228,
-        "visitors": 773,
+        "visit_duration": 133,
+        "visitors": 2315,
         "workflows": [
             {
                 "creators": [],
-                "description": "metaquantome-data-creation",
+                "description": "DIA Analysis Training using HEK Ecoli data in OSW",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nExperiment_Design\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nFASTA_db\"]\n  3[label=\"mzml to mgf\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Search GUI\"]\n  2 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"Peptide Shaker\"]\n  4 -> 5 [label=\"searchgui_results\"]\n  6[label=\"Replace Text\"]\n  5 -> 6 [label=\"output_psm\"]\n  7[label=\"Remove beginning\"]\n  5 -> 7 [label=\"output_peptides\"]\n  8[label=\"Unipept_lca\"]\n  5 -> 8 [label=\"output_peptides\"]\n  9[label=\"FlashLFQ\"]\n  1 -> 9 [label=\"output\"]\n  6 -> 9 [label=\"outfile\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"Unipept_peptinfo\"]\n  7 -> 10 [label=\"out_file1\"]\n  11[label=\"Replace Text\"]\n  8 -> 11 [label=\"output_tsv\"]\n  12[label=\"Regex Find And Replace\"]\n  9 -> 12 [label=\"quantifiedPeptides\"]\n  13[label=\"selecting EC column\"]\n  10 -> 13 [label=\"output_ec_tsv\"]\n  14[label=\"filter 5% All_funct\"]\n  10 -> 14 [label=\"output_go_tsv\"]\n  15[label=\"GO_EC\"]\n  13 -> 15 [label=\"out_file1\"]\n  16[label=\"GO_BP\"]\n  14 -> 16 [label=\"output\"]\n  17[label=\"GO_CC\"]\n  14 -> 17 [label=\"output\"]\n  18[label=\"GO_MF\"]\n  14 -> 18 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput exp. design annotation\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\niRTassays.tsv\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSpectral library\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Collection\\n\u201dInput Dataset Collection\u201d\"]\n  4[label=\"msconvert\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"OpenSwathWorkflow\"]\n  4 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"PyProphet merge\"]\n  5 -> 6 [label=\"out_osw\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"PyProphet score\"]\n  6 -> 7 [label=\"output\"]\n  8[label=\"PyProphet peptide\"]\n  7 -> 8 [label=\"output\"]\n  9[label=\"PyProphet peptide\"]\n  8 -> 9 [label=\"output\"]\n  10[label=\"PyProphet protein\"]\n  9 -> 10 [label=\"output\"]\n  11[label=\"PyProphet protein\"]\n  10 -> 11 [label=\"output\"]\n  12[label=\"PyProphet export\"]\n  0 -> 12 [label=\"output\"]\n  11 -> 12 [label=\"output\"]\n  13[label=\"Ecoli protein expression matrix\"]\n  12 -> 13 [label=\"protein_signal\"]\n}",
                 "history": [
                     {
-                        "hash": "72e53ea9af53237e2b615f69b8c95f7e1371396d",
-                        "message": "Rename workflow.ga to main_workflow.ga",
-                        "num": 14,
-                        "short_hash": "72e53ea9a",
-                        "unix": "1636569874"
-                    },
-                    {
-                        "hash": "b63d3bd0727a2182c18a765dc776ec8e35677046",
-                        "message": "Rename main_workflow.ga to workflow.ga",
-                        "num": 13,
-                        "short_hash": "b63d3bd07",
-                        "unix": "1636567614"
-                    },
-                    {
-                        "hash": "02a2548eca97ef7b2a0d5ac8b4ae145280ec9918",
-                        "message": "Update main_workflow.ga",
-                        "num": 12,
-                        "short_hash": "02a2548ec",
-                        "unix": "1636474235"
-                    },
-                    {
-                        "hash": "d4a710e9f76a5f0037efdf0e93711e87408ac272",
-                        "message": "Update main_workflow.ga",
-                        "num": 11,
-                        "short_hash": "d4a710e9f",
-                        "unix": "1636473894"
-                    },
-                    {
-                        "hash": "d0478e7ffd03b7adb6957eebf7fd90625fef7581",
-                        "message": "Update main_workflow.ga",
-                        "num": 10,
-                        "short_hash": "d0478e7ff",
-                        "unix": "1636473603"
-                    },
-                    {
-                        "hash": "2c4ad397f2f8887a6b0138d30f2e416d60341efd",
-                        "message": "Fixed tool_state.",
-                        "num": 9,
-                        "short_hash": "2c4ad397f",
-                        "unix": "1602877288"
-                    },
-                    {
-                        "hash": "f81d5946b9364c6a7b2a061e804c638db7f6a583",
-                        "message": "Added collection to test.",
-                        "num": 8,
-                        "short_hash": "f81d5946b",
-                        "unix": "1602873698"
-                    },
-                    {
-                        "hash": "70b86ecbfbcb239fe109e9e2e109a8a982f35fec",
-                        "message": "Updated workflow.",
-                        "num": 7,
-                        "short_hash": "70b86ecbf",
-                        "unix": "1602870731"
-                    },
-                    {
-                        "hash": "b8a5ce3d4a7d76e0453c2b25d34fadad21bc06c5",
-                        "message": "Update main_workflow.ga",
-                        "num": 6,
-                        "short_hash": "b8a5ce3d4",
-                        "unix": "1602803075"
-                    },
-                    {
-                        "hash": "71d516d05c099ba378eafd7eb1f7dedc3a288b65",
-                        "message": "Update main_workflow.ga",
-                        "num": 5,
-                        "short_hash": "71d516d05",
-                        "unix": "1602790259"
-                    },
-                    {
-                        "hash": "aa695993e63aa8d5ac99b842f23035d74a17978d",
-                        "message": "Update main_workflow.ga",
-                        "num": 4,
-                        "short_hash": "aa695993e",
-                        "unix": "1602507576"
-                    },
-                    {
-                        "hash": "dadb44fb528517637c96e074c9459bfd1c5a9ebb",
-                        "message": "Update main_workflow.ga",
-                        "num": 3,
-                        "short_hash": "dadb44fb5",
-                        "unix": "1602469286"
-                    },
-                    {
-                        "hash": "a45af5ea946c3fab63e502255a48edc8770b3237",
-                        "message": "Update main_workflow.ga",
+                        "hash": "15a13c3667af0db6a6ca380ca1b998c9faf625d3",
+                        "message": "updated workflow annotation and name",
                         "num": 2,
-                        "short_hash": "a45af5ea9",
-                        "unix": "1602469238"
+                        "short_hash": "15a13c366",
+                        "unix": "1606931443"
                     },
                     {
-                        "hash": "c042f2b7195179d8e45abac8d41122ab94538264",
-                        "message": "planemo workflow-to-tutorial",
+                        "hash": "e8f20c190bc7a0d319835969a36114d939bd4dce",
+                        "message": "generated three tutorials on DIA data analysis in galaxy",
                         "num": 1,
-                        "short_hash": "c042f2b71",
-                        "unix": "1600357793"
+                        "short_hash": "e8f20c190",
+                        "unix": "1606930318"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "metaquantome-data-creation",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "Input dataset collection",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Input exp. design annotation"
+                            }
+                        ],
+                        "label": "Input exp. design annotation",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 134,
-                            "height": 81,
-                            "left": 347.53125,
-                            "right": 547.53125,
-                            "top": 53,
+                            "bottom": 646.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 490.5,
+                            "right": 690.5,
+                            "top": 564,
                             "width": 200,
-                            "x": 347.53125,
-                            "y": 53
+                            "x": 490.5,
+                            "y": 564
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "a00a1b36-1600-4833-8cd3-df6ceec33349",
-                        "workflow_outputs": []
+                        "type": "data_input",
+                        "uuid": "a5d35883-fba0-4de7-a883-8bb6b2be333d",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "c5372600-b105-4692-8d32-60b4e882c235"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
@@ -186427,28 +188480,34 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Experiment_Design"
+                                "name": "iRTassays.tsv"
                             }
                         ],
-                        "label": "Experiment_Design",
+                        "label": "iRTassays.tsv",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 401.96875,
-                            "height": 81,
-                            "left": 525.640625,
-                            "right": 725.640625,
-                            "top": 320.96875,
+                            "bottom": 184.8000030517578,
+                            "height": 61.80000305175781,
+                            "left": -1122.5,
+                            "right": -922.5,
+                            "top": 123,
                             "width": 200,
-                            "x": 525.640625,
-                            "y": 320.96875
+                            "x": -1122.5,
+                            "y": 123
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "8dd6e50f-9951-4e8e-af47-783625e46786",
-                        "workflow_outputs": []
+                        "uuid": "03ffba1e-879b-47ae-995d-ceb262b4ff4e",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "8307748d-8fe6-4cee-8ac8-4d65bb598b0a"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
@@ -186459,48 +188518,244 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "FASTA_db"
+                                "name": "Spectral library"
                             }
                         ],
-                        "label": "FASTA_db",
+                        "label": "Spectral library",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 629.03125,
-                            "height": 61,
-                            "left": -408,
-                            "right": -208,
-                            "top": 568.03125,
+                            "bottom": 426.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": -1117.5,
+                            "right": -917.5,
+                            "top": 344,
                             "width": 200,
-                            "x": -408,
-                            "y": 568.03125
+                            "x": -1117.5,
+                            "y": 344
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "a9156286-a9e9-402f-b1d9-3e55ddd86ce8",
-                        "workflow_outputs": []
+                        "uuid": "a2c7f825-ad7c-4966-ad08-a1634f7b5453",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "1caaf3b7-2710-4835-89da-816d079a9e8a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "\"Input Dataset Collection\""
+                            }
+                        ],
+                        "label": "\"Input Dataset Collection\"",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 469.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": -1330.5,
+                            "right": -1130.5,
+                            "top": 387,
+                            "width": 200,
+                            "x": -1330.5,
+                            "y": 387
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "e5b0dbc4-3478-4d5b-a220-ca720f06c787",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "dee72339-437a-4b71-8aab-85fce61e7369"
+                            }
+                        ]
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nExperiment_Design\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nFASTA_db\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"mzml to mgf\"];\n  0 -->|output| 3;\n  4[\"Search GUI\"];\n  2 -->|output| 4;\n  3 -->|output| 4;\n  5[\"Peptide Shaker\"];\n  4 -->|searchgui_results| 5;\n  6[\"Replace Text\"];\n  5 -->|output_psm| 6;\n  7[\"Remove beginning\"];\n  5 -->|output_peptides| 7;\n  8[\"Unipept_lca\"];\n  5 -->|output_peptides| 8;\n  9[\"FlashLFQ\"];\n  1 -->|output| 9;\n  6 -->|outfile| 9;\n  0 -->|output| 9;\n  10[\"Unipept_peptinfo\"];\n  7 -->|out_file1| 10;\n  11[\"Replace Text\"];\n  8 -->|output_tsv| 11;\n  12[\"Regex Find And Replace\"];\n  9 -->|quantifiedPeptides| 12;\n  13[\"selecting EC column\"];\n  10 -->|output_ec_tsv| 13;\n  14[\"filter 5% All_funct\"];\n  10 -->|output_go_tsv| 14;\n  15[\"GO_EC\"];\n  13 -->|out_file1| 15;\n  16[\"GO_BP\"];\n  14 -->|output| 16;\n  17[\"GO_CC\"];\n  14 -->|output| 17;\n  18[\"GO_MF\"];\n  14 -->|output| 18;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "metaQuantome_datacreation_workflow",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput exp. design annotation\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\niRTassays.tsv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nSpectral library\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Collection\\n\u201dInput Dataset Collection\u201d\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"msconvert\"];\n  3 -->|output| 4;\n  5[\"OpenSwathWorkflow\"];\n  4 -->|output| 5;\n  2 -->|output| 5;\n  1 -->|output| 5;\n  6[\"PyProphet merge\"];\n  5 -->|out_osw| 6;\n  2 -->|output| 6;\n  7[\"PyProphet score\"];\n  6 -->|output| 7;\n  8[\"PyProphet peptide\"];\n  7 -->|output| 8;\n  9[\"PyProphet peptide\"];\n  8 -->|output| 9;\n  10[\"PyProphet protein\"];\n  9 -->|output| 10;\n  11[\"PyProphet protein\"];\n  10 -->|output| 11;\n  12[\"PyProphet export\"];\n  0 -->|output| 12;\n  11 -->|output| 12;\n  13[\"Ecoli protein expression matrix\"];\n  12 -->|protein_signal| 13;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "DIA_Analysis_OSW",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.0",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Input exp. design annotation"
+                            }
+                        ],
+                        "label": "Input exp. design annotation",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 646.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 490.5,
+                            "right": 690.5,
+                            "top": 564,
+                            "width": 200,
+                            "x": 490.5,
+                            "y": 564
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "a5d35883-fba0-4de7-a883-8bb6b2be333d",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "c5372600-b105-4692-8d32-60b4e882c235"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "iRTassays.tsv"
+                            }
+                        ],
+                        "label": "iRTassays.tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 184.8000030517578,
+                            "height": 61.80000305175781,
+                            "left": -1122.5,
+                            "right": -922.5,
+                            "top": 123,
+                            "width": 200,
+                            "x": -1122.5,
+                            "y": 123
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "03ffba1e-879b-47ae-995d-ceb262b4ff4e",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "8307748d-8fe6-4cee-8ac8-4d65bb598b0a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Spectral library"
+                            }
+                        ],
+                        "label": "Spectral library",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 426.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": -1117.5,
+                            "right": -917.5,
+                            "top": 344,
+                            "width": 200,
+                            "x": -1117.5,
+                            "y": 344
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "a2c7f825-ad7c-4966-ad08-a1634f7b5453",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "1caaf3b7-2710-4835-89da-816d079a9e8a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
                         "errors": null,
                         "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "\"Input Dataset Collection\""
+                            }
+                        ],
+                        "label": "\"Input Dataset Collection\"",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 469.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": -1330.5,
+                            "right": -1130.5,
+                            "top": 387,
+                            "width": 200,
+                            "x": -1330.5,
+                            "y": 387
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "e5b0dbc4-3478-4d5b-a220-ca720f06c787",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "dee72339-437a-4b71-8aab-85fce61e7369"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.1",
+                        "errors": null,
+                        "id": 4,
                         "input_connections": {
                             "input": {
-                                "id": 0,
+                                "id": 3,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "mzml to mgf",
+                        "label": null,
                         "name": "msconvert",
                         "outputs": [
                             {
@@ -186509,654 +188764,573 @@
                             }
                         ],
                         "position": {
-                            "bottom": 587.5,
-                            "height": 132,
-                            "left": -35.515625,
-                            "right": 164.484375,
-                            "top": 455.5,
+                            "bottom": 596.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": -1122.5,
+                            "right": -922.5,
+                            "top": 483,
                             "width": 200,
-                            "x": -35.515625,
-                            "y": 455.5
+                            "x": -1122.5,
+                            "y": 483
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "9ec469ff191a",
+                            "changeset_revision": "3cf310697624",
                             "name": "msconvert",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"data_processing\": {\"peak_picking\": {\"pick_peaks\": \"false\", \"__current_case__\": 0}, \"precursor_refinement\": {\"use_mzrefinement\": \"false\", \"__current_case__\": 0}, \"charge_state_calculation\": {\"charge_state_calculation_method\": \"false\", \"__current_case__\": 0}, \"thresholds\": [], \"filter_mz_windows\": {\"do_mzwindow_filter\": \"false\", \"__current_case__\": 0}, \"etd_filtering\": {\"do_etd_filtering\": \"false\", \"__current_case__\": 0}, \"ms2denoise\": {\"denoise\": \"false\", \"__current_case__\": 1}, \"ms2deisotope\": \"false\"}, \"filtering\": {\"activation\": \"false\", \"indices\": [], \"scan_numbers\": [], \"strip_it\": \"false\", \"filter_ms_levels\": {\"do_ms_level_filter\": \"false\", \"__current_case__\": 0}, \"polarity\": \"false\", \"analyzer\": \"false\"}, \"general_options\": {\"combineIonMobilitySpectra\": \"false\", \"scan_summing\": {\"do_scan_summing\": \"false\", \"__current_case__\": 0}, \"simAsSpectra\": \"false\", \"srmAsSpectra\": \"false\", \"acceptZeroLengthSpectra\": \"false\", \"ignoreUnknownInstrumentError\": \"false\", \"multi_run_output\": {\"do_multi_run_output\": \"false\", \"__current_case__\": 0, \"runIndexSet\": \"0\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"license_agreement\": \"true\", \"output_type\": \"mgf\", \"settings\": {\"mz_encoding\": \"64\", \"intensity_encoding\": \"32\", \"binary_compression\": \"zlib\", \"gzip_compression\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.0.19052.0",
+                        "tool_state": "{\"data_processing\": {\"peak_picking\": {\"pick_peaks\": \"true\", \"__current_case__\": 1, \"pick_peaks_ms_levels\": \"1-\", \"pick_peaks_algorithm\": \"vendor\"}, \"precursor_refinement\": {\"use_mzrefinement\": \"false\", \"__current_case__\": 0}, \"charge_state_calculation\": {\"charge_state_calculation_method\": \"false\", \"__current_case__\": 0}, \"thresholds\": [], \"filter_mz_windows\": {\"do_mzwindow_filter\": \"false\", \"__current_case__\": 0}, \"etd_filtering\": {\"do_etd_filtering\": \"false\", \"__current_case__\": 0}, \"ms2denoise\": {\"denoise\": \"false\", \"__current_case__\": 1}, \"ms2deisotope\": \"false\", \"demultiplex\": {\"demultiplex_on\": \"true\", \"__current_case__\": 0, \"massError\": \"10.0\", \"massErrorUnits\": \"PPM\", \"nnlsMaxIter\": \"50\", \"nnlsEps\": \"1e-10\", \"demuxBlockExtra\": \"0.0\", \"variableFill\": \"false\", \"noSumNormalize\": \"true\", \"optimization\": \"overlap_only\", \"interpolateRT\": \"true\", \"noWeighting\": \"true\", \"minWindowSize\": \"0.2\"}}, \"filtering\": {\"activation\": \"false\", \"indices\": [], \"scan_numbers\": [], \"strip_it\": \"false\", \"filter_ms_levels\": {\"do_ms_level_filter\": \"false\", \"__current_case__\": 0}, \"polarity\": \"false\", \"analyzer\": \"false\"}, \"general_options\": {\"combineIonMobilitySpectra\": \"false\", \"scan_summing\": {\"do_scan_summing\": \"false\", \"__current_case__\": 0}, \"simAsSpectra\": \"true\", \"srmAsSpectra\": \"false\", \"acceptZeroLengthSpectra\": \"false\", \"ignoreUnknownInstrumentError\": \"true\", \"multi_run_output\": {\"do_multi_run_output\": \"false\", \"__current_case__\": 0, \"runIndexSet\": \"0\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"license_agreement\": \"true\", \"output_type\": \"mzML\", \"settings\": {\"mz_encoding\": \"64\", \"intensity_encoding\": \"64\", \"binary_compression\": \"zlib\", \"gzip_compression\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.0.19052.1",
                         "type": "tool",
-                        "uuid": "4d7e9227-49af-4722-b4c3-b8976ba3ed80",
+                        "uuid": "e83c6a83-748d-478f-a2cb-0992b2e8b780",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "2dc2ec3e-d5c7-47ac-a7f7-7559cde14f84"
+                                "uuid": "0fd858b9-4bca-44c8-baa3-e0e50e45ac1d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/2.5+galaxy0",
                         "errors": null,
                         "id": 5,
                         "input_connections": {
-                            "searchgui_input": {
+                            "in": {
                                 "id": 4,
-                                "output_name": "searchgui_results"
+                                "output_name": "output"
+                            },
+                            "tr": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "tr_irt": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Peptide Shaker",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "mzidentML",
-                                "type": "mzid"
+                                "description": "runtime parameter for tool OpenSwathWorkflow",
+                                "name": "adv_opts_cond"
                             },
                             {
-                                "name": "output_certificate",
-                                "type": "txt"
+                                "description": "runtime parameter for tool OpenSwathWorkflow",
+                                "name": "swath_windows_file"
                             },
                             {
-                                "name": "output_psm",
-                                "type": "tabular"
-                            },
+                                "description": "runtime parameter for tool OpenSwathWorkflow",
+                                "name": "tr_irt_nonlinear"
+                            }
+                        ],
+                        "label": null,
+                        "name": "OpenSwathWorkflow",
+                        "outputs": [
                             {
-                                "name": "output_peptides",
-                                "type": "tabular"
+                                "name": "out_osw",
+                                "type": "osw"
                             },
                             {
-                                "name": "output_proteins",
-                                "type": "tabular"
+                                "name": "ctd_out",
+                                "type": "xml"
                             }
                         ],
                         "position": {
-                            "bottom": 1001.046875,
-                            "height": 452,
-                            "left": 253.984375,
-                            "right": 453.984375,
-                            "top": 549.046875,
+                            "bottom": 903.7999877929688,
+                            "height": 540.7999877929688,
+                            "left": -839.5,
+                            "right": -639.5,
+                            "top": 363,
                             "width": 200,
-                            "x": 253.984375,
-                            "y": 549.046875
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionmzidentML": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "mzidentML"
-                            },
-                            "HideDatasetActionoutput_certificate": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_certificate"
-                            },
-                            "HideDatasetActionoutput_proteins": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_proteins"
-                            },
-                            "RenameDatasetActionoutput_peptides": {
-                                "action_arguments": {
-                                    "newname": "PS: Peptide Report"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_peptides"
-                            },
-                            "RenameDatasetActionoutput_psm": {
-                                "action_arguments": {
-                                    "newname": "PS: PSM report"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_psm"
-                            }
+                            "x": -839.5,
+                            "y": 363
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/2.5+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "7fdd9119cc4f",
-                            "name": "peptideshaker",
+                            "changeset_revision": "2aebe58de46e",
+                            "name": "openms_openswathworkflow",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"contact_options\": {\"contact_options_selector\": \"no\", \"__current_case__\": 0}, \"exporting_options\": {\"mzidentml_conditional\": {\"mzidentml_creation\": \"true\", \"__current_case__\": 0, \"include_sequences\": \"false\"}, \"zip_conditional\": {\"zip_output_boolean\": \"false\", \"__current_case__\": 0, \"export_cps\": \"false\"}, \"output_reports\": [\"3\", \"6\", \"9\", \"0\"]}, \"filtering_options\": {\"filtering_options_selector\": \"yes\", \"__current_case__\": 1, \"min_peptide_length\": \"6\", \"max_peptide_length\": \"60\", \"max_precursor_error\": \"10.0\", \"max_precursor_error_type\": \"1\", \"exclude_unknown_ptms\": \"true\"}, \"processing_options\": {\"processing_options_selector\": \"yes\", \"__current_case__\": 1, \"protein_fdr\": \"1.0\", \"peptide_fdr\": \"1.0\", \"psm_fdr\": \"1.0\", \"protein_fraction_mw_confidence\": \"95.0\", \"ptm_score\": {\"ptm_score_selector\": \"0\", \"__current_case__\": 0}, \"ptm_sequence_matching_type\": \"1\", \"ptm_alignment\": \"true\"}, \"searchgui_input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16.36.3",
+                        "tool_state": "{\"Calibration\": {\"ms1_im_calibration\": \"false\", \"im_correction_function\": \"linear\", \"debug_im_file\": \"\", \"debug_mz_file\": \"\"}, \"Library\": {\"retentionTimeInterpretation\": \"iRT\", \"override_group_label_check\": \"false\", \"force_invalid_mods\": \"false\"}, \"OPTIONAL_OUTPUTS\": [\"out_osw_FLAG\", \"ctd_out_FLAG\"], \"RTNormalization\": {\"alignmentMethod\": \"linear\", \"outlierMethod\": \"none\", \"useIterativeChauvenet\": \"false\", \"RANSACMaxIterations\": \"1000\", \"RANSACMaxPercentRTThreshold\": \"3\", \"RANSACSamplingSize\": \"10\", \"estimateBestPeptides\": \"true\", \"InitialQualityCutoff\": \"0.5\", \"OverallQualityCutoff\": \"5.5\", \"NrRTBins\": \"10\", \"MinPeptidesPerBin\": \"1\", \"MinBinsFilled\": \"7\", \"lowess\": {\"span\": \"0.666666666666667\"}, \"b_spline\": {\"num_nodes\": \"5\"}}, \"Scoring\": {\"stop_report_after_feature\": \"5\", \"rt_normalization_factor\": \"100.0\", \"quantification_cutoff\": \"0.0\", \"write_convex_hull\": \"false\", \"spectrum_addition_method\": \"simple\", \"add_up_spectra\": \"1\", \"spacing_for_spectra_resampling\": \"0.005\", \"uis_threshold_sn\": \"0\", \"uis_threshold_peak_area\": \"0\", \"scoring_model\": \"default\", \"im_extra_drift\": \"0.0\", \"strict\": \"true\", \"TransitionGroupPicker\": {\"stop_after_feature\": \"-1\", \"min_peak_width\": \"5.0\", \"peak_integration\": \"original\", \"background_subtraction\": \"none\", \"recalculate_peaks\": \"true\", \"use_precursors\": \"false\", \"use_consensus\": \"true\", \"recalculate_peaks_max_z\": \"0.75\", \"minimal_quality\": \"-1.5\", \"resample_boundary\": \"15.0\", \"compute_peak_quality\": \"false\", \"compute_peak_shape_metrics\": \"false\", \"compute_total_mi\": \"false\", \"boundary_selection_method\": \"largest\", \"PeakPickerMRM\": {\"sgolay_frame_length\": \"11\", \"sgolay_polynomial_order\": \"3\", \"gauss_width\": \"30.0\", \"use_gauss\": \"false\", \"peak_width\": \"-1.0\", \"signal_to_noise\": \"0.1\", \"write_sn_log_messages\": \"false\", \"remove_overlapping_peaks\": \"true\", \"method\": \"corrected\"}, \"PeakIntegrator\": {\"integration_type\": \"intensity_sum\", \"baseline_type\": \"base_to_base\", \"fit_EMG\": \"false\"}}, \"DIAScoring\": {\"dia_extraction_window\": \"0.05\", \"dia_extraction_unit\": \"Th\", \"dia_centroided\": \"false\", \"dia_byseries_intensity_min\": \"300.0\", \"dia_byseries_ppm_diff\": \"10.0\", \"dia_nr_isotopes\": \"4\", \"dia_nr_charges\": \"4\", \"peak_before_mono_max_ppm_diff\": \"20.0\"}, \"EMGScoring\": {\"max_iteration\": \"10\"}, \"Scores\": {\"use_shape_score\": \"true\", \"use_coelution_score\": \"true\", \"use_rt_score\": \"true\", \"use_library_score\": \"true\", \"use_intensity_score\": \"true\", \"use_nr_peaks_score\": \"true\", \"use_total_xic_score\": \"true\", \"use_total_mi_score\": \"false\", \"use_sn_score\": \"true\", \"use_mi_score\": \"false\", \"use_dia_scores\": \"true\", \"use_ms1_correlation\": \"false\", \"use_sonar_scores\": \"false\", \"use_ion_mobility_scores\": \"false\", \"use_ms1_fullscan\": \"false\", \"use_ms1_mi\": \"true\", \"use_uis_scores\": \"false\"}}, \"adv_opts_cond\": {\"adv_opts_selector\": \"advanced\", \"__current_case__\": 1, \"rt_norm\": {\"__class__\": \"RuntimeValue\"}, \"sort_swath_maps\": \"false\", \"enable_ms1\": \"true\", \"enable_ipf\": \"true\", \"out_chrom_type\": \"mzML\", \"min_upper_edge_dist\": \"0.0\", \"extra_rt_extraction_window\": \"100.0\", \"mz_extraction_window_unit\": \"ppm\", \"mz_extraction_window_ms1_unit\": \"ppm\", \"use_ms1_ion_mobility\": \"false\", \"matching_window_only\": \"false\", \"irt_mz_extraction_window\": \"10.0\", \"irt_mz_extraction_window_unit\": \"ppm\", \"irt_im_extraction_window\": \"-1.0\", \"min_rsq\": \"0.95\", \"min_coverage\": \"0.6\", \"split_file_input\": \"false\", \"use_elution_model_score\": \"false\", \"readOptions\": \"cacheWorkingInMemory\", \"mz_correction_function\": \"regression_delta_ppm\", \"extraction_function\": \"tophat\", \"batchSize\": \"1000\", \"ms1_isotopes\": \"3\", \"force\": \"false\", \"test\": \"False\"}, \"im_extraction_window_ms1\": \"-1.0\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"ion_mobility_window\": \"-1.0\", \"mz_extraction_window\": \"10.0\", \"mz_extraction_window_ms1\": \"10.0\", \"rt_extraction_window\": \"600.0\", \"sonar\": \"false\", \"swath_windows_file\": {\"__class__\": \"RuntimeValue\"}, \"tr\": {\"__class__\": \"ConnectedValue\"}, \"tr_irt\": {\"__class__\": \"ConnectedValue\"}, \"tr_irt_nonlinear\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
                         "type": "tool",
-                        "uuid": "8fd27751-3809-4345-9c6d-9c39a87e8497",
+                        "uuid": "77259b26-ee12-4fff-a26b-4233bd95bf2c",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_peptides",
-                                "uuid": "a0c21a57-e285-44ce-9799-cfdf6d0a3909"
+                                "output_name": "out_osw",
+                                "uuid": "263858ee-f576-4b39-9f4b-1487bf60212e"
                             },
                             {
                                 "label": null,
-                                "output_name": "output_psm",
-                                "uuid": "c1c7a55c-a8fd-4191-94b9-9da22f9f7dba"
+                                "output_name": "ctd_out",
+                                "uuid": "7a6e422b-1246-4ed9-945e-fa215225e53a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_merge/pyprophet_merge/2.1.4.0",
                         "errors": null,
                         "id": 6,
                         "input_connections": {
-                            "infile": {
+                            "inputs": {
                                 "id": 5,
-                                "output_name": "output_psm"
+                                "output_name": "out_osw"
+                            },
+                            "template": {
+                                "id": 2,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Replace Text",
-                                "name": "infile"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Replace Text",
+                        "name": "PyProphet merge",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "input"
+                                "name": "output",
+                                "type": "osw"
                             }
                         ],
                         "position": {
-                            "bottom": 525.46875,
-                            "height": 112,
-                            "left": 540.53125,
-                            "right": 740.53125,
-                            "top": 413.46875,
+                            "bottom": 307.8000030517578,
+                            "height": 184.8000030517578,
+                            "left": -682.5,
+                            "right": -482.5,
+                            "top": 123,
                             "width": 200,
-                            "x": 540.53125,
-                            "y": 413.46875
+                            "x": -682.5,
+                            "y": 123
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_merge/pyprophet_merge/2.1.4.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "a67b508b1dc5",
+                            "name": "pyprophet_merge",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"infile\": {\"__class__\": \"RuntimeValue\"}, \"replacements\": [{\"__index__\": 0, \"column\": \"10\", \"find_pattern\": \".mzml.mgf\", \"replace_pattern\": \"\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.3",
+                        "tool_state": "{\"__input_ext\": \"osw\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"inputs\": {\"__class__\": \"ConnectedValue\"}, \"same_run\": \"false\", \"template\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.4.0",
                         "type": "tool",
-                        "uuid": "02703525-ccb2-4e08-8492-7369408ebd0f",
+                        "uuid": "cfe13aec-2644-4a6e-8a2b-d3dc6cd0aec8",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "e8950200-a8b8-4496-a374-9b18638fc258"
+                                "output_name": "output",
+                                "uuid": "61dd81a7-9a2d-4e9b-b8cb-a93245e9dbbb"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/flashlfq/flashlfq/1.0.3.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_score/pyprophet_score/2.1.4.2",
                         "errors": null,
-                        "id": 9,
+                        "id": 7,
                         "input_connections": {
-                            "experiment|experimental_design": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "idt": {
+                            "input": {
                                 "id": 6,
-                                "output_name": "outfile"
-                            },
-                            "peak_lists": {
-                                "id": 0,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "FlashLFQ",
+                        "name": "PyProphet score",
                         "outputs": [
                             {
-                                "name": "log",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "toml",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "quantifiedPeaks",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "quantifiedPeptides",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "quantifiedProteins",
-                                "type": "tabular"
+                                "name": "output",
+                                "type": "osw"
                             },
                             {
-                                "name": "foldChange",
-                                "type": "tabular"
+                                "name": "score_report",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "bottom": 762.984375,
-                            "height": 602,
-                            "left": 829.640625,
-                            "right": 1029.640625,
-                            "top": 160.984375,
+                            "bottom": 399.3999938964844,
+                            "height": 276.3999938964844,
+                            "left": -462.5,
+                            "right": -262.5,
+                            "top": 123,
                             "width": 200,
-                            "x": 829.640625,
-                            "y": 160.984375
+                            "x": -462.5,
+                            "y": 123
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/flashlfq/flashlfq/1.0.3.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_score/pyprophet_score/2.1.4.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "878f6725c4f3",
-                            "name": "flashlfq",
+                            "changeset_revision": "77f068ba47dd",
+                            "name": "pyprophet_score",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"chg\": \"false\", \"experiment\": {\"use_design\": \"true\", \"__current_case__\": 1, \"experimental_design\": {\"__class__\": \"ConnectedValue\"}, \"nor\": \"true\", \"bayesian\": {\"calculate\": \"true\", \"__current_case__\": 1, \"ctr\": \"\", \"fcc\": null, \"sha\": \"false\", \"rmc\": \"false\", \"mcm\": \"500\", \"rns\": null}}, \"idt\": {\"__class__\": \"ConnectedValue\"}, \"int\": \"false\", \"iso\": \"5.0\", \"mbr\": \"true\", \"mrt\": \"2.5\", \"nis\": \"2\", \"peak_lists\": {\"__class__\": \"ConnectedValue\"}, \"ppm\": \"10.0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.3.0",
+                        "tool_state": "{\"__input_ext\": \"osw\", \"apply_weights\": null, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"conditional_classifier\": {\"classifier\": \"XGBoost\", \"__current_case__\": 1, \"xgb_autotune\": \"false\"}, \"group_id\": \"group_id\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"ipf_max_peakgroup_pep\": \"0.7\", \"ipf_max_peakgroup_rank\": \"1\", \"ipf_max_transition_isotope_overlap\": \"0.5\", \"ipf_min_transition_sn\": \"0.0\", \"level\": \"ms1ms2\", \"lfdr_adj\": \"1.5\", \"lfdr_eps\": \"1e-08\", \"lfdr_monotone\": \"true\", \"lfdr_transformation\": \"probit\", \"lfdr_truncate\": \"true\", \"parametric\": \"false\", \"pfdr\": \"false\", \"pi0_lambda_end\": \"0.5\", \"pi0_lambda_start\": \"0.1\", \"pi0_lambda_steps\": \"0.05\", \"pi0_method\": \"bootstrap\", \"pi0_smooth_df\": \"3\", \"pi0_smooth_log\": \"false\", \"ss_initial_fdr\": \"0.15\", \"ss_iteration_fdr\": \"0.05\", \"ss_main_score\": \"var_xcorr_shape\", \"ss_num_iter\": \"10\", \"test_mode\": \"false\", \"tric_chromprob\": \"false\", \"xeval_fraction\": \"0.5\", \"xeval_num_iter\": \"10\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.4.2",
                         "type": "tool",
-                        "uuid": "4973090f-a0e3-49a2-8f7d-35e4e4711ba1",
+                        "uuid": "40fc02c5-56f8-4e65-9e52-cd59ed321f5b",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "log",
-                                "uuid": "392d5313-7ebd-4cf4-aa57-07a70bbd1f17"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "quantifiedPeptides",
-                                "uuid": "0898ffbe-32cc-4c19-b9ab-0e3c8df1087d"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "quantifiedProteins",
-                                "uuid": "567e65b3-8a11-4bef-a8d0-c9164ee77f57"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "toml",
-                                "uuid": "a3668df7-3900-4ddf-a61e-9c9cedd6811c"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "foldChange",
-                                "uuid": "bdc79312-a96a-4d6a-9eec-b1f473a9d79b"
+                                "output_name": "score_report",
+                                "uuid": "78b03dbb-9561-4ccb-aa47-5ab90bf063ef"
                             },
                             {
                                 "label": null,
-                                "output_name": "quantifiedPeaks",
-                                "uuid": "bf3be654-975b-4881-883a-f5abce69ccea"
+                                "output_name": "output",
+                                "uuid": "70ab8388-f777-4fd3-8b5b-e34ef9b351f3"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_peptide/pyprophet_peptide/2.1.4.0",
                         "errors": null,
-                        "id": 11,
+                        "id": 8,
                         "input_connections": {
-                            "infile": {
-                                "id": 8,
-                                "output_name": "output_tsv"
+                            "input": {
+                                "id": 7,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Replace Text",
+                        "name": "PyProphet peptide",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "input"
+                                "name": "peptide_plots",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "output",
+                                "type": "osw"
                             }
                         ],
                         "position": {
-                            "bottom": 1211.46875,
-                            "height": 112,
-                            "left": 1204.453125,
-                            "right": 1404.453125,
-                            "top": 1099.46875,
+                            "bottom": 348.6000061035156,
+                            "height": 225.60000610351562,
+                            "left": -242.5,
+                            "right": -42.5,
+                            "top": 123,
                             "width": 200,
-                            "x": 1204.453125,
-                            "y": 1099.46875
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutfile": {
-                                "action_arguments": {
-                                    "newname": "taxa"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "outfile"
-                            }
+                            "x": -242.5,
+                            "y": 123
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_peptide/pyprophet_peptide/2.1.4.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "4504b3bc1eed",
+                            "name": "pyprophet_peptide",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"find_pattern\": \"#peptide\", \"replace_pattern\": \"peptide\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.2",
+                        "tool_state": "{\"__input_ext\": \"osw\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"context\": \"experiment-wide\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"lfdr_adj\": \"1.5\", \"lfdr_eps\": \"1e-08\", \"lfdr_monotone\": \"true\", \"lfdr_transformation\": \"probit\", \"lfdr_truncate\": \"true\", \"parametric\": \"false\", \"pfdr\": \"false\", \"pi0_lambda_end\": \"0.5\", \"pi0_lambda_start\": \"0.1\", \"pi0_lambda_steps\": \"0.05\", \"pi0_method\": \"bootstrap\", \"pi0_smooth_df\": \"3\", \"pi0_smooth_log\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.4.0",
                         "type": "tool",
-                        "uuid": "294c390d-3c9b-43b8-a29e-c0f2f6ea8e8a",
+                        "uuid": "e1f109cb-bc55-4b81-9f74-d9d02553a91b",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "04a9fbe7-a95c-4a53-a7de-b101da2cae96"
+                                "output_name": "output",
+                                "uuid": "a4dc51f3-11f6-457b-aff8-0ea597114b92"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "peptide_plots",
+                                "uuid": "f998ff80-a2ab-4b82-8b76-bb13ed2d207b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_peptide/pyprophet_peptide/2.1.4.0",
                         "errors": null,
-                        "id": 12,
+                        "id": 9,
                         "input_connections": {
                             "input": {
-                                "id": 9,
-                                "output_name": "quantifiedPeptides"
+                                "id": 8,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Regex Find And Replace",
+                        "name": "PyProphet peptide",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 422,
-                            "height": 112,
-                            "left": 1185.609375,
-                            "right": 1385.609375,
-                            "top": 310,
-                            "width": 200,
-                            "x": 1185.609375,
-                            "y": 310
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Intensity_file"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "209b7c5ee9d7",
-                            "name": "regex_find_replace",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \"NH2-\", \"replacement\": \"\"}, {\"__index__\": 1, \"pattern\": \"-COOH\", \"replacement\": \"\"}, {\"__index__\": 2, \"pattern\": \"Sequence\", \"replacement\": \"peptide\"}, {\"__index__\": 3, \"pattern\": \"Intensity_\", \"replacement\": \"\"}], \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "98ced7a1-b64e-40bf-bebf-76d5526424f4",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "de9f47ae-fd6f-4a94-b3ec-2eae5d1d8a1c"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
-                        "errors": null,
-                        "id": 14,
-                        "input_connections": {
-                            "tables_0|table": {
-                                "id": 10,
-                                "output_name": "output_go_tsv"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Query Tabular",
-                                "name": "add_to_database"
-                            }
-                        ],
-                        "label": "filter 5% (All_funct)",
-                        "name": "Query Tabular",
-                        "outputs": [
+                                "name": "peptide_plots",
+                                "type": "pdf"
+                            },
                             {
                                 "name": "output",
-                                "type": "tabular"
+                                "type": "osw"
                             }
                         ],
                         "position": {
-                            "bottom": 1102.03125,
-                            "height": 202,
-                            "left": 1158.046875,
-                            "right": 1358.046875,
-                            "top": 900.03125,
+                            "bottom": 348.6000061035156,
+                            "height": 225.60000610351562,
+                            "left": -22.5,
+                            "right": 177.5,
+                            "top": 123,
                             "width": 200,
-                            "x": 1158.046875,
-                            "y": 900.03125
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "ALL_functions"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
+                            "x": -22.5,
+                            "y": 123
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_peptide/pyprophet_peptide/2.1.4.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "33d61c89fb8d",
-                            "name": "query_tabular",
-                            "owner": "iuc",
+                            "changeset_revision": "4504b3bc1eed",
+                            "name": "pyprophet_peptide",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"\"}, \"save_db\": \"false\", \"sqlquery\": \"SELECT Goterm.*\\nFROM Goterm \\nWHERE ((1.0*Goterm.protein_count)/(1.0*Goterm.total_protein_count)) >= 0.05\\n\\n\\n\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"Goterm\", \"column_names_from_first_line\": \"false\", \"col_names\": \"peptide,total_protein_count,go_term,protein_count,go_name,go_funct\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.0.0",
+                        "tool_state": "{\"__input_ext\": \"osw\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"context\": \"global\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"lfdr_adj\": \"1.5\", \"lfdr_eps\": \"1e-08\", \"lfdr_monotone\": \"true\", \"lfdr_transformation\": \"probit\", \"lfdr_truncate\": \"true\", \"parametric\": \"false\", \"pfdr\": \"false\", \"pi0_lambda_end\": \"0.5\", \"pi0_lambda_start\": \"0.1\", \"pi0_lambda_steps\": \"0.05\", \"pi0_method\": \"bootstrap\", \"pi0_smooth_df\": \"3\", \"pi0_smooth_log\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.4.0",
                         "type": "tool",
-                        "uuid": "de18b739-d785-4c22-b291-713134e68d5d",
+                        "uuid": "68693bad-fc8d-4e7a-94aa-137d8dcb3d98",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "25c14890-63ec-422f-be57-0377cd5fe7ff"
+                                "uuid": "d1fb3ae7-3b84-4be6-8bb1-126a181c9269"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "peptide_plots",
+                                "uuid": "bc401b01-b1a5-420a-a455-8fdd9cbc2b5c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_protein/pyprophet_protein/2.1.4.0",
                         "errors": null,
-                        "id": 15,
+                        "id": 10,
                         "input_connections": {
-                            "tables_0|table": {
-                                "id": 13,
-                                "output_name": "out_file1"
+                            "input": {
+                                "id": 9,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Query Tabular",
-                                "name": "add_to_database"
-                            }
-                        ],
-                        "label": "GO_EC",
-                        "name": "Query Tabular",
+                        "inputs": [],
+                        "label": null,
+                        "name": "PyProphet protein",
                         "outputs": [
                             {
                                 "name": "output",
-                                "type": "tabular"
+                                "type": "osw"
+                            },
+                            {
+                                "name": "protein_plots",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "bottom": 699.5,
-                            "height": 182,
-                            "left": 1423.09375,
-                            "right": 1623.09375,
-                            "top": 517.5,
+                            "bottom": 348.6000061035156,
+                            "height": 225.60000610351562,
+                            "left": 197.5,
+                            "right": 397.5,
+                            "top": 123,
                             "width": 200,
-                            "x": 1423.09375,
-                            "y": 517.5
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "go_ec"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
+                            "x": 197.5,
+                            "y": 123
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_protein/pyprophet_protein/2.1.4.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "33d61c89fb8d",
-                            "name": "query_tabular",
-                            "owner": "iuc",
+                            "changeset_revision": "2320f48209fc",
+                            "name": "pyprophet_protein",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": null}, \"save_db\": \"false\", \"sqlquery\": \"SELECT *\\nFROM ec\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"ec\", \"column_names_from_first_line\": \"false\", \"col_names\": \"peptide,go_ec\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.0.0",
+                        "tool_state": "{\"__input_ext\": \"osw\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"context\": \"experiment-wide\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"lfdr_adj\": \"1.5\", \"lfdr_eps\": \"1e-08\", \"lfdr_monotone\": \"true\", \"lfdr_transformation\": \"probit\", \"lfdr_truncate\": \"true\", \"parametric\": \"false\", \"pfdr\": \"false\", \"pi0_lambda_end\": \"0.5\", \"pi0_lambda_start\": \"0.1\", \"pi0_lambda_steps\": \"0.05\", \"pi0_method\": \"bootstrap\", \"pi0_smooth_df\": \"3\", \"pi0_smooth_log\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.4.0",
                         "type": "tool",
-                        "uuid": "85158e37-3fc6-405f-9ad1-bf9ff70308e2",
+                        "uuid": "e8bc07ea-ba5d-4e3d-b439-894a786d7a63",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "6e69f54b-5573-463c-9c5d-1c34b09fcb20"
+                                "uuid": "c2b6fd5f-add6-477f-892f-e282df6345d0"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "protein_plots",
+                                "uuid": "699f4df0-df42-4acb-bd74-74aad82f3040"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Filter1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_protein/pyprophet_protein/2.1.4.0",
                         "errors": null,
-                        "id": 16,
+                        "id": 11,
                         "input_connections": {
                             "input": {
-                                "id": 14,
+                                "id": 10,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "GO_BP",
-                        "name": "Filter",
+                        "label": null,
+                        "name": "PyProphet protein",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "output",
+                                "type": "osw"
+                            },
+                            {
+                                "name": "protein_plots",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "bottom": 832.96875,
-                            "height": 92,
-                            "left": 1489.109375,
-                            "right": 1689.109375,
-                            "top": 740.96875,
+                            "bottom": 348.6000061035156,
+                            "height": 225.60000610351562,
+                            "left": 417.5,
+                            "right": 617.5,
+                            "top": 123,
                             "width": 200,
-                            "x": 1489.109375,
-                            "y": 740.96875
+                            "x": 417.5,
+                            "y": 123
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "go_bp"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_protein/pyprophet_protein/2.1.4.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2320f48209fc",
+                            "name": "pyprophet_protein",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"cond\": \"c6=='biological process'\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_state": "{\"__input_ext\": \"osw\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"context\": \"global\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"lfdr_adj\": \"1.5\", \"lfdr_eps\": \"1e-08\", \"lfdr_monotone\": \"true\", \"lfdr_transformation\": \"probit\", \"lfdr_truncate\": \"true\", \"parametric\": \"false\", \"pfdr\": \"false\", \"pi0_lambda_end\": \"0.5\", \"pi0_lambda_start\": \"0.1\", \"pi0_lambda_steps\": \"0.05\", \"pi0_method\": \"bootstrap\", \"pi0_smooth_df\": \"3\", \"pi0_smooth_log\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.4.0",
                         "type": "tool",
-                        "uuid": "b48f9e25-9725-404d-a77d-06a5a722dd29",
+                        "uuid": "3d0fc6f5-1027-4074-bcd1-5f73b1493f5b",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "07473a74-e477-4a19-8368-d437ecab74bd"
+                                "output_name": "protein_plots",
+                                "uuid": "168a4e50-79f9-458c-876a-79cb5cad5198"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "ec047143-40ef-4061-8c1a-2fb6e81a6e62"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Filter1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_export/pyprophet_export/2.1.4.1",
                         "errors": null,
-                        "id": 17,
+                        "id": 12,
                         "input_connections": {
+                            "conditional_swath2stats|study_design": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
                             "input": {
-                                "id": 14,
+                                "id": 11,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "GO_CC",
-                        "name": "Filter",
+                        "label": null,
+                        "name": "PyProphet export",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "export_file",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "summary",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "peptide_signal",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "protein_signal",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "msstats_input",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 985.9375,
-                            "height": 92,
-                            "left": 1493.140625,
-                            "right": 1693.140625,
-                            "top": 893.9375,
+                            "bottom": 666.7999877929688,
+                            "height": 530.7999877929688,
+                            "left": 754.5,
+                            "right": 954.5,
+                            "top": 136,
                             "width": 200,
-                            "x": 1493.140625,
-                            "y": 893.9375
+                            "x": 754.5,
+                            "y": 136
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "go_cc"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_export/pyprophet_export/2.1.4.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3cf580bf28e2",
+                            "name": "pyprophet_export",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"cond\": \"c6=='cellular component'\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_state": "{\"__input_ext\": \"osw\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"conditional_output\": {\"format\": \"legacy_merged\", \"__current_case__\": 1, \"transition_quant\": \"true\", \"max_transition_pep\": \"0.7\", \"ipf\": \"peptidoform\", \"ipf_max_peptidoform_pep\": \"0.4\", \"max_rs_peakgroup_qvalue\": \"0.05\", \"max_global_peptide_qvalue\": \"0.01\", \"max_global_protein_qvalue\": \"0.01\"}, \"conditional_swath2stats\": {\"swath2stats\": \"yes_swath2stats\", \"__current_case__\": 0, \"study_design\": {\"__class__\": \"ConnectedValue\"}, \"conditional_fdr_replica\": {\"calc_fdr_replica\": \"calc_fdr_replica_yes\", \"__current_case__\": 0, \"fft\": \"0.5\", \"n_range\": \"10.0\", \"fdr_target\": \"0.05\", \"n_replica\": \"2\"}, \"conditional_max_pep\": {\"filter_max_pep\": \"filter_max_pep_yes\", \"__current_case__\": 0, \"n_peptides_max\": \"10\"}, \"conditional_min_pep\": {\"filter_min_pep\": \"filter_min_pep_yes\", \"__current_case__\": 0, \"n_peptides_min\": \"2\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"peptide_error\": \"true\", \"protein_error\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.4.1",
                         "type": "tool",
-                        "uuid": "2ad4113b-583f-48f1-9fa2-8bc111f84f81",
+                        "uuid": "48d5be06-8816-4da4-a70d-12b5a219f07b",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "68fadf94-d8c4-4e25-8093-48c783fa65e6"
+                                "output_name": "msstats_input",
+                                "uuid": "e287c3d3-cb72-4d70-809b-acb86932a2db"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "summary",
+                                "uuid": "f5be16a2-f5a0-4abb-807c-079bddfaeb5c"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "export_file",
+                                "uuid": "6d808fed-9f94-4a95-a0ad-ce0f41170e69"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "peptide_signal",
+                                "uuid": "d044b25c-c339-4bdf-8c18-422a88f029b0"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "protein_signal",
+                                "uuid": "d45a777c-0af4-4569-a427-8ae99e0314ff"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Filter1",
+                        "content_id": "Grep1",
                         "errors": null,
-                        "id": 18,
+                        "id": 13,
                         "input_connections": {
                             "input": {
-                                "id": 14,
-                                "output_name": "output"
+                                "id": 12,
+                                "output_name": "protein_signal"
                             }
                         },
-                        "inputs": [],
-                        "label": "GO_MF",
-                        "name": "Filter",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Select",
+                                "name": "input"
+                            }
+                        ],
+                        "label": "Ecoli protein expression matrix",
+                        "name": "Select",
                         "outputs": [
                             {
                                 "name": "out_file1",
@@ -187164,74 +189338,61 @@
                             }
                         ],
                         "position": {
-                            "bottom": 1116.0625,
-                            "height": 92,
-                            "left": 1484.109375,
-                            "right": 1684.109375,
-                            "top": 1024.0625,
+                            "bottom": 483.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": 1058.5,
+                            "right": 1258.5,
+                            "top": 370,
                             "width": 200,
-                            "x": 1484.109375,
-                            "y": 1024.0625
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "go_mf"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
+                            "x": 1058.5,
+                            "y": 370
                         },
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"cond\": \"c6=='molecular function'\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "post_job_actions": {},
+                        "tool_id": "Grep1",
+                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"invert\": \"false\", \"pattern\": \"(ECOLI)|(Spike-in)\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.1",
                         "type": "tool",
-                        "uuid": "a5249831-e466-4ae6-8490-cb62ea43611e",
+                        "uuid": "5282f24d-8985-472e-9669-f5484a9a2594",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "out_file1",
-                                "uuid": "400504d4-18ba-4c89-a6db-388e72af8923"
+                                "uuid": "26ace007-a011-453e-b37e-1a2056a6184b"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/metaquantome-data-creation",
-                "path": "topics/proteomics/tutorials/metaquantome-data-creation/workflows/main_workflow.ga",
+                "parent_id": "proteomics/DIA_Analysis_OSW",
+                "path": "topics/proteomics/tutorials/DIA_Analysis_OSW/workflows/Galaxy-Workflow-_DIA_Training_using_HEK_Ecoli_3_EG_data_.ga",
                 "tags": [
                     "proteomics"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "metaQuantome_datacreation_workflow",
+                "tests": false,
+                "title": "DIA_Analysis_OSW",
                 "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-metaquantome-data-creation/versions/main-workflow",
-                "tutorial_id": "metaquantome-data-creation",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaquantome-data-creation/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaquantome-data-creation/workflows/main_workflow.html",
-                "version": 3,
-                "wfid": "proteomics-metaquantome-data-creation",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-DIA_Analysis_OSW/versions/galaxy-workflow--dia-training-using-hek-ecoli-3-eg-data-",
+                "tutorial_id": "DIA_Analysis_OSW",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/DIA_Analysis_OSW/workflows/Galaxy-Workflow-_DIA_Training_using_HEK_Ecoli_3_EG_data_.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/DIA_Analysis_OSW/workflows/Galaxy-Workflow-_DIA_Training_using_HEK_Ecoli_3_EG_data_.html",
+                "version": 1,
+                "wfid": "proteomics-DIA_Analysis_OSW",
+                "wfname": "galaxy-workflow--dia-training-using-hek-ecoli-3-eg-data-",
+                "workflow": "Galaxy-Workflow-_DIA_Training_using_HEK_Ecoli_3_EG_data_.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "Filter1",
-                    "Remove beginning1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/flashlfq/flashlfq/1.0.3.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0"
+                    "Grep1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/2.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_export/pyprophet_export/2.1.4.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_merge/pyprophet_merge/2.1.4.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_peptide/pyprophet_peptide/2.1.4.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_protein/pyprophet_protein/2.1.4.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet_score/pyprophet_score/2.1.4.2"
                 ],
-                "workflowhub_id": "1177"
+                "workflowhub_id": "1180"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.4037137"
+        "zenodo_link": "https://zenodo.org/record/4307762"
     },
     {
         "admin_install": {
@@ -187240,24 +189401,24 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "ncbi_blast_plus",
-                    "owner": "devteam",
-                    "revisions": "2889433c7ae1",
-                    "tool_panel_section_label": "NCBI Blast",
+                    "name": "peptideshaker",
+                    "owner": "galaxyp",
+                    "revisions": "7fdd9119cc4f",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pep_pointer",
+                    "name": "peptideshaker",
                     "owner": "galaxyp",
-                    "revisions": "073a2965e3b2",
+                    "revisions": "7fdd9119cc4f",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "peptide_genomic_coordinate",
+                    "name": "unipept",
                     "owner": "galaxyp",
-                    "revisions": "5f49ffce52cb",
-                    "tool_panel_section_label": "Proteomics",
+                    "revisions": "9aaa46d45472",
+                    "tool_panel_section_label": "Get Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
@@ -187266,24 +189427,19 @@
                     "revisions": "33d61c89fb8d",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sqlite_to_tabular",
+                    "owner": "iuc",
+                    "revisions": "b722161a845a",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: 2889433c7ae1\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pep_pointer\n  owner: galaxyp\n  revisions: 073a2965e3b2\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptide_genomic_coordinate\n  owner: galaxyp\n  revisions: 5f49ffce52cb\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n  owner: iuc\n  revisions: 33d61c89fb8d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 7fdd9119cc4f\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 7fdd9119cc4f\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unipept\n  owner: galaxyp\n  revisions: 9aaa46d45472\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n  owner: iuc\n  revisions: 33d61c89fb8d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sqlite_to_tabular\n  owner: iuc\n  revisions: b722161a845a\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaproteomics/tutorial.json",
         "contributors": [
-            {
-                "email": "subinamehta@gmail.com",
-                "id": "subinamehta",
-                "joined": "2018-06",
-                "linkedin": "subinamehta",
-                "matrix": "subinamehta:matrix.org",
-                "name": "Subina Mehta",
-                "orcid": "0000-0001-9818-0537",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
-                "twitter": "Subina_Mehta",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
-            },
             {
                 "email": "tgriffin@umn.edu",
                 "github": false,
@@ -187303,14 +189459,6 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
             },
-            {
-                "email": "rsajulga@umn.edu",
-                "id": "jraysajulga",
-                "joined": "2018-11",
-                "name": "Ray Sajulga",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jraysajulga/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jraysajulga.json"
-            },
             {
                 "email": "jj@umn.edu",
                 "id": "jj-umn",
@@ -187321,80 +189469,106 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/jj-umn.json"
             },
             {
-                "email": "kumar207@umn.edu",
-                "id": "pravs3683",
-                "joined": "2019-04",
-                "name": "Praveen Kumar",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pravs3683/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pravs3683.json"
+                "elixir_node": "de",
+                "email": "blankclemens@gmail.com",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "blankclemens",
+                "joined": "2017-09",
+                "name": "Clemens Blank",
+                "orcid": "0000-0002-1726-2256",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankclemens/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankclemens.json"
+            },
+            {
+                "email": "subinamehta@gmail.com",
+                "id": "subinamehta",
+                "joined": "2018-06",
+                "linkedin": "subinamehta",
+                "matrix": "subinamehta:matrix.org",
+                "name": "Subina Mehta",
+                "orcid": "0000-0001-9818-0537",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
+                "twitter": "Subina_Mehta",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis",
-        "edam_operation": [],
-        "edam_topic": [],
+        "dir": "topics/proteomics/tutorials/metaproteomics",
+        "edam_ontology": [
+            "topic_0121",
+            "topic_3922",
+            "topic_3050",
+            "topic_0637"
+        ],
+        "edam_operation": [
+            "Prediction and recognition",
+            "Visualisation"
+        ],
+        "edam_topic": [
+            "Proteomics",
+            "Proteogenomics",
+            "Biodiversity",
+            "Taxonomy"
+        ],
         "exact_supported_servers": [
             "UseGalaxy.eu",
+            "UseGalaxy.no",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "proteomics",
-                "tutorials": [
-                    "proteogenomics-dbcreation",
-                    "proteogenomics-dbsearch"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "proteomics/proteogenomics-novel-peptide-analysis",
+        "id": "proteomics/metaproteomics",
         "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.no"
+            "UseGalaxy.be",
+            "UseGalaxy.cz"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Learning how to visualize proteomic data and to perform its genomic allocation"
+            "Use dataset collections",
+            "With SearchGUI and PeptideShaker you can gain access to multiple search engines",
+            "Learning the basics of SQL queries can pay off"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-09",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "How to assign and visualize the genomic localization of these identified novel proteoforms?"
+            "A taxonomy and functional analysis of metaproteomic mass spectrometry data."
         ],
-        "pageviews": 1822,
-        "pub_date": "2018-11-20",
+        "pageviews": 3828,
+        "pub_date": "2017-06-28",
         "questions": [
-            "How to verify the spectra of novel proteoforms?",
-            "How to assign genomic allocation to these novel proteoforms?"
+            "How can I match metaproteomic mass spectrometry data to peptide sequences derived from shotgun metagenomic data?",
+            "How can I perform taxonomy analysis and visualize metaproteomics data?",
+            "How can I perform functional analysis on this metaproteomics data?"
         ],
         "recordings": [
             {
                 "captioners": [
-                    "subinamehta"
+                    "emmaleith"
                 ],
                 "date": "2021-02-15",
                 "galaxy_version": "21.01",
-                "length": "40M",
+                "length": "1H",
                 "speakers": [
-                    "subinamehta"
+                    "pratikdjagtap"
                 ],
-                "youtube_id": "Ku274KwFh1Y"
+                "youtube_id": "3_yaPp-RCFw"
             }
         ],
-        "short_id": "T00233",
+        "short_id": "T00221",
         "short_tools": [
-            "pep_pointer",
-            "peptide_genomic_coordinate",
             "query_tabular",
-            "ncbi_blastp_wrapper"
+            "peptide_shaker",
+            "search_gui",
+            "unipept",
+            "sqlite_to_tabular"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -187406,6 +189580,11 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -187419,28 +189598,29 @@
             ],
             "inexact": [
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 }
             ]
         },
         "symlink": null,
         "tags": [
-            "proteogenomics"
+            "microgalaxy"
         ],
-        "time_estimation": "30m",
-        "title": "Proteogenomics 3: Novel peptide analysis",
+        "time_estimation": "2h",
+        "title": "Metaproteomics tutorial",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/pep_pointer/pep_pointer/0.1.3",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptide_genomic_coordinate/peptide_genomic_coordinate/0.1.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0"
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0"
         ],
         "topic_name": "proteomics",
         "topic_name_human": "Proteomics",
@@ -187450,79 +189630,100 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "proteogenomics-novel-peptide-analysis",
+        "tutorial_name": "metaproteomics",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaproteomics/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaproteomics/tutorial.json"
         },
-        "version": 19,
+        "version": 41,
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 157,
-        "visitors": 1219,
+        "visit_duration": 158,
+        "visitors": 2310,
         "workflows": [
             {
                 "creators": [],
-                "description": "Proteogenomics 3: Novel peptide analysis",
+                "description": "Metaproteomics tutorial",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nEdited_Mus_Musculus.GRCm38.86\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\npeptides for blast\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPSM Report\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmz_sqlite\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ngenomic mapping sqlite db\"]\n  5[label=\"NCBI BLAST+ blastp\"]\n  1 -> 5 [label=\"output\"]\n  k88461c74131241d5bd54e7d7297ccd76[color=lightseagreen,label=\"Output\\nBLASTP_results\"]\n  5 -> k88461c74131241d5bd54e7d7297ccd76\n  6[label=\"PSM_Novel_Peptides\"]\n  5 -> 6 [label=\"output1\"]\n  2 -> 6 [label=\"output\"]\n  k29c9a368a7e64e8b81ca131f63293093[color=lightseagreen,label=\"Output\\nPSM_Novel_Peptides\"]\n  6 -> k29c9a368a7e64e8b81ca131f63293093\n  7[label=\"Novel_Peptides\"]\n  6 -> 7 [label=\"output\"]\n  k569546687aac423a89afaecf2b405b94[color=lightseagreen,label=\"Output\\nNovel_Peptides\"]\n  7 -> k569546687aac423a89afaecf2b405b94\n  8[label=\"Peptide Genomic Coodinate\"]\n  4 -> 8 [label=\"output\"]\n  3 -> 8 [label=\"output\"]\n  7 -> 8 [label=\"output\"]\n  k60fd3e418cb74a49b5852a43117e9cf8[color=lightseagreen,label=\"Output\\nPeptide Genomic Coodinate on input dataset(s)\"]\n  8 -> k60fd3e418cb74a49b5852a43117e9cf8\n  9[label=\"PepPointer\"]\n  8 -> 9 [label=\"peptide_bed\"]\n  0 -> 9 [label=\"output\"]\n  k3c410bedff794774b75c48659d291160[color=lightseagreen,label=\"Output\\nPepPointer on input dataset(s)\"]\n  9 -> k3c410bedff794774b75c48659d291160\n  10[label=\"Final_Summary_Novel_Peptides\"]\n  9 -> 10 [label=\"classified\"]\n  6 -> 10 [label=\"output\"]\n  k50e64c95cd6847cb9e0cb3714b2f2431[color=lightseagreen,label=\"Output\\nFinal_Summary_Novel_Peptides\"]\n  10 -> k50e64c95cd6847cb9e0cb3714b2f2431\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSixgill generated protein FASTA File\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nDataset Collection of Bering Strait MGF Files\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGene Ontology Terms Selected\"]\n  3[label=\"Search GUI\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  k7516674ab5aa45b5b2e838c1889ad2e9[color=lightseagreen,label=\"Output\\nSearch GUI on input dataset(s)\"]\n  3 -> k7516674ab5aa45b5b2e838c1889ad2e9\n  4[label=\"Peptide Shaker\"]\n  3 -> 4 [label=\"searchgui_results\"]\n  kddfe8d62a7b74e30a84d91c92fc60bd0[color=lightseagreen,label=\"Output\\nPeptide Shaker on input dataset(s): mzidentML file\"]\n  4 -> kddfe8d62a7b74e30a84d91c92fc60bd0\n  5[label=\"Query Tabular Select Peptides\"]\n  4 -> 5 [label=\"output_psm\"]\n  6[label=\"Unipept pept2prot\"]\n  5 -> 6 [label=\"output\"]\n  7[label=\"Unipept lca\"]\n  5 -> 7 [label=\"output\"]\n  8[label=\"Go Pop2Prot DB\"]\n  2 -> 8 [label=\"output\"]\n  6 -> 8 [label=\"output_tsv\"]\n  6 -> 8 [label=\"output_tsv\"]\n  4 -> 8 [label=\"output_psm\"]\n  9[label=\"Genera | PSMs | Peptides\"]\n  4 -> 9 [label=\"output_psm\"]\n  7 -> 9 [label=\"output_tsv\"]\n  10[label=\"GO Terms: Biological Processes\"]\n  8 -> 10 [label=\"sqlitedb\"]\n  11[label=\"GO Terms: Molecular Functions\"]\n  8 -> 11 [label=\"sqlitedb\"]\n  12[label=\"GO Terms: Cellular Localization\"]\n  8 -> 12 [label=\"sqlitedb\"]\n}",
                 "history": [
                     {
-                        "hash": "6d0c1e528390a4617e1f467a5f24a4ffd240d039",
-                        "message": "Update galaxy-workflow-mouse_novel_peptide_analysis.ga",
-                        "num": 7,
-                        "short_hash": "6d0c1e528",
-                        "unix": "1611782322"
+                        "hash": "aab73d220b58b8cb43227624f29fa6ea618133e6",
+                        "message": "Update workflow.ga",
+                        "num": 10,
+                        "short_hash": "aab73d220",
+                        "unix": "1612840176"
                     },
                     {
-                        "hash": "3284d3ba74c4cf199a07c5efcad7c911dc5b9658",
-                        "message": "Update galaxy-workflow-mouse_novel_peptide_analysis.ga",
-                        "num": 6,
-                        "short_hash": "3284d3ba7",
-                        "unix": "1611781479"
+                        "hash": "1386c22b289e346728ded8a2c88f940af9ed2247",
+                        "message": "Update workflow.ga",
+                        "num": 9,
+                        "short_hash": "1386c22b2",
+                        "unix": "1612834619"
                     },
                     {
-                        "hash": "a17d756120453ccf9c9ba819da787dc7e378c649",
-                        "message": "Update galaxy-workflow-mouse_novel_peptide_analysis.ga",
-                        "num": 5,
-                        "short_hash": "a17d75612",
-                        "unix": "1611585589"
+                        "hash": "65c8cf73a1d5371e2cb99f59ab1eab2aea941dfc",
+                        "message": "Update workflow.ga",
+                        "num": 8,
+                        "short_hash": "65c8cf73a",
+                        "unix": "1612473524"
+                    },
+                    {
+                        "hash": "277c504ce90837b1883239a00872839f674aea8c",
+                        "message": "Update workflow.ga",
+                        "num": 7,
+                        "short_hash": "277c504ce",
+                        "unix": "1612473274"
                     },
                     {
                         "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
                         "message": "annotation",
-                        "num": 4,
+                        "num": 6,
                         "short_hash": "667ff3de9",
                         "unix": "1579690769"
                     },
                     {
                         "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
                         "message": "Workflow renaming",
-                        "num": 3,
+                        "num": 5,
                         "short_hash": "eb4d724e0",
                         "unix": "1579084895"
                     },
                     {
-                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
-                        "message": "Changed format of workflows",
+                        "hash": "e4a786cd7a8c7abebd27fa8a6d945a197290345b",
+                        "message": "Installing tools from workflows (#1269)",
+                        "num": 4,
+                        "short_hash": "e4a786cd7",
+                        "unix": "1550581735"
+                    },
+                    {
+                        "hash": "30b28d4c0288107f216b1a9339bd043c511bfe80",
+                        "message": "broken workflow",
+                        "num": 3,
+                        "short_hash": "30b28d4c0",
+                        "unix": "1512315861"
+                    },
+                    {
+                        "hash": "2e53c11bf8ac4f010ef72c879a36e96df6ec0202",
+                        "message": "Update workflow",
                         "num": 2,
-                        "short_hash": "361236c41",
-                        "unix": "1554368414"
+                        "short_hash": "2e53c11bf",
+                        "unix": "1502111726"
                     },
                     {
-                        "hash": "715d5f2ee1d9cfa74c5230a0a4bf746df8758e87",
-                        "message": "fix folder names",
+                        "hash": "f6e08e286c8531ae382c7db6128ba2f419dc7d03",
+                        "message": "Metaproteomics tutorial (#393)",
                         "num": 1,
-                        "short_hash": "715d5f2ee",
-                        "unix": "1542746779"
+                        "short_hash": "f6e08e286",
+                        "unix": "1498643437"
                     }
                 ],
                 "inputs": [
@@ -187535,32 +189736,32 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Edited_Mus_Musculus.GRCm38.86"
+                                "name": "Sixgill generated protein FASTA File"
                             }
                         ],
-                        "label": "Edited_Mus_Musculus.GRCm38.86",
+                        "label": "Sixgill generated protein FASTA File",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 404.25001525878906,
-                            "height": 84,
-                            "left": 448.75,
-                            "right": 608.75,
-                            "top": 320.25001525878906,
-                            "width": 160,
-                            "x": 448.75,
-                            "y": 320.25001525878906
+                            "bottom": 109.09375,
+                            "height": 81,
+                            "left": -232.5,
+                            "right": -32.5,
+                            "top": 28.09375,
+                            "width": 200,
+                            "x": -232.5,
+                            "y": 28.09375
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "f4bb779b-d830-4b6e-974d-73a5b5111d2a",
+                        "uuid": "a3a731aa-022c-4d9b-89d3-475fc855e82e",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "77cd0e85-207b-4572-ab26-be78e1b4b3a8"
+                                "uuid": "1ca164ee-d66f-4b6c-b1de-e0841cb0b662"
                             }
                         ]
                     },
@@ -187573,32 +189774,32 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "peptides for blast"
+                                "name": "Dataset Collection of Bering Strait MGF Files"
                             }
                         ],
-                        "label": "peptides for blast",
-                        "name": "Input dataset",
+                        "label": "Dataset Collection of Bering Strait MGF Files",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "bottom": 548.2468795776367,
-                            "height": 67.20001220703125,
-                            "left": 442.96875,
-                            "right": 602.96875,
-                            "top": 481.04686737060547,
-                            "width": 160,
-                            "x": 442.96875,
-                            "y": 481.04686737060547
+                            "bottom": 288.03125,
+                            "height": 101,
+                            "left": -229.546875,
+                            "right": -29.546875,
+                            "top": 187.03125,
+                            "width": 200,
+                            "x": -229.546875,
+                            "y": 187.03125
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "14d01a35-1699-4246-9759-41156c9881d8",
+                        "type": "data_collection_input",
+                        "uuid": "ae22c03f-32ee-47af-9c46-064f32e93ee9",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "1bfa1662-4420-42e0-a189-0f9d16f4afa7"
+                                "uuid": "1864b353-ca39-4da9-82d4-4ba5124df3b0"
                             }
                         ]
                     },
@@ -187611,70 +189812,76 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "PSM Report"
+                                "name": "Gene Ontology Terms (Selected)"
                             }
                         ],
-                        "label": "PSM Report",
+                        "label": "Gene Ontology Terms (Selected)",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 647.4312744140625,
-                            "height": 50.4000244140625,
-                            "left": 440.98438262939453,
-                            "right": 600.9843521118164,
-                            "top": 597.03125,
-                            "width": 159.99996948242188,
-                            "x": 440.98438262939453,
-                            "y": 597.03125
+                            "bottom": 108.5,
+                            "height": 81,
+                            "left": 977.90625,
+                            "right": 1177.90625,
+                            "top": 27.5,
+                            "width": 200,
+                            "x": 977.90625,
+                            "y": 27.5
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "6d7fee9d-ae62-4c9b-80af-94067aee67af",
+                        "uuid": "1dfff1a0-d645-4272-b524-39538fcdc95b",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "3460165b-5fad-4884-8688-2138be1419f5"
+                                "uuid": "f3de0677-7d91-4e64-b644-e384a9b556cb"
                             }
                         ]
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSixgill generated protein FASTA File\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nDataset Collection of Bering Strait MGF Files\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nGene Ontology Terms Selected\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Search GUI\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  7516674a-b5aa-45b5-b2e8-38c1889ad2e9[\"Output\\nSearch GUI on input dataset(s)\"];\n  3 --> 7516674a-b5aa-45b5-b2e8-38c1889ad2e9;\n  style 7516674a-b5aa-45b5-b2e8-38c1889ad2e9 stroke:#2c3143,stroke-width:4px;\n  4[\"Peptide Shaker\"];\n  3 -->|searchgui_results| 4;\n  ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0[\"Output\\nPeptide Shaker on input dataset(s): mzidentML file\"];\n  4 --> ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0;\n  style ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0 stroke:#2c3143,stroke-width:4px;\n  5[\"Query Tabular Select Peptides\"];\n  4 -->|output_psm| 5;\n  6[\"Unipept pept2prot\"];\n  5 -->|output| 6;\n  7[\"Unipept lca\"];\n  5 -->|output| 7;\n  8[\"Go Pop2Prot DB\"];\n  2 -->|output| 8;\n  6 -->|output_tsv| 8;\n  6 -->|output_tsv| 8;\n  4 -->|output_psm| 8;\n  9[\"Genera | PSMs | Peptides\"];\n  4 -->|output_psm| 9;\n  7 -->|output_tsv| 9;\n  10[\"GO Terms: Biological Processes\"];\n  8 -->|sqlitedb| 10;\n  11[\"GO Terms: Molecular Functions\"];\n  8 -->|sqlitedb| 11;\n  12[\"GO Terms: Cellular Localization\"];\n  8 -->|sqlitedb| 12;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Metaproteomics_GTN",
+                "outputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "mz_sqlite"
+                                "name": "Sixgill generated protein FASTA File"
                             }
                         ],
-                        "label": "mz_sqlite",
+                        "label": "Sixgill generated protein FASTA File",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 770.4468688964844,
-                            "height": 50.4000244140625,
-                            "left": 440,
-                            "right": 600,
-                            "top": 720.0468444824219,
-                            "width": 160,
-                            "x": 440,
-                            "y": 720.0468444824219
+                            "bottom": 109.09375,
+                            "height": 81,
+                            "left": -232.5,
+                            "right": -32.5,
+                            "top": 28.09375,
+                            "width": 200,
+                            "x": -232.5,
+                            "y": 28.09375
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "368d1a7a-f4f2-4b37-af4d-0410be56af33",
+                        "uuid": "a3a731aa-022c-4d9b-89d3-475fc855e82e",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "ce93f0ba-2e12-4ba9-92bc-e2c119a558d6"
+                                "uuid": "1ca164ee-d66f-4b6c-b1de-e0841cb0b662"
                             }
                         ]
                     },
@@ -187682,291 +189889,371 @@
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 4,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "genomic mapping sqlite db"
+                                "name": "Dataset Collection of Bering Strait MGF Files"
                             }
                         ],
-                        "label": "genomic mapping sqlite db",
-                        "name": "Input dataset",
+                        "label": "Dataset Collection of Bering Strait MGF Files",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "bottom": 857.2156524658203,
-                            "height": 67.20001220703125,
-                            "left": 440.15625,
-                            "right": 600.15625,
-                            "top": 790.0156402587891,
-                            "width": 160,
-                            "x": 440.15625,
-                            "y": 790.0156402587891
+                            "bottom": 288.03125,
+                            "height": 101,
+                            "left": -229.546875,
+                            "right": -29.546875,
+                            "top": 187.03125,
+                            "width": 200,
+                            "x": -229.546875,
+                            "y": 187.03125
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "35ef98c3-607e-4903-9f89-84ec48aaa385",
+                        "type": "data_collection_input",
+                        "uuid": "ae22c03f-32ee-47af-9c46-064f32e93ee9",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "3aefda19-8fd0-42cd-a3c1-3480eb1364b4"
+                                "uuid": "1864b353-ca39-4da9-82d4-4ba5124df3b0"
                             }
                         ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nEdited_Mus_Musculus.GRCm38.86\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\npeptides for blast\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nPSM Report\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nmz_sqlite\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\ngenomic mapping sqlite db\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"NCBI BLAST+ blastp\"];\n  1 -->|output| 5;\n  88461c74-1312-41d5-bd54-e7d7297ccd76[\"Output\\nBLASTP_results\"];\n  5 --> 88461c74-1312-41d5-bd54-e7d7297ccd76;\n  style 88461c74-1312-41d5-bd54-e7d7297ccd76 stroke:#2c3143,stroke-width:4px;\n  6[\"PSM_Novel_Peptides\"];\n  5 -->|output1| 6;\n  2 -->|output| 6;\n  29c9a368-a7e6-4e8b-81ca-131f63293093[\"Output\\nPSM_Novel_Peptides\"];\n  6 --> 29c9a368-a7e6-4e8b-81ca-131f63293093;\n  style 29c9a368-a7e6-4e8b-81ca-131f63293093 stroke:#2c3143,stroke-width:4px;\n  7[\"Novel_Peptides\"];\n  6 -->|output| 7;\n  56954668-7aac-423a-89af-aecf2b405b94[\"Output\\nNovel_Peptides\"];\n  7 --> 56954668-7aac-423a-89af-aecf2b405b94;\n  style 56954668-7aac-423a-89af-aecf2b405b94 stroke:#2c3143,stroke-width:4px;\n  8[\"Peptide Genomic Coodinate\"];\n  4 -->|output| 8;\n  3 -->|output| 8;\n  7 -->|output| 8;\n  60fd3e41-8cb7-4a49-b585-2a43117e9cf8[\"Output\\nPeptide Genomic Coodinate on input dataset(s)\"];\n  8 --> 60fd3e41-8cb7-4a49-b585-2a43117e9cf8;\n  style 60fd3e41-8cb7-4a49-b585-2a43117e9cf8 stroke:#2c3143,stroke-width:4px;\n  9[\"PepPointer\"];\n  8 -->|peptide_bed| 9;\n  0 -->|output| 9;\n  3c410bed-ff79-4774-b75c-48659d291160[\"Output\\nPepPointer on input dataset(s)\"];\n  9 --> 3c410bed-ff79-4774-b75c-48659d291160;\n  style 3c410bed-ff79-4774-b75c-48659d291160 stroke:#2c3143,stroke-width:4px;\n  10[\"Final_Summary_Novel_Peptides\"];\n  9 -->|classified| 10;\n  6 -->|output| 10;\n  50e64c95-cd68-47cb-9e0c-b3714b2f2431[\"Output\\nFinal_Summary_Novel_Peptides\"];\n  10 --> 50e64c95-cd68-47cb-9e0c-b3714b2f2431;\n  style 50e64c95-cd68-47cb-9e0c-b3714b2f2431 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "GTN Proteogemics3 Novel Peptide Analysis",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Edited_Mus_Musculus.GRCm38.86"
+                                "name": "Gene Ontology Terms (Selected)"
                             }
                         ],
-                        "label": "Edited_Mus_Musculus.GRCm38.86",
+                        "label": "Gene Ontology Terms (Selected)",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 404.25001525878906,
-                            "height": 84,
-                            "left": 448.75,
-                            "right": 608.75,
-                            "top": 320.25001525878906,
-                            "width": 160,
-                            "x": 448.75,
-                            "y": 320.25001525878906
+                            "bottom": 108.5,
+                            "height": 81,
+                            "left": 977.90625,
+                            "right": 1177.90625,
+                            "top": 27.5,
+                            "width": 200,
+                            "x": 977.90625,
+                            "y": 27.5
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "f4bb779b-d830-4b6e-974d-73a5b5111d2a",
+                        "uuid": "1dfff1a0-d645-4272-b524-39538fcdc95b",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "77cd0e85-207b-4572-ab26-be78e1b4b3a8"
+                                "uuid": "f3de0677-7d91-4e64-b644-e384a9b556cb"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 3,
+                        "input_connections": {
+                            "input_database": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "peak_lists": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Search GUI",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "peptides for blast"
+                                "name": "searchgui_results",
+                                "type": "searchgui_archive"
                             }
                         ],
-                        "label": "peptides for blast",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 548.2468795776367,
-                            "height": 67.20001220703125,
-                            "left": 442.96875,
-                            "right": 602.96875,
-                            "top": 481.04686737060547,
-                            "width": 160,
-                            "x": 442.96875,
-                            "y": 481.04686737060547
+                            "bottom": 204,
+                            "height": 162,
+                            "left": -2.546875,
+                            "right": 197.453125,
+                            "top": 42,
+                            "width": 200,
+                            "x": -2.546875,
+                            "y": 42
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "14d01a35-1699-4246-9759-41156c9881d8",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "7fdd9119cc4f",
+                            "name": "peptideshaker",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"advanced_options\": {\"searchgui_advanced\": {\"searchgui_advanced_selector\": \"basic\", \"__current_case__\": 0}, \"xtandem\": {\"xtandem_advanced\": \"no\", \"__current_case__\": 0}, \"omssa\": {\"omssa_advanced\": \"no\", \"__current_case__\": 0}, \"msgf\": {\"msgf_advanced\": \"no\", \"__current_case__\": 0}, \"ms_amanda\": {\"ms_amanda_advanced\": \"no\", \"__current_case__\": 0}, \"tide\": {\"tide_advanced\": \"no\", \"__current_case__\": 0}, \"myrimatch\": {\"myrimatch_advanced\": \"no\", \"__current_case__\": 0}, \"comet\": {\"comet_advanced\": \"no\", \"__current_case__\": 0}, \"directtag\": {\"directtag_advanced\": \"no\", \"__current_case__\": 0}, \"novor\": {\"novor_advanced\": \"no\", \"__current_case__\": 0}}, \"input_database\": {\"__class__\": \"ConnectedValue\"}, \"peak_lists\": {\"__class__\": \"ConnectedValue\"}, \"precursor_options\": {\"precursor_ion_tol_units\": \"1\", \"precursor_ion_tol\": \"10.0\", \"fragment_tol_units\": \"0\", \"fragment_tol\": \"0.5\", \"min_charge\": \"2\", \"max_charge\": \"4\", \"forward_ion\": \"b\", \"reverse_ion\": \"y\", \"min_isotope\": \"0\", \"max_isotope\": \"1\"}, \"protein_database_options\": {\"create_decoy\": \"true\", \"use_gene_mapping\": \"false\", \"update_gene_mapping\": \"false\"}, \"protein_digest_options\": {\"digestion\": {\"cleavage\": \"0\", \"__current_case__\": 0, \"digests\": [{\"__index__\": 0, \"enzyme\": \"Trypsin\", \"missed_cleavages\": \"2\"}]}}, \"protein_modification_options\": {\"fixed_modifications\": null, \"variable_modifications\": null}, \"search_engines_options\": {\"engines\": [\"X!Tandem\", \"MSGF\"]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.3.10.1",
+                        "type": "tool",
+                        "uuid": "7ebb4019-93b4-4bf0-8fab-c4a786040001",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1bfa1662-4420-42e0-a189-0f9d16f4afa7"
+                                "label": "Search GUI on input dataset(s)",
+                                "output_name": "searchgui_results",
+                                "uuid": "7516674a-b5aa-45b5-b2e8-38c1889ad2e9"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 4,
+                        "input_connections": {
+                            "searchgui_input": {
+                                "id": 3,
+                                "output_name": "searchgui_results"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Peptide Shaker",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "PSM Report"
+                                "name": "mzidentML",
+                                "type": "mzid"
+                            },
+                            {
+                                "name": "output_psm",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "output_peptides",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "output_proteins",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "PSM Report",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 647.4312744140625,
-                            "height": 50.4000244140625,
-                            "left": 440.98438262939453,
-                            "right": 600.9843521118164,
-                            "top": 597.03125,
-                            "width": 159.99996948242188,
-                            "x": 440.98438262939453,
-                            "y": 597.03125
+                            "bottom": 683,
+                            "height": 382,
+                            "left": 80.453125,
+                            "right": 280.453125,
+                            "top": 301,
+                            "width": 200,
+                            "x": 80.453125,
+                            "y": 301
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "6d7fee9d-ae62-4c9b-80af-94067aee67af",
+                        "post_job_actions": {
+                            "HideDatasetActionoutput_peptides": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_peptides"
+                            },
+                            "HideDatasetActionoutput_proteins": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_proteins"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "7fdd9119cc4f",
+                            "name": "peptideshaker",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"contact_options\": {\"contact_options_selector\": \"no\", \"__current_case__\": 0}, \"exporting_options\": {\"mzidentml_conditional\": {\"mzidentml_creation\": \"true\", \"__current_case__\": 0, \"include_sequences\": \"false\"}, \"zip_conditional\": {\"zip_output_boolean\": \"false\", \"__current_case__\": 0, \"export_cps\": \"false\"}, \"output_reports\": [\"3\", \"6\", \"9\"]}, \"filtering_options\": {\"filtering_options_selector\": \"no\", \"__current_case__\": 0}, \"processing_options\": {\"processing_options_selector\": \"no\", \"__current_case__\": 0}, \"searchgui_input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.36.3",
+                        "type": "tool",
+                        "uuid": "56edf0bc-6512-4191-8c36-b02bea23df83",
                         "workflow_outputs": [
+                            {
+                                "label": "Peptide Shaker on input dataset(s): mzidentML file",
+                                "output_name": "mzidentML",
+                                "uuid": "ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0"
+                            },
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "3460165b-5fad-4884-8688-2138be1419f5"
+                                "output_name": "output_psm",
+                                "uuid": "5bd10721-63b1-4b4b-a4bb-12f13d576e48"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "errors": null,
-                        "id": 3,
-                        "input_connections": {},
+                        "id": 5,
+                        "input_connections": {
+                            "tables_0|table": {
+                                "id": 4,
+                                "output_name": "output_psm"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "mz_sqlite"
+                                "description": "runtime parameter for tool Query Tabular",
+                                "name": "add_to_database"
+                            }
+                        ],
+                        "label": "Query Tabular Select Peptides",
+                        "name": "Query Tabular",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "mz_sqlite",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 770.4468688964844,
-                            "height": 50.4000244140625,
-                            "left": 440,
-                            "right": 600,
-                            "top": 720.0468444824219,
-                            "width": 160,
-                            "x": 440,
-                            "y": 720.0468444824219
+                            "bottom": 349.109375,
+                            "height": 182,
+                            "left": 415.5,
+                            "right": 615.5,
+                            "top": 167.109375,
+                            "width": 200,
+                            "x": 415.5,
+                            "y": 167.109375
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "368d1a7a-f4f2-4b37-af4d-0410be56af33",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "33d61c89fb8d",
+                            "name": "query_tabular",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"no\", \"__current_case__\": 1}, \"save_db\": \"false\", \"sqlquery\": \"SELECT distinct sequence \\nFROM psm \\nWHERE confidence >= 95 \\nORDER BY sequence\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"regex\", \"__current_case__\": 6, \"regex_pattern\": \"^\\\\d\", \"regex_action\": \"include_match\"}}]}, \"tbl_opts\": {\"table_name\": \"psm\", \"column_names_from_first_line\": \"false\", \"col_names\": \"id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\", \"load_named_columns\": \"true\", \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.0.0",
+                        "type": "tool",
+                        "uuid": "2e566329-0e53-4dac-a62b-d9acbe971e53",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "ce93f0ba-2e12-4ba9-92bc-e2c119a558d6"
+                                "uuid": "4fc155b2-ff21-492f-9a9f-541989357012"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0",
                         "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 6,
+                        "input_connections": {
+                            "peptide_src|input_tsv": {
+                                "id": 5,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Unipept pept2prot",
+                        "name": "Unipept",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "genomic mapping sqlite db"
+                                "name": "output_tsv",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "genomic mapping sqlite db",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 857.2156524658203,
-                            "height": 67.20001220703125,
-                            "left": 440.15625,
-                            "right": 600.15625,
-                            "top": 790.0156402587891,
-                            "width": 160,
-                            "x": 440.15625,
-                            "y": 790.0156402587891
+                            "bottom": 214.46875,
+                            "height": 152,
+                            "left": 686.90625,
+                            "right": 886.90625,
+                            "top": 62.46875,
+                            "width": 200,
+                            "x": 686.90625,
+                            "y": 62.46875
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "35ef98c3-607e-4903-9f89-84ec48aaa385",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "9aaa46d45472",
+                            "name": "unipept",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"peptide_src\": {\"fmt\": \"tabular\", \"__current_case__\": 1, \"input_tsv\": {\"__class__\": \"ConnectedValue\"}, \"column\": \"1\"}, \"selected_outputs\": \"tsv\", \"strict\": \"false\", \"unipept\": {\"api\": \"pept2prot\", \"__current_case__\": 2, \"equate_il\": \"true\", \"extra\": \"true\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.3.0",
+                        "type": "tool",
+                        "uuid": "87abdf8e-c93e-4383-8e0e-79504d6a1c8f",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "3aefda19-8fd0-42cd-a3c1-3480eb1364b4"
+                                "output_name": "output_tsv",
+                                "uuid": "0ee1d427-69d3-4cda-afd4-d86dbd654c5f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0",
                         "errors": null,
-                        "id": 5,
+                        "id": 7,
                         "input_connections": {
-                            "query": {
-                                "id": 1,
+                            "peptide_src|input_tsv": {
+                                "id": 5,
                                 "output_name": "output"
                             }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "NCBI BLAST+ blastp",
-                        "outputs": [
-                            {
-                                "name": "output1",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 569.8031387329102,
-                            "height": 109.60000610351562,
-                            "left": 673.5469055175781,
-                            "right": 833.5469055175781,
-                            "top": 460.20313262939453,
-                            "width": 160,
-                            "x": 673.5469055175781,
-                            "y": 460.20313262939453
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput1": {
-                                "action_arguments": {
-                                    "newname": "BLASTP_results"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output1"
+                        },
+                        "inputs": [],
+                        "label": "Unipept lca",
+                        "name": "Unipept",
+                        "outputs": [
+                            {
+                                "name": "output_json",
+                                "type": "d3_hierarchy"
+                            },
+                            {
+                                "name": "output_tsv",
+                                "type": "tabular"
                             }
+                        ],
+                        "position": {
+                            "bottom": 687.484375,
+                            "height": 202,
+                            "left": 670.96875,
+                            "right": 870.96875,
+                            "top": 485.484375,
+                            "width": 200,
+                            "x": 670.96875,
+                            "y": 485.484375
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "2889433c7ae1",
-                            "name": "ncbi_blast_plus",
-                            "owner": "devteam",
+                            "changeset_revision": "9aaa46d45472",
+                            "name": "unipept",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"advanced\", \"__current_case__\": 1, \"filter_query\": \"false\", \"matrix_gapcosts\": {\"matrix\": \"PAM30\", \"__current_case__\": 8, \"gap_costs\": \"-gapopen 9 -gapextend 1\"}, \"max_hits\": \"1\", \"max_hsps\": \"1\", \"word_size\": \"2\", \"window_size\": \"40\", \"threshold\": \"11\", \"comp_based_stats\": \"0\", \"parse_deflines\": \"false\", \"adv_optional_id_files_opts\": {\"adv_optional_id_files_opts_selector\": \"none\", \"__current_case__\": 0}, \"qcov_hsp_perc\": \"0.0\", \"use_sw_tback\": \"false\"}, \"blast_type\": \"blastp-short\", \"db_opts\": {\"db_opts_selector\": \"db\", \"__current_case__\": 0, \"database\": [\"nr_2018-01-22\"], \"histdb\": \"\", \"subject\": \"\"}, \"evalue_cutoff\": \"200000.0\", \"output\": {\"out_format\": \"ext\", \"__current_case__\": 1}, \"query\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3.3",
+                        "tool_state": "{\"peptide_src\": {\"fmt\": \"tabular\", \"__current_case__\": 1, \"input_tsv\": {\"__class__\": \"ConnectedValue\"}, \"column\": \"1\"}, \"selected_outputs\": [\"tsv\", \"json\"], \"strict\": \"false\", \"unipept\": {\"api\": \"pept2lca\", \"__current_case__\": 0, \"equate_il\": \"true\", \"extra\": \"false\", \"names\": \"true\", \"allfields\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.3.0",
                         "type": "tool",
-                        "uuid": "8304a4ed-e1e4-45f3-a868-1d8eb6127968",
+                        "uuid": "ea4ed3b9-6907-4feb-a656-b16f4a657a3e",
                         "workflow_outputs": [
                             {
-                                "label": "BLASTP_results",
-                                "output_name": "output1",
-                                "uuid": "88461c74-1312-41d5-bd54-e7d7297ccd76"
+                                "label": null,
+                                "output_name": "output_json",
+                                "uuid": "4d83f563-1cd9-4db0-8f22-8e32b499f040"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_tsv",
+                                "uuid": "0d262aad-5472-41b4-8926-a5335dac8610"
                             }
                         ]
                     },
@@ -187974,15 +190261,23 @@
                         "annotation": "",
                         "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "errors": null,
-                        "id": 6,
+                        "id": 8,
                         "input_connections": {
                             "tables_0|table": {
-                                "id": 5,
-                                "output_name": "output1"
-                            },
-                            "tables_1|table": {
                                 "id": 2,
                                 "output_name": "output"
+                            },
+                            "tables_1|table": {
+                                "id": 6,
+                                "output_name": "output_tsv"
+                            },
+                            "tables_2|table": {
+                                "id": 6,
+                                "output_name": "output_tsv"
+                            },
+                            "tables_3|table": {
+                                "id": 4,
+                                "output_name": "output_psm"
                             }
                         },
                         "inputs": [
@@ -187991,28 +190286,32 @@
                                 "name": "add_to_database"
                             }
                         ],
-                        "label": "PSM_Novel_Peptides",
+                        "label": "Go Pop2Prot DB",
                         "name": "Query Tabular",
                         "outputs": [
+                            {
+                                "name": "sqlitedb",
+                                "type": "sqlite"
+                            },
                             {
                                 "name": "output",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 673.8656387329102,
-                            "height": 209.60000610351562,
-                            "left": 897.0468902587891,
-                            "right": 1057.046890258789,
-                            "top": 464.26563262939453,
-                            "width": 160,
-                            "x": 897.0468902587891,
-                            "y": 464.26563262939453
+                            "bottom": 580.109375,
+                            "height": 382,
+                            "left": 902.5,
+                            "right": 1102.5,
+                            "top": 198.109375,
+                            "width": 200,
+                            "x": 902.5,
+                            "y": 198.109375
                         },
                         "post_job_actions": {
                             "RenameDatasetActionoutput": {
                                 "action_arguments": {
-                                    "newname": "PSM_Novel_Peptides"
+                                    "newname": "Peptides and PSMs"
                                 },
                                 "action_type": "RenameDatasetAction",
                                 "output_name": "output"
@@ -188025,15 +190324,20 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"save_db\": \"false\", \"sqlquery\": \"SELECT distinct psm.*\\nFROM psm join blast ON psm.Sequence = blast.qseqid\\nWHERE blast.pident < 100 OR blast.gapopen >= 1 OR blast.length < blast.qlen\\nORDER BY psm.Sequence, psm.ID\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"blast\", \"column_names_from_first_line\": \"false\", \"col_names\": \"qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles\", \"load_named_columns\": \"true\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"qseqid\"}]}}, {\"__index__\": 1, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"skip\", \"__current_case__\": 0, \"skip_lines\": \"1\"}}]}, \"tbl_opts\": {\"table_name\": \"psm\", \"column_names_from_first_line\": \"false\", \"col_names\": \"ID,Proteins,Sequence,AAs_Before,AAs_After,Position,Modified_Sequence,Variable_Modifications,Fixed_Modifications,Spectrum_File,Spectrum_Title,Spectrum_Scan_Number,RT,mz,Measured_Charge,Identification_Charge,Theoretical_Mass,Isotope_Number,Precursor_mz_Error_ppm,Localization_Confidence,Probabilistic_PTM_score,Dscore,Confidence,Validation\", \"load_named_columns\": \"true\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"Sequence\"}]}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"save_db\": \"true\", \"sqlquery\": \"SELECT sequence as \\\"peptide\\\", count(id) as \\\"PSMs\\\"\\nFROM bering_psms\\nWHERE confidence >= 95\\nGROUP BY sequence\\nORDER BY sequence\\n\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"skip\", \"__current_case__\": 0, \"skip_lines\": \"1\"}}]}, \"tbl_opts\": {\"table_name\": \"go\", \"column_names_from_first_line\": \"false\", \"col_names\": \"aspect,go_id,description\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"aspect,go_id\"}]}}, {\"__index__\": 1, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"skip\", \"__current_case__\": 0, \"skip_lines\": \"1\"}}, {\"__index__\": 1, \"filter\": {\"filter_type\": \"prepend_line_num\", \"__current_case__\": 2}}]}, \"tbl_opts\": {\"table_name\": \"bering_prot\", \"column_names_from_first_line\": \"false\", \"col_names\": \"id,peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_references,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"id,peptide\"}]}}, {\"__index__\": 2, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"skip\", \"__current_case__\": 0, \"skip_lines\": \"1\"}}, {\"__index__\": 1, \"filter\": {\"filter_type\": \"prepend_line_num\", \"__current_case__\": 2}}, {\"__index__\": 2, \"filter\": {\"filter_type\": \"select_columns\", \"__current_case__\": 7, \"columns\": \"1,7\"}}, {\"__index__\": 3, \"filter\": {\"filter_type\": \"normalize\", \"__current_case__\": 9, \"columns\": \"2\", \"separator\": \" \"}}]}, \"tbl_opts\": {\"table_name\": \"bering_prot_go\", \"column_names_from_first_line\": \"false\", \"col_names\": \"id,go_reference\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"go_reference,id\"}]}}, {\"__index__\": 3, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"regex\", \"__current_case__\": 6, \"regex_pattern\": \"^\\\\d\", \"regex_action\": \"include_match\"}}, {\"__index__\": 1, \"filter\": {\"filter_type\": \"select_columns\", \"__current_case__\": 7, \"columns\": \"1,3,23,24\"}}]}, \"tbl_opts\": {\"table_name\": \"bering_psms\", \"column_names_from_first_line\": \"false\", \"col_names\": \"id,sequence,confidence,validation\", \"load_named_columns\": \"true\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"sequence,id\"}]}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "3.0.0",
                         "type": "tool",
-                        "uuid": "0da3b9ec-f964-4386-b150-a2e81adfd05d",
+                        "uuid": "9c62adb5-c8ad-4692-98d2-f3e6964ee408",
                         "workflow_outputs": [
                             {
-                                "label": "PSM_Novel_Peptides",
+                                "label": null,
                                 "output_name": "output",
-                                "uuid": "29c9a368-a7e6-4e8b-81ca-131f63293093"
+                                "uuid": "5aa6b89c-9d27-453e-b898-fde8f34196e2"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "sqlitedb",
+                                "uuid": "1c5e9fbb-cf66-4369-a0ac-be3637359966"
                             }
                         ]
                     },
@@ -188041,11 +190345,15 @@
                         "annotation": "",
                         "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "errors": null,
-                        "id": 7,
+                        "id": 9,
                         "input_connections": {
                             "tables_0|table": {
-                                "id": 6,
-                                "output_name": "output"
+                                "id": 4,
+                                "output_name": "output_psm"
+                            },
+                            "tables_1|table": {
+                                "id": 7,
+                                "output_name": "output_tsv"
                             }
                         },
                         "inputs": [
@@ -188054,28 +190362,32 @@
                                 "name": "add_to_database"
                             }
                         ],
-                        "label": "Novel_Peptides",
+                        "label": "Genera | PSMs | Peptides",
                         "name": "Query Tabular",
                         "outputs": [
+                            {
+                                "name": "sqlitedb",
+                                "type": "sqlite"
+                            },
                             {
                                 "name": "output",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 644.25,
-                            "height": 168,
-                            "left": 1143.046875,
-                            "right": 1303.046875,
-                            "top": 476.25,
-                            "width": 160,
-                            "x": 1143.046875,
-                            "y": 476.25
+                            "bottom": 911.109375,
+                            "height": 282,
+                            "left": 955.5,
+                            "right": 1155.5,
+                            "top": 629.109375,
+                            "width": 200,
+                            "x": 955.5,
+                            "y": 629.109375
                         },
                         "post_job_actions": {
                             "RenameDatasetActionoutput": {
                                 "action_arguments": {
-                                    "newname": "Novel_Peptides"
+                                    "newname": "Genera | PSMs | Peptides"
                                 },
                                 "action_type": "RenameDatasetAction",
                                 "output_name": "output"
@@ -188088,225 +190400,226 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"no\", \"__current_case__\": 1}, \"save_db\": \"false\", \"sqlquery\": \"SELECT distinct Sequence FROM psm\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"skip\", \"__current_case__\": 0, \"skip_lines\": \"1\"}}]}, \"tbl_opts\": {\"table_name\": \"psm\", \"column_names_from_first_line\": \"false\", \"col_names\": \"ID,Proteins,Sequence\", \"load_named_columns\": \"true\", \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"save_db\": \"true\", \"sqlquery\": \"SELECT lca.genus,count(psm.sequence) as \\\"PSMs\\\",count(distinct psm.sequence) as \\\"DISTINCT PEPTIDES\\\" \\nFROM psm LEFT JOIN lca ON psm.sequence = lca.peptide \\nWHERE confidence >= 95 \\nGROUP BY lca.genus \\nORDER BY PSMs desc, 'DISTINCT PEPTIDES' desc\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"regex\", \"__current_case__\": 6, \"regex_pattern\": \"^\\\\d\", \"regex_action\": \"include_match\"}}]}, \"tbl_opts\": {\"table_name\": \"psm\", \"column_names_from_first_line\": \"false\", \"col_names\": \",,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\", \"load_named_columns\": \"true\", \"pkey_autoincr\": \"\", \"indexes\": []}}, {\"__index__\": 1, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"regex\", \"__current_case__\": 6, \"regex_pattern\": \"#peptide\", \"regex_action\": \"exclude_match\"}}]}, \"tbl_opts\": {\"table_name\": \"lca\", \"column_names_from_first_line\": \"false\", \"col_names\": \"peptide,,,,,,,,,,,,,,,,,,,,,genus\", \"load_named_columns\": \"true\", \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "3.0.0",
                         "type": "tool",
-                        "uuid": "5ad1e99c-bf3c-4e87-9fb6-1b5e305ee3fc",
+                        "uuid": "70beb05c-8f4f-49d8-8d51-101a116e3084",
                         "workflow_outputs": [
                             {
-                                "label": "Novel_Peptides",
+                                "label": null,
+                                "output_name": "sqlitedb",
+                                "uuid": "2679b146-1262-4a79-87e3-6eef09d2ac9b"
+                            },
+                            {
+                                "label": null,
                                 "output_name": "output",
-                                "uuid": "56954668-7aac-423a-89af-aecf2b405b94"
+                                "uuid": "f9a3fa9f-6984-4e69-8d40-e60702ea2e66"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptide_genomic_coordinate/peptide_genomic_coordinate/0.1.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
                         "errors": null,
-                        "id": 8,
+                        "id": 10,
                         "input_connections": {
-                            "mapping": {
-                                "id": 4,
-                                "output_name": "output"
-                            },
-                            "mzsqlite": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "peptideinput": {
-                                "id": 7,
-                                "output_name": "output"
+                            "sqlitedb": {
+                                "id": 8,
+                                "output_name": "sqlitedb"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Peptide Genomic Coodinate",
+                        "label": "GO Terms: Biological Processes",
+                        "name": "SQLite to tabular",
                         "outputs": [
                             {
-                                "name": "peptide_bed",
-                                "type": "bed"
+                                "name": "query_results",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 825.3500137329102,
-                            "height": 209.60000610351562,
-                            "left": 1368.9999389648438,
-                            "right": 1528.9999389648438,
-                            "top": 615.7500076293945,
-                            "width": 160,
-                            "x": 1368.9999389648438,
-                            "y": 615.7500076293945
+                            "bottom": 247.609375,
+                            "height": 112,
+                            "left": 1298,
+                            "right": 1498,
+                            "top": 135.609375,
+                            "width": 200,
+                            "x": 1298,
+                            "y": 135.609375
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptide_genomic_coordinate/peptide_genomic_coordinate/0.1.1",
+                        "post_job_actions": {
+                            "RenameDatasetActionquery_results": {
+                                "action_arguments": {
+                                    "newname": "GO Terms: Biological Processes"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "query_results"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "5f49ffce52cb",
-                            "name": "peptide_genomic_coordinate",
-                            "owner": "galaxyp",
+                            "changeset_revision": "b722161a845a",
+                            "name": "sqlite_to_tabular",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"mapping\": {\"__class__\": \"ConnectedValue\"}, \"mzsqlite\": {\"__class__\": \"ConnectedValue\"}, \"peptideinput\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.1",
+                        "tool_state": "{\"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"sqlitedb\": {\"__class__\": \"ConnectedValue\"}, \"sqlquery\": \"SELECT go.description, \\ncount(distinct bering_psms.sequence) as \\\"bering_peptides\\\", count(distinct bering_psms.id) as \\\"bering_psms\\\" \\nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\\nWHERE go.aspect = 'biological_process'\\nGROUP BY go.description\\nORDER BY  bering_peptides desc,bering_psms desc\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.0",
                         "type": "tool",
-                        "uuid": "8eae5eda-e1aa-4d74-8cb9-78172a809ddb",
+                        "uuid": "d189e68e-b1de-4f30-89a7-319810b7d536",
                         "workflow_outputs": [
                             {
-                                "label": "Peptide Genomic Coodinate on input dataset(s)",
-                                "output_name": "peptide_bed",
-                                "uuid": "60fd3e41-8cb7-4a49-b585-2a43117e9cf8"
+                                "label": null,
+                                "output_name": "query_results",
+                                "uuid": "baad84e0-4201-4275-923d-dd5a0956ecef"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pep_pointer/pep_pointer/0.1.3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
                         "errors": null,
-                        "id": 9,
+                        "id": 11,
                         "input_connections": {
-                            "bed": {
+                            "sqlitedb": {
                                 "id": 8,
-                                "output_name": "peptide_bed"
-                            },
-                            "gtf_input|gtf": {
-                                "id": 0,
-                                "output_name": "output"
+                                "output_name": "sqlitedb"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "PepPointer",
+                        "label": "GO Terms: Molecular Functions",
+                        "name": "SQLite to tabular",
                         "outputs": [
                             {
-                                "name": "classified",
+                                "name": "query_results",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 560.4656143188477,
-                            "height": 151.19998168945312,
-                            "left": 1601.5780639648438,
-                            "right": 1761.5780639648438,
-                            "top": 409.26563262939453,
-                            "width": 160,
-                            "x": 1601.5780639648438,
-                            "y": 409.26563262939453
+                            "bottom": 386.609375,
+                            "height": 112,
+                            "left": 1310,
+                            "right": 1510,
+                            "top": 274.609375,
+                            "width": 200,
+                            "x": 1310,
+                            "y": 274.609375
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pep_pointer/pep_pointer/0.1.3",
+                        "post_job_actions": {
+                            "RenameDatasetActionquery_results": {
+                                "action_arguments": {
+                                    "newname": "GO Terms: Molecular Functions"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "query_results"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "073a2965e3b2",
-                            "name": "pep_pointer",
-                            "owner": "galaxyp",
+                            "changeset_revision": "b722161a845a",
+                            "name": "sqlite_to_tabular",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"bed\": {\"__class__\": \"ConnectedValue\"}, \"gtf_input\": {\"gtf_source\": \"history\", \"__current_case__\": 1, \"gtf\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.3",
+                        "tool_state": "{\"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"sqlitedb\": {\"__class__\": \"ConnectedValue\"}, \"sqlquery\": \"SELECT go.description, \\ncount(distinct bering_psms.sequence) as \\\"bering_peptides\\\", count(distinct bering_psms.id) as \\\"bering_psms\\\" \\nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\\nWHERE go.aspect = 'molecular_function'\\nGROUP BY go.description\\nORDER BY  bering_peptides desc,bering_psms desc\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.0",
                         "type": "tool",
-                        "uuid": "54174fe8-f646-43b5-9491-0e117aaf75bd",
+                        "uuid": "d2a2e7cb-26be-4db9-b275-e805116f1832",
                         "workflow_outputs": [
                             {
-                                "label": "PepPointer on input dataset(s)",
-                                "output_name": "classified",
-                                "uuid": "3c410bed-ff79-4774-b75c-48659d291160"
+                                "label": null,
+                                "output_name": "query_results",
+                                "uuid": "62313ee8-9c3b-4f3e-92ae-cc095a3313a7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
                         "errors": null,
-                        "id": 10,
+                        "id": 12,
                         "input_connections": {
-                            "tables_0|table": {
-                                "id": 9,
-                                "output_name": "classified"
-                            },
-                            "tables_1|table": {
-                                "id": 6,
-                                "output_name": "output"
+                            "sqlitedb": {
+                                "id": 8,
+                                "output_name": "sqlitedb"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Query Tabular",
-                                "name": "add_to_database"
-                            }
-                        ],
-                        "label": "Final_Summary_Novel_Peptides",
-                        "name": "Query Tabular",
+                        "inputs": [],
+                        "label": "GO Terms: Cellular Localization",
+                        "name": "SQLite to tabular",
                         "outputs": [
                             {
-                                "name": "output",
+                                "name": "query_results",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 585.9500274658203,
-                            "height": 243.20001220703125,
-                            "left": 1888.0000305175781,
-                            "right": 2048.000030517578,
-                            "top": 342.75001525878906,
-                            "width": 160,
-                            "x": 1888.0000305175781,
-                            "y": 342.75001525878906
+                            "bottom": 546.609375,
+                            "height": 112,
+                            "left": 1311,
+                            "right": 1511,
+                            "top": 434.609375,
+                            "width": 200,
+                            "x": 1311,
+                            "y": 434.609375
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput": {
+                            "RenameDatasetActionquery_results": {
                                 "action_arguments": {
-                                    "newname": "Final_Summary_Novel_Peptides"
+                                    "newname": "GO Terms: Cellular Localization"
                                 },
                                 "action_type": "RenameDatasetAction",
-                                "output_name": "output"
+                                "output_name": "query_results"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "33d61c89fb8d",
-                            "name": "query_tabular",
+                            "changeset_revision": "b722161a845a",
+                            "name": "sqlite_to_tabular",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"save_db\": \"false\", \"sqlquery\": \"SELECT psm.Sequence as PeptideSequence, count(psm.Sequence) as SpectralCount, psm.Proteins as Proteins, bed_pep_pointer.chrom as Chromosome, bed_pep_pointer.start as Start, bed_pep_pointer.end as End, bed_pep_pointer.strand as Strand, bed_pep_pointer.annot as Annotation, bed_pep_pointer.chrom||':'||bed_pep_pointer.start||'-'||bed_pep_pointer.end as GenomeCoordinate,'https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='||bed_pep_pointer.chrom||'%3A'||bed_pep_pointer.start||'-'||bed_pep_pointer.end as UCSC_Genome_Browser \\nFROM psm \\nINNER JOIN bed_pep_pointer on bed_pep_pointer.peptide = psm.Sequence \\nGROUP BY psm.Sequence\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"bed_pep_pointer\", \"column_names_from_first_line\": \"false\", \"col_names\": \"chrom,start,end,peptide,score,strand,annot\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": []}}, {\"__index__\": 1, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"skip\", \"__current_case__\": 0, \"skip_lines\": \"1\"}}]}, \"tbl_opts\": {\"table_name\": \"psm\", \"column_names_from_first_line\": \"false\", \"col_names\": \"ID,Proteins,Sequence,AAs_Before,AAs_After,Position,Modified_Sequence,Variable_Modifications,Fixed_Modifications,Spectrum_File,Spectrum_Title,Spectrum_Scan_Number,RT,mz,Measured_Charge,Identification_Charge,Theoretical_Mass,Isotope_Number,Precursor_mz_Error_ppm,Localization_Confidence,Probabilistic_PTM_score,Dscore,Confidence,Validation\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.0.0",
+                        "tool_state": "{\"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"sqlitedb\": {\"__class__\": \"ConnectedValue\"}, \"sqlquery\": \"SELECT go.description, \\ncount(distinct bering_psms.sequence) as \\\"bering_peptides\\\", count(distinct bering_psms.id) as \\\"bering_psms\\\" \\nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\\nWHERE go.aspect = 'cellular_component'\\nGROUP BY go.description\\nORDER BY  bering_peptides desc,bering_psms desc\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.0",
                         "type": "tool",
-                        "uuid": "d962e688-4af1-49fc-907c-6e2f5d6c6d0f",
+                        "uuid": "0068d768-bedb-4222-8fa7-741dcc41ce84",
                         "workflow_outputs": [
                             {
-                                "label": "Final_Summary_Novel_Peptides",
-                                "output_name": "output",
-                                "uuid": "50e64c95-cd68-47cb-9e0c-b3714b2f2431"
+                                "label": null,
+                                "output_name": "query_results",
+                                "uuid": "191c2b4f-e525-451a-be37-4c24f0490d83"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/proteogenomics-novel-peptide-analysis",
-                "path": "topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/workflows/galaxy-workflow-mouse_novel_peptide_analysis.ga",
+                "parent_id": "proteomics/metaproteomics",
+                "path": "topics/proteomics/tutorials/metaproteomics/workflows/workflow.ga",
                 "tags": [
                     "proteomics"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "GTN Proteogemics3 Novel Peptide Analysis",
+                "title": "Metaproteomics_GTN",
                 "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-proteogenomics-novel-peptide-analysis/versions/galaxy-workflow-mouse-novel-peptide-analysis",
-                "tutorial_id": "proteogenomics-novel-peptide-analysis",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/workflows/galaxy-workflow-mouse_novel_peptide_analysis.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/workflows/galaxy-workflow-mouse_novel_peptide_analysis.html",
-                "version": 6,
-                "wfid": "proteomics-proteogenomics-novel-peptide-analysis",
-                "wfname": "galaxy-workflow-mouse-novel-peptide-analysis",
-                "workflow": "galaxy-workflow-mouse_novel_peptide_analysis.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-metaproteomics/versions/workflow",
+                "tutorial_id": "metaproteomics",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaproteomics/workflows/workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaproteomics/workflows/workflow.html",
+                "version": 7,
+                "wfid": "proteomics-metaproteomics",
+                "wfname": "workflow",
+                "workflow": "workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/pep_pointer/pep_pointer/0.1.3",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptide_genomic_coordinate/peptide_genomic_coordinate/0.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0"
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0"
                 ],
-                "workflowhub_id": "1236"
+                "workflowhub_id": "1159"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.1489208"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.839701"
     },
     {
         "admin_install": {
@@ -188315,298 +190628,126 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_to_tabular",
-                    "owner": "devteam",
-                    "revisions": "7e801ab2b70e",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "dbbuilder",
-                    "owner": "galaxyp",
-                    "revisions": "983bf725dfc2",
-                    "tool_panel_section_label": "Get Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_merge_files_and_filter_unique_sequences",
-                    "owner": "galaxyp",
-                    "revisions": "f546e7278f04",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "maxquant",
-                    "owner": "galaxyp",
-                    "revisions": "9c52362ae7bb",
+                    "name": "pdaug_addclasslabel",
+                    "owner": "jay",
+                    "revisions": "7160bfd77aef",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "msconvert",
-                    "owner": "galaxyp",
-                    "revisions": "6153e8ada1ee",
-                    "tool_panel_section_label": "Convert Formats",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "peptideshaker",
-                    "owner": "galaxyp",
-                    "revisions": "3ec27b4cee7c",
+                    "name": "pdaug_basic_plots",
+                    "owner": "jay",
+                    "revisions": "15b6eec94c40",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "peptideshaker",
-                    "owner": "galaxyp",
-                    "revisions": "3ec27b4cee7c",
+                    "name": "pdaug_merge_dataframes",
+                    "owner": "jay",
+                    "revisions": "2dbfb42d34bc",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "peptideshaker",
-                    "owner": "galaxyp",
-                    "revisions": "3ec27b4cee7c",
+                    "name": "pdaug_ml_models",
+                    "owner": "jay",
+                    "revisions": "aa0b1cb1260c",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "peptideshaker",
-                    "owner": "galaxyp",
-                    "revisions": "3ec27b4cee7c",
+                    "name": "pdaug_sequence_property_based_descriptors",
+                    "owner": "jay",
+                    "revisions": "187c6f2d3b55",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "filter_tabular",
-                    "owner": "iuc",
-                    "revisions": "557ec8d7087d",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "query_tabular",
-                    "owner": "iuc",
-                    "revisions": "cf34c344508d",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_to_tabular\n  owner: devteam\n  revisions: 7e801ab2b70e\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dbbuilder\n  owner: galaxyp\n  revisions: 983bf725dfc2\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_merge_files_and_filter_unique_sequences\n  owner: galaxyp\n  revisions: f546e7278f04\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maxquant\n  owner: galaxyp\n  revisions: 9c52362ae7bb\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msconvert\n  owner: galaxyp\n  revisions: 6153e8ada1ee\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 3ec27b4cee7c\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 3ec27b4cee7c\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 3ec27b4cee7c\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 3ec27b4cee7c\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filter_tabular\n  owner: iuc\n  revisions: 557ec8d7087d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n  owner: iuc\n  revisions: cf34c344508d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "subinamehta",
-                "katherine-d21",
-                "dechendb"
-            ],
-            "editing": [
-                "pratikdjagtap",
-                "timothygriffin"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: pdaug_addclasslabel\n  owner: jay\n  revisions: 7160bfd77aef\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_basic_plots\n  owner: jay\n  revisions: 15b6eec94c40\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_merge_dataframes\n  owner: jay\n  revisions: 2dbfb42d34bc\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_ml_models\n  owner: jay\n  revisions: aa0b1cb1260c\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_sequence_property_based_descriptors\n  owner: jay\n  revisions: 187c6f2d3b55\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/tutorial.json",
         "contributors": [
             {
-                "email": "subinamehta@gmail.com",
-                "id": "subinamehta",
-                "joined": "2018-06",
-                "linkedin": "subinamehta",
-                "matrix": "subinamehta:matrix.org",
-                "name": "Subina Mehta",
-                "orcid": "0000-0001-9818-0537",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
-                "twitter": "Subina_Mehta",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
-            },
-            {
-                "id": "katherine-d21",
-                "joined": "2023-08",
-                "name": "Katherine Do",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/katherine-d21/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/katherine-d21.json"
-            },
-            {
-                "id": "dechendb",
-                "joined": "2023-06",
-                "name": "Dechen Bhuming",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dechendb/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/dechendb.json"
-            },
-            {
-                "email": "pjagtap@umn.edu",
-                "id": "pratikdjagtap",
-                "joined": "2017-09",
-                "name": "Pratik Jagtap",
-                "orcid": "0000-0003-0984-0973",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
+                "id": "jaidevjoshi83",
+                "joined": "2020-11",
+                "name": "Jayadev Joshi",
+                "orcid": "0000-0001-7589-5230",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jaidevjoshi83/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jaidevjoshi83.json"
             },
             {
-                "email": "tgriffin@umn.edu",
-                "github": false,
-                "id": "timothygriffin",
-                "joined": "2017-09",
-                "name": "Timothy J. Griffin",
-                "orcid": "0000-0001-6801-2559",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
+                "id": "blankenberg",
+                "joined": "2018-07",
+                "name": "Daniel Blankenberg",
+                "orcid": "0000-0002-6833-9049",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankenberg/",
+                "twitter": "dblankenberg",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankenberg.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/clinical-mp-2-discovery",
-        "edam_operation": [
-            "Visualisation",
-            "Imputation",
-            "Heat map generation",
-            "Standardisation and normalisation",
-            "Formatting",
-            "Principal component plotting",
-            "Protein quantification",
-            "Filtering",
-            "Clustering",
-            "Statistical calculation"
-        ],
+        "dir": "topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides",
+        "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.org.au"
+            "UseGalaxy.be"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "proteomics",
-                "tutorials": [
-                    "clinical-mp-3-verification"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "proteomics/clinical-mp-2-discovery",
+        "id": "proteomics/ml-modeling-of-anti-cancer-peptides",
         "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": [
-            "Employ SearchGUI/PeptideShaker and MaxQuant for database searching",
-            "Extraction of confident microbial peptides for verification"
-        ],
         "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-08",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Perform Database searching using two algorithms",
-            "Extract confident peptides and proteins",
-            "Generate a microbial peptide panel for verification"
+            "Learn, how to calculate peptide descriptor",
+            "Learn, how to create training data set from features?",
+            "Assessment of best ML algorithm in predicting anticancer peptide"
         ],
-        "pageviews": 139,
-        "pub_date": "2024-02-06",
+        "pageviews": 1335,
+        "pub_date": "2021-01-22",
         "questions": [
-            "How to perform database searching?",
-            "How to extract microbial and Human protein and peptide sequences from the results"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "katherine-d21"
-                ],
-                "date": "2024-06-21",
-                "galaxy_version": "23.1",
-                "length": "16M",
-                "speakers": [
-                    "katherine-d21"
-                ],
-                "youtube_id": "5Pg9LLfFGX4"
-            }
-        ],
-        "redirect_from": [
-            "/topics/proteomics/tutorials/clinical-mp-discovery/tutorial",
-            "/short/proteomics/clinical-mp-2-discovery",
-            "/short/T00414"
-        ],
-        "requirements": [
-            {
-                "topic_name": "proteomics",
-                "type": "internal"
-            }
+            "Which machine learning (ML) algorithm is superior in classifying anticancer peptides (ACPs) and non-anticancer peptides (non-ACPs)?"
         ],
-        "short_id": "T00414",
+        "short_id": "T00225",
         "short_tools": [
-            "Grep1",
-            "Grouping1",
-            "msconvert",
-            "fasta_cli",
-            "peptide_shaker",
-            "ident_params",
-            "maxquant",
-            "dbbuilder",
-            "search_gui",
-            "tp_cat",
-            "filter_tabular",
-            "Cut1",
-            "Filter1",
-            "query_tabular",
-            "fasta2tab",
-            "Remove beginning1",
-            "fasta_merge_files_and_filter_unique_sequences"
+            "pdaug_basic_plots",
+            "pdaug_ml_models",
+            "pdaug_addclasslabel",
+            "pdaug_merge_dataframes",
+            "pdaug_sequence_property_based_descriptors"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "clinical-metaproteomics",
+        "subtopic": "property-prediction",
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
                 }
             ],
             "inexact": []
         },
         "symlink": null,
         "tags": [
-            "label-TMT11"
+            "ML",
+            "cancer"
         ],
-        "time_estimation": "3H",
-        "title": "Clinical Metaproteomics 2: Discovery",
+        "time_estimation": "30m",
+        "title": "Machine Learning Modeling of Anticancer Peptides",
         "tools": [
-            "Cut1",
-            "Filter1",
-            "Grep1",
-            "Grouping1",
-            "Remove beginning1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/2.0.3.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/fasta_cli/4.0.41+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/ident_params/4.0.41+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/2.0.33+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/4.0.41+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0"
+            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_addclasslabel/pdaug_addclasslabel/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_basic_plots/pdaug_basic_plots/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_merge_dataframes/pdaug_merge_dataframes/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_ml_models/pdaug_ml_models/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_sequence_property_based_descriptors/pdaug_sequence_property_based_descriptors/0.1.0"
         ],
         "topic_name": "proteomics",
         "topic_name_human": "Proteomics",
@@ -188616,943 +190757,509 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "clinical-mp-2-discovery",
+        "tutorial_name": "ml-modeling-of-anti-cancer-peptides",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/tutorial.json"
         },
-        "version": 2,
+        "version": 8,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 451,
-        "visitors": 87,
+        "visit_duration": 115,
+        "visitors": 874,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Organization",
-                        "identifier": "0000-0001-9818-0537",
-                        "name": "Subina Mehta"
-                    }
-                ],
-                "description": "Discovery workflow with SG/PS and MaxQuant to generate microbial peptides",
+                "creators": [],
+                "description": "ML Modeling of Anti-cancer Peptides",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHuman UniProt Microbial Proteins from MetaNovo and cRAP \"]\n  1[label=\"Identification Parameters: PAR file\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nRAW files Dataset Collection\"]\n  3[label=\"Human SwissProt reviewed only\"]\n  ke0de9f90a7104b55af6241ba1c2d8e1f[color=lightseagreen,label=\"Output\\nHuman SwissProt (reviewed only)\"]\n  3 -> ke0de9f90a7104b55af6241ba1c2d8e1f\n  4[label=\"Contaminants cRAP\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nExperimental Design Discovery MaxQuant\"]\n  6[label=\"FastaCLI__MetaNovo_Human_SwissProt_cRAP_with_decoys_on_data_1_MetaNovo_Human_SwissProt_cRAP_concatenated_target_decoy.fasta\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"msconvert\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"Human SwissProt+cRAP\"]\n  3 -> 8 [label=\"output_database\"]\n  4 -> 8 [label=\"output_database\"]\n  k2f14902fb0054c08b6d16d7ee0b4b199[color=lightseagreen,label=\"Output\\nHuman SwissProt+cRAP\"]\n  8 -> k2f14902fb0054c08b6d16d7ee0b4b199\n  9[label=\"MaxQuant\"]\n  0 -> 9 [label=\"output\"]\n  2 -> 9 [label=\"output\"]\n  5 -> 9 [label=\"output\"]\n  10[label=\"Search GUI\"]\n  6 -> 10 [label=\"input_database_concatenated_target_decoy\"]\n  1 -> 10 [label=\"Identification_Parameters_File\"]\n  7 -> 10 [label=\"output\"]\n  11[label=\"FASTA-to-Tabular\"]\n  8 -> 11 [label=\"output\"]\n  12[label=\"Select microbial peptides MQ\"]\n  9 -> 12 [label=\"peptides\"]\n  kd7718bab9e754729bfb603bc3112a0e2[color=lightseagreen,label=\"Output\\nSelect microbial peptides (MQ)\"]\n  12 -> kd7718bab9e754729bfb603bc3112a0e2\n  13[label=\"Peptide Shaker\"]\n  10 -> 13 [label=\"searchgui_results\"]\n  14[label=\"Filter Tabular\"]\n  11 -> 14 [label=\"output\"]\n  15[label=\"MQ Peptide Sequences\"]\n  12 -> 15 [label=\"out_file1\"]\n  16[label=\"Select microbial peptides SGPS\"]\n  13 -> 16 [label=\"output_peptides\"]\n  k14fd9080df924c61b1f13f700a166700[color=lightseagreen,label=\"Output\\nSelect microbial peptides (SGPS)\"]\n  16 -> k14fd9080df924c61b1f13f700a166700\n  17[label=\"Select microbial PSMs\"]\n  13 -> 17 [label=\"output_psm\"]\n  18[label=\"Remove beginning\"]\n  15 -> 18 [label=\"out_file1\"]\n  19[label=\"Filter confident microbial peptides\"]\n  16 -> 19 [label=\"out_file1\"]\n  k1c6c953fd1924953938a9f401315bc0d[color=lightseagreen,label=\"Output\\nFilter confident microbial peptides\"]\n  19 -> k1c6c953fd1924953938a9f401315bc0d\n  20[label=\"Filter confident microbial PSMs\"]\n  17 -> 20 [label=\"out_file1\"]\n  kd8ec7f0c7ba14733a3dc74a9ef298dc2[color=lightseagreen,label=\"Output\\nFilter confident microbial PSMs\"]\n  20 -> kd8ec7f0c7ba14733a3dc74a9ef298dc2\n  21[label=\"MQ Distinct Peptides\"]\n  18 -> 21 [label=\"out_file1\"]\n  k07cae0170b394065b83eb5f2e27fe740[color=lightseagreen,label=\"Output\\nMQ Peptides\"]\n  21 -> k07cae0170b394065b83eb5f2e27fe740\n  22[label=\"Query Tabular\"]\n  20 -> 22 [label=\"out_file1\"]\n  20 -> 22 [label=\"out_file1\"]\n  14 -> 22 [label=\"output\"]\n  23[label=\"Cut\"]\n  22 -> 23 [label=\"output\"]\n  24[label=\"SGPS Distinct Peptides\"]\n  23 -> 24 [label=\"out_file1\"]\n  kb6c61697ff5243c08fb4765d7b4204cc[color=lightseagreen,label=\"Output\\nSGPS Distinct Peptides\"]\n  24 -> kb6c61697ff5243c08fb4765d7b4204cc\n  25[label=\"SGPS-MQ Peptides\"]\n  21 -> 25 [label=\"out_file1\"]\n  24 -> 25 [label=\"out_file1\"]\n  ka8c2de2ee32248309d282f79bf937013[color=lightseagreen,label=\"Output\\nSGPS-MQ Peptides\"]\n  25 -> ka8c2de2ee32248309d282f79bf937013\n  26[label=\"Distinct Peptides\"]\n  25 -> 26 [label=\"out_file1\"]\n  kef0d91b1042f4a9fa2b6bf73d82f24f7[color=lightseagreen,label=\"Output\\nDistinct Peptides\"]\n  26 -> kef0d91b1042f4a9fa2b6bf73d82f24f7\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nACPs\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nnon-ACPs\"]\n  2[label=\"PDAUG Sequence Property Based Descriptors\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"PDAUG Sequence Property Based Descriptors\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"PDAUG Add Class Label\"]\n  2 -> 4 [label=\"output1\"]\n  5[label=\"PDAUG Add Class Label\"]\n  3 -> 5 [label=\"output1\"]\n  6[label=\"PDAUG Merge Dataframes\"]\n  4 -> 6 [label=\"OutFile1\"]\n  5 -> 6 [label=\"OutFile1\"]\n  7[label=\"PDAUG ML Models\"]\n  6 -> 7 [label=\"output1\"]\n  8[label=\"PDAUG ML Models\"]\n  6 -> 8 [label=\"output1\"]\n  9[label=\"PDAUG ML Models\"]\n  6 -> 9 [label=\"output1\"]\n  10[label=\"PDAUG ML Models\"]\n  6 -> 10 [label=\"output1\"]\n  11[label=\"PDAUG ML Models\"]\n  6 -> 11 [label=\"output1\"]\n  12[label=\"PDAUG ML Models\"]\n  6 -> 12 [label=\"output1\"]\n  13[label=\"PDAUG Merge Dataframes\"]\n  7 -> 13 [label=\"output1\"]\n  9 -> 13 [label=\"output1\"]\n  8 -> 13 [label=\"output1\"]\n  10 -> 13 [label=\"output1\"]\n  11 -> 13 [label=\"output1\"]\n  12 -> 13 [label=\"output1\"]\n  14[label=\"PDAUG Basic Plots\"]\n  13 -> 14 [label=\"output1\"]\n}",
                 "history": [
                     {
-                        "hash": "e0464fd1787b4ca7dea72ca77b7ab2ad03a8292a",
-                        "message": "add workflows",
+                        "hash": "c6cb67762f0c2d329bb52c6e6fb805df376f9ea0",
+                        "message": "Tutorials for PDAUG tool suite (#2150)",
                         "num": 1,
-                        "short_hash": "e0464fd17",
-                        "unix": "1723118192"
+                        "short_hash": "c6cb67762",
+                        "unix": "1611340147"
                     }
                 ],
                 "inputs": [
-                    {
-                        "annotation": "FastaCLI: MetaNovo Human SwissProt cRAP with decoys on data 1 (MetaNovo Human SwissProt cRAP_concatenated_target_decoy) (49,076 sequences)",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "FastaCLI: MetaNovo Human SwissProt cRAP with decoys on data 1 (MetaNovo Human SwissProt cRAP_concatenated_target_decoy) (49,076 sequences)",
-                                "name": "Human UniProt Microbial Proteins (from MetaNovo) and cRAP "
-                            }
-                        ],
-                        "label": "Human UniProt Microbial Proteins (from MetaNovo) and cRAP ",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 249.51593017578125,
-                            "top": 272.60801696777344
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "c0c1c1cf-e899-4b8e-b1b1-6a4f24d87ad1",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "RAW files (Dataset Collection)"
-                            }
-                        ],
-                        "label": "RAW files (Dataset Collection)",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 833.7075958251953
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"thermo.raw\"], \"tag\": null, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "c0f85358-244a-4254-ac94-e920a6cdbe39",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Experimental Design Discovery MaxQuant"
-                            }
-                        ],
-                        "label": "Experimental Design Discovery MaxQuant",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 881.6298217773438,
-                            "top": 922.0535430908203
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "9652a70a-de8c-4966-b7cf-121f1b9f0b54",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nHuman UniProt Microbial Proteins from MetaNovo and cRAP \"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Identification Parameters: PAR file\"];\n  2[\"\u2139\ufe0f Input Collection\\nRAW files Dataset Collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Human SwissProt reviewed only\"];\n  e0de9f90-a710-4b55-af62-41ba1c2d8e1f[\"Output\\nHuman SwissProt (reviewed only)\"];\n  3 --> e0de9f90-a710-4b55-af62-41ba1c2d8e1f;\n  style e0de9f90-a710-4b55-af62-41ba1c2d8e1f stroke:#2c3143,stroke-width:4px;\n  4[\"Contaminants cRAP\"];\n  5[\"\u2139\ufe0f Input Dataset\\nExperimental Design Discovery MaxQuant\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"FastaCLI__MetaNovo_Human_SwissProt_cRAP_with_decoys_on_data_1_MetaNovo_Human_SwissProt_cRAP_concatenated_target_decoy.fasta\"];\n  0 -->|output| 6;\n  7[\"msconvert\"];\n  2 -->|output| 7;\n  8[\"Human SwissProt+cRAP\"];\n  3 -->|output_database| 8;\n  4 -->|output_database| 8;\n  2f14902f-b005-4c08-b6d1-6d7ee0b4b199[\"Output\\nHuman SwissProt+cRAP\"];\n  8 --> 2f14902f-b005-4c08-b6d1-6d7ee0b4b199;\n  style 2f14902f-b005-4c08-b6d1-6d7ee0b4b199 stroke:#2c3143,stroke-width:4px;\n  9[\"MaxQuant\"];\n  0 -->|output| 9;\n  2 -->|output| 9;\n  5 -->|output| 9;\n  10[\"Search GUI\"];\n  6 -->|input_database_concatenated_target_decoy| 10;\n  1 -->|Identification_Parameters_File| 10;\n  7 -->|output| 10;\n  11[\"FASTA-to-Tabular\"];\n  8 -->|output| 11;\n  12[\"Select microbial peptides MQ\"];\n  9 -->|peptides| 12;\n  d7718bab-9e75-4729-bfb6-03bc3112a0e2[\"Output\\nSelect microbial peptides (MQ)\"];\n  12 --> d7718bab-9e75-4729-bfb6-03bc3112a0e2;\n  style d7718bab-9e75-4729-bfb6-03bc3112a0e2 stroke:#2c3143,stroke-width:4px;\n  13[\"Peptide Shaker\"];\n  10 -->|searchgui_results| 13;\n  14[\"Filter Tabular\"];\n  11 -->|output| 14;\n  15[\"MQ Peptide Sequences\"];\n  12 -->|out_file1| 15;\n  16[\"Select microbial peptides SGPS\"];\n  13 -->|output_peptides| 16;\n  14fd9080-df92-4c61-b1f1-3f700a166700[\"Output\\nSelect microbial peptides (SGPS)\"];\n  16 --> 14fd9080-df92-4c61-b1f1-3f700a166700;\n  style 14fd9080-df92-4c61-b1f1-3f700a166700 stroke:#2c3143,stroke-width:4px;\n  17[\"Select microbial PSMs\"];\n  13 -->|output_psm| 17;\n  18[\"Remove beginning\"];\n  15 -->|out_file1| 18;\n  19[\"Filter confident microbial peptides\"];\n  16 -->|out_file1| 19;\n  1c6c953f-d192-4953-938a-9f401315bc0d[\"Output\\nFilter confident microbial peptides\"];\n  19 --> 1c6c953f-d192-4953-938a-9f401315bc0d;\n  style 1c6c953f-d192-4953-938a-9f401315bc0d stroke:#2c3143,stroke-width:4px;\n  20[\"Filter confident microbial PSMs\"];\n  17 -->|out_file1| 20;\n  d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2[\"Output\\nFilter confident microbial PSMs\"];\n  20 --> d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2;\n  style d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2 stroke:#2c3143,stroke-width:4px;\n  21[\"MQ Distinct Peptides\"];\n  18 -->|out_file1| 21;\n  07cae017-0b39-4065-b83e-b5f2e27fe740[\"Output\\nMQ Peptides\"];\n  21 --> 07cae017-0b39-4065-b83e-b5f2e27fe740;\n  style 07cae017-0b39-4065-b83e-b5f2e27fe740 stroke:#2c3143,stroke-width:4px;\n  22[\"Query Tabular\"];\n  20 -->|out_file1| 22;\n  20 -->|out_file1| 22;\n  14 -->|output| 22;\n  23[\"Cut\"];\n  22 -->|output| 23;\n  24[\"SGPS Distinct Peptides\"];\n  23 -->|out_file1| 24;\n  b6c61697-ff52-43c0-8fb4-765d7b4204cc[\"Output\\nSGPS Distinct Peptides\"];\n  24 --> b6c61697-ff52-43c0-8fb4-765d7b4204cc;\n  style b6c61697-ff52-43c0-8fb4-765d7b4204cc stroke:#2c3143,stroke-width:4px;\n  25[\"SGPS-MQ Peptides\"];\n  21 -->|out_file1| 25;\n  24 -->|out_file1| 25;\n  a8c2de2e-e322-4830-9d28-2f79bf937013[\"Output\\nSGPS-MQ Peptides\"];\n  25 --> a8c2de2e-e322-4830-9d28-2f79bf937013;\n  style a8c2de2e-e322-4830-9d28-2f79bf937013 stroke:#2c3143,stroke-width:4px;\n  26[\"Distinct Peptides\"];\n  25 -->|out_file1| 26;\n  ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7[\"Output\\nDistinct Peptides\"];\n  26 --> ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7;\n  style ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "WF2_Discovery-Workflow",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/ident_params/4.0.41+galaxy1",
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "Identification Parameters: PAR file",
-                        "name": "Identification Parameters",
-                        "outputs": [
-                            {
-                                "name": "Identification_Parameters_File",
-                                "type": "json"
-                            }
-                        ],
-                        "position": {
-                            "left": 814.9930419921875,
-                            "top": 0
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionIdentification_Parameters_File": {
-                                "action_arguments": {
-                                    "newname": "Identification Parameters (PAR)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "Identification_Parameters_File"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/ident_params/4.0.41+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3ec27b4cee7c",
-                            "name": "peptideshaker",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"advanced_options\": {\"spectrum_annotation_options\": {\"annotation_level\": \"0.75\", \"annotation_mz_tolerance\": \"0.5\", \"annotation_high_resolution\": true}, \"sequence_matching_options\": {\"sequence_matching_type\": \"2\", \"sequence_matching_x\": \"0.25\", \"sequence_matching_enzymatic_tags\": false, \"sequence_matching_max_ptms_per_tag\": \"3\", \"sequence_matching_min_amino_acid_score\": \"30\", \"sequence_matching_min_tag_length\": \"3\"}, \"import_filters_options\": {\"min_peptide_length\": \"8\", \"max_peptide_length\": \"30\", \"max_precursor_error\": \"10.0\", \"max_precursor_error_type\": \"1\", \"missed_cleavages_min\": null, \"missed_cleavages_max\": null, \"exclude_unknown_ptms\": true}, \"ptm_localization_options\": {\"ptm_score\": {\"ptm_score_selector\": \"1\", \"__current_case__\": 0, \"score_neutral_losses\": false, \"ptm_threshold\": \"95.0\"}, \"ptm_sequence_matching_type\": \"1\", \"ptm_alignment\": true}, \"gene_annotation_options\": {\"use_gene_mapping\": false, \"update_gene_mapping\": false}, \"protein_inference_options\": {\"simplify_protein_groups_conditional\": {\"simplify_protein_groups_selector\": \"yes\", \"__current_case__\": 1, \"simplify_protein_groups_evidence\": true, \"simplify_protein_groups_confidence\": true, \"simplify_protein_groups_confidence_threshold\": \"0.05\", \"simplify_protein_groups_enzymaticity\": true, \"simplify_protein_groups_variant\": true}, \"simplify_protein_pi_modifications\": true}, \"validation_levels_options\": {\"protein_fdr\": \"1.0\", \"peptide_fdr\": \"1.0\", \"psm_fdr\": \"1.0\"}, \"fraction_analysis_options\": {\"protein_fraction_mw_confidence\": \"95.0\"}, \"database_processing_options\": {\"decoy_conditional\": {\"create_decoy_selector\": \"yes\", \"__current_case__\": 1, \"decoy_tag\": \"_REVERSED\", \"decoy_type\": \"1\"}, \"decoy_file_tag\": \"_concatenated_target_decoy\"}}, \"searchengines_options\": {\"xtandem\": {\"xtandem_advanced\": \"no\", \"__current_case__\": 0}, \"myrimatch\": {\"myrimatch_advanced\": \"no\", \"__current_case__\": 0}, \"msgf\": {\"msgf_advanced\": \"no\", \"__current_case__\": 0}, \"ms_amanda\": {\"ms_amanda_advanced\": \"no\", \"__current_case__\": 0}, \"omssa\": {\"omssa_advanced\": \"no\", \"__current_case__\": 0}, \"comet\": {\"comet_advanced\": \"no\", \"__current_case__\": 0}, \"tide\": {\"tide_advanced\": \"no\", \"__current_case__\": 0}, \"directtag\": {\"directtag_advanced\": \"no\", \"__current_case__\": 0}, \"metamorpheus\": {\"metamorpheus_advanced\": \"no\", \"__current_case__\": 0}, \"novor\": {\"novor_advanced\": \"no\", \"__current_case__\": 0}, \"pepnovo\": {\"pepnovo_advanced\": \"no\", \"__current_case__\": 0}, \"pnovo\": {\"pnovo_advanced\": \"no\", \"__current_case__\": 0}}, \"spectrum_matching_options\": {\"fixed_modifications\": [\"Carbamidomethylation of C\", \"TMT 11-plex of K+4\", \"TMT 11-plex of peptide N-term\"], \"variable_modifications\": [\"Oxidation of M\"], \"digestion\": {\"cleavage\": \"0\", \"__current_case__\": 0, \"digests\": [{\"__index__\": 0, \"enzyme\": \"Trypsin\", \"missed_cleavages\": \"2\", \"specificity\": \"0\"}]}, \"precursor_ion_tol_units\": \"1\", \"precursor_ion_tol\": \"10.0\", \"fragment_tol_units\": \"0\", \"fragment_tol\": \"0.6\", \"min_charge\": \"2\", \"max_charge\": \"6\", \"forward_ion\": \"b\", \"reverse_ion\": \"y\", \"min_isotope\": \"0\", \"max_isotope\": \"1\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.0.41+galaxy1",
-                        "type": "tool",
-                        "uuid": "abaf5892-7976-4526-9cf6-a0c96b9222ea",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "Identification_Parameters_File",
-                                "uuid": "4a0e51c2-f558-4c3b-bf33-3616f4583771"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "Human SwissProt (reviewed only)",
-                        "name": "Protein Database Downloader",
-                        "outputs": [
-                            {
-                                "name": "output_database",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "left": 634.6446672462531,
-                            "top": 607.9219329733031
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_database": {
-                                "action_arguments": {
-                                    "newname": "Human SwissProt (reviewed only)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_database"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
-                        "tool_shed_repository": {
-                            "changeset_revision": "983bf725dfc2",
-                            "name": "dbbuilder",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"9606\", \"taxon_id\": null, \"reviewed\": \"reviewed:true\", \"set\": \"keyword:KW-1185\", \"include_isoform\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3.4",
-                        "type": "tool",
-                        "uuid": "5b0de886-9f18-4dd2-8e81-4b29467e727a",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Human SwissProt (reviewed only)",
-                                "output_name": "output_database",
-                                "uuid": "e0de9f90-a710-4b55-af62-41ba1c2d8e1f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "batchmode|input_fastas_0|input_fasta": {
-                                "id": 3,
-                                "output_name": "output_database"
-                            },
-                            "batchmode|input_fastas_1|input_fasta": {
-                                "id": 4,
-                                "output_name": "output_database"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Human SwissProt+cRAP",
-                        "name": "FASTA Merge Files and Filter Unique Sequences",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "left": 902.4973253039605,
-                            "top": 577.0886700391638
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Human SwissProt+cRAP"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f546e7278f04",
-                            "name": "fasta_merge_files_and_filter_unique_sequences",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"accession_parser\": \"^>([^ ]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"uniqueness_criterion\": \"sequence\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.0",
-                        "type": "tool",
-                        "uuid": "a35c2efa-70f2-41e8-bc46-cb2a245fdf57",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Human SwissProt+cRAP",
-                                "output_name": "output",
-                                "uuid": "2f14902f-b005-4c08-b6d1-6d7ee0b4b199"
-                            }
-                        ]
-                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/2.0.3.0+galaxy0",
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "input_opts|fasta_files": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "paramGroups_0|files": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "search_opts|template": {
-                                "id": 5,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool MaxQuant",
-                                "name": "input_opts"
-                            },
-                            {
-                                "description": "runtime parameter for tool MaxQuant",
-                                "name": "search_opts"
-                            }
-                        ],
-                        "label": null,
-                        "name": "MaxQuant",
-                        "outputs": [
-                            {
-                                "name": "proteinGroups",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "mqpar",
-                                "type": "xml"
-                            },
-                            {
-                                "name": "peptides",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "msms",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "msmsScans",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "summary",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "log",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "config",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 1389.0771241398825,
-                            "top": 778.3294605307798
-                        },
-                        "post_job_actions": {
-                            "TagDatasetActionpeptides": {
-                                "action_arguments": {
-                                    "tags": "#MQ_Peptides"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "peptides"
-                            },
-                            "TagDatasetActionproteinGroups": {
-                                "action_arguments": {
-                                    "tags": "#MQ_ProteinGroups"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "proteinGroups"
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "ACPs"
                             }
+                        ],
+                        "label": "ACPs",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 136.59375,
+                            "top": 125.359375
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/2.0.3.0+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9c52362ae7bb",
-                            "name": "maxquant",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input_opts\": {\"ftype\": \".thermo.raw\", \"fasta_files\": {\"__class__\": \"ConnectedValue\"}, \"identifier_parse_rule\": \">([^\\\\s]*)\", \"description_parse_rule\": \">(.*)\"}, \"output_opts\": {\"dry_run\": false, \"output\": [\"proteinGroups\", \"mqpar\", \"peptides\", \"msms\", \"msmsScans\", \"summary\", \"log\", \"config\"]}, \"paramGroups\": [{\"__index__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}, \"maxMissedCleavages\": \"2\", \"fixedModifications\": [\"Carbamidomethyl (C)\"], \"variableModifications\": [\"Oxidation (M)\"], \"enzymes\": [\"Trypsin/P\"], \"digestion_mode\": \"0\", \"quant_method\": {\"select_quant_method\": \"reporter_ion_ms2\", \"__current_case__\": 3, \"iso_labels\": {\"labeling\": \"tmt11plex\", \"__current_case__\": 4}, \"filter_by_pif\": {\"filter_pif\": \"True\", \"__current_case__\": 0, \"reporter_pif\": \"0.75\"}}}], \"protein_quant\": {\"peptides_for_quantification\": \"1\", \"only_unmod_prot\": {\"unmod_prot\": \"True\", \"__current_case__\": 0, \"mods_used_prot_quant\": [\"Oxidation (M)\"], \"discard_unmod_cpart_peptides\": true}, \"lfq_opts\": {\"separateLfq\": false, \"lfqStabilizeLargeRatios\": true, \"lfqRequireMsms\": true, \"do_ibaq\": {\"ibaq\": \"False\", \"__current_case__\": 1}, \"advancedSiteIntensities\": true}}, \"qc\": {\"do_it\": \"false\", \"__current_case__\": 1}, \"search_opts\": {\"template\": {\"__class__\": \"ConnectedValue\"}, \"min_peptide_len\": \"8\", \"max_peptide_mass\": \"4600\", \"min_unique_pep\": \"0\", \"calc_peak_properties\": false, \"mbr\": {\"match_between_runs\": \"True\", \"__current_case__\": 1, \"matching_time_window\": \"0.7\", \"matching_ion_mobility_window\": \"0.05\", \"alignment_time_window\": \"20\", \"alignment_ion_mobility_window\": \"1\", \"match_unidentified_features\": false}, \"incl_contaminants\": false, \"decoy_mode\": \"revert\", \"psm_fdr\": \"0.01\", \"protein_fdr\": \"0.01\", \"min_pep_length\": \"8\", \"max_pep_length\": \"50\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.3.0+galaxy0",
-                        "type": "tool",
-                        "uuid": "46c61a69-355c-44ac-9945-0e4d43f0b2ec",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "471cb99c-89a3-4e6e-930a-b344d2b44b14",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "proteinGroups",
-                                "uuid": "5306e0c0-bd4c-44ea-9f3c-817f959ed3d4"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "peptides",
-                                "uuid": "a2bbaad0-27ba-491c-9462-efd4a1e8efb6"
+                                "output_name": "output",
+                                "uuid": "6b2eaf3c-5598-44ce-a7e8-5f6e262c92b0"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Grep1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 12,
-                        "input_connections": {
-                            "input": {
-                                "id": 9,
-                                "output_name": "peptides"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Select microbial peptides (MQ)",
-                        "name": "Select",
-                        "outputs": [
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "description": "",
+                                "name": "non-ACPs"
                             }
                         ],
+                        "label": "non-ACPs",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1644.1114561742336,
-                            "top": 809.3114768624164
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Select microbial peptides (MQ)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
+                            "left": 134,
+                            "top": 202.328125
                         },
-                        "tool_id": "Grep1",
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"-v\", \"keep_header\": true, \"pattern\": \"(_HUMAN)|(_REVERSED)|(CON)|(con)\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.4",
-                        "type": "tool",
-                        "uuid": "cb9b81ce-c86e-4b07-ba18-3d1deddeded5",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "1690c4bb-afa2-47cf-9a34-381d59ac348d",
                         "workflow_outputs": [
                             {
-                                "label": "Select microbial peptides (MQ)",
-                                "output_name": "out_file1",
-                                "uuid": "d7718bab-9e75-4729-bfb6-03bc3112a0e2"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "6449070c-3e6b-4088-98a4-dcb7449bf279"
                             }
                         ]
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nACPs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nnon-ACPs\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"PDAUG Sequence Property Based Descriptors\"];\n  0 -->|output| 2;\n  3[\"PDAUG Sequence Property Based Descriptors\"];\n  1 -->|output| 3;\n  4[\"PDAUG Add Class Label\"];\n  2 -->|output1| 4;\n  5[\"PDAUG Add Class Label\"];\n  3 -->|output1| 5;\n  6[\"PDAUG Merge Dataframes\"];\n  4 -->|OutFile1| 6;\n  5 -->|OutFile1| 6;\n  7[\"PDAUG ML Models\"];\n  6 -->|output1| 7;\n  8[\"PDAUG ML Models\"];\n  6 -->|output1| 8;\n  9[\"PDAUG ML Models\"];\n  6 -->|output1| 9;\n  10[\"PDAUG ML Models\"];\n  6 -->|output1| 10;\n  11[\"PDAUG ML Models\"];\n  6 -->|output1| 11;\n  12[\"PDAUG ML Models\"];\n  6 -->|output1| 12;\n  13[\"PDAUG Merge Dataframes\"];\n  7 -->|output1| 13;\n  9 -->|output1| 13;\n  8 -->|output1| 13;\n  10 -->|output1| 13;\n  11 -->|output1| 13;\n  12 -->|output1| 13;\n  14[\"PDAUG Basic Plots\"];\n  13 -->|output1| 14;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "PeptideML",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/2.0.33+galaxy1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 13,
-                        "input_connections": {
-                            "searchgui_input": {
-                                "id": 10,
-                                "output_name": "searchgui_results"
-                            }
-                        },
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Peptide Shaker",
-                                "name": "optional_main_parameters"
-                            },
-                            {
-                                "description": "runtime parameter for tool Peptide Shaker",
-                                "name": "optional_main_parameters"
-                            },
-                            {
-                                "description": "runtime parameter for tool Peptide Shaker",
-                                "name": "optional_main_parameters"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Peptide Shaker",
-                        "outputs": [
-                            {
-                                "name": "mzidentML",
-                                "type": "mzid"
-                            },
-                            {
-                                "name": "output_certificate",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "output_psm",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "output_peptides",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "output_proteins",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "ACPs"
                             }
                         ],
+                        "label": "ACPs",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1376.5616292921313,
-                            "top": 136.11307746315038
-                        },
-                        "post_job_actions": {
-                            "TagDatasetActionoutput_peptides": {
-                                "action_arguments": {
-                                    "tags": "#PS_Peptides"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "output_peptides"
-                            },
-                            "TagDatasetActionoutput_psm": {
-                                "action_arguments": {
-                                    "tags": "#PS_PSM"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "output_psm"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/2.0.33+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "a6ff76e057fd",
-                            "name": "peptideshaker",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 136.59375,
+                            "top": 125.359375
                         },
-                        "tool_state": "{\"exporting_options\": {\"zip_conditional\": {\"zip_output_boolean\": false, \"__current_case__\": 0, \"export_psdb\": false}, \"mzidentml_conditional\": {\"mzidentml_creation\": true, \"__current_case__\": 0, \"include_sequences\": false, \"contact_options\": {\"contact_options_selector\": \"no\", \"__current_case__\": 0}}, \"followup_conditional\": {\"followup_conditional_selector\": \"no\", \"__current_case__\": 0}, \"output_reports\": [\"3\", \"6\", \"9\", \"0\"]}, \"optional_main_parameters\": {\"input_optional_identification_parameters\": {\"__class__\": \"RuntimeValue\"}, \"input_fasta_file\": {\"__class__\": \"RuntimeValue\"}, \"input_optional_spectrum_files\": {\"__class__\": \"RuntimeValue\"}}, \"searchgui_input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.33+galaxy1",
-                        "type": "tool",
-                        "uuid": "d8293305-e003-4c82-9085-a6a6e27563f3",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "471cb99c-89a3-4e6e-930a-b344d2b44b14",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_proteins",
-                                "uuid": "3dfa370b-aaa1-4b0b-ab51-801ed5abf804"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_peptides",
-                                "uuid": "062fabe0-3631-4888-9a0e-5ea16af9c564"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "mzidentML",
-                                "uuid": "275ca0b9-f609-4cb7-8a1f-3ada482634fe"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_psm",
-                                "uuid": "39e82c48-26d6-4717-9efe-06a73e37dfdc"
+                                "output_name": "output",
+                                "uuid": "6b2eaf3c-5598-44ce-a7e8-5f6e262c92b0"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Grep1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 16,
-                        "input_connections": {
-                            "input": {
-                                "id": 13,
-                                "output_name": "output_peptides"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Select microbial peptides (SGPS)",
-                        "name": "Select",
-                        "outputs": [
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "description": "",
+                                "name": "non-ACPs"
                             }
                         ],
+                        "label": "non-ACPs",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1624.5012303811463,
-                            "top": 133.08277443284737
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Select microbial peptides (SGPS)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
+                            "left": 134,
+                            "top": 202.328125
                         },
-                        "tool_id": "Grep1",
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"-v\", \"keep_header\": true, \"pattern\": \"(_HUMAN)|(_REVERSED)|(CON)|(con)\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.4",
-                        "type": "tool",
-                        "uuid": "088c67e2-5680-45ac-8fc6-58107304378b",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "1690c4bb-afa2-47cf-9a34-381d59ac348d",
                         "workflow_outputs": [
                             {
-                                "label": "Select microbial peptides (SGPS)",
-                                "output_name": "out_file1",
-                                "uuid": "14fd9080-df92-4c61-b1f1-3f700a166700"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "6449070c-3e6b-4088-98a4-dcb7449bf279"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Filter1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_sequence_property_based_descriptors/pdaug_sequence_property_based_descriptors/0.1.0",
                         "errors": null,
-                        "id": 19,
+                        "id": 2,
                         "input_connections": {
-                            "input": {
-                                "id": 16,
-                                "output_name": "out_file1"
+                            "input1": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "Filter confident microbial peptides",
-                        "name": "Filter",
+                        "label": null,
+                        "name": "PDAUG Sequence Property Based Descriptors",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "output1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1882.4063928456353,
-                            "top": 138.52877496551775
+                            "left": 325.609375,
+                            "top": 142.703125
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Filter confident microbial peptides"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_sequence_property_based_descriptors/pdaug_sequence_property_based_descriptors/0.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "6b6aec52638d",
+                            "name": "pdaug_sequence_property_based_descriptors",
+                            "owner": "jay",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"cond\": \"c17=='Confident'\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_state": "{\"SelectDiscriptor\": {\"DesType\": \"CTD\", \"__current_case__\": 9}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0",
                         "type": "tool",
-                        "uuid": "a2763f6c-4bb4-4637-b9a5-4319b8176e57",
-                        "when": null,
+                        "uuid": "d751bc15-62a7-4c2b-959d-ec32b7bf9929",
                         "workflow_outputs": [
                             {
-                                "label": "Filter confident microbial peptides",
-                                "output_name": "out_file1",
-                                "uuid": "1c6c953f-d192-4953-938a-9f401315bc0d"
+                                "label": null,
+                                "output_name": "output1",
+                                "uuid": "4ce6e57c-1fb3-4ccb-857a-13f1a50e3fe7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Filter1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_addclasslabel/pdaug_addclasslabel/0.1.0",
                         "errors": null,
-                        "id": 20,
+                        "id": 4,
                         "input_connections": {
-                            "input": {
-                                "id": 17,
-                                "output_name": "out_file1"
+                            "input1": {
+                                "id": 2,
+                                "output_name": "output1"
                             }
                         },
                         "inputs": [],
-                        "label": "Filter confident microbial PSMs",
-                        "name": "Filter",
+                        "label": null,
+                        "name": "PDAUG Add Class Label",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "OutFile1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1892.8411851041578,
-                            "top": 346.8881407177668
+                            "left": 517.234375,
+                            "top": 142.703125
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Filter confident microbial PSMs"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_addclasslabel/pdaug_addclasslabel/0.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2df11ea23f10",
+                            "name": "pdaug_addclasslabel",
+                            "owner": "jay",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"cond\": \"c24=='Confident'\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_state": "{\"ClassLabel\": \"0\", \"ClassLabelTitle\": \"Class_label\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0",
                         "type": "tool",
-                        "uuid": "2986ffd8-f797-4bdd-ba33-e3383bb3cbd1",
-                        "when": null,
+                        "uuid": "37498ada-bad4-456d-91e6-f21a6fe98c5d",
                         "workflow_outputs": [
                             {
-                                "label": "Filter confident microbial PSMs",
-                                "output_name": "out_file1",
-                                "uuid": "d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2"
+                                "label": null,
+                                "output_name": "OutFile1",
+                                "uuid": "47d6dd33-c08f-4818-87f5-02eb73dc97b5"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Grouping1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_merge_dataframes/pdaug_merge_dataframes/0.1.0",
                         "errors": null,
-                        "id": 21,
+                        "id": 6,
                         "input_connections": {
-                            "input1": {
-                                "id": 18,
-                                "output_name": "out_file1"
-                            }
+                            "input1": [
+                                {
+                                    "id": 4,
+                                    "output_name": "OutFile1"
+                                },
+                                {
+                                    "id": 5,
+                                    "output_name": "OutFile1"
+                                }
+                            ]
                         },
                         "inputs": [],
-                        "label": "MQ Distinct Peptides",
-                        "name": "Group",
+                        "label": null,
+                        "name": "PDAUG Merge Dataframes",
                         "outputs": [
                             {
-                                "name": "out_file1",
+                                "name": "output1",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 2692.1307728764114,
-                            "top": 524.4947117996797
+                            "left": 708.859375,
+                            "top": 142.703125
                         },
-                        "post_job_actions": {
-                            "EmailActionout_file1": {
-                                "action_arguments": {
-                                    "host": "usegalaxy.eu"
-                                },
-                                "action_type": "EmailAction",
-                                "output_name": "out_file1"
-                            },
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "MQ Peptides"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_merge_dataframes/pdaug_merge_dataframes/0.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "5bb52d4bf172",
+                            "name": "pdaug_merge_dataframes",
+                            "owner": "jay",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": "Grouping1",
-                        "tool_state": "{\"groupcol\": \"1\", \"ignorecase\": false, \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.4",
+                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0",
                         "type": "tool",
-                        "uuid": "eadd5e67-4653-4895-bd99-d7ec8e8514f7",
-                        "when": null,
+                        "uuid": "f8d1b048-a859-40d0-9572-f3a21230229d",
                         "workflow_outputs": [
                             {
-                                "label": "MQ Peptides",
-                                "output_name": "out_file1",
-                                "uuid": "07cae017-0b39-4065-b83e-b5f2e27fe740"
+                                "label": null,
+                                "output_name": "output1",
+                                "uuid": "98bb1ac8-f0a1-48fa-9e77-55f0df88c35f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Grouping1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_ml_models/pdaug_ml_models/0.1.0",
                         "errors": null,
-                        "id": 24,
+                        "id": 7,
                         "input_connections": {
                             "input1": {
-                                "id": 23,
-                                "output_name": "out_file1"
+                                "id": 6,
+                                "output_name": "output1"
                             }
                         },
-                        "inputs": [],
-                        "label": "SGPS Distinct Peptides",
-                        "name": "Group",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool PDAUG ML Models",
+                                "name": "input1"
+                            }
+                        ],
+                        "label": null,
+                        "name": "PDAUG ML Models",
                         "outputs": [
                             {
-                                "name": "out_file1",
+                                "name": "output1",
                                 "type": "tabular"
+                            },
+                            {
+                                "name": "output2",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 2692.21992119554,
-                            "top": 329.70161173161625
+                            "left": 900.46875,
+                            "top": 142.703125
                         },
-                        "post_job_actions": {
-                            "EmailActionout_file1": {
-                                "action_arguments": {
-                                    "host": "usegalaxy.eu"
-                                },
-                                "action_type": "EmailAction",
-                                "output_name": "out_file1"
-                            },
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "SGPS Distinct Peptides"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_ml_models/pdaug_ml_models/0.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "0973f093d98f",
+                            "name": "pdaug_ml_models",
+                            "owner": "jay",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": "Grouping1",
-                        "tool_state": "{\"groupcol\": \"1\", \"ignorecase\": false, \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.4",
+                        "tool_state": "{\"SelMLAlgo\": {\"MLAlgo\": \"SVMC\", \"__current_case__\": 0, \"settings\": {\"advanced\": \"simple\", \"__current_case__\": 0}}, \"TestMethods\": {\"SelTestMethods\": \"Internal\", \"__current_case__\": 0, \"nFolds\": \"10\"}, \"input1\": {\"__class__\": \"RuntimeValue\"}, \"scalling\": \"Min_Max\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0",
                         "type": "tool",
-                        "uuid": "17433c88-5d56-453f-9371-dc2943eecac2",
-                        "when": null,
+                        "uuid": "670d3053-75fe-4e1f-80a3-ca5a8d46448c",
                         "workflow_outputs": [
                             {
-                                "label": "SGPS Distinct Peptides",
-                                "output_name": "out_file1",
-                                "uuid": "b6c61697-ff52-43c0-8fb4-765d7b4204cc"
+                                "label": null,
+                                "output_name": "output1",
+                                "uuid": "bf8f300a-b4d8-448b-9b6a-ce55bb5cb1a1"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output2",
+                                "uuid": "18a6b311-3cf4-4d6e-9fea-62b9633a9953"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_merge_dataframes/pdaug_merge_dataframes/0.1.0",
                         "errors": null,
-                        "id": 25,
+                        "id": 13,
                         "input_connections": {
-                            "inputs": [
+                            "input1": [
                                 {
-                                    "id": 21,
-                                    "output_name": "out_file1"
+                                    "id": 7,
+                                    "output_name": "output1"
                                 },
                                 {
-                                    "id": 24,
-                                    "output_name": "out_file1"
+                                    "id": 9,
+                                    "output_name": "output1"
+                                },
+                                {
+                                    "id": 8,
+                                    "output_name": "output1"
+                                },
+                                {
+                                    "id": 10,
+                                    "output_name": "output1"
+                                },
+                                {
+                                    "id": 11,
+                                    "output_name": "output1"
+                                },
+                                {
+                                    "id": 12,
+                                    "output_name": "output1"
                                 }
                             ]
                         },
                         "inputs": [],
-                        "label": "SGPS-MQ Peptides",
-                        "name": "Concatenate datasets",
+                        "label": null,
+                        "name": "PDAUG Merge Dataframes",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "output1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 3005.427930624518,
-                            "top": 411.55050647320707
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "SGPS-MQ Peptides"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
+                            "left": 1092.09375,
+                            "top": 142.703125
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_merge_dataframes/pdaug_merge_dataframes/0.1.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "d698c222f354",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "5bb52d4bf172",
+                            "name": "pdaug_merge_dataframes",
+                            "owner": "jay",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.1",
+                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0",
                         "type": "tool",
-                        "uuid": "967a29c5-8ef9-45de-918a-f99e3f9a058f",
-                        "when": null,
+                        "uuid": "c5de6791-d223-450d-af1b-df0334d30290",
                         "workflow_outputs": [
                             {
-                                "label": "SGPS-MQ Peptides",
-                                "output_name": "out_file1",
-                                "uuid": "a8c2de2e-e322-4830-9d28-2f79bf937013"
+                                "label": null,
+                                "output_name": "output1",
+                                "uuid": "1261809f-eb67-4012-84bb-24770f3177a2"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Grouping1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_basic_plots/pdaug_basic_plots/0.1.0",
                         "errors": null,
-                        "id": 26,
+                        "id": 14,
                         "input_connections": {
-                            "input1": {
-                                "id": 25,
-                                "output_name": "out_file1"
+                            "SelPlotting|InFile": {
+                                "id": 13,
+                                "output_name": "output1"
                             }
                         },
                         "inputs": [],
-                        "label": "Distinct Peptides",
-                        "name": "Group",
+                        "label": null,
+                        "name": "PDAUG Basic Plots",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "tabular"
+                                "name": "output",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 3283.0311189112367,
-                            "top": 419.0948684617405
+                            "left": 1283.6875,
+                            "top": 142.703125
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Distinct Peptides"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_basic_plots/pdaug_basic_plots/0.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "7d247e27ff11",
+                            "name": "pdaug_basic_plots",
+                            "owner": "jay",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": "Grouping1",
-                        "tool_state": "{\"groupcol\": \"1\", \"ignorecase\": false, \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.4",
+                        "tool_state": "{\"SelPlotting\": {\"Plot\": \"HeatMap\", \"__current_case__\": 0, \"InFile\": {\"__class__\": \"ConnectedValue\"}, \"IndexColumn\": \"Algo\", \"x_label\": \"Performance measures\", \"y_label\": \"ML algorithms \"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0",
                         "type": "tool",
-                        "uuid": "b5462dd0-3af9-41d4-a011-65d4244525a9",
-                        "when": null,
+                        "uuid": "dad0ec0d-cef5-49f9-8592-f83bb8cb03e5",
                         "workflow_outputs": [
                             {
-                                "label": "Distinct Peptides",
-                                "output_name": "out_file1",
-                                "uuid": "ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "8e28f651-ba58-43dc-b894-074fe90aa50a"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/clinical-mp-2-discovery",
-                "path": "topics/proteomics/tutorials/clinical-mp-2-discovery/workflows/WF2_Discovery-Workflow.ga",
+                "parent_id": "proteomics/ml-modeling-of-anti-cancer-peptides",
+                "path": "topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/workflows/PeptideML.ga",
                 "tags": [
-                    "name:clinicalMP"
+                    "proteomics"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "WF2_Discovery-Workflow",
+                "title": "PeptideML",
                 "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-clinical-mp-2-discovery/versions/wf2-discovery-workflow",
-                "tutorial_id": "clinical-mp-2-discovery",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-2-discovery/workflows/WF2_Discovery-Workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-2-discovery/workflows/WF2_Discovery-Workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-ml-modeling-of-anti-cancer-peptides/versions/peptideml",
+                "tutorial_id": "ml-modeling-of-anti-cancer-peptides",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/workflows/PeptideML.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/ml-modeling-of-anti-cancer-peptides/workflows/PeptideML.html",
                 "version": 1,
-                "wfid": "proteomics-clinical-mp-2-discovery",
-                "wfname": "wf2-discovery-workflow",
-                "workflow": "WF2_Discovery-Workflow.ga",
+                "wfid": "proteomics-ml-modeling-of-anti-cancer-peptides",
+                "wfname": "peptideml",
+                "workflow": "PeptideML.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "Filter1",
-                    "Grep1",
-                    "Grouping1",
-                    "Remove beginning1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/2.0.3.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/fasta_cli/4.0.41+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/ident_params/4.0.41+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/2.0.33+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/4.0.41+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0"
+                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_addclasslabel/pdaug_addclasslabel/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_basic_plots/pdaug_basic_plots/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_merge_dataframes/pdaug_merge_dataframes/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_ml_models/pdaug_ml_models/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_sequence_property_based_descriptors/pdaug_sequence_property_based_descriptors/0.1.0"
                 ],
-                "workflowhub_id": "1354"
+                "workflowhub_id": "1196"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.10105821"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.4111092"
     },
     {
         "admin_install": {
@@ -189561,128 +191268,51 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "ddf54b12c295",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_to_tabular",
-                    "owner": "devteam",
-                    "revisions": "e7ed3c310b74",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "freebayes",
-                    "owner": "devteam",
-                    "revisions": "ef2c525bd8cd",
-                    "tool_panel_section_label": "Variant Calling",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "tabular_to_fasta",
-                    "owner": "devteam",
-                    "revisions": "0a7799698fe5",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bed_to_protein_map",
+                    "name": "metaquantome_db",
                     "owner": "galaxyp",
-                    "revisions": "a7c58b43cbaa",
-                    "tool_panel_section_label": "Convert Formats",
+                    "revisions": "7c45aa1c9464",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "custom_pro_db",
+                    "name": "metaquantome_expand",
                     "owner": "galaxyp",
-                    "revisions": "2c7df0077d28",
+                    "revisions": "eb65ab160a10",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fasta_merge_files_and_filter_unique_sequences",
+                    "name": "metaquantome_filter",
                     "owner": "galaxyp",
-                    "revisions": "f546e7278f04",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "7d1c20b315ff",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "gffcompare_to_bed",
+                    "name": "metaquantome_sample",
                     "owner": "galaxyp",
-                    "revisions": "ba5368c19dbd",
-                    "tool_panel_section_label": "Convert Formats",
+                    "revisions": "49a957fb353a",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "regex_find_replace",
+                    "name": "metaquantome_stat",
                     "owner": "galaxyp",
-                    "revisions": "209b7c5ee9d7",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "revisions": "982a442a98dd",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "translate_bed",
+                    "name": "metaquantome_viz",
                     "owner": "galaxyp",
-                    "revisions": "038ecf54cbec",
-                    "tool_panel_section_label": "Operate on Genomic Intervals",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "filter_tabular",
-                    "owner": "iuc",
-                    "revisions": "34d29339abab",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gffcompare",
-                    "owner": "iuc",
-                    "revisions": "0f710191a66d",
-                    "tool_panel_section_label": "Filter and Sort",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "hisat2",
-                    "owner": "iuc",
-                    "revisions": "a86e80d3c09c",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "query_tabular",
-                    "owner": "iuc",
-                    "revisions": "33d61c89fb8d",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "sqlite_to_tabular",
-                    "owner": "iuc",
-                    "revisions": "b722161a845a",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "stringtie",
-                    "owner": "iuc",
-                    "revisions": "1ebd14235b92",
-                    "tool_panel_section_label": "RNA Analysis",
+                    "revisions": "02da24eac445",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: ddf54b12c295\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_to_tabular\n  owner: devteam\n  revisions: e7ed3c310b74\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: freebayes\n  owner: devteam\n  revisions: ef2c525bd8cd\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tabular_to_fasta\n  owner: devteam\n  revisions: 0a7799698fe5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bed_to_protein_map\n  owner: galaxyp\n  revisions: a7c58b43cbaa\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: custom_pro_db\n  owner: galaxyp\n  revisions: 2c7df0077d28\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_merge_files_and_filter_unique_sequences\n  owner: galaxyp\n  revisions: f546e7278f04\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gffcompare_to_bed\n  owner: galaxyp\n  revisions: ba5368c19dbd\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 209b7c5ee9d7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: translate_bed\n  owner: galaxyp\n  revisions: '038ecf54cbec'\n  tool_panel_section_label: Operate on Genomic Intervals\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filter_tabular\n  owner: iuc\n  revisions: 34d29339abab\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gffcompare\n  owner: iuc\n  revisions: 0f710191a66d\n  tool_panel_section_label: Filter and Sort\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: hisat2\n  owner: iuc\n  revisions: a86e80d3c09c\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n  owner: iuc\n  revisions: 33d61c89fb8d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sqlite_to_tabular\n  owner: iuc\n  revisions: b722161a845a\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stringtie\n  owner: iuc\n  revisions: 1ebd14235b92\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: metaquantome_db\n  owner: galaxyp\n  revisions: 7c45aa1c9464\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_expand\n  owner: galaxyp\n  revisions: eb65ab160a10\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_filter\n  owner: galaxyp\n  revisions: 7d1c20b315ff\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_sample\n  owner: galaxyp\n  revisions: 49a957fb353a\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_stat\n  owner: galaxyp\n  revisions: 982a442a98dd\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_viz\n  owner: galaxyp\n  revisions: 02da24eac445\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.json",
         "contributors": [
             {
                 "email": "subinamehta@gmail.com",
@@ -189716,21 +191346,20 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
             },
             {
-                "email": "rsajulga@umn.edu",
-                "id": "jraysajulga",
-                "joined": "2018-11",
-                "name": "Ray Sajulga",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jraysajulga/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jraysajulga.json"
+                "email": "leith023@umn.edu",
+                "id": "emmaleith",
+                "joined": "2019-07",
+                "name": "Emma Leith",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/emmaleith/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/emmaleith.json"
             },
             {
-                "email": "jj@umn.edu",
-                "id": "jj-umn",
-                "in_memoriam": "<a href=\"https://galaxyproject.org/news/2024-03-19-remembrances-of-jj/\">James \u2018JJ\u2019 Johnson, was a Galaxy community rock star most known for his indispensable contributions to the Galaxy Proteomics community.</a>\n\nJJ\u2019s works will live on in so many Galaxy tools and workflows for years to come.",
-                "joined": "2017-09",
-                "name": "James Johnson",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jj-umn/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jj-umn.json"
+                "email": "crane136@umn.edu",
+                "id": "mariecrane",
+                "joined": "2019-05",
+                "name": "Marie Crane",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mariecrane/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mariecrane.json"
             },
             {
                 "email": "kumar207@umn.edu",
@@ -189741,19 +191370,38 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/pravs3683.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/proteogenomics-dbcreation",
+        "dir": "topics/proteomics/tutorials/metaquantome-taxonomy",
+        "edam_ontology": [
+            "topic_0121",
+            "topic_3922",
+            "topic_3941",
+            "topic_3697",
+            "topic_3174",
+            "topic_0637"
+        ],
         "edam_operation": [
-            "Variant calling",
-            "Transcriptome assembly",
-            "Sequence annotation",
-            "Sequence alignment",
-            "RNA-Seq analysis",
-            "Statistical calculation"
+            "Visualisation",
+            "Indexing",
+            "Differential protein expression analysis",
+            "Functional clustering",
+            "Statistical inference",
+            "Principal component visualisation",
+            "Query and retrieval",
+            "Heat map generation",
+            "Quantification",
+            "Filtering"
+        ],
+        "edam_topic": [
+            "Proteomics",
+            "Proteogenomics",
+            "Metatranscriptomics",
+            "Microbial ecology",
+            "Metagenomics",
+            "Taxonomy"
         ],
-        "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.be",
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
@@ -189761,14 +191409,14 @@
             {
                 "topic_name": "proteomics",
                 "tutorials": [
-                    "proteogenomics-dbsearch",
-                    "proteogenomics-novel-peptide-analysis"
+                    "metaproteomics",
+                    "metaquantome-function"
                 ],
                 "type": "internal"
             }
         ],
         "hands_on": true,
-        "id": "proteomics/proteogenomics-dbcreation",
+        "id": "proteomics/metaquantome-taxonomy",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
             "UseGalaxy.no",
@@ -189779,54 +191427,40 @@
             "mermaid": false
         },
         "key_points": [
-            "Generating variant protein database",
-            "Generating genomic and variant mapping files for visualization"
+            "All the inputs should have one column in common i.e. peptides.",
+            "Learning different tools such as Unipept, MEGAN, MetaGOmics etc. for taxonomic annotation of peptides will benefit."
         ],
         "layout": "tutorial_hands_on",
         "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-09",
+        "mod_date": "2024-03-15",
         "objectives": [
-            "Generating a customized Protein sequence database with variants, indels, splice junctions and known sequences."
+            "A taxonomy and quantitational analysis of metaproteomic mass spectrometry data."
         ],
-        "pageviews": 7820,
-        "pub_date": "2018-11-20",
+        "pageviews": 509,
+        "pub_date": "2020-10-29",
         "questions": [
-            "How to create a customized Protein Database from RNAseq data?"
+            "How do I look at differentially expressed taxa?",
+            "Can we get top 5 or 10 taxa present in the sample?",
+            "How can I visualize my results?"
         ],
-        "recordings": [
+        "requirements": [
             {
-                "captioners": [
-                    "emmaleith"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "40M",
-                "speakers": [
-                    "jj-umn"
+                "topic_name": "proteomics",
+                "tutorials": [
+                    "metaquantome-data-creation"
                 ],
-                "youtube_id": "b_kZf8mXHdo"
+                "type": "internal"
             }
         ],
-        "short_id": "T00231",
+        "short_id": "T00224",
         "short_tools": [
-            "hisat2",
-            "tab2fasta",
-            "sqlite_to_tabular",
-            "freebayes",
-            "custom_pro_db",
-            "gffcompare_to_bed",
-            "tp_cat",
-            "bed_to_protein_map",
-            "filter_tabular",
-            "translate_bed",
-            "gffcompare",
-            "query_tabular",
-            "fasta2tab",
-            "fasta_merge_files_and_filter_unique_sequences",
-            "regexColumn1",
-            "tp_replace_in_column",
-            "stringtie"
+            "metaquantome_filter",
+            "metaquantome_sample",
+            "metaquantome_stat",
+            "metaquantome_expand",
+            "metaquantome_viz",
+            "metaquantome_db"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -189834,13 +191468,13 @@
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 }
             ],
@@ -189864,28 +191498,17 @@
         },
         "symlink": null,
         "tags": [
-            "proteogenomics"
+            "microgalaxy"
         ],
-        "time_estimation": "30m",
-        "title": "Proteogenomics 1: Database Creation",
+        "time_estimation": "1h",
+        "title": "metaQuantome 3: Taxonomy",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/bed_to_protein_map/bed_to_protein_map/0.2.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.22.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/gffcompare_to_bed/gffcompare_to_bed/0.2.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed/translate_bed/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.11.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5",
-            "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1"
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.0-0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.0-0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.0-0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.0-0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.0-0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0"
         ],
         "topic_name": "proteomics",
         "topic_name_human": "Proteomics",
@@ -189895,114 +191518,51 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "proteogenomics-dbcreation",
+        "tutorial_name": "metaquantome-taxonomy",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.json"
         },
-        "version": 27,
+        "version": 14,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 154,
-        "visitors": 4508,
+        "visit_duration": 164,
+        "visitors": 377,
         "workflows": [
             {
                 "creators": [],
-                "description": "Proteogenomics Galaxy Training Network Database Creation",
+                "description": "metaquantome-taxonomy",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nFASTQ_ProB_22LIST.fastqsanger\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMus_musculus.GRCm38.86.gtf\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTrimmed_ref_5000_uniprot_cRAP.fasta\"]\n  3[label=\"HISAT2\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Editing GTF File\"]\n  1 -> 4 [label=\"output\"]\n  k70b6f719803f4fa98394a3b64b71ec01[color=lightseagreen,label=\"Output\\nchr_corrected_gtf\"]\n  4 -> k70b6f719803f4fa98394a3b64b71ec01\n  5[label=\"FASTA-to-Tabular\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"FreeBayes\"]\n  3 -> 6 [label=\"output_alignments\"]\n  7[label=\"StringTie\"]\n  4 -> 7 [label=\"outfile\"]\n  3 -> 7 [label=\"output_alignments\"]\n  8[label=\"Filter Tabular\"]\n  5 -> 8 [label=\"output\"]\n  9[label=\"CustomProDB\"]\n  3 -> 9 [label=\"output_alignments\"]\n  6 -> 9 [label=\"output_vcf\"]\n  10[label=\"GffCompare\"]\n  4 -> 10 [label=\"outfile\"]\n  7 -> 10 [label=\"output_gtf\"]\n  11[label=\"SQLite to tabular\"]\n  9 -> 11 [label=\"output_genomic_mapping_sqlite\"]\n  12[label=\"SQLite to tabular\"]\n  9 -> 12 [label=\"output_variant_annotation_sqlite\"]\n  13[label=\"FASTA Merge Files and Filter Unique Sequences\"]\n  9 -> 13 [label=\"output_rpkm\"]\n  9 -> 13 [label=\"output_snv\"]\n  9 -> 13 [label=\"output_indel\"]\n  ka5054be9dd744d60a4c6494fdbcb97a1[color=lightseagreen,label=\"Output\\nCustomProDB_FASTA\"]\n  13 -> ka5054be9dd744d60a4c6494fdbcb97a1\n  14[label=\"FASTA-to-Tabular\"]\n  9 -> 14 [label=\"output_rpkm\"]\n  15[label=\"Convert gffCompare annotated GTF to BED\"]\n  10 -> 15 [label=\"transcripts_annotated\"]\n  16[label=\"Column Regex Find And Replace\"]\n  11 -> 16 [label=\"query_results\"]\n  17[label=\"Column Regex Find And Replace\"]\n  12 -> 17 [label=\"query_results\"]\n  18[label=\"FASTA-to-Tabular\"]\n  13 -> 18 [label=\"output\"]\n  19[label=\"Filter Tabular\"]\n  14 -> 19 [label=\"output\"]\n  20[label=\"Translate BED transcripts\"]\n  15 -> 20 [label=\"output\"]\n  21[label=\"Query Tabular\"]\n  17 -> 21 [label=\"out_file1\"]\n  ke94684794ebd4ced8086c10e916b97c5[color=lightseagreen,label=\"Output\\nvariant_annoation_sqlite\"]\n  21 -> ke94684794ebd4ced8086c10e916b97c5\n  22[label=\"Column Regex Find And Replace\"]\n  18 -> 22 [label=\"output\"]\n  23[label=\"Reference Protein Accessions\"]\n  19 -> 23 [label=\"output\"]\n  8 -> 23 [label=\"output\"]\n  k19aa5a8559334ab5ae76e4b1ec5b2f85[color=lightseagreen,label=\"Output\\nReference_Protein_Accessions\"]\n  23 -> k19aa5a8559334ab5ae76e4b1ec5b2f85\n  24[label=\"bed to protein map\"]\n  20 -> 24 [label=\"translation_bed\"]\n  25[label=\"Tabular-to-FASTA\"]\n  22 -> 25 [label=\"out_file1\"]\n  26[label=\"Concatenate datasets\"]\n  24 -> 26 [label=\"output\"]\n  16 -> 26 [label=\"out_file1\"]\n  27[label=\"FASTA Merge Files and Filter Unique Sequences\"]\n  2 -> 27 [label=\"output\"]\n  25 -> 27 [label=\"output\"]\n  20 -> 27 [label=\"translation_fasta\"]\n  k924bce7c5c6a4cb3a45918784a55ae01[color=lightseagreen,label=\"Output\\nUniprot_cRAP_SAV_indel_translatedbed_FASTA\"]\n  27 -> k924bce7c5c6a4cb3a45918784a55ae01\n  28[label=\"Genomic_mapping_sqlite\"]\n  26 -> 28 [label=\"out_file1\"]\n  k6542c4e5289a4be49b427a4e170ba198[color=lightseagreen,label=\"Output\\ngenomic_mapping_sqlite\"]\n  28 -> k6542c4e5289a4be49b427a4e170ba198\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"metaQuantome: create samples file\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTaxa\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIntensity\"]\n  3[label=\"metaQuantome: database\"]\n  4[label=\"metaQuantome: expand\"]\n  3 -> 4 [label=\"outfile\"]\n  2 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  0 -> 4 [label=\"samples_file\"]\n  5[label=\"metaQuantome: filter\"]\n  4 -> 5 [label=\"outfile\"]\n  0 -> 5 [label=\"samples_file\"]\n  6[label=\"metaQuantome: stat\"]\n  5 -> 6 [label=\"outfile\"]\n  0 -> 6 [label=\"samples_file\"]\n  7[label=\"T2-Bar-Plot\"]\n  6 -> 7 [label=\"outfile\"]\n  0 -> 7 [label=\"samples_file\"]\n  8[label=\"T7-T2_volcano-plot\"]\n  6 -> 8 [label=\"outfile\"]\n  0 -> 8 [label=\"samples_file\"]\n  9[label=\"T4-Bar-Plot\"]\n  6 -> 9 [label=\"outfile\"]\n  0 -> 9 [label=\"samples_file\"]\n  10[label=\"T7-Bar-Plot\"]\n  6 -> 10 [label=\"outfile\"]\n  0 -> 10 [label=\"samples_file\"]\n  11[label=\"T4-T2_volcano-plot\"]\n  6 -> 11 [label=\"outfile\"]\n  0 -> 11 [label=\"samples_file\"]\n}",
                 "history": [
                     {
-                        "hash": "28fc28c45aa8516e99a6f1f975814904be546a3a",
-                        "message": "Update galaxy-workflow-mouse_rnaseq_dbcreation.ga",
-                        "num": 12,
-                        "short_hash": "28fc28c45",
-                        "unix": "1612811929"
-                    },
-                    {
-                        "hash": "1eca54ca9d40ba883df90c41f9e671ffd4e45d59",
-                        "message": "Update galaxy-workflow-mouse_rnaseq_dbcreation.ga",
-                        "num": 11,
-                        "short_hash": "1eca54ca9",
-                        "unix": "1611784076"
-                    },
-                    {
-                        "hash": "0db38ae94eb41e0f3a8af428a741559473c8543f",
-                        "message": "Update galaxy-workflow-mouse_rnaseq_dbcreation.ga",
-                        "num": 10,
-                        "short_hash": "0db38ae94",
-                        "unix": "1611783698"
-                    },
-                    {
-                        "hash": "13e2ffc4d065eb5e76df61af4d1627e1e74ad103",
-                        "message": "Update galaxy-workflow-mouse_rnaseq_dbcreation.ga",
-                        "num": 9,
-                        "short_hash": "13e2ffc4d",
-                        "unix": "1611782854"
-                    },
-                    {
-                        "hash": "2c4b4646c61b3da411901fd4edc3e7f2270cd8bf",
-                        "message": "Update galaxy-workflow-mouse_rnaseq_dbcreation.ga",
-                        "num": 8,
-                        "short_hash": "2c4b4646c",
-                        "unix": "1611782235"
-                    },
-                    {
-                        "hash": "f99b54e3c22e74a3572ee864041f4726f4838727",
-                        "message": "Update galaxy-workflow-mouse_rnaseq_dbcreation.ga",
-                        "num": 7,
-                        "short_hash": "f99b54e3c",
-                        "unix": "1611781308"
-                    },
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 6,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 5,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "55fe079b2828d71aabb21fa0700f6f77ac76052c",
-                        "message": "WoLF PSORT WF",
-                        "num": 4,
-                        "short_hash": "55fe079b2",
-                        "unix": "1578933056"
-                    },
-                    {
-                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
-                        "message": "Changed format of workflows",
-                        "num": 3,
-                        "short_hash": "361236c41",
-                        "unix": "1554368414"
+                        "hash": "23fe00a8ab231d19aad201787b67446f76d72128",
+                        "message": "Update main_workflow.ga",
+                        "num": 3,
+                        "short_hash": "23fe00a8a",
+                        "unix": "1636494825"
                     },
                     {
-                        "hash": "6eef55b7e8306d8ce46ac08e7799f6f65ae106aa",
-                        "message": "Updated install_tutorial_requirements.sh + minor fixes (#1275)",
+                        "hash": "6508b46449968fac766df69a5fee4295fa7e362f",
+                        "message": "Update main_workflow.ga",
                         "num": 2,
-                        "short_hash": "6eef55b7e",
-                        "unix": "1551293676"
+                        "short_hash": "6508b4644",
+                        "unix": "1603158930"
                     },
                     {
-                        "hash": "a928824de1a4881491bd2c63f7b60ba800319437",
-                        "message": "add protegenomics dbcreation tutorial",
+                        "hash": "426a2746eee3945edd669f81b15b222493c46c82",
+                        "message": "tutorial skeletons generated by planemo",
                         "num": 1,
-                        "short_hash": "a928824de",
-                        "unix": "1535188370"
+                        "short_hash": "426a2746e",
+                        "unix": "1602853461"
                     }
                 ],
                 "inputs": [
@@ -190010,37 +191570,31 @@
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "FASTQ_ProB_22LIST.fastqsanger"
+                                "name": "Taxa"
                             }
                         ],
-                        "label": "FASTQ_ProB_22LIST.fastqsanger",
+                        "label": "Taxa",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 479.57811737060547,
-                            "height": 84,
-                            "left": 465.49999237060547,
-                            "right": 625.5000228881836,
-                            "top": 395.57811737060547,
-                            "width": 160.00003051757812,
-                            "x": 465.49999237060547,
-                            "y": 395.57811737060547
+                            "left": 306.6493225097656,
+                            "top": 535.6250152587891
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "a4deaec6-bac9-4c6d-9b55-1db09bd68be5",
+                        "uuid": "dea4289e-33b0-4215-8768-da6c65f8cd83",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "8ce4f9b5-2fc0-4a8b-977c-0042f2f4bc60"
+                                "uuid": "fbf383a9-1774-483c-a1f1-1aa4d0a5659f"
                             }
                         ]
                     },
@@ -190048,119 +191602,108 @@
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Mus_musculus.GRCm38.86.gtf"
+                                "name": "Intensity"
                             }
                         ],
-                        "label": "Mus_musculus.GRCm38.86.gtf",
+                        "label": "Intensity",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 717.5468978881836,
-                            "height": 84.00003051757812,
-                            "left": 448.46874237060547,
-                            "right": 608.4687728881836,
-                            "top": 633.5468673706055,
-                            "width": 160.00003051757812,
-                            "x": 448.46874237060547,
-                            "y": 633.5468673706055
+                            "left": 304.6180725097656,
+                            "top": 659.6180877685547
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "39d9897f-14c7-476a-a85d-08425745e5a3",
+                        "uuid": "be000472-cc47-456f-8791-b62c1a6308ec",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "66e6bfc3-7f7f-415b-91be-a8d5deabe21f"
+                                "uuid": "42e60127-395b-451f-a31c-191f6f82f2e0"
                             }
                         ]
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"metaQuantome: create samples file\"];\n  1[\"\u2139\ufe0f Input Dataset\\nTaxa\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nIntensity\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"metaQuantome: database\"];\n  4[\"metaQuantome: expand\"];\n  3 -->|outfile| 4;\n  2 -->|output| 4;\n  1 -->|output| 4;\n  0 -->|samples_file| 4;\n  5[\"metaQuantome: filter\"];\n  4 -->|outfile| 5;\n  0 -->|samples_file| 5;\n  6[\"metaQuantome: stat\"];\n  5 -->|outfile| 6;\n  0 -->|samples_file| 6;\n  7[\"T2-Bar-Plot\"];\n  6 -->|outfile| 7;\n  0 -->|samples_file| 7;\n  8[\"T7-T2_volcano-plot\"];\n  6 -->|outfile| 8;\n  0 -->|samples_file| 8;\n  9[\"T4-Bar-Plot\"];\n  6 -->|outfile| 9;\n  0 -->|samples_file| 9;\n  10[\"T7-Bar-Plot\"];\n  6 -->|outfile| 10;\n  0 -->|samples_file| 10;\n  11[\"T4-T2_volcano-plot\"];\n  6 -->|outfile| 11;\n  0 -->|samples_file| 11;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "metaquantome-taxonomy-workflow",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.0-0",
                         "errors": null,
-                        "id": 2,
+                        "id": 0,
                         "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "metaQuantome: create samples file",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Trimmed_ref_5000_uniprot_cRAP.fasta"
+                                "name": "samples_file",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "Trimmed_ref_5000_uniprot_cRAP.fasta",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 186.8125,
-                            "height": 84,
-                            "left": 2539.6719360351562,
-                            "right": 2699.6719360351562,
-                            "top": 102.8125,
-                            "width": 160,
-                            "x": 2539.6719360351562,
-                            "y": 102.8125
+                            "left": 324.2882385253906,
+                            "top": 367.9861297607422
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "4ae4a7cf-adbd-4529-b4a5-e3a37d7c0120",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.0-0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "40ca115438d2",
+                            "name": "metaquantome_sample",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"samps_args\": {\"samps_src\": \"build\", \"__current_case__\": 0, \"samps\": [{\"__index__\": 0, \"group_name\": \"T2\", \"col_names\": \"T2_A1,T2_B1\"}, {\"__index__\": 1, \"group_name\": \"T4\", \"col_names\": \"T4A_1,T4B_1\"}, {\"__index__\": 2, \"group_name\": \"T7\", \"col_names\": \"T7A_1,T7B_1\"}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
+                        "type": "tool",
+                        "uuid": "8f8b3a5c-1ada-4b83-988b-46ff7e2e9468",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "f8446100-0e31-437c-a642-27c70ec4d7ef"
+                                "output_name": "samples_file",
+                                "uuid": "d0b1aed8-8212-4e20-b1b4-b10bf76a394d"
                             }
                         ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nFASTQ_ProB_22LIST.fastqsanger\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nMus_musculus.GRCm38.86.gtf\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nTrimmed_ref_5000_uniprot_cRAP.fasta\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"HISAT2\"];\n  0 -->|output| 3;\n  4[\"Editing GTF File\"];\n  1 -->|output| 4;\n  70b6f719-803f-4fa9-8394-a3b64b71ec01[\"Output\\nchr_corrected_gtf\"];\n  4 --> 70b6f719-803f-4fa9-8394-a3b64b71ec01;\n  style 70b6f719-803f-4fa9-8394-a3b64b71ec01 stroke:#2c3143,stroke-width:4px;\n  5[\"FASTA-to-Tabular\"];\n  2 -->|output| 5;\n  6[\"FreeBayes\"];\n  3 -->|output_alignments| 6;\n  7[\"StringTie\"];\n  4 -->|outfile| 7;\n  3 -->|output_alignments| 7;\n  8[\"Filter Tabular\"];\n  5 -->|output| 8;\n  9[\"CustomProDB\"];\n  3 -->|output_alignments| 9;\n  6 -->|output_vcf| 9;\n  10[\"GffCompare\"];\n  4 -->|outfile| 10;\n  7 -->|output_gtf| 10;\n  11[\"SQLite to tabular\"];\n  9 -->|output_genomic_mapping_sqlite| 11;\n  12[\"SQLite to tabular\"];\n  9 -->|output_variant_annotation_sqlite| 12;\n  13[\"FASTA Merge Files and Filter Unique Sequences\"];\n  9 -->|output_rpkm| 13;\n  9 -->|output_snv| 13;\n  9 -->|output_indel| 13;\n  a5054be9-dd74-4d60-a4c6-494fdbcb97a1[\"Output\\nCustomProDB_FASTA\"];\n  13 --> a5054be9-dd74-4d60-a4c6-494fdbcb97a1;\n  style a5054be9-dd74-4d60-a4c6-494fdbcb97a1 stroke:#2c3143,stroke-width:4px;\n  14[\"FASTA-to-Tabular\"];\n  9 -->|output_rpkm| 14;\n  15[\"Convert gffCompare annotated GTF to BED\"];\n  10 -->|transcripts_annotated| 15;\n  16[\"Column Regex Find And Replace\"];\n  11 -->|query_results| 16;\n  17[\"Column Regex Find And Replace\"];\n  12 -->|query_results| 17;\n  18[\"FASTA-to-Tabular\"];\n  13 -->|output| 18;\n  19[\"Filter Tabular\"];\n  14 -->|output| 19;\n  20[\"Translate BED transcripts\"];\n  15 -->|output| 20;\n  21[\"Query Tabular\"];\n  17 -->|out_file1| 21;\n  e9468479-4ebd-4ced-8086-c10e916b97c5[\"Output\\nvariant_annoation_sqlite\"];\n  21 --> e9468479-4ebd-4ced-8086-c10e916b97c5;\n  style e9468479-4ebd-4ced-8086-c10e916b97c5 stroke:#2c3143,stroke-width:4px;\n  22[\"Column Regex Find And Replace\"];\n  18 -->|output| 22;\n  23[\"Reference Protein Accessions\"];\n  19 -->|output| 23;\n  8 -->|output| 23;\n  19aa5a85-5933-4ab5-ae76-e4b1ec5b2f85[\"Output\\nReference_Protein_Accessions\"];\n  23 --> 19aa5a85-5933-4ab5-ae76-e4b1ec5b2f85;\n  style 19aa5a85-5933-4ab5-ae76-e4b1ec5b2f85 stroke:#2c3143,stroke-width:4px;\n  24[\"bed to protein map\"];\n  20 -->|translation_bed| 24;\n  25[\"Tabular-to-FASTA\"];\n  22 -->|out_file1| 25;\n  26[\"Concatenate datasets\"];\n  24 -->|output| 26;\n  16 -->|out_file1| 26;\n  27[\"FASTA Merge Files and Filter Unique Sequences\"];\n  2 -->|output| 27;\n  25 -->|output| 27;\n  20 -->|translation_fasta| 27;\n  924bce7c-5c6a-4cb3-a459-18784a55ae01[\"Output\\nUniprot_cRAP_SAV_indel_translatedbed_FASTA\"];\n  27 --> 924bce7c-5c6a-4cb3-a459-18784a55ae01;\n  style 924bce7c-5c6a-4cb3-a459-18784a55ae01 stroke:#2c3143,stroke-width:4px;\n  28[\"Genomic_mapping_sqlite\"];\n  26 -->|out_file1| 28;\n  6542c4e5-289a-4be4-9b42-7a4e170ba198[\"Output\\ngenomic_mapping_sqlite\"];\n  28 --> 6542c4e5-289a-4be4-9b42-7a4e170ba198;\n  style 6542c4e5-289a-4be4-9b42-7a4e170ba198 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "GTN Proteogenomics1 Database Creation",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "FASTQ_ProB_22LIST.fastqsanger"
+                                "name": "Taxa"
                             }
                         ],
-                        "label": "FASTQ_ProB_22LIST.fastqsanger",
+                        "label": "Taxa",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 479.57811737060547,
-                            "height": 84,
-                            "left": 465.49999237060547,
-                            "right": 625.5000228881836,
-                            "top": 395.57811737060547,
-                            "width": 160.00003051757812,
-                            "x": 465.49999237060547,
-                            "y": 395.57811737060547
+                            "left": 306.6493225097656,
+                            "top": 535.6250152587891
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "a4deaec6-bac9-4c6d-9b55-1db09bd68be5",
+                        "uuid": "dea4289e-33b0-4215-8768-da6c65f8cd83",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "8ce4f9b5-2fc0-4a8b-977c-0042f2f4bc60"
+                                "uuid": "fbf383a9-1774-483c-a1f1-1aa4d0a5659f"
                             }
                         ]
                     },
@@ -190168,690 +191711,1069 @@
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Mus_musculus.GRCm38.86.gtf"
+                                "name": "Intensity"
                             }
                         ],
-                        "label": "Mus_musculus.GRCm38.86.gtf",
+                        "label": "Intensity",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 717.5468978881836,
-                            "height": 84.00003051757812,
-                            "left": 448.46874237060547,
-                            "right": 608.4687728881836,
-                            "top": 633.5468673706055,
-                            "width": 160.00003051757812,
-                            "x": 448.46874237060547,
-                            "y": 633.5468673706055
+                            "left": 304.6180725097656,
+                            "top": 659.6180877685547
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "39d9897f-14c7-476a-a85d-08425745e5a3",
+                        "uuid": "be000472-cc47-456f-8791-b62c1a6308ec",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "66e6bfc3-7f7f-415b-91be-a8d5deabe21f"
+                                "uuid": "42e60127-395b-451f-a31c-191f6f82f2e0"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.0-0",
                         "errors": null,
-                        "id": 2,
+                        "id": 3,
                         "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "metaQuantome: database",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Trimmed_ref_5000_uniprot_cRAP.fasta"
+                                "name": "outfile",
+                                "type": "tar"
                             }
                         ],
-                        "label": "Trimmed_ref_5000_uniprot_cRAP.fasta",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 186.8125,
-                            "height": 84,
-                            "left": 2539.6719360351562,
-                            "right": 2699.6719360351562,
-                            "top": 102.8125,
-                            "width": 160,
-                            "x": 2539.6719360351562,
-                            "y": 102.8125
+                            "left": 293.2986145019531,
+                            "top": 780.0000152587891
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "4ae4a7cf-adbd-4529-b4a5-e3a37d7c0120",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.0-0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "860429737408",
+                            "name": "metaquantome_db",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"databases\": [\"ncbi\", \"go\", \"ec\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
+                        "type": "tool",
+                        "uuid": "25b0969d-52fb-4942-b37f-d9bfb88d048b",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "f8446100-0e31-437c-a642-27c70ec4d7ef"
+                                "output_name": "outfile",
+                                "uuid": "4136ae07-b54f-4dea-bb43-b79259ea1df2"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.0-0",
                         "errors": null,
-                        "id": 3,
+                        "id": 4,
                         "input_connections": {
-                            "library|input_1": {
-                                "id": 0,
+                            "db_tar": {
+                                "id": 3,
+                                "output_name": "outfile"
+                            },
+                            "int_file": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "mode_args|tax_file": {
+                                "id": 1,
                                 "output_name": "output"
+                            },
+                            "samps": {
+                                "id": 0,
+                                "output_name": "samples_file"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "HISAT2",
+                        "name": "metaQuantome: expand",
                         "outputs": [
                             {
-                                "name": "output_alignments",
-                                "type": "bam"
+                                "name": "outfile",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 504.17813873291016,
-                            "height": 109.60000610351562,
-                            "left": 716.5000152587891,
-                            "right": 876.5000152587891,
-                            "top": 394.57813262939453,
-                            "width": 160,
-                            "x": 716.5000152587891,
-                            "y": 394.57813262939453
+                            "left": 595.2430725097656,
+                            "top": 528.0034942626953
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.0-0",
                         "tool_shed_repository": {
-                            "changeset_revision": "a86e80d3c09c",
-                            "name": "hisat2",
-                            "owner": "iuc",
+                            "changeset_revision": "4187b6df1a40",
+                            "name": "metaquantome_expand",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"input_options\": {\"input_options_selector\": \"defaults\", \"__current_case__\": 0}, \"alignment_options\": {\"alignment_options_selector\": \"defaults\", \"__current_case__\": 0}, \"scoring_options\": {\"scoring_options_selector\": \"defaults\", \"__current_case__\": 0}, \"spliced_options\": {\"spliced_options_selector\": \"defaults\", \"__current_case__\": 0}, \"reporting_options\": {\"reporting_options_selector\": \"defaults\", \"__current_case__\": 0}, \"output_options\": {\"output_options_selector\": \"defaults\", \"__current_case__\": 0}, \"other_options\": {\"other_options_selector\": \"defaults\", \"__current_case__\": 0}}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"rna_strandness\": \"\"}, \"reference_genome\": {\"source\": \"indexed\", \"__current_case__\": 0, \"index\": \"mm10\"}, \"sum\": {\"new_summary\": \"false\", \"summary_file\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"__input_ext\": \"tar\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"db_tar\": {\"__class__\": \"ConnectedValue\"}, \"int_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"t\", \"__current_case__\": 1, \"tax_file\": {\"__class__\": \"ConnectedValue\"}, \"pep_colname_tax\": \"peptide\", \"tax_colname\": \"taxon_id\"}, \"pep_colname_int\": \"peptide\", \"samps\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
                         "type": "tool",
-                        "uuid": "6ebfb19c-ad93-4506-96f8-8c6ecbff76d0",
+                        "uuid": "6d9549b9-849e-4412-8a51-1aa88f34eb8c",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_alignments",
-                                "uuid": "e3257606-a1f4-4a0e-9cfa-f2a5a5aee993"
+                                "output_name": "outfile",
+                                "uuid": "8cc0c4b0-53d3-40b0-aae4-609a33c3de73"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.0-0",
                         "errors": null,
-                        "id": 4,
+                        "id": 5,
                         "input_connections": {
-                            "infile": {
-                                "id": 1,
-                                "output_name": "output"
+                            "expand_file": {
+                                "id": 4,
+                                "output_name": "outfile"
+                            },
+                            "samps": {
+                                "id": 0,
+                                "output_name": "samples_file"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "metaQuantome: filter",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool Replace Text",
-                                "name": "infile"
+                                "name": "outfile",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "Editing GTF File",
-                        "name": "Replace Text",
+                        "position": {
+                            "left": 626.2674255371094,
+                            "top": 899.0104522705078
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.0-0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "a1daafbf5233",
+                            "name": "metaquantome_filter",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"expand_file\": {\"__class__\": \"ConnectedValue\"}, \"min_child_nsamp\": \"1\", \"min_children_non_leaf\": \"2\", \"min_pep_nsamp\": \"1\", \"min_peptides\": \"1\", \"mode_args\": {\"mode\": \"t\", \"__current_case__\": 1}, \"qthreshold\": \"2\", \"samps\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
+                        "type": "tool",
+                        "uuid": "afab6ea9-b83d-426f-badc-14ca1e4596d9",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "6d31b51a-5045-4a68-ba38-507d06331904"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.0-0",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "file": {
+                                "id": 5,
+                                "output_name": "outfile"
+                            },
+                            "samps": {
+                                "id": 0,
+                                "output_name": "samples_file"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "metaQuantome: stat",
                         "outputs": [
                             {
                                 "name": "outfile",
-                                "type": "input"
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 949.1468658447266,
-                            "height": 109.5999755859375,
-                            "left": 715.5625152587891,
-                            "right": 875.5625152587891,
-                            "top": 839.5468902587891,
-                            "width": 160,
-                            "x": 715.5625152587891,
-                            "y": 839.5468902587891
+                            "left": 890.2951354980469,
+                            "top": 523.9930877685547
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutfile": {
-                                "action_arguments": {
-                                    "newname": "Edited_Mus_Musculus.GRCm38.86"
-                                },
-                                "action_type": "RenameDatasetAction",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.0-0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "b648e45fd3cf",
+                            "name": "metaquantome_stat",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"control_group\": \"T2\", \"file\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"t\", \"__current_case__\": 1}, \"paired\": \"true\", \"parametric\": \"True\", \"samps\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
+                        "type": "tool",
+                        "uuid": "06bf363c-be87-4342-b803-38e5b0b9b1e0",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "b66b5425-b16e-4034-899e-033f15f94bbf"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "infile": {
+                                "id": 6,
                                 "output_name": "outfile"
+                            },
+                            "samps": {
+                                "id": 0,
+                                "output_name": "samples_file"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+                        "inputs": [],
+                        "label": "T2-Bar-Plot",
+                        "name": "metaQuantome: visualize",
+                        "outputs": [
+                            {
+                                "name": "wrapped_outfile",
+                                "type": "html"
+                            },
+                            {
+                                "name": "plotdata",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 1236.3020935058594,
+                            "top": 200.00000762939453
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
                         "tool_shed_repository": {
-                            "changeset_revision": "a6f147a050a2",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "eb811f3018ea",
+                            "name": "metaquantome_viz",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"infile\": {\"__class__\": \"RuntimeValue\"}, \"replacements\": [{\"__index__\": 0, \"column\": \"1\", \"find_pattern\": \"^([1-9][0-9]*)$\", \"replace_pattern\": \"chr\\\\\\\\1\"}, {\"__index__\": 1, \"column\": \"1\", \"find_pattern\": \"^([XY])$\", \"replace_pattern\": \"chr\\\\\\\\1\"}, {\"__index__\": 2, \"column\": \"1\", \"find_pattern\": \"^MT$\", \"replace_pattern\": \"chrM\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"t\", \"__current_case__\": 1, \"plot\": {\"plottype\": \"bar\", \"__current_case__\": 0, \"target_rank\": \"genus\", \"meancol\": \"T2_mean\", \"nterms\": \"5\", \"barcol\": \"1\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
                         "type": "tool",
-                        "uuid": "1771bf89-9c60-4d45-bbf9-15c937b5aa3a",
+                        "uuid": "403554ac-e02a-423c-8342-a2813b4f160a",
                         "workflow_outputs": [
                             {
-                                "label": "chr_corrected_gtf",
-                                "output_name": "outfile",
-                                "uuid": "70b6f719-803f-4fa9-8394-a3b64b71ec01"
+                                "label": null,
+                                "output_name": "plotdata",
+                                "uuid": "0f00b678-12ee-40a4-919a-736998f1da10"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "wrapped_outfile",
+                                "uuid": "5ce4440c-d524-47a1-a990-069824a9c20e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
                         "errors": null,
-                        "id": 5,
+                        "id": 8,
                         "input_connections": {
-                            "input": {
-                                "id": 2,
-                                "output_name": "output"
+                            "infile": {
+                                "id": 6,
+                                "output_name": "outfile"
+                            },
+                            "samps": {
+                                "id": 0,
+                                "output_name": "samples_file"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "FASTA-to-Tabular",
+                        "label": "T7-T2_volcano-plot",
+                        "name": "metaQuantome: visualize",
                         "outputs": [
                             {
-                                "name": "output",
+                                "name": "wrapped_outfile",
+                                "type": "html"
+                            },
+                            {
+                                "name": "plotdata",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 209.8312530517578,
-                            "height": 92.80000305175781,
-                            "left": 2793.7655639648438,
-                            "right": 2953.7655639648438,
-                            "top": 117.03125,
-                            "width": 160,
-                            "x": 2793.7655639648438,
-                            "y": 117.03125
+                            "left": 931.5625915527344,
+                            "top": 947.6042022705078
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
                         "tool_shed_repository": {
-                            "changeset_revision": "7e801ab2b70e",
-                            "name": "fasta_to_tabular",
-                            "owner": "devteam",
+                            "changeset_revision": "eb811f3018ea",
+                            "name": "metaquantome_viz",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"descr_columns\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"t\", \"__current_case__\": 1, \"plot\": {\"plottype\": \"volcano\", \"__current_case__\": 1, \"fc_name\": \"log2fc_T7_over_T2\", \"fc_corr_p\": \"corrected_p_T7_over_T2\", \"textannot\": \"\", \"flip_fc\": \"false\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
                         "type": "tool",
-                        "uuid": "1c90c734-44df-433a-8431-da0dae1e46d0",
+                        "uuid": "56b5e0c8-654f-48a1-80f2-5dee80f2ea28",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "55a4c3db-64ee-4631-aecd-11e9dc0d8bac"
+                                "output_name": "plotdata",
+                                "uuid": "8a5b5357-fdf6-4a08-80fc-ccc961e197d3"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "wrapped_outfile",
+                                "uuid": "1885e756-240c-4c52-9a92-3031c86fa28b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
                         "errors": null,
-                        "id": 6,
+                        "id": 9,
                         "input_connections": {
-                            "reference_source|batchmode|input_bams": {
-                                "id": 3,
-                                "output_name": "output_alignments"
+                            "infile": {
+                                "id": 6,
+                                "output_name": "outfile"
+                            },
+                            "samps": {
+                                "id": 0,
+                                "output_name": "samples_file"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "FreeBayes",
+                        "label": "T4-Bar-Plot",
+                        "name": "metaQuantome: visualize",
                         "outputs": [
                             {
-                                "name": "output_vcf",
-                                "type": "vcf"
+                                "name": "wrapped_outfile",
+                                "type": "html"
+                            },
+                            {
+                                "name": "plotdata",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 534.3468780517578,
-                            "height": 92.80001831054688,
-                            "left": 1046.5625,
-                            "right": 1206.5625,
-                            "top": 441.54685974121094,
-                            "width": 160,
-                            "x": 1046.5625,
-                            "y": 441.54685974121094
+                            "left": 1236.3020935058594,
+                            "top": 540.0000152587891
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
                         "tool_shed_repository": {
-                            "changeset_revision": "ef2c525bd8cd",
-                            "name": "freebayes",
-                            "owner": "devteam",
+                            "changeset_revision": "eb811f3018ea",
+                            "name": "metaquantome_viz",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"coverage_options\": {\"coverage_options_selector\": \"do_not_set\", \"__current_case__\": 1}, \"options_type\": {\"options_type_selector\": \"simple\", \"__current_case__\": 1}, \"reference_source\": {\"reference_source_selector\": \"cached\", \"__current_case__\": 0, \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_bams\": {\"__class__\": \"ConnectedValue\"}}, \"ref_file\": \"mm10full\"}, \"target_limit_type\": {\"target_limit_type_selector\": \"do_not_limit\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"t\", \"__current_case__\": 1, \"plot\": {\"plottype\": \"bar\", \"__current_case__\": 0, \"target_rank\": \"genus\", \"meancol\": \"T4_mean\", \"nterms\": \"5\", \"barcol\": \"1\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
                         "type": "tool",
-                        "uuid": "c02258e7-9b87-4a32-9a49-a4edb44a293f",
+                        "uuid": "a4d4199a-6fac-4027-9403-317561ea3ca0",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_vcf",
-                                "uuid": "3ce080ca-cae9-457f-8606-4357fd9c5736"
+                                "output_name": "wrapped_outfile",
+                                "uuid": "5db21144-afd7-486a-ad2e-e2186ccb2759"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "plotdata",
+                                "uuid": "a6fb4b9a-b0fb-4a0e-af13-6cd78d2a804b"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {
+                            "infile": {
+                                "id": 6,
+                                "output_name": "outfile"
+                            },
+                            "samps": {
+                                "id": 0,
+                                "output_name": "samples_file"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "T7-Bar-Plot",
+                        "name": "metaQuantome: visualize",
+                        "outputs": [
+                            {
+                                "name": "wrapped_outfile",
+                                "type": "html"
+                            },
+                            {
+                                "name": "plotdata",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 1244.3056335449219,
+                            "top": 834.0104522705078
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "eb811f3018ea",
+                            "name": "metaquantome_viz",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"t\", \"__current_case__\": 1, \"plot\": {\"plottype\": \"bar\", \"__current_case__\": 0, \"target_rank\": \"genus\", \"meancol\": \"T7_mean\", \"nterms\": \"5\", \"barcol\": \"1\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
+                        "type": "tool",
+                        "uuid": "3e71e1e5-5f29-4e02-87d4-431a93d72eb0",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "wrapped_outfile",
+                                "uuid": "c49669b7-f4c9-4e84-89bf-86484a3e11d0"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "plotdata",
+                                "uuid": "b17119dd-9b47-40ba-9610-53f1fbffab04"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
+                        "errors": null,
+                        "id": 11,
+                        "input_connections": {
+                            "infile": {
+                                "id": 6,
+                                "output_name": "outfile"
+                            },
+                            "samps": {
+                                "id": 0,
+                                "output_name": "samples_file"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "T4-T2_volcano-plot",
+                        "name": "metaQuantome: visualize",
+                        "outputs": [
+                            {
+                                "name": "wrapped_outfile",
+                                "type": "html"
+                            },
+                            {
+                                "name": "plotdata",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 1275.2778015136719,
+                            "top": 1161.0069732666016
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "eb811f3018ea",
+                            "name": "metaquantome_viz",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"t\", \"__current_case__\": 1, \"plot\": {\"plottype\": \"volcano\", \"__current_case__\": 1, \"fc_name\": \"log2fc_T4_over_T2\", \"fc_corr_p\": \"corrected_p_T4_over_T2\", \"textannot\": \"\", \"flip_fc\": \"false\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
+                        "type": "tool",
+                        "uuid": "6d7fa5d9-4ece-4f7c-9a5c-21366e78b7de",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "wrapped_outfile",
+                                "uuid": "c06ba8b9-d6ae-409a-8418-01a21e80c209"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "plotdata",
+                                "uuid": "f18da0f4-0758-472d-94fa-737119726861"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "proteomics/metaquantome-taxonomy",
+                "path": "topics/proteomics/tutorials/metaquantome-taxonomy/workflows/main_workflow.ga",
+                "tags": [
+                    "proteomics"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "metaquantome-taxonomy-workflow",
+                "topic_id": "proteomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-metaquantome-taxonomy/versions/main-workflow",
+                "tutorial_id": "metaquantome-taxonomy",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaquantome-taxonomy/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaquantome-taxonomy/workflows/main_workflow.html",
+                "version": 2,
+                "wfid": "proteomics-metaquantome-taxonomy",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.0-0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.0-0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.0-0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.0-0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.0-0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0"
+                ],
+                "workflowhub_id": "1155"
+            }
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.4110725"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_to_tabular",
+                    "owner": "devteam",
+                    "revisions": "7e801ab2b70e",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "dbbuilder",
+                    "owner": "galaxyp",
+                    "revisions": "983bf725dfc2",
+                    "tool_panel_section_label": "Get Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_merge_files_and_filter_unique_sequences",
+                    "owner": "galaxyp",
+                    "revisions": "f546e7278f04",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "maxquant",
+                    "owner": "galaxyp",
+                    "revisions": "9c52362ae7bb",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "msconvert",
+                    "owner": "galaxyp",
+                    "revisions": "6153e8ada1ee",
+                    "tool_panel_section_label": "Convert Formats",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "peptideshaker",
+                    "owner": "galaxyp",
+                    "revisions": "3ec27b4cee7c",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "peptideshaker",
+                    "owner": "galaxyp",
+                    "revisions": "3ec27b4cee7c",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "peptideshaker",
+                    "owner": "galaxyp",
+                    "revisions": "3ec27b4cee7c",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "peptideshaker",
+                    "owner": "galaxyp",
+                    "revisions": "3ec27b4cee7c",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "filter_tabular",
+                    "owner": "iuc",
+                    "revisions": "557ec8d7087d",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "query_tabular",
+                    "owner": "iuc",
+                    "revisions": "cf34c344508d",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_to_tabular\n  owner: devteam\n  revisions: 7e801ab2b70e\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dbbuilder\n  owner: galaxyp\n  revisions: 983bf725dfc2\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_merge_files_and_filter_unique_sequences\n  owner: galaxyp\n  revisions: f546e7278f04\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maxquant\n  owner: galaxyp\n  revisions: 9c52362ae7bb\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msconvert\n  owner: galaxyp\n  revisions: 6153e8ada1ee\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 3ec27b4cee7c\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 3ec27b4cee7c\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 3ec27b4cee7c\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 3ec27b4cee7c\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filter_tabular\n  owner: iuc\n  revisions: 557ec8d7087d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n  owner: iuc\n  revisions: cf34c344508d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "subinamehta",
+                "katherine-d21",
+                "dechendb"
+            ],
+            "editing": [
+                "pratikdjagtap",
+                "timothygriffin"
+            ]
+        },
+        "contributors": [
+            {
+                "email": "subinamehta@gmail.com",
+                "id": "subinamehta",
+                "joined": "2018-06",
+                "linkedin": "subinamehta",
+                "matrix": "subinamehta:matrix.org",
+                "name": "Subina Mehta",
+                "orcid": "0000-0001-9818-0537",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
+                "twitter": "Subina_Mehta",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
+            },
+            {
+                "id": "katherine-d21",
+                "joined": "2023-08",
+                "name": "Katherine Do",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/katherine-d21/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/katherine-d21.json"
+            },
+            {
+                "id": "dechendb",
+                "joined": "2023-06",
+                "name": "Dechen Bhuming",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dechendb/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/dechendb.json"
+            },
+            {
+                "email": "pjagtap@umn.edu",
+                "id": "pratikdjagtap",
+                "joined": "2017-09",
+                "name": "Pratik Jagtap",
+                "orcid": "0000-0003-0984-0973",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
+            },
+            {
+                "email": "tgriffin@umn.edu",
+                "github": false,
+                "id": "timothygriffin",
+                "joined": "2017-09",
+                "name": "Timothy J. Griffin",
+                "orcid": "0000-0001-6801-2559",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
+            }
+        ],
+        "dir": "topics/proteomics/tutorials/clinical-mp-2-discovery",
+        "edam_operation": [
+            "Principal component plotting",
+            "Visualisation",
+            "Clustering",
+            "Protein quantification",
+            "Standardisation and normalisation",
+            "Imputation",
+            "Statistical calculation",
+            "Heat map generation",
+            "Filtering",
+            "Formatting"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "proteomics",
+                "tutorials": [
+                    "clinical-mp-3-verification"
+                ],
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "proteomics/clinical-mp-2-discovery",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Employ SearchGUI/PeptideShaker and MaxQuant for database searching",
+            "Extraction of confident microbial peptides for verification"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-08-08",
+        "objectives": [
+            "Perform Database searching using two algorithms",
+            "Extract confident peptides and proteins",
+            "Generate a microbial peptide panel for verification"
+        ],
+        "pageviews": 166,
+        "pub_date": "2024-02-06",
+        "questions": [
+            "How to perform database searching?",
+            "How to extract microbial and Human protein and peptide sequences from the results"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "katherine-d21"
+                ],
+                "date": "2024-06-21",
+                "galaxy_version": "23.1",
+                "length": "16M",
+                "speakers": [
+                    "katherine-d21"
+                ],
+                "youtube_id": "5Pg9LLfFGX4"
+            }
+        ],
+        "redirect_from": [
+            "/topics/proteomics/tutorials/clinical-mp-discovery/tutorial",
+            "/short/proteomics/clinical-mp-2-discovery",
+            "/short/T00414"
+        ],
+        "requirements": [
+            {
+                "topic_name": "proteomics",
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00414",
+        "short_tools": [
+            "query_tabular",
+            "tp_cat",
+            "fasta_merge_files_and_filter_unique_sequences",
+            "filter_tabular",
+            "Filter1",
+            "dbbuilder",
+            "peptide_shaker",
+            "ident_params",
+            "msconvert",
+            "search_gui",
+            "Grep1",
+            "Cut1",
+            "maxquant",
+            "Remove beginning1",
+            "fasta2tab",
+            "fasta_cli",
+            "Grouping1"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "clinical-metaproteomics",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "label-TMT11"
+        ],
+        "time_estimation": "3H",
+        "title": "Clinical Metaproteomics 2: Discovery",
+        "tools": [
+            "Cut1",
+            "Filter1",
+            "Grep1",
+            "Grouping1",
+            "Remove beginning1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/2.0.3.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/fasta_cli/4.0.41+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/ident_params/4.0.41+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/2.0.33+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/4.0.41+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0"
+        ],
+        "topic_name": "proteomics",
+        "topic_name_human": "Proteomics",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "clinical-mp-2-discovery",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-2-discovery/tutorial.json"
+        },
+        "version": 2,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 432,
+        "visitors": 111,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Organization",
+                        "identifier": "0000-0001-9818-0537",
+                        "name": "Subina Mehta"
+                    }
+                ],
+                "description": "Discovery workflow with SG/PS and MaxQuant to generate microbial peptides",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHuman UniProt Microbial Proteins from MetaNovo and cRAP \"]\n  1[label=\"Identification Parameters: PAR file\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nRAW files Dataset Collection\"]\n  3[label=\"Human SwissProt reviewed only\"]\n  ke0de9f90a7104b55af6241ba1c2d8e1f[color=lightseagreen,label=\"Output\\nHuman SwissProt (reviewed only)\"]\n  3 -> ke0de9f90a7104b55af6241ba1c2d8e1f\n  4[label=\"Contaminants cRAP\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nExperimental Design Discovery MaxQuant\"]\n  6[label=\"FastaCLI__MetaNovo_Human_SwissProt_cRAP_with_decoys_on_data_1_MetaNovo_Human_SwissProt_cRAP_concatenated_target_decoy.fasta\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"msconvert\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"Human SwissProt+cRAP\"]\n  3 -> 8 [label=\"output_database\"]\n  4 -> 8 [label=\"output_database\"]\n  k2f14902fb0054c08b6d16d7ee0b4b199[color=lightseagreen,label=\"Output\\nHuman SwissProt+cRAP\"]\n  8 -> k2f14902fb0054c08b6d16d7ee0b4b199\n  9[label=\"MaxQuant\"]\n  0 -> 9 [label=\"output\"]\n  2 -> 9 [label=\"output\"]\n  5 -> 9 [label=\"output\"]\n  10[label=\"Search GUI\"]\n  6 -> 10 [label=\"input_database_concatenated_target_decoy\"]\n  1 -> 10 [label=\"Identification_Parameters_File\"]\n  7 -> 10 [label=\"output\"]\n  11[label=\"FASTA-to-Tabular\"]\n  8 -> 11 [label=\"output\"]\n  12[label=\"Select microbial peptides MQ\"]\n  9 -> 12 [label=\"peptides\"]\n  kd7718bab9e754729bfb603bc3112a0e2[color=lightseagreen,label=\"Output\\nSelect microbial peptides (MQ)\"]\n  12 -> kd7718bab9e754729bfb603bc3112a0e2\n  13[label=\"Peptide Shaker\"]\n  10 -> 13 [label=\"searchgui_results\"]\n  14[label=\"Filter Tabular\"]\n  11 -> 14 [label=\"output\"]\n  15[label=\"MQ Peptide Sequences\"]\n  12 -> 15 [label=\"out_file1\"]\n  16[label=\"Select microbial peptides SGPS\"]\n  13 -> 16 [label=\"output_peptides\"]\n  k14fd9080df924c61b1f13f700a166700[color=lightseagreen,label=\"Output\\nSelect microbial peptides (SGPS)\"]\n  16 -> k14fd9080df924c61b1f13f700a166700\n  17[label=\"Select microbial PSMs\"]\n  13 -> 17 [label=\"output_psm\"]\n  18[label=\"Remove beginning\"]\n  15 -> 18 [label=\"out_file1\"]\n  19[label=\"Filter confident microbial peptides\"]\n  16 -> 19 [label=\"out_file1\"]\n  k1c6c953fd1924953938a9f401315bc0d[color=lightseagreen,label=\"Output\\nFilter confident microbial peptides\"]\n  19 -> k1c6c953fd1924953938a9f401315bc0d\n  20[label=\"Filter confident microbial PSMs\"]\n  17 -> 20 [label=\"out_file1\"]\n  kd8ec7f0c7ba14733a3dc74a9ef298dc2[color=lightseagreen,label=\"Output\\nFilter confident microbial PSMs\"]\n  20 -> kd8ec7f0c7ba14733a3dc74a9ef298dc2\n  21[label=\"MQ Distinct Peptides\"]\n  18 -> 21 [label=\"out_file1\"]\n  k07cae0170b394065b83eb5f2e27fe740[color=lightseagreen,label=\"Output\\nMQ Peptides\"]\n  21 -> k07cae0170b394065b83eb5f2e27fe740\n  22[label=\"Query Tabular\"]\n  20 -> 22 [label=\"out_file1\"]\n  20 -> 22 [label=\"out_file1\"]\n  14 -> 22 [label=\"output\"]\n  23[label=\"Cut\"]\n  22 -> 23 [label=\"output\"]\n  24[label=\"SGPS Distinct Peptides\"]\n  23 -> 24 [label=\"out_file1\"]\n  kb6c61697ff5243c08fb4765d7b4204cc[color=lightseagreen,label=\"Output\\nSGPS Distinct Peptides\"]\n  24 -> kb6c61697ff5243c08fb4765d7b4204cc\n  25[label=\"SGPS-MQ Peptides\"]\n  21 -> 25 [label=\"out_file1\"]\n  24 -> 25 [label=\"out_file1\"]\n  ka8c2de2ee32248309d282f79bf937013[color=lightseagreen,label=\"Output\\nSGPS-MQ Peptides\"]\n  25 -> ka8c2de2ee32248309d282f79bf937013\n  26[label=\"Distinct Peptides\"]\n  25 -> 26 [label=\"out_file1\"]\n  kef0d91b1042f4a9fa2b6bf73d82f24f7[color=lightseagreen,label=\"Output\\nDistinct Peptides\"]\n  26 -> kef0d91b1042f4a9fa2b6bf73d82f24f7\n}",
+                "history": [
+                    {
+                        "hash": "e0464fd1787b4ca7dea72ca77b7ab2ad03a8292a",
+                        "message": "add workflows",
+                        "num": 1,
+                        "short_hash": "e0464fd17",
+                        "unix": "1723118192"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "FastaCLI: MetaNovo Human SwissProt cRAP with decoys on data 1 (MetaNovo Human SwissProt cRAP_concatenated_target_decoy) (49,076 sequences)",
+                        "content_id": null,
                         "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "guide|guide_source|ref_hist": {
-                                "id": 4,
-                                "output_name": "outfile"
-                            },
-                            "input_bam": {
-                                "id": 3,
-                                "output_name": "output_alignments"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "StringTie",
-                        "outputs": [
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output_gtf",
-                                "type": "gtf"
+                                "description": "FastaCLI: MetaNovo Human SwissProt cRAP with decoys on data 1 (MetaNovo Human SwissProt cRAP_concatenated_target_decoy) (49,076 sequences)",
+                                "name": "Human UniProt Microbial Proteins (from MetaNovo) and cRAP "
                             }
                         ],
+                        "label": "Human UniProt Microbial Proteins (from MetaNovo) and cRAP ",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 808.7781372070312,
-                            "height": 151.20001220703125,
-                            "left": 1039.53125,
-                            "right": 1199.53125,
-                            "top": 657.578125,
-                            "width": 160,
-                            "x": 1039.53125,
-                            "y": 657.578125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "1ebd14235b92",
-                            "name": "stringtie",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 249.51593017578125,
+                            "top": 272.60801696777344
                         },
-                        "tool_state": "{\"__input_ext\": \"bam\", \"adv\": {\"abundance_estimation\": \"false\", \"omit_sequences\": \"\", \"name_prefix\": \"\", \"fraction\": \"0.15\", \"min_tlen\": \"200\", \"min_anchor_len\": \"10\", \"min_anchor_cov\": \"1\", \"min_bundle_cov\": \"2\", \"bdist\": \"50\", \"bundle_fraction\": \"0.95\", \"disable_trimming\": \"false\", \"multi_mapping\": \"false\"}, \"chromInfo\": \"/panfs/roc/website/galaxyp.msi.umn.edu/galaxy/tool-data/shared/ucsc/chrom/mm10.len\", \"guide\": {\"use_guide\": \"yes\", \"__current_case__\": 1, \"guide_source\": {\"guide_gff_select\": \"history\", \"__current_case__\": 1, \"ref_hist\": {\"__class__\": \"ConnectedValue\"}}, \"input_estimation\": \"false\", \"special_outputs\": {\"special_outputs_select\": \"no\", \"__current_case__\": 2}, \"coverage_file\": \"false\"}, \"input_bam\": {\"__class__\": \"ConnectedValue\"}, \"long_reads\": \"false\", \"rna_strandness\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "fad69441-c09f-410c-8c49-34832d8e297d",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_gtf",
-                                "uuid": "12837520-843e-49c1-be1e-06a44985c2b9"
-                            }
-                        ]
+                        "type": "data_input",
+                        "uuid": "c0c1c1cf-e899-4b8e-b1b1-6a4f24d87ad1",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "input": {
-                                "id": 5,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Filter Tabular",
-                        "outputs": [
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "RAW files (Dataset Collection)"
                             }
                         ],
+                        "label": "RAW files (Dataset Collection)",
+                        "name": "Input dataset collection",
+                        "outputs": [],
                         "position": {
-                            "bottom": 252.8000030517578,
-                            "height": 92.80000305175781,
-                            "left": 3066.40625,
-                            "right": 3226.40625,
-                            "top": 160,
-                            "width": 160,
-                            "x": 3066.40625,
-                            "y": 160
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "34d29339abab",
-                            "name": "filter_tabular",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 833.7075958251953
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"select_columns\", \"__current_case__\": 7, \"columns\": \"1\"}}, {\"__index__\": 1, \"filter\": {\"filter_type\": \"replace\", \"__current_case__\": 8, \"column\": \"1\", \"regex_pattern\": \"^[^|]+[|]([^| ]+).*$\", \"regex_replace\": \"\\\\1\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"thermo.raw\"], \"tag\": null, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "067ce402-0494-4d31-860f-50097b76449d",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "adbd3988-0a8e-409c-b1b2-4939fe9611a4"
-                            }
-                        ]
+                        "type": "data_collection_input",
+                        "uuid": "c0f85358-244a-4254-ac94-e920a6cdbe39",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.22.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "genome_annotation|bamInput": {
-                                "id": 3,
-                                "output_name": "output_alignments"
-                            },
-                            "genome_annotation|vcfInput": {
-                                "id": 6,
-                                "output_name": "output_vcf"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "CustomProDB",
-                        "outputs": [
-                            {
-                                "name": "output_rpkm",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "output_snv",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "output_indel",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "output_variant_annotation_rdata",
-                                "type": "rdata"
-                            },
-                            {
-                                "name": "output_genomic_mapping_sqlite",
-                                "type": "sqlite"
-                            },
+                        "id": 5,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output_variant_annotation_sqlite",
-                                "type": "sqlite"
+                                "description": "",
+                                "name": "Experimental Design Discovery MaxQuant"
                             }
                         ],
+                        "label": "Experimental Design Discovery MaxQuant",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 391.89999198913574,
-                            "height": 342.3999938964844,
-                            "left": 1294.6719360351562,
-                            "right": 1454.6719360351562,
-                            "top": 49.49999809265137,
-                            "width": 160,
-                            "x": 1294.6719360351562,
-                            "y": 49.49999809265137
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.22.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2c7df0077d28",
-                            "name": "custom_pro_db",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 881.6298217773438,
+                            "top": 922.0535430908203
                         },
-                        "tool_state": "{\"genome_annotation\": {\"source\": \"builtin\", \"__current_case__\": 0, \"builtin\": \"mm10_GRCm38.p5\", \"bamInput\": {\"__class__\": \"ConnectedValue\"}, \"vcfInput\": {\"__class__\": \"ConnectedValue\"}, \"dbsnpInCoding\": \"false\", \"cosmic\": \"false\"}, \"outputIndels\": \"true\", \"outputRData\": \"true\", \"outputSQLite\": \"true\", \"rpkmCutoff\": \"1.0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "3268fd0d-0aa0-45d2-ad2d-2ba443d94a2b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_rpkm",
-                                "uuid": "2e2725cd-de12-4fa3-ae65-dfc52dbe45bf"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_snv",
-                                "uuid": "9dddcd8b-25bc-4bc0-9240-fd3157340cbd"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_indel",
-                                "uuid": "d8ba561c-2dc7-4668-ab3c-8d11a0bbc8db"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_variant_annotation_rdata",
-                                "uuid": "951816e4-4410-4bf9-982c-0604ecfc5a4b"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_genomic_mapping_sqlite",
-                                "uuid": "a856b8cf-185e-435a-8c5c-0e87fa5fb7ac"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_variant_annotation_sqlite",
-                                "uuid": "045869cc-5493-439c-b870-b2be30170137"
-                            }
-                        ]
-                    },
+                        "type": "data_input",
+                        "uuid": "9652a70a-de8c-4966-b7cf-121f1b9f0b54",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nHuman UniProt Microbial Proteins from MetaNovo and cRAP \"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Identification Parameters: PAR file\"];\n  2[\"\u2139\ufe0f Input Collection\\nRAW files Dataset Collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Human SwissProt reviewed only\"];\n  e0de9f90-a710-4b55-af62-41ba1c2d8e1f[\"Output\\nHuman SwissProt (reviewed only)\"];\n  3 --> e0de9f90-a710-4b55-af62-41ba1c2d8e1f;\n  style e0de9f90-a710-4b55-af62-41ba1c2d8e1f stroke:#2c3143,stroke-width:4px;\n  4[\"Contaminants cRAP\"];\n  5[\"\u2139\ufe0f Input Dataset\\nExperimental Design Discovery MaxQuant\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"FastaCLI__MetaNovo_Human_SwissProt_cRAP_with_decoys_on_data_1_MetaNovo_Human_SwissProt_cRAP_concatenated_target_decoy.fasta\"];\n  0 -->|output| 6;\n  7[\"msconvert\"];\n  2 -->|output| 7;\n  8[\"Human SwissProt+cRAP\"];\n  3 -->|output_database| 8;\n  4 -->|output_database| 8;\n  2f14902f-b005-4c08-b6d1-6d7ee0b4b199[\"Output\\nHuman SwissProt+cRAP\"];\n  8 --> 2f14902f-b005-4c08-b6d1-6d7ee0b4b199;\n  style 2f14902f-b005-4c08-b6d1-6d7ee0b4b199 stroke:#2c3143,stroke-width:4px;\n  9[\"MaxQuant\"];\n  0 -->|output| 9;\n  2 -->|output| 9;\n  5 -->|output| 9;\n  10[\"Search GUI\"];\n  6 -->|input_database_concatenated_target_decoy| 10;\n  1 -->|Identification_Parameters_File| 10;\n  7 -->|output| 10;\n  11[\"FASTA-to-Tabular\"];\n  8 -->|output| 11;\n  12[\"Select microbial peptides MQ\"];\n  9 -->|peptides| 12;\n  d7718bab-9e75-4729-bfb6-03bc3112a0e2[\"Output\\nSelect microbial peptides (MQ)\"];\n  12 --> d7718bab-9e75-4729-bfb6-03bc3112a0e2;\n  style d7718bab-9e75-4729-bfb6-03bc3112a0e2 stroke:#2c3143,stroke-width:4px;\n  13[\"Peptide Shaker\"];\n  10 -->|searchgui_results| 13;\n  14[\"Filter Tabular\"];\n  11 -->|output| 14;\n  15[\"MQ Peptide Sequences\"];\n  12 -->|out_file1| 15;\n  16[\"Select microbial peptides SGPS\"];\n  13 -->|output_peptides| 16;\n  14fd9080-df92-4c61-b1f1-3f700a166700[\"Output\\nSelect microbial peptides (SGPS)\"];\n  16 --> 14fd9080-df92-4c61-b1f1-3f700a166700;\n  style 14fd9080-df92-4c61-b1f1-3f700a166700 stroke:#2c3143,stroke-width:4px;\n  17[\"Select microbial PSMs\"];\n  13 -->|output_psm| 17;\n  18[\"Remove beginning\"];\n  15 -->|out_file1| 18;\n  19[\"Filter confident microbial peptides\"];\n  16 -->|out_file1| 19;\n  1c6c953f-d192-4953-938a-9f401315bc0d[\"Output\\nFilter confident microbial peptides\"];\n  19 --> 1c6c953f-d192-4953-938a-9f401315bc0d;\n  style 1c6c953f-d192-4953-938a-9f401315bc0d stroke:#2c3143,stroke-width:4px;\n  20[\"Filter confident microbial PSMs\"];\n  17 -->|out_file1| 20;\n  d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2[\"Output\\nFilter confident microbial PSMs\"];\n  20 --> d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2;\n  style d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2 stroke:#2c3143,stroke-width:4px;\n  21[\"MQ Distinct Peptides\"];\n  18 -->|out_file1| 21;\n  07cae017-0b39-4065-b83e-b5f2e27fe740[\"Output\\nMQ Peptides\"];\n  21 --> 07cae017-0b39-4065-b83e-b5f2e27fe740;\n  style 07cae017-0b39-4065-b83e-b5f2e27fe740 stroke:#2c3143,stroke-width:4px;\n  22[\"Query Tabular\"];\n  20 -->|out_file1| 22;\n  20 -->|out_file1| 22;\n  14 -->|output| 22;\n  23[\"Cut\"];\n  22 -->|output| 23;\n  24[\"SGPS Distinct Peptides\"];\n  23 -->|out_file1| 24;\n  b6c61697-ff52-43c0-8fb4-765d7b4204cc[\"Output\\nSGPS Distinct Peptides\"];\n  24 --> b6c61697-ff52-43c0-8fb4-765d7b4204cc;\n  style b6c61697-ff52-43c0-8fb4-765d7b4204cc stroke:#2c3143,stroke-width:4px;\n  25[\"SGPS-MQ Peptides\"];\n  21 -->|out_file1| 25;\n  24 -->|out_file1| 25;\n  a8c2de2e-e322-4830-9d28-2f79bf937013[\"Output\\nSGPS-MQ Peptides\"];\n  25 --> a8c2de2e-e322-4830-9d28-2f79bf937013;\n  style a8c2de2e-e322-4830-9d28-2f79bf937013 stroke:#2c3143,stroke-width:4px;\n  26[\"Distinct Peptides\"];\n  25 -->|out_file1| 26;\n  ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7[\"Output\\nDistinct Peptides\"];\n  26 --> ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7;\n  style ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "WF2_Discovery-Workflow",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.11.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/ident_params/4.0.41+galaxy1",
                         "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "annotation|ref_source|reference_annotation": {
-                                "id": 4,
-                                "output_name": "outfile"
-                            },
-                            "gffinputs": {
-                                "id": 7,
-                                "output_name": "output_gtf"
-                            }
-                        },
+                        "id": 1,
+                        "input_connections": {},
                         "inputs": [],
-                        "label": null,
-                        "name": "GffCompare",
+                        "label": "Identification Parameters: PAR file",
+                        "name": "Identification Parameters",
                         "outputs": [
                             {
-                                "name": "refmap_output",
-                                "type": "input"
-                            },
-                            {
-                                "name": "tmap_output",
-                                "type": "input"
-                            },
-                            {
-                                "name": "transcripts_stats",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "transcripts_loci",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "transcripts_tracking",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "transcripts_annotated",
-                                "type": "gtf"
+                                "name": "Identification_Parameters_File",
+                                "type": "json"
                             }
                         ],
                         "position": {
-                            "bottom": 1232.715576171875,
-                            "height": 359.199951171875,
-                            "left": 1283.6563110351562,
-                            "right": 1443.6563110351562,
-                            "top": 873.515625,
-                            "width": 160,
-                            "x": 1283.6563110351562,
-                            "y": 873.515625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.11.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "0f710191a66d",
-                            "name": "gffcompare",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"gtf\", \"adv_output\": {\"p\": \"TCONS\", \"C\": \"false\", \"A\": \"false\", \"X\": \"false\", \"K\": \"false\"}, \"annotation\": {\"use_ref_annotation\": \"Yes\", \"__current_case__\": 0, \"ref_source\": {\"ref_source_sel\": \"history\", \"__current_case__\": 1, \"reference_annotation\": {\"__class__\": \"ConnectedValue\"}}, \"ignore_nonoverlapping_reference\": \"false\", \"ignore_nonoverlapping_transfrags\": \"false\", \"strict_match\": \"false\", \"refmap_tmap\": [\"refmap\", \"tmap\"]}, \"chr_stats\": \"false\", \"chromInfo\": \"/panfs/roc/website/galaxyp.msi.umn.edu/galaxy/tool-data/shared/ucsc/chrom/mm10.len\", \"discard_duplicates\": \"\", \"discard_single_exon\": \"\", \"gffinputs\": {\"__class__\": \"ConnectedValue\"}, \"max_dist_exon\": \"100\", \"max_dist_group\": \"100\", \"no_merge\": \"false\", \"seq_data\": {\"use_seq_data\": \"No\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
-                        "type": "tool",
-                        "uuid": "6b917971-f710-4e39-b795-edda6bb0042e",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "transcripts_annotated",
-                                "uuid": "94d389ff-4147-4d17-9a88-ee40b51b1385"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "transcripts_loci",
-                                "uuid": "6572f472-1780-465a-94b1-194bc90100f5"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "transcripts_tracking",
-                                "uuid": "b98508c8-733f-4a08-ad97-4878dea87ec7"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "transcripts_stats",
-                                "uuid": "9b35be89-e7d9-4e01-b410-b5c3006879c8"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "refmap_output",
-                                "uuid": "e9e58252-6620-43f7-88aa-be97ca06eda2"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "tmap_output",
-                                "uuid": "48258492-2e3d-4e61-9789-b2e347306a17"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
-                        "errors": null,
-                        "id": 11,
-                        "input_connections": {
-                            "sqlitedb": {
-                                "id": 9,
-                                "output_name": "output_genomic_mapping_sqlite"
-                            }
+                            "left": 814.9930419921875,
+                            "top": 0
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "SQLite to tabular",
-                        "outputs": [
-                            {
-                                "name": "query_results",
-                                "type": "tabular"
+                        "post_job_actions": {
+                            "RenameDatasetActionIdentification_Parameters_File": {
+                                "action_arguments": {
+                                    "newname": "Identification Parameters (PAR)"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "Identification_Parameters_File"
                             }
-                        ],
-                        "position": {
-                            "bottom": 637.3312377929688,
-                            "height": 92.79998779296875,
-                            "left": 1521.1563110351562,
-                            "right": 1681.1563110351562,
-                            "top": 544.53125,
-                            "width": 160,
-                            "x": 1521.1563110351562,
-                            "y": 544.53125
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/ident_params/4.0.41+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "b722161a845a",
-                            "name": "sqlite_to_tabular",
-                            "owner": "iuc",
+                            "changeset_revision": "3ec27b4cee7c",
+                            "name": "peptideshaker",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"sqlite\", \"chromInfo\": \"/panfs/roc/website/galaxyp.msi.umn.edu/galaxy/tool-data/shared/ucsc/chrom/mm10.len\", \"query_result\": {\"header\": \"no\", \"__current_case__\": 1}, \"sqlitedb\": {\"__class__\": \"ConnectedValue\"}, \"sqlquery\": \"SELECT pro_name, chr_name, cds_chr_start - 1, cds_chr_end,strand,cds_start - 1, cds_end\\n  FROM genomic_mapping\\n  ORDER BY pro_name, cds_start, cds_end\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"advanced_options\": {\"spectrum_annotation_options\": {\"annotation_level\": \"0.75\", \"annotation_mz_tolerance\": \"0.5\", \"annotation_high_resolution\": true}, \"sequence_matching_options\": {\"sequence_matching_type\": \"2\", \"sequence_matching_x\": \"0.25\", \"sequence_matching_enzymatic_tags\": false, \"sequence_matching_max_ptms_per_tag\": \"3\", \"sequence_matching_min_amino_acid_score\": \"30\", \"sequence_matching_min_tag_length\": \"3\"}, \"import_filters_options\": {\"min_peptide_length\": \"8\", \"max_peptide_length\": \"30\", \"max_precursor_error\": \"10.0\", \"max_precursor_error_type\": \"1\", \"missed_cleavages_min\": null, \"missed_cleavages_max\": null, \"exclude_unknown_ptms\": true}, \"ptm_localization_options\": {\"ptm_score\": {\"ptm_score_selector\": \"1\", \"__current_case__\": 0, \"score_neutral_losses\": false, \"ptm_threshold\": \"95.0\"}, \"ptm_sequence_matching_type\": \"1\", \"ptm_alignment\": true}, \"gene_annotation_options\": {\"use_gene_mapping\": false, \"update_gene_mapping\": false}, \"protein_inference_options\": {\"simplify_protein_groups_conditional\": {\"simplify_protein_groups_selector\": \"yes\", \"__current_case__\": 1, \"simplify_protein_groups_evidence\": true, \"simplify_protein_groups_confidence\": true, \"simplify_protein_groups_confidence_threshold\": \"0.05\", \"simplify_protein_groups_enzymaticity\": true, \"simplify_protein_groups_variant\": true}, \"simplify_protein_pi_modifications\": true}, \"validation_levels_options\": {\"protein_fdr\": \"1.0\", \"peptide_fdr\": \"1.0\", \"psm_fdr\": \"1.0\"}, \"fraction_analysis_options\": {\"protein_fraction_mw_confidence\": \"95.0\"}, \"database_processing_options\": {\"decoy_conditional\": {\"create_decoy_selector\": \"yes\", \"__current_case__\": 1, \"decoy_tag\": \"_REVERSED\", \"decoy_type\": \"1\"}, \"decoy_file_tag\": \"_concatenated_target_decoy\"}}, \"searchengines_options\": {\"xtandem\": {\"xtandem_advanced\": \"no\", \"__current_case__\": 0}, \"myrimatch\": {\"myrimatch_advanced\": \"no\", \"__current_case__\": 0}, \"msgf\": {\"msgf_advanced\": \"no\", \"__current_case__\": 0}, \"ms_amanda\": {\"ms_amanda_advanced\": \"no\", \"__current_case__\": 0}, \"omssa\": {\"omssa_advanced\": \"no\", \"__current_case__\": 0}, \"comet\": {\"comet_advanced\": \"no\", \"__current_case__\": 0}, \"tide\": {\"tide_advanced\": \"no\", \"__current_case__\": 0}, \"directtag\": {\"directtag_advanced\": \"no\", \"__current_case__\": 0}, \"metamorpheus\": {\"metamorpheus_advanced\": \"no\", \"__current_case__\": 0}, \"novor\": {\"novor_advanced\": \"no\", \"__current_case__\": 0}, \"pepnovo\": {\"pepnovo_advanced\": \"no\", \"__current_case__\": 0}, \"pnovo\": {\"pnovo_advanced\": \"no\", \"__current_case__\": 0}}, \"spectrum_matching_options\": {\"fixed_modifications\": [\"Carbamidomethylation of C\", \"TMT 11-plex of K+4\", \"TMT 11-plex of peptide N-term\"], \"variable_modifications\": [\"Oxidation of M\"], \"digestion\": {\"cleavage\": \"0\", \"__current_case__\": 0, \"digests\": [{\"__index__\": 0, \"enzyme\": \"Trypsin\", \"missed_cleavages\": \"2\", \"specificity\": \"0\"}]}, \"precursor_ion_tol_units\": \"1\", \"precursor_ion_tol\": \"10.0\", \"fragment_tol_units\": \"0\", \"fragment_tol\": \"0.6\", \"min_charge\": \"2\", \"max_charge\": \"6\", \"forward_ion\": \"b\", \"reverse_ion\": \"y\", \"min_isotope\": \"0\", \"max_isotope\": \"1\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.0.41+galaxy1",
                         "type": "tool",
-                        "uuid": "235f73d3-b7b1-4c7b-956b-e4942ccd8a96",
+                        "uuid": "abaf5892-7976-4526-9cf6-a0c96b9222ea",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "query_results",
-                                "uuid": "78c872b0-6405-4398-a4ce-217b5aea935d"
+                                "output_name": "Identification_Parameters_File",
+                                "uuid": "4a0e51c2-f558-4c3b-bf33-3616f4583771"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
                         "errors": null,
-                        "id": 12,
-                        "input_connections": {
-                            "sqlitedb": {
-                                "id": 9,
-                                "output_name": "output_variant_annotation_sqlite"
-                            }
-                        },
+                        "id": 3,
+                        "input_connections": {},
                         "inputs": [],
-                        "label": null,
-                        "name": "SQLite to tabular",
+                        "label": "Human SwissProt (reviewed only)",
+                        "name": "Protein Database Downloader",
                         "outputs": [
                             {
-                                "name": "query_results",
-                                "type": "tabular"
+                                "name": "output_database",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "bottom": 774.7062683105469,
-                            "height": 92.79998779296875,
-                            "left": 1518.1562805175781,
-                            "right": 1678.1562805175781,
-                            "top": 681.9062805175781,
-                            "width": 160,
-                            "x": 1518.1562805175781,
-                            "y": 681.9062805175781
+                            "left": 634.6446672462531,
+                            "top": 607.9219329733031
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_database": {
+                                "action_arguments": {
+                                    "newname": "Human SwissProt (reviewed only)"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_database"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
                         "tool_shed_repository": {
-                            "changeset_revision": "b722161a845a",
-                            "name": "sqlite_to_tabular",
-                            "owner": "iuc",
+                            "changeset_revision": "983bf725dfc2",
+                            "name": "dbbuilder",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"sqlite\", \"chromInfo\": \"/panfs/roc/website/galaxyp.msi.umn.edu/galaxy/tool-data/shared/ucsc/chrom/mm10.len\", \"query_result\": {\"header\": \"no\", \"__current_case__\": 1}, \"sqlitedb\": {\"__class__\": \"ConnectedValue\"}, \"sqlquery\": \"SELECT var_pro_name,pro_name,cigar,annotation\\nFROM variant_annotation\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"9606\", \"taxon_id\": null, \"reviewed\": \"reviewed:true\", \"set\": \"keyword:KW-1185\", \"include_isoform\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3.4",
                         "type": "tool",
-                        "uuid": "0f9a44cc-2215-4576-96b1-0d58c71972ae",
+                        "uuid": "5b0de886-9f18-4dd2-8e81-4b29467e727a",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "query_results",
-                                "uuid": "a43002ec-42c3-4796-9c37-5fd478a16534"
+                                "label": "Human SwissProt (reviewed only)",
+                                "output_name": "output_database",
+                                "uuid": "e0de9f90-a710-4b55-af62-41ba1c2d8e1f"
                             }
                         ]
                     },
@@ -190859,23 +192781,19 @@
                         "annotation": "",
                         "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
                         "errors": null,
-                        "id": 13,
+                        "id": 8,
                         "input_connections": {
                             "batchmode|input_fastas_0|input_fasta": {
-                                "id": 9,
-                                "output_name": "output_rpkm"
+                                "id": 3,
+                                "output_name": "output_database"
                             },
                             "batchmode|input_fastas_1|input_fasta": {
-                                "id": 9,
-                                "output_name": "output_snv"
-                            },
-                            "batchmode|input_fastas_2|input_fasta": {
-                                "id": 9,
-                                "output_name": "output_indel"
+                                "id": 4,
+                                "output_name": "output_database"
                             }
                         },
                         "inputs": [],
-                        "label": null,
+                        "label": "Human SwissProt+cRAP",
                         "name": "FASTA Merge Files and Filter Unique Sequences",
                         "outputs": [
                             {
@@ -190884,19 +192802,13 @@
                             }
                         ],
                         "position": {
-                            "bottom": 432.9000053405762,
-                            "height": 226.40000915527344,
-                            "left": 1772.6718139648438,
-                            "right": 1932.6718139648438,
-                            "top": 206.49999618530273,
-                            "width": 160,
-                            "x": 1772.6718139648438,
-                            "y": 206.49999618530273
+                            "left": 902.4973253039605,
+                            "top": 577.0886700391638
                         },
                         "post_job_actions": {
                             "RenameDatasetActionoutput": {
                                 "action_arguments": {
-                                    "newname": "CustomProDB_FASTA"
+                                    "newname": "Human SwissProt+cRAP"
                                 },
                                 "action_type": "RenameDatasetAction",
                                 "output_name": "output"
@@ -190909,182 +192821,143 @@
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"accession_parser\": \"^>([^ |]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"uniqueness_criterion\": \"sequence\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"accession_parser\": \"^>([^ ]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"uniqueness_criterion\": \"sequence\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.0",
                         "type": "tool",
-                        "uuid": "5f8e4568-d12e-4a43-86d1-f68fbb3b9da0",
+                        "uuid": "a35c2efa-70f2-41e8-bc46-cb2a245fdf57",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "CustomProDB_FASTA",
+                                "label": "Human SwissProt+cRAP",
                                 "output_name": "output",
-                                "uuid": "a5054be9-dd74-4d60-a4c6-494fdbcb97a1"
+                                "uuid": "2f14902f-b005-4c08-b6d1-6d7ee0b4b199"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/2.0.3.0+galaxy0",
                         "errors": null,
-                        "id": 14,
+                        "id": 9,
                         "input_connections": {
-                            "input": {
-                                "id": 9,
-                                "output_name": "output_rpkm"
+                            "input_opts|fasta_files": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "paramGroups_0|files": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "search_opts|template": {
+                                "id": 5,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "FASTA-to-Tabular",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 75.04999923706055,
-                            "height": 92.79999542236328,
-                            "left": 2794.2657470703125,
-                            "right": 2954.2657470703125,
-                            "top": -17.749996185302734,
-                            "width": 160,
-                            "x": 2794.2657470703125,
-                            "y": -17.749996185302734
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "7e801ab2b70e",
-                            "name": "fasta_to_tabular",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"descr_columns\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
-                        "type": "tool",
-                        "uuid": "3b77287d-b9c2-4bc9-968d-c98db680292f",
-                        "workflow_outputs": [
+                                "description": "runtime parameter for tool MaxQuant",
+                                "name": "input_opts"
+                            },
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "5ec3c54b-c7a8-45b5-99c2-b9768bd8c037"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/gffcompare_to_bed/gffcompare_to_bed/0.2.1",
-                        "errors": null,
-                        "id": 15,
-                        "input_connections": {
-                            "input": {
-                                "id": 10,
-                                "output_name": "transcripts_annotated"
+                                "description": "runtime parameter for tool MaxQuant",
+                                "name": "search_opts"
                             }
-                        },
-                        "inputs": [],
+                        ],
                         "label": null,
-                        "name": "Convert gffCompare annotated GTF to BED",
+                        "name": "MaxQuant",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "bed"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 1182.9781036376953,
-                            "height": 126.39996337890625,
-                            "left": 1517.6406860351562,
-                            "right": 1677.6406860351562,
-                            "top": 1056.578140258789,
-                            "width": 160,
-                            "x": 1517.6406860351562,
-                            "y": 1056.578140258789
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/gffcompare_to_bed/gffcompare_to_bed/0.2.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ba5368c19dbd",
-                            "name": "gffcompare_to_bed",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"gtf\", \"chromInfo\": \"/panfs/roc/website/galaxyp.msi.umn.edu/galaxy/tool-data/shared/ucsc/chrom/mm10.len\", \"class_codes\": [\"j\", \"e\", \"i\", \"p\", \"u\"], \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
-                        "type": "tool",
-                        "uuid": "397b735d-cfc5-4a63-8d8c-3cbda7dcf0ad",
-                        "workflow_outputs": [
+                                "name": "proteinGroups",
+                                "type": "tabular"
+                            },
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "a294134b-17fd-4590-affe-f1363a292ff1"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
-                        "errors": null,
-                        "id": 16,
-                        "input_connections": {
-                            "input": {
-                                "id": 11,
-                                "output_name": "query_results"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Column Regex Find And Replace",
-                        "outputs": [
+                                "name": "mqpar",
+                                "type": "xml"
+                            },
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "peptides",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "msms",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "msmsScans",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "summary",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "log",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "config",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 636.8468475341797,
-                            "height": 92.79998779296875,
-                            "left": 1767.96875,
-                            "right": 1927.96875,
-                            "top": 544.0468597412109,
-                            "width": 160,
-                            "x": 1767.96875,
-                            "y": 544.0468597412109
+                            "left": 1389.0771241398825,
+                            "top": 778.3294605307798
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
+                        "post_job_actions": {
+                            "TagDatasetActionpeptides": {
+                                "action_arguments": {
+                                    "tags": "#MQ_Peptides"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "peptides"
+                            },
+                            "TagDatasetActionproteinGroups": {
+                                "action_arguments": {
+                                    "tags": "#MQ_ProteinGroups"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "proteinGroups"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/2.0.3.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "209b7c5ee9d7",
-                            "name": "regex_find_replace",
+                            "changeset_revision": "9c52362ae7bb",
+                            "name": "maxquant",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \"^(ENS[^_]+_\\\\d+:)([ACGTacgt]+)>([ACGTacgt]+)\\\\s*\", \"replacement\": \"\\\\1\\\\2_\\\\3\"}, {\"__index__\": 1, \"pattern\": \",([A-Y]\\\\d+[A-Y]?)\\\\s*\", \"replacement\": \".\\\\1\"}, {\"__index__\": 2, \"pattern\": \"^(ENS[^ |]*)\\\\s*\", \"replacement\": \"\\\\1\"}], \"field\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"input_opts\": {\"ftype\": \".thermo.raw\", \"fasta_files\": {\"__class__\": \"ConnectedValue\"}, \"identifier_parse_rule\": \">([^\\\\s]*)\", \"description_parse_rule\": \">(.*)\"}, \"output_opts\": {\"dry_run\": false, \"output\": [\"proteinGroups\", \"mqpar\", \"peptides\", \"msms\", \"msmsScans\", \"summary\", \"log\", \"config\"]}, \"paramGroups\": [{\"__index__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}, \"maxMissedCleavages\": \"2\", \"fixedModifications\": [\"Carbamidomethyl (C)\"], \"variableModifications\": [\"Oxidation (M)\"], \"enzymes\": [\"Trypsin/P\"], \"digestion_mode\": \"0\", \"quant_method\": {\"select_quant_method\": \"reporter_ion_ms2\", \"__current_case__\": 3, \"iso_labels\": {\"labeling\": \"tmt11plex\", \"__current_case__\": 4}, \"filter_by_pif\": {\"filter_pif\": \"True\", \"__current_case__\": 0, \"reporter_pif\": \"0.75\"}}}], \"protein_quant\": {\"peptides_for_quantification\": \"1\", \"only_unmod_prot\": {\"unmod_prot\": \"True\", \"__current_case__\": 0, \"mods_used_prot_quant\": [\"Oxidation (M)\"], \"discard_unmod_cpart_peptides\": true}, \"lfq_opts\": {\"separateLfq\": false, \"lfqStabilizeLargeRatios\": true, \"lfqRequireMsms\": true, \"do_ibaq\": {\"ibaq\": \"False\", \"__current_case__\": 1}, \"advancedSiteIntensities\": true}}, \"qc\": {\"do_it\": \"false\", \"__current_case__\": 1}, \"search_opts\": {\"template\": {\"__class__\": \"ConnectedValue\"}, \"min_peptide_len\": \"8\", \"max_peptide_mass\": \"4600\", \"min_unique_pep\": \"0\", \"calc_peak_properties\": false, \"mbr\": {\"match_between_runs\": \"True\", \"__current_case__\": 1, \"matching_time_window\": \"0.7\", \"matching_ion_mobility_window\": \"0.05\", \"alignment_time_window\": \"20\", \"alignment_ion_mobility_window\": \"1\", \"match_unidentified_features\": false}, \"incl_contaminants\": false, \"decoy_mode\": \"revert\", \"psm_fdr\": \"0.01\", \"protein_fdr\": \"0.01\", \"min_pep_length\": \"8\", \"max_pep_length\": \"50\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.3.0+galaxy0",
                         "type": "tool",
-                        "uuid": "286d169c-079e-42a3-beb5-7515c2109f3c",
+                        "uuid": "46c61a69-355c-44ac-9945-0e4d43f0b2ec",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "4ade9d67-ccc6-481c-b749-b3363871ea56"
+                                "output_name": "proteinGroups",
+                                "uuid": "5306e0c0-bd4c-44ea-9f3c-817f959ed3d4"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "peptides",
+                                "uuid": "a2bbaad0-27ba-491c-9462-efd4a1e8efb6"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
+                        "content_id": "Grep1",
                         "errors": null,
-                        "id": 17,
+                        "id": 12,
                         "input_connections": {
                             "input": {
-                                "id": 12,
-                                "output_name": "query_results"
+                                "id": 9,
+                                "output_name": "peptides"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Column Regex Find And Replace",
+                        "label": "Select microbial peptides (MQ)",
+                        "name": "Select",
                         "outputs": [
                             {
                                 "name": "out_file1",
@@ -191092,271 +192965,150 @@
                             }
                         ],
                         "position": {
-                            "bottom": 807.5812530517578,
-                            "height": 92.79998779296875,
-                            "left": 1745.5781555175781,
-                            "right": 1905.5781555175781,
-                            "top": 714.7812652587891,
-                            "width": 160,
-                            "x": 1745.5781555175781,
-                            "y": 714.7812652587891
+                            "left": 1644.1114561742336,
+                            "top": 809.3114768624164
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "209b7c5ee9d7",
-                            "name": "regex_find_replace",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Select microbial peptides (MQ)"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
                         },
-                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \"^(ENS[^_]+_\\\\d+:)([ACGTacgt]+)>([ACGTacgt]+)\\\\s*\", \"replacement\": \"\\\\1\\\\2_\\\\3\"}, {\"__index__\": 1, \"pattern\": \",([A-Y]\\\\d+[A-Y]?)\\\\s*\", \"replacement\": \".\\\\1\"}, {\"__index__\": 2, \"pattern\": \"^(ENS[^ |]*)\\\\s*\", \"replacement\": \"\\\\1\"}], \"field\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_id": "Grep1",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"-v\", \"keep_header\": true, \"pattern\": \"(_HUMAN)|(_REVERSED)|(CON)|(con)\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.4",
                         "type": "tool",
-                        "uuid": "3c96276e-032e-43cb-a7d0-8045941b9674",
+                        "uuid": "cb9b81ce-c86e-4b07-ba18-3d1deddeded5",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "Select microbial peptides (MQ)",
                                 "output_name": "out_file1",
-                                "uuid": "f6507937-030f-40b0-aff6-828d6e28aeae"
+                                "uuid": "d7718bab-9e75-4729-bfb6-03bc3112a0e2"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/2.0.33+galaxy1",
                         "errors": null,
-                        "id": 18,
+                        "id": 13,
                         "input_connections": {
-                            "input": {
-                                "id": 13,
-                                "output_name": "output"
+                            "searchgui_input": {
+                                "id": 10,
+                                "output_name": "searchgui_results"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "FASTA-to-Tabular",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 416.9874954223633,
-                            "height": 92.79998779296875,
-                            "left": 2049.640655517578,
-                            "right": 2209.640655517578,
-                            "top": 324.18750762939453,
-                            "width": 160,
-                            "x": 2049.640655517578,
-                            "y": 324.18750762939453
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "7e801ab2b70e",
-                            "name": "fasta_to_tabular",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"descr_columns\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
-                        "type": "tool",
-                        "uuid": "f77ceead-9781-4122-a033-e5e675d1d0af",
-                        "workflow_outputs": [
+                                "description": "runtime parameter for tool Peptide Shaker",
+                                "name": "optional_main_parameters"
+                            },
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "6f986155-b096-40f3-981b-edf3f3b75617"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
-                        "errors": null,
-                        "id": 19,
-                        "input_connections": {
-                            "input": {
-                                "id": 14,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Filter Tabular",
-                        "outputs": [
+                                "description": "runtime parameter for tool Peptide Shaker",
+                                "name": "optional_main_parameters"
+                            },
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "description": "runtime parameter for tool Peptide Shaker",
+                                "name": "optional_main_parameters"
                             }
                         ],
-                        "position": {
-                            "bottom": 105.04999923706055,
-                            "height": 92.79999542236328,
-                            "left": 3064.4061279296875,
-                            "right": 3224.4061279296875,
-                            "top": 12.250003814697266,
-                            "width": 160,
-                            "x": 3064.4061279296875,
-                            "y": 12.250003814697266
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "34d29339abab",
-                            "name": "filter_tabular",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"select_columns\", \"__current_case__\": 7, \"columns\": \"1\"}}, {\"__index__\": 1, \"filter\": {\"filter_type\": \"replace\", \"__current_case__\": 8, \"column\": \"1\", \"regex_pattern\": \"^([^ |]+).*$\", \"regex_replace\": \"\\\\1\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
-                        "type": "tool",
-                        "uuid": "c5a70a7c-b161-4468-8fe6-c5aa7a62ea97",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "02d27417-7639-4052-8f09-4d97225efb7b"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed/translate_bed/0.1.0",
-                        "errors": null,
-                        "id": 20,
-                        "input_connections": {
-                            "input": {
-                                "id": 15,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
                         "label": null,
-                        "name": "Translate BED transcripts",
+                        "name": "Peptide Shaker",
                         "outputs": [
                             {
-                                "name": "translation_bed",
-                                "type": "bed"
+                                "name": "mzidentML",
+                                "type": "mzid"
                             },
                             {
-                                "name": "translation_fasta",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 1166.1468811035156,
-                            "height": 117.5999755859375,
-                            "left": 1742.6094055175781,
-                            "right": 1902.6094055175781,
-                            "top": 1048.5469055175781,
-                            "width": 160,
-                            "x": 1742.6094055175781,
-                            "y": 1048.5469055175781
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed/translate_bed/0.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "038ecf54cbec",
-                            "name": "translate_bed",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"bed\", \"bed_filters\": {\"regions\": \"\", \"biotypes\": \"\"}, \"chromInfo\": \"/panfs/roc/website/galaxyp.msi.umn.edu/galaxy/tool-data/shared/ucsc/chrom/mm10.len\", \"fa_id\": {\"reference\": \"\", \"fa_db\": \"generic\", \"fa_sep\": \"\", \"id_prefix\": \"\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ref\": {\"ref_source\": \"cached\", \"__current_case__\": 0, \"ref_loc\": \"mm10\"}, \"translations\": {\"translate\": \"cDNA_minus_CDS\", \"min_length\": \"10\", \"start_codon\": \"false\", \"enzyme\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
-                        "type": "tool",
-                        "uuid": "23639fe3-f5d9-40e7-9377-f0a9657a70df",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "translation_fasta",
-                                "uuid": "9de63997-d103-4efa-a7ec-0720d7b35b5e"
+                                "name": "output_certificate",
+                                "type": "txt"
                             },
                             {
-                                "label": null,
-                                "output_name": "translation_bed",
-                                "uuid": "5512409b-e1d2-4722-9398-4af66e2df909"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
-                        "errors": null,
-                        "id": 21,
-                        "input_connections": {
-                            "tables_0|table": {
-                                "id": 17,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [
+                                "name": "output_psm",
+                                "type": "tabular"
+                            },
                             {
-                                "description": "runtime parameter for tool Query Tabular",
-                                "name": "add_to_database"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Query Tabular",
-                        "outputs": [
+                                "name": "output_peptides",
+                                "type": "tabular"
+                            },
                             {
-                                "name": "sqlitedb",
-                                "type": "sqlite"
+                                "name": "output_proteins",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 831.2187652587891,
-                            "height": 168,
-                            "left": 1982.6406860351562,
-                            "right": 2142.6406860351562,
-                            "top": 663.2187652587891,
-                            "width": 160,
-                            "x": 1982.6406860351562,
-                            "y": 663.2187652587891
+                            "left": 1376.5616292921313,
+                            "top": 136.11307746315038
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionsqlitedb": {
+                            "TagDatasetActionoutput_peptides": {
                                 "action_arguments": {
-                                    "newname": "variant_annoation.sqlite"
+                                    "tags": "#PS_Peptides"
                                 },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "sqlitedb"
+                                "action_type": "TagDatasetAction",
+                                "output_name": "output_peptides"
+                            },
+                            "TagDatasetActionoutput_psm": {
+                                "action_arguments": {
+                                    "tags": "#PS_PSM"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "output_psm"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/2.0.33+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "33d61c89fb8d",
-                            "name": "query_tabular",
-                            "owner": "iuc",
+                            "changeset_revision": "a6ff76e057fd",
+                            "name": "peptideshaker",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"save_db\": \"true\", \"sqlquery\": \"\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"variant_annotation\", \"column_names_from_first_line\": \"false\", \"col_names\": \"name,reference,cigar,annotation\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"name,cigar\"}]}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"exporting_options\": {\"zip_conditional\": {\"zip_output_boolean\": false, \"__current_case__\": 0, \"export_psdb\": false}, \"mzidentml_conditional\": {\"mzidentml_creation\": true, \"__current_case__\": 0, \"include_sequences\": false, \"contact_options\": {\"contact_options_selector\": \"no\", \"__current_case__\": 0}}, \"followup_conditional\": {\"followup_conditional_selector\": \"no\", \"__current_case__\": 0}, \"output_reports\": [\"3\", \"6\", \"9\", \"0\"]}, \"optional_main_parameters\": {\"input_optional_identification_parameters\": {\"__class__\": \"RuntimeValue\"}, \"input_fasta_file\": {\"__class__\": \"RuntimeValue\"}, \"input_optional_spectrum_files\": {\"__class__\": \"RuntimeValue\"}}, \"searchgui_input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.33+galaxy1",
                         "type": "tool",
-                        "uuid": "81d10709-f407-43c9-b867-b23d52759775",
+                        "uuid": "d8293305-e003-4c82-9085-a6a6e27563f3",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "variant_annoation_sqlite",
-                                "output_name": "sqlitedb",
-                                "uuid": "e9468479-4ebd-4ced-8086-c10e916b97c5"
+                                "label": null,
+                                "output_name": "output_proteins",
+                                "uuid": "3dfa370b-aaa1-4b0b-ab51-801ed5abf804"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_peptides",
+                                "uuid": "062fabe0-3631-4888-9a0e-5ea16af9c564"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "mzidentML",
+                                "uuid": "275ca0b9-f609-4cb7-8a1f-3ada482634fe"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_psm",
+                                "uuid": "39e82c48-26d6-4717-9efe-06a73e37dfdc"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
+                        "content_id": "Grep1",
                         "errors": null,
-                        "id": 22,
+                        "id": 16,
                         "input_connections": {
                             "input": {
-                                "id": 18,
-                                "output_name": "output"
+                                "id": 13,
+                                "output_name": "output_peptides"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Column Regex Find And Replace",
+                        "label": "Select microbial peptides (SGPS)",
+                        "name": "Select",
                         "outputs": [
                             {
                                 "name": "out_file1",
@@ -191364,55 +193116,46 @@
                             }
                         ],
                         "position": {
-                            "bottom": 427.9718780517578,
-                            "height": 92.79998779296875,
-                            "left": 2311.671905517578,
-                            "right": 2471.671905517578,
-                            "top": 335.17189025878906,
-                            "width": 160,
-                            "x": 2311.671905517578,
-                            "y": 335.17189025878906
+                            "left": 1624.5012303811463,
+                            "top": 133.08277443284737
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "209b7c5ee9d7",
-                            "name": "regex_find_replace",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Select microbial peptides (SGPS)"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
                         },
-                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \"^(ENS[^_]+_\\\\d+:)([ACGTacgt]+)>([ACGTacgt]+)\\\\s*\", \"replacement\": \"\\\\1\\\\2_\\\\3\"}, {\"__index__\": 1, \"pattern\": \",([A-Y]\\\\d+[A-Y]?)\\\\s*\", \"replacement\": \".\\\\1\"}, {\"__index__\": 2, \"pattern\": \"^(ENS[^ |]*)\\\\s*\", \"replacement\": \"\\\\1\"}, {\"__index__\": 3, \"pattern\": \"^(.*)$\", \"replacement\": \"generic|\\\\1\"}], \"field\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_id": "Grep1",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"-v\", \"keep_header\": true, \"pattern\": \"(_HUMAN)|(_REVERSED)|(CON)|(con)\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.4",
                         "type": "tool",
-                        "uuid": "4fe7754b-ecb7-4447-b66d-5f8ab520c6ea",
+                        "uuid": "088c67e2-5680-45ac-8fc6-58107304378b",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "Select microbial peptides (SGPS)",
                                 "output_name": "out_file1",
-                                "uuid": "1c721b4b-9acf-4f5c-b5e6-4a5bad5aa3f7"
+                                "uuid": "14fd9080-df92-4c61-b1f1-3f700a166700"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
+                        "content_id": "Filter1",
                         "errors": null,
-                        "id": 23,
+                        "id": 19,
                         "input_connections": {
-                            "inputs": [
-                                {
-                                    "id": 19,
-                                    "output_name": "output"
-                                },
-                                {
-                                    "id": 8,
-                                    "output_name": "output"
-                                }
-                            ]
+                            "input": {
+                                "id": 16,
+                                "output_name": "out_file1"
+                            }
                         },
                         "inputs": [],
-                        "label": "Reference Protein Accessions",
-                        "name": "Concatenate datasets",
+                        "label": "Filter confident microbial peptides",
+                        "name": "Filter",
                         "outputs": [
                             {
                                 "name": "out_file1",
@@ -191420,369 +193163,334 @@
                             }
                         ],
                         "position": {
-                            "bottom": 209.64999961853027,
-                            "height": 126.4000015258789,
-                            "left": 3312.6251220703125,
-                            "right": 3472.6251220703125,
-                            "top": 83.24999809265137,
-                            "width": 160,
-                            "x": 3312.6251220703125,
-                            "y": 83.24999809265137
+                            "left": 1882.4063928456353,
+                            "top": 138.52877496551775
                         },
                         "post_job_actions": {
                             "RenameDatasetActionout_file1": {
                                 "action_arguments": {
-                                    "newname": "Reference_Protein_Accessions"
+                                    "newname": "Filter confident microbial peptides"
                                 },
                                 "action_type": "RenameDatasetAction",
                                 "output_name": "out_file1"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "20344ce0c811",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"cond\": \"c17=='Confident'\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
                         "type": "tool",
-                        "uuid": "815c5137-f521-4c1c-9d38-e959ac23bfa6",
+                        "uuid": "a2763f6c-4bb4-4637-b9a5-4319b8176e57",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Reference_Protein_Accessions",
+                                "label": "Filter confident microbial peptides",
                                 "output_name": "out_file1",
-                                "uuid": "19aa5a85-5933-4ab5-ae76-e4b1ec5b2f85"
+                                "uuid": "1c6c953f-d192-4953-938a-9f401315bc0d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/bed_to_protein_map/bed_to_protein_map/0.2.0",
+                        "content_id": "Filter1",
                         "errors": null,
-                        "id": 24,
+                        "id": 20,
                         "input_connections": {
                             "input": {
-                                "id": 20,
-                                "output_name": "translation_bed"
+                                "id": 17,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "bed to protein map",
+                        "label": "Filter confident microbial PSMs",
+                        "name": "Filter",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 1037.8718719482422,
-                            "height": 143.20001220703125,
-                            "left": 1954.1719055175781,
-                            "right": 2114.171905517578,
-                            "top": 894.6718597412109,
-                            "width": 160,
-                            "x": 1954.1719055175781,
-                            "y": 894.6718597412109
+                            "left": 1892.8411851041578,
+                            "top": 346.8881407177668
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/bed_to_protein_map/bed_to_protein_map/0.2.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "a7c58b43cbaa",
-                            "name": "bed_to_protein_map",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Filter confident microbial PSMs"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"cond\": \"c24=='Confident'\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
                         "type": "tool",
-                        "uuid": "f32d0b6f-c434-47ea-88b1-391147c88f92",
+                        "uuid": "2986ffd8-f797-4bdd-ba33-e3383bb3cbd1",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "ec2b95fe-e600-490e-abde-a8b0d80d1ac9"
+                                "label": "Filter confident microbial PSMs",
+                                "output_name": "out_file1",
+                                "uuid": "d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+                        "content_id": "Grouping1",
                         "errors": null,
-                        "id": 25,
+                        "id": 21,
                         "input_connections": {
-                            "input": {
-                                "id": 22,
+                            "input1": {
+                                "id": 18,
                                 "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Tabular-to-FASTA",
+                        "label": "MQ Distinct Peptides",
+                        "name": "Group",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "fasta"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 478.0031204223633,
-                            "height": 92.79998779296875,
-                            "left": 2557.6718139648438,
-                            "right": 2717.6718139648438,
-                            "top": 385.20313262939453,
-                            "width": 160,
-                            "x": 2557.6718139648438,
-                            "y": 385.20313262939453
+                            "left": 2692.1307728764114,
+                            "top": 524.4947117996797
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "0b4e36026794",
-                            "name": "tabular_to_fasta",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        "post_job_actions": {
+                            "EmailActionout_file1": {
+                                "action_arguments": {
+                                    "host": "usegalaxy.eu"
+                                },
+                                "action_type": "EmailAction",
+                                "output_name": "out_file1"
+                            },
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "MQ Peptides"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"seq_col\": \"2\", \"title_col\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_id": "Grouping1",
+                        "tool_state": "{\"groupcol\": \"1\", \"ignorecase\": false, \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.4",
                         "type": "tool",
-                        "uuid": "10d46847-b9e3-43b5-868c-bc34ab8e16b5",
+                        "uuid": "eadd5e67-4653-4895-bd99-d7ec8e8514f7",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "a20fd7ce-326c-4fb2-845b-ba93bc2d24a5"
+                                "label": "MQ Peptides",
+                                "output_name": "out_file1",
+                                "uuid": "07cae017-0b39-4065-b83e-b5f2e27fe740"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
+                        "content_id": "Grouping1",
                         "errors": null,
-                        "id": 26,
+                        "id": 24,
                         "input_connections": {
-                            "inputs": [
-                                {
-                                    "id": 24,
-                                    "output_name": "output"
-                                },
-                                {
-                                    "id": 16,
-                                    "output_name": "out_file1"
-                                }
-                            ]
+                            "input1": {
+                                "id": 23,
+                                "output_name": "out_file1"
+                            }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Concatenate datasets",
+                        "label": "SGPS Distinct Peptides",
+                        "name": "Group",
                         "outputs": [
                             {
                                 "name": "out_file1",
-                                "type": "input"
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 662.2062606811523,
-                            "height": 92.80001831054688,
-                            "left": 2288.093719482422,
-                            "right": 2448.093719482422,
-                            "top": 569.4062423706055,
-                            "width": 160,
-                            "x": 2288.093719482422,
-                            "y": 569.4062423706055
+                            "left": 2692.21992119554,
+                            "top": 329.70161173161625
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "20344ce0c811",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        "post_job_actions": {
+                            "EmailActionout_file1": {
+                                "action_arguments": {
+                                    "host": "usegalaxy.eu"
+                                },
+                                "action_type": "EmailAction",
+                                "output_name": "out_file1"
+                            },
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "SGPS Distinct Peptides"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
                         },
-                        "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_id": "Grouping1",
+                        "tool_state": "{\"groupcol\": \"1\", \"ignorecase\": false, \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.4",
                         "type": "tool",
-                        "uuid": "943dd8be-c5e3-45cf-9b22-8b6d92e2fe4f",
+                        "uuid": "17433c88-5d56-453f-9371-dc2943eecac2",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "SGPS Distinct Peptides",
                                 "output_name": "out_file1",
-                                "uuid": "e24d9b68-120f-43da-91a1-34f0daaceb7f"
+                                "uuid": "b6c61697-ff52-43c0-8fb4-765d7b4204cc"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
                         "errors": null,
-                        "id": 27,
+                        "id": 25,
                         "input_connections": {
-                            "batchmode|input_fastas_0|input_fasta": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "batchmode|input_fastas_1|input_fasta": {
-                                "id": 25,
-                                "output_name": "output"
-                            },
-                            "batchmode|input_fastas_2|input_fasta": {
-                                "id": 20,
-                                "output_name": "translation_fasta"
-                            }
+                            "inputs": [
+                                {
+                                    "id": 21,
+                                    "output_name": "out_file1"
+                                },
+                                {
+                                    "id": 24,
+                                    "output_name": "out_file1"
+                                }
+                            ]
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "FASTA Merge Files and Filter Unique Sequences",
+                        "label": "SGPS-MQ Peptides",
+                        "name": "Concatenate datasets",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "fasta"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 801.796875,
-                            "height": 260,
-                            "left": 2996.5780639648438,
-                            "right": 3156.5780639648438,
-                            "top": 541.796875,
-                            "width": 160,
-                            "x": 2996.5780639648438,
-                            "y": 541.796875
+                            "left": 3005.427930624518,
+                            "top": 411.55050647320707
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput": {
+                            "RenameDatasetActionout_file1": {
                                 "action_arguments": {
-                                    "newname": "Uniprot_cRAP_SAV_indel_translatedbed.FASTA"
+                                    "newname": "SGPS-MQ Peptides"
                                 },
                                 "action_type": "RenameDatasetAction",
-                                "output_name": "output"
+                                "output_name": "out_file1"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "f546e7278f04",
-                            "name": "fasta_merge_files_and_filter_unique_sequences",
-                            "owner": "galaxyp",
+                            "changeset_revision": "d698c222f354",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"accession_parser\": \"^>([^ ]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"uniqueness_criterion\": \"sequence\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.1",
                         "type": "tool",
-                        "uuid": "ee552030-2599-41c9-9bd1-0c6e3d311cae",
+                        "uuid": "967a29c5-8ef9-45de-918a-f99e3f9a058f",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Uniprot_cRAP_SAV_indel_translatedbed_FASTA",
-                                "output_name": "output",
-                                "uuid": "924bce7c-5c6a-4cb3-a459-18784a55ae01"
+                                "label": "SGPS-MQ Peptides",
+                                "output_name": "out_file1",
+                                "uuid": "a8c2de2e-e322-4830-9d28-2f79bf937013"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                        "content_id": "Grouping1",
                         "errors": null,
-                        "id": 28,
+                        "id": 26,
                         "input_connections": {
-                            "tables_0|table": {
-                                "id": 26,
+                            "input1": {
+                                "id": 25,
                                 "output_name": "out_file1"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Query Tabular",
-                                "name": "add_to_database"
-                            }
-                        ],
-                        "label": "Genomic_mapping_sqlite",
-                        "name": "Query Tabular",
+                        "inputs": [],
+                        "label": "Distinct Peptides",
+                        "name": "Group",
                         "outputs": [
                             {
-                                "name": "sqlitedb",
-                                "type": "sqlite"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 735.6281509399414,
-                            "height": 184.80001831054688,
-                            "left": 2532.6718139648438,
-                            "right": 2692.6718139648438,
-                            "top": 550.8281326293945,
-                            "width": 160,
-                            "x": 2532.6718139648438,
-                            "y": 550.8281326293945
+                            "left": 3283.0311189112367,
+                            "top": 419.0948684617405
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionsqlitedb": {
+                            "RenameDatasetActionout_file1": {
                                 "action_arguments": {
-                                    "newname": "genomic_mapping.sqlite"
+                                    "newname": "Distinct Peptides"
                                 },
                                 "action_type": "RenameDatasetAction",
-                                "output_name": "sqlitedb"
+                                "output_name": "out_file1"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "33d61c89fb8d",
-                            "name": "query_tabular",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"save_db\": \"true\", \"sqlquery\": \"\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"feature_cds_map\", \"column_names_from_first_line\": \"false\", \"col_names\": \"name,chrom,start,end,strand,cds_start,cds_end\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"name,cds_start,cds_end\"}]}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_id": "Grouping1",
+                        "tool_state": "{\"groupcol\": \"1\", \"ignorecase\": false, \"ignorelines\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"operations\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.4",
                         "type": "tool",
-                        "uuid": "0af1f230-f319-41ab-946a-98ada6900f17",
+                        "uuid": "b5462dd0-3af9-41d4-a011-65d4244525a9",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "genomic_mapping_sqlite",
-                                "output_name": "sqlitedb",
-                                "uuid": "6542c4e5-289a-4be4-9b42-7a4e170ba198"
+                                "label": "Distinct Peptides",
+                                "output_name": "out_file1",
+                                "uuid": "ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/proteogenomics-dbcreation",
-                "path": "topics/proteomics/tutorials/proteogenomics-dbcreation/workflows/galaxy-workflow-mouse_rnaseq_dbcreation.ga",
+                "parent_id": "proteomics/clinical-mp-2-discovery",
+                "path": "topics/proteomics/tutorials/clinical-mp-2-discovery/workflows/WF2_Discovery-Workflow.ga",
                 "tags": [
-                    "proteomics"
+                    "name:clinicalMP"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "GTN Proteogenomics1 Database Creation",
+                "title": "WF2_Discovery-Workflow",
                 "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-proteogenomics-dbcreation/versions/galaxy-workflow-mouse-rnaseq-dbcreation",
-                "tutorial_id": "proteogenomics-dbcreation",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteogenomics-dbcreation/workflows/galaxy-workflow-mouse_rnaseq_dbcreation.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteogenomics-dbcreation/workflows/galaxy-workflow-mouse_rnaseq_dbcreation.html",
-                "version": 8,
-                "wfid": "proteomics-proteogenomics-dbcreation",
-                "wfname": "galaxy-workflow-mouse-rnaseq-dbcreation",
-                "workflow": "galaxy-workflow-mouse_rnaseq_dbcreation.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-clinical-mp-2-discovery/versions/wf2-discovery-workflow",
+                "tutorial_id": "clinical-mp-2-discovery",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-2-discovery/workflows/WF2_Discovery-Workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-2-discovery/workflows/WF2_Discovery-Workflow.html",
+                "version": 1,
+                "wfid": "proteomics-clinical-mp-2-discovery",
+                "wfname": "wf2-discovery-workflow",
+                "workflow": "WF2_Discovery-Workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/bed_to_protein_map/bed_to_protein_map/0.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.22.0",
+                    "Cut1",
+                    "Filter1",
+                    "Grep1",
+                    "Grouping1",
+                    "Remove beginning1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
                     "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/gffcompare_to_bed/gffcompare_to_bed/0.2.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed/translate_bed/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.11.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1"
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/2.0.3.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/fasta_cli/4.0.41+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/ident_params/4.0.41+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/2.0.33+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/4.0.41+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0"
                 ],
-                "workflowhub_id": "1201"
+                "workflowhub_id": "1354"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.1489208"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.10105821"
     },
     {
         "admin_install": {
@@ -191791,45 +193499,106 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "peptideshaker",
+                    "name": "metaquantome_db",
                     "owner": "galaxyp",
-                    "revisions": "7fdd9119cc4f",
+                    "revisions": "7c45aa1c9464",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "peptideshaker",
+                    "name": "metaquantome_db",
                     "owner": "galaxyp",
-                    "revisions": "7fdd9119cc4f",
+                    "revisions": "e63db1aa82ee",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "unipept",
+                    "name": "metaquantome_expand",
                     "owner": "galaxyp",
-                    "revisions": "9aaa46d45472",
-                    "tool_panel_section_label": "Get Data",
+                    "revisions": "eb65ab160a10",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "query_tabular",
-                    "owner": "iuc",
-                    "revisions": "33d61c89fb8d",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "metaquantome_expand",
+                    "owner": "galaxyp",
+                    "revisions": "767c1d761aaf",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sqlite_to_tabular",
-                    "owner": "iuc",
-                    "revisions": "b722161a845a",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "metaquantome_filter",
+                    "owner": "galaxyp",
+                    "revisions": "7d1c20b315ff",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "metaquantome_filter",
+                    "owner": "galaxyp",
+                    "revisions": "35cc7ca0bdc7",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "metaquantome_sample",
+                    "owner": "galaxyp",
+                    "revisions": "49a957fb353a",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "metaquantome_sample",
+                    "owner": "galaxyp",
+                    "revisions": "06f6826d380c",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "metaquantome_stat",
+                    "owner": "galaxyp",
+                    "revisions": "982a442a98dd",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "metaquantome_stat",
+                    "owner": "galaxyp",
+                    "revisions": "b9d453dca8d3",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "metaquantome_viz",
+                    "owner": "galaxyp",
+                    "revisions": "02da24eac445",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "metaquantome_viz",
+                    "owner": "galaxyp",
+                    "revisions": "8bd7734309f6",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 7fdd9119cc4f\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 7fdd9119cc4f\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unipept\n  owner: galaxyp\n  revisions: 9aaa46d45472\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n  owner: iuc\n  revisions: 33d61c89fb8d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sqlite_to_tabular\n  owner: iuc\n  revisions: b722161a845a\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaproteomics/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: metaquantome_db\n  owner: galaxyp\n  revisions: 7c45aa1c9464\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_db\n  owner: galaxyp\n  revisions: e63db1aa82ee\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_expand\n  owner: galaxyp\n  revisions: eb65ab160a10\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_expand\n  owner: galaxyp\n  revisions: 767c1d761aaf\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_filter\n  owner: galaxyp\n  revisions: 7d1c20b315ff\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_filter\n  owner: galaxyp\n  revisions: 35cc7ca0bdc7\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_sample\n  owner: galaxyp\n  revisions: 49a957fb353a\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_sample\n  owner: galaxyp\n  revisions: 06f6826d380c\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_stat\n  owner: galaxyp\n  revisions: 982a442a98dd\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_stat\n  owner: galaxyp\n  revisions: b9d453dca8d3\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_viz\n  owner: galaxyp\n  revisions: 02da24eac445\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metaquantome_viz\n  owner: galaxyp\n  revisions: 8bd7734309f6\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-function/tutorial.json",
         "contributors": [
+            {
+                "email": "subinamehta@gmail.com",
+                "id": "subinamehta",
+                "joined": "2018-06",
+                "linkedin": "subinamehta",
+                "matrix": "subinamehta:matrix.org",
+                "name": "Subina Mehta",
+                "orcid": "0000-0001-9818-0537",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
+                "twitter": "Subina_Mehta",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
+            },
             {
                 "email": "tgriffin@umn.edu",
                 "github": false,
@@ -191850,114 +193619,126 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
             },
             {
-                "email": "jj@umn.edu",
-                "id": "jj-umn",
-                "in_memoriam": "<a href=\"https://galaxyproject.org/news/2024-03-19-remembrances-of-jj/\">James \u2018JJ\u2019 Johnson, was a Galaxy community rock star most known for his indispensable contributions to the Galaxy Proteomics community.</a>\n\nJJ\u2019s works will live on in so many Galaxy tools and workflows for years to come.",
-                "joined": "2017-09",
-                "name": "James Johnson",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jj-umn/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/jj-umn.json"
+                "email": "leith023@umn.edu",
+                "id": "emmaleith",
+                "joined": "2019-07",
+                "name": "Emma Leith",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/emmaleith/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/emmaleith.json"
             },
             {
-                "elixir_node": "de",
-                "email": "blankclemens@gmail.com",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "blankclemens",
-                "joined": "2017-09",
-                "name": "Clemens Blank",
-                "orcid": "0000-0002-1726-2256",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankclemens/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankclemens.json"
+                "email": "crane136@umn.edu",
+                "id": "mariecrane",
+                "joined": "2019-05",
+                "name": "Marie Crane",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mariecrane/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mariecrane.json"
             },
             {
-                "email": "subinamehta@gmail.com",
-                "id": "subinamehta",
-                "joined": "2018-06",
-                "linkedin": "subinamehta",
-                "matrix": "subinamehta:matrix.org",
-                "name": "Subina Mehta",
-                "orcid": "0000-0001-9818-0537",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
-                "twitter": "Subina_Mehta",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
+                "email": "kumar207@umn.edu",
+                "id": "pravs3683",
+                "joined": "2019-04",
+                "name": "Praveen Kumar",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pravs3683/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pravs3683.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/metaproteomics",
+        "dir": "topics/proteomics/tutorials/metaquantome-function",
         "edam_ontology": [
             "topic_0121",
             "topic_3922",
-            "topic_3050",
-            "topic_0637"
+            "topic_3941",
+            "topic_3697",
+            "topic_3174"
         ],
         "edam_operation": [
             "Visualisation",
-            "Prediction and recognition"
+            "Indexing",
+            "Differential protein expression analysis",
+            "Functional clustering",
+            "Statistical inference",
+            "Principal component visualisation",
+            "Query and retrieval",
+            "Heat map generation",
+            "Quantification",
+            "Filtering"
         ],
         "edam_topic": [
             "Proteomics",
             "Proteogenomics",
-            "Biodiversity",
-            "Taxonomy"
+            "Metatranscriptomics",
+            "Microbial ecology",
+            "Metagenomics"
         ],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "proteomics",
+                "tutorials": [
+                    "metaproteomics"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "proteomics",
+                "tutorials": [
+                    "metaquantome-taxonomy"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "proteomics/metaproteomics",
+        "id": "proteomics/metaquantome-function",
         "inexact_supported_servers": [
-            "UseGalaxy.cz"
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Use dataset collections",
-            "With SearchGUI and PeptideShaker you can gain access to multiple search engines",
-            "Learning the basics of SQL queries can pay off"
+            "All the inputs should have one column in common i.e. peptides.",
+            "Functional annotation can be performed using GO terms and EC numbers",
+            "Having basic knowledge regarding tools that can perform functional annotation can come in handy"
         ],
         "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-03-15",
         "objectives": [
-            "A taxonomy and functional analysis of metaproteomic mass spectrometry data."
+            "A functional and quantitational analysis of metaproteomic mass spectrometry data."
         ],
-        "pageviews": 3750,
-        "pub_date": "2017-06-28",
+        "pageviews": 508,
+        "pub_date": "2020-10-29",
         "questions": [
-            "How can I match metaproteomic mass spectrometry data to peptide sequences derived from shotgun metagenomic data?",
-            "How can I perform taxonomy analysis and visualize metaproteomics data?",
-            "How can I perform functional analysis on this metaproteomics data?"
+            "How do I look at differentially expressed proteins?",
+            "How do I get top 5 or 10 function present in the sample?",
+            "How can I visualize my results?"
         ],
-        "recordings": [
+        "requirements": [
             {
-                "captioners": [
-                    "emmaleith"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "1H",
-                "speakers": [
-                    "pratikdjagtap"
+                "topic_name": "proteomics",
+                "tutorials": [
+                    "metaquantome-data-creation"
                 ],
-                "youtube_id": "3_yaPp-RCFw"
+                "type": "internal"
             }
         ],
-        "short_id": "T00221",
+        "short_id": "T00223",
         "short_tools": [
-            "sqlite_to_tabular",
-            "peptide_shaker",
-            "search_gui",
-            "unipept",
-            "query_tabular"
+            "metaquantome_filter",
+            "metaquantome_sample",
+            "metaquantome_stat",
+            "metaquantome_expand",
+            "metaquantome_viz",
+            "metaquantome_db"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -191968,43 +193749,50 @@
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
                 }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                }
             ]
         },
         "symlink": null,
         "tags": [
             "microgalaxy"
         ],
-        "time_estimation": "2h",
-        "title": "Metaproteomics tutorial",
+        "time_estimation": "1h",
+        "title": "metaQuantome 2: Function",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0"
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.0-0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.0-0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.0-0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.0-0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.0-0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0"
         ],
         "topic_name": "proteomics",
         "topic_name_human": "Proteomics",
@@ -192014,100 +193802,58 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "metaproteomics",
+        "tutorial_name": "metaquantome-function",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaproteomics/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaproteomics/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-function/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-function/tutorial.json"
         },
-        "version": 41,
+        "version": 14,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 157,
-        "visitors": 2256,
+        "visit_duration": 226,
+        "visitors": 352,
         "workflows": [
             {
                 "creators": [],
-                "description": "Metaproteomics tutorial",
+                "description": "metaquantome-function",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSixgill generated protein FASTA File\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nDataset Collection of Bering Strait MGF Files\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGene Ontology Terms Selected\"]\n  3[label=\"Search GUI\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  k7516674ab5aa45b5b2e838c1889ad2e9[color=lightseagreen,label=\"Output\\nSearch GUI on input dataset(s)\"]\n  3 -> k7516674ab5aa45b5b2e838c1889ad2e9\n  4[label=\"Peptide Shaker\"]\n  3 -> 4 [label=\"searchgui_results\"]\n  kddfe8d62a7b74e30a84d91c92fc60bd0[color=lightseagreen,label=\"Output\\nPeptide Shaker on input dataset(s): mzidentML file\"]\n  4 -> kddfe8d62a7b74e30a84d91c92fc60bd0\n  5[label=\"Query Tabular Select Peptides\"]\n  4 -> 5 [label=\"output_psm\"]\n  6[label=\"Unipept pept2prot\"]\n  5 -> 6 [label=\"output\"]\n  7[label=\"Unipept lca\"]\n  5 -> 7 [label=\"output\"]\n  8[label=\"Go Pop2Prot DB\"]\n  2 -> 8 [label=\"output\"]\n  6 -> 8 [label=\"output_tsv\"]\n  6 -> 8 [label=\"output_tsv\"]\n  4 -> 8 [label=\"output_psm\"]\n  9[label=\"Genera | PSMs | Peptides\"]\n  4 -> 9 [label=\"output_psm\"]\n  7 -> 9 [label=\"output_tsv\"]\n  10[label=\"GO Terms: Biological Processes\"]\n  8 -> 10 [label=\"sqlitedb\"]\n  11[label=\"GO Terms: Molecular Functions\"]\n  8 -> 11 [label=\"sqlitedb\"]\n  12[label=\"GO Terms: Cellular Localization\"]\n  8 -> 12 [label=\"sqlitedb\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"metaQuantome: database\"]\n  1[label=\"metaQuantome: create samples file\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nFunctional file\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIntensity file\"]\n  4[label=\"metaQuantome: expand\"]\n  0 -> 4 [label=\"outfile\"]\n  3 -> 4 [label=\"output\"]\n  2 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"samples_file\"]\n  5[label=\"metaQuantome: filter\"]\n  4 -> 5 [label=\"outfile\"]\n  1 -> 5 [label=\"samples_file\"]\n  6[label=\"metaQuantome: stat\"]\n  5 -> 6 [label=\"outfile\"]\n  1 -> 6 [label=\"samples_file\"]\n  7[label=\"T2-Bar-Plot\"]\n  6 -> 7 [label=\"outfile\"]\n  6 -> 7 [label=\"outfile\"]\n  8[label=\"T4-Bar-Plot\"]\n  6 -> 8 [label=\"outfile\"]\n  1 -> 8 [label=\"samples_file\"]\n  9[label=\"T7-Bar-Plot\"]\n  6 -> 9 [label=\"outfile\"]\n  1 -> 9 [label=\"samples_file\"]\n  10[label=\"T7-T2-Volcano-Plot\"]\n  6 -> 10 [label=\"outfile\"]\n  1 -> 10 [label=\"samples_file\"]\n  11[label=\"T4-T2-Volcano-Plot\"]\n  6 -> 11 [label=\"outfile\"]\n  1 -> 11 [label=\"samples_file\"]\n}",
                 "history": [
                     {
-                        "hash": "aab73d220b58b8cb43227624f29fa6ea618133e6",
-                        "message": "Update workflow.ga",
-                        "num": 10,
-                        "short_hash": "aab73d220",
-                        "unix": "1612840176"
-                    },
-                    {
-                        "hash": "1386c22b289e346728ded8a2c88f940af9ed2247",
-                        "message": "Update workflow.ga",
-                        "num": 9,
-                        "short_hash": "1386c22b2",
-                        "unix": "1612834619"
-                    },
-                    {
-                        "hash": "65c8cf73a1d5371e2cb99f59ab1eab2aea941dfc",
-                        "message": "Update workflow.ga",
-                        "num": 8,
-                        "short_hash": "65c8cf73a",
-                        "unix": "1612473524"
-                    },
-                    {
-                        "hash": "277c504ce90837b1883239a00872839f674aea8c",
-                        "message": "Update workflow.ga",
-                        "num": 7,
-                        "short_hash": "277c504ce",
-                        "unix": "1612473274"
-                    },
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 6,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 5,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "e4a786cd7a8c7abebd27fa8a6d945a197290345b",
-                        "message": "Installing tools from workflows (#1269)",
+                        "hash": "9d12ea3f6c949d0485659fb58ac0eda7c8814a74",
+                        "message": "Update main_workflow.ga",
                         "num": 4,
-                        "short_hash": "e4a786cd7",
-                        "unix": "1550581735"
+                        "short_hash": "9d12ea3f6",
+                        "unix": "1636475724"
                     },
                     {
-                        "hash": "30b28d4c0288107f216b1a9339bd043c511bfe80",
-                        "message": "broken workflow",
+                        "hash": "b44e7f7c70e9638f17ca09238d425e0d8542d2a9",
+                        "message": "Update main_workflow.ga",
                         "num": 3,
-                        "short_hash": "30b28d4c0",
-                        "unix": "1512315861"
+                        "short_hash": "b44e7f7c7",
+                        "unix": "1603726491"
                     },
                     {
-                        "hash": "2e53c11bf8ac4f010ef72c879a36e96df6ec0202",
-                        "message": "Update workflow",
+                        "hash": "619a94b389406eacd755598aa6ce4fab95f867f6",
+                        "message": "Update main_workflow.ga",
                         "num": 2,
-                        "short_hash": "2e53c11bf",
-                        "unix": "1502111726"
+                        "short_hash": "619a94b38",
+                        "unix": "1603158677"
                     },
                     {
-                        "hash": "f6e08e286c8531ae382c7db6128ba2f419dc7d03",
-                        "message": "Metaproteomics tutorial (#393)",
+                        "hash": "426a2746eee3945edd669f81b15b222493c46c82",
+                        "message": "tutorial skeletons generated by planemo",
                         "num": 1,
-                        "short_hash": "f6e08e286",
-                        "unix": "1498643437"
+                        "short_hash": "426a2746e",
+                        "unix": "1602853461"
                     }
                 ],
                 "inputs": [
@@ -192115,895 +193861,677 @@
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Sixgill generated protein FASTA File"
+                                "name": "Functional file"
                             }
                         ],
-                        "label": "Sixgill generated protein FASTA File",
+                        "label": "Functional file",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 109.09375,
+                            "bottom": 856.578125,
                             "height": 81,
-                            "left": -232.5,
-                            "right": -32.5,
-                            "top": 28.09375,
+                            "left": 397.546875,
+                            "right": 597.546875,
+                            "top": 775.578125,
                             "width": 200,
-                            "x": -232.5,
-                            "y": 28.09375
+                            "x": 397.546875,
+                            "y": 775.578125
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "a3a731aa-022c-4d9b-89d3-475fc855e82e",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1ca164ee-d66f-4b6c-b1de-e0841cb0b662"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Dataset Collection of Bering Strait MGF Files"
-                            }
-                        ],
-                        "label": "Dataset Collection of Bering Strait MGF Files",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 288.03125,
-                            "height": 101,
-                            "left": -229.546875,
-                            "right": -29.546875,
-                            "top": 187.03125,
-                            "width": 200,
-                            "x": -229.546875,
-                            "y": 187.03125
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "ae22c03f-32ee-47af-9c46-064f32e93ee9",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1864b353-ca39-4da9-82d4-4ba5124df3b0"
-                            }
-                        ]
+                        "uuid": "7d436bc0-0e63-4445-93d5-5600c9a5c383",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 3,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Gene Ontology Terms (Selected)"
+                                "name": "Intensity file"
                             }
                         ],
-                        "label": "Gene Ontology Terms (Selected)",
+                        "label": "Intensity file",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 108.5,
-                            "height": 81,
-                            "left": 977.90625,
-                            "right": 1177.90625,
-                            "top": 27.5,
+                            "bottom": 953.578125,
+                            "height": 61,
+                            "left": 391.5625,
+                            "right": 591.5625,
+                            "top": 892.578125,
                             "width": 200,
-                            "x": 977.90625,
-                            "y": 27.5
+                            "x": 391.5625,
+                            "y": 892.578125
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "1dfff1a0-d645-4272-b524-39538fcdc95b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "f3de0677-7d91-4e64-b644-e384a9b556cb"
-                            }
-                        ]
+                        "uuid": "1e20e3c4-3b6f-4e0c-a5b6-8f8f3d220441",
+                        "workflow_outputs": []
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSixgill generated protein FASTA File\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nDataset Collection of Bering Strait MGF Files\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nGene Ontology Terms Selected\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Search GUI\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  7516674a-b5aa-45b5-b2e8-38c1889ad2e9[\"Output\\nSearch GUI on input dataset(s)\"];\n  3 --> 7516674a-b5aa-45b5-b2e8-38c1889ad2e9;\n  style 7516674a-b5aa-45b5-b2e8-38c1889ad2e9 stroke:#2c3143,stroke-width:4px;\n  4[\"Peptide Shaker\"];\n  3 -->|searchgui_results| 4;\n  ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0[\"Output\\nPeptide Shaker on input dataset(s): mzidentML file\"];\n  4 --> ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0;\n  style ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0 stroke:#2c3143,stroke-width:4px;\n  5[\"Query Tabular Select Peptides\"];\n  4 -->|output_psm| 5;\n  6[\"Unipept pept2prot\"];\n  5 -->|output| 6;\n  7[\"Unipept lca\"];\n  5 -->|output| 7;\n  8[\"Go Pop2Prot DB\"];\n  2 -->|output| 8;\n  6 -->|output_tsv| 8;\n  6 -->|output_tsv| 8;\n  4 -->|output_psm| 8;\n  9[\"Genera | PSMs | Peptides\"];\n  4 -->|output_psm| 9;\n  7 -->|output_tsv| 9;\n  10[\"GO Terms: Biological Processes\"];\n  8 -->|sqlitedb| 10;\n  11[\"GO Terms: Molecular Functions\"];\n  8 -->|sqlitedb| 11;\n  12[\"GO Terms: Cellular Localization\"];\n  8 -->|sqlitedb| 12;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Metaproteomics_GTN",
+                "mermaid": "flowchart TD\n  0[\"metaQuantome: database\"];\n  1[\"metaQuantome: create samples file\"];\n  2[\"\u2139\ufe0f Input Dataset\\nFunctional file\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nIntensity file\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"metaQuantome: expand\"];\n  0 -->|outfile| 4;\n  3 -->|output| 4;\n  2 -->|output| 4;\n  1 -->|samples_file| 4;\n  5[\"metaQuantome: filter\"];\n  4 -->|outfile| 5;\n  1 -->|samples_file| 5;\n  6[\"metaQuantome: stat\"];\n  5 -->|outfile| 6;\n  1 -->|samples_file| 6;\n  7[\"T2-Bar-Plot\"];\n  6 -->|outfile| 7;\n  6 -->|outfile| 7;\n  8[\"T4-Bar-Plot\"];\n  6 -->|outfile| 8;\n  1 -->|samples_file| 8;\n  9[\"T7-Bar-Plot\"];\n  6 -->|outfile| 9;\n  1 -->|samples_file| 9;\n  10[\"T7-T2-Volcano-Plot\"];\n  6 -->|outfile| 10;\n  1 -->|samples_file| 10;\n  11[\"T4-T2-Volcano-Plot\"];\n  6 -->|outfile| 11;\n  1 -->|samples_file| 11;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "metaquantome-function-worklow",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.2+galaxy0",
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Sixgill generated protein FASTA File"
-                            }
-                        ],
-                        "label": "Sixgill generated protein FASTA File",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 109.09375,
-                            "height": 81,
-                            "left": -232.5,
-                            "right": -32.5,
-                            "top": 28.09375,
-                            "width": 200,
-                            "x": -232.5,
-                            "y": 28.09375
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "a3a731aa-022c-4d9b-89d3-475fc855e82e",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1ca164ee-d66f-4b6c-b1de-e0841cb0b662"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "metaQuantome: database",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Dataset Collection of Bering Strait MGF Files"
+                                "name": "outfile",
+                                "type": "tar"
                             }
                         ],
-                        "label": "Dataset Collection of Bering Strait MGF Files",
-                        "name": "Input dataset collection",
-                        "outputs": [],
                         "position": {
-                            "bottom": 288.03125,
+                            "bottom": 555.953125,
                             "height": 101,
-                            "left": -229.546875,
-                            "right": -29.546875,
-                            "top": 187.03125,
+                            "left": 380.078125,
+                            "right": 580.078125,
+                            "top": 454.953125,
                             "width": 200,
-                            "x": -229.546875,
-                            "y": 187.03125
+                            "x": 380.078125,
+                            "y": 454.953125
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "ae22c03f-32ee-47af-9c46-064f32e93ee9",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1864b353-ca39-4da9-82d4-4ba5124df3b0"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Gene Ontology Terms (Selected)"
-                            }
-                        ],
-                        "label": "Gene Ontology Terms (Selected)",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 108.5,
-                            "height": 81,
-                            "left": 977.90625,
-                            "right": 1177.90625,
-                            "top": 27.5,
-                            "width": 200,
-                            "x": 977.90625,
-                            "y": 27.5
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.2+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "860429737408",
+                            "name": "metaquantome_db",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "1dfff1a0-d645-4272-b524-39538fcdc95b",
+                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"databases\": [\"ncbi\", \"go\", \"ec\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
+                        "type": "tool",
+                        "uuid": "8d2913b3-9c27-4a7e-989b-3e99642caa7e",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "f3de0677-7d91-4e64-b644-e384a9b556cb"
+                                "output_name": "outfile",
+                                "uuid": "f0040af5-b737-40da-8965-4c1ff91aa3ed"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.2+galaxy0",
                         "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "input_database": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "peak_lists": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
+                        "id": 1,
+                        "input_connections": {},
                         "inputs": [],
                         "label": null,
-                        "name": "Search GUI",
+                        "name": "metaQuantome: create samples file",
                         "outputs": [
                             {
-                                "name": "searchgui_results",
-                                "type": "searchgui_archive"
+                                "name": "samples_file",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 204,
-                            "height": 162,
-                            "left": -2.546875,
-                            "right": 197.453125,
-                            "top": 42,
+                            "bottom": 742,
+                            "height": 141,
+                            "left": 386.09375,
+                            "right": 586.09375,
+                            "top": 601,
                             "width": 200,
-                            "x": -2.546875,
-                            "y": 42
+                            "x": 386.09375,
+                            "y": 601
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "7fdd9119cc4f",
-                            "name": "peptideshaker",
+                            "changeset_revision": "40ca115438d2",
+                            "name": "metaquantome_sample",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_options\": {\"searchgui_advanced\": {\"searchgui_advanced_selector\": \"basic\", \"__current_case__\": 0}, \"xtandem\": {\"xtandem_advanced\": \"no\", \"__current_case__\": 0}, \"omssa\": {\"omssa_advanced\": \"no\", \"__current_case__\": 0}, \"msgf\": {\"msgf_advanced\": \"no\", \"__current_case__\": 0}, \"ms_amanda\": {\"ms_amanda_advanced\": \"no\", \"__current_case__\": 0}, \"tide\": {\"tide_advanced\": \"no\", \"__current_case__\": 0}, \"myrimatch\": {\"myrimatch_advanced\": \"no\", \"__current_case__\": 0}, \"comet\": {\"comet_advanced\": \"no\", \"__current_case__\": 0}, \"directtag\": {\"directtag_advanced\": \"no\", \"__current_case__\": 0}, \"novor\": {\"novor_advanced\": \"no\", \"__current_case__\": 0}}, \"input_database\": {\"__class__\": \"ConnectedValue\"}, \"peak_lists\": {\"__class__\": \"ConnectedValue\"}, \"precursor_options\": {\"precursor_ion_tol_units\": \"1\", \"precursor_ion_tol\": \"10.0\", \"fragment_tol_units\": \"0\", \"fragment_tol\": \"0.5\", \"min_charge\": \"2\", \"max_charge\": \"4\", \"forward_ion\": \"b\", \"reverse_ion\": \"y\", \"min_isotope\": \"0\", \"max_isotope\": \"1\"}, \"protein_database_options\": {\"create_decoy\": \"true\", \"use_gene_mapping\": \"false\", \"update_gene_mapping\": \"false\"}, \"protein_digest_options\": {\"digestion\": {\"cleavage\": \"0\", \"__current_case__\": 0, \"digests\": [{\"__index__\": 0, \"enzyme\": \"Trypsin\", \"missed_cleavages\": \"2\"}]}}, \"protein_modification_options\": {\"fixed_modifications\": null, \"variable_modifications\": null}, \"search_engines_options\": {\"engines\": [\"X!Tandem\", \"MSGF\"]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.3.10.1",
+                        "tool_state": "{\"samps_args\": {\"samps_src\": \"build\", \"__current_case__\": 0, \"samps\": [{\"__index__\": 0, \"group_name\": \"T2\", \"col_names\": \"T2_A1,T2_B1\"}, {\"__index__\": 1, \"group_name\": \"T4\", \"col_names\": \"T4A_1,T4B_1\"}, {\"__index__\": 2, \"group_name\": \"T7\", \"col_names\": \"T7A_1,T7B_1\"}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
                         "type": "tool",
-                        "uuid": "7ebb4019-93b4-4bf0-8fab-c4a786040001",
+                        "uuid": "9f37b361-1999-45f1-bdff-91e40d1b7783",
                         "workflow_outputs": [
                             {
-                                "label": "Search GUI on input dataset(s)",
-                                "output_name": "searchgui_results",
-                                "uuid": "7516674a-b5aa-45b5-b2e8-38c1889ad2e9"
+                                "label": null,
+                                "output_name": "samples_file",
+                                "uuid": "729e43a9-27eb-4ab8-b89d-af815d52defd"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.2+galaxy0",
                         "errors": null,
                         "id": 4,
                         "input_connections": {
-                            "searchgui_input": {
+                            "db_tar": {
+                                "id": 0,
+                                "output_name": "outfile"
+                            },
+                            "int_file": {
                                 "id": 3,
-                                "output_name": "searchgui_results"
+                                "output_name": "output"
+                            },
+                            "mode_args|func_file": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "samps": {
+                                "id": 1,
+                                "output_name": "samples_file"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Peptide Shaker",
+                        "name": "metaQuantome: expand",
                         "outputs": [
                             {
-                                "name": "mzidentML",
-                                "type": "mzid"
-                            },
-                            {
-                                "name": "output_psm",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "output_peptides",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "output_proteins",
+                                "name": "outfile",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 683,
-                            "height": 382,
-                            "left": 80.453125,
-                            "right": 280.453125,
-                            "top": 301,
+                            "bottom": 552.96875,
+                            "height": 242,
+                            "left": 713.109375,
+                            "right": 913.109375,
+                            "top": 310.96875,
                             "width": 200,
-                            "x": 80.453125,
-                            "y": 301
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionoutput_peptides": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_peptides"
-                            },
-                            "HideDatasetActionoutput_proteins": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_proteins"
-                            }
+                            "x": 713.109375,
+                            "y": 310.96875
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "7fdd9119cc4f",
-                            "name": "peptideshaker",
+                            "changeset_revision": "4187b6df1a40",
+                            "name": "metaquantome_expand",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"contact_options\": {\"contact_options_selector\": \"no\", \"__current_case__\": 0}, \"exporting_options\": {\"mzidentml_conditional\": {\"mzidentml_creation\": \"true\", \"__current_case__\": 0, \"include_sequences\": \"false\"}, \"zip_conditional\": {\"zip_output_boolean\": \"false\", \"__current_case__\": 0, \"export_cps\": \"false\"}, \"output_reports\": [\"3\", \"6\", \"9\"]}, \"filtering_options\": {\"filtering_options_selector\": \"no\", \"__current_case__\": 0}, \"processing_options\": {\"processing_options_selector\": \"no\", \"__current_case__\": 0}, \"searchgui_input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16.36.3",
+                        "tool_state": "{\"db_tar\": {\"__class__\": \"ConnectedValue\"}, \"int_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"f\", \"__current_case__\": 0, \"func_file\": {\"__class__\": \"ConnectedValue\"}, \"pep_colname_func\": \"peptide\", \"ontology_args\": {\"ontology\": \"go\", \"__current_case__\": 0, \"slim_down\": \"false\"}, \"func_colname\": \"go_term\"}, \"pep_colname_int\": \"peptide\", \"samps\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
                         "type": "tool",
-                        "uuid": "56edf0bc-6512-4191-8c36-b02bea23df83",
+                        "uuid": "6ba916f3-e8d2-4efb-bee8-d190d4497e99",
                         "workflow_outputs": [
-                            {
-                                "label": "Peptide Shaker on input dataset(s): mzidentML file",
-                                "output_name": "mzidentML",
-                                "uuid": "ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0"
-                            },
                             {
                                 "label": null,
-                                "output_name": "output_psm",
-                                "uuid": "5bd10721-63b1-4b4b-a4bb-12f13d576e48"
+                                "output_name": "outfile",
+                                "uuid": "a695a223-52de-4b99-a457-fc002123d7f4"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.2+galaxy0",
                         "errors": null,
                         "id": 5,
                         "input_connections": {
-                            "tables_0|table": {
+                            "expand_file": {
                                 "id": 4,
-                                "output_name": "output_psm"
+                                "output_name": "outfile"
+                            },
+                            "samps": {
+                                "id": 1,
+                                "output_name": "samples_file"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Query Tabular",
-                                "name": "add_to_database"
-                            }
-                        ],
-                        "label": "Query Tabular Select Peptides",
-                        "name": "Query Tabular",
+                        "inputs": [],
+                        "label": null,
+                        "name": "metaQuantome: filter",
                         "outputs": [
                             {
-                                "name": "output",
+                                "name": "outfile",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 349.109375,
+                            "bottom": 986.984375,
                             "height": 182,
-                            "left": 415.5,
-                            "right": 615.5,
-                            "top": 167.109375,
+                            "left": 712.109375,
+                            "right": 912.109375,
+                            "top": 804.984375,
                             "width": 200,
-                            "x": 415.5,
-                            "y": 167.109375
+                            "x": 712.109375,
+                            "y": 804.984375
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "33d61c89fb8d",
-                            "name": "query_tabular",
-                            "owner": "iuc",
+                            "changeset_revision": "a1daafbf5233",
+                            "name": "metaquantome_filter",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"no\", \"__current_case__\": 1}, \"save_db\": \"false\", \"sqlquery\": \"SELECT distinct sequence \\nFROM psm \\nWHERE confidence >= 95 \\nORDER BY sequence\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"regex\", \"__current_case__\": 6, \"regex_pattern\": \"^\\\\d\", \"regex_action\": \"include_match\"}}]}, \"tbl_opts\": {\"table_name\": \"psm\", \"column_names_from_first_line\": \"false\", \"col_names\": \"id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\", \"load_named_columns\": \"true\", \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.0.0",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"expand_file\": {\"__class__\": \"ConnectedValue\"}, \"min_child_nsamp\": \"1\", \"min_children_non_leaf\": \"2\", \"min_pep_nsamp\": \"1\", \"min_peptides\": \"1\", \"mode_args\": {\"mode\": \"f\", \"__current_case__\": 0, \"ontology_args\": {\"ontology\": \"go\", \"__current_case__\": 0, \"slim_down\": \"false\"}}, \"qthreshold\": \"2\", \"samps\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
                         "type": "tool",
-                        "uuid": "2e566329-0e53-4dac-a62b-d9acbe971e53",
+                        "uuid": "4d85cd84-63b6-4822-a1c1-b4555317fc92",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "4fc155b2-ff21-492f-9a9f-541989357012"
+                                "output_name": "outfile",
+                                "uuid": "1fcbebef-7f9d-4c46-90e4-ecce3dc87c3c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.2+galaxy0",
                         "errors": null,
                         "id": 6,
                         "input_connections": {
-                            "peptide_src|input_tsv": {
+                            "file": {
                                 "id": 5,
-                                "output_name": "output"
+                                "output_name": "outfile"
+                            },
+                            "samps": {
+                                "id": 1,
+                                "output_name": "samples_file"
                             }
                         },
                         "inputs": [],
-                        "label": "Unipept pept2prot",
-                        "name": "Unipept",
+                        "label": null,
+                        "name": "metaQuantome: stat",
                         "outputs": [
                             {
-                                "name": "output_tsv",
+                                "name": "outfile",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 214.46875,
-                            "height": 152,
-                            "left": 686.90625,
-                            "right": 886.90625,
-                            "top": 62.46875,
+                            "bottom": 683,
+                            "height": 202,
+                            "left": 1001.109375,
+                            "right": 1201.109375,
+                            "top": 481,
                             "width": 200,
-                            "x": 686.90625,
-                            "y": 62.46875
+                            "x": 1001.109375,
+                            "y": 481
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "9aaa46d45472",
-                            "name": "unipept",
+                            "changeset_revision": "b648e45fd3cf",
+                            "name": "metaquantome_stat",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"peptide_src\": {\"fmt\": \"tabular\", \"__current_case__\": 1, \"input_tsv\": {\"__class__\": \"ConnectedValue\"}, \"column\": \"1\"}, \"selected_outputs\": \"tsv\", \"strict\": \"false\", \"unipept\": {\"api\": \"pept2prot\", \"__current_case__\": 2, \"equate_il\": \"true\", \"extra\": \"true\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.3.0",
+                        "tool_state": "{\"control_group\": \"T2\", \"file\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"f\", \"__current_case__\": 0, \"ontology_args\": {\"ontology\": \"go\", \"__current_case__\": 0, \"slim_down\": \"false\"}}, \"paired\": \"true\", \"parametric\": \"True\", \"samps\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
                         "type": "tool",
-                        "uuid": "87abdf8e-c93e-4383-8e0e-79504d6a1c8f",
+                        "uuid": "53c9d15f-ef26-4bed-a07c-e5aae09c6ec2",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_tsv",
-                                "uuid": "0ee1d427-69d3-4cda-afd4-d86dbd654c5f"
+                                "output_name": "outfile",
+                                "uuid": "114546bc-4c2f-484d-9f4f-e6af605f30a4"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
                         "errors": null,
                         "id": 7,
                         "input_connections": {
-                            "peptide_src|input_tsv": {
-                                "id": 5,
-                                "output_name": "output"
+                            "infile": {
+                                "id": 6,
+                                "output_name": "outfile"
+                            },
+                            "samps": {
+                                "id": 6,
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
-                        "label": "Unipept lca",
-                        "name": "Unipept",
+                        "label": "T2-Bar-Plot",
+                        "name": "metaQuantome: visualize",
                         "outputs": [
                             {
-                                "name": "output_json",
-                                "type": "d3_hierarchy"
+                                "name": "wrapped_outfile",
+                                "type": "html"
                             },
                             {
-                                "name": "output_tsv",
+                                "name": "plotdata",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 687.484375,
-                            "height": 202,
-                            "left": 670.96875,
-                            "right": 870.96875,
-                            "top": 485.484375,
+                            "bottom": 683,
+                            "height": 292,
+                            "left": 1344.078125,
+                            "right": 1544.078125,
+                            "top": 391,
                             "width": 200,
-                            "x": 670.96875,
-                            "y": 485.484375
+                            "x": 1344.078125,
+                            "y": 391
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "9aaa46d45472",
-                            "name": "unipept",
+                            "changeset_revision": "eb811f3018ea",
+                            "name": "metaquantome_viz",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"peptide_src\": {\"fmt\": \"tabular\", \"__current_case__\": 1, \"input_tsv\": {\"__class__\": \"ConnectedValue\"}, \"column\": \"1\"}, \"selected_outputs\": [\"tsv\", \"json\"], \"strict\": \"false\", \"unipept\": {\"api\": \"pept2lca\", \"__current_case__\": 0, \"equate_il\": \"true\", \"extra\": \"false\", \"names\": \"true\", \"allfields\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.3.0",
+                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"f\", \"__current_case__\": 0, \"ontology\": \"go\", \"plot\": {\"plottype\": \"bar\", \"__current_case__\": 0, \"meancol\": \"T2_mean\", \"nterms\": \"5\", \"target_onto\": \"mf\", \"barcol\": \"2\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
                         "type": "tool",
-                        "uuid": "ea4ed3b9-6907-4feb-a656-b16f4a657a3e",
+                        "uuid": "22e19420-d346-4080-a941-d7f6eeb34bf1",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_json",
-                                "uuid": "4d83f563-1cd9-4db0-8f22-8e32b499f040"
+                                "output_name": "plotdata",
+                                "uuid": "f5f8721f-3fee-4164-b155-565ecba9c15f"
                             },
                             {
                                 "label": null,
-                                "output_name": "output_tsv",
-                                "uuid": "0d262aad-5472-41b4-8926-a5335dac8610"
+                                "output_name": "wrapped_outfile",
+                                "uuid": "3a1f5a00-68cd-4b78-a231-377f15278758"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
                         "errors": null,
                         "id": 8,
                         "input_connections": {
-                            "tables_0|table": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "tables_1|table": {
-                                "id": 6,
-                                "output_name": "output_tsv"
-                            },
-                            "tables_2|table": {
+                            "infile": {
                                 "id": 6,
-                                "output_name": "output_tsv"
+                                "output_name": "outfile"
                             },
-                            "tables_3|table": {
-                                "id": 4,
-                                "output_name": "output_psm"
+                            "samps": {
+                                "id": 1,
+                                "output_name": "samples_file"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Query Tabular",
-                                "name": "add_to_database"
-                            }
-                        ],
-                        "label": "Go Pop2Prot DB",
-                        "name": "Query Tabular",
+                        "inputs": [],
+                        "label": "T4-Bar-Plot",
+                        "name": "metaQuantome: visualize",
                         "outputs": [
                             {
-                                "name": "sqlitedb",
-                                "type": "sqlite"
+                                "name": "wrapped_outfile",
+                                "type": "html"
                             },
                             {
-                                "name": "output",
+                                "name": "plotdata",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 580.109375,
-                            "height": 382,
-                            "left": 902.5,
-                            "right": 1102.5,
-                            "top": 198.109375,
+                            "bottom": 985.578125,
+                            "height": 292,
+                            "left": 1358.5625,
+                            "right": 1558.5625,
+                            "top": 693.578125,
                             "width": 200,
-                            "x": 902.5,
-                            "y": 198.109375
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Peptides and PSMs"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
+                            "x": 1358.5625,
+                            "y": 693.578125
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "33d61c89fb8d",
-                            "name": "query_tabular",
-                            "owner": "iuc",
+                            "changeset_revision": "eb811f3018ea",
+                            "name": "metaquantome_viz",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"save_db\": \"true\", \"sqlquery\": \"SELECT sequence as \\\"peptide\\\", count(id) as \\\"PSMs\\\"\\nFROM bering_psms\\nWHERE confidence >= 95\\nGROUP BY sequence\\nORDER BY sequence\\n\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"skip\", \"__current_case__\": 0, \"skip_lines\": \"1\"}}]}, \"tbl_opts\": {\"table_name\": \"go\", \"column_names_from_first_line\": \"false\", \"col_names\": \"aspect,go_id,description\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"aspect,go_id\"}]}}, {\"__index__\": 1, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"skip\", \"__current_case__\": 0, \"skip_lines\": \"1\"}}, {\"__index__\": 1, \"filter\": {\"filter_type\": \"prepend_line_num\", \"__current_case__\": 2}}]}, \"tbl_opts\": {\"table_name\": \"bering_prot\", \"column_names_from_first_line\": \"false\", \"col_names\": \"id,peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_references,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"id,peptide\"}]}}, {\"__index__\": 2, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"skip\", \"__current_case__\": 0, \"skip_lines\": \"1\"}}, {\"__index__\": 1, \"filter\": {\"filter_type\": \"prepend_line_num\", \"__current_case__\": 2}}, {\"__index__\": 2, \"filter\": {\"filter_type\": \"select_columns\", \"__current_case__\": 7, \"columns\": \"1,7\"}}, {\"__index__\": 3, \"filter\": {\"filter_type\": \"normalize\", \"__current_case__\": 9, \"columns\": \"2\", \"separator\": \" \"}}]}, \"tbl_opts\": {\"table_name\": \"bering_prot_go\", \"column_names_from_first_line\": \"false\", \"col_names\": \"id,go_reference\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"go_reference,id\"}]}}, {\"__index__\": 3, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"regex\", \"__current_case__\": 6, \"regex_pattern\": \"^\\\\d\", \"regex_action\": \"include_match\"}}, {\"__index__\": 1, \"filter\": {\"filter_type\": \"select_columns\", \"__current_case__\": 7, \"columns\": \"1,3,23,24\"}}]}, \"tbl_opts\": {\"table_name\": \"bering_psms\", \"column_names_from_first_line\": \"false\", \"col_names\": \"id,sequence,confidence,validation\", \"load_named_columns\": \"true\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"sequence,id\"}]}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.0.0",
+                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"f\", \"__current_case__\": 0, \"ontology\": \"go\", \"plot\": {\"plottype\": \"bar\", \"__current_case__\": 0, \"meancol\": \"T4_mean\", \"nterms\": \"5\", \"target_onto\": \"mf\", \"barcol\": \"2\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
                         "type": "tool",
-                        "uuid": "9c62adb5-c8ad-4692-98d2-f3e6964ee408",
+                        "uuid": "be87379d-46ef-458e-941d-6b74d95056b2",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "5aa6b89c-9d27-453e-b898-fde8f34196e2"
+                                "output_name": "plotdata",
+                                "uuid": "3690aff1-2671-4667-8b30-82e69cd93ae4"
                             },
                             {
                                 "label": null,
-                                "output_name": "sqlitedb",
-                                "uuid": "1c5e9fbb-cf66-4369-a0ac-be3637359966"
+                                "output_name": "wrapped_outfile",
+                                "uuid": "46b92417-58a7-47f1-b144-21b4ec612962"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
                         "errors": null,
                         "id": 9,
                         "input_connections": {
-                            "tables_0|table": {
-                                "id": 4,
-                                "output_name": "output_psm"
+                            "infile": {
+                                "id": 6,
+                                "output_name": "outfile"
                             },
-                            "tables_1|table": {
-                                "id": 7,
-                                "output_name": "output_tsv"
+                            "samps": {
+                                "id": 1,
+                                "output_name": "samples_file"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Query Tabular",
-                                "name": "add_to_database"
-                            }
-                        ],
-                        "label": "Genera | PSMs | Peptides",
-                        "name": "Query Tabular",
+                        "inputs": [],
+                        "label": "T7-Bar-Plot",
+                        "name": "metaQuantome: visualize",
                         "outputs": [
                             {
-                                "name": "sqlitedb",
-                                "type": "sqlite"
+                                "name": "wrapped_outfile",
+                                "type": "html"
                             },
                             {
-                                "name": "output",
+                                "name": "plotdata",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 911.109375,
-                            "height": 282,
-                            "left": 955.5,
-                            "right": 1155.5,
-                            "top": 629.109375,
+                            "bottom": 1273.5625,
+                            "height": 292,
+                            "left": 1358.484375,
+                            "right": 1558.484375,
+                            "top": 981.5625,
                             "width": 200,
-                            "x": 955.5,
-                            "y": 629.109375
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Genera | PSMs | Peptides"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
+                            "x": 1358.484375,
+                            "y": 981.5625
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "33d61c89fb8d",
-                            "name": "query_tabular",
-                            "owner": "iuc",
+                            "changeset_revision": "eb811f3018ea",
+                            "name": "metaquantome_viz",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"save_db\": \"true\", \"sqlquery\": \"SELECT lca.genus,count(psm.sequence) as \\\"PSMs\\\",count(distinct psm.sequence) as \\\"DISTINCT PEPTIDES\\\" \\nFROM psm LEFT JOIN lca ON psm.sequence = lca.peptide \\nWHERE confidence >= 95 \\nGROUP BY lca.genus \\nORDER BY PSMs desc, 'DISTINCT PEPTIDES' desc\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"regex\", \"__current_case__\": 6, \"regex_pattern\": \"^\\\\d\", \"regex_action\": \"include_match\"}}]}, \"tbl_opts\": {\"table_name\": \"psm\", \"column_names_from_first_line\": \"false\", \"col_names\": \",,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\", \"load_named_columns\": \"true\", \"pkey_autoincr\": \"\", \"indexes\": []}}, {\"__index__\": 1, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"regex\", \"__current_case__\": 6, \"regex_pattern\": \"#peptide\", \"regex_action\": \"exclude_match\"}}]}, \"tbl_opts\": {\"table_name\": \"lca\", \"column_names_from_first_line\": \"false\", \"col_names\": \"peptide,,,,,,,,,,,,,,,,,,,,,genus\", \"load_named_columns\": \"true\", \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.0.0",
+                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"f\", \"__current_case__\": 0, \"ontology\": \"go\", \"plot\": {\"plottype\": \"bar\", \"__current_case__\": 0, \"meancol\": \"T7_mean\", \"nterms\": \"5\", \"target_onto\": \"mf\", \"barcol\": \"2\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
                         "type": "tool",
-                        "uuid": "70beb05c-8f4f-49d8-8d51-101a116e3084",
+                        "uuid": "d9b6f1d7-671d-4d7a-915f-2cb12a2e1d7f",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "sqlitedb",
-                                "uuid": "2679b146-1262-4a79-87e3-6eef09d2ac9b"
+                                "output_name": "plotdata",
+                                "uuid": "48d40170-76bb-4b9e-a014-9b7f16d4212b"
                             },
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "f9a3fa9f-6984-4e69-8d40-e60702ea2e66"
+                                "output_name": "wrapped_outfile",
+                                "uuid": "51f1a1c6-960d-4f74-9cce-bf7d03f57297"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
                         "errors": null,
                         "id": 10,
                         "input_connections": {
-                            "sqlitedb": {
-                                "id": 8,
-                                "output_name": "sqlitedb"
+                            "infile": {
+                                "id": 6,
+                                "output_name": "outfile"
+                            },
+                            "samps": {
+                                "id": 1,
+                                "output_name": "samples_file"
                             }
                         },
                         "inputs": [],
-                        "label": "GO Terms: Biological Processes",
-                        "name": "SQLite to tabular",
+                        "label": "T7-T2-Volcano-Plot",
+                        "name": "metaQuantome: visualize",
                         "outputs": [
                             {
-                                "name": "query_results",
+                                "name": "wrapped_outfile",
+                                "type": "html"
+                            },
+                            {
+                                "name": "plotdata",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 247.609375,
-                            "height": 112,
-                            "left": 1298,
-                            "right": 1498,
-                            "top": 135.609375,
+                            "bottom": 783.9375,
+                            "height": 332,
+                            "left": 1647.078125,
+                            "right": 1847.078125,
+                            "top": 451.9375,
                             "width": 200,
-                            "x": 1298,
-                            "y": 135.609375
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionquery_results": {
-                                "action_arguments": {
-                                    "newname": "GO Terms: Biological Processes"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "query_results"
-                            }
+                            "x": 1647.078125,
+                            "y": 451.9375
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "b722161a845a",
-                            "name": "sqlite_to_tabular",
-                            "owner": "iuc",
+                            "changeset_revision": "eb811f3018ea",
+                            "name": "metaquantome_viz",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"sqlitedb\": {\"__class__\": \"ConnectedValue\"}, \"sqlquery\": \"SELECT go.description, \\ncount(distinct bering_psms.sequence) as \\\"bering_peptides\\\", count(distinct bering_psms.id) as \\\"bering_psms\\\" \\nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\\nWHERE go.aspect = 'biological_process'\\nGROUP BY go.description\\nORDER BY  bering_peptides desc,bering_psms desc\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.0",
+                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"f\", \"__current_case__\": 0, \"ontology\": \"go\", \"plot\": {\"plottype\": \"volcano\", \"__current_case__\": 1, \"fc_name\": \"log2fc_T7_over_T2\", \"fc_corr_p\": \"corrected_p_T7_over_T2\", \"textannot\": \"id\", \"flip_fc\": \"false\", \"gosplit\": \"true\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
                         "type": "tool",
-                        "uuid": "d189e68e-b1de-4f30-89a7-319810b7d536",
+                        "uuid": "19539885-0990-4eda-8f07-deb39f11343f",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "query_results",
-                                "uuid": "baad84e0-4201-4275-923d-dd5a0956ecef"
+                                "output_name": "plotdata",
+                                "uuid": "f78ca1ea-8601-49a4-b816-7c1b9f97b06a"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "wrapped_outfile",
+                                "uuid": "48985efc-d6ef-4560-bc06-be28aec7e6d8"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
                         "errors": null,
                         "id": 11,
                         "input_connections": {
-                            "sqlitedb": {
-                                "id": 8,
-                                "output_name": "sqlitedb"
+                            "infile": {
+                                "id": 6,
+                                "output_name": "outfile"
+                            },
+                            "samps": {
+                                "id": 1,
+                                "output_name": "samples_file"
                             }
                         },
                         "inputs": [],
-                        "label": "GO Terms: Molecular Functions",
-                        "name": "SQLite to tabular",
+                        "label": "T4-T2-Volcano-Plot",
+                        "name": "metaQuantome: visualize",
                         "outputs": [
                             {
-                                "name": "query_results",
+                                "name": "wrapped_outfile",
+                                "type": "html"
+                            },
+                            {
+                                "name": "plotdata",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 386.609375,
-                            "height": 112,
-                            "left": 1310,
-                            "right": 1510,
-                            "top": 274.609375,
+                            "bottom": 1148.53125,
+                            "height": 332,
+                            "left": 1644.46875,
+                            "right": 1844.46875,
+                            "top": 816.53125,
                             "width": 200,
-                            "x": 1310,
-                            "y": 274.609375
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionquery_results": {
-                                "action_arguments": {
-                                    "newname": "GO Terms: Molecular Functions"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "query_results"
-                            }
+                            "x": 1644.46875,
+                            "y": 816.53125
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "b722161a845a",
-                            "name": "sqlite_to_tabular",
-                            "owner": "iuc",
+                            "changeset_revision": "eb811f3018ea",
+                            "name": "metaquantome_viz",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"sqlitedb\": {\"__class__\": \"ConnectedValue\"}, \"sqlquery\": \"SELECT go.description, \\ncount(distinct bering_psms.sequence) as \\\"bering_peptides\\\", count(distinct bering_psms.id) as \\\"bering_psms\\\" \\nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\\nWHERE go.aspect = 'molecular_function'\\nGROUP BY go.description\\nORDER BY  bering_peptides desc,bering_psms desc\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.0",
+                        "tool_state": "{\"height\": null, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"mode_args\": {\"mode\": \"f\", \"__current_case__\": 0, \"ontology\": \"go\", \"plot\": {\"plottype\": \"volcano\", \"__current_case__\": 1, \"fc_name\": \"log2fc_T4_over_T2\", \"fc_corr_p\": \"corrected_p_T4_over_T2\", \"textannot\": \"id\", \"flip_fc\": \"false\", \"gosplit\": \"true\"}}, \"samps\": {\"__class__\": \"ConnectedValue\"}, \"width\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy0",
                         "type": "tool",
-                        "uuid": "d2a2e7cb-26be-4db9-b275-e805116f1832",
+                        "uuid": "80ea05c8-f9c1-46f1-a0d0-a66c494d22fd",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "query_results",
-                                "uuid": "62313ee8-9c3b-4f3e-92ae-cc095a3313a7"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
-                        "errors": null,
-                        "id": 12,
-                        "input_connections": {
-                            "sqlitedb": {
-                                "id": 8,
-                                "output_name": "sqlitedb"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "GO Terms: Cellular Localization",
-                        "name": "SQLite to tabular",
-                        "outputs": [
-                            {
-                                "name": "query_results",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 546.609375,
-                            "height": 112,
-                            "left": 1311,
-                            "right": 1511,
-                            "top": 434.609375,
-                            "width": 200,
-                            "x": 1311,
-                            "y": 434.609375
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionquery_results": {
-                                "action_arguments": {
-                                    "newname": "GO Terms: Cellular Localization"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "query_results"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b722161a845a",
-                            "name": "sqlite_to_tabular",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"sqlitedb\": {\"__class__\": \"ConnectedValue\"}, \"sqlquery\": \"SELECT go.description, \\ncount(distinct bering_psms.sequence) as \\\"bering_peptides\\\", count(distinct bering_psms.id) as \\\"bering_psms\\\" \\nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\\nWHERE go.aspect = 'cellular_component'\\nGROUP BY go.description\\nORDER BY  bering_peptides desc,bering_psms desc\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.0",
-                        "type": "tool",
-                        "uuid": "0068d768-bedb-4222-8fa7-741dcc41ce84",
-                        "workflow_outputs": [
+                                "output_name": "plotdata",
+                                "uuid": "2fbd499f-b9e7-403e-bbc9-e13670cacd52"
+                            },
                             {
                                 "label": null,
-                                "output_name": "query_results",
-                                "uuid": "191c2b4f-e525-451a-be37-4c24f0490d83"
+                                "output_name": "wrapped_outfile",
+                                "uuid": "4be072a7-8373-4d49-a71a-ffdc1ac318de"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/metaproteomics",
-                "path": "topics/proteomics/tutorials/metaproteomics/workflows/workflow.ga",
+                "parent_id": "proteomics/metaquantome-function",
+                "path": "topics/proteomics/tutorials/metaquantome-function/workflows/main_workflow.ga",
                 "tags": [
                     "proteomics"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Metaproteomics_GTN",
+                "title": "metaquantome-function-worklow",
                 "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-metaproteomics/versions/workflow",
-                "tutorial_id": "metaproteomics",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaproteomics/workflows/workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaproteomics/workflows/workflow.html",
-                "version": 7,
-                "wfid": "proteomics-metaproteomics",
-                "wfname": "workflow",
-                "workflow": "workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-metaquantome-function/versions/main-workflow",
+                "tutorial_id": "metaquantome-function",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaquantome-function/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaquantome-function/workflows/main_workflow.html",
+                "version": 2,
+                "wfid": "proteomics-metaquantome-function",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0"
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0"
                 ],
-                "workflowhub_id": "1159"
+                "workflowhub_id": "1221"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.839701"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.4110725"
     },
     {
         "admin_install": {
@@ -193012,142 +194540,240 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "maxquant",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "dbbuilder",
                     "owner": "galaxyp",
-                    "revisions": "e42225f8a659",
-                    "tool_panel_section_label": "Proteomics",
+                    "revisions": "983bf725dfc2",
+                    "tool_panel_section_label": "Get Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "msstatstmt",
+                    "name": "fasta_merge_files_and_filter_unique_sequences",
                     "owner": "galaxyp",
-                    "revisions": "a5e394b36d87",
+                    "revisions": "f546e7278f04",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pepquery2",
+                    "owner": "galaxyp",
+                    "revisions": "a07976bbc4d9",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "uniprotxml_downloader",
+                    "owner": "galaxyp",
+                    "revisions": "a371252a2cf6",
+                    "tool_panel_section_label": "Get Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "query_tabular",
+                    "owner": "iuc",
+                    "revisions": "cf34c344508d",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "90981f86000f",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: maxquant\n  owner: galaxyp\n  revisions: e42225f8a659\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msstatstmt\n  owner: galaxyp\n  revisions: a5e394b36d87\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/maxquant-msstats-tmt/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dbbuilder\n  owner: galaxyp\n  revisions: 983bf725dfc2\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_merge_files_and_filter_unique_sequences\n  owner: galaxyp\n  revisions: f546e7278f04\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pepquery2\n  owner: galaxyp\n  revisions: a07976bbc4d9\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: uniprotxml_downloader\n  owner: galaxyp\n  revisions: a371252a2cf6\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n  owner: iuc\n  revisions: cf34c344508d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "subinamehta",
+                "katherine-d21",
+                "dechendb"
+            ],
+            "editing": [
+                "pratikdjagtap",
+                "timothygriffin"
+            ]
+        },
         "contributors": [
             {
-                "id": "KlemensFroehlich",
-                "joined": "2021-08",
-                "name": "Klemens Fr\u00f6hlich",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/KlemensFroehlich/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/KlemensFroehlich.json"
+                "email": "subinamehta@gmail.com",
+                "id": "subinamehta",
+                "joined": "2018-06",
+                "linkedin": "subinamehta",
+                "matrix": "subinamehta:matrix.org",
+                "name": "Subina Mehta",
+                "orcid": "0000-0001-9818-0537",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
+                "twitter": "Subina_Mehta",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
             },
             {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "email": "melanie.foell@mol-med.uni-freiburg.de",
-                "id": "foellmelanie",
-                "joined": "2018-10",
-                "matrix": "foellmelanie:matrix.org",
-                "name": "Melanie F\u00f6ll",
-                "orcid": "0000-0002-1887-7543",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
-                "twitter": "MCFoell",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
+                "id": "katherine-d21",
+                "joined": "2023-08",
+                "name": "Katherine Do",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/katherine-d21/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/katherine-d21.json"
             },
             {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "email": "matthias.fahrner@uniklinik-freiburg.de",
-                "id": "matthias313",
-                "joined": "2019-03",
-                "name": "Matthias Fahrner",
-                "orcid": "0000-0001-7955-2518",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/matthias313/",
-                "twitter": "mfahrner313",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/matthias313.json"
+                "id": "dechendb",
+                "joined": "2023-06",
+                "name": "Dechen Bhuming",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dechendb/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/dechendb.json"
+            },
+            {
+                "email": "pjagtap@umn.edu",
+                "id": "pratikdjagtap",
+                "joined": "2017-09",
+                "name": "Pratik Jagtap",
+                "orcid": "0000-0003-0984-0973",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
+            },
+            {
+                "email": "tgriffin@umn.edu",
+                "github": false,
+                "id": "timothygriffin",
+                "joined": "2017-09",
+                "name": "Timothy J. Griffin",
+                "orcid": "0000-0001-6801-2559",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/maxquant-msstats-tmt",
-        "edam_operation": [
-            "Visualisation",
-            "Imputation",
-            "Heat map generation",
-            "Standardisation and normalisation",
-            "Principal component plotting",
-            "Protein quantification",
-            "Clustering",
-            "Statistical calculation"
-        ],
+        "dir": "topics/proteomics/tutorials/clinical-mp-3-verification",
+        "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org.au"
+            "UseGalaxy.cz",
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "proteomics",
+                "tutorials": [
+                    "clinical-mp-4-quantitation"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "proteomics/maxquant-msstats-tmt",
+        "id": "proteomics/clinical-mp-3-verification",
         "inexact_supported_servers": [
-            "UseGalaxy.cz"
+            "UseGalaxy.org.au"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "MaxQuant in combination with MSstatsTMT enables quantitative analysis of TMT data."
+            "Perform verification",
+            "Extraction of accession numbers for getting protein sequences"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-08-08",
         "objectives": [
-            "Learn how to use MaxQuant and MSstats for the analysis of TMT labelled shotgun (DDA) data",
-            "Learn how to create an experimental design template for fractionated data in MaxQuant",
-            "Learn how to create an annotation file for MSstatsTMT"
+            "Verification of peptides helps in confirming the presence of the peptides in our samplle"
         ],
-        "pageviews": 4621,
-        "pub_date": "2021-08-13",
+        "pageviews": 89,
+        "pub_date": "2024-02-06",
         "questions": [
-            "How to analyze tandem-mass-tag (TMT) labelled shotgun (DDA) data analysis in MaxQuant and MSstats?",
-            "Which proteins are differentially abundant between KMT9\u03b1 knock-down and control cells?"
+            "Why do we need to verify our identified peptides",
+            "What is the importance of making a new database for quantification"
         ],
-        "short_id": "T00220",
+        "recordings": [
+            {
+                "captioners": [
+                    "katherine-d21"
+                ],
+                "date": "2024-06-21",
+                "galaxy_version": "23.1",
+                "length": "16M",
+                "speakers": [
+                    "katherine-d21"
+                ],
+                "youtube_id": "wCVzWMQANGE"
+            }
+        ],
+        "redirect_from": [
+            "/topics/proteomics/tutorials/clinical-mp-data-verification/tutorial",
+            "/short/proteomics/clinical-mp-3-verification",
+            "/short/T00415"
+        ],
+        "requirements": [
+            {
+                "topic_name": "proteomics",
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00415",
         "short_tools": [
-            "maxquant",
-            "msstatstmt"
+            "query_tabular",
+            "tp_cat",
+            "fasta_merge_files_and_filter_unique_sequences",
+            "Filter1",
+            "dbbuilder",
+            "Cut1",
+            "uniprotxml_downloader",
+            "collapse_dataset",
+            "Remove beginning1",
+            "pepquery2",
+            "Grouping1"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "id-quant",
+        "subtopic": "clinical-metaproteomics",
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 }
             ],
             "inexact": [
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
         "tags": [
-            "DDA",
-            "TMT"
+            "label-TMT11"
         ],
         "time_estimation": "3H",
-        "title": "MaxQuant and MSstats for the analysis of TMT data",
+        "title": "Clinical Metaproteomics 3: Verification",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.17.0+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/msstatstmt/msstatstmt/2.0.0+galaxy0"
+            "Cut1",
+            "Filter1",
+            "Grouping1",
+            "Remove beginning1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery2/pepquery2/2.0.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.4.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
         ],
         "topic_name": "proteomics",
         "topic_name_human": "Proteomics",
@@ -193157,44 +194783,43 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "maxquant-msstats-tmt",
+        "tutorial_name": "clinical-mp-3-verification",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-msstats-tmt/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/maxquant-msstats-tmt/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/maxquant-msstats-tmt/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.json"
         },
-        "version": 10,
+        "version": 4,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 102,
-        "visitors": 3357,
+        "visit_duration": 634,
+        "visitors": 53,
         "workflows": [
             {
-                "creators": [],
-                "description": "MaxQuant and MSstats for the analysis of TMT data",
+                "creators": [
+                    {
+                        "class": "Organization",
+                        "identifier": "0000-0001-9818-0537",
+                        "name": "Subina Mehta"
+                    }
+                ],
+                "description": "WF3- Peptide verification/validaiton workflow",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nExperimental design template\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMSstats annotation file\"]\n  3[label=\"MaxQuant\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"MSstatsTMT\"]\n  2 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"evidence\"]\n  3 -> 4 [label=\"proteinGroups\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Human UniProt+Isoforms FASTA\"]\n  k4bdae9fbeb484821a806e7dd3a8c7101[color=lightseagreen,label=\"Output\\nHuman UniProt+Isoforms FASTA\"]\n  0 -> k4bdae9fbeb484821a806e7dd3a8c7101\n  1[label=\"cRAP\"]\n  k13ddaf34d3464cc4b5b6fee2b5e0c1aa[color=lightseagreen,label=\"Output\\ncRAP\"]\n  1 -> k13ddaf34d3464cc4b5b6fee2b5e0c1aa\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput MGFs Dataset Collection\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSGPS_peptide-report\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDistinct Peptides for PepQuery\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMaxQuant-peptide-report\"]\n  6[label=\"Human UniProt+Isoforms+cRAP FASTA\"]\n  0 -> 6 [label=\"output_database\"]\n  1 -> 6 [label=\"output_database\"]\n  k62c376eb85a349768024bd72ac528af3[color=lightseagreen,label=\"Output\\nHuman UniProt+Isoforms+cRAP FASTA\"]\n  6 -> k62c376eb85a349768024bd72ac528af3\n  7[label=\"Cut\"]\n  3 -> 7 [label=\"output\"]\n  8[label=\"Cut\"]\n  5 -> 8 [label=\"output\"]\n  9[label=\"PepQuery2\"]\n  6 -> 9 [label=\"output\"]\n  4 -> 9 [label=\"output\"]\n  2 -> 9 [label=\"output\"]\n  10[label=\"Remove beginning\"]\n  7 -> 10 [label=\"out_file1\"]\n  11[label=\"Remove beginning\"]\n  8 -> 11 [label=\"out_file1\"]\n  12[label=\"Collapse Collection\"]\n  9 -> 12 [label=\"psm_rank_txt\"]\n  13[label=\"Concatenate datasets\"]\n  10 -> 13 [label=\"out_file1\"]\n  11 -> 13 [label=\"out_file1\"]\n  14[label=\"Filter\"]\n  12 -> 14 [label=\"output\"]\n  15[label=\"Remove beginning\"]\n  14 -> 15 [label=\"out_file1\"]\n  16[label=\"Cut\"]\n  15 -> 16 [label=\"out_file1\"]\n  17[label=\"Peptide and Protein from Peptide reports\"]\n  16 -> 17 [label=\"out_file1\"]\n  13 -> 17 [label=\"out_file1\"]\n  kbc4e33da40644b78bb155732b08b9316[color=lightseagreen,label=\"Output\\nPeptide and Protein from Peptide reports\"]\n  17 -> kbc4e33da40644b78bb155732b08b9316\n  18[label=\"Remove beginning\"]\n  17 -> 18 [label=\"output\"]\n  19[label=\"Group\"]\n  18 -> 19 [label=\"out_file1\"]\n  20[label=\"Uniprot-ID from verified Peptides\"]\n  19 -> 20 [label=\"out_file1\"]\n  kcd6c81d81f444129b5052ee4dde10cd2[color=lightseagreen,label=\"Output\\nUniprot-ID from verified Peptides\"]\n  20 -> kcd6c81d81f444129b5052ee4dde10cd2\n  21[label=\"UniProt\"]\n  20 -> 21 [label=\"output\"]\n  22[label=\"Quantitation Database for MaxQuant\"]\n  0 -> 22 [label=\"output_database\"]\n  1 -> 22 [label=\"output_database\"]\n  21 -> 22 [label=\"proteome\"]\n  ka52b5136db74496f9b66ec1064f2301d[color=lightseagreen,label=\"Output\\nQuantitation Database for MaxQuant\"]\n  22 -> ka52b5136db74496f9b66ec1064f2301d\n}",
                 "history": [
                     {
-                        "hash": "8926310c66f250b5e34d1b68039572f5ec8024d9",
-                        "message": "correcting workflow",
-                        "num": 2,
-                        "short_hash": "8926310c6",
-                        "unix": "1628863550"
-                    },
-                    {
-                        "hash": "0d66511e27870d0346a8da4d1a84e697501d055d",
-                        "message": "new maxquant msstats tmt training",
+                        "hash": "e0464fd1787b4ca7dea72ca77b7ab2ad03a8292a",
+                        "message": "add workflows",
                         "num": 1,
-                        "short_hash": "0d66511e2",
-                        "unix": "1628863148"
+                        "short_hash": "e0464fd17",
+                        "unix": "1723118192"
                     }
                 ],
                 "inputs": [
@@ -193202,437 +194827,475 @@
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Input Dataset Collection"
+                                "name": "Input MGFs Dataset Collection"
                             }
                         ],
-                        "label": "Input Dataset Collection",
+                        "label": "Input MGFs Dataset Collection",
                         "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "bottom": 241.5500030517578,
-                            "height": 82.55000305175781,
-                            "left": 567,
-                            "right": 767,
-                            "top": 159,
-                            "width": 200,
-                            "x": 567,
-                            "y": 159
+                            "left": 26.467106653090468,
+                            "top": 441.64657624309564
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
                         "tool_version": null,
                         "type": "data_collection_input",
-                        "uuid": "75fdd4a0-50ea-4d89-833e-13119df2b7fe",
-                        "workflow_outputs": [
+                        "uuid": "4c4f20b4-3fa6-48a2-b4b0-6480a0dd230a",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "2f2012bd-d7fe-43be-86d8-4c6d233ae83d"
+                                "description": "",
+                                "name": "SGPS_peptide-report"
                             }
-                        ]
+                        ],
+                        "label": "SGPS_peptide-report",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 49.219598040314054,
+                            "top": 775.0615167366277
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "2d7b777c-8bb9-4de8-af72-4cae64cd5eaf",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 4,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Experimental design template"
+                                "name": "Distinct Peptides for PepQuery"
                             }
                         ],
-                        "label": "Experimental design template",
+                        "label": "Distinct Peptides for PepQuery",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 393.5500030517578,
-                            "height": 82.55000305175781,
-                            "left": 571,
-                            "right": 771,
-                            "top": 311,
-                            "width": 200,
-                            "x": 571,
-                            "y": 311
+                            "left": 974.964669791108,
+                            "top": 210.36937340005647
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "1b701c96-82fe-441d-afcc-51e4f7a1b09a",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1796d087-a179-4174-aec3-a89f45c9a367"
-                            }
-                        ]
+                        "uuid": "dbc1b4b1-bb63-4c13-8adb-d9a0febc8e17",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 5,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "MSstats annotation file"
+                                "name": "MaxQuant-peptide-report"
                             }
                         ],
-                        "label": "MSstats annotation file",
+                        "label": "MaxQuant-peptide-report",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 851.5500030517578,
-                            "height": 82.55000305175781,
-                            "left": 813,
-                            "right": 1013,
-                            "top": 769,
-                            "width": 200,
-                            "x": 813,
-                            "y": 769
+                            "left": 29.12351833088178,
+                            "top": 1007.203580787368
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "01633bc9-8d2d-4b03-9100-958febc2cbec",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1ff0fa8b-cf25-420f-acda-ac8a2d18b29e"
-                            }
-                        ]
+                        "uuid": "2c07aebc-8b9e-4f4e-9020-9a50664ac648",
+                        "when": null,
+                        "workflow_outputs": []
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nExperimental design template\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nMSstats annotation file\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"MaxQuant\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  4[\"MSstatsTMT\"];\n  2 -->|output| 4;\n  3 -->|evidence| 4;\n  3 -->|proteinGroups| 4;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "MaxQuant MSstatsTMT Training",
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"Human UniProt+Isoforms FASTA\"];\n  4bdae9fb-eb48-4821-a806-e7dd3a8c7101[\"Output\\nHuman UniProt+Isoforms FASTA\"];\n  0 --> 4bdae9fb-eb48-4821-a806-e7dd3a8c7101;\n  style 4bdae9fb-eb48-4821-a806-e7dd3a8c7101 stroke:#2c3143,stroke-width:4px;\n  1[\"cRAP\"];\n  13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa[\"Output\\ncRAP\"];\n  1 --> 13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa;\n  style 13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nInput MGFs Dataset Collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nSGPS_peptide-report\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nDistinct Peptides for PepQuery\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nMaxQuant-peptide-report\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"Human UniProt+Isoforms+cRAP FASTA\"];\n  0 -->|output_database| 6;\n  1 -->|output_database| 6;\n  62c376eb-85a3-4976-8024-bd72ac528af3[\"Output\\nHuman UniProt+Isoforms+cRAP FASTA\"];\n  6 --> 62c376eb-85a3-4976-8024-bd72ac528af3;\n  style 62c376eb-85a3-4976-8024-bd72ac528af3 stroke:#2c3143,stroke-width:4px;\n  7[\"Cut\"];\n  3 -->|output| 7;\n  8[\"Cut\"];\n  5 -->|output| 8;\n  9[\"PepQuery2\"];\n  6 -->|output| 9;\n  4 -->|output| 9;\n  2 -->|output| 9;\n  10[\"Remove beginning\"];\n  7 -->|out_file1| 10;\n  11[\"Remove beginning\"];\n  8 -->|out_file1| 11;\n  12[\"Collapse Collection\"];\n  9 -->|psm_rank_txt| 12;\n  13[\"Concatenate datasets\"];\n  10 -->|out_file1| 13;\n  11 -->|out_file1| 13;\n  14[\"Filter\"];\n  12 -->|output| 14;\n  15[\"Remove beginning\"];\n  14 -->|out_file1| 15;\n  16[\"Cut\"];\n  15 -->|out_file1| 16;\n  17[\"Peptide and Protein from Peptide reports\"];\n  16 -->|out_file1| 17;\n  13 -->|out_file1| 17;\n  bc4e33da-4064-4b78-bb15-5732b08b9316[\"Output\\nPeptide and Protein from Peptide reports\"];\n  17 --> bc4e33da-4064-4b78-bb15-5732b08b9316;\n  style bc4e33da-4064-4b78-bb15-5732b08b9316 stroke:#2c3143,stroke-width:4px;\n  18[\"Remove beginning\"];\n  17 -->|output| 18;\n  19[\"Group\"];\n  18 -->|out_file1| 19;\n  20[\"Uniprot-ID from verified Peptides\"];\n  19 -->|out_file1| 20;\n  cd6c81d8-1f44-4129-b505-2ee4dde10cd2[\"Output\\nUniprot-ID from verified Peptides\"];\n  20 --> cd6c81d8-1f44-4129-b505-2ee4dde10cd2;\n  style cd6c81d8-1f44-4129-b505-2ee4dde10cd2 stroke:#2c3143,stroke-width:4px;\n  21[\"UniProt\"];\n  20 -->|output| 21;\n  22[\"Quantitation Database for MaxQuant\"];\n  0 -->|output_database| 22;\n  1 -->|output_database| 22;\n  21 -->|proteome| 22;\n  a52b5136-db74-496f-9b66-ec1064f2301d[\"Output\\nQuantitation Database for MaxQuant\"];\n  22 --> a52b5136-db74-496f-9b66-ec1064f2301d;\n  style a52b5136-db74-496f-9b66-ec1064f2301d stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "WF3_VERIFICATION_WORKFLOW",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": "Human UniProt+Isoforms FASTA",
+                        "name": "Protein Database Downloader",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Input Dataset Collection"
+                                "name": "output_database",
+                                "type": "fasta"
                             }
                         ],
-                        "label": "Input Dataset Collection",
-                        "name": "Input dataset collection",
-                        "outputs": [],
                         "position": {
-                            "bottom": 241.5500030517578,
-                            "height": 82.55000305175781,
-                            "left": 567,
-                            "right": 767,
-                            "top": 159,
-                            "width": 200,
-                            "x": 567,
-                            "y": 159
+                            "left": 0,
+                            "top": 0
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "75fdd4a0-50ea-4d89-833e-13119df2b7fe",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_database": {
+                                "action_arguments": {
+                                    "newname": "Human UniProt+Isoforms FASTA"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_database"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "983bf725dfc2",
+                            "name": "dbbuilder",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"data\", \"__workflow_invocation_uuid__\": \"08a702aa736d11ee91a5001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"9606\", \"taxon_id\": null, \"reviewed\": \"\", \"set\": \"keyword:KW-1185\", \"include_isoform\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3.4",
+                        "type": "tool",
+                        "uuid": "ff0bbbc9-35b4-44a6-b6bb-a1969ca01eb6",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "2f2012bd-d7fe-43be-86d8-4c6d233ae83d"
+                                "label": "Human UniProt+Isoforms FASTA",
+                                "output_name": "output_database",
+                                "uuid": "4bdae9fb-eb48-4821-a806-e7dd3a8c7101"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": "cRAP",
+                        "name": "Protein Database Downloader",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Experimental design template"
+                                "name": "output_database",
+                                "type": "fasta"
                             }
                         ],
-                        "label": "Experimental design template",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 393.5500030517578,
-                            "height": 82.55000305175781,
-                            "left": 571,
-                            "right": 771,
-                            "top": 311,
-                            "width": 200,
-                            "x": 571,
-                            "y": 311
+                            "left": 20.775440205938253,
+                            "top": 196.89138890513698
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "1b701c96-82fe-441d-afcc-51e4f7a1b09a",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_database": {
+                                "action_arguments": {
+                                    "newname": "cRAP"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_database"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "983bf725dfc2",
+                            "name": "dbbuilder",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"data\", \"__workflow_invocation_uuid__\": \"08a702aa736d11ee91a5001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"cRAP\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3.4",
+                        "type": "tool",
+                        "uuid": "fa25fdbf-2cec-48fc-94f3-7c47888753b0",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1796d087-a179-4174-aec3-a89f45c9a367"
+                                "label": "cRAP",
+                                "output_name": "output_database",
+                                "uuid": "13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 6,
+                        "input_connections": {
+                            "batchmode|input_fastas_0|input_fasta": {
+                                "id": 0,
+                                "output_name": "output_database"
+                            },
+                            "batchmode|input_fastas_1|input_fasta": {
+                                "id": 1,
+                                "output_name": "output_database"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Human UniProt+Isoforms+cRAP FASTA",
+                        "name": "FASTA Merge Files and Filter Unique Sequences",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "MSstats annotation file"
+                                "name": "output",
+                                "type": "fasta"
                             }
                         ],
-                        "label": "MSstats annotation file",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 851.5500030517578,
-                            "height": 82.55000305175781,
-                            "left": 813,
-                            "right": 1013,
-                            "top": 769,
-                            "width": 200,
-                            "x": 813,
-                            "y": 769
+                            "left": 497.09213191562515,
+                            "top": 177.90819833483664
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "01633bc9-8d2d-4b03-9100-958febc2cbec",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Human UniProt+Isoforms+cRAP FASTA"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f546e7278f04",
+                            "name": "fasta_merge_files_and_filter_unique_sequences",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"__workflow_invocation_uuid__\": \"08a702aa736d11ee91a5001e67d2ec02\", \"accession_parser\": \"^>([^ ]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"uniqueness_criterion\": \"sequence\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.0",
+                        "type": "tool",
+                        "uuid": "67f1d2d4-d347-49ff-a941-885987a8254e",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "Human UniProt+Isoforms+cRAP FASTA",
                                 "output_name": "output",
-                                "uuid": "1ff0fa8b-cf25-420f-acda-ac8a2d18b29e"
+                                "uuid": "62c376eb-85a3-4976-8024-bd72ac528af3"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.17.0+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0",
                         "errors": null,
-                        "id": 3,
+                        "id": 17,
                         "input_connections": {
-                            "input_opts|fasta_files": {
-                                "id": 0,
-                                "output_name": "output"
+                            "tables_0|table": {
+                                "id": 16,
+                                "output_name": "out_file1"
                             },
-                            "search_opts|template": {
-                                "id": 1,
-                                "output_name": "output"
+                            "tables_1|table": {
+                                "id": 13,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "MaxQuant",
+                        "label": "Peptide and Protein from Peptide reports",
+                        "name": "Query Tabular",
                         "outputs": [
                             {
-                                "name": "proteinGroups",
+                                "name": "output",
                                 "type": "tabular"
-                            },
+                            }
+                        ],
+                        "position": {
+                            "left": 2219.7817115852936,
+                            "top": 625.4286563925251
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Peptide and Protein from Peptide reports"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "cf34c344508d",
+                            "name": "query_tabular",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"__workflow_invocation_uuid__\": \"08a702aa736d11ee91a5001e67d2ec02\", \"add_to_database\": {\"withdb\": null}, \"addqueries\": {\"queries\": []}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"\"}, \"save_db\": false, \"sqlquery\": \"select pep.mpep, prot.prot\\nFROM pep\\nINNER JOIN  prot on pep.mpep=prot.pep \", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"pep\", \"column_names_from_first_line\": false, \"col_names\": \"mpep\", \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"indexes\": []}}, {\"__index__\": 1, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"prot\", \"column_names_from_first_line\": false, \"col_names\": \"pep,prot\", \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.3.0",
+                        "type": "tool",
+                        "uuid": "93abe6e7-0034-460f-b517-418c4ed9d43a",
+                        "when": null,
+                        "workflow_outputs": [
                             {
-                                "name": "mqpar",
-                                "type": "xml"
-                            },
+                                "label": "Peptide and Protein from Peptide reports",
+                                "output_name": "output",
+                                "uuid": "bc4e33da-4064-4b78-bb15-5732b08b9316"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0",
+                        "errors": null,
+                        "id": 20,
+                        "input_connections": {
+                            "tables_0|table": {
+                                "id": 19,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Uniprot-ID from verified Peptides",
+                        "name": "Query Tabular",
+                        "outputs": [
                             {
-                                "name": "evidence",
+                                "name": "output",
                                 "type": "tabular"
-                            },
-                            {
-                                "name": "log",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "ptxqc_report",
-                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "bottom": 677.6666870117188,
-                            "height": 459.66668701171875,
-                            "left": 855,
-                            "right": 1055,
-                            "top": 218,
-                            "width": 200,
-                            "x": 855,
-                            "y": 218
+                            "left": 2545.114966014936,
+                            "top": 878.0953618681222
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.17.0+galaxy2",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Uniprot-ID from verified Peptides"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "e42225f8a659",
-                            "name": "maxquant",
-                            "owner": "galaxyp",
+                            "changeset_revision": "cf34c344508d",
+                            "name": "query_tabular",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"__workflow_invocation_uuid__\": \"8b08afb0ed1d11eb85dd001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_opts\": {\"ftype\": \".thermo.raw\", \"fasta_files\": {\"__class__\": \"ConnectedValue\"}, \"identifier_parse_rule\": \">([^\\\\s]*)\", \"description_parse_rule\": \">(.*)\"}, \"output_opts\": {\"dry_run\": \"false\", \"output\": [\"proteinGroups\", \"mqpar\", \"evidence\", \"log\"]}, \"paramGroups\": [{\"__index__\": 0, \"files\": null, \"maxMissedCleavages\": \"2\", \"fixedModifications\": [\"Carbamidomethyl (C)\"], \"variableModifications\": [\"Acetyl (Protein N-term)\", \"Oxidation (M)\"], \"enzymes\": [\"Trypsin/P\"], \"digestion_mode\": \"0\", \"quant_method\": {\"select_quant_method\": \"reporter_ion_ms2\", \"__current_case__\": 3, \"iso_labels\": {\"labeling\": \"tmt11plex\", \"__current_case__\": 4}, \"filter_by_pif\": {\"filter_pif\": \"false\", \"__current_case__\": 1}}}], \"protein_quant\": {\"peptides_for_quantification\": \"1\", \"only_unmod_prot\": {\"unmod_prot\": \"True\", \"__current_case__\": 0, \"mods_used_prot_quant\": [\"Acetyl (Protein N-term)\", \"Oxidation (M)\"], \"discard_unmod_cpart_peptides\": \"true\"}, \"lfq_opts\": {\"separateLfq\": \"false\", \"lfqStabilizeLargeRatios\": \"true\", \"lfqRequireMsms\": \"true\", \"do_ibaq\": {\"ibaq\": \"False\", \"__current_case__\": 1}, \"advancedSiteIntensities\": \"true\"}}, \"qc\": {\"do_it\": \"true\", \"__current_case__\": 0, \"parameters\": \"true\", \"summary\": \"true\", \"proteingroups\": \"true\", \"evidence\": \"true\", \"msms\": \"true\", \"msmsscans\": \"true\"}, \"search_opts\": {\"template\": {\"__class__\": \"ConnectedValue\"}, \"min_peptide_len\": \"7\", \"max_peptide_mass\": \"4600\", \"min_unique_pep\": \"0\", \"calc_peak_properties\": \"false\", \"mbr\": {\"match_between_runs\": \"False\", \"__current_case__\": 0}, \"incl_contaminants\": \"true\", \"decoy_mode\": \"revert\", \"psm_fdr\": \"0.01\", \"protein_fdr\": \"0.01\", \"min_pep_length\": \"8\", \"max_pep_length\": \"25\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.6.17.0+galaxy2",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"__workflow_invocation_uuid__\": \"08a702aa736d11ee91a5001e67d2ec02\", \"add_to_database\": {\"withdb\": null}, \"addqueries\": {\"queries\": []}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"no\", \"__current_case__\": 1}, \"save_db\": false, \"sqlquery\": \"SELECT distinct(prot) AS Accession \\nfrom t1\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"normalize\", \"__current_case__\": 12, \"columns\": \"2\", \"separator\": \";\"}}, {\"__index__\": 1, \"filter\": {\"filter_type\": \"replace\", \"__current_case__\": 11, \"column\": \"2\", \"regex_pattern\": \"(tr|sp)[|]\", \"regex_replace\": \"\", \"add\": null}}, {\"__index__\": 2, \"filter\": {\"filter_type\": \"replace\", \"__current_case__\": 11, \"column\": \"2\", \"regex_pattern\": \"[ ]+\", \"regex_replace\": \"\", \"add\": null}}, {\"__index__\": 3, \"filter\": {\"filter_type\": \"replace\", \"__current_case__\": 11, \"column\": \"2\", \"regex_pattern\": \"[|].*$\", \"regex_replace\": \"\", \"add\": null}}, {\"__index__\": 4, \"filter\": {\"filter_type\": \"normalize\", \"__current_case__\": 12, \"columns\": \"2\", \"separator\": \",\"}}]}, \"tbl_opts\": {\"table_name\": \"t1\", \"column_names_from_first_line\": true, \"col_names\": \"pep,prot\", \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.3.0",
                         "type": "tool",
-                        "uuid": "3027c4ed-81fa-4116-961e-7242cf99be29",
+                        "uuid": "fcf0a38b-8b4c-4b11-8152-ef3f5375b9e6",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "evidence",
-                                "uuid": "16cb3dce-2b9e-47bc-99ee-84ddfa57847c"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "proteinGroups",
-                                "uuid": "55166a25-0f2d-49dc-91d3-c815fbc12aa0"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "ptxqc_report",
-                                "uuid": "fcde55d8-f460-4e1e-a49c-d896fab5cf91"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "log",
-                                "uuid": "83760cea-4e21-42be-b1ae-05408528ed3e"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "mqpar",
-                                "uuid": "3d492abd-7e61-41c3-8238-4f7532a535a7"
+                                "label": "Uniprot-ID from verified Peptides",
+                                "output_name": "output",
+                                "uuid": "cd6c81d8-1f44-4129-b505-2ee4dde10cd2"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msstatstmt/msstatstmt/2.0.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
                         "errors": null,
-                        "id": 4,
+                        "id": 22,
                         "input_connections": {
-                            "input|annotation": {
-                                "id": 2,
-                                "output_name": "output"
+                            "batchmode|input_fastas_0|input_fasta": {
+                                "id": 0,
+                                "output_name": "output_database"
                             },
-                            "input|evidence": {
-                                "id": 3,
-                                "output_name": "evidence"
+                            "batchmode|input_fastas_1|input_fasta": {
+                                "id": 1,
+                                "output_name": "output_database"
                             },
-                            "input|proteinGroups": {
-                                "id": 3,
-                                "output_name": "proteinGroups"
+                            "batchmode|input_fastas_2|input_fasta": {
+                                "id": 21,
+                                "output_name": "proteome"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "MSstatsTMT",
+                        "label": "Quantitation Database for MaxQuant",
+                        "name": "FASTA Merge Files and Filter Unique Sequences",
                         "outputs": [
                             {
-                                "name": "out_qc_plot",
-                                "type": "pdf"
-                            },
-                            {
-                                "name": "out_group_comp",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "out_group_volcano_plot",
-                                "type": "pdf"
-                            },
-                            {
-                                "name": "out_group_comp_plot",
-                                "type": "pdf"
+                                "name": "output",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "bottom": 710.6666870117188,
-                            "height": 449.66668701171875,
-                            "left": 1234,
-                            "right": 1434,
-                            "top": 261,
-                            "width": 200,
-                            "x": 1234,
-                            "y": 261
+                            "left": 3070.223999018992,
+                            "top": 1289.3686346167783
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msstatstmt/msstatstmt/2.0.0+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Quantitation Database for MaxQuant"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "8375a0035d79",
-                            "name": "msstatstmt",
+                            "changeset_revision": "f546e7278f04",
+                            "name": "fasta_merge_files_and_filter_unique_sequences",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"group\": {\"group_comparison\": \"true\", \"__current_case__\": 1, \"use_comp_matrix\": {\"select\": \"false\", \"__current_case__\": 0}, \"moderated\": \"false\", \"adj_method\": \"BH\", \"remove_norm_channel\": \"true\", \"remove_empty_channel\": \"true\", \"selected_group_outputs\": [\"comparison_result\", \"VolcanoPlot\", \"ComparisonPlot\"], \"comparison_plots_opt\": {\"sig\": \"0.05\", \"FCcutoff\": null, \"logBase_pvalue\": \"10\", \"ylimUp\": null, \"ylimDown\": null, \"xlimUp\": null, \"axis_size\": \"10\", \"x_axis_size\": \"10\", \"y_axis_size\": \"10\", \"dot_size\": \"3\", \"text_size\": \"4\", \"text_angle\": \"90\", \"legend_size\": \"7\", \"ProteinName\": \"false\", \"colorkey\": \"true\", \"numProtein\": \"100\", \"clustering\": \"protein\", \"width\": \"8\", \"height\": \"5\", \"which_Protein\": {\"select\": \"all\", \"__current_case__\": 0}, \"which_Comparison\": {\"select\": \"all\", \"__current_case__\": 0}}}, \"input\": {\"input_src\": \"MaxQuant\", \"__current_case__\": 1, \"evidence\": {\"__class__\": \"ConnectedValue\"}, \"proteinGroups\": {\"__class__\": \"ConnectedValue\"}, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"proteinID\": \"Proteins\", \"input_options\": {\"rmProt_Onlyidentifiedbysite\": \"false\", \"useUniquePeptide\": \"true\", \"rmPSM_withMissing_withinRun\": \"false\", \"rmPSM_withfewMea_withinRun\": \"true\", \"rmProtein_with1Feature\": \"false\", \"summaryforMultipleRows\": \"sum\"}}, \"out_plots_opt\": {\"which_Protein\": {\"select\": \"all\", \"__current_case__\": 0}, \"width\": \"10\", \"height\": \"10\", \"adv\": {\"ylimUp\": \"false\", \"ylimDown\": \"false\", \"x_axis_size\": \"10\", \"y_axis_size\": \"10\", \"text_size\": \"4\", \"text_angle\": \"90\", \"legend_size\": \"7\", \"dot_size_profile\": \"2\", \"ncol_guide\": \"5\", \"originalPlot\": \"true\", \"summaryPlot\": \"true\"}}, \"proteinSummarization\": {\"method\": \"msstats\", \"global_norm\": \"true\", \"reference_norm\": \"true\", \"remove_norm_channel\": \"true\", \"remove_empty_channel\": \"true\", \"MBimpute\": \"true\", \"maxQuantileforCensored\": null}, \"selected_outputs\": [\"QCPlot\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.0+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"__workflow_invocation_uuid__\": \"08a702aa736d11ee91a5001e67d2ec02\", \"accession_parser\": \"^>([^ ]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"uniqueness_criterion\": \"sequence\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.0",
                         "type": "tool",
-                        "uuid": "b73daf20-e3e4-4a1d-bfd9-8597e5679cbb",
+                        "uuid": "a6060517-ee4f-4196-991f-6adf06e192c4",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_group_comp_plot",
-                                "uuid": "64c98726-4129-45b4-85e5-b8417982fff7"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_group_volcano_plot",
-                                "uuid": "d3e07901-b18b-4727-80b8-086cdce12f9b"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_group_comp",
-                                "uuid": "f387d202-696e-435a-adee-9c0f18e72538"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_qc_plot",
-                                "uuid": "6b598ae7-595d-44bf-b677-a83a41724329"
+                                "label": "Quantitation Database for MaxQuant",
+                                "output_name": "output",
+                                "uuid": "a52b5136-db74-496f-9b66-ec1064f2301d"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/maxquant-msstats-tmt",
-                "path": "topics/proteomics/tutorials/maxquant-msstats-tmt/workflows/main_workflow.ga",
+                "parent_id": "proteomics/clinical-mp-3-verification",
+                "path": "topics/proteomics/tutorials/clinical-mp-3-verification/workflows/WF3_Verification_Workflow.ga",
                 "tags": [
-                    "proteomics"
+                    "name:clinicalMP"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "MaxQuant MSstatsTMT Training",
+                "title": "WF3_VERIFICATION_WORKFLOW",
                 "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-maxquant-msstats-tmt/versions/main-workflow",
-                "tutorial_id": "maxquant-msstats-tmt",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/maxquant-msstats-tmt/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/maxquant-msstats-tmt/workflows/main_workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-clinical-mp-3-verification/versions/wf3-verification-workflow",
+                "tutorial_id": "clinical-mp-3-verification",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-3-verification/workflows/WF3_Verification_Workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-3-verification/workflows/WF3_Verification_Workflow.html",
                 "version": 1,
-                "wfid": "proteomics-maxquant-msstats-tmt",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "wfid": "proteomics-clinical-mp-3-verification",
+                "wfname": "wf3-verification-workflow",
+                "workflow": "WF3_Verification_Workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.17.0+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msstatstmt/msstatstmt/2.0.0+galaxy0"
+                    "Cut1",
+                    "Filter1",
+                    "Grouping1",
+                    "Remove beginning1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery2/pepquery2/2.0.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.4.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0",
+                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
                 ],
-                "workflowhub_id": "1227"
+                "workflowhub_id": "1351"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/5195800"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.10105821"
     },
     {
         "admin_install": {
@@ -193641,188 +195304,182 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "proteore_clusterprofiler",
-                    "owner": "proteore",
-                    "revisions": "2f67202ffdb3",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "proteore_expression_rnaseq_abbased",
-                    "owner": "proteore",
-                    "revisions": "dbeabf9bf091",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "proteore_filter_keywords_values",
-                    "owner": "proteore",
-                    "revisions": "b4641c0f8a82",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "proteore_id_converter",
-                    "owner": "proteore",
-                    "revisions": "1e45ea50f145",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "proteore_reactome",
-                    "owner": "proteore",
-                    "revisions": "9cc475dcd0f2",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "proteore_reactome",
-                    "owner": "proteore",
-                    "revisions": "6c95f1b88627",
-                    "tool_panel_section_label": "Proteomics",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "proteore_tissue_specific_expression_data",
-                    "owner": "proteore",
-                    "revisions": "3e65e0249976",
+                    "name": "cardinal_data_exporter",
+                    "owner": "galaxyp",
+                    "revisions": "d94770c22f13",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "proteore_venn_diagram",
-                    "owner": "proteore",
-                    "revisions": "98b7912a9ceb",
+                    "name": "cardinal_quality_report",
+                    "owner": "galaxyp",
+                    "revisions": "16556ca0196b",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: proteore_clusterprofiler\n  owner: proteore\n  revisions: 2f67202ffdb3\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_expression_rnaseq_abbased\n  owner: proteore\n  revisions: dbeabf9bf091\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_filter_keywords_values\n  owner: proteore\n  revisions: b4641c0f8a82\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_id_converter\n  owner: proteore\n  revisions: 1e45ea50f145\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_reactome\n  owner: proteore\n  revisions: 9cc475dcd0f2\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_reactome\n  owner: proteore\n  revisions: 6c95f1b88627\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_tissue_specific_expression_data\n  owner: proteore\n  revisions: 3e65e0249976\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_venn_diagram\n  owner: proteore\n  revisions: 98b7912a9ceb\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteome_annotation/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_data_exporter\n  owner: galaxyp\n  revisions: d94770c22f13\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_quality_report\n  owner: galaxyp\n  revisions: 16556ca0196b\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/tutorial.json",
         "contributors": [
             {
-                "id": "vloux",
-                "joined": "2019-04",
-                "name": "Valentin Loux",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/vloux/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/vloux.json"
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "email": "melanie.foell@mol-med.uni-freiburg.de",
+                "id": "foellmelanie",
+                "joined": "2018-10",
+                "matrix": "foellmelanie:matrix.org",
+                "name": "Melanie F\u00f6ll",
+                "orcid": "0000-0002-1887-7543",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
+                "twitter": "MCFoell",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
             },
             {
                 "affiliations": [
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
                     "elixir-europe"
                 ],
-                "elixir_node": "fr",
-                "email": "florence.combes@cea.fr",
-                "id": "combesf",
-                "joined": "2019-04",
-                "name": "Florence Combes",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/combesf/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/combesf.json"
-            },
-            {
-                "id": "davidchristiany",
-                "joined": "2019-04",
-                "name": "David Christiany",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/davidchristiany/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/davidchristiany.json"
-            },
-            {
-                "id": "yvandenb",
-                "joined": "2019-04",
-                "name": "Yves Vandenbrouck",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvandenb/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/yvandenb.json"
+                "contact_for_training": true,
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
+                "fediverse_flavor": "mastodon",
+                "id": "bgruening",
+                "joined": "2017-09",
+                "linkedin": "bgruening",
+                "location": {
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
+                },
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/proteome_annotation",
+        "dir": "topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data",
+        "edam_ontology": [
+            "topic_0121"
+        ],
         "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
+        "edam_topic": [
+            "Proteomics"
+        ],
+        "exact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.eu"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "proteomics/proteome_annotation",
+        "id": "proteomics/mass-spectrometry-imaging-loading-exploring-data",
         "inexact_supported_servers": [
-            "UseGalaxy.fr"
+            "UseGalaxy.cz",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "The Human Protein Atlas is a valuable resource for annotation and exploration of protein data",
-            "Conversion between different gene identifiers is sometimes required",
-            "The Reactome pathway database can be used to browse biological pathways"
+            "imzML (continuous or processed file type) and Analyze7.5 can be uploaded into Galaxy via the composite upload.",
+            "The MSI Qualitycontrol tool gives valuable information before starting the analysis.",
+            "The MSI data exporter can be used any time during the analysis when it is necessary to dig deeper into the data. Galaxy provides many text manipulation tools that can directly be applied on the exported tabular file to filter, sort, plot, ... the data."
         ],
         "layout": "tutorial_hands_on",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Execute a complete annotation pipeline of a protein list identified by LC-MS/MS experiments"
+            "How to upload an imzML file into Galaxy",
+            "Getting an overview of the MSI data with the MSI quality control tool",
+            "How to export MSI data as tabular files"
         ],
-        "pageviews": 3633,
-        "pub_date": "2019-09-12",
+        "pageviews": 3657,
+        "pub_date": "2018-11-27",
         "questions": [
-            "How to filter out technical contaminants?",
-            "How to check for tissue-specificity?",
-            "How to perform enrichment analysis?",
-            "How to map your protein list to pathways (Reactome)?",
-            "How to compare your proteome with other studies?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "combesf"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "30M",
-                "speakers": [
-                    "yvesvdb"
-                ],
-                "youtube_id": "qG7GZc6BeGY"
-            }
+            "Did the tryptic digestions work?",
+            "Is there an intensity gradient in the data?",
+            "How good is the m/z accuracy?"
         ],
-        "short_id": "T00234",
+        "short_id": "T00217",
         "short_tools": [
-            "IDconverter",
-            "MQoutputfilter",
-            "reactome_analysis",
-            "retrieve_from_hpa",
-            "rna_abbased_data",
-            "cluter_profiler",
-            "Jvenn"
+            "tp_sort_header_tool",
+            "Grep1",
+            "cardinal_quality_report",
+            "cardinal_data_exporter"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "post-process",
+        "subtopic": "special",
         "supported_servers": {
-            "exact": [],
+            "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
             "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.fr",
                     "url": "https://usegalaxy.fr/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
         "tags": [
-            "DDA",
-            "human"
+            "mouse",
+            "imaging"
         ],
-        "time_estimation": "1H",
-        "title": "Annotating a protein list identified by LC-MS/MS experiments",
+        "time_estimation": "45m",
+        "title": "Mass spectrometry imaging: Loading and exploring MSI data",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_clusterprofiler/cluter_profiler/2019.02.18",
-            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_expression_rnaseq_abbased/rna_abbased_data/2019.03.07",
-            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_filter_keywords_values/MQoutputfilter/2019.03.11",
-            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_id_converter/IDconverter/2019.03.07",
-            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_reactome/reactome_analysis/2018.12.12",
-            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_reactome/reactome_analysis/2019.03.05",
-            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_tissue_specific_expression_data/retrieve_from_hpa/2019.02.27",
-            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/Jvenn/2019.02.21"
+            "Grep1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/1.12.1.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.2"
         ],
         "topic_name": "proteomics",
         "topic_name_human": "Proteomics",
@@ -193832,176 +195489,30 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "proteome_annotation",
+        "tutorial_name": "mass-spectrometry-imaging-loading-exploring-data",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/proteome_annotation/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteome_annotation/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteome_annotation/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/tutorial.json"
         },
-        "version": 11,
+        "version": 17,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 175,
-        "visitors": 2408,
+        "visit_duration": 103,
+        "visitors": 2273,
         "workflows": [
             {
                 "creators": [],
-                "description": "Annotating a protein list identified by LC-MS/MS experiments",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  3[label=\"Build tissue-specific expression dataset\"]\n  4[label=\"Filter by keywords and/or numerical value\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"ID Converter\"]\n  3 -> 5 [label=\"output\"]\n  6[label=\"ID Converter\"]\n  4 -> 6 [label=\"kept_lines\"]\n  7[label=\"Venn diagram\"]\n  4 -> 7 [label=\"kept_lines\"]\n  0 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"Add expression data\"]\n  6 -> 8 [label=\"output\"]\n  9[label=\"Filter by keywords and/or numerical value\"]\n  8 -> 9 [label=\"output\"]\n  10[label=\"GO terms classification and enrichment analysis\"]\n  5 -> 10 [label=\"output\"]\n  9 -> 10 [label=\"kept_lines\"]\n  11[label=\"Query pathway database\"]\n  9 -> 11 [label=\"kept_lines\"]\n}",
-                "history": [
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 3,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 2,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "a959d88d0da58e17d87c7a39b0d89e03765629df",
-                        "message": "workflow update by Flo",
-                        "num": 1,
-                        "short_hash": "a959d88d0",
-                        "unix": "1560843795"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Bredberg.txt"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 10
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Bredberg.txt\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "98762c87-4a74-4e99-a0a8-b61360e4e123",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Lacombe_et_al_2017_OK.txt"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 130
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Lacombe_et_al_2017_OK.txt\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "90836b07-3f58-40a5-914b-1f9036993489",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Mucilli.txt"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 250
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Mucilli.txt\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "30b559f3-322c-4323-ae32-b6e6d6c9d210",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Build tissue-specific expression dataset\"];\n  4[\"Filter by keywords and/or numerical value\"];\n  1 -->|output| 4;\n  5[\"ID Converter\"];\n  3 -->|output| 5;\n  6[\"ID Converter\"];\n  4 -->|kept_lines| 6;\n  7[\"Venn diagram\"];\n  4 -->|kept_lines| 7;\n  0 -->|output| 7;\n  2 -->|output| 7;\n  8[\"Add expression data\"];\n  6 -->|output| 8;\n  9[\"Filter by keywords and/or numerical value\"];\n  8 -->|output| 9;\n  10[\"GO terms classification and enrichment analysis\"];\n  5 -->|output| 10;\n  9 -->|kept_lines| 10;\n  11[\"Query pathway database\"];\n  9 -->|kept_lines| 11;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "'Proteome Annotation'",
-                "outputs": [],
-                "parent_id": "proteomics/proteome_annotation",
-                "path": "topics/proteomics/tutorials/proteome_annotation/workflows/Galaxy-Workflow-_Proteome_annotation_.ga",
-                "tags": [
-                    "proteomics"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "'Proteome Annotation'",
-                "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-proteome_annotation/versions/galaxy-workflow--proteome-annotation-",
-                "tutorial_id": "proteome_annotation",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteome_annotation/workflows/Galaxy-Workflow-_Proteome_annotation_.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteome_annotation/workflows/Galaxy-Workflow-_Proteome_annotation_.html",
-                "version": 3,
-                "wfid": "proteomics-proteome_annotation",
-                "wfname": "galaxy-workflow--proteome-annotation-",
-                "workflow": "Galaxy-Workflow-_Proteome_annotation_.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_clusterprofiler/cluter_profiler/2019.02.18",
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_expression_rnaseq_abbased/rna_abbased_data/2019.03.07",
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_filter_keywords_values/MQoutputfilter/2019.03.11",
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_id_converter/IDconverter/2019.03.07",
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_reactome/reactome_analysis/2019.03.05",
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_tissue_specific_expression_data/retrieve_from_hpa/2019.02.27",
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/Jvenn/2019.02.21"
-                ],
-                "workflowhub_id": "1207"
-            },
-            {
-                "creators": [],
-                "description": "Annotating a protein list identified by LC-MS/MS experiments",
+                "description": "Mass spectrometry imaging: Loading and exploring MSI data",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nLacombe_et_al_2017.txt\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBredberg.txt\"]\n  10[label=\"View proteins on Reactome maps\"]\n  9 -> 10 [label=\"kept_lines\"]\n  11[label=\"GO terms classification and enrichment analysis\"]\n  5 -> 11 [label=\"output\"]\n  9 -> 11 [label=\"kept_lines\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMucilli.txt\"]\n  3[label=\"Build a lung proteome as a background \"]\n  4[label=\"Filter technical contaminants\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"ID Converter\"]\n  3 -> 5 [label=\"output\"]\n  6[label=\"ID mapping UniProt <-> ENSG ID\"]\n  4 -> 6 [label=\"kept_lines\"]\n  7[label=\"MS/MS datasets comparison\"]\n  4 -> 7 [label=\"kept_lines\"]\n  1 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"Add expression data\"]\n  6 -> 8 [label=\"output\"]\n  9[label=\"Filter biological contaminants\"]\n  8 -> 9 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmouse_kidney_cut.i\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ninternal calibrants.tab\"]\n  2[label=\"MSI data exporter\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"MSI Qualitycontrol\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Sort\"]\n  2 -> 4 [label=\"feature_output\"]\n  5[label=\"Select\"]\n  2 -> 5 [label=\"pixel_output\"]\n}",
                 "history": [
                     {
                         "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
@@ -194018,18 +195529,18 @@
                         "unix": "1579084895"
                     },
                     {
-                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
-                        "message": "unflatten workflows",
+                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
+                        "message": "Changed format of workflows",
                         "num": 2,
-                        "short_hash": "faf6d298a",
-                        "unix": "1576155753"
+                        "short_hash": "361236c41",
+                        "unix": "1554368414"
                     },
                     {
-                        "hash": "a853f1694294a719690d1818388c4358460d12b1",
-                        "message": "First draft of proteome annotation tutorial",
+                        "hash": "862b5b0bcff3928a16de9b43d6061c689fef9d7b",
+                        "message": "Rename MS_imaging_loading_exploring_data.ga to ms_imaging_loading_exploring_data.ga",
                         "num": 1,
-                        "short_hash": "a853f1694",
-                        "unix": "1556281728"
+                        "short_hash": "862b5b0bc",
+                        "unix": "1551717714"
                     }
                 ],
                 "inputs": [
@@ -194042,21 +195553,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Lacombe_et_al_2017.txt"
+                                "name": "mouse_kidney_cut.i"
                             }
                         ],
-                        "label": "Lacombe_et_al_2017.txt",
+                        "label": "mouse_kidney_cut.i",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 284,
-                            "top": 272
+                            "left": 208.9204559326172,
+                            "top": 239.99999237060547
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"Lacombe_et_al_2017.txt\"}",
+                        "tool_state": "{\"name\": \"mouse_kidney_cut.i\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "6e05c374-5a8c-45cc-bc41-060403961b92",
+                        "uuid": "bd40d0ba-d5ce-496f-9988-c8be1f81a75d",
                         "workflow_outputs": []
                     },
                     {
@@ -194068,85 +195579,56 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Bredberg.txt"
-                            }
-                        ],
-                        "label": "Bredberg.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 511,
-                            "top": 454
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Bredberg.txt\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "c59cd601-5021-4665-a225-5881a856d796",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Mucilli.txt"
+                                "name": "internal calibrants.tab"
                             }
                         ],
-                        "label": "Mucilli.txt",
+                        "label": "internal calibrants.tab",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 512,
-                            "top": 532
+                            "left": 199.92897033691406,
+                            "top": 417.0028305053711
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"Mucilli.txt\"}",
+                        "tool_state": "{\"name\": \"internal calibrants.tab\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "aa14863c-2183-4e0e-be4a-3c34972ae040",
+                        "uuid": "15455ea4-e2cc-4872-a441-d40e979c7660",
                         "workflow_outputs": []
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nLacombe_et_al_2017.txt\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nBredberg.txt\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"View proteins on Reactome maps\"];\n  9 -->|kept_lines| 10;\n  11[\"GO terms classification and enrichment analysis\"];\n  5 -->|output| 11;\n  9 -->|kept_lines| 11;\n  2[\"\u2139\ufe0f Input Dataset\\nMucilli.txt\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Build a lung proteome as a background \"];\n  4[\"Filter technical contaminants\"];\n  0 -->|output| 4;\n  5[\"ID Converter\"];\n  3 -->|output| 5;\n  6[\"ID mapping UniProt <-> ENSG ID\"];\n  4 -->|kept_lines| 6;\n  7[\"MS/MS datasets comparison\"];\n  4 -->|kept_lines| 7;\n  1 -->|output| 7;\n  2 -->|output| 7;\n  8[\"Add expression data\"];\n  6 -->|output| 8;\n  9[\"Filter biological contaminants\"];\n  8 -->|output| 9;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "ProteoRE ProteomeAnnotation Tutorial (release 2.0)",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nmouse_kidney_cut.i\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ninternal calibrants.tab\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"MSI data exporter\"];\n  0 -->|output| 2;\n  3[\"MSI Qualitycontrol\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  4[\"Sort\"];\n  2 -->|feature_output| 4;\n  5[\"Select\"];\n  2 -->|pixel_output| 5;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "MS Imaging Loading Exploring Data",
                 "outputs": [],
-                "parent_id": "proteomics/proteome_annotation",
-                "path": "topics/proteomics/tutorials/proteome_annotation/workflows/main_workflow.ga",
+                "parent_id": "proteomics/mass-spectrometry-imaging-loading-exploring-data",
+                "path": "topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/workflows/ms_imaging_loading_exploring_data.ga",
                 "tags": [
                     "proteomics"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "ProteoRE ProteomeAnnotation Tutorial (release 2.0)",
+                "title": "MS Imaging Loading Exploring Data",
                 "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-proteome_annotation/versions/main-workflow",
-                "tutorial_id": "proteome_annotation",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteome_annotation/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteome_annotation/workflows/main_workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-mass-spectrometry-imaging-loading-exploring-data/versions/ms-imaging-loading-exploring-data",
+                "tutorial_id": "mass-spectrometry-imaging-loading-exploring-data",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/workflows/ms_imaging_loading_exploring_data.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/workflows/ms_imaging_loading_exploring_data.html",
                 "version": 4,
-                "wfid": "proteomics-proteome_annotation",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "wfid": "proteomics-mass-spectrometry-imaging-loading-exploring-data",
+                "wfname": "ms-imaging-loading-exploring-data",
+                "workflow": "ms_imaging_loading_exploring_data.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_clusterprofiler/cluter_profiler/2019.02.18",
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_expression_rnaseq_abbased/rna_abbased_data/2019.03.07",
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_filter_keywords_values/MQoutputfilter/2019.03.11",
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_id_converter/IDconverter/2019.03.07",
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_reactome/reactome_analysis/2018.12.12",
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_tissue_specific_expression_data/retrieve_from_hpa/2019.02.27",
-                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/Jvenn/2019.02.21"
+                    "Grep1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/1.12.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.2"
                 ],
-                "workflowhub_id": "1209"
+                "workflowhub_id": "1184"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/3405119"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.1560645"
     },
     {
         "admin_install": {
@@ -194155,127 +195637,117 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "uniprot_rest_interface",
-                    "owner": "bgruening",
-                    "revisions": "054483e27a35",
-                    "tool_panel_section_label": "Convert Formats",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_to_tabular",
-                    "owner": "devteam",
-                    "revisions": "e7ed3c310b74",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "encyclopedia_quantify",
+                    "owner": "galaxyp",
+                    "revisions": "4081e4faa4ab",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "maxquant",
+                    "name": "encyclopedia_quantify",
                     "owner": "galaxyp",
-                    "revisions": "37d669de2828",
+                    "revisions": "1c5cbf8f79ce",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "maxquant",
+                    "name": "encyclopedia_searchtolib",
                     "owner": "galaxyp",
-                    "revisions": "f522c08e900c",
+                    "revisions": "62a718b76f62",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "msstats",
+                    "name": "encyclopedia_searchtolib",
                     "owner": "galaxyp",
-                    "revisions": "593839e1f2c3",
+                    "revisions": "36880dfd9fa7",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "msstats",
+                    "name": "msconvert",
                     "owner": "galaxyp",
-                    "revisions": "28434abe6c5c",
-                    "tool_panel_section_label": "Proteomics",
+                    "revisions": "3cf310697624",
+                    "tool_panel_section_label": "Convert Formats",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ggplot2_heatmap2",
-                    "owner": "iuc",
-                    "revisions": "ca7cb0eaad62",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "name": "msconvert",
+                    "owner": "galaxyp",
+                    "revisions": "6153e8ada1ee",
+                    "tool_panel_section_label": "Convert Formats",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: uniprot_rest_interface\n  owner: bgruening\n  revisions: '054483e27a35'\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_to_tabular\n  owner: devteam\n  revisions: e7ed3c310b74\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maxquant\n  owner: galaxyp\n  revisions: 37d669de2828\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maxquant\n  owner: galaxyp\n  revisions: f522c08e900c\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msstats\n  owner: galaxyp\n  revisions: 593839e1f2c3\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msstats\n  owner: galaxyp\n  revisions: 28434abe6c5c\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ggplot2_heatmap2\n  owner: iuc\n  revisions: ca7cb0eaad62\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: encyclopedia_quantify\n  owner: galaxyp\n  revisions: 4081e4faa4ab\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: encyclopedia_quantify\n  owner: galaxyp\n  revisions: 1c5cbf8f79ce\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: encyclopedia_searchtolib\n  owner: galaxyp\n  revisions: 62a718b76f62\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: encyclopedia_searchtolib\n  owner: galaxyp\n  revisions: 36880dfd9fa7\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msconvert\n  owner: galaxyp\n  revisions: 3cf310697624\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msconvert\n  owner: galaxyp\n  revisions: 6153e8ada1ee\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/encyclopedia/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "email": "melanie.foell@mol-med.uni-freiburg.de",
-                "id": "foellmelanie",
-                "joined": "2018-10",
-                "matrix": "foellmelanie:matrix.org",
-                "name": "Melanie F\u00f6ll",
-                "orcid": "0000-0002-1887-7543",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
-                "twitter": "MCFoell",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
+                "email": "leith023@umn.edu",
+                "id": "emmaleith",
+                "joined": "2019-07",
+                "name": "Emma Leith",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/emmaleith/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/emmaleith.json"
             },
             {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "email": "matthias.fahrner@uniklinik-freiburg.de",
-                "id": "matthias313",
-                "joined": "2019-03",
-                "name": "Matthias Fahrner",
-                "orcid": "0000-0001-7955-2518",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/matthias313/",
-                "twitter": "mfahrner313",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/matthias313.json"
+                "email": "subinamehta@gmail.com",
+                "id": "subinamehta",
+                "joined": "2018-06",
+                "linkedin": "subinamehta",
+                "matrix": "subinamehta:matrix.org",
+                "name": "Subina Mehta",
+                "orcid": "0000-0001-9818-0537",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
+                "twitter": "Subina_Mehta",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
+            },
+            {
+                "email": "jj@umn.edu",
+                "id": "jj-umn",
+                "in_memoriam": "<a href=\"https://galaxyproject.org/news/2024-03-19-remembrances-of-jj/\">James \u2018JJ\u2019 Johnson, was a Galaxy community rock star most known for his indispensable contributions to the Galaxy Proteomics community.</a>\n\nJJ\u2019s works will live on in so many Galaxy tools and workflows for years to come.",
+                "joined": "2017-09",
+                "name": "James Johnson",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jj-umn/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jj-umn.json"
+            },
+            {
+                "email": "pjagtap@umn.edu",
+                "id": "pratikdjagtap",
+                "joined": "2017-09",
+                "name": "Pratik Jagtap",
+                "orcid": "0000-0003-0984-0973",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
+            },
+            {
+                "email": "tgriffin@umn.edu",
+                "github": false,
+                "id": "timothygriffin",
+                "joined": "2017-09",
+                "name": "Timothy J. Griffin",
+                "orcid": "0000-0001-6801-2559",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/maxquant-msstats-dda-lfq",
+        "dir": "topics/proteomics/tutorials/encyclopedia",
         "edam_operation": [
-            "Visualisation",
-            "Imputation",
-            "Heat map generation",
-            "Tag-based peptide identification",
-            "Standardisation and normalisation",
-            "Principal component plotting",
-            "Differential protein expression profiling",
-            "Protein quantification",
-            "Spectrum calculation",
-            "Clustering",
-            "Statistical calculation"
+            "Filtering",
+            "Formatting"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "proteomics/maxquant-msstats-dda-lfq",
+        "id": "proteomics/encyclopedia",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
         "js_requirements": {
@@ -194283,59 +195755,43 @@
             "mermaid": false
         },
         "key_points": [
-            "MaxQuant offers a single tool solution for protein identification and quantification.",
-            "Label-free quantitation reveals the most abundant proteins in serum samples."
+            "With SearchToLib, Chromatogram Libraries can be created",
+            "Learning conversion of file types using msconvert"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-09-30",
         "objectives": [
-            "Learn how to use MaxQuant and MSstats for the analysis of label-free shotgun (DDA) data"
+            "Understand the difference between DDA and DIA methods",
+            "Performing quantitative analysis using DIA data",
+            "Understand the purpose and benefits of using a Chromatogram Library for the detection of peptides",
+            "You can use Bloom's Taxonomy to write effective learning objectives"
         ],
-        "pageviews": 10460,
-        "pub_date": "2021-02-17",
+        "pageviews": 2029,
+        "pub_date": "2021-06-21",
         "questions": [
-            "How to perform label-free shotgun (DDA) data analysis in MaxQuant and MSstats?",
-            "Which proteins are differentially abundant in the two types of cutaneous squamous cell carcinomas?"
+            "How to perform quantitative analysis using DIA data with the help of EncyclopeDIA?",
+            "How to perform quantitation with or without Chromatogram Libraries?"
         ],
         "recordings": [
             {
                 "captioners": [
-                    "foellmelanie"
+                    "mtekman"
                 ],
-                "date": "2021-02-15",
+                "date": "2021-06-25",
                 "galaxy_version": "21.01",
-                "length": "1H",
+                "length": "30M",
                 "speakers": [
-                    "foellmelanie"
-                ],
-                "youtube_id": "IXdLAt2PAT4"
-            }
-        ],
-        "requirements": [
-            {
-                "topic_name": "proteomics",
-                "tutorials": [
-                    "maxquant-label-free"
+                    "emmaleith"
                 ],
-                "type": "internal"
+                "youtube_id": "eCEjHtbZLVg"
             }
         ],
-        "short_id": "T00219",
+        "short_id": "T00215",
         "short_tools": [
-            "Grep1",
-            "msstats",
-            "datamash_ops",
-            "maxquant",
-            "uniprot",
-            "ggplot2_heatmap2",
-            "tp_easyjoin_tool",
-            "tp_replace_in_column",
-            "Cut1",
-            "Filter1",
-            "fasta2tab",
-            "Summary_Statistics1"
+            "encyclopedia_searchtolib",
+            "encyclopedia_quantify",
+            "msconvert"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -194346,6 +195802,11 @@
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 }
             ],
             "inexact": [
@@ -194354,16 +195815,6 @@
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
@@ -194373,25 +195824,17 @@
         },
         "symlink": null,
         "tags": [
-            "label-free"
+            "DIA"
         ],
-        "time_estimation": "2H",
-        "title": "MaxQuant and MSstats for the analysis of label-free data",
+        "time_estimation": "6H",
+        "title": "EncyclopeDIA",
         "tools": [
-            "Cut1",
-            "Filter1",
-            "Grep1",
-            "Summary_Statistics1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy4",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.22.0.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/4.0.0.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/datamash_ops/1.0.6",
-            "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1"
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_quantify/encyclopedia_quantify/0.9.5.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_quantify/encyclopedia_quantify/1.2.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_searchtolib/encyclopedia_searchtolib/0.9.5.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_searchtolib/encyclopedia_searchtolib/1.2.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2"
         ],
         "topic_name": "proteomics",
         "topic_name_human": "Proteomics",
@@ -194401,957 +195844,1203 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "maxquant-msstats-dda-lfq",
+        "tutorial_name": "encyclopedia",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/encyclopedia/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/encyclopedia/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/encyclopedia/tutorial.json"
         },
-        "version": 13,
+        "version": 9,
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 162,
-        "visitors": 6154,
+        "visit_duration": 112,
+        "visitors": 1417,
         "workflows": [
             {
-                "creators": [],
-                "description": "MaxQuant and MSstats for the analysis of label-free data",
+                "creators": [
+                    {
+                        "class": "Organization",
+                        "name": "GalaxyP"
+                    }
+                ],
+                "description": "encyclopedia- DIA Metaproteomics",
                 "features": {
                     "comments": false,
                     "parameters": false,
-                    "report": null,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                    },
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nannotation file\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncomparison matrix\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nfasta protein database\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nraw files\"]\n  4[label=\"MaxQuant\"]\n  2 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"Select\"]\n  4 -> 5 [label=\"proteinGroups\"]\n  6[label=\"Select\"]\n  4 -> 6 [label=\"evidence\"]\n  7[label=\"Replace Text\"]\n  5 -> 7 [label=\"out_file1\"]\n  8[label=\"Replace Text\"]\n  6 -> 8 [label=\"out_file1\"]\n  9[label=\"MSstats\"]\n  1 -> 9 [label=\"output\"]\n  0 -> 9 [label=\"output\"]\n  8 -> 9 [label=\"outfile\"]\n  7 -> 9 [label=\"outfile\"]\n  10[label=\"Datamash\"]\n  9 -> 10 [label=\"runlevel_data\"]\n  11[label=\"Summary Statistics\"]\n  9 -> 11 [label=\"runlevel_data\"]\n  12[label=\"Replace Text\"]\n  9 -> 12 [label=\"comparison_result\"]\n  13[label=\"Replace Text\"]\n  9 -> 13 [label=\"quant_sample_matrix\"]\n  14[label=\"Filter\"]\n  12 -> 14 [label=\"outfile\"]\n  15[label=\"Filter\"]\n  14 -> 15 [label=\"out_file1\"]\n  16[label=\"Filter\"]\n  14 -> 16 [label=\"out_file1\"]\n  17[label=\"Filter\"]\n  15 -> 17 [label=\"out_file1\"]\n  18[label=\"Filter\"]\n  16 -> 18 [label=\"out_file1\"]\n  19[label=\"Cut\"]\n  17 -> 19 [label=\"out_file1\"]\n  20[label=\"Cut\"]\n  18 -> 20 [label=\"out_file1\"]\n  21[label=\"Join\"]\n  13 -> 21 [label=\"outfile\"]\n  19 -> 21 [label=\"out_file1\"]\n  22[label=\"Join\"]\n  13 -> 22 [label=\"outfile\"]\n  20 -> 22 [label=\"out_file1\"]\n  23[label=\"heatmap2\"]\n  21 -> 23 [label=\"output\"]\n  24[label=\"UniProt\"]\n  21 -> 24 [label=\"output\"]\n  25[label=\"heatmap2\"]\n  22 -> 25 [label=\"output\"]\n  26[label=\"UniProt\"]\n  22 -> 26 [label=\"output\"]\n  27[label=\"FASTA-to-Tabular\"]\n  24 -> 27 [label=\"outfile_retrieve_fasta\"]\n  28[label=\"FASTA-to-Tabular\"]\n  26 -> 28 [label=\"outfile_retrieve_fasta\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nGPF DIA RAW Files Dataset collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nEXPERIMENTAL DIA RAW FILES WIDE\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSPECTRAL OR PROSIT LIBRARY\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBACKGROUND PROTEIN FASTA FILE\"]\n  4[label=\"Converting RAW to mzml \"]\n  0 -> 4 [label=\"output\"]\n  kee41b00e11e5494396d0bb64a0dd976c[color=lightseagreen,label=\"Output\\nGPF_MZML\"]\n  4 -> kee41b00e11e5494396d0bb64a0dd976c\n  5[label=\"msconvert\"]\n  1 -> 5 [label=\"output\"]\n  k982b398874ff4755b03f564fd72adad9[color=lightseagreen,label=\"Output\\nExperimental-dataset-MZML\"]\n  5 -> k982b398874ff4755b03f564fd72adad9\n  6[label=\"Library searching\"]\n  3 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  4 -> 6 [label=\"output\"]\n  ka6ae2431c813408eb67f4df16f4d9816[color=lightseagreen,label=\"Output\\nCHROMATOGRAM LIBRARY\"]\n  6 -> ka6ae2431c813408eb67f4df16f4d9816\n  k1c3b0d2e87864f818ac5a932fe3759c6[color=lightseagreen,label=\"Output\\nLOG\"]\n  6 -> k1c3b0d2e87864f818ac5a932fe3759c6\n  7[label=\"EncyclopeDIA Quantify\"]\n  3 -> 7 [label=\"output\"]\n  6 -> 7 [label=\"elib\"]\n  5 -> 7 [label=\"output\"]\n  k6fcebd600aa24833ab18bf3fad5f2e34[color=lightseagreen,label=\"Output\\nQuant-LOG\"]\n  7 -> k6fcebd600aa24833ab18bf3fad5f2e34\n  k31f9b9fa9e6c4531b207e6a4547f96a0[color=lightseagreen,label=\"Output\\nQUANT LIBRARY\"]\n  7 -> k31f9b9fa9e6c4531b207e6a4547f96a0\n  ka6d58aaffd7b4d1492cec217e2fbad18[color=lightseagreen,label=\"Output\\nPEPTIDE QUANTITATION OUTPUT\"]\n  7 -> ka6d58aaffd7b4d1492cec217e2fbad18\n  k5cc9b38b83554367ab3e382333a73eff[color=lightseagreen,label=\"Output\\nPROTEIN QUANTITATION OUTPUT\"]\n  7 -> k5cc9b38b83554367ab3e382333a73eff\n}",
                 "history": [
                     {
-                        "hash": "e1daddc515c5b61f6c9170e1415a3ea9a43ea096",
-                        "message": "fixing broken boxes, adjusting results for actual set MSstats parameters",
+                        "hash": "dec1b6f1da6aa47a9d1748f0cbc3406f38653d23",
+                        "message": "remove ga",
+                        "num": 7,
+                        "short_hash": "dec1b6f1d",
+                        "unix": "1724967741"
+                    },
+                    {
+                        "hash": "cb6a5053b811d2fc5c7cf75af32db15532c2fd61",
+                        "message": "Update main_workflow.ga",
+                        "num": 6,
+                        "short_hash": "cb6a5053b",
+                        "unix": "1724859297"
+                    },
+                    {
+                        "hash": "3a53b7e1d818adb147f4783f3589a16a6b053f6d",
+                        "message": "Update main_workflow.ga",
+                        "num": 5,
+                        "short_hash": "3a53b7e1d",
+                        "unix": "1724858686"
+                    },
+                    {
+                        "hash": "9126f68f0d5565a9630e9f3e92784308a4a24662",
+                        "message": "Update main_workflow.ga",
+                        "num": 4,
+                        "short_hash": "9126f68f0",
+                        "unix": "1623859793"
+                    },
+                    {
+                        "hash": "0a1ee8353f1a3c919f53904b61c778db04495f6b",
+                        "message": "Rename Workflow-May19_EncyclopeDIA_raw_inputs.ga to main_workflow.ga",
                         "num": 3,
-                        "short_hash": "e1daddc51",
-                        "unix": "1622784375"
+                        "short_hash": "0a1ee8353",
+                        "unix": "1623859630"
                     },
                     {
-                        "hash": "0463f30a6b57a55c89db3bffafeef808eb170a51",
-                        "message": "changed Maxquant parameters and removed middle part of training",
+                        "hash": "c07e80f5e0a299c6c0abc2abc70fac0baa4a99f0",
+                        "message": "Delete main_workflow.ga",
                         "num": 2,
-                        "short_hash": "0463f30a6",
-                        "unix": "1622722954"
+                        "short_hash": "c07e80f5e",
+                        "unix": "1623859613"
                     },
                     {
-                        "hash": "ae8154eef553947defbdf59c7ae4460dffbb33d9",
-                        "message": "Adding new maxquant msstats tutorial",
+                        "hash": "34e20aef08d95022e0a31d81ca9b28f3627d975d",
+                        "message": "add tutorial skeleton",
                         "num": 1,
-                        "short_hash": "ae8154eef",
-                        "unix": "1613563165"
+                        "short_hash": "34e20aef0",
+                        "unix": "1607964775"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "",
+                        "annotation": "encyclopedia- Gas phase fractionation files for library",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "annotation file"
+                                "description": "encyclopedia- Gas phase fractionation files for library",
+                                "name": "GPF DIA RAW Files (Dataset collection)"
                             }
                         ],
-                        "label": "annotation file",
-                        "name": "Input dataset",
+                        "label": "GPF DIA RAW Files (Dataset collection)",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "bottom": 315.78334045410156,
-                            "height": 81.95001220703125,
-                            "left": -341.33331298828125,
-                            "right": -141.33331298828125,
-                            "top": 233.8333282470703,
-                            "width": 200,
-                            "x": -341.33331298828125,
-                            "y": 233.8333282470703
+                            "left": 9.765625,
+                            "top": 117
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "1884c487-3263-45f5-a735-61c3a466b830",
+                        "type": "data_collection_input",
+                        "uuid": "1fadab79-360f-43e9-9514-d72404a9390c",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Input raw files",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "comparison matrix"
+                                "description": "Input raw files",
+                                "name": "EXPERIMENTAL DIA RAW FILES (WIDE)"
                             }
                         ],
-                        "label": "comparison matrix",
-                        "name": "Input dataset",
+                        "label": "EXPERIMENTAL DIA RAW FILES (WIDE)",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "bottom": 491.7833251953125,
-                            "height": 81.95001220703125,
-                            "left": -341.33331298828125,
-                            "right": -141.33331298828125,
-                            "top": 409.83331298828125,
-                            "width": 200,
-                            "x": -341.33331298828125,
-                            "y": 409.83331298828125
+                            "left": 268.875,
+                            "top": 0
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ba82de42-628d-44c4-9795-33d8924a37b1",
+                        "type": "data_collection_input",
+                        "uuid": "7f653814-bf62-4211-bc22-31a6e9a90b1a",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Library from Prosit",
                         "content_id": null,
                         "errors": null,
                         "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "fasta protein database"
+                                "description": "Library from Prosit",
+                                "name": "SPECTRAL OR PROSIT LIBRARY"
                             }
                         ],
-                        "label": "fasta protein database",
+                        "label": "SPECTRAL OR PROSIT LIBRARY",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 633.7833251953125,
-                            "height": 81.95001220703125,
-                            "left": -264.48333740234375,
-                            "right": -64.48333740234375,
-                            "top": 551.8333129882812,
-                            "width": 200,
-                            "x": -264.48333740234375,
-                            "y": 551.8333129882812
+                            "left": 20,
+                            "top": 332
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "740e4036-bc46-44cc-b270-1b3962760293",
+                        "uuid": "a4626ff3-d652-4c83-9cae-6651c231146f",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Input Protein Database file",
                         "content_id": null,
                         "errors": null,
                         "id": 3,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "raw files"
+                                "description": "Input Protein Database file",
+                                "name": "BACKGROUND PROTEIN FASTA FILE"
                             }
                         ],
-                        "label": "raw files",
-                        "name": "Input dataset collection",
+                        "label": "BACKGROUND PROTEIN FASTA FILE",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 737.3833160400391,
-                            "height": 61.55000305175781,
-                            "left": -273.816650390625,
-                            "right": -73.816650390625,
-                            "top": 675.8333129882812,
-                            "width": 200,
-                            "x": -273.816650390625,
-                            "y": 675.8333129882812
+                            "left": 0,
+                            "top": 522
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "20726c07-2b97-4f61-8ece-02d09df86a21",
+                        "type": "data_input",
+                        "uuid": "dbadbb9c-c942-496b-a395-94dded270781",
+                        "when": null,
                         "workflow_outputs": []
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nannotation file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ncomparison matrix\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nfasta protein database\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Collection\\nraw files\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"MaxQuant\"];\n  2 -->|output| 4;\n  3 -->|output| 4;\n  5[\"Select\"];\n  4 -->|proteinGroups| 5;\n  6[\"Select\"];\n  4 -->|evidence| 6;\n  7[\"Replace Text\"];\n  5 -->|out_file1| 7;\n  8[\"Replace Text\"];\n  6 -->|out_file1| 8;\n  9[\"MSstats\"];\n  1 -->|output| 9;\n  0 -->|output| 9;\n  8 -->|outfile| 9;\n  7 -->|outfile| 9;\n  10[\"Datamash\"];\n  9 -->|runlevel_data| 10;\n  11[\"Summary Statistics\"];\n  9 -->|runlevel_data| 11;\n  12[\"Replace Text\"];\n  9 -->|comparison_result| 12;\n  13[\"Replace Text\"];\n  9 -->|quant_sample_matrix| 13;\n  14[\"Filter\"];\n  12 -->|outfile| 14;\n  15[\"Filter\"];\n  14 -->|out_file1| 15;\n  16[\"Filter\"];\n  14 -->|out_file1| 16;\n  17[\"Filter\"];\n  15 -->|out_file1| 17;\n  18[\"Filter\"];\n  16 -->|out_file1| 18;\n  19[\"Cut\"];\n  17 -->|out_file1| 19;\n  20[\"Cut\"];\n  18 -->|out_file1| 20;\n  21[\"Join\"];\n  13 -->|outfile| 21;\n  19 -->|out_file1| 21;\n  22[\"Join\"];\n  13 -->|outfile| 22;\n  20 -->|out_file1| 22;\n  23[\"heatmap2\"];\n  21 -->|output| 23;\n  24[\"UniProt\"];\n  21 -->|output| 24;\n  25[\"heatmap2\"];\n  22 -->|output| 25;\n  26[\"UniProt\"];\n  22 -->|output| 26;\n  27[\"FASTA-to-Tabular\"];\n  24 -->|outfile_retrieve_fasta| 27;\n  28[\"FASTA-to-Tabular\"];\n  26 -->|outfile_retrieve_fasta| 28;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Proteomics: MaxQuant and MSstats LFQ workflow",
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nGPF DIA RAW Files Dataset collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nEXPERIMENTAL DIA RAW FILES WIDE\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nSPECTRAL OR PROSIT LIBRARY\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nBACKGROUND PROTEIN FASTA FILE\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Converting RAW to mzml \"];\n  0 -->|output| 4;\n  ee41b00e-11e5-4943-96d0-bb64a0dd976c[\"Output\\nGPF_MZML\"];\n  4 --> ee41b00e-11e5-4943-96d0-bb64a0dd976c;\n  style ee41b00e-11e5-4943-96d0-bb64a0dd976c stroke:#2c3143,stroke-width:4px;\n  5[\"msconvert\"];\n  1 -->|output| 5;\n  982b3988-74ff-4755-b03f-564fd72adad9[\"Output\\nExperimental-dataset-MZML\"];\n  5 --> 982b3988-74ff-4755-b03f-564fd72adad9;\n  style 982b3988-74ff-4755-b03f-564fd72adad9 stroke:#2c3143,stroke-width:4px;\n  6[\"Library searching\"];\n  3 -->|output| 6;\n  2 -->|output| 6;\n  4 -->|output| 6;\n  a6ae2431-c813-408e-b67f-4df16f4d9816[\"Output\\nCHROMATOGRAM LIBRARY\"];\n  6 --> a6ae2431-c813-408e-b67f-4df16f4d9816;\n  style a6ae2431-c813-408e-b67f-4df16f4d9816 stroke:#2c3143,stroke-width:4px;\n  1c3b0d2e-8786-4f81-8ac5-a932fe3759c6[\"Output\\nLOG\"];\n  6 --> 1c3b0d2e-8786-4f81-8ac5-a932fe3759c6;\n  style 1c3b0d2e-8786-4f81-8ac5-a932fe3759c6 stroke:#2c3143,stroke-width:4px;\n  7[\"EncyclopeDIA Quantify\"];\n  3 -->|output| 7;\n  6 -->|elib| 7;\n  5 -->|output| 7;\n  6fcebd60-0aa2-4833-ab18-bf3fad5f2e34[\"Output\\nQuant-LOG\"];\n  7 --> 6fcebd60-0aa2-4833-ab18-bf3fad5f2e34;\n  style 6fcebd60-0aa2-4833-ab18-bf3fad5f2e34 stroke:#2c3143,stroke-width:4px;\n  31f9b9fa-9e6c-4531-b207-e6a4547f96a0[\"Output\\nQUANT LIBRARY\"];\n  7 --> 31f9b9fa-9e6c-4531-b207-e6a4547f96a0;\n  style 31f9b9fa-9e6c-4531-b207-e6a4547f96a0 stroke:#2c3143,stroke-width:4px;\n  a6d58aaf-fd7b-4d14-92ce-c217e2fbad18[\"Output\\nPEPTIDE QUANTITATION OUTPUT\"];\n  7 --> a6d58aaf-fd7b-4d14-92ce-c217e2fbad18;\n  style a6d58aaf-fd7b-4d14-92ce-c217e2fbad18 stroke:#2c3143,stroke-width:4px;\n  5cc9b38b-8355-4367-ab3e-382333a73eff[\"Output\\nPROTEIN QUANTITATION OUTPUT\"];\n  7 --> 5cc9b38b-8355-4367-ab3e-382333a73eff;\n  style 5cc9b38b-8355-4367-ab3e-382333a73eff stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "EncyclopeDIA-GTN",
                 "outputs": [
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy4",
+                        "annotation": "convert to mzml for encyclopedia",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2",
                         "errors": null,
                         "id": 4,
                         "input_connections": {
-                            "input_opts|fasta_files": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "paramGroups_0|files": {
-                                "id": 3,
+                            "input": {
+                                "id": 0,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "MaxQuant",
+                        "label": "Converting RAW to mzml ",
+                        "name": "msconvert",
                         "outputs": [
                             {
-                                "name": "proteinGroups",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "evidence",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "ptxqc_report",
-                                "type": "pdf"
+                                "name": "output",
+                                "type": "mzml"
                             }
                         ],
                         "position": {
-                            "bottom": 825.7666625976562,
-                            "height": 357.26666259765625,
-                            "left": 61.33332824707031,
-                            "right": 261.3333282470703,
-                            "top": 468.5,
-                            "width": 200,
-                            "x": 61.33332824707031,
-                            "y": 468.5
+                            "left": 299,
+                            "top": 234.5
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy4",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "GPF_MZML"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "f522c08e900c",
-                            "name": "maxquant",
+                            "changeset_revision": "6153e8ada1ee",
+                            "name": "msconvert",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"__workflow_invocation_uuid__\": \"a5b196c8c2c611eb9ee3001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_opts\": {\"ftype\": \".thermo.raw\", \"fasta_files\": {\"__class__\": \"ConnectedValue\"}, \"identifier_parse_rule\": \">([^\\\\s]*)\", \"description_parse_rule\": \">(.*)\"}, \"output_opts\": {\"dry_run\": \"false\", \"output\": [\"proteinGroups\", \"evidence\"]}, \"paramGroups\": [{\"__index__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}, \"maxMissedCleavages\": \"2\", \"fixedModifications\": [\"Carbamidomethyl (C)\"], \"variableModifications\": [\"Acetyl (Protein N-term)\", \"Oxidation (M)\"], \"enzymes\": [\"Trypsin/P\"], \"digestion_mode\": \"0\", \"quant_method\": {\"select_quant_method\": \"lfq\", \"__current_case__\": 2, \"lfqMinRatioCount\": \"2\", \"lfqMinEdgesPerNode\": \"3\", \"lfqAvEdgesPerNode\": \"6\", \"lfqSkipNorm\": \"true\"}}], \"protein_quant\": {\"peptides_for_quantification\": \"1\", \"only_unmod_prot\": {\"unmod_prot\": \"True\", \"__current_case__\": 0, \"mods_used_prot_quant\": [\"Acetyl (Protein N-term)\", \"Oxidation (M)\"], \"discard_unmod_cpart_peptides\": \"true\"}, \"lfq_opts\": {\"separateLfq\": \"false\", \"lfqStabilizeLargeRatios\": \"true\", \"lfqRequireMsms\": \"true\", \"do_ibaq\": {\"ibaq\": \"False\", \"__current_case__\": 1}, \"advancedSiteIntensities\": \"true\"}}, \"qc\": {\"do_it\": \"true\", \"__current_case__\": 0, \"parameters\": \"true\", \"summary\": \"true\", \"proteingroups\": \"true\", \"evidence\": \"true\", \"msms\": \"true\", \"msmsscans\": \"true\"}, \"search_opts\": {\"template\": null, \"min_peptide_len\": \"7\", \"max_peptide_mass\": \"4600\", \"min_unique_pep\": \"1\", \"calc_peak_properties\": \"false\", \"mbr\": {\"match_between_runs\": \"True\", \"__current_case__\": 1, \"matching_time_window\": \"0.7\", \"matching_ion_mobility_window\": \"0.05\", \"alignment_time_window\": \"20\", \"alignment_ion_mobility_window\": \"1\", \"match_unidentified_features\": \"false\"}, \"incl_contaminants\": \"true\", \"decoy_mode\": \"revert\", \"psm_fdr\": \"0.01\", \"protein_fdr\": \"0.01\", \"min_pep_length\": \"8\", \"max_pep_length\": \"25\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.6.10.43+galaxy4",
+                        "tool_state": "{\"data_processing\": {\"peak_picking\": {\"pick_peaks\": false, \"__current_case__\": 0}, \"precursor_refinement\": {\"use_mzrefinement\": false, \"__current_case__\": 0}, \"charge_state_calculation\": {\"charge_state_calculation_method\": \"false\", \"__current_case__\": 0}, \"thresholds\": [], \"filter_mz_windows\": {\"do_mzwindow_filter\": false, \"__current_case__\": 0}, \"etd_filtering\": {\"do_etd_filtering\": false, \"__current_case__\": 0}, \"ms2denoise\": {\"denoise\": false, \"__current_case__\": 1}, \"ms2deisotope\": false, \"demultiplex\": {\"demultiplex_on\": false, \"__current_case__\": 1}}, \"filtering\": {\"activation\": \"false\", \"indices\": [], \"scan_numbers\": [], \"strip_it\": false, \"filter_ms_levels\": {\"do_ms_level_filter\": false, \"__current_case__\": 0}, \"polarity\": \"false\", \"analyzer\": \"false\"}, \"general_options\": {\"combineIonMobilitySpectra\": false, \"scan_summing\": {\"do_scan_summing\": false, \"__current_case__\": 0}, \"simAsSpectra\": false, \"srmAsSpectra\": false, \"acceptZeroLengthSpectra\": false, \"ignoreUnknownInstrumentError\": false, \"multi_run_output\": {\"do_multi_run_output\": false, \"__current_case__\": 0, \"runIndexSet\": \"0\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"license_agreement\": true, \"output_type\": \"mzML\", \"settings\": {\"mz_encoding\": \"64\", \"intensity_encoding\": \"32\", \"binary_compression\": \"zlib\", \"gzip_compression\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.0.20287.2",
                         "type": "tool",
-                        "uuid": "8eb1e949-4cfc-402e-971a-1ab02dd124db",
+                        "uuid": "b7867e76-7310-4283-8621-f5d862f2a00a",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "ptxqc_report",
-                                "uuid": "934770a0-48e9-4901-b9a5-8c9dd97f6ef1"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "proteinGroups",
-                                "uuid": "f6a17442-5d9b-4972-9b94-2ff2f55c02ff"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "evidence",
-                                "uuid": "51525532-28c7-4e01-951f-8886fc19dedf"
+                                "label": "GPF_MZML",
+                                "output_name": "output",
+                                "uuid": "ee41b00e-11e5-4943-96d0-bb64a0dd976c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Grep1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2",
                         "errors": null,
                         "id": 5,
                         "input_connections": {
                             "input": {
-                                "id": 4,
-                                "output_name": "proteinGroups"
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Select",
+                        "name": "msconvert",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "output",
+                                "type": "mzml"
                             }
                         ],
                         "position": {
-                            "bottom": 268.03334045410156,
-                            "height": 92.86666870117188,
-                            "left": 76,
-                            "right": 276,
-                            "top": 175.1666717529297,
-                            "width": 200,
-                            "x": 76,
-                            "y": 175.1666717529297
+                            "left": 569,
+                            "top": 75.5
                         },
-                        "post_job_actions": {},
-                        "tool_id": "Grep1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"false\", \"pattern\": \"(HUMAN)|(Majority)\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.1",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Experimental-dataset-MZML"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "6153e8ada1ee",
+                            "name": "msconvert",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"data_processing\": {\"peak_picking\": {\"pick_peaks\": false, \"__current_case__\": 0}, \"precursor_refinement\": {\"use_mzrefinement\": false, \"__current_case__\": 0}, \"charge_state_calculation\": {\"charge_state_calculation_method\": \"false\", \"__current_case__\": 0}, \"thresholds\": [], \"filter_mz_windows\": {\"do_mzwindow_filter\": false, \"__current_case__\": 0}, \"etd_filtering\": {\"do_etd_filtering\": false, \"__current_case__\": 0}, \"ms2denoise\": {\"denoise\": false, \"__current_case__\": 1}, \"ms2deisotope\": false, \"demultiplex\": {\"demultiplex_on\": false, \"__current_case__\": 1}}, \"filtering\": {\"activation\": \"false\", \"indices\": [], \"scan_numbers\": [], \"strip_it\": false, \"filter_ms_levels\": {\"do_ms_level_filter\": false, \"__current_case__\": 0}, \"polarity\": \"false\", \"analyzer\": \"false\"}, \"general_options\": {\"combineIonMobilitySpectra\": false, \"scan_summing\": {\"do_scan_summing\": false, \"__current_case__\": 0}, \"simAsSpectra\": false, \"srmAsSpectra\": false, \"acceptZeroLengthSpectra\": false, \"ignoreUnknownInstrumentError\": false, \"multi_run_output\": {\"do_multi_run_output\": false, \"__current_case__\": 0, \"runIndexSet\": \"0\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"license_agreement\": true, \"output_type\": \"mzML\", \"settings\": {\"mz_encoding\": \"64\", \"intensity_encoding\": \"32\", \"binary_compression\": \"zlib\", \"gzip_compression\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.0.20287.2",
                         "type": "tool",
-                        "uuid": "955e509e-f02c-4b30-ac4f-b2dd66a23468",
+                        "uuid": "9e6a4dd9-06b9-4b51-a99f-0855ec529569",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "e36fbdbe-c076-4efd-b792-1c6e3f190b14"
+                                "label": "Experimental-dataset-MZML",
+                                "output_name": "output",
+                                "uuid": "982b3988-74ff-4755-b03f-564fd72adad9"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": "Grep1",
+                        "annotation": "Searching the mzml files against the Prosit library and the protein FASTA database.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_searchtolib/encyclopedia_searchtolib/1.2.2+galaxy0",
                         "errors": null,
                         "id": 6,
                         "input_connections": {
-                            "input": {
+                            "fasta": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "library": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "scan_inputs": {
                                 "id": 4,
-                                "output_name": "evidence"
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Select",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "description": "runtime parameter for tool SearchToLib",
+                                "name": "target_fasta"
                             }
                         ],
-                        "position": {
-                            "bottom": 388.0333557128906,
-                            "height": 92.86666870117188,
-                            "left": 76,
-                            "right": 276,
-                            "top": 295.16668701171875,
-                            "width": 200,
-                            "x": 76,
-                            "y": 295.16668701171875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "Grep1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"false\", \"pattern\": \"(HUMAN)|(Sequence)\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.1",
-                        "type": "tool",
-                        "uuid": "5e5ab4af-2096-4cd6-a93d-adec152e4bdd",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "d5069d61-91f6-4580-9574-a80962e19a43"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "infile": {
-                                "id": 5,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Replace Text",
+                        "label": "Library searching",
+                        "name": "SearchToLib",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "input"
+                                "name": "log",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "elib",
+                                "type": "elib"
                             }
                         ],
                         "position": {
-                            "bottom": 268.03334045410156,
-                            "height": 92.86666870117188,
-                            "left": 296,
-                            "right": 496,
-                            "top": 175.1666717529297,
-                            "width": 200,
-                            "x": 296,
-                            "y": 175.1666717529297
+                            "left": 469,
+                            "top": 420.73828125
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+                        "post_job_actions": {
+                            "RenameDatasetActionelib": {
+                                "action_arguments": {
+                                    "newname": "CHROMATOGRAM LIBRARY"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "elib"
+                            },
+                            "RenameDatasetActionlog": {
+                                "action_arguments": {
+                                    "newname": "LOG"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "log"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_searchtolib/encyclopedia_searchtolib/1.2.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "36880dfd9fa7",
+                            "name": "encyclopedia_searchtolib",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"column\": \"118\", \"find_pattern\": \"+\", \"replace_pattern\": \"\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.3",
+                        "tool_state": "{\"a\": false, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"library\": {\"__class__\": \"ConnectedValue\"}, \"options\": {\"acquisition\": {\"set_acquisition\": \"no\", \"__current_case__\": 0}, \"tolerance\": {\"set_tolerance\": \"no\", \"__current_case__\": 0}, \"percolator\": {\"set_percolator\": \"no\", \"__current_case__\": 0}, \"peak\": {\"set_peak\": \"no\", \"__current_case__\": 0}, \"window\": {\"set_window\": \"no\", \"__current_case__\": 0}, \"modifications\": {\"set_modifications\": \"no\", \"__current_case__\": 0}, \"search\": {\"set_search\": \"no\", \"__current_case__\": 0}}, \"scan_inputs\": {\"__class__\": \"ConnectedValue\"}, \"select_outputs\": [\"log\", \"elib\"], \"target_fasta\": {\"__class__\": \"RuntimeValue\"}, \"tp\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.2+galaxy0",
                         "type": "tool",
-                        "uuid": "fdeab669-5c90-4169-9b10-969ed89bbdc7",
+                        "uuid": "2e3e8b7b-5ff1-4518-86fb-7a07830cf2b7",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "0e37dd18-2246-456e-b03b-9da9f7b11ebd"
+                                "label": "CHROMATOGRAM LIBRARY",
+                                "output_name": "elib",
+                                "uuid": "a6ae2431-c813-408e-b67f-4df16f4d9816"
+                            },
+                            {
+                                "label": "LOG",
+                                "output_name": "log",
+                                "uuid": "1c3b0d2e-8786-4f81-8ac5-a932fe3759c6"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_quantify/encyclopedia_quantify/1.2.2+galaxy0",
                         "errors": null,
-                        "id": 8,
+                        "id": 7,
                         "input_connections": {
-                            "infile": {
+                            "fasta": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "library": {
                                 "id": 6,
-                                "output_name": "out_file1"
+                                "output_name": "elib"
+                            },
+                            "scan_inputs": {
+                                "id": 5,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool EncyclopeDIA Quantify",
+                                "name": "target_fasta"
+                            }
+                        ],
                         "label": null,
-                        "name": "Replace Text",
+                        "name": "EncyclopeDIA Quantify",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "input"
+                                "name": "log",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "elib",
+                                "type": "elib"
+                            },
+                            {
+                                "name": "results",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "peptides",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "proteins",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 388.0333557128906,
-                            "height": 92.86666870117188,
-                            "left": 296,
-                            "right": 496,
-                            "top": 295.16668701171875,
-                            "width": 200,
-                            "x": 296,
-                            "y": 295.16668701171875
+                            "left": 739.453125,
+                            "top": 296
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+                        "post_job_actions": {
+                            "HideDatasetActionelib": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "elib"
+                            },
+                            "HideDatasetActionresults": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "results"
+                            },
+                            "RenameDatasetActionelib": {
+                                "action_arguments": {
+                                    "newname": "QUANT LIBRARY"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "elib"
+                            },
+                            "RenameDatasetActionlog": {
+                                "action_arguments": {
+                                    "newname": "Quant-LOG"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "log"
+                            },
+                            "RenameDatasetActionpeptides": {
+                                "action_arguments": {
+                                    "newname": "PEPTIDE QUANTITATION OUTPUT"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "peptides"
+                            },
+                            "RenameDatasetActionproteins": {
+                                "action_arguments": {
+                                    "newname": "PROTEIN QUANTITATION OUTPUT"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "proteins"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_quantify/encyclopedia_quantify/1.2.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "1c5cbf8f79ce",
+                            "name": "encyclopedia_quantify",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"column\": \"54\", \"find_pattern\": \"+\", \"replace_pattern\": \"\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.3",
+                        "tool_state": "{\"a\": true, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"library\": {\"__class__\": \"ConnectedValue\"}, \"options\": {\"acquisition\": {\"set_acquisition\": \"no\", \"__current_case__\": 0}, \"tolerance\": {\"set_tolerance\": \"no\", \"__current_case__\": 0}, \"percolator\": {\"set_percolator\": \"no\", \"__current_case__\": 0}, \"peak\": {\"set_peak\": \"no\", \"__current_case__\": 0}, \"window\": {\"set_window\": \"no\", \"__current_case__\": 0}, \"modifications\": {\"set_modifications\": \"no\", \"__current_case__\": 0}, \"search\": {\"set_search\": \"no\", \"__current_case__\": 0}}, \"scan_inputs\": {\"__class__\": \"ConnectedValue\"}, \"select_outputs\": [\"log\", \"elib\", \"results\", \"peptides\", \"proteins\"], \"target_fasta\": {\"__class__\": \"RuntimeValue\"}, \"tp\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.2+galaxy0",
                         "type": "tool",
-                        "uuid": "3e0d0a18-3cfb-4c90-a9e2-9fdc3af29786",
+                        "uuid": "52497828-9e08-4418-92e8-7e4dd2c7cc1d",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "00a0fa1a-91e7-4034-9484-cb788ccf6b16"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.22.0.1",
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "group|comparison_matrix": {
-                                "id": 1,
-                                "output_name": "output"
+                                "label": "Quant-LOG",
+                                "output_name": "log",
+                                "uuid": "6fcebd60-0aa2-4833-ab18-bf3fad5f2e34"
                             },
-                            "input|annotation": {
-                                "id": 0,
-                                "output_name": "output"
+                            {
+                                "label": "QUANT LIBRARY",
+                                "output_name": "elib",
+                                "uuid": "31f9b9fa-9e6c-4531-b207-e6a4547f96a0"
                             },
-                            "input|evidence": {
-                                "id": 8,
-                                "output_name": "outfile"
+                            {
+                                "label": "PEPTIDE QUANTITATION OUTPUT",
+                                "output_name": "peptides",
+                                "uuid": "a6d58aaf-fd7b-4d14-92ce-c217e2fbad18"
                             },
-                            "input|proteinGroups": {
-                                "id": 7,
-                                "output_name": "outfile"
+                            {
+                                "label": "PROTEIN QUANTITATION OUTPUT",
+                                "output_name": "proteins",
+                                "uuid": "5cc9b38b-8355-4367-ab3e-382333a73eff"
                             }
-                        },
+                        ]
+                    }
+                ],
+                "parent_id": "proteomics/encyclopedia",
+                "path": "topics/proteomics/tutorials/encyclopedia/workflows/main_workflow.ga",
+                "tags": [
+                    "proteomics"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "EncyclopeDIA-GTN",
+                "topic_id": "proteomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-encyclopedia/versions/main-workflow",
+                "tutorial_id": "encyclopedia",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/encyclopedia/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/encyclopedia/workflows/main_workflow.html",
+                "version": 2,
+                "wfid": "proteomics-encyclopedia",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_quantify/encyclopedia_quantify/1.2.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_searchtolib/encyclopedia_searchtolib/1.2.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2"
+                ],
+                "workflowhub_id": "1146"
+            }
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.13505774"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "diapysef",
+                    "owner": "galaxyp",
+                    "revisions": "8eed818f5d48",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "maxquant",
+                    "owner": "galaxyp",
+                    "revisions": "37d669de2828",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_openswathassaygenerator",
+                    "owner": "galaxyp",
+                    "revisions": "df72ca515420",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_openswathassaygenerator",
+                    "owner": "galaxyp",
+                    "revisions": "2a9ff56cb279",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_openswathdecoygenerator",
+                    "owner": "galaxyp",
+                    "revisions": "965413f29bf5",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_openswathdecoygenerator",
+                    "owner": "galaxyp",
+                    "revisions": "f861ec9fbe59",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_targetedfileconverter",
+                    "owner": "galaxyp",
+                    "revisions": "aa62f8f48dd4",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_targetedfileconverter",
+                    "owner": "galaxyp",
+                    "revisions": "dd71e020e2aa",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: diapysef\n  owner: galaxyp\n  revisions: 8eed818f5d48\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maxquant\n  owner: galaxyp\n  revisions: 37d669de2828\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_openswathassaygenerator\n  owner: galaxyp\n  revisions: df72ca515420\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_openswathassaygenerator\n  owner: galaxyp\n  revisions: 2a9ff56cb279\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_openswathdecoygenerator\n  owner: galaxyp\n  revisions: 965413f29bf5\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_openswathdecoygenerator\n  owner: galaxyp\n  revisions: f861ec9fbe59\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_targetedfileconverter\n  owner: galaxyp\n  revisions: aa62f8f48dd4\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_targetedfileconverter\n  owner: galaxyp\n  revisions: dd71e020e2aa\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/DIA_lib_OSW/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "email": "matthias.fahrner@uniklinik-freiburg.de",
+                "id": "matthias313",
+                "joined": "2019-03",
+                "name": "Matthias Fahrner",
+                "orcid": "0000-0001-7955-2518",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/matthias313/",
+                "twitter": "mfahrner313",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/matthias313.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "email": "melanie.foell@mol-med.uni-freiburg.de",
+                "id": "foellmelanie",
+                "joined": "2018-10",
+                "matrix": "foellmelanie:matrix.org",
+                "name": "Melanie F\u00f6ll",
+                "orcid": "0000-0002-1887-7543",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
+                "twitter": "MCFoell",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
+            }
+        ],
+        "dir": "topics/proteomics/tutorials/DIA_lib_OSW",
+        "edam_operation": [
+            "Principal component plotting",
+            "Visualisation",
+            "Clustering",
+            "Protein quantification",
+            "Standardisation and normalisation",
+            "Imputation",
+            "Statistical calculation",
+            "Heat map generation"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "proteomics/DIA_lib_OSW",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "MaxQuant, diapysef and OpenSwath tools enable the generation of spectral libraries from DDA data",
+            "Generated spectral libraries can be used for the analysis of DIA data"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": [
+            "Generating a spectral library from data dependent acquisition (DDA) MS data",
+            "Understanding DIA data principles and characteristics",
+            "Optimizing and refining a spectral library for the analysis of DIA data"
+        ],
+        "pageviews": 5003,
+        "pub_date": "2020-12-02",
+        "questions": [
+            "How does the peptide identification work in data independent acquisition (DIA) mass spectrometry (MS) data?",
+            "What is a spectral library and how to generate a spectral library using Maxquant, diapysef and OpenSwath tools?"
+        ],
+        "short_id": "T00212",
+        "short_tools": [
+            "Filter1",
+            "OpenSwathDecoyGenerator",
+            "diapysef",
+            "maxquant",
+            "OpenSwathAssayGenerator",
+            "TargetedFileConverter"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "id-quant",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "DIA"
+        ],
+        "time_estimation": "1H",
+        "title": "Library Generation for DIA Analysis",
+        "tools": [
+            "Filter1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/diapysef/diapysef/0.3.5.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathassaygenerator/OpenSwathAssayGenerator/2.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathassaygenerator/OpenSwathAssayGenerator/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator/2.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_targetedfileconverter/TargetedFileConverter/2.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_targetedfileconverter/TargetedFileConverter/2.6+galaxy0"
+        ],
+        "topic_name": "proteomics",
+        "topic_name_human": "Proteomics",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "DIA_lib_OSW",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/DIA_lib_OSW/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/DIA_lib_OSW/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/DIA_lib_OSW/tutorial.json"
+        },
+        "version": 10,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 82,
+        "visitors": 3790,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "DIA library Training HEK Ecoli data",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHEK_Ecoli_exp_design.txt\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\niRTassays.tsv\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nFASTA collection\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nDDA_data collection\"]\n  4[label=\"MaxQuant\"]\n  2 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Filter\"]\n  4 -> 5 [label=\"evidence\"]\n  6[label=\"Filter\"]\n  4 -> 6 [label=\"msms\"]\n  7[label=\"diapysef library generation\"]\n  5 -> 7 [label=\"out_file1\"]\n  1 -> 7 [label=\"output\"]\n  6 -> 7 [label=\"out_file1\"]\n  8[label=\"OpenSwathAssayGenerator\"]\n  7 -> 8 [label=\"output_tabular\"]\n  9[label=\"OpenSwathDecoyGenerator\"]\n  8 -> 9 [label=\"out\"]\n  10[label=\"TargetedFileConverter\"]\n  9 -> 10 [label=\"out\"]\n}",
+                "history": [
+                    {
+                        "hash": "15a13c3667af0db6a6ca380ca1b998c9faf625d3",
+                        "message": "updated workflow annotation and name",
+                        "num": 2,
+                        "short_hash": "15a13c366",
+                        "unix": "1606931443"
+                    },
+                    {
+                        "hash": "e8f20c190bc7a0d319835969a36114d939bd4dce",
+                        "message": "generated three tutorials on DIA data analysis in galaxy",
+                        "num": 1,
+                        "short_hash": "e8f20c190",
+                        "unix": "1606930318"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool MSstats",
-                                "name": "group"
-                            },
-                            {
-                                "description": "runtime parameter for tool MSstats",
-                                "name": "input"
-                            },
-                            {
-                                "description": "runtime parameter for tool MSstats",
-                                "name": "input"
-                            },
-                            {
-                                "description": "runtime parameter for tool MSstats",
-                                "name": "input"
-                            }
-                        ],
-                        "label": null,
-                        "name": "MSstats",
-                        "outputs": [
-                            {
-                                "name": "log",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "processed_data",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "runlevel_data",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "QCPlot",
-                                "type": "pdf"
-                            },
-                            {
-                                "name": "quant_sample_matrix",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "quant_group_matrix",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "comparison_result",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "VolcanoPlot",
-                                "type": "pdf"
+                                "description": "",
+                                "name": "HEK_Ecoli_exp_design.txt"
                             }
                         ],
+                        "label": "HEK_Ecoli_exp_design.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 918.8332977294922,
-                            "height": 743.6666259765625,
-                            "left": 516,
-                            "right": 716,
-                            "top": 175.1666717529297,
+                            "bottom": 253.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": -302.5,
+                            "right": -102.5,
+                            "top": 171,
                             "width": 200,
-                            "x": 516,
-                            "y": 175.1666717529297
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.22.0.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "593839e1f2c3",
-                            "name": "msstats",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "x": -302.5,
+                            "y": 171
                         },
-                        "tool_state": "{\"dp_options\": {\"selected_outputs\": [\"log\", \"processed_data\", \"runlevel_data\", \"quant_sample_matrix\", \"quant_group_matrix\"], \"logTrans\": \"2\", \"norm\": {\"normalization\": \"equalizeMedians\", \"__current_case__\": 0}, \"fillIncompleteRows\": \"true\", \"features\": {\"featureSubset\": \"all\", \"__current_case__\": 0}, \"summarize\": {\"summaryMethod\": \"TMP\", \"__current_case__\": 0, \"MBimpute\": \"true\", \"remove50missing\": \"false\"}, \"censoredInt\": \"NA\", \"cutoffCensored\": \"minFeature\", \"maxQuantileforCensored\": \"0.999\", \"out_plots_opt\": {\"selected_vis_outputs\": [\"QCPlot\"], \"which_Protein\": {\"select\": \"allonly\", \"__current_case__\": 1}, \"width\": \"8\", \"height\": \"5\", \"proc_plots_advanced\": {\"featureName\": \"Transition\", \"ylimUp\": null, \"ylimDown\": null, \"scale\": \"false\", \"interval\": \"CI\", \"x_axis_size\": \"10\", \"y_axis_size\": \"10\", \"text_size\": \"4\", \"text_angle\": \"0\", \"legend_size\": \"7\", \"dot_size_profile\": \"2\", \"dot_size_condition\": \"3\", \"remove_uninformative_feature_outlier\": \"false\"}}}, \"group\": {\"group_comparison\": \"yes\", \"__current_case__\": 1, \"comparison_matrix\": {\"__class__\": \"RuntimeValue\"}, \"select_outputs\": [\"comparison_result\"], \"comparison_plots_opt\": {\"select_comparison_plots\": [\"VolcanoPlot\"], \"width\": \"8\", \"height\": \"5\", \"which_Protein\": {\"select\": \"all\", \"__current_case__\": 0}, \"comparison_vis_options\": {\"sig\": \"0.05\", \"FCcutoff\": \"1.5\", \"logBase_pvalue\": \"10\", \"ylimUp\": null, \"ylimDown\": null, \"xlimUp\": null, \"axis_size\": \"10\", \"x_axis_size\": \"10\", \"y_axis_size\": \"10\", \"dot_size\": \"3\", \"text_size\": \"4\", \"text_angle\": \"90\", \"legend_size\": \"7\", \"ProteinName\": \"false\", \"colorkey\": \"true\", \"numProtein\": \"100\", \"clustering\": \"protein\", \"which_Comparison\": {\"select\": \"all\", \"__current_case__\": 0}}}}, \"input\": {\"input_src\": \"MaxQuant\", \"__current_case__\": 1, \"evidence\": {\"__class__\": \"RuntimeValue\"}, \"proteinGroups\": {\"__class__\": \"RuntimeValue\"}, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"proteinID\": \"Leading.razor.protein\", \"input_options\": {\"useUniquePeptide\": \"true\", \"summaryforMultipleRows\": \"max\", \"fewMeasurements\": \"remove\", \"removeMpeptides\": \"false\", \"removeOxidationMpeptides\": \"false\", \"removeProtein_with1Peptide\": \"true\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.22.0.1",
-                        "type": "tool",
-                        "uuid": "b3968b97-c518-4333-be78-a10676d0c260",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "b7a2d992-bc43-4699-8914-4315558acf72",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "comparison_result",
-                                "uuid": "5d3ee1c6-32bb-4899-b7e7-e84477cc2127"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "log",
-                                "uuid": "1dd1ac5c-eb19-4b9c-8786-b72776ebb1a4"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "processed_data",
-                                "uuid": "7549686d-4219-4c17-9f4d-5d1ed7bb92cf"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "QCPlot",
-                                "uuid": "44092c24-df36-4d05-91ae-5fca98f4bc36"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "quant_sample_matrix",
-                                "uuid": "6aa35c51-4144-4aec-a597-4591386279b1"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "quant_group_matrix",
-                                "uuid": "0c980fd2-d34a-4fb0-8adb-2e974c8261f0"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "runlevel_data",
-                                "uuid": "14636105-8e4d-4f00-8da1-5468aa830132"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "VolcanoPlot",
-                                "uuid": "91943356-70a8-4598-a24e-4ac6f6354e1c"
+                                "output_name": "output",
+                                "uuid": "be397353-5730-4e2d-a975-5342da357935"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/datamash_ops/1.0.6",
+                        "content_id": null,
                         "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "in_file": {
-                                "id": 9,
-                                "output_name": "runlevel_data"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Datamash",
-                        "outputs": [
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "iRTassays.tsv"
                             }
                         ],
+                        "label": "iRTassays.tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 288.43333435058594,
-                            "height": 113.26666259765625,
-                            "left": 736,
-                            "right": 936,
-                            "top": 175.1666717529297,
+                            "bottom": 369.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": -347.5,
+                            "right": -147.5,
+                            "top": 287,
                             "width": 200,
-                            "x": 736,
-                            "y": 175.1666717529297
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/datamash_ops/1.0.6",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2f3c6f2dcf39",
-                            "name": "datamash_ops",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "x": -347.5,
+                            "y": 287
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"grouping\": \"8\", \"header_in\": \"true\", \"header_out\": \"true\", \"ignore_case\": \"false\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"need_sort\": \"true\", \"operations\": [{\"__index__\": 0, \"op_name\": \"count\", \"op_column\": \"1\"}], \"print_full_line\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.6",
-                        "type": "tool",
-                        "uuid": "4c334a37-a534-46b0-9d1c-9d0c1e91b8e7",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "2020e579-6339-4c24-baf0-556c6e07d94e",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file",
-                                "uuid": "9897b924-bd51-46f3-8e86-2282f96be68b"
+                                "output_name": "output",
+                                "uuid": "facf90b8-ddac-410e-a894-c966b56f21a2"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Summary_Statistics1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 11,
-                        "input_connections": {
-                            "input": {
-                                "id": 9,
-                                "output_name": "runlevel_data"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Summary Statistics",
-                        "outputs": [
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "FASTA collection"
                             }
                         ],
+                        "label": "FASTA collection",
+                        "name": "Input dataset collection",
+                        "outputs": [],
                         "position": {
-                            "bottom": 408.433349609375,
-                            "height": 113.26666259765625,
-                            "left": 736,
-                            "right": 936,
-                            "top": 295.16668701171875,
+                            "bottom": 478.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": -337.5,
+                            "right": -137.5,
+                            "top": 396,
                             "width": 200,
-                            "x": 736,
-                            "y": 295.16668701171875
+                            "x": -337.5,
+                            "y": 396
                         },
-                        "post_job_actions": {},
-                        "tool_id": "Summary_Statistics1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c4\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.2",
-                        "type": "tool",
-                        "uuid": "14d4f8b8-2729-41b1-9f10-58eafdb43d5f",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "b990e20a-52da-44de-9a00-22ae2e400e5e",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "105467da-afe7-470f-b3d3-1868ab1e2e50"
+                                "output_name": "output",
+                                "uuid": "7867b0df-a52a-4c04-a488-c03e1db17631"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+                        "content_id": null,
                         "errors": null,
-                        "id": 12,
-                        "input_connections": {
-                            "infile": {
-                                "id": 9,
-                                "output_name": "comparison_result"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Replace Text",
-                        "outputs": [
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "outfile",
-                                "type": "input"
+                                "description": "",
+                                "name": "DDA_data collection"
                             }
                         ],
+                        "label": "DDA_data collection",
+                        "name": "Input dataset collection",
+                        "outputs": [],
                         "position": {
-                            "bottom": 508.0333557128906,
-                            "height": 92.86666870117188,
-                            "left": 736,
-                            "right": 936,
-                            "top": 415.16668701171875,
+                            "bottom": 608.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": -344.5,
+                            "right": -144.5,
+                            "top": 526,
                             "width": 200,
-                            "x": 736,
-                            "y": 415.16668701171875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "x": -344.5,
+                            "y": 526
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"column\": \"1\", \"find_pattern\": \"sp\\\\|\", \"replace_pattern\": \"\"}, {\"__index__\": 1, \"column\": \"1\", \"find_pattern\": \"\\\\|.*\", \"replace_pattern\": \"\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.3",
-                        "type": "tool",
-                        "uuid": "d79c82bc-9b4d-43b9-bb39-42b4cdf81bdb",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "2a32fc5d-36c4-46ee-a2cd-b80be12da5e3",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "851024bd-132d-4bd6-87c6-5249211d6666"
+                                "output_name": "output",
+                                "uuid": "14a26fc5-5e3e-4bca-84fc-057c6f828155"
                             }
                         ]
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nHEK_Ecoli_exp_design.txt\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\niRTassays.tsv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nFASTA collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Collection\\nDDA_data collection\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"MaxQuant\"];\n  2 -->|output| 4;\n  3 -->|output| 4;\n  0 -->|output| 4;\n  5[\"Filter\"];\n  4 -->|evidence| 5;\n  6[\"Filter\"];\n  4 -->|msms| 6;\n  7[\"diapysef library generation\"];\n  5 -->|out_file1| 7;\n  1 -->|output| 7;\n  6 -->|out_file1| 7;\n  8[\"OpenSwathAssayGenerator\"];\n  7 -->|output_tabular| 8;\n  9[\"OpenSwathDecoyGenerator\"];\n  8 -->|out| 9;\n  10[\"TargetedFileConverter\"];\n  9 -->|out| 10;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "DIA_lib_OSW",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+                        "content_id": null,
                         "errors": null,
-                        "id": 13,
-                        "input_connections": {
-                            "infile": {
-                                "id": 9,
-                                "output_name": "quant_sample_matrix"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Replace Text",
-                        "outputs": [
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "outfile",
-                                "type": "input"
+                                "description": "",
+                                "name": "HEK_Ecoli_exp_design.txt"
                             }
                         ],
+                        "label": "HEK_Ecoli_exp_design.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 628.0333557128906,
-                            "height": 92.86666870117188,
-                            "left": 736,
-                            "right": 936,
-                            "top": 535.1666870117188,
+                            "bottom": 253.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": -302.5,
+                            "right": -102.5,
+                            "top": 171,
                             "width": 200,
-                            "x": 736,
-                            "y": 535.1666870117188
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "x": -302.5,
+                            "y": 171
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"column\": \"1\", \"find_pattern\": \"sp\\\\|\", \"replace_pattern\": \"\"}, {\"__index__\": 1, \"column\": \"1\", \"find_pattern\": \"\\\\|.*\", \"replace_pattern\": \"\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.3",
-                        "type": "tool",
-                        "uuid": "e3f8c7ce-c2cf-488a-bf80-eb18d677d8a7",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "b7a2d992-bc43-4699-8914-4315558acf72",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "02878b52-bd9d-4e3d-914a-3925430524d9"
+                                "output_name": "output",
+                                "uuid": "be397353-5730-4e2d-a975-5342da357935"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Filter1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 14,
-                        "input_connections": {
-                            "input": {
-                                "id": 12,
-                                "output_name": "outfile"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Filter",
-                        "outputs": [
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "description": "",
+                                "name": "iRTassays.tsv"
                             }
                         ],
+                        "label": "iRTassays.tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 268.03334045410156,
-                            "height": 92.86666870117188,
-                            "left": 956,
-                            "right": 1156,
-                            "top": 175.1666717529297,
+                            "bottom": 369.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": -347.5,
+                            "right": -147.5,
+                            "top": 287,
                             "width": 200,
-                            "x": 956,
-                            "y": 175.1666717529297
+                            "x": -347.5,
+                            "y": 287
                         },
-                        "post_job_actions": {},
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c8<0.05\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
-                        "type": "tool",
-                        "uuid": "a8c17ba0-9fd9-45cb-a195-bd3f6af256e8",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "2020e579-6339-4c24-baf0-556c6e07d94e",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "3c3a85e8-3934-4439-9836-cfff976035e7"
+                                "output_name": "output",
+                                "uuid": "facf90b8-ddac-410e-a894-c966b56f21a2"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Filter1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 15,
-                        "input_connections": {
-                            "input": {
-                                "id": 14,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Filter",
-                        "outputs": [
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "description": "",
+                                "name": "FASTA collection"
                             }
                         ],
+                        "label": "FASTA collection",
+                        "name": "Input dataset collection",
+                        "outputs": [],
                         "position": {
-                            "bottom": 268.03334045410156,
-                            "height": 92.86666870117188,
-                            "left": 1176,
-                            "right": 1376,
-                            "top": 175.1666717529297,
+                            "bottom": 478.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": -337.5,
+                            "right": -137.5,
+                            "top": 396,
                             "width": 200,
-                            "x": 1176,
-                            "y": 175.1666717529297
+                            "x": -337.5,
+                            "y": 396
                         },
-                        "post_job_actions": {},
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c3>0.58\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
-                        "type": "tool",
-                        "uuid": "d27bb3b9-ff30-4004-8cc1-60b0085bbeea",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "b990e20a-52da-44de-9a00-22ae2e400e5e",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "01a2b15e-f55e-4485-acf6-b24063e79b7c"
+                                "output_name": "output",
+                                "uuid": "7867b0df-a52a-4c04-a488-c03e1db17631"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Filter1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 16,
-                        "input_connections": {
-                            "input": {
-                                "id": 14,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Filter",
-                        "outputs": [
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "description": "",
+                                "name": "DDA_data collection"
                             }
                         ],
+                        "label": "DDA_data collection",
+                        "name": "Input dataset collection",
+                        "outputs": [],
                         "position": {
-                            "bottom": 388.0333557128906,
-                            "height": 92.86666870117188,
-                            "left": 1176,
-                            "right": 1376,
-                            "top": 295.16668701171875,
+                            "bottom": 608.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": -344.5,
+                            "right": -144.5,
+                            "top": 526,
                             "width": 200,
-                            "x": 1176,
-                            "y": 295.16668701171875
+                            "x": -344.5,
+                            "y": 526
                         },
-                        "post_job_actions": {},
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c3<-0.58\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
-                        "type": "tool",
-                        "uuid": "8cd26d6e-9eab-4329-aa4f-4baeb79cba8e",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "2a32fc5d-36c4-46ee-a2cd-b80be12da5e3",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "9878106d-9970-49e2-9498-12786bf87859"
+                                "output_name": "output",
+                                "uuid": "14a26fc5-5e3e-4bca-84fc-057c6f828155"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Filter1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3",
                         "errors": null,
-                        "id": 17,
+                        "id": 4,
                         "input_connections": {
-                            "input": {
-                                "id": 15,
-                                "output_name": "out_file1"
+                            "input_opts|fasta_files": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "paramGroups_0|files": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "search_opts|template": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Filter",
+                        "name": "MaxQuant",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "proteinGroups",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "mqpar",
+                                "type": "xml"
+                            },
+                            {
+                                "name": "peptides",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "evidence",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "msms",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "ptxqc_report",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "bottom": 268.03334045410156,
-                            "height": 92.86666870117188,
-                            "left": 1396,
-                            "right": 1596,
-                            "top": 175.1666717529297,
+                            "bottom": 681,
+                            "height": 510,
+                            "left": -82.5,
+                            "right": 117.5,
+                            "top": 171,
                             "width": 200,
-                            "x": 1396,
-                            "y": 175.1666717529297
+                            "x": -82.5,
+                            "y": 171
                         },
                         "post_job_actions": {},
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c8>0\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ea0a1d50c83f",
+                            "name": "maxquant",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_opts\": {\"ftype\": \".thermo.raw\", \"fasta_files\": {\"__class__\": \"ConnectedValue\"}, \"identifier_parse_rule\": \">([^ ]*)\", \"description_parse_rule\": \"^>.*\\\\|.*\\\\|[^ ]+ (.*) OS.*$\"}, \"output_opts\": {\"dry_run\": \"false\", \"output\": [\"proteinGroups\", \"mqpar\", \"peptides\", \"evidence\", \"msms\"]}, \"paramGroups\": [{\"__index__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}, \"maxMissedCleavages\": \"1\", \"fixedModifications\": [\"Carbamidomethyl (C)\"], \"variableModifications\": [\"Oxidation (M)\"], \"enzymes\": [\"Trypsin/P\"], \"digestion_mode\": \"0\", \"quant_method\": {\"select_quant_method\": \"\", \"__current_case__\": 0}}], \"protein_quant\": {\"peptides_for_quantification\": \"1\", \"only_unmod_prot\": {\"unmod_prot\": \"False\", \"__current_case__\": 1}, \"lfq_opts\": {\"separateLfq\": \"false\", \"lfqStabilizeLargeRatios\": \"true\", \"lfqRequireMsms\": \"true\", \"do_ibaq\": {\"ibaq\": \"False\", \"__current_case__\": 1}, \"advancedSiteIntensities\": \"true\"}}, \"qc\": {\"do_it\": \"true\", \"__current_case__\": 0, \"parameters\": \"true\", \"summary\": \"true\", \"proteingroups\": \"true\", \"evidence\": \"true\", \"msms\": \"true\", \"msmsscans\": \"true\"}, \"search_opts\": {\"template\": {\"__class__\": \"ConnectedValue\"}, \"min_peptide_len\": \"7\", \"max_peptide_mass\": \"4600\", \"min_unique_pep\": \"1\", \"calc_peak_properties\": \"false\", \"match_between_runs\": \"true\", \"incl_contaminants\": \"true\", \"decoy_mode\": \"revert\", \"psm_fdr\": \"0.01\", \"protein_fdr\": \"0.01\", \"min_pep_length\": \"8\", \"max_pep_length\": \"25\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.6.10.43+galaxy3",
                         "type": "tool",
-                        "uuid": "d748fc5d-a609-472d-b6cb-0b6ec18affe0",
+                        "uuid": "0ee17766-fdba-4ff9-b274-5a3c6a7f1e3d",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "6c12e078-7e56-47c5-9524-462cc9e285c7"
+                                "output_name": "proteinGroups",
+                                "uuid": "59c88bb8-68af-43df-991b-0a012cc639be"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "msms",
+                                "uuid": "e1310278-385d-404f-b9ba-68d2fbd2dd25"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "evidence",
+                                "uuid": "a9bef4a5-cdb4-4b74-a46e-fe7249f1e771"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "peptides",
+                                "uuid": "c1a3b7df-3441-458c-9fef-8fdab2f19576"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "mqpar",
+                                "uuid": "65605a07-5a17-4d31-b92b-afaf5dcb8837"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "ptxqc_report",
+                                "uuid": "0b1667be-be49-4ea7-a3b2-48d099a44103"
                             }
                         ]
                     },
@@ -195359,11 +197048,11 @@
                         "annotation": "",
                         "content_id": "Filter1",
                         "errors": null,
-                        "id": 18,
+                        "id": 5,
                         "input_connections": {
                             "input": {
-                                "id": 16,
-                                "output_name": "out_file1"
+                                "id": 4,
+                                "output_name": "evidence"
                             }
                         },
                         "inputs": [],
@@ -195376,561 +197065,343 @@
                             }
                         ],
                         "position": {
-                            "bottom": 388.0333557128906,
-                            "height": 92.86666870117188,
-                            "left": 1396,
-                            "right": 1596,
-                            "top": 295.16668701171875,
+                            "bottom": 264.1999969482422,
+                            "height": 93.19999694824219,
+                            "left": 137.5,
+                            "right": 337.5,
+                            "top": 171,
                             "width": 200,
-                            "x": 1396,
-                            "y": 295.16668701171875
+                            "x": 137.5,
+                            "y": 171
                         },
                         "post_job_actions": {},
                         "tool_id": "Filter1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c8>0\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"len(c9.split(';')) < 2\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.1.1",
                         "type": "tool",
-                        "uuid": "fc4b67ba-8f8d-41b4-a797-20221cc7bcbd",
+                        "uuid": "22368d26-e6a2-41f8-99d2-321bddd04840",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "out_file1",
-                                "uuid": "de5996ce-55a9-45dc-876b-3877fa1b778b"
+                                "uuid": "44b9a121-c925-41a9-945f-52c7c8aeceb9"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Cut1",
+                        "content_id": "Filter1",
                         "errors": null,
-                        "id": 19,
+                        "id": 6,
                         "input_connections": {
                             "input": {
-                                "id": 17,
-                                "output_name": "out_file1"
+                                "id": 4,
+                                "output_name": "msms"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Cut",
+                        "name": "Filter",
                         "outputs": [
                             {
                                 "name": "out_file1",
-                                "type": "tabular"
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 268.03334045410156,
-                            "height": 92.86666870117188,
-                            "left": 1616,
-                            "right": 1816,
-                            "top": 175.1666717529297,
+                            "bottom": 384.1999969482422,
+                            "height": 93.19999694824219,
+                            "left": 137.5,
+                            "right": 337.5,
+                            "top": 291,
                             "width": 200,
-                            "x": 1616,
-                            "y": 175.1666717529297
+                            "x": 137.5,
+                            "y": 291
                         },
                         "post_job_actions": {},
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c1\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2",
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"len(c12.split(';')) < 2\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
                         "type": "tool",
-                        "uuid": "85e52e8f-4bc9-4c0f-9ea3-99e2f5939a83",
+                        "uuid": "eb4fa570-9fdd-40a3-a980-f494cde96317",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "out_file1",
-                                "uuid": "466eb4ff-3685-425d-b1aa-4f6fb834dd70"
+                                "uuid": "95eda6f0-e8b5-4cdc-8cf6-d6ed53933077"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Cut1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/diapysef/diapysef/0.3.5.0",
                         "errors": null,
-                        "id": 20,
+                        "id": 7,
                         "input_connections": {
-                            "input": {
-                                "id": 18,
+                            "input_evidence": {
+                                "id": 5,
                                 "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cut",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 388.0333557128906,
-                            "height": 92.86666870117188,
-                            "left": 1616,
-                            "right": 1816,
-                            "top": 295.16668701171875,
-                            "width": 200,
-                            "x": 1616,
-                            "y": 295.16668701171875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c1\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2",
-                        "type": "tool",
-                        "uuid": "bf3841cb-6e7f-4a3d-988f-df196aca874a",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "9d0a535d-ed5b-448f-bbc4-795ec0b7ae4b"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-                        "errors": null,
-                        "id": 21,
-                        "input_connections": {
-                            "infile1": {
-                                "id": 13,
-                                "output_name": "outfile"
                             },
-                            "infile2": {
-                                "id": 19,
+                            "input_irtassays": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "input_msms": {
+                                "id": 6,
                                 "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Join",
+                        "name": "diapysef library generation",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 298.43333435058594,
-                            "height": 123.26666259765625,
-                            "left": 1836,
-                            "right": 2036,
-                            "top": 175.1666717529297,
-                            "width": 200,
-                            "x": 1836,
-                            "y": 175.1666717529297
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": \"true\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.2",
-                        "type": "tool",
-                        "uuid": "a006f45e-d6ee-457f-b9af-84d5d86c24b7",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "f24e4056-f3ba-40bd-ac6e-0421584ff7b9"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-                        "errors": null,
-                        "id": 22,
-                        "input_connections": {
-                            "infile1": {
-                                "id": 13,
-                                "output_name": "outfile"
+                                "name": "output_tabular",
+                                "type": "tabular"
                             },
-                            "infile2": {
-                                "id": 20,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Join",
-                        "outputs": [
                             {
-                                "name": "output",
-                                "type": "input"
+                                "name": "output_pdf",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "bottom": 418.433349609375,
-                            "height": 123.26666259765625,
-                            "left": 1836,
-                            "right": 2036,
-                            "top": 295.16668701171875,
+                            "bottom": 559.3999938964844,
+                            "height": 388.3999938964844,
+                            "left": 357.5,
+                            "right": 557.5,
+                            "top": 171,
                             "width": 200,
-                            "x": 1836,
-                            "y": 295.16668701171875
+                            "x": 357.5,
+                            "y": 171
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/diapysef/diapysef/0.3.5.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "8eed818f5d48",
+                            "name": "diapysef",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": \"true\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.2",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"alignment\": \"linear\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_evidence\": {\"__class__\": \"ConnectedValue\"}, \"input_irtassays\": {\"__class__\": \"ConnectedValue\"}, \"input_msms\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3.5.0",
                         "type": "tool",
-                        "uuid": "33d235ba-6450-4f5a-8f41-8611e2153ed9",
+                        "uuid": "50c157a3-ceb5-4d34-aadf-a635f2d9c62c",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "9a2e9e3a-6e50-4ee8-b599-b6186975f1fc"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1",
-                        "errors": null,
-                        "id": 23,
-                        "input_connections": {
-                            "input1": {
-                                "id": 21,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "heatmap2",
-                        "outputs": [
-                            {
-                                "name": "output1",
-                                "type": "pdf"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 308.8333282470703,
-                            "height": 133.66665649414062,
-                            "left": 2056,
-                            "right": 2256,
-                            "top": 175.1666717529297,
-                            "width": 200,
-                            "x": 2056,
-                            "y": 175.1666717529297
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ca7cb0eaad62",
-                            "name": "ggplot2_heatmap2",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cluster_cond\": {\"cluster\": \"\", \"__current_case__\": 1}, \"colorscheme\": \"whrd\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"key\": \"\", \"labels\": \"both\", \"scale\": \"row\", \"title\": \"Upregulated proteins in metastasized cSCC\", \"transform\": \"none\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.0.1",
-                        "type": "tool",
-                        "uuid": "bee1e0b5-2251-4f85-8737-243dacef01a7",
-                        "workflow_outputs": [
+                                "output_name": "output_pdf",
+                                "uuid": "3dde2b97-a71d-40e6-bfd5-a818577596c7"
+                            },
                             {
                                 "label": null,
-                                "output_name": "output1",
-                                "uuid": "cf47dbb9-afc4-4d9b-985b-0a18bd95ebfe"
+                                "output_name": "output_tabular",
+                                "uuid": "9db078b5-7289-4de8-80e0-3af5466d5f4b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathassaygenerator/OpenSwathAssayGenerator/2.5+galaxy0",
                         "errors": null,
-                        "id": 24,
+                        "id": 8,
                         "input_connections": {
-                            "infile": {
-                                "id": 21,
-                                "output_name": "output"
+                            "in": {
+                                "id": 7,
+                                "output_name": "output_tabular"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "UniProt",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "outfile_retrieve_fasta",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 548.8333435058594,
-                            "height": 133.66665649414062,
-                            "left": 2056,
-                            "right": 2256,
-                            "top": 415.16668701171875,
-                            "width": 200,
-                            "x": 2056,
-                            "y": 415.16668701171875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "054483e27a35",
-                            "name": "uniprot_rest_interface",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"id_column\": \"1\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"tool\": {\"tool_choice\": \"retrieve\", \"__current_case__\": 1, \"format\": \"fasta\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.2",
-                        "type": "tool",
-                        "uuid": "5f1dd559-3d47-464d-ac73-72684267aaf4",
-                        "workflow_outputs": [
+                                "description": "runtime parameter for tool OpenSwathAssayGenerator",
+                                "name": "in"
+                            },
                             {
-                                "label": null,
-                                "output_name": "outfile_retrieve_fasta",
-                                "uuid": "141b0dcd-080b-440d-81d0-85f7297d8054"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1",
-                        "errors": null,
-                        "id": 25,
-                        "input_connections": {
-                            "input1": {
-                                "id": 22,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "heatmap2",
-                        "outputs": [
+                                "description": "runtime parameter for tool OpenSwathAssayGenerator",
+                                "name": "swath_windows_file"
+                            },
                             {
-                                "name": "output1",
-                                "type": "pdf"
+                                "description": "runtime parameter for tool OpenSwathAssayGenerator",
+                                "name": "unimod_file"
                             }
                         ],
-                        "position": {
-                            "bottom": 428.8333435058594,
-                            "height": 133.66665649414062,
-                            "left": 2056,
-                            "right": 2256,
-                            "top": 295.16668701171875,
-                            "width": 200,
-                            "x": 2056,
-                            "y": 295.16668701171875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ca7cb0eaad62",
-                            "name": "ggplot2_heatmap2",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cluster_cond\": {\"cluster\": \"\", \"__current_case__\": 1}, \"colorscheme\": \"whrd\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"key\": \"\", \"labels\": \"both\", \"scale\": \"row\", \"title\": \"Upregulated proteins in RDEB cSCC\", \"transform\": \"none\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.0.1",
-                        "type": "tool",
-                        "uuid": "df17ae43-0885-4132-b75a-6917049e573c",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output1",
-                                "uuid": "1dd011a1-b91e-4b39-8fa6-c9585946df63"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2",
-                        "errors": null,
-                        "id": 26,
-                        "input_connections": {
-                            "infile": {
-                                "id": 22,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
                         "label": null,
-                        "name": "UniProt",
+                        "name": "OpenSwathAssayGenerator",
                         "outputs": [
                             {
-                                "name": "outfile_retrieve_fasta",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 668.8333435058594,
-                            "height": 133.66665649414062,
-                            "left": 2056,
-                            "right": 2256,
-                            "top": 535.1666870117188,
+                                "name": "out",
+                                "type": "data"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 590.2000122070312,
+                            "height": 419.20001220703125,
+                            "left": 577.5,
+                            "right": 777.5,
+                            "top": 171,
                             "width": 200,
-                            "x": 2056,
-                            "y": 535.1666870117188
+                            "x": 577.5,
+                            "y": 171
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathassaygenerator/OpenSwathAssayGenerator/2.5+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "054483e27a35",
-                            "name": "uniprot_rest_interface",
-                            "owner": "bgruening",
+                            "changeset_revision": "2a9ff56cb279",
+                            "name": "openms_openswathassaygenerator",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"id_column\": \"1\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"tool\": {\"tool_choice\": \"retrieve\", \"__current_case__\": 1, \"format\": \"fasta\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.2",
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"adv_opts_cond\": {\"adv_opts_selector\": \"advanced\", \"__current_case__\": 1, \"max_num_alternative_localizations\": \"10000\", \"disable_identification_ms2_precursors\": \"false\", \"disable_identification_specific_losses\": \"false\", \"enable_identification_unspecific_losses\": \"false\", \"enable_swath_specifity\": \"false\", \"force\": \"false\", \"test\": \"False\"}, \"allowed_fragment_charges\": \"1,2,3,4\", \"allowed_fragment_types\": \"b,y\", \"enable_detection_specific_losses\": \"false\", \"enable_detection_unspecific_losses\": \"false\", \"enable_ipf\": \"false\", \"in\": {\"__class__\": \"RuntimeValue\"}, \"max_transitions\": \"6\", \"min_transitions\": \"6\", \"out_type\": \"tsv\", \"precursor_lower_mz_limit\": \"400.0\", \"precursor_mz_threshold\": \"0.015\", \"precursor_upper_mz_limit\": \"1000.0\", \"product_lower_mz_limit\": \"350.0\", \"product_mz_threshold\": \"0.015\", \"product_upper_mz_limit\": \"2000.0\", \"swath_windows_file\": {\"__class__\": \"RuntimeValue\"}, \"unimod_file\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
                         "type": "tool",
-                        "uuid": "c8c7914e-7c65-40b3-931b-c64b3848d383",
+                        "uuid": "ed923bff-cb4e-4d69-9b95-90c85e709fa2",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile_retrieve_fasta",
-                                "uuid": "ce31b047-1193-4937-9d7b-2a5c5d2c9d6d"
+                                "output_name": "out",
+                                "uuid": "b759b71c-1b1a-4240-9ee5-8294990dc07d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator/2.5+galaxy0",
                         "errors": null,
-                        "id": 27,
+                        "id": 9,
                         "input_connections": {
-                            "input": {
-                                "id": 24,
-                                "output_name": "outfile_retrieve_fasta"
+                            "in": {
+                                "id": 8,
+                                "output_name": "out"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool OpenSwathDecoyGenerator",
+                                "name": "in"
+                            }
+                        ],
                         "label": null,
-                        "name": "FASTA-to-Tabular",
+                        "name": "OpenSwathDecoyGenerator",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "name": "out",
+                                "type": "data"
                             }
                         ],
                         "position": {
-                            "bottom": 288.43333435058594,
-                            "height": 113.26666259765625,
-                            "left": 2276,
-                            "right": 2476,
-                            "top": 175.1666717529297,
+                            "bottom": 345.8000030517578,
+                            "height": 174.8000030517578,
+                            "left": 797.5,
+                            "right": 997.5,
+                            "top": 171,
                             "width": 200,
-                            "x": 2276,
-                            "y": 175.1666717529297
+                            "x": 797.5,
+                            "y": 171
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator/2.5+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "e7ed3c310b74",
-                            "name": "fasta_to_tabular",
-                            "owner": "devteam",
+                            "changeset_revision": "f861ec9fbe59",
+                            "name": "openms_openswathdecoygenerator",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"descr_columns\": \"2\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"adv_opts_cond\": {\"adv_opts_selector\": \"advanced\", \"__current_case__\": 1, \"min_decoy_fraction\": \"0.8\", \"aim_decoy_fraction\": \"1.0\", \"shuffle_max_attempts\": \"30\", \"shuffle_sequence_identity_threshold\": \"0.5\", \"shift_precursor_mz_shift\": \"0.0\", \"shift_product_mz_shift\": \"20.0\", \"product_mz_threshold\": \"0.015\", \"allowed_fragment_types\": \"b,y\", \"allowed_fragment_charges\": \"1,2,3,4\", \"enable_detection_specific_losses\": \"false\", \"enable_detection_unspecific_losses\": \"false\", \"separate\": \"false\", \"force\": \"false\", \"test\": \"False\"}, \"decoy_tag\": \"DECOY_\", \"in\": {\"__class__\": \"RuntimeValue\"}, \"method\": \"shuffle\", \"out_type\": \"tsv\", \"switchKR\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
                         "type": "tool",
-                        "uuid": "da7d791d-50c8-4c98-80dd-dc5fdee242d4",
+                        "uuid": "fb0b6f0e-4a95-4fa0-80d3-8a6dfa0edf25",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "bff31e15-ee6c-4972-9795-b478d0a0e9e7"
+                                "output_name": "out",
+                                "uuid": "c068a0cc-c6e9-44ac-bc64-9714b89841f7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_targetedfileconverter/TargetedFileConverter/2.5+galaxy0",
                         "errors": null,
-                        "id": 28,
+                        "id": 10,
                         "input_connections": {
-                            "input": {
-                                "id": 26,
-                                "output_name": "outfile_retrieve_fasta"
+                            "in": {
+                                "id": 9,
+                                "output_name": "out"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool TargetedFileConverter",
+                                "name": "in"
+                            }
+                        ],
                         "label": null,
-                        "name": "FASTA-to-Tabular",
+                        "name": "TargetedFileConverter",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "name": "out",
+                                "type": "data"
                             }
                         ],
                         "position": {
-                            "bottom": 408.433349609375,
-                            "height": 113.26666259765625,
-                            "left": 2276,
-                            "right": 2476,
-                            "top": 295.16668701171875,
+                            "bottom": 325.3999938964844,
+                            "height": 154.39999389648438,
+                            "left": 1017.5,
+                            "right": 1217.5,
+                            "top": 171,
                             "width": 200,
-                            "x": 2276,
-                            "y": 295.16668701171875
+                            "x": 1017.5,
+                            "y": 171
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_targetedfileconverter/TargetedFileConverter/2.5+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "e7ed3c310b74",
-                            "name": "fasta_to_tabular",
-                            "owner": "devteam",
+                            "changeset_revision": "dd71e020e2aa",
+                            "name": "openms_targetedfileconverter",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"descr_columns\": \"2\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"adv_opts_cond\": {\"adv_opts_selector\": \"advanced\", \"__current_case__\": 1, \"legacy_traml_id\": \"false\", \"force\": \"false\", \"test\": \"False\"}, \"algorithm\": {\"retentionTimeInterpretation\": \"iRT\", \"override_group_label_check\": \"false\", \"force_invalid_mods\": \"false\"}, \"in\": {\"__class__\": \"RuntimeValue\"}, \"out_type\": \"pqp\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
                         "type": "tool",
-                        "uuid": "6df99dbd-ac3d-4574-90dd-11f93c65d4c4",
+                        "uuid": "c91c0e6d-282a-46ae-bb47-1425f1b0f1f3",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "f661462b-ca82-4621-9f2a-1c7892b89918"
+                                "output_name": "out",
+                                "uuid": "5721be8a-32ce-4d4d-8d50-6deeae3b61d2"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/maxquant-msstats-dda-lfq",
-                "path": "topics/proteomics/tutorials/maxquant-msstats-dda-lfq/workflows/main_workflow.ga",
+                "parent_id": "proteomics/DIA_lib_OSW",
+                "path": "topics/proteomics/tutorials/DIA_lib_OSW/workflows/Galaxy-Workflow-DIA_lib_Training_HEK_Ecoli_3_EG_data.ga",
                 "tags": [
                     "proteomics"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Proteomics: MaxQuant and MSstats LFQ workflow",
+                "title": "DIA_lib_OSW",
                 "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-maxquant-msstats-dda-lfq/versions/main-workflow",
-                "tutorial_id": "maxquant-msstats-dda-lfq",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/maxquant-msstats-dda-lfq/workflows/main_workflow.html",
-                "version": 3,
-                "wfid": "proteomics-maxquant-msstats-dda-lfq",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-DIA_lib_OSW/versions/galaxy-workflow-dia-lib-training-hek-ecoli-3-eg-data",
+                "tutorial_id": "DIA_lib_OSW",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/DIA_lib_OSW/workflows/Galaxy-Workflow-DIA_lib_Training_HEK_Ecoli_3_EG_data.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/DIA_lib_OSW/workflows/Galaxy-Workflow-DIA_lib_Training_HEK_Ecoli_3_EG_data.html",
+                "version": 1,
+                "wfid": "proteomics-DIA_lib_OSW",
+                "wfname": "galaxy-workflow-dia-lib-training-hek-ecoli-3-eg-data",
+                "workflow": "Galaxy-Workflow-DIA_lib_Training_HEK_Ecoli_3_EG_data.ga",
                 "workflow_tools": [
-                    "Cut1",
                     "Filter1",
-                    "Grep1",
-                    "Summary_Statistics1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy4",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.22.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/datamash_ops/1.0.6",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1"
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/diapysef/diapysef/0.3.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathassaygenerator/OpenSwathAssayGenerator/2.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator/2.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_targetedfileconverter/TargetedFileConverter/2.5+galaxy0"
                 ],
-                "workflowhub_id": "1240"
+                "workflowhub_id": "1224"
             }
         ],
-        "zenodo_link": ""
+        "zenodo_link": "https://zenodo.org/record/4293493"
     },
     {
         "admin_install": {
@@ -196025,7 +197496,7 @@
         "objectives": [
             "Protein identification from LC-MS/MS raw files."
         ],
-        "pageviews": 4025,
+        "pageviews": 4157,
         "pub_date": "2017-06-12",
         "questions": [
             "How to convert LC-MS/MS raw files?",
@@ -196035,10 +197506,10 @@
         ],
         "short_id": "T00229",
         "short_tools": [
-            "Grep1",
-            "peptide_shaker",
             "PeakPickerHiRes",
+            "peptide_shaker",
             "search_gui",
+            "Grep1",
             "FileConverter"
         ],
         "slides": false,
@@ -196082,7 +197553,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 124,
-        "visitors": 2316,
+        "visitors": 2412,
         "workflows": [
             {
                 "creators": [],
@@ -196192,7 +197663,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput: Protein Database\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput: mzML file\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"PeakPickerHiRes\"];\n  1 -->|output| 2;\n  3[\"FileConverter\"];\n  2 -->|param_out| 3;\n  4[\"Search GUI\"];\n  0 -->|output| 4;\n  3 -->|param_out| 4;\n  5[\"Peptide Shaker\"];\n  4 -->|searchgui_results| 5;\n  6[\"Select\"];\n  5 -->|output_proteins| 6;\n  7[\"Select\"];\n  5 -->|output_proteins| 7;\n  8[\"Select\"];\n  7 -->|out_file1| 8;",
-                "modified": "2024-08-18 00:06:24 +0000",
+                "modified": "2024-10-02 12:08:09 +0000",
                 "name": "Peptide And Protein ID Tutorial",
                 "outputs": [
                     {
@@ -196675,7 +198146,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"PeakPickerHiRes\"];\n  1 -->|output| 2;\n  3[\"FileConverter\"];\n  2 -->|param_out| 3;\n  4[\"Search GUI\"];\n  0 -->|output| 4;\n  3 -->|param_out| 4;\n  5[\"Peptide Shaker\"];\n  4 -->|searchgui_results| 5;\n  6[\"Select\"];\n  5 -->|output_proteins| 6;\n  7[\"Select\"];\n  5 -->|output_proteins| 7;\n  8[\"Select\"];\n  7 -->|out_file1| 8;",
-                "modified": "2024-08-18 00:06:24 +0000",
+                "modified": "2024-10-02 12:08:09 +0000",
                 "name": "ProteinID SG PS Tutorial WF datasetCollection",
                 "outputs": [
                     {
@@ -196855,51 +198326,44 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "288462ec2630",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "288462ec2630",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "fasta_to_tabular",
+                    "owner": "devteam",
+                    "revisions": "e7ed3c310b74",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "288462ec2630",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "tabular_to_fasta",
+                    "owner": "devteam",
+                    "revisions": "0a7799698fe5",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "uniprot_rest_interface",
-                    "owner": "bgruening",
-                    "revisions": "f7ebd1b4783b",
-                    "tool_panel_section_label": "Convert Formats",
+                    "name": "dbbuilder",
+                    "owner": "galaxyp",
+                    "revisions": "c1b437242fee",
+                    "tool_panel_section_label": "Get Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "unique",
-                    "owner": "bgruening",
-                    "revisions": "7ce75adb93be",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "fasta_merge_files_and_filter_unique_sequences",
+                    "owner": "galaxyp",
+                    "revisions": "f546e7278f04",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "tmhmm_and_signalp",
-                    "owner": "peterjc",
-                    "revisions": "e6cc27d182a8",
-                    "tool_panel_section_label": "Annotation",
+                    "name": "openms_decoydatabase",
+                    "owner": "galaxyp",
+                    "revisions": "370141bc0da3",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: 288462ec2630\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 288462ec2630\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 288462ec2630\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: uniprot_rest_interface\n  owner: bgruening\n  revisions: f7ebd1b4783b\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unique\n  owner: bgruening\n  revisions: 7ce75adb93be\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tmhmm_and_signalp\n  owner: peterjc\n  revisions: e6cc27d182a8\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/secretome-prediction/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fasta_to_tabular\n  owner: devteam\n  revisions: e7ed3c310b74\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tabular_to_fasta\n  owner: devteam\n  revisions: 0a7799698fe5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dbbuilder\n  owner: galaxyp\n  revisions: c1b437242fee\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_merge_files_and_filter_unique_sequences\n  owner: galaxyp\n  revisions: f546e7278f04\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_decoydatabase\n  owner: galaxyp\n  revisions: 370141bc0da3\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/database-handling/tutorial.json",
         "contributors": [
             {
                 "email": "sigloch+github@mailbox.org",
@@ -196944,81 +198408,102 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/secretome-prediction",
-        "draft": true,
+        "dir": "topics/proteomics/tutorials/database-handling",
+        "edam_ontology": [
+            "topic_0121"
+        ],
         "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
+        "edam_topic": [
+            "Proteomics"
+        ],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org.au"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "proteomics/secretome-prediction",
-        "inexact_supported_servers": [],
+        "id": "proteomics/database-handling",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.no"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "The cellular secretome contains more than the classically secreted proteins.",
-            "Localization predictions by multiple different algorithms can improve sensitivity and/or specificity."
+            "There are several types of Uniprot databases.",
+            "Search databases should always include possible contaminants.",
+            "For analyzing cell culture or organic samples, search databases should include mycoplasma databases.",
+            "Some peptide search engines depend on decoys to calculate the FDR."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
         "mod_date": "2023-11-09",
         "objectives": [
-            "Predict proteins in the cellular secretome by using GO-terms.",
-            "Predict proteins in the cellular secretome by using WolfPSORT.",
-            "Combine the results of both predictions."
+            "Creation of a protein FASTA database ready for use with database search algorithms."
         ],
-        "pageviews": 865,
-        "pub_date": "2017-04-13",
+        "pageviews": 6523,
+        "pub_date": "2017-02-14",
         "questions": [
-            "How to predict cellular protein localization based upon GO-terms?",
-            "How to combine multiple localization predictions?"
+            "How to download protein FASTA databases of a certain organism?",
+            "How to download a contaminant database?",
+            "How to create a decoy database?",
+            "How to combine databases?"
         ],
-        "short_id": "T00235",
+        "short_id": "T00214",
         "short_tools": [
-            "Grep1",
-            "bg_uniq",
-            "get_subontology_from",
-            "tp_cut_tool",
-            "uniprot",
-            "wolf_psort",
-            "Convert characters1",
-            "term_id_vs_term_name",
-            "tp_easyjoin_tool",
-            "Filter1",
-            "comp1",
-            "tp_sorted_uniq"
+            "DecoyDatabase",
+            "fasta_merge_files_and_filter_unique_sequences",
+            "dbbuilder",
+            "tab2fasta",
+            "fasta2tab",
+            "addValue"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "post-process",
+        "subtopic": "id-quant",
         "supported_servers": {
-            "exact": [],
-            "inexact": []
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                }
+            ]
         },
         "symlink": null,
         "tags": [
-            "human",
-            "work-in-progress"
+            "DDA"
         ],
         "time_estimation": "30m",
-        "title": "Secretome Prediction",
+        "title": "Protein FASTA Database Handling",
         "tools": [
-            "Convert characters1",
-            "Filter1",
-            "Grep1",
-            "comp1",
-            "get_subontology_from",
-            "term_id_vs_term_name",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.0.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.0.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.0.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
-            "toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/wolf_psort/0.0.8"
+            "addValue",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.6+galaxy0"
         ],
         "topic_name": "proteomics",
         "topic_name_human": "Proteomics",
@@ -197028,44 +198513,498 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "secretome-prediction",
+        "tutorial_name": "database-handling",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/secretome-prediction/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/database-handling/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/secretome-prediction/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/secretome-prediction/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/database-handling/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/database-handling/tutorial.json"
         },
-        "version": 14,
+        "version": 29,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 90,
-        "visitors": 564,
+        "visit_duration": 120,
+        "visitors": 3941,
         "workflows": [
             {
                 "creators": [],
-                "description": "version 1.0, 160318, published at https://github.com/Stortebecker/secretome_prediction",
+                "description": "Protein FASTA Database Handling",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  3[label=\"UniProt\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Select\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Get subontology from a given OBO term\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"Get subontology from a given OBO term\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"Get subontology from a given OBO term\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"Get subontology from a given OBO term\"]\n  2 -> 8 [label=\"output\"]\n  9[label=\"Get subontology from a given OBO term\"]\n  2 -> 9 [label=\"output\"]\n  10[label=\"WoLF PSORT\"]\n  3 -> 10 [label=\"outfile_retrieve_fasta\"]\n  11[label=\"Join\"]\n  0 -> 11 [label=\"output\"]\n  4 -> 11 [label=\"out_file1\"]\n  12[label=\"Get all the term IDs and term names of a given OBO ontology\"]\n  5 -> 12 [label=\"output\"]\n  13[label=\"Get all the term IDs and term names of a given OBO ontology\"]\n  6 -> 13 [label=\"output\"]\n  14[label=\"Get all the term IDs and term names of a given OBO ontology\"]\n  7 -> 14 [label=\"output\"]\n  15[label=\"Get all the term IDs and term names of a given OBO ontology\"]\n  8 -> 15 [label=\"output\"]\n  16[label=\"Get all the term IDs and term names of a given OBO ontology\"]\n  9 -> 16 [label=\"output\"]\n  17[label=\"Filter\"]\n  10 -> 17 [label=\"tabular_file\"]\n  18[label=\"Filter\"]\n  10 -> 18 [label=\"tabular_file\"]\n  19[label=\"Join\"]\n  12 -> 19 [label=\"output\"]\n  13 -> 19 [label=\"output\"]\n  20[label=\"Join\"]\n  14 -> 20 [label=\"output\"]\n  15 -> 20 [label=\"output\"]\n  21[label=\"Join\"]\n  17 -> 21 [label=\"out_file1\"]\n  18 -> 21 [label=\"out_file1\"]\n  22[label=\"Join\"]\n  19 -> 22 [label=\"output\"]\n  20 -> 22 [label=\"output\"]\n  23[label=\"Convert\"]\n  21 -> 23 [label=\"output\"]\n  24[label=\"Join\"]\n  22 -> 24 [label=\"output\"]\n  16 -> 24 [label=\"output\"]\n  25[label=\"Cut\"]\n  23 -> 25 [label=\"out_file1\"]\n  26[label=\"Compare two Datasets\"]\n  11 -> 26 [label=\"output\"]\n  24 -> 26 [label=\"output\"]\n  27[label=\"Unique\"]\n  26 -> 27 [label=\"out_file1\"]\n  28[label=\"Cut\"]\n  27 -> 28 [label=\"outfile\"]\n  29[label=\"Join\"]\n  25 -> 29 [label=\"output\"]\n  28 -> 29 [label=\"output\"]\n  30[label=\"Unique\"]\n  29 -> 30 [label=\"output\"]\n  k14e0c6dc436b4c4c9292d5e00cca8c92[color=lightseagreen,label=\"Output\\nSecretome proteins\"]\n  30 -> k14e0c6dc436b4c4c9292d5e00cca8c92\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Protein Database Downloader\"]\n  1[label=\"Protein Database Downloader\"]\n  2[label=\"FASTA-to-Tabular\"]\n  0 -> 2 [label=\"output_database\"]\n  3[label=\"Add column\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Tabular-to-FASTA\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"FASTA Merge Files and Filter Unique Sequences\"]\n  4 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output_database\"]\n  6[label=\"DecoyDatabase\"]\n  5 -> 6 [label=\"output\"]\n}",
                 "history": [
+                    {
+                        "hash": "54b4d9fcc78b1394f71f7affd51ca15e83b211d5",
+                        "message": "Adding tags to workflows",
+                        "num": 6,
+                        "short_hash": "54b4d9fcc",
+                        "unix": "1604224600"
+                    },
+                    {
+                        "hash": "ca84d739509bdb1ef8f3cfc64c15242ef0363407",
+                        "message": "Updating Tutorials to OpenMS 2.6, adjusting of parameters and tools, adding tool versions",
+                        "num": 5,
+                        "short_hash": "ca84d7395",
+                        "unix": "1604176914"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 4,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
                     {
                         "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
                         "message": "Workflow renaming",
-                        "num": 4,
+                        "num": 3,
                         "short_hash": "eb4d724e0",
                         "unix": "1579084895"
                     },
                     {
-                        "hash": "55fe079b2828d71aabb21fa0700f6f77ac76052c",
-                        "message": "WoLF PSORT WF",
+                        "hash": "7da80b34185f4165852feb3bfe80d692609685db",
+                        "message": "Workflows fix",
+                        "num": 2,
+                        "short_hash": "7da80b341",
+                        "unix": "1578668175"
+                    },
+                    {
+                        "hash": "2c1271b670d336517fb123fb632ce13c93c40465",
+                        "message": "Restructure proteomics",
+                        "num": 1,
+                        "short_hash": "2c1271b67",
+                        "unix": "1495544862"
+                    }
+                ],
+                "inputs": [],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"Protein Database Downloader\"];\n  1[\"Protein Database Downloader\"];\n  2[\"FASTA-to-Tabular\"];\n  0 -->|output_database| 2;\n  3[\"Add column\"];\n  2 -->|output| 3;\n  4[\"Tabular-to-FASTA\"];\n  3 -->|out_file1| 4;\n  5[\"FASTA Merge Files and Filter Unique Sequences\"];\n  4 -->|output| 5;\n  1 -->|output_database| 5;\n  6[\"DecoyDatabase\"];\n  5 -->|output| 6;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Proteomics: database handling",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": null,
+                        "name": "Protein Database Downloader",
+                        "outputs": [
+                            {
+                                "name": "output_database",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 380.6000061035156,
+                            "height": 102.60000610351562,
+                            "left": -110,
+                            "right": 90,
+                            "top": 278,
+                            "width": 200,
+                            "x": -110,
+                            "y": 278
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "c1b437242fee",
+                            "name": "dbbuilder",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"cRAP\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3.1",
+                        "type": "tool",
+                        "uuid": "6613b72c-2bab-423c-88fc-05edfe9ea8ec",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_database",
+                                "uuid": "2d289b03-c396-46a2-a725-987b6c75ada9"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": null,
+                        "name": "Protein Database Downloader",
+                        "outputs": [
+                            {
+                                "name": "output_database",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 632.6000061035156,
+                            "height": 102.60000610351562,
+                            "left": -83,
+                            "right": 117,
+                            "top": 530,
+                            "width": 200,
+                            "x": -83,
+                            "y": 530
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "c1b437242fee",
+                            "name": "dbbuilder",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"9606\", \"reviewed\": \"+reviewed%3Ayes\", \"set\": \"+keyword%3a1185\", \"include_isoform\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3.1",
+                        "type": "tool",
+                        "uuid": "ee46d245-5fdd-4d02-9148-49a26c98ed81",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_database",
+                                "uuid": "8b345bac-fbae-4fee-aced-a3f56e72aa21"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output_database"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FASTA-to-Tabular",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 383.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": 146,
+                            "right": 346,
+                            "top": 270,
+                            "width": 200,
+                            "x": 146,
+                            "y": 270
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e7ed3c310b74",
+                            "name": "fasta_to_tabular",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"descr_columns\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
+                        "type": "tool",
+                        "uuid": "c7bafec5-de51-4a49-80f8-402e443fa3fb",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "d320cd9d-fa50-41ab-96f9-0715e2467d55"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "addValue",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "input": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Add column",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 363.1999969482422,
+                            "height": 93.19999694824219,
+                            "left": 366,
+                            "right": 566,
+                            "top": 270,
+                            "width": 200,
+                            "x": 366,
+                            "y": 270
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "addValue",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"exp\": \"CONTAMINANT\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "27172bb3-7f15-49d9-961e-4a87401812c7",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "12d78b53-8f63-4349-89b5-4f5770d3ac4d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "input": {
+                                "id": 3,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Tabular-to-FASTA",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 383.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": 586,
+                            "right": 786,
+                            "top": 270,
+                            "width": 200,
+                            "x": 586,
+                            "y": 270
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "0a7799698fe5",
+                            "name": "tabular_to_fasta",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"seq_col\": \"2\", \"title_col\": [\"1\", \"3\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
+                        "type": "tool",
+                        "uuid": "d8a59abc-1be6-41e9-8df0-c8b06d8430c7",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "a1dccdc6-a13f-4326-bb33-a75581b22d9b"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "batchmode|input_fastas_0|input_fasta": {
+                                "id": 4,
+                                "output_name": "output"
+                            },
+                            "batchmode|input_fastas_1|input_fasta": {
+                                "id": 1,
+                                "output_name": "output_database"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FASTA Merge Files and Filter Unique Sequences",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 516,
+                            "height": 246,
+                            "left": 806,
+                            "right": 1006,
+                            "top": 270,
+                            "width": 200,
+                            "x": 806,
+                            "y": 270
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "650d553c1fda",
+                            "name": "fasta_merge_files_and_filter_unique_sequences",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"accession_parser\": \"^>([^ ]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"uniqueness_criterion\": \"accession\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.0",
+                        "type": "tool",
+                        "uuid": "609ed0b7-37b3-459b-ab69-e10ff898b372",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "b7b9b10b-9f63-4e66-b25a-da521756b75d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.6+galaxy0",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "in": {
+                                "id": 5,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "DecoyDatabase",
+                        "outputs": [
+                            {
+                                "name": "out",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 428.3999938964844,
+                            "height": 154.39999389648438,
+                            "left": 1137,
+                            "right": 1337,
+                            "top": 274,
+                            "width": 200,
+                            "x": 1137,
+                            "y": 274
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "71a6c870aa48",
+                            "name": "openms_decoydatabase",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"Decoy\": {\"non_shuffle_pattern\": \"\", \"keepPeptideNTerm\": \"true\", \"keepPeptideCTerm\": \"true\"}, \"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"decoy_string\": \"DECOY_\", \"decoy_string_position\": \"prefix\", \"enzyme\": \"Trypsin\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"method\": \"reverse\", \"only_decoy\": \"false\", \"type\": \"protein\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "053fc094-7146-4bf7-91bd-df3f8fdc3f05",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out",
+                                "uuid": "54465c5a-911c-46a7-91d2-78e40ba9e92f"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "proteomics/database-handling",
+                "path": "topics/proteomics/tutorials/database-handling/workflows/wf_database-handling.ga",
+                "tags": [
+                    "proteomics"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Proteomics: database handling",
+                "topic_id": "proteomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-database-handling/versions/wf-database-handling",
+                "tutorial_id": "database-handling",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/database-handling/workflows/wf_database-handling.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/database-handling/workflows/wf_database-handling.html",
+                "version": 5,
+                "wfid": "proteomics-database-handling",
+                "wfname": "wf-database-handling",
+                "workflow": "wf_database-handling.ga",
+                "workflow_tools": [
+                    "addValue",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.6+galaxy0"
+                ],
+                "workflowhub_id": "1204"
+            },
+            {
+                "creators": [],
+                "description": "Protein FASTA Database Handling",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Protein Database Downloader\"]\n  1[label=\"Protein Database Downloader\"]\n  2[label=\"Protein Database Downloader\"]\n  3[label=\"Protein Database Downloader\"]\n  4[label=\"Protein Database Downloader\"]\n  5[label=\"Protein Database Downloader\"]\n  6[label=\"Protein Database Downloader\"]\n  7[label=\"Protein Database Downloader\"]\n  8[label=\"FASTA-to-Tabular\"]\n  2 -> 8 [label=\"output_database\"]\n  9[label=\"FASTA Merge Files and Filter Unique Sequences\"]\n  5 -> 9 [label=\"output_database\"]\n  4 -> 9 [label=\"output_database\"]\n  3 -> 9 [label=\"output_database\"]\n  1 -> 9 [label=\"output_database\"]\n  0 -> 9 [label=\"output_database\"]\n  6 -> 9 [label=\"output_database\"]\n  10[label=\"Add column\"]\n  8 -> 10 [label=\"output\"]\n  11[label=\"FASTA-to-Tabular\"]\n  9 -> 11 [label=\"output\"]\n  12[label=\"Tabular-to-FASTA\"]\n  10 -> 12 [label=\"out_file1\"]\n  13[label=\"Add column\"]\n  11 -> 13 [label=\"output\"]\n  14[label=\"Tabular-to-FASTA\"]\n  13 -> 14 [label=\"out_file1\"]\n  15[label=\"FASTA Merge Files and Filter Unique Sequences\"]\n  12 -> 15 [label=\"output\"]\n  7 -> 15 [label=\"output_database\"]\n  14 -> 15 [label=\"output\"]\n  16[label=\"DecoyDatabase\"]\n  15 -> 16 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "30b5abb36b9cfef5ca43d0f8c6fc504dd9bc459a",
+                        "message": "Update wf_database-handling_mycoplasma.ga",
+                        "num": 8,
+                        "short_hash": "30b5abb36",
+                        "unix": "1608207012"
+                    },
+                    {
+                        "hash": "30e6e1ac18f3e4e93c1f1d322d8423070cf3a4a5",
+                        "message": "Update wf_database-handling_mycoplasma.ga workflow",
+                        "num": 7,
+                        "short_hash": "30e6e1ac1",
+                        "unix": "1608205362"
+                    },
+                    {
+                        "hash": "54b4d9fcc78b1394f71f7affd51ca15e83b211d5",
+                        "message": "Adding tags to workflows",
+                        "num": 6,
+                        "short_hash": "54b4d9fcc",
+                        "unix": "1604224600"
+                    },
+                    {
+                        "hash": "ca84d739509bdb1ef8f3cfc64c15242ef0363407",
+                        "message": "Updating Tutorials to OpenMS 2.6, adjusting of parameters and tools, adding tool versions",
+                        "num": 5,
+                        "short_hash": "ca84d7395",
+                        "unix": "1604176914"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 4,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
                         "num": 3,
-                        "short_hash": "55fe079b2",
-                        "unix": "1578933056"
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
                     },
                     {
                         "hash": "7da80b34185f4165852feb3bfe80d692609685db",
@@ -197082,620 +199021,818 @@
                         "unix": "1495544862"
                     }
                 ],
-                "inputs": [
+                "inputs": [],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"Protein Database Downloader\"];\n  1[\"Protein Database Downloader\"];\n  2[\"Protein Database Downloader\"];\n  3[\"Protein Database Downloader\"];\n  4[\"Protein Database Downloader\"];\n  5[\"Protein Database Downloader\"];\n  6[\"Protein Database Downloader\"];\n  7[\"Protein Database Downloader\"];\n  8[\"FASTA-to-Tabular\"];\n  2 -->|output_database| 8;\n  9[\"FASTA Merge Files and Filter Unique Sequences\"];\n  5 -->|output_database| 9;\n  4 -->|output_database| 9;\n  3 -->|output_database| 9;\n  1 -->|output_database| 9;\n  0 -->|output_database| 9;\n  6 -->|output_database| 9;\n  10[\"Add column\"];\n  8 -->|output| 10;\n  11[\"FASTA-to-Tabular\"];\n  9 -->|output| 11;\n  12[\"Tabular-to-FASTA\"];\n  10 -->|out_file1| 12;\n  13[\"Add column\"];\n  11 -->|output| 13;\n  14[\"Tabular-to-FASTA\"];\n  13 -->|out_file1| 14;\n  15[\"FASTA Merge Files and Filter Unique Sequences\"];\n  12 -->|output| 15;\n  7 -->|output_database| 15;\n  14 -->|output| 15;\n  16[\"DecoyDatabase\"];\n  15 -->|output| 16;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Proteomics: database handling including mycoplasma",
+                "outputs": [
                     {
-                        "annotation": "Input: Protein ID list\nFirst column has to be uniprot accessions",
-                        "content_id": null,
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Protein Database Downloader",
+                        "outputs": [
+                            {
+                                "name": "output_database",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 186.171875,
+                            "height": 101,
+                            "left": 489.96875,
+                            "right": 689.96875,
+                            "top": 85.171875,
+                            "width": 200,
+                            "x": 489.96875,
+                            "y": 85.171875
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "c1b437242fee",
+                            "name": "dbbuilder",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"2121\", \"reviewed\": \"+\", \"set\": \"+keyword%3a1185\", \"include_isoform\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3.1",
+                        "type": "tool",
+                        "uuid": "4114a759-55b3-41e4-866d-b4ce95b7064a",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_database",
+                                "uuid": "7139701a-2418-4a54-8708-69e50cdf64b1"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": null,
+                        "name": "Protein Database Downloader",
+                        "outputs": [
+                            {
+                                "name": "output_database",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 293.171875,
+                            "height": 101,
+                            "left": 508.96875,
+                            "right": 708.96875,
+                            "top": 192.171875,
+                            "width": 200,
+                            "x": 508.96875,
+                            "y": 192.171875
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "c1b437242fee",
+                            "name": "dbbuilder",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"2100\", \"reviewed\": \"+\", \"set\": \"+keyword%3a1185\", \"include_isoform\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3.1",
+                        "type": "tool",
+                        "uuid": "9d6509a8-45b2-463c-a37c-5330280a2302",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_database",
+                                "uuid": "02415048-af7f-482d-bc30-af3315ae63b2"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": null,
+                        "name": "Protein Database Downloader",
+                        "outputs": [
+                            {
+                                "name": "output_database",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "bottom": -196.828125,
+                            "height": 101,
+                            "left": 471.96875,
+                            "right": 671.96875,
+                            "top": -297.828125,
+                            "width": 200,
+                            "x": 471.96875,
+                            "y": -297.828125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "c1b437242fee",
+                            "name": "dbbuilder",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"cRAP\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3.1",
+                        "type": "tool",
+                        "uuid": "357e8c0f-93cd-4ebc-81ac-6ece5de019e5",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_database",
+                                "uuid": "1605ec3f-5755-43d4-813d-a865518bda07"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": null,
+                        "name": "Protein Database Downloader",
+                        "outputs": [
+                            {
+                                "name": "output_database",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 413.171875,
+                            "height": 101,
+                            "left": 508.96875,
+                            "right": 708.96875,
+                            "top": 312.171875,
+                            "width": 200,
+                            "x": 508.96875,
+                            "y": 312.171875
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "c1b437242fee",
+                            "name": "dbbuilder",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"2094\", \"reviewed\": \"+\", \"set\": \"+keyword%3a1185\", \"include_isoform\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3.1",
+                        "type": "tool",
+                        "uuid": "6124a009-45b4-44f3-a143-61d47fbe17a9",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_database",
+                                "uuid": "55cd7e71-a1f9-4dea-8355-462fefce371a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": null,
+                        "name": "Protein Database Downloader",
+                        "outputs": [
                             {
-                                "description": "Input: Protein ID list\nFirst column has to be uniprot accessions",
-                                "name": "Custom Protein list (uniprot accession)"
+                                "name": "output_database",
+                                "type": "fasta"
                             }
                         ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 293,
-                            "top": 377
+                            "bottom": 533.171875,
+                            "height": 101,
+                            "left": 508.96875,
+                            "right": 708.96875,
+                            "top": 432.171875,
+                            "width": 200,
+                            "x": 508.96875,
+                            "y": 432.171875
                         },
-                        "tool_errors": null,
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Custom Protein list (uniprot accession)\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "4d60060c-188b-4a93-8320-36f9b43e5765",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "c1b437242fee",
+                            "name": "dbbuilder",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"2115\", \"reviewed\": \"+\", \"set\": \"+keyword%3a1185\", \"include_isoform\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3.1",
+                        "type": "tool",
+                        "uuid": "f01d73bd-e427-40f1-94d0-732836dc3c32",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "27022e50-f5dc-46b1-8b54-979f955eb050"
+                                "output_name": "output_database",
+                                "uuid": "180b1779-a0dc-4a20-aeb8-c451b67e589f"
                             }
                         ]
                     },
                     {
-                        "annotation": "Input: Uniprot GO database file (choose the right organism)\nExample: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gene_association.goa_human.gz",
-                        "content_id": null,
-                        "id": 1,
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "errors": null,
+                        "id": 5,
                         "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Protein Database Downloader",
+                        "outputs": [
                             {
-                                "description": "Input: Uniprot GO database file (choose the right organism)\nExample: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gene_association.goa_human.gz",
-                                "name": "Uniprot GO database"
+                                "name": "output_database",
+                                "type": "fasta"
                             }
                         ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 290,
-                            "top": 507
+                            "bottom": 653.171875,
+                            "height": 101,
+                            "left": 508.96875,
+                            "right": 708.96875,
+                            "top": 552.171875,
+                            "width": 200,
+                            "x": 508.96875,
+                            "y": 552.171875
                         },
-                        "tool_errors": null,
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Uniprot GO database\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "e8f4a577-7b6a-4cd0-9a74-2e68c4ae6c5a",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "c1b437242fee",
+                            "name": "dbbuilder",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"2098\", \"reviewed\": \"+\", \"set\": \"+keyword%3a1185\", \"include_isoform\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3.1",
+                        "type": "tool",
+                        "uuid": "b725bbfe-011f-4ebf-b94d-235db3811db5",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "b8fa36c2-6bbf-40c1-a472-8d4a6a7096c3"
+                                "output_name": "output_database",
+                                "uuid": "8458bb43-85bd-4b58-810b-d87277b0fa51"
                             }
                         ]
                     },
                     {
-                        "annotation": "Input: Please downlad the Open Biomedical Ontology (OBO), i.e. \"GO term tree\" from\nhttp://purl.obolibrary.org/obo/go/go.obo",
-                        "content_id": null,
-                        "id": 2,
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "errors": null,
+                        "id": 6,
                         "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Protein Database Downloader",
+                        "outputs": [
                             {
-                                "description": "Input: Please downlad the Open Biomedical Ontology (OBO), i.e. \"GO term tree\" from\nhttp://purl.obolibrary.org/obo/go/go.obo",
-                                "name": "Open Biomedical Ontology (OBO)"
+                                "name": "output_database",
+                                "type": "fasta"
                             }
                         ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 293,
-                            "top": 790
+                            "bottom": 770.171875,
+                            "height": 101,
+                            "left": 512.5625,
+                            "right": 712.5625,
+                            "top": 669.171875,
+                            "width": 200,
+                            "x": 512.5625,
+                            "y": 669.171875
                         },
-                        "tool_errors": null,
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Open Biomedical Ontology (OBO)\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "0640e1c4-4d77-49da-8473-0018e0a5db09",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "c1b437242fee",
+                            "name": "dbbuilder",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"2148\", \"reviewed\": \"+\", \"set\": \"+keyword%3a1185\", \"include_isoform\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3.1",
+                        "type": "tool",
+                        "uuid": "0b7814d9-5511-4278-9ca3-19748a1f9ece",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "4725c10d-9e7a-4e3f-9874-c302c34687cb"
+                                "output_name": "output_database",
+                                "uuid": "cc6b866c-4912-421d-a342-23baef5d2c95"
                             }
                         ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"UniProt\"];\n  0 -->|output| 3;\n  4[\"Select\"];\n  1 -->|output| 4;\n  5[\"Get subontology from a given OBO term\"];\n  2 -->|output| 5;\n  6[\"Get subontology from a given OBO term\"];\n  2 -->|output| 6;\n  7[\"Get subontology from a given OBO term\"];\n  2 -->|output| 7;\n  8[\"Get subontology from a given OBO term\"];\n  2 -->|output| 8;\n  9[\"Get subontology from a given OBO term\"];\n  2 -->|output| 9;\n  10[\"WoLF PSORT\"];\n  3 -->|outfile_retrieve_fasta| 10;\n  11[\"Join\"];\n  0 -->|output| 11;\n  4 -->|out_file1| 11;\n  12[\"Get all the term IDs and term names of a given OBO ontology\"];\n  5 -->|output| 12;\n  13[\"Get all the term IDs and term names of a given OBO ontology\"];\n  6 -->|output| 13;\n  14[\"Get all the term IDs and term names of a given OBO ontology\"];\n  7 -->|output| 14;\n  15[\"Get all the term IDs and term names of a given OBO ontology\"];\n  8 -->|output| 15;\n  16[\"Get all the term IDs and term names of a given OBO ontology\"];\n  9 -->|output| 16;\n  17[\"Filter\"];\n  10 -->|tabular_file| 17;\n  18[\"Filter\"];\n  10 -->|tabular_file| 18;\n  19[\"Join\"];\n  12 -->|output| 19;\n  13 -->|output| 19;\n  20[\"Join\"];\n  14 -->|output| 20;\n  15 -->|output| 20;\n  21[\"Join\"];\n  17 -->|out_file1| 21;\n  18 -->|out_file1| 21;\n  22[\"Join\"];\n  19 -->|output| 22;\n  20 -->|output| 22;\n  23[\"Convert\"];\n  21 -->|output| 23;\n  24[\"Join\"];\n  22 -->|output| 24;\n  16 -->|output| 24;\n  25[\"Cut\"];\n  23 -->|out_file1| 25;\n  26[\"Compare two Datasets\"];\n  11 -->|output| 26;\n  24 -->|output| 26;\n  27[\"Unique\"];\n  26 -->|out_file1| 27;\n  28[\"Cut\"];\n  27 -->|outfile| 28;\n  29[\"Join\"];\n  25 -->|output| 29;\n  28 -->|output| 29;\n  30[\"Unique\"];\n  29 -->|output| 30;\n  14e0c6dc-436b-4c4c-9292-d5e00cca8c92[\"Output\\nSecretome proteins\"];\n  30 --> 14e0c6dc-436b-4c4c-9292-d5e00cca8c92;\n  style 14e0c6dc-436b-4c4c-9292-d5e00cca8c92 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Secreted Proteins Via GO Annotation And WoLF PSORT For shCTSB Paper",
-                "outputs": [
+                    },
                     {
-                        "annotation": "Input: Protein ID list\nFirst column has to be uniprot accessions",
-                        "content_id": null,
-                        "id": 0,
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "errors": null,
+                        "id": 7,
                         "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Protein Database Downloader",
+                        "outputs": [
                             {
-                                "description": "Input: Protein ID list\nFirst column has to be uniprot accessions",
-                                "name": "Custom Protein list (uniprot accession)"
+                                "name": "output_database",
+                                "type": "fasta"
                             }
                         ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 293,
-                            "top": 377
+                            "bottom": 358.171875,
+                            "height": 101,
+                            "left": 1149.96875,
+                            "right": 1349.96875,
+                            "top": 257.171875,
+                            "width": 200,
+                            "x": 1149.96875,
+                            "y": 257.171875
                         },
-                        "tool_errors": null,
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Custom Protein list (uniprot accession)\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "4d60060c-188b-4a93-8320-36f9b43e5765",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "c1b437242fee",
+                            "name": "dbbuilder",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"data\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"9606\", \"reviewed\": \"+reviewed%3Ayes\", \"set\": \"+keyword%3a1185\", \"include_isoform\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3.1",
+                        "type": "tool",
+                        "uuid": "8edafc35-59c1-4043-adf2-9413a5959ffe",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "27022e50-f5dc-46b1-8b54-979f955eb050"
+                                "output_name": "output_database",
+                                "uuid": "9b9e1bc5-f179-47e7-bb74-0979ca293e8a"
                             }
                         ]
                     },
                     {
-                        "annotation": "Input: Uniprot GO database file (choose the right organism)\nExample: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gene_association.goa_human.gz",
-                        "content_id": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "input": {
+                                "id": 2,
+                                "output_name": "output_database"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FASTA-to-Tabular",
+                        "outputs": [
                             {
-                                "description": "Input: Uniprot GO database file (choose the right organism)\nExample: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gene_association.goa_human.gz",
-                                "name": "Uniprot GO database"
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 290,
-                            "top": 507
+                            "bottom": -55.828125,
+                            "height": 112,
+                            "left": 728.96875,
+                            "right": 928.96875,
+                            "top": -167.828125,
+                            "width": 200,
+                            "x": 728.96875,
+                            "y": -167.828125
                         },
-                        "tool_errors": null,
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Uniprot GO database\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "e8f4a577-7b6a-4cd0-9a74-2e68c4ae6c5a",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e7ed3c310b74",
+                            "name": "fasta_to_tabular",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"descr_columns\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
+                        "type": "tool",
+                        "uuid": "43204d4a-03b7-46c1-b96f-d9cce74ad707",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "b8fa36c2-6bbf-40c1-a472-8d4a6a7096c3"
+                                "uuid": "28ec9532-c442-4b0a-889e-5809098b1b7f"
                             }
                         ]
                     },
                     {
-                        "annotation": "Input: Please downlad the Open Biomedical Ontology (OBO), i.e. \"GO term tree\" from\nhttp://purl.obolibrary.org/obo/go/go.obo",
-                        "content_id": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {
+                            "batchmode|input_fastas_0|input_fasta": {
+                                "id": 5,
+                                "output_name": "output_database"
+                            },
+                            "batchmode|input_fastas_1|input_fasta": {
+                                "id": 4,
+                                "output_name": "output_database"
+                            },
+                            "batchmode|input_fastas_2|input_fasta": {
+                                "id": 3,
+                                "output_name": "output_database"
+                            },
+                            "batchmode|input_fastas_3|input_fasta": {
+                                "id": 1,
+                                "output_name": "output_database"
+                            },
+                            "batchmode|input_fastas_4|input_fasta": {
+                                "id": 0,
+                                "output_name": "output_database"
+                            },
+                            "batchmode|input_fastas_5|input_fasta": {
+                                "id": 6,
+                                "output_name": "output_database"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FASTA Merge Files and Filter Unique Sequences",
+                        "outputs": [
                             {
-                                "description": "Input: Please downlad the Open Biomedical Ontology (OBO), i.e. \"GO term tree\" from\nhttp://purl.obolibrary.org/obo/go/go.obo",
-                                "name": "Open Biomedical Ontology (OBO)"
+                                "name": "output",
+                                "type": "fasta"
                             }
                         ],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 293,
-                            "top": 790
+                            "bottom": 394.171875,
+                            "height": 442,
+                            "left": 728.96875,
+                            "right": 928.96875,
+                            "top": -47.828125,
+                            "width": 200,
+                            "x": 728.96875,
+                            "y": -47.828125
                         },
-                        "tool_errors": null,
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Open Biomedical Ontology (OBO)\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "0640e1c4-4d77-49da-8473-0018e0a5db09",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f546e7278f04",
+                            "name": "fasta_merge_files_and_filter_unique_sequences",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"accession_parser\": \"^>([^ ]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 3, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 4, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 5, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"uniqueness_criterion\": \"sequence\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.0",
+                        "type": "tool",
+                        "uuid": "2f3e5008-14dc-4078-ab3d-72faf16b21ce",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "4725c10d-9e7a-4e3f-9874-c302c34687cb"
+                                "uuid": "0a40b18e-1b8a-4f70-a134-44a449069a6b"
                             }
                         ]
                     },
                     {
-                        "annotation": "Final output. Unique entries of all proteins that are either predicted by WoLF PSORT to be shed or secreted or annotated in the GO database to be shed or secreted.",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.0.0",
-                        "id": 30,
+                        "annotation": "",
+                        "content_id": "addValue",
+                        "errors": null,
+                        "id": 10,
                         "input_connections": {
-                            "infile": {
-                                "id": 29,
+                            "input": {
+                                "id": 8,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Unique",
+                        "name": "Add column",
                         "outputs": [
                             {
-                                "name": "outfile",
+                                "name": "out_file1",
                                 "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 1964.75,
-                            "top": 787.75
+                            "bottom": -75.828125,
+                            "height": 92,
+                            "left": 948.96875,
+                            "right": 1148.96875,
+                            "top": -167.828125,
+                            "width": 200,
+                            "x": 948.96875,
+                            "y": -167.828125
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutfile": {
-                                "action_arguments": {
-                                    "newname": "secretome_proteins"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "outfile"
+                        "post_job_actions": {},
+                        "tool_id": "addValue",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"exp\": \"CONTAMINANT\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "74c42033-1c6c-4647-b99b-d50eeba95063",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "1d442a40-1bcf-4d3b-979f-0ef7233c7db9"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                        "errors": null,
+                        "id": 11,
+                        "input_connections": {
+                            "input": {
+                                "id": 9,
+                                "output_name": "output"
                             }
                         },
-                        "tool_errors": null,
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.0.0",
+                        "inputs": [],
+                        "label": null,
+                        "name": "FASTA-to-Tabular",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 64.171875,
+                            "height": 112,
+                            "left": 948.96875,
+                            "right": 1148.96875,
+                            "top": -47.828125,
+                            "width": 200,
+                            "x": 948.96875,
+                            "y": -47.828125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "288462ec2630",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "e7ed3c310b74",
+                            "name": "fasta_to_tabular",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": 0, \"ignore_case\": \"\\\"False\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"is_numeric\": \"\\\"False\\\"\", \"infile\": \"null\"}",
-                        "tool_version": "1.0.0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"descr_columns\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"keep_first\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
                         "type": "tool",
-                        "uuid": "5ca3dd78-27ed-4f4f-95f6-c25fa4fd43b6",
+                        "uuid": "c9832b4a-7f75-4763-bd5e-d7de8a80ed3a",
                         "workflow_outputs": [
                             {
-                                "label": "Secretome proteins",
-                                "output_name": "outfile",
-                                "uuid": "14e0c6dc-436b-4c4c-9292-d5e00cca8c92"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "b549c26c-0f66-438f-9c44-e45372fe4cd1"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "proteomics/secretome-prediction",
-                "path": "topics/proteomics/tutorials/secretome-prediction/workflows/WF_secretomePrediction_goWolfpsort.ga",
-                "tags": [
-                    "proteomics"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Secreted Proteins Via GO Annotation And WoLF PSORT For shCTSB Paper",
-                "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-secretome-prediction/versions/wf-secretomeprediction-gowolfpsort",
-                "tutorial_id": "secretome-prediction",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/secretome-prediction/workflows/WF_secretomePrediction_goWolfpsort.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/secretome-prediction/workflows/WF_secretomePrediction_goWolfpsort.html",
-                "version": 3,
-                "wfid": "proteomics-secretome-prediction",
-                "wfname": "wf-secretomeprediction-gowolfpsort",
-                "workflow": "WF_secretomePrediction_goWolfpsort.ga",
-                "workflow_tools": [
-                    "Convert characters1",
-                    "Filter1",
-                    "Grep1",
-                    "comp1",
-                    "get_subontology_from",
-                    "term_id_vs_term_name",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
-                    "toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/wolf_psort/0.0.8"
-                ],
-                "workflowhub_id": "1143"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/519260"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cardinal_data_exporter",
-                    "owner": "galaxyp",
-                    "revisions": "d94770c22f13",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cardinal_quality_report",
-                    "owner": "galaxyp",
-                    "revisions": "16556ca0196b",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_data_exporter\n  owner: galaxyp\n  revisions: d94770c22f13\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cardinal_quality_report\n  owner: galaxyp\n  revisions: 16556ca0196b\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "email": "melanie.foell@mol-med.uni-freiburg.de",
-                "id": "foellmelanie",
-                "joined": "2018-10",
-                "matrix": "foellmelanie:matrix.org",
-                "name": "Melanie F\u00f6ll",
-                "orcid": "0000-0002-1887-7543",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
-                "twitter": "MCFoell",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
-            },
-            {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
-                "fediverse_flavor": "mastodon",
-                "id": "bgruening",
-                "joined": "2017-09",
-                "linkedin": "bgruening",
-                "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
-                },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
-            }
-        ],
-        "dir": "topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data",
-        "edam_ontology": [
-            "topic_0121"
-        ],
-        "edam_operation": [],
-        "edam_topic": [
-            "Proteomics"
-        ],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "proteomics/mass-spectrometry-imaging-loading-exploring-data",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "imzML (continuous or processed file type) and Analyze7.5 can be uploaded into Galaxy via the composite upload.",
-            "The MSI Qualitycontrol tool gives valuable information before starting the analysis.",
-            "The MSI data exporter can be used any time during the analysis when it is necessary to dig deeper into the data. Galaxy provides many text manipulation tools that can directly be applied on the exported tabular file to filter, sort, plot, ... the data."
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Introductory",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "How to upload an imzML file into Galaxy",
-            "Getting an overview of the MSI data with the MSI quality control tool",
-            "How to export MSI data as tabular files"
-        ],
-        "pageviews": 3612,
-        "pub_date": "2018-11-27",
-        "questions": [
-            "Did the tryptic digestions work?",
-            "Is there an intensity gradient in the data?",
-            "How good is the m/z accuracy?"
-        ],
-        "short_id": "T00217",
-        "short_tools": [
-            "Grep1",
-            "cardinal_quality_report",
-            "tp_sort_header_tool",
-            "cardinal_data_exporter"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "special",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "mouse",
-            "imaging"
-        ],
-        "time_estimation": "45m",
-        "title": "Mass spectrometry imaging: Loading and exploring MSI data",
-        "tools": [
-            "Grep1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/1.12.1.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.2"
-        ],
-        "topic_name": "proteomics",
-        "topic_name_human": "Proteomics",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "mass-spectrometry-imaging-loading-exploring-data",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/tutorial.json"
-        },
-        "version": 17,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 104,
-        "visitors": 2232,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Mass spectrometry imaging: Loading and exploring MSI data",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmouse_kidney_cut.i\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ninternal calibrants.tab\"]\n  2[label=\"MSI data exporter\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"MSI Qualitycontrol\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Sort\"]\n  2 -> 4 [label=\"feature_output\"]\n  5[label=\"Select\"]\n  2 -> 5 [label=\"pixel_output\"]\n}",
-                "history": [
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 4,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
                     },
                     {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 3,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {
+                            "input": {
+                                "id": 10,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Tabular-to-FASTA",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "bottom": -55.828125,
+                            "height": 112,
+                            "left": 1168.96875,
+                            "right": 1368.96875,
+                            "top": -167.828125,
+                            "width": 200,
+                            "x": 1168.96875,
+                            "y": -167.828125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "0a7799698fe5",
+                            "name": "tabular_to_fasta",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"seq_col\": \"2\", \"title_col\": [\"1\", \"3\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
+                        "type": "tool",
+                        "uuid": "396df67c-421c-4a4a-9965-d5eee8d20982",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "d27e6997-b84e-4671-806b-ec8ac62e8fb5"
+                            }
+                        ]
                     },
                     {
-                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
-                        "message": "Changed format of workflows",
-                        "num": 2,
-                        "short_hash": "361236c41",
-                        "unix": "1554368414"
+                        "annotation": "",
+                        "content_id": "addValue",
+                        "errors": null,
+                        "id": 13,
+                        "input_connections": {
+                            "input": {
+                                "id": 11,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Add column",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 44.171875,
+                            "height": 92,
+                            "left": 1168.96875,
+                            "right": 1368.96875,
+                            "top": -47.828125,
+                            "width": 200,
+                            "x": 1168.96875,
+                            "y": -47.828125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "addValue",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"exp\": \"MYCOPLASMA_CONTAMINANT\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "5a462916-3e19-4344-80b4-e1b1f0d3fb9d",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "36488f81-9674-4e5c-ab0a-73c91d2b71fd"
+                            }
+                        ]
                     },
-                    {
-                        "hash": "862b5b0bcff3928a16de9b43d6061c689fef9d7b",
-                        "message": "Rename MS_imaging_loading_exploring_data.ga to ms_imaging_loading_exploring_data.ga",
-                        "num": 1,
-                        "short_hash": "862b5b0bc",
-                        "unix": "1551717714"
-                    }
-                ],
-                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 14,
+                        "input_connections": {
+                            "input": {
+                                "id": 13,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Tabular-to-FASTA",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "mouse_kidney_cut.i"
+                                "name": "output",
+                                "type": "fasta"
                             }
                         ],
-                        "label": "mouse_kidney_cut.i",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 208.9204559326172,
-                            "top": 239.99999237060547
+                            "bottom": 125.171875,
+                            "height": 112,
+                            "left": 1379.96875,
+                            "right": 1579.96875,
+                            "top": 13.171875,
+                            "width": 200,
+                            "x": 1379.96875,
+                            "y": 13.171875
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"mouse_kidney_cut.i\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "bd40d0ba-d5ce-496f-9988-c8be1f81a75d",
-                        "workflow_outputs": []
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "0a7799698fe5",
+                            "name": "tabular_to_fasta",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"seq_col\": \"2\", \"title_col\": [\"1\", \"3\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
+                        "type": "tool",
+                        "uuid": "688b1790-2b96-46cc-849f-7c981b8d6e8c",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "c7b7f6bf-b83f-424d-b1ca-63161427c7ab"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 15,
+                        "input_connections": {
+                            "batchmode|input_fastas_0|input_fasta": {
+                                "id": 12,
+                                "output_name": "output"
+                            },
+                            "batchmode|input_fastas_1|input_fasta": {
+                                "id": 7,
+                                "output_name": "output_database"
+                            },
+                            "batchmode|input_fastas_2|input_fasta": {
+                                "id": 14,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FASTA Merge Files and Filter Unique Sequences",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "internal calibrants.tab"
+                                "name": "output",
+                                "type": "fasta"
                             }
                         ],
-                        "label": "internal calibrants.tab",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 199.92897033691406,
-                            "top": 417.0028305053711
+                            "bottom": 533.171875,
+                            "height": 292,
+                            "left": 1521.96875,
+                            "right": 1721.96875,
+                            "top": 241.171875,
+                            "width": 200,
+                            "x": 1521.96875,
+                            "y": 241.171875
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"internal calibrants.tab\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "15455ea4-e2cc-4872-a441-d40e979c7660",
-                        "workflow_outputs": []
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f546e7278f04",
+                            "name": "fasta_merge_files_and_filter_unique_sequences",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"accession_parser\": \"^>([^ ]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"uniqueness_criterion\": \"accession\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.0",
+                        "type": "tool",
+                        "uuid": "a6d6aafa-1474-44ee-812a-3d700643e350",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "7571d011-cfdf-4c97-bd1b-65a13f26b044"
+                            }
+                        ]
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nmouse_kidney_cut.i\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ninternal calibrants.tab\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"MSI data exporter\"];\n  0 -->|output| 2;\n  3[\"MSI Qualitycontrol\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  4[\"Sort\"];\n  2 -->|feature_output| 4;\n  5[\"Select\"];\n  2 -->|pixel_output| 5;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "MS Imaging Loading Exploring Data",
-                "outputs": [],
-                "parent_id": "proteomics/mass-spectrometry-imaging-loading-exploring-data",
-                "path": "topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/workflows/ms_imaging_loading_exploring_data.ga",
+                "parent_id": "proteomics/database-handling",
+                "path": "topics/proteomics/tutorials/database-handling/workflows/wf_database-handling_mycoplasma.ga",
                 "tags": [
                     "proteomics"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "MS Imaging Loading Exploring Data",
+                "title": "Proteomics: database handling including mycoplasma",
                 "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-mass-spectrometry-imaging-loading-exploring-data/versions/ms-imaging-loading-exploring-data",
-                "tutorial_id": "mass-spectrometry-imaging-loading-exploring-data",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/workflows/ms_imaging_loading_exploring_data.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/workflows/ms_imaging_loading_exploring_data.html",
-                "version": 4,
-                "wfid": "proteomics-mass-spectrometry-imaging-loading-exploring-data",
-                "wfname": "ms-imaging-loading-exploring-data",
-                "workflow": "ms_imaging_loading_exploring_data.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-database-handling/versions/wf-database-handling-mycoplasma",
+                "tutorial_id": "database-handling",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/database-handling/workflows/wf_database-handling_mycoplasma.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/database-handling/workflows/wf_database-handling_mycoplasma.html",
+                "version": 6,
+                "wfid": "proteomics-database-handling",
+                "wfname": "wf-database-handling-mycoplasma",
+                "workflow": "wf_database-handling_mycoplasma.ga",
                 "workflow_tools": [
-                    "Grep1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/1.12.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.2"
+                    "addValue",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.6+galaxy0"
                 ],
-                "workflowhub_id": "1184"
+                "workflowhub_id": "1199"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.1560645"
+        "zenodo_link": ""
     },
     {
         "admin_install": {
@@ -197704,232 +199841,196 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "proteore_clusterprofiler",
+                    "owner": "proteore",
+                    "revisions": "2f67202ffdb3",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "dbbuilder",
-                    "owner": "galaxyp",
-                    "revisions": "983bf725dfc2",
-                    "tool_panel_section_label": "Get Data",
+                    "name": "proteore_expression_rnaseq_abbased",
+                    "owner": "proteore",
+                    "revisions": "dbeabf9bf091",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fasta_merge_files_and_filter_unique_sequences",
-                    "owner": "galaxyp",
-                    "revisions": "f546e7278f04",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "proteore_filter_keywords_values",
+                    "owner": "proteore",
+                    "revisions": "b4641c0f8a82",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pepquery2",
-                    "owner": "galaxyp",
-                    "revisions": "a07976bbc4d9",
+                    "name": "proteore_id_converter",
+                    "owner": "proteore",
+                    "revisions": "1e45ea50f145",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "uniprotxml_downloader",
-                    "owner": "galaxyp",
-                    "revisions": "a371252a2cf6",
-                    "tool_panel_section_label": "Get Data",
+                    "name": "proteore_reactome",
+                    "owner": "proteore",
+                    "revisions": "9cc475dcd0f2",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "query_tabular",
-                    "owner": "iuc",
-                    "revisions": "cf34c344508d",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "proteore_reactome",
+                    "owner": "proteore",
+                    "revisions": "6c95f1b88627",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "90981f86000f",
-                    "tool_panel_section_label": "Collection Operations",
+                    "name": "proteore_tissue_specific_expression_data",
+                    "owner": "proteore",
+                    "revisions": "3e65e0249976",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dbbuilder\n  owner: galaxyp\n  revisions: 983bf725dfc2\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_merge_files_and_filter_unique_sequences\n  owner: galaxyp\n  revisions: f546e7278f04\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pepquery2\n  owner: galaxyp\n  revisions: a07976bbc4d9\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: uniprotxml_downloader\n  owner: galaxyp\n  revisions: a371252a2cf6\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n  owner: iuc\n  revisions: cf34c344508d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "subinamehta",
-                "katherine-d21",
-                "dechendb"
-            ],
-            "editing": [
-                "pratikdjagtap",
-                "timothygriffin"
+                },
+                {
+                    "name": "proteore_venn_diagram",
+                    "owner": "proteore",
+                    "revisions": "98b7912a9ceb",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
             ]
         },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: proteore_clusterprofiler\n  owner: proteore\n  revisions: 2f67202ffdb3\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_expression_rnaseq_abbased\n  owner: proteore\n  revisions: dbeabf9bf091\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_filter_keywords_values\n  owner: proteore\n  revisions: b4641c0f8a82\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_id_converter\n  owner: proteore\n  revisions: 1e45ea50f145\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_reactome\n  owner: proteore\n  revisions: 9cc475dcd0f2\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_reactome\n  owner: proteore\n  revisions: 6c95f1b88627\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_tissue_specific_expression_data\n  owner: proteore\n  revisions: 3e65e0249976\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_venn_diagram\n  owner: proteore\n  revisions: 98b7912a9ceb\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteome_annotation/tutorial.json",
         "contributors": [
             {
-                "email": "subinamehta@gmail.com",
-                "id": "subinamehta",
-                "joined": "2018-06",
-                "linkedin": "subinamehta",
-                "matrix": "subinamehta:matrix.org",
-                "name": "Subina Mehta",
-                "orcid": "0000-0001-9818-0537",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
-                "twitter": "Subina_Mehta",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
-            },
-            {
-                "id": "katherine-d21",
-                "joined": "2023-08",
-                "name": "Katherine Do",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/katherine-d21/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/katherine-d21.json"
+                "id": "vloux",
+                "joined": "2019-04",
+                "name": "Valentin Loux",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/vloux/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/vloux.json"
             },
             {
-                "id": "dechendb",
-                "joined": "2023-06",
-                "name": "Dechen Bhuming",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dechendb/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/dechendb.json"
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "fr",
+                "email": "florence.combes@cea.fr",
+                "id": "combesf",
+                "joined": "2019-04",
+                "name": "Florence Combes",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/combesf/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/combesf.json"
             },
             {
-                "email": "pjagtap@umn.edu",
-                "id": "pratikdjagtap",
-                "joined": "2017-09",
-                "name": "Pratik Jagtap",
-                "orcid": "0000-0003-0984-0973",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
+                "id": "davidchristiany",
+                "joined": "2019-04",
+                "name": "David Christiany",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/davidchristiany/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/davidchristiany.json"
             },
             {
-                "email": "tgriffin@umn.edu",
-                "github": false,
-                "id": "timothygriffin",
-                "joined": "2017-09",
-                "name": "Timothy J. Griffin",
-                "orcid": "0000-0001-6801-2559",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
+                "id": "yvandenb",
+                "joined": "2019-04",
+                "name": "Yves Vandenbrouck",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvandenb/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/yvandenb.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/clinical-mp-3-verification",
+        "dir": "topics/proteomics/tutorials/proteome_annotation",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu"
+            "UseGalaxy.be"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "proteomics",
-                "tutorials": [
-                    "clinical-mp-4-quantitation"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "proteomics/clinical-mp-3-verification",
-        "inexact_supported_servers": [],
+        "id": "proteomics/proteome_annotation",
+        "inexact_supported_servers": [
+            "UseGalaxy.fr"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Perform verification",
-            "Extraction of accession numbers for getting protein sequences"
+            "The Human Protein Atlas is a valuable resource for annotation and exploration of protein data",
+            "Conversion between different gene identifiers is sometimes required",
+            "The Reactome pathway database can be used to browse biological pathways"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-08",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Verification of peptides helps in confirming the presence of the peptides in our samplle"
+            "Execute a complete annotation pipeline of a protein list identified by LC-MS/MS experiments"
         ],
-        "pageviews": 78,
-        "pub_date": "2024-02-06",
+        "pageviews": 3736,
+        "pub_date": "2019-09-12",
         "questions": [
-            "Why do we need to verify our identified peptides",
-            "What is the importance of making a new database for quantification"
+            "How to filter out technical contaminants?",
+            "How to check for tissue-specificity?",
+            "How to perform enrichment analysis?",
+            "How to map your protein list to pathways (Reactome)?",
+            "How to compare your proteome with other studies?"
         ],
         "recordings": [
             {
                 "captioners": [
-                    "katherine-d21"
+                    "combesf"
                 ],
-                "date": "2024-06-21",
-                "galaxy_version": "23.1",
-                "length": "16M",
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "30M",
                 "speakers": [
-                    "katherine-d21"
+                    "yvesvdb"
                 ],
-                "youtube_id": "wCVzWMQANGE"
-            }
-        ],
-        "redirect_from": [
-            "/topics/proteomics/tutorials/clinical-mp-data-verification/tutorial",
-            "/short/proteomics/clinical-mp-3-verification",
-            "/short/T00415"
-        ],
-        "requirements": [
-            {
-                "topic_name": "proteomics",
-                "type": "internal"
+                "youtube_id": "qG7GZc6BeGY"
             }
         ],
-        "short_id": "T00415",
+        "short_id": "T00234",
         "short_tools": [
-            "Grouping1",
-            "pepquery2",
-            "uniprotxml_downloader",
-            "dbbuilder",
-            "tp_cat",
-            "Cut1",
-            "Filter1",
-            "query_tabular",
-            "Remove beginning1",
-            "fasta_merge_files_and_filter_unique_sequences",
-            "collapse_dataset"
+            "MQoutputfilter",
+            "Jvenn",
+            "IDconverter",
+            "rna_abbased_data",
+            "reactome_analysis",
+            "retrieve_from_hpa",
+            "cluter_profiler"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "clinical-metaproteomics",
+        "subtopic": "post-process",
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
                 }
             ],
-            "inexact": []
+            "inexact": [
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                }
+            ]
         },
         "symlink": null,
         "tags": [
-            "label-TMT11"
+            "DDA",
+            "human"
         ],
-        "time_estimation": "3H",
-        "title": "Clinical Metaproteomics 3: Verification",
+        "time_estimation": "1H",
+        "title": "Annotating a protein list identified by LC-MS/MS experiments",
         "tools": [
-            "Cut1",
-            "Filter1",
-            "Grouping1",
-            "Remove beginning1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery2/pepquery2/2.0.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.4.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
+            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_clusterprofiler/cluter_profiler/2019.02.18",
+            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_expression_rnaseq_abbased/rna_abbased_data/2019.03.07",
+            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_filter_keywords_values/MQoutputfilter/2019.03.11",
+            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_id_converter/IDconverter/2019.03.07",
+            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_reactome/reactome_analysis/2018.12.12",
+            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_reactome/reactome_analysis/2019.03.05",
+            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_tissue_specific_expression_data/retrieve_from_hpa/2019.02.27",
+            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/Jvenn/2019.02.21"
         ],
         "topic_name": "proteomics",
         "topic_name_human": "Proteomics",
@@ -197939,43 +200040,51 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "clinical-mp-3-verification",
+        "tutorial_name": "proteome_annotation",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/proteome_annotation/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-3-verification/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteome_annotation/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteome_annotation/tutorial.json"
         },
-        "version": 4,
+        "version": 11,
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 634,
-        "visitors": 42,
+        "visit_duration": 174,
+        "visitors": 2483,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Organization",
-                        "identifier": "0000-0001-9818-0537",
-                        "name": "Subina Mehta"
-                    }
-                ],
-                "description": "WF3- Peptide verification/validaiton workflow",
+                "creators": [],
+                "description": "Annotating a protein list identified by LC-MS/MS experiments",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Human UniProt+Isoforms FASTA\"]\n  k4bdae9fbeb484821a806e7dd3a8c7101[color=lightseagreen,label=\"Output\\nHuman UniProt+Isoforms FASTA\"]\n  0 -> k4bdae9fbeb484821a806e7dd3a8c7101\n  1[label=\"cRAP\"]\n  k13ddaf34d3464cc4b5b6fee2b5e0c1aa[color=lightseagreen,label=\"Output\\ncRAP\"]\n  1 -> k13ddaf34d3464cc4b5b6fee2b5e0c1aa\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput MGFs Dataset Collection\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSGPS_peptide-report\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDistinct Peptides for PepQuery\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMaxQuant-peptide-report\"]\n  6[label=\"Human UniProt+Isoforms+cRAP FASTA\"]\n  0 -> 6 [label=\"output_database\"]\n  1 -> 6 [label=\"output_database\"]\n  k62c376eb85a349768024bd72ac528af3[color=lightseagreen,label=\"Output\\nHuman UniProt+Isoforms+cRAP FASTA\"]\n  6 -> k62c376eb85a349768024bd72ac528af3\n  7[label=\"Cut\"]\n  3 -> 7 [label=\"output\"]\n  8[label=\"Cut\"]\n  5 -> 8 [label=\"output\"]\n  9[label=\"PepQuery2\"]\n  6 -> 9 [label=\"output\"]\n  4 -> 9 [label=\"output\"]\n  2 -> 9 [label=\"output\"]\n  10[label=\"Remove beginning\"]\n  7 -> 10 [label=\"out_file1\"]\n  11[label=\"Remove beginning\"]\n  8 -> 11 [label=\"out_file1\"]\n  12[label=\"Collapse Collection\"]\n  9 -> 12 [label=\"psm_rank_txt\"]\n  13[label=\"Concatenate datasets\"]\n  10 -> 13 [label=\"out_file1\"]\n  11 -> 13 [label=\"out_file1\"]\n  14[label=\"Filter\"]\n  12 -> 14 [label=\"output\"]\n  15[label=\"Remove beginning\"]\n  14 -> 15 [label=\"out_file1\"]\n  16[label=\"Cut\"]\n  15 -> 16 [label=\"out_file1\"]\n  17[label=\"Peptide and Protein from Peptide reports\"]\n  16 -> 17 [label=\"out_file1\"]\n  13 -> 17 [label=\"out_file1\"]\n  kbc4e33da40644b78bb155732b08b9316[color=lightseagreen,label=\"Output\\nPeptide and Protein from Peptide reports\"]\n  17 -> kbc4e33da40644b78bb155732b08b9316\n  18[label=\"Remove beginning\"]\n  17 -> 18 [label=\"output\"]\n  19[label=\"Group\"]\n  18 -> 19 [label=\"out_file1\"]\n  20[label=\"Uniprot-ID from verified Peptides\"]\n  19 -> 20 [label=\"out_file1\"]\n  kcd6c81d81f444129b5052ee4dde10cd2[color=lightseagreen,label=\"Output\\nUniprot-ID from verified Peptides\"]\n  20 -> kcd6c81d81f444129b5052ee4dde10cd2\n  21[label=\"UniProt\"]\n  20 -> 21 [label=\"output\"]\n  22[label=\"Quantitation Database for MaxQuant\"]\n  0 -> 22 [label=\"output_database\"]\n  1 -> 22 [label=\"output_database\"]\n  21 -> 22 [label=\"proteome\"]\n  ka52b5136db74496f9b66ec1064f2301d[color=lightseagreen,label=\"Output\\nQuantitation Database for MaxQuant\"]\n  22 -> ka52b5136db74496f9b66ec1064f2301d\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  3[label=\"Build tissue-specific expression dataset\"]\n  4[label=\"Filter by keywords and/or numerical value\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"ID Converter\"]\n  3 -> 5 [label=\"output\"]\n  6[label=\"ID Converter\"]\n  4 -> 6 [label=\"kept_lines\"]\n  7[label=\"Venn diagram\"]\n  4 -> 7 [label=\"kept_lines\"]\n  0 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"Add expression data\"]\n  6 -> 8 [label=\"output\"]\n  9[label=\"Filter by keywords and/or numerical value\"]\n  8 -> 9 [label=\"output\"]\n  10[label=\"GO terms classification and enrichment analysis\"]\n  5 -> 10 [label=\"output\"]\n  9 -> 10 [label=\"kept_lines\"]\n  11[label=\"Query pathway database\"]\n  9 -> 11 [label=\"kept_lines\"]\n}",
                 "history": [
                     {
-                        "hash": "e0464fd1787b4ca7dea72ca77b7ab2ad03a8292a",
-                        "message": "add workflows",
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 3,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 2,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "a959d88d0da58e17d87c7a39b0d89e03765629df",
+                        "message": "workflow update by Flo",
                         "num": 1,
-                        "short_hash": "e0464fd17",
-                        "unix": "1723118192"
+                        "short_hash": "a959d88d0",
+                        "unix": "1560843795"
                     }
                 ],
                 "inputs": [
@@ -197983,591 +200092,279 @@
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Input MGFs Dataset Collection"
+                                "name": "Bredberg.txt"
                             }
                         ],
-                        "label": "Input MGFs Dataset Collection",
-                        "name": "Input dataset collection",
+                        "label": null,
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 26.467106653090468,
-                            "top": 441.64657624309564
+                            "left": 10,
+                            "top": 10
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"name\": \"Bredberg.txt\"}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "4c4f20b4-3fa6-48a2-b4b0-6480a0dd230a",
-                        "when": null,
+                        "type": "data_input",
+                        "uuid": "98762c87-4a74-4e99-a0a8-b61360e4e123",
                         "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "SGPS_peptide-report"
+                                "name": "Lacombe_et_al_2017_OK.txt"
                             }
                         ],
-                        "label": "SGPS_peptide-report",
+                        "label": null,
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 49.219598040314054,
-                            "top": 775.0615167366277
+                            "left": 10,
+                            "top": 130
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"name\": \"Lacombe_et_al_2017_OK.txt\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "2d7b777c-8bb9-4de8-af72-4cae64cd5eaf",
-                        "when": null,
+                        "uuid": "90836b07-3f58-40a5-914b-1f9036993489",
                         "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 4,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Distinct Peptides for PepQuery"
+                                "name": "Mucilli.txt"
                             }
                         ],
-                        "label": "Distinct Peptides for PepQuery",
+                        "label": null,
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 974.964669791108,
-                            "top": 210.36937340005647
+                            "left": 10,
+                            "top": 250
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"name\": \"Mucilli.txt\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "dbc1b4b1-bb63-4c13-8adb-d9a0febc8e17",
-                        "when": null,
+                        "uuid": "30b559f3-322c-4323-ae32-b6e6d6c9d210",
                         "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Build tissue-specific expression dataset\"];\n  4[\"Filter by keywords and/or numerical value\"];\n  1 -->|output| 4;\n  5[\"ID Converter\"];\n  3 -->|output| 5;\n  6[\"ID Converter\"];\n  4 -->|kept_lines| 6;\n  7[\"Venn diagram\"];\n  4 -->|kept_lines| 7;\n  0 -->|output| 7;\n  2 -->|output| 7;\n  8[\"Add expression data\"];\n  6 -->|output| 8;\n  9[\"Filter by keywords and/or numerical value\"];\n  8 -->|output| 9;\n  10[\"GO terms classification and enrichment analysis\"];\n  5 -->|output| 10;\n  9 -->|kept_lines| 10;\n  11[\"Query pathway database\"];\n  9 -->|kept_lines| 11;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "'Proteome Annotation'",
+                "outputs": [],
+                "parent_id": "proteomics/proteome_annotation",
+                "path": "topics/proteomics/tutorials/proteome_annotation/workflows/Galaxy-Workflow-_Proteome_annotation_.ga",
+                "tags": [
+                    "proteomics"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "'Proteome Annotation'",
+                "topic_id": "proteomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-proteome_annotation/versions/galaxy-workflow--proteome-annotation-",
+                "tutorial_id": "proteome_annotation",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteome_annotation/workflows/Galaxy-Workflow-_Proteome_annotation_.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteome_annotation/workflows/Galaxy-Workflow-_Proteome_annotation_.html",
+                "version": 3,
+                "wfid": "proteomics-proteome_annotation",
+                "wfname": "galaxy-workflow--proteome-annotation-",
+                "workflow": "Galaxy-Workflow-_Proteome_annotation_.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_clusterprofiler/cluter_profiler/2019.02.18",
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_expression_rnaseq_abbased/rna_abbased_data/2019.03.07",
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_filter_keywords_values/MQoutputfilter/2019.03.11",
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_id_converter/IDconverter/2019.03.07",
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_reactome/reactome_analysis/2019.03.05",
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_tissue_specific_expression_data/retrieve_from_hpa/2019.02.27",
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/Jvenn/2019.02.21"
+                ],
+                "workflowhub_id": "1207"
+            },
+            {
+                "creators": [],
+                "description": "Annotating a protein list identified by LC-MS/MS experiments",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nLacombe_et_al_2017.txt\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBredberg.txt\"]\n  10[label=\"View proteins on Reactome maps\"]\n  9 -> 10 [label=\"kept_lines\"]\n  11[label=\"GO terms classification and enrichment analysis\"]\n  5 -> 11 [label=\"output\"]\n  9 -> 11 [label=\"kept_lines\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMucilli.txt\"]\n  3[label=\"Build a lung proteome as a background \"]\n  4[label=\"Filter technical contaminants\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"ID Converter\"]\n  3 -> 5 [label=\"output\"]\n  6[label=\"ID mapping UniProt <-> ENSG ID\"]\n  4 -> 6 [label=\"kept_lines\"]\n  7[label=\"MS/MS datasets comparison\"]\n  4 -> 7 [label=\"kept_lines\"]\n  1 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"Add expression data\"]\n  6 -> 8 [label=\"output\"]\n  9[label=\"Filter biological contaminants\"]\n  8 -> 9 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 4,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 3,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
+                        "message": "unflatten workflows",
+                        "num": 2,
+                        "short_hash": "faf6d298a",
+                        "unix": "1576155753"
                     },
+                    {
+                        "hash": "a853f1694294a719690d1818388c4358460d12b1",
+                        "message": "First draft of proteome annotation tutorial",
+                        "num": 1,
+                        "short_hash": "a853f1694",
+                        "unix": "1556281728"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 5,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "MaxQuant-peptide-report"
+                                "name": "Lacombe_et_al_2017.txt"
                             }
                         ],
-                        "label": "MaxQuant-peptide-report",
+                        "label": "Lacombe_et_al_2017.txt",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 29.12351833088178,
-                            "top": 1007.203580787368
+                            "left": 284,
+                            "top": 272
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"name\": \"Lacombe_et_al_2017.txt\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "2c07aebc-8b9e-4f4e-9020-9a50664ac648",
-                        "when": null,
+                        "uuid": "6e05c374-5a8c-45cc-bc41-060403961b92",
                         "workflow_outputs": []
-                    }
-                ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"Human UniProt+Isoforms FASTA\"];\n  4bdae9fb-eb48-4821-a806-e7dd3a8c7101[\"Output\\nHuman UniProt+Isoforms FASTA\"];\n  0 --> 4bdae9fb-eb48-4821-a806-e7dd3a8c7101;\n  style 4bdae9fb-eb48-4821-a806-e7dd3a8c7101 stroke:#2c3143,stroke-width:4px;\n  1[\"cRAP\"];\n  13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa[\"Output\\ncRAP\"];\n  1 --> 13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa;\n  style 13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nInput MGFs Dataset Collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nSGPS_peptide-report\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nDistinct Peptides for PepQuery\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nMaxQuant-peptide-report\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"Human UniProt+Isoforms+cRAP FASTA\"];\n  0 -->|output_database| 6;\n  1 -->|output_database| 6;\n  62c376eb-85a3-4976-8024-bd72ac528af3[\"Output\\nHuman UniProt+Isoforms+cRAP FASTA\"];\n  6 --> 62c376eb-85a3-4976-8024-bd72ac528af3;\n  style 62c376eb-85a3-4976-8024-bd72ac528af3 stroke:#2c3143,stroke-width:4px;\n  7[\"Cut\"];\n  3 -->|output| 7;\n  8[\"Cut\"];\n  5 -->|output| 8;\n  9[\"PepQuery2\"];\n  6 -->|output| 9;\n  4 -->|output| 9;\n  2 -->|output| 9;\n  10[\"Remove beginning\"];\n  7 -->|out_file1| 10;\n  11[\"Remove beginning\"];\n  8 -->|out_file1| 11;\n  12[\"Collapse Collection\"];\n  9 -->|psm_rank_txt| 12;\n  13[\"Concatenate datasets\"];\n  10 -->|out_file1| 13;\n  11 -->|out_file1| 13;\n  14[\"Filter\"];\n  12 -->|output| 14;\n  15[\"Remove beginning\"];\n  14 -->|out_file1| 15;\n  16[\"Cut\"];\n  15 -->|out_file1| 16;\n  17[\"Peptide and Protein from Peptide reports\"];\n  16 -->|out_file1| 17;\n  13 -->|out_file1| 17;\n  bc4e33da-4064-4b78-bb15-5732b08b9316[\"Output\\nPeptide and Protein from Peptide reports\"];\n  17 --> bc4e33da-4064-4b78-bb15-5732b08b9316;\n  style bc4e33da-4064-4b78-bb15-5732b08b9316 stroke:#2c3143,stroke-width:4px;\n  18[\"Remove beginning\"];\n  17 -->|output| 18;\n  19[\"Group\"];\n  18 -->|out_file1| 19;\n  20[\"Uniprot-ID from verified Peptides\"];\n  19 -->|out_file1| 20;\n  cd6c81d8-1f44-4129-b505-2ee4dde10cd2[\"Output\\nUniprot-ID from verified Peptides\"];\n  20 --> cd6c81d8-1f44-4129-b505-2ee4dde10cd2;\n  style cd6c81d8-1f44-4129-b505-2ee4dde10cd2 stroke:#2c3143,stroke-width:4px;\n  21[\"UniProt\"];\n  20 -->|output| 21;\n  22[\"Quantitation Database for MaxQuant\"];\n  0 -->|output_database| 22;\n  1 -->|output_database| 22;\n  21 -->|proteome| 22;\n  a52b5136-db74-496f-9b66-ec1064f2301d[\"Output\\nQuantitation Database for MaxQuant\"];\n  22 --> a52b5136-db74-496f-9b66-ec1064f2301d;\n  style a52b5136-db74-496f-9b66-ec1064f2301d stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "WF3_VERIFICATION_WORKFLOW",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "Human UniProt+Isoforms FASTA",
-                        "name": "Protein Database Downloader",
-                        "outputs": [
-                            {
-                                "name": "output_database",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "left": 0,
-                            "top": 0
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_database": {
-                                "action_arguments": {
-                                    "newname": "Human UniProt+Isoforms FASTA"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_database"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
-                        "tool_shed_repository": {
-                            "changeset_revision": "983bf725dfc2",
-                            "name": "dbbuilder",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"data\", \"__workflow_invocation_uuid__\": \"08a702aa736d11ee91a5001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"uniprot\", \"__current_case__\": 0, \"taxon\": \"9606\", \"taxon_id\": null, \"reviewed\": \"\", \"set\": \"keyword:KW-1185\", \"include_isoform\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3.4",
-                        "type": "tool",
-                        "uuid": "ff0bbbc9-35b4-44a6-b6bb-a1969ca01eb6",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Human UniProt+Isoforms FASTA",
-                                "output_name": "output_database",
-                                "uuid": "4bdae9fb-eb48-4821-a806-e7dd3a8c7101"
-                            }
-                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
+                        "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "cRAP",
-                        "name": "Protein Database Downloader",
-                        "outputs": [
-                            {
-                                "name": "output_database",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "left": 20.775440205938253,
-                            "top": 196.89138890513698
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_database": {
-                                "action_arguments": {
-                                    "newname": "cRAP"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_database"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
-                        "tool_shed_repository": {
-                            "changeset_revision": "983bf725dfc2",
-                            "name": "dbbuilder",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"data\", \"__workflow_invocation_uuid__\": \"08a702aa736d11ee91a5001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"source\": {\"from\": \"cRAP\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.3.4",
-                        "type": "tool",
-                        "uuid": "fa25fdbf-2cec-48fc-94f3-7c47888753b0",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "cRAP",
-                                "output_name": "output_database",
-                                "uuid": "13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "batchmode|input_fastas_0|input_fasta": {
-                                "id": 0,
-                                "output_name": "output_database"
-                            },
-                            "batchmode|input_fastas_1|input_fasta": {
-                                "id": 1,
-                                "output_name": "output_database"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Human UniProt+Isoforms+cRAP FASTA",
-                        "name": "FASTA Merge Files and Filter Unique Sequences",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "left": 497.09213191562515,
-                            "top": 177.90819833483664
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Human UniProt+Isoforms+cRAP FASTA"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f546e7278f04",
-                            "name": "fasta_merge_files_and_filter_unique_sequences",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"__workflow_invocation_uuid__\": \"08a702aa736d11ee91a5001e67d2ec02\", \"accession_parser\": \"^>([^ ]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"uniqueness_criterion\": \"sequence\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.0",
-                        "type": "tool",
-                        "uuid": "67f1d2d4-d347-49ff-a941-885987a8254e",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Human UniProt+Isoforms+cRAP FASTA",
-                                "output_name": "output",
-                                "uuid": "62c376eb-85a3-4976-8024-bd72ac528af3"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0",
-                        "errors": null,
-                        "id": 17,
-                        "input_connections": {
-                            "tables_0|table": {
-                                "id": 16,
-                                "output_name": "out_file1"
-                            },
-                            "tables_1|table": {
-                                "id": 13,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Peptide and Protein from Peptide reports",
-                        "name": "Query Tabular",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 2219.7817115852936,
-                            "top": 625.4286563925251
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Peptide and Protein from Peptide reports"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "cf34c344508d",
-                            "name": "query_tabular",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"__workflow_invocation_uuid__\": \"08a702aa736d11ee91a5001e67d2ec02\", \"add_to_database\": {\"withdb\": null}, \"addqueries\": {\"queries\": []}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"\"}, \"save_db\": false, \"sqlquery\": \"select pep.mpep, prot.prot\\nFROM pep\\nINNER JOIN  prot on pep.mpep=prot.pep \", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"pep\", \"column_names_from_first_line\": false, \"col_names\": \"mpep\", \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"indexes\": []}}, {\"__index__\": 1, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"prot\", \"column_names_from_first_line\": false, \"col_names\": \"pep,prot\", \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.3.0",
-                        "type": "tool",
-                        "uuid": "93abe6e7-0034-460f-b517-418c4ed9d43a",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Peptide and Protein from Peptide reports",
-                                "output_name": "output",
-                                "uuid": "bc4e33da-4064-4b78-bb15-5732b08b9316"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0",
-                        "errors": null,
-                        "id": 20,
-                        "input_connections": {
-                            "tables_0|table": {
-                                "id": 19,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Uniprot-ID from verified Peptides",
-                        "name": "Query Tabular",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "Bredberg.txt"
                             }
                         ],
+                        "label": "Bredberg.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2545.114966014936,
-                            "top": 878.0953618681222
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Uniprot-ID from verified Peptides"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "cf34c344508d",
-                            "name": "query_tabular",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 511,
+                            "top": 454
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"__workflow_invocation_uuid__\": \"08a702aa736d11ee91a5001e67d2ec02\", \"add_to_database\": {\"withdb\": null}, \"addqueries\": {\"queries\": []}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"no\", \"__current_case__\": 1}, \"save_db\": false, \"sqlquery\": \"SELECT distinct(prot) AS Accession \\nfrom t1\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"normalize\", \"__current_case__\": 12, \"columns\": \"2\", \"separator\": \";\"}}, {\"__index__\": 1, \"filter\": {\"filter_type\": \"replace\", \"__current_case__\": 11, \"column\": \"2\", \"regex_pattern\": \"(tr|sp)[|]\", \"regex_replace\": \"\", \"add\": null}}, {\"__index__\": 2, \"filter\": {\"filter_type\": \"replace\", \"__current_case__\": 11, \"column\": \"2\", \"regex_pattern\": \"[ ]+\", \"regex_replace\": \"\", \"add\": null}}, {\"__index__\": 3, \"filter\": {\"filter_type\": \"replace\", \"__current_case__\": 11, \"column\": \"2\", \"regex_pattern\": \"[|].*$\", \"regex_replace\": \"\", \"add\": null}}, {\"__index__\": 4, \"filter\": {\"filter_type\": \"normalize\", \"__current_case__\": 12, \"columns\": \"2\", \"separator\": \",\"}}]}, \"tbl_opts\": {\"table_name\": \"t1\", \"column_names_from_first_line\": true, \"col_names\": \"pep,prot\", \"load_named_columns\": false, \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.3.0",
-                        "type": "tool",
-                        "uuid": "fcf0a38b-8b4c-4b11-8152-ef3f5375b9e6",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Uniprot-ID from verified Peptides",
-                                "output_name": "output",
-                                "uuid": "cd6c81d8-1f44-4129-b505-2ee4dde10cd2"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Bredberg.txt\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "c59cd601-5021-4665-a225-5881a856d796",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 22,
-                        "input_connections": {
-                            "batchmode|input_fastas_0|input_fasta": {
-                                "id": 0,
-                                "output_name": "output_database"
-                            },
-                            "batchmode|input_fastas_1|input_fasta": {
-                                "id": 1,
-                                "output_name": "output_database"
-                            },
-                            "batchmode|input_fastas_2|input_fasta": {
-                                "id": 21,
-                                "output_name": "proteome"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Quantitation Database for MaxQuant",
-                        "name": "FASTA Merge Files and Filter Unique Sequences",
-                        "outputs": [
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "Mucilli.txt"
                             }
                         ],
+                        "label": "Mucilli.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 3070.223999018992,
-                            "top": 1289.3686346167783
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Quantitation Database for MaxQuant"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f546e7278f04",
-                            "name": "fasta_merge_files_and_filter_unique_sequences",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 512,
+                            "top": 532
                         },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"__workflow_invocation_uuid__\": \"08a702aa736d11ee91a5001e67d2ec02\", \"accession_parser\": \"^>([^ ]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"uniqueness_criterion\": \"sequence\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.0",
-                        "type": "tool",
-                        "uuid": "a6060517-ee4f-4196-991f-6adf06e192c4",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Quantitation Database for MaxQuant",
-                                "output_name": "output",
-                                "uuid": "a52b5136-db74-496f-9b66-ec1064f2301d"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Mucilli.txt\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "aa14863c-2183-4e0e-be4a-3c34972ae040",
+                        "workflow_outputs": []
                     }
                 ],
-                "parent_id": "proteomics/clinical-mp-3-verification",
-                "path": "topics/proteomics/tutorials/clinical-mp-3-verification/workflows/WF3_Verification_Workflow.ga",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nLacombe_et_al_2017.txt\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nBredberg.txt\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"View proteins on Reactome maps\"];\n  9 -->|kept_lines| 10;\n  11[\"GO terms classification and enrichment analysis\"];\n  5 -->|output| 11;\n  9 -->|kept_lines| 11;\n  2[\"\u2139\ufe0f Input Dataset\\nMucilli.txt\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Build a lung proteome as a background \"];\n  4[\"Filter technical contaminants\"];\n  0 -->|output| 4;\n  5[\"ID Converter\"];\n  3 -->|output| 5;\n  6[\"ID mapping UniProt <-> ENSG ID\"];\n  4 -->|kept_lines| 6;\n  7[\"MS/MS datasets comparison\"];\n  4 -->|kept_lines| 7;\n  1 -->|output| 7;\n  2 -->|output| 7;\n  8[\"Add expression data\"];\n  6 -->|output| 8;\n  9[\"Filter biological contaminants\"];\n  8 -->|output| 9;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "ProteoRE ProteomeAnnotation Tutorial (release 2.0)",
+                "outputs": [],
+                "parent_id": "proteomics/proteome_annotation",
+                "path": "topics/proteomics/tutorials/proteome_annotation/workflows/main_workflow.ga",
                 "tags": [
-                    "name:clinicalMP"
+                    "proteomics"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "WF3_VERIFICATION_WORKFLOW",
+                "title": "ProteoRE ProteomeAnnotation Tutorial (release 2.0)",
                 "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-clinical-mp-3-verification/versions/wf3-verification-workflow",
-                "tutorial_id": "clinical-mp-3-verification",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-3-verification/workflows/WF3_Verification_Workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-3-verification/workflows/WF3_Verification_Workflow.html",
-                "version": 1,
-                "wfid": "proteomics-clinical-mp-3-verification",
-                "wfname": "wf3-verification-workflow",
-                "workflow": "WF3_Verification_Workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-proteome_annotation/versions/main-workflow",
+                "tutorial_id": "proteome_annotation",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteome_annotation/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteome_annotation/workflows/main_workflow.html",
+                "version": 4,
+                "wfid": "proteomics-proteome_annotation",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "Filter1",
-                    "Grouping1",
-                    "Remove beginning1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery2/pepquery2/2.0.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.4.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0",
-                    "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_clusterprofiler/cluter_profiler/2019.02.18",
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_expression_rnaseq_abbased/rna_abbased_data/2019.03.07",
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_filter_keywords_values/MQoutputfilter/2019.03.11",
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_id_converter/IDconverter/2019.03.07",
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_reactome/reactome_analysis/2018.12.12",
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_tissue_specific_expression_data/retrieve_from_hpa/2019.02.27",
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/Jvenn/2019.02.21"
                 ],
-                "workflowhub_id": "1351"
+                "workflowhub_id": "1209"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.10105821"
+        "zenodo_link": "https://zenodo.org/record/3405119"
     },
     {
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "histogram",
-                    "owner": "devteam",
-                    "revisions": "6f134426c2b0",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_falsediscoveryrate",
-                    "owner": "galaxyp",
-                    "revisions": "c9eff69a7c62",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_featurefindermultiplex",
-                    "owner": "galaxyp",
-                    "revisions": "5e948629bc73",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_fidoadapter",
-                    "owner": "galaxyp",
-                    "revisions": "658494a2cb00",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_fileinfo",
-                    "owner": "galaxyp",
-                    "revisions": "52ba9695e752",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_idconflictresolver",
-                    "owner": "galaxyp",
-                    "revisions": "c28f13cab67a",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_idmapper",
-                    "owner": "galaxyp",
-                    "revisions": "39caaa778d2e",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_idposteriorerrorprobability",
-                    "owner": "galaxyp",
-                    "revisions": "111c3a00136d",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_idscoreswitcher",
-                    "owner": "galaxyp",
-                    "revisions": "be74a8cd7d66",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_multiplexresolver",
-                    "owner": "galaxyp",
-                    "revisions": "fb647b7cf2c1",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_peptideindexer",
-                    "owner": "galaxyp",
-                    "revisions": "dd173849c3d8",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_proteinquantifier",
-                    "owner": "galaxyp",
-                    "revisions": "16026cdb1330",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_textexporter",
-                    "owner": "galaxyp",
-                    "revisions": "9020199dba0a",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_xtandemadapter",
-                    "owner": "galaxyp",
-                    "revisions": "7f6a1f27553e",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
+            "tools": []
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: histogram\n  owner: devteam\n  revisions: 6f134426c2b0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_falsediscoveryrate\n  owner: galaxyp\n  revisions: c9eff69a7c62\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_featurefindermultiplex\n  owner: galaxyp\n  revisions: 5e948629bc73\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_fidoadapter\n  owner: galaxyp\n  revisions: 658494a2cb00\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_fileinfo\n  owner: galaxyp\n  revisions: 52ba9695e752\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idconflictresolver\n  owner: galaxyp\n  revisions: c28f13cab67a\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idmapper\n  owner: galaxyp\n  revisions: 39caaa778d2e\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idposteriorerrorprobability\n  owner: galaxyp\n  revisions: 111c3a00136d\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idscoreswitcher\n  owner: galaxyp\n  revisions: be74a8cd7d66\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_multiplexresolver\n  owner: galaxyp\n  revisions: fb647b7cf2c1\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_peptideindexer\n  owner: galaxyp\n  revisions: dd173849c3d8\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_proteinquantifier\n  owner: galaxyp\n  revisions: 16026cdb1330\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_textexporter\n  owner: galaxyp\n  revisions: 9020199dba0a\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_xtandemadapter\n  owner: galaxyp\n  revisions: 7f6a1f27553e\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/protein-quant-sil/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/ntails/tutorial.json",
         "contributors": [
             {
                 "email": "sigloch+github@mailbox.org",
@@ -198610,146 +200407,85 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
                 "twitter": "bjoerngruening",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "email": "matthias.fahrner@uniklinik-freiburg.de",
-                "id": "matthias313",
-                "joined": "2019-03",
-                "name": "Matthias Fahrner",
-                "orcid": "0000-0001-7955-2518",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/matthias313/",
-                "twitter": "mfahrner313",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/matthias313.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/protein-quant-sil",
+        "dir": "topics/proteomics/tutorials/ntails",
+        "edam_ontology": [
+            "topic_0121"
+        ],
         "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
+        "edam_topic": [
+            "Proteomics"
         ],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "proteomics/protein-quant-sil",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
-        ],
+        "id": "proteomics/ntails",
+        "inexact_supported_servers": [],
         "js_requirements": {
-            "mathjax": 8638,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Peptides labelled with stable isotopes result in multiple parallel MS1 ion traces.",
-            "MS1 features can be used for relative protein quantitation.",
-            "Quantitations have to be mapped to PSMs.",
-            "PSM quantitations can be used to calculate protein quantitations.",
-            "Proper quantitation and mapping needs careful evaluation and optimization."
+            "N-TAILS enriches natural protein N-termini and neo-N-termini.",
+            "neo-N-termini are typically generated by protease cleavage.",
+            "N-TAILS can be used for analysis of protease cleavage."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Advanced",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2023-05-16",
         "objectives": [
-            "MS1 feature quantitation and mapping of quantitations to peptide and protein IDs."
+            "Run an N-TAILS data analysis."
         ],
-        "pageviews": 1586,
-        "pub_date": "2017-03-17",
+        "pageviews": 982,
+        "pub_date": "2017-02-14",
         "questions": [
-            "What are MS1 features?",
-            "How to quantify based on MS1 features?",
-            "How to map MS1 features to MS2 identifications?",
-            "How to evaluate and optimize the results?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "proteomics",
-                "tutorials": [
-                    "database-handling",
-                    "protein-id-oms"
-                ],
-                "type": "internal"
-            }
+            "How can protein N-termini be enriched for LC-MS/MS?",
+            "How to analyze the LC-MS/MS data?"
         ],
-        "short_id": "T00230",
+        "short_id": "T00226",
         "short_tools": [
-            "Grep1",
-            "IDPosteriorErrorProbability",
-            "ProteinQuantifier",
-            "IDConflictResolver",
+            "IDMapper",
             "FalseDiscoveryRate",
-            "FidoAdapter",
-            "TextExporter",
-            "tp_tail_tool",
+            "MSGFPlusAdapter",
+            "FileFilter",
+            "HighResPrecursorMassCorrector",
+            "IDConflictResolver",
+            "IDFilter",
+            "MzTabExporter",
+            "ConsensusID",
             "FeatureFinderMultiplex",
-            "IDScoreSwitcher",
-            "PeptideIndexer",
-            "MultiplexResolver",
-            "histogram_rpy",
-            "Summary_Statistics1",
-            "FileInfo",
-            "XTandemAdapter",
-            "IDMapper"
+            "IDMerger",
+            "FileMerger",
+            "PeptideIndexer"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "id-quant",
+        "subtopic": "special",
         "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "DDA",
-            "SILAC"
-        ],
-        "time_estimation": "1h",
-        "title": "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)",
-        "tools": [
-            "Grep1",
-            "Summary_Statistics1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_multiplexresolver/MultiplexResolver/2.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0"
+            "exact": [],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [],
+        "time_estimation": "1h",
+        "title": "Detection and quantitation of N-termini (degradomics) via N-TAILS",
+        "tools": [
+            "ConsensusID",
+            "FalseDiscoveryRate",
+            "FeatureFinderMultiplex",
+            "FileFilter",
+            "FileMerger",
+            "HighResPrecursorMassCorrector",
+            "IDConflictResolver",
+            "IDFilter",
+            "IDMapper",
+            "IDMerger",
+            "MSGFPlusAdapter",
+            "MzTabExporter",
+            "PeptideIndexer"
         ],
         "topic_name": "proteomics",
         "topic_name_human": "Proteomics",
@@ -198759,100 +200495,51 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "protein-quant-sil",
+        "tutorial_name": "ntails",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/protein-quant-sil/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/ntails/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/protein-quant-sil/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/protein-quant-sil/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/ntails/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/ntails/tutorial.json"
         },
-        "version": 31,
+        "version": 15,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 96,
-        "visitors": 1095,
+        "visit_duration": 84,
+        "visitors": 674,
         "workflows": [
             {
                 "creators": [],
-                "description": "Peptide and Protein Quantification via Stable Isotope Labelling (SIL)",
+                "description": "Detection and quantitation of N-termini (degradomics) via N-TAILS",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmzml raw file\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nfasta file\"]\n  2[label=\"FeatureFinderMultiplex\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"XTandemAdapter\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"FileInfo\"]\n  3 -> 4 [label=\"out\"]\n  5[label=\"PeptideIndexer\"]\n  1 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"out\"]\n  6[label=\"IDPosteriorErrorProbability\"]\n  5 -> 6 [label=\"out\"]\n  7[label=\"FalseDiscoveryRate\"]\n  6 -> 7 [label=\"out\"]\n  8[label=\"IDScoreSwitcher\"]\n  7 -> 8 [label=\"out\"]\n  9[label=\"FileInfo\"]\n  8 -> 9 [label=\"out\"]\n  10[label=\"FidoAdapter\"]\n  8 -> 10 [label=\"out\"]\n  11[label=\"FalseDiscoveryRate\"]\n  10 -> 11 [label=\"out\"]\n  12[label=\"FileInfo\"]\n  11 -> 12 [label=\"out\"]\n  13[label=\"TextExporter\"]\n  11 -> 13 [label=\"out\"]\n  14[label=\"IDMapper\"]\n  11 -> 14 [label=\"out\"]\n  2 -> 14 [label=\"out_multiplets\"]\n  15[label=\"Select\"]\n  13 -> 15 [label=\"out\"]\n  16[label=\"Select\"]\n  13 -> 16 [label=\"out\"]\n  17[label=\"IDConflictResolver\"]\n  14 -> 17 [label=\"out\"]\n  18[label=\"MultiplexResolver\"]\n  17 -> 18 [label=\"out\"]\n  19[label=\"ProteinQuantifier\"]\n  18 -> 19 [label=\"out\"]\n  11 -> 19 [label=\"out\"]\n  20[label=\"Summary Statistics\"]\n  19 -> 20 [label=\"out\"]\n  21[label=\"Select last\"]\n  19 -> 21 [label=\"out\"]\n  22[label=\"Histogram\"]\n  21 -> 22 [label=\"outfile\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[label=\"FeatureFinderMultiplex\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"HighResPrecursorMassCorrector\"]\n  2 -> 3 [label=\"param_out_features\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"MSGFPlusAdapter\"]\n  1 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"param_out\"]\n  5[label=\"MSGFPlusAdapter\"]\n  1 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"param_out\"]\n  6[label=\"MSGFPlusAdapter\"]\n  3 -> 6 [label=\"param_out\"]\n  7[label=\"PeptideIndexer\"]\n  1 -> 7 [label=\"output\"]\n  4 -> 7 [label=\"param_out\"]\n  8[label=\"PeptideIndexer\"]\n  1 -> 8 [label=\"output\"]\n  5 -> 8 [label=\"param_out\"]\n  9[label=\"PeptideIndexer\"]\n  1 -> 9 [label=\"output\"]\n  6 -> 9 [label=\"param_out\"]\n  10[label=\"IDMerger\"]\n  7 -> 10 [label=\"param_out\"]\n  8 -> 10 [label=\"param_out\"]\n  9 -> 10 [label=\"param_out\"]\n  11[label=\"ConsensusID\"]\n  10 -> 11 [label=\"param_out\"]\n  12[label=\"PeptideIndexer\"]\n  1 -> 12 [label=\"output\"]\n  11 -> 12 [label=\"param_out\"]\n  13[label=\"FalseDiscoveryRate\"]\n  12 -> 13 [label=\"param_out\"]\n  14[label=\"IDFilter\"]\n  13 -> 14 [label=\"param_out\"]\n  15[label=\"IDMapper\"]\n  14 -> 15 [label=\"param_out\"]\n  2 -> 15 [label=\"param_out\"]\n  16[label=\"IDConflictResolver\"]\n  15 -> 16 [label=\"param_out\"]\n  17[label=\"FileFilter\"]\n  16 -> 17 [label=\"param_out\"]\n  18[label=\"FileMerger\"]\n  17 -> 18 [label=\"param_out\"]\n  19[label=\"MzTabExporter\"]\n  18 -> 19 [label=\"param_out\"]\n}",
                 "history": [
-                    {
-                        "hash": "54b4d9fcc78b1394f71f7affd51ca15e83b211d5",
-                        "message": "Adding tags to workflows",
-                        "num": 11,
-                        "short_hash": "54b4d9fcc",
-                        "unix": "1604224600"
-                    },
-                    {
-                        "hash": "ca84d739509bdb1ef8f3cfc64c15242ef0363407",
-                        "message": "Updating Tutorials to OpenMS 2.6, adjusting of parameters and tools, adding tool versions",
-                        "num": 10,
-                        "short_hash": "ca84d7395",
-                        "unix": "1604176914"
-                    },
-                    {
-                        "hash": "c5002c655c4206fb1d6712d1c1543f9b7ea2e3cb",
-                        "message": "protein-quant-sil",
-                        "num": 9,
-                        "short_hash": "c5002c655",
-                        "unix": "1601688681"
-                    },
                     {
                         "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
                         "message": "annotation",
-                        "num": 8,
+                        "num": 4,
                         "short_hash": "667ff3de9",
                         "unix": "1579690769"
                     },
                     {
                         "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
                         "message": "Workflow renaming",
-                        "num": 7,
+                        "num": 3,
                         "short_hash": "eb4d724e0",
                         "unix": "1579084895"
                     },
                     {
-                        "hash": "e42145c47e6b093c441a431ec3c5671b7ddfc176",
-                        "message": "Updated workflow",
-                        "num": 6,
-                        "short_hash": "e42145c47",
-                        "unix": "1553096121"
-                    },
-                    {
-                        "hash": "3a0757df3e7b39d74c5e9e124018710702ca0ab0",
-                        "message": "Enabled FFMult advanced options without changing any parameter",
-                        "num": 5,
-                        "short_hash": "3a0757df3",
-                        "unix": "1511966670"
-                    },
-                    {
-                        "hash": "66e504fe259577c3473db9b51c320674d62eb504",
-                        "message": "Workaround for ProteinQuantifier bug: changed '-include_all' to TRUE",
-                        "num": 4,
-                        "short_hash": "66e504fe2",
-                        "unix": "1511867833"
-                    },
-                    {
-                        "hash": "ed8674c45632a609171092f22c9e16fbb69e1342",
-                        "message": "Updated workflow parameters",
-                        "num": 3,
-                        "short_hash": "ed8674c45",
-                        "unix": "1511865952"
-                    },
-                    {
-                        "hash": "c7d698525c66e52498ec708408d5045883619da2",
-                        "message": "Fill workflow file with an empty workflow",
+                        "hash": "7da80b34185f4165852feb3bfe80d692609685db",
+                        "message": "Workflows fix",
                         "num": 2,
-                        "short_hash": "c7d698525",
-                        "unix": "1496938362"
+                        "short_hash": "7da80b341",
+                        "unix": "1578668175"
                     },
                     {
                         "hash": "2c1271b670d336517fb123fb632ce13c93c40465",
@@ -198866,1259 +200553,1131 @@
                     {
                         "annotation": "",
                         "content_id": null,
-                        "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "mzml raw file"
+                                "name": "Input Dataset Collection (mzML files)"
                             }
                         ],
-                        "label": "mzml raw file",
-                        "name": "Input dataset",
+                        "label": null,
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "bottom": 307.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": -1679,
-                            "right": -1479,
-                            "top": 225,
-                            "width": 200,
-                            "x": -1679,
-                            "y": 225
+                            "left": 199.9666748046875,
+                            "top": 435.20001220703125
                         },
+                        "tool_errors": null,
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection (mzML files)\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "a2382c96-bff3-4807-bbb7-20f74d014134",
+                        "type": "data_collection_input",
+                        "uuid": "7bf13771-4620-4563-b972-efaf74887ce5",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "da762be8-3c8c-42a9-b749-8a38a004b944"
+                                "uuid": "11ba0e33-3924-43e2-a8f9-85e0e6c12cfe"
                             }
                         ]
                     },
                     {
                         "annotation": "",
                         "content_id": null,
-                        "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "fasta file"
+                                "name": "UniProt database (FASTA file)"
                             }
                         ],
-                        "label": "fasta file",
+                        "label": null,
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 466.8000030517578,
-                            "height": 61.80000305175781,
-                            "left": -1680,
-                            "right": -1480,
-                            "top": 405,
-                            "width": 200,
-                            "x": -1680,
-                            "y": 405
+                            "left": 241,
+                            "top": 603.2166748046875
                         },
+                        "tool_errors": null,
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"name\": \"UniProt database (FASTA file)\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "94c0bbb8-89a2-43a2-980b-65f44c21aa51",
+                        "uuid": "05f5cbd8-8459-47a0-8faf-95c0821f25fc",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "c9862313-9f50-4042-a35a-7db1f3af9a4d"
+                                "uuid": "3d25e478-d053-4d4e-9c7f-92fec2d6b09c"
                             }
                         ]
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nmzml raw file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nfasta file\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"FeatureFinderMultiplex\"];\n  0 -->|output| 2;\n  3[\"XTandemAdapter\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  4[\"FileInfo\"];\n  3 -->|out| 4;\n  5[\"PeptideIndexer\"];\n  1 -->|output| 5;\n  3 -->|out| 5;\n  6[\"IDPosteriorErrorProbability\"];\n  5 -->|out| 6;\n  7[\"FalseDiscoveryRate\"];\n  6 -->|out| 7;\n  8[\"IDScoreSwitcher\"];\n  7 -->|out| 8;\n  9[\"FileInfo\"];\n  8 -->|out| 9;\n  10[\"FidoAdapter\"];\n  8 -->|out| 10;\n  11[\"FalseDiscoveryRate\"];\n  10 -->|out| 11;\n  12[\"FileInfo\"];\n  11 -->|out| 12;\n  13[\"TextExporter\"];\n  11 -->|out| 13;\n  14[\"IDMapper\"];\n  11 -->|out| 14;\n  2 -->|out_multiplets| 14;\n  15[\"Select\"];\n  13 -->|out| 15;\n  16[\"Select\"];\n  13 -->|out| 16;\n  17[\"IDConflictResolver\"];\n  14 -->|out| 17;\n  18[\"MultiplexResolver\"];\n  17 -->|out| 18;\n  19[\"ProteinQuantifier\"];\n  18 -->|out| 19;\n  11 -->|out| 19;\n  20[\"Summary Statistics\"];\n  19 -->|out| 20;\n  21[\"Select last\"];\n  19 -->|out| 21;\n  22[\"Histogram\"];\n  21 -->|outfile| 22;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Proteomics: Peptide and Protein Quantification via stable istobe labeling",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"FeatureFinderMultiplex\"];\n  0 -->|output| 2;\n  3[\"HighResPrecursorMassCorrector\"];\n  2 -->|param_out_features| 3;\n  0 -->|output| 3;\n  4[\"MSGFPlusAdapter\"];\n  1 -->|output| 4;\n  3 -->|param_out| 4;\n  5[\"MSGFPlusAdapter\"];\n  1 -->|output| 5;\n  3 -->|param_out| 5;\n  6[\"MSGFPlusAdapter\"];\n  3 -->|param_out| 6;\n  7[\"PeptideIndexer\"];\n  1 -->|output| 7;\n  4 -->|param_out| 7;\n  8[\"PeptideIndexer\"];\n  1 -->|output| 8;\n  5 -->|param_out| 8;\n  9[\"PeptideIndexer\"];\n  1 -->|output| 9;\n  6 -->|param_out| 9;\n  10[\"IDMerger\"];\n  7 -->|param_out| 10;\n  8 -->|param_out| 10;\n  9 -->|param_out| 10;\n  11[\"ConsensusID\"];\n  10 -->|param_out| 11;\n  12[\"PeptideIndexer\"];\n  1 -->|output| 12;\n  11 -->|param_out| 12;\n  13[\"FalseDiscoveryRate\"];\n  12 -->|param_out| 13;\n  14[\"IDFilter\"];\n  13 -->|param_out| 14;\n  15[\"IDMapper\"];\n  14 -->|param_out| 15;\n  2 -->|param_out| 15;\n  16[\"IDConflictResolver\"];\n  15 -->|param_out| 16;\n  17[\"FileFilter\"];\n  16 -->|param_out| 17;\n  18[\"FileMerger\"];\n  17 -->|param_out| 18;\n  19[\"MzTabExporter\"];\n  18 -->|param_out| 19;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Tails Triple Dimethyl OpenMS2.1",
                 "outputs": [
                     {
                         "annotation": "",
                         "content_id": null,
-                        "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "mzml raw file"
+                                "name": "Input Dataset Collection (mzML files)"
                             }
                         ],
-                        "label": "mzml raw file",
-                        "name": "Input dataset",
+                        "label": null,
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "bottom": 307.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": -1679,
-                            "right": -1479,
-                            "top": 225,
-                            "width": 200,
-                            "x": -1679,
-                            "y": 225
+                            "left": 199.9666748046875,
+                            "top": 435.20001220703125
                         },
+                        "tool_errors": null,
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection (mzML files)\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "a2382c96-bff3-4807-bbb7-20f74d014134",
+                        "type": "data_collection_input",
+                        "uuid": "7bf13771-4620-4563-b972-efaf74887ce5",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "da762be8-3c8c-42a9-b749-8a38a004b944"
+                                "uuid": "11ba0e33-3924-43e2-a8f9-85e0e6c12cfe"
                             }
                         ]
                     },
                     {
                         "annotation": "",
                         "content_id": null,
-                        "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "fasta file"
+                                "name": "UniProt database (FASTA file)"
                             }
                         ],
-                        "label": "fasta file",
+                        "label": null,
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 466.8000030517578,
-                            "height": 61.80000305175781,
-                            "left": -1680,
-                            "right": -1480,
-                            "top": 405,
-                            "width": 200,
-                            "x": -1680,
-                            "y": 405
+                            "left": 241,
+                            "top": 603.2166748046875
                         },
+                        "tool_errors": null,
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"name\": \"UniProt database (FASTA file)\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "94c0bbb8-89a2-43a2-980b-65f44c21aa51",
+                        "uuid": "05f5cbd8-8459-47a0-8faf-95c0821f25fc",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "c9862313-9f50-4042-a35a-7db1f3af9a4d"
+                                "uuid": "3d25e478-d053-4d4e-9c7f-92fec2d6b09c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.6+galaxy0",
-                        "errors": null,
+                        "content_id": "FeatureFinderMultiplex",
                         "id": 2,
                         "input_connections": {
-                            "in": {
+                            "param_in": {
                                 "id": 0,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool FeatureFinderMultiplex",
+                                "name": "param_in"
+                            }
+                        ],
                         "label": null,
                         "name": "FeatureFinderMultiplex",
                         "outputs": [
                             {
-                                "name": "out_multiplets",
+                                "name": "param_out",
                                 "type": "consensusxml"
+                            },
+                            {
+                                "name": "param_out_features",
+                                "type": "featurexml"
+                            },
+                            {
+                                "name": "param_out_mzq",
+                                "type": "mzq"
                             }
                         ],
                         "position": {
-                            "bottom": 587.1999969482422,
-                            "height": 195.1999969482422,
-                            "left": -1373,
-                            "right": -1173,
-                            "top": 392,
-                            "width": 200,
-                            "x": -1373,
-                            "y": 392
+                            "left": 1228.9666748046875,
+                            "top": 1174.88330078125
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.6+galaxy0",
+                        "post_job_actions": {
+                            "HideDatasetActionparam_out_mzq": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "param_out_mzq"
+                            }
+                        },
+                        "tool_errors": null,
+                        "tool_id": "FeatureFinderMultiplex",
                         "tool_shed_repository": {
-                            "changeset_revision": "5e5771b511a3",
+                            "changeset_revision": "ca88bd28f116",
                             "name": "openms_featurefindermultiplex",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": [\"out_multiplets_FLAG\"], \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"algorithm\": {\"labels\": \"[ ][Arg6,Lys6]\", \"charge\": \"1:4\", \"isotopes_per_peptide\": \"3:6\", \"rt_typical\": \"40.0\", \"rt_band\": \"0.0\", \"rt_min\": \"2.0\", \"mz_tolerance\": \"10.0\", \"mz_unit\": \"ppm\", \"intensity_cutoff\": \"1000.0\", \"peptide_similarity\": \"0.5\", \"averagine_similarity\": \"0.4\", \"averagine_similarity_scaling\": \"0.95\", \"missed_cleavages\": \"1\", \"spectrum_type\": \"automatic\", \"averagine_type\": \"peptide\", \"knock_out\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"labels\": {\"Arg6\": \"6.0201290268\", \"Arg10\": \"10.0082686\", \"Lys4\": \"4.0251069836\", \"Lys6\": \"6.0201290268\", \"Lys8\": \"8.0141988132\", \"Leu3\": \"3.01883\", \"Dimethyl0\": \"28.0313\", \"Dimethyl4\": \"32.056407\", \"Dimethyl6\": \"34.063117\", \"Dimethyl8\": \"36.07567\", \"ICPL0\": \"105.021464\", \"ICPL4\": \"109.046571\", \"ICPL6\": \"111.041593\", \"ICPL10\": \"115.0667\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"param_algorithm_averagine_similarity\": \"\\\"0.6\\\"\", \"param_algorithm_rt_min\": \"\\\"3.0\\\"\", \"__page__\": 0, \"param_algorithm_missed_cleavages\": \"\\\"2\\\"\", \"param_algorithm_peptide_similarity\": \"\\\"0.7\\\"\", \"adv_opts\": \"{\\\"param_algorithm_knock_out\\\": \\\"true\\\", \\\"param_labels_Dimethyl4\\\": \\\"32.056407\\\", \\\"param_algorithm_isotopes_per_peptide\\\": \\\"3:6\\\", \\\"param_labels_Lys4\\\": \\\"4.0251069836\\\", \\\"param_labels_Dimethyl0\\\": \\\"28.0313\\\", \\\"param_labels_Lys8\\\": \\\"8.0141988132\\\", \\\"param_labels_ICPL10\\\": \\\"115.0667\\\", \\\"param_labels_Lys6\\\": \\\"6.0201290268\\\", \\\"param_labels_Arg10\\\": \\\"10.0082686\\\", \\\"param_labels_Dimethyl8\\\": \\\"36.07567\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"param_labels_ICPL6\\\": \\\"111.041593\\\", \\\"param_force\\\": \\\"false\\\", \\\"param_labels_Dimethyl6\\\": \\\"34.063117\\\", \\\"param_labels_Arg6\\\": \\\"6.0201290268\\\", \\\"__current_case__\\\": 1, \\\"param_algorithm_averagine_type\\\": \\\"peptide\\\", \\\"param_labels_ICPL0\\\": \\\"105.021464\\\", \\\"param_labels_Leu3\\\": \\\"3.01883\\\", \\\"param_labels_ICPL4\\\": \\\"109.046571\\\", \\\"param_algorithm_averagine_similarity_scaling\\\": \\\"0.6\\\"}\", \"param_algorithm_mz_tolerance\": \"\\\"15.0\\\"\", \"param_algorithm_charge\": \"\\\"1:5\\\"\", \"param_algorithm_mz_unit\": \"\\\"ppm\\\"\", \"param_algorithm_labels\": \"\\\"[Dimethyl0][Dimethyl4][Dimethyl8]\\\"\", \"param_algorithm_intensity_cutoff\": \"\\\"10.0\\\"\", \"param_algorithm_rt_typical\": \"\\\"50.0\\\"\", \"__rerun_remap_job_id__\": null, \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "2.1.0",
                         "type": "tool",
-                        "uuid": "eaa992c7-823d-46df-8e6c-161733ed043c",
+                        "uuid": "627672fc-feef-4e31-9208-182a27df2533",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_multiplets",
-                                "uuid": "c4519437-723f-4033-884e-90686600a9cd"
+                                "output_name": "param_out",
+                                "uuid": "6e1e9231-52a0-4d05-9491-31f4b162d405"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "param_out_features",
+                                "uuid": "a8b8b589-661b-49ca-9832-556069bf98bc"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0",
-                        "errors": null,
+                        "content_id": "HighResPrecursorMassCorrector",
                         "id": 3,
                         "input_connections": {
-                            "database": {
-                                "id": 1,
-                                "output_name": "output"
+                            "param_feature_in": {
+                                "id": 2,
+                                "output_name": "param_out_features"
                             },
-                            "in": {
+                            "param_in": {
                                 "id": 0,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool HighResPrecursorMassCorrector",
+                                "name": "param_feature_in"
+                            },
+                            {
+                                "description": "runtime parameter for tool HighResPrecursorMassCorrector",
+                                "name": "param_in"
+                            }
+                        ],
                         "label": null,
-                        "name": "XTandemAdapter",
+                        "name": "HighResPrecursorMassCorrector",
                         "outputs": [
                             {
-                                "name": "out",
-                                "type": "idxml"
+                                "name": "param_out",
+                                "type": "mzml"
+                            },
+                            {
+                                "name": "param_out_csv",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 317.1999969482422,
-                            "height": 215.1999969482422,
-                            "left": -1381,
-                            "right": -1181,
-                            "top": 102,
-                            "width": 200,
-                            "x": -1381,
-                            "y": 102
+                            "left": 484.54998779296875,
+                            "top": 151.1999969482422
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0",
+                        "post_job_actions": {
+                            "HideDatasetActionparam_out_csv": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "param_out_csv"
+                            },
+                            "RenameDatasetActionparam_out": {
+                                "action_arguments": {
+                                    "newname": "HighRes_out"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "param_out"
+                            }
+                        },
+                        "tool_errors": null,
+                        "tool_id": "HighResPrecursorMassCorrector",
                         "tool_shed_repository": {
-                            "changeset_revision": "1add9bacdccd",
-                            "name": "openms_xtandemadapter",
+                            "changeset_revision": "9e26f5c770f8",
+                            "name": "openms_highresprecursormasscorrector",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": [\"out_FLAG\"], \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"database\": {\"__class__\": \"ConnectedValue\"}, \"default_config_file\": null, \"enzyme\": \"Trypsin\", \"fixed_modifications\": [\"Carbamidomethyl (C)\"], \"fragment_error_units\": \"ppm\", \"fragment_mass_tolerance\": \"10.0\", \"ignore_adapter_param\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"max_precursor_charge\": \"4\", \"max_valid_expect\": \"0.1\", \"minimum_fragment_mz\": \"150.0\", \"missed_cleavages\": \"1\", \"no_isotope_error\": \"false\", \"output_results\": \"all\", \"precursor_error_units\": \"ppm\", \"precursor_mass_tolerance\": \"10.0\", \"semi_cleavage\": \"false\", \"variable_modifications\": [\"Label:13C(6) (K)\", \"Label:13C(6) (R)\", \"Oxidation (M)\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_feature_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_feature_rt_tolerance\": \"\\\"15.0\\\"\", \"param_nearest_peak_mz_tolerance_unit\": \"\\\"ppm\\\"\", \"param_feature_mz_tolerance_unit\": \"\\\"ppm\\\"\", \"param_feature_mz_tolerance\": \"\\\"40.0\\\"\", \"param_feature_keep_original\": \"\\\"false\\\"\", \"param_feature_assign_all_matching\": \"\\\"false\\\"\", \"param_feature_believe_charge\": \"\\\"false\\\"\", \"param_nearest_peak_mz_tolerance\": \"\\\"0.0\\\"\"}",
+                        "tool_version": "2.1.0",
                         "type": "tool",
-                        "uuid": "0118ed37-ce01-4abd-9551-e84807f0b008",
+                        "uuid": "3d7f4c8b-1896-4365-b41a-77b152ec84b4",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "2c114d65-1bd5-451a-9cd3-eaa334d3000b"
+                                "output_name": "param_out",
+                                "uuid": "be0344fb-dccf-4d28-a45e-9d1aded44e41"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
-                        "errors": null,
+                        "content_id": "MSGFPlusAdapter",
                         "id": 4,
                         "input_connections": {
-                            "in": {
+                            "param_database": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "param_in": {
                                 "id": 3,
-                                "output_name": "out"
+                                "output_name": "param_out"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool MSGFPlusAdapter",
+                                "name": "param_in"
+                            },
+                            {
+                                "description": "runtime parameter for tool MSGFPlusAdapter",
+                                "name": "param_database"
+                            }
+                        ],
                         "label": null,
-                        "name": "FileInfo",
+                        "name": "MSGFPlusAdapter",
                         "outputs": [
                             {
-                                "name": "out",
-                                "type": "txt"
+                                "name": "param_out",
+                                "type": "idxml"
+                            },
+                            {
+                                "name": "param_mzid_out",
+                                "type": "mzid"
                             }
                         ],
                         "position": {
-                            "bottom": 385.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": -1153,
-                            "right": -953,
-                            "top": 272,
-                            "width": 200,
-                            "x": -1153,
-                            "y": 272
+                            "left": 849.0500030517578,
+                            "top": 186.21665954589844
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
+                        "post_job_actions": {
+                            "HideDatasetActionparam_mzid_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "param_mzid_out"
+                            }
+                        },
+                        "tool_errors": null,
+                        "tool_id": "MSGFPlusAdapter",
                         "tool_shed_repository": {
-                            "changeset_revision": "e8dce5e07fa5",
-                            "name": "openms_fileinfo",
+                            "changeset_revision": "2b2a7551a857",
+                            "name": "openms_msgfplusadapter",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"c\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"d\": \"false\", \"i\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"false\", \"p\": \"false\", \"s\": \"false\", \"v\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"param_java_executable\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_max_precursor_charge\": \"\\\"4\\\"\", \"param_min_precursor_charge\": \"\\\"2\\\"\", \"param_min_peptide_length\": \"\\\"7\\\"\", \"param_precursor_error_units\": \"\\\"ppm\\\"\", \"param_protocol\": \"\\\"none\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"param_tryptic\": \"\\\"semi\\\"\", \"param_max_mods\": \"\\\"3\\\"\", \"rep_param_fixed_modifications\": \"[{\\\"__index__\\\": 0, \\\"param_fixed_modifications\\\": \\\"Carbamidomethyl (C)\\\"}, {\\\"__index__\\\": 1, \\\"param_fixed_modifications\\\": \\\"Dimethyl (K)\\\"}, {\\\"__index__\\\": 2, \\\"param_fixed_modifications\\\": \\\"Dimethyl (N-term)\\\"}]\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_add_decoys\": \"\\\"false\\\"\", \"param_matches_per_spec\": \"\\\"1\\\"\", \"param_max_peptide_length\": \"\\\"40\\\"\", \"param_instrument\": \"\\\"Q_Exactive\\\"\", \"param_precursor_mass_tolerance\": \"\\\"20.0\\\"\", \"rep_param_variable_modifications\": \"[]\", \"param_add_features\": \"\\\"true\\\"\", \"param_enzyme\": \"\\\"ArgC\\\"\", \"param_database\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_fragment_method\": \"\\\"from_spectrum\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"param_java_memory\": \"\\\"3500\\\"\", \"param_isotope_error_range\": \"\\\"0,0\\\"\"}",
+                        "tool_version": "2.1.0",
                         "type": "tool",
-                        "uuid": "a2a5218c-cdd7-4d84-904a-4fe5d9763927",
+                        "uuid": "cc98863a-5f1a-42ef-bd30-a7c6002f3efa",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "4d3e6847-d51d-410f-9bbf-168ab598b108"
+                                "output_name": "param_out",
+                                "uuid": "7066dfd9-e896-462b-8877-68580da0cc08"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0",
-                        "errors": null,
+                        "content_id": "MSGFPlusAdapter",
                         "id": 5,
                         "input_connections": {
-                            "fasta": {
+                            "param_database": {
                                 "id": 1,
                                 "output_name": "output"
                             },
-                            "in": {
+                            "param_in": {
                                 "id": 3,
-                                "output_name": "out"
+                                "output_name": "param_out"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool MSGFPlusAdapter",
+                                "name": "param_in"
+                            },
+                            {
+                                "description": "runtime parameter for tool MSGFPlusAdapter",
+                                "name": "param_database"
+                            }
+                        ],
                         "label": null,
-                        "name": "PeptideIndexer",
+                        "name": "MSGFPlusAdapter",
                         "outputs": [
                             {
-                                "name": "out",
+                                "name": "param_out",
                                 "type": "idxml"
+                            },
+                            {
+                                "name": "param_mzid_out",
+                                "type": "mzid"
                             }
                         ],
                         "position": {
-                            "bottom": 597.1999969482422,
-                            "height": 205.1999969482422,
-                            "left": -1153,
-                            "right": -953,
-                            "top": 392,
-                            "width": 200,
-                            "x": -1153,
-                            "y": 392
+                            "left": 887,
+                            "top": 394.20001220703125
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0",
+                        "post_job_actions": {
+                            "HideDatasetActionparam_mzid_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "param_mzid_out"
+                            }
+                        },
+                        "tool_errors": null,
+                        "tool_id": "MSGFPlusAdapter",
                         "tool_shed_repository": {
-                            "changeset_revision": "d8ee5700c66b",
-                            "name": "openms_peptideindexer",
+                            "changeset_revision": "2b2a7551a857",
+                            "name": "openms_msgfplusadapter",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"IL_equivalent\": \"false\", \"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"aaa_max\": \"3\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"decoy_string\": \"\", \"decoy_string_position\": \"prefix\", \"enzyme\": {\"name\": \"auto\", \"specificity\": \"none\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"in\": {\"__class__\": \"ConnectedValue\"}, \"keep_unreferenced_proteins\": \"false\", \"mismatches_max\": \"0\", \"missing_decoy_action\": \"error\", \"unmatched_action\": \"error\", \"write_protein_description\": \"true\", \"write_protein_sequence\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"param_java_executable\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_max_precursor_charge\": \"\\\"4\\\"\", \"param_min_precursor_charge\": \"\\\"2\\\"\", \"param_min_peptide_length\": \"\\\"7\\\"\", \"param_precursor_error_units\": \"\\\"ppm\\\"\", \"param_protocol\": \"\\\"none\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"param_tryptic\": \"\\\"semi\\\"\", \"param_max_mods\": \"\\\"3\\\"\", \"rep_param_fixed_modifications\": \"[{\\\"__index__\\\": 0, \\\"param_fixed_modifications\\\": \\\"Carbamidomethyl (C)\\\"}, {\\\"__index__\\\": 1, \\\"param_fixed_modifications\\\": \\\"Dimethyl:2H(4) (K)\\\"}, {\\\"__index__\\\": 2, \\\"param_fixed_modifications\\\": \\\"Dimethyl:2H(4) (N-term)\\\"}]\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_add_decoys\": \"\\\"false\\\"\", \"param_matches_per_spec\": \"\\\"1\\\"\", \"param_max_peptide_length\": \"\\\"40\\\"\", \"param_instrument\": \"\\\"Q_Exactive\\\"\", \"param_precursor_mass_tolerance\": \"\\\"20.0\\\"\", \"rep_param_variable_modifications\": \"[]\", \"param_add_features\": \"\\\"true\\\"\", \"param_enzyme\": \"\\\"ArgC\\\"\", \"param_database\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_fragment_method\": \"\\\"from_spectrum\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"param_java_memory\": \"\\\"3500\\\"\", \"param_isotope_error_range\": \"\\\"0,0\\\"\"}",
+                        "tool_version": "2.1.0",
                         "type": "tool",
-                        "uuid": "d7e47129-c738-4174-b7e4-4d387a5b24f1",
+                        "uuid": "3a2ce94c-c7c0-43e8-a95a-29773f41ff83",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "dc35fedb-9094-4984-9936-0aeb83d98e72"
+                                "output_name": "param_out",
+                                "uuid": "7d1226d5-80ff-4f81-b2f8-1298517f98f8"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy0",
-                        "errors": null,
+                        "content_id": "MSGFPlusAdapter",
                         "id": 6,
                         "input_connections": {
-                            "in": {
-                                "id": 5,
-                                "output_name": "out"
+                            "param_in": {
+                                "id": 3,
+                                "output_name": "param_out"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool MSGFPlusAdapter",
+                                "name": "param_in"
+                            },
+                            {
+                                "description": "runtime parameter for tool MSGFPlusAdapter",
+                                "name": "param_database"
+                            }
+                        ],
                         "label": null,
-                        "name": "IDPosteriorErrorProbability",
+                        "name": "MSGFPlusAdapter",
                         "outputs": [
                             {
-                                "name": "out",
+                                "name": "param_out",
                                 "type": "idxml"
+                            },
+                            {
+                                "name": "param_mzid_out",
+                                "type": "mzid"
                             }
                         ],
                         "position": {
-                            "bottom": 446.8000030517578,
-                            "height": 174.8000030517578,
-                            "left": -933,
-                            "right": -733,
-                            "top": 272,
-                            "width": 200,
-                            "x": -933,
-                            "y": 272
+                            "left": 892.5,
+                            "top": 590
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy0",
+                        "post_job_actions": {
+                            "HideDatasetActionparam_mzid_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "param_mzid_out"
+                            }
+                        },
+                        "tool_errors": null,
+                        "tool_id": "MSGFPlusAdapter",
                         "tool_shed_repository": {
-                            "changeset_revision": "711a081d80ba",
-                            "name": "openms_idposteriorerrorprobability",
+                            "changeset_revision": "2b2a7551a857",
+                            "name": "openms_msgfplusadapter",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fit_algorithm\": {\"number_of_bins\": \"100\", \"incorrectly_assigned\": \"Gumbel\", \"max_nr_iterations\": \"1000\", \"neg_log_delta\": \"6\", \"outlier_handling\": \"ignore_iqr_outliers\"}, \"ignore_bad_data\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"prob_correct\": \"true\", \"split_charge\": \"false\", \"top_hits_only\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"param_java_executable\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_max_precursor_charge\": \"\\\"4\\\"\", \"param_min_precursor_charge\": \"\\\"2\\\"\", \"param_min_peptide_length\": \"\\\"7\\\"\", \"param_precursor_error_units\": \"\\\"ppm\\\"\", \"param_protocol\": \"\\\"none\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"param_tryptic\": \"\\\"semi\\\"\", \"param_max_mods\": \"\\\"3\\\"\", \"rep_param_fixed_modifications\": \"[{\\\"__index__\\\": 0, \\\"param_fixed_modifications\\\": \\\"Carbamidomethyl (C)\\\"}, {\\\"__index__\\\": 1, \\\"param_fixed_modifications\\\": \\\"Dimethyl:2H(6)13C(2) (K)\\\"}, {\\\"__index__\\\": 2, \\\"param_fixed_modifications\\\": \\\"Dimethyl:2H(6)13C(2) (N-term)\\\"}]\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_add_decoys\": \"\\\"false\\\"\", \"param_matches_per_spec\": \"\\\"1\\\"\", \"param_max_peptide_length\": \"\\\"40\\\"\", \"param_instrument\": \"\\\"Q_Exactive\\\"\", \"param_precursor_mass_tolerance\": \"\\\"20.0\\\"\", \"rep_param_variable_modifications\": \"[]\", \"param_add_features\": \"\\\"true\\\"\", \"param_enzyme\": \"\\\"ArgC\\\"\", \"param_database\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_fragment_method\": \"\\\"from_spectrum\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"param_java_memory\": \"\\\"3500\\\"\", \"param_isotope_error_range\": \"\\\"0,0\\\"\"}",
+                        "tool_version": "2.1.0",
                         "type": "tool",
-                        "uuid": "3d87b974-366d-4ffa-b626-bb0c63bef28e",
+                        "uuid": "05593ca7-2056-4201-9ce7-60b4abc82ff5",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "c24e8bab-c848-46d1-b469-2537f21d4b69"
+                                "output_name": "param_out",
+                                "uuid": "22b3fa5a-a162-4ce1-8c07-8c3f84fc0551"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
-                        "errors": null,
+                        "content_id": "PeptideIndexer",
                         "id": 7,
                         "input_connections": {
-                            "in": {
-                                "id": 6,
-                                "output_name": "out"
+                            "param_fasta": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "param_in": {
+                                "id": 4,
+                                "output_name": "param_out"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool PeptideIndexer",
+                                "name": "param_fasta"
+                            },
+                            {
+                                "description": "runtime parameter for tool PeptideIndexer",
+                                "name": "param_in"
+                            }
+                        ],
                         "label": null,
-                        "name": "FalseDiscoveryRate",
+                        "name": "PeptideIndexer",
                         "outputs": [
                             {
-                                "name": "out",
+                                "name": "param_out",
                                 "type": "idxml"
                             }
                         ],
                         "position": {
-                            "bottom": 446.8000030517578,
-                            "height": 174.8000030517578,
-                            "left": -713,
-                            "right": -513,
-                            "top": 272,
-                            "width": 200,
-                            "x": -713,
-                            "y": 272
+                            "left": 1191,
+                            "top": 181.1999969482422
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
+                        "tool_errors": null,
+                        "tool_id": "PeptideIndexer",
                         "tool_shed_repository": {
-                            "changeset_revision": "469690558892",
-                            "name": "openms_falsediscoveryrate",
+                            "changeset_revision": "539a3a4dcc9e",
+                            "name": "openms_peptideindexer",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"FDR\": {\"PSM\": \"0.01\", \"protein\": \"1.0\", \"cleanup\": {\"remove_proteins_without_psms\": \"true\", \"remove_psms_without_proteins\": \"true\", \"remove_spectra_without_psms\": \"true\"}}, \"OPTIONAL_OUTPUTS\": null, \"PSM\": \"true\", \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"algorithm\": {\"no_qvalues\": \"false\", \"use_all_hits\": \"false\", \"split_charge_variants\": \"false\", \"treat_runs_separately\": \"false\", \"add_decoy_peptides\": \"true\", \"add_decoy_proteins\": \"false\", \"conservative\": \"true\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"protein\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"param_write_protein_sequence\": \"\\\"true\\\"\", \"param_missing_decoy_action\": \"\\\"error\\\"\", \"param_filter_aaa_proteins\": \"\\\"false\\\"\", \"param_prefix\": \"\\\"true\\\"\", \"param_keep_unreferenced_proteins\": \"\\\"false\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"param_allow_unmatched\": \"\\\"true\\\"\", \"param_decoy_string_position\": \"\\\"prefix\\\"\", \"param_mismatches_max\": \"\\\"0\\\"\", \"param_enzyme_name\": \"\\\"Trypsin/P\\\"\", \"param_enzyme_specificity\": \"\\\"semi\\\"\", \"param_decoy_string\": \"\\\"dec_\\\"\", \"__rerun_remap_job_id__\": null, \"param_write_protein_description\": \"\\\"true\\\"\", \"param_full_tolerant_search\": \"\\\"false\\\"\", \"param_fasta\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_aaa_max\": \"\\\"4\\\"\", \"param_annotate_proteins\": \"\\\"True\\\"\", \"param_IL_equivalent\": \"\\\"false\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "2.1.0",
                         "type": "tool",
-                        "uuid": "b9a62ef4-7758-41ed-a57f-07a761f34ea7",
+                        "uuid": "6d75c013-51d3-49f5-8b26-876a8b1c06d5",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "13259070-1f50-4f87-84b0-c1d3640db605"
+                                "output_name": "param_out",
+                                "uuid": "92afc5d3-a20f-4f89-8b80-f6618ba430d0"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.6+galaxy0",
-                        "errors": null,
+                        "content_id": "PeptideIndexer",
                         "id": 8,
                         "input_connections": {
-                            "in": {
-                                "id": 7,
-                                "output_name": "out"
+                            "param_fasta": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "param_in": {
+                                "id": 5,
+                                "output_name": "param_out"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "IDScoreSwitcher",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "out",
-                                "type": "idxml"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 406,
-                            "height": 134,
-                            "left": -493,
-                            "right": -293,
-                            "top": 272,
-                            "width": 200,
-                            "x": -493,
-                            "y": 272
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.6+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ec0d05b20eed",
-                            "name": "openms_idscoreswitcher",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"new_score\": \"Posterior Probability_score\", \"new_score_orientation\": \"higher_better\", \"new_score_type\": \"\", \"old_score\": \"\", \"proteins\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
-                        "type": "tool",
-                        "uuid": "659bd32d-fbc8-4c81-a48e-6f1c118b9416",
-                        "workflow_outputs": [
+                                "description": "runtime parameter for tool PeptideIndexer",
+                                "name": "param_fasta"
+                            },
                             {
-                                "label": null,
-                                "output_name": "out",
-                                "uuid": "01759e5a-51ec-4358-89bf-040a35560402"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "in": {
-                                "id": 8,
-                                "output_name": "out"
+                                "description": "runtime parameter for tool PeptideIndexer",
+                                "name": "param_in"
                             }
-                        },
-                        "inputs": [],
+                        ],
                         "label": null,
-                        "name": "FileInfo",
+                        "name": "PeptideIndexer",
                         "outputs": [
                             {
-                                "name": "out",
-                                "type": "txt"
+                                "name": "param_out",
+                                "type": "idxml"
                             }
                         ],
                         "position": {
-                            "bottom": 385.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": -273,
-                            "right": -73,
-                            "top": 272,
-                            "width": 200,
-                            "x": -273,
-                            "y": 272
+                            "left": 1155,
+                            "top": 398.2166748046875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
+                        "tool_errors": null,
+                        "tool_id": "PeptideIndexer",
                         "tool_shed_repository": {
-                            "changeset_revision": "e8dce5e07fa5",
-                            "name": "openms_fileinfo",
+                            "changeset_revision": "539a3a4dcc9e",
+                            "name": "openms_peptideindexer",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"c\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"d\": \"false\", \"i\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"false\", \"p\": \"false\", \"s\": \"false\", \"v\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"param_write_protein_sequence\": \"\\\"true\\\"\", \"param_missing_decoy_action\": \"\\\"error\\\"\", \"param_filter_aaa_proteins\": \"\\\"false\\\"\", \"param_prefix\": \"\\\"true\\\"\", \"param_keep_unreferenced_proteins\": \"\\\"false\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"param_allow_unmatched\": \"\\\"true\\\"\", \"param_decoy_string_position\": \"\\\"prefix\\\"\", \"param_mismatches_max\": \"\\\"0\\\"\", \"param_enzyme_name\": \"\\\"Trypsin/P\\\"\", \"param_enzyme_specificity\": \"\\\"semi\\\"\", \"param_decoy_string\": \"\\\"dec_\\\"\", \"__rerun_remap_job_id__\": null, \"param_write_protein_description\": \"\\\"true\\\"\", \"param_full_tolerant_search\": \"\\\"false\\\"\", \"param_fasta\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_aaa_max\": \"\\\"4\\\"\", \"param_annotate_proteins\": \"\\\"True\\\"\", \"param_IL_equivalent\": \"\\\"false\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "2.1.0",
                         "type": "tool",
-                        "uuid": "a871c553-362d-4e80-bbdb-9cb7b866e370",
+                        "uuid": "8cd335cb-9d51-4c04-99b3-38fed4f3c3b6",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "21b6c69b-b138-4db8-9950-de68dac93a05"
+                                "output_name": "param_out",
+                                "uuid": "9774a600-1f91-4927-932a-b887a1b6f73a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0",
-                        "errors": null,
+                        "content_id": "IDMerger",
                         "id": 10,
                         "input_connections": {
-                            "in": {
-                                "id": 8,
-                                "output_name": "out"
-                            }
+                            "param_in": [
+                                {
+                                    "id": 7,
+                                    "output_name": "param_out"
+                                },
+                                {
+                                    "id": 8,
+                                    "output_name": "param_out"
+                                },
+                                {
+                                    "id": 9,
+                                    "output_name": "param_out"
+                                }
+                            ]
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool IDMerger",
+                                "name": "param_add_to"
+                            },
+                            {
+                                "description": "runtime parameter for tool IDMerger",
+                                "name": "param_in"
+                            }
+                        ],
                         "label": null,
-                        "name": "FidoAdapter",
+                        "name": "IDMerger",
                         "outputs": [
                             {
-                                "name": "out",
+                                "name": "param_out",
                                 "type": "idxml"
                             }
                         ],
                         "position": {
-                            "bottom": 505.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": -273,
-                            "right": -73,
-                            "top": 392,
-                            "width": 200,
-                            "x": -273,
-                            "y": 392
+                            "left": 1441,
+                            "top": 352.20001220703125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0",
+                        "tool_errors": null,
+                        "tool_id": "IDMerger",
                         "tool_shed_repository": {
-                            "changeset_revision": "c3a5cd016963",
-                            "name": "openms_fidoadapter",
+                            "changeset_revision": "18f93351f8b6",
+                            "name": "openms_idmerger",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"all_PSMs\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"greedy_group_resolution\": \"true\", \"group_level\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"log2_states\": \"0\", \"no_cleanup\": \"false\", \"prob\": {\"protein\": \"0.0\", \"peptide\": \"0.0\", \"spurious\": \"0.0\"}, \"separate_runs\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"inputs\": \"[{\\\"__index__\\\": 0, \\\"param_in\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"__index__\\\": 1, \\\"param_in\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}]\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"param_annotate_file_origin\": \"\\\"false\\\"\", \"param_pepxml_protxml\": \"\\\"false\\\"\", \"param_add_to\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_in1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "2.1.0",
                         "type": "tool",
-                        "uuid": "404e63ae-e855-4cef-9352-8fcb43de3f13",
+                        "uuid": "3616471f-09c7-4c6a-8118-e92619874f09",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "e1a8b9e2-3fe9-4c6d-b8c7-b292ce47374f"
+                                "output_name": "param_out",
+                                "uuid": "f78b508e-7e25-4d72-a870-9f12371c95ea"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
-                        "errors": null,
+                        "content_id": "ConsensusID",
                         "id": 11,
                         "input_connections": {
-                            "in": {
+                            "param_in": {
                                 "id": 10,
-                                "output_name": "out"
+                                "output_name": "param_out"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "FalseDiscoveryRate",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "out",
-                                "type": "idxml"
+                                "description": "runtime parameter for tool ConsensusID",
+                                "name": "param_in"
                             }
                         ],
-                        "position": {
-                            "bottom": 446.8000030517578,
-                            "height": 174.8000030517578,
-                            "left": -53,
-                            "right": 147,
-                            "top": 272,
-                            "width": 200,
-                            "x": -53,
-                            "y": 272
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "469690558892",
-                            "name": "openms_falsediscoveryrate",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"FDR\": {\"PSM\": \"1.0\", \"protein\": \"0.01\", \"cleanup\": {\"remove_proteins_without_psms\": \"true\", \"remove_psms_without_proteins\": \"true\", \"remove_spectra_without_psms\": \"true\"}}, \"OPTIONAL_OUTPUTS\": null, \"PSM\": \"false\", \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"algorithm\": {\"no_qvalues\": \"false\", \"use_all_hits\": \"false\", \"split_charge_variants\": \"false\", \"treat_runs_separately\": \"false\", \"add_decoy_peptides\": \"false\", \"add_decoy_proteins\": \"false\", \"conservative\": \"true\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"protein\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
-                        "type": "tool",
-                        "uuid": "886f5485-8805-494f-99aa-f50c7c84e156",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out",
-                                "uuid": "a047eec1-fc49-4adb-a48b-eebfcf86b4ba"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
-                        "errors": null,
-                        "id": 12,
-                        "input_connections": {
-                            "in": {
-                                "id": 11,
-                                "output_name": "out"
-                            }
-                        },
-                        "inputs": [],
                         "label": null,
-                        "name": "FileInfo",
+                        "name": "ConsensusID",
                         "outputs": [
                             {
-                                "name": "out",
-                                "type": "txt"
+                                "name": "param_out",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 385.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": 167,
-                            "right": 367,
-                            "top": 272,
-                            "width": 200,
-                            "x": 167,
-                            "y": 272
+                            "left": 1609,
+                            "top": 470.20001220703125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
+                        "tool_errors": null,
+                        "tool_id": "ConsensusID",
                         "tool_shed_repository": {
-                            "changeset_revision": "e8dce5e07fa5",
-                            "name": "openms_fileinfo",
+                            "changeset_revision": "8960fb791701",
+                            "name": "openms_consensusid",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"c\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"d\": \"false\", \"i\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"false\", \"p\": \"false\", \"s\": \"false\", \"v\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"__page__\": 0, \"param_algorithm\": \"\\\"best\\\"\", \"param_filter_considered_hits\": \"\\\"0\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"param_filter_count_empty\": \"\\\"false\\\"\", \"param_PEPIons_mass_tolerance\": \"\\\"0.5\\\"\", \"param_PEPIons_min_shared\": \"\\\"2\\\"\", \"param_PEPMatrix_penalty\": \"\\\"5\\\"\", \"param_filter_min_support\": \"\\\"0.0\\\"\", \"param_rt_delta\": \"\\\"0.1\\\"\", \"param_PEPMatrix_matrix\": \"\\\"identity\\\"\", \"param_mz_delta\": \"\\\"0.1\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "2.1.0",
                         "type": "tool",
-                        "uuid": "d13e8538-3432-4a00-9cca-7e8280947bb9",
+                        "uuid": "a397db69-017e-4988-9f94-7ecbc119e3f3",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "28b66dcf-19db-4d93-959d-ec6af66ed496"
+                                "output_name": "param_out",
+                                "uuid": "b05c7e3e-e094-4366-9163-e0c1984974b9"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.6+galaxy0",
-                        "errors": null,
-                        "id": 13,
+                        "content_id": "PeptideIndexer",
+                        "id": 12,
                         "input_connections": {
-                            "in": {
+                            "param_fasta": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "param_in": {
                                 "id": 11,
-                                "output_name": "out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "TextExporter",
-                        "outputs": [
-                            {
-                                "name": "out",
-                                "type": "tabular"
+                                "output_name": "param_out"
                             }
-                        ],
-                        "position": {
-                            "bottom": 505.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": 167,
-                            "right": 367,
-                            "top": 392,
-                            "width": 200,
-                            "x": 167,
-                            "y": 392
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.6+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "1c596fdaf34a",
-                            "name": "openms_textexporter",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"consensus\": {\"sorting_method\": \"none\", \"sort_by_maps\": \"false\", \"sort_by_size\": \"false\"}, \"feature\": {\"minimal\": \"false\", \"add_metavalues\": \"-1\"}, \"id\": {\"proteins_only\": \"false\", \"peptides_only\": \"false\", \"protein_groups\": \"false\", \"first_dim_rt\": \"false\", \"add_metavalues\": \"-1\", \"add_hit_metavalues\": \"-1\", \"add_protein_hit_metavalues\": \"-1\"}, \"in\": {\"__class__\": \"ConnectedValue\"}, \"no_ids\": \"false\", \"quoting\": \"none\", \"replacement\": \"_\", \"separator\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
-                        "type": "tool",
-                        "uuid": "e206c716-a374-4810-a560-e57e6761aa2c",
-                        "workflow_outputs": [
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "out",
-                                "uuid": "b9156da0-a6b3-47d9-a352-836aee0451bc"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.6+galaxy0",
-                        "errors": null,
-                        "id": 14,
-                        "input_connections": {
-                            "id": {
-                                "id": 11,
-                                "output_name": "out"
+                                "description": "runtime parameter for tool PeptideIndexer",
+                                "name": "param_fasta"
                             },
-                            "in": {
-                                "id": 2,
-                                "output_name": "out_multiplets"
+                            {
+                                "description": "runtime parameter for tool PeptideIndexer",
+                                "name": "param_in"
                             }
-                        },
-                        "inputs": [],
+                        ],
                         "label": null,
-                        "name": "IDMapper",
+                        "name": "PeptideIndexer",
                         "outputs": [
                             {
-                                "name": "out",
-                                "type": "input"
+                                "name": "param_out",
+                                "type": "idxml"
                             }
                         ],
                         "position": {
-                            "bottom": 788.3999938964844,
-                            "height": 276.3999938964844,
-                            "left": 167,
-                            "right": 367,
-                            "top": 512,
-                            "width": 200,
-                            "x": 167,
-                            "y": 512
+                            "left": 1003,
+                            "top": 820.2000122070312
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.6+galaxy0",
+                        "tool_errors": null,
+                        "tool_id": "PeptideIndexer",
                         "tool_shed_repository": {
-                            "changeset_revision": "2517c03f5cd3",
-                            "name": "openms_idmapper",
+                            "changeset_revision": "539a3a4dcc9e",
+                            "name": "openms_peptideindexer",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"consensus\": {\"use_subelements\": \"true\", \"annotate_ids_with_subelements\": \"true\"}, \"feature\": {\"use_centroid_rt\": \"false\", \"use_centroid_mz\": \"true\"}, \"id\": {\"__class__\": \"ConnectedValue\"}, \"in\": {\"__class__\": \"ConnectedValue\"}, \"mz_measure\": \"ppm\", \"mz_reference\": \"peptide\", \"mz_tolerance\": \"10.0\", \"rt_tolerance\": \"20.0\", \"spectra\": {\"_in\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
-                        "type": "tool",
-                        "uuid": "f368bcfb-dcd6-4006-b0fb-54684f73f36c",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out",
-                                "uuid": "2385a34d-3bf9-4b1e-8c09-ececeec35479"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "Grep1",
-                        "errors": null,
-                        "id": 15,
-                        "input_connections": {
-                            "input": {
-                                "id": 13,
-                                "output_name": "out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Select",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 365.1999969482422,
-                            "height": 93.19999694824219,
-                            "left": 387,
-                            "right": 587,
-                            "top": 272,
-                            "width": 200,
-                            "x": 387,
-                            "y": 272
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "Grep1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"false\", \"pattern\": \"CONTAMINANT\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.1",
-                        "type": "tool",
-                        "uuid": "bd3098ce-6f2f-4c3d-8580-35a559c5a07b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "57f19087-b67a-40f4-9fcd-ab338a853e59"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "Grep1",
-                        "errors": null,
-                        "id": 16,
-                        "input_connections": {
-                            "input": {
-                                "id": 13,
-                                "output_name": "out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Select",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 485.1999969482422,
-                            "height": 93.19999694824219,
-                            "left": 387,
-                            "right": 587,
-                            "top": 392,
-                            "width": 200,
-                            "x": 387,
-                            "y": 392
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "Grep1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"__workflow_invocation_uuid__\": \"9603dea81b7711eb9fdd001b21d75532\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"false\", \"pattern\": \"HUMAN\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.1",
+                        "tool_state": "{\"param_write_protein_sequence\": \"\\\"true\\\"\", \"param_missing_decoy_action\": \"\\\"error\\\"\", \"param_filter_aaa_proteins\": \"\\\"false\\\"\", \"param_prefix\": \"\\\"true\\\"\", \"param_keep_unreferenced_proteins\": \"\\\"false\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"param_allow_unmatched\": \"\\\"true\\\"\", \"param_decoy_string_position\": \"\\\"prefix\\\"\", \"param_mismatches_max\": \"\\\"0\\\"\", \"param_enzyme_name\": \"\\\"Trypsin/P\\\"\", \"param_enzyme_specificity\": \"\\\"none\\\"\", \"param_decoy_string\": \"\\\"dec_\\\"\", \"__rerun_remap_job_id__\": null, \"param_write_protein_description\": \"\\\"true\\\"\", \"param_full_tolerant_search\": \"\\\"false\\\"\", \"param_fasta\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_aaa_max\": \"\\\"4\\\"\", \"param_annotate_proteins\": \"\\\"True\\\"\", \"param_IL_equivalent\": \"\\\"false\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "2.1.0",
                         "type": "tool",
-                        "uuid": "24029aca-9eb6-423a-9474-b05961073a01",
+                        "uuid": "868442d2-bb81-4d9a-b783-448377dce6d7",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "19884cc2-1a3c-4f84-ab1d-192c8238ecd1"
+                                "output_name": "param_out",
+                                "uuid": "f026ce76-91ea-40df-99bb-00ae4bacf3f6"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.6+galaxy0",
-                        "errors": null,
-                        "id": 17,
+                        "content_id": "IDFilter",
+                        "id": 14,
                         "input_connections": {
-                            "in": {
-                                "id": 14,
-                                "output_name": "out"
+                            "param_in": {
+                                "id": 13,
+                                "output_name": "param_out"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool IDFilter",
+                                "name": "param_whitelist_peptides"
+                            },
+                            {
+                                "description": "runtime parameter for tool IDFilter",
+                                "name": "param_whitelist_proteins"
+                            },
+                            {
+                                "description": "runtime parameter for tool IDFilter",
+                                "name": "param_blacklist_proteins"
+                            },
+                            {
+                                "description": "runtime parameter for tool IDFilter",
+                                "name": "param_in"
+                            },
+                            {
+                                "description": "runtime parameter for tool IDFilter",
+                                "name": "param_blacklist_peptides"
+                            }
+                        ],
                         "label": null,
-                        "name": "IDConflictResolver",
+                        "name": "IDFilter",
                         "outputs": [
                             {
-                                "name": "out",
-                                "type": "input"
+                                "name": "param_out",
+                                "type": "idxml"
                             }
                         ],
                         "position": {
-                            "bottom": 666.3999938964844,
-                            "height": 154.39999389648438,
-                            "left": 387,
-                            "right": 587,
-                            "top": 512,
-                            "width": 200,
-                            "x": 387,
-                            "y": 512
+                            "left": 1647.9666748046875,
+                            "top": 808.88330078125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.6+galaxy0",
+                        "tool_errors": null,
+                        "tool_id": "IDFilter",
                         "tool_shed_repository": {
-                            "changeset_revision": "fb0e6f70a1df",
-                            "name": "openms_idconflictresolver",
+                            "changeset_revision": "c427a8628cbe",
+                            "name": "openms_idfilter",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"resolve_between_features\": \"off\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"param_whitelist_peptides\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_length\": \"\\\":\\\"\", \"param_keep_unreferenced_protein_hits\": \"\\\"false\\\"\", \"param_unique\": \"\\\"false\\\"\", \"param_whitelist_proteins\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_unique_per_protein\": \"\\\"false\\\"\", \"param_remove_decoys\": \"\\\"false\\\"\", \"param_score_prot\": \"\\\"0.0\\\"\", \"param_rt_p_value_1st_dim\": \"\\\"0.0\\\"\", \"param_best_n_protein_hits\": \"\\\"0\\\"\", \"param_min_length\": \"\\\"0\\\"\", \"__rerun_remap_job_id__\": null, \"param_precursor_mz\": \"\\\":\\\"\", \"param_mz_error\": \"\\\"-1.0\\\"\", \"rep_param_blacklist_modifications\": \"[]\", \"param_precursor_allow_missing\": \"\\\"false\\\"\", \"param_blacklist_proteins\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_delete_unreferenced_peptide_hits\": \"\\\"false\\\"\", \"param_precursor_rt\": \"\\\":\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0, \"param_charge\": \"\\\":\\\"\", \"param_var_mods\": \"\\\"false\\\"\", \"param_max_length\": \"\\\"0\\\"\", \"param_best_strict\": \"\\\"false\\\"\", \"rep_param_whitelist_protein_accessions\": \"[]\", \"rep_param_whitelist_modifications\": \"[]\", \"param_thresh_pep\": \"\\\"0.0\\\"\", \"param_mz_unit\": \"\\\"ppm\\\"\", \"param_best_n_peptide_hits\": \"\\\"0\\\"\", \"param_whitelist_by_seq_only\": \"\\\"false\\\"\", \"param_blacklist_peptides\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"param_score_pep\": \"\\\"0.05\\\"\", \"param_rt_p_value\": \"\\\"0.0\\\"\", \"param_min_charge\": \"\\\"1\\\"\", \"param_blacklist_ignore_modifications\": \"\\\"false\\\"\", \"rep_param_blacklist_protein_accessions\": \"[]\", \"param_whitelist_ignore_modifications\": \"\\\"false\\\"\", \"param_thresh_prot\": \"\\\"0.0\\\"\"}",
+                        "tool_version": "2.1.0",
                         "type": "tool",
-                        "uuid": "29e2c398-4df7-40c8-8fa7-b03eaeb86eb7",
+                        "uuid": "458f5b98-62dd-4650-86dc-f3fc3da4584e",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "b261502d-5f97-4263-b79e-575000d63c07"
+                                "output_name": "param_out",
+                                "uuid": "ac38c879-b0a6-4260-a659-32bc6f531232"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_multiplexresolver/MultiplexResolver/2.5+galaxy0",
-                        "errors": null,
-                        "id": 18,
+                        "content_id": "IDMapper",
+                        "id": 15,
                         "input_connections": {
-                            "in": {
-                                "id": 17,
-                                "output_name": "out"
+                            "param_id": {
+                                "id": 14,
+                                "output_name": "param_out"
+                            },
+                            "param_in": {
+                                "id": 2,
+                                "output_name": "param_out"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool IDMapper",
+                                "name": "param_id"
+                            },
+                            {
+                                "description": "runtime parameter for tool IDMapper",
+                                "name": "param_in"
+                            }
+                        ],
                         "label": null,
-                        "name": "MultiplexResolver",
+                        "name": "IDMapper",
                         "outputs": [
                             {
-                                "name": "out",
-                                "type": "consensusxml"
+                                "name": "param_out",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 538.3999938964844,
-                            "height": 266.3999938964844,
-                            "left": 607,
-                            "right": 807,
-                            "top": 272,
-                            "width": 200,
-                            "x": 607,
-                            "y": 272
+                            "left": 1979.9666748046875,
+                            "top": 843.88330078125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_multiplexresolver/MultiplexResolver/2.5+galaxy0",
+                        "tool_errors": null,
+                        "tool_id": "IDMapper",
                         "tool_shed_repository": {
-                            "changeset_revision": "fb647b7cf2c1",
-                            "name": "openms_multiplexresolver",
+                            "changeset_revision": "b5d0905419da",
+                            "name": "openms_idmapper",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"algorithm\": {\"labels\": \"[ ][Arg6,Lys6]\", \"missed_cleavages\": \"1\", \"mass_tolerance\": \"0.1\", \"mz_tolerance\": \"10\", \"rt_tolerance\": \"5\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"in_blacklist\": null, \"labels\": {\"Arg6\": \"6.0201290268\", \"Arg10\": \"10.0082686\", \"Lys4\": \"4.0251069836\", \"Lys6\": \"6.0201290268\", \"Lys8\": \"8.0141988132\", \"Leu3\": \"3.01883\", \"Dimethyl0\": \"28.0313\", \"Dimethyl4\": \"32.056407\", \"Dimethyl6\": \"34.063117\", \"Dimethyl8\": \"36.07567\", \"ICPL0\": \"105.021464\", \"ICPL4\": \"109.046571\", \"ICPL6\": \"111.041593\", \"ICPL10\": \"115.0667\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.5+galaxy0",
+                        "tool_state": "{\"param_mz_tolerance\": \"\\\"30.0\\\"\", \"param_ignore_charge\": \"\\\"true\\\"\", \"param_feature_use_centroid_rt\": \"\\\"false\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"param_mz_measure\": \"\\\"ppm\\\"\", \"param_mz_reference\": \"\\\"precursor\\\"\", \"param_id\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_rt_tolerance\": \"\\\"50.0\\\"\", \"param_consensus_use_subelements\": \"\\\"true\\\"\", \"param_feature_use_centroid_mz\": \"\\\"false\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "2.1.0",
                         "type": "tool",
-                        "uuid": "c8cead64-a291-4bbc-b400-df3b0c87cb05",
+                        "uuid": "f199e8c6-c243-4fce-8dac-a62d504c9cdd",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "2d191fe3-d682-4bc1-ac64-f5a5a2cdc04a"
+                                "output_name": "param_out",
+                                "uuid": "84923098-0cc0-4c3b-ac19-aa12ef6a5244"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.6+galaxy0",
-                        "errors": null,
-                        "id": 19,
+                        "content_id": "IDConflictResolver",
+                        "id": 16,
                         "input_connections": {
-                            "in": {
-                                "id": 18,
-                                "output_name": "out"
-                            },
-                            "protein_groups": {
-                                "id": 11,
-                                "output_name": "out"
+                            "param_in": {
+                                "id": 15,
+                                "output_name": "param_out"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool IDConflictResolver",
+                                "name": "param_in"
+                            }
+                        ],
                         "label": null,
-                        "name": "ProteinQuantifier",
+                        "name": "IDConflictResolver",
                         "outputs": [
                             {
-                                "name": "out",
-                                "type": "csv"
-                            },
-                            {
-                                "name": "peptide_out",
-                                "type": "csv"
+                                "name": "param_out",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 619.6000061035156,
-                            "height": 347.6000061035156,
-                            "left": 827,
-                            "right": 1027,
-                            "top": 272,
-                            "width": 200,
-                            "x": 827,
-                            "y": 272
+                            "left": 2220.449951171875,
+                            "top": 881.88330078125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.6+galaxy0",
+                        "tool_errors": null,
+                        "tool_id": "IDConflictResolver",
                         "tool_shed_repository": {
-                            "changeset_revision": "bb1e75938909",
-                            "name": "openms_proteinquantifier",
+                            "changeset_revision": "8a04ed1c1d1b",
+                            "name": "openms_idconflictresolver",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": [\"out_FLAG\", \"peptide_out_FLAG\"], \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"average\": \"sum\", \"best_charge_and_fraction\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"consensus\": {\"normalize\": \"false\", \"fix_peptides\": \"false\"}, \"design\": null, \"format\": {\"separator\": \"\", \"quoting\": \"double\", \"replacement\": \"_\"}, \"greedy_group_resolution\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"include_all\": \"false\", \"protein_groups\": {\"__class__\": \"ConnectedValue\"}, \"ratios\": \"true\", \"ratiosSILAC\": \"false\", \"top\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"adv_opts\": \"{\\\"param_force\\\": \\\"false\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "2.1.0",
                         "type": "tool",
-                        "uuid": "f45eb629-cead-420b-b277-a1d9dd781c70",
+                        "uuid": "6f4dc17d-b0fd-4b66-9487-3fda71316199",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "69c464ef-cf41-4bd2-b8ea-e10560b8d6fd"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "peptide_out",
-                                "uuid": "a9eeea33-4858-402a-a526-4ce950474f6f"
+                                "output_name": "param_out",
+                                "uuid": "485d4684-835d-4ff0-9ca5-3400a0b8fa22"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Summary_Statistics1",
-                        "errors": null,
-                        "id": 20,
+                        "content_id": "FileFilter",
+                        "id": 17,
                         "input_connections": {
-                            "input": {
-                                "id": 19,
-                                "output_name": "out"
+                            "param_in": {
+                                "id": 16,
+                                "output_name": "param_out"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool FileFilter",
+                                "name": "param_in"
+                            },
+                            {
+                                "description": "runtime parameter for tool FileFilter",
+                                "name": "param_id_blacklist"
+                            },
+                            {
+                                "description": "runtime parameter for tool FileFilter",
+                                "name": "param_consensus_blackorwhitelist_file"
+                            }
+                        ],
                         "label": null,
-                        "name": "Summary Statistics",
+                        "name": "FileFilter",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "tabular"
+                                "name": "param_out",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 385.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": 1047,
-                            "right": 1247,
-                            "top": 272,
-                            "width": 200,
-                            "x": 1047,
-                            "y": 272
+                            "left": 2531,
+                            "top": 786.88330078125
                         },
                         "post_job_actions": {},
-                        "tool_id": "Summary_Statistics1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c8\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.2",
+                        "tool_errors": null,
+                        "tool_id": "FileFilter",
+                        "tool_shed_repository": {
+                            "changeset_revision": "d6878d27f051",
+                            "name": "openms_filefilter",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"rep_param_id_sequences_whitelist\": \"[]\", \"param_algorithm_SignalToNoise_win_len\": \"\\\"200.0\\\"\", \"param_algorithm_SignalToNoise_bin_count\": \"\\\"30\\\"\", \"param_peak_options_sn\": \"\\\"0.0\\\"\", \"param_id_mz\": \"\\\"0.001\\\"\", \"param_spectra_select_polarity\": \"null\", \"param_spectra_remove_collision_energy\": \"\\\":\\\"\", \"param_id_blacklist_imperfect\": \"\\\"false\\\"\", \"param_mz\": \"\\\":\\\"\", \"param_int\": \"\\\":\\\"\", \"param_spectra_select_isolation_window_width\": \"\\\":\\\"\", \"param_peak_options_indexed_file\": \"\\\"false\\\"\", \"param_spectra_select_activation\": \"null\", \"param_id_remove_annotated_features\": \"\\\"false\\\"\", \"__page__\": 0, \"param_peak_options_no_chromatograms\": \"\\\"false\\\"\", \"rep_param_peak_options_pc_mz_list\": \"[]\", \"param_peak_options_numpress_masstime\": \"\\\"none\\\"\", \"param_peak_options_remove_chromatograms\": \"\\\"false\\\"\", \"rep_param_consensus_map\": \"[]\", \"param_peak_options_numpress_intensity\": \"\\\"none\\\"\", \"param_pc_mz\": \"\\\":\\\"\", \"__rerun_remap_job_id__\": null, \"param_spectra_select_mode\": \"null\", \"param_rt\": \"\\\":\\\"\", \"param_algorithm_SignalToNoise_write_log_messages\": \"\\\"true\\\"\", \"param_consensus_blackorwhitelist_use_ppm_tolerance\": \"\\\"false\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_id_remove_unannotated_features\": \"\\\"true\\\"\", \"param_peak_options_sort_peaks\": \"\\\"false\\\"\", \"param_peak_options_int_precision\": \"\\\"32\\\"\", \"rep_param_id_accessions_whitelist\": \"[]\", \"param_peak_options_pc_mz_range\": \"\\\":\\\"\", \"param_out_type\": \"\\\"consensusXML\\\"\", \"param_spectra_remove_mode\": \"null\", \"param_consensus_blackorwhitelist_blacklist\": \"\\\"true\\\"\", \"rep_param_peak_options_level\": \"[{\\\"__index__\\\": 0, \\\"param_peak_options_level\\\": \\\"1 2 3\\\"}]\", \"rep_param_f_and_c_remove_meta\": \"[]\", \"param_f_and_c_size\": \"\\\":\\\"\", \"param_id_remove_unassigned_ids\": \"\\\"true\\\"\", \"param_spectra_remove_zoom\": \"\\\"false\\\"\", \"param_peak_options_mz_precision\": \"\\\"64\\\"\", \"param_sort\": \"\\\"false\\\"\", \"param_algorithm_SignalToNoise_min_required_elements\": \"\\\"10\\\"\", \"param_consensus_blackorwhitelist_rt\": \"\\\"60.0\\\"\", \"rep_param_peak_options_rm_pc_charge\": \"[]\", \"param_peak_options_numpress_intensity_error\": \"\\\"0.0001\\\"\", \"param_id_rt\": \"\\\"0.1\\\"\", \"param_id_keep_best_score_id\": \"\\\"false\\\"\", \"param_id_blacklist\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_spectra_select_collision_energy\": \"\\\":\\\"\", \"param_feature_q\": \"\\\":\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"param_f_and_c_charge\": \"\\\":\\\"\", \"param_consensus_map_and\": \"\\\"false\\\"\", \"param_spectra_select_zoom\": \"\\\"false\\\"\", \"param_consensus_blackorwhitelist_mz\": \"\\\"0.01\\\"\", \"param_consensus_blackorwhitelist_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"rep_param_consensus_blackorwhitelist_maps\": \"[]\", \"param_spectra_remove_activation\": \"null\", \"param_peak_options_numpress_masstime_error\": \"\\\"0.0001\\\"\", \"param_spectra_remove_isolation_window_width\": \"\\\":\\\"\"}",
+                        "tool_version": "2.1.0",
                         "type": "tool",
-                        "uuid": "2271282e-d599-4d40-9b0c-42adb142874f",
+                        "uuid": "77e6a295-f6e2-4d72-a7e3-94f682d916a7",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "ed52356c-4179-444a-9761-f7c0edf4c642"
+                                "output_name": "param_out",
+                                "uuid": "55dc6d2b-f473-4496-abaf-86630ad0151b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
-                        "errors": null,
-                        "id": 21,
+                        "content_id": "FileMerger",
+                        "id": 18,
                         "input_connections": {
-                            "infile": {
-                                "id": 19,
-                                "output_name": "out"
+                            "param_in": {
+                                "id": 17,
+                                "output_name": "param_out"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool FileMerger",
+                                "name": "param_in"
+                            }
+                        ],
                         "label": null,
-                        "name": "Select last",
+                        "name": "FileMerger",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "input"
+                                "name": "param_out",
+                                "type": "featurexml"
+                            },
+                            {
+                                "name": "param_rt_concat_trafo_out",
+                                "type": "trafoxml"
                             }
                         ],
                         "position": {
-                            "bottom": 485.1999969482422,
-                            "height": 93.19999694824219,
-                            "left": 1047,
-                            "right": 1247,
-                            "top": 392,
-                            "width": 200,
-                            "x": 1047,
-                            "y": 392
+                            "left": 2832.966552734375,
+                            "top": 1062.9000244140625
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
+                        "tool_errors": null,
+                        "tool_id": "FileMerger",
                         "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "39e8fde08881",
+                            "name": "openms_filemerger",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"csv\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"complement\": \"+\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"num_lines\": \"4\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.0",
+                        "tool_state": "{\"param_raw_user_ms_level\": \"\\\"False\\\"\", \"param_raw_rt_auto\": \"\\\"false\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"param_raw_rt_filename\": \"\\\"false\\\"\", \"param_rt_concat_gap\": \"\\\"0.0\\\"\", \"param_annotate_file_origin\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"param_raw_ms_level\": \"\\\"2\\\"\", \"rep_param_raw_rt_custom\": \"[]\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "2.1.0",
                         "type": "tool",
-                        "uuid": "522bc5dc-d39a-4448-b887-848bb5cf5c55",
+                        "uuid": "d82505c8-6f1c-43a9-a9c7-c572ad2aa3c8",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "52919249-1fb8-4481-95fc-ba6c40d4399c"
+                                "output_name": "param_out",
+                                "uuid": "db9ffdb1-ef2f-4d53-9808-bef6de3d85b4"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "param_rt_concat_trafo_out",
+                                "uuid": "47af80c0-5efb-43b3-a830-c3df9fc0528d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
-                        "errors": null,
-                        "id": 22,
+                        "content_id": "MzTabExporter",
+                        "id": 19,
                         "input_connections": {
-                            "input": {
-                                "id": 21,
-                                "output_name": "outfile"
+                            "param_in": {
+                                "id": 18,
+                                "output_name": "param_out"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool MzTabExporter",
+                                "name": "param_in"
+                            }
+                        ],
                         "label": null,
-                        "name": "Histogram",
+                        "name": "MzTabExporter",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "pdf"
+                                "name": "param_out",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 365.1999969482422,
-                            "height": 93.19999694824219,
-                            "left": 1267,
-                            "right": 1467,
-                            "top": 272,
-                            "width": 200,
-                            "x": 1267,
-                            "y": 272
+                            "left": 3076.5,
+                            "top": 1061.88330078125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
+                        "tool_errors": null,
+                        "tool_id": "MzTabExporter",
                         "tool_shed_repository": {
-                            "changeset_revision": "6f134426c2b0",
-                            "name": "histogram",
-                            "owner": "devteam",
+                            "changeset_revision": "bf32e0bcf554",
+                            "name": "openms_mztabexporter",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"breaks\": \"20\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"density\": \"true\", \"frequency\": \"false\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"numerical_column\": \"8\", \"title\": \"Histogram\", \"xlab\": \"V1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.4",
+                        "tool_state": "{\"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "2.1.0",
                         "type": "tool",
-                        "uuid": "67a0985f-236d-4b84-a51e-86c4cbf657b4",
+                        "uuid": "3f6cb69e-8629-4fea-ab74-dec388ed0fd4",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "11f0da6d-4f57-487a-ae21-042b1d8badf6"
+                                "output_name": "param_out",
+                                "uuid": "a6361de3-6865-4c6b-9920-d7a8c6a27645"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/protein-quant-sil",
-                "path": "topics/proteomics/tutorials/protein-quant-sil/workflows/workflow.ga",
+                "parent_id": "proteomics/ntails",
+                "path": "topics/proteomics/tutorials/ntails/workflows/WF_ntails.ga",
                 "tags": [
                     "proteomics"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "Proteomics: Peptide and Protein Quantification via stable istobe labeling",
+                "tests": false,
+                "title": "Tails Triple Dimethyl OpenMS2.1",
                 "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-protein-quant-sil/versions/workflow",
-                "tutorial_id": "protein-quant-sil",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/protein-quant-sil/workflows/workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/protein-quant-sil/workflows/workflow.html",
-                "version": 7,
-                "wfid": "proteomics-protein-quant-sil",
-                "wfname": "workflow",
-                "workflow": "workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-ntails/versions/wf-ntails",
+                "tutorial_id": "ntails",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/ntails/workflows/WF_ntails.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/ntails/workflows/WF_ntails.html",
+                "version": 4,
+                "wfid": "proteomics-ntails",
+                "wfname": "wf-ntails",
+                "workflow": "WF_ntails.ga",
                 "workflow_tools": [
-                    "Grep1",
-                    "Summary_Statistics1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_multiplexresolver/MultiplexResolver/2.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0"
+                    "ConsensusID",
+                    "FalseDiscoveryRate",
+                    "FeatureFinderMultiplex",
+                    "FileFilter",
+                    "FileMerger",
+                    "HighResPrecursorMassCorrector",
+                    "IDConflictResolver",
+                    "IDFilter",
+                    "IDMapper",
+                    "IDMerger",
+                    "MSGFPlusAdapter",
+                    "MzTabExporter",
+                    "PeptideIndexer"
                 ],
-                "workflowhub_id": "1215"
+                "workflowhub_id": "1213"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/1051552"
+        "zenodo_link": ""
     },
     {
         "admin_install": {
@@ -200127,27 +201686,44 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "maxquant",
+                    "name": "tabular_to_fasta",
+                    "owner": "devteam",
+                    "revisions": "0a7799698fe5",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mz_to_sqlite",
                     "owner": "galaxyp",
-                    "revisions": "1f39c833f65f",
+                    "revisions": "f5c632894818",
+                    "tool_panel_section_label": "Convert Formats",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "peptideshaker",
+                    "owner": "galaxyp",
+                    "revisions": "7fdd9119cc4f",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "peptideshaker",
+                    "owner": "galaxyp",
+                    "revisions": "7fdd9119cc4f",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "query_tabular",
+                    "owner": "iuc",
+                    "revisions": "33d61c89fb8d",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: maxquant\n  owner: galaxyp\n  revisions: 1f39c833f65f\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "subinamehta",
-                "katherine-d21",
-                "dechendb"
-            ],
-            "editing": [
-                "pratikdjagtap",
-                "timothygriffin"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: tabular_to_fasta\n  owner: devteam\n  revisions: 0a7799698fe5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mz_to_sqlite\n  owner: galaxyp\n  revisions: f5c632894818\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 7fdd9119cc4f\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 7fdd9119cc4f\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n  owner: iuc\n  revisions: 33d61c89fb8d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.json",
         "contributors": [
             {
                 "email": "subinamehta@gmail.com",
@@ -200162,18 +201738,14 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
             },
             {
-                "id": "katherine-d21",
-                "joined": "2023-08",
-                "name": "Katherine Do",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/katherine-d21/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/katherine-d21.json"
-            },
-            {
-                "id": "dechendb",
-                "joined": "2023-06",
-                "name": "Dechen Bhuming",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dechendb/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/dechendb.json"
+                "email": "tgriffin@umn.edu",
+                "github": false,
+                "id": "timothygriffin",
+                "joined": "2017-09",
+                "name": "Timothy J. Griffin",
+                "orcid": "0000-0001-6801-2559",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
             },
             {
                 "email": "pjagtap@umn.edu",
@@ -200185,30 +201757,40 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
             },
             {
-                "email": "tgriffin@umn.edu",
-                "github": false,
-                "id": "timothygriffin",
+                "email": "rsajulga@umn.edu",
+                "id": "jraysajulga",
+                "joined": "2018-11",
+                "name": "Ray Sajulga",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jraysajulga/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jraysajulga.json"
+            },
+            {
+                "email": "jj@umn.edu",
+                "id": "jj-umn",
+                "in_memoriam": "<a href=\"https://galaxyproject.org/news/2024-03-19-remembrances-of-jj/\">James \u2018JJ\u2019 Johnson, was a Galaxy community rock star most known for his indispensable contributions to the Galaxy Proteomics community.</a>\n\nJJ\u2019s works will live on in so many Galaxy tools and workflows for years to come.",
                 "joined": "2017-09",
-                "name": "Timothy J. Griffin",
-                "orcid": "0000-0001-6801-2559",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
+                "name": "James Johnson",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jj-umn/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jj-umn.json"
+            },
+            {
+                "email": "kumar207@umn.edu",
+                "id": "pravs3683",
+                "joined": "2019-04",
+                "name": "Praveen Kumar",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pravs3683/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pravs3683.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/clinical-mp-4-quantitation",
+        "dir": "topics/proteomics/tutorials/proteogenomics-dbsearch",
         "edam_operation": [
-            "Visualisation",
-            "Imputation",
-            "Heat map generation",
-            "Standardisation and normalisation",
-            "Principal component plotting",
-            "Protein quantification",
-            "Clustering",
-            "Statistical calculation"
+            "Conversion",
+            "Peptide database search"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu",
+            "UseGalaxy.no",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
@@ -200218,572 +201800,72 @@
             {
                 "topic_name": "proteomics",
                 "tutorials": [
-                    "clinical-mp-5-data-interpretation"
-                ],
-                "type": "internal"
-            }
-        ],
-        "hands_on": true,
-        "id": "proteomics/clinical-mp-4-quantitation",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.no"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Quantified Microbial and Human peptides/proteins can be analyzed separately so that the results are more comparative."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-08-08",
-        "objectives": [
-            "Perform quantitation using MaxQuant and extract microbial and human proteins and peptides."
-        ],
-        "pageviews": 66,
-        "pub_date": "2024-02-06",
-        "questions": [
-            "How to perform quantitation?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "katherine-d21"
-                ],
-                "date": "2024-06-21",
-                "galaxy_version": "23.1",
-                "length": "8M",
-                "speakers": [
-                    "katherine-d21"
-                ],
-                "youtube_id": "_e0l1AtfZ4Y"
-            }
-        ],
-        "redirect_from": [
-            "/topics/proteomics/tutorials/clinical-mp-quantitation/tutorial",
-            "/short/proteomics/clinical-mp-4-quantitation",
-            "/short/T00416"
-        ],
-        "requirements": [
-            {
-                "topic_name": "proteomics",
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00416",
-        "short_tools": [
-            "Grep1",
-            "Cut1",
-            "Grouping1",
-            "maxquant"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "clinical-metaproteomics",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "label-TMT11"
-        ],
-        "time_estimation": "3H",
-        "title": "Clinical Metaproteomics 4: Quantitation",
-        "tools": [
-            "Cut1",
-            "Grep1",
-            "Grouping1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.17.0+galaxy4"
-        ],
-        "topic_name": "proteomics",
-        "topic_name_human": "Proteomics",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "clinical-mp-4-quantitation",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-4-quantitation/tutorial.json"
-        },
-        "version": 2,
-        "video": false,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 331,
-        "visitors": 40,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Organization",
-                        "identifier": "0000-0001-9818-0537",
-                        "name": "Subina Mehta"
-                    }
-                ],
-                "description": "Quantification using the MaxQuant tool",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nQuantitation_Database-For-MaxQuant\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nExperimental-Design Discovery MaxQuant\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Raw-files\"]\n  3[label=\"MaxQuant\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Select\"]\n  3 -> 4 [label=\"proteinGroups\"]\n  5[label=\"Select\"]\n  3 -> 5 [label=\"peptides\"]\n  6[label=\"Cut\"]\n  4 -> 6 [label=\"out_file1\"]\n  7[label=\"Cut\"]\n  5 -> 7 [label=\"out_file1\"]\n  8[label=\"Group\"]\n  6 -> 8 [label=\"out_file1\"]\n  9[label=\"Group\"]\n  7 -> 9 [label=\"out_file1\"]\n}",
-                "history": [
-                    {
-                        "hash": "40391e78410baebc3f2ffd02ffbd1a3642903251",
-                        "message": "add missing metadata",
-                        "num": 2,
-                        "short_hash": "40391e784",
-                        "unix": "1723120010"
-                    },
-                    {
-                        "hash": "e0464fd1787b4ca7dea72ca77b7ab2ad03a8292a",
-                        "message": "add workflows",
-                        "num": 1,
-                        "short_hash": "e0464fd17",
-                        "unix": "1723118192"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Quantitation_Database-For-MaxQuant"
-                            }
-                        ],
-                        "label": "Quantitation_Database-For-MaxQuant",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0.0,
-                            "top": 0.0
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "c2311b55-b0c7-4237-bed1-4b25bf1a1655",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Experimental-Design Discovery MaxQuant"
-                            }
-                        ],
-                        "label": "Experimental-Design Discovery MaxQuant",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 69.76104736328125,
-                            "top": 268.9728088378906
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "d957f00d-79a9-4e2e-8e15-088444ca5605",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Input Raw-files"
-                            }
-                        ],
-                        "label": "Input Raw-files",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 41.42888775537051,
-                            "top": 531.8779602050781
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "2864b493-6d12-4313-ad29-f3b1e2564aba",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQuantitation_Database-For-MaxQuant\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nExperimental-Design Discovery MaxQuant\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nInput Raw-files\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"MaxQuant\"];\n  0 -->|output| 3;\n  2 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Select\"];\n  3 -->|proteinGroups| 4;\n  5[\"Select\"];\n  3 -->|peptides| 5;\n  6[\"Cut\"];\n  4 -->|out_file1| 6;\n  7[\"Cut\"];\n  5 -->|out_file1| 7;\n  8[\"Group\"];\n  6 -->|out_file1| 8;\n  9[\"Group\"];\n  7 -->|out_file1| 9;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "WF4_Quantitation_Workflow",
-                "outputs": [],
-                "parent_id": "proteomics/clinical-mp-4-quantitation",
-                "path": "topics/proteomics/tutorials/clinical-mp-4-quantitation/workflows/WF4_Quantitation_Workflow.ga",
-                "tags": [
-                    "name:clinicalMP"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "WF4_Quantitation_Workflow",
-                "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-clinical-mp-4-quantitation/versions/wf4-quantitation-workflow",
-                "tutorial_id": "clinical-mp-4-quantitation",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-4-quantitation/workflows/WF4_Quantitation_Workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-4-quantitation/workflows/WF4_Quantitation_Workflow.html",
-                "version": 1,
-                "wfid": "proteomics-clinical-mp-4-quantitation",
-                "wfname": "wf4-quantitation-workflow",
-                "workflow": "WF4_Quantitation_Workflow.ga",
-                "workflow_tools": [
-                    "Cut1",
-                    "Grep1",
-                    "Grouping1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.17.0+galaxy4"
-                ],
-                "workflowhub_id": "1353"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.10105821"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "msconvert",
-                    "owner": "galaxyp",
-                    "revisions": "3cf310697624",
-                    "tool_panel_section_label": "Convert Formats",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_consensusid",
-                    "owner": "galaxyp",
-                    "revisions": "4e77b8f12cd3",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_falsediscoveryrate",
-                    "owner": "galaxyp",
-                    "revisions": "f7fef900f5b2",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_falsediscoveryrate",
-                    "owner": "galaxyp",
-                    "revisions": "c9eff69a7c62",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_fidoadapter",
-                    "owner": "galaxyp",
-                    "revisions": "890025d6e426",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_fidoadapter",
-                    "owner": "galaxyp",
-                    "revisions": "658494a2cb00",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_fileinfo",
-                    "owner": "galaxyp",
-                    "revisions": "5ad830edc021",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_fileinfo",
-                    "owner": "galaxyp",
-                    "revisions": "52ba9695e752",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_idfilter",
-                    "owner": "galaxyp",
-                    "revisions": "382cde407f81",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_idmerger",
-                    "owner": "galaxyp",
-                    "revisions": "1c5f31b8d632",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_idposteriorerrorprobability",
-                    "owner": "galaxyp",
-                    "revisions": "c69f69d7867a",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_idposteriorerrorprobability",
-                    "owner": "galaxyp",
-                    "revisions": "111c3a00136d",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_idscoreswitcher",
-                    "owner": "galaxyp",
-                    "revisions": "476b5e296979",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_idscoreswitcher",
-                    "owner": "galaxyp",
-                    "revisions": "be74a8cd7d66",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_msgfplusadapter",
-                    "owner": "galaxyp",
-                    "revisions": "a407b6790342",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_peakpickerhires",
-                    "owner": "galaxyp",
-                    "revisions": "3d8d4ada5405",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_peptideindexer",
-                    "owner": "galaxyp",
-                    "revisions": "e039cc5c7aed",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_peptideindexer",
-                    "owner": "galaxyp",
-                    "revisions": "dd173849c3d8",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_textexporter",
-                    "owner": "galaxyp",
-                    "revisions": "9020199dba0a",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_xtandemadapter",
-                    "owner": "galaxyp",
-                    "revisions": "c8b225c69a7f",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "openms_xtandemadapter",
-                    "owner": "galaxyp",
-                    "revisions": "7f6a1f27553e",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: msconvert\n  owner: galaxyp\n  revisions: 3cf310697624\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_consensusid\n  owner: galaxyp\n  revisions: 4e77b8f12cd3\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_falsediscoveryrate\n  owner: galaxyp\n  revisions: f7fef900f5b2\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_falsediscoveryrate\n  owner: galaxyp\n  revisions: c9eff69a7c62\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_fidoadapter\n  owner: galaxyp\n  revisions: 890025d6e426\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_fidoadapter\n  owner: galaxyp\n  revisions: 658494a2cb00\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_fileinfo\n  owner: galaxyp\n  revisions: 5ad830edc021\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_fileinfo\n  owner: galaxyp\n  revisions: 52ba9695e752\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idfilter\n  owner: galaxyp\n  revisions: 382cde407f81\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idmerger\n  owner: galaxyp\n  revisions: 1c5f31b8d632\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idposteriorerrorprobability\n  owner: galaxyp\n  revisions: c69f69d7867a\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idposteriorerrorprobability\n  owner: galaxyp\n  revisions: 111c3a00136d\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idscoreswitcher\n  owner: galaxyp\n  revisions: 476b5e296979\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idscoreswitcher\n  owner: galaxyp\n  revisions: be74a8cd7d66\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_msgfplusadapter\n  owner: galaxyp\n  revisions: a407b6790342\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_peakpickerhires\n  owner: galaxyp\n  revisions: 3d8d4ada5405\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_peptideindexer\n  owner: galaxyp\n  revisions: e039cc5c7aed\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_peptideindexer\n  owner: galaxyp\n  revisions: dd173849c3d8\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_textexporter\n  owner: galaxyp\n  revisions: 9020199dba0a\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_xtandemadapter\n  owner: galaxyp\n  revisions: c8b225c69a7f\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_xtandemadapter\n  owner: galaxyp\n  revisions: 7f6a1f27553e\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/protein-id-oms/tutorial.json",
-        "contributors": [
-            {
-                "email": "sigloch+github@mailbox.org",
-                "former_affiliations": [
-                    "uni-freiburg"
-                ],
-                "id": "stortebecker",
-                "joined": "2017-09",
-                "name": "Florian Christoph Sigloch",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stortebecker/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/stortebecker.json"
-            },
-            {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
-                "fediverse_flavor": "mastodon",
-                "id": "bgruening",
-                "joined": "2017-09",
-                "linkedin": "bgruening",
-                "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
-                },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
-            }
-        ],
-        "dir": "topics/proteomics/tutorials/protein-id-oms",
-        "edam_operation": [
-            "Filtering",
-            "Formatting"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "proteomics",
-                "tutorials": [
-                    "protein-quant-sil"
+                    "proteogenomics-novel-peptide-analysis"
                 ],
                 "type": "internal"
             }
         ],
         "hands_on": true,
-        "id": "proteomics/protein-id-oms",
+        "id": "proteomics/proteogenomics-dbsearch",
         "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
+            "UseGalaxy.be",
+            "UseGalaxy.cz"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "LC-MS/MS raw files have to be converted to mzML before using GalaxyP on most GalaxyP servers.",
-            "OpenMS provides many tools for proteomic analysis and guarantees compatibility by using open file formats.",
-            "OpenMS provides several thirdparty search engines and Fido for protein inference."
+            "With SearchGUI and PeptideShaker you can gain access to multiple search engines"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Advanced",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-08-09",
         "objectives": [
-            "Protein identification from LC-MS/MS raw files."
+            "A proteogenomic data analysis of mass spectrometry data to identify and visualize variant peptides."
         ],
-        "pageviews": 4651,
-        "pub_date": "2017-10-16",
+        "pageviews": 1926,
+        "pub_date": "2018-11-20",
         "questions": [
-            "How to convert LC-MS/MS raw files?",
-            "How to identify peptides?",
-            "How to identify proteins?",
-            "How to evaluate the results?"
+            "How to identify variant proteoforms in MS data by searching with the customized Protein database?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "emmaleith"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "30M",
+                "speakers": [
+                    "andrewr"
+                ],
+                "youtube_id": "q1OjmTcbvBA"
+            }
         ],
         "requirements": [
             {
                 "topic_name": "proteomics",
                 "tutorials": [
-                    "database-handling"
+                    "proteogenomics-dbcreation"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00228",
+        "short_id": "T00232",
         "short_tools": [
-            "Grep1",
-            "msconvert",
-            "IDMerger",
-            "IDPosteriorErrorProbability",
-            "PeakPickerHiRes",
-            "FidoAdapter",
-            "FalseDiscoveryRate",
-            "MSGFPlusAdapter",
-            "TextExporter",
-            "IDScoreSwitcher",
-            "ConsensusID",
-            "IDFilter",
-            "FileInfo",
-            "XTandemAdapter",
-            "PeptideIndexer"
+            "query_tabular",
+            "peptide_shaker",
+            "tab2fasta",
+            "search_gui",
+            "mz_to_sqlite"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "id-quant",
+        "subtopic": "multi-omics",
         "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
+            "exact": [
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
@@ -200794,44 +201876,42 @@
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
                 }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
             ]
         },
         "symlink": null,
         "tags": [
-            "DDA",
-            "HeLa"
+            "proteogenomics"
         ],
-        "time_estimation": "45m",
-        "title": "Peptide and Protein ID using OpenMS tools",
+        "time_estimation": "15m",
+        "title": "Proteogenomics 2: Database Search",
         "tools": [
-            "Grep1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_consensusid/ConsensusID/2.2.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.2.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.2.0.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.2.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmerger/IDMerger/2.2.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.2.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.2.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/2.2.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerhires/PeakPickerHiRes/2.3.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.2.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.2.0.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0"
+            "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite/mz_to_sqlite/2.0.4+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0"
         ],
         "topic_name": "proteomics",
         "topic_name_human": "Proteomics",
@@ -200841,93 +201921,86 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "protein-id-oms",
+        "tutorial_name": "proteogenomics-dbsearch",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/protein-id-oms/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/protein-id-oms/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/protein-id-oms/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.json"
         },
-        "version": 31,
+        "version": 23,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 168,
-        "visitors": 2673,
+        "visit_duration": 301,
+        "visitors": 1242,
         "workflows": [
             {
                 "creators": [],
-                "description": "Peptide and Protein ID using OpenMS tools",
+                "description": "Proteogenomics 2: Database Search",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmzml input\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nfasta input\"]\n  2[label=\"PeakPickerHiRes\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"XTandemAdapter\"]\n  1 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"param_out\"]\n  4[label=\"FileInfo\"]\n  3 -> 4 [label=\"out\"]\n  5[label=\"PeptideIndexer\"]\n  1 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"out\"]\n  6[label=\"IDPosteriorErrorProbability\"]\n  5 -> 6 [label=\"out\"]\n  7[label=\"FalseDiscoveryRate\"]\n  6 -> 7 [label=\"out\"]\n  8[label=\"IDScoreSwitcher\"]\n  7 -> 8 [label=\"out\"]\n  9[label=\"FileInfo\"]\n  8 -> 9 [label=\"out\"]\n  10[label=\"FidoAdapter\"]\n  8 -> 10 [label=\"out\"]\n  11[label=\"FalseDiscoveryRate\"]\n  10 -> 11 [label=\"out\"]\n  12[label=\"FileInfo\"]\n  11 -> 12 [label=\"out\"]\n  13[label=\"TextExporter\"]\n  11 -> 13 [label=\"out\"]\n  14[label=\"Select\"]\n  13 -> 14 [label=\"out\"]\n  15[label=\"Select\"]\n  13 -> 15 [label=\"out\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nUniprot_cRAP_SAV_indel_translatedbed.FASTA\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nMGF Collection\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference Protein Accessions\"]\n  3[label=\"Search GUI\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  kd14f948180db4c158afc6fa38ef61deb[color=lightseagreen,label=\"Output\\nSearch GUI on input dataset(s)\"]\n  3 -> kd14f948180db4c158afc6fa38ef61deb\n  4[label=\"Peptide Shaker\"]\n  3 -> 4 [label=\"searchgui_results\"]\n  kafe0f1a528bb44bdb32bc634aa2154f3[color=lightseagreen,label=\"Output\\nPeptide Shaker on input dataset(s): mzidentML file\"]\n  4 -> kafe0f1a528bb44bdb32bc634aa2154f3\n  5[label=\"mz to sqlite\"]\n  4 -> 5 [label=\"mzidentML\"]\n  1 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  kb43a2136cf594fb0bb2b0d5b446c8ba9[color=lightseagreen,label=\"Output\\nmz to sqlite on input dataset(s)\"]\n  5 -> kb43a2136cf594fb0bb2b0d5b446c8ba9\n  6[label=\"Removing reference proteins\"]\n  4 -> 6 [label=\"output_psm\"]\n  4 -> 6 [label=\"output_psm\"]\n  2 -> 6 [label=\"output\"]\n  ka06ad5fa9a004867b9763745c5e59c80[color=lightseagreen,label=\"Output\\nRemoving reference proteins\"]\n  6 -> ka06ad5fa9a004867b9763745c5e59c80\n  7[label=\"Selecting sequence with length >6 and <30\"]\n  6 -> 7 [label=\"output\"]\n  kb71e541728644712b5c1c90725976baf[color=lightseagreen,label=\"Output\\nSelecting sequence with length >6 and <30\"]\n  7 -> kb71e541728644712b5c1c90725976baf\n  8[label=\"Peptides for BlastP analysis\"]\n  7 -> 8 [label=\"output\"]\n  k1ac3c77680954db185183643dc081006[color=lightseagreen,label=\"Output\\nPeptides_for_BlastP_analysis\"]\n  8 -> k1ac3c77680954db185183643dc081006\n}",
                 "history": [
                     {
-                        "hash": "54b4d9fcc78b1394f71f7affd51ca15e83b211d5",
-                        "message": "Adding tags to workflows",
-                        "num": 9,
-                        "short_hash": "54b4d9fcc",
-                        "unix": "1604224600"
+                        "hash": "6474a188df5601dc13cccb8fcfcd99cab9c6d1f4",
+                        "message": "Update galaxy-workflow-mouse_rnaseq_dbsearch.ga",
+                        "num": 8,
+                        "short_hash": "6474a188d",
+                        "unix": "1612811785"
                     },
                     {
-                        "hash": "ca84d739509bdb1ef8f3cfc64c15242ef0363407",
-                        "message": "Updating Tutorials to OpenMS 2.6, adjusting of parameters and tools, adding tool versions",
-                        "num": 8,
-                        "short_hash": "ca84d7395",
-                        "unix": "1604176914"
+                        "hash": "42e6b15fc35a261ef9aed129c2d28385e747e1d1",
+                        "message": "Update galaxy-workflow-mouse_rnaseq_dbsearch.ga",
+                        "num": 7,
+                        "short_hash": "42e6b15fc",
+                        "unix": "1611782271"
+                    },
+                    {
+                        "hash": "8011373088f966876016f1afc71237d842ba13d7",
+                        "message": "Update galaxy-workflow-mouse_rnaseq_dbsearch.ga",
+                        "num": 6,
+                        "short_hash": "801137308",
+                        "unix": "1611781407"
                     },
                     {
                         "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
                         "message": "annotation",
-                        "num": 7,
+                        "num": 5,
                         "short_hash": "667ff3de9",
                         "unix": "1579690769"
                     },
                     {
                         "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
                         "message": "Workflow renaming",
-                        "num": 6,
+                        "num": 4,
                         "short_hash": "eb4d724e0",
                         "unix": "1579084895"
                     },
                     {
-                        "hash": "775a0b42554fad0d7106779b50b758f34f9388f0",
-                        "message": "Updated workflow containing all follow up tools",
-                        "num": 5,
-                        "short_hash": "775a0b425",
-                        "unix": "1553092201"
-                    },
-                    {
-                        "hash": "08f1e0dc3f10498a73acb658e65375b6589b7ce2",
-                        "message": "Updated workflow for ID training",
-                        "num": 4,
-                        "short_hash": "08f1e0dc3",
-                        "unix": "1553088979"
-                    },
-                    {
-                        "hash": "dbcc48eaa51d95815ca6a19bd643264e9db81825",
-                        "message": "fix workflow name",
+                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
+                        "message": "Changed format of workflows",
                         "num": 3,
-                        "short_hash": "dbcc48eaa",
-                        "unix": "1510677790"
+                        "short_hash": "361236c41",
+                        "unix": "1554368414"
                     },
                     {
-                        "hash": "b916508e1e11168c289f744f7acfc847e906285a",
-                        "message": "Added workflow for two search engines, deleted ms2 PeakPicking and updated old workflow, added link to workflow in tutorial",
+                        "hash": "6eef55b7e8306d8ce46ac08e7799f6f65ae106aa",
+                        "message": "Updated install_tutorial_requirements.sh + minor fixes (#1275)",
                         "num": 2,
-                        "short_hash": "b916508e1",
-                        "unix": "1510655977"
+                        "short_hash": "6eef55b7e",
+                        "unix": "1551293676"
                     },
                     {
-                        "hash": "a6411f26e23a9e4754177332839416165c9b4658",
-                        "message": "New tutorial \"Protein ID using OpenMS\" and major revision of \"Protein ID using SG/PS\" (#570)",
+                        "hash": "715d5f2ee1d9cfa74c5230a0a4bf746df8758e87",
+                        "message": "fix folder names",
                         "num": 1,
-                        "short_hash": "a6411f26e",
-                        "unix": "1508148807"
+                        "short_hash": "715d5f2ee",
+                        "unix": "1542746779"
                     }
                 ],
                 "inputs": [
@@ -200940,32 +202013,32 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "mzml input"
+                                "name": "Uniprot_cRAP_SAV_indel_translatedbed.FASTA"
                             }
                         ],
-                        "label": "mzml input",
+                        "label": "Uniprot_cRAP_SAV_indel_translatedbed.FASTA",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 218.8000030517578,
-                            "height": 61.80000305175781,
-                            "left": 546,
-                            "right": 746,
-                            "top": 157,
+                            "bottom": 290,
+                            "height": 105,
+                            "left": -277.5,
+                            "right": -77.5,
+                            "top": 185,
                             "width": 200,
-                            "x": 546,
-                            "y": 157
+                            "x": -277.5,
+                            "y": 185
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "1604c094-ef2d-4094-a0f4-dc530fe8e359",
+                        "uuid": "eb7142ae-40cc-4c61-b744-bf7f3c8ed096",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "c7aacc63-3815-4e28-9c1d-9b2378799a97"
+                                "uuid": "a125ba5f-316b-4f95-a8f2-978e9a9affda"
                             }
                         ]
                     },
@@ -200978,40 +202051,78 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "fasta input"
+                                "name": "MGF Collection"
                             }
                         ],
-                        "label": "fasta input",
+                        "label": "MGF Collection",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 433.984375,
+                            "height": 84,
+                            "left": -277.46875,
+                            "right": -77.46875,
+                            "top": 349.984375,
+                            "width": 200,
+                            "x": -277.46875,
+                            "y": 349.984375
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "d7429ce1-2fc7-4ffa-87dd-4c4c343f8496",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "f0af224e-c8cd-412b-803b-ee636c1b924c"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Reference Protein Accessions"
+                            }
+                        ],
+                        "label": "Reference Protein Accessions",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 430.8000030517578,
-                            "height": 61.80000305175781,
-                            "left": 541,
-                            "right": 741,
-                            "top": 369,
+                            "bottom": 592.625,
+                            "height": 84,
+                            "left": -264.5,
+                            "right": -64.5,
+                            "top": 508.625,
                             "width": 200,
-                            "x": 541,
-                            "y": 369
+                            "x": -264.5,
+                            "y": 508.625
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "d948aea0-6741-4a7f-a07c-fd451674714e",
+                        "uuid": "99f0374c-ea36-4def-822a-2feb64aee67b",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "b3071ae5-c01b-4cba-a31a-0b36943c2aca"
+                                "uuid": "4a838c43-d3ba-4037-9ce1-0a47f919ac94"
                             }
                         ]
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nmzml input\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nfasta input\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"PeakPickerHiRes\"];\n  0 -->|output| 2;\n  3[\"XTandemAdapter\"];\n  1 -->|output| 3;\n  2 -->|param_out| 3;\n  4[\"FileInfo\"];\n  3 -->|out| 4;\n  5[\"PeptideIndexer\"];\n  1 -->|output| 5;\n  3 -->|out| 5;\n  6[\"IDPosteriorErrorProbability\"];\n  5 -->|out| 6;\n  7[\"FalseDiscoveryRate\"];\n  6 -->|out| 7;\n  8[\"IDScoreSwitcher\"];\n  7 -->|out| 8;\n  9[\"FileInfo\"];\n  8 -->|out| 9;\n  10[\"FidoAdapter\"];\n  8 -->|out| 10;\n  11[\"FalseDiscoveryRate\"];\n  10 -->|out| 11;\n  12[\"FileInfo\"];\n  11 -->|out| 12;\n  13[\"TextExporter\"];\n  11 -->|out| 13;\n  14[\"Select\"];\n  13 -->|out| 14;\n  15[\"Select\"];\n  13 -->|out| 15;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Proteomics: Peptide and Protein ID using OpenMS",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nUniprot_cRAP_SAV_indel_translatedbed.FASTA\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nMGF Collection\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nReference Protein Accessions\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Search GUI\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  d14f9481-80db-4c15-8afc-6fa38ef61deb[\"Output\\nSearch GUI on input dataset(s)\"];\n  3 --> d14f9481-80db-4c15-8afc-6fa38ef61deb;\n  style d14f9481-80db-4c15-8afc-6fa38ef61deb stroke:#2c3143,stroke-width:4px;\n  4[\"Peptide Shaker\"];\n  3 -->|searchgui_results| 4;\n  afe0f1a5-28bb-44bd-b32b-c634aa2154f3[\"Output\\nPeptide Shaker on input dataset(s): mzidentML file\"];\n  4 --> afe0f1a5-28bb-44bd-b32b-c634aa2154f3;\n  style afe0f1a5-28bb-44bd-b32b-c634aa2154f3 stroke:#2c3143,stroke-width:4px;\n  5[\"mz to sqlite\"];\n  4 -->|mzidentML| 5;\n  1 -->|output| 5;\n  0 -->|output| 5;\n  b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9[\"Output\\nmz to sqlite on input dataset(s)\"];\n  5 --> b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9;\n  style b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9 stroke:#2c3143,stroke-width:4px;\n  6[\"Removing reference proteins\"];\n  4 -->|output_psm| 6;\n  4 -->|output_psm| 6;\n  2 -->|output| 6;\n  a06ad5fa-9a00-4867-b976-3745c5e59c80[\"Output\\nRemoving reference proteins\"];\n  6 --> a06ad5fa-9a00-4867-b976-3745c5e59c80;\n  style a06ad5fa-9a00-4867-b976-3745c5e59c80 stroke:#2c3143,stroke-width:4px;\n  7[\"Selecting sequence with length >6 and <30\"];\n  6 -->|output| 7;\n  b71e5417-2864-4712-b5c1-c90725976baf[\"Output\\nSelecting sequence with length >6 and <30\"];\n  7 --> b71e5417-2864-4712-b5c1-c90725976baf;\n  style b71e5417-2864-4712-b5c1-c90725976baf stroke:#2c3143,stroke-width:4px;\n  8[\"Peptides for BlastP analysis\"];\n  7 -->|output| 8;\n  1ac3c776-8095-4db1-8518-3643dc081006[\"Output\\nPeptides_for_BlastP_analysis\"];\n  8 --> 1ac3c776-8095-4db1-8518-3643dc081006;\n  style 1ac3c776-8095-4db1-8518-3643dc081006 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "GTN Proteogemics2 Database Search",
                 "outputs": [
                     {
                         "annotation": "",
@@ -201022,32 +202133,32 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "mzml input"
+                                "name": "Uniprot_cRAP_SAV_indel_translatedbed.FASTA"
                             }
                         ],
-                        "label": "mzml input",
+                        "label": "Uniprot_cRAP_SAV_indel_translatedbed.FASTA",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 218.8000030517578,
-                            "height": 61.80000305175781,
-                            "left": 546,
-                            "right": 746,
-                            "top": 157,
+                            "bottom": 290,
+                            "height": 105,
+                            "left": -277.5,
+                            "right": -77.5,
+                            "top": 185,
                             "width": 200,
-                            "x": 546,
-                            "y": 157
+                            "x": -277.5,
+                            "y": 185
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "1604c094-ef2d-4094-a0f4-dc530fe8e359",
+                        "uuid": "eb7142ae-40cc-4c61-b744-bf7f3c8ed096",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "c7aacc63-3815-4e28-9c1d-9b2378799a97"
+                                "uuid": "a125ba5f-316b-4f95-a8f2-978e9a9affda"
                             }
                         ]
                     },
@@ -201060,763 +202171,1749 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "fasta input"
+                                "name": "MGF Collection"
                             }
                         ],
-                        "label": "fasta input",
+                        "label": "MGF Collection",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 433.984375,
+                            "height": 84,
+                            "left": -277.46875,
+                            "right": -77.46875,
+                            "top": 349.984375,
+                            "width": 200,
+                            "x": -277.46875,
+                            "y": 349.984375
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "d7429ce1-2fc7-4ffa-87dd-4c4c343f8496",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "f0af224e-c8cd-412b-803b-ee636c1b924c"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Reference Protein Accessions"
+                            }
+                        ],
+                        "label": "Reference Protein Accessions",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 430.8000030517578,
-                            "height": 61.80000305175781,
-                            "left": 541,
-                            "right": 741,
-                            "top": 369,
+                            "bottom": 592.625,
+                            "height": 84,
+                            "left": -264.5,
+                            "right": -64.5,
+                            "top": 508.625,
                             "width": 200,
-                            "x": 541,
-                            "y": 369
+                            "x": -264.5,
+                            "y": 508.625
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "d948aea0-6741-4a7f-a07c-fd451674714e",
+                        "uuid": "99f0374c-ea36-4def-822a-2feb64aee67b",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "b3071ae5-c01b-4cba-a31a-0b36943c2aca"
+                                "uuid": "4a838c43-d3ba-4037-9ce1-0a47f919ac94"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerhires/PeakPickerHiRes/2.3.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
                         "errors": null,
-                        "id": 2,
+                        "id": 3,
                         "input_connections": {
-                            "param_in": {
+                            "input_database": {
                                 "id": 0,
                                 "output_name": "output"
+                            },
+                            "peak_lists": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "PeakPickerHiRes",
+                        "name": "Search GUI",
                         "outputs": [
                             {
-                                "name": "param_out",
-                                "type": "mzml"
+                                "name": "searchgui_results",
+                                "type": "searchgui_archive"
                             }
                         ],
                         "position": {
-                            "bottom": 325.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": 852,
-                            "right": 1052,
-                            "top": 212,
+                            "bottom": 514,
+                            "height": 168,
+                            "left": 22.53125,
+                            "right": 222.53125,
+                            "top": 346,
                             "width": 200,
-                            "x": 852,
-                            "y": 212
+                            "x": 22.53125,
+                            "y": 346
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerhires/PeakPickerHiRes/2.3.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "3d8d4ada5405",
-                            "name": "openms_peakpickerhires",
+                            "changeset_revision": "7fdd9119cc4f",
+                            "name": "peptideshaker",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"mzml\", \"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"param_algorithm_SignalToNoise_bin_count\": \"30\", \"param_algorithm_SignalToNoise_min_required_elements\": \"10\", \"param_algorithm_SignalToNoise_win_len\": \"200.0\", \"param_algorithm_SignalToNoise_write_log_messages\": \"true\", \"param_algorithm_report_FWHM\": \"false\", \"param_algorithm_report_FWHM_unit\": \"relative\", \"param_algorithm_signal_to_noise\": \"0.0\", \"param_in\": {\"__class__\": \"ConnectedValue\"}, \"rep_param_algorithm_ms_levels\": [{\"__index__\": 0, \"param_algorithm_ms_levels\": \"2\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.3.0",
+                        "tool_state": "{\"advanced_options\": {\"searchgui_advanced\": {\"searchgui_advanced_selector\": \"basic\", \"__current_case__\": 0}, \"xtandem\": {\"xtandem_advanced\": \"no\", \"__current_case__\": 0}, \"omssa\": {\"omssa_advanced\": \"no\", \"__current_case__\": 0}, \"msgf\": {\"msgf_advanced\": \"no\", \"__current_case__\": 0}, \"ms_amanda\": {\"ms_amanda_advanced\": \"no\", \"__current_case__\": 0}, \"tide\": {\"tide_advanced\": \"no\", \"__current_case__\": 0}, \"myrimatch\": {\"myrimatch_advanced\": \"no\", \"__current_case__\": 0}, \"comet\": {\"comet_advanced\": \"no\", \"__current_case__\": 0}, \"directtag\": {\"directtag_advanced\": \"no\", \"__current_case__\": 0}, \"novor\": {\"novor_advanced\": \"no\", \"__current_case__\": 0}}, \"input_database\": {\"__class__\": \"ConnectedValue\"}, \"peak_lists\": {\"__class__\": \"ConnectedValue\"}, \"precursor_options\": {\"precursor_ion_tol_units\": \"1\", \"precursor_ion_tol\": \"10.0\", \"fragment_tol_units\": \"0\", \"fragment_tol\": \"0.5\", \"min_charge\": \"2\", \"max_charge\": \"6\", \"forward_ion\": \"b\", \"reverse_ion\": \"y\", \"min_isotope\": \"0\", \"max_isotope\": \"1\"}, \"protein_database_options\": {\"create_decoy\": \"true\", \"use_gene_mapping\": \"false\", \"update_gene_mapping\": \"false\"}, \"protein_digest_options\": {\"digestion\": {\"cleavage\": \"0\", \"__current_case__\": 0, \"digests\": [{\"__index__\": 0, \"enzyme\": \"Trypsin\", \"missed_cleavages\": \"2\"}]}}, \"protein_modification_options\": {\"fixed_modifications\": [\"Carbamidomethylation of C\", \"iTRAQ 4-plex of K\", \"iTRAQ 4-plex of peptide N-term\"], \"variable_modifications\": [\"Oxidation of M\", \"iTRAQ 4-plex of Y\"]}, \"search_engines_options\": {\"engines\": [\"X!Tandem\"]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.3.10.1",
                         "type": "tool",
-                        "uuid": "09ceeb02-6c71-4ee3-b70a-ad879b4904e1",
+                        "uuid": "41bfe37f-62de-44cd-9a2c-26f007258c61",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "param_out",
-                                "uuid": "058dedba-3334-4687-8e34-c995a1d019c4"
+                                "label": "Search GUI on input dataset(s)",
+                                "output_name": "searchgui_results",
+                                "uuid": "d14f9481-80db-4c15-8afc-6fa38ef61deb"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
                         "errors": null,
-                        "id": 3,
+                        "id": 4,
                         "input_connections": {
-                            "database": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "in": {
-                                "id": 2,
-                                "output_name": "param_out"
+                            "searchgui_input": {
+                                "id": 3,
+                                "output_name": "searchgui_results"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "XTandemAdapter",
+                        "name": "Peptide Shaker",
                         "outputs": [
                             {
-                                "name": "out",
-                                "type": "idxml"
+                                "name": "mzidentML",
+                                "type": "mzid"
+                            },
+                            {
+                                "name": "output_certificate",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "output_psm",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "output_peptides",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "output_proteins",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 427.1999969482422,
-                            "height": 215.1999969482422,
-                            "left": 1072,
-                            "right": 1272,
-                            "top": 212,
+                            "bottom": 704.125,
+                            "height": 471,
+                            "left": 309.53125,
+                            "right": 509.53125,
+                            "top": 233.125,
                             "width": 200,
-                            "x": 1072,
-                            "y": 212
+                            "x": 309.53125,
+                            "y": 233.125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "1add9bacdccd",
-                            "name": "openms_xtandemadapter",
+                            "changeset_revision": "7fdd9119cc4f",
+                            "name": "peptideshaker",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": [\"out_FLAG\"], \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"database\": {\"__class__\": \"ConnectedValue\"}, \"default_config_file\": null, \"enzyme\": \"Trypsin\", \"fixed_modifications\": [\"Carbamidomethyl (C)\"], \"fragment_error_units\": \"ppm\", \"fragment_mass_tolerance\": \"10.0\", \"ignore_adapter_param\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"max_precursor_charge\": \"4\", \"max_valid_expect\": \"0.1\", \"minimum_fragment_mz\": \"150.0\", \"missed_cleavages\": \"1\", \"no_isotope_error\": \"false\", \"output_results\": \"all\", \"precursor_error_units\": \"ppm\", \"precursor_mass_tolerance\": \"10.0\", \"semi_cleavage\": \"false\", \"variable_modifications\": [\"Oxidation (M)\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"contact_options\": {\"contact_options_selector\": \"no\", \"__current_case__\": 0}, \"exporting_options\": {\"mzidentml_conditional\": {\"mzidentml_creation\": \"true\", \"__current_case__\": 0, \"include_sequences\": \"false\"}, \"zip_conditional\": {\"zip_output_boolean\": \"false\", \"__current_case__\": 0, \"export_cps\": \"false\"}, \"output_reports\": [\"3\", \"6\", \"9\", \"0\"]}, \"filtering_options\": {\"filtering_options_selector\": \"no\", \"__current_case__\": 0}, \"processing_options\": {\"processing_options_selector\": \"no\", \"__current_case__\": 0}, \"searchgui_input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.36.3",
                         "type": "tool",
-                        "uuid": "5fe07f26-b2e1-4a10-a4ae-439ee6146c8b",
+                        "uuid": "3d435aa3-cc94-4320-94a4-a49503f7e82e",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "893e0901-e84a-4212-837d-63036f8b4d51"
+                                "output_name": "output_certificate",
+                                "uuid": "1c33ea40-12f5-4e28-b4da-5b7975f2c13f"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_psm",
+                                "uuid": "6425fbc7-08cf-4633-ac15-74993be5851f"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_proteins",
+                                "uuid": "a52e58b1-de72-4bd6-a434-674f20c5d19d"
+                            },
+                            {
+                                "label": "Peptide Shaker on input dataset(s): mzidentML file",
+                                "output_name": "mzidentML",
+                                "uuid": "afe0f1a5-28bb-44bd-b32b-c634aa2154f3"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_peptides",
+                                "uuid": "75e03205-eb1a-4cfd-847f-c70dd5c3209a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite/mz_to_sqlite/2.0.4+galaxy1",
                         "errors": null,
-                        "id": 4,
+                        "id": 5,
                         "input_connections": {
-                            "in": {
-                                "id": 3,
-                                "output_name": "out"
+                            "mzinput": {
+                                "id": 4,
+                                "output_name": "mzidentML"
+                            },
+                            "scanfiles": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "searchdbs": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "FileInfo",
+                        "name": "mz to sqlite",
                         "outputs": [
                             {
-                                "name": "out",
-                                "type": "txt"
+                                "name": "sqlite_db",
+                                "type": "mz.sqlite"
                             }
                         ],
                         "position": {
-                            "bottom": 325.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": 1292,
-                            "right": 1492,
-                            "top": 212,
+                            "bottom": 411.484375,
+                            "height": 220,
+                            "left": 651.546875,
+                            "right": 851.546875,
+                            "top": 191.484375,
                             "width": 200,
-                            "x": 1292,
-                            "y": 212
+                            "x": 651.546875,
+                            "y": 191.484375
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActionsqlite_db": {
+                                "action_arguments": {
+                                    "newname": "Mz to sqlite"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "sqlite_db"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite/mz_to_sqlite/2.0.4+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "e8dce5e07fa5",
-                            "name": "openms_fileinfo",
+                            "changeset_revision": "f5c632894818",
+                            "name": "mz_to_sqlite",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"c\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"d\": \"false\", \"i\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"false\", \"p\": \"false\", \"s\": \"false\", \"v\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"mzinput\": {\"__class__\": \"ConnectedValue\"}, \"scanfiles\": {\"__class__\": \"ConnectedValue\"}, \"searchdbs\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.4+galaxy1",
                         "type": "tool",
-                        "uuid": "0afb93c4-71a2-481a-a64d-936b394dde64",
+                        "uuid": "1985019a-af9a-4ebc-82c6-448a6ae62166",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out",
-                                "uuid": "0e8d24f3-79a8-4914-802b-5f50f34bafa5"
+                                "label": "mz to sqlite on input dataset(s)",
+                                "output_name": "sqlite_db",
+                                "uuid": "b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "errors": null,
-                        "id": 5,
+                        "id": 6,
                         "input_connections": {
-                            "fasta": {
-                                "id": 1,
-                                "output_name": "output"
+                            "tables_0|table": {
+                                "id": 4,
+                                "output_name": "output_psm"
                             },
-                            "in": {
-                                "id": 3,
-                                "output_name": "out"
+                            "tables_1|table": {
+                                "id": 4,
+                                "output_name": "output_psm"
+                            },
+                            "tables_2|table": {
+                                "id": 2,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "PeptideIndexer",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Query Tabular",
+                                "name": "add_to_database"
+                            }
+                        ],
+                        "label": "Removing reference proteins",
+                        "name": "Query Tabular",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 821.640625,
+                            "height": 314,
+                            "left": 609.546875,
+                            "right": 809.546875,
+                            "top": 507.640625,
+                            "width": 200,
+                            "x": 609.546875,
+                            "y": 507.640625
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Removing reference proteins"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "33d61c89fb8d",
+                            "name": "query_tabular",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"save_db\": \"false\", \"sqlquery\": \"SELECT psms.*\\nFROM psms\\nWHERE psms.id NOT IN\\n(SELECT distinct prots.id\\nFROM prots JOIN uniprot ON prots.prot = uniprot.prot)\\nORDER BY psms.id\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"skip\", \"__current_case__\": 0, \"skip_lines\": \"1\"}}]}, \"tbl_opts\": {\"table_name\": \"psms\", \"column_names_from_first_line\": \"false\", \"col_names\": \"id,Proteins,Sequence\", \"load_named_columns\": \"true\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"id\"}]}}, {\"__index__\": 1, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"skip\", \"__current_case__\": 0, \"skip_lines\": \"1\"}}, {\"__index__\": 1, \"filter\": {\"filter_type\": \"select_columns\", \"__current_case__\": 7, \"columns\": \"1,2\"}}, {\"__index__\": 2, \"filter\": {\"filter_type\": \"normalize\", \"__current_case__\": 9, \"columns\": \"2\", \"separator\": \",\"}}]}, \"tbl_opts\": {\"table_name\": \"prots\", \"column_names_from_first_line\": \"false\", \"col_names\": \"id,prot\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"prot,id\"}]}}, {\"__index__\": 2, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"Uniprot\", \"column_names_from_first_line\": \"false\", \"col_names\": \"prot\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"prot\"}]}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.0.0",
+                        "type": "tool",
+                        "uuid": "90f1b13e-0ba1-4373-92c5-8b31adbdcdbb",
+                        "workflow_outputs": [
+                            {
+                                "label": "Removing reference proteins",
+                                "output_name": "output",
+                                "uuid": "a06ad5fa-9a00-4867-b976-3745c5e59c80"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "tables_0|table": {
+                                "id": 6,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Query Tabular",
+                                "name": "add_to_database"
+                            }
+                        ],
+                        "label": "Selecting sequence with length >6 and <30",
+                        "name": "Query Tabular",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 767.140625,
+                            "height": 252,
+                            "left": 836.546875,
+                            "right": 1036.546875,
+                            "top": 515.140625,
+                            "width": 200,
+                            "x": 836.546875,
+                            "y": 515.140625
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Selecting sequence with length >6 and <30"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "33d61c89fb8d",
+                            "name": "query_tabular",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"save_db\": \"false\", \"sqlquery\": \"SELECT Sequence || ' PSM=' || group_concat(id,',') || ' length='\\n|| length(Sequence) as \\\"ID\\\",Sequence\\nFROM  psm\\nWHERE length(Sequence) >6\\nAND length(Sequence) <= 30\\nGROUP BY Sequence\\nORDER BY length(Sequence),Sequence\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"skip\", \"__current_case__\": 0, \"skip_lines\": \"1\"}}]}, \"tbl_opts\": {\"table_name\": \"psm\", \"column_names_from_first_line\": \"false\", \"col_names\": \"id,Proteins,Sequence\", \"load_named_columns\": \"true\", \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.0.0",
+                        "type": "tool",
+                        "uuid": "7a40e039-01e2-4b13-b72f-7bb91061c50a",
+                        "workflow_outputs": [
+                            {
+                                "label": "Selecting sequence with length >6 and <30",
+                                "output_name": "output",
+                                "uuid": "b71e5417-2864-4712-b5c1-c90725976baf"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "input": {
+                                "id": 7,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Tabular-to-FASTA",
+                                "name": "input"
+                            }
+                        ],
+                        "label": "Peptides for BlastP analysis",
+                        "name": "Tabular-to-FASTA",
                         "outputs": [
                             {
-                                "name": "out",
-                                "type": "idxml"
+                                "name": "output",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 724.9375,
+                            "height": 158,
+                            "left": 1066.546875,
+                            "right": 1266.546875,
+                            "top": 566.9375,
+                            "width": 200,
+                            "x": 1066.546875,
+                            "y": 566.9375
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Peptides for BlastP analysis"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "0a7799698fe5",
+                            "name": "tabular_to_fasta",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"seq_col\": \"2\", \"title_col\": \"1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
+                        "type": "tool",
+                        "uuid": "135caaf1-ceda-47b6-9f1a-8b0659d8e6a2",
+                        "workflow_outputs": [
+                            {
+                                "label": "Peptides_for_BlastP_analysis",
+                                "output_name": "output",
+                                "uuid": "1ac3c776-8095-4db1-8518-3643dc081006"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "proteomics/proteogenomics-dbsearch",
+                "path": "topics/proteomics/tutorials/proteogenomics-dbsearch/workflows/galaxy-workflow-mouse_rnaseq_dbsearch.ga",
+                "tags": [
+                    "proteomics"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "GTN Proteogemics2 Database Search",
+                "topic_id": "proteomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-proteogenomics-dbsearch/versions/galaxy-workflow-mouse-rnaseq-dbsearch",
+                "tutorial_id": "proteogenomics-dbsearch",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteogenomics-dbsearch/workflows/galaxy-workflow-mouse_rnaseq_dbsearch.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteogenomics-dbsearch/workflows/galaxy-workflow-mouse_rnaseq_dbsearch.html",
+                "version": 7,
+                "wfid": "proteomics-proteogenomics-dbsearch",
+                "wfname": "galaxy-workflow-mouse-rnaseq-dbsearch",
+                "workflow": "galaxy-workflow-mouse_rnaseq_dbsearch.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite/mz_to_sqlite/2.0.4+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0"
+                ],
+                "workflowhub_id": "1151"
+            }
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.1489208"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "288462ec2630",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "288462ec2630",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "288462ec2630",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "uniprot_rest_interface",
+                    "owner": "bgruening",
+                    "revisions": "f7ebd1b4783b",
+                    "tool_panel_section_label": "Convert Formats",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "unique",
+                    "owner": "bgruening",
+                    "revisions": "7ce75adb93be",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "tmhmm_and_signalp",
+                    "owner": "peterjc",
+                    "revisions": "e6cc27d182a8",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: 288462ec2630\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 288462ec2630\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 288462ec2630\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: uniprot_rest_interface\n  owner: bgruening\n  revisions: f7ebd1b4783b\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unique\n  owner: bgruening\n  revisions: 7ce75adb93be\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tmhmm_and_signalp\n  owner: peterjc\n  revisions: e6cc27d182a8\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/secretome-prediction/tutorial.json",
+        "contributors": [
+            {
+                "email": "sigloch+github@mailbox.org",
+                "former_affiliations": [
+                    "uni-freiburg"
+                ],
+                "id": "stortebecker",
+                "joined": "2017-09",
+                "name": "Florian Christoph Sigloch",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stortebecker/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/stortebecker.json"
+            },
+            {
+                "affiliations": [
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
+                "fediverse_flavor": "mastodon",
+                "id": "bgruening",
+                "joined": "2017-09",
+                "linkedin": "bgruening",
+                "location": {
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
+                },
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+            }
+        ],
+        "dir": "topics/proteomics/tutorials/secretome-prediction",
+        "draft": true,
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "proteomics/secretome-prediction",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "The cellular secretome contains more than the classically secreted proteins.",
+            "Localization predictions by multiple different algorithms can improve sensitivity and/or specificity."
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": [
+            "Predict proteins in the cellular secretome by using GO-terms.",
+            "Predict proteins in the cellular secretome by using WolfPSORT.",
+            "Combine the results of both predictions."
+        ],
+        "pageviews": 873,
+        "pub_date": "2017-04-13",
+        "questions": [
+            "How to predict cellular protein localization based upon GO-terms?",
+            "How to combine multiple localization predictions?"
+        ],
+        "short_id": "T00235",
+        "short_tools": [
+            "tp_sorted_uniq",
+            "tp_easyjoin_tool",
+            "wolf_psort",
+            "comp1",
+            "Filter1",
+            "Convert characters1",
+            "get_subontology_from",
+            "bg_uniq",
+            "term_id_vs_term_name",
+            "Grep1",
+            "tp_cut_tool",
+            "uniprot"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "post-process",
+        "supported_servers": {
+            "exact": [],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "human",
+            "work-in-progress"
+        ],
+        "time_estimation": "30m",
+        "title": "Secretome Prediction",
+        "tools": [
+            "Convert characters1",
+            "Filter1",
+            "Grep1",
+            "comp1",
+            "get_subontology_from",
+            "term_id_vs_term_name",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.0.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.0.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.0.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
+            "toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/wolf_psort/0.0.8"
+        ],
+        "topic_name": "proteomics",
+        "topic_name_human": "Proteomics",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "secretome-prediction",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/secretome-prediction/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/secretome-prediction/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/secretome-prediction/tutorial.json"
+        },
+        "version": 14,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 89,
+        "visitors": 571,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "version 1.0, 160318, published at https://github.com/Stortebecker/secretome_prediction",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  3[label=\"UniProt\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Select\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Get subontology from a given OBO term\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"Get subontology from a given OBO term\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"Get subontology from a given OBO term\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"Get subontology from a given OBO term\"]\n  2 -> 8 [label=\"output\"]\n  9[label=\"Get subontology from a given OBO term\"]\n  2 -> 9 [label=\"output\"]\n  10[label=\"WoLF PSORT\"]\n  3 -> 10 [label=\"outfile_retrieve_fasta\"]\n  11[label=\"Join\"]\n  0 -> 11 [label=\"output\"]\n  4 -> 11 [label=\"out_file1\"]\n  12[label=\"Get all the term IDs and term names of a given OBO ontology\"]\n  5 -> 12 [label=\"output\"]\n  13[label=\"Get all the term IDs and term names of a given OBO ontology\"]\n  6 -> 13 [label=\"output\"]\n  14[label=\"Get all the term IDs and term names of a given OBO ontology\"]\n  7 -> 14 [label=\"output\"]\n  15[label=\"Get all the term IDs and term names of a given OBO ontology\"]\n  8 -> 15 [label=\"output\"]\n  16[label=\"Get all the term IDs and term names of a given OBO ontology\"]\n  9 -> 16 [label=\"output\"]\n  17[label=\"Filter\"]\n  10 -> 17 [label=\"tabular_file\"]\n  18[label=\"Filter\"]\n  10 -> 18 [label=\"tabular_file\"]\n  19[label=\"Join\"]\n  12 -> 19 [label=\"output\"]\n  13 -> 19 [label=\"output\"]\n  20[label=\"Join\"]\n  14 -> 20 [label=\"output\"]\n  15 -> 20 [label=\"output\"]\n  21[label=\"Join\"]\n  17 -> 21 [label=\"out_file1\"]\n  18 -> 21 [label=\"out_file1\"]\n  22[label=\"Join\"]\n  19 -> 22 [label=\"output\"]\n  20 -> 22 [label=\"output\"]\n  23[label=\"Convert\"]\n  21 -> 23 [label=\"output\"]\n  24[label=\"Join\"]\n  22 -> 24 [label=\"output\"]\n  16 -> 24 [label=\"output\"]\n  25[label=\"Cut\"]\n  23 -> 25 [label=\"out_file1\"]\n  26[label=\"Compare two Datasets\"]\n  11 -> 26 [label=\"output\"]\n  24 -> 26 [label=\"output\"]\n  27[label=\"Unique\"]\n  26 -> 27 [label=\"out_file1\"]\n  28[label=\"Cut\"]\n  27 -> 28 [label=\"outfile\"]\n  29[label=\"Join\"]\n  25 -> 29 [label=\"output\"]\n  28 -> 29 [label=\"output\"]\n  30[label=\"Unique\"]\n  29 -> 30 [label=\"output\"]\n  k14e0c6dc436b4c4c9292d5e00cca8c92[color=lightseagreen,label=\"Output\\nSecretome proteins\"]\n  30 -> k14e0c6dc436b4c4c9292d5e00cca8c92\n}",
+                "history": [
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 4,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "55fe079b2828d71aabb21fa0700f6f77ac76052c",
+                        "message": "WoLF PSORT WF",
+                        "num": 3,
+                        "short_hash": "55fe079b2",
+                        "unix": "1578933056"
+                    },
+                    {
+                        "hash": "7da80b34185f4165852feb3bfe80d692609685db",
+                        "message": "Workflows fix",
+                        "num": 2,
+                        "short_hash": "7da80b341",
+                        "unix": "1578668175"
+                    },
+                    {
+                        "hash": "2c1271b670d336517fb123fb632ce13c93c40465",
+                        "message": "Restructure proteomics",
+                        "num": 1,
+                        "short_hash": "2c1271b67",
+                        "unix": "1495544862"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "Input: Protein ID list\nFirst column has to be uniprot accessions",
+                        "content_id": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Input: Protein ID list\nFirst column has to be uniprot accessions",
+                                "name": "Custom Protein list (uniprot accession)"
                             }
                         ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 537.1999969482422,
-                            "height": 205.1999969482422,
-                            "left": 1292,
-                            "right": 1492,
-                            "top": 332,
-                            "width": 200,
-                            "x": 1292,
-                            "y": 332
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "d8ee5700c66b",
-                            "name": "openms_peptideindexer",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 293,
+                            "top": 377
                         },
-                        "tool_state": "{\"IL_equivalent\": \"false\", \"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"aaa_max\": \"3\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"decoy_string\": \"\", \"decoy_string_position\": \"prefix\", \"enzyme\": {\"name\": \"auto\", \"specificity\": \"none\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"in\": {\"__class__\": \"ConnectedValue\"}, \"keep_unreferenced_proteins\": \"false\", \"mismatches_max\": \"0\", \"missing_decoy_action\": \"error\", \"unmatched_action\": \"error\", \"write_protein_description\": \"true\", \"write_protein_sequence\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
-                        "type": "tool",
-                        "uuid": "39045d4c-f666-40f2-8c21-677271e734cc",
+                        "tool_errors": null,
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Custom Protein list (uniprot accession)\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "4d60060c-188b-4a93-8320-36f9b43e5765",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "ca346fb2-f01e-4374-bce7-8fe6eddf5d3c"
+                                "output_name": "output",
+                                "uuid": "27022e50-f5dc-46b1-8b54-979f955eb050"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy0",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "in": {
-                                "id": 5,
-                                "output_name": "out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "IDPosteriorErrorProbability",
-                        "outputs": [
+                        "annotation": "Input: Uniprot GO database file (choose the right organism)\nExample: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gene_association.goa_human.gz",
+                        "content_id": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out",
-                                "type": "idxml"
+                                "description": "Input: Uniprot GO database file (choose the right organism)\nExample: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gene_association.goa_human.gz",
+                                "name": "Uniprot GO database"
                             }
                         ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 386.8000030517578,
-                            "height": 174.8000030517578,
-                            "left": 1512,
-                            "right": 1712,
-                            "top": 212,
-                            "width": 200,
-                            "x": 1512,
-                            "y": 212
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "711a081d80ba",
-                            "name": "openms_idposteriorerrorprobability",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 290,
+                            "top": 507
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fit_algorithm\": {\"number_of_bins\": \"100\", \"incorrectly_assigned\": \"Gumbel\", \"max_nr_iterations\": \"1000\", \"neg_log_delta\": \"6\", \"outlier_handling\": \"ignore_iqr_outliers\"}, \"ignore_bad_data\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"prob_correct\": \"true\", \"split_charge\": \"false\", \"top_hits_only\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
-                        "type": "tool",
-                        "uuid": "e0bdc6ec-b1ff-436e-8ebc-0fdd5f7206b7",
+                        "tool_errors": null,
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Uniprot GO database\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "e8f4a577-7b6a-4cd0-9a74-2e68c4ae6c5a",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "584f8b3b-6e0c-492b-92ee-9996e27f4769"
+                                "output_name": "output",
+                                "uuid": "b8fa36c2-6bbf-40c1-a472-8d4a6a7096c3"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "in": {
-                                "id": 6,
-                                "output_name": "out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "FalseDiscoveryRate",
-                        "outputs": [
+                        "annotation": "Input: Please downlad the Open Biomedical Ontology (OBO), i.e. \"GO term tree\" from\nhttp://purl.obolibrary.org/obo/go/go.obo",
+                        "content_id": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out",
-                                "type": "idxml"
+                                "description": "Input: Please downlad the Open Biomedical Ontology (OBO), i.e. \"GO term tree\" from\nhttp://purl.obolibrary.org/obo/go/go.obo",
+                                "name": "Open Biomedical Ontology (OBO)"
                             }
                         ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 386.8000030517578,
-                            "height": 174.8000030517578,
-                            "left": 1732,
-                            "right": 1932,
-                            "top": 212,
-                            "width": 200,
-                            "x": 1732,
-                            "y": 212
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "469690558892",
-                            "name": "openms_falsediscoveryrate",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 293,
+                            "top": 790
                         },
-                        "tool_state": "{\"FDR\": {\"PSM\": \"0.01\", \"protein\": \"1.0\", \"cleanup\": {\"remove_proteins_without_psms\": \"true\", \"remove_psms_without_proteins\": \"true\", \"remove_spectra_without_psms\": \"true\"}}, \"OPTIONAL_OUTPUTS\": null, \"PSM\": \"true\", \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"algorithm\": {\"no_qvalues\": \"false\", \"use_all_hits\": \"false\", \"split_charge_variants\": \"false\", \"treat_runs_separately\": \"false\", \"add_decoy_peptides\": \"true\", \"add_decoy_proteins\": \"false\", \"conservative\": \"true\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"protein\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
-                        "type": "tool",
-                        "uuid": "b0e90f52-67ab-497c-8cc0-81997cda5ec0",
+                        "tool_errors": null,
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Open Biomedical Ontology (OBO)\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0640e1c4-4d77-49da-8473-0018e0a5db09",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "7d94c074-055a-4348-969f-c5e3e3404cd1"
+                                "output_name": "output",
+                                "uuid": "4725c10d-9e7a-4e3f-9874-c302c34687cb"
                             }
                         ]
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"UniProt\"];\n  0 -->|output| 3;\n  4[\"Select\"];\n  1 -->|output| 4;\n  5[\"Get subontology from a given OBO term\"];\n  2 -->|output| 5;\n  6[\"Get subontology from a given OBO term\"];\n  2 -->|output| 6;\n  7[\"Get subontology from a given OBO term\"];\n  2 -->|output| 7;\n  8[\"Get subontology from a given OBO term\"];\n  2 -->|output| 8;\n  9[\"Get subontology from a given OBO term\"];\n  2 -->|output| 9;\n  10[\"WoLF PSORT\"];\n  3 -->|outfile_retrieve_fasta| 10;\n  11[\"Join\"];\n  0 -->|output| 11;\n  4 -->|out_file1| 11;\n  12[\"Get all the term IDs and term names of a given OBO ontology\"];\n  5 -->|output| 12;\n  13[\"Get all the term IDs and term names of a given OBO ontology\"];\n  6 -->|output| 13;\n  14[\"Get all the term IDs and term names of a given OBO ontology\"];\n  7 -->|output| 14;\n  15[\"Get all the term IDs and term names of a given OBO ontology\"];\n  8 -->|output| 15;\n  16[\"Get all the term IDs and term names of a given OBO ontology\"];\n  9 -->|output| 16;\n  17[\"Filter\"];\n  10 -->|tabular_file| 17;\n  18[\"Filter\"];\n  10 -->|tabular_file| 18;\n  19[\"Join\"];\n  12 -->|output| 19;\n  13 -->|output| 19;\n  20[\"Join\"];\n  14 -->|output| 20;\n  15 -->|output| 20;\n  21[\"Join\"];\n  17 -->|out_file1| 21;\n  18 -->|out_file1| 21;\n  22[\"Join\"];\n  19 -->|output| 22;\n  20 -->|output| 22;\n  23[\"Convert\"];\n  21 -->|output| 23;\n  24[\"Join\"];\n  22 -->|output| 24;\n  16 -->|output| 24;\n  25[\"Cut\"];\n  23 -->|out_file1| 25;\n  26[\"Compare two Datasets\"];\n  11 -->|output| 26;\n  24 -->|output| 26;\n  27[\"Unique\"];\n  26 -->|out_file1| 27;\n  28[\"Cut\"];\n  27 -->|outfile| 28;\n  29[\"Join\"];\n  25 -->|output| 29;\n  28 -->|output| 29;\n  30[\"Unique\"];\n  29 -->|output| 30;\n  14e0c6dc-436b-4c4c-9292-d5e00cca8c92[\"Output\\nSecretome proteins\"];\n  30 --> 14e0c6dc-436b-4c4c-9292-d5e00cca8c92;\n  style 14e0c6dc-436b-4c4c-9292-d5e00cca8c92 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Secreted Proteins Via GO Annotation And WoLF PSORT For shCTSB Paper",
+                "outputs": [
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.6+galaxy0",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "in": {
-                                "id": 7,
-                                "output_name": "out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "IDScoreSwitcher",
-                        "outputs": [
+                        "annotation": "Input: Protein ID list\nFirst column has to be uniprot accessions",
+                        "content_id": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out",
-                                "type": "idxml"
+                                "description": "Input: Protein ID list\nFirst column has to be uniprot accessions",
+                                "name": "Custom Protein list (uniprot accession)"
                             }
                         ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 346,
-                            "height": 134,
-                            "left": 1952,
-                            "right": 2152,
-                            "top": 212,
-                            "width": 200,
-                            "x": 1952,
-                            "y": 212
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.6+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ec0d05b20eed",
-                            "name": "openms_idscoreswitcher",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 293,
+                            "top": 377
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"new_score\": \"Posterior Probability_score\", \"new_score_orientation\": \"higher_better\", \"new_score_type\": \"\", \"old_score\": \"\", \"proteins\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
-                        "type": "tool",
-                        "uuid": "37c738f6-b896-4d1f-a9e6-2f962cca61a2",
+                        "tool_errors": null,
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Custom Protein list (uniprot accession)\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "4d60060c-188b-4a93-8320-36f9b43e5765",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "e5270102-64f5-4c7b-b798-ce031275dfc0"
+                                "output_name": "output",
+                                "uuid": "27022e50-f5dc-46b1-8b54-979f955eb050"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "in": {
-                                "id": 8,
-                                "output_name": "out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "FileInfo",
-                        "outputs": [
+                        "annotation": "Input: Uniprot GO database file (choose the right organism)\nExample: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gene_association.goa_human.gz",
+                        "content_id": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out",
-                                "type": "txt"
+                                "description": "Input: Uniprot GO database file (choose the right organism)\nExample: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gene_association.goa_human.gz",
+                                "name": "Uniprot GO database"
                             }
                         ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 325.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": 2172,
-                            "right": 2372,
-                            "top": 212,
-                            "width": 200,
-                            "x": 2172,
-                            "y": 212
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "e8dce5e07fa5",
-                            "name": "openms_fileinfo",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 290,
+                            "top": 507
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"c\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"d\": \"false\", \"i\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"false\", \"p\": \"false\", \"s\": \"false\", \"v\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
-                        "type": "tool",
-                        "uuid": "64dd3889-3bd5-49b9-a84c-3d563764fa5a",
+                        "tool_errors": null,
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Uniprot GO database\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "e8f4a577-7b6a-4cd0-9a74-2e68c4ae6c5a",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "5bbfd315-1b89-4565-9297-dcde01c15619"
+                                "output_name": "output",
+                                "uuid": "b8fa36c2-6bbf-40c1-a472-8d4a6a7096c3"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0",
-                        "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "in": {
-                                "id": 8,
-                                "output_name": "out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "FidoAdapter",
-                        "outputs": [
+                        "annotation": "Input: Please downlad the Open Biomedical Ontology (OBO), i.e. \"GO term tree\" from\nhttp://purl.obolibrary.org/obo/go/go.obo",
+                        "content_id": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out",
-                                "type": "idxml"
+                                "description": "Input: Please downlad the Open Biomedical Ontology (OBO), i.e. \"GO term tree\" from\nhttp://purl.obolibrary.org/obo/go/go.obo",
+                                "name": "Open Biomedical Ontology (OBO)"
                             }
                         ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 445.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": 2172,
-                            "right": 2372,
-                            "top": 332,
-                            "width": 200,
-                            "x": 2172,
-                            "y": 332
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "c3a5cd016963",
-                            "name": "openms_fidoadapter",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 293,
+                            "top": 790
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"all_PSMs\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"greedy_group_resolution\": \"true\", \"group_level\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"log2_states\": \"0\", \"no_cleanup\": \"false\", \"prob\": {\"protein\": \"0.0\", \"peptide\": \"0.0\", \"spurious\": \"0.0\"}, \"separate_runs\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
-                        "type": "tool",
-                        "uuid": "27b53d06-d3a7-42e4-8ad4-1b861ae38777",
+                        "tool_errors": null,
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Open Biomedical Ontology (OBO)\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0640e1c4-4d77-49da-8473-0018e0a5db09",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "24c9df2d-4ed0-46cd-a949-60c8f21bc8eb"
+                                "output_name": "output",
+                                "uuid": "4725c10d-9e7a-4e3f-9874-c302c34687cb"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
-                        "errors": null,
-                        "id": 11,
+                        "annotation": "Final output. Unique entries of all proteins that are either predicted by WoLF PSORT to be shed or secreted or annotated in the GO database to be shed or secreted.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.0.0",
+                        "id": 30,
                         "input_connections": {
-                            "in": {
-                                "id": 10,
-                                "output_name": "out"
+                            "infile": {
+                                "id": 29,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "FalseDiscoveryRate",
+                        "name": "Unique",
                         "outputs": [
                             {
-                                "name": "out",
-                                "type": "idxml"
+                                "name": "outfile",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 386.8000030517578,
-                            "height": 174.8000030517578,
-                            "left": 2392,
-                            "right": 2592,
-                            "top": 212,
-                            "width": 200,
-                            "x": 2392,
-                            "y": 212
+                            "left": 1964.75,
+                            "top": 787.75
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutfile": {
+                                "action_arguments": {
+                                    "newname": "secretome_proteins"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "outfile"
+                            }
+                        },
+                        "tool_errors": null,
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "469690558892",
-                            "name": "openms_falsediscoveryrate",
-                            "owner": "galaxyp",
+                            "changeset_revision": "288462ec2630",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"FDR\": {\"PSM\": \"1.0\", \"protein\": \"0.01\", \"cleanup\": {\"remove_proteins_without_psms\": \"true\", \"remove_psms_without_proteins\": \"true\", \"remove_spectra_without_psms\": \"true\"}}, \"OPTIONAL_OUTPUTS\": null, \"PSM\": \"false\", \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"algorithm\": {\"no_qvalues\": \"false\", \"use_all_hits\": \"false\", \"split_charge_variants\": \"false\", \"treat_runs_separately\": \"false\", \"add_decoy_peptides\": \"false\", \"add_decoy_proteins\": \"false\", \"conservative\": \"true\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"protein\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"__page__\": 0, \"ignore_case\": \"\\\"False\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"is_numeric\": \"\\\"False\\\"\", \"infile\": \"null\"}",
+                        "tool_version": "1.0.0",
                         "type": "tool",
-                        "uuid": "e6fdc81c-b3b9-4916-9810-ebba68cde517",
+                        "uuid": "5ca3dd78-27ed-4f4f-95f6-c25fa4fd43b6",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out",
-                                "uuid": "bb2738e8-0258-4b31-a6e8-14ac4b750750"
+                                "label": "Secretome proteins",
+                                "output_name": "outfile",
+                                "uuid": "14e0c6dc-436b-4c4c-9292-d5e00cca8c92"
                             }
                         ]
-                    },
+                    }
+                ],
+                "parent_id": "proteomics/secretome-prediction",
+                "path": "topics/proteomics/tutorials/secretome-prediction/workflows/WF_secretomePrediction_goWolfpsort.ga",
+                "tags": [
+                    "proteomics"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Secreted Proteins Via GO Annotation And WoLF PSORT For shCTSB Paper",
+                "topic_id": "proteomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-secretome-prediction/versions/wf-secretomeprediction-gowolfpsort",
+                "tutorial_id": "secretome-prediction",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/secretome-prediction/workflows/WF_secretomePrediction_goWolfpsort.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/secretome-prediction/workflows/WF_secretomePrediction_goWolfpsort.html",
+                "version": 3,
+                "wfid": "proteomics-secretome-prediction",
+                "wfname": "wf-secretomeprediction-gowolfpsort",
+                "workflow": "WF_secretomePrediction_goWolfpsort.ga",
+                "workflow_tools": [
+                    "Convert characters1",
+                    "Filter1",
+                    "Grep1",
+                    "comp1",
+                    "get_subontology_from",
+                    "term_id_vs_term_name",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
+                    "toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/wolf_psort/0.0.8"
+                ],
+                "workflowhub_id": "1143"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/519260"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "pdaug_addclasslabel",
+                    "owner": "jay",
+                    "revisions": "7160bfd77aef",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pdaug_basic_plots",
+                    "owner": "jay",
+                    "revisions": "15b6eec94c40",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pdaug_fishers_plot",
+                    "owner": "jay",
+                    "revisions": "2fe62dfbdc9d",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pdaug_merge_dataframes",
+                    "owner": "jay",
+                    "revisions": "2dbfb42d34bc",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pdaug_peptide_data_access",
+                    "owner": "jay",
+                    "revisions": "7cf1e907c31d",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pdaug_peptide_sequence_analysis",
+                    "owner": "jay",
+                    "revisions": "90e3b1968ae6",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pdaug_sequence_property_based_descriptors",
+                    "owner": "jay",
+                    "revisions": "187c6f2d3b55",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pdaug_tsvtofasta",
+                    "owner": "jay",
+                    "revisions": "03f954dd8360",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: pdaug_addclasslabel\n  owner: jay\n  revisions: 7160bfd77aef\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_basic_plots\n  owner: jay\n  revisions: 15b6eec94c40\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_fishers_plot\n  owner: jay\n  revisions: 2fe62dfbdc9d\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_merge_dataframes\n  owner: jay\n  revisions: 2dbfb42d34bc\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_peptide_data_access\n  owner: jay\n  revisions: 7cf1e907c31d\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_peptide_sequence_analysis\n  owner: jay\n  revisions: 90e3b1968ae6\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_sequence_property_based_descriptors\n  owner: jay\n  revisions: 187c6f2d3b55\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pdaug_tsvtofasta\n  owner: jay\n  revisions: 03f954dd8360\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/peptide-library-data-analysis/tutorial.json",
+        "contributors": [
+            {
+                "id": "jaidevjoshi83",
+                "joined": "2020-11",
+                "name": "Jayadev Joshi",
+                "orcid": "0000-0001-7589-5230",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jaidevjoshi83/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jaidevjoshi83.json"
+            },
+            {
+                "id": "blankenberg",
+                "joined": "2018-07",
+                "name": "Daniel Blankenberg",
+                "orcid": "0000-0002-6833-9049",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankenberg/",
+                "twitter": "dblankenberg",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankenberg.json"
+            }
+        ],
+        "dir": "topics/proteomics/tutorials/peptide-library-data-analysis",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.be"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "proteomics/peptide-library-data-analysis",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": [
+            "Calculate descriptors",
+            "Quantitative analysis of peptide sequence properties"
+        ],
+        "pageviews": 821,
+        "pub_date": "2021-01-22",
+        "questions": [
+            "How to utilize quantitative properties of amino acids and peptide sequence to analyse peptide data?"
+        ],
+        "short_id": "T00227",
+        "short_tools": [
+            "pdaug_peptide_sequence_analysis",
+            "pdaug_basic_plots",
+            "pdaug_peptide_data_access",
+            "pdaug_addclasslabel",
+            "pdaug_fishers_plot",
+            "pdaug_tsvtofasta",
+            "pdaug_merge_dataframes",
+            "pdaug_sequence_property_based_descriptors"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "property-prediction",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [],
+        "time_estimation": "20m",
+        "title": "Peptide Library Data Analysis",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_addclasslabel/pdaug_addclasslabel/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_basic_plots/pdaug_basic_plots/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_fishers_plot/pdaug_fishers_plot/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_merge_dataframes/pdaug_merge_dataframes/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_peptide_data_access/pdaug_peptide_data_access/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_peptide_sequence_analysis/pdaug_peptide_sequence_analysis/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_sequence_property_based_descriptors/pdaug_sequence_property_based_descriptors/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/jay/pdaug_tsvtofasta/pdaug_tsvtofasta/0.1.0"
+        ],
+        "topic_name": "proteomics",
+        "topic_name_human": "Proteomics",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "peptide-library-data-analysis",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/peptide-library-data-analysis/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/peptide-library-data-analysis/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/peptide-library-data-analysis/tutorial.json"
+        },
+        "version": 5,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 159,
+        "visitors": 589,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Peptide Library Data Analysis",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"PDAUG Peptide Data Access\"]\n  1[label=\"PDAUG TSVtoFASTA\"]\n  0 -> 1 [label=\"output1\"]\n  2[label=\"PDAUG Peptide Sequence Analysis\"]\n  1 -> 2 [label=\"output3\"]\n  1 -> 2 [label=\"output2\"]\n  3[label=\"PDAUG Sequence Property Based Descriptors\"]\n  1 -> 3 [label=\"output2\"]\n  4[label=\"PDAUG Sequence Property Based Descriptors\"]\n  1 -> 4 [label=\"output3\"]\n  5[label=\"PDAUG Fisher\u2019s Plot\"]\n  1 -> 5 [label=\"output3\"]\n  1 -> 5 [label=\"output2\"]\n  6[label=\"AMP\"]\n  3 -> 6 [label=\"output1\"]\n  7[label=\"TMP\"]\n  4 -> 7 [label=\"output1\"]\n  8[label=\"PDAUG Merge Dataframes\"]\n  6 -> 8 [label=\"OutFile1\"]\n  7 -> 8 [label=\"OutFile1\"]\n  9[label=\"PDAUG Basic Plots\"]\n  8 -> 9 [label=\"output1\"]\n}",
+                "history": [
+                    {
+                        "hash": "c6cb67762f0c2d329bb52c6e6fb805df376f9ea0",
+                        "message": "Tutorials for PDAUG tool suite (#2150)",
+                        "num": 1,
+                        "short_hash": "c6cb67762",
+                        "unix": "1611340147"
+                    }
+                ],
+                "inputs": [],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"PDAUG Peptide Data Access\"];\n  1[\"PDAUG TSVtoFASTA\"];\n  0 -->|output1| 1;\n  2[\"PDAUG Peptide Sequence Analysis\"];\n  1 -->|output3| 2;\n  1 -->|output2| 2;\n  3[\"PDAUG Sequence Property Based Descriptors\"];\n  1 -->|output2| 3;\n  4[\"PDAUG Sequence Property Based Descriptors\"];\n  1 -->|output3| 4;\n  5[\"PDAUG Fisher\u2019s Plot\"];\n  1 -->|output3| 5;\n  1 -->|output2| 5;\n  6[\"AMP\"];\n  3 -->|output1| 6;\n  7[\"TMP\"];\n  4 -->|output1| 7;\n  8[\"PDAUG Merge Dataframes\"];\n  6 -->|OutFile1| 8;\n  7 -->|OutFile1| 8;\n  9[\"PDAUG Basic Plots\"];\n  8 -->|output1| 9;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Copy of PeptideDataAnalysis (imported from uploaded file)",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_peptide_data_access/pdaug_peptide_data_access/0.1.0",
                         "errors": null,
-                        "id": 12,
-                        "input_connections": {
-                            "in": {
-                                "id": 11,
-                                "output_name": "out"
-                            }
-                        },
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [],
                         "label": null,
-                        "name": "FileInfo",
+                        "name": "PDAUG Peptide Data Access",
                         "outputs": [
                             {
-                                "name": "out",
-                                "type": "txt"
+                                "name": "output1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 325.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": 2612,
-                            "right": 2812,
-                            "top": 212,
-                            "width": 200,
-                            "x": 2612,
-                            "y": 212
+                            "left": 200,
+                            "top": 200
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_peptide_data_access/pdaug_peptide_data_access/0.1.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "e8dce5e07fa5",
-                            "name": "openms_fileinfo",
-                            "owner": "galaxyp",
+                            "changeset_revision": "3eb014f169cf",
+                            "name": "pdaug_peptide_data_access",
+                            "owner": "jay",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"c\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"d\": \"false\", \"i\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"false\", \"p\": \"false\", \"s\": \"false\", \"v\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"SelectDatasets\": {\"DataBaseType\": \"AMPvsTMP\", \"__current_case__\": 4}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0",
                         "type": "tool",
-                        "uuid": "8f9e92ab-8d06-460c-9c2f-b4b8d701f3ee",
+                        "uuid": "cc540442-0f77-4623-acac-962820250573",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "f0910911-bcff-45c0-93b4-d966174ea637"
+                                "output_name": "output1",
+                                "uuid": "18bdb5f0-767f-4f38-a49d-daaf38287b79"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.6+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_fishers_plot/pdaug_fishers_plot/0.1.0",
                         "errors": null,
-                        "id": 13,
+                        "id": 5,
                         "input_connections": {
-                            "in": {
-                                "id": 11,
-                                "output_name": "out"
+                            "Fasta1": {
+                                "id": 1,
+                                "output_name": "output3"
+                            },
+                            "Fasta2": {
+                                "id": 1,
+                                "output_name": "output2"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "TextExporter",
+                        "name": "PDAUG Fisher's Plot",
                         "outputs": [
                             {
-                                "name": "out",
-                                "type": "tabular"
+                                "name": "output2",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": 445.6000061035156,
-                            "height": 113.60000610351562,
-                            "left": 2612,
-                            "right": 2812,
-                            "top": 332,
-                            "width": 200,
-                            "x": 2612,
-                            "y": 332
+                            "left": 770.99609375,
+                            "top": 912.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.6+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_fishers_plot/pdaug_fishers_plot/0.1.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "1c596fdaf34a",
-                            "name": "openms_textexporter",
-                            "owner": "galaxyp",
+                            "changeset_revision": "7a9f6ac448bc",
+                            "name": "pdaug_fishers_plot",
+                            "owner": "jay",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"consensus\": {\"sorting_method\": \"none\", \"sort_by_maps\": \"false\", \"sort_by_size\": \"false\"}, \"feature\": {\"minimal\": \"false\", \"add_metavalues\": \"-1\"}, \"id\": {\"proteins_only\": \"false\", \"peptides_only\": \"false\", \"protein_groups\": \"false\", \"first_dim_rt\": \"false\", \"add_metavalues\": \"-1\", \"add_hit_metavalues\": \"-1\", \"add_protein_hit_metavalues\": \"-1\"}, \"in\": {\"__class__\": \"ConnectedValue\"}, \"no_ids\": \"false\", \"quoting\": \"none\", \"replacement\": \"_\", \"separator\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6+galaxy0",
+                        "tool_state": "{\"Fasta1\": {\"__class__\": \"ConnectedValue\"}, \"Fasta2\": {\"__class__\": \"ConnectedValue\"}, \"overlap_factor\": \"5\", \"pop1_label\": \"TMPs\", \"pop2_label\": \"AMPs\", \"windows_per_frame\": \"5\", \"xlabel\": \"Mean volume\", \"ylabel\": \"Mean hydropathy\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0",
                         "type": "tool",
-                        "uuid": "2fc7c7a5-4ae4-4205-b02e-e587b3c0ce68",
+                        "uuid": "61d70923-d629-49a4-be01-0ead9c18bdb8",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out",
-                                "uuid": "293612b7-8f5c-4727-9805-5c060187883a"
+                                "output_name": "output2",
+                                "uuid": "c5869465-89c0-4183-9834-04d34f90233f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Grep1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_basic_plots/pdaug_basic_plots/0.1.0",
                         "errors": null,
-                        "id": 14,
+                        "id": 9,
                         "input_connections": {
-                            "input": {
-                                "id": 13,
-                                "output_name": "out"
+                            "SelPlotting|InFile": {
+                                "id": 8,
+                                "output_name": "output1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Select",
+                        "name": "PDAUG Basic Plots",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "output",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "bottom": 305.1999969482422,
-                            "height": 93.19999694824219,
-                            "left": 2832,
-                            "right": 3032,
-                            "top": 212,
-                            "width": 200,
-                            "x": 2832,
-                            "y": 212
+                            "left": 1627.5,
+                            "top": 200
                         },
                         "post_job_actions": {},
-                        "tool_id": "Grep1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"false\", \"pattern\": \"CONTAMINANT\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.1",
-                        "type": "tool",
-                        "uuid": "ab75d88c-15ca-48e5-ad26-effb00dd1dc9",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "cf9ac306-35ad-4846-a68d-ae635df7686e"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "Grep1",
-                        "errors": null,
-                        "id": 15,
-                        "input_connections": {
-                            "input": {
-                                "id": 13,
-                                "output_name": "out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Select",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 425.1999969482422,
-                            "height": 93.19999694824219,
-                            "left": 2832,
-                            "right": 3032,
-                            "top": 332,
-                            "width": 200,
-                            "x": 2832,
-                            "y": 332
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/jay/pdaug_basic_plots/pdaug_basic_plots/0.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "080b372fe513",
+                            "name": "pdaug_basic_plots",
+                            "owner": "jay",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "post_job_actions": {},
-                        "tool_id": "Grep1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"false\", \"pattern\": \"HUMAN\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.1",
+                        "tool_state": "{\"SelPlotting\": {\"Plot\": \"ScatterPlot\", \"__current_case__\": 2, \"InFile\": {\"__class__\": \"ConnectedValue\"}, \"PlotType\": {\"SelectPlot\": \"3D\", \"__current_case__\": 1, \"Features1\": \"_SecondaryStrD1100\", \"Features2\": \"_SolventAccessibilityD2001\", \"Features3\": \"_NormalizedVDWVD3050\"}, \"Label\": \"Class_label\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.0",
                         "type": "tool",
-                        "uuid": "3a18c2c5-f301-47b0-b446-deb0726ee889",
+                        "uuid": "457cfde2-d691-4e9c-af64-5416ae609770",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "5f0e93ec-df5f-4c23-8b11-e298abec7fb7"
+                                "output_name": "output",
+                                "uuid": "269a24c3-8cf7-4ab6-b08d-f91fd9996756"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/protein-id-oms",
-                "path": "topics/proteomics/tutorials/protein-id-oms/workflows/workflow.ga",
-                "tags": [
-                    "proteomics"
+                "parent_id": "proteomics/peptide-library-data-analysis",
+                "path": "topics/proteomics/tutorials/peptide-library-data-analysis/workflows/PeptideDataAnalysis.ga",
+                "tags": [
+                    "proteomics"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Copy of PeptideDataAnalysis (imported from uploaded file)",
+                "topic_id": "proteomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-peptide-library-data-analysis/versions/peptidedataanalysis",
+                "tutorial_id": "peptide-library-data-analysis",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/peptide-library-data-analysis/workflows/PeptideDataAnalysis.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/peptide-library-data-analysis/workflows/PeptideDataAnalysis.html",
+                "version": 1,
+                "wfid": "proteomics-peptide-library-data-analysis",
+                "wfname": "peptidedataanalysis",
+                "workflow": "PeptideDataAnalysis.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_addclasslabel/pdaug_addclasslabel/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_basic_plots/pdaug_basic_plots/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_fishers_plot/pdaug_fishers_plot/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_merge_dataframes/pdaug_merge_dataframes/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_peptide_data_access/pdaug_peptide_data_access/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_peptide_sequence_analysis/pdaug_peptide_sequence_analysis/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_sequence_property_based_descriptors/pdaug_sequence_property_based_descriptors/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/jay/pdaug_tsvtofasta/pdaug_tsvtofasta/0.1.0"
+                ],
+                "workflowhub_id": "1244"
+            }
+        ]
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "msconvert",
+                    "owner": "galaxyp",
+                    "revisions": "3cf310697624",
+                    "tool_panel_section_label": "Convert Formats",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_consensusid",
+                    "owner": "galaxyp",
+                    "revisions": "4e77b8f12cd3",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_falsediscoveryrate",
+                    "owner": "galaxyp",
+                    "revisions": "f7fef900f5b2",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_falsediscoveryrate",
+                    "owner": "galaxyp",
+                    "revisions": "c9eff69a7c62",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_fidoadapter",
+                    "owner": "galaxyp",
+                    "revisions": "890025d6e426",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_fidoadapter",
+                    "owner": "galaxyp",
+                    "revisions": "658494a2cb00",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_fileinfo",
+                    "owner": "galaxyp",
+                    "revisions": "5ad830edc021",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_fileinfo",
+                    "owner": "galaxyp",
+                    "revisions": "52ba9695e752",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_idfilter",
+                    "owner": "galaxyp",
+                    "revisions": "382cde407f81",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_idmerger",
+                    "owner": "galaxyp",
+                    "revisions": "1c5f31b8d632",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_idposteriorerrorprobability",
+                    "owner": "galaxyp",
+                    "revisions": "c69f69d7867a",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_idposteriorerrorprobability",
+                    "owner": "galaxyp",
+                    "revisions": "111c3a00136d",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_idscoreswitcher",
+                    "owner": "galaxyp",
+                    "revisions": "476b5e296979",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_idscoreswitcher",
+                    "owner": "galaxyp",
+                    "revisions": "be74a8cd7d66",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_msgfplusadapter",
+                    "owner": "galaxyp",
+                    "revisions": "a407b6790342",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_peakpickerhires",
+                    "owner": "galaxyp",
+                    "revisions": "3d8d4ada5405",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_peptideindexer",
+                    "owner": "galaxyp",
+                    "revisions": "e039cc5c7aed",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_peptideindexer",
+                    "owner": "galaxyp",
+                    "revisions": "dd173849c3d8",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_textexporter",
+                    "owner": "galaxyp",
+                    "revisions": "9020199dba0a",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_xtandemadapter",
+                    "owner": "galaxyp",
+                    "revisions": "c8b225c69a7f",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "openms_xtandemadapter",
+                    "owner": "galaxyp",
+                    "revisions": "7f6a1f27553e",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: msconvert\n  owner: galaxyp\n  revisions: 3cf310697624\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_consensusid\n  owner: galaxyp\n  revisions: 4e77b8f12cd3\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_falsediscoveryrate\n  owner: galaxyp\n  revisions: f7fef900f5b2\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_falsediscoveryrate\n  owner: galaxyp\n  revisions: c9eff69a7c62\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_fidoadapter\n  owner: galaxyp\n  revisions: 890025d6e426\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_fidoadapter\n  owner: galaxyp\n  revisions: 658494a2cb00\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_fileinfo\n  owner: galaxyp\n  revisions: 5ad830edc021\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_fileinfo\n  owner: galaxyp\n  revisions: 52ba9695e752\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idfilter\n  owner: galaxyp\n  revisions: 382cde407f81\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idmerger\n  owner: galaxyp\n  revisions: 1c5f31b8d632\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idposteriorerrorprobability\n  owner: galaxyp\n  revisions: c69f69d7867a\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idposteriorerrorprobability\n  owner: galaxyp\n  revisions: 111c3a00136d\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idscoreswitcher\n  owner: galaxyp\n  revisions: 476b5e296979\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_idscoreswitcher\n  owner: galaxyp\n  revisions: be74a8cd7d66\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_msgfplusadapter\n  owner: galaxyp\n  revisions: a407b6790342\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_peakpickerhires\n  owner: galaxyp\n  revisions: 3d8d4ada5405\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_peptideindexer\n  owner: galaxyp\n  revisions: e039cc5c7aed\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_peptideindexer\n  owner: galaxyp\n  revisions: dd173849c3d8\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_textexporter\n  owner: galaxyp\n  revisions: 9020199dba0a\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_xtandemadapter\n  owner: galaxyp\n  revisions: c8b225c69a7f\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: openms_xtandemadapter\n  owner: galaxyp\n  revisions: 7f6a1f27553e\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/protein-id-oms/tutorial.json",
+        "contributors": [
+            {
+                "email": "sigloch+github@mailbox.org",
+                "former_affiliations": [
+                    "uni-freiburg"
+                ],
+                "id": "stortebecker",
+                "joined": "2017-09",
+                "name": "Florian Christoph Sigloch",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stortebecker/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/stortebecker.json"
+            },
+            {
+                "affiliations": [
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
+                "fediverse_flavor": "mastodon",
+                "id": "bgruening",
+                "joined": "2017-09",
+                "linkedin": "bgruening",
+                "location": {
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
+                },
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+            }
+        ],
+        "dir": "topics/proteomics/tutorials/protein-id-oms",
+        "edam_operation": [
+            "Filtering",
+            "Formatting"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "proteomics",
+                "tutorials": [
+                    "protein-quant-sil"
                 ],
-                "test_results": null,
-                "tests": false,
-                "title": "Proteomics: Peptide and Protein ID using OpenMS",
-                "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-protein-id-oms/versions/workflow",
-                "tutorial_id": "protein-id-oms",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/protein-id-oms/workflows/workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/protein-id-oms/workflows/workflow.html",
-                "version": 6,
-                "wfid": "proteomics-protein-id-oms",
-                "wfname": "workflow",
-                "workflow": "workflow.ga",
-                "workflow_tools": [
-                    "Grep1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerhires/PeakPickerHiRes/2.3.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0"
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "proteomics/protein-id-oms",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "LC-MS/MS raw files have to be converted to mzML before using GalaxyP on most GalaxyP servers.",
+            "OpenMS provides many tools for proteomic analysis and guarantees compatibility by using open file formats.",
+            "OpenMS provides several thirdparty search engines and Fido for protein inference."
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Advanced",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": [
+            "Protein identification from LC-MS/MS raw files."
+        ],
+        "pageviews": 4800,
+        "pub_date": "2017-10-16",
+        "questions": [
+            "How to convert LC-MS/MS raw files?",
+            "How to identify peptides?",
+            "How to identify proteins?",
+            "How to evaluate the results?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "proteomics",
+                "tutorials": [
+                    "database-handling"
                 ],
-                "workflowhub_id": "1188"
-            },
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00228",
+        "short_tools": [
+            "MSGFPlusAdapter",
+            "FalseDiscoveryRate",
+            "PeakPickerHiRes",
+            "IDScoreSwitcher",
+            "TextExporter",
+            "FileInfo",
+            "XTandemAdapter",
+            "msconvert",
+            "IDFilter",
+            "Grep1",
+            "ConsensusID",
+            "IDMerger",
+            "IDPosteriorErrorProbability",
+            "PeptideIndexer",
+            "FidoAdapter"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "id-quant",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "DDA",
+            "HeLa"
+        ],
+        "time_estimation": "45m",
+        "title": "Peptide and Protein ID using OpenMS tools",
+        "tools": [
+            "Grep1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_consensusid/ConsensusID/2.2.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.2.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.2.0.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.2.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmerger/IDMerger/2.2.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.2.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.2.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/2.2.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerhires/PeakPickerHiRes/2.3.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.2.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.6+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.2.0.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0"
+        ],
+        "topic_name": "proteomics",
+        "topic_name_human": "Proteomics",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "protein-id-oms",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/protein-id-oms/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/protein-id-oms/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/protein-id-oms/tutorial.json"
+        },
+        "version": 31,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 172,
+        "visitors": 2767,
+        "workflows": [
             {
                 "creators": [],
                 "description": "Peptide and Protein ID using OpenMS tools",
@@ -201826,35 +203923,70 @@
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmzML_test_dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHuman_database_including_decoys\"]\n  2[label=\"XTandemAdapter\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"MSGFPlusAdapter\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"IDPosteriorErrorProbability\"]\n  2 -> 4 [label=\"param_out\"]\n  5[label=\"IDPosteriorErrorProbability\"]\n  3 -> 5 [label=\"param_out\"]\n  6[label=\"IDMerger\"]\n  5 -> 6 [label=\"param_out\"]\n  4 -> 6 [label=\"param_out\"]\n  7[label=\"ConsensusID\"]\n  6 -> 7 [label=\"param_out\"]\n  8[label=\"PeptideIndexer\"]\n  1 -> 8 [label=\"output\"]\n  7 -> 8 [label=\"param_out\"]\n  9[label=\"FalseDiscoveryRate\"]\n  8 -> 9 [label=\"param_out\"]\n  10[label=\"IDScoreSwitcher\"]\n  9 -> 10 [label=\"param_out\"]\n  11[label=\"FileInfo\"]\n  9 -> 11 [label=\"param_out\"]\n  12[label=\"FidoAdapter\"]\n  10 -> 12 [label=\"param_out\"]\n  13[label=\"FalseDiscoveryRate\"]\n  12 -> 13 [label=\"param_out\"]\n  14[label=\"IDFilter\"]\n  13 -> 14 [label=\"param_out\"]\n  15[label=\"FileInfo\"]\n  14 -> 15 [label=\"param_out\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmzml input\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nfasta input\"]\n  2[label=\"PeakPickerHiRes\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"XTandemAdapter\"]\n  1 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"param_out\"]\n  4[label=\"FileInfo\"]\n  3 -> 4 [label=\"out\"]\n  5[label=\"PeptideIndexer\"]\n  1 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"out\"]\n  6[label=\"IDPosteriorErrorProbability\"]\n  5 -> 6 [label=\"out\"]\n  7[label=\"FalseDiscoveryRate\"]\n  6 -> 7 [label=\"out\"]\n  8[label=\"IDScoreSwitcher\"]\n  7 -> 8 [label=\"out\"]\n  9[label=\"FileInfo\"]\n  8 -> 9 [label=\"out\"]\n  10[label=\"FidoAdapter\"]\n  8 -> 10 [label=\"out\"]\n  11[label=\"FalseDiscoveryRate\"]\n  10 -> 11 [label=\"out\"]\n  12[label=\"FileInfo\"]\n  11 -> 12 [label=\"out\"]\n  13[label=\"TextExporter\"]\n  11 -> 13 [label=\"out\"]\n  14[label=\"Select\"]\n  13 -> 14 [label=\"out\"]\n  15[label=\"Select\"]\n  13 -> 15 [label=\"out\"]\n}",
                 "history": [
+                    {
+                        "hash": "54b4d9fcc78b1394f71f7affd51ca15e83b211d5",
+                        "message": "Adding tags to workflows",
+                        "num": 9,
+                        "short_hash": "54b4d9fcc",
+                        "unix": "1604224600"
+                    },
+                    {
+                        "hash": "ca84d739509bdb1ef8f3cfc64c15242ef0363407",
+                        "message": "Updating Tutorials to OpenMS 2.6, adjusting of parameters and tools, adding tool versions",
+                        "num": 8,
+                        "short_hash": "ca84d7395",
+                        "unix": "1604176914"
+                    },
                     {
                         "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
                         "message": "annotation",
-                        "num": 4,
+                        "num": 7,
                         "short_hash": "667ff3de9",
                         "unix": "1579690769"
                     },
                     {
                         "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
                         "message": "Workflow renaming",
-                        "num": 3,
+                        "num": 6,
                         "short_hash": "eb4d724e0",
                         "unix": "1579084895"
                     },
                     {
-                        "hash": "643fab24d5e16da68d2ad7ec87252b68f520f62f",
-                        "message": "update workflow",
-                        "num": 2,
-                        "short_hash": "643fab24d",
-                        "unix": "1538518838"
+                        "hash": "775a0b42554fad0d7106779b50b758f34f9388f0",
+                        "message": "Updated workflow containing all follow up tools",
+                        "num": 5,
+                        "short_hash": "775a0b425",
+                        "unix": "1553092201"
+                    },
+                    {
+                        "hash": "08f1e0dc3f10498a73acb658e65375b6589b7ce2",
+                        "message": "Updated workflow for ID training",
+                        "num": 4,
+                        "short_hash": "08f1e0dc3",
+                        "unix": "1553088979"
+                    },
+                    {
+                        "hash": "dbcc48eaa51d95815ca6a19bd643264e9db81825",
+                        "message": "fix workflow name",
+                        "num": 3,
+                        "short_hash": "dbcc48eaa",
+                        "unix": "1510677790"
                     },
                     {
                         "hash": "b916508e1e11168c289f744f7acfc847e906285a",
                         "message": "Added workflow for two search engines, deleted ms2 PeakPicking and updated old workflow, added link to workflow in tutorial",
-                        "num": 1,
+                        "num": 2,
                         "short_hash": "b916508e1",
                         "unix": "1510655977"
+                    },
+                    {
+                        "hash": "a6411f26e23a9e4754177332839416165c9b4658",
+                        "message": "New tutorial \"Protein ID using OpenMS\" and major revision of \"Protein ID using SG/PS\" (#570)",
+                        "num": 1,
+                        "short_hash": "a6411f26e",
+                        "unix": "1508148807"
                     }
                 ],
                 "inputs": [
@@ -201867,26 +203999,32 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "mzML_test_dataset"
+                                "name": "mzml input"
                             }
                         ],
-                        "label": "mzML_test_dataset",
+                        "label": "mzml input",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 219
+                            "bottom": 218.8000030517578,
+                            "height": 61.80000305175781,
+                            "left": 546,
+                            "right": 746,
+                            "top": 157,
+                            "width": 200,
+                            "x": 546,
+                            "y": 157
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"mzML_test_dataset\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "f388c78b-a105-4a24-897f-d2f3510d3cc4",
+                        "uuid": "1604c094-ef2d-4094-a0f4-dc530fe8e359",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "643ec67a-7144-4d78-a58a-527d2a582bbc"
+                                "uuid": "c7aacc63-3815-4e28-9c1d-9b2378799a97"
                             }
                         ]
                     },
@@ -201899,34 +204037,40 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Human_database_including_decoys"
+                                "name": "fasta input"
                             }
                         ],
-                        "label": "Human_database_including_decoys",
+                        "label": "fasta input",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 324
+                            "bottom": 430.8000030517578,
+                            "height": 61.80000305175781,
+                            "left": 541,
+                            "right": 741,
+                            "top": 369,
+                            "width": 200,
+                            "x": 541,
+                            "y": 369
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"Human_database_including_decoys\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "7b1b1907-1591-45af-a841-4c54ea936d81",
+                        "uuid": "d948aea0-6741-4a7f-a07c-fd451674714e",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "fbb8c863-7d41-4261-8651-a407818ca5c1"
+                                "uuid": "b3071ae5-c01b-4cba-a31a-0b36943c2aca"
                             }
                         ]
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nmzML_test_dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nHuman_database_including_decoys\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"XTandemAdapter\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"MSGFPlusAdapter\"];\n  1 -->|output| 3;\n  4[\"IDPosteriorErrorProbability\"];\n  2 -->|param_out| 4;\n  5[\"IDPosteriorErrorProbability\"];\n  3 -->|param_out| 5;\n  6[\"IDMerger\"];\n  5 -->|param_out| 6;\n  4 -->|param_out| 6;\n  7[\"ConsensusID\"];\n  6 -->|param_out| 7;\n  8[\"PeptideIndexer\"];\n  1 -->|output| 8;\n  7 -->|param_out| 8;\n  9[\"FalseDiscoveryRate\"];\n  8 -->|param_out| 9;\n  10[\"IDScoreSwitcher\"];\n  9 -->|param_out| 10;\n  11[\"FileInfo\"];\n  9 -->|param_out| 11;\n  12[\"FidoAdapter\"];\n  10 -->|param_out| 12;\n  13[\"FalseDiscoveryRate\"];\n  12 -->|param_out| 13;\n  14[\"IDFilter\"];\n  13 -->|param_out| 14;\n  15[\"FileInfo\"];\n  14 -->|param_out| 15;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Peptide And Protein ID Via OMS Using Two Search Engines",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nmzml input\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nfasta input\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"PeakPickerHiRes\"];\n  0 -->|output| 2;\n  3[\"XTandemAdapter\"];\n  1 -->|output| 3;\n  2 -->|param_out| 3;\n  4[\"FileInfo\"];\n  3 -->|out| 4;\n  5[\"PeptideIndexer\"];\n  1 -->|output| 5;\n  3 -->|out| 5;\n  6[\"IDPosteriorErrorProbability\"];\n  5 -->|out| 6;\n  7[\"FalseDiscoveryRate\"];\n  6 -->|out| 7;\n  8[\"IDScoreSwitcher\"];\n  7 -->|out| 8;\n  9[\"FileInfo\"];\n  8 -->|out| 9;\n  10[\"FidoAdapter\"];\n  8 -->|out| 10;\n  11[\"FalseDiscoveryRate\"];\n  10 -->|out| 11;\n  12[\"FileInfo\"];\n  11 -->|out| 12;\n  13[\"TextExporter\"];\n  11 -->|out| 13;\n  14[\"Select\"];\n  13 -->|out| 14;\n  15[\"Select\"];\n  13 -->|out| 15;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Proteomics: Peptide and Protein ID using OpenMS",
                 "outputs": [
                     {
                         "annotation": "",
@@ -201937,26 +204081,32 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "mzML_test_dataset"
+                                "name": "mzml input"
                             }
                         ],
-                        "label": "mzML_test_dataset",
+                        "label": "mzml input",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 219
+                            "bottom": 218.8000030517578,
+                            "height": 61.80000305175781,
+                            "left": 546,
+                            "right": 746,
+                            "top": 157,
+                            "width": 200,
+                            "x": 546,
+                            "y": 157
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"mzML_test_dataset\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "f388c78b-a105-4a24-897f-d2f3510d3cc4",
+                        "uuid": "1604c094-ef2d-4094-a0f4-dc530fe8e359",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "643ec67a-7144-4d78-a58a-527d2a582bbc"
+                                "uuid": "c7aacc63-3815-4e28-9c1d-9b2378799a97"
                             }
                         ]
                     },
@@ -201969,984 +204119,640 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Human_database_including_decoys"
+                                "name": "fasta input"
                             }
                         ],
-                        "label": "Human_database_including_decoys",
+                        "label": "fasta input",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 324
+                            "bottom": 430.8000030517578,
+                            "height": 61.80000305175781,
+                            "left": 541,
+                            "right": 741,
+                            "top": 369,
+                            "width": 200,
+                            "x": 541,
+                            "y": 369
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"Human_database_including_decoys\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "7b1b1907-1591-45af-a841-4c54ea936d81",
+                        "uuid": "d948aea0-6741-4a7f-a07c-fd451674714e",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "fbb8c863-7d41-4261-8651-a407818ca5c1"
+                                "uuid": "b3071ae5-c01b-4cba-a31a-0b36943c2aca"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.2.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerhires/PeakPickerHiRes/2.3.0",
                         "errors": null,
-                        "id": 9,
+                        "id": 2,
                         "input_connections": {
                             "param_in": {
-                                "id": 8,
-                                "output_name": "param_out"
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool FalseDiscoveryRate",
-                                "name": "param_in"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "FalseDiscoveryRate",
+                        "name": "PeakPickerHiRes",
                         "outputs": [
                             {
                                 "name": "param_out",
-                                "type": "idxml"
+                                "type": "mzml"
                             }
                         ],
                         "position": {
-                            "left": 1888,
-                            "top": 219
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionparam_out": {
-                                "action_arguments": {
-                                    "newname": "Peptide IDs (idXML)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "param_out"
-                            }
+                            "bottom": 325.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": 852,
+                            "right": 1052,
+                            "top": 212,
+                            "width": 200,
+                            "x": 852,
+                            "y": 212
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.2.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerhires/PeakPickerHiRes/2.3.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "f7fef900f5b2",
-                            "name": "openms_falsediscoveryrate",
+                            "changeset_revision": "3d8d4ada5405",
+                            "name": "openms_peakpickerhires",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"param_algorithm_use_all_hits\": \"\\\"false\\\"\", \"param_PSM\": \"\\\"true\\\"\", \"param_FDR_PSM\": \"\\\"0.01\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"param_algorithm_split_charge_variants\": \"\\\"false\\\"\", \"param_algorithm_no_qvalues\": \"\\\"false\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_algorithm_treat_runs_separately\": \"\\\"false\\\"\", \"param_protein\": \"\\\"false\\\"\", \"param_FDR_protein\": \"\\\"1.0\\\"\", \"param_algorithm_add_decoy_peptides\": \"\\\"true\\\"\"}",
-                        "tool_version": "2.2.0",
+                        "tool_state": "{\"__input_ext\": \"mzml\", \"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"param_algorithm_SignalToNoise_bin_count\": \"30\", \"param_algorithm_SignalToNoise_min_required_elements\": \"10\", \"param_algorithm_SignalToNoise_win_len\": \"200.0\", \"param_algorithm_SignalToNoise_write_log_messages\": \"true\", \"param_algorithm_report_FWHM\": \"false\", \"param_algorithm_report_FWHM_unit\": \"relative\", \"param_algorithm_signal_to_noise\": \"0.0\", \"param_in\": {\"__class__\": \"ConnectedValue\"}, \"rep_param_algorithm_ms_levels\": [{\"__index__\": 0, \"param_algorithm_ms_levels\": \"2\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.3.0",
                         "type": "tool",
-                        "uuid": "c5dabcee-14be-4494-8a87-6b03843ebbd6",
+                        "uuid": "09ceeb02-6c71-4ee3-b70a-ad879b4904e1",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "param_out",
-                                "uuid": "e42e42c6-0fec-49c4-a5fb-67e140445752"
+                                "uuid": "058dedba-3334-4687-8e34-c995a1d019c4"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0",
                         "errors": null,
-                        "id": 11,
+                        "id": 3,
                         "input_connections": {
-                            "param_in": {
-                                "id": 9,
+                            "database": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "in": {
+                                "id": 2,
                                 "output_name": "param_out"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool FileInfo",
-                                "name": "param_in"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "FileInfo",
+                        "name": "XTandemAdapter",
                         "outputs": [
                             {
-                                "name": "param_out",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "param_out_tsv",
-                                "type": "tabular"
+                                "name": "out",
+                                "type": "idxml"
                             }
                         ],
                         "position": {
-                            "left": 2217,
-                            "top": 352.5
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionparam_out": {
-                                "action_arguments": {
-                                    "newname": "FileInfo Peptide IDs (txt)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "param_out"
-                            },
-                            "RenameDatasetActionparam_out_tsv": {
-                                "action_arguments": {
-                                    "newname": "FileInfo Peptide IDs (tabular)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "param_out_tsv"
-                            }
+                            "bottom": 427.1999969482422,
+                            "height": 215.1999969482422,
+                            "left": 1072,
+                            "right": 1272,
+                            "top": 212,
+                            "width": 200,
+                            "x": 1072,
+                            "y": 212
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "5ad830edc021",
-                            "name": "openms_fileinfo",
+                            "changeset_revision": "1add9bacdccd",
+                            "name": "openms_xtandemadapter",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"param_v\": \"\\\"false\\\"\", \"param_p\": \"\\\"false\\\"\", \"param_s\": \"\\\"false\\\"\", \"param_m\": \"\\\"false\\\"\", \"param_i\": \"\\\"false\\\"\", \"param_d\": \"\\\"false\\\"\", \"param_c\": \"\\\"false\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "2.2.0",
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": [\"out_FLAG\"], \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"database\": {\"__class__\": \"ConnectedValue\"}, \"default_config_file\": null, \"enzyme\": \"Trypsin\", \"fixed_modifications\": [\"Carbamidomethyl (C)\"], \"fragment_error_units\": \"ppm\", \"fragment_mass_tolerance\": \"10.0\", \"ignore_adapter_param\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"max_precursor_charge\": \"4\", \"max_valid_expect\": \"0.1\", \"minimum_fragment_mz\": \"150.0\", \"missed_cleavages\": \"1\", \"no_isotope_error\": \"false\", \"output_results\": \"all\", \"precursor_error_units\": \"ppm\", \"precursor_mass_tolerance\": \"10.0\", \"semi_cleavage\": \"false\", \"variable_modifications\": [\"Oxidation (M)\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
                         "type": "tool",
-                        "uuid": "7c834594-54f3-4201-a45a-4c75c41825f0",
+                        "uuid": "5fe07f26-b2e1-4a10-a4ae-439ee6146c8b",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "param_out_tsv",
-                                "uuid": "118d2874-3da7-4133-ae7d-b6e47d2c5a1a"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "param_out",
-                                "uuid": "36885b5d-64c4-46e4-8388-43c1058c6251"
+                                "output_name": "out",
+                                "uuid": "893e0901-e84a-4212-837d-63036f8b4d51"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.2.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
                         "errors": null,
-                        "id": 14,
+                        "id": 4,
                         "input_connections": {
-                            "param_in": {
-                                "id": 13,
-                                "output_name": "param_out"
+                            "in": {
+                                "id": 3,
+                                "output_name": "out"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool IDFilter",
-                                "name": "param_whitelist_peptides"
-                            },
-                            {
-                                "description": "runtime parameter for tool IDFilter",
-                                "name": "param_whitelist_proteins"
-                            },
-                            {
-                                "description": "runtime parameter for tool IDFilter",
-                                "name": "param_blacklist_proteins"
-                            },
-                            {
-                                "description": "runtime parameter for tool IDFilter",
-                                "name": "param_in"
-                            },
-                            {
-                                "description": "runtime parameter for tool IDFilter",
-                                "name": "param_blacklist_peptides"
-                            },
-                            {
-                                "description": "runtime parameter for tool IDFilter",
-                                "name": "param_digest_fasta"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "IDFilter",
+                        "name": "FileInfo",
                         "outputs": [
                             {
-                                "name": "param_out",
-                                "type": "idxml"
+                                "name": "out",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 3042,
-                            "top": 220
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionparam_out": {
-                                "action_arguments": {
-                                    "newname": "Protein IDs (idXML)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "param_out"
-                            }
+                            "bottom": 325.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": 1292,
+                            "right": 1492,
+                            "top": 212,
+                            "width": 200,
+                            "x": 1292,
+                            "y": 212
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.2.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "382cde407f81",
-                            "name": "openms_idfilter",
+                            "changeset_revision": "e8dce5e07fa5",
+                            "name": "openms_fileinfo",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"param_whitelist_peptides\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_length\": \"\\\":\\\"\", \"param_keep_unreferenced_protein_hits\": \"\\\"false\\\"\", \"param_unique\": \"\\\"false\\\"\", \"param_whitelist_proteins\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_unique_per_protein\": \"\\\"false\\\"\", \"param_remove_decoys\": \"\\\"false\\\"\", \"param_score_prot\": \"\\\"0.01\\\"\", \"__rerun_remap_job_id__\": null, \"param_precursor_mz\": \"\\\":\\\"\", \"param_mz_error\": \"\\\"-1.0\\\"\", \"rep_param_blacklist_modifications\": \"[]\", \"param_blacklist_proteins\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_delete_unreferenced_peptide_hits\": \"\\\"false\\\"\", \"param_blacklist_ignore_modifications\": \"\\\"false\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null, \"param_charge\": \"\\\":\\\"\", \"param_var_mods\": \"\\\"false\\\"\", \"param_best_strict\": \"\\\"false\\\"\", \"param_digest_specificity\": \"\\\"full\\\"\", \"param_digest_missed_cleavages\": \"\\\"-1\\\"\", \"rep_param_whitelist_modifications\": \"[]\", \"param_mz_unit\": \"\\\"ppm\\\"\", \"rep_param_whitelist_protein_accessions\": \"[]\", \"param_best_n_peptide_hits\": \"\\\"0\\\"\", \"param_blacklist_peptides\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"param_score_pep\": \"\\\"0.0\\\"\", \"param_digest_methionine_cleavage\": \"\\\"false\\\"\", \"param_best_n_protein_hits\": \"\\\"0\\\"\", \"param_precursor_rt\": \"\\\":\\\"\", \"param_digest_fasta\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"rep_param_blacklist_protein_accessions\": \"[]\", \"param_whitelist_ignore_modifications\": \"\\\"false\\\"\", \"param_digest_enzyme\": \"\\\"Trypsin\\\"\"}",
-                        "tool_version": "2.2.0",
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"c\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"d\": \"false\", \"i\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"false\", \"p\": \"false\", \"s\": \"false\", \"v\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
                         "type": "tool",
-                        "uuid": "7955e91e-a52b-4153-8222-3b16ae99fd94",
+                        "uuid": "0afb93c4-71a2-481a-a64d-936b394dde64",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "param_out",
-                                "uuid": "fe8099a0-d4c5-4e0d-a21e-62406c69c137"
+                                "output_name": "out",
+                                "uuid": "0e8d24f3-79a8-4914-802b-5f50f34bafa5"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0",
                         "errors": null,
-                        "id": 15,
+                        "id": 5,
                         "input_connections": {
-                            "param_in": {
-                                "id": 14,
-                                "output_name": "param_out"
+                            "fasta": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "in": {
+                                "id": 3,
+                                "output_name": "out"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool FileInfo",
-                                "name": "param_in"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "FileInfo",
+                        "name": "PeptideIndexer",
                         "outputs": [
                             {
-                                "name": "param_out",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "param_out_tsv",
-                                "type": "tabular"
+                                "name": "out",
+                                "type": "idxml"
                             }
                         ],
                         "position": {
-                            "left": 3370,
-                            "top": 219
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionparam_out": {
-                                "action_arguments": {
-                                    "newname": "FileInfo Protein IDs (txt)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "param_out"
-                            },
-                            "RenameDatasetActionparam_out_tsv": {
-                                "action_arguments": {
-                                    "newname": "FileInfo Protein IDs (tabular)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "param_out_tsv"
-                            }
+                            "bottom": 537.1999969482422,
+                            "height": 205.1999969482422,
+                            "left": 1292,
+                            "right": 1492,
+                            "top": 332,
+                            "width": 200,
+                            "x": 1292,
+                            "y": 332
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "5ad830edc021",
-                            "name": "openms_fileinfo",
+                            "changeset_revision": "d8ee5700c66b",
+                            "name": "openms_peptideindexer",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"param_v\": \"\\\"false\\\"\", \"param_p\": \"\\\"false\\\"\", \"param_s\": \"\\\"false\\\"\", \"param_m\": \"\\\"false\\\"\", \"param_i\": \"\\\"false\\\"\", \"param_d\": \"\\\"false\\\"\", \"param_c\": \"\\\"false\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "2.2.0",
+                        "tool_state": "{\"IL_equivalent\": \"false\", \"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"aaa_max\": \"3\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"decoy_string\": \"\", \"decoy_string_position\": \"prefix\", \"enzyme\": {\"name\": \"auto\", \"specificity\": \"none\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"in\": {\"__class__\": \"ConnectedValue\"}, \"keep_unreferenced_proteins\": \"false\", \"mismatches_max\": \"0\", \"missing_decoy_action\": \"error\", \"unmatched_action\": \"error\", \"write_protein_description\": \"true\", \"write_protein_sequence\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
                         "type": "tool",
-                        "uuid": "0a22ddc7-00a6-424f-9ce2-5816423d49ba",
+                        "uuid": "39045d4c-f666-40f2-8c21-677271e734cc",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "param_out_tsv",
-                                "uuid": "97b4b4e9-1745-49fd-8b0c-bc5bce0ab5b2"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "param_out",
-                                "uuid": "dc6535dd-cc02-4be9-bd2e-6a37f8e164c0"
+                                "output_name": "out",
+                                "uuid": "ca346fb2-f01e-4374-bce7-8fe6eddf5d3c"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "proteomics/protein-id-oms",
-                "path": "topics/proteomics/tutorials/protein-id-oms/workflows/workflow_two-search-engines.ga",
-                "tags": [
-                    "proteomics"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Peptide And Protein ID Via OMS Using Two Search Engines",
-                "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-protein-id-oms/versions/workflow-two-search-engines",
-                "tutorial_id": "protein-id-oms",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/protein-id-oms/workflows/workflow_two-search-engines.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/protein-id-oms/workflows/workflow_two-search-engines.html",
-                "version": 4,
-                "wfid": "proteomics-protein-id-oms",
-                "wfname": "workflow-two-search-engines",
-                "workflow": "workflow_two-search-engines.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_consensusid/ConsensusID/2.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.2.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmerger/IDMerger/2.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/2.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.2.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.2.0.1"
-                ],
-                "workflowhub_id": "1191"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/546301"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "column_maker",
-                    "owner": "devteam",
-                    "revisions": "be25c075ed54",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "histogram",
-                    "owner": "devteam",
-                    "revisions": "6f134426c2b0",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "maxquant",
-                    "owner": "galaxyp",
-                    "revisions": "37d669de2828",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "msstats",
-                    "owner": "galaxyp",
-                    "revisions": "52ac6fde9a5b",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: be25c075ed54\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: histogram\n  owner: devteam\n  revisions: 6f134426c2b0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: maxquant\n  owner: galaxyp\n  revisions: 37d669de2828\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msstats\n  owner: galaxyp\n  revisions: 52ac6fde9a5b\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/maxquant-label-free/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "email": "melanie.foell@mol-med.uni-freiburg.de",
-                "id": "foellmelanie",
-                "joined": "2018-10",
-                "matrix": "foellmelanie:matrix.org",
-                "name": "Melanie F\u00f6ll",
-                "orcid": "0000-0002-1887-7543",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
-                "twitter": "MCFoell",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "email": "matthias.fahrner@uniklinik-freiburg.de",
-                "id": "matthias313",
-                "joined": "2019-03",
-                "name": "Matthias Fahrner",
-                "orcid": "0000-0001-7955-2518",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/matthias313/",
-                "twitter": "mfahrner313",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/matthias313.json"
-            }
-        ],
-        "dir": "topics/proteomics/tutorials/maxquant-label-free",
-        "edam_operation": [
-            "Visualisation",
-            "Imputation",
-            "Heat map generation",
-            "Tag-based peptide identification",
-            "Standardisation and normalisation",
-            "Principal component plotting",
-            "Differential protein expression profiling",
-            "Protein quantification",
-            "Spectrum calculation",
-            "Clustering",
-            "Statistical calculation"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "proteomics/maxquant-label-free",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.org.au"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "MaxQuant offers a single tool solution for protein identification and quantification.",
-            "Label-free quantitation reveals the most abundant proteins in serum samples."
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Introductory",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Analysis of human serum proteome samples with label-free quantification in MaxQuant"
-        ],
-        "pageviews": 23901,
-        "pub_date": "2020-04-29",
-        "questions": [
-            "How to perform label-free analysis in Maxquant?",
-            "Which are the most abundant proteins in serum?",
-            "How successful was the depletion of those in our experiment?"
-        ],
-        "short_id": "T00218",
-        "short_tools": [
-            "Grep1",
-            "msstats",
-            "maxquant",
-            "Cut1",
-            "Filter1",
-            "tp_sort_header_tool",
-            "Add_a_column1",
-            "histogram_rpy"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "id-quant",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "DDA",
-            "label-free"
-        ],
-        "time_estimation": "1H",
-        "title": "Label-free data analysis using MaxQuant",
-        "tools": [
-            "Cut1",
-            "Filter1",
-            "Grep1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.20.1.0"
-        ],
-        "topic_name": "proteomics",
-        "topic_name_human": "Proteomics",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "maxquant-label-free",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-label-free/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/maxquant-label-free/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/maxquant-label-free/tutorial.json"
-        },
-        "version": 12,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 102,
-        "visitors": 16079,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Label-free data analysis using MaxQuant",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nProtein_database\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSample1\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSample2\"]\n  3[label=\"MaxQuant\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Filter\"]\n  3 -> 4 [label=\"proteinGroups\"]\n  5[label=\"Select\"]\n  4 -> 5 [label=\"out_file1\"]\n  6[label=\"Cut\"]\n  5 -> 6 [label=\"out_file1\"]\n  7[label=\"Sort\"]\n  6 -> 7 [label=\"out_file1\"]\n  8[label=\"Compute\"]\n  6 -> 8 [label=\"out_file1\"]\n  9[label=\"Sort\"]\n  7 -> 9 [label=\"outfile\"]\n  10[label=\"Compute\"]\n  8 -> 10 [label=\"out_file1\"]\n  11[label=\"Cut\"]\n  10 -> 11 [label=\"out_file1\"]\n  12[label=\"Compute\"]\n  10 -> 12 [label=\"out_file1\"]\n  13[label=\"Histogram\"]\n  12 -> 13 [label=\"out_file1\"]\n}",
-                "history": [
-                    {
-                        "hash": "1a316efffa5d21398409e859952e3f99ae0aac9a",
-                        "message": "update wf parameter",
-                        "num": 8,
-                        "short_hash": "1a316efff",
-                        "unix": "1605483358"
-                    },
-                    {
-                        "hash": "dffe67cc1cd22e5f34204ccd105a156188c88fc8",
-                        "message": "Updating figure and workflow",
-                        "num": 7,
-                        "short_hash": "dffe67cc1",
-                        "unix": "1604174052"
-                    },
-                    {
-                        "hash": "3fd8e24d19128f02d08c3dd8d44ca034fd0bba9d",
-                        "message": "Adding steps to workflow",
-                        "num": 6,
-                        "short_hash": "3fd8e24d1",
-                        "unix": "1603366973"
-                    },
-                    {
-                        "hash": "cf8b1cb0509e73e534c234076c8bd055379823c5",
-                        "message": "Update some workflow names for consistency",
-                        "num": 5,
-                        "short_hash": "cf8b1cb05",
-                        "unix": "1598836271"
-                    },
-                    {
-                        "hash": "cdab43efb540f8228bce6af36097b4ce2f7b8019",
-                        "message": "update maxquant workflow histogram version to 1.0.4, add test",
-                        "num": 4,
-                        "short_hash": "cdab43efb",
-                        "unix": "1596427673"
-                    },
-                    {
-                        "hash": "ba67a0dfefa95ef6538d0c229146b475ba806f0a",
-                        "message": "Adding a few more follow up steps and improving some older training content",
-                        "num": 3,
-                        "short_hash": "ba67a0dfe",
-                        "unix": "1591567276"
-                    },
-                    {
-                        "hash": "5d041fcf71bb9e8c35d11b00a7531b32de608ce2",
-                        "message": "adding more stuff to the workflow",
-                        "num": 2,
-                        "short_hash": "5d041fcf7",
-                        "unix": "1588178974"
                     },
-                    {
-                        "hash": "83de9bde8bfd5f709f0e1347841e30664057b6c2",
-                        "message": "Adding MaxQuant training and levels for other proteomics tutorials",
-                        "num": 1,
-                        "short_hash": "83de9bde8",
-                        "unix": "1588175696"
-                    }
-                ],
-                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy0",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 6,
+                        "input_connections": {
+                            "in": {
+                                "id": 5,
+                                "output_name": "out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "IDPosteriorErrorProbability",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Protein_database"
+                                "name": "out",
+                                "type": "idxml"
                             }
                         ],
-                        "label": "Protein_database",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 525.6999969482422,
-                            "height": 82.19999694824219,
-                            "left": -15,
-                            "right": 185,
-                            "top": 443.5,
+                            "bottom": 386.8000030517578,
+                            "height": 174.8000030517578,
+                            "left": 1512,
+                            "right": 1712,
+                            "top": 212,
                             "width": 200,
-                            "x": -15,
-                            "y": 443.5
+                            "x": 1512,
+                            "y": 212
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "90cc78f2-681e-4855-8e66-e4884558be47",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "711a081d80ba",
+                            "name": "openms_idposteriorerrorprobability",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fit_algorithm\": {\"number_of_bins\": \"100\", \"incorrectly_assigned\": \"Gumbel\", \"max_nr_iterations\": \"1000\", \"neg_log_delta\": \"6\", \"outlier_handling\": \"ignore_iqr_outliers\"}, \"ignore_bad_data\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"prob_correct\": \"true\", \"split_charge\": \"false\", \"top_hits_only\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "e0bdc6ec-b1ff-436e-8ebc-0fdd5f7206b7",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "bc660f8d-110e-4c33-909b-66c0c29748c9"
+                                "output_name": "out",
+                                "uuid": "584f8b3b-6e0c-492b-92ee-9996e27f4769"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 7,
+                        "input_connections": {
+                            "in": {
+                                "id": 6,
+                                "output_name": "out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FalseDiscoveryRate",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Sample1"
+                                "name": "out",
+                                "type": "idxml"
                             }
                         ],
-                        "label": "Sample1",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 637.3000030517578,
-                            "height": 61.80000305175781,
-                            "left": -49,
-                            "right": 151,
-                            "top": 575.5,
+                            "bottom": 386.8000030517578,
+                            "height": 174.8000030517578,
+                            "left": 1732,
+                            "right": 1932,
+                            "top": 212,
                             "width": 200,
-                            "x": -49,
-                            "y": 575.5
+                            "x": 1732,
+                            "y": 212
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "eb754bfe-49b1-406d-8eb9-842b8f1fab22",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "469690558892",
+                            "name": "openms_falsediscoveryrate",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"FDR\": {\"PSM\": \"0.01\", \"protein\": \"1.0\", \"cleanup\": {\"remove_proteins_without_psms\": \"true\", \"remove_psms_without_proteins\": \"true\", \"remove_spectra_without_psms\": \"true\"}}, \"OPTIONAL_OUTPUTS\": null, \"PSM\": \"true\", \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"algorithm\": {\"no_qvalues\": \"false\", \"use_all_hits\": \"false\", \"split_charge_variants\": \"false\", \"treat_runs_separately\": \"false\", \"add_decoy_peptides\": \"true\", \"add_decoy_proteins\": \"false\", \"conservative\": \"true\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"protein\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "b0e90f52-67ab-497c-8cc0-81997cda5ec0",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "9a0693dc-6c4d-4fe8-8c8d-4846938278c3"
+                                "output_name": "out",
+                                "uuid": "7d94c074-055a-4348-969f-c5e3e3404cd1"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.6+galaxy0",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 8,
+                        "input_connections": {
+                            "in": {
+                                "id": 7,
+                                "output_name": "out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "IDScoreSwitcher",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Sample2"
+                                "name": "out",
+                                "type": "idxml"
                             }
                         ],
-                        "label": "Sample2",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 766.3000030517578,
-                            "height": 61.80000305175781,
-                            "left": -42,
-                            "right": 158,
-                            "top": 704.5,
+                            "bottom": 346,
+                            "height": 134,
+                            "left": 1952,
+                            "right": 2152,
+                            "top": 212,
                             "width": 200,
-                            "x": -42,
-                            "y": 704.5
+                            "x": 1952,
+                            "y": 212
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "321c3baa-dd58-45ce-9a28-ee1eb7332f0f",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ec0d05b20eed",
+                            "name": "openms_idscoreswitcher",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"new_score\": \"Posterior Probability_score\", \"new_score_orientation\": \"higher_better\", \"new_score_type\": \"\", \"old_score\": \"\", \"proteins\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "37c738f6-b896-4d1f-a9e6-2f962cca61a2",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "0a8fcb2d-5b66-4e0f-bb8c-46017c426cf2"
+                                "output_name": "out",
+                                "uuid": "e5270102-64f5-4c7b-b798-ce031275dfc0"
                             }
                         ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nProtein_database\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSample1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nSample2\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"MaxQuant\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  2 -->|output| 3;\n  4[\"Filter\"];\n  3 -->|proteinGroups| 4;\n  5[\"Select\"];\n  4 -->|out_file1| 5;\n  6[\"Cut\"];\n  5 -->|out_file1| 6;\n  7[\"Sort\"];\n  6 -->|out_file1| 7;\n  8[\"Compute\"];\n  6 -->|out_file1| 8;\n  9[\"Sort\"];\n  7 -->|outfile| 9;\n  10[\"Compute\"];\n  8 -->|out_file1| 10;\n  11[\"Cut\"];\n  10 -->|out_file1| 11;\n  12[\"Compute\"];\n  10 -->|out_file1| 12;\n  13[\"Histogram\"];\n  12 -->|out_file1| 13;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Proteomics: MaxQuant workflow",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 9,
+                        "input_connections": {
+                            "in": {
+                                "id": 8,
+                                "output_name": "out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FileInfo",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Protein_database"
+                                "name": "out",
+                                "type": "txt"
                             }
                         ],
-                        "label": "Protein_database",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 525.6999969482422,
-                            "height": 82.19999694824219,
-                            "left": -15,
-                            "right": 185,
-                            "top": 443.5,
+                            "bottom": 325.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": 2172,
+                            "right": 2372,
+                            "top": 212,
                             "width": 200,
-                            "x": -15,
-                            "y": 443.5
+                            "x": 2172,
+                            "y": 212
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "90cc78f2-681e-4855-8e66-e4884558be47",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e8dce5e07fa5",
+                            "name": "openms_fileinfo",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"c\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"d\": \"false\", \"i\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"false\", \"p\": \"false\", \"s\": \"false\", \"v\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "64dd3889-3bd5-49b9-a84c-3d563764fa5a",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "bc660f8d-110e-4c33-909b-66c0c29748c9"
+                                "output_name": "out",
+                                "uuid": "5bbfd315-1b89-4565-9297-dcde01c15619"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 10,
+                        "input_connections": {
+                            "in": {
+                                "id": 8,
+                                "output_name": "out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FidoAdapter",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Sample1"
+                                "name": "out",
+                                "type": "idxml"
                             }
                         ],
-                        "label": "Sample1",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 637.3000030517578,
-                            "height": 61.80000305175781,
-                            "left": -49,
-                            "right": 151,
-                            "top": 575.5,
+                            "bottom": 445.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": 2172,
+                            "right": 2372,
+                            "top": 332,
                             "width": 200,
-                            "x": -49,
-                            "y": 575.5
+                            "x": 2172,
+                            "y": 332
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "eb754bfe-49b1-406d-8eb9-842b8f1fab22",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "c3a5cd016963",
+                            "name": "openms_fidoadapter",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"all_PSMs\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"greedy_group_resolution\": \"true\", \"group_level\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"log2_states\": \"0\", \"no_cleanup\": \"false\", \"prob\": {\"protein\": \"0.0\", \"peptide\": \"0.0\", \"spurious\": \"0.0\"}, \"separate_runs\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "27b53d06-d3a7-42e4-8ad4-1b861ae38777",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "9a0693dc-6c4d-4fe8-8c8d-4846938278c3"
+                                "output_name": "out",
+                                "uuid": "24c9df2d-4ed0-46cd-a949-60c8f21bc8eb"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 11,
+                        "input_connections": {
+                            "in": {
+                                "id": 10,
+                                "output_name": "out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FalseDiscoveryRate",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Sample2"
+                                "name": "out",
+                                "type": "idxml"
                             }
                         ],
-                        "label": "Sample2",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 766.3000030517578,
-                            "height": 61.80000305175781,
-                            "left": -42,
-                            "right": 158,
-                            "top": 704.5,
+                            "bottom": 386.8000030517578,
+                            "height": 174.8000030517578,
+                            "left": 2392,
+                            "right": 2592,
+                            "top": 212,
                             "width": 200,
-                            "x": -42,
-                            "y": 704.5
+                            "x": 2392,
+                            "y": 212
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "321c3baa-dd58-45ce-9a28-ee1eb7332f0f",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "469690558892",
+                            "name": "openms_falsediscoveryrate",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"FDR\": {\"PSM\": \"1.0\", \"protein\": \"0.01\", \"cleanup\": {\"remove_proteins_without_psms\": \"true\", \"remove_psms_without_proteins\": \"true\", \"remove_spectra_without_psms\": \"true\"}}, \"OPTIONAL_OUTPUTS\": null, \"PSM\": \"false\", \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"algorithm\": {\"no_qvalues\": \"false\", \"use_all_hits\": \"false\", \"split_charge_variants\": \"false\", \"treat_runs_separately\": \"false\", \"add_decoy_peptides\": \"false\", \"add_decoy_proteins\": \"false\", \"conservative\": \"true\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"protein\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
+                        "type": "tool",
+                        "uuid": "e6fdc81c-b3b9-4916-9810-ebba68cde517",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "0a8fcb2d-5b66-4e0f-bb8c-46017c426cf2"
+                                "output_name": "out",
+                                "uuid": "bb2738e8-0258-4b31-a6e8-14ac4b750750"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
                         "errors": null,
-                        "id": 3,
+                        "id": 12,
                         "input_connections": {
-                            "input_opts|fasta_files": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "paramGroups_0|files": [
-                                {
-                                    "id": 1,
-                                    "output_name": "output"
-                                },
-                                {
-                                    "id": 2,
-                                    "output_name": "output"
-                                }
-                            ]
+                            "in": {
+                                "id": 11,
+                                "output_name": "out"
+                            }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "MaxQuant",
+                        "name": "FileInfo",
                         "outputs": [
                             {
-                                "name": "proteinGroups",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "mqpar",
-                                "type": "xml"
-                            },
-                            {
-                                "name": "peptides",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "ptxqc_report",
-                                "type": "pdf"
+                                "name": "out",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 780.8999938964844,
-                            "height": 408.3999938964844,
-                            "left": 310,
-                            "right": 510,
-                            "top": 372.5,
+                            "bottom": 325.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": 2612,
+                            "right": 2812,
+                            "top": 212,
                             "width": 200,
-                            "x": 310,
-                            "y": 372.5
+                            "x": 2612,
+                            "y": 212
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "ea0a1d50c83f",
-                            "name": "maxquant",
+                            "changeset_revision": "e8dce5e07fa5",
+                            "name": "openms_fileinfo",
                             "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_opts\": {\"ftype\": \".thermo.raw\", \"fasta_files\": {\"__class__\": \"ConnectedValue\"}, \"identifier_parse_rule\": \">.*\\\\|(.*)\\\\|\", \"description_parse_rule\": \">(.*) OS\"}, \"output_opts\": {\"dry_run\": \"false\", \"output\": [\"proteinGroups\", \"mqpar\", \"peptides\"]}, \"paramGroups\": [{\"__index__\": 0, \"files\": {\"__class__\": \"ConnectedValue\"}, \"maxMissedCleavages\": \"1\", \"fixedModifications\": [\"Carbamidomethyl (C)\"], \"variableModifications\": null, \"enzymes\": [\"Trypsin/P\"], \"digestion_mode\": \"0\", \"quant_method\": {\"select_quant_method\": \"lfq\", \"__current_case__\": 2, \"lfqMinRatioCount\": \"2\", \"lfqMinEdgesPerNode\": \"3\", \"lfqAvEdgesPerNode\": \"6\", \"lfqSkipNorm\": \"true\"}}], \"protein_quant\": {\"peptides_for_quantification\": \"1\", \"only_unmod_prot\": {\"unmod_prot\": \"True\", \"__current_case__\": 0, \"mods_used_prot_quant\": [\"Acetyl (Protein N-term)\", \"Oxidation (M)\"], \"discard_unmod_cpart_peptides\": \"true\"}, \"lfq_opts\": {\"separateLfq\": \"false\", \"lfqStabilizeLargeRatios\": \"true\", \"lfqRequireMsms\": \"true\", \"do_ibaq\": {\"ibaq\": \"False\", \"__current_case__\": 1}, \"advancedSiteIntensities\": \"true\"}}, \"qc\": {\"do_it\": \"true\", \"__current_case__\": 0, \"parameters\": \"true\", \"summary\": \"true\", \"proteingroups\": \"true\", \"evidence\": \"true\", \"msms\": \"true\", \"msmsscans\": \"true\"}, \"search_opts\": {\"template\": null, \"min_peptide_len\": \"7\", \"max_peptide_mass\": \"4600\", \"min_unique_pep\": \"1\", \"calc_peak_properties\": \"false\", \"match_between_runs\": \"false\", \"incl_contaminants\": \"true\", \"decoy_mode\": \"revert\", \"psm_fdr\": \"0.01\", \"protein_fdr\": \"0.01\", \"min_pep_length\": \"8\", \"max_pep_length\": \"25\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.6.10.43+galaxy3",
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"c\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"d\": \"false\", \"i\": \"false\", \"in\": {\"__class__\": \"ConnectedValue\"}, \"m\": \"false\", \"p\": \"false\", \"s\": \"false\", \"v\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
                         "type": "tool",
-                        "uuid": "ae1d3f39-d1a8-4cd3-9534-64cc69f175a9",
+                        "uuid": "8f9e92ab-8d06-460c-9c2f-b4b8d701f3ee",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "peptides",
-                                "uuid": "fe9cec5c-de9c-4c39-bddd-e7dd199f2564"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "ptxqc_report",
-                                "uuid": "360aa96f-bebf-46b6-9b30-1d6940779216"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "proteinGroups",
-                                "uuid": "c155ddc4-7084-4830-836d-b71f7557a86e"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "mqpar",
-                                "uuid": "23b1a6e3-3da7-4c60-951b-71b1f4da33ba"
+                                "output_name": "out",
+                                "uuid": "f0910911-bcff-45c0-93b4-d966174ea637"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Filter1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.6+galaxy0",
                         "errors": null,
-                        "id": 4,
+                        "id": 13,
                         "input_connections": {
-                            "input": {
-                                "id": 3,
-                                "output_name": "proteinGroups"
+                            "in": {
+                                "id": 11,
+                                "output_name": "out"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Filter",
+                        "name": "TextExporter",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "out",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 465.6999969482422,
-                            "height": 93.19999694824219,
-                            "left": 530,
-                            "right": 730,
-                            "top": 372.5,
+                            "bottom": 445.6000061035156,
+                            "height": 113.60000610351562,
+                            "left": 2612,
+                            "right": 2812,
+                            "top": 332,
                             "width": 200,
-                            "x": 530,
-                            "y": 372.5
+                            "x": 2612,
+                            "y": 332
                         },
                         "post_job_actions": {},
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c38!=\\\"+\\\"\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.6+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "1c596fdaf34a",
+                            "name": "openms_textexporter",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"OPTIONAL_OUTPUTS\": null, \"__input_ext\": \"input\", \"adv_opts_cond\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"consensus\": {\"sorting_method\": \"none\", \"sort_by_maps\": \"false\", \"sort_by_size\": \"false\"}, \"feature\": {\"minimal\": \"false\", \"add_metavalues\": \"-1\"}, \"id\": {\"proteins_only\": \"false\", \"peptides_only\": \"false\", \"protein_groups\": \"false\", \"first_dim_rt\": \"false\", \"add_metavalues\": \"-1\", \"add_hit_metavalues\": \"-1\", \"add_protein_hit_metavalues\": \"-1\"}, \"in\": {\"__class__\": \"ConnectedValue\"}, \"no_ids\": \"false\", \"quoting\": \"none\", \"replacement\": \"_\", \"separator\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6+galaxy0",
                         "type": "tool",
-                        "uuid": "295e41a6-0642-414e-a939-8179f8b5f47d",
+                        "uuid": "2fc7c7a5-4ae4-4205-b02e-e587b3c0ce68",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "7d51c925-9c11-4125-98f3-abe19bc22825"
+                                "output_name": "out",
+                                "uuid": "293612b7-8f5c-4727-9805-5c060187883a"
                             }
                         ]
                     },
@@ -202954,11 +204760,11 @@
                         "annotation": "",
                         "content_id": "Grep1",
                         "errors": null,
-                        "id": 5,
+                        "id": 14,
                         "input_connections": {
                             "input": {
-                                "id": 4,
-                                "output_name": "out_file1"
+                                "id": 13,
+                                "output_name": "out"
                             }
                         },
                         "inputs": [],
@@ -202971,728 +204777,1061 @@
                             }
                         ],
                         "position": {
-                            "bottom": 470.6999969482422,
+                            "bottom": 305.1999969482422,
                             "height": 93.19999694824219,
-                            "left": 745,
-                            "right": 945,
-                            "top": 377.5,
+                            "left": 2832,
+                            "right": 3032,
+                            "top": 212,
                             "width": 200,
-                            "x": 745,
-                            "y": 377.5
+                            "x": 2832,
+                            "y": 212
                         },
                         "post_job_actions": {},
                         "tool_id": "Grep1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"false\", \"pattern\": \"(HUMAN)|(Majority)\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"false\", \"pattern\": \"CONTAMINANT\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.0.1",
                         "type": "tool",
-                        "uuid": "f582f3e8-8308-49c3-a1ee-3ba9051f5a85",
+                        "uuid": "ab75d88c-15ca-48e5-ad26-effb00dd1dc9",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "out_file1",
-                                "uuid": "e88a2cae-98f1-471d-9131-338a6e1169fd"
+                                "uuid": "cf9ac306-35ad-4846-a68d-ae635df7686e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Cut1",
+                        "content_id": "Grep1",
                         "errors": null,
-                        "id": 6,
+                        "id": 15,
                         "input_connections": {
                             "input": {
-                                "id": 5,
-                                "output_name": "out_file1"
+                                "id": 13,
+                                "output_name": "out"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Cut",
+                        "name": "Select",
                         "outputs": [
                             {
                                 "name": "out_file1",
-                                "type": "tabular"
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "bottom": 465.6999969482422,
+                            "bottom": 425.1999969482422,
                             "height": 93.19999694824219,
-                            "left": 970,
-                            "right": 1170,
-                            "top": 372.5,
+                            "left": 2832,
+                            "right": 3032,
+                            "top": 332,
                             "width": 200,
-                            "x": 970,
-                            "y": 372.5
+                            "x": 2832,
+                            "y": 332
                         },
                         "post_job_actions": {},
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c8,c32,c33\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2",
+                        "tool_id": "Grep1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"false\", \"pattern\": \"HUMAN\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.1",
                         "type": "tool",
-                        "uuid": "99557c29-6927-4736-afff-9a2be53e967e",
+                        "uuid": "3a18c2c5-f301-47b0-b446-deb0726ee889",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "out_file1",
-                                "uuid": "a97baff1-6f76-4400-98c7-138666974448"
+                                "uuid": "5f0e93ec-df5f-4c23-8b11-e298abec7fb7"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "proteomics/protein-id-oms",
+                "path": "topics/proteomics/tutorials/protein-id-oms/workflows/workflow.ga",
+                "tags": [
+                    "proteomics"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Proteomics: Peptide and Protein ID using OpenMS",
+                "topic_id": "proteomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-protein-id-oms/versions/workflow",
+                "tutorial_id": "protein-id-oms",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/protein-id-oms/workflows/workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/protein-id-oms/workflows/workflow.html",
+                "version": 6,
+                "wfid": "proteomics-protein-id-oms",
+                "wfname": "workflow",
+                "workflow": "workflow.ga",
+                "workflow_tools": [
+                    "Grep1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerhires/PeakPickerHiRes/2.3.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0"
+                ],
+                "workflowhub_id": "1188"
+            },
+            {
+                "creators": [],
+                "description": "Peptide and Protein ID using OpenMS tools",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmzML_test_dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHuman_database_including_decoys\"]\n  2[label=\"XTandemAdapter\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"MSGFPlusAdapter\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"IDPosteriorErrorProbability\"]\n  2 -> 4 [label=\"param_out\"]\n  5[label=\"IDPosteriorErrorProbability\"]\n  3 -> 5 [label=\"param_out\"]\n  6[label=\"IDMerger\"]\n  5 -> 6 [label=\"param_out\"]\n  4 -> 6 [label=\"param_out\"]\n  7[label=\"ConsensusID\"]\n  6 -> 7 [label=\"param_out\"]\n  8[label=\"PeptideIndexer\"]\n  1 -> 8 [label=\"output\"]\n  7 -> 8 [label=\"param_out\"]\n  9[label=\"FalseDiscoveryRate\"]\n  8 -> 9 [label=\"param_out\"]\n  10[label=\"IDScoreSwitcher\"]\n  9 -> 10 [label=\"param_out\"]\n  11[label=\"FileInfo\"]\n  9 -> 11 [label=\"param_out\"]\n  12[label=\"FidoAdapter\"]\n  10 -> 12 [label=\"param_out\"]\n  13[label=\"FalseDiscoveryRate\"]\n  12 -> 13 [label=\"param_out\"]\n  14[label=\"IDFilter\"]\n  13 -> 14 [label=\"param_out\"]\n  15[label=\"FileInfo\"]\n  14 -> 15 [label=\"param_out\"]\n}",
+                "history": [
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 4,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 3,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "643fab24d5e16da68d2ad7ec87252b68f520f62f",
+                        "message": "update workflow",
+                        "num": 2,
+                        "short_hash": "643fab24d",
+                        "unix": "1538518838"
                     },
+                    {
+                        "hash": "b916508e1e11168c289f744f7acfc847e906285a",
+                        "message": "Added workflow for two search engines, deleted ms2 PeakPicking and updated old workflow, added link to workflow in tutorial",
+                        "num": 1,
+                        "short_hash": "b916508e1",
+                        "unix": "1510655977"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "infile": {
-                                "id": 6,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Sort",
-                        "outputs": [
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "outfile",
-                                "type": "input"
+                                "description": "",
+                                "name": "mzML_test_dataset"
                             }
                         ],
+                        "label": "mzML_test_dataset",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 344.6999969482422,
-                            "height": 93.19999694824219,
-                            "left": 1162,
-                            "right": 1362,
-                            "top": 251.5,
-                            "width": 200,
-                            "x": 1162,
-                            "y": 251.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 200,
+                            "top": 219
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"header\": \"1\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"2\", \"order\": \"r\", \"style\": \"g\"}], \"unique\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
-                        "type": "tool",
-                        "uuid": "c6da37e8-98fc-4ab2-8ec1-9a55510b09c5",
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"mzML_test_dataset\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "f388c78b-a105-4a24-897f-d2f3510d3cc4",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "44df6e3d-01b3-4136-b18b-694f4d153b32"
+                                "output_name": "output",
+                                "uuid": "643ec67a-7144-4d78-a58a-527d2a582bbc"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "input": {
-                                "id": 6,
-                                "output_name": "out_file1"
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Human_database_including_decoys"
                             }
+                        ],
+                        "label": "Human_database_including_decoys",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 324
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Compute",
-                        "outputs": [
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Human_database_including_decoys\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "7b1b1907-1591-45af-a841-4c54ea936d81",
+                        "workflow_outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "fbb8c863-7d41-4261-8651-a407818ca5c1"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nmzML_test_dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nHuman_database_including_decoys\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"XTandemAdapter\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"MSGFPlusAdapter\"];\n  1 -->|output| 3;\n  4[\"IDPosteriorErrorProbability\"];\n  2 -->|param_out| 4;\n  5[\"IDPosteriorErrorProbability\"];\n  3 -->|param_out| 5;\n  6[\"IDMerger\"];\n  5 -->|param_out| 6;\n  4 -->|param_out| 6;\n  7[\"ConsensusID\"];\n  6 -->|param_out| 7;\n  8[\"PeptideIndexer\"];\n  1 -->|output| 8;\n  7 -->|param_out| 8;\n  9[\"FalseDiscoveryRate\"];\n  8 -->|param_out| 9;\n  10[\"IDScoreSwitcher\"];\n  9 -->|param_out| 10;\n  11[\"FileInfo\"];\n  9 -->|param_out| 11;\n  12[\"FidoAdapter\"];\n  10 -->|param_out| 12;\n  13[\"FalseDiscoveryRate\"];\n  12 -->|param_out| 13;\n  14[\"IDFilter\"];\n  13 -->|param_out| 14;\n  15[\"FileInfo\"];\n  14 -->|param_out| 15;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Peptide And Protein ID Via OMS Using Two Search Engines",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "mzML_test_dataset"
                             }
                         ],
+                        "label": "mzML_test_dataset",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 585.6999969482422,
-                            "height": 93.19999694824219,
-                            "left": 1190,
-                            "right": 1390,
-                            "top": 492.5,
-                            "width": 200,
-                            "x": 1190,
-                            "y": 492.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "be25c075ed54",
-                            "name": "column_maker",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 200,
+                            "top": 219
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"avoid_scientific_notation\": \"no\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"log(c2,2)\", \"header_lines_conditional\": {\"header_lines_select\": \"yes\", \"__current_case__\": 1, \"header_new_column_name\": \"log2 intensity sample1\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"round\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3.0",
-                        "type": "tool",
-                        "uuid": "a73294a5-050b-436a-95c2-7042aa30bab3",
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"mzML_test_dataset\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "f388c78b-a105-4a24-897f-d2f3510d3cc4",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "ec3d0fb2-8ce0-48d9-92d5-590c2644e326"
+                                "output_name": "output",
+                                "uuid": "643ec67a-7144-4d78-a58a-527d2a582bbc"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "infile": {
-                                "id": 7,
-                                "output_name": "outfile"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Sort",
-                        "outputs": [
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "outfile",
-                                "type": "input"
+                                "description": "",
+                                "name": "Human_database_including_decoys"
                             }
                         ],
+                        "label": "Human_database_including_decoys",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 339.6999969482422,
-                            "height": 93.19999694824219,
-                            "left": 1410,
-                            "right": 1610,
-                            "top": 246.5,
-                            "width": 200,
-                            "x": 1410,
-                            "y": 246.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 200,
+                            "top": 324
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"header\": \"1\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"3\", \"order\": \"r\", \"style\": \"g\"}], \"unique\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
-                        "type": "tool",
-                        "uuid": "3f46dbc8-6684-4e43-bfca-114671eff459",
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Human_database_including_decoys\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "7b1b1907-1591-45af-a841-4c54ea936d81",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "9ea6d4d3-05a4-4b64-a36c-eb4417be546d"
+                                "output_name": "output",
+                                "uuid": "fbb8c863-7d41-4261-8651-a407818ca5c1"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.2.0",
                         "errors": null,
-                        "id": 10,
+                        "id": 9,
                         "input_connections": {
-                            "input": {
+                            "param_in": {
                                 "id": 8,
-                                "output_name": "out_file1"
+                                "output_name": "param_out"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool FalseDiscoveryRate",
+                                "name": "param_in"
+                            }
+                        ],
                         "label": null,
-                        "name": "Compute",
+                        "name": "FalseDiscoveryRate",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "param_out",
+                                "type": "idxml"
                             }
                         ],
                         "position": {
-                            "bottom": 585.6999969482422,
-                            "height": 93.19999694824219,
-                            "left": 1410,
-                            "right": 1610,
-                            "top": 492.5,
-                            "width": 200,
-                            "x": 1410,
-                            "y": 492.5
+                            "left": 1888,
+                            "top": 219
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                        "post_job_actions": {
+                            "RenameDatasetActionparam_out": {
+                                "action_arguments": {
+                                    "newname": "Peptide IDs (idXML)"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "param_out"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.2.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "be25c075ed54",
-                            "name": "column_maker",
-                            "owner": "devteam",
+                            "changeset_revision": "f7fef900f5b2",
+                            "name": "openms_falsediscoveryrate",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"avoid_scientific_notation\": \"no\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"log(c3,2)\", \"header_lines_conditional\": {\"header_lines_select\": \"yes\", \"__current_case__\": 1, \"header_new_column_name\": \"log2 intensity sample2\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"round\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3.0",
+                        "tool_state": "{\"__page__\": null, \"param_algorithm_use_all_hits\": \"\\\"false\\\"\", \"param_PSM\": \"\\\"true\\\"\", \"param_FDR_PSM\": \"\\\"0.01\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"param_algorithm_split_charge_variants\": \"\\\"false\\\"\", \"param_algorithm_no_qvalues\": \"\\\"false\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_algorithm_treat_runs_separately\": \"\\\"false\\\"\", \"param_protein\": \"\\\"false\\\"\", \"param_FDR_protein\": \"\\\"1.0\\\"\", \"param_algorithm_add_decoy_peptides\": \"\\\"true\\\"\"}",
+                        "tool_version": "2.2.0",
                         "type": "tool",
-                        "uuid": "f164eec0-10d2-446d-ada7-db67303384f9",
+                        "uuid": "c5dabcee-14be-4494-8a87-6b03843ebbd6",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "1905e349-23d8-4b81-a156-7e22977d3593"
+                                "output_name": "param_out",
+                                "uuid": "e42e42c6-0fec-49c4-a5fb-67e140445752"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Cut1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0",
                         "errors": null,
                         "id": 11,
                         "input_connections": {
-                            "input": {
-                                "id": 10,
-                                "output_name": "out_file1"
+                            "param_in": {
+                                "id": 9,
+                                "output_name": "param_out"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool FileInfo",
+                                "name": "param_in"
+                            }
+                        ],
                         "label": null,
-                        "name": "Cut",
+                        "name": "FileInfo",
                         "outputs": [
                             {
-                                "name": "out_file1",
+                                "name": "param_out",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "param_out_tsv",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 766.6999969482422,
-                            "height": 93.19999694824219,
-                            "left": 1568,
-                            "right": 1768,
-                            "top": 673.5,
-                            "width": 200,
-                            "x": 1568,
-                            "y": 673.5
+                            "left": 2217,
+                            "top": 352.5
                         },
-                        "post_job_actions": {},
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"columnList\": \"c4,c5\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2",
+                        "post_job_actions": {
+                            "RenameDatasetActionparam_out": {
+                                "action_arguments": {
+                                    "newname": "FileInfo Peptide IDs (txt)"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "param_out"
+                            },
+                            "RenameDatasetActionparam_out_tsv": {
+                                "action_arguments": {
+                                    "newname": "FileInfo Peptide IDs (tabular)"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "param_out_tsv"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "5ad830edc021",
+                            "name": "openms_fileinfo",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"param_v\": \"\\\"false\\\"\", \"param_p\": \"\\\"false\\\"\", \"param_s\": \"\\\"false\\\"\", \"param_m\": \"\\\"false\\\"\", \"param_i\": \"\\\"false\\\"\", \"param_d\": \"\\\"false\\\"\", \"param_c\": \"\\\"false\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "2.2.0",
                         "type": "tool",
-                        "uuid": "7e308945-aa0f-494a-a59f-b960614e0a03",
+                        "uuid": "7c834594-54f3-4201-a45a-4c75c41825f0",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "70c5c495-69e5-41e2-aefa-2bcc18aa5fd4"
+                                "output_name": "param_out_tsv",
+                                "uuid": "118d2874-3da7-4133-ae7d-b6e47d2c5a1a"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "param_out",
+                                "uuid": "36885b5d-64c4-46e4-8388-43c1058c6251"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.2.0",
                         "errors": null,
-                        "id": 12,
+                        "id": 14,
                         "input_connections": {
-                            "input": {
-                                "id": 10,
-                                "output_name": "out_file1"
+                            "param_in": {
+                                "id": 13,
+                                "output_name": "param_out"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool IDFilter",
+                                "name": "param_whitelist_peptides"
+                            },
+                            {
+                                "description": "runtime parameter for tool IDFilter",
+                                "name": "param_whitelist_proteins"
+                            },
+                            {
+                                "description": "runtime parameter for tool IDFilter",
+                                "name": "param_blacklist_proteins"
+                            },
+                            {
+                                "description": "runtime parameter for tool IDFilter",
+                                "name": "param_in"
+                            },
+                            {
+                                "description": "runtime parameter for tool IDFilter",
+                                "name": "param_blacklist_peptides"
+                            },
+                            {
+                                "description": "runtime parameter for tool IDFilter",
+                                "name": "param_digest_fasta"
+                            }
+                        ],
                         "label": null,
-                        "name": "Compute",
+                        "name": "IDFilter",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "param_out",
+                                "type": "idxml"
                             }
                         ],
                         "position": {
-                            "bottom": 598.6999969482422,
-                            "height": 93.19999694824219,
-                            "left": 1707,
-                            "right": 1907,
-                            "top": 505.5,
-                            "width": 200,
-                            "x": 1707,
-                            "y": 505.5
+                            "left": 3042,
+                            "top": 220
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
+                        "post_job_actions": {
+                            "RenameDatasetActionparam_out": {
+                                "action_arguments": {
+                                    "newname": "Protein IDs (idXML)"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "param_out"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.2.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "be25c075ed54",
-                            "name": "column_maker",
-                            "owner": "devteam",
+                            "changeset_revision": "382cde407f81",
+                            "name": "openms_idfilter",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"avoid_scientific_notation\": \"no\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"cond\": \"c4-c5\", \"header_lines_conditional\": {\"header_lines_select\": \"yes\", \"__current_case__\": 1, \"header_new_column_name\": \"log2 Fold Change\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"round\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3.0",
+                        "tool_state": "{\"param_whitelist_peptides\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_length\": \"\\\":\\\"\", \"param_keep_unreferenced_protein_hits\": \"\\\"false\\\"\", \"param_unique\": \"\\\"false\\\"\", \"param_whitelist_proteins\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_unique_per_protein\": \"\\\"false\\\"\", \"param_remove_decoys\": \"\\\"false\\\"\", \"param_score_prot\": \"\\\"0.01\\\"\", \"__rerun_remap_job_id__\": null, \"param_precursor_mz\": \"\\\":\\\"\", \"param_mz_error\": \"\\\"-1.0\\\"\", \"rep_param_blacklist_modifications\": \"[]\", \"param_blacklist_proteins\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"param_delete_unreferenced_peptide_hits\": \"\\\"false\\\"\", \"param_blacklist_ignore_modifications\": \"\\\"false\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null, \"param_charge\": \"\\\":\\\"\", \"param_var_mods\": \"\\\"false\\\"\", \"param_best_strict\": \"\\\"false\\\"\", \"param_digest_specificity\": \"\\\"full\\\"\", \"param_digest_missed_cleavages\": \"\\\"-1\\\"\", \"rep_param_whitelist_modifications\": \"[]\", \"param_mz_unit\": \"\\\"ppm\\\"\", \"rep_param_whitelist_protein_accessions\": \"[]\", \"param_best_n_peptide_hits\": \"\\\"0\\\"\", \"param_blacklist_peptides\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"param_score_pep\": \"\\\"0.0\\\"\", \"param_digest_methionine_cleavage\": \"\\\"false\\\"\", \"param_best_n_protein_hits\": \"\\\"0\\\"\", \"param_precursor_rt\": \"\\\":\\\"\", \"param_digest_fasta\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"rep_param_blacklist_protein_accessions\": \"[]\", \"param_whitelist_ignore_modifications\": \"\\\"false\\\"\", \"param_digest_enzyme\": \"\\\"Trypsin\\\"\"}",
+                        "tool_version": "2.2.0",
                         "type": "tool",
-                        "uuid": "55d7d873-c11c-47ce-8c53-022ab234f8e1",
+                        "uuid": "7955e91e-a52b-4153-8222-3b16ae99fd94",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "f61c7a19-b543-4f5a-afe0-44c06bb28cd4"
+                                "output_name": "param_out",
+                                "uuid": "fe8099a0-d4c5-4e0d-a21e-62406c69c137"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0",
                         "errors": null,
-                        "id": 13,
+                        "id": 15,
                         "input_connections": {
-                            "input": {
-                                "id": 12,
-                                "output_name": "out_file1"
+                            "param_in": {
+                                "id": 14,
+                                "output_name": "param_out"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool FileInfo",
+                                "name": "param_in"
+                            }
+                        ],
                         "label": null,
-                        "name": "Histogram",
+                        "name": "FileInfo",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "pdf"
+                                "name": "param_out",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "param_out_tsv",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 465.6999969482422,
-                            "height": 93.19999694824219,
-                            "left": 1850,
-                            "right": 2050,
-                            "top": 372.5,
-                            "width": 200,
-                            "x": 1850,
-                            "y": 372.5
+                            "left": 3370,
+                            "top": 219
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
+                        "post_job_actions": {
+                            "RenameDatasetActionparam_out": {
+                                "action_arguments": {
+                                    "newname": "FileInfo Protein IDs (txt)"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "param_out"
+                            },
+                            "RenameDatasetActionparam_out_tsv": {
+                                "action_arguments": {
+                                    "newname": "FileInfo Protein IDs (tabular)"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "param_out_tsv"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "6f134426c2b0",
-                            "name": "histogram",
-                            "owner": "devteam",
+                            "changeset_revision": "5ad830edc021",
+                            "name": "openms_fileinfo",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"breaks\": \"0\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"density\": \"true\", \"frequency\": \"false\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"numerical_column\": \"6\", \"title\": \"log2 Fold Change\", \"xlab\": \"V1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.4",
+                        "tool_state": "{\"__page__\": null, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"param_v\": \"\\\"false\\\"\", \"param_p\": \"\\\"false\\\"\", \"param_s\": \"\\\"false\\\"\", \"param_m\": \"\\\"false\\\"\", \"param_i\": \"\\\"false\\\"\", \"param_d\": \"\\\"false\\\"\", \"param_c\": \"\\\"false\\\"\", \"param_in\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "2.2.0",
                         "type": "tool",
-                        "uuid": "0cffa4b8-d1df-4339-a6f8-18041a18c7e2",
+                        "uuid": "0a22ddc7-00a6-424f-9ce2-5816423d49ba",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "8b6f54e6-bea6-4dac-9226-f5468661fcd5"
+                                "output_name": "param_out_tsv",
+                                "uuid": "97b4b4e9-1745-49fd-8b0c-bc5bce0ab5b2"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "param_out",
+                                "uuid": "dc6535dd-cc02-4be9-bd2e-6a37f8e164c0"
                             }
                         ]
                     }
                 ],
-                "parent_id": "proteomics/maxquant-label-free",
-                "path": "topics/proteomics/tutorials/maxquant-label-free/workflows/maxquant_label_free.ga",
+                "parent_id": "proteomics/protein-id-oms",
+                "path": "topics/proteomics/tutorials/protein-id-oms/workflows/workflow_two-search-engines.ga",
                 "tags": [
                     "proteomics"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "Proteomics: MaxQuant workflow",
+                "tests": false,
+                "title": "Peptide And Protein ID Via OMS Using Two Search Engines",
                 "topic_id": "proteomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-maxquant-label-free/versions/maxquant-label-free",
-                "tutorial_id": "maxquant-label-free",
-                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/maxquant-label-free/workflows/maxquant_label_free.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/maxquant-label-free/workflows/maxquant_label_free.html",
-                "version": 6,
-                "wfid": "proteomics-maxquant-label-free",
-                "wfname": "maxquant-label-free",
-                "workflow": "maxquant_label_free.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-protein-id-oms/versions/workflow-two-search-engines",
+                "tutorial_id": "protein-id-oms",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/protein-id-oms/workflows/workflow_two-search-engines.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/protein-id-oms/workflows/workflow_two-search-engines.html",
+                "version": 4,
+                "wfid": "proteomics-protein-id-oms",
+                "wfname": "workflow-two-search-engines",
+                "workflow": "workflow_two-search-engines.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "Filter1",
-                    "Grep1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3"
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_consensusid/ConsensusID/2.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.2.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmerger/IDMerger/2.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/2.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.2.0.1"
                 ],
-                "workflowhub_id": "1140"
+                "workflowhub_id": "1191"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/3774452"
+        "zenodo_link": "https://zenodo.org/record/546301"
     },
     {
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": []
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "288462ec2630",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "proteore_expression_rnaseq_abbased",
+                    "owner": "proteore",
+                    "revisions": "dbeabf9bf091",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "proteore_filter_keywords_values",
+                    "owner": "proteore",
+                    "revisions": "33ca9ba2495a",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "proteore_id_converter",
+                    "owner": "proteore",
+                    "revisions": "b6607b7e683f",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "proteore_ms_observation_pepatlas",
+                    "owner": "proteore",
+                    "revisions": "299eb4a62e0c",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "proteore_prot_features",
+                    "owner": "proteore",
+                    "revisions": "8df559ad14a7",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "proteore_tissue_specific_expression_data",
+                    "owner": "proteore",
+                    "revisions": "3e65e0249976",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "proteore_venn_diagram",
+                    "owner": "proteore",
+                    "revisions": "d1fd04dcb13a",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/introduction/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: 288462ec2630\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_expression_rnaseq_abbased\n  owner: proteore\n  revisions: dbeabf9bf091\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_filter_keywords_values\n  owner: proteore\n  revisions: 33ca9ba2495a\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_id_converter\n  owner: proteore\n  revisions: b6607b7e683f\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_ms_observation_pepatlas\n  owner: proteore\n  revisions: 299eb4a62e0c\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_prot_features\n  owner: proteore\n  revisions: 8df559ad14a7\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_tissue_specific_expression_data\n  owner: proteore\n  revisions: 3e65e0249976\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: proteore_venn_diagram\n  owner: proteore\n  revisions: d1fd04dcb13a\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/biomarker_selection/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
-                    "uni-freiburg"
+                    "elixir-europe"
                 ],
-                "email": "melanie.foell@mol-med.uni-freiburg.de",
-                "id": "foellmelanie",
-                "joined": "2018-10",
-                "matrix": "foellmelanie:matrix.org",
-                "name": "Melanie F\u00f6ll",
-                "orcid": "0000-0002-1887-7543",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
-                "twitter": "MCFoell",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
+                "elixir_node": "fr",
+                "email": "florence.combes@cea.fr",
+                "id": "combesf",
+                "joined": "2019-04",
+                "name": "Florence Combes",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/combesf/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/combesf.json"
+            },
+            {
+                "id": "davidchristiany",
+                "joined": "2019-04",
+                "name": "David Christiany",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/davidchristiany/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/davidchristiany.json"
+            },
+            {
+                "id": "vloux",
+                "joined": "2019-04",
+                "name": "Valentin Loux",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/vloux/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/vloux.json"
+            },
+            {
+                "id": "yvandenb",
+                "joined": "2019-04",
+                "name": "Yves Vandenbrouck",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/yvandenb/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/yvandenb.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/introduction",
+        "dir": "topics/proteomics/tutorials/biomarker_selection",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": false,
-        "id": "proteomics/introduction",
+        "hands_on": true,
+        "id": "proteomics/biomarker_selection",
         "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
+            "UseGalaxy.be",
             "UseGalaxy.fr"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "layout": "introduction_slides",
+        "key_points": [
+            "Public proteomics databases are useful resources for annotation of biomarker candidates"
+        ],
+        "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "logo": "GTN",
-        "mod_date": "2024-08-08",
-        "pageviews": 5726884,
-        "priority": 1,
-        "pub_date": "2017-12-01",
-        "recordings": [
-            {
-                "captioners": [
-                    "foellmelanie"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "20M",
-                "speakers": [
-                    "awspolly"
-                ],
-                "youtube_id": "2C96AvrFT38"
-            }
+        "mod_date": "2023-11-09",
+        "objectives": [
+            "Build a workflow implementing a strategy for the selection of tissue-leakage biomarkers using ProteoRE"
         ],
-        "redirect_from": [
-            "/topics/proteomics/slides/introduction",
-            "/short/proteomics/introduction/slides",
-            "/short/S00080"
+        "pageviews": 1926,
+        "pub_date": "2019-06-13",
+        "questions": [
+            "How to mine public databases to retrieve info?",
+            "How to build a selection strategy by applying successive biochemical/cellular criteria to a list of gene/protein?",
+            "How to select biomarkers candidates using experimental information (transcriptomics & proteomics) and annotation from public databases?"
         ],
-        "short_id": "S00080",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": [
-            {
-                "captioners": [
-                    "foellmelanie"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "20M",
-                "speakers": [
-                    "awspolly"
-                ],
-                "youtube_id": "2C96AvrFT38"
-            }
+        "short_id": "T00213",
+        "short_tools": [
+            "prot_features",
+            "MQoutputfilter",
+            "retr_pepatlas1",
+            "rna_abbased_data",
+            "Jvenn",
+            "IDconverter",
+            "tp_cut_tool",
+            "retrieve_from_hpa"
         ],
-        "subtopic": "intro",
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "post-process",
         "supported_servers": {
             "exact": [],
             "inexact": [
                 {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
                 },
                 {
-                    "human": "Galaxy France",
-                    "id": "fr",
                     "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
                 }
             ]
         },
         "symlink": null,
-        "title": "Introduction to proteomics, protein identification, quantification and statistical modelling",
-        "tools": [],
+        "tags": [
+            "DDA",
+            "human"
+        ],
+        "time_estimation": "3H",
+        "title": "Biomarker candidate identification",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.0.0",
+            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_expression_rnaseq_abbased/rna_abbased_data/2019.03.07",
+            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_filter_keywords_values/MQoutputfilter/2019.03.05",
+            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_id_converter/IDconverter/2019.01.28",
+            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_ms_observation_pepatlas/retr_pepatlas1/2019.02.01.1",
+            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_prot_features/prot_features/2019.01.18",
+            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_tissue_specific_expression_data/retrieve_from_hpa/2019.02.27",
+            "toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/Jvenn/2018.12.18"
+        ],
         "topic_name": "proteomics",
         "topic_name_human": "Proteomics",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": true
+            "video": false
         },
-        "tutorial_name": "introduction",
+        "tutorial_name": "biomarker_selection",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/introduction/slides.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/biomarker_selection/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/introduction/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/introduction/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/biomarker_selection/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/biomarker_selection/tutorial.json"
         },
-        "version": 3,
-        "video": true,
-        "video_versions": 1,
+        "version": 9,
+        "video": false,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758
+        "visit_duration": 159,
+        "visitors": 1393,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Biomarker candidate identification",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Build tissue-specific expression dataset\"]\n  1[label=\"Build tissue-specific expression dataset\"]\n  2[label=\"Filter by keywords and/or numerical value\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"Venn diagram\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"kept_lines\"]\n  4[label=\"Cut\"]\n  3 -> 4 [label=\"output_text\"]\n  5[label=\"Filter by keywords and/or numerical value\"]\n  4 -> 5 [label=\"output\"]\n  6[label=\"Add expression data\"]\n  5 -> 6 [label=\"kept_lines\"]\n  7[label=\"Filter by keywords and/or numerical value\"]\n  6 -> 7 [label=\"output\"]\n  8[label=\"ID Converter\"]\n  7 -> 8 [label=\"kept_lines\"]\n  9[label=\"Add protein features\"]\n  8 -> 9 [label=\"output\"]\n  10[label=\"Filter by keywords and/or numerical value\"]\n  9 -> 10 [label=\"output\"]\n  11[label=\"Get MS/MS observations in tissue/fluid\"]\n  10 -> 11 [label=\"kept_lines\"]\n  12[label=\"Filter by keywords and/or numerical value\"]\n  11 -> 12 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 3,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 2,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "efe1128541cbed0185333343ba7bd94fb3bab869",
+                        "message": "Add first version of biomarker selection tutorial",
+                        "num": 1,
+                        "short_hash": "efe112854",
+                        "unix": "1556267888"
+                    }
+                ],
+                "inputs": [],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"Build tissue-specific expression dataset\"];\n  1[\"Build tissue-specific expression dataset\"];\n  2[\"Filter by keywords and/or numerical value\"];\n  1 -->|output| 2;\n  3[\"Venn diagram\"];\n  0 -->|output| 3;\n  2 -->|kept_lines| 3;\n  4[\"Cut\"];\n  3 -->|output_text| 4;\n  5[\"Filter by keywords and/or numerical value\"];\n  4 -->|output| 5;\n  6[\"Add expression data\"];\n  5 -->|kept_lines| 6;\n  7[\"Filter by keywords and/or numerical value\"];\n  6 -->|output| 7;\n  8[\"ID Converter\"];\n  7 -->|kept_lines| 8;\n  9[\"Add protein features\"];\n  8 -->|output| 9;\n  10[\"Filter by keywords and/or numerical value\"];\n  9 -->|output| 10;\n  11[\"Get MS/MS observations in tissue/fluid\"];\n  10 -->|kept_lines| 11;\n  12[\"Filter by keywords and/or numerical value\"];\n  11 -->|output| 12;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "'Biomarkers4Paris' Workflow",
+                "outputs": [],
+                "parent_id": "proteomics/biomarker_selection",
+                "path": "topics/proteomics/tutorials/biomarker_selection/workflows/main_workflow.ga",
+                "tags": [
+                    "proteomics"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "'Biomarkers4Paris' Workflow",
+                "topic_id": "proteomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-biomarker_selection/versions/main-workflow",
+                "tutorial_id": "biomarker_selection",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/biomarker_selection/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/biomarker_selection/workflows/main_workflow.html",
+                "version": 3,
+                "wfid": "proteomics-biomarker_selection",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_expression_rnaseq_abbased/rna_abbased_data/2019.03.07",
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_filter_keywords_values/MQoutputfilter/2019.03.05",
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_id_converter/IDconverter/2019.01.28",
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_ms_observation_pepatlas/retr_pepatlas1/2019.02.01.1",
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_prot_features/prot_features/2019.01.18",
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_tissue_specific_expression_data/retrieve_from_hpa/2019.02.27",
+                    "toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/Jvenn/2018.12.18"
+                ],
+                "workflowhub_id": "1232"
+            }
+        ],
+        "zenodo_link": ""
     },
     {
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": []
+            "tools": [
+                {
+                    "name": "msstatstmt",
+                    "owner": "galaxyp",
+                    "revisions": "bd1535813cfe",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "unipept",
+                    "owner": "galaxyp",
+                    "revisions": "21a560af5913",
+                    "tool_panel_section_label": "Get Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: msstatstmt\n  owner: galaxyp\n  revisions: bd1535813cfe\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unipept\n  owner: galaxyp\n  revisions: 21a560af5913\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-5-data-interpretation/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "subinamehta",
+                "katherine-d21",
+                "dechendb"
+            ],
+            "editing": [
+                "pratikdjagtap",
+                "timothygriffin"
+            ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/labelfree-vs-labelled/tutorial.json",
         "contributors": [
             {
-                "email": "sigloch+github@mailbox.org",
-                "former_affiliations": [
-                    "uni-freiburg"
-                ],
-                "id": "stortebecker",
+                "email": "subinamehta@gmail.com",
+                "id": "subinamehta",
+                "joined": "2018-06",
+                "linkedin": "subinamehta",
+                "matrix": "subinamehta:matrix.org",
+                "name": "Subina Mehta",
+                "orcid": "0000-0001-9818-0537",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
+                "twitter": "Subina_Mehta",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
+            },
+            {
+                "id": "katherine-d21",
+                "joined": "2023-08",
+                "name": "Katherine Do",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/katherine-d21/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/katherine-d21.json"
+            },
+            {
+                "id": "dechendb",
+                "joined": "2023-06",
+                "name": "Dechen Bhuming",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dechendb/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/dechendb.json"
+            },
+            {
+                "email": "pjagtap@umn.edu",
+                "id": "pratikdjagtap",
                 "joined": "2017-09",
-                "name": "Florian Christoph Sigloch",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stortebecker/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/stortebecker.json"
+                "name": "Pratik Jagtap",
+                "orcid": "0000-0003-0984-0973",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
             },
             {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
-                "fediverse_flavor": "mastodon",
-                "id": "bgruening",
+                "email": "tgriffin@umn.edu",
+                "github": false,
+                "id": "timothygriffin",
                 "joined": "2017-09",
-                "linkedin": "bgruening",
-                "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
-                },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+                "name": "Timothy J. Griffin",
+                "orcid": "0000-0001-6801-2559",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
             }
         ],
-        "dir": "topics/proteomics/tutorials/labelfree-vs-labelled",
-        "edam_operation": [],
+        "dir": "topics/proteomics/tutorials/clinical-mp-5-data-interpretation",
+        "edam_operation": [
+            "Prediction and recognition",
+            "Visualisation"
+        ],
         "edam_topic": [],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.org.au"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": true,
-        "id": "proteomics/labelfree-vs-labelled",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
+        "follow_up_training": [
+            {
+                "topic_name": "proteomics",
+                "tutorials": [
+                    "metaproteomics"
+                ],
+                "type": "internal"
+            }
         ],
+        "hands_on": true,
+        "id": "proteomics/clinical-mp-5-data-interpretation",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Label-free and labelled methods are not better or worse *per se*.",
-            "Different scientific question call for different quantitation methods.",
-            "Be wise in choosing the right method before starting your LC-MS/MS runs."
+            "Data interpretation and visualization of clinical samples."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2022-10-18",
+        "mod_date": "2024-08-08",
         "objectives": [
-            "Choose your quantitation method."
+            "Perform group comparison analysis.",
+            "Analyze significant proteins",
+            "Look at the taxonomic distribution of the quantified peptides"
         ],
-        "pageviews": 11544,
-        "pub_date": "2017-03-17",
+        "pageviews": 88,
+        "pub_date": "2024-02-06",
         "questions": [
-            "What are benefits and drawbacks of different quantitation methods?",
-            "How to choose which quantitation method bests suits my need?"
+            "Why do we need to interpret the data?",
+            "Can we visualize the data?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "katherine-d21"
+                ],
+                "date": "2024-06-21",
+                "galaxy_version": "23.1",
+                "length": "20M",
+                "speakers": [
+                    "katherine-d21"
+                ],
+                "youtube_id": "uDs9bXAwCHo"
+            }
+        ],
+        "redirect_from": [
+            "/topics/proteomics/tutorials/clinical-mp-data-interpretation/tutorial",
+            "/short/proteomics/clinical-mp-5-data-interpretation",
+            "/short/T00417"
+        ],
+        "requirements": [
+            {
+                "topic_name": "proteomics",
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00417",
+        "short_tools": [
+            "unipept",
+            "Grep1",
+            "msstatstmt"
         ],
-        "short_id": "T00216",
-        "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "id-quant",
+        "subtopic": "clinical-metaproteomics",
         "supported_servers": {
-            "exact": [],
-            "inexact": [
+            "exact": [
                 {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
                 },
                 {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
                 {
-                    "human": "Galaxy Australia",
-                    "id": "au",
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
                 }
-            ]
+            ],
+            "inexact": []
         },
         "symlink": null,
         "tags": [
-            "DDA"
+            "label-TMT11"
+        ],
+        "time_estimation": "3H",
+        "title": "Clinical Metaproteomics 5: Data Interpretation",
+        "tools": [
+            "Grep1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/msstatstmt/msstatstmt/2.0.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.5.1"
         ],
-        "time_estimation": "15m",
-        "title": "Label-free versus Labelled - How to Choose Your Quantitation Method",
-        "tools": [],
         "topic_name": "proteomics",
         "topic_name_human": "Proteomics",
         "tours": false,
@@ -203701,20 +205840,220 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "labelfree-vs-labelled",
+        "tutorial_name": "clinical-mp-5-data-interpretation",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/labelfree-vs-labelled/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-5-data-interpretation/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/labelfree-vs-labelled/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/labelfree-vs-labelled/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-5-data-interpretation/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-5-data-interpretation/tutorial.json"
         },
-        "version": 16,
+        "version": 2,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 55,
-        "visitors": 6916,
-        "zenodo_link": ""
+        "visit_duration": 539,
+        "visitors": 63,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Organization",
+                        "identifier": "0000-0001-9818-0537",
+                        "name": "Subina Mehta"
+                    }
+                ],
+                "description": "Interpreting MaxQuant data using MSstats involves applying a rigorous statistical framework to glean meaningful insights from quantitative proteomic datasets",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nQuantified Peptides\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMaxQuant Protein Groups\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMaxQuant Evidence\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAnnotation.txt\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nComparison Matrix\"]\n  5[label=\"Unipept\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Microbial Proteins\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"Select\"]\n  1 -> 7 [label=\"output\"]\n  8[label=\"MSstatsTMT\"]\n  4 -> 8 [label=\"output\"]\n  3 -> 8 [label=\"output\"]\n  2 -> 8 [label=\"output\"]\n  6 -> 8 [label=\"out_file1\"]\n  9[label=\"HUMAN-Proteins\"]\n  7 -> 9 [label=\"out_file1\"]\n  10[label=\"MSstatsTMT\"]\n  4 -> 10 [label=\"output\"]\n  3 -> 10 [label=\"output\"]\n  2 -> 10 [label=\"output\"]\n  9 -> 10 [label=\"out_file1\"]\n}",
+                "history": [
+                    {
+                        "hash": "e8db145f1d7e42048e01ecc851e6c2bf5caf0f1a",
+                        "message": "add missing metadata",
+                        "num": 2,
+                        "short_hash": "e8db145f1",
+                        "unix": "1723120021"
+                    },
+                    {
+                        "hash": "e0464fd1787b4ca7dea72ca77b7ab2ad03a8292a",
+                        "message": "add workflows",
+                        "num": 1,
+                        "short_hash": "e0464fd17",
+                        "unix": "1723118192"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Quantified Peptides"
+                            }
+                        ],
+                        "label": "Quantified Peptides",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 189.871337890625,
+                            "top": 0
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "cd669a99-182a-48db-a2c6-f8d24323e353",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "MaxQuant Protein Groups"
+                            }
+                        ],
+                        "label": "MaxQuant Protein Groups",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 289.65196228027344
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "2ecd2d61-5e94-4dbd-a0cc-c30c343b38b4",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "MaxQuant Evidence"
+                            }
+                        ],
+                        "label": "MaxQuant Evidence",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 221.97045898437503,
+                            "top": 568.7156335895269
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "11afae12-7cc4-402b-a0e3-cf6e53276674",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Annotation.txt"
+                            }
+                        ],
+                        "label": "Annotation.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 293.3940978424075,
+                            "top": 851.982536255788
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "4ed9cd3d-2473-4b69-8ac8-3404e5628f85",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Comparison Matrix"
+                            }
+                        ],
+                        "label": "Comparison Matrix",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 307.5031433105469,
+                            "top": 973.9487421100347
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "6c47825f-c68c-4f0e-a99b-a961f27c7719",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQuantified Peptides\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nMaxQuant Protein Groups\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nMaxQuant Evidence\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nAnnotation.txt\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nComparison Matrix\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Unipept\"];\n  0 -->|output| 5;\n  6[\"Microbial Proteins\"];\n  1 -->|output| 6;\n  7[\"Select\"];\n  1 -->|output| 7;\n  8[\"MSstatsTMT\"];\n  4 -->|output| 8;\n  3 -->|output| 8;\n  2 -->|output| 8;\n  6 -->|out_file1| 8;\n  9[\"HUMAN-Proteins\"];\n  7 -->|out_file1| 9;\n  10[\"MSstatsTMT\"];\n  4 -->|output| 10;\n  3 -->|output| 10;\n  2 -->|output| 10;\n  9 -->|out_file1| 10;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "WF5_Data_Interpretation_Worklow",
+                "outputs": [],
+                "parent_id": "proteomics/clinical-mp-5-data-interpretation",
+                "path": "topics/proteomics/tutorials/clinical-mp-5-data-interpretation/workflows/WF5_Data_Interpretation_Worklow.ga",
+                "tags": [
+                    "name:clinicalMP"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "WF5_Data_Interpretation_Worklow",
+                "topic_id": "proteomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-clinical-mp-5-data-interpretation/versions/wf5-data-interpretation-worklow",
+                "tutorial_id": "clinical-mp-5-data-interpretation",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-5-data-interpretation/workflows/WF5_Data_Interpretation_Worklow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-5-data-interpretation/workflows/WF5_Data_Interpretation_Worklow.html",
+                "version": 1,
+                "wfid": "proteomics-clinical-mp-5-data-interpretation",
+                "wfname": "wf5-data-interpretation-worklow",
+                "workflow": "WF5_Data_Interpretation_Worklow.ga",
+                "workflow_tools": [
+                    "Grep1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msstatstmt/msstatstmt/2.0.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.5.1"
+                ],
+                "workflowhub_id": "1352"
+            }
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.10105821"
     },
     {
         "admin_install": {
@@ -203723,177 +206062,171 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bwa",
+                    "name": "ncbi_blast_plus",
                     "owner": "devteam",
-                    "revisions": "e188dc7a68e6",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_fastx",
-                    "owner": "iuc",
-                    "revisions": "a8d69aee190e",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "revisions": "2889433c7ae1",
+                    "tool_panel_section_label": "NCBI Blast",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "seqtk",
-                    "owner": "iuc",
-                    "revisions": "3da72230c066",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "pep_pointer",
+                    "owner": "galaxyp",
+                    "revisions": "073a2965e3b2",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "trimmomatic",
-                    "owner": "pjbriggs",
-                    "revisions": "898b67846b47",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "peptide_genomic_coordinate",
+                    "owner": "galaxyp",
+                    "revisions": "5f49ffce52cb",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "trimmomatic",
-                    "owner": "pjbriggs",
-                    "revisions": "d94aff5ee623",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "query_tabular",
+                    "owner": "iuc",
+                    "revisions": "33d61c89fb8d",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_fastx\n  owner: iuc\n  revisions: a8d69aee190e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n  owner: pjbriggs\n  revisions: 898b67846b47\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n  owner: pjbriggs\n  revisions: d94aff5ee623\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: 2889433c7ae1\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pep_pointer\n  owner: galaxyp\n  revisions: 073a2965e3b2\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptide_genomic_coordinate\n  owner: galaxyp\n  revisions: 5f49ffce52cb\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n  owner: iuc\n  revisions: 33d61c89fb8d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "by-covid",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "fediverse": "https://scholar.social/@zerodivision",
-                "fediverse_flavor": "mastodon",
-                "id": "wm75",
+                "email": "subinamehta@gmail.com",
+                "id": "subinamehta",
+                "joined": "2018-06",
+                "linkedin": "subinamehta",
+                "matrix": "subinamehta:matrix.org",
+                "name": "Subina Mehta",
+                "orcid": "0000-0001-9818-0537",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
+                "twitter": "Subina_Mehta",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
+            },
+            {
+                "email": "tgriffin@umn.edu",
+                "github": false,
+                "id": "timothygriffin",
                 "joined": "2017-09",
-                "matrix": "wm75:matrix.org",
-                "name": "Wolfgang Maier",
-                "orcid": "0000-0002-9464-6640",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
+                "name": "Timothy J. Griffin",
+                "orcid": "0000-0001-6801-2559",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
+            },
+            {
+                "email": "pjagtap@umn.edu",
+                "id": "pratikdjagtap",
+                "joined": "2017-09",
+                "name": "Pratik Jagtap",
+                "orcid": "0000-0003-0984-0973",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
+            },
+            {
+                "email": "rsajulga@umn.edu",
+                "id": "jraysajulga",
+                "joined": "2018-11",
+                "name": "Ray Sajulga",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jraysajulga/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jraysajulga.json"
+            },
+            {
+                "email": "jj@umn.edu",
+                "id": "jj-umn",
+                "in_memoriam": "<a href=\"https://galaxyproject.org/news/2024-03-19-remembrances-of-jj/\">James \u2018JJ\u2019 Johnson, was a Galaxy community rock star most known for his indispensable contributions to the Galaxy Proteomics community.</a>\n\nJJ\u2019s works will live on in so many Galaxy tools and workflows for years to come.",
+                "joined": "2017-09",
+                "name": "James Johnson",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/jj-umn/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/jj-umn.json"
+            },
+            {
+                "email": "kumar207@umn.edu",
+                "id": "pravs3683",
+                "joined": "2019-04",
+                "name": "Praveen Kumar",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pravs3683/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pravs3683.json"
             }
         ],
-        "dir": "topics/sequence-analysis/tutorials/human-reads-removal",
-        "edam_operation": [
-            "Generation",
-            "Data handling",
-            "Sequence file editing",
-            "Sequence alignment",
-            "Genome indexing",
-            "Read mapping"
-        ],
+        "dir": "topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis",
+        "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.be",
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "proteomics",
+                "tutorials": [
+                    "proteogenomics-dbcreation",
+                    "proteogenomics-dbsearch"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "sequence-analysis/human-reads-removal",
+        "id": "proteomics/proteogenomics-novel-peptide-analysis",
         "inexact_supported_servers": [
-            "Galaxy@AuBi",
-            "GalaxyTrakr",
             "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
+            "UseGalaxy.no"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Before submitting raw viral sequencing data to public databases you will want to remove human sequence traces",
-            "Human reads can be identified by mapping the data to the human reference genome",
-            "After mapping, you can extract the read identifiers of the non-human reads and use these to extract just the desired original sequenced reads from the input data"
+            "Learning how to visualize proteomic data and to perform its genomic allocation"
         ],
         "layout": "tutorial_hands_on",
         "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-08-09",
         "objectives": [
-            "Obtain viral (SARS-CoV-2) sequencing data with contaminating human reads from public sources",
-            "Organize the data into a collection",
-            "Preprocess and map the data against the human reference genome",
-            "Eliminate reads/read pairs that map to the human genome from the original data"
+            "How to assign and visualize the genomic localization of these identified novel proteoforms?"
         ],
-        "pageviews": 4759,
-        "pub_date": "2021-08-04",
+        "pageviews": 1853,
+        "pub_date": "2018-11-20",
         "questions": [
-            "How can you remove traces of human sequence data from a sequenced viral sample?"
+            "How to verify the spectra of novel proteoforms?",
+            "How to assign genomic allocation to these novel proteoforms?"
         ],
-        "requirements": [
+        "recordings": [
             {
-                "topic_name": "sequence-analysis",
-                "tutorials": [
-                    "quality-control",
-                    "mapping"
+                "captioners": [
+                    "subinamehta"
                 ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "collections"
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "40M",
+                "speakers": [
+                    "subinamehta"
                 ],
-                "type": "internal"
+                "youtube_id": "Ku274KwFh1Y"
             }
         ],
-        "short_id": "T00236",
+        "short_id": "T00233",
         "short_tools": [
-            "Grep1",
-            "__UNZIP_COLLECTION__",
-            "samtools_fastx",
-            "__ZIP_COLLECTION__",
-            "seqtk_subseq",
-            "tp_replace_in_line",
-            "bwa_mem",
-            "trimmomatic"
+            "ncbi_blastp_wrapper",
+            "peptide_genomic_coordinate",
+            "query_tabular",
+            "pep_pointer"
         ],
         "slides": false,
         "slides_recordings": false,
+        "subtopic": "multi-omics",
         "supported_servers": {
             "exact": [
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
                 {
@@ -203902,80 +206235,122 @@
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
                 }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                }
             ]
         },
         "symlink": null,
         "tags": [
-            "covid19"
+            "proteogenomics"
         ],
-        "time_estimation": "1h",
-        "title": "Removal of human reads from SARS-CoV-2 sequencing data",
+        "time_estimation": "30m",
+        "title": "Proteogenomics 3: Novel peptide analysis",
         "tools": [
-            "Grep1",
-            "__UNZIP_COLLECTION__",
-            "__ZIP_COLLECTION__",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-            "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
-            "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1"
+            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/pep_pointer/pep_pointer/0.1.3",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptide_genomic_coordinate/peptide_genomic_coordinate/0.1.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0"
         ],
-        "topic_name": "sequence-analysis",
-        "topic_name_human": "Sequence analysis",
+        "topic_name": "proteomics",
+        "topic_name_human": "Proteomics",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "human-reads-removal",
+        "tutorial_name": "proteogenomics-novel-peptide-analysis",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.json"
         },
-        "version": 5,
+        "version": 19,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 141,
-        "visitors": 3347,
+        "visit_duration": 158,
+        "visitors": 1246,
         "workflows": [
             {
                 "creators": [],
-                "description": "Removal of human reads from SARS-CoV-2 sequencing data",
+                "description": "Proteogenomics 3: Novel peptide analysis",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  1[label=\"Trimmomatic\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Unzip Collection\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Map with BWA-MEM\"]\n  1 -> 3 [label=\"fastq_out_paired\"]\n  4[label=\"Samtools fastx\"]\n  3 -> 4 [label=\"bam_output\"]\n  5[label=\"Select\"]\n  4 -> 5 [label=\"forward\"]\n  6[label=\"Replace Text\"]\n  5 -> 6 [label=\"out_file1\"]\n  7[label=\"seqtk_subseq\"]\n  2 -> 7 [label=\"forward\"]\n  6 -> 7 [label=\"outfile\"]\n  8[label=\"seqtk_subseq\"]\n  2 -> 8 [label=\"reverse\"]\n  6 -> 8 [label=\"outfile\"]\n  9[label=\"Paired-end collection of cleaned reads\"]\n  7 -> 9 [label=\"default\"]\n  8 -> 9 [label=\"default\"]\n  kf24bbf28dc51440fa758ac05033f0645[color=lightseagreen,label=\"Output\\nCleaned Data\"]\n  9 -> kf24bbf28dc51440fa758ac05033f0645\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nEdited_Mus_Musculus.GRCm38.86\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\npeptides for blast\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPSM Report\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmz_sqlite\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ngenomic mapping sqlite db\"]\n  5[label=\"NCBI BLAST+ blastp\"]\n  1 -> 5 [label=\"output\"]\n  k88461c74131241d5bd54e7d7297ccd76[color=lightseagreen,label=\"Output\\nBLASTP_results\"]\n  5 -> k88461c74131241d5bd54e7d7297ccd76\n  6[label=\"PSM_Novel_Peptides\"]\n  5 -> 6 [label=\"output1\"]\n  2 -> 6 [label=\"output\"]\n  k29c9a368a7e64e8b81ca131f63293093[color=lightseagreen,label=\"Output\\nPSM_Novel_Peptides\"]\n  6 -> k29c9a368a7e64e8b81ca131f63293093\n  7[label=\"Novel_Peptides\"]\n  6 -> 7 [label=\"output\"]\n  k569546687aac423a89afaecf2b405b94[color=lightseagreen,label=\"Output\\nNovel_Peptides\"]\n  7 -> k569546687aac423a89afaecf2b405b94\n  8[label=\"Peptide Genomic Coodinate\"]\n  4 -> 8 [label=\"output\"]\n  3 -> 8 [label=\"output\"]\n  7 -> 8 [label=\"output\"]\n  k60fd3e418cb74a49b5852a43117e9cf8[color=lightseagreen,label=\"Output\\nPeptide Genomic Coodinate on input dataset(s)\"]\n  8 -> k60fd3e418cb74a49b5852a43117e9cf8\n  9[label=\"PepPointer\"]\n  8 -> 9 [label=\"peptide_bed\"]\n  0 -> 9 [label=\"output\"]\n  k3c410bedff794774b75c48659d291160[color=lightseagreen,label=\"Output\\nPepPointer on input dataset(s)\"]\n  9 -> k3c410bedff794774b75c48659d291160\n  10[label=\"Final_Summary_Novel_Peptides\"]\n  9 -> 10 [label=\"classified\"]\n  6 -> 10 [label=\"output\"]\n  k50e64c95cd6847cb9e0cb3714b2f2431[color=lightseagreen,label=\"Output\\nFinal_Summary_Novel_Peptides\"]\n  10 -> k50e64c95cd6847cb9e0cb3714b2f2431\n}",
                 "history": [
                     {
-                        "hash": "f71f6dde01e2dfe86a4b43526f119d9050693f84",
-                        "message": "Address WF linting issues",
+                        "hash": "6d0c1e528390a4617e1f467a5f24a4ffd240d039",
+                        "message": "Update galaxy-workflow-mouse_novel_peptide_analysis.ga",
+                        "num": 7,
+                        "short_hash": "6d0c1e528",
+                        "unix": "1611782322"
+                    },
+                    {
+                        "hash": "3284d3ba74c4cf199a07c5efcad7c911dc5b9658",
+                        "message": "Update galaxy-workflow-mouse_novel_peptide_analysis.ga",
+                        "num": 6,
+                        "short_hash": "3284d3ba7",
+                        "unix": "1611781479"
+                    },
+                    {
+                        "hash": "a17d756120453ccf9c9ba819da787dc7e378c649",
+                        "message": "Update galaxy-workflow-mouse_novel_peptide_analysis.ga",
+                        "num": 5,
+                        "short_hash": "a17d75612",
+                        "unix": "1611585589"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 4,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 3,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
+                        "message": "Changed format of workflows",
                         "num": 2,
-                        "short_hash": "f71f6dde0",
-                        "unix": "1628012579"
+                        "short_hash": "361236c41",
+                        "unix": "1554368414"
                     },
                     {
-                        "hash": "f232ad426455a30be4a74af21054384c23b07275",
-                        "message": "Add new tutorial for cleaning SARS-CoV-2 data",
+                        "hash": "715d5f2ee1d9cfa74c5230a0a4bf746df8758e87",
+                        "message": "fix folder names",
                         "num": 1,
-                        "short_hash": "f232ad426",
-                        "unix": "1628010649"
+                        "short_hash": "715d5f2ee",
+                        "unix": "1542746779"
                     }
                 ],
                 "inputs": [
@@ -203988,1090 +206363,778 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Input Dataset Collection"
+                                "name": "Edited_Mus_Musculus.GRCm38.86"
                             }
                         ],
-                        "label": "Input Dataset Collection",
-                        "name": "Input dataset collection",
+                        "label": "Edited_Mus_Musculus.GRCm38.86",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 564,
-                            "height": 81,
-                            "left": 296,
-                            "right": 496,
-                            "top": 483,
-                            "width": 200,
-                            "x": 296,
-                            "y": 483
+                            "bottom": 404.25001525878906,
+                            "height": 84,
+                            "left": 448.75,
+                            "right": 608.75,
+                            "top": 320.25001525878906,
+                            "width": 160,
+                            "x": 448.75,
+                            "y": 320.25001525878906
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list:paired\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "d61c43e8-23ee-4f9a-9fd8-f58ffc134735",
+                        "type": "data_input",
+                        "uuid": "f4bb779b-d830-4b6e-974d-73a5b5111d2a",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "b14c9326-21d3-4e0e-be24-7654e6b31b43"
+                                "uuid": "77cd0e85-207b-4572-ab26-be78e1b4b3a8"
                             }
                         ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Trimmomatic\"];\n  0 -->|output| 1;\n  2[\"Unzip Collection\"];\n  0 -->|output| 2;\n  3[\"Map with BWA-MEM\"];\n  1 -->|fastq_out_paired| 3;\n  4[\"Samtools fastx\"];\n  3 -->|bam_output| 4;\n  5[\"Select\"];\n  4 -->|forward| 5;\n  6[\"Replace Text\"];\n  5 -->|out_file1| 6;\n  7[\"seqtk_subseq\"];\n  2 -->|forward| 7;\n  6 -->|outfile| 7;\n  8[\"seqtk_subseq\"];\n  2 -->|reverse| 8;\n  6 -->|outfile| 8;\n  9[\"Paired-end collection of cleaned reads\"];\n  7 -->|default| 9;\n  8 -->|default| 9;\n  f24bbf28-dc51-440f-a758-ac05033f0645[\"Output\\nCleaned Data\"];\n  9 --> f24bbf28-dc51-440f-a758-ac05033f0645;\n  style f24bbf28-dc51-440f-a758-ac05033f0645 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "GTN - Sequence Analyses - Removal of human reads from SARS-CoV-2 sequencing data",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Input Dataset Collection"
+                                "name": "peptides for blast"
                             }
                         ],
-                        "label": "Input Dataset Collection",
-                        "name": "Input dataset collection",
+                        "label": "peptides for blast",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 564,
-                            "height": 81,
-                            "left": 296,
-                            "right": 496,
-                            "top": 483,
-                            "width": 200,
-                            "x": 296,
-                            "y": 483
+                            "bottom": 548.2468795776367,
+                            "height": 67.20001220703125,
+                            "left": 442.96875,
+                            "right": 602.96875,
+                            "top": 481.04686737060547,
+                            "width": 160,
+                            "x": 442.96875,
+                            "y": 481.04686737060547
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list:paired\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "d61c43e8-23ee-4f9a-9fd8-f58ffc134735",
+                        "type": "data_input",
+                        "uuid": "14d01a35-1699-4246-9759-41156c9881d8",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "b14c9326-21d3-4e0e-be24-7654e6b31b43"
+                                "uuid": "1bfa1662-4420-42e0-a189-0f9d16f4afa7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {
-                            "readtype|fastq_pair": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Trimmomatic",
-                        "outputs": [
-                            {
-                                "name": "fastq_out_paired",
-                                "type": "input"
-                            },
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "fastq_out_unpaired",
-                                "type": "input"
+                                "description": "",
+                                "name": "PSM Report"
                             }
                         ],
+                        "label": "PSM Report",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 515,
-                            "height": 202,
-                            "left": 532,
-                            "right": 732,
-                            "top": 313,
-                            "width": 200,
-                            "x": 532,
-                            "y": 313
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "d94aff5ee623",
-                            "name": "trimmomatic",
-                            "owner": "pjbriggs",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 647.4312744140625,
+                            "height": 50.4000244140625,
+                            "left": 440.98438262939453,
+                            "right": 600.9843521118164,
+                            "top": 597.03125,
+                            "width": 159.99996948242188,
+                            "x": 440.98438262939453,
+                            "y": 597.03125
                         },
-                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"illuminaclip\": {\"do_illuminaclip\": \"false\", \"__current_case__\": 1}, \"operations\": [{\"__index__\": 0, \"operation\": {\"name\": \"SLIDINGWINDOW\", \"__current_case__\": 0, \"window_size\": \"4\", \"required_quality\": \"20\"}}], \"output_err\": \"false\", \"output_logs\": \"false\", \"readtype\": {\"single_or_paired\": \"collection\", \"__current_case__\": 2, \"fastq_pair\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.38.1",
-                        "type": "tool",
-                        "uuid": "ced9a15d-ca78-4cf5-b1a0-267920691879",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "6d7fee9d-ae62-4c9b-80af-94067aee67af",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "fastq_out_unpaired",
-                                "uuid": "88e4c149-85d2-4c19-8a53-f242a3703e5e"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "fastq_out_paired",
-                                "uuid": "fd0243b9-ef6a-445d-8fb9-f76d47c3f6fc"
+                                "output_name": "output",
+                                "uuid": "3460165b-5fad-4884-8688-2138be1419f5"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "__UNZIP_COLLECTION__",
+                        "content_id": null,
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Unzip Collection",
-                        "outputs": [
-                            {
-                                "name": "forward",
-                                "type": "input"
-                            },
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "reverse",
-                                "type": "input"
+                                "description": "",
+                                "name": "mz_sqlite"
                             }
                         ],
+                        "label": "mz_sqlite",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 746,
-                            "height": 182,
-                            "left": 735,
-                            "right": 935,
-                            "top": 564,
-                            "width": 200,
-                            "x": 735,
-                            "y": 564
+                            "bottom": 770.4468688964844,
+                            "height": 50.4000244140625,
+                            "left": 440,
+                            "right": 600,
+                            "top": 720.0468444824219,
+                            "width": 160,
+                            "x": 440,
+                            "y": 720.0468444824219
                         },
-                        "post_job_actions": {},
-                        "tool_id": "__UNZIP_COLLECTION__",
-                        "tool_state": "{\"input\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "f6552b12-5845-486b-95f5-35a3eefaa109",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "368d1a7a-f4f2-4b37-af4d-0410be56af33",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "forward",
-                                "uuid": "5fabd686-3611-4d28-aff3-c1286b461bbf"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "reverse",
-                                "uuid": "9b0c1a5f-6d39-46c7-a16d-afbb9e34bcfe"
+                                "output_name": "output",
+                                "uuid": "ce93f0ba-2e12-4ba9-92bc-e2c119a558d6"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+                        "content_id": null,
                         "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "fastq_input|fastq_input1": {
-                                "id": 1,
-                                "output_name": "fastq_out_paired"
-                            }
-                        },
+                        "id": 4,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Map with BWA-MEM",
-                                "name": "fastq_input"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Map with BWA-MEM",
-                        "outputs": [
-                            {
-                                "name": "bam_output",
-                                "type": "bam"
+                                "description": "",
+                                "name": "genomic mapping sqlite db"
                             }
                         ],
+                        "label": "genomic mapping sqlite db",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 487,
-                            "height": 192,
-                            "left": 753,
-                            "right": 953,
-                            "top": 295,
-                            "width": 200,
-                            "x": 753,
-                            "y": 295
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "64f11cf59c6e",
-                            "name": "bwa",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 857.2156524658203,
+                            "height": 67.20001220703125,
+                            "left": 440.15625,
+                            "right": 600.15625,
+                            "top": 790.0156402587891,
+                            "width": 160,
+                            "x": 440.15625,
+                            "y": 790.0156402587891
                         },
-                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"illumina\", \"__current_case__\": 0}, \"fastq_input\": {\"fastq_input_selector\": \"paired_collection\", \"__current_case__\": 2, \"fastq_input1\": {\"__class__\": \"RuntimeValue\"}, \"iset_stats\": \"\"}, \"output_sort\": \"coordinate\", \"reference_source\": {\"reference_source_selector\": \"cached\", \"__current_case__\": 0, \"ref_file\": \"hg38\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.17.2",
-                        "type": "tool",
-                        "uuid": "c21129e8-b54f-4a7d-9af2-b8202434c342",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "35ef98c3-607e-4903-9f89-84ec48aaa385",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "bam_output",
-                                "uuid": "f0ca56d9-f544-465c-ad37-6380ba0ac2ea"
+                                "output_name": "output",
+                                "uuid": "3aefda19-8fd0-42cd-a3c1-3480eb1364b4"
                             }
                         ]
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nEdited_Mus_Musculus.GRCm38.86\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\npeptides for blast\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nPSM Report\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nmz_sqlite\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\ngenomic mapping sqlite db\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"NCBI BLAST+ blastp\"];\n  1 -->|output| 5;\n  88461c74-1312-41d5-bd54-e7d7297ccd76[\"Output\\nBLASTP_results\"];\n  5 --> 88461c74-1312-41d5-bd54-e7d7297ccd76;\n  style 88461c74-1312-41d5-bd54-e7d7297ccd76 stroke:#2c3143,stroke-width:4px;\n  6[\"PSM_Novel_Peptides\"];\n  5 -->|output1| 6;\n  2 -->|output| 6;\n  29c9a368-a7e6-4e8b-81ca-131f63293093[\"Output\\nPSM_Novel_Peptides\"];\n  6 --> 29c9a368-a7e6-4e8b-81ca-131f63293093;\n  style 29c9a368-a7e6-4e8b-81ca-131f63293093 stroke:#2c3143,stroke-width:4px;\n  7[\"Novel_Peptides\"];\n  6 -->|output| 7;\n  56954668-7aac-423a-89af-aecf2b405b94[\"Output\\nNovel_Peptides\"];\n  7 --> 56954668-7aac-423a-89af-aecf2b405b94;\n  style 56954668-7aac-423a-89af-aecf2b405b94 stroke:#2c3143,stroke-width:4px;\n  8[\"Peptide Genomic Coodinate\"];\n  4 -->|output| 8;\n  3 -->|output| 8;\n  7 -->|output| 8;\n  60fd3e41-8cb7-4a49-b585-2a43117e9cf8[\"Output\\nPeptide Genomic Coodinate on input dataset(s)\"];\n  8 --> 60fd3e41-8cb7-4a49-b585-2a43117e9cf8;\n  style 60fd3e41-8cb7-4a49-b585-2a43117e9cf8 stroke:#2c3143,stroke-width:4px;\n  9[\"PepPointer\"];\n  8 -->|peptide_bed| 9;\n  0 -->|output| 9;\n  3c410bed-ff79-4774-b75c-48659d291160[\"Output\\nPepPointer on input dataset(s)\"];\n  9 --> 3c410bed-ff79-4774-b75c-48659d291160;\n  style 3c410bed-ff79-4774-b75c-48659d291160 stroke:#2c3143,stroke-width:4px;\n  10[\"Final_Summary_Novel_Peptides\"];\n  9 -->|classified| 10;\n  6 -->|output| 10;\n  50e64c95-cd68-47cb-9e0c-b3714b2f2431[\"Output\\nFinal_Summary_Novel_Peptides\"];\n  10 --> 50e64c95-cd68-47cb-9e0c-b3714b2f2431;\n  style 50e64c95-cd68-47cb-9e0c-b3714b2f2431 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "GTN Proteogemics3 Novel Peptide Analysis",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "input": {
-                                "id": 3,
-                                "output_name": "bam_output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Samtools fastx",
-                        "outputs": [
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "forward",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "Edited_Mus_Musculus.GRCm38.86"
                             }
                         ],
+                        "label": "Edited_Mus_Musculus.GRCm38.86",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 447,
-                            "height": 152,
-                            "left": 973,
-                            "right": 1173,
-                            "top": 295,
-                            "width": 200,
-                            "x": 973,
-                            "y": 295
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "a8d69aee190e",
-                            "name": "samtools_fastx",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 404.25001525878906,
+                            "height": 84,
+                            "left": 448.75,
+                            "right": 608.75,
+                            "top": 320.25001525878906,
+                            "width": 160,
+                            "x": 448.75,
+                            "y": 320.25001525878906
                         },
-                        "tool_state": "{\"__input_ext\": \"bam\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"copy_arb_tags\": \"\", \"copy_tags\": \"false\", \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"idxout_cond\": {\"idxout_select\": \"no\", \"__current_case__\": 0}, \"inclusive_filter\": [\"4\", \"8\"], \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"1085990\", \"output_fmt_cond\": {\"output_fmt_select\": \"fasta\", \"__current_case__\": 1}, \"outputs\": [\"r1\"], \"read_numbering\": \"-n\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9+galaxy1",
-                        "type": "tool",
-                        "uuid": "756ca036-b6b5-46e8-a230-81ed522ba950",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "f4bb779b-d830-4b6e-974d-73a5b5111d2a",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "forward",
-                                "uuid": "e82ae014-e75a-486c-93d6-af8cdd6e6f95"
+                                "output_name": "output",
+                                "uuid": "77cd0e85-207b-4572-ab26-be78e1b4b3a8"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Grep1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "input": {
-                                "id": 4,
-                                "output_name": "forward"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Select",
-                        "outputs": [
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "description": "",
+                                "name": "peptides for blast"
                             }
                         ],
+                        "label": "peptides for blast",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 387,
-                            "height": 92,
-                            "left": 1193,
-                            "right": 1393,
-                            "top": 295,
-                            "width": 200,
-                            "x": 1193,
-                            "y": 295
+                            "bottom": 548.2468795776367,
+                            "height": 67.20001220703125,
+                            "left": 442.96875,
+                            "right": 602.96875,
+                            "top": 481.04686737060547,
+                            "width": 160,
+                            "x": 442.96875,
+                            "y": 481.04686737060547
                         },
-                        "post_job_actions": {},
-                        "tool_id": "Grep1",
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"1085990\", \"invert\": \"\", \"keep_header\": \"false\", \"pattern\": \"^>.+\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.3",
-                        "type": "tool",
-                        "uuid": "5ab56d83-be12-4498-a88e-16d37ef2e904",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "14d01a35-1699-4246-9759-41156c9881d8",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "04aaed7c-6c4c-44d6-89b0-5bba0a58927b"
+                                "output_name": "output",
+                                "uuid": "1bfa1662-4420-42e0-a189-0f9d16f4afa7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                        "content_id": null,
                         "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "infile": {
-                                "id": 5,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Replace Text",
-                        "outputs": [
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "outfile",
-                                "type": "input"
+                                "description": "",
+                                "name": "PSM Report"
                             }
                         ],
+                        "label": "PSM Report",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 387,
-                            "height": 92,
-                            "left": 1413,
-                            "right": 1613,
-                            "top": 295,
-                            "width": 200,
-                            "x": 1413,
-                            "y": 295
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 647.4312744140625,
+                            "height": 50.4000244140625,
+                            "left": 440.98438262939453,
+                            "right": 600.9843521118164,
+                            "top": 597.03125,
+                            "width": 159.99996948242188,
+                            "x": 440.98438262939453,
+                            "y": 597.03125
                         },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"infile|__identifier__\": \"1085990\", \"replacements\": [{\"__index__\": 0, \"find_pattern\": \"^>(.+)\", \"replace_pattern\": \"\\\\1\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.2",
-                        "type": "tool",
-                        "uuid": "030b177e-2375-4856-b640-8ffd7f591aaf",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "6d7fee9d-ae62-4c9b-80af-94067aee67af",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile",
-                                "uuid": "f81d7560-8835-4307-b876-f56e22edf40e"
+                                "output_name": "output",
+                                "uuid": "3460165b-5fad-4884-8688-2138be1419f5"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "in_file": {
-                                "id": 2,
-                                "output_name": "forward"
-                            },
-                            "source|name_list": {
-                                "id": 6,
-                                "output_name": "outfile"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "seqtk_subseq",
-                        "outputs": [
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "default",
-                                "type": "input"
+                                "description": "",
+                                "name": "mz_sqlite"
                             }
                         ],
+                        "label": "mz_sqlite",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 416,
-                            "height": 142,
-                            "left": 1653,
-                            "right": 1853,
-                            "top": 274,
-                            "width": 200,
-                            "x": 1653,
-                            "y": 274
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "58c8ece95b53",
-                            "name": "seqtk",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 770.4468688964844,
+                            "height": 50.4000244140625,
+                            "left": 440,
+                            "right": 600,
+                            "top": 720.0468444824219,
+                            "width": 160,
+                            "x": 440,
+                            "y": 720.0468444824219
                         },
-                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"in_file|__identifier__\": \"1085990\", \"l\": \"0\", \"name_list|__identifier__\": \"1085990\", \"source\": {\"type\": \"name\", \"__current_case__\": 1, \"name_list\": {\"__class__\": \"ConnectedValue\"}}, \"t\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3.1",
-                        "type": "tool",
-                        "uuid": "50599db8-7c04-4f0f-8cc7-ca9fbeb405ea",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "368d1a7a-f4f2-4b37-af4d-0410be56af33",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "default",
-                                "uuid": "75989c7c-9b50-4286-b59a-e2ebefcd6206"
+                                "output_name": "output",
+                                "uuid": "ce93f0ba-2e12-4ba9-92bc-e2c119a558d6"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "in_file": {
-                                "id": 2,
-                                "output_name": "reverse"
-                            },
-                            "source|name_list": {
-                                "id": 6,
-                                "output_name": "outfile"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "seqtk_subseq",
-                        "outputs": [
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "default",
-                                "type": "input"
+                                "description": "",
+                                "name": "genomic mapping sqlite db"
                             }
                         ],
+                        "label": "genomic mapping sqlite db",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 572,
-                            "height": 142,
-                            "left": 1658,
-                            "right": 1858,
-                            "top": 430,
-                            "width": 200,
-                            "x": 1658,
-                            "y": 430
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "58c8ece95b53",
-                            "name": "seqtk",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 857.2156524658203,
+                            "height": 67.20001220703125,
+                            "left": 440.15625,
+                            "right": 600.15625,
+                            "top": 790.0156402587891,
+                            "width": 160,
+                            "x": 440.15625,
+                            "y": 790.0156402587891
                         },
-                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"in_file|__identifier__\": \"1085990\", \"l\": \"0\", \"name_list|__identifier__\": \"1085990\", \"source\": {\"type\": \"name\", \"__current_case__\": 1, \"name_list\": {\"__class__\": \"ConnectedValue\"}}, \"t\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3.1",
-                        "type": "tool",
-                        "uuid": "6b8ac606-6490-4355-9111-001dbe15fd22",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "35ef98c3-607e-4903-9f89-84ec48aaa385",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "default",
-                                "uuid": "1787644d-4796-4928-9458-7fc0779eb500"
+                                "output_name": "output",
+                                "uuid": "3aefda19-8fd0-42cd-a3c1-3480eb1364b4"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "__ZIP_COLLECTION__",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3",
                         "errors": null,
-                        "id": 9,
+                        "id": 5,
                         "input_connections": {
-                            "input_forward": {
-                                "id": 7,
-                                "output_name": "default"
-                            },
-                            "input_reverse": {
-                                "id": 8,
-                                "output_name": "default"
+                            "query": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Zip Collection",
-                                "name": "input_forward"
-                            },
-                            {
-                                "description": "runtime parameter for tool Zip Collection",
-                                "name": "input_reverse"
-                            }
-                        ],
-                        "label": "Paired-end collection of cleaned reads",
-                        "name": "Zip Collection",
+                        "inputs": [],
+                        "label": null,
+                        "name": "NCBI BLAST+ blastp",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "input"
+                                "name": "output1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 490.5,
-                            "height": 142,
-                            "left": 1939,
-                            "right": 2139,
-                            "top": 348.5,
-                            "width": 200,
-                            "x": 1939,
-                            "y": 348.5
+                            "bottom": 569.8031387329102,
+                            "height": 109.60000610351562,
+                            "left": 673.5469055175781,
+                            "right": 833.5469055175781,
+                            "top": 460.20313262939453,
+                            "width": 160,
+                            "x": 673.5469055175781,
+                            "y": 460.20313262939453
                         },
-                        "post_job_actions": {},
-                        "tool_id": "__ZIP_COLLECTION__",
-                        "tool_state": "{\"input_forward\": {\"__class__\": \"RuntimeValue\"}, \"input_reverse\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput1": {
+                                "action_arguments": {
+                                    "newname": "BLASTP_results"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output1"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2889433c7ae1",
+                            "name": "ncbi_blast_plus",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"advanced\", \"__current_case__\": 1, \"filter_query\": \"false\", \"matrix_gapcosts\": {\"matrix\": \"PAM30\", \"__current_case__\": 8, \"gap_costs\": \"-gapopen 9 -gapextend 1\"}, \"max_hits\": \"1\", \"max_hsps\": \"1\", \"word_size\": \"2\", \"window_size\": \"40\", \"threshold\": \"11\", \"comp_based_stats\": \"0\", \"parse_deflines\": \"false\", \"adv_optional_id_files_opts\": {\"adv_optional_id_files_opts_selector\": \"none\", \"__current_case__\": 0}, \"qcov_hsp_perc\": \"0.0\", \"use_sw_tback\": \"false\"}, \"blast_type\": \"blastp-short\", \"db_opts\": {\"db_opts_selector\": \"db\", \"__current_case__\": 0, \"database\": [\"nr_2018-01-22\"], \"histdb\": \"\", \"subject\": \"\"}, \"evalue_cutoff\": \"200000.0\", \"output\": {\"out_format\": \"ext\", \"__current_case__\": 1}, \"query\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.3.3",
                         "type": "tool",
-                        "uuid": "381d0485-0164-410f-801d-7dfb7891663d",
+                        "uuid": "8304a4ed-e1e4-45f3-a868-1d8eb6127968",
                         "workflow_outputs": [
                             {
-                                "label": "Cleaned Data",
-                                "output_name": "output",
-                                "uuid": "f24bbf28-dc51-440f-a758-ac05033f0645"
+                                "label": "BLASTP_results",
+                                "output_name": "output1",
+                                "uuid": "88461c74-1312-41d5-bd54-e7d7297ccd76"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "sequence-analysis/human-reads-removal",
-                "path": "topics/sequence-analysis/tutorials/human-reads-removal/workflows/human-reads-removal.ga",
-                "tags": [
-                    "sequence-analysis"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "GTN - Sequence Analyses - Removal of human reads from SARS-CoV-2 sequencing data",
-                "topic_id": "sequence-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/sequence-analysis-human-reads-removal/versions/human-reads-removal",
-                "tutorial_id": "human-reads-removal",
-                "url": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/human-reads-removal/workflows/human-reads-removal.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/human-reads-removal/workflows/human-reads-removal.html",
-                "version": 1,
-                "wfid": "sequence-analysis-human-reads-removal",
-                "wfname": "human-reads-removal",
-                "workflow": "human-reads-removal.ga",
-                "workflow_tools": [
-                    "Grep1",
-                    "__UNZIP_COLLECTION__",
-                    "__ZIP_COLLECTION__",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-                    "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1"
-                ],
-                "workflowhub_id": "1276"
-            }
-        ]
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "ncbi_fcs_gx",
-                    "owner": "iuc",
-                    "revisions": "49f8eae39606",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ncbi_fcs_adaptor",
-                    "owner": "richard-burhans",
-                    "revisions": "d55ad8533d58",
-                    "tool_panel_section_label": "Sequence Contamination Filtering",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: ncbi_fcs_gx\n  owner: iuc\n  revisions: 49f8eae39606\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_fcs_adaptor\n  owner: richard-burhans\n  revisions: d55ad8533d58\n  tool_panel_section_label: Sequence Contamination Filtering\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/ncbi-fcs/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "tvedtees"
-            ],
-            "editing": [
-                "hexylena"
-            ],
-            "funding": [
-                "NIH"
-            ]
-        },
-        "contributors": [
-            {
-                "id": "tvedtees",
-                "joined": "2024-03",
-                "name": "Eric Tvedte",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tvedtees/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tvedtees.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/nih.png",
-                "funder": true,
-                "github": false,
-                "id": "NIH",
-                "name": "National Institutes of Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/NIH/",
-                "short_name": "NIH",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/NIH.json"
-            }
-        ],
-        "dir": "topics/sequence-analysis/tutorials/ncbi-fcs",
-        "edam_operation": [
-            "Sequence assembly validation",
-            "Sequence contamination filtering",
-            "Sequence trimming"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.org (Main)"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "sequence-analysis/ncbi-fcs",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Contamination can arise from multiple sources and occur at multiple stages of a genome assembly project.",
-            "Contamination cleanup is essential for reliable comparative genomics analyses."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-04-16",
-        "objectives": [
-            "Learn how to screen a genome assembly for adaptor and vector contamination.",
-            "Learn how to screen a genome assembly for non-host organism contamination."
-        ],
-        "pageviews": 425,
-        "pub_date": "2024-04-16",
-        "questions": [
-            "Are the sequences in a genome assembly contaminant-free?"
-        ],
-        "short_id": "T00439",
-        "short_tools": [
-            "ncbi_fcs_adaptor",
-            "ncbi_fcs_gx"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": []
-        },
-        "symlink": null,
-        "time_estimation": "90M",
-        "title": "Screening assembled genomes for contamination using NCBI FCS",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/richard-burhans/ncbi_fcs_adaptor/ncbi_fcs_adaptor/0.5.0+galaxy0"
-        ],
-        "topic_name": "sequence-analysis",
-        "topic_name_human": "Sequence analysis",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "ncbi-fcs",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/ncbi-fcs/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/ncbi-fcs/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/ncbi-fcs/tutorial.json"
-        },
-        "version": 2,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 135,
-        "visitors": 302,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Organization",
-                        "name": "National Center for Biotechnology Information",
-                        "url": "https://github.com/ncbi/fcs"
-                    }
-                ],
-                "description": "This workflow performs contamination cleaning steps on assembled genomes. Users specify an input genome (fasta/fasta.gz) and taxonomic information corresponding to the source organism. There are two screening steps for foreign organism sequences (FCS-GX) and adaptors (FCS-adaptor), each followed by a cleaning step to remove identified contaminants. The final output is a cleaned genome. ",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput genome\"]\n  1[label=\"FCS-GX screen\"]\n  0 -> 1 [label=\"output\"]\n  k9741edf24be645a3980d99b1aea18380[color=lightseagreen,label=\"Output\\nfcs_gx_action_report\"]\n  1 -> k9741edf24be645a3980d99b1aea18380\n  kddedd49f8c574e3ea1583d66ce12f05c[color=lightseagreen,label=\"Output\\nfcs_gx_taxonomy_report\"]\n  1 -> kddedd49f8c574e3ea1583d66ce12f05c\n  2[label=\"FCS-GX clean\"]\n  1 -> 2 [label=\"action_report\"]\n  0 -> 2 [label=\"output\"]\n  kf3a37b43d3044ec0a023197c9e0ce2e1[color=lightseagreen,label=\"Output\\ngx_contam_fasta\"]\n  2 -> kf3a37b43d3044ec0a023197c9e0ce2e1\n  k56716c7cac7f42f7bbef62a36b4d3810[color=lightseagreen,label=\"Output\\ngx_clean_fasta\"]\n  2 -> k56716c7cac7f42f7bbef62a36b4d3810\n  3[label=\"FCS-adaptor screen\"]\n  2 -> 3 [label=\"clean_fasta\"]\n  k6a4baf4680b04a96b8649201fc80cdb7[color=lightseagreen,label=\"Output\\nfcs_adaptor_report\"]\n  3 -> k6a4baf4680b04a96b8649201fc80cdb7\n  k1cad7ab4a817436c9a63fd4e3c6b4bbb[color=lightseagreen,label=\"Output\\nadaptor_clean_fasta\"]\n  3 -> k1cad7ab4a817436c9a63fd4e3c6b4bbb\n  4[label=\"FCS-adaptor clean\"]\n  3 -> 4 [label=\"adaptor_report\"]\n  2 -> 4 [label=\"clean_fasta\"]\n  k0da685707490408786c8739522e1a776[color=lightseagreen,label=\"Output\\nadaptor_contam_fasta\"]\n  4 -> k0da685707490408786c8739522e1a776\n  k4985eb0730b04872ab8352ffeb619900[color=lightseagreen,label=\"Output\\nfinal_clean_fasta\"]\n  4 -> k4985eb0730b04872ab8352ffeb619900\n}",
-                "history": [
-                    {
-                        "hash": "3cc782f4789a4e769a903fb810a7ad5c72385c6d",
-                        "message": "Modify NIH funder. Add workflow license URL",
-                        "num": 2,
-                        "short_hash": "3cc782f47",
-                        "unix": "1713210183"
                     },
-                    {
-                        "hash": "05ae375a039cfb4ac8f226d77c106a6fed0764ae",
-                        "message": "Suggested tutorial changes. Add workflow test.",
-                        "num": 1,
-                        "short_hash": "05ae375a0",
-                        "unix": "1712757577"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "input must be an assembled genome in fasta/fasta.gz format. FCS is not intended to identify contaminants in sequencing reads inputs.",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "input must be an assembled genome in fasta/fasta.gz format. FCS is not intended to identify contaminants in sequencing reads inputs.",
-                                "name": "Input genome"
-                            }
-                        ],
-                        "label": "Input genome",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 3.9375
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta.gz\", \" fasta\"], \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "a2066ff6-a9c6-4152-9537-a7d05d2bea00",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "http://www.usa.gov/publicdomain/label/1.0/",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput genome\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"FCS-GX screen\"];\n  0 -->|output| 1;\n  9741edf2-4be6-45a3-980d-99b1aea18380[\"Output\\nfcs_gx_action_report\"];\n  1 --> 9741edf2-4be6-45a3-980d-99b1aea18380;\n  style 9741edf2-4be6-45a3-980d-99b1aea18380 stroke:#2c3143,stroke-width:4px;\n  ddedd49f-8c57-4e3e-a158-3d66ce12f05c[\"Output\\nfcs_gx_taxonomy_report\"];\n  1 --> ddedd49f-8c57-4e3e-a158-3d66ce12f05c;\n  style ddedd49f-8c57-4e3e-a158-3d66ce12f05c stroke:#2c3143,stroke-width:4px;\n  2[\"FCS-GX clean\"];\n  1 -->|action_report| 2;\n  0 -->|output| 2;\n  f3a37b43-d304-4ec0-a023-197c9e0ce2e1[\"Output\\ngx_contam_fasta\"];\n  2 --> f3a37b43-d304-4ec0-a023-197c9e0ce2e1;\n  style f3a37b43-d304-4ec0-a023-197c9e0ce2e1 stroke:#2c3143,stroke-width:4px;\n  56716c7c-ac7f-42f7-bbef-62a36b4d3810[\"Output\\ngx_clean_fasta\"];\n  2 --> 56716c7c-ac7f-42f7-bbef-62a36b4d3810;\n  style 56716c7c-ac7f-42f7-bbef-62a36b4d3810 stroke:#2c3143,stroke-width:4px;\n  3[\"FCS-adaptor screen\"];\n  2 -->|clean_fasta| 3;\n  6a4baf46-80b0-4a96-b864-9201fc80cdb7[\"Output\\nfcs_adaptor_report\"];\n  3 --> 6a4baf46-80b0-4a96-b864-9201fc80cdb7;\n  style 6a4baf46-80b0-4a96-b864-9201fc80cdb7 stroke:#2c3143,stroke-width:4px;\n  1cad7ab4-a817-436c-9a63-fd4e3c6b4bbb[\"Output\\nadaptor_clean_fasta\"];\n  3 --> 1cad7ab4-a817-436c-9a63-fd4e3c6b4bbb;\n  style 1cad7ab4-a817-436c-9a63-fd4e3c6b4bbb stroke:#2c3143,stroke-width:4px;\n  4[\"FCS-adaptor clean\"];\n  3 -->|adaptor_report| 4;\n  2 -->|clean_fasta| 4;\n  0da68570-7490-4087-86c8-739522e1a776[\"Output\\nadaptor_contam_fasta\"];\n  4 --> 0da68570-7490-4087-86c8-739522e1a776;\n  style 0da68570-7490-4087-86c8-739522e1a776 stroke:#2c3143,stroke-width:4px;\n  4985eb07-30b0-4872-ab83-52ffeb619900[\"Output\\nfinal_clean_fasta\"];\n  4 --> 4985eb07-30b0-4872-ab83-52ffeb619900;\n  style 4985eb07-30b0-4872-ab83-52ffeb619900 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "NCBI Foreign Contamination Screen",
-                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "errors": null,
-                        "id": 1,
+                        "id": 6,
                         "input_connections": {
-                            "mode|fasta": {
-                                "id": 0,
+                            "tables_0|table": {
+                                "id": 5,
+                                "output_name": "output1"
+                            },
+                            "tables_1|table": {
+                                "id": 2,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool NCBI FCS GX",
-                                "name": "mode"
+                                "description": "runtime parameter for tool Query Tabular",
+                                "name": "add_to_database"
                             }
                         ],
-                        "label": "FCS-GX screen",
-                        "name": "NCBI FCS GX",
+                        "label": "PSM_Novel_Peptides",
+                        "name": "Query Tabular",
                         "outputs": [
                             {
-                                "name": "taxonomy_report",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "action_report",
+                                "name": "output",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 355.5156127405953,
-                            "top": 3.28126838910714
+                            "bottom": 673.8656387329102,
+                            "height": 209.60000610351562,
+                            "left": 897.0468902587891,
+                            "right": 1057.046890258789,
+                            "top": 464.26563262939453,
+                            "width": 160,
+                            "x": 897.0468902587891,
+                            "y": 464.26563262939453
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "PSM_Novel_Peptides"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "3cdb96f2855d",
-                            "name": "ncbi_fcs_gx",
+                            "changeset_revision": "33d61c89fb8d",
+                            "name": "query_tabular",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"mode\": {\"mode_selector\": \"screen\", \"__current_case__\": 0, \"config_tag\": \"all\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"id\": {\"id_selector\": \"gx_div\", \"__current_case__\": 0, \"div\": \"fung:budding yeasts\"}, \"species\": null, \"screen_adv\": {\"gx_align_exclude_taxa\": \"\", \"gx_extra_contam_divs\": null, \"split_fasta\": true, \"div\": \"\", \"database\": \"/cvmfs/data.galaxyproject.org/byhand/ncbi_fcs_gx/all\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.5.0+galaxy0",
+                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"save_db\": \"false\", \"sqlquery\": \"SELECT distinct psm.*\\nFROM psm join blast ON psm.Sequence = blast.qseqid\\nWHERE blast.pident < 100 OR blast.gapopen >= 1 OR blast.length < blast.qlen\\nORDER BY psm.Sequence, psm.ID\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"blast\", \"column_names_from_first_line\": \"false\", \"col_names\": \"qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles\", \"load_named_columns\": \"true\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"qseqid\"}]}}, {\"__index__\": 1, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"skip\", \"__current_case__\": 0, \"skip_lines\": \"1\"}}]}, \"tbl_opts\": {\"table_name\": \"psm\", \"column_names_from_first_line\": \"false\", \"col_names\": \"ID,Proteins,Sequence,AAs_Before,AAs_After,Position,Modified_Sequence,Variable_Modifications,Fixed_Modifications,Spectrum_File,Spectrum_Title,Spectrum_Scan_Number,RT,mz,Measured_Charge,Identification_Charge,Theoretical_Mass,Isotope_Number,Precursor_mz_Error_ppm,Localization_Confidence,Probabilistic_PTM_score,Dscore,Confidence,Validation\", \"load_named_columns\": \"true\", \"pkey_autoincr\": \"\", \"indexes\": [{\"__index__\": 0, \"unique\": \"false\", \"index_columns\": \"Sequence\"}]}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.0.0",
                         "type": "tool",
-                        "uuid": "7907456b-eaa7-4a3f-b53b-c250110a117a",
-                        "when": null,
+                        "uuid": "0da3b9ec-f964-4386-b150-a2e81adfd05d",
                         "workflow_outputs": [
                             {
-                                "label": "fcs_gx_action_report",
-                                "output_name": "action_report",
-                                "uuid": "9741edf2-4be6-45a3-980d-99b1aea18380"
-                            },
-                            {
-                                "label": "fcs_gx_taxonomy_report",
-                                "output_name": "taxonomy_report",
-                                "uuid": "ddedd49f-8c57-4e3e-a158-3d66ce12f05c"
+                                "label": "PSM_Novel_Peptides",
+                                "output_name": "output",
+                                "uuid": "29c9a368-a7e6-4e8b-81ca-131f63293093"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "errors": null,
-                        "id": 2,
+                        "id": 7,
                         "input_connections": {
-                            "mode|action_report": {
-                                "id": 1,
-                                "output_name": "action_report"
-                            },
-                            "mode|input": {
-                                "id": 0,
+                            "tables_0|table": {
+                                "id": 6,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool NCBI FCS GX",
-                                "name": "mode"
-                            },
-                            {
-                                "description": "runtime parameter for tool NCBI FCS GX",
-                                "name": "mode"
+                                "description": "runtime parameter for tool Query Tabular",
+                                "name": "add_to_database"
                             }
                         ],
-                        "label": "FCS-GX clean",
-                        "name": "NCBI FCS GX",
+                        "label": "Novel_Peptides",
+                        "name": "Query Tabular",
                         "outputs": [
                             {
-                                "name": "contam_fasta",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "clean_fasta",
-                                "type": "fasta"
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 351.484375,
-                            "top": 301.109375
+                            "bottom": 644.25,
+                            "height": 168,
+                            "left": 1143.046875,
+                            "right": 1303.046875,
+                            "top": 476.25,
+                            "width": 160,
+                            "x": 1143.046875,
+                            "y": 476.25
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Novel_Peptides"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "3cdb96f2855d",
-                            "name": "ncbi_fcs_gx",
+                            "changeset_revision": "33d61c89fb8d",
+                            "name": "query_tabular",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"mode\": {\"mode_selector\": \"clean\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}, \"action_report\": {\"__class__\": \"ConnectedValue\"}, \"min_seq_len\": \"200\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.5.0+galaxy0",
+                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"no\", \"__current_case__\": 1}, \"save_db\": \"false\", \"sqlquery\": \"SELECT distinct Sequence FROM psm\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"skip\", \"__current_case__\": 0, \"skip_lines\": \"1\"}}]}, \"tbl_opts\": {\"table_name\": \"psm\", \"column_names_from_first_line\": \"false\", \"col_names\": \"ID,Proteins,Sequence\", \"load_named_columns\": \"true\", \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.0.0",
                         "type": "tool",
-                        "uuid": "0eba0bee-4d7a-4a8d-824c-76d5ae5dcdaa",
-                        "when": null,
+                        "uuid": "5ad1e99c-bf3c-4e87-9fb6-1b5e305ee3fc",
                         "workflow_outputs": [
                             {
-                                "label": "gx_contam_fasta",
-                                "output_name": "contam_fasta",
-                                "uuid": "f3a37b43-d304-4ec0-a023-197c9e0ce2e1"
+                                "label": "Novel_Peptides",
+                                "output_name": "output",
+                                "uuid": "56954668-7aac-423a-89af-aecf2b405b94"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptide_genomic_coordinate/peptide_genomic_coordinate/0.1.1",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "mapping": {
+                                "id": 4,
+                                "output_name": "output"
+                            },
+                            "mzsqlite": {
+                                "id": 3,
+                                "output_name": "output"
                             },
+                            "peptideinput": {
+                                "id": 7,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Peptide Genomic Coodinate",
+                        "outputs": [
                             {
-                                "label": "gx_clean_fasta",
-                                "output_name": "clean_fasta",
-                                "uuid": "56716c7c-ac7f-42f7-bbef-62a36b4d3810"
+                                "name": "peptide_bed",
+                                "type": "bed"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 825.3500137329102,
+                            "height": 209.60000610351562,
+                            "left": 1368.9999389648438,
+                            "right": 1528.9999389648438,
+                            "top": 615.7500076293945,
+                            "width": 160,
+                            "x": 1368.9999389648438,
+                            "y": 615.7500076293945
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptide_genomic_coordinate/peptide_genomic_coordinate/0.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "5f49ffce52cb",
+                            "name": "peptide_genomic_coordinate",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"mapping\": {\"__class__\": \"ConnectedValue\"}, \"mzsqlite\": {\"__class__\": \"ConnectedValue\"}, \"peptideinput\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.1",
+                        "type": "tool",
+                        "uuid": "8eae5eda-e1aa-4d74-8cb9-78172a809ddb",
+                        "workflow_outputs": [
+                            {
+                                "label": "Peptide Genomic Coodinate on input dataset(s)",
+                                "output_name": "peptide_bed",
+                                "uuid": "60fd3e41-8cb7-4a49-b585-2a43117e9cf8"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/richard-burhans/ncbi_fcs_adaptor/ncbi_fcs_adaptor/0.5.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pep_pointer/pep_pointer/0.1.3",
                         "errors": null,
-                        "id": 3,
+                        "id": 9,
                         "input_connections": {
-                            "input": {
-                                "id": 2,
-                                "output_name": "clean_fasta"
+                            "bed": {
+                                "id": 8,
+                                "output_name": "peptide_bed"
+                            },
+                            "gtf_input|gtf": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "FCS-adaptor screen",
-                        "name": "NCBI FCS Adaptor",
+                        "label": null,
+                        "name": "PepPointer",
                         "outputs": [
                             {
-                                "name": "adaptor_report",
+                                "name": "classified",
                                 "type": "tabular"
-                            },
-                            {
-                                "name": "clean_fasta",
-                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 701.53125,
-                            "top": 0
+                            "bottom": 560.4656143188477,
+                            "height": 151.19998168945312,
+                            "left": 1601.5780639648438,
+                            "right": 1761.5780639648438,
+                            "top": 409.26563262939453,
+                            "width": 160,
+                            "x": 1601.5780639648438,
+                            "y": 409.26563262939453
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/richard-burhans/ncbi_fcs_adaptor/ncbi_fcs_adaptor/0.5.0+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/pep_pointer/pep_pointer/0.1.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "d55ad8533d58",
-                            "name": "ncbi_fcs_adaptor",
-                            "owner": "richard-burhans",
+                            "changeset_revision": "073a2965e3b2",
+                            "name": "pep_pointer",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced\": {\"optional_log\": null}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"tax\": \"--euk\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.5.0+galaxy0",
+                        "tool_state": "{\"bed\": {\"__class__\": \"ConnectedValue\"}, \"gtf_input\": {\"gtf_source\": \"history\", \"__current_case__\": 1, \"gtf\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.3",
                         "type": "tool",
-                        "uuid": "1c9a5183-76a7-4cd9-9511-72fd75101c13",
-                        "when": null,
+                        "uuid": "54174fe8-f646-43b5-9491-0e117aaf75bd",
                         "workflow_outputs": [
                             {
-                                "label": "fcs_adaptor_report",
-                                "output_name": "adaptor_report",
-                                "uuid": "6a4baf46-80b0-4a96-b864-9201fc80cdb7"
-                            },
-                            {
-                                "label": "adaptor_clean_fasta",
-                                "output_name": "clean_fasta",
-                                "uuid": "1cad7ab4-a817-436c-9a63-fd4e3c6b4bbb"
+                                "label": "PepPointer on input dataset(s)",
+                                "output_name": "classified",
+                                "uuid": "3c410bed-ff79-4774-b75c-48659d291160"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "errors": null,
-                        "id": 4,
+                        "id": 10,
                         "input_connections": {
-                            "mode|action_report": {
-                                "id": 3,
-                                "output_name": "adaptor_report"
+                            "tables_0|table": {
+                                "id": 9,
+                                "output_name": "classified"
                             },
-                            "mode|input": {
-                                "id": 2,
-                                "output_name": "clean_fasta"
+                            "tables_1|table": {
+                                "id": 6,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool NCBI FCS GX",
-                                "name": "mode"
-                            },
-                            {
-                                "description": "runtime parameter for tool NCBI FCS GX",
-                                "name": "mode"
+                                "description": "runtime parameter for tool Query Tabular",
+                                "name": "add_to_database"
                             }
                         ],
-                        "label": "FCS-adaptor clean",
-                        "name": "NCBI FCS GX",
+                        "label": "Final_Summary_Novel_Peptides",
+                        "name": "Query Tabular",
                         "outputs": [
                             {
-                                "name": "contam_fasta",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "clean_fasta",
-                                "type": "fasta"
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 699,
-                            "top": 302.78125
+                            "bottom": 585.9500274658203,
+                            "height": 243.20001220703125,
+                            "left": 1888.0000305175781,
+                            "right": 2048.000030517578,
+                            "top": 342.75001525878906,
+                            "width": 160,
+                            "x": 1888.0000305175781,
+                            "y": 342.75001525878906
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Final_Summary_Novel_Peptides"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "3cdb96f2855d",
-                            "name": "ncbi_fcs_gx",
+                            "changeset_revision": "33d61c89fb8d",
+                            "name": "query_tabular",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"mode\": {\"mode_selector\": \"clean\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}, \"action_report\": {\"__class__\": \"ConnectedValue\"}, \"min_seq_len\": \"200\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.5.0+galaxy0",
+                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"save_db\": \"false\", \"sqlquery\": \"SELECT psm.Sequence as PeptideSequence, count(psm.Sequence) as SpectralCount, psm.Proteins as Proteins, bed_pep_pointer.chrom as Chromosome, bed_pep_pointer.start as Start, bed_pep_pointer.end as End, bed_pep_pointer.strand as Strand, bed_pep_pointer.annot as Annotation, bed_pep_pointer.chrom||':'||bed_pep_pointer.start||'-'||bed_pep_pointer.end as GenomeCoordinate,'https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='||bed_pep_pointer.chrom||'%3A'||bed_pep_pointer.start||'-'||bed_pep_pointer.end as UCSC_Genome_Browser \\nFROM psm \\nINNER JOIN bed_pep_pointer on bed_pep_pointer.peptide = psm.Sequence \\nGROUP BY psm.Sequence\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"bed_pep_pointer\", \"column_names_from_first_line\": \"false\", \"col_names\": \"chrom,start,end,peptide,score,strand,annot\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": []}}, {\"__index__\": 1, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": [{\"__index__\": 0, \"filter\": {\"filter_type\": \"skip\", \"__current_case__\": 0, \"skip_lines\": \"1\"}}]}, \"tbl_opts\": {\"table_name\": \"psm\", \"column_names_from_first_line\": \"false\", \"col_names\": \"ID,Proteins,Sequence,AAs_Before,AAs_After,Position,Modified_Sequence,Variable_Modifications,Fixed_Modifications,Spectrum_File,Spectrum_Title,Spectrum_Scan_Number,RT,mz,Measured_Charge,Identification_Charge,Theoretical_Mass,Isotope_Number,Precursor_mz_Error_ppm,Localization_Confidence,Probabilistic_PTM_score,Dscore,Confidence,Validation\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.0.0",
                         "type": "tool",
-                        "uuid": "ee8b7bac-42a5-4b17-b8ef-f432c626bb80",
-                        "when": null,
+                        "uuid": "d962e688-4af1-49fc-907c-6e2f5d6c6d0f",
                         "workflow_outputs": [
                             {
-                                "label": "adaptor_contam_fasta",
-                                "output_name": "contam_fasta",
-                                "uuid": "0da68570-7490-4087-86c8-739522e1a776"
-                            },
-                            {
-                                "label": "final_clean_fasta",
-                                "output_name": "clean_fasta",
-                                "uuid": "4985eb07-30b0-4872-ab83-52ffeb619900"
+                                "label": "Final_Summary_Novel_Peptides",
+                                "output_name": "output",
+                                "uuid": "50e64c95-cd68-47cb-9e0c-b3714b2f2431"
                             }
                         ]
                     }
                 ],
-                "parent_id": "sequence-analysis/ncbi-fcs",
-                "path": "topics/sequence-analysis/tutorials/ncbi-fcs/workflows/NCBI-Foreign-Contamination-Screen.ga",
+                "parent_id": "proteomics/proteogenomics-novel-peptide-analysis",
+                "path": "topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/workflows/galaxy-workflow-mouse_novel_peptide_analysis.ga",
                 "tags": [
-                    "NCBI"
+                    "proteomics"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "NCBI Foreign Contamination Screen",
-                "topic_id": "sequence-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/sequence-analysis-ncbi-fcs/versions/ncbi-foreign-contamination-screen",
-                "tutorial_id": "ncbi-fcs",
-                "url": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/ncbi-fcs/workflows/NCBI-Foreign-Contamination-Screen.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/ncbi-fcs/workflows/NCBI-Foreign-Contamination-Screen.html",
-                "version": 1,
-                "wfid": "sequence-analysis-ncbi-fcs",
-                "wfname": "ncbi-foreign-contamination-screen",
-                "workflow": "NCBI-Foreign-Contamination-Screen.ga",
+                "tests": false,
+                "title": "GTN Proteogemics3 Novel Peptide Analysis",
+                "topic_id": "proteomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-proteogenomics-novel-peptide-analysis/versions/galaxy-workflow-mouse-novel-peptide-analysis",
+                "tutorial_id": "proteogenomics-novel-peptide-analysis",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/workflows/galaxy-workflow-mouse_novel_peptide_analysis.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/workflows/galaxy-workflow-mouse_novel_peptide_analysis.html",
+                "version": 6,
+                "wfid": "proteomics-proteogenomics-novel-peptide-analysis",
+                "wfname": "galaxy-workflow-mouse-novel-peptide-analysis",
+                "workflow": "galaxy-workflow-mouse_novel_peptide_analysis.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/richard-burhans/ncbi_fcs_adaptor/ncbi_fcs_adaptor/0.5.0+galaxy0"
+                    "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/pep_pointer/pep_pointer/0.1.3",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptide_genomic_coordinate/peptide_genomic_coordinate/0.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0"
                 ],
-                "workflowhub_id": null
+                "workflowhub_id": "1236"
             }
         ],
-        "zenodo_link": "https://zenodo.org/records/10932013"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.1489208"
     },
     {
         "admin_install": {
@@ -205080,873 +207143,606 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "5ec9f6bceaee",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bracken",
-                    "owner": "iuc",
-                    "revisions": "978ae4147c29",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bracken",
-                    "owner": "iuc",
-                    "revisions": "1d4bd12f01cf",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastp",
-                    "owner": "iuc",
-                    "revisions": "65b93b623c77",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "dbbuilder",
+                    "owner": "galaxyp",
+                    "revisions": "983bf725dfc2",
+                    "tool_panel_section_label": "Get Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fastp",
-                    "owner": "iuc",
-                    "revisions": "c59d48774d03",
+                    "name": "fasta_merge_files_and_filter_unique_sequences",
+                    "owner": "galaxyp",
+                    "revisions": "f546e7278f04",
                     "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "kraken2",
-                    "owner": "iuc",
-                    "revisions": "20e2f64aa1fe",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "kraken2",
-                    "owner": "iuc",
-                    "revisions": "cdee7158adf3",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "name": "metanovo",
+                    "owner": "galaxyp",
+                    "revisions": "d6dcd3173bdf",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "recentrifuge",
-                    "owner": "iuc",
-                    "revisions": "b5407cc2bf51",
-                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "name": "uniprotxml_downloader",
+                    "owner": "galaxyp",
+                    "revisions": "265c35540faa",
+                    "tool_panel_section_label": "Get Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bracken\n  owner: iuc\n  revisions: 978ae4147c29\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bracken\n  owner: iuc\n  revisions: 1d4bd12f01cf\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: c59d48774d03\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: 20e2f64aa1fe\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: cdee7158adf3\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: recentrifuge\n  owner: iuc\n  revisions: b5407cc2bf51\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: dbbuilder\n  owner: galaxyp\n  revisions: 983bf725dfc2\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_merge_files_and_filter_unique_sequences\n  owner: galaxyp\n  revisions: f546e7278f04\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: metanovo\n  owner: galaxyp\n  revisions: d6dcd3173bdf\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: uniprotxml_downloader\n  owner: galaxyp\n  revisions: 265c35540faa\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.json",
         "contributions": {
             "authorship": [
-                "bebatut",
-                "clsiguret"
+                "subinamehta",
+                "katherine-d21",
+                "dechendb"
             ],
-            "funding": [
-                "abromics"
+            "editing": [
+                "pratikdjagtap",
+                "timothygriffin"
             ]
         },
         "contributors": [
             {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+                "email": "subinamehta@gmail.com",
+                "id": "subinamehta",
+                "joined": "2018-06",
+                "linkedin": "subinamehta",
+                "matrix": "subinamehta:matrix.org",
+                "name": "Subina Mehta",
+                "orcid": "0000-0001-9818-0537",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
+                "twitter": "Subina_Mehta",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
             },
             {
-                "affiliations": [
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "elixir_node": "fr",
-                "email": "clea.siguret@gmail.com",
-                "id": "clsiguret",
-                "joined": "2024-04",
-                "linkedin": "cl\u00e9a-siguret-58423b107",
-                "matrix": "clsiguret:matrix.org",
-                "name": "Clea Siguret",
-                "orcid": "0009-0005-6140-0379",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/clsiguret/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/clsiguret.json"
+                "id": "katherine-d21",
+                "joined": "2023-08",
+                "name": "Katherine Do",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/katherine-d21/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/katherine-d21.json"
             },
             {
-                "avatar": "/training-material/assets/images/abromics.png",
-                "funder": true,
+                "id": "dechendb",
+                "joined": "2023-06",
+                "name": "Dechen Bhuming",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/dechendb/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/dechendb.json"
+            },
+            {
+                "email": "pjagtap@umn.edu",
+                "id": "pratikdjagtap",
+                "joined": "2017-09",
+                "name": "Pratik Jagtap",
+                "orcid": "0000-0003-0984-0973",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
+            },
+            {
+                "email": "tgriffin@umn.edu",
                 "github": false,
-                "id": "abromics",
-                "joined": "2024-01",
-                "name": "ABRomics",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abromics/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/abromics.json"
+                "id": "timothygriffin",
+                "joined": "2017-09",
+                "name": "Timothy J. Griffin",
+                "orcid": "0000-0001-6801-2559",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
             }
         ],
-        "dir": "topics/sequence-analysis/tutorials/quality-contamination-control",
-        "edam_ontology": [
-            "topic_3673",
-            "topic_0622",
-            "topic_3301",
-            "topic_3697"
-        ],
+        "dir": "topics/proteomics/tutorials/clinical-mp-1-database-generation",
         "edam_operation": [
-            "Sequencing quality control",
-            "Sequence contamination filtering",
-            "Cross-assembly",
-            "Sequence composition calculation",
-            "Taxonomic classification",
+            "Target-Decoy",
             "Expression analysis",
-            "Statistical calculation"
-        ],
-        "edam_topic": [
-            "Whole genome sequencing",
-            "Genomics",
-            "Microbiology",
-            "Microbial ecology"
+            "Tag-based peptide identification",
+            "de Novo sequencing",
+            "Protein identification"
         ],
+        "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.fr"
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": true,
-        "id": "sequence-analysis/quality-contamination-control",
-        "inexact_supported_servers": [
-            "Galaxy@AuBi",
-            "GalaxyTrakr",
-            "UseGalaxy.cz",
-            "UseGalaxy.org (Main)"
+        "follow_up_training": [
+            {
+                "topic_name": "proteomics",
+                "tutorials": [
+                    "clinical-mp-2-discovery"
+                ],
+                "type": "internal"
+            }
         ],
+        "hands_on": true,
+        "id": "proteomics/clinical-mp-1-database-generation",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Conduct quality control on every dataset before performing any other bioinformatics analysis",
-            "Review the quality metrics and, if necessary, improve the quality of your data",
-            "Check the impact of the quality control",
-            "Detect witch microorganisms are present and extract the species level",
-            "Check possible contamination in a bacterial isolate"
+            "Create a customized proteomics database from 16SrRNA results."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-15",
+        "mod_date": "2024-08-08",
         "objectives": [
-            "Run tools to evaluate sequencing data on quality and quantity",
-            "Evaluate the output of quality control tools",
-            "Improve the quality of sequencing data",
-            "Run a series of tool to identify species in bacterial isolate sequencing data",
-            "Visualize the species abundance"
+            "Downloading databases related to 16SrRNA data",
+            "For better identification results, combine host and microbial proteins.",
+            "Reduced database provides better FDR stats."
         ],
-        "pageviews": 76,
-        "pub_date": "2024-07-15",
+        "pageviews": 362,
+        "pub_date": "2024-02-06",
         "questions": [
-            "How to check the quality of MiSeq data?",
-            "What are the species in bacterial isolate sequencing data?"
+            "Why do we need to generate a customized database for metaproteomics research?",
+            "How do we reduce the size of the database?"
         ],
-        "short_id": "T00446",
+        "recordings": [
+            {
+                "captioners": [
+                    "katherine-d21"
+                ],
+                "date": "2024-06-21",
+                "galaxy_version": "23.1",
+                "length": "15M",
+                "speakers": [
+                    "katherine-d21"
+                ],
+                "youtube_id": "FEAEyqcjxkE"
+            }
+        ],
+        "redirect_from": [
+            "/topics/proteomics/tutorials/clinical-mp-database-generation/tutorial",
+            "/short/proteomics/clinical-mp-1-database-generation",
+            "/short/T00413"
+        ],
+        "requirements": [
+            {
+                "topic_name": "proteomics",
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00413",
         "short_tools": [
-            "fastp",
-            "est_abundance",
-            "fastqc",
-            "kraken2",
-            "recentrifuge",
-            "upload1"
+            "uniprotxml_downloader",
+            "dbbuilder",
+            "fasta_merge_files_and_filter_unique_sequences",
+            "metanovo"
         ],
         "slides": false,
         "slides_recordings": false,
+        "subtopic": "clinical-metaproteomics",
         "supported_servers": {
             "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
                 }
-            ]
+            ],
+            "inexact": []
         },
         "symlink": null,
         "tags": [
-            "illumina",
-            "bacteria",
-            "microgalaxy"
+            "label-TMT11"
         ],
-        "time_estimation": "2H",
-        "title": "Quality and contamination control in bacterial isolate using Illumina MiSeq Data",
+        "time_estimation": "3H",
+        "title": "Clinical Metaproteiomics 1: Database-Generation",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.8+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0",
-            "upload1"
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/metanovo/metanovo/1.9.4+galaxy4",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.3.0"
         ],
-        "topic_name": "sequence-analysis",
-        "topic_name_human": "Sequence analysis",
+        "topic_name": "proteomics",
+        "topic_name_human": "Proteomics",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "quality-contamination-control",
+        "tutorial_name": "clinical-mp-1-database-generation",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.json"
         },
-        "version": 1,
+        "version": 2,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 233,
-        "visitors": 61,
+        "visit_duration": 225,
+        "visitors": 215,
         "workflows": [
             {
                 "creators": [
                     {
-                        "alternateName": "bebatut",
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0001-9852-1987",
-                        "name": "B\u00e9r\u00e9nice Batut"
-                    },
-                    {
-                        "alternateName": "clsiguret",
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0009-0005-6140-0379",
-                        "name": "Clea Siguret"
+                        "class": "Organization",
+                        "identifier": "0000-0001-9818-0537",
+                        "name": "Subina Mehta"
                     }
                 ],
-                "description": "Quality and contamination control in bacterial isolate using Illumina MiSeq Data",
+                "description": "Generating a large database and then reducing it to a compact database using Metanovo",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDRR187559_1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDRR187559_2\"]\n  2[label=\"FastQC forward\"]\n  0 -> 2 [label=\"output\"]\n  kd3aed14e51b840b09d6d548fff2ab63a[color=lightseagreen,label=\"Output\\nFastQC text_file (forward)\"]\n  2 -> kd3aed14e51b840b09d6d548fff2ab63a\n  k6c9273387e024599a01d014a35a529e8[color=lightseagreen,label=\"Output\\nFastQC html_file (forward)\"]\n  2 -> k6c9273387e024599a01d014a35a529e8\n  3[label=\"FastQC reverse\"]\n  1 -> 3 [label=\"output\"]\n  k30d76c09809d4415a1e6f244cfc34065[color=lightseagreen,label=\"Output\\nFastQC html_file (reverse)\"]\n  3 -> k30d76c09809d4415a1e6f244cfc34065\n  kbbafb0728b124908ae0f10cc7f9086d3[color=lightseagreen,label=\"Output\\nFastQC text_file (reverse)\"]\n  3 -> kbbafb0728b124908ae0f10cc7f9086d3\n  4[label=\"fastp\"]\n  0 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  k1a089ca0445a4322b74f60c7aefc7cd8[color=lightseagreen,label=\"Output\\nfastp report_html\"]\n  4 -> k1a089ca0445a4322b74f60c7aefc7cd8\n  kb634addfdcb843e68016341de7eb5b87[color=lightseagreen,label=\"Output\\nDRR187559_filtered_\"]\n  4 -> kb634addfdcb843e68016341de7eb5b87\n  k0a57afa4e75e470dad7b13e567ce54a3[color=lightseagreen,label=\"Output\\nDRR187559_filtered_1\"]\n  4 -> k0a57afa4e75e470dad7b13e567ce54a3\n  kbb98c4d1bd1d47bdac564ac0e1e49d50[color=lightseagreen,label=\"Output\\nfastp_json\"]\n  4 -> kbb98c4d1bd1d47bdac564ac0e1e49d50\n  5[label=\"Kraken2\"]\n  4 -> 5 [label=\"out1\"]\n  4 -> 5 [label=\"out2\"]\n  k54b85a5372ee4b73b1867fd55e8aab9b[color=lightseagreen,label=\"Output\\nkraken_report_tabular\"]\n  5 -> k54b85a5372ee4b73b1867fd55e8aab9b\n  ka408a64458cd4f5eaf2515b5ea63aa76[color=lightseagreen,label=\"Output\\nkraken_report_reads\"]\n  5 -> ka408a64458cd4f5eaf2515b5ea63aa76\n  6[label=\"Bracken\"]\n  5 -> 6 [label=\"report_output\"]\n  k8ca52af9f83942b6aa74f1a6a1dfbbc8[color=lightseagreen,label=\"Output\\nbracken_kraken_report\"]\n  6 -> k8ca52af9f83942b6aa74f1a6a1dfbbc8\n  kae6c6464f5f54e5bb616d38166fc0133[color=lightseagreen,label=\"Output\\nbracken_report_tsv\"]\n  6 -> kae6c6464f5f54e5bb616d38166fc0133\n  7[label=\"Recentrifuge\"]\n  5 -> 7 [label=\"output\"]\n  kbd947a1d0443465f86585d76d9ce69f8[color=lightseagreen,label=\"Output\\nrecentrifuge_report_html\"]\n  7 -> kbd947a1d0443465f86585d76d9ce69f8\n  kc7457acb41bc4191b3fb6716e15fbe57[color=lightseagreen,label=\"Output\\nrecentrifuge_data_tabular\"]\n  7 -> kc7457acb41bc4191b3fb6716e15fbe57\n  kb5694f2dc8cd4460bfff74fd0792ecb3[color=lightseagreen,label=\"Output\\nrecentrifuge_stats_tabular\"]\n  7 -> kb5694f2dc8cd4460bfff74fd0792ecb3\n  k94f6ff070e0647ad88f8a058d0808537[color=lightseagreen,label=\"Output\\nrecentrifuge_logfile\"]\n  7 -> k94f6ff070e0647ad88f8a058d0808537\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHUMAN SwissProt Protein Database\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput MGF files Dataset Collection\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSpecies_UniProt_FASTA\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nContaminants cRAP Protein Database \"]\n  4[label=\"Human UniProt Microbial Proteins cRAP for MetaNovo\"]\n  0 -> 4 [label=\"output\"]\n  2 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  k286f5bd4fb0d46498dacf191acc72722[color=lightseagreen,label=\"Output\\nHuman UniProt Microbial Proteins cRAP for MetaNovo\"]\n  4 -> k286f5bd4fb0d46498dacf191acc72722\n  5[label=\"MetaNovo\"]\n  4 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"FASTA Merge Files and Filter Unique Sequences\"]\n  0 -> 6 [label=\"output\"]\n  5 -> 6 [label=\"output_fasta\"]\n  3 -> 6 [label=\"output\"]\n  kde57cd9dac0543979d44e65620913447[color=lightseagreen,label=\"Output\\nHuman UniProt Microbial Proteins (from MetaNovo) and cRAP \"]\n  6 -> kde57cd9dac0543979d44e65620913447\n}",
                 "history": [
                     {
-                        "hash": "b415560c3b517c8332ed6762dc86a54d0968b2f2",
-                        "message": "Add tuto 'quality-contamination-control' + update learning pathway 'amr-gene-detection'",
+                        "hash": "9a94b97ceccea577f680e7b454b6b8b7995801de",
+                        "message": "add workflow",
                         "num": 1,
-                        "short_hash": "b415560c3",
-                        "unix": "1718877309"
+                        "short_hash": "9a94b97ce",
+                        "unix": "1723116168"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "forward read",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "forward read",
-                                "name": "DRR187559_1"
+                                "description": "",
+                                "name": "HUMAN SwissProt Protein Database"
                             }
                         ],
-                        "label": "DRR187559_1",
+                        "label": "HUMAN SwissProt Protein Database",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
                             "left": 0,
-                            "top": 275.20001220703125
+                            "top": 204.86580898284382
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "a39893cf-49cb-4c5c-9e71-0f8004a2a1ee",
+                        "uuid": "bb037df4-ef56-42ad-8b3e-93425bc7bdfa",
                         "when": null,
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "reverse read",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "reverse read",
-                                "name": "DRR187559_2"
+                                "description": "",
+                                "name": "Input MGF files (Dataset Collection)"
                             }
                         ],
-                        "label": "DRR187559_2",
-                        "name": "Input dataset",
+                        "label": "Input MGF files (Dataset Collection)",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 24,
-                            "top": 530.1999969482422
+                            "left": 260.9789733886719,
+                            "top": 0
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ca539dfd-e173-42d6-998a-0fc4c5f3d5b8",
+                        "type": "data_collection_input",
+                        "uuid": "d6bb6e3e-ebf6-4c65-bcf7-ea9527cf8653",
                         "when": null,
                         "workflow_outputs": []
-                    }
-                ],
-                "license": "GPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nDRR187559_1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nDRR187559_2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"FastQC forward\"];\n  0 -->|output| 2;\n  d3aed14e-51b8-40b0-9d6d-548fff2ab63a[\"Output\\nFastQC text_file (forward)\"];\n  2 --> d3aed14e-51b8-40b0-9d6d-548fff2ab63a;\n  style d3aed14e-51b8-40b0-9d6d-548fff2ab63a stroke:#2c3143,stroke-width:4px;\n  6c927338-7e02-4599-a01d-014a35a529e8[\"Output\\nFastQC html_file (forward)\"];\n  2 --> 6c927338-7e02-4599-a01d-014a35a529e8;\n  style 6c927338-7e02-4599-a01d-014a35a529e8 stroke:#2c3143,stroke-width:4px;\n  3[\"FastQC reverse\"];\n  1 -->|output| 3;\n  30d76c09-809d-4415-a1e6-f244cfc34065[\"Output\\nFastQC html_file (reverse)\"];\n  3 --> 30d76c09-809d-4415-a1e6-f244cfc34065;\n  style 30d76c09-809d-4415-a1e6-f244cfc34065 stroke:#2c3143,stroke-width:4px;\n  bbafb072-8b12-4908-ae0f-10cc7f9086d3[\"Output\\nFastQC text_file (reverse)\"];\n  3 --> bbafb072-8b12-4908-ae0f-10cc7f9086d3;\n  style bbafb072-8b12-4908-ae0f-10cc7f9086d3 stroke:#2c3143,stroke-width:4px;\n  4[\"fastp\"];\n  0 -->|output| 4;\n  1 -->|output| 4;\n  1a089ca0-445a-4322-b74f-60c7aefc7cd8[\"Output\\nfastp report_html\"];\n  4 --> 1a089ca0-445a-4322-b74f-60c7aefc7cd8;\n  style 1a089ca0-445a-4322-b74f-60c7aefc7cd8 stroke:#2c3143,stroke-width:4px;\n  b634addf-dcb8-43e6-8016-341de7eb5b87[\"Output\\nDRR187559_filtered_\"];\n  4 --> b634addf-dcb8-43e6-8016-341de7eb5b87;\n  style b634addf-dcb8-43e6-8016-341de7eb5b87 stroke:#2c3143,stroke-width:4px;\n  0a57afa4-e75e-470d-ad7b-13e567ce54a3[\"Output\\nDRR187559_filtered_1\"];\n  4 --> 0a57afa4-e75e-470d-ad7b-13e567ce54a3;\n  style 0a57afa4-e75e-470d-ad7b-13e567ce54a3 stroke:#2c3143,stroke-width:4px;\n  bb98c4d1-bd1d-47bd-ac56-4ac0e1e49d50[\"Output\\nfastp_json\"];\n  4 --> bb98c4d1-bd1d-47bd-ac56-4ac0e1e49d50;\n  style bb98c4d1-bd1d-47bd-ac56-4ac0e1e49d50 stroke:#2c3143,stroke-width:4px;\n  5[\"Kraken2\"];\n  4 -->|out1| 5;\n  4 -->|out2| 5;\n  54b85a53-72ee-4b73-b186-7fd55e8aab9b[\"Output\\nkraken_report_tabular\"];\n  5 --> 54b85a53-72ee-4b73-b186-7fd55e8aab9b;\n  style 54b85a53-72ee-4b73-b186-7fd55e8aab9b stroke:#2c3143,stroke-width:4px;\n  a408a644-58cd-4f5e-af25-15b5ea63aa76[\"Output\\nkraken_report_reads\"];\n  5 --> a408a644-58cd-4f5e-af25-15b5ea63aa76;\n  style a408a644-58cd-4f5e-af25-15b5ea63aa76 stroke:#2c3143,stroke-width:4px;\n  6[\"Bracken\"];\n  5 -->|report_output| 6;\n  8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8[\"Output\\nbracken_kraken_report\"];\n  6 --> 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8;\n  style 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8 stroke:#2c3143,stroke-width:4px;\n  ae6c6464-f5f5-4e5b-b616-d38166fc0133[\"Output\\nbracken_report_tsv\"];\n  6 --> ae6c6464-f5f5-4e5b-b616-d38166fc0133;\n  style ae6c6464-f5f5-4e5b-b616-d38166fc0133 stroke:#2c3143,stroke-width:4px;\n  7[\"Recentrifuge\"];\n  5 -->|output| 7;\n  bd947a1d-0443-465f-8658-5d76d9ce69f8[\"Output\\nrecentrifuge_report_html\"];\n  7 --> bd947a1d-0443-465f-8658-5d76d9ce69f8;\n  style bd947a1d-0443-465f-8658-5d76d9ce69f8 stroke:#2c3143,stroke-width:4px;\n  c7457acb-41bc-4191-b3fb-6716e15fbe57[\"Output\\nrecentrifuge_data_tabular\"];\n  7 --> c7457acb-41bc-4191-b3fb-6716e15fbe57;\n  style c7457acb-41bc-4191-b3fb-6716e15fbe57 stroke:#2c3143,stroke-width:4px;\n  b5694f2d-c8cd-4460-bfff-74fd0792ecb3[\"Output\\nrecentrifuge_stats_tabular\"];\n  7 --> b5694f2d-c8cd-4460-bfff-74fd0792ecb3;\n  style b5694f2d-c8cd-4460-bfff-74fd0792ecb3 stroke:#2c3143,stroke-width:4px;\n  94f6ff07-0e06-47ad-88f8-a058d0808537[\"Output\\nrecentrifuge_logfile\"];\n  7 --> 94f6ff07-0e06-47ad-88f8-a058d0808537;\n  style 94f6ff07-0e06-47ad-88f8-a058d0808537 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Quality and contamination control in bacterial isolate using Illumina MiSeq Data",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+                        "content_id": null,
                         "errors": null,
                         "id": 2,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "FastQC (forward)",
-                        "name": "FastQC",
-                        "outputs": [
-                            {
-                                "name": "html_file",
-                                "type": "html"
-                            },
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "text_file",
-                                "type": "txt"
+                                "description": "",
+                                "name": "Species_UniProt_FASTA"
                             }
                         ],
+                        "label": "Species_UniProt_FASTA",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 340,
-                            "top": 0
-                        },
-                        "post_job_actions": {
-                            "TagDatasetActionhtml_file": {
-                                "action_arguments": {
-                                    "tags": "#unfiltered"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "html_file"
-                            },
-                            "TagDatasetActiontext_file": {
-                                "action_arguments": {
-                                    "tags": "#unfiltered"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "text_file"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "5ec9f6bceaee",
-                            "name": "fastqc",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 2.443389892578125,
+                            "top": 369.4779610824532
                         },
-                        "tool_state": "{\"__input_ext\": \"fastqsanger.bz2\", \"adapters\": null, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"contaminants\": null, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": null, \"min_length\": null, \"nogroup\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.74+galaxy0",
-                        "type": "tool",
-                        "uuid": "1dd908a7-85da-4c90-b506-73fe598e0ce0",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "b4b90dcd-9228-4aad-b51d-2f08b2d4cc0d",
                         "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "FastQC text_file (forward)",
-                                "output_name": "text_file",
-                                "uuid": "d3aed14e-51b8-40b0-9d6d-548fff2ab63a"
-                            },
-                            {
-                                "label": "FastQC html_file (forward)",
-                                "output_name": "html_file",
-                                "uuid": "6c927338-7e02-4599-a01d-014a35a529e8"
-                            }
-                        ]
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+                        "content_id": null,
                         "errors": null,
                         "id": 3,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "FastQC (reverse)",
-                        "name": "FastQC",
-                        "outputs": [
-                            {
-                                "name": "html_file",
-                                "type": "html"
-                            },
-                            {
-                                "name": "text_file",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 323,
-                            "top": 612.5999755859375
-                        },
-                        "post_job_actions": {
-                            "TagDatasetActionhtml_file": {
-                                "action_arguments": {
-                                    "tags": "#unfiltered"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "html_file"
-                            },
-                            "TagDatasetActiontext_file": {
-                                "action_arguments": {
-                                    "tags": "#unfiltered"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "text_file"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "5ec9f6bceaee",
-                            "name": "fastqc",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"fastqsanger.bz2\", \"adapters\": null, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"contaminants\": null, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": null, \"min_length\": null, \"nogroup\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.74+galaxy0",
-                        "type": "tool",
-                        "uuid": "198542e7-06ed-42ed-a725-6c8902cda430",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "FastQC html_file (reverse)",
-                                "output_name": "html_file",
-                                "uuid": "30d76c09-809d-4415-a1e6-f244cfc34065"
-                            },
-                            {
-                                "label": "FastQC text_file (reverse)",
-                                "output_name": "text_file",
-                                "uuid": "bbafb072-8b12-4908-ae0f-10cc7f9086d3"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "single_paired|in1": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "single_paired|in2": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "fastp",
-                        "outputs": [
-                            {
-                                "name": "out1",
-                                "type": "input"
-                            },
-                            {
-                                "name": "out2",
-                                "type": "input"
-                            },
-                            {
-                                "name": "report_html",
-                                "type": "html"
-                            },
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "report_json",
-                                "type": "json"
+                                "description": "",
+                                "name": "Contaminants (cRAP) Protein Database "
                             }
                         ],
+                        "label": "Contaminants (cRAP) Protein Database ",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 578.603249768338,
-                            "top": 384.1144483914405
-                        },
-                        "post_job_actions": {
-                            "TagDatasetActionout1": {
-                                "action_arguments": {
-                                    "tags": "#filtered"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "out1"
-                            },
-                            "TagDatasetActionout2": {
-                                "action_arguments": {
-                                    "tags": "#filtered"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "out2"
-                            },
-                            "TagDatasetActionreport_html": {
-                                "action_arguments": {
-                                    "tags": "#filtered"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "report_html"
-                            },
-                            "TagDatasetActionreport_json": {
-                                "action_arguments": {
-                                    "tags": "#filtered"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "report_json"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "65b93b623c77",
-                            "name": "fastp",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 14.413701296714208,
+                            "top": 468.23383463562413
                         },
-                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": \"30\", \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": null, \"umi_len\": null, \"umi_prefix\": null}, \"cutting_by_quality_options\": {\"cut_by_quality5\": true, \"cut_by_quality3\": true, \"cut_window_size\": \"4\", \"cut_mean_quality\": \"20\"}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired\", \"__current_case__\": 1, \"in1\": {\"__class__\": \"ConnectedValue\"}, \"in2\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": null, \"adapter_sequence2\": null}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.23.2+galaxy0",
-                        "type": "tool",
-                        "uuid": "2e9aba48-2b99-46a1-a4de-72a8a2f6db84",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "fastp report_html",
-                                "output_name": "report_html",
-                                "uuid": "1a089ca0-445a-4322-b74f-60c7aefc7cd8"
-                            },
-                            {
-                                "label": "DRR187559_filtered_",
-                                "output_name": "out2",
-                                "uuid": "b634addf-dcb8-43e6-8016-341de7eb5b87"
-                            },
-                            {
-                                "label": "DRR187559_filtered_1",
-                                "output_name": "out1",
-                                "uuid": "0a57afa4-e75e-470d-ad7b-13e567ce54a3"
-                            },
-                            {
-                                "label": "fastp_json",
-                                "output_name": "report_json",
-                                "uuid": "bb98c4d1-bd1d-47bd-ac56-4ac0e1e49d50"
-                            }
-                        ]
-                    },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ca7de659-6e60-4bd5-aa4c-a88f2860e8c9",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nHUMAN SwissProt Protein Database\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nInput MGF files Dataset Collection\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nSpecies_UniProt_FASTA\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nContaminants cRAP Protein Database \"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Human UniProt Microbial Proteins cRAP for MetaNovo\"];\n  0 -->|output| 4;\n  2 -->|output| 4;\n  3 -->|output| 4;\n  286f5bd4-fb0d-4649-8dac-f191acc72722[\"Output\\nHuman UniProt Microbial Proteins cRAP for MetaNovo\"];\n  4 --> 286f5bd4-fb0d-4649-8dac-f191acc72722;\n  style 286f5bd4-fb0d-4649-8dac-f191acc72722 stroke:#2c3143,stroke-width:4px;\n  5[\"MetaNovo\"];\n  4 -->|output| 5;\n  1 -->|output| 5;\n  6[\"FASTA Merge Files and Filter Unique Sequences\"];\n  0 -->|output| 6;\n  5 -->|output_fasta| 6;\n  3 -->|output| 6;\n  de57cd9d-ac05-4397-9d44-e65620913447[\"Output\\nHuman UniProt Microbial Proteins (from MetaNovo) and cRAP \"];\n  6 --> de57cd9d-ac05-4397-9d44-e65620913447;\n  style de57cd9d-ac05-4397-9d44-e65620913447 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "WF1_Database_Generation_Workflow",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
                         "errors": null,
-                        "id": 5,
+                        "id": 4,
                         "input_connections": {
-                            "single_paired|forward_input": {
-                                "id": 4,
-                                "output_name": "out1"
+                            "batchmode|input_fastas_0|input_fasta": {
+                                "id": 0,
+                                "output_name": "output"
                             },
-                            "single_paired|reverse_input": {
-                                "id": 4,
-                                "output_name": "out2"
+                            "batchmode|input_fastas_1|input_fasta": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "batchmode|input_fastas_2|input_fasta": {
+                                "id": 3,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Kraken2",
+                        "label": "Human UniProt Microbial Proteins cRAP for MetaNovo",
+                        "name": "FASTA Merge Files and Filter Unique Sequences",
                         "outputs": [
-                            {
-                                "name": "report_output",
-                                "type": "tabular"
-                            },
                             {
                                 "name": "output",
-                                "type": "tabular"
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 850.4914977412587,
-                            "top": 397.42238822577673
+                            "left": 332.14166641631607,
+                            "top": 272.4446413680965
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                        "post_job_actions": {
+                            "EmailActionoutput": {
+                                "action_arguments": {
+                                    "host": "usegalaxy.eu"
+                                },
+                                "action_type": "EmailAction",
+                                "output_name": "output"
+                            },
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Human UniProt Microbial Proteins cRAP for MetaNovo"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "20e2f64aa1fe",
-                            "name": "kraken2",
-                            "owner": "iuc",
+                            "changeset_revision": "f546e7278f04",
+                            "name": "fasta_merge_files_and_filter_unique_sequences",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"confidence\": \"0.0\", \"kraken2_database\": \"2023-08-24T153645Z_standard_prebuilt_pluspf_16gb_2022-06-07\", \"min_base_quality\": \"10\", \"minimum_hit_groups\": \"2\", \"quick\": false, \"report\": {\"create_report\": true, \"use_mpa_style\": false, \"report_zero_counts\": false, \"report_minimizer_data\": false}, \"single_paired\": {\"single_paired_selector\": \"yes\", \"__current_case__\": 1, \"forward_input\": {\"__class__\": \"ConnectedValue\"}, \"reverse_input\": {\"__class__\": \"ConnectedValue\"}}, \"split_reads\": false, \"use_names\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.1+galaxy1",
+                        "tool_state": "{\"accession_parser\": \"^>([^ ]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"uniqueness_criterion\": \"sequence\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.0",
                         "type": "tool",
-                        "uuid": "75b7f2b8-2b63-4f1a-a877-4babef16a08b",
+                        "uuid": "4c1b21ac-9ceb-49be-9c48-771a3fda8db4",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "kraken_report_tabular",
-                                "output_name": "report_output",
-                                "uuid": "54b85a53-72ee-4b73-b186-7fd55e8aab9b"
-                            },
-                            {
-                                "label": "kraken_report_reads",
+                                "label": "Human UniProt Microbial Proteins cRAP for MetaNovo",
                                 "output_name": "output",
-                                "uuid": "a408a644-58cd-4f5e-af25-15b5ea63aa76"
+                                "uuid": "286f5bd4-fb0d-4649-8dac-f191acc72722"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.8+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metanovo/metanovo/1.9.4+galaxy4",
                         "errors": null,
-                        "id": 6,
+                        "id": 5,
                         "input_connections": {
-                            "input": {
-                                "id": 5,
-                                "output_name": "report_output"
+                            "input_fasta": {
+                                "id": 4,
+                                "output_name": "output"
+                            },
+                            "input_type|input_mgf_collection": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool MetaNovo",
+                                "name": "input_type"
+                            }
+                        ],
                         "label": null,
-                        "name": "Bracken",
+                        "name": "MetaNovo",
                         "outputs": [
                             {
-                                "name": "report",
-                                "type": "tabular"
+                                "name": "output_fasta",
+                                "type": "fasta"
                             },
                             {
-                                "name": "kraken_report",
-                                "type": "tabular"
+                                "name": "output_csv",
+                                "type": "csv"
                             }
                         ],
                         "position": {
-                            "left": 1140.1325234308401,
-                            "top": 326.57184790597137
+                            "left": 641.8293151855469,
+                            "top": 171.08148193359375
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionkraken_report": {
-                                "action_arguments": {
-                                    "newname": "bracken_kraken_report"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "kraken_report"
-                            },
-                            "RenameDatasetActionreport": {
+                            "RenameDatasetActionoutput_fasta": {
                                 "action_arguments": {
-                                    "newname": "bracken_report_tsv"
+                                    "newname": "Metanovo Compact database"
                                 },
                                 "action_type": "RenameDatasetAction",
-                                "output_name": "report"
+                                "output_name": "output_fasta"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.8+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/metanovo/metanovo/1.9.4+galaxy4",
                         "tool_shed_repository": {
-                            "changeset_revision": "978ae4147c29",
-                            "name": "bracken",
-                            "owner": "iuc",
+                            "changeset_revision": "d6dcd3173bdf",
+                            "name": "metanovo",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"kmer_distr\": \"bf6177af-7f5b-4005-9bec-fc7c89c3cb1c\", \"level\": \"S\", \"logfile_output\": false, \"out_report\": true, \"threshold\": \"10\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.8+galaxy0",
+                        "tool_state": "{\"directag\": {\"directag_tic_cutoff\": \"85\", \"directag_max_peak_count\": \"400\", \"directag_intensity_classes\": \"3\", \"directag_adjust_precursor\": false, \"directag_min_adjustment\": \"-2.5\", \"directag_max_adjustment\": \"2.5\", \"directag_adjustment_step\": \"0.1\", \"directag_charge_states\": \"3\", \"directag_ms_charge_state\": false, \"directag_duplicate_spectra\": true, \"directag_deisotoping\": \"0\", \"directag_isotope_tolerance\": \"0.25\", \"directag_complement_tolerance\": \"0.5\", \"directag_tag_length\": \"4\", \"directag_max_var_mods\": \"2\", \"directag_max_tag_count\": \"5\", \"directag_intensity_weight\": \"1.0\", \"directag_fidelity_weight\": \"1.0\", \"directag_complement_weight\": \"1.0\"}, \"fraction_analysis\": {\"protein_fraction_mw_confidence\": \"95.0\"}, \"gene_annotation\": {\"useGeneMapping\": true, \"updateGeneMapping\": true}, \"import_filters\": {\"import_peptide_length_min\": \"8\", \"import_peptide_length_max\": \"50\", \"import_precursor_mz_ppm\": \"0\", \"exclude_unknown_ptms\": true}, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}, \"input_type\": {\"type\": \"collection\", \"__current_case__\": 1, \"input_mgf_collection\": {\"__class__\": \"ConnectedValue\"}}, \"metanovo_parameters\": {\"mn_specificity\": \"specific\", \"mn_enzymes\": \"Trypsin, no P rule\", \"mn_max_missed_cleavages\": \"2\"}, \"processing_control\": {\"CHUNKSIZE\": \"100000\"}, \"protein_inference\": {\"simplify_groups\": true, \"simplify_score\": true, \"simplify_enzymaticity\": true, \"simplify_evidence\": true, \"simplify_uncharacterized\": true}, \"ptm_localization\": {\"ptm_score\": \"1\", \"score_neutral_losses\": false, \"ptm_sequence_matching_type\": \"1\", \"ptm_alignment\": true}, \"sequence_matching\": {\"sequence_index_type\": \"0\", \"sequence_matching_type\": \"2\", \"sequence_matching_x\": \"0.25\"}, \"spectrum_annotation\": {\"annotation_level\": \"0.75\", \"annotation_high_resolution\": true}, \"spectrum_matching_parameters\": {\"prec_tol\": \"10.0\", \"prec_ppm\": \"1\", \"frag_tol\": \"0.01\", \"frag_ppm\": \"0\", \"digestion\": \"0\", \"enzyme\": [\"Trypsin (no P rule)\"], \"specificity\": \"0\", \"mc\": \"2\", \"fixed_mods\": [\"Carbamidomethylation of C\", \"TMT 10-plex of K\", \"TMT 10-plex of peptide N-term\"], \"variable_mods\": [\"Oxidation of M\"], \"min_charge\": \"2\", \"max_charge\": \"5\", \"fi\": \"b\", \"ri\": \"y\", \"min_isotope\": \"0\", \"max_isotope\": \"1\"}, \"validation_levels\": {\"psm_fdr\": \"1\", \"peptide_fdr\": \"1\", \"protein_fdr\": \"1\", \"group_psms\": true, \"group_peptides\": true, \"merge_subgroups\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.4+galaxy4",
                         "type": "tool",
-                        "uuid": "53b9c80b-f5f4-4fee-9778-fb4fd6b76165",
+                        "uuid": "07d51088-eb68-4ffd-b505-7228a21de93c",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "bracken_kraken_report",
-                                "output_name": "kraken_report",
-                                "uuid": "8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8"
+                                "label": null,
+                                "output_name": "output_fasta",
+                                "uuid": "7d35c0ce-359a-4b99-bc50-7898bbb9f6c7"
                             },
                             {
-                                "label": "bracken_report_tsv",
-                                "output_name": "report",
-                                "uuid": "ae6c6464-f5f5-4e5b-b616-d38166fc0133"
+                                "label": null,
+                                "output_name": "output_csv",
+                                "uuid": "a37b2a24-df14-4ce0-9bec-38cc327a044d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
                         "errors": null,
-                        "id": 7,
+                        "id": 6,
                         "input_connections": {
-                            "input_file": {
+                            "batchmode|input_fastas_0|input_fasta": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "batchmode|input_fastas_1|input_fasta": {
                                 "id": 5,
+                                "output_name": "output_fasta"
+                            },
+                            "batchmode|input_fastas_2|input_fasta": {
+                                "id": 3,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Recentrifuge",
+                        "name": "FASTA Merge Files and Filter Unique Sequences",
                         "outputs": [
                             {
-                                "name": "html_report",
-                                "type": "html"
-                            },
-                            {
-                                "name": "logfile",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "data_tsv",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "stat_tsv",
-                                "type": "tabular"
+                                "name": "output",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 1132.0995834632697,
-                            "top": 578.6187243531585
+                            "left": 924.9069441945012,
+                            "top": 319.6465149119742
                         },
                         "post_job_actions": {
-                            "RenameDatasetActiondata_tsv": {
-                                "action_arguments": {
-                                    "newname": "recentrifuge_data_tabular"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "data_tsv"
-                            },
-                            "RenameDatasetActionhtml_report": {
-                                "action_arguments": {
-                                    "newname": "recentrifuge_report_html"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "html_report"
-                            },
-                            "RenameDatasetActionlogfile": {
+                            "EmailActionoutput": {
                                 "action_arguments": {
-                                    "newname": "recentrifuge_logfile"
+                                    "host": "usegalaxy.eu"
                                 },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "logfile"
+                                "action_type": "EmailAction",
+                                "output_name": "output"
                             },
-                            "RenameDatasetActionstat_tsv": {
+                            "RenameDatasetActionoutput": {
                                 "action_arguments": {
-                                    "newname": "recentrifuge_stats_tabular"
+                                    "newname": "Human UniProt Microbial Proteins (from MetaNovo) and cRAP "
                                 },
                                 "action_type": "RenameDatasetAction",
-                                "output_name": "stat_tsv"
+                                "output_name": "output"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "b5407cc2bf51",
-                            "name": "recentrifuge",
-                            "owner": "iuc",
+                            "changeset_revision": "f546e7278f04",
+                            "name": "fasta_merge_files_and_filter_unique_sequences",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_option\": {\"controls\": \"0\", \"scoring\": null, \"minscore_value\": \"0\", \"mintaxa\": \"0\", \"exclude_taxa_name\": null, \"include_taxa_name\": null, \"avoidcross\": false}, \"database\": {\"database_name\": \"ncbi-2023-06-27\"}, \"file_type\": {\"filetype\": \"kraken\", \"__current_case__\": 3}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"more_advanced_option\": {\"ctrlminscore\": \"0\", \"ctrlmintaxa\": \"0\", \"summary\": \"ADD\", \"takeoutroot\": false, \"nokollapse\": false, \"strain\": true, \"sequential\": false}, \"output_option\": {\"extra\": \"TSV\", \"nohtml\": false, \"no_logfile\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.12.1+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"accession_parser\": \"^>([^ ]+).*$\", \"batchmode\": {\"processmode\": \"individual\", \"__current_case__\": 0, \"input_fastas\": [{\"__index__\": 0, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}}]}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"uniqueness_criterion\": \"sequence\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.0",
                         "type": "tool",
-                        "uuid": "4b3b34ad-2352-4e93-abbc-69da3ab9ee3a",
+                        "uuid": "3880c712-4f3c-4edc-bda0-ee348ab1a2c4",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "recentrifuge_report_html",
-                                "output_name": "html_report",
-                                "uuid": "bd947a1d-0443-465f-8658-5d76d9ce69f8"
-                            },
-                            {
-                                "label": "recentrifuge_data_tabular",
-                                "output_name": "data_tsv",
-                                "uuid": "c7457acb-41bc-4191-b3fb-6716e15fbe57"
-                            },
-                            {
-                                "label": "recentrifuge_stats_tabular",
-                                "output_name": "stat_tsv",
-                                "uuid": "b5694f2d-c8cd-4460-bfff-74fd0792ecb3"
-                            },
-                            {
-                                "label": "recentrifuge_logfile",
-                                "output_name": "logfile",
-                                "uuid": "94f6ff07-0e06-47ad-88f8-a058d0808537"
+                                "label": "Human UniProt Microbial Proteins (from MetaNovo) and cRAP ",
+                                "output_name": "output",
+                                "uuid": "de57cd9d-ac05-4397-9d44-e65620913447"
                             }
                         ]
                     }
                 ],
-                "parent_id": "sequence-analysis/quality-contamination-control",
-                "path": "topics/sequence-analysis/tutorials/quality-contamination-control/workflows/Quality_and_contamination_control_in_bacterial_isolate_using_Illumina_MiSeq_Data.ga",
+                "parent_id": "proteomics/clinical-mp-1-database-generation",
+                "path": "topics/proteomics/tutorials/clinical-mp-1-database-generation/workflows/WF1_Database_Generation_Workflow.ga",
                 "tags": [
-                    "sequence-analysis"
+                    "name:clinicalMP"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "Quality and contamination control in bacterial isolate using Illumina MiSeq Data",
-                "topic_id": "sequence-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/sequence-analysis-quality-contamination-control/versions/quality-and-contamination-control-in-bacterial-isolate-using-illumina-miseq-data",
-                "tutorial_id": "quality-contamination-control",
-                "url": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-contamination-control/workflows/Quality_and_contamination_control_in_bacterial_isolate_using_Illumina_MiSeq_Data.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-contamination-control/workflows/Quality_and_contamination_control_in_bacterial_isolate_using_Illumina_MiSeq_Data.html",
+                "tests": false,
+                "title": "WF1_Database_Generation_Workflow",
+                "topic_id": "proteomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-clinical-mp-1-database-generation/versions/wf1-database-generation-workflow",
+                "tutorial_id": "clinical-mp-1-database-generation",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-1-database-generation/workflows/WF1_Database_Generation_Workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-1-database-generation/workflows/WF1_Database_Generation_Workflow.html",
                 "version": 1,
-                "wfid": "sequence-analysis-quality-contamination-control",
-                "wfname": "quality-and-contamination-control-in-bacterial-isolate-using-illumina-miseq-data",
-                "workflow": "Quality_and_contamination_control_in_bacterial_isolate_using_Illumina_MiSeq_Data.ga",
+                "wfid": "proteomics-clinical-mp-1-database-generation",
+                "wfname": "wf1-database-generation-workflow",
+                "workflow": "WF1_Database_Generation_Workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.8+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0"
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/metanovo/metanovo/1.9.4+galaxy4"
                 ],
-                "workflowhub_id": "1344"
+                "workflowhub_id": "1350"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/10669812"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.10105821"
     },
     {
         "admin_install": {
@@ -205955,345 +207751,431 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "fastq_groomer",
-                    "owner": "devteam",
-                    "revisions": "47e5dbc3e790",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastq_masker_by_quality",
-                    "owner": "devteam",
-                    "revisions": "9dfda4e310ed",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastq_to_fasta",
-                    "owner": "devteam",
-                    "revisions": "77b41c89d856",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastq_to_tabular",
-                    "owner": "devteam",
-                    "revisions": "4b347702c4aa",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastx_reverse_complement",
-                    "owner": "devteam",
-                    "revisions": "6027ef51ef91",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ncbi_blast_plus",
-                    "owner": "devteam",
-                    "revisions": "0e3cf9594bb7",
-                    "tool_panel_section_label": "NCBI Blast",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "tabular_to_fasta",
-                    "owner": "devteam",
-                    "revisions": "0a7799698fe5",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "flashlfq",
+                    "owner": "galaxyp",
+                    "revisions": "878f6725c4f3",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ab1_fastq_converter",
-                    "owner": "ecology",
-                    "revisions": "307518fb51af",
+                    "name": "msconvert",
+                    "owner": "galaxyp",
+                    "revisions": "9ec469ff191a",
                     "tool_panel_section_label": "Convert Formats",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "aligned_to_consensus",
-                    "owner": "ecology",
-                    "revisions": "0ccbe1c20fc3",
-                    "tool_panel_section_label": "Assembly",
+                    "name": "peptideshaker",
+                    "owner": "galaxyp",
+                    "revisions": "7fdd9119cc4f",
+                    "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "filter_by_fasta_ids",
+                    "name": "peptideshaker",
                     "owner": "galaxyp",
-                    "revisions": "dff7df6fcab5",
+                    "revisions": "7fdd9119cc4f",
                     "tool_panel_section_label": "Proteomics",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "regex_find_replace",
                     "owner": "galaxyp",
-                    "revisions": "503bcd6ebe4b",
+                    "revisions": "209b7c5ee9d7",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "unzip",
-                    "owner": "imgteam",
-                    "revisions": "57f0914ddb7b",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collection_element_identifiers",
-                    "owner": "iuc",
-                    "revisions": "d3c07d270a50",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_degap_seqs",
-                    "owner": "iuc",
-                    "revisions": "6f08af23888a",
-                    "tool_panel_section_label": "Mothur",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mothur_merge_files",
-                    "owner": "iuc",
-                    "revisions": "bc20680d28d5",
-                    "tool_panel_section_label": "Mothur",
+                    "name": "unipept",
+                    "owner": "galaxyp",
+                    "revisions": "4953dcd7dd39",
+                    "tool_panel_section_label": "Get Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "qiime_align_seqs",
-                    "owner": "iuc",
-                    "revisions": "e8bb88f051ec",
-                    "tool_panel_section_label": "Sequence analysis",
+                    "name": "unipept",
+                    "owner": "galaxyp",
+                    "revisions": "9aaa46d45472",
+                    "tool_panel_section_label": "Get Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "seqtk",
-                    "owner": "iuc",
-                    "revisions": "3da72230c066",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "unipept",
+                    "owner": "galaxyp",
+                    "revisions": "75b3b3d0adbf",
+                    "tool_panel_section_label": "Get Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "seqtk",
+                    "name": "query_tabular",
                     "owner": "iuc",
-                    "revisions": "3da72230c066",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "33d61c89fb8d",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastq_groomer\n  owner: devteam\n  revisions: 47e5dbc3e790\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastq_masker_by_quality\n  owner: devteam\n  revisions: 9dfda4e310ed\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastq_to_fasta\n  owner: devteam\n  revisions: 77b41c89d856\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastq_to_tabular\n  owner: devteam\n  revisions: 4b347702c4aa\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastx_reverse_complement\n  owner: devteam\n  revisions: 6027ef51ef91\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: 0e3cf9594bb7\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tabular_to_fasta\n  owner: devteam\n  revisions: 0a7799698fe5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ab1_fastq_converter\n  owner: ecology\n  revisions: 307518fb51af\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: aligned_to_consensus\n  owner: ecology\n  revisions: 0ccbe1c20fc3\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filter_by_fasta_ids\n  owner: galaxyp\n  revisions: dff7df6fcab5\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 503bcd6ebe4b\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unzip\n  owner: imgteam\n  revisions: 57f0914ddb7b\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_element_identifiers\n  owner: iuc\n  revisions: d3c07d270a50\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_degap_seqs\n  owner: iuc\n  revisions: 6f08af23888a\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_merge_files\n  owner: iuc\n  revisions: bc20680d28d5\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qiime_align_seqs\n  owner: iuc\n  revisions: e8bb88f051ec\n  tool_panel_section_label: Sequence analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: flashlfq\n  owner: galaxyp\n  revisions: 878f6725c4f3\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msconvert\n  owner: galaxyp\n  revisions: 9ec469ff191a\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 7fdd9119cc4f\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: peptideshaker\n  owner: galaxyp\n  revisions: 7fdd9119cc4f\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 209b7c5ee9d7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unipept\n  owner: galaxyp\n  revisions: 4953dcd7dd39\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unipept\n  owner: galaxyp\n  revisions: 9aaa46d45472\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unipept\n  owner: galaxyp\n  revisions: 75b3b3d0adbf\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n  owner: iuc\n  revisions: 33d61c89fb8d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "pndb",
-                    "gallantries",
-                    "elixir-europe"
-                ],
-                "elixir_node": "fr",
-                "email": "coline.royaux@mnhn.fr",
-                "id": "colineroyaux",
-                "joined": "2020-11",
-                "name": "Coline Royaux",
-                "orcid": "0000-0003-4308-5617",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/",
-                "twitter": "ColineRoyaux",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/colineroyaux.json"
+                "email": "subinamehta@gmail.com",
+                "id": "subinamehta",
+                "joined": "2018-06",
+                "linkedin": "subinamehta",
+                "matrix": "subinamehta:matrix.org",
+                "name": "Subina Mehta",
+                "orcid": "0000-0001-9818-0537",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/subinamehta/",
+                "twitter": "Subina_Mehta",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/subinamehta.json"
+            },
+            {
+                "email": "tgriffin@umn.edu",
+                "github": false,
+                "id": "timothygriffin",
+                "joined": "2017-09",
+                "name": "Timothy J. Griffin",
+                "orcid": "0000-0001-6801-2559",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timothygriffin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/timothygriffin.json"
+            },
+            {
+                "email": "pjagtap@umn.edu",
+                "id": "pratikdjagtap",
+                "joined": "2017-09",
+                "name": "Pratik Jagtap",
+                "orcid": "0000-0003-0984-0973",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pratikdjagtap/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pratikdjagtap.json"
+            },
+            {
+                "email": "leith023@umn.edu",
+                "id": "emmaleith",
+                "joined": "2019-07",
+                "name": "Emma Leith",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/emmaleith/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/emmaleith.json"
+            },
+            {
+                "email": "crane136@umn.edu",
+                "id": "mariecrane",
+                "joined": "2019-05",
+                "name": "Marie Crane",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mariecrane/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mariecrane.json"
             }
         ],
-        "dir": "topics/sequence-analysis/tutorials/Manage_AB1_Sanger",
+        "dir": "topics/proteomics/tutorials/metaquantome-data-creation",
+        "edam_ontology": [
+            "topic_0121",
+            "topic_3922",
+            "topic_3050",
+            "topic_0637"
+        ],
         "edam_operation": [
+            "Prediction and recognition",
             "Visualisation",
-            "Sequencing quality control",
-            "Sequence file editing",
-            "Demultiplexing",
-            "Phylogenetic analysis",
-            "Taxonomic classification",
-            "Data handling",
-            "Sequence read processing",
-            "DNA barcoding",
-            "Sequence clustering"
+            "Filtering",
+            "Label-free quantification",
+            "Formatting"
+        ],
+        "edam_topic": [
+            "Proteomics",
+            "Proteogenomics",
+            "Biodiversity",
+            "Taxonomy"
         ],
-        "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "proteomics",
+                "tutorials": [
+                    "metaproteomics"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "sequence-analysis/Manage_AB1_Sanger",
-        "inexact_supported_servers": [],
+        "id": "proteomics/metaquantome-data-creation",
+        "inexact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Check your data and results for mistakes afterward !!!! This procedure is useful but not perfect"
+            "Use dataset collections",
+            "With SearchGUI and PeptideShaker you can gain access to multiple search engines",
+            "Learning the basics of SQL queries can pay off"
         ],
         "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-05",
+        "mod_date": "2024-03-14",
         "objectives": [
-            "Learn how to manage sequencing files (AB1, FASTQ, FASTA)",
-            "Learn how to clean your Sanger sequences in an automated and reproducible way"
+            "A taxonomy, functional and quantitational analysis of metaproteomic mass spectrometry data."
         ],
-        "pageviews": 1709,
-        "pub_date": "2024-01-08",
+        "pageviews": 1353,
+        "pub_date": "2020-10-16",
         "questions": [
-            "How to clean Sanger sequencing files?"
+            "How do I perform functional and taxonomy analysis on metaproteomics data?",
+            "How can I perform quantitation on metaproteomics data?",
+            "How do I create inputs that can be used in metaquantome to examine differentially expressed proteins?"
         ],
-        "short_id": "T00383",
+        "short_id": "T00222",
         "short_tools": [
-            "filter_by_fasta_ids",
-            "mothur_merge_files",
-            "ncbi_blastn_wrapper",
-            "__SORTLIST__",
-            "qiime_align_seqs",
-            "fastq_masker_by_quality",
-            "unzip",
-            "seqtk_trimfq",
-            "fastq_groomer",
+            "query_tabular",
+            "flashlfq",
+            "Filter1",
+            "peptide_shaker",
             "regex1",
-            "tab2fasta",
-            "mothur_degap_seqs",
-            "seqtk_mergepe",
-            "collection_element_identifiers",
-            "cshl_fastx_reverse_complement",
-            "ab1_fastq_converter",
-            "cshl_fastq_to_fasta",
-            "__FILTER_FROM_FILE__",
-            "fastq_to_tabular",
-            "aligned_to_consensus"
+            "tp_replace_in_line",
+            "msconvert",
+            "search_gui",
+            "unipept",
+            "Grep1",
+            "Cut1",
+            "Remove beginning1",
+            "tp_replace_in_column"
         ],
         "slides": false,
         "slides_recordings": false,
+        "subtopic": "multi-omics",
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
-            ],
-            "inexact": []
+            ]
         },
         "symlink": null,
-        "time_estimation": "1H",
-        "title": "Clean and manage Sanger sequences from raw files to aligned consensus",
+        "tags": [
+            "microgalaxy"
+        ],
+        "time_estimation": "1h",
+        "title": "metaQuantome 1: Data creation",
         "tools": [
-            "__FILTER_FROM_FILE__",
-            "__SORTLIST__",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastq_masker_by_quality/fastq_masker_by_quality/1.1.5",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.2+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.5",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter/1.20.0",
-            "toolshed.g2.bx.psu.edu/repos/ecology/aligned_to_consensus/aligned_to_consensus/1.0.0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.3",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_degap_seqs/mothur_degap_seqs/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.3.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1"
+            "Cut1",
+            "Filter1",
+            "Grep1",
+            "Remove beginning1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/flashlfq/flashlfq/1.0.3.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.0.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0"
         ],
-        "topic_name": "sequence-analysis",
-        "topic_name_human": "Sequence analysis",
+        "topic_name": "proteomics",
+        "topic_name_human": "Proteomics",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "Manage_AB1_Sanger",
+        "tutorial_name": "metaquantome-data-creation",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.json"
         },
-        "version": 2,
+        "version": 20,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 137,
-        "visitors": 1316,
+        "visit_duration": 229,
+        "visitors": 781,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Organization",
-                        "name": "Coline Royaux"
-                    }
-                ],
-                "description": "",
+                "creators": [],
+                "description": "metaquantome-data-creation",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nL sequences Forward\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nH sequences Reverse\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nLCOI primers\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHCOI primers\"]\n  4[label=\"ab1 to FASTQ converter\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"ab1 to FASTQ converter\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"What\u2019s your LCOI primer sequence identifier ?\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"What\u2019s your HCOI primer sequence identifier ?\"]\n  3 -> 7 [label=\"output\"]\n  8[label=\"seqtk_trimfq\"]\n  4 -> 8 [label=\"output\"]\n  9[label=\"seqtk_trimfq\"]\n  5 -> 9 [label=\"output\"]\n  10[label=\"Degap.seqs\"]\n  6 -> 10 [label=\"output\"]\n  11[label=\"Degap.seqs\"]\n  7 -> 11 [label=\"output\"]\n  12[label=\"Sort collection\"]\n  8 -> 12 [label=\"default\"]\n  13[label=\"FASTQ Groomer\"]\n  9 -> 13 [label=\"default\"]\n  14[label=\"Reverse-Complement\"]\n  11 -> 14 [label=\"out_fasta\"]\n  15[label=\"Reverse-Complement\"]\n  13 -> 15 [label=\"output_file\"]\n  16[label=\"Sort collection\"]\n  15 -> 16 [label=\"output\"]\n  17[label=\"seqtk_mergepe\"]\n  12 -> 17 [label=\"output\"]\n  16 -> 17 [label=\"output\"]\n  18[label=\"FASTQ Groomer\"]\n  17 -> 18 [label=\"default\"]\n  19[label=\"FASTQ to Tabular\"]\n  18 -> 19 [label=\"output_file\"]\n  20[label=\"Tabular-to-FASTA\"]\n  19 -> 20 [label=\"output_file\"]\n  21[label=\"Align sequences\"]\n  20 -> 21 [label=\"output\"]\n  22[label=\"Consensus sequence from aligned FASTA\"]\n  21 -> 22 [label=\"aligned_sequences\"]\n  23[label=\"Merge.files\"]\n  22 -> 23 [label=\"output\"]\n  24[label=\"Merge.files\"]\n  23 -> 24 [label=\"output\"]\n  14 -> 24 [label=\"output\"]\n  10 -> 24 [label=\"out_fasta\"]\n  25[label=\"Regex Find And Replace\"]\n  24 -> 25 [label=\"output\"]\n  26[label=\"Align sequences\"]\n  25 -> 26 [label=\"out_file1\"]\n  27[label=\"NCBI BLAST+ blastn\"]\n  25 -> 27 [label=\"out_file1\"]\n  k31c2dd1a918e4648a407d0e3d7172253[color=lightseagreen,label=\"Output\\nw_blast_output\"]\n  27 -> k31c2dd1a918e4648a407d0e3d7172253\n  k7514514f809a4a148981cb08c950b523[color=lightseagreen,label=\"Output\\nw_consensus_aligned_sequences\"]\n  27 -> k7514514f809a4a148981cb08c950b523\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nExperiment_Design\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nFASTA_db\"]\n  3[label=\"mzml to mgf\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Search GUI\"]\n  2 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"Peptide Shaker\"]\n  4 -> 5 [label=\"searchgui_results\"]\n  6[label=\"Replace Text\"]\n  5 -> 6 [label=\"output_psm\"]\n  7[label=\"Remove beginning\"]\n  5 -> 7 [label=\"output_peptides\"]\n  8[label=\"Unipept_lca\"]\n  5 -> 8 [label=\"output_peptides\"]\n  9[label=\"FlashLFQ\"]\n  1 -> 9 [label=\"output\"]\n  6 -> 9 [label=\"outfile\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"Unipept_peptinfo\"]\n  7 -> 10 [label=\"out_file1\"]\n  11[label=\"Replace Text\"]\n  8 -> 11 [label=\"output_tsv\"]\n  12[label=\"Regex Find And Replace\"]\n  9 -> 12 [label=\"quantifiedPeptides\"]\n  13[label=\"selecting EC column\"]\n  10 -> 13 [label=\"output_ec_tsv\"]\n  14[label=\"filter 5% All_funct\"]\n  10 -> 14 [label=\"output_go_tsv\"]\n  15[label=\"GO_EC\"]\n  13 -> 15 [label=\"out_file1\"]\n  16[label=\"GO_BP\"]\n  14 -> 16 [label=\"output\"]\n  17[label=\"GO_CC\"]\n  14 -> 17 [label=\"output\"]\n  18[label=\"GO_MF\"]\n  14 -> 18 [label=\"output\"]\n}",
                 "history": [
                     {
-                        "hash": "bf907f6d3bcd09d391c9143bb2464b50c0fb9d7a",
-                        "message": "Add creator and license",
+                        "hash": "72e53ea9af53237e2b615f69b8c95f7e1371396d",
+                        "message": "Rename workflow.ga to main_workflow.ga",
+                        "num": 14,
+                        "short_hash": "72e53ea9a",
+                        "unix": "1636569874"
+                    },
+                    {
+                        "hash": "b63d3bd0727a2182c18a765dc776ec8e35677046",
+                        "message": "Rename main_workflow.ga to workflow.ga",
+                        "num": 13,
+                        "short_hash": "b63d3bd07",
+                        "unix": "1636567614"
+                    },
+                    {
+                        "hash": "02a2548eca97ef7b2a0d5ac8b4ae145280ec9918",
+                        "message": "Update main_workflow.ga",
+                        "num": 12,
+                        "short_hash": "02a2548ec",
+                        "unix": "1636474235"
+                    },
+                    {
+                        "hash": "d4a710e9f76a5f0037efdf0e93711e87408ac272",
+                        "message": "Update main_workflow.ga",
+                        "num": 11,
+                        "short_hash": "d4a710e9f",
+                        "unix": "1636473894"
+                    },
+                    {
+                        "hash": "d0478e7ffd03b7adb6957eebf7fd90625fef7581",
+                        "message": "Update main_workflow.ga",
+                        "num": 10,
+                        "short_hash": "d0478e7ff",
+                        "unix": "1636473603"
+                    },
+                    {
+                        "hash": "2c4ad397f2f8887a6b0138d30f2e416d60341efd",
+                        "message": "Fixed tool_state.",
+                        "num": 9,
+                        "short_hash": "2c4ad397f",
+                        "unix": "1602877288"
+                    },
+                    {
+                        "hash": "f81d5946b9364c6a7b2a061e804c638db7f6a583",
+                        "message": "Added collection to test.",
+                        "num": 8,
+                        "short_hash": "f81d5946b",
+                        "unix": "1602873698"
+                    },
+                    {
+                        "hash": "70b86ecbfbcb239fe109e9e2e109a8a982f35fec",
+                        "message": "Updated workflow.",
+                        "num": 7,
+                        "short_hash": "70b86ecbf",
+                        "unix": "1602870731"
+                    },
+                    {
+                        "hash": "b8a5ce3d4a7d76e0453c2b25d34fadad21bc06c5",
+                        "message": "Update main_workflow.ga",
+                        "num": 6,
+                        "short_hash": "b8a5ce3d4",
+                        "unix": "1602803075"
+                    },
+                    {
+                        "hash": "71d516d05c099ba378eafd7eb1f7dedc3a288b65",
+                        "message": "Update main_workflow.ga",
+                        "num": 5,
+                        "short_hash": "71d516d05",
+                        "unix": "1602790259"
+                    },
+                    {
+                        "hash": "aa695993e63aa8d5ac99b842f23035d74a17978d",
+                        "message": "Update main_workflow.ga",
+                        "num": 4,
+                        "short_hash": "aa695993e",
+                        "unix": "1602507576"
+                    },
+                    {
+                        "hash": "dadb44fb528517637c96e074c9459bfd1c5a9ebb",
+                        "message": "Update main_workflow.ga",
+                        "num": 3,
+                        "short_hash": "dadb44fb5",
+                        "unix": "1602469286"
+                    },
+                    {
+                        "hash": "a45af5ea946c3fab63e502255a48edc8770b3237",
+                        "message": "Update main_workflow.ga",
                         "num": 2,
-                        "short_hash": "bf907f6d3",
-                        "unix": "1704192784"
+                        "short_hash": "a45af5ea9",
+                        "unix": "1602469238"
                     },
                     {
-                        "hash": "03e5a4f54d25895ffe16fa5557c895ffa7b81262",
-                        "message": "Remove colons",
+                        "hash": "c042f2b7195179d8e45abac8d41122ab94538264",
+                        "message": "planemo workflow-to-tutorial",
                         "num": 1,
-                        "short_hash": "03e5a4f54",
-                        "unix": "1702999279"
+                        "short_hash": "c042f2b71",
+                        "unix": "1600357793"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "",
+                        "annotation": "metaquantome-data-creation",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "L sequences (Forward)"
-                            }
-                        ],
-                        "label": "L sequences (Forward)",
+                        "inputs": [],
+                        "label": null,
                         "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 125.19532716773591
+                            "bottom": 134,
+                            "height": 81,
+                            "left": 347.53125,
+                            "right": 547.53125,
+                            "top": 53,
+                            "width": 200,
+                            "x": 347.53125,
+                            "y": 53
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"ab1\"], \"tag\": \"\", \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
                         "tool_version": null,
                         "type": "data_collection_input",
-                        "uuid": "8a638477-d771-41a6-8c73-c6bc548d2a63",
-                        "when": null,
+                        "uuid": "a00a1b36-1600-4833-8cd3-df6ceec33349",
                         "workflow_outputs": []
                     },
                     {
@@ -206305,22 +208187,27 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "H sequences (Reverse)"
+                                "name": "Experiment_Design"
                             }
                         ],
-                        "label": "H sequences (Reverse)",
-                        "name": "Input dataset collection",
+                        "label": "Experiment_Design",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 11.09375,
-                            "top": 453.7578937515429
+                            "bottom": 401.96875,
+                            "height": 81,
+                            "left": 525.640625,
+                            "right": 725.640625,
+                            "top": 320.96875,
+                            "width": 200,
+                            "x": 525.640625,
+                            "y": 320.96875
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"ab1\"], \"tag\": \"\", \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "79715df2-d3e0-4491-af3f-2ab6bf8d0065",
-                        "when": null,
+                        "type": "data_input",
+                        "uuid": "8dd6e50f-9951-4e8e-af47-783625e46786",
                         "workflow_outputs": []
                     },
                     {
@@ -206332,1144 +208219,1717 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "LCOI primers"
+                                "name": "FASTA_db"
                             }
                         ],
-                        "label": "LCOI primers",
+                        "label": "FASTA_db",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 2404.8908903486745,
-                            "top": 220.80473862021637
+                            "bottom": 629.03125,
+                            "height": 61,
+                            "left": -408,
+                            "right": -208,
+                            "top": 568.03125,
+                            "width": 200,
+                            "x": -408,
+                            "y": 568.03125
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "711c7d32-6d82-46d7-8ee9-3258e1e11a05",
-                        "when": null,
+                        "uuid": "a9156286-a9e9-402f-b1d9-3e55ddd86ce8",
                         "workflow_outputs": []
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nExperiment_Design\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nFASTA_db\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"mzml to mgf\"];\n  0 -->|output| 3;\n  4[\"Search GUI\"];\n  2 -->|output| 4;\n  3 -->|output| 4;\n  5[\"Peptide Shaker\"];\n  4 -->|searchgui_results| 5;\n  6[\"Replace Text\"];\n  5 -->|output_psm| 6;\n  7[\"Remove beginning\"];\n  5 -->|output_peptides| 7;\n  8[\"Unipept_lca\"];\n  5 -->|output_peptides| 8;\n  9[\"FlashLFQ\"];\n  1 -->|output| 9;\n  6 -->|outfile| 9;\n  0 -->|output| 9;\n  10[\"Unipept_peptinfo\"];\n  7 -->|out_file1| 10;\n  11[\"Replace Text\"];\n  8 -->|output_tsv| 11;\n  12[\"Regex Find And Replace\"];\n  9 -->|quantifiedPeptides| 12;\n  13[\"selecting EC column\"];\n  10 -->|output_ec_tsv| 13;\n  14[\"filter 5% All_funct\"];\n  10 -->|output_go_tsv| 14;\n  15[\"GO_EC\"];\n  13 -->|out_file1| 15;\n  16[\"GO_BP\"];\n  14 -->|output| 16;\n  17[\"GO_CC\"];\n  14 -->|output| 17;\n  18[\"GO_MF\"];\n  14 -->|output| 18;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "metaQuantome_datacreation_workflow",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.0",
                         "errors": null,
                         "id": 3,
-                        "input_connections": {},
-                        "inputs": [
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "mzml to mgf",
+                        "name": "msconvert",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "HCOI primers"
+                                "name": "output",
+                                "type": "mzml"
                             }
                         ],
-                        "label": "HCOI primers",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 2408.903404638635,
-                            "top": 389.37482504451754
+                            "bottom": 587.5,
+                            "height": 132,
+                            "left": -35.515625,
+                            "right": 164.484375,
+                            "top": 455.5,
+                            "width": 200,
+                            "x": -35.515625,
+                            "y": 455.5
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "d23f0e22-e2ac-4c88-b7dc-f70035cfb1c2",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nL sequences Forward\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nH sequences Reverse\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nLCOI primers\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nHCOI primers\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"ab1 to FASTQ converter\"];\n  0 -->|output| 4;\n  5[\"ab1 to FASTQ converter\"];\n  1 -->|output| 5;\n  6[\"What\u2019s your LCOI primer sequence identifier ?\"];\n  2 -->|output| 6;\n  7[\"What\u2019s your HCOI primer sequence identifier ?\"];\n  3 -->|output| 7;\n  8[\"seqtk_trimfq\"];\n  4 -->|output| 8;\n  9[\"seqtk_trimfq\"];\n  5 -->|output| 9;\n  10[\"Degap.seqs\"];\n  6 -->|output| 10;\n  11[\"Degap.seqs\"];\n  7 -->|output| 11;\n  12[\"Sort collection\"];\n  8 -->|default| 12;\n  13[\"FASTQ Groomer\"];\n  9 -->|default| 13;\n  14[\"Reverse-Complement\"];\n  11 -->|out_fasta| 14;\n  15[\"Reverse-Complement\"];\n  13 -->|output_file| 15;\n  16[\"Sort collection\"];\n  15 -->|output| 16;\n  17[\"seqtk_mergepe\"];\n  12 -->|output| 17;\n  16 -->|output| 17;\n  18[\"FASTQ Groomer\"];\n  17 -->|default| 18;\n  19[\"FASTQ to Tabular\"];\n  18 -->|output_file| 19;\n  20[\"Tabular-to-FASTA\"];\n  19 -->|output_file| 20;\n  21[\"Align sequences\"];\n  20 -->|output| 21;\n  22[\"Consensus sequence from aligned FASTA\"];\n  21 -->|aligned_sequences| 22;\n  23[\"Merge.files\"];\n  22 -->|output| 23;\n  24[\"Merge.files\"];\n  23 -->|output| 24;\n  14 -->|output| 24;\n  10 -->|out_fasta| 24;\n  25[\"Regex Find And Replace\"];\n  24 -->|output| 25;\n  26[\"Align sequences\"];\n  25 -->|out_file1| 26;\n  27[\"NCBI BLAST+ blastn\"];\n  25 -->|out_file1| 27;\n  31c2dd1a-918e-4648-a407-d0e3d7172253[\"Output\\nw_blast_output\"];\n  27 --> 31c2dd1a-918e-4648-a407-d0e3d7172253;\n  style 31c2dd1a-918e-4648-a407-d0e3d7172253 stroke:#2c3143,stroke-width:4px;\n  7514514f-809a-4a14-8981-cb08c950b523[\"Output\\nw_consensus_aligned_sequences\"];\n  27 --> 7514514f-809a-4a14-8981-cb08c950b523;\n  style 7514514f-809a-4a14-8981-cb08c950b523 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Sanger1 : From AB1 to aligned consensus and primers fasta + BLAST",
-                "outputs": [
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "9ec469ff191a",
+                            "name": "msconvert",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"data_processing\": {\"peak_picking\": {\"pick_peaks\": \"false\", \"__current_case__\": 0}, \"precursor_refinement\": {\"use_mzrefinement\": \"false\", \"__current_case__\": 0}, \"charge_state_calculation\": {\"charge_state_calculation_method\": \"false\", \"__current_case__\": 0}, \"thresholds\": [], \"filter_mz_windows\": {\"do_mzwindow_filter\": \"false\", \"__current_case__\": 0}, \"etd_filtering\": {\"do_etd_filtering\": \"false\", \"__current_case__\": 0}, \"ms2denoise\": {\"denoise\": \"false\", \"__current_case__\": 1}, \"ms2deisotope\": \"false\"}, \"filtering\": {\"activation\": \"false\", \"indices\": [], \"scan_numbers\": [], \"strip_it\": \"false\", \"filter_ms_levels\": {\"do_ms_level_filter\": \"false\", \"__current_case__\": 0}, \"polarity\": \"false\", \"analyzer\": \"false\"}, \"general_options\": {\"combineIonMobilitySpectra\": \"false\", \"scan_summing\": {\"do_scan_summing\": \"false\", \"__current_case__\": 0}, \"simAsSpectra\": \"false\", \"srmAsSpectra\": \"false\", \"acceptZeroLengthSpectra\": \"false\", \"ignoreUnknownInstrumentError\": \"false\", \"multi_run_output\": {\"do_multi_run_output\": \"false\", \"__current_case__\": 0, \"runIndexSet\": \"0\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"license_agreement\": \"true\", \"output_type\": \"mgf\", \"settings\": {\"mz_encoding\": \"64\", \"intensity_encoding\": \"32\", \"binary_compression\": \"zlib\", \"gzip_compression\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.0.19052.0",
+                        "type": "tool",
+                        "uuid": "4d7e9227-49af-4722-b4c3-b8976ba3ed80",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "2dc2ec3e-d5c7-47ac-a7f7-7559cde14f84"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter/1.20.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
                         "errors": null,
-                        "id": 4,
+                        "id": 5,
                         "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
+                            "searchgui_input": {
+                                "id": 4,
+                                "output_name": "searchgui_results"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "ab1 to FASTQ converter",
+                        "name": "Peptide Shaker",
+                        "outputs": [
+                            {
+                                "name": "mzidentML",
+                                "type": "mzid"
+                            },
+                            {
+                                "name": "output_certificate",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "output_psm",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "output_peptides",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "output_proteins",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 1001.046875,
+                            "height": 452,
+                            "left": 253.984375,
+                            "right": 453.984375,
+                            "top": 549.046875,
+                            "width": 200,
+                            "x": 253.984375,
+                            "y": 549.046875
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionmzidentML": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "mzidentML"
+                            },
+                            "HideDatasetActionoutput_certificate": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_certificate"
+                            },
+                            "HideDatasetActionoutput_proteins": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_proteins"
+                            },
+                            "RenameDatasetActionoutput_peptides": {
+                                "action_arguments": {
+                                    "newname": "PS: Peptide Report"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_peptides"
+                            },
+                            "RenameDatasetActionoutput_psm": {
+                                "action_arguments": {
+                                    "newname": "PS: PSM report"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_psm"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "7fdd9119cc4f",
+                            "name": "peptideshaker",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"contact_options\": {\"contact_options_selector\": \"no\", \"__current_case__\": 0}, \"exporting_options\": {\"mzidentml_conditional\": {\"mzidentml_creation\": \"true\", \"__current_case__\": 0, \"include_sequences\": \"false\"}, \"zip_conditional\": {\"zip_output_boolean\": \"false\", \"__current_case__\": 0, \"export_cps\": \"false\"}, \"output_reports\": [\"3\", \"6\", \"9\", \"0\"]}, \"filtering_options\": {\"filtering_options_selector\": \"yes\", \"__current_case__\": 1, \"min_peptide_length\": \"6\", \"max_peptide_length\": \"60\", \"max_precursor_error\": \"10.0\", \"max_precursor_error_type\": \"1\", \"exclude_unknown_ptms\": \"true\"}, \"processing_options\": {\"processing_options_selector\": \"yes\", \"__current_case__\": 1, \"protein_fdr\": \"1.0\", \"peptide_fdr\": \"1.0\", \"psm_fdr\": \"1.0\", \"protein_fraction_mw_confidence\": \"95.0\", \"ptm_score\": {\"ptm_score_selector\": \"0\", \"__current_case__\": 0}, \"ptm_sequence_matching_type\": \"1\", \"ptm_alignment\": \"true\"}, \"searchgui_input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.36.3",
+                        "type": "tool",
+                        "uuid": "8fd27751-3809-4345-9c6d-9c39a87e8497",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_peptides",
+                                "uuid": "a0c21a57-e285-44ce-9799-cfdf6d0a3909"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_psm",
+                                "uuid": "c1c7a55c-a8fd-4191-94b9-9da22f9f7dba"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "infile": {
+                                "id": 5,
+                                "output_name": "output_psm"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Replace Text",
+                                "name": "infile"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Replace Text",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "fastq"
+                                "name": "outfile",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 262.40633877840924,
-                            "top": 88.5911568019689
-                        },
-                        "post_job_actions": {
-                            "TagDatasetActionoutput": {
-                                "action_arguments": {
-                                    "tags": "#Forward"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "output"
-                            }
+                            "bottom": 525.46875,
+                            "height": 112,
+                            "left": 540.53125,
+                            "right": 740.53125,
+                            "top": 413.46875,
+                            "width": 200,
+                            "x": 540.53125,
+                            "y": 413.46875
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter/1.20.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "307518fb51af",
-                            "name": "ab1_fastq_converter",
-                            "owner": "ecology",
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"tr\": {\"trim\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.20.0",
+                        "tool_state": "{\"infile\": {\"__class__\": \"RuntimeValue\"}, \"replacements\": [{\"__index__\": 0, \"column\": \"10\", \"find_pattern\": \".mzml.mgf\", \"replace_pattern\": \"\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.3",
                         "type": "tool",
-                        "uuid": "54cdaa74-a83e-4c0b-baf7-90c854b6e65e",
-                        "when": null,
+                        "uuid": "02703525-ccb2-4e08-8492-7369408ebd0f",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "fcaa483b-90d1-40fc-b681-d8a5d421ccca"
+                                "output_name": "outfile",
+                                "uuid": "e8950200-a8b8-4496-a374-9b18638fc258"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/flashlfq/flashlfq/1.0.3.0",
                         "errors": null,
-                        "id": 8,
+                        "id": 9,
                         "input_connections": {
-                            "in_file": {
-                                "id": 4,
+                            "experiment|experimental_design": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "idt": {
+                                "id": 6,
+                                "output_name": "outfile"
+                            },
+                            "peak_lists": {
+                                "id": 0,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool seqtk_trimfq",
-                                "name": "mode"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "seqtk_trimfq",
+                        "name": "FlashLFQ",
                         "outputs": [
                             {
-                                "name": "default",
-                                "type": "input"
+                                "name": "log",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "toml",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "quantifiedPeaks",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "quantifiedPeptides",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "quantifiedProteins",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "foldChange",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 510.1667695686167,
-                            "top": 97.48960601311335
-                        },
-                        "post_job_actions": {
-                            "TagDatasetActiondefault": {
-                                "action_arguments": {
-                                    "tags": "TrimmedFastq"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "default"
-                            }
+                            "bottom": 762.984375,
+                            "height": 602,
+                            "left": 829.640625,
+                            "right": 1029.640625,
+                            "top": 160.984375,
+                            "width": 200,
+                            "x": 829.640625,
+                            "y": 160.984375
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/flashlfq/flashlfq/1.0.3.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "3da72230c066",
-                            "name": "seqtk",
-                            "owner": "iuc",
+                            "changeset_revision": "878f6725c4f3",
+                            "name": "flashlfq",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"in_file\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"mode_select\": \"quality\", \"__current_case__\": 0, \"q\": \"0.05\", \"l\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3.1",
+                        "tool_state": "{\"chg\": \"false\", \"experiment\": {\"use_design\": \"true\", \"__current_case__\": 1, \"experimental_design\": {\"__class__\": \"ConnectedValue\"}, \"nor\": \"true\", \"bayesian\": {\"calculate\": \"true\", \"__current_case__\": 1, \"ctr\": \"\", \"fcc\": null, \"sha\": \"false\", \"rmc\": \"false\", \"mcm\": \"500\", \"rns\": null}}, \"idt\": {\"__class__\": \"ConnectedValue\"}, \"int\": \"false\", \"iso\": \"5.0\", \"mbr\": \"true\", \"mrt\": \"2.5\", \"nis\": \"2\", \"peak_lists\": {\"__class__\": \"ConnectedValue\"}, \"ppm\": \"10.0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.3.0",
                         "type": "tool",
-                        "uuid": "915f5560-b853-4b0a-bd5f-126d831e8f8c",
-                        "when": null,
+                        "uuid": "4973090f-a0e3-49a2-8f7d-35e4e4711ba1",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "default",
-                                "uuid": "d65ac032-9ff6-4fb7-9aa2-1931ed709384"
+                                "output_name": "log",
+                                "uuid": "392d5313-7ebd-4cf4-aa57-07a70bbd1f17"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "quantifiedPeptides",
+                                "uuid": "0898ffbe-32cc-4c19-b9ab-0e3c8df1087d"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "quantifiedProteins",
+                                "uuid": "567e65b3-8a11-4bef-a8d0-c9164ee77f57"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "toml",
+                                "uuid": "a3668df7-3900-4ddf-a61e-9c9cedd6811c"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "foldChange",
+                                "uuid": "bdc79312-a96a-4d6a-9eec-b1f473a9d79b"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "quantifiedPeaks",
+                                "uuid": "bf3be654-975b-4881-883a-f5abce69ccea"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
                         "errors": null,
-                        "id": 9,
+                        "id": 11,
                         "input_connections": {
-                            "in_file": {
-                                "id": 5,
-                                "output_name": "output"
+                            "infile": {
+                                "id": 8,
+                                "output_name": "output_tsv"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool seqtk_trimfq",
-                                "name": "mode"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "seqtk_trimfq",
+                        "name": "Replace Text",
                         "outputs": [
                             {
-                                "name": "default",
+                                "name": "outfile",
                                 "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 516.8334128639917,
-                            "top": 432.987075214611
+                            "bottom": 1211.46875,
+                            "height": 112,
+                            "left": 1204.453125,
+                            "right": 1404.453125,
+                            "top": 1099.46875,
+                            "width": 200,
+                            "x": 1204.453125,
+                            "y": 1099.46875
                         },
                         "post_job_actions": {
-                            "TagDatasetActiondefault": {
+                            "RenameDatasetActionoutfile": {
                                 "action_arguments": {
-                                    "tags": "TrimmedFastq"
+                                    "newname": "taxa"
                                 },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "default"
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "outfile"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "3da72230c066",
-                            "name": "seqtk",
-                            "owner": "iuc",
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"in_file\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"mode_select\": \"quality\", \"__current_case__\": 0, \"q\": \"0.05\", \"l\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3.1",
+                        "tool_state": "{\"infile\": {\"__class__\": \"ConnectedValue\"}, \"replacements\": [{\"__index__\": 0, \"find_pattern\": \"#peptide\", \"replace_pattern\": \"peptide\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.2",
                         "type": "tool",
-                        "uuid": "979d668f-f8e9-4a09-8d79-e02ed0c027b5",
-                        "when": null,
+                        "uuid": "294c390d-3c9b-43b8-a29e-c0f2f6ea8e8a",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "default",
-                                "uuid": "d1bf6174-2eec-4589-b890-9336c46f3623"
+                                "output_name": "outfile",
+                                "uuid": "04a9fbe7-a95c-4a53-a7de-b101da2cae96"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "__SORTLIST__",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0",
                         "errors": null,
                         "id": 12,
                         "input_connections": {
                             "input": {
-                                "id": 8,
-                                "output_name": "default"
+                                "id": 9,
+                                "output_name": "quantifiedPeptides"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Sort collection",
+                        "name": "Regex Find And Replace",
                         "outputs": [
                             {
-                                "name": "output",
+                                "name": "out_file1",
                                 "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 913.747383567731,
-                            "top": 82.22452721670341
+                            "bottom": 422,
+                            "height": 112,
+                            "left": 1185.609375,
+                            "right": 1385.609375,
+                            "top": 310,
+                            "width": 200,
+                            "x": 1185.609375,
+                            "y": 310
                         },
-                        "post_job_actions": {},
-                        "tool_id": "__SORTLIST__",
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"sort_type\": {\"sort_type\": \"alpha\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Intensity_file"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "209b7c5ee9d7",
+                            "name": "regex_find_replace",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \"NH2-\", \"replacement\": \"\"}, {\"__index__\": 1, \"pattern\": \"-COOH\", \"replacement\": \"\"}, {\"__index__\": 2, \"pattern\": \"Sequence\", \"replacement\": \"peptide\"}, {\"__index__\": 3, \"pattern\": \"Intensity_\", \"replacement\": \"\"}], \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.0.0",
                         "type": "tool",
-                        "uuid": "dbaab406-5db7-44e6-8694-04e78a7a5f11",
-                        "when": null,
+                        "uuid": "98ced7a1-b64e-40bf-bebf-76d5526424f4",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "be7cfe5d-d40b-40ca-b334-671f2f680e05"
+                                "output_name": "out_file1",
+                                "uuid": "de9f47ae-fd6f-4a94-b3ec-2eae5d1d8a1c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "errors": null,
-                        "id": 13,
+                        "id": 14,
                         "input_connections": {
-                            "input_file": {
-                                "id": 9,
-                                "output_name": "default"
+                            "tables_0|table": {
+                                "id": 10,
+                                "output_name": "output_go_tsv"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "FASTQ Groomer",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Query Tabular",
+                                "name": "add_to_database"
+                            }
+                        ],
+                        "label": "filter 5% (All_funct)",
+                        "name": "Query Tabular",
                         "outputs": [
                             {
-                                "name": "output_file",
-                                "type": "fastqsanger"
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 771.7188193581324,
-                            "top": 347.4557364362019
+                            "bottom": 1102.03125,
+                            "height": 202,
+                            "left": 1158.046875,
+                            "right": 1358.046875,
+                            "top": 900.03125,
+                            "width": 200,
+                            "x": 1158.046875,
+                            "y": 900.03125
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "ALL_functions"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "47e5dbc3e790",
-                            "name": "fastq_groomer",
-                            "owner": "devteam",
+                            "changeset_revision": "33d61c89fb8d",
+                            "name": "query_tabular",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"input_type\": \"sanger\", \"options_type\": {\"options_type_selector\": \"advanced\", \"__current_case__\": 1, \"output_type\": \"sanger\", \"force_quality_encoding\": \"ascii\", \"summarize_input\": \"dont_summarize_input\", \"fix_id\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.5",
+                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"\"}, \"save_db\": \"false\", \"sqlquery\": \"SELECT Goterm.*\\nFROM Goterm \\nWHERE ((1.0*Goterm.protein_count)/(1.0*Goterm.total_protein_count)) >= 0.05\\n\\n\\n\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"Goterm\", \"column_names_from_first_line\": \"false\", \"col_names\": \"peptide,total_protein_count,go_term,protein_count,go_name,go_funct\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.0.0",
                         "type": "tool",
-                        "uuid": "f4f69d89-8133-4ad1-ac1f-de948e788511",
-                        "when": null,
+                        "uuid": "de18b739-d785-4c22-b291-713134e68d5d",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_file",
-                                "uuid": "64bbe1c0-fc65-4fb0-a4de-f6b0eb35086a"
+                                "output_name": "output",
+                                "uuid": "25c14890-63ec-422f-be57-0377cd5fe7ff"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "errors": null,
                         "id": 15,
                         "input_connections": {
-                            "input": {
+                            "tables_0|table": {
                                 "id": 13,
-                                "output_name": "output_file"
+                                "output_name": "out_file1"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Reverse-Complement",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Query Tabular",
+                                "name": "add_to_database"
+                            }
+                        ],
+                        "label": "GO_EC",
+                        "name": "Query Tabular",
                         "outputs": [
                             {
                                 "name": "output",
-                                "type": "input"
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1011.3125887784095,
-                            "top": 401.88283826503715
+                            "bottom": 699.5,
+                            "height": 182,
+                            "left": 1423.09375,
+                            "right": 1623.09375,
+                            "top": 517.5,
+                            "width": 200,
+                            "x": 1423.09375,
+                            "y": 517.5
                         },
                         "post_job_actions": {
-                            "TagDatasetActionoutput": {
+                            "RenameDatasetActionoutput": {
                                 "action_arguments": {
-                                    "tags": "Reversed"
+                                    "newname": "go_ec"
                                 },
-                                "action_type": "TagDatasetAction",
+                                "action_type": "RenameDatasetAction",
                                 "output_name": "output"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "6027ef51ef91",
-                            "name": "fastx_reverse_complement",
-                            "owner": "devteam",
+                            "changeset_revision": "33d61c89fb8d",
+                            "name": "query_tabular",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2+galaxy0",
+                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": null}, \"save_db\": \"false\", \"sqlquery\": \"SELECT *\\nFROM ec\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"ConnectedValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"ec\", \"column_names_from_first_line\": \"false\", \"col_names\": \"peptide,go_ec\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.0.0",
                         "type": "tool",
-                        "uuid": "fc621ad3-5725-4f10-8f1e-b5afa01a059c",
-                        "when": null,
+                        "uuid": "85158e37-3fc6-405f-9ad1-bf9ff70308e2",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "6d261e5a-8d3c-4055-ae85-5fd4fd6bb268"
+                                "uuid": "6e69f54b-5573-463c-9c5d-1c34b09fcb20"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "__SORTLIST__",
+                        "content_id": "Filter1",
                         "errors": null,
                         "id": 16,
                         "input_connections": {
                             "input": {
-                                "id": 15,
+                                "id": 14,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Sort collection",
+                        "label": "GO_BP",
+                        "name": "Filter",
                         "outputs": [
                             {
-                                "name": "output",
+                                "name": "out_file1",
                                 "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 1242.4584406072447,
-                            "top": 399.60162155694064
+                            "bottom": 832.96875,
+                            "height": 92,
+                            "left": 1489.109375,
+                            "right": 1689.109375,
+                            "top": 740.96875,
+                            "width": 200,
+                            "x": 1489.109375,
+                            "y": 740.96875
                         },
-                        "post_job_actions": {},
-                        "tool_id": "__SORTLIST__",
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"sort_type\": {\"sort_type\": \"alpha\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "go_bp"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"cond\": \"c6=='biological process'\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
                         "type": "tool",
-                        "uuid": "db0e7202-78c6-4726-a70d-64cd2627fb85",
-                        "when": null,
+                        "uuid": "b48f9e25-9725-404d-a77d-06a5a722dd29",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "408d419f-bcae-4bcc-8b3a-e38fdbafcdd3"
+                                "output_name": "out_file1",
+                                "uuid": "07473a74-e477-4a19-8368-d437ecab74bd"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.3.1",
+                        "content_id": "Filter1",
                         "errors": null,
                         "id": 17,
                         "input_connections": {
-                            "in_fq1": {
-                                "id": 12,
-                                "output_name": "output"
-                            },
-                            "in_fq2": {
-                                "id": 16,
+                            "input": {
+                                "id": 14,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "seqtk_mergepe",
+                        "label": "GO_CC",
+                        "name": "Filter",
                         "outputs": [
                             {
-                                "name": "default",
+                                "name": "out_file1",
                                 "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 1253.306789106719,
-                            "top": 45.2514467179884
+                            "bottom": 985.9375,
+                            "height": 92,
+                            "left": 1493.140625,
+                            "right": 1693.140625,
+                            "top": 893.9375,
+                            "width": 200,
+                            "x": 1493.140625,
+                            "y": 893.9375
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.3.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3da72230c066",
-                            "name": "seqtk",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "go_cc"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
                         },
-                        "tool_state": "{\"in_fq1\": {\"__class__\": \"ConnectedValue\"}, \"in_fq2\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.3.1",
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"cond\": \"c6=='cellular component'\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
                         "type": "tool",
-                        "uuid": "6010e92a-afb0-49ca-a73c-dacd0c5567e2",
-                        "when": null,
+                        "uuid": "2ad4113b-583f-48f1-9fa2-8bc111f84f81",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "default",
-                                "uuid": "9b2849cd-587d-438a-b77a-077f033c8ac1"
+                                "output_name": "out_file1",
+                                "uuid": "68fadf94-d8c4-4e25-8093-48c783fa65e6"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
+                        "content_id": "Filter1",
                         "errors": null,
                         "id": 18,
                         "input_connections": {
-                            "input_file": {
-                                "id": 17,
-                                "output_name": "default"
+                            "input": {
+                                "id": 14,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "FASTQ Groomer",
+                        "label": "GO_MF",
+                        "name": "Filter",
                         "outputs": [
                             {
-                                "name": "output_file",
-                                "type": "fastqsanger"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 1504.6579138638374,
-                            "top": 31.193468490200797
+                            "bottom": 1116.0625,
+                            "height": 92,
+                            "left": 1484.109375,
+                            "right": 1684.109375,
+                            "top": 1024.0625,
+                            "width": 200,
+                            "x": 1484.109375,
+                            "y": 1024.0625
                         },
                         "post_job_actions": {
-                            "ChangeDatatypeActionoutput_file": {
+                            "RenameDatasetActionout_file1": {
                                 "action_arguments": {
-                                    "newtype": "fastqsanger"
+                                    "newname": "go_mf"
                                 },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "output_file"
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
-                        "tool_shed_repository": {
-                            "changeset_revision": "47e5dbc3e790",
-                            "name": "fastq_groomer",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"input_type\": \"sanger\", \"options_type\": {\"options_type_selector\": \"advanced\", \"__current_case__\": 1, \"output_type\": \"sanger\", \"force_quality_encoding\": \"ascii\", \"summarize_input\": \"dont_summarize_input\", \"fix_id\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.5",
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"cond\": \"c6=='molecular function'\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
                         "type": "tool",
-                        "uuid": "467c139a-27d3-42e9-af9c-83ffdf8dc339",
-                        "when": null,
+                        "uuid": "a5249831-e466-4ae6-8490-cb62ea43611e",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_file",
-                                "uuid": "64bbe1c0-fc65-4fb0-a4de-f6b0eb35086a"
+                                "output_name": "out_file1",
+                                "uuid": "400504d4-18ba-4c89-a6db-388e72af8923"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "proteomics/metaquantome-data-creation",
+                "path": "topics/proteomics/tutorials/metaquantome-data-creation/workflows/main_workflow.ga",
+                "tags": [
+                    "proteomics"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "metaQuantome_datacreation_workflow",
+                "topic_id": "proteomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-metaquantome-data-creation/versions/main-workflow",
+                "tutorial_id": "metaquantome-data-creation",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaquantome-data-creation/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaquantome-data-creation/workflows/main_workflow.html",
+                "version": 3,
+                "wfid": "proteomics-metaquantome-data-creation",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "Cut1",
+                    "Filter1",
+                    "Remove beginning1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/flashlfq/flashlfq/1.0.3.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0"
+                ],
+                "workflowhub_id": "1177"
+            }
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.4037137"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "maxquant",
+                    "owner": "galaxyp",
+                    "revisions": "e42225f8a659",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "msstatstmt",
+                    "owner": "galaxyp",
+                    "revisions": "a5e394b36d87",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: maxquant\n  owner: galaxyp\n  revisions: e42225f8a659\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: msstatstmt\n  owner: galaxyp\n  revisions: a5e394b36d87\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/maxquant-msstats-tmt/tutorial.json",
+        "contributors": [
+            {
+                "id": "KlemensFroehlich",
+                "joined": "2021-08",
+                "name": "Klemens Fr\u00f6hlich",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/KlemensFroehlich/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/KlemensFroehlich.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "email": "melanie.foell@mol-med.uni-freiburg.de",
+                "id": "foellmelanie",
+                "joined": "2018-10",
+                "matrix": "foellmelanie:matrix.org",
+                "name": "Melanie F\u00f6ll",
+                "orcid": "0000-0002-1887-7543",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
+                "twitter": "MCFoell",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "email": "matthias.fahrner@uniklinik-freiburg.de",
+                "id": "matthias313",
+                "joined": "2019-03",
+                "name": "Matthias Fahrner",
+                "orcid": "0000-0001-7955-2518",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/matthias313/",
+                "twitter": "mfahrner313",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/matthias313.json"
+            }
+        ],
+        "dir": "topics/proteomics/tutorials/maxquant-msstats-tmt",
+        "edam_operation": [
+            "Principal component plotting",
+            "Visualisation",
+            "Clustering",
+            "Protein quantification",
+            "Standardisation and normalisation",
+            "Imputation",
+            "Statistical calculation",
+            "Heat map generation"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "proteomics/maxquant-msstats-tmt",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "MaxQuant in combination with MSstatsTMT enables quantitative analysis of TMT data."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": [
+            "Learn how to use MaxQuant and MSstats for the analysis of TMT labelled shotgun (DDA) data",
+            "Learn how to create an experimental design template for fractionated data in MaxQuant",
+            "Learn how to create an annotation file for MSstatsTMT"
+        ],
+        "pageviews": 4762,
+        "pub_date": "2021-08-13",
+        "questions": [
+            "How to analyze tandem-mass-tag (TMT) labelled shotgun (DDA) data analysis in MaxQuant and MSstats?",
+            "Which proteins are differentially abundant between KMT9\u03b1 knock-down and control cells?"
+        ],
+        "short_id": "T00220",
+        "short_tools": [
+            "msstatstmt",
+            "maxquant"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "id-quant",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "DDA",
+            "TMT"
+        ],
+        "time_estimation": "3H",
+        "title": "MaxQuant and MSstats for the analysis of TMT data",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.17.0+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/msstatstmt/msstatstmt/2.0.0+galaxy0"
+        ],
+        "topic_name": "proteomics",
+        "topic_name_human": "Proteomics",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "maxquant-msstats-tmt",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/maxquant-msstats-tmt/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/maxquant-msstats-tmt/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/maxquant-msstats-tmt/tutorial.json"
+        },
+        "version": 10,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 101,
+        "visitors": 3472,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "MaxQuant and MSstats for the analysis of TMT data",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nExperimental design template\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMSstats annotation file\"]\n  3[label=\"MaxQuant\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"MSstatsTMT\"]\n  2 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"evidence\"]\n  3 -> 4 [label=\"proteinGroups\"]\n}",
+                "history": [
+                    {
+                        "hash": "8926310c66f250b5e34d1b68039572f5ec8024d9",
+                        "message": "correcting workflow",
+                        "num": 2,
+                        "short_hash": "8926310c6",
+                        "unix": "1628863550"
                     },
+                    {
+                        "hash": "0d66511e27870d0346a8da4d1a84e697501d055d",
+                        "message": "new maxquant msstats tmt training",
+                        "num": 1,
+                        "short_hash": "0d66511e2",
+                        "unix": "1628863148"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 21,
-                        "input_connections": {
-                            "input_fasta_fp": {
-                                "id": 20,
-                                "output_name": "output"
-                            }
-                        },
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Align sequences",
-                                "name": "min_length"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Align sequences",
-                        "outputs": [
-                            {
-                                "name": "aligned_sequences",
-                                "type": "fasta"
-                            },
-                            {
-                                "name": "log",
-                                "type": "txt"
+                                "description": "",
+                                "name": "Input Dataset Collection"
                             }
                         ],
+                        "label": "Input Dataset Collection",
+                        "name": "Input dataset collection",
+                        "outputs": [],
                         "position": {
-                            "left": 2240.20532371138,
-                            "top": 0
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "e8bb88f051ec",
-                            "name": "qiime_align_seqs",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 241.5500030517578,
+                            "height": 82.55000305175781,
+                            "left": 567,
+                            "right": 767,
+                            "top": 159,
+                            "width": 200,
+                            "x": 567,
+                            "y": 159
                         },
-                        "tool_state": "{\"alignment\": {\"alignment_method\": \"clustalw\", \"__current_case__\": 2}, \"input_fasta_fp\": {\"__class__\": \"ConnectedValue\"}, \"min_length\": {\"__class__\": \"RuntimeValue\"}, \"min_percent_id\": \"0.1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.1.0",
-                        "type": "tool",
-                        "uuid": "5283fe90-38e1-4a44-a9c3-f54f29cbad85",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "75fdd4a0-50ea-4d89-833e-13119df2b7fe",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "log",
-                                "uuid": "d63ff33a-4e1a-4900-a59c-f3c14da1b7fc"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "aligned_sequences",
-                                "uuid": "c049c7ef-cc65-487c-a3c7-28b6845273b7"
+                                "output_name": "output",
+                                "uuid": "2f2012bd-d7fe-43be-86d8-4c6d233ae83d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/aligned_to_consensus/aligned_to_consensus/1.0.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 22,
-                        "input_connections": {
-                            "input": {
-                                "id": 21,
-                                "output_name": "aligned_sequences"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Consensus sequence from aligned FASTA",
-                        "outputs": [
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "Experimental design template"
                             }
                         ],
+                        "label": "Experimental design template",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2499.008880503396,
-                            "top": 0.8750031686378801
-                        },
-                        "post_job_actions": {
-                            "RemoveTagDatasetActionoutput": {
-                                "action_arguments": {
-                                    "tags": "#Forward; #Reverse"
-                                },
-                                "action_type": "RemoveTagDatasetAction",
-                                "output_name": "output"
-                            },
-                            "TagDatasetActionoutput": {
-                                "action_arguments": {
-                                    "tags": "#Consensus"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/aligned_to_consensus/aligned_to_consensus/1.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "0ccbe1c20fc3",
-                            "name": "aligned_to_consensus",
-                            "owner": "ecology",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 393.5500030517578,
+                            "height": 82.55000305175781,
+                            "left": 571,
+                            "right": 771,
+                            "top": 311,
+                            "width": 200,
+                            "x": 571,
+                            "y": 311
                         },
-                        "tool_state": "{\"gaps\": false, \"input\": {\"__class__\": \"ConnectedValue\"}, \"method\": \"chr_ambiguity\", \"outog\": false, \"seqtype\": \"DNA\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "69865435-ac6e-44d7-b0db-42bf338372a9",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "1b701c96-82fe-441d-afcc-51e4f7a1b09a",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "15b69469-bba8-4af3-8f1e-816cebc96645"
+                                "uuid": "1796d087-a179-4174-aec3-a89f45c9a367"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 23,
-                        "input_connections": {
-                            "merge|inputs": {
-                                "id": 22,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Merge.files",
-                        "outputs": [
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "input"
+                                "description": "",
+                                "name": "MSstats annotation file"
                             }
                         ],
+                        "label": "MSstats annotation file",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2763.411217150582,
-                            "top": 15.925027274602481
-                        },
-                        "post_job_actions": {
-                            "TagDatasetActionoutput": {
-                                "action_arguments": {
-                                    "tags": "#AllSeqs"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "7bd37d6decd9",
-                            "name": "mothur_merge_files",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 851.5500030517578,
+                            "height": 82.55000305175781,
+                            "left": 813,
+                            "right": 1013,
+                            "top": 769,
+                            "width": 200,
+                            "x": 813,
+                            "y": 769
                         },
-                        "tool_state": "{\"merge\": {\"type\": \"fasta\", \"__current_case__\": 0, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"savelog\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
-                        "type": "tool",
-                        "uuid": "bc874b27-7222-46e1-9753-64fa1a1b98bd",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "01633bc9-8d2d-4b03-9100-958febc2cbec",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "356f874b-c4d6-419c-afb7-15df5d285738"
+                                "uuid": "1ff0fa8b-cf25-420f-acda-ac8a2d18b29e"
                             }
                         ]
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nExperimental design template\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nMSstats annotation file\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"MaxQuant\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  4[\"MSstatsTMT\"];\n  2 -->|output| 4;\n  3 -->|evidence| 4;\n  3 -->|proteinGroups| 4;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "MaxQuant MSstatsTMT Training",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 24,
-                        "input_connections": {
-                            "merge|inputs": [
-                                {
-                                    "id": 23,
-                                    "output_name": "output"
-                                },
-                                {
-                                    "id": 14,
-                                    "output_name": "output"
-                                },
-                                {
-                                    "id": 10,
-                                    "output_name": "out_fasta"
-                                }
-                            ]
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Merge.files",
-                        "outputs": [
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "input"
+                                "description": "",
+                                "name": "Input Dataset Collection"
                             }
                         ],
+                        "label": "Input Dataset Collection",
+                        "name": "Input dataset collection",
+                        "outputs": [],
                         "position": {
-                            "left": 3443.4000227757297,
-                            "top": 228.33828312924055
-                        },
-                        "post_job_actions": {
-                            "RemoveTagDatasetActionoutput": {
-                                "action_arguments": {
-                                    "tags": "#Forward ; #Reverse"
-                                },
-                                "action_type": "RemoveTagDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "7bd37d6decd9",
-                            "name": "mothur_merge_files",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 241.5500030517578,
+                            "height": 82.55000305175781,
+                            "left": 567,
+                            "right": 767,
+                            "top": 159,
+                            "width": 200,
+                            "x": 567,
+                            "y": 159
                         },
-                        "tool_state": "{\"merge\": {\"type\": \"fasta\", \"__current_case__\": 0, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"savelog\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.39.5.0",
-                        "type": "tool",
-                        "uuid": "5f3ca9fa-eed1-45a5-8300-031268c7783d",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "75fdd4a0-50ea-4d89-833e-13119df2b7fe",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "356f874b-c4d6-419c-afb7-15df5d285738"
+                                "uuid": "2f2012bd-d7fe-43be-86d8-4c6d233ae83d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3",
+                        "content_id": null,
                         "errors": null,
-                        "id": 25,
-                        "input_connections": {
-                            "input": {
-                                "id": 24,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Regex Find And Replace",
-                        "outputs": [
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "description": "",
+                                "name": "Experimental design template"
                             }
                         ],
+                        "label": "Experimental design template",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 3700.2137599467087,
-                            "top": 225.93423217156686
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "503bcd6ebe4b",
-                            "name": "regex_find_replace",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 393.5500030517578,
+                            "height": 82.55000305175781,
+                            "left": 571,
+                            "right": 771,
+                            "top": 311,
+                            "width": 200,
+                            "x": 571,
+                            "y": 311
                         },
-                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \"([A-Z-])>\", \"replacement\": \"\\\\1\\\\n>\"}], \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.3",
-                        "type": "tool",
-                        "uuid": "8eb5a8e5-5935-4052-a5d3-000426e25a99",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "1b701c96-82fe-441d-afcc-51e4f7a1b09a",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "b0c0361f-3434-4f77-b1e6-0fd97c225559"
+                                "output_name": "output",
+                                "uuid": "1796d087-a179-4174-aec3-a89f45c9a367"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 26,
-                        "input_connections": {
-                            "input_fasta_fp": {
-                                "id": 25,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Align sequences",
-                        "outputs": [
-                            {
-                                "name": "aligned_sequences",
-                                "type": "fasta"
-                            },
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "log",
-                                "type": "txt"
+                                "description": "",
+                                "name": "MSstats annotation file"
                             }
                         ],
+                        "label": "MSstats annotation file",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 3971.6876053119054,
-                            "top": 187.59371966347155
-                        },
-                        "post_job_actions": {
-                            "TagDatasetActionaligned_sequences": {
-                                "action_arguments": {
-                                    "tags": "#Aligned"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "aligned_sequences"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "e8bb88f051ec",
-                            "name": "qiime_align_seqs",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 851.5500030517578,
+                            "height": 82.55000305175781,
+                            "left": 813,
+                            "right": 1013,
+                            "top": 769,
+                            "width": 200,
+                            "x": 813,
+                            "y": 769
                         },
-                        "tool_state": "{\"alignment\": {\"alignment_method\": \"mafft\", \"__current_case__\": 4}, \"input_fasta_fp\": {\"__class__\": \"ConnectedValue\"}, \"min_length\": null, \"min_percent_id\": \"0.1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.1.0",
-                        "type": "tool",
-                        "uuid": "a6fde88b-d89a-4fe2-ac12-0c82f16429e0",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "01633bc9-8d2d-4b03-9100-958febc2cbec",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "aligned_sequences",
-                                "uuid": "c049c7ef-cc65-487c-a3c7-28b6845273b7"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "log",
-                                "uuid": "d63ff33a-4e1a-4900-a59c-f3c14da1b7fc"
+                                "output_name": "output",
+                                "uuid": "1ff0fa8b-cf25-420f-acda-ac8a2d18b29e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.17.0+galaxy2",
                         "errors": null,
-                        "id": 27,
+                        "id": 3,
                         "input_connections": {
-                            "query": {
-                                "id": 25,
-                                "output_name": "out_file1"
+                            "input_opts|fasta_files": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "search_opts|template": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "NCBI BLAST+ blastn",
+                        "name": "MaxQuant",
                         "outputs": [
                             {
-                                "name": "output1",
+                                "name": "proteinGroups",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "mqpar",
+                                "type": "xml"
+                            },
+                            {
+                                "name": "evidence",
                                 "type": "tabular"
+                            },
+                            {
+                                "name": "log",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "ptxqc_report",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "left": 3984.640583018545,
-                            "top": 451.7552266775396
+                            "bottom": 677.6666870117188,
+                            "height": 459.66668701171875,
+                            "left": 855,
+                            "right": 1055,
+                            "top": 218,
+                            "width": 200,
+                            "x": 855,
+                            "y": 218
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.17.0+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "0e3cf9594bb7",
-                            "name": "ncbi_blast_plus",
-                            "owner": "devteam",
+                            "changeset_revision": "e42225f8a659",
+                            "name": "maxquant",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"advanced\", \"__current_case__\": 1, \"filter_query\": true, \"strand\": \"-strand both\", \"max_hits\": \"10\", \"max_hsps\": null, \"identity_cutoff\": \"0.0\", \"word_size\": null, \"ungapped\": false, \"parse_deflines\": false, \"adv_optional_id_files_opts\": {\"adv_optional_id_files_opts_selector\": \"none\", \"__current_case__\": 0}, \"qcov_hsp_perc\": \"0.0\", \"window_size\": null, \"gapopen\": null, \"gapextend\": null}, \"blast_type\": \"megablast\", \"db_opts\": {\"db_opts_selector\": \"db\", \"__current_case__\": 0, \"database\": [\"nt_2021-6-21\"], \"histdb\": \"\", \"subject\": \"\"}, \"evalue_cutoff\": \"0.001\", \"output\": {\"out_format\": \"cols\", \"__current_case__\": 2, \"std_cols\": [\"qseqid\", \"pident\", \"mismatch\", \"gapopen\"], \"ext_cols\": [\"gaps\", \"salltitles\"], \"ids_cols\": [\"saccver\"], \"misc_cols\": null, \"tax_cols\": null}, \"query\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.10.1+galaxy2",
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"__workflow_invocation_uuid__\": \"8b08afb0ed1d11eb85dd001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_opts\": {\"ftype\": \".thermo.raw\", \"fasta_files\": {\"__class__\": \"ConnectedValue\"}, \"identifier_parse_rule\": \">([^\\\\s]*)\", \"description_parse_rule\": \">(.*)\"}, \"output_opts\": {\"dry_run\": \"false\", \"output\": [\"proteinGroups\", \"mqpar\", \"evidence\", \"log\"]}, \"paramGroups\": [{\"__index__\": 0, \"files\": null, \"maxMissedCleavages\": \"2\", \"fixedModifications\": [\"Carbamidomethyl (C)\"], \"variableModifications\": [\"Acetyl (Protein N-term)\", \"Oxidation (M)\"], \"enzymes\": [\"Trypsin/P\"], \"digestion_mode\": \"0\", \"quant_method\": {\"select_quant_method\": \"reporter_ion_ms2\", \"__current_case__\": 3, \"iso_labels\": {\"labeling\": \"tmt11plex\", \"__current_case__\": 4}, \"filter_by_pif\": {\"filter_pif\": \"false\", \"__current_case__\": 1}}}], \"protein_quant\": {\"peptides_for_quantification\": \"1\", \"only_unmod_prot\": {\"unmod_prot\": \"True\", \"__current_case__\": 0, \"mods_used_prot_quant\": [\"Acetyl (Protein N-term)\", \"Oxidation (M)\"], \"discard_unmod_cpart_peptides\": \"true\"}, \"lfq_opts\": {\"separateLfq\": \"false\", \"lfqStabilizeLargeRatios\": \"true\", \"lfqRequireMsms\": \"true\", \"do_ibaq\": {\"ibaq\": \"False\", \"__current_case__\": 1}, \"advancedSiteIntensities\": \"true\"}}, \"qc\": {\"do_it\": \"true\", \"__current_case__\": 0, \"parameters\": \"true\", \"summary\": \"true\", \"proteingroups\": \"true\", \"evidence\": \"true\", \"msms\": \"true\", \"msmsscans\": \"true\"}, \"search_opts\": {\"template\": {\"__class__\": \"ConnectedValue\"}, \"min_peptide_len\": \"7\", \"max_peptide_mass\": \"4600\", \"min_unique_pep\": \"0\", \"calc_peak_properties\": \"false\", \"mbr\": {\"match_between_runs\": \"False\", \"__current_case__\": 0}, \"incl_contaminants\": \"true\", \"decoy_mode\": \"revert\", \"psm_fdr\": \"0.01\", \"protein_fdr\": \"0.01\", \"min_pep_length\": \"8\", \"max_pep_length\": \"25\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.6.17.0+galaxy2",
                         "type": "tool",
-                        "uuid": "335762a1-b65e-4510-a3bc-c6148648c8c2",
-                        "when": null,
+                        "uuid": "3027c4ed-81fa-4116-961e-7242cf99be29",
                         "workflow_outputs": [
                             {
-                                "label": "w_blast_output",
-                                "output_name": "blast_output",
-                                "uuid": "31c2dd1a-918e-4648-a407-d0e3d7172253"
+                                "label": null,
+                                "output_name": "evidence",
+                                "uuid": "16cb3dce-2b9e-47bc-99ee-84ddfa57847c"
                             },
                             {
-                                "label": "w_consensus_aligned_sequences",
-                                "output_name": "consensus_aligned_sequences",
-                                "uuid": "7514514f-809a-4a14-8981-cb08c950b523"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "sequence-analysis/Manage_AB1_Sanger",
-                "path": "topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Sanger1_From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST.ga",
-                "tags": [],
-                "test_results": null,
-                "tests": true,
-                "title": "Sanger1 : From AB1 to aligned consensus and primers fasta + BLAST",
-                "topic_id": "sequence-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/sequence-analysis-Manage_AB1_Sanger/versions/sanger1-from-ab1-to-aligned-consensus-and-primers-fasta---blast",
-                "tutorial_id": "Manage_AB1_Sanger",
-                "url": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Sanger1_From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Sanger1_From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST.html",
-                "version": 1,
-                "wfid": "sequence-analysis-Manage_AB1_Sanger",
-                "wfname": "sanger1-from-ab1-to-aligned-consensus-and-primers-fasta---blast",
-                "workflow": "Sanger1_From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST.ga",
-                "workflow_tools": [
-                    "__SORTLIST__",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.5",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter/1.20.0",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/aligned_to_consensus/aligned_to_consensus/1.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.3",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_degap_seqs/mothur_degap_seqs/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.3.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1"
-                ],
-                "workflowhub_id": "1287"
-            },
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0003-4308-5617",
-                        "name": "Coline Royaux"
-                    }
-                ],
-                "description": "",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAOPEP_and_CHD8_sequences_20220907.zip?download=1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPrim\"]\n  2[label=\"Unzip\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Filter FASTA\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Filter FASTA\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Extract element identifiers\"]\n  2 -> 5 [label=\"unzipped\"]\n  6[label=\"Degap.seqs\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"Degap.seqs\"]\n  4 -> 7 [label=\"output\"]\n  8[label=\"Regex Find And Replace\"]\n  5 -> 8 [label=\"output\"]\n  9[label=\"Regex Find And Replace\"]\n  5 -> 9 [label=\"output\"]\n  10[label=\"Reverse-Complement\"]\n  7 -> 10 [label=\"out_fasta\"]\n  11[label=\"Filter collection\"]\n  8 -> 11 [label=\"out_file1\"]\n  2 -> 11 [label=\"unzipped\"]\n  12[label=\"Filter collection\"]\n  9 -> 12 [label=\"out_file1\"]\n  11 -> 12 [label=\"output_discarded\"]\n  13[label=\"ab1 to FASTQ converter\"]\n  11 -> 13 [label=\"output_filtered\"]\n  14[label=\"ab1 to FASTQ converter\"]\n  12 -> 14 [label=\"output_filtered\"]\n  15[label=\"seqtk_trimfq\"]\n  13 -> 15 [label=\"output\"]\n  16[label=\"seqtk_trimfq\"]\n  14 -> 16 [label=\"output\"]\n  17[label=\"FASTQ Groomer\"]\n  15 -> 17 [label=\"default\"]\n  18[label=\"Sort collection\"]\n  16 -> 18 [label=\"default\"]\n  19[label=\"Sort collection\"]\n  17 -> 19 [label=\"output_file\"]\n  20[label=\"Reverse-Complement\"]\n  19 -> 20 [label=\"output\"]\n  21[label=\"seqtk_mergepe\"]\n  18 -> 21 [label=\"output\"]\n  20 -> 21 [label=\"output\"]\n  22[label=\"FASTQ Groomer\"]\n  21 -> 22 [label=\"default\"]\n  23[label=\"FASTQ to Tabular\"]\n  22 -> 23 [label=\"output_file\"]\n  24[label=\"Tabular-to-FASTA\"]\n  23 -> 24 [label=\"output_file\"]\n  25[label=\"Align sequences\"]\n  24 -> 25 [label=\"output\"]\n  26[label=\"Consensus sequence from aligned FASTA\"]\n  25 -> 26 [label=\"aligned_sequences\"]\n  27[label=\"Merge.files\"]\n  26 -> 27 [label=\"output\"]\n  28[label=\"Merge.files\"]\n  27 -> 28 [label=\"output\"]\n  10 -> 28 [label=\"output\"]\n  6 -> 28 [label=\"out_fasta\"]\n  29[label=\"Regex Find And Replace\"]\n  28 -> 29 [label=\"output\"]\n  30[label=\"Align sequences\"]\n  29 -> 30 [label=\"out_file1\"]\n  31[label=\"NCBI BLAST+ blastn\"]\n  29 -> 31 [label=\"out_file1\"]\n}",
-                "history": [
-                    {
-                        "hash": "9b2a39983d90c6094d400a9288bf711577ef5690",
-                        "message": "Update workflow",
-                        "num": 2,
-                        "short_hash": "9b2a39983",
-                        "unix": "1704193918"
-                    },
-                    {
-                        "hash": "1d51e2dc3ebda3fca99a60be425d69edd4681702",
-                        "message": "Move files from ecology to sequence analysis",
-                        "num": 1,
-                        "short_hash": "1d51e2dc3",
-                        "unix": "1702992927"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                                "label": null,
+                                "output_name": "proteinGroups",
+                                "uuid": "55166a25-0f2d-49dc-91d3-c815fbc12aa0"
+                            },
                             {
-                                "description": "",
-                                "name": "AOPEP_and_CHD8_sequences_20220907.zip?download=1"
-                            }
-                        ],
-                        "label": "AOPEP_and_CHD8_sequences_20220907.zip?download=1",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 658.2072063088361
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "2113bd7f-ee7f-462e-9d96-0181a1cd8219",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                                "label": null,
+                                "output_name": "ptxqc_report",
+                                "uuid": "fcde55d8-f460-4e1e-a49c-d896fab5cf91"
+                            },
                             {
-                                "description": "",
-                                "name": "Prim"
+                                "label": null,
+                                "output_name": "log",
+                                "uuid": "83760cea-4e21-42be-b1ae-05408528ed3e"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "mqpar",
+                                "uuid": "3d492abd-7e61-41c3-8238-4f7532a535a7"
                             }
-                        ],
-                        "label": "Prim",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 4123.210210680649,
-                            "top": 561.120359751304
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ceb12523-7e38-428e-a26d-c05ff85e0749",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAOPEP_and_CHD8_sequences_20220907.zip?download=1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nPrim\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Unzip\"];\n  0 -->|output| 2;\n  3[\"Filter FASTA\"];\n  1 -->|output| 3;\n  4[\"Filter FASTA\"];\n  1 -->|output| 4;\n  5[\"Extract element identifiers\"];\n  2 -->|unzipped| 5;\n  6[\"Degap.seqs\"];\n  3 -->|output| 6;\n  7[\"Degap.seqs\"];\n  4 -->|output| 7;\n  8[\"Regex Find And Replace\"];\n  5 -->|output| 8;\n  9[\"Regex Find And Replace\"];\n  5 -->|output| 9;\n  10[\"Reverse-Complement\"];\n  7 -->|out_fasta| 10;\n  11[\"Filter collection\"];\n  8 -->|out_file1| 11;\n  2 -->|unzipped| 11;\n  12[\"Filter collection\"];\n  9 -->|out_file1| 12;\n  11 -->|output_discarded| 12;\n  13[\"ab1 to FASTQ converter\"];\n  11 -->|output_filtered| 13;\n  14[\"ab1 to FASTQ converter\"];\n  12 -->|output_filtered| 14;\n  15[\"seqtk_trimfq\"];\n  13 -->|output| 15;\n  16[\"seqtk_trimfq\"];\n  14 -->|output| 16;\n  17[\"FASTQ Groomer\"];\n  15 -->|default| 17;\n  18[\"Sort collection\"];\n  16 -->|default| 18;\n  19[\"Sort collection\"];\n  17 -->|output_file| 19;\n  20[\"Reverse-Complement\"];\n  19 -->|output| 20;\n  21[\"seqtk_mergepe\"];\n  18 -->|output| 21;\n  20 -->|output| 21;\n  22[\"FASTQ Groomer\"];\n  21 -->|default| 22;\n  23[\"FASTQ to Tabular\"];\n  22 -->|output_file| 23;\n  24[\"Tabular-to-FASTA\"];\n  23 -->|output_file| 24;\n  25[\"Align sequences\"];\n  24 -->|output| 25;\n  26[\"Consensus sequence from aligned FASTA\"];\n  25 -->|aligned_sequences| 26;\n  27[\"Merge.files\"];\n  26 -->|output| 27;\n  28[\"Merge.files\"];\n  27 -->|output| 28;\n  10 -->|output| 28;\n  6 -->|out_fasta| 28;\n  29[\"Regex Find And Replace\"];\n  28 -->|output| 29;\n  30[\"Align sequences\"];\n  29 -->|out_file1| 30;\n  31[\"NCBI BLAST+ blastn\"];\n  29 -->|out_file1| 31;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "Training Sanger sequences CHD8",
-                "outputs": [
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msstatstmt/msstatstmt/2.0.0+galaxy0",
                         "errors": null,
-                        "id": 20,
+                        "id": 4,
                         "input_connections": {
-                            "input": {
-                                "id": 19,
+                            "input|annotation": {
+                                "id": 2,
                                 "output_name": "output"
+                            },
+                            "input|evidence": {
+                                "id": 3,
+                                "output_name": "evidence"
+                            },
+                            "input|proteinGroups": {
+                                "id": 3,
+                                "output_name": "proteinGroups"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Reverse-Complement",
+                        "name": "MSstatsTMT",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "input"
+                                "name": "out_qc_plot",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "out_group_comp",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "out_group_volcano_plot",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "out_group_comp_plot",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "left": 2835.744215956759,
-                            "top": 0
+                            "bottom": 710.6666870117188,
+                            "height": 449.66668701171875,
+                            "left": 1234,
+                            "right": 1434,
+                            "top": 261,
+                            "width": 200,
+                            "x": 1234,
+                            "y": 261
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/msstatstmt/msstatstmt/2.0.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "6027ef51ef91",
-                            "name": "fastx_reverse_complement",
-                            "owner": "devteam",
+                            "changeset_revision": "8375a0035d79",
+                            "name": "msstatstmt",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"fastqsanger\", \"__workflow_invocation_uuid__\": \"f12bdb84904311eeb9fd00505691a2f4\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"group\": {\"group_comparison\": \"true\", \"__current_case__\": 1, \"use_comp_matrix\": {\"select\": \"false\", \"__current_case__\": 0}, \"moderated\": \"false\", \"adj_method\": \"BH\", \"remove_norm_channel\": \"true\", \"remove_empty_channel\": \"true\", \"selected_group_outputs\": [\"comparison_result\", \"VolcanoPlot\", \"ComparisonPlot\"], \"comparison_plots_opt\": {\"sig\": \"0.05\", \"FCcutoff\": null, \"logBase_pvalue\": \"10\", \"ylimUp\": null, \"ylimDown\": null, \"xlimUp\": null, \"axis_size\": \"10\", \"x_axis_size\": \"10\", \"y_axis_size\": \"10\", \"dot_size\": \"3\", \"text_size\": \"4\", \"text_angle\": \"90\", \"legend_size\": \"7\", \"ProteinName\": \"false\", \"colorkey\": \"true\", \"numProtein\": \"100\", \"clustering\": \"protein\", \"width\": \"8\", \"height\": \"5\", \"which_Protein\": {\"select\": \"all\", \"__current_case__\": 0}, \"which_Comparison\": {\"select\": \"all\", \"__current_case__\": 0}}}, \"input\": {\"input_src\": \"MaxQuant\", \"__current_case__\": 1, \"evidence\": {\"__class__\": \"ConnectedValue\"}, \"proteinGroups\": {\"__class__\": \"ConnectedValue\"}, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"proteinID\": \"Proteins\", \"input_options\": {\"rmProt_Onlyidentifiedbysite\": \"false\", \"useUniquePeptide\": \"true\", \"rmPSM_withMissing_withinRun\": \"false\", \"rmPSM_withfewMea_withinRun\": \"true\", \"rmProtein_with1Feature\": \"false\", \"summaryforMultipleRows\": \"sum\"}}, \"out_plots_opt\": {\"which_Protein\": {\"select\": \"all\", \"__current_case__\": 0}, \"width\": \"10\", \"height\": \"10\", \"adv\": {\"ylimUp\": \"false\", \"ylimDown\": \"false\", \"x_axis_size\": \"10\", \"y_axis_size\": \"10\", \"text_size\": \"4\", \"text_angle\": \"90\", \"legend_size\": \"7\", \"dot_size_profile\": \"2\", \"ncol_guide\": \"5\", \"originalPlot\": \"true\", \"summaryPlot\": \"true\"}}, \"proteinSummarization\": {\"method\": \"msstats\", \"global_norm\": \"true\", \"reference_norm\": \"true\", \"remove_norm_channel\": \"true\", \"remove_empty_channel\": \"true\", \"MBimpute\": \"true\", \"maxQuantileforCensored\": null}, \"selected_outputs\": [\"QCPlot\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.0+galaxy0",
                         "type": "tool",
-                        "uuid": "1933ab2e-90bb-4535-899b-1379d85fbd64",
-                        "when": null,
+                        "uuid": "b73daf20-e3e4-4a1d-bfd9-8597e5679cbb",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "c999ceff-4f83-4cf6-bd3b-c38f2128b86d"
+                                "output_name": "out_group_comp_plot",
+                                "uuid": "64c98726-4129-45b4-85e5-b8417982fff7"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_group_volcano_plot",
+                                "uuid": "d3e07901-b18b-4727-80b8-086cdce12f9b"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_group_comp",
+                                "uuid": "f387d202-696e-435a-adee-9c0f18e72538"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_qc_plot",
+                                "uuid": "6b598ae7-595d-44bf-b677-a83a41724329"
                             }
                         ]
                     }
                 ],
-                "parent_id": "sequence-analysis/Manage_AB1_Sanger",
-                "path": "topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Training-Sanger-sequences-CHD8.ga",
-                "tags": [],
+                "parent_id": "proteomics/maxquant-msstats-tmt",
+                "path": "topics/proteomics/tutorials/maxquant-msstats-tmt/workflows/main_workflow.ga",
+                "tags": [
+                    "proteomics"
+                ],
                 "test_results": null,
-                "tests": true,
-                "title": "Training Sanger sequences CHD8",
-                "topic_id": "sequence-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/sequence-analysis-Manage_AB1_Sanger/versions/training-sanger-sequences-chd8",
-                "tutorial_id": "Manage_AB1_Sanger",
-                "url": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Training-Sanger-sequences-CHD8.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Training-Sanger-sequences-CHD8.html",
+                "tests": false,
+                "title": "MaxQuant MSstatsTMT Training",
+                "topic_id": "proteomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/proteomics-maxquant-msstats-tmt/versions/main-workflow",
+                "tutorial_id": "maxquant-msstats-tmt",
+                "url": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/maxquant-msstats-tmt/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/maxquant-msstats-tmt/workflows/main_workflow.html",
                 "version": 1,
-                "wfid": "sequence-analysis-Manage_AB1_Sanger",
-                "wfname": "training-sanger-sequences-chd8",
-                "workflow": "Training-Sanger-sequences-CHD8.ga",
+                "wfid": "proteomics-maxquant-msstats-tmt",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "__FILTER_FROM_FILE__",
-                    "__SORTLIST__",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.5",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter/1.20.0",
-                    "toolshed.g2.bx.psu.edu/repos/ecology/aligned_to_consensus/aligned_to_consensus/1.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.3",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3",
-                    "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_degap_seqs/mothur_degap_seqs/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.3.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1"
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.17.0+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/msstatstmt/msstatstmt/2.0.0+galaxy0"
                 ],
-                "workflowhub_id": "1292"
+                "workflowhub_id": "1227"
             }
         ],
-        "zenodo_link": "https://zenodo.org/records/7104640"
+        "zenodo_link": "https://zenodo.org/record/5195800"
     },
     {
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": [
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/introduction/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "email": "melanie.foell@mol-med.uni-freiburg.de",
+                "id": "foellmelanie",
+                "joined": "2018-10",
+                "matrix": "foellmelanie:matrix.org",
+                "name": "Melanie F\u00f6ll",
+                "orcid": "0000-0002-1887-7543",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/foellmelanie/",
+                "twitter": "MCFoell",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/foellmelanie.json"
+            }
+        ],
+        "dir": "topics/proteomics/tutorials/introduction",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": false,
+        "id": "proteomics/introduction",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "layout": "introduction_slides",
+        "license": "CC-BY-4.0",
+        "logo": "GTN",
+        "mod_date": "2024-08-08",
+        "pageviews": 5897557,
+        "priority": 1,
+        "pub_date": "2017-12-01",
+        "recordings": [
+            {
+                "captioners": [
+                    "foellmelanie"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "20M",
+                "speakers": [
+                    "awspolly"
+                ],
+                "youtube_id": "2C96AvrFT38"
+            }
+        ],
+        "redirect_from": [
+            "/topics/proteomics/slides/introduction",
+            "/short/proteomics/introduction/slides",
+            "/short/S00080"
+        ],
+        "short_id": "S00080",
+        "short_tools": [],
+        "slides": true,
+        "slides_recordings": [
+            {
+                "captioners": [
+                    "foellmelanie"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "20M",
+                "speakers": [
+                    "awspolly"
+                ],
+                "youtube_id": "2C96AvrFT38"
+            }
+        ],
+        "subtopic": "intro",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
                 {
-                    "name": "trim_galore",
-                    "owner": "bgruening",
-                    "revisions": "949f01671246",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
                 },
                 {
-                    "name": "bamtools_filter",
-                    "owner": "devteam",
-                    "revisions": "cb20f99fd45b",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 },
                 {
-                    "name": "bamtools_filter",
-                    "owner": "devteam",
-                    "revisions": "993b19f20c76",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 },
                 {
-                    "name": "bowtie2",
-                    "owner": "devteam",
-                    "revisions": "a6d65b0c67af",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "title": "Introduction to proteomics, protein identification, quantification and statistical modelling",
+        "tools": [],
+        "topic_name": "proteomics",
+        "topic_name_human": "Proteomics",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": true
+        },
+        "tutorial_name": "introduction",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/introduction/slides.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/introduction/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/introduction/slides.json"
+        },
+        "version": 3,
+        "video": true,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 152,
+        "visitors": 2133613
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/labelfree-vs-labelled/tutorial.json",
+        "contributors": [
+            {
+                "email": "sigloch+github@mailbox.org",
+                "former_affiliations": [
+                    "uni-freiburg"
+                ],
+                "id": "stortebecker",
+                "joined": "2017-09",
+                "name": "Florian Christoph Sigloch",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stortebecker/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/stortebecker.json"
+            },
+            {
+                "affiliations": [
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
+                "fediverse_flavor": "mastodon",
+                "id": "bgruening",
+                "joined": "2017-09",
+                "linkedin": "bgruening",
+                "location": {
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
+                },
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+            }
+        ],
+        "dir": "topics/proteomics/tutorials/labelfree-vs-labelled",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "proteomics/labelfree-vs-labelled",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Label-free and labelled methods are not better or worse *per se*.",
+            "Different scientific question call for different quantitation methods.",
+            "Be wise in choosing the right method before starting your LC-MS/MS runs."
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2022-10-18",
+        "objectives": [
+            "Choose your quantitation method."
+        ],
+        "pageviews": 11642,
+        "pub_date": "2017-03-17",
+        "questions": [
+            "What are benefits and drawbacks of different quantitation methods?",
+            "How to choose which quantitation method bests suits my need?"
+        ],
+        "short_id": "T00216",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "id-quant",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "DDA"
+        ],
+        "time_estimation": "15m",
+        "title": "Label-free versus Labelled - How to Choose Your Quantitation Method",
+        "tools": [],
+        "topic_name": "proteomics",
+        "topic_name_human": "Proteomics",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "labelfree-vs-labelled",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/proteomics/tutorials/labelfree-vs-labelled/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/labelfree-vs-labelled/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/proteomics/tutorials/labelfree-vs-labelled/tutorial.json"
+        },
+        "version": 16,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 54,
+        "visitors": 7004,
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
                 {
                     "name": "fastqc",
                     "owner": "devteam",
@@ -207478,72 +209938,59 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "samtools_stats",
+                    "name": "fastqc",
                     "owner": "devteam",
-                    "revisions": "24c5d43cb545",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "revisions": "3d0c7bdf12f5",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "samtools_stats",
-                    "owner": "devteam",
-                    "revisions": "145f6d74ff5e",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "name": "fastqe",
+                    "owner": "iuc",
+                    "revisions": "89d299153577",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "samtools_stats",
-                    "owner": "devteam",
-                    "revisions": "fed4aa48ba09",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "75c93c70d094",
+                    "tool_panel_section_label": "Quality Control",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "jbrowse",
+                    "name": "nanoplot",
                     "owner": "iuc",
-                    "revisions": "1cfc579079a6",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "revisions": "0f1c34698076",
+                    "tool_panel_section_label": "Nanopore",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "jbrowse",
+                    "name": "pycoqc",
                     "owner": "iuc",
-                    "revisions": "4542035c1075",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "revisions": "fae03f3d4bf7",
+                    "tool_panel_section_label": "Nanopore",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "c1a4b5f3b432",
-                    "tool_panel_section_label": "Quality Control",
+                    "name": "cutadapt",
+                    "owner": "lparsons",
+                    "revisions": "660cffd8d92a",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "75c93c70d094",
-                    "tool_panel_section_label": "Quality Control",
+                    "name": "cutadapt",
+                    "owner": "lparsons",
+                    "revisions": "44e2cc14f75b",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: trim_galore\n  owner: bgruening\n  revisions: 949f01671246\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_filter\n  owner: devteam\n  revisions: cb20f99fd45b\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_filter\n  owner: devteam\n  revisions: 993b19f20c76\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie2\n  owner: devteam\n  revisions: a6d65b0c67af\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 24c5d43cb545\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 145f6d74ff5e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: fed4aa48ba09\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 1cfc579079a6\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 4542035c1075\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: c1a4b5f3b432\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 75c93c70d094\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/mapping/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqe\n  owner: iuc\n  revisions: 89d299153577\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 75c93c70d094\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: 0f1c34698076\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pycoqc\n  owner: iuc\n  revisions: fae03f3d4bf7\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 660cffd8d92a\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 44e2cc14f75b\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/quality-control/tutorial.json",
         "contributors": [
-            {
-                "elixir_node": "de",
-                "email": "wolffj@informatik.uni-freiburg.de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "joachimwolff",
-                "joined": "2017-09",
-                "name": "Joachim Wolff",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/joachimwolff.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
@@ -207570,56 +210017,131 @@
                 "twitter": "bebatut",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             },
+            {
+                "id": "mblue9",
+                "joined": "2018-09",
+                "name": "Maria Doyle",
+                "orcid": "0000-0003-4847-8436",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
+            },
+            {
+                "email": "alexandre.cormier@ifremer.fr",
+                "id": "alexcorm",
+                "joined": "2021-11",
+                "name": "Alexandre Cormier",
+                "orcid": "0000-0002-7775-8413",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/",
+                "twitter": "allanssx",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/alexcorm.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
+                    "eurosciencegateway",
+                    "elixir-europe"
                 ],
-                "id": "hexylena",
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "anthony.bretaudeau@inrae.fr",
+                "fediverse": "https://genomic.social/@abretaud",
+                "fediverse_flavor": "mastodon",
+                "id": "abretaud",
                 "joined": "2017-09",
                 "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
+                    "country": "FR",
+                    "lat": 48.11,
+                    "lon": -1.64
                 },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+                "matrix": "abretaud:matrix.org",
+                "name": "Anthony Bretaudeau",
+                "orcid": "0000-0003-0914-2470",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
+                "twitter": "abretau",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
+            },
+            {
+                "email": "laura.leroi@ifremer.fr",
+                "id": "lleroi",
+                "joined": "2021-11",
+                "name": "Laura Leroi",
+                "orcid": "0000-0003-3748-4179",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lleroi/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/lleroi.json"
+            },
+            {
+                "email": "erwan.corre@sb-roscoff.fr",
+                "id": "r1corre",
+                "joined": "2019-04",
+                "name": "Erwan Corre",
+                "orcid": "0000-0001-6354-2278",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/r1corre/",
+                "twitter": "r1corre",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/r1corre.json"
+            },
+            {
+                "email": "stephanie.robin@inrae.fr",
+                "id": "stephanierobin",
+                "joined": "2021-11",
+                "name": "St\u00e9phanie Robin",
+                "orcid": "0000-0001-7379-9173",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/",
+                "twitter": "robinstphanie1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/stephanierobin.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "au",
+                "email": "c.hyde@qcif.edu.au",
+                "id": "neoformit",
+                "joined": "2022-02",
+                "name": "Cameron Hyde",
+                "orcid": "0000-0002-5913-9766",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/neoformit/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/neoformit.json"
             }
         ],
-        "dir": "topics/sequence-analysis/tutorials/mapping",
-        "edam_ontology": [
-            "topic_0102"
-        ],
+        "dir": "topics/sequence-analysis/tutorials/quality-control",
         "edam_operation": [
+            "Scatter plot plotting",
+            "Sequence trimming",
             "Sequencing quality control",
-            "Primer removal",
-            "Read mapping",
-            "Sequence alignment analysis",
+            "Box-Whisker plot plotting",
+            "Statistical calculation",
+            "Validation",
             "Sequence composition calculation",
             "Read pre-processing",
-            "Data handling",
-            "Validation",
-            "Genome visualisation",
-            "Sequence trimming",
-            "Statistical calculation"
-        ],
-        "edam_topic": [
-            "Mapping"
+            "Primer removal"
         ],
+        "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org (Main)",
@@ -207629,100 +210151,100 @@
         "feedback_number": 0,
         "follow_up_training": [
             {
-                "topic_name": "transcriptomics",
-                "tutorials": [
-                    "ref-based"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "epigenetics",
+                "topic_name": "sequence-analysis",
                 "tutorials": [
-                    "formation_of_super-structures_on_xi"
+                    "mapping"
                 ],
                 "type": "internal"
             }
         ],
         "hands_on": true,
-        "id": "sequence-analysis/mapping",
+        "id": "sequence-analysis/quality-control",
         "inexact_supported_servers": [
             "Galaxy@AuBi",
-            "GalaxyTrakr",
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
-            "UseGalaxy.no"
+            "UseGalaxy.fr"
         ],
         "js_requirements": {
-            "mathjax": null,
+            "mathjax": 23197,
             "mermaid": false
         },
         "key_points": [
-            "Know your data!",
-            "Mapping is not trivial",
-            "There are many mapping algorithms, it depends on your data which one to choose"
+            "Perform quality control on every dataset before running any other bioinformatics analysis",
+            "Assess the quality metrics and improve quality if necessary",
+            "Check the impact of the quality control",
+            "Different tools are available to provide additional quality metrics",
+            "For paired-end reads analyze the forward and reverse reads together"
         ],
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
         "mod_date": "2024-06-14",
         "objectives": [
-            "Run a tool to map reads to a reference genome",
-            "Explain what is a BAM file and what it contains",
-            "Use genome browser to understand your data"
+            "Assess short reads FASTQ quality using FASTQE \ud83e\uddec\ud83d\ude0e and FastQC",
+            "Assess long reads FASTQ quality using Nanoplot and PycoQC",
+            "Perform quality correction with Cutadapt (short reads)",
+            "Summarise quality metrics MultiQC",
+            "Process single-end and paired-end data"
         ],
-        "pageviews": 5821018,
+        "pageviews": 6060186,
         "pub_date": "2016-10-04",
         "questions": [
-            "What is mapping?",
-            "What two things are crucial for a correct mapping?",
-            "What is BAM?"
+            "How to perform quality control of NGS raw data?",
+            "What are the quality parameters to check for a dataset?",
+            "How to improve the quality of a dataset?"
         ],
         "recordings": [
             {
                 "captioners": [
+                    "LonsBio"
+                ],
+                "date": "2023-05-19",
+                "length": "50M",
+                "speakers": [
+                    "LonsBio"
+                ],
+                "youtube_id": "coaMGvZazoc"
+            },
+            {
+                "captioners": [
+                    "bebatut",
+                    "nagoue",
                     "shiltemann"
                 ],
                 "date": "2021-02-15",
                 "galaxy_version": "21.01",
-                "length": "20M",
+                "length": "1H10M",
                 "speakers": [
-                    "pvanheus"
-                ],
-                "youtube_id": "1wm-62E2NkY"
-            }
-        ],
-        "requirements": [
-            {
-                "topic_name": "sequence-analysis",
-                "tutorials": [
-                    "quality-control"
+                    "heylf"
                 ],
-                "type": "internal"
+                "youtube_id": "QJRlX2hWDKM"
             }
         ],
-        "short_id": "T00237",
+        "short_id": "T00239",
         "short_tools": [
-            "samtools_stats",
-            "jbrowse",
+            "cutadapt",
+            "pycoqc",
             "multiqc",
-            "bowtie2",
-            "bamFilter",
+            "nanoplot",
             "fastqc",
-            "trim_galore"
+            "fastqe"
         ],
         "slides": true,
         "slides_recordings": [
             {
                 "captioners": [
-                    "blankenberg"
+                    "ennovytje",
+                    "nagoue",
+                    "hexylena"
                 ],
                 "date": "2021-02-15",
                 "galaxy_version": "21.01",
-                "length": "10M",
+                "length": "40M",
                 "speakers": [
-                    "pvanheus"
+                    "heylf"
                 ],
-                "youtube_id": "7FhHb8EV3EU"
+                "youtube_id": "BWonTPS4zB8"
             }
         ],
         "supported_servers": {
@@ -207749,11 +210271,6 @@
                     "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
                 },
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -207763,30 +210280,21 @@
                     "name": "UseGalaxy.fr",
                     "url": "https://usegalaxy.fr/",
                     "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
                 }
             ]
         },
         "symlink": null,
-        "time_estimation": "1h",
-        "title": "Mapping",
+        "time_estimation": "1H30M",
+        "title": "Quality Control",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1"
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastqe/fastqe/0.2.6+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/pycoqc/pycoqc/2.5.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3",
+            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.4+galaxy2"
         ],
         "topic_name": "sequence-analysis",
         "topic_name_human": "Sequence analysis",
@@ -207796,65 +210304,72 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "mapping",
+        "tutorial_name": "quality-control",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/mapping/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-control/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/mapping/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/mapping/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/quality-control/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/quality-control/tutorial.json"
         },
-        "version": 40,
+        "version": 41,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 314,
-        "visitors": 2116959,
+        "visit_duration": 335,
+        "visitors": 2218100,
         "workflows": [
             {
                 "creators": [],
-                "description": "Mapping",
+                "description": "Quality Control",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreads_1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreads_2\"]\n  2[label=\"FastQC\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"FastQC\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Trim Galore!\"]\n  0 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"MultiQC\"]\n  3 -> 5 [label=\"text_file\"]\n  2 -> 5 [label=\"text_file\"]\n  6[label=\"Bowtie2\"]\n  4 -> 6 [label=\"trimmed_reads_pair1\"]\n  4 -> 6 [label=\"trimmed_reads_pair2\"]\n  kcb22563afece4b639d85ff5817edb5c3[color=lightseagreen,label=\"Output\\nbowtie2_mapping_stats\"]\n  6 -> kcb22563afece4b639d85ff5817edb5c3\n  7[label=\"Samtools stats\"]\n  6 -> 7 [label=\"output\"]\n  k490620d4f0834999bb3373a2a1f736b4[color=lightseagreen,label=\"Output\\nbam_stats_1\"]\n  7 -> k490620d4f0834999bb3373a2a1f736b4\n  8[label=\"JBrowse\"]\n  6 -> 8 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreads_2\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreads_1\"]\n  2[label=\"FastQC\"]\n  0 -> 2 [label=\"output\"]\n  k1f4fad7b11e74ec5b73d835080c47e70[color=lightseagreen,label=\"Output\\nreads_2_fastqc\"]\n  2 -> k1f4fad7b11e74ec5b73d835080c47e70\n  3[label=\"Cutadapt\"]\n  1 -> 3 [label=\"output\"]\n  k12a1bc96cfdd4ed8b062433833e09aee[color=lightseagreen,label=\"Output\\nreads_1_cutadapt\"]\n  3 -> k12a1bc96cfdd4ed8b062433833e09aee\n  4[label=\"FastQC\"]\n  1 -> 4 [label=\"output\"]\n  k12e19f0b102a44709bc8e362bb4e2c91[color=lightseagreen,label=\"Output\\nreads_1_fastqc\"]\n  4 -> k12e19f0b102a44709bc8e362bb4e2c91\n  5[label=\"Cutadapt\"]\n  1 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  kb7c138cc10d04bd0b960a3b5e60f29cd[color=lightseagreen,label=\"Output\\nreads_cutadapt\"]\n  5 -> kb7c138cc10d04bd0b960a3b5e60f29cd\n  6[label=\"MultiQC\"]\n  4 -> 6 [label=\"text_file\"]\n  2 -> 6 [label=\"text_file\"]\n  kfa7f541db9be4283afa18398d89f345e[color=lightseagreen,label=\"Output\\nmultiqc\"]\n  6 -> kfa7f541db9be4283afa18398d89f345e\n}",
                 "history": [
                     {
                         "hash": "505f7550f2798d344c73ae11ff158fa77cf90584",
                         "message": "update-workflows",
-                        "num": 5,
+                        "num": 6,
                         "short_hash": "505f7550f",
                         "unix": "1618939337"
                     },
                     {
                         "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
                         "message": "annotation",
-                        "num": 4,
+                        "num": 5,
                         "short_hash": "667ff3de9",
                         "unix": "1579690769"
                     },
                     {
                         "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
                         "message": "Workflow renaming",
-                        "num": 3,
+                        "num": 4,
                         "short_hash": "eb4d724e0",
                         "unix": "1579084895"
                     },
                     {
-                        "hash": "469053ce23c700f73325c5f1b668b8fa48d48252",
-                        "message": "avoiding duplicate name",
+                        "hash": "7b4cb6d1d70496ae6f59dbbc4383d5ec6c16c8ad",
+                        "message": "Replace Trim Galore with Cutadapt",
+                        "num": 3,
+                        "short_hash": "7b4cb6d1d",
+                        "unix": "1537804789"
+                    },
+                    {
+                        "hash": "2204ebb5ee73708e3ade6ece3b20a34cbe333236",
+                        "message": "Expand the QC tutorial and add workflow testing",
                         "num": 2,
-                        "short_hash": "469053ce2",
-                        "unix": "1578995047"
+                        "short_hash": "2204ebb5e",
+                        "unix": "1536843430"
                     },
                     {
-                        "hash": "27d11fd7fc4673db6c431f3a7d9529fd5ade273d",
-                        "message": "add variant with jbrowse output",
+                        "hash": "3048a0c69fe2aee55827dcadb806c11636496884",
+                        "message": "workflows",
                         "num": 1,
-                        "short_hash": "27d11fd7f",
-                        "unix": "1557229186"
+                        "short_hash": "3048a0c69",
+                        "unix": "1498583960"
                     }
                 ],
                 "inputs": [
@@ -207867,27 +210382,27 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "reads_1"
+                                "name": "reads_2"
                             }
                         ],
-                        "label": "reads_1",
+                        "label": "reads_2",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 285.5,
+                            "bottom": -144,
                             "height": 61,
-                            "left": 405.5,
-                            "right": 605.5,
-                            "top": 224.5,
+                            "left": 359,
+                            "right": 559,
+                            "top": -205,
                             "width": 200,
-                            "x": 405.5,
-                            "y": 224.5
+                            "x": 359,
+                            "y": -205
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "71f77373-c9b8-441c-bbf3-b168fbb69220",
+                        "uuid": "11e6b420-32a1-431d-8eb4-b707a1e9b2df",
                         "workflow_outputs": []
                     },
                     {
@@ -207899,876 +210414,470 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "reads_2"
+                                "name": "reads_1"
                             }
                         ],
-                        "label": "reads_2",
+                        "label": "reads_1",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 710.5,
+                            "bottom": -231,
                             "height": 61,
-                            "left": 330.5,
-                            "right": 530.5,
-                            "top": 649.5,
+                            "left": 359,
+                            "right": 559,
+                            "top": -292,
                             "width": 200,
-                            "x": 330.5,
-                            "y": 649.5
+                            "x": 359,
+                            "y": -292
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "3da9f126-0edf-4243-88f7-e1d1528840f6",
+                        "uuid": "3ba96dd1-e62d-4c22-b5b9-92a03e9b0c46",
                         "workflow_outputs": []
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nreads_1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nreads_2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"FastQC\"];\n  0 -->|output| 2;\n  3[\"FastQC\"];\n  1 -->|output| 3;\n  4[\"Trim Galore!\"];\n  0 -->|output| 4;\n  1 -->|output| 4;\n  5[\"MultiQC\"];\n  3 -->|text_file| 5;\n  2 -->|text_file| 5;\n  6[\"Bowtie2\"];\n  4 -->|trimmed_reads_pair1| 6;\n  4 -->|trimmed_reads_pair2| 6;\n  cb22563a-fece-4b63-9d85-ff5817edb5c3[\"Output\\nbowtie2_mapping_stats\"];\n  6 --> cb22563a-fece-4b63-9d85-ff5817edb5c3;\n  style cb22563a-fece-4b63-9d85-ff5817edb5c3 stroke:#2c3143,stroke-width:4px;\n  7[\"Samtools stats\"];\n  6 -->|output| 7;\n  490620d4-f083-4999-bb33-73a2a1f736b4[\"Output\\nbam_stats_1\"];\n  7 --> 490620d4-f083-4999-bb33-73a2a1f736b4;\n  style 490620d4-f083-4999-bb33-73a2a1f736b4 stroke:#2c3143,stroke-width:4px;\n  8[\"JBrowse\"];\n  6 -->|output| 8;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "GTN - Sequence Analyses - Mapping - Jbrowse (imported from uploaded file)",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nreads_2\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nreads_1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"FastQC\"];\n  0 -->|output| 2;\n  1f4fad7b-11e7-4ec5-b73d-835080c47e70[\"Output\\nreads_2_fastqc\"];\n  2 --> 1f4fad7b-11e7-4ec5-b73d-835080c47e70;\n  style 1f4fad7b-11e7-4ec5-b73d-835080c47e70 stroke:#2c3143,stroke-width:4px;\n  3[\"Cutadapt\"];\n  1 -->|output| 3;\n  12a1bc96-cfdd-4ed8-b062-433833e09aee[\"Output\\nreads_1_cutadapt\"];\n  3 --> 12a1bc96-cfdd-4ed8-b062-433833e09aee;\n  style 12a1bc96-cfdd-4ed8-b062-433833e09aee stroke:#2c3143,stroke-width:4px;\n  4[\"FastQC\"];\n  1 -->|output| 4;\n  12e19f0b-102a-4470-9bc8-e362bb4e2c91[\"Output\\nreads_1_fastqc\"];\n  4 --> 12e19f0b-102a-4470-9bc8-e362bb4e2c91;\n  style 12e19f0b-102a-4470-9bc8-e362bb4e2c91 stroke:#2c3143,stroke-width:4px;\n  5[\"Cutadapt\"];\n  1 -->|output| 5;\n  0 -->|output| 5;\n  b7c138cc-10d0-4bd0-b960-a3b5e60f29cd[\"Output\\nreads_cutadapt\"];\n  5 --> b7c138cc-10d0-4bd0-b960-a3b5e60f29cd;\n  style b7c138cc-10d0-4bd0-b960-a3b5e60f29cd stroke:#2c3143,stroke-width:4px;\n  6[\"MultiQC\"];\n  4 -->|text_file| 6;\n  2 -->|text_file| 6;\n  fa7f541d-b9be-4283-afa1-8398d89f345e[\"Output\\nmultiqc\"];\n  6 --> fa7f541d-b9be-4283-afa1-8398d89f345e;\n  style fa7f541d-b9be-4283-afa1-8398d89f345e stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "GTN - Sequence Analyses - Quality Control (imported from uploaded file)",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
                         "errors": null,
-                        "id": 5,
+                        "id": 2,
                         "input_connections": {
-                            "results_0|software_cond|output_0|input": [
-                                {
-                                    "id": 3,
-                                    "output_name": "text_file"
-                                },
-                                {
-                                    "id": 2,
-                                    "output_name": "text_file"
-                                }
-                            ]
+                            "input_file": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "adapters"
+                            },
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "contaminants"
+                            },
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "input_file"
+                            },
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "limits"
+                            }
+                        ],
                         "label": null,
-                        "name": "MultiQC",
+                        "name": "FastQC",
                         "outputs": [
                             {
-                                "name": "stats",
-                                "type": "input"
+                                "name": "html_file",
+                                "type": "html"
                             },
                             {
-                                "name": "html_report",
-                                "type": "html"
+                                "name": "text_file",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 513.5,
-                            "height": 182,
-                            "left": 1150.5,
-                            "right": 1350.5,
-                            "top": 331.5,
+                            "bottom": 199,
+                            "height": 272,
+                            "left": 617,
+                            "right": 817,
+                            "top": -73,
                             "width": 200,
-                            "x": 1150.5,
-                            "y": 331.5
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionstats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "stats"
-                            }
+                            "x": 617,
+                            "y": -73
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "75c93c70d094",
-                            "name": "multiqc",
-                            "owner": "iuc",
+                            "changeset_revision": "e7b2202befea",
+                            "name": "fastqc",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"comment\": \"\", \"export\": \"false\", \"flat\": \"false\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9+galaxy1",
+                        "tool_state": "{\"adapters\": {\"__class__\": \"RuntimeValue\"}, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"RuntimeValue\"}, \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"min_length\": null, \"nogroup\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.72+galaxy1",
                         "type": "tool",
-                        "uuid": "cb721d2b-697e-4722-9c26-4909ee315e42",
+                        "uuid": "f48fa351-4a73-4daa-b993-2210274ae84d",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "html_report",
-                                "uuid": "1d156863-b350-4bf7-b68c-406c6c1ef582"
+                                "output_name": "html_file",
+                                "uuid": "aa19933c-2d76-4fd2-ab45-7a4f0a3baab1"
+                            },
+                            {
+                                "label": "reads_2_fastqc",
+                                "output_name": "text_file",
+                                "uuid": "1f4fad7b-11e7-4ec5-b73d-835080c47e70"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3",
                         "errors": null,
-                        "id": 6,
+                        "id": 3,
                         "input_connections": {
                             "library|input_1": {
-                                "id": 4,
-                                "output_name": "trimmed_reads_pair1"
-                            },
-                            "library|input_2": {
-                                "id": 4,
-                                "output_name": "trimmed_reads_pair2"
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Bowtie2",
+                        "name": "Cutadapt",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "bam"
+                                "name": "out1",
+                                "type": "fastqsanger"
                             },
                             {
-                                "name": "mapping_stats",
+                                "name": "report",
                                 "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 989.5,
-                            "height": 252,
-                            "left": 1170.5,
-                            "right": 1370.5,
-                            "top": 737.5,
+                            "bottom": 306,
+                            "height": 162,
+                            "left": 617,
+                            "right": 817,
+                            "top": 144,
                             "width": 200,
-                            "x": 1170.5,
-                            "y": 737.5
+                            "x": 617,
+                            "y": 144
                         },
                         "post_job_actions": {
-                            "HideDatasetActionoutput": {
+                            "HideDatasetActionout1": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "09b2cdb7ace5",
-                            "name": "bowtie2",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"no_presets\"}, \"library\": {\"type\": \"paired\", \"__current_case__\": 1, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"input_2\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": \"false\", \"aligned_file\": \"false\", \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"reference_genome\": {\"source\": \"indexed\", \"__current_case__\": 0, \"index\": \"mm10\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.4.2+galaxy0",
-                        "type": "tool",
-                        "uuid": "7e2ff666-517c-46d8-9a25-c31bd6ffa55a",
-                        "workflow_outputs": [
-                            {
-                                "label": "bowtie2_mapping_stats",
-                                "output_name": "mapping_stats",
-                                "uuid": "cb22563a-fece-4b63-9d85-ff5817edb5c3"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "input": {
-                                "id": 6,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Samtools stats",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "tabular"
+                                "output_name": "out1"
                             }
-                        ],
-                        "position": {
-                            "bottom": 352.5,
-                            "height": 112,
-                            "left": 1532.5,
-                            "right": 1732.5,
-                            "top": 240.5,
-                            "width": 200,
-                            "x": 1532.5,
-                            "y": 240.5
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "145f6d74ff5e",
-                            "name": "samtools_stats",
-                            "owner": "devteam",
+                            "changeset_revision": "660cffd8d92a",
+                            "name": "cutadapt",
+                            "owner": "lparsons",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cov_threshold\": null, \"coverage_cond\": {\"coverage_select\": \"no\", \"__current_case__\": 0}, \"filter_by_flags\": {\"filter_flags\": \"nofilter\", \"__current_case__\": 1}, \"gc_depth\": \"20000.0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"insert_size\": \"8000\", \"most_inserts\": \"0.99\", \"read_length\": null, \"remove_dups\": \"false\", \"remove_overlaps\": \"false\", \"sparse\": \"false\", \"split_output_cond\": {\"split_output_selector\": \"no\", \"__current_case__\": 0}, \"trim_quality\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.2+galaxy2",
+                        "tool_state": "{\"adapter_options\": {\"error_rate\": \"0.1\", \"no_indels\": \"false\", \"count\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \"false\"}, \"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"discard\": \"false\", \"discard_untrimmed\": \"false\", \"min\": \"20\", \"max\": \"0\", \"no_trim\": \"false\", \"mask_adapter\": \"false\", \"max_n\": null, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}}, \"output_options\": {\"report\": \"true\", \"info_file\": \"false\", \"rest_file\": \"false\", \"wildcard_file\": \"false\", \"too_short_file\": \"false\", \"too_long_file\": \"false\", \"untrimmed_file\": \"false\"}, \"read_mod_options\": {\"quality_cutoff\": \"20\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"prefix\": \"\", \"suffix\": \"\", \"strip_suffix\": \"\", \"length\": \"0\", \"length_tag\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.3",
                         "type": "tool",
-                        "uuid": "8b468a5b-01e5-4beb-8aef-fa079e3f7c2a",
+                        "uuid": "ddd70253-72b8-4a5e-8025-56a579b01975",
                         "workflow_outputs": [
                             {
-                                "label": "bam_stats_1",
-                                "output_name": "output",
-                                "uuid": "490620d4-f083-4999-bb33-73a2a1f736b4"
+                                "label": "reads_1_cutadapt",
+                                "output_name": "report",
+                                "uuid": "12a1bc96-cfdd-4ed8-b062-433833e09aee"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
                         "errors": null,
-                        "id": 8,
+                        "id": 4,
                         "input_connections": {
-                            "track_groups_0|data_tracks_0|data_format|annotation": {
-                                "id": 6,
+                            "input_file": {
+                                "id": 1,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "JBrowse",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "html"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 1019.5,
-                            "height": 132,
-                            "left": 1536.5,
-                            "right": 1736.5,
-                            "top": 887.5,
-                            "width": 200,
-                            "x": 1536.5,
-                            "y": 887.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "1cfc579079a6",
-                            "name": "jbrowse",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"indexed\", \"__current_case__\": 0, \"genomes\": \"mm10full\"}, \"standalone\": \"true\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Default\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"auto_snp\": \"true\", \"chunkSizeLimit\": \"5000000\", \"track_visibility\": \"default_on\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "90ba0a17-0370-4cdf-8ddb-6d60f17f1b49",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "d62f841d-3f68-485b-8da6-af60a48f404d"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "sequence-analysis/mapping",
-                "path": "topics/sequence-analysis/tutorials/mapping/workflows/mapping-jbrowse.ga",
-                "tags": [
-                    "sequence-analysis"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "GTN - Sequence Analyses - Mapping - Jbrowse (imported from uploaded file)",
-                "topic_id": "sequence-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/sequence-analysis-mapping/versions/mapping-jbrowse",
-                "tutorial_id": "mapping",
-                "url": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/workflows/mapping-jbrowse.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/workflows/mapping-jbrowse.html",
-                "version": 5,
-                "wfid": "sequence-analysis-mapping",
-                "wfname": "mapping-jbrowse",
-                "workflow": "mapping-jbrowse.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1"
-                ],
-                "workflowhub_id": "1269"
-            },
-            {
-                "creators": [],
-                "description": "Mapping",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreads_1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreads_2\"]\n  2[label=\"FastQC\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"FastQC\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Trim Galore!\"]\n  0 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"MultiQC\"]\n  3 -> 5 [label=\"text_file\"]\n  2 -> 5 [label=\"text_file\"]\n  6[label=\"Bowtie2\"]\n  4 -> 6 [label=\"trimmed_reads_pair1\"]\n  4 -> 6 [label=\"trimmed_reads_pair2\"]\n  kd267491228a645f3ac486635eabe47b7[color=lightseagreen,label=\"Output\\nbowtie2_mapping_stats\"]\n  6 -> kd267491228a645f3ac486635eabe47b7\n  7[label=\"Stats\"]\n  6 -> 7 [label=\"output\"]\n  k96de3c0c4d7e423b8e9b9a12a011d726[color=lightseagreen,label=\"Output\\nbam_stats_1\"]\n  7 -> k96de3c0c4d7e423b8e9b9a12a011d726\n  8[label=\"Filter\"]\n  6 -> 8 [label=\"output\"]\n  9[label=\"Stats\"]\n  8 -> 9 [label=\"out_file1\"]\n  k9603a94adcd84c1f89cdbb31d8572783[color=lightseagreen,label=\"Output\\nbam_stats_2\"]\n  9 -> k9603a94adcd84c1f89cdbb31d8572783\n}",
-                "history": [
-                    {
-                        "hash": "505f7550f2798d344c73ae11ff158fa77cf90584",
-                        "message": "update-workflows",
-                        "num": 4,
-                        "short_hash": "505f7550f",
-                        "unix": "1618939337"
-                    },
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 3,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 2,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "c06c5b15160d8a4e1f1fc6d254c0590b82865f43",
-                        "message": "Expand mapping tutorial and add workflow + tests",
-                        "num": 1,
-                        "short_hash": "c06c5b151",
-                        "unix": "1536937277"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "reads_1"
-                            }
-                        ],
-                        "label": "reads_1",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": -18,
-                            "height": 61,
-                            "left": -85,
-                            "right": 115,
-                            "top": -79,
-                            "width": 200,
-                            "x": -85,
-                            "y": -79
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "71f77373-c9b8-441c-bbf3-b168fbb69220",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "adapters"
+                            },
                             {
-                                "description": "",
-                                "name": "reads_2"
-                            }
-                        ],
-                        "label": "reads_2",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 407,
-                            "height": 61,
-                            "left": -160,
-                            "right": 40,
-                            "top": 346,
-                            "width": 200,
-                            "x": -160,
-                            "y": 346
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "3da9f126-0edf-4243-88f7-e1d1528840f6",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nreads_1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nreads_2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"FastQC\"];\n  0 -->|output| 2;\n  3[\"FastQC\"];\n  1 -->|output| 3;\n  4[\"Trim Galore!\"];\n  0 -->|output| 4;\n  1 -->|output| 4;\n  5[\"MultiQC\"];\n  3 -->|text_file| 5;\n  2 -->|text_file| 5;\n  6[\"Bowtie2\"];\n  4 -->|trimmed_reads_pair1| 6;\n  4 -->|trimmed_reads_pair2| 6;\n  d2674912-28a6-45f3-ac48-6635eabe47b7[\"Output\\nbowtie2_mapping_stats\"];\n  6 --> d2674912-28a6-45f3-ac48-6635eabe47b7;\n  style d2674912-28a6-45f3-ac48-6635eabe47b7 stroke:#2c3143,stroke-width:4px;\n  7[\"Stats\"];\n  6 -->|output| 7;\n  96de3c0c-4d7e-423b-8e9b-9a12a011d726[\"Output\\nbam_stats_1\"];\n  7 --> 96de3c0c-4d7e-423b-8e9b-9a12a011d726;\n  style 96de3c0c-4d7e-423b-8e9b-9a12a011d726 stroke:#2c3143,stroke-width:4px;\n  8[\"Filter\"];\n  6 -->|output| 8;\n  9[\"Stats\"];\n  8 -->|out_file1| 9;\n  9603a94a-dcd8-4c1f-89cd-bb31d8572783[\"Output\\nbam_stats_2\"];\n  9 --> 9603a94a-dcd8-4c1f-89cd-bb31d8572783;\n  style 9603a94a-dcd8-4c1f-89cd-bb31d8572783 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "GTN - Sequence Analyses - Mapping (imported from uploaded file)",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "library|input_1": {
-                                "id": 4,
-                                "output_name": "trimmed_reads_pair1"
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "contaminants"
                             },
-                            "library|input_2": {
-                                "id": 4,
-                                "output_name": "trimmed_reads_pair2"
-                            }
-                        },
-                        "inputs": [
                             {
-                                "description": "runtime parameter for tool Bowtie2",
-                                "name": "library"
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "input_file"
                             },
                             {
-                                "description": "runtime parameter for tool Bowtie2",
-                                "name": "library"
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "limits"
                             }
                         ],
                         "label": null,
-                        "name": "Bowtie2",
+                        "name": "FastQC",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "bam"
+                                "name": "html_file",
+                                "type": "html"
                             },
                             {
-                                "name": "mapping_stats",
+                                "name": "text_file",
                                 "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 684,
-                            "height": 252,
-                            "left": 594,
-                            "right": 794,
-                            "top": 432,
+                            "bottom": -20,
+                            "height": 272,
+                            "left": 617,
+                            "right": 817,
+                            "top": -292,
                             "width": 200,
-                            "x": 594,
-                            "y": 432
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionoutput": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output"
-                            }
+                            "x": 617,
+                            "y": -292
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "09b2cdb7ace5",
-                            "name": "bowtie2",
+                            "changeset_revision": "e7b2202befea",
+                            "name": "fastqc",
                             "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"no_presets\"}, \"library\": {\"type\": \"paired\", \"__current_case__\": 1, \"input_1\": {\"__class__\": \"RuntimeValue\"}, \"input_2\": {\"__class__\": \"RuntimeValue\"}, \"unaligned_file\": \"false\", \"aligned_file\": \"false\", \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"reference_genome\": {\"source\": \"indexed\", \"__current_case__\": 0, \"index\": \"mm10\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.4.2+galaxy0",
+                        "tool_state": "{\"adapters\": {\"__class__\": \"RuntimeValue\"}, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"RuntimeValue\"}, \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"min_length\": null, \"nogroup\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.72+galaxy1",
                         "type": "tool",
-                        "uuid": "2d04b2e4-a2fe-4ce6-8894-5a752031171b",
+                        "uuid": "026332e1-70ba-4705-b75e-d228fafacc92",
                         "workflow_outputs": [
                             {
-                                "label": "bowtie2_mapping_stats",
-                                "output_name": "mapping_stats",
-                                "uuid": "d2674912-28a6-45f3-ac48-6635eabe47b7"
+                                "label": null,
+                                "output_name": "html_file",
+                                "uuid": "2b5a1c8d-a6e7-46f3-bf0a-3ccc35102538"
+                            },
+                            {
+                                "label": "reads_1_fastqc",
+                                "output_name": "text_file",
+                                "uuid": "12e19f0b-102a-4470-9bc8-e362bb4e2c91"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3",
                         "errors": null,
-                        "id": 7,
+                        "id": 5,
                         "input_connections": {
-                            "input_file": {
-                                "id": 6,
+                            "library|input_1": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "library|input_2": {
+                                "id": 0,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Stats",
+                        "name": "Cutadapt",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 29,
-                            "height": 92,
-                            "left": 1042,
-                            "right": 1242,
-                            "top": -63,
-                            "width": 200,
-                            "x": 1042,
-                            "y": -63
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "24c5d43cb545",
-                            "name": "samtools_stats",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm10.len\", \"coverage_max\": \"1000\", \"coverage_min\": \"1\", \"coverage_step\": \"1\", \"filter_by_flags\": {\"filter_flags\": \"nofilter\", \"__current_case__\": 1}, \"gc_depth\": \"20000.0\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"insert_size\": \"8000\", \"most_inserts\": \"0.99\", \"read_length\": null, \"remove_dups\": \"false\", \"split_output\": {\"split_output_selector\": \"no\", \"__current_case__\": 0}, \"trim_quality\": \"0\", \"use_reference\": {\"use_ref_selector\": \"yes\", \"__current_case__\": 0, \"reference_source\": {\"reference_source_selector\": \"cached\", \"__current_case__\": 0, \"ref_file\": \"mm10full\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.1",
-                        "type": "tool",
-                        "uuid": "898dd71d-9b58-4286-a6ae-5403cb284341",
-                        "workflow_outputs": [
+                                "name": "out1",
+                                "type": "fastqsanger"
+                            },
                             {
-                                "label": "bam_stats_1",
-                                "output_name": "output",
-                                "uuid": "96de3c0c-4d7e-423b-8e9b-9a12a011d726"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 8,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Stats",
-                        "outputs": [
+                                "name": "out2",
+                                "type": "fastqsanger"
+                            },
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "name": "report",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 619,
-                            "height": 92,
-                            "left": 1172,
-                            "right": 1372,
-                            "top": 527,
+                            "bottom": 848,
+                            "height": 262,
+                            "left": 617,
+                            "right": 817,
+                            "top": 586,
                             "width": 200,
-                            "x": 1172,
-                            "y": 527
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "24c5d43cb545",
-                            "name": "samtools_stats",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "x": 617,
+                            "y": 586
                         },
-                        "tool_state": "{\"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm10.len\", \"coverage_max\": \"1000\", \"coverage_min\": \"1\", \"coverage_step\": \"1\", \"filter_by_flags\": {\"filter_flags\": \"nofilter\", \"__current_case__\": 1}, \"gc_depth\": \"20000.0\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"insert_size\": \"8000\", \"most_inserts\": \"0.99\", \"read_length\": null, \"remove_dups\": \"false\", \"split_output\": {\"split_output_selector\": \"no\", \"__current_case__\": 0}, \"trim_quality\": \"0\", \"use_reference\": {\"use_ref_selector\": \"yes\", \"__current_case__\": 0, \"reference_source\": {\"reference_source_selector\": \"cached\", \"__current_case__\": 0, \"ref_file\": \"mm10full\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.0.1",
-                        "type": "tool",
-                        "uuid": "cb1e8297-24f1-4553-8111-1a2a48bfc12a",
-                        "workflow_outputs": [
-                            {
-                                "label": "bam_stats_2",
-                                "output_name": "output",
-                                "uuid": "9603a94a-dcd8-4c1f-89cd-bb31d8572783"
+                        "post_job_actions": {
+                            "HideDatasetActionout1": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "out1"
+                            },
+                            "HideDatasetActionout2": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "out2"
                             }
-                        ]
-                    }
-                ],
-                "parent_id": "sequence-analysis/mapping",
-                "path": "topics/sequence-analysis/tutorials/mapping/workflows/mapping.ga",
-                "tags": [
-                    "sequence-analysis"
-                ],
-                "test_results": {
-                    "eu": {
-                        "summary": {
-                            "num_errors": 0,
-                            "num_failures": 0,
-                            "num_skips": 0,
-                            "num_tests": 1
                         },
-                        "tests": [
-                            {
-                                "data": {
-                                    "end_datetime": "2023-05-19T16:33:47.079379",
-                                    "inputs": "---\nreads_1:\n  class: File\n  location: https://zenodo.org/record/1324070/files/wt_H3K4me3_read1.fastq.gz\nreads_2:\n  class: File\n  location: https://zenodo.org/record/1324070/files/wt_H3K4me3_read2.fastq.gz\n",
-                                    "invocation_details": {
-                                        "details": {
-                                            "error_message": "",
-                                            "history_id": "2e96b0bf6abd6b74",
-                                            "history_state": "ok",
-                                            "invocation_id": "6284e34d09b1b06d",
-                                            "invocation_state": "scheduled",
-                                            "workflow_id": "507e9a109418ad9c"
-                                        },
-                                        "steps": {
-                                            "0. reads_1": {
-                                                "action": null,
-                                                "id": "239cd24984e05a43",
-                                                "job_id": null,
-                                                "jobs": [],
-                                                "model_class": "WorkflowInvocationStep",
-                                                "order_index": 0,
-                                                "output_collections": {},
-                                                "outputs": {
-                                                    "output": {
-                                                        "id": "4838ba20a6d86765ce9b5492a01ba912",
-                                                        "src": "hda",
-                                                        "uuid": "689bd625-8e53-484d-a369-e8f88e298ae8"
-                                                    }
-                                                },
-                                                "state": "scheduled",
-                                                "subworkflow": null,
-                                                "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-19T14:30:12.217904",
-                                                "workflow_step_id": "a07c7d9026192889",
-                                                "workflow_step_label": "reads_1",
-                                                "workflow_step_uuid": "71f77373-c9b8-441c-bbf3-b168fbb69220"
-                                            },
-                                            "1. reads_2": {
-                                                "action": null,
-                                                "id": "1da8d9ea66ac45a3",
-                                                "job_id": null,
-                                                "jobs": [],
-                                                "model_class": "WorkflowInvocationStep",
-                                                "order_index": 1,
-                                                "output_collections": {},
-                                                "outputs": {
-                                                    "output": {
-                                                        "id": "4838ba20a6d8676511241aa0be025fbe",
-                                                        "src": "hda",
-                                                        "uuid": "654f0d1a-35d6-4c17-863b-1ed725a10d3c"
-                                                    }
-                                                },
-                                                "state": "scheduled",
-                                                "subworkflow": null,
-                                                "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-19T14:30:12.217908",
-                                                "workflow_step_id": "8b783f04ae56b16d",
-                                                "workflow_step_label": "reads_2",
-                                                "workflow_step_uuid": "3da9f126-0edf-4243-88f7-e1d1528840f6"
-                                            },
-                                            "2. Unnamed step": {
-                                                "action": null,
-                                                "id": "d11da588620ce6e9",
-                                                "job_id": "11ac94870d0bb33adde30cbebfc7b5aa",
-                                                "jobs": [
-                                                    {
-                                                        "command_line": "ln -s '/data/dnb08/galaxy_db/files/6/8/9/dataset_689bd625-8e53-484d-a369-e8f88e298ae8.dat' 'wt_H3K4me3_read1_fastq_gz.gz' && mkdir -p '/data/jwd05e/main/060/058/60058034/working/dataset_efc9b134-bbc0-4a68-9655-0ee02cf880af_files' && fastqc --outdir '/data/jwd05e/main/060/058/60058034/working/dataset_efc9b134-bbc0-4a68-9655-0ee02cf880af_files'    --quiet --extract  --kmers 7 -f 'fastq' 'wt_H3K4me3_read1_fastq_gz.gz'  && cp '/data/jwd05e/main/060/058/60058034/working/dataset_efc9b134-bbc0-4a68-9655-0ee02cf880af_files'/*/fastqc_data.txt output.txt && cp '/data/jwd05e/main/060/058/60058034/working/dataset_efc9b134-bbc0-4a68-9655-0ee02cf880af_files'/*\\.html output.html",
-                                                        "command_version": null,
-                                                        "create_time": "2023-05-19T14:30:12.209933",
-                                                        "dependencies": [
-                                                            {
-                                                                "cacheable": false,
-                                                                "dependency_resolver": {
-                                                                    "auto_init": true,
-                                                                    "auto_install": false,
-                                                                    "can_uninstall_dependencies": true,
-                                                                    "ensure_channels": "conda-forge,bioconda",
-                                                                    "model_class": "CondaDependencyResolver",
-                                                                    "prefix": "/usr/local/tools/_conda",
-                                                                    "read_only": false,
-                                                                    "resolver_type": "conda",
-                                                                    "resolves_simple_dependencies": true,
-                                                                    "use_local": false,
-                                                                    "versionless": false
-                                                                },
-                                                                "dependency_type": "conda",
-                                                                "environment_path": "/usr/local/tools/_conda/envs/__fastqc@0.11.8",
-                                                                "exact": true,
-                                                                "model_class": "MergedCondaDependency",
-                                                                "name": "fastqc",
-                                                                "version": "0.11.8"
-                                                            }
-                                                        ],
-                                                        "exit_code": 0,
-                                                        "external_id": "43534317",
-                                                        "galaxy_version": "23.0",
-                                                        "history_id": "2e96b0bf6abd6b74",
-                                                        "id": "11ac94870d0bb33adde30cbebfc7b5aa",
-                                                        "inputs": {
-                                                            "input_file": {
-                                                                "id": "4838ba20a6d86765ce9b5492a01ba912",
-                                                                "src": "hda",
-                                                                "uuid": "689bd625-8e53-484d-a369-e8f88e298ae8"
-                                                            }
-                                                        },
-                                                        "job_messages": [],
-                                                        "job_metrics": [
-                                                            {
-                                                                "name": "hostname",
-                                                                "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c125m425-1589.novalocal",
-                                                                "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c125m425-1589.novalocal"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_slots",
-                                                                "plugin": "core",
-                                                                "raw_value": "8.0000000",
-                                                                "title": "Cores Allocated",
-                                                                "value": "8"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_memory_mb",
-                                                                "plugin": "core",
-                                                                "raw_value": "31129.0000000",
-                                                                "title": "Memory Allocated (MB)",
-                                                                "value": "31129"
-                                                            },
-                                                            {
-                                                                "name": "start_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684506662.0000000",
-                                                                "title": "Job Start Time",
-                                                                "value": "2023-05-19 16:31:02"
-                                                            },
-                                                            {
-                                                                "name": "end_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684506713.0000000",
-                                                                "title": "Job End Time",
-                                                                "value": "2023-05-19 16:31:53"
-                                                            },
-                                                            {
-                                                                "name": "runtime_seconds",
-                                                                "plugin": "core",
-                                                                "raw_value": "51.0000000",
-                                                                "title": "Job Runtime (Wall Clock)",
-                                                                "value": "51 seconds"
-                                                            },
-                                                            {
-                                                                "name": "cpuacct.usage",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "12375662744.0000000",
-                                                                "title": "CPU Time",
-                                                                "value": "12.375662744 seconds"
-                                                            },
-                                                            {
-                                                                "name": "memory.failcnt",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Failed to allocate memory count",
-                                                                "value": 0.0
-                                                            },
-                                                            {
-                                                                "name": "memory.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "32749125632.0000000",
-                                                                "title": "Memory limit on cgroup (MEM)",
-                                                                "value": "30.5 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "268595200.0000000",
-                                                                "title": "Max memory usage (MEM)",
-                                                                "value": "256.2 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "9223372036854771712.0000000",
-                                                                "title": "Memory limit on cgroup (MEM+SWP)",
-                                                                "value": "8.0 EB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "268595200.0000000",
-                                                                "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "256.2 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.oom_kill_disable",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "OOM Control enabled",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.under_oom",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Was OOM Killer active?",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.soft_limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Memory softlimit on cgroup",
-                                                                "value": "0 bytes"
-                                                            }
-                                                        ],
-                                                        "job_stderr": "",
-                                                        "job_stdout": "",
-                                                        "model_class": "Job",
-                                                        "output_collections": {},
-                                                        "outputs": {
-                                                            "html_file": {
-                                                                "id": "4838ba20a6d8676572288659e6a2bd0b",
-                                                                "src": "hda",
-                                                                "uuid": "efc9b134-bbc0-4a68-9655-0ee02cf880af"
-                                                            },
-                                                            "text_file": {
-                                                                "id": "4838ba20a6d86765100e931edbfb8029",
-                                                                "src": "hda",
-                                                                "uuid": "718a2f6a-6747-4754-a9da-60a98a6c5957"
-                                                            }
-                                                        },
-                                                        "params": {
-                                                            "__input_ext": "\"fastqsanger.gz\"",
-                                                            "__workflow_invocation_uuid__": "\"9ef558e0f65111eda6f2001e67d2ec02\"",
-                                                            "adapters": null,
-                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
-                                                            "contaminants": null,
-                                                            "dbkey": "\"?\"",
-                                                            "kmers": "\"7\"",
-                                                            "limits": null,
-                                                            "min_length": null,
-                                                            "nogroup": "false"
-                                                        },
-                                                        "state": "ok",
-                                                        "stderr": "",
-                                                        "stdout": "",
-                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-                                                        "tool_stderr": "",
-                                                        "tool_stdout": "",
-                                                        "traceback": null,
-                                                        "update_time": "2023-05-19T14:31:54.552522",
-                                                        "user_email": "hxr@informatik.uni-freiburg.de"
-                                                    }
-                                                ],
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "660cffd8d92a",
+                            "name": "cutadapt",
+                            "owner": "lparsons",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adapter_options\": {\"error_rate\": \"0.1\", \"no_indels\": \"false\", \"count\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \"false\"}, \"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"discard\": \"false\", \"discard_untrimmed\": \"false\", \"min\": \"20\", \"max\": \"0\", \"no_trim\": \"false\", \"mask_adapter\": \"false\", \"max_n\": null, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"paired\", \"__current_case__\": 1, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"input_2\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}, \"r2\": {\"adapters2\": [], \"front_adapters2\": [], \"anywhere_adapters2\": [], \"cut2\": \"0\"}}, \"output_options\": {\"report\": \"true\", \"info_file\": \"false\", \"rest_file\": \"false\", \"wildcard_file\": \"false\", \"too_short_file\": \"false\", \"too_long_file\": \"false\", \"untrimmed_file\": \"false\"}, \"read_mod_options\": {\"quality_cutoff\": \"20\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"prefix\": \"\", \"suffix\": \"\", \"strip_suffix\": \"\", \"length\": \"0\", \"length_tag\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.3",
+                        "type": "tool",
+                        "uuid": "5ff1e523-c42b-42cd-8857-84d7d83802f8",
+                        "workflow_outputs": [
+                            {
+                                "label": "reads_cutadapt",
+                                "output_name": "report",
+                                "uuid": "b7c138cc-10d0-4bd0-b960-a3b5e60f29cd"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "results_0|software_cond|output_0|input": [
+                                {
+                                    "id": 4,
+                                    "output_name": "text_file"
+                                },
+                                {
+                                    "id": 2,
+                                    "output_name": "text_file"
+                                }
+                            ]
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "MultiQC",
+                        "outputs": [
+                            {
+                                "name": "stats",
+                                "type": "input"
+                            },
+                            {
+                                "name": "html_report",
+                                "type": "html"
+                            }
+                        ],
+                        "position": {
+                            "bottom": -130,
+                            "height": 162,
+                            "left": 945,
+                            "right": 1145,
+                            "top": -292,
+                            "width": 200,
+                            "x": 945,
+                            "y": -292
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "75c93c70d094",
+                            "name": "multiqc",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"comment\": \"\", \"export\": \"false\", \"flat\": \"false\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"RuntimeValue\"}}]}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9+galaxy1",
+                        "type": "tool",
+                        "uuid": "abf34a41-0150-42fc-b56a-a29eb92c24c3",
+                        "workflow_outputs": [
+                            {
+                                "label": "multiqc",
+                                "output_name": "html_report",
+                                "uuid": "fa7f541d-b9be-4283-afa1-8398d89f345e"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "sequence-analysis/quality-control",
+                "path": "topics/sequence-analysis/tutorials/quality-control/workflows/quality_control.ga",
+                "tags": [
+                    "sequence-analysis"
+                ],
+                "test_results": {
+                    "eu": {
+                        "summary": {
+                            "num_errors": 0,
+                            "num_failures": 0,
+                            "num_skips": 0,
+                            "num_tests": 1
+                        },
+                        "tests": [
+                            {
+                                "data": {
+                                    "end_datetime": "2023-05-19T17:08:59.654933",
+                                    "inputs": "---\nreads_1:\n  class: File\n  location: https://zenodo.org/record/61771/files/GSM461178_untreat_paired_subset_1.fastq\nreads_2:\n  class: File\n  location: https://zenodo.org/record/61771/files/GSM461178_untreat_paired_subset_2.fastq\n",
+                                    "invocation_details": {
+                                        "details": {
+                                            "error_message": "",
+                                            "history_id": "2f1f9fa04aab9b59",
+                                            "history_state": "ok",
+                                            "invocation_id": "1375254bd7688d41",
+                                            "invocation_state": "scheduled",
+                                            "workflow_id": "8d2820cd545d11e7"
+                                        },
+                                        "steps": {
+                                            "0. reads_1": {
+                                                "action": null,
+                                                "id": "09aab9ccfa6260cb",
+                                                "job_id": null,
+                                                "jobs": [],
                                                 "model_class": "WorkflowInvocationStep",
-                                                "order_index": 2,
+                                                "order_index": 0,
                                                 "output_collections": {},
                                                 "outputs": {
-                                                    "html_file": {
-                                                        "id": "4838ba20a6d8676572288659e6a2bd0b",
+                                                    "output": {
+                                                        "id": "4838ba20a6d86765ff25d30589db09fe",
                                                         "src": "hda",
-                                                        "uuid": "efc9b134-bbc0-4a68-9655-0ee02cf880af"
-                                                    },
-                                                    "text_file": {
-                                                        "id": "4838ba20a6d86765100e931edbfb8029",
+                                                        "uuid": "3835c7cb-1707-4e6f-85d2-6f1ad5c31bc4"
+                                                    }
+                                                },
+                                                "state": "scheduled",
+                                                "subworkflow": null,
+                                                "subworkflow_invocation_id": null,
+                                                "update_time": "2023-05-19T14:59:03.317312",
+                                                "workflow_step_id": "41e0f8150fe3cff2",
+                                                "workflow_step_label": "reads_1",
+                                                "workflow_step_uuid": "3ba96dd1-e62d-4c22-b5b9-92a03e9b0c46"
+                                            },
+                                            "1. reads_2": {
+                                                "action": null,
+                                                "id": "53088303de376bb8",
+                                                "job_id": null,
+                                                "jobs": [],
+                                                "model_class": "WorkflowInvocationStep",
+                                                "order_index": 1,
+                                                "output_collections": {},
+                                                "outputs": {
+                                                    "output": {
+                                                        "id": "4838ba20a6d867656914ebcc68e736a5",
                                                         "src": "hda",
-                                                        "uuid": "718a2f6a-6747-4754-a9da-60a98a6c5957"
+                                                        "uuid": "9968668a-3051-4e02-aa3d-4997838a0985"
                                                     }
                                                 },
                                                 "state": "scheduled",
                                                 "subworkflow": null,
                                                 "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-19T14:31:54.529698",
-                                                "workflow_step_id": "1e8dd70f0c41cadf",
-                                                "workflow_step_label": null,
-                                                "workflow_step_uuid": "f9d0ea7d-f2e3-41b2-bc11-4d40665a4439"
+                                                "update_time": "2023-05-19T14:59:03.317318",
+                                                "workflow_step_id": "ada35db989250a9c",
+                                                "workflow_step_label": "reads_2",
+                                                "workflow_step_uuid": "11e6b420-32a1-431d-8eb4-b707a1e9b2df"
                                             },
-                                            "3. Unnamed step": {
+                                            "2. Unnamed step": {
                                                 "action": null,
-                                                "id": "76778945e7e793e5",
-                                                "job_id": "11ac94870d0bb33af53ebe6a5976a7e4",
+                                                "id": "d94b4b21ddc3e0c3",
+                                                "job_id": "11ac94870d0bb33a2a3328a31b8b1d2e",
                                                 "jobs": [
                                                     {
-                                                        "command_line": "ln -s '/data/dnb08/galaxy_db/files/6/5/4/dataset_654f0d1a-35d6-4c17-863b-1ed725a10d3c.dat' 'wt_H3K4me3_read2_fastq_gz.gz' && mkdir -p '/data/jwd02f/main/060/058/60058035/working/dataset_5f25fcad-3405-4aa3-a343-8eb710d98761_files' && fastqc --outdir '/data/jwd02f/main/060/058/60058035/working/dataset_5f25fcad-3405-4aa3-a343-8eb710d98761_files'    --quiet --extract  --kmers 7 -f 'fastq' 'wt_H3K4me3_read2_fastq_gz.gz'  && cp '/data/jwd02f/main/060/058/60058035/working/dataset_5f25fcad-3405-4aa3-a343-8eb710d98761_files'/*/fastqc_data.txt output.txt && cp '/data/jwd02f/main/060/058/60058035/working/dataset_5f25fcad-3405-4aa3-a343-8eb710d98761_files'/*\\.html output.html",
+                                                        "command_line": "ln -s '/data/dnb08/galaxy_db/files/3/8/3/dataset_3835c7cb-1707-4e6f-85d2-6f1ad5c31bc4.dat' 'GSM461178_untreat_paired_subset_1_fastq' && mkdir -p '/data/jwd01/main/060/059/60059402/working/dataset_a0107efb-9924-481b-99eb-5e7c74c4c697_files' && fastqc --outdir '/data/jwd01/main/060/059/60059402/working/dataset_a0107efb-9924-481b-99eb-5e7c74c4c697_files'    --quiet --extract  --kmers 7 -f 'fastq' 'GSM461178_untreat_paired_subset_1_fastq'  && cp '/data/jwd01/main/060/059/60059402/working/dataset_a0107efb-9924-481b-99eb-5e7c74c4c697_files'/*/fastqc_data.txt output.txt && cp '/data/jwd01/main/060/059/60059402/working/dataset_a0107efb-9924-481b-99eb-5e7c74c4c697_files'/*\\.html output.html",
                                                         "command_version": null,
-                                                        "create_time": "2023-05-19T14:30:12.324932",
+                                                        "create_time": "2023-05-19T14:59:03.313089",
                                                         "dependencies": [
                                                             {
                                                                 "cacheable": false,
@@ -208794,15 +210903,15 @@
                                                             }
                                                         ],
                                                         "exit_code": 0,
-                                                        "external_id": "43534318",
+                                                        "external_id": "43535387",
                                                         "galaxy_version": "23.0",
-                                                        "history_id": "2e96b0bf6abd6b74",
-                                                        "id": "11ac94870d0bb33af53ebe6a5976a7e4",
+                                                        "history_id": "2f1f9fa04aab9b59",
+                                                        "id": "11ac94870d0bb33a2a3328a31b8b1d2e",
                                                         "inputs": {
                                                             "input_file": {
-                                                                "id": "4838ba20a6d8676511241aa0be025fbe",
+                                                                "id": "4838ba20a6d86765ff25d30589db09fe",
                                                                 "src": "hda",
-                                                                "uuid": "654f0d1a-35d6-4c17-863b-1ed725a10d3c"
+                                                                "uuid": "3835c7cb-1707-4e6f-85d2-6f1ad5c31bc4"
                                                             }
                                                         },
                                                         "job_messages": [],
@@ -208831,30 +210940,30 @@
                                                             {
                                                                 "name": "start_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684506662.0000000",
+                                                                "raw_value": "1684508692.0000000",
                                                                 "title": "Job Start Time",
-                                                                "value": "2023-05-19 16:31:02"
+                                                                "value": "2023-05-19 17:04:52"
                                                             },
                                                             {
                                                                 "name": "end_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684506721.0000000",
+                                                                "raw_value": "1684508707.0000000",
                                                                 "title": "Job End Time",
-                                                                "value": "2023-05-19 16:32:01"
+                                                                "value": "2023-05-19 17:05:07"
                                                             },
                                                             {
                                                                 "name": "runtime_seconds",
                                                                 "plugin": "core",
-                                                                "raw_value": "59.0000000",
+                                                                "raw_value": "15.0000000",
                                                                 "title": "Job Runtime (Wall Clock)",
-                                                                "value": "59 seconds"
+                                                                "value": "15 seconds"
                                                             },
                                                             {
                                                                 "name": "cpuacct.usage",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "13599783917.0000000",
+                                                                "raw_value": "12194724984.0000000",
                                                                 "title": "CPU Time",
-                                                                "value": "13.599783917 seconds"
+                                                                "value": "12.194724984 seconds"
                                                             },
                                                             {
                                                                 "name": "memory.failcnt",
@@ -208873,9 +210982,9 @@
                                                             {
                                                                 "name": "memory.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "231440384.0000000",
+                                                                "raw_value": "357576704.0000000",
                                                                 "title": "Max memory usage (MEM)",
-                                                                "value": "220.7 MB"
+                                                                "value": "341.0 MB"
                                                             },
                                                             {
                                                                 "name": "memory.memsw.limit_in_bytes",
@@ -208887,9 +210996,9 @@
                                                             {
                                                                 "name": "memory.memsw.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "231440384.0000000",
+                                                                "raw_value": "357576704.0000000",
                                                                 "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "220.7 MB"
+                                                                "value": "341.0 MB"
                                                             },
                                                             {
                                                                 "name": "memory.oom_control.oom_kill_disable",
@@ -208919,19 +211028,19 @@
                                                         "output_collections": {},
                                                         "outputs": {
                                                             "html_file": {
-                                                                "id": "4838ba20a6d8676521dd17a9b62d385f",
+                                                                "id": "4838ba20a6d867651957556f6b54741b",
                                                                 "src": "hda",
-                                                                "uuid": "5f25fcad-3405-4aa3-a343-8eb710d98761"
+                                                                "uuid": "a0107efb-9924-481b-99eb-5e7c74c4c697"
                                                             },
                                                             "text_file": {
-                                                                "id": "4838ba20a6d8676577d1d2d4d95b125f",
+                                                                "id": "4838ba20a6d86765967c147adffa4ae2",
                                                                 "src": "hda",
-                                                                "uuid": "0a0a3867-f5f7-4690-9776-09274436e562"
+                                                                "uuid": "8aadb0d6-4752-43b3-9a70-b58359fe1659"
                                                             }
                                                         },
                                                         "params": {
-                                                            "__input_ext": "\"fastqsanger.gz\"",
-                                                            "__workflow_invocation_uuid__": "\"9ef558e0f65111eda6f2001e67d2ec02\"",
+                                                            "__input_ext": "\"fastqsanger\"",
+                                                            "__workflow_invocation_uuid__": "\"a085c588f65511ed82b7001e67d2ec02\"",
                                                             "adapters": null,
                                                             "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
                                                             "contaminants": null,
@@ -208948,81 +211057,53 @@
                                                         "tool_stderr": "",
                                                         "tool_stdout": "",
                                                         "traceback": null,
-                                                        "update_time": "2023-05-19T14:32:05.448601",
+                                                        "update_time": "2023-05-19T15:05:09.851510",
                                                         "user_email": "hxr@informatik.uni-freiburg.de"
                                                     }
                                                 ],
                                                 "model_class": "WorkflowInvocationStep",
-                                                "order_index": 3,
+                                                "order_index": 2,
                                                 "output_collections": {},
                                                 "outputs": {
                                                     "html_file": {
-                                                        "id": "4838ba20a6d8676521dd17a9b62d385f",
+                                                        "id": "4838ba20a6d867651957556f6b54741b",
                                                         "src": "hda",
-                                                        "uuid": "5f25fcad-3405-4aa3-a343-8eb710d98761"
+                                                        "uuid": "a0107efb-9924-481b-99eb-5e7c74c4c697"
                                                     },
                                                     "text_file": {
-                                                        "id": "4838ba20a6d8676577d1d2d4d95b125f",
+                                                        "id": "4838ba20a6d86765967c147adffa4ae2",
                                                         "src": "hda",
-                                                        "uuid": "0a0a3867-f5f7-4690-9776-09274436e562"
+                                                        "uuid": "8aadb0d6-4752-43b3-9a70-b58359fe1659"
                                                     }
                                                 },
                                                 "state": "scheduled",
                                                 "subworkflow": null,
                                                 "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-19T14:32:05.428308",
-                                                "workflow_step_id": "7c2802e0bfd4ecd0",
+                                                "update_time": "2023-05-19T15:05:09.811263",
+                                                "workflow_step_id": "4b6834f9ae6537d8",
                                                 "workflow_step_label": null,
-                                                "workflow_step_uuid": "faa4b55f-0b0c-4696-b61e-f281007aa8a1"
+                                                "workflow_step_uuid": "026332e1-70ba-4705-b75e-d228fafacc92"
                                             },
-                                            "4. Unnamed step": {
+                                            "3. Unnamed step": {
                                                 "action": null,
-                                                "id": "1504cb0a755f30bb",
-                                                "job_id": "11ac94870d0bb33a0920faa96345e33f",
+                                                "id": "c5c312487856832c",
+                                                "job_id": "11ac94870d0bb33a14ad54e496e129b6",
                                                 "jobs": [
                                                     {
-                                                        "command_line": "ln -s '/data/dnb08/galaxy_db/files/6/8/9/dataset_689bd625-8e53-484d-a369-e8f88e298ae8.dat' input_1.fastq.gz &&  ln -s '/data/dnb08/galaxy_db/files/6/5/4/dataset_654f0d1a-35d6-4c17-863b-1ed725a10d3c.dat' input_2.fastq.gz &&  trim_galore  --phred33    --output_dir ./      --paired      input_1.fastq.gz input_2.fastq.gz   && if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi",
-                                                        "command_version": "Quality-/Adapter-/RRBS-Trimming\n                               (powered by Cutadapt)\n                                  version 0.4.3\n\n                             Last update: 07 12 2016",
-                                                        "create_time": "2023-05-19T14:30:12.446388",
-                                                        "dependencies": [
-                                                            {
-                                                                "cacheable": false,
-                                                                "dependency_resolver": {
-                                                                    "auto_init": true,
-                                                                    "auto_install": false,
-                                                                    "can_uninstall_dependencies": true,
-                                                                    "ensure_channels": "conda-forge,bioconda",
-                                                                    "model_class": "CondaDependencyResolver",
-                                                                    "prefix": "/usr/local/tools/_conda",
-                                                                    "read_only": false,
-                                                                    "resolver_type": "conda",
-                                                                    "resolves_simple_dependencies": true,
-                                                                    "use_local": false,
-                                                                    "versionless": false
-                                                                },
-                                                                "dependency_type": "conda",
-                                                                "environment_path": "/usr/local/tools/_conda/envs/__trim-galore@0.4.3",
-                                                                "exact": true,
-                                                                "model_class": "MergedCondaDependency",
-                                                                "name": "trim-galore",
-                                                                "version": "0.4.3"
-                                                            }
-                                                        ],
+                                                        "command_line": "ln -f -s '/data/dnb08/galaxy_db/files/3/8/3/dataset_3835c7cb-1707-4e6f-85d2-6f1ad5c31bc4.dat' 'GSM461178_untreat_paired_subset_1_fastq.fq' &&    cutadapt  -j ${GALAXY_SLOTS:-1}          --output='out1.fq'  --error-rate=0.1 --times=1 --overlap=3         --minimum-length=20   --quality-cutoff=20   'GSM461178_untreat_paired_subset_1_fastq.fq'  > report.txt",
+                                                        "command_version": "1.16",
+                                                        "create_time": "2023-05-19T14:59:03.399654",
+                                                        "dependencies": [],
                                                         "exit_code": 0,
-                                                        "external_id": "43534319",
+                                                        "external_id": "43535389",
                                                         "galaxy_version": "23.0",
-                                                        "history_id": "2e96b0bf6abd6b74",
-                                                        "id": "11ac94870d0bb33a0920faa96345e33f",
+                                                        "history_id": "2f1f9fa04aab9b59",
+                                                        "id": "11ac94870d0bb33a14ad54e496e129b6",
                                                         "inputs": {
-                                                            "input_mate1": {
-                                                                "id": "4838ba20a6d86765ce9b5492a01ba912",
-                                                                "src": "hda",
-                                                                "uuid": "689bd625-8e53-484d-a369-e8f88e298ae8"
-                                                            },
-                                                            "input_mate2": {
-                                                                "id": "4838ba20a6d8676511241aa0be025fbe",
+                                                            "input_1": {
+                                                                "id": "4838ba20a6d86765ff25d30589db09fe",
                                                                 "src": "hda",
-                                                                "uuid": "654f0d1a-35d6-4c17-863b-1ed725a10d3c"
+                                                                "uuid": "3835c7cb-1707-4e6f-85d2-6f1ad5c31bc4"
                                                             }
                                                         },
                                                         "job_messages": [],
@@ -209030,9 +211111,9 @@
                                                             {
                                                                 "name": "hostname",
                                                                 "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c36m100-8763.novalocal",
+                                                                "raw_value": "vgcnbwc-worker-c125m425-6547.novalocal",
                                                                 "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c36m100-8763.novalocal"
+                                                                "value": "vgcnbwc-worker-c125m425-6547.novalocal"
                                                             },
                                                             {
                                                                 "name": "galaxy_slots",
@@ -209051,30 +211132,30 @@
                                                             {
                                                                 "name": "start_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684506638.0000000",
+                                                                "raw_value": "1684508382.0000000",
                                                                 "title": "Job Start Time",
-                                                                "value": "2023-05-19 16:30:38"
+                                                                "value": "2023-05-19 16:59:42"
                                                             },
                                                             {
                                                                 "name": "end_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684506671.0000000",
+                                                                "raw_value": "1684508412.0000000",
                                                                 "title": "Job End Time",
-                                                                "value": "2023-05-19 16:31:11"
+                                                                "value": "2023-05-19 17:00:12"
                                                             },
                                                             {
                                                                 "name": "runtime_seconds",
                                                                 "plugin": "core",
-                                                                "raw_value": "33.0000000",
+                                                                "raw_value": "30.0000000",
                                                                 "title": "Job Runtime (Wall Clock)",
-                                                                "value": "33 seconds"
+                                                                "value": "30 seconds"
                                                             },
                                                             {
                                                                 "name": "cpuacct.usage",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "15323583745.0000000",
+                                                                "raw_value": "7314785524.0000000",
                                                                 "title": "CPU Time",
-                                                                "value": "15.323583745 seconds"
+                                                                "value": "7.314785524 seconds"
                                                             },
                                                             {
                                                                 "name": "memory.failcnt",
@@ -209093,9 +211174,9 @@
                                                             {
                                                                 "name": "memory.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "216088576.0000000",
+                                                                "raw_value": "251256832.0000000",
                                                                 "title": "Max memory usage (MEM)",
-                                                                "value": "206.1 MB"
+                                                                "value": "239.6 MB"
                                                             },
                                                             {
                                                                 "name": "memory.memsw.limit_in_bytes",
@@ -209107,9 +211188,9 @@
                                                             {
                                                                 "name": "memory.memsw.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "216088576.0000000",
+                                                                "raw_value": "251256832.0000000",
                                                                 "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "206.1 MB"
+                                                                "value": "239.6 MB"
                                                             },
                                                             {
                                                                 "name": "memory.oom_control.oom_kill_disable",
@@ -209138,302 +211219,105 @@
                                                         "model_class": "Job",
                                                         "output_collections": {},
                                                         "outputs": {
-                                                            "trimmed_reads_pair1": {
-                                                                "id": "4838ba20a6d86765439b06bcf8677007",
+                                                            "out1": {
+                                                                "id": "4838ba20a6d8676528f2966e438993df",
                                                                 "src": "hda",
-                                                                "uuid": "64981dba-44f7-4768-8b63-e63defba2ecf"
+                                                                "uuid": "5096388f-425a-42a1-b99e-4f0174665371"
                                                             },
-                                                            "trimmed_reads_pair2": {
-                                                                "id": "4838ba20a6d867658f72f66dd1d7e6cc",
+                                                            "report": {
+                                                                "id": "4838ba20a6d8676504b9c2c33c839b66",
                                                                 "src": "hda",
-                                                                "uuid": "0764cea4-72ed-4a8c-93b2-88bd066afc4e"
+                                                                "uuid": "b9909c1d-09b1-47ec-9135-48915855c294"
                                                             }
                                                         },
                                                         "params": {
                                                             "__input_ext": "\"input\"",
-                                                            "__workflow_invocation_uuid__": "\"9ef558e0f65111eda6f2001e67d2ec02\"",
+                                                            "__workflow_invocation_uuid__": "\"a085c588f65511ed82b7001e67d2ec02\"",
+                                                            "adapter_options": "{\"count\": \"1\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"overlap\": \"3\"}",
                                                             "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
                                                             "dbkey": "\"?\"",
-                                                            "params": "{\"__current_case__\": 0, \"settingsType\": \"default\"}",
-                                                            "rrbs": "{\"__current_case__\": 0, \"settingsType\": \"default\"}",
-                                                            "singlePaired": "{\"__current_case__\": 1, \"input_mate1\": {\"values\": [{\"id\": 137415404, \"src\": \"hda\"}]}, \"input_mate2\": {\"values\": [{\"id\": 137415461, \"src\": \"hda\"}]}, \"sPaired\": \"paired\", \"three_prime_clip_R1\": null, \"three_prime_clip_R2\": null, \"trim1\": false, \"trimming\": {\"__current_case__\": 0, \"trimming_select\": \"\"}}"
+                                                            "filter_options": "{\"discard\": false, \"discard_untrimmed\": false, \"mask_adapter\": false, \"max\": \"0\", \"max_n\": null, \"min\": \"20\", \"no_trim\": false, \"pair_filter\": \"any\"}",
+                                                            "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 137417465, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\", \"front_adapters\": []}, \"type\": \"single\"}",
+                                                            "output_options": "{\"info_file\": false, \"report\": true, \"rest_file\": false, \"too_long_file\": false, \"too_short_file\": false, \"untrimmed_file\": false, \"wildcard_file\": false}",
+                                                            "read_mod_options": "{\"length\": \"0\", \"length_tag\": \"\", \"nextseq_trim\": \"0\", \"prefix\": \"\", \"quality_cutoff\": \"20\", \"strip_suffix\": \"\", \"suffix\": \"\", \"trim_n\": false}"
                                                         },
                                                         "state": "ok",
-                                                        "stderr": "Path to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\n\n\nAUTO-DETECTING ADAPTER TYPE\n===========================\nAttempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq.gz <<)\n\nFound perfect matches for the following adapter sequences:\nAdapter type\tCount\tSequence\tSequences analysed\tPercentage\nIllumina\t2\tAGATCGGAAGAGC\t50000\t0.00\nsmallRNA\t0\tTGGAATTCTCGG\t50000\t0.00\nNextera\t0\tCTGTCTCTTATA\t50000\t0.00\nUsing Illumina adapter for trimming (count: 2). Second best hit was smallRNA (count: 0)\n\nWriting report to './input_1.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq.gz\nTrimming mode: paired-end\nTrim Galore version: 0.4.3\nCutadapt version: 1.13\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nWriting final adapter and quality trimmed output to input_1_trimmed.fq.gz\n\n\n  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq.gz <<< \nThis is cutadapt 1.13 with Python 3.6.1\nCommand line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz\nTrimming 1 adapter with at most 10.0% errors in single-end mode ...\nFinished in 0.85 s (17 us/read; 3.52 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed:                  50,000\nReads with adapters:                    14,011 (28.0%)\nReads written (passing filters):        50,000 (100.0%)\n\nTotal basepairs processed:     2,550,000 bp\nQuality-trimmed:                  34,012 bp (1.3%)\nTotal written (filtered):      2,495,795 bp (97.9%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14011 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n  A: 27.3%\n  C: 33.3%\n  G: 24.8%\n  T: 14.6%\n  none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t9379\t12500.0\t0\t9379\n2\t3646\t3125.0\t0\t3646\n3\t791\t781.2\t0\t791\n4\t134\t195.3\t0\t134\n5\t33\t48.8\t0\t33\n6\t9\t12.2\t0\t9\n7\t3\t3.1\t0\t3\n8\t1\t0.8\t0\t1\n9\t1\t0.2\t0\t0 1\n10\t3\t0.0\t1\t0 3\n11\t1\t0.0\t1\t1\n15\t1\t0.0\t1\t1\n16\t1\t0.0\t1\t0 1\n19\t1\t0.0\t1\t1\n27\t1\t0.0\t1\t0 1\n28\t1\t0.0\t1\t0 1\n32\t1\t0.0\t1\t0 1\n36\t1\t0.0\t1\t0 1\n43\t1\t0.0\t1\t0 1\n49\t1\t0.0\t1\t0 1\n50\t1\t0.0\t1\t0 1\n\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq.gz\n=============================================\n50000 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nWriting report to './input_2.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_2.fastq.gz\nTrimming mode: paired-end\nTrim Galore version: 0.4.3\nCutadapt version: 1.13\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nWriting final adapter and quality trimmed output to input_2_trimmed.fq.gz\n\n\n  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_2.fastq.gz <<< \nThis is cutadapt 1.13 with Python 3.6.1\nCommand line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_2.fastq.gz\nTrimming 1 adapter with at most 10.0% errors in single-end mode ...\nFinished in 0.91 s (18 us/read; 3.30 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed:                  50,000\nReads with adapters:                    13,787 (27.6%)\nReads written (passing filters):        50,000 (100.0%)\n\nTotal basepairs processed:     2,550,000 bp\nQuality-trimmed:                 120,340 bp (4.7%)\nTotal written (filtered):      2,410,008 bp (94.5%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13787 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n  A: 27.6%\n  C: 32.8%\n  G: 24.6%\n  T: 15.0%\n  none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t9236\t12500.0\t0\t9236\n2\t3546\t3125.0\t0\t3546\n3\t827\t781.2\t0\t827\n4\t131\t195.3\t0\t131\n5\t36\t48.8\t0\t36\n6\t3\t12.2\t0\t3\n7\t2\t3.1\t0\t2\n9\t1\t0.2\t0\t0 1\n11\t2\t0.0\t1\t1 1\n15\t1\t0.0\t1\t1\n19\t1\t0.0\t1\t1\n42\t1\t0.0\t1\t0 1\n\n\nRUN STATISTICS FOR INPUT FILE: input_2.fastq.gz\n=============================================\n50000 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nValidate paired-end files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz\nfile_1: input_1_trimmed.fq.gz, file_2: input_2_trimmed.fq.gz\n\n\n>>>>> Now validing the length of the 2 paired-end infiles: input_1_trimmed.fq.gz and input_2_trimmed.fq.gz <<<<<\nWriting validated paired-end read 1 reads to input_1_val_1.fq.gz\nWriting validated paired-end read 2 reads to input_2_val_2.fq.gz\n\nTotal number of sequences analysed: 50000\n\nNumber of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1639 (3.28%)\n\nDeleting both intermediate output files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz\n\n====================================================================================================\n\n\ngzip: stdout: Broken pipe\n",
-                                                        "stdout": "1.13\n",
-                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1",
-                                                        "tool_stderr": "Path to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\n\n\nAUTO-DETECTING ADAPTER TYPE\n===========================\nAttempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq.gz <<)\n\nFound perfect matches for the following adapter sequences:\nAdapter type\tCount\tSequence\tSequences analysed\tPercentage\nIllumina\t2\tAGATCGGAAGAGC\t50000\t0.00\nsmallRNA\t0\tTGGAATTCTCGG\t50000\t0.00\nNextera\t0\tCTGTCTCTTATA\t50000\t0.00\nUsing Illumina adapter for trimming (count: 2). Second best hit was smallRNA (count: 0)\n\nWriting report to './input_1.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq.gz\nTrimming mode: paired-end\nTrim Galore version: 0.4.3\nCutadapt version: 1.13\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nWriting final adapter and quality trimmed output to input_1_trimmed.fq.gz\n\n\n  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq.gz <<< \nThis is cutadapt 1.13 with Python 3.6.1\nCommand line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz\nTrimming 1 adapter with at most 10.0% errors in single-end mode ...\nFinished in 0.85 s (17 us/read; 3.52 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed:                  50,000\nReads with adapters:                    14,011 (28.0%)\nReads written (passing filters):        50,000 (100.0%)\n\nTotal basepairs processed:     2,550,000 bp\nQuality-trimmed:                  34,012 bp (1.3%)\nTotal written (filtered):      2,495,795 bp (97.9%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14011 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n  A: 27.3%\n  C: 33.3%\n  G: 24.8%\n  T: 14.6%\n  none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t9379\t12500.0\t0\t9379\n2\t3646\t3125.0\t0\t3646\n3\t791\t781.2\t0\t791\n4\t134\t195.3\t0\t134\n5\t33\t48.8\t0\t33\n6\t9\t12.2\t0\t9\n7\t3\t3.1\t0\t3\n8\t1\t0.8\t0\t1\n9\t1\t0.2\t0\t0 1\n10\t3\t0.0\t1\t0 3\n11\t1\t0.0\t1\t1\n15\t1\t0.0\t1\t1\n16\t1\t0.0\t1\t0 1\n19\t1\t0.0\t1\t1\n27\t1\t0.0\t1\t0 1\n28\t1\t0.0\t1\t0 1\n32\t1\t0.0\t1\t0 1\n36\t1\t0.0\t1\t0 1\n43\t1\t0.0\t1\t0 1\n49\t1\t0.0\t1\t0 1\n50\t1\t0.0\t1\t0 1\n\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq.gz\n=============================================\n50000 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nWriting report to './input_2.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_2.fastq.gz\nTrimming mode: paired-end\nTrim Galore version: 0.4.3\nCutadapt version: 1.13\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nWriting final adapter and quality trimmed output to input_2_trimmed.fq.gz\n\n\n  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_2.fastq.gz <<< \nThis is cutadapt 1.13 with Python 3.6.1\nCommand line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_2.fastq.gz\nTrimming 1 adapter with at most 10.0% errors in single-end mode ...\nFinished in 0.91 s (18 us/read; 3.30 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed:                  50,000\nReads with adapters:                    13,787 (27.6%)\nReads written (passing filters):        50,000 (100.0%)\n\nTotal basepairs processed:     2,550,000 bp\nQuality-trimmed:                 120,340 bp (4.7%)\nTotal written (filtered):      2,410,008 bp (94.5%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13787 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n  A: 27.6%\n  C: 32.8%\n  G: 24.6%\n  T: 15.0%\n  none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t9236\t12500.0\t0\t9236\n2\t3546\t3125.0\t0\t3546\n3\t827\t781.2\t0\t827\n4\t131\t195.3\t0\t131\n5\t36\t48.8\t0\t36\n6\t3\t12.2\t0\t3\n7\t2\t3.1\t0\t2\n9\t1\t0.2\t0\t0 1\n11\t2\t0.0\t1\t1 1\n15\t1\t0.0\t1\t1\n19\t1\t0.0\t1\t1\n42\t1\t0.0\t1\t0 1\n\n\nRUN STATISTICS FOR INPUT FILE: input_2.fastq.gz\n=============================================\n50000 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nValidate paired-end files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz\nfile_1: input_1_trimmed.fq.gz, file_2: input_2_trimmed.fq.gz\n\n\n>>>>> Now validing the length of the 2 paired-end infiles: input_1_trimmed.fq.gz and input_2_trimmed.fq.gz <<<<<\nWriting validated paired-end read 1 reads to input_1_val_1.fq.gz\nWriting validated paired-end read 2 reads to input_2_val_2.fq.gz\n\nTotal number of sequences analysed: 50000\n\nNumber of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1639 (3.28%)\n\nDeleting both intermediate output files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz\n\n====================================================================================================\n\n\ngzip: stdout: Broken pipe\n",
-                                                        "tool_stdout": "1.13\n",
+                                                        "stderr": "",
+                                                        "stdout": "",
+                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3",
+                                                        "tool_stderr": "",
+                                                        "tool_stdout": "",
                                                         "traceback": null,
-                                                        "update_time": "2023-05-19T14:31:12.868610",
+                                                        "update_time": "2023-05-19T15:00:22.417608",
                                                         "user_email": "hxr@informatik.uni-freiburg.de"
                                                     }
                                                 ],
                                                 "model_class": "WorkflowInvocationStep",
-                                                "order_index": 4,
+                                                "order_index": 3,
                                                 "output_collections": {},
                                                 "outputs": {
-                                                    "trimmed_reads_pair1": {
-                                                        "id": "4838ba20a6d86765439b06bcf8677007",
+                                                    "out1": {
+                                                        "id": "4838ba20a6d8676528f2966e438993df",
                                                         "src": "hda",
-                                                        "uuid": "64981dba-44f7-4768-8b63-e63defba2ecf"
+                                                        "uuid": "5096388f-425a-42a1-b99e-4f0174665371"
                                                     },
-                                                    "trimmed_reads_pair2": {
-                                                        "id": "4838ba20a6d867658f72f66dd1d7e6cc",
+                                                    "report": {
+                                                        "id": "4838ba20a6d8676504b9c2c33c839b66",
                                                         "src": "hda",
-                                                        "uuid": "0764cea4-72ed-4a8c-93b2-88bd066afc4e"
+                                                        "uuid": "b9909c1d-09b1-47ec-9135-48915855c294"
                                                     }
                                                 },
                                                 "state": "scheduled",
                                                 "subworkflow": null,
                                                 "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-19T14:31:12.847743",
-                                                "workflow_step_id": "0cdaaf28f2c92138",
+                                                "update_time": "2023-05-19T15:00:21.982154",
+                                                "workflow_step_id": "17cb0d9cde915ee1",
                                                 "workflow_step_label": null,
-                                                "workflow_step_uuid": "ba2566a8-447f-45ed-98d1-1fd1a5ba6ab4"
+                                                "workflow_step_uuid": "ddd70253-72b8-4a5e-8025-56a579b01975"
                                             },
-                                            "5. Unnamed step": {
+                                            "4. Unnamed step": {
                                                 "action": null,
-                                                "id": "c06c2ed6eeedc161",
-                                                "job_id": "11ac94870d0bb33a0cd484c99b4bfb1e",
+                                                "id": "a380f2e9cccfcc65",
+                                                "job_id": "11ac94870d0bb33aae939aa0a3d41382",
                                                 "jobs": [
                                                     {
-                                                        "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&    mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/data/dnb08/galaxy_db/files/0/a/0/dataset_0a0a3867-f5f7-4690-9776-09274436e562.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_1' && ln -s '/data/dnb08/galaxy_db/files/7/1/8/dataset_718a2f6a-6747-4754-a9da-60a98a6c5957.dat' 'multiqc_WDir/fastqc_0/data_0/file_1/fastqc_data.txt' &&  multiqc multiqc_WDir --filename \"report\"",
+                                                        "command_line": "ln -s '/data/dnb08/galaxy_db/files/9/9/6/dataset_9968668a-3051-4e02-aa3d-4997838a0985.dat' 'GSM461178_untreat_paired_subset_2_fastq' && mkdir -p '/data/jwd05e/main/060/059/60059404/working/dataset_3bc9888e-ec3f-4ae0-b61c-db19dec8e43e_files' && fastqc --outdir '/data/jwd05e/main/060/059/60059404/working/dataset_3bc9888e-ec3f-4ae0-b61c-db19dec8e43e_files'    --quiet --extract  --kmers 7 -f 'fastq' 'GSM461178_untreat_paired_subset_2_fastq'  && cp '/data/jwd05e/main/060/059/60059404/working/dataset_3bc9888e-ec3f-4ae0-b61c-db19dec8e43e_files'/*/fastqc_data.txt output.txt && cp '/data/jwd05e/main/060/059/60059404/working/dataset_3bc9888e-ec3f-4ae0-b61c-db19dec8e43e_files'/*\\.html output.html",
                                                         "command_version": null,
-                                                        "create_time": "2023-05-19T14:30:12.574335",
-                                                        "dependencies": [],
-                                                        "exit_code": 0,
-                                                        "external_id": "43534360",
-                                                        "galaxy_version": "23.0",
-                                                        "history_id": "2e96b0bf6abd6b74",
-                                                        "id": "11ac94870d0bb33a0cd484c99b4bfb1e",
-                                                        "inputs": {
-                                                            "results_0|software_cond|output_0|input": {
-                                                                "id": "4838ba20a6d8676577d1d2d4d95b125f",
-                                                                "src": "hda",
-                                                                "uuid": "0a0a3867-f5f7-4690-9776-09274436e562"
-                                                            },
-                                                            "results_0|software_cond|output_0|input1": {
-                                                                "id": "4838ba20a6d8676577d1d2d4d95b125f",
-                                                                "src": "hda",
-                                                                "uuid": "0a0a3867-f5f7-4690-9776-09274436e562"
-                                                            },
-                                                            "results_0|software_cond|output_0|input2": {
-                                                                "id": "4838ba20a6d86765100e931edbfb8029",
-                                                                "src": "hda",
-                                                                "uuid": "718a2f6a-6747-4754-a9da-60a98a6c5957"
-                                                            }
-                                                        },
-                                                        "job_messages": [],
-                                                        "job_metrics": [
-                                                            {
-                                                                "name": "hostname",
-                                                                "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c125m425-4973.novalocal",
-                                                                "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c125m425-4973.novalocal"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_slots",
-                                                                "plugin": "core",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "Cores Allocated",
-                                                                "value": "1"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_memory_mb",
-                                                                "plugin": "core",
-                                                                "raw_value": "11673.0000000",
-                                                                "title": "Memory Allocated (MB)",
-                                                                "value": "11673"
-                                                            },
-                                                            {
-                                                                "name": "start_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684506732.0000000",
-                                                                "title": "Job Start Time",
-                                                                "value": "2023-05-19 16:32:12"
-                                                            },
-                                                            {
-                                                                "name": "end_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684506804.0000000",
-                                                                "title": "Job End Time",
-                                                                "value": "2023-05-19 16:33:24"
-                                                            },
-                                                            {
-                                                                "name": "runtime_seconds",
-                                                                "plugin": "core",
-                                                                "raw_value": "72.0000000",
-                                                                "title": "Job Runtime (Wall Clock)",
-                                                                "value": "1 minute"
-                                                            },
-                                                            {
-                                                                "name": "cpuacct.usage",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "11111220478.0000000",
-                                                                "title": "CPU Time",
-                                                                "value": "11.111220478 seconds"
-                                                            },
-                                                            {
-                                                                "name": "memory.failcnt",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Failed to allocate memory count",
-                                                                "value": 0.0
-                                                            },
-                                                            {
-                                                                "name": "memory.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "21474836480.0000000",
-                                                                "title": "Memory limit on cgroup (MEM)",
-                                                                "value": "20.0 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "246882304.0000000",
-                                                                "title": "Max memory usage (MEM)",
-                                                                "value": "235.4 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "9223372036854771712.0000000",
-                                                                "title": "Memory limit on cgroup (MEM+SWP)",
-                                                                "value": "8.0 EB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "246882304.0000000",
-                                                                "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "235.4 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.oom_kill_disable",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "OOM Control enabled",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.under_oom",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Was OOM Killer active?",
-                                                                "value": "No"
-                                                            },
+                                                        "create_time": "2023-05-19T14:59:03.488111",
+                                                        "dependencies": [
                                                             {
-                                                                "name": "memory.soft_limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Memory softlimit on cgroup",
-                                                                "value": "0 bytes"
+                                                                "cacheable": false,
+                                                                "dependency_resolver": {
+                                                                    "auto_init": true,
+                                                                    "auto_install": false,
+                                                                    "can_uninstall_dependencies": true,
+                                                                    "ensure_channels": "conda-forge,bioconda",
+                                                                    "model_class": "CondaDependencyResolver",
+                                                                    "prefix": "/usr/local/tools/_conda",
+                                                                    "read_only": false,
+                                                                    "resolver_type": "conda",
+                                                                    "resolves_simple_dependencies": true,
+                                                                    "use_local": false,
+                                                                    "versionless": false
+                                                                },
+                                                                "dependency_type": "conda",
+                                                                "environment_path": "/usr/local/tools/_conda/envs/__fastqc@0.11.8",
+                                                                "exact": true,
+                                                                "model_class": "MergedCondaDependency",
+                                                                "name": "fastqc",
+                                                                "version": "0.11.8"
                                                             }
                                                         ],
-                                                        "job_stderr": "",
-                                                        "job_stdout": "",
-                                                        "model_class": "Job",
-                                                        "output_collections": {
-                                                            "stats": {
-                                                                "id": "cfa32fe2043782fe",
-                                                                "src": "hdca"
-                                                            }
-                                                        },
-                                                        "outputs": {
-                                                            "__new_primary_file_stats|fastqc__": {
-                                                                "id": "4838ba20a6d86765af3f1d3773b3e6e6",
-                                                                "src": "hda",
-                                                                "uuid": "3b7d0c75-6916-4fe8-b043-2f548a0b6178"
-                                                            },
-                                                            "__new_primary_file_stats|general_stats__": {
-                                                                "id": "4838ba20a6d86765eeebdf0f28fa6046",
-                                                                "src": "hda",
-                                                                "uuid": "25a75644-bd77-40a5-b740-fbc4cf4b2873"
-                                                            },
-                                                            "__new_primary_file_stats|sources__": {
-                                                                "id": "4838ba20a6d8676552f11ea459caefac",
-                                                                "src": "hda",
-                                                                "uuid": "707ab880-1526-47de-be63-f6466c1857ff"
-                                                            },
-                                                            "html_report": {
-                                                                "id": "4838ba20a6d86765ec54819e54cbe660",
-                                                                "src": "hda",
-                                                                "uuid": "a7901748-d8a1-40f0-a656-40796763ae98"
-                                                            }
-                                                        },
-                                                        "params": {
-                                                            "__input_ext": "\"txt\"",
-                                                            "__workflow_invocation_uuid__": "\"9ef558e0f65111eda6f2001e67d2ec02\"",
-                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
-                                                            "comment": "\"\"",
-                                                            "dbkey": "\"?\"",
-                                                            "export": "false",
-                                                            "flat": "false",
-                                                            "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"input\": {\"values\": [{\"id\": 137415695, \"src\": \"hda\"}, {\"id\": 137415693, \"src\": \"hda\"}]}, \"type\": \"data\"}], \"software\": \"fastqc\"}}]",
-                                                            "saveLog": "false",
-                                                            "title": "\"\""
-                                                        },
-                                                        "state": "ok",
-                                                        "stderr": "[WARNING]         multiqc : MultiQC Version v1.14 now available!\n[INFO   ]         multiqc : This is MultiQC v1.9\n[INFO   ]         multiqc : Template    : default\n[INFO   ]         multiqc : Searching   : /data/jwd02f/main/060/058/60058037/working/multiqc_WDir\n[INFO   ]          fastqc : Found 2 reports\n[INFO   ]         multiqc : Compressing plot data\n[INFO   ]         multiqc : Report      : report.html\n[INFO   ]         multiqc : Data        : report_data\n[INFO   ]         multiqc : MultiQC complete\n",
-                                                        "stdout": "",
-                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9",
-                                                        "tool_stderr": "[WARNING]         multiqc : MultiQC Version v1.14 now available!\n[INFO   ]         multiqc : This is MultiQC v1.9\n[INFO   ]         multiqc : Template    : default\n[INFO   ]         multiqc : Searching   : /data/jwd02f/main/060/058/60058037/working/multiqc_WDir\n[INFO   ]          fastqc : Found 2 reports\n[INFO   ]         multiqc : Compressing plot data\n[INFO   ]         multiqc : Report      : report.html\n[INFO   ]         multiqc : Data        : report_data\n[INFO   ]         multiqc : MultiQC complete\n",
-                                                        "tool_stdout": "",
-                                                        "traceback": null,
-                                                        "update_time": "2023-05-19T14:33:25.724813",
-                                                        "user_email": "hxr@informatik.uni-freiburg.de"
-                                                    }
-                                                ],
-                                                "model_class": "WorkflowInvocationStep",
-                                                "order_index": 5,
-                                                "output_collections": {
-                                                    "stats": {
-                                                        "id": "cfa32fe2043782fe",
-                                                        "src": "hdca"
-                                                    }
-                                                },
-                                                "outputs": {
-                                                    "html_report": {
-                                                        "id": "4838ba20a6d86765ec54819e54cbe660",
-                                                        "src": "hda",
-                                                        "uuid": "a7901748-d8a1-40f0-a656-40796763ae98"
-                                                    }
-                                                },
-                                                "state": "scheduled",
-                                                "subworkflow": null,
-                                                "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-19T14:33:25.705737",
-                                                "workflow_step_id": "076bed37af53db03",
-                                                "workflow_step_label": null,
-                                                "workflow_step_uuid": "0f4492d6-2e63-466f-98e7-9f2921d4c039"
-                                            },
-                                            "6. Unnamed step": {
-                                                "action": null,
-                                                "id": "ac35c3e9e0f36f77",
-                                                "job_id": "11ac94870d0bb33a600088ef54ecdb6d",
-                                                "jobs": [
-                                                    {
-                                                        "command_line": "set -o | grep -q pipefail && set -o pipefail;   ln -f -s '/data/dnb08/galaxy_db/files/6/4/9/dataset_64981dba-44f7-4768-8b63-e63defba2ecf.dat' input_f.fastq.gz &&  ln -f -s '/data/dnb08/galaxy_db/files/0/7/6/dataset_0764cea4-72ed-4a8c-93b2-88bd066afc4e.dat' input_r.fastq.gz &&   bowtie2  -p ${GALAXY_SLOTS:-4}  -x '/data/db/reference_genomes/mm10/bowtie2_index/mm10'   -1 'input_f.fastq.gz' -2 'input_r.fastq.gz'                2> '/data/jwd02f/main/060/058/60058038/outputs/galaxy_dataset_b1360a80-c9bb-4fb9-ac3e-00aac0213e44.dat'  | samtools sort --no-PG -@${GALAXY_SLOTS:-2} -T \"${TMPDIR:-.}\" -O bam -o '/data/jwd02f/main/060/058/60058038/outputs/galaxy_dataset_014de858-c517-4e2a-a491-c14c99491b03.dat'",
-                                                        "command_version": "/usr/local/tools/_conda/envs/mulled-v1-2c9d0d73d81f016cd458c97e185f638410841f3ecf7ae79158d90e0d58249513/bin/bowtie2-align-s version 2.4.2\n64-bit\nBuilt on default-bf91a638-95fa-4b77-97c5-abccd9855c3e\nMon Nov  2 17:36:36 UTC 2020\nCompiler: gcc version 7.5.0 (crosstool-NG 1.24.0.131_87df0e6_dirty) \nOptions: -O3 -msse2 -funroll-loops -g3 -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/tools/_conda/envs/mulled-v1-2c9d0d73d81f016cd458c97e185f638410841f3ecf7ae79158d90e0d58249513/include -fdebug-prefix-map=/opt/conda/conda-bld/bowtie2_1604337828546/work=/usr/local/src/conda/bowtie2-2.4.2 -fdebug-prefix-map=/usr/local/tools/_conda/envs/mulled-v1-2c9d0d73d81f016cd458c97e185f638410841f3ecf7ae79158d90e0d58249513=/usr/local/src/conda-prefix -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}",
-                                                        "create_time": "2023-05-19T14:30:12.695266",
-                                                        "dependencies": [],
                                                         "exit_code": 0,
-                                                        "external_id": "43534339",
+                                                        "external_id": "43535386",
                                                         "galaxy_version": "23.0",
-                                                        "history_id": "2e96b0bf6abd6b74",
-                                                        "id": "11ac94870d0bb33a600088ef54ecdb6d",
+                                                        "history_id": "2f1f9fa04aab9b59",
+                                                        "id": "11ac94870d0bb33aae939aa0a3d41382",
                                                         "inputs": {
-                                                            "input_1": {
-                                                                "id": "4838ba20a6d86765439b06bcf8677007",
-                                                                "src": "hda",
-                                                                "uuid": "64981dba-44f7-4768-8b63-e63defba2ecf"
-                                                            },
-                                                            "input_2": {
-                                                                "id": "4838ba20a6d867658f72f66dd1d7e6cc",
+                                                            "input_file": {
+                                                                "id": "4838ba20a6d867656914ebcc68e736a5",
                                                                 "src": "hda",
-                                                                "uuid": "0764cea4-72ed-4a8c-93b2-88bd066afc4e"
+                                                                "uuid": "9968668a-3051-4e02-aa3d-4997838a0985"
                                                             }
                                                         },
                                                         "job_messages": [],
@@ -209441,9 +211325,9 @@
                                                             {
                                                                 "name": "hostname",
                                                                 "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c125m425-4973.novalocal",
+                                                                "raw_value": "vgcnbwc-worker-c125m425-1589.novalocal",
                                                                 "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c125m425-4973.novalocal"
+                                                                "value": "vgcnbwc-worker-c125m425-1589.novalocal"
                                                             },
                                                             {
                                                                 "name": "galaxy_slots",
@@ -209455,37 +211339,37 @@
                                                             {
                                                                 "name": "galaxy_memory_mb",
                                                                 "plugin": "core",
-                                                                "raw_value": "20480.0000000",
+                                                                "raw_value": "31129.0000000",
                                                                 "title": "Memory Allocated (MB)",
-                                                                "value": "20480"
+                                                                "value": "31129"
                                                             },
                                                             {
                                                                 "name": "start_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684506680.0000000",
+                                                                "raw_value": "1684508676.0000000",
                                                                 "title": "Job Start Time",
-                                                                "value": "2023-05-19 16:31:20"
+                                                                "value": "2023-05-19 17:04:36"
                                                             },
                                                             {
                                                                 "name": "end_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684506731.0000000",
+                                                                "raw_value": "1684508692.0000000",
                                                                 "title": "Job End Time",
-                                                                "value": "2023-05-19 16:32:11"
+                                                                "value": "2023-05-19 17:04:52"
                                                             },
                                                             {
                                                                 "name": "runtime_seconds",
                                                                 "plugin": "core",
-                                                                "raw_value": "51.0000000",
+                                                                "raw_value": "16.0000000",
                                                                 "title": "Job Runtime (Wall Clock)",
-                                                                "value": "51 seconds"
+                                                                "value": "16 seconds"
                                                             },
                                                             {
                                                                 "name": "cpuacct.usage",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "36889533091.0000000",
+                                                                "raw_value": "13539752576.0000000",
                                                                 "title": "CPU Time",
-                                                                "value": "36.889533091 seconds"
+                                                                "value": "13.539752576 seconds"
                                                             },
                                                             {
                                                                 "name": "memory.failcnt",
@@ -209497,16 +211381,16 @@
                                                             {
                                                                 "name": "memory.limit_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "21474836480.0000000",
+                                                                "raw_value": "32749125632.0000000",
                                                                 "title": "Memory limit on cgroup (MEM)",
-                                                                "value": "20.0 GB"
+                                                                "value": "30.5 GB"
                                                             },
                                                             {
                                                                 "name": "memory.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "6388858880.0000000",
+                                                                "raw_value": "411770880.0000000",
                                                                 "title": "Max memory usage (MEM)",
-                                                                "value": "6.0 GB"
+                                                                "value": "392.7 MB"
                                                             },
                                                             {
                                                                 "name": "memory.memsw.limit_in_bytes",
@@ -209518,9 +211402,9 @@
                                                             {
                                                                 "name": "memory.memsw.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "6388858880.0000000",
+                                                                "raw_value": "411770880.0000000",
                                                                 "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "6.0 GB"
+                                                                "value": "392.7 MB"
                                                             },
                                                             {
                                                                 "name": "memory.oom_control.oom_kill_disable",
@@ -209549,72 +211433,72 @@
                                                         "model_class": "Job",
                                                         "output_collections": {},
                                                         "outputs": {
-                                                            "mapping_stats": {
-                                                                "id": "4838ba20a6d867656446378f71ad820b",
+                                                            "html_file": {
+                                                                "id": "4838ba20a6d867650e70120b79b974b3",
                                                                 "src": "hda",
-                                                                "uuid": "b1360a80-c9bb-4fb9-ac3e-00aac0213e44"
+                                                                "uuid": "3bc9888e-ec3f-4ae0-b61c-db19dec8e43e"
                                                             },
-                                                            "output": {
-                                                                "id": "4838ba20a6d86765af291d8ab2af5e96",
+                                                            "text_file": {
+                                                                "id": "4838ba20a6d867656a6422c26474bdc5",
                                                                 "src": "hda",
-                                                                "uuid": "014de858-c517-4e2a-a491-c14c99491b03"
+                                                                "uuid": "edecc2ea-fa52-4947-9c41-f5956870688a"
                                                             }
                                                         },
                                                         "params": {
-                                                            "__input_ext": "\"input\"",
-                                                            "__workflow_invocation_uuid__": "\"9ef558e0f65111eda6f2001e67d2ec02\"",
-                                                            "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"simple\", \"presets\": \"no_presets\"}",
+                                                            "__input_ext": "\"fastqsanger\"",
+                                                            "__workflow_invocation_uuid__": "\"a085c588f65511ed82b7001e67d2ec02\"",
+                                                            "adapters": null,
                                                             "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
+                                                            "contaminants": null,
                                                             "dbkey": "\"?\"",
-                                                            "library": "{\"__current_case__\": 1, \"aligned_file\": false, \"input_1\": {\"values\": [{\"id\": 137415696, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 137415697, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 1, \"paired_options_selector\": \"no\"}, \"type\": \"paired\", \"unaligned_file\": false}",
-                                                            "reference_genome": "{\"__current_case__\": 0, \"index\": \"mm10\", \"source\": \"indexed\"}",
-                                                            "rg": "{\"__current_case__\": 3, \"rg_selector\": \"do_not_set\"}",
-                                                            "sam_options": "{\"__current_case__\": 1, \"sam_options_selector\": \"no\"}",
-                                                            "save_mapping_stats": "true"
+                                                            "kmers": "\"7\"",
+                                                            "limits": null,
+                                                            "min_length": null,
+                                                            "nogroup": "false"
                                                         },
                                                         "state": "ok",
-                                                        "stderr": "[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n",
+                                                        "stderr": "",
                                                         "stdout": "",
-                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0",
-                                                        "tool_stderr": "[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n",
+                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                                                        "tool_stderr": "",
                                                         "tool_stdout": "",
                                                         "traceback": null,
-                                                        "update_time": "2023-05-19T14:32:13.080341",
+                                                        "update_time": "2023-05-19T15:04:54.529461",
                                                         "user_email": "hxr@informatik.uni-freiburg.de"
                                                     }
                                                 ],
                                                 "model_class": "WorkflowInvocationStep",
-                                                "order_index": 6,
+                                                "order_index": 4,
                                                 "output_collections": {},
                                                 "outputs": {
-                                                    "mapping_stats": {
-                                                        "id": "4838ba20a6d867656446378f71ad820b",
+                                                    "html_file": {
+                                                        "id": "4838ba20a6d867650e70120b79b974b3",
                                                         "src": "hda",
-                                                        "uuid": "b1360a80-c9bb-4fb9-ac3e-00aac0213e44"
+                                                        "uuid": "3bc9888e-ec3f-4ae0-b61c-db19dec8e43e"
                                                     },
-                                                    "output": {
-                                                        "id": "4838ba20a6d86765af291d8ab2af5e96",
+                                                    "text_file": {
+                                                        "id": "4838ba20a6d867656a6422c26474bdc5",
                                                         "src": "hda",
-                                                        "uuid": "014de858-c517-4e2a-a491-c14c99491b03"
+                                                        "uuid": "edecc2ea-fa52-4947-9c41-f5956870688a"
                                                     }
                                                 },
                                                 "state": "scheduled",
                                                 "subworkflow": null,
                                                 "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-19T14:32:13.062698",
-                                                "workflow_step_id": "de91ab1f4d5a7cd4",
+                                                "update_time": "2023-05-19T15:04:54.499181",
+                                                "workflow_step_id": "fc590094641a1ae9",
                                                 "workflow_step_label": null,
-                                                "workflow_step_uuid": "2d04b2e4-a2fe-4ce6-8894-5a752031171b"
+                                                "workflow_step_uuid": "f48fa351-4a73-4daa-b993-2210274ae84d"
                                             },
-                                            "7. Unnamed step": {
+                                            "5. Unnamed step": {
                                                 "action": null,
-                                                "id": "83d212dd0df7f7f8",
-                                                "job_id": "11ac94870d0bb33a8145f91d85cf7ba7",
+                                                "id": "6a0711aa69933475",
+                                                "job_id": "11ac94870d0bb33abd6fe235967051f6",
                                                 "jobs": [
                                                     {
-                                                        "command_line": "samtools stats '/data/dnb08/galaxy_db/files/0/1/4/dataset_014de858-c517-4e2a-a491-c14c99491b03.dat' --coverage 1,1000,1    --GC-depth 20000.0 --insert-size 8000    --most-inserts 0.99 --trim-quality 0  --ref-seq '/data/db/reference_genomes/mm10/seq/mm10.fa' > '/data/jwd01/main/060/058/60058039/outputs/galaxy_dataset_9de6afbf-b266-439b-b405-215a8d1d90f4.dat'",
-                                                        "command_version": "Version: 1.3.1 (using htslib 1.3.1)",
-                                                        "create_time": "2023-05-19T14:30:12.801865",
+                                                        "command_line": "ln -f -s '/data/dnb08/galaxy_db/files/3/8/3/dataset_3835c7cb-1707-4e6f-85d2-6f1ad5c31bc4.dat' 'GSM461178_untreat_paired_subset_1_fastq.fq' &&  ln -f -s '/data/dnb08/galaxy_db/files/9/9/6/dataset_9968668a-3051-4e02-aa3d-4997838a0985.dat' 'GSM461178_untreat_paired_subset_2_fastq.fq' &&   cutadapt  -j ${GALAXY_SLOTS:-1}                  --output='out1.fq' --paired-output='out2.fq'  --error-rate=0.1 --times=1 --overlap=3         --minimum-length=20 --pair-filter=any   --quality-cutoff=20   'GSM461178_untreat_paired_subset_1_fastq.fq' 'GSM461178_untreat_paired_subset_2_fastq.fq'  > report.txt",
+                                                        "command_version": "1.16",
+                                                        "create_time": "2023-05-19T14:59:03.590819",
                                                         "dependencies": [
                                                             {
                                                                 "cacheable": false,
@@ -209632,211 +211516,28 @@
                                                                     "versionless": false
                                                                 },
                                                                 "dependency_type": "conda",
-                                                                "environment_path": "/usr/local/tools/_conda/envs/__samtools@1.3.1",
+                                                                "environment_path": "/usr/local/tools/_conda/envs/__cutadapt@1.16",
                                                                 "exact": true,
                                                                 "model_class": "MergedCondaDependency",
-                                                                "name": "samtools",
-                                                                "version": "1.3.1"
+                                                                "name": "cutadapt",
+                                                                "version": "1.16"
                                                             }
                                                         ],
                                                         "exit_code": 0,
-                                                        "external_id": "43534364",
+                                                        "external_id": "43535388",
                                                         "galaxy_version": "23.0",
-                                                        "history_id": "2e96b0bf6abd6b74",
-                                                        "id": "11ac94870d0bb33a8145f91d85cf7ba7",
+                                                        "history_id": "2f1f9fa04aab9b59",
+                                                        "id": "11ac94870d0bb33abd6fe235967051f6",
                                                         "inputs": {
-                                                            "input_file": {
-                                                                "id": "4838ba20a6d86765af291d8ab2af5e96",
+                                                            "input_1": {
+                                                                "id": "4838ba20a6d86765ff25d30589db09fe",
                                                                 "src": "hda",
-                                                                "uuid": "014de858-c517-4e2a-a491-c14c99491b03"
-                                                            }
-                                                        },
-                                                        "job_messages": [],
-                                                        "job_metrics": [
-                                                            {
-                                                                "name": "hostname",
-                                                                "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c28m475-1207.novalocal",
-                                                                "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c28m475-1207.novalocal"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_slots",
-                                                                "plugin": "core",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "Cores Allocated",
-                                                                "value": "1"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_memory_mb",
-                                                                "plugin": "core",
-                                                                "raw_value": "3891.0000000",
-                                                                "title": "Memory Allocated (MB)",
-                                                                "value": "3891"
-                                                            },
-                                                            {
-                                                                "name": "start_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684506752.0000000",
-                                                                "title": "Job Start Time",
-                                                                "value": "2023-05-19 16:32:32"
-                                                            },
-                                                            {
-                                                                "name": "end_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684506806.0000000",
-                                                                "title": "Job End Time",
-                                                                "value": "2023-05-19 16:33:26"
-                                                            },
-                                                            {
-                                                                "name": "runtime_seconds",
-                                                                "plugin": "core",
-                                                                "raw_value": "54.0000000",
-                                                                "title": "Job Runtime (Wall Clock)",
-                                                                "value": "54 seconds"
-                                                            },
-                                                            {
-                                                                "name": "cpuacct.usage",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "17841669661.0000000",
-                                                                "title": "CPU Time",
-                                                                "value": "17.841669661 seconds"
-                                                            },
-                                                            {
-                                                                "name": "memory.failcnt",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Failed to allocate memory count",
-                                                                "value": 0.0
-                                                            },
-                                                            {
-                                                                "name": "memory.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "4160749568.0000000",
-                                                                "title": "Memory limit on cgroup (MEM)",
-                                                                "value": "3.9 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "1402118144.0000000",
-                                                                "title": "Max memory usage (MEM)",
-                                                                "value": "1.3 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "9223372036854771712.0000000",
-                                                                "title": "Memory limit on cgroup (MEM+SWP)",
-                                                                "value": "8.0 EB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "1402118144.0000000",
-                                                                "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "1.3 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.oom_kill_disable",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "OOM Control enabled",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.under_oom",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Was OOM Killer active?",
-                                                                "value": "No"
+                                                                "uuid": "3835c7cb-1707-4e6f-85d2-6f1ad5c31bc4"
                                                             },
-                                                            {
-                                                                "name": "memory.soft_limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Memory softlimit on cgroup",
-                                                                "value": "0 bytes"
-                                                            }
-                                                        ],
-                                                        "job_stderr": "",
-                                                        "job_stdout": "",
-                                                        "model_class": "Job",
-                                                        "output_collections": {},
-                                                        "outputs": {
-                                                            "output": {
-                                                                "id": "4838ba20a6d8676528f7337e9709f706",
-                                                                "src": "hda",
-                                                                "uuid": "9de6afbf-b266-439b-b405-215a8d1d90f4"
-                                                            }
-                                                        },
-                                                        "params": {
-                                                            "__input_ext": "\"bam\"",
-                                                            "__workflow_invocation_uuid__": "\"9ef558e0f65111eda6f2001e67d2ec02\"",
-                                                            "chromInfo": "\"/data/db/data_managers/mm10/len/mm10.len\"",
-                                                            "coverage_max": "\"1000\"",
-                                                            "coverage_min": "\"1\"",
-                                                            "coverage_step": "\"1\"",
-                                                            "dbkey": "\"mm10\"",
-                                                            "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}",
-                                                            "gc_depth": "\"20000.0\"",
-                                                            "insert_size": "\"8000\"",
-                                                            "most_inserts": "\"0.99\"",
-                                                            "read_length": null,
-                                                            "remove_dups": "false",
-                                                            "split_output": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}",
-                                                            "trim_quality": "\"0\"",
-                                                            "use_reference": "{\"__current_case__\": 0, \"reference_source\": {\"__current_case__\": 0, \"ref_file\": \"mm10full\", \"reference_source_selector\": \"cached\"}, \"use_ref_selector\": \"yes\"}"
-                                                        },
-                                                        "state": "ok",
-                                                        "stderr": "",
-                                                        "stdout": "",
-                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
-                                                        "tool_stderr": "",
-                                                        "tool_stdout": "",
-                                                        "traceback": null,
-                                                        "update_time": "2023-05-19T14:33:37.050310",
-                                                        "user_email": "hxr@informatik.uni-freiburg.de"
-                                                    }
-                                                ],
-                                                "model_class": "WorkflowInvocationStep",
-                                                "order_index": 7,
-                                                "output_collections": {},
-                                                "outputs": {
-                                                    "output": {
-                                                        "id": "4838ba20a6d8676528f7337e9709f706",
-                                                        "src": "hda",
-                                                        "uuid": "9de6afbf-b266-439b-b405-215a8d1d90f4"
-                                                    }
-                                                },
-                                                "state": "scheduled",
-                                                "subworkflow": null,
-                                                "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-19T14:33:36.956022",
-                                                "workflow_step_id": "74a208880456b021",
-                                                "workflow_step_label": null,
-                                                "workflow_step_uuid": "898dd71d-9b58-4286-a6ae-5403cb284341"
-                                            },
-                                            "8. Unnamed step": {
-                                                "action": null,
-                                                "id": "53b676dcfcf6d669",
-                                                "job_id": "11ac94870d0bb33a4dcd57b031359dae",
-                                                "jobs": [
-                                                    {
-                                                        "command_line": "cp '/data/jwd05e/main/060/058/60058040/configs/tmpr1btgj1_' '/data/jwd05e/main/060/058/60058040/outputs/galaxy_dataset_b3362212-c40a-470a-b0e0-89a4c7bc6d26.dat' && ln -s '/data/dnb08/galaxy_db/files/0/1/4/dataset_014de858-c517-4e2a-a491-c14c99491b03.dat' localbam.bam && ln -s '/data/dnb08/galaxy_db/files/_metadata_files/3/b/6/metadata_3b6f911b-633e-41e4-a35b-86b3615b2257.dat' localbam.bam.bai && cat '/data/jwd05e/main/060/058/60058040/configs/tmpr1btgj1_' && bamtools filter -script '/data/jwd05e/main/060/058/60058040/configs/tmpr1btgj1_' -in localbam.bam -out '/data/jwd05e/main/060/058/60058040/outputs/galaxy_dataset_11b4a85c-d4af-4e9d-9890-63e2517ff346.dat'",
-                                                        "command_version": null,
-                                                        "create_time": "2023-05-19T14:30:12.913255",
-                                                        "dependencies": [],
-                                                        "exit_code": 0,
-                                                        "external_id": "43534362",
-                                                        "galaxy_version": "23.0",
-                                                        "history_id": "2e96b0bf6abd6b74",
-                                                        "id": "11ac94870d0bb33a4dcd57b031359dae",
-                                                        "inputs": {
-                                                            "input_bam": {
-                                                                "id": "4838ba20a6d86765af291d8ab2af5e96",
+                                                            "input_2": {
+                                                                "id": "4838ba20a6d867656914ebcc68e736a5",
                                                                 "src": "hda",
-                                                                "uuid": "014de858-c517-4e2a-a491-c14c99491b03"
+                                                                "uuid": "9968668a-3051-4e02-aa3d-4997838a0985"
                                                             }
                                                         },
                                                         "job_messages": [],
@@ -209844,51 +211545,51 @@
                                                             {
                                                                 "name": "hostname",
                                                                 "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c36m225-7327.novalocal",
+                                                                "raw_value": "vgcnbwc-worker-c125m425-6547.novalocal",
                                                                 "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c36m225-7327.novalocal"
+                                                                "value": "vgcnbwc-worker-c125m425-6547.novalocal"
                                                             },
                                                             {
                                                                 "name": "galaxy_slots",
                                                                 "plugin": "core",
-                                                                "raw_value": "1.0000000",
+                                                                "raw_value": "5.0000000",
                                                                 "title": "Cores Allocated",
-                                                                "value": "1"
+                                                                "value": "5"
                                                             },
                                                             {
                                                                 "name": "galaxy_memory_mb",
                                                                 "plugin": "core",
-                                                                "raw_value": "3891.0000000",
+                                                                "raw_value": "19456.0000000",
                                                                 "title": "Memory Allocated (MB)",
-                                                                "value": "3891"
+                                                                "value": "19456"
                                                             },
                                                             {
                                                                 "name": "start_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684506749.0000000",
+                                                                "raw_value": "1684508356.0000000",
                                                                 "title": "Job Start Time",
-                                                                "value": "2023-05-19 16:32:29"
+                                                                "value": "2023-05-19 16:59:16"
                                                             },
                                                             {
                                                                 "name": "end_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684506773.0000000",
+                                                                "raw_value": "1684508381.0000000",
                                                                 "title": "Job End Time",
-                                                                "value": "2023-05-19 16:32:53"
+                                                                "value": "2023-05-19 16:59:41"
                                                             },
                                                             {
                                                                 "name": "runtime_seconds",
                                                                 "plugin": "core",
-                                                                "raw_value": "24.0000000",
+                                                                "raw_value": "25.0000000",
                                                                 "title": "Job Runtime (Wall Clock)",
-                                                                "value": "24 seconds"
+                                                                "value": "25 seconds"
                                                             },
                                                             {
                                                                 "name": "cpuacct.usage",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "13735913869.0000000",
+                                                                "raw_value": "8873728303.0000000",
                                                                 "title": "CPU Time",
-                                                                "value": "13.735913869 seconds"
+                                                                "value": "8.873728303 seconds"
                                                             },
                                                             {
                                                                 "name": "memory.failcnt",
@@ -209900,16 +211601,16 @@
                                                             {
                                                                 "name": "memory.limit_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "4160749568.0000000",
+                                                                "raw_value": "20401094656.0000000",
                                                                 "title": "Memory limit on cgroup (MEM)",
-                                                                "value": "3.9 GB"
+                                                                "value": "19.0 GB"
                                                             },
                                                             {
                                                                 "name": "memory.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "218013696.0000000",
+                                                                "raw_value": "362237952.0000000",
                                                                 "title": "Max memory usage (MEM)",
-                                                                "value": "207.9 MB"
+                                                                "value": "345.5 MB"
                                                             },
                                                             {
                                                                 "name": "memory.memsw.limit_in_bytes",
@@ -209921,9 +211622,9 @@
                                                             {
                                                                 "name": "memory.memsw.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "218013696.0000000",
+                                                                "raw_value": "362237952.0000000",
                                                                 "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "207.9 MB"
+                                                                "value": "345.5 MB"
                                                             },
                                                             {
                                                                 "name": "memory.oom_control.oom_kill_disable",
@@ -209952,79 +211653,125 @@
                                                         "model_class": "Job",
                                                         "output_collections": {},
                                                         "outputs": {
-                                                            "out_file1": {
-                                                                "id": "4838ba20a6d8676586fc63a32e96cd1a",
+                                                            "out1": {
+                                                                "id": "4838ba20a6d867658b181ea162b2bff2",
                                                                 "src": "hda",
-                                                                "uuid": "11b4a85c-d4af-4e9d-9890-63e2517ff346"
+                                                                "uuid": "5647f1a7-5cfe-4e7e-8a12-733901cbbc2f"
                                                             },
-                                                            "out_file2": {
-                                                                "id": "4838ba20a6d86765332d056e72acf04a",
+                                                            "out2": {
+                                                                "id": "4838ba20a6d8676511267a23c1bb707d",
                                                                 "src": "hda",
-                                                                "uuid": "b3362212-c40a-470a-b0e0-89a4c7bc6d26"
+                                                                "uuid": "7936d330-0e1e-43d9-abc8-e01e2e8ce871"
+                                                            },
+                                                            "report": {
+                                                                "id": "4838ba20a6d86765b7823a727e8a67cd",
+                                                                "src": "hda",
+                                                                "uuid": "d3748a3d-cb92-4c98-a590-d687c708ddc8"
                                                             }
                                                         },
                                                         "params": {
-                                                            "__input_ext": "\"bam\"",
-                                                            "__workflow_invocation_uuid__": "\"9ef558e0f65111eda6f2001e67d2ec02\"",
-                                                            "chromInfo": "\"/data/db/data_managers/mm10/len/mm10.len\"",
-                                                            "conditions": "[{\"__index__\": 0, \"filters\": [{\"__index__\": 0, \"bam_property\": {\"__current_case__\": 14, \"bam_property_selector\": \"mapQuality\", \"bam_property_value\": \">=20\"}}]}]",
-                                                            "dbkey": "\"mm10\"",
-                                                            "rule_configuration": "{\"__current_case__\": 0, \"rules_selector\": false}"
+                                                            "__input_ext": "\"input\"",
+                                                            "__workflow_invocation_uuid__": "\"a085c588f65511ed82b7001e67d2ec02\"",
+                                                            "adapter_options": "{\"count\": \"1\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"overlap\": \"3\"}",
+                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
+                                                            "dbkey": "\"?\"",
+                                                            "filter_options": "{\"discard\": false, \"discard_untrimmed\": false, \"mask_adapter\": false, \"max\": \"0\", \"max_n\": null, \"min\": \"20\", \"no_trim\": false, \"pair_filter\": \"any\"}",
+                                                            "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 137417465, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 137417509, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\", \"front_adapters\": []}, \"r2\": {\"adapters2\": [], \"anywhere_adapters2\": [], \"cut2\": \"0\", \"front_adapters2\": []}, \"type\": \"paired\"}",
+                                                            "output_options": "{\"info_file\": false, \"report\": true, \"rest_file\": false, \"too_long_file\": false, \"too_short_file\": false, \"untrimmed_file\": false, \"wildcard_file\": false}",
+                                                            "read_mod_options": "{\"length\": \"0\", \"length_tag\": \"\", \"nextseq_trim\": \"0\", \"prefix\": \"\", \"quality_cutoff\": \"20\", \"strip_suffix\": \"\", \"suffix\": \"\", \"trim_n\": false}"
                                                         },
                                                         "state": "ok",
                                                         "stderr": "",
-                                                        "stdout": "\n\n\n        \n{\n    \"filters\": [\n        {\n            \"id\": \"1\",\n            \"mapQuality\": \">=20\"\n        }\n    ]\n}\n\n        ",
-                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
+                                                        "stdout": "",
+                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3",
                                                         "tool_stderr": "",
-                                                        "tool_stdout": "\n\n\n        \n{\n    \"filters\": [\n        {\n            \"id\": \"1\",\n            \"mapQuality\": \">=20\"\n        }\n    ]\n}\n\n        ",
+                                                        "tool_stdout": "",
                                                         "traceback": null,
-                                                        "update_time": "2023-05-19T14:32:55.076647",
+                                                        "update_time": "2023-05-19T14:59:42.633522",
                                                         "user_email": "hxr@informatik.uni-freiburg.de"
                                                     }
                                                 ],
                                                 "model_class": "WorkflowInvocationStep",
-                                                "order_index": 8,
+                                                "order_index": 5,
                                                 "output_collections": {},
                                                 "outputs": {
-                                                    "out_file1": {
-                                                        "id": "4838ba20a6d8676586fc63a32e96cd1a",
+                                                    "out1": {
+                                                        "id": "4838ba20a6d867658b181ea162b2bff2",
                                                         "src": "hda",
-                                                        "uuid": "11b4a85c-d4af-4e9d-9890-63e2517ff346"
+                                                        "uuid": "5647f1a7-5cfe-4e7e-8a12-733901cbbc2f"
                                                     },
-                                                    "out_file2": {
-                                                        "id": "4838ba20a6d86765332d056e72acf04a",
+                                                    "out2": {
+                                                        "id": "4838ba20a6d8676511267a23c1bb707d",
                                                         "src": "hda",
-                                                        "uuid": "b3362212-c40a-470a-b0e0-89a4c7bc6d26"
+                                                        "uuid": "7936d330-0e1e-43d9-abc8-e01e2e8ce871"
+                                                    },
+                                                    "report": {
+                                                        "id": "4838ba20a6d86765b7823a727e8a67cd",
+                                                        "src": "hda",
+                                                        "uuid": "d3748a3d-cb92-4c98-a590-d687c708ddc8"
                                                     }
                                                 },
                                                 "state": "scheduled",
                                                 "subworkflow": null,
                                                 "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-19T14:32:55.059256",
-                                                "workflow_step_id": "4964c8b8ced0b316",
+                                                "update_time": "2023-05-19T14:59:42.614406",
+                                                "workflow_step_id": "1c99f44f251d0c5a",
                                                 "workflow_step_label": null,
-                                                "workflow_step_uuid": "9fca8663-299c-4a3e-9d21-c3f5b89936c9"
+                                                "workflow_step_uuid": "5ff1e523-c42b-42cd-8857-84d7d83802f8"
                                             },
-                                            "9. Unnamed step": {
+                                            "6. Unnamed step": {
                                                 "action": null,
-                                                "id": "d10aa175eaaa29cb",
-                                                "job_id": "11ac94870d0bb33a4d625b480e3a88e5",
+                                                "id": "c0e9eb97be074ab9",
+                                                "job_id": "11ac94870d0bb33a3e4f5384f33fb7c3",
                                                 "jobs": [
                                                     {
-                                                        "command_line": "samtools stats '/data/dnb08/galaxy_db/files/1/1/b/dataset_11b4a85c-d4af-4e9d-9890-63e2517ff346.dat' --coverage 1,1000,1    --GC-depth 20000.0 --insert-size 8000    --most-inserts 0.99 --trim-quality 0  --ref-seq '/data/db/reference_genomes/mm10/seq/mm10.fa' > '/data/jwd05e/main/060/058/60058041/outputs/galaxy_dataset_94cccd62-deee-4ce5-8952-739603b253f7.dat'",
-                                                        "command_version": "Version: 1.3.1 (using htslib 1.3.1)",
-                                                        "create_time": "2023-05-19T14:30:13.010837",
-                                                        "dependencies": [],
+                                                        "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&    mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/data/dnb08/galaxy_db/files/8/a/a/dataset_8aadb0d6-4752-43b3-9a70-b58359fe1659.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_1' && ln -s '/data/dnb08/galaxy_db/files/e/d/e/dataset_edecc2ea-fa52-4947-9c41-f5956870688a.dat' 'multiqc_WDir/fastqc_0/data_0/file_1/fastqc_data.txt' &&  multiqc multiqc_WDir --filename \"report\"",
+                                                        "command_version": null,
+                                                        "create_time": "2023-05-19T14:59:03.693709",
+                                                        "dependencies": [
+                                                            {
+                                                                "cacheable": false,
+                                                                "dependency_resolver": {
+                                                                    "auto_init": true,
+                                                                    "auto_install": false,
+                                                                    "can_uninstall_dependencies": true,
+                                                                    "ensure_channels": "conda-forge,bioconda",
+                                                                    "model_class": "CondaDependencyResolver",
+                                                                    "prefix": "/usr/local/tools/_conda",
+                                                                    "read_only": false,
+                                                                    "resolver_type": "conda",
+                                                                    "resolves_simple_dependencies": true,
+                                                                    "use_local": false,
+                                                                    "versionless": false
+                                                                },
+                                                                "dependency_type": "conda",
+                                                                "environment_path": "/usr/local/tools/_conda/envs/__multiqc@1.9",
+                                                                "exact": true,
+                                                                "model_class": "MergedCondaDependency",
+                                                                "name": "multiqc",
+                                                                "version": "1.9"
+                                                            }
+                                                        ],
                                                         "exit_code": 0,
-                                                        "external_id": "43534369",
+                                                        "external_id": "43535462",
                                                         "galaxy_version": "23.0",
-                                                        "history_id": "2e96b0bf6abd6b74",
-                                                        "id": "11ac94870d0bb33a4d625b480e3a88e5",
+                                                        "history_id": "2f1f9fa04aab9b59",
+                                                        "id": "11ac94870d0bb33a3e4f5384f33fb7c3",
                                                         "inputs": {
-                                                            "input_file": {
-                                                                "id": "4838ba20a6d8676586fc63a32e96cd1a",
+                                                            "results_0|software_cond|output_0|input": {
+                                                                "id": "4838ba20a6d86765967c147adffa4ae2",
                                                                 "src": "hda",
-                                                                "uuid": "11b4a85c-d4af-4e9d-9890-63e2517ff346"
+                                                                "uuid": "8aadb0d6-4752-43b3-9a70-b58359fe1659"
+                                                            },
+                                                            "results_0|software_cond|output_0|input1": {
+                                                                "id": "4838ba20a6d86765967c147adffa4ae2",
+                                                                "src": "hda",
+                                                                "uuid": "8aadb0d6-4752-43b3-9a70-b58359fe1659"
+                                                            },
+                                                            "results_0|software_cond|output_0|input2": {
+                                                                "id": "4838ba20a6d867656a6422c26474bdc5",
+                                                                "src": "hda",
+                                                                "uuid": "edecc2ea-fa52-4947-9c41-f5956870688a"
                                                             }
                                                         },
                                                         "job_messages": [],
@@ -210032,9 +211779,9 @@
                                                             {
                                                                 "name": "hostname",
                                                                 "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c28m475-1207.novalocal",
+                                                                "raw_value": "vgcnbwc-worker-c36m225-7634.novalocal",
                                                                 "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c28m475-1207.novalocal"
+                                                                "value": "vgcnbwc-worker-c36m225-7634.novalocal"
                                                             },
                                                             {
                                                                 "name": "galaxy_slots",
@@ -210046,37 +211793,37 @@
                                                             {
                                                                 "name": "galaxy_memory_mb",
                                                                 "plugin": "core",
-                                                                "raw_value": "3891.0000000",
+                                                                "raw_value": "11673.0000000",
                                                                 "title": "Memory Allocated (MB)",
-                                                                "value": "3891"
+                                                                "value": "11673"
                                                             },
                                                             {
                                                                 "name": "start_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684506791.0000000",
+                                                                "raw_value": "1684508719.0000000",
                                                                 "title": "Job Start Time",
-                                                                "value": "2023-05-19 16:33:11"
+                                                                "value": "2023-05-19 17:05:19"
                                                             },
                                                             {
                                                                 "name": "end_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684506812.0000000",
+                                                                "raw_value": "1684508927.0000000",
                                                                 "title": "Job End Time",
-                                                                "value": "2023-05-19 16:33:32"
+                                                                "value": "2023-05-19 17:08:47"
                                                             },
                                                             {
                                                                 "name": "runtime_seconds",
                                                                 "plugin": "core",
-                                                                "raw_value": "21.0000000",
+                                                                "raw_value": "208.0000000",
                                                                 "title": "Job Runtime (Wall Clock)",
-                                                                "value": "21 seconds"
+                                                                "value": "3 minutes"
                                                             },
                                                             {
                                                                 "name": "cpuacct.usage",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "16061028698.0000000",
+                                                                "raw_value": "15451533789.0000000",
                                                                 "title": "CPU Time",
-                                                                "value": "16.061028698 seconds"
+                                                                "value": "15.451533789 seconds"
                                                             },
                                                             {
                                                                 "name": "memory.failcnt",
@@ -210088,16 +211835,16 @@
                                                             {
                                                                 "name": "memory.limit_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "4160749568.0000000",
+                                                                "raw_value": "12348030976.0000000",
                                                                 "title": "Memory limit on cgroup (MEM)",
-                                                                "value": "3.9 GB"
+                                                                "value": "11.5 GB"
                                                             },
                                                             {
                                                                 "name": "memory.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "199102464.0000000",
+                                                                "raw_value": "243441664.0000000",
                                                                 "title": "Max memory usage (MEM)",
-                                                                "value": "189.9 MB"
+                                                                "value": "232.2 MB"
                                                             },
                                                             {
                                                                 "name": "memory.memsw.limit_in_bytes",
@@ -210109,9 +211856,9 @@
                                                             {
                                                                 "name": "memory.memsw.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "199102464.0000000",
+                                                                "raw_value": "243441664.0000000",
                                                                 "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "189.9 MB"
+                                                                "value": "232.2 MB"
                                                             },
                                                             {
                                                                 "name": "memory.oom_control.oom_kill_disable",
@@ -210138,99 +211885,980 @@
                                                         "job_stderr": "",
                                                         "job_stdout": "",
                                                         "model_class": "Job",
-                                                        "output_collections": {},
+                                                        "output_collections": {
+                                                            "stats": {
+                                                                "id": "b2ed5bced30ea70a",
+                                                                "src": "hdca"
+                                                            }
+                                                        },
                                                         "outputs": {
-                                                            "output": {
-                                                                "id": "4838ba20a6d86765c665b3763e979c0a",
+                                                            "__new_primary_file_stats|fastqc__": {
+                                                                "id": "4838ba20a6d8676552151abe856ca468",
                                                                 "src": "hda",
-                                                                "uuid": "94cccd62-deee-4ce5-8952-739603b253f7"
+                                                                "uuid": "a0afcc44-22b6-4019-938e-4c8b313de6ea"
+                                                            },
+                                                            "__new_primary_file_stats|general_stats__": {
+                                                                "id": "4838ba20a6d867656f4643c70fbd40cc",
+                                                                "src": "hda",
+                                                                "uuid": "d41e3789-24ea-4080-868b-0edab34c49a6"
+                                                            },
+                                                            "__new_primary_file_stats|sources__": {
+                                                                "id": "4838ba20a6d8676518ad2e8586cc7f6b",
+                                                                "src": "hda",
+                                                                "uuid": "b697c224-e6d6-4f53-a3df-16fe5ca4444c"
+                                                            },
+                                                            "html_report": {
+                                                                "id": "4838ba20a6d867657c9b5bfe8c22949d",
+                                                                "src": "hda",
+                                                                "uuid": "a42df514-e2c2-4f72-a9b8-e065ef58237f"
                                                             }
                                                         },
                                                         "params": {
-                                                            "__input_ext": "\"bam\"",
-                                                            "__workflow_invocation_uuid__": "\"9ef558e0f65111eda6f2001e67d2ec02\"",
-                                                            "chromInfo": "\"/data/db/data_managers/mm10/len/mm10.len\"",
-                                                            "coverage_max": "\"1000\"",
-                                                            "coverage_min": "\"1\"",
-                                                            "coverage_step": "\"1\"",
-                                                            "dbkey": "\"mm10\"",
-                                                            "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}",
-                                                            "gc_depth": "\"20000.0\"",
-                                                            "insert_size": "\"8000\"",
-                                                            "most_inserts": "\"0.99\"",
-                                                            "read_length": null,
-                                                            "remove_dups": "false",
-                                                            "split_output": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}",
-                                                            "trim_quality": "\"0\"",
-                                                            "use_reference": "{\"__current_case__\": 0, \"reference_source\": {\"__current_case__\": 0, \"ref_file\": \"mm10full\", \"reference_source_selector\": \"cached\"}, \"use_ref_selector\": \"yes\"}"
+                                                            "__input_ext": "\"txt\"",
+                                                            "__workflow_invocation_uuid__": "\"a085c588f65511ed82b7001e67d2ec02\"",
+                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
+                                                            "comment": "\"\"",
+                                                            "dbkey": "\"?\"",
+                                                            "export": "false",
+                                                            "flat": "false",
+                                                            "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"input\": {\"values\": [{\"id\": 137417582, \"src\": \"hda\"}, {\"id\": 137417586, \"src\": \"hda\"}]}, \"type\": \"data\"}], \"software\": \"fastqc\"}}]",
+                                                            "saveLog": "false",
+                                                            "title": "\"\""
                                                         },
                                                         "state": "ok",
-                                                        "stderr": "",
+                                                        "stderr": "[WARNING]         multiqc : MultiQC Version v1.14 now available!\n[INFO   ]         multiqc : This is MultiQC v1.9\n[INFO   ]         multiqc : Template    : default\n[INFO   ]         multiqc : Searching   : /data/jwd05e/main/060/059/60059406/working/multiqc_WDir\n[INFO   ]          fastqc : Found 2 reports\n[INFO   ]         multiqc : Compressing plot data\n[INFO   ]         multiqc : Report      : report.html\n[INFO   ]         multiqc : Data        : report_data\n[INFO   ]         multiqc : MultiQC complete\n",
                                                         "stdout": "",
-                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
-                                                        "tool_stderr": "",
+                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
+                                                        "tool_stderr": "[WARNING]         multiqc : MultiQC Version v1.14 now available!\n[INFO   ]         multiqc : This is MultiQC v1.9\n[INFO   ]         multiqc : Template    : default\n[INFO   ]         multiqc : Searching   : /data/jwd05e/main/060/059/60059406/working/multiqc_WDir\n[INFO   ]          fastqc : Found 2 reports\n[INFO   ]         multiqc : Compressing plot data\n[INFO   ]         multiqc : Report      : report.html\n[INFO   ]         multiqc : Data        : report_data\n[INFO   ]         multiqc : MultiQC complete\n",
                                                         "tool_stdout": "",
                                                         "traceback": null,
-                                                        "update_time": "2023-05-19T14:33:32.811917",
+                                                        "update_time": "2023-05-19T15:08:50.825299",
                                                         "user_email": "hxr@informatik.uni-freiburg.de"
                                                     }
                                                 ],
                                                 "model_class": "WorkflowInvocationStep",
-                                                "order_index": 9,
-                                                "output_collections": {},
+                                                "order_index": 6,
+                                                "output_collections": {
+                                                    "stats": {
+                                                        "id": "b2ed5bced30ea70a",
+                                                        "src": "hdca"
+                                                    }
+                                                },
                                                 "outputs": {
-                                                    "output": {
-                                                        "id": "4838ba20a6d86765c665b3763e979c0a",
+                                                    "html_report": {
+                                                        "id": "4838ba20a6d867657c9b5bfe8c22949d",
                                                         "src": "hda",
-                                                        "uuid": "94cccd62-deee-4ce5-8952-739603b253f7"
+                                                        "uuid": "a42df514-e2c2-4f72-a9b8-e065ef58237f"
                                                     }
                                                 },
                                                 "state": "scheduled",
                                                 "subworkflow": null,
                                                 "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-19T14:33:32.796651",
-                                                "workflow_step_id": "d00ffb828650fb93",
+                                                "update_time": "2023-05-19T15:08:50.808688",
+                                                "workflow_step_id": "40e61d72c5cedf2a",
                                                 "workflow_step_label": null,
-                                                "workflow_step_uuid": "cb1e8297-24f1-4553-8111-1a2a48bfc12a"
+                                                "workflow_step_uuid": "abf34a41-0150-42fc-b56a-a29eb92c24c3"
                                             }
                                         }
                                     },
                                     "problem_log": "No log for this engine type.",
-                                    "start_datetime": "2023-05-19T16:26:39.476426",
+                                    "start_datetime": "2023-05-19T16:55:58.620842",
                                     "status": "success"
                                 },
-                                "doc": "Test sample data for Sequence analysis:Mapping",
+                                "doc": "Test sample data for Sequence-analyses:Quality-control",
                                 "has_data": true,
-                                "id": "mapping.ga_0",
+                                "id": "quality_control.ga_0",
                                 "test_type": "galaxy_workflow"
                             }
                         ],
-                        "version": "0.1"
+                        "version": "0.1"
+                    }
+                },
+                "tests": true,
+                "title": "GTN - Sequence Analyses - Quality Control (imported from uploaded file)",
+                "topic_id": "sequence-analysis",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/sequence-analysis-quality-control/versions/quality-control",
+                "tutorial_id": "quality-control",
+                "url": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/workflows/quality_control.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/workflows/quality_control.html",
+                "version": 5,
+                "wfid": "sequence-analysis-quality-control",
+                "wfname": "quality-control",
+                "workflow": "quality_control.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3"
+                ],
+                "workflowhub_id": "1282"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/records/61771"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bwa",
+                    "owner": "devteam",
+                    "revisions": "e188dc7a68e6",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "samtools_fastx",
+                    "owner": "iuc",
+                    "revisions": "a8d69aee190e",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seqtk",
+                    "owner": "iuc",
+                    "revisions": "3da72230c066",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "trimmomatic",
+                    "owner": "pjbriggs",
+                    "revisions": "898b67846b47",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "trimmomatic",
+                    "owner": "pjbriggs",
+                    "revisions": "d94aff5ee623",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_fastx\n  owner: iuc\n  revisions: a8d69aee190e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n  owner: pjbriggs\n  revisions: 898b67846b47\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n  owner: pjbriggs\n  revisions: d94aff5ee623\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "by-covid",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "elixir_node": "de",
+                "fediverse": "https://scholar.social/@zerodivision",
+                "fediverse_flavor": "mastodon",
+                "id": "wm75",
+                "joined": "2017-09",
+                "matrix": "wm75:matrix.org",
+                "name": "Wolfgang Maier",
+                "orcid": "0000-0002-9464-6640",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
+            }
+        ],
+        "dir": "topics/sequence-analysis/tutorials/human-reads-removal",
+        "edam_operation": [
+            "Generation",
+            "Data handling",
+            "Sequence alignment",
+            "Sequence file editing",
+            "Read mapping",
+            "Genome indexing"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "sequence-analysis/human-reads-removal",
+        "inexact_supported_servers": [
+            "Galaxy@AuBi",
+            "GalaxyTrakr",
+            "MISSISSIPPI",
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Before submitting raw viral sequencing data to public databases you will want to remove human sequence traces",
+            "Human reads can be identified by mapping the data to the human reference genome",
+            "After mapping, you can extract the read identifiers of the non-human reads and use these to extract just the desired original sequenced reads from the input data"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": [
+            "Obtain viral (SARS-CoV-2) sequencing data with contaminating human reads from public sources",
+            "Organize the data into a collection",
+            "Preprocess and map the data against the human reference genome",
+            "Eliminate reads/read pairs that map to the human genome from the original data"
+        ],
+        "pageviews": 4842,
+        "pub_date": "2021-08-04",
+        "questions": [
+            "How can you remove traces of human sequence data from a sequenced viral sample?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "sequence-analysis",
+                "tutorials": [
+                    "quality-control",
+                    "mapping"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "collections"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00236",
+        "short_tools": [
+            "bwa_mem",
+            "seqtk_subseq",
+            "tp_replace_in_line",
+            "samtools_fastx",
+            "Grep1",
+            "__UNZIP_COLLECTION__",
+            "trimmomatic",
+            "__ZIP_COLLECTION__"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "covid19"
+        ],
+        "time_estimation": "1h",
+        "title": "Removal of human reads from SARS-CoV-2 sequencing data",
+        "tools": [
+            "Grep1",
+            "__UNZIP_COLLECTION__",
+            "__ZIP_COLLECTION__",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+            "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0",
+            "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1"
+        ],
+        "topic_name": "sequence-analysis",
+        "topic_name_human": "Sequence analysis",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "human-reads-removal",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/human-reads-removal/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/human-reads-removal/tutorial.json"
+        },
+        "version": 5,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 140,
+        "visitors": 3422,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Removal of human reads from SARS-CoV-2 sequencing data",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"]\n  1[label=\"Trimmomatic\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Unzip Collection\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Map with BWA-MEM\"]\n  1 -> 3 [label=\"fastq_out_paired\"]\n  4[label=\"Samtools fastx\"]\n  3 -> 4 [label=\"bam_output\"]\n  5[label=\"Select\"]\n  4 -> 5 [label=\"forward\"]\n  6[label=\"Replace Text\"]\n  5 -> 6 [label=\"out_file1\"]\n  7[label=\"seqtk_subseq\"]\n  2 -> 7 [label=\"forward\"]\n  6 -> 7 [label=\"outfile\"]\n  8[label=\"seqtk_subseq\"]\n  2 -> 8 [label=\"reverse\"]\n  6 -> 8 [label=\"outfile\"]\n  9[label=\"Paired-end collection of cleaned reads\"]\n  7 -> 9 [label=\"default\"]\n  8 -> 9 [label=\"default\"]\n  kf24bbf28dc51440fa758ac05033f0645[color=lightseagreen,label=\"Output\\nCleaned Data\"]\n  9 -> kf24bbf28dc51440fa758ac05033f0645\n}",
+                "history": [
+                    {
+                        "hash": "f71f6dde01e2dfe86a4b43526f119d9050693f84",
+                        "message": "Address WF linting issues",
+                        "num": 2,
+                        "short_hash": "f71f6dde0",
+                        "unix": "1628012579"
+                    },
+                    {
+                        "hash": "f232ad426455a30be4a74af21054384c23b07275",
+                        "message": "Add new tutorial for cleaning SARS-CoV-2 data",
+                        "num": 1,
+                        "short_hash": "f232ad426",
+                        "unix": "1628010649"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Input Dataset Collection"
+                            }
+                        ],
+                        "label": "Input Dataset Collection",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 564,
+                            "height": 81,
+                            "left": 296,
+                            "right": 496,
+                            "top": 483,
+                            "width": 200,
+                            "x": 296,
+                            "y": 483
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list:paired\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "d61c43e8-23ee-4f9a-9fd8-f58ffc134735",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "b14c9326-21d3-4e0e-be24-7654e6b31b43"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Trimmomatic\"];\n  0 -->|output| 1;\n  2[\"Unzip Collection\"];\n  0 -->|output| 2;\n  3[\"Map with BWA-MEM\"];\n  1 -->|fastq_out_paired| 3;\n  4[\"Samtools fastx\"];\n  3 -->|bam_output| 4;\n  5[\"Select\"];\n  4 -->|forward| 5;\n  6[\"Replace Text\"];\n  5 -->|out_file1| 6;\n  7[\"seqtk_subseq\"];\n  2 -->|forward| 7;\n  6 -->|outfile| 7;\n  8[\"seqtk_subseq\"];\n  2 -->|reverse| 8;\n  6 -->|outfile| 8;\n  9[\"Paired-end collection of cleaned reads\"];\n  7 -->|default| 9;\n  8 -->|default| 9;\n  f24bbf28-dc51-440f-a758-ac05033f0645[\"Output\\nCleaned Data\"];\n  9 --> f24bbf28-dc51-440f-a758-ac05033f0645;\n  style f24bbf28-dc51-440f-a758-ac05033f0645 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "GTN - Sequence Analyses - Removal of human reads from SARS-CoV-2 sequencing data",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Input Dataset Collection"
+                            }
+                        ],
+                        "label": "Input Dataset Collection",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 564,
+                            "height": 81,
+                            "left": 296,
+                            "right": 496,
+                            "top": 483,
+                            "width": 200,
+                            "x": 296,
+                            "y": 483
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list:paired\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "d61c43e8-23ee-4f9a-9fd8-f58ffc134735",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "b14c9326-21d3-4e0e-be24-7654e6b31b43"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1",
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {
+                            "readtype|fastq_pair": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Trimmomatic",
+                        "outputs": [
+                            {
+                                "name": "fastq_out_paired",
+                                "type": "input"
+                            },
+                            {
+                                "name": "fastq_out_unpaired",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 515,
+                            "height": 202,
+                            "left": 532,
+                            "right": 732,
+                            "top": 313,
+                            "width": 200,
+                            "x": 532,
+                            "y": 313
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "d94aff5ee623",
+                            "name": "trimmomatic",
+                            "owner": "pjbriggs",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"illuminaclip\": {\"do_illuminaclip\": \"false\", \"__current_case__\": 1}, \"operations\": [{\"__index__\": 0, \"operation\": {\"name\": \"SLIDINGWINDOW\", \"__current_case__\": 0, \"window_size\": \"4\", \"required_quality\": \"20\"}}], \"output_err\": \"false\", \"output_logs\": \"false\", \"readtype\": {\"single_or_paired\": \"collection\", \"__current_case__\": 2, \"fastq_pair\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.38.1",
+                        "type": "tool",
+                        "uuid": "ced9a15d-ca78-4cf5-b1a0-267920691879",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "fastq_out_unpaired",
+                                "uuid": "88e4c149-85d2-4c19-8a53-f242a3703e5e"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "fastq_out_paired",
+                                "uuid": "fd0243b9-ef6a-445d-8fb9-f76d47c3f6fc"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "__UNZIP_COLLECTION__",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Unzip Collection",
+                        "outputs": [
+                            {
+                                "name": "forward",
+                                "type": "input"
+                            },
+                            {
+                                "name": "reverse",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 746,
+                            "height": 182,
+                            "left": 735,
+                            "right": 935,
+                            "top": 564,
+                            "width": 200,
+                            "x": 735,
+                            "y": 564
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "__UNZIP_COLLECTION__",
+                        "tool_state": "{\"input\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "f6552b12-5845-486b-95f5-35a3eefaa109",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "forward",
+                                "uuid": "5fabd686-3611-4d28-aff3-c1286b461bbf"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "reverse",
+                                "uuid": "9b0c1a5f-6d39-46c7-a16d-afbb9e34bcfe"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "fastq_input|fastq_input1": {
+                                "id": 1,
+                                "output_name": "fastq_out_paired"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Map with BWA-MEM",
+                                "name": "fastq_input"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Map with BWA-MEM",
+                        "outputs": [
+                            {
+                                "name": "bam_output",
+                                "type": "bam"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 487,
+                            "height": 192,
+                            "left": 753,
+                            "right": 953,
+                            "top": 295,
+                            "width": 200,
+                            "x": 753,
+                            "y": 295
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "64f11cf59c6e",
+                            "name": "bwa",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"illumina\", \"__current_case__\": 0}, \"fastq_input\": {\"fastq_input_selector\": \"paired_collection\", \"__current_case__\": 2, \"fastq_input1\": {\"__class__\": \"RuntimeValue\"}, \"iset_stats\": \"\"}, \"output_sort\": \"coordinate\", \"reference_source\": {\"reference_source_selector\": \"cached\", \"__current_case__\": 0, \"ref_file\": \"hg38\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.17.2",
+                        "type": "tool",
+                        "uuid": "c21129e8-b54f-4a7d-9af2-b8202434c342",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "bam_output",
+                                "uuid": "f0ca56d9-f544-465c-ad37-6380ba0ac2ea"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "input": {
+                                "id": 3,
+                                "output_name": "bam_output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Samtools fastx",
+                        "outputs": [
+                            {
+                                "name": "forward",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 447,
+                            "height": 152,
+                            "left": 973,
+                            "right": 1173,
+                            "top": 295,
+                            "width": 200,
+                            "x": 973,
+                            "y": 295
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "a8d69aee190e",
+                            "name": "samtools_fastx",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"bam\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"copy_arb_tags\": \"\", \"copy_tags\": \"false\", \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"idxout_cond\": {\"idxout_select\": \"no\", \"__current_case__\": 0}, \"inclusive_filter\": [\"4\", \"8\"], \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"1085990\", \"output_fmt_cond\": {\"output_fmt_select\": \"fasta\", \"__current_case__\": 1}, \"outputs\": [\"r1\"], \"read_numbering\": \"-n\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9+galaxy1",
+                        "type": "tool",
+                        "uuid": "756ca036-b6b5-46e8-a230-81ed522ba950",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "forward",
+                                "uuid": "e82ae014-e75a-486c-93d6-af8cdd6e6f95"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "Grep1",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "input": {
+                                "id": 4,
+                                "output_name": "forward"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Select",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 387,
+                            "height": 92,
+                            "left": 1193,
+                            "right": 1393,
+                            "top": 295,
+                            "width": 200,
+                            "x": 1193,
+                            "y": 295
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "Grep1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"1085990\", \"invert\": \"\", \"keep_header\": \"false\", \"pattern\": \"^>.+\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.3",
+                        "type": "tool",
+                        "uuid": "5ab56d83-be12-4498-a88e-16d37ef2e904",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "04aaed7c-6c4c-44d6-89b0-5bba0a58927b"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "infile": {
+                                "id": 5,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Replace Text",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 387,
+                            "height": 92,
+                            "left": 1413,
+                            "right": 1613,
+                            "top": 295,
+                            "width": 200,
+                            "x": 1413,
+                            "y": 295
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"infile|__identifier__\": \"1085990\", \"replacements\": [{\"__index__\": 0, \"find_pattern\": \"^>(.+)\", \"replace_pattern\": \"\\\\1\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.2",
+                        "type": "tool",
+                        "uuid": "030b177e-2375-4856-b640-8ffd7f591aaf",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "f81d7560-8835-4307-b876-f56e22edf40e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "in_file": {
+                                "id": 2,
+                                "output_name": "forward"
+                            },
+                            "source|name_list": {
+                                "id": 6,
+                                "output_name": "outfile"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "seqtk_subseq",
+                        "outputs": [
+                            {
+                                "name": "default",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 416,
+                            "height": 142,
+                            "left": 1653,
+                            "right": 1853,
+                            "top": 274,
+                            "width": 200,
+                            "x": 1653,
+                            "y": 274
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "58c8ece95b53",
+                            "name": "seqtk",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"in_file|__identifier__\": \"1085990\", \"l\": \"0\", \"name_list|__identifier__\": \"1085990\", \"source\": {\"type\": \"name\", \"__current_case__\": 1, \"name_list\": {\"__class__\": \"ConnectedValue\"}}, \"t\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3.1",
+                        "type": "tool",
+                        "uuid": "50599db8-7c04-4f0f-8cc7-ca9fbeb405ea",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "default",
+                                "uuid": "75989c7c-9b50-4286-b59a-e2ebefcd6206"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "in_file": {
+                                "id": 2,
+                                "output_name": "reverse"
+                            },
+                            "source|name_list": {
+                                "id": 6,
+                                "output_name": "outfile"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "seqtk_subseq",
+                        "outputs": [
+                            {
+                                "name": "default",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 572,
+                            "height": 142,
+                            "left": 1658,
+                            "right": 1858,
+                            "top": 430,
+                            "width": 200,
+                            "x": 1658,
+                            "y": 430
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "58c8ece95b53",
+                            "name": "seqtk",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"in_file|__identifier__\": \"1085990\", \"l\": \"0\", \"name_list|__identifier__\": \"1085990\", \"source\": {\"type\": \"name\", \"__current_case__\": 1, \"name_list\": {\"__class__\": \"ConnectedValue\"}}, \"t\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3.1",
+                        "type": "tool",
+                        "uuid": "6b8ac606-6490-4355-9111-001dbe15fd22",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "default",
+                                "uuid": "1787644d-4796-4928-9458-7fc0779eb500"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "__ZIP_COLLECTION__",
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {
+                            "input_forward": {
+                                "id": 7,
+                                "output_name": "default"
+                            },
+                            "input_reverse": {
+                                "id": 8,
+                                "output_name": "default"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Zip Collection",
+                                "name": "input_forward"
+                            },
+                            {
+                                "description": "runtime parameter for tool Zip Collection",
+                                "name": "input_reverse"
+                            }
+                        ],
+                        "label": "Paired-end collection of cleaned reads",
+                        "name": "Zip Collection",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 490.5,
+                            "height": 142,
+                            "left": 1939,
+                            "right": 2139,
+                            "top": 348.5,
+                            "width": 200,
+                            "x": 1939,
+                            "y": 348.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "__ZIP_COLLECTION__",
+                        "tool_state": "{\"input_forward\": {\"__class__\": \"RuntimeValue\"}, \"input_reverse\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "381d0485-0164-410f-801d-7dfb7891663d",
+                        "workflow_outputs": [
+                            {
+                                "label": "Cleaned Data",
+                                "output_name": "output",
+                                "uuid": "f24bbf28-dc51-440f-a758-ac05033f0645"
+                            }
+                        ]
                     }
-                },
-                "tests": true,
-                "title": "GTN - Sequence Analyses - Mapping (imported from uploaded file)",
+                ],
+                "parent_id": "sequence-analysis/human-reads-removal",
+                "path": "topics/sequence-analysis/tutorials/human-reads-removal/workflows/human-reads-removal.ga",
+                "tags": [
+                    "sequence-analysis"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "GTN - Sequence Analyses - Removal of human reads from SARS-CoV-2 sequencing data",
                 "topic_id": "sequence-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/sequence-analysis-mapping/versions/mapping",
-                "tutorial_id": "mapping",
-                "url": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/workflows/mapping.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/workflows/mapping.html",
-                "version": 4,
-                "wfid": "sequence-analysis-mapping",
-                "wfname": "mapping",
-                "workflow": "mapping.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/sequence-analysis-human-reads-removal/versions/human-reads-removal",
+                "tutorial_id": "human-reads-removal",
+                "url": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/human-reads-removal/workflows/human-reads-removal.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/human-reads-removal/workflows/human-reads-removal.html",
+                "version": 1,
+                "wfid": "sequence-analysis-human-reads-removal",
+                "wfname": "human-reads-removal",
+                "workflow": "human-reads-removal.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9"
+                    "Grep1",
+                    "__UNZIP_COLLECTION__",
+                    "__ZIP_COLLECTION__",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+                    "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1"
                 ],
-                "workflowhub_id": "1265"
+                "workflowhub_id": "1276"
             }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.1324070"
+        ]
     },
     {
         "admin_install": {
@@ -210238,6 +212866,34 @@
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
             "tools": [
+                {
+                    "name": "trim_galore",
+                    "owner": "bgruening",
+                    "revisions": "949f01671246",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bamtools_filter",
+                    "owner": "devteam",
+                    "revisions": "cb20f99fd45b",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bamtools_filter",
+                    "owner": "devteam",
+                    "revisions": "993b19f20c76",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bowtie2",
+                    "owner": "devteam",
+                    "revisions": "a6d65b0c67af",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "fastqc",
                     "owner": "devteam",
@@ -210246,59 +212902,72 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fastqc",
+                    "name": "samtools_stats",
                     "owner": "devteam",
-                    "revisions": "3d0c7bdf12f5",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "24c5d43cb545",
+                    "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fastqe",
-                    "owner": "iuc",
-                    "revisions": "89d299153577",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "samtools_stats",
+                    "owner": "devteam",
+                    "revisions": "145f6d74ff5e",
+                    "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "75c93c70d094",
-                    "tool_panel_section_label": "Quality Control",
+                    "name": "samtools_stats",
+                    "owner": "devteam",
+                    "revisions": "541082d03bef",
+                    "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "nanoplot",
+                    "name": "jbrowse",
                     "owner": "iuc",
-                    "revisions": "0f1c34698076",
-                    "tool_panel_section_label": "Nanopore",
+                    "revisions": "1cfc579079a6",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pycoqc",
+                    "name": "jbrowse",
                     "owner": "iuc",
-                    "revisions": "fae03f3d4bf7",
-                    "tool_panel_section_label": "Nanopore",
+                    "revisions": "4542035c1075",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cutadapt",
-                    "owner": "lparsons",
-                    "revisions": "660cffd8d92a",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "c1a4b5f3b432",
+                    "tool_panel_section_label": "Quality Control",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cutadapt",
-                    "owner": "lparsons",
-                    "revisions": "44e2cc14f75b",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "75c93c70d094",
+                    "tool_panel_section_label": "Quality Control",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqe\n  owner: iuc\n  revisions: 89d299153577\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 75c93c70d094\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nanoplot\n  owner: iuc\n  revisions: 0f1c34698076\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pycoqc\n  owner: iuc\n  revisions: fae03f3d4bf7\n  tool_panel_section_label: Nanopore\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 660cffd8d92a\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 44e2cc14f75b\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/quality-control/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: trim_galore\n  owner: bgruening\n  revisions: 949f01671246\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_filter\n  owner: devteam\n  revisions: cb20f99fd45b\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_filter\n  owner: devteam\n  revisions: 993b19f20c76\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bowtie2\n  owner: devteam\n  revisions: a6d65b0c67af\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 24c5d43cb545\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 145f6d74ff5e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 541082d03bef\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 1cfc579079a6\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 4542035c1075\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: c1a4b5f3b432\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 75c93c70d094\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/mapping/tutorial.json",
         "contributors": [
+            {
+                "elixir_node": "de",
+                "email": "wolffj@informatik.uni-freiburg.de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "joachimwolff",
+                "joined": "2017-09",
+                "name": "Joachim Wolff",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/joachimwolff.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
@@ -210325,131 +212994,56 @@
                 "twitter": "bebatut",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             },
-            {
-                "id": "mblue9",
-                "joined": "2018-09",
-                "name": "Maria Doyle",
-                "orcid": "0000-0003-4847-8436",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
-            },
-            {
-                "email": "alexandre.cormier@ifremer.fr",
-                "id": "alexcorm",
-                "joined": "2021-11",
-                "name": "Alexandre Cormier",
-                "orcid": "0000-0002-7775-8413",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/alexcorm/",
-                "twitter": "allanssx",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/alexcorm.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
-                    "eurosciencegateway",
-                    "elixir-europe"
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
                 ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "anthony.bretaudeau@inrae.fr",
-                "fediverse": "https://genomic.social/@abretaud",
-                "fediverse_flavor": "mastodon",
-                "id": "abretaud",
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
                 "joined": "2017-09",
                 "location": {
-                    "country": "FR",
-                    "lat": 48.11,
-                    "lon": -1.64
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
                 },
-                "matrix": "abretaud:matrix.org",
-                "name": "Anthony Bretaudeau",
-                "orcid": "0000-0003-0914-2470",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abretaud/",
-                "twitter": "abretau",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/abretaud.json"
-            },
-            {
-                "email": "laura.leroi@ifremer.fr",
-                "id": "lleroi",
-                "joined": "2021-11",
-                "name": "Laura Leroi",
-                "orcid": "0000-0003-3748-4179",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/lleroi/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/lleroi.json"
-            },
-            {
-                "email": "erwan.corre@sb-roscoff.fr",
-                "id": "r1corre",
-                "joined": "2019-04",
-                "name": "Erwan Corre",
-                "orcid": "0000-0001-6354-2278",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/r1corre/",
-                "twitter": "r1corre",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/r1corre.json"
-            },
-            {
-                "email": "stephanie.robin@inrae.fr",
-                "id": "stephanierobin",
-                "joined": "2021-11",
-                "name": "St\u00e9phanie Robin",
-                "orcid": "0000-0001-7379-9173",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/stephanierobin/",
-                "twitter": "robinstphanie1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/stephanierobin.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "au",
-                "email": "c.hyde@qcif.edu.au",
-                "id": "neoformit",
-                "joined": "2022-02",
-                "name": "Cameron Hyde",
-                "orcid": "0000-0002-5913-9766",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/neoformit/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/neoformit.json"
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/sequence-analysis/tutorials/quality-control",
+        "dir": "topics/sequence-analysis/tutorials/mapping",
+        "edam_ontology": [
+            "topic_0102"
+        ],
         "edam_operation": [
+            "Data handling",
+            "Sequence trimming",
+            "Read mapping",
             "Sequencing quality control",
-            "Primer removal",
-            "Box-Whisker plot plotting",
+            "Genome visualisation",
+            "Sequence alignment analysis",
+            "Statistical calculation",
+            "Validation",
             "Sequence composition calculation",
             "Read pre-processing",
-            "Scatter plot plotting",
-            "Validation",
-            "Sequence trimming",
-            "Statistical calculation"
+            "Primer removal"
+        ],
+        "edam_topic": [
+            "Mapping"
         ],
-        "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org (Main)",
@@ -210459,100 +213053,114 @@
         "feedback_number": 0,
         "follow_up_training": [
             {
-                "topic_name": "sequence-analysis",
+                "topic_name": "transcriptomics",
                 "tutorials": [
-                    "mapping"
+                    "ref-based"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "epigenetics",
+                "tutorials": [
+                    "formation_of_super-structures_on_xi"
                 ],
                 "type": "internal"
             }
         ],
         "hands_on": true,
-        "id": "sequence-analysis/quality-control",
+        "id": "sequence-analysis/mapping",
         "inexact_supported_servers": [
             "Galaxy@AuBi",
+            "GalaxyTrakr",
+            "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.fr"
+            "UseGalaxy.fr",
+            "UseGalaxy.no"
         ],
         "js_requirements": {
-            "mathjax": 23197,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Perform quality control on every dataset before running any other bioinformatics analysis",
-            "Assess the quality metrics and improve quality if necessary",
-            "Check the impact of the quality control",
-            "Different tools are available to provide additional quality metrics",
-            "For paired-end reads analyze the forward and reverse reads together"
+            "Know your data!",
+            "Mapping is not trivial",
+            "There are many mapping algorithms, it depends on your data which one to choose"
         ],
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-09-22",
         "objectives": [
-            "Assess short reads FASTQ quality using FASTQE \ud83e\uddec\ud83d\ude0e and FastQC",
-            "Assess long reads FASTQ quality using Nanoplot and PycoQC",
-            "Perform quality correction with Cutadapt (short reads)",
-            "Summarise quality metrics MultiQC",
-            "Process single-end and paired-end data"
+            "Run a tool to map reads to a reference genome",
+            "Explain what is a BAM file and what it contains",
+            "Use genome browser to understand your data"
         ],
-        "pageviews": 5886178,
+        "pageviews": 5993272,
         "pub_date": "2016-10-04",
         "questions": [
-            "How to perform quality control of NGS raw data?",
-            "What are the quality parameters to check for a dataset?",
-            "How to improve the quality of a dataset?"
+            "What is mapping?",
+            "What two things are crucial for a correct mapping?",
+            "What is BAM?"
         ],
         "recordings": [
             {
                 "captioners": [
-                    "LonsBio"
+                    "shiltemann"
                 ],
-                "date": "2023-05-19",
-                "length": "50M",
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "20M",
                 "speakers": [
-                    "LonsBio"
+                    "pvanheus"
                 ],
-                "youtube_id": "coaMGvZazoc"
+                "youtube_id": "1wm-62E2NkY"
             },
             {
+                "bot-timestamp": 1725707919,
                 "captioners": [
-                    "bebatut",
-                    "nagoue",
-                    "shiltemann"
+                    "DinithiRajapaksha"
                 ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "1H10M",
+                "date": "2024-09-07",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "24M",
                 "speakers": [
-                    "heylf"
+                    "DinithiRajapaksha"
                 ],
-                "youtube_id": "QJRlX2hWDKM"
+                "youtube_id": "B-CFWSkZzRc"
             }
         ],
-        "short_id": "T00239",
+        "requirements": [
+            {
+                "topic_name": "sequence-analysis",
+                "tutorials": [
+                    "quality-control"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00237",
         "short_tools": [
-            "nanoplot",
-            "pycoqc",
-            "fastqe",
+            "jbrowse",
+            "samtools_stats",
+            "bamFilter",
             "multiqc",
             "fastqc",
-            "cutadapt"
+            "bowtie2",
+            "trim_galore"
         ],
         "slides": true,
         "slides_recordings": [
             {
                 "captioners": [
-                    "ennovytje",
-                    "nagoue",
-                    "hexylena"
+                    "blankenberg"
                 ],
                 "date": "2021-02-15",
                 "galaxy_version": "21.01",
-                "length": "40M",
+                "length": "10M",
                 "speakers": [
-                    "heylf"
+                    "pvanheus"
                 ],
-                "youtube_id": "BWonTPS4zB8"
+                "youtube_id": "7FhHb8EV3EU"
             }
         ],
         "supported_servers": {
@@ -210579,6 +213187,16 @@
                     "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
                 },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -210588,21 +213206,30 @@
                     "name": "UseGalaxy.fr",
                     "url": "https://usegalaxy.fr/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
                 }
             ]
         },
         "symlink": null,
-        "time_estimation": "1H30M",
-        "title": "Quality Control",
+        "time_estimation": "1h",
+        "title": "Mapping",
         "tools": [
+            "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastqe/fastqe/0.2.6+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/pycoqc/pycoqc/2.5.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3",
-            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.4+galaxy2"
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1"
         ],
         "topic_name": "sequence-analysis",
         "topic_name_human": "Sequence analysis",
@@ -210612,72 +213239,65 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "quality-control",
+        "tutorial_name": "mapping",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-control/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/mapping/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/quality-control/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/quality-control/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/mapping/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/mapping/tutorial.json"
         },
         "version": 41,
         "video": false,
         "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 336,
-        "visitors": 2145817,
+        "visit_duration": 314,
+        "visitors": 2188054,
         "workflows": [
             {
                 "creators": [],
-                "description": "Quality Control",
+                "description": "Mapping",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreads_2\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreads_1\"]\n  2[label=\"FastQC\"]\n  0 -> 2 [label=\"output\"]\n  k1f4fad7b11e74ec5b73d835080c47e70[color=lightseagreen,label=\"Output\\nreads_2_fastqc\"]\n  2 -> k1f4fad7b11e74ec5b73d835080c47e70\n  3[label=\"Cutadapt\"]\n  1 -> 3 [label=\"output\"]\n  k12a1bc96cfdd4ed8b062433833e09aee[color=lightseagreen,label=\"Output\\nreads_1_cutadapt\"]\n  3 -> k12a1bc96cfdd4ed8b062433833e09aee\n  4[label=\"FastQC\"]\n  1 -> 4 [label=\"output\"]\n  k12e19f0b102a44709bc8e362bb4e2c91[color=lightseagreen,label=\"Output\\nreads_1_fastqc\"]\n  4 -> k12e19f0b102a44709bc8e362bb4e2c91\n  5[label=\"Cutadapt\"]\n  1 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  kb7c138cc10d04bd0b960a3b5e60f29cd[color=lightseagreen,label=\"Output\\nreads_cutadapt\"]\n  5 -> kb7c138cc10d04bd0b960a3b5e60f29cd\n  6[label=\"MultiQC\"]\n  4 -> 6 [label=\"text_file\"]\n  2 -> 6 [label=\"text_file\"]\n  kfa7f541db9be4283afa18398d89f345e[color=lightseagreen,label=\"Output\\nmultiqc\"]\n  6 -> kfa7f541db9be4283afa18398d89f345e\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreads_1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreads_2\"]\n  2[label=\"FastQC\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"FastQC\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Trim Galore!\"]\n  0 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"MultiQC\"]\n  3 -> 5 [label=\"text_file\"]\n  2 -> 5 [label=\"text_file\"]\n  6[label=\"Bowtie2\"]\n  4 -> 6 [label=\"trimmed_reads_pair1\"]\n  4 -> 6 [label=\"trimmed_reads_pair2\"]\n  kcb22563afece4b639d85ff5817edb5c3[color=lightseagreen,label=\"Output\\nbowtie2_mapping_stats\"]\n  6 -> kcb22563afece4b639d85ff5817edb5c3\n  7[label=\"Samtools stats\"]\n  6 -> 7 [label=\"output\"]\n  k490620d4f0834999bb3373a2a1f736b4[color=lightseagreen,label=\"Output\\nbam_stats_1\"]\n  7 -> k490620d4f0834999bb3373a2a1f736b4\n  8[label=\"JBrowse\"]\n  6 -> 8 [label=\"output\"]\n}",
                 "history": [
                     {
                         "hash": "505f7550f2798d344c73ae11ff158fa77cf90584",
                         "message": "update-workflows",
-                        "num": 6,
+                        "num": 5,
                         "short_hash": "505f7550f",
                         "unix": "1618939337"
                     },
                     {
                         "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
                         "message": "annotation",
-                        "num": 5,
+                        "num": 4,
                         "short_hash": "667ff3de9",
                         "unix": "1579690769"
                     },
                     {
                         "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
                         "message": "Workflow renaming",
-                        "num": 4,
+                        "num": 3,
                         "short_hash": "eb4d724e0",
                         "unix": "1579084895"
                     },
                     {
-                        "hash": "7b4cb6d1d70496ae6f59dbbc4383d5ec6c16c8ad",
-                        "message": "Replace Trim Galore with Cutadapt",
-                        "num": 3,
-                        "short_hash": "7b4cb6d1d",
-                        "unix": "1537804789"
-                    },
-                    {
-                        "hash": "2204ebb5ee73708e3ade6ece3b20a34cbe333236",
-                        "message": "Expand the QC tutorial and add workflow testing",
+                        "hash": "469053ce23c700f73325c5f1b668b8fa48d48252",
+                        "message": "avoiding duplicate name",
                         "num": 2,
-                        "short_hash": "2204ebb5e",
-                        "unix": "1536843430"
+                        "short_hash": "469053ce2",
+                        "unix": "1578995047"
                     },
                     {
-                        "hash": "3048a0c69fe2aee55827dcadb806c11636496884",
-                        "message": "workflows",
+                        "hash": "27d11fd7fc4673db6c431f3a7d9529fd5ade273d",
+                        "message": "add variant with jbrowse output",
                         "num": 1,
-                        "short_hash": "3048a0c69",
-                        "unix": "1498583960"
+                        "short_hash": "27d11fd7f",
+                        "unix": "1557229186"
                     }
                 ],
                 "inputs": [
@@ -210690,27 +213310,27 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "reads_2"
+                                "name": "reads_1"
                             }
                         ],
-                        "label": "reads_2",
+                        "label": "reads_1",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": -144,
+                            "bottom": 285.5,
                             "height": 61,
-                            "left": 359,
-                            "right": 559,
-                            "top": -205,
+                            "left": 405.5,
+                            "right": 605.5,
+                            "top": 224.5,
                             "width": 200,
-                            "x": 359,
-                            "y": -205
+                            "x": 405.5,
+                            "y": 224.5
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "11e6b420-32a1-431d-8eb4-b707a1e9b2df",
+                        "uuid": "71f77373-c9b8-441c-bbf3-b168fbb69220",
                         "workflow_outputs": []
                     },
                     {
@@ -210722,389 +213342,580 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "reads_1"
+                                "name": "reads_2"
                             }
                         ],
-                        "label": "reads_1",
+                        "label": "reads_2",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": -231,
+                            "bottom": 710.5,
                             "height": 61,
-                            "left": 359,
-                            "right": 559,
-                            "top": -292,
+                            "left": 330.5,
+                            "right": 530.5,
+                            "top": 649.5,
                             "width": 200,
-                            "x": 359,
-                            "y": -292
+                            "x": 330.5,
+                            "y": 649.5
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "3ba96dd1-e62d-4c22-b5b9-92a03e9b0c46",
+                        "uuid": "3da9f126-0edf-4243-88f7-e1d1528840f6",
                         "workflow_outputs": []
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nreads_2\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nreads_1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"FastQC\"];\n  0 -->|output| 2;\n  1f4fad7b-11e7-4ec5-b73d-835080c47e70[\"Output\\nreads_2_fastqc\"];\n  2 --> 1f4fad7b-11e7-4ec5-b73d-835080c47e70;\n  style 1f4fad7b-11e7-4ec5-b73d-835080c47e70 stroke:#2c3143,stroke-width:4px;\n  3[\"Cutadapt\"];\n  1 -->|output| 3;\n  12a1bc96-cfdd-4ed8-b062-433833e09aee[\"Output\\nreads_1_cutadapt\"];\n  3 --> 12a1bc96-cfdd-4ed8-b062-433833e09aee;\n  style 12a1bc96-cfdd-4ed8-b062-433833e09aee stroke:#2c3143,stroke-width:4px;\n  4[\"FastQC\"];\n  1 -->|output| 4;\n  12e19f0b-102a-4470-9bc8-e362bb4e2c91[\"Output\\nreads_1_fastqc\"];\n  4 --> 12e19f0b-102a-4470-9bc8-e362bb4e2c91;\n  style 12e19f0b-102a-4470-9bc8-e362bb4e2c91 stroke:#2c3143,stroke-width:4px;\n  5[\"Cutadapt\"];\n  1 -->|output| 5;\n  0 -->|output| 5;\n  b7c138cc-10d0-4bd0-b960-a3b5e60f29cd[\"Output\\nreads_cutadapt\"];\n  5 --> b7c138cc-10d0-4bd0-b960-a3b5e60f29cd;\n  style b7c138cc-10d0-4bd0-b960-a3b5e60f29cd stroke:#2c3143,stroke-width:4px;\n  6[\"MultiQC\"];\n  4 -->|text_file| 6;\n  2 -->|text_file| 6;\n  fa7f541d-b9be-4283-afa1-8398d89f345e[\"Output\\nmultiqc\"];\n  6 --> fa7f541d-b9be-4283-afa1-8398d89f345e;\n  style fa7f541d-b9be-4283-afa1-8398d89f345e stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:24 +0000",
-                "name": "GTN - Sequence Analyses - Quality Control (imported from uploaded file)",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nreads_1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nreads_2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"FastQC\"];\n  0 -->|output| 2;\n  3[\"FastQC\"];\n  1 -->|output| 3;\n  4[\"Trim Galore!\"];\n  0 -->|output| 4;\n  1 -->|output| 4;\n  5[\"MultiQC\"];\n  3 -->|text_file| 5;\n  2 -->|text_file| 5;\n  6[\"Bowtie2\"];\n  4 -->|trimmed_reads_pair1| 6;\n  4 -->|trimmed_reads_pair2| 6;\n  cb22563a-fece-4b63-9d85-ff5817edb5c3[\"Output\\nbowtie2_mapping_stats\"];\n  6 --> cb22563a-fece-4b63-9d85-ff5817edb5c3;\n  style cb22563a-fece-4b63-9d85-ff5817edb5c3 stroke:#2c3143,stroke-width:4px;\n  7[\"Samtools stats\"];\n  6 -->|output| 7;\n  490620d4-f083-4999-bb33-73a2a1f736b4[\"Output\\nbam_stats_1\"];\n  7 --> 490620d4-f083-4999-bb33-73a2a1f736b4;\n  style 490620d4-f083-4999-bb33-73a2a1f736b4 stroke:#2c3143,stroke-width:4px;\n  8[\"JBrowse\"];\n  6 -->|output| 8;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "GTN - Sequence Analyses - Mapping - Jbrowse (imported from uploaded file)",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
                         "errors": null,
-                        "id": 2,
+                        "id": 5,
                         "input_connections": {
-                            "input_file": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
+                            "results_0|software_cond|output_0|input": [
+                                {
+                                    "id": 3,
+                                    "output_name": "text_file"
+                                },
+                                {
+                                    "id": 2,
+                                    "output_name": "text_file"
+                                }
+                            ]
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "adapters"
-                            },
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "contaminants"
-                            },
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "input_file"
-                            },
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "limits"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "FastQC",
+                        "name": "MultiQC",
                         "outputs": [
                             {
-                                "name": "html_file",
-                                "type": "html"
+                                "name": "stats",
+                                "type": "input"
                             },
                             {
-                                "name": "text_file",
-                                "type": "txt"
+                                "name": "html_report",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "bottom": 199,
-                            "height": 272,
-                            "left": 617,
-                            "right": 817,
-                            "top": -73,
+                            "bottom": 513.5,
+                            "height": 182,
+                            "left": 1150.5,
+                            "right": 1350.5,
+                            "top": 331.5,
                             "width": 200,
-                            "x": 617,
-                            "y": -73
+                            "x": 1150.5,
+                            "y": 331.5
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                        "post_job_actions": {
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "e7b2202befea",
-                            "name": "fastqc",
-                            "owner": "devteam",
+                            "changeset_revision": "75c93c70d094",
+                            "name": "multiqc",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adapters\": {\"__class__\": \"RuntimeValue\"}, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"RuntimeValue\"}, \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"min_length\": null, \"nogroup\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.72+galaxy1",
+                        "tool_state": "{\"comment\": \"\", \"export\": \"false\", \"flat\": \"false\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9+galaxy1",
                         "type": "tool",
-                        "uuid": "f48fa351-4a73-4daa-b993-2210274ae84d",
+                        "uuid": "cb721d2b-697e-4722-9c26-4909ee315e42",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "html_file",
-                                "uuid": "aa19933c-2d76-4fd2-ab45-7a4f0a3baab1"
-                            },
-                            {
-                                "label": "reads_2_fastqc",
-                                "output_name": "text_file",
-                                "uuid": "1f4fad7b-11e7-4ec5-b73d-835080c47e70"
+                                "output_name": "html_report",
+                                "uuid": "1d156863-b350-4bf7-b68c-406c6c1ef582"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0",
                         "errors": null,
-                        "id": 3,
+                        "id": 6,
                         "input_connections": {
                             "library|input_1": {
-                                "id": 1,
-                                "output_name": "output"
+                                "id": 4,
+                                "output_name": "trimmed_reads_pair1"
+                            },
+                            "library|input_2": {
+                                "id": 4,
+                                "output_name": "trimmed_reads_pair2"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Cutadapt",
+                        "name": "Bowtie2",
                         "outputs": [
                             {
-                                "name": "out1",
-                                "type": "fastqsanger"
+                                "name": "output",
+                                "type": "bam"
                             },
                             {
-                                "name": "report",
+                                "name": "mapping_stats",
                                 "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 306,
-                            "height": 162,
-                            "left": 617,
-                            "right": 817,
-                            "top": 144,
+                            "bottom": 989.5,
+                            "height": 252,
+                            "left": 1170.5,
+                            "right": 1370.5,
+                            "top": 737.5,
                             "width": 200,
-                            "x": 617,
-                            "y": 144
+                            "x": 1170.5,
+                            "y": 737.5
                         },
                         "post_job_actions": {
-                            "HideDatasetActionout1": {
+                            "HideDatasetActionoutput": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "out1"
+                                "output_name": "output"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "660cffd8d92a",
-                            "name": "cutadapt",
-                            "owner": "lparsons",
+                            "changeset_revision": "09b2cdb7ace5",
+                            "name": "bowtie2",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adapter_options\": {\"error_rate\": \"0.1\", \"no_indels\": \"false\", \"count\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \"false\"}, \"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"discard\": \"false\", \"discard_untrimmed\": \"false\", \"min\": \"20\", \"max\": \"0\", \"no_trim\": \"false\", \"mask_adapter\": \"false\", \"max_n\": null, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}}, \"output_options\": {\"report\": \"true\", \"info_file\": \"false\", \"rest_file\": \"false\", \"wildcard_file\": \"false\", \"too_short_file\": \"false\", \"too_long_file\": \"false\", \"untrimmed_file\": \"false\"}, \"read_mod_options\": {\"quality_cutoff\": \"20\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"prefix\": \"\", \"suffix\": \"\", \"strip_suffix\": \"\", \"length\": \"0\", \"length_tag\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16.3",
+                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"no_presets\"}, \"library\": {\"type\": \"paired\", \"__current_case__\": 1, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"input_2\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": \"false\", \"aligned_file\": \"false\", \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"reference_genome\": {\"source\": \"indexed\", \"__current_case__\": 0, \"index\": \"mm10\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.4.2+galaxy0",
                         "type": "tool",
-                        "uuid": "ddd70253-72b8-4a5e-8025-56a579b01975",
+                        "uuid": "7e2ff666-517c-46d8-9a25-c31bd6ffa55a",
                         "workflow_outputs": [
                             {
-                                "label": "reads_1_cutadapt",
-                                "output_name": "report",
-                                "uuid": "12a1bc96-cfdd-4ed8-b062-433833e09aee"
+                                "label": "bowtie2_mapping_stats",
+                                "output_name": "mapping_stats",
+                                "uuid": "cb22563a-fece-4b63-9d85-ff5817edb5c3"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
                         "errors": null,
-                        "id": 4,
+                        "id": 7,
                         "input_connections": {
-                            "input_file": {
-                                "id": 1,
+                            "input": {
+                                "id": 6,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "adapters"
-                            },
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "contaminants"
-                            },
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "input_file"
-                            },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Samtools stats",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "limits"
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
+                        "position": {
+                            "bottom": 352.5,
+                            "height": 112,
+                            "left": 1532.5,
+                            "right": 1732.5,
+                            "top": 240.5,
+                            "width": 200,
+                            "x": 1532.5,
+                            "y": 240.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "145f6d74ff5e",
+                            "name": "samtools_stats",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cov_threshold\": null, \"coverage_cond\": {\"coverage_select\": \"no\", \"__current_case__\": 0}, \"filter_by_flags\": {\"filter_flags\": \"nofilter\", \"__current_case__\": 1}, \"gc_depth\": \"20000.0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"insert_size\": \"8000\", \"most_inserts\": \"0.99\", \"read_length\": null, \"remove_dups\": \"false\", \"remove_overlaps\": \"false\", \"sparse\": \"false\", \"split_output_cond\": {\"split_output_selector\": \"no\", \"__current_case__\": 0}, \"trim_quality\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.2+galaxy2",
+                        "type": "tool",
+                        "uuid": "8b468a5b-01e5-4beb-8aef-fa079e3f7c2a",
+                        "workflow_outputs": [
+                            {
+                                "label": "bam_stats_1",
+                                "output_name": "output",
+                                "uuid": "490620d4-f083-4999-bb33-73a2a1f736b4"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.1+galaxy0",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "track_groups_0|data_tracks_0|data_format|annotation": {
+                                "id": 6,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
                         "label": null,
-                        "name": "FastQC",
+                        "name": "JBrowse",
                         "outputs": [
                             {
-                                "name": "html_file",
+                                "name": "output",
                                 "type": "html"
-                            },
-                            {
-                                "name": "text_file",
-                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": -20,
-                            "height": 272,
-                            "left": 617,
-                            "right": 817,
-                            "top": -292,
+                            "bottom": 1019.5,
+                            "height": 132,
+                            "left": 1536.5,
+                            "right": 1736.5,
+                            "top": 887.5,
                             "width": 200,
-                            "x": 617,
-                            "y": -292
+                            "x": 1536.5,
+                            "y": 887.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "e7b2202befea",
-                            "name": "fastqc",
-                            "owner": "devteam",
+                            "changeset_revision": "1cfc579079a6",
+                            "name": "jbrowse",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adapters\": {\"__class__\": \"RuntimeValue\"}, \"contaminants\": {\"__class__\": \"RuntimeValue\"}, \"input_file\": {\"__class__\": \"RuntimeValue\"}, \"kmers\": \"7\", \"limits\": {\"__class__\": \"RuntimeValue\"}, \"min_length\": null, \"nogroup\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.72+galaxy1",
+                        "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"indexed\", \"__current_case__\": 0, \"genomes\": \"mm10full\"}, \"standalone\": \"true\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Default\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"pileup\", \"__current_case__\": 3, \"annotation\": {\"__class__\": \"ConnectedValue\"}, \"auto_snp\": \"true\", \"chunkSizeLimit\": \"5000000\", \"track_visibility\": \"default_on\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.1+galaxy0",
                         "type": "tool",
-                        "uuid": "026332e1-70ba-4705-b75e-d228fafacc92",
+                        "uuid": "90ba0a17-0370-4cdf-8ddb-6d60f17f1b49",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "html_file",
-                                "uuid": "2b5a1c8d-a6e7-46f3-bf0a-3ccc35102538"
-                            },
-                            {
-                                "label": "reads_1_fastqc",
-                                "output_name": "text_file",
-                                "uuid": "12e19f0b-102a-4470-9bc8-e362bb4e2c91"
+                                "output_name": "output",
+                                "uuid": "d62f841d-3f68-485b-8da6-af60a48f404d"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "sequence-analysis/mapping",
+                "path": "topics/sequence-analysis/tutorials/mapping/workflows/mapping-jbrowse.ga",
+                "tags": [
+                    "sequence-analysis"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "GTN - Sequence Analyses - Mapping - Jbrowse (imported from uploaded file)",
+                "topic_id": "sequence-analysis",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/sequence-analysis-mapping/versions/mapping-jbrowse",
+                "tutorial_id": "mapping",
+                "url": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/workflows/mapping-jbrowse.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/workflows/mapping-jbrowse.html",
+                "version": 5,
+                "wfid": "sequence-analysis-mapping",
+                "wfname": "mapping-jbrowse",
+                "workflow": "mapping-jbrowse.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1"
+                ],
+                "workflowhub_id": "1269"
+            },
+            {
+                "creators": [],
+                "description": "Mapping",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreads_1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreads_2\"]\n  2[label=\"FastQC\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"FastQC\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Trim Galore!\"]\n  0 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"MultiQC\"]\n  3 -> 5 [label=\"text_file\"]\n  2 -> 5 [label=\"text_file\"]\n  6[label=\"Bowtie2\"]\n  4 -> 6 [label=\"trimmed_reads_pair1\"]\n  4 -> 6 [label=\"trimmed_reads_pair2\"]\n  kd267491228a645f3ac486635eabe47b7[color=lightseagreen,label=\"Output\\nbowtie2_mapping_stats\"]\n  6 -> kd267491228a645f3ac486635eabe47b7\n  7[label=\"Stats\"]\n  6 -> 7 [label=\"output\"]\n  k96de3c0c4d7e423b8e9b9a12a011d726[color=lightseagreen,label=\"Output\\nbam_stats_1\"]\n  7 -> k96de3c0c4d7e423b8e9b9a12a011d726\n  8[label=\"Filter\"]\n  6 -> 8 [label=\"output\"]\n  9[label=\"Stats\"]\n  8 -> 9 [label=\"out_file1\"]\n  k9603a94adcd84c1f89cdbb31d8572783[color=lightseagreen,label=\"Output\\nbam_stats_2\"]\n  9 -> k9603a94adcd84c1f89cdbb31d8572783\n}",
+                "history": [
+                    {
+                        "hash": "505f7550f2798d344c73ae11ff158fa77cf90584",
+                        "message": "update-workflows",
+                        "num": 4,
+                        "short_hash": "505f7550f",
+                        "unix": "1618939337"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 3,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 2,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
                     },
+                    {
+                        "hash": "c06c5b15160d8a4e1f1fc6d254c0590b82865f43",
+                        "message": "Expand mapping tutorial and add workflow + tests",
+                        "num": 1,
+                        "short_hash": "c06c5b151",
+                        "unix": "1536937277"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3",
+                        "content_id": null,
                         "errors": null,
-                        "id": 5,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "reads_1"
+                            }
+                        ],
+                        "label": "reads_1",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": -18,
+                            "height": 61,
+                            "left": -85,
+                            "right": 115,
+                            "top": -79,
+                            "width": 200,
+                            "x": -85,
+                            "y": -79
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "71f77373-c9b8-441c-bbf3-b168fbb69220",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "reads_2"
+                            }
+                        ],
+                        "label": "reads_2",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 407,
+                            "height": 61,
+                            "left": -160,
+                            "right": 40,
+                            "top": 346,
+                            "width": 200,
+                            "x": -160,
+                            "y": 346
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "3da9f126-0edf-4243-88f7-e1d1528840f6",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nreads_1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nreads_2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"FastQC\"];\n  0 -->|output| 2;\n  3[\"FastQC\"];\n  1 -->|output| 3;\n  4[\"Trim Galore!\"];\n  0 -->|output| 4;\n  1 -->|output| 4;\n  5[\"MultiQC\"];\n  3 -->|text_file| 5;\n  2 -->|text_file| 5;\n  6[\"Bowtie2\"];\n  4 -->|trimmed_reads_pair1| 6;\n  4 -->|trimmed_reads_pair2| 6;\n  d2674912-28a6-45f3-ac48-6635eabe47b7[\"Output\\nbowtie2_mapping_stats\"];\n  6 --> d2674912-28a6-45f3-ac48-6635eabe47b7;\n  style d2674912-28a6-45f3-ac48-6635eabe47b7 stroke:#2c3143,stroke-width:4px;\n  7[\"Stats\"];\n  6 -->|output| 7;\n  96de3c0c-4d7e-423b-8e9b-9a12a011d726[\"Output\\nbam_stats_1\"];\n  7 --> 96de3c0c-4d7e-423b-8e9b-9a12a011d726;\n  style 96de3c0c-4d7e-423b-8e9b-9a12a011d726 stroke:#2c3143,stroke-width:4px;\n  8[\"Filter\"];\n  6 -->|output| 8;\n  9[\"Stats\"];\n  8 -->|out_file1| 9;\n  9603a94a-dcd8-4c1f-89cd-bb31d8572783[\"Output\\nbam_stats_2\"];\n  9 --> 9603a94a-dcd8-4c1f-89cd-bb31d8572783;\n  style 9603a94a-dcd8-4c1f-89cd-bb31d8572783 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "GTN - Sequence Analyses - Mapping (imported from uploaded file)",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0",
+                        "errors": null,
+                        "id": 6,
                         "input_connections": {
                             "library|input_1": {
-                                "id": 1,
-                                "output_name": "output"
+                                "id": 4,
+                                "output_name": "trimmed_reads_pair1"
                             },
                             "library|input_2": {
-                                "id": 0,
-                                "output_name": "output"
+                                "id": 4,
+                                "output_name": "trimmed_reads_pair2"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cutadapt",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "out1",
-                                "type": "fastqsanger"
+                                "description": "runtime parameter for tool Bowtie2",
+                                "name": "library"
                             },
                             {
-                                "name": "out2",
-                                "type": "fastqsanger"
+                                "description": "runtime parameter for tool Bowtie2",
+                                "name": "library"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Bowtie2",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "bam"
                             },
                             {
-                                "name": "report",
+                                "name": "mapping_stats",
                                 "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 848,
-                            "height": 262,
-                            "left": 617,
-                            "right": 817,
-                            "top": 586,
+                            "bottom": 684,
+                            "height": 252,
+                            "left": 594,
+                            "right": 794,
+                            "top": 432,
                             "width": 200,
-                            "x": 617,
-                            "y": 586
+                            "x": 594,
+                            "y": 432
                         },
                         "post_job_actions": {
-                            "HideDatasetActionout1": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "out1"
-                            },
-                            "HideDatasetActionout2": {
+                            "HideDatasetActionoutput": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "out2"
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "09b2cdb7ace5",
+                            "name": "bowtie2",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"no_presets\"}, \"library\": {\"type\": \"paired\", \"__current_case__\": 1, \"input_1\": {\"__class__\": \"RuntimeValue\"}, \"input_2\": {\"__class__\": \"RuntimeValue\"}, \"unaligned_file\": \"false\", \"aligned_file\": \"false\", \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"reference_genome\": {\"source\": \"indexed\", \"__current_case__\": 0, \"index\": \"mm10\"}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.4.2+galaxy0",
+                        "type": "tool",
+                        "uuid": "2d04b2e4-a2fe-4ce6-8894-5a752031171b",
+                        "workflow_outputs": [
+                            {
+                                "label": "bowtie2_mapping_stats",
+                                "output_name": "mapping_stats",
+                                "uuid": "d2674912-28a6-45f3-ac48-6635eabe47b7"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 6,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Stats",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "tabular"
                             }
+                        ],
+                        "position": {
+                            "bottom": 29,
+                            "height": 92,
+                            "left": 1042,
+                            "right": 1242,
+                            "top": -63,
+                            "width": 200,
+                            "x": 1042,
+                            "y": -63
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "660cffd8d92a",
-                            "name": "cutadapt",
-                            "owner": "lparsons",
+                            "changeset_revision": "24c5d43cb545",
+                            "name": "samtools_stats",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adapter_options\": {\"error_rate\": \"0.1\", \"no_indels\": \"false\", \"count\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \"false\"}, \"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"discard\": \"false\", \"discard_untrimmed\": \"false\", \"min\": \"20\", \"max\": \"0\", \"no_trim\": \"false\", \"mask_adapter\": \"false\", \"max_n\": null, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"paired\", \"__current_case__\": 1, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"input_2\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}, \"r2\": {\"adapters2\": [], \"front_adapters2\": [], \"anywhere_adapters2\": [], \"cut2\": \"0\"}}, \"output_options\": {\"report\": \"true\", \"info_file\": \"false\", \"rest_file\": \"false\", \"wildcard_file\": \"false\", \"too_short_file\": \"false\", \"too_long_file\": \"false\", \"untrimmed_file\": \"false\"}, \"read_mod_options\": {\"quality_cutoff\": \"20\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"prefix\": \"\", \"suffix\": \"\", \"strip_suffix\": \"\", \"length\": \"0\", \"length_tag\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16.3",
+                        "tool_state": "{\"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm10.len\", \"coverage_max\": \"1000\", \"coverage_min\": \"1\", \"coverage_step\": \"1\", \"filter_by_flags\": {\"filter_flags\": \"nofilter\", \"__current_case__\": 1}, \"gc_depth\": \"20000.0\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"insert_size\": \"8000\", \"most_inserts\": \"0.99\", \"read_length\": null, \"remove_dups\": \"false\", \"split_output\": {\"split_output_selector\": \"no\", \"__current_case__\": 0}, \"trim_quality\": \"0\", \"use_reference\": {\"use_ref_selector\": \"yes\", \"__current_case__\": 0, \"reference_source\": {\"reference_source_selector\": \"cached\", \"__current_case__\": 0, \"ref_file\": \"mm10full\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.1",
                         "type": "tool",
-                        "uuid": "5ff1e523-c42b-42cd-8857-84d7d83802f8",
+                        "uuid": "898dd71d-9b58-4286-a6ae-5403cb284341",
                         "workflow_outputs": [
                             {
-                                "label": "reads_cutadapt",
-                                "output_name": "report",
-                                "uuid": "b7c138cc-10d0-4bd0-b960-a3b5e60f29cd"
+                                "label": "bam_stats_1",
+                                "output_name": "output",
+                                "uuid": "96de3c0c-4d7e-423b-8e9b-9a12a011d726"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
                         "errors": null,
-                        "id": 6,
+                        "id": 9,
                         "input_connections": {
-                            "results_0|software_cond|output_0|input": [
-                                {
-                                    "id": 4,
-                                    "output_name": "text_file"
-                                },
-                                {
-                                    "id": 2,
-                                    "output_name": "text_file"
-                                }
-                            ]
+                            "input_file": {
+                                "id": 8,
+                                "output_name": "out_file1"
+                            }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "MultiQC",
+                        "name": "Stats",
                         "outputs": [
                             {
-                                "name": "stats",
-                                "type": "input"
-                            },
-                            {
-                                "name": "html_report",
-                                "type": "html"
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": -130,
-                            "height": 162,
-                            "left": 945,
-                            "right": 1145,
-                            "top": -292,
+                            "bottom": 619,
+                            "height": 92,
+                            "left": 1172,
+                            "right": 1372,
+                            "top": 527,
                             "width": 200,
-                            "x": 945,
-                            "y": -292
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionstats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "stats"
-                            }
+                            "x": 1172,
+                            "y": 527
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "75c93c70d094",
-                            "name": "multiqc",
-                            "owner": "iuc",
+                            "changeset_revision": "24c5d43cb545",
+                            "name": "samtools_stats",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"comment\": \"\", \"export\": \"false\", \"flat\": \"false\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"RuntimeValue\"}}]}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9+galaxy1",
+                        "tool_state": "{\"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm10.len\", \"coverage_max\": \"1000\", \"coverage_min\": \"1\", \"coverage_step\": \"1\", \"filter_by_flags\": {\"filter_flags\": \"nofilter\", \"__current_case__\": 1}, \"gc_depth\": \"20000.0\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"insert_size\": \"8000\", \"most_inserts\": \"0.99\", \"read_length\": null, \"remove_dups\": \"false\", \"split_output\": {\"split_output_selector\": \"no\", \"__current_case__\": 0}, \"trim_quality\": \"0\", \"use_reference\": {\"use_ref_selector\": \"yes\", \"__current_case__\": 0, \"reference_source\": {\"reference_source_selector\": \"cached\", \"__current_case__\": 0, \"ref_file\": \"mm10full\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.0.1",
                         "type": "tool",
-                        "uuid": "abf34a41-0150-42fc-b56a-a29eb92c24c3",
+                        "uuid": "cb1e8297-24f1-4553-8111-1a2a48bfc12a",
                         "workflow_outputs": [
                             {
-                                "label": "multiqc",
-                                "output_name": "html_report",
-                                "uuid": "fa7f541d-b9be-4283-afa1-8398d89f345e"
+                                "label": "bam_stats_2",
+                                "output_name": "output",
+                                "uuid": "9603a94a-dcd8-4c1f-89cd-bb31d8572783"
                             }
                         ]
                     }
                 ],
-                "parent_id": "sequence-analysis/quality-control",
-                "path": "topics/sequence-analysis/tutorials/quality-control/workflows/quality_control.ga",
+                "parent_id": "sequence-analysis/mapping",
+                "path": "topics/sequence-analysis/tutorials/mapping/workflows/mapping.ga",
                 "tags": [
                     "sequence-analysis"
                 ],
@@ -211119,21 +213930,21 @@
                         "tests": [
                             {
                                 "data": {
-                                    "end_datetime": "2023-05-19T17:08:59.654933",
-                                    "inputs": "---\nreads_1:\n  class: File\n  location: https://zenodo.org/record/61771/files/GSM461178_untreat_paired_subset_1.fastq\nreads_2:\n  class: File\n  location: https://zenodo.org/record/61771/files/GSM461178_untreat_paired_subset_2.fastq\n",
+                                    "end_datetime": "2023-05-19T16:33:47.079379",
+                                    "inputs": "---\nreads_1:\n  class: File\n  location: https://zenodo.org/record/1324070/files/wt_H3K4me3_read1.fastq.gz\nreads_2:\n  class: File\n  location: https://zenodo.org/record/1324070/files/wt_H3K4me3_read2.fastq.gz\n",
                                     "invocation_details": {
                                         "details": {
                                             "error_message": "",
-                                            "history_id": "2f1f9fa04aab9b59",
+                                            "history_id": "2e96b0bf6abd6b74",
                                             "history_state": "ok",
-                                            "invocation_id": "1375254bd7688d41",
+                                            "invocation_id": "6284e34d09b1b06d",
                                             "invocation_state": "scheduled",
-                                            "workflow_id": "8d2820cd545d11e7"
+                                            "workflow_id": "507e9a109418ad9c"
                                         },
                                         "steps": {
                                             "0. reads_1": {
                                                 "action": null,
-                                                "id": "09aab9ccfa6260cb",
+                                                "id": "239cd24984e05a43",
                                                 "job_id": null,
                                                 "jobs": [],
                                                 "model_class": "WorkflowInvocationStep",
@@ -211141,22 +213952,22 @@
                                                 "output_collections": {},
                                                 "outputs": {
                                                     "output": {
-                                                        "id": "4838ba20a6d86765ff25d30589db09fe",
+                                                        "id": "4838ba20a6d86765ce9b5492a01ba912",
                                                         "src": "hda",
-                                                        "uuid": "3835c7cb-1707-4e6f-85d2-6f1ad5c31bc4"
+                                                        "uuid": "689bd625-8e53-484d-a369-e8f88e298ae8"
                                                     }
                                                 },
                                                 "state": "scheduled",
                                                 "subworkflow": null,
                                                 "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-19T14:59:03.317312",
-                                                "workflow_step_id": "41e0f8150fe3cff2",
+                                                "update_time": "2023-05-19T14:30:12.217904",
+                                                "workflow_step_id": "a07c7d9026192889",
                                                 "workflow_step_label": "reads_1",
-                                                "workflow_step_uuid": "3ba96dd1-e62d-4c22-b5b9-92a03e9b0c46"
+                                                "workflow_step_uuid": "71f77373-c9b8-441c-bbf3-b168fbb69220"
                                             },
                                             "1. reads_2": {
                                                 "action": null,
-                                                "id": "53088303de376bb8",
+                                                "id": "1da8d9ea66ac45a3",
                                                 "job_id": null,
                                                 "jobs": [],
                                                 "model_class": "WorkflowInvocationStep",
@@ -211164,28 +213975,28 @@
                                                 "output_collections": {},
                                                 "outputs": {
                                                     "output": {
-                                                        "id": "4838ba20a6d867656914ebcc68e736a5",
+                                                        "id": "4838ba20a6d8676511241aa0be025fbe",
                                                         "src": "hda",
-                                                        "uuid": "9968668a-3051-4e02-aa3d-4997838a0985"
+                                                        "uuid": "654f0d1a-35d6-4c17-863b-1ed725a10d3c"
                                                     }
                                                 },
                                                 "state": "scheduled",
                                                 "subworkflow": null,
                                                 "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-19T14:59:03.317318",
-                                                "workflow_step_id": "ada35db989250a9c",
+                                                "update_time": "2023-05-19T14:30:12.217908",
+                                                "workflow_step_id": "8b783f04ae56b16d",
                                                 "workflow_step_label": "reads_2",
-                                                "workflow_step_uuid": "11e6b420-32a1-431d-8eb4-b707a1e9b2df"
+                                                "workflow_step_uuid": "3da9f126-0edf-4243-88f7-e1d1528840f6"
                                             },
                                             "2. Unnamed step": {
                                                 "action": null,
-                                                "id": "d94b4b21ddc3e0c3",
-                                                "job_id": "11ac94870d0bb33a2a3328a31b8b1d2e",
+                                                "id": "d11da588620ce6e9",
+                                                "job_id": "11ac94870d0bb33adde30cbebfc7b5aa",
                                                 "jobs": [
                                                     {
-                                                        "command_line": "ln -s '/data/dnb08/galaxy_db/files/3/8/3/dataset_3835c7cb-1707-4e6f-85d2-6f1ad5c31bc4.dat' 'GSM461178_untreat_paired_subset_1_fastq' && mkdir -p '/data/jwd01/main/060/059/60059402/working/dataset_a0107efb-9924-481b-99eb-5e7c74c4c697_files' && fastqc --outdir '/data/jwd01/main/060/059/60059402/working/dataset_a0107efb-9924-481b-99eb-5e7c74c4c697_files'    --quiet --extract  --kmers 7 -f 'fastq' 'GSM461178_untreat_paired_subset_1_fastq'  && cp '/data/jwd01/main/060/059/60059402/working/dataset_a0107efb-9924-481b-99eb-5e7c74c4c697_files'/*/fastqc_data.txt output.txt && cp '/data/jwd01/main/060/059/60059402/working/dataset_a0107efb-9924-481b-99eb-5e7c74c4c697_files'/*\\.html output.html",
+                                                        "command_line": "ln -s '/data/dnb08/galaxy_db/files/6/8/9/dataset_689bd625-8e53-484d-a369-e8f88e298ae8.dat' 'wt_H3K4me3_read1_fastq_gz.gz' && mkdir -p '/data/jwd05e/main/060/058/60058034/working/dataset_efc9b134-bbc0-4a68-9655-0ee02cf880af_files' && fastqc --outdir '/data/jwd05e/main/060/058/60058034/working/dataset_efc9b134-bbc0-4a68-9655-0ee02cf880af_files'    --quiet --extract  --kmers 7 -f 'fastq' 'wt_H3K4me3_read1_fastq_gz.gz'  && cp '/data/jwd05e/main/060/058/60058034/working/dataset_efc9b134-bbc0-4a68-9655-0ee02cf880af_files'/*/fastqc_data.txt output.txt && cp '/data/jwd05e/main/060/058/60058034/working/dataset_efc9b134-bbc0-4a68-9655-0ee02cf880af_files'/*\\.html output.html",
                                                         "command_version": null,
-                                                        "create_time": "2023-05-19T14:59:03.313089",
+                                                        "create_time": "2023-05-19T14:30:12.209933",
                                                         "dependencies": [
                                                             {
                                                                 "cacheable": false,
@@ -211211,15 +214022,15 @@
                                                             }
                                                         ],
                                                         "exit_code": 0,
-                                                        "external_id": "43535387",
+                                                        "external_id": "43534317",
                                                         "galaxy_version": "23.0",
-                                                        "history_id": "2f1f9fa04aab9b59",
-                                                        "id": "11ac94870d0bb33a2a3328a31b8b1d2e",
+                                                        "history_id": "2e96b0bf6abd6b74",
+                                                        "id": "11ac94870d0bb33adde30cbebfc7b5aa",
                                                         "inputs": {
                                                             "input_file": {
-                                                                "id": "4838ba20a6d86765ff25d30589db09fe",
+                                                                "id": "4838ba20a6d86765ce9b5492a01ba912",
                                                                 "src": "hda",
-                                                                "uuid": "3835c7cb-1707-4e6f-85d2-6f1ad5c31bc4"
+                                                                "uuid": "689bd625-8e53-484d-a369-e8f88e298ae8"
                                                             }
                                                         },
                                                         "job_messages": [],
@@ -211248,30 +214059,30 @@
                                                             {
                                                                 "name": "start_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684508692.0000000",
+                                                                "raw_value": "1684506662.0000000",
                                                                 "title": "Job Start Time",
-                                                                "value": "2023-05-19 17:04:52"
+                                                                "value": "2023-05-19 16:31:02"
                                                             },
                                                             {
                                                                 "name": "end_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684508707.0000000",
+                                                                "raw_value": "1684506713.0000000",
                                                                 "title": "Job End Time",
-                                                                "value": "2023-05-19 17:05:07"
+                                                                "value": "2023-05-19 16:31:53"
                                                             },
                                                             {
                                                                 "name": "runtime_seconds",
                                                                 "plugin": "core",
-                                                                "raw_value": "15.0000000",
+                                                                "raw_value": "51.0000000",
                                                                 "title": "Job Runtime (Wall Clock)",
-                                                                "value": "15 seconds"
+                                                                "value": "51 seconds"
                                                             },
                                                             {
                                                                 "name": "cpuacct.usage",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "12194724984.0000000",
+                                                                "raw_value": "12375662744.0000000",
                                                                 "title": "CPU Time",
-                                                                "value": "12.194724984 seconds"
+                                                                "value": "12.375662744 seconds"
                                                             },
                                                             {
                                                                 "name": "memory.failcnt",
@@ -211290,9 +214101,9 @@
                                                             {
                                                                 "name": "memory.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "357576704.0000000",
+                                                                "raw_value": "268595200.0000000",
                                                                 "title": "Max memory usage (MEM)",
-                                                                "value": "341.0 MB"
+                                                                "value": "256.2 MB"
                                                             },
                                                             {
                                                                 "name": "memory.memsw.limit_in_bytes",
@@ -211304,9 +214115,9 @@
                                                             {
                                                                 "name": "memory.memsw.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "357576704.0000000",
+                                                                "raw_value": "268595200.0000000",
                                                                 "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "341.0 MB"
+                                                                "value": "256.2 MB"
                                                             },
                                                             {
                                                                 "name": "memory.oom_control.oom_kill_disable",
@@ -211336,19 +214147,19 @@
                                                         "output_collections": {},
                                                         "outputs": {
                                                             "html_file": {
-                                                                "id": "4838ba20a6d867651957556f6b54741b",
+                                                                "id": "4838ba20a6d8676572288659e6a2bd0b",
                                                                 "src": "hda",
-                                                                "uuid": "a0107efb-9924-481b-99eb-5e7c74c4c697"
+                                                                "uuid": "efc9b134-bbc0-4a68-9655-0ee02cf880af"
                                                             },
                                                             "text_file": {
-                                                                "id": "4838ba20a6d86765967c147adffa4ae2",
+                                                                "id": "4838ba20a6d86765100e931edbfb8029",
                                                                 "src": "hda",
-                                                                "uuid": "8aadb0d6-4752-43b3-9a70-b58359fe1659"
+                                                                "uuid": "718a2f6a-6747-4754-a9da-60a98a6c5957"
                                                             }
                                                         },
                                                         "params": {
-                                                            "__input_ext": "\"fastqsanger\"",
-                                                            "__workflow_invocation_uuid__": "\"a085c588f65511ed82b7001e67d2ec02\"",
+                                                            "__input_ext": "\"fastqsanger.gz\"",
+                                                            "__workflow_invocation_uuid__": "\"9ef558e0f65111eda6f2001e67d2ec02\"",
                                                             "adapters": null,
                                                             "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
                                                             "contaminants": null,
@@ -211365,7 +214176,7 @@
                                                         "tool_stderr": "",
                                                         "tool_stdout": "",
                                                         "traceback": null,
-                                                        "update_time": "2023-05-19T15:05:09.851510",
+                                                        "update_time": "2023-05-19T14:31:54.552522",
                                                         "user_email": "hxr@informatik.uni-freiburg.de"
                                                     }
                                                 ],
@@ -211374,44 +214185,67 @@
                                                 "output_collections": {},
                                                 "outputs": {
                                                     "html_file": {
-                                                        "id": "4838ba20a6d867651957556f6b54741b",
+                                                        "id": "4838ba20a6d8676572288659e6a2bd0b",
                                                         "src": "hda",
-                                                        "uuid": "a0107efb-9924-481b-99eb-5e7c74c4c697"
+                                                        "uuid": "efc9b134-bbc0-4a68-9655-0ee02cf880af"
                                                     },
                                                     "text_file": {
-                                                        "id": "4838ba20a6d86765967c147adffa4ae2",
+                                                        "id": "4838ba20a6d86765100e931edbfb8029",
                                                         "src": "hda",
-                                                        "uuid": "8aadb0d6-4752-43b3-9a70-b58359fe1659"
+                                                        "uuid": "718a2f6a-6747-4754-a9da-60a98a6c5957"
                                                     }
                                                 },
                                                 "state": "scheduled",
                                                 "subworkflow": null,
                                                 "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-19T15:05:09.811263",
-                                                "workflow_step_id": "4b6834f9ae6537d8",
+                                                "update_time": "2023-05-19T14:31:54.529698",
+                                                "workflow_step_id": "1e8dd70f0c41cadf",
                                                 "workflow_step_label": null,
-                                                "workflow_step_uuid": "026332e1-70ba-4705-b75e-d228fafacc92"
+                                                "workflow_step_uuid": "f9d0ea7d-f2e3-41b2-bc11-4d40665a4439"
                                             },
                                             "3. Unnamed step": {
                                                 "action": null,
-                                                "id": "c5c312487856832c",
-                                                "job_id": "11ac94870d0bb33a14ad54e496e129b6",
+                                                "id": "76778945e7e793e5",
+                                                "job_id": "11ac94870d0bb33af53ebe6a5976a7e4",
                                                 "jobs": [
                                                     {
-                                                        "command_line": "ln -f -s '/data/dnb08/galaxy_db/files/3/8/3/dataset_3835c7cb-1707-4e6f-85d2-6f1ad5c31bc4.dat' 'GSM461178_untreat_paired_subset_1_fastq.fq' &&    cutadapt  -j ${GALAXY_SLOTS:-1}          --output='out1.fq'  --error-rate=0.1 --times=1 --overlap=3         --minimum-length=20   --quality-cutoff=20   'GSM461178_untreat_paired_subset_1_fastq.fq'  > report.txt",
-                                                        "command_version": "1.16",
-                                                        "create_time": "2023-05-19T14:59:03.399654",
-                                                        "dependencies": [],
+                                                        "command_line": "ln -s '/data/dnb08/galaxy_db/files/6/5/4/dataset_654f0d1a-35d6-4c17-863b-1ed725a10d3c.dat' 'wt_H3K4me3_read2_fastq_gz.gz' && mkdir -p '/data/jwd02f/main/060/058/60058035/working/dataset_5f25fcad-3405-4aa3-a343-8eb710d98761_files' && fastqc --outdir '/data/jwd02f/main/060/058/60058035/working/dataset_5f25fcad-3405-4aa3-a343-8eb710d98761_files'    --quiet --extract  --kmers 7 -f 'fastq' 'wt_H3K4me3_read2_fastq_gz.gz'  && cp '/data/jwd02f/main/060/058/60058035/working/dataset_5f25fcad-3405-4aa3-a343-8eb710d98761_files'/*/fastqc_data.txt output.txt && cp '/data/jwd02f/main/060/058/60058035/working/dataset_5f25fcad-3405-4aa3-a343-8eb710d98761_files'/*\\.html output.html",
+                                                        "command_version": null,
+                                                        "create_time": "2023-05-19T14:30:12.324932",
+                                                        "dependencies": [
+                                                            {
+                                                                "cacheable": false,
+                                                                "dependency_resolver": {
+                                                                    "auto_init": true,
+                                                                    "auto_install": false,
+                                                                    "can_uninstall_dependencies": true,
+                                                                    "ensure_channels": "conda-forge,bioconda",
+                                                                    "model_class": "CondaDependencyResolver",
+                                                                    "prefix": "/usr/local/tools/_conda",
+                                                                    "read_only": false,
+                                                                    "resolver_type": "conda",
+                                                                    "resolves_simple_dependencies": true,
+                                                                    "use_local": false,
+                                                                    "versionless": false
+                                                                },
+                                                                "dependency_type": "conda",
+                                                                "environment_path": "/usr/local/tools/_conda/envs/__fastqc@0.11.8",
+                                                                "exact": true,
+                                                                "model_class": "MergedCondaDependency",
+                                                                "name": "fastqc",
+                                                                "version": "0.11.8"
+                                                            }
+                                                        ],
                                                         "exit_code": 0,
-                                                        "external_id": "43535389",
+                                                        "external_id": "43534318",
                                                         "galaxy_version": "23.0",
-                                                        "history_id": "2f1f9fa04aab9b59",
-                                                        "id": "11ac94870d0bb33a14ad54e496e129b6",
+                                                        "history_id": "2e96b0bf6abd6b74",
+                                                        "id": "11ac94870d0bb33af53ebe6a5976a7e4",
                                                         "inputs": {
-                                                            "input_1": {
-                                                                "id": "4838ba20a6d86765ff25d30589db09fe",
+                                                            "input_file": {
+                                                                "id": "4838ba20a6d8676511241aa0be025fbe",
                                                                 "src": "hda",
-                                                                "uuid": "3835c7cb-1707-4e6f-85d2-6f1ad5c31bc4"
+                                                                "uuid": "654f0d1a-35d6-4c17-863b-1ed725a10d3c"
                                                             }
                                                         },
                                                         "job_messages": [],
@@ -211419,9 +214253,229 @@
                                                             {
                                                                 "name": "hostname",
                                                                 "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c125m425-6547.novalocal",
+                                                                "raw_value": "vgcnbwc-worker-c125m425-1589.novalocal",
                                                                 "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c125m425-6547.novalocal"
+                                                                "value": "vgcnbwc-worker-c125m425-1589.novalocal"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_slots",
+                                                                "plugin": "core",
+                                                                "raw_value": "8.0000000",
+                                                                "title": "Cores Allocated",
+                                                                "value": "8"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_memory_mb",
+                                                                "plugin": "core",
+                                                                "raw_value": "31129.0000000",
+                                                                "title": "Memory Allocated (MB)",
+                                                                "value": "31129"
+                                                            },
+                                                            {
+                                                                "name": "start_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684506662.0000000",
+                                                                "title": "Job Start Time",
+                                                                "value": "2023-05-19 16:31:02"
+                                                            },
+                                                            {
+                                                                "name": "end_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684506721.0000000",
+                                                                "title": "Job End Time",
+                                                                "value": "2023-05-19 16:32:01"
+                                                            },
+                                                            {
+                                                                "name": "runtime_seconds",
+                                                                "plugin": "core",
+                                                                "raw_value": "59.0000000",
+                                                                "title": "Job Runtime (Wall Clock)",
+                                                                "value": "59 seconds"
+                                                            },
+                                                            {
+                                                                "name": "cpuacct.usage",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "13599783917.0000000",
+                                                                "title": "CPU Time",
+                                                                "value": "13.599783917 seconds"
+                                                            },
+                                                            {
+                                                                "name": "memory.failcnt",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Failed to allocate memory count",
+                                                                "value": 0.0
+                                                            },
+                                                            {
+                                                                "name": "memory.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "32749125632.0000000",
+                                                                "title": "Memory limit on cgroup (MEM)",
+                                                                "value": "30.5 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "231440384.0000000",
+                                                                "title": "Max memory usage (MEM)",
+                                                                "value": "220.7 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "9223372036854771712.0000000",
+                                                                "title": "Memory limit on cgroup (MEM+SWP)",
+                                                                "value": "8.0 EB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "231440384.0000000",
+                                                                "title": "Max memory usage (MEM+SWP)",
+                                                                "value": "220.7 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.oom_kill_disable",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "OOM Control enabled",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.under_oom",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Was OOM Killer active?",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.soft_limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Memory softlimit on cgroup",
+                                                                "value": "0 bytes"
+                                                            }
+                                                        ],
+                                                        "job_stderr": "",
+                                                        "job_stdout": "",
+                                                        "model_class": "Job",
+                                                        "output_collections": {},
+                                                        "outputs": {
+                                                            "html_file": {
+                                                                "id": "4838ba20a6d8676521dd17a9b62d385f",
+                                                                "src": "hda",
+                                                                "uuid": "5f25fcad-3405-4aa3-a343-8eb710d98761"
+                                                            },
+                                                            "text_file": {
+                                                                "id": "4838ba20a6d8676577d1d2d4d95b125f",
+                                                                "src": "hda",
+                                                                "uuid": "0a0a3867-f5f7-4690-9776-09274436e562"
+                                                            }
+                                                        },
+                                                        "params": {
+                                                            "__input_ext": "\"fastqsanger.gz\"",
+                                                            "__workflow_invocation_uuid__": "\"9ef558e0f65111eda6f2001e67d2ec02\"",
+                                                            "adapters": null,
+                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
+                                                            "contaminants": null,
+                                                            "dbkey": "\"?\"",
+                                                            "kmers": "\"7\"",
+                                                            "limits": null,
+                                                            "min_length": null,
+                                                            "nogroup": "false"
+                                                        },
+                                                        "state": "ok",
+                                                        "stderr": "",
+                                                        "stdout": "",
+                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                                                        "tool_stderr": "",
+                                                        "tool_stdout": "",
+                                                        "traceback": null,
+                                                        "update_time": "2023-05-19T14:32:05.448601",
+                                                        "user_email": "hxr@informatik.uni-freiburg.de"
+                                                    }
+                                                ],
+                                                "model_class": "WorkflowInvocationStep",
+                                                "order_index": 3,
+                                                "output_collections": {},
+                                                "outputs": {
+                                                    "html_file": {
+                                                        "id": "4838ba20a6d8676521dd17a9b62d385f",
+                                                        "src": "hda",
+                                                        "uuid": "5f25fcad-3405-4aa3-a343-8eb710d98761"
+                                                    },
+                                                    "text_file": {
+                                                        "id": "4838ba20a6d8676577d1d2d4d95b125f",
+                                                        "src": "hda",
+                                                        "uuid": "0a0a3867-f5f7-4690-9776-09274436e562"
+                                                    }
+                                                },
+                                                "state": "scheduled",
+                                                "subworkflow": null,
+                                                "subworkflow_invocation_id": null,
+                                                "update_time": "2023-05-19T14:32:05.428308",
+                                                "workflow_step_id": "7c2802e0bfd4ecd0",
+                                                "workflow_step_label": null,
+                                                "workflow_step_uuid": "faa4b55f-0b0c-4696-b61e-f281007aa8a1"
+                                            },
+                                            "4. Unnamed step": {
+                                                "action": null,
+                                                "id": "1504cb0a755f30bb",
+                                                "job_id": "11ac94870d0bb33a0920faa96345e33f",
+                                                "jobs": [
+                                                    {
+                                                        "command_line": "ln -s '/data/dnb08/galaxy_db/files/6/8/9/dataset_689bd625-8e53-484d-a369-e8f88e298ae8.dat' input_1.fastq.gz &&  ln -s '/data/dnb08/galaxy_db/files/6/5/4/dataset_654f0d1a-35d6-4c17-863b-1ed725a10d3c.dat' input_2.fastq.gz &&  trim_galore  --phred33    --output_dir ./      --paired      input_1.fastq.gz input_2.fastq.gz   && if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi",
+                                                        "command_version": "Quality-/Adapter-/RRBS-Trimming\n                               (powered by Cutadapt)\n                                  version 0.4.3\n\n                             Last update: 07 12 2016",
+                                                        "create_time": "2023-05-19T14:30:12.446388",
+                                                        "dependencies": [
+                                                            {
+                                                                "cacheable": false,
+                                                                "dependency_resolver": {
+                                                                    "auto_init": true,
+                                                                    "auto_install": false,
+                                                                    "can_uninstall_dependencies": true,
+                                                                    "ensure_channels": "conda-forge,bioconda",
+                                                                    "model_class": "CondaDependencyResolver",
+                                                                    "prefix": "/usr/local/tools/_conda",
+                                                                    "read_only": false,
+                                                                    "resolver_type": "conda",
+                                                                    "resolves_simple_dependencies": true,
+                                                                    "use_local": false,
+                                                                    "versionless": false
+                                                                },
+                                                                "dependency_type": "conda",
+                                                                "environment_path": "/usr/local/tools/_conda/envs/__trim-galore@0.4.3",
+                                                                "exact": true,
+                                                                "model_class": "MergedCondaDependency",
+                                                                "name": "trim-galore",
+                                                                "version": "0.4.3"
+                                                            }
+                                                        ],
+                                                        "exit_code": 0,
+                                                        "external_id": "43534319",
+                                                        "galaxy_version": "23.0",
+                                                        "history_id": "2e96b0bf6abd6b74",
+                                                        "id": "11ac94870d0bb33a0920faa96345e33f",
+                                                        "inputs": {
+                                                            "input_mate1": {
+                                                                "id": "4838ba20a6d86765ce9b5492a01ba912",
+                                                                "src": "hda",
+                                                                "uuid": "689bd625-8e53-484d-a369-e8f88e298ae8"
+                                                            },
+                                                            "input_mate2": {
+                                                                "id": "4838ba20a6d8676511241aa0be025fbe",
+                                                                "src": "hda",
+                                                                "uuid": "654f0d1a-35d6-4c17-863b-1ed725a10d3c"
+                                                            }
+                                                        },
+                                                        "job_messages": [],
+                                                        "job_metrics": [
+                                                            {
+                                                                "name": "hostname",
+                                                                "plugin": "hostname",
+                                                                "raw_value": "vgcnbwc-worker-c36m100-8763.novalocal",
+                                                                "title": "hostname",
+                                                                "value": "vgcnbwc-worker-c36m100-8763.novalocal"
                                                             },
                                                             {
                                                                 "name": "galaxy_slots",
@@ -211440,30 +214494,30 @@
                                                             {
                                                                 "name": "start_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684508382.0000000",
+                                                                "raw_value": "1684506638.0000000",
                                                                 "title": "Job Start Time",
-                                                                "value": "2023-05-19 16:59:42"
+                                                                "value": "2023-05-19 16:30:38"
                                                             },
                                                             {
                                                                 "name": "end_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684508412.0000000",
+                                                                "raw_value": "1684506671.0000000",
                                                                 "title": "Job End Time",
-                                                                "value": "2023-05-19 17:00:12"
+                                                                "value": "2023-05-19 16:31:11"
                                                             },
                                                             {
                                                                 "name": "runtime_seconds",
                                                                 "plugin": "core",
-                                                                "raw_value": "30.0000000",
+                                                                "raw_value": "33.0000000",
                                                                 "title": "Job Runtime (Wall Clock)",
-                                                                "value": "30 seconds"
+                                                                "value": "33 seconds"
                                                             },
                                                             {
                                                                 "name": "cpuacct.usage",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "7314785524.0000000",
+                                                                "raw_value": "15323583745.0000000",
                                                                 "title": "CPU Time",
-                                                                "value": "7.314785524 seconds"
+                                                                "value": "15.323583745 seconds"
                                                             },
                                                             {
                                                                 "name": "memory.failcnt",
@@ -211482,9 +214536,9 @@
                                                             {
                                                                 "name": "memory.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "251256832.0000000",
+                                                                "raw_value": "216088576.0000000",
                                                                 "title": "Max memory usage (MEM)",
-                                                                "value": "239.6 MB"
+                                                                "value": "206.1 MB"
                                                             },
                                                             {
                                                                 "name": "memory.memsw.limit_in_bytes",
@@ -211496,9 +214550,9 @@
                                                             {
                                                                 "name": "memory.memsw.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "251256832.0000000",
+                                                                "raw_value": "216088576.0000000",
                                                                 "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "239.6 MB"
+                                                                "value": "206.1 MB"
                                                             },
                                                             {
                                                                 "name": "memory.oom_control.oom_kill_disable",
@@ -211527,71 +214581,483 @@
                                                         "model_class": "Job",
                                                         "output_collections": {},
                                                         "outputs": {
-                                                            "out1": {
-                                                                "id": "4838ba20a6d8676528f2966e438993df",
+                                                            "trimmed_reads_pair1": {
+                                                                "id": "4838ba20a6d86765439b06bcf8677007",
                                                                 "src": "hda",
-                                                                "uuid": "5096388f-425a-42a1-b99e-4f0174665371"
+                                                                "uuid": "64981dba-44f7-4768-8b63-e63defba2ecf"
                                                             },
-                                                            "report": {
-                                                                "id": "4838ba20a6d8676504b9c2c33c839b66",
+                                                            "trimmed_reads_pair2": {
+                                                                "id": "4838ba20a6d867658f72f66dd1d7e6cc",
                                                                 "src": "hda",
-                                                                "uuid": "b9909c1d-09b1-47ec-9135-48915855c294"
+                                                                "uuid": "0764cea4-72ed-4a8c-93b2-88bd066afc4e"
                                                             }
                                                         },
                                                         "params": {
                                                             "__input_ext": "\"input\"",
-                                                            "__workflow_invocation_uuid__": "\"a085c588f65511ed82b7001e67d2ec02\"",
-                                                            "adapter_options": "{\"count\": \"1\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"overlap\": \"3\"}",
+                                                            "__workflow_invocation_uuid__": "\"9ef558e0f65111eda6f2001e67d2ec02\"",
                                                             "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
                                                             "dbkey": "\"?\"",
-                                                            "filter_options": "{\"discard\": false, \"discard_untrimmed\": false, \"mask_adapter\": false, \"max\": \"0\", \"max_n\": null, \"min\": \"20\", \"no_trim\": false, \"pair_filter\": \"any\"}",
-                                                            "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 137417465, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\", \"front_adapters\": []}, \"type\": \"single\"}",
-                                                            "output_options": "{\"info_file\": false, \"report\": true, \"rest_file\": false, \"too_long_file\": false, \"too_short_file\": false, \"untrimmed_file\": false, \"wildcard_file\": false}",
-                                                            "read_mod_options": "{\"length\": \"0\", \"length_tag\": \"\", \"nextseq_trim\": \"0\", \"prefix\": \"\", \"quality_cutoff\": \"20\", \"strip_suffix\": \"\", \"suffix\": \"\", \"trim_n\": false}"
+                                                            "params": "{\"__current_case__\": 0, \"settingsType\": \"default\"}",
+                                                            "rrbs": "{\"__current_case__\": 0, \"settingsType\": \"default\"}",
+                                                            "singlePaired": "{\"__current_case__\": 1, \"input_mate1\": {\"values\": [{\"id\": 137415404, \"src\": \"hda\"}]}, \"input_mate2\": {\"values\": [{\"id\": 137415461, \"src\": \"hda\"}]}, \"sPaired\": \"paired\", \"three_prime_clip_R1\": null, \"three_prime_clip_R2\": null, \"trim1\": false, \"trimming\": {\"__current_case__\": 0, \"trimming_select\": \"\"}}"
                                                         },
                                                         "state": "ok",
-                                                        "stderr": "",
+                                                        "stderr": "Path to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\n\n\nAUTO-DETECTING ADAPTER TYPE\n===========================\nAttempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq.gz <<)\n\nFound perfect matches for the following adapter sequences:\nAdapter type\tCount\tSequence\tSequences analysed\tPercentage\nIllumina\t2\tAGATCGGAAGAGC\t50000\t0.00\nsmallRNA\t0\tTGGAATTCTCGG\t50000\t0.00\nNextera\t0\tCTGTCTCTTATA\t50000\t0.00\nUsing Illumina adapter for trimming (count: 2). Second best hit was smallRNA (count: 0)\n\nWriting report to './input_1.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq.gz\nTrimming mode: paired-end\nTrim Galore version: 0.4.3\nCutadapt version: 1.13\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nWriting final adapter and quality trimmed output to input_1_trimmed.fq.gz\n\n\n  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq.gz <<< \nThis is cutadapt 1.13 with Python 3.6.1\nCommand line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz\nTrimming 1 adapter with at most 10.0% errors in single-end mode ...\nFinished in 0.85 s (17 us/read; 3.52 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed:                  50,000\nReads with adapters:                    14,011 (28.0%)\nReads written (passing filters):        50,000 (100.0%)\n\nTotal basepairs processed:     2,550,000 bp\nQuality-trimmed:                  34,012 bp (1.3%)\nTotal written (filtered):      2,495,795 bp (97.9%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14011 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n  A: 27.3%\n  C: 33.3%\n  G: 24.8%\n  T: 14.6%\n  none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t9379\t12500.0\t0\t9379\n2\t3646\t3125.0\t0\t3646\n3\t791\t781.2\t0\t791\n4\t134\t195.3\t0\t134\n5\t33\t48.8\t0\t33\n6\t9\t12.2\t0\t9\n7\t3\t3.1\t0\t3\n8\t1\t0.8\t0\t1\n9\t1\t0.2\t0\t0 1\n10\t3\t0.0\t1\t0 3\n11\t1\t0.0\t1\t1\n15\t1\t0.0\t1\t1\n16\t1\t0.0\t1\t0 1\n19\t1\t0.0\t1\t1\n27\t1\t0.0\t1\t0 1\n28\t1\t0.0\t1\t0 1\n32\t1\t0.0\t1\t0 1\n36\t1\t0.0\t1\t0 1\n43\t1\t0.0\t1\t0 1\n49\t1\t0.0\t1\t0 1\n50\t1\t0.0\t1\t0 1\n\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq.gz\n=============================================\n50000 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nWriting report to './input_2.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_2.fastq.gz\nTrimming mode: paired-end\nTrim Galore version: 0.4.3\nCutadapt version: 1.13\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nWriting final adapter and quality trimmed output to input_2_trimmed.fq.gz\n\n\n  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_2.fastq.gz <<< \nThis is cutadapt 1.13 with Python 3.6.1\nCommand line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_2.fastq.gz\nTrimming 1 adapter with at most 10.0% errors in single-end mode ...\nFinished in 0.91 s (18 us/read; 3.30 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed:                  50,000\nReads with adapters:                    13,787 (27.6%)\nReads written (passing filters):        50,000 (100.0%)\n\nTotal basepairs processed:     2,550,000 bp\nQuality-trimmed:                 120,340 bp (4.7%)\nTotal written (filtered):      2,410,008 bp (94.5%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13787 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n  A: 27.6%\n  C: 32.8%\n  G: 24.6%\n  T: 15.0%\n  none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t9236\t12500.0\t0\t9236\n2\t3546\t3125.0\t0\t3546\n3\t827\t781.2\t0\t827\n4\t131\t195.3\t0\t131\n5\t36\t48.8\t0\t36\n6\t3\t12.2\t0\t3\n7\t2\t3.1\t0\t2\n9\t1\t0.2\t0\t0 1\n11\t2\t0.0\t1\t1 1\n15\t1\t0.0\t1\t1\n19\t1\t0.0\t1\t1\n42\t1\t0.0\t1\t0 1\n\n\nRUN STATISTICS FOR INPUT FILE: input_2.fastq.gz\n=============================================\n50000 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nValidate paired-end files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz\nfile_1: input_1_trimmed.fq.gz, file_2: input_2_trimmed.fq.gz\n\n\n>>>>> Now validing the length of the 2 paired-end infiles: input_1_trimmed.fq.gz and input_2_trimmed.fq.gz <<<<<\nWriting validated paired-end read 1 reads to input_1_val_1.fq.gz\nWriting validated paired-end read 2 reads to input_2_val_2.fq.gz\n\nTotal number of sequences analysed: 50000\n\nNumber of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1639 (3.28%)\n\nDeleting both intermediate output files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz\n\n====================================================================================================\n\n\ngzip: stdout: Broken pipe\n",
+                                                        "stdout": "1.13\n",
+                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1",
+                                                        "tool_stderr": "Path to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\n\n\nAUTO-DETECTING ADAPTER TYPE\n===========================\nAttempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq.gz <<)\n\nFound perfect matches for the following adapter sequences:\nAdapter type\tCount\tSequence\tSequences analysed\tPercentage\nIllumina\t2\tAGATCGGAAGAGC\t50000\t0.00\nsmallRNA\t0\tTGGAATTCTCGG\t50000\t0.00\nNextera\t0\tCTGTCTCTTATA\t50000\t0.00\nUsing Illumina adapter for trimming (count: 2). Second best hit was smallRNA (count: 0)\n\nWriting report to './input_1.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq.gz\nTrimming mode: paired-end\nTrim Galore version: 0.4.3\nCutadapt version: 1.13\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nWriting final adapter and quality trimmed output to input_1_trimmed.fq.gz\n\n\n  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq.gz <<< \nThis is cutadapt 1.13 with Python 3.6.1\nCommand line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz\nTrimming 1 adapter with at most 10.0% errors in single-end mode ...\nFinished in 0.85 s (17 us/read; 3.52 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed:                  50,000\nReads with adapters:                    14,011 (28.0%)\nReads written (passing filters):        50,000 (100.0%)\n\nTotal basepairs processed:     2,550,000 bp\nQuality-trimmed:                  34,012 bp (1.3%)\nTotal written (filtered):      2,495,795 bp (97.9%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14011 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n  A: 27.3%\n  C: 33.3%\n  G: 24.8%\n  T: 14.6%\n  none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t9379\t12500.0\t0\t9379\n2\t3646\t3125.0\t0\t3646\n3\t791\t781.2\t0\t791\n4\t134\t195.3\t0\t134\n5\t33\t48.8\t0\t33\n6\t9\t12.2\t0\t9\n7\t3\t3.1\t0\t3\n8\t1\t0.8\t0\t1\n9\t1\t0.2\t0\t0 1\n10\t3\t0.0\t1\t0 3\n11\t1\t0.0\t1\t1\n15\t1\t0.0\t1\t1\n16\t1\t0.0\t1\t0 1\n19\t1\t0.0\t1\t1\n27\t1\t0.0\t1\t0 1\n28\t1\t0.0\t1\t0 1\n32\t1\t0.0\t1\t0 1\n36\t1\t0.0\t1\t0 1\n43\t1\t0.0\t1\t0 1\n49\t1\t0.0\t1\t0 1\n50\t1\t0.0\t1\t0 1\n\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq.gz\n=============================================\n50000 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nWriting report to './input_2.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_2.fastq.gz\nTrimming mode: paired-end\nTrim Galore version: 0.4.3\nCutadapt version: 1.13\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nWriting final adapter and quality trimmed output to input_2_trimmed.fq.gz\n\n\n  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_2.fastq.gz <<< \nThis is cutadapt 1.13 with Python 3.6.1\nCommand line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_2.fastq.gz\nTrimming 1 adapter with at most 10.0% errors in single-end mode ...\nFinished in 0.91 s (18 us/read; 3.30 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed:                  50,000\nReads with adapters:                    13,787 (27.6%)\nReads written (passing filters):        50,000 (100.0%)\n\nTotal basepairs processed:     2,550,000 bp\nQuality-trimmed:                 120,340 bp (4.7%)\nTotal written (filtered):      2,410,008 bp (94.5%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13787 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n  A: 27.6%\n  C: 32.8%\n  G: 24.6%\n  T: 15.0%\n  none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t9236\t12500.0\t0\t9236\n2\t3546\t3125.0\t0\t3546\n3\t827\t781.2\t0\t827\n4\t131\t195.3\t0\t131\n5\t36\t48.8\t0\t36\n6\t3\t12.2\t0\t3\n7\t2\t3.1\t0\t2\n9\t1\t0.2\t0\t0 1\n11\t2\t0.0\t1\t1 1\n15\t1\t0.0\t1\t1\n19\t1\t0.0\t1\t1\n42\t1\t0.0\t1\t0 1\n\n\nRUN STATISTICS FOR INPUT FILE: input_2.fastq.gz\n=============================================\n50000 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nValidate paired-end files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz\nfile_1: input_1_trimmed.fq.gz, file_2: input_2_trimmed.fq.gz\n\n\n>>>>> Now validing the length of the 2 paired-end infiles: input_1_trimmed.fq.gz and input_2_trimmed.fq.gz <<<<<\nWriting validated paired-end read 1 reads to input_1_val_1.fq.gz\nWriting validated paired-end read 2 reads to input_2_val_2.fq.gz\n\nTotal number of sequences analysed: 50000\n\nNumber of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1639 (3.28%)\n\nDeleting both intermediate output files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz\n\n====================================================================================================\n\n\ngzip: stdout: Broken pipe\n",
+                                                        "tool_stdout": "1.13\n",
+                                                        "traceback": null,
+                                                        "update_time": "2023-05-19T14:31:12.868610",
+                                                        "user_email": "hxr@informatik.uni-freiburg.de"
+                                                    }
+                                                ],
+                                                "model_class": "WorkflowInvocationStep",
+                                                "order_index": 4,
+                                                "output_collections": {},
+                                                "outputs": {
+                                                    "trimmed_reads_pair1": {
+                                                        "id": "4838ba20a6d86765439b06bcf8677007",
+                                                        "src": "hda",
+                                                        "uuid": "64981dba-44f7-4768-8b63-e63defba2ecf"
+                                                    },
+                                                    "trimmed_reads_pair2": {
+                                                        "id": "4838ba20a6d867658f72f66dd1d7e6cc",
+                                                        "src": "hda",
+                                                        "uuid": "0764cea4-72ed-4a8c-93b2-88bd066afc4e"
+                                                    }
+                                                },
+                                                "state": "scheduled",
+                                                "subworkflow": null,
+                                                "subworkflow_invocation_id": null,
+                                                "update_time": "2023-05-19T14:31:12.847743",
+                                                "workflow_step_id": "0cdaaf28f2c92138",
+                                                "workflow_step_label": null,
+                                                "workflow_step_uuid": "ba2566a8-447f-45ed-98d1-1fd1a5ba6ab4"
+                                            },
+                                            "5. Unnamed step": {
+                                                "action": null,
+                                                "id": "c06c2ed6eeedc161",
+                                                "job_id": "11ac94870d0bb33a0cd484c99b4bfb1e",
+                                                "jobs": [
+                                                    {
+                                                        "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&    mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/data/dnb08/galaxy_db/files/0/a/0/dataset_0a0a3867-f5f7-4690-9776-09274436e562.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_1' && ln -s '/data/dnb08/galaxy_db/files/7/1/8/dataset_718a2f6a-6747-4754-a9da-60a98a6c5957.dat' 'multiqc_WDir/fastqc_0/data_0/file_1/fastqc_data.txt' &&  multiqc multiqc_WDir --filename \"report\"",
+                                                        "command_version": null,
+                                                        "create_time": "2023-05-19T14:30:12.574335",
+                                                        "dependencies": [],
+                                                        "exit_code": 0,
+                                                        "external_id": "43534360",
+                                                        "galaxy_version": "23.0",
+                                                        "history_id": "2e96b0bf6abd6b74",
+                                                        "id": "11ac94870d0bb33a0cd484c99b4bfb1e",
+                                                        "inputs": {
+                                                            "results_0|software_cond|output_0|input": {
+                                                                "id": "4838ba20a6d8676577d1d2d4d95b125f",
+                                                                "src": "hda",
+                                                                "uuid": "0a0a3867-f5f7-4690-9776-09274436e562"
+                                                            },
+                                                            "results_0|software_cond|output_0|input1": {
+                                                                "id": "4838ba20a6d8676577d1d2d4d95b125f",
+                                                                "src": "hda",
+                                                                "uuid": "0a0a3867-f5f7-4690-9776-09274436e562"
+                                                            },
+                                                            "results_0|software_cond|output_0|input2": {
+                                                                "id": "4838ba20a6d86765100e931edbfb8029",
+                                                                "src": "hda",
+                                                                "uuid": "718a2f6a-6747-4754-a9da-60a98a6c5957"
+                                                            }
+                                                        },
+                                                        "job_messages": [],
+                                                        "job_metrics": [
+                                                            {
+                                                                "name": "hostname",
+                                                                "plugin": "hostname",
+                                                                "raw_value": "vgcnbwc-worker-c125m425-4973.novalocal",
+                                                                "title": "hostname",
+                                                                "value": "vgcnbwc-worker-c125m425-4973.novalocal"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_slots",
+                                                                "plugin": "core",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "Cores Allocated",
+                                                                "value": "1"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_memory_mb",
+                                                                "plugin": "core",
+                                                                "raw_value": "11673.0000000",
+                                                                "title": "Memory Allocated (MB)",
+                                                                "value": "11673"
+                                                            },
+                                                            {
+                                                                "name": "start_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684506732.0000000",
+                                                                "title": "Job Start Time",
+                                                                "value": "2023-05-19 16:32:12"
+                                                            },
+                                                            {
+                                                                "name": "end_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684506804.0000000",
+                                                                "title": "Job End Time",
+                                                                "value": "2023-05-19 16:33:24"
+                                                            },
+                                                            {
+                                                                "name": "runtime_seconds",
+                                                                "plugin": "core",
+                                                                "raw_value": "72.0000000",
+                                                                "title": "Job Runtime (Wall Clock)",
+                                                                "value": "1 minute"
+                                                            },
+                                                            {
+                                                                "name": "cpuacct.usage",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "11111220478.0000000",
+                                                                "title": "CPU Time",
+                                                                "value": "11.111220478 seconds"
+                                                            },
+                                                            {
+                                                                "name": "memory.failcnt",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Failed to allocate memory count",
+                                                                "value": 0.0
+                                                            },
+                                                            {
+                                                                "name": "memory.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "21474836480.0000000",
+                                                                "title": "Memory limit on cgroup (MEM)",
+                                                                "value": "20.0 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "246882304.0000000",
+                                                                "title": "Max memory usage (MEM)",
+                                                                "value": "235.4 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "9223372036854771712.0000000",
+                                                                "title": "Memory limit on cgroup (MEM+SWP)",
+                                                                "value": "8.0 EB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "246882304.0000000",
+                                                                "title": "Max memory usage (MEM+SWP)",
+                                                                "value": "235.4 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.oom_kill_disable",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "OOM Control enabled",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.under_oom",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Was OOM Killer active?",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.soft_limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Memory softlimit on cgroup",
+                                                                "value": "0 bytes"
+                                                            }
+                                                        ],
+                                                        "job_stderr": "",
+                                                        "job_stdout": "",
+                                                        "model_class": "Job",
+                                                        "output_collections": {
+                                                            "stats": {
+                                                                "id": "cfa32fe2043782fe",
+                                                                "src": "hdca"
+                                                            }
+                                                        },
+                                                        "outputs": {
+                                                            "__new_primary_file_stats|fastqc__": {
+                                                                "id": "4838ba20a6d86765af3f1d3773b3e6e6",
+                                                                "src": "hda",
+                                                                "uuid": "3b7d0c75-6916-4fe8-b043-2f548a0b6178"
+                                                            },
+                                                            "__new_primary_file_stats|general_stats__": {
+                                                                "id": "4838ba20a6d86765eeebdf0f28fa6046",
+                                                                "src": "hda",
+                                                                "uuid": "25a75644-bd77-40a5-b740-fbc4cf4b2873"
+                                                            },
+                                                            "__new_primary_file_stats|sources__": {
+                                                                "id": "4838ba20a6d8676552f11ea459caefac",
+                                                                "src": "hda",
+                                                                "uuid": "707ab880-1526-47de-be63-f6466c1857ff"
+                                                            },
+                                                            "html_report": {
+                                                                "id": "4838ba20a6d86765ec54819e54cbe660",
+                                                                "src": "hda",
+                                                                "uuid": "a7901748-d8a1-40f0-a656-40796763ae98"
+                                                            }
+                                                        },
+                                                        "params": {
+                                                            "__input_ext": "\"txt\"",
+                                                            "__workflow_invocation_uuid__": "\"9ef558e0f65111eda6f2001e67d2ec02\"",
+                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
+                                                            "comment": "\"\"",
+                                                            "dbkey": "\"?\"",
+                                                            "export": "false",
+                                                            "flat": "false",
+                                                            "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"input\": {\"values\": [{\"id\": 137415695, \"src\": \"hda\"}, {\"id\": 137415693, \"src\": \"hda\"}]}, \"type\": \"data\"}], \"software\": \"fastqc\"}}]",
+                                                            "saveLog": "false",
+                                                            "title": "\"\""
+                                                        },
+                                                        "state": "ok",
+                                                        "stderr": "[WARNING]         multiqc : MultiQC Version v1.14 now available!\n[INFO   ]         multiqc : This is MultiQC v1.9\n[INFO   ]         multiqc : Template    : default\n[INFO   ]         multiqc : Searching   : /data/jwd02f/main/060/058/60058037/working/multiqc_WDir\n[INFO   ]          fastqc : Found 2 reports\n[INFO   ]         multiqc : Compressing plot data\n[INFO   ]         multiqc : Report      : report.html\n[INFO   ]         multiqc : Data        : report_data\n[INFO   ]         multiqc : MultiQC complete\n",
                                                         "stdout": "",
-                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3",
-                                                        "tool_stderr": "",
+                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9",
+                                                        "tool_stderr": "[WARNING]         multiqc : MultiQC Version v1.14 now available!\n[INFO   ]         multiqc : This is MultiQC v1.9\n[INFO   ]         multiqc : Template    : default\n[INFO   ]         multiqc : Searching   : /data/jwd02f/main/060/058/60058037/working/multiqc_WDir\n[INFO   ]          fastqc : Found 2 reports\n[INFO   ]         multiqc : Compressing plot data\n[INFO   ]         multiqc : Report      : report.html\n[INFO   ]         multiqc : Data        : report_data\n[INFO   ]         multiqc : MultiQC complete\n",
                                                         "tool_stdout": "",
                                                         "traceback": null,
-                                                        "update_time": "2023-05-19T15:00:22.417608",
+                                                        "update_time": "2023-05-19T14:33:25.724813",
                                                         "user_email": "hxr@informatik.uni-freiburg.de"
                                                     }
                                                 ],
                                                 "model_class": "WorkflowInvocationStep",
-                                                "order_index": 3,
+                                                "order_index": 5,
+                                                "output_collections": {
+                                                    "stats": {
+                                                        "id": "cfa32fe2043782fe",
+                                                        "src": "hdca"
+                                                    }
+                                                },
+                                                "outputs": {
+                                                    "html_report": {
+                                                        "id": "4838ba20a6d86765ec54819e54cbe660",
+                                                        "src": "hda",
+                                                        "uuid": "a7901748-d8a1-40f0-a656-40796763ae98"
+                                                    }
+                                                },
+                                                "state": "scheduled",
+                                                "subworkflow": null,
+                                                "subworkflow_invocation_id": null,
+                                                "update_time": "2023-05-19T14:33:25.705737",
+                                                "workflow_step_id": "076bed37af53db03",
+                                                "workflow_step_label": null,
+                                                "workflow_step_uuid": "0f4492d6-2e63-466f-98e7-9f2921d4c039"
+                                            },
+                                            "6. Unnamed step": {
+                                                "action": null,
+                                                "id": "ac35c3e9e0f36f77",
+                                                "job_id": "11ac94870d0bb33a600088ef54ecdb6d",
+                                                "jobs": [
+                                                    {
+                                                        "command_line": "set -o | grep -q pipefail && set -o pipefail;   ln -f -s '/data/dnb08/galaxy_db/files/6/4/9/dataset_64981dba-44f7-4768-8b63-e63defba2ecf.dat' input_f.fastq.gz &&  ln -f -s '/data/dnb08/galaxy_db/files/0/7/6/dataset_0764cea4-72ed-4a8c-93b2-88bd066afc4e.dat' input_r.fastq.gz &&   bowtie2  -p ${GALAXY_SLOTS:-4}  -x '/data/db/reference_genomes/mm10/bowtie2_index/mm10'   -1 'input_f.fastq.gz' -2 'input_r.fastq.gz'                2> '/data/jwd02f/main/060/058/60058038/outputs/galaxy_dataset_b1360a80-c9bb-4fb9-ac3e-00aac0213e44.dat'  | samtools sort --no-PG -@${GALAXY_SLOTS:-2} -T \"${TMPDIR:-.}\" -O bam -o '/data/jwd02f/main/060/058/60058038/outputs/galaxy_dataset_014de858-c517-4e2a-a491-c14c99491b03.dat'",
+                                                        "command_version": "/usr/local/tools/_conda/envs/mulled-v1-2c9d0d73d81f016cd458c97e185f638410841f3ecf7ae79158d90e0d58249513/bin/bowtie2-align-s version 2.4.2\n64-bit\nBuilt on default-bf91a638-95fa-4b77-97c5-abccd9855c3e\nMon Nov  2 17:36:36 UTC 2020\nCompiler: gcc version 7.5.0 (crosstool-NG 1.24.0.131_87df0e6_dirty) \nOptions: -O3 -msse2 -funroll-loops -g3 -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/tools/_conda/envs/mulled-v1-2c9d0d73d81f016cd458c97e185f638410841f3ecf7ae79158d90e0d58249513/include -fdebug-prefix-map=/opt/conda/conda-bld/bowtie2_1604337828546/work=/usr/local/src/conda/bowtie2-2.4.2 -fdebug-prefix-map=/usr/local/tools/_conda/envs/mulled-v1-2c9d0d73d81f016cd458c97e185f638410841f3ecf7ae79158d90e0d58249513=/usr/local/src/conda-prefix -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}",
+                                                        "create_time": "2023-05-19T14:30:12.695266",
+                                                        "dependencies": [],
+                                                        "exit_code": 0,
+                                                        "external_id": "43534339",
+                                                        "galaxy_version": "23.0",
+                                                        "history_id": "2e96b0bf6abd6b74",
+                                                        "id": "11ac94870d0bb33a600088ef54ecdb6d",
+                                                        "inputs": {
+                                                            "input_1": {
+                                                                "id": "4838ba20a6d86765439b06bcf8677007",
+                                                                "src": "hda",
+                                                                "uuid": "64981dba-44f7-4768-8b63-e63defba2ecf"
+                                                            },
+                                                            "input_2": {
+                                                                "id": "4838ba20a6d867658f72f66dd1d7e6cc",
+                                                                "src": "hda",
+                                                                "uuid": "0764cea4-72ed-4a8c-93b2-88bd066afc4e"
+                                                            }
+                                                        },
+                                                        "job_messages": [],
+                                                        "job_metrics": [
+                                                            {
+                                                                "name": "hostname",
+                                                                "plugin": "hostname",
+                                                                "raw_value": "vgcnbwc-worker-c125m425-4973.novalocal",
+                                                                "title": "hostname",
+                                                                "value": "vgcnbwc-worker-c125m425-4973.novalocal"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_slots",
+                                                                "plugin": "core",
+                                                                "raw_value": "8.0000000",
+                                                                "title": "Cores Allocated",
+                                                                "value": "8"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_memory_mb",
+                                                                "plugin": "core",
+                                                                "raw_value": "20480.0000000",
+                                                                "title": "Memory Allocated (MB)",
+                                                                "value": "20480"
+                                                            },
+                                                            {
+                                                                "name": "start_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684506680.0000000",
+                                                                "title": "Job Start Time",
+                                                                "value": "2023-05-19 16:31:20"
+                                                            },
+                                                            {
+                                                                "name": "end_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684506731.0000000",
+                                                                "title": "Job End Time",
+                                                                "value": "2023-05-19 16:32:11"
+                                                            },
+                                                            {
+                                                                "name": "runtime_seconds",
+                                                                "plugin": "core",
+                                                                "raw_value": "51.0000000",
+                                                                "title": "Job Runtime (Wall Clock)",
+                                                                "value": "51 seconds"
+                                                            },
+                                                            {
+                                                                "name": "cpuacct.usage",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "36889533091.0000000",
+                                                                "title": "CPU Time",
+                                                                "value": "36.889533091 seconds"
+                                                            },
+                                                            {
+                                                                "name": "memory.failcnt",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Failed to allocate memory count",
+                                                                "value": 0.0
+                                                            },
+                                                            {
+                                                                "name": "memory.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "21474836480.0000000",
+                                                                "title": "Memory limit on cgroup (MEM)",
+                                                                "value": "20.0 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "6388858880.0000000",
+                                                                "title": "Max memory usage (MEM)",
+                                                                "value": "6.0 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "9223372036854771712.0000000",
+                                                                "title": "Memory limit on cgroup (MEM+SWP)",
+                                                                "value": "8.0 EB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "6388858880.0000000",
+                                                                "title": "Max memory usage (MEM+SWP)",
+                                                                "value": "6.0 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.oom_kill_disable",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "OOM Control enabled",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.under_oom",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Was OOM Killer active?",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.soft_limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Memory softlimit on cgroup",
+                                                                "value": "0 bytes"
+                                                            }
+                                                        ],
+                                                        "job_stderr": "",
+                                                        "job_stdout": "",
+                                                        "model_class": "Job",
+                                                        "output_collections": {},
+                                                        "outputs": {
+                                                            "mapping_stats": {
+                                                                "id": "4838ba20a6d867656446378f71ad820b",
+                                                                "src": "hda",
+                                                                "uuid": "b1360a80-c9bb-4fb9-ac3e-00aac0213e44"
+                                                            },
+                                                            "output": {
+                                                                "id": "4838ba20a6d86765af291d8ab2af5e96",
+                                                                "src": "hda",
+                                                                "uuid": "014de858-c517-4e2a-a491-c14c99491b03"
+                                                            }
+                                                        },
+                                                        "params": {
+                                                            "__input_ext": "\"input\"",
+                                                            "__workflow_invocation_uuid__": "\"9ef558e0f65111eda6f2001e67d2ec02\"",
+                                                            "analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"simple\", \"presets\": \"no_presets\"}",
+                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
+                                                            "dbkey": "\"?\"",
+                                                            "library": "{\"__current_case__\": 1, \"aligned_file\": false, \"input_1\": {\"values\": [{\"id\": 137415696, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 137415697, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 1, \"paired_options_selector\": \"no\"}, \"type\": \"paired\", \"unaligned_file\": false}",
+                                                            "reference_genome": "{\"__current_case__\": 0, \"index\": \"mm10\", \"source\": \"indexed\"}",
+                                                            "rg": "{\"__current_case__\": 3, \"rg_selector\": \"do_not_set\"}",
+                                                            "sam_options": "{\"__current_case__\": 1, \"sam_options_selector\": \"no\"}",
+                                                            "save_mapping_stats": "true"
+                                                        },
+                                                        "state": "ok",
+                                                        "stderr": "[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n",
+                                                        "stdout": "",
+                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0",
+                                                        "tool_stderr": "[bam_sort_core] merging from 0 files and 8 in-memory blocks...\n",
+                                                        "tool_stdout": "",
+                                                        "traceback": null,
+                                                        "update_time": "2023-05-19T14:32:13.080341",
+                                                        "user_email": "hxr@informatik.uni-freiburg.de"
+                                                    }
+                                                ],
+                                                "model_class": "WorkflowInvocationStep",
+                                                "order_index": 6,
                                                 "output_collections": {},
                                                 "outputs": {
-                                                    "out1": {
-                                                        "id": "4838ba20a6d8676528f2966e438993df",
+                                                    "mapping_stats": {
+                                                        "id": "4838ba20a6d867656446378f71ad820b",
                                                         "src": "hda",
-                                                        "uuid": "5096388f-425a-42a1-b99e-4f0174665371"
+                                                        "uuid": "b1360a80-c9bb-4fb9-ac3e-00aac0213e44"
                                                     },
-                                                    "report": {
-                                                        "id": "4838ba20a6d8676504b9c2c33c839b66",
+                                                    "output": {
+                                                        "id": "4838ba20a6d86765af291d8ab2af5e96",
                                                         "src": "hda",
-                                                        "uuid": "b9909c1d-09b1-47ec-9135-48915855c294"
+                                                        "uuid": "014de858-c517-4e2a-a491-c14c99491b03"
                                                     }
                                                 },
                                                 "state": "scheduled",
                                                 "subworkflow": null,
                                                 "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-19T15:00:21.982154",
-                                                "workflow_step_id": "17cb0d9cde915ee1",
+                                                "update_time": "2023-05-19T14:32:13.062698",
+                                                "workflow_step_id": "de91ab1f4d5a7cd4",
                                                 "workflow_step_label": null,
-                                                "workflow_step_uuid": "ddd70253-72b8-4a5e-8025-56a579b01975"
+                                                "workflow_step_uuid": "2d04b2e4-a2fe-4ce6-8894-5a752031171b"
                                             },
-                                            "4. Unnamed step": {
+                                            "7. Unnamed step": {
                                                 "action": null,
-                                                "id": "a380f2e9cccfcc65",
-                                                "job_id": "11ac94870d0bb33aae939aa0a3d41382",
+                                                "id": "83d212dd0df7f7f8",
+                                                "job_id": "11ac94870d0bb33a8145f91d85cf7ba7",
                                                 "jobs": [
                                                     {
-                                                        "command_line": "ln -s '/data/dnb08/galaxy_db/files/9/9/6/dataset_9968668a-3051-4e02-aa3d-4997838a0985.dat' 'GSM461178_untreat_paired_subset_2_fastq' && mkdir -p '/data/jwd05e/main/060/059/60059404/working/dataset_3bc9888e-ec3f-4ae0-b61c-db19dec8e43e_files' && fastqc --outdir '/data/jwd05e/main/060/059/60059404/working/dataset_3bc9888e-ec3f-4ae0-b61c-db19dec8e43e_files'    --quiet --extract  --kmers 7 -f 'fastq' 'GSM461178_untreat_paired_subset_2_fastq'  && cp '/data/jwd05e/main/060/059/60059404/working/dataset_3bc9888e-ec3f-4ae0-b61c-db19dec8e43e_files'/*/fastqc_data.txt output.txt && cp '/data/jwd05e/main/060/059/60059404/working/dataset_3bc9888e-ec3f-4ae0-b61c-db19dec8e43e_files'/*\\.html output.html",
-                                                        "command_version": null,
-                                                        "create_time": "2023-05-19T14:59:03.488111",
+                                                        "command_line": "samtools stats '/data/dnb08/galaxy_db/files/0/1/4/dataset_014de858-c517-4e2a-a491-c14c99491b03.dat' --coverage 1,1000,1    --GC-depth 20000.0 --insert-size 8000    --most-inserts 0.99 --trim-quality 0  --ref-seq '/data/db/reference_genomes/mm10/seq/mm10.fa' > '/data/jwd01/main/060/058/60058039/outputs/galaxy_dataset_9de6afbf-b266-439b-b405-215a8d1d90f4.dat'",
+                                                        "command_version": "Version: 1.3.1 (using htslib 1.3.1)",
+                                                        "create_time": "2023-05-19T14:30:12.801865",
                                                         "dependencies": [
                                                             {
                                                                 "cacheable": false,
@@ -211609,23 +215075,23 @@
                                                                     "versionless": false
                                                                 },
                                                                 "dependency_type": "conda",
-                                                                "environment_path": "/usr/local/tools/_conda/envs/__fastqc@0.11.8",
+                                                                "environment_path": "/usr/local/tools/_conda/envs/__samtools@1.3.1",
                                                                 "exact": true,
                                                                 "model_class": "MergedCondaDependency",
-                                                                "name": "fastqc",
-                                                                "version": "0.11.8"
+                                                                "name": "samtools",
+                                                                "version": "1.3.1"
                                                             }
                                                         ],
                                                         "exit_code": 0,
-                                                        "external_id": "43535386",
+                                                        "external_id": "43534364",
                                                         "galaxy_version": "23.0",
-                                                        "history_id": "2f1f9fa04aab9b59",
-                                                        "id": "11ac94870d0bb33aae939aa0a3d41382",
+                                                        "history_id": "2e96b0bf6abd6b74",
+                                                        "id": "11ac94870d0bb33a8145f91d85cf7ba7",
                                                         "inputs": {
                                                             "input_file": {
-                                                                "id": "4838ba20a6d867656914ebcc68e736a5",
+                                                                "id": "4838ba20a6d86765af291d8ab2af5e96",
                                                                 "src": "hda",
-                                                                "uuid": "9968668a-3051-4e02-aa3d-4997838a0985"
+                                                                "uuid": "014de858-c517-4e2a-a491-c14c99491b03"
                                                             }
                                                         },
                                                         "job_messages": [],
@@ -211633,51 +215099,51 @@
                                                             {
                                                                 "name": "hostname",
                                                                 "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c125m425-1589.novalocal",
+                                                                "raw_value": "vgcnbwc-worker-c28m475-1207.novalocal",
                                                                 "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c125m425-1589.novalocal"
+                                                                "value": "vgcnbwc-worker-c28m475-1207.novalocal"
                                                             },
                                                             {
                                                                 "name": "galaxy_slots",
                                                                 "plugin": "core",
-                                                                "raw_value": "8.0000000",
+                                                                "raw_value": "1.0000000",
                                                                 "title": "Cores Allocated",
-                                                                "value": "8"
+                                                                "value": "1"
                                                             },
                                                             {
                                                                 "name": "galaxy_memory_mb",
                                                                 "plugin": "core",
-                                                                "raw_value": "31129.0000000",
+                                                                "raw_value": "3891.0000000",
                                                                 "title": "Memory Allocated (MB)",
-                                                                "value": "31129"
+                                                                "value": "3891"
                                                             },
                                                             {
                                                                 "name": "start_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684508676.0000000",
+                                                                "raw_value": "1684506752.0000000",
                                                                 "title": "Job Start Time",
-                                                                "value": "2023-05-19 17:04:36"
+                                                                "value": "2023-05-19 16:32:32"
                                                             },
                                                             {
                                                                 "name": "end_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684508692.0000000",
+                                                                "raw_value": "1684506806.0000000",
                                                                 "title": "Job End Time",
-                                                                "value": "2023-05-19 17:04:52"
+                                                                "value": "2023-05-19 16:33:26"
                                                             },
                                                             {
                                                                 "name": "runtime_seconds",
                                                                 "plugin": "core",
-                                                                "raw_value": "16.0000000",
+                                                                "raw_value": "54.0000000",
                                                                 "title": "Job Runtime (Wall Clock)",
-                                                                "value": "16 seconds"
+                                                                "value": "54 seconds"
                                                             },
                                                             {
                                                                 "name": "cpuacct.usage",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "13539752576.0000000",
+                                                                "raw_value": "17841669661.0000000",
                                                                 "title": "CPU Time",
-                                                                "value": "13.539752576 seconds"
+                                                                "value": "17.841669661 seconds"
                                                             },
                                                             {
                                                                 "name": "memory.failcnt",
@@ -211689,16 +215155,16 @@
                                                             {
                                                                 "name": "memory.limit_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "32749125632.0000000",
+                                                                "raw_value": "4160749568.0000000",
                                                                 "title": "Memory limit on cgroup (MEM)",
-                                                                "value": "30.5 GB"
+                                                                "value": "3.9 GB"
                                                             },
                                                             {
                                                                 "name": "memory.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "411770880.0000000",
+                                                                "raw_value": "1402118144.0000000",
                                                                 "title": "Max memory usage (MEM)",
-                                                                "value": "392.7 MB"
+                                                                "value": "1.3 GB"
                                                             },
                                                             {
                                                                 "name": "memory.memsw.limit_in_bytes",
@@ -211710,9 +215176,9 @@
                                                             {
                                                                 "name": "memory.memsw.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "411770880.0000000",
+                                                                "raw_value": "1402118144.0000000",
                                                                 "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "392.7 MB"
+                                                                "value": "1.3 GB"
                                                             },
                                                             {
                                                                 "name": "memory.oom_control.oom_kill_disable",
@@ -211741,111 +215207,79 @@
                                                         "model_class": "Job",
                                                         "output_collections": {},
                                                         "outputs": {
-                                                            "html_file": {
-                                                                "id": "4838ba20a6d867650e70120b79b974b3",
-                                                                "src": "hda",
-                                                                "uuid": "3bc9888e-ec3f-4ae0-b61c-db19dec8e43e"
-                                                            },
-                                                            "text_file": {
-                                                                "id": "4838ba20a6d867656a6422c26474bdc5",
+                                                            "output": {
+                                                                "id": "4838ba20a6d8676528f7337e9709f706",
                                                                 "src": "hda",
-                                                                "uuid": "edecc2ea-fa52-4947-9c41-f5956870688a"
+                                                                "uuid": "9de6afbf-b266-439b-b405-215a8d1d90f4"
                                                             }
                                                         },
                                                         "params": {
-                                                            "__input_ext": "\"fastqsanger\"",
-                                                            "__workflow_invocation_uuid__": "\"a085c588f65511ed82b7001e67d2ec02\"",
-                                                            "adapters": null,
-                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
-                                                            "contaminants": null,
-                                                            "dbkey": "\"?\"",
-                                                            "kmers": "\"7\"",
-                                                            "limits": null,
-                                                            "min_length": null,
-                                                            "nogroup": "false"
+                                                            "__input_ext": "\"bam\"",
+                                                            "__workflow_invocation_uuid__": "\"9ef558e0f65111eda6f2001e67d2ec02\"",
+                                                            "chromInfo": "\"/data/db/data_managers/mm10/len/mm10.len\"",
+                                                            "coverage_max": "\"1000\"",
+                                                            "coverage_min": "\"1\"",
+                                                            "coverage_step": "\"1\"",
+                                                            "dbkey": "\"mm10\"",
+                                                            "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}",
+                                                            "gc_depth": "\"20000.0\"",
+                                                            "insert_size": "\"8000\"",
+                                                            "most_inserts": "\"0.99\"",
+                                                            "read_length": null,
+                                                            "remove_dups": "false",
+                                                            "split_output": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}",
+                                                            "trim_quality": "\"0\"",
+                                                            "use_reference": "{\"__current_case__\": 0, \"reference_source\": {\"__current_case__\": 0, \"ref_file\": \"mm10full\", \"reference_source_selector\": \"cached\"}, \"use_ref_selector\": \"yes\"}"
                                                         },
                                                         "state": "ok",
                                                         "stderr": "",
                                                         "stdout": "",
-                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
                                                         "tool_stderr": "",
                                                         "tool_stdout": "",
                                                         "traceback": null,
-                                                        "update_time": "2023-05-19T15:04:54.529461",
+                                                        "update_time": "2023-05-19T14:33:37.050310",
                                                         "user_email": "hxr@informatik.uni-freiburg.de"
                                                     }
                                                 ],
                                                 "model_class": "WorkflowInvocationStep",
-                                                "order_index": 4,
+                                                "order_index": 7,
                                                 "output_collections": {},
                                                 "outputs": {
-                                                    "html_file": {
-                                                        "id": "4838ba20a6d867650e70120b79b974b3",
-                                                        "src": "hda",
-                                                        "uuid": "3bc9888e-ec3f-4ae0-b61c-db19dec8e43e"
-                                                    },
-                                                    "text_file": {
-                                                        "id": "4838ba20a6d867656a6422c26474bdc5",
+                                                    "output": {
+                                                        "id": "4838ba20a6d8676528f7337e9709f706",
                                                         "src": "hda",
-                                                        "uuid": "edecc2ea-fa52-4947-9c41-f5956870688a"
+                                                        "uuid": "9de6afbf-b266-439b-b405-215a8d1d90f4"
                                                     }
                                                 },
                                                 "state": "scheduled",
                                                 "subworkflow": null,
                                                 "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-19T15:04:54.499181",
-                                                "workflow_step_id": "fc590094641a1ae9",
+                                                "update_time": "2023-05-19T14:33:36.956022",
+                                                "workflow_step_id": "74a208880456b021",
                                                 "workflow_step_label": null,
-                                                "workflow_step_uuid": "f48fa351-4a73-4daa-b993-2210274ae84d"
+                                                "workflow_step_uuid": "898dd71d-9b58-4286-a6ae-5403cb284341"
                                             },
-                                            "5. Unnamed step": {
+                                            "8. Unnamed step": {
                                                 "action": null,
-                                                "id": "6a0711aa69933475",
-                                                "job_id": "11ac94870d0bb33abd6fe235967051f6",
+                                                "id": "53b676dcfcf6d669",
+                                                "job_id": "11ac94870d0bb33a4dcd57b031359dae",
                                                 "jobs": [
                                                     {
-                                                        "command_line": "ln -f -s '/data/dnb08/galaxy_db/files/3/8/3/dataset_3835c7cb-1707-4e6f-85d2-6f1ad5c31bc4.dat' 'GSM461178_untreat_paired_subset_1_fastq.fq' &&  ln -f -s '/data/dnb08/galaxy_db/files/9/9/6/dataset_9968668a-3051-4e02-aa3d-4997838a0985.dat' 'GSM461178_untreat_paired_subset_2_fastq.fq' &&   cutadapt  -j ${GALAXY_SLOTS:-1}                  --output='out1.fq' --paired-output='out2.fq'  --error-rate=0.1 --times=1 --overlap=3         --minimum-length=20 --pair-filter=any   --quality-cutoff=20   'GSM461178_untreat_paired_subset_1_fastq.fq' 'GSM461178_untreat_paired_subset_2_fastq.fq'  > report.txt",
-                                                        "command_version": "1.16",
-                                                        "create_time": "2023-05-19T14:59:03.590819",
-                                                        "dependencies": [
-                                                            {
-                                                                "cacheable": false,
-                                                                "dependency_resolver": {
-                                                                    "auto_init": true,
-                                                                    "auto_install": false,
-                                                                    "can_uninstall_dependencies": true,
-                                                                    "ensure_channels": "conda-forge,bioconda",
-                                                                    "model_class": "CondaDependencyResolver",
-                                                                    "prefix": "/usr/local/tools/_conda",
-                                                                    "read_only": false,
-                                                                    "resolver_type": "conda",
-                                                                    "resolves_simple_dependencies": true,
-                                                                    "use_local": false,
-                                                                    "versionless": false
-                                                                },
-                                                                "dependency_type": "conda",
-                                                                "environment_path": "/usr/local/tools/_conda/envs/__cutadapt@1.16",
-                                                                "exact": true,
-                                                                "model_class": "MergedCondaDependency",
-                                                                "name": "cutadapt",
-                                                                "version": "1.16"
-                                                            }
-                                                        ],
+                                                        "command_line": "cp '/data/jwd05e/main/060/058/60058040/configs/tmpr1btgj1_' '/data/jwd05e/main/060/058/60058040/outputs/galaxy_dataset_b3362212-c40a-470a-b0e0-89a4c7bc6d26.dat' && ln -s '/data/dnb08/galaxy_db/files/0/1/4/dataset_014de858-c517-4e2a-a491-c14c99491b03.dat' localbam.bam && ln -s '/data/dnb08/galaxy_db/files/_metadata_files/3/b/6/metadata_3b6f911b-633e-41e4-a35b-86b3615b2257.dat' localbam.bam.bai && cat '/data/jwd05e/main/060/058/60058040/configs/tmpr1btgj1_' && bamtools filter -script '/data/jwd05e/main/060/058/60058040/configs/tmpr1btgj1_' -in localbam.bam -out '/data/jwd05e/main/060/058/60058040/outputs/galaxy_dataset_11b4a85c-d4af-4e9d-9890-63e2517ff346.dat'",
+                                                        "command_version": null,
+                                                        "create_time": "2023-05-19T14:30:12.913255",
+                                                        "dependencies": [],
                                                         "exit_code": 0,
-                                                        "external_id": "43535388",
+                                                        "external_id": "43534362",
                                                         "galaxy_version": "23.0",
-                                                        "history_id": "2f1f9fa04aab9b59",
-                                                        "id": "11ac94870d0bb33abd6fe235967051f6",
+                                                        "history_id": "2e96b0bf6abd6b74",
+                                                        "id": "11ac94870d0bb33a4dcd57b031359dae",
                                                         "inputs": {
-                                                            "input_1": {
-                                                                "id": "4838ba20a6d86765ff25d30589db09fe",
-                                                                "src": "hda",
-                                                                "uuid": "3835c7cb-1707-4e6f-85d2-6f1ad5c31bc4"
-                                                            },
-                                                            "input_2": {
-                                                                "id": "4838ba20a6d867656914ebcc68e736a5",
+                                                            "input_bam": {
+                                                                "id": "4838ba20a6d86765af291d8ab2af5e96",
                                                                 "src": "hda",
-                                                                "uuid": "9968668a-3051-4e02-aa3d-4997838a0985"
+                                                                "uuid": "014de858-c517-4e2a-a491-c14c99491b03"
                                                             }
                                                         },
                                                         "job_messages": [],
@@ -211853,51 +215287,51 @@
                                                             {
                                                                 "name": "hostname",
                                                                 "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c125m425-6547.novalocal",
+                                                                "raw_value": "vgcnbwc-worker-c36m225-7327.novalocal",
                                                                 "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c125m425-6547.novalocal"
+                                                                "value": "vgcnbwc-worker-c36m225-7327.novalocal"
                                                             },
                                                             {
                                                                 "name": "galaxy_slots",
                                                                 "plugin": "core",
-                                                                "raw_value": "5.0000000",
+                                                                "raw_value": "1.0000000",
                                                                 "title": "Cores Allocated",
-                                                                "value": "5"
+                                                                "value": "1"
                                                             },
                                                             {
                                                                 "name": "galaxy_memory_mb",
                                                                 "plugin": "core",
-                                                                "raw_value": "19456.0000000",
+                                                                "raw_value": "3891.0000000",
                                                                 "title": "Memory Allocated (MB)",
-                                                                "value": "19456"
+                                                                "value": "3891"
                                                             },
                                                             {
                                                                 "name": "start_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684508356.0000000",
+                                                                "raw_value": "1684506749.0000000",
                                                                 "title": "Job Start Time",
-                                                                "value": "2023-05-19 16:59:16"
+                                                                "value": "2023-05-19 16:32:29"
                                                             },
                                                             {
                                                                 "name": "end_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684508381.0000000",
+                                                                "raw_value": "1684506773.0000000",
                                                                 "title": "Job End Time",
-                                                                "value": "2023-05-19 16:59:41"
+                                                                "value": "2023-05-19 16:32:53"
                                                             },
                                                             {
                                                                 "name": "runtime_seconds",
                                                                 "plugin": "core",
-                                                                "raw_value": "25.0000000",
+                                                                "raw_value": "24.0000000",
                                                                 "title": "Job Runtime (Wall Clock)",
-                                                                "value": "25 seconds"
+                                                                "value": "24 seconds"
                                                             },
                                                             {
                                                                 "name": "cpuacct.usage",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "8873728303.0000000",
+                                                                "raw_value": "13735913869.0000000",
                                                                 "title": "CPU Time",
-                                                                "value": "8.873728303 seconds"
+                                                                "value": "13.735913869 seconds"
                                                             },
                                                             {
                                                                 "name": "memory.failcnt",
@@ -211909,16 +215343,16 @@
                                                             {
                                                                 "name": "memory.limit_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "20401094656.0000000",
+                                                                "raw_value": "4160749568.0000000",
                                                                 "title": "Memory limit on cgroup (MEM)",
-                                                                "value": "19.0 GB"
+                                                                "value": "3.9 GB"
                                                             },
                                                             {
                                                                 "name": "memory.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "362237952.0000000",
+                                                                "raw_value": "218013696.0000000",
                                                                 "title": "Max memory usage (MEM)",
-                                                                "value": "345.5 MB"
+                                                                "value": "207.9 MB"
                                                             },
                                                             {
                                                                 "name": "memory.memsw.limit_in_bytes",
@@ -211930,9 +215364,9 @@
                                                             {
                                                                 "name": "memory.memsw.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "362237952.0000000",
+                                                                "raw_value": "218013696.0000000",
                                                                 "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "345.5 MB"
+                                                                "value": "207.9 MB"
                                                             },
                                                             {
                                                                 "name": "memory.oom_control.oom_kill_disable",
@@ -211961,125 +215395,79 @@
                                                         "model_class": "Job",
                                                         "output_collections": {},
                                                         "outputs": {
-                                                            "out1": {
-                                                                "id": "4838ba20a6d867658b181ea162b2bff2",
-                                                                "src": "hda",
-                                                                "uuid": "5647f1a7-5cfe-4e7e-8a12-733901cbbc2f"
-                                                            },
-                                                            "out2": {
-                                                                "id": "4838ba20a6d8676511267a23c1bb707d",
+                                                            "out_file1": {
+                                                                "id": "4838ba20a6d8676586fc63a32e96cd1a",
                                                                 "src": "hda",
-                                                                "uuid": "7936d330-0e1e-43d9-abc8-e01e2e8ce871"
+                                                                "uuid": "11b4a85c-d4af-4e9d-9890-63e2517ff346"
                                                             },
-                                                            "report": {
-                                                                "id": "4838ba20a6d86765b7823a727e8a67cd",
+                                                            "out_file2": {
+                                                                "id": "4838ba20a6d86765332d056e72acf04a",
                                                                 "src": "hda",
-                                                                "uuid": "d3748a3d-cb92-4c98-a590-d687c708ddc8"
+                                                                "uuid": "b3362212-c40a-470a-b0e0-89a4c7bc6d26"
                                                             }
                                                         },
                                                         "params": {
-                                                            "__input_ext": "\"input\"",
-                                                            "__workflow_invocation_uuid__": "\"a085c588f65511ed82b7001e67d2ec02\"",
-                                                            "adapter_options": "{\"count\": \"1\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"overlap\": \"3\"}",
-                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
-                                                            "dbkey": "\"?\"",
-                                                            "filter_options": "{\"discard\": false, \"discard_untrimmed\": false, \"mask_adapter\": false, \"max\": \"0\", \"max_n\": null, \"min\": \"20\", \"no_trim\": false, \"pair_filter\": \"any\"}",
-                                                            "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 137417465, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 137417509, \"src\": \"hda\"}]}, \"r1\": {\"adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\", \"front_adapters\": []}, \"r2\": {\"adapters2\": [], \"anywhere_adapters2\": [], \"cut2\": \"0\", \"front_adapters2\": []}, \"type\": \"paired\"}",
-                                                            "output_options": "{\"info_file\": false, \"report\": true, \"rest_file\": false, \"too_long_file\": false, \"too_short_file\": false, \"untrimmed_file\": false, \"wildcard_file\": false}",
-                                                            "read_mod_options": "{\"length\": \"0\", \"length_tag\": \"\", \"nextseq_trim\": \"0\", \"prefix\": \"\", \"quality_cutoff\": \"20\", \"strip_suffix\": \"\", \"suffix\": \"\", \"trim_n\": false}"
+                                                            "__input_ext": "\"bam\"",
+                                                            "__workflow_invocation_uuid__": "\"9ef558e0f65111eda6f2001e67d2ec02\"",
+                                                            "chromInfo": "\"/data/db/data_managers/mm10/len/mm10.len\"",
+                                                            "conditions": "[{\"__index__\": 0, \"filters\": [{\"__index__\": 0, \"bam_property\": {\"__current_case__\": 14, \"bam_property_selector\": \"mapQuality\", \"bam_property_value\": \">=20\"}}]}]",
+                                                            "dbkey": "\"mm10\"",
+                                                            "rule_configuration": "{\"__current_case__\": 0, \"rules_selector\": false}"
                                                         },
                                                         "state": "ok",
                                                         "stderr": "",
-                                                        "stdout": "",
-                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3",
+                                                        "stdout": "\n\n\n        \n{\n    \"filters\": [\n        {\n            \"id\": \"1\",\n            \"mapQuality\": \">=20\"\n        }\n    ]\n}\n\n        ",
+                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
                                                         "tool_stderr": "",
-                                                        "tool_stdout": "",
+                                                        "tool_stdout": "\n\n\n        \n{\n    \"filters\": [\n        {\n            \"id\": \"1\",\n            \"mapQuality\": \">=20\"\n        }\n    ]\n}\n\n        ",
                                                         "traceback": null,
-                                                        "update_time": "2023-05-19T14:59:42.633522",
+                                                        "update_time": "2023-05-19T14:32:55.076647",
                                                         "user_email": "hxr@informatik.uni-freiburg.de"
                                                     }
                                                 ],
                                                 "model_class": "WorkflowInvocationStep",
-                                                "order_index": 5,
+                                                "order_index": 8,
                                                 "output_collections": {},
                                                 "outputs": {
-                                                    "out1": {
-                                                        "id": "4838ba20a6d867658b181ea162b2bff2",
-                                                        "src": "hda",
-                                                        "uuid": "5647f1a7-5cfe-4e7e-8a12-733901cbbc2f"
-                                                    },
-                                                    "out2": {
-                                                        "id": "4838ba20a6d8676511267a23c1bb707d",
+                                                    "out_file1": {
+                                                        "id": "4838ba20a6d8676586fc63a32e96cd1a",
                                                         "src": "hda",
-                                                        "uuid": "7936d330-0e1e-43d9-abc8-e01e2e8ce871"
+                                                        "uuid": "11b4a85c-d4af-4e9d-9890-63e2517ff346"
                                                     },
-                                                    "report": {
-                                                        "id": "4838ba20a6d86765b7823a727e8a67cd",
+                                                    "out_file2": {
+                                                        "id": "4838ba20a6d86765332d056e72acf04a",
                                                         "src": "hda",
-                                                        "uuid": "d3748a3d-cb92-4c98-a590-d687c708ddc8"
+                                                        "uuid": "b3362212-c40a-470a-b0e0-89a4c7bc6d26"
                                                     }
                                                 },
                                                 "state": "scheduled",
                                                 "subworkflow": null,
                                                 "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-19T14:59:42.614406",
-                                                "workflow_step_id": "1c99f44f251d0c5a",
+                                                "update_time": "2023-05-19T14:32:55.059256",
+                                                "workflow_step_id": "4964c8b8ced0b316",
                                                 "workflow_step_label": null,
-                                                "workflow_step_uuid": "5ff1e523-c42b-42cd-8857-84d7d83802f8"
+                                                "workflow_step_uuid": "9fca8663-299c-4a3e-9d21-c3f5b89936c9"
                                             },
-                                            "6. Unnamed step": {
+                                            "9. Unnamed step": {
                                                 "action": null,
-                                                "id": "c0e9eb97be074ab9",
-                                                "job_id": "11ac94870d0bb33a3e4f5384f33fb7c3",
+                                                "id": "d10aa175eaaa29cb",
+                                                "job_id": "11ac94870d0bb33a4d625b480e3a88e5",
                                                 "jobs": [
                                                     {
-                                                        "command_line": "die() { echo \"$@\" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/fastqc_0 &&    mkdir 'multiqc_WDir/fastqc_0/data_0' &&  mkdir 'multiqc_WDir/fastqc_0/data_0/file_0' && ln -s '/data/dnb08/galaxy_db/files/8/a/a/dataset_8aadb0d6-4752-43b3-9a70-b58359fe1659.dat' 'multiqc_WDir/fastqc_0/data_0/file_0/fastqc_data.txt' && mkdir 'multiqc_WDir/fastqc_0/data_0/file_1' && ln -s '/data/dnb08/galaxy_db/files/e/d/e/dataset_edecc2ea-fa52-4947-9c41-f5956870688a.dat' 'multiqc_WDir/fastqc_0/data_0/file_1/fastqc_data.txt' &&  multiqc multiqc_WDir --filename \"report\"",
-                                                        "command_version": null,
-                                                        "create_time": "2023-05-19T14:59:03.693709",
-                                                        "dependencies": [
-                                                            {
-                                                                "cacheable": false,
-                                                                "dependency_resolver": {
-                                                                    "auto_init": true,
-                                                                    "auto_install": false,
-                                                                    "can_uninstall_dependencies": true,
-                                                                    "ensure_channels": "conda-forge,bioconda",
-                                                                    "model_class": "CondaDependencyResolver",
-                                                                    "prefix": "/usr/local/tools/_conda",
-                                                                    "read_only": false,
-                                                                    "resolver_type": "conda",
-                                                                    "resolves_simple_dependencies": true,
-                                                                    "use_local": false,
-                                                                    "versionless": false
-                                                                },
-                                                                "dependency_type": "conda",
-                                                                "environment_path": "/usr/local/tools/_conda/envs/__multiqc@1.9",
-                                                                "exact": true,
-                                                                "model_class": "MergedCondaDependency",
-                                                                "name": "multiqc",
-                                                                "version": "1.9"
-                                                            }
-                                                        ],
+                                                        "command_line": "samtools stats '/data/dnb08/galaxy_db/files/1/1/b/dataset_11b4a85c-d4af-4e9d-9890-63e2517ff346.dat' --coverage 1,1000,1    --GC-depth 20000.0 --insert-size 8000    --most-inserts 0.99 --trim-quality 0  --ref-seq '/data/db/reference_genomes/mm10/seq/mm10.fa' > '/data/jwd05e/main/060/058/60058041/outputs/galaxy_dataset_94cccd62-deee-4ce5-8952-739603b253f7.dat'",
+                                                        "command_version": "Version: 1.3.1 (using htslib 1.3.1)",
+                                                        "create_time": "2023-05-19T14:30:13.010837",
+                                                        "dependencies": [],
                                                         "exit_code": 0,
-                                                        "external_id": "43535462",
+                                                        "external_id": "43534369",
                                                         "galaxy_version": "23.0",
-                                                        "history_id": "2f1f9fa04aab9b59",
-                                                        "id": "11ac94870d0bb33a3e4f5384f33fb7c3",
+                                                        "history_id": "2e96b0bf6abd6b74",
+                                                        "id": "11ac94870d0bb33a4d625b480e3a88e5",
                                                         "inputs": {
-                                                            "results_0|software_cond|output_0|input": {
-                                                                "id": "4838ba20a6d86765967c147adffa4ae2",
-                                                                "src": "hda",
-                                                                "uuid": "8aadb0d6-4752-43b3-9a70-b58359fe1659"
-                                                            },
-                                                            "results_0|software_cond|output_0|input1": {
-                                                                "id": "4838ba20a6d86765967c147adffa4ae2",
-                                                                "src": "hda",
-                                                                "uuid": "8aadb0d6-4752-43b3-9a70-b58359fe1659"
-                                                            },
-                                                            "results_0|software_cond|output_0|input2": {
-                                                                "id": "4838ba20a6d867656a6422c26474bdc5",
+                                                            "input_file": {
+                                                                "id": "4838ba20a6d8676586fc63a32e96cd1a",
                                                                 "src": "hda",
-                                                                "uuid": "edecc2ea-fa52-4947-9c41-f5956870688a"
+                                                                "uuid": "11b4a85c-d4af-4e9d-9890-63e2517ff346"
                                                             }
                                                         },
                                                         "job_messages": [],
@@ -212087,9 +215475,9 @@
                                                             {
                                                                 "name": "hostname",
                                                                 "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c36m225-7634.novalocal",
+                                                                "raw_value": "vgcnbwc-worker-c28m475-1207.novalocal",
                                                                 "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c36m225-7634.novalocal"
+                                                                "value": "vgcnbwc-worker-c28m475-1207.novalocal"
                                                             },
                                                             {
                                                                 "name": "galaxy_slots",
@@ -212101,37 +215489,37 @@
                                                             {
                                                                 "name": "galaxy_memory_mb",
                                                                 "plugin": "core",
-                                                                "raw_value": "11673.0000000",
+                                                                "raw_value": "3891.0000000",
                                                                 "title": "Memory Allocated (MB)",
-                                                                "value": "11673"
+                                                                "value": "3891"
                                                             },
                                                             {
                                                                 "name": "start_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684508719.0000000",
+                                                                "raw_value": "1684506791.0000000",
                                                                 "title": "Job Start Time",
-                                                                "value": "2023-05-19 17:05:19"
+                                                                "value": "2023-05-19 16:33:11"
                                                             },
                                                             {
                                                                 "name": "end_epoch",
                                                                 "plugin": "core",
-                                                                "raw_value": "1684508927.0000000",
+                                                                "raw_value": "1684506812.0000000",
                                                                 "title": "Job End Time",
-                                                                "value": "2023-05-19 17:08:47"
+                                                                "value": "2023-05-19 16:33:32"
                                                             },
                                                             {
                                                                 "name": "runtime_seconds",
                                                                 "plugin": "core",
-                                                                "raw_value": "208.0000000",
+                                                                "raw_value": "21.0000000",
                                                                 "title": "Job Runtime (Wall Clock)",
-                                                                "value": "3 minutes"
+                                                                "value": "21 seconds"
                                                             },
                                                             {
                                                                 "name": "cpuacct.usage",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "15451533789.0000000",
+                                                                "raw_value": "16061028698.0000000",
                                                                 "title": "CPU Time",
-                                                                "value": "15.451533789 seconds"
+                                                                "value": "16.061028698 seconds"
                                                             },
                                                             {
                                                                 "name": "memory.failcnt",
@@ -212143,16 +215531,16 @@
                                                             {
                                                                 "name": "memory.limit_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "12348030976.0000000",
+                                                                "raw_value": "4160749568.0000000",
                                                                 "title": "Memory limit on cgroup (MEM)",
-                                                                "value": "11.5 GB"
+                                                                "value": "3.9 GB"
                                                             },
                                                             {
                                                                 "name": "memory.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "243441664.0000000",
+                                                                "raw_value": "199102464.0000000",
                                                                 "title": "Max memory usage (MEM)",
-                                                                "value": "232.2 MB"
+                                                                "value": "189.9 MB"
                                                             },
                                                             {
                                                                 "name": "memory.memsw.limit_in_bytes",
@@ -212164,9 +215552,9 @@
                                                             {
                                                                 "name": "memory.memsw.max_usage_in_bytes",
                                                                 "plugin": "cgroup",
-                                                                "raw_value": "243441664.0000000",
+                                                                "raw_value": "199102464.0000000",
                                                                 "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "232.2 MB"
+                                                                "value": "189.9 MB"
                                                             },
                                                             {
                                                                 "name": "memory.oom_control.oom_kill_disable",
@@ -212193,89 +215581,70 @@
                                                         "job_stderr": "",
                                                         "job_stdout": "",
                                                         "model_class": "Job",
-                                                        "output_collections": {
-                                                            "stats": {
-                                                                "id": "b2ed5bced30ea70a",
-                                                                "src": "hdca"
-                                                            }
-                                                        },
+                                                        "output_collections": {},
                                                         "outputs": {
-                                                            "__new_primary_file_stats|fastqc__": {
-                                                                "id": "4838ba20a6d8676552151abe856ca468",
-                                                                "src": "hda",
-                                                                "uuid": "a0afcc44-22b6-4019-938e-4c8b313de6ea"
-                                                            },
-                                                            "__new_primary_file_stats|general_stats__": {
-                                                                "id": "4838ba20a6d867656f4643c70fbd40cc",
-                                                                "src": "hda",
-                                                                "uuid": "d41e3789-24ea-4080-868b-0edab34c49a6"
-                                                            },
-                                                            "__new_primary_file_stats|sources__": {
-                                                                "id": "4838ba20a6d8676518ad2e8586cc7f6b",
-                                                                "src": "hda",
-                                                                "uuid": "b697c224-e6d6-4f53-a3df-16fe5ca4444c"
-                                                            },
-                                                            "html_report": {
-                                                                "id": "4838ba20a6d867657c9b5bfe8c22949d",
+                                                            "output": {
+                                                                "id": "4838ba20a6d86765c665b3763e979c0a",
                                                                 "src": "hda",
-                                                                "uuid": "a42df514-e2c2-4f72-a9b8-e065ef58237f"
+                                                                "uuid": "94cccd62-deee-4ce5-8952-739603b253f7"
                                                             }
                                                         },
                                                         "params": {
-                                                            "__input_ext": "\"txt\"",
-                                                            "__workflow_invocation_uuid__": "\"a085c588f65511ed82b7001e67d2ec02\"",
-                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
-                                                            "comment": "\"\"",
-                                                            "dbkey": "\"?\"",
-                                                            "export": "false",
-                                                            "flat": "false",
-                                                            "results": "[{\"__index__\": 0, \"software_cond\": {\"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"input\": {\"values\": [{\"id\": 137417582, \"src\": \"hda\"}, {\"id\": 137417586, \"src\": \"hda\"}]}, \"type\": \"data\"}], \"software\": \"fastqc\"}}]",
-                                                            "saveLog": "false",
-                                                            "title": "\"\""
+                                                            "__input_ext": "\"bam\"",
+                                                            "__workflow_invocation_uuid__": "\"9ef558e0f65111eda6f2001e67d2ec02\"",
+                                                            "chromInfo": "\"/data/db/data_managers/mm10/len/mm10.len\"",
+                                                            "coverage_max": "\"1000\"",
+                                                            "coverage_min": "\"1\"",
+                                                            "coverage_step": "\"1\"",
+                                                            "dbkey": "\"mm10\"",
+                                                            "filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}",
+                                                            "gc_depth": "\"20000.0\"",
+                                                            "insert_size": "\"8000\"",
+                                                            "most_inserts": "\"0.99\"",
+                                                            "read_length": null,
+                                                            "remove_dups": "false",
+                                                            "split_output": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}",
+                                                            "trim_quality": "\"0\"",
+                                                            "use_reference": "{\"__current_case__\": 0, \"reference_source\": {\"__current_case__\": 0, \"ref_file\": \"mm10full\", \"reference_source_selector\": \"cached\"}, \"use_ref_selector\": \"yes\"}"
                                                         },
                                                         "state": "ok",
-                                                        "stderr": "[WARNING]         multiqc : MultiQC Version v1.14 now available!\n[INFO   ]         multiqc : This is MultiQC v1.9\n[INFO   ]         multiqc : Template    : default\n[INFO   ]         multiqc : Searching   : /data/jwd05e/main/060/059/60059406/working/multiqc_WDir\n[INFO   ]          fastqc : Found 2 reports\n[INFO   ]         multiqc : Compressing plot data\n[INFO   ]         multiqc : Report      : report.html\n[INFO   ]         multiqc : Data        : report_data\n[INFO   ]         multiqc : MultiQC complete\n",
+                                                        "stderr": "",
                                                         "stdout": "",
-                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
-                                                        "tool_stderr": "[WARNING]         multiqc : MultiQC Version v1.14 now available!\n[INFO   ]         multiqc : This is MultiQC v1.9\n[INFO   ]         multiqc : Template    : default\n[INFO   ]         multiqc : Searching   : /data/jwd05e/main/060/059/60059406/working/multiqc_WDir\n[INFO   ]          fastqc : Found 2 reports\n[INFO   ]         multiqc : Compressing plot data\n[INFO   ]         multiqc : Report      : report.html\n[INFO   ]         multiqc : Data        : report_data\n[INFO   ]         multiqc : MultiQC complete\n",
+                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
+                                                        "tool_stderr": "",
                                                         "tool_stdout": "",
                                                         "traceback": null,
-                                                        "update_time": "2023-05-19T15:08:50.825299",
+                                                        "update_time": "2023-05-19T14:33:32.811917",
                                                         "user_email": "hxr@informatik.uni-freiburg.de"
                                                     }
                                                 ],
                                                 "model_class": "WorkflowInvocationStep",
-                                                "order_index": 6,
-                                                "output_collections": {
-                                                    "stats": {
-                                                        "id": "b2ed5bced30ea70a",
-                                                        "src": "hdca"
-                                                    }
-                                                },
+                                                "order_index": 9,
+                                                "output_collections": {},
                                                 "outputs": {
-                                                    "html_report": {
-                                                        "id": "4838ba20a6d867657c9b5bfe8c22949d",
+                                                    "output": {
+                                                        "id": "4838ba20a6d86765c665b3763e979c0a",
                                                         "src": "hda",
-                                                        "uuid": "a42df514-e2c2-4f72-a9b8-e065ef58237f"
+                                                        "uuid": "94cccd62-deee-4ce5-8952-739603b253f7"
                                                     }
                                                 },
                                                 "state": "scheduled",
                                                 "subworkflow": null,
                                                 "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-19T15:08:50.808688",
-                                                "workflow_step_id": "40e61d72c5cedf2a",
+                                                "update_time": "2023-05-19T14:33:32.796651",
+                                                "workflow_step_id": "d00ffb828650fb93",
                                                 "workflow_step_label": null,
-                                                "workflow_step_uuid": "abf34a41-0150-42fc-b56a-a29eb92c24c3"
+                                                "workflow_step_uuid": "cb1e8297-24f1-4553-8111-1a2a48bfc12a"
                                             }
                                         }
                                     },
                                     "problem_log": "No log for this engine type.",
-                                    "start_datetime": "2023-05-19T16:55:58.620842",
+                                    "start_datetime": "2023-05-19T16:26:39.476426",
                                     "status": "success"
                                 },
-                                "doc": "Test sample data for Sequence-analyses:Quality-control",
+                                "doc": "Test sample data for Sequence analysis:Mapping",
                                 "has_data": true,
-                                "id": "quality_control.ga_0",
+                                "id": "mapping.ga_0",
                                 "test_type": "galaxy_workflow"
                             }
                         ],
@@ -212283,25 +215652,28 @@
                     }
                 },
                 "tests": true,
-                "title": "GTN - Sequence Analyses - Quality Control (imported from uploaded file)",
+                "title": "GTN - Sequence Analyses - Mapping (imported from uploaded file)",
                 "topic_id": "sequence-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/sequence-analysis-quality-control/versions/quality-control",
-                "tutorial_id": "quality-control",
-                "url": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/workflows/quality_control.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/workflows/quality_control.html",
-                "version": 5,
-                "wfid": "sequence-analysis-quality-control",
-                "wfname": "quality-control",
-                "workflow": "quality_control.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/sequence-analysis-mapping/versions/mapping",
+                "tutorial_id": "mapping",
+                "url": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/workflows/mapping.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/mapping/workflows/mapping.html",
+                "version": 4,
+                "wfid": "sequence-analysis-mapping",
+                "wfname": "mapping",
+                "workflow": "mapping.ga",
                 "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0",
                     "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3"
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9"
                 ],
-                "workflowhub_id": "1282"
+                "workflowhub_id": "1265"
             }
         ],
-        "zenodo_link": "https://zenodo.org/records/61771"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.1324070"
     },
     {
         "admin_install": {
@@ -212310,184 +215682,146 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "diamond",
-                    "owner": "bgruening",
-                    "revisions": "e8ac2b53f262",
-                    "tool_panel_section_label": "NCBI Blast",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ncbi_blast_plus",
-                    "owner": "devteam",
-                    "revisions": "0e3cf9594bb7",
-                    "tool_panel_section_label": "NCBI Blast",
+                    "name": "ncbi_fcs_gx",
+                    "owner": "iuc",
+                    "revisions": "49f8eae39606",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ncbi_blast_plus",
-                    "owner": "devteam",
-                    "revisions": "0e3cf9594bb7",
-                    "tool_panel_section_label": "NCBI Blast",
+                    "name": "ncbi_fcs_adaptor",
+                    "owner": "richard-burhans",
+                    "revisions": "d55ad8533d58",
+                    "tool_panel_section_label": "Sequence Contamination Filtering",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: diamond\n  owner: bgruening\n  revisions: e8ac2b53f262\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: 0e3cf9594bb7\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: 0e3cf9594bb7\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: ncbi_fcs_gx\n  owner: iuc\n  revisions: 49f8eae39606\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_fcs_adaptor\n  owner: richard-burhans\n  revisions: d55ad8533d58\n  tool_panel_section_label: Sequence Contamination Filtering\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/ncbi-fcs/tutorial.json",
         "contributions": {
             "authorship": [
-                "deeptivarshney"
+                "tvedtees"
+            ],
+            "editing": [
+                "hexylena"
             ],
             "funding": [
-                "madland",
-                "nfdi4plants"
+                "NIH"
             ]
         },
         "contributors": [
+            {
+                "id": "tvedtees",
+                "joined": "2024-03",
+                "name": "Eric Tvedte",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tvedtees/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tvedtees.json"
+            },
             {
                 "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
                 ],
-                "id": "deeptivarshney",
-                "joined": "2022-12",
-                "name": "Deepti Varshney",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/deeptivarshney.json"
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
             {
-                "avatar": "/training-material/shared/images/logo-madland.jpg",
+                "avatar": "/training-material/shared/images/nih.png",
                 "funder": true,
                 "github": false,
-                "id": "madland",
-                "joined": "2024-07",
-                "name": "MAdLand",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/madland/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/madland.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/logo-dataplant.svg",
-                "funder": true,
-                "id": "nfdi4plants",
-                "joined": "2024-07",
-                "name": "DataPLANT",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nfdi4plants/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/nfdi4plants.json"
+                "id": "NIH",
+                "name": "National Institutes of Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/NIH/",
+                "short_name": "NIH",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/NIH.json"
             }
         ],
-        "dir": "topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland",
+        "dir": "topics/sequence-analysis/tutorials/ncbi-fcs",
         "edam_operation": [
-            "Sequence alignment analysis"
+            "Sequence assembly validation",
+            "Sequence trimming",
+            "Sequence contamination filtering"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
+            "GalaxyTrakr",
+            "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "sequence-analysis/ncbi-blast-against-the-madland",
-        "inexact_supported_servers": [
-            "Center for Phage Technology (CPT)",
-            "Galaxy@AuBi",
-            "GalaxyTrakr",
-            "UseGalaxy.no"
-        ],
+        "id": "sequence-analysis/ncbi-fcs",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Blast tool searches a database of sequences for similar sequences to a query sequence.",
-            "Diamond  quickly aligns large-scale data sets using a compressed version of the reference sequences called a \"database diamond\".",
-            "MAdLand is a database of fully sequenced plant and algal genomes, with an emphasis on non-seed plants and streptophyte algae that can be use for sequence similarity search."
+            "Contamination can arise from multiple sources and occur at multiple stages of a genome assembly project.",
+            "Contamination cleanup is essential for reliable comparative genomics analyses."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-31",
+        "mod_date": "2024-04-16",
         "objectives": [
-            "Load FASTA sequence into Galaxy",
-            "Perform NCBI-Blast+ analysis against MAdLandDB"
+            "Learn how to screen a genome assembly for adaptor and vector contamination.",
+            "Learn how to screen a genome assembly for non-host organism contamination."
         ],
-        "pageviews": 1348,
-        "pub_date": "2023-01-16",
+        "pageviews": 634,
+        "pub_date": "2024-04-16",
         "questions": [
-            "What is MAdLand DB?",
-            "How can we perform Blast analysis on Galaxy?"
+            "Are the sequences in a genome assembly contaminant-free?"
         ],
-        "short_id": "T00238",
+        "short_id": "T00439",
         "short_tools": [
-            "ncbi_blastx_wrapper",
-            "ncbi_blastp_wrapper",
-            "bg_diamond"
+            "ncbi_fcs_gx",
+            "ncbi_fcs_adaptor"
         ],
         "slides": false,
         "slides_recordings": false,
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
                     "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
                 }
             ],
-            "inexact": [
-                {
-                    "name": "Center for Phage Technology (CPT)",
-                    "url": "https://cpt.tamu.edu/galaxy-public/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                }
-            ]
+            "inexact": []
         },
         "symlink": null,
-        "tags": [
-            "plants"
-        ],
-        "time_estimation": "15m",
-        "title": "NCBI BLAST+ against the MAdLand",
+        "time_estimation": "90M",
+        "title": "Screening assembled genomes for contamination using NCBI FCS",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/2.10.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/2.10.1+galaxy2"
+            "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/richard-burhans/ncbi_fcs_adaptor/ncbi_fcs_adaptor/0.5.0+galaxy0"
         ],
         "topic_name": "sequence-analysis",
         "topic_name_human": "Sequence analysis",
@@ -212497,20 +215831,359 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "ncbi-blast-against-the-madland",
+        "tutorial_name": "ncbi-fcs",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/ncbi-fcs/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/ncbi-fcs/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/ncbi-fcs/tutorial.json"
         },
-        "version": 9,
+        "version": 2,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 166,
-        "visitors": 1042,
-        "zenodo_link": "https://zenodo.org/records/7524427"
+        "visit_duration": 142,
+        "visitors": 448,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Organization",
+                        "name": "National Center for Biotechnology Information",
+                        "url": "https://github.com/ncbi/fcs"
+                    }
+                ],
+                "description": "This workflow performs contamination cleaning steps on assembled genomes. Users specify an input genome (fasta/fasta.gz) and taxonomic information corresponding to the source organism. There are two screening steps for foreign organism sequences (FCS-GX) and adaptors (FCS-adaptor), each followed by a cleaning step to remove identified contaminants. The final output is a cleaned genome. ",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput genome\"]\n  1[label=\"FCS-GX screen\"]\n  0 -> 1 [label=\"output\"]\n  k9741edf24be645a3980d99b1aea18380[color=lightseagreen,label=\"Output\\nfcs_gx_action_report\"]\n  1 -> k9741edf24be645a3980d99b1aea18380\n  kddedd49f8c574e3ea1583d66ce12f05c[color=lightseagreen,label=\"Output\\nfcs_gx_taxonomy_report\"]\n  1 -> kddedd49f8c574e3ea1583d66ce12f05c\n  2[label=\"FCS-GX clean\"]\n  1 -> 2 [label=\"action_report\"]\n  0 -> 2 [label=\"output\"]\n  kf3a37b43d3044ec0a023197c9e0ce2e1[color=lightseagreen,label=\"Output\\ngx_contam_fasta\"]\n  2 -> kf3a37b43d3044ec0a023197c9e0ce2e1\n  k56716c7cac7f42f7bbef62a36b4d3810[color=lightseagreen,label=\"Output\\ngx_clean_fasta\"]\n  2 -> k56716c7cac7f42f7bbef62a36b4d3810\n  3[label=\"FCS-adaptor screen\"]\n  2 -> 3 [label=\"clean_fasta\"]\n  k6a4baf4680b04a96b8649201fc80cdb7[color=lightseagreen,label=\"Output\\nfcs_adaptor_report\"]\n  3 -> k6a4baf4680b04a96b8649201fc80cdb7\n  k1cad7ab4a817436c9a63fd4e3c6b4bbb[color=lightseagreen,label=\"Output\\nadaptor_clean_fasta\"]\n  3 -> k1cad7ab4a817436c9a63fd4e3c6b4bbb\n  4[label=\"FCS-adaptor clean\"]\n  3 -> 4 [label=\"adaptor_report\"]\n  2 -> 4 [label=\"clean_fasta\"]\n  k0da685707490408786c8739522e1a776[color=lightseagreen,label=\"Output\\nadaptor_contam_fasta\"]\n  4 -> k0da685707490408786c8739522e1a776\n  k4985eb0730b04872ab8352ffeb619900[color=lightseagreen,label=\"Output\\nfinal_clean_fasta\"]\n  4 -> k4985eb0730b04872ab8352ffeb619900\n}",
+                "history": [
+                    {
+                        "hash": "3cc782f4789a4e769a903fb810a7ad5c72385c6d",
+                        "message": "Modify NIH funder. Add workflow license URL",
+                        "num": 2,
+                        "short_hash": "3cc782f47",
+                        "unix": "1713210183"
+                    },
+                    {
+                        "hash": "05ae375a039cfb4ac8f226d77c106a6fed0764ae",
+                        "message": "Suggested tutorial changes. Add workflow test.",
+                        "num": 1,
+                        "short_hash": "05ae375a0",
+                        "unix": "1712757577"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "input must be an assembled genome in fasta/fasta.gz format. FCS is not intended to identify contaminants in sequencing reads inputs.",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "input must be an assembled genome in fasta/fasta.gz format. FCS is not intended to identify contaminants in sequencing reads inputs.",
+                                "name": "Input genome"
+                            }
+                        ],
+                        "label": "Input genome",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 3.9375
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta.gz\", \" fasta\"], \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "a2066ff6-a9c6-4152-9537-a7d05d2bea00",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "http://www.usa.gov/publicdomain/label/1.0/",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput genome\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"FCS-GX screen\"];\n  0 -->|output| 1;\n  9741edf2-4be6-45a3-980d-99b1aea18380[\"Output\\nfcs_gx_action_report\"];\n  1 --> 9741edf2-4be6-45a3-980d-99b1aea18380;\n  style 9741edf2-4be6-45a3-980d-99b1aea18380 stroke:#2c3143,stroke-width:4px;\n  ddedd49f-8c57-4e3e-a158-3d66ce12f05c[\"Output\\nfcs_gx_taxonomy_report\"];\n  1 --> ddedd49f-8c57-4e3e-a158-3d66ce12f05c;\n  style ddedd49f-8c57-4e3e-a158-3d66ce12f05c stroke:#2c3143,stroke-width:4px;\n  2[\"FCS-GX clean\"];\n  1 -->|action_report| 2;\n  0 -->|output| 2;\n  f3a37b43-d304-4ec0-a023-197c9e0ce2e1[\"Output\\ngx_contam_fasta\"];\n  2 --> f3a37b43-d304-4ec0-a023-197c9e0ce2e1;\n  style f3a37b43-d304-4ec0-a023-197c9e0ce2e1 stroke:#2c3143,stroke-width:4px;\n  56716c7c-ac7f-42f7-bbef-62a36b4d3810[\"Output\\ngx_clean_fasta\"];\n  2 --> 56716c7c-ac7f-42f7-bbef-62a36b4d3810;\n  style 56716c7c-ac7f-42f7-bbef-62a36b4d3810 stroke:#2c3143,stroke-width:4px;\n  3[\"FCS-adaptor screen\"];\n  2 -->|clean_fasta| 3;\n  6a4baf46-80b0-4a96-b864-9201fc80cdb7[\"Output\\nfcs_adaptor_report\"];\n  3 --> 6a4baf46-80b0-4a96-b864-9201fc80cdb7;\n  style 6a4baf46-80b0-4a96-b864-9201fc80cdb7 stroke:#2c3143,stroke-width:4px;\n  1cad7ab4-a817-436c-9a63-fd4e3c6b4bbb[\"Output\\nadaptor_clean_fasta\"];\n  3 --> 1cad7ab4-a817-436c-9a63-fd4e3c6b4bbb;\n  style 1cad7ab4-a817-436c-9a63-fd4e3c6b4bbb stroke:#2c3143,stroke-width:4px;\n  4[\"FCS-adaptor clean\"];\n  3 -->|adaptor_report| 4;\n  2 -->|clean_fasta| 4;\n  0da68570-7490-4087-86c8-739522e1a776[\"Output\\nadaptor_contam_fasta\"];\n  4 --> 0da68570-7490-4087-86c8-739522e1a776;\n  style 0da68570-7490-4087-86c8-739522e1a776 stroke:#2c3143,stroke-width:4px;\n  4985eb07-30b0-4872-ab83-52ffeb619900[\"Output\\nfinal_clean_fasta\"];\n  4 --> 4985eb07-30b0-4872-ab83-52ffeb619900;\n  style 4985eb07-30b0-4872-ab83-52ffeb619900 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "NCBI Foreign Contamination Screen",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0",
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {
+                            "mode|fasta": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool NCBI FCS GX",
+                                "name": "mode"
+                            }
+                        ],
+                        "label": "FCS-GX screen",
+                        "name": "NCBI FCS GX",
+                        "outputs": [
+                            {
+                                "name": "taxonomy_report",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "action_report",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 355.5156127405953,
+                            "top": 3.28126838910714
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3cdb96f2855d",
+                            "name": "ncbi_fcs_gx",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"mode\": {\"mode_selector\": \"screen\", \"__current_case__\": 0, \"config_tag\": \"all\", \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"id\": {\"id_selector\": \"gx_div\", \"__current_case__\": 0, \"div\": \"fung:budding yeasts\"}, \"species\": null, \"screen_adv\": {\"gx_align_exclude_taxa\": \"\", \"gx_extra_contam_divs\": null, \"split_fasta\": true, \"div\": \"\", \"database\": \"/cvmfs/data.galaxyproject.org/byhand/ncbi_fcs_gx/all\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.5.0+galaxy0",
+                        "type": "tool",
+                        "uuid": "7907456b-eaa7-4a3f-b53b-c250110a117a",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "fcs_gx_action_report",
+                                "output_name": "action_report",
+                                "uuid": "9741edf2-4be6-45a3-980d-99b1aea18380"
+                            },
+                            {
+                                "label": "fcs_gx_taxonomy_report",
+                                "output_name": "taxonomy_report",
+                                "uuid": "ddedd49f-8c57-4e3e-a158-3d66ce12f05c"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "mode|action_report": {
+                                "id": 1,
+                                "output_name": "action_report"
+                            },
+                            "mode|input": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool NCBI FCS GX",
+                                "name": "mode"
+                            },
+                            {
+                                "description": "runtime parameter for tool NCBI FCS GX",
+                                "name": "mode"
+                            }
+                        ],
+                        "label": "FCS-GX clean",
+                        "name": "NCBI FCS GX",
+                        "outputs": [
+                            {
+                                "name": "contam_fasta",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "clean_fasta",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "left": 351.484375,
+                            "top": 301.109375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3cdb96f2855d",
+                            "name": "ncbi_fcs_gx",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"mode\": {\"mode_selector\": \"clean\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}, \"action_report\": {\"__class__\": \"ConnectedValue\"}, \"min_seq_len\": \"200\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.5.0+galaxy0",
+                        "type": "tool",
+                        "uuid": "0eba0bee-4d7a-4a8d-824c-76d5ae5dcdaa",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "gx_contam_fasta",
+                                "output_name": "contam_fasta",
+                                "uuid": "f3a37b43-d304-4ec0-a023-197c9e0ce2e1"
+                            },
+                            {
+                                "label": "gx_clean_fasta",
+                                "output_name": "clean_fasta",
+                                "uuid": "56716c7c-ac7f-42f7-bbef-62a36b4d3810"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/richard-burhans/ncbi_fcs_adaptor/ncbi_fcs_adaptor/0.5.0+galaxy0",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "input": {
+                                "id": 2,
+                                "output_name": "clean_fasta"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "FCS-adaptor screen",
+                        "name": "NCBI FCS Adaptor",
+                        "outputs": [
+                            {
+                                "name": "adaptor_report",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "clean_fasta",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "left": 701.53125,
+                            "top": 0
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/richard-burhans/ncbi_fcs_adaptor/ncbi_fcs_adaptor/0.5.0+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "d55ad8533d58",
+                            "name": "ncbi_fcs_adaptor",
+                            "owner": "richard-burhans",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"advanced\": {\"optional_log\": null}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"tax\": \"--euk\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.5.0+galaxy0",
+                        "type": "tool",
+                        "uuid": "1c9a5183-76a7-4cd9-9511-72fd75101c13",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "fcs_adaptor_report",
+                                "output_name": "adaptor_report",
+                                "uuid": "6a4baf46-80b0-4a96-b864-9201fc80cdb7"
+                            },
+                            {
+                                "label": "adaptor_clean_fasta",
+                                "output_name": "clean_fasta",
+                                "uuid": "1cad7ab4-a817-436c-9a63-fd4e3c6b4bbb"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "mode|action_report": {
+                                "id": 3,
+                                "output_name": "adaptor_report"
+                            },
+                            "mode|input": {
+                                "id": 2,
+                                "output_name": "clean_fasta"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool NCBI FCS GX",
+                                "name": "mode"
+                            },
+                            {
+                                "description": "runtime parameter for tool NCBI FCS GX",
+                                "name": "mode"
+                            }
+                        ],
+                        "label": "FCS-adaptor clean",
+                        "name": "NCBI FCS GX",
+                        "outputs": [
+                            {
+                                "name": "contam_fasta",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "clean_fasta",
+                                "type": "fasta"
+                            }
+                        ],
+                        "position": {
+                            "left": 699,
+                            "top": 302.78125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3cdb96f2855d",
+                            "name": "ncbi_fcs_gx",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"mode\": {\"mode_selector\": \"clean\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}, \"action_report\": {\"__class__\": \"ConnectedValue\"}, \"min_seq_len\": \"200\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.5.0+galaxy0",
+                        "type": "tool",
+                        "uuid": "ee8b7bac-42a5-4b17-b8ef-f432c626bb80",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "adaptor_contam_fasta",
+                                "output_name": "contam_fasta",
+                                "uuid": "0da68570-7490-4087-86c8-739522e1a776"
+                            },
+                            {
+                                "label": "final_clean_fasta",
+                                "output_name": "clean_fasta",
+                                "uuid": "4985eb07-30b0-4872-ab83-52ffeb619900"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "sequence-analysis/ncbi-fcs",
+                "path": "topics/sequence-analysis/tutorials/ncbi-fcs/workflows/NCBI-Foreign-Contamination-Screen.ga",
+                "tags": [
+                    "NCBI"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "NCBI Foreign Contamination Screen",
+                "topic_id": "sequence-analysis",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/sequence-analysis-ncbi-fcs/versions/ncbi-foreign-contamination-screen",
+                "tutorial_id": "ncbi-fcs",
+                "url": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/ncbi-fcs/workflows/NCBI-Foreign-Contamination-Screen.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/ncbi-fcs/workflows/NCBI-Foreign-Contamination-Screen.html",
+                "version": 1,
+                "wfid": "sequence-analysis-ncbi-fcs",
+                "wfname": "ncbi-foreign-contamination-screen",
+                "workflow": "NCBI-Foreign-Contamination-Screen.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/0.5.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/richard-burhans/ncbi_fcs_adaptor/ncbi_fcs_adaptor/0.5.0+galaxy0"
+                ],
+                "workflowhub_id": null
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/records/10932013"
     },
     {
         "admin_install": {
@@ -212519,458 +216192,221 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "bwa",
+                    "name": "fastq_groomer",
                     "owner": "devteam",
-                    "revisions": "e188dc7a68e6",
-                    "tool_panel_section_label": "Mapping",
+                    "revisions": "47e5dbc3e790",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastq_masker_by_quality",
+                    "owner": "devteam",
+                    "revisions": "9dfda4e310ed",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastq_to_fasta",
+                    "owner": "devteam",
+                    "revisions": "77b41c89d856",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastq_to_tabular",
+                    "owner": "devteam",
+                    "revisions": "4b347702c4aa",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastx_reverse_complement",
+                    "owner": "devteam",
+                    "revisions": "6027ef51ef91",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ncbi_blast_plus",
+                    "owner": "devteam",
+                    "revisions": "0e3cf9594bb7",
+                    "tool_panel_section_label": "NCBI Blast",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fastqc",
+                    "name": "tabular_to_fasta",
                     "owner": "devteam",
-                    "revisions": "3d0c7bdf12f5",
+                    "revisions": "0a7799698fe5",
                     "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "jbrowse",
-                    "owner": "iuc",
-                    "revisions": "17359b808b01",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "name": "ab1_fastq_converter",
+                    "owner": "ecology",
+                    "revisions": "307518fb51af",
+                    "tool_panel_section_label": "Convert Formats",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 17359b808b01\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "nakucher",
-                "avahoffman",
-                "robertmeller"
-            ],
-            "editing": [
-                "katherinecox",
-                "cutsort",
-                "nakucher"
-            ],
-            "funding": [
-                "nhgri-gdscn",
-                "nhgri-anvil"
-            ],
-            "infrastructure": [
-                "cansavvy",
-                "avahoffman",
-                "katherinecox",
-                "ehumph",
-                "cutsort"
-            ]
-        },
-        "contributors": [
-            {
-                "email": "nkucher3@jhu.edu",
-                "id": "nakucher",
-                "joined": "2023-06",
-                "name": "Natalie Kucher",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nakucher/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nakucher.json"
-            },
-            {
-                "id": "avahoffman",
-                "joined": "2023-06",
-                "name": "Ava Hoffman",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avahoffman/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/avahoffman.json"
-            },
-            {
-                "id": "robertmeller",
-                "joined": "2023-06",
-                "name": "Robert Meller",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/robertmeller/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/robertmeller.json"
-            },
-            {
-                "id": "katherinecox",
-                "joined": "2023-06",
-                "name": "Katherine Cox",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/katherinecox/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/katherinecox.json"
-            },
-            {
-                "id": "cutsort",
-                "joined": "2023-06",
-                "name": "Frederick Tan",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cutsort/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/cutsort.json"
-            },
-            {
-                "email": "nkucher3@jhu.edu",
-                "id": "nakucher",
-                "joined": "2023-06",
-                "name": "Natalie Kucher",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nakucher/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nakucher.json"
-            },
-            {
-                "id": "cansavvy",
-                "joined": "2023-06",
-                "name": "Candace Savonen",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cansavvy/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/cansavvy.json"
-            },
-            {
-                "id": "avahoffman",
-                "joined": "2023-06",
-                "name": "Ava Hoffman",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avahoffman/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/avahoffman.json"
-            },
-            {
-                "id": "katherinecox",
-                "joined": "2023-06",
-                "name": "Katherine Cox",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/katherinecox/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/katherinecox.json"
-            },
-            {
-                "id": "ehumph",
-                "joined": "2023-06",
-                "name": "Elizabeth Humphries",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ehumph/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/ehumph.json"
-            },
-            {
-                "id": "cutsort",
-                "joined": "2023-06",
-                "name": "Frederick Tan",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cutsort/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/cutsort.json"
-            },
-            {
-                "avatar": "https://www.ashg.org/wp-content/uploads/2021/07/nhgri-logo-800x167-1.png",
-                "funder": true,
-                "funding_id": "75N92022P00232",
-                "github": false,
-                "id": "nhgri-gdscn",
-                "joined": "2023-06",
-                "name": "National Human Genome Research Institute Genomic Data Science Community Network",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nhgri-gdscn/",
-                "short_name": "NHGRI GDS Community Network",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/nhgri-gdscn.json"
-            },
-            {
-                "avatar": "https://www.ashg.org/wp-content/uploads/2021/07/nhgri-logo-800x167-1.png",
-                "funder": true,
-                "funding_id": "U24HG010263",
-                "github": false,
-                "id": "nhgri-anvil",
-                "joined": "2023-06",
-                "name": "National Human Genome Research Institute Genomic Data Science Analysis, Visualization, and Informatics Lab-Space",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nhgri-anvil/",
-                "short_name": "NHGRI ANVIL",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/nhgri-anvil.json"
-            }
-        ],
-        "dir": "topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil",
-        "edam_operation": [
-            "Sequencing quality control",
-            "Generation",
-            "Read mapping",
-            "Genome visualisation",
-            "Genome indexing",
-            "Sequence alignment",
-            "Sequence composition calculation",
-            "Statistical calculation"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "sequence-analysis/sars-with-galaxy-on-anvil",
-        "inexact_supported_servers": [
-            "Galaxy@AuBi",
-            "GalaxyTrakr",
-            "UseGalaxy.cz"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Use Galaxy on the AnVIL cloud computing resource to check data, perform an alignment, and visualize the results."
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Introductory",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-02-29",
-        "objectives": [
-            "Gather and evaluate experimental evidence, including qualitative and quantitative data",
-            "Generate and interpret graphs displaying experimental results",
-            "Critique large data sets and use bioinformatics to assess genetics data",
-            "Tap into the interdisciplinary nature of science"
-        ],
-        "pageviews": 899,
-        "pub_date": "2023-07-10",
-        "questions": [
-            "How do I check my data quality?",
-            "How do I put together my dataset of fragmented sequences into a full sequence?",
-            "How do I visually explore the variants in my SARS-CoV-2 sample?"
-        ],
-        "short_id": "T00356",
-        "short_tools": [
-            "fastqc",
-            "bwa_mem",
-            "jbrowse"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
+                    "name": "aligned_to_consensus",
+                    "owner": "ecology",
+                    "revisions": "0ccbe1c20fc3",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
+                    "name": "filter_by_fasta_ids",
+                    "owner": "galaxyp",
+                    "revisions": "dff7df6fcab5",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
+                    "name": "regex_find_replace",
+                    "owner": "galaxyp",
+                    "revisions": "503bcd6ebe4b",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
+                    "name": "unzip",
+                    "owner": "imgteam",
+                    "revisions": "57f0914ddb7b",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
+                    "name": "collection_element_identifiers",
+                    "owner": "iuc",
+                    "revisions": "d3c07d270a50",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "covid19",
-            "gmod",
-            "jbrowse1"
-        ],
-        "time_estimation": "1H",
-        "title": "SARS-CoV-2 Viral Sample Alignment and Variant Visualization",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0"
-        ],
-        "topic_name": "sequence-analysis",
-        "topic_name_human": "Sequence analysis",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "sars-with-galaxy-on-anvil",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.json"
-        },
-        "version": 2,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 283,
-        "visitors": 691,
-        "zenodo_link": "https://doi.org/10.5281/zenodo.8115178"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
+                    "name": "mothur_degap_seqs",
+                    "owner": "iuc",
+                    "revisions": "6f08af23888a",
+                    "tool_panel_section_label": "Mothur",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
-                    "name": "music_construct_eset",
-                    "owner": "bgruening",
-                    "revisions": "2cfd0db49bbc",
-                    "tool_panel_section_label": "Single-cell",
+                    "name": "mothur_merge_files",
+                    "owner": "iuc",
+                    "revisions": "bc20680d28d5",
+                    "tool_panel_section_label": "Mothur",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "music_construct_eset",
-                    "owner": "bgruening",
-                    "revisions": "7ffaa0968da3",
-                    "tool_panel_section_label": "Single-cell",
+                    "name": "qiime_align_seqs",
+                    "owner": "iuc",
+                    "revisions": "e8bb88f051ec",
+                    "tool_panel_section_label": "Sequence analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "music_deconvolution",
-                    "owner": "bgruening",
-                    "revisions": "56371b5a2da9",
-                    "tool_panel_section_label": "Single-cell",
+                    "name": "seqtk",
+                    "owner": "iuc",
+                    "revisions": "3da72230c066",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "music_inspect_eset",
-                    "owner": "bgruening",
-                    "revisions": "8c64a2da3869",
-                    "tool_panel_section_label": "Single-cell",
+                    "name": "seqtk",
+                    "owner": "iuc",
+                    "revisions": "3da72230c066",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: music_construct_eset\n  owner: bgruening\n  revisions: 2cfd0db49bbc\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: music_construct_eset\n  owner: bgruening\n  revisions: 7ffaa0968da3\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: music_deconvolution\n  owner: bgruening\n  revisions: 56371b5a2da9\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: music_inspect_eset\n  owner: bgruening\n  revisions: 8c64a2da3869\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastq_groomer\n  owner: devteam\n  revisions: 47e5dbc3e790\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastq_masker_by_quality\n  owner: devteam\n  revisions: 9dfda4e310ed\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastq_to_fasta\n  owner: devteam\n  revisions: 77b41c89d856\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastq_to_tabular\n  owner: devteam\n  revisions: 4b347702c4aa\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastx_reverse_complement\n  owner: devteam\n  revisions: 6027ef51ef91\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: 0e3cf9594bb7\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tabular_to_fasta\n  owner: devteam\n  revisions: 0a7799698fe5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ab1_fastq_converter\n  owner: ecology\n  revisions: 307518fb51af\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: aligned_to_consensus\n  owner: ecology\n  revisions: 0ccbe1c20fc3\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filter_by_fasta_ids\n  owner: galaxyp\n  revisions: dff7df6fcab5\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 503bcd6ebe4b\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unzip\n  owner: imgteam\n  revisions: 57f0914ddb7b\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_element_identifiers\n  owner: iuc\n  revisions: d3c07d270a50\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_degap_seqs\n  owner: iuc\n  revisions: 6f08af23888a\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mothur_merge_files\n  owner: iuc\n  revisions: bc20680d28d5\n  tool_panel_section_label: Mothur\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qiime_align_seqs\n  owner: iuc\n  revisions: e8bb88f051ec\n  tool_panel_section_label: Sequence analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
-                    "uni-freiburg"
-                ],
-                "elixir_node": "de",
-                "email": "mtekman89@gmail.com",
-                "former_affiliations": [
-                    "elixir-europe"
-                ],
-                "id": "mtekman",
-                "joined": "2018-11",
-                "name": "Mehmet Tekman",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
-            },
-            {
-                "affiliations": [
+                    "pndb",
+                    "gallantries",
                     "elixir-europe"
                 ],
-                "bio": "Senior Lecturer at The Open University",
-                "elixir_node": "uk",
-                "email": "wendi.bacon@open.ac.uk",
-                "fediverse": "https://mstdn.science/@wendibacon1",
-                "fediverse_flavor": "mastodon",
-                "id": "nomadscientist",
-                "joined": "2020-03",
-                "matrix": "nomadscientist:matrix.org",
-                "name": "Wendi Bacon",
-                "orcid": "0000-0002-8170-8806",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
-                "twitter": "WendiBacon1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+                "elixir_node": "fr",
+                "email": "coline.royaux@mnhn.fr",
+                "id": "colineroyaux",
+                "joined": "2020-11",
+                "name": "Coline Royaux",
+                "orcid": "0000-0003-4308-5617",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/colineroyaux/",
+                "twitter": "ColineRoyaux",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/colineroyaux.json"
             }
         ],
-        "dir": "topics/single-cell/tutorials/bulk-music",
-        "edam_operation": [],
+        "dir": "topics/sequence-analysis/tutorials/Manage_AB1_Sanger",
+        "edam_operation": [
+            "Data handling",
+            "DNA barcoding",
+            "Visualisation",
+            "Phylogenetic analysis",
+            "Sequencing quality control",
+            "Demultiplexing",
+            "Taxonomic classification",
+            "Sequence read processing",
+            "Sequence file editing",
+            "Sequence clustering"
+        ],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
+            "UseGalaxy.fr"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "bulk-music-2-preparescref"
-                ],
-                "type": "internal"
-            }
-        ],
-        "gitter": "Galaxy-Training-Network/galaxy-single-cell",
         "hands_on": true,
-        "id": "single-cell/bulk-music",
+        "id": "sequence-analysis/Manage_AB1_Sanger",
         "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Deconvolution tools show individual cell type proportions in bulk RNA-seq data",
-            "Bulk RNA-seq can be complimented by scRNA-seq data"
+            "Check your data and results for mistakes afterward !!!! This procedure is useful but not perfect"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-03-05",
         "objectives": [
-            "Construct Bulk and scRNA Expression Set Objects",
-            "Inspect these objects for various properties",
-            "Measure the abundance of certain cell type cluster markers compared to others"
+            "Learn how to manage sequencing files (AB1, FASTQ, FASTA)",
+            "Learn how to clean your Sanger sequences in an automated and reproducible way"
         ],
-        "pageviews": 3553,
-        "priority": 1,
-        "pub_date": "2022-02-11",
+        "pageviews": 1988,
+        "pub_date": "2024-01-08",
         "questions": [
-            "How do we infer cell type proportions from bulk RNA-seq data?",
-            "How are these cell types grouped together?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "mtekman",
-                    "nomadscientist"
-                ],
-                "date": "2021-03-08",
-                "galaxy_version": "21.09",
-                "length": "20M",
-                "speakers": [
-                    "nomadscientist"
-                ],
-                "youtube_id": "nfAUXP3W-jM"
-            }
-        ],
-        "redirect_from": [
-            "/topics/transcriptomics/tutorials/bulk-music/tutorial",
-            "/short/single-cell/bulk-music",
-            "/short/T00240"
-        ],
-        "requirements": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-intro"
-                ],
-                "type": "internal"
-            }
+            "How to clean Sanger sequencing files?"
         ],
-        "short_id": "T00240",
+        "short_id": "T00383",
         "short_tools": [
-            "music_construct_eset",
-            "music_inspect_eset",
-            "music_deconvolution"
+            "filter_by_fasta_ids",
+            "seqtk_trimfq",
+            "fastq_groomer",
+            "tab2fasta",
+            "unzip",
+            "fastq_to_tabular",
+            "collection_element_identifiers",
+            "fastq_masker_by_quality",
+            "mothur_degap_seqs",
+            "qiime_align_seqs",
+            "regex1",
+            "mothur_merge_files",
+            "ncbi_blastn_wrapper",
+            "cshl_fastq_to_fasta",
+            "ab1_fastq_converter",
+            "cshl_fastx_reverse_complement",
+            "seqtk_mergepe",
+            "aligned_to_consensus",
+            "__SORTLIST__",
+            "__FILTER_FROM_FILE__"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "deconvo",
         "supported_servers": {
             "exact": [
                 {
@@ -212984,389 +216420,1113 @@
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
                 }
             ],
             "inexact": []
         },
         "symlink": null,
-        "tags": [
-            "transcriptomics"
-        ],
-        "time_estimation": "2h",
-        "title": "Bulk RNA Deconvolution with MuSiC",
+        "time_estimation": "1H",
+        "title": "Clean and manage Sanger sequences from raw files to aligned consensus",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3"
+            "__FILTER_FROM_FILE__",
+            "__SORTLIST__",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastq_masker_by_quality/fastq_masker_by_quality/1.1.5",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.2+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.5",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter/1.20.0",
+            "toolshed.g2.bx.psu.edu/repos/ecology/aligned_to_consensus/aligned_to_consensus/1.0.0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.3",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_degap_seqs/mothur_degap_seqs/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.3.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1"
         ],
-        "topic_name": "single-cell",
-        "topic_name_human": "Single Cell",
+        "topic_name": "sequence-analysis",
+        "topic_name_human": "Sequence analysis",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "bulk-music",
+        "tutorial_name": "Manage_AB1_Sanger",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/tutorial.json"
         },
-        "version": 7,
+        "version": 2,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 98,
-        "visitors": 2774,
+        "visit_duration": 128,
+        "visitors": 1530,
         "workflows": [
             {
-                "creators": [],
-                "description": "Bulk RNA Deconvolution with MuSiC",
+                "creators": [
+                    {
+                        "class": "Organization",
+                        "name": "Coline Royaux"
+                    }
+                ],
+                "description": "",
                 "features": {
                     "comments": false,
-                    "parameters": true,
+                    "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nscRNA Assay Tabular\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nscRNA Phenotype Tabular\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nscRNA Metadata\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBulk RNA Assay Tabular\"]\n  4[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nBulk RNA Annotation\"]\n  5[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nCell Types List\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCell Markers C1\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCell Markers C2\"]\n  8[label=\"Construct scRNA ESet Object\"]\n  0 -> 8 [label=\"output\"]\n  2 -> 8 [label=\"output\"]\n  1 -> 8 [label=\"output\"]\n  k872b3dd2322c47ccb5b9071a9f939320[color=lightseagreen,label=\"Output\\nConstruct Expression Set Object on input dataset(s): RData ESet Object\"]\n  8 -> k872b3dd2322c47ccb5b9071a9f939320\n  9[label=\"Construct Bulk RNA ESet Object\"]\n  4 -> 9 [label=\"output\"]\n  3 -> 9 [label=\"output\"]\n  10[label=\"Extract Cell Types\"]\n  8 -> 10 [label=\"out_rds\"]\n  11[label=\"Extract General Info\"]\n  8 -> 11 [label=\"out_rds\"]\n  k1733593f847d4adb91f4fd78c077b074[color=lightseagreen,label=\"Output\\nInspect Expression Set Object on input dataset(s): Inspection Result\"]\n  11 -> k1733593f847d4adb91f4fd78c077b074\n  12[label=\"Extract General Info Bulk\"]\n  9 -> 12 [label=\"out_rds\"]\n  13[label=\"Music: Estimate Cell Proportions\"]\n  9 -> 13 [label=\"out_rds\"]\n  5 -> 13 [label=\"output\"]\n  8 -> 13 [label=\"out_rds\"]\n  14[label=\"Music: Compute Dendrogram\"]\n  9 -> 14 [label=\"out_rds\"]\n  6 -> 14 [label=\"output\"]\n  7 -> 14 [label=\"output\"]\n  8 -> 14 [label=\"out_rds\"]\n  kdf2e83a5ac67460f8b0fac3f3b63280f[color=lightseagreen,label=\"Output\\nMuSiC on input dataset(s): PDF Plots\"]\n  14 -> kdf2e83a5ac67460f8b0fac3f3b63280f\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nL sequences Forward\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nH sequences Reverse\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nLCOI primers\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHCOI primers\"]\n  4[label=\"ab1 to FASTQ converter\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"ab1 to FASTQ converter\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"What\u2019s your LCOI primer sequence identifier ?\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"What\u2019s your HCOI primer sequence identifier ?\"]\n  3 -> 7 [label=\"output\"]\n  8[label=\"seqtk_trimfq\"]\n  4 -> 8 [label=\"output\"]\n  9[label=\"seqtk_trimfq\"]\n  5 -> 9 [label=\"output\"]\n  10[label=\"Degap.seqs\"]\n  6 -> 10 [label=\"output\"]\n  11[label=\"Degap.seqs\"]\n  7 -> 11 [label=\"output\"]\n  12[label=\"Sort collection\"]\n  8 -> 12 [label=\"default\"]\n  13[label=\"FASTQ Groomer\"]\n  9 -> 13 [label=\"default\"]\n  14[label=\"Reverse-Complement\"]\n  11 -> 14 [label=\"out_fasta\"]\n  15[label=\"Reverse-Complement\"]\n  13 -> 15 [label=\"output_file\"]\n  16[label=\"Sort collection\"]\n  15 -> 16 [label=\"output\"]\n  17[label=\"seqtk_mergepe\"]\n  12 -> 17 [label=\"output\"]\n  16 -> 17 [label=\"output\"]\n  18[label=\"FASTQ Groomer\"]\n  17 -> 18 [label=\"default\"]\n  19[label=\"FASTQ to Tabular\"]\n  18 -> 19 [label=\"output_file\"]\n  20[label=\"Tabular-to-FASTA\"]\n  19 -> 20 [label=\"output_file\"]\n  21[label=\"Align sequences\"]\n  20 -> 21 [label=\"output\"]\n  22[label=\"Consensus sequence from aligned FASTA\"]\n  21 -> 22 [label=\"aligned_sequences\"]\n  23[label=\"Merge.files\"]\n  22 -> 23 [label=\"output\"]\n  24[label=\"Merge.files\"]\n  23 -> 24 [label=\"output\"]\n  14 -> 24 [label=\"output\"]\n  10 -> 24 [label=\"out_fasta\"]\n  25[label=\"Regex Find And Replace\"]\n  24 -> 25 [label=\"output\"]\n  26[label=\"Align sequences\"]\n  25 -> 26 [label=\"out_file1\"]\n  27[label=\"NCBI BLAST+ blastn\"]\n  25 -> 27 [label=\"out_file1\"]\n  k31c2dd1a918e4648a407d0e3d7172253[color=lightseagreen,label=\"Output\\nw_blast_output\"]\n  27 -> k31c2dd1a918e4648a407d0e3d7172253\n  k7514514f809a4a148981cb08c950b523[color=lightseagreen,label=\"Output\\nw_consensus_aligned_sequences\"]\n  27 -> k7514514f809a4a148981cb08c950b523\n}",
                 "history": [
                     {
-                        "hash": "e2453dfb588ab6bdcb28a0991c6800683e9947fe",
-                        "message": "use full tool ID",
+                        "hash": "bf907f6d3bcd09d391c9143bb2464b50c0fb9d7a",
+                        "message": "Add creator and license",
                         "num": 2,
-                        "short_hash": "e2453dfb5",
-                        "unix": "1684159247"
+                        "short_hash": "bf907f6d3",
+                        "unix": "1704192784"
                     },
                     {
-                        "hash": "327fd2b842f45de3dc2a30067714352675ad69ae",
-                        "message": "Making a single cell topics",
+                        "hash": "03e5a4f54d25895ffe16fa5557c895ffa7b81262",
+                        "message": "Remove colons",
                         "num": 1,
-                        "short_hash": "327fd2b84",
-                        "unix": "1668273265"
+                        "short_hash": "03e5a4f54",
+                        "unix": "1702999279"
                     }
                 ],
                 "inputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "L sequences (Forward)"
+                            }
+                        ],
+                        "label": "L sequences (Forward)",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 125.19532716773591
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"ab1\"], \"tag\": \"\", \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "8a638477-d771-41a6-8c73-c6bc548d2a63",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "H sequences (Reverse)"
+                            }
+                        ],
+                        "label": "H sequences (Reverse)",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 11.09375,
+                            "top": 453.7578937515429
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"ab1\"], \"tag\": \"\", \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "79715df2-d3e0-4491-af3f-2ab6bf8d0065",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "LCOI primers"
+                            }
+                        ],
+                        "label": "LCOI primers",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 2404.8908903486745,
+                            "top": 220.80473862021637
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "711c7d32-6d82-46d7-8ee9-3258e1e11a05",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "HCOI primers"
+                            }
+                        ],
+                        "label": "HCOI primers",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 2408.903404638635,
+                            "top": 389.37482504451754
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "d23f0e22-e2ac-4c88-b7dc-f70035cfb1c2",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nL sequences Forward\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nH sequences Reverse\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nLCOI primers\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nHCOI primers\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"ab1 to FASTQ converter\"];\n  0 -->|output| 4;\n  5[\"ab1 to FASTQ converter\"];\n  1 -->|output| 5;\n  6[\"What\u2019s your LCOI primer sequence identifier ?\"];\n  2 -->|output| 6;\n  7[\"What\u2019s your HCOI primer sequence identifier ?\"];\n  3 -->|output| 7;\n  8[\"seqtk_trimfq\"];\n  4 -->|output| 8;\n  9[\"seqtk_trimfq\"];\n  5 -->|output| 9;\n  10[\"Degap.seqs\"];\n  6 -->|output| 10;\n  11[\"Degap.seqs\"];\n  7 -->|output| 11;\n  12[\"Sort collection\"];\n  8 -->|default| 12;\n  13[\"FASTQ Groomer\"];\n  9 -->|default| 13;\n  14[\"Reverse-Complement\"];\n  11 -->|out_fasta| 14;\n  15[\"Reverse-Complement\"];\n  13 -->|output_file| 15;\n  16[\"Sort collection\"];\n  15 -->|output| 16;\n  17[\"seqtk_mergepe\"];\n  12 -->|output| 17;\n  16 -->|output| 17;\n  18[\"FASTQ Groomer\"];\n  17 -->|default| 18;\n  19[\"FASTQ to Tabular\"];\n  18 -->|output_file| 19;\n  20[\"Tabular-to-FASTA\"];\n  19 -->|output_file| 20;\n  21[\"Align sequences\"];\n  20 -->|output| 21;\n  22[\"Consensus sequence from aligned FASTA\"];\n  21 -->|aligned_sequences| 22;\n  23[\"Merge.files\"];\n  22 -->|output| 23;\n  24[\"Merge.files\"];\n  23 -->|output| 24;\n  14 -->|output| 24;\n  10 -->|out_fasta| 24;\n  25[\"Regex Find And Replace\"];\n  24 -->|output| 25;\n  26[\"Align sequences\"];\n  25 -->|out_file1| 26;\n  27[\"NCBI BLAST+ blastn\"];\n  25 -->|out_file1| 27;\n  31c2dd1a-918e-4648-a407-d0e3d7172253[\"Output\\nw_blast_output\"];\n  27 --> 31c2dd1a-918e-4648-a407-d0e3d7172253;\n  style 31c2dd1a-918e-4648-a407-d0e3d7172253 stroke:#2c3143,stroke-width:4px;\n  7514514f-809a-4a14-8981-cb08c950b523[\"Output\\nw_consensus_aligned_sequences\"];\n  27 --> 7514514f-809a-4a14-8981-cb08c950b523;\n  style 7514514f-809a-4a14-8981-cb08c950b523 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Sanger1 : From AB1 to aligned consensus and primers fasta + BLAST",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter/1.20.0",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "ab1 to FASTQ converter",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "fastq"
+                            }
+                        ],
+                        "position": {
+                            "left": 262.40633877840924,
+                            "top": 88.5911568019689
+                        },
+                        "post_job_actions": {
+                            "TagDatasetActionoutput": {
+                                "action_arguments": {
+                                    "tags": "#Forward"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter/1.20.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "307518fb51af",
+                            "name": "ab1_fastq_converter",
+                            "owner": "ecology",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"tr\": {\"trim\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.20.0",
+                        "type": "tool",
+                        "uuid": "54cdaa74-a83e-4c0b-baf7-90c854b6e65e",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "fcaa483b-90d1-40fc-b681-d8a5d421ccca"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "in_file": {
+                                "id": 4,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool seqtk_trimfq",
+                                "name": "mode"
+                            }
+                        ],
+                        "label": null,
+                        "name": "seqtk_trimfq",
+                        "outputs": [
+                            {
+                                "name": "default",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 510.1667695686167,
+                            "top": 97.48960601311335
+                        },
+                        "post_job_actions": {
+                            "TagDatasetActiondefault": {
+                                "action_arguments": {
+                                    "tags": "TrimmedFastq"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "default"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3da72230c066",
+                            "name": "seqtk",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"in_file\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"mode_select\": \"quality\", \"__current_case__\": 0, \"q\": \"0.05\", \"l\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3.1",
+                        "type": "tool",
+                        "uuid": "915f5560-b853-4b0a-bd5f-126d831e8f8c",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "default",
+                                "uuid": "d65ac032-9ff6-4fb7-9aa2-1931ed709384"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1",
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {
+                            "in_file": {
+                                "id": 5,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool seqtk_trimfq",
+                                "name": "mode"
+                            }
+                        ],
+                        "label": null,
+                        "name": "seqtk_trimfq",
+                        "outputs": [
+                            {
+                                "name": "default",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 516.8334128639917,
+                            "top": 432.987075214611
+                        },
+                        "post_job_actions": {
+                            "TagDatasetActiondefault": {
+                                "action_arguments": {
+                                    "tags": "TrimmedFastq"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "default"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3da72230c066",
+                            "name": "seqtk",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"in_file\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"mode_select\": \"quality\", \"__current_case__\": 0, \"q\": \"0.05\", \"l\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3.1",
+                        "type": "tool",
+                        "uuid": "979d668f-f8e9-4a09-8d79-e02ed0c027b5",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "default",
+                                "uuid": "d1bf6174-2eec-4589-b890-9336c46f3623"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "__SORTLIST__",
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {
+                            "input": {
+                                "id": 8,
+                                "output_name": "default"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Sort collection",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 913.747383567731,
+                            "top": 82.22452721670341
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "__SORTLIST__",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"sort_type\": {\"sort_type\": \"alpha\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "dbaab406-5db7-44e6-8694-04e78a7a5f11",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "be7cfe5d-d40b-40ca-b334-671f2f680e05"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
+                        "errors": null,
+                        "id": 13,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 9,
+                                "output_name": "default"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FASTQ Groomer",
+                        "outputs": [
+                            {
+                                "name": "output_file",
+                                "type": "fastqsanger"
+                            }
+                        ],
+                        "position": {
+                            "left": 771.7188193581324,
+                            "top": 347.4557364362019
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
+                        "tool_shed_repository": {
+                            "changeset_revision": "47e5dbc3e790",
+                            "name": "fastq_groomer",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"input_type\": \"sanger\", \"options_type\": {\"options_type_selector\": \"advanced\", \"__current_case__\": 1, \"output_type\": \"sanger\", \"force_quality_encoding\": \"ascii\", \"summarize_input\": \"dont_summarize_input\", \"fix_id\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.5",
+                        "type": "tool",
+                        "uuid": "f4f69d89-8133-4ad1-ac1f-de948e788511",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_file",
+                                "uuid": "64bbe1c0-fc65-4fb0-a4de-f6b0eb35086a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0",
+                        "errors": null,
+                        "id": 15,
+                        "input_connections": {
+                            "input": {
+                                "id": 13,
+                                "output_name": "output_file"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Reverse-Complement",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1011.3125887784095,
+                            "top": 401.88283826503715
+                        },
+                        "post_job_actions": {
+                            "TagDatasetActionoutput": {
+                                "action_arguments": {
+                                    "tags": "Reversed"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "6027ef51ef91",
+                            "name": "fastx_reverse_complement",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2+galaxy0",
+                        "type": "tool",
+                        "uuid": "fc621ad3-5725-4f10-8f1e-b5afa01a059c",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "6d261e5a-8d3c-4055-ae85-5fd4fd6bb268"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "__SORTLIST__",
+                        "errors": null,
+                        "id": 16,
+                        "input_connections": {
+                            "input": {
+                                "id": 15,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Sort collection",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1242.4584406072447,
+                            "top": 399.60162155694064
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "__SORTLIST__",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"sort_type\": {\"sort_type\": \"alpha\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "db0e7202-78c6-4726-a70d-64cd2627fb85",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "408d419f-bcae-4bcc-8b3a-e38fdbafcdd3"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.3.1",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 17,
+                        "input_connections": {
+                            "in_fq1": {
+                                "id": 12,
+                                "output_name": "output"
+                            },
+                            "in_fq2": {
+                                "id": 16,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "seqtk_mergepe",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "scRNA Assay Tabular"
+                                "name": "default",
+                                "type": "input"
                             }
                         ],
-                        "label": "scRNA Assay Tabular",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 234.6999969482422,
-                            "height": 82.19999694824219,
-                            "left": 360,
-                            "right": 560,
-                            "top": 152.5,
-                            "width": 200,
-                            "x": 360,
-                            "y": 152.5
+                            "left": 1253.306789106719,
+                            "top": 45.2514467179884
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "0d219185-0933-4459-ade3-30f96b00511d",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.3.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3da72230c066",
+                            "name": "seqtk",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"in_fq1\": {\"__class__\": \"ConnectedValue\"}, \"in_fq2\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.3.1",
+                        "type": "tool",
+                        "uuid": "6010e92a-afb0-49ca-a73c-dacd0c5567e2",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "c67225bf-f947-45ed-ae5b-5c9367ef8cab"
+                                "output_name": "default",
+                                "uuid": "9b2849cd-587d-438a-b77a-077f033c8ac1"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 18,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 17,
+                                "output_name": "default"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "FASTQ Groomer",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "scRNA Phenotype Tabular"
+                                "name": "output_file",
+                                "type": "fastqsanger"
                             }
                         ],
-                        "label": "scRNA Phenotype Tabular",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 338.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 359,
-                            "right": 559,
-                            "top": 256,
-                            "width": 200,
-                            "x": 359,
-                            "y": 256
+                            "left": 1504.6579138638374,
+                            "top": 31.193468490200797
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "9ca6d554-decc-4b57-b6f4-723a60e5a0cc",
+                        "post_job_actions": {
+                            "ChangeDatatypeActionoutput_file": {
+                                "action_arguments": {
+                                    "newtype": "fastqsanger"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "output_file"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
+                        "tool_shed_repository": {
+                            "changeset_revision": "47e5dbc3e790",
+                            "name": "fastq_groomer",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"input_type\": \"sanger\", \"options_type\": {\"options_type_selector\": \"advanced\", \"__current_case__\": 1, \"output_type\": \"sanger\", \"force_quality_encoding\": \"ascii\", \"summarize_input\": \"dont_summarize_input\", \"fix_id\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.5",
+                        "type": "tool",
+                        "uuid": "467c139a-27d3-42e9-af9c-83ffdf8dc339",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "59f0e53a-13ee-4ab6-8cdf-40482dfc0f75"
+                                "output_name": "output_file",
+                                "uuid": "64bbe1c0-fc65-4fb0-a4de-f6b0eb35086a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
+                        "id": 21,
+                        "input_connections": {
+                            "input_fasta_fp": {
+                                "id": 20,
+                                "output_name": "output"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "scRNA Metadata"
+                                "description": "runtime parameter for tool Align sequences",
+                                "name": "min_length"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Align sequences",
+                        "outputs": [
+                            {
+                                "name": "aligned_sequences",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "log",
+                                "type": "txt"
                             }
                         ],
-                        "label": "scRNA Metadata",
-                        "name": "Input parameter",
-                        "outputs": [],
                         "position": {
-                            "bottom": 424.8000030517578,
-                            "height": 61.80000305175781,
-                            "left": 357,
-                            "right": 557,
-                            "top": 363,
-                            "width": 200,
-                            "x": 357,
-                            "y": 363
+                            "left": 2240.20532371138,
+                            "top": 0
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "4efc5ad2-5000-4b60-92e8-df022c6f8a7f",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e8bb88f051ec",
+                            "name": "qiime_align_seqs",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"alignment\": {\"alignment_method\": \"clustalw\", \"__current_case__\": 2}, \"input_fasta_fp\": {\"__class__\": \"ConnectedValue\"}, \"min_length\": {\"__class__\": \"RuntimeValue\"}, \"min_percent_id\": \"0.1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.1.0",
+                        "type": "tool",
+                        "uuid": "5283fe90-38e1-4a44-a9c3-f54f29cbad85",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "f45df54a-4591-49bb-91be-06a497ceb14d"
+                                "output_name": "log",
+                                "uuid": "d63ff33a-4e1a-4900-a59c-f3c14da1b7fc"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "aligned_sequences",
+                                "uuid": "c049c7ef-cc65-487c-a3c7-28b6845273b7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ecology/aligned_to_consensus/aligned_to_consensus/1.0.0",
                         "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 22,
+                        "input_connections": {
+                            "input": {
+                                "id": 21,
+                                "output_name": "aligned_sequences"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Consensus sequence from aligned FASTA",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Bulk RNA Assay Tabular"
+                                "name": "output",
+                                "type": "fasta"
                             }
                         ],
-                        "label": "Bulk RNA Assay Tabular",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 544.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 358,
-                            "right": 558,
-                            "top": 462,
-                            "width": 200,
-                            "x": 358,
-                            "y": 462
+                            "left": 2499.008880503396,
+                            "top": 0.8750031686378801
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "809894bc-62b0-43a8-af73-d19c359b2e4e",
+                        "post_job_actions": {
+                            "RemoveTagDatasetActionoutput": {
+                                "action_arguments": {
+                                    "tags": "#Forward; #Reverse"
+                                },
+                                "action_type": "RemoveTagDatasetAction",
+                                "output_name": "output"
+                            },
+                            "TagDatasetActionoutput": {
+                                "action_arguments": {
+                                    "tags": "#Consensus"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/aligned_to_consensus/aligned_to_consensus/1.0.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "0ccbe1c20fc3",
+                            "name": "aligned_to_consensus",
+                            "owner": "ecology",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"gaps\": false, \"input\": {\"__class__\": \"ConnectedValue\"}, \"method\": \"chr_ambiguity\", \"outog\": false, \"seqtype\": \"DNA\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "69865435-ac6e-44d7-b0db-42bf338372a9",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "4a8ebd19-87c9-4b3d-89ad-26316b1460f9"
+                                "uuid": "15b69469-bba8-4af3-8f1e-816cebc96645"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0",
                         "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 23,
+                        "input_connections": {
+                            "merge|inputs": {
+                                "id": 22,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Merge.files",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Bulk RNA Annotation"
+                                "name": "output",
+                                "type": "input"
                             }
                         ],
-                        "label": "Bulk RNA Annotation",
-                        "name": "Input parameter",
-                        "outputs": [],
                         "position": {
-                            "bottom": 645.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 358,
-                            "right": 558,
-                            "top": 563,
-                            "width": 200,
-                            "x": 358,
-                            "y": 563
+                            "left": 2763.411217150582,
+                            "top": 15.925027274602481
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "1c008bcf-8ea8-4f48-89ec-623190301fc9",
+                        "post_job_actions": {
+                            "TagDatasetActionoutput": {
+                                "action_arguments": {
+                                    "tags": "#AllSeqs"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "7bd37d6decd9",
+                            "name": "mothur_merge_files",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"merge\": {\"type\": \"fasta\", \"__current_case__\": 0, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"savelog\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
+                        "type": "tool",
+                        "uuid": "bc874b27-7222-46e1-9753-64fa1a1b98bd",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "5663f93d-b38f-4f7c-9ed2-7aa5a5e0273e"
+                                "uuid": "356f874b-c4d6-419c-afb7-15df5d285738"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0",
                         "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 24,
+                        "input_connections": {
+                            "merge|inputs": [
+                                {
+                                    "id": 23,
+                                    "output_name": "output"
+                                },
+                                {
+                                    "id": 14,
+                                    "output_name": "output"
+                                },
+                                {
+                                    "id": 10,
+                                    "output_name": "out_fasta"
+                                }
+                            ]
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Merge.files",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Cell Types List"
+                                "name": "output",
+                                "type": "input"
                             }
                         ],
-                        "label": "Cell Types List",
-                        "name": "Input parameter",
-                        "outputs": [],
                         "position": {
-                            "bottom": 314.3000030517578,
-                            "height": 61.80000305175781,
-                            "left": 928,
-                            "right": 1128,
-                            "top": 252.5,
-                            "width": 200,
-                            "x": 928,
-                            "y": 252.5
+                            "left": 3443.4000227757297,
+                            "top": 228.33828312924055
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "f98985a7-458a-4b2f-a924-8ca4ecdaa037",
+                        "post_job_actions": {
+                            "RemoveTagDatasetActionoutput": {
+                                "action_arguments": {
+                                    "tags": "#Forward ; #Reverse"
+                                },
+                                "action_type": "RemoveTagDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "7bd37d6decd9",
+                            "name": "mothur_merge_files",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"merge\": {\"type\": \"fasta\", \"__current_case__\": 0, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"savelog\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.39.5.0",
+                        "type": "tool",
+                        "uuid": "5f3ca9fa-eed1-45a5-8300-031268c7783d",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "6440740d-b72c-422b-a46c-d3de32c25076"
+                                "uuid": "356f874b-c4d6-419c-afb7-15df5d285738"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3",
                         "errors": null,
-                        "id": 6,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 25,
+                        "input_connections": {
+                            "input": {
+                                "id": 24,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Regex Find And Replace",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Cell Markers C1"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
-                        "label": "Cell Markers C1",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 388.3000030517578,
-                            "height": 61.80000305175781,
-                            "left": 927,
-                            "right": 1127,
-                            "top": 326.5,
-                            "width": 200,
-                            "x": 927,
-                            "y": 326.5
+                            "left": 3700.2137599467087,
+                            "top": 225.93423217156686
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "d2940a2a-808b-43ec-9ed7-59a8915b4fbd",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "503bcd6ebe4b",
+                            "name": "regex_find_replace",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \"([A-Z-])>\", \"replacement\": \"\\\\1\\\\n>\"}], \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.3",
+                        "type": "tool",
+                        "uuid": "8eb5a8e5-5935-4052-a5d3-000426e25a99",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "b87c6860-8b9d-4412-8aa7-506ea09bfc16"
+                                "output_name": "out_file1",
+                                "uuid": "b0c0361f-3434-4f77-b1e6-0fd97c225559"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0",
                         "errors": null,
-                        "id": 7,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 26,
+                        "input_connections": {
+                            "input_fasta_fp": {
+                                "id": 25,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Align sequences",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Cell Markers C2"
+                                "name": "aligned_sequences",
+                                "type": "fasta"
+                            },
+                            {
+                                "name": "log",
+                                "type": "txt"
                             }
                         ],
-                        "label": "Cell Markers C2",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 459.3000030517578,
-                            "height": 61.80000305175781,
-                            "left": 932,
-                            "right": 1132,
-                            "top": 397.5,
-                            "width": 200,
-                            "x": 932,
-                            "y": 397.5
+                            "left": 3971.6876053119054,
+                            "top": 187.59371966347155
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "b13d3354-a633-4eeb-8edf-4f14c4209240",
+                        "post_job_actions": {
+                            "TagDatasetActionaligned_sequences": {
+                                "action_arguments": {
+                                    "tags": "#Aligned"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "aligned_sequences"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e8bb88f051ec",
+                            "name": "qiime_align_seqs",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"alignment\": {\"alignment_method\": \"mafft\", \"__current_case__\": 4}, \"input_fasta_fp\": {\"__class__\": \"ConnectedValue\"}, \"min_length\": null, \"min_percent_id\": \"0.1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.1.0",
+                        "type": "tool",
+                        "uuid": "a6fde88b-d89a-4fe2-ac12-0c82f16429e0",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "3f07162a-d2f4-411e-a276-6437c7149ecc"
+                                "output_name": "aligned_sequences",
+                                "uuid": "c049c7ef-cc65-487c-a3c7-28b6845273b7"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "log",
+                                "uuid": "d63ff33a-4e1a-4900-a59c-f3c14da1b7fc"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy2",
+                        "errors": null,
+                        "id": 27,
+                        "input_connections": {
+                            "query": {
+                                "id": 25,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "NCBI BLAST+ blastn",
+                        "outputs": [
+                            {
+                                "name": "output1",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 3984.640583018545,
+                            "top": 451.7552266775396
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "0e3cf9594bb7",
+                            "name": "ncbi_blast_plus",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"advanced\", \"__current_case__\": 1, \"filter_query\": true, \"strand\": \"-strand both\", \"max_hits\": \"10\", \"max_hsps\": null, \"identity_cutoff\": \"0.0\", \"word_size\": null, \"ungapped\": false, \"parse_deflines\": false, \"adv_optional_id_files_opts\": {\"adv_optional_id_files_opts_selector\": \"none\", \"__current_case__\": 0}, \"qcov_hsp_perc\": \"0.0\", \"window_size\": null, \"gapopen\": null, \"gapextend\": null}, \"blast_type\": \"megablast\", \"db_opts\": {\"db_opts_selector\": \"db\", \"__current_case__\": 0, \"database\": [\"nt_2021-6-21\"], \"histdb\": \"\", \"subject\": \"\"}, \"evalue_cutoff\": \"0.001\", \"output\": {\"out_format\": \"cols\", \"__current_case__\": 2, \"std_cols\": [\"qseqid\", \"pident\", \"mismatch\", \"gapopen\"], \"ext_cols\": [\"gaps\", \"salltitles\"], \"ids_cols\": [\"saccver\"], \"misc_cols\": null, \"tax_cols\": null}, \"query\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.10.1+galaxy2",
+                        "type": "tool",
+                        "uuid": "335762a1-b65e-4510-a3bc-c6148648c8c2",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "w_blast_output",
+                                "output_name": "blast_output",
+                                "uuid": "31c2dd1a-918e-4648-a407-d0e3d7172253"
+                            },
+                            {
+                                "label": "w_consensus_aligned_sequences",
+                                "output_name": "consensus_aligned_sequences",
+                                "uuid": "7514514f-809a-4a14-8981-cb08c950b523"
                             }
                         ]
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nscRNA Assay Tabular\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nscRNA Phenotype Tabular\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nscRNA Metadata\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nBulk RNA Assay Tabular\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nBulk RNA Annotation\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Parameter\\nCell Types List\"];\n  style 5 fill:#ded,stroke:#393,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nCell Markers C1\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nCell Markers C2\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"Construct scRNA ESet Object\"];\n  0 -->|output| 8;\n  2 -->|output| 8;\n  1 -->|output| 8;\n  872b3dd2-322c-47cc-b5b9-071a9f939320[\"Output\\nConstruct Expression Set Object on input dataset(s): RData ESet Object\"];\n  8 --> 872b3dd2-322c-47cc-b5b9-071a9f939320;\n  style 872b3dd2-322c-47cc-b5b9-071a9f939320 stroke:#2c3143,stroke-width:4px;\n  9[\"Construct Bulk RNA ESet Object\"];\n  4 -->|output| 9;\n  3 -->|output| 9;\n  10[\"Extract Cell Types\"];\n  8 -->|out_rds| 10;\n  11[\"Extract General Info\"];\n  8 -->|out_rds| 11;\n  1733593f-847d-4adb-91f4-fd78c077b074[\"Output\\nInspect Expression Set Object on input dataset(s): Inspection Result\"];\n  11 --> 1733593f-847d-4adb-91f4-fd78c077b074;\n  style 1733593f-847d-4adb-91f4-fd78c077b074 stroke:#2c3143,stroke-width:4px;\n  12[\"Extract General Info Bulk\"];\n  9 -->|out_rds| 12;\n  13[\"Music: Estimate Cell Proportions\"];\n  9 -->|out_rds| 13;\n  5 -->|output| 13;\n  8 -->|out_rds| 13;\n  14[\"Music: Compute Dendrogram\"];\n  9 -->|out_rds| 14;\n  6 -->|output| 14;\n  7 -->|output| 14;\n  8 -->|out_rds| 14;\n  df2e83a5-ac67-460f-8b0f-ac3f3b63280f[\"Output\\nMuSiC on input dataset(s): PDF Plots\"];\n  14 --> df2e83a5-ac67-460f-8b0f-ac3f3b63280f;\n  style df2e83a5-ac67-460f-8b0f-ac3f3b63280f stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "MuSiC Workflow",
-                "outputs": [
+                "parent_id": "sequence-analysis/Manage_AB1_Sanger",
+                "path": "topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Sanger1_From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST.ga",
+                "tags": [],
+                "test_results": null,
+                "tests": true,
+                "title": "Sanger1 : From AB1 to aligned consensus and primers fasta + BLAST",
+                "topic_id": "sequence-analysis",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/sequence-analysis-Manage_AB1_Sanger/versions/sanger1-from-ab1-to-aligned-consensus-and-primers-fasta---blast",
+                "tutorial_id": "Manage_AB1_Sanger",
+                "url": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Sanger1_From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Sanger1_From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST.html",
+                "version": 1,
+                "wfid": "sequence-analysis-Manage_AB1_Sanger",
+                "wfname": "sanger1-from-ab1-to-aligned-consensus-and-primers-fasta---blast",
+                "workflow": "Sanger1_From-AB1-to-aligned-consensus-and-primers-fasta-+-BLAST.ga",
+                "workflow_tools": [
+                    "__SORTLIST__",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.5",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter/1.20.0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/aligned_to_consensus/aligned_to_consensus/1.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.3",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_degap_seqs/mothur_degap_seqs/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.3.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1"
+                ],
+                "workflowhub_id": "1287"
+            },
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0003-4308-5617",
+                        "name": "Coline Royaux"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAOPEP_and_CHD8_sequences_20220907.zip?download=1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPrim\"]\n  2[label=\"Unzip\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Filter FASTA\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Filter FASTA\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Extract element identifiers\"]\n  2 -> 5 [label=\"unzipped\"]\n  6[label=\"Degap.seqs\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"Degap.seqs\"]\n  4 -> 7 [label=\"output\"]\n  8[label=\"Regex Find And Replace\"]\n  5 -> 8 [label=\"output\"]\n  9[label=\"Regex Find And Replace\"]\n  5 -> 9 [label=\"output\"]\n  10[label=\"Reverse-Complement\"]\n  7 -> 10 [label=\"out_fasta\"]\n  11[label=\"Filter collection\"]\n  8 -> 11 [label=\"out_file1\"]\n  2 -> 11 [label=\"unzipped\"]\n  12[label=\"Filter collection\"]\n  9 -> 12 [label=\"out_file1\"]\n  11 -> 12 [label=\"output_discarded\"]\n  13[label=\"ab1 to FASTQ converter\"]\n  11 -> 13 [label=\"output_filtered\"]\n  14[label=\"ab1 to FASTQ converter\"]\n  12 -> 14 [label=\"output_filtered\"]\n  15[label=\"seqtk_trimfq\"]\n  13 -> 15 [label=\"output\"]\n  16[label=\"seqtk_trimfq\"]\n  14 -> 16 [label=\"output\"]\n  17[label=\"FASTQ Groomer\"]\n  15 -> 17 [label=\"default\"]\n  18[label=\"Sort collection\"]\n  16 -> 18 [label=\"default\"]\n  19[label=\"Sort collection\"]\n  17 -> 19 [label=\"output_file\"]\n  20[label=\"Reverse-Complement\"]\n  19 -> 20 [label=\"output\"]\n  21[label=\"seqtk_mergepe\"]\n  18 -> 21 [label=\"output\"]\n  20 -> 21 [label=\"output\"]\n  22[label=\"FASTQ Groomer\"]\n  21 -> 22 [label=\"default\"]\n  23[label=\"FASTQ to Tabular\"]\n  22 -> 23 [label=\"output_file\"]\n  24[label=\"Tabular-to-FASTA\"]\n  23 -> 24 [label=\"output_file\"]\n  25[label=\"Align sequences\"]\n  24 -> 25 [label=\"output\"]\n  26[label=\"Consensus sequence from aligned FASTA\"]\n  25 -> 26 [label=\"aligned_sequences\"]\n  27[label=\"Merge.files\"]\n  26 -> 27 [label=\"output\"]\n  28[label=\"Merge.files\"]\n  27 -> 28 [label=\"output\"]\n  10 -> 28 [label=\"output\"]\n  6 -> 28 [label=\"out_fasta\"]\n  29[label=\"Regex Find And Replace\"]\n  28 -> 29 [label=\"output\"]\n  30[label=\"Align sequences\"]\n  29 -> 30 [label=\"out_file1\"]\n  31[label=\"NCBI BLAST+ blastn\"]\n  29 -> 31 [label=\"out_file1\"]\n}",
+                "history": [
+                    {
+                        "hash": "9b2a39983d90c6094d400a9288bf711577ef5690",
+                        "message": "Update workflow",
+                        "num": 2,
+                        "short_hash": "9b2a39983",
+                        "unix": "1704193918"
+                    },
+                    {
+                        "hash": "1d51e2dc3ebda3fca99a60be425d69edd4681702",
+                        "message": "Move files from ecology to sequence analysis",
+                        "num": 1,
+                        "short_hash": "1d51e2dc3",
+                        "unix": "1702992927"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
                         "content_id": null,
@@ -213376,34 +217536,23 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "scRNA Assay Tabular"
+                                "name": "AOPEP_and_CHD8_sequences_20220907.zip?download=1"
                             }
                         ],
-                        "label": "scRNA Assay Tabular",
+                        "label": "AOPEP_and_CHD8_sequences_20220907.zip?download=1",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 234.6999969482422,
-                            "height": 82.19999694824219,
-                            "left": 360,
-                            "right": 560,
-                            "top": 152.5,
-                            "width": 200,
-                            "x": 360,
-                            "y": 152.5
+                            "left": 0,
+                            "top": 658.2072063088361
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "0d219185-0933-4459-ade3-30f96b00511d",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "c67225bf-f947-45ed-ae5b-5c9367ef8cab"
-                            }
-                        ]
+                        "uuid": "2113bd7f-ee7f-462e-9d96-0181a1cd8219",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
@@ -213414,763 +217563,1005 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "scRNA Phenotype Tabular"
+                                "name": "Prim"
                             }
                         ],
-                        "label": "scRNA Phenotype Tabular",
+                        "label": "Prim",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 338.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 359,
-                            "right": 559,
-                            "top": 256,
-                            "width": 200,
-                            "x": 359,
-                            "y": 256
+                            "left": 4123.210210680649,
+                            "top": 561.120359751304
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "9ca6d554-decc-4b57-b6f4-723a60e5a0cc",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "59f0e53a-13ee-4ab6-8cdf-40482dfc0f75"
-                            }
-                        ]
-                    },
+                        "uuid": "ceb12523-7e38-428e-a26d-c05ff85e0749",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAOPEP_and_CHD8_sequences_20220907.zip?download=1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nPrim\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Unzip\"];\n  0 -->|output| 2;\n  3[\"Filter FASTA\"];\n  1 -->|output| 3;\n  4[\"Filter FASTA\"];\n  1 -->|output| 4;\n  5[\"Extract element identifiers\"];\n  2 -->|unzipped| 5;\n  6[\"Degap.seqs\"];\n  3 -->|output| 6;\n  7[\"Degap.seqs\"];\n  4 -->|output| 7;\n  8[\"Regex Find And Replace\"];\n  5 -->|output| 8;\n  9[\"Regex Find And Replace\"];\n  5 -->|output| 9;\n  10[\"Reverse-Complement\"];\n  7 -->|out_fasta| 10;\n  11[\"Filter collection\"];\n  8 -->|out_file1| 11;\n  2 -->|unzipped| 11;\n  12[\"Filter collection\"];\n  9 -->|out_file1| 12;\n  11 -->|output_discarded| 12;\n  13[\"ab1 to FASTQ converter\"];\n  11 -->|output_filtered| 13;\n  14[\"ab1 to FASTQ converter\"];\n  12 -->|output_filtered| 14;\n  15[\"seqtk_trimfq\"];\n  13 -->|output| 15;\n  16[\"seqtk_trimfq\"];\n  14 -->|output| 16;\n  17[\"FASTQ Groomer\"];\n  15 -->|default| 17;\n  18[\"Sort collection\"];\n  16 -->|default| 18;\n  19[\"Sort collection\"];\n  17 -->|output_file| 19;\n  20[\"Reverse-Complement\"];\n  19 -->|output| 20;\n  21[\"seqtk_mergepe\"];\n  18 -->|output| 21;\n  20 -->|output| 21;\n  22[\"FASTQ Groomer\"];\n  21 -->|default| 22;\n  23[\"FASTQ to Tabular\"];\n  22 -->|output_file| 23;\n  24[\"Tabular-to-FASTA\"];\n  23 -->|output_file| 24;\n  25[\"Align sequences\"];\n  24 -->|output| 25;\n  26[\"Consensus sequence from aligned FASTA\"];\n  25 -->|aligned_sequences| 26;\n  27[\"Merge.files\"];\n  26 -->|output| 27;\n  28[\"Merge.files\"];\n  27 -->|output| 28;\n  10 -->|output| 28;\n  6 -->|out_fasta| 28;\n  29[\"Regex Find And Replace\"];\n  28 -->|output| 29;\n  30[\"Align sequences\"];\n  29 -->|out_file1| 30;\n  31[\"NCBI BLAST+ blastn\"];\n  29 -->|out_file1| 31;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Training Sanger sequences CHD8",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 20,
+                        "input_connections": {
+                            "input": {
+                                "id": 19,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Reverse-Complement",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "scRNA Metadata"
+                                "name": "output",
+                                "type": "input"
                             }
                         ],
-                        "label": "scRNA Metadata",
-                        "name": "Input parameter",
-                        "outputs": [],
                         "position": {
-                            "bottom": 424.8000030517578,
-                            "height": 61.80000305175781,
-                            "left": 357,
-                            "right": 557,
-                            "top": 363,
-                            "width": 200,
-                            "x": 357,
-                            "y": 363
+                            "left": 2835.744215956759,
+                            "top": 0
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "4efc5ad2-5000-4b60-92e8-df022c6f8a7f",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "6027ef51ef91",
+                            "name": "fastx_reverse_complement",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"fastqsanger\", \"__workflow_invocation_uuid__\": \"f12bdb84904311eeb9fd00505691a2f4\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2+galaxy0",
+                        "type": "tool",
+                        "uuid": "1933ab2e-90bb-4535-899b-1379d85fbd64",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "f45df54a-4591-49bb-91be-06a497ceb14d"
+                                "uuid": "c999ceff-4f83-4cf6-bd3b-c38f2128b86d"
                             }
                         ]
-                    },
+                    }
+                ],
+                "parent_id": "sequence-analysis/Manage_AB1_Sanger",
+                "path": "topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Training-Sanger-sequences-CHD8.ga",
+                "tags": [],
+                "test_results": null,
+                "tests": true,
+                "title": "Training Sanger sequences CHD8",
+                "topic_id": "sequence-analysis",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/sequence-analysis-Manage_AB1_Sanger/versions/training-sanger-sequences-chd8",
+                "tutorial_id": "Manage_AB1_Sanger",
+                "url": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Training-Sanger-sequences-CHD8.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Training-Sanger-sequences-CHD8.html",
+                "version": 1,
+                "wfid": "sequence-analysis-Manage_AB1_Sanger",
+                "wfname": "training-sanger-sequences-chd8",
+                "workflow": "Training-Sanger-sequences-CHD8.ga",
+                "workflow_tools": [
+                    "__FILTER_FROM_FILE__",
+                    "__SORTLIST__",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.5",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter/1.20.0",
+                    "toolshed.g2.bx.psu.edu/repos/ecology/aligned_to_consensus/aligned_to_consensus/1.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.3",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3",
+                    "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_degap_seqs/mothur_degap_seqs/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.3.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1"
+                ],
+                "workflowhub_id": "1292"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/records/7104640"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "5ec9f6bceaee",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bracken",
+                    "owner": "iuc",
+                    "revisions": "978ae4147c29",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bracken",
+                    "owner": "iuc",
+                    "revisions": "1d4bd12f01cf",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastp",
+                    "owner": "iuc",
+                    "revisions": "65b93b623c77",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastp",
+                    "owner": "iuc",
+                    "revisions": "c59d48774d03",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "kraken2",
+                    "owner": "iuc",
+                    "revisions": "20e2f64aa1fe",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "kraken2",
+                    "owner": "iuc",
+                    "revisions": "cdee7158adf3",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "recentrifuge",
+                    "owner": "iuc",
+                    "revisions": "b5407cc2bf51",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bracken\n  owner: iuc\n  revisions: 978ae4147c29\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bracken\n  owner: iuc\n  revisions: 1d4bd12f01cf\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: c59d48774d03\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: 20e2f64aa1fe\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: cdee7158adf3\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: recentrifuge\n  owner: iuc\n  revisions: b5407cc2bf51\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "bebatut",
+                "clsiguret"
+            ],
+            "funding": [
+                "abromics"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "affiliations": [
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "elixir_node": "fr",
+                "email": "clea.siguret@gmail.com",
+                "id": "clsiguret",
+                "joined": "2024-04",
+                "linkedin": "cl\u00e9a-siguret-58423b107",
+                "matrix": "clsiguret:matrix.org",
+                "name": "Clea Siguret",
+                "orcid": "0009-0005-6140-0379",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/clsiguret/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/clsiguret.json"
+            },
+            {
+                "avatar": "/training-material/assets/images/abromics.png",
+                "funder": true,
+                "github": false,
+                "id": "abromics",
+                "joined": "2024-01",
+                "name": "ABRomics",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/abromics/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/abromics.json"
+            }
+        ],
+        "dir": "topics/sequence-analysis/tutorials/quality-contamination-control",
+        "edam_ontology": [
+            "topic_3673",
+            "topic_0622",
+            "topic_3301",
+            "topic_3697"
+        ],
+        "edam_operation": [
+            "Cross-assembly",
+            "Sequencing quality control",
+            "Sequence contamination filtering",
+            "Statistical calculation",
+            "Taxonomic classification",
+            "Expression analysis",
+            "Sequence composition calculation"
+        ],
+        "edam_topic": [
+            "Whole genome sequencing",
+            "Genomics",
+            "Microbiology",
+            "Microbial ecology"
+        ],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.fr"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "sequence-analysis/quality-contamination-control",
+        "inexact_supported_servers": [
+            "Galaxy@AuBi",
+            "GalaxyTrakr",
+            "UseGalaxy.cz",
+            "UseGalaxy.org (Main)"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Conduct quality control on every dataset before performing any other bioinformatics analysis",
+            "Review the quality metrics and, if necessary, improve the quality of your data",
+            "Check the impact of the quality control",
+            "Detect witch microorganisms are present and extract the species level",
+            "Check possible contamination in a bacterial isolate"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-02",
+        "objectives": [
+            "Run tools to evaluate sequencing data on quality and quantity",
+            "Evaluate the output of quality control tools",
+            "Improve the quality of sequencing data",
+            "Run a series of tool to identify species in bacterial isolate sequencing data",
+            "Visualize the species abundance"
+        ],
+        "pageviews": 225,
+        "pub_date": "2024-07-15",
+        "questions": [
+            "How to check the quality of MiSeq data?",
+            "What are the species in bacterial isolate sequencing data?"
+        ],
+        "recordings": [
+            {
+                "bot-timestamp": 1722527209,
+                "captioners": [
+                    "clsiguret"
+                ],
+                "date": "2024-08-01",
+                "galaxy_version": "24.0.4.dev0",
+                "length": "34M",
+                "speakers": [
+                    "clsiguret"
+                ],
+                "youtube_id": "Cx31r5emUJk"
+            }
+        ],
+        "short_id": "T00446",
+        "short_tools": [
+            "fastp",
+            "est_abundance",
+            "recentrifuge",
+            "upload1",
+            "kraken2",
+            "fastqc"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "illumina",
+            "bacteria",
+            "microgalaxy"
+        ],
+        "time_estimation": "2H",
+        "title": "Quality and contamination control in bacterial isolate using Illumina MiSeq Data",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.8+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0",
+            "upload1"
+        ],
+        "topic_name": "sequence-analysis",
+        "topic_name_human": "Sequence analysis",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "quality-contamination-control",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.json"
+        },
+        "version": 2,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 151,
+        "visitors": 185,
+        "workflows": [
+            {
+                "creators": [
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Bulk RNA Assay Tabular"
-                            }
-                        ],
-                        "label": "Bulk RNA Assay Tabular",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 544.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 358,
-                            "right": 558,
-                            "top": 462,
-                            "width": 200,
-                            "x": 358,
-                            "y": 462
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "809894bc-62b0-43a8-af73-d19c359b2e4e",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "4a8ebd19-87c9-4b3d-89ad-26316b1460f9"
-                            }
-                        ]
+                        "alternateName": "bebatut",
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0001-9852-1987",
+                        "name": "B\u00e9r\u00e9nice Batut"
                     },
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Bulk RNA Annotation"
-                            }
-                        ],
-                        "label": "Bulk RNA Annotation",
-                        "name": "Input parameter",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 645.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 358,
-                            "right": 558,
-                            "top": 563,
-                            "width": 200,
-                            "x": 358,
-                            "y": 563
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "1c008bcf-8ea8-4f48-89ec-623190301fc9",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "5663f93d-b38f-4f7c-9ed2-7aa5a5e0273e"
-                            }
-                        ]
-                    },
+                        "alternateName": "clsiguret",
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0009-0005-6140-0379",
+                        "name": "Clea Siguret"
+                    }
+                ],
+                "description": "Quality and contamination control in bacterial isolate using Illumina MiSeq Data",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDRR187559_1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDRR187559_2\"]\n  2[label=\"FastQC forward\"]\n  0 -> 2 [label=\"output\"]\n  kd3aed14e51b840b09d6d548fff2ab63a[color=lightseagreen,label=\"Output\\nFastQC text_file (forward)\"]\n  2 -> kd3aed14e51b840b09d6d548fff2ab63a\n  k6c9273387e024599a01d014a35a529e8[color=lightseagreen,label=\"Output\\nFastQC html_file (forward)\"]\n  2 -> k6c9273387e024599a01d014a35a529e8\n  3[label=\"FastQC reverse\"]\n  1 -> 3 [label=\"output\"]\n  k30d76c09809d4415a1e6f244cfc34065[color=lightseagreen,label=\"Output\\nFastQC html_file (reverse)\"]\n  3 -> k30d76c09809d4415a1e6f244cfc34065\n  kbbafb0728b124908ae0f10cc7f9086d3[color=lightseagreen,label=\"Output\\nFastQC text_file (reverse)\"]\n  3 -> kbbafb0728b124908ae0f10cc7f9086d3\n  4[label=\"fastp\"]\n  0 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  k1a089ca0445a4322b74f60c7aefc7cd8[color=lightseagreen,label=\"Output\\nfastp report_html\"]\n  4 -> k1a089ca0445a4322b74f60c7aefc7cd8\n  kb634addfdcb843e68016341de7eb5b87[color=lightseagreen,label=\"Output\\nDRR187559_filtered_\"]\n  4 -> kb634addfdcb843e68016341de7eb5b87\n  k0a57afa4e75e470dad7b13e567ce54a3[color=lightseagreen,label=\"Output\\nDRR187559_filtered_1\"]\n  4 -> k0a57afa4e75e470dad7b13e567ce54a3\n  kbb98c4d1bd1d47bdac564ac0e1e49d50[color=lightseagreen,label=\"Output\\nfastp_json\"]\n  4 -> kbb98c4d1bd1d47bdac564ac0e1e49d50\n  5[label=\"Kraken2\"]\n  4 -> 5 [label=\"out1\"]\n  4 -> 5 [label=\"out2\"]\n  k54b85a5372ee4b73b1867fd55e8aab9b[color=lightseagreen,label=\"Output\\nkraken_report_tabular\"]\n  5 -> k54b85a5372ee4b73b1867fd55e8aab9b\n  ka408a64458cd4f5eaf2515b5ea63aa76[color=lightseagreen,label=\"Output\\nkraken_report_reads\"]\n  5 -> ka408a64458cd4f5eaf2515b5ea63aa76\n  6[label=\"Bracken\"]\n  5 -> 6 [label=\"report_output\"]\n  k8ca52af9f83942b6aa74f1a6a1dfbbc8[color=lightseagreen,label=\"Output\\nbracken_kraken_report\"]\n  6 -> k8ca52af9f83942b6aa74f1a6a1dfbbc8\n  kae6c6464f5f54e5bb616d38166fc0133[color=lightseagreen,label=\"Output\\nbracken_report_tsv\"]\n  6 -> kae6c6464f5f54e5bb616d38166fc0133\n  7[label=\"Recentrifuge\"]\n  5 -> 7 [label=\"output\"]\n  kbd947a1d0443465f86585d76d9ce69f8[color=lightseagreen,label=\"Output\\nrecentrifuge_report_html\"]\n  7 -> kbd947a1d0443465f86585d76d9ce69f8\n  kc7457acb41bc4191b3fb6716e15fbe57[color=lightseagreen,label=\"Output\\nrecentrifuge_data_tabular\"]\n  7 -> kc7457acb41bc4191b3fb6716e15fbe57\n  kb5694f2dc8cd4460bfff74fd0792ecb3[color=lightseagreen,label=\"Output\\nrecentrifuge_stats_tabular\"]\n  7 -> kb5694f2dc8cd4460bfff74fd0792ecb3\n  k94f6ff070e0647ad88f8a058d0808537[color=lightseagreen,label=\"Output\\nrecentrifuge_logfile\"]\n  7 -> k94f6ff070e0647ad88f8a058d0808537\n}",
+                "history": [
                     {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Cell Types List"
-                            }
-                        ],
-                        "label": "Cell Types List",
-                        "name": "Input parameter",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 314.3000030517578,
-                            "height": 61.80000305175781,
-                            "left": 928,
-                            "right": 1128,
-                            "top": 252.5,
-                            "width": 200,
-                            "x": 928,
-                            "y": 252.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "f98985a7-458a-4b2f-a924-8ca4ecdaa037",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "6440740d-b72c-422b-a46c-d3de32c25076"
-                            }
-                        ]
-                    },
+                        "hash": "b415560c3b517c8332ed6762dc86a54d0968b2f2",
+                        "message": "Add tuto 'quality-contamination-control' + update learning pathway 'amr-gene-detection'",
+                        "num": 1,
+                        "short_hash": "b415560c3",
+                        "unix": "1718877309"
+                    }
+                ],
+                "inputs": [
                     {
-                        "annotation": "",
+                        "annotation": "forward read",
                         "content_id": null,
                         "errors": null,
-                        "id": 6,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Cell Markers C1"
+                                "description": "forward read",
+                                "name": "DRR187559_1"
                             }
                         ],
-                        "label": "Cell Markers C1",
+                        "label": "DRR187559_1",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 388.3000030517578,
-                            "height": 61.80000305175781,
-                            "left": 927,
-                            "right": 1127,
-                            "top": 326.5,
-                            "width": 200,
-                            "x": 927,
-                            "y": 326.5
+                            "left": 0,
+                            "top": 275.20001220703125
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "d2940a2a-808b-43ec-9ed7-59a8915b4fbd",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "b87c6860-8b9d-4412-8aa7-506ea09bfc16"
-                            }
-                        ]
+                        "uuid": "a39893cf-49cb-4c5c-9e71-0f8004a2a1ee",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "reverse read",
                         "content_id": null,
                         "errors": null,
-                        "id": 7,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Cell Markers C2"
+                                "description": "reverse read",
+                                "name": "DRR187559_2"
                             }
                         ],
-                        "label": "Cell Markers C2",
+                        "label": "DRR187559_2",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 459.3000030517578,
-                            "height": 61.80000305175781,
-                            "left": 932,
-                            "right": 1132,
-                            "top": 397.5,
-                            "width": 200,
-                            "x": 932,
-                            "y": 397.5
+                            "left": 24,
+                            "top": 530.1999969482422
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "b13d3354-a633-4eeb-8edf-4f14c4209240",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "3f07162a-d2f4-411e-a276-6437c7149ecc"
-                            }
-                        ]
-                    },
+                        "uuid": "ca539dfd-e173-42d6-998a-0fc4c5f3d5b8",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "GPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nDRR187559_1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nDRR187559_2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"FastQC forward\"];\n  0 -->|output| 2;\n  d3aed14e-51b8-40b0-9d6d-548fff2ab63a[\"Output\\nFastQC text_file (forward)\"];\n  2 --> d3aed14e-51b8-40b0-9d6d-548fff2ab63a;\n  style d3aed14e-51b8-40b0-9d6d-548fff2ab63a stroke:#2c3143,stroke-width:4px;\n  6c927338-7e02-4599-a01d-014a35a529e8[\"Output\\nFastQC html_file (forward)\"];\n  2 --> 6c927338-7e02-4599-a01d-014a35a529e8;\n  style 6c927338-7e02-4599-a01d-014a35a529e8 stroke:#2c3143,stroke-width:4px;\n  3[\"FastQC reverse\"];\n  1 -->|output| 3;\n  30d76c09-809d-4415-a1e6-f244cfc34065[\"Output\\nFastQC html_file (reverse)\"];\n  3 --> 30d76c09-809d-4415-a1e6-f244cfc34065;\n  style 30d76c09-809d-4415-a1e6-f244cfc34065 stroke:#2c3143,stroke-width:4px;\n  bbafb072-8b12-4908-ae0f-10cc7f9086d3[\"Output\\nFastQC text_file (reverse)\"];\n  3 --> bbafb072-8b12-4908-ae0f-10cc7f9086d3;\n  style bbafb072-8b12-4908-ae0f-10cc7f9086d3 stroke:#2c3143,stroke-width:4px;\n  4[\"fastp\"];\n  0 -->|output| 4;\n  1 -->|output| 4;\n  1a089ca0-445a-4322-b74f-60c7aefc7cd8[\"Output\\nfastp report_html\"];\n  4 --> 1a089ca0-445a-4322-b74f-60c7aefc7cd8;\n  style 1a089ca0-445a-4322-b74f-60c7aefc7cd8 stroke:#2c3143,stroke-width:4px;\n  b634addf-dcb8-43e6-8016-341de7eb5b87[\"Output\\nDRR187559_filtered_\"];\n  4 --> b634addf-dcb8-43e6-8016-341de7eb5b87;\n  style b634addf-dcb8-43e6-8016-341de7eb5b87 stroke:#2c3143,stroke-width:4px;\n  0a57afa4-e75e-470d-ad7b-13e567ce54a3[\"Output\\nDRR187559_filtered_1\"];\n  4 --> 0a57afa4-e75e-470d-ad7b-13e567ce54a3;\n  style 0a57afa4-e75e-470d-ad7b-13e567ce54a3 stroke:#2c3143,stroke-width:4px;\n  bb98c4d1-bd1d-47bd-ac56-4ac0e1e49d50[\"Output\\nfastp_json\"];\n  4 --> bb98c4d1-bd1d-47bd-ac56-4ac0e1e49d50;\n  style bb98c4d1-bd1d-47bd-ac56-4ac0e1e49d50 stroke:#2c3143,stroke-width:4px;\n  5[\"Kraken2\"];\n  4 -->|out1| 5;\n  4 -->|out2| 5;\n  54b85a53-72ee-4b73-b186-7fd55e8aab9b[\"Output\\nkraken_report_tabular\"];\n  5 --> 54b85a53-72ee-4b73-b186-7fd55e8aab9b;\n  style 54b85a53-72ee-4b73-b186-7fd55e8aab9b stroke:#2c3143,stroke-width:4px;\n  a408a644-58cd-4f5e-af25-15b5ea63aa76[\"Output\\nkraken_report_reads\"];\n  5 --> a408a644-58cd-4f5e-af25-15b5ea63aa76;\n  style a408a644-58cd-4f5e-af25-15b5ea63aa76 stroke:#2c3143,stroke-width:4px;\n  6[\"Bracken\"];\n  5 -->|report_output| 6;\n  8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8[\"Output\\nbracken_kraken_report\"];\n  6 --> 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8;\n  style 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8 stroke:#2c3143,stroke-width:4px;\n  ae6c6464-f5f5-4e5b-b616-d38166fc0133[\"Output\\nbracken_report_tsv\"];\n  6 --> ae6c6464-f5f5-4e5b-b616-d38166fc0133;\n  style ae6c6464-f5f5-4e5b-b616-d38166fc0133 stroke:#2c3143,stroke-width:4px;\n  7[\"Recentrifuge\"];\n  5 -->|output| 7;\n  bd947a1d-0443-465f-8658-5d76d9ce69f8[\"Output\\nrecentrifuge_report_html\"];\n  7 --> bd947a1d-0443-465f-8658-5d76d9ce69f8;\n  style bd947a1d-0443-465f-8658-5d76d9ce69f8 stroke:#2c3143,stroke-width:4px;\n  c7457acb-41bc-4191-b3fb-6716e15fbe57[\"Output\\nrecentrifuge_data_tabular\"];\n  7 --> c7457acb-41bc-4191-b3fb-6716e15fbe57;\n  style c7457acb-41bc-4191-b3fb-6716e15fbe57 stroke:#2c3143,stroke-width:4px;\n  b5694f2d-c8cd-4460-bfff-74fd0792ecb3[\"Output\\nrecentrifuge_stats_tabular\"];\n  7 --> b5694f2d-c8cd-4460-bfff-74fd0792ecb3;\n  style b5694f2d-c8cd-4460-bfff-74fd0792ecb3 stroke:#2c3143,stroke-width:4px;\n  94f6ff07-0e06-47ad-88f8-a058d0808537[\"Output\\nrecentrifuge_logfile\"];\n  7 --> 94f6ff07-0e06-47ad-88f8-a058d0808537;\n  style 94f6ff07-0e06-47ad-88f8-a058d0808537 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:09 +0000",
+                "name": "Quality and contamination control in bacterial isolate using Illumina MiSeq Data",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
                         "errors": null,
-                        "id": 8,
+                        "id": 2,
                         "input_connections": {
-                            "exprs_file": {
+                            "input_file": {
                                 "id": 0,
                                 "output_name": "output"
-                            },
-                            "metadata_0|row_names": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "pdata_file": {
-                                "id": 1,
-                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Construct Expression Set Object",
-                                "name": "exprs_file"
-                            },
-                            {
-                                "description": "runtime parameter for tool Construct Expression Set Object",
-                                "name": "pdata_file"
-                            }
-                        ],
-                        "label": "Construct scRNA ESet Object",
-                        "name": "Construct Expression Set Object",
+                        "inputs": [],
+                        "label": "FastQC (forward)",
+                        "name": "FastQC",
                         "outputs": [
                             {
-                                "name": "out_tab",
-                                "type": "tabular"
+                                "name": "html_file",
+                                "type": "html"
                             },
                             {
-                                "name": "out_rds",
-                                "type": "rdata"
+                                "name": "text_file",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 435.8999938964844,
-                            "height": 286.3999938964844,
-                            "left": 637,
-                            "right": 837,
-                            "top": 149.5,
-                            "width": 200,
-                            "x": 637,
-                            "y": 149.5
+                            "left": 340,
+                            "top": 0
                         },
                         "post_job_actions": {
-                            "HideDatasetActionout_tab": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "out_tab"
+                            "TagDatasetActionhtml_file": {
+                                "action_arguments": {
+                                    "tags": "#unfiltered"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "html_file"
+                            },
+                            "TagDatasetActiontext_file": {
+                                "action_arguments": {
+                                    "tags": "#unfiltered"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "text_file"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "2cfd0db49bbc",
-                            "name": "music_construct_eset",
-                            "owner": "bgruening",
+                            "changeset_revision": "5ec9f6bceaee",
+                            "name": "fastqc",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"annotation\": \"\", \"expdata\": {\"name\": \"\", \"lab\": \"\", \"contact\": \"\", \"title\": \"\", \"abstract\": \"\", \"url\": \"\", \"other\": [{\"__index__\": 0, \"field\": \"notes\", \"comment\": \"Created in Galaxy\"}]}, \"exprs_file\": {\"__class__\": \"RuntimeValue\"}, \"metadata\": [{\"__index__\": 0, \"row_names\": {\"__class__\": \"ConnectedValue\"}, \"label_desc\": \"\"}], \"pdata_file\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.1+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"fastqsanger.bz2\", \"adapters\": null, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"contaminants\": null, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": null, \"min_length\": null, \"nogroup\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.74+galaxy0",
                         "type": "tool",
-                        "uuid": "2e56a895-db92-4961-9d04-9860ef4d6007",
+                        "uuid": "1dd908a7-85da-4c90-b506-73fe598e0ce0",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Construct Expression Set Object on input dataset(s): RData ESet Object",
-                                "output_name": "out_rds",
-                                "uuid": "872b3dd2-322c-47cc-b5b9-071a9f939320"
+                                "label": "FastQC text_file (forward)",
+                                "output_name": "text_file",
+                                "uuid": "d3aed14e-51b8-40b0-9d6d-548fff2ab63a"
+                            },
+                            {
+                                "label": "FastQC html_file (forward)",
+                                "output_name": "html_file",
+                                "uuid": "6c927338-7e02-4599-a01d-014a35a529e8"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
                         "errors": null,
-                        "id": 9,
+                        "id": 3,
                         "input_connections": {
-                            "annotation": {
-                                "id": 4,
-                                "output_name": "output"
-                            },
-                            "exprs_file": {
-                                "id": 3,
+                            "input_file": {
+                                "id": 1,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Construct Expression Set Object",
-                                "name": "exprs_file"
-                            },
-                            {
-                                "description": "runtime parameter for tool Construct Expression Set Object",
-                                "name": "pdata_file"
-                            }
-                        ],
-                        "label": "Construct Bulk RNA ESet Object",
-                        "name": "Construct Expression Set Object",
+                        "inputs": [],
+                        "label": "FastQC (reverse)",
+                        "name": "FastQC",
                         "outputs": [
                             {
-                                "name": "out_tab",
-                                "type": "tabular"
+                                "name": "html_file",
+                                "type": "html"
                             },
                             {
-                                "name": "out_rds",
-                                "type": "rdata"
+                                "name": "text_file",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 746.3999938964844,
-                            "height": 286.3999938964844,
-                            "left": 638,
-                            "right": 838,
-                            "top": 460,
-                            "width": 200,
-                            "x": 638,
-                            "y": 460
+                            "left": 323,
+                            "top": 612.5999755859375
                         },
                         "post_job_actions": {
-                            "HideDatasetActionout_tab": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "out_tab"
+                            "TagDatasetActionhtml_file": {
+                                "action_arguments": {
+                                    "tags": "#unfiltered"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "html_file"
+                            },
+                            "TagDatasetActiontext_file": {
+                                "action_arguments": {
+                                    "tags": "#unfiltered"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "text_file"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "2cfd0db49bbc",
-                            "name": "music_construct_eset",
-                            "owner": "bgruening",
+                            "changeset_revision": "5ec9f6bceaee",
+                            "name": "fastqc",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"annotation\": {\"__class__\": \"ConnectedValue\"}, \"expdata\": {\"name\": \"\", \"lab\": \"\", \"contact\": \"\", \"title\": \"\", \"abstract\": \"\", \"url\": \"\", \"other\": [{\"__index__\": 0, \"field\": \"notes\", \"comment\": \"Created in Galaxy\"}]}, \"exprs_file\": {\"__class__\": \"RuntimeValue\"}, \"metadata\": [], \"pdata_file\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.1+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"fastqsanger.bz2\", \"adapters\": null, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"contaminants\": null, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": null, \"min_length\": null, \"nogroup\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.74+galaxy0",
                         "type": "tool",
-                        "uuid": "4646fe87-4f29-48cf-b751-a1edb4e9fd7d",
+                        "uuid": "198542e7-06ed-42ed-a725-6c8902cda430",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_rds",
-                                "uuid": "f27399d6-39f8-4712-a632-ee34b891306d"
+                                "label": "FastQC html_file (reverse)",
+                                "output_name": "html_file",
+                                "uuid": "30d76c09-809d-4415-a1e6-f244cfc34065"
+                            },
+                            {
+                                "label": "FastQC text_file (reverse)",
+                                "output_name": "text_file",
+                                "uuid": "bbafb072-8b12-4908-ae0f-10cc7f9086d3"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
                         "errors": null,
-                        "id": 10,
+                        "id": 4,
                         "input_connections": {
-                            "rds_eset": {
-                                "id": 8,
-                                "output_name": "out_rds"
+                            "single_paired|in1": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "single_paired|in2": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Inspect Expression Set Object",
-                                "name": "rds_eset"
-                            }
-                        ],
-                        "label": "Extract Cell Types",
-                        "name": "Inspect Expression Set Object",
+                        "inputs": [],
+                        "label": null,
+                        "name": "fastp",
                         "outputs": [
                             {
-                                "name": "out_tab",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 244.39999389648438,
-                            "height": 154.39999389648438,
-                            "left": 926,
-                            "right": 1126,
-                            "top": 90,
-                            "width": 200,
-                            "x": 926,
-                            "y": 90
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "8c64a2da3869",
-                            "name": "music_inspect_eset",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"inspector\": \"fData\", \"rds_eset\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "04fa6a76-2262-4608-bf42-f0bd17419226",
-                        "workflow_outputs": [
+                                "name": "out1",
+                                "type": "input"
+                            },
                             {
-                                "label": null,
-                                "output_name": "out_tab",
-                                "uuid": "3c2f499e-2f78-4aeb-bd5b-82b4606dea16"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3",
-                        "errors": null,
-                        "id": 11,
-                        "input_connections": {
-                            "rds_eset": {
-                                "id": 8,
-                                "output_name": "out_rds"
-                            }
-                        },
-                        "inputs": [
+                                "name": "out2",
+                                "type": "input"
+                            },
                             {
-                                "description": "runtime parameter for tool Inspect Expression Set Object",
-                                "name": "rds_eset"
-                            }
-                        ],
-                        "label": "Extract General Info",
-                        "name": "Inspect Expression Set Object",
-                        "outputs": [
+                                "name": "report_html",
+                                "type": "html"
+                            },
                             {
-                                "name": "out_tab",
-                                "type": "tabular"
+                                "name": "report_json",
+                                "type": "json"
                             }
                         ],
                         "position": {
-                            "bottom": 692.8999938964844,
-                            "height": 154.39999389648438,
-                            "left": 948,
-                            "right": 1148,
-                            "top": 538.5,
-                            "width": 200,
-                            "x": 948,
-                            "y": 538.5
+                            "left": 578.603249768338,
+                            "top": 384.1144483914405
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3",
+                        "post_job_actions": {
+                            "TagDatasetActionout1": {
+                                "action_arguments": {
+                                    "tags": "#filtered"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "out1"
+                            },
+                            "TagDatasetActionout2": {
+                                "action_arguments": {
+                                    "tags": "#filtered"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "out2"
+                            },
+                            "TagDatasetActionreport_html": {
+                                "action_arguments": {
+                                    "tags": "#filtered"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "report_html"
+                            },
+                            "TagDatasetActionreport_json": {
+                                "action_arguments": {
+                                    "tags": "#filtered"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "report_json"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "8c64a2da3869",
-                            "name": "music_inspect_eset",
-                            "owner": "bgruening",
+                            "changeset_revision": "65b93b623c77",
+                            "name": "fastp",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"inspector\": \"print\", \"rds_eset\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.1+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": \"30\", \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": null, \"umi_len\": null, \"umi_prefix\": null}, \"cutting_by_quality_options\": {\"cut_by_quality5\": true, \"cut_by_quality3\": true, \"cut_window_size\": \"4\", \"cut_mean_quality\": \"20\"}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired\", \"__current_case__\": 1, \"in1\": {\"__class__\": \"ConnectedValue\"}, \"in2\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": null, \"adapter_sequence2\": null}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.23.2+galaxy0",
                         "type": "tool",
-                        "uuid": "4a8ff055-fa99-4867-97e5-a3d1ec49b9bc",
+                        "uuid": "2e9aba48-2b99-46a1-a4de-72a8a2f6db84",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Inspect Expression Set Object on input dataset(s): Inspection Result",
-                                "output_name": "out_tab",
-                                "uuid": "1733593f-847d-4adb-91f4-fd78c077b074"
+                                "label": "fastp report_html",
+                                "output_name": "report_html",
+                                "uuid": "1a089ca0-445a-4322-b74f-60c7aefc7cd8"
+                            },
+                            {
+                                "label": "DRR187559_filtered_",
+                                "output_name": "out2",
+                                "uuid": "b634addf-dcb8-43e6-8016-341de7eb5b87"
+                            },
+                            {
+                                "label": "DRR187559_filtered_1",
+                                "output_name": "out1",
+                                "uuid": "0a57afa4-e75e-470d-ad7b-13e567ce54a3"
+                            },
+                            {
+                                "label": "fastp_json",
+                                "output_name": "report_json",
+                                "uuid": "bb98c4d1-bd1d-47bd-ac56-4ac0e1e49d50"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
                         "errors": null,
-                        "id": 12,
+                        "id": 5,
                         "input_connections": {
-                            "rds_eset": {
-                                "id": 9,
-                                "output_name": "out_rds"
+                            "single_paired|forward_input": {
+                                "id": 4,
+                                "output_name": "out1"
+                            },
+                            "single_paired|reverse_input": {
+                                "id": 4,
+                                "output_name": "out2"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Inspect Expression Set Object",
-                                "name": "rds_eset"
-                            }
-                        ],
-                        "label": "Extract General Info (Bulk)",
-                        "name": "Inspect Expression Set Object",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Kraken2",
                         "outputs": [
                             {
-                                "name": "out_tab",
+                                "name": "report_output",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "output",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 861.3999938964844,
-                            "height": 154.39999389648438,
-                            "left": 945,
-                            "right": 1145,
-                            "top": 707,
-                            "width": 200,
-                            "x": 945,
-                            "y": 707
+                            "left": 850.4914977412587,
+                            "top": 397.42238822577673
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "8c64a2da3869",
-                            "name": "music_inspect_eset",
-                            "owner": "bgruening",
+                            "changeset_revision": "20e2f64aa1fe",
+                            "name": "kraken2",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"inspector\": \"print\", \"rds_eset\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.1+galaxy0",
+                        "tool_state": "{\"confidence\": \"0.0\", \"kraken2_database\": \"2023-08-24T153645Z_standard_prebuilt_pluspf_16gb_2022-06-07\", \"min_base_quality\": \"10\", \"minimum_hit_groups\": \"2\", \"quick\": false, \"report\": {\"create_report\": true, \"use_mpa_style\": false, \"report_zero_counts\": false, \"report_minimizer_data\": false}, \"single_paired\": {\"single_paired_selector\": \"yes\", \"__current_case__\": 1, \"forward_input\": {\"__class__\": \"ConnectedValue\"}, \"reverse_input\": {\"__class__\": \"ConnectedValue\"}}, \"split_reads\": false, \"use_names\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.1+galaxy1",
                         "type": "tool",
-                        "uuid": "83ae4dc4-ff8a-4df7-8d47-c52e4f79c97f",
+                        "uuid": "75b7f2b8-2b63-4f1a-a877-4babef16a08b",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_tab",
-                                "uuid": "d2312cc5-cea1-4f07-a0cf-0574a0923c28"
+                                "label": "kraken_report_tabular",
+                                "output_name": "report_output",
+                                "uuid": "54b85a53-72ee-4b73-b186-7fd55e8aab9b"
+                            },
+                            {
+                                "label": "kraken_report_reads",
+                                "output_name": "output",
+                                "uuid": "a408a644-58cd-4f5e-af25-15b5ea63aa76"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.8+galaxy0",
                         "errors": null,
-                        "id": 13,
+                        "id": 6,
                         "input_connections": {
-                            "bulk_eset": {
-                                "id": 9,
-                                "output_name": "out_rds"
-                            },
-                            "do|celltypes": {
+                            "input": {
                                 "id": 5,
-                                "output_name": "output"
-                            },
-                            "scrna_eset": {
-                                "id": 8,
-                                "output_name": "out_rds"
+                                "output_name": "report_output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool MuSiC",
-                                "name": "bulk_eset"
-                            },
-                            {
-                                "description": "runtime parameter for tool MuSiC",
-                                "name": "scrna_eset"
-                            }
-                        ],
-                        "label": "Music: Estimate Cell Proportions",
-                        "name": "MuSiC",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Bracken",
                         "outputs": [
                             {
-                                "name": "summaries",
-                                "type": "input"
+                                "name": "report",
+                                "type": "tabular"
                             },
                             {
-                                "name": "out_pdf",
-                                "type": "pdf"
+                                "name": "kraken_report",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 536.3999938964844,
-                            "height": 286.3999938964844,
-                            "left": 1325,
-                            "right": 1525,
-                            "top": 250,
-                            "width": 200,
-                            "x": 1325,
-                            "y": 250
+                            "left": 1140.1325234308401,
+                            "top": 326.57184790597137
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3",
+                        "post_job_actions": {
+                            "RenameDatasetActionkraken_report": {
+                                "action_arguments": {
+                                    "newname": "bracken_kraken_report"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "kraken_report"
+                            },
+                            "RenameDatasetActionreport": {
+                                "action_arguments": {
+                                    "newname": "bracken_report_tsv"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "report"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.8+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "56371b5a2da9",
-                            "name": "music_deconvolution",
-                            "owner": "bgruening",
+                            "changeset_revision": "978ae4147c29",
+                            "name": "bracken",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"bulk_eset\": {\"__class__\": \"RuntimeValue\"}, \"do\": {\"method\": \"estimateprops\", \"__current_case__\": 0, \"celltypes_label\": \"cellType\", \"samples_label\": \"sampleID\", \"celltypes\": {\"__class__\": \"ConnectedValue\"}, \"methods\": [\"MuSiC\", \"NNLS\"], \"phenotype_factors\": \"\", \"phenotype_gene\": \"\", \"sample_groups\": \"\", \"sample_disease_group\": \"\", \"sample_disease_group_scale\": \"5\", \"healthy_phenotype\": \"\", \"compare_title\": \"\"}, \"scrna_eset\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.1+galaxy0",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"kmer_distr\": \"bf6177af-7f5b-4005-9bec-fc7c89c3cb1c\", \"level\": \"S\", \"logfile_output\": false, \"out_report\": true, \"threshold\": \"10\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.8+galaxy0",
                         "type": "tool",
-                        "uuid": "d5ff6923-3386-4407-8c50-0ec641a7fe0e",
+                        "uuid": "53b9c80b-f5f4-4fee-9778-fb4fd6b76165",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "summaries",
-                                "uuid": "ff64eeaa-56f4-4ef0-b458-5cf7c402ff84"
+                                "label": "bracken_kraken_report",
+                                "output_name": "kraken_report",
+                                "uuid": "8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8"
                             },
                             {
-                                "label": null,
-                                "output_name": "out_pdf",
-                                "uuid": "30e55eec-e403-4b10-a62c-5a503be0fb9f"
+                                "label": "bracken_report_tsv",
+                                "output_name": "report",
+                                "uuid": "ae6c6464-f5f5-4e5b-b616-d38166fc0133"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0",
                         "errors": null,
-                        "id": 14,
+                        "id": 7,
                         "input_connections": {
-                            "bulk_eset": {
-                                "id": 9,
-                                "output_name": "out_rds"
-                            },
-                            "do|cluster_groups_0|marker_list": {
-                                "id": 6,
-                                "output_name": "output"
-                            },
-                            "do|cluster_groups_1|marker_list": {
-                                "id": 7,
+                            "input_file": {
+                                "id": 5,
                                 "output_name": "output"
-                            },
-                            "scrna_eset": {
-                                "id": 8,
-                                "output_name": "out_rds"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Recentrifuge",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool MuSiC",
-                                "name": "bulk_eset"
+                                "name": "html_report",
+                                "type": "html"
                             },
                             {
-                                "description": "runtime parameter for tool MuSiC",
-                                "name": "scrna_eset"
-                            }
-                        ],
-                        "label": "Music: Compute Dendrogram",
-                        "name": "MuSiC",
-                        "outputs": [
+                                "name": "logfile",
+                                "type": "txt"
+                            },
                             {
-                                "name": "out_pdf",
-                                "type": "pdf"
+                                "name": "data_tsv",
+                                "type": "tabular"
                             },
                             {
-                                "name": "out_tab",
+                                "name": "stat_tsv",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 898.7000122070312,
-                            "height": 337.20001220703125,
-                            "left": 1333,
-                            "right": 1533,
-                            "top": 561.5,
-                            "width": 200,
-                            "x": 1333,
-                            "y": 561.5
+                            "left": 1132.0995834632697,
+                            "top": 578.6187243531585
                         },
                         "post_job_actions": {
-                            "HideDatasetActionout_tab": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "out_tab"
+                            "RenameDatasetActiondata_tsv": {
+                                "action_arguments": {
+                                    "newname": "recentrifuge_data_tabular"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "data_tsv"
+                            },
+                            "RenameDatasetActionhtml_report": {
+                                "action_arguments": {
+                                    "newname": "recentrifuge_report_html"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "html_report"
+                            },
+                            "RenameDatasetActionlogfile": {
+                                "action_arguments": {
+                                    "newname": "recentrifuge_logfile"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "logfile"
+                            },
+                            "RenameDatasetActionstat_tsv": {
+                                "action_arguments": {
+                                    "newname": "recentrifuge_stats_tabular"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "stat_tsv"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "56371b5a2da9",
-                            "name": "music_deconvolution",
-                            "owner": "bgruening",
+                            "changeset_revision": "b5407cc2bf51",
+                            "name": "recentrifuge",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"bulk_eset\": {\"__class__\": \"RuntimeValue\"}, \"do\": {\"method\": \"dendrogram\", \"__current_case__\": 1, \"celltypes_label\": \"cellType\", \"clustertype_label\": \"clusterType\", \"samples_label\": \"sampleID\", \"celltypes\": \"\", \"cluster_groups\": [{\"__index__\": 0, \"cluster_id\": \"C1\", \"celltypes\": \"\", \"marker_name\": \"\", \"marker_list\": {\"__class__\": \"RuntimeValue\"}}, {\"__index__\": 1, \"cluster_id\": \"C2\", \"celltypes\": \"\", \"marker_name\": \"\", \"marker_list\": {\"__class__\": \"RuntimeValue\"}}]}, \"scrna_eset\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.1+galaxy0",
+                        "tool_state": "{\"advanced_option\": {\"controls\": \"0\", \"scoring\": null, \"minscore_value\": \"0\", \"mintaxa\": \"0\", \"exclude_taxa_name\": null, \"include_taxa_name\": null, \"avoidcross\": false}, \"database\": {\"database_name\": \"ncbi-2023-06-27\"}, \"file_type\": {\"filetype\": \"kraken\", \"__current_case__\": 3}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"more_advanced_option\": {\"ctrlminscore\": \"0\", \"ctrlmintaxa\": \"0\", \"summary\": \"ADD\", \"takeoutroot\": false, \"nokollapse\": false, \"strain\": true, \"sequential\": false}, \"output_option\": {\"extra\": \"TSV\", \"nohtml\": false, \"no_logfile\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.12.1+galaxy0",
                         "type": "tool",
-                        "uuid": "86a3a936-ef2a-4eee-80e9-63f247463719",
+                        "uuid": "4b3b34ad-2352-4e93-abbc-69da3ab9ee3a",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "MuSiC on input dataset(s): PDF Plots",
-                                "output_name": "out_pdf",
-                                "uuid": "df2e83a5-ac67-460f-8b0f-ac3f3b63280f"
+                                "label": "recentrifuge_report_html",
+                                "output_name": "html_report",
+                                "uuid": "bd947a1d-0443-465f-8658-5d76d9ce69f8"
+                            },
+                            {
+                                "label": "recentrifuge_data_tabular",
+                                "output_name": "data_tsv",
+                                "uuid": "c7457acb-41bc-4191-b3fb-6716e15fbe57"
+                            },
+                            {
+                                "label": "recentrifuge_stats_tabular",
+                                "output_name": "stat_tsv",
+                                "uuid": "b5694f2d-c8cd-4460-bfff-74fd0792ecb3"
+                            },
+                            {
+                                "label": "recentrifuge_logfile",
+                                "output_name": "logfile",
+                                "uuid": "94f6ff07-0e06-47ad-88f8-a058d0808537"
                             }
                         ]
                     }
                 ],
-                "parent_id": "single-cell/bulk-music",
-                "path": "topics/single-cell/tutorials/bulk-music/workflows/main_workflow.ga",
+                "parent_id": "sequence-analysis/quality-contamination-control",
+                "path": "topics/sequence-analysis/tutorials/quality-contamination-control/workflows/Quality_and_contamination_control_in_bacterial_isolate_using_Illumina_MiSeq_Data.ga",
                 "tags": [
-                    "transcriptomics",
-                    "single-cell"
+                    "sequence-analysis"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "MuSiC Workflow",
-                "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-bulk-music/versions/main-workflow",
-                "tutorial_id": "bulk-music",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music/workflows/main_workflow.html",
-                "version": 2,
-                "wfid": "single-cell-bulk-music",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "tests": true,
+                "title": "Quality and contamination control in bacterial isolate using Illumina MiSeq Data",
+                "topic_id": "sequence-analysis",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/sequence-analysis-quality-contamination-control/versions/quality-and-contamination-control-in-bacterial-isolate-using-illumina-miseq-data",
+                "tutorial_id": "quality-contamination-control",
+                "url": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-contamination-control/workflows/Quality_and_contamination_control_in_bacterial_isolate_using_Illumina_MiSeq_Data.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-contamination-control/workflows/Quality_and_contamination_control_in_bacterial_isolate_using_Illumina_MiSeq_Data.html",
+                "version": 1,
+                "wfid": "sequence-analysis-quality-contamination-control",
+                "wfname": "quality-and-contamination-control-in-bacterial-isolate-using-illumina-miseq-data",
+                "workflow": "Quality_and_contamination_control_in_bacterial_isolate_using_Illumina_MiSeq_Data.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3"
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.8+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0"
                 ],
-                "workflowhub_id": "1234"
+                "workflowhub_id": "1344"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/5719228"
+        "zenodo_link": "https://zenodo.org/record/10669812"
     },
     {
         "admin_install": {
@@ -214179,218 +218570,122 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "dropletutils",
-                    "owner": "iuc",
-                    "revisions": "a9caad671439",
-                    "tool_panel_section_label": "Single-cell",
+                    "name": "diamond",
+                    "owner": "bgruening",
+                    "revisions": "e8ac2b53f262",
+                    "tool_panel_section_label": "NCBI Blast",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "75c93c70d094",
-                    "tool_panel_section_label": "Quality Control",
+                    "name": "ncbi_blast_plus",
+                    "owner": "devteam",
+                    "revisions": "0e3cf9594bb7",
+                    "tool_panel_section_label": "NCBI Blast",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "rna_starsolo",
-                    "owner": "iuc",
-                    "revisions": "13022c3d3076",
-                    "tool_panel_section_label": "Mapping",
+                    "name": "ncbi_blast_plus",
+                    "owner": "devteam",
+                    "revisions": "0e3cf9594bb7",
+                    "tool_panel_section_label": "NCBI Blast",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: dropletutils\n  owner: iuc\n  revisions: a9caad671439\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 75c93c70d094\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rna_starsolo\n  owner: iuc\n  revisions: 13022c3d3076\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "elixir_node": "de",
-                "email": "mtekman89@gmail.com",
-                "former_affiliations": [
-                    "elixir-europe"
-                ],
-                "id": "mtekman",
-                "joined": "2018-11",
-                "name": "Mehmet Tekman",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "ch",
-                "email": "hrhotz@googlemail.com",
-                "fediverse": "https://genomic.social/@hrhotz",
-                "fediverse_flavor": "mastodon",
-                "id": "hrhotz",
-                "joined": "2017-09",
-                "linkedin": "hans-rudolf-hotz-542b31",
-                "location": {
-                    "country": "CH",
-                    "lat": 47.57,
-                    "lon": 7.6
-                },
-                "matrix": "hrhotz:matrix.org",
-                "name": "Hans-Rudolf Hotz",
-                "orcid": "0000-0002-2799-424X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hrhotz/",
-                "twitter": "hrhotz",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hrhotz.json"
-            },
-            {
-                "id": "blankenberg",
-                "joined": "2018-07",
-                "name": "Daniel Blankenberg",
-                "orcid": "0000-0002-6833-9049",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankenberg/",
-                "twitter": "dblankenberg",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankenberg.json"
-            },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: diamond\n  owner: bgruening\n  revisions: e8ac2b53f262\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: 0e3cf9594bb7\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ncbi_blast_plus\n  owner: devteam\n  revisions: 0e3cf9594bb7\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "deeptivarshney"
+            ],
+            "funding": [
+                "madland",
+                "nfdi4plants"
+            ]
+        },
+        "contributors": [
             {
                 "affiliations": [
+                    "uni-freiburg",
                     "elixir-europe"
                 ],
-                "bio": "Senior Lecturer at The Open University",
-                "elixir_node": "uk",
-                "email": "wendi.bacon@open.ac.uk",
-                "fediverse": "https://mstdn.science/@wendibacon1",
-                "fediverse_flavor": "mastodon",
-                "id": "nomadscientist",
-                "joined": "2020-03",
-                "matrix": "nomadscientist:matrix.org",
-                "name": "Wendi Bacon",
-                "orcid": "0000-0002-8170-8806",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
-                "twitter": "WendiBacon1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+                "id": "deeptivarshney",
+                "joined": "2022-12",
+                "name": "Deepti Varshney",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/deeptivarshney/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/deeptivarshney.json"
             },
             {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "pavanvidem",
-                "joined": "2017-09",
-                "name": "Pavankumar Videm",
-                "orcid": "0000-0002-5192-126X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
+                "avatar": "/training-material/shared/images/logo-madland.jpg",
+                "funder": true,
+                "github": false,
+                "id": "madland",
+                "joined": "2024-07",
+                "name": "MAdLand",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/madland/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/madland.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/logo-dataplant.svg",
+                "funder": true,
+                "id": "nfdi4plants",
+                "joined": "2024-07",
+                "name": "DataPLANT",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nfdi4plants/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/nfdi4plants.json"
             }
         ],
-        "dir": "topics/single-cell/tutorials/scrna-preprocessing-tenx",
+        "dir": "topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland",
         "edam_operation": [
-            "Sequencing quality control",
-            "Community profiling",
-            "Validation",
-            "Sequence alignment",
-            "Loading"
+            "Sequence alignment analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.cz",
             "UseGalaxy.eu",
+            "UseGalaxy.fr",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-scanpy-pbmc3k"
-                ],
-                "type": "internal"
-            }
-        ],
-        "gitter": "Galaxy-Training-Network/galaxy-single-cell",
         "hands_on": true,
-        "id": "single-cell/scrna-preprocessing-tenx",
+        "id": "sequence-analysis/ncbi-blast-against-the-madland",
         "inexact_supported_servers": [
-            "HyPhy HIV NGS Tools",
-            "UseGalaxy.fr",
+            "Galaxy@AuBi",
+            "GalaxyTrakr",
             "UseGalaxy.no"
         ],
         "js_requirements": {
-            "mathjax": 12940,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Barcode FASTQ Reads are used to parse cDNA sequencing Reads.",
-            "A raw matrix is too large to process alone, and need to be filtered into a high quality one for downstream analysis"
+            "Blast tool searches a database of sequences for similar sequences to a query sequence.",
+            "Diamond  quickly aligns large-scale data sets using a compressed version of the reference sequences called a \"database diamond\".",
+            "MAdLand is a database of fully sequenced plant and algal genomes, with an emphasis on non-seed plants and streptophyte algae that can be use for sequence similarity search."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-07-31",
         "objectives": [
-            "Demultiplex single-cell FASTQ data from 10X Genomics",
-            "Learn about transparent matrix formats",
-            "Understand the importance of high and low quality cells"
+            "Load FASTA sequence into Galaxy",
+            "Perform NCBI-Blast+ analysis against MAdLandDB"
         ],
-        "pageviews": 10662,
-        "priority": 1,
-        "pub_date": "2019-09-11",
+        "pageviews": 1414,
+        "pub_date": "2023-01-16",
         "questions": [
-            "What is 10X?",
-            "What is STARsolo and what is Cell Ranger?",
-            "What are BCL and MTX files?",
-            "What is an HDF5 file, and why is it important?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "pavanvidem"
-                ],
-                "date": "2023-05-19",
-                "galaxy_version": "23.01",
-                "length": "19M",
-                "speakers": [
-                    "pavanvidem"
-                ],
-                "youtube_id": "IIiOcgiXviE"
-            },
-            {
-                "captioners": [
-                    "khanteymoori"
-                ],
-                "date": "2021-03-18",
-                "galaxy_version": "21.01",
-                "length": "5M",
-                "speakers": [
-                    "nomadscientist"
-                ],
-                "youtube_id": "vNBNFkF0L4U"
-            }
-        ],
-        "redirect_from": [
-            "/topics/transcriptomics/tutorials/scrna-preprocessing-tenx/tutorial",
-            "/short/single-cell/scrna-preprocessing-tenx",
-            "/short/T00252"
-        ],
-        "requirements": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-preprocessing"
-                ],
-                "type": "internal"
-            }
+            "What is MAdLand DB?",
+            "How can we perform Blast analysis on Galaxy?"
         ],
-        "short_id": "T00252",
+        "short_id": "T00238",
         "short_tools": [
-            "rna_starsolo",
-            "dropletutils",
-            "multiqc"
+            "ncbi_blastp_wrapper",
+            "ncbi_blastx_wrapper",
+            "bg_diamond"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "firstsc",
         "supported_servers": {
             "exact": [
                 {
@@ -214403,6 +218698,11 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -214416,13 +218716,13 @@
             ],
             "inexact": [
                 {
-                    "name": "HyPhy HIV NGS Tools",
-                    "url": "https://galaxy.hyphy.org/",
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
                     "usegalaxy": false
                 },
                 {
@@ -214434,291 +218734,37 @@
         },
         "symlink": null,
         "tags": [
-            "10x"
+            "plants"
         ],
-        "time_estimation": "1h",
-        "title": "Pre-processing of 10X Single-Cell RNA Datasets",
+        "time_estimation": "15m",
+        "title": "NCBI BLAST+ against the MAdLand",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.10b+galaxy3"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.0.15+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/2.10.1+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/2.10.1+galaxy2"
         ],
-        "topic_name": "single-cell",
-        "topic_name_human": "Single Cell",
+        "topic_name": "sequence-analysis",
+        "topic_name_human": "Sequence analysis",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "scrna-preprocessing-tenx",
+        "tutorial_name": "ncbi-blast-against-the-madland",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/ncbi-blast-against-the-madland/tutorial.json"
         },
-        "version": 8,
+        "version": 9,
         "video": false,
-        "video_versions": 2,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 107,
-        "visitors": 8207,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-8170-8806",
-                        "name": "Wendi Bacon"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-5192-126X",
-                        "name": "Pavankumar Videm"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-4181-2676",
-                        "name": "Mehmet Tekman"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-2799-424X",
-                        "name": "Hans-Rudolf Hotz"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-6833-9049",
-                        "name": "Daniel Blankenberg"
-                    }
-                ],
-                "description": "",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHomo_sapiens.GRCh37.75.gtf\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nsubset_pbmc_1k_v3_S1_L001_R1_001.fastq.gz\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nsubset_pbmc_1k_v3_S1_L002_R1_001.fastq.gz\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nsubset_pbmc_1k_v3_S1_L002_R2_001.fastq.gz\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nsubset_pbmc_1k_v3_S1_L001_R2_001.fastq.gz\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\n3M-february-2018.txt.gz\"]\n  6[label=\"RNA STARSolo\"]\n  0 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  4 -> 6 [label=\"output\"]\n  5 -> 6 [label=\"output\"]\n  7[label=\"DropletUtils\"]\n  6 -> 7 [label=\"output_matrix\"]\n  6 -> 7 [label=\"output_barcodes\"]\n  6 -> 7 [label=\"output_genes\"]\n  8[label=\"DropletUtils\"]\n  6 -> 8 [label=\"output_matrix\"]\n  6 -> 8 [label=\"output_barcodes\"]\n  6 -> 8 [label=\"output_genes\"]\n  9[label=\"DropletUtils\"]\n  6 -> 9 [label=\"output_matrix\"]\n  6 -> 9 [label=\"output_barcodes\"]\n  6 -> 9 [label=\"output_genes\"]\n}",
-                "history": [
-                    {
-                        "hash": "a72ffa88609dce58d84066d5e173ab7f7dfaaa8a",
-                        "message": "add author ids",
-                        "num": 3,
-                        "short_hash": "a72ffa886",
-                        "unix": "1684436873"
-                    },
-                    {
-                        "hash": "3dead543d9798a6456c609bf50844dff6a42ea60",
-                        "message": "Update workflow authors",
-                        "num": 2,
-                        "short_hash": "3dead543d",
-                        "unix": "1684436577"
-                    },
-                    {
-                        "hash": "5d8104ecc67f388338f9bb292c56453b8556542d",
-                        "message": "Update 10x scRNA preprocessing tutorial",
-                        "num": 1,
-                        "short_hash": "5d8104ecc",
-                        "unix": "1684419217"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Homo_sapiens.GRCh37.75.gtf"
-                            }
-                        ],
-                        "label": "Homo_sapiens.GRCh37.75.gtf",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 0
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "8b20f887-9a5a-4a62-9ec5-20ae950c4af3",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "subset_pbmc_1k_v3_S1_L001_R1_001.fastq.gz"
-                            }
-                        ],
-                        "label": "subset_pbmc_1k_v3_S1_L001_R1_001.fastq.gz",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 123
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "e6ecb480-0530-406f-b10d-542769def2ee",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "subset_pbmc_1k_v3_S1_L002_R1_001.fastq.gz"
-                            }
-                        ],
-                        "label": "subset_pbmc_1k_v3_S1_L002_R1_001.fastq.gz",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 266
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "c45a8335-5384-4904-9735-0711a9928c6f",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "subset_pbmc_1k_v3_S1_L002_R2_001.fastq.gz"
-                            }
-                        ],
-                        "label": "subset_pbmc_1k_v3_S1_L002_R2_001.fastq.gz",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 409
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "727d1244-f775-4709-bbea-eecaca8588f3",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "subset_pbmc_1k_v3_S1_L001_R2_001.fastq.gz"
-                            }
-                        ],
-                        "label": "subset_pbmc_1k_v3_S1_L001_R2_001.fastq.gz",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 552
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "183c20fc-aa5a-43bf-a3f2-e496bbe30f43",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "3M-february-2018.txt.gz"
-                            }
-                        ],
-                        "label": "3M-february-2018.txt.gz",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 695
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "9be1bade-3ff5-4d99-9ffb-cc909273464c",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nHomo_sapiens.GRCh37.75.gtf\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nsubset_pbmc_1k_v3_S1_L001_R1_001.fastq.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nsubset_pbmc_1k_v3_S1_L002_R1_001.fastq.gz\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nsubset_pbmc_1k_v3_S1_L002_R2_001.fastq.gz\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nsubset_pbmc_1k_v3_S1_L001_R2_001.fastq.gz\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\n3M-february-2018.txt.gz\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"RNA STARSolo\"];\n  0 -->|output| 6;\n  1 -->|output| 6;\n  2 -->|output| 6;\n  3 -->|output| 6;\n  4 -->|output| 6;\n  5 -->|output| 6;\n  7[\"DropletUtils\"];\n  6 -->|output_matrix| 7;\n  6 -->|output_barcodes| 7;\n  6 -->|output_genes| 7;\n  8[\"DropletUtils\"];\n  6 -->|output_matrix| 8;\n  6 -->|output_barcodes| 8;\n  6 -->|output_genes| 8;\n  9[\"DropletUtils\"];\n  6 -->|output_matrix| 9;\n  6 -->|output_barcodes| 9;\n  6 -->|output_genes| 9;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Preprocessing of 10X scRNA-seq data",
-                "outputs": [],
-                "parent_id": "single-cell/scrna-preprocessing-tenx",
-                "path": "topics/single-cell/tutorials/scrna-preprocessing-tenx/workflows/scRNA-seq-Preprocessing-TenX.ga",
-                "tags": [
-                    "single-cell",
-                    "transcriptomics"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "Preprocessing of 10X scRNA-seq data",
-                "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-preprocessing-tenx/versions/scrna-seq-preprocessing-tenx",
-                "tutorial_id": "scrna-preprocessing-tenx",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-preprocessing-tenx/workflows/scRNA-seq-Preprocessing-TenX.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-preprocessing-tenx/workflows/scRNA-seq-Preprocessing-TenX.html",
-                "version": 1,
-                "wfid": "single-cell-scrna-preprocessing-tenx",
-                "wfname": "scrna-seq-preprocessing-tenx",
-                "workflow": "scRNA-seq-Preprocessing-TenX.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.10b+galaxy3"
-                ],
-                "workflowhub_id": "1220"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/3457880"
+        "visit_duration": 158,
+        "visitors": 1103,
+        "zenodo_link": "https://zenodo.org/records/7524427"
     },
     {
         "admin_install": {
@@ -214726,13 +218772,6 @@
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
             "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
                 {
                     "name": "bwa",
                     "owner": "devteam",
@@ -214748,131 +218787,173 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "anndata_inspect",
-                    "owner": "iuc",
-                    "revisions": "ee98d611afc6",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bedtools",
-                    "owner": "iuc",
-                    "revisions": "a1a923cd89e8",
-                    "tool_panel_section_label": "BED",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "episcanpy_build_matrix",
-                    "owner": "iuc",
-                    "revisions": "31a21ba2c5ea",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "episcanpy_preprocess",
-                    "owner": "iuc",
-                    "revisions": "29f5f25b9935",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "macs2",
-                    "owner": "iuc",
-                    "revisions": "424aefbd7777",
-                    "tool_panel_section_label": "Peak Calling",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "macs2",
-                    "owner": "iuc",
-                    "revisions": "640d3af5d833",
-                    "tool_panel_section_label": "Peak Calling",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_plot",
-                    "owner": "iuc",
-                    "revisions": "6adf98e782f3",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_plot",
-                    "owner": "iuc",
-                    "revisions": "aa0c474463c2",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "sinto_barcode",
-                    "owner": "iuc",
-                    "revisions": "d1b34ac42b8f",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "sinto_fragments",
+                    "name": "jbrowse",
                     "owner": "iuc",
-                    "revisions": "29e6bfb2cf49",
-                    "tool_panel_section_label": "Single-cell",
+                    "revisions": "17359b808b01",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_inspect\n  owner: iuc\n  revisions: ee98d611afc6\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: a1a923cd89e8\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: episcanpy_build_matrix\n  owner: iuc\n  revisions: 31a21ba2c5ea\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: episcanpy_preprocess\n  owner: iuc\n  revisions: 29f5f25b9935\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: macs2\n  owner: iuc\n  revisions: 424aefbd7777\n  tool_panel_section_label: Peak Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: macs2\n  owner: iuc\n  revisions: 640d3af5d833\n  tool_panel_section_label: Peak Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot\n  owner: iuc\n  revisions: 6adf98e782f3\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot\n  owner: iuc\n  revisions: aa0c474463c2\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sinto_barcode\n  owner: iuc\n  revisions: d1b34ac42b8f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sinto_fragments\n  owner: iuc\n  revisions: 29e6bfb2cf49\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: 17359b808b01\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "nakucher",
+                "avahoffman",
+                "robertmeller"
+            ],
+            "editing": [
+                "katherinecox",
+                "cutsort",
+                "nakucher"
+            ],
+            "funding": [
+                "nhgri-gdscn",
+                "nhgri-anvil"
+            ],
+            "infrastructure": [
+                "cansavvy",
+                "avahoffman",
+                "katherinecox",
+                "ehumph",
+                "cutsort"
+            ]
+        },
         "contributors": [
             {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "pavanvidem",
-                "joined": "2017-09",
-                "name": "Pavankumar Videm",
-                "orcid": "0000-0002-5192-126X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
+                "email": "nkucher3@jhu.edu",
+                "id": "nakucher",
+                "joined": "2023-06",
+                "name": "Natalie Kucher",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nakucher/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nakucher.json"
+            },
+            {
+                "id": "avahoffman",
+                "joined": "2023-06",
+                "name": "Ava Hoffman",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avahoffman/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/avahoffman.json"
+            },
+            {
+                "id": "robertmeller",
+                "joined": "2023-06",
+                "name": "Robert Meller",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/robertmeller/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/robertmeller.json"
+            },
+            {
+                "id": "katherinecox",
+                "joined": "2023-06",
+                "name": "Katherine Cox",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/katherinecox/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/katherinecox.json"
+            },
+            {
+                "id": "cutsort",
+                "joined": "2023-06",
+                "name": "Frederick Tan",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cutsort/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/cutsort.json"
+            },
+            {
+                "email": "nkucher3@jhu.edu",
+                "id": "nakucher",
+                "joined": "2023-06",
+                "name": "Natalie Kucher",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nakucher/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nakucher.json"
+            },
+            {
+                "id": "cansavvy",
+                "joined": "2023-06",
+                "name": "Candace Savonen",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cansavvy/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/cansavvy.json"
+            },
+            {
+                "id": "avahoffman",
+                "joined": "2023-06",
+                "name": "Ava Hoffman",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avahoffman/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/avahoffman.json"
+            },
+            {
+                "id": "katherinecox",
+                "joined": "2023-06",
+                "name": "Katherine Cox",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/katherinecox/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/katherinecox.json"
+            },
+            {
+                "id": "ehumph",
+                "joined": "2023-06",
+                "name": "Elizabeth Humphries",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ehumph/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/ehumph.json"
+            },
+            {
+                "id": "cutsort",
+                "joined": "2023-06",
+                "name": "Frederick Tan",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cutsort/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/cutsort.json"
+            },
+            {
+                "avatar": "https://www.ashg.org/wp-content/uploads/2021/07/nhgri-logo-800x167-1.png",
+                "funder": true,
+                "funding_id": "75N92022P00232",
+                "github": false,
+                "id": "nhgri-gdscn",
+                "joined": "2023-06",
+                "name": "National Human Genome Research Institute Genomic Data Science Community Network",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nhgri-gdscn/",
+                "short_name": "NHGRI GDS Community Network",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/nhgri-gdscn.json"
+            },
+            {
+                "avatar": "https://www.ashg.org/wp-content/uploads/2021/07/nhgri-logo-800x167-1.png",
+                "funder": true,
+                "funding_id": "U24HG010263",
+                "github": false,
+                "id": "nhgri-anvil",
+                "joined": "2023-06",
+                "name": "National Human Genome Research Institute Genomic Data Science Analysis, Visualization, and Informatics Lab-Space",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nhgri-anvil/",
+                "short_name": "NHGRI ANVIL",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/nhgri-anvil.json"
             }
         ],
-        "dir": "topics/single-cell/tutorials/scatac-preprocessing-tenx",
+        "dir": "topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil",
         "edam_operation": [
-            "Sequencing quality control",
-            "Imputation",
-            "Peak calling",
-            "Enrichment analysis",
+            "Generation",
+            "Statistical calculation",
             "Sequence alignment",
-            "Mapping",
-            "Sequence composition calculation",
             "Read mapping",
-            "Genome indexing",
-            "Gene regulatory network analysis",
-            "Generation",
-            "Differential gene expression analysis",
-            "Statistical calculation"
+            "Sequencing quality control",
+            "Sequence composition calculation",
+            "Genome visualisation",
+            "Genome indexing"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-scanpy-pbmc3k",
-                    "scatac-standard-processing-snapatac2"
-                ],
-                "type": "internal"
-            }
-        ],
-        "gitter": "Galaxy-Training-Network/galaxy-single-cell",
         "hands_on": true,
-        "id": "single-cell/scatac-preprocessing-tenx",
+        "id": "sequence-analysis/sars-with-galaxy-on-anvil",
         "inexact_supported_servers": [
+            "Galaxy@AuBi",
+            "Galaxy@Pasteur",
+            "GalaxyTrakr",
+            "MISSISSIPPI",
+            "UseGalaxy.be",
             "UseGalaxy.cz"
         ],
         "js_requirements": {
@@ -214880,56 +218961,33 @@
             "mermaid": false
         },
         "key_points": [
-            "Bulk ATAC-seq like mapping and peak calling",
-            "Creating a scATAC-seq count matrix requires positions of open chromatin regions"
+            "Use Galaxy on the AnVIL cloud computing resource to check data, perform an alignment, and visualize the results."
         ],
         "layout": "tutorial_hands_on",
+        "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-11",
+        "mod_date": "2024-02-29",
         "objectives": [
-            "Demultiplex single-cell FASTQ data from 10X Genomics",
-            "Learn about transparent matrix formats",
-            "Create a high-quality count matrix starting from scATAC-seq FASTQ files"
+            "Gather and evaluate experimental evidence, including qualitative and quantitative data",
+            "Generate and interpret graphs displaying experimental results",
+            "Critique large data sets and use bioinformatics to assess genetics data",
+            "Tap into the interdisciplinary nature of science"
         ],
-        "pageviews": 4163,
-        "priority": 1,
-        "pub_date": "2023-04-24",
+        "pageviews": 956,
+        "pub_date": "2023-07-10",
         "questions": [
-            "What is 10X?",
-            "What are single-cell ATAC fragments and MTX files?",
-            "What is an Anndata file, and why is it important?"
-        ],
-        "redirect_from": [
-            "/topics/transcriptomics/tutorials/satac-preprocessing-tenx/tutorial",
-            "/short/single-cell/scatac-preprocessing-tenx",
-            "/short/T00335"
-        ],
-        "requirements": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-preprocessing-tenx"
-                ],
-                "type": "internal"
-            }
+            "How do I check my data quality?",
+            "How do I put together my dataset of fragmented sequences into a full sequence?",
+            "How do I visually explore the variants in my SARS-CoV-2 sample?"
         ],
-        "short_id": "T00335",
+        "short_id": "T00356",
         "short_tools": [
-            "episcanpy_preprocess",
-            "anndata_inspect",
-            "sinto_fragments",
-            "scanpy_plot",
-            "bedtools_sortbed",
-            "sinto_barcode",
+            "bwa_mem",
             "fastqc",
-            "macs2_callpeak",
-            "episcanpy_build_matrix",
-            "tp_sorted_uniq",
-            "bwa_mem"
+            "jbrowse"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "scmultiomics",
         "supported_servers": {
             "exact": [
                 {
@@ -214937,292 +218995,95 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "10x",
-            "epigenetics"
-        ],
-        "time_estimation": "1h",
-        "title": "Pre-processing of 10X Single-Cell ATAC-seq Datasets",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/episcanpy_build_matrix/episcanpy_build_matrix/0.3.2+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/episcanpy_preprocess/episcanpy_preprocess/0.3.2+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6",
-            "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/sinto_barcode/sinto_barcode/0.9.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/sinto_fragments/sinto_fragments/0.9.0+galaxy1"
-        ],
-        "topic_name": "single-cell",
-        "topic_name_human": "Single Cell",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "scatac-preprocessing-tenx",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.json"
-        },
-        "version": 8,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 67,
-        "visitors": 3511,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-5192-126X",
-                        "name": "Pavankumar Videm"
-                    }
-                ],
-                "description": "",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nscATAC-seq Anndata\"]\n  1[label=\"scATAC-seq Preprocessing\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"scATAC-seq Preprocessing\"]\n  1 -> 2 [label=\"anndata_out\"]\n  3[label=\"scATAC-seq Preprocessing\"]\n  2 -> 3 [label=\"anndata_out\"]\n  4[label=\"Plot\"]\n  3 -> 4 [label=\"anndata_out\"]\n  5[label=\"scATAC-seq Preprocessing\"]\n  3 -> 5 [label=\"anndata_out\"]\n  6[label=\"scATAC-seq Preprocessing\"]\n  3 -> 6 [label=\"anndata_out\"]\n  7[label=\"scATAC-seq Preprocessing\"]\n  3 -> 7 [label=\"anndata_out\"]\n  8[label=\"scATAC-seq Preprocessing\"]\n  3 -> 8 [label=\"anndata_out\"]\n  9[label=\"scATAC-seq Preprocessing\"]\n  8 -> 9 [label=\"anndata_out\"]\n  10[label=\"scATAC-seq Preprocessing\"]\n  9 -> 10 [label=\"anndata_out\"]\n  11[label=\"scATAC-seq Preprocessing\"]\n  10 -> 11 [label=\"anndata_out\"]\n  12[label=\"Plot\"]\n  11 -> 12 [label=\"anndata_out\"]\n}",
-                "history": [
-                    {
-                        "hash": "094d1948af4063fe1165b564f128a8a3a447b037",
-                        "message": "Add workflow tests",
-                        "num": 1,
-                        "short_hash": "094d1948a",
-                        "unix": "1682339007"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "scATAC-seq Anndata"
-                            }
-                        ],
-                        "label": "scATAC-seq Anndata",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 522
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "2e2b15be-c7c1-4ebb-bb2c-5b269c563ae4",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nscATAC-seq Anndata\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"scATAC-seq Preprocessing\"];\n  0 -->|output| 1;\n  2[\"scATAC-seq Preprocessing\"];\n  1 -->|anndata_out| 2;\n  3[\"scATAC-seq Preprocessing\"];\n  2 -->|anndata_out| 3;\n  4[\"Plot\"];\n  3 -->|anndata_out| 4;\n  5[\"scATAC-seq Preprocessing\"];\n  3 -->|anndata_out| 5;\n  6[\"scATAC-seq Preprocessing\"];\n  3 -->|anndata_out| 6;\n  7[\"scATAC-seq Preprocessing\"];\n  3 -->|anndata_out| 7;\n  8[\"scATAC-seq Preprocessing\"];\n  3 -->|anndata_out| 8;\n  9[\"scATAC-seq Preprocessing\"];\n  8 -->|anndata_out| 9;\n  10[\"scATAC-seq Preprocessing\"];\n  9 -->|anndata_out| 10;\n  11[\"scATAC-seq Preprocessing\"];\n  10 -->|anndata_out| 11;\n  12[\"Plot\"];\n  11 -->|anndata_out| 12;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "scATAC-seq Count Matrix Filtering",
-                "outputs": [],
-                "parent_id": "single-cell/scatac-preprocessing-tenx",
-                "path": "topics/single-cell/tutorials/scatac-preprocessing-tenx/workflows/scATAC-seq-Count-Matrix-Filtering.ga",
-                "tags": [],
-                "test_results": null,
-                "tests": true,
-                "title": "scATAC-seq Count Matrix Filtering",
-                "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scatac-preprocessing-tenx/versions/scatac-seq-count-matrix-filtering",
-                "tutorial_id": "scatac-preprocessing-tenx",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-preprocessing-tenx/workflows/scATAC-seq-Count-Matrix-Filtering.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-preprocessing-tenx/workflows/scATAC-seq-Count-Matrix-Filtering.html",
-                "version": 1,
-                "wfid": "single-cell-scatac-preprocessing-tenx",
-                "wfname": "scatac-seq-count-matrix-filtering",
-                "workflow": "scATAC-seq-Count-Matrix-Filtering.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/episcanpy_preprocess/episcanpy_preprocess/0.3.2+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1"
-                ],
-                "workflowhub_id": "1275"
-            },
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-5192-126X",
-                        "name": "Pavankumar Videm"
-                    }
-                ],
-                "description": "",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nForward reads FASTQ R1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBarcodes FASTQ R2\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReverse reads FASTQ R3\"]\n  3[label=\"Sinto barcode\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"FastQC\"]\n  3 -> 4 [label=\"read1_out\"]\n  5[label=\"FastQC\"]\n  3 -> 5 [label=\"read2_out\"]\n  6[label=\"Map with BWA-MEM\"]\n  3 -> 6 [label=\"read1_out\"]\n  3 -> 6 [label=\"read2_out\"]\n  7[label=\"Sinto fragments\"]\n  6 -> 7 [label=\"bam_output\"]\n  8[label=\"bedtools SortBED\"]\n  7 -> 8 [label=\"fragments\"]\n  9[label=\"MACS2 callpeak\"]\n  8 -> 9 [label=\"output\"]\n  10[label=\"Unique\"]\n  9 -> 10 [label=\"output_narrowpeaks\"]\n  11[label=\"Build count matrix\"]\n  8 -> 11 [label=\"output\"]\n  10 -> 11 [label=\"outfile\"]\n  12[label=\"Inspect AnnData\"]\n  11 -> 12 [label=\"anndata_out\"]\n  13[label=\"Inspect AnnData\"]\n  11 -> 13 [label=\"anndata_out\"]\n  14[label=\"Inspect AnnData\"]\n  11 -> 14 [label=\"anndata_out\"]\n  15[label=\"Inspect AnnData\"]\n  11 -> 15 [label=\"anndata_out\"]\n}",
-                "history": [
-                    {
-                        "hash": "094d1948af4063fe1165b564f128a8a3a447b037",
-                        "message": "Add workflow tests",
-                        "num": 1,
-                        "short_hash": "094d1948a",
-                        "unix": "1682339007"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Forward reads FASTQ (R1)"
-                            }
-                        ],
-                        "label": "Forward reads FASTQ (R1)",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 0
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ec67a5c0-4854-4344-af16-7772c1c0742b",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Barcodes FASTQ (R2)"
-                            }
-                        ],
-                        "label": "Barcodes FASTQ (R2)",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 120
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "50c6de05-b355-4733-bc1d-96dc1ca058e1",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Reverse reads FASTQ (R3)"
-                            }
-                        ],
-                        "label": "Reverse reads FASTQ (R3)",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 240
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "8a73ff78-6e0a-41ab-9ac3-523cbd486021",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nForward reads FASTQ R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nBarcodes FASTQ R2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nReverse reads FASTQ R3\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Sinto barcode\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  2 -->|output| 3;\n  4[\"FastQC\"];\n  3 -->|read1_out| 4;\n  5[\"FastQC\"];\n  3 -->|read2_out| 5;\n  6[\"Map with BWA-MEM\"];\n  3 -->|read1_out| 6;\n  3 -->|read2_out| 6;\n  7[\"Sinto fragments\"];\n  6 -->|bam_output| 7;\n  8[\"bedtools SortBED\"];\n  7 -->|fragments| 8;\n  9[\"MACS2 callpeak\"];\n  8 -->|output| 9;\n  10[\"Unique\"];\n  9 -->|output_narrowpeaks| 10;\n  11[\"Build count matrix\"];\n  8 -->|output| 11;\n  10 -->|outfile| 11;\n  12[\"Inspect AnnData\"];\n  11 -->|anndata_out| 12;\n  13[\"Inspect AnnData\"];\n  11 -->|anndata_out| 13;\n  14[\"Inspect AnnData\"];\n  11 -->|anndata_out| 14;\n  15[\"Inspect AnnData\"];\n  11 -->|anndata_out| 15;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "scATAC-seq FASTQ to Count Matrix",
-                "outputs": [],
-                "parent_id": "single-cell/scatac-preprocessing-tenx",
-                "path": "topics/single-cell/tutorials/scatac-preprocessing-tenx/workflows/scATAC-seq-FASTQ-to-Count-Matrix.ga",
-                "tags": [],
-                "test_results": null,
-                "tests": true,
-                "title": "scATAC-seq FASTQ to Count Matrix",
-                "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scatac-preprocessing-tenx/versions/scatac-seq-fastq-to-count-matrix",
-                "tutorial_id": "scatac-preprocessing-tenx",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-preprocessing-tenx/workflows/scATAC-seq-FASTQ-to-Count-Matrix.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-preprocessing-tenx/workflows/scATAC-seq-FASTQ-to-Count-Matrix.html",
-                "version": 1,
-                "wfid": "single-cell-scatac-preprocessing-tenx",
-                "wfname": "scatac-seq-fastq-to-count-matrix",
-                "workflow": "scATAC-seq-FASTQ-to-Count-Matrix.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/episcanpy_build_matrix/episcanpy_build_matrix/0.3.2+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/sinto_barcode/sinto_barcode/0.9.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/sinto_fragments/sinto_fragments/0.9.0+galaxy1"
-                ],
-                "workflowhub_id": "1208"
-            }
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "covid19",
+            "gmod",
+            "jbrowse1"
         ],
-        "zenodo_link": "https://zenodo.org/record/7855968"
+        "time_estimation": "1H",
+        "title": "SARS-CoV-2 Viral Sample Alignment and Variant Visualization",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0"
+        ],
+        "topic_name": "sequence-analysis",
+        "topic_name_human": "Sequence analysis",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "sars-with-galaxy-on-anvil",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/sars-with-galaxy-on-anvil/tutorial.json"
+        },
+        "version": 2,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 271,
+        "visitors": 739,
+        "zenodo_link": "https://doi.org/10.5281/zenodo.8115178"
     },
     {
         "admin_install": {
@@ -215231,143 +219092,124 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "scater_create_qcmetric_ready_sce",
-                    "owner": "iuc",
-                    "revisions": "fd808de478b1",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scater_filter",
-                    "owner": "iuc",
-                    "revisions": "b7ea9f09c02f",
-                    "tool_panel_section_label": "Single-cell",
+                    "name": "split_file_on_column",
+                    "owner": "bgruening",
+                    "revisions": "37a53100b67e",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scater_plot_dist_scatter",
+                    "name": "goenrichment",
                     "owner": "iuc",
-                    "revisions": "2e41b35b5bdd",
-                    "tool_panel_section_label": "Single-cell",
+                    "revisions": "2c7c9646ccf0",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scater_plot_pca",
+                    "name": "gprofiler_gost",
                     "owner": "iuc",
-                    "revisions": "46fc6751d746",
-                    "tool_panel_section_label": "Single-cell",
+                    "revisions": "bf39cdd007f5",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: scater_create_qcmetric_ready_sce\n  owner: iuc\n  revisions: fd808de478b1\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scater_filter\n  owner: iuc\n  revisions: b7ea9f09c02f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scater_plot_dist_scatter\n  owner: iuc\n  revisions: 2e41b35b5bdd\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scater_plot_pca\n  owner: iuc\n  revisions: 46fc6751d746\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-scater-qc/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: split_file_on_column\n  owner: bgruening\n  revisions: 37a53100b67e\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: goenrichment\n  owner: iuc\n  revisions: 2c7c9646ccf0\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gprofiler_gost\n  owner: iuc\n  revisions: bf39cdd007f5\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/GO-enrichment/tutorial.json",
         "contributors": [
-            {
-                "id": "ethering",
-                "joined": "2019-10",
-                "name": "Graham Etherington",
-                "orcid": "0000-0002-5003-1425",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ethering/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/ethering.json"
-            },
             {
                 "affiliations": [
-                    "earlham",
                     "elixir-europe"
                 ],
+                "bio": "Senior Lecturer at The Open University",
                 "elixir_node": "uk",
-                "fediverse": "https://mstdn.science/@nsoranzo",
+                "email": "wendi.bacon@open.ac.uk",
+                "fediverse": "https://mstdn.science/@wendibacon1",
                 "fediverse_flavor": "mastodon",
-                "id": "nsoranzo",
-                "joined": "2017-09",
-                "linkedin": "nicola-soranzo-7884125",
-                "matrix": "nsoranzo:matrix.org",
-                "name": "Nicola Soranzo",
-                "orcid": "0000-0003-3627-5340",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
-                "twitter": "NicolaSoranzo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
+                "id": "nomadscientist",
+                "joined": "2020-03",
+                "matrix": "nomadscientist:matrix.org",
+                "name": "Wendi Bacon",
+                "orcid": "0000-0002-8170-8806",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
+                "twitter": "WendiBacon1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+            },
+            {
+                "email": "mennayoussef@live.com",
+                "id": "MennaGamal",
+                "joined": "2024-09",
+                "name": "Menna Gamal",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/MennaGamal/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/MennaGamal.json"
             }
         ],
-        "dir": "topics/single-cell/tutorials/scrna-scater-qc",
+        "dir": "topics/single-cell/tutorials/GO-enrichment",
         "edam_operation": [
-            "Sequencing quality control",
-            "Sequence visualisation",
-            "Read pre-processing"
+            "Gene-set enrichment analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.cz",
             "UseGalaxy.eu",
             "UseGalaxy.no",
-            "UseGalaxy.org.au"
+            "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-raceid"
-                ],
-                "type": "internal"
-            }
-        ],
-        "gitter": "Galaxy-Training-Network/galaxy-single-cell",
         "hands_on": true,
-        "id": "single-cell/scrna-scater-qc",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz"
-        ],
+        "id": "single-cell/GO-enrichment",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Single-cell RNA-seq data is often noisy",
-            "scater can be used to apply the visualise-filter-visualise paradigm of quality control"
+            "GO enrichment helps make sense of your data and understand what makes each cell cluster/condition unique.",
+            "GO enrichment analysis is used to discover new insights about how cells work, which can lead to better understanding of biological processes and diseases."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-09-27",
         "objectives": [
-            "Examine scRNA-seq data for low-quality cells",
-            "Visualise data with various types of plots",
-            "Filtering low-quality cells with the appropriate approach"
+            "Understand the Role of GO Enrichment in Single-Cell Analysis.",
+            "Use marker genes from different cell clusters or conditions for GO enrichment analysis.",
+            "Compare enrichment across experimental conditions (e.g., wild type vs. knockout) to uncover functional changes associated with genetic or environmental perturbations.",
+            "Link GO enrichment results with previously annotated cell clusters, providing a clearer picture of the functional roles of different cell populations."
         ],
-        "pageviews": 609,
-        "priority": 1,
-        "pub_date": "2019-10-23",
+        "pageviews": 70216,
+        "pub_date": "2024-09-17",
         "questions": [
-            "How to ensure the quality of single-cell RNA-seq data?",
-            "What are the confounding factors that may affect the interpretation of downstream analyses?"
-        ],
-        "redirect_from": [
-            "/topics/transcriptomics/tutorials/scrna-scater-qc/tutorial",
-            "/short/single-cell/scrna-scater-qc",
-            "/short/T00255"
+            "What is Gene Ontology (GO) enrichment analysis, and why should I perform it on my marker genes?",
+            "How can I use GO enrichment analysis to better understand the biological functions of the genes in my clusters?",
+            "Can GO enrichment analysis help me confirm that my clusters represent distinct cell types or states?",
+            "How can I visualize my GO enrichment results to make them easier to understand and interpret?"
         ],
         "requirements": [
             {
                 "topic_name": "single-cell",
                 "tutorials": [
-                    "scrna-plates-batches-barcodes"
+                    "scrna-case_basic-pipeline"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00255",
+        "short_id": "T00456",
         "short_tools": [
-            "scater_plot_dist_scatter",
-            "scater_filter",
-            "scater_plot_pca",
-            "scater_create_qcmetric_ready_sce"
+            "gprofiler_gost",
+            "Cut1",
+            "tp_split_on_column",
+            "goenrichment"
         ],
-        "slides": false,
+        "slides": true,
         "slides_recordings": false,
-        "subtopic": "tricks",
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
@@ -215379,28 +219221,25 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 }
             ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                }
-            ]
+            "inexact": []
         },
         "symlink": null,
-        "tags": null,
-        "time_estimation": "1H",
-        "title": "Single-cell quality control with scater",
+        "tags": [
+            "single cell",
+            "GO enrichment"
+        ],
+        "time_estimation": "3H",
+        "title": "GO Enrichment Analysis on Single-Cell RNA-Seq Data",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.12.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.12.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.12.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.12.2"
+            "Cut1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/goenrichment/goenrichment/2.0.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/gprofiler_gost/gprofiler_gost/0.1.7+galaxy11"
         ],
         "topic_name": "single-cell",
         "topic_name_human": "Single Cell",
@@ -215410,37 +219249,73 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "scrna-scater-qc",
+        "tutorial_name": "GO-enrichment",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-scater-qc/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/GO-enrichment/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-scater-qc/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-scater-qc/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/GO-enrichment/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/GO-enrichment/tutorial.json"
         },
-        "version": 4,
+        "version": 2,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 45,
-        "visitors": 536,
+        "visit_duration": 339,
+        "visitors": 28604,
         "workflows": [
             {
-                "creators": [],
-                "description": "Single-cell quality control with scater",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0009-0009-7422-4764",
+                        "name": "Menna Gamal"
+                    }
+                ],
+                "description": "",
                 "features": {
                     "comments": false,
                     "parameters": false,
-                    "report": null,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                    },
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nannotation.txt\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncounts.txt\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmt_controls.txt\"]\n  3[label=\"Scater: Calculate QC metrics\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Scater: plot library QC\"]\n  3 -> 4 [label=\"output_loom\"]\n  5[label=\"Scater: filter SCE\"]\n  3 -> 5 [label=\"output_loom\"]\n  6[label=\"Scater: plot library QC\"]\n  5 -> 6 [label=\"output_loom\"]\n  7[label=\"Scater: PCA plot\"]\n  5 -> 7 [label=\"output_loom\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMarker Genes\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGO\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAnnotation\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBackground\"]\n  4[label=\"Split file\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Cut\"]\n  4 -> 5 [label=\"split_output\"]\n  6[label=\"GOEnrichment\"]\n  2 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  5 -> 6 [label=\"out_file1\"]\n  7[label=\"gProfiler GOSt\"]\n  5 -> 7 [label=\"out_file1\"]\n}",
                 "history": [
                     {
-                        "hash": "327fd2b842f45de3dc2a30067714352675ad69ae",
-                        "message": "Making a single cell topics",
+                        "hash": "2d8afbe273867d79cd8d5c0a841f13e1711dd27c",
+                        "message": "Update main_workflow.ga",
+                        "num": 5,
+                        "short_hash": "2d8afbe27",
+                        "unix": "1726234110"
+                    },
+                    {
+                        "hash": "8b5a810af6e7811032b0818567a8f0c9514798e9",
+                        "message": "Update main_workflow.ga",
+                        "num": 4,
+                        "short_hash": "8b5a810af",
+                        "unix": "1726225705"
+                    },
+                    {
+                        "hash": "627cef42b3f74c9b0d0e93383abe57d25542157d",
+                        "message": "Update main_workflow.ga",
+                        "num": 3,
+                        "short_hash": "627cef42b",
+                        "unix": "1726221346"
+                    },
+                    {
+                        "hash": "53a1b9f1b468ced73497862338e4ff9ce44a4987",
+                        "message": "Update main_workflow.ga",
+                        "num": 2,
+                        "short_hash": "53a1b9f1b",
+                        "unix": "1726220765"
+                    },
+                    {
+                        "hash": "0093a305ae2f9f147f5aa042596085f1822dc55d",
+                        "message": "adding files",
                         "num": 1,
-                        "short_hash": "327fd2b84",
-                        "unix": "1668273265"
+                        "short_hash": "0093a305a",
+                        "unix": "1724923969"
                     }
                 ],
                 "inputs": [
@@ -215453,21 +219328,22 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "annotation.txt"
+                                "name": "Marker Genes"
                             }
                         ],
-                        "label": "annotation.txt",
+                        "label": "Marker Genes",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 200
+                            "left": 0,
+                            "top": 0
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"annotation.txt\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "3575b170-465d-4e4a-bae1-ff4c1efa142a",
+                        "uuid": "6dfe267d-399f-425d-ab90-e12fde8ca444",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
@@ -215479,21 +219355,22 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "counts.txt"
+                                "name": "GO"
                             }
                         ],
-                        "label": "counts.txt",
+                        "label": "GO",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 320
+                            "left": 575.6925283858866,
+                            "top": 132.70019640716558
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"counts.txt\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "03bc455e-52cc-4a2e-9a00-049f0fab721f",
+                        "uuid": "49623772-0ee0-4a7d-b587-3940c57f6d39",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
@@ -215505,56 +219382,82 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "mt_controls.txt"
+                                "name": "Annotation"
                             }
                         ],
-                        "label": "mt_controls.txt",
+                        "label": "Annotation",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 440
+                            "left": 578.5792471358866,
+                            "top": 229.41113390716558
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"mt_controls.txt\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "f59c9ecb-0d03-4e93-8f46-5d3ed1b75aea",
+                        "uuid": "32519c71-1699-4942-b34b-44cfc177808c",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Background"
+                            }
+                        ],
+                        "label": "Background",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 583.3644033858866,
+                            "top": 330.2314464071656
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "49c3498d-d1dc-4743-a60d-7ca56195b072",
+                        "when": null,
                         "workflow_outputs": []
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nannotation.txt\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ncounts.txt\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nmt_controls.txt\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Scater: Calculate QC metrics\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  2 -->|output| 3;\n  4[\"Scater: plot library QC\"];\n  3 -->|output_loom| 4;\n  5[\"Scater: filter SCE\"];\n  3 -->|output_loom| 5;\n  6[\"Scater: plot library QC\"];\n  5 -->|output_loom| 6;\n  7[\"Scater: PCA plot\"];\n  5 -->|output_loom| 7;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Scater",
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nMarker Genes\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGO\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nAnnotation\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nBackground\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Split file\"];\n  0 -->|output| 4;\n  5[\"Cut\"];\n  4 -->|split_output| 5;\n  6[\"GOEnrichment\"];\n  2 -->|output| 6;\n  1 -->|output| 6;\n  3 -->|output| 6;\n  5 -->|out_file1| 6;\n  7[\"gProfiler GOSt\"];\n  5 -->|out_file1| 7;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "GO Enrichment Workflow",
                 "outputs": [],
-                "parent_id": "single-cell/scrna-scater-qc",
-                "path": "topics/single-cell/tutorials/scrna-scater-qc/workflows/main_workflow.ga",
-                "tags": [
-                    "transcriptomics"
-                ],
+                "parent_id": "single-cell/GO-enrichment",
+                "path": "topics/single-cell/tutorials/GO-enrichment/workflows/main_workflow.ga",
+                "tags": [],
                 "test_results": null,
-                "tests": false,
-                "title": "Scater",
+                "tests": true,
+                "title": "GO Enrichment Workflow",
                 "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-scater-qc/versions/main-workflow",
-                "tutorial_id": "scrna-scater-qc",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-scater-qc/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-scater-qc/workflows/main_workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-GO-enrichment/versions/main-workflow",
+                "tutorial_id": "GO-enrichment",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/GO-enrichment/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/GO-enrichment/workflows/main_workflow.html",
                 "version": 1,
-                "wfid": "single-cell-scrna-scater-qc",
+                "wfid": "single-cell-GO-enrichment",
                 "wfname": "main-workflow",
                 "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.12.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.12.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.12.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.12.2"
+                    "Cut1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.4",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/goenrichment/goenrichment/2.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/gprofiler_gost/gprofiler_gost/0.1.7+galaxy11"
                 ],
-                "workflowhub_id": "1241"
+                "workflowhub_id": "1365"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/3386291"
+        "zenodo_link": "https://zenodo.org/records/13461890"
     },
     {
         "admin_install": {
@@ -215563,107 +219466,37 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
+                    "name": "music_construct_eset",
                     "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bamtools_filter",
-                    "owner": "devteam",
-                    "revisions": "cb20f99fd45b",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_stats",
-                    "owner": "devteam",
-                    "revisions": "24c5d43cb545",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collection_column_join",
-                    "owner": "iuc",
-                    "revisions": "3ddd99c7efee",
-                    "tool_panel_section_label": "Join, Subtract and Group",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "featurecounts",
-                    "owner": "iuc",
-                    "revisions": "f3a5f075498f",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "featurecounts",
-                    "owner": "iuc",
-                    "revisions": "ea04b737afa0",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "df99138d2776",
-                    "tool_panel_section_label": "Quality Control",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "c1a4b5f3b432",
-                    "tool_panel_section_label": "Quality Control",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "rgrnastar",
-                    "owner": "iuc",
-                    "revisions": "2055c2667eb3",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "rgrnastar",
-                    "owner": "iuc",
-                    "revisions": "7ed2edc1337f",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "umi_tools_count",
-                    "owner": "iuc",
-                    "revisions": "b557acca0b56",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "2cfd0db49bbc",
+                    "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "umi_tools_count",
-                    "owner": "iuc",
-                    "revisions": "8250ea3a1501",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "music_construct_eset",
+                    "owner": "bgruening",
+                    "revisions": "7ffaa0968da3",
+                    "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "umi_tools_extract",
-                    "owner": "iuc",
-                    "revisions": "828dba98cdb4",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "music_deconvolution",
+                    "owner": "bgruening",
+                    "revisions": "56371b5a2da9",
+                    "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "umi_tools_extract",
-                    "owner": "iuc",
-                    "revisions": "6a675c3aa610",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "music_inspect_eset",
+                    "owner": "bgruening",
+                    "revisions": "8c64a2da3869",
+                    "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_filter\n  owner: devteam\n  revisions: cb20f99fd45b\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 24c5d43cb545\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_column_join\n  owner: iuc\n  revisions: 3ddd99c7efee\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: featurecounts\n  owner: iuc\n  revisions: f3a5f075498f\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: featurecounts\n  owner: iuc\n  revisions: ea04b737afa0\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: df99138d2776\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: c1a4b5f3b432\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n  owner: iuc\n  revisions: 2055c2667eb3\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n  owner: iuc\n  revisions: 7ed2edc1337f\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: umi_tools_count\n  owner: iuc\n  revisions: b557acca0b56\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: umi_tools_count\n  owner: iuc\n  revisions: 8250ea3a1501\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: umi_tools_extract\n  owner: iuc\n  revisions: 828dba98cdb4\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: umi_tools_extract\n  owner: iuc\n  revisions: 6a675c3aa610\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-preprocessing/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: music_construct_eset\n  owner: bgruening\n  revisions: 2cfd0db49bbc\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: music_construct_eset\n  owner: bgruening\n  revisions: 7ffaa0968da3\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: music_deconvolution\n  owner: bgruening\n  revisions: 56371b5a2da9\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: music_inspect_eset\n  owner: bgruening\n  revisions: 8c64a2da3869\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
@@ -215682,76 +219515,31 @@
             },
             {
                 "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "email": "anikaerxleben@gmail.com",
-                "id": "erxleben",
-                "joined": "2017-09",
-                "name": "Anika Erxleben",
-                "orcid": "0000-0002-7427-6478",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/erxleben/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/erxleben.json"
-            },
-            {
-                "affiliations": [
-                    "by-covid",
-                    "uni-freiburg",
                     "elixir-europe"
                 ],
-                "elixir_node": "de",
-                "fediverse": "https://scholar.social/@zerodivision",
+                "bio": "Senior Lecturer at The Open University",
+                "elixir_node": "uk",
+                "email": "wendi.bacon@open.ac.uk",
+                "fediverse": "https://mstdn.science/@wendibacon1",
                 "fediverse_flavor": "mastodon",
-                "id": "wm75",
-                "joined": "2017-09",
-                "matrix": "wm75:matrix.org",
-                "name": "Wolfgang Maier",
-                "orcid": "0000-0002-9464-6640",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
+                "id": "nomadscientist",
+                "joined": "2020-03",
+                "matrix": "nomadscientist:matrix.org",
+                "name": "Wendi Bacon",
+                "orcid": "0000-0002-8170-8806",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
+                "twitter": "WendiBacon1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
             }
         ],
-        "dir": "topics/single-cell/tutorials/scrna-preprocessing",
-        "edam_operation": [
-            "Sequencing quality control",
-            "RNA-Seq quantification",
-            "Read summarisation",
-            "Data handling",
-            "Validation",
-            "Sequence alignment",
-            "Sequence alignment analysis"
-        ],
+        "dir": "topics/single-cell/tutorials/bulk-music",
+        "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
@@ -215759,54 +219547,57 @@
             {
                 "topic_name": "single-cell",
                 "tutorials": [
-                    "scrna-umis"
+                    "bulk-music-2-preparescref"
                 ],
                 "type": "internal"
             }
         ],
         "gitter": "Galaxy-Training-Network/galaxy-single-cell",
         "hands_on": true,
-        "id": "single-cell/scrna-preprocessing",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
+        "id": "single-cell/bulk-music",
+        "inexact_supported_servers": [],
         "js_requirements": {
-            "mathjax": 39191,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Verifying the distribution of barcodes via a FASTQC plot",
-            "Relocating barcodes into headers",
-            "Merging matrices from different batches together",
-            "Removing unwanted barcodes"
+            "Deconvolution tools show individual cell type proportions in bulk RNA-seq data",
+            "Bulk RNA-seq can be complimented by scRNA-seq data"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-10-10",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Demultiplex FASTQ data via UMI-tools",
-            "Understand and validate the extraction of barcodes",
-            "Obtain an overview of general alignment and quantification techniques",
-            "Generate a count matrix for downstream single-cell RNA analysis"
+            "Construct Bulk and scRNA Expression Set Objects",
+            "Inspect these objects for various properties",
+            "Measure the abundance of certain cell type cluster markers compared to others"
         ],
-        "pageviews": 5732812,
+        "pageviews": 3662,
         "priority": 1,
-        "pub_date": "2019-02-22",
+        "pub_date": "2022-02-11",
         "questions": [
-            "What is single-cell?",
-            "How do we process a batch?",
-            "How do we process multiple batches?",
-            "How do we check for cross-contamination?"
+            "How do we infer cell type proportions from bulk RNA-seq data?",
+            "How are these cell types grouped together?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "mtekman",
+                    "nomadscientist"
+                ],
+                "date": "2021-03-08",
+                "galaxy_version": "21.09",
+                "length": "20M",
+                "speakers": [
+                    "nomadscientist"
+                ],
+                "youtube_id": "nfAUXP3W-jM"
+            }
         ],
         "redirect_from": [
-            "/topics/transcriptomics/tutorials/scrna_preprocessing/tutorial",
-            "/topics/transcriptomics/tutorials/scrna-preprocessing/tutorial",
-            "/short/single-cell/scrna-preprocessing",
-            "/short/T00251"
+            "/topics/transcriptomics/tutorials/bulk-music/tutorial",
+            "/short/single-cell/bulk-music",
+            "/short/T00240"
         ],
         "requirements": [
             {
@@ -215817,45 +219608,26 @@
                 "type": "internal"
             }
         ],
-        "short_id": "T00251",
+        "short_id": "T00240",
         "short_tools": [
-            "samtools_stats",
-            "multiqc",
-            "umi_tools_count",
-            "umi_tools_extract",
-            "collection_column_join",
-            "bamFilter",
-            "featurecounts",
-            "tp_sed_tool",
-            "rna_star",
-            "__FLATTEN__"
+            "music_construct_eset",
+            "music_deconvolution",
+            "music_inspect_eset"
         ],
-        "slides": true,
+        "slides": false,
         "slides_recordings": false,
-        "subtopic": "end-to-end",
+        "subtopic": "deconvo",
         "supported_servers": {
             "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
                 },
                 {
                     "name": "UseGalaxy.org (Main)",
@@ -215867,28 +219639,20 @@
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
                 }
-            ]
+            ],
+            "inexact": []
         },
         "symlink": null,
-        "tags": null,
-        "time_estimation": "3h",
-        "title": "Pre-processing of Single-Cell RNA Data",
+        "tags": [
+            "transcriptomics"
+        ],
+        "time_estimation": "2h",
+        "title": "Bulk RNA Deconvolution with MuSiC",
         "tools": [
-            "__FLATTEN__",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9",
-            "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.7a",
-            "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3"
         ],
         "topic_name": "single-cell",
         "topic_name_human": "Single Cell",
@@ -215898,31 +219662,38 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "scrna-preprocessing",
+        "tutorial_name": "bulk-music",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-preprocessing/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-preprocessing/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-preprocessing/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music/tutorial.json"
         },
-        "version": 2,
+        "version": 7,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 290,
-        "visitors": 2068274,
+        "visit_duration": 98,
+        "visitors": 2865,
         "workflows": [
             {
                 "creators": [],
-                "description": "Pre-processing of Single-Cell RNA Data",
+                "description": "Bulk RNA Deconvolution with MuSiC",
                 "features": {
                     "comments": false,
-                    "parameters": false,
+                    "parameters": true,
                     "report": null,
-                    "subworkflows": true
+                    "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nList of FACS pairs\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBarcodes\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGTF file UCSC\"]\n  3[label=\"Flatten Collection\"]\n  0 -> 3 [label=\"output\"]\n  4[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nCelSeq2: Single Batch mm10\"]\n  1 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Column Join\"]\n  4 -> 5 [label=\"9:out_counts\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nscRNA Assay Tabular\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nscRNA Phenotype Tabular\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nscRNA Metadata\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBulk RNA Assay Tabular\"]\n  4[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nBulk RNA Annotation\"]\n  5[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nCell Types List\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCell Markers C1\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCell Markers C2\"]\n  8[label=\"Construct scRNA ESet Object\"]\n  0 -> 8 [label=\"output\"]\n  2 -> 8 [label=\"output\"]\n  1 -> 8 [label=\"output\"]\n  k872b3dd2322c47ccb5b9071a9f939320[color=lightseagreen,label=\"Output\\nConstruct Expression Set Object on input dataset(s): RData ESet Object\"]\n  8 -> k872b3dd2322c47ccb5b9071a9f939320\n  9[label=\"Construct Bulk RNA ESet Object\"]\n  4 -> 9 [label=\"output\"]\n  3 -> 9 [label=\"output\"]\n  10[label=\"Extract Cell Types\"]\n  8 -> 10 [label=\"out_rds\"]\n  11[label=\"Extract General Info\"]\n  8 -> 11 [label=\"out_rds\"]\n  k1733593f847d4adb91f4fd78c077b074[color=lightseagreen,label=\"Output\\nInspect Expression Set Object on input dataset(s): Inspection Result\"]\n  11 -> k1733593f847d4adb91f4fd78c077b074\n  12[label=\"Extract General Info Bulk\"]\n  9 -> 12 [label=\"out_rds\"]\n  13[label=\"Music: Estimate Cell Proportions\"]\n  9 -> 13 [label=\"out_rds\"]\n  5 -> 13 [label=\"output\"]\n  8 -> 13 [label=\"out_rds\"]\n  14[label=\"Music: Compute Dendrogram\"]\n  9 -> 14 [label=\"out_rds\"]\n  6 -> 14 [label=\"output\"]\n  7 -> 14 [label=\"output\"]\n  8 -> 14 [label=\"out_rds\"]\n  kdf2e83a5ac67460f8b0fac3f3b63280f[color=lightseagreen,label=\"Output\\nMuSiC on input dataset(s): PDF Plots\"]\n  14 -> kdf2e83a5ac67460f8b0fac3f3b63280f\n}",
                 "history": [
+                    {
+                        "hash": "e2453dfb588ab6bdcb28a0991c6800683e9947fe",
+                        "message": "use full tool ID",
+                        "num": 2,
+                        "short_hash": "e2453dfb5",
+                        "unix": "1684159247"
+                    },
                     {
                         "hash": "327fd2b842f45de3dc2a30067714352675ad69ae",
                         "message": "Making a single cell topics",
@@ -215936,26 +219707,385 @@
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "scRNA Assay Tabular"
+                            }
+                        ],
+                        "label": "scRNA Assay Tabular",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 234.6999969482422,
+                            "height": 82.19999694824219,
+                            "left": 360,
+                            "right": 560,
+                            "top": 152.5,
+                            "width": 200,
+                            "x": 360,
+                            "y": 152.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0d219185-0933-4459-ade3-30f96b00511d",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "c67225bf-f947-45ed-ae5b-5c9367ef8cab"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "scRNA Phenotype Tabular"
+                            }
+                        ],
+                        "label": "scRNA Phenotype Tabular",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 338.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 359,
+                            "right": 559,
+                            "top": 256,
+                            "width": 200,
+                            "x": 359,
+                            "y": 256
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "9ca6d554-decc-4b57-b6f4-723a60e5a0cc",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "59f0e53a-13ee-4ab6-8cdf-40482dfc0f75"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "scRNA Metadata"
+                            }
+                        ],
+                        "label": "scRNA Metadata",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 424.8000030517578,
+                            "height": 61.80000305175781,
+                            "left": 357,
+                            "right": 557,
+                            "top": 363,
+                            "width": 200,
+                            "x": 357,
+                            "y": 363
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "4efc5ad2-5000-4b60-92e8-df022c6f8a7f",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "f45df54a-4591-49bb-91be-06a497ceb14d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Bulk RNA Assay Tabular"
+                            }
+                        ],
+                        "label": "Bulk RNA Assay Tabular",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 544.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 358,
+                            "right": 558,
+                            "top": 462,
+                            "width": 200,
+                            "x": 358,
+                            "y": 462
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "809894bc-62b0-43a8-af73-d19c359b2e4e",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "4a8ebd19-87c9-4b3d-89ad-26316b1460f9"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Bulk RNA Annotation"
+                            }
+                        ],
+                        "label": "Bulk RNA Annotation",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 645.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 358,
+                            "right": 558,
+                            "top": 563,
+                            "width": 200,
+                            "x": 358,
+                            "y": 563
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "1c008bcf-8ea8-4f48-89ec-623190301fc9",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "5663f93d-b38f-4f7c-9ed2-7aa5a5e0273e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Cell Types List"
+                            }
+                        ],
+                        "label": "Cell Types List",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 314.3000030517578,
+                            "height": 61.80000305175781,
+                            "left": 928,
+                            "right": 1128,
+                            "top": 252.5,
+                            "width": 200,
+                            "x": 928,
+                            "y": 252.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "f98985a7-458a-4b2f-a924-8ca4ecdaa037",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "6440740d-b72c-422b-a46c-d3de32c25076"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Cell Markers C1"
+                            }
+                        ],
+                        "label": "Cell Markers C1",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 388.3000030517578,
+                            "height": 61.80000305175781,
+                            "left": 927,
+                            "right": 1127,
+                            "top": 326.5,
+                            "width": 200,
+                            "x": 927,
+                            "y": 326.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "d2940a2a-808b-43ec-9ed7-59a8915b4fbd",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "b87c6860-8b9d-4412-8aa7-506ea09bfc16"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Cell Markers C2"
+                            }
+                        ],
+                        "label": "Cell Markers C2",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 459.3000030517578,
+                            "height": 61.80000305175781,
+                            "left": 932,
+                            "right": 1132,
+                            "top": 397.5,
+                            "width": 200,
+                            "x": 932,
+                            "y": 397.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "b13d3354-a633-4eeb-8edf-4f14c4209240",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "3f07162a-d2f4-411e-a276-6437c7149ecc"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nscRNA Assay Tabular\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nscRNA Phenotype Tabular\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nscRNA Metadata\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nBulk RNA Assay Tabular\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nBulk RNA Annotation\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Parameter\\nCell Types List\"];\n  style 5 fill:#ded,stroke:#393,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nCell Markers C1\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nCell Markers C2\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"Construct scRNA ESet Object\"];\n  0 -->|output| 8;\n  2 -->|output| 8;\n  1 -->|output| 8;\n  872b3dd2-322c-47cc-b5b9-071a9f939320[\"Output\\nConstruct Expression Set Object on input dataset(s): RData ESet Object\"];\n  8 --> 872b3dd2-322c-47cc-b5b9-071a9f939320;\n  style 872b3dd2-322c-47cc-b5b9-071a9f939320 stroke:#2c3143,stroke-width:4px;\n  9[\"Construct Bulk RNA ESet Object\"];\n  4 -->|output| 9;\n  3 -->|output| 9;\n  10[\"Extract Cell Types\"];\n  8 -->|out_rds| 10;\n  11[\"Extract General Info\"];\n  8 -->|out_rds| 11;\n  1733593f-847d-4adb-91f4-fd78c077b074[\"Output\\nInspect Expression Set Object on input dataset(s): Inspection Result\"];\n  11 --> 1733593f-847d-4adb-91f4-fd78c077b074;\n  style 1733593f-847d-4adb-91f4-fd78c077b074 stroke:#2c3143,stroke-width:4px;\n  12[\"Extract General Info Bulk\"];\n  9 -->|out_rds| 12;\n  13[\"Music: Estimate Cell Proportions\"];\n  9 -->|out_rds| 13;\n  5 -->|output| 13;\n  8 -->|out_rds| 13;\n  14[\"Music: Compute Dendrogram\"];\n  9 -->|out_rds| 14;\n  6 -->|output| 14;\n  7 -->|output| 14;\n  8 -->|out_rds| 14;\n  df2e83a5-ac67-460f-8b0f-ac3f3b63280f[\"Output\\nMuSiC on input dataset(s): PDF Plots\"];\n  14 --> df2e83a5-ac67-460f-8b0f-ac3f3b63280f;\n  style df2e83a5-ac67-460f-8b0f-ac3f3b63280f stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "MuSiC Workflow",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "scRNA Assay Tabular"
+                            }
+                        ],
+                        "label": "scRNA Assay Tabular",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 234.6999969482422,
+                            "height": 82.19999694824219,
+                            "left": 360,
+                            "right": 560,
+                            "top": 152.5,
+                            "width": 200,
+                            "x": 360,
+                            "y": 152.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0d219185-0933-4459-ade3-30f96b00511d",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "c67225bf-f947-45ed-ae5b-5c9367ef8cab"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "List of FACS pairs",
-                        "name": "Input dataset collection",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "scRNA Phenotype Tabular"
+                            }
+                        ],
+                        "label": "scRNA Phenotype Tabular",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 119.5,
-                            "top": 260
+                            "bottom": 338.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 359,
+                            "right": 559,
+                            "top": 256,
+                            "width": 200,
+                            "x": 359,
+                            "y": 256
                         },
                         "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list:paired\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "c50ee411-e25e-4570-97bf-f0a05af2458e",
+                        "type": "data_input",
+                        "uuid": "9ca6d554-decc-4b57-b6f4-723a60e5a0cc",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "37307bc9-a8de-4fb4-8482-4a3554c9af36"
+                                "uuid": "59f0e53a-13ee-4ab6-8cdf-40482dfc0f75"
                             }
                         ]
                     },
@@ -215963,26 +220093,37 @@
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 2,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "Barcodes",
-                        "name": "Input dataset",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "scRNA Metadata"
+                            }
+                        ],
+                        "label": "scRNA Metadata",
+                        "name": "Input parameter",
                         "outputs": [],
                         "position": {
-                            "left": 566.5,
-                            "top": 429.5
+                            "bottom": 424.8000030517578,
+                            "height": 61.80000305175781,
+                            "left": 357,
+                            "right": 557,
+                            "top": 363,
+                            "width": 200,
+                            "x": 357,
+                            "y": 363
                         },
                         "tool_id": null,
-                        "tool_state": "{}",
+                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "cb331533-4896-419f-83ca-196c5daf2c03",
+                        "type": "parameter_input",
+                        "uuid": "4efc5ad2-5000-4b60-92e8-df022c6f8a7f",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "d863899f-2ea8-49d1-acc9-a2cca1f9fce3"
+                                "uuid": "f45df54a-4591-49bb-91be-06a497ceb14d"
                             }
                         ]
                     },
@@ -215990,59 +220131,75 @@
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 3,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "GTF file (UCSC)",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Bulk RNA Assay Tabular"
+                            }
+                        ],
+                        "label": "Bulk RNA Assay Tabular",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 568.5,
-                            "top": 521
+                            "bottom": 544.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 358,
+                            "right": 558,
+                            "top": 462,
+                            "width": 200,
+                            "x": 358,
+                            "y": 462
                         },
                         "tool_id": null,
-                        "tool_state": "{}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ac1f89bb-52b9-41ac-a6d4-f8dfd4d21550",
+                        "uuid": "809894bc-62b0-43a8-af73-d19c359b2e4e",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "51046a1f-f629-4e6a-aac1-eb563eeb693b"
+                                "uuid": "4a8ebd19-87c9-4b3d-89ad-26316b1460f9"
                             }
                         ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nList of FACS pairs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nBarcodes\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nGTF file UCSC\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Flatten Collection\"];\n  0 -->|output| 3;\n  4[\"\ud83d\udee0\ufe0f Subworkflow\\nCelSeq2: Single Batch mm10\"];\n  style 4 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 4;\n  3 -->|output| 4;\n  2 -->|output| 4;\n  5[\"Column Join\"];\n  4 -->|9:out_counts| 5;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "CelSeq2: Multi Batch (mm10)",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 4,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "List of FACS pairs",
-                        "name": "Input dataset collection",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Bulk RNA Annotation"
+                            }
+                        ],
+                        "label": "Bulk RNA Annotation",
+                        "name": "Input parameter",
                         "outputs": [],
                         "position": {
-                            "left": 119.5,
-                            "top": 260
+                            "bottom": 645.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 358,
+                            "right": 558,
+                            "top": 563,
+                            "width": 200,
+                            "x": 358,
+                            "y": 563
                         },
                         "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list:paired\"}",
+                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "c50ee411-e25e-4570-97bf-f0a05af2458e",
+                        "type": "parameter_input",
+                        "uuid": "1c008bcf-8ea8-4f48-89ec-623190301fc9",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "37307bc9-a8de-4fb4-8482-4a3554c9af36"
+                                "uuid": "5663f93d-b38f-4f7c-9ed2-7aa5a5e0273e"
                             }
                         ]
                     },
@@ -216050,26 +220207,75 @@
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 5,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "Barcodes",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Cell Types List"
+                            }
+                        ],
+                        "label": "Cell Types List",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 314.3000030517578,
+                            "height": 61.80000305175781,
+                            "left": 928,
+                            "right": 1128,
+                            "top": 252.5,
+                            "width": 200,
+                            "x": 928,
+                            "y": 252.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "f98985a7-458a-4b2f-a924-8ca4ecdaa037",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "6440740d-b72c-422b-a46c-d3de32c25076"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Cell Markers C1"
+                            }
+                        ],
+                        "label": "Cell Markers C1",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 566.5,
-                            "top": 429.5
+                            "bottom": 388.3000030517578,
+                            "height": 61.80000305175781,
+                            "left": 927,
+                            "right": 1127,
+                            "top": 326.5,
+                            "width": 200,
+                            "x": 927,
+                            "y": 326.5
                         },
                         "tool_id": null,
-                        "tool_state": "{}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "cb331533-4896-419f-83ca-196c5daf2c03",
+                        "uuid": "d2940a2a-808b-43ec-9ed7-59a8915b4fbd",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "d863899f-2ea8-49d1-acc9-a2cca1f9fce3"
+                                "uuid": "b87c6860-8b9d-4412-8aa7-506ea09bfc16"
                             }
                         ]
                     },
@@ -216077,913 +220283,1211 @@
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 7,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "GTF file (UCSC)",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Cell Markers C2"
+                            }
+                        ],
+                        "label": "Cell Markers C2",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 568.5,
-                            "top": 521
+                            "bottom": 459.3000030517578,
+                            "height": 61.80000305175781,
+                            "left": 932,
+                            "right": 1132,
+                            "top": 397.5,
+                            "width": 200,
+                            "x": 932,
+                            "y": 397.5
                         },
                         "tool_id": null,
-                        "tool_state": "{}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ac1f89bb-52b9-41ac-a6d4-f8dfd4d21550",
+                        "uuid": "b13d3354-a633-4eeb-8edf-4f14c4209240",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "51046a1f-f629-4e6a-aac1-eb563eeb693b"
+                                "uuid": "3f07162a-d2f4-411e-a276-6437c7149ecc"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "id": 4,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0",
+                        "errors": null,
+                        "id": 8,
                         "input_connections": {
-                            "Barcodes (single-col)": {
-                                "id": 1,
-                                "input_subworkflow_step_id": 1,
+                            "exprs_file": {
+                                "id": 0,
                                 "output_name": "output"
                             },
-                            "Batch": {
-                                "id": 3,
-                                "input_subworkflow_step_id": 0,
+                            "metadata_0|row_names": {
+                                "id": 2,
                                 "output_name": "output"
                             },
-                            "GTF file (UCSC)": {
-                                "id": 2,
-                                "input_subworkflow_step_id": 2,
+                            "pdata_file": {
+                                "id": 1,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "CelSeq2: Single Batch mm10",
-                        "outputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Construct Expression Set Object",
+                                "name": "exprs_file"
+                            },
+                            {
+                                "description": "runtime parameter for tool Construct Expression Set Object",
+                                "name": "pdata_file"
+                            }
+                        ],
+                        "label": "Construct scRNA ESet Object",
+                        "name": "Construct Expression Set Object",
+                        "outputs": [
+                            {
+                                "name": "out_tab",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "out_rds",
+                                "type": "rdata"
+                            }
+                        ],
                         "position": {
-                            "left": 879,
-                            "top": 293.5
+                            "bottom": 435.8999938964844,
+                            "height": 286.3999938964844,
+                            "left": 637,
+                            "right": 837,
+                            "top": 149.5,
+                            "width": 200,
+                            "x": 637,
+                            "y": 149.5
                         },
-                        "subworkflow": {
-                            "a_galaxy_workflow": "true",
-                            "annotation": "",
-                            "format-version": "0.1",
-                            "name": "CelSeq2: Single Batch mm10",
-                            "steps": {
-                                "0": {
-                                    "annotation": "",
-                                    "content_id": null,
-                                    "errors": null,
-                                    "id": 0,
-                                    "input_connections": {},
-                                    "inputs": [],
-                                    "label": "Batch",
-                                    "name": "Input dataset collection",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 286,
-                                        "top": 470.90625
-                                    },
-                                    "tool_id": null,
-                                    "tool_state": "{\"collection_type\": \"paired\"}",
-                                    "tool_version": null,
-                                    "type": "data_collection_input",
-                                    "uuid": "c451df86-a25e-409c-9f2e-33c22a0f1bb9",
-                                    "workflow_outputs": [
-                                        {
-                                            "label": null,
-                                            "output_name": "output",
-                                            "uuid": "d46989fb-ef46-4506-8932-d66cee38e62a"
-                                        }
-                                    ]
-                                },
-                                "1": {
-                                    "annotation": "",
-                                    "content_id": null,
-                                    "errors": null,
-                                    "id": 1,
-                                    "input_connections": {},
-                                    "inputs": [],
-                                    "label": "Barcodes (single-col)",
-                                    "name": "Input dataset",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 302.5,
-                                        "top": 552
-                                    },
-                                    "tool_id": null,
-                                    "tool_state": "{}",
-                                    "tool_version": null,
-                                    "type": "data_input",
-                                    "uuid": "4ac7860e-01d4-4009-b1fd-899fab778eb5",
-                                    "workflow_outputs": [
-                                        {
-                                            "label": null,
-                                            "output_name": "output",
-                                            "uuid": "2c66b77f-5ee0-4991-971c-3c43d8e7841d"
-                                        }
-                                    ]
-                                },
-                                "10": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-                                    "errors": null,
-                                    "id": 10,
-                                    "input_connections": {
-                                        "infile": {
-                                            "id": 9,
-                                            "output_name": "out_counts"
-                                        }
-                                    },
-                                    "inputs": [
-                                        {
-                                            "description": "runtime parameter for tool Text transformation",
-                                            "name": "infile"
-                                        }
-                                    ],
-                                    "label": "Fix Headers",
-                                    "name": "Text transformation",
-                                    "outputs": [
-                                        {
-                                            "name": "output",
-                                            "type": "input"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 1919.90625,
-                                        "top": 528.40625
-                                    },
-                                    "post_job_actions": {},
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "a6f147a050a2",
-                                        "name": "text_processing",
-                                        "owner": "bgruening",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"adv_opts\": \"{\\\"__current_case__\\\": 0, \\\"adv_opts_selector\\\": \\\"basic\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"code\": \"\\\"1 s|\\\\\\\\w+_([ACTG]+)\\\\\\\\b|\\\\\\\\1|g\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                                    "tool_version": "1.1.1",
-                                    "type": "tool",
-                                    "uuid": "1d1e09f7-119f-4086-b8b7-a9fb61cea637",
-                                    "workflow_outputs": [
-                                        {
-                                            "label": null,
-                                            "output_name": "output",
-                                            "uuid": "2aa0f119-75c6-4b6b-8260-ff66f54167a4"
-                                        }
-                                    ]
-                                },
-                                "2": {
-                                    "annotation": "",
-                                    "content_id": null,
-                                    "errors": null,
-                                    "id": 2,
-                                    "input_connections": {},
-                                    "inputs": [],
-                                    "label": "GTF file (UCSC)",
-                                    "name": "Input dataset",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 313.5,
-                                        "top": 828.90625
-                                    },
-                                    "tool_id": null,
-                                    "tool_state": "{}",
-                                    "tool_version": null,
-                                    "type": "data_input",
-                                    "uuid": "0455bae6-58da-4ec3-9688-72aba9f676fe",
-                                    "workflow_outputs": [
-                                        {
-                                            "label": null,
-                                            "output_name": "output",
-                                            "uuid": "7ca9e0df-159c-43f7-a0b3-e546fcd9b2c9"
-                                        }
-                                    ]
-                                },
-                                "3": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2",
-                                    "errors": null,
-                                    "id": 3,
-                                    "input_connections": {
-                                        "barcodes|filter_barcode_file": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        },
-                                        "input_type|input_readpair": {
-                                            "id": 0,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [
-                                        {
-                                            "description": "runtime parameter for tool UMI-tools extract",
-                                            "name": "input_type"
-                                        },
-                                        {
-                                            "description": "runtime parameter for tool UMI-tools extract",
-                                            "name": "barcodes"
-                                        }
-                                    ],
-                                    "label": null,
-                                    "name": "UMI-tools extract",
-                                    "outputs": [
-                                        {
-                                            "name": "out",
-                                            "type": "input"
-                                        },
-                                        {
-                                            "name": "out1",
-                                            "type": "input"
-                                        },
-                                        {
-                                            "name": "out2",
-                                            "type": "input"
-                                        },
-                                        {
-                                            "name": "out_log",
-                                            "type": "txt"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 554.5,
-                                        "top": 469.90625
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionout": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "out"
-                                        },
-                                        "HideDatasetActionout1": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "out1"
-                                        },
-                                        "HideDatasetActionout_log": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "out_log"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "99aea37a7ff7",
-                                        "name": "umi_tools_extract",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"__page__\": null, \"extract_method\": \"\\\"string\\\"\", \"input_type\": \"{\\\"__current_case__\\\": 2, \\\"barcode\\\": {\\\"__current_case__\\\": 0, \\\"barcode_select\\\": \\\"first_read_only\\\"}, \\\"input_readpair\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"type\\\": \\\"paired_collection\\\"}\", \"__rerun_remap_job_id__\": null, \"bc_pattern\": \"\\\"NNNNNNCCCCCC\\\"\", \"print_log\": \"\\\"true\\\"\", \"prime3\": \"\\\"true\\\"\", \"quality\": \"{\\\"__current_case__\\\": 0, \\\"quality_selector\\\": \\\"false\\\"}\", \"barcodes\": \"{\\\"__current_case__\\\": 1, \\\"filter_barcode_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"filter_correct\\\": \\\"false\\\", \\\"use_barcodes\\\": \\\"yes\\\"}\"}",
-                                    "tool_version": "0.5.3.2",
-                                    "type": "tool",
-                                    "uuid": "0b94d2ea-1889-4b88-b0a2-ac7b0a3452e5",
-                                    "workflow_outputs": [
-                                        {
-                                            "label": null,
-                                            "output_name": "out2",
-                                            "uuid": "c24e1482-bbff-4a22-8747-2ab0330fb5af"
-                                        }
-                                    ]
-                                },
-                                "4": {
-                                    "annotation": "The genome should match that of the GTF file",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2",
-                                    "errors": null,
-                                    "id": 4,
-                                    "input_connections": {
-                                        "refGenomeSource|GTFconditional|sjdbGTFfile": {
-                                            "id": 2,
-                                            "output_name": "output"
-                                        },
-                                        "singlePaired|input1": {
-                                            "id": 3,
-                                            "output_name": "out2"
-                                        }
-                                    },
-                                    "inputs": [
-                                        {
-                                            "description": "runtime parameter for tool RNA STAR",
-                                            "name": "quantMode"
-                                        },
-                                        {
-                                            "description": "runtime parameter for tool RNA STAR",
-                                            "name": "singlePaired"
-                                        }
-                                    ],
-                                    "label": "Alignment (mm10)",
-                                    "name": "RNA STAR",
-                                    "outputs": [
-                                        {
-                                            "name": "output_log",
-                                            "type": "txt"
-                                        },
-                                        {
-                                            "name": "chimeric_junctions",
-                                            "type": "interval"
-                                        },
-                                        {
-                                            "name": "chimeric_reads",
-                                            "type": "bam"
-                                        },
-                                        {
-                                            "name": "splice_junctions",
-                                            "type": "interval"
-                                        },
-                                        {
-                                            "name": "mapped_reads",
-                                            "type": "bam"
-                                        },
-                                        {
-                                            "name": "reads_per_gene",
-                                            "type": "tabular"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 832.5,
-                                        "top": 581.90625
-                                    },
-                                    "post_job_actions": {},
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "2055c2667eb3",
-                                        "name": "rgrnastar",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"__page__\": null, \"singlePaired\": \"{\\\"__current_case__\\\": 0, \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sPaired\\\": \\\"single\\\"}\", \"output_params\": \"{\\\"__current_case__\\\": 1, \\\"output_select\\\": \\\"no\\\"}\", \"__rerun_remap_job_id__\": null, \"params\": \"{\\\"__current_case__\\\": 0, \\\"settingsType\\\": \\\"default\\\"}\", \"refGenomeSource\": \"{\\\"GTFconditional\\\": {\\\"GTFselect\\\": \\\"without-gtf\\\", \\\"__current_case__\\\": 1, \\\"genomeDir\\\": \\\"mm10\\\", \\\"sjdbGTFfile\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sjdbOverhang\\\": \\\"100\\\"}, \\\"__current_case__\\\": 0, \\\"geneSource\\\": \\\"indexed\\\"}\", \"quantMode\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                                    "tool_version": "2.5.2b-2",
-                                    "type": "tool",
-                                    "uuid": "1e4a54be-b2fb-496a-8247-ccba4ffe6f3b",
-                                    "workflow_outputs": [
-                                        {
-                                            "label": null,
-                                            "output_name": "chimeric_reads",
-                                            "uuid": "f44d1ce2-b0a0-4aca-b9da-d47a9151dd8f"
-                                        },
-                                        {
-                                            "label": null,
-                                            "output_name": "chimeric_junctions",
-                                            "uuid": "a70f8d45-eaa8-40f4-a755-99e7004ad0ee"
-                                        },
-                                        {
-                                            "label": null,
-                                            "output_name": "reads_per_gene",
-                                            "uuid": "70ef8c03-6a54-4c88-81b6-e178dbf776c7"
-                                        },
-                                        {
-                                            "label": null,
-                                            "output_name": "splice_junctions",
-                                            "uuid": "0896bee8-d853-4467-8143-96a4d314774c"
-                                        },
-                                        {
-                                            "label": null,
-                                            "output_name": "mapped_reads",
-                                            "uuid": "956818b5-dc81-440c-8c2a-b10869547c70"
-                                        },
-                                        {
-                                            "label": null,
-                                            "output_name": "output_log",
-                                            "uuid": "5714f89a-1d7f-4634-95ce-2b089e5cc83d"
-                                        }
-                                    ]
-                                },
-                                "5": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
-                                    "errors": null,
-                                    "id": 5,
-                                    "input_connections": {
-                                        "input_file": {
-                                            "id": 4,
-                                            "output_name": "mapped_reads"
-                                        }
-                                    },
-                                    "inputs": [
-                                        {
-                                            "description": "runtime parameter for tool Stats",
-                                            "name": "input_file"
-                                        }
-                                    ],
-                                    "label": null,
-                                    "name": "Stats",
-                                    "outputs": [
-                                        {
-                                            "name": "output",
-                                            "type": "tabular"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 1338.5,
-                                        "top": 403
-                                    },
-                                    "post_job_actions": {},
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "24c5d43cb545",
-                                        "name": "samtools_stats",
-                                        "owner": "devteam",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"coverage_max\": \"\\\"1000\\\"\", \"__page__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"gc_depth\": \"\\\"20000.0\\\"\", \"insert_size\": \"\\\"8000\\\"\", \"most_inserts\": \"\\\"0.99\\\"\", \"coverage_step\": \"\\\"1\\\"\", \"coverage_min\": \"\\\"1\\\"\", \"read_length\": \"\\\"\\\"\", \"trim_quality\": \"\\\"0\\\"\", \"filter_by_flags\": \"{\\\"__current_case__\\\": 1, \\\"filter_flags\\\": \\\"nofilter\\\"}\", \"split_output\": \"{\\\"__current_case__\\\": 0, \\\"split_output_selector\\\": \\\"no\\\"}\", \"use_reference\": \"{\\\"__current_case__\\\": 1, \\\"use_ref_selector\\\": \\\"no\\\"}\", \"__rerun_remap_job_id__\": null, \"remove_dups\": \"\\\"false\\\"\"}",
-                                    "tool_version": "2.0.1",
-                                    "type": "tool",
-                                    "uuid": "36ad81d4-f920-4ca6-83c2-66516b2229f2",
-                                    "workflow_outputs": [
-                                        {
-                                            "label": null,
-                                            "output_name": "output",
-                                            "uuid": "eed5af2c-48f7-4227-8d76-0686c0537ccc"
-                                        }
-                                    ]
-                                },
-                                "6": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2",
-                                    "errors": null,
-                                    "id": 6,
-                                    "input_connections": {
-                                        "alignment": {
-                                            "id": 4,
-                                            "output_name": "mapped_reads"
-                                        },
-                                        "anno|reference_gene_sets": {
-                                            "id": 2,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [
-                                        {
-                                            "description": "runtime parameter for tool featureCounts",
-                                            "name": "anno"
-                                        },
-                                        {
-                                            "description": "runtime parameter for tool featureCounts",
-                                            "name": "alignment"
-                                        }
-                                    ],
-                                    "label": null,
-                                    "name": "featureCounts",
-                                    "outputs": [
-                                        {
-                                            "name": "output_medium",
-                                            "type": "tabular"
-                                        },
-                                        {
-                                            "name": "output_bam",
-                                            "type": "bam"
-                                        },
-                                        {
-                                            "name": "output_short",
-                                            "type": "tabular"
-                                        },
-                                        {
-                                            "name": "output_full",
-                                            "type": "tabular"
-                                        },
-                                        {
-                                            "name": "output_summary",
-                                            "type": "tabular"
-                                        },
-                                        {
-                                            "name": "output_feature_lengths",
-                                            "type": "tabular"
-                                        },
-                                        {
-                                            "name": "output_jcounts",
-                                            "type": "tabular"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 1141.5,
-                                        "top": 814
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionoutput_feature_lengths": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "output_feature_lengths"
-                                        },
-                                        "HideDatasetActionoutput_full": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "output_full"
-                                        },
-                                        "HideDatasetActionoutput_jcounts": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "output_jcounts"
-                                        },
-                                        "HideDatasetActionoutput_medium": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "output_medium"
-                                        },
-                                        "HideDatasetActionoutput_short": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "output_short"
-                                        },
-                                        "HideDatasetActionoutput_summary": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "output_summary"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "f3a5f075498f",
-                                        "name": "featurecounts",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"pe_parameters\": \"{\\\"exclude_chimerics\\\": \\\"true\\\", \\\"fragment_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"fragment_counting\\\": \\\"\\\"}, \\\"only_both_ends\\\": \\\"false\\\"}\", \"strand_specificity\": \"\\\"0\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"format\": \"\\\"tabdel_short\\\"\", \"include_feature_length_file\": \"\\\"false\\\"\", \"anno\": \"{\\\"__current_case__\\\": 2, \\\"anno_select\\\": \\\"history\\\", \\\"reference_gene_sets\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"extended_parameters\": \"{\\\"R\\\": \\\"true\\\", \\\"by_read_group\\\": \\\"false\\\", \\\"contribute_to_multiple_features\\\": \\\"false\\\", \\\"count_split_alignments_only\\\": \\\"false\\\", \\\"exon_exon_junction_read_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"count_exon_exon_junction_reads\\\": \\\"false\\\"}, \\\"frac_overlap\\\": \\\"0\\\", \\\"frac_overlap_feature\\\": \\\"0\\\", \\\"gff_feature_attribute\\\": \\\"gene_id\\\", \\\"gff_feature_type\\\": \\\"exon\\\", \\\"ignore_dup\\\": \\\"false\\\", \\\"largest_overlap\\\": \\\"false\\\", \\\"long_reads\\\": \\\"false\\\", \\\"mapping_quality\\\": \\\"12\\\", \\\"min_overlap\\\": \\\"1\\\", \\\"multimapping_enabled\\\": {\\\"__current_case__\\\": 1, \\\"multimapping_counts\\\": \\\"\\\"}, \\\"primary\\\": \\\"false\\\", \\\"read_extension_3p\\\": \\\"0\\\", \\\"read_extension_5p\\\": \\\"0\\\", \\\"read_reduction\\\": \\\"\\\", \\\"summarization_level\\\": \\\"false\\\"}\", \"alignment\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                                    "tool_version": "1.6.2",
-                                    "type": "tool",
-                                    "uuid": "9506153d-d997-43a4-8ce1-216690415561",
-                                    "workflow_outputs": [
-                                        {
-                                            "label": null,
-                                            "output_name": "output_bam",
-                                            "uuid": "87abf585-aae9-4af3-aed7-541795d65faf"
-                                        }
-                                    ]
-                                },
-                                "7": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.0",
-                                    "errors": null,
-                                    "id": 7,
-                                    "input_connections": {
-                                        "results_0|software_cond|output_0|type|input": {
-                                            "id": 5,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": null,
-                                    "name": "MultiQC",
-                                    "outputs": [
-                                        {
-                                            "name": "stats",
-                                            "type": "input"
-                                        },
-                                        {
-                                            "name": "html_report",
-                                            "type": "html"
-                                        },
-                                        {
-                                            "name": "log",
-                                            "type": "txt"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 1643.5,
-                                        "top": 200
-                                    },
-                                    "post_job_actions": {},
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.0",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "df99138d2776",
-                                        "name": "multiqc",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"comment\": \"\\\"\\\"\", \"__page__\": null, \"title\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"results\": \"[{\\\"__index__\\\": 0, \\\"software_cond\\\": {\\\"__current_case__\\\": 20, \\\"output\\\": [{\\\"__index__\\\": 0, \\\"type\\\": {\\\"__current_case__\\\": 0, \\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"type\\\": \\\"stats\\\"}}], \\\"software\\\": \\\"samtools\\\"}}, {\\\"__index__\\\": 1, \\\"software_cond\\\": {\\\"__current_case__\\\": 7, \\\"output\\\": [{\\\"__index__\\\": 0, \\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"type\\\": \\\"data\\\"}], \\\"software\\\": \\\"fastqc\\\"}}, {\\\"__index__\\\": 2, \\\"software_cond\\\": {\\\"__current_case__\\\": 7, \\\"output\\\": [{\\\"__index__\\\": 0, \\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"type\\\": \\\"data\\\"}], \\\"software\\\": \\\"fastqc\\\"}}]\", \"saveLog\": \"\\\"false\\\"\"}",
-                                    "tool_version": "1.5.0",
-                                    "type": "tool",
-                                    "uuid": "c56b2cfb-18c4-4f17-9f5c-a84009e00050",
-                                    "workflow_outputs": [
-                                        {
-                                            "label": null,
-                                            "output_name": "stats",
-                                            "uuid": "2845973b-96f5-44c6-b454-b3e09601972b"
-                                        },
-                                        {
-                                            "label": null,
-                                            "output_name": "log",
-                                            "uuid": "9dfc4543-d1d9-40f4-b703-61993f05fbee"
-                                        },
-                                        {
-                                            "label": null,
-                                            "output_name": "html_report",
-                                            "uuid": "452d04bd-cdcc-4074-839d-6a70ad44ba55"
-                                        }
-                                    ]
-                                },
-                                "8": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
-                                    "errors": null,
-                                    "id": 8,
-                                    "input_connections": {
-                                        "input_bam": {
-                                            "id": 6,
-                                            "output_name": "output_bam"
-                                        }
-                                    },
-                                    "inputs": [
-                                        {
-                                            "description": "runtime parameter for tool Filter",
-                                            "name": "input_bam"
-                                        }
-                                    ],
-                                    "label": null,
-                                    "name": "Filter",
-                                    "outputs": [
-                                        {
-                                            "name": "out_file2",
-                                            "type": "txt"
-                                        },
-                                        {
-                                            "name": "out_file1",
-                                            "type": "bam"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 1440.5,
-                                        "top": 627.5
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionout_file2": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "out_file2"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "bd735cae4ce6",
-                                        "name": "bamtools_filter",
-                                        "owner": "devteam",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"input_bam\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"rule_configuration\": \"{\\\"__current_case__\\\": 1, \\\"rules\\\": \\\"(1 | 2) & 3 & 4\\\", \\\"rules_selector\\\": \\\"true\\\"}\", \"conditions\": \"[{\\\"__index__\\\": 0, \\\"filters\\\": [{\\\"__index__\\\": 0, \\\"bam_property\\\": {\\\"__current_case__\\\": 0, \\\"bam_property_selector\\\": \\\"alignmentFlag\\\", \\\"bam_property_value\\\": \\\"0\\\"}}]}, {\\\"__index__\\\": 1, \\\"filters\\\": [{\\\"__index__\\\": 0, \\\"bam_property\\\": {\\\"__current_case__\\\": 0, \\\"bam_property_selector\\\": \\\"alignmentFlag\\\", \\\"bam_property_value\\\": \\\"16\\\"}}]}, {\\\"__index__\\\": 2, \\\"filters\\\": [{\\\"__index__\\\": 0, \\\"bam_property\\\": {\\\"__current_case__\\\": 21, \\\"bam_property_selector\\\": \\\"tag\\\", \\\"bam_property_value\\\": \\\"nM:<3\\\"}}]}, {\\\"__index__\\\": 3, \\\"filters\\\": [{\\\"__index__\\\": 0, \\\"bam_property\\\": {\\\"__current_case__\\\": 21, \\\"bam_property_selector\\\": \\\"tag\\\", \\\"bam_property_value\\\": \\\"NH:<2\\\"}}]}]\", \"__page__\": null}",
-                                    "tool_version": "2.4.1",
-                                    "type": "tool",
-                                    "uuid": "e65c9b1a-65d2-46dc-8199-0f87acf7f6b1",
-                                    "workflow_outputs": [
-                                        {
-                                            "label": null,
-                                            "output_name": "out_file1",
-                                            "uuid": "50f1d2af-ca7e-46b1-a9a6-99931ee1fcb5"
-                                        }
-                                    ]
-                                },
-                                "9": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2",
-                                    "errors": null,
-                                    "id": 9,
-                                    "input_connections": {
-                                        "input_bam": {
-                                            "id": 8,
-                                            "output_name": "out_file1"
-                                        }
-                                    },
-                                    "inputs": [
-                                        {
-                                            "description": "runtime parameter for tool UMI-tools count",
-                                            "name": "input_bam"
-                                        }
-                                    ],
-                                    "label": null,
-                                    "name": "UMI-tools count",
-                                    "outputs": [
-                                        {
-                                            "name": "out_counts",
-                                            "type": "tabular"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 1703.5,
-                                        "top": 590
-                                    },
-                                    "post_job_actions": {},
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "b557acca0b56",
-                                        "name": "umi_tools_count",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"wide_format_cell_counts\": \"\\\"true\\\"\", \"cond_extra\": \"{\\\"__current_case__\\\": 1, \\\"prepender\\\": \\\"dataset name\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"edit_distance_threshold\": \"\\\"1\\\"\", \"paired\": \"\\\"false\\\"\", \"input_bam\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"method\": \"\\\"unique\\\"\", \"advanced\": \"{\\\"gene_tag\\\": \\\"XT\\\", \\\"mapping_quality\\\": \\\"0\\\", \\\"per_cell\\\": \\\"true\\\", \\\"per_contig\\\": \\\"false\\\", \\\"random_seed\\\": \\\"0\\\", \\\"skip_tags_regex\\\": \\\"\\\"}\", \"barcodes\": \"{\\\"__current_case__\\\": 0, \\\"extract_umi_method\\\": \\\"read_id\\\", \\\"umi_separator\\\": \\\"_\\\"}\"}",
-                                    "tool_version": "0.5.3.2",
-                                    "type": "tool",
-                                    "uuid": "89675c5a-ef94-49a5-889c-c53ba1074f80",
-                                    "workflow_outputs": [
-                                        {
-                                            "label": null,
-                                            "output_name": "out_counts",
-                                            "uuid": "209f3dd6-974f-4e76-a206-c86114a6697f"
-                                        }
-                                    ]
-                                }
+                        "post_job_actions": {
+                            "HideDatasetActionout_tab": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "out_tab"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2cfd0db49bbc",
+                            "name": "music_construct_eset",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"annotation\": \"\", \"expdata\": {\"name\": \"\", \"lab\": \"\", \"contact\": \"\", \"title\": \"\", \"abstract\": \"\", \"url\": \"\", \"other\": [{\"__index__\": 0, \"field\": \"notes\", \"comment\": \"Created in Galaxy\"}]}, \"exprs_file\": {\"__class__\": \"RuntimeValue\"}, \"metadata\": [{\"__index__\": 0, \"row_names\": {\"__class__\": \"ConnectedValue\"}, \"label_desc\": \"\"}], \"pdata_file\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.1+galaxy0",
+                        "type": "tool",
+                        "uuid": "2e56a895-db92-4961-9d04-9860ef4d6007",
+                        "workflow_outputs": [
+                            {
+                                "label": "Construct Expression Set Object on input dataset(s): RData ESet Object",
+                                "output_name": "out_rds",
+                                "uuid": "872b3dd2-322c-47cc-b5b9-071a9f939320"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0",
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {
+                            "annotation": {
+                                "id": 4,
+                                "output_name": "output"
                             },
-                            "tags": "",
-                            "uuid": "ee17e23b-42b1-48e8-ad5e-bcb0b7fa8cf0"
+                            "exprs_file": {
+                                "id": 3,
+                                "output_name": "output"
+                            }
                         },
-                        "tool_id": "0600e24fe786d72f",
-                        "type": "subworkflow",
-                        "uuid": "e86d6331-50b9-412a-b895-0bda5408d366",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Construct Expression Set Object",
+                                "name": "exprs_file"
+                            },
+                            {
+                                "description": "runtime parameter for tool Construct Expression Set Object",
+                                "name": "pdata_file"
+                            }
+                        ],
+                        "label": "Construct Bulk RNA ESet Object",
+                        "name": "Construct Expression Set Object",
+                        "outputs": [
+                            {
+                                "name": "out_tab",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "out_rds",
+                                "type": "rdata"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 746.3999938964844,
+                            "height": 286.3999938964844,
+                            "left": 638,
+                            "right": 838,
+                            "top": 460,
+                            "width": 200,
+                            "x": 638,
+                            "y": 460
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionout_tab": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "out_tab"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2cfd0db49bbc",
+                            "name": "music_construct_eset",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"annotation\": {\"__class__\": \"ConnectedValue\"}, \"expdata\": {\"name\": \"\", \"lab\": \"\", \"contact\": \"\", \"title\": \"\", \"abstract\": \"\", \"url\": \"\", \"other\": [{\"__index__\": 0, \"field\": \"notes\", \"comment\": \"Created in Galaxy\"}]}, \"exprs_file\": {\"__class__\": \"RuntimeValue\"}, \"metadata\": [], \"pdata_file\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.1+galaxy0",
+                        "type": "tool",
+                        "uuid": "4646fe87-4f29-48cf-b751-a1edb4e9fd7d",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "4:mapped_reads",
-                                "uuid": "0a5f54e7-09dc-4c35-980a-b617fcfaa2eb"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "7:html_report",
-                                "uuid": "fea13497-e4cb-47b1-a64d-6883e19def0f"
-                            },
+                                "output_name": "out_rds",
+                                "uuid": "f27399d6-39f8-4712-a632-ee34b891306d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3",
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {
+                            "rds_eset": {
+                                "id": 8,
+                                "output_name": "out_rds"
+                            }
+                        },
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "0:output",
-                                "uuid": "65f46424-6d76-4d1f-acd0-aef24e26d10b"
-                            },
+                                "description": "runtime parameter for tool Inspect Expression Set Object",
+                                "name": "rds_eset"
+                            }
+                        ],
+                        "label": "Extract Cell Types",
+                        "name": "Inspect Expression Set Object",
+                        "outputs": [
                             {
-                                "label": null,
-                                "output_name": "10:output",
-                                "uuid": "cc791e7c-9cbb-481d-8deb-39d33f7b2857"
-                            },
+                                "name": "out_tab",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 244.39999389648438,
+                            "height": 154.39999389648438,
+                            "left": 926,
+                            "right": 1126,
+                            "top": 90,
+                            "width": 200,
+                            "x": 926,
+                            "y": 90
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "8c64a2da3869",
+                            "name": "music_inspect_eset",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"inspector\": \"fData\", \"rds_eset\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.1+galaxy0",
+                        "type": "tool",
+                        "uuid": "04fa6a76-2262-4608-bf42-f0bd17419226",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "4:chimeric_reads",
-                                "uuid": "c6ad66bf-5fde-4440-ab54-4997211c2c3d"
-                            },
+                                "output_name": "out_tab",
+                                "uuid": "3c2f499e-2f78-4aeb-bd5b-82b4606dea16"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3",
+                        "errors": null,
+                        "id": 11,
+                        "input_connections": {
+                            "rds_eset": {
+                                "id": 8,
+                                "output_name": "out_rds"
+                            }
+                        },
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "4:reads_per_gene",
-                                "uuid": "b4ea5261-7733-4b7e-8e30-1d3535e9cb57"
-                            },
+                                "description": "runtime parameter for tool Inspect Expression Set Object",
+                                "name": "rds_eset"
+                            }
+                        ],
+                        "label": "Extract General Info",
+                        "name": "Inspect Expression Set Object",
+                        "outputs": [
                             {
-                                "label": null,
-                                "output_name": "9:out_counts",
-                                "uuid": "58562166-7b2d-4b0d-9172-14a02d7a989a"
-                            },
+                                "name": "out_tab",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 692.8999938964844,
+                            "height": 154.39999389648438,
+                            "left": 948,
+                            "right": 1148,
+                            "top": 538.5,
+                            "width": 200,
+                            "x": 948,
+                            "y": 538.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "8c64a2da3869",
+                            "name": "music_inspect_eset",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"inspector\": \"print\", \"rds_eset\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.1+galaxy0",
+                        "type": "tool",
+                        "uuid": "4a8ff055-fa99-4867-97e5-a3d1ec49b9bc",
+                        "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "4:chimeric_junctions",
-                                "uuid": "c33a7acd-f5bc-4ac5-b3d3-a6fb2892c9f6"
-                            },
+                                "label": "Inspect Expression Set Object on input dataset(s): Inspection Result",
+                                "output_name": "out_tab",
+                                "uuid": "1733593f-847d-4adb-91f4-fd78c077b074"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3",
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {
+                            "rds_eset": {
+                                "id": 9,
+                                "output_name": "out_rds"
+                            }
+                        },
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "6:output_bam",
-                                "uuid": "1601b4a1-a302-425d-bad6-7b71d14f9726"
-                            },
+                                "description": "runtime parameter for tool Inspect Expression Set Object",
+                                "name": "rds_eset"
+                            }
+                        ],
+                        "label": "Extract General Info (Bulk)",
+                        "name": "Inspect Expression Set Object",
+                        "outputs": [
                             {
-                                "label": null,
-                                "output_name": "8:out_file1",
-                                "uuid": "a7b1aa8e-61cd-4b1c-8fa9-3c85d4113ea5"
-                            },
+                                "name": "out_tab",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 861.3999938964844,
+                            "height": 154.39999389648438,
+                            "left": 945,
+                            "right": 1145,
+                            "top": 707,
+                            "width": 200,
+                            "x": 945,
+                            "y": 707
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "8c64a2da3869",
+                            "name": "music_inspect_eset",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"inspector\": \"print\", \"rds_eset\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.1+galaxy0",
+                        "type": "tool",
+                        "uuid": "83ae4dc4-ff8a-4df7-8d47-c52e4f79c97f",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "7:stats",
-                                "uuid": "ac17c572-784c-456e-b3c7-ebaf15c2109e"
+                                "output_name": "out_tab",
+                                "uuid": "d2312cc5-cea1-4f07-a0cf-0574a0923c28"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3",
+                        "errors": null,
+                        "id": 13,
+                        "input_connections": {
+                            "bulk_eset": {
+                                "id": 9,
+                                "output_name": "out_rds"
                             },
-                            {
-                                "label": null,
-                                "output_name": "5:output",
-                                "uuid": "5c220f46-2525-471f-8fd6-0eb17dc689ad"
+                            "do|celltypes": {
+                                "id": 5,
+                                "output_name": "output"
                             },
+                            "scrna_eset": {
+                                "id": 8,
+                                "output_name": "out_rds"
+                            }
+                        },
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "7:log",
-                                "uuid": "3ad7aac8-e4a0-4df1-beb6-88cdcb106e7a"
+                                "description": "runtime parameter for tool MuSiC",
+                                "name": "bulk_eset"
                             },
                             {
-                                "label": null,
-                                "output_name": "3:out2",
-                                "uuid": "4ff34341-786c-4c66-95c7-6985e4c66ad7"
-                            },
+                                "description": "runtime parameter for tool MuSiC",
+                                "name": "scrna_eset"
+                            }
+                        ],
+                        "label": "Music: Estimate Cell Proportions",
+                        "name": "MuSiC",
+                        "outputs": [
                             {
-                                "label": null,
-                                "output_name": "1:output",
-                                "uuid": "78bfe4ce-528c-4d16-8e73-f721b09676be"
+                                "name": "summaries",
+                                "type": "input"
                             },
                             {
-                                "label": null,
-                                "output_name": "2:output",
-                                "uuid": "603d0608-7866-4f1d-be85-6a4f3116d5b8"
-                            },
+                                "name": "out_pdf",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 536.3999938964844,
+                            "height": 286.3999938964844,
+                            "left": 1325,
+                            "right": 1525,
+                            "top": 250,
+                            "width": 200,
+                            "x": 1325,
+                            "y": 250
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "56371b5a2da9",
+                            "name": "music_deconvolution",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"bulk_eset\": {\"__class__\": \"RuntimeValue\"}, \"do\": {\"method\": \"estimateprops\", \"__current_case__\": 0, \"celltypes_label\": \"cellType\", \"samples_label\": \"sampleID\", \"celltypes\": {\"__class__\": \"ConnectedValue\"}, \"methods\": [\"MuSiC\", \"NNLS\"], \"phenotype_factors\": \"\", \"phenotype_gene\": \"\", \"sample_groups\": \"\", \"sample_disease_group\": \"\", \"sample_disease_group_scale\": \"5\", \"healthy_phenotype\": \"\", \"compare_title\": \"\"}, \"scrna_eset\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.1+galaxy0",
+                        "type": "tool",
+                        "uuid": "d5ff6923-3386-4407-8c50-0ec641a7fe0e",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "4:splice_junctions",
-                                "uuid": "7f85f228-75da-4933-8157-e6eb4f15bd98"
+                                "output_name": "summaries",
+                                "uuid": "ff64eeaa-56f4-4ef0-b458-5cf7c402ff84"
                             },
                             {
                                 "label": null,
-                                "output_name": "4:output_log",
-                                "uuid": "86003cab-1a90-4871-b489-27eb49715574"
+                                "output_name": "out_pdf",
+                                "uuid": "30e55eec-e403-4b10-a62c-5a503be0fb9f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3",
                         "errors": null,
-                        "id": 5,
+                        "id": 14,
                         "input_connections": {
-                            "input_tabular": {
-                                "id": 4,
-                                "output_name": "9:out_counts"
+                            "bulk_eset": {
+                                "id": 9,
+                                "output_name": "out_rds"
+                            },
+                            "do|cluster_groups_0|marker_list": {
+                                "id": 6,
+                                "output_name": "output"
+                            },
+                            "do|cluster_groups_1|marker_list": {
+                                "id": 7,
+                                "output_name": "output"
+                            },
+                            "scrna_eset": {
+                                "id": 8,
+                                "output_name": "out_rds"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Column Join",
-                                "name": "input_tabular"
+                                "description": "runtime parameter for tool MuSiC",
+                                "name": "bulk_eset"
+                            },
+                            {
+                                "description": "runtime parameter for tool MuSiC",
+                                "name": "scrna_eset"
                             }
                         ],
-                        "label": null,
-                        "name": "Column Join",
+                        "label": "Music: Compute Dendrogram",
+                        "name": "MuSiC",
                         "outputs": [
                             {
-                                "name": "tabular_output",
-                                "type": "tabular"
+                                "name": "out_pdf",
+                                "type": "pdf"
                             },
                             {
-                                "name": "script_output",
-                                "type": "txt"
+                                "name": "out_tab",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1277.5,
-                            "top": 288
+                            "bottom": 898.7000122070312,
+                            "height": 337.20001220703125,
+                            "left": 1333,
+                            "right": 1533,
+                            "top": 561.5,
+                            "width": 200,
+                            "x": 1333,
+                            "y": 561.5
                         },
                         "post_job_actions": {
-                            "HideDatasetActionscript_output": {
+                            "HideDatasetActionout_tab": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "script_output"
+                                "output_name": "out_tab"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3",
                         "tool_shed_repository": {
-                            "changeset_revision": "58228a4d58fe",
-                            "name": "collection_column_join",
-                            "owner": "iuc",
+                            "changeset_revision": "56371b5a2da9",
+                            "name": "music_deconvolution",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"identifier_column\": \"\\\"1\\\"\", \"include_outputs\": \"null\", \"__rerun_remap_job_id__\": null, \"input_tabular\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"fill_char\": \"\\\".\\\"\", \"old_col_in_header\": \"\\\"true\\\"\", \"has_header\": \"\\\"1\\\"\"}",
-                        "tool_version": "0.0.3",
+                        "tool_state": "{\"bulk_eset\": {\"__class__\": \"RuntimeValue\"}, \"do\": {\"method\": \"dendrogram\", \"__current_case__\": 1, \"celltypes_label\": \"cellType\", \"clustertype_label\": \"clusterType\", \"samples_label\": \"sampleID\", \"celltypes\": \"\", \"cluster_groups\": [{\"__index__\": 0, \"cluster_id\": \"C1\", \"celltypes\": \"\", \"marker_name\": \"\", \"marker_list\": {\"__class__\": \"RuntimeValue\"}}, {\"__index__\": 1, \"cluster_id\": \"C2\", \"celltypes\": \"\", \"marker_name\": \"\", \"marker_list\": {\"__class__\": \"RuntimeValue\"}}]}, \"scrna_eset\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.1+galaxy0",
                         "type": "tool",
-                        "uuid": "174c32b6-444c-4762-b9c1-c84201e656ab",
+                        "uuid": "86a3a936-ef2a-4eee-80e9-63f247463719",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "tabular_output",
-                                "uuid": "2167fa1b-4865-40b1-9c61-82dd6ba8ccc7"
+                                "label": "MuSiC on input dataset(s): PDF Plots",
+                                "output_name": "out_pdf",
+                                "uuid": "df2e83a5-ac67-460f-8b0f-ac3f3b63280f"
                             }
                         ]
                     }
                 ],
-                "parent_id": "single-cell/scrna-preprocessing",
-                "path": "topics/single-cell/tutorials/scrna-preprocessing/workflows/scrna_mp_celseq.ga",
-                "tags": [
-                    "transcriptomics"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "CelSeq2: Multi Batch (mm10)",
-                "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-preprocessing/versions/scrna-mp-celseq",
-                "tutorial_id": "scrna-preprocessing",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-preprocessing/workflows/scrna_mp_celseq.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-preprocessing/workflows/scrna_mp_celseq.html",
-                "version": 1,
-                "wfid": "single-cell-scrna-preprocessing",
-                "wfname": "scrna-mp-celseq",
-                "workflow": "scrna_mp_celseq.ga",
-                "workflow_tools": [
-                    "__FLATTEN__",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2"
-                ],
-                "workflowhub_id": "1218"
-            },
-            {
-                "creators": [],
-                "description": "Pre-processing of Single-Cell RNA Data",
+                "parent_id": "single-cell/bulk-music",
+                "path": "topics/single-cell/tutorials/bulk-music/workflows/main_workflow.ga",
+                "tags": [
+                    "transcriptomics",
+                    "single-cell"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "MuSiC Workflow",
+                "topic_id": "single-cell",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-bulk-music/versions/main-workflow",
+                "tutorial_id": "bulk-music",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music/workflows/main_workflow.html",
+                "version": 2,
+                "wfid": "single-cell-bulk-music",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3"
+                ],
+                "workflowhub_id": "1234"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/5719228"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "scater_create_qcmetric_ready_sce",
+                    "owner": "iuc",
+                    "revisions": "fd808de478b1",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scater_filter",
+                    "owner": "iuc",
+                    "revisions": "b7ea9f09c02f",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scater_plot_dist_scatter",
+                    "owner": "iuc",
+                    "revisions": "2e41b35b5bdd",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scater_plot_pca",
+                    "owner": "iuc",
+                    "revisions": "46fc6751d746",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: scater_create_qcmetric_ready_sce\n  owner: iuc\n  revisions: fd808de478b1\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scater_filter\n  owner: iuc\n  revisions: b7ea9f09c02f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scater_plot_dist_scatter\n  owner: iuc\n  revisions: 2e41b35b5bdd\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scater_plot_pca\n  owner: iuc\n  revisions: 46fc6751d746\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-scater-qc/tutorial.json",
+        "contributors": [
+            {
+                "id": "ethering",
+                "joined": "2019-10",
+                "name": "Graham Etherington",
+                "orcid": "0000-0002-5003-1425",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ethering/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/ethering.json"
+            },
+            {
+                "affiliations": [
+                    "earlham",
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "fediverse": "https://mstdn.science/@nsoranzo",
+                "fediverse_flavor": "mastodon",
+                "id": "nsoranzo",
+                "joined": "2017-09",
+                "linkedin": "nicola-soranzo-7884125",
+                "matrix": "nsoranzo:matrix.org",
+                "name": "Nicola Soranzo",
+                "orcid": "0000-0003-3627-5340",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
+                "twitter": "NicolaSoranzo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
+            }
+        ],
+        "dir": "topics/single-cell/tutorials/scrna-scater-qc",
+        "edam_operation": [
+            "Sequence visualisation",
+            "Sequencing quality control",
+            "Read pre-processing"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.eu",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-raceid"
+                ],
+                "type": "internal"
+            }
+        ],
+        "gitter": "Galaxy-Training-Network/galaxy-single-cell",
+        "hands_on": true,
+        "id": "single-cell/scrna-scater-qc",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Single-cell RNA-seq data is often noisy",
+            "scater can be used to apply the visualise-filter-visualise paradigm of quality control"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": [
+            "Examine scRNA-seq data for low-quality cells",
+            "Visualise data with various types of plots",
+            "Filtering low-quality cells with the appropriate approach"
+        ],
+        "pageviews": 645,
+        "priority": 1,
+        "pub_date": "2019-10-23",
+        "questions": [
+            "How to ensure the quality of single-cell RNA-seq data?",
+            "What are the confounding factors that may affect the interpretation of downstream analyses?"
+        ],
+        "redirect_from": [
+            "/topics/transcriptomics/tutorials/scrna-scater-qc/tutorial",
+            "/short/single-cell/scrna-scater-qc",
+            "/short/T00255"
+        ],
+        "requirements": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-plates-batches-barcodes"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00255",
+        "short_tools": [
+            "scater_create_qcmetric_ready_sce",
+            "scater_filter",
+            "scater_plot_pca",
+            "scater_plot_dist_scatter"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "tricks",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": null,
+        "time_estimation": "1H",
+        "title": "Single-cell quality control with scater",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.12.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.12.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.12.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.12.2"
+        ],
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "scrna-scater-qc",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-scater-qc/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-scater-qc/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-scater-qc/tutorial.json"
+        },
+        "version": 4,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 44,
+        "visitors": 565,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Single-cell quality control with scater",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nannotation.txt\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncounts.txt\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmt_controls.txt\"]\n  3[label=\"Scater: Calculate QC metrics\"]\n  0 -> 3 [label=\"output\"]\n  1 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Scater: plot library QC\"]\n  3 -> 4 [label=\"output_loom\"]\n  5[label=\"Scater: filter SCE\"]\n  3 -> 5 [label=\"output_loom\"]\n  6[label=\"Scater: plot library QC\"]\n  5 -> 6 [label=\"output_loom\"]\n  7[label=\"Scater: PCA plot\"]\n  5 -> 7 [label=\"output_loom\"]\n}",
+                "history": [
+                    {
+                        "hash": "327fd2b842f45de3dc2a30067714352675ad69ae",
+                        "message": "Making a single cell topics",
+                        "num": 1,
+                        "short_hash": "327fd2b84",
+                        "unix": "1668273265"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "annotation.txt"
+                            }
+                        ],
+                        "label": "annotation.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 200
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"annotation.txt\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "3575b170-465d-4e4a-bae1-ff4c1efa142a",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "counts.txt"
+                            }
+                        ],
+                        "label": "counts.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 320
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"counts.txt\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "03bc455e-52cc-4a2e-9a00-049f0fab721f",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "mt_controls.txt"
+                            }
+                        ],
+                        "label": "mt_controls.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 440
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"mt_controls.txt\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "f59c9ecb-0d03-4e93-8f46-5d3ed1b75aea",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nannotation.txt\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ncounts.txt\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nmt_controls.txt\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Scater: Calculate QC metrics\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  2 -->|output| 3;\n  4[\"Scater: plot library QC\"];\n  3 -->|output_loom| 4;\n  5[\"Scater: filter SCE\"];\n  3 -->|output_loom| 5;\n  6[\"Scater: plot library QC\"];\n  5 -->|output_loom| 6;\n  7[\"Scater: PCA plot\"];\n  5 -->|output_loom| 7;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "Scater",
+                "outputs": [],
+                "parent_id": "single-cell/scrna-scater-qc",
+                "path": "topics/single-cell/tutorials/scrna-scater-qc/workflows/main_workflow.ga",
+                "tags": [
+                    "transcriptomics"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Scater",
+                "topic_id": "single-cell",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-scater-qc/versions/main-workflow",
+                "tutorial_id": "scrna-scater-qc",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-scater-qc/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-scater-qc/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "single-cell-scrna-scater-qc",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.12.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.12.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.12.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.12.2"
+                ],
+                "workflowhub_id": "1241"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/3386291"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "alevin",
+                    "owner": "bgruening",
+                    "revisions": "e32b215b7c04",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "droplet_barcode_plot",
+                    "owner": "ebi-gxa",
+                    "revisions": "8f605643ccfd",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "dropletutils_empty_drops",
+                    "owner": "ebi-gxa",
+                    "revisions": "fa662ca7ae7f",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "dropletutils_read_10x",
+                    "owner": "ebi-gxa",
+                    "revisions": "ca62f52e0d7f",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "gtf2gene_list",
+                    "owner": "ebi-gxa",
+                    "revisions": "14b3f2a4523b",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "salmon_kallisto_mtx_to_10x",
+                    "owner": "ebi-gxa",
+                    "revisions": "88f5a0a6a818",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sceasy_convert",
+                    "owner": "iuc",
+                    "revisions": "2062be7efc84",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: alevin\n  owner: bgruening\n  revisions: e32b215b7c04\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: droplet_barcode_plot\n  owner: ebi-gxa\n  revisions: 8f605643ccfd\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dropletutils_empty_drops\n  owner: ebi-gxa\n  revisions: fa662ca7ae7f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dropletutils_read_10x\n  owner: ebi-gxa\n  revisions: ca62f52e0d7f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gtf2gene_list\n  owner: ebi-gxa\n  revisions: 14b3f2a4523b\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: salmon_kallisto_mtx_to_10x\n  owner: ebi-gxa\n  revisions: 88f5a0a6a818\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sceasy_convert\n  owner: iuc\n  revisions: 2062be7efc84\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "answer_histories": [
+            {
+                "date": "2024-03-22",
+                "history": "https://usegalaxy.eu/u/j.jakiela/h/generating-a-single-cell-matrix-alevin",
+                "label": "UseGalaxy.eu"
+            },
+            {
+                "date": "2024-01-01",
+                "history": "https://humancellatlas.usegalaxy.eu/u/wendi.bacon.training/h/cs1pre-processing-with-alevin---answer-key",
+                "label": "Older Alevin version"
+            }
+        ],
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_alevin/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "nomadscientist",
+                "pinin4fjords"
+            ],
+            "editing": [
+                "hexylena"
+            ],
+            "testing": [
+                "wee-snufkin"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "bio": "Senior Lecturer at The Open University",
+                "elixir_node": "uk",
+                "email": "wendi.bacon@open.ac.uk",
+                "fediverse": "https://mstdn.science/@wendibacon1",
+                "fediverse_flavor": "mastodon",
+                "id": "nomadscientist",
+                "joined": "2020-03",
+                "matrix": "nomadscientist:matrix.org",
+                "name": "Wendi Bacon",
+                "orcid": "0000-0002-8170-8806",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
+                "twitter": "WendiBacon1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+            },
+            {
+                "email": "jmanning@ebi.ac.uk",
+                "id": "pinin4fjords",
+                "joined": "2021-02",
+                "name": "Jonathan Manning",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pinin4fjords/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pinin4fjords.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "elixir_node": "uk",
+                "email": "juliajot36@gmail.com",
+                "id": "wee-snufkin",
+                "joined": "2022-06",
+                "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
+            }
+        ],
+        "dir": "topics/single-cell/tutorials/scrna-case_alevin",
+        "edam_operation": [
+            "Gene expression analysis",
+            "RNA-Seq quantification",
+            "Sequence composition calculation"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-case_alevin-combine-datasets"
+                ],
+                "type": "internal"
+            }
+        ],
+        "gitter": "Galaxy-Training-Network/galaxy-single-cell",
+        "hands_on": true,
+        "id": "single-cell/scrna-case_alevin",
+        "inexact_supported_servers": [],
+        "input_histories": [
+            {
+                "history": "https://humancellatlas.usegalaxy.eu/u/wendi.bacon.training/h/cs1pre-processing-with-alevin---input-1",
+                "label": "UseGalaxy.eu"
+            }
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Create a scanpy-accessible AnnData object from FASTQ files, including relevant gene metadata"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-14",
+        "objectives": [
+            "Generate a cellxgene matrix for droplet-based single cell sequencing data",
+            "Interpret quality control (QC) plots to make informed decisions on cell thresholds",
+            "Find relevant information in GTF files for the particulars of their study, and include this in data matrix metadata"
+        ],
+        "pageviews": 4069,
+        "priority": 1,
+        "pub_date": "2021-03-03",
+        "questions": [
+            "I have some single cell FASTQ files I want to analyse. Where do I start?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "nomadscientist"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "30M",
+                "speakers": [
+                    "nomadscientist"
+                ],
+                "youtube_id": "3ytm2AU6QUc"
+            }
+        ],
+        "redirect_from": [
+            "/topics/transcriptomics/tutorials/droplet-quantification-preprocessing/tutorial",
+            "/topics/transcriptomics/tutorials/scrna-case_alevin/tutorial",
+            "/short/single-cell/scrna-case_alevin",
+            "/short/T00245"
+        ],
+        "requirements": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-intro",
+                    "scrna-umis"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00245",
+        "short_tools": [
+            "join1",
+            "alevin",
+            "dropletutils_read_10x",
+            "dropletutils_empty_drops",
+            "_dropletBarcodePlot",
+            "_ensembl_gtf2gene_list",
+            "Cut1",
+            "sceasy_convert",
+            "_salmon_kallisto_mtx_to_10x"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "single-cell-CS",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "10x",
+            "paper-replication"
+        ],
+        "time_estimation": "2H",
+        "title": "Generating a single cell matrix using Alevin",
+        "tools": [
+            "Cut1",
+            "join1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x/0.0.1+galaxy6",
+            "toolshed.g2.bx.psu.edu/repos/iuc/sceasy_convert/sceasy_convert/0.0.7+galaxy2"
+        ],
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "scrna-case_alevin",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_alevin/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_alevin/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_alevin/tutorial.json"
+        },
+        "version": 17,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 202,
+        "visitors": 2590,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0009-0001-2017-8805",
+                        "name": "Julia Jakiela"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-8170-8806",
+                        "name": "Wendi Bacon"
+                    }
+                ],
+                "description": "This workflow generates a single cell matrix using Alevin. ",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nBatch\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBarcodes single-col\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGTF file UCSC\"]\n  3[label=\"UMI-tools extract\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Alignment Choose a Genome\"]\n  2 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"out2\"]\n  5[label=\"Filter\"]\n  4 -> 5 [label=\"mapped_reads\"]\n  6[label=\"featureCounts\"]\n  5 -> 6 [label=\"out_file1\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"UMI-tools count\"]\n  6 -> 7 [label=\"output_bam\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGTF file\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference FASTA\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nRead 1 - containing cell barcode & UMI\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nRead 2 - containing transcript\"]\n  4[label=\"GTF2GeneList\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Transcript-gene mapping\"]\n  1 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  k773cb4ae56c349c0b582ee69d620def3[color=lightseagreen,label=\"Output\\nfasta_output\"]\n  5 -> k773cb4ae56c349c0b582ee69d620def3\n  ka30424b51ddc43249ff6dc5883adcce0[color=lightseagreen,label=\"Output\\nfeature_annotation\"]\n  5 -> ka30424b51ddc43249ff6dc5883adcce0\n  6[label=\"Alevin Processed\"]\n  2 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  5 -> 6 [label=\"fasta_output\"]\n  1 -> 6 [label=\"output\"]\n  5 -> 6 [label=\"feature_annotation\"]\n  ka87beb551baf458ebd09bb5ac6ea6e9a[color=lightseagreen,label=\"Output\\nraw_cb_frequency_txt\"]\n  6 -> ka87beb551baf458ebd09bb5ac6ea6e9a\n  kc9390a50775c4f0f88e50984d570902c[color=lightseagreen,label=\"Output\\nsalmon_quant_log\"]\n  6 -> kc9390a50775c4f0f88e50984d570902c\n  k2cebc438ddc041e089ba49b4bd3e2160[color=lightseagreen,label=\"Output\\nquants_mat_mtx\"]\n  6 -> k2cebc438ddc041e089ba49b4bd3e2160\n  k89fa1aad9ec6435197d5f05cac09e08e[color=lightseagreen,label=\"Output\\nquants_mat_cols_txt\"]\n  6 -> k89fa1aad9ec6435197d5f05cac09e08e\n  k3b3dda805d354c519ca090a2f909755f[color=lightseagreen,label=\"Output\\nquants_mat_rows_txt\"]\n  6 -> k3b3dda805d354c519ca090a2f909755f\n  7[label=\"Alevin - no processing\"]\n  2 -> 7 [label=\"output\"]\n  3 -> 7 [label=\"output\"]\n  5 -> 7 [label=\"fasta_output\"]\n  1 -> 7 [label=\"output\"]\n  5 -> 7 [label=\"feature_annotation\"]\n  k25d4d8f6d166447080fed0fdb0702371[color=lightseagreen,label=\"Output\\nquants_mat_rows_txt_1\"]\n  7 -> k25d4d8f6d166447080fed0fdb0702371\n  kd9ed1457792b4eafa9fc2407bcd90da7[color=lightseagreen,label=\"Output\\nquants_mat_mtx_1\"]\n  7 -> kd9ed1457792b4eafa9fc2407bcd90da7\n  k40df6aa83dfa4946bbc8cacf4ca2a20e[color=lightseagreen,label=\"Output\\nquants_mat_cols_txt_1\"]\n  7 -> k40df6aa83dfa4946bbc8cacf4ca2a20e\n  8[label=\"Droplet rank plot - raw barcodes\"]\n  6 -> 8 [label=\"raw_cb_frequency_txt\"]\n  9[label=\"Droplet rank plot - Alevin barcodes\"]\n  6 -> 9 [label=\"quants_mat_mtx\"]\n  10[label=\"salmonKallistoMtxTo10x\"]\n  7 -> 10 [label=\"quants_mat_rows_txt\"]\n  7 -> 10 [label=\"quants_mat_cols_txt\"]\n  7 -> 10 [label=\"quants_mat_mtx\"]\n  11[label=\"Join two Datasets\"]\n  10 -> 11 [label=\"genes_out\"]\n  4 -> 11 [label=\"feature_annotation\"]\n  12[label=\"Cut\"]\n  11 -> 12 [label=\"out_file1\"]\n  13[label=\"DropletUtils Read10x\"]\n  10 -> 13 [label=\"barcodes_out\"]\n  12 -> 13 [label=\"out_file1\"]\n  10 -> 13 [label=\"matrix_out\"]\n  14[label=\"DropletUtils emptyDrops\"]\n  13 -> 14 [label=\"output_rds\"]\n  15[label=\"SCEasy Converter\"]\n  14 -> 15 [label=\"output_rdata\"]\n}",
                 "history": [
+                    {
+                        "hash": "927da941a1ce7627ff0d5d5635d74cfa8abdff1f",
+                        "message": "add workflow tests",
+                        "num": 2,
+                        "short_hash": "927da941a",
+                        "unix": "1711095976"
+                    },
                     {
                         "hash": "327fd2b842f45de3dc2a30067714352675ad69ae",
                         "message": "Making a single cell topics",
@@ -216994,546 +221498,1015 @@
                 ],
                 "inputs": [
                     {
-                        "annotation": "",
+                        "annotation": "You can find the file containing the gene information for your species here: \nhttp://www.ensembl.org/info/data/ftp/index.html/",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "Batch",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 286,
-                            "top": 293.9166717529297
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"paired\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "c451df86-a25e-409c-9f2e-33c22a0f1bb9",
-                        "workflow_outputs": [
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "d46989fb-ef46-4506-8932-d66cee38e62a"
+                                "description": "You can find the file containing the gene information for your species here: \nhttp://www.ensembl.org/info/data/ftp/index.html/",
+                                "name": "GTF file"
                             }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "Barcodes (single-col)",
+                        ],
+                        "label": "GTF file",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 302.5,
-                            "top": 375
+                            "left": 58.60616823526459,
+                            "top": 88.90721532236475
                         },
                         "tool_id": null,
-                        "tool_state": "{}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "4ac7860e-01d4-4009-b1fd-899fab778eb5",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "2c66b77f-5ee0-4991-971c-3c43d8e7841d"
-                            }
-                        ]
+                        "uuid": "09e96b1f-f0e5-4e1a-b418-cd4ecc706e35",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "You can find this file for your species here: http://www.ensembl.org/info/data/ftp/index.html/",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 1,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "GTF file (UCSC)",
+                        "inputs": [
+                            {
+                                "description": "You can find this file for your species here: http://www.ensembl.org/info/data/ftp/index.html/",
+                                "name": "Reference FASTA"
+                            }
+                        ],
+                        "label": "Reference FASTA",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 313.5,
-                            "top": 651.9166717529297
+                            "left": 83.54487198456434,
+                            "top": 288.0815521308393
                         },
                         "tool_id": null,
-                        "tool_state": "{}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "0455bae6-58da-4ec3-9688-72aba9f676fe",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "7ca9e0df-159c-43f7-a0b3-e546fcd9b2c9"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nBatch\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nBarcodes single-col\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nGTF file UCSC\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"UMI-tools extract\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  4[\"Alignment Choose a Genome\"];\n  2 -->|output| 4;\n  3 -->|out2| 4;\n  5[\"Filter\"];\n  4 -->|mapped_reads| 5;\n  6[\"featureCounts\"];\n  5 -->|out_file1| 6;\n  2 -->|output| 6;\n  7[\"UMI-tools count\"];\n  6 -->|output_bam| 7;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "CelSeq2: Single Batch (mm10)",
-                "outputs": [
+                        "uuid": "43c0a6ac-36dc-4b35-9bca-83063de43a8a",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
                     {
-                        "annotation": "",
+                        "annotation": "This should be a fast file containing the shorter read - i.e. the cell barcode and the unique molecular identifier",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 2,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "Batch",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 286,
-                            "top": 293.9166717529297
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"paired\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "c451df86-a25e-409c-9f2e-33c22a0f1bb9",
-                        "workflow_outputs": [
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "d46989fb-ef46-4506-8932-d66cee38e62a"
+                                "description": "This should be a fast file containing the shorter read - i.e. the cell barcode and the unique molecular identifier",
+                                "name": "Read 1 - containing cell barcode & UMI"
                             }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "Barcodes (single-col)",
+                        ],
+                        "label": "Read 1 - containing cell barcode & UMI",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 302.5,
-                            "top": 375
+                            "left": 0.18723338168473447,
+                            "top": 439.63352912048805
                         },
                         "tool_id": null,
-                        "tool_state": "{}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "4ac7860e-01d4-4009-b1fd-899fab778eb5",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "2c66b77f-5ee0-4991-971c-3c43d8e7841d"
-                            }
-                        ]
+                        "uuid": "ed68f7dd-faa4-453e-9050-8fbfb0027928",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "This should be the read containing the transcript",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 3,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "GTF file (UCSC)",
+                        "inputs": [
+                            {
+                                "description": "This should be the read containing the transcript",
+                                "name": "Read 2 - containing transcript"
+                            }
+                        ],
+                        "label": "Read 2 - containing transcript",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 313.5,
-                            "top": 651.9166717529297
+                            "left": 0,
+                            "top": 611.9759545962928
                         },
                         "tool_id": null,
-                        "tool_state": "{}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "0455bae6-58da-4ec3-9688-72aba9f676fe",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "7ca9e0df-159c-43f7-a0b3-e546fcd9b2c9"
-                            }
-                        ]
-                    },
+                        "uuid": "508c574e-8ca2-46b0-b753-b96c5b797fd2",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGTF file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference FASTA\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nRead 1 - containing cell barcode & UMI\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nRead 2 - containing transcript\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"GTF2GeneList\"];\n  0 -->|output| 4;\n  5[\"Transcript-gene mapping\"];\n  1 -->|output| 5;\n  0 -->|output| 5;\n  773cb4ae-56c3-49c0-b582-ee69d620def3[\"Output\\nfasta_output\"];\n  5 --> 773cb4ae-56c3-49c0-b582-ee69d620def3;\n  style 773cb4ae-56c3-49c0-b582-ee69d620def3 stroke:#2c3143,stroke-width:4px;\n  a30424b5-1ddc-4324-9ff6-dc5883adcce0[\"Output\\nfeature_annotation\"];\n  5 --> a30424b5-1ddc-4324-9ff6-dc5883adcce0;\n  style a30424b5-1ddc-4324-9ff6-dc5883adcce0 stroke:#2c3143,stroke-width:4px;\n  6[\"Alevin Processed\"];\n  2 -->|output| 6;\n  3 -->|output| 6;\n  5 -->|fasta_output| 6;\n  1 -->|output| 6;\n  5 -->|feature_annotation| 6;\n  a87beb55-1baf-458e-bd09-bb5ac6ea6e9a[\"Output\\nraw_cb_frequency_txt\"];\n  6 --> a87beb55-1baf-458e-bd09-bb5ac6ea6e9a;\n  style a87beb55-1baf-458e-bd09-bb5ac6ea6e9a stroke:#2c3143,stroke-width:4px;\n  c9390a50-775c-4f0f-88e5-0984d570902c[\"Output\\nsalmon_quant_log\"];\n  6 --> c9390a50-775c-4f0f-88e5-0984d570902c;\n  style c9390a50-775c-4f0f-88e5-0984d570902c stroke:#2c3143,stroke-width:4px;\n  2cebc438-ddc0-41e0-89ba-49b4bd3e2160[\"Output\\nquants_mat_mtx\"];\n  6 --> 2cebc438-ddc0-41e0-89ba-49b4bd3e2160;\n  style 2cebc438-ddc0-41e0-89ba-49b4bd3e2160 stroke:#2c3143,stroke-width:4px;\n  89fa1aad-9ec6-4351-97d5-f05cac09e08e[\"Output\\nquants_mat_cols_txt\"];\n  6 --> 89fa1aad-9ec6-4351-97d5-f05cac09e08e;\n  style 89fa1aad-9ec6-4351-97d5-f05cac09e08e stroke:#2c3143,stroke-width:4px;\n  3b3dda80-5d35-4c51-9ca0-90a2f909755f[\"Output\\nquants_mat_rows_txt\"];\n  6 --> 3b3dda80-5d35-4c51-9ca0-90a2f909755f;\n  style 3b3dda80-5d35-4c51-9ca0-90a2f909755f stroke:#2c3143,stroke-width:4px;\n  7[\"Alevin - no processing\"];\n  2 -->|output| 7;\n  3 -->|output| 7;\n  5 -->|fasta_output| 7;\n  1 -->|output| 7;\n  5 -->|feature_annotation| 7;\n  25d4d8f6-d166-4470-80fe-d0fdb0702371[\"Output\\nquants_mat_rows_txt_1\"];\n  7 --> 25d4d8f6-d166-4470-80fe-d0fdb0702371;\n  style 25d4d8f6-d166-4470-80fe-d0fdb0702371 stroke:#2c3143,stroke-width:4px;\n  d9ed1457-792b-4eaf-a9fc-2407bcd90da7[\"Output\\nquants_mat_mtx_1\"];\n  7 --> d9ed1457-792b-4eaf-a9fc-2407bcd90da7;\n  style d9ed1457-792b-4eaf-a9fc-2407bcd90da7 stroke:#2c3143,stroke-width:4px;\n  40df6aa8-3dfa-4946-bbc8-cacf4ca2a20e[\"Output\\nquants_mat_cols_txt_1\"];\n  7 --> 40df6aa8-3dfa-4946-bbc8-cacf4ca2a20e;\n  style 40df6aa8-3dfa-4946-bbc8-cacf4ca2a20e stroke:#2c3143,stroke-width:4px;\n  8[\"Droplet rank plot - raw barcodes\"];\n  6 -->|raw_cb_frequency_txt| 8;\n  9[\"Droplet rank plot - Alevin barcodes\"];\n  6 -->|quants_mat_mtx| 9;\n  10[\"salmonKallistoMtxTo10x\"];\n  7 -->|quants_mat_rows_txt| 10;\n  7 -->|quants_mat_cols_txt| 10;\n  7 -->|quants_mat_mtx| 10;\n  11[\"Join two Datasets\"];\n  10 -->|genes_out| 11;\n  4 -->|feature_annotation| 11;\n  12[\"Cut\"];\n  11 -->|out_file1| 12;\n  13[\"DropletUtils Read10x\"];\n  10 -->|barcodes_out| 13;\n  12 -->|out_file1| 13;\n  10 -->|matrix_out| 13;\n  14[\"DropletUtils emptyDrops\"];\n  13 -->|output_rds| 14;\n  15[\"SCEasy Converter\"];\n  14 -->|output_rdata| 15;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "Generating a single cell matrix using Alevin",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0",
                         "errors": null,
-                        "id": 3,
+                        "id": 5,
                         "input_connections": {
-                            "barcodes|filter_barcode_file": {
+                            "cdnas|fasta_input": {
                                 "id": 1,
                                 "output_name": "output"
                             },
-                            "input_type|input_readpair": {
+                            "gtf_input": {
                                 "id": 0,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool UMI-tools extract",
-                                "name": "input_type"
-                            },
-                            {
-                                "description": "runtime parameter for tool UMI-tools extract",
-                                "name": "barcodes"
-                            }
-                        ],
-                        "label": null,
-                        "name": "UMI-tools extract",
+                        "inputs": [],
+                        "label": "Transcript-gene mapping",
+                        "name": "GTF2GeneList",
                         "outputs": [
                             {
-                                "name": "out",
-                                "type": "input"
-                            },
-                            {
-                                "name": "out1",
-                                "type": "input"
-                            },
-                            {
-                                "name": "out2",
-                                "type": "input"
+                                "name": "feature_annotation",
+                                "type": "tsv"
                             },
                             {
-                                "name": "out_log",
-                                "type": "txt"
+                                "name": "fasta_output",
+                                "type": "fasta.gz"
                             }
                         ],
                         "position": {
-                            "left": 554.5,
-                            "top": 292.9166717529297
+                            "left": 374.4625157115551,
+                            "top": 351.46516186147346
                         },
                         "post_job_actions": {
-                            "HideDatasetActionout": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "out"
-                            },
-                            "HideDatasetActionout1": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "out1"
+                            "RenameDatasetActionfasta_output": {
+                                "action_arguments": {
+                                    "newname": "Filtered fasta"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "fasta_output"
                             },
-                            "HideDatasetActionout_log": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "out_log"
+                            "RenameDatasetActionfeature_annotation": {
+                                "action_arguments": {
+                                    "newname": "Map"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "feature_annotation"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "99aea37a7ff7",
-                            "name": "umi_tools_extract",
-                            "owner": "iuc",
+                            "changeset_revision": "14b3f2a4523b",
+                            "name": "gtf2gene_list",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"extract_method\": \"\\\"string\\\"\", \"input_type\": \"{\\\"input_readpair\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"barcode\\\": {\\\"barcode_select\\\": \\\"first_read_only\\\", \\\"__current_case__\\\": 0}, \\\"type\\\": \\\"paired_collection\\\", \\\"__current_case__\\\": 2}\", \"__rerun_remap_job_id__\": null, \"bc_pattern\": \"\\\"NNNNNNCCCCCC\\\"\", \"print_log\": \"\\\"true\\\"\", \"prime3\": \"\\\"true\\\"\", \"quality\": \"{\\\"quality_selector\\\": \\\"false\\\", \\\"__current_case__\\\": 0}\", \"barcodes\": \"{\\\"filter_correct\\\": \\\"false\\\", \\\"filter_barcode_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"use_barcodes\\\": \\\"yes\\\"}\"}",
-                        "tool_version": "0.5.3.2",
+                        "tool_state": "{\"__input_ext\": \"input\", \"cdnas\": {\"parse_cdnas\": true, \"__current_case__\": 0, \"fasta_input\": {\"__class__\": \"ConnectedValue\"}, \"cdnas_field\": \"transcript_id\", \"parse_cdna_names\": false, \"filter_cdnas\": true}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"feature_type\": \"transcript\", \"fields\": \"transcript_id,gene_id\", \"fill_empty\": \"\", \"first_field\": \"transcript_id\", \"gtf_input\": {\"__class__\": \"ConnectedValue\"}, \"mito\": {\"mark_mito\": false, \"__current_case__\": 1}, \"noheader\": true, \"version_transcripts\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.52.0+galaxy0",
                         "type": "tool",
-                        "uuid": "0b94d2ea-1889-4b88-b0a2-ac7b0a3452e5",
+                        "uuid": "098be95e-54cb-4d1f-96a7-3e79ec4870b6",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out2",
-                                "uuid": "c24e1482-bbff-4a22-8747-2ab0330fb5af"
+                                "label": "fasta_output",
+                                "output_name": "fasta_output",
+                                "uuid": "773cb4ae-56c3-49c0-b582-ee69d620def3"
+                            },
+                            {
+                                "label": "feature_annotation",
+                                "output_name": "feature_annotation",
+                                "uuid": "a30424b5-1ddc-4324-9ff6-dc5883adcce0"
                             }
                         ]
                     },
                     {
-                        "annotation": "The genome should match that of the GTF file",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0",
                         "errors": null,
-                        "id": 4,
+                        "id": 6,
                         "input_connections": {
-                            "refGenomeSource|GTFconditional|sjdbGTFfile": {
+                            "pairstraight|file1": {
                                 "id": 2,
                                 "output_name": "output"
                             },
-                            "singlePaired|input1": {
+                            "pairstraight|file2": {
                                 "id": 3,
-                                "output_name": "out2"
+                                "output_name": "output"
+                            },
+                            "refTranscriptSource|s_index|fasta": {
+                                "id": 5,
+                                "output_name": "fasta_output"
+                            },
+                            "refTranscriptSource|s_index|genome": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "tgmap": {
+                                "id": 5,
+                                "output_name": "feature_annotation"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool RNA STAR",
-                                "name": "singlePaired"
-                            }
-                        ],
-                        "label": "Alignment (Choose a Genome)",
-                        "name": "RNA STAR",
+                        "inputs": [],
+                        "label": "Alevin Processed",
+                        "name": "Alevin",
                         "outputs": [
                             {
-                                "name": "output_log",
+                                "name": "quants_mat_mtx",
+                                "type": "mtx"
+                            },
+                            {
+                                "name": "quants_mat_gz",
+                                "type": "gz"
+                            },
+                            {
+                                "name": "quants_mat_cols_txt",
                                 "type": "txt"
                             },
                             {
-                                "name": "chimeric_junctions",
-                                "type": "interval"
+                                "name": "quants_mat_rows_txt",
+                                "type": "txt"
                             },
                             {
-                                "name": "chimeric_reads",
-                                "type": "bam"
+                                "name": "quants_tier_mat",
+                                "type": "gz"
                             },
                             {
-                                "name": "splice_junctions",
-                                "type": "interval"
+                                "name": "featureDump_txt",
+                                "type": "txt"
                             },
                             {
-                                "name": "mapped_reads",
-                                "type": "bam"
+                                "name": "raw_cb_frequency_txt",
+                                "type": "txt"
                             },
                             {
-                                "name": "reads_per_gene",
-                                "type": "tabular"
+                                "name": "whitelist_txt",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "salmon_quant_log",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 832.5,
-                            "top": 404.9166717529297
+                            "left": 646.2074090941105,
+                            "top": 77.77185227276172
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2",
+                        "post_job_actions": {
+                            "HideDatasetActionfeatureDump_txt": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "featureDump_txt"
+                            },
+                            "HideDatasetActionquants_tier_mat": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "quants_tier_mat"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "2055c2667eb3",
-                            "name": "rgrnastar",
-                            "owner": "iuc",
+                            "changeset_revision": "e32b215b7c04",
+                            "name": "alevin",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"singlePaired\": \"{\\\"sPaired\\\": \\\"single\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"output_params\": \"{\\\"__current_case__\\\": 1, \\\"output_select\\\": \\\"no\\\"}\", \"__rerun_remap_job_id__\": null, \"params\": \"{\\\"settingsType\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\", \"refGenomeSource\": \"{\\\"GTFconditional\\\": {\\\"genomeDir\\\": \\\"mm10\\\", \\\"sjdbGTFfile\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"GTFselect\\\": \\\"without-gtf\\\", \\\"__current_case__\\\": 1, \\\"sjdbOverhang\\\": \\\"100\\\"}, \\\"geneSource\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0}\", \"quantMode\": \"\\\"false\\\"\"}",
-                        "tool_version": "2.5.2b-2",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"optional\": {\"whitelist\": null, \"noDedup\": false, \"mrna\": null, \"rrna\": null, \"dumpMtx\": true, \"forceCells\": null, \"expectCells\": null, \"numCellBootstraps\": \"0\", \"minScoreFraction\": null, \"keepCBFraction\": null, \"maxNumBarcodes\": \"100000\", \"freqThreshold\": \"10\"}, \"output_files\": [\"salmon_log\", \"dumpFeatures\"], \"pairstraight\": {\"readselect\": \"paired\", \"__current_case__\": 0, \"file1\": {\"__class__\": \"ConnectedValue\"}, \"file2\": {\"__class__\": \"ConnectedValue\"}, \"libtype\": {\"strandedness\": \"A\", \"__current_case__\": 0}}, \"protocol_cond\": {\"protocol\": \"--dropseq\", \"__current_case__\": 0}, \"refTranscriptSource\": {\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"__class__\": \"ConnectedValue\"}, \"genome\": {\"__class__\": \"ConnectedValue\"}, \"kmer\": \"31\", \"phash\": false}}, \"tgmap\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.10.1+galaxy0",
                         "type": "tool",
-                        "uuid": "1e4a54be-b2fb-496a-8247-ccba4ffe6f3b",
+                        "uuid": "7e94ce4f-e45d-4be8-8994-df14c329cba8",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "chimeric_reads",
-                                "uuid": "f44d1ce2-b0a0-4aca-b9da-d47a9151dd8f"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "chimeric_junctions",
-                                "uuid": "a70f8d45-eaa8-40f4-a755-99e7004ad0ee"
+                                "label": "raw_cb_frequency_txt",
+                                "output_name": "raw_cb_frequency_txt",
+                                "uuid": "a87beb55-1baf-458e-bd09-bb5ac6ea6e9a"
                             },
                             {
-                                "label": null,
-                                "output_name": "reads_per_gene",
-                                "uuid": "70ef8c03-6a54-4c88-81b6-e178dbf776c7"
+                                "label": "salmon_quant_log",
+                                "output_name": "salmon_quant_log",
+                                "uuid": "c9390a50-775c-4f0f-88e5-0984d570902c"
                             },
                             {
-                                "label": null,
-                                "output_name": "splice_junctions",
-                                "uuid": "0896bee8-d853-4467-8143-96a4d314774c"
+                                "label": "quants_mat_mtx",
+                                "output_name": "quants_mat_mtx",
+                                "uuid": "2cebc438-ddc0-41e0-89ba-49b4bd3e2160"
                             },
                             {
-                                "label": null,
-                                "output_name": "mapped_reads",
-                                "uuid": "956818b5-dc81-440c-8c2a-b10869547c70"
+                                "label": "quants_mat_cols_txt",
+                                "output_name": "quants_mat_cols_txt",
+                                "uuid": "89fa1aad-9ec6-4351-97d5-f05cac09e08e"
                             },
                             {
-                                "label": null,
-                                "output_name": "output_log",
-                                "uuid": "5714f89a-1d7f-4634-95ce-2b089e5cc83d"
+                                "label": "quants_mat_rows_txt",
+                                "output_name": "quants_mat_rows_txt",
+                                "uuid": "3b3dda80-5d35-4c51-9ca0-90a2f909755f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0",
                         "errors": null,
-                        "id": 6,
+                        "id": 7,
                         "input_connections": {
-                            "alignment": {
+                            "pairstraight|file1": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "pairstraight|file2": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "refTranscriptSource|s_index|fasta": {
                                 "id": 5,
-                                "output_name": "out_file1"
+                                "output_name": "fasta_output"
                             },
-                            "anno|reference_gene_sets": {
-                                "id": 2,
+                            "refTranscriptSource|s_index|genome": {
+                                "id": 1,
                                 "output_name": "output"
+                            },
+                            "tgmap": {
+                                "id": 5,
+                                "output_name": "feature_annotation"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": "Alevin - no processing",
+                        "name": "Alevin",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool featureCounts",
-                                "name": "anno"
+                                "name": "quants_mat_mtx",
+                                "type": "mtx"
                             },
                             {
-                                "description": "runtime parameter for tool featureCounts",
-                                "name": "alignment"
-                            }
-                        ],
-                        "label": null,
-                        "name": "featureCounts",
-                        "outputs": [
+                                "name": "quants_mat_gz",
+                                "type": "gz"
+                            },
                             {
-                                "name": "output_medium",
-                                "type": "tabular"
+                                "name": "quants_mat_cols_txt",
+                                "type": "txt"
                             },
                             {
-                                "name": "output_bam",
-                                "type": "bam"
+                                "name": "quants_mat_rows_txt",
+                                "type": "txt"
                             },
                             {
-                                "name": "output_short",
-                                "type": "tabular"
+                                "name": "quants_tier_mat",
+                                "type": "gz"
                             },
                             {
-                                "name": "output_full",
-                                "type": "tabular"
+                                "name": "featureDump_txt",
+                                "type": "txt"
                             },
                             {
-                                "name": "output_summary",
-                                "type": "tabular"
+                                "name": "raw_cb_frequency_txt",
+                                "type": "txt"
                             },
                             {
-                                "name": "output_feature_lengths",
-                                "type": "tabular"
+                                "name": "whitelist_txt",
+                                "type": "txt"
                             },
                             {
-                                "name": "output_jcounts",
-                                "type": "tabular"
+                                "name": "salmon_quant_log",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 1224.5,
-                            "top": 717
+                            "left": 746.3694565659698,
+                            "top": 916.0501011256805
                         },
                         "post_job_actions": {
-                            "HideDatasetActionoutput_feature_lengths": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_feature_lengths"
-                            },
-                            "HideDatasetActionoutput_full": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_full"
-                            },
-                            "HideDatasetActionoutput_jcounts": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_jcounts"
-                            },
-                            "HideDatasetActionoutput_medium": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_medium"
-                            },
-                            "HideDatasetActionoutput_short": {
+                            "HideDatasetActionfeatureDump_txt": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "output_short"
+                                "output_name": "featureDump_txt"
                             },
-                            "HideDatasetActionoutput_summary": {
+                            "HideDatasetActionquants_tier_mat": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "output_summary"
+                                "output_name": "quants_tier_mat"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "f3a5f075498f",
-                            "name": "featurecounts",
-                            "owner": "iuc",
+                            "changeset_revision": "e32b215b7c04",
+                            "name": "alevin",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"pe_parameters\": \"{\\\"only_both_ends\\\": \\\"false\\\", \\\"exclude_chimerics\\\": \\\"true\\\", \\\"fragment_counting_enabled\\\": {\\\"fragment_counting\\\": \\\"\\\", \\\"__current_case__\\\": 1}}\", \"format\": \"\\\"tabdel_short\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"strand_specificity\": \"\\\"1\\\"\", \"include_feature_length_file\": \"\\\"false\\\"\", \"anno\": \"{\\\"anno_select\\\": \\\"history\\\", \\\"reference_gene_sets\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 2}\", \"extended_parameters\": \"{\\\"gff_feature_attribute\\\": \\\"gene_id\\\", \\\"exon_exon_junction_read_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"count_exon_exon_junction_reads\\\": \\\"false\\\"}, \\\"read_extension_3p\\\": \\\"0\\\", \\\"frac_overlap_feature\\\": \\\"0\\\", \\\"min_overlap\\\": \\\"1\\\", \\\"read_extension_5p\\\": \\\"0\\\", \\\"contribute_to_multiple_features\\\": \\\"false\\\", \\\"frac_overlap\\\": \\\"0\\\", \\\"primary\\\": \\\"false\\\", \\\"count_split_alignments_only\\\": \\\"false\\\", \\\"by_read_group\\\": \\\"false\\\", \\\"ignore_dup\\\": \\\"false\\\", \\\"mapping_quality\\\": \\\"12\\\", \\\"summarization_level\\\": \\\"false\\\", \\\"R\\\": \\\"true\\\", \\\"largest_overlap\\\": \\\"false\\\", \\\"read_reduction\\\": \\\"\\\", \\\"multimapping_enabled\\\": {\\\"multimapping_counts\\\": \\\"\\\", \\\"__current_case__\\\": 1}, \\\"long_reads\\\": \\\"false\\\", \\\"gff_feature_type\\\": \\\"exon\\\"}\", \"alignment\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "1.6.2",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"optional\": {\"whitelist\": null, \"noDedup\": false, \"mrna\": null, \"rrna\": null, \"dumpMtx\": true, \"forceCells\": null, \"expectCells\": null, \"numCellBootstraps\": \"0\", \"minScoreFraction\": null, \"keepCBFraction\": \"1.0\", \"maxNumBarcodes\": \"100000\", \"freqThreshold\": \"3\"}, \"output_files\": [\"salmon_log\", \"dumpFeatures\"], \"pairstraight\": {\"readselect\": \"paired\", \"__current_case__\": 0, \"file1\": {\"__class__\": \"ConnectedValue\"}, \"file2\": {\"__class__\": \"ConnectedValue\"}, \"libtype\": {\"strandedness\": \"A\", \"__current_case__\": 0}}, \"protocol_cond\": {\"protocol\": \"--dropseq\", \"__current_case__\": 0}, \"refTranscriptSource\": {\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"__class__\": \"ConnectedValue\"}, \"genome\": {\"__class__\": \"ConnectedValue\"}, \"kmer\": \"31\", \"phash\": false}}, \"tgmap\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.10.1+galaxy0",
                         "type": "tool",
-                        "uuid": "9506153d-d997-43a4-8ce1-216690415561",
+                        "uuid": "ee90c5ca-c7be-4544-b49e-e6568486ab8d",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_bam",
-                                "uuid": "87abf585-aae9-4af3-aed7-541795d65faf"
+                                "label": "quants_mat_rows_txt_1",
+                                "output_name": "quants_mat_rows_txt",
+                                "uuid": "25d4d8f6-d166-4470-80fe-d0fdb0702371"
+                            },
+                            {
+                                "label": "quants_mat_mtx_1",
+                                "output_name": "quants_mat_mtx",
+                                "uuid": "d9ed1457-792b-4eaf-a9fc-2407bcd90da7"
+                            },
+                            {
+                                "label": "quants_mat_cols_txt_1",
+                                "output_name": "quants_mat_cols_txt",
+                                "uuid": "40df6aa8-3dfa-4946-bbc8-cacf4ca2a20e"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "single-cell/scrna-case_alevin",
+                "path": "topics/single-cell/tutorials/scrna-case_alevin/workflows/Generating-a-single-cell-matrix-using-Alevin.ga",
+                "tags": [],
+                "test_results": null,
+                "tests": true,
+                "title": "Generating a single cell matrix using Alevin",
+                "topic_id": "single-cell",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-case_alevin/versions/generating-a-single-cell-matrix-using-alevin",
+                "tutorial_id": "scrna-case_alevin",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_alevin/workflows/Generating-a-single-cell-matrix-using-Alevin.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_alevin/workflows/Generating-a-single-cell-matrix-using-Alevin.html",
+                "version": 2,
+                "wfid": "single-cell-scrna-case_alevin",
+                "wfname": "generating-a-single-cell-matrix-using-alevin",
+                "workflow": "Generating-a-single-cell-matrix-using-Alevin.ga",
+                "workflow_tools": [
+                    "Cut1",
+                    "join1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x/0.0.1+galaxy6",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/sceasy_convert/sceasy_convert/0.0.7+galaxy2"
+                ],
+                "workflowhub_id": "1263"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/4574153"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "dropletutils",
+                    "owner": "iuc",
+                    "revisions": "a9caad671439",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "75c93c70d094",
+                    "tool_panel_section_label": "Quality Control",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rna_starsolo",
+                    "owner": "iuc",
+                    "revisions": "13022c3d3076",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: dropletutils\n  owner: iuc\n  revisions: a9caad671439\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 75c93c70d094\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rna_starsolo\n  owner: iuc\n  revisions: 13022c3d3076\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "elixir_node": "de",
+                "email": "mtekman89@gmail.com",
+                "former_affiliations": [
+                    "elixir-europe"
+                ],
+                "id": "mtekman",
+                "joined": "2018-11",
+                "name": "Mehmet Tekman",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "ch",
+                "email": "hrhotz@googlemail.com",
+                "fediverse": "https://genomic.social/@hrhotz",
+                "fediverse_flavor": "mastodon",
+                "id": "hrhotz",
+                "joined": "2017-09",
+                "linkedin": "hans-rudolf-hotz-542b31",
+                "location": {
+                    "country": "CH",
+                    "lat": 47.57,
+                    "lon": 7.6
+                },
+                "matrix": "hrhotz:matrix.org",
+                "name": "Hans-Rudolf Hotz",
+                "orcid": "0000-0002-2799-424X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hrhotz/",
+                "twitter": "hrhotz",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hrhotz.json"
+            },
+            {
+                "id": "blankenberg",
+                "joined": "2018-07",
+                "name": "Daniel Blankenberg",
+                "orcid": "0000-0002-6833-9049",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankenberg/",
+                "twitter": "dblankenberg",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankenberg.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "bio": "Senior Lecturer at The Open University",
+                "elixir_node": "uk",
+                "email": "wendi.bacon@open.ac.uk",
+                "fediverse": "https://mstdn.science/@wendibacon1",
+                "fediverse_flavor": "mastodon",
+                "id": "nomadscientist",
+                "joined": "2020-03",
+                "matrix": "nomadscientist:matrix.org",
+                "name": "Wendi Bacon",
+                "orcid": "0000-0002-8170-8806",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
+                "twitter": "WendiBacon1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "pavanvidem",
+                "joined": "2017-09",
+                "name": "Pavankumar Videm",
+                "orcid": "0000-0002-5192-126X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
+            }
+        ],
+        "dir": "topics/single-cell/tutorials/scrna-preprocessing-tenx",
+        "edam_operation": [
+            "Sequence alignment",
+            "Validation",
+            "Sequencing quality control",
+            "Community profiling",
+            "Loading"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-scanpy-pbmc3k"
+                ],
+                "type": "internal"
+            }
+        ],
+        "gitter": "Galaxy-Training-Network/galaxy-single-cell",
+        "hands_on": true,
+        "id": "single-cell/scrna-preprocessing-tenx",
+        "inexact_supported_servers": [
+            "HyPhy HIV NGS Tools",
+            "UseGalaxy.be",
+            "UseGalaxy.fr",
+            "UseGalaxy.no"
+        ],
+        "js_requirements": {
+            "mathjax": 12940,
+            "mermaid": false
+        },
+        "key_points": [
+            "Barcode FASTQ Reads are used to parse cDNA sequencing Reads.",
+            "A raw matrix is too large to process alone, and need to be filtered into a high quality one for downstream analysis"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-14",
+        "objectives": [
+            "Demultiplex single-cell FASTQ data from 10X Genomics",
+            "Learn about transparent matrix formats",
+            "Understand the importance of high and low quality cells"
+        ],
+        "pageviews": 11241,
+        "priority": 1,
+        "pub_date": "2019-09-11",
+        "questions": [
+            "What is 10X?",
+            "What is STARsolo and what is Cell Ranger?",
+            "What are BCL and MTX files?",
+            "What is an HDF5 file, and why is it important?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "pavanvidem"
+                ],
+                "date": "2023-05-19",
+                "galaxy_version": "23.01",
+                "length": "19M",
+                "speakers": [
+                    "pavanvidem"
+                ],
+                "youtube_id": "IIiOcgiXviE"
+            },
+            {
+                "captioners": [
+                    "khanteymoori"
+                ],
+                "date": "2021-03-18",
+                "galaxy_version": "21.01",
+                "length": "5M",
+                "speakers": [
+                    "nomadscientist"
+                ],
+                "youtube_id": "vNBNFkF0L4U"
+            }
+        ],
+        "redirect_from": [
+            "/topics/transcriptomics/tutorials/scrna-preprocessing-tenx/tutorial",
+            "/short/single-cell/scrna-preprocessing-tenx",
+            "/short/T00252"
+        ],
+        "requirements": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-preprocessing"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00252",
+        "short_tools": [
+            "multiqc",
+            "dropletutils",
+            "rna_starsolo"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "firstsc",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "10x"
+        ],
+        "time_estimation": "1h",
+        "title": "Pre-processing of 10X Single-Cell RNA Datasets",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.10b+galaxy3"
+        ],
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "scrna-preprocessing-tenx",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.json"
+        },
+        "version": 8,
+        "video": false,
+        "video_versions": 2,
+        "video_view": 0,
+        "visit_duration": 107,
+        "visitors": 8671,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-8170-8806",
+                        "name": "Wendi Bacon"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-5192-126X",
+                        "name": "Pavankumar Videm"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-4181-2676",
+                        "name": "Mehmet Tekman"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-2799-424X",
+                        "name": "Hans-Rudolf Hotz"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-6833-9049",
+                        "name": "Daniel Blankenberg"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nHomo_sapiens.GRCh37.75.gtf\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nsubset_pbmc_1k_v3_S1_L001_R1_001.fastq.gz\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nsubset_pbmc_1k_v3_S1_L002_R1_001.fastq.gz\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nsubset_pbmc_1k_v3_S1_L002_R2_001.fastq.gz\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nsubset_pbmc_1k_v3_S1_L001_R2_001.fastq.gz\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\n3M-february-2018.txt.gz\"]\n  6[label=\"RNA STARSolo\"]\n  0 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  4 -> 6 [label=\"output\"]\n  5 -> 6 [label=\"output\"]\n  7[label=\"DropletUtils\"]\n  6 -> 7 [label=\"output_matrix\"]\n  6 -> 7 [label=\"output_barcodes\"]\n  6 -> 7 [label=\"output_genes\"]\n  8[label=\"DropletUtils\"]\n  6 -> 8 [label=\"output_matrix\"]\n  6 -> 8 [label=\"output_barcodes\"]\n  6 -> 8 [label=\"output_genes\"]\n  9[label=\"DropletUtils\"]\n  6 -> 9 [label=\"output_matrix\"]\n  6 -> 9 [label=\"output_barcodes\"]\n  6 -> 9 [label=\"output_genes\"]\n}",
+                "history": [
+                    {
+                        "hash": "a72ffa88609dce58d84066d5e173ab7f7dfaaa8a",
+                        "message": "add author ids",
+                        "num": 3,
+                        "short_hash": "a72ffa886",
+                        "unix": "1684436873"
+                    },
+                    {
+                        "hash": "3dead543d9798a6456c609bf50844dff6a42ea60",
+                        "message": "Update workflow authors",
+                        "num": 2,
+                        "short_hash": "3dead543d",
+                        "unix": "1684436577"
+                    },
+                    {
+                        "hash": "5d8104ecc67f388338f9bb292c56453b8556542d",
+                        "message": "Update 10x scRNA preprocessing tutorial",
+                        "num": 1,
+                        "short_hash": "5d8104ecc",
+                        "unix": "1684419217"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Homo_sapiens.GRCh37.75.gtf"
+                            }
+                        ],
+                        "label": "Homo_sapiens.GRCh37.75.gtf",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 0
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "8b20f887-9a5a-4a62-9ec5-20ae950c4af3",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "subset_pbmc_1k_v3_S1_L001_R1_001.fastq.gz"
+                            }
+                        ],
+                        "label": "subset_pbmc_1k_v3_S1_L001_R1_001.fastq.gz",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 123
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "e6ecb480-0530-406f-b10d-542769def2ee",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2",
+                        "content_id": null,
                         "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "input_bam": {
-                                "id": 6,
-                                "output_name": "output_bam"
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "subset_pbmc_1k_v3_S1_L002_R1_001.fastq.gz"
                             }
+                        ],
+                        "label": "subset_pbmc_1k_v3_S1_L002_R1_001.fastq.gz",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 266
                         },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "c45a8335-5384-4904-9735-0711a9928c6f",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool UMI-tools count",
-                                "name": "input_bam"
+                                "description": "",
+                                "name": "subset_pbmc_1k_v3_S1_L002_R2_001.fastq.gz"
                             }
                         ],
-                        "label": null,
-                        "name": "UMI-tools count",
-                        "outputs": [
+                        "label": "subset_pbmc_1k_v3_S1_L002_R2_001.fastq.gz",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 409
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "727d1244-f775-4709-bbea-eecaca8588f3",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_counts",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "subset_pbmc_1k_v3_S1_L001_R2_001.fastq.gz"
                             }
                         ],
+                        "label": "subset_pbmc_1k_v3_S1_L001_R2_001.fastq.gz",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1536.5,
-                            "top": 802
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b557acca0b56",
-                            "name": "umi_tools_count",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 552
                         },
-                        "tool_state": "{\"wide_format_cell_counts\": \"\\\"true\\\"\", \"cond_extra\": \"{\\\"prepender\\\": \\\"none\\\", \\\"__current_case__\\\": 0}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"edit_distance_threshold\": \"\\\"1\\\"\", \"paired\": \"\\\"false\\\"\", \"input_bam\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"method\": \"\\\"unique\\\"\", \"advanced\": \"{\\\"random_seed\\\": \\\"0\\\", \\\"gene_tag\\\": \\\"XT\\\", \\\"per_contig\\\": \\\"false\\\", \\\"mapping_quality\\\": \\\"0\\\", \\\"skip_tags_regex\\\": \\\"\\\", \\\"per_cell\\\": \\\"true\\\"}\", \"barcodes\": \"{\\\"umi_separator\\\": \\\"_\\\", \\\"extract_umi_method\\\": \\\"read_id\\\", \\\"__current_case__\\\": 0}\"}",
-                        "tool_version": "0.5.3.2",
-                        "type": "tool",
-                        "uuid": "89675c5a-ef94-49a5-889c-c53ba1074f80",
-                        "workflow_outputs": [
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "183c20fc-aa5a-43bf-a3f2-e496bbe30f43",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "out_counts",
-                                "uuid": "209f3dd6-974f-4e76-a206-c86114a6697f"
+                                "description": "",
+                                "name": "3M-february-2018.txt.gz"
                             }
-                        ]
+                        ],
+                        "label": "3M-february-2018.txt.gz",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 695
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "9be1bade-3ff5-4d99-9ffb-cc909273464c",
+                        "when": null,
+                        "workflow_outputs": []
                     }
                 ],
-                "parent_id": "single-cell/scrna-preprocessing",
-                "path": "topics/single-cell/tutorials/scrna-preprocessing/workflows/scrna_pp_celseq.ga",
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nHomo_sapiens.GRCh37.75.gtf\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nsubset_pbmc_1k_v3_S1_L001_R1_001.fastq.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nsubset_pbmc_1k_v3_S1_L002_R1_001.fastq.gz\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nsubset_pbmc_1k_v3_S1_L002_R2_001.fastq.gz\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nsubset_pbmc_1k_v3_S1_L001_R2_001.fastq.gz\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\n3M-february-2018.txt.gz\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"RNA STARSolo\"];\n  0 -->|output| 6;\n  1 -->|output| 6;\n  2 -->|output| 6;\n  3 -->|output| 6;\n  4 -->|output| 6;\n  5 -->|output| 6;\n  7[\"DropletUtils\"];\n  6 -->|output_matrix| 7;\n  6 -->|output_barcodes| 7;\n  6 -->|output_genes| 7;\n  8[\"DropletUtils\"];\n  6 -->|output_matrix| 8;\n  6 -->|output_barcodes| 8;\n  6 -->|output_genes| 8;\n  9[\"DropletUtils\"];\n  6 -->|output_matrix| 9;\n  6 -->|output_barcodes| 9;\n  6 -->|output_genes| 9;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "Preprocessing of 10X scRNA-seq data",
+                "outputs": [],
+                "parent_id": "single-cell/scrna-preprocessing-tenx",
+                "path": "topics/single-cell/tutorials/scrna-preprocessing-tenx/workflows/scRNA-seq-Preprocessing-TenX.ga",
                 "tags": [
+                    "single-cell",
                     "transcriptomics"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "CelSeq2: Single Batch (mm10)",
+                "tests": true,
+                "title": "Preprocessing of 10X scRNA-seq data",
                 "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-preprocessing/versions/scrna-pp-celseq",
-                "tutorial_id": "scrna-preprocessing",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-preprocessing/workflows/scrna_pp_celseq.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-preprocessing/workflows/scrna_pp_celseq.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-preprocessing-tenx/versions/scrna-seq-preprocessing-tenx",
+                "tutorial_id": "scrna-preprocessing-tenx",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-preprocessing-tenx/workflows/scRNA-seq-Preprocessing-TenX.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-preprocessing-tenx/workflows/scRNA-seq-Preprocessing-TenX.html",
                 "version": 1,
-                "wfid": "single-cell-scrna-preprocessing",
-                "wfname": "scrna-pp-celseq",
-                "workflow": "scrna_pp_celseq.ga",
+                "wfid": "single-cell-scrna-preprocessing-tenx",
+                "wfname": "scrna-seq-preprocessing-tenx",
+                "workflow": "scRNA-seq-Preprocessing-TenX.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.10b+galaxy3"
                 ],
-                "workflowhub_id": "1214"
+                "workflowhub_id": "1220"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/3253142"
+        "zenodo_link": "https://zenodo.org/record/3457880"
     },
     {
         "admin_install": {
@@ -217542,156 +222515,135 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "alevin",
+                    "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "e32b215b7c04",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bwa",
+                    "owner": "devteam",
+                    "revisions": "e188dc7a68e6",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "3d0c7bdf12f5",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "anndata_inspect",
+                    "owner": "iuc",
+                    "revisions": "ee98d611afc6",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "droplet_barcode_plot",
-                    "owner": "ebi-gxa",
-                    "revisions": "8f605643ccfd",
+                    "name": "bedtools",
+                    "owner": "iuc",
+                    "revisions": "a1a923cd89e8",
+                    "tool_panel_section_label": "BED",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "episcanpy_build_matrix",
+                    "owner": "iuc",
+                    "revisions": "31a21ba2c5ea",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "dropletutils_empty_drops",
-                    "owner": "ebi-gxa",
-                    "revisions": "fa662ca7ae7f",
+                    "name": "episcanpy_preprocess",
+                    "owner": "iuc",
+                    "revisions": "29f5f25b9935",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "dropletutils_read_10x",
-                    "owner": "ebi-gxa",
-                    "revisions": "ca62f52e0d7f",
+                    "name": "macs2",
+                    "owner": "iuc",
+                    "revisions": "424aefbd7777",
+                    "tool_panel_section_label": "Peak Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "macs2",
+                    "owner": "iuc",
+                    "revisions": "640d3af5d833",
+                    "tool_panel_section_label": "Peak Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_plot",
+                    "owner": "iuc",
+                    "revisions": "6adf98e782f3",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "gtf2gene_list",
-                    "owner": "ebi-gxa",
-                    "revisions": "14b3f2a4523b",
+                    "name": "scanpy_plot",
+                    "owner": "iuc",
+                    "revisions": "aa0c474463c2",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "salmon_kallisto_mtx_to_10x",
-                    "owner": "ebi-gxa",
-                    "revisions": "88f5a0a6a818",
+                    "name": "sinto_barcode",
+                    "owner": "iuc",
+                    "revisions": "d1b34ac42b8f",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sceasy_convert",
+                    "name": "sinto_fragments",
                     "owner": "iuc",
-                    "revisions": "2062be7efc84",
+                    "revisions": "29e6bfb2cf49",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: alevin\n  owner: bgruening\n  revisions: e32b215b7c04\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: droplet_barcode_plot\n  owner: ebi-gxa\n  revisions: 8f605643ccfd\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dropletutils_empty_drops\n  owner: ebi-gxa\n  revisions: fa662ca7ae7f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dropletutils_read_10x\n  owner: ebi-gxa\n  revisions: ca62f52e0d7f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gtf2gene_list\n  owner: ebi-gxa\n  revisions: 14b3f2a4523b\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: salmon_kallisto_mtx_to_10x\n  owner: ebi-gxa\n  revisions: 88f5a0a6a818\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sceasy_convert\n  owner: iuc\n  revisions: 2062be7efc84\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "answer_histories": [
-            {
-                "date": "2024-03-22",
-                "history": "https://usegalaxy.eu/u/j.jakiela/h/generating-a-single-cell-matrix-alevin",
-                "label": "UseGalaxy.eu"
-            },
-            {
-                "date": "2024-01-01",
-                "history": "https://humancellatlas.usegalaxy.eu/u/wendi.bacon.training/h/cs1pre-processing-with-alevin---answer-key",
-                "label": "Older Alevin version"
-            }
-        ],
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_alevin/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "nomadscientist",
-                "pinin4fjords"
-            ],
-            "editing": [
-                "hexylena"
-            ],
-            "testing": [
-                "wee-snufkin"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_inspect\n  owner: iuc\n  revisions: ee98d611afc6\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: a1a923cd89e8\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: episcanpy_build_matrix\n  owner: iuc\n  revisions: 31a21ba2c5ea\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: episcanpy_preprocess\n  owner: iuc\n  revisions: 29f5f25b9935\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: macs2\n  owner: iuc\n  revisions: 424aefbd7777\n  tool_panel_section_label: Peak Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: macs2\n  owner: iuc\n  revisions: 640d3af5d833\n  tool_panel_section_label: Peak Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot\n  owner: iuc\n  revisions: 6adf98e782f3\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot\n  owner: iuc\n  revisions: aa0c474463c2\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sinto_barcode\n  owner: iuc\n  revisions: d1b34ac42b8f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sinto_fragments\n  owner: iuc\n  revisions: 29e6bfb2cf49\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
+                    "uni-freiburg",
                     "elixir-europe"
                 ],
-                "bio": "Senior Lecturer at The Open University",
-                "elixir_node": "uk",
-                "email": "wendi.bacon@open.ac.uk",
-                "fediverse": "https://mstdn.science/@wendibacon1",
-                "fediverse_flavor": "mastodon",
-                "id": "nomadscientist",
-                "joined": "2020-03",
-                "matrix": "nomadscientist:matrix.org",
-                "name": "Wendi Bacon",
-                "orcid": "0000-0002-8170-8806",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
-                "twitter": "WendiBacon1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
-            },
-            {
-                "email": "jmanning@ebi.ac.uk",
-                "id": "pinin4fjords",
-                "joined": "2021-02",
-                "name": "Jonathan Manning",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pinin4fjords/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pinin4fjords.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
+                "id": "pavanvidem",
                 "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "email": "juliajot36@gmail.com",
-                "id": "wee-snufkin",
-                "joined": "2022-06",
-                "name": "Julia Jakiela",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
+                "name": "Pavankumar Videm",
+                "orcid": "0000-0002-5192-126X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
             }
         ],
-        "dir": "topics/single-cell/tutorials/scrna-case_alevin",
+        "dir": "topics/single-cell/tutorials/scatac-preprocessing-tenx",
         "edam_operation": [
-            "RNA-Seq quantification",
+            "Peak calling",
+            "Sequence alignment",
+            "Differential gene expression analysis",
+            "Read mapping",
+            "Sequencing quality control",
+            "Genome indexing",
             "Sequence composition calculation",
-            "Gene expression analysis"
+            "Imputation",
+            "Generation",
+            "Statistical calculation",
+            "Gene regulatory network analysis",
+            "Mapping",
+            "Enrichment analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
@@ -217699,114 +222651,120 @@
             {
                 "topic_name": "single-cell",
                 "tutorials": [
-                    "scrna-case_alevin-combine-datasets"
+                    "scrna-scanpy-pbmc3k",
+                    "scatac-standard-processing-snapatac2"
                 ],
                 "type": "internal"
             }
         ],
         "gitter": "Galaxy-Training-Network/galaxy-single-cell",
         "hands_on": true,
-        "id": "single-cell/scrna-case_alevin",
-        "inexact_supported_servers": [],
-        "input_histories": [
-            {
-                "history": "https://humancellatlas.usegalaxy.eu/u/wendi.bacon.training/h/cs1pre-processing-with-alevin---input-1",
-                "label": "UseGalaxy.eu"
-            }
+        "id": "single-cell/scatac-preprocessing-tenx",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Create a scanpy-accessible AnnData object from FASTQ files, including relevant gene metadata"
+            "Bulk ATAC-seq like mapping and peak calling",
+            "Creating a scATAC-seq count matrix requires positions of open chromatin regions"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-07-11",
         "objectives": [
-            "Generate a cellxgene matrix for droplet-based single cell sequencing data",
-            "Interpret quality control (QC) plots to make informed decisions on cell thresholds",
-            "Find relevant information in GTF files for the particulars of their study, and include this in data matrix metadata"
+            "Demultiplex single-cell FASTQ data from 10X Genomics",
+            "Learn about transparent matrix formats",
+            "Create a high-quality count matrix starting from scATAC-seq FASTQ files"
         ],
-        "pageviews": 3412,
+        "pageviews": 4539,
         "priority": 1,
-        "pub_date": "2021-03-03",
+        "pub_date": "2023-04-24",
         "questions": [
-            "I have some single cell FASTQ files I want to analyse. Where do I start?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "nomadscientist"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "30M",
-                "speakers": [
-                    "nomadscientist"
-                ],
-                "youtube_id": "3ytm2AU6QUc"
-            }
+            "What is 10X?",
+            "What are single-cell ATAC fragments and MTX files?",
+            "What is an Anndata file, and why is it important?"
         ],
         "redirect_from": [
-            "/topics/transcriptomics/tutorials/droplet-quantification-preprocessing/tutorial",
-            "/topics/transcriptomics/tutorials/scrna-case_alevin/tutorial",
-            "/short/single-cell/scrna-case_alevin",
-            "/short/T00245"
+            "/topics/transcriptomics/tutorials/satac-preprocessing-tenx/tutorial",
+            "/short/single-cell/scatac-preprocessing-tenx",
+            "/short/T00335"
         ],
         "requirements": [
             {
                 "topic_name": "single-cell",
                 "tutorials": [
-                    "scrna-intro",
-                    "scrna-umis"
+                    "scrna-preprocessing-tenx"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00245",
+        "short_id": "T00335",
         "short_tools": [
-            "dropletutils_read_10x",
-            "sceasy_convert",
-            "_dropletBarcodePlot",
-            "Cut1",
-            "alevin",
-            "dropletutils_empty_drops",
-            "join1",
-            "_ensembl_gtf2gene_list",
-            "_salmon_kallisto_mtx_to_10x"
+            "bwa_mem",
+            "tp_sorted_uniq",
+            "sinto_fragments",
+            "episcanpy_preprocess",
+            "bedtools_sortbed",
+            "scanpy_plot",
+            "anndata_inspect",
+            "sinto_barcode",
+            "macs2_callpeak",
+            "fastqc",
+            "episcanpy_build_matrix"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "single-cell-CS",
+        "subtopic": "scmultiomics",
         "supported_servers": {
             "exact": [
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ],
-            "inexact": []
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
         },
         "symlink": null,
         "tags": [
             "10x",
-            "paper-replication"
+            "epigenetics"
         ],
-        "time_estimation": "2H",
-        "title": "Generating a single cell matrix using Alevin",
+        "time_estimation": "1h",
+        "title": "Pre-processing of 10X Single-Cell ATAC-seq Datasets",
         "tools": [
-            "Cut1",
-            "join1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x/0.0.1+galaxy6",
-            "toolshed.g2.bx.psu.edu/repos/iuc/sceasy_convert/sceasy_convert/0.0.7+galaxy2"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/episcanpy_build_matrix/episcanpy_build_matrix/0.3.2+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/episcanpy_preprocess/episcanpy_preprocess/0.3.2+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6",
+            "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/sinto_barcode/sinto_barcode/0.9.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/sinto_fragments/sinto_fragments/0.9.0+galaxy1"
         ],
         "topic_name": "single-cell",
         "topic_name_human": "Single Cell",
@@ -217816,514 +222774,243 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "scrna-case_alevin",
+        "tutorial_name": "scatac-preprocessing-tenx",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_alevin/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_alevin/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_alevin/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.json"
         },
-        "version": 16,
+        "version": 8,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 169,
-        "visitors": 2300,
+        "visit_duration": 67,
+        "visitors": 3827,
         "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "0009-0001-2017-8805",
-                        "name": "Julia Jakiela"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-8170-8806",
-                        "name": "Wendi Bacon"
+                        "identifier": "0000-0002-5192-126X",
+                        "name": "Pavankumar Videm"
                     }
                 ],
-                "description": "This workflow generates a single cell matrix using Alevin. ",
+                "description": "",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGTF file\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference FASTA\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nRead 1 - containing cell barcode & UMI\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nRead 2 - containing transcript\"]\n  4[label=\"GTF2GeneList\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Transcript-gene mapping\"]\n  1 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  k773cb4ae56c349c0b582ee69d620def3[color=lightseagreen,label=\"Output\\nfasta_output\"]\n  5 -> k773cb4ae56c349c0b582ee69d620def3\n  ka30424b51ddc43249ff6dc5883adcce0[color=lightseagreen,label=\"Output\\nfeature_annotation\"]\n  5 -> ka30424b51ddc43249ff6dc5883adcce0\n  6[label=\"Alevin Processed\"]\n  2 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  5 -> 6 [label=\"fasta_output\"]\n  1 -> 6 [label=\"output\"]\n  5 -> 6 [label=\"feature_annotation\"]\n  ka87beb551baf458ebd09bb5ac6ea6e9a[color=lightseagreen,label=\"Output\\nraw_cb_frequency_txt\"]\n  6 -> ka87beb551baf458ebd09bb5ac6ea6e9a\n  kc9390a50775c4f0f88e50984d570902c[color=lightseagreen,label=\"Output\\nsalmon_quant_log\"]\n  6 -> kc9390a50775c4f0f88e50984d570902c\n  k2cebc438ddc041e089ba49b4bd3e2160[color=lightseagreen,label=\"Output\\nquants_mat_mtx\"]\n  6 -> k2cebc438ddc041e089ba49b4bd3e2160\n  k89fa1aad9ec6435197d5f05cac09e08e[color=lightseagreen,label=\"Output\\nquants_mat_cols_txt\"]\n  6 -> k89fa1aad9ec6435197d5f05cac09e08e\n  k3b3dda805d354c519ca090a2f909755f[color=lightseagreen,label=\"Output\\nquants_mat_rows_txt\"]\n  6 -> k3b3dda805d354c519ca090a2f909755f\n  7[label=\"Alevin - no processing\"]\n  2 -> 7 [label=\"output\"]\n  3 -> 7 [label=\"output\"]\n  5 -> 7 [label=\"fasta_output\"]\n  1 -> 7 [label=\"output\"]\n  5 -> 7 [label=\"feature_annotation\"]\n  k25d4d8f6d166447080fed0fdb0702371[color=lightseagreen,label=\"Output\\nquants_mat_rows_txt_1\"]\n  7 -> k25d4d8f6d166447080fed0fdb0702371\n  kd9ed1457792b4eafa9fc2407bcd90da7[color=lightseagreen,label=\"Output\\nquants_mat_mtx_1\"]\n  7 -> kd9ed1457792b4eafa9fc2407bcd90da7\n  k40df6aa83dfa4946bbc8cacf4ca2a20e[color=lightseagreen,label=\"Output\\nquants_mat_cols_txt_1\"]\n  7 -> k40df6aa83dfa4946bbc8cacf4ca2a20e\n  8[label=\"Droplet rank plot - raw barcodes\"]\n  6 -> 8 [label=\"raw_cb_frequency_txt\"]\n  9[label=\"Droplet rank plot - Alevin barcodes\"]\n  6 -> 9 [label=\"quants_mat_mtx\"]\n  10[label=\"salmonKallistoMtxTo10x\"]\n  7 -> 10 [label=\"quants_mat_rows_txt\"]\n  7 -> 10 [label=\"quants_mat_cols_txt\"]\n  7 -> 10 [label=\"quants_mat_mtx\"]\n  11[label=\"Join two Datasets\"]\n  10 -> 11 [label=\"genes_out\"]\n  4 -> 11 [label=\"feature_annotation\"]\n  12[label=\"Cut\"]\n  11 -> 12 [label=\"out_file1\"]\n  13[label=\"DropletUtils Read10x\"]\n  10 -> 13 [label=\"barcodes_out\"]\n  12 -> 13 [label=\"out_file1\"]\n  10 -> 13 [label=\"matrix_out\"]\n  14[label=\"DropletUtils emptyDrops\"]\n  13 -> 14 [label=\"output_rds\"]\n  15[label=\"SCEasy Converter\"]\n  14 -> 15 [label=\"output_rdata\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nscATAC-seq Anndata\"]\n  1[label=\"scATAC-seq Preprocessing\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"scATAC-seq Preprocessing\"]\n  1 -> 2 [label=\"anndata_out\"]\n  3[label=\"scATAC-seq Preprocessing\"]\n  2 -> 3 [label=\"anndata_out\"]\n  4[label=\"Plot\"]\n  3 -> 4 [label=\"anndata_out\"]\n  5[label=\"scATAC-seq Preprocessing\"]\n  3 -> 5 [label=\"anndata_out\"]\n  6[label=\"scATAC-seq Preprocessing\"]\n  3 -> 6 [label=\"anndata_out\"]\n  7[label=\"scATAC-seq Preprocessing\"]\n  3 -> 7 [label=\"anndata_out\"]\n  8[label=\"scATAC-seq Preprocessing\"]\n  3 -> 8 [label=\"anndata_out\"]\n  9[label=\"scATAC-seq Preprocessing\"]\n  8 -> 9 [label=\"anndata_out\"]\n  10[label=\"scATAC-seq Preprocessing\"]\n  9 -> 10 [label=\"anndata_out\"]\n  11[label=\"scATAC-seq Preprocessing\"]\n  10 -> 11 [label=\"anndata_out\"]\n  12[label=\"Plot\"]\n  11 -> 12 [label=\"anndata_out\"]\n}",
                 "history": [
                     {
-                        "hash": "927da941a1ce7627ff0d5d5635d74cfa8abdff1f",
-                        "message": "add workflow tests",
-                        "num": 2,
-                        "short_hash": "927da941a",
-                        "unix": "1711095976"
-                    },
-                    {
-                        "hash": "327fd2b842f45de3dc2a30067714352675ad69ae",
-                        "message": "Making a single cell topics",
+                        "hash": "094d1948af4063fe1165b564f128a8a3a447b037",
+                        "message": "Add workflow tests",
                         "num": 1,
-                        "short_hash": "327fd2b84",
-                        "unix": "1668273265"
+                        "short_hash": "094d1948a",
+                        "unix": "1682339007"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "You can find the file containing the gene information for your species here: \nhttp://www.ensembl.org/info/data/ftp/index.html/",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "You can find the file containing the gene information for your species here: \nhttp://www.ensembl.org/info/data/ftp/index.html/",
-                                "name": "GTF file"
+                                "description": "",
+                                "name": "scATAC-seq Anndata"
                             }
                         ],
-                        "label": "GTF file",
+                        "label": "scATAC-seq Anndata",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 58.60616823526459,
-                            "top": 88.90721532236475
+                            "left": 0,
+                            "top": 522
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "09e96b1f-f0e5-4e1a-b418-cd4ecc706e35",
+                        "uuid": "2e2b15be-c7c1-4ebb-bb2c-5b269c563ae4",
                         "when": null,
                         "workflow_outputs": []
-                    },
+                    }
+                ],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nscATAC-seq Anndata\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"scATAC-seq Preprocessing\"];\n  0 -->|output| 1;\n  2[\"scATAC-seq Preprocessing\"];\n  1 -->|anndata_out| 2;\n  3[\"scATAC-seq Preprocessing\"];\n  2 -->|anndata_out| 3;\n  4[\"Plot\"];\n  3 -->|anndata_out| 4;\n  5[\"scATAC-seq Preprocessing\"];\n  3 -->|anndata_out| 5;\n  6[\"scATAC-seq Preprocessing\"];\n  3 -->|anndata_out| 6;\n  7[\"scATAC-seq Preprocessing\"];\n  3 -->|anndata_out| 7;\n  8[\"scATAC-seq Preprocessing\"];\n  3 -->|anndata_out| 8;\n  9[\"scATAC-seq Preprocessing\"];\n  8 -->|anndata_out| 9;\n  10[\"scATAC-seq Preprocessing\"];\n  9 -->|anndata_out| 10;\n  11[\"scATAC-seq Preprocessing\"];\n  10 -->|anndata_out| 11;\n  12[\"Plot\"];\n  11 -->|anndata_out| 12;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "scATAC-seq Count Matrix Filtering",
+                "outputs": [],
+                "parent_id": "single-cell/scatac-preprocessing-tenx",
+                "path": "topics/single-cell/tutorials/scatac-preprocessing-tenx/workflows/scATAC-seq-Count-Matrix-Filtering.ga",
+                "tags": [],
+                "test_results": null,
+                "tests": true,
+                "title": "scATAC-seq Count Matrix Filtering",
+                "topic_id": "single-cell",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scatac-preprocessing-tenx/versions/scatac-seq-count-matrix-filtering",
+                "tutorial_id": "scatac-preprocessing-tenx",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-preprocessing-tenx/workflows/scATAC-seq-Count-Matrix-Filtering.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-preprocessing-tenx/workflows/scATAC-seq-Count-Matrix-Filtering.html",
+                "version": 1,
+                "wfid": "single-cell-scatac-preprocessing-tenx",
+                "wfname": "scatac-seq-count-matrix-filtering",
+                "workflow": "scATAC-seq-Count-Matrix-Filtering.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/iuc/episcanpy_preprocess/episcanpy_preprocess/0.3.2+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1"
+                ],
+                "workflowhub_id": "1275"
+            },
+            {
+                "creators": [
                     {
-                        "annotation": "You can find this file for your species here: http://www.ensembl.org/info/data/ftp/index.html/",
+                        "class": "Person",
+                        "identifier": "0000-0002-5192-126X",
+                        "name": "Pavankumar Videm"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nForward reads FASTQ R1\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBarcodes FASTQ R2\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReverse reads FASTQ R3\"]\n  3[label=\"Sinto barcode\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"FastQC\"]\n  3 -> 4 [label=\"read1_out\"]\n  5[label=\"FastQC\"]\n  3 -> 5 [label=\"read2_out\"]\n  6[label=\"Map with BWA-MEM\"]\n  3 -> 6 [label=\"read1_out\"]\n  3 -> 6 [label=\"read2_out\"]\n  7[label=\"Sinto fragments\"]\n  6 -> 7 [label=\"bam_output\"]\n  8[label=\"bedtools SortBED\"]\n  7 -> 8 [label=\"fragments\"]\n  9[label=\"MACS2 callpeak\"]\n  8 -> 9 [label=\"output\"]\n  10[label=\"Unique\"]\n  9 -> 10 [label=\"output_narrowpeaks\"]\n  11[label=\"Build count matrix\"]\n  8 -> 11 [label=\"output\"]\n  10 -> 11 [label=\"outfile\"]\n  12[label=\"Inspect AnnData\"]\n  11 -> 12 [label=\"anndata_out\"]\n  13[label=\"Inspect AnnData\"]\n  11 -> 13 [label=\"anndata_out\"]\n  14[label=\"Inspect AnnData\"]\n  11 -> 14 [label=\"anndata_out\"]\n  15[label=\"Inspect AnnData\"]\n  11 -> 15 [label=\"anndata_out\"]\n}",
+                "history": [
+                    {
+                        "hash": "094d1948af4063fe1165b564f128a8a3a447b037",
+                        "message": "Add workflow tests",
+                        "num": 1,
+                        "short_hash": "094d1948a",
+                        "unix": "1682339007"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "You can find this file for your species here: http://www.ensembl.org/info/data/ftp/index.html/",
-                                "name": "Reference FASTA"
+                                "description": "",
+                                "name": "Forward reads FASTQ (R1)"
                             }
                         ],
-                        "label": "Reference FASTA",
+                        "label": "Forward reads FASTQ (R1)",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 83.54487198456434,
-                            "top": 288.0815521308393
+                            "left": 0,
+                            "top": 0
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "43c0a6ac-36dc-4b35-9bca-83063de43a8a",
+                        "uuid": "ec67a5c0-4854-4344-af16-7772c1c0742b",
                         "when": null,
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "This should be a fast file containing the shorter read - i.e. the cell barcode and the unique molecular identifier",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "This should be a fast file containing the shorter read - i.e. the cell barcode and the unique molecular identifier",
-                                "name": "Read 1 - containing cell barcode & UMI"
+                                "description": "",
+                                "name": "Barcodes FASTQ (R2)"
                             }
                         ],
-                        "label": "Read 1 - containing cell barcode & UMI",
+                        "label": "Barcodes FASTQ (R2)",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0.18723338168473447,
-                            "top": 439.63352912048805
+                            "left": 0,
+                            "top": 120
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ed68f7dd-faa4-453e-9050-8fbfb0027928",
+                        "uuid": "50c6de05-b355-4733-bc1d-96dc1ca058e1",
                         "when": null,
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "This should be the read containing the transcript",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "This should be the read containing the transcript",
-                                "name": "Read 2 - containing transcript"
+                                "description": "",
+                                "name": "Reverse reads FASTQ (R3)"
                             }
                         ],
-                        "label": "Read 2 - containing transcript",
+                        "label": "Reverse reads FASTQ (R3)",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
                             "left": 0,
-                            "top": 611.9759545962928
+                            "top": 240
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "508c574e-8ca2-46b0-b753-b96c5b797fd2",
+                        "uuid": "8a73ff78-6e0a-41ab-9ac3-523cbd486021",
                         "when": null,
                         "workflow_outputs": []
                     }
                 ],
                 "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGTF file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference FASTA\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nRead 1 - containing cell barcode & UMI\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nRead 2 - containing transcript\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"GTF2GeneList\"];\n  0 -->|output| 4;\n  5[\"Transcript-gene mapping\"];\n  1 -->|output| 5;\n  0 -->|output| 5;\n  773cb4ae-56c3-49c0-b582-ee69d620def3[\"Output\\nfasta_output\"];\n  5 --> 773cb4ae-56c3-49c0-b582-ee69d620def3;\n  style 773cb4ae-56c3-49c0-b582-ee69d620def3 stroke:#2c3143,stroke-width:4px;\n  a30424b5-1ddc-4324-9ff6-dc5883adcce0[\"Output\\nfeature_annotation\"];\n  5 --> a30424b5-1ddc-4324-9ff6-dc5883adcce0;\n  style a30424b5-1ddc-4324-9ff6-dc5883adcce0 stroke:#2c3143,stroke-width:4px;\n  6[\"Alevin Processed\"];\n  2 -->|output| 6;\n  3 -->|output| 6;\n  5 -->|fasta_output| 6;\n  1 -->|output| 6;\n  5 -->|feature_annotation| 6;\n  a87beb55-1baf-458e-bd09-bb5ac6ea6e9a[\"Output\\nraw_cb_frequency_txt\"];\n  6 --> a87beb55-1baf-458e-bd09-bb5ac6ea6e9a;\n  style a87beb55-1baf-458e-bd09-bb5ac6ea6e9a stroke:#2c3143,stroke-width:4px;\n  c9390a50-775c-4f0f-88e5-0984d570902c[\"Output\\nsalmon_quant_log\"];\n  6 --> c9390a50-775c-4f0f-88e5-0984d570902c;\n  style c9390a50-775c-4f0f-88e5-0984d570902c stroke:#2c3143,stroke-width:4px;\n  2cebc438-ddc0-41e0-89ba-49b4bd3e2160[\"Output\\nquants_mat_mtx\"];\n  6 --> 2cebc438-ddc0-41e0-89ba-49b4bd3e2160;\n  style 2cebc438-ddc0-41e0-89ba-49b4bd3e2160 stroke:#2c3143,stroke-width:4px;\n  89fa1aad-9ec6-4351-97d5-f05cac09e08e[\"Output\\nquants_mat_cols_txt\"];\n  6 --> 89fa1aad-9ec6-4351-97d5-f05cac09e08e;\n  style 89fa1aad-9ec6-4351-97d5-f05cac09e08e stroke:#2c3143,stroke-width:4px;\n  3b3dda80-5d35-4c51-9ca0-90a2f909755f[\"Output\\nquants_mat_rows_txt\"];\n  6 --> 3b3dda80-5d35-4c51-9ca0-90a2f909755f;\n  style 3b3dda80-5d35-4c51-9ca0-90a2f909755f stroke:#2c3143,stroke-width:4px;\n  7[\"Alevin - no processing\"];\n  2 -->|output| 7;\n  3 -->|output| 7;\n  5 -->|fasta_output| 7;\n  1 -->|output| 7;\n  5 -->|feature_annotation| 7;\n  25d4d8f6-d166-4470-80fe-d0fdb0702371[\"Output\\nquants_mat_rows_txt_1\"];\n  7 --> 25d4d8f6-d166-4470-80fe-d0fdb0702371;\n  style 25d4d8f6-d166-4470-80fe-d0fdb0702371 stroke:#2c3143,stroke-width:4px;\n  d9ed1457-792b-4eaf-a9fc-2407bcd90da7[\"Output\\nquants_mat_mtx_1\"];\n  7 --> d9ed1457-792b-4eaf-a9fc-2407bcd90da7;\n  style d9ed1457-792b-4eaf-a9fc-2407bcd90da7 stroke:#2c3143,stroke-width:4px;\n  40df6aa8-3dfa-4946-bbc8-cacf4ca2a20e[\"Output\\nquants_mat_cols_txt_1\"];\n  7 --> 40df6aa8-3dfa-4946-bbc8-cacf4ca2a20e;\n  style 40df6aa8-3dfa-4946-bbc8-cacf4ca2a20e stroke:#2c3143,stroke-width:4px;\n  8[\"Droplet rank plot - raw barcodes\"];\n  6 -->|raw_cb_frequency_txt| 8;\n  9[\"Droplet rank plot - Alevin barcodes\"];\n  6 -->|quants_mat_mtx| 9;\n  10[\"salmonKallistoMtxTo10x\"];\n  7 -->|quants_mat_rows_txt| 10;\n  7 -->|quants_mat_cols_txt| 10;\n  7 -->|quants_mat_mtx| 10;\n  11[\"Join two Datasets\"];\n  10 -->|genes_out| 11;\n  4 -->|feature_annotation| 11;\n  12[\"Cut\"];\n  11 -->|out_file1| 12;\n  13[\"DropletUtils Read10x\"];\n  10 -->|barcodes_out| 13;\n  12 -->|out_file1| 13;\n  10 -->|matrix_out| 13;\n  14[\"DropletUtils emptyDrops\"];\n  13 -->|output_rds| 14;\n  15[\"SCEasy Converter\"];\n  14 -->|output_rdata| 15;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Generating a single cell matrix using Alevin",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "cdnas|fasta_input": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "gtf_input": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Transcript-gene mapping",
-                        "name": "GTF2GeneList",
-                        "outputs": [
-                            {
-                                "name": "feature_annotation",
-                                "type": "tsv"
-                            },
-                            {
-                                "name": "fasta_output",
-                                "type": "fasta.gz"
-                            }
-                        ],
-                        "position": {
-                            "left": 374.4625157115551,
-                            "top": 351.46516186147346
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionfasta_output": {
-                                "action_arguments": {
-                                    "newname": "Filtered fasta"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "fasta_output"
-                            },
-                            "RenameDatasetActionfeature_annotation": {
-                                "action_arguments": {
-                                    "newname": "Map"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "feature_annotation"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "14b3f2a4523b",
-                            "name": "gtf2gene_list",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"cdnas\": {\"parse_cdnas\": true, \"__current_case__\": 0, \"fasta_input\": {\"__class__\": \"ConnectedValue\"}, \"cdnas_field\": \"transcript_id\", \"parse_cdna_names\": false, \"filter_cdnas\": true}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"feature_type\": \"transcript\", \"fields\": \"transcript_id,gene_id\", \"fill_empty\": \"\", \"first_field\": \"transcript_id\", \"gtf_input\": {\"__class__\": \"ConnectedValue\"}, \"mito\": {\"mark_mito\": false, \"__current_case__\": 1}, \"noheader\": true, \"version_transcripts\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.52.0+galaxy0",
-                        "type": "tool",
-                        "uuid": "098be95e-54cb-4d1f-96a7-3e79ec4870b6",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "fasta_output",
-                                "output_name": "fasta_output",
-                                "uuid": "773cb4ae-56c3-49c0-b582-ee69d620def3"
-                            },
-                            {
-                                "label": "feature_annotation",
-                                "output_name": "feature_annotation",
-                                "uuid": "a30424b5-1ddc-4324-9ff6-dc5883adcce0"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "pairstraight|file1": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "pairstraight|file2": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "refTranscriptSource|s_index|fasta": {
-                                "id": 5,
-                                "output_name": "fasta_output"
-                            },
-                            "refTranscriptSource|s_index|genome": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "tgmap": {
-                                "id": 5,
-                                "output_name": "feature_annotation"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Alevin Processed",
-                        "name": "Alevin",
-                        "outputs": [
-                            {
-                                "name": "quants_mat_mtx",
-                                "type": "mtx"
-                            },
-                            {
-                                "name": "quants_mat_gz",
-                                "type": "gz"
-                            },
-                            {
-                                "name": "quants_mat_cols_txt",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "quants_mat_rows_txt",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "quants_tier_mat",
-                                "type": "gz"
-                            },
-                            {
-                                "name": "featureDump_txt",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "raw_cb_frequency_txt",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "whitelist_txt",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "salmon_quant_log",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 646.2074090941105,
-                            "top": 77.77185227276172
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionfeatureDump_txt": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "featureDump_txt"
-                            },
-                            "HideDatasetActionquants_tier_mat": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "quants_tier_mat"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "e32b215b7c04",
-                            "name": "alevin",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"optional\": {\"whitelist\": null, \"noDedup\": false, \"mrna\": null, \"rrna\": null, \"dumpMtx\": true, \"forceCells\": null, \"expectCells\": null, \"numCellBootstraps\": \"0\", \"minScoreFraction\": null, \"keepCBFraction\": null, \"maxNumBarcodes\": \"100000\", \"freqThreshold\": \"10\"}, \"output_files\": [\"salmon_log\", \"dumpFeatures\"], \"pairstraight\": {\"readselect\": \"paired\", \"__current_case__\": 0, \"file1\": {\"__class__\": \"ConnectedValue\"}, \"file2\": {\"__class__\": \"ConnectedValue\"}, \"libtype\": {\"strandedness\": \"A\", \"__current_case__\": 0}}, \"protocol_cond\": {\"protocol\": \"--dropseq\", \"__current_case__\": 0}, \"refTranscriptSource\": {\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"__class__\": \"ConnectedValue\"}, \"genome\": {\"__class__\": \"ConnectedValue\"}, \"kmer\": \"31\", \"phash\": false}}, \"tgmap\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.10.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "7e94ce4f-e45d-4be8-8994-df14c329cba8",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "raw_cb_frequency_txt",
-                                "output_name": "raw_cb_frequency_txt",
-                                "uuid": "a87beb55-1baf-458e-bd09-bb5ac6ea6e9a"
-                            },
-                            {
-                                "label": "salmon_quant_log",
-                                "output_name": "salmon_quant_log",
-                                "uuid": "c9390a50-775c-4f0f-88e5-0984d570902c"
-                            },
-                            {
-                                "label": "quants_mat_mtx",
-                                "output_name": "quants_mat_mtx",
-                                "uuid": "2cebc438-ddc0-41e0-89ba-49b4bd3e2160"
-                            },
-                            {
-                                "label": "quants_mat_cols_txt",
-                                "output_name": "quants_mat_cols_txt",
-                                "uuid": "89fa1aad-9ec6-4351-97d5-f05cac09e08e"
-                            },
-                            {
-                                "label": "quants_mat_rows_txt",
-                                "output_name": "quants_mat_rows_txt",
-                                "uuid": "3b3dda80-5d35-4c51-9ca0-90a2f909755f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "pairstraight|file1": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "pairstraight|file2": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "refTranscriptSource|s_index|fasta": {
-                                "id": 5,
-                                "output_name": "fasta_output"
-                            },
-                            "refTranscriptSource|s_index|genome": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "tgmap": {
-                                "id": 5,
-                                "output_name": "feature_annotation"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Alevin - no processing",
-                        "name": "Alevin",
-                        "outputs": [
-                            {
-                                "name": "quants_mat_mtx",
-                                "type": "mtx"
-                            },
-                            {
-                                "name": "quants_mat_gz",
-                                "type": "gz"
-                            },
-                            {
-                                "name": "quants_mat_cols_txt",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "quants_mat_rows_txt",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "quants_tier_mat",
-                                "type": "gz"
-                            },
-                            {
-                                "name": "featureDump_txt",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "raw_cb_frequency_txt",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "whitelist_txt",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "salmon_quant_log",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 746.3694565659698,
-                            "top": 916.0501011256805
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionfeatureDump_txt": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "featureDump_txt"
-                            },
-                            "HideDatasetActionquants_tier_mat": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "quants_tier_mat"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "e32b215b7c04",
-                            "name": "alevin",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"optional\": {\"whitelist\": null, \"noDedup\": false, \"mrna\": null, \"rrna\": null, \"dumpMtx\": true, \"forceCells\": null, \"expectCells\": null, \"numCellBootstraps\": \"0\", \"minScoreFraction\": null, \"keepCBFraction\": \"1.0\", \"maxNumBarcodes\": \"100000\", \"freqThreshold\": \"3\"}, \"output_files\": [\"salmon_log\", \"dumpFeatures\"], \"pairstraight\": {\"readselect\": \"paired\", \"__current_case__\": 0, \"file1\": {\"__class__\": \"ConnectedValue\"}, \"file2\": {\"__class__\": \"ConnectedValue\"}, \"libtype\": {\"strandedness\": \"A\", \"__current_case__\": 0}}, \"protocol_cond\": {\"protocol\": \"--dropseq\", \"__current_case__\": 0}, \"refTranscriptSource\": {\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"__class__\": \"ConnectedValue\"}, \"genome\": {\"__class__\": \"ConnectedValue\"}, \"kmer\": \"31\", \"phash\": false}}, \"tgmap\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.10.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "ee90c5ca-c7be-4544-b49e-e6568486ab8d",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "quants_mat_rows_txt_1",
-                                "output_name": "quants_mat_rows_txt",
-                                "uuid": "25d4d8f6-d166-4470-80fe-d0fdb0702371"
-                            },
-                            {
-                                "label": "quants_mat_mtx_1",
-                                "output_name": "quants_mat_mtx",
-                                "uuid": "d9ed1457-792b-4eaf-a9fc-2407bcd90da7"
-                            },
-                            {
-                                "label": "quants_mat_cols_txt_1",
-                                "output_name": "quants_mat_cols_txt",
-                                "uuid": "40df6aa8-3dfa-4946-bbc8-cacf4ca2a20e"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "single-cell/scrna-case_alevin",
-                "path": "topics/single-cell/tutorials/scrna-case_alevin/workflows/Generating-a-single-cell-matrix-using-Alevin.ga",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nForward reads FASTQ R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nBarcodes FASTQ R2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nReverse reads FASTQ R3\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Sinto barcode\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  2 -->|output| 3;\n  4[\"FastQC\"];\n  3 -->|read1_out| 4;\n  5[\"FastQC\"];\n  3 -->|read2_out| 5;\n  6[\"Map with BWA-MEM\"];\n  3 -->|read1_out| 6;\n  3 -->|read2_out| 6;\n  7[\"Sinto fragments\"];\n  6 -->|bam_output| 7;\n  8[\"bedtools SortBED\"];\n  7 -->|fragments| 8;\n  9[\"MACS2 callpeak\"];\n  8 -->|output| 9;\n  10[\"Unique\"];\n  9 -->|output_narrowpeaks| 10;\n  11[\"Build count matrix\"];\n  8 -->|output| 11;\n  10 -->|outfile| 11;\n  12[\"Inspect AnnData\"];\n  11 -->|anndata_out| 12;\n  13[\"Inspect AnnData\"];\n  11 -->|anndata_out| 13;\n  14[\"Inspect AnnData\"];\n  11 -->|anndata_out| 14;\n  15[\"Inspect AnnData\"];\n  11 -->|anndata_out| 15;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "scATAC-seq FASTQ to Count Matrix",
+                "outputs": [],
+                "parent_id": "single-cell/scatac-preprocessing-tenx",
+                "path": "topics/single-cell/tutorials/scatac-preprocessing-tenx/workflows/scATAC-seq-FASTQ-to-Count-Matrix.ga",
                 "tags": [],
                 "test_results": null,
                 "tests": true,
-                "title": "Generating a single cell matrix using Alevin",
+                "title": "scATAC-seq FASTQ to Count Matrix",
                 "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-case_alevin/versions/generating-a-single-cell-matrix-using-alevin",
-                "tutorial_id": "scrna-case_alevin",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_alevin/workflows/Generating-a-single-cell-matrix-using-Alevin.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_alevin/workflows/Generating-a-single-cell-matrix-using-Alevin.html",
-                "version": 2,
-                "wfid": "single-cell-scrna-case_alevin",
-                "wfname": "generating-a-single-cell-matrix-using-alevin",
-                "workflow": "Generating-a-single-cell-matrix-using-Alevin.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scatac-preprocessing-tenx/versions/scatac-seq-fastq-to-count-matrix",
+                "tutorial_id": "scatac-preprocessing-tenx",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-preprocessing-tenx/workflows/scATAC-seq-FASTQ-to-Count-Matrix.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-preprocessing-tenx/workflows/scATAC-seq-FASTQ-to-Count-Matrix.html",
+                "version": 1,
+                "wfid": "single-cell-scatac-preprocessing-tenx",
+                "wfname": "scatac-seq-fastq-to-count-matrix",
+                "workflow": "scATAC-seq-FASTQ-to-Count-Matrix.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "join1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.10.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/droplet_barcode_plot/_dropletBarcodePlot/1.6.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_empty_drops/dropletutils_empty_drops/1.0.4+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/salmon_kallisto_mtx_to_10x/_salmon_kallisto_mtx_to_10x/0.0.1+galaxy6",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/sceasy_convert/sceasy_convert/0.0.7+galaxy2"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.30.0+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/episcanpy_build_matrix/episcanpy_build_matrix/0.3.2+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/sinto_barcode/sinto_barcode/0.9.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/sinto_fragments/sinto_fragments/0.9.0+galaxy1"
                 ],
-                "workflowhub_id": "1263"
+                "workflowhub_id": "1208"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/4574153"
+        "zenodo_link": "https://zenodo.org/record/7855968"
     },
     {
         "admin_install": {
@@ -218480,10 +223167,12 @@
         },
         "contributors": [
             {
+                "elixir_node": "uk",
                 "email": "juliajot36@gmail.com",
                 "id": "wee-snufkin",
                 "joined": "2022-06",
                 "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
             },
@@ -218586,8 +223275,8 @@
         ],
         "dir": "topics/single-cell/tutorials/scrna-data-ingest",
         "edam_operation": [
-            "Loading",
-            "Community profiling"
+            "Community profiling",
+            "Loading"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -218622,7 +223311,7 @@
             "You will perform conversions between the most common single cell formats.",
             "You will downsample FASTQ files."
         ],
-        "pageviews": 779,
+        "pageviews": 1011,
         "priority": 1,
         "pub_date": "2024-02-13",
         "questions": [
@@ -218634,23 +223323,23 @@
         ],
         "short_id": "T00418",
         "short_tools": [
-            "anndata_ops",
-            "dropletutils_read_10x",
-            "anndata_inspect",
-            "sceasy_convert",
-            "tp_cut_tool",
-            "scanpy_filter_cells",
+            "monocle3_create",
+            "join1",
             "datamash_transpose",
-            "tp_tail_tool",
-            "seurat_read10x",
-            "Cut1",
-            "tabular_to_fastq",
+            "dropletutils_read_10x",
             "Filter1",
+            "seurat_read10x",
+            "anndata_ops",
             "fastq_to_tabular",
-            "monocle3_create",
+            "scanpy_filter_cells",
+            "sceasy_convert",
+            "Cut1",
+            "anndata_inspect",
             "dropletutils",
-            "join1",
-            "regexColumn1"
+            "regexColumn1",
+            "tp_cut_tool",
+            "tp_tail_tool",
+            "tabular_to_fastq"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -218714,8 +223403,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 113,
-        "visitors": 632,
+        "visit_duration": 101,
+        "visitors": 826,
         "workflows": [
             {
                 "creators": [
@@ -218787,7 +223476,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAnnData\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Inspect AnnData\"];\n  0 -->|output| 1;\n  7bdb825c-6a89-4a34-bbd9-a79c309c9750[\"Output\\nInspect AnnData: obs\"];\n  1 --> 7bdb825c-6a89-4a34-bbd9-a79c309c9750;\n  style 7bdb825c-6a89-4a34-bbd9-a79c309c9750 stroke:#2c3143,stroke-width:4px;\n  2[\"Inspect AnnData\"];\n  0 -->|output| 2;\n  79a2e3e5-4bd6-42de-864c-a5dc2412cb86[\"Output\\nInspect AnnData: var\"];\n  2 --> 79a2e3e5-4bd6-42de-864c-a5dc2412cb86;\n  style 79a2e3e5-4bd6-42de-864c-a5dc2412cb86 stroke:#2c3143,stroke-width:4px;\n  3[\"Inspect AnnData\"];\n  0 -->|output| 3;\n  7a254954-7e32-4e8a-bd4c-a79abf9db8d8[\"Output\\nInspect AnnData: X\"];\n  3 --> 7a254954-7e32-4e8a-bd4c-a79abf9db8d8;\n  style 7a254954-7e32-4e8a-bd4c-a79abf9db8d8 stroke:#2c3143,stroke-width:4px;\n  4[\"Transpose\"];\n  3 -->|X| 4;\n  5[\"Monocle3 create\"];\n  1 -->|obs| 5;\n  4 -->|out_file| 5;\n  2 -->|var| 5;\n  6bf4a0ea-3cb9-470c-9863-0a7eb0bc3d8c[\"Output\\nCDS Monocle file\"];\n  5 --> 6bf4a0ea-3cb9-470c-9863-0a7eb0bc3d8c;\n  style 6bf4a0ea-3cb9-470c-9863-0a7eb0bc3d8c stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:25 +0000",
+                "modified": "2024-10-02 12:08:10 +0000",
                 "name": "AnnData to Cell Data Set (CDS) conversion",
                 "outputs": [
                     {
@@ -219108,7 +223797,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAnnData\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Inspect AnnData\"];\n  0 -->|output| 1;\n  6d03d713-8d71-4f6a-9f83-cd999f423ebf[\"Output\\nInspect AnnData: obs\"];\n  1 --> 6d03d713-8d71-4f6a-9f83-cd999f423ebf;\n  style 6d03d713-8d71-4f6a-9f83-cd999f423ebf stroke:#2c3143,stroke-width:4px;\n  2[\"Inspect AnnData\"];\n  0 -->|output| 2;\n  ea025a8a-6f3a-4e38-a3af-db406886c7de[\"Output\\nInspect AnnData: X\"];\n  2 --> ea025a8a-6f3a-4e38-a3af-db406886c7de;\n  style ea025a8a-6f3a-4e38-a3af-db406886c7de stroke:#2c3143,stroke-width:4px;\n  3[\"Transpose\"];\n  2 -->|X| 3;\n  4[\"DropletUtils\"];\n  3 -->|out_file| 4;\n  5[\"Seurat Read10x\"];\n  4 -->|barcodes_out| 5;\n  4 -->|genes_out| 5;\n  4 -->|matrix_out| 5;\n  1 -->|obs| 5;\n  e5fec5dc-4706-48e5-8326-05e70290552d[\"Output\\nConverted Seurat object\"];\n  5 --> e5fec5dc-4706-48e5-8326-05e70290552d;\n  style e5fec5dc-4706-48e5-8326-05e70290552d stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:25 +0000",
+                "modified": "2024-10-02 12:08:10 +0000",
                 "name": "AnnData to Seurat conversion",
                 "outputs": [
                     {
@@ -219414,7 +224103,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAnnData\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nCell ID column\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"Inspect AnnData\"];\n  0 -->|output| 2;\n  8b9200c2-96e6-40fa-a8e9-1e99638c733f[\"Output\\nInspect AnnData: obs\"];\n  2 --> 8b9200c2-96e6-40fa-a8e9-1e99638c733f;\n  style 8b9200c2-96e6-40fa-a8e9-1e99638c733f stroke:#2c3143,stroke-width:4px;\n  3[\"Inspect AnnData\"];\n  0 -->|output| 3;\n  9fc4ce5a-8384-484d-b1cd-c0f5137cf821[\"Output\\nInspect AnnData: X\"];\n  3 --> 9fc4ce5a-8384-484d-b1cd-c0f5137cf821;\n  style 9fc4ce5a-8384-484d-b1cd-c0f5137cf821 stroke:#2c3143,stroke-width:4px;\n  4[\"Transpose\"];\n  3 -->|X| 4;\n  5[\"DropletUtils\"];\n  4 -->|out_file| 5;\n  6[\"DropletUtils Read10x\"];\n  1 -->|output| 6;\n  2 -->|obs| 6;\n  5 -->|barcodes_out| 6;\n  5 -->|genes_out| 6;\n  5 -->|matrix_out| 6;\n  3256e23f-2026-407d-aa25-0f8c0f3ae3f7[\"Output\\nConverted SCE object\"];\n  6 --> 3256e23f-2026-407d-aa25-0f8c0f3ae3f7;\n  style 3256e23f-2026-407d-aa25-0f8c0f3ae3f7 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:25 +0000",
+                "modified": "2024-10-02 12:08:10 +0000",
                 "name": "AnnData to SingleCellExperiment (SCE) conversion",
                 "outputs": [
                     {
@@ -219528,541 +224217,129 @@
                             "top": 230.26711592888955
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionX": {
-                                "action_arguments": {
-                                    "newname": "Matrix"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "X"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6f0d0c784f09",
-                            "name": "anndata_inspect",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"h5ad\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"X\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.10.3+galaxy0",
-                        "type": "tool",
-                        "uuid": "21e60473-83c4-4458-84c1-4fd7853e49b5",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Inspect AnnData: X",
-                                "output_name": "X",
-                                "uuid": "9fc4ce5a-8384-484d-b1cd-c0f5137cf821"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "add_metadata|cell_id_column": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "add_metadata|metadata_files": {
-                                "id": 2,
-                                "output_name": "obs"
-                            },
-                            "barcodes": {
-                                "id": 5,
-                                "output_name": "barcodes_out"
-                            },
-                            "genes": {
-                                "id": 5,
-                                "output_name": "genes_out"
-                            },
-                            "matrix": {
-                                "id": 5,
-                                "output_name": "matrix_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "DropletUtils Read10x",
-                        "outputs": [
-                            {
-                                "name": "output_rds",
-                                "type": "rdata"
-                            }
-                        ],
-                        "position": {
-                            "left": 1197.34937037914,
-                            "top": 645.5739866720206
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_rds": {
-                                "action_arguments": {
-                                    "newname": "Converted SCE object"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_rds"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ca62f52e0d7f",
-                            "name": "dropletutils_read_10x",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"add_metadata\": {\"add_metadata_file\": true, \"__current_case__\": 0, \"metadata_files\": {\"__class__\": \"ConnectedValue\"}, \"cell_id_column\": {\"__class__\": \"ConnectedValue\"}}, \"barcodes\": {\"__class__\": \"ConnectedValue\"}, \"genes\": {\"__class__\": \"ConnectedValue\"}, \"matrix\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.4+galaxy0",
-                        "type": "tool",
-                        "uuid": "a9f92b9d-af96-43ad-b3b3-b8a42089f32f",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Converted SCE object",
-                                "output_name": "output_rds",
-                                "uuid": "3256e23f-2026-407d-aa25-0f8c0f3ae3f7"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "single-cell/scrna-data-ingest",
-                "path": "topics/single-cell/tutorials/scrna-data-ingest/workflows/AnnData-to-SingleCellExperiment-(SCE)-conversion.ga",
-                "tags": [],
-                "test_results": null,
-                "tests": true,
-                "title": "AnnData to SingleCellExperiment (SCE) conversion",
-                "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-data-ingest/versions/anndata-to-singlecellexperiment--sce--conversion",
-                "tutorial_id": "scrna-data-ingest",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-data-ingest/workflows/AnnData-to-SingleCellExperiment-(SCE)-conversion.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-data-ingest/workflows/AnnData-to-SingleCellExperiment-(SCE)-conversion.html",
-                "version": 1,
-                "wfid": "single-cell-scrna-data-ingest",
-                "wfname": "anndata-to-singlecellexperiment--sce--conversion",
-                "workflow": "AnnData-to-SingleCellExperiment-(SCE)-conversion.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2"
-                ],
-                "workflowhub_id": "1247"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/4574153"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-intro/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "elixir_node": "de",
-                "email": "mtekman89@gmail.com",
-                "former_affiliations": [
-                    "elixir-europe"
-                ],
-                "id": "mtekman",
-                "joined": "2018-11",
-                "name": "Mehmet Tekman",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
-            }
-        ],
-        "dir": "topics/single-cell/tutorials/scrna-intro",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-preprocessing"
-                ],
-                "type": "internal"
-            }
-        ],
-        "hands_on": false,
-        "id": "single-cell/scrna-intro",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": 20144,
-            "mermaid": false
-        },
-        "key_points": [
-            "scRNA-seq requires much pre-processing before analysis can be performed.",
-            "Groups of similarly profiled-cells are compared against other groups.",
-            "Detectability issues requires careful consideration at all stages.",
-            "Clustering is an integral part of an analysis."
-        ],
-        "layout": "tutorial_slides",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "logo": "GTN",
-        "mod_date": "2024-08-08",
-        "objectives": [
-            "To understand the pitfalls in scRNA-seq sequencing and amplification, and how they are overcome.",
-            "Know the types of variation in an analysis and how to control for them.",
-            "Grasp what dimension reduction is, and how it might be performed.",
-            "Be familiarised with the main types of clustering techniques and when to use them."
-        ],
-        "pageviews": 5612842,
-        "priority": 1,
-        "pub_date": "2021-01-29",
-        "questions": [
-            "How are samples compared?",
-            "How are cells captured?",
-            "How does bulk RNA-seq differ from scRNA-seq?",
-            "Why is clustering important?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "mtekman"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "20M",
-                "speakers": [
-                    "awspolly"
-                ],
-                "youtube_id": "D3qvYWZMFa0"
-            }
-        ],
-        "redirect_from": [
-            "/topics/transcriptomics/tutorials/scrna-intro/slides",
-            "/short/single-cell/scrna-intro/slides",
-            "/short/S00084"
-        ],
-        "short_id": "S00084",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": [
-            {
-                "captioners": [
-                    "mtekman"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "20M",
-                "speakers": [
-                    "awspolly"
-                ],
-                "youtube_id": "D3qvYWZMFa0"
-            }
-        ],
-        "subtopic": "scintroduction",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": null,
-        "time_estimation": "30m",
-        "title": "An introduction to scRNA-seq data analysis",
-        "tools": [],
-        "topic_name": "single-cell",
-        "topic_name_human": "Single Cell",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": true
-        },
-        "tutorial_name": "scrna-intro",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-intro/slides.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-intro/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-intro/slides.json"
-        },
-        "version": 5,
-        "video": true,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2029238,
-        "zenodo_link": ""
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/alevin-commandline/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "wee-snufkin",
-                "nomadscientist"
-            ],
-            "editing": [
-                "pavanvidem",
-                "mtekman"
-            ],
-            "funding": [
-                "eosc-life"
-            ],
-            "testing": [
-                "pavanvidem"
-            ]
-        },
-        "contributors": [
-            {
-                "email": "juliajot36@gmail.com",
-                "id": "wee-snufkin",
-                "joined": "2022-06",
-                "name": "Julia Jakiela",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "bio": "Senior Lecturer at The Open University",
-                "elixir_node": "uk",
-                "email": "wendi.bacon@open.ac.uk",
-                "fediverse": "https://mstdn.science/@wendibacon1",
-                "fediverse_flavor": "mastodon",
-                "id": "nomadscientist",
-                "joined": "2020-03",
-                "matrix": "nomadscientist:matrix.org",
-                "name": "Wendi Bacon",
-                "orcid": "0000-0002-8170-8806",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
-                "twitter": "WendiBacon1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "pavanvidem",
-                "joined": "2017-09",
-                "name": "Pavankumar Videm",
-                "orcid": "0000-0002-5192-126X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "elixir_node": "de",
-                "email": "mtekman89@gmail.com",
-                "former_affiliations": [
-                    "elixir-europe"
-                ],
-                "id": "mtekman",
-                "joined": "2018-11",
-                "name": "Mehmet Tekman",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "pavanvidem",
-                "joined": "2017-09",
-                "name": "Pavankumar Videm",
-                "orcid": "0000-0002-5192-126X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
-            },
-            {
-                "avatar": "https://www.eosc-life.eu/wp-content/themes/eosc-life-v2/assets/images/eosclogo.png",
-                "funder": true,
-                "funding_id": "824087",
-                "funding_statement": "EOSC-Life has received funding from the European Union\u2019s Horizon 2020 programme under grant agreement number 824087",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "eosc-life",
-                "joined": "2023-04",
-                "members": [
-                    "bgruening"
-                ],
-                "name": "EOSC-Life",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eosc-life/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/eosc-life.json"
-            }
-        ],
-        "dir": "topics/single-cell/tutorials/alevin-commandline",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-case_alevin-combine-datasets"
+                            "RenameDatasetActionX": {
+                                "action_arguments": {
+                                    "newname": "Matrix"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "X"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "6f0d0c784f09",
+                            "name": "anndata_inspect",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"h5ad\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"X\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.10.3+galaxy0",
+                        "type": "tool",
+                        "uuid": "21e60473-83c4-4458-84c1-4fd7853e49b5",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Inspect AnnData: X",
+                                "output_name": "X",
+                                "uuid": "9fc4ce5a-8384-484d-b1cd-c0f5137cf821"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "add_metadata|cell_id_column": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "add_metadata|metadata_files": {
+                                "id": 2,
+                                "output_name": "obs"
+                            },
+                            "barcodes": {
+                                "id": 5,
+                                "output_name": "barcodes_out"
+                            },
+                            "genes": {
+                                "id": 5,
+                                "output_name": "genes_out"
+                            },
+                            "matrix": {
+                                "id": 5,
+                                "output_name": "matrix_out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "DropletUtils Read10x",
+                        "outputs": [
+                            {
+                                "name": "output_rds",
+                                "type": "rdata"
+                            }
+                        ],
+                        "position": {
+                            "left": 1197.34937037914,
+                            "top": 645.5739866720206
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_rds": {
+                                "action_arguments": {
+                                    "newname": "Converted SCE object"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_rds"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ca62f52e0d7f",
+                            "name": "dropletutils_read_10x",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"add_metadata\": {\"add_metadata_file\": true, \"__current_case__\": 0, \"metadata_files\": {\"__class__\": \"ConnectedValue\"}, \"cell_id_column\": {\"__class__\": \"ConnectedValue\"}}, \"barcodes\": {\"__class__\": \"ConnectedValue\"}, \"genes\": {\"__class__\": \"ConnectedValue\"}, \"matrix\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.4+galaxy0",
+                        "type": "tool",
+                        "uuid": "a9f92b9d-af96-43ad-b3b3-b8a42089f32f",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Converted SCE object",
+                                "output_name": "output_rds",
+                                "uuid": "3256e23f-2026-407d-aa25-0f8c0f3ae3f7"
+                            }
+                        ]
+                    }
                 ],
-                "type": "internal"
-            }
-        ],
-        "hands_on": true,
-        "id": "single-cell/alevin-commandline",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Create a SCE object from FASTQ files, including relevant gene and cell metadata, and do it all in Jupyter Notebook!"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-02-13",
-        "notebook": {
-            "language": "bash",
-            "snippet": "topics/single-cell/tutorials/alevin-commandline/preamble.md"
-        },
-        "objectives": [
-            "Generate a cellxgene matrix for droplet-based single cell sequencing data",
-            "Interpret quality control (QC) plots to make informed decisions on cell thresholds",
-            "Find relevant information in GTF files for the particulars of their study, and include this in data matrix metadata"
-        ],
-        "pageviews": 241,
-        "priority": 1,
-        "pub_date": "2023-12-08",
-        "questions": [
-            "I have some single cell FASTQ files I want to analyse. Where do I start?",
-            "How to generate a single cell matrix using command line?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-case_alevin"
+                "parent_id": "single-cell/scrna-data-ingest",
+                "path": "topics/single-cell/tutorials/scrna-data-ingest/workflows/AnnData-to-SingleCellExperiment-(SCE)-conversion.ga",
+                "tags": [],
+                "test_results": null,
+                "tests": true,
+                "title": "AnnData to SingleCellExperiment (SCE) conversion",
+                "topic_id": "single-cell",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-data-ingest/versions/anndata-to-singlecellexperiment--sce--conversion",
+                "tutorial_id": "scrna-data-ingest",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-data-ingest/workflows/AnnData-to-SingleCellExperiment-(SCE)-conversion.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-data-ingest/workflows/AnnData-to-SingleCellExperiment-(SCE)-conversion.html",
+                "version": 1,
+                "wfid": "single-cell-scrna-data-ingest",
+                "wfname": "anndata-to-singlecellexperiment--sce--conversion",
+                "workflow": "AnnData-to-SingleCellExperiment-(SCE)-conversion.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2"
                 ],
-                "type": "internal"
+                "workflowhub_id": "1247"
             }
         ],
-        "short_id": "T00378",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "single-cell-CS-code",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "10x",
-            "paper-replication"
-        ],
-        "time_estimation": "2H",
-        "title": "Generating a single cell matrix using Alevin and combining datasets (bash + R)",
-        "tools": [],
-        "topic_name": "single-cell",
-        "topic_name_human": "Single Cell",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "alevin-commandline",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/alevin-commandline/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/alevin-commandline/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/alevin-commandline/tutorial.json"
-        },
-        "version": 2,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 146,
-        "visitors": 205,
-        "zenodo_link": null
+        "zenodo_link": "https://zenodo.org/record/4574153"
     },
     {
         "admin_install": {
@@ -220073,147 +224350,190 @@
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "12615d397df7",
+                    "revisions": "d698c222f354",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "anndata_ops",
-                    "owner": "ebi-gxa",
-                    "revisions": "a4774b7b2e85",
-                    "tool_panel_section_label": "Single-cell",
+                    "name": "bamtools_filter",
+                    "owner": "devteam",
+                    "revisions": "cb20f99fd45b",
+                    "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "retrieve_scxa",
-                    "owner": "ebi-gxa",
-                    "revisions": "72b6e1747e37",
-                    "tool_panel_section_label": "Single-cell",
+                    "name": "samtools_stats",
+                    "owner": "devteam",
+                    "revisions": "24c5d43cb545",
+                    "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_read_10x",
-                    "owner": "ebi-gxa",
-                    "revisions": "9afcfcd1d215",
-                    "tool_panel_section_label": "Single-cell",
+                    "name": "collection_column_join",
+                    "owner": "iuc",
+                    "revisions": "3ddd99c7efee",
+                    "tool_panel_section_label": "Join, Subtract and Group",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "anndata_inspect",
+                    "name": "featurecounts",
                     "owner": "iuc",
-                    "revisions": "6f0d0c784f09",
-                    "tool_panel_section_label": "Single-cell",
+                    "revisions": "f3a5f075498f",
+                    "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "anndata_inspect",
+                    "name": "featurecounts",
                     "owner": "iuc",
-                    "revisions": "ee98d611afc6",
-                    "tool_panel_section_label": "Single-cell",
+                    "revisions": "ea04b737afa0",
+                    "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "anndata_manipulate",
+                    "name": "multiqc",
                     "owner": "iuc",
-                    "revisions": "ed4996a16f7f",
-                    "tool_panel_section_label": "Single-cell",
+                    "revisions": "df99138d2776",
+                    "tool_panel_section_label": "Quality Control",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "c1a4b5f3b432",
+                    "tool_panel_section_label": "Quality Control",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rgrnastar",
+                    "owner": "iuc",
+                    "revisions": "2055c2667eb3",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rgrnastar",
+                    "owner": "iuc",
+                    "revisions": "7ed2edc1337f",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "umi_tools_count",
+                    "owner": "iuc",
+                    "revisions": "b557acca0b56",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "umi_tools_count",
+                    "owner": "iuc",
+                    "revisions": "8250ea3a1501",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "umi_tools_extract",
+                    "owner": "iuc",
+                    "revisions": "828dba98cdb4",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "umi_tools_extract",
+                    "owner": "iuc",
+                    "revisions": "6a675c3aa610",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: 12615d397df7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_ops\n  owner: ebi-gxa\n  revisions: a4774b7b2e85\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: retrieve_scxa\n  owner: ebi-gxa\n  revisions: 72b6e1747e37\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_read_10x\n  owner: ebi-gxa\n  revisions: 9afcfcd1d215\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_inspect\n  owner: iuc\n  revisions: 6f0d0c784f09\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_inspect\n  owner: iuc\n  revisions: ee98d611afc6\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n  owner: iuc\n  revisions: ed4996a16f7f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "answer_histories": [
-            {
-                "date": "2024-03-26",
-                "history": "https://usegalaxy.eu/u/j.jakiela/h/combining-datasets-key-history",
-                "label": "UseGalaxy.eu"
-            },
-            {
-                "date": "2024-03-26",
-                "history": "https://usegalaxy.eu/u/j.jakiela/h/all-total-samples-processed-after-alevin-into-single-object",
-                "label": "All total samples - processed after Alevin into single object (UseGalaxy.eu)"
-            }
-        ],
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "nomadscientist",
-                "pinin4fjords"
-            ],
-            "editing": [
-                "hexylena"
-            ],
-            "testing": [
-                "wee-snufkin"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_filter\n  owner: devteam\n  revisions: cb20f99fd45b\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 24c5d43cb545\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_column_join\n  owner: iuc\n  revisions: 3ddd99c7efee\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: featurecounts\n  owner: iuc\n  revisions: f3a5f075498f\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: featurecounts\n  owner: iuc\n  revisions: ea04b737afa0\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: df99138d2776\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: c1a4b5f3b432\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n  owner: iuc\n  revisions: 2055c2667eb3\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n  owner: iuc\n  revisions: 7ed2edc1337f\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: umi_tools_count\n  owner: iuc\n  revisions: b557acca0b56\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: umi_tools_count\n  owner: iuc\n  revisions: 8250ea3a1501\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: umi_tools_extract\n  owner: iuc\n  revisions: 828dba98cdb4\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: umi_tools_extract\n  owner: iuc\n  revisions: 6a675c3aa610\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-preprocessing/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
+                    "uni-freiburg"
+                ],
+                "elixir_node": "de",
+                "email": "mtekman89@gmail.com",
+                "former_affiliations": [
                     "elixir-europe"
                 ],
-                "bio": "Senior Lecturer at The Open University",
-                "elixir_node": "uk",
-                "email": "wendi.bacon@open.ac.uk",
-                "fediverse": "https://mstdn.science/@wendibacon1",
-                "fediverse_flavor": "mastodon",
-                "id": "nomadscientist",
-                "joined": "2020-03",
-                "matrix": "nomadscientist:matrix.org",
-                "name": "Wendi Bacon",
-                "orcid": "0000-0002-8170-8806",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
-                "twitter": "WendiBacon1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
-            },
-            {
-                "email": "jmanning@ebi.ac.uk",
-                "id": "pinin4fjords",
-                "joined": "2021-02",
-                "name": "Jonathan Manning",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pinin4fjords/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pinin4fjords.json"
+                "id": "mtekman",
+                "joined": "2018-11",
+                "name": "Mehmet Tekman",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
             },
             {
                 "affiliations": [
                     "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
+                    "ifb",
+                    "elixir-europe"
                 ],
-                "id": "hexylena",
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
                 "joined": "2017-09",
+                "linkedin": "berenicebatut",
                 "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
                 },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             },
             {
-                "email": "juliajot36@gmail.com",
-                "id": "wee-snufkin",
-                "joined": "2022-06",
-                "name": "Julia Jakiela",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
+                "affiliations": [
+                    "eurosciencegateway",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "elixir_node": "de",
+                "email": "anikaerxleben@gmail.com",
+                "id": "erxleben",
+                "joined": "2017-09",
+                "name": "Anika Erxleben",
+                "orcid": "0000-0002-7427-6478",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/erxleben/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/erxleben.json"
+            },
+            {
+                "affiliations": [
+                    "by-covid",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "elixir_node": "de",
+                "fediverse": "https://scholar.social/@zerodivision",
+                "fediverse_flavor": "mastodon",
+                "id": "wm75",
+                "joined": "2017-09",
+                "matrix": "wm75:matrix.org",
+                "name": "Wolfgang Maier",
+                "orcid": "0000-0002-9464-6640",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
             }
         ],
-        "dir": "topics/single-cell/tutorials/scrna-case_alevin-combine-datasets",
-        "edam_operation": [],
+        "dir": "topics/single-cell/tutorials/scrna-preprocessing",
+        "edam_operation": [
+            "RNA-Seq quantification",
+            "Data handling",
+            "Sequence alignment",
+            "Validation",
+            "Sequencing quality control",
+            "Sequence alignment analysis",
+            "Read summarisation"
+        ],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu"
@@ -220224,104 +224544,81 @@
             {
                 "topic_name": "single-cell",
                 "tutorials": [
-                    "scrna-case_basic-pipeline"
+                    "scrna-umis"
                 ],
                 "type": "internal"
             }
         ],
         "gitter": "Galaxy-Training-Network/galaxy-single-cell",
         "hands_on": true,
-        "id": "single-cell/scrna-case_alevin-combine-datasets",
+        "id": "single-cell/scrna-preprocessing",
         "inexact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
-        "input_histories": [
-            {
-                "history": "https://usegalaxy.eu/u/j.jakiela/h/combining-datasets-input",
-                "label": "UseGalaxy.eu"
-            },
-            {
-                "history": "https://usegalaxy.org/u/juliajot/h/combining-datasets-input",
-                "label": "UseGalaxy.org"
-            }
-        ],
         "js_requirements": {
-            "mathjax": null,
+            "mathjax": 39191,
             "mermaid": false
         },
         "key_points": [
-            "Create a single scanpy-accessible AnnData object from multiple AnnData files, including relevant cell metadata according to the study design",
-            "Retreive partially analysed data from a public repository"
+            "Verifying the distribution of barcodes via a FASTQC plot",
+            "Relocating barcodes into headers",
+            "Merging matrices from different batches together",
+            "Removing unwanted barcodes"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2023-10-10",
         "objectives": [
-            "Combine data matrices from different samples in the same experiment",
-            "Label the metadata for downstream processing"
+            "Demultiplex FASTQ data via UMI-tools",
+            "Understand and validate the extraction of barcodes",
+            "Obtain an overview of general alignment and quantification techniques",
+            "Generate a count matrix for downstream single-cell RNA analysis"
         ],
-        "pageviews": 2373,
-        "priority": 2,
-        "pub_date": "2022-09-08",
+        "pageviews": 5903735,
+        "priority": 1,
+        "pub_date": "2019-02-22",
         "questions": [
-            "I have some AnnData files from different samples that I want to combine into a single file. How can I combine these and label them within the object?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "hrukkudyr"
-                ],
-                "date": "2023-05-09",
-                "length": "11M",
-                "speakers": [
-                    "hrukkudyr"
-                ],
-                "youtube_id": "22t-4qvHnow"
-            },
-            {
-                "captioners": [
-                    "nomadscientist"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.09",
-                "length": "11M",
-                "speakers": [
-                    "nomadscientist"
-                ],
-                "youtube_id": "U8pVa6csmUE"
-            }
+            "What is single-cell?",
+            "How do we process a batch?",
+            "How do we process multiple batches?",
+            "How do we check for cross-contamination?"
         ],
         "redirect_from": [
-            "/topics/transcriptomics/tutorials/scrna-case_alevin-combine-datasets/tutorial",
-            "/short/single-cell/scrna-case_alevin-combine-datasets",
-            "/short/T00246"
+            "/topics/transcriptomics/tutorials/scrna_preprocessing/tutorial",
+            "/topics/transcriptomics/tutorials/scrna-preprocessing/tutorial",
+            "/short/single-cell/scrna-preprocessing",
+            "/short/T00251"
         ],
         "requirements": [
             {
                 "topic_name": "single-cell",
                 "tutorials": [
-                    "scrna-intro",
-                    "scrna-umis",
-                    "scrna-case_alevin"
+                    "scrna-intro"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00246",
+        "short_id": "T00251",
         "short_tools": [
-            "anndata_ops",
-            "anndata_manipulate",
-            "scanpy_read_10x",
-            "anndata_inspect",
-            "Paste1",
-            "Cut1",
-            "retrieve_scxa",
-            "tp_replace_in_column"
+            "rna_star",
+            "samtools_stats",
+            "tp_sed_tool",
+            "umi_tools_count",
+            "bamFilter",
+            "multiqc",
+            "umi_tools_extract",
+            "collection_column_join",
+            "__FLATTEN__",
+            "featurecounts"
         ],
-        "slides": false,
+        "slides": true,
         "slides_recordings": false,
-        "subtopic": "single-cell-CS",
+        "subtopic": "end-to-end",
         "supported_servers": {
             "exact": [
                 {
@@ -220331,6 +224628,26 @@
                 }
             ],
             "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -220344,22 +224661,25 @@
             ]
         },
         "symlink": null,
-        "tags": [
-            "10x",
-            "paper-replication"
-        ],
-        "time_estimation": "1H",
-        "title": "Combining single cell datasets after pre-processing",
+        "tags": null,
+        "time_estimation": "3h",
+        "title": "Pre-processing of Single-Cell RNA Data",
         "tools": [
-            "Cut1",
-            "Paste1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0"
+            "__FLATTEN__",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9",
+            "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.7a",
+            "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.5.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1"
         ],
         "topic_name": "single-cell",
         "topic_name_human": "Single Cell",
@@ -220369,909 +224689,1091 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "scrna-case_alevin-combine-datasets",
+        "tutorial_name": "scrna-preprocessing",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-preprocessing/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-preprocessing/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-preprocessing/tutorial.json"
         },
-        "version": 16,
+        "version": 2,
         "video": false,
-        "video_versions": 2,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 131,
-        "visitors": 1673,
+        "visit_duration": 291,
+        "visitors": 2138310,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0009-0001-2017-8805",
-                        "name": "Julia Jakiela"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-8170-8806",
-                        "name": "Wendi Bacon"
-                    }
-                ],
-                "description": "Updated March 2024",
+                "creators": [],
+                "description": "Pre-processing of Single-Cell RNA Data",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
-                    "subworkflows": false
+                    "subworkflows": true
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nN701\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nN702\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nN703\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nN704\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nN705\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nN706\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nN707\"]\n  7[label=\"Concatenating Datasets\"]\n  0 -> 7 [label=\"output\"]\n  1 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  3 -> 7 [label=\"output\"]\n  4 -> 7 [label=\"output\"]\n  5 -> 7 [label=\"output\"]\n  6 -> 7 [label=\"output\"]\n  k168d4710570a43b1998a2164154eebc5[color=lightseagreen,label=\"Output\\nCombined Object\"]\n  7 -> k168d4710570a43b1998a2164154eebc5\n  8[label=\"Inspect AnnData\"]\n  7 -> 8 [label=\"anndata\"]\n  9[label=\"Inspect AnnData\"]\n  7 -> 9 [label=\"anndata\"]\n  10[label=\"Inspect AnnData\"]\n  7 -> 10 [label=\"anndata\"]\n  11[label=\"Replace Text\"]\n  9 -> 11 [label=\"obs\"]\n  12[label=\"Replace Text\"]\n  9 -> 12 [label=\"obs\"]\n  13[label=\"Cut\"]\n  11 -> 13 [label=\"outfile\"]\n  k8b026c35f9db4bcd8cf554b7d6fb5aea[color=lightseagreen,label=\"Output\\nSex metadata\"]\n  13 -> k8b026c35f9db4bcd8cf554b7d6fb5aea\n  14[label=\"Cut\"]\n  12 -> 14 [label=\"outfile\"]\n  k6f55548b5ded42b8b2f7c7f1a327a068[color=lightseagreen,label=\"Output\\nGenotype metadata\"]\n  14 -> k6f55548b5ded42b8b2f7c7f1a327a068\n  15[label=\"Paste\"]\n  14 -> 15 [label=\"out_file1\"]\n  13 -> 15 [label=\"out_file1\"]\n  k2f0ea0f3f2f744b2b8f005d8cbb364a6[color=lightseagreen,label=\"Output\\nCell metadata\"]\n  15 -> k2f0ea0f3f2f744b2b8f005d8cbb364a6\n  16[label=\"Adding in cell metadata\"]\n  7 -> 16 [label=\"anndata\"]\n  15 -> 16 [label=\"out_file1\"]\n  k2720386c727349d6abb09bd14f6cb68c[color=lightseagreen,label=\"Output\\nAnnData with Cell Metadata\"]\n  16 -> k2720386c727349d6abb09bd14f6cb68c\n  17[label=\"Batching Cell Metadata\"]\n  16 -> 17 [label=\"anndata\"]\n  kb950c8dbabe14cb0af58d291d3b74a83[color=lightseagreen,label=\"Output\\nBatched Object\"]\n  17 -> kb950c8dbabe14cb0af58d291d3b74a83\n  18[label=\"Calculating mitochondrial \"]\n  17 -> 18 [label=\"anndata\"]\n  k2417284d825243ff84bf6f15ef11cd05[color=lightseagreen,label=\"Output\\nAnnotated AnnData\"]\n  18 -> k2417284d825243ff84bf6f15ef11cd05\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nList of FACS pairs\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBarcodes\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGTF file UCSC\"]\n  3[label=\"Flatten Collection\"]\n  0 -> 3 [label=\"output\"]\n  4[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nCelSeq2: Single Batch mm10\"]\n  1 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Column Join\"]\n  4 -> 5 [label=\"9:out_counts\"]\n}",
                 "history": [
                     {
-                        "hash": "923c71c756c805a4ce7f2b794fa721aa6a4966f4",
-                        "message": "workflow tests",
+                        "hash": "327fd2b842f45de3dc2a30067714352675ad69ae",
+                        "message": "Making a single cell topics",
                         "num": 1,
-                        "short_hash": "923c71c75",
-                        "unix": "1711487790"
+                        "short_hash": "327fd2b84",
+                        "unix": "1668273265"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "Dataset to be combined",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Dataset to be combined",
-                                "name": "N701"
-                            }
-                        ],
-                        "label": "N701",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 12.9765625,
-                            "top": 159.9921875
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f5f24f48-9a1d-49f2-b351-ec3dbea3a6c6",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "Dataset to be combined",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Dataset to be combined",
-                                "name": "N702"
-                            }
-                        ],
-                        "label": "N702",
-                        "name": "Input dataset",
+                        "inputs": [],
+                        "label": "List of FACS pairs",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 8.9921875,
-                            "top": 241
+                            "left": 119.5,
+                            "top": 260
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{\"collection_type\": \"list:paired\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "509506fb-e5ef-4509-92dd-196aa797870a",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "Dataset to be combined",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "type": "data_collection_input",
+                        "uuid": "c50ee411-e25e-4570-97bf-f0a05af2458e",
+                        "workflow_outputs": [
                             {
-                                "description": "Dataset to be combined",
-                                "name": "N703"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "37307bc9-a8de-4fb4-8482-4a3554c9af36"
                             }
-                        ],
-                        "label": "N703",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 322.9921875
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f4726f7b-d956-45b7-b1e0-b9df93b9892c",
-                        "when": null,
-                        "workflow_outputs": []
+                        ]
                     },
                     {
-                        "annotation": "Dataset to be combined",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 1,
                         "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Dataset to be combined",
-                                "name": "N704"
-                            }
-                        ],
-                        "label": "N704",
+                        "inputs": [],
+                        "label": "Barcodes",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 4.984375,
-                            "top": 434
+                            "left": 566.5,
+                            "top": 429.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "908341bb-6451-4360-a2ec-a1af73fb941e",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "Dataset to be combined",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
+                        "uuid": "cb331533-4896-419f-83ca-196c5daf2c03",
+                        "workflow_outputs": [
                             {
-                                "description": "Dataset to be combined",
-                                "name": "N705"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "d863899f-2ea8-49d1-acc9-a2cca1f9fce3"
                             }
-                        ],
-                        "label": "N705",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 6,
-                            "top": 538.9921875
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "6c534b76-c5cc-4bbe-b180-376200e29b75",
-                        "when": null,
-                        "workflow_outputs": []
+                        ]
                     },
                     {
-                        "annotation": "Dataset to be combined",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 5,
+                        "id": 2,
                         "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Dataset to be combined",
-                                "name": "N706"
-                            }
-                        ],
-                        "label": "N706",
+                        "inputs": [],
+                        "label": "GTF file (UCSC)",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 7.000041058980229,
-                            "top": 640.0000146155871
+                            "left": 568.5,
+                            "top": 521
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "b512e8b6-85f2-45b7-a057-d0af216b26f0",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "Dataset to be combined",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {},
-                        "inputs": [
+                        "uuid": "ac1f89bb-52b9-41ac-a6d4-f8dfd4d21550",
+                        "workflow_outputs": [
                             {
-                                "description": "Dataset to be combined",
-                                "name": "N707"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "51046a1f-f629-4e6a-aac1-eb563eeb693b"
                             }
-                        ],
-                        "label": "N707",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 7,
-                            "top": 741
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "6aee1bd4-2698-4572-aa78-1b166f27eff2",
-                        "when": null,
-                        "workflow_outputs": []
+                        ]
                     }
                 ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nN701\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nN702\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nN703\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nN704\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nN705\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nN706\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nN707\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"Concatenating Datasets\"];\n  0 -->|output| 7;\n  1 -->|output| 7;\n  2 -->|output| 7;\n  3 -->|output| 7;\n  4 -->|output| 7;\n  5 -->|output| 7;\n  6 -->|output| 7;\n  168d4710-570a-43b1-998a-2164154eebc5[\"Output\\nCombined Object\"];\n  7 --> 168d4710-570a-43b1-998a-2164154eebc5;\n  style 168d4710-570a-43b1-998a-2164154eebc5 stroke:#2c3143,stroke-width:4px;\n  8[\"Inspect AnnData\"];\n  7 -->|anndata| 8;\n  9[\"Inspect AnnData\"];\n  7 -->|anndata| 9;\n  10[\"Inspect AnnData\"];\n  7 -->|anndata| 10;\n  11[\"Replace Text\"];\n  9 -->|obs| 11;\n  12[\"Replace Text\"];\n  9 -->|obs| 12;\n  13[\"Cut\"];\n  11 -->|outfile| 13;\n  8b026c35-f9db-4bcd-8cf5-54b7d6fb5aea[\"Output\\nSex metadata\"];\n  13 --> 8b026c35-f9db-4bcd-8cf5-54b7d6fb5aea;\n  style 8b026c35-f9db-4bcd-8cf5-54b7d6fb5aea stroke:#2c3143,stroke-width:4px;\n  14[\"Cut\"];\n  12 -->|outfile| 14;\n  6f55548b-5ded-42b8-b2f7-c7f1a327a068[\"Output\\nGenotype metadata\"];\n  14 --> 6f55548b-5ded-42b8-b2f7-c7f1a327a068;\n  style 6f55548b-5ded-42b8-b2f7-c7f1a327a068 stroke:#2c3143,stroke-width:4px;\n  15[\"Paste\"];\n  14 -->|out_file1| 15;\n  13 -->|out_file1| 15;\n  2f0ea0f3-f2f7-44b2-b8f0-05d8cbb364a6[\"Output\\nCell metadata\"];\n  15 --> 2f0ea0f3-f2f7-44b2-b8f0-05d8cbb364a6;\n  style 2f0ea0f3-f2f7-44b2-b8f0-05d8cbb364a6 stroke:#2c3143,stroke-width:4px;\n  16[\"Adding in cell metadata\"];\n  7 -->|anndata| 16;\n  15 -->|out_file1| 16;\n  2720386c-7273-49d6-abb0-9bd14f6cb68c[\"Output\\nAnnData with Cell Metadata\"];\n  16 --> 2720386c-7273-49d6-abb0-9bd14f6cb68c;\n  style 2720386c-7273-49d6-abb0-9bd14f6cb68c stroke:#2c3143,stroke-width:4px;\n  17[\"Batching Cell Metadata\"];\n  16 -->|anndata| 17;\n  b950c8db-abe1-4cb0-af58-d291d3b74a83[\"Output\\nBatched Object\"];\n  17 --> b950c8db-abe1-4cb0-af58-d291d3b74a83;\n  style b950c8db-abe1-4cb0-af58-d291d3b74a83 stroke:#2c3143,stroke-width:4px;\n  18[\"Calculating mitochondrial \"];\n  17 -->|anndata| 18;\n  2417284d-8252-43ff-84bf-6f15ef11cd05[\"Output\\nAnnotated AnnData\"];\n  18 --> 2417284d-8252-43ff-84bf-6f15ef11cd05;\n  style 2417284d-8252-43ff-84bf-6f15ef11cd05 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Combining datasets after pre-processing",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nList of FACS pairs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nBarcodes\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nGTF file UCSC\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Flatten Collection\"];\n  0 -->|output| 3;\n  4[\"\ud83d\udee0\ufe0f Subworkflow\\nCelSeq2: Single Batch mm10\"];\n  style 4 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 4;\n  3 -->|output| 4;\n  2 -->|output| 4;\n  5[\"Column Join\"];\n  4 -->|9:out_counts| 5;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "CelSeq2: Multi Batch (mm10)",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "manipulate|other_adatas": [
-                                {
-                                    "id": 1,
-                                    "output_name": "output"
-                                },
-                                {
-                                    "id": 2,
-                                    "output_name": "output"
-                                },
-                                {
-                                    "id": 3,
-                                    "output_name": "output"
-                                },
-                                {
-                                    "id": 4,
-                                    "output_name": "output"
-                                },
-                                {
-                                    "id": 5,
-                                    "output_name": "output"
-                                },
-                                {
-                                    "id": 6,
-                                    "output_name": "output"
-                                }
-                            ]
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Manipulate AnnData",
-                                "name": "manipulate"
-                            }
-                        ],
-                        "label": "Concatenating Datasets",
-                        "name": "Manipulate AnnData",
-                        "outputs": [
-                            {
-                                "name": "anndata",
-                                "type": "h5ad"
-                            }
-                        ],
-                        "position": {
-                            "left": 295.0234375,
-                            "top": 410
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionanndata": {
-                                "action_arguments": {
-                                    "newname": "Combined AnnData"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "anndata"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ed4996a16f7f",
-                            "name": "anndata_manipulate",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"concatenate\", \"__current_case__\": 0, \"other_adatas\": {\"__class__\": \"ConnectedValue\"}, \"join\": \"inner\", \"batch_key\": \"batch\", \"index_unique\": \"-\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.10.3+galaxy0",
-                        "type": "tool",
-                        "uuid": "4dfd7670-2dd9-46d4-9c97-aaf33524d076",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Combined Object",
-                                "output_name": "anndata",
-                                "uuid": "168d4710-570a-43b1-998a-2164154eebc5"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "Cut1",
-                        "errors": null,
-                        "id": 13,
-                        "input_connections": {
-                            "input": {
-                                "id": 11,
-                                "output_name": "outfile"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cut",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 1129.03125,
-                            "top": 280
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Sex metadata"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"columnList\": \"c8\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2",
-                        "type": "tool",
-                        "uuid": "731604ed-f075-49b5-9beb-752b69cdc388",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Sex metadata",
-                                "output_name": "out_file1",
-                                "uuid": "8b026c35-f9db-4bcd-8cf5-54b7d6fb5aea"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "Cut1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 14,
-                        "input_connections": {
-                            "input": {
-                                "id": 12,
-                                "output_name": "outfile"
-                            }
-                        },
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [],
-                        "label": null,
-                        "name": "Cut",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "tabular"
-                            }
-                        ],
+                        "label": "List of FACS pairs",
+                        "name": "Input dataset collection",
+                        "outputs": [],
                         "position": {
-                            "left": 1129.03125,
-                            "top": 423.9921875
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Genotype metadata"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"columnList\": \"c8\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2",
-                        "type": "tool",
-                        "uuid": "1021770e-eb6d-4e23-b75f-76f5827e37e1",
-                        "when": null,
+                            "left": 119.5,
+                            "top": 260
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"collection_type\": \"list:paired\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "c50ee411-e25e-4570-97bf-f0a05af2458e",
                         "workflow_outputs": [
                             {
-                                "label": "Genotype metadata",
-                                "output_name": "out_file1",
-                                "uuid": "6f55548b-5ded-42b8-b2f7-c7f1a327a068"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "37307bc9-a8de-4fb4-8482-4a3554c9af36"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Paste1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 15,
-                        "input_connections": {
-                            "input1": {
-                                "id": 14,
-                                "output_name": "out_file1"
-                            },
-                            "input2": {
-                                "id": 13,
-                                "output_name": "out_file1"
-                            }
-                        },
+                        "id": 1,
+                        "input_connections": {},
                         "inputs": [],
-                        "label": null,
-                        "name": "Paste",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
+                        "label": "Barcodes",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1407.046875,
-                            "top": 380.984375
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Cell metadata"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
+                            "left": 566.5,
+                            "top": 429.5
                         },
-                        "tool_id": "Paste1",
-                        "tool_state": "{\"delimiter\": \"T\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "78b0f142-dc1d-4c64-8ea8-58d704646c55",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "cb331533-4896-419f-83ca-196c5daf2c03",
                         "workflow_outputs": [
                             {
-                                "label": "Cell metadata",
-                                "output_name": "out_file1",
-                                "uuid": "2f0ea0f3-f2f7-44b2-b8f0-05d8cbb364a6"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "d863899f-2ea8-49d1-acc9-a2cca1f9fce3"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 16,
-                        "input_connections": {
-                            "input": {
-                                "id": 7,
-                                "output_name": "anndata"
-                            },
-                            "manipulate|new_annot": {
-                                "id": 15,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Manipulate AnnData",
-                                "name": "manipulate"
-                            }
-                        ],
-                        "label": "Adding in cell metadata",
-                        "name": "Manipulate AnnData",
-                        "outputs": [
-                            {
-                                "name": "anndata",
-                                "type": "h5ad"
-                            }
-                        ],
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "GTF file (UCSC)",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 557.03125,
-                            "top": 630.9765625
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionanndata": {
-                                "action_arguments": {
-                                    "newname": "AnnData with Cell Metadata"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "anndata"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ed4996a16f7f",
-                            "name": "anndata_manipulate",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 568.5,
+                            "top": 521
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"add_annotation\", \"__current_case__\": 6, \"var_obs\": \"obs\", \"new_annot\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.10.3+galaxy0",
-                        "type": "tool",
-                        "uuid": "d30f8445-4d7d-43d4-a5b2-06b62286a70d",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ac1f89bb-52b9-41ac-a6d4-f8dfd4d21550",
                         "workflow_outputs": [
                             {
-                                "label": "AnnData with Cell Metadata",
-                                "output_name": "anndata",
-                                "uuid": "2720386c-7273-49d6-abb0-9bd14f6cb68c"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "51046a1f-f629-4e6a-aac1-eb563eeb693b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
-                        "errors": null,
-                        "id": 17,
+                        "id": 4,
                         "input_connections": {
-                            "input": {
-                                "id": 16,
-                                "output_name": "anndata"
+                            "Barcodes (single-col)": {
+                                "id": 1,
+                                "input_subworkflow_step_id": 1,
+                                "output_name": "output"
+                            },
+                            "Batch": {
+                                "id": 3,
+                                "input_subworkflow_step_id": 0,
+                                "output_name": "output"
+                            },
+                            "GTF file (UCSC)": {
+                                "id": 2,
+                                "input_subworkflow_step_id": 2,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "Batching Cell Metadata",
-                        "name": "Manipulate AnnData",
-                        "outputs": [
-                            {
-                                "name": "anndata",
-                                "type": "h5ad"
-                            }
-                        ],
+                        "label": null,
+                        "name": "CelSeq2: Single Batch mm10",
+                        "outputs": [],
                         "position": {
-                            "left": 795.03125,
-                            "top": 644.9765625
+                            "left": 879,
+                            "top": 293.5
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionanndata": {
-                                "action_arguments": {
-                                    "newname": "Batched AnnData"
+                        "subworkflow": {
+                            "a_galaxy_workflow": "true",
+                            "annotation": "",
+                            "format-version": "0.1",
+                            "name": "CelSeq2: Single Batch mm10",
+                            "steps": {
+                                "0": {
+                                    "annotation": "",
+                                    "content_id": null,
+                                    "errors": null,
+                                    "id": 0,
+                                    "input_connections": {},
+                                    "inputs": [],
+                                    "label": "Batch",
+                                    "name": "Input dataset collection",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 286,
+                                        "top": 470.90625
+                                    },
+                                    "tool_id": null,
+                                    "tool_state": "{\"collection_type\": \"paired\"}",
+                                    "tool_version": null,
+                                    "type": "data_collection_input",
+                                    "uuid": "c451df86-a25e-409c-9f2e-33c22a0f1bb9",
+                                    "workflow_outputs": [
+                                        {
+                                            "label": null,
+                                            "output_name": "output",
+                                            "uuid": "d46989fb-ef46-4506-8932-d66cee38e62a"
+                                        }
+                                    ]
                                 },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "anndata"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ed4996a16f7f",
-                            "name": "anndata_manipulate",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                                "1": {
+                                    "annotation": "",
+                                    "content_id": null,
+                                    "errors": null,
+                                    "id": 1,
+                                    "input_connections": {},
+                                    "inputs": [],
+                                    "label": "Barcodes (single-col)",
+                                    "name": "Input dataset",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 302.5,
+                                        "top": 552
+                                    },
+                                    "tool_id": null,
+                                    "tool_state": "{}",
+                                    "tool_version": null,
+                                    "type": "data_input",
+                                    "uuid": "4ac7860e-01d4-4009-b1fd-899fab778eb5",
+                                    "workflow_outputs": [
+                                        {
+                                            "label": null,
+                                            "output_name": "output",
+                                            "uuid": "2c66b77f-5ee0-4991-971c-3c43d8e7841d"
+                                        }
+                                    ]
+                                },
+                                "10": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+                                    "errors": null,
+                                    "id": 10,
+                                    "input_connections": {
+                                        "infile": {
+                                            "id": 9,
+                                            "output_name": "out_counts"
+                                        }
+                                    },
+                                    "inputs": [
+                                        {
+                                            "description": "runtime parameter for tool Text transformation",
+                                            "name": "infile"
+                                        }
+                                    ],
+                                    "label": "Fix Headers",
+                                    "name": "Text transformation",
+                                    "outputs": [
+                                        {
+                                            "name": "output",
+                                            "type": "input"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 1919.90625,
+                                        "top": 528.40625
+                                    },
+                                    "post_job_actions": {},
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "a6f147a050a2",
+                                        "name": "text_processing",
+                                        "owner": "bgruening",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"adv_opts\": \"{\\\"__current_case__\\\": 0, \\\"adv_opts_selector\\\": \\\"basic\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"code\": \"\\\"1 s|\\\\\\\\w+_([ACTG]+)\\\\\\\\b|\\\\\\\\1|g\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                                    "tool_version": "1.1.1",
+                                    "type": "tool",
+                                    "uuid": "1d1e09f7-119f-4086-b8b7-a9fb61cea637",
+                                    "workflow_outputs": [
+                                        {
+                                            "label": null,
+                                            "output_name": "output",
+                                            "uuid": "2aa0f119-75c6-4b6b-8260-ff66f54167a4"
+                                        }
+                                    ]
+                                },
+                                "2": {
+                                    "annotation": "",
+                                    "content_id": null,
+                                    "errors": null,
+                                    "id": 2,
+                                    "input_connections": {},
+                                    "inputs": [],
+                                    "label": "GTF file (UCSC)",
+                                    "name": "Input dataset",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 313.5,
+                                        "top": 828.90625
+                                    },
+                                    "tool_id": null,
+                                    "tool_state": "{}",
+                                    "tool_version": null,
+                                    "type": "data_input",
+                                    "uuid": "0455bae6-58da-4ec3-9688-72aba9f676fe",
+                                    "workflow_outputs": [
+                                        {
+                                            "label": null,
+                                            "output_name": "output",
+                                            "uuid": "7ca9e0df-159c-43f7-a0b3-e546fcd9b2c9"
+                                        }
+                                    ]
+                                },
+                                "3": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2",
+                                    "errors": null,
+                                    "id": 3,
+                                    "input_connections": {
+                                        "barcodes|filter_barcode_file": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        },
+                                        "input_type|input_readpair": {
+                                            "id": 0,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [
+                                        {
+                                            "description": "runtime parameter for tool UMI-tools extract",
+                                            "name": "input_type"
+                                        },
+                                        {
+                                            "description": "runtime parameter for tool UMI-tools extract",
+                                            "name": "barcodes"
+                                        }
+                                    ],
+                                    "label": null,
+                                    "name": "UMI-tools extract",
+                                    "outputs": [
+                                        {
+                                            "name": "out",
+                                            "type": "input"
+                                        },
+                                        {
+                                            "name": "out1",
+                                            "type": "input"
+                                        },
+                                        {
+                                            "name": "out2",
+                                            "type": "input"
+                                        },
+                                        {
+                                            "name": "out_log",
+                                            "type": "txt"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 554.5,
+                                        "top": 469.90625
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionout": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "out"
+                                        },
+                                        "HideDatasetActionout1": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "out1"
+                                        },
+                                        "HideDatasetActionout_log": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "out_log"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "99aea37a7ff7",
+                                        "name": "umi_tools_extract",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"__page__\": null, \"extract_method\": \"\\\"string\\\"\", \"input_type\": \"{\\\"__current_case__\\\": 2, \\\"barcode\\\": {\\\"__current_case__\\\": 0, \\\"barcode_select\\\": \\\"first_read_only\\\"}, \\\"input_readpair\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"type\\\": \\\"paired_collection\\\"}\", \"__rerun_remap_job_id__\": null, \"bc_pattern\": \"\\\"NNNNNNCCCCCC\\\"\", \"print_log\": \"\\\"true\\\"\", \"prime3\": \"\\\"true\\\"\", \"quality\": \"{\\\"__current_case__\\\": 0, \\\"quality_selector\\\": \\\"false\\\"}\", \"barcodes\": \"{\\\"__current_case__\\\": 1, \\\"filter_barcode_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"filter_correct\\\": \\\"false\\\", \\\"use_barcodes\\\": \\\"yes\\\"}\"}",
+                                    "tool_version": "0.5.3.2",
+                                    "type": "tool",
+                                    "uuid": "0b94d2ea-1889-4b88-b0a2-ac7b0a3452e5",
+                                    "workflow_outputs": [
+                                        {
+                                            "label": null,
+                                            "output_name": "out2",
+                                            "uuid": "c24e1482-bbff-4a22-8747-2ab0330fb5af"
+                                        }
+                                    ]
+                                },
+                                "4": {
+                                    "annotation": "The genome should match that of the GTF file",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2",
+                                    "errors": null,
+                                    "id": 4,
+                                    "input_connections": {
+                                        "refGenomeSource|GTFconditional|sjdbGTFfile": {
+                                            "id": 2,
+                                            "output_name": "output"
+                                        },
+                                        "singlePaired|input1": {
+                                            "id": 3,
+                                            "output_name": "out2"
+                                        }
+                                    },
+                                    "inputs": [
+                                        {
+                                            "description": "runtime parameter for tool RNA STAR",
+                                            "name": "quantMode"
+                                        },
+                                        {
+                                            "description": "runtime parameter for tool RNA STAR",
+                                            "name": "singlePaired"
+                                        }
+                                    ],
+                                    "label": "Alignment (mm10)",
+                                    "name": "RNA STAR",
+                                    "outputs": [
+                                        {
+                                            "name": "output_log",
+                                            "type": "txt"
+                                        },
+                                        {
+                                            "name": "chimeric_junctions",
+                                            "type": "interval"
+                                        },
+                                        {
+                                            "name": "chimeric_reads",
+                                            "type": "bam"
+                                        },
+                                        {
+                                            "name": "splice_junctions",
+                                            "type": "interval"
+                                        },
+                                        {
+                                            "name": "mapped_reads",
+                                            "type": "bam"
+                                        },
+                                        {
+                                            "name": "reads_per_gene",
+                                            "type": "tabular"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 832.5,
+                                        "top": 581.90625
+                                    },
+                                    "post_job_actions": {},
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "2055c2667eb3",
+                                        "name": "rgrnastar",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"__page__\": null, \"singlePaired\": \"{\\\"__current_case__\\\": 0, \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sPaired\\\": \\\"single\\\"}\", \"output_params\": \"{\\\"__current_case__\\\": 1, \\\"output_select\\\": \\\"no\\\"}\", \"__rerun_remap_job_id__\": null, \"params\": \"{\\\"__current_case__\\\": 0, \\\"settingsType\\\": \\\"default\\\"}\", \"refGenomeSource\": \"{\\\"GTFconditional\\\": {\\\"GTFselect\\\": \\\"without-gtf\\\", \\\"__current_case__\\\": 1, \\\"genomeDir\\\": \\\"mm10\\\", \\\"sjdbGTFfile\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sjdbOverhang\\\": \\\"100\\\"}, \\\"__current_case__\\\": 0, \\\"geneSource\\\": \\\"indexed\\\"}\", \"quantMode\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                                    "tool_version": "2.5.2b-2",
+                                    "type": "tool",
+                                    "uuid": "1e4a54be-b2fb-496a-8247-ccba4ffe6f3b",
+                                    "workflow_outputs": [
+                                        {
+                                            "label": null,
+                                            "output_name": "chimeric_reads",
+                                            "uuid": "f44d1ce2-b0a0-4aca-b9da-d47a9151dd8f"
+                                        },
+                                        {
+                                            "label": null,
+                                            "output_name": "chimeric_junctions",
+                                            "uuid": "a70f8d45-eaa8-40f4-a755-99e7004ad0ee"
+                                        },
+                                        {
+                                            "label": null,
+                                            "output_name": "reads_per_gene",
+                                            "uuid": "70ef8c03-6a54-4c88-81b6-e178dbf776c7"
+                                        },
+                                        {
+                                            "label": null,
+                                            "output_name": "splice_junctions",
+                                            "uuid": "0896bee8-d853-4467-8143-96a4d314774c"
+                                        },
+                                        {
+                                            "label": null,
+                                            "output_name": "mapped_reads",
+                                            "uuid": "956818b5-dc81-440c-8c2a-b10869547c70"
+                                        },
+                                        {
+                                            "label": null,
+                                            "output_name": "output_log",
+                                            "uuid": "5714f89a-1d7f-4634-95ce-2b089e5cc83d"
+                                        }
+                                    ]
+                                },
+                                "5": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
+                                    "errors": null,
+                                    "id": 5,
+                                    "input_connections": {
+                                        "input_file": {
+                                            "id": 4,
+                                            "output_name": "mapped_reads"
+                                        }
+                                    },
+                                    "inputs": [
+                                        {
+                                            "description": "runtime parameter for tool Stats",
+                                            "name": "input_file"
+                                        }
+                                    ],
+                                    "label": null,
+                                    "name": "Stats",
+                                    "outputs": [
+                                        {
+                                            "name": "output",
+                                            "type": "tabular"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 1338.5,
+                                        "top": 403
+                                    },
+                                    "post_job_actions": {},
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "24c5d43cb545",
+                                        "name": "samtools_stats",
+                                        "owner": "devteam",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"coverage_max\": \"\\\"1000\\\"\", \"__page__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"gc_depth\": \"\\\"20000.0\\\"\", \"insert_size\": \"\\\"8000\\\"\", \"most_inserts\": \"\\\"0.99\\\"\", \"coverage_step\": \"\\\"1\\\"\", \"coverage_min\": \"\\\"1\\\"\", \"read_length\": \"\\\"\\\"\", \"trim_quality\": \"\\\"0\\\"\", \"filter_by_flags\": \"{\\\"__current_case__\\\": 1, \\\"filter_flags\\\": \\\"nofilter\\\"}\", \"split_output\": \"{\\\"__current_case__\\\": 0, \\\"split_output_selector\\\": \\\"no\\\"}\", \"use_reference\": \"{\\\"__current_case__\\\": 1, \\\"use_ref_selector\\\": \\\"no\\\"}\", \"__rerun_remap_job_id__\": null, \"remove_dups\": \"\\\"false\\\"\"}",
+                                    "tool_version": "2.0.1",
+                                    "type": "tool",
+                                    "uuid": "36ad81d4-f920-4ca6-83c2-66516b2229f2",
+                                    "workflow_outputs": [
+                                        {
+                                            "label": null,
+                                            "output_name": "output",
+                                            "uuid": "eed5af2c-48f7-4227-8d76-0686c0537ccc"
+                                        }
+                                    ]
+                                },
+                                "6": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2",
+                                    "errors": null,
+                                    "id": 6,
+                                    "input_connections": {
+                                        "alignment": {
+                                            "id": 4,
+                                            "output_name": "mapped_reads"
+                                        },
+                                        "anno|reference_gene_sets": {
+                                            "id": 2,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [
+                                        {
+                                            "description": "runtime parameter for tool featureCounts",
+                                            "name": "anno"
+                                        },
+                                        {
+                                            "description": "runtime parameter for tool featureCounts",
+                                            "name": "alignment"
+                                        }
+                                    ],
+                                    "label": null,
+                                    "name": "featureCounts",
+                                    "outputs": [
+                                        {
+                                            "name": "output_medium",
+                                            "type": "tabular"
+                                        },
+                                        {
+                                            "name": "output_bam",
+                                            "type": "bam"
+                                        },
+                                        {
+                                            "name": "output_short",
+                                            "type": "tabular"
+                                        },
+                                        {
+                                            "name": "output_full",
+                                            "type": "tabular"
+                                        },
+                                        {
+                                            "name": "output_summary",
+                                            "type": "tabular"
+                                        },
+                                        {
+                                            "name": "output_feature_lengths",
+                                            "type": "tabular"
+                                        },
+                                        {
+                                            "name": "output_jcounts",
+                                            "type": "tabular"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 1141.5,
+                                        "top": 814
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionoutput_feature_lengths": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "output_feature_lengths"
+                                        },
+                                        "HideDatasetActionoutput_full": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "output_full"
+                                        },
+                                        "HideDatasetActionoutput_jcounts": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "output_jcounts"
+                                        },
+                                        "HideDatasetActionoutput_medium": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "output_medium"
+                                        },
+                                        "HideDatasetActionoutput_short": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "output_short"
+                                        },
+                                        "HideDatasetActionoutput_summary": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "output_summary"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "f3a5f075498f",
+                                        "name": "featurecounts",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"pe_parameters\": \"{\\\"exclude_chimerics\\\": \\\"true\\\", \\\"fragment_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"fragment_counting\\\": \\\"\\\"}, \\\"only_both_ends\\\": \\\"false\\\"}\", \"strand_specificity\": \"\\\"0\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"format\": \"\\\"tabdel_short\\\"\", \"include_feature_length_file\": \"\\\"false\\\"\", \"anno\": \"{\\\"__current_case__\\\": 2, \\\"anno_select\\\": \\\"history\\\", \\\"reference_gene_sets\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"extended_parameters\": \"{\\\"R\\\": \\\"true\\\", \\\"by_read_group\\\": \\\"false\\\", \\\"contribute_to_multiple_features\\\": \\\"false\\\", \\\"count_split_alignments_only\\\": \\\"false\\\", \\\"exon_exon_junction_read_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"count_exon_exon_junction_reads\\\": \\\"false\\\"}, \\\"frac_overlap\\\": \\\"0\\\", \\\"frac_overlap_feature\\\": \\\"0\\\", \\\"gff_feature_attribute\\\": \\\"gene_id\\\", \\\"gff_feature_type\\\": \\\"exon\\\", \\\"ignore_dup\\\": \\\"false\\\", \\\"largest_overlap\\\": \\\"false\\\", \\\"long_reads\\\": \\\"false\\\", \\\"mapping_quality\\\": \\\"12\\\", \\\"min_overlap\\\": \\\"1\\\", \\\"multimapping_enabled\\\": {\\\"__current_case__\\\": 1, \\\"multimapping_counts\\\": \\\"\\\"}, \\\"primary\\\": \\\"false\\\", \\\"read_extension_3p\\\": \\\"0\\\", \\\"read_extension_5p\\\": \\\"0\\\", \\\"read_reduction\\\": \\\"\\\", \\\"summarization_level\\\": \\\"false\\\"}\", \"alignment\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                                    "tool_version": "1.6.2",
+                                    "type": "tool",
+                                    "uuid": "9506153d-d997-43a4-8ce1-216690415561",
+                                    "workflow_outputs": [
+                                        {
+                                            "label": null,
+                                            "output_name": "output_bam",
+                                            "uuid": "87abf585-aae9-4af3-aed7-541795d65faf"
+                                        }
+                                    ]
+                                },
+                                "7": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.0",
+                                    "errors": null,
+                                    "id": 7,
+                                    "input_connections": {
+                                        "results_0|software_cond|output_0|type|input": {
+                                            "id": 5,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": null,
+                                    "name": "MultiQC",
+                                    "outputs": [
+                                        {
+                                            "name": "stats",
+                                            "type": "input"
+                                        },
+                                        {
+                                            "name": "html_report",
+                                            "type": "html"
+                                        },
+                                        {
+                                            "name": "log",
+                                            "type": "txt"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 1643.5,
+                                        "top": 200
+                                    },
+                                    "post_job_actions": {},
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.0",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "df99138d2776",
+                                        "name": "multiqc",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"comment\": \"\\\"\\\"\", \"__page__\": null, \"title\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"results\": \"[{\\\"__index__\\\": 0, \\\"software_cond\\\": {\\\"__current_case__\\\": 20, \\\"output\\\": [{\\\"__index__\\\": 0, \\\"type\\\": {\\\"__current_case__\\\": 0, \\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"type\\\": \\\"stats\\\"}}], \\\"software\\\": \\\"samtools\\\"}}, {\\\"__index__\\\": 1, \\\"software_cond\\\": {\\\"__current_case__\\\": 7, \\\"output\\\": [{\\\"__index__\\\": 0, \\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"type\\\": \\\"data\\\"}], \\\"software\\\": \\\"fastqc\\\"}}, {\\\"__index__\\\": 2, \\\"software_cond\\\": {\\\"__current_case__\\\": 7, \\\"output\\\": [{\\\"__index__\\\": 0, \\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"type\\\": \\\"data\\\"}], \\\"software\\\": \\\"fastqc\\\"}}]\", \"saveLog\": \"\\\"false\\\"\"}",
+                                    "tool_version": "1.5.0",
+                                    "type": "tool",
+                                    "uuid": "c56b2cfb-18c4-4f17-9f5c-a84009e00050",
+                                    "workflow_outputs": [
+                                        {
+                                            "label": null,
+                                            "output_name": "stats",
+                                            "uuid": "2845973b-96f5-44c6-b454-b3e09601972b"
+                                        },
+                                        {
+                                            "label": null,
+                                            "output_name": "log",
+                                            "uuid": "9dfc4543-d1d9-40f4-b703-61993f05fbee"
+                                        },
+                                        {
+                                            "label": null,
+                                            "output_name": "html_report",
+                                            "uuid": "452d04bd-cdcc-4074-839d-6a70ad44ba55"
+                                        }
+                                    ]
+                                },
+                                "8": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
+                                    "errors": null,
+                                    "id": 8,
+                                    "input_connections": {
+                                        "input_bam": {
+                                            "id": 6,
+                                            "output_name": "output_bam"
+                                        }
+                                    },
+                                    "inputs": [
+                                        {
+                                            "description": "runtime parameter for tool Filter",
+                                            "name": "input_bam"
+                                        }
+                                    ],
+                                    "label": null,
+                                    "name": "Filter",
+                                    "outputs": [
+                                        {
+                                            "name": "out_file2",
+                                            "type": "txt"
+                                        },
+                                        {
+                                            "name": "out_file1",
+                                            "type": "bam"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 1440.5,
+                                        "top": 627.5
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionout_file2": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "out_file2"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "bd735cae4ce6",
+                                        "name": "bamtools_filter",
+                                        "owner": "devteam",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"input_bam\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"rule_configuration\": \"{\\\"__current_case__\\\": 1, \\\"rules\\\": \\\"(1 | 2) & 3 & 4\\\", \\\"rules_selector\\\": \\\"true\\\"}\", \"conditions\": \"[{\\\"__index__\\\": 0, \\\"filters\\\": [{\\\"__index__\\\": 0, \\\"bam_property\\\": {\\\"__current_case__\\\": 0, \\\"bam_property_selector\\\": \\\"alignmentFlag\\\", \\\"bam_property_value\\\": \\\"0\\\"}}]}, {\\\"__index__\\\": 1, \\\"filters\\\": [{\\\"__index__\\\": 0, \\\"bam_property\\\": {\\\"__current_case__\\\": 0, \\\"bam_property_selector\\\": \\\"alignmentFlag\\\", \\\"bam_property_value\\\": \\\"16\\\"}}]}, {\\\"__index__\\\": 2, \\\"filters\\\": [{\\\"__index__\\\": 0, \\\"bam_property\\\": {\\\"__current_case__\\\": 21, \\\"bam_property_selector\\\": \\\"tag\\\", \\\"bam_property_value\\\": \\\"nM:<3\\\"}}]}, {\\\"__index__\\\": 3, \\\"filters\\\": [{\\\"__index__\\\": 0, \\\"bam_property\\\": {\\\"__current_case__\\\": 21, \\\"bam_property_selector\\\": \\\"tag\\\", \\\"bam_property_value\\\": \\\"NH:<2\\\"}}]}]\", \"__page__\": null}",
+                                    "tool_version": "2.4.1",
+                                    "type": "tool",
+                                    "uuid": "e65c9b1a-65d2-46dc-8199-0f87acf7f6b1",
+                                    "workflow_outputs": [
+                                        {
+                                            "label": null,
+                                            "output_name": "out_file1",
+                                            "uuid": "50f1d2af-ca7e-46b1-a9a6-99931ee1fcb5"
+                                        }
+                                    ]
+                                },
+                                "9": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2",
+                                    "errors": null,
+                                    "id": 9,
+                                    "input_connections": {
+                                        "input_bam": {
+                                            "id": 8,
+                                            "output_name": "out_file1"
+                                        }
+                                    },
+                                    "inputs": [
+                                        {
+                                            "description": "runtime parameter for tool UMI-tools count",
+                                            "name": "input_bam"
+                                        }
+                                    ],
+                                    "label": null,
+                                    "name": "UMI-tools count",
+                                    "outputs": [
+                                        {
+                                            "name": "out_counts",
+                                            "type": "tabular"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 1703.5,
+                                        "top": 590
+                                    },
+                                    "post_job_actions": {},
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "b557acca0b56",
+                                        "name": "umi_tools_count",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"wide_format_cell_counts\": \"\\\"true\\\"\", \"cond_extra\": \"{\\\"__current_case__\\\": 1, \\\"prepender\\\": \\\"dataset name\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"edit_distance_threshold\": \"\\\"1\\\"\", \"paired\": \"\\\"false\\\"\", \"input_bam\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"method\": \"\\\"unique\\\"\", \"advanced\": \"{\\\"gene_tag\\\": \\\"XT\\\", \\\"mapping_quality\\\": \\\"0\\\", \\\"per_cell\\\": \\\"true\\\", \\\"per_contig\\\": \\\"false\\\", \\\"random_seed\\\": \\\"0\\\", \\\"skip_tags_regex\\\": \\\"\\\"}\", \"barcodes\": \"{\\\"__current_case__\\\": 0, \\\"extract_umi_method\\\": \\\"read_id\\\", \\\"umi_separator\\\": \\\"_\\\"}\"}",
+                                    "tool_version": "0.5.3.2",
+                                    "type": "tool",
+                                    "uuid": "89675c5a-ef94-49a5-889c-c53ba1074f80",
+                                    "workflow_outputs": [
+                                        {
+                                            "label": null,
+                                            "output_name": "out_counts",
+                                            "uuid": "209f3dd6-974f-4e76-a206-c86114a6697f"
+                                        }
+                                    ]
+                                }
+                            },
+                            "tags": "",
+                            "uuid": "ee17e23b-42b1-48e8-ad5e-bcb0b7fa8cf0"
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"rename_categories\", \"__current_case__\": 3, \"key\": \"batch\", \"categories\": \"N701,N702,N703,N704,N705,N706,N707\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.10.3+galaxy0",
-                        "type": "tool",
-                        "uuid": "e3e2f437-6fd1-432b-8dc0-2133c1b3fee3",
-                        "when": null,
+                        "tool_id": "0600e24fe786d72f",
+                        "type": "subworkflow",
+                        "uuid": "e86d6331-50b9-412a-b895-0bda5408d366",
                         "workflow_outputs": [
                             {
-                                "label": "Batched Object",
-                                "output_name": "anndata",
-                                "uuid": "b950c8db-abe1-4cb0-af58-d291d3b74a83"
+                                "label": null,
+                                "output_name": "4:mapped_reads",
+                                "uuid": "0a5f54e7-09dc-4c35-980a-b617fcfaa2eb"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "7:html_report",
+                                "uuid": "fea13497-e4cb-47b1-a64d-6883e19def0f"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "0:output",
+                                "uuid": "65f46424-6d76-4d1f-acd0-aef24e26d10b"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "10:output",
+                                "uuid": "cc791e7c-9cbb-481d-8deb-39d33f7b2857"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "4:chimeric_reads",
+                                "uuid": "c6ad66bf-5fde-4440-ab54-4997211c2c3d"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "4:reads_per_gene",
+                                "uuid": "b4ea5261-7733-4b7e-8e30-1d3535e9cb57"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "9:out_counts",
+                                "uuid": "58562166-7b2d-4b0d-9172-14a02d7a989a"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "4:chimeric_junctions",
+                                "uuid": "c33a7acd-f5bc-4ac5-b3d3-a6fb2892c9f6"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "6:output_bam",
+                                "uuid": "1601b4a1-a302-425d-bad6-7b71d14f9726"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "8:out_file1",
+                                "uuid": "a7b1aa8e-61cd-4b1c-8fa9-3c85d4113ea5"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "7:stats",
+                                "uuid": "ac17c572-784c-456e-b3c7-ebaf15c2109e"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "5:output",
+                                "uuid": "5c220f46-2525-471f-8fd6-0eb17dc689ad"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "7:log",
+                                "uuid": "3ad7aac8-e4a0-4df1-beb6-88cdcb106e7a"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "3:out2",
+                                "uuid": "4ff34341-786c-4c66-95c7-6985e4c66ad7"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "1:output",
+                                "uuid": "78bfe4ce-528c-4d16-8e73-f721b09676be"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "2:output",
+                                "uuid": "603d0608-7866-4f1d-be85-6a4f3116d5b8"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "4:splice_junctions",
+                                "uuid": "7f85f228-75da-4933-8157-e6eb4f15bd98"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "4:output_log",
+                                "uuid": "86003cab-1a90-4871-b489-27eb49715574"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
                         "errors": null,
-                        "id": 18,
+                        "id": 5,
                         "input_connections": {
-                            "input_obj_file": {
-                                "id": 17,
-                                "output_name": "anndata"
+                            "input_tabular": {
+                                "id": 4,
+                                "output_name": "9:out_counts"
                             }
                         },
-                        "inputs": [],
-                        "label": "Calculating mitochondrial ",
-                        "name": "AnnData Operations",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Column Join",
+                                "name": "input_tabular"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Column Join",
                         "outputs": [
                             {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
+                                "name": "tabular_output",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "script_output",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 1041.03125,
-                            "top": 641
+                            "left": 1277.5,
+                            "top": 288
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput_h5ad": {
-                                "action_arguments": {
-                                    "newname": "Annotated AnnData"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_h5ad"
+                            "HideDatasetActionscript_output": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "script_output"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
                         "tool_shed_repository": {
-                            "changeset_revision": "a4774b7b2e85",
-                            "name": "anndata_ops",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "58228a4d58fe",
+                            "name": "collection_column_join",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"add_cell_metadata\": {\"default\": false, \"__current_case__\": 1}, \"copy_adata_to_raw\": false, \"copy_e\": {\"default\": false, \"__current_case__\": 1}, \"copy_l\": {\"default\": false, \"__current_case__\": 1}, \"copy_o\": {\"default\": false, \"__current_case__\": 1}, \"copy_r\": {\"default\": false, \"__current_case__\": 1}, \"copy_u\": {\"default\": false, \"__current_case__\": 1}, \"copy_x\": {\"default\": false, \"__current_case__\": 1}, \"field_unique\": null, \"gene_flags\": [{\"__index__\": 0, \"startswith\": \"True\", \"flag\": \"mito\"}], \"gene_symbols_field\": \"NA.\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": false, \"split_on_obs\": {\"default\": false, \"__current_case__\": 1}, \"swap_layer_to_x\": {\"default\": false, \"__current_case__\": 1}, \"top_genes\": \"50\", \"var_modifications\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.3+galaxy0",
+                        "tool_state": "{\"__page__\": null, \"identifier_column\": \"\\\"1\\\"\", \"include_outputs\": \"null\", \"__rerun_remap_job_id__\": null, \"input_tabular\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"fill_char\": \"\\\".\\\"\", \"old_col_in_header\": \"\\\"true\\\"\", \"has_header\": \"\\\"1\\\"\"}",
+                        "tool_version": "0.0.3",
                         "type": "tool",
-                        "uuid": "0db28a98-06c8-43a6-b72a-da2e84965d3a",
-                        "when": null,
+                        "uuid": "174c32b6-444c-4762-b9c1-c84201e656ab",
                         "workflow_outputs": [
                             {
-                                "label": "Annotated AnnData",
-                                "output_name": "output_h5ad",
-                                "uuid": "2417284d-8252-43ff-84bf-6f15ef11cd05"
+                                "label": null,
+                                "output_name": "tabular_output",
+                                "uuid": "2167fa1b-4865-40b1-9c61-82dd6ba8ccc7"
                             }
                         ]
                     }
                 ],
-                "parent_id": "single-cell/scrna-case_alevin-combine-datasets",
-                "path": "topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/workflows/Combining-datasets-after-pre-processing.ga",
+                "parent_id": "single-cell/scrna-preprocessing",
+                "path": "topics/single-cell/tutorials/scrna-preprocessing/workflows/scrna_mp_celseq.ga",
                 "tags": [
-                    "name:training",
-                    "name:single-cell"
+                    "transcriptomics"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "Combining datasets after pre-processing",
+                "tests": false,
+                "title": "CelSeq2: Multi Batch (mm10)",
                 "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-case_alevin-combine-datasets/versions/combining-datasets-after-pre-processing",
-                "tutorial_id": "scrna-case_alevin-combine-datasets",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/workflows/Combining-datasets-after-pre-processing.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/workflows/Combining-datasets-after-pre-processing.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-preprocessing/versions/scrna-mp-celseq",
+                "tutorial_id": "scrna-preprocessing",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-preprocessing/workflows/scrna_mp_celseq.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-preprocessing/workflows/scrna_mp_celseq.html",
                 "version": 1,
-                "wfid": "single-cell-scrna-case_alevin-combine-datasets",
-                "wfname": "combining-datasets-after-pre-processing",
-                "workflow": "Combining-datasets-after-pre-processing.ga",
+                "wfid": "single-cell-scrna-preprocessing",
+                "wfname": "scrna-mp-celseq",
+                "workflow": "scrna_mp_celseq.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "Paste1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0"
-                ],
-                "workflowhub_id": "1225"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/records/10852529"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "datamash_ops",
-                    "owner": "iuc",
-                    "revisions": "562f3c677828",
-                    "tool_panel_section_label": "Join, Subtract and Group",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "datamash_transpose",
-                    "owner": "iuc",
-                    "revisions": "22c2a1ac7ae3",
-                    "tool_panel_section_label": "Join, Subtract and Group",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "raceid_clustering",
-                    "owner": "iuc",
-                    "revisions": "a4b734cd253b",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "raceid_filtnormconf",
-                    "owner": "iuc",
-                    "revisions": "43c146e25a43",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "raceid_inspectclusters",
-                    "owner": "iuc",
-                    "revisions": "41f34e925bd5",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "raceid_inspecttrajectory",
-                    "owner": "iuc",
-                    "revisions": "c8434a623268",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "raceid_trajectory",
-                    "owner": "iuc",
-                    "revisions": "72979cac22b2",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 562f3c677828\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_transpose\n  owner: iuc\n  revisions: 22c2a1ac7ae3\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: raceid_clustering\n  owner: iuc\n  revisions: a4b734cd253b\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: raceid_filtnormconf\n  owner: iuc\n  revisions: 43c146e25a43\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: raceid_inspectclusters\n  owner: iuc\n  revisions: 41f34e925bd5\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: raceid_inspecttrajectory\n  owner: iuc\n  revisions: c8434a623268\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: raceid_trajectory\n  owner: iuc\n  revisions: 72979cac22b2\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-raceid/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "elixir_node": "de",
-                "email": "mtekman89@gmail.com",
-                "former_affiliations": [
-                    "elixir-europe"
+                    "__FLATTEN__",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2"
                 ],
-                "id": "mtekman",
-                "joined": "2018-11",
-                "name": "Mehmet Tekman",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
+                "workflowhub_id": "1218"
             },
-            {
-                "email": "a.ostrovsky@mac.com",
-                "id": "astrovsky01",
-                "joined": "2019-06",
-                "name": "Alex Ostrovsky",
-                "orcid": "0000-0002-7901-7109",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/astrovsky01/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/astrovsky01.json"
-            }
-        ],
-        "dir": "topics/single-cell/tutorials/scrna-raceid",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-preprocessing-tenx"
-                ],
-                "type": "internal"
-            }
-        ],
-        "gitter": "Galaxy-Training-Network/galaxy-single-cell",
-        "hands_on": true,
-        "id": "single-cell/scrna-raceid",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": 10933,
-            "mermaid": false
-        },
-        "key_points": [
-            "Clustering single-cell RNA-seq data is often noisy",
-            "RaceID can be used to cluster cells based on the their gene expression profiles",
-            "StemID describes a hierarchical relationship between clusters to find multipotent progenitor stem cells to provide an understanding of cell development",
-            "FateID predicts the potential lineages that cells within specific clusters are inclined towards"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Filtering, normalising, and clustering cells in a matrix",
-            "Assessing the quality of individual clusters",
-            "Inferring cell type lineages",
-            "Examining gene expression",
-            "Determining the top most expressive genes per cluster",
-            "Correcting for unwanted variation"
-        ],
-        "pageviews": 885,
-        "priority": 2,
-        "pub_date": "2019-03-25",
-        "questions": [
-            "What is normalisation and why is it necessary?",
-            "How many types of unwanted variation are there?",
-            "How are biological phenotypes clustered?",
-            "What is the difference between PCA and tSNE?",
-            "What is the difference between cell trajectory and cell fate?"
-        ],
-        "redirect_from": [
-            "/topics/transcriptomics/tutorials/scrna-raceid/tutorial",
-            "/short/single-cell/scrna-raceid",
-            "/short/T00253"
-        ],
-        "requirements": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-scater-qc"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00253",
-        "short_tools": [
-            "datamash_ops",
-            "raceid_inspecttrajectory",
-            "datamash_transpose",
-            "tp_head_tool",
-            "raceid_clustering",
-            "tp_sed_tool",
-            "raceid_filtnormconf",
-            "raceid_trajectory",
-            "raceid_inspectclusters"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "end-to-end",
-        "supported_servers": {
-            "exact": [],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": null,
-        "time_estimation": "3H",
-        "title": "Downstream Single-cell RNA analysis with RaceID",
-        "tools": [
-            "raceid_clustering",
-            "raceid_filtnormconf",
-            "raceid_inspectclusters",
-            "raceid_inspecttrajectory",
-            "raceid_trajectory",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy0"
-        ],
-        "topic_name": "single-cell",
-        "topic_name_human": "Single Cell",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "scrna-raceid",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-raceid/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-raceid/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-raceid/tutorial.json"
-        },
-        "version": 5,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 78,
-        "visitors": 749,
-        "workflows": [
             {
                 "creators": [],
-                "description": "Downstream Single-cell RNA analysis with RaceID",
+                "description": "Pre-processing of Single-Cell RNA Data",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTabular Matrix\"]\n  1[label=\"Initial processing using RaceID\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Clustering using RaceID\"]\n  1 -> 2 [label=\"outrdat\"]\n  3[label=\"Lineage computation using StemID\"]\n  2 -> 3 [label=\"outrdat\"]\n  4[label=\"Cluster Inspection using RaceID\"]\n  2 -> 4 [label=\"outrdat\"]\n  5[label=\"Cluster Inspection using RaceID\"]\n  2 -> 5 [label=\"outrdat\"]\n  6[label=\"Cluster Inspection using RaceID\"]\n  2 -> 6 [label=\"outrdat\"]\n  7[label=\"Lineage Branch Analysis using StemID\"]\n  3 -> 7 [label=\"outrdat\"]\n  8[label=\"Lineage Branch Analysis using StemID\"]\n  3 -> 8 [label=\"outrdat\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nBatch\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBarcodes single-col\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGTF file UCSC\"]\n  3[label=\"UMI-tools extract\"]\n  1 -> 3 [label=\"output\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Alignment Choose a Genome\"]\n  2 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"out2\"]\n  5[label=\"Filter\"]\n  4 -> 5 [label=\"mapped_reads\"]\n  6[label=\"featureCounts\"]\n  5 -> 6 [label=\"out_file1\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"UMI-tools count\"]\n  6 -> 7 [label=\"output_bam\"]\n}",
                 "history": [
                     {
                         "hash": "327fd2b842f45de3dc2a30067714352675ad69ae",
@@ -221288,43 +225790,86 @@
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": "Batch",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 286,
+                            "top": 293.9166717529297
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"collection_type\": \"paired\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "c451df86-a25e-409c-9f2e-33c22a0f1bb9",
+                        "workflow_outputs": [
                             {
-                                "description": "",
-                                "name": "Tabular Matrix"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "d46989fb-ef46-4506-8932-d66cee38e62a"
                             }
-                        ],
-                        "label": "Tabular Matrix",
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "Barcodes (single-col)",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 167.21666717529297,
-                            "height": 48.96665954589844,
-                            "left": 38.75,
-                            "right": 198.75,
-                            "top": 118.25000762939453,
-                            "width": 160,
-                            "x": 38.75,
-                            "y": 118.25000762939453
+                            "left": 302.5,
+                            "top": 375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ba3fe014-c728-486e-8ce4-55be24df0682",
+                        "uuid": "4ac7860e-01d4-4009-b1fd-899fab778eb5",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "0c858705-5e28-44e0-8023-46aec4a01725"
+                                "uuid": "2c66b77f-5ee0-4991-971c-3c43d8e7841d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "GTF file (UCSC)",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 313.5,
+                            "top": 651.9166717529297
+                        },
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0455bae6-58da-4ec3-9688-72aba9f676fe",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "7ca9e0df-159c-43f7-a0b3-e546fcd9b2c9"
                             }
                         ]
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nTabular Matrix\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Initial processing using RaceID\"];\n  0 -->|output| 1;\n  2[\"Clustering using RaceID\"];\n  1 -->|outrdat| 2;\n  3[\"Lineage computation using StemID\"];\n  2 -->|outrdat| 3;\n  4[\"Cluster Inspection using RaceID\"];\n  2 -->|outrdat| 4;\n  5[\"Cluster Inspection using RaceID\"];\n  2 -->|outrdat| 5;\n  6[\"Cluster Inspection using RaceID\"];\n  2 -->|outrdat| 6;\n  7[\"Lineage Branch Analysis using StemID\"];\n  3 -->|outrdat| 7;\n  8[\"Lineage Branch Analysis using StemID\"];\n  3 -->|outrdat| 8;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "RaceID Workflow",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nBatch\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nBarcodes single-col\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nGTF file UCSC\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"UMI-tools extract\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  4[\"Alignment Choose a Genome\"];\n  2 -->|output| 4;\n  3 -->|out2| 4;\n  5[\"Filter\"];\n  4 -->|mapped_reads| 5;\n  6[\"featureCounts\"];\n  5 -->|out_file1| 6;\n  2 -->|output| 6;\n  7[\"UMI-tools count\"];\n  6 -->|output_bam| 7;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "CelSeq2: Single Batch (mm10)",
                 "outputs": [
                     {
                         "annotation": "",
@@ -221332,546 +225877,875 @@
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Tabular Matrix"
-                            }
-                        ],
-                        "label": "Tabular Matrix",
-                        "name": "Input dataset",
+                        "inputs": [],
+                        "label": "Batch",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "bottom": 167.21666717529297,
-                            "height": 48.96665954589844,
-                            "left": 38.75,
-                            "right": 198.75,
-                            "top": 118.25000762939453,
-                            "width": 160,
-                            "x": 38.75,
-                            "y": 118.25000762939453
+                            "left": 286,
+                            "top": 293.9166717529297
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"collection_type\": \"paired\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ba3fe014-c728-486e-8ce4-55be24df0682",
+                        "type": "data_collection_input",
+                        "uuid": "c451df86-a25e-409c-9f2e-33c22a0f1bb9",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "0c858705-5e28-44e0-8023-46aec4a01725"
+                                "uuid": "d46989fb-ef46-4506-8932-d66cee38e62a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "raceid_filtnormconf",
+                        "content_id": null,
                         "errors": null,
                         "id": 1,
-                        "input_connections": {
-                            "intable": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
+                        "input_connections": {},
                         "inputs": [],
-                        "label": null,
-                        "name": "Initial processing using RaceID",
-                        "outputs": [
-                            {
-                                "name": "outtable",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "outpdf",
-                                "type": "pdf"
-                            },
-                            {
-                                "name": "outrdat",
-                                "type": "rdata"
-                            },
-                            {
-                                "name": "outlog",
-                                "type": "txt"
-                            }
-                        ],
+                        "label": "Barcodes (single-col)",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 410.7666702270508,
-                            "height": 293.76666259765625,
-                            "left": 272.5,
-                            "right": 432.5,
-                            "top": 117.00000762939453,
-                            "width": 160,
-                            "x": 272.5,
-                            "y": 117.00000762939453
+                            "left": 302.5,
+                            "top": 375
                         },
-                        "post_job_actions": {},
-                        "tool_id": "raceid_filtnormconf",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"filt\": {\"mintotal\": \"3000\", \"minexpr\": \"5\", \"minnumber\": \"5\", \"hist_geq_one\": \"false\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"intable\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.2.3+galaxy0",
-                        "type": "tool",
-                        "uuid": "6fd8dbde-93d2-4903-865f-78cc3c2fa299",
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "4ac7860e-01d4-4009-b1fd-899fab778eb5",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outtable",
-                                "uuid": "d9293468-efef-4a10-89a6-0064a1740afd"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "outpdf",
-                                "uuid": "358ddb8a-a6ca-4162-8d53-354902f905cf"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "outrdat",
-                                "uuid": "68451b36-8875-45ca-bdb9-e315cc836e49"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "outlog",
-                                "uuid": "35505252-c65a-4572-9d66-b0e69893c01b"
+                                "output_name": "output",
+                                "uuid": "2c66b77f-5ee0-4991-971c-3c43d8e7841d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "raceid_clustering",
+                        "content_id": null,
                         "errors": null,
                         "id": 2,
-                        "input_connections": {
-                            "inputrds": {
-                                "id": 1,
-                                "output_name": "outrdat"
-                            }
-                        },
+                        "input_connections": {},
                         "inputs": [],
-                        "label": null,
-                        "name": "Clustering using RaceID",
-                        "outputs": [
-                            {
-                                "name": "outpdf",
-                                "type": "pdf"
-                            },
-                            {
-                                "name": "outrdat",
-                                "type": "rdata"
-                            },
-                            {
-                                "name": "outassignments",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "outgenelist",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "outlog",
-                                "type": "txt"
-                            }
-                        ],
+                        "label": "GTF file (UCSC)",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 466.46668243408203,
-                            "height": 350.7166748046875,
-                            "left": 520,
-                            "right": 680,
-                            "top": 115.75000762939453,
-                            "width": 160,
-                            "x": 520,
-                            "y": 115.75000762939453
+                            "left": 313.5,
+                            "top": 651.9166717529297
                         },
-                        "post_job_actions": {},
-                        "tool_id": "raceid_clustering",
-                        "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"clust\": {\"metric\": \"pearson\", \"funcluster\": \"kmedoids\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"extra\": {\"tablelim\": \"25\", \"plotlim\": \"10\", \"foldchange\": \"1.0\", \"pvalue\": \"0.01\"}, \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"outlier\": {\"outminc\": \"5\", \"outlg\": \"2\", \"final\": \"false\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"tsne\": {\"perplexity\": \"30\", \"knn\": \"10\", \"umap_nn\": \"15\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.2.3+galaxy0",
-                        "type": "tool",
-                        "uuid": "ca88c6cb-03e0-400c-8942-4c7ac0545a67",
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0455bae6-58da-4ec3-9688-72aba9f676fe",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outpdf",
-                                "uuid": "48b02eb6-1b70-4d1f-a210-03aa93a189d8"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "outrdat",
-                                "uuid": "e59d7dff-7e4b-42b4-ba62-09858f83c75c"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "outassignments",
-                                "uuid": "2514a8cc-48a9-4cf2-9640-8663f81d6cd6"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "outgenelist",
-                                "uuid": "b69f7d2f-4efe-41ca-ac2f-c74d45c2327e"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "outlog",
-                                "uuid": "68cbc6ab-4697-4042-b5a0-0d9cd842e09a"
+                                "output_name": "output",
+                                "uuid": "7ca9e0df-159c-43f7-a0b3-e546fcd9b2c9"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "raceid_trajectory",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2",
                         "errors": null,
                         "id": 3,
                         "input_connections": {
-                            "inputrds": {
-                                "id": 2,
-                                "output_name": "outrdat"
+                            "barcodes|filter_barcode_file": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "input_type|input_readpair": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool UMI-tools extract",
+                                "name": "input_type"
+                            },
+                            {
+                                "description": "runtime parameter for tool UMI-tools extract",
+                                "name": "barcodes"
+                            }
+                        ],
                         "label": null,
-                        "name": "Lineage computation using StemID",
+                        "name": "UMI-tools extract",
                         "outputs": [
                             {
-                                "name": "outpdf",
-                                "type": "pdf"
+                                "name": "out",
+                                "type": "input"
                             },
                             {
-                                "name": "outrdat",
-                                "type": "rdata"
+                                "name": "out1",
+                                "type": "input"
+                            },
+                            {
+                                "name": "out2",
+                                "type": "input"
+                            },
+                            {
+                                "name": "out_log",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 298.08333587646484,
-                            "height": 179.8333282470703,
-                            "left": 778.75,
-                            "right": 938.75,
-                            "top": 118.25000762939453,
-                            "width": 160,
-                            "x": 778.75,
-                            "y": 118.25000762939453
+                            "left": 554.5,
+                            "top": 292.9166717529297
                         },
-                        "post_job_actions": {},
-                        "tool_id": "raceid_trajectory",
-                        "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"comppval\": {\"pthr\": \"0.01\", \"sensitive\": \"false\"}, \"compscore\": {\"nn\": \"1\", \"scthr\": \"0.0\"}, \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"plotgraph\": {\"showcells\": \"false\", \"scthr\": \"0.0\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"projback\": {\"pdishuf\": \"2000\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"projcell\": {\"knn\": \"3\", \"cthr\": \"5\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"use_log\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.2.3+galaxy0",
+                        "post_job_actions": {
+                            "HideDatasetActionout": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "out"
+                            },
+                            "HideDatasetActionout1": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "out1"
+                            },
+                            "HideDatasetActionout_log": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "out_log"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "99aea37a7ff7",
+                            "name": "umi_tools_extract",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"extract_method\": \"\\\"string\\\"\", \"input_type\": \"{\\\"input_readpair\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"barcode\\\": {\\\"barcode_select\\\": \\\"first_read_only\\\", \\\"__current_case__\\\": 0}, \\\"type\\\": \\\"paired_collection\\\", \\\"__current_case__\\\": 2}\", \"__rerun_remap_job_id__\": null, \"bc_pattern\": \"\\\"NNNNNNCCCCCC\\\"\", \"print_log\": \"\\\"true\\\"\", \"prime3\": \"\\\"true\\\"\", \"quality\": \"{\\\"quality_selector\\\": \\\"false\\\", \\\"__current_case__\\\": 0}\", \"barcodes\": \"{\\\"filter_correct\\\": \\\"false\\\", \\\"filter_barcode_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"use_barcodes\\\": \\\"yes\\\"}\"}",
+                        "tool_version": "0.5.3.2",
                         "type": "tool",
-                        "uuid": "515732a4-cba5-402a-9cc8-11980c4815c6",
+                        "uuid": "0b94d2ea-1889-4b88-b0a2-ac7b0a3452e5",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outpdf",
-                                "uuid": "5de0f2cb-41a8-4278-8faa-20cdb534f3c4"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "outrdat",
-                                "uuid": "91b567ed-cf6e-4ff4-a84d-186d49502dff"
+                                "output_name": "out2",
+                                "uuid": "c24e1482-bbff-4a22-8747-2ab0330fb5af"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": "raceid_inspectclusters",
+                        "annotation": "The genome should match that of the GTF file",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2",
                         "errors": null,
                         "id": 4,
                         "input_connections": {
-                            "inputrds": {
+                            "refGenomeSource|GTFconditional|sjdbGTFfile": {
                                 "id": 2,
-                                "output_name": "outrdat"
+                                "output_name": "output"
+                            },
+                            "singlePaired|input1": {
+                                "id": 3,
+                                "output_name": "out2"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cluster Inspection using RaceID",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool RNA STAR",
+                                "name": "singlePaired"
+                            }
+                        ],
+                        "label": "Alignment (Choose a Genome)",
+                        "name": "RNA STAR",
                         "outputs": [
                             {
-                                "name": "outpdf",
-                                "type": "pdf"
+                                "name": "output_log",
+                                "type": "txt"
                             },
                             {
-                                "name": "outlog",
-                                "type": "txt"
+                                "name": "chimeric_junctions",
+                                "type": "interval"
+                            },
+                            {
+                                "name": "chimeric_reads",
+                                "type": "bam"
+                            },
+                            {
+                                "name": "splice_junctions",
+                                "type": "interval"
+                            },
+                            {
+                                "name": "mapped_reads",
+                                "type": "bam"
+                            },
+                            {
+                                "name": "reads_per_gene",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 512.9500045776367,
-                            "height": 147.1999969482422,
-                            "left": 773.75,
-                            "right": 933.75,
-                            "top": 365.75000762939453,
-                            "width": 160,
-                            "x": 773.75,
-                            "y": 365.75000762939453
+                            "left": 832.5,
+                            "top": 404.9166717529297
                         },
                         "post_job_actions": {},
-                        "tool_id": "raceid_inspectclusters",
-                        "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"diffgtest\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"gois\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"plotgen\": {\"do_opt\": \"yes\", \"__current_case__\": 1, \"clusts_plot\": \"\"}, \"plotsym\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.2.3+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2055c2667eb3",
+                            "name": "rgrnastar",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"singlePaired\": \"{\\\"sPaired\\\": \\\"single\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"output_params\": \"{\\\"__current_case__\\\": 1, \\\"output_select\\\": \\\"no\\\"}\", \"__rerun_remap_job_id__\": null, \"params\": \"{\\\"settingsType\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\", \"refGenomeSource\": \"{\\\"GTFconditional\\\": {\\\"genomeDir\\\": \\\"mm10\\\", \\\"sjdbGTFfile\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"GTFselect\\\": \\\"without-gtf\\\", \\\"__current_case__\\\": 1, \\\"sjdbOverhang\\\": \\\"100\\\"}, \\\"geneSource\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0}\", \"quantMode\": \"\\\"false\\\"\"}",
+                        "tool_version": "2.5.2b-2",
                         "type": "tool",
-                        "uuid": "727ee241-4de7-408f-867a-fc1ed21c23cb",
+                        "uuid": "1e4a54be-b2fb-496a-8247-ccba4ffe6f3b",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outpdf",
-                                "uuid": "051cbdaa-6513-4239-91b6-e22004f6469f"
+                                "output_name": "chimeric_reads",
+                                "uuid": "f44d1ce2-b0a0-4aca-b9da-d47a9151dd8f"
                             },
                             {
                                 "label": null,
-                                "output_name": "outlog",
-                                "uuid": "bf324238-9739-4960-90c0-2935d225bd42"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "raceid_inspectclusters",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "inputrds": {
-                                "id": 2,
-                                "output_name": "outrdat"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cluster Inspection using RaceID",
-                        "outputs": [
+                                "output_name": "chimeric_junctions",
+                                "uuid": "a70f8d45-eaa8-40f4-a755-99e7004ad0ee"
+                            },
                             {
-                                "name": "outpdf",
-                                "type": "pdf"
+                                "label": null,
+                                "output_name": "reads_per_gene",
+                                "uuid": "70ef8c03-6a54-4c88-81b6-e178dbf776c7"
                             },
                             {
-                                "name": "outlog",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 712.9500045776367,
-                            "height": 147.1999969482422,
-                            "left": 773.75,
-                            "right": 933.75,
-                            "top": 565.7500076293945,
-                            "width": 160,
-                            "x": 773.75,
-                            "y": 565.7500076293945
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "raceid_inspectclusters",
-                        "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"diffgtest\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"gois\": {\"do_opt\": \"yes\", \"__current_case__\": 1, \"inspect_goi_genes\": \"Gstm3, St3gal4, Gna11\", \"inspect_goi_cells\": \"\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"plotgen\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"plotsym\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.2.3+galaxy0",
-                        "type": "tool",
-                        "uuid": "6db63f68-65bc-4bb5-96a2-9d3e75712287",
-                        "workflow_outputs": [
+                                "label": null,
+                                "output_name": "splice_junctions",
+                                "uuid": "0896bee8-d853-4467-8143-96a4d314774c"
+                            },
                             {
                                 "label": null,
-                                "output_name": "outpdf",
-                                "uuid": "344cd8bc-01a1-4614-8def-806815a615af"
+                                "output_name": "mapped_reads",
+                                "uuid": "956818b5-dc81-440c-8c2a-b10869547c70"
                             },
                             {
                                 "label": null,
-                                "output_name": "outlog",
-                                "uuid": "3268d277-37a0-4081-ae95-8c7a83efb903"
+                                "output_name": "output_log",
+                                "uuid": "5714f89a-1d7f-4634-95ce-2b089e5cc83d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "raceid_inspectclusters",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2",
                         "errors": null,
                         "id": 6,
                         "input_connections": {
-                            "inputrds": {
+                            "alignment": {
+                                "id": 5,
+                                "output_name": "out_file1"
+                            },
+                            "anno|reference_gene_sets": {
                                 "id": 2,
-                                "output_name": "outrdat"
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cluster Inspection using RaceID",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "outpdf",
-                                "type": "pdf"
+                                "description": "runtime parameter for tool featureCounts",
+                                "name": "anno"
                             },
                             {
-                                "name": "outlog",
-                                "type": "txt"
+                                "description": "runtime parameter for tool featureCounts",
+                                "name": "alignment"
                             }
                         ],
-                        "position": {
-                            "bottom": 827.9499664306641,
-                            "height": 147.1999969482422,
-                            "left": 1035,
-                            "right": 1195,
-                            "top": 680.7499694824219,
-                            "width": 160,
-                            "x": 1035,
-                            "y": 680.7499694824219
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "raceid_inspectclusters",
-                        "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"diffgtest\": {\"do_opt\": \"yes\", \"__current_case__\": 1, \"set_a\": {\"name_set\": \"Cells in 1\", \"meth\": {\"type\": \"cln\", \"__current_case__\": 0, \"selector\": \"1\"}}, \"set_b\": {\"name_set\": \"Cells in 3\", \"meth\": {\"type\": \"cln\", \"__current_case__\": 0, \"selector\": \"3\"}}, \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"gois\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"plotgen\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"plotsym\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.2.3+galaxy0",
-                        "type": "tool",
-                        "uuid": "57c7332a-c6f5-484f-8a5c-d5467d320e72",
-                        "workflow_outputs": [
+                        "label": null,
+                        "name": "featureCounts",
+                        "outputs": [
                             {
-                                "label": null,
-                                "output_name": "outpdf",
-                                "uuid": "d028c3e8-3acb-44ba-968a-74b1cdfb4bb1"
+                                "name": "output_medium",
+                                "type": "tabular"
                             },
                             {
-                                "label": null,
-                                "output_name": "outlog",
-                                "uuid": "8f9f3e29-3c56-4fcf-af0a-f2bea2c10234"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "raceid_inspecttrajectory",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "inputrds": {
-                                "id": 3,
-                                "output_name": "outrdat"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Lineage Branch Analysis using StemID",
-                        "outputs": [
+                                "name": "output_bam",
+                                "type": "bam"
+                            },
                             {
-                                "name": "outpdf",
-                                "type": "pdf"
+                                "name": "output_short",
+                                "type": "tabular"
                             },
                             {
-                                "name": "outdiffgenes",
+                                "name": "output_full",
                                 "type": "tabular"
                             },
                             {
-                                "name": "outlog",
-                                "type": "txt"
+                                "name": "output_summary",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "output_feature_lengths",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "output_jcounts",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 372.61666107177734,
-                            "height": 253.1166534423828,
-                            "left": 1041.25,
-                            "right": 1201.25,
-                            "top": 119.50000762939453,
-                            "width": 160,
-                            "x": 1041.25,
-                            "y": 119.50000762939453
+                            "left": 1224.5,
+                            "top": 717
                         },
-                        "post_job_actions": {},
-                        "tool_id": "raceid_inspecttrajectory",
-                        "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"trjfid\": {\"basic\": {\"doit\": \"no\", \"__current_case__\": 0}}, \"trjsid\": {\"basic\": {\"doit\": \"yes\", \"__current_case__\": 1, \"i\": \"3\", \"br\": \"1,3,5\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.2.3+galaxy0",
-                        "type": "tool",
-                        "uuid": "4a519b59-2319-4811-969e-3b872f95c377",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outpdf",
-                                "uuid": "1e19e4d3-802d-4713-b920-ba8264bce2d0"
+                        "post_job_actions": {
+                            "HideDatasetActionoutput_feature_lengths": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_feature_lengths"
                             },
-                            {
-                                "label": null,
-                                "output_name": "outdiffgenes",
-                                "uuid": "814ac5ce-500d-4ea2-bbc7-ab8c4f5d2962"
+                            "HideDatasetActionoutput_full": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_full"
+                            },
+                            "HideDatasetActionoutput_jcounts": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_jcounts"
+                            },
+                            "HideDatasetActionoutput_medium": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_medium"
+                            },
+                            "HideDatasetActionoutput_short": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_short"
                             },
+                            "HideDatasetActionoutput_summary": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_summary"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f3a5f075498f",
+                            "name": "featurecounts",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"pe_parameters\": \"{\\\"only_both_ends\\\": \\\"false\\\", \\\"exclude_chimerics\\\": \\\"true\\\", \\\"fragment_counting_enabled\\\": {\\\"fragment_counting\\\": \\\"\\\", \\\"__current_case__\\\": 1}}\", \"format\": \"\\\"tabdel_short\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"strand_specificity\": \"\\\"1\\\"\", \"include_feature_length_file\": \"\\\"false\\\"\", \"anno\": \"{\\\"anno_select\\\": \\\"history\\\", \\\"reference_gene_sets\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 2}\", \"extended_parameters\": \"{\\\"gff_feature_attribute\\\": \\\"gene_id\\\", \\\"exon_exon_junction_read_counting_enabled\\\": {\\\"__current_case__\\\": 1, \\\"count_exon_exon_junction_reads\\\": \\\"false\\\"}, \\\"read_extension_3p\\\": \\\"0\\\", \\\"frac_overlap_feature\\\": \\\"0\\\", \\\"min_overlap\\\": \\\"1\\\", \\\"read_extension_5p\\\": \\\"0\\\", \\\"contribute_to_multiple_features\\\": \\\"false\\\", \\\"frac_overlap\\\": \\\"0\\\", \\\"primary\\\": \\\"false\\\", \\\"count_split_alignments_only\\\": \\\"false\\\", \\\"by_read_group\\\": \\\"false\\\", \\\"ignore_dup\\\": \\\"false\\\", \\\"mapping_quality\\\": \\\"12\\\", \\\"summarization_level\\\": \\\"false\\\", \\\"R\\\": \\\"true\\\", \\\"largest_overlap\\\": \\\"false\\\", \\\"read_reduction\\\": \\\"\\\", \\\"multimapping_enabled\\\": {\\\"multimapping_counts\\\": \\\"\\\", \\\"__current_case__\\\": 1}, \\\"long_reads\\\": \\\"false\\\", \\\"gff_feature_type\\\": \\\"exon\\\"}\", \"alignment\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "1.6.2",
+                        "type": "tool",
+                        "uuid": "9506153d-d997-43a4-8ce1-216690415561",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outlog",
-                                "uuid": "4404cdf2-ee33-4e08-8fed-83b52bbfad88"
+                                "output_name": "output_bam",
+                                "uuid": "87abf585-aae9-4af3-aed7-541795d65faf"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "raceid_inspecttrajectory",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2",
                         "errors": null,
-                        "id": 8,
+                        "id": 7,
                         "input_connections": {
-                            "inputrds": {
-                                "id": 3,
-                                "output_name": "outrdat"
+                            "input_bam": {
+                                "id": 6,
+                                "output_name": "output_bam"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool UMI-tools count",
+                                "name": "input_bam"
+                            }
+                        ],
                         "label": null,
-                        "name": "Lineage Branch Analysis using StemID",
+                        "name": "UMI-tools count",
                         "outputs": [
                             {
-                                "name": "outpdf",
-                                "type": "pdf"
-                            },
-                            {
-                                "name": "outlog",
-                                "type": "txt"
+                                "name": "out_counts",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 625.5833358764648,
-                            "height": 179.8333282470703,
-                            "left": 1040,
-                            "right": 1200,
-                            "top": 445.75000762939453,
-                            "width": 160,
-                            "x": 1040,
-                            "y": 445.75000762939453
+                            "left": 1536.5,
+                            "top": 802
                         },
                         "post_job_actions": {},
-                        "tool_id": "raceid_inspecttrajectory",
-                        "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"trjfid\": {\"basic\": {\"doit\": \"yes\", \"__current_case__\": 1, \"cellsfromz\": \"1,3,5\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}, \"som\": {\"doit\": \"no\", \"__current_case__\": 0}}}, \"trjsid\": {\"basic\": {\"doit\": \"no\", \"__current_case__\": 0}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.2.3+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "b557acca0b56",
+                            "name": "umi_tools_count",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"wide_format_cell_counts\": \"\\\"true\\\"\", \"cond_extra\": \"{\\\"prepender\\\": \\\"none\\\", \\\"__current_case__\\\": 0}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"edit_distance_threshold\": \"\\\"1\\\"\", \"paired\": \"\\\"false\\\"\", \"input_bam\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"method\": \"\\\"unique\\\"\", \"advanced\": \"{\\\"random_seed\\\": \\\"0\\\", \\\"gene_tag\\\": \\\"XT\\\", \\\"per_contig\\\": \\\"false\\\", \\\"mapping_quality\\\": \\\"0\\\", \\\"skip_tags_regex\\\": \\\"\\\", \\\"per_cell\\\": \\\"true\\\"}\", \"barcodes\": \"{\\\"umi_separator\\\": \\\"_\\\", \\\"extract_umi_method\\\": \\\"read_id\\\", \\\"__current_case__\\\": 0}\"}",
+                        "tool_version": "0.5.3.2",
                         "type": "tool",
-                        "uuid": "883ffd05-1545-449f-8028-c45c0f9edfd5",
+                        "uuid": "89675c5a-ef94-49a5-889c-c53ba1074f80",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outpdf",
-                                "uuid": "8ef7bad4-ff15-42d2-acc4-6c5bc5de89e4"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "outlog",
-                                "uuid": "23f0fab3-0128-443a-a26a-a3e40cee4578"
+                                "output_name": "out_counts",
+                                "uuid": "209f3dd6-974f-4e76-a206-c86114a6697f"
                             }
                         ]
                     }
                 ],
-                "parent_id": "single-cell/scrna-raceid",
-                "path": "topics/single-cell/tutorials/scrna-raceid/workflows/main_workflow.ga",
-                "tags": [
-                    "transcriptomics",
-                    "single-cell"
+                "parent_id": "single-cell/scrna-preprocessing",
+                "path": "topics/single-cell/tutorials/scrna-preprocessing/workflows/scrna_pp_celseq.ga",
+                "tags": [
+                    "transcriptomics"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "CelSeq2: Single Batch (mm10)",
+                "topic_id": "single-cell",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-preprocessing/versions/scrna-pp-celseq",
+                "tutorial_id": "scrna-preprocessing",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-preprocessing/workflows/scrna_pp_celseq.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-preprocessing/workflows/scrna_pp_celseq.html",
+                "version": 1,
+                "wfid": "single-cell-scrna-preprocessing",
+                "wfname": "scrna-pp-celseq",
+                "workflow": "scrna_pp_celseq.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2"
+                ],
+                "workflowhub_id": "1214"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/3253142"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-intro/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "elixir_node": "de",
+                "email": "mtekman89@gmail.com",
+                "former_affiliations": [
+                    "elixir-europe"
+                ],
+                "id": "mtekman",
+                "joined": "2018-11",
+                "name": "Mehmet Tekman",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
+            }
+        ],
+        "dir": "topics/single-cell/tutorials/scrna-intro",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-preprocessing"
+                ],
+                "type": "internal"
+            }
+        ],
+        "hands_on": false,
+        "id": "single-cell/scrna-intro",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": 20144,
+            "mermaid": false
+        },
+        "key_points": [
+            "scRNA-seq requires much pre-processing before analysis can be performed.",
+            "Groups of similarly profiled-cells are compared against other groups.",
+            "Detectability issues requires careful consideration at all stages.",
+            "Clustering is an integral part of an analysis."
+        ],
+        "layout": "tutorial_slides",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "logo": "GTN",
+        "mod_date": "2024-08-08",
+        "objectives": [
+            "To understand the pitfalls in scRNA-seq sequencing and amplification, and how they are overcome.",
+            "Know the types of variation in an analysis and how to control for them.",
+            "Grasp what dimension reduction is, and how it might be performed.",
+            "Be familiarised with the main types of clustering techniques and when to use them."
+        ],
+        "pageviews": 5783519,
+        "priority": 1,
+        "pub_date": "2021-01-29",
+        "questions": [
+            "How are samples compared?",
+            "How are cells captured?",
+            "How does bulk RNA-seq differ from scRNA-seq?",
+            "Why is clustering important?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "mtekman"
                 ],
-                "test_results": null,
-                "tests": false,
-                "title": "RaceID Workflow",
-                "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-raceid/versions/main-workflow",
-                "tutorial_id": "scrna-raceid",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-raceid/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-raceid/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "single-cell-scrna-raceid",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "raceid_clustering",
-                    "raceid_filtnormconf",
-                    "raceid_inspectclusters",
-                    "raceid_inspecttrajectory",
-                    "raceid_trajectory"
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "20M",
+                "speakers": [
+                    "awspolly"
                 ],
-                "workflowhub_id": "1205"
+                "youtube_id": "D3qvYWZMFa0"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/1511582"
+        "redirect_from": [
+            "/topics/transcriptomics/tutorials/scrna-intro/slides",
+            "/short/single-cell/scrna-intro/slides",
+            "/short/S00084"
+        ],
+        "short_id": "S00084",
+        "short_tools": [],
+        "slides": true,
+        "slides_recordings": [
+            {
+                "captioners": [
+                    "mtekman"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "20M",
+                "speakers": [
+                    "awspolly"
+                ],
+                "youtube_id": "D3qvYWZMFa0"
+            }
+        ],
+        "subtopic": "scintroduction",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": null,
+        "time_estimation": "30m",
+        "title": "An introduction to scRNA-seq data analysis",
+        "tools": [],
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": true
+        },
+        "tutorial_name": "scrna-intro",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-intro/slides.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-intro/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-intro/slides.json"
+        },
+        "version": 5,
+        "video": true,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 152,
+        "visitors": 2101226,
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "answer_histories": [
+            {
+                "date": "2024-09-08",
+                "history": "https://colab.research.google.com/drive/1nRidlpiU-_qUG1zLgpc8mJZewr_EQL0N?usp=sharing",
+                "label": "Backup Jupyter Notebook for Google Collab"
+            }
+        ],
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/alevin-commandline/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "wee-snufkin",
+                "nomadscientist"
+            ],
+            "editing": [
+                "pavanvidem",
+                "mtekman"
+            ],
+            "funding": [
+                "eosc-life"
+            ],
+            "testing": [
+                "pavanvidem"
+            ]
+        },
+        "contributors": [
+            {
+                "elixir_node": "uk",
+                "email": "juliajot36@gmail.com",
+                "id": "wee-snufkin",
+                "joined": "2022-06",
+                "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "bio": "Senior Lecturer at The Open University",
+                "elixir_node": "uk",
+                "email": "wendi.bacon@open.ac.uk",
+                "fediverse": "https://mstdn.science/@wendibacon1",
+                "fediverse_flavor": "mastodon",
+                "id": "nomadscientist",
+                "joined": "2020-03",
+                "matrix": "nomadscientist:matrix.org",
+                "name": "Wendi Bacon",
+                "orcid": "0000-0002-8170-8806",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
+                "twitter": "WendiBacon1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "pavanvidem",
+                "joined": "2017-09",
+                "name": "Pavankumar Videm",
+                "orcid": "0000-0002-5192-126X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "elixir_node": "de",
+                "email": "mtekman89@gmail.com",
+                "former_affiliations": [
+                    "elixir-europe"
+                ],
+                "id": "mtekman",
+                "joined": "2018-11",
+                "name": "Mehmet Tekman",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "pavanvidem",
+                "joined": "2017-09",
+                "name": "Pavankumar Videm",
+                "orcid": "0000-0002-5192-126X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
+            },
+            {
+                "avatar": "https://www.eosc-life.eu/wp-content/themes/eosc-life-v2/assets/images/eosclogo.png",
+                "funder": true,
+                "funding_id": "824087",
+                "funding_statement": "EOSC-Life has received funding from the European Union\u2019s Horizon 2020 programme under grant agreement number 824087",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "eosc-life",
+                "joined": "2023-04",
+                "members": [
+                    "bgruening"
+                ],
+                "name": "EOSC-Life",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eosc-life/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/eosc-life.json"
+            }
+        ],
+        "dir": "topics/single-cell/tutorials/alevin-commandline",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-case_alevin-combine-datasets"
+                ],
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "single-cell/alevin-commandline",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Create a SCE object from FASTQ files, including relevant gene and cell metadata, and do it all in Jupyter Notebook!"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-13",
+        "notebook": {
+            "language": "bash",
+            "snippet": "topics/single-cell/tutorials/alevin-commandline/preamble.md"
+        },
+        "objectives": [
+            "Generate a cellxgene matrix for droplet-based single cell sequencing data",
+            "Interpret quality control (QC) plots to make informed decisions on cell thresholds",
+            "Find relevant information in GTF files for the particulars of their study, and include this in data matrix metadata"
+        ],
+        "pageviews": 560,
+        "priority": 1,
+        "pub_date": "2023-12-08",
+        "questions": [
+            "I have some single cell FASTQ files I want to analyse. Where do I start?",
+            "How to generate a single cell matrix using command line?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-case_alevin"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00378",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "single-cell-CS-code",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "10x",
+            "paper-replication"
+        ],
+        "time_estimation": "2H",
+        "title": "Generating a single cell matrix using Alevin and combining datasets (bash + R)",
+        "tools": [],
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "alevin-commandline",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/alevin-commandline/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/alevin-commandline/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/alevin-commandline/tutorial.json"
+        },
+        "version": 3,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 285,
+        "visitors": 363,
+        "zenodo_link": null
     },
     {
         "admin_install": {
@@ -221914,6 +226788,13 @@
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "anndata_import",
+                    "owner": "iuc",
+                    "revisions": "d330b3082107",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "anndata_inspect",
                     "owner": "iuc",
@@ -221921,6 +226802,13 @@
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "anndata_inspect",
+                    "owner": "iuc",
+                    "revisions": "0bf7fddf90c7",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "anndata_manipulate",
                     "owner": "iuc",
@@ -221928,6 +226816,13 @@
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "anndata_manipulate",
+                    "owner": "iuc",
+                    "revisions": "7e8c677a7b71",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "datamash_ops",
                     "owner": "iuc",
@@ -221935,6 +226830,13 @@
                     "tool_panel_section_label": "Join, Subtract and Group",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "scanpy_cluster_reduce_dimension",
+                    "owner": "iuc",
+                    "revisions": "38db3fef7aad",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "scanpy_cluster_reduce_dimension",
                     "owner": "iuc",
@@ -221942,6 +226844,13 @@
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "scanpy_filter",
+                    "owner": "iuc",
+                    "revisions": "8cb783c81905",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "scanpy_filter",
                     "owner": "iuc",
@@ -221949,6 +226858,13 @@
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "scanpy_inspect",
+                    "owner": "iuc",
+                    "revisions": "d1cd8c147809",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "scanpy_inspect",
                     "owner": "iuc",
@@ -221956,6 +226872,13 @@
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "scanpy_normalize",
+                    "owner": "iuc",
+                    "revisions": "56c0d4acef02",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "scanpy_normalize",
                     "owner": "iuc",
@@ -221963,6 +226886,13 @@
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "scanpy_plot",
+                    "owner": "iuc",
+                    "revisions": "0185bd174ea0",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "scanpy_plot",
                     "owner": "iuc",
@@ -221970,6 +226900,13 @@
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "scanpy_remove_confounders",
+                    "owner": "iuc",
+                    "revisions": "9fb627495ec2",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "scanpy_remove_confounders",
                     "owner": "iuc",
@@ -221979,7 +226916,7 @@
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_import\n  owner: iuc\n  revisions: 93dd15e13e6a\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_inspect\n  owner: iuc\n  revisions: 6f0d0c784f09\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n  owner: iuc\n  revisions: ed4996a16f7f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 4c07ddedc198\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_cluster_reduce_dimension\n  owner: iuc\n  revisions: 6acb08931836\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter\n  owner: iuc\n  revisions: a03ff8633507\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_inspect\n  owner: iuc\n  revisions: 3081ff5c84a3\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_normalize\n  owner: iuc\n  revisions: 94c19fb1281c\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot\n  owner: iuc\n  revisions: 9b0cdb8cf6be\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_remove_confounders\n  owner: iuc\n  revisions: 458e8f43a775\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_import\n  owner: iuc\n  revisions: 93dd15e13e6a\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_import\n  owner: iuc\n  revisions: d330b3082107\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_inspect\n  owner: iuc\n  revisions: 6f0d0c784f09\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_inspect\n  owner: iuc\n  revisions: 0bf7fddf90c7\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n  owner: iuc\n  revisions: ed4996a16f7f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n  owner: iuc\n  revisions: 7e8c677a7b71\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 4c07ddedc198\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_cluster_reduce_dimension\n  owner: iuc\n  revisions: 38db3fef7aad\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_cluster_reduce_dimension\n  owner: iuc\n  revisions: 6acb08931836\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter\n  owner: iuc\n  revisions: 8cb783c81905\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter\n  owner: iuc\n  revisions: a03ff8633507\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_inspect\n  owner: iuc\n  revisions: d1cd8c147809\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_inspect\n  owner: iuc\n  revisions: 3081ff5c84a3\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_normalize\n  owner: iuc\n  revisions: 56c0d4acef02\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_normalize\n  owner: iuc\n  revisions: 94c19fb1281c\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot\n  owner: iuc\n  revisions: '0185bd174ea0'\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot\n  owner: iuc\n  revisions: 9b0cdb8cf6be\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_remove_confounders\n  owner: iuc\n  revisions: 9fb627495ec2\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_remove_confounders\n  owner: iuc\n  revisions: 458e8f43a775\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
         "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.json",
         "contributors": [
             {
@@ -222085,6 +227022,7 @@
         "hands_on": true,
         "id": "single-cell/scrna-scanpy-pbmc3k",
         "inexact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.no"
         ],
@@ -222098,7 +227036,7 @@
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-16",
+        "mod_date": "2024-09-23",
         "objectives": [
             "Describe an AnnData object to store single-cell data",
             "Explain the preprocessing steps for single-cell data",
@@ -222110,7 +227048,7 @@
             "Identify marker genes for the clusters",
             "Construct and run a cell type annotation for the clusters"
         ],
-        "pageviews": 5734803,
+        "pageviews": 5905859,
         "priority": 2,
         "pub_date": "2019-12-19",
         "questions": [
@@ -222148,22 +227086,21 @@
         ],
         "short_id": "T00254",
         "short_tools": [
-            "anndata_manipulate",
-            "cat1",
-            "anndata_inspect",
-            "scanpy_inspect",
-            "scanpy_plot",
-            "datamash_ops",
-            "scanpy_normalize",
-            "tp_grep_tool",
+            "scanpy_remove_confounders",
             "tp_awk_tool",
-            "tp_tail_tool",
-            "scanpy_cluster_reduce_dimension",
-            "Filter1",
             "anndata_import",
+            "scanpy_plot",
+            "tp_grep_tool",
             "tp_replace_in_line",
+            "scanpy_cluster_reduce_dimension",
+            "datamash_ops",
+            "anndata_inspect",
+            "anndata_manipulate",
             "scanpy_filter",
-            "scanpy_remove_confounders"
+            "scanpy_inspect",
+            "scanpy_normalize",
+            "tp_tail_tool",
+            "cat1"
         ],
         "slides": true,
         "slides_recordings": false,
@@ -222187,6 +227124,11 @@
                 }
             ],
             "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -222206,21 +227148,29 @@
         "time_estimation": "8H",
         "title": "Clustering 3K PBMCs with Scanpy",
         "tools": [
-            "Filter1",
             "cat1",
             "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
             "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
             "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
             "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
             "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.9+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.10.2+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.9.6+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1",
             "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.10.2+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.10.2+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.9.6+galaxy1"
         ],
         "topic_name": "single-cell",
@@ -222238,12 +227188,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.json"
         },
-        "version": 9,
+        "version": 11,
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 274,
-        "visitors": 2069109,
+        "visit_duration": 272,
+        "visitors": 2139256,
         "workflows": [
             {
                 "creators": [
@@ -222379,621 +227329,49 @@
                         "type": "data_input",
                         "uuid": "e08d9bbd-0761-47dd-b87a-9a0aff2b963b",
                         "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "mito header"
-                            }
-                        ],
-                        "label": "mito header",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 1679.9999999999977,
-                            "top": 1106
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "d798c58a-1b8e-4b1a-be24-3703fa627c0d",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nBarcodes\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGenes\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nMatrix\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nmito header\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Import Anndata and loom\"];\n  2 -->|output| 4;\n  0 -->|output| 4;\n  1 -->|output| 4;\n  5[\"Inspect AnnData\"];\n  4 -->|anndata| 5;\n  6[\"Inspect AnnData\"];\n  4 -->|anndata| 6;\n  7[\"Inspect AnnData\"];\n  4 -->|anndata| 7;\n  8[\"Filter\"];\n  4 -->|anndata| 8;\n  9[\"Inspect AnnData\"];\n  4 -->|anndata| 9;\n  10[\"Inspect AnnData\"];\n  8 -->|anndata_out| 10;\n  11[\"Select last\"];\n  10 -->|var| 11;\n  12[\"Text reformatting\"];\n  11 -->|outfile| 12;\n  13[\"Search in textfiles\"];\n  11 -->|outfile| 13;\n  14[\"Replace Text\"];\n  12 -->|outfile| 14;\n  15[\"Concatenate datasets\"];\n  3 -->|output| 15;\n  14 -->|outfile| 15;\n  16[\"Manipulate AnnData\"];\n  8 -->|anndata_out| 16;\n  15 -->|out_file1| 16;\n  17[\"Inspect and manipulate\"];\n  16 -->|anndata| 17;\n  18[\"Inspect AnnData\"];\n  16 -->|anndata| 18;\n  19[\"Plot\"];\n  17 -->|anndata_out| 19;\n  4ab8b810-4e79-46b2-b740-74e267f5e209[\"Output\\nout_png\"];\n  19 --> 4ab8b810-4e79-46b2-b740-74e267f5e209;\n  style 4ab8b810-4e79-46b2-b740-74e267f5e209 stroke:#2c3143,stroke-width:4px;\n  20[\"Filter\"];\n  17 -->|anndata_out| 20;\n  21[\"Plot\"];\n  17 -->|anndata_out| 21;\n  02478047-eb04-4a4e-b1ff-f3cb3c7673d5[\"Output\\nout_png\"];\n  21 --> 02478047-eb04-4a4e-b1ff-f3cb3c7673d5;\n  style 02478047-eb04-4a4e-b1ff-f3cb3c7673d5 stroke:#2c3143,stroke-width:4px;\n  22[\"Plot\"];\n  17 -->|anndata_out| 22;\n  3eb66a4a-79fe-43a3-889b-d43daeae5e17[\"Output\\nout_png\"];\n  22 --> 3eb66a4a-79fe-43a3-889b-d43daeae5e17;\n  style 3eb66a4a-79fe-43a3-889b-d43daeae5e17 stroke:#2c3143,stroke-width:4px;\n  23[\"Filter\"];\n  20 -->|anndata_out| 23;\n  24[\"Manipulate AnnData\"];\n  23 -->|anndata_out| 24;\n  25[\"Normalize\"];\n  24 -->|anndata| 25;\n  26[\"Inspect and manipulate\"];\n  25 -->|anndata_out| 26;\n  27[\"Manipulate AnnData\"];\n  26 -->|anndata_out| 27;\n  28[\"Filter\"];\n  27 -->|anndata| 28;\n  29[\"Manipulate AnnData\"];\n  28 -->|anndata_out| 29;\n  30[\"Plot\"];\n  28 -->|anndata_out| 30;\n  31[\"Remove confounders\"];\n  29 -->|anndata| 31;\n  32[\"Inspect and manipulate\"];\n  31 -->|anndata_out| 32;\n  33[\"Cluster, infer trajectories and embed\"];\n  32 -->|anndata_out| 33;\n  96cbb37e-e755-4479-9f14-f0e14f689868[\"Output\\nanndata_out\"];\n  33 --> 96cbb37e-e755-4479-9f14-f0e14f689868;\n  style 96cbb37e-e755-4479-9f14-f0e14f689868 stroke:#2c3143,stroke-width:4px;\n  34[\"Plot\"];\n  33 -->|anndata_out| 34;\n  35[\"Plot\"];\n  33 -->|anndata_out| 35;\n  5dc45ef9-c56e-4dbd-9817-367c981a2041[\"Output\\nout_png\"];\n  35 --> 5dc45ef9-c56e-4dbd-9817-367c981a2041;\n  style 5dc45ef9-c56e-4dbd-9817-367c981a2041 stroke:#2c3143,stroke-width:4px;\n  36[\"Inspect and manipulate\"];\n  33 -->|anndata_out| 36;\n  37[\"Plot\"];\n  33 -->|anndata_out| 37;\n  38[\"Plot\"];\n  33 -->|anndata_out| 38;\n  39[\"Cluster, infer trajectories and embed\"];\n  36 -->|anndata_out| 39;\n  40[\"Cluster, infer trajectories and embed\"];\n  39 -->|anndata_out| 40;\n  41[\"Plot\"];\n  39 -->|anndata_out| 41;\n  29513947-d16c-48b2-93ff-dd78cd99ecb7[\"Output\\nout_png\"];\n  41 --> 29513947-d16c-48b2-93ff-dd78cd99ecb7;\n  style 29513947-d16c-48b2-93ff-dd78cd99ecb7 stroke:#2c3143,stroke-width:4px;\n  42[\"Inspect and manipulate\"];\n  40 -->|anndata_out| 42;\n  43[\"Inspect and manipulate\"];\n  40 -->|anndata_out| 43;\n  da91ad5a-dd9c-482e-accc-8e42d645e7b1[\"Output\\nanndata_out\"];\n  43 --> da91ad5a-dd9c-482e-accc-8e42d645e7b1;\n  style da91ad5a-dd9c-482e-accc-8e42d645e7b1 stroke:#2c3143,stroke-width:4px;\n  44[\"Plot\"];\n  40 -->|anndata_out| 44;\n  45[\"Inspect AnnData\"];\n  42 -->|anndata_out| 45;\n  868797a3-ab74-45bf-96d1-84451a16f882[\"Output\\nuns_rank_genes_groups_names\"];\n  45 --> 868797a3-ab74-45bf-96d1-84451a16f882;\n  style 868797a3-ab74-45bf-96d1-84451a16f882 stroke:#2c3143,stroke-width:4px;\n  46[\"Plot\"];\n  42 -->|anndata_out| 46;\n  47[\"Plot\"];\n  43 -->|anndata_out| 47;\n  2d042636-8fd1-42e3-af8d-83b4d613f075[\"Output\\nout_png\"];\n  47 --> 2d042636-8fd1-42e3-af8d-83b4d613f075;\n  style 2d042636-8fd1-42e3-af8d-83b4d613f075 stroke:#2c3143,stroke-width:4px;\n  48[\"Manipulate AnnData\"];\n  43 -->|anndata_out| 48;\n  51289df3-101f-4c6c-ae85-a8f46c2f33ea[\"Output\\nanndata\"];\n  48 --> 51289df3-101f-4c6c-ae85-a8f46c2f33ea;\n  style 51289df3-101f-4c6c-ae85-a8f46c2f33ea stroke:#2c3143,stroke-width:4px;\n  49[\"Inspect and manipulate\"];\n  43 -->|anndata_out| 49;\n  50[\"Inspect AnnData\"];\n  43 -->|anndata_out| 50;\n  e617acd1-e59d-4f20-b39d-9dc0f832b0db[\"Output\\nuns_rank_genes_groups_names\"];\n  50 --> e617acd1-e59d-4f20-b39d-9dc0f832b0db;\n  style e617acd1-e59d-4f20-b39d-9dc0f832b0db stroke:#2c3143,stroke-width:4px;\n  51[\"Plot\"];\n  43 -->|anndata_out| 51;\n  983e7cee-7028-456c-9db2-bf0ad3e52de5[\"Output\\nout_png\"];\n  51 --> 983e7cee-7028-456c-9db2-bf0ad3e52de5;\n  style 983e7cee-7028-456c-9db2-bf0ad3e52de5 stroke:#2c3143,stroke-width:4px;\n  52[\"Inspect clusters\"];\n  43 -->|anndata_out| 52;\n  53[\"Plot\"];\n  43 -->|anndata_out| 53;\n  734099bb-f454-4d8c-bc78-a269b0570c41[\"Output\\nout_png\"];\n  53 --> 734099bb-f454-4d8c-bc78-a269b0570c41;\n  style 734099bb-f454-4d8c-bc78-a269b0570c41 stroke:#2c3143,stroke-width:4px;\n  54[\"Plot\"];\n  43 -->|anndata_out| 54;\n  55[\"Plot\"];\n  43 -->|anndata_out| 55;\n  39f2d4b6-f2e8-41b3-a00a-a2c5b54face2[\"Output\\nout_png\"];\n  55 --> 39f2d4b6-f2e8-41b3-a00a-a2c5b54face2;\n  style 39f2d4b6-f2e8-41b3-a00a-a2c5b54face2 stroke:#2c3143,stroke-width:4px;\n  56[\"Plot\"];\n  48 -->|anndata| 56;\n  e0979d1e-eb87-4a7b-904f-a5116c7b8fff[\"Output\\nout_svg\"];\n  56 --> e0979d1e-eb87-4a7b-904f-a5116c7b8fff;\n  style e0979d1e-eb87-4a7b-904f-a5116c7b8fff stroke:#2c3143,stroke-width:4px;\n  57[\"Plot\"];\n  48 -->|anndata| 57;\n  58[\"Plot\"];\n  48 -->|anndata| 58;\n  bd14e644-2a32-4a81-bd83-042ee46d118a[\"Output\\nout_png\"];\n  58 --> bd14e644-2a32-4a81-bd83-042ee46d118a;\n  style bd14e644-2a32-4a81-bd83-042ee46d118a stroke:#2c3143,stroke-width:4px;\n  59[\"Plot\"];\n  49 -->|anndata_out| 59;\n  e9cf90db-ac42-4876-8abd-183fea271666[\"Output\\ncollection_png\"];\n  59 --> e9cf90db-ac42-4876-8abd-183fea271666;\n  style e9cf90db-ac42-4876-8abd-183fea271666 stroke:#2c3143,stroke-width:4px;\n  60[\"Plot\"];\n  49 -->|anndata_out| 60;\n  aef215b1-dbb4-447b-9297-c90536842c8e[\"Output\\nout_png\"];\n  60 --> aef215b1-dbb4-447b-9297-c90536842c8e;\n  style aef215b1-dbb4-447b-9297-c90536842c8e stroke:#2c3143,stroke-width:4px;\n  61[\"Datamash\"];\n  52 -->|obs| 61;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Clustering 3k PBMC with Scanpy",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
-                        "errors": null,
-                        "id": 19,
-                        "input_connections": {
-                            "adata": {
-                                "id": 17,
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Plot",
-                        "outputs": [
-                            {
-                                "name": "out_png",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 2799.999999999996,
-                            "top": 931
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9b0cdb8cf6be",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.scatter\", \"__current_case__\": 0, \"type\": {\"type\": \"xy\", \"__current_case__\": 0, \"x\": \"n_genes_by_counts\", \"y\": \"pct_counts_mito\", \"log\": false, \"color\": \"\", \"layers\": {\"use_layers\": \"false\", \"__current_case__\": 1}}, \"use_raw\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"color_map\": null, \"palette\": null, \"frameon\": true, \"size\": null, \"title\": \"\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.6+galaxy1",
-                        "type": "tool",
-                        "uuid": "8cd94050-8147-45a7-8c16-274bdc987a35",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "out_png",
-                                "output_name": "out_png",
-                                "uuid": "4ab8b810-4e79-46b2-b740-74e267f5e209"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
-                        "errors": null,
-                        "id": 21,
-                        "input_connections": {
-                            "adata": {
-                                "id": 17,
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Plot",
-                        "outputs": [
-                            {
-                                "name": "out_png",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 2799.999999999996,
-                            "top": 1199
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9b0cdb8cf6be",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.scatter\", \"__current_case__\": 0, \"type\": {\"type\": \"xy\", \"__current_case__\": 0, \"x\": \"total_counts\", \"y\": \"n_genes_by_counts\", \"log\": false, \"color\": \"\", \"layers\": {\"use_layers\": \"false\", \"__current_case__\": 1}}, \"use_raw\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"color_map\": null, \"palette\": null, \"frameon\": true, \"size\": null, \"title\": \"\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.6+galaxy1",
-                        "type": "tool",
-                        "uuid": "748883c6-9abf-464b-8dad-746f9d7ae9af",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "out_png",
-                                "output_name": "out_png",
-                                "uuid": "02478047-eb04-4a4e-b1ff-f3cb3c7673d5"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
-                        "errors": null,
-                        "id": 22,
-                        "input_connections": {
-                            "adata": {
-                                "id": 17,
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Plot",
-                        "outputs": [
-                            {
-                                "name": "out_png",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 2799.999999999996,
-                            "top": 1333
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9b0cdb8cf6be",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"n_genes_by_counts, total_counts, pct_counts_mito\"}, \"groupby\": \"\", \"log\": false, \"use_raw\": false, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"True\", \"__current_case__\": 0, \"width\": null, \"height\": null}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": null, \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.6+galaxy1",
-                        "type": "tool",
-                        "uuid": "dbea9c99-c513-45bb-be11-f1e995ea29cc",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "out_png",
-                                "output_name": "out_png",
-                                "uuid": "3eb66a4a-79fe-43a3-889b-d43daeae5e17"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
-                        "errors": null,
-                        "id": 30,
-                        "input_connections": {
-                            "adata": {
-                                "id": 28,
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Plot",
-                        "outputs": [
-                            {
-                                "name": "out_png",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 4759.999999999994,
-                            "top": 1209
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9b0cdb8cf6be",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.highly_variable_genes\", \"__current_case__\": 7, \"log\": false, \"highly_variable_genes\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.6+galaxy1",
-                        "type": "tool",
-                        "uuid": "b74ac6fe-664f-4751-aa40-e584c4846be3",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_png",
-                                "uuid": "2dfc6706-ccdb-43ca-87b6-40cf80f8e31c"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.9.6+galaxy1",
-                        "errors": null,
-                        "id": 33,
-                        "input_connections": {
-                            "adata": {
-                                "id": 32,
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cluster, infer trajectories and embed",
-                        "outputs": [
-                            {
-                                "name": "anndata_out",
-                                "type": "h5ad"
-                            }
-                        ],
-                        "position": {
-                            "left": 5599.999999999994,
-                            "top": 1055
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionanndata_out": {
-                                "action_arguments": {
-                                    "newname": "3k PBMC with only HVG, after scaling and PCA"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.9.6+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6acb08931836",
-                            "name": "scanpy_cluster_reduce_dimension",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"tl.pca\", \"__current_case__\": 3, \"n_comps\": \"50\", \"dtype\": \"float32\", \"pca\": {\"chunked\": \"False\", \"__current_case__\": 1, \"zero_center\": true, \"svd_solver\": \"arpack\", \"random_state\": \"0\"}, \"use_highly_variable\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.6+galaxy1",
-                        "type": "tool",
-                        "uuid": "ae913706-975b-4b63-8432-313b325a4306",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "anndata_out",
-                                "output_name": "anndata_out",
-                                "uuid": "96cbb37e-e755-4479-9f14-f0e14f689868"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
-                        "errors": null,
-                        "id": 34,
-                        "input_connections": {
-                            "adata": {
-                                "id": 33,
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Plot",
-                        "outputs": [
-                            {
-                                "name": "out_png",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 5879.999999999994,
-                            "top": 787
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9b0cdb8cf6be",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.pca_loadings\", \"__current_case__\": 10, \"components\": \"1,2,3\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.6+galaxy1",
-                        "type": "tool",
-                        "uuid": "e074111c-968e-444a-827d-9928727e9792",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_png",
-                                "uuid": "630f48d2-915e-4d59-b25b-b99a957b1cce"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
-                        "errors": null,
-                        "id": 35,
-                        "input_connections": {
-                            "adata": {
-                                "id": 33,
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Plot",
-                        "outputs": [
-                            {
-                                "name": "out_png",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 5879.999999999994,
-                            "top": 921
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9b0cdb8cf6be",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.pca_variance_ratio\", \"__current_case__\": 11, \"n_pcs\": \"30\", \"log\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.6+galaxy1",
-                        "type": "tool",
-                        "uuid": "bb708b36-d4d4-424e-8262-4a792dd2098f",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "out_png",
-                                "output_name": "out_png",
-                                "uuid": "5dc45ef9-c56e-4dbd-9817-367c981a2041"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
-                        "errors": null,
-                        "id": 37,
-                        "input_connections": {
-                            "adata": {
-                                "id": 33,
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Plot",
-                        "outputs": [
-                            {
-                                "name": "out_png",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 5879.999999999994,
-                            "top": 1209
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9b0cdb8cf6be",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.pca_overview\", \"__current_case__\": 12, \"color\": \"\", \"use_raw\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [{\"__index__\": 0, \"axis1\": \"1\", \"axis2\": \"2\"}, {\"__index__\": 1, \"axis1\": \"2\", \"axis2\": \"3\"}], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": null, \"palette\": null, \"frameon\": true, \"ncols\": \"2\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.6+galaxy1",
-                        "type": "tool",
-                        "uuid": "bd73b843-6b62-4b87-8712-6e2ded015eb1",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_png",
-                                "uuid": "630f48d2-915e-4d59-b25b-b99a957b1cce"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
-                        "errors": null,
-                        "id": 38,
-                        "input_connections": {
-                            "adata": {
-                                "id": 33,
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Plot",
-                        "outputs": [
-                            {
-                                "name": "out_png",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 5879.999999999994,
-                            "top": 1343
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9b0cdb8cf6be",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.pca_overview\", \"__current_case__\": 12, \"color\": \"CST3, NKG7, PPBP\", \"use_raw\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [{\"__index__\": 0, \"axis1\": \"1\", \"axis2\": \"2\"}, {\"__index__\": 1, \"axis1\": \"2\", \"axis2\": \"3\"}], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": null, \"palette\": null, \"frameon\": true, \"ncols\": \"2\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.6+galaxy1",
-                        "type": "tool",
-                        "uuid": "4884a876-9340-4e66-843f-f1849df0f52b",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_png",
-                                "uuid": "630f48d2-915e-4d59-b25b-b99a957b1cce"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
-                        "errors": null,
-                        "id": 41,
-                        "input_connections": {
-                            "adata": {
-                                "id": 39,
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Plot",
-                        "outputs": [
-                            {
-                                "name": "out_png",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 6439.999999999994,
-                            "top": 1209
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "9b0cdb8cf6be",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"CST3, NKG7, PPBP\", \"use_raw\": false, \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": null, \"palette\": null, \"frameon\": true, \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.6+galaxy1",
-                        "type": "tool",
-                        "uuid": "efe6eab5-4014-4c80-a425-809d20cf6672",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "out_png",
-                                "output_name": "out_png",
-                                "uuid": "29513947-d16c-48b2-93ff-dd78cd99ecb7"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy1",
-                        "errors": null,
-                        "id": 43,
-                        "input_connections": {
-                            "adata": {
-                                "id": 40,
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Inspect and manipulate",
-                        "outputs": [
-                            {
-                                "name": "anndata_out",
-                                "type": "h5ad"
-                            }
-                        ],
-                        "position": {
-                            "left": 6719.999999999994,
-                            "top": 1055
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionanndata_out": {
-                                "action_arguments": {
-                                    "newname": "3k PBMC with only HVG, after scaling, PCA, KNN graph, UMAP, clustering, marker genes with Wilcoxon test"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3081ff5c84a3",
-                            "name": "scanpy_inspect",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"method\": {\"method\": \"tl.rank_genes_groups\", \"__current_case__\": 4, \"groupby\": \"louvain\", \"use_raw\": true, \"groups\": \"\", \"ref\": {\"rest\": \"rest\", \"__current_case__\": 0}, \"n_genes\": \"100\", \"tl_rank_genes_groups_method\": {\"method\": \"wilcoxon\", \"__current_case__\": 1, \"corr_method\": \"benjamini-hochberg\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.6+galaxy1",
-                        "type": "tool",
-                        "uuid": "636ce34b-e448-4108-8c36-08bb9552f3d9",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "anndata_out",
-                                "output_name": "anndata_out",
-                                "uuid": "da91ad5a-dd9c-482e-accc-8e42d645e7b1"
-                            }
-                        ]
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 45,
-                        "input_connections": {
-                            "input": {
-                                "id": 42,
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Inspect AnnData",
-                        "outputs": [
-                            {
-                                "name": "uns_rank_genes_groups_names",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "uns_rank_genes_groups_scores",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "uns_rank_genes_groups_logfoldchanges",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "uns_rank_genes_groups_pvals",
-                                "type": "tabular"
-                            },
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "uns_rank_genes_groups_pvals_adj",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "mito header"
                             }
                         ],
+                        "label": "mito header",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 6999.999999999994,
-                            "top": 0
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6f0d0c784f09",
-                            "name": "anndata_inspect",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 1679.9999999999977,
+                            "top": 1106
                         },
-                        "tool_state": "{\"__input_ext\": \"h5ad\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"uns\", \"__current_case__\": 5, \"uns_info\": \"rank_genes_groups\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.10.3+galaxy0",
-                        "type": "tool",
-                        "uuid": "a4ce5de4-7791-48f6-bcdf-97a9a6c930cb",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "d798c58a-1b8e-4b1a-be24-3703fa627c0d",
                         "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "uns_rank_genes_groups_names",
-                                "output_name": "uns_rank_genes_groups_names",
-                                "uuid": "868797a3-ab74-45bf-96d1-84451a16f882"
-                            }
-                        ]
-                    },
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nBarcodes\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGenes\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nMatrix\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nmito header\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Import Anndata and loom\"];\n  2 -->|output| 4;\n  0 -->|output| 4;\n  1 -->|output| 4;\n  5[\"Inspect AnnData\"];\n  4 -->|anndata| 5;\n  6[\"Inspect AnnData\"];\n  4 -->|anndata| 6;\n  7[\"Inspect AnnData\"];\n  4 -->|anndata| 7;\n  8[\"Filter\"];\n  4 -->|anndata| 8;\n  9[\"Inspect AnnData\"];\n  4 -->|anndata| 9;\n  10[\"Inspect AnnData\"];\n  8 -->|anndata_out| 10;\n  11[\"Select last\"];\n  10 -->|var| 11;\n  12[\"Text reformatting\"];\n  11 -->|outfile| 12;\n  13[\"Search in textfiles\"];\n  11 -->|outfile| 13;\n  14[\"Replace Text\"];\n  12 -->|outfile| 14;\n  15[\"Concatenate datasets\"];\n  3 -->|output| 15;\n  14 -->|outfile| 15;\n  16[\"Manipulate AnnData\"];\n  8 -->|anndata_out| 16;\n  15 -->|out_file1| 16;\n  17[\"Inspect and manipulate\"];\n  16 -->|anndata| 17;\n  18[\"Inspect AnnData\"];\n  16 -->|anndata| 18;\n  19[\"Plot\"];\n  17 -->|anndata_out| 19;\n  4ab8b810-4e79-46b2-b740-74e267f5e209[\"Output\\nout_png\"];\n  19 --> 4ab8b810-4e79-46b2-b740-74e267f5e209;\n  style 4ab8b810-4e79-46b2-b740-74e267f5e209 stroke:#2c3143,stroke-width:4px;\n  20[\"Filter\"];\n  17 -->|anndata_out| 20;\n  21[\"Plot\"];\n  17 -->|anndata_out| 21;\n  02478047-eb04-4a4e-b1ff-f3cb3c7673d5[\"Output\\nout_png\"];\n  21 --> 02478047-eb04-4a4e-b1ff-f3cb3c7673d5;\n  style 02478047-eb04-4a4e-b1ff-f3cb3c7673d5 stroke:#2c3143,stroke-width:4px;\n  22[\"Plot\"];\n  17 -->|anndata_out| 22;\n  3eb66a4a-79fe-43a3-889b-d43daeae5e17[\"Output\\nout_png\"];\n  22 --> 3eb66a4a-79fe-43a3-889b-d43daeae5e17;\n  style 3eb66a4a-79fe-43a3-889b-d43daeae5e17 stroke:#2c3143,stroke-width:4px;\n  23[\"Filter\"];\n  20 -->|anndata_out| 23;\n  24[\"Manipulate AnnData\"];\n  23 -->|anndata_out| 24;\n  25[\"Normalize\"];\n  24 -->|anndata| 25;\n  26[\"Inspect and manipulate\"];\n  25 -->|anndata_out| 26;\n  27[\"Manipulate AnnData\"];\n  26 -->|anndata_out| 27;\n  28[\"Filter\"];\n  27 -->|anndata| 28;\n  29[\"Manipulate AnnData\"];\n  28 -->|anndata_out| 29;\n  30[\"Plot\"];\n  28 -->|anndata_out| 30;\n  31[\"Remove confounders\"];\n  29 -->|anndata| 31;\n  32[\"Inspect and manipulate\"];\n  31 -->|anndata_out| 32;\n  33[\"Cluster, infer trajectories and embed\"];\n  32 -->|anndata_out| 33;\n  96cbb37e-e755-4479-9f14-f0e14f689868[\"Output\\nanndata_out\"];\n  33 --> 96cbb37e-e755-4479-9f14-f0e14f689868;\n  style 96cbb37e-e755-4479-9f14-f0e14f689868 stroke:#2c3143,stroke-width:4px;\n  34[\"Plot\"];\n  33 -->|anndata_out| 34;\n  35[\"Plot\"];\n  33 -->|anndata_out| 35;\n  5dc45ef9-c56e-4dbd-9817-367c981a2041[\"Output\\nout_png\"];\n  35 --> 5dc45ef9-c56e-4dbd-9817-367c981a2041;\n  style 5dc45ef9-c56e-4dbd-9817-367c981a2041 stroke:#2c3143,stroke-width:4px;\n  36[\"Inspect and manipulate\"];\n  33 -->|anndata_out| 36;\n  37[\"Plot\"];\n  33 -->|anndata_out| 37;\n  38[\"Plot\"];\n  33 -->|anndata_out| 38;\n  39[\"Cluster, infer trajectories and embed\"];\n  36 -->|anndata_out| 39;\n  40[\"Cluster, infer trajectories and embed\"];\n  39 -->|anndata_out| 40;\n  41[\"Plot\"];\n  39 -->|anndata_out| 41;\n  29513947-d16c-48b2-93ff-dd78cd99ecb7[\"Output\\nout_png\"];\n  41 --> 29513947-d16c-48b2-93ff-dd78cd99ecb7;\n  style 29513947-d16c-48b2-93ff-dd78cd99ecb7 stroke:#2c3143,stroke-width:4px;\n  42[\"Inspect and manipulate\"];\n  40 -->|anndata_out| 42;\n  43[\"Inspect and manipulate\"];\n  40 -->|anndata_out| 43;\n  da91ad5a-dd9c-482e-accc-8e42d645e7b1[\"Output\\nanndata_out\"];\n  43 --> da91ad5a-dd9c-482e-accc-8e42d645e7b1;\n  style da91ad5a-dd9c-482e-accc-8e42d645e7b1 stroke:#2c3143,stroke-width:4px;\n  44[\"Plot\"];\n  40 -->|anndata_out| 44;\n  45[\"Inspect AnnData\"];\n  42 -->|anndata_out| 45;\n  868797a3-ab74-45bf-96d1-84451a16f882[\"Output\\nuns_rank_genes_groups_names\"];\n  45 --> 868797a3-ab74-45bf-96d1-84451a16f882;\n  style 868797a3-ab74-45bf-96d1-84451a16f882 stroke:#2c3143,stroke-width:4px;\n  46[\"Plot\"];\n  42 -->|anndata_out| 46;\n  47[\"Plot\"];\n  43 -->|anndata_out| 47;\n  2d042636-8fd1-42e3-af8d-83b4d613f075[\"Output\\nout_png\"];\n  47 --> 2d042636-8fd1-42e3-af8d-83b4d613f075;\n  style 2d042636-8fd1-42e3-af8d-83b4d613f075 stroke:#2c3143,stroke-width:4px;\n  48[\"Manipulate AnnData\"];\n  43 -->|anndata_out| 48;\n  51289df3-101f-4c6c-ae85-a8f46c2f33ea[\"Output\\nanndata\"];\n  48 --> 51289df3-101f-4c6c-ae85-a8f46c2f33ea;\n  style 51289df3-101f-4c6c-ae85-a8f46c2f33ea stroke:#2c3143,stroke-width:4px;\n  49[\"Inspect and manipulate\"];\n  43 -->|anndata_out| 49;\n  50[\"Inspect AnnData\"];\n  43 -->|anndata_out| 50;\n  e617acd1-e59d-4f20-b39d-9dc0f832b0db[\"Output\\nuns_rank_genes_groups_names\"];\n  50 --> e617acd1-e59d-4f20-b39d-9dc0f832b0db;\n  style e617acd1-e59d-4f20-b39d-9dc0f832b0db stroke:#2c3143,stroke-width:4px;\n  51[\"Plot\"];\n  43 -->|anndata_out| 51;\n  983e7cee-7028-456c-9db2-bf0ad3e52de5[\"Output\\nout_png\"];\n  51 --> 983e7cee-7028-456c-9db2-bf0ad3e52de5;\n  style 983e7cee-7028-456c-9db2-bf0ad3e52de5 stroke:#2c3143,stroke-width:4px;\n  52[\"Inspect clusters\"];\n  43 -->|anndata_out| 52;\n  53[\"Plot\"];\n  43 -->|anndata_out| 53;\n  734099bb-f454-4d8c-bc78-a269b0570c41[\"Output\\nout_png\"];\n  53 --> 734099bb-f454-4d8c-bc78-a269b0570c41;\n  style 734099bb-f454-4d8c-bc78-a269b0570c41 stroke:#2c3143,stroke-width:4px;\n  54[\"Plot\"];\n  43 -->|anndata_out| 54;\n  55[\"Plot\"];\n  43 -->|anndata_out| 55;\n  39f2d4b6-f2e8-41b3-a00a-a2c5b54face2[\"Output\\nout_png\"];\n  55 --> 39f2d4b6-f2e8-41b3-a00a-a2c5b54face2;\n  style 39f2d4b6-f2e8-41b3-a00a-a2c5b54face2 stroke:#2c3143,stroke-width:4px;\n  56[\"Plot\"];\n  48 -->|anndata| 56;\n  e0979d1e-eb87-4a7b-904f-a5116c7b8fff[\"Output\\nout_svg\"];\n  56 --> e0979d1e-eb87-4a7b-904f-a5116c7b8fff;\n  style e0979d1e-eb87-4a7b-904f-a5116c7b8fff stroke:#2c3143,stroke-width:4px;\n  57[\"Plot\"];\n  48 -->|anndata| 57;\n  58[\"Plot\"];\n  48 -->|anndata| 58;\n  bd14e644-2a32-4a81-bd83-042ee46d118a[\"Output\\nout_png\"];\n  58 --> bd14e644-2a32-4a81-bd83-042ee46d118a;\n  style bd14e644-2a32-4a81-bd83-042ee46d118a stroke:#2c3143,stroke-width:4px;\n  59[\"Plot\"];\n  49 -->|anndata_out| 59;\n  e9cf90db-ac42-4876-8abd-183fea271666[\"Output\\ncollection_png\"];\n  59 --> e9cf90db-ac42-4876-8abd-183fea271666;\n  style e9cf90db-ac42-4876-8abd-183fea271666 stroke:#2c3143,stroke-width:4px;\n  60[\"Plot\"];\n  49 -->|anndata_out| 60;\n  aef215b1-dbb4-447b-9297-c90536842c8e[\"Output\\nout_png\"];\n  60 --> aef215b1-dbb4-447b-9297-c90536842c8e;\n  style aef215b1-dbb4-447b-9297-c90536842c8e stroke:#2c3143,stroke-width:4px;\n  61[\"Datamash\"];\n  52 -->|obs| 61;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "Clustering 3k PBMC with Scanpy",
+                "outputs": [
                     {
                         "annotation": "",
                         "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "errors": null,
-                        "id": 47,
+                        "id": 19,
                         "input_connections": {
                             "adata": {
-                                "id": 43,
+                                "id": 17,
                                 "output_name": "anndata_out"
                             }
                         },
@@ -223007,8 +227385,8 @@
                             }
                         ],
                         "position": {
-                            "left": 6999.999999999994,
-                            "top": 614
+                            "left": 2799.999999999996,
+                            "top": 931
                         },
                         "post_job_actions": {},
                         "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
@@ -223018,130 +227396,106 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"CST3, NKG7, PPBP\"}, \"groupby\": \"louvain\", \"log\": false, \"use_raw\": false, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.scatter\", \"__current_case__\": 0, \"type\": {\"type\": \"xy\", \"__current_case__\": 0, \"x\": \"n_genes_by_counts\", \"y\": \"pct_counts_mito\", \"log\": false, \"color\": \"\", \"layers\": {\"use_layers\": \"false\", \"__current_case__\": 1}}, \"use_raw\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"color_map\": null, \"palette\": null, \"frameon\": true, \"size\": null, \"title\": \"\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.9.6+galaxy1",
                         "type": "tool",
-                        "uuid": "8030a8a4-0fb2-41b4-b7b6-a3fee0e1348c",
+                        "uuid": "8cd94050-8147-45a7-8c16-274bdc987a35",
                         "when": null,
                         "workflow_outputs": [
                             {
                                 "label": "out_png",
                                 "output_name": "out_png",
-                                "uuid": "2d042636-8fd1-42e3-af8d-83b4d613f075"
+                                "uuid": "4ab8b810-4e79-46b2-b740-74e267f5e209"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "errors": null,
-                        "id": 48,
+                        "id": 21,
                         "input_connections": {
-                            "input": {
-                                "id": 43,
+                            "adata": {
+                                "id": 17,
                                 "output_name": "anndata_out"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Manipulate AnnData",
+                        "name": "Plot",
                         "outputs": [
                             {
-                                "name": "anndata",
-                                "type": "h5ad"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 6999.999999999994,
-                            "top": 748
+                            "left": 2799.999999999996,
+                            "top": 1199
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "ed4996a16f7f",
-                            "name": "anndata_manipulate",
+                            "changeset_revision": "9b0cdb8cf6be",
+                            "name": "scanpy_plot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"h5ad\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"rename_categories\", \"__current_case__\": 3, \"key\": \"louvain\", \"categories\": \"CD4+ T, CD14+, B, CD8+ T, FCGR3A+, NK, Dendritic, Megakaryocytes\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.10.3+galaxy0",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.scatter\", \"__current_case__\": 0, \"type\": {\"type\": \"xy\", \"__current_case__\": 0, \"x\": \"total_counts\", \"y\": \"n_genes_by_counts\", \"log\": false, \"color\": \"\", \"layers\": {\"use_layers\": \"false\", \"__current_case__\": 1}}, \"use_raw\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"color_map\": null, \"palette\": null, \"frameon\": true, \"size\": null, \"title\": \"\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.6+galaxy1",
                         "type": "tool",
-                        "uuid": "6ac832fd-39f6-4e07-b386-56001eacc343",
+                        "uuid": "748883c6-9abf-464b-8dad-746f9d7ae9af",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "anndata",
-                                "output_name": "anndata",
-                                "uuid": "51289df3-101f-4c6c-ae85-a8f46c2f33ea"
+                                "label": "out_png",
+                                "output_name": "out_png",
+                                "uuid": "02478047-eb04-4a4e-b1ff-f3cb3c7673d5"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "errors": null,
-                        "id": 50,
+                        "id": 22,
                         "input_connections": {
-                            "input": {
-                                "id": 43,
+                            "adata": {
+                                "id": 17,
                                 "output_name": "anndata_out"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Inspect AnnData",
+                        "name": "Plot",
                         "outputs": [
                             {
-                                "name": "uns_rank_genes_groups_names",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "uns_rank_genes_groups_scores",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "uns_rank_genes_groups_logfoldchanges",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "uns_rank_genes_groups_pvals",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "uns_rank_genes_groups_pvals_adj",
-                                "type": "tabular"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 6999.999999999994,
-                            "top": 1056
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionuns_rank_genes_groups_names": {
-                                "action_arguments": {
-                                    "newname": "Ranked genes with Wilcoxon test"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "uns_rank_genes_groups_names"
-                            }
+                            "left": 2799.999999999996,
+                            "top": 1333
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "6f0d0c784f09",
-                            "name": "anndata_inspect",
+                            "changeset_revision": "9b0cdb8cf6be",
+                            "name": "scanpy_plot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"h5ad\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"uns\", \"__current_case__\": 5, \"uns_info\": \"rank_genes_groups\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.10.3+galaxy0",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"n_genes_by_counts, total_counts, pct_counts_mito\"}, \"groupby\": \"\", \"log\": false, \"use_raw\": false, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"True\", \"__current_case__\": 0, \"width\": null, \"height\": null}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": null, \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.6+galaxy1",
                         "type": "tool",
-                        "uuid": "4755a9d9-1cda-4ade-8b1b-4514835fd3d1",
+                        "uuid": "dbea9c99-c513-45bb-be11-f1e995ea29cc",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "uns_rank_genes_groups_names",
-                                "output_name": "uns_rank_genes_groups_names",
-                                "uuid": "e617acd1-e59d-4f20-b39d-9dc0f832b0db"
+                                "label": "out_png",
+                                "output_name": "out_png",
+                                "uuid": "3eb66a4a-79fe-43a3-889b-d43daeae5e17"
                             }
                         ]
                     },
@@ -223149,10 +227503,10 @@
                         "annotation": "",
                         "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "errors": null,
-                        "id": 51,
+                        "id": 30,
                         "input_connections": {
                             "adata": {
-                                "id": 43,
+                                "id": 28,
                                 "output_name": "anndata_out"
                             }
                         },
@@ -223166,8 +227520,8 @@
                             }
                         ],
                         "position": {
-                            "left": 6999.999999999994,
-                            "top": 1536
+                            "left": 4759.999999999994,
+                            "top": 1209
                         },
                         "post_job_actions": {},
                         "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
@@ -223177,61 +227531,69 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.rank_genes_groups_heatmap\", \"__current_case__\": 26, \"groups\": \"\", \"n_genes\": \"20\", \"key\": \"\", \"log\": false, \"use_raw\": true, \"dendrogram\": true, \"var_group_positions\": [], \"var_group_rotation\": null, \"figsize\": {\"test\": \"no\", \"__current_case__\": 1}, \"layer\": \"\", \"gene_symbols\": \"\", \"swap_axes\": false, \"show_gene_labels\": false, \"matplotlib_pyplot_imshow\": {\"cmap\": \"viridis\", \"interpolation\": \"None\", \"alpha\": null, \"vmin\": null, \"vmax\": null, \"origin\": \"upper\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.highly_variable_genes\", \"__current_case__\": 7, \"log\": false, \"highly_variable_genes\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.9.6+galaxy1",
                         "type": "tool",
-                        "uuid": "92ad3339-6642-4452-a993-aade06db8c56",
+                        "uuid": "b74ac6fe-664f-4751-aa40-e584c4846be3",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "out_png",
+                                "label": null,
                                 "output_name": "out_png",
-                                "uuid": "983e7cee-7028-456c-9db2-bf0ad3e52de5"
+                                "uuid": "2dfc6706-ccdb-43ca-87b6-40cf80f8e31c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.9.6+galaxy1",
                         "errors": null,
-                        "id": 53,
+                        "id": 33,
                         "input_connections": {
                             "adata": {
-                                "id": 43,
+                                "id": 32,
                                 "output_name": "anndata_out"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Plot",
+                        "name": "Cluster, infer trajectories and embed",
                         "outputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "name": "anndata_out",
+                                "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 6999.999999999994,
-                            "top": 1824
+                            "left": 5599.999999999994,
+                            "top": 1055
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
+                        "post_job_actions": {
+                            "RenameDatasetActionanndata_out": {
+                                "action_arguments": {
+                                    "newname": "3k PBMC with only HVG, after scaling and PCA"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "anndata_out"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.9.6+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "9b0cdb8cf6be",
-                            "name": "scanpy_plot",
+                            "changeset_revision": "6acb08931836",
+                            "name": "scanpy_cluster_reduce_dimension",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"louvain, LDHB, LYZ, CD74, CCL5, LST1, NKG7, HLA-DPA1, PF4\", \"use_raw\": true, \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": null, \"palette\": null, \"frameon\": true, \"ncols\": \"2\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"tl.pca\", \"__current_case__\": 3, \"n_comps\": \"50\", \"dtype\": \"float32\", \"pca\": {\"chunked\": \"False\", \"__current_case__\": 1, \"zero_center\": true, \"svd_solver\": \"arpack\", \"random_state\": \"0\"}, \"use_highly_variable\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.9.6+galaxy1",
                         "type": "tool",
-                        "uuid": "f54debde-f7a9-4615-8a81-6a4406ebcc02",
+                        "uuid": "ae913706-975b-4b63-8432-313b325a4306",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "out_png",
-                                "output_name": "out_png",
-                                "uuid": "734099bb-f454-4d8c-bc78-a269b0570c41"
+                                "label": "anndata_out",
+                                "output_name": "anndata_out",
+                                "uuid": "96cbb37e-e755-4479-9f14-f0e14f689868"
                             }
                         ]
                     },
@@ -223239,10 +227601,10 @@
                         "annotation": "",
                         "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "errors": null,
-                        "id": 55,
+                        "id": 34,
                         "input_connections": {
                             "adata": {
-                                "id": 43,
+                                "id": 33,
                                 "output_name": "anndata_out"
                             }
                         },
@@ -223256,8 +227618,8 @@
                             }
                         ],
                         "position": {
-                            "left": 6999.999999999994,
-                            "top": 2092
+                            "left": 5879.999999999994,
+                            "top": 787
                         },
                         "post_job_actions": {},
                         "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
@@ -223267,16 +227629,16 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.stacked_violin\", \"__current_case__\": 4, \"var_names\": {\"type\": \"custom\", \"__current_case__\": 1, \"var_names\": \"LDHB, LYZ, CD74, CCL5, LST1, NKG7, HLA-DPA1, PF4\"}, \"groupby\": \"louvain\", \"num_categories\": \"8\", \"gene_symbols\": \"\", \"log\": false, \"use_raw\": true, \"dendrogram\": false, \"var_group_positions\": [], \"var_group_rotation\": null, \"figsize\": {\"test\": \"yes\", \"__current_case__\": 0, \"width\": \"10\", \"height\": \"10\"}, \"layer\": \"\", \"swap_axes\": true, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"scale\": \"width\"}, \"row_palette\": \"muted\", \"standard_scale\": \"None\", \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.pca_loadings\", \"__current_case__\": 10, \"components\": \"1,2,3\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.9.6+galaxy1",
                         "type": "tool",
-                        "uuid": "9386a889-5f57-4c24-b804-d1018a2c4d24",
+                        "uuid": "e074111c-968e-444a-827d-9928727e9792",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "out_png",
+                                "label": null,
                                 "output_name": "out_png",
-                                "uuid": "39f2d4b6-f2e8-41b3-a00a-a2c5b54face2"
+                                "uuid": "630f48d2-915e-4d59-b25b-b99a957b1cce"
                             }
                         ]
                     },
@@ -223284,11 +227646,11 @@
                         "annotation": "",
                         "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "errors": null,
-                        "id": 56,
+                        "id": 35,
                         "input_connections": {
                             "adata": {
-                                "id": 48,
-                                "output_name": "anndata"
+                                "id": 33,
+                                "output_name": "anndata_out"
                             }
                         },
                         "inputs": [],
@@ -223296,13 +227658,13 @@
                         "name": "Plot",
                         "outputs": [
                             {
-                                "name": "out_svg",
-                                "type": "svg"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 7279.999999999994,
-                            "top": 529
+                            "left": 5879.999999999994,
+                            "top": 921
                         },
                         "post_job_actions": {},
                         "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
@@ -223312,16 +227674,16 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"svg\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"louvain\", \"use_raw\": true, \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"on data\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": null, \"palette\": null, \"frameon\": true, \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.pca_variance_ratio\", \"__current_case__\": 11, \"n_pcs\": \"30\", \"log\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.9.6+galaxy1",
                         "type": "tool",
-                        "uuid": "90fc9851-6092-46b7-a5ec-c3f5b49345c9",
+                        "uuid": "bb708b36-d4d4-424e-8262-4a792dd2098f",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "out_svg",
-                                "output_name": "out_svg",
-                                "uuid": "e0979d1e-eb87-4a7b-904f-a5116c7b8fff"
+                                "label": "out_png",
+                                "output_name": "out_png",
+                                "uuid": "5dc45ef9-c56e-4dbd-9817-367c981a2041"
                             }
                         ]
                     },
@@ -223329,11 +227691,11 @@
                         "annotation": "",
                         "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "errors": null,
-                        "id": 58,
+                        "id": 37,
                         "input_connections": {
                             "adata": {
-                                "id": 48,
-                                "output_name": "anndata"
+                                "id": 33,
+                                "output_name": "anndata_out"
                             }
                         },
                         "inputs": [],
@@ -223346,8 +227708,8 @@
                             }
                         ],
                         "position": {
-                            "left": 7279.999999999994,
-                            "top": 797
+                            "left": 5879.999999999994,
+                            "top": 1209
                         },
                         "post_job_actions": {},
                         "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
@@ -223357,16 +227719,16 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.dotplot\", \"__current_case__\": 2, \"var_names\": {\"type\": \"custom\", \"__current_case__\": 1, \"var_names\": \"IL7R, CCR7, CD8A, CD14, LYZ, MS4A1, CD79A, GNLY, NKG7, KLRB1, FCER1A, CST3, PPBP, FCGR3A\"}, \"groupby\": \"louvain\", \"num_categories\": \"8\", \"gene_symbols\": \"\", \"log\": false, \"use_raw\": true, \"dendrogram\": true, \"var_group_positions\": [{\"__index__\": 0, \"start\": \"0\", \"end\": \"1\", \"label\": \"CD4+T\"}, {\"__index__\": 1, \"start\": \"2\", \"end\": \"2\", \"label\": \"CD8\"}, {\"__index__\": 2, \"start\": \"3\", \"end\": \"4\", \"label\": \"CD14+\"}, {\"__index__\": 3, \"start\": \"5\", \"end\": \"6\", \"label\": \"B\"}, {\"__index__\": 4, \"start\": \"7\", \"end\": \"9\", \"label\": \"NK\"}, {\"__index__\": 5, \"start\": \"10\", \"end\": \"11\", \"label\": \"Dendritic\"}, {\"__index__\": 6, \"start\": \"12\", \"end\": \"12\", \"label\": \"Megakaryocytes\"}, {\"__index__\": 7, \"start\": \"13\", \"end\": \"13\", \"label\": \"FCGR3A+\"}], \"var_group_rotation\": null, \"figsize\": {\"test\": \"no\", \"__current_case__\": 1}, \"layer\": \"\", \"color_map\": \"viridis\", \"dot_max\": null, \"dot_min\": null, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.pca_overview\", \"__current_case__\": 12, \"color\": \"\", \"use_raw\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [{\"__index__\": 0, \"axis1\": \"1\", \"axis2\": \"2\"}, {\"__index__\": 1, \"axis1\": \"2\", \"axis2\": \"3\"}], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": null, \"palette\": null, \"frameon\": true, \"ncols\": \"2\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.9.6+galaxy1",
                         "type": "tool",
-                        "uuid": "7234b677-3502-42bb-a1ca-7c62a6118a52",
+                        "uuid": "bd73b843-6b62-4b87-8712-6e2ded015eb1",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "out_png",
+                                "label": null,
                                 "output_name": "out_png",
-                                "uuid": "bd14e644-2a32-4a81-bd83-042ee46d118a"
+                                "uuid": "630f48d2-915e-4d59-b25b-b99a957b1cce"
                             }
                         ]
                     },
@@ -223374,10 +227736,10 @@
                         "annotation": "",
                         "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "errors": null,
-                        "id": 59,
+                        "id": 38,
                         "input_connections": {
                             "adata": {
-                                "id": 49,
+                                "id": 33,
                                 "output_name": "anndata_out"
                             }
                         },
@@ -223386,13 +227748,13 @@
                         "name": "Plot",
                         "outputs": [
                             {
-                                "name": "collection_png",
-                                "type": "input"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 7279.999999999994,
-                            "top": 931
+                            "left": 5879.999999999994,
+                            "top": 1343
                         },
                         "post_job_actions": {},
                         "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
@@ -223402,16 +227764,16 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.rank_genes_groups_violin\", \"__current_case__\": 24, \"groups\": \"\", \"genes\": {\"select\": \"n_genes\", \"__current_case__\": 0, \"n_genes\": \"10\"}, \"gene_symbols\": \"\", \"use_raw\": true, \"split\": true, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"scale\": \"width\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.pca_overview\", \"__current_case__\": 12, \"color\": \"CST3, NKG7, PPBP\", \"use_raw\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [{\"__index__\": 0, \"axis1\": \"1\", \"axis2\": \"2\"}, {\"__index__\": 1, \"axis1\": \"2\", \"axis2\": \"3\"}], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": null, \"palette\": null, \"frameon\": true, \"ncols\": \"2\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.9.6+galaxy1",
                         "type": "tool",
-                        "uuid": "1f003b20-da10-4f6f-84f6-2d335b3b1102",
+                        "uuid": "4884a876-9340-4e66-843f-f1849df0f52b",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "collection_png",
-                                "output_name": "collection_png",
-                                "uuid": "e9cf90db-ac42-4876-8abd-183fea271666"
+                                "label": null,
+                                "output_name": "out_png",
+                                "uuid": "630f48d2-915e-4d59-b25b-b99a957b1cce"
                             }
                         ]
                     },
@@ -223419,10 +227781,10 @@
                         "annotation": "",
                         "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "errors": null,
-                        "id": 60,
+                        "id": 41,
                         "input_connections": {
                             "adata": {
-                                "id": 49,
+                                "id": 39,
                                 "output_name": "anndata_out"
                             }
                         },
@@ -223436,8 +227798,8 @@
                             }
                         ],
                         "position": {
-                            "left": 7279.999999999994,
-                            "top": 1065
+                            "left": 6439.999999999994,
+                            "top": 1209
                         },
                         "post_job_actions": {},
                         "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
@@ -223447,702 +227809,147 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.rank_genes_groups\", \"__current_case__\": 23, \"groups\": \"\", \"n_genes\": \"20\", \"gene_symbols\": \"\", \"fontsize\": \"8\", \"ncols\": \"4\", \"sharey\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"CST3, NKG7, PPBP\", \"use_raw\": false, \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": null, \"palette\": null, \"frameon\": true, \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.9.6+galaxy1",
                         "type": "tool",
-                        "uuid": "c2a9e741-d871-45e3-b71e-813b08500091",
+                        "uuid": "efe6eab5-4014-4c80-a425-809d20cf6672",
                         "when": null,
                         "workflow_outputs": [
                             {
                                 "label": "out_png",
                                 "output_name": "out_png",
-                                "uuid": "aef215b1-dbb4-447b-9297-c90536842c8e"
+                                "uuid": "29513947-d16c-48b2-93ff-dd78cd99ecb7"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "single-cell/scrna-scanpy-pbmc3k",
-                "path": "topics/single-cell/tutorials/scrna-scanpy-pbmc3k/workflows/Clustering-3k-PBMC-with-Scanpy.ga",
-                "tags": [
-                    "name:scRNA-seq",
-                    "name:single-cell"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "Clustering 3k PBMC with Scanpy",
-                "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-scanpy-pbmc3k/versions/clustering-3k-pbmc-with-scanpy",
-                "tutorial_id": "scrna-scanpy-pbmc3k",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/workflows/Clustering-3k-PBMC-with-Scanpy.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/workflows/Clustering-3k-PBMC-with-Scanpy.html",
-                "version": 1,
-                "wfid": "single-cell-scrna-scanpy-pbmc3k",
-                "wfname": "clustering-3k-pbmc-with-scanpy",
-                "workflow": "Clustering-3k-PBMC-with-Scanpy.ga",
-                "workflow_tools": [
-                    "cat1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.9.6+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.9.6+galaxy1"
-                ],
-                "workflowhub_id": "1259"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/3581213"
-    },
-    {
-        "abbreviations": {
-            "PBMCs": "peripheral blood mononuclear cells",
-            "QC": "quality control",
-            "TSS": "transcription start sites",
-            "TSSe": "transcription start site enrichment",
-            "UMAP": "Uniform Manifold Approximation and Projection",
-            "scATAC-seq": "Single-cell Assay for Transposase-Accessible Chromatin using sequencing"
-        },
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "replace_column_by_key_value_file",
-                    "owner": "bgruening",
-                    "revisions": "d533e4b75800",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bwa",
-                    "owner": "devteam",
-                    "revisions": "2477830927ec",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cut_columns",
-                    "owner": "devteam",
-                    "revisions": "cec635fab700",
-                    "tool_panel_section_label": "Single Cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fasta_compute_length",
-                    "owner": "devteam",
-                    "revisions": "7d37cfda8e00",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "anndata_ops",
-                    "owner": "ebi-gxa",
-                    "revisions": "a4774b7b2e85",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "anndata_inspect",
-                    "owner": "iuc",
-                    "revisions": "6f0d0c784f09",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "anndata_manipulate",
-                    "owner": "iuc",
-                    "revisions": "ed4996a16f7f",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_filter",
-                    "owner": "iuc",
-                    "revisions": "d636ce5cde16",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_inspect",
-                    "owner": "iuc",
-                    "revisions": "f54f0f0598ad",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_normalize",
-                    "owner": "iuc",
-                    "revisions": "d844935c906c",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_plot",
-                    "owner": "iuc",
-                    "revisions": "f7446fd8d5e7",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "snapatac2_clustering",
-                    "owner": "iuc",
-                    "revisions": "afb90d3485df",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "snapatac2_peaks_and_motif",
-                    "owner": "iuc",
-                    "revisions": "88192fe25375",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "snapatac2_plotting",
-                    "owner": "iuc",
-                    "revisions": "370d45e0d1a8",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "snapatac2_preprocessing",
-                    "owner": "iuc",
-                    "revisions": "fef8f61cb34c",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: replace_column_by_key_value_file\n  owner: bgruening\n  revisions: d533e4b75800\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: 2477830927ec\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cut_columns\n  owner: devteam\n  revisions: cec635fab700\n  tool_panel_section_label: Single Cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_compute_length\n  owner: devteam\n  revisions: 7d37cfda8e00\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_ops\n  owner: ebi-gxa\n  revisions: a4774b7b2e85\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_inspect\n  owner: iuc\n  revisions: 6f0d0c784f09\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n  owner: iuc\n  revisions: ed4996a16f7f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter\n  owner: iuc\n  revisions: d636ce5cde16\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_inspect\n  owner: iuc\n  revisions: f54f0f0598ad\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_normalize\n  owner: iuc\n  revisions: d844935c906c\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot\n  owner: iuc\n  revisions: f7446fd8d5e7\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snapatac2_clustering\n  owner: iuc\n  revisions: afb90d3485df\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snapatac2_peaks_and_motif\n  owner: iuc\n  revisions: 88192fe25375\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snapatac2_plotting\n  owner: iuc\n  revisions: 370d45e0d1a8\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snapatac2_preprocessing\n  owner: iuc\n  revisions: fef8f61cb34c\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "timonschlegel"
-            ],
-            "editing": [
-                "pavanvidem",
-                "bgruening"
-            ],
-            "testing": [
-                "pavanvidem"
-            ]
-        },
-        "contributors": [
-            {
-                "id": "timonschlegel",
-                "joined": "2024-05",
-                "name": "Timon Schlegel",
-                "orcid": "0009-0001-3228-105X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timonschlegel/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/timonschlegel.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "pavanvidem",
-                "joined": "2017-09",
-                "name": "Pavankumar Videm",
-                "orcid": "0000-0002-5192-126X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
-            },
-            {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
-                "fediverse_flavor": "mastodon",
-                "id": "bgruening",
-                "joined": "2017-09",
-                "linkedin": "bgruening",
-                "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
-                },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "pavanvidem",
-                "joined": "2017-09",
-                "name": "Pavankumar Videm",
-                "orcid": "0000-0002-5192-126X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
-            }
-        ],
-        "dir": "topics/single-cell/tutorials/scatac-standard-processing-snapatac2",
-        "edam_operation": [
-            "Generation",
-            "Genome indexing",
-            "Sequence alignment",
-            "Read mapping",
-            "Differential gene expression analysis"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "gitter": "Galaxy-Training-Network/galaxy-single-cell",
-        "hands_on": true,
-        "id": "single-cell/scatac-standard-processing-snapatac2",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Single-cell ATAC-seq can identify open chromatin sites",
-            "Dimension reduction is required to simplify the data while preserving important information about the relationships of cells to each other.",
-            "Clusters of similar cells can be annotated to their respective cell-types"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-08-09",
-        "objectives": [
-            "Learn how single-cell ATAC-seq data is processed",
-            "Create a count-matrix from a 10X fragment file",
-            "Perform filtering, dimension reduction and clustering on AnnData matrices",
-            "Generate and filter a cell-by-gene matrix",
-            "Identify marker genes for the clusters and annotate the cell types"
-        ],
-        "pageviews": 240,
-        "priority": 2,
-        "pub_date": "2024-07-11",
-        "questions": [
-            "What does ATAC-seq data tell us about the cell?",
-            "Which steps are necessary to cluster the cells of single-cell ATAC-seq data?",
-            "Why is dimension reduction important for the analysis of single-cell data?"
-        ],
-        "redirect_from": [
-            "/topics/transcriptomics/tutorials/scatac-standard-processing-snapatac2/tutorial",
-            "/short/single-cell/scatac-standard-processing-snapatac2",
-            "/short/T00445"
-        ],
-        "requirements": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scatac-preprocessing-tenx"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00445",
-        "short_tools": [
-            "anndata_ops",
-            "anndata_manipulate",
-            "anndata_inspect",
-            "snapatac2_clustering",
-            "scanpy_inspect",
-            "scanpy_plot",
-            "snapatac2_plotting",
-            "replace_column_with_key_value_file",
-            "scanpy_normalize",
-            "snapatac2_peaks_and_motif",
-            "snapatac2_preprocessing",
-            "Cut1",
-            "fasta_compute_length",
-            "scanpy_filter",
-            "bwa_mem"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "scmultiomics",
-        "supported_servers": {
-            "exact": [],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "10x",
-            "epigenetics",
-            "single-cell"
-        ],
-        "time_estimation": "4H",
-        "title": "Single-cell ATAC-seq standard processing with SnapATAC2",
-        "tools": [
-            "Cut1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18",
-            "toolshed.g2.bx.psu.edu/repos/devteam/cut_columns/Cut1/1.0.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_peaks_and_motif/snapatac2_peaks_and_motif/2.6.4+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1"
-        ],
-        "topic_name": "single-cell",
-        "topic_name_human": "Single Cell",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "scatac-standard-processing-snapatac2",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.json"
-        },
-        "version": 2,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 66,
-        "visitors": 170,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0009-0001-3228-105X",
-                        "name": "Timon Schlegel"
-                    }
-                ],
-                "description": "Workflow of Tutorial \"Single-cell ATAC-seq standard processing with SnapATAC2\".\nThis workflow takes a fragment file as input and performs the standard steps of scATAC-seq analysis: filtering, dimension reduction, embedding and visualization of marker genes with SnapATAC2.\nIn an alternative step, the fragment file can also be generated from a BAM file. ",
-                "features": {
-                    "comments": true,
-                    "parameters": true,
-                    "report": {
-                        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
-                    },
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nFragment_file\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nchromosome_sizes.tabular\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ngene_annotation\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBam-file\"]\n  4[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nKeys for annotations of obs/cells or vars/genes\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReplace_file\"]\n  6[label=\"pp.import_data\"]\n  1 -> 6 [label=\"output\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"pp.make_fragment_file\"]\n  3 -> 7 [label=\"output\"]\n  8[label=\"pl.frag_size_distr\"]\n  6 -> 8 [label=\"anndata_out\"]\n  k265d602044e2408c9eb602cbc9ac23a7[color=lightseagreen,label=\"Output\\nplot frag_size\"]\n  8 -> k265d602044e2408c9eb602cbc9ac23a7\n  9[label=\"pl.frag_size_distr_log\"]\n  6 -> 9 [label=\"anndata_out\"]\n  ka37cd3c3e07e4bea899fee44cee8370b[color=lightseagreen,label=\"Output\\nplot log frag_size\"]\n  9 -> ka37cd3c3e07e4bea899fee44cee8370b\n  10[label=\"metrics.tsse\"]\n  6 -> 10 [label=\"anndata_out\"]\n  2 -> 10 [label=\"output\"]\n  k233284e5c1844330a1d32d03951c4ce7[color=lightseagreen,label=\"Output\\nanndata tsse\"]\n  10 -> k233284e5c1844330a1d32d03951c4ce7\n  11[label=\"pp.import_data-sorted_by_barcodes\"]\n  1 -> 11 [label=\"output\"]\n  7 -> 11 [label=\"fragments_out\"]\n  k50ef9fe7bb084957bc45079ed78f9ee8[color=lightseagreen,label=\"Output\\nanndata\"]\n  11 -> k50ef9fe7bb084957bc45079ed78f9ee8\n  12[label=\"pl.tsse\"]\n  10 -> 12 [label=\"anndata_out\"]\n  k9a5c0f9c04234822871eba8317f2fa7b[color=lightseagreen,label=\"Output\\nplot tsse\"]\n  12 -> k9a5c0f9c04234822871eba8317f2fa7b\n  13[label=\"pp.filter_cells\"]\n  10 -> 13 [label=\"anndata_out\"]\n  kb58dc4ad6bf04f3199f44f8deb13427c[color=lightseagreen,label=\"Output\\nanndata filter cells\"]\n  13 -> kb58dc4ad6bf04f3199f44f8deb13427c\n  14[label=\"pp.add_tile_matrix\"]\n  13 -> 14 [label=\"anndata_out\"]\n  kd4b64fc4fd354781b7990d07fe8fe438[color=lightseagreen,label=\"Output\\nanndata tile matrix\"]\n  14 -> kd4b64fc4fd354781b7990d07fe8fe438\n  15[label=\"pp.select_features\"]\n  14 -> 15 [label=\"anndata_out\"]\n  kf531f6bd3fc648b9bb3366de7928e670[color=lightseagreen,label=\"Output\\nanndata select features\"]\n  15 -> kf531f6bd3fc648b9bb3366de7928e670\n  16[label=\"pp.scrublet\"]\n  15 -> 16 [label=\"anndata_out\"]\n  k5b17aa3a3694440f9022cf9761feb760[color=lightseagreen,label=\"Output\\nanndata scrublet\"]\n  16 -> k5b17aa3a3694440f9022cf9761feb760\n  17[label=\"pp.filter_doublets\"]\n  16 -> 17 [label=\"anndata_out\"]\n  k3838cf9da0184aa78852893b2f60ec2a[color=lightseagreen,label=\"Output\\nanndata filter doublets\"]\n  17 -> k3838cf9da0184aa78852893b2f60ec2a\n  18[label=\"tl.spectral\"]\n  17 -> 18 [label=\"anndata_out\"]\n  k778835168ac440b58b755750639d9fc4[color=lightseagreen,label=\"Output\\nanndata spectral\"]\n  18 -> k778835168ac440b58b755750639d9fc4\n  19[label=\"tl.umap\"]\n  18 -> 19 [label=\"anndata_out\"]\n  k062a54717b7a4d9bbf6cfe9bbbc5d2ad[color=lightseagreen,label=\"Output\\nanndata umap\"]\n  19 -> k062a54717b7a4d9bbf6cfe9bbbc5d2ad\n  20[label=\"pp.knn\"]\n  19 -> 20 [label=\"anndata_out\"]\n  kb7ebe580993848e587184df197126615[color=lightseagreen,label=\"Output\\nanndata knn\"]\n  20 -> kb7ebe580993848e587184df197126615\n  21[label=\"tl.leiden\"]\n  20 -> 21 [label=\"anndata_out\"]\n  k9970eb96013b4d97bbbf2d1f4663b73c[color=lightseagreen,label=\"Output\\nanndata_leiden_clustering\"]\n  21 -> k9970eb96013b4d97bbbf2d1f4663b73c\n  22[label=\"pl.umap\"]\n  21 -> 22 [label=\"anndata_out\"]\n  k4fff8ec87d6f48719e42d6c1791d6aa9[color=lightseagreen,label=\"Output\\numap_leiden-clusters\"]\n  22 -> k4fff8ec87d6f48719e42d6c1791d6aa9\n  23[label=\"make_gene_matrix\"]\n  21 -> 23 [label=\"anndata_out\"]\n  2 -> 23 [label=\"output\"]\n  k9a5c2e235b5941aeaceb0e47ce9e7b1a[color=lightseagreen,label=\"Output\\nanndata gene matrix\"]\n  23 -> k9a5c2e235b5941aeaceb0e47ce9e7b1a\n  24[label=\"scanpy_filter_genes\"]\n  23 -> 24 [label=\"anndata_out\"]\n  k7a9b22dfe0e549d99fa12efe316d6d66[color=lightseagreen,label=\"Output\\nanndata filter genes\"]\n  24 -> k7a9b22dfe0e549d99fa12efe316d6d66\n  25[label=\"Normalize\"]\n  24 -> 25 [label=\"anndata_out\"]\n  k7dddd4c819444f50b331857d03cc9631[color=lightseagreen,label=\"Output\\nanndata normalize\"]\n  25 -> k7dddd4c819444f50b331857d03cc9631\n  26[label=\"pp.log1p\"]\n  25 -> 26 [label=\"anndata_out\"]\n  k40ace30a21e14bf28e08ad93b62fb2ee[color=lightseagreen,label=\"Output\\nanndata log1p\"]\n  26 -> k40ace30a21e14bf28e08ad93b62fb2ee\n  27[label=\"external.pp.magic\"]\n  26 -> 27 [label=\"anndata_out\"]\n  k8c1c7aa9b9dd467b971573773aea093f[color=lightseagreen,label=\"Output\\nanndata_magic\"]\n  27 -> k8c1c7aa9b9dd467b971573773aea093f\n  28[label=\"Copy obsm\"]\n  21 -> 28 [label=\"anndata_out\"]\n  27 -> 28 [label=\"anndata_out\"]\n  k2c3825d371514eef97d0c8a31ca6fd3e[color=lightseagreen,label=\"Output\\nanndata_gene-matrix_leiden\"]\n  28 -> k2c3825d371514eef97d0c8a31ca6fd3e\n  29[label=\"umap_plot_with_scanpy\"]\n  28 -> 29 [label=\"output_h5ad\"]\n  4 -> 29 [label=\"output\"]\n  k4cfbbb70156b48d7b14bdb21198d9b6d[color=lightseagreen,label=\"Output\\numap_marker-genes\"]\n  29 -> k4cfbbb70156b48d7b14bdb21198d9b6d\n  30[label=\"Inspect observations\"]\n  28 -> 30 [label=\"output_h5ad\"]\n  31[label=\"Cut leiden from table\"]\n  30 -> 31 [label=\"obs\"]\n  k11c22200a54e458582c48457dbbfb53c[color=lightseagreen,label=\"Output\\nleiden annotation\"]\n  31 -> k11c22200a54e458582c48457dbbfb53c\n  32[label=\"Replace leiden\"]\n  31 -> 32 [label=\"out_file1\"]\n  5 -> 32 [label=\"output\"]\n  k467de06179e641488a65c06383a14012[color=lightseagreen,label=\"Output\\ncell type annotation\"]\n  32 -> k467de06179e641488a65c06383a14012\n  33[label=\"Manipulate AnnData\"]\n  28 -> 33 [label=\"output_h5ad\"]\n  32 -> 33 [label=\"outfile_replace\"]\n  kcbba6173f4394fd58423946aa625112b[color=lightseagreen,label=\"Output\\nanndata_cell_type\"]\n  33 -> kcbba6173f4394fd58423946aa625112b\n  34[label=\"Plot cell types\"]\n  33 -> 34 [label=\"anndata\"]\n  kc28c53ae8ee747d78a00352908bb7c1a[color=lightseagreen,label=\"Output\\numap_cell-type\"]\n  34 -> kc28c53ae8ee747d78a00352908bb7c1a\n  35[label=\"Final Anndata general info\"]\n  33 -> 35 [label=\"anndata\"]\n  k379a85d1a2044b0b8b3386e5582fc51f[color=lightseagreen,label=\"Output\\ngeneral\"]\n  35 -> k379a85d1a2044b0b8b3386e5582fc51f\n}",
-                "history": [
-                    {
-                        "hash": "747cf76eb0ac7e1a046715c274e302d31ea720f5",
-                        "message": "updated snapatac2 version to 2.6.4",
-                        "num": 2,
-                        "short_hash": "747cf76eb",
-                        "unix": "1723136381"
-                    },
-                    {
-                        "hash": "9740cbbaddce4bd770c90ec91e8990d0cddf3bc8",
-                        "message": "Update workflow and add tests",
-                        "num": 1,
-                        "short_hash": "9740cbbad",
-                        "unix": "1720704591"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Fragment_file"
-                            }
-                        ],
-                        "label": "Fragment_file",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 67.17018491581389,
-                            "top": 354.56754754491556
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "4f5ba41c-e6b0-4650-ad92-59029b87ef44",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "chromosome_sizes.tabular"
-                            }
-                        ],
-                        "label": "chromosome_sizes.tabular",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 68.17018491581389,
-                            "top": 455.5596085802506
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "9431a94a-1399-458c-8e40-d19725a52701",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "gene_annotation"
-                            }
-                        ],
-                        "label": "gene_annotation",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 59.084574366332504,
-                            "top": 597.3149223682577
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "a1de7d61-0483-4217-84d9-89e3dc46f403",
-                        "when": null,
-                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy1",
                         "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Bam-file"
+                        "id": 43,
+                        "input_connections": {
+                            "adata": {
+                                "id": 40,
+                                "output_name": "anndata_out"
                             }
-                        ],
-                        "label": "Bam-file",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 67.53440796800412,
-                            "top": 743.7297383396873
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ddc6a5b2-45e6-4a49-a2b5-2d36b98bee2d",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "Comma-separated list of obs/cells and vars/genes",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Inspect and manipulate",
+                        "outputs": [
                             {
-                                "description": "Comma-separated list of obs/cells and vars/genes",
-                                "name": "Keys for annotations of obs/cells or vars/genes"
+                                "name": "anndata_out",
+                                "type": "h5ad"
                             }
                         ],
-                        "label": "Keys for annotations of obs/cells or vars/genes",
-                        "name": "Input parameter",
-                        "outputs": [],
                         "position": {
-                            "left": 6317.296690866118,
-                            "top": 925.3289621684261
+                            "left": 6719.999999999994,
+                            "top": 1055
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "2bced0d9-2c35-4a59-a2d7-295312b09948",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "591d2291-9647-4a37-bf54-984a153a049f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Replace_file"
+                        "post_job_actions": {
+                            "RenameDatasetActionanndata_out": {
+                                "action_arguments": {
+                                    "newname": "3k PBMC with only HVG, after scaling, PCA, KNN graph, UMAP, clustering, marker genes with Wilcoxon test"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "anndata_out"
                             }
-                        ],
-                        "label": "Replace_file",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 7286.446262020649,
-                            "top": 972.2617918997179
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "d741c4c6-0e32-46b8-9167-ee1d168839d9",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nFragment_file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nchromosome_sizes.tabular\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ngene_annotation\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nBam-file\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nKeys for annotations of obs/cells or vars/genes\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nReplace_file\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"pp.import_data\"];\n  1 -->|output| 6;\n  0 -->|output| 6;\n  7[\"pp.make_fragment_file\"];\n  3 -->|output| 7;\n  8[\"pl.frag_size_distr\"];\n  6 -->|anndata_out| 8;\n  265d6020-44e2-408c-9eb6-02cbc9ac23a7[\"Output\\nplot frag_size\"];\n  8 --> 265d6020-44e2-408c-9eb6-02cbc9ac23a7;\n  style 265d6020-44e2-408c-9eb6-02cbc9ac23a7 stroke:#2c3143,stroke-width:4px;\n  9[\"pl.frag_size_distr_log\"];\n  6 -->|anndata_out| 9;\n  a37cd3c3-e07e-4bea-899f-ee44cee8370b[\"Output\\nplot log frag_size\"];\n  9 --> a37cd3c3-e07e-4bea-899f-ee44cee8370b;\n  style a37cd3c3-e07e-4bea-899f-ee44cee8370b stroke:#2c3143,stroke-width:4px;\n  10[\"metrics.tsse\"];\n  6 -->|anndata_out| 10;\n  2 -->|output| 10;\n  233284e5-c184-4330-a1d3-2d03951c4ce7[\"Output\\nanndata tsse\"];\n  10 --> 233284e5-c184-4330-a1d3-2d03951c4ce7;\n  style 233284e5-c184-4330-a1d3-2d03951c4ce7 stroke:#2c3143,stroke-width:4px;\n  11[\"pp.import_data-sorted_by_barcodes\"];\n  1 -->|output| 11;\n  7 -->|fragments_out| 11;\n  50ef9fe7-bb08-4957-bc45-079ed78f9ee8[\"Output\\nanndata\"];\n  11 --> 50ef9fe7-bb08-4957-bc45-079ed78f9ee8;\n  style 50ef9fe7-bb08-4957-bc45-079ed78f9ee8 stroke:#2c3143,stroke-width:4px;\n  12[\"pl.tsse\"];\n  10 -->|anndata_out| 12;\n  9a5c0f9c-0423-4822-871e-ba8317f2fa7b[\"Output\\nplot tsse\"];\n  12 --> 9a5c0f9c-0423-4822-871e-ba8317f2fa7b;\n  style 9a5c0f9c-0423-4822-871e-ba8317f2fa7b stroke:#2c3143,stroke-width:4px;\n  13[\"pp.filter_cells\"];\n  10 -->|anndata_out| 13;\n  b58dc4ad-6bf0-4f31-99f4-4f8deb13427c[\"Output\\nanndata filter cells\"];\n  13 --> b58dc4ad-6bf0-4f31-99f4-4f8deb13427c;\n  style b58dc4ad-6bf0-4f31-99f4-4f8deb13427c stroke:#2c3143,stroke-width:4px;\n  14[\"pp.add_tile_matrix\"];\n  13 -->|anndata_out| 14;\n  d4b64fc4-fd35-4781-b799-0d07fe8fe438[\"Output\\nanndata tile matrix\"];\n  14 --> d4b64fc4-fd35-4781-b799-0d07fe8fe438;\n  style d4b64fc4-fd35-4781-b799-0d07fe8fe438 stroke:#2c3143,stroke-width:4px;\n  15[\"pp.select_features\"];\n  14 -->|anndata_out| 15;\n  f531f6bd-3fc6-48b9-bb33-66de7928e670[\"Output\\nanndata select features\"];\n  15 --> f531f6bd-3fc6-48b9-bb33-66de7928e670;\n  style f531f6bd-3fc6-48b9-bb33-66de7928e670 stroke:#2c3143,stroke-width:4px;\n  16[\"pp.scrublet\"];\n  15 -->|anndata_out| 16;\n  5b17aa3a-3694-440f-9022-cf9761feb760[\"Output\\nanndata scrublet\"];\n  16 --> 5b17aa3a-3694-440f-9022-cf9761feb760;\n  style 5b17aa3a-3694-440f-9022-cf9761feb760 stroke:#2c3143,stroke-width:4px;\n  17[\"pp.filter_doublets\"];\n  16 -->|anndata_out| 17;\n  3838cf9d-a018-4aa7-8852-893b2f60ec2a[\"Output\\nanndata filter doublets\"];\n  17 --> 3838cf9d-a018-4aa7-8852-893b2f60ec2a;\n  style 3838cf9d-a018-4aa7-8852-893b2f60ec2a stroke:#2c3143,stroke-width:4px;\n  18[\"tl.spectral\"];\n  17 -->|anndata_out| 18;\n  77883516-8ac4-40b5-8b75-5750639d9fc4[\"Output\\nanndata spectral\"];\n  18 --> 77883516-8ac4-40b5-8b75-5750639d9fc4;\n  style 77883516-8ac4-40b5-8b75-5750639d9fc4 stroke:#2c3143,stroke-width:4px;\n  19[\"tl.umap\"];\n  18 -->|anndata_out| 19;\n  062a5471-7b7a-4d9b-bf6c-fe9bbbc5d2ad[\"Output\\nanndata umap\"];\n  19 --> 062a5471-7b7a-4d9b-bf6c-fe9bbbc5d2ad;\n  style 062a5471-7b7a-4d9b-bf6c-fe9bbbc5d2ad stroke:#2c3143,stroke-width:4px;\n  20[\"pp.knn\"];\n  19 -->|anndata_out| 20;\n  b7ebe580-9938-48e5-8718-4df197126615[\"Output\\nanndata knn\"];\n  20 --> b7ebe580-9938-48e5-8718-4df197126615;\n  style b7ebe580-9938-48e5-8718-4df197126615 stroke:#2c3143,stroke-width:4px;\n  21[\"tl.leiden\"];\n  20 -->|anndata_out| 21;\n  9970eb96-013b-4d97-bbbf-2d1f4663b73c[\"Output\\nanndata_leiden_clustering\"];\n  21 --> 9970eb96-013b-4d97-bbbf-2d1f4663b73c;\n  style 9970eb96-013b-4d97-bbbf-2d1f4663b73c stroke:#2c3143,stroke-width:4px;\n  22[\"pl.umap\"];\n  21 -->|anndata_out| 22;\n  4fff8ec8-7d6f-4871-9e42-d6c1791d6aa9[\"Output\\numap_leiden-clusters\"];\n  22 --> 4fff8ec8-7d6f-4871-9e42-d6c1791d6aa9;\n  style 4fff8ec8-7d6f-4871-9e42-d6c1791d6aa9 stroke:#2c3143,stroke-width:4px;\n  23[\"make_gene_matrix\"];\n  21 -->|anndata_out| 23;\n  2 -->|output| 23;\n  9a5c2e23-5b59-41ae-aceb-0e47ce9e7b1a[\"Output\\nanndata gene matrix\"];\n  23 --> 9a5c2e23-5b59-41ae-aceb-0e47ce9e7b1a;\n  style 9a5c2e23-5b59-41ae-aceb-0e47ce9e7b1a stroke:#2c3143,stroke-width:4px;\n  24[\"scanpy_filter_genes\"];\n  23 -->|anndata_out| 24;\n  7a9b22df-e0e5-49d9-9fa1-2efe316d6d66[\"Output\\nanndata filter genes\"];\n  24 --> 7a9b22df-e0e5-49d9-9fa1-2efe316d6d66;\n  style 7a9b22df-e0e5-49d9-9fa1-2efe316d6d66 stroke:#2c3143,stroke-width:4px;\n  25[\"Normalize\"];\n  24 -->|anndata_out| 25;\n  7dddd4c8-1944-4f50-b331-857d03cc9631[\"Output\\nanndata normalize\"];\n  25 --> 7dddd4c8-1944-4f50-b331-857d03cc9631;\n  style 7dddd4c8-1944-4f50-b331-857d03cc9631 stroke:#2c3143,stroke-width:4px;\n  26[\"pp.log1p\"];\n  25 -->|anndata_out| 26;\n  40ace30a-21e1-4bf2-8e08-ad93b62fb2ee[\"Output\\nanndata log1p\"];\n  26 --> 40ace30a-21e1-4bf2-8e08-ad93b62fb2ee;\n  style 40ace30a-21e1-4bf2-8e08-ad93b62fb2ee stroke:#2c3143,stroke-width:4px;\n  27[\"external.pp.magic\"];\n  26 -->|anndata_out| 27;\n  8c1c7aa9-b9dd-467b-9715-73773aea093f[\"Output\\nanndata_magic\"];\n  27 --> 8c1c7aa9-b9dd-467b-9715-73773aea093f;\n  style 8c1c7aa9-b9dd-467b-9715-73773aea093f stroke:#2c3143,stroke-width:4px;\n  28[\"Copy obsm\"];\n  21 -->|anndata_out| 28;\n  27 -->|anndata_out| 28;\n  2c3825d3-7151-4eef-97d0-c8a31ca6fd3e[\"Output\\nanndata_gene-matrix_leiden\"];\n  28 --> 2c3825d3-7151-4eef-97d0-c8a31ca6fd3e;\n  style 2c3825d3-7151-4eef-97d0-c8a31ca6fd3e stroke:#2c3143,stroke-width:4px;\n  29[\"umap_plot_with_scanpy\"];\n  28 -->|output_h5ad| 29;\n  4 -->|output| 29;\n  4cfbbb70-156b-48d7-b14b-db21198d9b6d[\"Output\\numap_marker-genes\"];\n  29 --> 4cfbbb70-156b-48d7-b14b-db21198d9b6d;\n  style 4cfbbb70-156b-48d7-b14b-db21198d9b6d stroke:#2c3143,stroke-width:4px;\n  30[\"Inspect observations\"];\n  28 -->|output_h5ad| 30;\n  31[\"Cut leiden from table\"];\n  30 -->|obs| 31;\n  11c22200-a54e-4585-82c4-8457dbbfb53c[\"Output\\nleiden annotation\"];\n  31 --> 11c22200-a54e-4585-82c4-8457dbbfb53c;\n  style 11c22200-a54e-4585-82c4-8457dbbfb53c stroke:#2c3143,stroke-width:4px;\n  32[\"Replace leiden\"];\n  31 -->|out_file1| 32;\n  5 -->|output| 32;\n  467de061-79e6-4148-8a65-c06383a14012[\"Output\\ncell type annotation\"];\n  32 --> 467de061-79e6-4148-8a65-c06383a14012;\n  style 467de061-79e6-4148-8a65-c06383a14012 stroke:#2c3143,stroke-width:4px;\n  33[\"Manipulate AnnData\"];\n  28 -->|output_h5ad| 33;\n  32 -->|outfile_replace| 33;\n  cbba6173-f439-4fd5-8423-946aa625112b[\"Output\\nanndata_cell_type\"];\n  33 --> cbba6173-f439-4fd5-8423-946aa625112b;\n  style cbba6173-f439-4fd5-8423-946aa625112b stroke:#2c3143,stroke-width:4px;\n  34[\"Plot cell types\"];\n  33 -->|anndata| 34;\n  c28c53ae-8ee7-47d7-8a00-352908bb7c1a[\"Output\\numap_cell-type\"];\n  34 --> c28c53ae-8ee7-47d7-8a00-352908bb7c1a;\n  style c28c53ae-8ee7-47d7-8a00-352908bb7c1a stroke:#2c3143,stroke-width:4px;\n  35[\"Final Anndata general info\"];\n  33 -->|anndata| 35;\n  379a85d1-a204-4b0b-8b33-86e5582fc51f[\"Output\\ngeneral\"];\n  35 --> 379a85d1-a204-4b0b-8b33-86e5582fc51f;\n  style 379a85d1-a204-4b0b-8b33-86e5582fc51f stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2",
-                "outputs": [
-                    {
-                        "annotation": "Comma-separated list of obs/cells and vars/genes",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Comma-separated list of obs/cells and vars/genes",
-                                "name": "Keys for annotations of obs/cells or vars/genes"
-                            }
-                        ],
-                        "label": "Keys for annotations of obs/cells or vars/genes",
-                        "name": "Input parameter",
-                        "outputs": [],
-                        "position": {
-                            "left": 6317.296690866118,
-                            "top": 925.3289621684261
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3081ff5c84a3",
+                            "name": "scanpy_inspect",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "2bced0d9-2c35-4a59-a2d7-295312b09948",
+                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"method\": {\"method\": \"tl.rank_genes_groups\", \"__current_case__\": 4, \"groupby\": \"louvain\", \"use_raw\": true, \"groups\": \"\", \"ref\": {\"rest\": \"rest\", \"__current_case__\": 0}, \"n_genes\": \"100\", \"tl_rank_genes_groups_method\": {\"method\": \"wilcoxon\", \"__current_case__\": 1, \"corr_method\": \"benjamini-hochberg\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.6+galaxy1",
+                        "type": "tool",
+                        "uuid": "636ce34b-e448-4108-8c36-08bb9552f3d9",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "591d2291-9647-4a37-bf54-984a153a049f"
+                                "label": "anndata_out",
+                                "output_name": "anndata_out",
+                                "uuid": "da91ad5a-dd9c-482e-accc-8e42d645e7b1"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
                         "errors": null,
-                        "id": 8,
+                        "id": 45,
                         "input_connections": {
-                            "method|adata": {
-                                "id": 6,
+                            "input": {
+                                "id": 42,
                                 "output_name": "anndata_out"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool SnapATAC2 Plotting",
-                                "name": "method"
-                            }
-                        ],
-                        "label": "pl.frag_size_distr",
-                        "name": "SnapATAC2 Plotting",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Inspect AnnData",
                         "outputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "name": "uns_rank_genes_groups_names",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "uns_rank_genes_groups_scores",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "uns_rank_genes_groups_logfoldchanges",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "uns_rank_genes_groups_pvals",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "uns_rank_genes_groups_pvals_adj",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 976.2484628301277,
-                            "top": 50.363557618794744
+                            "left": 6999.999999999994,
+                            "top": 0
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "c01f0a08ab43",
-                            "name": "snapatac2_plotting",
+                            "changeset_revision": "6f0d0c784f09",
+                            "name": "anndata_inspect",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pl.frag_size_distr\", \"__current_case__\": 0, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"log_scale\": false, \"width\": \"600\", \"height\": \"400\", \"out_file\": \"png\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.4+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"h5ad\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"uns\", \"__current_case__\": 5, \"uns_info\": \"rank_genes_groups\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.10.3+galaxy0",
                         "type": "tool",
-                        "uuid": "62b9a255-2b4a-42a7-93a2-b8790d36148f",
+                        "uuid": "a4ce5de4-7791-48f6-bcdf-97a9a6c930cb",
                         "when": null,
                         "workflow_outputs": [
-                            {
-                                "label": "plot frag_size",
-                                "output_name": "out_png",
-                                "uuid": "265d6020-44e2-408c-9eb6-02cbc9ac23a7"
+                            {
+                                "label": "uns_rank_genes_groups_names",
+                                "output_name": "uns_rank_genes_groups_names",
+                                "uuid": "868797a3-ab74-45bf-96d1-84451a16f882"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "errors": null,
-                        "id": 9,
+                        "id": 47,
                         "input_connections": {
-                            "method|adata": {
-                                "id": 6,
+                            "adata": {
+                                "id": 43,
                                 "output_name": "anndata_out"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool SnapATAC2 Plotting",
-                                "name": "method"
-                            }
-                        ],
-                        "label": "pl.frag_size_distr_log",
-                        "name": "SnapATAC2 Plotting",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot",
                         "outputs": [
                             {
                                 "name": "out_png",
@@ -224150,177 +227957,158 @@
                             }
                         ],
                         "position": {
-                            "left": 971.9878217859592,
-                            "top": 178.50521031008577
+                            "left": 6999.999999999994,
+                            "top": 614
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "c01f0a08ab43",
-                            "name": "snapatac2_plotting",
+                            "changeset_revision": "9b0cdb8cf6be",
+                            "name": "scanpy_plot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pl.frag_size_distr\", \"__current_case__\": 0, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"log_scale\": true, \"width\": \"600\", \"height\": \"400\", \"out_file\": \"png\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.4+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"CST3, NKG7, PPBP\"}, \"groupby\": \"louvain\", \"log\": false, \"use_raw\": false, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.6+galaxy1",
                         "type": "tool",
-                        "uuid": "6665080c-ba86-4a70-b901-394770382862",
+                        "uuid": "8030a8a4-0fb2-41b4-b7b6-a3fee0e1348c",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "plot log frag_size",
+                                "label": "out_png",
                                 "output_name": "out_png",
-                                "uuid": "a37cd3c3-e07e-4bea-899f-ee44cee8370b"
+                                "uuid": "2d042636-8fd1-42e3-af8d-83b4d613f075"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
                         "errors": null,
-                        "id": 10,
+                        "id": 48,
                         "input_connections": {
-                            "method|adata": {
-                                "id": 6,
+                            "input": {
+                                "id": 43,
                                 "output_name": "anndata_out"
-                            },
-                            "method|gene_anno": {
-                                "id": 2,
-                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
-                                "name": "method"
-                            },
-                            {
-                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
-                                "name": "method"
-                            }
-                        ],
-                        "label": "metrics.tsse",
-                        "name": "SnapATAC2 Preprocessing",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Manipulate AnnData",
                         "outputs": [
                             {
-                                "name": "anndata_out",
+                                "name": "anndata",
                                 "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 976.5191068126845,
-                            "top": 321.5929676948151
-                        },
-                        "post_job_actions": {
-                            "TagDatasetActionanndata_out": {
-                                "action_arguments": {
-                                    "tags": "non_filtered_matrix"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "anndata_out"
-                            }
+                            "left": 6999.999999999994,
+                            "top": 748
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "48d9421bf176",
-                            "name": "snapatac2_preprocessing",
+                            "changeset_revision": "ed4996a16f7f",
+                            "name": "anndata_manipulate",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"metrics.tsse\", \"__current_case__\": 12, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"gene_anno\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.4+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"h5ad\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"rename_categories\", \"__current_case__\": 3, \"key\": \"louvain\", \"categories\": \"CD4+ T, CD14+, B, CD8+ T, FCGR3A+, NK, Dendritic, Megakaryocytes\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.10.3+galaxy0",
                         "type": "tool",
-                        "uuid": "1d16ec89-ce71-4f81-a6c9-b785247666f0",
+                        "uuid": "6ac832fd-39f6-4e07-b386-56001eacc343",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "anndata tsse",
-                                "output_name": "anndata_out",
-                                "uuid": "233284e5-c184-4330-a1d3-2d03951c4ce7"
+                                "label": "anndata",
+                                "output_name": "anndata",
+                                "uuid": "51289df3-101f-4c6c-ae85-a8f46c2f33ea"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
                         "errors": null,
-                        "id": 11,
+                        "id": 50,
                         "input_connections": {
-                            "method|chrom_sizes": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "method|fragment_file": {
-                                "id": 7,
-                                "output_name": "fragments_out"
+                            "input": {
+                                "id": 43,
+                                "output_name": "anndata_out"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Inspect AnnData",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
-                                "name": "method"
+                                "name": "uns_rank_genes_groups_names",
+                                "type": "tabular"
                             },
                             {
-                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
-                                "name": "method"
+                                "name": "uns_rank_genes_groups_scores",
+                                "type": "tabular"
                             },
                             {
-                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
-                                "name": "method"
-                            }
-                        ],
-                        "label": "pp.import_data-sorted_by_barcodes",
-                        "name": "SnapATAC2 Preprocessing",
-                        "outputs": [
+                                "name": "uns_rank_genes_groups_logfoldchanges",
+                                "type": "tabular"
+                            },
                             {
-                                "name": "anndata_out",
-                                "type": "h5ad"
+                                "name": "uns_rank_genes_groups_pvals",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "uns_rank_genes_groups_pvals_adj",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1033.1679120853273,
-                            "top": 703.9571480740287
+                            "left": 6999.999999999994,
+                            "top": 1056
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
+                        "post_job_actions": {
+                            "RenameDatasetActionuns_rank_genes_groups_names": {
+                                "action_arguments": {
+                                    "newname": "Ranked genes with Wilcoxon test"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "uns_rank_genes_groups_names"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "48d9421bf176",
-                            "name": "snapatac2_preprocessing",
+                            "changeset_revision": "6f0d0c784f09",
+                            "name": "anndata_inspect",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.import_data\", \"__current_case__\": 1, \"fragment_file\": {\"__class__\": \"ConnectedValue\"}, \"chrom_sizes\": {\"__class__\": \"ConnectedValue\"}, \"min_num_fragments\": \"200\", \"sorted_by_barcode\": true, \"whitelist\": {\"__class__\": \"RuntimeValue\"}, \"chrM\": \"chrM, M\", \"shift_left\": \"0\", \"shift_right\": \"0\", \"chunk_size\": \"2000\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.4+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"h5ad\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"uns\", \"__current_case__\": 5, \"uns_info\": \"rank_genes_groups\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.10.3+galaxy0",
                         "type": "tool",
-                        "uuid": "b92fe42b-af1d-4f83-b1cd-7e4c173d8c2c",
+                        "uuid": "4755a9d9-1cda-4ade-8b1b-4514835fd3d1",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "anndata",
-                                "output_name": "anndata_out",
-                                "uuid": "50ef9fe7-bb08-4957-bc45-079ed78f9ee8"
+                                "label": "uns_rank_genes_groups_names",
+                                "output_name": "uns_rank_genes_groups_names",
+                                "uuid": "e617acd1-e59d-4f20-b39d-9dc0f832b0db"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "errors": null,
-                        "id": 12,
+                        "id": 51,
                         "input_connections": {
-                            "method|adata": {
-                                "id": 10,
+                            "adata": {
+                                "id": 43,
                                 "output_name": "anndata_out"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool SnapATAC2 Plotting",
-                                "name": "method"
-                            }
-                        ],
-                        "label": "pl.tsse",
-                        "name": "SnapATAC2 Plotting",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot",
                         "outputs": [
                             {
                                 "name": "out_png",
@@ -224328,1485 +228116,1831 @@
                             }
                         ],
                         "position": {
-                            "left": 1234.1672018887232,
-                            "top": 181.36234265283736
+                            "left": 6999.999999999994,
+                            "top": 1536
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "c01f0a08ab43",
-                            "name": "snapatac2_plotting",
+                            "changeset_revision": "9b0cdb8cf6be",
+                            "name": "scanpy_plot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pl.tsse\", \"__current_case__\": 1, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"min_fragment\": \"500\", \"width\": \"600\", \"height\": \"400\", \"out_file\": \"png\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.4+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.rank_genes_groups_heatmap\", \"__current_case__\": 26, \"groups\": \"\", \"n_genes\": \"20\", \"key\": \"\", \"log\": false, \"use_raw\": true, \"dendrogram\": true, \"var_group_positions\": [], \"var_group_rotation\": null, \"figsize\": {\"test\": \"no\", \"__current_case__\": 1}, \"layer\": \"\", \"gene_symbols\": \"\", \"swap_axes\": false, \"show_gene_labels\": false, \"matplotlib_pyplot_imshow\": {\"cmap\": \"viridis\", \"interpolation\": \"None\", \"alpha\": null, \"vmin\": null, \"vmax\": null, \"origin\": \"upper\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.6+galaxy1",
                         "type": "tool",
-                        "uuid": "9db3b159-cfe6-4f24-ad2e-79e6ab1f1c6c",
+                        "uuid": "92ad3339-6642-4452-a993-aade06db8c56",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "plot tsse",
+                                "label": "out_png",
                                 "output_name": "out_png",
-                                "uuid": "9a5c0f9c-0423-4822-871e-ba8317f2fa7b"
+                                "uuid": "983e7cee-7028-456c-9db2-bf0ad3e52de5"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "errors": null,
-                        "id": 13,
+                        "id": 53,
                         "input_connections": {
-                            "method|adata": {
-                                "id": 10,
+                            "adata": {
+                                "id": 43,
                                 "output_name": "anndata_out"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
-                                "name": "method"
-                            }
-                        ],
-                        "label": "pp.filter_cells",
-                        "name": "SnapATAC2 Preprocessing",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot",
                         "outputs": [
                             {
-                                "name": "anndata_out",
-                                "type": "h5ad"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 1900.828125,
-                            "top": 498.703125
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionanndata_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "anndata_out"
-                            }
+                            "left": 6999.999999999994,
+                            "top": 1824
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "48d9421bf176",
-                            "name": "snapatac2_preprocessing",
+                            "changeset_revision": "9b0cdb8cf6be",
+                            "name": "scanpy_plot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.filter_cells\", \"__current_case__\": 4, \"adata\": {\"__class__\": \"RuntimeValue\"}, \"min_counts\": \"5000\", \"min_tsse\": \"10.0\", \"max_counts\": \"100000\", \"max_tsse\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.4+galaxy1",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"louvain, LDHB, LYZ, CD74, CCL5, LST1, NKG7, HLA-DPA1, PF4\", \"use_raw\": true, \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": null, \"palette\": null, \"frameon\": true, \"ncols\": \"2\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.6+galaxy1",
                         "type": "tool",
-                        "uuid": "067a4964-4e96-456e-848e-ea414a745d66",
+                        "uuid": "f54debde-f7a9-4615-8a81-6a4406ebcc02",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "anndata filter cells",
-                                "output_name": "anndata_out",
-                                "uuid": "b58dc4ad-6bf0-4f31-99f4-4f8deb13427c"
+                                "label": "out_png",
+                                "output_name": "out_png",
+                                "uuid": "734099bb-f454-4d8c-bc78-a269b0570c41"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "errors": null,
-                        "id": 14,
+                        "id": 55,
                         "input_connections": {
-                            "method|adata": {
-                                "id": 13,
+                            "adata": {
+                                "id": 43,
                                 "output_name": "anndata_out"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
-                                "name": "method"
-                            }
-                        ],
-                        "label": "pp.add_tile_matrix",
-                        "name": "SnapATAC2 Preprocessing",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot",
                         "outputs": [
                             {
-                                "name": "anndata_out",
-                                "type": "h5ad"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 2244.497498607226,
-                            "top": 531.5176822961781
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionanndata_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "anndata_out"
-                            }
+                            "left": 6999.999999999994,
+                            "top": 2092
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "48d9421bf176",
-                            "name": "snapatac2_preprocessing",
+                            "changeset_revision": "9b0cdb8cf6be",
+                            "name": "scanpy_plot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.add_tile_matrix\", \"__current_case__\": 2, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"bin_size\": \"500\", \"chunk_size\": \"500\", \"exclude_chroms\": \"chrM, chrY, M, Y\", \"min_frag_size\": null, \"max_frag_size\": null, \"count_frag_as_reads\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.4+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.stacked_violin\", \"__current_case__\": 4, \"var_names\": {\"type\": \"custom\", \"__current_case__\": 1, \"var_names\": \"LDHB, LYZ, CD74, CCL5, LST1, NKG7, HLA-DPA1, PF4\"}, \"groupby\": \"louvain\", \"num_categories\": \"8\", \"gene_symbols\": \"\", \"log\": false, \"use_raw\": true, \"dendrogram\": false, \"var_group_positions\": [], \"var_group_rotation\": null, \"figsize\": {\"test\": \"yes\", \"__current_case__\": 0, \"width\": \"10\", \"height\": \"10\"}, \"layer\": \"\", \"swap_axes\": true, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"scale\": \"width\"}, \"row_palette\": \"muted\", \"standard_scale\": \"None\", \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.6+galaxy1",
                         "type": "tool",
-                        "uuid": "de6e8e48-f792-4163-9289-f5fa7690fa3c",
+                        "uuid": "9386a889-5f57-4c24-b804-d1018a2c4d24",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "anndata tile matrix",
-                                "output_name": "anndata_out",
-                                "uuid": "d4b64fc4-fd35-4781-b799-0d07fe8fe438"
+                                "label": "out_png",
+                                "output_name": "out_png",
+                                "uuid": "39f2d4b6-f2e8-41b3-a00a-a2c5b54face2"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "errors": null,
-                        "id": 15,
+                        "id": 56,
                         "input_connections": {
-                            "method|adata": {
-                                "id": 14,
-                                "output_name": "anndata_out"
+                            "adata": {
+                                "id": 48,
+                                "output_name": "anndata"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
-                                "name": "method"
-                            },
-                            {
-                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
-                                "name": "method"
-                            },
-                            {
-                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
-                                "name": "method"
-                            }
-                        ],
-                        "label": "pp.select_features",
-                        "name": "SnapATAC2 Preprocessing",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot",
                         "outputs": [
                             {
-                                "name": "anndata_out",
-                                "type": "h5ad"
+                                "name": "out_svg",
+                                "type": "svg"
                             }
                         ],
                         "position": {
-                            "left": 2262.8393353215497,
-                            "top": 793.2107306253445
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionanndata_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "anndata_out"
-                            }
+                            "left": 7279.999999999994,
+                            "top": 529
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "48d9421bf176",
-                            "name": "snapatac2_preprocessing",
+                            "changeset_revision": "9b0cdb8cf6be",
+                            "name": "scanpy_plot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.select_features\", \"__current_case__\": 5, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"n_features\": \"250000\", \"filter_lower_quantile\": \"0.005\", \"filter_upper_quantile\": \"0.005\", \"whitelist\": {\"__class__\": \"RuntimeValue\"}, \"blacklist\": {\"__class__\": \"RuntimeValue\"}, \"max_iter\": \"1\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.4+galaxy1",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"svg\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"louvain\", \"use_raw\": true, \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"on data\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": null, \"palette\": null, \"frameon\": true, \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.6+galaxy1",
                         "type": "tool",
-                        "uuid": "0f99ab71-fb4c-4d8f-b248-854b7661e365",
+                        "uuid": "90fc9851-6092-46b7-a5ec-c3f5b49345c9",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "anndata select features",
-                                "output_name": "anndata_out",
-                                "uuid": "f531f6bd-3fc6-48b9-bb33-66de7928e670"
+                                "label": "out_svg",
+                                "output_name": "out_svg",
+                                "uuid": "e0979d1e-eb87-4a7b-904f-a5116c7b8fff"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "errors": null,
-                        "id": 16,
+                        "id": 58,
                         "input_connections": {
-                            "method|adata": {
-                                "id": 15,
-                                "output_name": "anndata_out"
+                            "adata": {
+                                "id": 48,
+                                "output_name": "anndata"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
-                                "name": "method"
-                            }
-                        ],
-                        "label": "pp.scrublet",
-                        "name": "SnapATAC2 Preprocessing",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot",
                         "outputs": [
                             {
-                                "name": "anndata_out",
-                                "type": "h5ad"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 2586.191666804627,
-                            "top": 949.4798428594668
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionanndata_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "anndata_out"
-                            }
+                            "left": 7279.999999999994,
+                            "top": 797
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "48d9421bf176",
-                            "name": "snapatac2_preprocessing",
+                            "changeset_revision": "9b0cdb8cf6be",
+                            "name": "scanpy_plot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.scrublet\", \"__current_case__\": 6, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"features\": \"\", \"n_comps\": \"15\", \"sim_doublet_ratio\": \"2.0\", \"expected_doublet_rate\": \"0.1\", \"n_neighbors\": null, \"use_approx_neighbors\": false, \"random_state\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.4+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.dotplot\", \"__current_case__\": 2, \"var_names\": {\"type\": \"custom\", \"__current_case__\": 1, \"var_names\": \"IL7R, CCR7, CD8A, CD14, LYZ, MS4A1, CD79A, GNLY, NKG7, KLRB1, FCER1A, CST3, PPBP, FCGR3A\"}, \"groupby\": \"louvain\", \"num_categories\": \"8\", \"gene_symbols\": \"\", \"log\": false, \"use_raw\": true, \"dendrogram\": true, \"var_group_positions\": [{\"__index__\": 0, \"start\": \"0\", \"end\": \"1\", \"label\": \"CD4+T\"}, {\"__index__\": 1, \"start\": \"2\", \"end\": \"2\", \"label\": \"CD8\"}, {\"__index__\": 2, \"start\": \"3\", \"end\": \"4\", \"label\": \"CD14+\"}, {\"__index__\": 3, \"start\": \"5\", \"end\": \"6\", \"label\": \"B\"}, {\"__index__\": 4, \"start\": \"7\", \"end\": \"9\", \"label\": \"NK\"}, {\"__index__\": 5, \"start\": \"10\", \"end\": \"11\", \"label\": \"Dendritic\"}, {\"__index__\": 6, \"start\": \"12\", \"end\": \"12\", \"label\": \"Megakaryocytes\"}, {\"__index__\": 7, \"start\": \"13\", \"end\": \"13\", \"label\": \"FCGR3A+\"}], \"var_group_rotation\": null, \"figsize\": {\"test\": \"no\", \"__current_case__\": 1}, \"layer\": \"\", \"color_map\": \"viridis\", \"dot_max\": null, \"dot_min\": null, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.6+galaxy1",
                         "type": "tool",
-                        "uuid": "a944b129-dedb-4a9a-a1c7-1a4ddd51fac6",
+                        "uuid": "7234b677-3502-42bb-a1ca-7c62a6118a52",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "anndata scrublet",
-                                "output_name": "anndata_out",
-                                "uuid": "5b17aa3a-3694-440f-9022-cf9761feb760"
+                                "label": "out_png",
+                                "output_name": "out_png",
+                                "uuid": "bd14e644-2a32-4a81-bd83-042ee46d118a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "errors": null,
-                        "id": 17,
+                        "id": 59,
                         "input_connections": {
-                            "method|adata": {
-                                "id": 16,
+                            "adata": {
+                                "id": 49,
                                 "output_name": "anndata_out"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
-                                "name": "method"
-                            }
-                        ],
-                        "label": "pp.filter_doublets",
-                        "name": "SnapATAC2 Preprocessing",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot",
                         "outputs": [
                             {
-                                "name": "anndata_out",
-                                "type": "h5ad"
+                                "name": "collection_png",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 2635.9329633142843,
-                            "top": 663.8944755224237
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionanndata_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "anndata_out"
-                            }
+                            "left": 7279.999999999994,
+                            "top": 931
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "48d9421bf176",
-                            "name": "snapatac2_preprocessing",
+                            "changeset_revision": "9b0cdb8cf6be",
+                            "name": "scanpy_plot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.filter_doublets\", \"__current_case__\": 7, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"probability_threshold\": \"0.5\", \"score_threshold\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.4+galaxy1",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.rank_genes_groups_violin\", \"__current_case__\": 24, \"groups\": \"\", \"genes\": {\"select\": \"n_genes\", \"__current_case__\": 0, \"n_genes\": \"10\"}, \"gene_symbols\": \"\", \"use_raw\": true, \"split\": true, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"scale\": \"width\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.6+galaxy1",
                         "type": "tool",
-                        "uuid": "edb303e1-aaf9-4f4c-ab5a-b4197997eb95",
+                        "uuid": "1f003b20-da10-4f6f-84f6-2d335b3b1102",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "anndata filter doublets",
-                                "output_name": "anndata_out",
-                                "uuid": "3838cf9d-a018-4aa7-8852-893b2f60ec2a"
+                                "label": "collection_png",
+                                "output_name": "collection_png",
+                                "uuid": "e9cf90db-ac42-4876-8abd-183fea271666"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "errors": null,
-                        "id": 18,
+                        "id": 60,
                         "input_connections": {
-                            "method|adata": {
-                                "id": 17,
+                            "adata": {
+                                "id": 49,
                                 "output_name": "anndata_out"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool SnapATAC2 Clustering",
-                                "name": "method"
-                            },
-                            {
-                                "description": "runtime parameter for tool SnapATAC2 Clustering",
-                                "name": "method"
-                            }
-                        ],
-                        "label": "tl.spectral",
-                        "name": "SnapATAC2 Clustering",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot",
                         "outputs": [
                             {
-                                "name": "anndata_out",
-                                "type": "h5ad"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 3084.96875,
-                            "top": 555.0625
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionanndata_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "anndata_out"
-                            }
+                            "left": 7279.999999999994,
+                            "top": 1065
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "94ae400dde2f",
-                            "name": "snapatac2_clustering",
+                            "changeset_revision": "9b0cdb8cf6be",
+                            "name": "scanpy_plot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"tl.spectral\", \"__current_case__\": 0, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"n_comps\": \"30\", \"features\": {\"__class__\": \"RuntimeValue\"}, \"random_state\": \"0\", \"sample_size\": null, \"chunk_size\": \"20000\", \"distance_metric\": \"cosine\", \"weighted_by_sd\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.4+galaxy1",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.rank_genes_groups\", \"__current_case__\": 23, \"groups\": \"\", \"n_genes\": \"20\", \"gene_symbols\": \"\", \"fontsize\": \"8\", \"ncols\": \"4\", \"sharey\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.6+galaxy1",
                         "type": "tool",
-                        "uuid": "282c336d-2ff5-460b-889d-58ef74574199",
+                        "uuid": "c2a9e741-d871-45e3-b71e-813b08500091",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "anndata spectral",
-                                "output_name": "anndata_out",
-                                "uuid": "77883516-8ac4-40b5-8b75-5750639d9fc4"
+                                "label": "out_png",
+                                "output_name": "out_png",
+                                "uuid": "aef215b1-dbb4-447b-9297-c90536842c8e"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "single-cell/scrna-scanpy-pbmc3k",
+                "path": "topics/single-cell/tutorials/scrna-scanpy-pbmc3k/workflows/Clustering-3k-PBMC-with-Scanpy.ga",
+                "tags": [
+                    "name:scRNA-seq",
+                    "name:single-cell"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "Clustering 3k PBMC with Scanpy",
+                "topic_id": "single-cell",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-scanpy-pbmc3k/versions/clustering-3k-pbmc-with-scanpy",
+                "tutorial_id": "scrna-scanpy-pbmc3k",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/workflows/Clustering-3k-PBMC-with-Scanpy.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/workflows/Clustering-3k-PBMC-with-Scanpy.html",
+                "version": 1,
+                "wfid": "single-cell-scrna-scanpy-pbmc3k",
+                "wfname": "clustering-3k-pbmc-with-scanpy",
+                "workflow": "Clustering-3k-PBMC-with-Scanpy.ga",
+                "workflow_tools": [
+                    "cat1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.9.6+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.9.6+galaxy1"
+                ],
+                "workflowhub_id": "1259"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/3581213"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "anndata_ops",
+                    "owner": "ebi-gxa",
+                    "revisions": "a0274bc43b7e",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "hca_matrix_downloader",
+                    "owner": "ebi-gxa",
+                    "revisions": "c3c85b67d118",
+                    "tool_panel_section_label": "Single Cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "retrieve_scxa",
+                    "owner": "ebi-gxa",
+                    "revisions": "72b6e1747e37",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_read_10x",
+                    "owner": "ebi-gxa",
+                    "revisions": "9afcfcd1d215",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seurat_read10x",
+                    "owner": "ebi-gxa",
+                    "revisions": "301cf1b4b43d",
+                    "tool_panel_section_label": "Seurat",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seurat_read10x",
+                    "owner": "ebi-gxa",
+                    "revisions": "f5db0e853f57",
+                    "tool_panel_section_label": "Seurat",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "regex_find_replace",
+                    "owner": "galaxyp",
+                    "revisions": "503bcd6ebe4b",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sceasy_convert",
+                    "owner": "iuc",
+                    "revisions": "d70139524747",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_ops\n  owner: ebi-gxa\n  revisions: a0274bc43b7e\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: hca_matrix_downloader\n  owner: ebi-gxa\n  revisions: c3c85b67d118\n  tool_panel_section_label: Single Cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: retrieve_scxa\n  owner: ebi-gxa\n  revisions: 72b6e1747e37\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_read_10x\n  owner: ebi-gxa\n  revisions: 9afcfcd1d215\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_read10x\n  owner: ebi-gxa\n  revisions: 301cf1b4b43d\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_read10x\n  owner: ebi-gxa\n  revisions: f5db0e853f57\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 503bcd6ebe4b\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sceasy_convert\n  owner: iuc\n  revisions: d70139524747\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "answer_histories": [
+            {
+                "date": "2024-01-10",
+                "history": "https://singlecell.usegalaxy.eu/u/j.jakiela/h/ebi-scxa---anndata-scanpy-or-seurat-object-1",
+                "label": "EBI SCXA retrieval tool (UseGalaxy.eu)"
+            },
+            {
+                "date": "2024-09-08",
+                "history": "https://singlecell.usegalaxy.eu/u/j.jakiela/h/hca-downloader---example-files-1",
+                "label": "HCA Downloader (UseGalaxy.eu)"
+            }
+        ],
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/EBI-retrieval/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "wee-snufkin",
+                "nomadscientist"
+            ],
+            "funding": [
+                "elixir-fair-data"
+            ]
+        },
+        "contributors": [
+            {
+                "elixir_node": "uk",
+                "email": "juliajot36@gmail.com",
+                "id": "wee-snufkin",
+                "joined": "2022-06",
+                "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "bio": "Senior Lecturer at The Open University",
+                "elixir_node": "uk",
+                "email": "wendi.bacon@open.ac.uk",
+                "fediverse": "https://mstdn.science/@wendibacon1",
+                "fediverse_flavor": "mastodon",
+                "id": "nomadscientist",
+                "joined": "2020-03",
+                "matrix": "nomadscientist:matrix.org",
+                "name": "Wendi Bacon",
+                "orcid": "0000-0002-8170-8806",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
+                "twitter": "WendiBacon1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+            },
+            {
+                "funder": true,
+                "funding_id": "MR/V038966/1",
+                "funding_statement": "This work has been funded by the ELIXIR-UK FAIR Data Stewardship training UKRI award (MR/V038966/1)",
+                "funding_system": "ukri",
+                "github": false,
+                "id": "elixir-fair-data",
+                "joined": "2023-06",
+                "name": "ELIXIR-UK: FAIR Data Stewardship training",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-fair-data/",
+                "short_name": "ELIXIR Fair Data",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-fair-data.json"
+            }
+        ],
+        "dir": "topics/single-cell/tutorials/EBI-retrieval",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-case_basic-pipeline"
+                ],
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "single-cell/EBI-retrieval",
+        "inexact_supported_servers": [],
+        "input_histories": [
+            {
+                "history": "https://singlecell.usegalaxy.eu/u/j.jakiela/h/input-history-ebi-scxa---anndata-scanpy-or-seurat-object",
+                "label": "UseGalaxy.eu"
+            }
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "The EMBL-EBI Single-cell Expression Atlas contains high quality datasets.",
+            "Metadata manipulation is key for generating the correctly formatted files.",
+            "To use Scanpy tools, you have to transform your metadata into an AnnData object.",
+            "To use Seurat tools, you have to transform your metadata into a Seurat object."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-13",
+        "objectives": [
+            "You will retrieve raw data from the EBI Single Cell Expression Atlas and Human Cell Atlas.",
+            "You will manipulate the metadata and matrix files.",
+            "You will combine the metadata and matrix files into an AnnData or Seurat object for downstream analysis."
+        ],
+        "pageviews": 416,
+        "priority": 2,
+        "pub_date": "2023-11-14",
+        "questions": [
+            "How do I use the EBI Single Cell Expression Atlas and Human Cell Atlas?",
+            "How can I reformat and manipulate the downloaded files to create the correct input for downstream analysis?"
+        ],
+        "recordings": [
+            {
+                "date": "2024-09-12",
+                "length": "18M54S",
+                "speakers": [
+                    "hexhowells"
+                ],
+                "youtube_id": "Yx7m7Uh4tVg"
+            }
+        ],
+        "requirements": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-case_alevin",
+                    "scrna-case_alevin-combine-datasets"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00374",
+        "short_tools": [
+            "hca_matrix_downloader",
+            "retrieve_scxa",
+            "seurat_read10x",
+            "anndata_ops",
+            "tp_grep_tool",
+            "tp_find_and_replace",
+            "sceasy_convert",
+            "regexColumn1",
+            "scanpy_read_10x"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "datamanipulation",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "data import",
+            "data management"
+        ],
+        "time_estimation": "15m",
+        "title": "Importing files from public atlases",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy92",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/hca_matrix_downloader/hca_matrix_downloader/v0.0.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/3.2.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/4.0.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/sceasy_convert/sceasy_convert/0.0.7+galaxy1"
+        ],
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "EBI-retrieval",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/EBI-retrieval/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/EBI-retrieval/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/EBI-retrieval/tutorial.json"
+        },
+        "version": 5,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 325,
+        "visitors": 272,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0009-0001-2017-8805",
+                        "name": "Julia Jakiela"
+                    }
+                ],
+                "description": "Creates input file for Filter, Plot, Explore tutorial",
+                "features": {
+                    "comments": false,
+                    "parameters": true,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nSC-Atlas experiment accession\"]\n  1[label=\"EBI SCXA Data Retrieval\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Rename batch numbers\"]\n  1 -> 2 [label=\"design_tsv\"]\n  3[label=\"Mito genes check\"]\n  1 -> 3 [label=\"genes_tsv\"]\n  kb0762cfd58bd4c39ae412dca4289c541[color=lightseagreen,label=\"Output\\nMito genes check\"]\n  3 -> kb0762cfd58bd4c39ae412dca4289c541\n  4[label=\"Rename cell metadata headers\"]\n  2 -> 4 [label=\"out_file1\"]\n  5[label=\"Create AnnData\"]\n  1 -> 5 [label=\"barcode_tsv\"]\n  4 -> 5 [label=\"outfile\"]\n  1 -> 5 [label=\"genes_tsv\"]\n  1 -> 5 [label=\"matrix_mtx\"]\n  k938cd59461cf4037a58bc09c065db505[color=lightseagreen,label=\"Output\\nAnnData object\"]\n  5 -> k938cd59461cf4037a58bc09c065db505\n  6[label=\"Seurat Read10x\"]\n  1 -> 6 [label=\"barcode_tsv\"]\n  1 -> 6 [label=\"genes_tsv\"]\n  1 -> 6 [label=\"matrix_mtx\"]\n  4 -> 6 [label=\"outfile\"]\n  kc24e9d83c17540a29c36eeb486fe323e[color=lightseagreen,label=\"Output\\nSeurat object\"]\n  6 -> kc24e9d83c17540a29c36eeb486fe323e\n  7[label=\"AnnData Operations\"]\n  5 -> 7 [label=\"output_h5ad\"]\n  kb47f801fbedb4136a5e9378a815a1799[color=lightseagreen,label=\"Output\\nMito-counted AnnData for downstream analysis\"]\n  7 -> kb47f801fbedb4136a5e9378a815a1799\n}",
+                "history": [
+                    {
+                        "hash": "a6e3cf848bad2cf19f48ca286c52821f558a6b52",
+                        "message": "new tests",
+                        "num": 2,
+                        "short_hash": "a6e3cf848",
+                        "unix": "1702552191"
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
+                        "hash": "914bf924a609d64b3f3f69d8b78b44a584d90581",
+                        "message": "ebi scxa updated workflow tests",
+                        "num": 1,
+                        "short_hash": "914bf924a",
+                        "unix": "1702547068"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "EBI Single Cell Atlas accession for the experiment that you want to retrieve.",
+                        "content_id": null,
                         "errors": null,
-                        "id": 19,
-                        "input_connections": {
-                            "method|adata": {
-                                "id": 18,
-                                "output_name": "anndata_out"
-                            }
-                        },
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool SnapATAC2 Clustering",
-                                "name": "method"
-                            }
-                        ],
-                        "label": "tl.umap",
-                        "name": "SnapATAC2 Clustering",
-                        "outputs": [
-                            {
-                                "name": "anndata_out",
-                                "type": "h5ad"
+                                "description": "EBI Single Cell Atlas accession for the experiment that you want to retrieve.",
+                                "name": "SC-Atlas experiment accession"
                             }
                         ],
+                        "label": "SC-Atlas experiment accession",
+                        "name": "Input parameter",
+                        "outputs": [],
                         "position": {
-                            "left": 3098.912527828772,
-                            "top": 841.6746200330715
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionanndata_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "94ae400dde2f",
-                            "name": "snapatac2_clustering",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 0
                         },
-                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"tl.umap\", \"__current_case__\": 1, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"n_comps\": \"2\", \"use_dims\": null, \"use_rep\": \"X_spectral\", \"key_added\": \"umap\", \"random_state\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.4+galaxy1",
-                        "type": "tool",
-                        "uuid": "ea0844bb-c3d7-45f7-bd12-73b8325e8816",
+                        "tool_id": null,
+                        "tool_state": "{\"default\": \"E-MTAB-6945\", \"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "ca016294-33ee-47fc-9a42-36a0288d353d",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "anndata umap",
-                                "output_name": "anndata_out",
-                                "uuid": "062a5471-7b7a-4d9b-bf6c-fe9bbbc5d2ad"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "dcf5b67e-9773-4ca5-8e33-b0f875e91d77"
                             }
                         ]
-                    },
+                    }
+                ],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nSC-Atlas experiment accession\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"EBI SCXA Data Retrieval\"];\n  0 -->|output| 1;\n  2[\"Rename batch numbers\"];\n  1 -->|design_tsv| 2;\n  3[\"Mito genes check\"];\n  1 -->|genes_tsv| 3;\n  b0762cfd-58bd-4c39-ae41-2dca4289c541[\"Output\\nMito genes check\"];\n  3 --> b0762cfd-58bd-4c39-ae41-2dca4289c541;\n  style b0762cfd-58bd-4c39-ae41-2dca4289c541 stroke:#2c3143,stroke-width:4px;\n  4[\"Rename cell metadata headers\"];\n  2 -->|out_file1| 4;\n  5[\"Create AnnData\"];\n  1 -->|barcode_tsv| 5;\n  4 -->|outfile| 5;\n  1 -->|genes_tsv| 5;\n  1 -->|matrix_mtx| 5;\n  938cd594-61cf-4037-a58b-c09c065db505[\"Output\\nAnnData object\"];\n  5 --> 938cd594-61cf-4037-a58b-c09c065db505;\n  style 938cd594-61cf-4037-a58b-c09c065db505 stroke:#2c3143,stroke-width:4px;\n  6[\"Seurat Read10x\"];\n  1 -->|barcode_tsv| 6;\n  1 -->|genes_tsv| 6;\n  1 -->|matrix_mtx| 6;\n  4 -->|outfile| 6;\n  c24e9d83-c175-40a2-9c36-eeb486fe323e[\"Output\\nSeurat object\"];\n  6 --> c24e9d83-c175-40a2-9c36-eeb486fe323e;\n  style c24e9d83-c175-40a2-9c36-eeb486fe323e stroke:#2c3143,stroke-width:4px;\n  7[\"AnnData Operations\"];\n  5 -->|output_h5ad| 7;\n  b47f801f-bedb-4136-a5e9-378a815a1799[\"Output\\nMito-counted AnnData for downstream analysis\"];\n  7 --> b47f801f-bedb-4136-a5e9-378a815a1799;\n  style b47f801f-bedb-4136-a5e9-378a815a1799 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "EBI SCXA to AnnData (Scanpy) or Seurat Object",
+                "outputs": [
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
+                        "annotation": "EBI Single Cell Atlas accession for the experiment that you want to retrieve.",
+                        "content_id": null,
                         "errors": null,
-                        "id": 20,
-                        "input_connections": {
-                            "method|adata": {
-                                "id": 19,
-                                "output_name": "anndata_out"
-                            }
-                        },
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool SnapATAC2 Clustering",
-                                "name": "method"
-                            }
-                        ],
-                        "label": "pp.knn",
-                        "name": "SnapATAC2 Clustering",
-                        "outputs": [
-                            {
-                                "name": "anndata_out",
-                                "type": "h5ad"
+                                "description": "EBI Single Cell Atlas accession for the experiment that you want to retrieve.",
+                                "name": "SC-Atlas experiment accession"
                             }
                         ],
+                        "label": "SC-Atlas experiment accession",
+                        "name": "Input parameter",
+                        "outputs": [],
                         "position": {
-                            "left": 3537.197366261425,
-                            "top": 667.2386060771821
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionanndata_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "94ae400dde2f",
-                            "name": "snapatac2_clustering",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 0
                         },
-                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.knn\", \"__current_case__\": 2, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"n_neighbors\": \"50\", \"use_dims\": \"\", \"use_rep\": \"X_spectral\", \"algorithm\": \"kdtree\", \"random_state\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.4+galaxy1",
-                        "type": "tool",
-                        "uuid": "8628dcfa-cec9-488a-9ea1-9b9caa315290",
+                        "tool_id": null,
+                        "tool_state": "{\"default\": \"E-MTAB-6945\", \"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "ca016294-33ee-47fc-9a42-36a0288d353d",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "anndata knn",
-                                "output_name": "anndata_out",
-                                "uuid": "b7ebe580-9938-48e5-8718-4df197126615"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "dcf5b67e-9773-4ca5-8e33-b0f875e91d77"
                             }
                         ]
                     },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
+                    {
+                        "annotation": "Shows how mitochondrial genes are annotated.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
                         "errors": null,
-                        "id": 21,
+                        "id": 3,
                         "input_connections": {
-                            "method|adata": {
-                                "id": 20,
-                                "output_name": "anndata_out"
+                            "infile": {
+                                "id": 1,
+                                "output_name": "genes_tsv"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool SnapATAC2 Clustering",
-                                "name": "method"
-                            }
-                        ],
-                        "label": "tl.leiden",
-                        "name": "SnapATAC2 Clustering",
+                        "inputs": [],
+                        "label": "Mito genes check",
+                        "name": "Search in textfiles",
                         "outputs": [
                             {
-                                "name": "anndata_out",
-                                "type": "h5ad"
+                                "name": "output",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 3836.579452840314,
-                            "top": 625.923381281925
+                            "left": 791.9068204609299,
+                            "top": 717.1702369809638
                         },
                         "post_job_actions": {
-                            "DeleteIntermediatesActionanndata_out": {
-                                "action_arguments": {},
-                                "action_type": "DeleteIntermediatesAction",
-                                "output_name": "anndata_out"
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Mito genes check"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "94ae400dde2f",
-                            "name": "snapatac2_clustering",
-                            "owner": "iuc",
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"tl.leiden\", \"__current_case__\": 3, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"resolution\": \"1.0\", \"objective_function\": \"modularity\", \"min_cluster_size\": \"5\", \"n_iterations\": \"-1\", \"random_state\": \"0\", \"key_added\": \"leiden\", \"weighted\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.4+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"tsv\", \"case_sensitive\": \"-i\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"color\": \"COLOR\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-P\", \"url_paste\": \"mt\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
                         "type": "tool",
-                        "uuid": "64840a63-5cb4-4bdd-a088-78e5739819a7",
+                        "uuid": "51b0361d-00dd-45cf-98db-90b2242b6cb3",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "anndata_leiden_clustering",
-                                "output_name": "anndata_out",
-                                "uuid": "9970eb96-013b-4d97-bbbf-2d1f4663b73c"
+                                "label": "Mito genes check",
+                                "output_name": "output",
+                                "uuid": "b0762cfd-58bd-4c39-ae41-2dca4289c541"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 22,
+                        "id": 5,
                         "input_connections": {
-                            "method|adata": {
-                                "id": 21,
-                                "output_name": "anndata_out"
+                            "barcodes": {
+                                "id": 1,
+                                "output_name": "barcode_tsv"
+                            },
+                            "cell_meta": {
+                                "id": 4,
+                                "output_name": "outfile"
+                            },
+                            "genes": {
+                                "id": 1,
+                                "output_name": "genes_tsv"
+                            },
+                            "matrix": {
+                                "id": 1,
+                                "output_name": "matrix_mtx"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool SnapATAC2 Plotting",
-                                "name": "method"
+                                "description": "runtime parameter for tool Scanpy Read10x",
+                                "name": "gene_meta"
                             }
                         ],
-                        "label": "pl.umap",
-                        "name": "SnapATAC2 Plotting",
+                        "label": "Create AnnData",
+                        "name": "Scanpy Read10x",
                         "outputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "name": "output_h5ad",
+                                "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 4174.404258334524,
-                            "top": 534.0748356757703
+                            "left": 1025.6788601346032,
+                            "top": 534.8213953419395
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_h5ad": {
+                                "action_arguments": {
+                                    "newname": "AnnData object"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy9",
                         "tool_shed_repository": {
-                            "changeset_revision": "c01f0a08ab43",
-                            "name": "snapatac2_plotting",
-                            "owner": "iuc",
+                            "changeset_revision": "9afcfcd1d215",
+                            "name": "scanpy_read_10x",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 2, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"color\": \"leiden\", \"use_rep\": \"X_umap\", \"marker_size\": null, \"marker_opacity\": \"1.0\", \"sample_size\": null, \"width\": \"600\", \"height\": \"500\", \"out_file\": \"png\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.4+galaxy1",
+                        "tool_state": "{\"barcodes\": {\"__class__\": \"ConnectedValue\"}, \"cell_meta\": {\"__class__\": \"ConnectedValue\"}, \"gene_meta\": {\"__class__\": \"RuntimeValue\"}, \"genes\": {\"__class__\": \"ConnectedValue\"}, \"matrix\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"var_names\": \"gene_ids\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "46564bf3-03e6-4a9b-b160-a10ddbb69197",
+                        "uuid": "e02346a9-9da0-40fc-85ef-3492cbb73b44",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "umap_leiden-clusters",
-                                "output_name": "out_png",
-                                "uuid": "4fff8ec8-7d6f-4871-9e42-d6c1791d6aa9"
+                                "label": "AnnData object",
+                                "output_name": "output_h5ad",
+                                "uuid": "938cd594-61cf-4037-a58b-c09c065db505"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/3.2.3+galaxy0",
                         "errors": null,
-                        "id": 23,
+                        "id": 6,
                         "input_connections": {
-                            "method|adata": {
-                                "id": 21,
-                                "output_name": "anndata_out"
+                            "input|barcodes": {
+                                "id": 1,
+                                "output_name": "barcode_tsv"
                             },
-                            "method|gene_anno": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
-                                "name": "method"
+                            "input|genes": {
+                                "id": 1,
+                                "output_name": "genes_tsv"
                             },
-                            {
-                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
-                                "name": "method"
+                            "input|matrix": {
+                                "id": 1,
+                                "output_name": "matrix_mtx"
+                            },
+                            "metadata": {
+                                "id": 4,
+                                "output_name": "outfile"
                             }
-                        ],
-                        "label": "make_gene_matrix",
-                        "name": "SnapATAC2 Preprocessing",
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Seurat Read10x",
                         "outputs": [
                             {
-                                "name": "anndata_out",
-                                "type": "h5ad"
+                                "name": "rds_seurat_file",
+                                "type": "rdata"
                             }
                         ],
                         "position": {
-                            "left": 4560.8801354196185,
-                            "top": 781.9723996031015
+                            "left": 1564.7962994380462,
+                            "top": 864.6368384275628
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
+                        "post_job_actions": {
+                            "RenameDatasetActionrds_seurat_file": {
+                                "action_arguments": {
+                                    "newname": "Seurat object"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "rds_seurat_file"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/3.2.3+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "48d9421bf176",
-                            "name": "snapatac2_preprocessing",
-                            "owner": "iuc",
+                            "changeset_revision": "301cf1b4b43d",
+                            "name": "seurat_read10x",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.make_gene_matrix\", \"__current_case__\": 3, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"gene_anno\": {\"__class__\": \"ConnectedValue\"}, \"chunk_size\": \"500\", \"use_x\": false, \"id_type\": \"gene\", \"transcript_name_key\": \"transcript_name\", \"transcript_id_key\": \"transcript_id\", \"gene_name_key\": \"gene_name\", \"gene_id_key\": \"gene_id\", \"min_frag_size\": null, \"max_frag_size\": null, \"count_frag_as_reads\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.6.4+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"rds_seurat\", \"input\": {\"format\": \"mtx\", \"__current_case__\": 1, \"matrix\": {\"__class__\": \"ConnectedValue\"}, \"genes\": {\"__class__\": \"ConnectedValue\"}, \"barcodes\": {\"__class__\": \"ConnectedValue\"}}, \"metadata\": {\"__class__\": \"ConnectedValue\"}, \"min_cells\": null, \"min_features\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.2.3+galaxy0",
                         "type": "tool",
-                        "uuid": "76286f1f-1153-487f-8146-22e9fbc0e843",
+                        "uuid": "1aa185bd-1392-438d-adea-21ed201bc9db",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "anndata gene matrix",
-                                "output_name": "anndata_out",
-                                "uuid": "9a5c2e23-5b59-41ae-aceb-0e47ce9e7b1a"
+                                "label": "Seurat object",
+                                "output_name": "rds_seurat_file",
+                                "uuid": "c24e9d83-c175-40a2-9c36-eeb486fe323e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy3",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy92",
                         "errors": null,
-                        "id": 24,
+                        "id": 7,
                         "input_connections": {
-                            "adata": {
-                                "id": 23,
-                                "output_name": "anndata_out"
+                            "input_obj_file": {
+                                "id": 5,
+                                "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
-                        "label": "scanpy_filter_genes",
-                        "name": "Filter",
+                        "label": null,
+                        "name": "AnnData Operations",
                         "outputs": [
                             {
-                                "name": "anndata_out",
+                                "name": "output_h5ad",
                                 "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 4914.636475213905,
-                            "top": 577.4812733437685
+                            "left": 1310.0874938964844,
+                            "top": 792.8125610351562
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy3",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_h5ad": {
+                                "action_arguments": {
+                                    "newname": "Mito-counted AnnData for downstream analysis"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy92",
                         "tool_shed_repository": {
-                            "changeset_revision": "d636ce5cde16",
-                            "name": "scanpy_filter",
-                            "owner": "iuc",
+                            "changeset_revision": "a0274bc43b7e",
+                            "name": "anndata_ops",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.filter_genes\", \"__current_case__\": 1, \"filter\": {\"filter\": \"min_cells\", \"__current_case__\": 2, \"min_cells\": \"5\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.6+galaxy3",
+                        "tool_state": "{\"add_cell_metadata\": {\"default\": false, \"__current_case__\": 1}, \"copy_adata_to_raw\": false, \"copy_e\": {\"default\": false, \"__current_case__\": 1}, \"copy_l\": {\"default\": false, \"__current_case__\": 1}, \"copy_o\": {\"default\": false, \"__current_case__\": 1}, \"copy_r\": {\"default\": false, \"__current_case__\": 1}, \"copy_u\": {\"default\": false, \"__current_case__\": 1}, \"copy_x\": {\"default\": false, \"__current_case__\": 1}, \"field_unique\": null, \"gene_flags\": [{\"__index__\": 0, \"startswith\": \"mt-\", \"flag\": \"mito\"}], \"gene_symbols_field\": \"Symbol\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": false, \"split_on_obs\": {\"default\": false, \"__current_case__\": 1}, \"swap_layer_to_x\": {\"default\": false, \"__current_case__\": 1}, \"top_genes\": \"50\", \"var_modifications\": [{\"__index__\": 0, \"from_var\": \"gene_symbols\", \"to_var\": \"Symbol\", \"keep_original\": false, \"make_unique\": false}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy92",
                         "type": "tool",
-                        "uuid": "7dfff544-95f9-4309-8094-31a0acfa525e",
+                        "uuid": "b4616c2c-96f1-4474-97f3-cdbecd37e65b",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "anndata filter genes",
-                                "output_name": "anndata_out",
-                                "uuid": "7a9b22df-e0e5-49d9-9fa1-2efe316d6d66"
+                                "label": "Mito-counted AnnData for downstream analysis",
+                                "output_name": "output_h5ad",
+                                "uuid": "b47f801f-bedb-4136-a5e9-378a815a1799"
                             }
                         ]
-                    },
+                    }
+                ],
+                "parent_id": "single-cell/EBI-retrieval",
+                "path": "topics/single-cell/tutorials/EBI-retrieval/workflows/EBI-SCXA-to-AnnData-(Scanpy)-or-Seurat-Object.ga",
+                "tags": [],
+                "test_results": null,
+                "tests": true,
+                "title": "EBI SCXA to AnnData (Scanpy) or Seurat Object",
+                "topic_id": "single-cell",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-EBI-retrieval/versions/ebi-scxa-to-anndata--scanpy--or-seurat-object",
+                "tutorial_id": "EBI-retrieval",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/EBI-retrieval/workflows/EBI-SCXA-to-AnnData-(Scanpy)-or-Seurat-Object.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/EBI-retrieval/workflows/EBI-SCXA-to-AnnData-(Scanpy)-or-Seurat-Object.html",
+                "version": 1,
+                "wfid": "single-cell-EBI-retrieval",
+                "wfname": "ebi-scxa-to-anndata--scanpy--or-seurat-object",
+                "workflow": "EBI-SCXA-to-AnnData-(Scanpy)-or-Seurat-Object.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy92",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/3.2.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3"
+                ],
+                "workflowhub_id": "1210"
+            }
+        ]
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "datamash_ops",
+                    "owner": "iuc",
+                    "revisions": "562f3c677828",
+                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "datamash_transpose",
+                    "owner": "iuc",
+                    "revisions": "22c2a1ac7ae3",
+                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "raceid_clustering",
+                    "owner": "iuc",
+                    "revisions": "a4b734cd253b",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "raceid_filtnormconf",
+                    "owner": "iuc",
+                    "revisions": "43c146e25a43",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "raceid_inspectclusters",
+                    "owner": "iuc",
+                    "revisions": "41f34e925bd5",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "raceid_inspecttrajectory",
+                    "owner": "iuc",
+                    "revisions": "c8434a623268",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "raceid_trajectory",
+                    "owner": "iuc",
+                    "revisions": "72979cac22b2",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 562f3c677828\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_transpose\n  owner: iuc\n  revisions: 22c2a1ac7ae3\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: raceid_clustering\n  owner: iuc\n  revisions: a4b734cd253b\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: raceid_filtnormconf\n  owner: iuc\n  revisions: 43c146e25a43\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: raceid_inspectclusters\n  owner: iuc\n  revisions: 41f34e925bd5\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: raceid_inspecttrajectory\n  owner: iuc\n  revisions: c8434a623268\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: raceid_trajectory\n  owner: iuc\n  revisions: 72979cac22b2\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-raceid/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "elixir_node": "de",
+                "email": "mtekman89@gmail.com",
+                "former_affiliations": [
+                    "elixir-europe"
+                ],
+                "id": "mtekman",
+                "joined": "2018-11",
+                "name": "Mehmet Tekman",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
+            },
+            {
+                "email": "a.ostrovsky@mac.com",
+                "id": "astrovsky01",
+                "joined": "2019-06",
+                "name": "Alex Ostrovsky",
+                "orcid": "0000-0002-7901-7109",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/astrovsky01/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/astrovsky01.json"
+            }
+        ],
+        "dir": "topics/single-cell/tutorials/scrna-raceid",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-preprocessing-tenx"
+                ],
+                "type": "internal"
+            }
+        ],
+        "gitter": "Galaxy-Training-Network/galaxy-single-cell",
+        "hands_on": true,
+        "id": "single-cell/scrna-raceid",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": 10933,
+            "mermaid": false
+        },
+        "key_points": [
+            "Clustering single-cell RNA-seq data is often noisy",
+            "RaceID can be used to cluster cells based on the their gene expression profiles",
+            "StemID describes a hierarchical relationship between clusters to find multipotent progenitor stem cells to provide an understanding of cell development",
+            "FateID predicts the potential lineages that cells within specific clusters are inclined towards"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": [
+            "Filtering, normalising, and clustering cells in a matrix",
+            "Assessing the quality of individual clusters",
+            "Inferring cell type lineages",
+            "Examining gene expression",
+            "Determining the top most expressive genes per cluster",
+            "Correcting for unwanted variation"
+        ],
+        "pageviews": 960,
+        "priority": 2,
+        "pub_date": "2019-03-25",
+        "questions": [
+            "What is normalisation and why is it necessary?",
+            "How many types of unwanted variation are there?",
+            "How are biological phenotypes clustered?",
+            "What is the difference between PCA and tSNE?",
+            "What is the difference between cell trajectory and cell fate?"
+        ],
+        "redirect_from": [
+            "/topics/transcriptomics/tutorials/scrna-raceid/tutorial",
+            "/short/single-cell/scrna-raceid",
+            "/short/T00253"
+        ],
+        "requirements": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-scater-qc"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00253",
+        "short_tools": [
+            "raceid_trajectory",
+            "tp_sed_tool",
+            "raceid_clustering",
+            "raceid_inspecttrajectory",
+            "raceid_filtnormconf",
+            "tp_head_tool",
+            "raceid_inspectclusters",
+            "datamash_transpose",
+            "datamash_ops"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "end-to-end",
+        "supported_servers": {
+            "exact": [],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": null,
+        "time_estimation": "3H",
+        "title": "Downstream Single-cell RNA analysis with RaceID",
+        "tools": [
+            "raceid_clustering",
+            "raceid_filtnormconf",
+            "raceid_inspectclusters",
+            "raceid_inspecttrajectory",
+            "raceid_trajectory",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/0.2.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/0.2.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/0.2.3+galaxy0"
+        ],
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "scrna-raceid",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-raceid/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-raceid/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-raceid/tutorial.json"
+        },
+        "version": 5,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 82,
+        "visitors": 800,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Downstream Single-cell RNA analysis with RaceID",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTabular Matrix\"]\n  1[label=\"Initial processing using RaceID\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Clustering using RaceID\"]\n  1 -> 2 [label=\"outrdat\"]\n  3[label=\"Lineage computation using StemID\"]\n  2 -> 3 [label=\"outrdat\"]\n  4[label=\"Cluster Inspection using RaceID\"]\n  2 -> 4 [label=\"outrdat\"]\n  5[label=\"Cluster Inspection using RaceID\"]\n  2 -> 5 [label=\"outrdat\"]\n  6[label=\"Cluster Inspection using RaceID\"]\n  2 -> 6 [label=\"outrdat\"]\n  7[label=\"Lineage Branch Analysis using StemID\"]\n  3 -> 7 [label=\"outrdat\"]\n  8[label=\"Lineage Branch Analysis using StemID\"]\n  3 -> 8 [label=\"outrdat\"]\n}",
+                "history": [
+                    {
+                        "hash": "327fd2b842f45de3dc2a30067714352675ad69ae",
+                        "message": "Making a single cell topics",
+                        "num": 1,
+                        "short_hash": "327fd2b84",
+                        "unix": "1668273265"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy3",
+                        "content_id": null,
                         "errors": null,
-                        "id": 25,
-                        "input_connections": {
-                            "adata": {
-                                "id": 24,
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Normalize",
-                        "outputs": [
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "anndata_out",
-                                "type": "h5ad"
+                                "description": "",
+                                "name": "Tabular Matrix"
                             }
                         ],
+                        "label": "Tabular Matrix",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 5246.771945926951,
-                            "top": 559.3328161085777
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "d844935c906c",
-                            "name": "scanpy_normalize",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 167.21666717529297,
+                            "height": 48.96665954589844,
+                            "left": 38.75,
+                            "right": 198.75,
+                            "top": 118.25000762939453,
+                            "width": 160,
+                            "x": 38.75,
+                            "y": 118.25000762939453
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.normalize_total\", \"__current_case__\": 0, \"target_sum\": null, \"exclude_highly_expressed\": {\"exclude_highly_expressed\": \"False\", \"__current_case__\": 1}, \"key_added\": \"\", \"layers\": \"\", \"layer_norm\": \"None\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.6+galaxy3",
-                        "type": "tool",
-                        "uuid": "7629e178-c715-4b96-b5c3-523050cac768",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ba3fe014-c728-486e-8ce4-55be24df0682",
                         "workflow_outputs": [
                             {
-                                "label": "anndata normalize",
-                                "output_name": "anndata_out",
-                                "uuid": "7dddd4c8-1944-4f50-b331-857d03cc9631"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "0c858705-5e28-44e0-8023-46aec4a01725"
                             }
                         ]
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nTabular Matrix\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Initial processing using RaceID\"];\n  0 -->|output| 1;\n  2[\"Clustering using RaceID\"];\n  1 -->|outrdat| 2;\n  3[\"Lineage computation using StemID\"];\n  2 -->|outrdat| 3;\n  4[\"Cluster Inspection using RaceID\"];\n  2 -->|outrdat| 4;\n  5[\"Cluster Inspection using RaceID\"];\n  2 -->|outrdat| 5;\n  6[\"Cluster Inspection using RaceID\"];\n  2 -->|outrdat| 6;\n  7[\"Lineage Branch Analysis using StemID\"];\n  3 -->|outrdat| 7;\n  8[\"Lineage Branch Analysis using StemID\"];\n  3 -->|outrdat| 8;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "RaceID Workflow",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy3",
+                        "content_id": null,
                         "errors": null,
-                        "id": 26,
-                        "input_connections": {
-                            "adata": {
-                                "id": 25,
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "pp.log1p",
-                        "name": "Inspect and manipulate",
-                        "outputs": [
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "anndata_out",
-                                "type": "h5ad"
+                                "description": "",
+                                "name": "Tabular Matrix"
                             }
                         ],
+                        "label": "Tabular Matrix",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 5571.598835062394,
-                            "top": 560.0237842861073
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f54f0f0598ad",
-                            "name": "scanpy_inspect",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 167.21666717529297,
+                            "height": 48.96665954589844,
+                            "left": 38.75,
+                            "right": 198.75,
+                            "top": 118.25000762939453,
+                            "width": 160,
+                            "x": 38.75,
+                            "y": 118.25000762939453
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.log1p\", \"__current_case__\": 5}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.6+galaxy3",
-                        "type": "tool",
-                        "uuid": "8a57a670-5511-462f-b342-d2a6c868a7a8",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ba3fe014-c728-486e-8ce4-55be24df0682",
                         "workflow_outputs": [
                             {
-                                "label": "anndata log1p",
-                                "output_name": "anndata_out",
-                                "uuid": "40ace30a-21e1-4bf2-8e08-ad93b62fb2ee"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "0c858705-5e28-44e0-8023-46aec4a01725"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy3",
+                        "content_id": "raceid_filtnormconf",
                         "errors": null,
-                        "id": 27,
+                        "id": 1,
                         "input_connections": {
-                            "adata": {
-                                "id": 26,
-                                "output_name": "anndata_out"
+                            "intable": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": "external.pp.magic",
-                        "name": "Normalize",
+                        "label": null,
+                        "name": "Initial processing using RaceID",
                         "outputs": [
                             {
-                                "name": "anndata_out",
-                                "type": "h5ad"
+                                "name": "outtable",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "outpdf",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "outrdat",
+                                "type": "rdata"
+                            },
+                            {
+                                "name": "outlog",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 5919.286956493308,
-                            "top": 543.2768617443896
+                            "bottom": 410.7666702270508,
+                            "height": 293.76666259765625,
+                            "left": 272.5,
+                            "right": 432.5,
+                            "top": 117.00000762939453,
+                            "width": 160,
+                            "x": 272.5,
+                            "y": 117.00000762939453
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "d844935c906c",
-                            "name": "scanpy_normalize",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"external.pp.magic\", \"__current_case__\": 4, \"name_list\": \"all_genes\", \"knn\": \"5\", \"decay\": \"1\", \"knn_max\": null, \"t\": \"3\", \"n_pca\": \"100\", \"solver\": \"approximate\", \"knn_dist\": \"euclidean\", \"random_state\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.6+galaxy3",
+                        "tool_id": "raceid_filtnormconf",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"filt\": {\"mintotal\": \"3000\", \"minexpr\": \"5\", \"minnumber\": \"5\", \"hist_geq_one\": \"false\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"intable\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.2.3+galaxy0",
                         "type": "tool",
-                        "uuid": "0bdfc7e0-2f37-4122-9c33-517e6743e971",
-                        "when": null,
+                        "uuid": "6fd8dbde-93d2-4903-865f-78cc3c2fa299",
                         "workflow_outputs": [
                             {
-                                "label": "anndata_magic",
-                                "output_name": "anndata_out",
-                                "uuid": "8c1c7aa9-b9dd-467b-9715-73773aea093f"
+                                "label": null,
+                                "output_name": "outtable",
+                                "uuid": "d9293468-efef-4a10-89a6-0064a1740afd"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outpdf",
+                                "uuid": "358ddb8a-a6ca-4162-8d53-354902f905cf"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outrdat",
+                                "uuid": "68451b36-8875-45ca-bdb9-e315cc836e49"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outlog",
+                                "uuid": "35505252-c65a-4572-9d66-b0e69893c01b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0",
+                        "content_id": "raceid_clustering",
                         "errors": null,
-                        "id": 28,
+                        "id": 2,
                         "input_connections": {
-                            "copy_e|embedding_sources": {
-                                "id": 21,
-                                "output_name": "anndata_out"
-                            },
-                            "input_obj_file": {
-                                "id": 27,
-                                "output_name": "anndata_out"
+                            "inputrds": {
+                                "id": 1,
+                                "output_name": "outrdat"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool AnnData Operations",
-                                "name": "copy_e"
-                            }
-                        ],
-                        "label": "Copy obsm",
-                        "name": "AnnData Operations",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Clustering using RaceID",
                         "outputs": [
                             {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
+                                "name": "outpdf",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "outrdat",
+                                "type": "rdata"
+                            },
+                            {
+                                "name": "outassignments",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "outgenelist",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "outlog",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 6310.074636497004,
-                            "top": 564.1397165041963
+                            "bottom": 466.46668243408203,
+                            "height": 350.7166748046875,
+                            "left": 520,
+                            "right": 680,
+                            "top": 115.75000762939453,
+                            "width": 160,
+                            "x": 520,
+                            "y": 115.75000762939453
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "a4774b7b2e85",
-                            "name": "anndata_ops",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"add_cell_metadata\": {\"default\": false, \"__current_case__\": 1}, \"copy_adata_to_raw\": false, \"copy_e\": {\"default\": true, \"__current_case__\": 0, \"embedding_keys\": [{\"__index__\": 0, \"contains\": null}], \"embedding_sources\": {\"__class__\": \"ConnectedValue\"}}, \"copy_l\": {\"default\": false, \"__current_case__\": 1}, \"copy_o\": {\"default\": false, \"__current_case__\": 1}, \"copy_r\": {\"default\": false, \"__current_case__\": 1}, \"copy_u\": {\"default\": false, \"__current_case__\": 1}, \"copy_x\": {\"default\": false, \"__current_case__\": 1}, \"field_unique\": null, \"gene_flags\": [], \"gene_symbols_field\": \"index\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": false, \"split_on_obs\": {\"default\": false, \"__current_case__\": 1}, \"swap_layer_to_x\": {\"default\": false, \"__current_case__\": 1}, \"top_genes\": \"50\", \"var_modifications\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.3+galaxy0",
+                        "tool_id": "raceid_clustering",
+                        "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"clust\": {\"metric\": \"pearson\", \"funcluster\": \"kmedoids\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"extra\": {\"tablelim\": \"25\", \"plotlim\": \"10\", \"foldchange\": \"1.0\", \"pvalue\": \"0.01\"}, \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"outlier\": {\"outminc\": \"5\", \"outlg\": \"2\", \"final\": \"false\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"tsne\": {\"perplexity\": \"30\", \"knn\": \"10\", \"umap_nn\": \"15\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.2.3+galaxy0",
                         "type": "tool",
-                        "uuid": "117972e9-cf57-4b98-a032-39acedadc428",
-                        "when": null,
+                        "uuid": "ca88c6cb-03e0-400c-8942-4c7ac0545a67",
                         "workflow_outputs": [
                             {
-                                "label": "anndata_gene-matrix_leiden",
-                                "output_name": "output_h5ad",
-                                "uuid": "2c3825d3-7151-4eef-97d0-c8a31ca6fd3e"
+                                "label": null,
+                                "output_name": "outpdf",
+                                "uuid": "48b02eb6-1b70-4d1f-a210-03aa93a189d8"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outrdat",
+                                "uuid": "e59d7dff-7e4b-42b4-ba62-09858f83c75c"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outassignments",
+                                "uuid": "2514a8cc-48a9-4cf2-9640-8663f81d6cd6"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outgenelist",
+                                "uuid": "b69f7d2f-4efe-41ca-ac2f-c74d45c2327e"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outlog",
+                                "uuid": "68cbc6ab-4697-4042-b5a0-0d9cd842e09a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy3",
+                        "content_id": "raceid_trajectory",
                         "errors": null,
-                        "id": 29,
+                        "id": 3,
                         "input_connections": {
-                            "adata": {
-                                "id": 28,
-                                "output_name": "output_h5ad"
-                            },
-                            "method|color": {
-                                "id": 4,
-                                "output_name": "output"
+                            "inputrds": {
+                                "id": 2,
+                                "output_name": "outrdat"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Plot",
-                                "name": "method"
-                            }
-                        ],
-                        "label": "umap_plot_with_scanpy",
-                        "name": "Plot",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Lineage computation using StemID",
                         "outputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "name": "outpdf",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "outrdat",
+                                "type": "rdata"
                             }
                         ],
                         "position": {
-                            "left": 6625.542217976416,
-                            "top": 759.4084323967407
+                            "bottom": 298.08333587646484,
+                            "height": 179.8333282470703,
+                            "left": 778.75,
+                            "right": 938.75,
+                            "top": 118.25000762939453,
+                            "width": 160,
+                            "x": 778.75,
+                            "y": 118.25000762939453
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f7446fd8d5e7",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": {\"__class__\": \"ConnectedValue\"}, \"use_raw\": false, \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": null, \"palette\": null, \"frameon\": true, \"ncols\": \"2\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.6+galaxy3",
+                        "tool_id": "raceid_trajectory",
+                        "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"comppval\": {\"pthr\": \"0.01\", \"sensitive\": \"false\"}, \"compscore\": {\"nn\": \"1\", \"scthr\": \"0.0\"}, \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"plotgraph\": {\"showcells\": \"false\", \"scthr\": \"0.0\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"projback\": {\"pdishuf\": \"2000\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"projcell\": {\"knn\": \"3\", \"cthr\": \"5\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"use_log\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.2.3+galaxy0",
                         "type": "tool",
-                        "uuid": "9a3a0713-a10d-40d1-80b8-7b66fdf4f6b9",
-                        "when": null,
+                        "uuid": "515732a4-cba5-402a-9cc8-11980c4815c6",
                         "workflow_outputs": [
                             {
-                                "label": "umap_marker-genes",
-                                "output_name": "out_png",
-                                "uuid": "4cfbbb70-156b-48d7-b14b-db21198d9b6d"
+                                "label": null,
+                                "output_name": "outpdf",
+                                "uuid": "5de0f2cb-41a8-4278-8faa-20cdb534f3c4"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outrdat",
+                                "uuid": "91b567ed-cf6e-4ff4-a84d-186d49502dff"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Cut1",
+                        "content_id": "raceid_inspectclusters",
                         "errors": null,
-                        "id": 31,
+                        "id": 4,
                         "input_connections": {
-                            "input": {
-                                "id": 30,
-                                "output_name": "obs"
+                            "inputrds": {
+                                "id": 2,
+                                "output_name": "outrdat"
                             }
                         },
                         "inputs": [],
-                        "label": "Cut leiden from table",
-                        "name": "Cut",
+                        "label": null,
+                        "name": "Cluster Inspection using RaceID",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "tabular"
+                                "name": "outpdf",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "outlog",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 7290.77139785132,
-                            "top": 805.5918074906932
+                            "bottom": 512.9500045776367,
+                            "height": 147.1999969482422,
+                            "left": 773.75,
+                            "right": 933.75,
+                            "top": 365.75000762939453,
+                            "width": 160,
+                            "x": 773.75,
+                            "y": 365.75000762939453
                         },
                         "post_job_actions": {},
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"columnList\": \"c8\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2",
+                        "tool_id": "raceid_inspectclusters",
+                        "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"diffgtest\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"gois\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"plotgen\": {\"do_opt\": \"yes\", \"__current_case__\": 1, \"clusts_plot\": \"\"}, \"plotsym\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.2.3+galaxy0",
                         "type": "tool",
-                        "uuid": "7c8a2055-a457-4001-baba-a46c75b9e506",
-                        "when": null,
+                        "uuid": "727ee241-4de7-408f-867a-fc1ed21c23cb",
                         "workflow_outputs": [
                             {
-                                "label": "leiden annotation",
-                                "output_name": "out_file1",
-                                "uuid": "11c22200-a54e-4585-82c4-8457dbbfb53c"
+                                "label": null,
+                                "output_name": "outpdf",
+                                "uuid": "051cbdaa-6513-4239-91b6-e22004f6469f"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outlog",
+                                "uuid": "bf324238-9739-4960-90c0-2935d225bd42"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2",
+                        "content_id": "raceid_inspectclusters",
                         "errors": null,
-                        "id": 32,
+                        "id": 5,
                         "input_connections": {
-                            "original_file": {
-                                "id": 31,
-                                "output_name": "out_file1"
-                            },
-                            "replace_information": {
-                                "id": 5,
-                                "output_name": "output"
+                            "inputrds": {
+                                "id": 2,
+                                "output_name": "outrdat"
                             }
                         },
                         "inputs": [],
-                        "label": "Replace leiden",
-                        "name": "Replace column",
+                        "label": null,
+                        "name": "Cluster Inspection using RaceID",
                         "outputs": [
                             {
-                                "name": "outfile_replace",
+                                "name": "outpdf",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "outlog",
                                 "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 7610.590154939628,
-                            "top": 714.8720707586833
-                        },
-                        "post_job_actions": {
-                            "ChangeDatatypeActionoutfile_replace": {
-                                "action_arguments": {
-                                    "newtype": "tabular"
-                                },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "outfile_replace"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "d533e4b75800",
-                            "name": "replace_column_by_key_value_file",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 712.9500045776367,
+                            "height": 147.1999969482422,
+                            "left": 773.75,
+                            "right": 933.75,
+                            "top": 565.7500076293945,
+                            "width": 160,
+                            "x": 773.75,
+                            "y": 565.7500076293945
                         },
-                        "tool_state": "{\"column_replace\": \"1\", \"delimiter\": \"tab\", \"original_file\": {\"__class__\": \"ConnectedValue\"}, \"pass_comments\": \"#\", \"replace_information\": {\"__class__\": \"ConnectedValue\"}, \"skip_lines\": \"0\", \"unknowns_strategy\": \"skip\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.2",
+                        "post_job_actions": {},
+                        "tool_id": "raceid_inspectclusters",
+                        "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"diffgtest\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"gois\": {\"do_opt\": \"yes\", \"__current_case__\": 1, \"inspect_goi_genes\": \"Gstm3, St3gal4, Gna11\", \"inspect_goi_cells\": \"\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"plotgen\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"plotsym\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.2.3+galaxy0",
                         "type": "tool",
-                        "uuid": "94ec122d-0eb2-43e7-bf79-3b3ad6e0a7e8",
-                        "when": null,
+                        "uuid": "6db63f68-65bc-4bb5-96a2-9d3e75712287",
                         "workflow_outputs": [
                             {
-                                "label": "cell type annotation",
-                                "output_name": "outfile_replace",
-                                "uuid": "467de061-79e6-4148-8a65-c06383a14012"
+                                "label": null,
+                                "output_name": "outpdf",
+                                "uuid": "344cd8bc-01a1-4614-8def-806815a615af"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outlog",
+                                "uuid": "3268d277-37a0-4081-ae95-8c7a83efb903"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
+                        "content_id": "raceid_inspectclusters",
                         "errors": null,
-                        "id": 33,
+                        "id": 6,
                         "input_connections": {
-                            "input": {
-                                "id": 28,
-                                "output_name": "output_h5ad"
-                            },
-                            "manipulate|new_annot": {
-                                "id": 32,
-                                "output_name": "outfile_replace"
+                            "inputrds": {
+                                "id": 2,
+                                "output_name": "outrdat"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Manipulate AnnData",
-                                "name": "manipulate"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Manipulate AnnData",
+                        "name": "Cluster Inspection using RaceID",
                         "outputs": [
                             {
-                                "name": "anndata",
-                                "type": "h5ad"
+                                "name": "outpdf",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "outlog",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 7951.665647831622,
-                            "top": 529.7790878349768
+                            "bottom": 827.9499664306641,
+                            "height": 147.1999969482422,
+                            "left": 1035,
+                            "right": 1195,
+                            "top": 680.7499694824219,
+                            "width": 160,
+                            "x": 1035,
+                            "y": 680.7499694824219
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ed4996a16f7f",
-                            "name": "anndata_manipulate",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"add_annotation\", \"__current_case__\": 6, \"var_obs\": \"obs\", \"new_annot\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.10.3+galaxy0",
+                        "tool_id": "raceid_inspectclusters",
+                        "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"diffgtest\": {\"do_opt\": \"yes\", \"__current_case__\": 1, \"set_a\": {\"name_set\": \"Cells in 1\", \"meth\": {\"type\": \"cln\", \"__current_case__\": 0, \"selector\": \"1\"}}, \"set_b\": {\"name_set\": \"Cells in 3\", \"meth\": {\"type\": \"cln\", \"__current_case__\": 0, \"selector\": \"3\"}}, \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}, \"gois\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"plotgen\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"plotsym\": {\"do_opt\": \"no\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.2.3+galaxy0",
                         "type": "tool",
-                        "uuid": "8002dcb8-d903-4a46-a2df-6a0cf4e4407f",
-                        "when": null,
+                        "uuid": "57c7332a-c6f5-484f-8a5c-d5467d320e72",
                         "workflow_outputs": [
                             {
-                                "label": "anndata_cell_type",
-                                "output_name": "anndata",
-                                "uuid": "cbba6173-f439-4fd5-8423-946aa625112b"
+                                "label": null,
+                                "output_name": "outpdf",
+                                "uuid": "d028c3e8-3acb-44ba-968a-74b1cdfb4bb1"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outlog",
+                                "uuid": "8f9f3e29-3c56-4fcf-af0a-f2bea2c10234"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy3",
+                        "content_id": "raceid_inspecttrajectory",
                         "errors": null,
-                        "id": 34,
+                        "id": 7,
                         "input_connections": {
-                            "adata": {
-                                "id": 33,
-                                "output_name": "anndata"
+                            "inputrds": {
+                                "id": 3,
+                                "output_name": "outrdat"
                             }
                         },
                         "inputs": [],
-                        "label": "Plot cell types",
-                        "name": "Plot",
+                        "label": null,
+                        "name": "Lineage Branch Analysis using StemID",
                         "outputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "name": "outpdf",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "outdiffgenes",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "outlog",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 8306.897077852367,
-                            "top": 563.5673448508458
+                            "bottom": 372.61666107177734,
+                            "height": 253.1166534423828,
+                            "left": 1041.25,
+                            "right": 1201.25,
+                            "top": 119.50000762939453,
+                            "width": 160,
+                            "x": 1041.25,
+                            "y": 119.50000762939453
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f7446fd8d5e7",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"cell_type\", \"use_raw\": false, \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"on data\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": null, \"palette\": null, \"frameon\": true, \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9.6+galaxy3",
+                        "tool_id": "raceid_inspecttrajectory",
+                        "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"trjfid\": {\"basic\": {\"doit\": \"no\", \"__current_case__\": 0}}, \"trjsid\": {\"basic\": {\"doit\": \"yes\", \"__current_case__\": 1, \"i\": \"3\", \"br\": \"1,3,5\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.2.3+galaxy0",
                         "type": "tool",
-                        "uuid": "ad9c86ff-9843-44f7-815d-026a3a4d6eef",
-                        "when": null,
+                        "uuid": "4a519b59-2319-4811-969e-3b872f95c377",
                         "workflow_outputs": [
                             {
-                                "label": "umap_cell-type",
-                                "output_name": "out_png",
-                                "uuid": "c28c53ae-8ee7-47d7-8a00-352908bb7c1a"
+                                "label": null,
+                                "output_name": "outpdf",
+                                "uuid": "1e19e4d3-802d-4713-b920-ba8264bce2d0"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outdiffgenes",
+                                "uuid": "814ac5ce-500d-4ea2-bbc7-ab8c4f5d2962"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outlog",
+                                "uuid": "4404cdf2-ee33-4e08-8fed-83b52bbfad88"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
+                        "content_id": "raceid_inspecttrajectory",
                         "errors": null,
-                        "id": 35,
+                        "id": 8,
                         "input_connections": {
-                            "input": {
-                                "id": 33,
-                                "output_name": "anndata"
+                            "inputrds": {
+                                "id": 3,
+                                "output_name": "outrdat"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Inspect AnnData",
-                                "name": "input"
-                            }
-                        ],
-                        "label": "Final Anndata general info",
-                        "name": "Inspect AnnData",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Lineage Branch Analysis using StemID",
                         "outputs": [
                             {
-                                "name": "general",
+                                "name": "outpdf",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "outlog",
                                 "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 8297.002377504208,
-                            "top": 760.6562767663465
+                            "bottom": 625.5833358764648,
+                            "height": 179.8333282470703,
+                            "left": 1040,
+                            "right": 1200,
+                            "top": 445.75000762939453,
+                            "width": 160,
+                            "x": 1040,
+                            "y": 445.75000762939453
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6f0d0c784f09",
-                            "name": "anndata_inspect",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"inspect\": {\"info\": \"general\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.10.3+galaxy0",
+                        "tool_id": "raceid_inspecttrajectory",
+                        "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/tmp/tmp8dp_jicw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\", \"inputrds\": {\"__class__\": \"ConnectedValue\"}, \"trjfid\": {\"basic\": {\"doit\": \"yes\", \"__current_case__\": 1, \"cellsfromz\": \"1,3,5\", \"use\": {\"def\": \"yes\", \"__current_case__\": 0}, \"som\": {\"doit\": \"no\", \"__current_case__\": 0}}}, \"trjsid\": {\"basic\": {\"doit\": \"no\", \"__current_case__\": 0}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.2.3+galaxy0",
                         "type": "tool",
-                        "uuid": "d178ea23-94a0-42c0-87db-44f2cc23d5dc",
-                        "when": null,
+                        "uuid": "883ffd05-1545-449f-8028-c45c0f9edfd5",
                         "workflow_outputs": [
                             {
-                                "label": "general",
-                                "output_name": "general",
-                                "uuid": "379a85d1-a204-4b0b-8b33-86e5582fc51f"
+                                "label": null,
+                                "output_name": "outpdf",
+                                "uuid": "8ef7bad4-ff15-42d2-acc4-6c5bc5de89e4"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outlog",
+                                "uuid": "23f0fab3-0128-443a-a26a-a3e40cee4578"
                             }
                         ]
                     }
                 ],
-                "parent_id": "single-cell/scatac-standard-processing-snapatac2",
-                "path": "topics/single-cell/tutorials/scatac-standard-processing-snapatac2/workflows/Standard-processing-of-10X-single-cell-ATAC-seq-data-with-SnapATAC2.ga",
+                "parent_id": "single-cell/scrna-raceid",
+                "path": "topics/single-cell/tutorials/scrna-raceid/workflows/main_workflow.ga",
                 "tags": [
-                    "scATAC-seq",
-                    "epigenetics"
+                    "transcriptomics",
+                    "single-cell"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2",
+                "tests": false,
+                "title": "RaceID Workflow",
                 "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scatac-standard-processing-snapatac2/versions/standard-processing-of-10x-single-cell-atac-seq-data-with-snapatac2",
-                "tutorial_id": "scatac-standard-processing-snapatac2",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/workflows/Standard-processing-of-10X-single-cell-ATAC-seq-data-with-SnapATAC2.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/workflows/Standard-processing-of-10X-single-cell-ATAC-seq-data-with-SnapATAC2.html",
-                "version": 2,
-                "wfid": "single-cell-scatac-standard-processing-snapatac2",
-                "wfname": "standard-processing-of-10x-single-cell-atac-seq-data-with-snapatac2",
-                "workflow": "Standard-processing-of-10X-single-cell-ATAC-seq-data-with-SnapATAC2.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-raceid/versions/main-workflow",
+                "tutorial_id": "scrna-raceid",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-raceid/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-raceid/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "single-cell-scrna-raceid",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1"
-                ],
-                "workflowhub_id": "1343"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/records/12707159"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRStudio/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "Camila-goclowski"
-            ],
-            "editing": [
-                "nomadscientist",
-                "hexylena",
-                "mtekman",
-                "shiltemann",
-                "pavanvidem"
-            ]
-        },
-        "contributors": [
-            {
-                "email": "camila.goclowski@gmail.com",
-                "id": "Camila-goclowski",
-                "joined": "2023-01",
-                "linkedin": "camila-goclowski",
-                "name": "Camila Goclowski",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Camila-goclowski/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/Camila-goclowski.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "bio": "Senior Lecturer at The Open University",
-                "elixir_node": "uk",
-                "email": "wendi.bacon@open.ac.uk",
-                "fediverse": "https://mstdn.science/@wendibacon1",
-                "fediverse_flavor": "mastodon",
-                "id": "nomadscientist",
-                "joined": "2020-03",
-                "matrix": "nomadscientist:matrix.org",
-                "name": "Wendi Bacon",
-                "orcid": "0000-0002-8170-8806",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
-                "twitter": "WendiBacon1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "elixir_node": "de",
-                "email": "mtekman89@gmail.com",
-                "former_affiliations": [
-                    "elixir-europe"
-                ],
-                "id": "mtekman",
-                "joined": "2018-11",
-                "name": "Mehmet Tekman",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "pavanvidem",
-                "joined": "2017-09",
-                "name": "Pavankumar Videm",
-                "orcid": "0000-0002-5192-126X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
-            }
-        ],
-        "dir": "topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRStudio",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "single-cell/scrna-case_FilterPlotandExploreRStudio",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Being able to switch between Galaxy and RStudio when analyzing datasets can be useful when looking to adjust default parameters within Seurat's functions and workflow.",
-            "Seurat in RStudio gives more flexibility and specificity of analyses, but Galaxy offers great reproducibility and ease of analysis.",
-            "Beginning to learn the syntax and use of R will expand your"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-07",
-        "notebook": {
-            "language": "r",
-            "snippet": "topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRStudio/preamble.md"
-        },
-        "objectives": [
-            "Interpret quality control plots to direct parameter decisions",
-            "Repeat analysis from matrix to clustering to labelling clusters",
-            "Identify decision-making points",
-            "Appraise data outputs and decisions",
-            "Explain why single cell analysis is an iterative process (i.e. the first plots you generate are not final, but rather you go back and re-analyse your data repeatedly)"
-        ],
-        "pageviews": 2151,
-        "priority": 2,
-        "pub_date": "2023-10-02",
-        "questions": [
-            "Is my single cell dataset a quality dataset?",
-            "How do I pick thresholds and parameters in my analysis? What\u2019s a \u201creasonable\u201d number, and will the world collapse if I pick the wrong one?",
-            "How do I generate and annotate cell clusters?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-case_alevin-combine-datasets",
-                    "scrna-case_basic-pipeline"
+                    "raceid_clustering",
+                    "raceid_filtnormconf",
+                    "raceid_inspectclusters",
+                    "raceid_inspecttrajectory",
+                    "raceid_trajectory"
                 ],
-                "type": "internal"
+                "workflowhub_id": "1205"
             }
         ],
-        "short_id": "T00366",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "single-cell-CS-code",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "10x",
-            "paper-replication",
-            "R"
-        ],
-        "time_estimation": "3H",
-        "title": "Filter, plot, and explore single cell RNA-seq data with Seurat (R)",
-        "tools": [],
-        "topic_name": "single-cell",
-        "topic_name_human": "Single Cell",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "scrna-case_FilterPlotandExploreRStudio",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRStudio/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRStudio/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRStudio/tutorial.json"
-        },
-        "version": 8,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 45,
-        "visitors": 1933,
-        "zenodo_link": "https://zenodo.org/record/7053673"
+        "zenodo_link": "https://zenodo.org/record/1511582"
     },
     {
         "admin_install": {
@@ -225822,89 +229956,86 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
+                    "name": "add_value",
+                    "owner": "devteam",
+                    "revisions": "745871c0b055",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "anndata_ops",
+                    "name": "scanpy_regress_variable",
                     "owner": "ebi-gxa",
-                    "revisions": "a0274bc43b7e",
+                    "revisions": "36daab33aecf",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "hca_matrix_downloader",
-                    "owner": "ebi-gxa",
-                    "revisions": "c3c85b67d118",
-                    "tool_panel_section_label": "Single Cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "retrieve_scxa",
-                    "owner": "ebi-gxa",
-                    "revisions": "72b6e1747e37",
+                    "name": "anndata_inspect",
+                    "owner": "iuc",
+                    "revisions": "ee98d611afc6",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_read_10x",
-                    "owner": "ebi-gxa",
-                    "revisions": "d253d69ff19f",
+                    "name": "anndata_manipulate",
+                    "owner": "iuc",
+                    "revisions": "3d748954434b",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_read_10x",
-                    "owner": "ebi-gxa",
-                    "revisions": "9afcfcd1d215",
+                    "name": "scanpy_cluster_reduce_dimension",
+                    "owner": "iuc",
+                    "revisions": "aaa5da8e73a9",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "seurat_read10x",
-                    "owner": "ebi-gxa",
-                    "revisions": "301cf1b4b43d",
-                    "tool_panel_section_label": "Seurat",
+                    "name": "scanpy_inspect",
+                    "owner": "iuc",
+                    "revisions": "c5d3684f7c4c",
+                    "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "regex_find_replace",
-                    "owner": "galaxyp",
-                    "revisions": "503bcd6ebe4b",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "scanpy_plot",
+                    "owner": "iuc",
+                    "revisions": "aa0c474463c2",
+                    "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sceasy_convert",
+                    "name": "table_compute",
                     "owner": "iuc",
-                    "revisions": "d70139524747",
-                    "tool_panel_section_label": "Single-cell",
+                    "revisions": "3bf5661c0280",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_ops\n  owner: ebi-gxa\n  revisions: a0274bc43b7e\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: hca_matrix_downloader\n  owner: ebi-gxa\n  revisions: c3c85b67d118\n  tool_panel_section_label: Single Cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: retrieve_scxa\n  owner: ebi-gxa\n  revisions: 72b6e1747e37\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_read_10x\n  owner: ebi-gxa\n  revisions: d253d69ff19f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_read_10x\n  owner: ebi-gxa\n  revisions: 9afcfcd1d215\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_read10x\n  owner: ebi-gxa\n  revisions: 301cf1b4b43d\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 503bcd6ebe4b\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sceasy_convert\n  owner: iuc\n  revisions: d70139524747\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/EBI-retrieval/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: add_value\n  owner: devteam\n  revisions: 745871c0b055\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_regress_variable\n  owner: ebi-gxa\n  revisions: 36daab33aecf\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_inspect\n  owner: iuc\n  revisions: ee98d611afc6\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n  owner: iuc\n  revisions: 3d748954434b\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_cluster_reduce_dimension\n  owner: iuc\n  revisions: aaa5da8e73a9\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_inspect\n  owner: iuc\n  revisions: c5d3684f7c4c\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot\n  owner: iuc\n  revisions: aa0c474463c2\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: table_compute\n  owner: iuc\n  revisions: 3bf5661c0280\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.json",
         "contributions": {
             "authorship": [
-                "wee-snufkin",
+                "MarisaJL"
+            ],
+            "editing": [
                 "nomadscientist"
             ],
-            "funding": [
-                "elixir-fair-data"
+            "testing": [
+                "hrukkudyr"
             ]
         },
         "contributors": [
             {
-                "email": "juliajot36@gmail.com",
-                "id": "wee-snufkin",
-                "joined": "2022-06",
-                "name": "Julia Jakiela",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
+                "email": "marisa.loach@open.ac.uk",
+                "id": "MarisaJL",
+                "joined": "2022-10",
+                "name": "Marisa Loach",
+                "orcid": "0000-0001-6979-6930",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/MarisaJL/",
+                "twitter": "Marisa_Loach",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/MarisaJL.json"
             },
             {
                 "affiliations": [
@@ -225925,89 +230056,80 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
             },
             {
-                "funder": true,
-                "funding_id": "MR/V038966/1",
-                "funding_statement": "This work has been funded by the ELIXIR-UK FAIR Data Stewardship training UKRI award (MR/V038966/1)",
-                "funding_system": "ukri",
-                "github": false,
-                "id": "elixir-fair-data",
-                "joined": "2023-06",
-                "name": "ELIXIR-UK: FAIR Data Stewardship training",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-fair-data/",
-                "short_name": "ELIXIR Fair Data",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-fair-data.json"
+                "email": "grt67@open.ac.uk",
+                "id": "hrukkudyr",
+                "joined": "2022-09",
+                "name": "Graeme Tyson",
+                "orcid": "0000-0002-1748-2806",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hrukkudyr/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hrukkudyr.json"
             }
         ],
-        "dir": "topics/single-cell/tutorials/EBI-retrieval",
-        "edam_operation": [],
+        "dir": "topics/single-cell/tutorials/scrna-case_cell-cycle",
+        "edam_operation": [
+            "Differential gene expression analysis"
+        ],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-case_basic-pipeline"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "single-cell/EBI-retrieval",
-        "inexact_supported_servers": [],
+        "id": "single-cell/scrna-case_cell-cycle",
+        "inexact_supported_servers": [
+            "UseGalaxy.org.au"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "The EMBL-EBI Single-cell Expression Atlas contains high quality datasets.",
-            "Metadata manipulation is key for generating the correctly formatted files.",
-            "To use Scanpy tools, you have to transform your metadata into an AnnData object.",
-            "To use Seurat tools, you have to transform your metadata into a Seurat object."
+            "Cell cycle genes can conceal what is happening in your data if cells are grouping together according to their stage in the cycle",
+            "Identifying the cell cycle genes and using them to regress out the effects of the cell cycle can reveal underlying patterns in the data"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-02-13",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "You will retrieve raw data from the EBI Single Cell Expression Atlas and Human Cell Atlas.",
-            "You will manipulate the metadata and matrix files.",
-            "You will combine the metadata and matrix files into an AnnData or Seurat object for downstream analysis."
+            "Identify the cell cycle genes",
+            "Use the cell cycle genes to regress out the effects of the cell cycle",
+            "Create PCA plots to understand the impact of the regression"
         ],
-        "pageviews": 226,
+        "pageviews": 1730,
         "priority": 2,
-        "pub_date": "2023-11-14",
+        "pub_date": "2023-01-25",
         "questions": [
-            "How do I use the EBI Single Cell Expression Atlas and Human Cell Atlas?",
-            "How can I reformat and manipulate the downloaded files to create the correct input for downstream analysis?"
+            "How can I reduce the effects of the cell cycle on my scRNA-seq data?"
         ],
         "requirements": [
             {
                 "topic_name": "single-cell",
                 "tutorials": [
                     "scrna-case_alevin",
-                    "scrna-case_alevin-combine-datasets"
+                    "scrna-case_alevin-combine-datasets",
+                    "scrna-case_basic-pipeline"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00374",
+        "short_id": "T00248",
         "short_tools": [
-            "anndata_ops",
-            "scanpy_read_10x",
-            "sceasy_convert",
-            "tp_find_and_replace",
-            "tp_grep_tool",
-            "hca_matrix_downloader",
-            "seurat_read10x",
-            "retrieve_scxa",
-            "regexColumn1"
+            "table_compute",
+            "tp_easyjoin_tool",
+            "sort1",
+            "scanpy_plot",
+            "scanpy_cluster_reduce_dimension",
+            "anndata_inspect",
+            "anndata_manipulate",
+            "scanpy_inspect",
+            "scanpy_regress_variable",
+            "cat1",
+            "addValue"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "datamanipulation",
+        "subtopic": "tricks",
         "supported_servers": {
             "exact": [
                 {
@@ -226016,26 +230138,32 @@
                     "usegalaxy": true
                 }
             ],
-            "inexact": []
+            "inexact": [
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
         },
         "symlink": null,
         "tags": [
-            "data import",
-            "data management"
+            "10x"
         ],
-        "time_estimation": "15m",
-        "title": "Importing files from public atlases",
+        "time_estimation": "1H",
+        "title": "Removing the effects of the cell cycle",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy92",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/hca_matrix_downloader/hca_matrix_downloader/v0.0.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/3.2.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/sceasy_convert/sceasy_convert/0.0.7+galaxy1"
+            "cat1",
+            "sort1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_regress_variable/scanpy_regress_variable/1.8.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0"
         ],
         "topic_name": "single-cell",
         "topic_name_human": "Single Cell",
@@ -226045,394 +230173,985 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "EBI-retrieval",
+        "tutorial_name": "scrna-case_cell-cycle",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/EBI-retrieval/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/EBI-retrieval/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/EBI-retrieval/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.json"
         },
-        "version": 3,
+        "version": 11,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 165,
-        "visitors": 166,
+        "visit_duration": 50,
+        "visitors": 1435,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0009-0001-2017-8805",
-                        "name": "Julia Jakiela"
-                    }
-                ],
-                "description": "Creates input file for Filter, Plot, Explore tutorial",
+                "creators": [],
+                "description": "",
                 "features": {
                     "comments": false,
-                    "parameters": true,
+                    "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nSC-Atlas experiment accession\"]\n  1[label=\"EBI SCXA Data Retrieval\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Rename batch numbers\"]\n  1 -> 2 [label=\"design_tsv\"]\n  3[label=\"Mito genes check\"]\n  1 -> 3 [label=\"genes_tsv\"]\n  kb0762cfd58bd4c39ae412dca4289c541[color=lightseagreen,label=\"Output\\nMito genes check\"]\n  3 -> kb0762cfd58bd4c39ae412dca4289c541\n  4[label=\"Rename cell metadata headers\"]\n  2 -> 4 [label=\"out_file1\"]\n  5[label=\"Create AnnData\"]\n  1 -> 5 [label=\"barcode_tsv\"]\n  4 -> 5 [label=\"outfile\"]\n  1 -> 5 [label=\"genes_tsv\"]\n  1 -> 5 [label=\"matrix_mtx\"]\n  k938cd59461cf4037a58bc09c065db505[color=lightseagreen,label=\"Output\\nAnnData object\"]\n  5 -> k938cd59461cf4037a58bc09c065db505\n  6[label=\"Seurat Read10x\"]\n  1 -> 6 [label=\"barcode_tsv\"]\n  1 -> 6 [label=\"genes_tsv\"]\n  1 -> 6 [label=\"matrix_mtx\"]\n  4 -> 6 [label=\"outfile\"]\n  kc24e9d83c17540a29c36eeb486fe323e[color=lightseagreen,label=\"Output\\nSeurat object\"]\n  6 -> kc24e9d83c17540a29c36eeb486fe323e\n  7[label=\"AnnData Operations\"]\n  5 -> 7 [label=\"output_h5ad\"]\n  kb47f801fbedb4136a5e9378a815a1799[color=lightseagreen,label=\"Output\\nMito-counted AnnData for downstream analysis\"]\n  7 -> kb47f801fbedb4136a5e9378a815a1799\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAnnData After QC, normalisation, scaling\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nS Phase Genes\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nG2M Phase Genes\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPasted Entry\"]\n  4[label=\"Inspect AnnData\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"All Cell Cycle Genes Concatenate S and G2M Genes\"]\n  1 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"Inspect and manipulate\"]\n  0 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"Table Compute\"]\n  4 -> 7 [label=\"var\"]\n  8[label=\"Add column\"]\n  5 -> 8 [label=\"out_file1\"]\n  9[label=\"Scanpy RegressOut\"]\n  6 -> 9 [label=\"anndata_out\"]\n  k026b02d397ee4847934740773ab76356[color=lightseagreen,label=\"Output\\nScanpy RegressOut on input dataset(s): Regressed out  AnnData\"]\n  9 -> k026b02d397ee4847934740773ab76356\n  10[label=\"Add column\"]\n  7 -> 10 [label=\"table\"]\n  11[label=\"Join\"]\n  10 -> 11 [label=\"out_file1\"]\n  8 -> 11 [label=\"out_file1\"]\n  12[label=\"Sort\"]\n  11 -> 12 [label=\"output\"]\n  13[label=\"Table Compute\"]\n  12 -> 13 [label=\"out_file1\"]\n  14[label=\"Concatenate datasets\"]\n  3 -> 14 [label=\"output\"]\n  13 -> 14 [label=\"table\"]\n  15[label=\"Manipulate AnnData\"]\n  6 -> 15 [label=\"anndata_out\"]\n  14 -> 15 [label=\"out_file1\"]\n  16[label=\"Manipulate AnnData\"]\n  9 -> 16 [label=\"output_h5ad\"]\n  14 -> 16 [label=\"out_file1\"]\n  17[label=\"Manipulate AnnData\"]\n  15 -> 17 [label=\"anndata\"]\n  18[label=\"Manipulate AnnData\"]\n  16 -> 18 [label=\"anndata\"]\n  19[label=\"Cluster, infer trajectories and embed\"]\n  17 -> 19 [label=\"anndata\"]\n  20[label=\"Cluster, infer trajectories and embed\"]\n  18 -> 20 [label=\"anndata\"]\n  k09d97ef7ed924d90a5972032581c2d4a[color=lightseagreen,label=\"Output\\nCluster, infer trajectories and embed (tl.louvain) on input dataset(s): Annotated data matrix\"]\n  20 -> k09d97ef7ed924d90a5972032581c2d4a\n  21[label=\"Plot\"]\n  19 -> 21 [label=\"anndata_out\"]\n  22[label=\"Plot\"]\n  20 -> 22 [label=\"anndata_out\"]\n}",
                 "history": [
                     {
-                        "hash": "a6e3cf848bad2cf19f48ca286c52821f558a6b52",
-                        "message": "new tests",
-                        "num": 2,
-                        "short_hash": "a6e3cf848",
-                        "unix": "1702552191"
+                        "hash": "f70e87e49ec1315f959cb4532d667ab976ae61f4",
+                        "message": "Moving to single cell",
+                        "num": 1,
+                        "short_hash": "f70e87e49",
+                        "unix": "1669054986"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "AnnData (After QC, normalisation, scaling)"
+                            }
+                        ],
+                        "label": "AnnData (After QC, normalisation, scaling)",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 646.9375,
+                            "top": 474.125
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "abf51bba-7bf3-442f-8d25-bb8008efdab1",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "S Phase Genes"
+                            }
+                        ],
+                        "label": "S Phase Genes",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 1029.3646240234375
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "20c44e44-d3da-47b3-a761-5b9714629e8e",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "G2M Phase Genes"
+                            }
+                        ],
+                        "label": "G2M Phase Genes",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 17.21875,
+                            "top": 1184.7708740234375
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "5ed158d1-a7eb-4750-892c-f123c80bfe89",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Pasted Entry"
+                            }
+                        ],
+                        "label": "Pasted Entry",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 1955.0625,
+                            "top": 0.0
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "bd171b20-fde0-4346-8d3e-274a3592485d",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAnnData After QC, normalisation, scaling\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nS Phase Genes\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nG2M Phase Genes\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nPasted Entry\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Inspect AnnData\"];\n  0 -->|output| 4;\n  5[\"All Cell Cycle Genes Concatenate S and G2M Genes\"];\n  1 -->|output| 5;\n  2 -->|output| 5;\n  6[\"Inspect and manipulate\"];\n  0 -->|output| 6;\n  2 -->|output| 6;\n  1 -->|output| 6;\n  7[\"Table Compute\"];\n  4 -->|var| 7;\n  8[\"Add column\"];\n  5 -->|out_file1| 8;\n  9[\"Scanpy RegressOut\"];\n  6 -->|anndata_out| 9;\n  026b02d3-97ee-4847-9347-40773ab76356[\"Output\\nScanpy RegressOut on input dataset(s): Regressed out  AnnData\"];\n  9 --> 026b02d3-97ee-4847-9347-40773ab76356;\n  style 026b02d3-97ee-4847-9347-40773ab76356 stroke:#2c3143,stroke-width:4px;\n  10[\"Add column\"];\n  7 -->|table| 10;\n  11[\"Join\"];\n  10 -->|out_file1| 11;\n  8 -->|out_file1| 11;\n  12[\"Sort\"];\n  11 -->|output| 12;\n  13[\"Table Compute\"];\n  12 -->|out_file1| 13;\n  14[\"Concatenate datasets\"];\n  3 -->|output| 14;\n  13 -->|table| 14;\n  15[\"Manipulate AnnData\"];\n  6 -->|anndata_out| 15;\n  14 -->|out_file1| 15;\n  16[\"Manipulate AnnData\"];\n  9 -->|output_h5ad| 16;\n  14 -->|out_file1| 16;\n  17[\"Manipulate AnnData\"];\n  15 -->|anndata| 17;\n  18[\"Manipulate AnnData\"];\n  16 -->|anndata| 18;\n  19[\"Cluster, infer trajectories and embed\"];\n  17 -->|anndata| 19;\n  20[\"Cluster, infer trajectories and embed\"];\n  18 -->|anndata| 20;\n  09d97ef7-ed92-4d90-a597-2032581c2d4a[\"Output\\nCluster, infer trajectories and embed (tl.louvain) on input dataset(s): Annotated data matrix\"];\n  20 --> 09d97ef7-ed92-4d90-a597-2032581c2d4a;\n  style 09d97ef7-ed92-4d90-a597-2032581c2d4a stroke:#2c3143,stroke-width:4px;\n  21[\"Plot\"];\n  19 -->|anndata_out| 21;\n  22[\"Plot\"];\n  20 -->|anndata_out| 22;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "Cell Cycle Regression Workflow",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Inspect AnnData",
+                        "outputs": [
+                            {
+                                "name": "var",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 459.125,
+                            "top": 133.625
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ee98d611afc6",
+                            "name": "anndata_inspect",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"var\", \"__current_case__\": 4}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "96b7447e-c65c-4955-b3c5-a381f707fb3d",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "var",
+                                "uuid": "1ffba0d7-dc80-4e44-bd74-77cf007f1446"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "cat1",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "input1": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "queries_0|input2": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "All Cell Cycle Genes (Concatenate S and G2M Genes)",
+                        "name": "Concatenate datasets",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 445.59375,
+                            "top": 1010.6666870117188
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "cat1",
+                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [{\"__index__\": 0, \"input2\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "7d0769c1-4b8d-4d29-bcc7-aed030503ccc",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "dd200c78-68fe-4a66-85e7-76710e20e4ae"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "adata": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "method|g2m_genes|file": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "method|s_genes|file": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Inspect and manipulate",
+                        "outputs": [
+                            {
+                                "name": "anndata_out",
+                                "type": "h5ad"
+                            }
+                        ],
+                        "position": {
+                            "left": 1839.84375,
+                            "top": 567.9375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "c5d3684f7c4c",
+                            "name": "scanpy_inspect",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"method\": {\"method\": \"tl.score_genes_cell_cycle\", \"__current_case__\": 3, \"s_genes\": {\"format\": \"file\", \"__current_case__\": 1, \"file\": {\"__class__\": \"ConnectedValue\"}}, \"g2m_genes\": {\"format\": \"file\", \"__current_case__\": 1, \"file\": {\"__class__\": \"ConnectedValue\"}}, \"n_bins\": \"25\", \"random_state\": \"0\", \"use_raw\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy0",
+                        "type": "tool",
+                        "uuid": "11e0487f-e5a9-44c1-b3e5-2fe50ee207d4",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "anndata_out",
+                                "uuid": "0852740e-92ea-496a-bfeb-86184b8f8570"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "singtabop|input": {
+                                "id": 4,
+                                "output_name": "var"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Table Compute",
+                        "outputs": [
+                            {
+                                "name": "table",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 781.4375,
+                            "top": 125.09375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "93a3ce78ce55",
+                            "name": "table_compute",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"out_opts\": [\"ignore_nas\"], \"precision\": \"6\", \"singtabop\": {\"use_type\": \"single\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"col_row_names\": null, \"adv\": {\"header\": null, \"nrows\": null, \"skipfooter\": null, \"skip_blank_lines\": \"true\"}, \"user\": {\"mode\": \"select\", \"__current_case__\": 1, \"select_cols_wanted\": \"1\", \"select_rows_wanted\": \"2:15396\", \"select_keepdupe\": [\"select_cols_keepdupe\", \"select_rows_keepdupe\"]}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.4+galaxy0",
+                        "type": "tool",
+                        "uuid": "e02f60d9-596f-4e18-9770-633ac1fc9a5a",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "table",
+                                "uuid": "ddb059b1-92b2-4989-8313-dbd144a11269"
+                            }
+                        ]
                     },
                     {
-                        "hash": "914bf924a609d64b3f3f69d8b78b44a584d90581",
-                        "message": "ebi scxa updated workflow tests",
-                        "num": 1,
-                        "short_hash": "914bf924a",
-                        "unix": "1702547068"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "EBI Single Cell Atlas accession for the experiment that you want to retrieve.",
-                        "content_id": null,
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 8,
+                        "input_connections": {
+                            "input": {
+                                "id": 5,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Add column",
+                        "outputs": [
                             {
-                                "description": "EBI Single Cell Atlas accession for the experiment that you want to retrieve.",
-                                "name": "SC-Atlas experiment accession"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
-                        "label": "SC-Atlas experiment accession",
-                        "name": "Input parameter",
-                        "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 0
+                            "left": 730.125,
+                            "top": 940.9375
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": \"E-MTAB-6945\", \"parameter_type\": \"text\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "ca016294-33ee-47fc-9a42-36a0288d353d",
-                        "when": null,
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "745871c0b055",
+                            "name": "add_value",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"exp\": \"TRUE\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "8270c2b8-343c-4a96-918e-7615844a9e08",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "dcf5b67e-9773-4ca5-8e33-b0f875e91d77"
+                                "output_name": "out_file1",
+                                "uuid": "11c1edc1-5969-4b69-939f-8b3ef484a28d"
                             }
                         ]
-                    }
-                ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nSC-Atlas experiment accession\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"EBI SCXA Data Retrieval\"];\n  0 -->|output| 1;\n  2[\"Rename batch numbers\"];\n  1 -->|design_tsv| 2;\n  3[\"Mito genes check\"];\n  1 -->|genes_tsv| 3;\n  b0762cfd-58bd-4c39-ae41-2dca4289c541[\"Output\\nMito genes check\"];\n  3 --> b0762cfd-58bd-4c39-ae41-2dca4289c541;\n  style b0762cfd-58bd-4c39-ae41-2dca4289c541 stroke:#2c3143,stroke-width:4px;\n  4[\"Rename cell metadata headers\"];\n  2 -->|out_file1| 4;\n  5[\"Create AnnData\"];\n  1 -->|barcode_tsv| 5;\n  4 -->|outfile| 5;\n  1 -->|genes_tsv| 5;\n  1 -->|matrix_mtx| 5;\n  938cd594-61cf-4037-a58b-c09c065db505[\"Output\\nAnnData object\"];\n  5 --> 938cd594-61cf-4037-a58b-c09c065db505;\n  style 938cd594-61cf-4037-a58b-c09c065db505 stroke:#2c3143,stroke-width:4px;\n  6[\"Seurat Read10x\"];\n  1 -->|barcode_tsv| 6;\n  1 -->|genes_tsv| 6;\n  1 -->|matrix_mtx| 6;\n  4 -->|outfile| 6;\n  c24e9d83-c175-40a2-9c36-eeb486fe323e[\"Output\\nSeurat object\"];\n  6 --> c24e9d83-c175-40a2-9c36-eeb486fe323e;\n  style c24e9d83-c175-40a2-9c36-eeb486fe323e stroke:#2c3143,stroke-width:4px;\n  7[\"AnnData Operations\"];\n  5 -->|output_h5ad| 7;\n  b47f801f-bedb-4136-a5e9-378a815a1799[\"Output\\nMito-counted AnnData for downstream analysis\"];\n  7 --> b47f801f-bedb-4136-a5e9-378a815a1799;\n  style b47f801f-bedb-4136-a5e9-378a815a1799 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "EBI SCXA to AnnData (Scanpy) or Seurat Object",
-                "outputs": [
+                    },
                     {
-                        "annotation": "EBI Single Cell Atlas accession for the experiment that you want to retrieve.",
-                        "content_id": null,
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_regress_variable/scanpy_regress_variable/1.8.1+galaxy0",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 9,
+                        "input_connections": {
+                            "input_obj_file": {
+                                "id": 6,
+                                "output_name": "anndata_out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Scanpy RegressOut",
+                        "outputs": [
                             {
-                                "description": "EBI Single Cell Atlas accession for the experiment that you want to retrieve.",
-                                "name": "SC-Atlas experiment accession"
+                                "name": "output_h5ad",
+                                "type": "h5ad"
                             }
                         ],
-                        "label": "SC-Atlas experiment accession",
-                        "name": "Input parameter",
-                        "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 0
+                            "left": 2373.3958740234375,
+                            "top": 934.0416870117188
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": \"E-MTAB-6945\", \"parameter_type\": \"text\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "ca016294-33ee-47fc-9a42-36a0288d353d",
-                        "when": null,
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_regress_variable/scanpy_regress_variable/1.8.1+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "36daab33aecf",
+                            "name": "scanpy_regress_variable",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"save_layer\": \"\", \"save_raw\": \"false\", \"variable_keys\": \"phase\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
+                        "type": "tool",
+                        "uuid": "5624944c-4504-4d72-8692-363ae5419e34",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "dcf5b67e-9773-4ca5-8e33-b0f875e91d77"
+                                "label": "Scanpy RegressOut on input dataset(s): Regressed out  AnnData",
+                                "output_name": "output_h5ad",
+                                "uuid": "026b02d3-97ee-4847-9347-40773ab76356"
                             }
                         ]
                     },
                     {
-                        "annotation": "Shows how mitochondrial genes are annotated.",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
                         "errors": null,
-                        "id": 3,
+                        "id": 10,
                         "input_connections": {
-                            "infile": {
-                                "id": 1,
-                                "output_name": "genes_tsv"
+                            "input": {
+                                "id": 7,
+                                "output_name": "table"
                             }
                         },
                         "inputs": [],
-                        "label": "Mito genes check",
-                        "name": "Search in textfiles",
+                        "label": null,
+                        "name": "Add column",
                         "outputs": [
                             {
-                                "name": "output",
+                                "name": "out_file1",
                                 "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 791.9068204609299,
-                            "top": 717.1702369809638
+                            "left": 1190.8125,
+                            "top": 142.65625
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Mito genes check"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "745871c0b055",
+                            "name": "add_value",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"exp\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"yes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "3920392c-5481-42be-aa3c-e0ae807d145d",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "27b6bae1-3786-4cbb-a943-e792f4320bc4"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                        "errors": null,
+                        "id": 11,
+                        "input_connections": {
+                            "infile1": {
+                                "id": 10,
+                                "output_name": "out_file1"
+                            },
+                            "infile2": {
+                                "id": 8,
+                                "output_name": "out_file1"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Join",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1471.15625,
+                            "top": 154.25
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
                         "tool_shed_repository": {
                             "changeset_revision": "ddf54b12c295",
                             "name": "text_processing",
                             "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tsv\", \"case_sensitive\": \"-i\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"color\": \"COLOR\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-P\", \"url_paste\": \"mt\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "tool_state": "{\"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \"FALSE\", \"header\": \"false\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \"-a 1 -a 2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.2",
                         "type": "tool",
-                        "uuid": "51b0361d-00dd-45cf-98db-90b2242b6cb3",
-                        "when": null,
+                        "uuid": "ea5dbe23-1636-4f14-ad7d-7d9c0926115c",
                         "workflow_outputs": [
                             {
-                                "label": "Mito genes check",
+                                "label": null,
                                 "output_name": "output",
-                                "uuid": "b0762cfd-58bd-4c39-ae41-2dca4289c541"
+                                "uuid": "48e95afc-ac2c-4ab8-80a6-224bf9486af8"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy9",
+                        "content_id": "sort1",
                         "errors": null,
-                        "id": 5,
+                        "id": 12,
                         "input_connections": {
-                            "barcodes": {
-                                "id": 1,
-                                "output_name": "barcode_tsv"
-                            },
-                            "cell_meta": {
-                                "id": 4,
-                                "output_name": "outfile"
-                            },
-                            "genes": {
-                                "id": 1,
-                                "output_name": "genes_tsv"
+                            "input": {
+                                "id": 11,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Sort",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1733.7083740234375,
+                            "top": 146.0625
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "sort1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"__workflow_invocation_uuid__\": \"4cdf4fce5b9d11edba32001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"column\": \"2\", \"column_set\": [], \"header_lines\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"order\": \"ASC\", \"style\": \"num\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.0",
+                        "type": "tool",
+                        "uuid": "0e870357-b257-4e99-9d7e-06775c763579",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "735a9c42-3440-4370-9ef4-755c081ef2cc"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0",
+                        "errors": null,
+                        "id": 13,
+                        "input_connections": {
+                            "singtabop|input": {
+                                "id": 12,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Table Compute",
+                        "outputs": [
+                            {
+                                "name": "table",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 1953.6875,
+                            "top": 146.0625
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "93a3ce78ce55",
+                            "name": "table_compute",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"out_opts\": [\"ignore_nas\"], \"precision\": \"6\", \"singtabop\": {\"use_type\": \"single\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"col_row_names\": null, \"adv\": {\"header\": null, \"nrows\": null, \"skipfooter\": null, \"skip_blank_lines\": \"true\"}, \"user\": {\"mode\": \"select\", \"__current_case__\": 1, \"select_cols_wanted\": \"3\", \"select_rows_wanted\": \"1:15395\", \"select_keepdupe\": [\"select_cols_keepdupe\", \"select_rows_keepdupe\"]}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.2.4+galaxy0",
+                        "type": "tool",
+                        "uuid": "45f07fc8-3ff4-4e21-a1a6-7a764986930f",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "table",
+                                "uuid": "58fbdecd-859a-42a6-a166-980a2625e01f"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "cat1",
+                        "errors": null,
+                        "id": 14,
+                        "input_connections": {
+                            "input1": {
+                                "id": 3,
+                                "output_name": "output"
                             },
-                            "matrix": {
-                                "id": 1,
-                                "output_name": "matrix_mtx"
+                            "queries_0|input2": {
+                                "id": 13,
+                                "output_name": "table"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Concatenate datasets",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool Scanpy Read10x",
-                                "name": "gene_meta"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
-                        "label": "Create AnnData",
-                        "name": "Scanpy Read10x",
+                        "position": {
+                            "left": 2173.65625,
+                            "top": 146.0625
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "cat1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"__workflow_invocation_uuid__\": \"4cdf4fce5b9d11edba32001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [{\"__index__\": 0, \"input2\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "92d869ca-9989-4699-8069-1632a4c3d159",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "b946b4c9-ad29-4f7e-b2bc-2023265bdc10"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
+                        "errors": null,
+                        "id": 16,
+                        "input_connections": {
+                            "input": {
+                                "id": 9,
+                                "output_name": "output_h5ad"
+                            },
+                            "manipulate|new_annot": {
+                                "id": 14,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Manipulate AnnData",
                         "outputs": [
                             {
-                                "name": "output_h5ad",
+                                "name": "anndata",
                                 "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 1025.6788601346032,
-                            "top": 534.8213953419395
+                            "left": 2813.729248046875,
+                            "top": 194.28125
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_h5ad": {
-                                "action_arguments": {
-                                    "newname": "AnnData object"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_h5ad"
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3d748954434b",
+                            "name": "anndata_manipulate",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"add_annotation\", \"__current_case__\": 6, \"var_obs\": \"var\", \"new_annot\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "b441e4be-4438-4e6e-8ba7-b4cfd3be4eb0",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "anndata",
+                                "uuid": "b7370b49-ef2f-4427-8ea0-70f8159efd3c"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
+                        "errors": null,
+                        "id": 17,
+                        "input_connections": {
+                            "input": {
+                                "id": 15,
+                                "output_name": "anndata"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy9",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Manipulate AnnData",
+                        "outputs": [
+                            {
+                                "name": "anndata",
+                                "type": "h5ad"
+                            }
+                        ],
+                        "position": {
+                            "left": 2794.041748046875,
+                            "top": 1071.2396240234375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "9afcfcd1d215",
-                            "name": "scanpy_read_10x",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "3d748954434b",
+                            "name": "anndata_manipulate",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"barcodes\": {\"__class__\": \"ConnectedValue\"}, \"cell_meta\": {\"__class__\": \"ConnectedValue\"}, \"gene_meta\": {\"__class__\": \"RuntimeValue\"}, \"genes\": {\"__class__\": \"ConnectedValue\"}, \"matrix\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"var_names\": \"gene_ids\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"filter\", \"__current_case__\": 7, \"var_obs\": \"var\", \"filter\": {\"filter\": \"key\", \"__current_case__\": 0, \"key\": \"CC_genes\", \"filter_key\": {\"type\": \"boolean\", \"__current_case__\": 2, \"value\": \"true\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.5+galaxy1",
                         "type": "tool",
-                        "uuid": "e02346a9-9da0-40fc-85ef-3492cbb73b44",
-                        "when": null,
+                        "uuid": "82e3a365-be59-4ca8-a82d-596c7b4056ba",
                         "workflow_outputs": [
                             {
-                                "label": "AnnData object",
-                                "output_name": "output_h5ad",
-                                "uuid": "938cd594-61cf-4037-a58b-c09c065db505"
+                                "label": null,
+                                "output_name": "anndata",
+                                "uuid": "3c56a2bd-26d8-4566-b9f9-0f0896651f8c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/3.2.3+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
                         "errors": null,
-                        "id": 6,
+                        "id": 18,
                         "input_connections": {
-                            "input|barcodes": {
-                                "id": 1,
-                                "output_name": "barcode_tsv"
-                            },
-                            "input|genes": {
-                                "id": 1,
-                                "output_name": "genes_tsv"
-                            },
-                            "input|matrix": {
-                                "id": 1,
-                                "output_name": "matrix_mtx"
-                            },
-                            "metadata": {
-                                "id": 4,
-                                "output_name": "outfile"
+                            "input": {
+                                "id": 16,
+                                "output_name": "anndata"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Seurat Read10x",
+                        "name": "Manipulate AnnData",
                         "outputs": [
                             {
-                                "name": "rds_seurat_file",
-                                "type": "rdata"
+                                "name": "anndata",
+                                "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 1564.7962994380462,
-                            "top": 864.6368384275628
+                            "left": 2826,
+                            "top": 690.625
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionrds_seurat_file": {
-                                "action_arguments": {
-                                    "newname": "Seurat object"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "rds_seurat_file"
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3d748954434b",
+                            "name": "anndata_manipulate",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"filter\", \"__current_case__\": 7, \"var_obs\": \"var\", \"filter\": {\"filter\": \"key\", \"__current_case__\": 0, \"key\": \"CC_genes\", \"filter_key\": {\"type\": \"boolean\", \"__current_case__\": 2, \"value\": \"true\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "77b6cf83-c02a-49c4-9ae4-c02fa88510d5",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "anndata",
+                                "uuid": "8968536f-6774-4b4f-b1cf-0535133911f7"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
+                        "errors": null,
+                        "id": 19,
+                        "input_connections": {
+                            "adata": {
+                                "id": 17,
+                                "output_name": "anndata"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/3.2.3+galaxy0",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Cluster, infer trajectories and embed",
+                        "outputs": [
+                            {
+                                "name": "anndata_out",
+                                "type": "h5ad"
+                            }
+                        ],
+                        "position": {
+                            "left": 3119.666748046875,
+                            "top": 1062.2396240234375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "301cf1b4b43d",
-                            "name": "seurat_read10x",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "aaa5da8e73a9",
+                            "name": "scanpy_cluster_reduce_dimension",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"rds_seurat\", \"input\": {\"format\": \"mtx\", \"__current_case__\": 1, \"matrix\": {\"__class__\": \"ConnectedValue\"}, \"genes\": {\"__class__\": \"ConnectedValue\"}, \"barcodes\": {\"__class__\": \"ConnectedValue\"}}, \"metadata\": {\"__class__\": \"ConnectedValue\"}, \"min_cells\": null, \"min_features\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.2.3+galaxy0",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"method\": {\"method\": \"tl.pca\", \"__current_case__\": 3, \"n_comps\": \"50\", \"dtype\": \"float32\", \"pca\": {\"chunked\": \"False\", \"__current_case__\": 1, \"zero_center\": \"true\", \"svd_solver\": \"auto\", \"random_state\": \"0\"}, \"use_highly_variable\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy0",
                         "type": "tool",
-                        "uuid": "1aa185bd-1392-438d-adea-21ed201bc9db",
-                        "when": null,
+                        "uuid": "0dc6efda-15c2-4c62-a381-887c3d29c017",
                         "workflow_outputs": [
                             {
-                                "label": "Seurat object",
-                                "output_name": "rds_seurat_file",
-                                "uuid": "c24e9d83-c175-40a2-9c36-eeb486fe323e"
+                                "label": null,
+                                "output_name": "anndata_out",
+                                "uuid": "b194bcae-6ae7-494d-ba15-68a6b14e59f3"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy92",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
                         "errors": null,
-                        "id": 7,
+                        "id": 20,
                         "input_connections": {
-                            "input_obj_file": {
-                                "id": 5,
-                                "output_name": "output_h5ad"
+                            "adata": {
+                                "id": 18,
+                                "output_name": "anndata"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "AnnData Operations",
+                        "name": "Cluster, infer trajectories and embed",
                         "outputs": [
                             {
-                                "name": "output_h5ad",
+                                "name": "anndata_out",
                                 "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 1310.0874938964844,
-                            "top": 792.8125610351562
+                            "left": 3115.635498046875,
+                            "top": 699.0
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_h5ad": {
-                                "action_arguments": {
-                                    "newname": "Mito-counted AnnData for downstream analysis"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_h5ad"
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "aaa5da8e73a9",
+                            "name": "scanpy_cluster_reduce_dimension",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"method\": {\"method\": \"tl.pca\", \"__current_case__\": 3, \"n_comps\": \"50\", \"dtype\": \"float32\", \"pca\": {\"chunked\": \"False\", \"__current_case__\": 1, \"zero_center\": \"true\", \"svd_solver\": \"auto\", \"random_state\": \"0\"}, \"use_highly_variable\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy0",
+                        "type": "tool",
+                        "uuid": "c776b1f6-4eac-40fa-9f19-1fb8fb2b530e",
+                        "workflow_outputs": [
+                            {
+                                "label": "Cluster, infer trajectories and embed (tl.louvain) on input dataset(s): Annotated data matrix",
+                                "output_name": "anndata_out",
+                                "uuid": "09d97ef7-ed92-4d90-a597-2032581c2d4a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "errors": null,
+                        "id": 21,
+                        "input_connections": {
+                            "adata": {
+                                "id": 19,
+                                "output_name": "anndata_out"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy92",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot",
+                        "outputs": [
+                            {
+                                "name": "out_png",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 3397.70849609375,
+                            "top": 1056.2708740234375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "a0274bc43b7e",
-                            "name": "anndata_ops",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "aa0c474463c2",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"add_cell_metadata\": {\"default\": false, \"__current_case__\": 1}, \"copy_adata_to_raw\": false, \"copy_e\": {\"default\": false, \"__current_case__\": 1}, \"copy_l\": {\"default\": false, \"__current_case__\": 1}, \"copy_o\": {\"default\": false, \"__current_case__\": 1}, \"copy_r\": {\"default\": false, \"__current_case__\": 1}, \"copy_u\": {\"default\": false, \"__current_case__\": 1}, \"copy_x\": {\"default\": false, \"__current_case__\": 1}, \"field_unique\": null, \"gene_flags\": [{\"__index__\": 0, \"startswith\": \"mt-\", \"flag\": \"mito\"}], \"gene_symbols_field\": \"Symbol\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": false, \"split_on_obs\": {\"default\": false, \"__current_case__\": 1}, \"swap_layer_to_x\": {\"default\": false, \"__current_case__\": 1}, \"top_genes\": \"50\", \"var_modifications\": [{\"__index__\": 0, \"from_var\": \"gene_symbols\", \"to_var\": \"Symbol\", \"keep_original\": false, \"make_unique\": false}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy92",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.pca_overview\", \"__current_case__\": 12, \"color\": \"phase\", \"use_raw\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy1",
                         "type": "tool",
-                        "uuid": "b4616c2c-96f1-4474-97f3-cdbecd37e65b",
-                        "when": null,
+                        "uuid": "500c400f-02e5-40ab-8e33-684ecef4aeff",
                         "workflow_outputs": [
                             {
-                                "label": "Mito-counted AnnData for downstream analysis",
-                                "output_name": "output_h5ad",
-                                "uuid": "b47f801f-bedb-4136-a5e9-378a815a1799"
+                                "label": null,
+                                "output_name": "out_png",
+                                "uuid": "908ff564-db8c-41e3-90e8-fee85df325d0"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "errors": null,
+                        "id": 22,
+                        "input_connections": {
+                            "adata": {
+                                "id": 20,
+                                "output_name": "anndata_out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot",
+                        "outputs": [
+                            {
+                                "name": "out_png",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 3411.70849609375,
+                            "top": 726.2291870117188
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "aa0c474463c2",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.pca_overview\", \"__current_case__\": 12, \"color\": \"phase\", \"use_raw\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy1",
+                        "type": "tool",
+                        "uuid": "beb0ba6d-3a0f-4bec-a045-3cdf62053d6d",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_png",
+                                "uuid": "9737f727-e959-4773-b964-38b225b7c7ee"
                             }
                         ]
                     }
                 ],
-                "parent_id": "single-cell/EBI-retrieval",
-                "path": "topics/single-cell/tutorials/EBI-retrieval/workflows/EBI-SCXA-to-AnnData-(Scanpy)-or-Seurat-Object.ga",
-                "tags": [],
+                "parent_id": "single-cell/scrna-case_cell-cycle",
+                "path": "topics/single-cell/tutorials/scrna-case_cell-cycle/workflows/main_workflow.ga",
+                "tags": [
+                    "single-cell",
+                    "10x",
+                    "transcriptomics"
+                ],
                 "test_results": null,
-                "tests": true,
-                "title": "EBI SCXA to AnnData (Scanpy) or Seurat Object",
+                "tests": false,
+                "title": "Cell Cycle Regression Workflow",
                 "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-EBI-retrieval/versions/ebi-scxa-to-anndata--scanpy--or-seurat-object",
-                "tutorial_id": "EBI-retrieval",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/EBI-retrieval/workflows/EBI-SCXA-to-AnnData-(Scanpy)-or-Seurat-Object.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/EBI-retrieval/workflows/EBI-SCXA-to-AnnData-(Scanpy)-or-Seurat-Object.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-case_cell-cycle/versions/main-workflow",
+                "tutorial_id": "scrna-case_cell-cycle",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_cell-cycle/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_cell-cycle/workflows/main_workflow.html",
                 "version": 1,
-                "wfid": "single-cell-EBI-retrieval",
-                "wfname": "ebi-scxa-to-anndata--scanpy--or-seurat-object",
-                "workflow": "EBI-SCXA-to-AnnData-(Scanpy)-or-Seurat-Object.ga",
+                "wfid": "single-cell-scrna-case_cell-cycle",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy92",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/3.2.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3"
+                    "cat1",
+                    "sort1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_regress_variable/scanpy_regress_variable/1.8.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0"
                 ],
-                "workflowhub_id": "1210"
+                "workflowhub_id": "1246"
             }
-        ]
+        ],
+        "zenodo_link": "https://zenodo.org/record/7311628/"
     },
     {
         "admin_install": {
@@ -226443,92 +231162,74 @@
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "add_value",
-                    "owner": "devteam",
-                    "revisions": "745871c0b055",
+                    "revisions": "12615d397df7",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_regress_variable",
+                    "name": "anndata_ops",
                     "owner": "ebi-gxa",
-                    "revisions": "36daab33aecf",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "anndata_inspect",
-                    "owner": "iuc",
-                    "revisions": "ee98d611afc6",
+                    "revisions": "a4774b7b2e85",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "anndata_manipulate",
-                    "owner": "iuc",
-                    "revisions": "3d748954434b",
+                    "name": "retrieve_scxa",
+                    "owner": "ebi-gxa",
+                    "revisions": "72b6e1747e37",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_cluster_reduce_dimension",
-                    "owner": "iuc",
-                    "revisions": "aaa5da8e73a9",
+                    "name": "scanpy_read_10x",
+                    "owner": "ebi-gxa",
+                    "revisions": "9afcfcd1d215",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_inspect",
+                    "name": "anndata_inspect",
                     "owner": "iuc",
-                    "revisions": "c5d3684f7c4c",
+                    "revisions": "6f0d0c784f09",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_plot",
+                    "name": "anndata_manipulate",
                     "owner": "iuc",
-                    "revisions": "aa0c474463c2",
+                    "revisions": "ed4996a16f7f",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "table_compute",
-                    "owner": "iuc",
-                    "revisions": "3bf5661c0280",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: add_value\n  owner: devteam\n  revisions: 745871c0b055\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_regress_variable\n  owner: ebi-gxa\n  revisions: 36daab33aecf\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_inspect\n  owner: iuc\n  revisions: ee98d611afc6\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n  owner: iuc\n  revisions: 3d748954434b\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_cluster_reduce_dimension\n  owner: iuc\n  revisions: aaa5da8e73a9\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_inspect\n  owner: iuc\n  revisions: c5d3684f7c4c\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot\n  owner: iuc\n  revisions: aa0c474463c2\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: table_compute\n  owner: iuc\n  revisions: 3bf5661c0280\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: 12615d397df7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_ops\n  owner: ebi-gxa\n  revisions: a4774b7b2e85\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: retrieve_scxa\n  owner: ebi-gxa\n  revisions: 72b6e1747e37\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_read_10x\n  owner: ebi-gxa\n  revisions: 9afcfcd1d215\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_inspect\n  owner: iuc\n  revisions: 6f0d0c784f09\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n  owner: iuc\n  revisions: ed4996a16f7f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "answer_histories": [
+            {
+                "date": "2024-03-26",
+                "history": "https://usegalaxy.eu/u/j.jakiela/h/combining-datasets-key-history",
+                "label": "UseGalaxy.eu"
+            },
+            {
+                "date": "2024-03-26",
+                "history": "https://usegalaxy.eu/u/j.jakiela/h/all-total-samples-processed-after-alevin-into-single-object",
+                "label": "All total samples - processed after Alevin into single object (UseGalaxy.eu)"
+            }
+        ],
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.json",
         "contributions": {
             "authorship": [
-                "MarisaJL"
+                "nomadscientist",
+                "pinin4fjords"
             ],
             "editing": [
-                "nomadscientist"
+                "hexylena"
             ],
             "testing": [
-                "hrukkudyr"
+                "wee-snufkin"
             ]
         },
         "contributors": [
-            {
-                "email": "marisa.loach@open.ac.uk",
-                "id": "MarisaJL",
-                "joined": "2022-10",
-                "name": "Marisa Loach",
-                "orcid": "0000-0001-6979-6930",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/MarisaJL/",
-                "twitter": "Marisa_Loach",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/MarisaJL.json"
-            },
             {
                 "affiliations": [
                     "elixir-europe"
@@ -226548,80 +231249,163 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
             },
             {
-                "email": "grt67@open.ac.uk",
-                "id": "hrukkudyr",
-                "joined": "2022-09",
-                "name": "Graeme Tyson",
-                "orcid": "0000-0002-1748-2806",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hrukkudyr/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hrukkudyr.json"
+                "email": "jmanning@ebi.ac.uk",
+                "id": "pinin4fjords",
+                "joined": "2021-02",
+                "name": "Jonathan Manning",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pinin4fjords/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pinin4fjords.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "elixir_node": "uk",
+                "email": "juliajot36@gmail.com",
+                "id": "wee-snufkin",
+                "joined": "2022-06",
+                "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
             }
         ],
-        "dir": "topics/single-cell/tutorials/scrna-case_cell-cycle",
-        "edam_operation": [
-            "Differential gene expression analysis"
-        ],
+        "dir": "topics/single-cell/tutorials/scrna-case_alevin-combine-datasets",
+        "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-case_basic-pipeline"
+                ],
+                "type": "internal"
+            }
+        ],
+        "gitter": "Galaxy-Training-Network/galaxy-single-cell",
         "hands_on": true,
-        "id": "single-cell/scrna-case_cell-cycle",
+        "id": "single-cell/scrna-case_alevin-combine-datasets",
         "inexact_supported_servers": [
+            "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
+        "input_histories": [
+            {
+                "history": "https://usegalaxy.eu/u/j.jakiela/h/combining-datasets-input",
+                "label": "UseGalaxy.eu"
+            },
+            {
+                "history": "https://usegalaxy.org/u/juliajot/h/combining-datasets-input",
+                "label": "UseGalaxy.org"
+            }
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Cell cycle genes can conceal what is happening in your data if cells are grouping together according to their stage in the cycle",
-            "Identifying the cell cycle genes and using them to regress out the effects of the cell cycle can reveal underlying patterns in the data"
+            "Create a single scanpy-accessible AnnData object from multiple AnnData files, including relevant cell metadata according to the study design",
+            "Retreive partially analysed data from a public repository"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-09-27",
         "objectives": [
-            "Identify the cell cycle genes",
-            "Use the cell cycle genes to regress out the effects of the cell cycle",
-            "Create PCA plots to understand the impact of the regression"
+            "Combine data matrices from different samples in the same experiment",
+            "Label the metadata for downstream processing"
         ],
-        "pageviews": 1603,
+        "pageviews": 2665,
         "priority": 2,
-        "pub_date": "2023-01-25",
+        "pub_date": "2022-09-08",
         "questions": [
-            "How can I reduce the effects of the cell cycle on my scRNA-seq data?"
+            "I have some AnnData files from different samples that I want to combine into a single file. How can I combine these and label them within the object?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "hrukkudyr"
+                ],
+                "date": "2023-05-09",
+                "length": "11M",
+                "speakers": [
+                    "hrukkudyr"
+                ],
+                "youtube_id": "22t-4qvHnow"
+            },
+            {
+                "captioners": [
+                    "nomadscientist"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.09",
+                "length": "11M",
+                "speakers": [
+                    "nomadscientist"
+                ],
+                "youtube_id": "U8pVa6csmUE"
+            }
+        ],
+        "redirect_from": [
+            "/topics/transcriptomics/tutorials/scrna-case_alevin-combine-datasets/tutorial",
+            "/short/single-cell/scrna-case_alevin-combine-datasets",
+            "/short/T00246"
         ],
         "requirements": [
             {
                 "topic_name": "single-cell",
                 "tutorials": [
-                    "scrna-case_alevin",
-                    "scrna-case_alevin-combine-datasets",
-                    "scrna-case_basic-pipeline"
+                    "scrna-intro",
+                    "scrna-umis",
+                    "scrna-case_alevin"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00248",
+        "short_id": "T00246",
         "short_tools": [
-            "anndata_manipulate",
-            "cat1",
+            "retrieve_scxa",
+            "Paste1",
+            "anndata_ops",
             "anndata_inspect",
-            "scanpy_inspect",
-            "scanpy_plot",
-            "sort1",
-            "tp_easyjoin_tool",
-            "scanpy_regress_variable",
-            "scanpy_cluster_reduce_dimension",
-            "table_compute",
-            "addValue"
+            "Cut1",
+            "anndata_manipulate",
+            "scanpy_read_10x",
+            "tp_replace_in_column"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "tricks",
+        "subtopic": "single-cell-CS",
         "supported_servers": {
             "exact": [
                 {
@@ -226631,6 +231415,11 @@
                 }
             ],
             "inexact": [
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
@@ -226640,22 +231429,20 @@
         },
         "symlink": null,
         "tags": [
-            "10x"
+            "10x",
+            "paper-replication"
         ],
         "time_estimation": "1H",
-        "title": "Removing the effects of the cell cycle",
+        "title": "Combining single cell datasets after pre-processing",
         "tools": [
-            "cat1",
-            "sort1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_regress_variable/scanpy_regress_variable/1.8.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0"
+            "Cut1",
+            "Paste1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0"
         ],
         "topic_name": "single-cell",
         "topic_name_human": "Single Cell",
@@ -226665,612 +231452,442 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "scrna-case_cell-cycle",
+        "tutorial_name": "scrna-case_alevin-combine-datasets",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_cell-cycle/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.json"
         },
-        "version": 11,
+        "version": 18,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 48,
-        "visitors": 1329,
+        "visit_duration": 144,
+        "visitors": 1846,
         "workflows": [
             {
-                "creators": [],
-                "description": "",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0009-0001-2017-8805",
+                        "name": "Julia Jakiela"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-8170-8806",
+                        "name": "Wendi Bacon"
+                    }
+                ],
+                "description": "Updated March 2024",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAnnData After QC, normalisation, scaling\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nS Phase Genes\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nG2M Phase Genes\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPasted Entry\"]\n  4[label=\"Inspect AnnData\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"All Cell Cycle Genes Concatenate S and G2M Genes\"]\n  1 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"Inspect and manipulate\"]\n  0 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"Table Compute\"]\n  4 -> 7 [label=\"var\"]\n  8[label=\"Add column\"]\n  5 -> 8 [label=\"out_file1\"]\n  9[label=\"Scanpy RegressOut\"]\n  6 -> 9 [label=\"anndata_out\"]\n  k026b02d397ee4847934740773ab76356[color=lightseagreen,label=\"Output\\nScanpy RegressOut on input dataset(s): Regressed out  AnnData\"]\n  9 -> k026b02d397ee4847934740773ab76356\n  10[label=\"Add column\"]\n  7 -> 10 [label=\"table\"]\n  11[label=\"Join\"]\n  10 -> 11 [label=\"out_file1\"]\n  8 -> 11 [label=\"out_file1\"]\n  12[label=\"Sort\"]\n  11 -> 12 [label=\"output\"]\n  13[label=\"Table Compute\"]\n  12 -> 13 [label=\"out_file1\"]\n  14[label=\"Concatenate datasets\"]\n  3 -> 14 [label=\"output\"]\n  13 -> 14 [label=\"table\"]\n  15[label=\"Manipulate AnnData\"]\n  6 -> 15 [label=\"anndata_out\"]\n  14 -> 15 [label=\"out_file1\"]\n  16[label=\"Manipulate AnnData\"]\n  9 -> 16 [label=\"output_h5ad\"]\n  14 -> 16 [label=\"out_file1\"]\n  17[label=\"Manipulate AnnData\"]\n  15 -> 17 [label=\"anndata\"]\n  18[label=\"Manipulate AnnData\"]\n  16 -> 18 [label=\"anndata\"]\n  19[label=\"Cluster, infer trajectories and embed\"]\n  17 -> 19 [label=\"anndata\"]\n  20[label=\"Cluster, infer trajectories and embed\"]\n  18 -> 20 [label=\"anndata\"]\n  k09d97ef7ed924d90a5972032581c2d4a[color=lightseagreen,label=\"Output\\nCluster, infer trajectories and embed (tl.louvain) on input dataset(s): Annotated data matrix\"]\n  20 -> k09d97ef7ed924d90a5972032581c2d4a\n  21[label=\"Plot\"]\n  19 -> 21 [label=\"anndata_out\"]\n  22[label=\"Plot\"]\n  20 -> 22 [label=\"anndata_out\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nN701\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nN702\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nN703\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nN704\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nN705\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nN706\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nN707\"]\n  7[label=\"Concatenating Datasets\"]\n  0 -> 7 [label=\"output\"]\n  1 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  3 -> 7 [label=\"output\"]\n  4 -> 7 [label=\"output\"]\n  5 -> 7 [label=\"output\"]\n  6 -> 7 [label=\"output\"]\n  k168d4710570a43b1998a2164154eebc5[color=lightseagreen,label=\"Output\\nCombined Object\"]\n  7 -> k168d4710570a43b1998a2164154eebc5\n  8[label=\"Inspect AnnData\"]\n  7 -> 8 [label=\"anndata\"]\n  9[label=\"Inspect AnnData\"]\n  7 -> 9 [label=\"anndata\"]\n  10[label=\"Inspect AnnData\"]\n  7 -> 10 [label=\"anndata\"]\n  11[label=\"Replace Text\"]\n  9 -> 11 [label=\"obs\"]\n  12[label=\"Replace Text\"]\n  9 -> 12 [label=\"obs\"]\n  13[label=\"Cut\"]\n  11 -> 13 [label=\"outfile\"]\n  k8b026c35f9db4bcd8cf554b7d6fb5aea[color=lightseagreen,label=\"Output\\nSex metadata\"]\n  13 -> k8b026c35f9db4bcd8cf554b7d6fb5aea\n  14[label=\"Cut\"]\n  12 -> 14 [label=\"outfile\"]\n  k6f55548b5ded42b8b2f7c7f1a327a068[color=lightseagreen,label=\"Output\\nGenotype metadata\"]\n  14 -> k6f55548b5ded42b8b2f7c7f1a327a068\n  15[label=\"Paste\"]\n  14 -> 15 [label=\"out_file1\"]\n  13 -> 15 [label=\"out_file1\"]\n  k2f0ea0f3f2f744b2b8f005d8cbb364a6[color=lightseagreen,label=\"Output\\nCell metadata\"]\n  15 -> k2f0ea0f3f2f744b2b8f005d8cbb364a6\n  16[label=\"Adding in cell metadata\"]\n  7 -> 16 [label=\"anndata\"]\n  15 -> 16 [label=\"out_file1\"]\n  k2720386c727349d6abb09bd14f6cb68c[color=lightseagreen,label=\"Output\\nAnnData with Cell Metadata\"]\n  16 -> k2720386c727349d6abb09bd14f6cb68c\n  17[label=\"Batching Cell Metadata\"]\n  16 -> 17 [label=\"anndata\"]\n  kb950c8dbabe14cb0af58d291d3b74a83[color=lightseagreen,label=\"Output\\nBatched Object\"]\n  17 -> kb950c8dbabe14cb0af58d291d3b74a83\n  18[label=\"Calculating mitochondrial \"]\n  17 -> 18 [label=\"anndata\"]\n  k2417284d825243ff84bf6f15ef11cd05[color=lightseagreen,label=\"Output\\nAnnotated AnnData\"]\n  18 -> k2417284d825243ff84bf6f15ef11cd05\n}",
                 "history": [
                     {
-                        "hash": "f70e87e49ec1315f959cb4532d667ab976ae61f4",
-                        "message": "Moving to single cell",
+                        "hash": "923c71c756c805a4ce7f2b794fa721aa6a4966f4",
+                        "message": "workflow tests",
                         "num": 1,
-                        "short_hash": "f70e87e49",
-                        "unix": "1669054986"
+                        "short_hash": "923c71c75",
+                        "unix": "1711487790"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "",
+                        "annotation": "Dataset to be combined",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "AnnData (After QC, normalisation, scaling)"
+                                "description": "Dataset to be combined",
+                                "name": "N701"
                             }
                         ],
-                        "label": "AnnData (After QC, normalisation, scaling)",
+                        "label": "N701",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 646.9375,
-                            "top": 474.125
+                            "left": 12.9765625,
+                            "top": 159.9921875
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "abf51bba-7bf3-442f-8d25-bb8008efdab1",
+                        "uuid": "f5f24f48-9a1d-49f2-b351-ec3dbea3a6c6",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Dataset to be combined",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "S Phase Genes"
+                                "description": "Dataset to be combined",
+                                "name": "N702"
                             }
                         ],
-                        "label": "S Phase Genes",
+                        "label": "N702",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 1029.3646240234375
+                            "left": 8.9921875,
+                            "top": 241
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "20c44e44-d3da-47b3-a761-5b9714629e8e",
+                        "uuid": "509506fb-e5ef-4509-92dd-196aa797870a",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Dataset to be combined",
                         "content_id": null,
                         "errors": null,
                         "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "G2M Phase Genes"
+                                "description": "Dataset to be combined",
+                                "name": "N703"
                             }
                         ],
-                        "label": "G2M Phase Genes",
+                        "label": "N703",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 17.21875,
-                            "top": 1184.7708740234375
+                            "left": 0,
+                            "top": 322.9921875
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "5ed158d1-a7eb-4750-892c-f123c80bfe89",
+                        "uuid": "f4726f7b-d956-45b7-b1e0-b9df93b9892c",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Dataset to be combined",
                         "content_id": null,
                         "errors": null,
                         "id": 3,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Pasted Entry"
+                                "description": "Dataset to be combined",
+                                "name": "N704"
                             }
                         ],
-                        "label": "Pasted Entry",
+                        "label": "N704",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 1955.0625,
-                            "top": 0.0
+                            "left": 4.984375,
+                            "top": 434
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "bd171b20-fde0-4346-8d3e-274a3592485d",
+                        "uuid": "908341bb-6451-4360-a2ec-a1af73fb941e",
+                        "when": null,
                         "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAnnData After QC, normalisation, scaling\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nS Phase Genes\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nG2M Phase Genes\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nPasted Entry\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Inspect AnnData\"];\n  0 -->|output| 4;\n  5[\"All Cell Cycle Genes Concatenate S and G2M Genes\"];\n  1 -->|output| 5;\n  2 -->|output| 5;\n  6[\"Inspect and manipulate\"];\n  0 -->|output| 6;\n  2 -->|output| 6;\n  1 -->|output| 6;\n  7[\"Table Compute\"];\n  4 -->|var| 7;\n  8[\"Add column\"];\n  5 -->|out_file1| 8;\n  9[\"Scanpy RegressOut\"];\n  6 -->|anndata_out| 9;\n  026b02d3-97ee-4847-9347-40773ab76356[\"Output\\nScanpy RegressOut on input dataset(s): Regressed out  AnnData\"];\n  9 --> 026b02d3-97ee-4847-9347-40773ab76356;\n  style 026b02d3-97ee-4847-9347-40773ab76356 stroke:#2c3143,stroke-width:4px;\n  10[\"Add column\"];\n  7 -->|table| 10;\n  11[\"Join\"];\n  10 -->|out_file1| 11;\n  8 -->|out_file1| 11;\n  12[\"Sort\"];\n  11 -->|output| 12;\n  13[\"Table Compute\"];\n  12 -->|out_file1| 13;\n  14[\"Concatenate datasets\"];\n  3 -->|output| 14;\n  13 -->|table| 14;\n  15[\"Manipulate AnnData\"];\n  6 -->|anndata_out| 15;\n  14 -->|out_file1| 15;\n  16[\"Manipulate AnnData\"];\n  9 -->|output_h5ad| 16;\n  14 -->|out_file1| 16;\n  17[\"Manipulate AnnData\"];\n  15 -->|anndata| 17;\n  18[\"Manipulate AnnData\"];\n  16 -->|anndata| 18;\n  19[\"Cluster, infer trajectories and embed\"];\n  17 -->|anndata| 19;\n  20[\"Cluster, infer trajectories and embed\"];\n  18 -->|anndata| 20;\n  09d97ef7-ed92-4d90-a597-2032581c2d4a[\"Output\\nCluster, infer trajectories and embed (tl.louvain) on input dataset(s): Annotated data matrix\"];\n  20 --> 09d97ef7-ed92-4d90-a597-2032581c2d4a;\n  style 09d97ef7-ed92-4d90-a597-2032581c2d4a stroke:#2c3143,stroke-width:4px;\n  21[\"Plot\"];\n  19 -->|anndata_out| 21;\n  22[\"Plot\"];\n  20 -->|anndata_out| 22;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Cell Cycle Regression Workflow",
-                "outputs": [
+                    },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "annotation": "Dataset to be combined",
+                        "content_id": null,
                         "errors": null,
                         "id": 4,
-                        "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Inspect AnnData",
-                        "outputs": [
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "var",
-                                "type": "tabular"
+                                "description": "Dataset to be combined",
+                                "name": "N705"
                             }
                         ],
+                        "label": "N705",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 459.125,
-                            "top": 133.625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ee98d611afc6",
-                            "name": "anndata_inspect",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 6,
+                            "top": 538.9921875
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"var\", \"__current_case__\": 4}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.5+galaxy1",
-                        "type": "tool",
-                        "uuid": "96b7447e-c65c-4955-b3c5-a381f707fb3d",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "var",
-                                "uuid": "1ffba0d7-dc80-4e44-bd74-77cf007f1446"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "6c534b76-c5cc-4bbe-b180-376200e29b75",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
-                        "content_id": "cat1",
+                        "annotation": "Dataset to be combined",
+                        "content_id": null,
                         "errors": null,
                         "id": 5,
-                        "input_connections": {
-                            "input1": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "queries_0|input2": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "All Cell Cycle Genes (Concatenate S and G2M Genes)",
-                        "name": "Concatenate datasets",
-                        "outputs": [
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "description": "Dataset to be combined",
+                                "name": "N706"
                             }
                         ],
+                        "label": "N706",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 445.59375,
-                            "top": 1010.6666870117188
+                            "left": 7.000041058980229,
+                            "top": 640.0000146155871
                         },
-                        "post_job_actions": {},
-                        "tool_id": "cat1",
-                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [{\"__index__\": 0, \"input2\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "7d0769c1-4b8d-4d29-bcc7-aed030503ccc",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "dd200c78-68fe-4a66-85e7-76710e20e4ae"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "b512e8b6-85f2-45b7-a057-d0af216b26f0",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0",
+                        "annotation": "Dataset to be combined",
+                        "content_id": null,
                         "errors": null,
                         "id": 6,
-                        "input_connections": {
-                            "adata": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "method|g2m_genes|file": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "method|s_genes|file": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Inspect and manipulate",
-                        "outputs": [
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "anndata_out",
-                                "type": "h5ad"
+                                "description": "Dataset to be combined",
+                                "name": "N707"
                             }
                         ],
+                        "label": "N707",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1839.84375,
-                            "top": 567.9375
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "c5d3684f7c4c",
-                            "name": "scanpy_inspect",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 7,
+                            "top": 741
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"method\": {\"method\": \"tl.score_genes_cell_cycle\", \"__current_case__\": 3, \"s_genes\": {\"format\": \"file\", \"__current_case__\": 1, \"file\": {\"__class__\": \"ConnectedValue\"}}, \"g2m_genes\": {\"format\": \"file\", \"__current_case__\": 1, \"file\": {\"__class__\": \"ConnectedValue\"}}, \"n_bins\": \"25\", \"random_state\": \"0\", \"use_raw\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "11e0487f-e5a9-44c1-b3e5-2fe50ee207d4",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "anndata_out",
-                                "uuid": "0852740e-92ea-496a-bfeb-86184b8f8570"
-                            }
-                        ]
-                    },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "6aee1bd4-2698-4572-aa78-1b166f27eff2",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nN701\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nN702\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nN703\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nN704\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nN705\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nN706\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nN707\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"Concatenating Datasets\"];\n  0 -->|output| 7;\n  1 -->|output| 7;\n  2 -->|output| 7;\n  3 -->|output| 7;\n  4 -->|output| 7;\n  5 -->|output| 7;\n  6 -->|output| 7;\n  168d4710-570a-43b1-998a-2164154eebc5[\"Output\\nCombined Object\"];\n  7 --> 168d4710-570a-43b1-998a-2164154eebc5;\n  style 168d4710-570a-43b1-998a-2164154eebc5 stroke:#2c3143,stroke-width:4px;\n  8[\"Inspect AnnData\"];\n  7 -->|anndata| 8;\n  9[\"Inspect AnnData\"];\n  7 -->|anndata| 9;\n  10[\"Inspect AnnData\"];\n  7 -->|anndata| 10;\n  11[\"Replace Text\"];\n  9 -->|obs| 11;\n  12[\"Replace Text\"];\n  9 -->|obs| 12;\n  13[\"Cut\"];\n  11 -->|outfile| 13;\n  8b026c35-f9db-4bcd-8cf5-54b7d6fb5aea[\"Output\\nSex metadata\"];\n  13 --> 8b026c35-f9db-4bcd-8cf5-54b7d6fb5aea;\n  style 8b026c35-f9db-4bcd-8cf5-54b7d6fb5aea stroke:#2c3143,stroke-width:4px;\n  14[\"Cut\"];\n  12 -->|outfile| 14;\n  6f55548b-5ded-42b8-b2f7-c7f1a327a068[\"Output\\nGenotype metadata\"];\n  14 --> 6f55548b-5ded-42b8-b2f7-c7f1a327a068;\n  style 6f55548b-5ded-42b8-b2f7-c7f1a327a068 stroke:#2c3143,stroke-width:4px;\n  15[\"Paste\"];\n  14 -->|out_file1| 15;\n  13 -->|out_file1| 15;\n  2f0ea0f3-f2f7-44b2-b8f0-05d8cbb364a6[\"Output\\nCell metadata\"];\n  15 --> 2f0ea0f3-f2f7-44b2-b8f0-05d8cbb364a6;\n  style 2f0ea0f3-f2f7-44b2-b8f0-05d8cbb364a6 stroke:#2c3143,stroke-width:4px;\n  16[\"Adding in cell metadata\"];\n  7 -->|anndata| 16;\n  15 -->|out_file1| 16;\n  2720386c-7273-49d6-abb0-9bd14f6cb68c[\"Output\\nAnnData with Cell Metadata\"];\n  16 --> 2720386c-7273-49d6-abb0-9bd14f6cb68c;\n  style 2720386c-7273-49d6-abb0-9bd14f6cb68c stroke:#2c3143,stroke-width:4px;\n  17[\"Batching Cell Metadata\"];\n  16 -->|anndata| 17;\n  b950c8db-abe1-4cb0-af58-d291d3b74a83[\"Output\\nBatched Object\"];\n  17 --> b950c8db-abe1-4cb0-af58-d291d3b74a83;\n  style b950c8db-abe1-4cb0-af58-d291d3b74a83 stroke:#2c3143,stroke-width:4px;\n  18[\"Calculating mitochondrial \"];\n  17 -->|anndata| 18;\n  2417284d-8252-43ff-84bf-6f15ef11cd05[\"Output\\nAnnotated AnnData\"];\n  18 --> 2417284d-8252-43ff-84bf-6f15ef11cd05;\n  style 2417284d-8252-43ff-84bf-6f15ef11cd05 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "Combining datasets after pre-processing",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
                         "errors": null,
                         "id": 7,
-                        "input_connections": {
-                            "singtabop|input": {
-                                "id": 4,
-                                "output_name": "var"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Table Compute",
-                        "outputs": [
-                            {
-                                "name": "table",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 781.4375,
-                            "top": 125.09375
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "93a3ce78ce55",
-                            "name": "table_compute",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"out_opts\": [\"ignore_nas\"], \"precision\": \"6\", \"singtabop\": {\"use_type\": \"single\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"col_row_names\": null, \"adv\": {\"header\": null, \"nrows\": null, \"skipfooter\": null, \"skip_blank_lines\": \"true\"}, \"user\": {\"mode\": \"select\", \"__current_case__\": 1, \"select_cols_wanted\": \"1\", \"select_rows_wanted\": \"2:15396\", \"select_keepdupe\": [\"select_cols_keepdupe\", \"select_rows_keepdupe\"]}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.4+galaxy0",
-                        "type": "tool",
-                        "uuid": "e02f60d9-596f-4e18-9770-633ac1fc9a5a",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "table",
-                                "uuid": "ddb059b1-92b2-4989-8313-dbd144a11269"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
-                        "errors": null,
-                        "id": 8,
                         "input_connections": {
                             "input": {
-                                "id": 5,
-                                "output_name": "out_file1"
-                            }
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "manipulate|other_adatas": [
+                                {
+                                    "id": 1,
+                                    "output_name": "output"
+                                },
+                                {
+                                    "id": 2,
+                                    "output_name": "output"
+                                },
+                                {
+                                    "id": 3,
+                                    "output_name": "output"
+                                },
+                                {
+                                    "id": 4,
+                                    "output_name": "output"
+                                },
+                                {
+                                    "id": 5,
+                                    "output_name": "output"
+                                },
+                                {
+                                    "id": 6,
+                                    "output_name": "output"
+                                }
+                            ]
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Add column",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "description": "runtime parameter for tool Manipulate AnnData",
+                                "name": "manipulate"
                             }
                         ],
-                        "position": {
-                            "left": 730.125,
-                            "top": 940.9375
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "745871c0b055",
-                            "name": "add_value",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"exp\": \"TRUE\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "8270c2b8-343c-4a96-918e-7615844a9e08",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "11c1edc1-5969-4b69-939f-8b3ef484a28d"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_regress_variable/scanpy_regress_variable/1.8.1+galaxy0",
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "input_obj_file": {
-                                "id": 6,
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy RegressOut",
+                        "label": "Concatenating Datasets",
+                        "name": "Manipulate AnnData",
                         "outputs": [
                             {
-                                "name": "output_h5ad",
+                                "name": "anndata",
                                 "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 2373.3958740234375,
-                            "top": 934.0416870117188
+                            "left": 295.0234375,
+                            "top": 410
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_regress_variable/scanpy_regress_variable/1.8.1+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActionanndata": {
+                                "action_arguments": {
+                                    "newname": "Combined AnnData"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "anndata"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "36daab33aecf",
-                            "name": "scanpy_regress_variable",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "ed4996a16f7f",
+                            "name": "anndata_manipulate",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"save_layer\": \"\", \"save_raw\": \"false\", \"variable_keys\": \"phase\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"concatenate\", \"__current_case__\": 0, \"other_adatas\": {\"__class__\": \"ConnectedValue\"}, \"join\": \"inner\", \"batch_key\": \"batch\", \"index_unique\": \"-\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.10.3+galaxy0",
                         "type": "tool",
-                        "uuid": "5624944c-4504-4d72-8692-363ae5419e34",
+                        "uuid": "4dfd7670-2dd9-46d4-9c97-aaf33524d076",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Scanpy RegressOut on input dataset(s): Regressed out  AnnData",
-                                "output_name": "output_h5ad",
-                                "uuid": "026b02d3-97ee-4847-9347-40773ab76356"
+                                "label": "Combined Object",
+                                "output_name": "anndata",
+                                "uuid": "168d4710-570a-43b1-998a-2164154eebc5"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
+                        "content_id": "Cut1",
                         "errors": null,
-                        "id": 10,
+                        "id": 13,
                         "input_connections": {
                             "input": {
-                                "id": 7,
-                                "output_name": "table"
+                                "id": 11,
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Add column",
+                        "name": "Cut",
                         "outputs": [
                             {
                                 "name": "out_file1",
-                                "type": "input"
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1190.8125,
-                            "top": 142.65625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "745871c0b055",
-                            "name": "add_value",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 1129.03125,
+                            "top": 280
                         },
-                        "tool_state": "{\"exp\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"yes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "3920392c-5481-42be-aa3c-e0ae807d145d",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "27b6bae1-3786-4cbb-a943-e792f4320bc4"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-                        "errors": null,
-                        "id": 11,
-                        "input_connections": {
-                            "infile1": {
-                                "id": 10,
-                                "output_name": "out_file1"
-                            },
-                            "infile2": {
-                                "id": 8,
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Sex metadata"
+                                },
+                                "action_type": "RenameDatasetAction",
                                 "output_name": "out_file1"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Join",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 1471.15625,
-                            "top": 154.25
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \"FALSE\", \"header\": \"false\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \"-a 1 -a 2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.2",
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"columnList\": \"c8\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2",
                         "type": "tool",
-                        "uuid": "ea5dbe23-1636-4f14-ad7d-7d9c0926115c",
+                        "uuid": "731604ed-f075-49b5-9beb-752b69cdc388",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "48e95afc-ac2c-4ab8-80a6-224bf9486af8"
+                                "label": "Sex metadata",
+                                "output_name": "out_file1",
+                                "uuid": "8b026c35-f9db-4bcd-8cf5-54b7d6fb5aea"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "sort1",
+                        "content_id": "Cut1",
                         "errors": null,
-                        "id": 12,
+                        "id": 14,
                         "input_connections": {
                             "input": {
-                                "id": 11,
-                                "output_name": "output"
+                                "id": 12,
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Sort",
+                        "name": "Cut",
                         "outputs": [
                             {
                                 "name": "out_file1",
-                                "type": "input"
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1733.7083740234375,
-                            "top": 146.0625
+                            "left": 1129.03125,
+                            "top": 423.9921875
                         },
-                        "post_job_actions": {},
-                        "tool_id": "sort1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"__workflow_invocation_uuid__\": \"4cdf4fce5b9d11edba32001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"column\": \"2\", \"column_set\": [], \"header_lines\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"order\": \"ASC\", \"style\": \"num\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.0",
-                        "type": "tool",
-                        "uuid": "0e870357-b257-4e99-9d7e-06775c763579",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "735a9c42-3440-4370-9ef4-755c081ef2cc"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0",
-                        "errors": null,
-                        "id": 13,
-                        "input_connections": {
-                            "singtabop|input": {
-                                "id": 12,
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Genotype metadata"
+                                },
+                                "action_type": "RenameDatasetAction",
                                 "output_name": "out_file1"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Table Compute",
-                        "outputs": [
-                            {
-                                "name": "table",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 1953.6875,
-                            "top": 146.0625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "93a3ce78ce55",
-                            "name": "table_compute",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"out_opts\": [\"ignore_nas\"], \"precision\": \"6\", \"singtabop\": {\"use_type\": \"single\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"col_row_names\": null, \"adv\": {\"header\": null, \"nrows\": null, \"skipfooter\": null, \"skip_blank_lines\": \"true\"}, \"user\": {\"mode\": \"select\", \"__current_case__\": 1, \"select_cols_wanted\": \"3\", \"select_rows_wanted\": \"1:15395\", \"select_keepdupe\": [\"select_cols_keepdupe\", \"select_rows_keepdupe\"]}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.2.4+galaxy0",
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"columnList\": \"c8\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2",
                         "type": "tool",
-                        "uuid": "45f07fc8-3ff4-4e21-a1a6-7a764986930f",
+                        "uuid": "1021770e-eb6d-4e23-b75f-76f5827e37e1",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "table",
-                                "uuid": "58fbdecd-859a-42a6-a166-980a2625e01f"
+                                "label": "Genotype metadata",
+                                "output_name": "out_file1",
+                                "uuid": "6f55548b-5ded-42b8-b2f7-c7f1a327a068"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "cat1",
+                        "content_id": "Paste1",
                         "errors": null,
-                        "id": 14,
+                        "id": 15,
                         "input_connections": {
                             "input1": {
-                                "id": 3,
-                                "output_name": "output"
+                                "id": 14,
+                                "output_name": "out_file1"
                             },
-                            "queries_0|input2": {
+                            "input2": {
                                 "id": 13,
-                                "output_name": "table"
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Concatenate datasets",
+                        "name": "Paste",
                         "outputs": [
                             {
                                 "name": "out_file1",
@@ -227278,84 +231895,54 @@
                             }
                         ],
                         "position": {
-                            "left": 2173.65625,
-                            "top": 146.0625
+                            "left": 1407.046875,
+                            "top": 380.984375
                         },
-                        "post_job_actions": {},
-                        "tool_id": "cat1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"__workflow_invocation_uuid__\": \"4cdf4fce5b9d11edba32001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [{\"__index__\": 0, \"input2\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Cell metadata"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "tool_id": "Paste1",
+                        "tool_state": "{\"delimiter\": \"T\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.0.0",
                         "type": "tool",
-                        "uuid": "92d869ca-9989-4699-8069-1632a4c3d159",
+                        "uuid": "78b0f142-dc1d-4c64-8ea8-58d704646c55",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "Cell metadata",
                                 "output_name": "out_file1",
-                                "uuid": "b946b4c9-ad29-4f7e-b2bc-2023265bdc10"
+                                "uuid": "2f0ea0f3-f2f7-44b2-b8f0-05d8cbb364a6"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
                         "errors": null,
                         "id": 16,
                         "input_connections": {
                             "input": {
-                                "id": 9,
-                                "output_name": "output_h5ad"
+                                "id": 7,
+                                "output_name": "anndata"
                             },
                             "manipulate|new_annot": {
-                                "id": 14,
+                                "id": 15,
                                 "output_name": "out_file1"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Manipulate AnnData",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "anndata",
-                                "type": "h5ad"
+                                "description": "runtime parameter for tool Manipulate AnnData",
+                                "name": "manipulate"
                             }
                         ],
-                        "position": {
-                            "left": 2813.729248046875,
-                            "top": 194.28125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3d748954434b",
-                            "name": "anndata_manipulate",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"add_annotation\", \"__current_case__\": 6, \"var_obs\": \"var\", \"new_annot\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.5+galaxy1",
-                        "type": "tool",
-                        "uuid": "b441e4be-4438-4e6e-8ba7-b4cfd3be4eb0",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "anndata",
-                                "uuid": "b7370b49-ef2f-4427-8ea0-70f8159efd3c"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
-                        "errors": null,
-                        "id": 17,
-                        "input_connections": {
-                            "input": {
-                                "id": 15,
-                                "output_name": "anndata"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
+                        "label": "Adding in cell metadata",
                         "name": "Manipulate AnnData",
                         "outputs": [
                             {
@@ -227364,34 +231951,43 @@
                             }
                         ],
                         "position": {
-                            "left": 2794.041748046875,
-                            "top": 1071.2396240234375
+                            "left": 557.03125,
+                            "top": 630.9765625
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
+                        "post_job_actions": {
+                            "RenameDatasetActionanndata": {
+                                "action_arguments": {
+                                    "newname": "AnnData with Cell Metadata"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "anndata"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "3d748954434b",
+                            "changeset_revision": "ed4996a16f7f",
                             "name": "anndata_manipulate",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"filter\", \"__current_case__\": 7, \"var_obs\": \"var\", \"filter\": {\"filter\": \"key\", \"__current_case__\": 0, \"key\": \"CC_genes\", \"filter_key\": {\"type\": \"boolean\", \"__current_case__\": 2, \"value\": \"true\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.5+galaxy1",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"add_annotation\", \"__current_case__\": 6, \"var_obs\": \"obs\", \"new_annot\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.10.3+galaxy0",
                         "type": "tool",
-                        "uuid": "82e3a365-be59-4ca8-a82d-596c7b4056ba",
+                        "uuid": "d30f8445-4d7d-43d4-a5b2-06b62286a70d",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "AnnData with Cell Metadata",
                                 "output_name": "anndata",
-                                "uuid": "3c56a2bd-26d8-4566-b9f9-0f0896651f8c"
+                                "uuid": "2720386c-7273-49d6-abb0-9bd14f6cb68c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
                         "errors": null,
-                        "id": 18,
+                        "id": 17,
                         "input_connections": {
                             "input": {
                                 "id": 16,
@@ -227399,7 +231995,7 @@
                             }
                         },
                         "inputs": [],
-                        "label": null,
+                        "label": "Batching Cell Metadata",
                         "name": "Manipulate AnnData",
                         "outputs": [
                             {
@@ -227408,242 +232004,122 @@
                             }
                         ],
                         "position": {
-                            "left": 2826,
-                            "top": 690.625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3d748954434b",
-                            "name": "anndata_manipulate",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 795.03125,
+                            "top": 644.9765625
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"filter\", \"__current_case__\": 7, \"var_obs\": \"var\", \"filter\": {\"filter\": \"key\", \"__current_case__\": 0, \"key\": \"CC_genes\", \"filter_key\": {\"type\": \"boolean\", \"__current_case__\": 2, \"value\": \"true\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.5+galaxy1",
-                        "type": "tool",
-                        "uuid": "77b6cf83-c02a-49c4-9ae4-c02fa88510d5",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "anndata",
-                                "uuid": "8968536f-6774-4b4f-b1cf-0535133911f7"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
-                        "errors": null,
-                        "id": 19,
-                        "input_connections": {
-                            "adata": {
-                                "id": 17,
+                        "post_job_actions": {
+                            "RenameDatasetActionanndata": {
+                                "action_arguments": {
+                                    "newname": "Batched AnnData"
+                                },
+                                "action_type": "RenameDatasetAction",
                                 "output_name": "anndata"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cluster, infer trajectories and embed",
-                        "outputs": [
-                            {
-                                "name": "anndata_out",
-                                "type": "h5ad"
-                            }
-                        ],
-                        "position": {
-                            "left": 3119.666748046875,
-                            "top": 1062.2396240234375
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "aaa5da8e73a9",
-                            "name": "scanpy_cluster_reduce_dimension",
+                            "changeset_revision": "ed4996a16f7f",
+                            "name": "anndata_manipulate",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"method\": {\"method\": \"tl.pca\", \"__current_case__\": 3, \"n_comps\": \"50\", \"dtype\": \"float32\", \"pca\": {\"chunked\": \"False\", \"__current_case__\": 1, \"zero_center\": \"true\", \"svd_solver\": \"auto\", \"random_state\": \"0\"}, \"use_highly_variable\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy0",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"rename_categories\", \"__current_case__\": 3, \"key\": \"batch\", \"categories\": \"N701,N702,N703,N704,N705,N706,N707\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.10.3+galaxy0",
                         "type": "tool",
-                        "uuid": "0dc6efda-15c2-4c62-a381-887c3d29c017",
+                        "uuid": "e3e2f437-6fd1-432b-8dc0-2133c1b3fee3",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "anndata_out",
-                                "uuid": "b194bcae-6ae7-494d-ba15-68a6b14e59f3"
+                                "label": "Batched Object",
+                                "output_name": "anndata",
+                                "uuid": "b950c8db-abe1-4cb0-af58-d291d3b74a83"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0",
                         "errors": null,
-                        "id": 20,
+                        "id": 18,
                         "input_connections": {
-                            "adata": {
-                                "id": 18,
+                            "input_obj_file": {
+                                "id": 17,
                                 "output_name": "anndata"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Cluster, infer trajectories and embed",
+                        "label": "Calculating mitochondrial ",
+                        "name": "AnnData Operations",
                         "outputs": [
                             {
-                                "name": "anndata_out",
+                                "name": "output_h5ad",
                                 "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 3115.635498046875,
-                            "top": 699.0
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "aaa5da8e73a9",
-                            "name": "scanpy_cluster_reduce_dimension",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"method\": {\"method\": \"tl.pca\", \"__current_case__\": 3, \"n_comps\": \"50\", \"dtype\": \"float32\", \"pca\": {\"chunked\": \"False\", \"__current_case__\": 1, \"zero_center\": \"true\", \"svd_solver\": \"auto\", \"random_state\": \"0\"}, \"use_highly_variable\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "c776b1f6-4eac-40fa-9f19-1fb8fb2b530e",
-                        "workflow_outputs": [
-                            {
-                                "label": "Cluster, infer trajectories and embed (tl.louvain) on input dataset(s): Annotated data matrix",
-                                "output_name": "anndata_out",
-                                "uuid": "09d97ef7-ed92-4d90-a597-2032581c2d4a"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
-                        "errors": null,
-                        "id": 21,
-                        "input_connections": {
-                            "adata": {
-                                "id": 19,
-                                "output_name": "anndata_out"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Plot",
-                        "outputs": [
-                            {
-                                "name": "out_png",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 3397.70849609375,
-                            "top": 1056.2708740234375
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "aa0c474463c2",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.pca_overview\", \"__current_case__\": 12, \"color\": \"phase\", \"use_raw\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy1",
-                        "type": "tool",
-                        "uuid": "500c400f-02e5-40ab-8e33-684ecef4aeff",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_png",
-                                "uuid": "908ff564-db8c-41e3-90e8-fee85df325d0"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
-                        "errors": null,
-                        "id": 22,
-                        "input_connections": {
-                            "adata": {
-                                "id": 20,
-                                "output_name": "anndata_out"
-                            }
+                            "left": 1041.03125,
+                            "top": 641
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Plot",
-                        "outputs": [
-                            {
-                                "name": "out_png",
-                                "type": "png"
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_h5ad": {
+                                "action_arguments": {
+                                    "newname": "Annotated AnnData"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_h5ad"
                             }
-                        ],
-                        "position": {
-                            "left": 3411.70849609375,
-                            "top": 726.2291870117188
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "aa0c474463c2",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
+                            "changeset_revision": "a4774b7b2e85",
+                            "name": "anndata_ops",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.pca_overview\", \"__current_case__\": 12, \"color\": \"phase\", \"use_raw\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy1",
+                        "tool_state": "{\"add_cell_metadata\": {\"default\": false, \"__current_case__\": 1}, \"copy_adata_to_raw\": false, \"copy_e\": {\"default\": false, \"__current_case__\": 1}, \"copy_l\": {\"default\": false, \"__current_case__\": 1}, \"copy_o\": {\"default\": false, \"__current_case__\": 1}, \"copy_r\": {\"default\": false, \"__current_case__\": 1}, \"copy_u\": {\"default\": false, \"__current_case__\": 1}, \"copy_x\": {\"default\": false, \"__current_case__\": 1}, \"field_unique\": null, \"gene_flags\": [{\"__index__\": 0, \"startswith\": \"True\", \"flag\": \"mito\"}], \"gene_symbols_field\": \"NA.\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": false, \"split_on_obs\": {\"default\": false, \"__current_case__\": 1}, \"swap_layer_to_x\": {\"default\": false, \"__current_case__\": 1}, \"top_genes\": \"50\", \"var_modifications\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.3+galaxy0",
                         "type": "tool",
-                        "uuid": "beb0ba6d-3a0f-4bec-a045-3cdf62053d6d",
+                        "uuid": "0db28a98-06c8-43a6-b72a-da2e84965d3a",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_png",
-                                "uuid": "9737f727-e959-4773-b964-38b225b7c7ee"
+                                "label": "Annotated AnnData",
+                                "output_name": "output_h5ad",
+                                "uuid": "2417284d-8252-43ff-84bf-6f15ef11cd05"
                             }
                         ]
                     }
                 ],
-                "parent_id": "single-cell/scrna-case_cell-cycle",
-                "path": "topics/single-cell/tutorials/scrna-case_cell-cycle/workflows/main_workflow.ga",
+                "parent_id": "single-cell/scrna-case_alevin-combine-datasets",
+                "path": "topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/workflows/Combining-datasets-after-pre-processing.ga",
                 "tags": [
-                    "single-cell",
-                    "10x",
-                    "transcriptomics"
+                    "name:training",
+                    "name:single-cell"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "Cell Cycle Regression Workflow",
+                "tests": true,
+                "title": "Combining datasets after pre-processing",
                 "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-case_cell-cycle/versions/main-workflow",
-                "tutorial_id": "scrna-case_cell-cycle",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_cell-cycle/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_cell-cycle/workflows/main_workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-case_alevin-combine-datasets/versions/combining-datasets-after-pre-processing",
+                "tutorial_id": "scrna-case_alevin-combine-datasets",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/workflows/Combining-datasets-after-pre-processing.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/workflows/Combining-datasets-after-pre-processing.html",
                 "version": 1,
-                "wfid": "single-cell-scrna-case_cell-cycle",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "wfid": "single-cell-scrna-case_alevin-combine-datasets",
+                "wfname": "combining-datasets-after-pre-processing",
+                "workflow": "Combining-datasets-after-pre-processing.ga",
                 "workflow_tools": [
-                    "cat1",
-                    "sort1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_regress_variable/scanpy_regress_variable/1.8.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0"
+                    "Cut1",
+                    "Paste1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0"
                 ],
-                "workflowhub_id": "1246"
+                "workflowhub_id": "1225"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/7311628/"
+        "zenodo_link": "https://zenodo.org/records/10852529"
     },
     {
         "admin_install": {
@@ -227653,60 +232129,142 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case-jupyter_basic-pipeline/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRStudio/tutorial.json",
         "contributions": {
             "authorship": [
-                "hexhowells",
-                "nomadscientist"
+                "Camila-goclowski"
+            ],
+            "editing": [
+                "nomadscientist",
+                "hexylena",
+                "mtekman",
+                "shiltemann",
+                "pavanvidem"
             ]
         },
         "contributors": [
             {
-                "email": "hexhowells@gmail.com",
-                "id": "hexhowells",
-                "joined": "2023-06",
-                "name": "Morgan Howells",
-                "orcid": "0009-0008-9422-6380",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexhowells/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexhowells.json"
+                "email": "camila.goclowski@gmail.com",
+                "id": "Camila-goclowski",
+                "joined": "2023-01",
+                "linkedin": "camila-goclowski",
+                "name": "Camila Goclowski",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Camila-goclowski/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Camila-goclowski.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "bio": "Senior Lecturer at The Open University",
+                "elixir_node": "uk",
+                "email": "wendi.bacon@open.ac.uk",
+                "fediverse": "https://mstdn.science/@wendibacon1",
+                "fediverse_flavor": "mastodon",
+                "id": "nomadscientist",
+                "joined": "2020-03",
+                "matrix": "nomadscientist:matrix.org",
+                "name": "Wendi Bacon",
+                "orcid": "0000-0002-8170-8806",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
+                "twitter": "WendiBacon1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             },
             {
                 "affiliations": [
+                    "uni-freiburg"
+                ],
+                "elixir_node": "de",
+                "email": "mtekman89@gmail.com",
+                "former_affiliations": [
                     "elixir-europe"
                 ],
-                "bio": "Senior Lecturer at The Open University",
-                "elixir_node": "uk",
-                "email": "wendi.bacon@open.ac.uk",
-                "fediverse": "https://mstdn.science/@wendibacon1",
+                "id": "mtekman",
+                "joined": "2018-11",
+                "name": "Mehmet Tekman",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
+            },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
                 "fediverse_flavor": "mastodon",
-                "id": "nomadscientist",
-                "joined": "2020-03",
-                "matrix": "nomadscientist:matrix.org",
-                "name": "Wendi Bacon",
-                "orcid": "0000-0002-8170-8806",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
-                "twitter": "WendiBacon1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "pavanvidem",
+                "joined": "2017-09",
+                "name": "Pavankumar Videm",
+                "orcid": "0000-0002-5192-126X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
             }
         ],
-        "dir": "topics/single-cell/tutorials/scrna-case-jupyter_basic-pipeline",
+        "dir": "topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRStudio",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-case_JUPYTER-trajectories",
-                    "scrna-case_monocle3-trajectories"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "single-cell/scrna-case-jupyter_basic-pipeline",
+        "id": "single-cell/scrna-case_FilterPlotandExploreRStudio",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -227718,57 +232276,43 @@
             "mermaid": false
         },
         "key_points": [
-            "Single cell data is huge, and must have its many (# genes) dimensions reduced for analysis",
-            "Analysis is more subjective than we think, and biological understanding of the samples as well as many iterations of analysis are important to give us our best change of attaining real biological insights"
+            "Being able to switch between Galaxy and RStudio when analyzing datasets can be useful when looking to adjust default parameters within Seurat's functions and workflow.",
+            "Seurat in RStudio gives more flexibility and specificity of analyses, but Galaxy offers great reproducibility and ease of analysis.",
+            "Beginning to learn the syntax and use of R will expand your"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-15",
+        "mod_date": "2024-06-07",
         "notebook": {
-            "language": "python",
-            "snippet": "topics/single-cell/tutorials/scrna-case-jupyter_basic-pipeline/preamble.md"
+            "language": "r",
+            "snippet": "topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRStudio/preamble.md"
         },
         "objectives": [
             "Interpret quality control plots to direct parameter decisions",
-            "Repeat analysis from matrix to clustering",
+            "Repeat analysis from matrix to clustering to labelling clusters",
             "Identify decision-making points",
             "Appraise data outputs and decisions",
-            "Explain why single cell analysis is an iterative (i.e. the first plots you generate are not final, but rather you go back and re-analyse your data repeatedly) process"
+            "Explain why single cell analysis is an iterative process (i.e. the first plots you generate are not final, but rather you go back and re-analyse your data repeatedly)"
         ],
-        "pageviews": 1903,
+        "pageviews": 2391,
         "priority": 2,
-        "pub_date": "2023-08-25",
+        "pub_date": "2023-10-02",
         "questions": [
             "Is my single cell dataset a quality dataset?",
-            "How do I generate and annotate cell clusters?",
-            "How do I pick thresholds and parameters in my analysis? What's a \"reasonable\" number, and will the world collapse if I pick the wrong one?"
-        ],
-        "recordings": [
-            {
-                "bot-timestamp": 1722971660,
-                "captioners": [
-                    "hexhowells"
-                ],
-                "date": "2024-08-06",
-                "galaxy_version": "24.1.2.dev0",
-                "length": "13M",
-                "speakers": [
-                    "hexhowells"
-                ],
-                "youtube_id": "40w0WVohv4E"
-            }
+            "How do I pick thresholds and parameters in my analysis? What\u2019s a \u201creasonable\u201d number, and will the world collapse if I pick the wrong one?",
+            "How do I generate and annotate cell clusters?"
         ],
         "requirements": [
             {
                 "topic_name": "single-cell",
                 "tutorials": [
-                    "scrna-case_alevin",
-                    "scrna-case_alevin-combine-datasets"
+                    "scrna-case_alevin-combine-datasets",
+                    "scrna-case_basic-pipeline"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00358",
+        "short_id": "T00366",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
@@ -227810,10 +232354,10 @@
         "tags": [
             "10x",
             "paper-replication",
-            "Python"
+            "R"
         ],
         "time_estimation": "3H",
-        "title": "Filter, plot and explore single-cell RNA-seq data with Scanpy (Python)",
+        "title": "Filter, plot, and explore single cell RNA-seq data with Seurat (R)",
         "tools": [],
         "topic_name": "single-cell",
         "topic_name_human": "Single Cell",
@@ -227823,413 +232367,329 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "scrna-case-jupyter_basic-pipeline",
+        "tutorial_name": "scrna-case_FilterPlotandExploreRStudio",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case-jupyter_basic-pipeline/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRStudio/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case-jupyter_basic-pipeline/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case-jupyter_basic-pipeline/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRStudio/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_FilterPlotandExploreRStudio/tutorial.json"
         },
-        "version": 10,
+        "version": 8,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 74,
-        "visitors": 1660,
+        "visit_duration": 50,
+        "visitors": 2134,
         "zenodo_link": "https://zenodo.org/record/7053673"
     },
     {
+        "abbreviations": {
+            "PBMCs": "peripheral blood mononuclear cells",
+            "QC": "quality control",
+            "TSS": "transcription start sites",
+            "TSSe": "transcription start site enrichment",
+            "UMAP": "Uniform Manifold Approximation and Projection",
+            "scATAC-seq": "Single-cell Assay for Transposase-Accessible Chromatin using sequencing"
+        },
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "e7b2202befea",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "replace_column_by_key_value_file",
+                    "owner": "bgruening",
+                    "revisions": "d533e4b75800",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "umi_tools_extract",
-                    "owner": "iuc",
-                    "revisions": "6a675c3aa610",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "bwa",
+                    "owner": "devteam",
+                    "revisions": "2477830927ec",
+                    "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "seq_filter_by_id",
-                    "owner": "peterjc",
-                    "revisions": "141612f8c3e3",
-                    "tool_panel_section_label": "Filter and Sort",
+                    "name": "cut_columns",
+                    "owner": "devteam",
+                    "revisions": "cec635fab700",
+                    "tool_panel_section_label": "Single Cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: umi_tools_extract\n  owner: iuc\n  revisions: 6a675c3aa610\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seq_filter_by_id\n  owner: peterjc\n  revisions: 141612f8c3e3\n  tool_panel_section_label: Filter and Sort\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-umis/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "elixir_node": "de",
-                "email": "mtekman89@gmail.com",
-                "former_affiliations": [
-                    "elixir-europe"
-                ],
-                "id": "mtekman",
-                "joined": "2018-11",
-                "name": "Mehmet Tekman",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
-            }
-        ],
-        "dir": "topics/single-cell/tutorials/scrna-umis",
-        "edam_operation": [
-            "Sequencing quality control",
-            "Sequence composition calculation",
-            "Statistical calculation"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "gitter": "Galaxy-Training-Network/galaxy-single-cell",
-        "hands_on": true,
-        "id": "single-cell/scrna-umis",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Verifying the distribution of barcodes via a FASTQC plot",
-            "Relocating barcodes into headers",
-            "Removing unwanted barcodes"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
-        "objectives": [
-            "Demultiplex FASTQ data via UMI-tools",
-            "Understand and validate the extraction of barcodes"
-        ],
-        "pageviews": 5963,
-        "priority": 2,
-        "pub_date": "2019-02-20",
-        "questions": [
-            "What are barcodes?",
-            "What is their purpose?",
-            "How are barcodes formatted?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "khanteymoori"
-                ],
-                "date": "2021-03-18",
-                "galaxy_version": "21.01",
-                "length": "10M",
-                "speakers": [
-                    "nomadscientist"
-                ],
-                "youtube_id": "AJ17BicjmYU"
-            }
-        ],
-        "redirect_from": [
-            "/topics/transcriptomics/tutorials/scrna-umis/tutorial",
-            "/short/single-cell/scrna-umis",
-            "/short/T00256"
-        ],
-        "short_id": "T00256",
-        "short_tools": [
-            "seq_filter_by_id",
-            "umi_tools_extract",
-            "fastqc"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "scintroduction",
-        "supported_servers": {
-            "exact": [
+                },
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "fasta_compute_length",
+                    "owner": "devteam",
+                    "revisions": "7d37cfda8e00",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
+                    "name": "anndata_ops",
+                    "owner": "ebi-gxa",
+                    "revisions": "a4774b7b2e85",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
+                    "name": "anndata_inspect",
+                    "owner": "iuc",
+                    "revisions": "6f0d0c784f09",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
+                    "name": "anndata_manipulate",
+                    "owner": "iuc",
+                    "revisions": "ed4996a16f7f",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
+                    "name": "scanpy_filter",
+                    "owner": "iuc",
+                    "revisions": "d636ce5cde16",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": null,
-        "time_estimation": "2h",
-        "title": "Understanding Barcodes",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1",
-            "toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7"
-        ],
-        "topic_name": "single-cell",
-        "topic_name_human": "Single Cell",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "scrna-umis",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-umis/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-umis/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-umis/tutorial.json"
-        },
-        "version": 7,
-        "video": false,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 70,
-        "visitors": 4694,
-        "zenodo_link": "https://zenodo.org/record/2573177"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
+                    "name": "scanpy_inspect",
+                    "owner": "iuc",
+                    "revisions": "f54f0f0598ad",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
-                    "name": "scanpy_compute_graph",
-                    "owner": "ebi-gxa",
-                    "revisions": "6417cccad133",
+                    "name": "scanpy_normalize",
+                    "owner": "iuc",
+                    "revisions": "d844935c906c",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_find_cluster",
-                    "owner": "ebi-gxa",
-                    "revisions": "2ccd9f9e2cd0",
+                    "name": "scanpy_plot",
+                    "owner": "iuc",
+                    "revisions": "f7446fd8d5e7",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_parameter_iterator",
-                    "owner": "ebi-gxa",
-                    "revisions": "73d43034c860",
+                    "name": "snapatac2_clustering",
+                    "owner": "iuc",
+                    "revisions": "afb90d3485df",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_plot_embed",
-                    "owner": "ebi-gxa",
-                    "revisions": "35f6611fb8c3",
+                    "name": "snapatac2_peaks_and_motif",
+                    "owner": "iuc",
+                    "revisions": "88192fe25375",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_run_tsne",
-                    "owner": "ebi-gxa",
-                    "revisions": "181d61d2f3cd",
+                    "name": "snapatac2_plotting",
+                    "owner": "iuc",
+                    "revisions": "370d45e0d1a8",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_run_umap",
-                    "owner": "ebi-gxa",
-                    "revisions": "bd4a244faeb8",
+                    "name": "snapatac2_preprocessing",
+                    "owner": "iuc",
+                    "revisions": "fef8f61cb34c",
                     "tool_panel_section_label": "Single-cell",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: scanpy_compute_graph\n  owner: ebi-gxa\n  revisions: 6417cccad133\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_find_cluster\n  owner: ebi-gxa\n  revisions: 2ccd9f9e2cd0\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_parameter_iterator\n  owner: ebi-gxa\n  revisions: 73d43034c860\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot_embed\n  owner: ebi-gxa\n  revisions: 35f6611fb8c3\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_tsne\n  owner: ebi-gxa\n  revisions: 181d61d2f3cd\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_umap\n  owner: ebi-gxa\n  revisions: bd4a244faeb8\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scanpy_parameter_iterator/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: replace_column_by_key_value_file\n  owner: bgruening\n  revisions: d533e4b75800\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: 2477830927ec\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cut_columns\n  owner: devteam\n  revisions: cec635fab700\n  tool_panel_section_label: Single Cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_compute_length\n  owner: devteam\n  revisions: 7d37cfda8e00\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_ops\n  owner: ebi-gxa\n  revisions: a4774b7b2e85\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_inspect\n  owner: iuc\n  revisions: 6f0d0c784f09\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n  owner: iuc\n  revisions: ed4996a16f7f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter\n  owner: iuc\n  revisions: d636ce5cde16\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_inspect\n  owner: iuc\n  revisions: f54f0f0598ad\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_normalize\n  owner: iuc\n  revisions: d844935c906c\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot\n  owner: iuc\n  revisions: f7446fd8d5e7\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snapatac2_clustering\n  owner: iuc\n  revisions: afb90d3485df\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snapatac2_peaks_and_motif\n  owner: iuc\n  revisions: 88192fe25375\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snapatac2_plotting\n  owner: iuc\n  revisions: 370d45e0d1a8\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snapatac2_preprocessing\n  owner: iuc\n  revisions: fef8f61cb34c\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.json",
         "contributions": {
             "authorship": [
-                "wee-snufkin"
+                "timonschlegel"
             ],
-            "funding": [
-                "eosc-life"
+            "editing": [
+                "pavanvidem",
+                "bgruening"
             ],
             "testing": [
-                "nomadscientist"
+                "pavanvidem"
             ]
         },
         "contributors": [
             {
-                "email": "juliajot36@gmail.com",
-                "id": "wee-snufkin",
-                "joined": "2022-06",
-                "name": "Julia Jakiela",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
+                "id": "timonschlegel",
+                "joined": "2024-05",
+                "name": "Timon Schlegel",
+                "orcid": "0009-0001-3228-105X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/timonschlegel/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/timonschlegel.json"
             },
             {
                 "affiliations": [
+                    "uni-freiburg",
                     "elixir-europe"
                 ],
-                "bio": "Senior Lecturer at The Open University",
-                "elixir_node": "uk",
-                "email": "wendi.bacon@open.ac.uk",
-                "fediverse": "https://mstdn.science/@wendibacon1",
+                "id": "pavanvidem",
+                "joined": "2017-09",
+                "name": "Pavankumar Videm",
+                "orcid": "0000-0002-5192-126X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
+            },
+            {
+                "affiliations": [
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
                 "fediverse_flavor": "mastodon",
-                "id": "nomadscientist",
-                "joined": "2020-03",
-                "matrix": "nomadscientist:matrix.org",
-                "name": "Wendi Bacon",
-                "orcid": "0000-0002-8170-8806",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
-                "twitter": "WendiBacon1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+                "id": "bgruening",
+                "joined": "2017-09",
+                "linkedin": "bgruening",
+                "location": {
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
+                },
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
             },
             {
-                "avatar": "https://www.eosc-life.eu/wp-content/themes/eosc-life-v2/assets/images/eosclogo.png",
-                "funder": true,
-                "funding_id": "824087",
-                "funding_statement": "EOSC-Life has received funding from the European Union\u2019s Horizon 2020 programme under grant agreement number 824087",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "eosc-life",
-                "joined": "2023-04",
-                "members": [
-                    "bgruening"
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
                 ],
-                "name": "EOSC-Life",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eosc-life/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/eosc-life.json"
+                "id": "pavanvidem",
+                "joined": "2017-09",
+                "name": "Pavankumar Videm",
+                "orcid": "0000-0002-5192-126X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
             }
         ],
-        "dir": "topics/single-cell/tutorials/scanpy_parameter_iterator",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)"
+        "dir": "topics/single-cell/tutorials/scatac-standard-processing-snapatac2",
+        "edam_operation": [
+            "Generation",
+            "Sequence alignment",
+            "Differential gene expression analysis",
+            "Read mapping",
+            "Genome indexing"
         ],
+        "edam_topic": [],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "gitter": "Galaxy-Training-Network/galaxy-single-cell",
         "hands_on": true,
-        "id": "single-cell/scanpy_parameter_iterator",
-        "inexact_supported_servers": [
-            "UseGalaxy.org.au"
-        ],
+        "id": "single-cell/scatac-standard-processing-snapatac2",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Scanpy ParameterIterator can be used for k nearest neighbours (Scanpy ComputeGraph), perplexity (Scanpy RunTSNE) and resolution (Scanpy FindCluster).",
-            "You can enter the parameter values either as a list or as values to be iterated in step.",
-            "Parameter Iterator is a useful tool to quickly and easily compare the differences in the outputs caused by changing parameter values. Hence it allows us to choose the optimal parameter values."
+            "Single-cell ATAC-seq can identify open chromatin sites",
+            "Dimension reduction is required to simplify the data while preserving important information about the relationships of cells to each other.",
+            "Clusters of similar cells can be annotated to their respective cell-types"
         ],
         "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-12-05",
+        "mod_date": "2024-08-09",
         "objectives": [
-            "Execute the Scanpy Parameter Iterator",
-            "Recognise what tools you can use Parameter Iterator with",
-            "Operate tools working on dataset collections",
-            "Compare plots resulting from different parameters values"
+            "Learn how single-cell ATAC-seq data is processed",
+            "Create a count-matrix from a 10X fragment file",
+            "Perform filtering, dimension reduction and clustering on AnnData matrices",
+            "Generate and filter a cell-by-gene matrix",
+            "Identify marker genes for the clusters and annotate the cell types"
         ],
-        "pageviews": 135,
-        "priority": 3,
-        "pub_date": "2023-07-19",
+        "pageviews": 421,
+        "priority": 2,
+        "pub_date": "2024-07-11",
         "questions": [
-            "How can I run a tool with multiple parameter values?",
-            "Do I have to enter parameter values manually each time I want to check a new value?",
-            "What tools can take multiple values at once and iterate over them?"
+            "What does ATAC-seq data tell us about the cell?",
+            "Which steps are necessary to cluster the cells of single-cell ATAC-seq data?",
+            "Why is dimension reduction important for the analysis of single-cell data?"
+        ],
+        "redirect_from": [
+            "/topics/transcriptomics/tutorials/scatac-standard-processing-snapatac2/tutorial",
+            "/short/single-cell/scatac-standard-processing-snapatac2",
+            "/short/T00445"
         ],
         "requirements": [
             {
                 "topic_name": "single-cell",
                 "tutorials": [
-                    "scrna-case_alevin",
-                    "scrna-case_alevin-combine-datasets",
-                    "scrna-case_basic-pipeline"
+                    "scatac-preprocessing-tenx"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00357",
+        "short_id": "T00445",
         "short_tools": [
-            "scanpy_plot_embed",
-            "scanpy_run_tsne",
-            "scanpy_find_cluster",
-            "scanpy_compute_graph",
-            "scanpy_parameter_iterator",
-            "scanpy_run_umap"
+            "bwa_mem",
+            "snapatac2_peaks_and_motif",
+            "fasta_compute_length",
+            "replace_column_with_key_value_file",
+            "snapatac2_clustering",
+            "snapatac2_preprocessing",
+            "anndata_ops",
+            "scanpy_plot",
+            "snapatac2_plotting",
+            "anndata_inspect",
+            "Cut1",
+            "anndata_manipulate",
+            "scanpy_filter",
+            "scanpy_inspect",
+            "scanpy_normalize"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "tricks",
+        "subtopic": "scmultiomics",
         "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
+            "exact": [],
+            "inexact": []
         },
         "symlink": null,
-        "tags": null,
-        "time_estimation": "2H",
-        "title": "Scanpy Parameter Iterator",
+        "tags": [
+            "10x",
+            "epigenetics",
+            "single-cell"
+        ],
+        "time_estimation": "4H",
+        "title": "Single-cell ATAC-seq standard processing with SnapATAC2",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9"
+            "Cut1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18",
+            "toolshed.g2.bx.psu.edu/repos/devteam/cut_columns/Cut1/1.0.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_peaks_and_motif/snapatac2_peaks_and_motif/2.6.4+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1"
         ],
         "topic_name": "single-cell",
         "topic_name_human": "Single Cell",
@@ -228239,50 +232699,52 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "scanpy_parameter_iterator",
+        "tutorial_name": "scatac-standard-processing-snapatac2",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scanpy_parameter_iterator/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scanpy_parameter_iterator/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scanpy_parameter_iterator/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.json"
         },
-        "version": 7,
+        "version": 2,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 94,
-        "visitors": 118,
+        "visit_duration": 61,
+        "visitors": 319,
         "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "0009-0001-2017-8805",
-                        "name": "Julia Jakiela"
+                        "identifier": "0009-0001-3228-105X",
+                        "name": "Timon Schlegel"
                     }
                 ],
-                "description": "",
+                "description": "Workflow of Tutorial \"Single-cell ATAC-seq standard processing with SnapATAC2\".\nThis workflow takes a fragment file as input and performs the standard steps of scATAC-seq analysis: filtering, dimension reduction, embedding and visualization of marker genes with SnapATAC2.\nIn an alternative step, the fragment file can also be generated from a BAM file. ",
                 "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
+                    "comments": true,
+                    "parameters": true,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                    },
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nScanpy RunPCA: AnnData object\"]\n  1[label=\"ParameterIterator n-neighbors\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nScanpy ComputeGraph on data X and data Y: Graph object AnnData\"]\n  3[label=\"ParameterIterator perplexity\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nScanpy RunUMAP on data X: UMAP object AnnData\"]\n  5[label=\"ParameterIterator resolution\"]\n  6[label=\"Scanpy ComputeGraph\"]\n  0 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"parameter_iteration\"]\n  k1e60c7cd7e02450fa403f3df1e548757[color=lightseagreen,label=\"Output\\nScanpy ComputeGraph on collection X: Graph object AnnData (n-neighbours)\"]\n  6 -> k1e60c7cd7e02450fa403f3df1e548757\n  7[label=\"Scanpy RunTSNE\"]\n  2 -> 7 [label=\"output\"]\n  3 -> 7 [label=\"parameter_iteration\"]\n  k15143fea5e2b4b25b5d10726da910f67[color=lightseagreen,label=\"Output\\nScanpy RunTSNE on collection X: tSNE object AnnData (perplexity)\"]\n  7 -> k15143fea5e2b4b25b5d10726da910f67\n  8[label=\"Scanpy FindCluster\"]\n  4 -> 8 [label=\"output\"]\n  5 -> 8 [label=\"parameter_iteration\"]\n  k6fdddfe7c4da442186a09819ce4c769c[color=lightseagreen,label=\"Output\\nScanpy FindCluster on collection X: Clusters AnnData (resolution)\"]\n  8 -> k6fdddfe7c4da442186a09819ce4c769c\n  9[label=\"Scanpy RunTSNE\"]\n  6 -> 9 [label=\"output_h5ad\"]\n  k7c988247b1674733859ffcd582f91959[color=lightseagreen,label=\"Output\\nScanpy RunTSNE on collection X: tSNE object AnnData (n-neighbours)\"]\n  9 -> k7c988247b1674733859ffcd582f91959\n  10[label=\"Scanpy RunUMAP\"]\n  7 -> 10 [label=\"output_h5ad\"]\n  k1f5abfa2845c47639f87e4b167aa7bc8[color=lightseagreen,label=\"Output\\nScanpy RunUMAP on collection X: UMAP object AnnData (perplexity)\"]\n  10 -> k1f5abfa2845c47639f87e4b167aa7bc8\n  11[label=\"Scanpy PlotEmbed\"]\n  8 -> 11 [label=\"output_h5ad\"]\n  k99185d1e047f47f2908107506e1c17df[color=lightseagreen,label=\"Output\\nresolution_pca_plots\"]\n  11 -> k99185d1e047f47f2908107506e1c17df\n  12[label=\"Scanpy PlotEmbed\"]\n  8 -> 12 [label=\"output_h5ad\"]\n  k65d7b619865940089e56db21fda6ce8c[color=lightseagreen,label=\"Output\\nresolution_umap_plots\"]\n  12 -> k65d7b619865940089e56db21fda6ce8c\n  13[label=\"Scanpy PlotEmbed\"]\n  8 -> 13 [label=\"output_h5ad\"]\n  kbdcaf8375fc44024a87aeabfa0110127[color=lightseagreen,label=\"Output\\nresolution_tsne_plots\"]\n  13 -> kbdcaf8375fc44024a87aeabfa0110127\n  14[label=\"Scanpy RunUMAP\"]\n  9 -> 14 [label=\"output_h5ad\"]\n  k8a0b3d69e7df4977b8ebec478b914a26[color=lightseagreen,label=\"Output\\nScanpy RunUMAP on collection X: UMAP object AnnData (n-neighbours)\"]\n  14 -> k8a0b3d69e7df4977b8ebec478b914a26\n  15[label=\"Scanpy FindCluster\"]\n  10 -> 15 [label=\"output_h5ad\"]\n  kc2e0d48f9f0e44528fb5e78420578c65[color=lightseagreen,label=\"Output\\nScanpy FindCluster on collection X: Clusters AnnData (perplexity)\"]\n  15 -> kc2e0d48f9f0e44528fb5e78420578c65\n  16[label=\"Scanpy FindCluster\"]\n  14 -> 16 [label=\"output_h5ad\"]\n  kc952b32e99d54b94a6d7be59439c4dca[color=lightseagreen,label=\"Output\\nScanpy FindCluster on collection X: Clusters AnnData (n-neighbours)\"]\n  16 -> kc952b32e99d54b94a6d7be59439c4dca\n  17[label=\"Scanpy PlotEmbed\"]\n  15 -> 17 [label=\"output_h5ad\"]\n  k44c0ec07b64e428f92545217e8041416[color=lightseagreen,label=\"Output\\nperplexity_plots\"]\n  17 -> k44c0ec07b64e428f92545217e8041416\n  18[label=\"Scanpy PlotEmbed\"]\n  16 -> 18 [label=\"output_h5ad\"]\n  k0b30f5738ebd45829bcd58ba5c778658[color=lightseagreen,label=\"Output\\nn-neighbors_plots\"]\n  18 -> k0b30f5738ebd45829bcd58ba5c778658\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nFragment_file\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nchromosome_sizes.tabular\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ngene_annotation\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nBam-file\"]\n  4[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nKeys for annotations of obs/cells or vars/genes\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReplace_file\"]\n  6[label=\"pp.import_data\"]\n  1 -> 6 [label=\"output\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"pp.make_fragment_file\"]\n  3 -> 7 [label=\"output\"]\n  8[label=\"pl.frag_size_distr\"]\n  6 -> 8 [label=\"anndata_out\"]\n  k265d602044e2408c9eb602cbc9ac23a7[color=lightseagreen,label=\"Output\\nplot frag_size\"]\n  8 -> k265d602044e2408c9eb602cbc9ac23a7\n  9[label=\"pl.frag_size_distr_log\"]\n  6 -> 9 [label=\"anndata_out\"]\n  ka37cd3c3e07e4bea899fee44cee8370b[color=lightseagreen,label=\"Output\\nplot log frag_size\"]\n  9 -> ka37cd3c3e07e4bea899fee44cee8370b\n  10[label=\"metrics.tsse\"]\n  6 -> 10 [label=\"anndata_out\"]\n  2 -> 10 [label=\"output\"]\n  k233284e5c1844330a1d32d03951c4ce7[color=lightseagreen,label=\"Output\\nanndata tsse\"]\n  10 -> k233284e5c1844330a1d32d03951c4ce7\n  11[label=\"pp.import_data-sorted_by_barcodes\"]\n  1 -> 11 [label=\"output\"]\n  7 -> 11 [label=\"fragments_out\"]\n  k50ef9fe7bb084957bc45079ed78f9ee8[color=lightseagreen,label=\"Output\\nanndata\"]\n  11 -> k50ef9fe7bb084957bc45079ed78f9ee8\n  12[label=\"pl.tsse\"]\n  10 -> 12 [label=\"anndata_out\"]\n  k9a5c0f9c04234822871eba8317f2fa7b[color=lightseagreen,label=\"Output\\nplot tsse\"]\n  12 -> k9a5c0f9c04234822871eba8317f2fa7b\n  13[label=\"pp.filter_cells\"]\n  10 -> 13 [label=\"anndata_out\"]\n  kb58dc4ad6bf04f3199f44f8deb13427c[color=lightseagreen,label=\"Output\\nanndata filter cells\"]\n  13 -> kb58dc4ad6bf04f3199f44f8deb13427c\n  14[label=\"pp.add_tile_matrix\"]\n  13 -> 14 [label=\"anndata_out\"]\n  kd4b64fc4fd354781b7990d07fe8fe438[color=lightseagreen,label=\"Output\\nanndata tile matrix\"]\n  14 -> kd4b64fc4fd354781b7990d07fe8fe438\n  15[label=\"pp.select_features\"]\n  14 -> 15 [label=\"anndata_out\"]\n  kf531f6bd3fc648b9bb3366de7928e670[color=lightseagreen,label=\"Output\\nanndata select features\"]\n  15 -> kf531f6bd3fc648b9bb3366de7928e670\n  16[label=\"pp.scrublet\"]\n  15 -> 16 [label=\"anndata_out\"]\n  k5b17aa3a3694440f9022cf9761feb760[color=lightseagreen,label=\"Output\\nanndata scrublet\"]\n  16 -> k5b17aa3a3694440f9022cf9761feb760\n  17[label=\"pp.filter_doublets\"]\n  16 -> 17 [label=\"anndata_out\"]\n  k3838cf9da0184aa78852893b2f60ec2a[color=lightseagreen,label=\"Output\\nanndata filter doublets\"]\n  17 -> k3838cf9da0184aa78852893b2f60ec2a\n  18[label=\"tl.spectral\"]\n  17 -> 18 [label=\"anndata_out\"]\n  k778835168ac440b58b755750639d9fc4[color=lightseagreen,label=\"Output\\nanndata spectral\"]\n  18 -> k778835168ac440b58b755750639d9fc4\n  19[label=\"tl.umap\"]\n  18 -> 19 [label=\"anndata_out\"]\n  k062a54717b7a4d9bbf6cfe9bbbc5d2ad[color=lightseagreen,label=\"Output\\nanndata umap\"]\n  19 -> k062a54717b7a4d9bbf6cfe9bbbc5d2ad\n  20[label=\"pp.knn\"]\n  19 -> 20 [label=\"anndata_out\"]\n  kb7ebe580993848e587184df197126615[color=lightseagreen,label=\"Output\\nanndata knn\"]\n  20 -> kb7ebe580993848e587184df197126615\n  21[label=\"tl.leiden\"]\n  20 -> 21 [label=\"anndata_out\"]\n  k9970eb96013b4d97bbbf2d1f4663b73c[color=lightseagreen,label=\"Output\\nanndata_leiden_clustering\"]\n  21 -> k9970eb96013b4d97bbbf2d1f4663b73c\n  22[label=\"pl.umap\"]\n  21 -> 22 [label=\"anndata_out\"]\n  k4fff8ec87d6f48719e42d6c1791d6aa9[color=lightseagreen,label=\"Output\\numap_leiden-clusters\"]\n  22 -> k4fff8ec87d6f48719e42d6c1791d6aa9\n  23[label=\"make_gene_matrix\"]\n  21 -> 23 [label=\"anndata_out\"]\n  2 -> 23 [label=\"output\"]\n  k9a5c2e235b5941aeaceb0e47ce9e7b1a[color=lightseagreen,label=\"Output\\nanndata gene matrix\"]\n  23 -> k9a5c2e235b5941aeaceb0e47ce9e7b1a\n  24[label=\"scanpy_filter_genes\"]\n  23 -> 24 [label=\"anndata_out\"]\n  k7a9b22dfe0e549d99fa12efe316d6d66[color=lightseagreen,label=\"Output\\nanndata filter genes\"]\n  24 -> k7a9b22dfe0e549d99fa12efe316d6d66\n  25[label=\"Normalize\"]\n  24 -> 25 [label=\"anndata_out\"]\n  k7dddd4c819444f50b331857d03cc9631[color=lightseagreen,label=\"Output\\nanndata normalize\"]\n  25 -> k7dddd4c819444f50b331857d03cc9631\n  26[label=\"pp.log1p\"]\n  25 -> 26 [label=\"anndata_out\"]\n  k40ace30a21e14bf28e08ad93b62fb2ee[color=lightseagreen,label=\"Output\\nanndata log1p\"]\n  26 -> k40ace30a21e14bf28e08ad93b62fb2ee\n  27[label=\"external.pp.magic\"]\n  26 -> 27 [label=\"anndata_out\"]\n  k8c1c7aa9b9dd467b971573773aea093f[color=lightseagreen,label=\"Output\\nanndata_magic\"]\n  27 -> k8c1c7aa9b9dd467b971573773aea093f\n  28[label=\"Copy obsm\"]\n  21 -> 28 [label=\"anndata_out\"]\n  27 -> 28 [label=\"anndata_out\"]\n  k2c3825d371514eef97d0c8a31ca6fd3e[color=lightseagreen,label=\"Output\\nanndata_gene-matrix_leiden\"]\n  28 -> k2c3825d371514eef97d0c8a31ca6fd3e\n  29[label=\"umap_plot_with_scanpy\"]\n  28 -> 29 [label=\"output_h5ad\"]\n  4 -> 29 [label=\"output\"]\n  k4cfbbb70156b48d7b14bdb21198d9b6d[color=lightseagreen,label=\"Output\\numap_marker-genes\"]\n  29 -> k4cfbbb70156b48d7b14bdb21198d9b6d\n  30[label=\"Inspect observations\"]\n  28 -> 30 [label=\"output_h5ad\"]\n  31[label=\"Cut leiden from table\"]\n  30 -> 31 [label=\"obs\"]\n  k11c22200a54e458582c48457dbbfb53c[color=lightseagreen,label=\"Output\\nleiden annotation\"]\n  31 -> k11c22200a54e458582c48457dbbfb53c\n  32[label=\"Replace leiden\"]\n  31 -> 32 [label=\"out_file1\"]\n  5 -> 32 [label=\"output\"]\n  k467de06179e641488a65c06383a14012[color=lightseagreen,label=\"Output\\ncell type annotation\"]\n  32 -> k467de06179e641488a65c06383a14012\n  33[label=\"Manipulate AnnData\"]\n  28 -> 33 [label=\"output_h5ad\"]\n  32 -> 33 [label=\"outfile_replace\"]\n  kcbba6173f4394fd58423946aa625112b[color=lightseagreen,label=\"Output\\nanndata_cell_type\"]\n  33 -> kcbba6173f4394fd58423946aa625112b\n  34[label=\"Plot cell types\"]\n  33 -> 34 [label=\"anndata\"]\n  kc28c53ae8ee747d78a00352908bb7c1a[color=lightseagreen,label=\"Output\\numap_cell-type\"]\n  34 -> kc28c53ae8ee747d78a00352908bb7c1a\n  35[label=\"Final Anndata general info\"]\n  33 -> 35 [label=\"anndata\"]\n  k379a85d1a2044b0b8b3386e5582fc51f[color=lightseagreen,label=\"Output\\ngeneral\"]\n  35 -> k379a85d1a2044b0b8b3386e5582fc51f\n}",
                 "history": [
                     {
-                        "hash": "331d2c1b553213fe663c01d608bba47638414644",
-                        "message": "updated workflow tests",
+                        "hash": "747cf76eb0ac7e1a046715c274e302d31ea720f5",
+                        "message": "updated snapatac2 version to 2.6.4",
                         "num": 2,
-                        "short_hash": "331d2c1b5",
-                        "unix": "1689307889"
+                        "short_hash": "747cf76eb",
+                        "unix": "1723136381"
                     },
                     {
-                        "hash": "68fc015a7fae9417a5365fb3edda17a5aaf9d87b",
-                        "message": "add workflow tests",
+                        "hash": "9740cbbaddce4bd770c90ec91e8990d0cddf3bc8",
+                        "message": "Update workflow and add tests",
                         "num": 1,
-                        "short_hash": "68fc015a7",
-                        "unix": "1686208349"
+                        "short_hash": "9740cbbad",
+                        "unix": "1720704591"
                     }
                 ],
                 "inputs": [
@@ -228295,21 +232757,48 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Scanpy RunPCA: AnnData object"
+                                "name": "Fragment_file"
                             }
                         ],
-                        "label": "Scanpy RunPCA: AnnData object",
+                        "label": "Fragment_file",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 25.151777265812267,
-                            "top": 0
+                            "left": 67.17018491581389,
+                            "top": 354.56754754491556
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ce25265d-8c04-490f-bd84-dd417a635456",
+                        "uuid": "4f5ba41c-e6b0-4650-ad92-59029b87ef44",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "chromosome_sizes.tabular"
+                            }
+                        ],
+                        "label": "chromosome_sizes.tabular",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 68.17018491581389,
+                            "top": 455.5596085802506
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "9431a94a-1399-458c-8e40-d19725a52701",
                         "when": null,
                         "workflow_outputs": []
                     },
@@ -228322,21 +232811,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Scanpy ComputeGraph on data X and data Y: Graph object AnnData"
+                                "name": "gene_annotation"
                             }
                         ],
-                        "label": "Scanpy ComputeGraph on data X and data Y: Graph object AnnData",
+                        "label": "gene_annotation",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 31.588610949585586,
-                            "top": 368.3566064231565
+                            "left": 59.084574366332504,
+                            "top": 597.3149223682577
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "fae9d652-9474-4b6c-9bd2-9e0eb6cb5ab4",
+                        "uuid": "a1de7d61-0483-4217-84d9-89e3dc46f403",
                         "when": null,
                         "workflow_outputs": []
                     },
@@ -228344,1498 +232833,1600 @@
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 4,
+                        "id": 3,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Scanpy RunUMAP on data X: UMAP object AnnData"
+                                "name": "Bam-file"
                             }
                         ],
-                        "label": "Scanpy RunUMAP on data X: UMAP object AnnData",
+                        "label": "Bam-file",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 12.794588175128467,
-                            "top": 688.9871973265816
+                            "left": 67.53440796800412,
+                            "top": 743.7297383396873
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "6f462fe5-e34b-4d8f-93bc-61b0d0e99488",
+                        "uuid": "ddc6a5b2-45e6-4a49-a2b5-2d36b98bee2d",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "Comma-separated list of obs/cells and vars/genes",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Comma-separated list of obs/cells and vars/genes",
+                                "name": "Keys for annotations of obs/cells or vars/genes"
+                            }
+                        ],
+                        "label": "Keys for annotations of obs/cells or vars/genes",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 6317.296690866118,
+                            "top": 925.3289621684261
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "2bced0d9-2c35-4a59-a2d7-295312b09948",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "591d2291-9647-4a37-bf54-984a153a049f"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Replace_file"
+                            }
+                        ],
+                        "label": "Replace_file",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 7286.446262020649,
+                            "top": 972.2617918997179
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "d741c4c6-0e32-46b8-9167-ee1d168839d9",
                         "when": null,
                         "workflow_outputs": []
                     }
                 ],
                 "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nScanpy RunPCA: AnnData object\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"ParameterIterator n-neighbors\"];\n  2[\"\u2139\ufe0f Input Dataset\\nScanpy ComputeGraph on data X and data Y: Graph object AnnData\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"ParameterIterator perplexity\"];\n  4[\"\u2139\ufe0f Input Dataset\\nScanpy RunUMAP on data X: UMAP object AnnData\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"ParameterIterator resolution\"];\n  6[\"Scanpy ComputeGraph\"];\n  0 -->|output| 6;\n  1 -->|parameter_iteration| 6;\n  1e60c7cd-7e02-450f-a403-f3df1e548757[\"Output\\nScanpy ComputeGraph on collection X: Graph object AnnData (n-neighbours)\"];\n  6 --> 1e60c7cd-7e02-450f-a403-f3df1e548757;\n  style 1e60c7cd-7e02-450f-a403-f3df1e548757 stroke:#2c3143,stroke-width:4px;\n  7[\"Scanpy RunTSNE\"];\n  2 -->|output| 7;\n  3 -->|parameter_iteration| 7;\n  15143fea-5e2b-4b25-b5d1-0726da910f67[\"Output\\nScanpy RunTSNE on collection X: tSNE object AnnData (perplexity)\"];\n  7 --> 15143fea-5e2b-4b25-b5d1-0726da910f67;\n  style 15143fea-5e2b-4b25-b5d1-0726da910f67 stroke:#2c3143,stroke-width:4px;\n  8[\"Scanpy FindCluster\"];\n  4 -->|output| 8;\n  5 -->|parameter_iteration| 8;\n  6fdddfe7-c4da-4421-86a0-9819ce4c769c[\"Output\\nScanpy FindCluster on collection X: Clusters AnnData (resolution)\"];\n  8 --> 6fdddfe7-c4da-4421-86a0-9819ce4c769c;\n  style 6fdddfe7-c4da-4421-86a0-9819ce4c769c stroke:#2c3143,stroke-width:4px;\n  9[\"Scanpy RunTSNE\"];\n  6 -->|output_h5ad| 9;\n  7c988247-b167-4733-859f-fcd582f91959[\"Output\\nScanpy RunTSNE on collection X: tSNE object AnnData (n-neighbours)\"];\n  9 --> 7c988247-b167-4733-859f-fcd582f91959;\n  style 7c988247-b167-4733-859f-fcd582f91959 stroke:#2c3143,stroke-width:4px;\n  10[\"Scanpy RunUMAP\"];\n  7 -->|output_h5ad| 10;\n  1f5abfa2-845c-4763-9f87-e4b167aa7bc8[\"Output\\nScanpy RunUMAP on collection X: UMAP object AnnData (perplexity)\"];\n  10 --> 1f5abfa2-845c-4763-9f87-e4b167aa7bc8;\n  style 1f5abfa2-845c-4763-9f87-e4b167aa7bc8 stroke:#2c3143,stroke-width:4px;\n  11[\"Scanpy PlotEmbed\"];\n  8 -->|output_h5ad| 11;\n  99185d1e-047f-47f2-9081-07506e1c17df[\"Output\\nresolution_pca_plots\"];\n  11 --> 99185d1e-047f-47f2-9081-07506e1c17df;\n  style 99185d1e-047f-47f2-9081-07506e1c17df stroke:#2c3143,stroke-width:4px;\n  12[\"Scanpy PlotEmbed\"];\n  8 -->|output_h5ad| 12;\n  65d7b619-8659-4008-9e56-db21fda6ce8c[\"Output\\nresolution_umap_plots\"];\n  12 --> 65d7b619-8659-4008-9e56-db21fda6ce8c;\n  style 65d7b619-8659-4008-9e56-db21fda6ce8c stroke:#2c3143,stroke-width:4px;\n  13[\"Scanpy PlotEmbed\"];\n  8 -->|output_h5ad| 13;\n  bdcaf837-5fc4-4024-a87a-eabfa0110127[\"Output\\nresolution_tsne_plots\"];\n  13 --> bdcaf837-5fc4-4024-a87a-eabfa0110127;\n  style bdcaf837-5fc4-4024-a87a-eabfa0110127 stroke:#2c3143,stroke-width:4px;\n  14[\"Scanpy RunUMAP\"];\n  9 -->|output_h5ad| 14;\n  8a0b3d69-e7df-4977-b8eb-ec478b914a26[\"Output\\nScanpy RunUMAP on collection X: UMAP object AnnData (n-neighbours)\"];\n  14 --> 8a0b3d69-e7df-4977-b8eb-ec478b914a26;\n  style 8a0b3d69-e7df-4977-b8eb-ec478b914a26 stroke:#2c3143,stroke-width:4px;\n  15[\"Scanpy FindCluster\"];\n  10 -->|output_h5ad| 15;\n  c2e0d48f-9f0e-4452-8fb5-e78420578c65[\"Output\\nScanpy FindCluster on collection X: Clusters AnnData (perplexity)\"];\n  15 --> c2e0d48f-9f0e-4452-8fb5-e78420578c65;\n  style c2e0d48f-9f0e-4452-8fb5-e78420578c65 stroke:#2c3143,stroke-width:4px;\n  16[\"Scanpy FindCluster\"];\n  14 -->|output_h5ad| 16;\n  c952b32e-99d5-4b94-a6d7-be59439c4dca[\"Output\\nScanpy FindCluster on collection X: Clusters AnnData (n-neighbours)\"];\n  16 --> c952b32e-99d5-4b94-a6d7-be59439c4dca;\n  style c952b32e-99d5-4b94-a6d7-be59439c4dca stroke:#2c3143,stroke-width:4px;\n  17[\"Scanpy PlotEmbed\"];\n  15 -->|output_h5ad| 17;\n  44c0ec07-b64e-428f-9254-5217e8041416[\"Output\\nperplexity_plots\"];\n  17 --> 44c0ec07-b64e-428f-9254-5217e8041416;\n  style 44c0ec07-b64e-428f-9254-5217e8041416 stroke:#2c3143,stroke-width:4px;\n  18[\"Scanpy PlotEmbed\"];\n  16 -->|output_h5ad| 18;\n  0b30f573-8ebd-4582-9bcd-58ba5c778658[\"Output\\nn-neighbors_plots\"];\n  18 --> 0b30f573-8ebd-4582-9bcd-58ba5c778658;\n  style 0b30f573-8ebd-4582-9bcd-58ba5c778658 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Scanpy Parameter Iterator workflow full (imported from URL)",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nFragment_file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nchromosome_sizes.tabular\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ngene_annotation\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nBam-file\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nKeys for annotations of obs/cells or vars/genes\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nReplace_file\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"pp.import_data\"];\n  1 -->|output| 6;\n  0 -->|output| 6;\n  7[\"pp.make_fragment_file\"];\n  3 -->|output| 7;\n  8[\"pl.frag_size_distr\"];\n  6 -->|anndata_out| 8;\n  265d6020-44e2-408c-9eb6-02cbc9ac23a7[\"Output\\nplot frag_size\"];\n  8 --> 265d6020-44e2-408c-9eb6-02cbc9ac23a7;\n  style 265d6020-44e2-408c-9eb6-02cbc9ac23a7 stroke:#2c3143,stroke-width:4px;\n  9[\"pl.frag_size_distr_log\"];\n  6 -->|anndata_out| 9;\n  a37cd3c3-e07e-4bea-899f-ee44cee8370b[\"Output\\nplot log frag_size\"];\n  9 --> a37cd3c3-e07e-4bea-899f-ee44cee8370b;\n  style a37cd3c3-e07e-4bea-899f-ee44cee8370b stroke:#2c3143,stroke-width:4px;\n  10[\"metrics.tsse\"];\n  6 -->|anndata_out| 10;\n  2 -->|output| 10;\n  233284e5-c184-4330-a1d3-2d03951c4ce7[\"Output\\nanndata tsse\"];\n  10 --> 233284e5-c184-4330-a1d3-2d03951c4ce7;\n  style 233284e5-c184-4330-a1d3-2d03951c4ce7 stroke:#2c3143,stroke-width:4px;\n  11[\"pp.import_data-sorted_by_barcodes\"];\n  1 -->|output| 11;\n  7 -->|fragments_out| 11;\n  50ef9fe7-bb08-4957-bc45-079ed78f9ee8[\"Output\\nanndata\"];\n  11 --> 50ef9fe7-bb08-4957-bc45-079ed78f9ee8;\n  style 50ef9fe7-bb08-4957-bc45-079ed78f9ee8 stroke:#2c3143,stroke-width:4px;\n  12[\"pl.tsse\"];\n  10 -->|anndata_out| 12;\n  9a5c0f9c-0423-4822-871e-ba8317f2fa7b[\"Output\\nplot tsse\"];\n  12 --> 9a5c0f9c-0423-4822-871e-ba8317f2fa7b;\n  style 9a5c0f9c-0423-4822-871e-ba8317f2fa7b stroke:#2c3143,stroke-width:4px;\n  13[\"pp.filter_cells\"];\n  10 -->|anndata_out| 13;\n  b58dc4ad-6bf0-4f31-99f4-4f8deb13427c[\"Output\\nanndata filter cells\"];\n  13 --> b58dc4ad-6bf0-4f31-99f4-4f8deb13427c;\n  style b58dc4ad-6bf0-4f31-99f4-4f8deb13427c stroke:#2c3143,stroke-width:4px;\n  14[\"pp.add_tile_matrix\"];\n  13 -->|anndata_out| 14;\n  d4b64fc4-fd35-4781-b799-0d07fe8fe438[\"Output\\nanndata tile matrix\"];\n  14 --> d4b64fc4-fd35-4781-b799-0d07fe8fe438;\n  style d4b64fc4-fd35-4781-b799-0d07fe8fe438 stroke:#2c3143,stroke-width:4px;\n  15[\"pp.select_features\"];\n  14 -->|anndata_out| 15;\n  f531f6bd-3fc6-48b9-bb33-66de7928e670[\"Output\\nanndata select features\"];\n  15 --> f531f6bd-3fc6-48b9-bb33-66de7928e670;\n  style f531f6bd-3fc6-48b9-bb33-66de7928e670 stroke:#2c3143,stroke-width:4px;\n  16[\"pp.scrublet\"];\n  15 -->|anndata_out| 16;\n  5b17aa3a-3694-440f-9022-cf9761feb760[\"Output\\nanndata scrublet\"];\n  16 --> 5b17aa3a-3694-440f-9022-cf9761feb760;\n  style 5b17aa3a-3694-440f-9022-cf9761feb760 stroke:#2c3143,stroke-width:4px;\n  17[\"pp.filter_doublets\"];\n  16 -->|anndata_out| 17;\n  3838cf9d-a018-4aa7-8852-893b2f60ec2a[\"Output\\nanndata filter doublets\"];\n  17 --> 3838cf9d-a018-4aa7-8852-893b2f60ec2a;\n  style 3838cf9d-a018-4aa7-8852-893b2f60ec2a stroke:#2c3143,stroke-width:4px;\n  18[\"tl.spectral\"];\n  17 -->|anndata_out| 18;\n  77883516-8ac4-40b5-8b75-5750639d9fc4[\"Output\\nanndata spectral\"];\n  18 --> 77883516-8ac4-40b5-8b75-5750639d9fc4;\n  style 77883516-8ac4-40b5-8b75-5750639d9fc4 stroke:#2c3143,stroke-width:4px;\n  19[\"tl.umap\"];\n  18 -->|anndata_out| 19;\n  062a5471-7b7a-4d9b-bf6c-fe9bbbc5d2ad[\"Output\\nanndata umap\"];\n  19 --> 062a5471-7b7a-4d9b-bf6c-fe9bbbc5d2ad;\n  style 062a5471-7b7a-4d9b-bf6c-fe9bbbc5d2ad stroke:#2c3143,stroke-width:4px;\n  20[\"pp.knn\"];\n  19 -->|anndata_out| 20;\n  b7ebe580-9938-48e5-8718-4df197126615[\"Output\\nanndata knn\"];\n  20 --> b7ebe580-9938-48e5-8718-4df197126615;\n  style b7ebe580-9938-48e5-8718-4df197126615 stroke:#2c3143,stroke-width:4px;\n  21[\"tl.leiden\"];\n  20 -->|anndata_out| 21;\n  9970eb96-013b-4d97-bbbf-2d1f4663b73c[\"Output\\nanndata_leiden_clustering\"];\n  21 --> 9970eb96-013b-4d97-bbbf-2d1f4663b73c;\n  style 9970eb96-013b-4d97-bbbf-2d1f4663b73c stroke:#2c3143,stroke-width:4px;\n  22[\"pl.umap\"];\n  21 -->|anndata_out| 22;\n  4fff8ec8-7d6f-4871-9e42-d6c1791d6aa9[\"Output\\numap_leiden-clusters\"];\n  22 --> 4fff8ec8-7d6f-4871-9e42-d6c1791d6aa9;\n  style 4fff8ec8-7d6f-4871-9e42-d6c1791d6aa9 stroke:#2c3143,stroke-width:4px;\n  23[\"make_gene_matrix\"];\n  21 -->|anndata_out| 23;\n  2 -->|output| 23;\n  9a5c2e23-5b59-41ae-aceb-0e47ce9e7b1a[\"Output\\nanndata gene matrix\"];\n  23 --> 9a5c2e23-5b59-41ae-aceb-0e47ce9e7b1a;\n  style 9a5c2e23-5b59-41ae-aceb-0e47ce9e7b1a stroke:#2c3143,stroke-width:4px;\n  24[\"scanpy_filter_genes\"];\n  23 -->|anndata_out| 24;\n  7a9b22df-e0e5-49d9-9fa1-2efe316d6d66[\"Output\\nanndata filter genes\"];\n  24 --> 7a9b22df-e0e5-49d9-9fa1-2efe316d6d66;\n  style 7a9b22df-e0e5-49d9-9fa1-2efe316d6d66 stroke:#2c3143,stroke-width:4px;\n  25[\"Normalize\"];\n  24 -->|anndata_out| 25;\n  7dddd4c8-1944-4f50-b331-857d03cc9631[\"Output\\nanndata normalize\"];\n  25 --> 7dddd4c8-1944-4f50-b331-857d03cc9631;\n  style 7dddd4c8-1944-4f50-b331-857d03cc9631 stroke:#2c3143,stroke-width:4px;\n  26[\"pp.log1p\"];\n  25 -->|anndata_out| 26;\n  40ace30a-21e1-4bf2-8e08-ad93b62fb2ee[\"Output\\nanndata log1p\"];\n  26 --> 40ace30a-21e1-4bf2-8e08-ad93b62fb2ee;\n  style 40ace30a-21e1-4bf2-8e08-ad93b62fb2ee stroke:#2c3143,stroke-width:4px;\n  27[\"external.pp.magic\"];\n  26 -->|anndata_out| 27;\n  8c1c7aa9-b9dd-467b-9715-73773aea093f[\"Output\\nanndata_magic\"];\n  27 --> 8c1c7aa9-b9dd-467b-9715-73773aea093f;\n  style 8c1c7aa9-b9dd-467b-9715-73773aea093f stroke:#2c3143,stroke-width:4px;\n  28[\"Copy obsm\"];\n  21 -->|anndata_out| 28;\n  27 -->|anndata_out| 28;\n  2c3825d3-7151-4eef-97d0-c8a31ca6fd3e[\"Output\\nanndata_gene-matrix_leiden\"];\n  28 --> 2c3825d3-7151-4eef-97d0-c8a31ca6fd3e;\n  style 2c3825d3-7151-4eef-97d0-c8a31ca6fd3e stroke:#2c3143,stroke-width:4px;\n  29[\"umap_plot_with_scanpy\"];\n  28 -->|output_h5ad| 29;\n  4 -->|output| 29;\n  4cfbbb70-156b-48d7-b14b-db21198d9b6d[\"Output\\numap_marker-genes\"];\n  29 --> 4cfbbb70-156b-48d7-b14b-db21198d9b6d;\n  style 4cfbbb70-156b-48d7-b14b-db21198d9b6d stroke:#2c3143,stroke-width:4px;\n  30[\"Inspect observations\"];\n  28 -->|output_h5ad| 30;\n  31[\"Cut leiden from table\"];\n  30 -->|obs| 31;\n  11c22200-a54e-4585-82c4-8457dbbfb53c[\"Output\\nleiden annotation\"];\n  31 --> 11c22200-a54e-4585-82c4-8457dbbfb53c;\n  style 11c22200-a54e-4585-82c4-8457dbbfb53c stroke:#2c3143,stroke-width:4px;\n  32[\"Replace leiden\"];\n  31 -->|out_file1| 32;\n  5 -->|output| 32;\n  467de061-79e6-4148-8a65-c06383a14012[\"Output\\ncell type annotation\"];\n  32 --> 467de061-79e6-4148-8a65-c06383a14012;\n  style 467de061-79e6-4148-8a65-c06383a14012 stroke:#2c3143,stroke-width:4px;\n  33[\"Manipulate AnnData\"];\n  28 -->|output_h5ad| 33;\n  32 -->|outfile_replace| 33;\n  cbba6173-f439-4fd5-8423-946aa625112b[\"Output\\nanndata_cell_type\"];\n  33 --> cbba6173-f439-4fd5-8423-946aa625112b;\n  style cbba6173-f439-4fd5-8423-946aa625112b stroke:#2c3143,stroke-width:4px;\n  34[\"Plot cell types\"];\n  33 -->|anndata| 34;\n  c28c53ae-8ee7-47d7-8a00-352908bb7c1a[\"Output\\numap_cell-type\"];\n  34 --> c28c53ae-8ee7-47d7-8a00-352908bb7c1a;\n  style c28c53ae-8ee7-47d7-8a00-352908bb7c1a stroke:#2c3143,stroke-width:4px;\n  35[\"Final Anndata general info\"];\n  33 -->|anndata| 35;\n  379a85d1-a204-4b0b-8b33-86e5582fc51f[\"Output\\ngeneral\"];\n  35 --> 379a85d1-a204-4b0b-8b33-86e5582fc51f;\n  style 379a85d1-a204-4b0b-8b33-86e5582fc51f stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2",
                 "outputs": [
+                    {
+                        "annotation": "Comma-separated list of obs/cells and vars/genes",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Comma-separated list of obs/cells and vars/genes",
+                                "name": "Keys for annotations of obs/cells or vars/genes"
+                            }
+                        ],
+                        "label": "Keys for annotations of obs/cells or vars/genes",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 6317.296690866118,
+                            "top": 925.3289621684261
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "2bced0d9-2c35-4a59-a2d7-295312b09948",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "591d2291-9647-4a37-bf54-984a153a049f"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
                         "errors": null,
-                        "id": 6,
+                        "id": 8,
                         "input_connections": {
-                            "input_obj_file": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "settings|n_neighbors_file": {
-                                "id": 1,
-                                "output_name": "parameter_iteration"
+                            "method|adata": {
+                                "id": 6,
+                                "output_name": "anndata_out"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy ComputeGraph",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool SnapATAC2 Plotting",
+                                "name": "method"
+                            }
+                        ],
+                        "label": "pl.frag_size_distr",
+                        "name": "SnapATAC2 Plotting",
                         "outputs": [
                             {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 311.6945808886878,
-                            "top": 0.08716619391159292
+                            "left": 976.2484628301277,
+                            "top": 50.363557618794744
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_h5ad": {
-                                "action_arguments": {
-                                    "newname": "Scanpy ComputeGraph on collection X: Graph object AnnData (n-neighbours)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_h5ad"
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "c01f0a08ab43",
+                            "name": "snapatac2_plotting",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pl.frag_size_distr\", \"__current_case__\": 0, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"log_scale\": false, \"width\": \"600\", \"height\": \"400\", \"out_file\": \"png\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.4+galaxy1",
+                        "type": "tool",
+                        "uuid": "62b9a255-2b4a-42a7-93a2-b8790d36148f",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "plot frag_size",
+                                "output_name": "out_png",
+                                "uuid": "265d6020-44e2-408c-9eb6-02cbc9ac23a7"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {
+                            "method|adata": {
+                                "id": 6,
+                                "output_name": "anndata_out"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool SnapATAC2 Plotting",
+                                "name": "method"
+                            }
+                        ],
+                        "label": "pl.frag_size_distr_log",
+                        "name": "SnapATAC2 Plotting",
+                        "outputs": [
+                            {
+                                "name": "out_png",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 971.9878217859592,
+                            "top": 178.50521031008577
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "6417cccad133",
-                            "name": "scanpy_compute_graph",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "c01f0a08ab43",
+                            "name": "snapatac2_plotting",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"n_neighbors_file|__identifier__\": \"n-neighbors_10\", \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": false, \"__current_case__\": 1, \"key_added\": \"\", \"n_neighbors\": \"15\", \"n_neighbors_file\": {\"__class__\": \"ConnectedValue\"}, \"use_rep\": \"X_pca\", \"n_pcs\": \"20\", \"knn\": true, \"method\": \"umap\", \"metric\": \"euclidean\", \"random_seed\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pl.frag_size_distr\", \"__current_case__\": 0, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"log_scale\": true, \"width\": \"600\", \"height\": \"400\", \"out_file\": \"png\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.4+galaxy1",
                         "type": "tool",
-                        "uuid": "d8928b9b-012d-469c-8916-7a42b88b8bd6",
+                        "uuid": "6665080c-ba86-4a70-b901-394770382862",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Scanpy ComputeGraph on collection X: Graph object AnnData (n-neighbours)",
-                                "output_name": "output_h5ad",
-                                "uuid": "1e60c7cd-7e02-450f-a403-f3df1e548757"
+                                "label": "plot log frag_size",
+                                "output_name": "out_png",
+                                "uuid": "a37cd3c3-e07e-4bea-899f-ee44cee8370b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
                         "errors": null,
-                        "id": 7,
+                        "id": 10,
                         "input_connections": {
-                            "input_obj_file": {
+                            "method|adata": {
+                                "id": 6,
+                                "output_name": "anndata_out"
+                            },
+                            "method|gene_anno": {
                                 "id": 2,
                                 "output_name": "output"
-                            },
-                            "settings|perplexity_file": {
-                                "id": 3,
-                                "output_name": "parameter_iteration"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy RunTSNE",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
+                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
+                                "name": "method"
                             },
                             {
-                                "name": "output_embed",
-                                "type": "tabular"
+                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
+                                "name": "method"
+                            }
+                        ],
+                        "label": "metrics.tsse",
+                        "name": "SnapATAC2 Preprocessing",
+                        "outputs": [
+                            {
+                                "name": "anndata_out",
+                                "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 284.8446053027503,
-                            "top": 367.1121982373686
+                            "left": 976.5191068126845,
+                            "top": 321.5929676948151
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput_h5ad": {
+                            "TagDatasetActionanndata_out": {
                                 "action_arguments": {
-                                    "newname": "Scanpy RunTSNE on collection X: tSNE object AnnData (perplexity)"
+                                    "tags": "non_filtered_matrix"
                                 },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_h5ad"
+                                "action_type": "TagDatasetAction",
+                                "output_name": "anndata_out"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "181d61d2f3cd",
-                            "name": "scanpy_run_tsne",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "48d9421bf176",
+                            "name": "snapatac2_preprocessing",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"embeddings\": true, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"perplexity_file|__identifier__\": \"perplexity_15.0\", \"settings\": {\"default\": false, \"__current_case__\": 1, \"key_added\": null, \"perplexity\": \"30.0\", \"perplexity_file\": {\"__class__\": \"ConnectedValue\"}, \"early_exaggeration\": \"12.0\", \"learning_rate\": \"1000.0\", \"fast_tsne\": false, \"n_job\": null, \"n_pc\": null, \"random_seed\": \"0\"}, \"use_rep\": \"X_pca\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"metrics.tsse\", \"__current_case__\": 12, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"gene_anno\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.4+galaxy1",
                         "type": "tool",
-                        "uuid": "90f289f5-8589-4094-a415-72105bd42346",
+                        "uuid": "1d16ec89-ce71-4f81-a6c9-b785247666f0",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Scanpy RunTSNE on collection X: tSNE object AnnData (perplexity)",
-                                "output_name": "output_h5ad",
-                                "uuid": "15143fea-5e2b-4b25-b5d1-0726da910f67"
+                                "label": "anndata tsse",
+                                "output_name": "anndata_out",
+                                "uuid": "233284e5-c184-4330-a1d3-2d03951c4ce7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
                         "errors": null,
-                        "id": 8,
+                        "id": 11,
                         "input_connections": {
-                            "input_obj_file": {
-                                "id": 4,
+                            "method|chrom_sizes": {
+                                "id": 1,
                                 "output_name": "output"
                             },
-                            "settings|resolution_file": {
-                                "id": 5,
-                                "output_name": "parameter_iteration"
+                            "method|fragment_file": {
+                                "id": 7,
+                                "output_name": "fragments_out"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
+                                "name": "method"
+                            },
+                            {
+                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
+                                "name": "method"
+                            },
+                            {
+                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
+                                "name": "method"
                             }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy FindCluster",
+                        ],
+                        "label": "pp.import_data-sorted_by_barcodes",
+                        "name": "SnapATAC2 Preprocessing",
                         "outputs": [
                             {
-                                "name": "output_h5ad",
+                                "name": "anndata_out",
                                 "type": "h5ad"
-                            },
-                            {
-                                "name": "output_txt",
-                                "type": "tsv"
                             }
                         ],
                         "position": {
-                            "left": 299.9946351604703,
-                            "top": 682.3122048475996
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_h5ad": {
-                                "action_arguments": {
-                                    "newname": "Scanpy FindCluster on collection X: Clusters AnnData (resolution)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_h5ad"
-                            }
+                            "left": 1033.1679120853273,
+                            "top": 703.9571480740287
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "2ccd9f9e2cd0",
-                            "name": "scanpy_find_cluster",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "48d9421bf176",
+                            "name": "snapatac2_preprocessing",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"method\": \"louvain\", \"output_cluster\": true, \"output_format\": \"anndata_h5ad\", \"resolution_file|__identifier__\": \"resolution_0.2\", \"settings\": {\"default\": false, \"__current_case__\": 1, \"neighbors_key\": \"neighbors\", \"layer\": \"\", \"key_added\": null, \"resolution\": \"1.0\", \"resolution_file\": {\"__class__\": \"ConnectedValue\"}, \"restrict_to\": null, \"use_weights\": false, \"random_seed\": \"0\", \"directed\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.import_data\", \"__current_case__\": 1, \"fragment_file\": {\"__class__\": \"ConnectedValue\"}, \"chrom_sizes\": {\"__class__\": \"ConnectedValue\"}, \"min_num_fragments\": \"200\", \"sorted_by_barcode\": true, \"whitelist\": {\"__class__\": \"RuntimeValue\"}, \"chrM\": \"chrM, M\", \"shift_left\": \"0\", \"shift_right\": \"0\", \"chunk_size\": \"2000\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.4+galaxy1",
                         "type": "tool",
-                        "uuid": "0854fbcc-e57c-421c-8320-3eb5d1fdba1e",
+                        "uuid": "b92fe42b-af1d-4f83-b1cd-7e4c173d8c2c",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Scanpy FindCluster on collection X: Clusters AnnData (resolution)",
-                                "output_name": "output_h5ad",
-                                "uuid": "6fdddfe7-c4da-4421-86a0-9819ce4c769c"
+                                "label": "anndata",
+                                "output_name": "anndata_out",
+                                "uuid": "50ef9fe7-bb08-4957-bc45-079ed78f9ee8"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
                         "errors": null,
-                        "id": 9,
+                        "id": 12,
                         "input_connections": {
-                            "input_obj_file": {
-                                "id": 6,
-                                "output_name": "output_h5ad"
+                            "method|adata": {
+                                "id": 10,
+                                "output_name": "anndata_out"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy RunTSNE",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
-                            },
+                                "description": "runtime parameter for tool SnapATAC2 Plotting",
+                                "name": "method"
+                            }
+                        ],
+                        "label": "pl.tsse",
+                        "name": "SnapATAC2 Plotting",
+                        "outputs": [
                             {
-                                "name": "output_embed",
-                                "type": "tabular"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 583.120210023914,
-                            "top": 5.5371860303373746
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_h5ad": {
-                                "action_arguments": {
-                                    "newname": "Scanpy RunTSNE on collection X: tSNE object AnnData (n-neighbours)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_h5ad"
-                            }
+                            "left": 1234.1672018887232,
+                            "top": 181.36234265283736
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "181d61d2f3cd",
-                            "name": "scanpy_run_tsne",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "c01f0a08ab43",
+                            "name": "snapatac2_plotting",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"embeddings\": true, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"n-neighbors_10\", \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": false, \"__current_case__\": 1, \"key_added\": null, \"perplexity\": \"30.0\", \"perplexity_file\": null, \"early_exaggeration\": \"12.0\", \"learning_rate\": \"1000.0\", \"fast_tsne\": false, \"n_job\": null, \"n_pc\": null, \"random_seed\": \"0\"}, \"use_rep\": \"X_pca\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pl.tsse\", \"__current_case__\": 1, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"min_fragment\": \"500\", \"width\": \"600\", \"height\": \"400\", \"out_file\": \"png\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.4+galaxy1",
                         "type": "tool",
-                        "uuid": "727487bc-89e8-478c-81f7-3b3a2db1d2d7",
+                        "uuid": "9db3b159-cfe6-4f24-ad2e-79e6ab1f1c6c",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Scanpy RunTSNE on collection X: tSNE object AnnData (n-neighbours)",
-                                "output_name": "output_h5ad",
-                                "uuid": "7c988247-b167-4733-859f-fcd582f91959"
+                                "label": "plot tsse",
+                                "output_name": "out_png",
+                                "uuid": "9a5c0f9c-0423-4822-871e-ba8317f2fa7b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
                         "errors": null,
-                        "id": 10,
+                        "id": 13,
                         "input_connections": {
-                            "input_obj_file": {
-                                "id": 7,
-                                "output_name": "output_h5ad"
+                            "method|adata": {
+                                "id": 10,
+                                "output_name": "anndata_out"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy RunUMAP",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
+                                "name": "method"
+                            }
+                        ],
+                        "label": "pp.filter_cells",
+                        "name": "SnapATAC2 Preprocessing",
                         "outputs": [
                             {
-                                "name": "output_h5ad",
+                                "name": "anndata_out",
                                 "type": "h5ad"
-                            },
-                            {
-                                "name": "output_embed",
-                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 580.3870931396372,
-                            "top": 371.3332390321145
+                            "left": 1900.828125,
+                            "top": 498.703125
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput_h5ad": {
-                                "action_arguments": {
-                                    "newname": "Scanpy RunUMAP on collection X: UMAP object AnnData (perplexity)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_h5ad"
+                            "HideDatasetActionanndata_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "anndata_out"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "bd4a244faeb8",
-                            "name": "scanpy_run_umap",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "48d9421bf176",
+                            "name": "snapatac2_preprocessing",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"embeddings\": true, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"perplexity_15.0\", \"key_added\": null, \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": true, \"__current_case__\": 0}, \"use_graph\": \"neighbors\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.filter_cells\", \"__current_case__\": 4, \"adata\": {\"__class__\": \"RuntimeValue\"}, \"min_counts\": \"5000\", \"min_tsse\": \"10.0\", \"max_counts\": \"100000\", \"max_tsse\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.4+galaxy1",
                         "type": "tool",
-                        "uuid": "2b98c2ef-aea6-4581-9155-e780f4d5c5eb",
+                        "uuid": "067a4964-4e96-456e-848e-ea414a745d66",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Scanpy RunUMAP on collection X: UMAP object AnnData (perplexity)",
-                                "output_name": "output_h5ad",
-                                "uuid": "1f5abfa2-845c-4763-9f87-e4b167aa7bc8"
+                                "label": "anndata filter cells",
+                                "output_name": "anndata_out",
+                                "uuid": "b58dc4ad-6bf0-4f31-99f4-4f8deb13427c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
                         "errors": null,
-                        "id": 11,
+                        "id": 14,
                         "input_connections": {
-                            "input_obj_file": {
-                                "id": 8,
-                                "output_name": "output_h5ad"
+                            "method|adata": {
+                                "id": 13,
+                                "output_name": "anndata_out"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy PlotEmbed",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
+                                "name": "method"
+                            }
+                        ],
+                        "label": "pp.add_tile_matrix",
+                        "name": "SnapATAC2 Preprocessing",
                         "outputs": [
                             {
-                                "name": "output_png",
-                                "type": "png"
+                                "name": "anndata_out",
+                                "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 610.8375710947927,
-                            "top": 629.3556101888285
+                            "left": 2244.497498607226,
+                            "top": 531.5176822961781
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                        "post_job_actions": {
+                            "HideDatasetActionanndata_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "anndata_out"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "35f6611fb8c3",
-                            "name": "scanpy_plot_embed",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "48d9421bf176",
+                            "name": "snapatac2_preprocessing",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"basis\": \"pca\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"color_by\": \"louvain\", \"components\": \"\", \"edges\": false, \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": false, \"fig_size\": \"4,4\", \"fig_title\": null, \"gene_symbols_field\": null, \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"resolution_0.2\", \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": false, \"use_raw\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.add_tile_matrix\", \"__current_case__\": 2, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"bin_size\": \"500\", \"chunk_size\": \"500\", \"exclude_chroms\": \"chrM, chrY, M, Y\", \"min_frag_size\": null, \"max_frag_size\": null, \"count_frag_as_reads\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.4+galaxy1",
                         "type": "tool",
-                        "uuid": "6dc51709-4987-4944-99d4-386cc9233d1b",
+                        "uuid": "de6e8e48-f792-4163-9289-f5fa7690fa3c",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "resolution_pca_plots",
-                                "output_name": "output_png",
-                                "uuid": "99185d1e-047f-47f2-9081-07506e1c17df"
+                                "label": "anndata tile matrix",
+                                "output_name": "anndata_out",
+                                "uuid": "d4b64fc4-fd35-4781-b799-0d07fe8fe438"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
                         "errors": null,
-                        "id": 12,
+                        "id": 15,
                         "input_connections": {
-                            "input_obj_file": {
-                                "id": 8,
-                                "output_name": "output_h5ad"
+                            "method|adata": {
+                                "id": 14,
+                                "output_name": "anndata_out"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy PlotEmbed",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
+                                "name": "method"
+                            },
+                            {
+                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
+                                "name": "method"
+                            },
+                            {
+                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
+                                "name": "method"
+                            }
+                        ],
+                        "label": "pp.select_features",
+                        "name": "SnapATAC2 Preprocessing",
                         "outputs": [
                             {
-                                "name": "output_png",
-                                "type": "png"
+                                "name": "anndata_out",
+                                "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 601.9354642911717,
-                            "top": 807.4162217137739
+                            "left": 2262.8393353215497,
+                            "top": 793.2107306253445
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                        "post_job_actions": {
+                            "HideDatasetActionanndata_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "anndata_out"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "35f6611fb8c3",
-                            "name": "scanpy_plot_embed",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "48d9421bf176",
+                            "name": "snapatac2_preprocessing",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"basis\": \"umap\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"color_by\": \"louvain\", \"components\": \"\", \"edges\": false, \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": false, \"fig_size\": \"4,4\", \"fig_title\": null, \"gene_symbols_field\": null, \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"resolution_0.2\", \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": false, \"use_raw\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.select_features\", \"__current_case__\": 5, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"n_features\": \"250000\", \"filter_lower_quantile\": \"0.005\", \"filter_upper_quantile\": \"0.005\", \"whitelist\": {\"__class__\": \"RuntimeValue\"}, \"blacklist\": {\"__class__\": \"RuntimeValue\"}, \"max_iter\": \"1\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.4+galaxy1",
                         "type": "tool",
-                        "uuid": "4098f10f-19d7-4745-aeb5-2d5ceb436fb1",
+                        "uuid": "0f99ab71-fb4c-4d8f-b248-854b7661e365",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "resolution_umap_plots",
-                                "output_name": "output_png",
-                                "uuid": "65d7b619-8659-4008-9e56-db21fda6ce8c"
+                                "label": "anndata select features",
+                                "output_name": "anndata_out",
+                                "uuid": "f531f6bd-3fc6-48b9-bb33-66de7928e670"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
                         "errors": null,
-                        "id": 13,
+                        "id": 16,
                         "input_connections": {
-                            "input_obj_file": {
-                                "id": 8,
-                                "output_name": "output_h5ad"
+                            "method|adata": {
+                                "id": 15,
+                                "output_name": "anndata_out"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy PlotEmbed",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
+                                "name": "method"
+                            }
+                        ],
+                        "label": "pp.scrublet",
+                        "name": "SnapATAC2 Preprocessing",
                         "outputs": [
                             {
-                                "name": "output_png",
-                                "type": "png"
+                                "name": "anndata_out",
+                                "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 593.5750000507026,
-                            "top": 977.1437760474608
+                            "left": 2586.191666804627,
+                            "top": 949.4798428594668
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                        "post_job_actions": {
+                            "HideDatasetActionanndata_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "anndata_out"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "35f6611fb8c3",
-                            "name": "scanpy_plot_embed",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "48d9421bf176",
+                            "name": "snapatac2_preprocessing",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"basis\": \"tsne\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"color_by\": \"louvain\", \"components\": \"\", \"edges\": false, \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": false, \"fig_size\": \"4,4\", \"fig_title\": null, \"gene_symbols_field\": null, \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"resolution_0.2\", \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": false, \"use_raw\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.scrublet\", \"__current_case__\": 6, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"features\": \"\", \"n_comps\": \"15\", \"sim_doublet_ratio\": \"2.0\", \"expected_doublet_rate\": \"0.1\", \"n_neighbors\": null, \"use_approx_neighbors\": false, \"random_state\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.4+galaxy1",
                         "type": "tool",
-                        "uuid": "b1d539e5-05cf-4359-87c9-19b2d22dcdb7",
+                        "uuid": "a944b129-dedb-4a9a-a1c7-1a4ddd51fac6",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "resolution_tsne_plots",
-                                "output_name": "output_png",
-                                "uuid": "bdcaf837-5fc4-4024-a87a-eabfa0110127"
+                                "label": "anndata scrublet",
+                                "output_name": "anndata_out",
+                                "uuid": "5b17aa3a-3694-440f-9022-cf9761feb760"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
                         "errors": null,
-                        "id": 14,
+                        "id": 17,
                         "input_connections": {
-                            "input_obj_file": {
-                                "id": 9,
-                                "output_name": "output_h5ad"
+                            "method|adata": {
+                                "id": 16,
+                                "output_name": "anndata_out"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy RunUMAP",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
+                                "name": "method"
+                            }
+                        ],
+                        "label": "pp.filter_doublets",
+                        "name": "SnapATAC2 Preprocessing",
                         "outputs": [
                             {
-                                "name": "output_h5ad",
+                                "name": "anndata_out",
                                 "type": "h5ad"
-                            },
-                            {
-                                "name": "output_embed",
-                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 843.1624694773969,
-                            "top": 18.380633385427693
+                            "left": 2635.9329633142843,
+                            "top": 663.8944755224237
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput_h5ad": {
-                                "action_arguments": {
-                                    "newname": "Scanpy RunUMAP on collection X: UMAP object AnnData (n-neighbours)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_h5ad"
+                            "HideDatasetActionanndata_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "anndata_out"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "bd4a244faeb8",
-                            "name": "scanpy_run_umap",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "48d9421bf176",
+                            "name": "snapatac2_preprocessing",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"embeddings\": true, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"n-neighbors_10\", \"key_added\": null, \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": true, \"__current_case__\": 0}, \"use_graph\": \"neighbors\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.filter_doublets\", \"__current_case__\": 7, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"probability_threshold\": \"0.5\", \"score_threshold\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.4+galaxy1",
                         "type": "tool",
-                        "uuid": "e61b46a4-847c-45d6-90e3-b1547fa95634",
+                        "uuid": "edb303e1-aaf9-4f4c-ab5a-b4197997eb95",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Scanpy RunUMAP on collection X: UMAP object AnnData (n-neighbours)",
-                                "output_name": "output_h5ad",
-                                "uuid": "8a0b3d69-e7df-4977-b8eb-ec478b914a26"
+                                "label": "anndata filter doublets",
+                                "output_name": "anndata_out",
+                                "uuid": "3838cf9d-a018-4aa7-8852-893b2f60ec2a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
                         "errors": null,
-                        "id": 15,
+                        "id": 18,
                         "input_connections": {
-                            "input_obj_file": {
-                                "id": 10,
-                                "output_name": "output_h5ad"
+                            "method|adata": {
+                                "id": 17,
+                                "output_name": "anndata_out"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy FindCluster",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
+                                "description": "runtime parameter for tool SnapATAC2 Clustering",
+                                "name": "method"
                             },
                             {
-                                "name": "output_txt",
-                                "type": "tsv"
+                                "description": "runtime parameter for tool SnapATAC2 Clustering",
+                                "name": "method"
+                            }
+                        ],
+                        "label": "tl.spectral",
+                        "name": "SnapATAC2 Clustering",
+                        "outputs": [
+                            {
+                                "name": "anndata_out",
+                                "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 860.8525296481835,
-                            "top": 354.84265238442265
+                            "left": 3084.96875,
+                            "top": 555.0625
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput_h5ad": {
-                                "action_arguments": {
-                                    "newname": "Scanpy FindCluster on collection X: Clusters AnnData (perplexity)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_h5ad"
+                            "HideDatasetActionanndata_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "anndata_out"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "2ccd9f9e2cd0",
-                            "name": "scanpy_find_cluster",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "94ae400dde2f",
+                            "name": "snapatac2_clustering",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"perplexity_15.0\", \"method\": \"louvain\", \"output_cluster\": true, \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": false, \"__current_case__\": 1, \"neighbors_key\": \"neighbors\", \"layer\": \"\", \"key_added\": null, \"resolution\": \"0.6\", \"resolution_file\": null, \"restrict_to\": null, \"use_weights\": false, \"random_seed\": \"0\", \"directed\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"tl.spectral\", \"__current_case__\": 0, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"n_comps\": \"30\", \"features\": {\"__class__\": \"RuntimeValue\"}, \"random_state\": \"0\", \"sample_size\": null, \"chunk_size\": \"20000\", \"distance_metric\": \"cosine\", \"weighted_by_sd\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.4+galaxy1",
                         "type": "tool",
-                        "uuid": "2ec67307-cf3a-45a7-b973-d0dd915ec5b5",
+                        "uuid": "282c336d-2ff5-460b-889d-58ef74574199",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Scanpy FindCluster on collection X: Clusters AnnData (perplexity)",
-                                "output_name": "output_h5ad",
-                                "uuid": "c2e0d48f-9f0e-4452-8fb5-e78420578c65"
+                                "label": "anndata spectral",
+                                "output_name": "anndata_out",
+                                "uuid": "77883516-8ac4-40b5-8b75-5750639d9fc4"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
                         "errors": null,
-                        "id": 16,
+                        "id": 19,
                         "input_connections": {
-                            "input_obj_file": {
-                                "id": 14,
-                                "output_name": "output_h5ad"
+                            "method|adata": {
+                                "id": 18,
+                                "output_name": "anndata_out"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy FindCluster",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool SnapATAC2 Clustering",
+                                "name": "method"
+                            }
+                        ],
+                        "label": "tl.umap",
+                        "name": "SnapATAC2 Clustering",
                         "outputs": [
                             {
-                                "name": "output_h5ad",
+                                "name": "anndata_out",
                                 "type": "h5ad"
-                            },
-                            {
-                                "name": "output_txt",
-                                "type": "tsv"
                             }
                         ],
                         "position": {
-                            "left": 1110.1696213010753,
-                            "top": 27.962176176922693
+                            "left": 3098.912527828772,
+                            "top": 841.6746200330715
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput_h5ad": {
-                                "action_arguments": {
-                                    "newname": "Scanpy FindCluster on collection X: Clusters AnnData (n-neighbours)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_h5ad"
+                            "HideDatasetActionanndata_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "anndata_out"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "2ccd9f9e2cd0",
-                            "name": "scanpy_find_cluster",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "94ae400dde2f",
+                            "name": "snapatac2_clustering",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"n-neighbors_10\", \"method\": \"louvain\", \"output_cluster\": true, \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": false, \"__current_case__\": 1, \"neighbors_key\": \"neighbors\", \"layer\": \"\", \"key_added\": null, \"resolution\": \"0.6\", \"resolution_file\": null, \"restrict_to\": null, \"use_weights\": false, \"random_seed\": \"0\", \"directed\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"tl.umap\", \"__current_case__\": 1, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"n_comps\": \"2\", \"use_dims\": null, \"use_rep\": \"X_spectral\", \"key_added\": \"umap\", \"random_state\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.4+galaxy1",
                         "type": "tool",
-                        "uuid": "a427d6bd-a860-4ff1-a614-3c48baa04737",
+                        "uuid": "ea0844bb-c3d7-45f7-bd12-73b8325e8816",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Scanpy FindCluster on collection X: Clusters AnnData (n-neighbours)",
-                                "output_name": "output_h5ad",
-                                "uuid": "c952b32e-99d5-4b94-a6d7-be59439c4dca"
+                                "label": "anndata umap",
+                                "output_name": "anndata_out",
+                                "uuid": "062a5471-7b7a-4d9b-bf6c-fe9bbbc5d2ad"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
                         "errors": null,
-                        "id": 17,
+                        "id": 20,
                         "input_connections": {
-                            "input_obj_file": {
-                                "id": 15,
-                                "output_name": "output_h5ad"
+                            "method|adata": {
+                                "id": 19,
+                                "output_name": "anndata_out"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy PlotEmbed",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool SnapATAC2 Clustering",
+                                "name": "method"
+                            }
+                        ],
+                        "label": "pp.knn",
+                        "name": "SnapATAC2 Clustering",
                         "outputs": [
                             {
-                                "name": "output_png",
-                                "type": "png"
+                                "name": "anndata_out",
+                                "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 1122.427370848608,
-                            "top": 356.74062604698014
+                            "left": 3537.197366261425,
+                            "top": 667.2386060771821
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                        "post_job_actions": {
+                            "HideDatasetActionanndata_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "anndata_out"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "35f6611fb8c3",
-                            "name": "scanpy_plot_embed",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "94ae400dde2f",
+                            "name": "snapatac2_clustering",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"basis\": \"tsne\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"color_by\": \"louvain\", \"components\": \"\", \"edges\": false, \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": false, \"fig_size\": \"4,4\", \"fig_title\": null, \"gene_symbols_field\": null, \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"perplexity_15.0\", \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": false, \"use_raw\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.knn\", \"__current_case__\": 2, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"n_neighbors\": \"50\", \"use_dims\": \"\", \"use_rep\": \"X_spectral\", \"algorithm\": \"kdtree\", \"random_state\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.4+galaxy1",
                         "type": "tool",
-                        "uuid": "900f5cef-ad85-4b7d-b4c3-1c3a86c64e29",
+                        "uuid": "8628dcfa-cec9-488a-9ea1-9b9caa315290",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "perplexity_plots",
-                                "output_name": "output_png",
-                                "uuid": "44c0ec07-b64e-428f-9254-5217e8041416"
+                                "label": "anndata knn",
+                                "output_name": "anndata_out",
+                                "uuid": "b7ebe580-9938-48e5-8718-4df197126615"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
                         "errors": null,
-                        "id": 18,
+                        "id": 21,
                         "input_connections": {
-                            "input_obj_file": {
-                                "id": 16,
-                                "output_name": "output_h5ad"
+                            "method|adata": {
+                                "id": 20,
+                                "output_name": "anndata_out"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy PlotEmbed",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool SnapATAC2 Clustering",
+                                "name": "method"
+                            }
+                        ],
+                        "label": "tl.leiden",
+                        "name": "SnapATAC2 Clustering",
                         "outputs": [
                             {
-                                "name": "output_png",
-                                "type": "png"
+                                "name": "anndata_out",
+                                "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 1378.4911495849283,
-                            "top": 64.43740029026476
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
-                        "tool_shed_repository": {
-                            "changeset_revision": "35f6611fb8c3",
-                            "name": "scanpy_plot_embed",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 3836.579452840314,
+                            "top": 625.923381281925
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"basis\": \"umap\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"color_by\": \"louvain\", \"components\": \"\", \"edges\": false, \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": false, \"fig_size\": \"4,4\", \"fig_title\": null, \"gene_symbols_field\": null, \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"n-neighbors_10\", \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": false, \"use_raw\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
-                        "type": "tool",
-                        "uuid": "b2682b86-da4c-427e-b793-24faa66f5c8f",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "n-neighbors_plots",
-                                "output_name": "output_png",
-                                "uuid": "0b30f573-8ebd-4582-9bcd-58ba5c778658"
+                        "post_job_actions": {
+                            "DeleteIntermediatesActionanndata_out": {
+                                "action_arguments": {},
+                                "action_type": "DeleteIntermediatesAction",
+                                "output_name": "anndata_out"
                             }
-                        ]
-                    }
-                ],
-                "parent_id": "single-cell/scanpy_parameter_iterator",
-                "path": "topics/single-cell/tutorials/scanpy_parameter_iterator/workflows/Scanpy-Parameter-Iterator-workflow-full.ga",
-                "tags": [],
-                "test_results": null,
-                "tests": true,
-                "title": "Scanpy Parameter Iterator workflow full (imported from URL)",
-                "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scanpy_parameter_iterator/versions/scanpy-parameter-iterator-workflow-full",
-                "tutorial_id": "scanpy_parameter_iterator",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scanpy_parameter_iterator/workflows/Scanpy-Parameter-Iterator-workflow-full.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scanpy_parameter_iterator/workflows/Scanpy-Parameter-Iterator-workflow-full.html",
-                "version": 1,
-                "wfid": "single-cell-scanpy_parameter_iterator",
-                "wfname": "scanpy-parameter-iterator-workflow-full",
-                "workflow": "Scanpy-Parameter-Iterator-workflow-full.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9"
-                ],
-                "workflowhub_id": "1243"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/8011681"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "anndata_ops",
-                    "owner": "ebi-gxa",
-                    "revisions": "890fb06a2893",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "anndata_ops",
-                    "owner": "ebi-gxa",
-                    "revisions": "825dfd66e3fb",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_filter_cells",
-                    "owner": "ebi-gxa",
-                    "revisions": "e9283529cba1",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "unzip",
-                    "owner": "imgteam",
-                    "revisions": "57f0914ddb7b",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "anndata_import",
-                    "owner": "iuc",
-                    "revisions": "fb9e030ffae4",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "anndata_inspect",
-                    "owner": "iuc",
-                    "revisions": "ee98d611afc6",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "anndata_manipulate",
-                    "owner": "iuc",
-                    "revisions": "3d748954434b",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_ops\n  owner: ebi-gxa\n  revisions: 890fb06a2893\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_ops\n  owner: ebi-gxa\n  revisions: 825dfd66e3fb\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter_cells\n  owner: ebi-gxa\n  revisions: e9283529cba1\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unzip\n  owner: imgteam\n  revisions: 57f0914ddb7b\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_import\n  owner: iuc\n  revisions: fb9e030ffae4\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_inspect\n  owner: iuc\n  revisions: ee98d611afc6\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n  owner: iuc\n  revisions: 3d748954434b\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "hexhowells"
-            ],
-            "editing": [
-                "nomadscientist",
-                "pavanvidem",
-                "mtekman",
-                "hexylena"
-            ],
-            "funding": [
-                "elixir-fair-data"
-            ],
-            "testing": [
-                "pavanvidem"
-            ]
-        },
-        "contributors": [
-            {
-                "email": "hexhowells@gmail.com",
-                "id": "hexhowells",
-                "joined": "2023-06",
-                "name": "Morgan Howells",
-                "orcid": "0009-0008-9422-6380",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexhowells/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexhowells.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "bio": "Senior Lecturer at The Open University",
-                "elixir_node": "uk",
-                "email": "wendi.bacon@open.ac.uk",
-                "fediverse": "https://mstdn.science/@wendibacon1",
-                "fediverse_flavor": "mastodon",
-                "id": "nomadscientist",
-                "joined": "2020-03",
-                "matrix": "nomadscientist:matrix.org",
-                "name": "Wendi Bacon",
-                "orcid": "0000-0002-8170-8806",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
-                "twitter": "WendiBacon1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "pavanvidem",
-                "joined": "2017-09",
-                "name": "Pavankumar Videm",
-                "orcid": "0000-0002-5192-126X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "elixir_node": "de",
-                "email": "mtekman89@gmail.com",
-                "former_affiliations": [
-                    "elixir-europe"
-                ],
-                "id": "mtekman",
-                "joined": "2018-11",
-                "name": "Mehmet Tekman",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "pavanvidem",
-                "joined": "2017-09",
-                "name": "Pavankumar Videm",
-                "orcid": "0000-0002-5192-126X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
-            },
-            {
-                "funder": true,
-                "funding_id": "MR/V038966/1",
-                "funding_statement": "This work has been funded by the ELIXIR-UK FAIR Data Stewardship training UKRI award (MR/V038966/1)",
-                "funding_system": "ukri",
-                "github": false,
-                "id": "elixir-fair-data",
-                "joined": "2023-06",
-                "name": "ELIXIR-UK: FAIR Data Stewardship training",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-fair-data/",
-                "short_name": "ELIXIR Fair Data",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-fair-data.json"
-            }
-        ],
-        "dir": "topics/single-cell/tutorials/scrna-ncbi-anndata",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "single-cell",
-                "type": "internal"
-            }
-        ],
-        "hands_on": true,
-        "id": "single-cell/scrna-ncbi-anndata",
-        "inexact_supported_servers": [
-            "UseGalaxy.org.au"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Single cell data often requires additional processing and conversion before it is able to be analysed.",
-            "Metadata and annotations can be added in both manually and automatically with various tools and resources."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-04-10",
-        "objectives": [
-            "Analyse gene data from NCBI.",
-            "Convert raw gene expression data into the AnnData format.",
-            "Add metadata to the AnnData object to prepare it for analysis."
-        ],
-        "pageviews": 183,
-        "priority": 3,
-        "pub_date": "2023-12-13",
-        "questions": [
-            "How do I understand NCBI data?",
-            "How can I convert raw gene data to the AnnData format?",
-            "How do I manually and automatically add metadata to my AnnData object?"
-        ],
-        "short_id": "T00380",
-        "short_tools": [
-            "anndata_ops",
-            "anndata_manipulate",
-            "anndata_inspect",
-            "scanpy_filter_cells",
-            "Paste1",
-            "Cut1",
-            "unzip",
-            "anndata_import",
-            "tp_replace_in_column"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "datamanipulation",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "data management",
-            "data import"
-        ],
-        "time_estimation": "1H",
-        "title": "Converting NCBI Data to the AnnData Format",
-        "tools": [
-            "Cut1",
-            "Paste1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1"
-        ],
-        "topic_name": "single-cell",
-        "topic_name_human": "Single Cell",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "scrna-ncbi-anndata",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.json"
-        },
-        "version": 3,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 87,
-        "visitors": 151,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0009-0008-9422-6380",
-                        "name": "Morgan Howells"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-5192-126X",
-                        "name": "Pavankumar Videm"
-                    }
-                ],
-                "description": "",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353219_PA_PB1B_Pool_2_S24_L001_dge.txt\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353223_PA_PB2B_Pool_2_S26_L001_dge.txt\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353218_PA_PB1B_Pool_1_2_S74_L003_dge.txt\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353216_PA_PB1A_Pool_1_3_S50_L002_dge.txt\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353221_PA_PB2A_Pool_1_3_S25_L001_dge.txt\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353215_PA_AUG_PB_1B_S2_dge.txt\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353222_PA_PB2B_Pool_1_3_S52_L002_dge.txt\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353220_PA_PB1B_Pool_3_S51_L002_dge.txt\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353217_PA_PB1A_Pool_2_S107_L004_dge.txt\"]\n  9[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353214_PA_AUG_PB_1A_S1_dge.txt\"]\n  10[label=\"Import Anndata and loom\"]\n  0 -> 10 [label=\"output\"]\n  11[label=\"Import Anndata and loom\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"Import Anndata and loom\"]\n  2 -> 12 [label=\"output\"]\n  13[label=\"Import Anndata and loom\"]\n  3 -> 13 [label=\"output\"]\n  14[label=\"Import Anndata and loom\"]\n  4 -> 14 [label=\"output\"]\n  15[label=\"Import Anndata and loom\"]\n  5 -> 15 [label=\"output\"]\n  16[label=\"Import Anndata and loom\"]\n  6 -> 16 [label=\"output\"]\n  17[label=\"Import Anndata and loom\"]\n  7 -> 17 [label=\"output\"]\n  18[label=\"Import Anndata and loom\"]\n  8 -> 18 [label=\"output\"]\n  19[label=\"Import Anndata and loom\"]\n  9 -> 19 [label=\"output\"]\n  20[label=\"Manipulate AnnData\"]\n  10 -> 20 [label=\"anndata\"]\n  21[label=\"Manipulate AnnData\"]\n  11 -> 21 [label=\"anndata\"]\n  22[label=\"Manipulate AnnData\"]\n  12 -> 22 [label=\"anndata\"]\n  23[label=\"Manipulate AnnData\"]\n  13 -> 23 [label=\"anndata\"]\n  24[label=\"Manipulate AnnData\"]\n  14 -> 24 [label=\"anndata\"]\n  25[label=\"Manipulate AnnData\"]\n  15 -> 25 [label=\"anndata\"]\n  26[label=\"Manipulate AnnData\"]\n  16 -> 26 [label=\"anndata\"]\n  27[label=\"Manipulate AnnData\"]\n  17 -> 27 [label=\"anndata\"]\n  28[label=\"Manipulate AnnData\"]\n  18 -> 28 [label=\"anndata\"]\n  29[label=\"Manipulate AnnData\"]\n  19 -> 29 [label=\"anndata\"]\n  30[label=\"Manipulate AnnData\"]\n  29 -> 30 [label=\"anndata\"]\n  23 -> 30 [label=\"anndata\"]\n  24 -> 30 [label=\"anndata\"]\n  21 -> 30 [label=\"anndata\"]\n  25 -> 30 [label=\"anndata\"]\n  22 -> 30 [label=\"anndata\"]\n  27 -> 30 [label=\"anndata\"]\n  28 -> 30 [label=\"anndata\"]\n  26 -> 30 [label=\"anndata\"]\n  20 -> 30 [label=\"anndata\"]\n  31[label=\"Inspect AnnData\"]\n  30 -> 31 [label=\"anndata\"]\n  32[label=\"Replace Text\"]\n  31 -> 32 [label=\"obs\"]\n  33[label=\"Replace Text\"]\n  31 -> 33 [label=\"obs\"]\n  34[label=\"Replace Text\"]\n  31 -> 34 [label=\"obs\"]\n  35[label=\"Replace Text\"]\n  31 -> 35 [label=\"obs\"]\n  36[label=\"Cut\"]\n  32 -> 36 [label=\"outfile\"]\n  37[label=\"Cut\"]\n  33 -> 37 [label=\"outfile\"]\n  38[label=\"Cut\"]\n  34 -> 38 [label=\"outfile\"]\n  39[label=\"Cut\"]\n  35 -> 39 [label=\"outfile\"]\n  40[label=\"Paste\"]\n  37 -> 40 [label=\"out_file1\"]\n  36 -> 40 [label=\"out_file1\"]\n  41[label=\"Paste\"]\n  40 -> 41 [label=\"out_file1\"]\n  38 -> 41 [label=\"out_file1\"]\n  42[label=\"Paste\"]\n  41 -> 42 [label=\"out_file1\"]\n  39 -> 42 [label=\"out_file1\"]\n  43[label=\"Manipulate AnnData\"]\n  30 -> 43 [label=\"anndata\"]\n  42 -> 43 [label=\"out_file1\"]\n  44[label=\"Scanpy FilterCells\"]\n  43 -> 44 [label=\"anndata\"]\n  45[label=\"AnnData Operations\"]\n  44 -> 45 [label=\"output_h5ad\"]\n  k98fdc0798b714841a9aaa3adda888616[color=lightseagreen,label=\"Output\\noutput_h5ad\"]\n  45 -> k98fdc0798b714841a9aaa3adda888616\n  46[label=\"Inspect AnnData\"]\n  45 -> 46 [label=\"output_h5ad\"]\n  ke4df84253c1e439cabe542b705eed1b3[color=lightseagreen,label=\"Output\\nobs\"]\n  46 -> ke4df84253c1e439cabe542b705eed1b3\n}",
-                "history": [
-                    {
-                        "hash": "5503254f3b981f79a46ba83ca14a882d772380e4",
-                        "message": "Update to a working worflow and change test files type to tabular",
-                        "num": 2,
-                        "short_hash": "5503254f3",
-                        "unix": "1702491243"
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "94ae400dde2f",
+                            "name": "snapatac2_clustering",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"tl.leiden\", \"__current_case__\": 3, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"resolution\": \"1.0\", \"objective_function\": \"modularity\", \"min_cluster_size\": \"5\", \"n_iterations\": \"-1\", \"random_state\": \"0\", \"key_added\": \"leiden\", \"weighted\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.4+galaxy1",
+                        "type": "tool",
+                        "uuid": "64840a63-5cb4-4bdd-a088-78e5739819a7",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "anndata_leiden_clustering",
+                                "output_name": "anndata_out",
+                                "uuid": "9970eb96-013b-4d97-bbbf-2d1f4663b73c"
+                            }
+                        ]
                     },
-                    {
-                        "hash": "cd3728b55641562a98d26242ac7862218c25aa09",
-                        "message": "add workflow",
-                        "num": 1,
-                        "short_hash": "cd3728b55",
-                        "unix": "1702408106"
-                    }
-                ],
-                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
+                        "id": 22,
+                        "input_connections": {
+                            "method|adata": {
+                                "id": 21,
+                                "output_name": "anndata_out"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "GSM5353219_PA_PB1B_Pool_2_S24_L001_dge.txt"
+                                "description": "runtime parameter for tool SnapATAC2 Plotting",
+                                "name": "method"
+                            }
+                        ],
+                        "label": "pl.umap",
+                        "name": "SnapATAC2 Plotting",
+                        "outputs": [
+                            {
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
-                        "label": "GSM5353219_PA_PB1B_Pool_2_S24_L001_dge.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 6
+                            "left": 4174.404258334524,
+                            "top": 534.0748356757703
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "fc2d53ef-3b4c-437b-bec7-e7b84f8f6c54",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "c01f0a08ab43",
+                            "name": "snapatac2_plotting",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 2, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"color\": \"leiden\", \"use_rep\": \"X_umap\", \"marker_size\": null, \"marker_opacity\": \"1.0\", \"sample_size\": null, \"width\": \"600\", \"height\": \"500\", \"out_file\": \"png\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.4+galaxy1",
+                        "type": "tool",
+                        "uuid": "46564bf3-03e6-4a9b-b160-a10ddbb69197",
                         "when": null,
-                        "workflow_outputs": []
+                        "workflow_outputs": [
+                            {
+                                "label": "umap_leiden-clusters",
+                                "output_name": "out_png",
+                                "uuid": "4fff8ec8-7d6f-4871-9e42-d6c1791d6aa9"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
+                        "id": 23,
+                        "input_connections": {
+                            "method|adata": {
+                                "id": 21,
+                                "output_name": "anndata_out"
+                            },
+                            "method|gene_anno": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "GSM5353223_PA_PB2B_Pool_2_S26_L001_dge.txt"
+                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
+                                "name": "method"
+                            },
+                            {
+                                "description": "runtime parameter for tool SnapATAC2 Preprocessing",
+                                "name": "method"
+                            }
+                        ],
+                        "label": "make_gene_matrix",
+                        "name": "SnapATAC2 Preprocessing",
+                        "outputs": [
+                            {
+                                "name": "anndata_out",
+                                "type": "h5ad"
                             }
                         ],
-                        "label": "GSM5353223_PA_PB2B_Pool_2_S26_L001_dge.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 160
+                            "left": 4560.8801354196185,
+                            "top": 781.9723996031015
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "7e556424-a80d-4114-be2e-7c9ced71f048",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "48d9421bf176",
+                            "name": "snapatac2_preprocessing",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.make_gene_matrix\", \"__current_case__\": 3, \"adata\": {\"__class__\": \"ConnectedValue\"}, \"gene_anno\": {\"__class__\": \"ConnectedValue\"}, \"chunk_size\": \"500\", \"use_x\": false, \"id_type\": \"gene\", \"transcript_name_key\": \"transcript_name\", \"transcript_id_key\": \"transcript_id\", \"gene_name_key\": \"gene_name\", \"gene_id_key\": \"gene_id\", \"min_frag_size\": null, \"max_frag_size\": null, \"count_frag_as_reads\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.6.4+galaxy1",
+                        "type": "tool",
+                        "uuid": "76286f1f-1153-487f-8146-22e9fbc0e843",
                         "when": null,
-                        "workflow_outputs": []
+                        "workflow_outputs": [
+                            {
+                                "label": "anndata gene matrix",
+                                "output_name": "anndata_out",
+                                "uuid": "9a5c2e23-5b59-41ae-aceb-0e47ce9e7b1a"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy3",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 24,
+                        "input_connections": {
+                            "adata": {
+                                "id": 23,
+                                "output_name": "anndata_out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "scanpy_filter_genes",
+                        "name": "Filter",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "GSM5353218_PA_PB1B_Pool_1_2_S74_L003_dge.txt"
+                                "name": "anndata_out",
+                                "type": "h5ad"
                             }
                         ],
-                        "label": "GSM5353218_PA_PB1B_Pool_1_2_S74_L003_dge.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 314
+                            "left": 4914.636475213905,
+                            "top": 577.4812733437685
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ea1f8502-ed3c-45ac-bf09-36a1771dec28",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "d636ce5cde16",
+                            "name": "scanpy_filter",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.filter_genes\", \"__current_case__\": 1, \"filter\": {\"filter\": \"min_cells\", \"__current_case__\": 2, \"min_cells\": \"5\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.6+galaxy3",
+                        "type": "tool",
+                        "uuid": "7dfff544-95f9-4309-8094-31a0acfa525e",
                         "when": null,
-                        "workflow_outputs": []
+                        "workflow_outputs": [
+                            {
+                                "label": "anndata filter genes",
+                                "output_name": "anndata_out",
+                                "uuid": "7a9b22df-e0e5-49d9-9fa1-2efe316d6d66"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy3",
                         "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 25,
+                        "input_connections": {
+                            "adata": {
+                                "id": 24,
+                                "output_name": "anndata_out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Normalize",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "GSM5353216_PA_PB1A_Pool_1_3_S50_L002_dge.txt"
+                                "name": "anndata_out",
+                                "type": "h5ad"
                             }
                         ],
-                        "label": "GSM5353216_PA_PB1A_Pool_1_3_S50_L002_dge.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 468
+                            "left": 5246.771945926951,
+                            "top": 559.3328161085777
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "473c66ce-eb30-483e-bf74-a04f0b452f67",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "d844935c906c",
+                            "name": "scanpy_normalize",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.normalize_total\", \"__current_case__\": 0, \"target_sum\": null, \"exclude_highly_expressed\": {\"exclude_highly_expressed\": \"False\", \"__current_case__\": 1}, \"key_added\": \"\", \"layers\": \"\", \"layer_norm\": \"None\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.6+galaxy3",
+                        "type": "tool",
+                        "uuid": "7629e178-c715-4b96-b5c3-523050cac768",
                         "when": null,
-                        "workflow_outputs": []
+                        "workflow_outputs": [
+                            {
+                                "label": "anndata normalize",
+                                "output_name": "anndata_out",
+                                "uuid": "7dddd4c8-1944-4f50-b331-857d03cc9631"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy3",
                         "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 26,
+                        "input_connections": {
+                            "adata": {
+                                "id": 25,
+                                "output_name": "anndata_out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "pp.log1p",
+                        "name": "Inspect and manipulate",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "GSM5353221_PA_PB2A_Pool_1_3_S25_L001_dge.txt"
+                                "name": "anndata_out",
+                                "type": "h5ad"
                             }
                         ],
-                        "label": "GSM5353221_PA_PB2A_Pool_1_3_S25_L001_dge.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 622
+                            "left": 5571.598835062394,
+                            "top": 560.0237842861073
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "6b5fc504-7162-4cbb-90a4-97b3fc4f792b",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f54f0f0598ad",
+                            "name": "scanpy_inspect",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"pp.log1p\", \"__current_case__\": 5}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.6+galaxy3",
+                        "type": "tool",
+                        "uuid": "8a57a670-5511-462f-b342-d2a6c868a7a8",
                         "when": null,
-                        "workflow_outputs": []
+                        "workflow_outputs": [
+                            {
+                                "label": "anndata log1p",
+                                "output_name": "anndata_out",
+                                "uuid": "40ace30a-21e1-4bf2-8e08-ad93b62fb2ee"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy3",
                         "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 27,
+                        "input_connections": {
+                            "adata": {
+                                "id": 26,
+                                "output_name": "anndata_out"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "external.pp.magic",
+                        "name": "Normalize",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "GSM5353215_PA_AUG_PB_1B_S2_dge.txt"
+                                "name": "anndata_out",
+                                "type": "h5ad"
                             }
                         ],
-                        "label": "GSM5353215_PA_AUG_PB_1B_S2_dge.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 776
+                            "left": 5919.286956493308,
+                            "top": 543.2768617443896
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "99d79b05-7b7a-4986-93e6-6957c34afdca",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "d844935c906c",
+                            "name": "scanpy_normalize",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"method\": {\"method\": \"external.pp.magic\", \"__current_case__\": 4, \"name_list\": \"all_genes\", \"knn\": \"5\", \"decay\": \"1\", \"knn_max\": null, \"t\": \"3\", \"n_pca\": \"100\", \"solver\": \"approximate\", \"knn_dist\": \"euclidean\", \"random_state\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.6+galaxy3",
+                        "type": "tool",
+                        "uuid": "0bdfc7e0-2f37-4122-9c33-517e6743e971",
                         "when": null,
-                        "workflow_outputs": []
+                        "workflow_outputs": [
+                            {
+                                "label": "anndata_magic",
+                                "output_name": "anndata_out",
+                                "uuid": "8c1c7aa9-b9dd-467b-9715-73773aea093f"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0",
                         "errors": null,
-                        "id": 6,
-                        "input_connections": {},
+                        "id": 28,
+                        "input_connections": {
+                            "copy_e|embedding_sources": {
+                                "id": 21,
+                                "output_name": "anndata_out"
+                            },
+                            "input_obj_file": {
+                                "id": 27,
+                                "output_name": "anndata_out"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "GSM5353222_PA_PB2B_Pool_1_3_S52_L002_dge.txt"
+                                "description": "runtime parameter for tool AnnData Operations",
+                                "name": "copy_e"
+                            }
+                        ],
+                        "label": "Copy obsm",
+                        "name": "AnnData Operations",
+                        "outputs": [
+                            {
+                                "name": "output_h5ad",
+                                "type": "h5ad"
                             }
                         ],
-                        "label": "GSM5353222_PA_PB2B_Pool_1_3_S52_L002_dge.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 930
+                            "left": 6310.074636497004,
+                            "top": 564.1397165041963
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "3f690013-56d0-4046-a64f-42ddd71ceb81",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "a4774b7b2e85",
+                            "name": "anndata_ops",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"add_cell_metadata\": {\"default\": false, \"__current_case__\": 1}, \"copy_adata_to_raw\": false, \"copy_e\": {\"default\": true, \"__current_case__\": 0, \"embedding_keys\": [{\"__index__\": 0, \"contains\": null}], \"embedding_sources\": {\"__class__\": \"ConnectedValue\"}}, \"copy_l\": {\"default\": false, \"__current_case__\": 1}, \"copy_o\": {\"default\": false, \"__current_case__\": 1}, \"copy_r\": {\"default\": false, \"__current_case__\": 1}, \"copy_u\": {\"default\": false, \"__current_case__\": 1}, \"copy_x\": {\"default\": false, \"__current_case__\": 1}, \"field_unique\": null, \"gene_flags\": [], \"gene_symbols_field\": \"index\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": false, \"split_on_obs\": {\"default\": false, \"__current_case__\": 1}, \"swap_layer_to_x\": {\"default\": false, \"__current_case__\": 1}, \"top_genes\": \"50\", \"var_modifications\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.3+galaxy0",
+                        "type": "tool",
+                        "uuid": "117972e9-cf57-4b98-a032-39acedadc428",
                         "when": null,
-                        "workflow_outputs": []
+                        "workflow_outputs": [
+                            {
+                                "label": "anndata_gene-matrix_leiden",
+                                "output_name": "output_h5ad",
+                                "uuid": "2c3825d3-7151-4eef-97d0-c8a31ca6fd3e"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy3",
                         "errors": null,
-                        "id": 7,
-                        "input_connections": {},
+                        "id": 29,
+                        "input_connections": {
+                            "adata": {
+                                "id": 28,
+                                "output_name": "output_h5ad"
+                            },
+                            "method|color": {
+                                "id": 4,
+                                "output_name": "output"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "GSM5353220_PA_PB1B_Pool_3_S51_L002_dge.txt"
+                                "description": "runtime parameter for tool Plot",
+                                "name": "method"
+                            }
+                        ],
+                        "label": "umap_plot_with_scanpy",
+                        "name": "Plot",
+                        "outputs": [
+                            {
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
-                        "label": "GSM5353220_PA_PB1B_Pool_3_S51_L002_dge.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 1084
+                            "left": 6625.542217976416,
+                            "top": 759.4084323967407
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "9fce1b9d-52e4-40e5-9c3c-32c1d901aeb1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f7446fd8d5e7",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": {\"__class__\": \"ConnectedValue\"}, \"use_raw\": false, \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": null, \"palette\": null, \"frameon\": true, \"ncols\": \"2\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.6+galaxy3",
+                        "type": "tool",
+                        "uuid": "9a3a0713-a10d-40d1-80b8-7b66fdf4f6b9",
                         "when": null,
-                        "workflow_outputs": []
+                        "workflow_outputs": [
+                            {
+                                "label": "umap_marker-genes",
+                                "output_name": "out_png",
+                                "uuid": "4cfbbb70-156b-48d7-b14b-db21198d9b6d"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "Cut1",
                         "errors": null,
-                        "id": 8,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 31,
+                        "input_connections": {
+                            "input": {
+                                "id": 30,
+                                "output_name": "obs"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Cut leiden from table",
+                        "name": "Cut",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "GSM5353217_PA_PB1A_Pool_2_S107_L004_dge.txt"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "GSM5353217_PA_PB1A_Pool_2_S107_L004_dge.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 1238
+                            "left": 7290.77139785132,
+                            "top": 805.5918074906932
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "2222b107-d0bc-4daf-bee0-d8573375ff43",
+                        "post_job_actions": {},
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"columnList\": \"c8\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2",
+                        "type": "tool",
+                        "uuid": "7c8a2055-a457-4001-baba-a46c75b9e506",
                         "when": null,
-                        "workflow_outputs": []
+                        "workflow_outputs": [
+                            {
+                                "label": "leiden annotation",
+                                "output_name": "out_file1",
+                                "uuid": "11c22200-a54e-4585-82c4-8457dbbfb53c"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2",
                         "errors": null,
-                        "id": 9,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 32,
+                        "input_connections": {
+                            "original_file": {
+                                "id": 31,
+                                "output_name": "out_file1"
+                            },
+                            "replace_information": {
+                                "id": 5,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Replace leiden",
+                        "name": "Replace column",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "GSM5353214_PA_AUG_PB_1A_S1_dge.txt"
+                                "name": "outfile_replace",
+                                "type": "txt"
                             }
                         ],
-                        "label": "GSM5353214_PA_AUG_PB_1A_S1_dge.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 1392
+                            "left": 7610.590154939628,
+                            "top": 714.8720707586833
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "7b4a0b40-4a1a-4d89-bb13-6f150be24c9c",
+                        "post_job_actions": {
+                            "ChangeDatatypeActionoutfile_replace": {
+                                "action_arguments": {
+                                    "newtype": "tabular"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "outfile_replace"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "d533e4b75800",
+                            "name": "replace_column_by_key_value_file",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"column_replace\": \"1\", \"delimiter\": \"tab\", \"original_file\": {\"__class__\": \"ConnectedValue\"}, \"pass_comments\": \"#\", \"replace_information\": {\"__class__\": \"ConnectedValue\"}, \"skip_lines\": \"0\", \"unknowns_strategy\": \"skip\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.2",
+                        "type": "tool",
+                        "uuid": "94ec122d-0eb2-43e7-bf79-3b3ad6e0a7e8",
                         "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGSM5353219_PA_PB1B_Pool_2_S24_L001_dge.txt\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGSM5353223_PA_PB2B_Pool_2_S26_L001_dge.txt\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nGSM5353218_PA_PB1B_Pool_1_2_S74_L003_dge.txt\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nGSM5353216_PA_PB1A_Pool_1_3_S50_L002_dge.txt\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nGSM5353221_PA_PB2A_Pool_1_3_S25_L001_dge.txt\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nGSM5353215_PA_AUG_PB_1B_S2_dge.txt\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nGSM5353222_PA_PB2B_Pool_1_3_S52_L002_dge.txt\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nGSM5353220_PA_PB1B_Pool_3_S51_L002_dge.txt\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nGSM5353217_PA_PB1A_Pool_2_S107_L004_dge.txt\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"\u2139\ufe0f Input Dataset\\nGSM5353214_PA_AUG_PB_1A_S1_dge.txt\"];\n  style 9 stroke:#2c3143,stroke-width:4px;\n  10[\"Import Anndata and loom\"];\n  0 -->|output| 10;\n  11[\"Import Anndata and loom\"];\n  1 -->|output| 11;\n  12[\"Import Anndata and loom\"];\n  2 -->|output| 12;\n  13[\"Import Anndata and loom\"];\n  3 -->|output| 13;\n  14[\"Import Anndata and loom\"];\n  4 -->|output| 14;\n  15[\"Import Anndata and loom\"];\n  5 -->|output| 15;\n  16[\"Import Anndata and loom\"];\n  6 -->|output| 16;\n  17[\"Import Anndata and loom\"];\n  7 -->|output| 17;\n  18[\"Import Anndata and loom\"];\n  8 -->|output| 18;\n  19[\"Import Anndata and loom\"];\n  9 -->|output| 19;\n  20[\"Manipulate AnnData\"];\n  10 -->|anndata| 20;\n  21[\"Manipulate AnnData\"];\n  11 -->|anndata| 21;\n  22[\"Manipulate AnnData\"];\n  12 -->|anndata| 22;\n  23[\"Manipulate AnnData\"];\n  13 -->|anndata| 23;\n  24[\"Manipulate AnnData\"];\n  14 -->|anndata| 24;\n  25[\"Manipulate AnnData\"];\n  15 -->|anndata| 25;\n  26[\"Manipulate AnnData\"];\n  16 -->|anndata| 26;\n  27[\"Manipulate AnnData\"];\n  17 -->|anndata| 27;\n  28[\"Manipulate AnnData\"];\n  18 -->|anndata| 28;\n  29[\"Manipulate AnnData\"];\n  19 -->|anndata| 29;\n  30[\"Manipulate AnnData\"];\n  29 -->|anndata| 30;\n  23 -->|anndata| 30;\n  24 -->|anndata| 30;\n  21 -->|anndata| 30;\n  25 -->|anndata| 30;\n  22 -->|anndata| 30;\n  27 -->|anndata| 30;\n  28 -->|anndata| 30;\n  26 -->|anndata| 30;\n  20 -->|anndata| 30;\n  31[\"Inspect AnnData\"];\n  30 -->|anndata| 31;\n  32[\"Replace Text\"];\n  31 -->|obs| 32;\n  33[\"Replace Text\"];\n  31 -->|obs| 33;\n  34[\"Replace Text\"];\n  31 -->|obs| 34;\n  35[\"Replace Text\"];\n  31 -->|obs| 35;\n  36[\"Cut\"];\n  32 -->|outfile| 36;\n  37[\"Cut\"];\n  33 -->|outfile| 37;\n  38[\"Cut\"];\n  34 -->|outfile| 38;\n  39[\"Cut\"];\n  35 -->|outfile| 39;\n  40[\"Paste\"];\n  37 -->|out_file1| 40;\n  36 -->|out_file1| 40;\n  41[\"Paste\"];\n  40 -->|out_file1| 41;\n  38 -->|out_file1| 41;\n  42[\"Paste\"];\n  41 -->|out_file1| 42;\n  39 -->|out_file1| 42;\n  43[\"Manipulate AnnData\"];\n  30 -->|anndata| 43;\n  42 -->|out_file1| 43;\n  44[\"Scanpy FilterCells\"];\n  43 -->|anndata| 44;\n  45[\"AnnData Operations\"];\n  44 -->|output_h5ad| 45;\n  98fdc079-8b71-4841-a9aa-a3adda888616[\"Output\\noutput_h5ad\"];\n  45 --> 98fdc079-8b71-4841-a9aa-a3adda888616;\n  style 98fdc079-8b71-4841-a9aa-a3adda888616 stroke:#2c3143,stroke-width:4px;\n  46[\"Inspect AnnData\"];\n  45 -->|output_h5ad| 46;\n  e4df8425-3c1e-439c-abe5-42b705eed1b3[\"Output\\nobs\"];\n  46 --> e4df8425-3c1e-439c-abe5-42b705eed1b3;\n  style e4df8425-3c1e-439c-abe5-42b705eed1b3 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "NCBI to Anndata",
-                "outputs": [
+                        "workflow_outputs": [
+                            {
+                                "label": "cell type annotation",
+                                "output_name": "outfile_replace",
+                                "uuid": "467de061-79e6-4148-8a65-c06383a14012"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
                         "errors": null,
-                        "id": 45,
+                        "id": 33,
                         "input_connections": {
-                            "input_obj_file": {
-                                "id": 44,
+                            "input": {
+                                "id": 28,
                                 "output_name": "output_h5ad"
+                            },
+                            "manipulate|new_annot": {
+                                "id": 32,
+                                "output_name": "outfile_replace"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Manipulate AnnData",
+                                "name": "manipulate"
+                            }
+                        ],
                         "label": null,
-                        "name": "AnnData Operations",
+                        "name": "Manipulate AnnData",
                         "outputs": [
                             {
-                                "name": "output_h5ad",
+                                "name": "anndata",
                                 "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 3369.999842902977,
-                            "top": 610
+                            "left": 7951.665647831622,
+                            "top": 529.7790878349768
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "890fb06a2893",
-                            "name": "anndata_ops",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "ed4996a16f7f",
+                            "name": "anndata_manipulate",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"copy_adata_to_raw\": false, \"copy_e\": {\"default\": false, \"__current_case__\": 1}, \"copy_l\": {\"default\": false, \"__current_case__\": 1}, \"copy_o\": {\"default\": false, \"__current_case__\": 1}, \"copy_r\": {\"default\": false, \"__current_case__\": 1}, \"copy_u\": {\"default\": false, \"__current_case__\": 1}, \"copy_x\": {\"default\": false, \"__current_case__\": 1}, \"gene_flags\": [{\"__index__\": 0, \"startswith\": \"MT-\", \"flag\": \"mito\"}], \"gene_symbols_field\": \"index\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": false, \"top_genes\": \"50\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"add_annotation\", \"__current_case__\": 6, \"var_obs\": \"obs\", \"new_annot\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.10.3+galaxy0",
                         "type": "tool",
-                        "uuid": "c53d106a-f45b-477d-ab64-ad266c248411",
+                        "uuid": "8002dcb8-d903-4a46-a2df-6a0cf4e4407f",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "output_h5ad",
-                                "output_name": "output_h5ad",
-                                "uuid": "98fdc079-8b71-4841-a9aa-a3adda888616"
+                                "label": "anndata_cell_type",
+                                "output_name": "anndata",
+                                "uuid": "cbba6173-f439-4fd5-8423-946aa625112b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy3",
                         "errors": null,
-                        "id": 46,
+                        "id": 34,
                         "input_connections": {
-                            "input": {
-                                "id": 45,
-                                "output_name": "output_h5ad"
+                            "adata": {
+                                "id": 33,
+                                "output_name": "anndata"
                             }
                         },
                         "inputs": [],
-                        "label": null,
+                        "label": "Plot cell types",
+                        "name": "Plot",
+                        "outputs": [
+                            {
+                                "name": "out_png",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 8306.897077852367,
+                            "top": 563.5673448508458
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f7446fd8d5e7",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"cell_type\", \"use_raw\": false, \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"on data\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": null, \"palette\": null, \"frameon\": true, \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9.6+galaxy3",
+                        "type": "tool",
+                        "uuid": "ad9c86ff-9843-44f7-815d-026a3a4d6eef",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "umap_cell-type",
+                                "output_name": "out_png",
+                                "uuid": "c28c53ae-8ee7-47d7-8a00-352908bb7c1a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
+                        "errors": null,
+                        "id": 35,
+                        "input_connections": {
+                            "input": {
+                                "id": 33,
+                                "output_name": "anndata"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Inspect AnnData",
+                                "name": "input"
+                            }
+                        ],
+                        "label": "Final Anndata general info",
                         "name": "Inspect AnnData",
                         "outputs": [
                             {
-                                "name": "obs",
-                                "type": "tabular"
+                                "name": "general",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 3649.9996418187607,
-                            "top": 642
+                            "left": 8297.002377504208,
+                            "top": 760.6562767663465
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "ee98d611afc6",
+                            "changeset_revision": "6f0d0c784f09",
                             "name": "anndata_inspect",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"h5ad\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"obs\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.5+galaxy1",
+                        "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"inspect\": {\"info\": \"general\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.10.3+galaxy0",
                         "type": "tool",
-                        "uuid": "60a81f95-32e1-47a7-8a95-07586eb9ed6a",
+                        "uuid": "d178ea23-94a0-42c0-87db-44f2cc23d5dc",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "obs",
-                                "output_name": "obs",
-                                "uuid": "e4df8425-3c1e-439c-abe5-42b705eed1b3"
+                                "label": "general",
+                                "output_name": "general",
+                                "uuid": "379a85d1-a204-4b0b-8b33-86e5582fc51f"
                             }
                         ]
                     }
                 ],
-                "parent_id": "single-cell/scrna-ncbi-anndata",
-                "path": "topics/single-cell/tutorials/scrna-ncbi-anndata/workflows/NCBI_to_Anndata.ga",
+                "parent_id": "single-cell/scatac-standard-processing-snapatac2",
+                "path": "topics/single-cell/tutorials/scatac-standard-processing-snapatac2/workflows/Standard-processing-of-10X-single-cell-ATAC-seq-data-with-SnapATAC2.ga",
                 "tags": [
-                    "name:single-cell",
-                    "name:data-management"
+                    "scATAC-seq",
+                    "epigenetics"
                 ],
                 "test_results": null,
                 "tests": true,
-                "title": "NCBI to Anndata",
+                "title": "Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2",
                 "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-ncbi-anndata/versions/ncbi-to-anndata",
-                "tutorial_id": "scrna-ncbi-anndata",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-ncbi-anndata/workflows/NCBI_to_Anndata.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-ncbi-anndata/workflows/NCBI_to_Anndata.html",
-                "version": 1,
-                "wfid": "single-cell-scrna-ncbi-anndata",
-                "wfname": "ncbi-to-anndata",
-                "workflow": "NCBI_to_Anndata.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scatac-standard-processing-snapatac2/versions/standard-processing-of-10x-single-cell-atac-seq-data-with-snapatac2",
+                "tutorial_id": "scatac-standard-processing-snapatac2",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/workflows/Standard-processing-of-10X-single-cell-ATAC-seq-data-with-SnapATAC2.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/workflows/Standard-processing-of-10X-single-cell-ATAC-seq-data-with-SnapATAC2.html",
+                "version": 2,
+                "wfid": "single-cell-scatac-standard-processing-snapatac2",
+                "wfname": "standard-processing-of-10x-single-cell-atac-seq-data-with-snapatac2",
+                "workflow": "Standard-processing-of-10X-single-cell-ATAC-seq-data-with-SnapATAC2.ga",
                 "workflow_tools": [
                     "Cut1",
-                    "Paste1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.9.6+galaxy3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.9.6+galaxy3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1"
                 ],
-                "workflowhub_id": "1272"
+                "workflowhub_id": "1343"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/10101768"
+        "zenodo_link": "https://zenodo.org/records/12707159"
     },
     {
         "admin_install": {
@@ -229844,237 +234435,221 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "anndata_ops",
-                    "owner": "ebi-gxa",
-                    "revisions": "890fb06a2893",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "anndata_ops",
-                    "owner": "ebi-gxa",
-                    "revisions": "7ebc22f77d86",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_compute_graph",
-                    "owner": "ebi-gxa",
-                    "revisions": "bc9e8de21efb",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_compute_graph",
-                    "owner": "ebi-gxa",
-                    "revisions": "6417cccad133",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_filter_cells",
-                    "owner": "ebi-gxa",
-                    "revisions": "55ccc0a121bc",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_filter_cells",
-                    "owner": "ebi-gxa",
-                    "revisions": "e9283529cba1",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_filter_genes",
-                    "owner": "ebi-gxa",
-                    "revisions": "da611a744112",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_filter_genes",
-                    "owner": "ebi-gxa",
-                    "revisions": "474a69c47184",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_find_cluster",
-                    "owner": "ebi-gxa",
-                    "revisions": "ad6995afd2e6",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_find_cluster",
-                    "owner": "ebi-gxa",
-                    "revisions": "2ccd9f9e2cd0",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_find_markers",
-                    "owner": "ebi-gxa",
-                    "revisions": "49653e680ea4",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_find_markers",
-                    "owner": "ebi-gxa",
-                    "revisions": "81c34e67f262",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_find_variable_genes",
-                    "owner": "ebi-gxa",
-                    "revisions": "4667fe07bd68",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_find_variable_genes",
-                    "owner": "ebi-gxa",
-                    "revisions": "2861ca3bfe4d",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_normalise_data",
-                    "owner": "ebi-gxa",
-                    "revisions": "8d9c22419c56",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_normalise_data",
-                    "owner": "ebi-gxa",
-                    "revisions": "6b97ffba31da",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_plot_embed",
-                    "owner": "ebi-gxa",
-                    "revisions": "56d22aa6cb3b",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_plot_embed",
-                    "owner": "ebi-gxa",
-                    "revisions": "35f6611fb8c3",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_run_pca",
-                    "owner": "ebi-gxa",
-                    "revisions": "3ee74b58c72d",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_run_pca",
-                    "owner": "ebi-gxa",
-                    "revisions": "59028945c857",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_run_tsne",
-                    "owner": "ebi-gxa",
-                    "revisions": "8b0d6f6f44c8",
-                    "tool_panel_section_label": "Single-cell",
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "e7b2202befea",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_run_tsne",
-                    "owner": "ebi-gxa",
-                    "revisions": "181d61d2f3cd",
-                    "tool_panel_section_label": "Single-cell",
+                    "name": "umi_tools_extract",
+                    "owner": "iuc",
+                    "revisions": "6a675c3aa610",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "scanpy_run_umap",
-                    "owner": "ebi-gxa",
-                    "revisions": "fe562424a0a6",
-                    "tool_panel_section_label": "Single-cell",
+                    "name": "seq_filter_by_id",
+                    "owner": "peterjc",
+                    "revisions": "141612f8c3e3",
+                    "tool_panel_section_label": "Filter and Sort",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: umi_tools_extract\n  owner: iuc\n  revisions: 6a675c3aa610\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seq_filter_by_id\n  owner: peterjc\n  revisions: 141612f8c3e3\n  tool_panel_section_label: Filter and Sort\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-umis/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "elixir_node": "de",
+                "email": "mtekman89@gmail.com",
+                "former_affiliations": [
+                    "elixir-europe"
+                ],
+                "id": "mtekman",
+                "joined": "2018-11",
+                "name": "Mehmet Tekman",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
+            }
+        ],
+        "dir": "topics/single-cell/tutorials/scrna-umis",
+        "edam_operation": [
+            "Sequencing quality control",
+            "Statistical calculation",
+            "Sequence composition calculation"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "gitter": "Galaxy-Training-Network/galaxy-single-cell",
+        "hands_on": true,
+        "id": "single-cell/scrna-umis",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Verifying the distribution of barcodes via a FASTQC plot",
+            "Relocating barcodes into headers",
+            "Removing unwanted barcodes"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-14",
+        "objectives": [
+            "Demultiplex FASTQ data via UMI-tools",
+            "Understand and validate the extraction of barcodes"
+        ],
+        "pageviews": 6185,
+        "priority": 2,
+        "pub_date": "2019-02-20",
+        "questions": [
+            "What are barcodes?",
+            "What is their purpose?",
+            "How are barcodes formatted?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "khanteymoori"
+                ],
+                "date": "2021-03-18",
+                "galaxy_version": "21.01",
+                "length": "10M",
+                "speakers": [
+                    "nomadscientist"
+                ],
+                "youtube_id": "AJ17BicjmYU"
+            }
+        ],
+        "redirect_from": [
+            "/topics/transcriptomics/tutorials/scrna-umis/tutorial",
+            "/short/single-cell/scrna-umis",
+            "/short/T00256"
+        ],
+        "short_id": "T00256",
+        "short_tools": [
+            "fastqc",
+            "seq_filter_by_id",
+            "umi_tools_extract"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "scintroduction",
+        "supported_servers": {
+            "exact": [
                 {
-                    "name": "scanpy_run_umap",
-                    "owner": "ebi-gxa",
-                    "revisions": "bd4a244faeb8",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
                 },
                 {
-                    "name": "scanpy_scale_data",
-                    "owner": "ebi-gxa",
-                    "revisions": "5605f8452eb3",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "scanpy_scale_data",
-                    "owner": "ebi-gxa",
-                    "revisions": "f86b2c3bc459",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 },
                 {
-                    "name": "anndata_inspect",
-                    "owner": "iuc",
-                    "revisions": "ee98d611afc6",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
                 {
-                    "name": "anndata_manipulate",
-                    "owner": "iuc",
-                    "revisions": "3d748954434b",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "scanpy_plot",
-                    "owner": "iuc",
-                    "revisions": "aa0c474463c2",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: anndata_ops\n  owner: ebi-gxa\n  revisions: 890fb06a2893\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_ops\n  owner: ebi-gxa\n  revisions: 7ebc22f77d86\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_compute_graph\n  owner: ebi-gxa\n  revisions: bc9e8de21efb\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_compute_graph\n  owner: ebi-gxa\n  revisions: 6417cccad133\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter_cells\n  owner: ebi-gxa\n  revisions: 55ccc0a121bc\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter_cells\n  owner: ebi-gxa\n  revisions: e9283529cba1\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter_genes\n  owner: ebi-gxa\n  revisions: da611a744112\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter_genes\n  owner: ebi-gxa\n  revisions: 474a69c47184\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_find_cluster\n  owner: ebi-gxa\n  revisions: ad6995afd2e6\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_find_cluster\n  owner: ebi-gxa\n  revisions: 2ccd9f9e2cd0\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_find_markers\n  owner: ebi-gxa\n  revisions: 49653e680ea4\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_find_markers\n  owner: ebi-gxa\n  revisions: 81c34e67f262\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_find_variable_genes\n  owner: ebi-gxa\n  revisions: 4667fe07bd68\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_find_variable_genes\n  owner: ebi-gxa\n  revisions: 2861ca3bfe4d\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_normalise_data\n  owner: ebi-gxa\n  revisions: 8d9c22419c56\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_normalise_data\n  owner: ebi-gxa\n  revisions: 6b97ffba31da\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot_embed\n  owner: ebi-gxa\n  revisions: 56d22aa6cb3b\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot_embed\n  owner: ebi-gxa\n  revisions: 35f6611fb8c3\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_pca\n  owner: ebi-gxa\n  revisions: 3ee74b58c72d\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_pca\n  owner: ebi-gxa\n  revisions: 59028945c857\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_tsne\n  owner: ebi-gxa\n  revisions: 8b0d6f6f44c8\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_tsne\n  owner: ebi-gxa\n  revisions: 181d61d2f3cd\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_umap\n  owner: ebi-gxa\n  revisions: fe562424a0a6\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_umap\n  owner: ebi-gxa\n  revisions: bd4a244faeb8\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_scale_data\n  owner: ebi-gxa\n  revisions: 5605f8452eb3\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_scale_data\n  owner: ebi-gxa\n  revisions: f86b2c3bc459\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_inspect\n  owner: iuc\n  revisions: ee98d611afc6\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n  owner: iuc\n  revisions: 3d748954434b\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot\n  owner: iuc\n  revisions: aa0c474463c2\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "symlink": null,
+        "tags": null,
+        "time_estimation": "2h",
+        "title": "Understanding Barcodes",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1",
+            "toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7"
+        ],
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "scrna-umis",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-umis/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-umis/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-umis/tutorial.json"
+        },
+        "version": 7,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 72,
+        "visitors": 4888,
+        "zenodo_link": "https://zenodo.org/record/2573177"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
         "answer_histories": [
             {
-                "date": "2023-10-10",
-                "history": "https://usegalaxy.eu/u/j.jakiela/h/filter-plot-and-explore-single-cell-rna-seq-data-updated",
-                "label": "UseGalaxy.eu"
-            },
-            {
-                "date": "2024-02-28",
-                "history": "https://usegalaxy.eu/u/wendi.bacon.training/h/cs3filter-plot-and-explore-single-cell-rna-seq-data---answer-key-2",
-                "label": "Older version"
+                "date": "2024-09-09",
+                "history": "https://colab.research.google.com/drive/1DkCysA77iaFAWoKJ1vwE5_qYV8Su7UsX?usp=sharing",
+                "label": "Backup Jupyter Notebook for Google Colab"
             }
         ],
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case-jupyter_basic-pipeline/tutorial.json",
         "contributions": {
             "authorship": [
+                "hexhowells",
                 "nomadscientist"
-            ],
-            "editing": [
-                "hexylena",
-                "wee-snufkin"
-            ],
-            "testing": [
-                "wee-snufkin"
             ]
         },
         "contributors": [
+            {
+                "email": "hexhowells@gmail.com",
+                "id": "hexhowells",
+                "joined": "2023-06",
+                "name": "Morgan Howells",
+                "orcid": "0009-0008-9422-6380",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexhowells/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexhowells.json"
+            },
             {
                 "affiliations": [
                     "elixir-europe"
@@ -230092,61 +234667,12 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
                 "twitter": "WendiBacon1",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "email": "juliajot36@gmail.com",
-                "id": "wee-snufkin",
-                "joined": "2022-06",
-                "name": "Julia Jakiela",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
-            },
-            {
-                "email": "juliajot36@gmail.com",
-                "id": "wee-snufkin",
-                "joined": "2022-06",
-                "name": "Julia Jakiela",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
             }
         ],
-        "dir": "topics/single-cell/tutorials/scrna-case_basic-pipeline",
-        "edam_operation": [
-            "Differential gene expression analysis"
-        ],
+        "dir": "topics/single-cell/tutorials/scrna-case-jupyter_basic-pipeline",
+        "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "follow_up_training": [
@@ -230160,13 +234686,16 @@
             }
         ],
         "hands_on": true,
-        "id": "single-cell/scrna-case_basic-pipeline",
+        "id": "single-cell/scrna-case-jupyter_basic-pipeline",
         "inexact_supported_servers": [
-            "UseGalaxy.org.au"
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
         ],
         "input_histories": [
             {
-                "history": "https://usegalaxy.eu/u/j.jakiela/h/filter-plot-explore-tutorial-input",
+                "history": "https://usegalaxy.eu/published/history?id=67ff4cea2adc574d",
                 "label": "UseGalaxy.eu"
             }
         ],
@@ -230180,7 +234709,11 @@
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-09-13",
+        "notebook": {
+            "language": "python",
+            "snippet": "topics/single-cell/tutorials/scrna-case-jupyter_basic-pipeline/preamble.md"
+        },
         "objectives": [
             "Interpret quality control plots to direct parameter decisions",
             "Repeat analysis from matrix to clustering",
@@ -230188,9 +234721,9 @@
             "Appraise data outputs and decisions",
             "Explain why single cell analysis is an iterative (i.e. the first plots you generate are not final, but rather you go back and re-analyse your data repeatedly) process"
         ],
-        "pageviews": 5840,
-        "priority": 3,
-        "pub_date": "2021-03-24",
+        "pageviews": 2296,
+        "priority": 2,
+        "pub_date": "2023-08-25",
         "questions": [
             "Is my single cell dataset a quality dataset?",
             "How do I generate and annotate cell clusters?",
@@ -230198,115 +234731,356 @@
         ],
         "recordings": [
             {
+                "bot-timestamp": 1722971660,
                 "captioners": [
-                    "nomadscientist"
+                    "hexhowells"
+                ],
+                "date": "2024-08-06",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "13M",
+                "speakers": [
+                    "hexhowells"
+                ],
+                "youtube_id": "40w0WVohv4E"
+            }
+        ],
+        "requirements": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-case_alevin",
+                    "scrna-case_alevin-combine-datasets"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00358",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "single-cell-CS-code",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "10x",
+            "paper-replication",
+            "Python"
+        ],
+        "time_estimation": "3H",
+        "title": "Filter, plot and explore single-cell RNA-seq data with Scanpy (Python)",
+        "tools": [],
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "scrna-case-jupyter_basic-pipeline",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case-jupyter_basic-pipeline/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case-jupyter_basic-pipeline/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case-jupyter_basic-pipeline/tutorial.json"
+        },
+        "version": 11,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 94,
+        "visitors": 1928,
+        "zenodo_link": "https://zenodo.org/record/7053673"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "anndata_import",
+                    "owner": "iuc",
+                    "revisions": "55e35e9203cf",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "anndata_manipulate",
+                    "owner": "iuc",
+                    "revisions": "9bd945a03d7b",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_cluster_reduce_dimension",
+                    "owner": "iuc",
+                    "revisions": "aaa5da8e73a9",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_filter",
+                    "owner": "iuc",
+                    "revisions": "b409c2486353",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_inspect",
+                    "owner": "iuc",
+                    "revisions": "c5d3684f7c4c",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_normalize",
+                    "owner": "iuc",
+                    "revisions": "ab55fe8030b6",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_plot",
+                    "owner": "iuc",
+                    "revisions": "6adf98e782f3",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_remove_confounders",
+                    "owner": "iuc",
+                    "revisions": "bf2017df9837",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: anndata_import\n  owner: iuc\n  revisions: 55e35e9203cf\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n  owner: iuc\n  revisions: 9bd945a03d7b\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_cluster_reduce_dimension\n  owner: iuc\n  revisions: aaa5da8e73a9\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter\n  owner: iuc\n  revisions: b409c2486353\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_inspect\n  owner: iuc\n  revisions: c5d3684f7c4c\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_normalize\n  owner: iuc\n  revisions: ab55fe8030b6\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot\n  owner: iuc\n  revisions: 6adf98e782f3\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_remove_confounders\n  owner: iuc\n  revisions: bf2017df9837\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plant/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "elixir_node": "de",
+                "email": "mtekman89@gmail.com",
+                "former_affiliations": [
+                    "elixir-europe"
+                ],
+                "id": "mtekman",
+                "joined": "2018-11",
+                "name": "Mehmet Tekman",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
+            },
+            {
+                "email": "beatrizserrano.galaxy@gmail.com",
+                "id": "beatrizserrano",
+                "joined": "2020-07",
+                "linkedin": "beatriz-serrano",
+                "matrix": "beatrizserrano:matrix.org",
+                "name": "Beatriz Serrano-Solano",
+                "orcid": "0000-0002-5862-6132",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/beatrizserrano/",
+                "twitter": "BSerranoSolano",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/beatrizserrano.json"
+            },
+            {
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "gallardoalba",
+                "joined": "2020-11",
+                "name": "Crist\u00f3bal Gallardo",
+                "orcid": "0000-0002-5752-2155",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "pavanvidem",
+                "joined": "2017-09",
+                "name": "Pavankumar Videm",
+                "orcid": "0000-0002-5192-126X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
+            }
+        ],
+        "dir": "topics/single-cell/tutorials/scrna-plant",
+        "edam_operation": [
+            "Differential gene expression analysis"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "gitter": "Galaxy-Training-Network/galaxy-single-cell",
+        "hands_on": true,
+        "id": "single-cell/scrna-plant",
+        "inexact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.no"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Filtering parameters are dependent on the dataset, and should be explored using scatter or violin plots",
+            "A DotPlot is a fantastic way to validate clusters across different analyses"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-14",
+        "objectives": [
+            "Perform filtering, dimensionality reduction, and clustering",
+            "Generate a DotPlot emulating the original paper using a different analysis tool",
+            "Determine robust clusters across scRNA-seq pipelines"
+        ],
+        "pageviews": 2483,
+        "priority": 3,
+        "pub_date": "2021-04-08",
+        "questions": [
+            "Can we reclaim cell markers using a different analysis method?",
+            "Are highly variable genes paramount to the analysis?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "mtekman"
                 ],
                 "date": "2021-02-15",
                 "galaxy_version": "21.01",
-                "length": "30M",
+                "length": "55M",
                 "speakers": [
-                    "nomadscientist"
+                    "mtekman"
                 ],
-                "youtube_id": "M6iepSJh0EQ"
+                "youtube_id": "yKlJ5ESri7o"
             }
         ],
         "redirect_from": [
-            "/topics/transcriptomics/tutorials/scrna-seq-basic-pipeline/tutorial",
-            "/topics/transcriptomics/tutorials/scrna-case_basic-pipeline/tutorial",
-            "/short/single-cell/scrna-case_basic-pipeline",
-            "/short/T00247"
+            "/topics/transcriptomics/tutorials/scrna-plant/tutorial",
+            "/short/single-cell/scrna-plant",
+            "/short/T00250"
         ],
         "requirements": [
             {
                 "topic_name": "single-cell",
                 "tutorials": [
-                    "scrna-case_alevin",
-                    "scrna-case_alevin-combine-datasets"
+                    "scrna-scanpy-pbmc3k"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00247",
+        "short_id": "T00250",
         "short_tools": [
-            "scanpy_normalise_data",
-            "scanpy_filter_cells",
-            "Cut1",
-            "scanpy_run_umap",
-            "scanpy_find_markers",
-            "scanpy_run_pca",
-            "anndata_manipulate",
-            "anndata_ops",
-            "scanpy_find_cluster",
-            "scanpy_filter_genes",
-            "join1",
-            "scanpy_scale_data",
-            "scanpy_plot_embed",
-            "anndata_inspect",
+            "scanpy_remove_confounders",
+            "anndata_import",
             "scanpy_plot",
-            "interactive_tool_cellxgene",
-            "scanpy_find_variable_genes",
-            "scanpy_run_tsne",
-            "scanpy_compute_graph"
+            "scanpy_cluster_reduce_dimension",
+            "anndata_manipulate",
+            "scanpy_filter",
+            "scanpy_inspect",
+            "scanpy_normalize"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "single-cell-CS",
+        "subtopic": "end-to-end",
         "supported_servers": {
             "exact": [
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                }
-            ],
-            "inexact": [
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
                 }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                }
             ]
         },
         "symlink": null,
         "tags": [
-            "10x",
+            "plants",
             "paper-replication"
         ],
-        "time_estimation": "3H",
-        "title": "Filter, plot and explore single-cell RNA-seq data with Scanpy",
+        "time_estimation": "2H",
+        "title": "Analysis of plant scRNA-Seq Data with Scanpy",
         "tools": [
-            "Cut1",
-            "interactive_tool_cellxgene",
-            "join1",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy91",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy9",
-            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1"
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0"
         ],
         "topic_name": "single-cell",
         "topic_name_human": "Single Cell",
@@ -230316,30 +235090,30 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "scrna-case_basic-pipeline",
+        "tutorial_name": "scrna-plant",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-plant/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plant/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plant/tutorial.json"
         },
-        "version": 18,
+        "version": 5,
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 144,
-        "visitors": 3733,
+        "visit_duration": 83,
+        "visitors": 1962,
         "workflows": [
             {
                 "creators": [],
-                "description": "Updated tool versions Aug 24 2022",
+                "description": "Downstream Single-cell RNA Plant analysis with ScanPy",
                 "features": {
                     "comments": false,
-                    "parameters": false,
+                    "parameters": true,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMito-counted AnnData\"]\n  1[label=\"Inspect AnnData\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Scanpy FilterCells\"]\n  0 -> 2 [label=\"output\"]\n  k08175d7ff4f4413cad86f59587ff692e[color=lightseagreen,label=\"Output\\nGenes-filtered Object\"]\n  2 -> k08175d7ff4f4413cad86f59587ff692e\n  3[label=\"Plot\"]\n  0 -> 3 [label=\"output\"]\n  kbfc499ee630a498b9be6696d9bb78837[color=lightseagreen,label=\"Output\\nScatter - genes x UMIs\"]\n  3 -> kbfc499ee630a498b9be6696d9bb78837\n  4[label=\"Plot\"]\n  0 -> 4 [label=\"output\"]\n  kf2c78ef37d314930954c0133cce27a41[color=lightseagreen,label=\"Output\\nScatter - mito x genes\"]\n  4 -> kf2c78ef37d314930954c0133cce27a41\n  5[label=\"Plot\"]\n  0 -> 5 [label=\"output\"]\n  k348818e69def41fda3906f8525c57cd8[color=lightseagreen,label=\"Output\\nViolin - genotype - log\"]\n  5 -> k348818e69def41fda3906f8525c57cd8\n  6[label=\"Plot\"]\n  0 -> 6 [label=\"output\"]\n  k844f5e7c78c84f288e15cea35ada8fef[color=lightseagreen,label=\"Output\\nViolin - batch - log\"]\n  6 -> k844f5e7c78c84f288e15cea35ada8fef\n  7[label=\"Inspect AnnData\"]\n  0 -> 7 [label=\"output\"]\n  8[label=\"Plot\"]\n  0 -> 8 [label=\"output\"]\n  k3b1232c5d16a434d806e79fd77f7c05f[color=lightseagreen,label=\"Output\\nScatter - mito x UMIs\"]\n  8 -> k3b1232c5d16a434d806e79fd77f7c05f\n  9[label=\"Inspect AnnData\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"Plot\"]\n  0 -> 10 [label=\"output\"]\n  ka639cdc0da404df9834823117528b24a[color=lightseagreen,label=\"Output\\nViolin - sex - log\"]\n  10 -> ka639cdc0da404df9834823117528b24a\n  11[label=\"Plot\"]\n  2 -> 11 [label=\"output_h5ad\"]\n  k69bf3e4263e24b5b9d635aac9d6b5691[color=lightseagreen,label=\"Output\\nViolin - Filterbygenes\"]\n  11 -> k69bf3e4263e24b5b9d635aac9d6b5691\n  12[label=\"Scanpy FilterCells\"]\n  2 -> 12 [label=\"output_h5ad\"]\n  kf378cb4e0a7749d9b92a752dbea4b09a[color=lightseagreen,label=\"Output\\nCounts-filtered Object\"]\n  12 -> kf378cb4e0a7749d9b92a752dbea4b09a\n  13[label=\"Inspect AnnData\"]\n  2 -> 13 [label=\"output_h5ad\"]\n  kf9e862dbeb2241248fe00fdcfcfb8393[color=lightseagreen,label=\"Output\\nGeneral - Filterbygenes\"]\n  13 -> kf9e862dbeb2241248fe00fdcfcfb8393\n  14[label=\"Inspect AnnData\"]\n  12 -> 14 [label=\"output_h5ad\"]\n  k794f72b5c2c346a0ac15b9f1e94941d2[color=lightseagreen,label=\"Output\\nGeneral - Filterbycounts\"]\n  14 -> k794f72b5c2c346a0ac15b9f1e94941d2\n  15[label=\"Scanpy FilterCells\"]\n  12 -> 15 [label=\"output_h5ad\"]\n  kb915da6664354871baa03e494ba73c96[color=lightseagreen,label=\"Output\\nMito-filtered Object\"]\n  15 -> kb915da6664354871baa03e494ba73c96\n  16[label=\"Plot\"]\n  12 -> 16 [label=\"output_h5ad\"]\n  k3aef86d7d34d4b24bc97bf8c97d8d2fa[color=lightseagreen,label=\"Output\\nViolin - Filterbycounts\"]\n  16 -> k3aef86d7d34d4b24bc97bf8c97d8d2fa\n  17[label=\"Inspect AnnData\"]\n  15 -> 17 [label=\"output_h5ad\"]\n  kcd94a4c656654bdf88ea4f4d41efa893[color=lightseagreen,label=\"Output\\nGeneral - Filterbymito\"]\n  17 -> kcd94a4c656654bdf88ea4f4d41efa893\n  18[label=\"Scanpy FilterGenes\"]\n  15 -> 18 [label=\"output_h5ad\"]\n  kee63ef0a98ed45cbb1441154f84ae452[color=lightseagreen,label=\"Output\\nFiltered Object\"]\n  18 -> kee63ef0a98ed45cbb1441154f84ae452\n  19[label=\"Plot\"]\n  15 -> 19 [label=\"output_h5ad\"]\n  k7e48a14f08fd45abb613606bf64dcf9d[color=lightseagreen,label=\"Output\\nViolin - Filterbymito\"]\n  19 -> k7e48a14f08fd45abb613606bf64dcf9d\n  20[label=\"Inspect AnnData\"]\n  18 -> 20 [label=\"output_h5ad\"]\n  kd59efa9bd0494f0e8bd88ae982a45d0a[color=lightseagreen,label=\"Output\\nGeneral - Filtered object\"]\n  20 -> kd59efa9bd0494f0e8bd88ae982a45d0a\n  21[label=\"Scanpy NormaliseData\"]\n  18 -> 21 [label=\"output_h5ad\"]\n  22[label=\"Scanpy FindVariableGenes\"]\n  21 -> 22 [label=\"output_h5ad\"]\n  23[label=\"Scanpy ScaleData\"]\n  22 -> 23 [label=\"output_h5ad\"]\n  24[label=\"Scanpy RunPCA\"]\n  23 -> 24 [label=\"output_h5ad\"]\n  25[label=\"Plot\"]\n  24 -> 25 [label=\"output_h5ad\"]\n  k993dea99990f460abeb946e5c97ee898[color=lightseagreen,label=\"Output\\nPCA Variance\"]\n  25 -> k993dea99990f460abeb946e5c97ee898\n  26[label=\"Scanpy ComputeGraph\"]\n  24 -> 26 [label=\"output_h5ad\"]\n  27[label=\"Scanpy RunTSNE\"]\n  26 -> 27 [label=\"output_h5ad\"]\n  28[label=\"Scanpy RunUMAP\"]\n  27 -> 28 [label=\"output_h5ad\"]\n  29[label=\"Scanpy FindCluster\"]\n  28 -> 29 [label=\"output_h5ad\"]\n  30[label=\"Scanpy FindMarkers\"]\n  29 -> 30 [label=\"output_h5ad\"]\n  k308b49614d50442b9bcabbb1992426ba[color=lightseagreen,label=\"Output\\nMarkers - cluster\"]\n  30 -> k308b49614d50442b9bcabbb1992426ba\n  k035bbbcefb5748c883d52b0cd0376541[color=lightseagreen,label=\"Output\\nFinal object\"]\n  30 -> k035bbbcefb5748c883d52b0cd0376541\n  31[label=\"Scanpy FindMarkers\"]\n  29 -> 31 [label=\"output_h5ad\"]\n  k1705e219192a4f529b2664fcbcd303ea[color=lightseagreen,label=\"Output\\nMarkers - genotype\"]\n  31 -> k1705e219192a4f529b2664fcbcd303ea\n  32[label=\"Scanpy PlotEmbed\"]\n  30 -> 32 [label=\"output_h5ad\"]\n  33[label=\"Scanpy PlotEmbed\"]\n  30 -> 33 [label=\"output_h5ad\"]\n  34[label=\"Manipulate AnnData\"]\n  30 -> 34 [label=\"output_h5ad\"]\n  35[label=\"Scanpy PlotEmbed\"]\n  30 -> 35 [label=\"output_h5ad\"]\n  36[label=\"Inspect AnnData\"]\n  30 -> 36 [label=\"output_h5ad\"]\n  37[label=\"AnnData Operations\"]\n  34 -> 37 [label=\"anndata\"]\n  30 -> 37 [label=\"output_h5ad\"]\n  38[label=\"Join two Datasets\"]\n  30 -> 38 [label=\"output_tsv\"]\n  36 -> 38 [label=\"var\"]\n  39[label=\"Join two Datasets\"]\n  31 -> 39 [label=\"output_tsv\"]\n  36 -> 39 [label=\"var\"]\n  40[label=\"AnnData Operations\"]\n  37 -> 40 [label=\"output_h5ad\"]\n  ka6d48df0403f4efca75f9504a960884e[color=lightseagreen,label=\"Output\\nFinal cell annotated object\"]\n  40 -> ka6d48df0403f4efca75f9504a960884e\n  41[label=\"Cut\"]\n  38 -> 41 [label=\"out_file1\"]\n  k0ee7f9b6b0654e2693df6e6e2fe458a9[color=lightseagreen,label=\"Output\\nMarkers - cluster - named\"]\n  41 -> k0ee7f9b6b0654e2693df6e6e2fe458a9\n  42[label=\"Cut\"]\n  39 -> 42 [label=\"out_file1\"]\n  kfdb88faa9b764edbb89b427c098a473e[color=lightseagreen,label=\"Output\\nMarkers - genotype - named\"]\n  42 -> kfdb88faa9b764edbb89b427c098a473e\n  43[label=\"Scanpy PlotEmbed\"]\n  40 -> 43 [label=\"output_h5ad\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nLeiden Resolution\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSHR CSV.gz\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nWT CSV.gz\"]\n  3[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMin Genes\"]\n  4[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMin Cells\"]\n  5[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMax Features\"]\n  6[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMax Lib Size\"]\n  7[label=\"Import Anndata and loom\"]\n  1 -> 7 [label=\"output\"]\n  8[label=\"Import Anndata and loom\"]\n  2 -> 8 [label=\"output\"]\n  9[label=\"Manipulate AnnData\"]\n  7 -> 9 [label=\"anndata\"]\n  8 -> 9 [label=\"anndata\"]\n  10[label=\"Rename Batches\"]\n  9 -> 10 [label=\"anndata\"]\n  k680180f6edfc4f66b2657a63aaa22b39[color=lightseagreen,label=\"Output\\nscRNA Concatenated Datasets\"]\n  10 -> k680180f6edfc4f66b2657a63aaa22b39\n  11[label=\"QC metrics\"]\n  10 -> 11 [label=\"anndata\"]\n  12[label=\"Filter genes\"]\n  11 -> 12 [label=\"anndata_out\"]\n  3 -> 12 [label=\"output\"]\n  13[label=\"Plot Violin\"]\n  11 -> 13 [label=\"anndata_out\"]\n  14[label=\"Filter Cells\"]\n  12 -> 14 [label=\"anndata_out\"]\n  4 -> 14 [label=\"output\"]\n  15[label=\"Filter Max Features\"]\n  14 -> 15 [label=\"anndata_out\"]\n  5 -> 15 [label=\"output\"]\n  16[label=\"Filter Max Library Size\"]\n  15 -> 16 [label=\"anndata\"]\n  6 -> 16 [label=\"output\"]\n  17[label=\"Save RAW\"]\n  16 -> 17 [label=\"anndata\"]\n  18[label=\"Norm to 1e4\"]\n  17 -> 18 [label=\"anndata\"]\n  19[label=\"Log1p\"]\n  18 -> 19 [label=\"anndata_out\"]\n  20[label=\"Regress total counts\"]\n  19 -> 20 [label=\"anndata_out\"]\n  21[label=\"Scale\"]\n  20 -> 21 [label=\"anndata_out\"]\n  22[label=\"PCA\"]\n  21 -> 22 [label=\"anndata_out\"]\n  23[label=\"Neighborhod\"]\n  22 -> 23 [label=\"anndata_out\"]\n  24[label=\"UMAP\"]\n  23 -> 24 [label=\"anndata_out\"]\n  25[label=\"Leiden\"]\n  24 -> 25 [label=\"anndata_out\"]\n  0 -> 25 [label=\"output\"]\n  k48cf046584ba461abdb961625626de42[color=lightseagreen,label=\"Output\\nscRNA with clusters Dataset\"]\n  25 -> k48cf046584ba461abdb961625626de42\n  26[label=\"Plot PCA batch\"]\n  24 -> 26 [label=\"anndata_out\"]\n  27[label=\"Plot UMAP batch\"]\n  24 -> 27 [label=\"anndata_out\"]\n  28[label=\"Plot UMAP leiden, batch\"]\n  25 -> 28 [label=\"anndata_out\"]\n  29[label=\"Rename Clusters\"]\n  25 -> 29 [label=\"anndata_out\"]\n  30[label=\"Complex DotPlot\"]\n  25 -> 30 [label=\"anndata_out\"]\n  31[label=\"Complex DotPlot with new labels\"]\n  29 -> 31 [label=\"anndata\"]\n  32[label=\"Plot UMAP with new labels\"]\n  29 -> 32 [label=\"anndata\"]\n}",
                 "history": [
                     {
                         "hash": "327fd2b842f45de3dc2a30067714352675ad69ae",
@@ -230359,390 +235133,290 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Mito-counted AnnData"
+                                "name": "Leiden Resolution"
                             }
                         ],
-                        "label": "Mito-counted AnnData",
-                        "name": "Input dataset",
+                        "label": "Leiden Resolution",
+                        "name": "Input parameter",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 736.1875
+                            "bottom": 195.5,
+                            "height": 84,
+                            "left": 121.5,
+                            "right": 321.5,
+                            "top": 111.5,
+                            "width": 200,
+                            "x": 121.5,
+                            "y": 111.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"default\": 0.35, \"parameter_type\": \"float\", \"optional\": true}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "60316d4a-07b0-4eea-a889-eef54798c5e0",
+                        "type": "parameter_input",
+                        "uuid": "eddf8108-6913-40d2-819d-a84677dee3f4",
                         "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nMito-counted AnnData\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Inspect AnnData\"];\n  0 -->|output| 1;\n  2[\"Scanpy FilterCells\"];\n  0 -->|output| 2;\n  08175d7f-f4f4-413c-ad86-f59587ff692e[\"Output\\nGenes-filtered Object\"];\n  2 --> 08175d7f-f4f4-413c-ad86-f59587ff692e;\n  style 08175d7f-f4f4-413c-ad86-f59587ff692e stroke:#2c3143,stroke-width:4px;\n  3[\"Plot\"];\n  0 -->|output| 3;\n  bfc499ee-630a-498b-9be6-696d9bb78837[\"Output\\nScatter - genes x UMIs\"];\n  3 --> bfc499ee-630a-498b-9be6-696d9bb78837;\n  style bfc499ee-630a-498b-9be6-696d9bb78837 stroke:#2c3143,stroke-width:4px;\n  4[\"Plot\"];\n  0 -->|output| 4;\n  f2c78ef3-7d31-4930-954c-0133cce27a41[\"Output\\nScatter - mito x genes\"];\n  4 --> f2c78ef3-7d31-4930-954c-0133cce27a41;\n  style f2c78ef3-7d31-4930-954c-0133cce27a41 stroke:#2c3143,stroke-width:4px;\n  5[\"Plot\"];\n  0 -->|output| 5;\n  348818e6-9def-41fd-a390-6f8525c57cd8[\"Output\\nViolin - genotype - log\"];\n  5 --> 348818e6-9def-41fd-a390-6f8525c57cd8;\n  style 348818e6-9def-41fd-a390-6f8525c57cd8 stroke:#2c3143,stroke-width:4px;\n  6[\"Plot\"];\n  0 -->|output| 6;\n  844f5e7c-78c8-4f28-8e15-cea35ada8fef[\"Output\\nViolin - batch - log\"];\n  6 --> 844f5e7c-78c8-4f28-8e15-cea35ada8fef;\n  style 844f5e7c-78c8-4f28-8e15-cea35ada8fef stroke:#2c3143,stroke-width:4px;\n  7[\"Inspect AnnData\"];\n  0 -->|output| 7;\n  8[\"Plot\"];\n  0 -->|output| 8;\n  3b1232c5-d16a-434d-806e-79fd77f7c05f[\"Output\\nScatter - mito x UMIs\"];\n  8 --> 3b1232c5-d16a-434d-806e-79fd77f7c05f;\n  style 3b1232c5-d16a-434d-806e-79fd77f7c05f stroke:#2c3143,stroke-width:4px;\n  9[\"Inspect AnnData\"];\n  0 -->|output| 9;\n  10[\"Plot\"];\n  0 -->|output| 10;\n  a639cdc0-da40-4df9-8348-23117528b24a[\"Output\\nViolin - sex - log\"];\n  10 --> a639cdc0-da40-4df9-8348-23117528b24a;\n  style a639cdc0-da40-4df9-8348-23117528b24a stroke:#2c3143,stroke-width:4px;\n  11[\"Plot\"];\n  2 -->|output_h5ad| 11;\n  69bf3e42-63e2-4b5b-9d63-5aac9d6b5691[\"Output\\nViolin - Filterbygenes\"];\n  11 --> 69bf3e42-63e2-4b5b-9d63-5aac9d6b5691;\n  style 69bf3e42-63e2-4b5b-9d63-5aac9d6b5691 stroke:#2c3143,stroke-width:4px;\n  12[\"Scanpy FilterCells\"];\n  2 -->|output_h5ad| 12;\n  f378cb4e-0a77-49d9-b92a-752dbea4b09a[\"Output\\nCounts-filtered Object\"];\n  12 --> f378cb4e-0a77-49d9-b92a-752dbea4b09a;\n  style f378cb4e-0a77-49d9-b92a-752dbea4b09a stroke:#2c3143,stroke-width:4px;\n  13[\"Inspect AnnData\"];\n  2 -->|output_h5ad| 13;\n  f9e862db-eb22-4124-8fe0-0fdcfcfb8393[\"Output\\nGeneral - Filterbygenes\"];\n  13 --> f9e862db-eb22-4124-8fe0-0fdcfcfb8393;\n  style f9e862db-eb22-4124-8fe0-0fdcfcfb8393 stroke:#2c3143,stroke-width:4px;\n  14[\"Inspect AnnData\"];\n  12 -->|output_h5ad| 14;\n  794f72b5-c2c3-46a0-ac15-b9f1e94941d2[\"Output\\nGeneral - Filterbycounts\"];\n  14 --> 794f72b5-c2c3-46a0-ac15-b9f1e94941d2;\n  style 794f72b5-c2c3-46a0-ac15-b9f1e94941d2 stroke:#2c3143,stroke-width:4px;\n  15[\"Scanpy FilterCells\"];\n  12 -->|output_h5ad| 15;\n  b915da66-6435-4871-baa0-3e494ba73c96[\"Output\\nMito-filtered Object\"];\n  15 --> b915da66-6435-4871-baa0-3e494ba73c96;\n  style b915da66-6435-4871-baa0-3e494ba73c96 stroke:#2c3143,stroke-width:4px;\n  16[\"Plot\"];\n  12 -->|output_h5ad| 16;\n  3aef86d7-d34d-4b24-bc97-bf8c97d8d2fa[\"Output\\nViolin - Filterbycounts\"];\n  16 --> 3aef86d7-d34d-4b24-bc97-bf8c97d8d2fa;\n  style 3aef86d7-d34d-4b24-bc97-bf8c97d8d2fa stroke:#2c3143,stroke-width:4px;\n  17[\"Inspect AnnData\"];\n  15 -->|output_h5ad| 17;\n  cd94a4c6-5665-4bdf-88ea-4f4d41efa893[\"Output\\nGeneral - Filterbymito\"];\n  17 --> cd94a4c6-5665-4bdf-88ea-4f4d41efa893;\n  style cd94a4c6-5665-4bdf-88ea-4f4d41efa893 stroke:#2c3143,stroke-width:4px;\n  18[\"Scanpy FilterGenes\"];\n  15 -->|output_h5ad| 18;\n  ee63ef0a-98ed-45cb-b144-1154f84ae452[\"Output\\nFiltered Object\"];\n  18 --> ee63ef0a-98ed-45cb-b144-1154f84ae452;\n  style ee63ef0a-98ed-45cb-b144-1154f84ae452 stroke:#2c3143,stroke-width:4px;\n  19[\"Plot\"];\n  15 -->|output_h5ad| 19;\n  7e48a14f-08fd-45ab-b613-606bf64dcf9d[\"Output\\nViolin - Filterbymito\"];\n  19 --> 7e48a14f-08fd-45ab-b613-606bf64dcf9d;\n  style 7e48a14f-08fd-45ab-b613-606bf64dcf9d stroke:#2c3143,stroke-width:4px;\n  20[\"Inspect AnnData\"];\n  18 -->|output_h5ad| 20;\n  d59efa9b-d049-4f0e-8bd8-8ae982a45d0a[\"Output\\nGeneral - Filtered object\"];\n  20 --> d59efa9b-d049-4f0e-8bd8-8ae982a45d0a;\n  style d59efa9b-d049-4f0e-8bd8-8ae982a45d0a stroke:#2c3143,stroke-width:4px;\n  21[\"Scanpy NormaliseData\"];\n  18 -->|output_h5ad| 21;\n  22[\"Scanpy FindVariableGenes\"];\n  21 -->|output_h5ad| 22;\n  23[\"Scanpy ScaleData\"];\n  22 -->|output_h5ad| 23;\n  24[\"Scanpy RunPCA\"];\n  23 -->|output_h5ad| 24;\n  25[\"Plot\"];\n  24 -->|output_h5ad| 25;\n  993dea99-990f-460a-beb9-46e5c97ee898[\"Output\\nPCA Variance\"];\n  25 --> 993dea99-990f-460a-beb9-46e5c97ee898;\n  style 993dea99-990f-460a-beb9-46e5c97ee898 stroke:#2c3143,stroke-width:4px;\n  26[\"Scanpy ComputeGraph\"];\n  24 -->|output_h5ad| 26;\n  27[\"Scanpy RunTSNE\"];\n  26 -->|output_h5ad| 27;\n  28[\"Scanpy RunUMAP\"];\n  27 -->|output_h5ad| 28;\n  29[\"Scanpy FindCluster\"];\n  28 -->|output_h5ad| 29;\n  30[\"Scanpy FindMarkers\"];\n  29 -->|output_h5ad| 30;\n  308b4961-4d50-442b-9bca-bbb1992426ba[\"Output\\nMarkers - cluster\"];\n  30 --> 308b4961-4d50-442b-9bca-bbb1992426ba;\n  style 308b4961-4d50-442b-9bca-bbb1992426ba stroke:#2c3143,stroke-width:4px;\n  035bbbce-fb57-48c8-83d5-2b0cd0376541[\"Output\\nFinal object\"];\n  30 --> 035bbbce-fb57-48c8-83d5-2b0cd0376541;\n  style 035bbbce-fb57-48c8-83d5-2b0cd0376541 stroke:#2c3143,stroke-width:4px;\n  31[\"Scanpy FindMarkers\"];\n  29 -->|output_h5ad| 31;\n  1705e219-192a-4f52-9b26-64fcbcd303ea[\"Output\\nMarkers - genotype\"];\n  31 --> 1705e219-192a-4f52-9b26-64fcbcd303ea;\n  style 1705e219-192a-4f52-9b26-64fcbcd303ea stroke:#2c3143,stroke-width:4px;\n  32[\"Scanpy PlotEmbed\"];\n  30 -->|output_h5ad| 32;\n  33[\"Scanpy PlotEmbed\"];\n  30 -->|output_h5ad| 33;\n  34[\"Manipulate AnnData\"];\n  30 -->|output_h5ad| 34;\n  35[\"Scanpy PlotEmbed\"];\n  30 -->|output_h5ad| 35;\n  36[\"Inspect AnnData\"];\n  30 -->|output_h5ad| 36;\n  37[\"AnnData Operations\"];\n  34 -->|anndata| 37;\n  30 -->|output_h5ad| 37;\n  38[\"Join two Datasets\"];\n  30 -->|output_tsv| 38;\n  36 -->|var| 38;\n  39[\"Join two Datasets\"];\n  31 -->|output_tsv| 39;\n  36 -->|var| 39;\n  40[\"AnnData Operations\"];\n  37 -->|output_h5ad| 40;\n  a6d48df0-403f-4efc-a75f-9504a960884e[\"Output\\nFinal cell annotated object\"];\n  40 --> a6d48df0-403f-4efc-a75f-9504a960884e;\n  style a6d48df0-403f-4efc-a75f-9504a960884e stroke:#2c3143,stroke-width:4px;\n  41[\"Cut\"];\n  38 -->|out_file1| 41;\n  0ee7f9b6-b065-4e26-93df-6e6e2fe458a9[\"Output\\nMarkers - cluster - named\"];\n  41 --> 0ee7f9b6-b065-4e26-93df-6e6e2fe458a9;\n  style 0ee7f9b6-b065-4e26-93df-6e6e2fe458a9 stroke:#2c3143,stroke-width:4px;\n  42[\"Cut\"];\n  39 -->|out_file1| 42;\n  fdb88faa-9b76-4edb-b89b-427c098a473e[\"Output\\nMarkers - genotype - named\"];\n  42 --> fdb88faa-9b76-4edb-b89b-427c098a473e;\n  style fdb88faa-9b76-4edb-b89b-427c098a473e stroke:#2c3143,stroke-width:4px;\n  43[\"Scanpy PlotEmbed\"];\n  40 -->|output_h5ad| 43;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "CS3_Filter, Plot and Explore Single-cell RNA-seq Data",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "content_id": null,
                         "errors": null,
                         "id": 1,
-                        "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Inspect AnnData",
-                        "outputs": [
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "obs",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "SHR (CSV.gz)"
                             }
                         ],
+                        "label": "SHR (CSV.gz)",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 277.8984375,
-                            "top": 21.0703125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ee98d611afc6",
-                            "name": "anndata_inspect",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 302,
+                            "height": 84,
+                            "left": 116,
+                            "right": 316,
+                            "top": 218,
+                            "width": 200,
+                            "x": 116,
+                            "y": 218
                         },
-                        "tool_state": "{\"__input_ext\": \"h5ad\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"obs\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.5+galaxy1",
-                        "type": "tool",
-                        "uuid": "99ffbf79-3be8-4905-b978-e56b02327314",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "obs",
-                                "uuid": "6e2bd8b0-8203-4dfe-9c28-054d863bd277"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "4cf4f111-d63b-47ad-bcbf-8ebb290b3431",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0",
+                        "content_id": null,
                         "errors": null,
                         "id": 2,
-                        "input_connections": {
-                            "input_obj_file": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy FilterCells",
-                        "outputs": [
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
+                                "description": "",
+                                "name": "WT (CSV.gz)"
                             }
                         ],
+                        "label": "WT (CSV.gz)",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 277.8984375,
-                            "top": 238.2421875
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_h5ad": {
-                                "action_arguments": {
-                                    "newname": "Genes-filtered Object"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "55ccc0a121bc",
-                            "name": "scanpy_filter_cells",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 403,
+                            "height": 84,
+                            "left": 114,
+                            "right": 314,
+                            "top": 319,
+                            "width": 200,
+                            "x": 114,
+                            "y": 319
                         },
-                        "tool_state": "{\"categories\": [], \"export_mtx\": \"false\", \"force_recalc\": \"false\", \"gene_name\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"parameters\": [{\"__index__\": 0, \"name\": \"log1p_n_genes_by_counts\", \"min\": \"5.7\", \"max\": \"20.0\"}], \"save_layer\": null, \"save_raw\": \"false\", \"subsets\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "ab02dab9-1c72-4987-929c-6b67baae1e6d",
-                        "workflow_outputs": [
-                            {
-                                "label": "Genes-filtered Object",
-                                "output_name": "output_h5ad",
-                                "uuid": "08175d7f-f4f4-413c-ad86-f59587ff692e"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "94fba59a-ba9d-452d-b325-cb558201f674",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "content_id": null,
                         "errors": null,
                         "id": 3,
-                        "input_connections": {
-                            "adata": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Plot",
-                        "outputs": [
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "description": "",
+                                "name": "Min Genes"
                             }
                         ],
+                        "label": "Min Genes",
+                        "name": "Input parameter",
+                        "outputs": [],
                         "position": {
-                            "left": 277.8984375,
-                            "top": 434.28125
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_png": {
-                                "action_arguments": {
-                                    "newname": "Scatter - genes x UMIs"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_png"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "aa0c474463c2",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 503.75,
+                            "height": 64.25,
+                            "left": 16,
+                            "right": 216,
+                            "top": 439.5,
+                            "width": 200,
+                            "x": 16,
+                            "y": 439.5
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.scatter\", \"__current_case__\": 0, \"type\": {\"type\": \"xy\", \"__current_case__\": 0, \"x\": \"log1p_total_counts\", \"y\": \"log1p_n_genes_by_counts\", \"color\": \"pct_counts_mito\", \"layers\": {\"use_layers\": \"false\", \"__current_case__\": 1}}, \"use_raw\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"color_map\": \"None\", \"palette\": \"default\", \"frameon\": \"true\", \"size\": null, \"title\": \"\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy1",
-                        "type": "tool",
-                        "uuid": "767da31e-dc80-4d11-9f8e-8b1589029dcc",
-                        "workflow_outputs": [
-                            {
-                                "label": "Scatter - genes x UMIs",
-                                "output_name": "out_png",
-                                "uuid": "bfc499ee-630a-498b-9be6-696d9bb78837"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"default\": 100, \"parameter_type\": \"integer\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "c9a62328-f049-43b6-92fb-df5c42982573",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "content_id": null,
                         "errors": null,
                         "id": 4,
-                        "input_connections": {
-                            "adata": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Plot",
-                        "outputs": [
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "description": "",
+                                "name": "Min Cells"
                             }
                         ],
+                        "label": "Min Cells",
+                        "name": "Input parameter",
+                        "outputs": [],
                         "position": {
-                            "left": 277.8984375,
-                            "top": 588.25
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_png": {
-                                "action_arguments": {
-                                    "newname": "Scatter - mito x genes"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_png"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "aa0c474463c2",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 578.75,
+                            "height": 64.25,
+                            "left": 17,
+                            "right": 217,
+                            "top": 514.5,
+                            "width": 200,
+                            "x": 17,
+                            "y": 514.5
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.scatter\", \"__current_case__\": 0, \"type\": {\"type\": \"xy\", \"__current_case__\": 0, \"x\": \"log1p_n_genes_by_counts\", \"y\": \"pct_counts_mito\", \"color\": \"\", \"layers\": {\"use_layers\": \"false\", \"__current_case__\": 1}}, \"use_raw\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"color_map\": \"None\", \"palette\": \"default\", \"frameon\": \"true\", \"size\": null, \"title\": \"\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy1",
-                        "type": "tool",
-                        "uuid": "ad0b1195-4bb2-46be-bb8a-8fd5de416372",
-                        "workflow_outputs": [
-                            {
-                                "label": "Scatter - mito x genes",
-                                "output_name": "out_png",
-                                "uuid": "f2c78ef3-7d31-4930-954c-0133cce27a41"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"default\": 2, \"parameter_type\": \"integer\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "7bf5f0e1-b482-45c3-9bcb-10ca93e6b7dc",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "content_id": null,
                         "errors": null,
                         "id": 5,
-                        "input_connections": {
-                            "adata": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Plot",
-                        "outputs": [
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "description": "",
+                                "name": "Max Features"
                             }
                         ],
+                        "label": "Max Features",
+                        "name": "Input parameter",
+                        "outputs": [],
                         "position": {
-                            "left": 277.8984375,
-                            "top": 742.28125
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_png": {
-                                "action_arguments": {
-                                    "newname": "Violin - genotype - log"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_png"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "aa0c474463c2",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 671.5,
+                            "height": 84,
+                            "left": 23,
+                            "right": 223,
+                            "top": 587.5,
+                            "width": 200,
+                            "x": 23,
+                            "y": 587.5
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"genotype\", \"log\": \"false\", \"use_raw\": \"false\", \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy1",
-                        "type": "tool",
-                        "uuid": "a6a5b2f9-9765-4f5d-b4cf-7c513b8eed3c",
-                        "workflow_outputs": [
-                            {
-                                "label": "Violin - genotype - log",
-                                "output_name": "out_png",
-                                "uuid": "348818e6-9def-41fd-a390-6f8525c57cd8"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"default\": 12000.0, \"parameter_type\": \"float\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "8902a917-75fb-49c6-9e5d-15f87bd91d46",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "content_id": null,
                         "errors": null,
                         "id": 6,
-                        "input_connections": {
-                            "adata": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Plot",
-                        "outputs": [
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "description": "",
+                                "name": "Max Lib Size"
                             }
                         ],
+                        "label": "Max Lib Size",
+                        "name": "Input parameter",
+                        "outputs": [],
                         "position": {
-                            "left": 277.8984375,
-                            "top": 896.3046875
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_png": {
-                                "action_arguments": {
-                                    "newname": "Violin - batch - log"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_png"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "aa0c474463c2",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 764.5,
+                            "height": 84,
+                            "left": 15,
+                            "right": 215,
+                            "top": 680.5,
+                            "width": 200,
+                            "x": 15,
+                            "y": 680.5
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"batch\", \"log\": \"false\", \"use_raw\": \"false\", \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy1",
-                        "type": "tool",
-                        "uuid": "a6d8ecf9-1510-4c1a-8665-ddf25b0ca395",
-                        "workflow_outputs": [
-                            {
-                                "label": "Violin - batch - log",
-                                "output_name": "out_png",
-                                "uuid": "844f5e7c-78c8-4f28-8e15-cea35ada8fef"
-                            }
-                        ]
-                    },
+                        "tool_id": null,
+                        "tool_state": "{\"default\": 120000.0, \"parameter_type\": \"float\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "db068cdb-53c4-48a3-95c2-141fa83c271b",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nLeiden Resolution\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSHR CSV.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nWT CSV.gz\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nMin Genes\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nMin Cells\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Parameter\\nMax Features\"];\n  style 5 fill:#ded,stroke:#393,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Parameter\\nMax Lib Size\"];\n  style 6 fill:#ded,stroke:#393,stroke-width:4px;\n  7[\"Import Anndata and loom\"];\n  1 -->|output| 7;\n  8[\"Import Anndata and loom\"];\n  2 -->|output| 8;\n  9[\"Manipulate AnnData\"];\n  7 -->|anndata| 9;\n  8 -->|anndata| 9;\n  10[\"Rename Batches\"];\n  9 -->|anndata| 10;\n  680180f6-edfc-4f66-b265-7a63aaa22b39[\"Output\\nscRNA Concatenated Datasets\"];\n  10 --> 680180f6-edfc-4f66-b265-7a63aaa22b39;\n  style 680180f6-edfc-4f66-b265-7a63aaa22b39 stroke:#2c3143,stroke-width:4px;\n  11[\"QC metrics\"];\n  10 -->|anndata| 11;\n  12[\"Filter genes\"];\n  11 -->|anndata_out| 12;\n  3 -->|output| 12;\n  13[\"Plot Violin\"];\n  11 -->|anndata_out| 13;\n  14[\"Filter Cells\"];\n  12 -->|anndata_out| 14;\n  4 -->|output| 14;\n  15[\"Filter Max Features\"];\n  14 -->|anndata_out| 15;\n  5 -->|output| 15;\n  16[\"Filter Max Library Size\"];\n  15 -->|anndata| 16;\n  6 -->|output| 16;\n  17[\"Save RAW\"];\n  16 -->|anndata| 17;\n  18[\"Norm to 1e4\"];\n  17 -->|anndata| 18;\n  19[\"Log1p\"];\n  18 -->|anndata_out| 19;\n  20[\"Regress total counts\"];\n  19 -->|anndata_out| 20;\n  21[\"Scale\"];\n  20 -->|anndata_out| 21;\n  22[\"PCA\"];\n  21 -->|anndata_out| 22;\n  23[\"Neighborhod\"];\n  22 -->|anndata_out| 23;\n  24[\"UMAP\"];\n  23 -->|anndata_out| 24;\n  25[\"Leiden\"];\n  24 -->|anndata_out| 25;\n  0 -->|output| 25;\n  48cf0465-84ba-461a-bdb9-61625626de42[\"Output\\nscRNA with clusters Dataset\"];\n  25 --> 48cf0465-84ba-461a-bdb9-61625626de42;\n  style 48cf0465-84ba-461a-bdb9-61625626de42 stroke:#2c3143,stroke-width:4px;\n  26[\"Plot PCA batch\"];\n  24 -->|anndata_out| 26;\n  27[\"Plot UMAP batch\"];\n  24 -->|anndata_out| 27;\n  28[\"Plot UMAP leiden, batch\"];\n  25 -->|anndata_out| 28;\n  29[\"Rename Clusters\"];\n  25 -->|anndata_out| 29;\n  30[\"Complex DotPlot\"];\n  25 -->|anndata_out| 30;\n  31[\"Complex DotPlot with new labels\"];\n  29 -->|anndata| 31;\n  32[\"Plot UMAP with new labels\"];\n  29 -->|anndata| 32;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "scRNA Plant Analysis",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0",
                         "errors": null,
-                        "id": 7,
+                        "id": 10,
                         "input_connections": {
                             "input": {
-                                "id": 0,
-                                "output_name": "output"
+                                "id": 9,
+                                "output_name": "anndata"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Inspect AnnData",
+                        "label": "Rename Batches",
+                        "name": "Manipulate AnnData",
                         "outputs": [
                             {
-                                "name": "var",
-                                "type": "tabular"
+                                "name": "anndata",
+                                "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 277.8984375,
-                            "top": 1029.3046875
+                            "bottom": 354.3999938964844,
+                            "height": 136.39999389648438,
+                            "left": 955,
+                            "right": 1155,
+                            "top": 218,
+                            "width": 200,
+                            "x": 955,
+                            "y": 218
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "ee98d611afc6",
-                            "name": "anndata_inspect",
+                            "changeset_revision": "8db95f488f0f",
+                            "name": "anndata_manipulate",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"h5ad\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"var\", \"__current_case__\": 4}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.5+galaxy1",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"rename_categories\", \"__current_case__\": 3, \"key\": \"batch\", \"categories\": \"shr, wt\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.5+galaxy0",
                         "type": "tool",
-                        "uuid": "9445c5ea-8c75-48f2-b7a1-fd0e43c625c7",
+                        "uuid": "0a25ffc3-ac58-4c17-9f22-b4127952027a",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "var",
-                                "uuid": "ba910718-a539-4b77-b3e8-087711e13eaf"
+                                "label": "scRNA Concatenated Datasets",
+                                "output_name": "anndata",
+                                "uuid": "680180f6-edfc-4f66-b265-7a63aaa22b39"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "errors": null,
-                        "id": 8,
+                        "id": 13,
                         "input_connections": {
                             "adata": {
-                                "id": 0,
-                                "output_name": "output"
+                                "id": 11,
+                                "output_name": "anndata_out"
                             }
                         },
                         "inputs": [],
-                        "label": null,
+                        "label": "Plot Violin",
                         "name": "Plot",
                         "outputs": [
                             {
@@ -230751,94 +235425,102 @@
                             }
                         ],
                         "position": {
-                            "left": 277.8984375,
-                            "top": 1267.2734375
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_png": {
-                                "action_arguments": {
-                                    "newname": "Scatter - mito x UMIs"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_png"
-                            }
+                            "bottom": 259.8000030517578,
+                            "height": 116.65000915527344,
+                            "left": 1867.2833251953125,
+                            "right": 2067.2833251953125,
+                            "top": 143.14999389648438,
+                            "width": 200,
+                            "x": 1867.2833251953125,
+                            "y": 143.14999389648438
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "aa0c474463c2",
+                            "changeset_revision": "6adf98e782f3",
                             "name": "scanpy_plot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.scatter\", \"__current_case__\": 0, \"type\": {\"type\": \"xy\", \"__current_case__\": 0, \"x\": \"log1p_total_counts\", \"y\": \"pct_counts_mito\", \"color\": \"\", \"layers\": {\"use_layers\": \"false\", \"__current_case__\": 1}}, \"use_raw\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"color_map\": \"None\", \"palette\": \"default\", \"frameon\": \"true\", \"size\": null, \"title\": \"\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy1",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"n_genes_by_counts, total_counts\"}, \"groupby\": \"batch\", \"log\": \"false\", \"use_raw\": \"false\", \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"0.4\"}}, \"multi_panel\": {\"multi_panel\": \"True\", \"__current_case__\": 0, \"width\": null, \"height\": null}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy0",
                         "type": "tool",
-                        "uuid": "7225da9d-e700-49f7-bb78-20f2954872bd",
+                        "uuid": "9dfc1e59-71aa-40b8-b504-2498a8dc5409",
                         "workflow_outputs": [
                             {
-                                "label": "Scatter - mito x UMIs",
+                                "label": null,
                                 "output_name": "out_png",
-                                "uuid": "3b1232c5-d16a-434d-806e-79fd77f7c05f"
+                                "uuid": "2fb1d919-0e60-4c81-92d2-83c28b1ef654"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
                         "errors": null,
-                        "id": 9,
+                        "id": 25,
                         "input_connections": {
-                            "input": {
+                            "adata": {
+                                "id": 24,
+                                "output_name": "anndata_out"
+                            },
+                            "method|resolution": {
                                 "id": 0,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Inspect AnnData",
+                        "label": "Leiden",
+                        "name": "Cluster, infer trajectories and embed",
                         "outputs": [
                             {
-                                "name": "general",
-                                "type": "txt"
+                                "name": "anndata_out",
+                                "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 277.8984375,
-                            "top": 1421.234375
+                            "bottom": 562.0500030517578,
+                            "height": 147.0500030517578,
+                            "left": 1389,
+                            "right": 1589,
+                            "top": 415,
+                            "width": 200,
+                            "x": 1389,
+                            "y": 415
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "ee98d611afc6",
-                            "name": "anndata_inspect",
+                            "changeset_revision": "35bc2eb568ed",
+                            "name": "scanpy_cluster_reduce_dimension",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"h5ad\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"general\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.5+galaxy1",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"method\": {\"method\": \"tl.leiden\", \"__current_case__\": 1, \"resolution\": {\"__class__\": \"ConnectedValue\"}, \"random_state\": \"0\", \"key_added\": \"leiden\", \"use_weights\": \"false\", \"n_iterations\": \"-1\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy0",
                         "type": "tool",
-                        "uuid": "549b599e-1b3d-4be4-bfe7-91c50cef7ef7",
+                        "uuid": "99494ea7-377c-4f3d-a45a-18bfd81b7888",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "general",
-                                "uuid": "8fbf3a0b-bf46-48ff-8f64-bb7018d51382"
+                                "label": "scRNA with clusters Dataset",
+                                "output_name": "anndata_out",
+                                "uuid": "48cf0465-84ba-461a-bdb9-61625626de42"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "errors": null,
-                        "id": 10,
+                        "id": 26,
                         "input_connections": {
                             "adata": {
-                                "id": 0,
-                                "output_name": "output"
+                                "id": 24,
+                                "output_name": "anndata_out"
                             }
                         },
                         "inputs": [],
-                        "label": null,
+                        "label": "Plot PCA (batch)",
                         "name": "Plot",
                         "outputs": [
                             {
@@ -230847,50 +235529,48 @@
                             }
                         ],
                         "position": {
-                            "left": 277.8984375,
-                            "top": 1617.2109375
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_png": {
-                                "action_arguments": {
-                                    "newname": "Violin - sex - log"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_png"
-                            }
+                            "bottom": 277.5500030517578,
+                            "height": 136.40000915527344,
+                            "left": 1629.433349609375,
+                            "right": 1829.433349609375,
+                            "top": 141.14999389648438,
+                            "width": 200,
+                            "x": 1629.433349609375,
+                            "y": 141.14999389648438
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "aa0c474463c2",
+                            "changeset_revision": "6adf98e782f3",
                             "name": "scanpy_plot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"sex\", \"log\": \"false\", \"use_raw\": \"false\", \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy1",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.pca\", \"__current_case__\": 9, \"color\": \"batch\", \"use_raw\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy0",
                         "type": "tool",
-                        "uuid": "d21d8d66-0488-4382-bed4-b8534c08169f",
+                        "uuid": "e2daa4c6-9a39-4c42-852e-4f61b65202c2",
                         "workflow_outputs": [
                             {
-                                "label": "Violin - sex - log",
+                                "label": null,
                                 "output_name": "out_png",
-                                "uuid": "a639cdc0-da40-4df9-8348-23117528b24a"
+                                "uuid": "72d1a264-3ace-4d2e-910a-5e2a0fa6721f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "errors": null,
-                        "id": 11,
+                        "id": 27,
                         "input_connections": {
                             "adata": {
-                                "id": 2,
-                                "output_name": "output_h5ad"
+                                "id": 24,
+                                "output_name": "anndata_out"
                             }
                         },
                         "inputs": [],
-                        "label": null,
+                        "label": "Plot UMAP (batch)",
                         "name": "Plot",
                         "outputs": [
                             {
@@ -230899,258 +235579,198 @@
                             }
                         ],
                         "position": {
-                            "left": 555.9140625,
-                            "top": 84.2109375
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_png": {
-                                "action_arguments": {
-                                    "newname": "Violin - Filterbygenes"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_png"
-                            }
+                            "bottom": 406.3999938964844,
+                            "height": 136.39999389648438,
+                            "left": 1862,
+                            "right": 2062,
+                            "top": 270,
+                            "width": 200,
+                            "x": 1862,
+                            "y": 270
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "aa0c474463c2",
+                            "changeset_revision": "6adf98e782f3",
                             "name": "scanpy_plot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"genotype\", \"log\": \"false\", \"use_raw\": \"false\", \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy1",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"batch\", \"use_raw\": \"false\", \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": \"14\", \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy0",
                         "type": "tool",
-                        "uuid": "0ceca44a-91f3-4c85-8dfe-7c958c373fed",
+                        "uuid": "e70d8e14-1983-4381-8feb-bba7d5dbb4d6",
                         "workflow_outputs": [
                             {
-                                "label": "Violin - Filterbygenes",
+                                "label": null,
                                 "output_name": "out_png",
-                                "uuid": "69bf3e42-63e2-4b5b-9d63-5aac9d6b5691"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0",
-                        "errors": null,
-                        "id": 12,
-                        "input_connections": {
-                            "input_obj_file": {
-                                "id": 2,
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy FilterCells",
-                        "outputs": [
-                            {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
-                            }
-                        ],
-                        "position": {
-                            "left": 555.9140625,
-                            "top": 238.2421875
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_h5ad": {
-                                "action_arguments": {
-                                    "newname": "Counts-filtered Object"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "55ccc0a121bc",
-                            "name": "scanpy_filter_cells",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"categories\": [], \"export_mtx\": \"false\", \"force_recalc\": \"false\", \"gene_name\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"parameters\": [{\"__index__\": 0, \"name\": \"log1p_total_counts\", \"min\": \"6.3\", \"max\": \"20.0\"}], \"save_layer\": null, \"save_raw\": \"false\", \"subsets\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "2b612ba2-7539-43a7-963c-da6172101f1f",
-                        "workflow_outputs": [
-                            {
-                                "label": "Counts-filtered Object",
-                                "output_name": "output_h5ad",
-                                "uuid": "f378cb4e-0a77-49d9-b92a-752dbea4b09a"
+                                "uuid": "c223e762-7e90-41e1-b354-bbe6e278b5c0"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "errors": null,
-                        "id": 13,
+                        "id": 28,
                         "input_connections": {
-                            "input": {
-                                "id": 2,
-                                "output_name": "output_h5ad"
+                            "adata": {
+                                "id": 25,
+                                "output_name": "anndata_out"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Inspect AnnData",
+                        "label": "Plot UMAP (leiden, batch)",
+                        "name": "Plot",
                         "outputs": [
                             {
-                                "name": "general",
-                                "type": "txt"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 555.9140625,
-                            "top": 434.28125
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActiongeneral": {
-                                "action_arguments": {
-                                    "newname": "General - Filterbygenes"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "general"
-                            }
+                            "bottom": 442.5500030517578,
+                            "height": 136.40000915527344,
+                            "left": 1630.433349609375,
+                            "right": 1830.433349609375,
+                            "top": 306.1499938964844,
+                            "width": 200,
+                            "x": 1630.433349609375,
+                            "y": 306.1499938964844
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "ee98d611afc6",
-                            "name": "anndata_inspect",
+                            "changeset_revision": "6adf98e782f3",
+                            "name": "scanpy_plot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"general\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.5+galaxy1",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"leiden, batch\", \"use_raw\": \"false\", \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": \"14\", \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy0",
                         "type": "tool",
-                        "uuid": "47b02be1-43e4-4bd3-a20f-ebfeddd29ad0",
+                        "uuid": "b88358ff-0dda-4c2e-bce6-124a0ab8fa28",
                         "workflow_outputs": [
                             {
-                                "label": "General - Filterbygenes",
-                                "output_name": "general",
-                                "uuid": "f9e862db-eb22-4124-8fe0-0fdcfcfb8393"
+                                "label": null,
+                                "output_name": "out_png",
+                                "uuid": "26c65cd9-74aa-4574-a5f3-ac10caced4da"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "errors": null,
-                        "id": 14,
+                        "id": 30,
                         "input_connections": {
-                            "input": {
-                                "id": 12,
-                                "output_name": "output_h5ad"
+                            "adata": {
+                                "id": 25,
+                                "output_name": "anndata_out"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Inspect AnnData",
+                        "label": "Complex DotPlot",
+                        "name": "Plot",
                         "outputs": [
                             {
-                                "name": "general",
-                                "type": "txt"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 834.046875,
-                            "top": 63.21875
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActiongeneral": {
-                                "action_arguments": {
-                                    "newname": "General - Filterbycounts"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "general"
-                            }
+                            "bottom": 557.3999938964844,
+                            "height": 136.39999389648438,
+                            "left": 1861,
+                            "right": 2061,
+                            "top": 421,
+                            "width": 200,
+                            "x": 1861,
+                            "y": 421
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "ee98d611afc6",
-                            "name": "anndata_inspect",
+                            "changeset_revision": "6adf98e782f3",
+                            "name": "scanpy_plot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"general\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.5+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.dotplot\", \"__current_case__\": 2, \"var_names\": {\"type\": \"custom\", \"__current_case__\": 1, \"var_names\": \"AT1G26680,COBL2,AT3G55180,NCED2,AT5G22550,ATL63,RGF8,TEL1,DUF9,AGL42,PLT1,PLT2,PER3,PER9,PBL15,TBL30,AT2G48130,AT3G22620,AED3,T3P18-7,MBK21-8,NPF6-4,CYP71B34,IAMT1,AT1G31950,F14G6-22,GL2,ANL2,PMEI4,MUD21-4,EXPA7,MES15,ADF8,COBL9,TPR14,BHLH144,MYB83,SCPL35,MYB46,COBL4,PIN7,PIN3   \"}, \"groupby\": \"leiden\", \"num_categories\": \"9\", \"log\": \"false\", \"use_raw\": \"true\", \"dendrogram\": \"false\", \"var_group_positions\": [{\"__index__\": 0, \"start\": \"0\", \"end\": \"5\", \"label\": \"Columella\"}, {\"__index__\": 1, \"start\": \"6\", \"end\": \"9\", \"label\": \"QC\"}, {\"__index__\": 2, \"start\": \"10\", \"end\": \"11\", \"label\": \"NC\"}, {\"__index__\": 3, \"start\": \"12\", \"end\": \"17\", \"label\": \"Endodermis\"}, {\"__index__\": 4, \"start\": \"18\", \"end\": \"23\", \"label\": \"Cortex\"}, {\"__index__\": 5, \"start\": \"24\", \"end\": \"29\", \"label\": \"Atrichoblast\"}, {\"__index__\": 6, \"start\": \"30\", \"end\": \"34\", \"label\": \"Trichoblast\"}, {\"__index__\": 7, \"start\": \"35\", \"end\": \"39\", \"label\": \"Xylem\"}, {\"__index__\": 8, \"start\": \"40\", \"end\": \"41\", \"label\": \"VC\"}], \"var_group_rotation\": null, \"figsize\": {\"test\": \"no\", \"__current_case__\": 1}, \"layer\": \"\", \"color_map\": \"viridis\", \"dot_max\": null, \"dot_min\": null, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy0",
                         "type": "tool",
-                        "uuid": "85d4b86e-cff4-41bf-92d5-a4d53c72f950",
+                        "uuid": "625a157f-f08f-4137-a27b-721bee0feb59",
                         "workflow_outputs": [
                             {
-                                "label": "General - Filterbycounts",
-                                "output_name": "general",
-                                "uuid": "794f72b5-c2c3-46a0-ac15-b9f1e94941d2"
+                                "label": null,
+                                "output_name": "out_png",
+                                "uuid": "b35ffb5a-5f29-4105-a016-c02ceee0d9da"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "errors": null,
-                        "id": 15,
+                        "id": 31,
                         "input_connections": {
-                            "input_obj_file": {
-                                "id": 12,
-                                "output_name": "output_h5ad"
+                            "adata": {
+                                "id": 29,
+                                "output_name": "anndata"
                             }
                         },
                         "inputs": [],
-                        "label": null,
-                        "name": "Scanpy FilterCells",
+                        "label": "Complex DotPlot with new labels",
+                        "name": "Plot",
                         "outputs": [
                             {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 834.046875,
-                            "top": 238.2421875
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_h5ad": {
-                                "action_arguments": {
-                                    "newname": "Mito-filtered Object"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_h5ad"
-                            }
+                            "bottom": 733.4666748046875,
+                            "height": 156.79998779296875,
+                            "left": 1860.449951171875,
+                            "right": 2060.449951171875,
+                            "top": 576.6666870117188,
+                            "width": 200,
+                            "x": 1860.449951171875,
+                            "y": 576.6666870117188
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "55ccc0a121bc",
-                            "name": "scanpy_filter_cells",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "6adf98e782f3",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"categories\": [], \"export_mtx\": \"false\", \"force_recalc\": \"false\", \"gene_name\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"parameters\": [{\"__index__\": 0, \"name\": \"pct_counts_mito\", \"min\": \"0.0\", \"max\": \"4.5\"}], \"save_layer\": null, \"save_raw\": \"false\", \"subsets\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.dotplot\", \"__current_case__\": 2, \"var_names\": {\"type\": \"custom\", \"__current_case__\": 1, \"var_names\": \"AT1G26680,COBL2,AT3G55180,NCED2,AT5G22550,ATL63,RGF8,TEL1,DUF9,AGL42,PLT1,PLT2,PER3,PER9,PBL15,TBL30,AT2G48130,AT3G22620,AED3,T3P18-7,MBK21-8,NPF6-4,CYP71B34,IAMT1,AT1G31950,F14G6-22,GL2,ANL2,PMEI4,MUD21-4,EXPA7,MES15,ADF8,COBL9,TPR14,BHLH144,MYB83,SCPL35,MYB46,COBL4,PIN7,PIN3   \"}, \"groupby\": \"leiden\", \"num_categories\": \"9\", \"log\": \"false\", \"use_raw\": \"true\", \"dendrogram\": \"false\", \"var_group_positions\": [{\"__index__\": 0, \"start\": \"0\", \"end\": \"5\", \"label\": \"Columella\"}, {\"__index__\": 1, \"start\": \"6\", \"end\": \"9\", \"label\": \"QC\"}, {\"__index__\": 2, \"start\": \"10\", \"end\": \"11\", \"label\": \"NC\"}, {\"__index__\": 3, \"start\": \"12\", \"end\": \"17\", \"label\": \"Endodermis\"}, {\"__index__\": 4, \"start\": \"18\", \"end\": \"23\", \"label\": \"Cortex\"}, {\"__index__\": 5, \"start\": \"24\", \"end\": \"29\", \"label\": \"Atrichoblast\"}, {\"__index__\": 6, \"start\": \"30\", \"end\": \"34\", \"label\": \"Trichoblast\"}, {\"__index__\": 7, \"start\": \"35\", \"end\": \"39\", \"label\": \"Xylem\"}, {\"__index__\": 8, \"start\": \"40\", \"end\": \"41\", \"label\": \"VC\"}], \"var_group_rotation\": null, \"figsize\": {\"test\": \"no\", \"__current_case__\": 1}, \"layer\": \"\", \"color_map\": \"viridis\", \"dot_max\": null, \"dot_min\": null, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy0",
                         "type": "tool",
-                        "uuid": "47ab6b8d-2130-4885-b972-84f3a444b707",
+                        "uuid": "a2f04375-1e67-4764-ae78-2678dcf2c03a",
                         "workflow_outputs": [
                             {
-                                "label": "Mito-filtered Object",
-                                "output_name": "output_h5ad",
-                                "uuid": "b915da66-6435-4871-baa0-3e494ba73c96"
+                                "label": null,
+                                "output_name": "out_png",
+                                "uuid": "329e95de-cf53-4c0b-9a9b-ad30632ceeb8"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "errors": null,
-                        "id": 16,
+                        "id": 32,
                         "input_connections": {
                             "adata": {
-                                "id": 12,
-                                "output_name": "output_h5ad"
+                                "id": 29,
+                                "output_name": "anndata"
                             }
                         },
                         "inputs": [],
-                        "label": null,
+                        "label": "Plot UMAP with new labels",
                         "name": "Plot",
                         "outputs": [
                             {
@@ -231159,965 +235779,1473 @@
                             }
                         ],
                         "position": {
-                            "left": 834.046875,
-                            "top": 434.28125
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_png": {
-                                "action_arguments": {
-                                    "newname": "Violin - Filterbycounts"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_png"
-                            }
+                            "bottom": 885.3999938964844,
+                            "height": 136.39999389648438,
+                            "left": 1863,
+                            "right": 2063,
+                            "top": 749,
+                            "width": 200,
+                            "x": 1863,
+                            "y": 749
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "aa0c474463c2",
+                            "changeset_revision": "6adf98e782f3",
                             "name": "scanpy_plot",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"genotype\", \"log\": \"false\", \"use_raw\": \"false\", \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"leiden, batch\", \"use_raw\": \"false\", \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"on data\", \"legend_fontsize\": \"14\", \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy0",
                         "type": "tool",
-                        "uuid": "dbf56597-b286-43b9-bc04-f1e3995f7bc0",
+                        "uuid": "c83c81b0-cd9e-41c5-8b72-4b024b7260dc",
                         "workflow_outputs": [
                             {
-                                "label": "Violin - Filterbycounts",
+                                "label": null,
                                 "output_name": "out_png",
-                                "uuid": "3aef86d7-d34d-4b24-bc97-bf8c97d8d2fa"
+                                "uuid": "579d19d3-a98c-4e3a-92aa-0b65e2ffcefd"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "single-cell/scrna-plant",
+                "path": "topics/single-cell/tutorials/scrna-plant/workflows/main_workflow.ga",
+                "tags": [
+                    "transcriptomics",
+                    "single-cell"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "scRNA Plant Analysis",
+                "topic_id": "single-cell",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-plant/versions/main-workflow",
+                "tutorial_id": "scrna-plant",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-plant/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-plant/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "single-cell-scrna-plant",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0"
+                ],
+                "workflowhub_id": "1266"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/4597857"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "anndata_ops",
+                    "owner": "ebi-gxa",
+                    "revisions": "890fb06a2893",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "anndata_ops",
+                    "owner": "ebi-gxa",
+                    "revisions": "825dfd66e3fb",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_filter_cells",
+                    "owner": "ebi-gxa",
+                    "revisions": "e9283529cba1",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "unzip",
+                    "owner": "imgteam",
+                    "revisions": "57f0914ddb7b",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "anndata_import",
+                    "owner": "iuc",
+                    "revisions": "fb9e030ffae4",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "anndata_inspect",
+                    "owner": "iuc",
+                    "revisions": "ee98d611afc6",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "anndata_manipulate",
+                    "owner": "iuc",
+                    "revisions": "3d748954434b",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_ops\n  owner: ebi-gxa\n  revisions: 890fb06a2893\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_ops\n  owner: ebi-gxa\n  revisions: 825dfd66e3fb\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter_cells\n  owner: ebi-gxa\n  revisions: e9283529cba1\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unzip\n  owner: imgteam\n  revisions: 57f0914ddb7b\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_import\n  owner: iuc\n  revisions: fb9e030ffae4\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_inspect\n  owner: iuc\n  revisions: ee98d611afc6\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n  owner: iuc\n  revisions: 3d748954434b\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "hexhowells"
+            ],
+            "editing": [
+                "nomadscientist",
+                "pavanvidem",
+                "mtekman",
+                "hexylena"
+            ],
+            "funding": [
+                "elixir-fair-data"
+            ],
+            "testing": [
+                "pavanvidem"
+            ]
+        },
+        "contributors": [
+            {
+                "email": "hexhowells@gmail.com",
+                "id": "hexhowells",
+                "joined": "2023-06",
+                "name": "Morgan Howells",
+                "orcid": "0009-0008-9422-6380",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexhowells/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexhowells.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "bio": "Senior Lecturer at The Open University",
+                "elixir_node": "uk",
+                "email": "wendi.bacon@open.ac.uk",
+                "fediverse": "https://mstdn.science/@wendibacon1",
+                "fediverse_flavor": "mastodon",
+                "id": "nomadscientist",
+                "joined": "2020-03",
+                "matrix": "nomadscientist:matrix.org",
+                "name": "Wendi Bacon",
+                "orcid": "0000-0002-8170-8806",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
+                "twitter": "WendiBacon1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "pavanvidem",
+                "joined": "2017-09",
+                "name": "Pavankumar Videm",
+                "orcid": "0000-0002-5192-126X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "elixir_node": "de",
+                "email": "mtekman89@gmail.com",
+                "former_affiliations": [
+                    "elixir-europe"
+                ],
+                "id": "mtekman",
+                "joined": "2018-11",
+                "name": "Mehmet Tekman",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "pavanvidem",
+                "joined": "2017-09",
+                "name": "Pavankumar Videm",
+                "orcid": "0000-0002-5192-126X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
+            },
+            {
+                "funder": true,
+                "funding_id": "MR/V038966/1",
+                "funding_statement": "This work has been funded by the ELIXIR-UK FAIR Data Stewardship training UKRI award (MR/V038966/1)",
+                "funding_system": "ukri",
+                "github": false,
+                "id": "elixir-fair-data",
+                "joined": "2023-06",
+                "name": "ELIXIR-UK: FAIR Data Stewardship training",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-fair-data/",
+                "short_name": "ELIXIR Fair Data",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-fair-data.json"
+            }
+        ],
+        "dir": "topics/single-cell/tutorials/scrna-ncbi-anndata",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "single-cell",
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "single-cell/scrna-ncbi-anndata",
+        "inexact_supported_servers": [
+            "UseGalaxy.org.au"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Single cell data often requires additional processing and conversion before it is able to be analysed.",
+            "Metadata and annotations can be added in both manually and automatically with various tools and resources."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-13",
+        "objectives": [
+            "Analyse gene data from NCBI.",
+            "Convert raw gene expression data into the AnnData format.",
+            "Add metadata to the AnnData object to prepare it for analysis."
+        ],
+        "pageviews": 213,
+        "priority": 3,
+        "pub_date": "2023-12-13",
+        "questions": [
+            "How do I understand NCBI data?",
+            "How can I convert raw gene data to the AnnData format?",
+            "How do I manually and automatically add metadata to my AnnData object?"
+        ],
+        "recordings": [
+            {
+                "date": "2020-09-12",
+                "length": "26M11S",
+                "speakers": [
+                    "hexhowells"
+                ],
+                "youtube_id": "abqwwwR1dbk"
+            }
+        ],
+        "short_id": "T00380",
+        "short_tools": [
+            "Paste1",
+            "anndata_ops",
+            "anndata_import",
+            "unzip",
+            "scanpy_filter_cells",
+            "anndata_inspect",
+            "Cut1",
+            "anndata_manipulate",
+            "tp_replace_in_column"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "datamanipulation",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "data management",
+            "data import"
+        ],
+        "time_estimation": "1H",
+        "title": "Converting NCBI Data to the AnnData Format",
+        "tools": [
+            "Cut1",
+            "Paste1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1"
+        ],
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "scrna-ncbi-anndata",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.json"
+        },
+        "version": 4,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 90,
+        "visitors": 179,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0009-0008-9422-6380",
+                        "name": "Morgan Howells"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-5192-126X",
+                        "name": "Pavankumar Videm"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353219_PA_PB1B_Pool_2_S24_L001_dge.txt\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353223_PA_PB2B_Pool_2_S26_L001_dge.txt\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353218_PA_PB1B_Pool_1_2_S74_L003_dge.txt\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353216_PA_PB1A_Pool_1_3_S50_L002_dge.txt\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353221_PA_PB2A_Pool_1_3_S25_L001_dge.txt\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353215_PA_AUG_PB_1B_S2_dge.txt\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353222_PA_PB2B_Pool_1_3_S52_L002_dge.txt\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353220_PA_PB1B_Pool_3_S51_L002_dge.txt\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353217_PA_PB1A_Pool_2_S107_L004_dge.txt\"]\n  9[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSM5353214_PA_AUG_PB_1A_S1_dge.txt\"]\n  10[label=\"Import Anndata and loom\"]\n  0 -> 10 [label=\"output\"]\n  11[label=\"Import Anndata and loom\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"Import Anndata and loom\"]\n  2 -> 12 [label=\"output\"]\n  13[label=\"Import Anndata and loom\"]\n  3 -> 13 [label=\"output\"]\n  14[label=\"Import Anndata and loom\"]\n  4 -> 14 [label=\"output\"]\n  15[label=\"Import Anndata and loom\"]\n  5 -> 15 [label=\"output\"]\n  16[label=\"Import Anndata and loom\"]\n  6 -> 16 [label=\"output\"]\n  17[label=\"Import Anndata and loom\"]\n  7 -> 17 [label=\"output\"]\n  18[label=\"Import Anndata and loom\"]\n  8 -> 18 [label=\"output\"]\n  19[label=\"Import Anndata and loom\"]\n  9 -> 19 [label=\"output\"]\n  20[label=\"Manipulate AnnData\"]\n  10 -> 20 [label=\"anndata\"]\n  21[label=\"Manipulate AnnData\"]\n  11 -> 21 [label=\"anndata\"]\n  22[label=\"Manipulate AnnData\"]\n  12 -> 22 [label=\"anndata\"]\n  23[label=\"Manipulate AnnData\"]\n  13 -> 23 [label=\"anndata\"]\n  24[label=\"Manipulate AnnData\"]\n  14 -> 24 [label=\"anndata\"]\n  25[label=\"Manipulate AnnData\"]\n  15 -> 25 [label=\"anndata\"]\n  26[label=\"Manipulate AnnData\"]\n  16 -> 26 [label=\"anndata\"]\n  27[label=\"Manipulate AnnData\"]\n  17 -> 27 [label=\"anndata\"]\n  28[label=\"Manipulate AnnData\"]\n  18 -> 28 [label=\"anndata\"]\n  29[label=\"Manipulate AnnData\"]\n  19 -> 29 [label=\"anndata\"]\n  30[label=\"Manipulate AnnData\"]\n  29 -> 30 [label=\"anndata\"]\n  23 -> 30 [label=\"anndata\"]\n  24 -> 30 [label=\"anndata\"]\n  21 -> 30 [label=\"anndata\"]\n  25 -> 30 [label=\"anndata\"]\n  22 -> 30 [label=\"anndata\"]\n  27 -> 30 [label=\"anndata\"]\n  28 -> 30 [label=\"anndata\"]\n  26 -> 30 [label=\"anndata\"]\n  20 -> 30 [label=\"anndata\"]\n  31[label=\"Inspect AnnData\"]\n  30 -> 31 [label=\"anndata\"]\n  32[label=\"Replace Text\"]\n  31 -> 32 [label=\"obs\"]\n  33[label=\"Replace Text\"]\n  31 -> 33 [label=\"obs\"]\n  34[label=\"Replace Text\"]\n  31 -> 34 [label=\"obs\"]\n  35[label=\"Replace Text\"]\n  31 -> 35 [label=\"obs\"]\n  36[label=\"Cut\"]\n  32 -> 36 [label=\"outfile\"]\n  37[label=\"Cut\"]\n  33 -> 37 [label=\"outfile\"]\n  38[label=\"Cut\"]\n  34 -> 38 [label=\"outfile\"]\n  39[label=\"Cut\"]\n  35 -> 39 [label=\"outfile\"]\n  40[label=\"Paste\"]\n  37 -> 40 [label=\"out_file1\"]\n  36 -> 40 [label=\"out_file1\"]\n  41[label=\"Paste\"]\n  40 -> 41 [label=\"out_file1\"]\n  38 -> 41 [label=\"out_file1\"]\n  42[label=\"Paste\"]\n  41 -> 42 [label=\"out_file1\"]\n  39 -> 42 [label=\"out_file1\"]\n  43[label=\"Manipulate AnnData\"]\n  30 -> 43 [label=\"anndata\"]\n  42 -> 43 [label=\"out_file1\"]\n  44[label=\"Scanpy FilterCells\"]\n  43 -> 44 [label=\"anndata\"]\n  45[label=\"AnnData Operations\"]\n  44 -> 45 [label=\"output_h5ad\"]\n  k98fdc0798b714841a9aaa3adda888616[color=lightseagreen,label=\"Output\\noutput_h5ad\"]\n  45 -> k98fdc0798b714841a9aaa3adda888616\n  46[label=\"Inspect AnnData\"]\n  45 -> 46 [label=\"output_h5ad\"]\n  ke4df84253c1e439cabe542b705eed1b3[color=lightseagreen,label=\"Output\\nobs\"]\n  46 -> ke4df84253c1e439cabe542b705eed1b3\n}",
+                "history": [
+                    {
+                        "hash": "5503254f3b981f79a46ba83ca14a882d772380e4",
+                        "message": "Update to a working worflow and change test files type to tabular",
+                        "num": 2,
+                        "short_hash": "5503254f3",
+                        "unix": "1702491243"
                     },
+                    {
+                        "hash": "cd3728b55641562a98d26242ac7862218c25aa09",
+                        "message": "add workflow",
+                        "num": 1,
+                        "short_hash": "cd3728b55",
+                        "unix": "1702408106"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 17,
-                        "input_connections": {
-                            "input": {
-                                "id": 15,
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Inspect AnnData",
-                        "outputs": [
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "general",
-                                "type": "txt"
+                                "description": "",
+                                "name": "GSM5353219_PA_PB1B_Pool_2_S24_L001_dge.txt"
                             }
                         ],
+                        "label": "GSM5353219_PA_PB1B_Pool_2_S24_L001_dge.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1111.96875,
-                            "top": 73.1796875
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActiongeneral": {
-                                "action_arguments": {
-                                    "newname": "General - Filterbymito"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "general"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ee98d611afc6",
-                            "name": "anndata_inspect",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 6
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"general\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.5+galaxy1",
-                        "type": "tool",
-                        "uuid": "d221b80d-63e9-42a8-8d4b-25f8f22b9696",
-                        "workflow_outputs": [
-                            {
-                                "label": "General - Filterbymito",
-                                "output_name": "general",
-                                "uuid": "cd94a4c6-5665-4bdf-88ea-4f4d41efa893"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "fc2d53ef-3b4c-437b-bec7-e7b84f8f6c54",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 18,
-                        "input_connections": {
-                            "input_obj_file": {
-                                "id": 15,
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy FilterGenes",
-                        "outputs": [
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
+                                "description": "",
+                                "name": "GSM5353223_PA_PB2B_Pool_2_S26_L001_dge.txt"
                             }
                         ],
+                        "label": "GSM5353223_PA_PB2B_Pool_2_S26_L001_dge.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1111.96875,
-                            "top": 248.21875
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_h5ad": {
-                                "action_arguments": {
-                                    "newname": "Filtered Object"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "da611a744112",
-                            "name": "scanpy_filter_genes",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 160
                         },
-                        "tool_state": "{\"categories\": [], \"export_mtx\": \"false\", \"force_recalc\": \"false\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"parameters\": [{\"__index__\": 0, \"name\": \"n_cells\", \"min\": \"3.0\", \"max\": \"1000000000.0\"}], \"save_layer\": null, \"save_raw\": \"false\", \"subsets\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "84dc3ac3-d79f-4dcd-b81b-f876de010f5e",
-                        "workflow_outputs": [
-                            {
-                                "label": "Filtered Object",
-                                "output_name": "output_h5ad",
-                                "uuid": "ee63ef0a-98ed-45cb-b144-1154f84ae452"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "7e556424-a80d-4114-be2e-7c9ced71f048",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 19,
-                        "input_connections": {
-                            "adata": {
-                                "id": 15,
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Plot",
-                        "outputs": [
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "description": "",
+                                "name": "GSM5353218_PA_PB1B_Pool_1_2_S74_L003_dge.txt"
                             }
                         ],
+                        "label": "GSM5353218_PA_PB1B_Pool_1_2_S74_L003_dge.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1111.96875,
-                            "top": 423.296875
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_png": {
-                                "action_arguments": {
-                                    "newname": "Violin - Filterbymito"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_png"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "aa0c474463c2",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 314
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"genotype\", \"log\": \"false\", \"use_raw\": \"false\", \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy1",
-                        "type": "tool",
-                        "uuid": "972b30ab-cf6c-43a7-a41d-9679cbae7be6",
-                        "workflow_outputs": [
-                            {
-                                "label": "Violin - Filterbymito",
-                                "output_name": "out_png",
-                                "uuid": "7e48a14f-08fd-45ab-b613-606bf64dcf9d"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ea1f8502-ed3c-45ac-bf09-36a1771dec28",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 20,
-                        "input_connections": {
-                            "input": {
-                                "id": 18,
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Inspect AnnData",
-                        "outputs": [
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "general",
-                                "type": "txt"
+                                "description": "",
+                                "name": "GSM5353216_PA_PB1A_Pool_1_3_S50_L002_dge.txt"
                             }
                         ],
+                        "label": "GSM5353216_PA_PB1A_Pool_1_3_S50_L002_dge.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1390.0078125,
-                            "top": 42.140625
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActiongeneral": {
-                                "action_arguments": {
-                                    "newname": "General - Filtered object"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "general"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ee98d611afc6",
-                            "name": "anndata_inspect",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 468
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"general\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.5+galaxy1",
-                        "type": "tool",
-                        "uuid": "78767f76-7f3c-416d-ac79-28f6104bb3b9",
-                        "workflow_outputs": [
-                            {
-                                "label": "General - Filtered object",
-                                "output_name": "general",
-                                "uuid": "d59efa9b-d049-4f0e-8bd8-8ae982a45d0a"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "473c66ce-eb30-483e-bf74-a04f0b452f67",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 21,
-                        "input_connections": {
-                            "input_obj_file": {
-                                "id": 18,
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy NormaliseData",
-                        "outputs": [
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
+                                "description": "",
+                                "name": "GSM5353221_PA_PB2A_Pool_1_3_S25_L001_dge.txt"
                             }
                         ],
+                        "label": "GSM5353221_PA_PB2A_Pool_1_3_S25_L001_dge.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1390.0078125,
-                            "top": 217.2421875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "8d9c22419c56",
-                            "name": "scanpy_normalise_data",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 622
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"export_mtx\": \"false\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"save_layer\": null, \"save_raw\": \"false\", \"settings\": {\"default\": \"true\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "405a3674-8eca-4444-abc8-9f79112efafe",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_h5ad",
-                                "uuid": "4b7c5849-0c06-4167-b1e5-f19a2f9204af"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "6b5fc504-7162-4cbb-90a4-97b3fc4f792b",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 22,
-                        "input_connections": {
-                            "input_obj_file": {
-                                "id": 21,
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy FindVariableGenes",
-                        "outputs": [
+                        "id": 5,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
+                                "description": "",
+                                "name": "GSM5353215_PA_AUG_PB_1B_S2_dge.txt"
                             }
                         ],
+                        "label": "GSM5353215_PA_AUG_PB_1B_S2_dge.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1668.9375,
-                            "top": 218.2421875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "4667fe07bd68",
-                            "name": "scanpy_find_variable_genes",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 776
                         },
-                        "tool_state": "{\"batch_key\": \"\", \"filter\": \"false\", \"flavor\": \"seurat\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"max_disp\": \"50.0\", \"max_mean\": \"3.0\", \"min_disp\": \"0.5\", \"min_mean\": \"0.0125\", \"n_bin\": \"20\", \"n_top_gene\": null, \"output_format\": \"anndata_h5ad\", \"span\": \"0.3\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "53fa19a2-55bd-43af-b0c9-a41d42554a6b",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_h5ad",
-                                "uuid": "2add5ce8-fffb-46ef-8d92-158b3f9a252b"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "99d79b05-7b7a-4986-93e6-6957c34afdca",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 23,
-                        "input_connections": {
-                            "input_obj_file": {
-                                "id": 22,
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy ScaleData",
-                        "outputs": [
+                        "id": 6,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
+                                "description": "",
+                                "name": "GSM5353222_PA_PB2B_Pool_1_3_S52_L002_dge.txt"
                             }
                         ],
+                        "label": "GSM5353222_PA_PB2B_Pool_1_3_S52_L002_dge.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1946.1875,
-                            "top": 227.203125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "5605f8452eb3",
-                            "name": "scanpy_scale_data",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 930
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"save_layer\": null, \"save_raw\": \"false\", \"scale_max\": \"10.0\", \"zero_center\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "a4106855-a661-4d6d-9208-99afcfc0eb55",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_h5ad",
-                                "uuid": "46ef29d8-4233-4cf9-b7d8-0b317dbfd37f"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "3f690013-56d0-4046-a64f-42ddd71ceb81",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 24,
-                        "input_connections": {
-                            "input_obj_file": {
-                                "id": 23,
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy RunPCA",
-                        "outputs": [
+                        "id": 7,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
+                                "description": "",
+                                "name": "GSM5353220_PA_PB1B_Pool_3_S51_L002_dge.txt"
                             }
                         ],
+                        "label": "GSM5353220_PA_PB1B_Pool_3_S51_L002_dge.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2224.1640625,
-                            "top": 227.203125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3ee74b58c72d",
-                            "name": "scanpy_run_pca",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 1084
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"extra_outputs\": null, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"n_pcs\": \"50\", \"output_format\": \"anndata_h5ad\", \"run_mode\": {\"chunked\": \"false\", \"__current_case__\": 1, \"zero_center\": \"true\", \"svd_solver\": null, \"random_seed\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "5a1ce297-23e9-46da-be5c-9c01a3a5a9dd",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_h5ad",
-                                "uuid": "7f75826e-ccd3-417b-9925-d1cbf231d27a"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "9fce1b9d-52e4-40e5-9c3c-32c1d901aeb1",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 25,
-                        "input_connections": {
-                            "adata": {
-                                "id": 24,
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Plot",
-                        "outputs": [
+                        "id": 8,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "description": "",
+                                "name": "GSM5353217_PA_PB1A_Pool_2_S107_L004_dge.txt"
                             }
                         ],
+                        "label": "GSM5353217_PA_PB1A_Pool_2_S107_L004_dge.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2502.1875,
-                            "top": 97.46875
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_png": {
-                                "action_arguments": {
-                                    "newname": "PCA Variance"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_png"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "aa0c474463c2",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 1238
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.pca_variance_ratio\", \"__current_case__\": 11, \"n_pcs\": \"50\", \"log\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy1",
-                        "type": "tool",
-                        "uuid": "04b47edc-87e5-4913-abe1-e525f62b9aa4",
-                        "workflow_outputs": [
-                            {
-                                "label": "PCA Variance",
-                                "output_name": "out_png",
-                                "uuid": "993dea99-990f-460a-beb9-46e5c97ee898"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "2222b107-d0bc-4daf-bee0-d8573375ff43",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 26,
-                        "input_connections": {
-                            "input_obj_file": {
-                                "id": 24,
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Scanpy ComputeGraph",
-                        "outputs": [
+                        "id": 9,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
+                                "description": "",
+                                "name": "GSM5353214_PA_AUG_PB_1A_S1_dge.txt"
                             }
                         ],
+                        "label": "GSM5353214_PA_AUG_PB_1A_S1_dge.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2502.1875,
-                            "top": 229.2265625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "bc9e8de21efb",
-                            "name": "scanpy_compute_graph",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 0,
+                            "top": 1392
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": \"false\", \"__current_case__\": 1, \"key_added\": \"\", \"n_neighbors\": \"15\", \"n_neighbors_file\": null, \"use_rep\": \"X_pca\", \"n_pcs\": \"20\", \"knn\": \"true\", \"method\": \"umap\", \"metric\": \"euclidean\", \"random_seed\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy1",
-                        "type": "tool",
-                        "uuid": "f0da837f-8547-4368-9160-f4416f91768f",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_h5ad",
-                                "uuid": "cf488e9d-4171-4ed2-9fa0-a9083077eed7"
-                            }
-                        ]
-                    },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "7b4a0b40-4a1a-4d89-bb13-6f150be24c9c",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGSM5353219_PA_PB1B_Pool_2_S24_L001_dge.txt\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGSM5353223_PA_PB2B_Pool_2_S26_L001_dge.txt\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nGSM5353218_PA_PB1B_Pool_1_2_S74_L003_dge.txt\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nGSM5353216_PA_PB1A_Pool_1_3_S50_L002_dge.txt\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nGSM5353221_PA_PB2A_Pool_1_3_S25_L001_dge.txt\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nGSM5353215_PA_AUG_PB_1B_S2_dge.txt\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nGSM5353222_PA_PB2B_Pool_1_3_S52_L002_dge.txt\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nGSM5353220_PA_PB1B_Pool_3_S51_L002_dge.txt\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nGSM5353217_PA_PB1A_Pool_2_S107_L004_dge.txt\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"\u2139\ufe0f Input Dataset\\nGSM5353214_PA_AUG_PB_1A_S1_dge.txt\"];\n  style 9 stroke:#2c3143,stroke-width:4px;\n  10[\"Import Anndata and loom\"];\n  0 -->|output| 10;\n  11[\"Import Anndata and loom\"];\n  1 -->|output| 11;\n  12[\"Import Anndata and loom\"];\n  2 -->|output| 12;\n  13[\"Import Anndata and loom\"];\n  3 -->|output| 13;\n  14[\"Import Anndata and loom\"];\n  4 -->|output| 14;\n  15[\"Import Anndata and loom\"];\n  5 -->|output| 15;\n  16[\"Import Anndata and loom\"];\n  6 -->|output| 16;\n  17[\"Import Anndata and loom\"];\n  7 -->|output| 17;\n  18[\"Import Anndata and loom\"];\n  8 -->|output| 18;\n  19[\"Import Anndata and loom\"];\n  9 -->|output| 19;\n  20[\"Manipulate AnnData\"];\n  10 -->|anndata| 20;\n  21[\"Manipulate AnnData\"];\n  11 -->|anndata| 21;\n  22[\"Manipulate AnnData\"];\n  12 -->|anndata| 22;\n  23[\"Manipulate AnnData\"];\n  13 -->|anndata| 23;\n  24[\"Manipulate AnnData\"];\n  14 -->|anndata| 24;\n  25[\"Manipulate AnnData\"];\n  15 -->|anndata| 25;\n  26[\"Manipulate AnnData\"];\n  16 -->|anndata| 26;\n  27[\"Manipulate AnnData\"];\n  17 -->|anndata| 27;\n  28[\"Manipulate AnnData\"];\n  18 -->|anndata| 28;\n  29[\"Manipulate AnnData\"];\n  19 -->|anndata| 29;\n  30[\"Manipulate AnnData\"];\n  29 -->|anndata| 30;\n  23 -->|anndata| 30;\n  24 -->|anndata| 30;\n  21 -->|anndata| 30;\n  25 -->|anndata| 30;\n  22 -->|anndata| 30;\n  27 -->|anndata| 30;\n  28 -->|anndata| 30;\n  26 -->|anndata| 30;\n  20 -->|anndata| 30;\n  31[\"Inspect AnnData\"];\n  30 -->|anndata| 31;\n  32[\"Replace Text\"];\n  31 -->|obs| 32;\n  33[\"Replace Text\"];\n  31 -->|obs| 33;\n  34[\"Replace Text\"];\n  31 -->|obs| 34;\n  35[\"Replace Text\"];\n  31 -->|obs| 35;\n  36[\"Cut\"];\n  32 -->|outfile| 36;\n  37[\"Cut\"];\n  33 -->|outfile| 37;\n  38[\"Cut\"];\n  34 -->|outfile| 38;\n  39[\"Cut\"];\n  35 -->|outfile| 39;\n  40[\"Paste\"];\n  37 -->|out_file1| 40;\n  36 -->|out_file1| 40;\n  41[\"Paste\"];\n  40 -->|out_file1| 41;\n  38 -->|out_file1| 41;\n  42[\"Paste\"];\n  41 -->|out_file1| 42;\n  39 -->|out_file1| 42;\n  43[\"Manipulate AnnData\"];\n  30 -->|anndata| 43;\n  42 -->|out_file1| 43;\n  44[\"Scanpy FilterCells\"];\n  43 -->|anndata| 44;\n  45[\"AnnData Operations\"];\n  44 -->|output_h5ad| 45;\n  98fdc079-8b71-4841-a9aa-a3adda888616[\"Output\\noutput_h5ad\"];\n  45 --> 98fdc079-8b71-4841-a9aa-a3adda888616;\n  style 98fdc079-8b71-4841-a9aa-a3adda888616 stroke:#2c3143,stroke-width:4px;\n  46[\"Inspect AnnData\"];\n  45 -->|output_h5ad| 46;\n  e4df8425-3c1e-439c-abe5-42b705eed1b3[\"Output\\nobs\"];\n  46 --> e4df8425-3c1e-439c-abe5-42b705eed1b3;\n  style e4df8425-3c1e-439c-abe5-42b705eed1b3 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "NCBI to Anndata",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
                         "errors": null,
-                        "id": 27,
+                        "id": 45,
                         "input_connections": {
                             "input_obj_file": {
-                                "id": 26,
+                                "id": 44,
                                 "output_name": "output_h5ad"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Scanpy RunTSNE",
-                                "name": "settings"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Scanpy RunTSNE",
+                        "name": "AnnData Operations",
                         "outputs": [
                             {
                                 "name": "output_h5ad",
                                 "type": "h5ad"
-                            },
-                            {
-                                "name": "output_embed",
-                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 2780.1875,
-                            "top": 289.234375
+                            "left": 3369.999842902977,
+                            "top": 610
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "8b0d6f6f44c8",
-                            "name": "scanpy_run_tsne",
+                            "changeset_revision": "890fb06a2893",
+                            "name": "anndata_ops",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"embeddings\": \"true\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": \"false\", \"__current_case__\": 1, \"key_added\": \"\", \"perplexity\": \"30.0\", \"perplexity_file\": {\"__class__\": \"RuntimeValue\"}, \"early_exaggeration\": \"12.0\", \"learning_rate\": \"1000.0\", \"fast_tsne\": \"false\", \"n_job\": null, \"n_pc\": null, \"random_seed\": \"0\"}, \"use_rep\": \"X_pca\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"copy_adata_to_raw\": false, \"copy_e\": {\"default\": false, \"__current_case__\": 1}, \"copy_l\": {\"default\": false, \"__current_case__\": 1}, \"copy_o\": {\"default\": false, \"__current_case__\": 1}, \"copy_r\": {\"default\": false, \"__current_case__\": 1}, \"copy_u\": {\"default\": false, \"__current_case__\": 1}, \"copy_x\": {\"default\": false, \"__current_case__\": 1}, \"gene_flags\": [{\"__index__\": 0, \"startswith\": \"MT-\", \"flag\": \"mito\"}], \"gene_symbols_field\": \"index\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": false, \"top_genes\": \"50\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
                         "type": "tool",
-                        "uuid": "1638ac03-a75c-4081-a33d-da080f0de1c7",
+                        "uuid": "c53d106a-f45b-477d-ab64-ad266c248411",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "output_h5ad",
                                 "output_name": "output_h5ad",
-                                "uuid": "1b78023b-ad9b-46d0-b75e-ffa3b12a52ee"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_embed",
-                                "uuid": "e1b399d8-fe94-438e-9bc3-22fe695f70a2"
+                                "uuid": "98fdc079-8b71-4841-a9aa-a3adda888616"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
                         "errors": null,
-                        "id": 28,
+                        "id": 46,
                         "input_connections": {
-                            "input_obj_file": {
-                                "id": 27,
+                            "input": {
+                                "id": 45,
                                 "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Scanpy RunUMAP",
+                        "name": "Inspect AnnData",
                         "outputs": [
                             {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
-                            },
-                            {
-                                "name": "output_embed",
+                                "name": "obs",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 3058.171875,
-                            "top": 371.296875
+                            "left": 3649.9996418187607,
+                            "top": 642
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "fe562424a0a6",
-                            "name": "scanpy_run_umap",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "ee98d611afc6",
+                            "name": "anndata_inspect",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"embeddings\": \"true\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"key_added\": \"\", \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": \"true\", \"__current_case__\": 0}, \"use_graph\": \"neighbors\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"h5ad\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"obs\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.5+galaxy1",
                         "type": "tool",
-                        "uuid": "f0847b39-f0b3-4422-a013-b1e0fc5d10af",
+                        "uuid": "60a81f95-32e1-47a7-8a95-07586eb9ed6a",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_embed",
-                                "uuid": "174f4c1d-9901-4fb8-be47-c53e3155d93f"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_h5ad",
-                                "uuid": "d7fad373-884b-4374-9e97-141302f576ab"
+                                "label": "obs",
+                                "output_name": "obs",
+                                "uuid": "e4df8425-3c1e-439c-abe5-42b705eed1b3"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "single-cell/scrna-ncbi-anndata",
+                "path": "topics/single-cell/tutorials/scrna-ncbi-anndata/workflows/NCBI_to_Anndata.ga",
+                "tags": [
+                    "name:single-cell",
+                    "name:data-management"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "NCBI to Anndata",
+                "topic_id": "single-cell",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-ncbi-anndata/versions/ncbi-to-anndata",
+                "tutorial_id": "scrna-ncbi-anndata",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-ncbi-anndata/workflows/NCBI_to_Anndata.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-ncbi-anndata/workflows/NCBI_to_Anndata.html",
+                "version": 1,
+                "wfid": "single-cell-scrna-ncbi-anndata",
+                "wfname": "ncbi-to-anndata",
+                "workflow": "NCBI_to_Anndata.ga",
+                "workflow_tools": [
+                    "Cut1",
+                    "Paste1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1"
+                ],
+                "workflowhub_id": "1272"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/10101768"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "scanpy_compute_graph",
+                    "owner": "ebi-gxa",
+                    "revisions": "6417cccad133",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_find_cluster",
+                    "owner": "ebi-gxa",
+                    "revisions": "2ccd9f9e2cd0",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_parameter_iterator",
+                    "owner": "ebi-gxa",
+                    "revisions": "73d43034c860",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_plot_embed",
+                    "owner": "ebi-gxa",
+                    "revisions": "35f6611fb8c3",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_run_tsne",
+                    "owner": "ebi-gxa",
+                    "revisions": "181d61d2f3cd",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_run_umap",
+                    "owner": "ebi-gxa",
+                    "revisions": "bd4a244faeb8",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: scanpy_compute_graph\n  owner: ebi-gxa\n  revisions: 6417cccad133\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_find_cluster\n  owner: ebi-gxa\n  revisions: 2ccd9f9e2cd0\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_parameter_iterator\n  owner: ebi-gxa\n  revisions: 73d43034c860\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot_embed\n  owner: ebi-gxa\n  revisions: 35f6611fb8c3\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_tsne\n  owner: ebi-gxa\n  revisions: 181d61d2f3cd\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_umap\n  owner: ebi-gxa\n  revisions: bd4a244faeb8\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scanpy_parameter_iterator/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "wee-snufkin"
+            ],
+            "funding": [
+                "eosc-life"
+            ],
+            "testing": [
+                "nomadscientist"
+            ]
+        },
+        "contributors": [
+            {
+                "elixir_node": "uk",
+                "email": "juliajot36@gmail.com",
+                "id": "wee-snufkin",
+                "joined": "2022-06",
+                "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "bio": "Senior Lecturer at The Open University",
+                "elixir_node": "uk",
+                "email": "wendi.bacon@open.ac.uk",
+                "fediverse": "https://mstdn.science/@wendibacon1",
+                "fediverse_flavor": "mastodon",
+                "id": "nomadscientist",
+                "joined": "2020-03",
+                "matrix": "nomadscientist:matrix.org",
+                "name": "Wendi Bacon",
+                "orcid": "0000-0002-8170-8806",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
+                "twitter": "WendiBacon1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+            },
+            {
+                "avatar": "https://www.eosc-life.eu/wp-content/themes/eosc-life-v2/assets/images/eosclogo.png",
+                "funder": true,
+                "funding_id": "824087",
+                "funding_statement": "EOSC-Life has received funding from the European Union\u2019s Horizon 2020 programme under grant agreement number 824087",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "eosc-life",
+                "joined": "2023-04",
+                "members": [
+                    "bgruening"
+                ],
+                "name": "EOSC-Life",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eosc-life/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/eosc-life.json"
+            }
+        ],
+        "dir": "topics/single-cell/tutorials/scanpy_parameter_iterator",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "single-cell/scanpy_parameter_iterator",
+        "inexact_supported_servers": [
+            "UseGalaxy.org.au"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Scanpy ParameterIterator can be used for k nearest neighbours (Scanpy ComputeGraph), perplexity (Scanpy RunTSNE) and resolution (Scanpy FindCluster).",
+            "You can enter the parameter values either as a list or as values to be iterated in step.",
+            "Parameter Iterator is a useful tool to quickly and easily compare the differences in the outputs caused by changing parameter values. Hence it allows us to choose the optimal parameter values."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-12-05",
+        "objectives": [
+            "Execute the Scanpy Parameter Iterator",
+            "Recognise what tools you can use Parameter Iterator with",
+            "Operate tools working on dataset collections",
+            "Compare plots resulting from different parameters values"
+        ],
+        "pageviews": 149,
+        "priority": 3,
+        "pub_date": "2023-07-19",
+        "questions": [
+            "How can I run a tool with multiple parameter values?",
+            "Do I have to enter parameter values manually each time I want to check a new value?",
+            "What tools can take multiple values at once and iterate over them?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-case_alevin",
+                    "scrna-case_alevin-combine-datasets",
+                    "scrna-case_basic-pipeline"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00357",
+        "short_tools": [
+            "scanpy_run_umap",
+            "scanpy_plot_embed",
+            "scanpy_find_cluster",
+            "scanpy_parameter_iterator",
+            "scanpy_compute_graph",
+            "scanpy_run_tsne"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "tricks",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": null,
+        "time_estimation": "2H",
+        "title": "Scanpy Parameter Iterator",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9"
+        ],
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "scanpy_parameter_iterator",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scanpy_parameter_iterator/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scanpy_parameter_iterator/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scanpy_parameter_iterator/tutorial.json"
+        },
+        "version": 7,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 83,
+        "visitors": 132,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0009-0001-2017-8805",
+                        "name": "Julia Jakiela"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nScanpy RunPCA: AnnData object\"]\n  1[label=\"ParameterIterator n-neighbors\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nScanpy ComputeGraph on data X and data Y: Graph object AnnData\"]\n  3[label=\"ParameterIterator perplexity\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nScanpy RunUMAP on data X: UMAP object AnnData\"]\n  5[label=\"ParameterIterator resolution\"]\n  6[label=\"Scanpy ComputeGraph\"]\n  0 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"parameter_iteration\"]\n  k1e60c7cd7e02450fa403f3df1e548757[color=lightseagreen,label=\"Output\\nScanpy ComputeGraph on collection X: Graph object AnnData (n-neighbours)\"]\n  6 -> k1e60c7cd7e02450fa403f3df1e548757\n  7[label=\"Scanpy RunTSNE\"]\n  2 -> 7 [label=\"output\"]\n  3 -> 7 [label=\"parameter_iteration\"]\n  k15143fea5e2b4b25b5d10726da910f67[color=lightseagreen,label=\"Output\\nScanpy RunTSNE on collection X: tSNE object AnnData (perplexity)\"]\n  7 -> k15143fea5e2b4b25b5d10726da910f67\n  8[label=\"Scanpy FindCluster\"]\n  4 -> 8 [label=\"output\"]\n  5 -> 8 [label=\"parameter_iteration\"]\n  k6fdddfe7c4da442186a09819ce4c769c[color=lightseagreen,label=\"Output\\nScanpy FindCluster on collection X: Clusters AnnData (resolution)\"]\n  8 -> k6fdddfe7c4da442186a09819ce4c769c\n  9[label=\"Scanpy RunTSNE\"]\n  6 -> 9 [label=\"output_h5ad\"]\n  k7c988247b1674733859ffcd582f91959[color=lightseagreen,label=\"Output\\nScanpy RunTSNE on collection X: tSNE object AnnData (n-neighbours)\"]\n  9 -> k7c988247b1674733859ffcd582f91959\n  10[label=\"Scanpy RunUMAP\"]\n  7 -> 10 [label=\"output_h5ad\"]\n  k1f5abfa2845c47639f87e4b167aa7bc8[color=lightseagreen,label=\"Output\\nScanpy RunUMAP on collection X: UMAP object AnnData (perplexity)\"]\n  10 -> k1f5abfa2845c47639f87e4b167aa7bc8\n  11[label=\"Scanpy PlotEmbed\"]\n  8 -> 11 [label=\"output_h5ad\"]\n  k99185d1e047f47f2908107506e1c17df[color=lightseagreen,label=\"Output\\nresolution_pca_plots\"]\n  11 -> k99185d1e047f47f2908107506e1c17df\n  12[label=\"Scanpy PlotEmbed\"]\n  8 -> 12 [label=\"output_h5ad\"]\n  k65d7b619865940089e56db21fda6ce8c[color=lightseagreen,label=\"Output\\nresolution_umap_plots\"]\n  12 -> k65d7b619865940089e56db21fda6ce8c\n  13[label=\"Scanpy PlotEmbed\"]\n  8 -> 13 [label=\"output_h5ad\"]\n  kbdcaf8375fc44024a87aeabfa0110127[color=lightseagreen,label=\"Output\\nresolution_tsne_plots\"]\n  13 -> kbdcaf8375fc44024a87aeabfa0110127\n  14[label=\"Scanpy RunUMAP\"]\n  9 -> 14 [label=\"output_h5ad\"]\n  k8a0b3d69e7df4977b8ebec478b914a26[color=lightseagreen,label=\"Output\\nScanpy RunUMAP on collection X: UMAP object AnnData (n-neighbours)\"]\n  14 -> k8a0b3d69e7df4977b8ebec478b914a26\n  15[label=\"Scanpy FindCluster\"]\n  10 -> 15 [label=\"output_h5ad\"]\n  kc2e0d48f9f0e44528fb5e78420578c65[color=lightseagreen,label=\"Output\\nScanpy FindCluster on collection X: Clusters AnnData (perplexity)\"]\n  15 -> kc2e0d48f9f0e44528fb5e78420578c65\n  16[label=\"Scanpy FindCluster\"]\n  14 -> 16 [label=\"output_h5ad\"]\n  kc952b32e99d54b94a6d7be59439c4dca[color=lightseagreen,label=\"Output\\nScanpy FindCluster on collection X: Clusters AnnData (n-neighbours)\"]\n  16 -> kc952b32e99d54b94a6d7be59439c4dca\n  17[label=\"Scanpy PlotEmbed\"]\n  15 -> 17 [label=\"output_h5ad\"]\n  k44c0ec07b64e428f92545217e8041416[color=lightseagreen,label=\"Output\\nperplexity_plots\"]\n  17 -> k44c0ec07b64e428f92545217e8041416\n  18[label=\"Scanpy PlotEmbed\"]\n  16 -> 18 [label=\"output_h5ad\"]\n  k0b30f5738ebd45829bcd58ba5c778658[color=lightseagreen,label=\"Output\\nn-neighbors_plots\"]\n  18 -> k0b30f5738ebd45829bcd58ba5c778658\n}",
+                "history": [
+                    {
+                        "hash": "331d2c1b553213fe663c01d608bba47638414644",
+                        "message": "updated workflow tests",
+                        "num": 2,
+                        "short_hash": "331d2c1b5",
+                        "unix": "1689307889"
                     },
+                    {
+                        "hash": "68fc015a7fae9417a5365fb3edda17a5aaf9d87b",
+                        "message": "add workflow tests",
+                        "num": 1,
+                        "short_hash": "68fc015a7",
+                        "unix": "1686208349"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 29,
-                        "input_connections": {
-                            "input_obj_file": {
-                                "id": 28,
-                                "output_name": "output_h5ad"
-                            }
-                        },
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Scanpy FindCluster",
-                                "name": "settings"
+                                "description": "",
+                                "name": "Scanpy RunPCA: AnnData object"
                             }
                         ],
-                        "label": null,
-                        "name": "Scanpy FindCluster",
-                        "outputs": [
-                            {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
-                            },
+                        "label": "Scanpy RunPCA: AnnData object",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 25.151777265812267,
+                            "top": 0
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ce25265d-8c04-490f-bd84-dd417a635456",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output_txt",
-                                "type": "tsv"
+                                "description": "",
+                                "name": "Scanpy ComputeGraph on data X and data Y: Graph object AnnData"
                             }
                         ],
+                        "label": "Scanpy ComputeGraph on data X and data Y: Graph object AnnData",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 3336.1796875,
-                            "top": 415.296875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ad6995afd2e6",
-                            "name": "scanpy_find_cluster",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 31.588610949585586,
+                            "top": 368.3566064231565
                         },
-                        "tool_state": "{\"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"method\": \"louvain\", \"output_cluster\": \"true\", \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": \"false\", \"__current_case__\": 1, \"neighbors_key\": \"neighbors\", \"layer\": \"\", \"key_added\": \"\", \"resolution\": \"0.6\", \"resolution_file\": {\"__class__\": \"RuntimeValue\"}, \"restrict_to\": \"\", \"use_weights\": \"false\", \"random_seed\": \"0\", \"directed\": \"true\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "684c6061-1703-4ed3-837a-f08aa49f496d",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_txt",
-                                "uuid": "8de66f85-2979-4d67-b9d6-a24ff1e480d3"
-                            },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "fae9d652-9474-4b6c-9bd2-9e0eb6cb5ab4",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "output_h5ad",
-                                "uuid": "980e4933-b0d6-4b92-aee8-ef76691aa958"
+                                "description": "",
+                                "name": "Scanpy RunUMAP on data X: UMAP object AnnData"
                             }
-                        ]
-                    },
+                        ],
+                        "label": "Scanpy RunUMAP on data X: UMAP object AnnData",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 12.794588175128467,
+                            "top": 688.9871973265816
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "6f462fe5-e34b-4d8f-93bc-61b0d0e99488",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nScanpy RunPCA: AnnData object\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"ParameterIterator n-neighbors\"];\n  2[\"\u2139\ufe0f Input Dataset\\nScanpy ComputeGraph on data X and data Y: Graph object AnnData\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"ParameterIterator perplexity\"];\n  4[\"\u2139\ufe0f Input Dataset\\nScanpy RunUMAP on data X: UMAP object AnnData\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"ParameterIterator resolution\"];\n  6[\"Scanpy ComputeGraph\"];\n  0 -->|output| 6;\n  1 -->|parameter_iteration| 6;\n  1e60c7cd-7e02-450f-a403-f3df1e548757[\"Output\\nScanpy ComputeGraph on collection X: Graph object AnnData (n-neighbours)\"];\n  6 --> 1e60c7cd-7e02-450f-a403-f3df1e548757;\n  style 1e60c7cd-7e02-450f-a403-f3df1e548757 stroke:#2c3143,stroke-width:4px;\n  7[\"Scanpy RunTSNE\"];\n  2 -->|output| 7;\n  3 -->|parameter_iteration| 7;\n  15143fea-5e2b-4b25-b5d1-0726da910f67[\"Output\\nScanpy RunTSNE on collection X: tSNE object AnnData (perplexity)\"];\n  7 --> 15143fea-5e2b-4b25-b5d1-0726da910f67;\n  style 15143fea-5e2b-4b25-b5d1-0726da910f67 stroke:#2c3143,stroke-width:4px;\n  8[\"Scanpy FindCluster\"];\n  4 -->|output| 8;\n  5 -->|parameter_iteration| 8;\n  6fdddfe7-c4da-4421-86a0-9819ce4c769c[\"Output\\nScanpy FindCluster on collection X: Clusters AnnData (resolution)\"];\n  8 --> 6fdddfe7-c4da-4421-86a0-9819ce4c769c;\n  style 6fdddfe7-c4da-4421-86a0-9819ce4c769c stroke:#2c3143,stroke-width:4px;\n  9[\"Scanpy RunTSNE\"];\n  6 -->|output_h5ad| 9;\n  7c988247-b167-4733-859f-fcd582f91959[\"Output\\nScanpy RunTSNE on collection X: tSNE object AnnData (n-neighbours)\"];\n  9 --> 7c988247-b167-4733-859f-fcd582f91959;\n  style 7c988247-b167-4733-859f-fcd582f91959 stroke:#2c3143,stroke-width:4px;\n  10[\"Scanpy RunUMAP\"];\n  7 -->|output_h5ad| 10;\n  1f5abfa2-845c-4763-9f87-e4b167aa7bc8[\"Output\\nScanpy RunUMAP on collection X: UMAP object AnnData (perplexity)\"];\n  10 --> 1f5abfa2-845c-4763-9f87-e4b167aa7bc8;\n  style 1f5abfa2-845c-4763-9f87-e4b167aa7bc8 stroke:#2c3143,stroke-width:4px;\n  11[\"Scanpy PlotEmbed\"];\n  8 -->|output_h5ad| 11;\n  99185d1e-047f-47f2-9081-07506e1c17df[\"Output\\nresolution_pca_plots\"];\n  11 --> 99185d1e-047f-47f2-9081-07506e1c17df;\n  style 99185d1e-047f-47f2-9081-07506e1c17df stroke:#2c3143,stroke-width:4px;\n  12[\"Scanpy PlotEmbed\"];\n  8 -->|output_h5ad| 12;\n  65d7b619-8659-4008-9e56-db21fda6ce8c[\"Output\\nresolution_umap_plots\"];\n  12 --> 65d7b619-8659-4008-9e56-db21fda6ce8c;\n  style 65d7b619-8659-4008-9e56-db21fda6ce8c stroke:#2c3143,stroke-width:4px;\n  13[\"Scanpy PlotEmbed\"];\n  8 -->|output_h5ad| 13;\n  bdcaf837-5fc4-4024-a87a-eabfa0110127[\"Output\\nresolution_tsne_plots\"];\n  13 --> bdcaf837-5fc4-4024-a87a-eabfa0110127;\n  style bdcaf837-5fc4-4024-a87a-eabfa0110127 stroke:#2c3143,stroke-width:4px;\n  14[\"Scanpy RunUMAP\"];\n  9 -->|output_h5ad| 14;\n  8a0b3d69-e7df-4977-b8eb-ec478b914a26[\"Output\\nScanpy RunUMAP on collection X: UMAP object AnnData (n-neighbours)\"];\n  14 --> 8a0b3d69-e7df-4977-b8eb-ec478b914a26;\n  style 8a0b3d69-e7df-4977-b8eb-ec478b914a26 stroke:#2c3143,stroke-width:4px;\n  15[\"Scanpy FindCluster\"];\n  10 -->|output_h5ad| 15;\n  c2e0d48f-9f0e-4452-8fb5-e78420578c65[\"Output\\nScanpy FindCluster on collection X: Clusters AnnData (perplexity)\"];\n  15 --> c2e0d48f-9f0e-4452-8fb5-e78420578c65;\n  style c2e0d48f-9f0e-4452-8fb5-e78420578c65 stroke:#2c3143,stroke-width:4px;\n  16[\"Scanpy FindCluster\"];\n  14 -->|output_h5ad| 16;\n  c952b32e-99d5-4b94-a6d7-be59439c4dca[\"Output\\nScanpy FindCluster on collection X: Clusters AnnData (n-neighbours)\"];\n  16 --> c952b32e-99d5-4b94-a6d7-be59439c4dca;\n  style c952b32e-99d5-4b94-a6d7-be59439c4dca stroke:#2c3143,stroke-width:4px;\n  17[\"Scanpy PlotEmbed\"];\n  15 -->|output_h5ad| 17;\n  44c0ec07-b64e-428f-9254-5217e8041416[\"Output\\nperplexity_plots\"];\n  17 --> 44c0ec07-b64e-428f-9254-5217e8041416;\n  style 44c0ec07-b64e-428f-9254-5217e8041416 stroke:#2c3143,stroke-width:4px;\n  18[\"Scanpy PlotEmbed\"];\n  16 -->|output_h5ad| 18;\n  0b30f573-8ebd-4582-9bcd-58ba5c778658[\"Output\\nn-neighbors_plots\"];\n  18 --> 0b30f573-8ebd-4582-9bcd-58ba5c778658;\n  style 0b30f573-8ebd-4582-9bcd-58ba5c778658 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "Scanpy Parameter Iterator workflow full (imported from URL)",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 30,
+                        "id": 6,
                         "input_connections": {
                             "input_obj_file": {
-                                "id": 29,
-                                "output_name": "output_h5ad"
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "settings|n_neighbors_file": {
+                                "id": 1,
+                                "output_name": "parameter_iteration"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Scanpy FindMarkers",
-                                "name": "groupby_file"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Scanpy FindMarkers",
+                        "name": "Scanpy ComputeGraph",
                         "outputs": [
                             {
                                 "name": "output_h5ad",
                                 "type": "h5ad"
-                            },
-                            {
-                                "name": "output_tsv",
-                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 3614.1640625,
-                            "top": 504.265625
+                            "left": 311.6945808886878,
+                            "top": 0.08716619391159292
                         },
                         "post_job_actions": {
                             "RenameDatasetActionoutput_h5ad": {
                                 "action_arguments": {
-                                    "newname": "Final object"
+                                    "newname": "Scanpy ComputeGraph on collection X: Graph object AnnData (n-neighbours)"
                                 },
                                 "action_type": "RenameDatasetAction",
                                 "output_name": "output_h5ad"
-                            },
-                            "RenameDatasetActionoutput_tsv": {
-                                "action_arguments": {
-                                    "newname": "Markers - cluster"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_tsv"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
                         "tool_shed_repository": {
-                            "changeset_revision": "49653e680ea4",
-                            "name": "scanpy_find_markers",
+                            "changeset_revision": "6417cccad133",
+                            "name": "scanpy_compute_graph",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"groupby\": \"louvain\", \"groupby_file\": {\"__class__\": \"RuntimeValue\"}, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"n_genes\": \"50\", \"output_format\": \"anndata_h5ad\", \"output_markers\": \"true\", \"settings\": {\"default\": \"true\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"n_neighbors_file|__identifier__\": \"n-neighbors_10\", \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": false, \"__current_case__\": 1, \"key_added\": \"\", \"n_neighbors\": \"15\", \"n_neighbors_file\": {\"__class__\": \"ConnectedValue\"}, \"use_rep\": \"X_pca\", \"n_pcs\": \"20\", \"knn\": true, \"method\": \"umap\", \"metric\": \"euclidean\", \"random_seed\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "b5fcde30-03d3-44b0-9d6a-094512e76172",
+                        "uuid": "d8928b9b-012d-469c-8916-7a42b88b8bd6",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Markers - cluster",
-                                "output_name": "output_tsv",
-                                "uuid": "308b4961-4d50-442b-9bca-bbb1992426ba"
-                            },
-                            {
-                                "label": "Final object",
+                                "label": "Scanpy ComputeGraph on collection X: Graph object AnnData (n-neighbours)",
                                 "output_name": "output_h5ad",
-                                "uuid": "035bbbce-fb57-48c8-83d5-2b0cd0376541"
+                                "uuid": "1e60c7cd-7e02-450f-a403-f3df1e548757"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 31,
+                        "id": 7,
                         "input_connections": {
                             "input_obj_file": {
-                                "id": 29,
-                                "output_name": "output_h5ad"
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "settings|perplexity_file": {
+                                "id": 3,
+                                "output_name": "parameter_iteration"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Scanpy FindMarkers",
-                                "name": "groupby_file"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Scanpy FindMarkers",
+                        "name": "Scanpy RunTSNE",
                         "outputs": [
                             {
                                 "name": "output_h5ad",
                                 "type": "h5ad"
                             },
                             {
-                                "name": "output_tsv",
+                                "name": "output_embed",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 3614.1640625,
-                            "top": 1110.296875
+                            "left": 284.8446053027503,
+                            "top": 367.1121982373686
                         },
                         "post_job_actions": {
-                            "HideDatasetActionoutput_h5ad": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_h5ad"
-                            },
-                            "RenameDatasetActionoutput_tsv": {
+                            "RenameDatasetActionoutput_h5ad": {
                                 "action_arguments": {
-                                    "newname": "Markers - genotype"
+                                    "newname": "Scanpy RunTSNE on collection X: tSNE object AnnData (perplexity)"
                                 },
                                 "action_type": "RenameDatasetAction",
-                                "output_name": "output_tsv"
+                                "output_name": "output_h5ad"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
                         "tool_shed_repository": {
-                            "changeset_revision": "49653e680ea4",
-                            "name": "scanpy_find_markers",
+                            "changeset_revision": "181d61d2f3cd",
+                            "name": "scanpy_run_tsne",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"groupby\": \"genotype\", \"groupby_file\": {\"__class__\": \"RuntimeValue\"}, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"n_genes\": \"50\", \"output_format\": \"anndata_h5ad\", \"output_markers\": \"true\", \"settings\": {\"default\": \"true\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"embeddings\": true, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"perplexity_file|__identifier__\": \"perplexity_15.0\", \"settings\": {\"default\": false, \"__current_case__\": 1, \"key_added\": null, \"perplexity\": \"30.0\", \"perplexity_file\": {\"__class__\": \"ConnectedValue\"}, \"early_exaggeration\": \"12.0\", \"learning_rate\": \"1000.0\", \"fast_tsne\": false, \"n_job\": null, \"n_pc\": null, \"random_seed\": \"0\"}, \"use_rep\": \"X_pca\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "cf2af5fd-4210-4a5a-b514-9786eebeb6f8",
+                        "uuid": "90f289f5-8589-4094-a415-72105bd42346",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Markers - genotype",
-                                "output_name": "output_tsv",
-                                "uuid": "1705e219-192a-4f52-9b26-64fcbcd303ea"
+                                "label": "Scanpy RunTSNE on collection X: tSNE object AnnData (perplexity)",
+                                "output_name": "output_h5ad",
+                                "uuid": "15143fea-5e2b-4b25-b5d1-0726da910f67"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 32,
+                        "id": 8,
                         "input_connections": {
                             "input_obj_file": {
-                                "id": 30,
-                                "output_name": "output_h5ad"
+                                "id": 4,
+                                "output_name": "output"
+                            },
+                            "settings|resolution_file": {
+                                "id": 5,
+                                "output_name": "parameter_iteration"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Scanpy PlotEmbed",
+                        "name": "Scanpy FindCluster",
                         "outputs": [
                             {
-                                "name": "output_png",
-                                "type": "png"
+                                "name": "output_h5ad",
+                                "type": "h5ad"
+                            },
+                            {
+                                "name": "output_txt",
+                                "type": "tsv"
                             }
                         ],
                         "position": {
-                            "left": 3902.203125,
-                            "top": 75.1328125
+                            "left": 299.9946351604703,
+                            "top": 682.3122048475996
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_h5ad": {
+                                "action_arguments": {
+                                    "newname": "Scanpy FindCluster on collection X: Clusters AnnData (resolution)"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
                         "tool_shed_repository": {
-                            "changeset_revision": "56d22aa6cb3b",
-                            "name": "scanpy_plot_embed",
+                            "changeset_revision": "2ccd9f9e2cd0",
+                            "name": "scanpy_find_cluster",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"basis\": \"tsne\", \"color_by\": \"louvain,sex,batch,genotype,Il2ra,Cd8b1,Cd8a,Cd4,Itm2a,Aif1,log1p_total_counts\", \"components\": \"\", \"edges\": \"false\", \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": \"false\", \"fig_size\": \"4,4\", \"fig_title\": \"\", \"gene_symbols_field\": \"Symbol\", \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": \"false\", \"use_raw\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"method\": \"louvain\", \"output_cluster\": true, \"output_format\": \"anndata_h5ad\", \"resolution_file|__identifier__\": \"resolution_0.2\", \"settings\": {\"default\": false, \"__current_case__\": 1, \"neighbors_key\": \"neighbors\", \"layer\": \"\", \"key_added\": null, \"resolution\": \"1.0\", \"resolution_file\": {\"__class__\": \"ConnectedValue\"}, \"restrict_to\": null, \"use_weights\": false, \"random_seed\": \"0\", \"directed\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "a41e2d67-8264-477d-9a61-9a9f86681a91",
+                        "uuid": "0854fbcc-e57c-421c-8320-3eb5d1fdba1e",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_png",
-                                "uuid": "a76a5c05-f1c3-414e-8663-4951fdbbb1f5"
+                                "label": "Scanpy FindCluster on collection X: Clusters AnnData (resolution)",
+                                "output_name": "output_h5ad",
+                                "uuid": "6fdddfe7-c4da-4421-86a0-9819ce4c769c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 33,
+                        "id": 9,
                         "input_connections": {
                             "input_obj_file": {
-                                "id": 30,
+                                "id": 6,
                                 "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Scanpy PlotEmbed",
+                        "name": "Scanpy RunTSNE",
                         "outputs": [
                             {
-                                "name": "output_png",
-                                "type": "png"
+                                "name": "output_h5ad",
+                                "type": "h5ad"
+                            },
+                            {
+                                "name": "output_embed",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 3902.203125,
-                            "top": 292.2421875
+                            "left": 583.120210023914,
+                            "top": 5.5371860303373746
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_h5ad": {
+                                "action_arguments": {
+                                    "newname": "Scanpy RunTSNE on collection X: tSNE object AnnData (n-neighbours)"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
                         "tool_shed_repository": {
-                            "changeset_revision": "56d22aa6cb3b",
-                            "name": "scanpy_plot_embed",
+                            "changeset_revision": "181d61d2f3cd",
+                            "name": "scanpy_run_tsne",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"basis\": \"umap\", \"color_by\": \"louvain,sex,batch,genotype,Il2ra,Cd8b1,Cd8a,Cd4,Itm2a,Aif1,log1p_total_counts\", \"components\": \"\", \"edges\": \"false\", \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": \"false\", \"fig_size\": \"4,4\", \"fig_title\": \"\", \"gene_symbols_field\": \"Symbol\", \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": \"false\", \"use_raw\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"embeddings\": true, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"n-neighbors_10\", \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": false, \"__current_case__\": 1, \"key_added\": null, \"perplexity\": \"30.0\", \"perplexity_file\": null, \"early_exaggeration\": \"12.0\", \"learning_rate\": \"1000.0\", \"fast_tsne\": false, \"n_job\": null, \"n_pc\": null, \"random_seed\": \"0\"}, \"use_rep\": \"X_pca\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "4402764b-f095-494c-abfe-97f8854c6c25",
+                        "uuid": "727487bc-89e8-478c-81f7-3b3a2db1d2d7",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_png",
-                                "uuid": "22e2c0b2-db19-4689-b2fc-7f9fcff14611"
+                                "label": "Scanpy RunTSNE on collection X: tSNE object AnnData (n-neighbours)",
+                                "output_name": "output_h5ad",
+                                "uuid": "7c988247-b167-4733-859f-fcd582f91959"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 34,
+                        "id": 10,
                         "input_connections": {
-                            "input": {
-                                "id": 30,
+                            "input_obj_file": {
+                                "id": 7,
                                 "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Manipulate AnnData",
+                        "name": "Scanpy RunUMAP",
                         "outputs": [
                             {
-                                "name": "anndata",
+                                "name": "output_h5ad",
                                 "type": "h5ad"
+                            },
+                            {
+                                "name": "output_embed",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 3902.203125,
-                            "top": 509.2890625
+                            "left": 580.3870931396372,
+                            "top": 371.3332390321145
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_h5ad": {
+                                "action_arguments": {
+                                    "newname": "Scanpy RunUMAP on collection X: UMAP object AnnData (perplexity)"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9",
                         "tool_shed_repository": {
-                            "changeset_revision": "3d748954434b",
-                            "name": "anndata_manipulate",
-                            "owner": "iuc",
+                            "changeset_revision": "bd4a244faeb8",
+                            "name": "scanpy_run_umap",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"rename_categories\", \"__current_case__\": 3, \"key\": \"louvain\", \"categories\": \"DP-M4,DP-M3,DP-M1,T-mat,DN,DP-L,DP-M2,Macrophages\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.5+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"embeddings\": true, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"perplexity_15.0\", \"key_added\": null, \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": true, \"__current_case__\": 0}, \"use_graph\": \"neighbors\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "91b502ec-5b8b-40a2-b70b-1d30581434ef",
+                        "uuid": "2b98c2ef-aea6-4581-9155-e780f4d5c5eb",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "anndata",
-                                "uuid": "8a35be0b-4004-4dce-810b-e5b9d33590b9"
+                                "label": "Scanpy RunUMAP on collection X: UMAP object AnnData (perplexity)",
+                                "output_name": "output_h5ad",
+                                "uuid": "1f5abfa2-845c-4763-9f87-e4b167aa7bc8"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 35,
+                        "id": 11,
                         "input_connections": {
                             "input_obj_file": {
-                                "id": 30,
+                                "id": 8,
                                 "output_name": "output_h5ad"
                             }
                         },
@@ -232131,366 +237259,348 @@
                             }
                         ],
                         "position": {
-                            "left": 3902.203125,
-                            "top": 705.234375
+                            "left": 610.8375710947927,
+                            "top": 629.3556101888285
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
                         "tool_shed_repository": {
-                            "changeset_revision": "56d22aa6cb3b",
+                            "changeset_revision": "35f6611fb8c3",
                             "name": "scanpy_plot_embed",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"basis\": \"pca\", \"color_by\": \"louvain,sex,batch,genotype,Il2ra,Cd8b1,Cd8a,Cd4,Itm2a,Aif1,log1p_total_counts\", \"components\": \"\", \"edges\": \"false\", \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": \"false\", \"fig_size\": \"4,4\", \"fig_title\": \"\", \"gene_symbols_field\": \"Symbol\", \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": \"false\", \"use_raw\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"basis\": \"pca\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"color_by\": \"louvain\", \"components\": \"\", \"edges\": false, \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": false, \"fig_size\": \"4,4\", \"fig_title\": null, \"gene_symbols_field\": null, \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"resolution_0.2\", \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": false, \"use_raw\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "2a77ae44-dc08-4b53-ae43-215ba91d6260",
+                        "uuid": "6dc51709-4987-4944-99d4-386cc9233d1b",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "resolution_pca_plots",
                                 "output_name": "output_png",
-                                "uuid": "ea42965c-0f03-404d-9a5a-a070170dc4b2"
+                                "uuid": "99185d1e-047f-47f2-9081-07506e1c17df"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 36,
+                        "id": 12,
                         "input_connections": {
-                            "input": {
-                                "id": 30,
+                            "input_obj_file": {
+                                "id": 8,
                                 "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Inspect AnnData",
+                        "name": "Scanpy PlotEmbed",
                         "outputs": [
                             {
-                                "name": "var",
-                                "type": "tabular"
+                                "name": "output_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 3902.203125,
-                            "top": 922.2890625
+                            "left": 601.9354642911717,
+                            "top": 807.4162217137739
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
                         "tool_shed_repository": {
-                            "changeset_revision": "ee98d611afc6",
-                            "name": "anndata_inspect",
-                            "owner": "iuc",
+                            "changeset_revision": "35f6611fb8c3",
+                            "name": "scanpy_plot_embed",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"h5ad\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"var\", \"__current_case__\": 4}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.5+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"basis\": \"umap\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"color_by\": \"louvain\", \"components\": \"\", \"edges\": false, \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": false, \"fig_size\": \"4,4\", \"fig_title\": null, \"gene_symbols_field\": null, \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"resolution_0.2\", \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": false, \"use_raw\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "c9832ad2-4cff-4316-a43a-11ba2691601d",
+                        "uuid": "4098f10f-19d7-4745-aeb5-2d5ceb436fb1",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "var",
-                                "uuid": "d890f37a-aa1e-4b3c-8f63-04ecfeaa8f73"
+                                "label": "resolution_umap_plots",
+                                "output_name": "output_png",
+                                "uuid": "65d7b619-8659-4008-9e56-db21fda6ce8c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 37,
+                        "id": 13,
                         "input_connections": {
-                            "copy_o|obs_sources": {
-                                "id": 34,
-                                "output_name": "anndata"
-                            },
                             "input_obj_file": {
-                                "id": 30,
+                                "id": 8,
                                 "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "AnnData Operations",
+                        "name": "Scanpy PlotEmbed",
                         "outputs": [
                             {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
+                                "name": "output_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 4386.2109375,
-                            "top": 257.1875
+                            "left": 593.5750000507026,
+                            "top": 977.1437760474608
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
                         "tool_shed_repository": {
-                            "changeset_revision": "890fb06a2893",
-                            "name": "anndata_ops",
+                            "changeset_revision": "35f6611fb8c3",
+                            "name": "scanpy_plot_embed",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"copy_adata_to_raw\": \"false\", \"copy_e\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_l\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_o\": {\"default\": \"true\", \"__current_case__\": 0, \"obs_keys\": [{\"__index__\": 0, \"contains\": \"louvain\"}], \"obs_sources\": {\"__class__\": \"ConnectedValue\"}}, \"copy_r\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_u\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_x\": {\"default\": \"false\", \"__current_case__\": 1}, \"gene_flags\": [], \"gene_symbols_field\": \"index\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": \"false\", \"top_genes\": \"50\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"basis\": \"tsne\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"color_by\": \"louvain\", \"components\": \"\", \"edges\": false, \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": false, \"fig_size\": \"4,4\", \"fig_title\": null, \"gene_symbols_field\": null, \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"resolution_0.2\", \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": false, \"use_raw\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "573bf376-2011-4572-ad91-84df828f1242",
+                        "uuid": "b1d539e5-05cf-4359-87c9-19b2d22dcdb7",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output_h5ad",
-                                "uuid": "50717627-47ed-40bc-bf18-17198416a57f"
+                                "label": "resolution_tsne_plots",
+                                "output_name": "output_png",
+                                "uuid": "bdcaf837-5fc4-4024-a87a-eabfa0110127"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "join1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 38,
+                        "id": 14,
                         "input_connections": {
-                            "input1": {
-                                "id": 30,
-                                "output_name": "output_tsv"
-                            },
-                            "input2": {
-                                "id": 36,
-                                "output_name": "var"
+                            "input_obj_file": {
+                                "id": 9,
+                                "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Join two Datasets",
+                        "name": "Scanpy RunUMAP",
                         "outputs": [
                             {
-                                "name": "out_file1",
+                                "name": "output_h5ad",
+                                "type": "h5ad"
+                            },
+                            {
+                                "name": "output_embed",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 4190.2109375,
-                            "top": 976.3046875
+                            "left": 843.1624694773969,
+                            "top": 18.380633385427693
                         },
-                        "post_job_actions": {},
-                        "tool_id": "join1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"field1\": \"4\", \"field2\": \"2\", \"fill_empty_columns\": {\"fill_empty_columns_switch\": \"no_fill\", \"__current_case__\": 0}, \"header\": \"-H\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"partial\": \"-p\", \"unmatched\": \"-u\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.3",
-                        "type": "tool",
-                        "uuid": "db6d5777-a3dd-467d-8541-91bb998e0e72",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "cb6967d5-7390-4d2e-b2c4-1d8a9e2d3c69"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "join1",
-                        "errors": null,
-                        "id": 39,
-                        "input_connections": {
-                            "input1": {
-                                "id": 31,
-                                "output_name": "output_tsv"
-                            },
-                            "input2": {
-                                "id": 36,
-                                "output_name": "var"
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_h5ad": {
+                                "action_arguments": {
+                                    "newname": "Scanpy RunUMAP on collection X: UMAP object AnnData (n-neighbours)"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_h5ad"
                             }
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Join two Datasets",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 4178.2109375,
-                            "top": 1199.2890625
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "bd4a244faeb8",
+                            "name": "scanpy_run_umap",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "post_job_actions": {},
-                        "tool_id": "join1",
-                        "tool_state": "{\"field1\": \"4\", \"field2\": \"2\", \"fill_empty_columns\": {\"fill_empty_columns_switch\": \"no_fill\", \"__current_case__\": 0}, \"header\": \"-H\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"partial\": \"-p\", \"unmatched\": \"-u\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.3",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"embeddings\": true, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"n-neighbors_10\", \"key_added\": null, \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": true, \"__current_case__\": 0}, \"use_graph\": \"neighbors\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "f4db0e7d-dfc8-4f77-bca0-997a0347304b",
+                        "uuid": "e61b46a4-847c-45d6-90e3-b1547fa95634",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "54cdb2bd-437b-47e4-90c1-e99e0b468574"
+                                "label": "Scanpy RunUMAP on collection X: UMAP object AnnData (n-neighbours)",
+                                "output_name": "output_h5ad",
+                                "uuid": "8a0b3d69-e7df-4977-b8eb-ec478b914a26"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 40,
+                        "id": 15,
                         "input_connections": {
                             "input_obj_file": {
-                                "id": 37,
+                                "id": 10,
                                 "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "AnnData Operations",
+                        "name": "Scanpy FindCluster",
                         "outputs": [
                             {
                                 "name": "output_h5ad",
                                 "type": "h5ad"
+                            },
+                            {
+                                "name": "output_txt",
+                                "type": "tsv"
                             }
                         ],
                         "position": {
-                            "left": 4468.2109375,
-                            "top": 0
+                            "left": 860.8525296481835,
+                            "top": 354.84265238442265
                         },
                         "post_job_actions": {
                             "RenameDatasetActionoutput_h5ad": {
                                 "action_arguments": {
-                                    "newname": "Final cell annotated object"
+                                    "newname": "Scanpy FindCluster on collection X: Clusters AnnData (perplexity)"
                                 },
                                 "action_type": "RenameDatasetAction",
                                 "output_name": "output_h5ad"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
                         "tool_shed_repository": {
-                            "changeset_revision": "890fb06a2893",
-                            "name": "anndata_ops",
+                            "changeset_revision": "2ccd9f9e2cd0",
+                            "name": "scanpy_find_cluster",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"copy_adata_to_raw\": \"false\", \"copy_e\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_l\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_o\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_r\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_u\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_x\": {\"default\": \"false\", \"__current_case__\": 1}, \"gene_flags\": [], \"gene_symbols_field\": \"index\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [{\"__index__\": 0, \"from_obs\": \"louvain_0\", \"to_obs\": \"cell_type\", \"keep_original\": \"false\"}], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": \"false\", \"top_genes\": \"50\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"perplexity_15.0\", \"method\": \"louvain\", \"output_cluster\": true, \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": false, \"__current_case__\": 1, \"neighbors_key\": \"neighbors\", \"layer\": \"\", \"key_added\": null, \"resolution\": \"0.6\", \"resolution_file\": null, \"restrict_to\": null, \"use_weights\": false, \"random_seed\": \"0\", \"directed\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "584bf7e3-05d7-4010-ba67-98375379c621",
+                        "uuid": "2ec67307-cf3a-45a7-b973-d0dd915ec5b5",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Final cell annotated object",
+                                "label": "Scanpy FindCluster on collection X: Clusters AnnData (perplexity)",
                                 "output_name": "output_h5ad",
-                                "uuid": "a6d48df0-403f-4efc-a75f-9504a960884e"
+                                "uuid": "c2e0d48f-9f0e-4452-8fb5-e78420578c65"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Cut1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 41,
+                        "id": 16,
                         "input_connections": {
-                            "input": {
-                                "id": 38,
-                                "output_name": "out_file1"
+                            "input_obj_file": {
+                                "id": 14,
+                                "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Cut",
+                        "name": "Scanpy FindCluster",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "tabular"
+                                "name": "output_h5ad",
+                                "type": "h5ad"
+                            },
+                            {
+                                "name": "output_txt",
+                                "type": "tsv"
                             }
                         ],
                         "position": {
-                            "left": 4468.2109375,
-                            "top": 1014.2890625
+                            "left": 1110.1696213010753,
+                            "top": 27.962176176922693
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
+                            "RenameDatasetActionoutput_h5ad": {
                                 "action_arguments": {
-                                    "newname": "Markers - cluster - named"
+                                    "newname": "Scanpy FindCluster on collection X: Clusters AnnData (n-neighbours)"
                                 },
                                 "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
+                                "output_name": "output_h5ad"
                             }
                         },
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"columnList\": \"c1,c2,c3,c4,c11,c5,c6,c7,c8\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2ccd9f9e2cd0",
+                            "name": "scanpy_find_cluster",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"n-neighbors_10\", \"method\": \"louvain\", \"output_cluster\": true, \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": false, \"__current_case__\": 1, \"neighbors_key\": \"neighbors\", \"layer\": \"\", \"key_added\": null, \"resolution\": \"0.6\", \"resolution_file\": null, \"restrict_to\": null, \"use_weights\": false, \"random_seed\": \"0\", \"directed\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "45fddc4f-1b9d-4464-b08b-c502d4d05a30",
+                        "uuid": "a427d6bd-a860-4ff1-a614-3c48baa04737",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Markers - cluster - named",
-                                "output_name": "out_file1",
-                                "uuid": "0ee7f9b6-b065-4e26-93df-6e6e2fe458a9"
+                                "label": "Scanpy FindCluster on collection X: Clusters AnnData (n-neighbours)",
+                                "output_name": "output_h5ad",
+                                "uuid": "c952b32e-99d5-4b94-a6d7-be59439c4dca"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Cut1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 42,
+                        "id": 17,
                         "input_connections": {
-                            "input": {
-                                "id": 39,
-                                "output_name": "out_file1"
+                            "input_obj_file": {
+                                "id": 15,
+                                "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Cut",
+                        "name": "Scanpy PlotEmbed",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "tabular"
+                                "name": "output_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 4468.2109375,
-                            "top": 1199.2890625
+                            "left": 1122.427370848608,
+                            "top": 356.74062604698014
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Markers - genotype - named"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "35f6611fb8c3",
+                            "name": "scanpy_plot_embed",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"columnList\": \"c1,c2,c3,c4,c11,c5,c6,c7,c8\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2",
+                        "tool_state": "{\"__input_ext\": \"input\", \"basis\": \"tsne\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"color_by\": \"louvain\", \"components\": \"\", \"edges\": false, \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": false, \"fig_size\": \"4,4\", \"fig_title\": null, \"gene_symbols_field\": null, \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"perplexity_15.0\", \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": false, \"use_raw\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "995cfd57-925a-470e-879b-8d7eb619c67b",
+                        "uuid": "900f5cef-ad85-4b7d-b4c3-1c3a86c64e29",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Markers - genotype - named",
-                                "output_name": "out_file1",
-                                "uuid": "fdb88faa-9b76-4edb-b89b-427c098a473e"
+                                "label": "perplexity_plots",
+                                "output_name": "output_png",
+                                "uuid": "44c0ec07-b64e-428f-9254-5217e8041416"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 43,
+                        "id": 18,
                         "input_connections": {
                             "input_obj_file": {
-                                "id": 40,
+                                "id": 16,
                                 "output_name": "output_h5ad"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Scanpy PlotEmbed",
-                                "name": "input_obj_file"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
                         "name": "Scanpy PlotEmbed",
                         "outputs": [
@@ -232500,99 +237610,573 @@
                             }
                         ],
                         "position": {
-                            "left": 4653.7109375,
-                            "top": 231.5
+                            "left": 1378.4911495849283,
+                            "top": 64.43740029026476
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
                         "tool_shed_repository": {
-                            "changeset_revision": "56d22aa6cb3b",
+                            "changeset_revision": "35f6611fb8c3",
                             "name": "scanpy_plot_embed",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"basis\": \"umap\", \"color_by\": \"sex,batch,genotype,Il2ra,Cd8b1,Cd8a,Cd4,Itm2a,Aif1,log1p_total_counts,Hba-a1,cell_type\", \"components\": \"\", \"edges\": \"false\", \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": \"false\", \"fig_size\": \"4,4\", \"fig_title\": \"\", \"gene_symbols_field\": \"Symbol\", \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"RuntimeValue\"}, \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": \"false\", \"use_raw\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"input\", \"basis\": \"umap\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"color_by\": \"louvain\", \"components\": \"\", \"edges\": false, \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": false, \"fig_size\": \"4,4\", \"fig_title\": null, \"gene_symbols_field\": null, \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"input_obj_file|__identifier__\": \"n-neighbors_10\", \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": false, \"use_raw\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "ff379bdf-e875-4803-baa0-b11bd71666db",
+                        "uuid": "b2682b86-da4c-427e-b793-24faa66f5c8f",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "n-neighbors_plots",
                                 "output_name": "output_png",
-                                "uuid": "cb97c2f3-8e23-45d0-bc96-faf2f06b59d0"
+                                "uuid": "0b30f573-8ebd-4582-9bcd-58ba5c778658"
                             }
                         ]
                     }
                 ],
-                "parent_id": "single-cell/scrna-case_basic-pipeline",
-                "path": "topics/single-cell/tutorials/scrna-case_basic-pipeline/workflows/CS3_Filter,_Plot_and_Explore_Single-cell_RNA-seq_Data.ga",
-                "tags": [
-                    "name:transcriptomics",
-                    "name:training",
-                    "name:singlecell"
-                ],
+                "parent_id": "single-cell/scanpy_parameter_iterator",
+                "path": "topics/single-cell/tutorials/scanpy_parameter_iterator/workflows/Scanpy-Parameter-Iterator-workflow-full.ga",
+                "tags": [],
                 "test_results": null,
-                "tests": false,
-                "title": "CS3_Filter, Plot and Explore Single-cell RNA-seq Data",
+                "tests": true,
+                "title": "Scanpy Parameter Iterator workflow full (imported from URL)",
                 "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-case_basic-pipeline/versions/cs3-filter--plot-and-explore-single-cell-rna-seq-data",
-                "tutorial_id": "scrna-case_basic-pipeline",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_basic-pipeline/workflows/CS3_Filter,_Plot_and_Explore_Single-cell_RNA-seq_Data.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_basic-pipeline/workflows/CS3_Filter,_Plot_and_Explore_Single-cell_RNA-seq_Data.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scanpy_parameter_iterator/versions/scanpy-parameter-iterator-workflow-full",
+                "tutorial_id": "scanpy_parameter_iterator",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scanpy_parameter_iterator/workflows/Scanpy-Parameter-Iterator-workflow-full.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scanpy_parameter_iterator/workflows/Scanpy-Parameter-Iterator-workflow-full.html",
                 "version": 1,
-                "wfid": "single-cell-scrna-case_basic-pipeline",
-                "wfname": "cs3-filter--plot-and-explore-single-cell-rna-seq-data",
-                "workflow": "CS3_Filter,_Plot_and_Explore_Single-cell_RNA-seq_Data.ga",
+                "wfid": "single-cell-scanpy_parameter_iterator",
+                "wfname": "scanpy-parameter-iterator-workflow-full",
+                "workflow": "Scanpy-Parameter-Iterator-workflow-full.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "join1",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1"
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9"
                 ],
-                "workflowhub_id": "1219"
+                "workflowhub_id": "1243"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/8011681"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "anndata_ops",
+                    "owner": "ebi-gxa",
+                    "revisions": "890fb06a2893",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "anndata_ops",
+                    "owner": "ebi-gxa",
+                    "revisions": "7ebc22f77d86",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_compute_graph",
+                    "owner": "ebi-gxa",
+                    "revisions": "bc9e8de21efb",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_compute_graph",
+                    "owner": "ebi-gxa",
+                    "revisions": "6417cccad133",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_filter_cells",
+                    "owner": "ebi-gxa",
+                    "revisions": "55ccc0a121bc",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_filter_cells",
+                    "owner": "ebi-gxa",
+                    "revisions": "e9283529cba1",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_filter_genes",
+                    "owner": "ebi-gxa",
+                    "revisions": "da611a744112",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_filter_genes",
+                    "owner": "ebi-gxa",
+                    "revisions": "474a69c47184",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_find_cluster",
+                    "owner": "ebi-gxa",
+                    "revisions": "ad6995afd2e6",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_find_cluster",
+                    "owner": "ebi-gxa",
+                    "revisions": "2ccd9f9e2cd0",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_find_markers",
+                    "owner": "ebi-gxa",
+                    "revisions": "49653e680ea4",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_find_markers",
+                    "owner": "ebi-gxa",
+                    "revisions": "81c34e67f262",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_find_variable_genes",
+                    "owner": "ebi-gxa",
+                    "revisions": "4667fe07bd68",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_find_variable_genes",
+                    "owner": "ebi-gxa",
+                    "revisions": "2861ca3bfe4d",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_normalise_data",
+                    "owner": "ebi-gxa",
+                    "revisions": "8d9c22419c56",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_normalise_data",
+                    "owner": "ebi-gxa",
+                    "revisions": "6b97ffba31da",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_plot_embed",
+                    "owner": "ebi-gxa",
+                    "revisions": "56d22aa6cb3b",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_plot_embed",
+                    "owner": "ebi-gxa",
+                    "revisions": "35f6611fb8c3",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_run_pca",
+                    "owner": "ebi-gxa",
+                    "revisions": "3ee74b58c72d",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_run_pca",
+                    "owner": "ebi-gxa",
+                    "revisions": "59028945c857",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_run_tsne",
+                    "owner": "ebi-gxa",
+                    "revisions": "8b0d6f6f44c8",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_run_tsne",
+                    "owner": "ebi-gxa",
+                    "revisions": "181d61d2f3cd",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_run_umap",
+                    "owner": "ebi-gxa",
+                    "revisions": "fe562424a0a6",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_run_umap",
+                    "owner": "ebi-gxa",
+                    "revisions": "bd4a244faeb8",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_scale_data",
+                    "owner": "ebi-gxa",
+                    "revisions": "5605f8452eb3",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_scale_data",
+                    "owner": "ebi-gxa",
+                    "revisions": "f86b2c3bc459",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "anndata_inspect",
+                    "owner": "iuc",
+                    "revisions": "ee98d611afc6",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "anndata_manipulate",
+                    "owner": "iuc",
+                    "revisions": "3d748954434b",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_plot",
+                    "owner": "iuc",
+                    "revisions": "aa0c474463c2",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: anndata_ops\n  owner: ebi-gxa\n  revisions: 890fb06a2893\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_ops\n  owner: ebi-gxa\n  revisions: 7ebc22f77d86\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_compute_graph\n  owner: ebi-gxa\n  revisions: bc9e8de21efb\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_compute_graph\n  owner: ebi-gxa\n  revisions: 6417cccad133\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter_cells\n  owner: ebi-gxa\n  revisions: 55ccc0a121bc\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter_cells\n  owner: ebi-gxa\n  revisions: e9283529cba1\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter_genes\n  owner: ebi-gxa\n  revisions: da611a744112\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter_genes\n  owner: ebi-gxa\n  revisions: 474a69c47184\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_find_cluster\n  owner: ebi-gxa\n  revisions: ad6995afd2e6\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_find_cluster\n  owner: ebi-gxa\n  revisions: 2ccd9f9e2cd0\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_find_markers\n  owner: ebi-gxa\n  revisions: 49653e680ea4\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_find_markers\n  owner: ebi-gxa\n  revisions: 81c34e67f262\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_find_variable_genes\n  owner: ebi-gxa\n  revisions: 4667fe07bd68\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_find_variable_genes\n  owner: ebi-gxa\n  revisions: 2861ca3bfe4d\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_normalise_data\n  owner: ebi-gxa\n  revisions: 8d9c22419c56\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_normalise_data\n  owner: ebi-gxa\n  revisions: 6b97ffba31da\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot_embed\n  owner: ebi-gxa\n  revisions: 56d22aa6cb3b\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot_embed\n  owner: ebi-gxa\n  revisions: 35f6611fb8c3\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_pca\n  owner: ebi-gxa\n  revisions: 3ee74b58c72d\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_pca\n  owner: ebi-gxa\n  revisions: 59028945c857\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_tsne\n  owner: ebi-gxa\n  revisions: 8b0d6f6f44c8\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_tsne\n  owner: ebi-gxa\n  revisions: 181d61d2f3cd\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_umap\n  owner: ebi-gxa\n  revisions: fe562424a0a6\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_run_umap\n  owner: ebi-gxa\n  revisions: bd4a244faeb8\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_scale_data\n  owner: ebi-gxa\n  revisions: 5605f8452eb3\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_scale_data\n  owner: ebi-gxa\n  revisions: f86b2c3bc459\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_inspect\n  owner: iuc\n  revisions: ee98d611afc6\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n  owner: iuc\n  revisions: 3d748954434b\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot\n  owner: iuc\n  revisions: aa0c474463c2\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "answer_histories": [
+            {
+                "date": "2023-10-10",
+                "history": "https://usegalaxy.eu/u/j.jakiela/h/filter-plot-and-explore-single-cell-rna-seq-data-updated",
+                "label": "UseGalaxy.eu"
+            },
+            {
+                "date": "2024-02-28",
+                "history": "https://usegalaxy.eu/u/wendi.bacon.training/h/cs3filter-plot-and-explore-single-cell-rna-seq-data---answer-key-2",
+                "label": "Older version"
+            }
+        ],
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "nomadscientist"
+            ],
+            "editing": [
+                "hexylena",
+                "wee-snufkin"
+            ],
+            "testing": [
+                "wee-snufkin"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "bio": "Senior Lecturer at The Open University",
+                "elixir_node": "uk",
+                "email": "wendi.bacon@open.ac.uk",
+                "fediverse": "https://mstdn.science/@wendibacon1",
+                "fediverse_flavor": "mastodon",
+                "id": "nomadscientist",
+                "joined": "2020-03",
+                "matrix": "nomadscientist:matrix.org",
+                "name": "Wendi Bacon",
+                "orcid": "0000-0002-8170-8806",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
+                "twitter": "WendiBacon1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "elixir_node": "uk",
+                "email": "juliajot36@gmail.com",
+                "id": "wee-snufkin",
+                "joined": "2022-06",
+                "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
             },
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-8170-8806",
-                        "name": "Wendi Bacon"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "0009-0001-2017-8805",
-                        "name": "Julia Jakiela"
-                    }
-                ],
-                "description": "Filter, Plot and Explore Single-cell RNA-seq Data",
+                "elixir_node": "uk",
+                "email": "juliajot36@gmail.com",
+                "id": "wee-snufkin",
+                "joined": "2022-06",
+                "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
+            }
+        ],
+        "dir": "topics/single-cell/tutorials/scrna-case_basic-pipeline",
+        "edam_operation": [
+            "Differential gene expression analysis"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-case_JUPYTER-trajectories",
+                    "scrna-case_monocle3-trajectories"
+                ],
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "single-cell/scrna-case_basic-pipeline",
+        "inexact_supported_servers": [
+            "UseGalaxy.org.au"
+        ],
+        "input_histories": [
+            {
+                "history": "https://usegalaxy.eu/published/history?id=67ff4cea2adc574d",
+                "label": "UseGalaxy.eu"
+            }
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Single cell data is huge, and must have its many (# genes) dimensions reduced for analysis",
+            "Analysis is more subjective than we think, and biological understanding of the samples as well as many iterations of analysis are important to give us our best change of attaining real biological insights"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-18",
+        "objectives": [
+            "Interpret quality control plots to direct parameter decisions",
+            "Repeat analysis from matrix to clustering",
+            "Identify decision-making points",
+            "Appraise data outputs and decisions",
+            "Explain why single cell analysis is an iterative (i.e. the first plots you generate are not final, but rather you go back and re-analyse your data repeatedly) process"
+        ],
+        "pageviews": 6346,
+        "priority": 3,
+        "pub_date": "2021-03-24",
+        "questions": [
+            "Is my single cell dataset a quality dataset?",
+            "How do I generate and annotate cell clusters?",
+            "How do I pick thresholds and parameters in my analysis? What's a \"reasonable\" number, and will the world collapse if I pick the wrong one?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "nomadscientist"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "30M",
+                "speakers": [
+                    "nomadscientist"
+                ],
+                "youtube_id": "M6iepSJh0EQ"
+            }
+        ],
+        "redirect_from": [
+            "/topics/transcriptomics/tutorials/scrna-seq-basic-pipeline/tutorial",
+            "/topics/transcriptomics/tutorials/scrna-case_basic-pipeline/tutorial",
+            "/short/single-cell/scrna-case_basic-pipeline",
+            "/short/T00247"
+        ],
+        "requirements": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-case_alevin",
+                    "scrna-case_alevin-combine-datasets"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00247",
+        "short_tools": [
+            "join1",
+            "scanpy_plot_embed",
+            "scanpy_run_pca",
+            "scanpy_run_tsne",
+            "scanpy_scale_data",
+            "anndata_manipulate",
+            "scanpy_filter_genes",
+            "scanpy_compute_graph",
+            "scanpy_find_variable_genes",
+            "scanpy_normalise_data",
+            "scanpy_run_umap",
+            "interactive_tool_cellxgene",
+            "scanpy_filter_cells",
+            "anndata_inspect",
+            "Cut1",
+            "scanpy_find_cluster",
+            "anndata_ops",
+            "scanpy_plot",
+            "scanpy_find_markers"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "single-cell-CS",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "10x",
+            "paper-replication"
+        ],
+        "time_estimation": "3H",
+        "title": "Filter, plot and explore single-cell RNA-seq data with Scanpy",
+        "tools": [
+            "Cut1",
+            "interactive_tool_cellxgene",
+            "join1",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy91",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy9",
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1"
+        ],
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "scrna-case_basic-pipeline",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.json"
+        },
+        "version": 20,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 160,
+        "visitors": 4039,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Updated tool versions Aug 24 2022",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMito-counted AnnData\"]\n  1[label=\"Inspect AnnData\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Scanpy FilterCells\"]\n  0 -> 2 [label=\"output\"]\n  k6a00b14bd3f84771963a76115c8eaf2f[color=lightseagreen,label=\"Output\\nGenes-filtered Object\"]\n  2 -> k6a00b14bd3f84771963a76115c8eaf2f\n  3[label=\"Plot\"]\n  0 -> 3 [label=\"output\"]\n  kc123842eb2d243ad81f06ba3b45d4021[color=lightseagreen,label=\"Output\\nScatter - genes x UMIs\"]\n  3 -> kc123842eb2d243ad81f06ba3b45d4021\n  4[label=\"Plot\"]\n  0 -> 4 [label=\"output\"]\n  kf1020d4d555e42faba2152a151b91a5b[color=lightseagreen,label=\"Output\\nScatter - mito x genes\"]\n  4 -> kf1020d4d555e42faba2152a151b91a5b\n  5[label=\"Plot\"]\n  0 -> 5 [label=\"output\"]\n  ka7fe60208f1e470a9ed3f2b5e95516e0[color=lightseagreen,label=\"Output\\nViolin - genotype - log\"]\n  5 -> ka7fe60208f1e470a9ed3f2b5e95516e0\n  6[label=\"Plot\"]\n  0 -> 6 [label=\"output\"]\n  k15e501bc8ddb451989ebdde431ea96c1[color=lightseagreen,label=\"Output\\nViolin - batch - log\"]\n  6 -> k15e501bc8ddb451989ebdde431ea96c1\n  7[label=\"Inspect AnnData\"]\n  0 -> 7 [label=\"output\"]\n  8[label=\"Plot\"]\n  0 -> 8 [label=\"output\"]\n  keff22f46baa64e00ba82d5e12ce26ff0[color=lightseagreen,label=\"Output\\nScatter - mito x UMIs\"]\n  8 -> keff22f46baa64e00ba82d5e12ce26ff0\n  9[label=\"Inspect AnnData\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"Plot\"]\n  0 -> 10 [label=\"output\"]\n  k56677ca4129c476c85ec69d1bb3d800d[color=lightseagreen,label=\"Output\\nViolin - sex - log\"]\n  10 -> k56677ca4129c476c85ec69d1bb3d800d\n  11[label=\"Plot\"]\n  2 -> 11 [label=\"output_h5ad\"]\n  kacb61ea4bcb945dbbeefe2bf1a176701[color=lightseagreen,label=\"Output\\nViolin - Filterbygenes\"]\n  11 -> kacb61ea4bcb945dbbeefe2bf1a176701\n  12[label=\"Scanpy FilterCells\"]\n  2 -> 12 [label=\"output_h5ad\"]\n  k5185366245194229a2eab22a53e7ef73[color=lightseagreen,label=\"Output\\nCounts-filtered Object\"]\n  12 -> k5185366245194229a2eab22a53e7ef73\n  13[label=\"Inspect AnnData\"]\n  2 -> 13 [label=\"output_h5ad\"]\n  k362a7fe624bb4398ae48870f4b4bb774[color=lightseagreen,label=\"Output\\nGeneral - Filterbygenes\"]\n  13 -> k362a7fe624bb4398ae48870f4b4bb774\n  14[label=\"Inspect AnnData\"]\n  12 -> 14 [label=\"output_h5ad\"]\n  kedf2414993414fe7b10c3fcf092faaa5[color=lightseagreen,label=\"Output\\nGeneral - Filterbycounts\"]\n  14 -> kedf2414993414fe7b10c3fcf092faaa5\n  15[label=\"Scanpy FilterCells\"]\n  12 -> 15 [label=\"output_h5ad\"]\n  ka88ec405265f4a59a75e34e3b05b0096[color=lightseagreen,label=\"Output\\nMito-filtered Object\"]\n  15 -> ka88ec405265f4a59a75e34e3b05b0096\n  16[label=\"Plot\"]\n  12 -> 16 [label=\"output_h5ad\"]\n  ka7c8b0d982d34438a212b5f7c56d36b8[color=lightseagreen,label=\"Output\\nViolin - Filterbycounts\"]\n  16 -> ka7c8b0d982d34438a212b5f7c56d36b8\n  17[label=\"Inspect AnnData\"]\n  15 -> 17 [label=\"output_h5ad\"]\n  k56882809e19f451a8010bc55dcee482f[color=lightseagreen,label=\"Output\\nGeneral - Filterbymito\"]\n  17 -> k56882809e19f451a8010bc55dcee482f\n  18[label=\"Scanpy FilterGenes\"]\n  15 -> 18 [label=\"output_h5ad\"]\n  k00846477dec5408a83b2105fff7ce05b[color=lightseagreen,label=\"Output\\nFiltered Object\"]\n  18 -> k00846477dec5408a83b2105fff7ce05b\n  19[label=\"Plot\"]\n  15 -> 19 [label=\"output_h5ad\"]\n  k7582e11320044255a1f3d3123373f342[color=lightseagreen,label=\"Output\\nViolin - Filterbymito\"]\n  19 -> k7582e11320044255a1f3d3123373f342\n  20[label=\"Inspect AnnData\"]\n  18 -> 20 [label=\"output_h5ad\"]\n  k2d870a40c6024a1cafef450489354d39[color=lightseagreen,label=\"Output\\nGeneral - Filtered object\"]\n  20 -> k2d870a40c6024a1cafef450489354d39\n  21[label=\"Scanpy NormaliseData\"]\n  18 -> 21 [label=\"output_h5ad\"]\n  22[label=\"Scanpy FindVariableGenes\"]\n  21 -> 22 [label=\"output_h5ad\"]\n  ka0eb92b102634179b7af4bd9bcc9c960[color=lightseagreen,label=\"Output\\nUse_me_FVG\"]\n  22 -> ka0eb92b102634179b7af4bd9bcc9c960\n  23[label=\"Scanpy ScaleData\"]\n  22 -> 23 [label=\"output_h5ad\"]\n  k5776dbb90cac40c09bae9accae16a7a0[color=lightseagreen,label=\"Output\\nUse_me_Scaled\"]\n  23 -> k5776dbb90cac40c09bae9accae16a7a0\n  24[label=\"Scanpy RunPCA\"]\n  23 -> 24 [label=\"output_h5ad\"]\n  25[label=\"Plot\"]\n  24 -> 25 [label=\"output_h5ad\"]\n  kf0b6f578050f49369ee79956b0760c6f[color=lightseagreen,label=\"Output\\nPCA Variance\"]\n  25 -> kf0b6f578050f49369ee79956b0760c6f\n  26[label=\"Scanpy ComputeGraph\"]\n  24 -> 26 [label=\"output_h5ad\"]\n  27[label=\"Scanpy RunTSNE\"]\n  26 -> 27 [label=\"output_h5ad\"]\n  28[label=\"Scanpy RunUMAP\"]\n  27 -> 28 [label=\"output_h5ad\"]\n  29[label=\"Scanpy FindCluster\"]\n  28 -> 29 [label=\"output_h5ad\"]\n  30[label=\"Scanpy FindMarkers\"]\n  29 -> 30 [label=\"output_h5ad\"]\n  k7cfe5c9c1c8041b4b669633b1d7d40e3[color=lightseagreen,label=\"Output\\nMarkers - cluster\"]\n  30 -> k7cfe5c9c1c8041b4b669633b1d7d40e3\n  k98e98405951e4c6cbe013c925ae35449[color=lightseagreen,label=\"Output\\nFinal object\"]\n  30 -> k98e98405951e4c6cbe013c925ae35449\n  31[label=\"Scanpy FindMarkers\"]\n  29 -> 31 [label=\"output_h5ad\"]\n  k1e9f229deb344a5ba6d9e70c7b0581f4[color=lightseagreen,label=\"Output\\nMarkers - genotype\"]\n  31 -> k1e9f229deb344a5ba6d9e70c7b0581f4\n  32[label=\"Scanpy PlotEmbed\"]\n  30 -> 32 [label=\"output_h5ad\"]\n  33[label=\"Scanpy PlotEmbed\"]\n  30 -> 33 [label=\"output_h5ad\"]\n  34[label=\"Manipulate AnnData\"]\n  30 -> 34 [label=\"output_h5ad\"]\n  35[label=\"Scanpy PlotEmbed\"]\n  30 -> 35 [label=\"output_h5ad\"]\n  36[label=\"Inspect AnnData\"]\n  30 -> 36 [label=\"output_h5ad\"]\n  37[label=\"AnnData Operations\"]\n  34 -> 37 [label=\"anndata\"]\n  30 -> 37 [label=\"output_h5ad\"]\n  38[label=\"Join two Datasets\"]\n  30 -> 38 [label=\"output_tsv\"]\n  36 -> 38 [label=\"var\"]\n  39[label=\"Join two Datasets\"]\n  31 -> 39 [label=\"output_tsv\"]\n  36 -> 39 [label=\"var\"]\n  40[label=\"AnnData Operations\"]\n  37 -> 40 [label=\"output_h5ad\"]\n  k10bd70f8ffcb442b9647e5b947b6d35e[color=lightseagreen,label=\"Output\\nFinal cell annotated object\"]\n  40 -> k10bd70f8ffcb442b9647e5b947b6d35e\n  41[label=\"Cut\"]\n  38 -> 41 [label=\"out_file1\"]\n  k4f822c1c91c54be48f9bd5bdda0a037e[color=lightseagreen,label=\"Output\\nMarkers - cluster - named\"]\n  41 -> k4f822c1c91c54be48f9bd5bdda0a037e\n  42[label=\"Cut\"]\n  39 -> 42 [label=\"out_file1\"]\n  k3b471f3d263d42999b7d8a8ae1aa556e[color=lightseagreen,label=\"Output\\nMarkers - genotype - named\"]\n  42 -> k3b471f3d263d42999b7d8a8ae1aa556e\n  43[label=\"Scanpy PlotEmbed\"]\n  40 -> 43 [label=\"output_h5ad\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMito-counted AnnData\"]\n  1[label=\"Inspect AnnData\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Scanpy FilterCells\"]\n  0 -> 2 [label=\"output\"]\n  k08175d7ff4f4413cad86f59587ff692e[color=lightseagreen,label=\"Output\\nGenes-filtered Object\"]\n  2 -> k08175d7ff4f4413cad86f59587ff692e\n  3[label=\"Plot\"]\n  0 -> 3 [label=\"output\"]\n  kbfc499ee630a498b9be6696d9bb78837[color=lightseagreen,label=\"Output\\nScatter - genes x UMIs\"]\n  3 -> kbfc499ee630a498b9be6696d9bb78837\n  4[label=\"Plot\"]\n  0 -> 4 [label=\"output\"]\n  kf2c78ef37d314930954c0133cce27a41[color=lightseagreen,label=\"Output\\nScatter - mito x genes\"]\n  4 -> kf2c78ef37d314930954c0133cce27a41\n  5[label=\"Plot\"]\n  0 -> 5 [label=\"output\"]\n  k348818e69def41fda3906f8525c57cd8[color=lightseagreen,label=\"Output\\nViolin - genotype - log\"]\n  5 -> k348818e69def41fda3906f8525c57cd8\n  6[label=\"Plot\"]\n  0 -> 6 [label=\"output\"]\n  k844f5e7c78c84f288e15cea35ada8fef[color=lightseagreen,label=\"Output\\nViolin - batch - log\"]\n  6 -> k844f5e7c78c84f288e15cea35ada8fef\n  7[label=\"Inspect AnnData\"]\n  0 -> 7 [label=\"output\"]\n  8[label=\"Plot\"]\n  0 -> 8 [label=\"output\"]\n  k3b1232c5d16a434d806e79fd77f7c05f[color=lightseagreen,label=\"Output\\nScatter - mito x UMIs\"]\n  8 -> k3b1232c5d16a434d806e79fd77f7c05f\n  9[label=\"Inspect AnnData\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"Plot\"]\n  0 -> 10 [label=\"output\"]\n  ka639cdc0da404df9834823117528b24a[color=lightseagreen,label=\"Output\\nViolin - sex - log\"]\n  10 -> ka639cdc0da404df9834823117528b24a\n  11[label=\"Plot\"]\n  2 -> 11 [label=\"output_h5ad\"]\n  k69bf3e4263e24b5b9d635aac9d6b5691[color=lightseagreen,label=\"Output\\nViolin - Filterbygenes\"]\n  11 -> k69bf3e4263e24b5b9d635aac9d6b5691\n  12[label=\"Scanpy FilterCells\"]\n  2 -> 12 [label=\"output_h5ad\"]\n  kf378cb4e0a7749d9b92a752dbea4b09a[color=lightseagreen,label=\"Output\\nCounts-filtered Object\"]\n  12 -> kf378cb4e0a7749d9b92a752dbea4b09a\n  13[label=\"Inspect AnnData\"]\n  2 -> 13 [label=\"output_h5ad\"]\n  kf9e862dbeb2241248fe00fdcfcfb8393[color=lightseagreen,label=\"Output\\nGeneral - Filterbygenes\"]\n  13 -> kf9e862dbeb2241248fe00fdcfcfb8393\n  14[label=\"Inspect AnnData\"]\n  12 -> 14 [label=\"output_h5ad\"]\n  k794f72b5c2c346a0ac15b9f1e94941d2[color=lightseagreen,label=\"Output\\nGeneral - Filterbycounts\"]\n  14 -> k794f72b5c2c346a0ac15b9f1e94941d2\n  15[label=\"Scanpy FilterCells\"]\n  12 -> 15 [label=\"output_h5ad\"]\n  kb915da6664354871baa03e494ba73c96[color=lightseagreen,label=\"Output\\nMito-filtered Object\"]\n  15 -> kb915da6664354871baa03e494ba73c96\n  16[label=\"Plot\"]\n  12 -> 16 [label=\"output_h5ad\"]\n  k3aef86d7d34d4b24bc97bf8c97d8d2fa[color=lightseagreen,label=\"Output\\nViolin - Filterbycounts\"]\n  16 -> k3aef86d7d34d4b24bc97bf8c97d8d2fa\n  17[label=\"Inspect AnnData\"]\n  15 -> 17 [label=\"output_h5ad\"]\n  kcd94a4c656654bdf88ea4f4d41efa893[color=lightseagreen,label=\"Output\\nGeneral - Filterbymito\"]\n  17 -> kcd94a4c656654bdf88ea4f4d41efa893\n  18[label=\"Scanpy FilterGenes\"]\n  15 -> 18 [label=\"output_h5ad\"]\n  kee63ef0a98ed45cbb1441154f84ae452[color=lightseagreen,label=\"Output\\nFiltered Object\"]\n  18 -> kee63ef0a98ed45cbb1441154f84ae452\n  19[label=\"Plot\"]\n  15 -> 19 [label=\"output_h5ad\"]\n  k7e48a14f08fd45abb613606bf64dcf9d[color=lightseagreen,label=\"Output\\nViolin - Filterbymito\"]\n  19 -> k7e48a14f08fd45abb613606bf64dcf9d\n  20[label=\"Inspect AnnData\"]\n  18 -> 20 [label=\"output_h5ad\"]\n  kd59efa9bd0494f0e8bd88ae982a45d0a[color=lightseagreen,label=\"Output\\nGeneral - Filtered object\"]\n  20 -> kd59efa9bd0494f0e8bd88ae982a45d0a\n  21[label=\"Scanpy NormaliseData\"]\n  18 -> 21 [label=\"output_h5ad\"]\n  22[label=\"Scanpy FindVariableGenes\"]\n  21 -> 22 [label=\"output_h5ad\"]\n  23[label=\"Scanpy ScaleData\"]\n  22 -> 23 [label=\"output_h5ad\"]\n  24[label=\"Scanpy RunPCA\"]\n  23 -> 24 [label=\"output_h5ad\"]\n  25[label=\"Plot\"]\n  24 -> 25 [label=\"output_h5ad\"]\n  k993dea99990f460abeb946e5c97ee898[color=lightseagreen,label=\"Output\\nPCA Variance\"]\n  25 -> k993dea99990f460abeb946e5c97ee898\n  26[label=\"Scanpy ComputeGraph\"]\n  24 -> 26 [label=\"output_h5ad\"]\n  27[label=\"Scanpy RunTSNE\"]\n  26 -> 27 [label=\"output_h5ad\"]\n  28[label=\"Scanpy RunUMAP\"]\n  27 -> 28 [label=\"output_h5ad\"]\n  29[label=\"Scanpy FindCluster\"]\n  28 -> 29 [label=\"output_h5ad\"]\n  30[label=\"Scanpy FindMarkers\"]\n  29 -> 30 [label=\"output_h5ad\"]\n  k308b49614d50442b9bcabbb1992426ba[color=lightseagreen,label=\"Output\\nMarkers - cluster\"]\n  30 -> k308b49614d50442b9bcabbb1992426ba\n  k035bbbcefb5748c883d52b0cd0376541[color=lightseagreen,label=\"Output\\nFinal object\"]\n  30 -> k035bbbcefb5748c883d52b0cd0376541\n  31[label=\"Scanpy FindMarkers\"]\n  29 -> 31 [label=\"output_h5ad\"]\n  k1705e219192a4f529b2664fcbcd303ea[color=lightseagreen,label=\"Output\\nMarkers - genotype\"]\n  31 -> k1705e219192a4f529b2664fcbcd303ea\n  32[label=\"Scanpy PlotEmbed\"]\n  30 -> 32 [label=\"output_h5ad\"]\n  33[label=\"Scanpy PlotEmbed\"]\n  30 -> 33 [label=\"output_h5ad\"]\n  34[label=\"Manipulate AnnData\"]\n  30 -> 34 [label=\"output_h5ad\"]\n  35[label=\"Scanpy PlotEmbed\"]\n  30 -> 35 [label=\"output_h5ad\"]\n  36[label=\"Inspect AnnData\"]\n  30 -> 36 [label=\"output_h5ad\"]\n  37[label=\"AnnData Operations\"]\n  34 -> 37 [label=\"anndata\"]\n  30 -> 37 [label=\"output_h5ad\"]\n  38[label=\"Join two Datasets\"]\n  30 -> 38 [label=\"output_tsv\"]\n  36 -> 38 [label=\"var\"]\n  39[label=\"Join two Datasets\"]\n  31 -> 39 [label=\"output_tsv\"]\n  36 -> 39 [label=\"var\"]\n  40[label=\"AnnData Operations\"]\n  37 -> 40 [label=\"output_h5ad\"]\n  ka6d48df0403f4efca75f9504a960884e[color=lightseagreen,label=\"Output\\nFinal cell annotated object\"]\n  40 -> ka6d48df0403f4efca75f9504a960884e\n  41[label=\"Cut\"]\n  38 -> 41 [label=\"out_file1\"]\n  k0ee7f9b6b0654e2693df6e6e2fe458a9[color=lightseagreen,label=\"Output\\nMarkers - cluster - named\"]\n  41 -> k0ee7f9b6b0654e2693df6e6e2fe458a9\n  42[label=\"Cut\"]\n  39 -> 42 [label=\"out_file1\"]\n  kfdb88faa9b764edbb89b427c098a473e[color=lightseagreen,label=\"Output\\nMarkers - genotype - named\"]\n  42 -> kfdb88faa9b764edbb89b427c098a473e\n  43[label=\"Scanpy PlotEmbed\"]\n  40 -> 43 [label=\"output_h5ad\"]\n}",
                 "history": [
                     {
-                        "hash": "9a3fc8a6dad6c8d1b7b9897056cc75af00a12c57",
-                        "message": "new workflow tests",
+                        "hash": "327fd2b842f45de3dc2a30067714352675ad69ae",
+                        "message": "Making a single cell topics",
                         "num": 1,
-                        "short_hash": "9a3fc8a6d",
-                        "unix": "1686345087"
+                        "short_hash": "327fd2b84",
+                        "unix": "1668273265"
                     }
                 ],
                 "inputs": [
@@ -232613,21 +238197,20 @@
                         "outputs": [],
                         "position": {
                             "left": 0,
-                            "top": 761.9687652587891
+                            "top": 736.1875
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "1d8303cb-de77-4164-923c-127a4e60d8e6",
-                        "when": null,
+                        "uuid": "60316d4a-07b0-4eea-a889-eef54798c5e0",
                         "workflow_outputs": []
                     }
                 ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nMito-counted AnnData\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Inspect AnnData\"];\n  0 -->|output| 1;\n  2[\"Scanpy FilterCells\"];\n  0 -->|output| 2;\n  6a00b14b-d3f8-4771-963a-76115c8eaf2f[\"Output\\nGenes-filtered Object\"];\n  2 --> 6a00b14b-d3f8-4771-963a-76115c8eaf2f;\n  style 6a00b14b-d3f8-4771-963a-76115c8eaf2f stroke:#2c3143,stroke-width:4px;\n  3[\"Plot\"];\n  0 -->|output| 3;\n  c123842e-b2d2-43ad-81f0-6ba3b45d4021[\"Output\\nScatter - genes x UMIs\"];\n  3 --> c123842e-b2d2-43ad-81f0-6ba3b45d4021;\n  style c123842e-b2d2-43ad-81f0-6ba3b45d4021 stroke:#2c3143,stroke-width:4px;\n  4[\"Plot\"];\n  0 -->|output| 4;\n  f1020d4d-555e-42fa-ba21-52a151b91a5b[\"Output\\nScatter - mito x genes\"];\n  4 --> f1020d4d-555e-42fa-ba21-52a151b91a5b;\n  style f1020d4d-555e-42fa-ba21-52a151b91a5b stroke:#2c3143,stroke-width:4px;\n  5[\"Plot\"];\n  0 -->|output| 5;\n  a7fe6020-8f1e-470a-9ed3-f2b5e95516e0[\"Output\\nViolin - genotype - log\"];\n  5 --> a7fe6020-8f1e-470a-9ed3-f2b5e95516e0;\n  style a7fe6020-8f1e-470a-9ed3-f2b5e95516e0 stroke:#2c3143,stroke-width:4px;\n  6[\"Plot\"];\n  0 -->|output| 6;\n  15e501bc-8ddb-4519-89eb-dde431ea96c1[\"Output\\nViolin - batch - log\"];\n  6 --> 15e501bc-8ddb-4519-89eb-dde431ea96c1;\n  style 15e501bc-8ddb-4519-89eb-dde431ea96c1 stroke:#2c3143,stroke-width:4px;\n  7[\"Inspect AnnData\"];\n  0 -->|output| 7;\n  8[\"Plot\"];\n  0 -->|output| 8;\n  eff22f46-baa6-4e00-ba82-d5e12ce26ff0[\"Output\\nScatter - mito x UMIs\"];\n  8 --> eff22f46-baa6-4e00-ba82-d5e12ce26ff0;\n  style eff22f46-baa6-4e00-ba82-d5e12ce26ff0 stroke:#2c3143,stroke-width:4px;\n  9[\"Inspect AnnData\"];\n  0 -->|output| 9;\n  10[\"Plot\"];\n  0 -->|output| 10;\n  56677ca4-129c-476c-85ec-69d1bb3d800d[\"Output\\nViolin - sex - log\"];\n  10 --> 56677ca4-129c-476c-85ec-69d1bb3d800d;\n  style 56677ca4-129c-476c-85ec-69d1bb3d800d stroke:#2c3143,stroke-width:4px;\n  11[\"Plot\"];\n  2 -->|output_h5ad| 11;\n  acb61ea4-bcb9-45db-beef-e2bf1a176701[\"Output\\nViolin - Filterbygenes\"];\n  11 --> acb61ea4-bcb9-45db-beef-e2bf1a176701;\n  style acb61ea4-bcb9-45db-beef-e2bf1a176701 stroke:#2c3143,stroke-width:4px;\n  12[\"Scanpy FilterCells\"];\n  2 -->|output_h5ad| 12;\n  51853662-4519-4229-a2ea-b22a53e7ef73[\"Output\\nCounts-filtered Object\"];\n  12 --> 51853662-4519-4229-a2ea-b22a53e7ef73;\n  style 51853662-4519-4229-a2ea-b22a53e7ef73 stroke:#2c3143,stroke-width:4px;\n  13[\"Inspect AnnData\"];\n  2 -->|output_h5ad| 13;\n  362a7fe6-24bb-4398-ae48-870f4b4bb774[\"Output\\nGeneral - Filterbygenes\"];\n  13 --> 362a7fe6-24bb-4398-ae48-870f4b4bb774;\n  style 362a7fe6-24bb-4398-ae48-870f4b4bb774 stroke:#2c3143,stroke-width:4px;\n  14[\"Inspect AnnData\"];\n  12 -->|output_h5ad| 14;\n  edf24149-9341-4fe7-b10c-3fcf092faaa5[\"Output\\nGeneral - Filterbycounts\"];\n  14 --> edf24149-9341-4fe7-b10c-3fcf092faaa5;\n  style edf24149-9341-4fe7-b10c-3fcf092faaa5 stroke:#2c3143,stroke-width:4px;\n  15[\"Scanpy FilterCells\"];\n  12 -->|output_h5ad| 15;\n  a88ec405-265f-4a59-a75e-34e3b05b0096[\"Output\\nMito-filtered Object\"];\n  15 --> a88ec405-265f-4a59-a75e-34e3b05b0096;\n  style a88ec405-265f-4a59-a75e-34e3b05b0096 stroke:#2c3143,stroke-width:4px;\n  16[\"Plot\"];\n  12 -->|output_h5ad| 16;\n  a7c8b0d9-82d3-4438-a212-b5f7c56d36b8[\"Output\\nViolin - Filterbycounts\"];\n  16 --> a7c8b0d9-82d3-4438-a212-b5f7c56d36b8;\n  style a7c8b0d9-82d3-4438-a212-b5f7c56d36b8 stroke:#2c3143,stroke-width:4px;\n  17[\"Inspect AnnData\"];\n  15 -->|output_h5ad| 17;\n  56882809-e19f-451a-8010-bc55dcee482f[\"Output\\nGeneral - Filterbymito\"];\n  17 --> 56882809-e19f-451a-8010-bc55dcee482f;\n  style 56882809-e19f-451a-8010-bc55dcee482f stroke:#2c3143,stroke-width:4px;\n  18[\"Scanpy FilterGenes\"];\n  15 -->|output_h5ad| 18;\n  00846477-dec5-408a-83b2-105fff7ce05b[\"Output\\nFiltered Object\"];\n  18 --> 00846477-dec5-408a-83b2-105fff7ce05b;\n  style 00846477-dec5-408a-83b2-105fff7ce05b stroke:#2c3143,stroke-width:4px;\n  19[\"Plot\"];\n  15 -->|output_h5ad| 19;\n  7582e113-2004-4255-a1f3-d3123373f342[\"Output\\nViolin - Filterbymito\"];\n  19 --> 7582e113-2004-4255-a1f3-d3123373f342;\n  style 7582e113-2004-4255-a1f3-d3123373f342 stroke:#2c3143,stroke-width:4px;\n  20[\"Inspect AnnData\"];\n  18 -->|output_h5ad| 20;\n  2d870a40-c602-4a1c-afef-450489354d39[\"Output\\nGeneral - Filtered object\"];\n  20 --> 2d870a40-c602-4a1c-afef-450489354d39;\n  style 2d870a40-c602-4a1c-afef-450489354d39 stroke:#2c3143,stroke-width:4px;\n  21[\"Scanpy NormaliseData\"];\n  18 -->|output_h5ad| 21;\n  22[\"Scanpy FindVariableGenes\"];\n  21 -->|output_h5ad| 22;\n  a0eb92b1-0263-4179-b7af-4bd9bcc9c960[\"Output\\nUse_me_FVG\"];\n  22 --> a0eb92b1-0263-4179-b7af-4bd9bcc9c960;\n  style a0eb92b1-0263-4179-b7af-4bd9bcc9c960 stroke:#2c3143,stroke-width:4px;\n  23[\"Scanpy ScaleData\"];\n  22 -->|output_h5ad| 23;\n  5776dbb9-0cac-40c0-9bae-9accae16a7a0[\"Output\\nUse_me_Scaled\"];\n  23 --> 5776dbb9-0cac-40c0-9bae-9accae16a7a0;\n  style 5776dbb9-0cac-40c0-9bae-9accae16a7a0 stroke:#2c3143,stroke-width:4px;\n  24[\"Scanpy RunPCA\"];\n  23 -->|output_h5ad| 24;\n  25[\"Plot\"];\n  24 -->|output_h5ad| 25;\n  f0b6f578-050f-4936-9ee7-9956b0760c6f[\"Output\\nPCA Variance\"];\n  25 --> f0b6f578-050f-4936-9ee7-9956b0760c6f;\n  style f0b6f578-050f-4936-9ee7-9956b0760c6f stroke:#2c3143,stroke-width:4px;\n  26[\"Scanpy ComputeGraph\"];\n  24 -->|output_h5ad| 26;\n  27[\"Scanpy RunTSNE\"];\n  26 -->|output_h5ad| 27;\n  28[\"Scanpy RunUMAP\"];\n  27 -->|output_h5ad| 28;\n  29[\"Scanpy FindCluster\"];\n  28 -->|output_h5ad| 29;\n  30[\"Scanpy FindMarkers\"];\n  29 -->|output_h5ad| 30;\n  7cfe5c9c-1c80-41b4-b669-633b1d7d40e3[\"Output\\nMarkers - cluster\"];\n  30 --> 7cfe5c9c-1c80-41b4-b669-633b1d7d40e3;\n  style 7cfe5c9c-1c80-41b4-b669-633b1d7d40e3 stroke:#2c3143,stroke-width:4px;\n  98e98405-951e-4c6c-be01-3c925ae35449[\"Output\\nFinal object\"];\n  30 --> 98e98405-951e-4c6c-be01-3c925ae35449;\n  style 98e98405-951e-4c6c-be01-3c925ae35449 stroke:#2c3143,stroke-width:4px;\n  31[\"Scanpy FindMarkers\"];\n  29 -->|output_h5ad| 31;\n  1e9f229d-eb34-4a5b-a6d9-e70c7b0581f4[\"Output\\nMarkers - genotype\"];\n  31 --> 1e9f229d-eb34-4a5b-a6d9-e70c7b0581f4;\n  style 1e9f229d-eb34-4a5b-a6d9-e70c7b0581f4 stroke:#2c3143,stroke-width:4px;\n  32[\"Scanpy PlotEmbed\"];\n  30 -->|output_h5ad| 32;\n  33[\"Scanpy PlotEmbed\"];\n  30 -->|output_h5ad| 33;\n  34[\"Manipulate AnnData\"];\n  30 -->|output_h5ad| 34;\n  35[\"Scanpy PlotEmbed\"];\n  30 -->|output_h5ad| 35;\n  36[\"Inspect AnnData\"];\n  30 -->|output_h5ad| 36;\n  37[\"AnnData Operations\"];\n  34 -->|anndata| 37;\n  30 -->|output_h5ad| 37;\n  38[\"Join two Datasets\"];\n  30 -->|output_tsv| 38;\n  36 -->|var| 38;\n  39[\"Join two Datasets\"];\n  31 -->|output_tsv| 39;\n  36 -->|var| 39;\n  40[\"AnnData Operations\"];\n  37 -->|output_h5ad| 40;\n  10bd70f8-ffcb-442b-9647-e5b947b6d35e[\"Output\\nFinal cell annotated object\"];\n  40 --> 10bd70f8-ffcb-442b-9647-e5b947b6d35e;\n  style 10bd70f8-ffcb-442b-9647-e5b947b6d35e stroke:#2c3143,stroke-width:4px;\n  41[\"Cut\"];\n  38 -->|out_file1| 41;\n  4f822c1c-91c5-4be4-8f9b-d5bdda0a037e[\"Output\\nMarkers - cluster - named\"];\n  41 --> 4f822c1c-91c5-4be4-8f9b-d5bdda0a037e;\n  style 4f822c1c-91c5-4be4-8f9b-d5bdda0a037e stroke:#2c3143,stroke-width:4px;\n  42[\"Cut\"];\n  39 -->|out_file1| 42;\n  3b471f3d-263d-4299-9b7d-8a8ae1aa556e[\"Output\\nMarkers - genotype - named\"];\n  42 --> 3b471f3d-263d-4299-9b7d-8a8ae1aa556e;\n  style 3b471f3d-263d-4299-9b7d-8a8ae1aa556e stroke:#2c3143,stroke-width:4px;\n  43[\"Scanpy PlotEmbed\"];\n  40 -->|output_h5ad| 43;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Filter, Plot and Explore Single-cell RNA-seq Data updated",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nMito-counted AnnData\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Inspect AnnData\"];\n  0 -->|output| 1;\n  2[\"Scanpy FilterCells\"];\n  0 -->|output| 2;\n  08175d7f-f4f4-413c-ad86-f59587ff692e[\"Output\\nGenes-filtered Object\"];\n  2 --> 08175d7f-f4f4-413c-ad86-f59587ff692e;\n  style 08175d7f-f4f4-413c-ad86-f59587ff692e stroke:#2c3143,stroke-width:4px;\n  3[\"Plot\"];\n  0 -->|output| 3;\n  bfc499ee-630a-498b-9be6-696d9bb78837[\"Output\\nScatter - genes x UMIs\"];\n  3 --> bfc499ee-630a-498b-9be6-696d9bb78837;\n  style bfc499ee-630a-498b-9be6-696d9bb78837 stroke:#2c3143,stroke-width:4px;\n  4[\"Plot\"];\n  0 -->|output| 4;\n  f2c78ef3-7d31-4930-954c-0133cce27a41[\"Output\\nScatter - mito x genes\"];\n  4 --> f2c78ef3-7d31-4930-954c-0133cce27a41;\n  style f2c78ef3-7d31-4930-954c-0133cce27a41 stroke:#2c3143,stroke-width:4px;\n  5[\"Plot\"];\n  0 -->|output| 5;\n  348818e6-9def-41fd-a390-6f8525c57cd8[\"Output\\nViolin - genotype - log\"];\n  5 --> 348818e6-9def-41fd-a390-6f8525c57cd8;\n  style 348818e6-9def-41fd-a390-6f8525c57cd8 stroke:#2c3143,stroke-width:4px;\n  6[\"Plot\"];\n  0 -->|output| 6;\n  844f5e7c-78c8-4f28-8e15-cea35ada8fef[\"Output\\nViolin - batch - log\"];\n  6 --> 844f5e7c-78c8-4f28-8e15-cea35ada8fef;\n  style 844f5e7c-78c8-4f28-8e15-cea35ada8fef stroke:#2c3143,stroke-width:4px;\n  7[\"Inspect AnnData\"];\n  0 -->|output| 7;\n  8[\"Plot\"];\n  0 -->|output| 8;\n  3b1232c5-d16a-434d-806e-79fd77f7c05f[\"Output\\nScatter - mito x UMIs\"];\n  8 --> 3b1232c5-d16a-434d-806e-79fd77f7c05f;\n  style 3b1232c5-d16a-434d-806e-79fd77f7c05f stroke:#2c3143,stroke-width:4px;\n  9[\"Inspect AnnData\"];\n  0 -->|output| 9;\n  10[\"Plot\"];\n  0 -->|output| 10;\n  a639cdc0-da40-4df9-8348-23117528b24a[\"Output\\nViolin - sex - log\"];\n  10 --> a639cdc0-da40-4df9-8348-23117528b24a;\n  style a639cdc0-da40-4df9-8348-23117528b24a stroke:#2c3143,stroke-width:4px;\n  11[\"Plot\"];\n  2 -->|output_h5ad| 11;\n  69bf3e42-63e2-4b5b-9d63-5aac9d6b5691[\"Output\\nViolin - Filterbygenes\"];\n  11 --> 69bf3e42-63e2-4b5b-9d63-5aac9d6b5691;\n  style 69bf3e42-63e2-4b5b-9d63-5aac9d6b5691 stroke:#2c3143,stroke-width:4px;\n  12[\"Scanpy FilterCells\"];\n  2 -->|output_h5ad| 12;\n  f378cb4e-0a77-49d9-b92a-752dbea4b09a[\"Output\\nCounts-filtered Object\"];\n  12 --> f378cb4e-0a77-49d9-b92a-752dbea4b09a;\n  style f378cb4e-0a77-49d9-b92a-752dbea4b09a stroke:#2c3143,stroke-width:4px;\n  13[\"Inspect AnnData\"];\n  2 -->|output_h5ad| 13;\n  f9e862db-eb22-4124-8fe0-0fdcfcfb8393[\"Output\\nGeneral - Filterbygenes\"];\n  13 --> f9e862db-eb22-4124-8fe0-0fdcfcfb8393;\n  style f9e862db-eb22-4124-8fe0-0fdcfcfb8393 stroke:#2c3143,stroke-width:4px;\n  14[\"Inspect AnnData\"];\n  12 -->|output_h5ad| 14;\n  794f72b5-c2c3-46a0-ac15-b9f1e94941d2[\"Output\\nGeneral - Filterbycounts\"];\n  14 --> 794f72b5-c2c3-46a0-ac15-b9f1e94941d2;\n  style 794f72b5-c2c3-46a0-ac15-b9f1e94941d2 stroke:#2c3143,stroke-width:4px;\n  15[\"Scanpy FilterCells\"];\n  12 -->|output_h5ad| 15;\n  b915da66-6435-4871-baa0-3e494ba73c96[\"Output\\nMito-filtered Object\"];\n  15 --> b915da66-6435-4871-baa0-3e494ba73c96;\n  style b915da66-6435-4871-baa0-3e494ba73c96 stroke:#2c3143,stroke-width:4px;\n  16[\"Plot\"];\n  12 -->|output_h5ad| 16;\n  3aef86d7-d34d-4b24-bc97-bf8c97d8d2fa[\"Output\\nViolin - Filterbycounts\"];\n  16 --> 3aef86d7-d34d-4b24-bc97-bf8c97d8d2fa;\n  style 3aef86d7-d34d-4b24-bc97-bf8c97d8d2fa stroke:#2c3143,stroke-width:4px;\n  17[\"Inspect AnnData\"];\n  15 -->|output_h5ad| 17;\n  cd94a4c6-5665-4bdf-88ea-4f4d41efa893[\"Output\\nGeneral - Filterbymito\"];\n  17 --> cd94a4c6-5665-4bdf-88ea-4f4d41efa893;\n  style cd94a4c6-5665-4bdf-88ea-4f4d41efa893 stroke:#2c3143,stroke-width:4px;\n  18[\"Scanpy FilterGenes\"];\n  15 -->|output_h5ad| 18;\n  ee63ef0a-98ed-45cb-b144-1154f84ae452[\"Output\\nFiltered Object\"];\n  18 --> ee63ef0a-98ed-45cb-b144-1154f84ae452;\n  style ee63ef0a-98ed-45cb-b144-1154f84ae452 stroke:#2c3143,stroke-width:4px;\n  19[\"Plot\"];\n  15 -->|output_h5ad| 19;\n  7e48a14f-08fd-45ab-b613-606bf64dcf9d[\"Output\\nViolin - Filterbymito\"];\n  19 --> 7e48a14f-08fd-45ab-b613-606bf64dcf9d;\n  style 7e48a14f-08fd-45ab-b613-606bf64dcf9d stroke:#2c3143,stroke-width:4px;\n  20[\"Inspect AnnData\"];\n  18 -->|output_h5ad| 20;\n  d59efa9b-d049-4f0e-8bd8-8ae982a45d0a[\"Output\\nGeneral - Filtered object\"];\n  20 --> d59efa9b-d049-4f0e-8bd8-8ae982a45d0a;\n  style d59efa9b-d049-4f0e-8bd8-8ae982a45d0a stroke:#2c3143,stroke-width:4px;\n  21[\"Scanpy NormaliseData\"];\n  18 -->|output_h5ad| 21;\n  22[\"Scanpy FindVariableGenes\"];\n  21 -->|output_h5ad| 22;\n  23[\"Scanpy ScaleData\"];\n  22 -->|output_h5ad| 23;\n  24[\"Scanpy RunPCA\"];\n  23 -->|output_h5ad| 24;\n  25[\"Plot\"];\n  24 -->|output_h5ad| 25;\n  993dea99-990f-460a-beb9-46e5c97ee898[\"Output\\nPCA Variance\"];\n  25 --> 993dea99-990f-460a-beb9-46e5c97ee898;\n  style 993dea99-990f-460a-beb9-46e5c97ee898 stroke:#2c3143,stroke-width:4px;\n  26[\"Scanpy ComputeGraph\"];\n  24 -->|output_h5ad| 26;\n  27[\"Scanpy RunTSNE\"];\n  26 -->|output_h5ad| 27;\n  28[\"Scanpy RunUMAP\"];\n  27 -->|output_h5ad| 28;\n  29[\"Scanpy FindCluster\"];\n  28 -->|output_h5ad| 29;\n  30[\"Scanpy FindMarkers\"];\n  29 -->|output_h5ad| 30;\n  308b4961-4d50-442b-9bca-bbb1992426ba[\"Output\\nMarkers - cluster\"];\n  30 --> 308b4961-4d50-442b-9bca-bbb1992426ba;\n  style 308b4961-4d50-442b-9bca-bbb1992426ba stroke:#2c3143,stroke-width:4px;\n  035bbbce-fb57-48c8-83d5-2b0cd0376541[\"Output\\nFinal object\"];\n  30 --> 035bbbce-fb57-48c8-83d5-2b0cd0376541;\n  style 035bbbce-fb57-48c8-83d5-2b0cd0376541 stroke:#2c3143,stroke-width:4px;\n  31[\"Scanpy FindMarkers\"];\n  29 -->|output_h5ad| 31;\n  1705e219-192a-4f52-9b26-64fcbcd303ea[\"Output\\nMarkers - genotype\"];\n  31 --> 1705e219-192a-4f52-9b26-64fcbcd303ea;\n  style 1705e219-192a-4f52-9b26-64fcbcd303ea stroke:#2c3143,stroke-width:4px;\n  32[\"Scanpy PlotEmbed\"];\n  30 -->|output_h5ad| 32;\n  33[\"Scanpy PlotEmbed\"];\n  30 -->|output_h5ad| 33;\n  34[\"Manipulate AnnData\"];\n  30 -->|output_h5ad| 34;\n  35[\"Scanpy PlotEmbed\"];\n  30 -->|output_h5ad| 35;\n  36[\"Inspect AnnData\"];\n  30 -->|output_h5ad| 36;\n  37[\"AnnData Operations\"];\n  34 -->|anndata| 37;\n  30 -->|output_h5ad| 37;\n  38[\"Join two Datasets\"];\n  30 -->|output_tsv| 38;\n  36 -->|var| 38;\n  39[\"Join two Datasets\"];\n  31 -->|output_tsv| 39;\n  36 -->|var| 39;\n  40[\"AnnData Operations\"];\n  37 -->|output_h5ad| 40;\n  a6d48df0-403f-4efc-a75f-9504a960884e[\"Output\\nFinal cell annotated object\"];\n  40 --> a6d48df0-403f-4efc-a75f-9504a960884e;\n  style a6d48df0-403f-4efc-a75f-9504a960884e stroke:#2c3143,stroke-width:4px;\n  41[\"Cut\"];\n  38 -->|out_file1| 41;\n  0ee7f9b6-b065-4e26-93df-6e6e2fe458a9[\"Output\\nMarkers - cluster - named\"];\n  41 --> 0ee7f9b6-b065-4e26-93df-6e6e2fe458a9;\n  style 0ee7f9b6-b065-4e26-93df-6e6e2fe458a9 stroke:#2c3143,stroke-width:4px;\n  42[\"Cut\"];\n  39 -->|out_file1| 42;\n  fdb88faa-9b76-4edb-b89b-427c098a473e[\"Output\\nMarkers - genotype - named\"];\n  42 --> fdb88faa-9b76-4edb-b89b-427c098a473e;\n  style fdb88faa-9b76-4edb-b89b-427c098a473e stroke:#2c3143,stroke-width:4px;\n  43[\"Scanpy PlotEmbed\"];\n  40 -->|output_h5ad| 43;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "CS3_Filter, Plot and Explore Single-cell RNA-seq Data",
                 "outputs": [
                     {
                         "annotation": "",
@@ -232650,8 +238233,8 @@
                             }
                         ],
                         "position": {
-                            "left": 277.87506103515625,
-                            "top": 46.953125
+                            "left": 277.8984375,
+                            "top": 21.0703125
                         },
                         "post_job_actions": {},
                         "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
@@ -232661,22 +238244,21 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"obs\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"__input_ext\": \"h5ad\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"obs\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "0.7.5+galaxy1",
                         "type": "tool",
-                        "uuid": "02ce9919-9e22-40cf-8d35-dd11bc87479d",
-                        "when": null,
+                        "uuid": "99ffbf79-3be8-4905-b978-e56b02327314",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "obs",
-                                "uuid": "71b6c011-cce0-476b-a468-ef4a8b6c3f2b"
+                                "uuid": "6e2bd8b0-8203-4dfe-9c28-054d863bd277"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0",
                         "errors": null,
                         "id": 2,
                         "input_connections": {
@@ -232695,8 +238277,8 @@
                             }
                         ],
                         "position": {
-                            "left": 277.87506103515625,
-                            "top": 264.01561737060547
+                            "left": 277.8984375,
+                            "top": 238.2421875
                         },
                         "post_job_actions": {
                             "RenameDatasetActionoutput_h5ad": {
@@ -232707,23 +238289,22 @@
                                 "output_name": "output_h5ad"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "e9283529cba1",
+                            "changeset_revision": "55ccc0a121bc",
                             "name": "scanpy_filter_cells",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"categories\": [], \"export_mtx\": false, \"force_recalc\": false, \"gene_name\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"parameters\": [{\"__index__\": 0, \"name\": \"log1p_n_genes_by_counts\", \"min\": \"5.7\", \"max\": \"20.0\"}], \"save_layer\": null, \"save_raw\": false, \"subsets\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"categories\": [], \"export_mtx\": \"false\", \"force_recalc\": \"false\", \"gene_name\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"parameters\": [{\"__index__\": 0, \"name\": \"log1p_n_genes_by_counts\", \"min\": \"5.7\", \"max\": \"20.0\"}], \"save_layer\": null, \"save_raw\": \"false\", \"subsets\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
                         "type": "tool",
-                        "uuid": "c7141742-50d6-4119-8e2e-827d3feb7cda",
-                        "when": null,
+                        "uuid": "ab02dab9-1c72-4987-929c-6b67baae1e6d",
                         "workflow_outputs": [
                             {
                                 "label": "Genes-filtered Object",
                                 "output_name": "output_h5ad",
-                                "uuid": "6a00b14b-d3f8-4771-963a-76115c8eaf2f"
+                                "uuid": "08175d7f-f4f4-413c-ad86-f59587ff692e"
                             }
                         ]
                     },
@@ -232748,8 +238329,8 @@
                             }
                         ],
                         "position": {
-                            "left": 277.87506103515625,
-                            "top": 460.0468444824219
+                            "left": 277.8984375,
+                            "top": 434.28125
                         },
                         "post_job_actions": {
                             "RenameDatasetActionout_png": {
@@ -232767,16 +238348,15 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.scatter\", \"__current_case__\": 0, \"type\": {\"type\": \"xy\", \"__current_case__\": 0, \"x\": \"log1p_total_counts\", \"y\": \"log1p_n_genes_by_counts\", \"color\": \"pct_counts_mito\", \"layers\": {\"use_layers\": \"false\", \"__current_case__\": 1}}, \"use_raw\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"color_map\": \"None\", \"palette\": \"default\", \"frameon\": true, \"size\": null, \"title\": \"\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.scatter\", \"__current_case__\": 0, \"type\": {\"type\": \"xy\", \"__current_case__\": 0, \"x\": \"log1p_total_counts\", \"y\": \"log1p_n_genes_by_counts\", \"color\": \"pct_counts_mito\", \"layers\": {\"use_layers\": \"false\", \"__current_case__\": 1}}, \"use_raw\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"color_map\": \"None\", \"palette\": \"default\", \"frameon\": \"true\", \"size\": null, \"title\": \"\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.7.1+galaxy1",
                         "type": "tool",
-                        "uuid": "f3193244-6053-47a5-89f9-eaa0993f3eca",
-                        "when": null,
+                        "uuid": "767da31e-dc80-4d11-9f8e-8b1589029dcc",
                         "workflow_outputs": [
                             {
                                 "label": "Scatter - genes x UMIs",
                                 "output_name": "out_png",
-                                "uuid": "c123842e-b2d2-43ad-81f0-6ba3b45d4021"
+                                "uuid": "bfc499ee-630a-498b-9be6-696d9bb78837"
                             }
                         ]
                     },
@@ -232801,8 +238381,8 @@
                             }
                         ],
                         "position": {
-                            "left": 277.87506103515625,
-                            "top": 614.0000152587891
+                            "left": 277.8984375,
+                            "top": 588.25
                         },
                         "post_job_actions": {
                             "RenameDatasetActionout_png": {
@@ -232820,16 +238400,15 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.scatter\", \"__current_case__\": 0, \"type\": {\"type\": \"xy\", \"__current_case__\": 0, \"x\": \"log1p_n_genes_by_counts\", \"y\": \"pct_counts_mito\", \"color\": \"\", \"layers\": {\"use_layers\": \"false\", \"__current_case__\": 1}}, \"use_raw\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"color_map\": \"None\", \"palette\": \"default\", \"frameon\": true, \"size\": null, \"title\": \"\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.scatter\", \"__current_case__\": 0, \"type\": {\"type\": \"xy\", \"__current_case__\": 0, \"x\": \"log1p_n_genes_by_counts\", \"y\": \"pct_counts_mito\", \"color\": \"\", \"layers\": {\"use_layers\": \"false\", \"__current_case__\": 1}}, \"use_raw\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"color_map\": \"None\", \"palette\": \"default\", \"frameon\": \"true\", \"size\": null, \"title\": \"\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.7.1+galaxy1",
                         "type": "tool",
-                        "uuid": "babba57e-e1e1-4af8-849e-7f1f88842b51",
-                        "when": null,
+                        "uuid": "ad0b1195-4bb2-46be-bb8a-8fd5de416372",
                         "workflow_outputs": [
                             {
                                 "label": "Scatter - mito x genes",
                                 "output_name": "out_png",
-                                "uuid": "f1020d4d-555e-42fa-ba21-52a151b91a5b"
+                                "uuid": "f2c78ef3-7d31-4930-954c-0133cce27a41"
                             }
                         ]
                     },
@@ -232854,8 +238433,8 @@
                             }
                         ],
                         "position": {
-                            "left": 278.98952554536163,
-                            "top": 768.0374811275927
+                            "left": 277.8984375,
+                            "top": 742.28125
                         },
                         "post_job_actions": {
                             "RenameDatasetActionout_png": {
@@ -232873,16 +238452,15 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"genotype\", \"log\": false, \"use_raw\": false, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"genotype\", \"log\": \"false\", \"use_raw\": \"false\", \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.7.1+galaxy1",
                         "type": "tool",
-                        "uuid": "a7b1206d-c867-4ffa-bc48-a7bd311b4cfb",
-                        "when": null,
+                        "uuid": "a6a5b2f9-9765-4f5d-b4cf-7c513b8eed3c",
                         "workflow_outputs": [
                             {
                                 "label": "Violin - genotype - log",
                                 "output_name": "out_png",
-                                "uuid": "a7fe6020-8f1e-470a-9ed3-f2b5e95516e0"
+                                "uuid": "348818e6-9def-41fd-a390-6f8525c57cd8"
                             }
                         ]
                     },
@@ -232907,8 +238485,8 @@
                             }
                         ],
                         "position": {
-                            "left": 277.87506103515625,
-                            "top": 922.0468902587891
+                            "left": 277.8984375,
+                            "top": 896.3046875
                         },
                         "post_job_actions": {
                             "RenameDatasetActionout_png": {
@@ -232926,16 +238504,15 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"batch\", \"log\": false, \"use_raw\": false, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"batch\", \"log\": \"false\", \"use_raw\": \"false\", \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.7.1+galaxy1",
                         "type": "tool",
-                        "uuid": "43e45438-9dda-4e43-90e9-bbfead684d40",
-                        "when": null,
+                        "uuid": "a6d8ecf9-1510-4c1a-8665-ddf25b0ca395",
                         "workflow_outputs": [
                             {
                                 "label": "Violin - batch - log",
                                 "output_name": "out_png",
-                                "uuid": "15e501bc-8ddb-4519-89eb-dde431ea96c1"
+                                "uuid": "844f5e7c-78c8-4f28-8e15-cea35ada8fef"
                             }
                         ]
                     },
@@ -232960,8 +238537,8 @@
                             }
                         ],
                         "position": {
-                            "left": 277.8749630368968,
-                            "top": 1055.0375737787456
+                            "left": 277.8984375,
+                            "top": 1029.3046875
                         },
                         "post_job_actions": {},
                         "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
@@ -232971,16 +238548,15 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"var\", \"__current_case__\": 4}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"__input_ext\": \"h5ad\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"var\", \"__current_case__\": 4}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "0.7.5+galaxy1",
                         "type": "tool",
-                        "uuid": "52409dab-0f57-417a-9aa2-0d14923b8820",
-                        "when": null,
+                        "uuid": "9445c5ea-8c75-48f2-b7a1-fd0e43c625c7",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "var",
-                                "uuid": "70ea04da-1d7b-47fa-939e-d01258f6f81d"
+                                "uuid": "ba910718-a539-4b77-b3e8-087711e13eaf"
                             }
                         ]
                     },
@@ -233005,8 +238581,8 @@
                             }
                         ],
                         "position": {
-                            "left": 279.20030309822187,
-                            "top": 1293.0249965988953
+                            "left": 277.8984375,
+                            "top": 1267.2734375
                         },
                         "post_job_actions": {
                             "RenameDatasetActionout_png": {
@@ -233024,16 +238600,15 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.scatter\", \"__current_case__\": 0, \"type\": {\"type\": \"xy\", \"__current_case__\": 0, \"x\": \"log1p_total_counts\", \"y\": \"pct_counts_mito\", \"color\": \"\", \"layers\": {\"use_layers\": \"false\", \"__current_case__\": 1}}, \"use_raw\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"color_map\": \"None\", \"palette\": \"default\", \"frameon\": true, \"size\": null, \"title\": \"\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.scatter\", \"__current_case__\": 0, \"type\": {\"type\": \"xy\", \"__current_case__\": 0, \"x\": \"log1p_total_counts\", \"y\": \"pct_counts_mito\", \"color\": \"\", \"layers\": {\"use_layers\": \"false\", \"__current_case__\": 1}}, \"use_raw\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"color_map\": \"None\", \"palette\": \"default\", \"frameon\": \"true\", \"size\": null, \"title\": \"\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.7.1+galaxy1",
                         "type": "tool",
-                        "uuid": "fea33591-4efa-488d-873c-2ef9ec1ad6e5",
-                        "when": null,
+                        "uuid": "7225da9d-e700-49f7-bb78-20f2954872bd",
                         "workflow_outputs": [
                             {
                                 "label": "Scatter - mito x UMIs",
                                 "output_name": "out_png",
-                                "uuid": "eff22f46-baa6-4e00-ba82-d5e12ce26ff0"
+                                "uuid": "3b1232c5-d16a-434d-806e-79fd77f7c05f"
                             }
                         ]
                     },
@@ -233058,8 +238633,8 @@
                             }
                         ],
                         "position": {
-                            "left": 277.87506103515625,
-                            "top": 1447.0156860351562
+                            "left": 277.8984375,
+                            "top": 1421.234375
                         },
                         "post_job_actions": {},
                         "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
@@ -233069,16 +238644,15 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"general\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"__input_ext\": \"h5ad\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"general\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "0.7.5+galaxy1",
                         "type": "tool",
-                        "uuid": "a6a5e239-9708-4044-9104-596fb6f130e8",
-                        "when": null,
+                        "uuid": "549b599e-1b3d-4be4-bfe7-91c50cef7ef7",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "general",
-                                "uuid": "9ddf445d-8b0f-4ffd-b71a-81ff28deb4a1"
+                                "uuid": "8fbf3a0b-bf46-48ff-8f64-bb7018d51382"
                             }
                         ]
                     },
@@ -233103,8 +238677,8 @@
                             }
                         ],
                         "position": {
-                            "left": 276.53750483025266,
-                            "top": 1641.8978917275417
+                            "left": 277.8984375,
+                            "top": 1617.2109375
                         },
                         "post_job_actions": {
                             "RenameDatasetActionout_png": {
@@ -233122,16 +238696,15 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"sex\", \"log\": false, \"use_raw\": false, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"sex\", \"log\": \"false\", \"use_raw\": \"false\", \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.7.1+galaxy1",
                         "type": "tool",
-                        "uuid": "64a75bd5-b091-45c1-a8f0-007efd803c16",
-                        "when": null,
+                        "uuid": "d21d8d66-0488-4382-bed4-b8534c08169f",
                         "workflow_outputs": [
                             {
                                 "label": "Violin - sex - log",
                                 "output_name": "out_png",
-                                "uuid": "56677ca4-129c-476c-85ec-69d1bb3d800d"
+                                "uuid": "a639cdc0-da40-4df9-8348-23117528b24a"
                             }
                         ]
                     },
@@ -233156,8 +238729,8 @@
                             }
                         ],
                         "position": {
-                            "left": 555.9375,
-                            "top": 110.03124237060547
+                            "left": 555.9140625,
+                            "top": 84.2109375
                         },
                         "post_job_actions": {
                             "RenameDatasetActionout_png": {
@@ -233175,22 +238748,21 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"genotype\", \"log\": false, \"use_raw\": false, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"genotype\", \"log\": \"false\", \"use_raw\": \"false\", \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.7.1+galaxy1",
                         "type": "tool",
-                        "uuid": "6b3eb9a5-8014-497f-a3db-aea4a39080e9",
-                        "when": null,
+                        "uuid": "0ceca44a-91f3-4c85-8dfe-7c958c373fed",
                         "workflow_outputs": [
                             {
                                 "label": "Violin - Filterbygenes",
                                 "output_name": "out_png",
-                                "uuid": "acb61ea4-bcb9-45db-beef-e2bf1a176701"
+                                "uuid": "69bf3e42-63e2-4b5b-9d63-5aac9d6b5691"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0",
                         "errors": null,
                         "id": 12,
                         "input_connections": {
@@ -233209,8 +238781,8 @@
                             }
                         ],
                         "position": {
-                            "left": 555.9375,
-                            "top": 264.01561737060547
+                            "left": 555.9140625,
+                            "top": 238.2421875
                         },
                         "post_job_actions": {
                             "RenameDatasetActionoutput_h5ad": {
@@ -233221,23 +238793,22 @@
                                 "output_name": "output_h5ad"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "e9283529cba1",
+                            "changeset_revision": "55ccc0a121bc",
                             "name": "scanpy_filter_cells",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"categories\": [], \"export_mtx\": false, \"force_recalc\": false, \"gene_name\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"parameters\": [{\"__index__\": 0, \"name\": \"log1p_total_counts\", \"min\": \"6.3\", \"max\": \"20.0\"}], \"save_layer\": null, \"save_raw\": false, \"subsets\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"categories\": [], \"export_mtx\": \"false\", \"force_recalc\": \"false\", \"gene_name\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"parameters\": [{\"__index__\": 0, \"name\": \"log1p_total_counts\", \"min\": \"6.3\", \"max\": \"20.0\"}], \"save_layer\": null, \"save_raw\": \"false\", \"subsets\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
                         "type": "tool",
-                        "uuid": "64f0c049-6f2a-47ad-bb7b-1a9516fceca6",
-                        "when": null,
+                        "uuid": "2b612ba2-7539-43a7-963c-da6172101f1f",
                         "workflow_outputs": [
                             {
                                 "label": "Counts-filtered Object",
                                 "output_name": "output_h5ad",
-                                "uuid": "51853662-4519-4229-a2ea-b22a53e7ef73"
+                                "uuid": "f378cb4e-0a77-49d9-b92a-752dbea4b09a"
                             }
                         ]
                     },
@@ -233262,8 +238833,8 @@
                             }
                         ],
                         "position": {
-                            "left": 555.9375,
-                            "top": 460.0468444824219
+                            "left": 555.9140625,
+                            "top": 434.28125
                         },
                         "post_job_actions": {
                             "RenameDatasetActiongeneral": {
@@ -233284,13 +238855,12 @@
                         "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"general\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "0.7.5+galaxy1",
                         "type": "tool",
-                        "uuid": "9691c915-a455-4c55-89c4-129afc19842d",
-                        "when": null,
+                        "uuid": "47b02be1-43e4-4bd3-a20f-ebfeddd29ad0",
                         "workflow_outputs": [
                             {
                                 "label": "General - Filterbygenes",
                                 "output_name": "general",
-                                "uuid": "362a7fe6-24bb-4398-ae48-870f4b4bb774"
+                                "uuid": "f9e862db-eb22-4124-8fe0-0fdcfcfb8393"
                             }
                         ]
                     },
@@ -233315,8 +238885,8 @@
                             }
                         ],
                         "position": {
-                            "left": 833.9688110351562,
-                            "top": 89.03125762939453
+                            "left": 834.046875,
+                            "top": 63.21875
                         },
                         "post_job_actions": {
                             "RenameDatasetActiongeneral": {
@@ -233337,19 +238907,18 @@
                         "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"general\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "0.7.5+galaxy1",
                         "type": "tool",
-                        "uuid": "d0fc1afa-8f79-4ba7-bc94-c7a5bddb27e1",
-                        "when": null,
+                        "uuid": "85d4b86e-cff4-41bf-92d5-a4d53c72f950",
                         "workflow_outputs": [
                             {
                                 "label": "General - Filterbycounts",
                                 "output_name": "general",
-                                "uuid": "edf24149-9341-4fe7-b10c-3fcf092faaa5"
+                                "uuid": "794f72b5-c2c3-46a0-ac15-b9f1e94941d2"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0",
                         "errors": null,
                         "id": 15,
                         "input_connections": {
@@ -233368,8 +238937,8 @@
                             }
                         ],
                         "position": {
-                            "left": 835.0770432726613,
-                            "top": 264.01253840544547
+                            "left": 834.046875,
+                            "top": 238.2421875
                         },
                         "post_job_actions": {
                             "RenameDatasetActionoutput_h5ad": {
@@ -233380,23 +238949,22 @@
                                 "output_name": "output_h5ad"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "e9283529cba1",
+                            "changeset_revision": "55ccc0a121bc",
                             "name": "scanpy_filter_cells",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"categories\": [], \"export_mtx\": false, \"force_recalc\": false, \"gene_name\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"parameters\": [{\"__index__\": 0, \"name\": \"pct_counts_mito\", \"min\": \"0.0\", \"max\": \"4.5\"}], \"save_layer\": null, \"save_raw\": false, \"subsets\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"categories\": [], \"export_mtx\": \"false\", \"force_recalc\": \"false\", \"gene_name\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"parameters\": [{\"__index__\": 0, \"name\": \"pct_counts_mito\", \"min\": \"0.0\", \"max\": \"4.5\"}], \"save_layer\": null, \"save_raw\": \"false\", \"subsets\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
                         "type": "tool",
-                        "uuid": "ddab098e-c545-4eeb-865a-d728213832a2",
-                        "when": null,
+                        "uuid": "47ab6b8d-2130-4885-b972-84f3a444b707",
                         "workflow_outputs": [
                             {
                                 "label": "Mito-filtered Object",
                                 "output_name": "output_h5ad",
-                                "uuid": "a88ec405-265f-4a59-a75e-34e3b05b0096"
+                                "uuid": "b915da66-6435-4871-baa0-3e494ba73c96"
                             }
                         ]
                     },
@@ -233421,8 +238989,8 @@
                             }
                         ],
                         "position": {
-                            "left": 833.9625270516542,
-                            "top": 458.9230379613743
+                            "left": 834.046875,
+                            "top": 434.28125
                         },
                         "post_job_actions": {
                             "RenameDatasetActionout_png": {
@@ -233440,16 +239008,15 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"genotype\", \"log\": false, \"use_raw\": false, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"genotype\", \"log\": \"false\", \"use_raw\": \"false\", \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.7.1+galaxy1",
                         "type": "tool",
-                        "uuid": "55957a47-4968-465c-8b31-fb044d3ed1e3",
-                        "when": null,
+                        "uuid": "dbf56597-b286-43b9-bc04-f1e3995f7bc0",
                         "workflow_outputs": [
                             {
                                 "label": "Violin - Filterbycounts",
                                 "output_name": "out_png",
-                                "uuid": "a7c8b0d9-82d3-4438-a212-b5f7c56d36b8"
+                                "uuid": "3aef86d7-d34d-4b24-bc97-bf8c97d8d2fa"
                             }
                         ]
                     },
@@ -233474,8 +239041,8 @@
                             }
                         ],
                         "position": {
-                            "left": 1111.9688415527344,
-                            "top": 98.99999618530273
+                            "left": 1111.96875,
+                            "top": 73.1796875
                         },
                         "post_job_actions": {
                             "RenameDatasetActiongeneral": {
@@ -233496,19 +239063,18 @@
                         "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"general\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "0.7.5+galaxy1",
                         "type": "tool",
-                        "uuid": "7c6883be-1a11-4b58-8c0c-0f5b87a84ec8",
-                        "when": null,
+                        "uuid": "d221b80d-63e9-42a8-8d4b-25f8f22b9696",
                         "workflow_outputs": [
                             {
                                 "label": "General - Filterbymito",
                                 "output_name": "general",
-                                "uuid": "56882809-e19f-451a-8010-bc55dcee482f"
+                                "uuid": "cd94a4c6-5665-4bdf-88ea-4f4d41efa893"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy0",
                         "errors": null,
                         "id": 18,
                         "input_connections": {
@@ -233527,8 +239093,8 @@
                             }
                         ],
                         "position": {
-                            "left": 1111.9688415527344,
-                            "top": 274.00001525878906
+                            "left": 1111.96875,
+                            "top": 248.21875
                         },
                         "post_job_actions": {
                             "RenameDatasetActionoutput_h5ad": {
@@ -233539,23 +239105,22 @@
                                 "output_name": "output_h5ad"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "474a69c47184",
+                            "changeset_revision": "da611a744112",
                             "name": "scanpy_filter_genes",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"categories\": [], \"export_mtx\": false, \"force_recalc\": false, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"parameters\": [{\"__index__\": 0, \"name\": \"n_cells\", \"min\": \"3.0\", \"max\": \"1000000000.0\"}], \"save_layer\": null, \"save_raw\": false, \"subsets\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"categories\": [], \"export_mtx\": \"false\", \"force_recalc\": \"false\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"parameters\": [{\"__index__\": 0, \"name\": \"n_cells\", \"min\": \"3.0\", \"max\": \"1000000000.0\"}], \"save_layer\": null, \"save_raw\": \"false\", \"subsets\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
                         "type": "tool",
-                        "uuid": "61272c94-406b-4a3f-9bf5-a7ebbf1e3dee",
-                        "when": null,
+                        "uuid": "84dc3ac3-d79f-4dcd-b81b-f876de010f5e",
                         "workflow_outputs": [
                             {
                                 "label": "Filtered Object",
                                 "output_name": "output_h5ad",
-                                "uuid": "00846477-dec5-408a-83b2-105fff7ce05b"
+                                "uuid": "ee63ef0a-98ed-45cb-b144-1154f84ae452"
                             }
                         ]
                     },
@@ -233580,8 +239145,8 @@
                             }
                         ],
                         "position": {
-                            "left": 1111.9688415527344,
-                            "top": 449.04685974121094
+                            "left": 1111.96875,
+                            "top": 423.296875
                         },
                         "post_job_actions": {
                             "RenameDatasetActionout_png": {
@@ -233599,16 +239164,15 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"genotype\", \"log\": false, \"use_raw\": false, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"genotype\", \"log\": \"false\", \"use_raw\": \"false\", \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.7.1+galaxy1",
                         "type": "tool",
-                        "uuid": "b192226f-02d2-4196-a4f1-1cd27b8434bd",
-                        "when": null,
+                        "uuid": "972b30ab-cf6c-43a7-a41d-9679cbae7be6",
                         "workflow_outputs": [
                             {
                                 "label": "Violin - Filterbymito",
                                 "output_name": "out_png",
-                                "uuid": "7582e113-2004-4255-a1f3-d3123373f342"
+                                "uuid": "7e48a14f-08fd-45ab-b613-606bf64dcf9d"
                             }
                         ]
                     },
@@ -233633,8 +239197,8 @@
                             }
                         ],
                         "position": {
-                            "left": 1389.9688720703125,
-                            "top": 68.01563262939453
+                            "left": 1390.0078125,
+                            "top": 42.140625
                         },
                         "post_job_actions": {
                             "RenameDatasetActiongeneral": {
@@ -233655,19 +239219,18 @@
                         "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"general\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "0.7.5+galaxy1",
                         "type": "tool",
-                        "uuid": "2aa06b62-4c69-45a1-9330-f69838076dab",
-                        "when": null,
+                        "uuid": "78767f76-7f3c-416d-ac79-28f6104bb3b9",
                         "workflow_outputs": [
                             {
                                 "label": "General - Filtered object",
                                 "output_name": "general",
-                                "uuid": "2d870a40-c602-4a1c-afef-450489354d39"
+                                "uuid": "d59efa9b-d049-4f0e-8bd8-8ae982a45d0a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy0",
                         "errors": null,
                         "id": 21,
                         "input_connections": {
@@ -233686,33 +239249,32 @@
                             }
                         ],
                         "position": {
-                            "left": 1389.9688720703125,
-                            "top": 243.03123474121094
+                            "left": 1390.0078125,
+                            "top": 217.2421875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "6b97ffba31da",
+                            "changeset_revision": "8d9c22419c56",
                             "name": "scanpy_normalise_data",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"export_mtx\": false, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"save_layer\": null, \"save_raw\": false, \"settings\": {\"default\": true, \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"export_mtx\": \"false\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"save_layer\": null, \"save_raw\": \"false\", \"settings\": {\"default\": \"true\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
                         "type": "tool",
-                        "uuid": "23a495af-28ed-40fb-8ed2-e0a9c0d6d5af",
-                        "when": null,
+                        "uuid": "405a3674-8eca-4444-abc8-9f79112efafe",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output_h5ad",
-                                "uuid": "182d3dbe-a691-48cb-a784-2bceb1f9fdeb"
+                                "uuid": "4b7c5849-0c06-4167-b1e5-f19a2f9204af"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy0",
                         "errors": null,
                         "id": 22,
                         "input_connections": {
@@ -233731,41 +239293,32 @@
                             }
                         ],
                         "position": {
-                            "left": 1666.8230043154201,
-                            "top": 243.02502669087463
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_h5ad": {
-                                "action_arguments": {
-                                    "newname": "Use_me_FVG"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_h5ad"
-                            }
+                            "left": 1668.9375,
+                            "top": 218.2421875
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy9",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "2861ca3bfe4d",
+                            "changeset_revision": "4667fe07bd68",
                             "name": "scanpy_find_variable_genes",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"batch_key\": \"\", \"filter\": false, \"flavor\": \"seurat\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"max_disp\": \"50.0\", \"max_mean\": \"3.0\", \"min_disp\": \"0.5\", \"min_mean\": \"0.0125\", \"n_bin\": \"20\", \"n_top_gene\": \"2000\", \"output_format\": \"anndata_h5ad\", \"span\": \"0.3\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"batch_key\": \"\", \"filter\": \"false\", \"flavor\": \"seurat\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"max_disp\": \"50.0\", \"max_mean\": \"3.0\", \"min_disp\": \"0.5\", \"min_mean\": \"0.0125\", \"n_bin\": \"20\", \"n_top_gene\": null, \"output_format\": \"anndata_h5ad\", \"span\": \"0.3\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
                         "type": "tool",
-                        "uuid": "a8525f8d-4acc-437e-8c29-3213f7b969e2",
-                        "when": null,
+                        "uuid": "53fa19a2-55bd-43af-b0c9-a41d42554a6b",
                         "workflow_outputs": [
                             {
-                                "label": "Use_me_FVG",
+                                "label": null,
                                 "output_name": "output_h5ad",
-                                "uuid": "a0eb92b1-0263-4179-b7af-4bd9bcc9c960"
+                                "uuid": "2add5ce8-fffb-46ef-8d92-158b3f9a252b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy0",
                         "errors": null,
                         "id": 23,
                         "input_connections": {
@@ -233784,41 +239337,32 @@
                             }
                         ],
                         "position": {
-                            "left": 1946.0000610351562,
-                            "top": 252.99999237060547
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_h5ad": {
-                                "action_arguments": {
-                                    "newname": "Use_me_Scaled"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_h5ad"
-                            }
+                            "left": 1946.1875,
+                            "top": 227.203125
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy9",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "f86b2c3bc459",
+                            "changeset_revision": "5605f8452eb3",
                             "name": "scanpy_scale_data",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"save_layer\": null, \"save_raw\": false, \"scale_max\": \"10.0\", \"zero_center\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"save_layer\": null, \"save_raw\": \"false\", \"scale_max\": \"10.0\", \"zero_center\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
                         "type": "tool",
-                        "uuid": "4bc539e1-2913-448f-bde6-d1ec35a10a51",
-                        "when": null,
+                        "uuid": "a4106855-a661-4d6d-9208-99afcfc0eb55",
                         "workflow_outputs": [
                             {
-                                "label": "Use_me_Scaled",
+                                "label": null,
                                 "output_name": "output_h5ad",
-                                "uuid": "5776dbb9-0cac-40c0-9bae-9accae16a7a0"
+                                "uuid": "46ef29d8-4233-4cf9-b7d8-0b317dbfd37f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy0",
                         "errors": null,
                         "id": 24,
                         "input_connections": {
@@ -233837,27 +239381,26 @@
                             }
                         ],
                         "position": {
-                            "left": 2225.1144284467173,
-                            "top": 251.885462533716
+                            "left": 2224.1640625,
+                            "top": 227.203125
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "59028945c857",
+                            "changeset_revision": "3ee74b58c72d",
                             "name": "scanpy_run_pca",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"extra_outputs\": null, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"n_pcs\": \"50\", \"output_format\": \"anndata_h5ad\", \"run_mode\": {\"chunked\": false, \"__current_case__\": 1, \"zero_center\": true, \"svd_solver\": null, \"random_seed\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"extra_outputs\": null, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"n_pcs\": \"50\", \"output_format\": \"anndata_h5ad\", \"run_mode\": {\"chunked\": \"false\", \"__current_case__\": 1, \"zero_center\": \"true\", \"svd_solver\": null, \"random_seed\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
                         "type": "tool",
-                        "uuid": "e71440f2-7c95-49ae-bb54-17ad4ee206bd",
-                        "when": null,
+                        "uuid": "5a1ce297-23e9-46da-be5c-9c01a3a5a9dd",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output_h5ad",
-                                "uuid": "608852db-340a-4ddd-9e62-744d0cb77dde"
+                                "uuid": "7f75826e-ccd3-417b-9925-d1cbf231d27a"
                             }
                         ]
                     },
@@ -233882,8 +239425,8 @@
                             }
                         ],
                         "position": {
-                            "left": 2502.000045776367,
-                            "top": 122.01560974121094
+                            "left": 2502.1875,
+                            "top": 97.46875
                         },
                         "post_job_actions": {
                             "RenameDatasetActionout_png": {
@@ -233901,22 +239444,21 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.pca_variance_ratio\", \"__current_case__\": 11, \"n_pcs\": \"50\", \"log\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.pca_variance_ratio\", \"__current_case__\": 11, \"n_pcs\": \"50\", \"log\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.7.1+galaxy1",
                         "type": "tool",
-                        "uuid": "1b34902c-7a3f-47cb-94c0-b96c6bd7ba1b",
-                        "when": null,
+                        "uuid": "04b47edc-87e5-4913-abe1-e525f62b9aa4",
                         "workflow_outputs": [
                             {
                                 "label": "PCA Variance",
                                 "output_name": "out_png",
-                                "uuid": "f0b6f578-050f-4936-9ee7-9956b0760c6f"
+                                "uuid": "993dea99-990f-460a-beb9-46e5c97ee898"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy1",
                         "errors": null,
                         "id": 26,
                         "input_connections": {
@@ -233925,12 +239467,7 @@
                                 "output_name": "output_h5ad"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Scanpy ComputeGraph",
-                                "name": "settings"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
                         "name": "Scanpy ComputeGraph",
                         "outputs": [
@@ -233940,33 +239477,32 @@
                             }
                         ],
                         "position": {
-                            "left": 2502.000045776367,
-                            "top": 255.03124237060547
+                            "left": 2502.1875,
+                            "top": 229.2265625
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "6417cccad133",
+                            "changeset_revision": "bc9e8de21efb",
                             "name": "scanpy_compute_graph",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": false, \"__current_case__\": 1, \"key_added\": \"\", \"n_neighbors\": \"15\", \"n_neighbors_file\": {\"__class__\": \"RuntimeValue\"}, \"use_rep\": \"X_pca\", \"n_pcs\": \"20\", \"knn\": true, \"method\": \"umap\", \"metric\": \"euclidean\", \"random_seed\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": \"false\", \"__current_case__\": 1, \"key_added\": \"\", \"n_neighbors\": \"15\", \"n_neighbors_file\": null, \"use_rep\": \"X_pca\", \"n_pcs\": \"20\", \"knn\": \"true\", \"method\": \"umap\", \"metric\": \"euclidean\", \"random_seed\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy1",
                         "type": "tool",
-                        "uuid": "6e66aa61-710a-46f2-bca6-b6e104ff28ca",
-                        "when": null,
+                        "uuid": "f0da837f-8547-4368-9160-f4416f91768f",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output_h5ad",
-                                "uuid": "019dc123-b822-47fb-960e-fd48cafc10e1"
+                                "uuid": "cf488e9d-4171-4ed2-9fa0-a9083077eed7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy1",
                         "errors": null,
                         "id": 27,
                         "input_connections": {
@@ -233994,38 +239530,37 @@
                             }
                         ],
                         "position": {
-                            "left": 2780.0000762939453,
-                            "top": 315.04688262939453
+                            "left": 2780.1875,
+                            "top": 289.234375
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "181d61d2f3cd",
+                            "changeset_revision": "8b0d6f6f44c8",
                             "name": "scanpy_run_tsne",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"embeddings\": true, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": false, \"__current_case__\": 1, \"key_added\": \"\", \"perplexity\": \"30.0\", \"perplexity_file\": {\"__class__\": \"RuntimeValue\"}, \"early_exaggeration\": \"12.0\", \"learning_rate\": \"1000.0\", \"fast_tsne\": false, \"n_job\": null, \"n_pc\": null, \"random_seed\": \"0\"}, \"use_rep\": \"X_pca\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"embeddings\": \"true\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": \"false\", \"__current_case__\": 1, \"key_added\": \"\", \"perplexity\": \"30.0\", \"perplexity_file\": {\"__class__\": \"RuntimeValue\"}, \"early_exaggeration\": \"12.0\", \"learning_rate\": \"1000.0\", \"fast_tsne\": \"false\", \"n_job\": null, \"n_pc\": null, \"random_seed\": \"0\"}, \"use_rep\": \"X_pca\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy1",
                         "type": "tool",
-                        "uuid": "a09fcea0-184d-472e-a22a-09567f10705d",
-                        "when": null,
+                        "uuid": "1638ac03-a75c-4081-a33d-da080f0de1c7",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_embed",
-                                "uuid": "91d7f71d-73df-4955-a0b7-fb86904e3b27"
+                                "output_name": "output_h5ad",
+                                "uuid": "1b78023b-ad9b-46d0-b75e-ffa3b12a52ee"
                             },
                             {
                                 "label": null,
-                                "output_name": "output_h5ad",
-                                "uuid": "2cdbd6fa-f4d7-46c5-83fa-200b8bf48501"
+                                "output_name": "output_embed",
+                                "uuid": "e1b399d8-fe94-438e-9bc3-22fe695f70a2"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy0",
                         "errors": null,
                         "id": 28,
                         "input_connections": {
@@ -234048,38 +239583,37 @@
                             }
                         ],
                         "position": {
-                            "left": 3058.000068664551,
-                            "top": 397.04689025878906
+                            "left": 3058.171875,
+                            "top": 371.296875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "bd4a244faeb8",
+                            "changeset_revision": "fe562424a0a6",
                             "name": "scanpy_run_umap",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"embeddings\": true, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"key_added\": \"\", \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": true, \"__current_case__\": 0}, \"use_graph\": \"neighbors\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"embeddings\": \"true\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"key_added\": \"\", \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": \"true\", \"__current_case__\": 0}, \"use_graph\": \"neighbors\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
                         "type": "tool",
-                        "uuid": "d657ab30-f8df-410a-a8f8-880b2a1842e1",
-                        "when": null,
+                        "uuid": "f0847b39-f0b3-4422-a013-b1e0fc5d10af",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_h5ad",
-                                "uuid": "ed6a1cd1-f7dc-4174-a083-6d634dbe1b34"
+                                "output_name": "output_embed",
+                                "uuid": "174f4c1d-9901-4fb8-be47-c53e3155d93f"
                             },
                             {
                                 "label": null,
-                                "output_name": "output_embed",
-                                "uuid": "a30c795c-9317-4f04-b206-89088235dc6d"
+                                "output_name": "output_h5ad",
+                                "uuid": "d7fad373-884b-4374-9e97-141302f576ab"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy0",
                         "errors": null,
                         "id": 29,
                         "input_connections": {
@@ -234107,715 +239641,229 @@
                             }
                         ],
                         "position": {
-                            "left": 3336.0000610351562,
-                            "top": 441.0469055175781
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2ccd9f9e2cd0",
-                            "name": "scanpy_find_cluster",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"method\": \"louvain\", \"output_cluster\": true, \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": false, \"__current_case__\": 1, \"neighbors_key\": \"neighbors\", \"layer\": \"\", \"key_added\": \"\", \"resolution\": \"0.6\", \"resolution_file\": {\"__class__\": \"RuntimeValue\"}, \"restrict_to\": \"\", \"use_weights\": false, \"random_seed\": \"0\", \"directed\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
-                        "type": "tool",
-                        "uuid": "21b1bed3-b826-4219-b99b-22c33061768e",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_txt",
-                                "uuid": "13459467-b675-4076-8529-91a8bedc5501"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_h5ad",
-                                "uuid": "cd0d1987-4c25-4ade-a499-9288342d52aa"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy9",
-                        "errors": null,
-                        "id": 30,
-                        "input_connections": {
-                            "input_obj_file": {
-                                "id": 29,
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Scanpy FindMarkers",
-                                "name": "groupby_file"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Scanpy FindMarkers",
-                        "outputs": [
-                            {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
-                            },
-                            {
-                                "name": "output_tsv",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 3614.0000534057617,
-                            "top": 530.0156402587891
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_h5ad": {
-                                "action_arguments": {
-                                    "newname": "Final object"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_h5ad"
-                            },
-                            "RenameDatasetActionoutput_tsv": {
-                                "action_arguments": {
-                                    "newname": "Markers - cluster"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_tsv"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy9",
-                        "tool_shed_repository": {
-                            "changeset_revision": "81c34e67f262",
-                            "name": "scanpy_find_markers",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"groupby\": \"louvain\", \"groupby_file\": {\"__class__\": \"RuntimeValue\"}, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"n_genes\": \"50\", \"output_format\": \"anndata_h5ad\", \"output_markers\": true, \"settings\": {\"default\": true, \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
-                        "type": "tool",
-                        "uuid": "bcd329a1-a1b2-401a-9f4e-ba3e01f062a7",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Markers - cluster",
-                                "output_name": "output_tsv",
-                                "uuid": "7cfe5c9c-1c80-41b4-b669-633b1d7d40e3"
-                            },
-                            {
-                                "label": "Final object",
-                                "output_name": "output_h5ad",
-                                "uuid": "98e98405-951e-4c6c-be01-3c925ae35449"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy9",
-                        "errors": null,
-                        "id": 31,
-                        "input_connections": {
-                            "input_obj_file": {
-                                "id": 29,
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Scanpy FindMarkers",
-                                "name": "groupby_file"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Scanpy FindMarkers",
-                        "outputs": [
-                            {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
-                            },
-                            {
-                                "name": "output_tsv",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 3614.0000534057617,
-                            "top": 1136.0469055175781
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionoutput_h5ad": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_h5ad"
-                            },
-                            "RenameDatasetActionoutput_tsv": {
-                                "action_arguments": {
-                                    "newname": "Markers - genotype"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_tsv"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy9",
-                        "tool_shed_repository": {
-                            "changeset_revision": "81c34e67f262",
-                            "name": "scanpy_find_markers",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"groupby\": \"genotype\", \"groupby_file\": {\"__class__\": \"RuntimeValue\"}, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"n_genes\": \"50\", \"output_format\": \"anndata_h5ad\", \"output_markers\": true, \"settings\": {\"default\": true, \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
-                        "type": "tool",
-                        "uuid": "fef645a2-5159-41f6-a910-fd99ca48b513",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Markers - genotype",
-                                "output_name": "output_tsv",
-                                "uuid": "1e9f229d-eb34-4a5b-a6d9-e70c7b0581f4"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
-                        "errors": null,
-                        "id": 32,
-                        "input_connections": {
-                            "input_obj_file": {
-                                "id": 30,
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Scanpy PlotEmbed",
-                                "name": "input_obj_file"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Scanpy PlotEmbed",
-                        "outputs": [
-                            {
-                                "name": "output_png",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 3900.885245493235,
-                            "top": 102.06455225986635
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
-                        "tool_shed_repository": {
-                            "changeset_revision": "35f6611fb8c3",
-                            "name": "scanpy_plot_embed",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"basis\": \"tsne\", \"color_by\": \"louvain,sex,batch,genotype,Il2ra,Cd8b1,Cd8a,Cd4,Itm2a,Aif1,log1p_total_counts\", \"components\": \"\", \"edges\": false, \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": false, \"fig_size\": \"4,4\", \"fig_title\": \"\", \"gene_symbols_field\": \"Symbol\", \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"RuntimeValue\"}, \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": false, \"use_raw\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
-                        "type": "tool",
-                        "uuid": "e2f88d64-42c4-42a3-8152-e9d680280a42",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_png",
-                                "uuid": "a3df76e7-84ab-4dc8-a08a-e45e8d2091c7"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
-                        "errors": null,
-                        "id": 33,
-                        "input_connections": {
-                            "input_obj_file": {
-                                "id": 30,
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Scanpy PlotEmbed",
-                                "name": "input_obj_file"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Scanpy PlotEmbed",
-                        "outputs": [
-                            {
-                                "name": "output_png",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 3905.3432253483716,
-                            "top": 319.15199020651033
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
-                        "tool_shed_repository": {
-                            "changeset_revision": "35f6611fb8c3",
-                            "name": "scanpy_plot_embed",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"basis\": \"umap\", \"color_by\": \"louvain,sex,batch,genotype,Il2ra,Cd8b1,Cd8a,Cd4,Itm2a,Aif1,log1p_total_counts\", \"components\": \"\", \"edges\": false, \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": false, \"fig_size\": \"4,4\", \"fig_title\": \"\", \"gene_symbols_field\": \"Symbol\", \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"RuntimeValue\"}, \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": false, \"use_raw\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
-                        "type": "tool",
-                        "uuid": "89c6456b-3f1c-4cc1-86c3-2a46debf6da9",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_png",
-                                "uuid": "41663669-5ea9-44e1-bd3d-f9515a6499d4"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
-                        "errors": null,
-                        "id": 34,
-                        "input_connections": {
-                            "input": {
-                                "id": 30,
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Manipulate AnnData",
-                        "outputs": [
-                            {
-                                "name": "anndata",
-                                "type": "h5ad"
-                            }
-                        ],
-                        "position": {
-                            "left": 3902.000045776367,
-                            "top": 535.0468444824219
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3d748954434b",
-                            "name": "anndata_manipulate",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"rename_categories\", \"__current_case__\": 3, \"key\": \"louvain\", \"categories\": \"DP-M4,DP-M3,DP-M1,T-mat,DN,DP-L,DP-M2,Macrophages\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.5+galaxy1",
-                        "type": "tool",
-                        "uuid": "5642c686-66c7-4462-af54-090fe91f83de",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "anndata",
-                                "uuid": "82521e5a-3438-4b2c-8164-fd111c0e9604"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
-                        "errors": null,
-                        "id": 35,
-                        "input_connections": {
-                            "input_obj_file": {
-                                "id": 30,
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Scanpy PlotEmbed",
-                                "name": "input_obj_file"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Scanpy PlotEmbed",
-                        "outputs": [
-                            {
-                                "name": "output_png",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 3902.000045776367,
-                            "top": 731.0312652587891
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
-                        "tool_shed_repository": {
-                            "changeset_revision": "35f6611fb8c3",
-                            "name": "scanpy_plot_embed",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"basis\": \"pca\", \"color_by\": \"louvain,sex,batch,genotype,Il2ra,Cd8b1,Cd8a,Cd4,Itm2a,Aif1,log1p_total_counts\", \"components\": \"\", \"edges\": false, \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": false, \"fig_size\": \"4,4\", \"fig_title\": \"\", \"gene_symbols_field\": \"Symbol\", \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"RuntimeValue\"}, \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": false, \"use_raw\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
-                        "type": "tool",
-                        "uuid": "d6331822-fde8-4172-b28e-0f4089d24901",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_png",
-                                "uuid": "986bfb38-fc90-4b28-aa46-c19856dd5ba9"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
-                        "errors": null,
-                        "id": 36,
-                        "input_connections": {
-                            "input": {
-                                "id": 30,
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Inspect AnnData",
-                        "outputs": [
-                            {
-                                "name": "var",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 3899.770771786677,
-                            "top": 948.0374627272056
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ee98d611afc6",
-                            "name": "anndata_inspect",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"var\", \"__current_case__\": 4}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.5+galaxy1",
-                        "type": "tool",
-                        "uuid": "58cb02fe-78cc-455c-a5ec-ba7091d909d6",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "var",
-                                "uuid": "60e229a4-73a2-45b4-95ef-894728376f7d"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy91",
-                        "errors": null,
-                        "id": 37,
-                        "input_connections": {
-                            "copy_o|obs_sources": {
-                                "id": 34,
-                                "output_name": "anndata"
-                            },
-                            "input_obj_file": {
-                                "id": 30,
-                                "output_name": "output_h5ad"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "AnnData Operations",
-                        "outputs": [
-                            {
-                                "name": "output_h5ad",
-                                "type": "h5ad"
-                            }
-                        ],
-                        "position": {
-                            "left": 4190.000076293945,
-                            "top": 0
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy91",
-                        "tool_shed_repository": {
-                            "changeset_revision": "7ebc22f77d86",
-                            "name": "anndata_ops",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"add_cell_metadata\": {\"default\": false, \"__current_case__\": 1}, \"copy_adata_to_raw\": false, \"copy_e\": {\"default\": false, \"__current_case__\": 1}, \"copy_l\": {\"default\": false, \"__current_case__\": 1}, \"copy_o\": {\"default\": true, \"__current_case__\": 0, \"obs_keys\": [{\"__index__\": 0, \"contains\": \"louvain\"}], \"obs_sources\": {\"__class__\": \"ConnectedValue\"}}, \"copy_r\": {\"default\": false, \"__current_case__\": 1}, \"copy_u\": {\"default\": false, \"__current_case__\": 1}, \"copy_x\": {\"default\": false, \"__current_case__\": 1}, \"field_unique\": null, \"gene_flags\": [], \"gene_symbols_field\": \"index\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": false, \"top_genes\": \"50\", \"var_modifications\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy91",
-                        "type": "tool",
-                        "uuid": "8e6882a9-3d0b-4b93-b5e9-5852643a7411",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_h5ad",
-                                "uuid": "28b9308e-7f03-44d5-a81b-2e654353f6f8"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "join1",
-                        "errors": null,
-                        "id": 38,
-                        "input_connections": {
-                            "input1": {
-                                "id": 30,
-                                "output_name": "output_tsv"
-                            },
-                            "input2": {
-                                "id": 36,
-                                "output_name": "var"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Join two Datasets",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 4190.000076293945,
-                            "top": 1002.0468902587891
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "join1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"field1\": \"4\", \"field2\": \"2\", \"fill_empty_columns\": {\"fill_empty_columns_switch\": \"no_fill\", \"__current_case__\": 0}, \"header\": \"-H\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"partial\": \"-p\", \"unmatched\": \"-u\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.3",
-                        "type": "tool",
-                        "uuid": "6e6e5028-78a9-47d7-8df0-d183075c3da6",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "fb12a596-f691-4045-ac12-a3909b084f3e"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "join1",
-                        "errors": null,
-                        "id": 39,
-                        "input_connections": {
-                            "input1": {
-                                "id": 31,
-                                "output_name": "output_tsv"
-                            },
-                            "input2": {
-                                "id": 36,
-                                "output_name": "var"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Join two Datasets",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 4190.000076293945,
-                            "top": 1187.0468139648438
+                            "left": 3336.1796875,
+                            "top": 415.296875
                         },
                         "post_job_actions": {},
-                        "tool_id": "join1",
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"field1\": \"4\", \"field2\": \"2\", \"fill_empty_columns\": {\"fill_empty_columns_switch\": \"no_fill\", \"__current_case__\": 0}, \"header\": \"-H\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"partial\": \"-p\", \"unmatched\": \"-u\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.3",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ad6995afd2e6",
+                            "name": "scanpy_find_cluster",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"method\": \"louvain\", \"output_cluster\": \"true\", \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": \"false\", \"__current_case__\": 1, \"neighbors_key\": \"neighbors\", \"layer\": \"\", \"key_added\": \"\", \"resolution\": \"0.6\", \"resolution_file\": {\"__class__\": \"RuntimeValue\"}, \"restrict_to\": \"\", \"use_weights\": \"false\", \"random_seed\": \"0\", \"directed\": \"true\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
                         "type": "tool",
-                        "uuid": "5f0e9d28-cad2-4716-8b07-616c521fcce1",
-                        "when": null,
+                        "uuid": "684c6061-1703-4ed3-837a-f08aa49f496d",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "ddf27680-03a3-44b6-8217-9e8d560f449f"
+                                "output_name": "output_txt",
+                                "uuid": "8de66f85-2979-4d67-b9d6-a24ff1e480d3"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_h5ad",
+                                "uuid": "980e4933-b0d6-4b92-aee8-ef76691aa958"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy91",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy0",
                         "errors": null,
-                        "id": 40,
+                        "id": 30,
                         "input_connections": {
                             "input_obj_file": {
-                                "id": 37,
+                                "id": 29,
                                 "output_name": "output_h5ad"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Scanpy FindMarkers",
+                                "name": "groupby_file"
+                            }
+                        ],
                         "label": null,
-                        "name": "AnnData Operations",
+                        "name": "Scanpy FindMarkers",
                         "outputs": [
                             {
                                 "name": "output_h5ad",
                                 "type": "h5ad"
+                            },
+                            {
+                                "name": "output_tsv",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 4468.000030517578,
-                            "top": 25.859375
+                            "left": 3614.1640625,
+                            "top": 504.265625
                         },
                         "post_job_actions": {
                             "RenameDatasetActionoutput_h5ad": {
                                 "action_arguments": {
-                                    "newname": "Final cell annotated object"
+                                    "newname": "Final object"
                                 },
                                 "action_type": "RenameDatasetAction",
                                 "output_name": "output_h5ad"
+                            },
+                            "RenameDatasetActionoutput_tsv": {
+                                "action_arguments": {
+                                    "newname": "Markers - cluster"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_tsv"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy91",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "7ebc22f77d86",
-                            "name": "anndata_ops",
+                            "changeset_revision": "49653e680ea4",
+                            "name": "scanpy_find_markers",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"add_cell_metadata\": {\"default\": false, \"__current_case__\": 1}, \"copy_adata_to_raw\": false, \"copy_e\": {\"default\": false, \"__current_case__\": 1}, \"copy_l\": {\"default\": false, \"__current_case__\": 1}, \"copy_o\": {\"default\": false, \"__current_case__\": 1}, \"copy_r\": {\"default\": false, \"__current_case__\": 1}, \"copy_u\": {\"default\": false, \"__current_case__\": 1}, \"copy_x\": {\"default\": false, \"__current_case__\": 1}, \"field_unique\": null, \"gene_flags\": [], \"gene_symbols_field\": \"index\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [{\"__index__\": 0, \"from_obs\": \"louvain_0\", \"to_obs\": \"cell_type\", \"keep_original\": false, \"make_unique\": false}], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": false, \"top_genes\": \"50\", \"var_modifications\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy91",
+                        "tool_state": "{\"groupby\": \"louvain\", \"groupby_file\": {\"__class__\": \"RuntimeValue\"}, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"n_genes\": \"50\", \"output_format\": \"anndata_h5ad\", \"output_markers\": \"true\", \"settings\": {\"default\": \"true\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
                         "type": "tool",
-                        "uuid": "4afeffe6-16b4-4a59-baef-ca0f15a6a6db",
-                        "when": null,
+                        "uuid": "b5fcde30-03d3-44b0-9d6a-094512e76172",
                         "workflow_outputs": [
                             {
-                                "label": "Final cell annotated object",
+                                "label": "Markers - cluster",
+                                "output_name": "output_tsv",
+                                "uuid": "308b4961-4d50-442b-9bca-bbb1992426ba"
+                            },
+                            {
+                                "label": "Final object",
                                 "output_name": "output_h5ad",
-                                "uuid": "10bd70f8-ffcb-442b-9647-e5b947b6d35e"
+                                "uuid": "035bbbce-fb57-48c8-83d5-2b0cd0376541"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Cut1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy0",
                         "errors": null,
-                        "id": 41,
+                        "id": 31,
                         "input_connections": {
-                            "input": {
-                                "id": 38,
-                                "output_name": "out_file1"
+                            "input_obj_file": {
+                                "id": 29,
+                                "output_name": "output_h5ad"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Scanpy FindMarkers",
+                                "name": "groupby_file"
+                            }
+                        ],
                         "label": null,
-                        "name": "Cut",
+                        "name": "Scanpy FindMarkers",
                         "outputs": [
                             {
-                                "name": "out_file1",
+                                "name": "output_h5ad",
+                                "type": "h5ad"
+                            },
+                            {
+                                "name": "output_tsv",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 4468.000030517578,
-                            "top": 1040.0468444824219
+                            "left": 3614.1640625,
+                            "top": 1110.296875
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
+                            "HideDatasetActionoutput_h5ad": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_h5ad"
+                            },
+                            "RenameDatasetActionoutput_tsv": {
                                 "action_arguments": {
-                                    "newname": "Markers - cluster - named"
+                                    "newname": "Markers - genotype"
                                 },
                                 "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
+                                "output_name": "output_tsv"
                             }
                         },
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"columnList\": \"c1,c2,c3,c4,c11,c5,c6,c7,c8\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "49653e680ea4",
+                            "name": "scanpy_find_markers",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"groupby\": \"genotype\", \"groupby_file\": {\"__class__\": \"RuntimeValue\"}, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"n_genes\": \"50\", \"output_format\": \"anndata_h5ad\", \"output_markers\": \"true\", \"settings\": {\"default\": \"true\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
                         "type": "tool",
-                        "uuid": "25c9cbaf-4543-455e-bc1f-22b57cb2d8be",
-                        "when": null,
+                        "uuid": "cf2af5fd-4210-4a5a-b514-9786eebeb6f8",
                         "workflow_outputs": [
                             {
-                                "label": "Markers - cluster - named",
-                                "output_name": "out_file1",
-                                "uuid": "4f822c1c-91c5-4be4-8f9b-d5bdda0a037e"
+                                "label": "Markers - genotype",
+                                "output_name": "output_tsv",
+                                "uuid": "1705e219-192a-4f52-9b26-64fcbcd303ea"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Cut1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
                         "errors": null,
-                        "id": 42,
+                        "id": 32,
                         "input_connections": {
-                            "input": {
-                                "id": 39,
-                                "output_name": "out_file1"
+                            "input_obj_file": {
+                                "id": 30,
+                                "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Cut",
+                        "name": "Scanpy PlotEmbed",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "tabular"
+                                "name": "output_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 4468.000030517578,
-                            "top": 1225.0468444824219
+                            "left": 3902.203125,
+                            "top": 75.1328125
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Markers - genotype - named"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "56d22aa6cb3b",
+                            "name": "scanpy_plot_embed",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"columnList\": \"c1,c2,c3,c4,c11,c5,c6,c7,c8\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2",
+                        "tool_state": "{\"basis\": \"tsne\", \"color_by\": \"louvain,sex,batch,genotype,Il2ra,Cd8b1,Cd8a,Cd4,Itm2a,Aif1,log1p_total_counts\", \"components\": \"\", \"edges\": \"false\", \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": \"false\", \"fig_size\": \"4,4\", \"fig_title\": \"\", \"gene_symbols_field\": \"Symbol\", \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": \"false\", \"use_raw\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
                         "type": "tool",
-                        "uuid": "7f87b07e-5b61-4429-a8d3-25d2f7f778ac",
-                        "when": null,
+                        "uuid": "a41e2d67-8264-477d-9a61-9a9f86681a91",
                         "workflow_outputs": [
                             {
-                                "label": "Markers - genotype - named",
-                                "output_name": "out_file1",
-                                "uuid": "3b471f3d-263d-4299-9b7d-8a8ae1aa556e"
+                                "label": null,
+                                "output_name": "output_png",
+                                "uuid": "a76a5c05-f1c3-414e-8663-4951fdbbb1f5"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
                         "errors": null,
-                        "id": 43,
+                        "id": 33,
                         "input_connections": {
                             "input_obj_file": {
-                                "id": 40,
+                                "id": 30,
                                 "output_name": "output_h5ad"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Scanpy PlotEmbed",
-                                "name": "input_obj_file"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
                         "name": "Scanpy PlotEmbed",
                         "outputs": [
@@ -234825,1996 +239873,556 @@
                             }
                         ],
                         "position": {
-                            "left": 4653.500061035156,
-                            "top": 257.28126525878906
+                            "left": 3902.203125,
+                            "top": 292.2421875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "35f6611fb8c3",
+                            "changeset_revision": "56d22aa6cb3b",
                             "name": "scanpy_plot_embed",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"basis\": \"umap\", \"color_by\": \"sex,batch,genotype,Il2ra,Cd8b1,Cd8a,Cd4,Itm2a,Aif1,Hba-a1,log1p_total_counts,cell_type\", \"components\": \"\", \"edges\": false, \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": false, \"fig_size\": \"4,4\", \"fig_title\": \"\", \"gene_symbols_field\": \"Symbol\", \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"RuntimeValue\"}, \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": false, \"use_raw\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.1+galaxy9",
+                        "tool_state": "{\"basis\": \"umap\", \"color_by\": \"louvain,sex,batch,genotype,Il2ra,Cd8b1,Cd8a,Cd4,Itm2a,Aif1,log1p_total_counts\", \"components\": \"\", \"edges\": \"false\", \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": \"false\", \"fig_size\": \"4,4\", \"fig_title\": \"\", \"gene_symbols_field\": \"Symbol\", \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": \"false\", \"use_raw\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
                         "type": "tool",
-                        "uuid": "d0930dc2-d747-49ff-ac8a-32bdda581012",
-                        "when": null,
+                        "uuid": "4402764b-f095-494c-abfe-97f8854c6c25",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output_png",
-                                "uuid": "180f366c-6007-4b0a-9c59-b05e2e4bb757"
+                                "uuid": "22e2c0b2-db19-4689-b2fc-7f9fcff14611"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "single-cell/scrna-case_basic-pipeline",
-                "path": "topics/single-cell/tutorials/scrna-case_basic-pipeline/workflows/Filter,-Plot-and-Explore-Single-cell-RNA-seq-Data-updated.ga",
-                "tags": [
-                    "transcriptomics"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "Filter, Plot and Explore Single-cell RNA-seq Data updated",
-                "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-case_basic-pipeline/versions/filter--plot-and-explore-single-cell-rna-seq-data-updated",
-                "tutorial_id": "scrna-case_basic-pipeline",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_basic-pipeline/workflows/Filter,-Plot-and-Explore-Single-cell-RNA-seq-Data-updated.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_basic-pipeline/workflows/Filter,-Plot-and-Explore-Single-cell-RNA-seq-Data-updated.html",
-                "version": 1,
-                "wfid": "single-cell-scrna-case_basic-pipeline",
-                "wfname": "filter--plot-and-explore-single-cell-rna-seq-data-updated",
-                "workflow": "Filter,-Plot-and-Explore-Single-cell-RNA-seq-Data-updated.ga",
-                "workflow_tools": [
-                    "Cut1",
-                    "join1",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy91",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1"
-                ],
-                "workflowhub_id": "1212"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/7053673"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "anndata_import",
-                    "owner": "iuc",
-                    "revisions": "55e35e9203cf",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "anndata_manipulate",
-                    "owner": "iuc",
-                    "revisions": "9bd945a03d7b",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_cluster_reduce_dimension",
-                    "owner": "iuc",
-                    "revisions": "aaa5da8e73a9",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_filter",
-                    "owner": "iuc",
-                    "revisions": "b409c2486353",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_inspect",
-                    "owner": "iuc",
-                    "revisions": "c5d3684f7c4c",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_normalize",
-                    "owner": "iuc",
-                    "revisions": "ab55fe8030b6",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_plot",
-                    "owner": "iuc",
-                    "revisions": "6adf98e782f3",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_remove_confounders",
-                    "owner": "iuc",
-                    "revisions": "bf2017df9837",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: anndata_import\n  owner: iuc\n  revisions: 55e35e9203cf\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_manipulate\n  owner: iuc\n  revisions: 9bd945a03d7b\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_cluster_reduce_dimension\n  owner: iuc\n  revisions: aaa5da8e73a9\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_filter\n  owner: iuc\n  revisions: b409c2486353\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_inspect\n  owner: iuc\n  revisions: c5d3684f7c4c\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_normalize\n  owner: iuc\n  revisions: ab55fe8030b6\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_plot\n  owner: iuc\n  revisions: 6adf98e782f3\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_remove_confounders\n  owner: iuc\n  revisions: bf2017df9837\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plant/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "elixir_node": "de",
-                "email": "mtekman89@gmail.com",
-                "former_affiliations": [
-                    "elixir-europe"
-                ],
-                "id": "mtekman",
-                "joined": "2018-11",
-                "name": "Mehmet Tekman",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
-            },
-            {
-                "email": "beatrizserrano.galaxy@gmail.com",
-                "id": "beatrizserrano",
-                "joined": "2020-07",
-                "linkedin": "beatriz-serrano",
-                "matrix": "beatrizserrano:matrix.org",
-                "name": "Beatriz Serrano-Solano",
-                "orcid": "0000-0002-5862-6132",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/beatrizserrano/",
-                "twitter": "BSerranoSolano",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/beatrizserrano.json"
-            },
-            {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "gallardoalba",
-                "joined": "2020-11",
-                "name": "Crist\u00f3bal Gallardo",
-                "orcid": "0000-0002-5752-2155",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "pavanvidem",
-                "joined": "2017-09",
-                "name": "Pavankumar Videm",
-                "orcid": "0000-0002-5192-126X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
-            }
-        ],
-        "dir": "topics/single-cell/tutorials/scrna-plant",
-        "edam_operation": [
-            "Differential gene expression analysis"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "gitter": "Galaxy-Training-Network/galaxy-single-cell",
-        "hands_on": true,
-        "id": "single-cell/scrna-plant",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.no"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Filtering parameters are dependent on the dataset, and should be explored using scatter or violin plots",
-            "A DotPlot is a fantastic way to validate clusters across different analyses"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
-        "objectives": [
-            "Perform filtering, dimensionality reduction, and clustering",
-            "Generate a DotPlot emulating the original paper using a different analysis tool",
-            "Determine robust clusters across scRNA-seq pipelines"
-        ],
-        "pageviews": 2387,
-        "priority": 3,
-        "pub_date": "2021-04-08",
-        "questions": [
-            "Can we reclaim cell markers using a different analysis method?",
-            "Are highly variable genes paramount to the analysis?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "mtekman"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "55M",
-                "speakers": [
-                    "mtekman"
-                ],
-                "youtube_id": "yKlJ5ESri7o"
-            }
-        ],
-        "redirect_from": [
-            "/topics/transcriptomics/tutorials/scrna-plant/tutorial",
-            "/short/single-cell/scrna-plant",
-            "/short/T00250"
-        ],
-        "requirements": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-scanpy-pbmc3k"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00250",
-        "short_tools": [
-            "anndata_manipulate",
-            "scanpy_inspect",
-            "scanpy_plot",
-            "scanpy_normalize",
-            "scanpy_cluster_reduce_dimension",
-            "anndata_import",
-            "scanpy_filter",
-            "scanpy_remove_confounders"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "end-to-end",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "plants",
-            "paper-replication"
-        ],
-        "time_estimation": "2H",
-        "title": "Analysis of plant scRNA-Seq Data with Scanpy",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0"
-        ],
-        "topic_name": "single-cell",
-        "topic_name_human": "Single Cell",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "scrna-plant",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-plant/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plant/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plant/tutorial.json"
-        },
-        "version": 5,
-        "video": false,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 85,
-        "visitors": 1878,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Downstream Single-cell RNA Plant analysis with ScanPy",
-                "features": {
-                    "comments": false,
-                    "parameters": true,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nLeiden Resolution\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSHR CSV.gz\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nWT CSV.gz\"]\n  3[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMin Genes\"]\n  4[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMin Cells\"]\n  5[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMax Features\"]\n  6[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMax Lib Size\"]\n  7[label=\"Import Anndata and loom\"]\n  1 -> 7 [label=\"output\"]\n  8[label=\"Import Anndata and loom\"]\n  2 -> 8 [label=\"output\"]\n  9[label=\"Manipulate AnnData\"]\n  7 -> 9 [label=\"anndata\"]\n  8 -> 9 [label=\"anndata\"]\n  10[label=\"Rename Batches\"]\n  9 -> 10 [label=\"anndata\"]\n  k680180f6edfc4f66b2657a63aaa22b39[color=lightseagreen,label=\"Output\\nscRNA Concatenated Datasets\"]\n  10 -> k680180f6edfc4f66b2657a63aaa22b39\n  11[label=\"QC metrics\"]\n  10 -> 11 [label=\"anndata\"]\n  12[label=\"Filter genes\"]\n  11 -> 12 [label=\"anndata_out\"]\n  3 -> 12 [label=\"output\"]\n  13[label=\"Plot Violin\"]\n  11 -> 13 [label=\"anndata_out\"]\n  14[label=\"Filter Cells\"]\n  12 -> 14 [label=\"anndata_out\"]\n  4 -> 14 [label=\"output\"]\n  15[label=\"Filter Max Features\"]\n  14 -> 15 [label=\"anndata_out\"]\n  5 -> 15 [label=\"output\"]\n  16[label=\"Filter Max Library Size\"]\n  15 -> 16 [label=\"anndata\"]\n  6 -> 16 [label=\"output\"]\n  17[label=\"Save RAW\"]\n  16 -> 17 [label=\"anndata\"]\n  18[label=\"Norm to 1e4\"]\n  17 -> 18 [label=\"anndata\"]\n  19[label=\"Log1p\"]\n  18 -> 19 [label=\"anndata_out\"]\n  20[label=\"Regress total counts\"]\n  19 -> 20 [label=\"anndata_out\"]\n  21[label=\"Scale\"]\n  20 -> 21 [label=\"anndata_out\"]\n  22[label=\"PCA\"]\n  21 -> 22 [label=\"anndata_out\"]\n  23[label=\"Neighborhod\"]\n  22 -> 23 [label=\"anndata_out\"]\n  24[label=\"UMAP\"]\n  23 -> 24 [label=\"anndata_out\"]\n  25[label=\"Leiden\"]\n  24 -> 25 [label=\"anndata_out\"]\n  0 -> 25 [label=\"output\"]\n  k48cf046584ba461abdb961625626de42[color=lightseagreen,label=\"Output\\nscRNA with clusters Dataset\"]\n  25 -> k48cf046584ba461abdb961625626de42\n  26[label=\"Plot PCA batch\"]\n  24 -> 26 [label=\"anndata_out\"]\n  27[label=\"Plot UMAP batch\"]\n  24 -> 27 [label=\"anndata_out\"]\n  28[label=\"Plot UMAP leiden, batch\"]\n  25 -> 28 [label=\"anndata_out\"]\n  29[label=\"Rename Clusters\"]\n  25 -> 29 [label=\"anndata_out\"]\n  30[label=\"Complex DotPlot\"]\n  25 -> 30 [label=\"anndata_out\"]\n  31[label=\"Complex DotPlot with new labels\"]\n  29 -> 31 [label=\"anndata\"]\n  32[label=\"Plot UMAP with new labels\"]\n  29 -> 32 [label=\"anndata\"]\n}",
-                "history": [
-                    {
-                        "hash": "327fd2b842f45de3dc2a30067714352675ad69ae",
-                        "message": "Making a single cell topics",
-                        "num": 1,
-                        "short_hash": "327fd2b84",
-                        "unix": "1668273265"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Leiden Resolution"
-                            }
-                        ],
-                        "label": "Leiden Resolution",
-                        "name": "Input parameter",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 195.5,
-                            "height": 84,
-                            "left": 121.5,
-                            "right": 321.5,
-                            "top": 111.5,
-                            "width": 200,
-                            "x": 121.5,
-                            "y": 111.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": 0.35, \"parameter_type\": \"float\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "eddf8108-6913-40d2-819d-a84677dee3f4",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "SHR (CSV.gz)"
-                            }
-                        ],
-                        "label": "SHR (CSV.gz)",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 302,
-                            "height": 84,
-                            "left": 116,
-                            "right": 316,
-                            "top": 218,
-                            "width": 200,
-                            "x": 116,
-                            "y": 218
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "4cf4f111-d63b-47ad-bcbf-8ebb290b3431",
-                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "WT (CSV.gz)"
+                        "id": 34,
+                        "input_connections": {
+                            "input": {
+                                "id": 30,
+                                "output_name": "output_h5ad"
                             }
-                        ],
-                        "label": "WT (CSV.gz)",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 403,
-                            "height": 84,
-                            "left": 114,
-                            "right": 314,
-                            "top": 319,
-                            "width": 200,
-                            "x": 114,
-                            "y": 319
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "94fba59a-ba9d-452d-b325-cb558201f674",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Manipulate AnnData",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Min Genes"
+                                "name": "anndata",
+                                "type": "h5ad"
                             }
                         ],
-                        "label": "Min Genes",
-                        "name": "Input parameter",
-                        "outputs": [],
                         "position": {
-                            "bottom": 503.75,
-                            "height": 64.25,
-                            "left": 16,
-                            "right": 216,
-                            "top": 439.5,
-                            "width": 200,
-                            "x": 16,
-                            "y": 439.5
+                            "left": 3902.203125,
+                            "top": 509.2890625
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": 100, \"parameter_type\": \"integer\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "c9a62328-f049-43b6-92fb-df5c42982573",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Min Cells"
-                            }
-                        ],
-                        "label": "Min Cells",
-                        "name": "Input parameter",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 578.75,
-                            "height": 64.25,
-                            "left": 17,
-                            "right": 217,
-                            "top": 514.5,
-                            "width": 200,
-                            "x": 17,
-                            "y": 514.5
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3d748954434b",
+                            "name": "anndata_manipulate",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": 2, \"parameter_type\": \"integer\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "7bf5f0e1-b482-45c3-9bcb-10ca93e6b7dc",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"rename_categories\", \"__current_case__\": 3, \"key\": \"louvain\", \"categories\": \"DP-M4,DP-M3,DP-M1,T-mat,DN,DP-L,DP-M2,Macrophages\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "91b502ec-5b8b-40a2-b70b-1d30581434ef",
+                        "workflow_outputs": [
                             {
-                                "description": "",
-                                "name": "Max Features"
+                                "label": null,
+                                "output_name": "anndata",
+                                "uuid": "8a35be0b-4004-4dce-810b-e5b9d33590b9"
                             }
-                        ],
-                        "label": "Max Features",
-                        "name": "Input parameter",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 671.5,
-                            "height": 84,
-                            "left": 23,
-                            "right": 223,
-                            "top": 587.5,
-                            "width": 200,
-                            "x": 23,
-                            "y": 587.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": 12000.0, \"parameter_type\": \"float\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "8902a917-75fb-49c6-9e5d-15f87bd91d46",
-                        "workflow_outputs": []
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Max Lib Size"
-                            }
-                        ],
-                        "label": "Max Lib Size",
-                        "name": "Input parameter",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 764.5,
-                            "height": 84,
-                            "left": 15,
-                            "right": 215,
-                            "top": 680.5,
-                            "width": 200,
-                            "x": 15,
-                            "y": 680.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"default\": 120000.0, \"parameter_type\": \"float\", \"optional\": true}",
-                        "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "db068cdb-53c4-48a3-95c2-141fa83c271b",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nLeiden Resolution\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSHR CSV.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nWT CSV.gz\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nMin Genes\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nMin Cells\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Parameter\\nMax Features\"];\n  style 5 fill:#ded,stroke:#393,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Parameter\\nMax Lib Size\"];\n  style 6 fill:#ded,stroke:#393,stroke-width:4px;\n  7[\"Import Anndata and loom\"];\n  1 -->|output| 7;\n  8[\"Import Anndata and loom\"];\n  2 -->|output| 8;\n  9[\"Manipulate AnnData\"];\n  7 -->|anndata| 9;\n  8 -->|anndata| 9;\n  10[\"Rename Batches\"];\n  9 -->|anndata| 10;\n  680180f6-edfc-4f66-b265-7a63aaa22b39[\"Output\\nscRNA Concatenated Datasets\"];\n  10 --> 680180f6-edfc-4f66-b265-7a63aaa22b39;\n  style 680180f6-edfc-4f66-b265-7a63aaa22b39 stroke:#2c3143,stroke-width:4px;\n  11[\"QC metrics\"];\n  10 -->|anndata| 11;\n  12[\"Filter genes\"];\n  11 -->|anndata_out| 12;\n  3 -->|output| 12;\n  13[\"Plot Violin\"];\n  11 -->|anndata_out| 13;\n  14[\"Filter Cells\"];\n  12 -->|anndata_out| 14;\n  4 -->|output| 14;\n  15[\"Filter Max Features\"];\n  14 -->|anndata_out| 15;\n  5 -->|output| 15;\n  16[\"Filter Max Library Size\"];\n  15 -->|anndata| 16;\n  6 -->|output| 16;\n  17[\"Save RAW\"];\n  16 -->|anndata| 17;\n  18[\"Norm to 1e4\"];\n  17 -->|anndata| 18;\n  19[\"Log1p\"];\n  18 -->|anndata_out| 19;\n  20[\"Regress total counts\"];\n  19 -->|anndata_out| 20;\n  21[\"Scale\"];\n  20 -->|anndata_out| 21;\n  22[\"PCA\"];\n  21 -->|anndata_out| 22;\n  23[\"Neighborhod\"];\n  22 -->|anndata_out| 23;\n  24[\"UMAP\"];\n  23 -->|anndata_out| 24;\n  25[\"Leiden\"];\n  24 -->|anndata_out| 25;\n  0 -->|output| 25;\n  48cf0465-84ba-461a-bdb9-61625626de42[\"Output\\nscRNA with clusters Dataset\"];\n  25 --> 48cf0465-84ba-461a-bdb9-61625626de42;\n  style 48cf0465-84ba-461a-bdb9-61625626de42 stroke:#2c3143,stroke-width:4px;\n  26[\"Plot PCA batch\"];\n  24 -->|anndata_out| 26;\n  27[\"Plot UMAP batch\"];\n  24 -->|anndata_out| 27;\n  28[\"Plot UMAP leiden, batch\"];\n  25 -->|anndata_out| 28;\n  29[\"Rename Clusters\"];\n  25 -->|anndata_out| 29;\n  30[\"Complex DotPlot\"];\n  25 -->|anndata_out| 30;\n  31[\"Complex DotPlot with new labels\"];\n  29 -->|anndata| 31;\n  32[\"Plot UMAP with new labels\"];\n  29 -->|anndata| 32;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "scRNA Plant Analysis",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
                         "errors": null,
-                        "id": 10,
+                        "id": 35,
                         "input_connections": {
-                            "input": {
-                                "id": 9,
-                                "output_name": "anndata"
+                            "input_obj_file": {
+                                "id": 30,
+                                "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
-                        "label": "Rename Batches",
-                        "name": "Manipulate AnnData",
+                        "label": null,
+                        "name": "Scanpy PlotEmbed",
                         "outputs": [
                             {
-                                "name": "anndata",
-                                "type": "h5ad"
+                                "name": "output_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": 354.3999938964844,
-                            "height": 136.39999389648438,
-                            "left": 955,
-                            "right": 1155,
-                            "top": 218,
-                            "width": 200,
-                            "x": 955,
-                            "y": 218
+                            "left": 3902.203125,
+                            "top": 705.234375
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "8db95f488f0f",
-                            "name": "anndata_manipulate",
-                            "owner": "iuc",
+                            "changeset_revision": "56d22aa6cb3b",
+                            "name": "scanpy_plot_embed",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"rename_categories\", \"__current_case__\": 3, \"key\": \"batch\", \"categories\": \"shr, wt\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.7.5+galaxy0",
+                        "tool_state": "{\"basis\": \"pca\", \"color_by\": \"louvain,sex,batch,genotype,Il2ra,Cd8b1,Cd8a,Cd4,Itm2a,Aif1,log1p_total_counts\", \"components\": \"\", \"edges\": \"false\", \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": \"false\", \"fig_size\": \"4,4\", \"fig_title\": \"\", \"gene_symbols_field\": \"Symbol\", \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": \"false\", \"use_raw\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
                         "type": "tool",
-                        "uuid": "0a25ffc3-ac58-4c17-9f22-b4127952027a",
+                        "uuid": "2a77ae44-dc08-4b53-ae43-215ba91d6260",
                         "workflow_outputs": [
                             {
-                                "label": "scRNA Concatenated Datasets",
-                                "output_name": "anndata",
-                                "uuid": "680180f6-edfc-4f66-b265-7a63aaa22b39"
+                                "label": null,
+                                "output_name": "output_png",
+                                "uuid": "ea42965c-0f03-404d-9a5a-a070170dc4b2"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
                         "errors": null,
-                        "id": 13,
+                        "id": 36,
                         "input_connections": {
-                            "adata": {
-                                "id": 11,
-                                "output_name": "anndata_out"
+                            "input": {
+                                "id": 30,
+                                "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
-                        "label": "Plot Violin",
-                        "name": "Plot",
+                        "label": null,
+                        "name": "Inspect AnnData",
                         "outputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "name": "var",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 259.8000030517578,
-                            "height": 116.65000915527344,
-                            "left": 1867.2833251953125,
-                            "right": 2067.2833251953125,
-                            "top": 143.14999389648438,
-                            "width": 200,
-                            "x": 1867.2833251953125,
-                            "y": 143.14999389648438
+                            "left": 3902.203125,
+                            "top": 922.2890625
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "6adf98e782f3",
-                            "name": "scanpy_plot",
+                            "changeset_revision": "ee98d611afc6",
+                            "name": "anndata_inspect",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"n_genes_by_counts, total_counts\"}, \"groupby\": \"batch\", \"log\": \"false\", \"use_raw\": \"false\", \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"0.4\"}}, \"multi_panel\": {\"multi_panel\": \"True\", \"__current_case__\": 0, \"width\": null, \"height\": null}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy0",
+                        "tool_state": "{\"__input_ext\": \"h5ad\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"var\", \"__current_case__\": 4}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.5+galaxy1",
                         "type": "tool",
-                        "uuid": "9dfc1e59-71aa-40b8-b504-2498a8dc5409",
+                        "uuid": "c9832ad2-4cff-4316-a43a-11ba2691601d",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_png",
-                                "uuid": "2fb1d919-0e60-4c81-92d2-83c28b1ef654"
+                                "output_name": "var",
+                                "uuid": "d890f37a-aa1e-4b3c-8f63-04ecfeaa8f73"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
                         "errors": null,
-                        "id": 25,
+                        "id": 37,
                         "input_connections": {
-                            "adata": {
-                                "id": 24,
-                                "output_name": "anndata_out"
+                            "copy_o|obs_sources": {
+                                "id": 34,
+                                "output_name": "anndata"
                             },
-                            "method|resolution": {
-                                "id": 0,
-                                "output_name": "output"
+                            "input_obj_file": {
+                                "id": 30,
+                                "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
-                        "label": "Leiden",
-                        "name": "Cluster, infer trajectories and embed",
+                        "label": null,
+                        "name": "AnnData Operations",
                         "outputs": [
                             {
-                                "name": "anndata_out",
+                                "name": "output_h5ad",
                                 "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "bottom": 562.0500030517578,
-                            "height": 147.0500030517578,
-                            "left": 1389,
-                            "right": 1589,
-                            "top": 415,
-                            "width": 200,
-                            "x": 1389,
-                            "y": 415
+                            "left": 4386.2109375,
+                            "top": 257.1875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "35bc2eb568ed",
-                            "name": "scanpy_cluster_reduce_dimension",
-                            "owner": "iuc",
+                            "changeset_revision": "890fb06a2893",
+                            "name": "anndata_ops",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"method\": {\"method\": \"tl.leiden\", \"__current_case__\": 1, \"resolution\": {\"__class__\": \"ConnectedValue\"}, \"random_state\": \"0\", \"key_added\": \"leiden\", \"use_weights\": \"false\", \"n_iterations\": \"-1\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy0",
+                        "tool_state": "{\"copy_adata_to_raw\": \"false\", \"copy_e\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_l\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_o\": {\"default\": \"true\", \"__current_case__\": 0, \"obs_keys\": [{\"__index__\": 0, \"contains\": \"louvain\"}], \"obs_sources\": {\"__class__\": \"ConnectedValue\"}}, \"copy_r\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_u\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_x\": {\"default\": \"false\", \"__current_case__\": 1}, \"gene_flags\": [], \"gene_symbols_field\": \"index\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": \"false\", \"top_genes\": \"50\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
                         "type": "tool",
-                        "uuid": "99494ea7-377c-4f3d-a45a-18bfd81b7888",
+                        "uuid": "573bf376-2011-4572-ad91-84df828f1242",
                         "workflow_outputs": [
                             {
-                                "label": "scRNA with clusters Dataset",
-                                "output_name": "anndata_out",
-                                "uuid": "48cf0465-84ba-461a-bdb9-61625626de42"
+                                "label": null,
+                                "output_name": "output_h5ad",
+                                "uuid": "50717627-47ed-40bc-bf18-17198416a57f"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "content_id": "join1",
                         "errors": null,
-                        "id": 26,
+                        "id": 38,
                         "input_connections": {
-                            "adata": {
-                                "id": 24,
-                                "output_name": "anndata_out"
+                            "input1": {
+                                "id": 30,
+                                "output_name": "output_tsv"
+                            },
+                            "input2": {
+                                "id": 36,
+                                "output_name": "var"
                             }
                         },
                         "inputs": [],
-                        "label": "Plot PCA (batch)",
-                        "name": "Plot",
+                        "label": null,
+                        "name": "Join two Datasets",
                         "outputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 277.5500030517578,
-                            "height": 136.40000915527344,
-                            "left": 1629.433349609375,
-                            "right": 1829.433349609375,
-                            "top": 141.14999389648438,
-                            "width": 200,
-                            "x": 1629.433349609375,
-                            "y": 141.14999389648438
+                            "left": 4190.2109375,
+                            "top": 976.3046875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6adf98e782f3",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.pca\", \"__current_case__\": 9, \"color\": \"batch\", \"use_raw\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy0",
+                        "tool_id": "join1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"field1\": \"4\", \"field2\": \"2\", \"fill_empty_columns\": {\"fill_empty_columns_switch\": \"no_fill\", \"__current_case__\": 0}, \"header\": \"-H\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"partial\": \"-p\", \"unmatched\": \"-u\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.3",
                         "type": "tool",
-                        "uuid": "e2daa4c6-9a39-4c42-852e-4f61b65202c2",
+                        "uuid": "db6d5777-a3dd-467d-8541-91bb998e0e72",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_png",
-                                "uuid": "72d1a264-3ace-4d2e-910a-5e2a0fa6721f"
+                                "output_name": "out_file1",
+                                "uuid": "cb6967d5-7390-4d2e-b2c4-1d8a9e2d3c69"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "content_id": "join1",
                         "errors": null,
-                        "id": 27,
+                        "id": 39,
                         "input_connections": {
-                            "adata": {
-                                "id": 24,
-                                "output_name": "anndata_out"
+                            "input1": {
+                                "id": 31,
+                                "output_name": "output_tsv"
+                            },
+                            "input2": {
+                                "id": 36,
+                                "output_name": "var"
                             }
                         },
                         "inputs": [],
-                        "label": "Plot UMAP (batch)",
-                        "name": "Plot",
+                        "label": null,
+                        "name": "Join two Datasets",
                         "outputs": [
-                            {
-                                "name": "out_png",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 406.3999938964844,
-                            "height": 136.39999389648438,
-                            "left": 1862,
-                            "right": 2062,
-                            "top": 270,
-                            "width": 200,
-                            "x": 1862,
-                            "y": 270
+                            {
+                                "name": "out_file1",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 4178.2109375,
+                            "top": 1199.2890625
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6adf98e782f3",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"batch\", \"use_raw\": \"false\", \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": \"14\", \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy0",
+                        "tool_id": "join1",
+                        "tool_state": "{\"field1\": \"4\", \"field2\": \"2\", \"fill_empty_columns\": {\"fill_empty_columns_switch\": \"no_fill\", \"__current_case__\": 0}, \"header\": \"-H\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"partial\": \"-p\", \"unmatched\": \"-u\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.3",
                         "type": "tool",
-                        "uuid": "e70d8e14-1983-4381-8feb-bba7d5dbb4d6",
+                        "uuid": "f4db0e7d-dfc8-4f77-bca0-997a0347304b",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_png",
-                                "uuid": "c223e762-7e90-41e1-b354-bbe6e278b5c0"
+                                "output_name": "out_file1",
+                                "uuid": "54cdb2bd-437b-47e4-90c1-e99e0b468574"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
                         "errors": null,
-                        "id": 28,
+                        "id": 40,
                         "input_connections": {
-                            "adata": {
-                                "id": 25,
-                                "output_name": "anndata_out"
+                            "input_obj_file": {
+                                "id": 37,
+                                "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
-                        "label": "Plot UMAP (leiden, batch)",
-                        "name": "Plot",
+                        "label": null,
+                        "name": "AnnData Operations",
                         "outputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "name": "output_h5ad",
+                                "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "bottom": 442.5500030517578,
-                            "height": 136.40000915527344,
-                            "left": 1630.433349609375,
-                            "right": 1830.433349609375,
-                            "top": 306.1499938964844,
-                            "width": 200,
-                            "x": 1630.433349609375,
-                            "y": 306.1499938964844
+                            "left": 4468.2109375,
+                            "top": 0
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_h5ad": {
+                                "action_arguments": {
+                                    "newname": "Final cell annotated object"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "6adf98e782f3",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
+                            "changeset_revision": "890fb06a2893",
+                            "name": "anndata_ops",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"leiden, batch\", \"use_raw\": \"false\", \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": \"14\", \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy0",
+                        "tool_state": "{\"copy_adata_to_raw\": \"false\", \"copy_e\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_l\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_o\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_r\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_u\": {\"default\": \"false\", \"__current_case__\": 1}, \"copy_x\": {\"default\": \"false\", \"__current_case__\": 1}, \"gene_flags\": [], \"gene_symbols_field\": \"index\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [{\"__index__\": 0, \"from_obs\": \"louvain_0\", \"to_obs\": \"cell_type\", \"keep_original\": \"false\"}], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": \"false\", \"top_genes\": \"50\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
                         "type": "tool",
-                        "uuid": "b88358ff-0dda-4c2e-bce6-124a0ab8fa28",
+                        "uuid": "584bf7e3-05d7-4010-ba67-98375379c621",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_png",
-                                "uuid": "26c65cd9-74aa-4574-a5f3-ac10caced4da"
+                                "label": "Final cell annotated object",
+                                "output_name": "output_h5ad",
+                                "uuid": "a6d48df0-403f-4efc-a75f-9504a960884e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "content_id": "Cut1",
                         "errors": null,
-                        "id": 30,
+                        "id": 41,
                         "input_connections": {
-                            "adata": {
-                                "id": 25,
-                                "output_name": "anndata_out"
+                            "input": {
+                                "id": 38,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
-                        "label": "Complex DotPlot",
-                        "name": "Plot",
+                        "label": null,
+                        "name": "Cut",
                         "outputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 557.3999938964844,
-                            "height": 136.39999389648438,
-                            "left": 1861,
-                            "right": 2061,
-                            "top": 421,
-                            "width": 200,
-                            "x": 1861,
-                            "y": 421
+                            "left": 4468.2109375,
+                            "top": 1014.2890625
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6adf98e782f3",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Markers - cluster - named"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.dotplot\", \"__current_case__\": 2, \"var_names\": {\"type\": \"custom\", \"__current_case__\": 1, \"var_names\": \"AT1G26680,COBL2,AT3G55180,NCED2,AT5G22550,ATL63,RGF8,TEL1,DUF9,AGL42,PLT1,PLT2,PER3,PER9,PBL15,TBL30,AT2G48130,AT3G22620,AED3,T3P18-7,MBK21-8,NPF6-4,CYP71B34,IAMT1,AT1G31950,F14G6-22,GL2,ANL2,PMEI4,MUD21-4,EXPA7,MES15,ADF8,COBL9,TPR14,BHLH144,MYB83,SCPL35,MYB46,COBL4,PIN7,PIN3   \"}, \"groupby\": \"leiden\", \"num_categories\": \"9\", \"log\": \"false\", \"use_raw\": \"true\", \"dendrogram\": \"false\", \"var_group_positions\": [{\"__index__\": 0, \"start\": \"0\", \"end\": \"5\", \"label\": \"Columella\"}, {\"__index__\": 1, \"start\": \"6\", \"end\": \"9\", \"label\": \"QC\"}, {\"__index__\": 2, \"start\": \"10\", \"end\": \"11\", \"label\": \"NC\"}, {\"__index__\": 3, \"start\": \"12\", \"end\": \"17\", \"label\": \"Endodermis\"}, {\"__index__\": 4, \"start\": \"18\", \"end\": \"23\", \"label\": \"Cortex\"}, {\"__index__\": 5, \"start\": \"24\", \"end\": \"29\", \"label\": \"Atrichoblast\"}, {\"__index__\": 6, \"start\": \"30\", \"end\": \"34\", \"label\": \"Trichoblast\"}, {\"__index__\": 7, \"start\": \"35\", \"end\": \"39\", \"label\": \"Xylem\"}, {\"__index__\": 8, \"start\": \"40\", \"end\": \"41\", \"label\": \"VC\"}], \"var_group_rotation\": null, \"figsize\": {\"test\": \"no\", \"__current_case__\": 1}, \"layer\": \"\", \"color_map\": \"viridis\", \"dot_max\": null, \"dot_min\": null, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy0",
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"columnList\": \"c1,c2,c3,c4,c11,c5,c6,c7,c8\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2",
                         "type": "tool",
-                        "uuid": "625a157f-f08f-4137-a27b-721bee0feb59",
+                        "uuid": "45fddc4f-1b9d-4464-b08b-c502d4d05a30",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_png",
-                                "uuid": "b35ffb5a-5f29-4105-a016-c02ceee0d9da"
+                                "label": "Markers - cluster - named",
+                                "output_name": "out_file1",
+                                "uuid": "0ee7f9b6-b065-4e26-93df-6e6e2fe458a9"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "content_id": "Cut1",
                         "errors": null,
-                        "id": 31,
+                        "id": 42,
                         "input_connections": {
-                            "adata": {
-                                "id": 29,
-                                "output_name": "anndata"
+                            "input": {
+                                "id": 39,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
-                        "label": "Complex DotPlot with new labels",
-                        "name": "Plot",
+                        "label": null,
+                        "name": "Cut",
                         "outputs": [
                             {
-                                "name": "out_png",
-                                "type": "png"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "bottom": 733.4666748046875,
-                            "height": 156.79998779296875,
-                            "left": 1860.449951171875,
-                            "right": 2060.449951171875,
-                            "top": 576.6666870117188,
-                            "width": 200,
-                            "x": 1860.449951171875,
-                            "y": 576.6666870117188
+                            "left": 4468.2109375,
+                            "top": 1199.2890625
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6adf98e782f3",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Markers - genotype - named"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.dotplot\", \"__current_case__\": 2, \"var_names\": {\"type\": \"custom\", \"__current_case__\": 1, \"var_names\": \"AT1G26680,COBL2,AT3G55180,NCED2,AT5G22550,ATL63,RGF8,TEL1,DUF9,AGL42,PLT1,PLT2,PER3,PER9,PBL15,TBL30,AT2G48130,AT3G22620,AED3,T3P18-7,MBK21-8,NPF6-4,CYP71B34,IAMT1,AT1G31950,F14G6-22,GL2,ANL2,PMEI4,MUD21-4,EXPA7,MES15,ADF8,COBL9,TPR14,BHLH144,MYB83,SCPL35,MYB46,COBL4,PIN7,PIN3   \"}, \"groupby\": \"leiden\", \"num_categories\": \"9\", \"log\": \"false\", \"use_raw\": \"true\", \"dendrogram\": \"false\", \"var_group_positions\": [{\"__index__\": 0, \"start\": \"0\", \"end\": \"5\", \"label\": \"Columella\"}, {\"__index__\": 1, \"start\": \"6\", \"end\": \"9\", \"label\": \"QC\"}, {\"__index__\": 2, \"start\": \"10\", \"end\": \"11\", \"label\": \"NC\"}, {\"__index__\": 3, \"start\": \"12\", \"end\": \"17\", \"label\": \"Endodermis\"}, {\"__index__\": 4, \"start\": \"18\", \"end\": \"23\", \"label\": \"Cortex\"}, {\"__index__\": 5, \"start\": \"24\", \"end\": \"29\", \"label\": \"Atrichoblast\"}, {\"__index__\": 6, \"start\": \"30\", \"end\": \"34\", \"label\": \"Trichoblast\"}, {\"__index__\": 7, \"start\": \"35\", \"end\": \"39\", \"label\": \"Xylem\"}, {\"__index__\": 8, \"start\": \"40\", \"end\": \"41\", \"label\": \"VC\"}], \"var_group_rotation\": null, \"figsize\": {\"test\": \"no\", \"__current_case__\": 1}, \"layer\": \"\", \"color_map\": \"viridis\", \"dot_max\": null, \"dot_min\": null, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy0",
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"columnList\": \"c1,c2,c3,c4,c11,c5,c6,c7,c8\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2",
                         "type": "tool",
-                        "uuid": "a2f04375-1e67-4764-ae78-2678dcf2c03a",
+                        "uuid": "995cfd57-925a-470e-879b-8d7eb619c67b",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_png",
-                                "uuid": "329e95de-cf53-4c0b-9a9b-ad30632ceeb8"
+                                "label": "Markers - genotype - named",
+                                "output_name": "out_file1",
+                                "uuid": "fdb88faa-9b76-4edb-b89b-427c098a473e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
                         "errors": null,
-                        "id": 32,
+                        "id": 43,
                         "input_connections": {
-                            "adata": {
-                                "id": 29,
-                                "output_name": "anndata"
+                            "input_obj_file": {
+                                "id": 40,
+                                "output_name": "output_h5ad"
                             }
                         },
-                        "inputs": [],
-                        "label": "Plot UMAP with new labels",
-                        "name": "Plot",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Scanpy PlotEmbed",
+                                "name": "input_obj_file"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Scanpy PlotEmbed",
                         "outputs": [
                             {
-                                "name": "out_png",
+                                "name": "output_png",
                                 "type": "png"
                             }
                         ],
                         "position": {
-                            "bottom": 885.3999938964844,
-                            "height": 136.39999389648438,
-                            "left": 1863,
-                            "right": 2063,
-                            "top": 749,
-                            "width": 200,
-                            "x": 1863,
-                            "y": 749
+                            "left": 4653.7109375,
+                            "top": 231.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "6adf98e782f3",
-                            "name": "scanpy_plot",
-                            "owner": "iuc",
+                            "changeset_revision": "56d22aa6cb3b",
+                            "name": "scanpy_plot_embed",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"format\": \"png\", \"method\": {\"method\": \"pl.umap\", \"__current_case__\": 14, \"color\": \"leiden, batch\", \"use_raw\": \"false\", \"edges\": {\"edges\": \"False\", \"__current_case__\": 1}, \"arrows\": \"false\", \"sort_order\": \"true\", \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"on data\", \"legend_fontsize\": \"14\", \"legend_fontweight\": \"normal\", \"size\": null, \"color_map\": \"None\", \"palette\": \"rainbow\", \"frameon\": \"true\", \"ncols\": \"4\", \"wspace\": \"0.1\", \"hspace\": \"0.25\", \"title\": \"\"}, \"matplotlib_pyplot_scatter\": {\"alpha\": null, \"vmin\": null, \"vmax\": null, \"linewidths\": \"0.0\", \"edgecolors\": \"face\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.1+galaxy0",
+                        "tool_state": "{\"basis\": \"umap\", \"color_by\": \"sex,batch,genotype,Il2ra,Cd8b1,Cd8a,Cd4,Itm2a,Aif1,log1p_total_counts,Hba-a1,cell_type\", \"components\": \"\", \"edges\": \"false\", \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": \"false\", \"fig_size\": \"4,4\", \"fig_title\": \"\", \"gene_symbols_field\": \"Symbol\", \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"RuntimeValue\"}, \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": \"false\", \"use_raw\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy0",
                         "type": "tool",
-                        "uuid": "c83c81b0-cd9e-41c5-8b72-4b024b7260dc",
+                        "uuid": "ff379bdf-e875-4803-baa0-b11bd71666db",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_png",
-                                "uuid": "579d19d3-a98c-4e3a-92aa-0b65e2ffcefd"
+                                "output_name": "output_png",
+                                "uuid": "cb97c2f3-8e23-45d0-bc96-faf2f06b59d0"
                             }
                         ]
                     }
                 ],
-                "parent_id": "single-cell/scrna-plant",
-                "path": "topics/single-cell/tutorials/scrna-plant/workflows/main_workflow.ga",
-                "tags": [
-                    "transcriptomics",
-                    "single-cell"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "scRNA Plant Analysis",
-                "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-plant/versions/main-workflow",
-                "tutorial_id": "scrna-plant",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-plant/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-plant/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "single-cell-scrna-plant",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0"
-                ],
-                "workflowhub_id": "1266"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/4597857"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plates-batches-barcodes/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "bio": "Senior Lecturer at The Open University",
-                "elixir_node": "uk",
-                "email": "wendi.bacon@open.ac.uk",
-                "fediverse": "https://mstdn.science/@wendibacon1",
-                "fediverse_flavor": "mastodon",
-                "id": "nomadscientist",
-                "joined": "2020-03",
-                "matrix": "nomadscientist:matrix.org",
-                "name": "Wendi Bacon",
-                "orcid": "0000-0002-8170-8806",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
-                "twitter": "WendiBacon1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "elixir_node": "de",
-                "email": "mtekman89@gmail.com",
-                "former_affiliations": [
-                    "elixir-europe"
-                ],
-                "id": "mtekman",
-                "joined": "2018-11",
-                "name": "Mehmet Tekman",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
-            },
-            {
-                "email": "a.ostrovsky@mac.com",
-                "id": "astrovsky01",
-                "joined": "2019-06",
-                "name": "Alex Ostrovsky",
-                "orcid": "0000-0002-7901-7109",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/astrovsky01/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/astrovsky01.json"
-            }
-        ],
-        "dir": "topics/single-cell/tutorials/scrna-plates-batches-barcodes",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": false,
-        "id": "single-cell/scrna-plates-batches-barcodes",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": 7126,
-            "mermaid": false
-        },
-        "key_points": [
-            "Balanced batches and replicates allow bioinformatic batch correction",
-            "A sequencing lane often contains multiple batches, and is itself a batch effect!"
-        ],
-        "layout": "tutorial_slides",
-        "license": "CC-BY-4.0",
-        "logo": "GTN",
-        "mod_date": "2023-10-10",
-        "objectives": [
-            "How to set up plates to prevent batch effect",
-            "Proper naming conventions when dealing with scRNA-seq samples"
-        ],
-        "pageviews": 5726884,
-        "priority": 3,
-        "pub_date": "2019-02-16",
-        "questions": [
-            "What is a batch when it comes to single cells?",
-            "What\u2019s the difference between a barcode and an index?",
-            "What is batch effect and how do you prevent it?",
-            "What is a lane?"
-        ],
-        "redirect_from": [
-            "/topics/transcriptomics/tutorials/scrna-plates-batches-barcodes/slides",
-            "/short/single-cell/scrna-plates-batches-barcodes/slides",
-            "/short/S00085"
-        ],
-        "short_id": "S00085",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
-        "subtopic": "scintroduction",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": null,
-        "time_estimation": "1h",
-        "title": "Plates, Batches, and Barcodes",
-        "tools": [],
-        "topic_name": "single-cell",
-        "topic_name_human": "Single Cell",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": true
-        },
-        "tutorial_name": "scrna-plates-batches-barcodes",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-plates-batches-barcodes/slides.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plates-batches-barcodes/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plates-batches-barcodes/slides.json"
-        },
-        "version": 2,
-        "video": true,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758,
-        "zenodo_link": ""
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_JUPYTER-trajectories/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "nomadscientist",
-                "wee-snufkin",
-                "mtekman"
-            ],
-            "editing": [
-                "hexylena"
-            ]
-        },
-        "contributors": [
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "bio": "Senior Lecturer at The Open University",
-                "elixir_node": "uk",
-                "email": "wendi.bacon@open.ac.uk",
-                "fediverse": "https://mstdn.science/@wendibacon1",
-                "fediverse_flavor": "mastodon",
-                "id": "nomadscientist",
-                "joined": "2020-03",
-                "matrix": "nomadscientist:matrix.org",
-                "name": "Wendi Bacon",
-                "orcid": "0000-0002-8170-8806",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
-                "twitter": "WendiBacon1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
-            },
-            {
-                "email": "juliajot36@gmail.com",
-                "id": "wee-snufkin",
-                "joined": "2022-06",
-                "name": "Julia Jakiela",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "elixir_node": "de",
-                "email": "mtekman89@gmail.com",
-                "former_affiliations": [
-                    "elixir-europe"
-                ],
-                "id": "mtekman",
-                "joined": "2018-11",
-                "name": "Mehmet Tekman",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            }
-        ],
-        "dir": "topics/single-cell/tutorials/scrna-case_JUPYTER-trajectories",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "single-cell/scrna-case_JUPYTER-trajectories",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Trajectory analysis is less robust than pure plotting methods, as such 'inferred relationships' are a bigger mathematical leap",
-            "As always with single-cell analysis, you must know enough biology to deduce if your analysis is reasonable, before exploring or deducing novel insight"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
-        "notebook": {
-            "language": "python",
-            "snippet": "topics/single-cell/tutorials/scrna-case_JUPYTER-trajectories/preamble.md"
-        },
-        "objectives": [
-            "Execute multiple plotting methods designed to maintain lineage relationships between cells",
-            "Interpret these plots"
-        ],
-        "pageviews": 3234,
-        "priority": 3,
-        "pub_date": "2021-04-07",
-        "questions": [
-            "How can I infer lineage relationships between single cells based on their RNA, without a time series?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "nomadscientist"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "10M",
-                "speakers": [
-                    "nomadscientist"
-                ],
-                "youtube_id": "VEyTmwDIgPI"
-            }
-        ],
-        "redirect_from": [
-            "/topics/transcriptomics/tutorials/scrna-JUPYTER-trajectories/tutorial",
-            "/topics/transcriptomics/tutorials/scrna-case_JUPYTER-trajectories/tutorial",
-            "/short/single-cell/scrna-case_JUPYTER-trajectories",
-            "/short/T00244"
-        ],
-        "requirements": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-case_alevin",
-                    "scrna-case_alevin-combine-datasets",
-                    "scrna-case_basic-pipeline"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "galaxy-intro-jupyter"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00244",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "single-cell-CS-code",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "10x",
-            "paper-replication",
-            "Python"
-        ],
-        "time_estimation": "2H",
-        "title": "Inferring single cell trajectories with Scanpy (Python)",
-        "tools": [],
-        "topic_name": "single-cell",
-        "topic_name_human": "Single Cell",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "scrna-case_JUPYTER-trajectories",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_JUPYTER-trajectories/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_JUPYTER-trajectories/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_JUPYTER-trajectories/tutorial.json"
-        },
-        "version": 15,
-        "video": false,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 80,
-        "visitors": 2724,
-        "zenodo_link": "https://zenodo.org/record/7075718"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "retrieve_scxa",
-                    "owner": "ebi-gxa",
-                    "revisions": "72b6e1747e37",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "seurat_filter_cells",
-                    "owner": "ebi-gxa",
-                    "revisions": "cd9f564bd63f",
-                    "tool_panel_section_label": "Seurat",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "seurat_find_clusters",
-                    "owner": "ebi-gxa",
-                    "revisions": "d541e9e62beb",
-                    "tool_panel_section_label": "Seurat",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "seurat_find_markers",
-                    "owner": "ebi-gxa",
-                    "revisions": "07fc9f4841b3",
-                    "tool_panel_section_label": "Seurat",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "seurat_find_neighbours",
-                    "owner": "ebi-gxa",
-                    "revisions": "ba897c57bdd9",
-                    "tool_panel_section_label": "Seurat",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "seurat_find_variable_genes",
-                    "owner": "ebi-gxa",
-                    "revisions": "948fc0276b4f",
-                    "tool_panel_section_label": "Seurat",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "seurat_normalise_data",
-                    "owner": "ebi-gxa",
-                    "revisions": "3f49bc9c9213",
-                    "tool_panel_section_label": "Seurat",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "seurat_plot",
-                    "owner": "ebi-gxa",
-                    "revisions": "95d79f1134f0",
-                    "tool_panel_section_label": "HCA-Scanpy",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "seurat_read10x",
-                    "owner": "ebi-gxa",
-                    "revisions": "f5db0e853f57",
-                    "tool_panel_section_label": "Seurat",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "seurat_run_pca",
-                    "owner": "ebi-gxa",
-                    "revisions": "8ded486b0014",
-                    "tool_panel_section_label": "Seurat",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "seurat_run_umap",
-                    "owner": "ebi-gxa",
-                    "revisions": "b9424c715a0d",
-                    "tool_panel_section_label": "HCA-Scanpy",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "seurat_scale_data",
-                    "owner": "ebi-gxa",
-                    "revisions": "5e9ba303f9e1",
-                    "tool_panel_section_label": "Seurat",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: retrieve_scxa\n  owner: ebi-gxa\n  revisions: 72b6e1747e37\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_filter_cells\n  owner: ebi-gxa\n  revisions: cd9f564bd63f\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_find_clusters\n  owner: ebi-gxa\n  revisions: d541e9e62beb\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_find_markers\n  owner: ebi-gxa\n  revisions: 07fc9f4841b3\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_find_neighbours\n  owner: ebi-gxa\n  revisions: ba897c57bdd9\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_find_variable_genes\n  owner: ebi-gxa\n  revisions: 948fc0276b4f\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_normalise_data\n  owner: ebi-gxa\n  revisions: 3f49bc9c9213\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_plot\n  owner: ebi-gxa\n  revisions: 95d79f1134f0\n  tool_panel_section_label: HCA-Scanpy\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_read10x\n  owner: ebi-gxa\n  revisions: f5db0e853f57\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_run_pca\n  owner: ebi-gxa\n  revisions: 8ded486b0014\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_run_umap\n  owner: ebi-gxa\n  revisions: b9424c715a0d\n  tool_panel_section_label: HCA-Scanpy\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_scale_data\n  owner: ebi-gxa\n  revisions: 5e9ba303f9e1\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "Camila-goclowski",
-                "pcm32"
-            ],
-            "editing": [
-                "pavanvidem",
-                "hexylena"
-            ]
-        },
-        "contributors": [
-            {
-                "email": "camila.goclowski@gmail.com",
-                "id": "Camila-goclowski",
-                "joined": "2023-01",
-                "linkedin": "camila-goclowski",
-                "name": "Camila Goclowski",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Camila-goclowski/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/Camila-goclowski.json"
-            },
-            {
-                "id": "pcm32",
-                "joined": "2019-06",
-                "name": "Pablo Moreno",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pcm32/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pcm32.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "pavanvidem",
-                "joined": "2017-09",
-                "name": "Pavankumar Videm",
-                "orcid": "0000-0002-5192-126X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            }
-        ],
-        "dir": "topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "single-cell/scrna-case_FilterPlotandExplore_SeuratTools",
-        "inexact_supported_servers": [],
-        "input_histories": [
-            {
-                "history": "https://singlecell.usegalaxy.eu/u/camila-goclowski/h/tool-based-seurat-fpe-input-data",
-                "label": "UseGalaxy.eu"
-            }
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-13",
-        "objectives": [
-            "Interpret quality control plots to direct parameter decisions",
-            "Repeat analysis from matrix to clustering to labelling clusters",
-            "Identify decision-making points",
-            "Appraise data outputs and decisions",
-            "Explain why single cell analysis is an iterative process (i.e. the first plots you generate are not final, but rather you go back and re-analyse your data repeatedly)"
-        ],
-        "pageviews": 391,
-        "priority": 3,
-        "pub_date": "2024-04-09",
-        "questions": [
-            "Is my single cell dataset a quality dataset?",
-            "How do I pick thresholds and parameters in my analysis? What\u2019s a \u201creasonable\u201d number, and will the world collapse if I pick the wrong one?",
-            "How do I generate and annotate cell clusters?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-intro",
-                    "scrna-preprocessing-tenx"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00438",
-        "short_tools": [
-            "seurat_find_markers",
-            "seurat_filter_cells",
-            "seurat_run_umap",
-            "seurat_scale_data",
-            "seurat_find_neighbours",
-            "seurat_find_variable_genes",
-            "seurat_read10x",
-            "retrieve_scxa",
-            "seurat_run_pca",
-            "seurat_find_clusters",
-            "seurat_normalise_data",
-            "seurat_plot"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "single-cell-CS",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "10x",
-            "paper-replication"
-        ],
-        "time_estimation": "3H",
-        "title": "Filter, plot, and explore single cell RNA-seq data with Seurat",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_filter_cells/seurat_filter_cells/4.0.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters/4.0.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_markers/seurat_find_markers/4.0.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_neighbours/seurat_find_neighbours/4.0.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes/4.0.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data/4.0.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_plot/seurat_plot/4.0.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/4.0.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_pca/seurat_run_pca/4.0.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_umap/seurat_run_umap/4.0.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_scale_data/seurat_scale_data/4.0.4+galaxy0"
-        ],
-        "topic_name": "single-cell",
-        "topic_name_human": "Single Cell",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "scrna-case_FilterPlotandExplore_SeuratTools",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.json"
-        },
-        "version": 3,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 25,
-        "visitors": 338,
-        "zenodo_link": "https://zenodo.org/record/7053673"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "music_compare",
-                    "owner": "bgruening",
-                    "revisions": "4447ed460308",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: music_compare\n  owner: bgruening\n  revisions: 4447ed460308\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music-4-compare/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "nomadscientist",
-                "mtekman"
-            ],
-            "testing": [
-                "MarisaJL"
-            ]
-        },
-        "contributors": [
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "bio": "Senior Lecturer at The Open University",
-                "elixir_node": "uk",
-                "email": "wendi.bacon@open.ac.uk",
-                "fediverse": "https://mstdn.science/@wendibacon1",
-                "fediverse_flavor": "mastodon",
-                "id": "nomadscientist",
-                "joined": "2020-03",
-                "matrix": "nomadscientist:matrix.org",
-                "name": "Wendi Bacon",
-                "orcid": "0000-0002-8170-8806",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
-                "twitter": "WendiBacon1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg"
+                "parent_id": "single-cell/scrna-case_basic-pipeline",
+                "path": "topics/single-cell/tutorials/scrna-case_basic-pipeline/workflows/CS3_Filter,_Plot_and_Explore_Single-cell_RNA-seq_Data.ga",
+                "tags": [
+                    "name:transcriptomics",
+                    "name:training",
+                    "name:singlecell"
                 ],
-                "elixir_node": "de",
-                "email": "mtekman89@gmail.com",
-                "former_affiliations": [
-                    "elixir-europe"
+                "test_results": null,
+                "tests": false,
+                "title": "CS3_Filter, Plot and Explore Single-cell RNA-seq Data",
+                "topic_id": "single-cell",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-case_basic-pipeline/versions/cs3-filter--plot-and-explore-single-cell-rna-seq-data",
+                "tutorial_id": "scrna-case_basic-pipeline",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_basic-pipeline/workflows/CS3_Filter,_Plot_and_Explore_Single-cell_RNA-seq_Data.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_basic-pipeline/workflows/CS3_Filter,_Plot_and_Explore_Single-cell_RNA-seq_Data.html",
+                "version": 1,
+                "wfid": "single-cell-scrna-case_basic-pipeline",
+                "wfname": "cs3-filter--plot-and-explore-single-cell-rna-seq-data",
+                "workflow": "CS3_Filter,_Plot_and_Explore_Single-cell_RNA-seq_Data.ga",
+                "workflow_tools": [
+                    "Cut1",
+                    "join1",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1"
                 ],
-                "id": "mtekman",
-                "joined": "2018-11",
-                "name": "Mehmet Tekman",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
+                "workflowhub_id": "1219"
             },
-            {
-                "email": "marisa.loach@open.ac.uk",
-                "id": "MarisaJL",
-                "joined": "2022-10",
-                "name": "Marisa Loach",
-                "orcid": "0000-0001-6979-6930",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/MarisaJL/",
-                "twitter": "Marisa_Loach",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/MarisaJL.json"
-            }
-        ],
-        "dir": "topics/single-cell/tutorials/bulk-music-4-compare",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "single-cell/bulk-music-4-compare",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Deconvolution can be used to compare cell type distributions from bulk RNA-seq datasets"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Apply the MuSiC deconvolution to samples and compare the cell type distributions",
-            "Compare the results from analysing different types of input, for example, whether combining disease and healthy references or not yields better results"
-        ],
-        "pageviews": 295,
-        "priority": 4,
-        "pub_date": "2023-01-20",
-        "questions": [
-            "How do the cell type distributions vary in bulk RNA samples across my variable of interest?",
-            "For example, are beta cell proportions different in the pancreas data from diabetes and healthy patients?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "bulk-music",
-                    "bulk-music-2-preparescref",
-                    "bulk-music-3-preparebulk"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00243",
-        "short_tools": [
-            "music_compare"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "deconvo",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "transcriptomics"
-        ],
-        "time_estimation": "1H",
-        "title": "Comparing inferred cell compositions using MuSiC deconvolution",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4"
-        ],
-        "topic_name": "single-cell",
-        "topic_name_human": "Single Cell",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "bulk-music-4-compare",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music-4-compare/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music-4-compare/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music-4-compare/tutorial.json"
-        },
-        "version": 8,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 49,
-        "visitors": 166,
-        "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "https://orcid.org/0000-0002-8170-8806",
+                        "identifier": "0000-0002-8170-8806",
                         "name": "Wendi Bacon"
                     },
                     {
                         "class": "Person",
-                        "identifier": "0000-0002-4181-2676",
-                        "name": "Mehmet Tekman"
+                        "identifier": "0009-0001-2017-8805",
+                        "name": "Julia Jakiela"
                     }
                 ],
-                "description": "This workflow runs 3 comparisons using MuSiC Deconvolution compare: where datasets cell compositions are inferred from a reference containing healthy and diseased cells; where diseased are inferred from disease and healthy from healthy; and where both diseased and healthy are inferred from a healthy reference.",
+                "description": "Filter, Plot and Explore Single-cell RNA-seq Data",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nESet Object - Single cell:T2D\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nESet Object - Single cell:normal\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nESet Object - Bulk:normal\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nESet Object - Bulk:T2D\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nESet Object - Single cell Total\"]\n  5[label=\"MuSiC Compare: Like with like\"]\n  2 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"MuSiC Compare: healthyscref\"]\n  2 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"MuSiC Compare - Altogether\"]\n  2 -> 7 [label=\"output\"]\n  3 -> 7 [label=\"output\"]\n  4 -> 7 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMito-counted AnnData\"]\n  1[label=\"Inspect AnnData\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Scanpy FilterCells\"]\n  0 -> 2 [label=\"output\"]\n  k6a00b14bd3f84771963a76115c8eaf2f[color=lightseagreen,label=\"Output\\nGenes-filtered Object\"]\n  2 -> k6a00b14bd3f84771963a76115c8eaf2f\n  3[label=\"Plot\"]\n  0 -> 3 [label=\"output\"]\n  kc123842eb2d243ad81f06ba3b45d4021[color=lightseagreen,label=\"Output\\nScatter - genes x UMIs\"]\n  3 -> kc123842eb2d243ad81f06ba3b45d4021\n  4[label=\"Plot\"]\n  0 -> 4 [label=\"output\"]\n  kf1020d4d555e42faba2152a151b91a5b[color=lightseagreen,label=\"Output\\nScatter - mito x genes\"]\n  4 -> kf1020d4d555e42faba2152a151b91a5b\n  5[label=\"Plot\"]\n  0 -> 5 [label=\"output\"]\n  ka7fe60208f1e470a9ed3f2b5e95516e0[color=lightseagreen,label=\"Output\\nViolin - genotype - log\"]\n  5 -> ka7fe60208f1e470a9ed3f2b5e95516e0\n  6[label=\"Plot\"]\n  0 -> 6 [label=\"output\"]\n  k15e501bc8ddb451989ebdde431ea96c1[color=lightseagreen,label=\"Output\\nViolin - batch - log\"]\n  6 -> k15e501bc8ddb451989ebdde431ea96c1\n  7[label=\"Inspect AnnData\"]\n  0 -> 7 [label=\"output\"]\n  8[label=\"Plot\"]\n  0 -> 8 [label=\"output\"]\n  keff22f46baa64e00ba82d5e12ce26ff0[color=lightseagreen,label=\"Output\\nScatter - mito x UMIs\"]\n  8 -> keff22f46baa64e00ba82d5e12ce26ff0\n  9[label=\"Inspect AnnData\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"Plot\"]\n  0 -> 10 [label=\"output\"]\n  k56677ca4129c476c85ec69d1bb3d800d[color=lightseagreen,label=\"Output\\nViolin - sex - log\"]\n  10 -> k56677ca4129c476c85ec69d1bb3d800d\n  11[label=\"Plot\"]\n  2 -> 11 [label=\"output_h5ad\"]\n  kacb61ea4bcb945dbbeefe2bf1a176701[color=lightseagreen,label=\"Output\\nViolin - Filterbygenes\"]\n  11 -> kacb61ea4bcb945dbbeefe2bf1a176701\n  12[label=\"Scanpy FilterCells\"]\n  2 -> 12 [label=\"output_h5ad\"]\n  k5185366245194229a2eab22a53e7ef73[color=lightseagreen,label=\"Output\\nCounts-filtered Object\"]\n  12 -> k5185366245194229a2eab22a53e7ef73\n  13[label=\"Inspect AnnData\"]\n  2 -> 13 [label=\"output_h5ad\"]\n  k362a7fe624bb4398ae48870f4b4bb774[color=lightseagreen,label=\"Output\\nGeneral - Filterbygenes\"]\n  13 -> k362a7fe624bb4398ae48870f4b4bb774\n  14[label=\"Inspect AnnData\"]\n  12 -> 14 [label=\"output_h5ad\"]\n  kedf2414993414fe7b10c3fcf092faaa5[color=lightseagreen,label=\"Output\\nGeneral - Filterbycounts\"]\n  14 -> kedf2414993414fe7b10c3fcf092faaa5\n  15[label=\"Scanpy FilterCells\"]\n  12 -> 15 [label=\"output_h5ad\"]\n  ka88ec405265f4a59a75e34e3b05b0096[color=lightseagreen,label=\"Output\\nMito-filtered Object\"]\n  15 -> ka88ec405265f4a59a75e34e3b05b0096\n  16[label=\"Plot\"]\n  12 -> 16 [label=\"output_h5ad\"]\n  ka7c8b0d982d34438a212b5f7c56d36b8[color=lightseagreen,label=\"Output\\nViolin - Filterbycounts\"]\n  16 -> ka7c8b0d982d34438a212b5f7c56d36b8\n  17[label=\"Inspect AnnData\"]\n  15 -> 17 [label=\"output_h5ad\"]\n  k56882809e19f451a8010bc55dcee482f[color=lightseagreen,label=\"Output\\nGeneral - Filterbymito\"]\n  17 -> k56882809e19f451a8010bc55dcee482f\n  18[label=\"Scanpy FilterGenes\"]\n  15 -> 18 [label=\"output_h5ad\"]\n  k00846477dec5408a83b2105fff7ce05b[color=lightseagreen,label=\"Output\\nFiltered Object\"]\n  18 -> k00846477dec5408a83b2105fff7ce05b\n  19[label=\"Plot\"]\n  15 -> 19 [label=\"output_h5ad\"]\n  k7582e11320044255a1f3d3123373f342[color=lightseagreen,label=\"Output\\nViolin - Filterbymito\"]\n  19 -> k7582e11320044255a1f3d3123373f342\n  20[label=\"Inspect AnnData\"]\n  18 -> 20 [label=\"output_h5ad\"]\n  k2d870a40c6024a1cafef450489354d39[color=lightseagreen,label=\"Output\\nGeneral - Filtered object\"]\n  20 -> k2d870a40c6024a1cafef450489354d39\n  21[label=\"Scanpy NormaliseData\"]\n  18 -> 21 [label=\"output_h5ad\"]\n  22[label=\"Scanpy FindVariableGenes\"]\n  21 -> 22 [label=\"output_h5ad\"]\n  ka0eb92b102634179b7af4bd9bcc9c960[color=lightseagreen,label=\"Output\\nUse_me_FVG\"]\n  22 -> ka0eb92b102634179b7af4bd9bcc9c960\n  23[label=\"Scanpy ScaleData\"]\n  22 -> 23 [label=\"output_h5ad\"]\n  k5776dbb90cac40c09bae9accae16a7a0[color=lightseagreen,label=\"Output\\nUse_me_Scaled\"]\n  23 -> k5776dbb90cac40c09bae9accae16a7a0\n  24[label=\"Scanpy RunPCA\"]\n  23 -> 24 [label=\"output_h5ad\"]\n  25[label=\"Plot\"]\n  24 -> 25 [label=\"output_h5ad\"]\n  kf0b6f578050f49369ee79956b0760c6f[color=lightseagreen,label=\"Output\\nPCA Variance\"]\n  25 -> kf0b6f578050f49369ee79956b0760c6f\n  26[label=\"Scanpy ComputeGraph\"]\n  24 -> 26 [label=\"output_h5ad\"]\n  27[label=\"Scanpy RunTSNE\"]\n  26 -> 27 [label=\"output_h5ad\"]\n  28[label=\"Scanpy RunUMAP\"]\n  27 -> 28 [label=\"output_h5ad\"]\n  29[label=\"Scanpy FindCluster\"]\n  28 -> 29 [label=\"output_h5ad\"]\n  30[label=\"Scanpy FindMarkers\"]\n  29 -> 30 [label=\"output_h5ad\"]\n  k7cfe5c9c1c8041b4b669633b1d7d40e3[color=lightseagreen,label=\"Output\\nMarkers - cluster\"]\n  30 -> k7cfe5c9c1c8041b4b669633b1d7d40e3\n  k98e98405951e4c6cbe013c925ae35449[color=lightseagreen,label=\"Output\\nFinal object\"]\n  30 -> k98e98405951e4c6cbe013c925ae35449\n  31[label=\"Scanpy FindMarkers\"]\n  29 -> 31 [label=\"output_h5ad\"]\n  k1e9f229deb344a5ba6d9e70c7b0581f4[color=lightseagreen,label=\"Output\\nMarkers - genotype\"]\n  31 -> k1e9f229deb344a5ba6d9e70c7b0581f4\n  32[label=\"Scanpy PlotEmbed\"]\n  30 -> 32 [label=\"output_h5ad\"]\n  33[label=\"Scanpy PlotEmbed\"]\n  30 -> 33 [label=\"output_h5ad\"]\n  34[label=\"Manipulate AnnData\"]\n  30 -> 34 [label=\"output_h5ad\"]\n  35[label=\"Scanpy PlotEmbed\"]\n  30 -> 35 [label=\"output_h5ad\"]\n  36[label=\"Inspect AnnData\"]\n  30 -> 36 [label=\"output_h5ad\"]\n  37[label=\"AnnData Operations\"]\n  34 -> 37 [label=\"anndata\"]\n  30 -> 37 [label=\"output_h5ad\"]\n  38[label=\"Join two Datasets\"]\n  30 -> 38 [label=\"output_tsv\"]\n  36 -> 38 [label=\"var\"]\n  39[label=\"Join two Datasets\"]\n  31 -> 39 [label=\"output_tsv\"]\n  36 -> 39 [label=\"var\"]\n  40[label=\"AnnData Operations\"]\n  37 -> 40 [label=\"output_h5ad\"]\n  k10bd70f8ffcb442b9647e5b947b6d35e[color=lightseagreen,label=\"Output\\nFinal cell annotated object\"]\n  40 -> k10bd70f8ffcb442b9647e5b947b6d35e\n  41[label=\"Cut\"]\n  38 -> 41 [label=\"out_file1\"]\n  k4f822c1c91c54be48f9bd5bdda0a037e[color=lightseagreen,label=\"Output\\nMarkers - cluster - named\"]\n  41 -> k4f822c1c91c54be48f9bd5bdda0a037e\n  42[label=\"Cut\"]\n  39 -> 42 [label=\"out_file1\"]\n  k3b471f3d263d42999b7d8a8ae1aa556e[color=lightseagreen,label=\"Output\\nMarkers - genotype - named\"]\n  42 -> k3b471f3d263d42999b7d8a8ae1aa556e\n  43[label=\"Scanpy PlotEmbed\"]\n  40 -> 43 [label=\"output_h5ad\"]\n}",
                 "history": [
                     {
-                        "hash": "9a561b3752745eab20cececd5346ee0a7449da28",
-                        "message": "update workflows",
+                        "hash": "9a3fc8a6dad6c8d1b7b9897056cc75af00a12c57",
+                        "message": "new workflow tests",
                         "num": 1,
-                        "short_hash": "9a561b375",
-                        "unix": "1669581042"
+                        "short_hash": "9a3fc8a6d",
+                        "unix": "1686345087"
                     }
                 ],
                 "inputs": [
@@ -236827,2466 +240435,3015 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "ESet Object - Single cell:T2D"
+                                "name": "Mito-counted AnnData"
                             }
                         ],
-                        "label": "ESet Object - Single cell:T2D",
+                        "label": "Mito-counted AnnData",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 2.0234375,
-                            "top": 87.03125
+                            "left": 0,
+                            "top": 761.9687652587891
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "16ac774b-2363-4b80-aef3-c931c2e7be39",
+                        "uuid": "1d8303cb-de77-4164-923c-127a4e60d8e6",
+                        "when": null,
                         "workflow_outputs": []
-                    },
+                    }
+                ],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nMito-counted AnnData\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Inspect AnnData\"];\n  0 -->|output| 1;\n  2[\"Scanpy FilterCells\"];\n  0 -->|output| 2;\n  6a00b14b-d3f8-4771-963a-76115c8eaf2f[\"Output\\nGenes-filtered Object\"];\n  2 --> 6a00b14b-d3f8-4771-963a-76115c8eaf2f;\n  style 6a00b14b-d3f8-4771-963a-76115c8eaf2f stroke:#2c3143,stroke-width:4px;\n  3[\"Plot\"];\n  0 -->|output| 3;\n  c123842e-b2d2-43ad-81f0-6ba3b45d4021[\"Output\\nScatter - genes x UMIs\"];\n  3 --> c123842e-b2d2-43ad-81f0-6ba3b45d4021;\n  style c123842e-b2d2-43ad-81f0-6ba3b45d4021 stroke:#2c3143,stroke-width:4px;\n  4[\"Plot\"];\n  0 -->|output| 4;\n  f1020d4d-555e-42fa-ba21-52a151b91a5b[\"Output\\nScatter - mito x genes\"];\n  4 --> f1020d4d-555e-42fa-ba21-52a151b91a5b;\n  style f1020d4d-555e-42fa-ba21-52a151b91a5b stroke:#2c3143,stroke-width:4px;\n  5[\"Plot\"];\n  0 -->|output| 5;\n  a7fe6020-8f1e-470a-9ed3-f2b5e95516e0[\"Output\\nViolin - genotype - log\"];\n  5 --> a7fe6020-8f1e-470a-9ed3-f2b5e95516e0;\n  style a7fe6020-8f1e-470a-9ed3-f2b5e95516e0 stroke:#2c3143,stroke-width:4px;\n  6[\"Plot\"];\n  0 -->|output| 6;\n  15e501bc-8ddb-4519-89eb-dde431ea96c1[\"Output\\nViolin - batch - log\"];\n  6 --> 15e501bc-8ddb-4519-89eb-dde431ea96c1;\n  style 15e501bc-8ddb-4519-89eb-dde431ea96c1 stroke:#2c3143,stroke-width:4px;\n  7[\"Inspect AnnData\"];\n  0 -->|output| 7;\n  8[\"Plot\"];\n  0 -->|output| 8;\n  eff22f46-baa6-4e00-ba82-d5e12ce26ff0[\"Output\\nScatter - mito x UMIs\"];\n  8 --> eff22f46-baa6-4e00-ba82-d5e12ce26ff0;\n  style eff22f46-baa6-4e00-ba82-d5e12ce26ff0 stroke:#2c3143,stroke-width:4px;\n  9[\"Inspect AnnData\"];\n  0 -->|output| 9;\n  10[\"Plot\"];\n  0 -->|output| 10;\n  56677ca4-129c-476c-85ec-69d1bb3d800d[\"Output\\nViolin - sex - log\"];\n  10 --> 56677ca4-129c-476c-85ec-69d1bb3d800d;\n  style 56677ca4-129c-476c-85ec-69d1bb3d800d stroke:#2c3143,stroke-width:4px;\n  11[\"Plot\"];\n  2 -->|output_h5ad| 11;\n  acb61ea4-bcb9-45db-beef-e2bf1a176701[\"Output\\nViolin - Filterbygenes\"];\n  11 --> acb61ea4-bcb9-45db-beef-e2bf1a176701;\n  style acb61ea4-bcb9-45db-beef-e2bf1a176701 stroke:#2c3143,stroke-width:4px;\n  12[\"Scanpy FilterCells\"];\n  2 -->|output_h5ad| 12;\n  51853662-4519-4229-a2ea-b22a53e7ef73[\"Output\\nCounts-filtered Object\"];\n  12 --> 51853662-4519-4229-a2ea-b22a53e7ef73;\n  style 51853662-4519-4229-a2ea-b22a53e7ef73 stroke:#2c3143,stroke-width:4px;\n  13[\"Inspect AnnData\"];\n  2 -->|output_h5ad| 13;\n  362a7fe6-24bb-4398-ae48-870f4b4bb774[\"Output\\nGeneral - Filterbygenes\"];\n  13 --> 362a7fe6-24bb-4398-ae48-870f4b4bb774;\n  style 362a7fe6-24bb-4398-ae48-870f4b4bb774 stroke:#2c3143,stroke-width:4px;\n  14[\"Inspect AnnData\"];\n  12 -->|output_h5ad| 14;\n  edf24149-9341-4fe7-b10c-3fcf092faaa5[\"Output\\nGeneral - Filterbycounts\"];\n  14 --> edf24149-9341-4fe7-b10c-3fcf092faaa5;\n  style edf24149-9341-4fe7-b10c-3fcf092faaa5 stroke:#2c3143,stroke-width:4px;\n  15[\"Scanpy FilterCells\"];\n  12 -->|output_h5ad| 15;\n  a88ec405-265f-4a59-a75e-34e3b05b0096[\"Output\\nMito-filtered Object\"];\n  15 --> a88ec405-265f-4a59-a75e-34e3b05b0096;\n  style a88ec405-265f-4a59-a75e-34e3b05b0096 stroke:#2c3143,stroke-width:4px;\n  16[\"Plot\"];\n  12 -->|output_h5ad| 16;\n  a7c8b0d9-82d3-4438-a212-b5f7c56d36b8[\"Output\\nViolin - Filterbycounts\"];\n  16 --> a7c8b0d9-82d3-4438-a212-b5f7c56d36b8;\n  style a7c8b0d9-82d3-4438-a212-b5f7c56d36b8 stroke:#2c3143,stroke-width:4px;\n  17[\"Inspect AnnData\"];\n  15 -->|output_h5ad| 17;\n  56882809-e19f-451a-8010-bc55dcee482f[\"Output\\nGeneral - Filterbymito\"];\n  17 --> 56882809-e19f-451a-8010-bc55dcee482f;\n  style 56882809-e19f-451a-8010-bc55dcee482f stroke:#2c3143,stroke-width:4px;\n  18[\"Scanpy FilterGenes\"];\n  15 -->|output_h5ad| 18;\n  00846477-dec5-408a-83b2-105fff7ce05b[\"Output\\nFiltered Object\"];\n  18 --> 00846477-dec5-408a-83b2-105fff7ce05b;\n  style 00846477-dec5-408a-83b2-105fff7ce05b stroke:#2c3143,stroke-width:4px;\n  19[\"Plot\"];\n  15 -->|output_h5ad| 19;\n  7582e113-2004-4255-a1f3-d3123373f342[\"Output\\nViolin - Filterbymito\"];\n  19 --> 7582e113-2004-4255-a1f3-d3123373f342;\n  style 7582e113-2004-4255-a1f3-d3123373f342 stroke:#2c3143,stroke-width:4px;\n  20[\"Inspect AnnData\"];\n  18 -->|output_h5ad| 20;\n  2d870a40-c602-4a1c-afef-450489354d39[\"Output\\nGeneral - Filtered object\"];\n  20 --> 2d870a40-c602-4a1c-afef-450489354d39;\n  style 2d870a40-c602-4a1c-afef-450489354d39 stroke:#2c3143,stroke-width:4px;\n  21[\"Scanpy NormaliseData\"];\n  18 -->|output_h5ad| 21;\n  22[\"Scanpy FindVariableGenes\"];\n  21 -->|output_h5ad| 22;\n  a0eb92b1-0263-4179-b7af-4bd9bcc9c960[\"Output\\nUse_me_FVG\"];\n  22 --> a0eb92b1-0263-4179-b7af-4bd9bcc9c960;\n  style a0eb92b1-0263-4179-b7af-4bd9bcc9c960 stroke:#2c3143,stroke-width:4px;\n  23[\"Scanpy ScaleData\"];\n  22 -->|output_h5ad| 23;\n  5776dbb9-0cac-40c0-9bae-9accae16a7a0[\"Output\\nUse_me_Scaled\"];\n  23 --> 5776dbb9-0cac-40c0-9bae-9accae16a7a0;\n  style 5776dbb9-0cac-40c0-9bae-9accae16a7a0 stroke:#2c3143,stroke-width:4px;\n  24[\"Scanpy RunPCA\"];\n  23 -->|output_h5ad| 24;\n  25[\"Plot\"];\n  24 -->|output_h5ad| 25;\n  f0b6f578-050f-4936-9ee7-9956b0760c6f[\"Output\\nPCA Variance\"];\n  25 --> f0b6f578-050f-4936-9ee7-9956b0760c6f;\n  style f0b6f578-050f-4936-9ee7-9956b0760c6f stroke:#2c3143,stroke-width:4px;\n  26[\"Scanpy ComputeGraph\"];\n  24 -->|output_h5ad| 26;\n  27[\"Scanpy RunTSNE\"];\n  26 -->|output_h5ad| 27;\n  28[\"Scanpy RunUMAP\"];\n  27 -->|output_h5ad| 28;\n  29[\"Scanpy FindCluster\"];\n  28 -->|output_h5ad| 29;\n  30[\"Scanpy FindMarkers\"];\n  29 -->|output_h5ad| 30;\n  7cfe5c9c-1c80-41b4-b669-633b1d7d40e3[\"Output\\nMarkers - cluster\"];\n  30 --> 7cfe5c9c-1c80-41b4-b669-633b1d7d40e3;\n  style 7cfe5c9c-1c80-41b4-b669-633b1d7d40e3 stroke:#2c3143,stroke-width:4px;\n  98e98405-951e-4c6c-be01-3c925ae35449[\"Output\\nFinal object\"];\n  30 --> 98e98405-951e-4c6c-be01-3c925ae35449;\n  style 98e98405-951e-4c6c-be01-3c925ae35449 stroke:#2c3143,stroke-width:4px;\n  31[\"Scanpy FindMarkers\"];\n  29 -->|output_h5ad| 31;\n  1e9f229d-eb34-4a5b-a6d9-e70c7b0581f4[\"Output\\nMarkers - genotype\"];\n  31 --> 1e9f229d-eb34-4a5b-a6d9-e70c7b0581f4;\n  style 1e9f229d-eb34-4a5b-a6d9-e70c7b0581f4 stroke:#2c3143,stroke-width:4px;\n  32[\"Scanpy PlotEmbed\"];\n  30 -->|output_h5ad| 32;\n  33[\"Scanpy PlotEmbed\"];\n  30 -->|output_h5ad| 33;\n  34[\"Manipulate AnnData\"];\n  30 -->|output_h5ad| 34;\n  35[\"Scanpy PlotEmbed\"];\n  30 -->|output_h5ad| 35;\n  36[\"Inspect AnnData\"];\n  30 -->|output_h5ad| 36;\n  37[\"AnnData Operations\"];\n  34 -->|anndata| 37;\n  30 -->|output_h5ad| 37;\n  38[\"Join two Datasets\"];\n  30 -->|output_tsv| 38;\n  36 -->|var| 38;\n  39[\"Join two Datasets\"];\n  31 -->|output_tsv| 39;\n  36 -->|var| 39;\n  40[\"AnnData Operations\"];\n  37 -->|output_h5ad| 40;\n  10bd70f8-ffcb-442b-9647-e5b947b6d35e[\"Output\\nFinal cell annotated object\"];\n  40 --> 10bd70f8-ffcb-442b-9647-e5b947b6d35e;\n  style 10bd70f8-ffcb-442b-9647-e5b947b6d35e stroke:#2c3143,stroke-width:4px;\n  41[\"Cut\"];\n  38 -->|out_file1| 41;\n  4f822c1c-91c5-4be4-8f9b-d5bdda0a037e[\"Output\\nMarkers - cluster - named\"];\n  41 --> 4f822c1c-91c5-4be4-8f9b-d5bdda0a037e;\n  style 4f822c1c-91c5-4be4-8f9b-d5bdda0a037e stroke:#2c3143,stroke-width:4px;\n  42[\"Cut\"];\n  39 -->|out_file1| 42;\n  3b471f3d-263d-4299-9b7d-8a8ae1aa556e[\"Output\\nMarkers - genotype - named\"];\n  42 --> 3b471f3d-263d-4299-9b7d-8a8ae1aa556e;\n  style 3b471f3d-263d-4299-9b7d-8a8ae1aa556e stroke:#2c3143,stroke-width:4px;\n  43[\"Scanpy PlotEmbed\"];\n  40 -->|output_h5ad| 43;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "Filter, Plot and Explore Single-cell RNA-seq Data updated",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
                         "errors": null,
                         "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Inspect AnnData",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "ESet Object - Single cell:normal"
+                                "name": "obs",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "ESet Object - Single cell:normal",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 2.0234375,
-                            "top": 194.046875
+                            "left": 277.87506103515625,
+                            "top": 46.953125
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "a12a2c75-60f9-4914-af0f-1e4c90d6232e",
-                        "workflow_outputs": []
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ee98d611afc6",
+                            "name": "anndata_inspect",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"obs\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "02ce9919-9e22-40cf-8d35-dd11bc87479d",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "obs",
+                                "uuid": "71b6c011-cce0-476b-a468-ef4a8b6c3f2b"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
                         "errors": null,
                         "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "input_connections": {
+                            "input_obj_file": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Scanpy FilterCells",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "ESet Object - Bulk:normal"
+                                "name": "output_h5ad",
+                                "type": "h5ad"
                             }
                         ],
-                        "label": "ESet Object - Bulk:normal",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 2.0234375,
-                            "top": 316.0546875
+                            "left": 277.87506103515625,
+                            "top": 264.01561737060547
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "631202df-1a51-4fac-8ca9-65b8e6959082",
-                        "workflow_outputs": []
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_h5ad": {
+                                "action_arguments": {
+                                    "newname": "Genes-filtered Object"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e9283529cba1",
+                            "name": "scanpy_filter_cells",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"categories\": [], \"export_mtx\": false, \"force_recalc\": false, \"gene_name\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"parameters\": [{\"__index__\": 0, \"name\": \"log1p_n_genes_by_counts\", \"min\": \"5.7\", \"max\": \"20.0\"}], \"save_layer\": null, \"save_raw\": false, \"subsets\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
+                        "type": "tool",
+                        "uuid": "c7141742-50d6-4119-8e2e-827d3feb7cda",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Genes-filtered Object",
+                                "output_name": "output_h5ad",
+                                "uuid": "6a00b14b-d3f8-4771-963a-76115c8eaf2f"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
                         "errors": null,
                         "id": 3,
-                        "input_connections": {},
-                        "inputs": [
+                        "input_connections": {
+                            "adata": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot",
+                        "outputs": [
+                            {
+                                "name": "out_png",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 277.87506103515625,
+                            "top": 460.0468444824219
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionout_png": {
+                                "action_arguments": {
+                                    "newname": "Scatter - genes x UMIs"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_png"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "aa0c474463c2",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.scatter\", \"__current_case__\": 0, \"type\": {\"type\": \"xy\", \"__current_case__\": 0, \"x\": \"log1p_total_counts\", \"y\": \"log1p_n_genes_by_counts\", \"color\": \"pct_counts_mito\", \"layers\": {\"use_layers\": \"false\", \"__current_case__\": 1}}, \"use_raw\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"color_map\": \"None\", \"palette\": \"default\", \"frameon\": true, \"size\": null, \"title\": \"\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy1",
+                        "type": "tool",
+                        "uuid": "f3193244-6053-47a5-89f9-eaa0993f3eca",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Scatter - genes x UMIs",
+                                "output_name": "out_png",
+                                "uuid": "c123842e-b2d2-43ad-81f0-6ba3b45d4021"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "adata": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot",
+                        "outputs": [
+                            {
+                                "name": "out_png",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 277.87506103515625,
+                            "top": 614.0000152587891
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionout_png": {
+                                "action_arguments": {
+                                    "newname": "Scatter - mito x genes"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_png"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "aa0c474463c2",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.scatter\", \"__current_case__\": 0, \"type\": {\"type\": \"xy\", \"__current_case__\": 0, \"x\": \"log1p_n_genes_by_counts\", \"y\": \"pct_counts_mito\", \"color\": \"\", \"layers\": {\"use_layers\": \"false\", \"__current_case__\": 1}}, \"use_raw\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"color_map\": \"None\", \"palette\": \"default\", \"frameon\": true, \"size\": null, \"title\": \"\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy1",
+                        "type": "tool",
+                        "uuid": "babba57e-e1e1-4af8-849e-7f1f88842b51",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Scatter - mito x genes",
+                                "output_name": "out_png",
+                                "uuid": "f1020d4d-555e-42fa-ba21-52a151b91a5b"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "adata": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot",
+                        "outputs": [
+                            {
+                                "name": "out_png",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 278.98952554536163,
+                            "top": 768.0374811275927
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionout_png": {
+                                "action_arguments": {
+                                    "newname": "Violin - genotype - log"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_png"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "aa0c474463c2",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"genotype\", \"log\": false, \"use_raw\": false, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy1",
+                        "type": "tool",
+                        "uuid": "a7b1206d-c867-4ffa-bc48-a7bd311b4cfb",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Violin - genotype - log",
+                                "output_name": "out_png",
+                                "uuid": "a7fe6020-8f1e-470a-9ed3-f2b5e95516e0"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "adata": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot",
+                        "outputs": [
+                            {
+                                "name": "out_png",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 277.87506103515625,
+                            "top": 922.0468902587891
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionout_png": {
+                                "action_arguments": {
+                                    "newname": "Violin - batch - log"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_png"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "aa0c474463c2",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"batch\", \"log\": false, \"use_raw\": false, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy1",
+                        "type": "tool",
+                        "uuid": "43e45438-9dda-4e43-90e9-bbfead684d40",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Violin - batch - log",
+                                "output_name": "out_png",
+                                "uuid": "15e501bc-8ddb-4519-89eb-dde431ea96c1"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Inspect AnnData",
+                        "outputs": [
+                            {
+                                "name": "var",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 277.8749630368968,
+                            "top": 1055.0375737787456
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ee98d611afc6",
+                            "name": "anndata_inspect",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"var\", \"__current_case__\": 4}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "52409dab-0f57-417a-9aa2-0d14923b8820",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "var",
+                                "uuid": "70ea04da-1d7b-47fa-939e-d01258f6f81d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "adata": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot",
+                        "outputs": [
+                            {
+                                "name": "out_png",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 279.20030309822187,
+                            "top": 1293.0249965988953
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionout_png": {
+                                "action_arguments": {
+                                    "newname": "Scatter - mito x UMIs"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_png"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "aa0c474463c2",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.scatter\", \"__current_case__\": 0, \"type\": {\"type\": \"xy\", \"__current_case__\": 0, \"x\": \"log1p_total_counts\", \"y\": \"pct_counts_mito\", \"color\": \"\", \"layers\": {\"use_layers\": \"false\", \"__current_case__\": 1}}, \"use_raw\": false, \"sort_order\": true, \"groups\": \"\", \"plot\": {\"components\": [], \"projection\": \"2d\", \"legend_loc\": \"right margin\", \"legend_fontsize\": null, \"legend_fontweight\": \"normal\", \"color_map\": \"None\", \"palette\": \"default\", \"frameon\": true, \"size\": null, \"title\": \"\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy1",
+                        "type": "tool",
+                        "uuid": "fea33591-4efa-488d-873c-2ef9ec1ad6e5",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Scatter - mito x UMIs",
+                                "output_name": "out_png",
+                                "uuid": "eff22f46-baa6-4e00-ba82-d5e12ce26ff0"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Inspect AnnData",
+                        "outputs": [
+                            {
+                                "name": "general",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 277.87506103515625,
+                            "top": 1447.0156860351562
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ee98d611afc6",
+                            "name": "anndata_inspect",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"general\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "a6a5e239-9708-4044-9104-596fb6f130e8",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "general",
+                                "uuid": "9ddf445d-8b0f-4ffd-b71a-81ff28deb4a1"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {
+                            "adata": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot",
+                        "outputs": [
+                            {
+                                "name": "out_png",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 276.53750483025266,
+                            "top": 1641.8978917275417
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionout_png": {
+                                "action_arguments": {
+                                    "newname": "Violin - sex - log"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_png"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "aa0c474463c2",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"sex\", \"log\": false, \"use_raw\": false, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy1",
+                        "type": "tool",
+                        "uuid": "64a75bd5-b091-45c1-a8f0-007efd803c16",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Violin - sex - log",
+                                "output_name": "out_png",
+                                "uuid": "56677ca4-129c-476c-85ec-69d1bb3d800d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "errors": null,
+                        "id": 11,
+                        "input_connections": {
+                            "adata": {
+                                "id": 2,
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot",
+                        "outputs": [
+                            {
+                                "name": "out_png",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 555.9375,
+                            "top": 110.03124237060547
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionout_png": {
+                                "action_arguments": {
+                                    "newname": "Violin - Filterbygenes"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_png"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "aa0c474463c2",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"genotype\", \"log\": false, \"use_raw\": false, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy1",
+                        "type": "tool",
+                        "uuid": "6b3eb9a5-8014-497f-a3db-aea4a39080e9",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Violin - Filterbygenes",
+                                "output_name": "out_png",
+                                "uuid": "acb61ea4-bcb9-45db-beef-e2bf1a176701"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {
+                            "input_obj_file": {
+                                "id": 2,
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Scanpy FilterCells",
+                        "outputs": [
+                            {
+                                "name": "output_h5ad",
+                                "type": "h5ad"
+                            }
+                        ],
+                        "position": {
+                            "left": 555.9375,
+                            "top": 264.01561737060547
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_h5ad": {
+                                "action_arguments": {
+                                    "newname": "Counts-filtered Object"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e9283529cba1",
+                            "name": "scanpy_filter_cells",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"categories\": [], \"export_mtx\": false, \"force_recalc\": false, \"gene_name\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"parameters\": [{\"__index__\": 0, \"name\": \"log1p_total_counts\", \"min\": \"6.3\", \"max\": \"20.0\"}], \"save_layer\": null, \"save_raw\": false, \"subsets\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
+                        "type": "tool",
+                        "uuid": "64f0c049-6f2a-47ad-bb7b-1a9516fceca6",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Counts-filtered Object",
+                                "output_name": "output_h5ad",
+                                "uuid": "51853662-4519-4229-a2ea-b22a53e7ef73"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "errors": null,
+                        "id": 13,
+                        "input_connections": {
+                            "input": {
+                                "id": 2,
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Inspect AnnData",
+                        "outputs": [
+                            {
+                                "name": "general",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 555.9375,
+                            "top": 460.0468444824219
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActiongeneral": {
+                                "action_arguments": {
+                                    "newname": "General - Filterbygenes"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "general"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ee98d611afc6",
+                            "name": "anndata_inspect",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"general\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "9691c915-a455-4c55-89c4-129afc19842d",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "General - Filterbygenes",
+                                "output_name": "general",
+                                "uuid": "362a7fe6-24bb-4398-ae48-870f4b4bb774"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "errors": null,
+                        "id": 14,
+                        "input_connections": {
+                            "input": {
+                                "id": 12,
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Inspect AnnData",
+                        "outputs": [
+                            {
+                                "name": "general",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 833.9688110351562,
+                            "top": 89.03125762939453
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActiongeneral": {
+                                "action_arguments": {
+                                    "newname": "General - Filterbycounts"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "general"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ee98d611afc6",
+                            "name": "anndata_inspect",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"general\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "d0fc1afa-8f79-4ba7-bc94-c7a5bddb27e1",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "General - Filterbycounts",
+                                "output_name": "general",
+                                "uuid": "edf24149-9341-4fe7-b10c-3fcf092faaa5"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
+                        "errors": null,
+                        "id": 15,
+                        "input_connections": {
+                            "input_obj_file": {
+                                "id": 12,
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Scanpy FilterCells",
+                        "outputs": [
+                            {
+                                "name": "output_h5ad",
+                                "type": "h5ad"
+                            }
+                        ],
+                        "position": {
+                            "left": 835.0770432726613,
+                            "top": 264.01253840544547
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_h5ad": {
+                                "action_arguments": {
+                                    "newname": "Mito-filtered Object"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e9283529cba1",
+                            "name": "scanpy_filter_cells",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"categories\": [], \"export_mtx\": false, \"force_recalc\": false, \"gene_name\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"parameters\": [{\"__index__\": 0, \"name\": \"pct_counts_mito\", \"min\": \"0.0\", \"max\": \"4.5\"}], \"save_layer\": null, \"save_raw\": false, \"subsets\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
+                        "type": "tool",
+                        "uuid": "ddab098e-c545-4eeb-865a-d728213832a2",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Mito-filtered Object",
+                                "output_name": "output_h5ad",
+                                "uuid": "a88ec405-265f-4a59-a75e-34e3b05b0096"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "errors": null,
+                        "id": 16,
+                        "input_connections": {
+                            "adata": {
+                                "id": 12,
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot",
+                        "outputs": [
+                            {
+                                "name": "out_png",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 833.9625270516542,
+                            "top": 458.9230379613743
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionout_png": {
+                                "action_arguments": {
+                                    "newname": "Violin - Filterbycounts"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_png"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "aa0c474463c2",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"genotype\", \"log\": false, \"use_raw\": false, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy1",
+                        "type": "tool",
+                        "uuid": "55957a47-4968-465c-8b31-fb044d3ed1e3",
+                        "when": null,
+                        "workflow_outputs": [
                             {
-                                "description": "",
-                                "name": "ESet Object - Bulk:T2D"
+                                "label": "Violin - Filterbycounts",
+                                "output_name": "out_png",
+                                "uuid": "a7c8b0d9-82d3-4438-a212-b5f7c56d36b8"
                             }
-                        ],
-                        "label": "ESet Object - Bulk:T2D",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 2.0234375,
-                            "top": 438.0390625
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "e841325f-0707-4ac9-9937-700d1bf5fa03",
-                        "workflow_outputs": []
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
                         "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 17,
+                        "input_connections": {
+                            "input": {
+                                "id": 15,
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Inspect AnnData",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "ESet Object - Single cell Total"
+                                "name": "general",
+                                "type": "txt"
                             }
                         ],
-                        "label": "ESet Object - Single cell Total",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 556.0390625
+                            "left": 1111.9688415527344,
+                            "top": 98.99999618530273
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "676d2c4b-58c3-438b-ae55-e294ee43e377",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nESet Object - Single cell:T2D\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nESet Object - Single cell:normal\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nESet Object - Bulk:normal\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nESet Object - Bulk:T2D\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nESet Object - Single cell Total\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"MuSiC Compare: Like with like\"];\n  2 -->|output| 5;\n  1 -->|output| 5;\n  3 -->|output| 5;\n  0 -->|output| 5;\n  6[\"MuSiC Compare: healthyscref\"];\n  2 -->|output| 6;\n  3 -->|output| 6;\n  1 -->|output| 6;\n  7[\"MuSiC Compare - Altogether\"];\n  2 -->|output| 7;\n  3 -->|output| 7;\n  4 -->|output| 7;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "MuSiC-Deconvolution: Compare",
-                "outputs": [
+                        "post_job_actions": {
+                            "RenameDatasetActiongeneral": {
+                                "action_arguments": {
+                                    "newname": "General - Filterbymito"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "general"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ee98d611afc6",
+                            "name": "anndata_inspect",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"general\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "7c6883be-1a11-4b58-8c0c-0f5b87a84ec8",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "General - Filterbymito",
+                                "output_name": "general",
+                                "uuid": "56882809-e19f-451a-8010-bc55dcee482f"
+                            }
+                        ]
+                    },
                     {
-                        "annotation": "Here the T2D bulk sample is inferred from the sc T2D sample, while the normal bulk sample is inferred from the sc normal sample",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 5,
+                        "id": 18,
                         "input_connections": {
-                            "scrna_groups_0|bulk_groups_0|bulk_eset": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "scrna_groups_0|scrna_eset": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "scrna_groups_1|bulk_groups_0|bulk_eset": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "scrna_groups_1|scrna_eset": {
-                                "id": 0,
-                                "output_name": "output"
+                            "input_obj_file": {
+                                "id": 15,
+                                "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
-                        "label": "MuSiC Compare: Like with like",
-                        "name": "MuSiC Compare",
+                        "label": null,
+                        "name": "Scanpy FilterGenes",
                         "outputs": [
                             {
-                                "name": "dtables",
-                                "type": "input"
-                            },
-                            {
-                                "name": "stats",
-                                "type": "input"
-                            },
-                            {
-                                "name": "out_heatmulti_pdf",
-                                "type": "pdf"
-                            },
-                            {
-                                "name": "out_heatsumm_pdf",
-                                "type": "pdf"
+                                "name": "output_h5ad",
+                                "type": "h5ad"
                             }
                         ],
                         "position": {
-                            "left": 730.265625,
-                            "top": 0
+                            "left": 1111.9688415527344,
+                            "top": 274.00001525878906
                         },
                         "post_job_actions": {
-                            "RemoveTagDatasetActiondtables": {
-                                "action_arguments": {
-                                    "tags": "#singlecell,#bulk"
-                                },
-                                "action_type": "RemoveTagDatasetAction",
-                                "output_name": "dtables"
-                            },
-                            "RemoveTagDatasetActionout_heatmulti_pdf": {
-                                "action_arguments": {
-                                    "tags": "#singlecell,#bulk"
-                                },
-                                "action_type": "RemoveTagDatasetAction",
-                                "output_name": "out_heatmulti_pdf"
-                            },
-                            "RemoveTagDatasetActionout_heatsumm_pdf": {
-                                "action_arguments": {
-                                    "tags": "#singlecell,#bulk"
-                                },
-                                "action_type": "RemoveTagDatasetAction",
-                                "output_name": "out_heatsumm_pdf"
-                            },
-                            "RemoveTagDatasetActionstats": {
-                                "action_arguments": {
-                                    "tags": "#singlecell,#bulk"
-                                },
-                                "action_type": "RemoveTagDatasetAction",
-                                "output_name": "stats"
-                            },
-                            "RenameDatasetActiondtables": {
-                                "action_arguments": {
-                                    "newname": "MuSiC-like4like-tables"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "dtables"
-                            },
-                            "RenameDatasetActionout_heatmulti_pdf": {
-                                "action_arguments": {
-                                    "newname": "MuSiC-like4like-plots"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_heatmulti_pdf"
-                            },
-                            "RenameDatasetActionout_heatsumm_pdf": {
-                                "action_arguments": {
-                                    "newname": "MuSiC-like4like-individualmaps"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_heatsumm_pdf"
-                            },
-                            "RenameDatasetActionstats": {
+                            "RenameDatasetActionoutput_h5ad": {
                                 "action_arguments": {
-                                    "newname": "MuSiC-like4like-stats"
+                                    "newname": "Filtered Object"
                                 },
                                 "action_type": "RenameDatasetAction",
-                                "output_name": "stats"
-                            },
-                            "TagDatasetActiondtables": {
-                                "action_arguments": {
-                                    "tags": "#like4like"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "dtables"
-                            },
-                            "TagDatasetActionout_heatmulti_pdf": {
-                                "action_arguments": {
-                                    "tags": "#like4like"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "out_heatmulti_pdf"
-                            },
-                            "TagDatasetActionout_heatsumm_pdf": {
-                                "action_arguments": {
-                                    "tags": "#like4like"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "out_heatsumm_pdf"
-                            },
-                            "TagDatasetActionstats": {
-                                "action_arguments": {
-                                    "tags": "#like4like"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "stats"
+                                "output_name": "output_h5ad"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy9",
                         "tool_shed_repository": {
-                            "changeset_revision": "4447ed460308",
-                            "name": "music_compare",
-                            "owner": "bgruening",
+                            "changeset_revision": "474a69c47184",
+                            "name": "scanpy_filter_genes",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"dendro_setting\": \"None\", \"est_method\": \"MuSiC\", \"filter\": {\"out_list_cells\": \"\", \"out_list_facts\": \"\"}, \"scrna_groups\": [{\"__index__\": 0, \"name\": \"scRNA_set:Normal\", \"scrna_eset\": {\"__class__\": \"ConnectedValue\"}, \"adv\": {\"celltypes_label\": \"Inferred cell type - author labels\", \"samples_label\": \"Individual\", \"celltypes\": \"alpha cell,beta cell,delta cell,gamma cell,acinar cell,ductal cell\"}, \"bulk_groups\": [{\"__index__\": 0, \"name\": \"Bulk_set:Normal\", \"bulk_eset\": {\"__class__\": \"ConnectedValue\"}, \"factor_group\": \"Disease\", \"adv\": {\"phenotype_factors\": \"\", \"phenotype_factors_always_exclude\": \"sampleID,SubjectName\"}}]}, {\"__index__\": 1, \"name\": \"scRNA_set:T2D\", \"scrna_eset\": {\"__class__\": \"ConnectedValue\"}, \"adv\": {\"celltypes_label\": \"Inferred cell type - author labels\", \"samples_label\": \"Individual\", \"celltypes\": \"alpha cell,beta cell,delta cell,gamma cell,acinar cell,ductal cell\"}, \"bulk_groups\": [{\"__index__\": 0, \"name\": \"bulk_set:T2D\", \"bulk_eset\": {\"__class__\": \"ConnectedValue\"}, \"factor_group\": \"Disease\", \"adv\": {\"phenotype_factors\": \"\", \"phenotype_factors_always_exclude\": \"sampleID,SubjectName\"}}]}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.1+galaxy4",
+                        "tool_state": "{\"categories\": [], \"export_mtx\": false, \"force_recalc\": false, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"parameters\": [{\"__index__\": 0, \"name\": \"n_cells\", \"min\": \"3.0\", \"max\": \"1000000000.0\"}], \"save_layer\": null, \"save_raw\": false, \"subsets\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "1aa07374-4bd9-4c8a-8e23-8c9c3b7faa78",
+                        "uuid": "61272c94-406b-4a3f-9bf5-a7ebbf1e3dee",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "stats",
-                                "uuid": "f23ddfe7-40e1-4232-985a-1deae154e13e"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "dtables",
-                                "uuid": "2a29e3ef-e447-4336-a5e4-c781f21eeeb6"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_heatsumm_pdf",
-                                "uuid": "ba82c5ac-05df-4ded-b6b4-0bac2cc3cc8b"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_heatmulti_pdf",
-                                "uuid": "f7f8627a-7a04-4ec4-8e65-7b4cd65ade13"
+                                "label": "Filtered Object",
+                                "output_name": "output_h5ad",
+                                "uuid": "00846477-dec5-408a-83b2-105fff7ce05b"
                             }
                         ]
                     },
                     {
-                        "annotation": "Here the T2D bulk sample and the normal sample are separately compared separately against the healthy sc reference only (excluding unhealthy sc reference)",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
                         "errors": null,
-                        "id": 6,
+                        "id": 19,
                         "input_connections": {
-                            "scrna_groups_0|bulk_groups_0|bulk_eset": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "scrna_groups_0|bulk_groups_1|bulk_eset": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "scrna_groups_0|scrna_eset": {
-                                "id": 1,
-                                "output_name": "output"
+                            "adata": {
+                                "id": 15,
+                                "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
-                        "label": "MuSiC Compare: healthyscref",
-                        "name": "MuSiC Compare",
+                        "label": null,
+                        "name": "Plot",
                         "outputs": [
                             {
-                                "name": "dtables",
-                                "type": "input"
-                            },
-                            {
-                                "name": "stats",
-                                "type": "input"
-                            },
-                            {
-                                "name": "out_heatmulti_pdf",
-                                "type": "pdf"
-                            },
-                            {
-                                "name": "out_heatsumm_pdf",
-                                "type": "pdf"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 992.265625,
-                            "top": 211
+                            "left": 1111.9688415527344,
+                            "top": 449.04685974121094
                         },
                         "post_job_actions": {
-                            "RemoveTagDatasetActiondtables": {
-                                "action_arguments": {
-                                    "tags": "#singlecell,#bulk"
-                                },
-                                "action_type": "RemoveTagDatasetAction",
-                                "output_name": "dtables"
-                            },
-                            "RemoveTagDatasetActionout_heatmulti_pdf": {
-                                "action_arguments": {
-                                    "tags": "#singlecell,#bulk"
-                                },
-                                "action_type": "RemoveTagDatasetAction",
-                                "output_name": "out_heatmulti_pdf"
-                            },
-                            "RemoveTagDatasetActionout_heatsumm_pdf": {
-                                "action_arguments": {
-                                    "tags": "#singlecell,#bulk"
-                                },
-                                "action_type": "RemoveTagDatasetAction",
-                                "output_name": "out_heatsumm_pdf"
-                            },
-                            "RemoveTagDatasetActionstats": {
-                                "action_arguments": {
-                                    "tags": "#singlecell,#bulk"
-                                },
-                                "action_type": "RemoveTagDatasetAction",
-                                "output_name": "stats"
-                            },
-                            "RenameDatasetActiondtables": {
-                                "action_arguments": {
-                                    "newname": "MuSiC-healthyscref-tables"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "dtables"
-                            },
-                            "RenameDatasetActionout_heatmulti_pdf": {
-                                "action_arguments": {
-                                    "newname": "MuSiC-healthyscref-plots"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_heatmulti_pdf"
-                            },
-                            "RenameDatasetActionout_heatsumm_pdf": {
-                                "action_arguments": {
-                                    "newname": "MuSiC-healthyscref-individualmaps"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_heatsumm_pdf"
-                            },
-                            "RenameDatasetActionstats": {
+                            "RenameDatasetActionout_png": {
                                 "action_arguments": {
-                                    "newname": "MuSiC-healthyscref-stats"
+                                    "newname": "Violin - Filterbymito"
                                 },
                                 "action_type": "RenameDatasetAction",
-                                "output_name": "stats"
-                            },
-                            "TagDatasetActiondtables": {
-                                "action_arguments": {
-                                    "tags": "#healthyscref"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "dtables"
-                            },
-                            "TagDatasetActionout_heatmulti_pdf": {
-                                "action_arguments": {
-                                    "tags": "#healthyscref"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "out_heatmulti_pdf"
-                            },
-                            "TagDatasetActionout_heatsumm_pdf": {
-                                "action_arguments": {
-                                    "tags": "#healthyscref"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "out_heatsumm_pdf"
-                            },
-                            "TagDatasetActionstats": {
-                                "action_arguments": {
-                                    "tags": "#healthyscref"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "stats"
+                                "output_name": "out_png"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "4447ed460308",
-                            "name": "music_compare",
-                            "owner": "bgruening",
+                            "changeset_revision": "aa0c474463c2",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"dendro_setting\": \"None\", \"est_method\": \"MuSiC\", \"filter\": {\"out_list_cells\": \"\", \"out_list_facts\": \"\"}, \"scrna_groups\": [{\"__index__\": 0, \"name\": \"scRNA_set:Normal\", \"scrna_eset\": {\"__class__\": \"ConnectedValue\"}, \"adv\": {\"celltypes_label\": \"Inferred cell type - author labels\", \"samples_label\": \"Individual\", \"celltypes\": \"alpha cell,beta cell,delta cell,gamma cell,acinar cell,ductal cell\"}, \"bulk_groups\": [{\"__index__\": 0, \"name\": \"Bulk_set:Normal\", \"bulk_eset\": {\"__class__\": \"ConnectedValue\"}, \"factor_group\": \"Disease\", \"adv\": {\"phenotype_factors\": \"\", \"phenotype_factors_always_exclude\": \"sampleID,SubjectName\"}}, {\"__index__\": 1, \"name\": \"Bulk_set:T2D\", \"bulk_eset\": {\"__class__\": \"ConnectedValue\"}, \"factor_group\": \"Disease\", \"adv\": {\"phenotype_factors\": \"\", \"phenotype_factors_always_exclude\": \"sampleID,SubjectName\"}}]}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.1+galaxy4",
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.violin\", \"__current_case__\": 3, \"key_variables\": {\"type\": \"custom\", \"__current_case__\": 2, \"keys\": \"log1p_total_counts,log1p_n_genes_by_counts,pct_counts_mito\"}, \"groupby\": \"genotype\", \"log\": false, \"use_raw\": false, \"violin_plot\": {\"stripplot\": {\"stripplot\": \"True\", \"__current_case__\": 0, \"jitter\": {\"jitter\": \"True\", \"__current_case__\": 0, \"size\": \"1.0\"}}, \"multi_panel\": {\"multi_panel\": \"False\", \"__current_case__\": 1}, \"scale\": \"width\"}, \"xlabel\": \"\", \"rotation\": null, \"seaborn_violinplot\": {\"bw\": \"scott\", \"orient\": null, \"linewidth\": \"0.0\", \"color\": \"AliceBlue\", \"saturation\": \"0.75\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy1",
                         "type": "tool",
-                        "uuid": "2d6961e3-6437-4fae-92d1-25695b55d4c4",
+                        "uuid": "b192226f-02d2-4196-a4f1-1cd27b8434bd",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_heatsumm_pdf",
-                                "uuid": "07325b72-c3f2-403e-bd83-a751603228ef"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_heatmulti_pdf",
-                                "uuid": "b75a92b4-f4eb-4bd6-a895-ba7285e80d65"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "stats",
-                                "uuid": "693bd310-705d-466b-9c35-1d7803bf16d7"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "dtables",
-                                "uuid": "e8a7c664-1510-4bc8-bb3a-bde0596dd2fd"
+                                "label": "Violin - Filterbymito",
+                                "output_name": "out_png",
+                                "uuid": "7582e113-2004-4255-a1f3-d3123373f342"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
                         "errors": null,
-                        "id": 7,
+                        "id": 20,
                         "input_connections": {
-                            "scrna_groups_0|bulk_groups_0|bulk_eset": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "scrna_groups_0|bulk_groups_1|bulk_eset": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "scrna_groups_0|scrna_eset": {
-                                "id": 4,
-                                "output_name": "output"
+                            "input": {
+                                "id": 18,
+                                "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
-                        "label": "MuSiC Compare - Altogether",
-                        "name": "MuSiC Compare",
+                        "label": null,
+                        "name": "Inspect AnnData",
                         "outputs": [
                             {
-                                "name": "dtables",
-                                "type": "input"
-                            },
-                            {
-                                "name": "stats",
-                                "type": "input"
-                            },
-                            {
-                                "name": "out_heatmulti_pdf",
-                                "type": "pdf"
-                            },
-                            {
-                                "name": "out_heatsumm_pdf",
-                                "type": "pdf"
+                                "name": "general",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 426.2890625,
-                            "top": 203.0390625
+                            "left": 1389.9688720703125,
+                            "top": 68.01563262939453
                         },
                         "post_job_actions": {
-                            "RemoveTagDatasetActiondtables": {
-                                "action_arguments": {
-                                    "tags": "#singlecell,#bulk"
-                                },
-                                "action_type": "RemoveTagDatasetAction",
-                                "output_name": "dtables"
-                            },
-                            "RemoveTagDatasetActionout_heatmulti_pdf": {
-                                "action_arguments": {
-                                    "tags": "#singlecell,#bulk"
-                                },
-                                "action_type": "RemoveTagDatasetAction",
-                                "output_name": "out_heatmulti_pdf"
-                            },
-                            "RemoveTagDatasetActionout_heatsumm_pdf": {
-                                "action_arguments": {
-                                    "tags": "#singlecell,#bulk"
-                                },
-                                "action_type": "RemoveTagDatasetAction",
-                                "output_name": "out_heatsumm_pdf"
-                            },
-                            "RemoveTagDatasetActionstats": {
-                                "action_arguments": {
-                                    "tags": "#singlecell,#bulk"
-                                },
-                                "action_type": "RemoveTagDatasetAction",
-                                "output_name": "stats"
-                            },
-                            "RenameDatasetActiondtables": {
-                                "action_arguments": {
-                                    "newname": "MuSiC-combined-tables"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "dtables"
-                            },
-                            "RenameDatasetActionout_heatmulti_pdf": {
-                                "action_arguments": {
-                                    "newname": "MuSiC-combined-plots"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_heatmulti_pdf"
-                            },
-                            "RenameDatasetActionout_heatsumm_pdf": {
-                                "action_arguments": {
-                                    "newname": "MuSiC-combined-individualmaps"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_heatsumm_pdf"
-                            },
-                            "RenameDatasetActionstats": {
+                            "RenameDatasetActiongeneral": {
                                 "action_arguments": {
-                                    "newname": "MuSiC-combined-stats"
+                                    "newname": "General - Filtered object"
                                 },
                                 "action_type": "RenameDatasetAction",
-                                "output_name": "stats"
-                            },
-                            "TagDatasetActiondtables": {
-                                "action_arguments": {
-                                    "tags": "#combined"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "dtables"
-                            },
-                            "TagDatasetActionout_heatmulti_pdf": {
-                                "action_arguments": {
-                                    "tags": "#combined"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "out_heatmulti_pdf"
-                            },
-                            "TagDatasetActionout_heatsumm_pdf": {
-                                "action_arguments": {
-                                    "tags": "#combined"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "out_heatsumm_pdf"
-                            },
-                            "TagDatasetActionstats": {
-                                "action_arguments": {
-                                    "tags": "#combined"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "stats"
+                                "output_name": "general"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "4447ed460308",
-                            "name": "music_compare",
-                            "owner": "bgruening",
+                            "changeset_revision": "ee98d611afc6",
+                            "name": "anndata_inspect",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"dendro_setting\": \"None\", \"est_method\": \"MuSiC\", \"filter\": {\"out_list_cells\": \"\", \"out_list_facts\": \"\"}, \"scrna_groups\": [{\"__index__\": 0, \"name\": \"scRNA_set\", \"scrna_eset\": {\"__class__\": \"ConnectedValue\"}, \"adv\": {\"celltypes_label\": \"Inferred cell type - author labels\", \"samples_label\": \"Individual\", \"celltypes\": \"alpha cell,beta cell,delta cell,gamma cell,acinar cell,ductal cell\"}, \"bulk_groups\": [{\"__index__\": 0, \"name\": \"Bulk_healthy\", \"bulk_eset\": {\"__class__\": \"ConnectedValue\"}, \"factor_group\": \"Disease\", \"adv\": {\"phenotype_factors\": \"\", \"phenotype_factors_always_exclude\": \"sampleID,SubjectName\"}}, {\"__index__\": 1, \"name\": \"Bulk_disease\", \"bulk_eset\": {\"__class__\": \"ConnectedValue\"}, \"factor_group\": \"Disease\", \"adv\": {\"phenotype_factors\": \"\", \"phenotype_factors_always_exclude\": \"sampleID,SubjectName\"}}]}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.1+galaxy4",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"general\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.5+galaxy1",
                         "type": "tool",
-                        "uuid": "bcea8743-e92e-4a04-b4da-34ca073ecd52",
+                        "uuid": "2aa06b62-4c69-45a1-9330-f69838076dab",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "dtables",
-                                "uuid": "812202ce-076d-46fa-8a80-a1f5f4c53a7a"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_heatmulti_pdf",
-                                "uuid": "cd5b8aa7-da07-49ba-8775-8bcbdd900150"
-                            },
+                                "label": "General - Filtered object",
+                                "output_name": "general",
+                                "uuid": "2d870a40-c602-4a1c-afef-450489354d39"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy9",
+                        "errors": null,
+                        "id": 21,
+                        "input_connections": {
+                            "input_obj_file": {
+                                "id": 18,
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Scanpy NormaliseData",
+                        "outputs": [
                             {
-                                "label": null,
-                                "output_name": "stats",
-                                "uuid": "93d46757-18b9-486b-ab59-b8bc1cb5fd7f"
-                            },
+                                "name": "output_h5ad",
+                                "type": "h5ad"
+                            }
+                        ],
+                        "position": {
+                            "left": 1389.9688720703125,
+                            "top": 243.03123474121094
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "6b97ffba31da",
+                            "name": "scanpy_normalise_data",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"export_mtx\": false, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"save_layer\": null, \"save_raw\": false, \"settings\": {\"default\": true, \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
+                        "type": "tool",
+                        "uuid": "23a495af-28ed-40fb-8ed2-e0a9c0d6d5af",
+                        "when": null,
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_heatsumm_pdf",
-                                "uuid": "35cfefba-a8e6-49b0-9cef-2a01b038ecb0"
+                                "output_name": "output_h5ad",
+                                "uuid": "182d3dbe-a691-48cb-a784-2bceb1f9fdeb"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "single-cell/bulk-music-4-compare",
-                "path": "topics/single-cell/tutorials/bulk-music-4-compare/workflows/compare.ga",
-                "tags": [
-                    "name:singlecell",
-                    "name:transcriptomics",
-                    "name:training"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "MuSiC-Deconvolution: Compare",
-                "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-bulk-music-4-compare/versions/compare",
-                "tutorial_id": "bulk-music-4-compare",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-4-compare/workflows/compare.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-4-compare/workflows/compare.html",
-                "version": 1,
-                "wfid": "single-cell-bulk-music-4-compare",
-                "wfname": "compare",
-                "workflow": "compare.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4"
-                ],
-                "workflowhub_id": "1223"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/7319925"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "add_line_to_file",
-                    "owner": "bgruening",
-                    "revisions": "8e251055b1a9",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "music_construct_eset",
-                    "owner": "bgruening",
-                    "revisions": "282819d09a4f",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "music_manipulate_eset",
-                    "owner": "bgruening",
-                    "revisions": "22232092be53",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "retrieve_scxa",
-                    "owner": "ebi-gxa",
-                    "revisions": "cd6b80f62fcc",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "retrieve_scxa",
-                    "owner": "ebi-gxa",
-                    "revisions": "72b6e1747e37",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "scanpy_read_10x",
-                    "owner": "ebi-gxa",
-                    "revisions": "d253d69ff19f",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "regex_find_replace",
-                    "owner": "galaxyp",
-                    "revisions": "399da6b5ec21",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "anndata_inspect",
-                    "owner": "iuc",
-                    "revisions": "ee98d611afc6",
-                    "tool_panel_section_label": "Single-cell",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "annotatemyids",
-                    "owner": "iuc",
-                    "revisions": "fe3ca740a485",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "datamash_transpose",
-                    "owner": "iuc",
-                    "revisions": "ac092723240d",
-                    "tool_panel_section_label": "Join, Subtract and Group",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "table_compute",
-                    "owner": "iuc",
-                    "revisions": "3bf5661c0280",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: add_line_to_file\n  owner: bgruening\n  revisions: 8e251055b1a9\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: music_construct_eset\n  owner: bgruening\n  revisions: 282819d09a4f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: music_manipulate_eset\n  owner: bgruening\n  revisions: 22232092be53\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: retrieve_scxa\n  owner: ebi-gxa\n  revisions: cd6b80f62fcc\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: retrieve_scxa\n  owner: ebi-gxa\n  revisions: 72b6e1747e37\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_read_10x\n  owner: ebi-gxa\n  revisions: d253d69ff19f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 399da6b5ec21\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_inspect\n  owner: iuc\n  revisions: ee98d611afc6\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: annotatemyids\n  owner: iuc\n  revisions: fe3ca740a485\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_transpose\n  owner: iuc\n  revisions: ac092723240d\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: table_compute\n  owner: iuc\n  revisions: 3bf5661c0280\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "nomadscientist",
-                "mtekman"
-            ],
-            "testing": [
-                "MarisaJL"
-            ]
-        },
-        "contributors": [
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "bio": "Senior Lecturer at The Open University",
-                "elixir_node": "uk",
-                "email": "wendi.bacon@open.ac.uk",
-                "fediverse": "https://mstdn.science/@wendibacon1",
-                "fediverse_flavor": "mastodon",
-                "id": "nomadscientist",
-                "joined": "2020-03",
-                "matrix": "nomadscientist:matrix.org",
-                "name": "Wendi Bacon",
-                "orcid": "0000-0002-8170-8806",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
-                "twitter": "WendiBacon1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "elixir_node": "de",
-                "email": "mtekman89@gmail.com",
-                "former_affiliations": [
-                    "elixir-europe"
-                ],
-                "id": "mtekman",
-                "joined": "2018-11",
-                "name": "Mehmet Tekman",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
-            },
-            {
-                "email": "marisa.loach@open.ac.uk",
-                "id": "MarisaJL",
-                "joined": "2022-10",
-                "name": "Marisa Loach",
-                "orcid": "0000-0001-6979-6930",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/MarisaJL/",
-                "twitter": "Marisa_Loach",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/MarisaJL.json"
-            }
-        ],
-        "dir": "topics/single-cell/tutorials/bulk-music-2-preparescref",
-        "edam_operation": [
-            "Annotation"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "bulk-music-3-preparebulk"
-                ],
-                "type": "internal"
-            }
-        ],
-        "hands_on": true,
-        "id": "single-cell/bulk-music-2-preparescref",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.org.au"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "The EMBL-EBI Single-cell expression atlas contains high quality datasets.",
-            "Metadata manipulation is key for generating the correctly formatted resource."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-02-13",
-        "objectives": [
-            "You will retrieve raw data from the EMBL-EBI Single cell expression atlas.",
-            "You will manipulate the metadata and matrix files.",
-            "You will combine the metadata and matrix files into an ESet object for MuSiC deconvolution.",
-            "You will create multiple ESet objects - both combined and separated out by disease phenotype for your single cell reference."
-        ],
-        "pageviews": 1029,
-        "priority": 4,
-        "pub_date": "2023-01-20",
-        "questions": [
-            "Where can I find good quality scRNA-seq reference datasets?",
-            "How can I reformat and manipulate these downloads to create the right format for MuSiC?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "bulk-music"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00241",
-        "short_tools": [
-            "scanpy_read_10x",
-            "regex1",
-            "anndata_inspect",
-            "music_construct_eset",
-            "sort1",
-            "tp_cut_tool",
-            "tp_awk_tool",
-            "tp_easyjoin_tool",
-            "datamash_transpose",
-            "Cut1",
-            "retrieve_scxa",
-            "music_manipulate_eset",
-            "tp_sed_tool",
-            "table_compute",
-            "annotatemyids",
-            "join1",
-            "add_line_to_file"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "datamanipulation",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "data management"
-        ],
-        "time_estimation": "1H",
-        "title": "Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution",
-        "tools": [
-            "Cut1",
-            "join1",
-            "sort1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0"
-        ],
-        "topic_name": "single-cell",
-        "topic_name_human": "Single Cell",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "bulk-music-2-preparescref",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.json"
-        },
-        "version": 8,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 126,
-        "visitors": 580,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-8170-8806",
-                        "name": "Wendi Bacon"
                     },
                     {
-                        "class": "Person",
-                        "identifier": "0000-0002-4181-2676",
-                        "name": "Mehmet Tekman"
-                    }
-                ],
-                "description": "This workflow creates an ESet object from scRNA metadata file and EBI SCXA retrieveal",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": true
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"EBI SCXA Data Retrieval\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSingle cell metadata\"]\n  2[label=\"Scanpy Read10x\"]\n  0 -> 2 [label=\"barcode_tsv\"]\n  0 -> 2 [label=\"genes_tsv\"]\n  0 -> 2 [label=\"matrix_mtx\"]\n  k6bd01730f0b548248cfcd563cc9c7f7d[color=lightseagreen,label=\"Output\\nScanpy Read10x on input dataset(s): anndata\"]\n  2 -> k6bd01730f0b548248cfcd563cc9c7f7d\n  3[label=\"Inspect AnnData\"]\n  2 -> 3 [label=\"output_h5\"]\n  4[label=\"Transpose\"]\n  3 -> 4 [label=\"X\"]\n  5[label=\"annotateMyIDs\"]\n  4 -> 5 [label=\"out_file\"]\n  kc39c7d69550e4b54a412317b599c5e55[color=lightseagreen,label=\"Output\\nannotateMyIDs on input dataset(s): Annotated IDs\"]\n  5 -> kc39c7d69550e4b54a412317b599c5e55\n  6[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\n1st step removed - Convert from Ensembl to GeneSymbol, summing duplicate genes\"]\n  5 -> 6 [label=\"out_tab\"]\n  4 -> 6 [label=\"out_file\"]\n  7[label=\"Construct Expression Set Object\"]\n  6 -> 7 [label=\"Gene Symbol Count Matrix\"]\n  1 -> 7 [label=\"output\"]\n  ke8c91df04e6c4eb29807c2679b494958[color=lightseagreen,label=\"Output\\nConstruct Expression Set Object on input dataset(s): RData ESet Object\"]\n  7 -> ke8c91df04e6c4eb29807c2679b494958\n  k2912d09bb1784035b7c87038392e2bf2[color=lightseagreen,label=\"Output\\nConstruct Expression Set Object on input dataset(s): General Info\"]\n  7 -> k2912d09bb1784035b7c87038392e2bf2\n  8[label=\"Manipulate Expression Set Object\"]\n  7 -> 8 [label=\"out_rds\"]\n  k08de92d832fe4b479038298cdd13fac5[color=lightseagreen,label=\"Output\\nManipulate Expression Set Object on input dataset(s): ExpressionSet Object\"]\n  8 -> k08de92d832fe4b479038298cdd13fac5\n  9[label=\"Manipulate Expression Set Object\"]\n  7 -> 9 [label=\"out_rds\"]\n}",
-                "history": [
-                    {
-                        "hash": "9a561b3752745eab20cececd5346ee0a7449da28",
-                        "message": "update workflows",
-                        "num": 1,
-                        "short_hash": "9a561b375",
-                        "unix": "1669581042"
-                    }
-                ],
-                "inputs": [
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy9",
+                        "errors": null,
+                        "id": 22,
+                        "input_connections": {
+                            "input_obj_file": {
+                                "id": 21,
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Scanpy FindVariableGenes",
+                        "outputs": [
+                            {
+                                "name": "output_h5ad",
+                                "type": "h5ad"
+                            }
+                        ],
+                        "position": {
+                            "left": 1666.8230043154201,
+                            "top": 243.02502669087463
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_h5ad": {
+                                "action_arguments": {
+                                    "newname": "Use_me_FVG"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2861ca3bfe4d",
+                            "name": "scanpy_find_variable_genes",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"batch_key\": \"\", \"filter\": false, \"flavor\": \"seurat\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"max_disp\": \"50.0\", \"max_mean\": \"3.0\", \"min_disp\": \"0.5\", \"min_mean\": \"0.0125\", \"n_bin\": \"20\", \"n_top_gene\": \"2000\", \"output_format\": \"anndata_h5ad\", \"span\": \"0.3\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
+                        "type": "tool",
+                        "uuid": "a8525f8d-4acc-437e-8c29-3213f7b969e2",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Use_me_FVG",
+                                "output_name": "output_h5ad",
+                                "uuid": "a0eb92b1-0263-4179-b7af-4bd9bcc9c960"
+                            }
+                        ]
+                    },
                     {
-                        "annotation": "This should be output from the MuSiC Deconvolution | Data generation | sc | metadata workflow",
-                        "content_id": null,
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 23,
+                        "input_connections": {
+                            "input_obj_file": {
+                                "id": 22,
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Scanpy ScaleData",
+                        "outputs": [
                             {
-                                "description": "This should be output from the MuSiC Deconvolution | Data generation | sc | metadata workflow",
-                                "name": "Single cell metadata"
+                                "name": "output_h5ad",
+                                "type": "h5ad"
                             }
                         ],
-                        "label": "Single cell metadata",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 1160.0208740234375,
-                            "top": 364
+                            "left": 1946.0000610351562,
+                            "top": 252.99999237060547
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f43195bc-96ef-4c07-8537-2e91c50b554c",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"EBI SCXA Data Retrieval\"];\n  1[\"\u2139\ufe0f Input Dataset\\nSingle cell metadata\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Scanpy Read10x\"];\n  0 -->|barcode_tsv| 2;\n  0 -->|genes_tsv| 2;\n  0 -->|matrix_mtx| 2;\n  6bd01730-f0b5-4824-8cfc-d563cc9c7f7d[\"Output\\nScanpy Read10x on input dataset(s): anndata\"];\n  2 --> 6bd01730-f0b5-4824-8cfc-d563cc9c7f7d;\n  style 6bd01730-f0b5-4824-8cfc-d563cc9c7f7d stroke:#2c3143,stroke-width:4px;\n  3[\"Inspect AnnData\"];\n  2 -->|output_h5| 3;\n  4[\"Transpose\"];\n  3 -->|X| 4;\n  5[\"annotateMyIDs\"];\n  4 -->|out_file| 5;\n  c39c7d69-550e-4b54-a412-317b599c5e55[\"Output\\nannotateMyIDs on input dataset(s): Annotated IDs\"];\n  5 --> c39c7d69-550e-4b54-a412-317b599c5e55;\n  style c39c7d69-550e-4b54-a412-317b599c5e55 stroke:#2c3143,stroke-width:4px;\n  6[\"\ud83d\udee0\ufe0f Subworkflow\\n1st step removed - Convert from Ensembl to GeneSymbol, summing duplicate genes\"];\n  style 6 fill:#edd,stroke:#900,stroke-width:4px;\n  5 -->|out_tab| 6;\n  4 -->|out_file| 6;\n  7[\"Construct Expression Set Object\"];\n  6 -->|Gene Symbol Count Matrix| 7;\n  1 -->|output| 7;\n  e8c91df0-4e6c-4eb2-9807-c2679b494958[\"Output\\nConstruct Expression Set Object on input dataset(s): RData ESet Object\"];\n  7 --> e8c91df0-4e6c-4eb2-9807-c2679b494958;\n  style e8c91df0-4e6c-4eb2-9807-c2679b494958 stroke:#2c3143,stroke-width:4px;\n  2912d09b-b178-4035-b7c8-7038392e2bf2[\"Output\\nConstruct Expression Set Object on input dataset(s): General Info\"];\n  7 --> 2912d09b-b178-4035-b7c8-7038392e2bf2;\n  style 2912d09b-b178-4035-b7c8-7038392e2bf2 stroke:#2c3143,stroke-width:4px;\n  8[\"Manipulate Expression Set Object\"];\n  7 -->|out_rds| 8;\n  08de92d8-32fe-4b47-9038-298cdd13fac5[\"Output\\nManipulate Expression Set Object on input dataset(s): ExpressionSet Object\"];\n  8 --> 08de92d8-32fe-4b47-9038-298cdd13fac5;\n  style 08de92d8-32fe-4b47-9038-298cdd13fac5 stroke:#2c3143,stroke-width:4px;\n  9[\"Manipulate Expression Set Object\"];\n  7 -->|out_rds| 9;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "MuSiC-Deconvolution: Data generation | sc | matrix + ESet",
-                "outputs": [
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_h5ad": {
+                                "action_arguments": {
+                                    "newname": "Use_me_Scaled"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f86b2c3bc459",
+                            "name": "scanpy_scale_data",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"save_layer\": null, \"save_raw\": false, \"scale_max\": \"10.0\", \"zero_center\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
+                        "type": "tool",
+                        "uuid": "4bc539e1-2913-448f-bde6-d1ec35a10a51",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Use_me_Scaled",
+                                "output_name": "output_h5ad",
+                                "uuid": "5776dbb9-0cac-40c0-9bae-9accae16a7a0"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
+                        "id": 24,
+                        "input_connections": {
+                            "input_obj_file": {
+                                "id": 23,
+                                "output_name": "output_h5ad"
+                            }
+                        },
                         "inputs": [],
                         "label": null,
-                        "name": "EBI SCXA Data Retrieval",
+                        "name": "Scanpy RunPCA",
                         "outputs": [
                             {
-                                "name": "matrix_mtx",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "genes_tsv",
-                                "type": "tsv"
-                            },
+                                "name": "output_h5ad",
+                                "type": "h5ad"
+                            }
+                        ],
+                        "position": {
+                            "left": 2225.1144284467173,
+                            "top": 251.885462533716
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "59028945c857",
+                            "name": "scanpy_run_pca",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"extra_outputs\": null, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"n_pcs\": \"50\", \"output_format\": \"anndata_h5ad\", \"run_mode\": {\"chunked\": false, \"__current_case__\": 1, \"zero_center\": true, \"svd_solver\": null, \"random_seed\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
+                        "type": "tool",
+                        "uuid": "e71440f2-7c95-49ae-bb54-17ad4ee206bd",
+                        "when": null,
+                        "workflow_outputs": [
                             {
-                                "name": "barcode_tsv",
-                                "type": "tsv"
-                            },
+                                "label": null,
+                                "output_name": "output_h5ad",
+                                "uuid": "608852db-340a-4ddd-9e62-744d0cb77dde"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+                        "errors": null,
+                        "id": 25,
+                        "input_connections": {
+                            "adata": {
+                                "id": 24,
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot",
+                        "outputs": [
                             {
-                                "name": "design_tsv",
-                                "type": "tsv"
+                                "name": "out_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 0.0,
-                            "top": 408.46875
+                            "left": 2502.000045776367,
+                            "top": 122.01560974121094
                         },
                         "post_job_actions": {
-                            "TagDatasetActionbarcode_tsv": {
-                                "action_arguments": {
-                                    "tags": "#ebi"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "barcode_tsv"
-                            },
-                            "TagDatasetActiondesign_tsv": {
-                                "action_arguments": {
-                                    "tags": "#ebi"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "design_tsv"
-                            },
-                            "TagDatasetActiongenes_tsv": {
-                                "action_arguments": {
-                                    "tags": "#ebi"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "genes_tsv"
-                            },
-                            "TagDatasetActionmatrix_mtx": {
+                            "RenameDatasetActionout_png": {
                                 "action_arguments": {
-                                    "tags": "#matrix,#ebi,#singlecell"
+                                    "newname": "PCA Variance"
                                 },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "matrix_mtx"
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_png"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "72b6e1747e37",
-                            "name": "retrieve_scxa",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "aa0c474463c2",
+                            "name": "scanpy_plot",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"accession\": \"E-MTAB-5061\", \"matrix_type\": \"raw\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"adata\": {\"__class__\": \"ConnectedValue\"}, \"advanced_common\": {\"show_log\": false}, \"format\": \"png\", \"method\": {\"method\": \"pl.pca_variance_ratio\", \"__current_case__\": 11, \"n_pcs\": \"50\", \"log\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.1+galaxy1",
                         "type": "tool",
-                        "uuid": "c6e24135-aa36-4d1f-83af-378c4882dba7",
+                        "uuid": "1b34902c-7a3f-47cb-94c0-b96c6bd7ba1b",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "barcode_tsv",
-                                "uuid": "c859047e-d5cd-42fd-9b79-3c6089279774"
-                            },
+                                "label": "PCA Variance",
+                                "output_name": "out_png",
+                                "uuid": "f0b6f578-050f-4936-9ee7-9956b0760c6f"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
+                        "errors": null,
+                        "id": 26,
+                        "input_connections": {
+                            "input_obj_file": {
+                                "id": 24,
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "design_tsv",
-                                "uuid": "974ffbbe-2218-4867-8775-e267b3311f95"
-                            },
+                                "description": "runtime parameter for tool Scanpy ComputeGraph",
+                                "name": "settings"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Scanpy ComputeGraph",
+                        "outputs": [
                             {
-                                "label": null,
-                                "output_name": "genes_tsv",
-                                "uuid": "6a8dd992-ccd9-403a-a94d-742a2249aaa7"
-                            },
+                                "name": "output_h5ad",
+                                "type": "h5ad"
+                            }
+                        ],
+                        "position": {
+                            "left": 2502.000045776367,
+                            "top": 255.03124237060547
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "6417cccad133",
+                            "name": "scanpy_compute_graph",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": false, \"__current_case__\": 1, \"key_added\": \"\", \"n_neighbors\": \"15\", \"n_neighbors_file\": {\"__class__\": \"RuntimeValue\"}, \"use_rep\": \"X_pca\", \"n_pcs\": \"20\", \"knn\": true, \"method\": \"umap\", \"metric\": \"euclidean\", \"random_seed\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
+                        "type": "tool",
+                        "uuid": "6e66aa61-710a-46f2-bca6-b6e104ff28ca",
+                        "when": null,
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "matrix_mtx",
-                                "uuid": "0273aaac-0d5b-40dd-a1d9-50a17e5f406a"
+                                "output_name": "output_h5ad",
+                                "uuid": "019dc123-b822-47fb-960e-fd48cafc10e1"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 2,
+                        "id": 27,
                         "input_connections": {
-                            "barcodes": {
-                                "id": 0,
-                                "output_name": "barcode_tsv"
-                            },
-                            "genes": {
-                                "id": 0,
-                                "output_name": "genes_tsv"
-                            },
-                            "matrix": {
-                                "id": 0,
-                                "output_name": "matrix_mtx"
+                            "input_obj_file": {
+                                "id": 26,
+                                "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Scanpy Read10x",
-                                "name": "cell_meta"
-                            },
-                            {
-                                "description": "runtime parameter for tool Scanpy Read10x",
-                                "name": "gene_meta"
+                                "description": "runtime parameter for tool Scanpy RunTSNE",
+                                "name": "settings"
                             }
                         ],
                         "label": null,
-                        "name": "Scanpy Read10x",
+                        "name": "Scanpy RunTSNE",
                         "outputs": [
                             {
-                                "name": "output_h5",
-                                "type": "h5"
+                                "name": "output_h5ad",
+                                "type": "h5ad"
+                            },
+                            {
+                                "name": "output_embed",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 277.97918701171875,
-                            "top": 325.96875
-                        },
-                        "post_job_actions": {
-                            "ChangeDatatypeActionoutput_h5": {
-                                "action_arguments": {
-                                    "newtype": "h5ad"
-                                },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "output_h5"
-                            }
+                            "left": 2780.0000762939453,
+                            "top": 315.04688262939453
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
                         "tool_shed_repository": {
-                            "changeset_revision": "d253d69ff19f",
-                            "name": "scanpy_read_10x",
+                            "changeset_revision": "181d61d2f3cd",
+                            "name": "scanpy_run_tsne",
                             "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"barcodes\": {\"__class__\": \"ConnectedValue\"}, \"cell_meta\": {\"__class__\": \"RuntimeValue\"}, \"gene_meta\": {\"__class__\": \"RuntimeValue\"}, \"genes\": {\"__class__\": \"ConnectedValue\"}, \"matrix\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata\", \"var_names\": \"gene_ids\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"embeddings\": true, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": false, \"__current_case__\": 1, \"key_added\": \"\", \"perplexity\": \"30.0\", \"perplexity_file\": {\"__class__\": \"RuntimeValue\"}, \"early_exaggeration\": \"12.0\", \"learning_rate\": \"1000.0\", \"fast_tsne\": false, \"n_job\": null, \"n_pc\": null, \"random_seed\": \"0\"}, \"use_rep\": \"X_pca\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "432bc2f8-5e5c-489a-ab84-fd3ccd40ec99",
+                        "uuid": "a09fcea0-184d-472e-a22a-09567f10705d",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Scanpy Read10x on input dataset(s): anndata",
-                                "output_name": "output_h5",
-                                "uuid": "6bd01730-f0b5-4824-8cfc-d563cc9c7f7d"
+                                "label": null,
+                                "output_name": "output_embed",
+                                "uuid": "91d7f71d-73df-4955-a0b7-fb86904e3b27"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_h5ad",
+                                "uuid": "2cdbd6fa-f4d7-46c5-83fa-200b8bf48501"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 3,
+                        "id": 28,
                         "input_connections": {
-                            "input": {
-                                "id": 2,
-                                "output_name": "output_h5"
+                            "input_obj_file": {
+                                "id": 27,
+                                "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Inspect AnnData",
+                        "name": "Scanpy RunUMAP",
                         "outputs": [
                             {
-                                "name": "X",
+                                "name": "output_h5ad",
+                                "type": "h5ad"
+                            },
+                            {
+                                "name": "output_embed",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 565.0208740234375,
-                            "top": 322.46875
+                            "left": 3058.000068664551,
+                            "top": 397.04689025878906
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9",
                         "tool_shed_repository": {
-                            "changeset_revision": "ee98d611afc6",
-                            "name": "anndata_inspect",
-                            "owner": "iuc",
+                            "changeset_revision": "bd4a244faeb8",
+                            "name": "scanpy_run_umap",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"X\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"embeddings\": true, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"key_added\": \"\", \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": true, \"__current_case__\": 0}, \"use_graph\": \"neighbors\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "27acc627-ce13-4572-b4bb-e8ecb9c80bb4",
+                        "uuid": "d657ab30-f8df-410a-a8f8-880b2a1842e1",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "X",
-                                "uuid": "e2548214-2e98-4faa-bd8a-ce539df4cef8"
+                                "output_name": "output_h5ad",
+                                "uuid": "ed6a1cd1-f7dc-4174-a083-6d634dbe1b34"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_embed",
+                                "uuid": "a30c795c-9317-4f04-b206-89088235dc6d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 4,
+                        "id": 29,
                         "input_connections": {
-                            "in_file": {
-                                "id": 3,
-                                "output_name": "X"
+                            "input_obj_file": {
+                                "id": 28,
+                                "output_name": "output_h5ad"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Scanpy FindCluster",
+                                "name": "settings"
+                            }
+                        ],
                         "label": null,
-                        "name": "Transpose",
+                        "name": "Scanpy FindCluster",
                         "outputs": [
                             {
-                                "name": "out_file",
-                                "type": "input"
+                                "name": "output_h5ad",
+                                "type": "h5ad"
+                            },
+                            {
+                                "name": "output_txt",
+                                "type": "tsv"
                             }
                         ],
                         "position": {
-                            "left": 831.010498046875,
-                            "top": 329.46875
+                            "left": 3336.0000610351562,
+                            "top": 441.0469055175781
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
                         "tool_shed_repository": {
-                            "changeset_revision": "ac092723240d",
-                            "name": "datamash_transpose",
-                            "owner": "iuc",
+                            "changeset_revision": "2ccd9f9e2cd0",
+                            "name": "scanpy_find_cluster",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"in_file\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"method\": \"louvain\", \"output_cluster\": true, \"output_format\": \"anndata_h5ad\", \"settings\": {\"default\": false, \"__current_case__\": 1, \"neighbors_key\": \"neighbors\", \"layer\": \"\", \"key_added\": \"\", \"resolution\": \"0.6\", \"resolution_file\": {\"__class__\": \"RuntimeValue\"}, \"restrict_to\": \"\", \"use_weights\": false, \"random_seed\": \"0\", \"directed\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "5ea8bf51-59c9-4074-960f-56a355d16bae",
+                        "uuid": "21b1bed3-b826-4219-b99b-22c33061768e",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file",
-                                "uuid": "4ca75360-6d9a-458c-a837-bd61fd5bdae1"
+                                "output_name": "output_txt",
+                                "uuid": "13459467-b675-4076-8529-91a8bedc5501"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_h5ad",
+                                "uuid": "cd0d1987-4c25-4ade-a499-9288342d52aa"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy9",
                         "errors": null,
-                        "id": 5,
+                        "id": 30,
                         "input_connections": {
-                            "id_file": {
-                                "id": 4,
-                                "output_name": "out_file"
+                            "input_obj_file": {
+                                "id": 29,
+                                "output_name": "output_h5ad"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Scanpy FindMarkers",
+                                "name": "groupby_file"
+                            }
+                        ],
                         "label": null,
-                        "name": "annotateMyIDs",
+                        "name": "Scanpy FindMarkers",
                         "outputs": [
                             {
-                                "name": "out_tab",
+                                "name": "output_h5ad",
+                                "type": "h5ad"
+                            },
+                            {
+                                "name": "output_tsv",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 881.5208740234375,
-                            "top": 67.5
+                            "left": 3614.0000534057617,
+                            "top": 530.0156402587891
                         },
                         "post_job_actions": {
-                            "RemoveTagDatasetActionout_tab": {
+                            "RenameDatasetActionoutput_h5ad": {
                                 "action_arguments": {
-                                    "tags": "#matrix"
+                                    "newname": "Final object"
                                 },
-                                "action_type": "RemoveTagDatasetAction",
-                                "output_name": "out_tab"
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_h5ad"
+                            },
+                            "RenameDatasetActionoutput_tsv": {
+                                "action_arguments": {
+                                    "newname": "Markers - cluster"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_tsv"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy9",
                         "tool_shed_repository": {
-                            "changeset_revision": "fe3ca740a485",
-                            "name": "annotatemyids",
-                            "owner": "iuc",
+                            "changeset_revision": "81c34e67f262",
+                            "name": "scanpy_find_markers",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"file_has_header\": \"true\", \"id_file\": {\"__class__\": \"ConnectedValue\"}, \"id_type\": \"ENSEMBL\", \"organism\": \"Hs\", \"output_cols\": [\"SYMBOL\"], \"remove_dups\": \"false\", \"rscriptOpt\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"groupby\": \"louvain\", \"groupby_file\": {\"__class__\": \"RuntimeValue\"}, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"n_genes\": \"50\", \"output_format\": \"anndata_h5ad\", \"output_markers\": true, \"settings\": {\"default\": true, \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "4e551e90-930f-4904-b859-8a107400eb1e",
+                        "uuid": "bcd329a1-a1b2-401a-9f4e-ba3e01f062a7",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "annotateMyIDs on input dataset(s): Annotated IDs",
-                                "output_name": "out_tab",
-                                "uuid": "c39c7d69-550e-4b54-a412-317b599c5e55"
+                                "label": "Markers - cluster",
+                                "output_name": "output_tsv",
+                                "uuid": "7cfe5c9c-1c80-41b4-b669-633b1d7d40e3"
+                            },
+                            {
+                                "label": "Final object",
+                                "output_name": "output_h5ad",
+                                "uuid": "98e98405-951e-4c6c-be01-3c925ae35449"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "id": 6,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy9",
+                        "errors": null,
+                        "id": 31,
                         "input_connections": {
-                            "Annotated IDs": {
-                                "id": 5,
-                                "input_subworkflow_step_id": 0,
-                                "output_name": "out_tab"
-                            },
-                            "Expression Matrix (Gene Rows)": {
-                                "id": 4,
-                                "input_subworkflow_step_id": 1,
-                                "output_name": "out_file"
+                            "input_obj_file": {
+                                "id": 29,
+                                "output_name": "output_h5ad"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Scanpy FindMarkers",
+                                "name": "groupby_file"
+                            }
+                        ],
                         "label": null,
-                        "name": "1st step removed - Convert from Ensembl to GeneSymbol, summing duplicate genes",
-                        "outputs": [],
-                        "position": {
-                            "left": 1184.510498046875,
-                            "top": 0
-                        },
-                        "subworkflow": {
-                            "a_galaxy_workflow": "true",
-                            "annotation": "",
-                            "creator": [
-                                {
-                                    "class": "Person",
-                                    "identifier": "",
-                                    "name": "Mehmet Tekman"
-                                }
-                            ],
-                            "format-version": "0.1",
-                            "name": "1st step removed - Convert from Ensembl to GeneSymbol, summing duplicate genes",
-                            "steps": {
-                                "0": {
-                                    "annotation": "",
-                                    "content_id": null,
-                                    "errors": null,
-                                    "id": 0,
-                                    "input_connections": {},
-                                    "inputs": [
-                                        {
-                                            "description": "",
-                                            "name": "Annotated IDs"
-                                        }
-                                    ],
-                                    "label": "Annotated IDs",
-                                    "name": "Input dataset",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 0.5,
-                                        "top": 127.52500915527344
-                                    },
-                                    "tool_id": null,
-                                    "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                                    "tool_version": null,
-                                    "type": "data_input",
-                                    "uuid": "d81929a3-775c-4421-ba06-6a4c69f74ff7",
-                                    "workflow_outputs": [
-                                        {
-                                            "label": null,
-                                            "output_name": "output",
-                                            "uuid": "8ac19ec5-b4f9-499b-93fb-c624b9c04b22"
-                                        }
-                                    ]
-                                },
-                                "1": {
-                                    "annotation": "",
-                                    "content_id": null,
-                                    "errors": null,
-                                    "id": 1,
-                                    "input_connections": {},
-                                    "inputs": [
-                                        {
-                                            "description": "",
-                                            "name": "Expression Matrix (Gene Rows)"
-                                        }
-                                    ],
-                                    "label": "Expression Matrix (Gene Rows)",
-                                    "name": "Input dataset",
-                                    "outputs": [],
-                                    "position": {
-                                        "left": 0.0,
-                                        "top": 237.01251220703125
-                                    },
-                                    "tool_id": null,
-                                    "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                                    "tool_version": null,
-                                    "type": "data_input",
-                                    "uuid": "cb8ea816-9239-421d-ae4c-8bba1b07d2f9",
-                                    "workflow_outputs": []
-                                },
-                                "10": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-                                    "errors": null,
-                                    "id": 10,
-                                    "input_connections": {
-                                        "infile": {
-                                            "id": 9,
-                                            "output_name": "table"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Final Count Matrix with Gene Symbol ID's",
-                                    "name": "Text transformation",
-                                    "outputs": [
-                                        {
-                                            "name": "output",
-                                            "type": "input"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 1284.0125732421875,
-                                        "top": 386.07501220703125
-                                    },
-                                    "post_job_actions": {},
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "f46f0e4f75c4",
-                                        "name": "text_processing",
-                                        "owner": "bgruening",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"1 s/^gene//\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": null,
-                                    "type": "tool",
-                                    "uuid": "417aedef-9d94-43b1-a3cd-adef81d7132a",
-                                    "workflow_outputs": [
-                                        {
-                                            "label": "Gene Symbol Count Matrix",
-                                            "output_name": "output",
-                                            "uuid": "3cefa576-db2d-44f6-8cf2-26c846cf5d88"
-                                        }
-                                    ]
-                                },
-                                "2": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-                                    "errors": null,
-                                    "id": 2,
-                                    "input_connections": {
-                                        "infile": {
-                                            "id": 0,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [
-                                        {
-                                            "description": "runtime parameter for tool Text reformatting",
-                                            "name": "infile"
-                                        }
-                                    ],
-                                    "label": "Group Ensembl Duplicates",
-                                    "name": "Text reformatting",
-                                    "outputs": [
-                                        {
-                                            "name": "outfile",
-                                            "type": "input"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 328.01251220703125,
-                                        "top": 220.0124969482422
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionoutfile": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "outfile"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "f46f0e4f75c4",
-                                        "name": "text_processing",
-                                        "owner": "bgruening",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"code\": \"BEGIN {\\n  ordering[\\\"test\\\"]\\n  delete ordering[\\\"test\\\"]\\n}\\nNR > 1 {\\n   if (gene[$1]){\\n      gene[$1] = gene[$1]\\\":\\\"$2\\n   } else {\\n      gene[$1] = $2\\n      ordering[length(ordering)+1] = $1\\n   }\\n   \\n}\\n\\nEND {\\n    for (o=0; o < length(ordering); ++o){\\n         print ordering[o]\\\"\\\\t\\\"gene[ordering[o]]\\n    }\\n}\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": null,
-                                    "type": "tool",
-                                    "uuid": "51d68e09-2af1-4c81-9ca8-b76afe06e9f7",
-                                    "workflow_outputs": []
-                                },
-                                "3": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-                                    "errors": null,
-                                    "id": 3,
-                                    "input_connections": {
-                                        "infile1": {
-                                            "id": 1,
-                                            "output_name": "output"
-                                        },
-                                        "infile2": {
-                                            "id": 2,
-                                            "output_name": "outfile"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Merge Gene Symbol and matrix together",
-                                    "name": "Join",
-                                    "outputs": [
-                                        {
-                                            "name": "output",
-                                            "type": "input"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 330.98748779296875,
-                                        "top": 352.0249938964844
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionoutput": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "f46f0e4f75c4",
-                                        "name": "text_processing",
-                                        "owner": "bgruening",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": \"true\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": null,
-                                    "type": "tool",
-                                    "uuid": "76d38310-a221-4b70-bcb9-296b4870bb52",
-                                    "workflow_outputs": []
-                                },
-                                "4": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-                                    "errors": null,
-                                    "id": 4,
-                                    "input_connections": {
-                                        "infile": {
-                                            "id": 3,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Relocate the Gene Symbol column to 1st column",
-                                    "name": "Text reformatting",
-                                    "outputs": [
-                                        {
-                                            "name": "outfile",
-                                            "type": "input"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 580.9625244140625,
-                                        "top": 381.01251220703125
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionoutfile": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "outfile"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "f46f0e4f75c4",
-                                        "name": "text_processing",
-                                        "owner": "bgruening",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"code\": \"{print $NF\\\"\\\\t\\\"$0}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": null,
-                                    "type": "tool",
-                                    "uuid": "f1d4e7aa-4ac7-4258-a1eb-a335cad2c861",
-                                    "workflow_outputs": []
-                                },
-                                "5": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-                                    "errors": null,
-                                    "id": 5,
-                                    "input_connections": {
-                                        "input": {
-                                            "id": 4,
-                                            "output_name": "outfile"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Remove second column with Ensembl ID's",
-                                    "name": "Advanced Cut",
-                                    "outputs": [
-                                        {
-                                            "name": "output",
-                                            "type": "tabular"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 580.0,
-                                        "top": 236.01251220703125
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionoutput": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "f46f0e4f75c4",
-                                        "name": "text_processing",
-                                        "owner": "bgruening",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"complement\": \"--complement\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"list\": \"2\"}, \"delimiter\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": null,
-                                    "type": "tool",
-                                    "uuid": "334f4810-84e0-4b5c-962f-0e2e6fbcc5f8",
-                                    "workflow_outputs": []
-                                },
-                                "6": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-                                    "errors": null,
-                                    "id": 6,
-                                    "input_connections": {
-                                        "infile": {
-                                            "id": 5,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Count Unique occurences of Gene Symbol",
-                                    "name": "Text reformatting",
-                                    "outputs": [
-                                        {
-                                            "name": "outfile",
-                                            "type": "input"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 832.987548828125,
-                                        "top": 0.0
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionoutfile": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "outfile"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "f46f0e4f75c4",
-                                        "name": "text_processing",
-                                        "owner": "bgruening",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"code\": \"{ gene[$1] = gene[$1] + 1 }\\n\\nEND {\\n     for (ge in gene){\\n         print ge\\\"\\\\t\\\"gene[ge]\\n     }\\n}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": null,
-                                    "type": "tool",
-                                    "uuid": "111ebd66-534f-4b17-9d60-aeff287fe500",
-                                    "workflow_outputs": []
-                                },
-                                "7": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-                                    "errors": null,
-                                    "id": 7,
-                                    "input_connections": {
-                                        "infile": {
-                                            "id": 5,
-                                            "output_name": "output"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Group rows by Gene Symbol and append their values (Long Format)",
-                                    "name": "Text reformatting",
-                                    "outputs": [
-                                        {
-                                            "name": "outfile",
-                                            "type": "input"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 833.9625244140625,
-                                        "top": 246.05001831054688
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActionoutfile": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "outfile"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "f46f0e4f75c4",
-                                        "name": "text_processing",
-                                        "owner": "bgruening",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"code\": \"NR == 1 {\\n    for (i=2; i <= NF; i++){\\n         cellorder[i] = $i\\n   }\\n}\\n\\nNR > 1 {\\n    for (i=2; i <= NF; i++){\\n         if (cellorder[i] == \\\"0\\\" || $1 == \\\"NA\\\"){\\n         } else {\\n             bc[$1\\\"\\\\t\\\"cellorder[i]] = bc[$1\\\"\\\\t\\\"cellorder[i]] + $i\\n         }\\n   }\\n}\\n\\nEND {\\n   print \\\"gene\\\\tbar\\\\tvalue\\\"\\n   for (key in bc){\\n       print key\\\"\\\\t\\\"bc[key]\\n   }\\n}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": null,
-                                    "type": "tool",
-                                    "uuid": "e2ce8f93-c8e2-490a-a3b6-3e580c0a6604",
-                                    "workflow_outputs": []
-                                },
-                                "8": {
-                                    "annotation": "",
-                                    "content_id": "sort1",
-                                    "errors": null,
-                                    "id": 8,
-                                    "input_connections": {
-                                        "input": {
-                                            "id": 6,
-                                            "output_name": "outfile"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Unique Gene Symbol Occurences, sorted in descending frequency.",
-                                    "name": "Sort",
-                                    "outputs": [
-                                        {
-                                            "name": "out_file1",
-                                            "type": "input"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 1067.9625244140625,
-                                        "top": 2.0625
-                                    },
-                                    "post_job_actions": {},
-                                    "tool_id": "sort1",
-                                    "tool_state": "{\"column\": \"2\", \"column_set\": [], \"header_lines\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"order\": \"DESC\", \"style\": \"num\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": null,
-                                    "type": "tool",
-                                    "uuid": "73ec3cc4-738e-4815-9ed0-a657e56f0706",
-                                    "workflow_outputs": [
-                                        {
-                                            "label": "Report of Duplicate Genes",
-                                            "output_name": "out_file1",
-                                            "uuid": "fb52cadb-3832-49bb-ac12-5ba2600ea26d"
-                                        }
-                                    ]
-                                },
-                                "9": {
-                                    "annotation": "",
-                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0",
-                                    "errors": null,
-                                    "id": 9,
-                                    "input_connections": {
-                                        "singtabop|input": {
-                                            "id": 7,
-                                            "output_name": "outfile"
-                                        }
-                                    },
-                                    "inputs": [],
-                                    "label": "Pivot Long Format to Wide Format (Matrix)",
-                                    "name": "Table Compute",
-                                    "outputs": [
-                                        {
-                                            "name": "table",
-                                            "type": "tabular"
-                                        }
-                                    ],
-                                    "position": {
-                                        "left": 1057.987548828125,
-                                        "top": 298.0249938964844
-                                    },
-                                    "post_job_actions": {
-                                        "HideDatasetActiontable": {
-                                            "action_arguments": {},
-                                            "action_type": "HideDatasetAction",
-                                            "output_name": "table"
-                                        }
-                                    },
-                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0",
-                                    "tool_shed_repository": {
-                                        "changeset_revision": "3bf5661c0280",
-                                        "name": "table_compute",
-                                        "owner": "iuc",
-                                        "tool_shed": "toolshed.g2.bx.psu.edu"
-                                    },
-                                    "tool_state": "{\"out_opts\": [\"output_headers_col\", \"output_headers_row\"], \"precision\": \"6\", \"singtabop\": {\"use_type\": \"single\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"col_row_names\": [\"has_col_names\"], \"adv\": {\"header\": null, \"nrows\": null, \"skipfooter\": null, \"skip_blank_lines\": \"true\"}, \"user\": {\"mode\": \"fulltable\", \"__current_case__\": 4, \"general\": {\"use\": \"pivot\", \"__current_case__\": 2, \"index\": \"gene\", \"column\": \"bar\", \"values\": \"value\", \"aggfunc\": null, \"colfun_map\": []}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                                    "tool_version": null,
-                                    "type": "tool",
-                                    "uuid": "571a650f-5b76-4103-98f1-7a8400f1abbd",
-                                    "workflow_outputs": []
-                                }
+                        "name": "Scanpy FindMarkers",
+                        "outputs": [
+                            {
+                                "name": "output_h5ad",
+                                "type": "h5ad"
+                            },
+                            {
+                                "name": "output_tsv",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 3614.0000534057617,
+                            "top": 1136.0469055175781
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionoutput_h5ad": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_h5ad"
                             },
-                            "tags": "",
-                            "uuid": "1eccbdc6-6b28-4cbf-abbe-59145eeee57e"
+                            "RenameDatasetActionoutput_tsv": {
+                                "action_arguments": {
+                                    "newname": "Markers - genotype"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_tsv"
+                            }
                         },
-                        "tool_id": 171553,
-                        "type": "subworkflow",
-                        "uuid": "ff79cab7-702d-4172-8a10-9e64815de427",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "81c34e67f262",
+                            "name": "scanpy_find_markers",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"groupby\": \"genotype\", \"groupby_file\": {\"__class__\": \"RuntimeValue\"}, \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"n_genes\": \"50\", \"output_format\": \"anndata_h5ad\", \"output_markers\": true, \"settings\": {\"default\": true, \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
+                        "type": "tool",
+                        "uuid": "fef645a2-5159-41f6-a910-fd99ca48b513",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Markers - genotype",
+                                "output_name": "output_tsv",
+                                "uuid": "1e9f229d-eb34-4a5b-a6d9-e70c7b0581f4"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                        "errors": null,
+                        "id": 32,
+                        "input_connections": {
+                            "input_obj_file": {
+                                "id": 30,
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Scanpy PlotEmbed",
+                                "name": "input_obj_file"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Scanpy PlotEmbed",
+                        "outputs": [
+                            {
+                                "name": "output_png",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 3900.885245493235,
+                            "top": 102.06455225986635
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "35f6611fb8c3",
+                            "name": "scanpy_plot_embed",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"basis\": \"tsne\", \"color_by\": \"louvain,sex,batch,genotype,Il2ra,Cd8b1,Cd8a,Cd4,Itm2a,Aif1,log1p_total_counts\", \"components\": \"\", \"edges\": false, \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": false, \"fig_size\": \"4,4\", \"fig_title\": \"\", \"gene_symbols_field\": \"Symbol\", \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"RuntimeValue\"}, \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": false, \"use_raw\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
+                        "type": "tool",
+                        "uuid": "e2f88d64-42c4-42a3-8152-e9d680280a42",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "Gene Symbol Count Matrix",
-                                "uuid": "bc5b731e-deb9-4117-ba1d-3f891cb61e66"
-                            },
+                                "output_name": "output_png",
+                                "uuid": "a3df76e7-84ab-4dc8-a08a-e45e8d2091c7"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                        "errors": null,
+                        "id": 33,
+                        "input_connections": {
+                            "input_obj_file": {
+                                "id": 30,
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Scanpy PlotEmbed",
+                                "name": "input_obj_file"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Scanpy PlotEmbed",
+                        "outputs": [
+                            {
+                                "name": "output_png",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 3905.3432253483716,
+                            "top": 319.15199020651033
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "35f6611fb8c3",
+                            "name": "scanpy_plot_embed",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"basis\": \"umap\", \"color_by\": \"louvain,sex,batch,genotype,Il2ra,Cd8b1,Cd8a,Cd4,Itm2a,Aif1,log1p_total_counts\", \"components\": \"\", \"edges\": false, \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": false, \"fig_size\": \"4,4\", \"fig_title\": \"\", \"gene_symbols_field\": \"Symbol\", \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"RuntimeValue\"}, \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": false, \"use_raw\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
+                        "type": "tool",
+                        "uuid": "89c6456b-3f1c-4cc1-86c3-2a46debf6da9",
+                        "when": null,
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "Report of Duplicate Genes",
-                                "uuid": "3dfa19cf-db53-4923-b2c1-abe2c37d3457"
+                                "output_name": "output_png",
+                                "uuid": "41663669-5ea9-44e1-bd3d-f9515a6499d4"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
                         "errors": null,
-                        "id": 7,
+                        "id": 34,
                         "input_connections": {
-                            "exprs_file": {
-                                "id": 6,
-                                "output_name": "Gene Symbol Count Matrix"
-                            },
-                            "pdata_file": {
-                                "id": 1,
-                                "output_name": "output"
+                            "input": {
+                                "id": 30,
+                                "output_name": "output_h5ad"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Construct Expression Set Object",
+                        "name": "Manipulate AnnData",
                         "outputs": [
                             {
-                                "name": "out_txt",
-                                "type": "txt"
-                            },
+                                "name": "anndata",
+                                "type": "h5ad"
+                            }
+                        ],
+                        "position": {
+                            "left": 3902.000045776367,
+                            "top": 535.0468444824219
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3d748954434b",
+                            "name": "anndata_manipulate",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"manipulate\": {\"function\": \"rename_categories\", \"__current_case__\": 3, \"key\": \"louvain\", \"categories\": \"DP-M4,DP-M3,DP-M1,T-mat,DN,DP-L,DP-M2,Macrophages\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "5642c686-66c7-4462-af54-090fe91f83de",
+                        "when": null,
+                        "workflow_outputs": [
                             {
-                                "name": "out_rds",
-                                "type": "rdata"
+                                "label": null,
+                                "output_name": "anndata",
+                                "uuid": "82521e5a-3438-4b2c-8164-fd111c0e9604"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                        "errors": null,
+                        "id": 35,
+                        "input_connections": {
+                            "input_obj_file": {
+                                "id": 30,
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Scanpy PlotEmbed",
+                                "name": "input_obj_file"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Scanpy PlotEmbed",
+                        "outputs": [
+                            {
+                                "name": "output_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 1439.0208740234375,
-                            "top": 151
+                            "left": 3902.000045776367,
+                            "top": 731.0312652587891
                         },
-                        "post_job_actions": {
-                            "RemoveTagDatasetActionout_rds": {
-                                "action_arguments": {
-                                    "tags": "#metadata,#matrix"
-                                },
-                                "action_type": "RemoveTagDatasetAction",
-                                "output_name": "out_rds"
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                        "tool_shed_repository": {
+                            "changeset_revision": "35f6611fb8c3",
+                            "name": "scanpy_plot_embed",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"basis\": \"pca\", \"color_by\": \"louvain,sex,batch,genotype,Il2ra,Cd8b1,Cd8a,Cd4,Itm2a,Aif1,log1p_total_counts\", \"components\": \"\", \"edges\": false, \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": false, \"fig_size\": \"4,4\", \"fig_title\": \"\", \"gene_symbols_field\": \"Symbol\", \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"RuntimeValue\"}, \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": false, \"use_raw\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
+                        "type": "tool",
+                        "uuid": "d6331822-fde8-4172-b28e-0f4089d24901",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_png",
+                                "uuid": "986bfb38-fc90-4b28-aa46-c19856dd5ba9"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "errors": null,
+                        "id": 36,
+                        "input_connections": {
+                            "input": {
+                                "id": 30,
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Inspect AnnData",
+                        "outputs": [
+                            {
+                                "name": "var",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 3899.770771786677,
+                            "top": 948.0374627272056
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ee98d611afc6",
+                            "name": "anndata_inspect",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"var\", \"__current_case__\": 4}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.7.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "58cb02fe-78cc-455c-a5ec-ba7091d909d6",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "var",
+                                "uuid": "60e229a4-73a2-45b4-95ef-894728376f7d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy91",
+                        "errors": null,
+                        "id": 37,
+                        "input_connections": {
+                            "copy_o|obs_sources": {
+                                "id": 34,
+                                "output_name": "anndata"
                             },
-                            "TagDatasetActionout_rds": {
-                                "action_arguments": {
-                                    "tags": "#combined"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "out_rds"
+                            "input_obj_file": {
+                                "id": 30,
+                                "output_name": "output_h5ad"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4",
+                        "inputs": [],
+                        "label": null,
+                        "name": "AnnData Operations",
+                        "outputs": [
+                            {
+                                "name": "output_h5ad",
+                                "type": "h5ad"
+                            }
+                        ],
+                        "position": {
+                            "left": 4190.000076293945,
+                            "top": 0
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy91",
                         "tool_shed_repository": {
-                            "changeset_revision": "282819d09a4f",
-                            "name": "music_construct_eset",
-                            "owner": "bgruening",
+                            "changeset_revision": "7ebc22f77d86",
+                            "name": "anndata_ops",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"annotation\": \"\", \"expdata\": {\"name\": \"\", \"lab\": \"\", \"contact\": \"\", \"title\": \"\", \"abstract\": \"\", \"url\": \"\", \"other\": [{\"__index__\": 0, \"field\": \"notes\", \"comment\": \"Created in Galaxy\"}]}, \"exprs_file\": {\"__class__\": \"ConnectedValue\"}, \"metadata\": [], \"pdata_file\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"add_cell_metadata\": {\"default\": false, \"__current_case__\": 1}, \"copy_adata_to_raw\": false, \"copy_e\": {\"default\": false, \"__current_case__\": 1}, \"copy_l\": {\"default\": false, \"__current_case__\": 1}, \"copy_o\": {\"default\": true, \"__current_case__\": 0, \"obs_keys\": [{\"__index__\": 0, \"contains\": \"louvain\"}], \"obs_sources\": {\"__class__\": \"ConnectedValue\"}}, \"copy_r\": {\"default\": false, \"__current_case__\": 1}, \"copy_u\": {\"default\": false, \"__current_case__\": 1}, \"copy_x\": {\"default\": false, \"__current_case__\": 1}, \"field_unique\": null, \"gene_flags\": [], \"gene_symbols_field\": \"index\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": false, \"top_genes\": \"50\", \"var_modifications\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy91",
                         "type": "tool",
-                        "uuid": "ca9a2794-404f-4460-8377-f2bc142b37a4",
+                        "uuid": "8e6882a9-3d0b-4b93-b5e9-5852643a7411",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Construct Expression Set Object on input dataset(s): RData ESet Object",
-                                "output_name": "out_rds",
-                                "uuid": "e8c91df0-4e6c-4eb2-9807-c2679b494958"
+                                "label": null,
+                                "output_name": "output_h5ad",
+                                "uuid": "28b9308e-7f03-44d5-a81b-2e654353f6f8"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "join1",
+                        "errors": null,
+                        "id": 38,
+                        "input_connections": {
+                            "input1": {
+                                "id": 30,
+                                "output_name": "output_tsv"
                             },
+                            "input2": {
+                                "id": 36,
+                                "output_name": "var"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Join two Datasets",
+                        "outputs": [
                             {
-                                "label": "Construct Expression Set Object on input dataset(s): General Info",
-                                "output_name": "out_txt",
-                                "uuid": "2912d09b-b178-4035-b7c8-7038392e2bf2"
+                                "name": "out_file1",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 4190.000076293945,
+                            "top": 1002.0468902587891
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "join1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"field1\": \"4\", \"field2\": \"2\", \"fill_empty_columns\": {\"fill_empty_columns_switch\": \"no_fill\", \"__current_case__\": 0}, \"header\": \"-H\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"partial\": \"-p\", \"unmatched\": \"-u\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.3",
+                        "type": "tool",
+                        "uuid": "6e6e5028-78a9-47d7-8df0-d183075c3da6",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "fb12a596-f691-4045-ac12-a3909b084f3e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4",
+                        "content_id": "join1",
                         "errors": null,
-                        "id": 8,
+                        "id": 39,
                         "input_connections": {
-                            "rds_eset": {
-                                "id": 7,
-                                "output_name": "out_rds"
+                            "input1": {
+                                "id": 31,
+                                "output_name": "output_tsv"
+                            },
+                            "input2": {
+                                "id": 36,
+                                "output_name": "var"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Manipulate Expression Set Object",
+                        "name": "Join two Datasets",
                         "outputs": [
                             {
-                                "name": "out_eset",
-                                "type": "rdata"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1729.52099609375,
-                            "top": 157.5
+                            "left": 4190.000076293945,
+                            "top": 1187.0468139648438
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "join1",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"__workflow_invocation_uuid__\": \"190c9dc088ac11eb8307001e67d2ec02\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"field1\": \"4\", \"field2\": \"2\", \"fill_empty_columns\": {\"fill_empty_columns_switch\": \"no_fill\", \"__current_case__\": 0}, \"header\": \"-H\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"partial\": \"-p\", \"unmatched\": \"-u\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.3",
+                        "type": "tool",
+                        "uuid": "5f0e9d28-cad2-4716-8b07-616c521fcce1",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "ddf27680-03a3-44b6-8217-9e8d560f449f"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy91",
+                        "errors": null,
+                        "id": 40,
+                        "input_connections": {
+                            "input_obj_file": {
+                                "id": 37,
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "AnnData Operations",
+                        "outputs": [
+                            {
+                                "name": "output_h5ad",
+                                "type": "h5ad"
+                            }
+                        ],
+                        "position": {
+                            "left": 4468.000030517578,
+                            "top": 25.859375
                         },
                         "post_job_actions": {
-                            "RemoveTagDatasetActionout_eset": {
-                                "action_arguments": {
-                                    "tags": "#combined"
-                                },
-                                "action_type": "RemoveTagDatasetAction",
-                                "output_name": "out_eset"
-                            },
-                            "TagDatasetActionout_eset": {
+                            "RenameDatasetActionoutput_h5ad": {
                                 "action_arguments": {
-                                    "tags": "#normal"
+                                    "newname": "Final cell annotated object"
                                 },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "out_eset"
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_h5ad"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy91",
                         "tool_shed_repository": {
-                            "changeset_revision": "22232092be53",
-                            "name": "music_manipulate_eset",
-                            "owner": "bgruening",
+                            "changeset_revision": "7ebc22f77d86",
+                            "name": "anndata_ops",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"combine_eset\": {\"do\": \"No\", \"__current_case__\": 0}, \"rds_eset\": {\"__class__\": \"ConnectedValue\"}, \"subset_eset\": {\"do\": \"Yes\", \"__current_case__\": 1, \"subset_yes\": {\"by\": \"phenotype\", \"__current_case__\": 3, \"pheno_samples\": [{\"__index__\": 0, \"column\": \"Disease\", \"values\": \"normal\"}], \"pheno_genes\": []}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"add_cell_metadata\": {\"default\": false, \"__current_case__\": 1}, \"copy_adata_to_raw\": false, \"copy_e\": {\"default\": false, \"__current_case__\": 1}, \"copy_l\": {\"default\": false, \"__current_case__\": 1}, \"copy_o\": {\"default\": false, \"__current_case__\": 1}, \"copy_r\": {\"default\": false, \"__current_case__\": 1}, \"copy_u\": {\"default\": false, \"__current_case__\": 1}, \"copy_x\": {\"default\": false, \"__current_case__\": 1}, \"field_unique\": null, \"gene_flags\": [], \"gene_symbols_field\": \"index\", \"input_obj_file\": {\"__class__\": \"ConnectedValue\"}, \"modifications\": [{\"__index__\": 0, \"from_obs\": \"louvain_0\", \"to_obs\": \"cell_type\", \"keep_original\": false, \"make_unique\": false}], \"output_format\": \"anndata_h5ad\", \"sanitize_varm\": false, \"top_genes\": \"50\", \"var_modifications\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy91",
                         "type": "tool",
-                        "uuid": "4f5f4bed-c2cf-4fe8-8d29-32b3e178932b",
+                        "uuid": "4afeffe6-16b4-4a59-baef-ca0f15a6a6db",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Manipulate Expression Set Object on input dataset(s): ExpressionSet Object",
-                                "output_name": "out_eset",
-                                "uuid": "08de92d8-32fe-4b47-9038-298cdd13fac5"
+                                "label": "Final cell annotated object",
+                                "output_name": "output_h5ad",
+                                "uuid": "10bd70f8-ffcb-442b-9647-e5b947b6d35e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4",
+                        "content_id": "Cut1",
                         "errors": null,
-                        "id": 9,
+                        "id": 41,
                         "input_connections": {
-                            "rds_eset": {
-                                "id": 7,
-                                "output_name": "out_rds"
+                            "input": {
+                                "id": 38,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Manipulate Expression Set Object",
+                        "name": "Cut",
                         "outputs": [
                             {
-                                "name": "out_eset",
-                                "type": "rdata"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1725.52099609375,
-                            "top": 402.4895935058594
+                            "left": 4468.000030517578,
+                            "top": 1040.0468444824219
                         },
                         "post_job_actions": {
-                            "RemoveTagDatasetActionout_eset": {
+                            "RenameDatasetActionout_file1": {
                                 "action_arguments": {
-                                    "tags": "#combined"
+                                    "newname": "Markers - cluster - named"
                                 },
-                                "action_type": "RemoveTagDatasetAction",
-                                "output_name": "out_eset"
-                            },
-                            "TagDatasetActionout_eset": {
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"columnList\": \"c1,c2,c3,c4,c11,c5,c6,c7,c8\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2",
+                        "type": "tool",
+                        "uuid": "25c9cbaf-4543-455e-bc1f-22b57cb2d8be",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Markers - cluster - named",
+                                "output_name": "out_file1",
+                                "uuid": "4f822c1c-91c5-4be4-8f9b-d5bdda0a037e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "Cut1",
+                        "errors": null,
+                        "id": 42,
+                        "input_connections": {
+                            "input": {
+                                "id": 39,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Cut",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 4468.000030517578,
+                            "top": 1225.0468444824219
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
                                 "action_arguments": {
-                                    "tags": "#T2D"
+                                    "newname": "Markers - genotype - named"
                                 },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "out_eset"
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4",
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"columnList\": \"c1,c2,c3,c4,c11,c5,c6,c7,c8\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2",
+                        "type": "tool",
+                        "uuid": "7f87b07e-5b61-4429-a8d3-25d2f7f778ac",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Markers - genotype - named",
+                                "output_name": "out_file1",
+                                "uuid": "3b471f3d-263d-4299-9b7d-8a8ae1aa556e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                        "errors": null,
+                        "id": 43,
+                        "input_connections": {
+                            "input_obj_file": {
+                                "id": 40,
+                                "output_name": "output_h5ad"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Scanpy PlotEmbed",
+                                "name": "input_obj_file"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Scanpy PlotEmbed",
+                        "outputs": [
+                            {
+                                "name": "output_png",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 4653.500061035156,
+                            "top": 257.28126525878906
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
                         "tool_shed_repository": {
-                            "changeset_revision": "22232092be53",
-                            "name": "music_manipulate_eset",
-                            "owner": "bgruening",
+                            "changeset_revision": "35f6611fb8c3",
+                            "name": "scanpy_plot_embed",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"combine_eset\": {\"do\": \"No\", \"__current_case__\": 0}, \"rds_eset\": {\"__class__\": \"ConnectedValue\"}, \"subset_eset\": {\"do\": \"Yes\", \"__current_case__\": 1, \"subset_yes\": {\"by\": \"phenotype\", \"__current_case__\": 3, \"pheno_samples\": [{\"__index__\": 0, \"column\": \"Disease\", \"values\": \"type II diabetes mellitus\"}], \"pheno_genes\": []}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"basis\": \"umap\", \"color_by\": \"sex,batch,genotype,Il2ra,Cd8b1,Cd8a,Cd4,Itm2a,Aif1,Hba-a1,log1p_total_counts,cell_type\", \"components\": \"\", \"edges\": false, \"edges_color\": \"\", \"edges_width\": \"0.1\", \"fig_dpi\": \"80\", \"fig_fontsize\": \"10\", \"fig_frame\": false, \"fig_size\": \"4,4\", \"fig_title\": \"\", \"gene_symbols_field\": \"Symbol\", \"groups\": \"\", \"input_format\": \"anndata\", \"input_obj_file\": {\"__class__\": \"RuntimeValue\"}, \"layer\": \"\", \"legend_fontsize\": \"15\", \"legend_loc\": \"right margin\", \"neighbors_key\": \"\", \"point_size\": null, \"projection\": \"2d\", \"sort_order\": false, \"use_raw\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.1+galaxy9",
                         "type": "tool",
-                        "uuid": "175ce542-ca00-4a2c-bb63-1f08bf41b16e",
+                        "uuid": "d0930dc2-d747-49ff-ac8a-32bdda581012",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_eset",
-                                "uuid": "bdf6c2ca-9ded-487f-8c7c-7b5e5e7ec42f"
+                                "output_name": "output_png",
+                                "uuid": "180f366c-6007-4b0a-9c59-b05e2e4bb757"
                             }
                         ]
                     }
                 ],
-                "parent_id": "single-cell/bulk-music-2-preparescref",
-                "path": "topics/single-cell/tutorials/bulk-music-2-preparescref/workflows/sc_matrix.ga",
+                "parent_id": "single-cell/scrna-case_basic-pipeline",
+                "path": "topics/single-cell/tutorials/scrna-case_basic-pipeline/workflows/Filter,-Plot-and-Explore-Single-cell-RNA-seq-Data-updated.ga",
                 "tags": [
-                    "name:singlecell",
-                    "name:training",
-                    "name:transcriptomics"
+                    "transcriptomics"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "MuSiC-Deconvolution: Data generation | sc | matrix + ESet",
+                "tests": true,
+                "title": "Filter, Plot and Explore Single-cell RNA-seq Data updated",
                 "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-bulk-music-2-preparescref/versions/sc-matrix",
-                "tutorial_id": "bulk-music-2-preparescref",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-2-preparescref/workflows/sc_matrix.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-2-preparescref/workflows/sc_matrix.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-case_basic-pipeline/versions/filter--plot-and-explore-single-cell-rna-seq-data-updated",
+                "tutorial_id": "scrna-case_basic-pipeline",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_basic-pipeline/workflows/Filter,-Plot-and-Explore-Single-cell-RNA-seq-Data-updated.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_basic-pipeline/workflows/Filter,-Plot-and-Explore-Single-cell-RNA-seq-Data-updated.html",
                 "version": 1,
-                "wfid": "single-cell-bulk-music-2-preparescref",
-                "wfname": "sc-matrix",
-                "workflow": "sc_matrix.ga",
+                "wfid": "single-cell-scrna-case_basic-pipeline",
+                "wfname": "filter--plot-and-explore-single-cell-rna-seq-data-updated",
+                "workflow": "Filter,-Plot-and-Explore-Single-cell-RNA-seq-Data-updated.ga",
                 "workflow_tools": [
-                    "sort1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy0",
+                    "Cut1",
+                    "join1",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy91",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy9",
                     "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1"
                 ],
-                "workflowhub_id": "1261"
+                "workflowhub_id": "1212"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/7053673"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plates-batches-barcodes/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "bio": "Senior Lecturer at The Open University",
+                "elixir_node": "uk",
+                "email": "wendi.bacon@open.ac.uk",
+                "fediverse": "https://mstdn.science/@wendibacon1",
+                "fediverse_flavor": "mastodon",
+                "id": "nomadscientist",
+                "joined": "2020-03",
+                "matrix": "nomadscientist:matrix.org",
+                "name": "Wendi Bacon",
+                "orcid": "0000-0002-8170-8806",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
+                "twitter": "WendiBacon1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
             },
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-8170-8806",
-                        "name": "Wendi Bacon"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0002-4181-2676",
-                        "name": "Mehmet Tekman"
-                    }
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "elixir_node": "de",
+                "email": "mtekman89@gmail.com",
+                "former_affiliations": [
+                    "elixir-europe"
+                ],
+                "id": "mtekman",
+                "joined": "2018-11",
+                "name": "Mehmet Tekman",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
+            },
+            {
+                "email": "a.ostrovsky@mac.com",
+                "id": "astrovsky01",
+                "joined": "2019-06",
+                "name": "Alex Ostrovsky",
+                "orcid": "0000-0002-7901-7109",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/astrovsky01/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/astrovsky01.json"
+            }
+        ],
+        "dir": "topics/single-cell/tutorials/scrna-plates-batches-barcodes",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": false,
+        "id": "single-cell/scrna-plates-batches-barcodes",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": 7126,
+            "mermaid": false
+        },
+        "key_points": [
+            "Balanced batches and replicates allow bioinformatic batch correction",
+            "A sequencing lane often contains multiple batches, and is itself a batch effect!"
+        ],
+        "layout": "tutorial_slides",
+        "license": "CC-BY-4.0",
+        "logo": "GTN",
+        "mod_date": "2023-10-10",
+        "objectives": [
+            "How to set up plates to prevent batch effect",
+            "Proper naming conventions when dealing with scRNA-seq samples"
+        ],
+        "pageviews": 5897561,
+        "priority": 3,
+        "pub_date": "2019-02-16",
+        "questions": [
+            "What is a batch when it comes to single cells?",
+            "What\u2019s the difference between a barcode and an index?",
+            "What is batch effect and how do you prevent it?",
+            "What is a lane?"
+        ],
+        "redirect_from": [
+            "/topics/transcriptomics/tutorials/scrna-plates-batches-barcodes/slides",
+            "/short/single-cell/scrna-plates-batches-barcodes/slides",
+            "/short/S00085"
+        ],
+        "short_id": "S00085",
+        "short_tools": [],
+        "slides": true,
+        "slides_recordings": false,
+        "subtopic": "scintroduction",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": null,
+        "time_estimation": "1h",
+        "title": "Plates, Batches, and Barcodes",
+        "tools": [],
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": true
+        },
+        "tutorial_name": "scrna-plates-batches-barcodes",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-plates-batches-barcodes/slides.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plates-batches-barcodes/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-plates-batches-barcodes/slides.json"
+        },
+        "version": 2,
+        "video": true,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 152,
+        "visitors": 2133613,
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "answer_histories": [
+            {
+                "date": "2024-09-08",
+                "history": "https://usegalaxy.eu/u/wendi.bacon.training/h/cs4inferring-trajectories-using-python-in-galaxyanswer-key",
+                "label": "Figures exported from the notebook to Galaxy history (UseGalaxy.eu)"
+            },
+            {
+                "date": "2024-09-10",
+                "history": "https://colab.research.google.com/drive/1-ENlIXM7TAoDGsMam7RyJIusIaBfF9e4?usp=sharing",
+                "label": "Backup Jupyter Notebook for Google Colab"
+            }
+        ],
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_JUPYTER-trajectories/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "nomadscientist",
+                "wee-snufkin",
+                "mtekman"
+            ],
+            "editing": [
+                "hexylena"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "bio": "Senior Lecturer at The Open University",
+                "elixir_node": "uk",
+                "email": "wendi.bacon@open.ac.uk",
+                "fediverse": "https://mstdn.science/@wendibacon1",
+                "fediverse_flavor": "mastodon",
+                "id": "nomadscientist",
+                "joined": "2020-03",
+                "matrix": "nomadscientist:matrix.org",
+                "name": "Wendi Bacon",
+                "orcid": "0000-0002-8170-8806",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
+                "twitter": "WendiBacon1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+            },
+            {
+                "elixir_node": "uk",
+                "email": "juliajot36@gmail.com",
+                "id": "wee-snufkin",
+                "joined": "2022-06",
+                "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "elixir_node": "de",
+                "email": "mtekman89@gmail.com",
+                "former_affiliations": [
+                    "elixir-europe"
+                ],
+                "id": "mtekman",
+                "joined": "2018-11",
+                "name": "Mehmet Tekman",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            }
+        ],
+        "dir": "topics/single-cell/tutorials/scrna-case_JUPYTER-trajectories",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "single-cell/scrna-case_JUPYTER-trajectories",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "input_histories": [
+            {
+                "history": "https://usegalaxy.eu/published/history?id=42cfa5176a883f43",
+                "label": "UseGalaxy.eu"
+            }
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Trajectory analysis is less robust than pure plotting methods, as such 'inferred relationships' are a bigger mathematical leap",
+            "As always with single-cell analysis, you must know enough biology to deduce if your analysis is reasonable, before exploring or deducing novel insight"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-19",
+        "notebook": {
+            "language": "python",
+            "snippet": "topics/single-cell/tutorials/scrna-case_JUPYTER-trajectories/preamble.md"
+        },
+        "objectives": [
+            "Execute multiple plotting methods designed to maintain lineage relationships between cells",
+            "Interpret these plots"
+        ],
+        "pageviews": 3602,
+        "priority": 3,
+        "pub_date": "2021-04-07",
+        "questions": [
+            "How can I infer lineage relationships between single cells based on their RNA, without a time series?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "nomadscientist"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "10M",
+                "speakers": [
+                    "nomadscientist"
+                ],
+                "youtube_id": "VEyTmwDIgPI"
+            }
+        ],
+        "redirect_from": [
+            "/topics/transcriptomics/tutorials/scrna-JUPYTER-trajectories/tutorial",
+            "/topics/transcriptomics/tutorials/scrna-case_JUPYTER-trajectories/tutorial",
+            "/short/single-cell/scrna-case_JUPYTER-trajectories",
+            "/short/T00244"
+        ],
+        "requirements": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-case_alevin",
+                    "scrna-case_alevin-combine-datasets",
+                    "scrna-case_basic-pipeline"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "galaxy-intro-jupyter"
                 ],
-                "description": "This workflow generates from only an EBI SCXA reference the metadata for creating an ESet object\n",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00244",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "single-cell-CS-code",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"EBI SCXA Data Retrieval\"]\n  1[label=\"Cut\"]\n  0 -> 1 [label=\"design_tsv\"]\n  2[label=\"Add line to file\"]\n  0 -> 2 [label=\"barcode_tsv\"]\n  3[label=\"Reformatting metadata columns\"]\n  1 -> 3 [label=\"out_file1\"]\n  4[label=\"Join two Datasets\"]\n  2 -> 4 [label=\"outfile\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"Advanced Cut\"]\n  4 -> 5 [label=\"out_file1\"]\n}",
-                "history": [
-                    {
-                        "hash": "9a561b3752745eab20cececd5346ee0a7449da28",
-                        "message": "update workflows",
-                        "num": 1,
-                        "short_hash": "9a561b375",
-                        "unix": "1669581042"
-                    }
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "10x",
+            "paper-replication",
+            "Python"
+        ],
+        "time_estimation": "2H",
+        "title": "Inferring single cell trajectories with Scanpy (Python)",
+        "tools": [],
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "scrna-case_JUPYTER-trajectories",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_JUPYTER-trajectories/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_JUPYTER-trajectories/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_JUPYTER-trajectories/tutorial.json"
+        },
+        "version": 17,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 88,
+        "visitors": 2983,
+        "zenodo_link": "https://zenodo.org/record/7075718"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "retrieve_scxa",
+                    "owner": "ebi-gxa",
+                    "revisions": "72b6e1747e37",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seurat_filter_cells",
+                    "owner": "ebi-gxa",
+                    "revisions": "cd9f564bd63f",
+                    "tool_panel_section_label": "Seurat",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seurat_find_clusters",
+                    "owner": "ebi-gxa",
+                    "revisions": "d541e9e62beb",
+                    "tool_panel_section_label": "Seurat",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seurat_find_markers",
+                    "owner": "ebi-gxa",
+                    "revisions": "07fc9f4841b3",
+                    "tool_panel_section_label": "Seurat",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seurat_find_neighbours",
+                    "owner": "ebi-gxa",
+                    "revisions": "ba897c57bdd9",
+                    "tool_panel_section_label": "Seurat",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seurat_find_variable_genes",
+                    "owner": "ebi-gxa",
+                    "revisions": "948fc0276b4f",
+                    "tool_panel_section_label": "Seurat",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seurat_normalise_data",
+                    "owner": "ebi-gxa",
+                    "revisions": "3f49bc9c9213",
+                    "tool_panel_section_label": "Seurat",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seurat_plot",
+                    "owner": "ebi-gxa",
+                    "revisions": "95d79f1134f0",
+                    "tool_panel_section_label": "HCA-Scanpy",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seurat_read10x",
+                    "owner": "ebi-gxa",
+                    "revisions": "f5db0e853f57",
+                    "tool_panel_section_label": "Seurat",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seurat_run_pca",
+                    "owner": "ebi-gxa",
+                    "revisions": "8ded486b0014",
+                    "tool_panel_section_label": "Seurat",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seurat_run_umap",
+                    "owner": "ebi-gxa",
+                    "revisions": "b9424c715a0d",
+                    "tool_panel_section_label": "HCA-Scanpy",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seurat_scale_data",
+                    "owner": "ebi-gxa",
+                    "revisions": "5e9ba303f9e1",
+                    "tool_panel_section_label": "Seurat",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: retrieve_scxa\n  owner: ebi-gxa\n  revisions: 72b6e1747e37\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_filter_cells\n  owner: ebi-gxa\n  revisions: cd9f564bd63f\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_find_clusters\n  owner: ebi-gxa\n  revisions: d541e9e62beb\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_find_markers\n  owner: ebi-gxa\n  revisions: 07fc9f4841b3\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_find_neighbours\n  owner: ebi-gxa\n  revisions: ba897c57bdd9\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_find_variable_genes\n  owner: ebi-gxa\n  revisions: 948fc0276b4f\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_normalise_data\n  owner: ebi-gxa\n  revisions: 3f49bc9c9213\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_plot\n  owner: ebi-gxa\n  revisions: 95d79f1134f0\n  tool_panel_section_label: HCA-Scanpy\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_read10x\n  owner: ebi-gxa\n  revisions: f5db0e853f57\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_run_pca\n  owner: ebi-gxa\n  revisions: 8ded486b0014\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_run_umap\n  owner: ebi-gxa\n  revisions: b9424c715a0d\n  tool_panel_section_label: HCA-Scanpy\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seurat_scale_data\n  owner: ebi-gxa\n  revisions: 5e9ba303f9e1\n  tool_panel_section_label: Seurat\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "Camila-goclowski",
+                "pcm32"
+            ],
+            "editing": [
+                "pavanvidem",
+                "hexylena"
+            ]
+        },
+        "contributors": [
+            {
+                "email": "camila.goclowski@gmail.com",
+                "id": "Camila-goclowski",
+                "joined": "2023-01",
+                "linkedin": "camila-goclowski",
+                "name": "Camila Goclowski",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Camila-goclowski/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Camila-goclowski.json"
+            },
+            {
+                "id": "pcm32",
+                "joined": "2019-06",
+                "name": "Pablo Moreno",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pcm32/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pcm32.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
                 ],
-                "inputs": [],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"EBI SCXA Data Retrieval\"];\n  1[\"Cut\"];\n  0 -->|design_tsv| 1;\n  2[\"Add line to file\"];\n  0 -->|barcode_tsv| 2;\n  3[\"Reformatting metadata columns\"];\n  1 -->|out_file1| 3;\n  4[\"Join two Datasets\"];\n  2 -->|outfile| 4;\n  3 -->|out_file1| 4;\n  5[\"Advanced Cut\"];\n  4 -->|out_file1| 5;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "MuSiC-Deconvolution: Data generation | sc | metadata",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.1+galaxy1",
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "EBI SCXA Data Retrieval",
-                        "outputs": [
-                            {
-                                "name": "matrix_mtx",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "genes_tsv",
-                                "type": "tsv"
-                            },
-                            {
-                                "name": "barcode_tsv",
-                                "type": "tsv"
-                            },
-                            {
-                                "name": "design_tsv",
-                                "type": "tsv"
-                            }
-                        ],
-                        "position": {
-                            "left": 0.0,
-                            "top": 10.5
-                        },
-                        "post_job_actions": {
-                            "ChangeDatatypeActionbarcode_tsv": {
-                                "action_arguments": {
-                                    "newtype": "tabular"
-                                },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "barcode_tsv"
-                            },
-                            "TagDatasetActionbarcode_tsv": {
-                                "action_arguments": {
-                                    "tags": "#ebi,#singlecell,#metadata"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "barcode_tsv"
-                            },
-                            "TagDatasetActiondesign_tsv": {
-                                "action_arguments": {
-                                    "tags": "#ebi"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "design_tsv"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.1+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "cd6b80f62fcc",
-                            "name": "retrieve_scxa",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"accession\": \"E-MTAB-5061\", \"matrix_type\": \"raw\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
-                        "type": "tool",
-                        "uuid": "836f6c68-fa15-4f1d-8db5-a432c6c783f8",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "matrix_mtx",
-                                "uuid": "ecafd465-5cb3-4484-868f-8922ae3db395"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "genes_tsv",
-                                "uuid": "25d87e34-ad87-4987-a626-589b42b0a10d"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "barcode_tsv",
-                                "uuid": "9f57847e-944c-4b00-a33b-bd60ef0814ec"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "design_tsv",
-                                "uuid": "d8857eeb-49da-4772-b8e7-7237c7a0ade0"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "Cut1",
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "design_tsv"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cut",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 282.01043701171875,
-                            "top": 270.5
-                        },
-                        "post_job_actions": {
-                            "TagDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "tags": "#singlecell"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"columnList\": \"c1,c4,c6,c8,c10,c14,c20,c24,c26,c30,c32,c34\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
-                        "type": "tool",
-                        "uuid": "fc140e5f-6659-4a8f-bacc-ccf78e50cf39",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "3d887d75-9e58-4a8b-b8c3-9f30b65d17aa"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0",
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {
-                            "infile": {
-                                "id": 0,
-                                "output_name": "barcode_tsv"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Add line to file",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 687.5,
-                            "top": 0
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "8e251055b1a9",
-                            "name": "add_line_to_file",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"infile\": {\"__class__\": \"ConnectedValue\"}, \"options\": \"header\", \"text_input\": \"Cell\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
-                        "type": "tool",
-                        "uuid": "e8ac2324-aa96-40c6-a4f4-e2f3896136c9",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "e07a7e35-8f57-479a-b328-6d988627d5fb"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "Adjust this step as necessary",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "input": {
-                                "id": 1,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Reformatting metadata columns",
-                        "name": "Regex Find And Replace",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 586.03125,
-                            "top": 150.45834350585938
-                        },
-                        "post_job_actions": {
-                            "ChangeDatatypeActionout_file1": {
-                                "action_arguments": {
-                                    "newtype": "tabular"
-                                },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "out_file1"
-                            },
-                            "TagDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "tags": "#metadata"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "399da6b5ec21",
-                            "name": "regex_find_replace",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \"\\\"Sample Characteristic\\\\[individual\\\\]\\\"\", \"replacement\": \"Individual\"}, {\"__index__\": 1, \"pattern\": \"\\\"Sample Characteristic\\\\[sex\\\\]\\\"\", \"replacement\": \"Sex\"}, {\"__index__\": 2, \"pattern\": \"\\\"Sample Characteristic\\\\[age\\\\]\\\"\", \"replacement\": \"Age\"}, {\"__index__\": 3, \"pattern\": \"\\\"Sample Characteristic\\\\[body mass index\\\\]\\\"\", \"replacement\": \"BMI\"}, {\"__index__\": 4, \"pattern\": \" kilogram per square meter\", \"replacement\": \"\"}, {\"__index__\": 5, \"pattern\": \"HbA1c \", \"replacement\": \"\"}, {\"__index__\": 6, \"pattern\": \"\\\"Sample Characteristic\\\\[clinical information\\\\]\\\"\", \"replacement\": \"HbA1c\"}, {\"__index__\": 7, \"pattern\": \"%\", \"replacement\": \"\"}, {\"__index__\": 8, \"pattern\": \"\\\"Sample Characteristic\\\\[disease\\\\]\\\"\", \"replacement\": \"Disease\"}, {\"__index__\": 9, \"pattern\": \"\\\"Sample Characteristic\\\\[single cell quality\\\\]\\\"\", \"replacement\": \"Single cell quality\"}, {\"__index__\": 10, \"pattern\": \"\\\"Sample Characteristic\\\\[submitted single cell quality\\\\]\\\"\", \"replacement\": \"Submitted single cell quality\"}, {\"__index__\": 11, \"pattern\": \"\\\"Factor Value\\\\[inferred cell type - ontology labels\\\\]\\\"\", \"replacement\": \"Inferred cell type - ontology label\"}, {\"__index__\": 12, \"pattern\": \"\\\"\\\"\", \"replacement\": \"\"}, {\"__index__\": 13, \"pattern\": \"\\\"\", \"replacement\": \"\"}, {\"__index__\": 14, \"pattern\": \"Factor Value\\\\[inferred cell type - authors labels\\\\]\", \"replacement\": \"Inferred cell type - author labels\"}], \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
-                        "type": "tool",
-                        "uuid": "e5b0bcd3-a94c-4942-bed0-6d8f51e36e22",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "45757c76-0453-426f-b729-4c9d7b5688c9"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "Experimental designs often include extra stuff (likely the barcodes not meeting the EBI pre-processing criteria), so this way we streamline down to only those barcodes in the barcodes file.",
-                        "content_id": "join1",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "input1": {
-                                "id": 2,
-                                "output_name": "outfile"
-                            },
-                            "input2": {
-                                "id": 3,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Join two Datasets",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 857.0208740234375,
-                            "top": 166.46875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "join1",
-                        "tool_state": "{\"field1\": \"1\", \"field2\": \"1\", \"fill_empty_columns\": {\"fill_empty_columns_switch\": \"no_fill\", \"__current_case__\": 0}, \"header\": \"-H\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"partial\": \"\", \"unmatched\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
-                        "type": "tool",
-                        "uuid": "0f40eba6-5e09-45de-a6b8-64b4bdcabd3f",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "39583bc2-7e06-4088-abcc-bb8b994767bb"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "Gets rid of the duplicated columns",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "input": {
-                                "id": 4,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Advanced Cut",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 1106.8125,
-                            "top": 110.29167175292969
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f46f0e4f75c4",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"complement\": \"--complement\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"list\": \"1\"}, \"delimiter\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
-                        "type": "tool",
-                        "uuid": "f5795ca8-4172-42d5-a898-ab71fe195024",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "f7c57eb1-71ae-4850-8e99-16fafe763bbf"
-                            }
-                        ]
-                    }
+                "id": "pavanvidem",
+                "joined": "2017-09",
+                "name": "Pavankumar Videm",
+                "orcid": "0000-0002-5192-126X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
                 ],
-                "parent_id": "single-cell/bulk-music-2-preparescref",
-                "path": "topics/single-cell/tutorials/bulk-music-2-preparescref/workflows/sc_metadata.ga",
-                "tags": [
-                    "name:singlecell",
-                    "name:transcriptomics",
-                    "name:training",
-                    "name:deconvolution"
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
                 ],
-                "test_results": null,
-                "tests": false,
-                "title": "MuSiC-Deconvolution: Data generation | sc | metadata",
-                "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-bulk-music-2-preparescref/versions/sc-metadata",
-                "tutorial_id": "bulk-music-2-preparescref",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-2-preparescref/workflows/sc_metadata.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-2-preparescref/workflows/sc_metadata.html",
-                "version": 1,
-                "wfid": "single-cell-bulk-music-2-preparescref",
-                "wfname": "sc-metadata",
-                "workflow": "sc_metadata.ga",
-                "workflow_tools": [
-                    "Cut1",
-                    "join1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2"
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            }
+        ],
+        "dir": "topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "single-cell/scrna-case_FilterPlotandExplore_SeuratTools",
+        "inexact_supported_servers": [],
+        "input_histories": [
+            {
+                "history": "https://singlecell.usegalaxy.eu/u/camila-goclowski/h/tool-based-seurat-fpe-input-data",
+                "label": "UseGalaxy.eu"
+            }
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-13",
+        "objectives": [
+            "Interpret quality control plots to direct parameter decisions",
+            "Repeat analysis from matrix to clustering to labelling clusters",
+            "Identify decision-making points",
+            "Appraise data outputs and decisions",
+            "Explain why single cell analysis is an iterative process (i.e. the first plots you generate are not final, but rather you go back and re-analyse your data repeatedly)"
+        ],
+        "pageviews": 561,
+        "priority": 3,
+        "pub_date": "2024-04-09",
+        "questions": [
+            "Is my single cell dataset a quality dataset?",
+            "How do I pick thresholds and parameters in my analysis? What\u2019s a \u201creasonable\u201d number, and will the world collapse if I pick the wrong one?",
+            "How do I generate and annotate cell clusters?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-intro",
+                    "scrna-preprocessing-tenx"
                 ],
-                "workflowhub_id": "1257"
+                "type": "internal"
             }
-        ]
+        ],
+        "short_id": "T00438",
+        "short_tools": [
+            "seurat_normalise_data",
+            "retrieve_scxa",
+            "seurat_find_variable_genes",
+            "seurat_plot",
+            "seurat_read10x",
+            "seurat_run_umap",
+            "seurat_filter_cells",
+            "seurat_find_markers",
+            "seurat_run_pca",
+            "seurat_find_clusters",
+            "seurat_find_neighbours",
+            "seurat_scale_data"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "single-cell-CS",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "10x",
+            "paper-replication"
+        ],
+        "time_estimation": "3H",
+        "title": "Filter, plot, and explore single cell RNA-seq data with Seurat",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_filter_cells/seurat_filter_cells/4.0.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters/4.0.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_markers/seurat_find_markers/4.0.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_neighbours/seurat_find_neighbours/4.0.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes/4.0.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data/4.0.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_plot/seurat_plot/4.0.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/4.0.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_pca/seurat_run_pca/4.0.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_umap/seurat_run_umap/4.0.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_scale_data/seurat_scale_data/4.0.4+galaxy0"
+        ],
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "scrna-case_FilterPlotandExplore_SeuratTools",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.json"
+        },
+        "version": 3,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 28,
+        "visitors": 467,
+        "zenodo_link": "https://zenodo.org/record/7053673"
     },
     {
         "admin_install": {
@@ -239410,10 +243567,12 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
             },
             {
+                "elixir_node": "uk",
                 "email": "juliajot36@gmail.com",
                 "id": "wee-snufkin",
                 "joined": "2022-06",
                 "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
             },
@@ -239477,17 +243636,12 @@
         "dir": "topics/single-cell/tutorials/scrna-case_trajectories",
         "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
         "id": "single-cell/scrna-case_trajectories",
-        "inexact_supported_servers": [
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
+        "inexact_supported_servers": [],
         "input_histories": [
             {
                 "history": "https://usegalaxy.eu/u/wendi.bacon.training/h/cs4inferred-trajectory-analysis-using-python-jupyter-notebook-in-galaxy---input",
@@ -239504,12 +243658,12 @@
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-13",
+        "mod_date": "2024-09-18",
         "objectives": [
             "Execute multiple plotting methods designed to identify lineage relationships between cells",
             "Interpret these plots"
         ],
-        "pageviews": 487,
+        "pageviews": 797,
         "priority": 4,
         "pub_date": "2023-12-08",
         "questions": [
@@ -239528,39 +243682,22 @@
         ],
         "short_id": "T00379",
         "short_tools": [
-            "anndata_manipulate",
             "scanpy_plot_embed",
+            "scanpy_run_fdg",
             "scanpy_run_diffmap",
-            "scanpy_run_dpt",
-            "scanpy_plot_trajectory",
             "scanpy_find_cluster",
-            "scanpy_compute_graph",
             "scanpy_run_paga",
-            "scanpy_run_fdg"
+            "scanpy_plot_trajectory",
+            "anndata_manipulate",
+            "scanpy_run_dpt",
+            "scanpy_compute_graph"
         ],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "single-cell-CS",
         "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
+            "exact": [],
+            "inexact": []
         },
         "symlink": null,
         "tags": [
@@ -239570,6 +243707,7 @@
         "time_estimation": "3H",
         "title": "Inferring single cell trajectories with Scanpy",
         "tools": [
+            "https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.9.3+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
             "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
@@ -239595,12 +243733,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_trajectories/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_trajectories/tutorial.json"
         },
-        "version": 5,
+        "version": 8,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 140,
-        "visitors": 405,
+        "visit_duration": 223,
+        "visitors": 578,
         "workflows": [
             {
                 "creators": [
@@ -239657,7 +243795,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput Anndata\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Manipulate AnnData\"];\n  0 -->|output| 1;\n  2[\"Scanpy RunFDG\"];\n  1 -->|anndata| 2;\n  3[\"Scanpy PlotEmbed\"];\n  2 -->|output_h5ad| 3;\n  4[\"Scanpy DiffusionMap\"];\n  2 -->|output_h5ad| 4;\n  5[\"Scanpy ComputeGraph\"];\n  4 -->|output_h5ad| 5;\n  6[\"Scanpy RunFDG\"];\n  5 -->|output_h5ad| 6;\n  7[\"Scanpy PlotEmbed\"];\n  6 -->|output_h5ad| 7;\n  8[\"Scanpy PAGA\"];\n  6 -->|output_h5ad| 8;\n  9[\"Scanpy PlotTrajectory\"];\n  8 -->|output_h5ad| 9;\n  10[\"Scanpy RunFDG\"];\n  9 -->|output_h5ad| 10;\n  11[\"Scanpy PlotEmbed\"];\n  10 -->|output_h5ad| 11;\n  12[\"Scanpy PlotEmbed\"];\n  10 -->|output_h5ad| 12;\n  13[\"Scanpy PlotEmbed\"];\n  10 -->|output_h5ad| 13;\n  14[\"Final Anndata with Trajectory and DPT\"];\n  10 -->|output_h5ad| 14;\n  15[\"Scanpy PlotEmbed\"];\n  14 -->|output_h5ad| 15;",
-                "modified": "2024-08-18 00:06:25 +0000",
+                "modified": "2024-10-02 12:08:10 +0000",
                 "name": "Inferring Trajectories with Scanpy Tutorial Workflow",
                 "outputs": [],
                 "parent_id": "single-cell/scrna-case_trajectories",
@@ -239680,391 +243818,45 @@
                 "workflow_tools": [
                     "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9",
                     "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_trajectory/scanpy_plot_trajectory/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_diffmap/scanpy_run_diffmap/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_dpt/scanpy_run_dpt/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_fdg/scanpy_run_fdg/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_paga/scanpy_run_paga/1.8.1+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1"
-                ],
-                "workflowhub_id": "1238"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/7075718"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-data-formats/tutorial.json",
-        "contributors": [
-            {
-                "email": "hexhowells@gmail.com",
-                "id": "hexhowells",
-                "joined": "2023-06",
-                "name": "Morgan Howells",
-                "orcid": "0009-0008-9422-6380",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexhowells/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexhowells.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "bio": "Senior Lecturer at The Open University",
-                "elixir_node": "uk",
-                "email": "wendi.bacon@open.ac.uk",
-                "fediverse": "https://mstdn.science/@wendibacon1",
-                "fediverse_flavor": "mastodon",
-                "id": "nomadscientist",
-                "joined": "2020-03",
-                "matrix": "nomadscientist:matrix.org",
-                "name": "Wendi Bacon",
-                "orcid": "0000-0002-8170-8806",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
-                "twitter": "WendiBacon1",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "uk",
-                "id": "kkamieniecka",
-                "joined": "2018-08",
-                "name": "Katarzyna Kamieniecka",
-                "orcid": "0009-0004-2454-5950",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/",
-                "twitter": "katemurat",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
-            }
-        ],
-        "dir": "topics/single-cell/tutorials/scrna-data-formats",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": false,
-        "id": "single-cell/scrna-data-formats",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Single-cell data consists of four main sections",
-            "Single-cell data can come in a variety of formats",
-            "Different data formats are required for different languages and packages",
-            "There are various public single-cell atlases that consist of useful data"
-        ],
-        "layout": "tutorial_slides",
-        "license": "CC-BY-4.0",
-        "logo": "GTN",
-        "mod_date": "2024-07-26",
-        "objectives": [
-            "Learn the basic structure of single-cell data",
-            "Be able to recognise different types of single-cell metadata",
-            "Learn the common data formats used for storing single-cell data",
-            "Become familiar with some popular sources for public single-cell data"
-        ],
-        "pageviews": 71655,
-        "priority": 4,
-        "pub_date": "2024-07-26",
-        "questions": [
-            "What does single-cell data look like?",
-            "What are the common single-cell formats?",
-            "Where can public single-cell data be found?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-intro"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "S00123",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
-        "subtopic": "scintroduction",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": null,
-        "title": "Single-cell Formats and Resources",
-        "tools": [],
-        "topic_name": "single-cell",
-        "topic_name_human": "Single Cell",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "scrna-data-formats",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-data-formats/slides.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-data-formats/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-data-formats/slides.json"
-        },
-        "version": 1,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 144,
-        "visitors": 29367
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case-cell-annotation/tutorial.json",
-        "contributors": [
-            {
-                "email": "hexhowells@gmail.com",
-                "id": "hexhowells",
-                "joined": "2023-06",
-                "name": "Morgan Howells",
-                "orcid": "0009-0008-9422-6380",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexhowells/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexhowells.json"
-            }
-        ],
-        "dir": "topics/single-cell/tutorials/scrna-case-cell-annotation",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": false,
-        "id": "single-cell/scrna-case-cell-annotation",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Automated cell annotation is a useful tool for automatically assigning cell type labels to cell data.",
-            "There are various algorithms and methods that can be used for conducting cell annotation with each method having its own strengths and weaknesses.",
-            "Automated cell annotation isn't perfect, when analysing results it's important to identify common issues that could occur."
-        ],
-        "layout": "tutorial_slides",
-        "license": "CC-BY-4.0",
-        "logo": "GTN",
-        "mod_date": "2023-10-10",
-        "objectives": [
-            "Learn the different methods underlying automated cell annotation",
-            "Understand the data needed to annotate cells",
-            "Be able to choose the most appropriate method for your data",
-            "Recognise the common issues and be able to resolve them"
-        ],
-        "pageviews": 1192560,
-        "priority": 4,
-        "pub_date": "2023-09-04",
-        "questions": [
-            "What is automated cell annotation?",
-            "How is automated cell annotation performed?",
-            "What methods are available?",
-            "What is the best method to choose for your data?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "single-cell",
-                "tutorials": [
-                    "scrna-intro"
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_trajectory/scanpy_plot_trajectory/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_diffmap/scanpy_run_diffmap/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_dpt/scanpy_run_dpt/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_fdg/scanpy_run_fdg/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_paga/scanpy_run_paga/1.8.1+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1"
                 ],
-                "type": "internal"
+                "workflowhub_id": "1238"
             }
         ],
-        "short_id": "S00110",
-        "short_tools": [],
-        "slides": true,
-        "slides_recordings": false,
-        "subtopic": "scintroduction",
-        "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy Australia",
-                    "id": "au",
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": null,
-        "title": "Automated Cell Annotation",
-        "tools": [],
-        "topic_name": "single-cell",
-        "topic_name_human": "Single Cell",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "scrna-case-cell-annotation",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case-cell-annotation/slides.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case-cell-annotation/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case-cell-annotation/slides.json"
-        },
-        "version": 3,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 147,
-        "visitors": 508507
+        "zenodo_link": "https://zenodo.org/record/7075718"
     },
     {
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": []
+            "tools": [
+                {
+                    "name": "music_compare",
+                    "owner": "bgruening",
+                    "revisions": "4447ed460308",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_monocle3-rstudio/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: music_compare\n  owner: bgruening\n  revisions: 4447ed460308\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music-4-compare/tutorial.json",
         "contributions": {
             "authorship": [
-                "wee-snufkin"
-            ],
-            "editing": [
-                "hexylena",
-                "pavanvidem",
-                "nomadscientist"
+                "nomadscientist",
+                "mtekman"
             ],
-            "funding": [
-                "eosc-life"
+            "testing": [
+                "MarisaJL"
             ]
         },
         "contributors": [
-            {
-                "email": "juliajot36@gmail.com",
-                "id": "wee-snufkin",
-                "joined": "2022-06",
-                "name": "Julia Jakiela",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "pavanvidem",
-                "joined": "2017-09",
-                "name": "Pavankumar Videm",
-                "orcid": "0000-0002-5192-126X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
-            },
             {
                 "affiliations": [
                     "elixir-europe"
@@ -240084,127 +243876,118 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
             },
             {
-                "avatar": "https://www.eosc-life.eu/wp-content/themes/eosc-life-v2/assets/images/eosclogo.png",
-                "funder": true,
-                "funding_id": "824087",
-                "funding_statement": "EOSC-Life has received funding from the European Union\u2019s Horizon 2020 programme under grant agreement number 824087",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "eosc-life",
-                "joined": "2023-04",
-                "members": [
-                    "bgruening"
+                "affiliations": [
+                    "uni-freiburg"
                 ],
-                "name": "EOSC-Life",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eosc-life/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/eosc-life.json"
+                "elixir_node": "de",
+                "email": "mtekman89@gmail.com",
+                "former_affiliations": [
+                    "elixir-europe"
+                ],
+                "id": "mtekman",
+                "joined": "2018-11",
+                "name": "Mehmet Tekman",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
+            },
+            {
+                "email": "marisa.loach@open.ac.uk",
+                "id": "MarisaJL",
+                "joined": "2022-10",
+                "name": "Marisa Loach",
+                "orcid": "0000-0001-6979-6930",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/MarisaJL/",
+                "twitter": "Marisa_Loach",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/MarisaJL.json"
             }
         ],
-        "dir": "topics/single-cell/tutorials/scrna-case_monocle3-rstudio",
+        "dir": "topics/single-cell/tutorials/bulk-music-4-compare",
         "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "single-cell/scrna-case_monocle3-rstudio",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
+        "id": "single-cell/bulk-music-4-compare",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Monocle3 in R gives more flexibility when it comes to differential expression analysis and plotting, but Galaxy offers great reproducibility and ease of analysis.",
-            "Comparing the output of several different methods applied on the same dataset might be useful to confirm the results, to ensure that the findings are reliable and even sometimes to find a new piece of information."
+            "Deconvolution can be used to compare cell type distributions from bulk RNA-seq datasets"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-07",
-        "notebook": {
-            "language": "r",
-            "snippet": "topics/single-cell/tutorials/scrna-case_monocle3-rstudio/preamble.md"
-        },
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Identify which operations are necessary to transform an AnnData object into the files needed for Monocle",
-            "Describe the Monocle3 functions in R",
-            "Recognise steps that can be performed in R, but not with current Galaxy tools",
-            "Repeat the Monocle3 workflow and choose appropriate parameter values",
-            "Compare the outputs from Scanpy, Monocle in Galaxy and Monocle in R",
-            "Describe differential expression analysis methods"
+            "Apply the MuSiC deconvolution to samples and compare the cell type distributions",
+            "Compare the results from analysing different types of input, for example, whether combining disease and healthy references or not yields better results"
         ],
-        "pageviews": 4140,
+        "pageviews": 314,
         "priority": 4,
-        "pub_date": "2023-04-12",
+        "pub_date": "2023-01-20",
         "questions": [
-            "How do I perform a trajectory analysis using Monocle3 in R?",
-            "What should I do when Galaxy's Monocle tools are not enough?",
-            "How do I assign cell types to the clusters?",
-            "How do I infer lineage relationships between clusters, without a time series?",
-            "How do I perform batch correction and differential expression analysis in Monocle?"
+            "How do the cell type distributions vary in bulk RNA samples across my variable of interest?",
+            "For example, are beta cell proportions different in the pancreas data from diabetes and healthy patients?"
         ],
         "requirements": [
             {
                 "topic_name": "single-cell",
                 "tutorials": [
-                    "scrna-case_alevin",
-                    "scrna-case_alevin-combine-datasets",
-                    "scrna-case_basic-pipeline"
+                    "bulk-music",
+                    "bulk-music-2-preparescref",
+                    "bulk-music-3-preparebulk"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00336",
-        "short_tools": [],
+        "short_id": "T00243",
+        "short_tools": [
+            "music_compare"
+        ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "single-cell-CS-code",
+        "subtopic": "deconvo",
         "supported_servers": {
-            "exact": [],
-            "inexact": [
+            "exact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
                 {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
                 {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
+                    "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 },
                 {
-                    "human": "Galaxy Australia",
-                    "id": "au",
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
                 }
-            ]
+            ],
+            "inexact": []
         },
         "symlink": null,
         "tags": [
-            "10x",
-            "paper-replication",
-            "R"
+            "transcriptomics"
+        ],
+        "time_estimation": "1H",
+        "title": "Comparing inferred cell compositions using MuSiC deconvolution",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4"
         ],
-        "time_estimation": "3H",
-        "title": "Inferring single cell trajectories with Monocle3 (R)",
-        "tools": [],
         "topic_name": "single-cell",
         "topic_name_human": "Single Cell",
         "tours": false,
@@ -240213,20 +243996,710 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "scrna-case_monocle3-rstudio",
+        "tutorial_name": "bulk-music-4-compare",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_monocle3-rstudio/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music-4-compare/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_monocle3-rstudio/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_monocle3-rstudio/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music-4-compare/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music-4-compare/tutorial.json"
         },
-        "version": 10,
+        "version": 8,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 53,
-        "visitors": 3575,
-        "zenodo_link": "https://zenodo.org/record/7455590"
+        "visit_duration": 67,
+        "visitors": 183,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0002-8170-8806",
+                        "name": "Wendi Bacon"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-4181-2676",
+                        "name": "Mehmet Tekman"
+                    }
+                ],
+                "description": "This workflow runs 3 comparisons using MuSiC Deconvolution compare: where datasets cell compositions are inferred from a reference containing healthy and diseased cells; where diseased are inferred from disease and healthy from healthy; and where both diseased and healthy are inferred from a healthy reference.",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nESet Object - Single cell:T2D\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nESet Object - Single cell:normal\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nESet Object - Bulk:normal\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nESet Object - Bulk:T2D\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nESet Object - Single cell Total\"]\n  5[label=\"MuSiC Compare: Like with like\"]\n  2 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"MuSiC Compare: healthyscref\"]\n  2 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"MuSiC Compare - Altogether\"]\n  2 -> 7 [label=\"output\"]\n  3 -> 7 [label=\"output\"]\n  4 -> 7 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "9a561b3752745eab20cececd5346ee0a7449da28",
+                        "message": "update workflows",
+                        "num": 1,
+                        "short_hash": "9a561b375",
+                        "unix": "1669581042"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "ESet Object - Single cell:T2D"
+                            }
+                        ],
+                        "label": "ESet Object - Single cell:T2D",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 2.0234375,
+                            "top": 87.03125
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "16ac774b-2363-4b80-aef3-c931c2e7be39",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "ESet Object - Single cell:normal"
+                            }
+                        ],
+                        "label": "ESet Object - Single cell:normal",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 2.0234375,
+                            "top": 194.046875
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "a12a2c75-60f9-4914-af0f-1e4c90d6232e",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "ESet Object - Bulk:normal"
+                            }
+                        ],
+                        "label": "ESet Object - Bulk:normal",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 2.0234375,
+                            "top": 316.0546875
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "631202df-1a51-4fac-8ca9-65b8e6959082",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "ESet Object - Bulk:T2D"
+                            }
+                        ],
+                        "label": "ESet Object - Bulk:T2D",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 2.0234375,
+                            "top": 438.0390625
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "e841325f-0707-4ac9-9937-700d1bf5fa03",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "ESet Object - Single cell Total"
+                            }
+                        ],
+                        "label": "ESet Object - Single cell Total",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 556.0390625
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "676d2c4b-58c3-438b-ae55-e294ee43e377",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nESet Object - Single cell:T2D\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nESet Object - Single cell:normal\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nESet Object - Bulk:normal\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nESet Object - Bulk:T2D\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nESet Object - Single cell Total\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"MuSiC Compare: Like with like\"];\n  2 -->|output| 5;\n  1 -->|output| 5;\n  3 -->|output| 5;\n  0 -->|output| 5;\n  6[\"MuSiC Compare: healthyscref\"];\n  2 -->|output| 6;\n  3 -->|output| 6;\n  1 -->|output| 6;\n  7[\"MuSiC Compare - Altogether\"];\n  2 -->|output| 7;\n  3 -->|output| 7;\n  4 -->|output| 7;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "MuSiC-Deconvolution: Compare",
+                "outputs": [
+                    {
+                        "annotation": "Here the T2D bulk sample is inferred from the sc T2D sample, while the normal bulk sample is inferred from the sc normal sample",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "scrna_groups_0|bulk_groups_0|bulk_eset": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "scrna_groups_0|scrna_eset": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "scrna_groups_1|bulk_groups_0|bulk_eset": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "scrna_groups_1|scrna_eset": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "MuSiC Compare: Like with like",
+                        "name": "MuSiC Compare",
+                        "outputs": [
+                            {
+                                "name": "dtables",
+                                "type": "input"
+                            },
+                            {
+                                "name": "stats",
+                                "type": "input"
+                            },
+                            {
+                                "name": "out_heatmulti_pdf",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "out_heatsumm_pdf",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "left": 730.265625,
+                            "top": 0
+                        },
+                        "post_job_actions": {
+                            "RemoveTagDatasetActiondtables": {
+                                "action_arguments": {
+                                    "tags": "#singlecell,#bulk"
+                                },
+                                "action_type": "RemoveTagDatasetAction",
+                                "output_name": "dtables"
+                            },
+                            "RemoveTagDatasetActionout_heatmulti_pdf": {
+                                "action_arguments": {
+                                    "tags": "#singlecell,#bulk"
+                                },
+                                "action_type": "RemoveTagDatasetAction",
+                                "output_name": "out_heatmulti_pdf"
+                            },
+                            "RemoveTagDatasetActionout_heatsumm_pdf": {
+                                "action_arguments": {
+                                    "tags": "#singlecell,#bulk"
+                                },
+                                "action_type": "RemoveTagDatasetAction",
+                                "output_name": "out_heatsumm_pdf"
+                            },
+                            "RemoveTagDatasetActionstats": {
+                                "action_arguments": {
+                                    "tags": "#singlecell,#bulk"
+                                },
+                                "action_type": "RemoveTagDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "RenameDatasetActiondtables": {
+                                "action_arguments": {
+                                    "newname": "MuSiC-like4like-tables"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "dtables"
+                            },
+                            "RenameDatasetActionout_heatmulti_pdf": {
+                                "action_arguments": {
+                                    "newname": "MuSiC-like4like-plots"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_heatmulti_pdf"
+                            },
+                            "RenameDatasetActionout_heatsumm_pdf": {
+                                "action_arguments": {
+                                    "newname": "MuSiC-like4like-individualmaps"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_heatsumm_pdf"
+                            },
+                            "RenameDatasetActionstats": {
+                                "action_arguments": {
+                                    "newname": "MuSiC-like4like-stats"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "TagDatasetActiondtables": {
+                                "action_arguments": {
+                                    "tags": "#like4like"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "dtables"
+                            },
+                            "TagDatasetActionout_heatmulti_pdf": {
+                                "action_arguments": {
+                                    "tags": "#like4like"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "out_heatmulti_pdf"
+                            },
+                            "TagDatasetActionout_heatsumm_pdf": {
+                                "action_arguments": {
+                                    "tags": "#like4like"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "out_heatsumm_pdf"
+                            },
+                            "TagDatasetActionstats": {
+                                "action_arguments": {
+                                    "tags": "#like4like"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "stats"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "4447ed460308",
+                            "name": "music_compare",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"dendro_setting\": \"None\", \"est_method\": \"MuSiC\", \"filter\": {\"out_list_cells\": \"\", \"out_list_facts\": \"\"}, \"scrna_groups\": [{\"__index__\": 0, \"name\": \"scRNA_set:Normal\", \"scrna_eset\": {\"__class__\": \"ConnectedValue\"}, \"adv\": {\"celltypes_label\": \"Inferred cell type - author labels\", \"samples_label\": \"Individual\", \"celltypes\": \"alpha cell,beta cell,delta cell,gamma cell,acinar cell,ductal cell\"}, \"bulk_groups\": [{\"__index__\": 0, \"name\": \"Bulk_set:Normal\", \"bulk_eset\": {\"__class__\": \"ConnectedValue\"}, \"factor_group\": \"Disease\", \"adv\": {\"phenotype_factors\": \"\", \"phenotype_factors_always_exclude\": \"sampleID,SubjectName\"}}]}, {\"__index__\": 1, \"name\": \"scRNA_set:T2D\", \"scrna_eset\": {\"__class__\": \"ConnectedValue\"}, \"adv\": {\"celltypes_label\": \"Inferred cell type - author labels\", \"samples_label\": \"Individual\", \"celltypes\": \"alpha cell,beta cell,delta cell,gamma cell,acinar cell,ductal cell\"}, \"bulk_groups\": [{\"__index__\": 0, \"name\": \"bulk_set:T2D\", \"bulk_eset\": {\"__class__\": \"ConnectedValue\"}, \"factor_group\": \"Disease\", \"adv\": {\"phenotype_factors\": \"\", \"phenotype_factors_always_exclude\": \"sampleID,SubjectName\"}}]}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.1+galaxy4",
+                        "type": "tool",
+                        "uuid": "1aa07374-4bd9-4c8a-8e23-8c9c3b7faa78",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "stats",
+                                "uuid": "f23ddfe7-40e1-4232-985a-1deae154e13e"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "dtables",
+                                "uuid": "2a29e3ef-e447-4336-a5e4-c781f21eeeb6"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_heatsumm_pdf",
+                                "uuid": "ba82c5ac-05df-4ded-b6b4-0bac2cc3cc8b"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_heatmulti_pdf",
+                                "uuid": "f7f8627a-7a04-4ec4-8e65-7b4cd65ade13"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Here the T2D bulk sample and the normal sample are separately compared separately against the healthy sc reference only (excluding unhealthy sc reference)",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "scrna_groups_0|bulk_groups_0|bulk_eset": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "scrna_groups_0|bulk_groups_1|bulk_eset": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "scrna_groups_0|scrna_eset": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "MuSiC Compare: healthyscref",
+                        "name": "MuSiC Compare",
+                        "outputs": [
+                            {
+                                "name": "dtables",
+                                "type": "input"
+                            },
+                            {
+                                "name": "stats",
+                                "type": "input"
+                            },
+                            {
+                                "name": "out_heatmulti_pdf",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "out_heatsumm_pdf",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "left": 992.265625,
+                            "top": 211
+                        },
+                        "post_job_actions": {
+                            "RemoveTagDatasetActiondtables": {
+                                "action_arguments": {
+                                    "tags": "#singlecell,#bulk"
+                                },
+                                "action_type": "RemoveTagDatasetAction",
+                                "output_name": "dtables"
+                            },
+                            "RemoveTagDatasetActionout_heatmulti_pdf": {
+                                "action_arguments": {
+                                    "tags": "#singlecell,#bulk"
+                                },
+                                "action_type": "RemoveTagDatasetAction",
+                                "output_name": "out_heatmulti_pdf"
+                            },
+                            "RemoveTagDatasetActionout_heatsumm_pdf": {
+                                "action_arguments": {
+                                    "tags": "#singlecell,#bulk"
+                                },
+                                "action_type": "RemoveTagDatasetAction",
+                                "output_name": "out_heatsumm_pdf"
+                            },
+                            "RemoveTagDatasetActionstats": {
+                                "action_arguments": {
+                                    "tags": "#singlecell,#bulk"
+                                },
+                                "action_type": "RemoveTagDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "RenameDatasetActiondtables": {
+                                "action_arguments": {
+                                    "newname": "MuSiC-healthyscref-tables"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "dtables"
+                            },
+                            "RenameDatasetActionout_heatmulti_pdf": {
+                                "action_arguments": {
+                                    "newname": "MuSiC-healthyscref-plots"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_heatmulti_pdf"
+                            },
+                            "RenameDatasetActionout_heatsumm_pdf": {
+                                "action_arguments": {
+                                    "newname": "MuSiC-healthyscref-individualmaps"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_heatsumm_pdf"
+                            },
+                            "RenameDatasetActionstats": {
+                                "action_arguments": {
+                                    "newname": "MuSiC-healthyscref-stats"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "TagDatasetActiondtables": {
+                                "action_arguments": {
+                                    "tags": "#healthyscref"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "dtables"
+                            },
+                            "TagDatasetActionout_heatmulti_pdf": {
+                                "action_arguments": {
+                                    "tags": "#healthyscref"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "out_heatmulti_pdf"
+                            },
+                            "TagDatasetActionout_heatsumm_pdf": {
+                                "action_arguments": {
+                                    "tags": "#healthyscref"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "out_heatsumm_pdf"
+                            },
+                            "TagDatasetActionstats": {
+                                "action_arguments": {
+                                    "tags": "#healthyscref"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "stats"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "4447ed460308",
+                            "name": "music_compare",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"dendro_setting\": \"None\", \"est_method\": \"MuSiC\", \"filter\": {\"out_list_cells\": \"\", \"out_list_facts\": \"\"}, \"scrna_groups\": [{\"__index__\": 0, \"name\": \"scRNA_set:Normal\", \"scrna_eset\": {\"__class__\": \"ConnectedValue\"}, \"adv\": {\"celltypes_label\": \"Inferred cell type - author labels\", \"samples_label\": \"Individual\", \"celltypes\": \"alpha cell,beta cell,delta cell,gamma cell,acinar cell,ductal cell\"}, \"bulk_groups\": [{\"__index__\": 0, \"name\": \"Bulk_set:Normal\", \"bulk_eset\": {\"__class__\": \"ConnectedValue\"}, \"factor_group\": \"Disease\", \"adv\": {\"phenotype_factors\": \"\", \"phenotype_factors_always_exclude\": \"sampleID,SubjectName\"}}, {\"__index__\": 1, \"name\": \"Bulk_set:T2D\", \"bulk_eset\": {\"__class__\": \"ConnectedValue\"}, \"factor_group\": \"Disease\", \"adv\": {\"phenotype_factors\": \"\", \"phenotype_factors_always_exclude\": \"sampleID,SubjectName\"}}]}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.1+galaxy4",
+                        "type": "tool",
+                        "uuid": "2d6961e3-6437-4fae-92d1-25695b55d4c4",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_heatsumm_pdf",
+                                "uuid": "07325b72-c3f2-403e-bd83-a751603228ef"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_heatmulti_pdf",
+                                "uuid": "b75a92b4-f4eb-4bd6-a895-ba7285e80d65"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "stats",
+                                "uuid": "693bd310-705d-466b-9c35-1d7803bf16d7"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "dtables",
+                                "uuid": "e8a7c664-1510-4bc8-bb3a-bde0596dd2fd"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "scrna_groups_0|bulk_groups_0|bulk_eset": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "scrna_groups_0|bulk_groups_1|bulk_eset": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "scrna_groups_0|scrna_eset": {
+                                "id": 4,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "MuSiC Compare - Altogether",
+                        "name": "MuSiC Compare",
+                        "outputs": [
+                            {
+                                "name": "dtables",
+                                "type": "input"
+                            },
+                            {
+                                "name": "stats",
+                                "type": "input"
+                            },
+                            {
+                                "name": "out_heatmulti_pdf",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "out_heatsumm_pdf",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "left": 426.2890625,
+                            "top": 203.0390625
+                        },
+                        "post_job_actions": {
+                            "RemoveTagDatasetActiondtables": {
+                                "action_arguments": {
+                                    "tags": "#singlecell,#bulk"
+                                },
+                                "action_type": "RemoveTagDatasetAction",
+                                "output_name": "dtables"
+                            },
+                            "RemoveTagDatasetActionout_heatmulti_pdf": {
+                                "action_arguments": {
+                                    "tags": "#singlecell,#bulk"
+                                },
+                                "action_type": "RemoveTagDatasetAction",
+                                "output_name": "out_heatmulti_pdf"
+                            },
+                            "RemoveTagDatasetActionout_heatsumm_pdf": {
+                                "action_arguments": {
+                                    "tags": "#singlecell,#bulk"
+                                },
+                                "action_type": "RemoveTagDatasetAction",
+                                "output_name": "out_heatsumm_pdf"
+                            },
+                            "RemoveTagDatasetActionstats": {
+                                "action_arguments": {
+                                    "tags": "#singlecell,#bulk"
+                                },
+                                "action_type": "RemoveTagDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "RenameDatasetActiondtables": {
+                                "action_arguments": {
+                                    "newname": "MuSiC-combined-tables"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "dtables"
+                            },
+                            "RenameDatasetActionout_heatmulti_pdf": {
+                                "action_arguments": {
+                                    "newname": "MuSiC-combined-plots"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_heatmulti_pdf"
+                            },
+                            "RenameDatasetActionout_heatsumm_pdf": {
+                                "action_arguments": {
+                                    "newname": "MuSiC-combined-individualmaps"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_heatsumm_pdf"
+                            },
+                            "RenameDatasetActionstats": {
+                                "action_arguments": {
+                                    "newname": "MuSiC-combined-stats"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "TagDatasetActiondtables": {
+                                "action_arguments": {
+                                    "tags": "#combined"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "dtables"
+                            },
+                            "TagDatasetActionout_heatmulti_pdf": {
+                                "action_arguments": {
+                                    "tags": "#combined"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "out_heatmulti_pdf"
+                            },
+                            "TagDatasetActionout_heatsumm_pdf": {
+                                "action_arguments": {
+                                    "tags": "#combined"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "out_heatsumm_pdf"
+                            },
+                            "TagDatasetActionstats": {
+                                "action_arguments": {
+                                    "tags": "#combined"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "stats"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "4447ed460308",
+                            "name": "music_compare",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"dendro_setting\": \"None\", \"est_method\": \"MuSiC\", \"filter\": {\"out_list_cells\": \"\", \"out_list_facts\": \"\"}, \"scrna_groups\": [{\"__index__\": 0, \"name\": \"scRNA_set\", \"scrna_eset\": {\"__class__\": \"ConnectedValue\"}, \"adv\": {\"celltypes_label\": \"Inferred cell type - author labels\", \"samples_label\": \"Individual\", \"celltypes\": \"alpha cell,beta cell,delta cell,gamma cell,acinar cell,ductal cell\"}, \"bulk_groups\": [{\"__index__\": 0, \"name\": \"Bulk_healthy\", \"bulk_eset\": {\"__class__\": \"ConnectedValue\"}, \"factor_group\": \"Disease\", \"adv\": {\"phenotype_factors\": \"\", \"phenotype_factors_always_exclude\": \"sampleID,SubjectName\"}}, {\"__index__\": 1, \"name\": \"Bulk_disease\", \"bulk_eset\": {\"__class__\": \"ConnectedValue\"}, \"factor_group\": \"Disease\", \"adv\": {\"phenotype_factors\": \"\", \"phenotype_factors_always_exclude\": \"sampleID,SubjectName\"}}]}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.1+galaxy4",
+                        "type": "tool",
+                        "uuid": "bcea8743-e92e-4a04-b4da-34ca073ecd52",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "dtables",
+                                "uuid": "812202ce-076d-46fa-8a80-a1f5f4c53a7a"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_heatmulti_pdf",
+                                "uuid": "cd5b8aa7-da07-49ba-8775-8bcbdd900150"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "stats",
+                                "uuid": "93d46757-18b9-486b-ab59-b8bc1cb5fd7f"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_heatsumm_pdf",
+                                "uuid": "35cfefba-a8e6-49b0-9cef-2a01b038ecb0"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "single-cell/bulk-music-4-compare",
+                "path": "topics/single-cell/tutorials/bulk-music-4-compare/workflows/compare.ga",
+                "tags": [
+                    "name:singlecell",
+                    "name:transcriptomics",
+                    "name:training"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "MuSiC-Deconvolution: Compare",
+                "topic_id": "single-cell",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-bulk-music-4-compare/versions/compare",
+                "tutorial_id": "bulk-music-4-compare",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-4-compare/workflows/compare.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-4-compare/workflows/compare.html",
+                "version": 1,
+                "wfid": "single-cell-bulk-music-4-compare",
+                "wfname": "compare",
+                "workflow": "compare.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4"
+                ],
+                "workflowhub_id": "1223"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/7319925"
     },
     {
         "admin_install": {
@@ -240234,6 +244707,13 @@
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
             "tools": [
+                {
+                    "name": "add_line_to_file",
+                    "owner": "bgruening",
+                    "revisions": "8e251055b1a9",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "music_construct_eset",
                     "owner": "bgruening",
@@ -240276,6 +244756,27 @@
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "retrieve_scxa",
+                    "owner": "ebi-gxa",
+                    "revisions": "cd6b80f62fcc",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "retrieve_scxa",
+                    "owner": "ebi-gxa",
+                    "revisions": "72b6e1747e37",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "scanpy_read_10x",
+                    "owner": "ebi-gxa",
+                    "revisions": "d253d69ff19f",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "regex_find_replace",
                     "owner": "galaxyp",
@@ -240283,6 +244784,13 @@
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "anndata_inspect",
+                    "owner": "iuc",
+                    "revisions": "ee98d611afc6",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "annotatemyids",
                     "owner": "iuc",
@@ -240291,10 +244799,10 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "column_remove_by_header",
+                    "name": "datamash_transpose",
                     "owner": "iuc",
-                    "revisions": "2040e4c2750a",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "revisions": "ac092723240d",
+                    "tool_panel_section_label": "Join, Subtract and Group",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
@@ -240306,8 +244814,8 @@
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: music_construct_eset\n  owner: bgruening\n  revisions: 282819d09a4f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: music_manipulate_eset\n  owner: bgruening\n  revisions: 22232092be53\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 399da6b5ec21\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: annotatemyids\n  owner: iuc\n  revisions: fe3ca740a485\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_remove_by_header\n  owner: iuc\n  revisions: 2040e4c2750a\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: table_compute\n  owner: iuc\n  revisions: 3bf5661c0280\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: add_line_to_file\n  owner: bgruening\n  revisions: 8e251055b1a9\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: music_construct_eset\n  owner: bgruening\n  revisions: 282819d09a4f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: music_manipulate_eset\n  owner: bgruening\n  revisions: 22232092be53\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: retrieve_scxa\n  owner: ebi-gxa\n  revisions: cd6b80f62fcc\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: retrieve_scxa\n  owner: ebi-gxa\n  revisions: 72b6e1747e37\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: scanpy_read_10x\n  owner: ebi-gxa\n  revisions: d253d69ff19f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 399da6b5ec21\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: anndata_inspect\n  owner: iuc\n  revisions: ee98d611afc6\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: annotatemyids\n  owner: iuc\n  revisions: fe3ca740a485\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_transpose\n  owner: iuc\n  revisions: ac092723240d\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: table_compute\n  owner: iuc\n  revisions: 3bf5661c0280\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.json",
         "contributions": {
             "authorship": [
                 "nomadscientist",
@@ -240362,115 +244870,124 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/MarisaJL.json"
             }
         ],
-        "dir": "topics/single-cell/tutorials/bulk-music-3-preparebulk",
+        "dir": "topics/single-cell/tutorials/bulk-music-2-preparescref",
         "edam_operation": [
             "Annotation"
         ],
         "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.org.au"
-        ],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "follow_up_training": [
             {
                 "topic_name": "single-cell",
                 "tutorials": [
-                    "bulk-music-4-compare"
+                    "bulk-music-3-preparebulk"
                 ],
                 "type": "internal"
             }
         ],
         "hands_on": true,
-        "id": "single-cell/bulk-music-3-preparebulk",
+        "id": "single-cell/bulk-music-2-preparescref",
         "inexact_supported_servers": [
-            "UseGalaxy.cz"
+            "UseGalaxy.cz",
+            "UseGalaxy.org.au"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "The EMBL-EBI Expression Atlas contains high quality datasets.",
+            "The EMBL-EBI Single-cell expression atlas contains high quality datasets.",
             "Metadata manipulation is key for generating the correctly formatted resource."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2024-02-13",
         "objectives": [
-            "You will retrieve raw data from the EMBL-EBI Expression Atlas.",
+            "You will retrieve raw data from the EMBL-EBI Single cell expression atlas.",
             "You will manipulate the metadata and matrix files.",
             "You will combine the metadata and matrix files into an ESet object for MuSiC deconvolution.",
-            "You will create multiple ESet objects - both combined and separated out by disease phenotype for your bulk dataset."
+            "You will create multiple ESet objects - both combined and separated out by disease phenotype for your single cell reference."
         ],
-        "pageviews": 854,
-        "priority": 5,
+        "pageviews": 1050,
+        "priority": 4,
         "pub_date": "2023-01-20",
         "questions": [
-            "Where can I find good quality RNA-seq datasets?",
+            "Where can I find good quality scRNA-seq reference datasets?",
             "How can I reformat and manipulate these downloads to create the right format for MuSiC?"
         ],
         "requirements": [
             {
                 "topic_name": "single-cell",
                 "tutorials": [
-                    "bulk-music",
-                    "bulk-music-2-preparescref"
+                    "bulk-music"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00242",
+        "short_id": "T00241",
         "short_tools": [
-            "music_construct_eset",
-            "tp_cut_tool",
-            "sort1",
-            "tp_awk_tool",
-            "tp_easyjoin_tool",
             "music_manipulate_eset",
+            "annotatemyids",
+            "join1",
             "tp_sed_tool",
             "table_compute",
-            "annotatemyids",
-            "regex1",
-            "column_remove_by_header"
+            "tp_easyjoin_tool",
+            "sort1",
+            "retrieve_scxa",
+            "tp_awk_tool",
+            "add_line_to_file",
+            "music_construct_eset",
+            "anndata_inspect",
+            "Cut1",
+            "tp_cut_tool",
+            "scanpy_read_10x",
+            "datamash_transpose",
+            "regex1"
         ],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "datamanipulation",
         "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
+            "exact": [],
             "inexact": [
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
         "tags": [
-            "transcriptomics",
             "data management"
         ],
         "time_estimation": "1H",
-        "title": "Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution",
+        "title": "Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution",
         "tools": [
+            "Cut1",
+            "join1",
             "sort1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0",
             "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4",
             "toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4",
             "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
             "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
             "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
             "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
             "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2",
             "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0"
         ],
         "topic_name": "single-cell",
@@ -240481,19 +244998,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "bulk-music-3-preparebulk",
+        "tutorial_name": "bulk-music-2-preparescref",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music-2-preparescref/tutorial.json"
         },
         "version": 8,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 100,
-        "visitors": 470,
+        "visit_duration": 122,
+        "visitors": 595,
         "workflows": [
             {
                 "creators": [
@@ -240508,14 +245025,14 @@
                         "name": "Mehmet Tekman"
                     }
                 ],
-                "description": "This workflow creates bulk ESet objects from uploaded raw matrix &amp; metadata files",
+                "description": "This workflow creates an ESet object from scRNA metadata file and EBI SCXA retrieveal",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": true
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Expression matrix\"]\n  1[label=\"Metadata\"]\n  2[label=\"annotateMyIDs\"]\n  0 -> 2 [label=\"output_tabular\"]\n  k8415bac06beb467da0fafb6465987ff7[color=lightseagreen,label=\"Output\\nannotateMyIDs on input dataset(s): Annotated IDs\"]\n  2 -> k8415bac06beb467da0fafb6465987ff7\n  3[label=\"Regex Find And Replace\"]\n  1 -> 3 [label=\"output\"]\n  4[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nCopy of Convert from Ensembl to GeneSymbol, summing duplicate genes\"]\n  2 -> 4 [label=\"out_tab\"]\n  0 -> 4 [label=\"output_tabular\"]\n  5[label=\"Construct Expression Set Object\"]\n  4 -> 5 [label=\"Gene Symbol Count Matrix\"]\n  3 -> 5 [label=\"out_file1\"]\n  6[label=\"Manipulate Expression Set Object\"]\n  5 -> 6 [label=\"out_rds\"]\n  k88196d0b72544794b08a5409f19c8323[color=lightseagreen,label=\"Output\\nManipulate Expression Set Object on input dataset(s): ExpressionSet Object\"]\n  6 -> k88196d0b72544794b08a5409f19c8323\n  7[label=\"Manipulate Expression Set Object\"]\n  5 -> 7 [label=\"out_rds\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"EBI SCXA Data Retrieval\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSingle cell metadata\"]\n  2[label=\"Scanpy Read10x\"]\n  0 -> 2 [label=\"barcode_tsv\"]\n  0 -> 2 [label=\"genes_tsv\"]\n  0 -> 2 [label=\"matrix_mtx\"]\n  k6bd01730f0b548248cfcd563cc9c7f7d[color=lightseagreen,label=\"Output\\nScanpy Read10x on input dataset(s): anndata\"]\n  2 -> k6bd01730f0b548248cfcd563cc9c7f7d\n  3[label=\"Inspect AnnData\"]\n  2 -> 3 [label=\"output_h5\"]\n  4[label=\"Transpose\"]\n  3 -> 4 [label=\"X\"]\n  5[label=\"annotateMyIDs\"]\n  4 -> 5 [label=\"out_file\"]\n  kc39c7d69550e4b54a412317b599c5e55[color=lightseagreen,label=\"Output\\nannotateMyIDs on input dataset(s): Annotated IDs\"]\n  5 -> kc39c7d69550e4b54a412317b599c5e55\n  6[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\n1st step removed - Convert from Ensembl to GeneSymbol, summing duplicate genes\"]\n  5 -> 6 [label=\"out_tab\"]\n  4 -> 6 [label=\"out_file\"]\n  7[label=\"Construct Expression Set Object\"]\n  6 -> 7 [label=\"Gene Symbol Count Matrix\"]\n  1 -> 7 [label=\"output\"]\n  ke8c91df04e6c4eb29807c2679b494958[color=lightseagreen,label=\"Output\\nConstruct Expression Set Object on input dataset(s): RData ESet Object\"]\n  7 -> ke8c91df04e6c4eb29807c2679b494958\n  k2912d09bb1784035b7c87038392e2bf2[color=lightseagreen,label=\"Output\\nConstruct Expression Set Object on input dataset(s): General Info\"]\n  7 -> k2912d09bb1784035b7c87038392e2bf2\n  8[label=\"Manipulate Expression Set Object\"]\n  7 -> 8 [label=\"out_rds\"]\n  k08de92d832fe4b479038298cdd13fac5[color=lightseagreen,label=\"Output\\nManipulate Expression Set Object on input dataset(s): ExpressionSet Object\"]\n  8 -> k08de92d832fe4b479038298cdd13fac5\n  9[label=\"Manipulate Expression Set Object\"]\n  7 -> 9 [label=\"out_rds\"]\n}",
                 "history": [
                     {
                         "hash": "9a561b3752745eab20cececd5346ee0a7449da28",
@@ -240525,244 +245042,365 @@
                         "unix": "1669581042"
                     }
                 ],
-                "inputs": [],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"Expression matrix\"];\n  1[\"Metadata\"];\n  2[\"annotateMyIDs\"];\n  0 -->|output_tabular| 2;\n  8415bac0-6beb-467d-a0fa-fb6465987ff7[\"Output\\nannotateMyIDs on input dataset(s): Annotated IDs\"];\n  2 --> 8415bac0-6beb-467d-a0fa-fb6465987ff7;\n  style 8415bac0-6beb-467d-a0fa-fb6465987ff7 stroke:#2c3143,stroke-width:4px;\n  3[\"Regex Find And Replace\"];\n  1 -->|output| 3;\n  4[\"\ud83d\udee0\ufe0f Subworkflow\\nCopy of Convert from Ensembl to GeneSymbol, summing duplicate genes\"];\n  style 4 fill:#edd,stroke:#900,stroke-width:4px;\n  2 -->|out_tab| 4;\n  0 -->|output_tabular| 4;\n  5[\"Construct Expression Set Object\"];\n  4 -->|Gene Symbol Count Matrix| 5;\n  3 -->|out_file1| 5;\n  6[\"Manipulate Expression Set Object\"];\n  5 -->|out_rds| 6;\n  88196d0b-7254-4794-b08a-5409f19c8323[\"Output\\nManipulate Expression Set Object on input dataset(s): ExpressionSet Object\"];\n  6 --> 88196d0b-7254-4794-b08a-5409f19c8323;\n  style 88196d0b-7254-4794-b08a-5409f19c8323 stroke:#2c3143,stroke-width:4px;\n  7[\"Manipulate Expression Set Object\"];\n  5 -->|out_rds| 7;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "MuSiC-Deconvolution: Data generation | bulk | ESet",
-                "outputs": [
+                "inputs": [
                     {
-                        "annotation": "While the EBI data has the gene symbols in it, these are duplicated, so we still need to thin down the duplications.",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0",
+                        "annotation": "This should be output from the MuSiC Deconvolution | Data generation | sc | metadata workflow",
+                        "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Remove columns",
-                                "name": "input_tabular"
+                                "description": "This should be output from the MuSiC Deconvolution | Data generation | sc | metadata workflow",
+                                "name": "Single cell metadata"
                             }
                         ],
-                        "label": "Expression matrix",
-                        "name": "Remove columns",
+                        "label": "Single cell metadata",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 1160.0208740234375,
+                            "top": 364
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "f43195bc-96ef-4c07-8537-2e91c50b554c",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"EBI SCXA Data Retrieval\"];\n  1[\"\u2139\ufe0f Input Dataset\\nSingle cell metadata\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Scanpy Read10x\"];\n  0 -->|barcode_tsv| 2;\n  0 -->|genes_tsv| 2;\n  0 -->|matrix_mtx| 2;\n  6bd01730-f0b5-4824-8cfc-d563cc9c7f7d[\"Output\\nScanpy Read10x on input dataset(s): anndata\"];\n  2 --> 6bd01730-f0b5-4824-8cfc-d563cc9c7f7d;\n  style 6bd01730-f0b5-4824-8cfc-d563cc9c7f7d stroke:#2c3143,stroke-width:4px;\n  3[\"Inspect AnnData\"];\n  2 -->|output_h5| 3;\n  4[\"Transpose\"];\n  3 -->|X| 4;\n  5[\"annotateMyIDs\"];\n  4 -->|out_file| 5;\n  c39c7d69-550e-4b54-a412-317b599c5e55[\"Output\\nannotateMyIDs on input dataset(s): Annotated IDs\"];\n  5 --> c39c7d69-550e-4b54-a412-317b599c5e55;\n  style c39c7d69-550e-4b54-a412-317b599c5e55 stroke:#2c3143,stroke-width:4px;\n  6[\"\ud83d\udee0\ufe0f Subworkflow\\n1st step removed - Convert from Ensembl to GeneSymbol, summing duplicate genes\"];\n  style 6 fill:#edd,stroke:#900,stroke-width:4px;\n  5 -->|out_tab| 6;\n  4 -->|out_file| 6;\n  7[\"Construct Expression Set Object\"];\n  6 -->|Gene Symbol Count Matrix| 7;\n  1 -->|output| 7;\n  e8c91df0-4e6c-4eb2-9807-c2679b494958[\"Output\\nConstruct Expression Set Object on input dataset(s): RData ESet Object\"];\n  7 --> e8c91df0-4e6c-4eb2-9807-c2679b494958;\n  style e8c91df0-4e6c-4eb2-9807-c2679b494958 stroke:#2c3143,stroke-width:4px;\n  2912d09b-b178-4035-b7c8-7038392e2bf2[\"Output\\nConstruct Expression Set Object on input dataset(s): General Info\"];\n  7 --> 2912d09b-b178-4035-b7c8-7038392e2bf2;\n  style 2912d09b-b178-4035-b7c8-7038392e2bf2 stroke:#2c3143,stroke-width:4px;\n  8[\"Manipulate Expression Set Object\"];\n  7 -->|out_rds| 8;\n  08de92d8-32fe-4b47-9038-298cdd13fac5[\"Output\\nManipulate Expression Set Object on input dataset(s): ExpressionSet Object\"];\n  8 --> 08de92d8-32fe-4b47-9038-298cdd13fac5;\n  style 08de92d8-32fe-4b47-9038-298cdd13fac5 stroke:#2c3143,stroke-width:4px;\n  9[\"Manipulate Expression Set Object\"];\n  7 -->|out_rds| 9;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "MuSiC-Deconvolution: Data generation | sc | matrix + ESet",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2",
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": null,
+                        "name": "EBI SCXA Data Retrieval",
                         "outputs": [
                             {
-                                "name": "output_tabular",
-                                "type": "tabular"
+                                "name": "matrix_mtx",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "genes_tsv",
+                                "type": "tsv"
+                            },
+                            {
+                                "name": "barcode_tsv",
+                                "type": "tsv"
+                            },
+                            {
+                                "name": "design_tsv",
+                                "type": "tsv"
                             }
                         ],
                         "position": {
                             "left": 0.0,
-                            "top": 262.5
+                            "top": 408.46875
                         },
                         "post_job_actions": {
-                            "TagDatasetActionoutput_tabular": {
+                            "TagDatasetActionbarcode_tsv": {
                                 "action_arguments": {
-                                    "tags": "#bulk,#ebi,#matrix"
+                                    "tags": "#ebi"
                                 },
                                 "action_type": "TagDatasetAction",
-                                "output_name": "output_tabular"
+                                "output_name": "barcode_tsv"
+                            },
+                            "TagDatasetActiondesign_tsv": {
+                                "action_arguments": {
+                                    "tags": "#ebi"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "design_tsv"
+                            },
+                            "TagDatasetActiongenes_tsv": {
+                                "action_arguments": {
+                                    "tags": "#ebi"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "genes_tsv"
+                            },
+                            "TagDatasetActionmatrix_mtx": {
+                                "action_arguments": {
+                                    "tags": "#matrix,#ebi,#singlecell"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "matrix_mtx"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "2040e4c2750a",
-                            "name": "column_remove_by_header",
-                            "owner": "iuc",
+                            "changeset_revision": "72b6e1747e37",
+                            "name": "retrieve_scxa",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"headers\": [{\"__index__\": 0, \"name\": \"Gene Name\"}], \"input_tabular\": {\"__class__\": \"RuntimeValue\"}, \"keep_columns\": \"false\", \"strip_characters\": \"#\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"accession\": \"E-MTAB-5061\", \"matrix_type\": \"raw\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
                         "type": "tool",
-                        "uuid": "aea0ab42-9fd6-4d16-a5f0-d1ce8cc698b1",
+                        "uuid": "c6e24135-aa36-4d1f-83af-378c4882dba7",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_tabular",
-                                "uuid": "88efcecd-d1c7-4946-8a18-491ad704f096"
+                                "output_name": "barcode_tsv",
+                                "uuid": "c859047e-d5cd-42fd-9b79-3c6089279774"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "design_tsv",
+                                "uuid": "974ffbbe-2218-4867-8775-e267b3311f95"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "genes_tsv",
+                                "uuid": "6a8dd992-ccd9-403a-a94d-742a2249aaa7"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "matrix_mtx",
+                                "uuid": "0273aaac-0d5b-40dd-a1d9-50a17e5f406a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy0",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
+                        "id": 2,
+                        "input_connections": {
+                            "barcodes": {
+                                "id": 0,
+                                "output_name": "barcode_tsv"
+                            },
+                            "genes": {
+                                "id": 0,
+                                "output_name": "genes_tsv"
+                            },
+                            "matrix": {
+                                "id": 0,
+                                "output_name": "matrix_mtx"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Advanced Cut",
-                                "name": "input"
+                                "description": "runtime parameter for tool Scanpy Read10x",
+                                "name": "cell_meta"
+                            },
+                            {
+                                "description": "runtime parameter for tool Scanpy Read10x",
+                                "name": "gene_meta"
                             }
                         ],
-                        "label": "Metadata",
-                        "name": "Advanced Cut",
+                        "label": null,
+                        "name": "Scanpy Read10x",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "name": "output_h5",
+                                "type": "h5"
                             }
                         ],
                         "position": {
-                            "left": 9.0,
-                            "top": 455.5
+                            "left": 277.97918701171875,
+                            "top": 325.96875
                         },
                         "post_job_actions": {
-                            "TagDatasetActionoutput": {
+                            "ChangeDatatypeActionoutput_h5": {
                                 "action_arguments": {
-                                    "tags": "#bulk,#ebi,#metadata"
+                                    "newtype": "h5ad"
                                 },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "output"
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "output_h5"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "f46f0e4f75c4",
-                            "name": "text_processing",
-                            "owner": "bgruening",
+                            "changeset_revision": "d253d69ff19f",
+                            "name": "scanpy_read_10x",
+                            "owner": "ebi-gxa",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"complement\": \"--complement\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"list\": \"3\\n5\\n7\\n8\\n9\\n10\\n11\\n12\\n13\\n15\\n16\\n17\\n18\"}, \"delimiter\": \"\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"barcodes\": {\"__class__\": \"ConnectedValue\"}, \"cell_meta\": {\"__class__\": \"RuntimeValue\"}, \"gene_meta\": {\"__class__\": \"RuntimeValue\"}, \"genes\": {\"__class__\": \"ConnectedValue\"}, \"matrix\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"anndata\", \"var_names\": \"gene_ids\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
                         "type": "tool",
-                        "uuid": "456f7c3d-3e34-44d4-b952-440927543a9c",
+                        "uuid": "432bc2f8-5e5c-489a-ab84-fd3ccd40ec99",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "71d445d7-061f-41bf-a968-a6705be82fdd"
+                                "label": "Scanpy Read10x on input dataset(s): anndata",
+                                "output_name": "output_h5",
+                                "uuid": "6bd01730-f0b5-4824-8cfc-d563cc9c7f7d"
                             }
                         ]
                     },
                     {
-                        "annotation": "Convert EnsemblID to Gene Symbol. Note that some EnsemblID's have multiple Gene Symbols.",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
                         "errors": null,
-                        "id": 2,
+                        "id": 3,
                         "input_connections": {
-                            "id_file": {
-                                "id": 0,
-                                "output_name": "output_tabular"
+                            "input": {
+                                "id": 2,
+                                "output_name": "output_h5"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool annotateMyIDs",
-                                "name": "id_file"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "annotateMyIDs",
+                        "name": "Inspect AnnData",
                         "outputs": [
                             {
-                                "name": "out_tab",
+                                "name": "X",
                                 "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 290.0,
-                            "top": 0
+                            "left": 565.0208740234375,
+                            "top": 322.46875
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "fe3ca740a485",
-                            "name": "annotatemyids",
+                            "changeset_revision": "ee98d611afc6",
+                            "name": "anndata_inspect",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"file_has_header\": \"true\", \"id_file\": {\"__class__\": \"RuntimeValue\"}, \"id_type\": \"ENSEMBL\", \"organism\": \"Hs\", \"output_cols\": [\"SYMBOL\"], \"remove_dups\": \"false\", \"rscriptOpt\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"inspect\": {\"info\": \"X\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
                         "type": "tool",
-                        "uuid": "faff29fb-e920-4767-9da2-f68820116c3b",
+                        "uuid": "27acc627-ce13-4572-b4bb-e8ecb9c80bb4",
                         "workflow_outputs": [
                             {
-                                "label": "annotateMyIDs on input dataset(s): Annotated IDs",
-                                "output_name": "out_tab",
-                                "uuid": "8415bac0-6beb-467d-a0fa-fb6465987ff7"
+                                "label": null,
+                                "output_name": "X",
+                                "uuid": "e2548214-2e98-4faa-bd8a-ce539df4cef8"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2",
                         "errors": null,
-                        "id": 3,
+                        "id": 4,
                         "input_connections": {
-                            "input": {
-                                "id": 1,
-                                "output_name": "output"
+                            "in_file": {
+                                "id": 3,
+                                "output_name": "X"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Transpose",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool Regex Find And Replace",
-                                "name": "input"
+                                "name": "out_file",
+                                "type": "input"
                             }
                         ],
+                        "position": {
+                            "left": 831.010498046875,
+                            "top": 329.46875
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ac092723240d",
+                            "name": "datamash_transpose",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"in_file\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "5ea8bf51-59c9-4074-960f-56a355d16bae",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file",
+                                "uuid": "4ca75360-6d9a-458c-a837-bd61fd5bdae1"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "id_file": {
+                                "id": 4,
+                                "output_name": "out_file"
+                            }
+                        },
+                        "inputs": [],
                         "label": null,
-                        "name": "Regex Find And Replace",
+                        "name": "annotateMyIDs",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "out_tab",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 466.0,
-                            "top": 422.5
+                            "left": 881.5208740234375,
+                            "top": 67.5
                         },
                         "post_job_actions": {
-                            "ChangeDatatypeActionout_file1": {
+                            "RemoveTagDatasetActionout_tab": {
                                 "action_arguments": {
-                                    "newtype": "tabular"
+                                    "tags": "#matrix"
                                 },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "out_file1"
+                                "action_type": "RemoveTagDatasetAction",
+                                "output_name": "out_tab"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "399da6b5ec21",
-                            "name": "regex_find_replace",
-                            "owner": "galaxyp",
+                            "changeset_revision": "fe3ca740a485",
+                            "name": "annotatemyids",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \"Sample Characteristic\\\\[age\\\\]\", \"replacement\": \"Age\"}, {\"__index__\": 1, \"pattern\": \" year\", \"replacement\": \"\"}, {\"__index__\": 2, \"pattern\": \"Sample Characteristic\\\\[body mass index\\\\]\", \"replacement\": \"BMI\"}, {\"__index__\": 3, \"pattern\": \"Sample Characteristic\\\\[disease\\\\]\", \"replacement\": \"Disease\"}, {\"__index__\": 4, \"pattern\": \"Sample Characteristic\\\\[individual\\\\]\", \"replacement\": \"Individual\"}, {\"__index__\": 5, \"pattern\": \"Sample Characteristic\\\\[sex\\\\]\", \"replacement\": \"Sex\"}], \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"file_has_header\": \"true\", \"id_file\": {\"__class__\": \"ConnectedValue\"}, \"id_type\": \"ENSEMBL\", \"organism\": \"Hs\", \"output_cols\": [\"SYMBOL\"], \"remove_dups\": \"false\", \"rscriptOpt\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
                         "type": "tool",
-                        "uuid": "e0bf890a-f327-424b-b6fa-353c4141c900",
+                        "uuid": "4e551e90-930f-4904-b859-8a107400eb1e",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "af0da388-91c7-4b22-b9a8-abe3c6655c1b"
+                                "label": "annotateMyIDs on input dataset(s): Annotated IDs",
+                                "output_name": "out_tab",
+                                "uuid": "c39c7d69-550e-4b54-a412-317b599c5e55"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "id": 4,
+                        "id": 6,
                         "input_connections": {
                             "Annotated IDs": {
-                                "id": 2,
+                                "id": 5,
                                 "input_subworkflow_step_id": 0,
                                 "output_name": "out_tab"
                             },
                             "Expression Matrix (Gene Rows)": {
-                                "id": 0,
+                                "id": 4,
                                 "input_subworkflow_step_id": 1,
-                                "output_name": "output_tabular"
+                                "output_name": "out_file"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Copy of Convert from Ensembl to GeneSymbol, summing duplicate genes",
+                        "name": "1st step removed - Convert from Ensembl to GeneSymbol, summing duplicate genes",
                         "outputs": [],
                         "position": {
-                            "left": 525.5,
-                            "top": 36.5
+                            "left": 1184.510498046875,
+                            "top": 0
                         },
                         "subworkflow": {
                             "a_galaxy_workflow": "true",
@@ -240775,7 +245413,7 @@
                                 }
                             ],
                             "format-version": "0.1",
-                            "name": "Copy of Convert from Ensembl to GeneSymbol, summing duplicate genes",
+                            "name": "1st step removed - Convert from Ensembl to GeneSymbol, summing duplicate genes",
                             "steps": {
                                 "0": {
                                     "annotation": "",
@@ -240800,12 +245438,12 @@
                                     "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                                     "tool_version": null,
                                     "type": "data_input",
-                                    "uuid": "a5355f15-68b7-4551-ac47-49ac73b00edf",
+                                    "uuid": "d81929a3-775c-4421-ba06-6a4c69f74ff7",
                                     "workflow_outputs": [
                                         {
                                             "label": null,
                                             "output_name": "output",
-                                            "uuid": "e6ac7216-b2c6-4232-b911-eb1285ed8a9f"
+                                            "uuid": "8ac19ec5-b4f9-499b-93fb-c624b9c04b22"
                                         }
                                     ]
                                 },
@@ -240832,7 +245470,7 @@
                                     "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                                     "tool_version": null,
                                     "type": "data_input",
-                                    "uuid": "9aa181ba-56bd-4360-9d50-907bee463505",
+                                    "uuid": "cb8ea816-9239-421d-ae4c-8bba1b07d2f9",
                                     "workflow_outputs": []
                                 },
                                 "10": {
@@ -240870,12 +245508,12 @@
                                     "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"1 s/^gene//\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                                     "tool_version": null,
                                     "type": "tool",
-                                    "uuid": "16452009-e11e-4aeb-8404-6c70e13490ac",
+                                    "uuid": "417aedef-9d94-43b1-a3cd-adef81d7132a",
                                     "workflow_outputs": [
                                         {
                                             "label": "Gene Symbol Count Matrix",
                                             "output_name": "output",
-                                            "uuid": "f7b8537e-6349-437a-9b89-d9bab0e1e581"
+                                            "uuid": "3cefa576-db2d-44f6-8cf2-26c846cf5d88"
                                         }
                                     ]
                                 },
@@ -240925,7 +245563,7 @@
                                     "tool_state": "{\"code\": \"BEGIN {\\n  ordering[\\\"test\\\"]\\n  delete ordering[\\\"test\\\"]\\n}\\nNR > 1 {\\n   if (gene[$1]){\\n      gene[$1] = gene[$1]\\\":\\\"$2\\n   } else {\\n      gene[$1] = $2\\n      ordering[length(ordering)+1] = $1\\n   }\\n   \\n}\\n\\nEND {\\n    for (o=0; o < length(ordering); ++o){\\n         print ordering[o]\\\"\\\\t\\\"gene[ordering[o]]\\n    }\\n}\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                                     "tool_version": null,
                                     "type": "tool",
-                                    "uuid": "e5b51c32-bd3a-440f-a05a-8c1c36384e3c",
+                                    "uuid": "51d68e09-2af1-4c81-9ca8-b76afe06e9f7",
                                     "workflow_outputs": []
                                 },
                                 "3": {
@@ -240973,7 +245611,7 @@
                                     "tool_state": "{\"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": \"true\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                                     "tool_version": null,
                                     "type": "tool",
-                                    "uuid": "0ac51cc9-c0b0-4b3d-961c-503860cf423f",
+                                    "uuid": "76d38310-a221-4b70-bcb9-296b4870bb52",
                                     "workflow_outputs": []
                                 },
                                 "4": {
@@ -241017,7 +245655,7 @@
                                     "tool_state": "{\"code\": \"{print $NF\\\"\\\\t\\\"$0}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                                     "tool_version": null,
                                     "type": "tool",
-                                    "uuid": "44880f2a-430c-4b00-a0b3-e4673fe395ce",
+                                    "uuid": "f1d4e7aa-4ac7-4258-a1eb-a335cad2c861",
                                     "workflow_outputs": []
                                 },
                                 "5": {
@@ -241061,7 +245699,7 @@
                                     "tool_state": "{\"complement\": \"--complement\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"list\": \"2\"}, \"delimiter\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                                     "tool_version": null,
                                     "type": "tool",
-                                    "uuid": "104cb55a-f297-4464-b3b6-7021ffd0ae9c",
+                                    "uuid": "334f4810-84e0-4b5c-962f-0e2e6fbcc5f8",
                                     "workflow_outputs": []
                                 },
                                 "6": {
@@ -241105,7 +245743,7 @@
                                     "tool_state": "{\"code\": \"{ gene[$1] = gene[$1] + 1 }\\n\\nEND {\\n     for (ge in gene){\\n         print ge\\\"\\\\t\\\"gene[ge]\\n     }\\n}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                                     "tool_version": null,
                                     "type": "tool",
-                                    "uuid": "1f84d0c1-b187-4299-a2bd-172964ef3732",
+                                    "uuid": "111ebd66-534f-4b17-9d60-aeff287fe500",
                                     "workflow_outputs": []
                                 },
                                 "7": {
@@ -241149,7 +245787,7 @@
                                     "tool_state": "{\"code\": \"NR == 1 {\\n    for (i=2; i <= NF; i++){\\n         cellorder[i] = $i\\n   }\\n}\\n\\nNR > 1 {\\n    for (i=2; i <= NF; i++){\\n         if (cellorder[i] == \\\"0\\\" || $1 == \\\"NA\\\"){\\n         } else {\\n             bc[$1\\\"\\\\t\\\"cellorder[i]] = bc[$1\\\"\\\\t\\\"cellorder[i]] + $i\\n         }\\n   }\\n}\\n\\nEND {\\n   print \\\"gene\\\\tbar\\\\tvalue\\\"\\n   for (key in bc){\\n       print key\\\"\\\\t\\\"bc[key]\\n   }\\n}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                                     "tool_version": null,
                                     "type": "tool",
-                                    "uuid": "8ac449d7-da88-44b0-bfe2-092d8cd47af9",
+                                    "uuid": "e2ce8f93-c8e2-490a-a3b6-3e580c0a6604",
                                     "workflow_outputs": []
                                 },
                                 "8": {
@@ -241181,12 +245819,12 @@
                                     "tool_state": "{\"column\": \"2\", \"column_set\": [], \"header_lines\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"order\": \"DESC\", \"style\": \"num\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                                     "tool_version": null,
                                     "type": "tool",
-                                    "uuid": "d3a9bfd0-372a-493c-a83a-578427a7fe17",
+                                    "uuid": "73ec3cc4-738e-4815-9ed0-a657e56f0706",
                                     "workflow_outputs": [
                                         {
                                             "label": "Report of Duplicate Genes",
                                             "output_name": "out_file1",
-                                            "uuid": "274c3805-5b98-4a64-8dcd-c269750b852e"
+                                            "uuid": "fb52cadb-3832-49bb-ac12-5ba2600ea26d"
                                         }
                                     ]
                                 },
@@ -241231,26 +245869,26 @@
                                     "tool_state": "{\"out_opts\": [\"output_headers_col\", \"output_headers_row\"], \"precision\": \"6\", \"singtabop\": {\"use_type\": \"single\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"col_row_names\": [\"has_col_names\"], \"adv\": {\"header\": null, \"nrows\": null, \"skipfooter\": null, \"skip_blank_lines\": \"true\"}, \"user\": {\"mode\": \"fulltable\", \"__current_case__\": 4, \"general\": {\"use\": \"pivot\", \"__current_case__\": 2, \"index\": \"gene\", \"column\": \"bar\", \"values\": \"value\", \"aggfunc\": null, \"colfun_map\": []}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                                     "tool_version": null,
                                     "type": "tool",
-                                    "uuid": "6c98c17e-43ca-4620-a2f7-a919c24bee20",
+                                    "uuid": "571a650f-5b76-4103-98f1-7a8400f1abbd",
                                     "workflow_outputs": []
                                 }
                             },
                             "tags": "",
-                            "uuid": "463a98af-e99f-47d8-9a05-f601d39b506a"
+                            "uuid": "1eccbdc6-6b28-4cbf-abbe-59145eeee57e"
                         },
-                        "tool_id": 171557,
+                        "tool_id": 171553,
                         "type": "subworkflow",
-                        "uuid": "319ba9b4-9af0-4a4d-a3d5-b700d1745d3f",
+                        "uuid": "ff79cab7-702d-4172-8a10-9e64815de427",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "Report of Duplicate Genes",
-                                "uuid": "915c757d-6fb1-41d2-a9f7-b8b30a29794a"
+                                "output_name": "Gene Symbol Count Matrix",
+                                "uuid": "bc5b731e-deb9-4117-ba1d-3f891cb61e66"
                             },
                             {
                                 "label": null,
-                                "output_name": "Gene Symbol Count Matrix",
-                                "uuid": "24ace210-3eac-4f62-8781-366e00cff2dc"
+                                "output_name": "Report of Duplicate Genes",
+                                "uuid": "3dfa19cf-db53-4923-b2c1-abe2c37d3457"
                             }
                         ]
                     },
@@ -241258,27 +245896,18 @@
                         "annotation": "",
                         "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4",
                         "errors": null,
-                        "id": 5,
+                        "id": 7,
                         "input_connections": {
                             "exprs_file": {
-                                "id": 4,
+                                "id": 6,
                                 "output_name": "Gene Symbol Count Matrix"
                             },
                             "pdata_file": {
-                                "id": 3,
-                                "output_name": "out_file1"
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Construct Expression Set Object",
-                                "name": "exprs_file"
-                            },
-                            {
-                                "description": "runtime parameter for tool Construct Expression Set Object",
-                                "name": "pdata_file"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
                         "name": "Construct Expression Set Object",
                         "outputs": [
@@ -241292,8 +245921,8 @@
                             }
                         ],
                         "position": {
-                            "left": 883.0,
-                            "top": 343.5
+                            "left": 1439.0208740234375,
+                            "top": 151
                         },
                         "post_job_actions": {
                             "RemoveTagDatasetActionout_rds": {
@@ -241318,20 +245947,20 @@
                             "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"annotation\": \"\", \"expdata\": {\"name\": \"\", \"lab\": \"\", \"contact\": \"\", \"title\": \"\", \"abstract\": \"\", \"url\": \"\", \"other\": [{\"__index__\": 0, \"field\": \"notes\", \"comment\": \"Created in Galaxy\"}]}, \"exprs_file\": {\"__class__\": \"RuntimeValue\"}, \"metadata\": [], \"pdata_file\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"annotation\": \"\", \"expdata\": {\"name\": \"\", \"lab\": \"\", \"contact\": \"\", \"title\": \"\", \"abstract\": \"\", \"url\": \"\", \"other\": [{\"__index__\": 0, \"field\": \"notes\", \"comment\": \"Created in Galaxy\"}]}, \"exprs_file\": {\"__class__\": \"ConnectedValue\"}, \"metadata\": [], \"pdata_file\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
                         "type": "tool",
-                        "uuid": "8e428b8e-bda7-4fdb-8daa-2197d1d1d357",
+                        "uuid": "ca9a2794-404f-4460-8377-f2bc142b37a4",
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "Construct Expression Set Object on input dataset(s): RData ESet Object",
                                 "output_name": "out_rds",
-                                "uuid": "28490366-fb29-40df-852c-2f5da6f1a6ce"
+                                "uuid": "e8c91df0-4e6c-4eb2-9807-c2679b494958"
                             },
                             {
-                                "label": null,
+                                "label": "Construct Expression Set Object on input dataset(s): General Info",
                                 "output_name": "out_txt",
-                                "uuid": "426d6040-bf0f-4312-babf-2ae9c928eff1"
+                                "uuid": "2912d09b-b178-4035-b7c8-7038392e2bf2"
                             }
                         ]
                     },
@@ -241339,19 +245968,14 @@
                         "annotation": "",
                         "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4",
                         "errors": null,
-                        "id": 6,
+                        "id": 8,
                         "input_connections": {
                             "rds_eset": {
-                                "id": 5,
+                                "id": 7,
                                 "output_name": "out_rds"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Manipulate Expression Set Object",
-                                "name": "rds_eset"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
                         "name": "Manipulate Expression Set Object",
                         "outputs": [
@@ -241361,8 +245985,8 @@
                             }
                         ],
                         "position": {
-                            "left": 1186.5,
-                            "top": 300.5
+                            "left": 1729.52099609375,
+                            "top": 157.5
                         },
                         "post_job_actions": {
                             "RemoveTagDatasetActionout_eset": {
@@ -241387,15 +246011,15 @@
                             "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"combine_eset\": {\"do\": \"No\", \"__current_case__\": 0}, \"rds_eset\": {\"__class__\": \"RuntimeValue\"}, \"subset_eset\": {\"do\": \"Yes\", \"__current_case__\": 1, \"subset_yes\": {\"by\": \"phenotype\", \"__current_case__\": 3, \"pheno_samples\": [{\"__index__\": 0, \"column\": \"Disease\", \"values\": \"normal\"}], \"pheno_genes\": []}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"combine_eset\": {\"do\": \"No\", \"__current_case__\": 0}, \"rds_eset\": {\"__class__\": \"ConnectedValue\"}, \"subset_eset\": {\"do\": \"Yes\", \"__current_case__\": 1, \"subset_yes\": {\"by\": \"phenotype\", \"__current_case__\": 3, \"pheno_samples\": [{\"__index__\": 0, \"column\": \"Disease\", \"values\": \"normal\"}], \"pheno_genes\": []}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
                         "type": "tool",
-                        "uuid": "f7cd1cd9-42bf-4a24-82a3-6720a7783771",
+                        "uuid": "4f5f4bed-c2cf-4fe8-8d29-32b3e178932b",
                         "workflow_outputs": [
                             {
                                 "label": "Manipulate Expression Set Object on input dataset(s): ExpressionSet Object",
                                 "output_name": "out_eset",
-                                "uuid": "88196d0b-7254-4794-b08a-5409f19c8323"
+                                "uuid": "08de92d8-32fe-4b47-9038-298cdd13fac5"
                             }
                         ]
                     },
@@ -241403,19 +246027,14 @@
                         "annotation": "",
                         "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4",
                         "errors": null,
-                        "id": 7,
+                        "id": 9,
                         "input_connections": {
                             "rds_eset": {
-                                "id": 5,
+                                "id": 7,
                                 "output_name": "out_rds"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Manipulate Expression Set Object",
-                                "name": "rds_eset"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
                         "name": "Manipulate Expression Set Object",
                         "outputs": [
@@ -241425,8 +246044,8 @@
                             }
                         ],
                         "position": {
-                            "left": 1183.5,
-                            "top": 528.5
+                            "left": 1725.52099609375,
+                            "top": 402.4895935058594
                         },
                         "post_job_actions": {
                             "RemoveTagDatasetActionout_eset": {
@@ -241451,38 +246070,38 @@
                             "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"combine_eset\": {\"do\": \"No\", \"__current_case__\": 0}, \"rds_eset\": {\"__class__\": \"RuntimeValue\"}, \"subset_eset\": {\"do\": \"Yes\", \"__current_case__\": 1, \"subset_yes\": {\"by\": \"phenotype\", \"__current_case__\": 3, \"pheno_samples\": [{\"__index__\": 0, \"column\": \"Disease\", \"values\": \"type II diabetes mellitus\"}], \"pheno_genes\": []}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"combine_eset\": {\"do\": \"No\", \"__current_case__\": 0}, \"rds_eset\": {\"__class__\": \"ConnectedValue\"}, \"subset_eset\": {\"do\": \"Yes\", \"__current_case__\": 1, \"subset_yes\": {\"by\": \"phenotype\", \"__current_case__\": 3, \"pheno_samples\": [{\"__index__\": 0, \"column\": \"Disease\", \"values\": \"type II diabetes mellitus\"}], \"pheno_genes\": []}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
                         "type": "tool",
-                        "uuid": "8dc9defa-1ae9-4e6b-8479-5034763c7c2f",
+                        "uuid": "175ce542-ca00-4a2c-bb63-1f08bf41b16e",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "out_eset",
-                                "uuid": "ecab164b-a19b-4b78-8b6d-491aa2d5c1e7"
+                                "uuid": "bdf6c2ca-9ded-487f-8c7c-7b5e5e7ec42f"
                             }
                         ]
                     }
                 ],
-                "parent_id": "single-cell/bulk-music-3-preparebulk",
-                "path": "topics/single-cell/tutorials/bulk-music-3-preparebulk/workflows/bulk_ESet.ga",
+                "parent_id": "single-cell/bulk-music-2-preparescref",
+                "path": "topics/single-cell/tutorials/bulk-music-2-preparescref/workflows/sc_matrix.ga",
                 "tags": [
                     "name:singlecell",
-                    "name:transcriptomics",
-                    "name:training"
+                    "name:training",
+                    "name:transcriptomics"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "MuSiC-Deconvolution: Data generation | bulk | ESet",
+                "title": "MuSiC-Deconvolution: Data generation | sc | matrix + ESet",
                 "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-bulk-music-3-preparebulk/versions/bulk-eset",
-                "tutorial_id": "bulk-music-3-preparebulk",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-3-preparebulk/workflows/bulk_ESet.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-3-preparebulk/workflows/bulk_ESet.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-bulk-music-2-preparescref/versions/sc-matrix",
+                "tutorial_id": "bulk-music-2-preparescref",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-2-preparescref/workflows/sc_matrix.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-2-preparescref/workflows/sc_matrix.html",
                 "version": 1,
-                "wfid": "single-cell-bulk-music-3-preparebulk",
-                "wfname": "bulk-eset",
-                "workflow": "bulk_ESet.ga",
+                "wfid": "single-cell-bulk-music-2-preparescref",
+                "wfname": "sc-matrix",
+                "workflow": "sc_matrix.ga",
                 "workflow_tools": [
                     "sort1",
                     "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4",
@@ -241491,15 +246110,944 @@
                     "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
                     "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
                     "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
                     "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2",
                     "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0"
                 ],
-                "workflowhub_id": "1230"
+                "workflowhub_id": "1261"
+            },
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-8170-8806",
+                        "name": "Wendi Bacon"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-4181-2676",
+                        "name": "Mehmet Tekman"
+                    }
+                ],
+                "description": "This workflow generates from only an EBI SCXA reference the metadata for creating an ESet object\n",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"EBI SCXA Data Retrieval\"]\n  1[label=\"Cut\"]\n  0 -> 1 [label=\"design_tsv\"]\n  2[label=\"Add line to file\"]\n  0 -> 2 [label=\"barcode_tsv\"]\n  3[label=\"Reformatting metadata columns\"]\n  1 -> 3 [label=\"out_file1\"]\n  4[label=\"Join two Datasets\"]\n  2 -> 4 [label=\"outfile\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"Advanced Cut\"]\n  4 -> 5 [label=\"out_file1\"]\n}",
+                "history": [
+                    {
+                        "hash": "9a561b3752745eab20cececd5346ee0a7449da28",
+                        "message": "update workflows",
+                        "num": 1,
+                        "short_hash": "9a561b375",
+                        "unix": "1669581042"
+                    }
+                ],
+                "inputs": [],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"EBI SCXA Data Retrieval\"];\n  1[\"Cut\"];\n  0 -->|design_tsv| 1;\n  2[\"Add line to file\"];\n  0 -->|barcode_tsv| 2;\n  3[\"Reformatting metadata columns\"];\n  1 -->|out_file1| 3;\n  4[\"Join two Datasets\"];\n  2 -->|outfile| 4;\n  3 -->|out_file1| 4;\n  5[\"Advanced Cut\"];\n  4 -->|out_file1| 5;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "MuSiC-Deconvolution: Data generation | sc | metadata",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.1+galaxy1",
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": null,
+                        "name": "EBI SCXA Data Retrieval",
+                        "outputs": [
+                            {
+                                "name": "matrix_mtx",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "genes_tsv",
+                                "type": "tsv"
+                            },
+                            {
+                                "name": "barcode_tsv",
+                                "type": "tsv"
+                            },
+                            {
+                                "name": "design_tsv",
+                                "type": "tsv"
+                            }
+                        ],
+                        "position": {
+                            "left": 0.0,
+                            "top": 10.5
+                        },
+                        "post_job_actions": {
+                            "ChangeDatatypeActionbarcode_tsv": {
+                                "action_arguments": {
+                                    "newtype": "tabular"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "barcode_tsv"
+                            },
+                            "TagDatasetActionbarcode_tsv": {
+                                "action_arguments": {
+                                    "tags": "#ebi,#singlecell,#metadata"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "barcode_tsv"
+                            },
+                            "TagDatasetActiondesign_tsv": {
+                                "action_arguments": {
+                                    "tags": "#ebi"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "design_tsv"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "cd6b80f62fcc",
+                            "name": "retrieve_scxa",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"accession\": \"E-MTAB-5061\", \"matrix_type\": \"raw\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "836f6c68-fa15-4f1d-8db5-a432c6c783f8",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "matrix_mtx",
+                                "uuid": "ecafd465-5cb3-4484-868f-8922ae3db395"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "genes_tsv",
+                                "uuid": "25d87e34-ad87-4987-a626-589b42b0a10d"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "barcode_tsv",
+                                "uuid": "9f57847e-944c-4b00-a33b-bd60ef0814ec"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "design_tsv",
+                                "uuid": "d8857eeb-49da-4772-b8e7-7237c7a0ade0"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "Cut1",
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "design_tsv"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Cut",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 282.01043701171875,
+                            "top": 270.5
+                        },
+                        "post_job_actions": {
+                            "TagDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "tags": "#singlecell"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"columnList\": \"c1,c4,c6,c8,c10,c14,c20,c24,c26,c30,c32,c34\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "fc140e5f-6659-4a8f-bacc-ccf78e50cf39",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "3d887d75-9e58-4a8b-b8c3-9f30b65d17aa"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "infile": {
+                                "id": 0,
+                                "output_name": "barcode_tsv"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Add line to file",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 687.5,
+                            "top": 0
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "8e251055b1a9",
+                            "name": "add_line_to_file",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"infile\": {\"__class__\": \"ConnectedValue\"}, \"options\": \"header\", \"text_input\": \"Cell\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "e8ac2324-aa96-40c6-a4f4-e2f3896136c9",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "e07a7e35-8f57-479a-b328-6d988627d5fb"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Adjust this step as necessary",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2",
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {
+                            "input": {
+                                "id": 1,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Reformatting metadata columns",
+                        "name": "Regex Find And Replace",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 586.03125,
+                            "top": 150.45834350585938
+                        },
+                        "post_job_actions": {
+                            "ChangeDatatypeActionout_file1": {
+                                "action_arguments": {
+                                    "newtype": "tabular"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "out_file1"
+                            },
+                            "TagDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "tags": "#metadata"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "399da6b5ec21",
+                            "name": "regex_find_replace",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \"\\\"Sample Characteristic\\\\[individual\\\\]\\\"\", \"replacement\": \"Individual\"}, {\"__index__\": 1, \"pattern\": \"\\\"Sample Characteristic\\\\[sex\\\\]\\\"\", \"replacement\": \"Sex\"}, {\"__index__\": 2, \"pattern\": \"\\\"Sample Characteristic\\\\[age\\\\]\\\"\", \"replacement\": \"Age\"}, {\"__index__\": 3, \"pattern\": \"\\\"Sample Characteristic\\\\[body mass index\\\\]\\\"\", \"replacement\": \"BMI\"}, {\"__index__\": 4, \"pattern\": \" kilogram per square meter\", \"replacement\": \"\"}, {\"__index__\": 5, \"pattern\": \"HbA1c \", \"replacement\": \"\"}, {\"__index__\": 6, \"pattern\": \"\\\"Sample Characteristic\\\\[clinical information\\\\]\\\"\", \"replacement\": \"HbA1c\"}, {\"__index__\": 7, \"pattern\": \"%\", \"replacement\": \"\"}, {\"__index__\": 8, \"pattern\": \"\\\"Sample Characteristic\\\\[disease\\\\]\\\"\", \"replacement\": \"Disease\"}, {\"__index__\": 9, \"pattern\": \"\\\"Sample Characteristic\\\\[single cell quality\\\\]\\\"\", \"replacement\": \"Single cell quality\"}, {\"__index__\": 10, \"pattern\": \"\\\"Sample Characteristic\\\\[submitted single cell quality\\\\]\\\"\", \"replacement\": \"Submitted single cell quality\"}, {\"__index__\": 11, \"pattern\": \"\\\"Factor Value\\\\[inferred cell type - ontology labels\\\\]\\\"\", \"replacement\": \"Inferred cell type - ontology label\"}, {\"__index__\": 12, \"pattern\": \"\\\"\\\"\", \"replacement\": \"\"}, {\"__index__\": 13, \"pattern\": \"\\\"\", \"replacement\": \"\"}, {\"__index__\": 14, \"pattern\": \"Factor Value\\\\[inferred cell type - authors labels\\\\]\", \"replacement\": \"Inferred cell type - author labels\"}], \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "e5b0bcd3-a94c-4942-bed0-6d8f51e36e22",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "45757c76-0453-426f-b729-4c9d7b5688c9"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Experimental designs often include extra stuff (likely the barcodes not meeting the EBI pre-processing criteria), so this way we streamline down to only those barcodes in the barcodes file.",
+                        "content_id": "join1",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "input1": {
+                                "id": 2,
+                                "output_name": "outfile"
+                            },
+                            "input2": {
+                                "id": 3,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Join two Datasets",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 857.0208740234375,
+                            "top": 166.46875
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "join1",
+                        "tool_state": "{\"field1\": \"1\", \"field2\": \"1\", \"fill_empty_columns\": {\"fill_empty_columns_switch\": \"no_fill\", \"__current_case__\": 0}, \"header\": \"-H\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"partial\": \"\", \"unmatched\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "0f40eba6-5e09-45de-a6b8-64b4bdcabd3f",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "39583bc2-7e06-4088-abcc-bb8b994767bb"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Gets rid of the duplicated columns",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "input": {
+                                "id": 4,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Advanced Cut",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 1106.8125,
+                            "top": 110.29167175292969
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f46f0e4f75c4",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"complement\": \"--complement\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"list\": \"1\"}, \"delimiter\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "f5795ca8-4172-42d5-a898-ab71fe195024",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "f7c57eb1-71ae-4850-8e99-16fafe763bbf"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "single-cell/bulk-music-2-preparescref",
+                "path": "topics/single-cell/tutorials/bulk-music-2-preparescref/workflows/sc_metadata.ga",
+                "tags": [
+                    "name:singlecell",
+                    "name:transcriptomics",
+                    "name:training",
+                    "name:deconvolution"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "MuSiC-Deconvolution: Data generation | sc | metadata",
+                "topic_id": "single-cell",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-bulk-music-2-preparescref/versions/sc-metadata",
+                "tutorial_id": "bulk-music-2-preparescref",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-2-preparescref/workflows/sc_metadata.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-2-preparescref/workflows/sc_metadata.html",
+                "version": 1,
+                "wfid": "single-cell-bulk-music-2-preparescref",
+                "wfname": "sc-metadata",
+                "workflow": "sc_metadata.ga",
+                "workflow_tools": [
+                    "Cut1",
+                    "join1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2"
+                ],
+                "workflowhub_id": "1257"
+            }
+        ]
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case-cell-annotation/tutorial.json",
+        "contributors": [
+            {
+                "email": "hexhowells@gmail.com",
+                "id": "hexhowells",
+                "joined": "2023-06",
+                "name": "Morgan Howells",
+                "orcid": "0009-0008-9422-6380",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexhowells/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexhowells.json"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/7319173"
+        "dir": "topics/single-cell/tutorials/scrna-case-cell-annotation",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": false,
+        "id": "single-cell/scrna-case-cell-annotation",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Automated cell annotation is a useful tool for automatically assigning cell type labels to cell data.",
+            "There are various algorithms and methods that can be used for conducting cell annotation with each method having its own strengths and weaknesses.",
+            "Automated cell annotation isn't perfect, when analysing results it's important to identify common issues that could occur."
+        ],
+        "layout": "tutorial_slides",
+        "license": "CC-BY-4.0",
+        "logo": "GTN",
+        "mod_date": "2023-10-10",
+        "objectives": [
+            "Learn the different methods underlying automated cell annotation",
+            "Understand the data needed to annotate cells",
+            "Be able to choose the most appropriate method for your data",
+            "Recognise the common issues and be able to resolve them"
+        ],
+        "pageviews": 1363237,
+        "priority": 4,
+        "pub_date": "2023-09-04",
+        "questions": [
+            "What is automated cell annotation?",
+            "How is automated cell annotation performed?",
+            "What methods are available?",
+            "What is the best method to choose for your data?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-intro"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "S00110",
+        "short_tools": [],
+        "slides": true,
+        "slides_recordings": false,
+        "subtopic": "scintroduction",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": null,
+        "title": "Automated Cell Annotation",
+        "tools": [],
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "scrna-case-cell-annotation",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case-cell-annotation/slides.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case-cell-annotation/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case-cell-annotation/slides.json"
+        },
+        "version": 3,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 148,
+        "visitors": 574600
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-data-formats/tutorial.json",
+        "contributors": [
+            {
+                "email": "hexhowells@gmail.com",
+                "id": "hexhowells",
+                "joined": "2023-06",
+                "name": "Morgan Howells",
+                "orcid": "0009-0008-9422-6380",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexhowells/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexhowells.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "bio": "Senior Lecturer at The Open University",
+                "elixir_node": "uk",
+                "email": "wendi.bacon@open.ac.uk",
+                "fediverse": "https://mstdn.science/@wendibacon1",
+                "fediverse_flavor": "mastodon",
+                "id": "nomadscientist",
+                "joined": "2020-03",
+                "matrix": "nomadscientist:matrix.org",
+                "name": "Wendi Bacon",
+                "orcid": "0000-0002-8170-8806",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
+                "twitter": "WendiBacon1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "id": "kkamieniecka",
+                "joined": "2018-08",
+                "name": "Katarzyna Kamieniecka",
+                "orcid": "0009-0004-2454-5950",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/",
+                "twitter": "katemurat",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
+            }
+        ],
+        "dir": "topics/single-cell/tutorials/scrna-data-formats",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": false,
+        "id": "single-cell/scrna-data-formats",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Single-cell data consists of four main sections",
+            "Single-cell data can come in a variety of formats",
+            "Different data formats are required for different languages and packages",
+            "There are various public single-cell atlases that consist of useful data"
+        ],
+        "layout": "tutorial_slides",
+        "license": "CC-BY-4.0",
+        "logo": "GTN",
+        "mod_date": "2024-07-26",
+        "objectives": [
+            "Learn the basic structure of single-cell data",
+            "Be able to recognise different types of single-cell metadata",
+            "Learn the common data formats used for storing single-cell data",
+            "Become familiar with some popular sources for public single-cell data"
+        ],
+        "pageviews": 242332,
+        "priority": 4,
+        "pub_date": "2024-07-26",
+        "questions": [
+            "What does single-cell data look like?",
+            "What are the common single-cell formats?",
+            "Where can public single-cell data be found?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-intro"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "S00123",
+        "short_tools": [],
+        "slides": true,
+        "slides_recordings": false,
+        "subtopic": "scintroduction",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": null,
+        "title": "Single-cell Formats and Resources",
+        "tools": [],
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "scrna-data-formats",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-data-formats/slides.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-data-formats/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-data-formats/slides.json"
+        },
+        "version": 1,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 151,
+        "visitors": 99484
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_monocle3-rstudio/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "wee-snufkin"
+            ],
+            "editing": [
+                "hexylena",
+                "pavanvidem",
+                "nomadscientist"
+            ],
+            "funding": [
+                "eosc-life"
+            ]
+        },
+        "contributors": [
+            {
+                "elixir_node": "uk",
+                "email": "juliajot36@gmail.com",
+                "id": "wee-snufkin",
+                "joined": "2022-06",
+                "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "pavanvidem",
+                "joined": "2017-09",
+                "name": "Pavankumar Videm",
+                "orcid": "0000-0002-5192-126X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
+            },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "bio": "Senior Lecturer at The Open University",
+                "elixir_node": "uk",
+                "email": "wendi.bacon@open.ac.uk",
+                "fediverse": "https://mstdn.science/@wendibacon1",
+                "fediverse_flavor": "mastodon",
+                "id": "nomadscientist",
+                "joined": "2020-03",
+                "matrix": "nomadscientist:matrix.org",
+                "name": "Wendi Bacon",
+                "orcid": "0000-0002-8170-8806",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
+                "twitter": "WendiBacon1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+            },
+            {
+                "avatar": "https://www.eosc-life.eu/wp-content/themes/eosc-life-v2/assets/images/eosclogo.png",
+                "funder": true,
+                "funding_id": "824087",
+                "funding_statement": "EOSC-Life has received funding from the European Union\u2019s Horizon 2020 programme under grant agreement number 824087",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "eosc-life",
+                "joined": "2023-04",
+                "members": [
+                    "bgruening"
+                ],
+                "name": "EOSC-Life",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/eosc-life/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/eosc-life.json"
+            }
+        ],
+        "dir": "topics/single-cell/tutorials/scrna-case_monocle3-rstudio",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "single-cell/scrna-case_monocle3-rstudio",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Monocle3 in R gives more flexibility when it comes to differential expression analysis and plotting, but Galaxy offers great reproducibility and ease of analysis.",
+            "Comparing the output of several different methods applied on the same dataset might be useful to confirm the results, to ensure that the findings are reliable and even sometimes to find a new piece of information."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-06-07",
+        "notebook": {
+            "language": "r",
+            "snippet": "topics/single-cell/tutorials/scrna-case_monocle3-rstudio/preamble.md"
+        },
+        "objectives": [
+            "Identify which operations are necessary to transform an AnnData object into the files needed for Monocle",
+            "Describe the Monocle3 functions in R",
+            "Recognise steps that can be performed in R, but not with current Galaxy tools",
+            "Repeat the Monocle3 workflow and choose appropriate parameter values",
+            "Compare the outputs from Scanpy, Monocle in Galaxy and Monocle in R",
+            "Describe differential expression analysis methods"
+        ],
+        "pageviews": 4485,
+        "priority": 4,
+        "pub_date": "2023-04-12",
+        "questions": [
+            "How do I perform a trajectory analysis using Monocle3 in R?",
+            "What should I do when Galaxy's Monocle tools are not enough?",
+            "How do I assign cell types to the clusters?",
+            "How do I infer lineage relationships between clusters, without a time series?",
+            "How do I perform batch correction and differential expression analysis in Monocle?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "scrna-case_alevin",
+                    "scrna-case_alevin-combine-datasets",
+                    "scrna-case_basic-pipeline"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00336",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "single-cell-CS-code",
+        "supported_servers": {
+            "exact": [],
+            "inexact": [
+                {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy Australia",
+                    "id": "au",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "10x",
+            "paper-replication",
+            "R"
+        ],
+        "time_estimation": "3H",
+        "title": "Inferring single cell trajectories with Monocle3 (R)",
+        "tools": [],
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "scrna-case_monocle3-rstudio",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/scrna-case_monocle3-rstudio/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_monocle3-rstudio/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-case_monocle3-rstudio/tutorial.json"
+        },
+        "version": 10,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 52,
+        "visitors": 3885,
+        "zenodo_link": "https://zenodo.org/record/7455590"
     },
     {
         "admin_install": {
@@ -241626,10 +247174,12 @@
         },
         "contributors": [
             {
+                "elixir_node": "uk",
                 "email": "juliajot36@gmail.com",
                 "id": "wee-snufkin",
                 "joined": "2022-06",
                 "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
             },
@@ -241746,7 +247296,7 @@
             "Compare the outputs from Scanpy and Monocle",
             "Interpet trajectory analysis results"
         ],
-        "pageviews": 3461,
+        "pageviews": 3613,
         "priority": 5,
         "pub_date": "2022-09-30",
         "questions": [
@@ -241787,22 +247337,22 @@
         ],
         "short_id": "T00249",
         "short_tools": [
-            "anndata_inspect",
             "monocle3_preprocess",
-            "monocle3_topmarkers",
-            "tp_cut_tool",
+            "monocle3_create",
+            "join1",
             "monocle3_partition",
+            "monocle3_plotCells",
+            "monocle3_reduceDim",
             "datamash_transpose",
-            "regexColumn1",
-            "monocle3_learnGraph",
-            "Cut1",
-            "monocle3_diffExp",
             "Filter1",
-            "monocle3_plotCells",
-            "monocle3_create",
-            "join1",
+            "monocle3_diffExp",
             "monocle3_orderCells",
-            "monocle3_reduceDim"
+            "anndata_inspect",
+            "Cut1",
+            "tp_cut_tool",
+            "monocle3_learnGraph",
+            "regexColumn1",
+            "monocle3_topmarkers"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -241866,8 +247416,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 93,
-        "visitors": 2742,
+        "visit_duration": 92,
+        "visitors": 2867,
         "workflows": [
             {
                 "creators": [],
@@ -241944,7 +247494,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAnnData to extract genes & cells annotations\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nAnnData before processing to extract clean expression matrix\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Extract cell annotations\"];\n  0 -->|output| 2;\n  9d66a217-4269-4fb4-9a4e-520eedbb0c9d[\"Output\\nExtracted cell annotations (obs)\"];\n  2 --> 9d66a217-4269-4fb4-9a4e-520eedbb0c9d;\n  style 9d66a217-4269-4fb4-9a4e-520eedbb0c9d stroke:#2c3143,stroke-width:4px;\n  3[\"Extract gene annotations\"];\n  0 -->|output| 3;\n  03537e97-d668-4ce2-ba6b-2952a18a2752[\"Output\\nExtracted gene annotations (var)\"];\n  3 --> 03537e97-d668-4ce2-ba6b-2952a18a2752;\n  style 03537e97-d668-4ce2-ba6b-2952a18a2752 stroke:#2c3143,stroke-width:4px;\n  4[\"Extract clean expression matrix\"];\n  1 -->|output| 4;\n  963462c8-4ae0-486c-8173-d98339127850[\"Output\\nUnprocessed expression matrix\"];\n  4 --> 963462c8-4ae0-486c-8173-d98339127850;\n  style 963462c8-4ae0-486c-8173-d98339127850 stroke:#2c3143,stroke-width:4px;\n  5[\"Filter out unwanted cell types\"];\n  2 -->|obs| 5;\n  5dcb7029-8d03-445d-bb3e-a3119e502be4[\"Output\\nCells without macrophages\"];\n  5 --> 5dcb7029-8d03-445d-bb3e-a3119e502be4;\n  style 5dcb7029-8d03-445d-bb3e-a3119e502be4 stroke:#2c3143,stroke-width:4px;\n  6[\"gene_short_name annotation\"];\n  3 -->|var| 6;\n  15fd415b-2d73-4a1d-92ad-200bb2e73853[\"Output\\nGenes table with gene_short_name colname\"];\n  6 --> 15fd415b-2d73-4a1d-92ad-200bb2e73853;\n  style 15fd415b-2d73-4a1d-92ad-200bb2e73853 stroke:#2c3143,stroke-width:4px;\n  7[\"Cut cells IDs\"];\n  5 -->|out_file1| 7;\n  f9bde249-43b9-4424-8285-e437549223e2[\"Output\\nFiltered cells IDs \"];\n  7 --> f9bde249-43b9-4424-8285-e437549223e2;\n  style f9bde249-43b9-4424-8285-e437549223e2 stroke:#2c3143,stroke-width:4px;\n  8[\"Cut genes IDs\"];\n  6 -->|out_file1| 8;\n  b22efa1d-db99-435f-9357-74150ac9a437[\"Output\\nGenes IDs\"];\n  8 --> b22efa1d-db99-435f-9357-74150ac9a437;\n  style b22efa1d-db99-435f-9357-74150ac9a437 stroke:#2c3143,stroke-width:4px;\n  9[\"Filter matrix by cells\"];\n  7 -->|out_file1| 9;\n  4 -->|X| 9;\n  b45f18b6-e385-41a1-a8f0-f94e6616e2b3[\"Output\\nPre-filtered matrix (by cells)\"];\n  9 --> b45f18b6-e385-41a1-a8f0-f94e6616e2b3;\n  style b45f18b6-e385-41a1-a8f0-f94e6616e2b3 stroke:#2c3143,stroke-width:4px;\n  10[\"Remove duplicate column cells IDs\"];\n  9 -->|out_file1| 10;\n  f4d6a581-9b42-41dc-9a4a-278fe5d6591c[\"Output\\nFiltered matrix (by cells) \"];\n  10 --> f4d6a581-9b42-41dc-9a4a-278fe5d6591c;\n  style f4d6a581-9b42-41dc-9a4a-278fe5d6591c stroke:#2c3143,stroke-width:4px;\n  11[\"Transpose matrix\"];\n  10 -->|output| 11;\n  e4eb8fb3-2028-41fb-8aca-b1c0a6e6bfe5[\"Output\\nfiltered matrix (by cells) transposed\"];\n  11 --> e4eb8fb3-2028-41fb-8aca-b1c0a6e6bfe5;\n  style e4eb8fb3-2028-41fb-8aca-b1c0a6e6bfe5 stroke:#2c3143,stroke-width:4px;\n  12[\"Filter matrix by genes\"];\n  8 -->|out_file1| 12;\n  11 -->|out_file| 12;\n  c0481255-0187-407c-9f29-f4c0069d9285[\"Output\\nPre-filtered matrix (by cells & genes)\"];\n  12 --> c0481255-0187-407c-9f29-f4c0069d9285;\n  style c0481255-0187-407c-9f29-f4c0069d9285 stroke:#2c3143,stroke-width:4px;\n  13[\"Remove duplicate column genes IDs\"];\n  12 -->|out_file1| 13;\n  4dcd8e60-1298-4886-be8f-af1eac9f20f7[\"Output\\nFiltered matrix (by cells & genes)\"];\n  13 --> 4dcd8e60-1298-4886-be8f-af1eac9f20f7;\n  style 4dcd8e60-1298-4886-be8f-af1eac9f20f7 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:25 +0000",
+                "modified": "2024-10-02 12:08:10 +0000",
                 "name": "AnnData object to Monocle input files",
                 "outputs": [
                     {
@@ -242695,7 +248245,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nExpression matrix input\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nCell annotations input\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nGene annotations input\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Monocle3 create\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  2 -->|output| 3;\n  30db218d-f9e5-426d-ac9b-7823743ab5fb[\"Output\\nMonocle3 create on input dataset(s): cds3\"];\n  3 --> 30db218d-f9e5-426d-ac9b-7823743ab5fb;\n  style 30db218d-f9e5-426d-ac9b-7823743ab5fb stroke:#2c3143,stroke-width:4px;\n  4[\"Monocle3 preprocess\"];\n  3 -->|output_rds| 4;\n  38996ee0-0c00-4a01-ad18-f2e505eaf780[\"Output\\nMonocle3 preprocess on input dataset(s): cds3\"];\n  4 --> 38996ee0-0c00-4a01-ad18-f2e505eaf780;\n  style 38996ee0-0c00-4a01-ad18-f2e505eaf780 stroke:#2c3143,stroke-width:4px;\n  5[\"Monocle3 reduceDim\"];\n  4 -->|output_rds| 5;\n  21edf68f-72df-457d-aad7-c5fc5afa2b6b[\"Output\\nMonocle3 reduceDim on input dataset(s): cds3\"];\n  5 --> 21edf68f-72df-457d-aad7-c5fc5afa2b6b;\n  style 21edf68f-72df-457d-aad7-c5fc5afa2b6b stroke:#2c3143,stroke-width:4px;\n  6[\"Monocle3 partition\"];\n  5 -->|output_rds| 6;\n  fdb0e520-27c4-43a0-8f27-a25832a0816d[\"Output\\nMonocle3 partition on input dataset(s): cds3\"];\n  6 --> fdb0e520-27c4-43a0-8f27-a25832a0816d;\n  style fdb0e520-27c4-43a0-8f27-a25832a0816d stroke:#2c3143,stroke-width:4px;\n  7[\"Plot cell type\"];\n  5 -->|output_rds| 7;\n  5e309658-e20f-4da1-8841-818f16fa8f01[\"Output\\nCell type plot\"];\n  7 --> 5e309658-e20f-4da1-8841-818f16fa8f01;\n  style 5e309658-e20f-4da1-8841-818f16fa8f01 stroke:#2c3143,stroke-width:4px;\n  8[\"Plot genotype\"];\n  5 -->|output_rds| 8;\n  aca3b2c0-2d3b-4a4e-8732-cf6ddc7844a4[\"Output\\nGenotype plot\"];\n  8 --> aca3b2c0-2d3b-4a4e-8732-cf6ddc7844a4;\n  style aca3b2c0-2d3b-4a4e-8732-cf6ddc7844a4 stroke:#2c3143,stroke-width:4px;\n  9[\"Plot batch\"];\n  5 -->|output_rds| 9;\n  c8eec2e4-1a64-47bb-812b-4002968c57c8[\"Output\\nBatch plot\"];\n  9 --> c8eec2e4-1a64-47bb-812b-4002968c57c8;\n  style c8eec2e4-1a64-47bb-812b-4002968c57c8 stroke:#2c3143,stroke-width:4px;\n  10[\"Plot sex\"];\n  5 -->|output_rds| 10;\n  c75954dd-34d5-4a20-bcf3-e5cd92d74885[\"Output\\nSex plot\"];\n  10 --> c75954dd-34d5-4a20-bcf3-e5cd92d74885;\n  style c75954dd-34d5-4a20-bcf3-e5cd92d74885 stroke:#2c3143,stroke-width:4px;\n  11[\"Monocle3 top markers\"];\n  6 -->|output_rds| 11;\n  12[\"Plot genes\"];\n  6 -->|output_rds| 12;\n  f91c22a3-8c6d-432a-92c5-cb010115fa86[\"Output\\nGene expression plot\"];\n  12 --> f91c22a3-8c6d-432a-92c5-cb010115fa86;\n  style f91c22a3-8c6d-432a-92c5-cb010115fa86 stroke:#2c3143,stroke-width:4px;\n  13[\"Plot partition\"];\n  6 -->|output_rds| 13;\n  f4c5f89b-edd7-489c-b4a2-a7a3e7d6a89d[\"Output\\nPartition plot\"];\n  13 --> f4c5f89b-edd7-489c-b4a2-a7a3e7d6a89d;\n  style f4c5f89b-edd7-489c-b4a2-a7a3e7d6a89d stroke:#2c3143,stroke-width:4px;\n  14[\"Plot cluster\"];\n  6 -->|output_rds| 14;\n  a2c1a628-d79d-4e37-ad33-de92033021a8[\"Output\\nCluster plot\"];\n  14 --> a2c1a628-d79d-4e37-ad33-de92033021a8;\n  style a2c1a628-d79d-4e37-ad33-de92033021a8 stroke:#2c3143,stroke-width:4px;\n  15[\"Monocle3 learnGraph\"];\n  6 -->|output_rds| 15;\n  ed2003aa-4680-409f-8d79-e79b878a786c[\"Output\\nMonocle3 learnGraph on input dataset(s): cds3\"];\n  15 --> ed2003aa-4680-409f-8d79-e79b878a786c;\n  style ed2003aa-4680-409f-8d79-e79b878a786c stroke:#2c3143,stroke-width:4px;\n  16[\"Plot learned trajectory\"];\n  15 -->|output_rds| 16;\n  6fa555f1-b4f2-4e5d-bce1-ed462d8e056d[\"Output\\nCell types & learned trajectory path plot\"];\n  16 --> 6fa555f1-b4f2-4e5d-bce1-ed462d8e056d;\n  style 6fa555f1-b4f2-4e5d-bce1-ed462d8e056d stroke:#2c3143,stroke-width:4px;\n  17[\"Monocle3 orderCells\"];\n  15 -->|output_rds| 17;\n  96d10412-3d7f-4970-b541-6f4367fa3f37[\"Output\\nMonocle3 orderCells on input dataset(s): cds3\"];\n  17 --> 96d10412-3d7f-4970-b541-6f4367fa3f37;\n  style 96d10412-3d7f-4970-b541-6f4367fa3f37 stroke:#2c3143,stroke-width:4px;\n  18[\"Monocle3 diffExp\"];\n  17 -->|output_rds| 18;\n  db1dc457-2d6e-47cc-b7ce-d0a4d23e9498[\"Output\\nDifferential expression of genes - table\"];\n  18 --> db1dc457-2d6e-47cc-b7ce-d0a4d23e9498;\n  style db1dc457-2d6e-47cc-b7ce-d0a4d23e9498 stroke:#2c3143,stroke-width:4px;\n  19[\"Plot pseudotime\"];\n  17 -->|output_rds| 19;\n  d1b3efd2-0a81-4dad-8652-589c2678fbaa[\"Output\\nPseudotime plot\"];\n  19 --> d1b3efd2-0a81-4dad-8652-589c2678fbaa;\n  style d1b3efd2-0a81-4dad-8652-589c2678fbaa stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:25 +0000",
+                "modified": "2024-10-02 12:08:10 +0000",
                 "name": "Monocle3 workflow",
                 "outputs": [
                     {
@@ -243679,7 +249229,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAnnData to extract genes & cells annotations\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nAnnData before processing to extract clean expression matrix\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Extract cell annotations\"];\n  0 -->|output| 2;\n  0646798d-3a5d-420a-a7cf-cde6cec722d5[\"Output\\nExtracted cell annotations (obs)\"];\n  2 --> 0646798d-3a5d-420a-a7cf-cde6cec722d5;\n  style 0646798d-3a5d-420a-a7cf-cde6cec722d5 stroke:#2c3143,stroke-width:4px;\n  3[\"Extract gene annotations\"];\n  0 -->|output| 3;\n  84162745-68b0-41a5-b06e-a285440ba095[\"Output\\nExtracted gene annotations (var)\"];\n  3 --> 84162745-68b0-41a5-b06e-a285440ba095;\n  style 84162745-68b0-41a5-b06e-a285440ba095 stroke:#2c3143,stroke-width:4px;\n  4[\"Extract clean expression matrix\"];\n  1 -->|output| 4;\n  3f03af0c-ac41-4450-b5ba-639a79ea543b[\"Output\\nUnprocessed expression matrix\"];\n  4 --> 3f03af0c-ac41-4450-b5ba-639a79ea543b;\n  style 3f03af0c-ac41-4450-b5ba-639a79ea543b stroke:#2c3143,stroke-width:4px;\n  5[\"Filter out macrophages\"];\n  2 -->|obs| 5;\n  fb81e9a1-0603-419a-83f5-0c9f94939b16[\"Output\\nCells without macrophages\"];\n  5 --> fb81e9a1-0603-419a-83f5-0c9f94939b16;\n  style fb81e9a1-0603-419a-83f5-0c9f94939b16 stroke:#2c3143,stroke-width:4px;\n  6[\"gene_short_name annotation\"];\n  3 -->|var| 6;\n  94a60e6c-cdf7-48e5-8b55-d221cef22688[\"Output\\nGenes table with gene_short_name colname\"];\n  6 --> 94a60e6c-cdf7-48e5-8b55-d221cef22688;\n  style 94a60e6c-cdf7-48e5-8b55-d221cef22688 stroke:#2c3143,stroke-width:4px;\n  7[\"Cut cells IDs\"];\n  5 -->|out_file1| 7;\n  34146c30-2666-481f-8d49-a849d5d3aa91[\"Output\\nFiltered cells IDs \"];\n  7 --> 34146c30-2666-481f-8d49-a849d5d3aa91;\n  style 34146c30-2666-481f-8d49-a849d5d3aa91 stroke:#2c3143,stroke-width:4px;\n  8[\"Cut genes IDs\"];\n  6 -->|out_file1| 8;\n  8f38fb93-cb30-4fbc-90c5-7f6bd023feea[\"Output\\nGenes IDs\"];\n  8 --> 8f38fb93-cb30-4fbc-90c5-7f6bd023feea;\n  style 8f38fb93-cb30-4fbc-90c5-7f6bd023feea stroke:#2c3143,stroke-width:4px;\n  9[\"Filter matrix by cells\"];\n  7 -->|out_file1| 9;\n  4 -->|X| 9;\n  f654c045-5fea-43f9-96d6-492c810593d2[\"Output\\nPre-filtered matrix (by cells)\"];\n  9 --> f654c045-5fea-43f9-96d6-492c810593d2;\n  style f654c045-5fea-43f9-96d6-492c810593d2 stroke:#2c3143,stroke-width:4px;\n  10[\"Remove duplicate column cells IDs\"];\n  9 -->|out_file1| 10;\n  f633c125-a4d0-4fa7-ab87-022349f4ac70[\"Output\\nFiltered matrix (by cells) \"];\n  10 --> f633c125-a4d0-4fa7-ab87-022349f4ac70;\n  style f633c125-a4d0-4fa7-ab87-022349f4ac70 stroke:#2c3143,stroke-width:4px;\n  11[\"Transpose matrix\"];\n  10 -->|output| 11;\n  3202091e-1afc-4f50-8922-1f9e50c490fc[\"Output\\nfiltered matrix (by cells) transposed\"];\n  11 --> 3202091e-1afc-4f50-8922-1f9e50c490fc;\n  style 3202091e-1afc-4f50-8922-1f9e50c490fc stroke:#2c3143,stroke-width:4px;\n  12[\"Filter matrix by genes\"];\n  8 -->|out_file1| 12;\n  11 -->|out_file| 12;\n  6c23cbd5-a1b5-428e-8ff9-ebac4893ad88[\"Output\\nPre-filtered matrix (by cells & genes)\"];\n  12 --> 6c23cbd5-a1b5-428e-8ff9-ebac4893ad88;\n  style 6c23cbd5-a1b5-428e-8ff9-ebac4893ad88 stroke:#2c3143,stroke-width:4px;\n  13[\"Remove duplicate column genes IDs\"];\n  12 -->|out_file1| 13;\n  25839326-0b5d-4e74-91ec-24e22c08f7c5[\"Output\\nFiltered matrix (by cells & genes)\"];\n  13 --> 25839326-0b5d-4e74-91ec-24e22c08f7c5;\n  style 25839326-0b5d-4e74-91ec-24e22c08f7c5 stroke:#2c3143,stroke-width:4px;\n  14[\"Monocle3 create\"];\n  5 -->|out_file1| 14;\n  13 -->|output| 14;\n  6 -->|out_file1| 14;\n  f8c5589c-a70d-416e-a9de-ebc987f61fc3[\"Output\\nMonocle3 create on input dataset(s): cds3\"];\n  14 --> f8c5589c-a70d-416e-a9de-ebc987f61fc3;\n  style f8c5589c-a70d-416e-a9de-ebc987f61fc3 stroke:#2c3143,stroke-width:4px;\n  15[\"Monocle3 preprocess\"];\n  14 -->|output_rds| 15;\n  c134942f-60e7-4cd0-8c32-da4a303b879d[\"Output\\nMonocle3 preprocess on input dataset(s): cds3\"];\n  15 --> c134942f-60e7-4cd0-8c32-da4a303b879d;\n  style c134942f-60e7-4cd0-8c32-da4a303b879d stroke:#2c3143,stroke-width:4px;\n  16[\"Monocle3 reduceDim\"];\n  15 -->|output_rds| 16;\n  2c9fb108-2a1c-41df-a8d8-81a18b66d2a1[\"Output\\nMonocle3 reduceDim on input dataset(s): cds3\"];\n  16 --> 2c9fb108-2a1c-41df-a8d8-81a18b66d2a1;\n  style 2c9fb108-2a1c-41df-a8d8-81a18b66d2a1 stroke:#2c3143,stroke-width:4px;\n  17[\"Monocle3 partition\"];\n  16 -->|output_rds| 17;\n  93371c10-6583-47fc-830f-9a90dc980766[\"Output\\nMonocle3 partition on input dataset(s): cds3\"];\n  17 --> 93371c10-6583-47fc-830f-9a90dc980766;\n  style 93371c10-6583-47fc-830f-9a90dc980766 stroke:#2c3143,stroke-width:4px;\n  18[\"Plot cell type\"];\n  16 -->|output_rds| 18;\n  f096d060-82e8-4847-9e8f-b22c9288f565[\"Output\\nCell type plot\"];\n  18 --> f096d060-82e8-4847-9e8f-b22c9288f565;\n  style f096d060-82e8-4847-9e8f-b22c9288f565 stroke:#2c3143,stroke-width:4px;\n  19[\"Plot genotype\"];\n  16 -->|output_rds| 19;\n  aab28bb1-e2e7-4b7d-9b2b-1cab64bea287[\"Output\\nGenotype plot\"];\n  19 --> aab28bb1-e2e7-4b7d-9b2b-1cab64bea287;\n  style aab28bb1-e2e7-4b7d-9b2b-1cab64bea287 stroke:#2c3143,stroke-width:4px;\n  20[\"Plot batch\"];\n  16 -->|output_rds| 20;\n  9b362eee-9238-47c5-a4c2-85f3995430f4[\"Output\\nBatch plot\"];\n  20 --> 9b362eee-9238-47c5-a4c2-85f3995430f4;\n  style 9b362eee-9238-47c5-a4c2-85f3995430f4 stroke:#2c3143,stroke-width:4px;\n  21[\"Plot sex\"];\n  16 -->|output_rds| 21;\n  c2a1e104-ef2d-4b66-ac2b-bf0251714434[\"Output\\nSex plot\"];\n  21 --> c2a1e104-ef2d-4b66-ac2b-bf0251714434;\n  style c2a1e104-ef2d-4b66-ac2b-bf0251714434 stroke:#2c3143,stroke-width:4px;\n  22[\"Monocle3 top markers\"];\n  17 -->|output_rds| 22;\n  23[\"Plot genes\"];\n  17 -->|output_rds| 23;\n  e8867379-82c6-4c32-a2d3-0b24670269ae[\"Output\\nGene expression plot\"];\n  23 --> e8867379-82c6-4c32-a2d3-0b24670269ae;\n  style e8867379-82c6-4c32-a2d3-0b24670269ae stroke:#2c3143,stroke-width:4px;\n  24[\"Plot partition\"];\n  17 -->|output_rds| 24;\n  3f7b0a7c-85d6-430b-8385-fa9a76385c0e[\"Output\\nPartition plot\"];\n  24 --> 3f7b0a7c-85d6-430b-8385-fa9a76385c0e;\n  style 3f7b0a7c-85d6-430b-8385-fa9a76385c0e stroke:#2c3143,stroke-width:4px;\n  25[\"Plot cluster\"];\n  17 -->|output_rds| 25;\n  40b65826-f73e-4054-a56d-b241985d6996[\"Output\\nCluster plot\"];\n  25 --> 40b65826-f73e-4054-a56d-b241985d6996;\n  style 40b65826-f73e-4054-a56d-b241985d6996 stroke:#2c3143,stroke-width:4px;\n  26[\"Monocle3 learnGraph\"];\n  17 -->|output_rds| 26;\n  294b1a49-cec6-49d0-bcd4-3a954da67bec[\"Output\\nMonocle3 learnGraph on input dataset(s): cds3\"];\n  26 --> 294b1a49-cec6-49d0-bcd4-3a954da67bec;\n  style 294b1a49-cec6-49d0-bcd4-3a954da67bec stroke:#2c3143,stroke-width:4px;\n  27[\"Plot learned trajectory\"];\n  26 -->|output_rds| 27;\n  c85ddefe-8eaf-4d21-93ed-ca0859286bf0[\"Output\\nCell types & learned trajectory path plot\"];\n  27 --> c85ddefe-8eaf-4d21-93ed-ca0859286bf0;\n  style c85ddefe-8eaf-4d21-93ed-ca0859286bf0 stroke:#2c3143,stroke-width:4px;\n  28[\"Monocle3 orderCells\"];\n  26 -->|output_rds| 28;\n  5aea5752-b767-4fc8-8741-1f4d1c659a41[\"Output\\nMonocle3 orderCells on input dataset(s): cds3\"];\n  28 --> 5aea5752-b767-4fc8-8741-1f4d1c659a41;\n  style 5aea5752-b767-4fc8-8741-1f4d1c659a41 stroke:#2c3143,stroke-width:4px;\n  29[\"Monocle3 diffExp\"];\n  28 -->|output_rds| 29;\n  3c298624-9f06-4e52-b2a8-fb834b87c296[\"Output\\nDifferential expression of genes - table\"];\n  29 --> 3c298624-9f06-4e52-b2a8-fb834b87c296;\n  style 3c298624-9f06-4e52-b2a8-fb834b87c296 stroke:#2c3143,stroke-width:4px;\n  30[\"Plot pseudotime\"];\n  28 -->|output_rds| 30;\n  813d15bb-0771-4aed-9226-4874c1ddba59[\"Output\\nPseudotime plot\"];\n  30 --> 813d15bb-0771-4aed-9226-4874c1ddba59;\n  style 813d15bb-0771-4aed-9226-4874c1ddba59 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:25 +0000",
+                "modified": "2024-10-02 12:08:10 +0000",
                 "name": "Trajectory analysis using Monocle3 - full tutorial workflow",
                 "outputs": [
                     {
@@ -244800,441 +250350,1714 @@
                         "name": "Monocle3 plotCells",
                         "outputs": [
                             {
-                                "name": "output_tsv",
-                                "type": "png"
+                                "name": "output_tsv",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 1774.0750000000003,
+                            "top": 548.3625
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_tsv": {
+                                "action_arguments": {
+                                    "newname": "Gene expression plot"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_tsv"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "91980addce5e",
+                            "name": "monocle3_plotcells",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"alpha\": \"1.0\", \"cell_size\": \"1.5\", \"color_cells_by\": \"cell_type\", \"genes\": \"Il2ra,Cd8b1,Cd8a,Cd4,Itm2a,Aif1,Hba-a1\", \"input_object_file\": {\"__class__\": \"ConnectedValue\"}, \"input_object_format\": \"cds3\", \"label_branch_points\": false, \"label_cell_groups\": true, \"label_groups_by_cluster\": false, \"label_leaves\": false, \"label_roots\": false, \"no_trajectory_graph\": false, \"norm_method\": \"log\", \"reduction_method\": \"UMAP\", \"verbose\": false, \"xdim\": \"1\", \"ydim\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "daea9f03-93e9-4af4-911c-f3fc73086560",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Gene expression plot",
+                                "output_name": "output_tsv",
+                                "uuid": "e8867379-82c6-4c32-a2d3-0b24670269ae"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
+                        "errors": null,
+                        "id": 24,
+                        "input_connections": {
+                            "input_object_file": {
+                                "id": 17,
+                                "output_name": "output_rds"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Plot partition",
+                        "name": "Monocle3 plotCells",
+                        "outputs": [
+                            {
+                                "name": "output_tsv",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 1773.85,
+                            "top": 694.45
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_tsv": {
+                                "action_arguments": {
+                                    "newname": "Partition plot"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_tsv"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "91980addce5e",
+                            "name": "monocle3_plotcells",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"alpha\": \"1.0\", \"cell_size\": \"1.5\", \"color_cells_by\": \"partition\", \"genes\": \"\", \"input_object_file\": {\"__class__\": \"ConnectedValue\"}, \"input_object_format\": \"cds3\", \"label_branch_points\": false, \"label_cell_groups\": true, \"label_groups_by_cluster\": false, \"label_leaves\": false, \"label_roots\": false, \"no_trajectory_graph\": false, \"norm_method\": \"log\", \"reduction_method\": \"UMAP\", \"verbose\": false, \"xdim\": \"1\", \"ydim\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "99fa4062-74c2-4236-94f0-e3e3dc85c7a2",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Partition plot",
+                                "output_name": "output_tsv",
+                                "uuid": "3f7b0a7c-85d6-430b-8385-fa9a76385c0e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
+                        "errors": null,
+                        "id": 25,
+                        "input_connections": {
+                            "input_object_file": {
+                                "id": 17,
+                                "output_name": "output_rds"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Plot cluster",
+                        "name": "Monocle3 plotCells",
+                        "outputs": [
+                            {
+                                "name": "output_tsv",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 1774.7625000000003,
+                            "top": 824.4875
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_tsv": {
+                                "action_arguments": {
+                                    "newname": "Cluster plot"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_tsv"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "91980addce5e",
+                            "name": "monocle3_plotcells",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"alpha\": \"1.0\", \"cell_size\": \"1.5\", \"color_cells_by\": \"cluster\", \"genes\": \"\", \"input_object_file\": {\"__class__\": \"ConnectedValue\"}, \"input_object_format\": \"cds3\", \"label_branch_points\": false, \"label_cell_groups\": true, \"label_groups_by_cluster\": false, \"label_leaves\": false, \"label_roots\": false, \"no_trajectory_graph\": false, \"norm_method\": \"log\", \"reduction_method\": \"UMAP\", \"verbose\": false, \"xdim\": \"1\", \"ydim\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "935fbc13-4775-48d9-bfda-96e065df3cbd",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Cluster plot",
+                                "output_name": "output_tsv",
+                                "uuid": "40b65826-f73e-4054-a56d-b241985d6996"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_learngraph/monocle3_learnGraph/0.1.4+galaxy0",
+                        "errors": null,
+                        "id": 26,
+                        "input_connections": {
+                            "input_object_file": {
+                                "id": 17,
+                                "output_name": "output_rds"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Monocle3 learnGraph",
+                        "outputs": [
+                            {
+                                "name": "output_rds",
+                                "type": "rdata"
+                            }
+                        ],
+                        "position": {
+                            "left": 1775.6375000000003,
+                            "top": 953.375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_learngraph/monocle3_learnGraph/0.1.4+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "5f877012f7af",
+                            "name": "monocle3_learngraph",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"euclidean_distance_ratio\": \"1.0\", \"geodesic_distance_ratio\": \"0.33\", \"input_object_file\": {\"__class__\": \"ConnectedValue\"}, \"input_object_format\": \"cds3\", \"introspective\": true, \"minimal_branch_len\": \"10\", \"no_close_loop\": false, \"no_partition\": false, \"no_prune_graph\": false, \"orthogonal_proj_tip\": false, \"output_object_format\": \"cds3\", \"verbose\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.4+galaxy0",
+                        "type": "tool",
+                        "uuid": "2afce1c2-6bd3-475c-88fd-7377a1698c24",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Monocle3 learnGraph on input dataset(s): cds3",
+                                "output_name": "output_rds",
+                                "uuid": "294b1a49-cec6-49d0-bcd4-3a954da67bec"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
+                        "errors": null,
+                        "id": 27,
+                        "input_connections": {
+                            "input_object_file": {
+                                "id": 26,
+                                "output_name": "output_rds"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Plot learned trajectory",
+                        "name": "Monocle3 plotCells",
+                        "outputs": [
+                            {
+                                "name": "output_tsv",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 2026.0750000000003,
+                            "top": 803.0125
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_tsv": {
+                                "action_arguments": {
+                                    "newname": "Learned trajectory plot"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_tsv"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "91980addce5e",
+                            "name": "monocle3_plotcells",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"alpha\": \"1.0\", \"cell_size\": \"1.5\", \"color_cells_by\": \"cell_type\", \"genes\": \"\", \"input_object_file\": {\"__class__\": \"ConnectedValue\"}, \"input_object_format\": \"cds3\", \"label_branch_points\": false, \"label_cell_groups\": true, \"label_groups_by_cluster\": false, \"label_leaves\": false, \"label_roots\": false, \"no_trajectory_graph\": false, \"norm_method\": \"log\", \"reduction_method\": \"UMAP\", \"verbose\": false, \"xdim\": \"1\", \"ydim\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "7284b7d6-792e-4e3e-b23a-9733ce8ba001",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Cell types & learned trajectory path plot",
+                                "output_name": "output_tsv",
+                                "uuid": "c85ddefe-8eaf-4d21-93ed-ca0859286bf0"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_ordercells/monocle3_orderCells/0.1.4+galaxy0",
+                        "errors": null,
+                        "id": 28,
+                        "input_connections": {
+                            "input_object_file": {
+                                "id": 26,
+                                "output_name": "output_rds"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Monocle3 orderCells",
+                        "outputs": [
+                            {
+                                "name": "output_rds",
+                                "type": "rdata"
+                            }
+                        ],
+                        "position": {
+                            "left": 2029.7000000000003,
+                            "top": 953.675
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_ordercells/monocle3_orderCells/0.1.4+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3e77dc421569",
+                            "name": "monocle3_ordercells",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"cell_phenotype\": \"cell_type\", \"input_object_file\": {\"__class__\": \"ConnectedValue\"}, \"input_object_format\": \"cds3\", \"introspective\": true, \"output_object_format\": \"cds3\", \"reduction_method\": \"UMAP\", \"root_cells\": \"\", \"root_pr_nodes\": \"\", \"root_type\": \"DN\", \"verbose\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.4+galaxy0",
+                        "type": "tool",
+                        "uuid": "e8c75441-228e-4a64-b80a-16c9dd763169",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Monocle3 orderCells on input dataset(s): cds3",
+                                "output_name": "output_rds",
+                                "uuid": "5aea5752-b767-4fc8-8741-1f4d1c659a41"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_diffexp/monocle3_diffExp/0.1.4+galaxy1",
+                        "errors": null,
+                        "id": 29,
+                        "input_connections": {
+                            "input_object_file": {
+                                "id": 28,
+                                "output_name": "output_rds"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Monocle3 diffExp",
+                        "outputs": [
+                            {
+                                "name": "output_tsv",
+                                "type": "tsv"
+                            }
+                        ],
+                        "position": {
+                            "left": 2274.4500000000003,
+                            "top": 828.1875
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_tsv": {
+                                "action_arguments": {
+                                    "newname": "Differential expression of genes - table"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_tsv"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_diffexp/monocle3_diffExp/0.1.4+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "d43a608d14ac",
+                            "name": "monocle3_diffexp",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"alternative\": \"greater\", \"input_object_file\": {\"__class__\": \"ConnectedValue\"}, \"input_object_format\": \"cds3\", \"knn\": \"20\", \"method\": \"Moran_I\", \"neighbor_graph\": \"knn\", \"reduction_method\": \"UMAP\", \"verbose\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.4+galaxy1",
+                        "type": "tool",
+                        "uuid": "6a7d9923-d68b-411b-a0e5-d1bf4716f7b1",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Differential expression of genes - table",
+                                "output_name": "output_tsv",
+                                "uuid": "3c298624-9f06-4e52-b2a8-fb834b87c296"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
+                        "errors": null,
+                        "id": 30,
+                        "input_connections": {
+                            "input_object_file": {
+                                "id": 28,
+                                "output_name": "output_rds"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Plot pseudotime",
+                        "name": "Monocle3 plotCells",
+                        "outputs": [
+                            {
+                                "name": "output_tsv",
+                                "type": "png"
+                            }
+                        ],
+                        "position": {
+                            "left": 2278.7625000000003,
+                            "top": 975.175
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput_tsv": {
+                                "action_arguments": {
+                                    "newname": "Pseudotime plot"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output_tsv"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "91980addce5e",
+                            "name": "monocle3_plotcells",
+                            "owner": "ebi-gxa",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"alpha\": \"1.0\", \"cell_size\": \"1.5\", \"color_cells_by\": \"pseudotime\", \"genes\": \"\", \"input_object_file\": {\"__class__\": \"ConnectedValue\"}, \"input_object_format\": \"cds3\", \"label_branch_points\": false, \"label_cell_groups\": true, \"label_groups_by_cluster\": false, \"label_leaves\": false, \"label_roots\": false, \"no_trajectory_graph\": false, \"norm_method\": \"log\", \"reduction_method\": \"UMAP\", \"verbose\": false, \"xdim\": \"1\", \"ydim\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.5+galaxy1",
+                        "type": "tool",
+                        "uuid": "1f9b4306-ec3c-4b2d-9c0e-40a2589afd1d",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Pseudotime plot",
+                                "output_name": "output_tsv",
+                                "uuid": "813d15bb-0771-4aed-9226-4874c1ddba59"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "single-cell/scrna-case_monocle3-trajectories",
+                "path": "topics/single-cell/tutorials/scrna-case_monocle3-trajectories/workflows/Trajectory-analysis-using-Monocle3---full-tutorial-workflow.ga",
+                "tags": [
+                    "name:trajectory_analysis",
+                    "name:transcriptomics",
+                    "name:scRNA-seq",
+                    "name:single_cell"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "Trajectory analysis using Monocle3 - full tutorial workflow",
+                "topic_id": "single-cell",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-case_monocle3-trajectories/versions/trajectory-analysis-using-monocle3---full-tutorial-workflow",
+                "tutorial_id": "scrna-case_monocle3-trajectories",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/workflows/Trajectory-analysis-using-Monocle3---full-tutorial-workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/workflows/Trajectory-analysis-using-Monocle3---full-tutorial-workflow.html",
+                "version": 1,
+                "wfid": "single-cell-scrna-case_monocle3-trajectories",
+                "wfname": "trajectory-analysis-using-monocle3---full-tutorial-workflow",
+                "workflow": "Trajectory-analysis-using-Monocle3---full-tutorial-workflow.ga",
+                "workflow_tools": [
+                    "Cut1",
+                    "Filter1",
+                    "join1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_create/monocle3_create/0.1.4+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_diffexp/monocle3_diffExp/0.1.4+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_learngraph/monocle3_learnGraph/0.1.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_ordercells/monocle3_orderCells/0.1.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_partition/monocle3_partition/0.1.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_preprocess/monocle3_preprocess/0.1.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_reducedim/monocle3_reduceDim/0.1.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_topmarkers/monocle3_topmarkers/0.1.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2"
+                ],
+                "workflowhub_id": "1228"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/records/10397366"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "music_construct_eset",
+                    "owner": "bgruening",
+                    "revisions": "282819d09a4f",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "music_manipulate_eset",
+                    "owner": "bgruening",
+                    "revisions": "22232092be53",
+                    "tool_panel_section_label": "Single-cell",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "regex_find_replace",
+                    "owner": "galaxyp",
+                    "revisions": "399da6b5ec21",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "annotatemyids",
+                    "owner": "iuc",
+                    "revisions": "fe3ca740a485",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "column_remove_by_header",
+                    "owner": "iuc",
+                    "revisions": "2040e4c2750a",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "table_compute",
+                    "owner": "iuc",
+                    "revisions": "3bf5661c0280",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: music_construct_eset\n  owner: bgruening\n  revisions: 282819d09a4f\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: music_manipulate_eset\n  owner: bgruening\n  revisions: 22232092be53\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: 399da6b5ec21\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: annotatemyids\n  owner: iuc\n  revisions: fe3ca740a485\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_remove_by_header\n  owner: iuc\n  revisions: 2040e4c2750a\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: table_compute\n  owner: iuc\n  revisions: 3bf5661c0280\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "nomadscientist",
+                "mtekman"
+            ],
+            "testing": [
+                "MarisaJL"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "bio": "Senior Lecturer at The Open University",
+                "elixir_node": "uk",
+                "email": "wendi.bacon@open.ac.uk",
+                "fediverse": "https://mstdn.science/@wendibacon1",
+                "fediverse_flavor": "mastodon",
+                "id": "nomadscientist",
+                "joined": "2020-03",
+                "matrix": "nomadscientist:matrix.org",
+                "name": "Wendi Bacon",
+                "orcid": "0000-0002-8170-8806",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/",
+                "twitter": "WendiBacon1",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nomadscientist.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "elixir_node": "de",
+                "email": "mtekman89@gmail.com",
+                "former_affiliations": [
+                    "elixir-europe"
+                ],
+                "id": "mtekman",
+                "joined": "2018-11",
+                "name": "Mehmet Tekman",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mtekman.json"
+            },
+            {
+                "email": "marisa.loach@open.ac.uk",
+                "id": "MarisaJL",
+                "joined": "2022-10",
+                "name": "Marisa Loach",
+                "orcid": "0000-0001-6979-6930",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/MarisaJL/",
+                "twitter": "Marisa_Loach",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/MarisaJL.json"
+            }
+        ],
+        "dir": "topics/single-cell/tutorials/bulk-music-3-preparebulk",
+        "edam_operation": [
+            "Annotation"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "bulk-music-4-compare"
+                ],
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "single-cell/bulk-music-3-preparebulk",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "The EMBL-EBI Expression Atlas contains high quality datasets.",
+            "Metadata manipulation is key for generating the correctly formatted resource."
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-02-13",
+        "objectives": [
+            "You will retrieve raw data from the EMBL-EBI Expression Atlas.",
+            "You will manipulate the metadata and matrix files.",
+            "You will combine the metadata and matrix files into an ESet object for MuSiC deconvolution.",
+            "You will create multiple ESet objects - both combined and separated out by disease phenotype for your bulk dataset."
+        ],
+        "pageviews": 877,
+        "priority": 5,
+        "pub_date": "2023-01-20",
+        "questions": [
+            "Where can I find good quality RNA-seq datasets?",
+            "How can I reformat and manipulate these downloads to create the right format for MuSiC?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "single-cell",
+                "tutorials": [
+                    "bulk-music",
+                    "bulk-music-2-preparescref"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00242",
+        "short_tools": [
+            "music_manipulate_eset",
+            "annotatemyids",
+            "tp_sed_tool",
+            "table_compute",
+            "tp_easyjoin_tool",
+            "sort1",
+            "column_remove_by_header",
+            "tp_awk_tool",
+            "music_construct_eset",
+            "tp_cut_tool",
+            "regex1"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "datamanipulation",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "transcriptomics",
+            "data management"
+        ],
+        "time_estimation": "1H",
+        "title": "Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution",
+        "tools": [
+            "sort1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0"
+        ],
+        "topic_name": "single-cell",
+        "topic_name_human": "Single Cell",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "bulk-music-3-preparebulk",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/bulk-music-3-preparebulk/tutorial.json"
+        },
+        "version": 8,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 103,
+        "visitors": 490,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-8170-8806",
+                        "name": "Wendi Bacon"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0002-4181-2676",
+                        "name": "Mehmet Tekman"
+                    }
+                ],
+                "description": "This workflow creates bulk ESet objects from uploaded raw matrix &amp; metadata files",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": true
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Expression matrix\"]\n  1[label=\"Metadata\"]\n  2[label=\"annotateMyIDs\"]\n  0 -> 2 [label=\"output_tabular\"]\n  k8415bac06beb467da0fafb6465987ff7[color=lightseagreen,label=\"Output\\nannotateMyIDs on input dataset(s): Annotated IDs\"]\n  2 -> k8415bac06beb467da0fafb6465987ff7\n  3[label=\"Regex Find And Replace\"]\n  1 -> 3 [label=\"output\"]\n  4[color=lightcoral,label=\"\ud83d\udee0\ufe0f Subworkflow\\nCopy of Convert from Ensembl to GeneSymbol, summing duplicate genes\"]\n  2 -> 4 [label=\"out_tab\"]\n  0 -> 4 [label=\"output_tabular\"]\n  5[label=\"Construct Expression Set Object\"]\n  4 -> 5 [label=\"Gene Symbol Count Matrix\"]\n  3 -> 5 [label=\"out_file1\"]\n  6[label=\"Manipulate Expression Set Object\"]\n  5 -> 6 [label=\"out_rds\"]\n  k88196d0b72544794b08a5409f19c8323[color=lightseagreen,label=\"Output\\nManipulate Expression Set Object on input dataset(s): ExpressionSet Object\"]\n  6 -> k88196d0b72544794b08a5409f19c8323\n  7[label=\"Manipulate Expression Set Object\"]\n  5 -> 7 [label=\"out_rds\"]\n}",
+                "history": [
+                    {
+                        "hash": "9a561b3752745eab20cececd5346ee0a7449da28",
+                        "message": "update workflows",
+                        "num": 1,
+                        "short_hash": "9a561b375",
+                        "unix": "1669581042"
+                    }
+                ],
+                "inputs": [],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"Expression matrix\"];\n  1[\"Metadata\"];\n  2[\"annotateMyIDs\"];\n  0 -->|output_tabular| 2;\n  8415bac0-6beb-467d-a0fa-fb6465987ff7[\"Output\\nannotateMyIDs on input dataset(s): Annotated IDs\"];\n  2 --> 8415bac0-6beb-467d-a0fa-fb6465987ff7;\n  style 8415bac0-6beb-467d-a0fa-fb6465987ff7 stroke:#2c3143,stroke-width:4px;\n  3[\"Regex Find And Replace\"];\n  1 -->|output| 3;\n  4[\"\ud83d\udee0\ufe0f Subworkflow\\nCopy of Convert from Ensembl to GeneSymbol, summing duplicate genes\"];\n  style 4 fill:#edd,stroke:#900,stroke-width:4px;\n  2 -->|out_tab| 4;\n  0 -->|output_tabular| 4;\n  5[\"Construct Expression Set Object\"];\n  4 -->|Gene Symbol Count Matrix| 5;\n  3 -->|out_file1| 5;\n  6[\"Manipulate Expression Set Object\"];\n  5 -->|out_rds| 6;\n  88196d0b-7254-4794-b08a-5409f19c8323[\"Output\\nManipulate Expression Set Object on input dataset(s): ExpressionSet Object\"];\n  6 --> 88196d0b-7254-4794-b08a-5409f19c8323;\n  style 88196d0b-7254-4794-b08a-5409f19c8323 stroke:#2c3143,stroke-width:4px;\n  7[\"Manipulate Expression Set Object\"];\n  5 -->|out_rds| 7;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "MuSiC-Deconvolution: Data generation | bulk | ESet",
+                "outputs": [
+                    {
+                        "annotation": "While the EBI data has the gene symbols in it, these are duplicated, so we still need to thin down the duplications.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0",
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Remove columns",
+                                "name": "input_tabular"
+                            }
+                        ],
+                        "label": "Expression matrix",
+                        "name": "Remove columns",
+                        "outputs": [
+                            {
+                                "name": "output_tabular",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1774.0750000000003,
-                            "top": 548.3625
+                            "left": 0.0,
+                            "top": 262.5
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput_tsv": {
+                            "TagDatasetActionoutput_tabular": {
                                 "action_arguments": {
-                                    "newname": "Gene expression plot"
+                                    "tags": "#bulk,#ebi,#matrix"
                                 },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_tsv"
+                                "action_type": "TagDatasetAction",
+                                "output_name": "output_tabular"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "91980addce5e",
-                            "name": "monocle3_plotcells",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "2040e4c2750a",
+                            "name": "column_remove_by_header",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"alpha\": \"1.0\", \"cell_size\": \"1.5\", \"color_cells_by\": \"cell_type\", \"genes\": \"Il2ra,Cd8b1,Cd8a,Cd4,Itm2a,Aif1,Hba-a1\", \"input_object_file\": {\"__class__\": \"ConnectedValue\"}, \"input_object_format\": \"cds3\", \"label_branch_points\": false, \"label_cell_groups\": true, \"label_groups_by_cluster\": false, \"label_leaves\": false, \"label_roots\": false, \"no_trajectory_graph\": false, \"norm_method\": \"log\", \"reduction_method\": \"UMAP\", \"verbose\": false, \"xdim\": \"1\", \"ydim\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.5+galaxy1",
+                        "tool_state": "{\"headers\": [{\"__index__\": 0, \"name\": \"Gene Name\"}], \"input_tabular\": {\"__class__\": \"RuntimeValue\"}, \"keep_columns\": \"false\", \"strip_characters\": \"#\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "daea9f03-93e9-4af4-911c-f3fc73086560",
-                        "when": null,
+                        "uuid": "aea0ab42-9fd6-4d16-a5f0-d1ce8cc698b1",
                         "workflow_outputs": [
                             {
-                                "label": "Gene expression plot",
-                                "output_name": "output_tsv",
-                                "uuid": "e8867379-82c6-4c32-a2d3-0b24670269ae"
+                                "label": null,
+                                "output_name": "output_tabular",
+                                "uuid": "88efcecd-d1c7-4946-8a18-491ad704f096"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
                         "errors": null,
-                        "id": 24,
-                        "input_connections": {
-                            "input_object_file": {
-                                "id": 17,
-                                "output_name": "output_rds"
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Advanced Cut",
+                                "name": "input"
                             }
-                        },
-                        "inputs": [],
-                        "label": "Plot partition",
-                        "name": "Monocle3 plotCells",
+                        ],
+                        "label": "Metadata",
+                        "name": "Advanced Cut",
                         "outputs": [
                             {
-                                "name": "output_tsv",
-                                "type": "png"
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1773.85,
-                            "top": 694.45
+                            "left": 9.0,
+                            "top": 455.5
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput_tsv": {
+                            "TagDatasetActionoutput": {
                                 "action_arguments": {
-                                    "newname": "Partition plot"
+                                    "tags": "#bulk,#ebi,#metadata"
                                 },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_tsv"
+                                "action_type": "TagDatasetAction",
+                                "output_name": "output"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "91980addce5e",
-                            "name": "monocle3_plotcells",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "f46f0e4f75c4",
+                            "name": "text_processing",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"alpha\": \"1.0\", \"cell_size\": \"1.5\", \"color_cells_by\": \"partition\", \"genes\": \"\", \"input_object_file\": {\"__class__\": \"ConnectedValue\"}, \"input_object_format\": \"cds3\", \"label_branch_points\": false, \"label_cell_groups\": true, \"label_groups_by_cluster\": false, \"label_leaves\": false, \"label_roots\": false, \"no_trajectory_graph\": false, \"norm_method\": \"log\", \"reduction_method\": \"UMAP\", \"verbose\": false, \"xdim\": \"1\", \"ydim\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.5+galaxy1",
+                        "tool_state": "{\"complement\": \"--complement\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"list\": \"3\\n5\\n7\\n8\\n9\\n10\\n11\\n12\\n13\\n15\\n16\\n17\\n18\"}, \"delimiter\": \"\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "99fa4062-74c2-4236-94f0-e3e3dc85c7a2",
-                        "when": null,
+                        "uuid": "456f7c3d-3e34-44d4-b952-440927543a9c",
                         "workflow_outputs": [
                             {
-                                "label": "Partition plot",
-                                "output_name": "output_tsv",
-                                "uuid": "3f7b0a7c-85d6-430b-8385-fa9a76385c0e"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "71d445d7-061f-41bf-a968-a6705be82fdd"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
+                        "annotation": "Convert EnsemblID to Gene Symbol. Note that some EnsemblID's have multiple Gene Symbols.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1",
                         "errors": null,
-                        "id": 25,
+                        "id": 2,
                         "input_connections": {
-                            "input_object_file": {
-                                "id": 17,
-                                "output_name": "output_rds"
+                            "id_file": {
+                                "id": 0,
+                                "output_name": "output_tabular"
                             }
                         },
-                        "inputs": [],
-                        "label": "Plot cluster",
-                        "name": "Monocle3 plotCells",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool annotateMyIDs",
+                                "name": "id_file"
+                            }
+                        ],
+                        "label": null,
+                        "name": "annotateMyIDs",
                         "outputs": [
                             {
-                                "name": "output_tsv",
-                                "type": "png"
+                                "name": "out_tab",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1774.7625000000003,
-                            "top": 824.4875
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_tsv": {
-                                "action_arguments": {
-                                    "newname": "Cluster plot"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_tsv"
-                            }
+                            "left": 290.0,
+                            "top": 0
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "91980addce5e",
-                            "name": "monocle3_plotcells",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "fe3ca740a485",
+                            "name": "annotatemyids",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"alpha\": \"1.0\", \"cell_size\": \"1.5\", \"color_cells_by\": \"cluster\", \"genes\": \"\", \"input_object_file\": {\"__class__\": \"ConnectedValue\"}, \"input_object_format\": \"cds3\", \"label_branch_points\": false, \"label_cell_groups\": true, \"label_groups_by_cluster\": false, \"label_leaves\": false, \"label_roots\": false, \"no_trajectory_graph\": false, \"norm_method\": \"log\", \"reduction_method\": \"UMAP\", \"verbose\": false, \"xdim\": \"1\", \"ydim\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.5+galaxy1",
+                        "tool_state": "{\"file_has_header\": \"true\", \"id_file\": {\"__class__\": \"RuntimeValue\"}, \"id_type\": \"ENSEMBL\", \"organism\": \"Hs\", \"output_cols\": [\"SYMBOL\"], \"remove_dups\": \"false\", \"rscriptOpt\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "935fbc13-4775-48d9-bfda-96e065df3cbd",
-                        "when": null,
+                        "uuid": "faff29fb-e920-4767-9da2-f68820116c3b",
                         "workflow_outputs": [
                             {
-                                "label": "Cluster plot",
-                                "output_name": "output_tsv",
-                                "uuid": "40b65826-f73e-4054-a56d-b241985d6996"
+                                "label": "annotateMyIDs on input dataset(s): Annotated IDs",
+                                "output_name": "out_tab",
+                                "uuid": "8415bac0-6beb-467d-a0fa-fb6465987ff7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_learngraph/monocle3_learnGraph/0.1.4+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2",
                         "errors": null,
-                        "id": 26,
+                        "id": 3,
                         "input_connections": {
-                            "input_object_file": {
-                                "id": 17,
-                                "output_name": "output_rds"
+                            "input": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Regex Find And Replace",
+                                "name": "input"
+                            }
+                        ],
                         "label": null,
-                        "name": "Monocle3 learnGraph",
+                        "name": "Regex Find And Replace",
                         "outputs": [
                             {
-                                "name": "output_rds",
-                                "type": "rdata"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 1775.6375000000003,
-                            "top": 953.375
+                            "left": 466.0,
+                            "top": 422.5
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_learngraph/monocle3_learnGraph/0.1.4+galaxy0",
+                        "post_job_actions": {
+                            "ChangeDatatypeActionout_file1": {
+                                "action_arguments": {
+                                    "newtype": "tabular"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "5f877012f7af",
-                            "name": "monocle3_learngraph",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "399da6b5ec21",
+                            "name": "regex_find_replace",
+                            "owner": "galaxyp",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"euclidean_distance_ratio\": \"1.0\", \"geodesic_distance_ratio\": \"0.33\", \"input_object_file\": {\"__class__\": \"ConnectedValue\"}, \"input_object_format\": \"cds3\", \"introspective\": true, \"minimal_branch_len\": \"10\", \"no_close_loop\": false, \"no_partition\": false, \"no_prune_graph\": false, \"orthogonal_proj_tip\": false, \"output_object_format\": \"cds3\", \"verbose\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.4+galaxy0",
+                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \"Sample Characteristic\\\\[age\\\\]\", \"replacement\": \"Age\"}, {\"__index__\": 1, \"pattern\": \" year\", \"replacement\": \"\"}, {\"__index__\": 2, \"pattern\": \"Sample Characteristic\\\\[body mass index\\\\]\", \"replacement\": \"BMI\"}, {\"__index__\": 3, \"pattern\": \"Sample Characteristic\\\\[disease\\\\]\", \"replacement\": \"Disease\"}, {\"__index__\": 4, \"pattern\": \"Sample Characteristic\\\\[individual\\\\]\", \"replacement\": \"Individual\"}, {\"__index__\": 5, \"pattern\": \"Sample Characteristic\\\\[sex\\\\]\", \"replacement\": \"Sex\"}], \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "2afce1c2-6bd3-475c-88fd-7377a1698c24",
-                        "when": null,
+                        "uuid": "e0bf890a-f327-424b-b6fa-353c4141c900",
                         "workflow_outputs": [
                             {
-                                "label": "Monocle3 learnGraph on input dataset(s): cds3",
-                                "output_name": "output_rds",
-                                "uuid": "294b1a49-cec6-49d0-bcd4-3a954da67bec"
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "af0da388-91c7-4b22-b9a8-abe3c6655c1b"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
-                        "errors": null,
-                        "id": 27,
+                        "id": 4,
                         "input_connections": {
-                            "input_object_file": {
-                                "id": 26,
-                                "output_name": "output_rds"
+                            "Annotated IDs": {
+                                "id": 2,
+                                "input_subworkflow_step_id": 0,
+                                "output_name": "out_tab"
+                            },
+                            "Expression Matrix (Gene Rows)": {
+                                "id": 0,
+                                "input_subworkflow_step_id": 1,
+                                "output_name": "output_tabular"
                             }
                         },
                         "inputs": [],
-                        "label": "Plot learned trajectory",
-                        "name": "Monocle3 plotCells",
-                        "outputs": [
-                            {
-                                "name": "output_tsv",
-                                "type": "png"
-                            }
-                        ],
+                        "label": null,
+                        "name": "Copy of Convert from Ensembl to GeneSymbol, summing duplicate genes",
+                        "outputs": [],
                         "position": {
-                            "left": 2026.0750000000003,
-                            "top": 803.0125
+                            "left": 525.5,
+                            "top": 36.5
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput_tsv": {
-                                "action_arguments": {
-                                    "newname": "Learned trajectory plot"
+                        "subworkflow": {
+                            "a_galaxy_workflow": "true",
+                            "annotation": "",
+                            "creator": [
+                                {
+                                    "class": "Person",
+                                    "identifier": "",
+                                    "name": "Mehmet Tekman"
+                                }
+                            ],
+                            "format-version": "0.1",
+                            "name": "Copy of Convert from Ensembl to GeneSymbol, summing duplicate genes",
+                            "steps": {
+                                "0": {
+                                    "annotation": "",
+                                    "content_id": null,
+                                    "errors": null,
+                                    "id": 0,
+                                    "input_connections": {},
+                                    "inputs": [
+                                        {
+                                            "description": "",
+                                            "name": "Annotated IDs"
+                                        }
+                                    ],
+                                    "label": "Annotated IDs",
+                                    "name": "Input dataset",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 0.5,
+                                        "top": 127.52500915527344
+                                    },
+                                    "tool_id": null,
+                                    "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                                    "tool_version": null,
+                                    "type": "data_input",
+                                    "uuid": "a5355f15-68b7-4551-ac47-49ac73b00edf",
+                                    "workflow_outputs": [
+                                        {
+                                            "label": null,
+                                            "output_name": "output",
+                                            "uuid": "e6ac7216-b2c6-4232-b911-eb1285ed8a9f"
+                                        }
+                                    ]
                                 },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_tsv"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "91980addce5e",
-                            "name": "monocle3_plotcells",
-                            "owner": "ebi-gxa",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                                "1": {
+                                    "annotation": "",
+                                    "content_id": null,
+                                    "errors": null,
+                                    "id": 1,
+                                    "input_connections": {},
+                                    "inputs": [
+                                        {
+                                            "description": "",
+                                            "name": "Expression Matrix (Gene Rows)"
+                                        }
+                                    ],
+                                    "label": "Expression Matrix (Gene Rows)",
+                                    "name": "Input dataset",
+                                    "outputs": [],
+                                    "position": {
+                                        "left": 0.0,
+                                        "top": 237.01251220703125
+                                    },
+                                    "tool_id": null,
+                                    "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                                    "tool_version": null,
+                                    "type": "data_input",
+                                    "uuid": "9aa181ba-56bd-4360-9d50-907bee463505",
+                                    "workflow_outputs": []
+                                },
+                                "10": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+                                    "errors": null,
+                                    "id": 10,
+                                    "input_connections": {
+                                        "infile": {
+                                            "id": 9,
+                                            "output_name": "table"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Final Count Matrix with Gene Symbol ID's",
+                                    "name": "Text transformation",
+                                    "outputs": [
+                                        {
+                                            "name": "output",
+                                            "type": "input"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 1284.0125732421875,
+                                        "top": 386.07501220703125
+                                    },
+                                    "post_job_actions": {},
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "f46f0e4f75c4",
+                                        "name": "text_processing",
+                                        "owner": "bgruening",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"1 s/^gene//\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": null,
+                                    "type": "tool",
+                                    "uuid": "16452009-e11e-4aeb-8404-6c70e13490ac",
+                                    "workflow_outputs": [
+                                        {
+                                            "label": "Gene Symbol Count Matrix",
+                                            "output_name": "output",
+                                            "uuid": "f7b8537e-6349-437a-9b89-d9bab0e1e581"
+                                        }
+                                    ]
+                                },
+                                "2": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+                                    "errors": null,
+                                    "id": 2,
+                                    "input_connections": {
+                                        "infile": {
+                                            "id": 0,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [
+                                        {
+                                            "description": "runtime parameter for tool Text reformatting",
+                                            "name": "infile"
+                                        }
+                                    ],
+                                    "label": "Group Ensembl Duplicates",
+                                    "name": "Text reformatting",
+                                    "outputs": [
+                                        {
+                                            "name": "outfile",
+                                            "type": "input"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 328.01251220703125,
+                                        "top": 220.0124969482422
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionoutfile": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "outfile"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "f46f0e4f75c4",
+                                        "name": "text_processing",
+                                        "owner": "bgruening",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"code\": \"BEGIN {\\n  ordering[\\\"test\\\"]\\n  delete ordering[\\\"test\\\"]\\n}\\nNR > 1 {\\n   if (gene[$1]){\\n      gene[$1] = gene[$1]\\\":\\\"$2\\n   } else {\\n      gene[$1] = $2\\n      ordering[length(ordering)+1] = $1\\n   }\\n   \\n}\\n\\nEND {\\n    for (o=0; o < length(ordering); ++o){\\n         print ordering[o]\\\"\\\\t\\\"gene[ordering[o]]\\n    }\\n}\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": null,
+                                    "type": "tool",
+                                    "uuid": "e5b51c32-bd3a-440f-a05a-8c1c36384e3c",
+                                    "workflow_outputs": []
+                                },
+                                "3": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                                    "errors": null,
+                                    "id": 3,
+                                    "input_connections": {
+                                        "infile1": {
+                                            "id": 1,
+                                            "output_name": "output"
+                                        },
+                                        "infile2": {
+                                            "id": 2,
+                                            "output_name": "outfile"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Merge Gene Symbol and matrix together",
+                                    "name": "Join",
+                                    "outputs": [
+                                        {
+                                            "name": "output",
+                                            "type": "input"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 330.98748779296875,
+                                        "top": 352.0249938964844
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionoutput": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "f46f0e4f75c4",
+                                        "name": "text_processing",
+                                        "owner": "bgruening",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": \"true\", \"ignore_case\": \"false\", \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": null,
+                                    "type": "tool",
+                                    "uuid": "0ac51cc9-c0b0-4b3d-961c-503860cf423f",
+                                    "workflow_outputs": []
+                                },
+                                "4": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+                                    "errors": null,
+                                    "id": 4,
+                                    "input_connections": {
+                                        "infile": {
+                                            "id": 3,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Relocate the Gene Symbol column to 1st column",
+                                    "name": "Text reformatting",
+                                    "outputs": [
+                                        {
+                                            "name": "outfile",
+                                            "type": "input"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 580.9625244140625,
+                                        "top": 381.01251220703125
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionoutfile": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "outfile"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "f46f0e4f75c4",
+                                        "name": "text_processing",
+                                        "owner": "bgruening",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"code\": \"{print $NF\\\"\\\\t\\\"$0}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": null,
+                                    "type": "tool",
+                                    "uuid": "44880f2a-430c-4b00-a0b3-e4673fe395ce",
+                                    "workflow_outputs": []
+                                },
+                                "5": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                                    "errors": null,
+                                    "id": 5,
+                                    "input_connections": {
+                                        "input": {
+                                            "id": 4,
+                                            "output_name": "outfile"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Remove second column with Ensembl ID's",
+                                    "name": "Advanced Cut",
+                                    "outputs": [
+                                        {
+                                            "name": "output",
+                                            "type": "tabular"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 580.0,
+                                        "top": 236.01251220703125
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionoutput": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "f46f0e4f75c4",
+                                        "name": "text_processing",
+                                        "owner": "bgruening",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"complement\": \"--complement\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"list\": \"2\"}, \"delimiter\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": null,
+                                    "type": "tool",
+                                    "uuid": "104cb55a-f297-4464-b3b6-7021ffd0ae9c",
+                                    "workflow_outputs": []
+                                },
+                                "6": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+                                    "errors": null,
+                                    "id": 6,
+                                    "input_connections": {
+                                        "infile": {
+                                            "id": 5,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Count Unique occurences of Gene Symbol",
+                                    "name": "Text reformatting",
+                                    "outputs": [
+                                        {
+                                            "name": "outfile",
+                                            "type": "input"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 832.987548828125,
+                                        "top": 0.0
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionoutfile": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "outfile"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "f46f0e4f75c4",
+                                        "name": "text_processing",
+                                        "owner": "bgruening",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"code\": \"{ gene[$1] = gene[$1] + 1 }\\n\\nEND {\\n     for (ge in gene){\\n         print ge\\\"\\\\t\\\"gene[ge]\\n     }\\n}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": null,
+                                    "type": "tool",
+                                    "uuid": "1f84d0c1-b187-4299-a2bd-172964ef3732",
+                                    "workflow_outputs": []
+                                },
+                                "7": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+                                    "errors": null,
+                                    "id": 7,
+                                    "input_connections": {
+                                        "infile": {
+                                            "id": 5,
+                                            "output_name": "output"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Group rows by Gene Symbol and append their values (Long Format)",
+                                    "name": "Text reformatting",
+                                    "outputs": [
+                                        {
+                                            "name": "outfile",
+                                            "type": "input"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 833.9625244140625,
+                                        "top": 246.05001831054688
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActionoutfile": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "outfile"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "f46f0e4f75c4",
+                                        "name": "text_processing",
+                                        "owner": "bgruening",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"code\": \"NR == 1 {\\n    for (i=2; i <= NF; i++){\\n         cellorder[i] = $i\\n   }\\n}\\n\\nNR > 1 {\\n    for (i=2; i <= NF; i++){\\n         if (cellorder[i] == \\\"0\\\" || $1 == \\\"NA\\\"){\\n         } else {\\n             bc[$1\\\"\\\\t\\\"cellorder[i]] = bc[$1\\\"\\\\t\\\"cellorder[i]] + $i\\n         }\\n   }\\n}\\n\\nEND {\\n   print \\\"gene\\\\tbar\\\\tvalue\\\"\\n   for (key in bc){\\n       print key\\\"\\\\t\\\"bc[key]\\n   }\\n}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": null,
+                                    "type": "tool",
+                                    "uuid": "8ac449d7-da88-44b0-bfe2-092d8cd47af9",
+                                    "workflow_outputs": []
+                                },
+                                "8": {
+                                    "annotation": "",
+                                    "content_id": "sort1",
+                                    "errors": null,
+                                    "id": 8,
+                                    "input_connections": {
+                                        "input": {
+                                            "id": 6,
+                                            "output_name": "outfile"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Unique Gene Symbol Occurences, sorted in descending frequency.",
+                                    "name": "Sort",
+                                    "outputs": [
+                                        {
+                                            "name": "out_file1",
+                                            "type": "input"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 1067.9625244140625,
+                                        "top": 2.0625
+                                    },
+                                    "post_job_actions": {},
+                                    "tool_id": "sort1",
+                                    "tool_state": "{\"column\": \"2\", \"column_set\": [], \"header_lines\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"order\": \"DESC\", \"style\": \"num\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": null,
+                                    "type": "tool",
+                                    "uuid": "d3a9bfd0-372a-493c-a83a-578427a7fe17",
+                                    "workflow_outputs": [
+                                        {
+                                            "label": "Report of Duplicate Genes",
+                                            "output_name": "out_file1",
+                                            "uuid": "274c3805-5b98-4a64-8dcd-c269750b852e"
+                                        }
+                                    ]
+                                },
+                                "9": {
+                                    "annotation": "",
+                                    "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0",
+                                    "errors": null,
+                                    "id": 9,
+                                    "input_connections": {
+                                        "singtabop|input": {
+                                            "id": 7,
+                                            "output_name": "outfile"
+                                        }
+                                    },
+                                    "inputs": [],
+                                    "label": "Pivot Long Format to Wide Format (Matrix)",
+                                    "name": "Table Compute",
+                                    "outputs": [
+                                        {
+                                            "name": "table",
+                                            "type": "tabular"
+                                        }
+                                    ],
+                                    "position": {
+                                        "left": 1057.987548828125,
+                                        "top": 298.0249938964844
+                                    },
+                                    "post_job_actions": {
+                                        "HideDatasetActiontable": {
+                                            "action_arguments": {},
+                                            "action_type": "HideDatasetAction",
+                                            "output_name": "table"
+                                        }
+                                    },
+                                    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0",
+                                    "tool_shed_repository": {
+                                        "changeset_revision": "3bf5661c0280",
+                                        "name": "table_compute",
+                                        "owner": "iuc",
+                                        "tool_shed": "toolshed.g2.bx.psu.edu"
+                                    },
+                                    "tool_state": "{\"out_opts\": [\"output_headers_col\", \"output_headers_row\"], \"precision\": \"6\", \"singtabop\": {\"use_type\": \"single\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"col_row_names\": [\"has_col_names\"], \"adv\": {\"header\": null, \"nrows\": null, \"skipfooter\": null, \"skip_blank_lines\": \"true\"}, \"user\": {\"mode\": \"fulltable\", \"__current_case__\": 4, \"general\": {\"use\": \"pivot\", \"__current_case__\": 2, \"index\": \"gene\", \"column\": \"bar\", \"values\": \"value\", \"aggfunc\": null, \"colfun_map\": []}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                                    "tool_version": null,
+                                    "type": "tool",
+                                    "uuid": "6c98c17e-43ca-4620-a2f7-a919c24bee20",
+                                    "workflow_outputs": []
+                                }
+                            },
+                            "tags": "",
+                            "uuid": "463a98af-e99f-47d8-9a05-f601d39b506a"
                         },
-                        "tool_state": "{\"alpha\": \"1.0\", \"cell_size\": \"1.5\", \"color_cells_by\": \"cell_type\", \"genes\": \"\", \"input_object_file\": {\"__class__\": \"ConnectedValue\"}, \"input_object_format\": \"cds3\", \"label_branch_points\": false, \"label_cell_groups\": true, \"label_groups_by_cluster\": false, \"label_leaves\": false, \"label_roots\": false, \"no_trajectory_graph\": false, \"norm_method\": \"log\", \"reduction_method\": \"UMAP\", \"verbose\": false, \"xdim\": \"1\", \"ydim\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.5+galaxy1",
-                        "type": "tool",
-                        "uuid": "7284b7d6-792e-4e3e-b23a-9733ce8ba001",
-                        "when": null,
+                        "tool_id": 171557,
+                        "type": "subworkflow",
+                        "uuid": "319ba9b4-9af0-4a4d-a3d5-b700d1745d3f",
                         "workflow_outputs": [
                             {
-                                "label": "Cell types & learned trajectory path plot",
-                                "output_name": "output_tsv",
-                                "uuid": "c85ddefe-8eaf-4d21-93ed-ca0859286bf0"
+                                "label": null,
+                                "output_name": "Report of Duplicate Genes",
+                                "uuid": "915c757d-6fb1-41d2-a9f7-b8b30a29794a"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "Gene Symbol Count Matrix",
+                                "uuid": "24ace210-3eac-4f62-8781-366e00cff2dc"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_ordercells/monocle3_orderCells/0.1.4+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4",
                         "errors": null,
-                        "id": 28,
+                        "id": 5,
                         "input_connections": {
-                            "input_object_file": {
-                                "id": 26,
-                                "output_name": "output_rds"
+                            "exprs_file": {
+                                "id": 4,
+                                "output_name": "Gene Symbol Count Matrix"
+                            },
+                            "pdata_file": {
+                                "id": 3,
+                                "output_name": "out_file1"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Construct Expression Set Object",
+                                "name": "exprs_file"
+                            },
+                            {
+                                "description": "runtime parameter for tool Construct Expression Set Object",
+                                "name": "pdata_file"
+                            }
+                        ],
                         "label": null,
-                        "name": "Monocle3 orderCells",
+                        "name": "Construct Expression Set Object",
                         "outputs": [
                             {
-                                "name": "output_rds",
+                                "name": "out_txt",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "out_rds",
                                 "type": "rdata"
                             }
                         ],
                         "position": {
-                            "left": 2029.7000000000003,
-                            "top": 953.675
+                            "left": 883.0,
+                            "top": 343.5
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_ordercells/monocle3_orderCells/0.1.4+galaxy0",
+                        "post_job_actions": {
+                            "RemoveTagDatasetActionout_rds": {
+                                "action_arguments": {
+                                    "tags": "#metadata,#matrix"
+                                },
+                                "action_type": "RemoveTagDatasetAction",
+                                "output_name": "out_rds"
+                            },
+                            "TagDatasetActionout_rds": {
+                                "action_arguments": {
+                                    "tags": "#combined"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "out_rds"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4",
                         "tool_shed_repository": {
-                            "changeset_revision": "3e77dc421569",
-                            "name": "monocle3_ordercells",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "282819d09a4f",
+                            "name": "music_construct_eset",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"cell_phenotype\": \"cell_type\", \"input_object_file\": {\"__class__\": \"ConnectedValue\"}, \"input_object_format\": \"cds3\", \"introspective\": true, \"output_object_format\": \"cds3\", \"reduction_method\": \"UMAP\", \"root_cells\": \"\", \"root_pr_nodes\": \"\", \"root_type\": \"DN\", \"verbose\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.4+galaxy0",
+                        "tool_state": "{\"annotation\": \"\", \"expdata\": {\"name\": \"\", \"lab\": \"\", \"contact\": \"\", \"title\": \"\", \"abstract\": \"\", \"url\": \"\", \"other\": [{\"__index__\": 0, \"field\": \"notes\", \"comment\": \"Created in Galaxy\"}]}, \"exprs_file\": {\"__class__\": \"RuntimeValue\"}, \"metadata\": [], \"pdata_file\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "e8c75441-228e-4a64-b80a-16c9dd763169",
-                        "when": null,
+                        "uuid": "8e428b8e-bda7-4fdb-8daa-2197d1d1d357",
                         "workflow_outputs": [
                             {
-                                "label": "Monocle3 orderCells on input dataset(s): cds3",
-                                "output_name": "output_rds",
-                                "uuid": "5aea5752-b767-4fc8-8741-1f4d1c659a41"
+                                "label": null,
+                                "output_name": "out_rds",
+                                "uuid": "28490366-fb29-40df-852c-2f5da6f1a6ce"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_txt",
+                                "uuid": "426d6040-bf0f-4312-babf-2ae9c928eff1"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_diffexp/monocle3_diffExp/0.1.4+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4",
                         "errors": null,
-                        "id": 29,
+                        "id": 6,
                         "input_connections": {
-                            "input_object_file": {
-                                "id": 28,
-                                "output_name": "output_rds"
+                            "rds_eset": {
+                                "id": 5,
+                                "output_name": "out_rds"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Manipulate Expression Set Object",
+                                "name": "rds_eset"
+                            }
+                        ],
                         "label": null,
-                        "name": "Monocle3 diffExp",
+                        "name": "Manipulate Expression Set Object",
                         "outputs": [
                             {
-                                "name": "output_tsv",
-                                "type": "tsv"
+                                "name": "out_eset",
+                                "type": "rdata"
                             }
                         ],
                         "position": {
-                            "left": 2274.4500000000003,
-                            "top": 828.1875
+                            "left": 1186.5,
+                            "top": 300.5
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput_tsv": {
+                            "RemoveTagDatasetActionout_eset": {
                                 "action_arguments": {
-                                    "newname": "Differential expression of genes - table"
+                                    "tags": "#combined"
                                 },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_tsv"
+                                "action_type": "RemoveTagDatasetAction",
+                                "output_name": "out_eset"
+                            },
+                            "TagDatasetActionout_eset": {
+                                "action_arguments": {
+                                    "tags": "#normal"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "out_eset"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_diffexp/monocle3_diffExp/0.1.4+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4",
                         "tool_shed_repository": {
-                            "changeset_revision": "d43a608d14ac",
-                            "name": "monocle3_diffexp",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "22232092be53",
+                            "name": "music_manipulate_eset",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"alternative\": \"greater\", \"input_object_file\": {\"__class__\": \"ConnectedValue\"}, \"input_object_format\": \"cds3\", \"knn\": \"20\", \"method\": \"Moran_I\", \"neighbor_graph\": \"knn\", \"reduction_method\": \"UMAP\", \"verbose\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.4+galaxy1",
+                        "tool_state": "{\"combine_eset\": {\"do\": \"No\", \"__current_case__\": 0}, \"rds_eset\": {\"__class__\": \"RuntimeValue\"}, \"subset_eset\": {\"do\": \"Yes\", \"__current_case__\": 1, \"subset_yes\": {\"by\": \"phenotype\", \"__current_case__\": 3, \"pheno_samples\": [{\"__index__\": 0, \"column\": \"Disease\", \"values\": \"normal\"}], \"pheno_genes\": []}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "6a7d9923-d68b-411b-a0e5-d1bf4716f7b1",
-                        "when": null,
+                        "uuid": "f7cd1cd9-42bf-4a24-82a3-6720a7783771",
                         "workflow_outputs": [
                             {
-                                "label": "Differential expression of genes - table",
-                                "output_name": "output_tsv",
-                                "uuid": "3c298624-9f06-4e52-b2a8-fb834b87c296"
+                                "label": "Manipulate Expression Set Object on input dataset(s): ExpressionSet Object",
+                                "output_name": "out_eset",
+                                "uuid": "88196d0b-7254-4794-b08a-5409f19c8323"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4",
                         "errors": null,
-                        "id": 30,
+                        "id": 7,
                         "input_connections": {
-                            "input_object_file": {
-                                "id": 28,
-                                "output_name": "output_rds"
+                            "rds_eset": {
+                                "id": 5,
+                                "output_name": "out_rds"
                             }
                         },
-                        "inputs": [],
-                        "label": "Plot pseudotime",
-                        "name": "Monocle3 plotCells",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Manipulate Expression Set Object",
+                                "name": "rds_eset"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Manipulate Expression Set Object",
                         "outputs": [
                             {
-                                "name": "output_tsv",
-                                "type": "png"
+                                "name": "out_eset",
+                                "type": "rdata"
                             }
                         ],
                         "position": {
-                            "left": 2278.7625000000003,
-                            "top": 975.175
+                            "left": 1183.5,
+                            "top": 528.5
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput_tsv": {
+                            "RemoveTagDatasetActionout_eset": {
                                 "action_arguments": {
-                                    "newname": "Pseudotime plot"
+                                    "tags": "#combined"
                                 },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output_tsv"
+                                "action_type": "RemoveTagDatasetAction",
+                                "output_name": "out_eset"
+                            },
+                            "TagDatasetActionout_eset": {
+                                "action_arguments": {
+                                    "tags": "#T2D"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "out_eset"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4",
                         "tool_shed_repository": {
-                            "changeset_revision": "91980addce5e",
-                            "name": "monocle3_plotcells",
-                            "owner": "ebi-gxa",
+                            "changeset_revision": "22232092be53",
+                            "name": "music_manipulate_eset",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"alpha\": \"1.0\", \"cell_size\": \"1.5\", \"color_cells_by\": \"pseudotime\", \"genes\": \"\", \"input_object_file\": {\"__class__\": \"ConnectedValue\"}, \"input_object_format\": \"cds3\", \"label_branch_points\": false, \"label_cell_groups\": true, \"label_groups_by_cluster\": false, \"label_leaves\": false, \"label_roots\": false, \"no_trajectory_graph\": false, \"norm_method\": \"log\", \"reduction_method\": \"UMAP\", \"verbose\": false, \"xdim\": \"1\", \"ydim\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.5+galaxy1",
+                        "tool_state": "{\"combine_eset\": {\"do\": \"No\", \"__current_case__\": 0}, \"rds_eset\": {\"__class__\": \"RuntimeValue\"}, \"subset_eset\": {\"do\": \"Yes\", \"__current_case__\": 1, \"subset_yes\": {\"by\": \"phenotype\", \"__current_case__\": 3, \"pheno_samples\": [{\"__index__\": 0, \"column\": \"Disease\", \"values\": \"type II diabetes mellitus\"}], \"pheno_genes\": []}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "1f9b4306-ec3c-4b2d-9c0e-40a2589afd1d",
-                        "when": null,
+                        "uuid": "8dc9defa-1ae9-4e6b-8479-5034763c7c2f",
                         "workflow_outputs": [
                             {
-                                "label": "Pseudotime plot",
-                                "output_name": "output_tsv",
-                                "uuid": "813d15bb-0771-4aed-9226-4874c1ddba59"
+                                "label": null,
+                                "output_name": "out_eset",
+                                "uuid": "ecab164b-a19b-4b78-8b6d-491aa2d5c1e7"
                             }
                         ]
                     }
                 ],
-                "parent_id": "single-cell/scrna-case_monocle3-trajectories",
-                "path": "topics/single-cell/tutorials/scrna-case_monocle3-trajectories/workflows/Trajectory-analysis-using-Monocle3---full-tutorial-workflow.ga",
+                "parent_id": "single-cell/bulk-music-3-preparebulk",
+                "path": "topics/single-cell/tutorials/bulk-music-3-preparebulk/workflows/bulk_ESet.ga",
                 "tags": [
-                    "name:trajectory_analysis",
+                    "name:singlecell",
                     "name:transcriptomics",
-                    "name:scRNA-seq",
-                    "name:single_cell"
+                    "name:training"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "Trajectory analysis using Monocle3 - full tutorial workflow",
+                "tests": false,
+                "title": "MuSiC-Deconvolution: Data generation | bulk | ESet",
                 "topic_id": "single-cell",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-scrna-case_monocle3-trajectories/versions/trajectory-analysis-using-monocle3---full-tutorial-workflow",
-                "tutorial_id": "scrna-case_monocle3-trajectories",
-                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/workflows/Trajectory-analysis-using-Monocle3---full-tutorial-workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_monocle3-trajectories/workflows/Trajectory-analysis-using-Monocle3---full-tutorial-workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/single-cell-bulk-music-3-preparebulk/versions/bulk-eset",
+                "tutorial_id": "bulk-music-3-preparebulk",
+                "url": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-3-preparebulk/workflows/bulk_ESet.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-3-preparebulk/workflows/bulk_ESet.html",
                 "version": 1,
-                "wfid": "single-cell-scrna-case_monocle3-trajectories",
-                "wfname": "trajectory-analysis-using-monocle3---full-tutorial-workflow",
-                "workflow": "Trajectory-analysis-using-Monocle3---full-tutorial-workflow.ga",
+                "wfid": "single-cell-bulk-music-3-preparebulk",
+                "wfname": "bulk-eset",
+                "workflow": "bulk_ESet.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "Filter1",
-                    "join1",
+                    "sort1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
                     "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_create/monocle3_create/0.1.4+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_diffexp/monocle3_diffExp/0.1.4+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_learngraph/monocle3_learnGraph/0.1.4+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_ordercells/monocle3_orderCells/0.1.4+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_partition/monocle3_partition/0.1.4+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_preprocess/monocle3_preprocess/0.1.4+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_reducedim/monocle3_reduceDim/0.1.4+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_topmarkers/monocle3_topmarkers/0.1.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0"
                 ],
-                "workflowhub_id": "1228"
+                "workflowhub_id": "1230"
             }
         ],
-        "zenodo_link": "https://zenodo.org/records/10397366"
+        "zenodo_link": "https://zenodo.org/record/7319173"
     },
     {
         "admin_install": {
@@ -245247,10 +252070,12 @@
         "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-trajectories/tutorial.json",
         "contributors": [
             {
+                "elixir_node": "uk",
                 "email": "juliajot36@gmail.com",
                 "id": "wee-snufkin",
                 "joined": "2022-06",
                 "name": "Julia Jakiela",
+                "orcid": "0009-0001-2017-8805",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wee-snufkin/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/wee-snufkin.json"
             }
@@ -245288,7 +252113,7 @@
             "Be able to choose the method appropriate for your specific data",
             "Gain insight into methods currently available in Galaxy"
         ],
-        "pageviews": 2640568,
+        "pageviews": 2811245,
         "priority": 5,
         "pub_date": "2022-09-30",
         "questions": [
@@ -245372,8 +252197,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 142,
-        "visitors": 1107674
+        "visit_duration": 143,
+        "visitors": 1177052
     },
     {
         "admin_install": {
@@ -245460,6 +252285,7 @@
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.eu",
             "UseGalaxy.no",
@@ -245490,7 +252316,7 @@
             "Learn how to make predictions using the training and test dataset.",
             "Visualize the predictions."
         ],
-        "pageviews": 9612,
+        "pageviews": 9658,
         "pub_date": "2019-03-07",
         "questions": [
             "what are classification and regression techniques?",
@@ -245508,6 +252334,11 @@
         "slides_recordings": false,
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -245565,7 +252396,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 42,
-        "visitors": 5179,
+        "visitors": 5216,
         "workflows": [
             {
                 "creators": [],
@@ -245706,7 +252537,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nbreast-w_train\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nbreast-w_targets\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nbreast-w_test\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Support vector machines SVMs\"];\n  0 -->|output| 3;\n  0 -->|output| 3;\n  4[\"Support vector machines SVMs\"];\n  2 -->|output| 4;\n  3 -->|outfile_fit| 4;\n  5[\"Plot confusion matrix, precision, recall and ROC and AUC curves\"];\n  3 -->|outfile_fit| 5;\n  4 -->|outfile_predict| 5;\n  1 -->|output| 5;\n  0fac82f3-c1b2-482f-a31f-30b623a0f223[\"Output\\noutput_roc\"];\n  5 --> 0fac82f3-c1b2-482f-a31f-30b623a0f223;\n  style 0fac82f3-c1b2-482f-a31f-30b623a0f223 stroke:#2c3143,stroke-width:4px;\n  431f3596-7b80-44f0-83ee-dda8c58e1e8c[\"Output\\noutput_confusion\"];\n  5 --> 431f3596-7b80-44f0-83ee-dda8c58e1e8c;\n  style 431f3596-7b80-44f0-83ee-dda8c58e1e8c stroke:#2c3143,stroke-width:4px;\n  ab62de11-fa69-4d59-9ebe-d5d0562f3c18[\"Output\\noutput_prf\"];\n  5 --> ab62de11-fa69-4d59-9ebe-d5d0562f3c18;\n  style ab62de11-fa69-4d59-9ebe-d5d0562f3c18 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:25 +0000",
+                "modified": "2024-10-02 12:08:10 +0000",
                 "name": "Classification LSVC",
                 "outputs": [
                     {
@@ -246072,7 +252903,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nbody_fat_test\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nbody_fat_train\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nbody_fat_test_labels\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Ensemble methods\"];\n  1 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Ensemble methods\"];\n  0 -->|output| 4;\n  3 -->|outfile_fit| 4;\n  5[\"Plot actual vs predicted curves and residual plots\"];\n  4 -->|outfile_predict| 5;\n  2 -->|output| 5;\n  cf1a5f94-f79d-4d13-b142-c3e20e25b658[\"Output\\noutput_scatter_plot\"];\n  5 --> cf1a5f94-f79d-4d13-b142-c3e20e25b658;\n  style cf1a5f94-f79d-4d13-b142-c3e20e25b658 stroke:#2c3143,stroke-width:4px;\n  e86ba3fd-3f85-4ba9-ad66-4c1e5caa875a[\"Output\\noutput_actual_vs_pred\"];\n  5 --> e86ba3fd-3f85-4ba9-ad66-4c1e5caa875a;\n  style e86ba3fd-3f85-4ba9-ad66-4c1e5caa875a stroke:#2c3143,stroke-width:4px;\n  2cbc04d3-d2d9-4623-b63d-51f1b024d611[\"Output\\noutput_residual_plot\"];\n  5 --> 2cbc04d3-d2d9-4623-b63d-51f1b024d611;\n  style 2cbc04d3-d2d9-4623-b63d-51f1b024d611 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:25 +0000",
+                "modified": "2024-10-02 12:08:10 +0000",
                 "name": "Regression GradientBoosting",
                 "outputs": [
                     {
@@ -246358,6 +253189,7 @@
         ],
         "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.eu",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)",
@@ -246390,21 +253222,26 @@
             "Apply clustering algorithms to different datasets",
             "Learn how to visualize clusters"
         ],
-        "pageviews": 13130,
+        "pageviews": 13270,
         "pub_date": "2020-05-08",
         "questions": [
             "How to use clustering algorithms to categorize data in different clusters"
         ],
         "short_id": "T00264",
         "short_tools": [
+            "sklearn_numeric_clustering",
             "ggplot2_point",
-            "csv_to_tabular",
-            "sklearn_numeric_clustering"
+            "csv_to_tabular"
         ],
         "slides": false,
         "slides_recordings": false,
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
@@ -246466,8 +253303,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 58,
-        "visitors": 7665,
+        "visit_duration": 57,
+        "visitors": 7784,
         "workflows": [
             {
                 "creators": [],
@@ -246577,7 +253414,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\niris\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ncircles\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Numeric Clustering\"];\n  2 -->|output| 10;\n  11[\"Numeric Clustering\"];\n  2 -->|output| 11;\n  12[\"Numeric Clustering\"];\n  3 -->|tabular| 12;\n  13[\"Numeric Clustering\"];\n  3 -->|tabular| 13;\n  14[\"Numeric Clustering\"];\n  3 -->|tabular| 14;\n  15[\"Scatterplot with ggplot2\"];\n  5 -->|outfile| 15;\n  275528af-4af3-4dc6-a958-737f4d2f89bd[\"Output\\nheirarchical_clustering_circles\"];\n  15 --> 275528af-4af3-4dc6-a958-737f4d2f89bd;\n  style 275528af-4af3-4dc6-a958-737f4d2f89bd stroke:#2c3143,stroke-width:4px;\n  16[\"Scatterplot with ggplot2\"];\n  6 -->|outfile| 16;\n  870b03ca-6b2c-42ab-bbcc-6c4bbecf8ea9[\"Output\\nkmeans_clustering_circles\"];\n  16 --> 870b03ca-6b2c-42ab-bbcc-6c4bbecf8ea9;\n  style 870b03ca-6b2c-42ab-bbcc-6c4bbecf8ea9 stroke:#2c3143,stroke-width:4px;\n  17[\"Scatterplot with ggplot2\"];\n  7 -->|outfile| 17;\n  9664ba05-4664-4ceb-8f93-0974b20bf9e1[\"Output\\ndbscan_clustering_circles\"];\n  17 --> 9664ba05-4664-4ceb-8f93-0974b20bf9e1;\n  style 9664ba05-4664-4ceb-8f93-0974b20bf9e1 stroke:#2c3143,stroke-width:4px;\n  18[\"Scatterplot with ggplot2\"];\n  9 -->|outfile| 18;\n  d82a4483-7f38-4614-96b4-2a9b3316c808[\"Output\\nheirarchical_clustering_moon\"];\n  18 --> d82a4483-7f38-4614-96b4-2a9b3316c808;\n  style d82a4483-7f38-4614-96b4-2a9b3316c808 stroke:#2c3143,stroke-width:4px;\n  19[\"Scatterplot with ggplot2\"];\n  10 -->|outfile| 19;\n  00c0ca58-4ee5-4606-8c1b-c172431e5dbd[\"Output\\ndbscan_clustering_moon\"];\n  19 --> 00c0ca58-4ee5-4606-8c1b-c172431e5dbd;\n  style 00c0ca58-4ee5-4606-8c1b-c172431e5dbd stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nmoon\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  20[\"Scatterplot with ggplot2\"];\n  11 -->|outfile| 20;\n  5717bf22-83e3-46a2-8f6d-12a1fa41439b[\"Output\\nkmeans_clustering_moon\"];\n  20 --> 5717bf22-83e3-46a2-8f6d-12a1fa41439b;\n  style 5717bf22-83e3-46a2-8f6d-12a1fa41439b stroke:#2c3143,stroke-width:4px;\n  21[\"Scatterplot with ggplot2\"];\n  12 -->|outfile| 21;\n  0ace8714-ff3a-4efd-a649-70924b1e6230[\"Output\\nheirarchical_clustering_iris\"];\n  21 --> 0ace8714-ff3a-4efd-a649-70924b1e6230;\n  style 0ace8714-ff3a-4efd-a649-70924b1e6230 stroke:#2c3143,stroke-width:4px;\n  22[\"Scatterplot with ggplot2\"];\n  13 -->|outfile| 22;\n  e6f69d7d-c9e3-4023-8daf-87f6b0afc3fd[\"Output\\nkmeans_clustering_iris\"];\n  22 --> e6f69d7d-c9e3-4023-8daf-87f6b0afc3fd;\n  style e6f69d7d-c9e3-4023-8daf-87f6b0afc3fd stroke:#2c3143,stroke-width:4px;\n  23[\"Scatterplot with ggplot2\"];\n  14 -->|outfile| 23;\n  119d1cde-567a-47f0-99de-00d3557c38a2[\"Output\\ndbscan_clustering_iris\"];\n  23 --> 119d1cde-567a-47f0-99de-00d3557c38a2;\n  style 119d1cde-567a-47f0-99de-00d3557c38a2 stroke:#2c3143,stroke-width:4px;\n  3[\"Convert CSV to tabular\"];\n  0 -->|output| 3;\n  4[\"Scatterplot with ggplot2\"];\n  1 -->|output| 4;\n  5[\"Numeric Clustering\"];\n  1 -->|output| 5;\n  6[\"Numeric Clustering\"];\n  1 -->|output| 6;\n  7[\"Numeric Clustering\"];\n  1 -->|output| 7;\n  8[\"Scatterplot with ggplot2\"];\n  2 -->|output| 8;\n  9[\"Numeric Clustering\"];\n  2 -->|output| 9;",
-                "modified": "2024-08-18 00:06:25 +0000",
+                "modified": "2024-10-02 12:08:10 +0000",
                 "name": "Clustering in Machine Learning",
                 "outputs": [
                     {
@@ -247015,42 +253852,77 @@
                 {
                     "name": "keras_model_builder",
                     "owner": "bgruening",
-                    "revisions": "66d7efc06000",
+                    "revisions": "772e0e89fc68",
                     "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "keras_model_config",
                     "owner": "bgruening",
-                    "revisions": "f22a9297440f",
+                    "revisions": "8a794e6d3388",
                     "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "keras_train_and_eval",
                     "owner": "bgruening",
-                    "revisions": "818f9b69d8a0",
+                    "revisions": "f1b9a42d6809",
+                    "tool_panel_section_label": "Machine Learning",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "keras_train_and_eval",
+                    "owner": "bgruening",
+                    "revisions": "b6ef6d0cb6b7",
+                    "tool_panel_section_label": "Machine Learning",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ml_visualization_ex",
+                    "owner": "bgruening",
+                    "revisions": "05143043ca13",
+                    "tool_panel_section_label": "Machine Learning",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ml_visualization_ex",
+                    "owner": "bgruening",
+                    "revisions": "947c2eacccb8",
                     "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "model_prediction",
                     "owner": "bgruening",
-                    "revisions": "9991c4ddde14",
+                    "revisions": "83228baae3c5",
                     "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "plotly_regression_performance_plots",
+                    "name": "model_prediction",
                     "owner": "bgruening",
-                    "revisions": "389227fa1864",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "revisions": "1552b8cb4a94",
+                    "tool_panel_section_label": "Machine Learning",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sklearn_to_categorical",
+                    "owner": "bgruening",
+                    "revisions": "ec69cbe34b73",
+                    "tool_panel_section_label": "Machine Learning",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: keras_model_builder\n  owner: bgruening\n  revisions: 66d7efc06000\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_model_config\n  owner: bgruening\n  revisions: f22a9297440f\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_train_and_eval\n  owner: bgruening\n  revisions: 818f9b69d8a0\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: model_prediction\n  owner: bgruening\n  revisions: 9991c4ddde14\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: plotly_regression_performance_plots\n  owner: bgruening\n  revisions: 389227fa1864\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/FNN/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: keras_model_builder\n  owner: bgruening\n  revisions: 772e0e89fc68\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_model_config\n  owner: bgruening\n  revisions: 8a794e6d3388\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_train_and_eval\n  owner: bgruening\n  revisions: f1b9a42d6809\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_train_and_eval\n  owner: bgruening\n  revisions: b6ef6d0cb6b7\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ml_visualization_ex\n  owner: bgruening\n  revisions: 05143043ca13\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ml_visualization_ex\n  owner: bgruening\n  revisions: 947c2eacccb8\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: model_prediction\n  owner: bgruening\n  revisions: 83228baae3c5\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: model_prediction\n  owner: bgruening\n  revisions: 1552b8cb4a94\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_to_categorical\n  owner: bgruening\n  revisions: ec69cbe34b73\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/fruit_360/tutorial.json",
         "contributors": [
             {
                 "email": "kxk302@gmail.com",
@@ -247061,7 +253933,7 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/kxk302.json"
             }
         ],
-        "dir": "topics/statistics/tutorials/FNN",
+        "dir": "topics/statistics/tutorials/fruit_360",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -247072,70 +253944,57 @@
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "statistics",
-                "tutorials": [
-                    "RNN"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "statistics/FNN",
-        "inexact_supported_servers": [
-            "UseGalaxy.no"
-        ],
+        "id": "statistics/fruit_360",
+        "inexact_supported_servers": [],
         "js_requirements": {
-            "mathjax": 2165,
+            "mathjax": 24661,
             "mermaid": false
         },
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-07-09",
         "objectives": [
-            "Understand the inspiration for neural networks",
-            "Learn various activation functions, and classification/regression problems solved by neural networks",
-            "Discuss various cost/loss functions and the backpropagation algorithm",
-            "Learn how to create a neural network using Galaxy's deep learning tools",
-            "Solve a simple regression problem, car purchase price prediction, via FNN in Galaxy"
+            "Learn how to create a CNN using Galaxy's deep learning tools",
+            "Solve an image classification problem on fruit 360 dataset using CNN in Galaxy"
         ],
-        "pageviews": 5180093,
-        "pub_date": "2021-04-28",
+        "pageviews": 4268424,
+        "pub_date": "2021-12-01",
         "questions": [
-            "What is a feedforward neural network (FNN)?",
-            "What are some applications of FNN?"
+            "How to solve an image classification problem using convolutional neural network (CNN)?"
         ],
         "recordings": [
             {
                 "captioners": [
                     "kxk302"
                 ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "1H10M",
+                "date": "2022-01-19",
+                "galaxy_version": "21.09",
+                "length": "1H",
                 "speakers": [
                     "kxk302"
                 ],
-                "youtube_id": "VbzJDkyPL4A"
+                "youtube_id": "EX8gZ1lxhNY"
             }
         ],
         "requirements": [
             {
                 "topic_name": "statistics",
                 "tutorials": [
-                    "intro_deep_learning"
+                    "CNN"
                 ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00258",
+        "short_id": "T00265",
         "short_tools": [
-            "keras_model_builder",
-            "keras_model_config",
             "model_prediction",
-            "plotly_regression_performance_plots",
-            "keras_train_and_eval"
+            "keras_model_config",
+            "tp_cut_tool",
+            "ml_visualization_ex",
+            "keras_train_and_eval",
+            "sklearn_to_categorical",
+            "keras_model_builder"
         ],
         "slides": true,
         "slides_recordings": false,
@@ -247162,23 +254021,22 @@
                     "usegalaxy": true
                 }
             ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                }
-            ]
+            "inexact": []
         },
         "symlink": null,
         "time_estimation": "2H",
-        "title": "Deep Learning (Part 1) - Feedforward neural networks (FNN)",
+        "title": "Image classification in Galaxy with fruit 360 dataset",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/1.0.10.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/1.0.10.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.10.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.10.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/0.5.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/0.5.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.3",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.3",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.3",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_to_categorical/sklearn_to_categorical/1.0.8.3",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0"
         ],
         "topic_name": "statistics",
         "topic_name_human": "Statistics and machine learning",
@@ -247188,43 +254046,70 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "FNN",
+        "tutorial_name": "fruit_360",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/FNN/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/fruit_360/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/FNN/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/FNN/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/fruit_360/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/fruit_360/tutorial.json"
         },
-        "version": 12,
+        "version": 8,
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 197,
-        "visitors": 1919945,
+        "visit_duration": 195,
+        "visitors": 1647157,
         "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "0000-0001-6585-3619",
                         "name": "Kaivan Kamali"
                     }
                 ],
-                "description": "",
+                "description": "Image classification with fruit 360 dataset",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nX_test\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nX_train\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ny_test\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ny_train\"]\n  4[label=\"Create a deep learning model architecture\"]\n  5[label=\"Create deep learning model\"]\n  4 -> 5 [label=\"outfile\"]\n  6[label=\"Deep learning training and evaluation\"]\n  5 -> 6 [label=\"outfile\"]\n  1 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"Model Prediction\"]\n  6 -> 7 [label=\"outfile_object\"]\n  0 -> 7 [label=\"output\"]\n  8[label=\"Plot actual vs predicted curves and residual plots\"]\n  2 -> 8 [label=\"output\"]\n  7 -> 8 [label=\"outfile_predict\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntest_y_10.tsv\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntrain_y_10.tsv\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntrain_X_10.tsv\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntest_X_10.tsv\"]\n  4[label=\"Create a deep learning model architecture\"]\n  5[label=\"Advanced Cut\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Advanced Cut\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"Create deep learning model\"]\n  4 -> 7 [label=\"outfile\"]\n  8[label=\"To categorical\"]\n  6 -> 8 [label=\"output\"]\n  9[label=\"Deep learning training and evaluation\"]\n  7 -> 9 [label=\"outfile\"]\n  2 -> 9 [label=\"output\"]\n  8 -> 9 [label=\"outfile\"]\n  10[label=\"Model Prediction\"]\n  9 -> 10 [label=\"outfile_object\"]\n  9 -> 10 [label=\"outfile_weights\"]\n  3 -> 10 [label=\"output\"]\n  11[label=\"Machine Learning Visualization Extension\"]\n  10 -> 11 [label=\"outfile_predict\"]\n  5 -> 11 [label=\"output\"]\n}",
                 "history": [
                     {
-                        "hash": "72508012689459bf074ee58d075b7e92d91044f0",
-                        "message": "Got rid of . in workflow name",
+                        "hash": "e5dd4d5746166c3bdb191f35b22435d1fe9627cc",
+                        "message": "Fixed an error in WF. Must cut test label data to get labels only",
+                        "num": 5,
+                        "short_hash": "e5dd4d574",
+                        "unix": "1639248119"
+                    },
+                    {
+                        "hash": "4b60e0407fb5348216da2c52c8bed4f7e0d8191c",
+                        "message": "Added Creator section to WF",
+                        "num": 4,
+                        "short_hash": "4b60e0407",
+                        "unix": "1638371876"
+                    },
+                    {
+                        "hash": "6dd9ffea125cd0c6858b425ac786eb37e1e64f67",
+                        "message": "Adde title and tag to WF",
+                        "num": 3,
+                        "short_hash": "6dd9ffea1",
+                        "unix": "1637350965"
+                    },
+                    {
+                        "hash": "d6c5afc6958f3deff1ac8b11c466e8dd35c9b3e5",
+                        "message": "Wrote parts of fruit image classification tutorial.",
+                        "num": 2,
+                        "short_hash": "d6c5afc69",
+                        "unix": "1637285151"
+                    },
+                    {
+                        "hash": "7d52835fb825a71e893a71304557c62c183cd929",
+                        "message": "Added the tutorial directory. Revising copied files now.",
                         "num": 1,
-                        "short_hash": "725080126",
-                        "unix": "1697492492"
+                        "short_hash": "7d52835fb",
+                        "unix": "1637156335"
                     }
                 ],
                 "inputs": [
@@ -247237,141 +254122,816 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "X_test"
+                                "name": "test_y_10.tsv"
                             }
                         ],
-                        "label": "X_test",
+                        "label": "test_y_10.tsv",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 10
+                            "bottom": 274,
+                            "height": 81,
+                            "left": 393,
+                            "right": 593,
+                            "top": 193,
+                            "width": 200,
+                            "x": 393,
+                            "y": 193
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "d9e33ebf-398b-41f5-83d4-aecd6f42817d",
-                        "when": null,
-                        "workflow_outputs": []
+                        "uuid": "af3547d0-573b-429a-8aa9-c653604221c1",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "24c728c7-3029-4732-ab49-fe4d3f8fb1b3"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "train_y_10.tsv"
+                            }
+                        ],
+                        "label": "train_y_10.tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 394,
+                            "height": 81,
+                            "left": 393,
+                            "right": 593,
+                            "top": 313,
+                            "width": 200,
+                            "x": 393,
+                            "y": 313
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "a43671c9-f8b4-4308-a223-e940be9ef115",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "8da8be9c-8ed0-44ae-80af-5f3cc69a95e2"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "train_X_10.tsv"
+                            }
+                        ],
+                        "label": "train_X_10.tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 514,
+                            "height": 81,
+                            "left": 393,
+                            "right": 593,
+                            "top": 433,
+                            "width": 200,
+                            "x": 393,
+                            "y": 433
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "d52183d4-71b5-4750-804a-9c8bb31087c1",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "a65e5725-c11d-4eb4-b163-925399acbb40"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "test_X_10.tsv"
+                            }
+                        ],
+                        "label": "test_X_10.tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 634,
+                            "height": 81,
+                            "left": 393,
+                            "right": 593,
+                            "top": 553,
+                            "width": 200,
+                            "x": 393,
+                            "y": 553
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "21548965-7cd1-453c-8fab-039f51f2320a",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "fd40d525-f72b-4121-bafc-6e380f6128bc"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ntest_y_10.tsv\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ntrain_y_10.tsv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ntrain_X_10.tsv\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\ntest_X_10.tsv\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Create a deep learning model architecture\"];\n  5[\"Advanced Cut\"];\n  0 -->|output| 5;\n  6[\"Advanced Cut\"];\n  1 -->|output| 6;\n  7[\"Create deep learning model\"];\n  4 -->|outfile| 7;\n  8[\"To categorical\"];\n  6 -->|output| 8;\n  9[\"Deep learning training and evaluation\"];\n  7 -->|outfile| 9;\n  2 -->|output| 9;\n  8 -->|outfile| 9;\n  10[\"Model Prediction\"];\n  9 -->|outfile_object| 10;\n  9 -->|outfile_weights| 10;\n  3 -->|output| 10;\n  11[\"Machine Learning Visualization Extension\"];\n  10 -->|outfile_predict| 11;\n  5 -->|output| 11;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "fruit_360",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "test_y_10.tsv"
+                            }
+                        ],
+                        "label": "test_y_10.tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 274,
+                            "height": 81,
+                            "left": 393,
+                            "right": 593,
+                            "top": 193,
+                            "width": 200,
+                            "x": 393,
+                            "y": 193
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "af3547d0-573b-429a-8aa9-c653604221c1",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "24c728c7-3029-4732-ab49-fe4d3f8fb1b3"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "train_y_10.tsv"
+                            }
+                        ],
+                        "label": "train_y_10.tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 394,
+                            "height": 81,
+                            "left": 393,
+                            "right": 593,
+                            "top": 313,
+                            "width": 200,
+                            "x": 393,
+                            "y": 313
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "a43671c9-f8b4-4308-a223-e940be9ef115",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "8da8be9c-8ed0-44ae-80af-5f3cc69a95e2"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "train_X_10.tsv"
+                            }
+                        ],
+                        "label": "train_X_10.tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 514,
+                            "height": 81,
+                            "left": 393,
+                            "right": 593,
+                            "top": 433,
+                            "width": 200,
+                            "x": 393,
+                            "y": 433
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "d52183d4-71b5-4750-804a-9c8bb31087c1",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "a65e5725-c11d-4eb4-b163-925399acbb40"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "test_X_10.tsv"
+                            }
+                        ],
+                        "label": "test_X_10.tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 634,
+                            "height": 81,
+                            "left": 393,
+                            "right": 593,
+                            "top": 553,
+                            "width": 200,
+                            "x": 393,
+                            "y": 553
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "21548965-7cd1-453c-8fab-039f51f2320a",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "fd40d525-f72b-4121-bafc-6e380f6128bc"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/0.5.0",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": null,
+                        "name": "Create a deep learning model architecture",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "json"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 794,
+                            "height": 121,
+                            "left": 393,
+                            "right": 593,
+                            "top": 673,
+                            "width": 200,
+                            "x": 393,
+                            "y": 673
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/0.5.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2b8d85927742",
+                            "name": "keras_model_config",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"model_selection\": {\"model_type\": \"sequential\", \"__current_case__\": 0, \"input_shape\": \"(30000, )\", \"layers\": [{\"__index__\": 0, \"layer_selection\": {\"layer_type\": \"Reshape\", \"__current_case__\": 4, \"target_shape\": \"(100, 100, 3)\"}}, {\"__index__\": 1, \"layer_selection\": {\"layer_type\": \"Conv2D\", \"__current_case__\": 13, \"filters\": \"16\", \"kernel_size\": \"5\", \"activation\": \"relu\", \"kwargs\": \"input_shape=(100, 100, 3)\"}}, {\"__index__\": 2, \"layer_selection\": {\"layer_type\": \"MaxPooling2D\", \"__current_case__\": 30, \"pool_size\": \"(2, 2)\", \"strides\": \"\", \"kwargs\": \"\"}}, {\"__index__\": 3, \"layer_selection\": {\"layer_type\": \"Conv2D\", \"__current_case__\": 13, \"filters\": \"32\", \"kernel_size\": \"5\", \"activation\": \"relu\", \"kwargs\": \"\"}}, {\"__index__\": 4, \"layer_selection\": {\"layer_type\": \"MaxPooling2D\", \"__current_case__\": 30, \"pool_size\": \"(2, 2)\", \"strides\": \"\", \"kwargs\": \"\"}}, {\"__index__\": 5, \"layer_selection\": {\"layer_type\": \"Conv2D\", \"__current_case__\": 13, \"filters\": \"64\", \"kernel_size\": \"5\", \"activation\": \"relu\", \"kwargs\": \"\"}}, {\"__index__\": 6, \"layer_selection\": {\"layer_type\": \"MaxPooling2D\", \"__current_case__\": 30, \"pool_size\": \"(2, 2)\", \"strides\": \"\", \"kwargs\": \"\"}}, {\"__index__\": 7, \"layer_selection\": {\"layer_type\": \"Flatten\", \"__current_case__\": 3, \"data_format\": \"channels_last\"}}, {\"__index__\": 8, \"layer_selection\": {\"layer_type\": \"Dense\", \"__current_case__\": 0, \"units\": \"256\", \"activation\": \"relu\", \"kwargs\": \"\"}}, {\"__index__\": 9, \"layer_selection\": {\"layer_type\": \"Dense\", \"__current_case__\": 0, \"units\": \"10\", \"activation\": \"softmax\", \"kwargs\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "e88ed344-23fb-4122-9af5-d8a75df0f049",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "061ae4fe-aec2-42f7-ac20-cd19cd57c7dc"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Advanced Cut",
+                                "name": "input"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Advanced Cut",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 213,
+                            "height": 112,
+                            "left": 972,
+                            "right": 1172,
+                            "top": 101,
+                            "width": 200,
+                            "x": 972,
+                            "y": 101
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f46f0e4f75c4",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"complement\": \"\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"list\": \"3\\n\"}, \"delimiter\": \"\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "c9066525-d9fb-4e8d-976c-0f9a3b030576",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "490b3818-84b5-4370-9b1f-34af163e1f9a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "input": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Advanced Cut",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 425,
+                            "height": 112,
+                            "left": 613,
+                            "right": 813,
+                            "top": 313,
+                            "width": 200,
+                            "x": 613,
+                            "y": 313
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f46f0e4f75c4",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"tsv\", \"__workflow_invocation_uuid__\": \"c39c89a6466311ec8344005056ba2773\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"complement\": \"\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"list\": [\"3\"]}, \"delimiter\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "9d569bfd-dfc6-4a0a-83ff-751385fb1881",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "388b3201-c37d-412b-b610-3d52983c0365"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/0.5.0",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "mode_selection|infile_json": {
+                                "id": 4,
+                                "output_name": "outfile"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Create deep learning model",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "zip"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 605,
+                            "height": 172,
+                            "left": 613,
+                            "right": 813,
+                            "top": 433,
+                            "width": 200,
+                            "x": 613,
+                            "y": 433
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/0.5.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "5b35833076f0",
+                            "name": "keras_model_builder",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"mode_selection\": {\"mode_type\": \"train_model\", \"__current_case__\": 0, \"infile_json\": {\"__class__\": \"ConnectedValue\"}, \"learning_type\": \"KerasGClassifier\", \"compile_params\": {\"loss\": \"categorical_crossentropy\", \"optimizer_selection\": {\"optimizer_type\": \"Adam\", \"__current_case__\": 4, \"optimizer_options\": {\"lr\": \"0.001\", \"decay\": \"0.0\", \"beta_1\": \"0.9\", \"beta_2\": \"0.999\", \"amsgrad\": \"false\"}}, \"metrics\": [\"acc\"]}, \"fit_params\": {\"epochs\": \"40\", \"batch_size\": \"50\", \"steps_per_epoch\": null, \"validation_steps\": null, \"callbacks\": [{\"__index__\": 0, \"callback_selection\": {\"callback_type\": \"None\", \"__current_case__\": 0}}]}, \"random_seed\": null, \"get_params\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "83b42cfe-b173-421f-999e-341f2891faa0",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "ea147ba5-e226-4529-bce2-3a6eadea74f0"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_to_categorical/sklearn_to_categorical/1.0.8.3",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "infile": {
+                                "id": 6,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool To categorical",
+                                "name": "infile"
+                            }
+                        ],
+                        "label": null,
+                        "name": "To categorical",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 486,
+                            "height": 112,
+                            "left": 838,
+                            "right": 1038,
+                            "top": 374,
+                            "width": 200,
+                            "x": 838,
+                            "y": 374
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_to_categorical/sklearn_to_categorical/1.0.8.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "612ca26c197d",
+                            "name": "sklearn_to_categorical",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"header0\": \"true\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"num_classes\": \"10\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "2daa2610-efc3-4e1e-9da3-532dfb960d62",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "9e1b61c9-cb6b-447c-aba7-376b69e38d6d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.3",
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {
+                            "experiment_schemes|infile_estimator": {
+                                "id": 7,
+                                "output_name": "outfile"
+                            },
+                            "input_options|infile1": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "input_options|infile2": {
+                                "id": 8,
+                                "output_name": "outfile"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Deep learning training and evaluation",
+                                "name": "experiment_schemes"
+                            },
+                            {
+                                "description": "runtime parameter for tool Deep learning training and evaluation",
+                                "name": "input_options"
+                            },
+                            {
+                                "description": "runtime parameter for tool Deep learning training and evaluation",
+                                "name": "input_options"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Deep learning training and evaluation",
+                        "outputs": [
+                            {
+                                "name": "outfile_result",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "outfile_object",
+                                "type": "zip"
+                            },
+                            {
+                                "name": "outfile_weights",
+                                "type": "h5"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 945,
+                            "height": 462,
+                            "left": 1049,
+                            "right": 1249,
+                            "top": 483,
+                            "width": 200,
+                            "x": 1049,
+                            "y": 483
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "470aed90aa41",
+                            "name": "keras_train_and_eval",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"experiment_schemes\": {\"selected_exp_scheme\": \"train_val\", \"__current_case__\": 0, \"infile_estimator\": {\"__class__\": \"RuntimeValue\"}, \"hyperparams_swapping\": {\"infile_params\": {\"__class__\": \"RuntimeValue\"}, \"param_set\": [{\"__index__\": 0, \"sp_name\": null, \"sp_value\": \"\"}]}, \"test_split\": {\"split_algos\": {\"shuffle\": \"simple\", \"__current_case__\": 1, \"test_size\": \"0.2\", \"random_state\": null}}, \"metrics\": {\"scoring\": {\"primary_scoring\": \"default\", \"__current_case__\": 0}}}, \"input_options\": {\"selected_input\": \"tabular\", \"__current_case__\": 0, \"infile1\": {\"__class__\": \"RuntimeValue\"}, \"header1\": \"false\", \"column_selector_options_1\": {\"selected_column_selector_option\": \"all_columns\", \"__current_case__\": 4}, \"infile2\": {\"__class__\": \"RuntimeValue\"}, \"header2\": \"false\", \"column_selector_options_2\": {\"selected_column_selector_option2\": \"all_columns\", \"__current_case__\": 4}}, \"save\": [\"save_estimator\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
+                        "type": "tool",
+                        "uuid": "caaf7c3c-b170-4cd7-b894-a4eecb898844",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile_result",
+                                "uuid": "2eb2e1bc-217d-4e93-a987-312934f9fc19"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outfile_object",
+                                "uuid": "fb9d855c-754d-4d32-8e6a-182664fa1f92"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outfile_weights",
+                                "uuid": "29e19193-b9b7-4ccc-b312-62409c2a7dcc"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.3",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
+                        "id": 10,
+                        "input_connections": {
+                            "infile_estimator": {
+                                "id": 9,
+                                "output_name": "outfile_object"
+                            },
+                            "infile_weights": {
+                                "id": 9,
+                                "output_name": "outfile_weights"
+                            },
+                            "input_options|infile1": {
+                                "id": 3,
+                                "output_name": "output"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "X_train"
+                                "description": "runtime parameter for tool Model Prediction",
+                                "name": "infile_estimator"
+                            },
+                            {
+                                "description": "runtime parameter for tool Model Prediction",
+                                "name": "infile_weights"
+                            },
+                            {
+                                "description": "runtime parameter for tool Model Prediction",
+                                "name": "input_options"
                             }
                         ],
-                        "label": "X_train",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 130
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ad5497f9-1638-4f14-835e-4ba48ccccfad",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "label": null,
+                        "name": "Model Prediction",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "y_test"
+                                "name": "outfile_predict",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "y_test",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 250
+                            "bottom": 877,
+                            "height": 252,
+                            "left": 1347,
+                            "right": 1547,
+                            "top": 625,
+                            "width": 200,
+                            "x": 1347,
+                            "y": 625
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "1e088aa741eb",
+                            "name": "model_prediction",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"infile_estimator\": {\"__class__\": \"RuntimeValue\"}, \"infile_weights\": {\"__class__\": \"RuntimeValue\"}, \"input_options\": {\"selected_input\": \"tabular\", \"__current_case__\": 0, \"infile1\": {\"__class__\": \"RuntimeValue\"}, \"header1\": \"false\", \"column_selector_options_1\": {\"selected_column_selector_option\": \"all_columns\", \"__current_case__\": 4}}, \"method\": \"predict\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "e9939b7b-c469-4823-9339-799a0b47397e",
-                        "when": null,
-                        "workflow_outputs": []
+                        "type": "tool",
+                        "uuid": "91789cf1-96a7-4e81-a989-4c60bed386b8",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile_predict",
+                                "uuid": "82004f35-b05d-4799-a082-1291e103c036"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.3",
                         "errors": null,
-                        "id": 3,
-                        "input_connections": {},
+                        "id": 11,
+                        "input_connections": {
+                            "plotting_selection|infile_predicted": {
+                                "id": 10,
+                                "output_name": "outfile_predict"
+                            },
+                            "plotting_selection|infile_true": {
+                                "id": 5,
+                                "output_name": "output"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "y_train"
+                                "description": "runtime parameter for tool Machine Learning Visualization Extension",
+                                "name": "plotting_selection"
+                            },
+                            {
+                                "description": "runtime parameter for tool Machine Learning Visualization Extension",
+                                "name": "plotting_selection"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Machine Learning Visualization Extension",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "html"
                             }
                         ],
-                        "label": "y_train",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 370
+                            "bottom": 567,
+                            "height": 242,
+                            "left": 1574,
+                            "right": 1774,
+                            "top": 325,
+                            "width": 200,
+                            "x": 1574,
+                            "y": 325
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.3",
+                        "tool_shed_repository": {
+                            "changeset_revision": "e88c782a127d",
+                            "name": "ml_visualization_ex",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"plotting_selection\": {\"plot_type\": \"classification_confusion_matrix\", \"__current_case__\": 6, \"infile_true\": {\"__class__\": \"RuntimeValue\"}, \"header_true\": \"true\", \"column_selector_options_true\": {\"selected_column_selector_option\": \"all_columns\", \"__current_case__\": 4}, \"infile_predicted\": {\"__class__\": \"RuntimeValue\"}, \"header_predicted\": \"true\", \"title\": \"Confusion matrix between true and predicted labels\", \"plot_format\": \"png\", \"plot_color\": \"Greens\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "978203ee-a2bc-4cf7-ad01-0793b7e27431",
-                        "when": null,
-                        "workflow_outputs": []
+                        "type": "tool",
+                        "uuid": "429e06e9-c9d0-447b-a9ab-4b36869beaf8",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "73af0f64-43f7-4b5e-815a-1c0326875a3a"
+                            }
+                        ]
                     }
                 ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nX_test\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nX_train\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ny_test\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\ny_train\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Create a deep learning model architecture\"];\n  5[\"Create deep learning model\"];\n  4 -->|outfile| 5;\n  6[\"Deep learning training and evaluation\"];\n  5 -->|outfile| 6;\n  1 -->|output| 6;\n  3 -->|output| 6;\n  7[\"Model Prediction\"];\n  6 -->|outfile_object| 7;\n  0 -->|output| 7;\n  8[\"Plot actual vs predicted curves and residual plots\"];\n  2 -->|output| 8;\n  7 -->|outfile_predict| 8;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Intro_To_FNN_v1_0_10_0",
-                "outputs": [],
-                "parent_id": "statistics/FNN",
-                "path": "topics/statistics/tutorials/FNN/workflows/Intro_To_FNN_v1_0_10_0.ga",
+                "parent_id": "statistics/fruit_360",
+                "path": "topics/statistics/tutorials/fruit_360/workflows/fruit_360.ga",
                 "tags": [
-                    "statistics",
-                    "ml",
-                    "fnn"
+                    "statistics"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "Intro_To_FNN_v1_0_10_0",
+                "tests": false,
+                "title": "fruit_360",
                 "topic_id": "statistics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-FNN/versions/intro-to-fnn-v1-0-10-0",
-                "tutorial_id": "FNN",
-                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/FNN/workflows/Intro_To_FNN_v1_0_10_0.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/FNN/workflows/Intro_To_FNN_v1_0_10_0.html",
-                "version": 1,
-                "wfid": "statistics-FNN",
-                "wfname": "intro-to-fnn-v1-0-10-0",
-                "workflow": "Intro_To_FNN_v1_0_10_0.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-fruit_360/versions/fruit-360",
+                "tutorial_id": "fruit_360",
+                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/fruit_360/workflows/fruit_360.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/fruit_360/workflows/fruit_360.html",
+                "version": 2,
+                "wfid": "statistics-fruit_360",
+                "wfname": "fruit-360",
+                "workflow": "fruit_360.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/1.0.10.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/1.0.10.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.10.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.10.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/0.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/0.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.3",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.3",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.3",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_to_categorical/sklearn_to_categorical/1.0.8.3",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0"
                 ],
-                "workflowhub_id": "1308"
+                "workflowhub_id": "1322"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/4660497"
+        "zenodo_link": "https://zenodo.org/record/5702887"
     },
     {
         "admin_install": {
@@ -247473,6 +255033,7 @@
         "hands_on": true,
         "id": "statistics/regression_machinelearning",
         "inexact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.no"
         ],
@@ -247493,7 +255054,7 @@
             "Learn ageing biomarkers and predict age from DNA methylation datasets",
             "Learn how visualizations can be used to analyze predictions"
         ],
-        "pageviews": 3093,
+        "pageviews": 3167,
         "pub_date": "2020-01-25",
         "questions": [
             "How to use regression techniques to create predictive models from biological datasets?"
@@ -247514,11 +255075,11 @@
         ],
         "short_id": "T00271",
         "short_tools": [
-            "sklearn_ensemble",
+            "sklearn_build_pipeline",
             "plotly_regression_performance_plots",
             "sklearn_generalized_linear",
+            "sklearn_ensemble",
             "Remove beginning1",
-            "sklearn_build_pipeline",
             "sklearn_searchcv"
         ],
         "slides": false,
@@ -247542,6 +255103,11 @@
                 }
             ],
             "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -247585,7 +255151,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 55,
-        "visitors": 2506,
+        "visitors": 2569,
         "workflows": [
             {
                 "creators": [
@@ -247697,7 +255263,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ntrain_rows\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ntest_rows_labels\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ntest_rows\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Pipeline Builder\"];\n  4[\"Generalized linear models\"];\n  0 -->|output| 4;\n  0 -->|output| 4;\n  5[\"Ensemble methods\"];\n  0 -->|output| 5;\n  0 -->|output| 5;\n  6[\"Remove beginning\"];\n  1 -->|output| 6;\n  7[\"Hyperparameter Search\"];\n  3 -->|outfile| 7;\n  0 -->|output| 7;\n  0 -->|output| 7;\n  8[\"Generalized linear models\"];\n  2 -->|output| 8;\n  4 -->|outfile_fit| 8;\n  9[\"Ensemble methods\"];\n  2 -->|output| 9;\n  5 -->|outfile_fit| 9;\n  10[\"Ensemble methods\"];\n  2 -->|output| 10;\n  7 -->|outfile_object| 10;\n  11[\"Plot actual vs predicted curves and residual plots\"];\n  6 -->|out_file1| 11;\n  8 -->|outfile_predict| 11;\n  12[\"Plot actual vs predicted curves and residual plots\"];\n  1 -->|output| 12;\n  9 -->|outfile_predict| 12;\n  13[\"Plot actual vs predicted curves and residual plots\"];\n  1 -->|output| 13;\n  10 -->|outfile_predict| 13;",
-                "modified": "2024-08-18 00:06:25 +0000",
+                "modified": "2024-10-02 12:08:10 +0000",
                 "name": "ml_regression",
                 "outputs": [],
                 "parent_id": "statistics/regression_machinelearning",
@@ -247727,805 +255293,10 @@
                     "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_generalized_linear/sklearn_generalized_linear/1.0.11.0",
                     "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0"
                 ],
-                "workflowhub_id": "1328"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/2545213"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "pancancer_alternative_genes_pathwaymapper",
-                    "owner": "vijay",
-                    "revisions": "c594c4333b76",
-                    "tool_panel_section_label": "Statistics and machine learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pancancer_apply_weights",
-                    "owner": "vijay",
-                    "revisions": "3543d3e66ecb",
-                    "tool_panel_section_label": "Statistics and machine learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pancancer_classifier",
-                    "owner": "vijay",
-                    "revisions": "20b049f5b3f5",
-                    "tool_panel_section_label": "Statistics and machine learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pancancer_compare_within_models",
-                    "owner": "vijay",
-                    "revisions": "84ac2a86bde1",
-                    "tool_panel_section_label": "Statistics and machine learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pancancer_external_sample_status_prediction",
-                    "owner": "vijay",
-                    "revisions": "8f426aeccfe3",
-                    "tool_panel_section_label": "Statistics and machine learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pancancer_map_mutation_class",
-                    "owner": "vijay",
-                    "revisions": "54c85c40dce1",
-                    "tool_panel_section_label": "Statistics and machine learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pancancer_pathway_count_heatmaps",
-                    "owner": "vijay",
-                    "revisions": "dc1d71493ebf",
-                    "tool_panel_section_label": "Statistics and machine learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pancancer_targene_cell_line_predictions",
-                    "owner": "vijay",
-                    "revisions": "872aab514d37",
-                    "tool_panel_section_label": "Statistics and machine learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pancancer_targene_pharmacology",
-                    "owner": "vijay",
-                    "revisions": "aa5e0e353148",
-                    "tool_panel_section_label": "Statistics and machine learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pancancer_targene_summary_figures",
-                    "owner": "vijay",
-                    "revisions": "d533f991e22e",
-                    "tool_panel_section_label": "Statistics and machine learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pancancer_visualize_decisions",
-                    "owner": "vijay",
-                    "revisions": "f6dd27775d28",
-                    "tool_panel_section_label": "Statistics and machine learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "pancancer_within_disease_analysis",
-                    "owner": "vijay",
-                    "revisions": "99d944bfe9b3",
-                    "tool_panel_section_label": "Statistics and machine learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: pancancer_alternative_genes_pathwaymapper\n  owner: vijay\n  revisions: c594c4333b76\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_apply_weights\n  owner: vijay\n  revisions: 3543d3e66ecb\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_classifier\n  owner: vijay\n  revisions: 20b049f5b3f5\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_compare_within_models\n  owner: vijay\n  revisions: 84ac2a86bde1\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_external_sample_status_prediction\n  owner: vijay\n  revisions: 8f426aeccfe3\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_map_mutation_class\n  owner: vijay\n  revisions: 54c85c40dce1\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_pathway_count_heatmaps\n  owner: vijay\n  revisions: dc1d71493ebf\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_targene_cell_line_predictions\n  owner: vijay\n  revisions: 872aab514d37\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_targene_pharmacology\n  owner: vijay\n  revisions: aa5e0e353148\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_targene_summary_figures\n  owner: vijay\n  revisions: d533f991e22e\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_visualize_decisions\n  owner: vijay\n  revisions: f6dd27775d28\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_within_disease_analysis\n  owner: vijay\n  revisions: 99d944bfe9b3\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.json",
-        "contributors": [
-            {
-                "id": "nvk747",
-                "joined": "2018-07",
-                "name": "Vijay",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nvk747/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nvk747.json"
-            },
-            {
-                "id": "blankenberg",
-                "joined": "2018-07",
-                "name": "Daniel Blankenberg",
-                "orcid": "0000-0002-6833-9049",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankenberg/",
-                "twitter": "dblankenberg",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankenberg.json"
-            }
-        ],
-        "dir": "topics/statistics/tutorials/aberrant_pi3k_pathway_analysis",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "statistics/aberrant_pi3k_pathway_analysis",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Machine learning based Aberrant pathway activity analysis can distinguish normal and tumor samples. Also can identify transcriptomic signature of tumors associated with oncogene or tumor suppressor gene mutations.",
-            "Correlations from classifier predictions and pharmacological responses determine drug sensitivity among cancer cell lines and can be useful in improving personalized medicine approaches.",
-            "Classifier models generated from the suite-papaa can identify potential biomarkers with in the transcriptomic signature of tumors."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Learn to predict aberrant pathway activity using RNA-Seq data, mutational status and copy number variation data from TCGA.",
-            "Apply logistic regression based machine learning algorithms on TCGA data."
-        ],
-        "pageviews": 1063,
-        "pub_date": "2021-05-06",
-        "questions": [
-            "How to predict aberrant pathway activity in The Cancer Genome Atlas (TCGA) using Machine learning approaches?"
-        ],
-        "short_id": "T00260",
-        "short_tools": [
-            "pancancer_alternative_genes_pathwaymapper",
-            "pancancer_visualize_decisions",
-            "pancancer_pathway_count_heatmaps",
-            "pancancer_external_sample_status_prediction",
-            "pancancer_targene_cell_line_predictions",
-            "pancancer_classifier",
-            "pancancer_map_mutation_class",
-            "pancancer_compare_within_models",
-            "pancancer_targene_summary_figures",
-            "pancancer_apply_weights",
-            "pancancer_targene_pharmacology",
-            "pancancer_within_disease_analysis"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "Machine learning",
-            "Pan-cancer",
-            "cancer biomarkers",
-            "oncogenes and tumor suppressor genes"
-        ],
-        "time_estimation": "1H30M",
-        "title": "PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_alternative_genes_pathwaymapper/pancancer_alternative_genes_pathwaymapper/0.1.9",
-            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_apply_weights/pancancer_apply_weights/0.1.9",
-            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_classifier/pancancer_classifier/0.1.9",
-            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_compare_within_models/pancancer_compare_within_models/0.1.9",
-            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_external_sample_status_prediction/pancancer_external_sample_status_prediction/0.1.9",
-            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_map_mutation_class/pancancer_map_mutation_class/0.1.9",
-            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_pathway_count_heatmaps/pancancer_pathway_count_heatmaps/0.1.9",
-            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_targene_cell_line_predictions/pancancer_targene_cell_line_predictions/0.1.9",
-            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_targene_pharmacology/pancancer_targene_pharmacology/0.1.9",
-            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_targene_summary_figures/pancancer_targene_summary_figures/0.1.9",
-            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_visualize_decisions/pancancer_visualize_decisions/0.1.9",
-            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_within_disease_analysis/pancancer_within_disease_analysis/0.1.9"
-        ],
-        "topic_name": "statistics",
-        "topic_name_human": "Statistics and machine learning",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "aberrant_pi3k_pathway_analysis",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.json"
-        },
-        "version": 7,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 202,
-        "visitors": 657,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "PanCancer Aberrant Pathway Activity Analysis: PI3K example",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\npancan_rnaseq_freeze.tsv\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\npancan_mutation_freeze.tsv\"]\n  10[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSE69822_pi3k_sign.txt\"]\n  11[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSE69822_pi3k_trans.csv\"]\n  12[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGDSC_CCLE_common_mut_cnv_binary.tsv.gz\"]\n  13[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nccle_rnaseq_genes_rpkm_20180929_mod.tsv.gz\"]\n  14[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGDSC_EXP_CCLE_converted_name.tsv.gz\"]\n  15[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCCLE_MUT_CNA_AMP_DEL_binary_Revealer.tsv\"]\n  16[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncompounds_of_interest.txt\"]\n  17[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncosmic_cancer_classification.tsv\"]\n  18[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\npath_rtk_ras_pi3k_genes.txt\"]\n  19[label=\"PAPAA: PanCancer classifier\"]\n  17 -> 19 [label=\"output\"]\n  3 -> 19 [label=\"output\"]\n  2 -> 19 [label=\"output\"]\n  1 -> 19 [label=\"output\"]\n  4 -> 19 [label=\"output\"]\n  5 -> 19 [label=\"output\"]\n  0 -> 19 [label=\"output\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncopy_number_loss_status.tsv\"]\n  20[label=\"PAPAA: PanCancer within disease analysis\"]\n  17 -> 20 [label=\"output\"]\n  3 -> 20 [label=\"output\"]\n  2 -> 20 [label=\"output\"]\n  1 -> 20 [label=\"output\"]\n  4 -> 20 [label=\"output\"]\n  5 -> 20 [label=\"output\"]\n  0 -> 20 [label=\"output\"]\n  21[label=\"PAPAA: PanCancer apply weights\"]\n  17 -> 21 [label=\"output\"]\n  3 -> 21 [label=\"output\"]\n  2 -> 21 [label=\"output\"]\n  1 -> 21 [label=\"output\"]\n  4 -> 21 [label=\"output\"]\n  5 -> 21 [label=\"output\"]\n  19 -> 21 [label=\"classifier_coefficients\"]\n  19 -> 21 [label=\"classifier_summary\"]\n  0 -> 21 [label=\"output\"]\n  22[label=\"PAPAA: PanCancer external sample status prediction\"]\n  19 -> 22 [label=\"classifier_summary\"]\n  11 -> 22 [label=\"output\"]\n  19 -> 22 [label=\"classifier_coefficients\"]\n  10 -> 22 [label=\"output\"]\n  23[label=\"PAPAA: PanCancer compare within models\"]\n  19 -> 23 [label=\"classifier_coefficients\"]\n  19 -> 23 [label=\"classifier_summary\"]\n  20 -> 23 [label=\"classifier_coefficients\"]\n  20 -> 23 [label=\"classifier_summary\"]\n  24[label=\"PAPAA: PanCancer visualize decisions\"]\n  21 -> 24 [label=\"classifier_decisions\"]\n  25[label=\"PAPAA: PanCancer alternative genes pathwaymapper\"]\n  21 -> 25 [label=\"classifier_decisions\"]\n  3 -> 25 [label=\"output\"]\n  2 -> 25 [label=\"output\"]\n  1 -> 25 [label=\"output\"]\n  5 -> 25 [label=\"output\"]\n  18 -> 25 [label=\"output\"]\n  26[label=\"PAPAA: PanCancer map mutation class\"]\n  21 -> 26 [label=\"classifier_decisions\"]\n  3 -> 26 [label=\"output\"]\n  2 -> 26 [label=\"output\"]\n  6 -> 26 [label=\"output\"]\n  18 -> 26 [label=\"output\"]\n  27[label=\"PAPAA: PanCancer pathway count heatmaps\"]\n  25 -> 27 [label=\"all_gene_metric_ranks\"]\n  21 -> 27 [label=\"classifier_decisions\"]\n  17 -> 27 [label=\"output\"]\n  3 -> 27 [label=\"output\"]\n  2 -> 27 [label=\"output\"]\n  1 -> 27 [label=\"output\"]\n  4 -> 27 [label=\"output\"]\n  5 -> 27 [label=\"output\"]\n  18 -> 27 [label=\"output\"]\n  25 -> 27 [label=\"pathway_metrics_pathwaymapper\"]\n  0 -> 27 [label=\"output\"]\n  28[label=\"PAPAA: PanCancer targene summary figures\"]\n  25 -> 28 [label=\"all_gene_metric_ranks\"]\n  19 -> 28 [label=\"classifier_summary\"]\n  26 -> 28 [label=\"mutation_classification_scores\"]\n  19 -> 28 [label=\"classifier_coefficients\"]\n  27 -> 28 [label=\"path_events_per_sample\"]\n  19 -> 28 [label=\"summary_counts\"]\n  29[label=\"PAPAA: PanCancer targene cell line predictions\"]\n  28 -> 29 [label=\"amino_acid_mutation_scores\"]\n  7 -> 29 [label=\"output\"]\n  15 -> 29 [label=\"output\"]\n  13 -> 29 [label=\"output\"]\n  19 -> 29 [label=\"classifier_summary\"]\n  8 -> 29 [label=\"output\"]\n  9 -> 29 [label=\"output\"]\n  12 -> 29 [label=\"output\"]\n  14 -> 29 [label=\"output\"]\n  28 -> 29 [label=\"nucleotide_mutation_scores\"]\n  19 -> 29 [label=\"classifier_coefficients\"]\n  18 -> 29 [label=\"output\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncopy_number_gain_status.tsv\"]\n  30[label=\"PAPAA: PanCancer targene pharmacology\"]\n  16 -> 30 [label=\"output\"]\n  29 -> 30 [label=\"gdsc1_ccle_targene_pharmacology_predictions\"]\n  29 -> 30 [label=\"gdsc1_targene_pharmacology_predictions\"]\n  29 -> 30 [label=\"gdsc2_ccle_targene_pharmacology_predictions\"]\n  29 -> 30 [label=\"gdsc2_targene_pharmacology_predictions\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmutation_burden_freeze.tsv\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nsample_freeze.tsv\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmc3.v0.2.8.PUBLIC.maf\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCCLE_DepMap_18Q1_maf_20180207.txt\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ngdsc1_ccle_pharm_fitted_dose_data.txt\"]\n  9[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ngdsc2_ccle_pharm_fitted_dose_data.txt\"]\n}",
-                "history": [
-                    {
-                        "hash": "7ea290c2bf6caf772265aa2a77f2b3c2ed976239",
-                        "message": "aberrant_pi3k_activity_tutorial update-18",
-                        "num": 5,
-                        "short_hash": "7ea290c2b",
-                        "unix": "1608318040"
-                    },
-                    {
-                        "hash": "34bebb50ba04a773e3548ca5648714a73baffb35",
-                        "message": "reformat workflow and add tags and annotation",
-                        "num": 4,
-                        "short_hash": "34bebb50b",
-                        "unix": "1608304565"
-                    },
-                    {
-                        "hash": "b0a2a036f47e662fcc522d0275deaf6579abf15b",
-                        "message": "aberrant_pi3k_activity_tutorial update-17",
-                        "num": 3,
-                        "short_hash": "b0a2a036f",
-                        "unix": "1608220697"
-                    },
-                    {
-                        "hash": "d49e2046f964c70efc6eddffdcdde0b424444d6c",
-                        "message": "pi3k_aberrant_activity_tutorial update-12",
-                        "num": 2,
-                        "short_hash": "d49e2046f",
-                        "unix": "1608048752"
-                    },
-                    {
-                        "hash": "5eeb04b8888e1cd2216696b70312102ecab548c5",
-                        "message": "pi3k_aberrant activity tutorial edit-8",
-                        "num": 1,
-                        "short_hash": "5eeb04b88",
-                        "unix": "1607726416"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "pancan_rnaseq_freeze.tsv"
-                            }
-                        ],
-                        "label": "pancan_rnaseq_freeze.tsv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 155.9921875,
-                            "top": 100
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "a5f07814-0162-40f0-bc9f-33c4aae981bd",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "pancan_mutation_freeze.tsv"
-                            }
-                        ],
-                        "label": "pancan_mutation_freeze.tsv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 155.9921875,
-                            "top": 154.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "085443c7-55ab-486a-9231-cbd7bf0f9f13",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 10,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "GSE69822_pi3k_sign.txt"
-                            }
-                        ],
-                        "label": "GSE69822_pi3k_sign.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 155.9921875,
-                            "top": 665
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "dc7daff3-f271-486a-873c-562122ae633f",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 11,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "GSE69822_pi3k_trans.csv"
-                            }
-                        ],
-                        "label": "GSE69822_pi3k_trans.csv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 155.9921875,
-                            "top": 719.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "eb46a60a-e122-4d04-817a-a77518b35495",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 12,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "GDSC_CCLE_common_mut_cnv_binary.tsv.gz"
-                            }
-                        ],
-                        "label": "GDSC_CCLE_common_mut_cnv_binary.tsv.gz",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 155.9921875,
-                            "top": 774
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "255c456d-686d-4509-b420-1ba0831a9300",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 13,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "ccle_rnaseq_genes_rpkm_20180929_mod.tsv.gz"
-                            }
-                        ],
-                        "label": "ccle_rnaseq_genes_rpkm_20180929_mod.tsv.gz",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 155.9921875,
-                            "top": 838.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "b4fae5c5-59ef-4c15-b796-8934c3988ace",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 14,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "GDSC_EXP_CCLE_converted_name.tsv.gz"
-                            }
-                        ],
-                        "label": "GDSC_EXP_CCLE_converted_name.tsv.gz",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 155.9921875,
-                            "top": 903
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "a20c0bf6-07ee-47f3-9170-4fa80c792e70",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 15,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "CCLE_MUT_CNA_AMP_DEL_binary_Revealer.tsv"
-                            }
-                        ],
-                        "label": "CCLE_MUT_CNA_AMP_DEL_binary_Revealer.tsv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 155.9921875,
-                            "top": 967.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "fb05135f-4178-44e4-bac6-05f00976098b",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 16,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "compounds_of_interest.txt"
-                            }
-                        ],
-                        "label": "compounds_of_interest.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 155.9921875,
-                            "top": 1032
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "9a2ce838-ed30-40c9-b7c8-1863ccbc020e",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 17,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "cosmic_cancer_classification.tsv"
-                            }
-                        ],
-                        "label": "cosmic_cancer_classification.tsv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 155.9921875,
-                            "top": 1086.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "4f425257-9b54-48c7-828c-72812aa6e8fa",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 18,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "path_rtk_ras_pi3k_genes.txt"
-                            }
-                        ],
-                        "label": "path_rtk_ras_pi3k_genes.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 155.9921875,
-                            "top": 1151
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "87edb72c-ff8c-4b05-902d-e31a6bdcefc8",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "copy_number_loss_status.tsv"
-                            }
-                        ],
-                        "label": "copy_number_loss_status.tsv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 155.9921875,
-                            "top": 209
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "e1e7ce2e-0dee-4cc7-bed0-428b1ef6045c",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "copy_number_gain_status.tsv"
-                            }
-                        ],
-                        "label": "copy_number_gain_status.tsv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 155.9921875,
-                            "top": 263.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "237f24d7-f089-47db-9bdb-89b804d346cb",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "mutation_burden_freeze.tsv"
-                            }
-                        ],
-                        "label": "mutation_burden_freeze.tsv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 155.9921875,
-                            "top": 318
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "297e1125-93e2-4dd6-ac9a-4728fef8862a",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "sample_freeze.tsv"
-                            }
-                        ],
-                        "label": "sample_freeze.tsv",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 155.9921875,
-                            "top": 372.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "0cbc8b0f-1933-46a9-8645-2ddf805198cd",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "mc3.v0.2.8.PUBLIC.maf"
-                            }
-                        ],
-                        "label": "mc3.v0.2.8.PUBLIC.maf",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 155.9921875,
-                            "top": 417
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "9c34e447-97a8-4f2d-b485-c4ca627f4021",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "CCLE_DepMap_18Q1_maf_20180207.txt"
-                            }
-                        ],
-                        "label": "CCLE_DepMap_18Q1_maf_20180207.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 155.9921875,
-                            "top": 471.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "e788af12-1a46-4b65-b714-6e4cea14b047",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "gdsc1_ccle_pharm_fitted_dose_data.txt"
-                            }
-                        ],
-                        "label": "gdsc1_ccle_pharm_fitted_dose_data.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 155.9921875,
-                            "top": 536
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f8953224-c89d-4980-8620-2f85e964bdea",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "gdsc2_ccle_pharm_fitted_dose_data.txt"
-                            }
-                        ],
-                        "label": "gdsc2_ccle_pharm_fitted_dose_data.txt",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 155.9921875,
-                            "top": 600.5
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "562ae27c-b15d-4732-89ab-82d5b6135f88",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\npancan_rnaseq_freeze.tsv\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\npancan_mutation_freeze.tsv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"\u2139\ufe0f Input Dataset\\nGSE69822_pi3k_sign.txt\"];\n  style 10 stroke:#2c3143,stroke-width:4px;\n  11[\"\u2139\ufe0f Input Dataset\\nGSE69822_pi3k_trans.csv\"];\n  style 11 stroke:#2c3143,stroke-width:4px;\n  12[\"\u2139\ufe0f Input Dataset\\nGDSC_CCLE_common_mut_cnv_binary.tsv.gz\"];\n  style 12 stroke:#2c3143,stroke-width:4px;\n  13[\"\u2139\ufe0f Input Dataset\\nccle_rnaseq_genes_rpkm_20180929_mod.tsv.gz\"];\n  style 13 stroke:#2c3143,stroke-width:4px;\n  14[\"\u2139\ufe0f Input Dataset\\nGDSC_EXP_CCLE_converted_name.tsv.gz\"];\n  style 14 stroke:#2c3143,stroke-width:4px;\n  15[\"\u2139\ufe0f Input Dataset\\nCCLE_MUT_CNA_AMP_DEL_binary_Revealer.tsv\"];\n  style 15 stroke:#2c3143,stroke-width:4px;\n  16[\"\u2139\ufe0f Input Dataset\\ncompounds_of_interest.txt\"];\n  style 16 stroke:#2c3143,stroke-width:4px;\n  17[\"\u2139\ufe0f Input Dataset\\ncosmic_cancer_classification.tsv\"];\n  style 17 stroke:#2c3143,stroke-width:4px;\n  18[\"\u2139\ufe0f Input Dataset\\npath_rtk_ras_pi3k_genes.txt\"];\n  style 18 stroke:#2c3143,stroke-width:4px;\n  19[\"PAPAA: PanCancer classifier\"];\n  17 -->|output| 19;\n  3 -->|output| 19;\n  2 -->|output| 19;\n  1 -->|output| 19;\n  4 -->|output| 19;\n  5 -->|output| 19;\n  0 -->|output| 19;\n  2[\"\u2139\ufe0f Input Dataset\\ncopy_number_loss_status.tsv\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  20[\"PAPAA: PanCancer within disease analysis\"];\n  17 -->|output| 20;\n  3 -->|output| 20;\n  2 -->|output| 20;\n  1 -->|output| 20;\n  4 -->|output| 20;\n  5 -->|output| 20;\n  0 -->|output| 20;\n  21[\"PAPAA: PanCancer apply weights\"];\n  17 -->|output| 21;\n  3 -->|output| 21;\n  2 -->|output| 21;\n  1 -->|output| 21;\n  4 -->|output| 21;\n  5 -->|output| 21;\n  19 -->|classifier_coefficients| 21;\n  19 -->|classifier_summary| 21;\n  0 -->|output| 21;\n  22[\"PAPAA: PanCancer external sample status prediction\"];\n  19 -->|classifier_summary| 22;\n  11 -->|output| 22;\n  19 -->|classifier_coefficients| 22;\n  10 -->|output| 22;\n  23[\"PAPAA: PanCancer compare within models\"];\n  19 -->|classifier_coefficients| 23;\n  19 -->|classifier_summary| 23;\n  20 -->|classifier_coefficients| 23;\n  20 -->|classifier_summary| 23;\n  24[\"PAPAA: PanCancer visualize decisions\"];\n  21 -->|classifier_decisions| 24;\n  25[\"PAPAA: PanCancer alternative genes pathwaymapper\"];\n  21 -->|classifier_decisions| 25;\n  3 -->|output| 25;\n  2 -->|output| 25;\n  1 -->|output| 25;\n  5 -->|output| 25;\n  18 -->|output| 25;\n  26[\"PAPAA: PanCancer map mutation class\"];\n  21 -->|classifier_decisions| 26;\n  3 -->|output| 26;\n  2 -->|output| 26;\n  6 -->|output| 26;\n  18 -->|output| 26;\n  27[\"PAPAA: PanCancer pathway count heatmaps\"];\n  25 -->|all_gene_metric_ranks| 27;\n  21 -->|classifier_decisions| 27;\n  17 -->|output| 27;\n  3 -->|output| 27;\n  2 -->|output| 27;\n  1 -->|output| 27;\n  4 -->|output| 27;\n  5 -->|output| 27;\n  18 -->|output| 27;\n  25 -->|pathway_metrics_pathwaymapper| 27;\n  0 -->|output| 27;\n  28[\"PAPAA: PanCancer targene summary figures\"];\n  25 -->|all_gene_metric_ranks| 28;\n  19 -->|classifier_summary| 28;\n  26 -->|mutation_classification_scores| 28;\n  19 -->|classifier_coefficients| 28;\n  27 -->|path_events_per_sample| 28;\n  19 -->|summary_counts| 28;\n  29[\"PAPAA: PanCancer targene cell line predictions\"];\n  28 -->|amino_acid_mutation_scores| 29;\n  7 -->|output| 29;\n  15 -->|output| 29;\n  13 -->|output| 29;\n  19 -->|classifier_summary| 29;\n  8 -->|output| 29;\n  9 -->|output| 29;\n  12 -->|output| 29;\n  14 -->|output| 29;\n  28 -->|nucleotide_mutation_scores| 29;\n  19 -->|classifier_coefficients| 29;\n  18 -->|output| 29;\n  3[\"\u2139\ufe0f Input Dataset\\ncopy_number_gain_status.tsv\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  30[\"PAPAA: PanCancer targene pharmacology\"];\n  16 -->|output| 30;\n  29 -->|gdsc1_ccle_targene_pharmacology_predictions| 30;\n  29 -->|gdsc1_targene_pharmacology_predictions| 30;\n  29 -->|gdsc2_ccle_targene_pharmacology_predictions| 30;\n  29 -->|gdsc2_targene_pharmacology_predictions| 30;\n  4[\"\u2139\ufe0f Input Dataset\\nmutation_burden_freeze.tsv\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nsample_freeze.tsv\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nmc3.v0.2.8.PUBLIC.maf\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nCCLE_DepMap_18Q1_maf_20180207.txt\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\ngdsc1_ccle_pharm_fitted_dose_data.txt\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"\u2139\ufe0f Input Dataset\\ngdsc2_ccle_pharm_fitted_dose_data.txt\"];\n  style 9 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "papaa@0.1.9_PI3K_OG_model_tutorial",
-                "outputs": [],
-                "parent_id": "statistics/aberrant_pi3k_pathway_analysis",
-                "path": "topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/workflows/main_workflow.ga",
-                "tags": [
-                    "statistics",
-                    "classification",
-                    "ml",
-                    "cancer"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "papaa@0.1.9_PI3K_OG_model_tutorial",
-                "topic_id": "statistics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-aberrant_pi3k_pathway_analysis/versions/main-workflow",
-                "tutorial_id": "aberrant_pi3k_pathway_analysis",
-                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "statistics-aberrant_pi3k_pathway_analysis",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_alternative_genes_pathwaymapper/pancancer_alternative_genes_pathwaymapper/0.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_apply_weights/pancancer_apply_weights/0.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_classifier/pancancer_classifier/0.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_compare_within_models/pancancer_compare_within_models/0.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_external_sample_status_prediction/pancancer_external_sample_status_prediction/0.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_map_mutation_class/pancancer_map_mutation_class/0.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_pathway_count_heatmaps/pancancer_pathway_count_heatmaps/0.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_targene_cell_line_predictions/pancancer_targene_cell_line_predictions/0.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_targene_pharmacology/pancancer_targene_pharmacology/0.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_targene_summary_figures/pancancer_targene_summary_figures/0.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_visualize_decisions/pancancer_visualize_decisions/0.1.9",
-                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_within_disease_analysis/pancancer_within_disease_analysis/0.1.9"
-                ],
-                "workflowhub_id": "1284"
+                "workflowhub_id": "1328"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/4306639"
+        "zenodo_link": "https://zenodo.org/record/2545213"
     },
     {
         "admin_install": {
@@ -248534,83 +255305,132 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "sklearn_svm_classifier",
+                    "name": "keras_model_builder",
                     "owner": "bgruening",
-                    "revisions": "f9639b488779",
+                    "revisions": "66d7efc06000",
+                    "tool_panel_section_label": "Machine Learning",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "keras_model_config",
+                    "owner": "bgruening",
+                    "revisions": "f22a9297440f",
+                    "tool_panel_section_label": "Machine Learning",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "keras_train_and_eval",
+                    "owner": "bgruening",
+                    "revisions": "818f9b69d8a0",
+                    "tool_panel_section_label": "Machine Learning",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "model_prediction",
+                    "owner": "bgruening",
+                    "revisions": "9991c4ddde14",
                     "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "plotly_regression_performance_plots",
+                    "owner": "bgruening",
+                    "revisions": "389227fa1864",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: sklearn_svm_classifier\n  owner: bgruening\n  revisions: f9639b488779\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/machinelearning/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: keras_model_builder\n  owner: bgruening\n  revisions: 66d7efc06000\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_model_config\n  owner: bgruening\n  revisions: f22a9297440f\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_train_and_eval\n  owner: bgruening\n  revisions: 818f9b69d8a0\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: model_prediction\n  owner: bgruening\n  revisions: 9991c4ddde14\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: plotly_regression_performance_plots\n  owner: bgruening\n  revisions: 389227fa1864\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/FNN/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "uni-freiburg",
-                    "eurosciencegateway",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "email": "anup.rulez@gmail.com",
-                "id": "anuprulez",
-                "joined": "2018-08",
-                "name": "Anup Kumar",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/anuprulez/",
-                "twitter": "musafirtweetsz",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/anuprulez.json"
+                "email": "kxk302@gmail.com",
+                "id": "kxk302",
+                "joined": "2021-02",
+                "name": "Kaivan Kamali",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kxk302/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/kxk302.json"
             }
         ],
-        "dir": "topics/statistics/tutorials/machinelearning",
+        "dir": "topics/statistics/tutorials/FNN",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.no",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "statistics",
+                "tutorials": [
+                    "RNN"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "statistics/machinelearning",
+        "id": "statistics/FNN",
         "inexact_supported_servers": [
-            "UseGalaxy.fr"
+            "UseGalaxy.be",
+            "UseGalaxy.no"
         ],
         "js_requirements": {
-            "mathjax": null,
+            "mathjax": 2165,
             "mermaid": false
         },
-        "key_points": [
-            "Machine learning algorithms learn features from data.",
-            "It is used for multiple tasks such as classification, regression, clustering and so on.",
-            "Multiple learning tasks can be performed using Galaxy's machine learning tools.",
-            "For the classification and regression tasks, data is divided into training and test sets.",
-            "Each sample/record in the training data has a category/class/label.",
-            "A machine learning algorithm learns features from the training data and do predictions on the test data."
-        ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-05",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Provide the basics of machine learning and its variants.",
-            "Learn how to do classification using the training and test data.",
-            "Learn how to use Galaxy's machine learning tools."
+            "Understand the inspiration for neural networks",
+            "Learn various activation functions, and classification/regression problems solved by neural networks",
+            "Discuss various cost/loss functions and the backpropagation algorithm",
+            "Learn how to create a neural network using Galaxy's deep learning tools",
+            "Solve a simple regression problem, car purchase price prediction, via FNN in Galaxy"
         ],
-        "pageviews": 2717,
-        "pub_date": "2018-11-05",
+        "pageviews": 5351360,
+        "pub_date": "2021-04-28",
         "questions": [
-            "What is machine learning?",
-            "Why is it useful?",
-            "What are its different approaches?"
+            "What is a feedforward neural network (FNN)?",
+            "What are some applications of FNN?"
         ],
-        "requirements": null,
-        "short_id": "T00270",
+        "recordings": [
+            {
+                "captioners": [
+                    "kxk302"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "1H10M",
+                "speakers": [
+                    "kxk302"
+                ],
+                "youtube_id": "VbzJDkyPL4A"
+            }
+        ],
+        "requirements": [
+            {
+                "topic_name": "statistics",
+                "tutorials": [
+                    "intro_deep_learning"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00258",
         "short_tools": [
-            "sklearn_svm_classifier"
+            "plotly_regression_performance_plots",
+            "model_prediction",
+            "keras_model_config",
+            "keras_train_and_eval",
+            "keras_model_builder"
         ],
-        "slides": false,
+        "slides": true,
         "slides_recordings": false,
         "supported_servers": {
             "exact": [
@@ -248624,11 +255444,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -248642,17 +255457,26 @@
             ],
             "inexact": [
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 }
             ]
         },
         "symlink": null,
-        "time_estimation": "30M",
-        "title": "Basics of machine learning",
+        "time_estimation": "2H",
+        "title": "Deep Learning (Part 1) - Feedforward neural networks (FNN)",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.8.1"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/1.0.10.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/1.0.10.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.10.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.10.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1"
         ],
         "topic_name": "statistics",
         "topic_name_human": "Statistics and machine learning",
@@ -248662,65 +255486,43 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "machinelearning",
+        "tutorial_name": "FNN",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/machinelearning/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/FNN/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/machinelearning/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/machinelearning/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/FNN/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/FNN/tutorial.json"
         },
-        "version": 13,
+        "version": 12,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 168,
-        "visitors": 1951,
+        "visit_duration": 197,
+        "visitors": 1989806,
         "workflows": [
             {
-                "creators": [],
-                "description": "Basics of machine learning",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0001-6585-3619",
+                        "name": "Kaivan Kamali"
+                    }
+                ],
+                "description": "",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nbreast-w_train\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nbreast-w_test\"]\n  2[label=\"Support vector machines SVMs\"]\n  0 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Support vector machines SVMs\"]\n  1 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"outfile_fit\"]\n  k03e30bebfc0141848649057c13bb626a[color=lightseagreen,label=\"Output\\noutfile_predict\"]\n  3 -> k03e30bebfc0141848649057c13bb626a\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nX_test\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nX_train\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ny_test\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ny_train\"]\n  4[label=\"Create a deep learning model architecture\"]\n  5[label=\"Create deep learning model\"]\n  4 -> 5 [label=\"outfile\"]\n  6[label=\"Deep learning training and evaluation\"]\n  5 -> 6 [label=\"outfile\"]\n  1 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"Model Prediction\"]\n  6 -> 7 [label=\"outfile_object\"]\n  0 -> 7 [label=\"output\"]\n  8[label=\"Plot actual vs predicted curves and residual plots\"]\n  2 -> 8 [label=\"output\"]\n  7 -> 8 [label=\"outfile_predict\"]\n}",
                 "history": [
                     {
-                        "hash": "6f18e04f0d03d9f42bc3dc88d708eadacd4acd96",
-                        "message": "Add workflow_outputs to machine_learning.ga for testing, add a test",
-                        "num": 5,
-                        "short_hash": "6f18e04f0",
-                        "unix": "1590540700"
-                    },
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 4,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 3,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "9f881ab875f38f8d4299a1fb0bc2f22b422d1eda",
-                        "message": "checking ML tutorials, updating workflows",
-                        "num": 2,
-                        "short_hash": "9f881ab87",
-                        "unix": "1578588754"
-                    },
-                    {
-                        "hash": "b6985b9499618c6ad25d58d67358618504d608a3",
-                        "message": "workflow for machine_learning",
+                        "hash": "72508012689459bf074ee58d075b7e92d91044f0",
+                        "message": "Got rid of . in workflow name",
                         "num": 1,
-                        "short_hash": "b6985b949",
-                        "unix": "1550745160"
+                        "short_hash": "725080126",
+                        "unix": "1697492492"
                     }
                 ],
                 "inputs": [
@@ -248733,21 +255535,22 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "breast-w_train"
+                                "name": "X_test"
                             }
                         ],
-                        "label": "breast-w_train",
+                        "label": "X_test",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 200
+                            "left": 10,
+                            "top": 10
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"breast-w_train\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "fa0bbf50-4881-407c-b9be-78cc96c2f00d",
+                        "uuid": "d9e33ebf-398b-41f5-83d4-aecd6f42817d",
+                        "when": null,
                         "workflow_outputs": []
                     },
                     {
@@ -248759,606 +255562,480 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "breast-w_test"
+                                "name": "X_train"
                             }
                         ],
-                        "label": "breast-w_test",
+                        "label": "X_train",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 289.76666259765625
+                            "left": 10,
+                            "top": 130
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"breast-w_test\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "b3b595f7-7a7a-416e-934d-84c6af042169",
+                        "uuid": "ad5497f9-1638-4f14-835e-4ba48ccccfad",
+                        "when": null,
                         "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nbreast-w_train\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nbreast-w_test\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Support vector machines SVMs\"];\n  0 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Support vector machines SVMs\"];\n  1 -->|output| 3;\n  2 -->|outfile_fit| 3;\n  03e30beb-fc01-4184-8649-057c13bb626a[\"Output\\noutfile_predict\"];\n  3 --> 03e30beb-fc01-4184-8649-057c13bb626a;\n  style 03e30beb-fc01-4184-8649-057c13bb626a stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Machine Learning",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.8.1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "selected_tasks|infile_data": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "selected_tasks|infile_model": {
-                                "id": 2,
-                                "output_name": "outfile_fit"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Support vector machines (SVMs)",
-                        "outputs": [
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "outfile_predict",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "y_test"
                             }
                         ],
+                        "label": "y_test",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 788.5333251953125,
-                            "top": 200
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.8.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2df8f5c30edc",
-                            "name": "sklearn_svm_classifier",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 10,
+                            "top": 250
                         },
-                        "tool_state": "{\"__page__\": null, \"selected_tasks\": \"{\\\"__current_case__\\\": 0, \\\"header\\\": \\\"true\\\", \\\"infile_data\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"infile_model\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"prediction_options\\\": {\\\"__current_case__\\\": 0, \\\"prediction_option\\\": \\\"predict\\\"}, \\\"selected_task\\\": \\\"load\\\"}\", \"chromInfo\": \"\\\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.8.1",
-                        "type": "tool",
-                        "uuid": "98bd60bb-4e32-4c11-9955-eade434a3817",
-                        "workflow_outputs": [
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "e9939b7b-c469-4823-9339-799a0b47397e",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": "outfile_predict",
-                                "output_name": "outfile_predict",
-                                "uuid": "03e30beb-fc01-4184-8649-057c13bb626a"
+                                "description": "",
+                                "name": "y_train"
                             }
-                        ]
+                        ],
+                        "label": "y_train",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 10,
+                            "top": 370
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "978203ee-a2bc-4cf7-ad01-0793b7e27431",
+                        "when": null,
+                        "workflow_outputs": []
                     }
                 ],
-                "parent_id": "statistics/machinelearning",
-                "path": "topics/statistics/tutorials/machinelearning/workflows/machine_learning.ga",
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nX_test\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nX_train\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ny_test\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\ny_train\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Create a deep learning model architecture\"];\n  5[\"Create deep learning model\"];\n  4 -->|outfile| 5;\n  6[\"Deep learning training and evaluation\"];\n  5 -->|outfile| 6;\n  1 -->|output| 6;\n  3 -->|output| 6;\n  7[\"Model Prediction\"];\n  6 -->|outfile_object| 7;\n  0 -->|output| 7;\n  8[\"Plot actual vs predicted curves and residual plots\"];\n  2 -->|output| 8;\n  7 -->|outfile_predict| 8;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "Intro_To_FNN_v1_0_10_0",
+                "outputs": [],
+                "parent_id": "statistics/FNN",
+                "path": "topics/statistics/tutorials/FNN/workflows/Intro_To_FNN_v1_0_10_0.ga",
                 "tags": [
+                    "statistics",
                     "ml",
-                    "statistics"
+                    "fnn"
                 ],
-                "test_results": {
-                    "eu": {
-                        "summary": {
-                            "num_errors": 0,
-                            "num_failures": 0,
-                            "num_skips": 0,
-                            "num_tests": 1
-                        },
-                        "tests": [
-                            {
-                                "data": {
-                                    "end_datetime": "2023-05-23T13:04:36.233588",
-                                    "inputs": {
-                                        "breast-w_test": {
-                                            "class": "File",
-                                            "filetype": "tabular",
-                                            "location": "https://zenodo.org/api/files/0d468136-5025-4c0f-bf8b-a8277a513a93/breast-w_test.tsv"
-                                        },
-                                        "breast-w_train": {
-                                            "class": "File",
-                                            "filetype": "tabular",
-                                            "location": "https://zenodo.org/api/files/0d468136-5025-4c0f-bf8b-a8277a513a93/breast-w_train.tsv"
-                                        }
-                                    },
-                                    "invocation_details": {
-                                        "details": {
-                                            "error_message": "",
-                                            "history_id": "2507553dd7587c83",
-                                            "history_state": "ok",
-                                            "invocation_id": "f5ae862b1590700e",
-                                            "invocation_state": "scheduled",
-                                            "workflow_id": "1017f47ddfcbe87f"
-                                        },
-                                        "steps": {
-                                            "0. breast-w_train": {
-                                                "action": null,
-                                                "id": "e6252d7ebd7b816c",
-                                                "job_id": null,
-                                                "jobs": [],
-                                                "model_class": "WorkflowInvocationStep",
-                                                "order_index": 0,
-                                                "output_collections": {},
-                                                "outputs": {
-                                                    "output": {
-                                                        "id": "4838ba20a6d86765c9cd0650a6a12ca3",
-                                                        "src": "hda",
-                                                        "uuid": "b175db07-7724-4a00-83b4-5a6cae8c6763"
-                                                    }
-                                                },
-                                                "state": "scheduled",
-                                                "subworkflow": null,
-                                                "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-23T10:59:49.573476",
-                                                "workflow_step_id": "646ce6c1fd8f1f07",
-                                                "workflow_step_label": "breast-w_train",
-                                                "workflow_step_uuid": "fa0bbf50-4881-407c-b9be-78cc96c2f00d"
-                                            },
-                                            "1. breast-w_test": {
-                                                "action": null,
-                                                "id": "9974f0360058d84f",
-                                                "job_id": null,
-                                                "jobs": [],
-                                                "model_class": "WorkflowInvocationStep",
-                                                "order_index": 1,
-                                                "output_collections": {},
-                                                "outputs": {
-                                                    "output": {
-                                                        "id": "4838ba20a6d867654de1bc22fefb9f52",
-                                                        "src": "hda",
-                                                        "uuid": "c438049f-86b6-415a-a9a0-554efa397b28"
-                                                    }
-                                                },
-                                                "state": "scheduled",
-                                                "subworkflow": null,
-                                                "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-23T10:59:49.573483",
-                                                "workflow_step_id": "5b42eb6dee4ed8f3",
-                                                "workflow_step_label": "breast-w_test",
-                                                "workflow_step_uuid": "b3b595f7-7a7a-416e-934d-84c6af042169"
-                                            },
-                                            "2. Unnamed step": {
-                                                "action": null,
-                                                "id": "1c214839f0e68f30",
-                                                "job_id": "11ac94870d0bb33a9209f9a6c46d5330",
-                                                "jobs": [
-                                                    {
-                                                        "command_line": "python '/data/jwd02f/main/060/156/60156804/configs/tmpyxkw996c' '/data/jwd02f/main/060/156/60156804/configs/tmp5q24hxye'",
-                                                        "command_version": "1.0.8.1",
-                                                        "create_time": "2023-05-23T10:59:49.569976",
-                                                        "dependencies": [],
-                                                        "exit_code": 0,
-                                                        "external_id": "43631361",
-                                                        "galaxy_version": "23.0",
-                                                        "history_id": "2507553dd7587c83",
-                                                        "id": "11ac94870d0bb33a9209f9a6c46d5330",
-                                                        "inputs": {
-                                                            "selected_tasks|selected_algorithms|infile1": {
-                                                                "id": "4838ba20a6d86765c9cd0650a6a12ca3",
-                                                                "src": "hda",
-                                                                "uuid": "b175db07-7724-4a00-83b4-5a6cae8c6763"
-                                                            },
-                                                            "selected_tasks|selected_algorithms|infile2": {
-                                                                "id": "4838ba20a6d86765c9cd0650a6a12ca3",
-                                                                "src": "hda",
-                                                                "uuid": "b175db07-7724-4a00-83b4-5a6cae8c6763"
-                                                            }
-                                                        },
-                                                        "job_messages": [],
-                                                        "job_metrics": [
-                                                            {
-                                                                "name": "hostname",
-                                                                "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c125m425-1660.novalocal",
-                                                                "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c125m425-1660.novalocal"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_slots",
-                                                                "plugin": "core",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "Cores Allocated",
-                                                                "value": "1"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_memory_mb",
-                                                                "plugin": "core",
-                                                                "raw_value": "3891.0000000",
-                                                                "title": "Memory Allocated (MB)",
-                                                                "value": "3891"
-                                                            },
-                                                            {
-                                                                "name": "start_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684839593.0000000",
-                                                                "title": "Job Start Time",
-                                                                "value": "2023-05-23 12:59:53"
-                                                            },
-                                                            {
-                                                                "name": "end_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684839787.0000000",
-                                                                "title": "Job End Time",
-                                                                "value": "2023-05-23 13:03:07"
-                                                            },
-                                                            {
-                                                                "name": "runtime_seconds",
-                                                                "plugin": "core",
-                                                                "raw_value": "194.0000000",
-                                                                "title": "Job Runtime (Wall Clock)",
-                                                                "value": "3 minutes"
-                                                            },
-                                                            {
-                                                                "name": "cpuacct.usage",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "22317680902.0000000",
-                                                                "title": "CPU Time",
-                                                                "value": "22.317680902 seconds"
-                                                            },
-                                                            {
-                                                                "name": "memory.failcnt",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Failed to allocate memory count",
-                                                                "value": 0.0
-                                                            },
-                                                            {
-                                                                "name": "memory.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "10737418240.0000000",
-                                                                "title": "Memory limit on cgroup (MEM)",
-                                                                "value": "10.0 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "427237376.0000000",
-                                                                "title": "Max memory usage (MEM)",
-                                                                "value": "407.4 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "9223372036854771712.0000000",
-                                                                "title": "Memory limit on cgroup (MEM+SWP)",
-                                                                "value": "8.0 EB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "427237376.0000000",
-                                                                "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "407.4 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.oom_kill_disable",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "OOM Control enabled",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.under_oom",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Was OOM Killer active?",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.soft_limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Memory softlimit on cgroup",
-                                                                "value": "0 bytes"
-                                                            }
-                                                        ],
-                                                        "job_stderr": "",
-                                                        "job_stdout": "",
-                                                        "model_class": "Job",
-                                                        "output_collections": {},
-                                                        "outputs": {
-                                                            "outfile_fit": {
-                                                                "id": "4838ba20a6d86765b565f48d5ac913b1",
-                                                                "src": "hda",
-                                                                "uuid": "1a17ebe9-c0e0-4ebd-bae0-5159331683bb"
-                                                            }
-                                                        },
-                                                        "params": {
-                                                            "__input_ext": "\"tabular\"",
-                                                            "__workflow_invocation_uuid__": "\"ebe5f326f95811ed916d001e67d2ec02\"",
-                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
-                                                            "dbkey": "\"?\"",
-                                                            "selected_tasks": "{\"__current_case__\": 1, \"selected_algorithms\": {\"__current_case__\": 2, \"input_options\": {\"__current_case__\": 0, \"column_selector_options_1\": {\"__current_case__\": 3, \"col1\": \"target\", \"selected_column_selector_option\": \"all_but_by_header_name\"}, \"column_selector_options_2\": {\"__current_case__\": 2, \"col2\": \"target\", \"selected_column_selector_option2\": \"by_header_name\"}, \"header1\": true, \"header2\": true, \"infile1\": {\"values\": [{\"id\": 137642769, \"src\": \"hda\"}]}, \"infile2\": {\"values\": [{\"id\": 137642769, \"src\": \"hda\"}]}, \"selected_input\": \"tabular\"}, \"options\": {\"C\": \"1.0\", \"dual\": true, \"fit_intercept\": true, \"intercept_scaling\": \"1.0\", \"loss\": \"squared_hinge\", \"max_iter\": \"1000\", \"multi_class\": \"ovr\", \"penalty\": \"l2\", \"random_state\": null, \"tol\": \"0.001\"}, \"selected_algorithm\": \"LinearSVC\"}, \"selected_task\": \"train\"}"
-                                                        },
-                                                        "state": "ok",
-                                                        "stderr": "OMP: Info #212: KMP_AFFINITY: decoding x2APIC ids.\nOMP: Info #210: KMP_AFFINITY: Affinity capable, using global cpuid leaf 11 info\nOMP: Info #154: KMP_AFFINITY: Initial OS proc set respected: 0-124\nOMP: Info #156: KMP_AFFINITY: 125 available OS procs\nOMP: Info #157: KMP_AFFINITY: Uniform topology\nOMP: Info #179: KMP_AFFINITY: 125 packages x 1 cores/pkg x 1 threads/core (125 total cores)\nOMP: Info #214: KMP_AFFINITY: OS proc to physical thread map:\nOMP: Info #171: KMP_AFFINITY: OS proc 0 maps to package 0 \nOMP: Info #171: KMP_AFFINITY: OS proc 1 maps to package 1 \nOMP: Info #171: KMP_AFFINITY: OS proc 2 maps to package 2 \nOMP: Info #171: KMP_AFFINITY: OS proc 3 maps to package 3 \nOMP: Info #171: KMP_AFFINITY: OS proc 4 maps to package 4 \nOMP: Info #171: KMP_AFFINITY: OS proc 5 maps to package 5 \nOMP: Info #171: KMP_AFFINITY: OS proc 6 maps to package 6 \nOMP: Info #171: KMP_AFFINITY: OS proc 7 maps to package 7 \nOMP: Info #171: KMP_AFFINITY: OS proc 8 maps to package 8 \nOMP: Info #171: KMP_AFFINITY: OS proc 9 maps to package 9 \nOMP: Info #171: KMP_AFFINITY: OS proc 10 maps to package 10 \nOMP: Info #171: KMP_AFFINITY: OS proc 11 maps to package 11 \nOMP: Info #171: KMP_AFFINITY: OS proc 12 maps to package 12 \nOMP: Info #171: KMP_AFFINITY: OS proc 13 maps to package 13 \nOMP: Info #171: KMP_AFFINITY: OS proc 14 maps to package 14 \nOMP: Info #171: KMP_AFFINITY: OS proc 15 maps to package 15 \nOMP: Info #171: KMP_AFFINITY: OS proc 16 maps to package 16 \nOMP: Info #171: KMP_AFFINITY: OS proc 17 maps to package 17 \nOMP: Info #171: KMP_AFFINITY: OS proc 18 maps to package 18 \nOMP: Info #171: KMP_AFFINITY: OS proc 19 maps to package 19 \nOMP: Info #171: KMP_AFFINITY: OS proc 20 maps to package 20 \nOMP: Info #171: KMP_AFFINITY: OS proc 21 maps to package 21 \nOMP: Info #171: KMP_AFFINITY: OS proc 22 maps to package 22 \nOMP: Info #171: KMP_AFFINITY: OS proc 23 maps to package 23 \nOMP: Info #171: KMP_AFFINITY: OS proc 24 maps to package 24 \nOMP: Info #171: KMP_AFFINITY: OS proc 25 maps to package 25 \nOMP: Info #171: KMP_AFFINITY: OS proc 26 maps to package 26 \nOMP: Info #171: KMP_AFFINITY: OS proc 27 maps to package 27 \nOMP: Info #171: KMP_AFFINITY: OS proc 28 maps to package 28 \nOMP: Info #171: KMP_AFFINITY: OS proc 29 maps to package 29 \nOMP: Info #171: KMP_AFFINITY: OS proc 30 maps to package 30 \nOMP: Info #171: KMP_AFFINITY: OS proc 31 maps to package 31 \nOMP: Info #171: KMP_AFFINITY: OS proc 32 maps to package 32 \nOMP: Info #171: KMP_AFFINITY: OS proc 33 maps to package 33 \nOMP: Info #171: KMP_AFFINITY: OS proc 34 maps to package 34 \nOMP: Info #171: KMP_AFFINITY: OS proc 35 maps to package 35 \nOMP: Info #171: KMP_AFFINITY: OS proc 36 maps to package 36 \nOMP: Info #171: KMP_AFFINITY: OS proc 37 maps to package 37 \nOMP: Info #171: KMP_AFFINITY: OS proc 38 maps to package 38 \nOMP: Info #171: KMP_AFFINITY: OS proc 39 maps to package 39 \nOMP: Info #171: KMP_AFFINITY: OS proc 40 maps to package 40 \nOMP: Info #171: KMP_AFFINITY: OS proc 41 maps to package 41 \nOMP: Info #171: KMP_AFFINITY: OS proc 42 maps to package 42 \nOMP: Info #171: KMP_AFFINITY: OS proc 43 maps to package 43 \nOMP: Info #171: KMP_AFFINITY: OS proc 44 maps to package 44 \nOMP: Info #171: KMP_AFFINITY: OS proc 45 maps to package 45 \nOMP: Info #171: KMP_AFFINITY: OS proc 46 maps to package 46 \nOMP: Info #171: KMP_AFFINITY: OS proc 47 maps to package 47 \nOMP: Info #171: KMP_AFFINITY: OS proc 48 maps to package 48 \nOMP: Info #171: KMP_AFFINITY: OS proc 49 maps to package 49 \nOMP: Info #171: KMP_AFFINITY: OS proc 50 maps to package 50 \nOMP: Info #171: KMP_AFFINITY: OS proc 51 maps to package 51 \nOMP: Info #171: KMP_AFFINITY: OS proc 52 maps to package 52 \nOMP: Info #171: KMP_AFFINITY: OS proc 53 maps to package 53 \nOMP: Info #171: KMP_AFFINITY: OS proc 54 maps to package 54 \nOMP: Info #171: KMP_AFFINITY: OS proc 55 maps to package 55 \nOMP: Info #171: KMP_AFFINITY: OS proc 56 maps to package 56 \nOMP: Info #171: KMP_AFFINITY: OS proc 57 maps to package 57 \nOMP: Info #171: KMP_AFFINITY: OS proc 58 maps to package 58 \nOMP: Info #171: KMP_AFFINITY: OS proc 59 maps to package 59 \nOMP: Info #171: KMP_AFFINITY: OS proc 60 maps to package 60 \nOMP: Info #171: KMP_AFFINITY: OS proc 61 maps to package 61 \nOMP: Info #171: KMP_AFFINITY: OS proc 62 maps to package 62 \nOMP: Info #171: KMP_AFFINITY: OS proc 63 maps to package 63 \nOMP: Info #171: KMP_AFFINITY: OS proc 64 maps to package 64 \nOMP: Info #171: KMP_AFFINITY: OS proc 65 maps to package 65 \nOMP: Info #171: KMP_AFFINITY: OS proc 66 maps to package 66 \nOMP: Info #171: KMP_AFFINITY: OS proc 67 maps to package 67 \nOMP: Info #171: KMP_AFFINITY: OS proc 68 maps to package 68 \nOMP: Info #171: KMP_AFFINITY: OS proc 69 maps to package 69 \nOMP: Info #171: KMP_AFFINITY: OS proc 70 maps to package 70 \nOMP: Info #171: KMP_AFFINITY: OS proc 71 maps to package 71 \nOMP: Info #171: KMP_AFFINITY: OS proc 72 maps to package 72 \nOMP: Info #171: KMP_AFFINITY: OS proc 73 maps to package 73 \nOMP: Info #171: KMP_AFFINITY: OS proc 74 maps to package 74 \nOMP: Info #171: KMP_AFFINITY: OS proc 75 maps to package 75 \nOMP: Info #171: KMP_AFFINITY: OS proc 76 maps to package 76 \nOMP: Info #171: KMP_AFFINITY: OS proc 77 maps to package 77 \nOMP: Info #171: KMP_AFFINITY: OS proc 78 maps to package 78 \nOMP: Info #171: KMP_AFFINITY: OS proc 79 maps to package 79 \nOMP: Info #171: KMP_AFFINITY: OS proc 80 maps to package 80 \nOMP: Info #171: KMP_AFFINITY: OS proc 81 maps to package 81 \nOMP: Info #171: KMP_AFFINITY: OS proc 82 maps to package 82 \nOMP: Info #171: KMP_AFFINITY: OS proc 83 maps to package 83 \nOMP: Info #171: KMP_AFFINITY: OS proc 84 maps to package 84 \nOMP: Info #171: KMP_AFFINITY: OS proc 85 maps to package 85 \nOMP: Info #171: KMP_AFFINITY: OS proc 86 maps to package 86 \nOMP: Info #171: KMP_AFFINITY: OS proc 87 maps to package 87 \nOMP: Info #171: KMP_AFFINITY: OS proc 88 maps to package 88 \nOMP: Info #171: KMP_AFFINITY: OS proc 89 maps to package 89 \nOMP: Info #171: KMP_AFFINITY: OS proc 90 maps to package 90 \nOMP: Info #171: KMP_AFFINITY: OS proc 91 maps to package 91 \nOMP: Info #171: KMP_AFFINITY: OS proc 92 maps to package 92 \nOMP: Info #171: KMP_AFFINITY: OS proc 93 maps to package 93 \nOMP: Info #171: KMP_AFFINITY: OS proc 94 maps to package 94 \nOMP: Info #171: KMP_AFFINITY: OS proc 95 maps to package 95 \nOMP: Info #171: KMP_AFFINITY: OS proc 96 maps to package 96 \nOMP: Info #171: KMP_AFFINITY: OS proc 97 maps to package 97 \nOMP: Info #171: KMP_AFFINITY: OS proc 98 maps to package 98 \nOMP: Info #171: KMP_AFFINITY: OS proc 99 maps to package 99 \nOMP: Info #171: KMP_AFFINITY: OS proc 100 maps to package 100 \nOMP: Info #171: KMP_AFFINITY: OS proc 101 maps to package 101 \nOMP: Info #171: KMP_AFFINITY: OS proc 102 maps to package 102 \nOMP: Info #171: KMP_AFFINITY: OS proc 103 maps to package 103 \nOMP: Info #171: KMP_AFFINITY: OS proc 104 maps to package 104 \nOMP: Info #171: KMP_AFFINITY: OS proc 105 maps to package 105 \nOMP: Info #171: KMP_AFFINITY: OS proc 106 maps to package 106 \nOMP: Info #171: KMP_AFFINITY: OS proc 107 maps to package 107 \nOMP: Info #171: KMP_AFFINITY: OS proc 108 maps to package 108 \nOMP: Info #171: KMP_AFFINITY: OS proc 109 maps to package 109 \nOMP: Info #171: KMP_AFFINITY: OS proc 110 maps to package 110 \nOMP: Info #171: KMP_AFFINITY: OS proc 111 maps to package 111 \nOMP: Info #171: KMP_AFFINITY: OS proc 112 maps to package 112 \nOMP: Info #171: KMP_AFFINITY: OS proc 113 maps to package 113 \nOMP: Info #171: KMP_AFFINITY: OS proc 114 maps to package 114 \nOMP: Info #171: KMP_AFFINITY: OS proc 115 maps to package 115 \nOMP: Info #171: KMP_AFFINITY: OS proc 116 maps to package 116 \nOMP: Info #171: KMP_AFFINITY: OS proc 117 maps to package 117 \nOMP: Info #171: KMP_AFFINITY: OS proc 118 maps to package 118 \nOMP: Info #171: KMP_AFFINITY: OS proc 119 maps to package 119 \nOMP: Info #171: KMP_AFFINITY: OS proc 120 maps to package 120 \nOMP: Info #171: KMP_AFFINITY: OS proc 121 maps to package 121 \nOMP: Info #171: KMP_AFFINITY: OS proc 122 maps to package 122 \nOMP: Info #171: KMP_AFFINITY: OS proc 123 maps to package 123 \nOMP: Info #171: KMP_AFFINITY: OS proc 124 maps to package 124 \nOMP: Info #250: KMP_AFFINITY: pid 2936157 tid 2936157 thread 0 bound to OS proc set 0\nUsing TensorFlow backend.\n/usr/local/tools/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.\n  warnings.warn(msg, category=DeprecationWarning)\n",
-                                                        "stdout": "",
-                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.8.1",
-                                                        "tool_stderr": "OMP: Info #212: KMP_AFFINITY: decoding x2APIC ids.\nOMP: Info #210: KMP_AFFINITY: Affinity capable, using global cpuid leaf 11 info\nOMP: Info #154: KMP_AFFINITY: Initial OS proc set respected: 0-124\nOMP: Info #156: KMP_AFFINITY: 125 available OS procs\nOMP: Info #157: KMP_AFFINITY: Uniform topology\nOMP: Info #179: KMP_AFFINITY: 125 packages x 1 cores/pkg x 1 threads/core (125 total cores)\nOMP: Info #214: KMP_AFFINITY: OS proc to physical thread map:\nOMP: Info #171: KMP_AFFINITY: OS proc 0 maps to package 0 \nOMP: Info #171: KMP_AFFINITY: OS proc 1 maps to package 1 \nOMP: Info #171: KMP_AFFINITY: OS proc 2 maps to package 2 \nOMP: Info #171: KMP_AFFINITY: OS proc 3 maps to package 3 \nOMP: Info #171: KMP_AFFINITY: OS proc 4 maps to package 4 \nOMP: Info #171: KMP_AFFINITY: OS proc 5 maps to package 5 \nOMP: Info #171: KMP_AFFINITY: OS proc 6 maps to package 6 \nOMP: Info #171: KMP_AFFINITY: OS proc 7 maps to package 7 \nOMP: Info #171: KMP_AFFINITY: OS proc 8 maps to package 8 \nOMP: Info #171: KMP_AFFINITY: OS proc 9 maps to package 9 \nOMP: Info #171: KMP_AFFINITY: OS proc 10 maps to package 10 \nOMP: Info #171: KMP_AFFINITY: OS proc 11 maps to package 11 \nOMP: Info #171: KMP_AFFINITY: OS proc 12 maps to package 12 \nOMP: Info #171: KMP_AFFINITY: OS proc 13 maps to package 13 \nOMP: Info #171: KMP_AFFINITY: OS proc 14 maps to package 14 \nOMP: Info #171: KMP_AFFINITY: OS proc 15 maps to package 15 \nOMP: Info #171: KMP_AFFINITY: OS proc 16 maps to package 16 \nOMP: Info #171: KMP_AFFINITY: OS proc 17 maps to package 17 \nOMP: Info #171: KMP_AFFINITY: OS proc 18 maps to package 18 \nOMP: Info #171: KMP_AFFINITY: OS proc 19 maps to package 19 \nOMP: Info #171: KMP_AFFINITY: OS proc 20 maps to package 20 \nOMP: Info #171: KMP_AFFINITY: OS proc 21 maps to package 21 \nOMP: Info #171: KMP_AFFINITY: OS proc 22 maps to package 22 \nOMP: Info #171: KMP_AFFINITY: OS proc 23 maps to package 23 \nOMP: Info #171: KMP_AFFINITY: OS proc 24 maps to package 24 \nOMP: Info #171: KMP_AFFINITY: OS proc 25 maps to package 25 \nOMP: Info #171: KMP_AFFINITY: OS proc 26 maps to package 26 \nOMP: Info #171: KMP_AFFINITY: OS proc 27 maps to package 27 \nOMP: Info #171: KMP_AFFINITY: OS proc 28 maps to package 28 \nOMP: Info #171: KMP_AFFINITY: OS proc 29 maps to package 29 \nOMP: Info #171: KMP_AFFINITY: OS proc 30 maps to package 30 \nOMP: Info #171: KMP_AFFINITY: OS proc 31 maps to package 31 \nOMP: Info #171: KMP_AFFINITY: OS proc 32 maps to package 32 \nOMP: Info #171: KMP_AFFINITY: OS proc 33 maps to package 33 \nOMP: Info #171: KMP_AFFINITY: OS proc 34 maps to package 34 \nOMP: Info #171: KMP_AFFINITY: OS proc 35 maps to package 35 \nOMP: Info #171: KMP_AFFINITY: OS proc 36 maps to package 36 \nOMP: Info #171: KMP_AFFINITY: OS proc 37 maps to package 37 \nOMP: Info #171: KMP_AFFINITY: OS proc 38 maps to package 38 \nOMP: Info #171: KMP_AFFINITY: OS proc 39 maps to package 39 \nOMP: Info #171: KMP_AFFINITY: OS proc 40 maps to package 40 \nOMP: Info #171: KMP_AFFINITY: OS proc 41 maps to package 41 \nOMP: Info #171: KMP_AFFINITY: OS proc 42 maps to package 42 \nOMP: Info #171: KMP_AFFINITY: OS proc 43 maps to package 43 \nOMP: Info #171: KMP_AFFINITY: OS proc 44 maps to package 44 \nOMP: Info #171: KMP_AFFINITY: OS proc 45 maps to package 45 \nOMP: Info #171: KMP_AFFINITY: OS proc 46 maps to package 46 \nOMP: Info #171: KMP_AFFINITY: OS proc 47 maps to package 47 \nOMP: Info #171: KMP_AFFINITY: OS proc 48 maps to package 48 \nOMP: Info #171: KMP_AFFINITY: OS proc 49 maps to package 49 \nOMP: Info #171: KMP_AFFINITY: OS proc 50 maps to package 50 \nOMP: Info #171: KMP_AFFINITY: OS proc 51 maps to package 51 \nOMP: Info #171: KMP_AFFINITY: OS proc 52 maps to package 52 \nOMP: Info #171: KMP_AFFINITY: OS proc 53 maps to package 53 \nOMP: Info #171: KMP_AFFINITY: OS proc 54 maps to package 54 \nOMP: Info #171: KMP_AFFINITY: OS proc 55 maps to package 55 \nOMP: Info #171: KMP_AFFINITY: OS proc 56 maps to package 56 \nOMP: Info #171: KMP_AFFINITY: OS proc 57 maps to package 57 \nOMP: Info #171: KMP_AFFINITY: OS proc 58 maps to package 58 \nOMP: Info #171: KMP_AFFINITY: OS proc 59 maps to package 59 \nOMP: Info #171: KMP_AFFINITY: OS proc 60 maps to package 60 \nOMP: Info #171: KMP_AFFINITY: OS proc 61 maps to package 61 \nOMP: Info #171: KMP_AFFINITY: OS proc 62 maps to package 62 \nOMP: Info #171: KMP_AFFINITY: OS proc 63 maps to package 63 \nOMP: Info #171: KMP_AFFINITY: OS proc 64 maps to package 64 \nOMP: Info #171: KMP_AFFINITY: OS proc 65 maps to package 65 \nOMP: Info #171: KMP_AFFINITY: OS proc 66 maps to package 66 \nOMP: Info #171: KMP_AFFINITY: OS proc 67 maps to package 67 \nOMP: Info #171: KMP_AFFINITY: OS proc 68 maps to package 68 \nOMP: Info #171: KMP_AFFINITY: OS proc 69 maps to package 69 \nOMP: Info #171: KMP_AFFINITY: OS proc 70 maps to package 70 \nOMP: Info #171: KMP_AFFINITY: OS proc 71 maps to package 71 \nOMP: Info #171: KMP_AFFINITY: OS proc 72 maps to package 72 \nOMP: Info #171: KMP_AFFINITY: OS proc 73 maps to package 73 \nOMP: Info #171: KMP_AFFINITY: OS proc 74 maps to package 74 \nOMP: Info #171: KMP_AFFINITY: OS proc 75 maps to package 75 \nOMP: Info #171: KMP_AFFINITY: OS proc 76 maps to package 76 \nOMP: Info #171: KMP_AFFINITY: OS proc 77 maps to package 77 \nOMP: Info #171: KMP_AFFINITY: OS proc 78 maps to package 78 \nOMP: Info #171: KMP_AFFINITY: OS proc 79 maps to package 79 \nOMP: Info #171: KMP_AFFINITY: OS proc 80 maps to package 80 \nOMP: Info #171: KMP_AFFINITY: OS proc 81 maps to package 81 \nOMP: Info #171: KMP_AFFINITY: OS proc 82 maps to package 82 \nOMP: Info #171: KMP_AFFINITY: OS proc 83 maps to package 83 \nOMP: Info #171: KMP_AFFINITY: OS proc 84 maps to package 84 \nOMP: Info #171: KMP_AFFINITY: OS proc 85 maps to package 85 \nOMP: Info #171: KMP_AFFINITY: OS proc 86 maps to package 86 \nOMP: Info #171: KMP_AFFINITY: OS proc 87 maps to package 87 \nOMP: Info #171: KMP_AFFINITY: OS proc 88 maps to package 88 \nOMP: Info #171: KMP_AFFINITY: OS proc 89 maps to package 89 \nOMP: Info #171: KMP_AFFINITY: OS proc 90 maps to package 90 \nOMP: Info #171: KMP_AFFINITY: OS proc 91 maps to package 91 \nOMP: Info #171: KMP_AFFINITY: OS proc 92 maps to package 92 \nOMP: Info #171: KMP_AFFINITY: OS proc 93 maps to package 93 \nOMP: Info #171: KMP_AFFINITY: OS proc 94 maps to package 94 \nOMP: Info #171: KMP_AFFINITY: OS proc 95 maps to package 95 \nOMP: Info #171: KMP_AFFINITY: OS proc 96 maps to package 96 \nOMP: Info #171: KMP_AFFINITY: OS proc 97 maps to package 97 \nOMP: Info #171: KMP_AFFINITY: OS proc 98 maps to package 98 \nOMP: Info #171: KMP_AFFINITY: OS proc 99 maps to package 99 \nOMP: Info #171: KMP_AFFINITY: OS proc 100 maps to package 100 \nOMP: Info #171: KMP_AFFINITY: OS proc 101 maps to package 101 \nOMP: Info #171: KMP_AFFINITY: OS proc 102 maps to package 102 \nOMP: Info #171: KMP_AFFINITY: OS proc 103 maps to package 103 \nOMP: Info #171: KMP_AFFINITY: OS proc 104 maps to package 104 \nOMP: Info #171: KMP_AFFINITY: OS proc 105 maps to package 105 \nOMP: Info #171: KMP_AFFINITY: OS proc 106 maps to package 106 \nOMP: Info #171: KMP_AFFINITY: OS proc 107 maps to package 107 \nOMP: Info #171: KMP_AFFINITY: OS proc 108 maps to package 108 \nOMP: Info #171: KMP_AFFINITY: OS proc 109 maps to package 109 \nOMP: Info #171: KMP_AFFINITY: OS proc 110 maps to package 110 \nOMP: Info #171: KMP_AFFINITY: OS proc 111 maps to package 111 \nOMP: Info #171: KMP_AFFINITY: OS proc 112 maps to package 112 \nOMP: Info #171: KMP_AFFINITY: OS proc 113 maps to package 113 \nOMP: Info #171: KMP_AFFINITY: OS proc 114 maps to package 114 \nOMP: Info #171: KMP_AFFINITY: OS proc 115 maps to package 115 \nOMP: Info #171: KMP_AFFINITY: OS proc 116 maps to package 116 \nOMP: Info #171: KMP_AFFINITY: OS proc 117 maps to package 117 \nOMP: Info #171: KMP_AFFINITY: OS proc 118 maps to package 118 \nOMP: Info #171: KMP_AFFINITY: OS proc 119 maps to package 119 \nOMP: Info #171: KMP_AFFINITY: OS proc 120 maps to package 120 \nOMP: Info #171: KMP_AFFINITY: OS proc 121 maps to package 121 \nOMP: Info #171: KMP_AFFINITY: OS proc 122 maps to package 122 \nOMP: Info #171: KMP_AFFINITY: OS proc 123 maps to package 123 \nOMP: Info #171: KMP_AFFINITY: OS proc 124 maps to package 124 \nOMP: Info #250: KMP_AFFINITY: pid 2936157 tid 2936157 thread 0 bound to OS proc set 0\nUsing TensorFlow backend.\n/usr/local/tools/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.\n  warnings.warn(msg, category=DeprecationWarning)\n",
-                                                        "tool_stdout": "",
-                                                        "traceback": null,
-                                                        "update_time": "2023-05-23T11:03:10.618603",
-                                                        "user_email": "hxr@informatik.uni-freiburg.de"
-                                                    }
-                                                ],
-                                                "model_class": "WorkflowInvocationStep",
-                                                "order_index": 2,
-                                                "output_collections": {},
-                                                "outputs": {
-                                                    "outfile_fit": {
-                                                        "id": "4838ba20a6d86765b565f48d5ac913b1",
-                                                        "src": "hda",
-                                                        "uuid": "1a17ebe9-c0e0-4ebd-bae0-5159331683bb"
-                                                    }
-                                                },
-                                                "state": "scheduled",
-                                                "subworkflow": null,
-                                                "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-23T11:03:10.590397",
-                                                "workflow_step_id": "3500dc3fab19a665",
-                                                "workflow_step_label": null,
-                                                "workflow_step_uuid": "159f5d0f-2ff6-46f3-8e42-7b7c1f9c346e"
-                                            },
-                                            "3. Unnamed step": {
-                                                "action": null,
-                                                "id": "06d0cb6c722a3ad0",
-                                                "job_id": "11ac94870d0bb33a7b20a18462093261",
-                                                "jobs": [
-                                                    {
-                                                        "command_line": "python '/data/jwd02f/main/060/156/60156805/configs/tmpsg_iolk6' '/data/jwd02f/main/060/156/60156805/configs/tmpbg5s306r'",
-                                                        "command_version": "1.0.8.1",
-                                                        "create_time": "2023-05-23T10:59:49.663928",
-                                                        "dependencies": [
-                                                            {
-                                                                "cacheable": false,
-                                                                "dependency_resolver": {
-                                                                    "auto_init": true,
-                                                                    "auto_install": false,
-                                                                    "can_uninstall_dependencies": true,
-                                                                    "ensure_channels": "conda-forge,bioconda",
-                                                                    "model_class": "CondaDependencyResolver",
-                                                                    "prefix": "/usr/local/tools/_conda",
-                                                                    "read_only": false,
-                                                                    "resolver_type": "conda",
-                                                                    "resolves_simple_dependencies": true,
-                                                                    "use_local": false,
-                                                                    "versionless": false
-                                                                },
-                                                                "dependency_type": "conda",
-                                                                "environment_path": "/usr/local/tools/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59",
-                                                                "exact": true,
-                                                                "model_class": "MergedCondaDependency",
-                                                                "name": "python",
-                                                                "version": "3.6"
-                                                            },
-                                                            {
-                                                                "cacheable": false,
-                                                                "dependency_resolver": {
-                                                                    "auto_init": true,
-                                                                    "auto_install": false,
-                                                                    "can_uninstall_dependencies": true,
-                                                                    "ensure_channels": "conda-forge,bioconda",
-                                                                    "model_class": "CondaDependencyResolver",
-                                                                    "prefix": "/usr/local/tools/_conda",
-                                                                    "read_only": false,
-                                                                    "resolver_type": "conda",
-                                                                    "resolves_simple_dependencies": true,
-                                                                    "use_local": false,
-                                                                    "versionless": false
-                                                                },
-                                                                "dependency_type": "conda",
-                                                                "environment_path": "/usr/local/tools/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59",
-                                                                "exact": true,
-                                                                "model_class": "MergedCondaDependency",
-                                                                "name": "Galaxy-ML",
-                                                                "version": "0.8.1"
-                                                            }
-                                                        ],
-                                                        "exit_code": 0,
-                                                        "external_id": "43631439",
-                                                        "galaxy_version": "23.0",
-                                                        "history_id": "2507553dd7587c83",
-                                                        "id": "11ac94870d0bb33a7b20a18462093261",
-                                                        "inputs": {
-                                                            "infile_data": {
-                                                                "id": "4838ba20a6d867654de1bc22fefb9f52",
-                                                                "src": "hda",
-                                                                "uuid": "c438049f-86b6-415a-a9a0-554efa397b28"
-                                                            },
-                                                            "infile_model": {
-                                                                "id": "4838ba20a6d86765b565f48d5ac913b1",
-                                                                "src": "hda",
-                                                                "uuid": "1a17ebe9-c0e0-4ebd-bae0-5159331683bb"
-                                                            }
-                                                        },
-                                                        "job_messages": [],
-                                                        "job_metrics": [
-                                                            {
-                                                                "name": "hostname",
-                                                                "plugin": "hostname",
-                                                                "raw_value": "vgcnbwc-worker-c28m475-9818.novalocal",
-                                                                "title": "hostname",
-                                                                "value": "vgcnbwc-worker-c28m475-9818.novalocal"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_slots",
-                                                                "plugin": "core",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "Cores Allocated",
-                                                                "value": "1"
-                                                            },
-                                                            {
-                                                                "name": "galaxy_memory_mb",
-                                                                "plugin": "core",
-                                                                "raw_value": "3891.0000000",
-                                                                "title": "Memory Allocated (MB)",
-                                                                "value": "3891"
-                                                            },
-                                                            {
-                                                                "name": "start_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684839797.0000000",
-                                                                "title": "Job Start Time",
-                                                                "value": "2023-05-23 13:03:17"
-                                                            },
-                                                            {
-                                                                "name": "end_epoch",
-                                                                "plugin": "core",
-                                                                "raw_value": "1684839860.0000000",
-                                                                "title": "Job End Time",
-                                                                "value": "2023-05-23 13:04:20"
-                                                            },
-                                                            {
-                                                                "name": "runtime_seconds",
-                                                                "plugin": "core",
-                                                                "raw_value": "63.0000000",
-                                                                "title": "Job Runtime (Wall Clock)",
-                                                                "value": "1 minute"
-                                                            },
-                                                            {
-                                                                "name": "cpuacct.usage",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "17604876182.0000000",
-                                                                "title": "CPU Time",
-                                                                "value": "17.604876182 seconds"
-                                                            },
-                                                            {
-                                                                "name": "memory.failcnt",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Failed to allocate memory count",
-                                                                "value": 0.0
-                                                            },
-                                                            {
-                                                                "name": "memory.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "12348030976.0000000",
-                                                                "title": "Memory limit on cgroup (MEM)",
-                                                                "value": "11.5 GB"
-                                                            },
-                                                            {
-                                                                "name": "memory.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "276676608.0000000",
-                                                                "title": "Max memory usage (MEM)",
-                                                                "value": "263.9 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "9223372036854771712.0000000",
-                                                                "title": "Memory limit on cgroup (MEM+SWP)",
-                                                                "value": "8.0 EB"
-                                                            },
-                                                            {
-                                                                "name": "memory.memsw.max_usage_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "276676608.0000000",
-                                                                "title": "Max memory usage (MEM+SWP)",
-                                                                "value": "263.9 MB"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.oom_kill_disable",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "1.0000000",
-                                                                "title": "OOM Control enabled",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.oom_control.under_oom",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Was OOM Killer active?",
-                                                                "value": "No"
-                                                            },
-                                                            {
-                                                                "name": "memory.soft_limit_in_bytes",
-                                                                "plugin": "cgroup",
-                                                                "raw_value": "0E-7",
-                                                                "title": "Memory softlimit on cgroup",
-                                                                "value": "0 bytes"
-                                                            }
-                                                        ],
-                                                        "job_stderr": "",
-                                                        "job_stdout": "",
-                                                        "model_class": "Job",
-                                                        "output_collections": {},
-                                                        "outputs": {
-                                                            "outfile_predict": {
-                                                                "id": "4838ba20a6d8676528bf3db1c2ee4fdf",
-                                                                "src": "hda",
-                                                                "uuid": "aa9ff12d-ae53-4540-a498-636aa43c3466"
-                                                            }
-                                                        },
-                                                        "params": {
-                                                            "__input_ext": "\"zip\"",
-                                                            "__workflow_invocation_uuid__": "\"ebe5f326f95811ed916d001e67d2ec02\"",
-                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
-                                                            "dbkey": "\"?\"",
-                                                            "selected_tasks": "{\"__current_case__\": 0, \"header\": true, \"infile_data\": {\"values\": [{\"id\": 137643085, \"src\": \"hda\"}]}, \"infile_model\": {\"values\": [{\"id\": 137643284, \"src\": \"hda\"}]}, \"prediction_options\": {\"__current_case__\": 0, \"prediction_option\": \"predict\"}, \"selected_task\": \"load\"}"
-                                                        },
-                                                        "state": "ok",
-                                                        "stderr": "OMP: Info #212: KMP_AFFINITY: decoding x2APIC ids.\nOMP: Info #210: KMP_AFFINITY: Affinity capable, using global cpuid leaf 11 info\nOMP: Info #154: KMP_AFFINITY: Initial OS proc set respected: 0-27\nOMP: Info #156: KMP_AFFINITY: 28 available OS procs\nOMP: Info #157: KMP_AFFINITY: Uniform topology\nOMP: Info #179: KMP_AFFINITY: 28 packages x 1 cores/pkg x 1 threads/core (28 total cores)\nOMP: Info #214: KMP_AFFINITY: OS proc to physical thread map:\nOMP: Info #171: KMP_AFFINITY: OS proc 0 maps to package 0 \nOMP: Info #171: KMP_AFFINITY: OS proc 1 maps to package 1 \nOMP: Info #171: KMP_AFFINITY: OS proc 2 maps to package 2 \nOMP: Info #171: KMP_AFFINITY: OS proc 3 maps to package 3 \nOMP: Info #171: KMP_AFFINITY: OS proc 4 maps to package 4 \nOMP: Info #171: KMP_AFFINITY: OS proc 5 maps to package 5 \nOMP: Info #171: KMP_AFFINITY: OS proc 6 maps to package 6 \nOMP: Info #171: KMP_AFFINITY: OS proc 7 maps to package 7 \nOMP: Info #171: KMP_AFFINITY: OS proc 8 maps to package 8 \nOMP: Info #171: KMP_AFFINITY: OS proc 9 maps to package 9 \nOMP: Info #171: KMP_AFFINITY: OS proc 10 maps to package 10 \nOMP: Info #171: KMP_AFFINITY: OS proc 11 maps to package 11 \nOMP: Info #171: KMP_AFFINITY: OS proc 12 maps to package 12 \nOMP: Info #171: KMP_AFFINITY: OS proc 13 maps to package 13 \nOMP: Info #171: KMP_AFFINITY: OS proc 14 maps to package 14 \nOMP: Info #171: KMP_AFFINITY: OS proc 15 maps to package 15 \nOMP: Info #171: KMP_AFFINITY: OS proc 16 maps to package 16 \nOMP: Info #171: KMP_AFFINITY: OS proc 17 maps to package 17 \nOMP: Info #171: KMP_AFFINITY: OS proc 18 maps to package 18 \nOMP: Info #171: KMP_AFFINITY: OS proc 19 maps to package 19 \nOMP: Info #171: KMP_AFFINITY: OS proc 20 maps to package 20 \nOMP: Info #171: KMP_AFFINITY: OS proc 21 maps to package 21 \nOMP: Info #171: KMP_AFFINITY: OS proc 22 maps to package 22 \nOMP: Info #171: KMP_AFFINITY: OS proc 23 maps to package 23 \nOMP: Info #171: KMP_AFFINITY: OS proc 24 maps to package 24 \nOMP: Info #171: KMP_AFFINITY: OS proc 25 maps to package 25 \nOMP: Info #171: KMP_AFFINITY: OS proc 26 maps to package 26 \nOMP: Info #171: KMP_AFFINITY: OS proc 27 maps to package 27 \nOMP: Info #250: KMP_AFFINITY: pid 2127423 tid 2127423 thread 0 bound to OS proc set 0\nUsing TensorFlow backend.\n/usr/local/tools/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.\n  warnings.warn(msg, category=DeprecationWarning)\n",
-                                                        "stdout": "",
-                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.8.1",
-                                                        "tool_stderr": "OMP: Info #212: KMP_AFFINITY: decoding x2APIC ids.\nOMP: Info #210: KMP_AFFINITY: Affinity capable, using global cpuid leaf 11 info\nOMP: Info #154: KMP_AFFINITY: Initial OS proc set respected: 0-27\nOMP: Info #156: KMP_AFFINITY: 28 available OS procs\nOMP: Info #157: KMP_AFFINITY: Uniform topology\nOMP: Info #179: KMP_AFFINITY: 28 packages x 1 cores/pkg x 1 threads/core (28 total cores)\nOMP: Info #214: KMP_AFFINITY: OS proc to physical thread map:\nOMP: Info #171: KMP_AFFINITY: OS proc 0 maps to package 0 \nOMP: Info #171: KMP_AFFINITY: OS proc 1 maps to package 1 \nOMP: Info #171: KMP_AFFINITY: OS proc 2 maps to package 2 \nOMP: Info #171: KMP_AFFINITY: OS proc 3 maps to package 3 \nOMP: Info #171: KMP_AFFINITY: OS proc 4 maps to package 4 \nOMP: Info #171: KMP_AFFINITY: OS proc 5 maps to package 5 \nOMP: Info #171: KMP_AFFINITY: OS proc 6 maps to package 6 \nOMP: Info #171: KMP_AFFINITY: OS proc 7 maps to package 7 \nOMP: Info #171: KMP_AFFINITY: OS proc 8 maps to package 8 \nOMP: Info #171: KMP_AFFINITY: OS proc 9 maps to package 9 \nOMP: Info #171: KMP_AFFINITY: OS proc 10 maps to package 10 \nOMP: Info #171: KMP_AFFINITY: OS proc 11 maps to package 11 \nOMP: Info #171: KMP_AFFINITY: OS proc 12 maps to package 12 \nOMP: Info #171: KMP_AFFINITY: OS proc 13 maps to package 13 \nOMP: Info #171: KMP_AFFINITY: OS proc 14 maps to package 14 \nOMP: Info #171: KMP_AFFINITY: OS proc 15 maps to package 15 \nOMP: Info #171: KMP_AFFINITY: OS proc 16 maps to package 16 \nOMP: Info #171: KMP_AFFINITY: OS proc 17 maps to package 17 \nOMP: Info #171: KMP_AFFINITY: OS proc 18 maps to package 18 \nOMP: Info #171: KMP_AFFINITY: OS proc 19 maps to package 19 \nOMP: Info #171: KMP_AFFINITY: OS proc 20 maps to package 20 \nOMP: Info #171: KMP_AFFINITY: OS proc 21 maps to package 21 \nOMP: Info #171: KMP_AFFINITY: OS proc 22 maps to package 22 \nOMP: Info #171: KMP_AFFINITY: OS proc 23 maps to package 23 \nOMP: Info #171: KMP_AFFINITY: OS proc 24 maps to package 24 \nOMP: Info #171: KMP_AFFINITY: OS proc 25 maps to package 25 \nOMP: Info #171: KMP_AFFINITY: OS proc 26 maps to package 26 \nOMP: Info #171: KMP_AFFINITY: OS proc 27 maps to package 27 \nOMP: Info #250: KMP_AFFINITY: pid 2127423 tid 2127423 thread 0 bound to OS proc set 0\nUsing TensorFlow backend.\n/usr/local/tools/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.\n  warnings.warn(msg, category=DeprecationWarning)\n",
-                                                        "tool_stdout": "",
-                                                        "traceback": null,
-                                                        "update_time": "2023-05-23T11:04:23.019377",
-                                                        "user_email": "hxr@informatik.uni-freiburg.de"
-                                                    }
-                                                ],
-                                                "model_class": "WorkflowInvocationStep",
-                                                "order_index": 3,
-                                                "output_collections": {},
-                                                "outputs": {
-                                                    "outfile_predict": {
-                                                        "id": "4838ba20a6d8676528bf3db1c2ee4fdf",
-                                                        "src": "hda",
-                                                        "uuid": "aa9ff12d-ae53-4540-a498-636aa43c3466"
-                                                    }
-                                                },
-                                                "state": "scheduled",
-                                                "subworkflow": null,
-                                                "subworkflow_invocation_id": null,
-                                                "update_time": "2023-05-23T11:04:23.001451",
-                                                "workflow_step_id": "2fb04d30a406970c",
-                                                "workflow_step_label": null,
-                                                "workflow_step_uuid": "98bd60bb-4e32-4c11-9955-eade434a3817"
-                                            }
-                                        }
-                                    },
-                                    "problem_log": "No log for this engine type.",
-                                    "start_datetime": "2023-05-23T12:56:36.643889",
-                                    "status": "success"
-                                },
-                                "doc": "Test Basics of Machine Learning workflow",
-                                "has_data": true,
-                                "id": "machine_learning.ga_0",
-                                "test_type": "galaxy_workflow"
+                "test_results": null,
+                "tests": true,
+                "title": "Intro_To_FNN_v1_0_10_0",
+                "topic_id": "statistics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-FNN/versions/intro-to-fnn-v1-0-10-0",
+                "tutorial_id": "FNN",
+                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/FNN/workflows/Intro_To_FNN_v1_0_10_0.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/FNN/workflows/Intro_To_FNN_v1_0_10_0.html",
+                "version": 1,
+                "wfid": "statistics-FNN",
+                "wfname": "intro-to-fnn-v1-0-10-0",
+                "workflow": "Intro_To_FNN_v1_0_10_0.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/1.0.10.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/1.0.10.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.10.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.10.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1"
+                ],
+                "workflowhub_id": "1308"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/4660497"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "keras_model_builder",
+                    "owner": "bgruening",
+                    "revisions": "66d7efc06000",
+                    "tool_panel_section_label": "Machine Learning",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "keras_model_config",
+                    "owner": "bgruening",
+                    "revisions": "f22a9297440f",
+                    "tool_panel_section_label": "Machine Learning",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "keras_train_and_eval",
+                    "owner": "bgruening",
+                    "revisions": "2af1346e68c9",
+                    "tool_panel_section_label": "Machine Learning",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ml_visualization_ex",
+                    "owner": "bgruening",
+                    "revisions": "8334dc98c48e",
+                    "tool_panel_section_label": "Machine Learning",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "model_prediction",
+                    "owner": "bgruening",
+                    "revisions": "25b46af53232",
+                    "tool_panel_section_label": "Machine Learning",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sklearn_to_categorical",
+                    "owner": "bgruening",
+                    "revisions": "61634a87efc7",
+                    "tool_panel_section_label": "Machine Learning",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: keras_model_builder\n  owner: bgruening\n  revisions: 66d7efc06000\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_model_config\n  owner: bgruening\n  revisions: f22a9297440f\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_train_and_eval\n  owner: bgruening\n  revisions: 2af1346e68c9\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ml_visualization_ex\n  owner: bgruening\n  revisions: 8334dc98c48e\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: model_prediction\n  owner: bgruening\n  revisions: 25b46af53232\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_to_categorical\n  owner: bgruening\n  revisions: 61634a87efc7\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/CNN/tutorial.json",
+        "contributors": [
+            {
+                "email": "kxk302@gmail.com",
+                "id": "kxk302",
+                "joined": "2021-02",
+                "name": "Kaivan Kamali",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kxk302/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/kxk302.json"
+            }
+        ],
+        "dir": "topics/statistics/tutorials/CNN",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "statistics/CNN",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": 1168,
+            "mermaid": false
+        },
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-07-09",
+        "objectives": [
+            "Understand the inspiration behind CNN and learn the CNN architecture",
+            "Learn the convolution operation and its parameters",
+            "Learn how to create a CNN using Galaxy's deep learning tools",
+            "Solve an image classification problem on MNIST digit classification dataset using CNN in Galaxy"
+        ],
+        "pageviews": 5364042,
+        "pub_date": "2021-04-19",
+        "questions": [
+            "What is a convolutional neural network (CNN)?",
+            "What are some applications of CNN?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "FilipposZ"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "1H",
+                "speakers": [
+                    "kxk302"
+                ],
+                "youtube_id": "P1NVYOJrv_4"
+            }
+        ],
+        "requirements": [
+            {
+                "topic_name": "statistics",
+                "tutorials": [
+                    "intro_deep_learning",
+                    "FNN",
+                    "RNN"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00257",
+        "short_tools": [
+            "model_prediction",
+            "keras_model_config",
+            "ml_visualization_ex",
+            "keras_train_and_eval",
+            "sklearn_to_categorical",
+            "keras_model_builder"
+        ],
+        "slides": true,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "time_estimation": "2H",
+        "title": "Deep Learning (Part 3) - Convolutional neural networks (CNN)",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/1.0.10.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/1.0.10.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.11.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.11.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.11.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_to_categorical/sklearn_to_categorical/1.0.10.0"
+        ],
+        "topic_name": "statistics",
+        "topic_name_human": "Statistics and machine learning",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "CNN",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/CNN/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/CNN/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/CNN/tutorial.json"
+        },
+        "version": 17,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 205,
+        "visitors": 1986810,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0001-6585-3619",
+                        "name": "Kaivan Kamali"
+                    }
+                ],
+                "description": "",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nX_test\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nX_train\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ny_test\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ny_train\"]\n  4[label=\"Create a deep learning model architecture\"]\n  5[label=\"To categorical\"]\n  3 -> 5 [label=\"output\"]\n  6[label=\"Create deep learning model\"]\n  4 -> 6 [label=\"outfile\"]\n  7[label=\"Deep learning training and evaluation\"]\n  6 -> 7 [label=\"outfile\"]\n  1 -> 7 [label=\"output\"]\n  5 -> 7 [label=\"outfile\"]\n  8[label=\"Model Prediction\"]\n  7 -> 8 [label=\"outfile_object\"]\n  0 -> 8 [label=\"output\"]\n  9[label=\"Machine Learning Visualization Extension\"]\n  8 -> 9 [label=\"outfile_predict\"]\n  2 -> 9 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "ce48b25d3253616efc9591ba44031331827b1f62",
+                        "message": "Fixed lint issues",
+                        "num": 2,
+                        "short_hash": "ce48b25d3",
+                        "unix": "1699469857"
+                    },
+                    {
+                        "hash": "0c206197dd1637890ad853b508f4c14009d1cd77",
+                        "message": "Renamed workflow and test yml file",
+                        "num": 1,
+                        "short_hash": "0c206197d",
+                        "unix": "1699461926"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "X_test"
                             }
                         ],
-                        "version": "0.1"
+                        "label": "X_test",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 0
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "67fe95aa-be8d-4ce8-89a3-844c55d4edf9",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "X_train"
+                            }
+                        ],
+                        "label": "X_train",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 120
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "cf3a589c-9683-47d0-a4b3-f56046633552",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "y_test"
+                            }
+                        ],
+                        "label": "y_test",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 240
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "5d37d651-f5c9-4af6-9ff1-211d7a145a30",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "y_train"
+                            }
+                        ],
+                        "label": "y_train",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 360
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ec126ab6-12b4-4559-9ade-321d6e5f37dd",
+                        "when": null,
+                        "workflow_outputs": []
                     }
-                },
+                ],
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nX_test\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nX_train\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ny_test\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\ny_train\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Create a deep learning model architecture\"];\n  5[\"To categorical\"];\n  3 -->|output| 5;\n  6[\"Create deep learning model\"];\n  4 -->|outfile| 6;\n  7[\"Deep learning training and evaluation\"];\n  6 -->|outfile| 7;\n  1 -->|output| 7;\n  5 -->|outfile| 7;\n  8[\"Model Prediction\"];\n  7 -->|outfile_object| 8;\n  0 -->|output| 8;\n  9[\"Machine Learning Visualization Extension\"];\n  8 -->|outfile_predict| 9;\n  2 -->|output| 9;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "Intro_To_CNN_v1.0.11.0",
+                "outputs": [],
+                "parent_id": "statistics/CNN",
+                "path": "topics/statistics/tutorials/CNN/workflows/Intro_To_CNN_v1_0_11_0.ga",
+                "tags": [],
+                "test_results": null,
                 "tests": true,
-                "title": "Machine Learning",
+                "title": "Intro_To_CNN_v1.0.11.0",
                 "topic_id": "statistics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-machinelearning/versions/machine-learning",
-                "tutorial_id": "machinelearning",
-                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/machinelearning/workflows/machine_learning.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/machinelearning/workflows/machine_learning.html",
-                "version": 5,
-                "wfid": "statistics-machinelearning",
-                "wfname": "machine-learning",
-                "workflow": "machine_learning.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-CNN/versions/intro-to-cnn-v1-0-11-0",
+                "tutorial_id": "CNN",
+                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/CNN/workflows/Intro_To_CNN_v1_0_11_0.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/CNN/workflows/Intro_To_CNN_v1_0_11_0.html",
+                "version": 1,
+                "wfid": "statistics-CNN",
+                "wfname": "intro-to-cnn-v1-0-11-0",
+                "workflow": "Intro_To_CNN_v1_0_11_0.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.8.1"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/1.0.10.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/1.0.10.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.11.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.11.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.11.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_to_categorical/sklearn_to_categorical/1.0.10.0"
                 ],
-                "workflowhub_id": "1320"
+                "workflowhub_id": "1313"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/1468039"
+        "zenodo_link": "https://zenodo.org/record/4697906"
     },
     {
         "admin_install": {
@@ -249367,61 +256044,79 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "iwtomics_loadandplot",
-                    "owner": "iuc",
-                    "revisions": "ce633cc8f5f9",
-                    "tool_panel_section_label": "Statistics",
+                    "name": "keras_model_builder",
+                    "owner": "bgruening",
+                    "revisions": "772e0e89fc68",
+                    "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "iwtomics_plotwithscale",
-                    "owner": "iuc",
-                    "revisions": "1bc9150ed125",
-                    "tool_panel_section_label": "Statistics",
+                    "name": "keras_model_config",
+                    "owner": "bgruening",
+                    "revisions": "8a794e6d3388",
+                    "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "iwtomics_testandplot",
-                    "owner": "iuc",
-                    "revisions": "94965e369be4",
-                    "tool_panel_section_label": "Statistics",
+                    "name": "keras_train_and_eval",
+                    "owner": "bgruening",
+                    "revisions": "f1b9a42d6809",
+                    "tool_panel_section_label": "Machine Learning",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ml_visualization_ex",
+                    "owner": "bgruening",
+                    "revisions": "05143043ca13",
+                    "tool_panel_section_label": "Machine Learning",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "model_prediction",
+                    "owner": "bgruening",
+                    "revisions": "83228baae3c5",
+                    "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: iwtomics_loadandplot\n  owner: iuc\n  revisions: ce633cc8f5f9\n  tool_panel_section_label: Statistics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: iwtomics_plotwithscale\n  owner: iuc\n  revisions: 1bc9150ed125\n  tool_panel_section_label: Statistics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: iwtomics_testandplot\n  owner: iuc\n  revisions: 94965e369be4\n  tool_panel_section_label: Statistics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/iwtomics/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: keras_model_builder\n  owner: bgruening\n  revisions: 772e0e89fc68\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_model_config\n  owner: bgruening\n  revisions: 8a794e6d3388\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_train_and_eval\n  owner: bgruening\n  revisions: f1b9a42d6809\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ml_visualization_ex\n  owner: bgruening\n  revisions: 05143043ca13\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: model_prediction\n  owner: bgruening\n  revisions: 83228baae3c5\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/intro_deep_learning/tutorial.json",
         "contributors": [
             {
-                "email": "mac78@psu.edu",
-                "id": "marziacremona",
-                "joined": "2018-02",
-                "name": "Marzia A Cremona",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/marziacremona/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/marziacremona.json"
+                "affiliations": [
+                    "uni-freiburg",
+                    "eurosciencegateway",
+                    "elixir-europe"
+                ],
+                "elixir_node": "de",
+                "email": "anup.rulez@gmail.com",
+                "id": "anuprulez",
+                "joined": "2018-08",
+                "name": "Anup Kumar",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/anuprulez/",
+                "twitter": "musafirtweetsz",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/anuprulez.json"
             },
             {
-                "email": "fabio.cumbo@gmail.com",
-                "id": "cumbof",
-                "joined": "2018-02",
-                "linkedin": "fabiocumbo",
-                "name": "Fabio Cumbo",
-                "orcid": "0000-0003-2920-5838",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cumbof/",
-                "twitter": "cumbofabio",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/cumbof.json"
+                "email": "khanteymoori@gmail.com",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "khanteymoori",
+                "joined": "2019-07",
+                "name": "Alireza Khanteymoori",
+                "orcid": "0000-0001-6811-9196",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/khanteymoori/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/khanteymoori.json"
             }
         ],
-        "dir": "topics/statistics/tutorials/iwtomics",
-        "edam_operation": [
-            "Peak calling",
-            "Genome annotation",
-            "Comparison",
-            "Differentially-methylated region identification",
-            "Differential gene expression analysis"
-        ],
+        "dir": "topics/statistics/tutorials/intro_deep_learning",
+        "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.eu",
             "UseGalaxy.no",
@@ -249431,47 +256126,49 @@
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "statistics/iwtomics",
+        "id": "statistics/intro_deep_learning",
         "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "High-resolution omics data can be represented as curves along the genome",
-            "IWTomics permits to visualize these data",
-            "The Interval-Wise Testing detects statistically significant differences between pairs of genomic regions",
-            "The Interval-Wise Testing corrects p-values taking into consideration the ordered nature of measurements along the genome",
-            "Locations and scales do not need to be specified at the outset, indeed IWTomics permits to detect them"
+            "Multiple tools to constitute a neural network architecture",
+            "Interpretation of predictions using visualisation tools"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-03-05",
         "objectives": [
-            "Pre-process high-resolution omics data",
-            "Create pointwise boxplots corresponding to different groups of genomic regions",
-            "Perform the Interval-Wise Testing between two groups of genomic regions",
-            "Visualize and inspect test results",
-            "Detect relevant locations and scales"
+            "Learn basic principles of deep learning",
+            "Learn about how to create an end-to-end neural network architecture",
+            "Learn about Galaxy deep learning tools",
+            "Learn how to interpret predictions"
         ],
-        "pageviews": 443,
-        "pub_date": "2018-06-14",
+        "pageviews": 2519,
+        "pub_date": "2020-03-26",
         "questions": [
-            "How to visualize high-resolution omics data in different groups of genomic regions?",
-            "How to evaluate differences in high-resolution omics data between groups of genomic regions?",
-            "How to detect locations and scales at which the significant effects unfold?"
+            "What are deep learning and neural networks?",
+            "Why is it useful?",
+            "How to create a neural network architecture for classification?"
         ],
-        "requirements": null,
-        "short_id": "T00269",
+        "short_id": "T00268",
         "short_tools": [
-            "iwtomics_plotwithscale",
-            "iwtomics_testandplot",
-            "iwtomics_loadandplot"
+            "model_prediction",
+            "keras_model_config",
+            "ml_visualization_ex",
+            "keras_train_and_eval",
+            "keras_model_builder"
         ],
         "slides": false,
         "slides_recordings": false,
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -249501,12 +256198,14 @@
             "inexact": []
         },
         "symlink": null,
-        "time_estimation": "1h",
-        "title": "Interval-Wise Testing for omics data",
+        "time_estimation": "1H",
+        "title": "Introduction to deep learning",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_loadandplot/iwtomics_loadandplot/1.0.0.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_plotwithscale/iwtomics_plotwithscale/1.0.0.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_testandplot/iwtomics_testandplot/1.0.0.0"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/0.5.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/0.5.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.2"
         ],
         "topic_name": "statistics",
         "topic_name_human": "Statistics and machine learning",
@@ -249516,72 +256215,58 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "iwtomics",
+        "tutorial_name": "intro_deep_learning",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/iwtomics/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/intro_deep_learning/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/iwtomics/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/iwtomics/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/intro_deep_learning/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/intro_deep_learning/tutorial.json"
         },
-        "version": 17,
+        "version": 8,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 196,
-        "visitors": 322,
+        "visit_duration": 99,
+        "visitors": 1946,
         "workflows": [
             {
                 "creators": [],
-                "description": "Interval-Wise Testing for omics data",
+                "description": "Introduction to Deep Learning",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nETn_fixed.bed\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nControl.bed\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nfeatures_header.tabular\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nregions_header.tabular\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nRecombination_hotspots.txt\"]\n  5[label=\"IWTomics Load\"]\n  4 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"output\"]\n  6[label=\"IWTomics Test\"]\n  5 -> 6 [label=\"outfeatures\"]\n  5 -> 6 [label=\"outrdata\"]\n  5 -> 6 [label=\"outregions\"]\n  7[label=\"IWTomics Plot with Threshold\"]\n  6 -> 7 [label=\"iwtomicsselectedfeatures\"]\n  6 -> 7 [label=\"iwtomicsrdata\"]\n  6 -> 7 [label=\"iwtomicstests\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nX_test\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nX_train\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ny_test\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ny_train\"]\n  4[label=\"Create a deep learning model architecture\"]\n  5[label=\"Create deep learning model\"]\n  4 -> 5 [label=\"outfile\"]\n  6[label=\"Deep learning training and evaluation\"]\n  5 -> 6 [label=\"outfile\"]\n  1 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"Model Prediction\"]\n  6 -> 7 [label=\"outfile_object\"]\n  6 -> 7 [label=\"outfile_weights\"]\n  0 -> 7 [label=\"output\"]\n  8[label=\"Machine Learning Visualization Extension\"]\n  7 -> 8 [label=\"outfile_predict\"]\n  2 -> 8 [label=\"output\"]\n}",
                 "history": [
                     {
-                        "hash": "b97fcf8dbc18d441d3e8e6eb7a2e4f01fda1cb14",
-                        "message": "Updating IWTomics data",
-                        "num": 6,
-                        "short_hash": "b97fcf8db",
-                        "unix": "1634825035"
-                    },
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 5,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
+                        "hash": "662ff162583df9ededd624afd29945d5c799df9b",
+                        "message": "Fixed input data labels (they were one off)",
                         "num": 4,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
+                        "short_hash": "662ff1625",
+                        "unix": "1611671063"
                     },
                     {
-                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
-                        "message": "Changed format of workflows",
+                        "hash": "6069e5afbdd15fea3ec1b9d22899c2cabdcd4abf",
+                        "message": "Added label for input data.",
                         "num": 3,
-                        "short_hash": "361236c41",
-                        "unix": "1554368414"
+                        "short_hash": "6069e5afb",
+                        "unix": "1611603134"
                     },
                     {
-                        "hash": "251bebcf11feffcbd9a103e1ac5898def74c861e",
-                        "message": "workflow fixed",
+                        "hash": "3250de162eff1978f2cc80d7732bad186d7a0006",
+                        "message": "Tagged the workflow and added a title.",
                         "num": 2,
-                        "short_hash": "251bebcf1",
-                        "unix": "1528895196"
+                        "short_hash": "3250de162",
+                        "unix": "1611418238"
                     },
                     {
-                        "hash": "5752bb6b95a47c674c4600c00537a015f6357967",
-                        "message": "IWTomics Workflow",
+                        "hash": "55c3b30a50a0c1cbfb02a7f028866d91ade386cf",
+                        "message": "Added workflow to Deep Learning Tutorial",
                         "num": 1,
-                        "short_hash": "5752bb6b9",
-                        "unix": "1528889546"
+                        "short_hash": "55c3b30a5",
+                        "unix": "1611351590"
                     }
                 ],
                 "inputs": [
@@ -249594,21 +256279,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "ETn_fixed.bed"
+                                "name": "X_test"
                             }
                         ],
-                        "label": "ETn_fixed.bed",
+                        "label": "X_test",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 200
+                            "left": 10,
+                            "top": 10
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"ETn_fixed.bed\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "7709e0ee-56fc-491d-afad-b10c18758c07",
+                        "uuid": "46c0a33e-73d7-4413-8872-dea66576377e",
                         "workflow_outputs": []
                     },
                     {
@@ -249620,21 +256305,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Control.bed"
+                                "name": "X_train"
                             }
                         ],
-                        "label": "Control.bed",
+                        "label": "X_train",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 320
+                            "left": 10,
+                            "top": 130
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"Control.bed\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "9c4be2e1-6f14-4ec4-a0e8-3ec4e21a6523",
+                        "uuid": "3939491d-5fc0-4eb0-9ece-32f87782d456",
                         "workflow_outputs": []
                     },
                     {
@@ -249646,21 +256331,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "features_header.tabular"
+                                "name": "y_test"
                             }
                         ],
-                        "label": "features_header.tabular",
+                        "label": "y_test",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 680
+                            "left": 10,
+                            "top": 250
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"features_header.tabular\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "4a071a64-59d3-481d-8d84-f063c38ddac7",
+                        "uuid": "7b284798-4e87-476c-9af1-514df24176f8",
                         "workflow_outputs": []
                     },
                     {
@@ -249672,83 +256357,59 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "regions_header.tabular"
-                            }
-                        ],
-                        "label": "regions_header.tabular",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 560
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"regions_header.tabular\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ac9cf2c6-9bbc-42b4-b4fb-f0fcf92dcee6",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Recombination_hotspots.txt"
+                                "name": "y_train"
                             }
                         ],
-                        "label": "Recombination_hotspots.txt",
+                        "label": "y_train",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 440
+                            "left": 10,
+                            "top": 370
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"Recombination_hotspots.txt\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "946f863d-0ef4-42b1-bb87-25247e31d4d9",
+                        "uuid": "d145f3ff-f7c9-4873-bb59-79d089262d6e",
                         "workflow_outputs": []
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nETn_fixed.bed\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nControl.bed\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nfeatures_header.tabular\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nregions_header.tabular\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nRecombination_hotspots.txt\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"IWTomics Load\"];\n  4 -->|output| 5;\n  2 -->|output| 5;\n  0 -->|output| 5;\n  1 -->|output| 5;\n  3 -->|output| 5;\n  6[\"IWTomics Test\"];\n  5 -->|outfeatures| 6;\n  5 -->|outrdata| 6;\n  5 -->|outregions| 6;\n  7[\"IWTomics Plot with Threshold\"];\n  6 -->|iwtomicsselectedfeatures| 7;\n  6 -->|iwtomicsrdata| 7;\n  6 -->|iwtomicstests| 7;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Workflow Constructed From History 'IWTomics Workflow'",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nX_test\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nX_train\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ny_test\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\ny_train\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Create a deep learning model architecture\"];\n  5[\"Create deep learning model\"];\n  4 -->|outfile| 5;\n  6[\"Deep learning training and evaluation\"];\n  5 -->|outfile| 6;\n  1 -->|output| 6;\n  3 -->|output| 6;\n  7[\"Model Prediction\"];\n  6 -->|outfile_object| 7;\n  6 -->|outfile_weights| 7;\n  0 -->|output| 7;\n  8[\"Machine Learning Visualization Extension\"];\n  7 -->|outfile_predict| 8;\n  2 -->|output| 8;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "Intro_To_Deep_Learning",
                 "outputs": [],
-                "parent_id": "statistics/iwtomics",
-                "path": "topics/statistics/tutorials/iwtomics/workflows/IWTomics_Workflow.ga",
+                "parent_id": "statistics/intro_deep_learning",
+                "path": "topics/statistics/tutorials/intro_deep_learning/workflows/Intro_To_Deep_Learning.ga",
                 "tags": [
-                    "genomics",
-                    "iwtomics",
-                    "statistics"
+                    "statistics",
+                    "deeplearning",
+                    "ml"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Workflow Constructed From History 'IWTomics Workflow'",
+                "title": "Intro_To_Deep_Learning",
                 "topic_id": "statistics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-iwtomics/versions/iwtomics-workflow",
-                "tutorial_id": "iwtomics",
-                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/iwtomics/workflows/IWTomics_Workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/iwtomics/workflows/IWTomics_Workflow.html",
-                "version": 5,
-                "wfid": "statistics-iwtomics",
-                "wfname": "iwtomics-workflow",
-                "workflow": "IWTomics_Workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-intro_deep_learning/versions/intro-to-deep-learning",
+                "tutorial_id": "intro_deep_learning",
+                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/intro_deep_learning/workflows/Intro_To_Deep_Learning.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/intro_deep_learning/workflows/Intro_To_Deep_Learning.html",
+                "version": 1,
+                "wfid": "statistics-intro_deep_learning",
+                "wfname": "intro-to-deep-learning",
+                "workflow": "Intro_To_Deep_Learning.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_loadandplot/iwtomics_loadandplot/1.0.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_plotwithscale/iwtomics_plotwithscale/1.0.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_testandplot/iwtomics_testandplot/1.0.0.0"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/0.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/0.5.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.2",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.2",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.2"
                 ],
-                "workflowhub_id": "1317"
+                "workflowhub_id": "1298"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.5589610"
+        "zenodo_link": "https://zenodo.org/record/3706539"
     },
     {
         "admin_install": {
@@ -249832,7 +256493,7 @@
             "Extract biomedical terms from the PubMed data for each biomedical entity",
             "Analyze the similarity among the biomedical entities based on the extracted data in an interactive app"
         ],
-        "pageviews": 549,
+        "pageviews": 560,
         "pub_date": "2021-04-05",
         "questions": [
             "How can I automatically collect PubMed data for a set of biomedical entities such as genes?",
@@ -249841,8 +256502,8 @@
         "short_id": "T00272",
         "short_tools": [
             "pmids_to_pubtator_matrix",
-            "interactive_tool_simtext_app",
-            "pubmed_by_queries"
+            "pubmed_by_queries",
+            "interactive_tool_simtext_app"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -249886,8 +256547,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 120,
-        "visitors": 389,
+        "visit_duration": 127,
+        "visitors": 398,
         "workflows": [
             {
                 "creators": [
@@ -249945,7 +256606,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"PubMed query\"];\n  0 -->|output| 1;\n  2[\"PMIDs to PubTator\"];\n  1 -->|output| 2;\n  3[\"simtext_app\"];\n  0 -->|output| 3;\n  2 -->|output| 3;",
-                "modified": "2024-08-18 00:06:25 +0000",
+                "modified": "2024-10-02 12:08:10 +0000",
                 "name": "Simtext training workflow",
                 "outputs": [
                     {
@@ -250128,428 +256789,6 @@
         ],
         "zenodo_link": "https://doi.org/10.5281/zenodo.4638516"
     },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/gpu_jupyter_lab/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "eurosciencegateway",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "email": "anup.rulez@gmail.com",
-                "id": "anuprulez",
-                "joined": "2018-08",
-                "name": "Anup Kumar",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/anuprulez/",
-                "twitter": "musafirtweetsz",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/anuprulez.json"
-            }
-        ],
-        "dir": "topics/statistics/tutorials/gpu_jupyter_lab",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "statistics/gpu_jupyter_lab",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-07-09",
-        "objectives": [
-            "Learn to use Jupyterlab - an online Python editor designed for developing AI algorithms",
-            "Explore several of its features such as Git, workflow of jupyter notebook, integration to Galaxy",
-            "Develop AI algorithms using Tensorflow",
-            "Send long-running jobs to Galaxy's cluster and save results in its history",
-            "Reproduce results from recent scientific publications - COVID CT scan segmentation and 3D protein structure prediction"
-        ],
-        "pageviews": 1101,
-        "pub_date": "2022-04-06",
-        "questions": [
-            "How to use Jupyterlab and it several features?",
-            "How to use it for creating input datasets and writing artificial intelligence (AI) algorithms?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "jupyterlab"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "statistics",
-                "tutorials": [
-                    "intro_deep_learning"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00266",
-        "short_tools": [
-            "Cut1",
-            "Filter1",
-            "interactive_tool_ml_jupyter_notebook"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "interactive-tools",
-            "machine-learning",
-            "deep-learning",
-            "jupyter-lab",
-            "image-segmentation",
-            "protein-3D-structure"
-        ],
-        "time_estimation": "1H",
-        "title": "A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy",
-        "tools": [
-            "Cut1",
-            "Filter1",
-            "interactive_tool_ml_jupyter_notebook"
-        ],
-        "topic_name": "statistics",
-        "topic_name_human": "Statistics and machine learning",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "gpu_jupyter_lab",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/gpu_jupyter_lab/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/gpu_jupyter_lab/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/gpu_jupyter_lab/tutorial.json"
-        },
-        "version": 8,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 79,
-        "visitors": 846,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIPynb notebook\"]\n  1[label=\"train_rows\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntest_rows\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntest_rows_labels\"]\n  4[label=\"GPU enabled Interactive Jupyter Notebook for Machine Learning\"]\n  0 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"out_file1\"]\n  2 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"Cut\"]\n  4 -> 5 [label=\"output_collection\"]\n}",
-                "history": [
-                    {
-                        "hash": "a13a2df4e05c8a59491ec3c2e896f9a2d6e57c43",
-                        "message": "add get data section",
-                        "num": 1,
-                        "short_hash": "a13a2df4e",
-                        "unix": "1673612716"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "IPynb notebook"
-                            }
-                        ],
-                        "label": "IPynb notebook",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0.0,
-                            "top": 49.46180725097656
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "9ddc6af5-38e4-4e13-9376-3540a8f94afb",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "test_rows"
-                            }
-                        ],
-                        "label": "test_rows",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 3.923614501953125,
-                            "top": 293.4548645019531
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "48752f10-3b93-4721-aac6-9217c9285e24",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "test_rows_labels"
-                            }
-                        ],
-                        "label": "test_rows_labels",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 2.986114501953125,
-                            "top": 389.4618225097656
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "d4e139b9-c90d-49b0-9600-dae8de4c04e5",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIPynb notebook\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"train_rows\"];\n  2[\"\u2139\ufe0f Input Dataset\\ntest_rows\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\ntest_rows_labels\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"GPU enabled Interactive Jupyter Notebook for Machine Learning\"];\n  0 -->|output| 4;\n  1 -->|out_file1| 4;\n  2 -->|output| 4;\n  3 -->|output| 4;\n  5[\"Cut\"];\n  4 -->|output_collection| 5;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "gpu_jupytool",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "Filter1",
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Filter",
-                                "name": "input"
-                            }
-                        ],
-                        "label": "train_rows",
-                        "name": "Filter",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 6.90972900390625,
-                            "top": 166.4757080078125
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "new_train_rows"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"cond\": \"c3==0\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
-                        "type": "tool",
-                        "uuid": "25b59910-1d66-4248-98a4-0a3e23193551",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "09c60184-4418-4a83-8d7c-eeac4cdca49e"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "interactive_tool_ml_jupyter_notebook",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "mode|ipynb": {
-                                "id": 0,
-                                "output_name": "output"
-                            },
-                            "user_inputs_0|input_type|input_value": {
-                                "id": 1,
-                                "output_name": "out_file1"
-                            },
-                            "user_inputs_1|input_type|input_value": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "user_inputs_2|input_type|input_value": {
-                                "id": 3,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool GPU enabled Interactive Jupyter Notebook for Machine Learning",
-                                "name": "mode"
-                            }
-                        ],
-                        "label": null,
-                        "name": "GPU enabled Interactive Jupyter Notebook for Machine Learning",
-                        "outputs": [
-                            {
-                                "name": "output_collection",
-                                "type": "input"
-                            },
-                            {
-                                "name": "jupyter_notebook",
-                                "type": "ipynb"
-                            }
-                        ],
-                        "position": {
-                            "left": 307.3437805175781,
-                            "top": 0.0
-                        },
-                        "post_job_actions": {
-                            "ChangeDatatypeActionoutput_collection": {
-                                "action_arguments": {
-                                    "newtype": "tabular"
-                                },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "output_collection"
-                            },
-                            "ChangeDatatypeActionoutput_dataset": {
-                                "action_arguments": {
-                                    "newtype": "tabular"
-                                },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "output_dataset"
-                            }
-                        },
-                        "tool_id": "interactive_tool_ml_jupyter_notebook",
-                        "tool_state": "{\"mode\": {\"mode_select\": \"previous\", \"__current_case__\": 1, \"ipynb\": {\"__class__\": \"RuntimeValue\"}, \"run_it\": \"true\"}, \"user_inputs\": [{\"__index__\": 0, \"input_name\": \"train\", \"description\": \"\", \"input_type\": {\"input_type_selector\": \"dataset\", \"__current_case__\": 0, \"input_value\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 1, \"input_name\": \"test\", \"description\": \"\", \"input_type\": {\"input_type_selector\": \"dataset\", \"__current_case__\": 0, \"input_value\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 2, \"input_name\": \"testlabels\", \"description\": \"\", \"input_type\": {\"input_type_selector\": \"dataset\", \"__current_case__\": 0, \"input_value\": {\"__class__\": \"RuntimeValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.2",
-                        "type": "tool",
-                        "uuid": "b0563c69-10cd-4024-b5de-309c828b8ea2",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output_collection",
-                                "uuid": "fe942416-e111-40c9-8b90-1102348a5b2c"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "jupyter_notebook",
-                                "uuid": "5a38221b-92db-4b48-9b4f-a5c8ecd6f8af"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "Cut1",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "input": {
-                                "id": 4,
-                                "output_name": "output_collection"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cut",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 617.9861755371094,
-                            "top": 52.44792175292969
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"columnList\": \"c1\", \"delimiter\": \"C\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2",
-                        "type": "tool",
-                        "uuid": "0909fb62-c832-4d1d-9d95-5b8ebac25dae",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "fd1c2370-a25e-41d3-8351-fb3aae79c394"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "statistics/gpu_jupyter_lab",
-                "path": "topics/statistics/tutorials/gpu_jupyter_lab/workflows/gpu_jupyterlab_as_jupytool.ga",
-                "tags": [],
-                "test_results": null,
-                "tests": false,
-                "title": "gpu_jupytool",
-                "topic_id": "statistics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-gpu_jupyter_lab/versions/gpu-jupyterlab-as-jupytool",
-                "tutorial_id": "gpu_jupyter_lab",
-                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/gpu_jupyter_lab/workflows/gpu_jupyterlab_as_jupytool.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/gpu_jupyter_lab/workflows/gpu_jupyterlab_as_jupytool.html",
-                "version": 1,
-                "wfid": "statistics-gpu_jupyter_lab",
-                "wfname": "gpu-jupyterlab-as-jupytool",
-                "workflow": "gpu_jupyterlab_as_jupytool.ga",
-                "workflow_tools": [
-                    "Cut1",
-                    "Filter1",
-                    "interactive_tool_ml_jupyter_notebook"
-                ],
-                "workflowhub_id": "1325"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/6091361"
-    },
     {
         "admin_install": {
             "install_repository_dependencies": true,
@@ -250557,177 +256796,140 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "plotly_ml_performance_plots",
-                    "owner": "bgruening",
-                    "revisions": "1c5dcef5ce0f",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "plotly_ml_performance_plots",
-                    "owner": "bgruening",
-                    "revisions": "f234e2e59d76",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "sklearn_build_pipeline",
-                    "owner": "bgruening",
-                    "revisions": "4c4ec859c31a",
-                    "tool_panel_section_label": "Machine Learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "sklearn_ensemble",
+                    "name": "keras_model_builder",
                     "owner": "bgruening",
-                    "revisions": "060ca94ac049",
+                    "revisions": "66d7efc06000",
                     "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sklearn_generalized_linear",
+                    "name": "keras_model_config",
                     "owner": "bgruening",
-                    "revisions": "d4808d5b83da",
+                    "revisions": "f22a9297440f",
                     "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sklearn_nn_classifier",
+                    "name": "keras_train_and_eval",
                     "owner": "bgruening",
-                    "revisions": "8b1b2b91f8d0",
+                    "revisions": "818f9b69d8a0",
                     "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sklearn_searchcv",
+                    "name": "ml_visualization_ex",
                     "owner": "bgruening",
-                    "revisions": "7626ea9c2e1b",
+                    "revisions": "1588f9076e32",
                     "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sklearn_svm_classifier",
+                    "name": "model_prediction",
                     "owner": "bgruening",
-                    "revisions": "80852884053f",
-                    "tool_panel_section_label": "Machine Learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: plotly_ml_performance_plots\n  owner: bgruening\n  revisions: 1c5dcef5ce0f\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: plotly_ml_performance_plots\n  owner: bgruening\n  revisions: f234e2e59d76\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_build_pipeline\n  owner: bgruening\n  revisions: 4c4ec859c31a\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_ensemble\n  owner: bgruening\n  revisions: 060ca94ac049\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_generalized_linear\n  owner: bgruening\n  revisions: d4808d5b83da\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_nn_classifier\n  owner: bgruening\n  revisions: 8b1b2b91f8d0\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_searchcv\n  owner: bgruening\n  revisions: 7626ea9c2e1b\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_svm_classifier\n  owner: bgruening\n  revisions: 80852884053f\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/classification_machinelearning/tutorial.json",
-        "contributors": [
-            {
-                "email": "khanteymoori@gmail.com",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "khanteymoori",
-                "joined": "2019-07",
-                "name": "Alireza Khanteymoori",
-                "orcid": "0000-0001-6811-9196",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/khanteymoori/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/khanteymoori.json"
-            },
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "eurosciencegateway",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "email": "anup.rulez@gmail.com",
-                "id": "anuprulez",
-                "joined": "2018-08",
-                "name": "Anup Kumar",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/anuprulez/",
-                "twitter": "musafirtweetsz",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/anuprulez.json"
-            },
+                    "revisions": "9991c4ddde14",
+                    "tool_panel_section_label": "Machine Learning",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: keras_model_builder\n  owner: bgruening\n  revisions: 66d7efc06000\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_model_config\n  owner: bgruening\n  revisions: f22a9297440f\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_train_and_eval\n  owner: bgruening\n  revisions: 818f9b69d8a0\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ml_visualization_ex\n  owner: bgruening\n  revisions: 1588f9076e32\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: model_prediction\n  owner: bgruening\n  revisions: 9991c4ddde14\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/RNN/tutorial.json",
+        "contributors": [
             {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "simonbray",
-                "joined": "2019-05",
-                "name": "Simon Bray",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
+                "email": "kxk302@gmail.com",
+                "id": "kxk302",
+                "joined": "2021-02",
+                "name": "Kaivan Kamali",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kxk302/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/kxk302.json"
             }
         ],
-        "dir": "topics/statistics/tutorials/classification_machinelearning",
+        "dir": "topics/statistics/tutorials/RNN",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.cz",
             "UseGalaxy.eu",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "statistics",
+                "tutorials": [
+                    "CNN"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "statistics/classification_machinelearning",
+        "id": "statistics/RNN",
         "inexact_supported_servers": [
-            "UseGalaxy.cz",
+            "UseGalaxy.be",
             "UseGalaxy.no"
         ],
         "js_requirements": {
-            "mathjax": null,
+            "mathjax": 22102,
             "mermaid": false
         },
-        "key_points": [
-            "Classification is a supervised approach in machine learning.",
-            "For classification tasks, data is divided into training and test sets.",
-            "Using classification, the samples are learned using the training set and predicted using the test set.",
-            "For each classification algorithm, it parameters should be optimised based on the dataset.",
-            "Machine learning algorithms can be applied to chemical datasets to predict important properties."
-        ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-12",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Learn classification background",
-            "Learn what a quantitative structure-analysis relationship (QSAR) model is and how it can be constructed in Galaxy",
-            "Learn to apply logistic regression, k-nearest neighbors, support verctor machines, random forests and bagging algorithms",
-            "Learn how visualizations can be used to analyze the classification results"
+            "Understand the difference between feedforward neural networks (FNN) and RNN",
+            "Learn various RNN types and architectures",
+            "Learn how to create a neural network using Galaxy's deep learning tools",
+            "Solve a sentiment analysis problem on IMDB movie review dataset using RNN in Galaxy"
         ],
-        "pageviews": 3064,
-        "pub_date": "2020-04-30",
+        "pageviews": 5646089,
+        "pub_date": "2021-02-23",
         "questions": [
-            "What is classification and how we can use classification techniques?"
+            "What is a recurrent neural network (RNN)?",
+            "What are some applications of RNN?"
         ],
         "recordings": [
             {
                 "captioners": [
-                    "anuprulez"
+                    "kxk302"
                 ],
                 "date": "2021-02-15",
                 "galaxy_version": "21.01",
-                "length": "1H50M",
+                "length": "50M",
                 "speakers": [
-                    "anuprulez"
+                    "kxk302"
                 ],
-                "youtube_id": "Gz2OdRPS2Nk"
+                "youtube_id": "1dwzEhjOAmw"
             }
         ],
-        "short_id": "T00262",
+        "requirements": [
+            {
+                "topic_name": "statistics",
+                "tutorials": [
+                    "intro_deep_learning",
+                    "FNN"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00259",
         "short_tools": [
-            "sklearn_ensemble",
-            "sklearn_nn_classifier",
-            "sklearn_generalized_linear",
-            "plotly_ml_performance_plots",
-            "Remove beginning1",
-            "sklearn_build_pipeline",
-            "sklearn_searchcv",
-            "sklearn_svm_classifier"
+            "model_prediction",
+            "keras_model_config",
+            "ml_visualization_ex",
+            "keras_train_and_eval",
+            "keras_model_builder"
         ],
-        "slides": false,
+        "slides": true,
         "slides_recordings": false,
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
@@ -250746,8 +256948,8 @@
             ],
             "inexact": [
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
                 {
@@ -250759,17 +256961,13 @@
         },
         "symlink": null,
         "time_estimation": "2H",
-        "title": "Classification in Machine Learning",
+        "title": "Deep Learning (Part 2) - Recurrent neural networks (RNN)",
         "tools": [
-            "Remove beginning1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.3",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.4",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.11.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_generalized_linear/sklearn_generalized_linear/1.0.11.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_nn_classifier/sklearn_nn_classifier/1.0.11.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.11.0"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/1.0.10.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/1.0.10.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.10.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.10.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.10.0"
         ],
         "topic_name": "statistics",
         "topic_name_human": "Statistics and machine learning",
@@ -250779,92 +256977,50 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "classification_machinelearning",
+        "tutorial_name": "RNN",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/classification_machinelearning/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/RNN/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/classification_machinelearning/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/classification_machinelearning/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/RNN/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/RNN/tutorial.json"
         },
         "version": 14,
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 119,
-        "visitors": 2004,
+        "visit_duration": 197,
+        "visitors": 2063610,
         "workflows": [
             {
                 "creators": [
                     {
-                        "class": "Organization",
-                        "identifier": "https://orcid.org/0000-0002-2068-4695",
-                        "name": "Anup Kumar"
+                        "class": "Person",
+                        "identifier": "0000-0001-6585-3619",
+                        "name": "Kaivan Kamali"
                     }
                 ],
-                "description": "Classification in Machine Learning",
+                "description": "",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntrain_rows.csv\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntest_rows_labels.csv\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntest_rows.csv\"]\n  3[label=\"Pipeline Builder\"]\n  4[label=\"Generalized linear models\"]\n  0 -> 4 [label=\"output\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Nearest Neighbors Classification\"]\n  0 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Support vector machines SVMs\"]\n  0 -> 6 [label=\"output\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Ensemble methods\"]\n  0 -> 7 [label=\"output\"]\n  0 -> 7 [label=\"output\"]\n  8[label=\"Remove beginning\"]\n  1 -> 8 [label=\"output\"]\n  9[label=\"Hyperparameter Search\"]\n  3 -> 9 [label=\"outfile\"]\n  0 -> 9 [label=\"output\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"Generalized linear models\"]\n  2 -> 10 [label=\"output\"]\n  4 -> 10 [label=\"outfile_fit\"]\n  11[label=\"Nearest Neighbors Classification\"]\n  2 -> 11 [label=\"output\"]\n  5 -> 11 [label=\"outfile_fit\"]\n  12[label=\"Support vector machines SVMs\"]\n  2 -> 12 [label=\"output\"]\n  6 -> 12 [label=\"outfile_fit\"]\n  13[label=\"Ensemble methods\"]\n  2 -> 13 [label=\"output\"]\n  7 -> 13 [label=\"outfile_fit\"]\n  14[label=\"Ensemble methods\"]\n  2 -> 14 [label=\"output\"]\n  9 -> 14 [label=\"outfile_object\"]\n  15[label=\"Plot confusion matrix, precision, recall and ROC and AUC curves\"]\n  8 -> 15 [label=\"out_file1\"]\n  10 -> 15 [label=\"outfile_predict\"]\n  4 -> 15 [label=\"outfile_fit\"]\n  16[label=\"Plot confusion matrix, precision, recall and ROC and AUC curves\"]\n  1 -> 16 [label=\"output\"]\n  11 -> 16 [label=\"outfile_predict\"]\n  5 -> 16 [label=\"outfile_fit\"]\n  17[label=\"Plot confusion matrix, precision, recall and ROC and AUC curves\"]\n  1 -> 17 [label=\"output\"]\n  12 -> 17 [label=\"outfile_predict\"]\n  6 -> 17 [label=\"outfile_fit\"]\n  18[label=\"Plot confusion matrix, precision, recall and ROC and AUC curves\"]\n  1 -> 18 [label=\"output\"]\n  13 -> 18 [label=\"outfile_predict\"]\n  7 -> 18 [label=\"outfile_fit\"]\n  19[label=\"Plot confusion matrix, precision, recall and ROC and AUC curves\"]\n  1 -> 19 [label=\"output\"]\n  14 -> 19 [label=\"outfile_predict\"]\n  9 -> 19 [label=\"outfile_object\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nX_test\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nX_train\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ny_test\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ny_train\"]\n  4[label=\"Create a deep learning model architecture\"]\n  5[label=\"Create deep learning model\"]\n  4 -> 5 [label=\"outfile\"]\n  6[label=\"Deep learning training and evaluation\"]\n  5 -> 6 [label=\"outfile\"]\n  1 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"Model Prediction\"]\n  6 -> 7 [label=\"outfile_object\"]\n  0 -> 7 [label=\"output\"]\n  8[label=\"Machine Learning Visualization Extension\"]\n  7 -> 8 [label=\"outfile_predict\"]\n  2 -> 8 [label=\"output\"]\n}",
                 "history": [
                     {
-                        "hash": "6439ff1d5b866f5eb249eff701851b538e0972f0",
-                        "message": "rename workflow file and add workflow test",
-                        "num": 8,
-                        "short_hash": "6439ff1d5",
-                        "unix": "1716281718"
-                    },
-                    {
-                        "hash": "502f6e6508564d450f0c1625e0324f11e36f14d0",
-                        "message": "rename workflow file and add workflow test",
-                        "num": 7,
-                        "short_hash": "502f6e650",
-                        "unix": "1716281168"
-                    },
-                    {
-                        "hash": "e6df909ee94fbedab4bfe0ad62927f8bbf2d5d4a",
-                        "message": "update workflows due to tool upgrade",
-                        "num": 6,
-                        "short_hash": "e6df909ee",
-                        "unix": "1715938213"
-                    },
-                    {
-                        "hash": "bdfa0296c91ec296d171375c5da00a304aa4e165",
-                        "message": "Update ml_classification.ga",
-                        "num": 5,
-                        "short_hash": "bdfa0296c",
-                        "unix": "1588252485"
-                    },
-                    {
-                        "hash": "2680ad593256d485316ebd30e52dbcf234f95211",
-                        "message": "some fixes",
-                        "num": 4,
-                        "short_hash": "2680ad593",
-                        "unix": "1588243701"
-                    },
-                    {
-                        "hash": "becca5c2776328e21e9acbb7da6601717fde7976",
-                        "message": "tags and annotation are added to workflow",
-                        "num": 3,
-                        "short_hash": "becca5c27",
-                        "unix": "1588181809"
-                    },
-                    {
-                        "hash": "0da8a889e86da886397ebb454a695e3286214eda",
-                        "message": "workflow format is changed",
+                        "hash": "f6fe5628d85d4263477b72d8c1ded5ab473fb97a",
+                        "message": "Fixed the extra WF step. Fixed instructions in model prediction",
                         "num": 2,
-                        "short_hash": "0da8a889e",
-                        "unix": "1588180978"
+                        "short_hash": "f6fe5628d",
+                        "unix": "1706115636"
                     },
                     {
-                        "hash": "28d2cd66bda9c8aa8f5fb0d2f4685af2b4b85820",
-                        "message": "workflow is added",
+                        "hash": "72508012689459bf074ee58d075b7e92d91044f0",
+                        "message": "Got rid of . in workflow name",
                         "num": 1,
-                        "short_hash": "28d2cd66b",
-                        "unix": "1588179550"
+                        "short_hash": "725080126",
+                        "unix": "1697492492"
                     }
                 ],
                 "inputs": [
@@ -250877,21 +257033,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "train_rows.csv"
+                                "name": "X_test"
                             }
                         ],
-                        "label": "train_rows.csv",
+                        "label": "X_test",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 21.98957654096855,
-                            "top": 439.5676907009551
+                            "left": 0,
+                            "top": 0
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "2b808085-c925-4327-8310-e45702344b59",
+                        "uuid": "c84eb1e9-61dc-4d37-b13e-999665b31337",
                         "when": null,
                         "workflow_outputs": []
                     },
@@ -250904,21 +257060,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "test_rows_labels.csv"
+                                "name": "X_train"
                             }
                         ],
-                        "label": "test_rows_labels.csv",
+                        "label": "X_train",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 13.333333333333329,
-                            "top": 532.2417024769386
+                            "left": 0,
+                            "top": 120
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "b04a2c8d-d019-49cd-8ef3-f2565cc9a2d5",
+                        "uuid": "0e7e1ec8-f422-4349-889a-4e3e66670c2f",
                         "when": null,
                         "workflow_outputs": []
                     },
@@ -250931,64 +257087,83 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "test_rows.csv"
+                                "name": "y_test"
                             }
                         ],
-                        "label": "test_rows.csv",
+                        "label": "y_test",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0.0,
-                            "top": 630.9083691436052
+                            "left": 0,
+                            "top": 240
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "0c0a1583-9e8c-4382-af2b-feae2d1fc845",
+                        "uuid": "ec09b380-de33-44e1-bce4-c203c10c47d6",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "y_train"
+                            }
+                        ],
+                        "label": "y_train",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 360
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "e0784c26-64c5-4135-ad67-03c62a362b7b",
                         "when": null,
                         "workflow_outputs": []
                     }
                 ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ntrain_rows.csv\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ntest_rows_labels.csv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ntest_rows.csv\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Pipeline Builder\"];\n  4[\"Generalized linear models\"];\n  0 -->|output| 4;\n  0 -->|output| 4;\n  5[\"Nearest Neighbors Classification\"];\n  0 -->|output| 5;\n  0 -->|output| 5;\n  6[\"Support vector machines SVMs\"];\n  0 -->|output| 6;\n  0 -->|output| 6;\n  7[\"Ensemble methods\"];\n  0 -->|output| 7;\n  0 -->|output| 7;\n  8[\"Remove beginning\"];\n  1 -->|output| 8;\n  9[\"Hyperparameter Search\"];\n  3 -->|outfile| 9;\n  0 -->|output| 9;\n  0 -->|output| 9;\n  10[\"Generalized linear models\"];\n  2 -->|output| 10;\n  4 -->|outfile_fit| 10;\n  11[\"Nearest Neighbors Classification\"];\n  2 -->|output| 11;\n  5 -->|outfile_fit| 11;\n  12[\"Support vector machines SVMs\"];\n  2 -->|output| 12;\n  6 -->|outfile_fit| 12;\n  13[\"Ensemble methods\"];\n  2 -->|output| 13;\n  7 -->|outfile_fit| 13;\n  14[\"Ensemble methods\"];\n  2 -->|output| 14;\n  9 -->|outfile_object| 14;\n  15[\"Plot confusion matrix, precision, recall and ROC and AUC curves\"];\n  8 -->|out_file1| 15;\n  10 -->|outfile_predict| 15;\n  4 -->|outfile_fit| 15;\n  16[\"Plot confusion matrix, precision, recall and ROC and AUC curves\"];\n  1 -->|output| 16;\n  11 -->|outfile_predict| 16;\n  5 -->|outfile_fit| 16;\n  17[\"Plot confusion matrix, precision, recall and ROC and AUC curves\"];\n  1 -->|output| 17;\n  12 -->|outfile_predict| 17;\n  6 -->|outfile_fit| 17;\n  18[\"Plot confusion matrix, precision, recall and ROC and AUC curves\"];\n  1 -->|output| 18;\n  13 -->|outfile_predict| 18;\n  7 -->|outfile_fit| 18;\n  19[\"Plot confusion matrix, precision, recall and ROC and AUC curves\"];\n  1 -->|output| 19;\n  14 -->|outfile_predict| 19;\n  9 -->|outfile_object| 19;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "ml_classification",
+                "license": "CC-BY-4.0",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nX_test\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nX_train\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ny_test\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\ny_train\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Create a deep learning model architecture\"];\n  5[\"Create deep learning model\"];\n  4 -->|outfile| 5;\n  6[\"Deep learning training and evaluation\"];\n  5 -->|outfile| 6;\n  1 -->|output| 6;\n  3 -->|output| 6;\n  7[\"Model Prediction\"];\n  6 -->|outfile_object| 7;\n  0 -->|output| 7;\n  8[\"Machine Learning Visualization Extension\"];\n  7 -->|outfile_predict| 8;\n  2 -->|output| 8;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "Intro_To_RNN_v1_0_10_0",
                 "outputs": [],
-                "parent_id": "statistics/classification_machinelearning",
-                "path": "topics/statistics/tutorials/classification_machinelearning/workflows/ml_classification.ga",
-                "tags": [
-                    "statistics",
-                    "classification",
-                    "ml",
-                    "cheminformatics"
-                ],
+                "parent_id": "statistics/RNN",
+                "path": "topics/statistics/tutorials/RNN/workflows/Intro_To_RNN_v1_0_10_0.ga",
+                "tags": [],
                 "test_results": null,
                 "tests": true,
-                "title": "ml_classification",
+                "title": "Intro_To_RNN_v1_0_10_0",
                 "topic_id": "statistics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-classification_machinelearning/versions/ml-classification",
-                "tutorial_id": "classification_machinelearning",
-                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/classification_machinelearning/workflows/ml_classification.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/classification_machinelearning/workflows/ml_classification.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-RNN/versions/intro-to-rnn-v1-0-10-0",
+                "tutorial_id": "RNN",
+                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/RNN/workflows/Intro_To_RNN_v1_0_10_0.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/RNN/workflows/Intro_To_RNN_v1_0_10_0.html",
                 "version": 2,
-                "wfid": "statistics-classification_machinelearning",
-                "wfname": "ml-classification",
-                "workflow": "ml_classification.ga",
+                "wfid": "statistics-RNN",
+                "wfname": "intro-to-rnn-v1-0-10-0",
+                "workflow": "Intro_To_RNN_v1_0_10_0.ga",
                 "workflow_tools": [
-                    "Remove beginning1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.3",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.11.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_generalized_linear/sklearn_generalized_linear/1.0.11.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_nn_classifier/sklearn_nn_classifier/1.0.11.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.11.0"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/1.0.10.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/1.0.10.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.10.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.10.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.10.0"
                 ],
-                "workflowhub_id": "1331"
+                "workflowhub_id": "1273"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/3738729"
+        "zenodo_link": "https://zenodo.org/record/4477881"
     },
     {
         "admin_install": {
@@ -250997,58 +257172,76 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "keras_model_builder",
+                    "name": "plotly_parallel_coordinates_plot",
                     "owner": "bgruening",
-                    "revisions": "66d7efc06000",
-                    "tool_panel_section_label": "Machine Learning",
+                    "revisions": "7b21a9b5922f",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "keras_model_config",
+                    "name": "plotly_regression_performance_plots",
                     "owner": "bgruening",
-                    "revisions": "f22a9297440f",
-                    "tool_panel_section_label": "Machine Learning",
+                    "revisions": "389227fa1864",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "keras_train_and_eval",
+                    "name": "sklearn_build_pipeline",
                     "owner": "bgruening",
-                    "revisions": "818f9b69d8a0",
+                    "revisions": "840f29aad145",
                     "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ml_visualization_ex",
+                    "name": "sklearn_ensemble",
                     "owner": "bgruening",
-                    "revisions": "1588f9076e32",
+                    "revisions": "1a53edc4b438",
                     "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "model_prediction",
+                    "name": "sklearn_searchcv",
                     "owner": "bgruening",
-                    "revisions": "9991c4ddde14",
+                    "revisions": "25ab6b4e376e",
                     "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: keras_model_builder\n  owner: bgruening\n  revisions: 66d7efc06000\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_model_config\n  owner: bgruening\n  revisions: f22a9297440f\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_train_and_eval\n  owner: bgruening\n  revisions: 818f9b69d8a0\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ml_visualization_ex\n  owner: bgruening\n  revisions: 1588f9076e32\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: model_prediction\n  owner: bgruening\n  revisions: 9991c4ddde14\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/RNN/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: plotly_parallel_coordinates_plot\n  owner: bgruening\n  revisions: 7b21a9b5922f\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: plotly_regression_performance_plots\n  owner: bgruening\n  revisions: 389227fa1864\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_build_pipeline\n  owner: bgruening\n  revisions: 840f29aad145\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_ensemble\n  owner: bgruening\n  revisions: 1a53edc4b438\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_searchcv\n  owner: bgruening\n  revisions: 25ab6b4e376e\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/age-prediction-with-ml/tutorial.json",
         "contributors": [
             {
-                "email": "kxk302@gmail.com",
-                "id": "kxk302",
-                "joined": "2021-02",
-                "name": "Kaivan Kamali",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kxk302/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/kxk302.json"
+                "affiliations": [
+                    "uni-freiburg"
+                ],
+                "id": "polkhe",
+                "joined": "2017-09",
+                "name": "Ekaterina Polkh",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/polkhe/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/polkhe.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "eurosciencegateway",
+                    "elixir-europe"
+                ],
+                "elixir_node": "de",
+                "email": "anup.rulez@gmail.com",
+                "id": "anuprulez",
+                "joined": "2018-08",
+                "name": "Anup Kumar",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/anuprulez/",
+                "twitter": "musafirtweetsz",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/anuprulez.json"
             }
         ],
-        "dir": "topics/statistics/tutorials/RNN",
+        "dir": "topics/statistics/tutorials/age-prediction-with-ml",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.eu",
             "UseGalaxy.org (Main)",
@@ -251056,75 +257249,50 @@
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "statistics",
-                "tutorials": [
-                    "CNN"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "statistics/RNN",
+        "id": "statistics/age-prediction-with-ml",
         "inexact_supported_servers": [
             "UseGalaxy.no"
         ],
         "js_requirements": {
-            "mathjax": 22102,
+            "mathjax": null,
             "mermaid": false
         },
+        "key_points": [
+            "Various machine learning algorithms should be used to find the best ones",
+            "For each machine learning algorithm, it hyperparameters should be optimised based on the dataset",
+            "Feature selection should be done for high-dimensional datasets"
+        ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-03-05",
         "objectives": [
-            "Understand the difference between feedforward neural networks (FNN) and RNN",
-            "Learn various RNN types and architectures",
-            "Learn how to create a neural network using Galaxy's deep learning tools",
-            "Solve a sentiment analysis problem on IMDB movie review dataset using RNN in Galaxy"
+            "Learn ageing biomarkers from RNA-seq and DNA methylation datasets",
+            "Apply regression based machine learning algorithms",
+            "Learn feature selection and hyperparameter optimisation"
         ],
-        "pageviews": 5475281,
-        "pub_date": "2021-02-23",
+        "pageviews": 20501,
+        "pub_date": "2019-01-25",
         "questions": [
-            "What is a recurrent neural network (RNN)?",
-            "What are some applications of RNN?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "kxk302"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "50M",
-                "speakers": [
-                    "kxk302"
-                ],
-                "youtube_id": "1dwzEhjOAmw"
-            }
-        ],
-        "requirements": [
-            {
-                "topic_name": "statistics",
-                "tutorials": [
-                    "intro_deep_learning",
-                    "FNN"
-                ],
-                "type": "internal"
-            }
+            "How to use machine learning to create predictive models from biological datasets (RNA-seq and DNA methylation)?"
         ],
-        "short_id": "T00259",
+        "short_id": "T00261",
         "short_tools": [
-            "keras_model_builder",
-            "keras_model_config",
-            "model_prediction",
-            "keras_train_and_eval",
-            "ml_visualization_ex"
+            "sklearn_build_pipeline",
+            "plotly_parallel_coordinates_plot",
+            "plotly_regression_performance_plots",
+            "sklearn_ensemble",
+            "sklearn_searchcv"
         ],
-        "slides": true,
+        "slides": false,
         "slides_recordings": false,
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -251156,13 +257324,13 @@
         },
         "symlink": null,
         "time_estimation": "2H",
-        "title": "Deep Learning (Part 2) - Recurrent neural networks (RNN)",
+        "title": "Age prediction using machine learning",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/1.0.10.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/1.0.10.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.10.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.10.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.10.0"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.8.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.8.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1"
         ],
         "topic_name": "statistics",
         "topic_name_human": "Statistics and machine learning",
@@ -251172,50 +257340,598 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "RNN",
+        "tutorial_name": "age-prediction-with-ml",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/RNN/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/age-prediction-with-ml/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/RNN/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/RNN/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/age-prediction-with-ml/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/age-prediction-with-ml/tutorial.json"
         },
-        "version": 14,
+        "version": 11,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 198,
-        "visitors": 1994160,
+        "visit_duration": 40,
+        "visitors": 12534,
         "workflows": [
             {
-                "creators": [
+                "creators": [],
+                "description": "Age prediction using machine learning",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Pipeline Builder\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntrain_dataset\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntest_dataset\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntest_labels_dataset\"]\n  4[label=\"Hyperparameter Search\"]\n  0 -> 4 [label=\"outfile_params\"]\n  0 -> 4 [label=\"outfile\"]\n  1 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Ensemble methods\"]\n  2 -> 5 [label=\"output\"]\n  4 -> 5 [label=\"outfile_object\"]\n  6[label=\"Plot actual vs predicted curves and residual plots\"]\n  5 -> 6 [label=\"outfile_predict\"]\n  3 -> 6 [label=\"output\"]\n}",
+                "history": [
                     {
-                        "class": "Person",
-                        "identifier": "0000-0001-6585-3619",
-                        "name": "Kaivan Kamali"
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 8,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "f7f017f3329dac306d19ca406c5e28f75bbf4ef8",
+                        "message": "dna and rna capitals",
+                        "num": 7,
+                        "short_hash": "f7f017f33",
+                        "unix": "1579092000"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 6,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "cad9f0a86642e5d5580ac0a3a2f7ffef6cd56311",
+                        "message": "Merge branch 'master' into ml_tools",
+                        "num": 5,
+                        "short_hash": "cad9f0a86",
+                        "unix": "1577658485"
+                    },
+                    {
+                        "hash": "0c8165c369cbc93a90c6f963d9fd5fcda86d4c5d",
+                        "message": "update workflow",
+                        "num": 4,
+                        "short_hash": "0c8165c36",
+                        "unix": "1577390920"
+                    },
+                    {
+                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
+                        "message": "unflatten workflows",
+                        "num": 3,
+                        "short_hash": "faf6d298a",
+                        "unix": "1576155753"
+                    },
+                    {
+                        "hash": "9d78b64348e1f3e59dc99c6860d4ae3c6a0619cc",
+                        "message": "Add workflows",
+                        "num": 2,
+                        "short_hash": "9d78b6434",
+                        "unix": "1560616699"
+                    },
+                    {
+                        "hash": "17a20f8e6367994c2dae74c93846a738275b9ee6",
+                        "message": "Fine-tuning formatting",
+                        "num": 1,
+                        "short_hash": "17a20f8e6",
+                        "unix": "1548412498"
                     }
                 ],
-                "description": "",
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "train_dataset",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 359.8828125,
+                            "top": 515.01953125
+                        },
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "7bcdbca8-beb1-4015-85f8-a289e0d5baa6",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "b53c6d64-e5a0-4fc9-bca1-6793352d93c5"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "test_dataset",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 409.375,
+                            "top": 641.875
+                        },
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "3bd54821-fc35-47ef-830f-eff3db757252",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "4588ddcc-8132-46a9-b1ed-00d8897790e0"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "test_labels_dataset",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 944.90234375,
+                            "top": 278.88671875
+                        },
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "40f96b3a-c0af-481b-beb0-4f98d711b5a5",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "fd8d51f2-0b16-4bab-97b8-b3e5a3f5c637"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"Pipeline Builder\"];\n  1[\"\u2139\ufe0f Input Dataset\\ntrain_dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ntest_dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\ntest_labels_dataset\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Hyperparameter Search\"];\n  0 -->|outfile_params| 4;\n  0 -->|outfile| 4;\n  1 -->|output| 4;\n  1 -->|output| 4;\n  5[\"Ensemble methods\"];\n  2 -->|output| 5;\n  4 -->|outfile_object| 5;\n  6[\"Plot actual vs predicted curves and residual plots\"];\n  5 -->|outfile_predict| 6;\n  3 -->|output| 6;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "Age Prediction DNA Methylation",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.8.1",
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": null,
+                        "name": "Pipeline Builder",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "zip"
+                            },
+                            {
+                                "name": "outfile_params",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 220.83984375,
+                            "top": 199.9609375
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.8.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3f3c6dc38f3e",
+                            "name": "sklearn_build_pipeline",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"final_estimator\": \"{\\\"estimator_selector\\\": {\\\"__current_case__\\\": 2, \\\"selected_estimator\\\": \\\"GradientBoostingRegressor\\\", \\\"selected_module\\\": \\\"ensemble\\\", \\\"text_params\\\": \\\"random_state=42\\\"}}\", \"pipeline_component\": \"[{\\\"__index__\\\": 0, \\\"component_selector\\\": {\\\"__current_case__\\\": 0, \\\"component_type\\\": \\\"None\\\"}}]\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"get_params\": \"\\\"true\\\"\"}",
+                        "tool_version": "1.0.8.1",
+                        "type": "tool",
+                        "uuid": "26db8419-6a23-48d3-bf72-33ca0416e645",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "2a7377ad-1474-4953-bd39-8bcdeccbc046"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outfile_params",
+                                "uuid": "19fe7f34-c119-479d-8cad-58338b1f9ce4"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "train_dataset",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 359.8828125,
+                            "top": 515.01953125
+                        },
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "7bcdbca8-beb1-4015-85f8-a289e0d5baa6",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "b53c6d64-e5a0-4fc9-bca1-6793352d93c5"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "test_dataset",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 409.375,
+                            "top": 641.875
+                        },
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "3bd54821-fc35-47ef-830f-eff3db757252",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "4588ddcc-8132-46a9-b1ed-00d8897790e0"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "test_labels_dataset",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 944.90234375,
+                            "top": 278.88671875
+                        },
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "40f96b3a-c0af-481b-beb0-4f98d711b5a5",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "fd8d51f2-0b16-4bab-97b8-b3e5a3f5c637"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "input_options|infile1": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "input_options|infile2": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "search_schemes|infile_estimator": {
+                                "id": 0,
+                                "output_name": "outfile"
+                            },
+                            "search_schemes|search_params_builder|infile_params": {
+                                "id": 0,
+                                "output_name": "outfile_params"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Hyperparameter Search",
+                                "name": "search_schemes"
+                            },
+                            {
+                                "description": "runtime parameter for tool Hyperparameter Search",
+                                "name": "input_options"
+                            },
+                            {
+                                "description": "runtime parameter for tool Hyperparameter Search",
+                                "name": "input_options"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Hyperparameter Search",
+                        "outputs": [
+                            {
+                                "name": "outfile_result",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "outfile_object",
+                                "type": "zip"
+                            }
+                        ],
+                        "position": {
+                            "left": 632.44140625,
+                            "top": 124.94140625
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "c1ca24a1509d",
+                            "name": "sklearn_searchcv",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"search_schemes\": \"{\\\"__current_case__\\\": 0, \\\"infile_estimator\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"is_deep_learning\\\": \\\"false\\\", \\\"options\\\": {\\\"cv_selector\\\": {\\\"__current_case__\\\": 1, \\\"n_splits\\\": \\\"5\\\", \\\"random_state\\\": \\\"3111696\\\", \\\"selected_cv\\\": \\\"KFold\\\", \\\"shuffle\\\": \\\"true\\\"}, \\\"error_score\\\": \\\"false\\\", \\\"iid\\\": \\\"true\\\", \\\"return_train_score\\\": \\\"false\\\", \\\"scoring\\\": {\\\"__current_case__\\\": 26, \\\"primary_scoring\\\": \\\"r2\\\", \\\"secondary_scoring\\\": null}, \\\"verbose\\\": \\\"0\\\"}, \\\"search_params_builder\\\": {\\\"infile_params\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"param_set\\\": [{\\\"__index__\\\": 0, \\\"sp_list\\\": \\\"[25, 50, 75, 100, 200]\\\", \\\"sp_name\\\": \\\"n_estimators\\\"}]}, \\\"selected_search_scheme\\\": \\\"GridSearchCV\\\"}\", \"__rerun_remap_job_id__\": null, \"save\": \"\\\"save_estimator\\\"\", \"input_options\": \"{\\\"__current_case__\\\": 0, \\\"column_selector_options_1\\\": {\\\"__current_case__\\\": 3, \\\"col1\\\": \\\"Age\\\", \\\"selected_column_selector_option\\\": \\\"all_but_by_header_name\\\"}, \\\"column_selector_options_2\\\": {\\\"__current_case__\\\": 2, \\\"col2\\\": \\\"Age\\\", \\\"selected_column_selector_option2\\\": \\\"by_header_name\\\"}, \\\"header1\\\": \\\"true\\\", \\\"header2\\\": \\\"true\\\", \\\"infile1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"infile2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"selected_input\\\": \\\"tabular\\\"}\", \"outer_split\": \"{\\\"__current_case__\\\": 0, \\\"split_mode\\\": \\\"no\\\"}\"}",
+                        "tool_version": "1.0.8.1",
+                        "type": "tool",
+                        "uuid": "4127ab12-dbd9-4888-bcda-b05748a05295",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile_object",
+                                "uuid": "48939329-f5f2-445e-bdb3-51dc28629f18"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outfile_result",
+                                "uuid": "5b78c8e6-1e98-4798-bab3-285cedbc8d85"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.8.1",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "selected_tasks|infile_data": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "selected_tasks|infile_model": {
+                                "id": 4,
+                                "output_name": "outfile_object"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Ensemble methods",
+                                "name": "selected_tasks"
+                            },
+                            {
+                                "description": "runtime parameter for tool Ensemble methods",
+                                "name": "selected_tasks"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Ensemble methods",
+                        "outputs": [
+                            {
+                                "name": "outfile_predict",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 710.87890625,
+                            "top": 558.92578125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.8.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "af0523c606a7",
+                            "name": "sklearn_ensemble",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"selected_tasks\": \"{\\\"__current_case__\\\": 0, \\\"header\\\": \\\"true\\\", \\\"infile_data\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"infile_model\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"prediction_options\\\": {\\\"__current_case__\\\": 0, \\\"prediction_option\\\": \\\"predict\\\"}, \\\"selected_task\\\": \\\"load\\\"}\", \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.8.1",
+                        "type": "tool",
+                        "uuid": "559f44ea-0d8b-4fce-85fb-079d010ab90d",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile_predict",
+                                "uuid": "d025d2be-6698-49a0-901e-0c9513f72255"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "infile_input": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "infile_output": {
+                                "id": 5,
+                                "output_name": "outfile_predict"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Plot actual vs predicted curves and residual plots",
+                        "outputs": [
+                            {
+                                "name": "output_actual_vs_pred",
+                                "type": "html"
+                            },
+                            {
+                                "name": "output_scatter_plot",
+                                "type": "html"
+                            },
+                            {
+                                "name": "output_residual_plot",
+                                "type": "html"
+                            }
+                        ],
+                        "position": {
+                            "left": 1058.3984375,
+                            "top": 452.890625
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "389227fa1864",
+                            "name": "plotly_regression_performance_plots",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"infile_output\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"infile_input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+                        "tool_version": "0.1",
+                        "type": "tool",
+                        "uuid": "8fd368d0-ef84-4414-9fc9-ef408947a080",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output_scatter_plot",
+                                "uuid": "043f8530-e77a-4768-abdc-365ff91127fa"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_actual_vs_pred",
+                                "uuid": "3a0f039e-b4c4-466a-9be9-b7d9ceeb73e7"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "output_residual_plot",
+                                "uuid": "1ec7ae83-9fd7-4b98-b613-3cb3802211ee"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "statistics/age-prediction-with-ml",
+                "path": "topics/statistics/tutorials/age-prediction-with-ml/workflows/age-prediction-dnam.ga",
+                "tags": [
+                    "statistics"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Age Prediction DNA Methylation",
+                "topic_id": "statistics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-age-prediction-with-ml/versions/age-prediction-dnam",
+                "tutorial_id": "age-prediction-with-ml",
+                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/age-prediction-with-ml/workflows/age-prediction-dnam.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/age-prediction-with-ml/workflows/age-prediction-dnam.html",
+                "version": 6,
+                "wfid": "statistics-age-prediction-with-ml",
+                "wfname": "age-prediction-dnam",
+                "workflow": "age-prediction-dnam.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.8.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.8.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1"
+                ],
+                "workflowhub_id": "1277"
+            },
+            {
+                "creators": [],
+                "description": "Age prediction using machine learning",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nX_test\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nX_train\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ny_test\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ny_train\"]\n  4[label=\"Create a deep learning model architecture\"]\n  5[label=\"Create deep learning model\"]\n  4 -> 5 [label=\"outfile\"]\n  6[label=\"Deep learning training and evaluation\"]\n  5 -> 6 [label=\"outfile\"]\n  1 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"Model Prediction\"]\n  6 -> 7 [label=\"outfile_object\"]\n  0 -> 7 [label=\"output\"]\n  8[label=\"Machine Learning Visualization Extension\"]\n  7 -> 8 [label=\"outfile_predict\"]\n  2 -> 8 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Pipeline Builder\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[label=\"Hyperparameter Search\"]\n  0 -> 2 [label=\"outfile_params\"]\n  0 -> 2 [label=\"outfile\"]\n  1 -> 2 [label=\"output\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"Parallel Coordinates Plot\"]\n  2 -> 3 [label=\"outfile_result\"]\n}",
                 "history": [
                     {
-                        "hash": "f6fe5628d85d4263477b72d8c1ded5ab473fb97a",
-                        "message": "Fixed the extra WF step. Fixed instructions in model prediction",
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 8,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "f7f017f3329dac306d19ca406c5e28f75bbf4ef8",
+                        "message": "dna and rna capitals",
+                        "num": 7,
+                        "short_hash": "f7f017f33",
+                        "unix": "1579092000"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 6,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "cad9f0a86642e5d5580ac0a3a2f7ffef6cd56311",
+                        "message": "Merge branch 'master' into ml_tools",
+                        "num": 5,
+                        "short_hash": "cad9f0a86",
+                        "unix": "1577658485"
+                    },
+                    {
+                        "hash": "0c8165c369cbc93a90c6f963d9fd5fcda86d4c5d",
+                        "message": "update workflow",
+                        "num": 4,
+                        "short_hash": "0c8165c36",
+                        "unix": "1577390920"
+                    },
+                    {
+                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
+                        "message": "unflatten workflows",
+                        "num": 3,
+                        "short_hash": "faf6d298a",
+                        "unix": "1576155753"
+                    },
+                    {
+                        "hash": "9d78b64348e1f3e59dc99c6860d4ae3c6a0619cc",
+                        "message": "Add workflows",
                         "num": 2,
-                        "short_hash": "f6fe5628d",
-                        "unix": "1706115636"
+                        "short_hash": "9d78b6434",
+                        "unix": "1560616699"
                     },
                     {
-                        "hash": "72508012689459bf074ee58d075b7e92d91044f0",
-                        "message": "Got rid of . in workflow name",
+                        "hash": "17a20f8e6367994c2dae74c93846a738275b9ee6",
+                        "message": "Fine-tuning formatting",
                         "num": 1,
-                        "short_hash": "725080126",
-                        "unix": "1697492492"
+                        "short_hash": "17a20f8e6",
+                        "unix": "1548412498"
                     }
                 ],
                 "inputs": [
@@ -251223,142 +257939,265 @@
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 1,
                         "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "X_test"
-                            }
-                        ],
-                        "label": "X_test",
+                        "inputs": [],
+                        "label": null,
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 0
+                            "left": 295.9375,
+                            "top": 391.09375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "c84eb1e9-61dc-4d37-b13e-999665b31337",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
+                        "uuid": "7bcdbca8-beb1-4015-85f8-a289e0d5baa6",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "f68ac118-2beb-41f3-9a64-41c66162c474"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"Pipeline Builder\"];\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Hyperparameter Search\"];\n  0 -->|outfile_params| 2;\n  0 -->|outfile| 2;\n  1 -->|output| 2;\n  1 -->|output| 2;\n  3[\"Parallel Coordinates Plot\"];\n  2 -->|outfile_result| 3;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "Age Prediction RNA-Seq",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.8.1",
                         "errors": null,
-                        "id": 1,
+                        "id": 0,
                         "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Pipeline Builder",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "X_train"
+                                "name": "outfile",
+                                "type": "zip"
+                            },
+                            {
+                                "name": "outfile_params",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "X_train",
+                        "position": {
+                            "left": 216.9140625,
+                            "top": 222.98828125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.8.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3f3c6dc38f3e",
+                            "name": "sklearn_build_pipeline",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"final_estimator\": \"{\\\"estimator_selector\\\": {\\\"__current_case__\\\": 1, \\\"selected_estimator\\\": \\\"ElasticNet\\\", \\\"selected_module\\\": \\\"linear_model\\\", \\\"text_params\\\": \\\"random_state=42\\\"}}\", \"pipeline_component\": \"[{\\\"__index__\\\": 0, \\\"component_selector\\\": {\\\"__current_case__\\\": 2, \\\"component_type\\\": \\\"feature_selection\\\", \\\"fs_algorithm_selector\\\": {\\\"__current_case__\\\": 2, \\\"options\\\": {\\\"k\\\": \\\"10\\\"}, \\\"score_func\\\": \\\"f_regression\\\", \\\"selected_algorithm\\\": \\\"SelectKBest\\\"}}}]\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"get_params\": \"\\\"true\\\"\"}",
+                        "tool_version": "1.0.8.1",
+                        "type": "tool",
+                        "uuid": "26db8419-6a23-48d3-bf72-33ca0416e645",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile_params",
+                                "uuid": "551e9e48-ff1b-42ec-90b6-98e6b5058b04"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "2a7377ad-1474-4953-bd39-8bcdeccbc046"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": null,
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 120
+                            "left": 295.9375,
+                            "top": 391.09375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "0e7e1ec8-f422-4349-889a-4e3e66670c2f",
-                        "when": null,
-                        "workflow_outputs": []
+                        "uuid": "7bcdbca8-beb1-4015-85f8-a289e0d5baa6",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "f68ac118-2beb-41f3-9a64-41c66162c474"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1",
                         "errors": null,
                         "id": 2,
-                        "input_connections": {},
+                        "input_connections": {
+                            "input_options|infile1": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "input_options|infile2": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "search_schemes|infile_estimator": {
+                                "id": 0,
+                                "output_name": "outfile"
+                            },
+                            "search_schemes|search_params_builder|infile_params": {
+                                "id": 0,
+                                "output_name": "outfile_params"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "y_test"
+                                "description": "runtime parameter for tool Hyperparameter Search",
+                                "name": "search_schemes"
+                            },
+                            {
+                                "description": "runtime parameter for tool Hyperparameter Search",
+                                "name": "input_options"
+                            },
+                            {
+                                "description": "runtime parameter for tool Hyperparameter Search",
+                                "name": "input_options"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Hyperparameter Search",
+                        "outputs": [
+                            {
+                                "name": "outfile_result",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "outfile_object",
+                                "type": "zip"
                             }
                         ],
-                        "label": "y_test",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 240
+                            "left": 647.5,
+                            "top": 180.99609375
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ec09b380-de33-44e1-bce4-c203c10c47d6",
-                        "when": null,
-                        "workflow_outputs": []
+                        "post_job_actions": {
+                            "HideDatasetActionoutfile_object": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "outfile_object"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "c1ca24a1509d",
+                            "name": "sklearn_searchcv",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"search_schemes\": \"{\\\"__current_case__\\\": 0, \\\"infile_estimator\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"is_deep_learning\\\": \\\"false\\\", \\\"options\\\": {\\\"cv_selector\\\": {\\\"__current_case__\\\": 1, \\\"n_splits\\\": \\\"5\\\", \\\"random_state\\\": \\\"3111696\\\", \\\"selected_cv\\\": \\\"KFold\\\", \\\"shuffle\\\": \\\"true\\\"}, \\\"error_score\\\": \\\"false\\\", \\\"iid\\\": \\\"true\\\", \\\"return_train_score\\\": \\\"false\\\", \\\"scoring\\\": {\\\"__current_case__\\\": 26, \\\"primary_scoring\\\": \\\"r2\\\", \\\"secondary_scoring\\\": null}, \\\"verbose\\\": \\\"0\\\"}, \\\"search_params_builder\\\": {\\\"infile_params\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"param_set\\\": [{\\\"__index__\\\": 0, \\\"sp_list\\\": \\\"[5880, 5890, 5895, 5900]\\\", \\\"sp_name\\\": \\\"selectkbest__k\\\"}, {\\\"__index__\\\": 1, \\\"sp_list\\\": \\\"[True, False]\\\", \\\"sp_name\\\": \\\"elasticnet__normalize\\\"}, {\\\"__index__\\\": 2, \\\"sp_list\\\": \\\"[0.00001, 0.0001, 0.001]\\\", \\\"sp_name\\\": \\\"elasticnet__alpha\\\"}]}, \\\"selected_search_scheme\\\": \\\"GridSearchCV\\\"}\", \"__rerun_remap_job_id__\": null, \"save\": \"\\\"save_estimator\\\"\", \"input_options\": \"{\\\"__current_case__\\\": 0, \\\"column_selector_options_1\\\": {\\\"__current_case__\\\": 3, \\\"col1\\\": \\\"age\\\", \\\"selected_column_selector_option\\\": \\\"all_but_by_header_name\\\"}, \\\"column_selector_options_2\\\": {\\\"__current_case__\\\": 2, \\\"col2\\\": \\\"age\\\", \\\"selected_column_selector_option2\\\": \\\"by_header_name\\\"}, \\\"header1\\\": \\\"true\\\", \\\"header2\\\": \\\"true\\\", \\\"infile1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"infile2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"selected_input\\\": \\\"tabular\\\"}\", \"outer_split\": \"{\\\"__current_case__\\\": 0, \\\"split_mode\\\": \\\"no\\\"}\"}",
+                        "tool_version": "1.0.8.1",
+                        "type": "tool",
+                        "uuid": "4127ab12-dbd9-4888-bcda-b05748a05295",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile_result",
+                                "uuid": "cd5488b6-e604-411d-9032-8189d9b0205f"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1",
                         "errors": null,
                         "id": 3,
-                        "input_connections": {},
+                        "input_connections": {
+                            "infile": {
+                                "id": 2,
+                                "output_name": "outfile_result"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "y_train"
+                                "description": "runtime parameter for tool Parallel Coordinates Plot",
+                                "name": "infile"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Parallel Coordinates Plot",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "html"
                             }
                         ],
-                        "label": "y_train",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 360
+                            "left": 961.0546875,
+                            "top": 252.05078125
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "e0784c26-64c5-4135-ad67-03c62a362b7b",
-                        "when": null,
-                        "workflow_outputs": []
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "7b2455348edf",
+                            "name": "plotly_parallel_coordinates_plot",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"col_color\": \"\\\"3\\\"\", \"col_dimensions\": \"\\\"4, 5, 6\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "0.1",
+                        "type": "tool",
+                        "uuid": "a208b2c4-9a3f-40a9-a55c-c98a7b552bcb",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "0dc1b427-05f1-40d5-b28b-9b2e73ce4a29"
+                            }
+                        ]
                     }
                 ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nX_test\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nX_train\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ny_test\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\ny_train\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Create a deep learning model architecture\"];\n  5[\"Create deep learning model\"];\n  4 -->|outfile| 5;\n  6[\"Deep learning training and evaluation\"];\n  5 -->|outfile| 6;\n  1 -->|output| 6;\n  3 -->|output| 6;\n  7[\"Model Prediction\"];\n  6 -->|outfile_object| 7;\n  0 -->|output| 7;\n  8[\"Machine Learning Visualization Extension\"];\n  7 -->|outfile_predict| 8;\n  2 -->|output| 8;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Intro_To_RNN_v1_0_10_0",
-                "outputs": [],
-                "parent_id": "statistics/RNN",
-                "path": "topics/statistics/tutorials/RNN/workflows/Intro_To_RNN_v1_0_10_0.ga",
-                "tags": [],
+                "parent_id": "statistics/age-prediction-with-ml",
+                "path": "topics/statistics/tutorials/age-prediction-with-ml/workflows/age-prediction-rna.ga",
+                "tags": [
+                    "statistics"
+                ],
                 "test_results": null,
-                "tests": true,
-                "title": "Intro_To_RNN_v1_0_10_0",
+                "tests": false,
+                "title": "Age Prediction RNA-Seq",
                 "topic_id": "statistics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-RNN/versions/intro-to-rnn-v1-0-10-0",
-                "tutorial_id": "RNN",
-                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/RNN/workflows/Intro_To_RNN_v1_0_10_0.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/RNN/workflows/Intro_To_RNN_v1_0_10_0.html",
-                "version": 2,
-                "wfid": "statistics-RNN",
-                "wfname": "intro-to-rnn-v1-0-10-0",
-                "workflow": "Intro_To_RNN_v1_0_10_0.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-age-prediction-with-ml/versions/age-prediction-rna",
+                "tutorial_id": "age-prediction-with-ml",
+                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/age-prediction-with-ml/workflows/age-prediction-rna.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/age-prediction-with-ml/workflows/age-prediction-rna.html",
+                "version": 6,
+                "wfid": "statistics-age-prediction-with-ml",
+                "wfname": "age-prediction-rna",
+                "workflow": "age-prediction-rna.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/1.0.10.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/1.0.10.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.10.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.10.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.10.0"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.8.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1"
                 ],
-                "workflowhub_id": "1273"
+                "workflowhub_id": "1280"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/4477881"
+        "zenodo_link": "https://zenodo.org/record/2545213"
     },
     {
         "admin_install": {
@@ -251367,44 +258206,16 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "keras_model_builder",
-                    "owner": "bgruening",
-                    "revisions": "772e0e89fc68",
-                    "tool_panel_section_label": "Machine Learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "keras_model_config",
-                    "owner": "bgruening",
-                    "revisions": "8a794e6d3388",
-                    "tool_panel_section_label": "Machine Learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "keras_train_and_eval",
-                    "owner": "bgruening",
-                    "revisions": "f1b9a42d6809",
-                    "tool_panel_section_label": "Machine Learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ml_visualization_ex",
-                    "owner": "bgruening",
-                    "revisions": "05143043ca13",
-                    "tool_panel_section_label": "Machine Learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "model_prediction",
+                    "name": "sklearn_svm_classifier",
                     "owner": "bgruening",
-                    "revisions": "83228baae3c5",
+                    "revisions": "f9639b488779",
                     "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: keras_model_builder\n  owner: bgruening\n  revisions: 772e0e89fc68\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_model_config\n  owner: bgruening\n  revisions: 8a794e6d3388\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_train_and_eval\n  owner: bgruening\n  revisions: f1b9a42d6809\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ml_visualization_ex\n  owner: bgruening\n  revisions: 05143043ca13\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: model_prediction\n  owner: bgruening\n  revisions: 83228baae3c5\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/intro_deep_learning/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: sklearn_svm_classifier\n  owner: bgruening\n  revisions: f9639b488779\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/machinelearning/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
@@ -251420,25 +258231,13 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/anuprulez/",
                 "twitter": "musafirtweetsz",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/anuprulez.json"
-            },
-            {
-                "email": "khanteymoori@gmail.com",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "khanteymoori",
-                "joined": "2019-07",
-                "name": "Alireza Khanteymoori",
-                "orcid": "0000-0001-6811-9196",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/khanteymoori/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/khanteymoori.json"
             }
         ],
-        "dir": "topics/statistics/tutorials/intro_deep_learning",
+        "dir": "topics/statistics/tutorials/machinelearning",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.eu",
             "UseGalaxy.no",
@@ -251448,44 +258247,51 @@
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "statistics/intro_deep_learning",
-        "inexact_supported_servers": [],
+        "id": "statistics/machinelearning",
+        "inexact_supported_servers": [
+            "UseGalaxy.fr"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Multiple tools to constitute a neural network architecture",
-            "Interpretation of predictions using visualisation tools"
+            "Machine learning algorithms learn features from data.",
+            "It is used for multiple tasks such as classification, regression, clustering and so on.",
+            "Multiple learning tasks can be performed using Galaxy's machine learning tools.",
+            "For the classification and regression tasks, data is divided into training and test sets.",
+            "Each sample/record in the training data has a category/class/label.",
+            "A machine learning algorithm learns features from the training data and do predictions on the test data."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2024-03-05",
         "objectives": [
-            "Learn basic principles of deep learning",
-            "Learn about how to create an end-to-end neural network architecture",
-            "Learn about Galaxy deep learning tools",
-            "Learn how to interpret predictions"
+            "Provide the basics of machine learning and its variants.",
+            "Learn how to do classification using the training and test data.",
+            "Learn how to use Galaxy's machine learning tools."
         ],
-        "pageviews": 2458,
-        "pub_date": "2020-03-26",
+        "pageviews": 2784,
+        "pub_date": "2018-11-05",
         "questions": [
-            "What are deep learning and neural networks?",
+            "What is machine learning?",
             "Why is it useful?",
-            "How to create a neural network architecture for classification?"
+            "What are its different approaches?"
         ],
-        "short_id": "T00268",
+        "requirements": null,
+        "short_id": "T00270",
         "short_tools": [
-            "keras_model_builder",
-            "keras_model_config",
-            "model_prediction",
-            "keras_train_and_eval",
-            "ml_visualization_ex"
+            "sklearn_svm_classifier"
         ],
         "slides": false,
         "slides_recordings": false,
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -251512,17 +258318,19 @@
                     "usegalaxy": true
                 }
             ],
-            "inexact": []
+            "inexact": [
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                }
+            ]
         },
         "symlink": null,
-        "time_estimation": "1H",
-        "title": "Introduction to deep learning",
+        "time_estimation": "30M",
+        "title": "Basics of machine learning",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/0.5.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/0.5.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.2"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.8.1"
         ],
         "topic_name": "statistics",
         "topic_name_human": "Statistics and machine learning",
@@ -251532,58 +258340,65 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "intro_deep_learning",
+        "tutorial_name": "machinelearning",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/intro_deep_learning/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/machinelearning/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/intro_deep_learning/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/intro_deep_learning/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/machinelearning/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/machinelearning/tutorial.json"
         },
-        "version": 8,
+        "version": 13,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 101,
-        "visitors": 1892,
+        "visit_duration": 170,
+        "visitors": 2008,
         "workflows": [
             {
                 "creators": [],
-                "description": "Introduction to Deep Learning",
+                "description": "Basics of machine learning",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nX_test\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nX_train\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ny_test\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ny_train\"]\n  4[label=\"Create a deep learning model architecture\"]\n  5[label=\"Create deep learning model\"]\n  4 -> 5 [label=\"outfile\"]\n  6[label=\"Deep learning training and evaluation\"]\n  5 -> 6 [label=\"outfile\"]\n  1 -> 6 [label=\"output\"]\n  3 -> 6 [label=\"output\"]\n  7[label=\"Model Prediction\"]\n  6 -> 7 [label=\"outfile_object\"]\n  6 -> 7 [label=\"outfile_weights\"]\n  0 -> 7 [label=\"output\"]\n  8[label=\"Machine Learning Visualization Extension\"]\n  7 -> 8 [label=\"outfile_predict\"]\n  2 -> 8 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nbreast-w_train\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nbreast-w_test\"]\n  2[label=\"Support vector machines SVMs\"]\n  0 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Support vector machines SVMs\"]\n  1 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"outfile_fit\"]\n  k03e30bebfc0141848649057c13bb626a[color=lightseagreen,label=\"Output\\noutfile_predict\"]\n  3 -> k03e30bebfc0141848649057c13bb626a\n}",
                 "history": [
                     {
-                        "hash": "662ff162583df9ededd624afd29945d5c799df9b",
-                        "message": "Fixed input data labels (they were one off)",
+                        "hash": "6f18e04f0d03d9f42bc3dc88d708eadacd4acd96",
+                        "message": "Add workflow_outputs to machine_learning.ga for testing, add a test",
+                        "num": 5,
+                        "short_hash": "6f18e04f0",
+                        "unix": "1590540700"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
                         "num": 4,
-                        "short_hash": "662ff1625",
-                        "unix": "1611671063"
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
                     },
                     {
-                        "hash": "6069e5afbdd15fea3ec1b9d22899c2cabdcd4abf",
-                        "message": "Added label for input data.",
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
                         "num": 3,
-                        "short_hash": "6069e5afb",
-                        "unix": "1611603134"
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
                     },
                     {
-                        "hash": "3250de162eff1978f2cc80d7732bad186d7a0006",
-                        "message": "Tagged the workflow and added a title.",
+                        "hash": "9f881ab875f38f8d4299a1fb0bc2f22b422d1eda",
+                        "message": "checking ML tutorials, updating workflows",
                         "num": 2,
-                        "short_hash": "3250de162",
-                        "unix": "1611418238"
+                        "short_hash": "9f881ab87",
+                        "unix": "1578588754"
                     },
                     {
-                        "hash": "55c3b30a50a0c1cbfb02a7f028866d91ade386cf",
-                        "message": "Added workflow to Deep Learning Tutorial",
+                        "hash": "b6985b9499618c6ad25d58d67358618504d608a3",
+                        "message": "workflow for machine_learning",
                         "num": 1,
-                        "short_hash": "55c3b30a5",
-                        "unix": "1611351590"
+                        "short_hash": "b6985b949",
+                        "unix": "1550745160"
                     }
                 ],
                 "inputs": [
@@ -251596,21 +258411,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "X_test"
+                                "name": "breast-w_train"
                             }
                         ],
-                        "label": "X_test",
+                        "label": "breast-w_train",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 10
+                            "left": 200,
+                            "top": 200
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"name\": \"breast-w_train\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "46c0a33e-73d7-4413-8872-dea66576377e",
+                        "uuid": "fa0bbf50-4881-407c-b9be-78cc96c2f00d",
                         "workflow_outputs": []
                     },
                     {
@@ -251622,168 +258437,617 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "X_train"
+                                "name": "breast-w_test"
                             }
                         ],
-                        "label": "X_train",
+                        "label": "breast-w_test",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 130
+                            "left": 200,
+                            "top": 289.76666259765625
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"name\": \"breast-w_test\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "3939491d-5fc0-4eb0-9ece-32f87782d456",
+                        "uuid": "b3b595f7-7a7a-416e-934d-84c6af042169",
                         "workflow_outputs": []
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nbreast-w_train\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nbreast-w_test\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Support vector machines SVMs\"];\n  0 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Support vector machines SVMs\"];\n  1 -->|output| 3;\n  2 -->|outfile_fit| 3;\n  03e30beb-fc01-4184-8649-057c13bb626a[\"Output\\noutfile_predict\"];\n  3 --> 03e30beb-fc01-4184-8649-057c13bb626a;\n  style 03e30beb-fc01-4184-8649-057c13bb626a stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "Machine Learning",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.8.1",
                         "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 3,
+                        "input_connections": {
+                            "selected_tasks|infile_data": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "selected_tasks|infile_model": {
+                                "id": 2,
+                                "output_name": "outfile_fit"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Support vector machines (SVMs)",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "y_test"
+                                "name": "outfile_predict",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "y_test",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 10,
-                            "top": 250
+                            "left": 788.5333251953125,
+                            "top": 200
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "7b284798-4e87-476c-9af1-514df24176f8",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.8.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "2df8f5c30edc",
+                            "name": "sklearn_svm_classifier",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"selected_tasks\": \"{\\\"__current_case__\\\": 0, \\\"header\\\": \\\"true\\\", \\\"infile_data\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"infile_model\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"prediction_options\\\": {\\\"__current_case__\\\": 0, \\\"prediction_option\\\": \\\"predict\\\"}, \\\"selected_task\\\": \\\"load\\\"}\", \"chromInfo\": \"\\\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.8.1",
+                        "type": "tool",
+                        "uuid": "98bd60bb-4e32-4c11-9955-eade434a3817",
+                        "workflow_outputs": [
                             {
-                                "description": "",
-                                "name": "y_train"
+                                "label": "outfile_predict",
+                                "output_name": "outfile_predict",
+                                "uuid": "03e30beb-fc01-4184-8649-057c13bb626a"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "statistics/machinelearning",
+                "path": "topics/statistics/tutorials/machinelearning/workflows/machine_learning.ga",
+                "tags": [
+                    "ml",
+                    "statistics"
+                ],
+                "test_results": {
+                    "eu": {
+                        "summary": {
+                            "num_errors": 0,
+                            "num_failures": 0,
+                            "num_skips": 0,
+                            "num_tests": 1
+                        },
+                        "tests": [
+                            {
+                                "data": {
+                                    "end_datetime": "2023-05-23T13:04:36.233588",
+                                    "inputs": {
+                                        "breast-w_test": {
+                                            "class": "File",
+                                            "filetype": "tabular",
+                                            "location": "https://zenodo.org/api/files/0d468136-5025-4c0f-bf8b-a8277a513a93/breast-w_test.tsv"
+                                        },
+                                        "breast-w_train": {
+                                            "class": "File",
+                                            "filetype": "tabular",
+                                            "location": "https://zenodo.org/api/files/0d468136-5025-4c0f-bf8b-a8277a513a93/breast-w_train.tsv"
+                                        }
+                                    },
+                                    "invocation_details": {
+                                        "details": {
+                                            "error_message": "",
+                                            "history_id": "2507553dd7587c83",
+                                            "history_state": "ok",
+                                            "invocation_id": "f5ae862b1590700e",
+                                            "invocation_state": "scheduled",
+                                            "workflow_id": "1017f47ddfcbe87f"
+                                        },
+                                        "steps": {
+                                            "0. breast-w_train": {
+                                                "action": null,
+                                                "id": "e6252d7ebd7b816c",
+                                                "job_id": null,
+                                                "jobs": [],
+                                                "model_class": "WorkflowInvocationStep",
+                                                "order_index": 0,
+                                                "output_collections": {},
+                                                "outputs": {
+                                                    "output": {
+                                                        "id": "4838ba20a6d86765c9cd0650a6a12ca3",
+                                                        "src": "hda",
+                                                        "uuid": "b175db07-7724-4a00-83b4-5a6cae8c6763"
+                                                    }
+                                                },
+                                                "state": "scheduled",
+                                                "subworkflow": null,
+                                                "subworkflow_invocation_id": null,
+                                                "update_time": "2023-05-23T10:59:49.573476",
+                                                "workflow_step_id": "646ce6c1fd8f1f07",
+                                                "workflow_step_label": "breast-w_train",
+                                                "workflow_step_uuid": "fa0bbf50-4881-407c-b9be-78cc96c2f00d"
+                                            },
+                                            "1. breast-w_test": {
+                                                "action": null,
+                                                "id": "9974f0360058d84f",
+                                                "job_id": null,
+                                                "jobs": [],
+                                                "model_class": "WorkflowInvocationStep",
+                                                "order_index": 1,
+                                                "output_collections": {},
+                                                "outputs": {
+                                                    "output": {
+                                                        "id": "4838ba20a6d867654de1bc22fefb9f52",
+                                                        "src": "hda",
+                                                        "uuid": "c438049f-86b6-415a-a9a0-554efa397b28"
+                                                    }
+                                                },
+                                                "state": "scheduled",
+                                                "subworkflow": null,
+                                                "subworkflow_invocation_id": null,
+                                                "update_time": "2023-05-23T10:59:49.573483",
+                                                "workflow_step_id": "5b42eb6dee4ed8f3",
+                                                "workflow_step_label": "breast-w_test",
+                                                "workflow_step_uuid": "b3b595f7-7a7a-416e-934d-84c6af042169"
+                                            },
+                                            "2. Unnamed step": {
+                                                "action": null,
+                                                "id": "1c214839f0e68f30",
+                                                "job_id": "11ac94870d0bb33a9209f9a6c46d5330",
+                                                "jobs": [
+                                                    {
+                                                        "command_line": "python '/data/jwd02f/main/060/156/60156804/configs/tmpyxkw996c' '/data/jwd02f/main/060/156/60156804/configs/tmp5q24hxye'",
+                                                        "command_version": "1.0.8.1",
+                                                        "create_time": "2023-05-23T10:59:49.569976",
+                                                        "dependencies": [],
+                                                        "exit_code": 0,
+                                                        "external_id": "43631361",
+                                                        "galaxy_version": "23.0",
+                                                        "history_id": "2507553dd7587c83",
+                                                        "id": "11ac94870d0bb33a9209f9a6c46d5330",
+                                                        "inputs": {
+                                                            "selected_tasks|selected_algorithms|infile1": {
+                                                                "id": "4838ba20a6d86765c9cd0650a6a12ca3",
+                                                                "src": "hda",
+                                                                "uuid": "b175db07-7724-4a00-83b4-5a6cae8c6763"
+                                                            },
+                                                            "selected_tasks|selected_algorithms|infile2": {
+                                                                "id": "4838ba20a6d86765c9cd0650a6a12ca3",
+                                                                "src": "hda",
+                                                                "uuid": "b175db07-7724-4a00-83b4-5a6cae8c6763"
+                                                            }
+                                                        },
+                                                        "job_messages": [],
+                                                        "job_metrics": [
+                                                            {
+                                                                "name": "hostname",
+                                                                "plugin": "hostname",
+                                                                "raw_value": "vgcnbwc-worker-c125m425-1660.novalocal",
+                                                                "title": "hostname",
+                                                                "value": "vgcnbwc-worker-c125m425-1660.novalocal"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_slots",
+                                                                "plugin": "core",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "Cores Allocated",
+                                                                "value": "1"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_memory_mb",
+                                                                "plugin": "core",
+                                                                "raw_value": "3891.0000000",
+                                                                "title": "Memory Allocated (MB)",
+                                                                "value": "3891"
+                                                            },
+                                                            {
+                                                                "name": "start_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684839593.0000000",
+                                                                "title": "Job Start Time",
+                                                                "value": "2023-05-23 12:59:53"
+                                                            },
+                                                            {
+                                                                "name": "end_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684839787.0000000",
+                                                                "title": "Job End Time",
+                                                                "value": "2023-05-23 13:03:07"
+                                                            },
+                                                            {
+                                                                "name": "runtime_seconds",
+                                                                "plugin": "core",
+                                                                "raw_value": "194.0000000",
+                                                                "title": "Job Runtime (Wall Clock)",
+                                                                "value": "3 minutes"
+                                                            },
+                                                            {
+                                                                "name": "cpuacct.usage",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "22317680902.0000000",
+                                                                "title": "CPU Time",
+                                                                "value": "22.317680902 seconds"
+                                                            },
+                                                            {
+                                                                "name": "memory.failcnt",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Failed to allocate memory count",
+                                                                "value": 0.0
+                                                            },
+                                                            {
+                                                                "name": "memory.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "10737418240.0000000",
+                                                                "title": "Memory limit on cgroup (MEM)",
+                                                                "value": "10.0 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "427237376.0000000",
+                                                                "title": "Max memory usage (MEM)",
+                                                                "value": "407.4 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "9223372036854771712.0000000",
+                                                                "title": "Memory limit on cgroup (MEM+SWP)",
+                                                                "value": "8.0 EB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "427237376.0000000",
+                                                                "title": "Max memory usage (MEM+SWP)",
+                                                                "value": "407.4 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.oom_kill_disable",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "OOM Control enabled",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.under_oom",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Was OOM Killer active?",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.soft_limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Memory softlimit on cgroup",
+                                                                "value": "0 bytes"
+                                                            }
+                                                        ],
+                                                        "job_stderr": "",
+                                                        "job_stdout": "",
+                                                        "model_class": "Job",
+                                                        "output_collections": {},
+                                                        "outputs": {
+                                                            "outfile_fit": {
+                                                                "id": "4838ba20a6d86765b565f48d5ac913b1",
+                                                                "src": "hda",
+                                                                "uuid": "1a17ebe9-c0e0-4ebd-bae0-5159331683bb"
+                                                            }
+                                                        },
+                                                        "params": {
+                                                            "__input_ext": "\"tabular\"",
+                                                            "__workflow_invocation_uuid__": "\"ebe5f326f95811ed916d001e67d2ec02\"",
+                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
+                                                            "dbkey": "\"?\"",
+                                                            "selected_tasks": "{\"__current_case__\": 1, \"selected_algorithms\": {\"__current_case__\": 2, \"input_options\": {\"__current_case__\": 0, \"column_selector_options_1\": {\"__current_case__\": 3, \"col1\": \"target\", \"selected_column_selector_option\": \"all_but_by_header_name\"}, \"column_selector_options_2\": {\"__current_case__\": 2, \"col2\": \"target\", \"selected_column_selector_option2\": \"by_header_name\"}, \"header1\": true, \"header2\": true, \"infile1\": {\"values\": [{\"id\": 137642769, \"src\": \"hda\"}]}, \"infile2\": {\"values\": [{\"id\": 137642769, \"src\": \"hda\"}]}, \"selected_input\": \"tabular\"}, \"options\": {\"C\": \"1.0\", \"dual\": true, \"fit_intercept\": true, \"intercept_scaling\": \"1.0\", \"loss\": \"squared_hinge\", \"max_iter\": \"1000\", \"multi_class\": \"ovr\", \"penalty\": \"l2\", \"random_state\": null, \"tol\": \"0.001\"}, \"selected_algorithm\": \"LinearSVC\"}, \"selected_task\": \"train\"}"
+                                                        },
+                                                        "state": "ok",
+                                                        "stderr": "OMP: Info #212: KMP_AFFINITY: decoding x2APIC ids.\nOMP: Info #210: KMP_AFFINITY: Affinity capable, using global cpuid leaf 11 info\nOMP: Info #154: KMP_AFFINITY: Initial OS proc set respected: 0-124\nOMP: Info #156: KMP_AFFINITY: 125 available OS procs\nOMP: Info #157: KMP_AFFINITY: Uniform topology\nOMP: Info #179: KMP_AFFINITY: 125 packages x 1 cores/pkg x 1 threads/core (125 total cores)\nOMP: Info #214: KMP_AFFINITY: OS proc to physical thread map:\nOMP: Info #171: KMP_AFFINITY: OS proc 0 maps to package 0 \nOMP: Info #171: KMP_AFFINITY: OS proc 1 maps to package 1 \nOMP: Info #171: KMP_AFFINITY: OS proc 2 maps to package 2 \nOMP: Info #171: KMP_AFFINITY: OS proc 3 maps to package 3 \nOMP: Info #171: KMP_AFFINITY: OS proc 4 maps to package 4 \nOMP: Info #171: KMP_AFFINITY: OS proc 5 maps to package 5 \nOMP: Info #171: KMP_AFFINITY: OS proc 6 maps to package 6 \nOMP: Info #171: KMP_AFFINITY: OS proc 7 maps to package 7 \nOMP: Info #171: KMP_AFFINITY: OS proc 8 maps to package 8 \nOMP: Info #171: KMP_AFFINITY: OS proc 9 maps to package 9 \nOMP: Info #171: KMP_AFFINITY: OS proc 10 maps to package 10 \nOMP: Info #171: KMP_AFFINITY: OS proc 11 maps to package 11 \nOMP: Info #171: KMP_AFFINITY: OS proc 12 maps to package 12 \nOMP: Info #171: KMP_AFFINITY: OS proc 13 maps to package 13 \nOMP: Info #171: KMP_AFFINITY: OS proc 14 maps to package 14 \nOMP: Info #171: KMP_AFFINITY: OS proc 15 maps to package 15 \nOMP: Info #171: KMP_AFFINITY: OS proc 16 maps to package 16 \nOMP: Info #171: KMP_AFFINITY: OS proc 17 maps to package 17 \nOMP: Info #171: KMP_AFFINITY: OS proc 18 maps to package 18 \nOMP: Info #171: KMP_AFFINITY: OS proc 19 maps to package 19 \nOMP: Info #171: KMP_AFFINITY: OS proc 20 maps to package 20 \nOMP: Info #171: KMP_AFFINITY: OS proc 21 maps to package 21 \nOMP: Info #171: KMP_AFFINITY: OS proc 22 maps to package 22 \nOMP: Info #171: KMP_AFFINITY: OS proc 23 maps to package 23 \nOMP: Info #171: KMP_AFFINITY: OS proc 24 maps to package 24 \nOMP: Info #171: KMP_AFFINITY: OS proc 25 maps to package 25 \nOMP: Info #171: KMP_AFFINITY: OS proc 26 maps to package 26 \nOMP: Info #171: KMP_AFFINITY: OS proc 27 maps to package 27 \nOMP: Info #171: KMP_AFFINITY: OS proc 28 maps to package 28 \nOMP: Info #171: KMP_AFFINITY: OS proc 29 maps to package 29 \nOMP: Info #171: KMP_AFFINITY: OS proc 30 maps to package 30 \nOMP: Info #171: KMP_AFFINITY: OS proc 31 maps to package 31 \nOMP: Info #171: KMP_AFFINITY: OS proc 32 maps to package 32 \nOMP: Info #171: KMP_AFFINITY: OS proc 33 maps to package 33 \nOMP: Info #171: KMP_AFFINITY: OS proc 34 maps to package 34 \nOMP: Info #171: KMP_AFFINITY: OS proc 35 maps to package 35 \nOMP: Info #171: KMP_AFFINITY: OS proc 36 maps to package 36 \nOMP: Info #171: KMP_AFFINITY: OS proc 37 maps to package 37 \nOMP: Info #171: KMP_AFFINITY: OS proc 38 maps to package 38 \nOMP: Info #171: KMP_AFFINITY: OS proc 39 maps to package 39 \nOMP: Info #171: KMP_AFFINITY: OS proc 40 maps to package 40 \nOMP: Info #171: KMP_AFFINITY: OS proc 41 maps to package 41 \nOMP: Info #171: KMP_AFFINITY: OS proc 42 maps to package 42 \nOMP: Info #171: KMP_AFFINITY: OS proc 43 maps to package 43 \nOMP: Info #171: KMP_AFFINITY: OS proc 44 maps to package 44 \nOMP: Info #171: KMP_AFFINITY: OS proc 45 maps to package 45 \nOMP: Info #171: KMP_AFFINITY: OS proc 46 maps to package 46 \nOMP: Info #171: KMP_AFFINITY: OS proc 47 maps to package 47 \nOMP: Info #171: KMP_AFFINITY: OS proc 48 maps to package 48 \nOMP: Info #171: KMP_AFFINITY: OS proc 49 maps to package 49 \nOMP: Info #171: KMP_AFFINITY: OS proc 50 maps to package 50 \nOMP: Info #171: KMP_AFFINITY: OS proc 51 maps to package 51 \nOMP: Info #171: KMP_AFFINITY: OS proc 52 maps to package 52 \nOMP: Info #171: KMP_AFFINITY: OS proc 53 maps to package 53 \nOMP: Info #171: KMP_AFFINITY: OS proc 54 maps to package 54 \nOMP: Info #171: KMP_AFFINITY: OS proc 55 maps to package 55 \nOMP: Info #171: KMP_AFFINITY: OS proc 56 maps to package 56 \nOMP: Info #171: KMP_AFFINITY: OS proc 57 maps to package 57 \nOMP: Info #171: KMP_AFFINITY: OS proc 58 maps to package 58 \nOMP: Info #171: KMP_AFFINITY: OS proc 59 maps to package 59 \nOMP: Info #171: KMP_AFFINITY: OS proc 60 maps to package 60 \nOMP: Info #171: KMP_AFFINITY: OS proc 61 maps to package 61 \nOMP: Info #171: KMP_AFFINITY: OS proc 62 maps to package 62 \nOMP: Info #171: KMP_AFFINITY: OS proc 63 maps to package 63 \nOMP: Info #171: KMP_AFFINITY: OS proc 64 maps to package 64 \nOMP: Info #171: KMP_AFFINITY: OS proc 65 maps to package 65 \nOMP: Info #171: KMP_AFFINITY: OS proc 66 maps to package 66 \nOMP: Info #171: KMP_AFFINITY: OS proc 67 maps to package 67 \nOMP: Info #171: KMP_AFFINITY: OS proc 68 maps to package 68 \nOMP: Info #171: KMP_AFFINITY: OS proc 69 maps to package 69 \nOMP: Info #171: KMP_AFFINITY: OS proc 70 maps to package 70 \nOMP: Info #171: KMP_AFFINITY: OS proc 71 maps to package 71 \nOMP: Info #171: KMP_AFFINITY: OS proc 72 maps to package 72 \nOMP: Info #171: KMP_AFFINITY: OS proc 73 maps to package 73 \nOMP: Info #171: KMP_AFFINITY: OS proc 74 maps to package 74 \nOMP: Info #171: KMP_AFFINITY: OS proc 75 maps to package 75 \nOMP: Info #171: KMP_AFFINITY: OS proc 76 maps to package 76 \nOMP: Info #171: KMP_AFFINITY: OS proc 77 maps to package 77 \nOMP: Info #171: KMP_AFFINITY: OS proc 78 maps to package 78 \nOMP: Info #171: KMP_AFFINITY: OS proc 79 maps to package 79 \nOMP: Info #171: KMP_AFFINITY: OS proc 80 maps to package 80 \nOMP: Info #171: KMP_AFFINITY: OS proc 81 maps to package 81 \nOMP: Info #171: KMP_AFFINITY: OS proc 82 maps to package 82 \nOMP: Info #171: KMP_AFFINITY: OS proc 83 maps to package 83 \nOMP: Info #171: KMP_AFFINITY: OS proc 84 maps to package 84 \nOMP: Info #171: KMP_AFFINITY: OS proc 85 maps to package 85 \nOMP: Info #171: KMP_AFFINITY: OS proc 86 maps to package 86 \nOMP: Info #171: KMP_AFFINITY: OS proc 87 maps to package 87 \nOMP: Info #171: KMP_AFFINITY: OS proc 88 maps to package 88 \nOMP: Info #171: KMP_AFFINITY: OS proc 89 maps to package 89 \nOMP: Info #171: KMP_AFFINITY: OS proc 90 maps to package 90 \nOMP: Info #171: KMP_AFFINITY: OS proc 91 maps to package 91 \nOMP: Info #171: KMP_AFFINITY: OS proc 92 maps to package 92 \nOMP: Info #171: KMP_AFFINITY: OS proc 93 maps to package 93 \nOMP: Info #171: KMP_AFFINITY: OS proc 94 maps to package 94 \nOMP: Info #171: KMP_AFFINITY: OS proc 95 maps to package 95 \nOMP: Info #171: KMP_AFFINITY: OS proc 96 maps to package 96 \nOMP: Info #171: KMP_AFFINITY: OS proc 97 maps to package 97 \nOMP: Info #171: KMP_AFFINITY: OS proc 98 maps to package 98 \nOMP: Info #171: KMP_AFFINITY: OS proc 99 maps to package 99 \nOMP: Info #171: KMP_AFFINITY: OS proc 100 maps to package 100 \nOMP: Info #171: KMP_AFFINITY: OS proc 101 maps to package 101 \nOMP: Info #171: KMP_AFFINITY: OS proc 102 maps to package 102 \nOMP: Info #171: KMP_AFFINITY: OS proc 103 maps to package 103 \nOMP: Info #171: KMP_AFFINITY: OS proc 104 maps to package 104 \nOMP: Info #171: KMP_AFFINITY: OS proc 105 maps to package 105 \nOMP: Info #171: KMP_AFFINITY: OS proc 106 maps to package 106 \nOMP: Info #171: KMP_AFFINITY: OS proc 107 maps to package 107 \nOMP: Info #171: KMP_AFFINITY: OS proc 108 maps to package 108 \nOMP: Info #171: KMP_AFFINITY: OS proc 109 maps to package 109 \nOMP: Info #171: KMP_AFFINITY: OS proc 110 maps to package 110 \nOMP: Info #171: KMP_AFFINITY: OS proc 111 maps to package 111 \nOMP: Info #171: KMP_AFFINITY: OS proc 112 maps to package 112 \nOMP: Info #171: KMP_AFFINITY: OS proc 113 maps to package 113 \nOMP: Info #171: KMP_AFFINITY: OS proc 114 maps to package 114 \nOMP: Info #171: KMP_AFFINITY: OS proc 115 maps to package 115 \nOMP: Info #171: KMP_AFFINITY: OS proc 116 maps to package 116 \nOMP: Info #171: KMP_AFFINITY: OS proc 117 maps to package 117 \nOMP: Info #171: KMP_AFFINITY: OS proc 118 maps to package 118 \nOMP: Info #171: KMP_AFFINITY: OS proc 119 maps to package 119 \nOMP: Info #171: KMP_AFFINITY: OS proc 120 maps to package 120 \nOMP: Info #171: KMP_AFFINITY: OS proc 121 maps to package 121 \nOMP: Info #171: KMP_AFFINITY: OS proc 122 maps to package 122 \nOMP: Info #171: KMP_AFFINITY: OS proc 123 maps to package 123 \nOMP: Info #171: KMP_AFFINITY: OS proc 124 maps to package 124 \nOMP: Info #250: KMP_AFFINITY: pid 2936157 tid 2936157 thread 0 bound to OS proc set 0\nUsing TensorFlow backend.\n/usr/local/tools/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.\n  warnings.warn(msg, category=DeprecationWarning)\n",
+                                                        "stdout": "",
+                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.8.1",
+                                                        "tool_stderr": "OMP: Info #212: KMP_AFFINITY: decoding x2APIC ids.\nOMP: Info #210: KMP_AFFINITY: Affinity capable, using global cpuid leaf 11 info\nOMP: Info #154: KMP_AFFINITY: Initial OS proc set respected: 0-124\nOMP: Info #156: KMP_AFFINITY: 125 available OS procs\nOMP: Info #157: KMP_AFFINITY: Uniform topology\nOMP: Info #179: KMP_AFFINITY: 125 packages x 1 cores/pkg x 1 threads/core (125 total cores)\nOMP: Info #214: KMP_AFFINITY: OS proc to physical thread map:\nOMP: Info #171: KMP_AFFINITY: OS proc 0 maps to package 0 \nOMP: Info #171: KMP_AFFINITY: OS proc 1 maps to package 1 \nOMP: Info #171: KMP_AFFINITY: OS proc 2 maps to package 2 \nOMP: Info #171: KMP_AFFINITY: OS proc 3 maps to package 3 \nOMP: Info #171: KMP_AFFINITY: OS proc 4 maps to package 4 \nOMP: Info #171: KMP_AFFINITY: OS proc 5 maps to package 5 \nOMP: Info #171: KMP_AFFINITY: OS proc 6 maps to package 6 \nOMP: Info #171: KMP_AFFINITY: OS proc 7 maps to package 7 \nOMP: Info #171: KMP_AFFINITY: OS proc 8 maps to package 8 \nOMP: Info #171: KMP_AFFINITY: OS proc 9 maps to package 9 \nOMP: Info #171: KMP_AFFINITY: OS proc 10 maps to package 10 \nOMP: Info #171: KMP_AFFINITY: OS proc 11 maps to package 11 \nOMP: Info #171: KMP_AFFINITY: OS proc 12 maps to package 12 \nOMP: Info #171: KMP_AFFINITY: OS proc 13 maps to package 13 \nOMP: Info #171: KMP_AFFINITY: OS proc 14 maps to package 14 \nOMP: Info #171: KMP_AFFINITY: OS proc 15 maps to package 15 \nOMP: Info #171: KMP_AFFINITY: OS proc 16 maps to package 16 \nOMP: Info #171: KMP_AFFINITY: OS proc 17 maps to package 17 \nOMP: Info #171: KMP_AFFINITY: OS proc 18 maps to package 18 \nOMP: Info #171: KMP_AFFINITY: OS proc 19 maps to package 19 \nOMP: Info #171: KMP_AFFINITY: OS proc 20 maps to package 20 \nOMP: Info #171: KMP_AFFINITY: OS proc 21 maps to package 21 \nOMP: Info #171: KMP_AFFINITY: OS proc 22 maps to package 22 \nOMP: Info #171: KMP_AFFINITY: OS proc 23 maps to package 23 \nOMP: Info #171: KMP_AFFINITY: OS proc 24 maps to package 24 \nOMP: Info #171: KMP_AFFINITY: OS proc 25 maps to package 25 \nOMP: Info #171: KMP_AFFINITY: OS proc 26 maps to package 26 \nOMP: Info #171: KMP_AFFINITY: OS proc 27 maps to package 27 \nOMP: Info #171: KMP_AFFINITY: OS proc 28 maps to package 28 \nOMP: Info #171: KMP_AFFINITY: OS proc 29 maps to package 29 \nOMP: Info #171: KMP_AFFINITY: OS proc 30 maps to package 30 \nOMP: Info #171: KMP_AFFINITY: OS proc 31 maps to package 31 \nOMP: Info #171: KMP_AFFINITY: OS proc 32 maps to package 32 \nOMP: Info #171: KMP_AFFINITY: OS proc 33 maps to package 33 \nOMP: Info #171: KMP_AFFINITY: OS proc 34 maps to package 34 \nOMP: Info #171: KMP_AFFINITY: OS proc 35 maps to package 35 \nOMP: Info #171: KMP_AFFINITY: OS proc 36 maps to package 36 \nOMP: Info #171: KMP_AFFINITY: OS proc 37 maps to package 37 \nOMP: Info #171: KMP_AFFINITY: OS proc 38 maps to package 38 \nOMP: Info #171: KMP_AFFINITY: OS proc 39 maps to package 39 \nOMP: Info #171: KMP_AFFINITY: OS proc 40 maps to package 40 \nOMP: Info #171: KMP_AFFINITY: OS proc 41 maps to package 41 \nOMP: Info #171: KMP_AFFINITY: OS proc 42 maps to package 42 \nOMP: Info #171: KMP_AFFINITY: OS proc 43 maps to package 43 \nOMP: Info #171: KMP_AFFINITY: OS proc 44 maps to package 44 \nOMP: Info #171: KMP_AFFINITY: OS proc 45 maps to package 45 \nOMP: Info #171: KMP_AFFINITY: OS proc 46 maps to package 46 \nOMP: Info #171: KMP_AFFINITY: OS proc 47 maps to package 47 \nOMP: Info #171: KMP_AFFINITY: OS proc 48 maps to package 48 \nOMP: Info #171: KMP_AFFINITY: OS proc 49 maps to package 49 \nOMP: Info #171: KMP_AFFINITY: OS proc 50 maps to package 50 \nOMP: Info #171: KMP_AFFINITY: OS proc 51 maps to package 51 \nOMP: Info #171: KMP_AFFINITY: OS proc 52 maps to package 52 \nOMP: Info #171: KMP_AFFINITY: OS proc 53 maps to package 53 \nOMP: Info #171: KMP_AFFINITY: OS proc 54 maps to package 54 \nOMP: Info #171: KMP_AFFINITY: OS proc 55 maps to package 55 \nOMP: Info #171: KMP_AFFINITY: OS proc 56 maps to package 56 \nOMP: Info #171: KMP_AFFINITY: OS proc 57 maps to package 57 \nOMP: Info #171: KMP_AFFINITY: OS proc 58 maps to package 58 \nOMP: Info #171: KMP_AFFINITY: OS proc 59 maps to package 59 \nOMP: Info #171: KMP_AFFINITY: OS proc 60 maps to package 60 \nOMP: Info #171: KMP_AFFINITY: OS proc 61 maps to package 61 \nOMP: Info #171: KMP_AFFINITY: OS proc 62 maps to package 62 \nOMP: Info #171: KMP_AFFINITY: OS proc 63 maps to package 63 \nOMP: Info #171: KMP_AFFINITY: OS proc 64 maps to package 64 \nOMP: Info #171: KMP_AFFINITY: OS proc 65 maps to package 65 \nOMP: Info #171: KMP_AFFINITY: OS proc 66 maps to package 66 \nOMP: Info #171: KMP_AFFINITY: OS proc 67 maps to package 67 \nOMP: Info #171: KMP_AFFINITY: OS proc 68 maps to package 68 \nOMP: Info #171: KMP_AFFINITY: OS proc 69 maps to package 69 \nOMP: Info #171: KMP_AFFINITY: OS proc 70 maps to package 70 \nOMP: Info #171: KMP_AFFINITY: OS proc 71 maps to package 71 \nOMP: Info #171: KMP_AFFINITY: OS proc 72 maps to package 72 \nOMP: Info #171: KMP_AFFINITY: OS proc 73 maps to package 73 \nOMP: Info #171: KMP_AFFINITY: OS proc 74 maps to package 74 \nOMP: Info #171: KMP_AFFINITY: OS proc 75 maps to package 75 \nOMP: Info #171: KMP_AFFINITY: OS proc 76 maps to package 76 \nOMP: Info #171: KMP_AFFINITY: OS proc 77 maps to package 77 \nOMP: Info #171: KMP_AFFINITY: OS proc 78 maps to package 78 \nOMP: Info #171: KMP_AFFINITY: OS proc 79 maps to package 79 \nOMP: Info #171: KMP_AFFINITY: OS proc 80 maps to package 80 \nOMP: Info #171: KMP_AFFINITY: OS proc 81 maps to package 81 \nOMP: Info #171: KMP_AFFINITY: OS proc 82 maps to package 82 \nOMP: Info #171: KMP_AFFINITY: OS proc 83 maps to package 83 \nOMP: Info #171: KMP_AFFINITY: OS proc 84 maps to package 84 \nOMP: Info #171: KMP_AFFINITY: OS proc 85 maps to package 85 \nOMP: Info #171: KMP_AFFINITY: OS proc 86 maps to package 86 \nOMP: Info #171: KMP_AFFINITY: OS proc 87 maps to package 87 \nOMP: Info #171: KMP_AFFINITY: OS proc 88 maps to package 88 \nOMP: Info #171: KMP_AFFINITY: OS proc 89 maps to package 89 \nOMP: Info #171: KMP_AFFINITY: OS proc 90 maps to package 90 \nOMP: Info #171: KMP_AFFINITY: OS proc 91 maps to package 91 \nOMP: Info #171: KMP_AFFINITY: OS proc 92 maps to package 92 \nOMP: Info #171: KMP_AFFINITY: OS proc 93 maps to package 93 \nOMP: Info #171: KMP_AFFINITY: OS proc 94 maps to package 94 \nOMP: Info #171: KMP_AFFINITY: OS proc 95 maps to package 95 \nOMP: Info #171: KMP_AFFINITY: OS proc 96 maps to package 96 \nOMP: Info #171: KMP_AFFINITY: OS proc 97 maps to package 97 \nOMP: Info #171: KMP_AFFINITY: OS proc 98 maps to package 98 \nOMP: Info #171: KMP_AFFINITY: OS proc 99 maps to package 99 \nOMP: Info #171: KMP_AFFINITY: OS proc 100 maps to package 100 \nOMP: Info #171: KMP_AFFINITY: OS proc 101 maps to package 101 \nOMP: Info #171: KMP_AFFINITY: OS proc 102 maps to package 102 \nOMP: Info #171: KMP_AFFINITY: OS proc 103 maps to package 103 \nOMP: Info #171: KMP_AFFINITY: OS proc 104 maps to package 104 \nOMP: Info #171: KMP_AFFINITY: OS proc 105 maps to package 105 \nOMP: Info #171: KMP_AFFINITY: OS proc 106 maps to package 106 \nOMP: Info #171: KMP_AFFINITY: OS proc 107 maps to package 107 \nOMP: Info #171: KMP_AFFINITY: OS proc 108 maps to package 108 \nOMP: Info #171: KMP_AFFINITY: OS proc 109 maps to package 109 \nOMP: Info #171: KMP_AFFINITY: OS proc 110 maps to package 110 \nOMP: Info #171: KMP_AFFINITY: OS proc 111 maps to package 111 \nOMP: Info #171: KMP_AFFINITY: OS proc 112 maps to package 112 \nOMP: Info #171: KMP_AFFINITY: OS proc 113 maps to package 113 \nOMP: Info #171: KMP_AFFINITY: OS proc 114 maps to package 114 \nOMP: Info #171: KMP_AFFINITY: OS proc 115 maps to package 115 \nOMP: Info #171: KMP_AFFINITY: OS proc 116 maps to package 116 \nOMP: Info #171: KMP_AFFINITY: OS proc 117 maps to package 117 \nOMP: Info #171: KMP_AFFINITY: OS proc 118 maps to package 118 \nOMP: Info #171: KMP_AFFINITY: OS proc 119 maps to package 119 \nOMP: Info #171: KMP_AFFINITY: OS proc 120 maps to package 120 \nOMP: Info #171: KMP_AFFINITY: OS proc 121 maps to package 121 \nOMP: Info #171: KMP_AFFINITY: OS proc 122 maps to package 122 \nOMP: Info #171: KMP_AFFINITY: OS proc 123 maps to package 123 \nOMP: Info #171: KMP_AFFINITY: OS proc 124 maps to package 124 \nOMP: Info #250: KMP_AFFINITY: pid 2936157 tid 2936157 thread 0 bound to OS proc set 0\nUsing TensorFlow backend.\n/usr/local/tools/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.\n  warnings.warn(msg, category=DeprecationWarning)\n",
+                                                        "tool_stdout": "",
+                                                        "traceback": null,
+                                                        "update_time": "2023-05-23T11:03:10.618603",
+                                                        "user_email": "hxr@informatik.uni-freiburg.de"
+                                                    }
+                                                ],
+                                                "model_class": "WorkflowInvocationStep",
+                                                "order_index": 2,
+                                                "output_collections": {},
+                                                "outputs": {
+                                                    "outfile_fit": {
+                                                        "id": "4838ba20a6d86765b565f48d5ac913b1",
+                                                        "src": "hda",
+                                                        "uuid": "1a17ebe9-c0e0-4ebd-bae0-5159331683bb"
+                                                    }
+                                                },
+                                                "state": "scheduled",
+                                                "subworkflow": null,
+                                                "subworkflow_invocation_id": null,
+                                                "update_time": "2023-05-23T11:03:10.590397",
+                                                "workflow_step_id": "3500dc3fab19a665",
+                                                "workflow_step_label": null,
+                                                "workflow_step_uuid": "159f5d0f-2ff6-46f3-8e42-7b7c1f9c346e"
+                                            },
+                                            "3. Unnamed step": {
+                                                "action": null,
+                                                "id": "06d0cb6c722a3ad0",
+                                                "job_id": "11ac94870d0bb33a7b20a18462093261",
+                                                "jobs": [
+                                                    {
+                                                        "command_line": "python '/data/jwd02f/main/060/156/60156805/configs/tmpsg_iolk6' '/data/jwd02f/main/060/156/60156805/configs/tmpbg5s306r'",
+                                                        "command_version": "1.0.8.1",
+                                                        "create_time": "2023-05-23T10:59:49.663928",
+                                                        "dependencies": [
+                                                            {
+                                                                "cacheable": false,
+                                                                "dependency_resolver": {
+                                                                    "auto_init": true,
+                                                                    "auto_install": false,
+                                                                    "can_uninstall_dependencies": true,
+                                                                    "ensure_channels": "conda-forge,bioconda",
+                                                                    "model_class": "CondaDependencyResolver",
+                                                                    "prefix": "/usr/local/tools/_conda",
+                                                                    "read_only": false,
+                                                                    "resolver_type": "conda",
+                                                                    "resolves_simple_dependencies": true,
+                                                                    "use_local": false,
+                                                                    "versionless": false
+                                                                },
+                                                                "dependency_type": "conda",
+                                                                "environment_path": "/usr/local/tools/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59",
+                                                                "exact": true,
+                                                                "model_class": "MergedCondaDependency",
+                                                                "name": "python",
+                                                                "version": "3.6"
+                                                            },
+                                                            {
+                                                                "cacheable": false,
+                                                                "dependency_resolver": {
+                                                                    "auto_init": true,
+                                                                    "auto_install": false,
+                                                                    "can_uninstall_dependencies": true,
+                                                                    "ensure_channels": "conda-forge,bioconda",
+                                                                    "model_class": "CondaDependencyResolver",
+                                                                    "prefix": "/usr/local/tools/_conda",
+                                                                    "read_only": false,
+                                                                    "resolver_type": "conda",
+                                                                    "resolves_simple_dependencies": true,
+                                                                    "use_local": false,
+                                                                    "versionless": false
+                                                                },
+                                                                "dependency_type": "conda",
+                                                                "environment_path": "/usr/local/tools/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59",
+                                                                "exact": true,
+                                                                "model_class": "MergedCondaDependency",
+                                                                "name": "Galaxy-ML",
+                                                                "version": "0.8.1"
+                                                            }
+                                                        ],
+                                                        "exit_code": 0,
+                                                        "external_id": "43631439",
+                                                        "galaxy_version": "23.0",
+                                                        "history_id": "2507553dd7587c83",
+                                                        "id": "11ac94870d0bb33a7b20a18462093261",
+                                                        "inputs": {
+                                                            "infile_data": {
+                                                                "id": "4838ba20a6d867654de1bc22fefb9f52",
+                                                                "src": "hda",
+                                                                "uuid": "c438049f-86b6-415a-a9a0-554efa397b28"
+                                                            },
+                                                            "infile_model": {
+                                                                "id": "4838ba20a6d86765b565f48d5ac913b1",
+                                                                "src": "hda",
+                                                                "uuid": "1a17ebe9-c0e0-4ebd-bae0-5159331683bb"
+                                                            }
+                                                        },
+                                                        "job_messages": [],
+                                                        "job_metrics": [
+                                                            {
+                                                                "name": "hostname",
+                                                                "plugin": "hostname",
+                                                                "raw_value": "vgcnbwc-worker-c28m475-9818.novalocal",
+                                                                "title": "hostname",
+                                                                "value": "vgcnbwc-worker-c28m475-9818.novalocal"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_slots",
+                                                                "plugin": "core",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "Cores Allocated",
+                                                                "value": "1"
+                                                            },
+                                                            {
+                                                                "name": "galaxy_memory_mb",
+                                                                "plugin": "core",
+                                                                "raw_value": "3891.0000000",
+                                                                "title": "Memory Allocated (MB)",
+                                                                "value": "3891"
+                                                            },
+                                                            {
+                                                                "name": "start_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684839797.0000000",
+                                                                "title": "Job Start Time",
+                                                                "value": "2023-05-23 13:03:17"
+                                                            },
+                                                            {
+                                                                "name": "end_epoch",
+                                                                "plugin": "core",
+                                                                "raw_value": "1684839860.0000000",
+                                                                "title": "Job End Time",
+                                                                "value": "2023-05-23 13:04:20"
+                                                            },
+                                                            {
+                                                                "name": "runtime_seconds",
+                                                                "plugin": "core",
+                                                                "raw_value": "63.0000000",
+                                                                "title": "Job Runtime (Wall Clock)",
+                                                                "value": "1 minute"
+                                                            },
+                                                            {
+                                                                "name": "cpuacct.usage",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "17604876182.0000000",
+                                                                "title": "CPU Time",
+                                                                "value": "17.604876182 seconds"
+                                                            },
+                                                            {
+                                                                "name": "memory.failcnt",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Failed to allocate memory count",
+                                                                "value": 0.0
+                                                            },
+                                                            {
+                                                                "name": "memory.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "12348030976.0000000",
+                                                                "title": "Memory limit on cgroup (MEM)",
+                                                                "value": "11.5 GB"
+                                                            },
+                                                            {
+                                                                "name": "memory.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "276676608.0000000",
+                                                                "title": "Max memory usage (MEM)",
+                                                                "value": "263.9 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "9223372036854771712.0000000",
+                                                                "title": "Memory limit on cgroup (MEM+SWP)",
+                                                                "value": "8.0 EB"
+                                                            },
+                                                            {
+                                                                "name": "memory.memsw.max_usage_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "276676608.0000000",
+                                                                "title": "Max memory usage (MEM+SWP)",
+                                                                "value": "263.9 MB"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.oom_kill_disable",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "1.0000000",
+                                                                "title": "OOM Control enabled",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.oom_control.under_oom",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Was OOM Killer active?",
+                                                                "value": "No"
+                                                            },
+                                                            {
+                                                                "name": "memory.soft_limit_in_bytes",
+                                                                "plugin": "cgroup",
+                                                                "raw_value": "0E-7",
+                                                                "title": "Memory softlimit on cgroup",
+                                                                "value": "0 bytes"
+                                                            }
+                                                        ],
+                                                        "job_stderr": "",
+                                                        "job_stdout": "",
+                                                        "model_class": "Job",
+                                                        "output_collections": {},
+                                                        "outputs": {
+                                                            "outfile_predict": {
+                                                                "id": "4838ba20a6d8676528bf3db1c2ee4fdf",
+                                                                "src": "hda",
+                                                                "uuid": "aa9ff12d-ae53-4540-a498-636aa43c3466"
+                                                            }
+                                                        },
+                                                        "params": {
+                                                            "__input_ext": "\"zip\"",
+                                                            "__workflow_invocation_uuid__": "\"ebe5f326f95811ed916d001e67d2ec02\"",
+                                                            "chromInfo": "\"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\"",
+                                                            "dbkey": "\"?\"",
+                                                            "selected_tasks": "{\"__current_case__\": 0, \"header\": true, \"infile_data\": {\"values\": [{\"id\": 137643085, \"src\": \"hda\"}]}, \"infile_model\": {\"values\": [{\"id\": 137643284, \"src\": \"hda\"}]}, \"prediction_options\": {\"__current_case__\": 0, \"prediction_option\": \"predict\"}, \"selected_task\": \"load\"}"
+                                                        },
+                                                        "state": "ok",
+                                                        "stderr": "OMP: Info #212: KMP_AFFINITY: decoding x2APIC ids.\nOMP: Info #210: KMP_AFFINITY: Affinity capable, using global cpuid leaf 11 info\nOMP: Info #154: KMP_AFFINITY: Initial OS proc set respected: 0-27\nOMP: Info #156: KMP_AFFINITY: 28 available OS procs\nOMP: Info #157: KMP_AFFINITY: Uniform topology\nOMP: Info #179: KMP_AFFINITY: 28 packages x 1 cores/pkg x 1 threads/core (28 total cores)\nOMP: Info #214: KMP_AFFINITY: OS proc to physical thread map:\nOMP: Info #171: KMP_AFFINITY: OS proc 0 maps to package 0 \nOMP: Info #171: KMP_AFFINITY: OS proc 1 maps to package 1 \nOMP: Info #171: KMP_AFFINITY: OS proc 2 maps to package 2 \nOMP: Info #171: KMP_AFFINITY: OS proc 3 maps to package 3 \nOMP: Info #171: KMP_AFFINITY: OS proc 4 maps to package 4 \nOMP: Info #171: KMP_AFFINITY: OS proc 5 maps to package 5 \nOMP: Info #171: KMP_AFFINITY: OS proc 6 maps to package 6 \nOMP: Info #171: KMP_AFFINITY: OS proc 7 maps to package 7 \nOMP: Info #171: KMP_AFFINITY: OS proc 8 maps to package 8 \nOMP: Info #171: KMP_AFFINITY: OS proc 9 maps to package 9 \nOMP: Info #171: KMP_AFFINITY: OS proc 10 maps to package 10 \nOMP: Info #171: KMP_AFFINITY: OS proc 11 maps to package 11 \nOMP: Info #171: KMP_AFFINITY: OS proc 12 maps to package 12 \nOMP: Info #171: KMP_AFFINITY: OS proc 13 maps to package 13 \nOMP: Info #171: KMP_AFFINITY: OS proc 14 maps to package 14 \nOMP: Info #171: KMP_AFFINITY: OS proc 15 maps to package 15 \nOMP: Info #171: KMP_AFFINITY: OS proc 16 maps to package 16 \nOMP: Info #171: KMP_AFFINITY: OS proc 17 maps to package 17 \nOMP: Info #171: KMP_AFFINITY: OS proc 18 maps to package 18 \nOMP: Info #171: KMP_AFFINITY: OS proc 19 maps to package 19 \nOMP: Info #171: KMP_AFFINITY: OS proc 20 maps to package 20 \nOMP: Info #171: KMP_AFFINITY: OS proc 21 maps to package 21 \nOMP: Info #171: KMP_AFFINITY: OS proc 22 maps to package 22 \nOMP: Info #171: KMP_AFFINITY: OS proc 23 maps to package 23 \nOMP: Info #171: KMP_AFFINITY: OS proc 24 maps to package 24 \nOMP: Info #171: KMP_AFFINITY: OS proc 25 maps to package 25 \nOMP: Info #171: KMP_AFFINITY: OS proc 26 maps to package 26 \nOMP: Info #171: KMP_AFFINITY: OS proc 27 maps to package 27 \nOMP: Info #250: KMP_AFFINITY: pid 2127423 tid 2127423 thread 0 bound to OS proc set 0\nUsing TensorFlow backend.\n/usr/local/tools/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.\n  warnings.warn(msg, category=DeprecationWarning)\n",
+                                                        "stdout": "",
+                                                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.8.1",
+                                                        "tool_stderr": "OMP: Info #212: KMP_AFFINITY: decoding x2APIC ids.\nOMP: Info #210: KMP_AFFINITY: Affinity capable, using global cpuid leaf 11 info\nOMP: Info #154: KMP_AFFINITY: Initial OS proc set respected: 0-27\nOMP: Info #156: KMP_AFFINITY: 28 available OS procs\nOMP: Info #157: KMP_AFFINITY: Uniform topology\nOMP: Info #179: KMP_AFFINITY: 28 packages x 1 cores/pkg x 1 threads/core (28 total cores)\nOMP: Info #214: KMP_AFFINITY: OS proc to physical thread map:\nOMP: Info #171: KMP_AFFINITY: OS proc 0 maps to package 0 \nOMP: Info #171: KMP_AFFINITY: OS proc 1 maps to package 1 \nOMP: Info #171: KMP_AFFINITY: OS proc 2 maps to package 2 \nOMP: Info #171: KMP_AFFINITY: OS proc 3 maps to package 3 \nOMP: Info #171: KMP_AFFINITY: OS proc 4 maps to package 4 \nOMP: Info #171: KMP_AFFINITY: OS proc 5 maps to package 5 \nOMP: Info #171: KMP_AFFINITY: OS proc 6 maps to package 6 \nOMP: Info #171: KMP_AFFINITY: OS proc 7 maps to package 7 \nOMP: Info #171: KMP_AFFINITY: OS proc 8 maps to package 8 \nOMP: Info #171: KMP_AFFINITY: OS proc 9 maps to package 9 \nOMP: Info #171: KMP_AFFINITY: OS proc 10 maps to package 10 \nOMP: Info #171: KMP_AFFINITY: OS proc 11 maps to package 11 \nOMP: Info #171: KMP_AFFINITY: OS proc 12 maps to package 12 \nOMP: Info #171: KMP_AFFINITY: OS proc 13 maps to package 13 \nOMP: Info #171: KMP_AFFINITY: OS proc 14 maps to package 14 \nOMP: Info #171: KMP_AFFINITY: OS proc 15 maps to package 15 \nOMP: Info #171: KMP_AFFINITY: OS proc 16 maps to package 16 \nOMP: Info #171: KMP_AFFINITY: OS proc 17 maps to package 17 \nOMP: Info #171: KMP_AFFINITY: OS proc 18 maps to package 18 \nOMP: Info #171: KMP_AFFINITY: OS proc 19 maps to package 19 \nOMP: Info #171: KMP_AFFINITY: OS proc 20 maps to package 20 \nOMP: Info #171: KMP_AFFINITY: OS proc 21 maps to package 21 \nOMP: Info #171: KMP_AFFINITY: OS proc 22 maps to package 22 \nOMP: Info #171: KMP_AFFINITY: OS proc 23 maps to package 23 \nOMP: Info #171: KMP_AFFINITY: OS proc 24 maps to package 24 \nOMP: Info #171: KMP_AFFINITY: OS proc 25 maps to package 25 \nOMP: Info #171: KMP_AFFINITY: OS proc 26 maps to package 26 \nOMP: Info #171: KMP_AFFINITY: OS proc 27 maps to package 27 \nOMP: Info #250: KMP_AFFINITY: pid 2127423 tid 2127423 thread 0 bound to OS proc set 0\nUsing TensorFlow backend.\n/usr/local/tools/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.\n  warnings.warn(msg, category=DeprecationWarning)\n",
+                                                        "tool_stdout": "",
+                                                        "traceback": null,
+                                                        "update_time": "2023-05-23T11:04:23.019377",
+                                                        "user_email": "hxr@informatik.uni-freiburg.de"
+                                                    }
+                                                ],
+                                                "model_class": "WorkflowInvocationStep",
+                                                "order_index": 3,
+                                                "output_collections": {},
+                                                "outputs": {
+                                                    "outfile_predict": {
+                                                        "id": "4838ba20a6d8676528bf3db1c2ee4fdf",
+                                                        "src": "hda",
+                                                        "uuid": "aa9ff12d-ae53-4540-a498-636aa43c3466"
+                                                    }
+                                                },
+                                                "state": "scheduled",
+                                                "subworkflow": null,
+                                                "subworkflow_invocation_id": null,
+                                                "update_time": "2023-05-23T11:04:23.001451",
+                                                "workflow_step_id": "2fb04d30a406970c",
+                                                "workflow_step_label": null,
+                                                "workflow_step_uuid": "98bd60bb-4e32-4c11-9955-eade434a3817"
+                                            }
+                                        }
+                                    },
+                                    "problem_log": "No log for this engine type.",
+                                    "start_datetime": "2023-05-23T12:56:36.643889",
+                                    "status": "success"
+                                },
+                                "doc": "Test Basics of Machine Learning workflow",
+                                "has_data": true,
+                                "id": "machine_learning.ga_0",
+                                "test_type": "galaxy_workflow"
                             }
                         ],
-                        "label": "y_train",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 10,
-                            "top": 370
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "d145f3ff-f7c9-4873-bb59-79d089262d6e",
-                        "workflow_outputs": []
+                        "version": "0.1"
                     }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nX_test\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nX_train\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ny_test\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\ny_train\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Create a deep learning model architecture\"];\n  5[\"Create deep learning model\"];\n  4 -->|outfile| 5;\n  6[\"Deep learning training and evaluation\"];\n  5 -->|outfile| 6;\n  1 -->|output| 6;\n  3 -->|output| 6;\n  7[\"Model Prediction\"];\n  6 -->|outfile_object| 7;\n  6 -->|outfile_weights| 7;\n  0 -->|output| 7;\n  8[\"Machine Learning Visualization Extension\"];\n  7 -->|outfile_predict| 8;\n  2 -->|output| 8;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Intro_To_Deep_Learning",
-                "outputs": [],
-                "parent_id": "statistics/intro_deep_learning",
-                "path": "topics/statistics/tutorials/intro_deep_learning/workflows/Intro_To_Deep_Learning.ga",
-                "tags": [
-                    "statistics",
-                    "deeplearning",
-                    "ml"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Intro_To_Deep_Learning",
+                },
+                "tests": true,
+                "title": "Machine Learning",
                 "topic_id": "statistics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-intro_deep_learning/versions/intro-to-deep-learning",
-                "tutorial_id": "intro_deep_learning",
-                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/intro_deep_learning/workflows/Intro_To_Deep_Learning.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/intro_deep_learning/workflows/Intro_To_Deep_Learning.html",
-                "version": 1,
-                "wfid": "statistics-intro_deep_learning",
-                "wfname": "intro-to-deep-learning",
-                "workflow": "Intro_To_Deep_Learning.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-machinelearning/versions/machine-learning",
+                "tutorial_id": "machinelearning",
+                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/machinelearning/workflows/machine_learning.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/machinelearning/workflows/machine_learning.html",
+                "version": 5,
+                "wfid": "statistics-machinelearning",
+                "wfname": "machine-learning",
+                "workflow": "machine_learning.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/0.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/0.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.2",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.2",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.2"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.8.1"
                 ],
-                "workflowhub_id": "1298"
+                "workflowhub_id": "1320"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/3706539"
+        "zenodo_link": "https://zenodo.org/record/1468039"
     },
     {
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "plotly_parallel_coordinates_plot",
-                    "owner": "bgruening",
-                    "revisions": "7b21a9b5922f",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "plotly_regression_performance_plots",
-                    "owner": "bgruening",
-                    "revisions": "389227fa1864",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "sklearn_build_pipeline",
-                    "owner": "bgruening",
-                    "revisions": "840f29aad145",
-                    "tool_panel_section_label": "Machine Learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "sklearn_ensemble",
-                    "owner": "bgruening",
-                    "revisions": "1a53edc4b438",
-                    "tool_panel_section_label": "Machine Learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "sklearn_searchcv",
-                    "owner": "bgruening",
-                    "revisions": "25ab6b4e376e",
-                    "tool_panel_section_label": "Machine Learning",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
+            "tools": []
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: plotly_parallel_coordinates_plot\n  owner: bgruening\n  revisions: 7b21a9b5922f\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: plotly_regression_performance_plots\n  owner: bgruening\n  revisions: 389227fa1864\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_build_pipeline\n  owner: bgruening\n  revisions: 840f29aad145\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_ensemble\n  owner: bgruening\n  revisions: 1a53edc4b438\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_searchcv\n  owner: bgruening\n  revisions: 25ab6b4e376e\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/age-prediction-with-ml/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/gpu_jupyter_lab/tutorial.json",
         "contributors": [
-            {
-                "affiliations": [
-                    "uni-freiburg"
-                ],
-                "id": "polkhe",
-                "joined": "2017-09",
-                "name": "Ekaterina Polkh",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/polkhe/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/polkhe.json"
-            },
             {
                 "affiliations": [
                     "uni-freiburg",
@@ -251800,94 +259064,86 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/anuprulez.json"
             }
         ],
-        "dir": "topics/statistics/tutorials/age-prediction-with-ml",
+        "dir": "topics/statistics/tutorials/gpu_jupyter_lab",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "statistics/age-prediction-with-ml",
-        "inexact_supported_servers": [
-            "UseGalaxy.no"
-        ],
+        "id": "statistics/gpu_jupyter_lab",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": [
-            "Various machine learning algorithms should be used to find the best ones",
-            "For each machine learning algorithm, it hyperparameters should be optimised based on the dataset",
-            "Feature selection should be done for high-dimensional datasets"
-        ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-05",
+        "mod_date": "2024-07-09",
         "objectives": [
-            "Learn ageing biomarkers from RNA-seq and DNA methylation datasets",
-            "Apply regression based machine learning algorithms",
-            "Learn feature selection and hyperparameter optimisation"
+            "Learn to use Jupyterlab - an online Python editor designed for developing AI algorithms",
+            "Explore several of its features such as Git, workflow of jupyter notebook, integration to Galaxy",
+            "Develop AI algorithms using Tensorflow",
+            "Send long-running jobs to Galaxy's cluster and save results in its history",
+            "Reproduce results from recent scientific publications - COVID CT scan segmentation and 3D protein structure prediction"
         ],
-        "pageviews": 20392,
-        "pub_date": "2019-01-25",
+        "pageviews": 1148,
+        "pub_date": "2022-04-06",
         "questions": [
-            "How to use machine learning to create predictive models from biological datasets (RNA-seq and DNA methylation)?"
+            "How to use Jupyterlab and it several features?",
+            "How to use it for creating input datasets and writing artificial intelligence (AI) algorithms?"
         ],
-        "short_id": "T00261",
+        "requirements": [
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "jupyterlab"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "statistics",
+                "tutorials": [
+                    "intro_deep_learning"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00266",
         "short_tools": [
-            "sklearn_ensemble",
-            "plotly_regression_performance_plots",
-            "sklearn_build_pipeline",
-            "sklearn_searchcv",
-            "plotly_parallel_coordinates_plot"
+            "Filter1",
+            "interactive_tool_ml_jupyter_notebook",
+            "Cut1"
         ],
         "slides": false,
         "slides_recordings": false,
         "supported_servers": {
             "exact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
                 }
             ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                }
-            ]
+            "inexact": []
         },
         "symlink": null,
-        "time_estimation": "2H",
-        "title": "Age prediction using machine learning",
+        "tags": [
+            "interactive-tools",
+            "machine-learning",
+            "deep-learning",
+            "jupyter-lab",
+            "image-segmentation",
+            "protein-3D-structure"
+        ],
+        "time_estimation": "1H",
+        "title": "A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.8.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.8.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1"
+            "Cut1",
+            "Filter1",
+            "interactive_tool_ml_jupyter_notebook"
         ],
         "topic_name": "statistics",
         "topic_name_human": "Statistics and machine learning",
@@ -251897,86 +259153,37 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "age-prediction-with-ml",
+        "tutorial_name": "gpu_jupyter_lab",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/age-prediction-with-ml/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/gpu_jupyter_lab/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/age-prediction-with-ml/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/age-prediction-with-ml/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/gpu_jupyter_lab/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/gpu_jupyter_lab/tutorial.json"
         },
-        "version": 11,
+        "version": 8,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 40,
-        "visitors": 12446,
+        "visit_duration": 78,
+        "visitors": 888,
         "workflows": [
             {
                 "creators": [],
-                "description": "Age prediction using machine learning",
+                "description": "",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Pipeline Builder\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntrain_dataset\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntest_dataset\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntest_labels_dataset\"]\n  4[label=\"Hyperparameter Search\"]\n  0 -> 4 [label=\"outfile_params\"]\n  0 -> 4 [label=\"outfile\"]\n  1 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Ensemble methods\"]\n  2 -> 5 [label=\"output\"]\n  4 -> 5 [label=\"outfile_object\"]\n  6[label=\"Plot actual vs predicted curves and residual plots\"]\n  5 -> 6 [label=\"outfile_predict\"]\n  3 -> 6 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nIPynb notebook\"]\n  1[label=\"train_rows\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntest_rows\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntest_rows_labels\"]\n  4[label=\"GPU enabled Interactive Jupyter Notebook for Machine Learning\"]\n  0 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"out_file1\"]\n  2 -> 4 [label=\"output\"]\n  3 -> 4 [label=\"output\"]\n  5[label=\"Cut\"]\n  4 -> 5 [label=\"output_collection\"]\n}",
                 "history": [
                     {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 8,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "f7f017f3329dac306d19ca406c5e28f75bbf4ef8",
-                        "message": "dna and rna capitals",
-                        "num": 7,
-                        "short_hash": "f7f017f33",
-                        "unix": "1579092000"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 6,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "cad9f0a86642e5d5580ac0a3a2f7ffef6cd56311",
-                        "message": "Merge branch 'master' into ml_tools",
-                        "num": 5,
-                        "short_hash": "cad9f0a86",
-                        "unix": "1577658485"
-                    },
-                    {
-                        "hash": "0c8165c369cbc93a90c6f963d9fd5fcda86d4c5d",
-                        "message": "update workflow",
-                        "num": 4,
-                        "short_hash": "0c8165c36",
-                        "unix": "1577390920"
-                    },
-                    {
-                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
-                        "message": "unflatten workflows",
-                        "num": 3,
-                        "short_hash": "faf6d298a",
-                        "unix": "1576155753"
-                    },
-                    {
-                        "hash": "9d78b64348e1f3e59dc99c6860d4ae3c6a0619cc",
-                        "message": "Add workflows",
-                        "num": 2,
-                        "short_hash": "9d78b6434",
-                        "unix": "1560616699"
-                    },
-                    {
-                        "hash": "17a20f8e6367994c2dae74c93846a738275b9ee6",
-                        "message": "Fine-tuning formatting",
+                        "hash": "a13a2df4e05c8a59491ec3c2e896f9a2d6e57c43",
+                        "message": "add get data section",
                         "num": 1,
-                        "short_hash": "17a20f8e6",
-                        "unix": "1548412498"
+                        "short_hash": "a13a2df4e",
+                        "unix": "1673612716"
                     }
                 ],
                 "inputs": [
@@ -251984,28 +259191,27 @@
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 0,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "train_dataset",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "IPynb notebook"
+                            }
+                        ],
+                        "label": "IPynb notebook",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 359.8828125,
-                            "top": 515.01953125
+                            "left": 0.0,
+                            "top": 49.46180725097656
                         },
                         "tool_id": null,
-                        "tool_state": "{}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "7bcdbca8-beb1-4015-85f8-a289e0d5baa6",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "b53c6d64-e5a0-4fc9-bca1-6793352d93c5"
-                            }
-                        ]
+                        "uuid": "9ddc6af5-38e4-4e13-9376-3540a8f94afb",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
@@ -252013,26 +259219,25 @@
                         "errors": null,
                         "id": 2,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "test_dataset",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "test_rows"
+                            }
+                        ],
+                        "label": "test_rows",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 409.375,
-                            "top": 641.875
+                            "left": 3.923614501953125,
+                            "top": 293.4548645019531
                         },
                         "tool_id": null,
-                        "tool_state": "{}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "3bd54821-fc35-47ef-830f-eff3db757252",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "4588ddcc-8132-46a9-b1ed-00d8897790e0"
-                            }
-                        ]
+                        "uuid": "48752f10-3b93-4721-aac6-9217c9285e24",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
@@ -252040,538 +259245,477 @@
                         "errors": null,
                         "id": 3,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "test_labels_dataset",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "test_rows_labels"
+                            }
+                        ],
+                        "label": "test_rows_labels",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 944.90234375,
-                            "top": 278.88671875
+                            "left": 2.986114501953125,
+                            "top": 389.4618225097656
                         },
                         "tool_id": null,
-                        "tool_state": "{}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "40f96b3a-c0af-481b-beb0-4f98d711b5a5",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "fd8d51f2-0b16-4bab-97b8-b3e5a3f5c637"
-                            }
-                        ]
+                        "uuid": "d4e139b9-c90d-49b0-9600-dae8de4c04e5",
+                        "workflow_outputs": []
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"Pipeline Builder\"];\n  1[\"\u2139\ufe0f Input Dataset\\ntrain_dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ntest_dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\ntest_labels_dataset\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Hyperparameter Search\"];\n  0 -->|outfile_params| 4;\n  0 -->|outfile| 4;\n  1 -->|output| 4;\n  1 -->|output| 4;\n  5[\"Ensemble methods\"];\n  2 -->|output| 5;\n  4 -->|outfile_object| 5;\n  6[\"Plot actual vs predicted curves and residual plots\"];\n  5 -->|outfile_predict| 6;\n  3 -->|output| 6;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Age Prediction DNA Methylation",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIPynb notebook\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"train_rows\"];\n  2[\"\u2139\ufe0f Input Dataset\\ntest_rows\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\ntest_rows_labels\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"GPU enabled Interactive Jupyter Notebook for Machine Learning\"];\n  0 -->|output| 4;\n  1 -->|out_file1| 4;\n  2 -->|output| 4;\n  3 -->|output| 4;\n  5[\"Cut\"];\n  4 -->|output_collection| 5;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "gpu_jupytool",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.8.1",
+                        "content_id": "Filter1",
                         "errors": null,
-                        "id": 0,
+                        "id": 1,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "Pipeline Builder",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "zip"
-                            },
+                        "inputs": [
                             {
-                                "name": "outfile_params",
-                                "type": "tabular"
+                                "description": "runtime parameter for tool Filter",
+                                "name": "input"
                             }
                         ],
-                        "position": {
-                            "left": 220.83984375,
-                            "top": 199.9609375
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.8.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3f3c6dc38f3e",
-                            "name": "sklearn_build_pipeline",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"final_estimator\": \"{\\\"estimator_selector\\\": {\\\"__current_case__\\\": 2, \\\"selected_estimator\\\": \\\"GradientBoostingRegressor\\\", \\\"selected_module\\\": \\\"ensemble\\\", \\\"text_params\\\": \\\"random_state=42\\\"}}\", \"pipeline_component\": \"[{\\\"__index__\\\": 0, \\\"component_selector\\\": {\\\"__current_case__\\\": 0, \\\"component_type\\\": \\\"None\\\"}}]\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"get_params\": \"\\\"true\\\"\"}",
-                        "tool_version": "1.0.8.1",
-                        "type": "tool",
-                        "uuid": "26db8419-6a23-48d3-bf72-33ca0416e645",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "2a7377ad-1474-4953-bd39-8bcdeccbc046"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "outfile_params",
-                                "uuid": "19fe7f34-c119-479d-8cad-58338b1f9ce4"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "train_dataset",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 359.8828125,
-                            "top": 515.01953125
-                        },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "7bcdbca8-beb1-4015-85f8-a289e0d5baa6",
-                        "workflow_outputs": [
+                        "label": "train_rows",
+                        "name": "Filter",
+                        "outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "b53c6d64-e5a0-4fc9-bca1-6793352d93c5"
+                                "name": "out_file1",
+                                "type": "input"
                             }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "test_dataset",
-                        "name": "Input dataset",
-                        "outputs": [],
+                        ],
                         "position": {
-                            "left": 409.375,
-                            "top": 641.875
+                            "left": 6.90972900390625,
+                            "top": 166.4757080078125
                         },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "3bd54821-fc35-47ef-830f-eff3db757252",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "4588ddcc-8132-46a9-b1ed-00d8897790e0"
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "new_train_rows"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
                             }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "test_labels_dataset",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 944.90234375,
-                            "top": 278.88671875
                         },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "40f96b3a-c0af-481b-beb0-4f98d711b5a5",
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"cond\": \"c3==0\", \"header_lines\": \"1\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
+                        "type": "tool",
+                        "uuid": "25b59910-1d66-4248-98a4-0a3e23193551",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "fd8d51f2-0b16-4bab-97b8-b3e5a3f5c637"
+                                "output_name": "out_file1",
+                                "uuid": "09c60184-4418-4a83-8d7c-eeac4cdca49e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1",
+                        "content_id": "interactive_tool_ml_jupyter_notebook",
                         "errors": null,
                         "id": 4,
                         "input_connections": {
-                            "input_options|infile1": {
-                                "id": 1,
+                            "mode|ipynb": {
+                                "id": 0,
                                 "output_name": "output"
                             },
-                            "input_options|infile2": {
+                            "user_inputs_0|input_type|input_value": {
                                 "id": 1,
-                                "output_name": "output"
+                                "output_name": "out_file1"
                             },
-                            "search_schemes|infile_estimator": {
-                                "id": 0,
-                                "output_name": "outfile"
+                            "user_inputs_1|input_type|input_value": {
+                                "id": 2,
+                                "output_name": "output"
                             },
-                            "search_schemes|search_params_builder|infile_params": {
-                                "id": 0,
-                                "output_name": "outfile_params"
+                            "user_inputs_2|input_type|input_value": {
+                                "id": 3,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Hyperparameter Search",
-                                "name": "search_schemes"
-                            },
-                            {
-                                "description": "runtime parameter for tool Hyperparameter Search",
-                                "name": "input_options"
-                            },
-                            {
-                                "description": "runtime parameter for tool Hyperparameter Search",
-                                "name": "input_options"
+                                "description": "runtime parameter for tool GPU enabled Interactive Jupyter Notebook for Machine Learning",
+                                "name": "mode"
                             }
                         ],
                         "label": null,
-                        "name": "Hyperparameter Search",
+                        "name": "GPU enabled Interactive Jupyter Notebook for Machine Learning",
                         "outputs": [
                             {
-                                "name": "outfile_result",
-                                "type": "tabular"
+                                "name": "output_collection",
+                                "type": "input"
                             },
                             {
-                                "name": "outfile_object",
-                                "type": "zip"
+                                "name": "jupyter_notebook",
+                                "type": "ipynb"
                             }
                         ],
                         "position": {
-                            "left": 632.44140625,
-                            "top": 124.94140625
+                            "left": 307.3437805175781,
+                            "top": 0.0
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "c1ca24a1509d",
-                            "name": "sklearn_searchcv",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        "post_job_actions": {
+                            "ChangeDatatypeActionoutput_collection": {
+                                "action_arguments": {
+                                    "newtype": "tabular"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "output_collection"
+                            },
+                            "ChangeDatatypeActionoutput_dataset": {
+                                "action_arguments": {
+                                    "newtype": "tabular"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "output_dataset"
+                            }
                         },
-                        "tool_state": "{\"__page__\": null, \"search_schemes\": \"{\\\"__current_case__\\\": 0, \\\"infile_estimator\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"is_deep_learning\\\": \\\"false\\\", \\\"options\\\": {\\\"cv_selector\\\": {\\\"__current_case__\\\": 1, \\\"n_splits\\\": \\\"5\\\", \\\"random_state\\\": \\\"3111696\\\", \\\"selected_cv\\\": \\\"KFold\\\", \\\"shuffle\\\": \\\"true\\\"}, \\\"error_score\\\": \\\"false\\\", \\\"iid\\\": \\\"true\\\", \\\"return_train_score\\\": \\\"false\\\", \\\"scoring\\\": {\\\"__current_case__\\\": 26, \\\"primary_scoring\\\": \\\"r2\\\", \\\"secondary_scoring\\\": null}, \\\"verbose\\\": \\\"0\\\"}, \\\"search_params_builder\\\": {\\\"infile_params\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"param_set\\\": [{\\\"__index__\\\": 0, \\\"sp_list\\\": \\\"[25, 50, 75, 100, 200]\\\", \\\"sp_name\\\": \\\"n_estimators\\\"}]}, \\\"selected_search_scheme\\\": \\\"GridSearchCV\\\"}\", \"__rerun_remap_job_id__\": null, \"save\": \"\\\"save_estimator\\\"\", \"input_options\": \"{\\\"__current_case__\\\": 0, \\\"column_selector_options_1\\\": {\\\"__current_case__\\\": 3, \\\"col1\\\": \\\"Age\\\", \\\"selected_column_selector_option\\\": \\\"all_but_by_header_name\\\"}, \\\"column_selector_options_2\\\": {\\\"__current_case__\\\": 2, \\\"col2\\\": \\\"Age\\\", \\\"selected_column_selector_option2\\\": \\\"by_header_name\\\"}, \\\"header1\\\": \\\"true\\\", \\\"header2\\\": \\\"true\\\", \\\"infile1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"infile2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"selected_input\\\": \\\"tabular\\\"}\", \"outer_split\": \"{\\\"__current_case__\\\": 0, \\\"split_mode\\\": \\\"no\\\"}\"}",
-                        "tool_version": "1.0.8.1",
+                        "tool_id": "interactive_tool_ml_jupyter_notebook",
+                        "tool_state": "{\"mode\": {\"mode_select\": \"previous\", \"__current_case__\": 1, \"ipynb\": {\"__class__\": \"RuntimeValue\"}, \"run_it\": \"true\"}, \"user_inputs\": [{\"__index__\": 0, \"input_name\": \"train\", \"description\": \"\", \"input_type\": {\"input_type_selector\": \"dataset\", \"__current_case__\": 0, \"input_value\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 1, \"input_name\": \"test\", \"description\": \"\", \"input_type\": {\"input_type_selector\": \"dataset\", \"__current_case__\": 0, \"input_value\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 2, \"input_name\": \"testlabels\", \"description\": \"\", \"input_type\": {\"input_type_selector\": \"dataset\", \"__current_case__\": 0, \"input_value\": {\"__class__\": \"RuntimeValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.2",
                         "type": "tool",
-                        "uuid": "4127ab12-dbd9-4888-bcda-b05748a05295",
+                        "uuid": "b0563c69-10cd-4024-b5de-309c828b8ea2",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outfile_object",
-                                "uuid": "48939329-f5f2-445e-bdb3-51dc28629f18"
+                                "output_name": "output_collection",
+                                "uuid": "fe942416-e111-40c9-8b90-1102348a5b2c"
                             },
                             {
                                 "label": null,
-                                "output_name": "outfile_result",
-                                "uuid": "5b78c8e6-1e98-4798-bab3-285cedbc8d85"
+                                "output_name": "jupyter_notebook",
+                                "uuid": "5a38221b-92db-4b48-9b4f-a5c8ecd6f8af"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.8.1",
+                        "content_id": "Cut1",
                         "errors": null,
                         "id": 5,
                         "input_connections": {
-                            "selected_tasks|infile_data": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "selected_tasks|infile_model": {
+                            "input": {
                                 "id": 4,
-                                "output_name": "outfile_object"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Ensemble methods",
-                                "name": "selected_tasks"
-                            },
-                            {
-                                "description": "runtime parameter for tool Ensemble methods",
-                                "name": "selected_tasks"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Ensemble methods",
-                        "outputs": [
-                            {
-                                "name": "outfile_predict",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 710.87890625,
-                            "top": 558.92578125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.8.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "af0523c606a7",
-                            "name": "sklearn_ensemble",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__page__\": null, \"selected_tasks\": \"{\\\"__current_case__\\\": 0, \\\"header\\\": \\\"true\\\", \\\"infile_data\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"infile_model\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"prediction_options\\\": {\\\"__current_case__\\\": 0, \\\"prediction_option\\\": \\\"predict\\\"}, \\\"selected_task\\\": \\\"load\\\"}\", \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.8.1",
-                        "type": "tool",
-                        "uuid": "559f44ea-0d8b-4fce-85fb-079d010ab90d",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile_predict",
-                                "uuid": "d025d2be-6698-49a0-901e-0c9513f72255"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "infile_input": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "infile_output": {
-                                "id": 5,
-                                "output_name": "outfile_predict"
+                                "output_name": "output_collection"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Plot actual vs predicted curves and residual plots",
+                        "name": "Cut",
                         "outputs": [
                             {
-                                "name": "output_actual_vs_pred",
-                                "type": "html"
-                            },
-                            {
-                                "name": "output_scatter_plot",
-                                "type": "html"
-                            },
-                            {
-                                "name": "output_residual_plot",
-                                "type": "html"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1058.3984375,
-                            "top": 452.890625
+                            "left": 617.9861755371094,
+                            "top": 52.44792175292969
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "389227fa1864",
-                            "name": "plotly_regression_performance_plots",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"infile_output\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"infile_input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
-                        "tool_version": "0.1",
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"columnList\": \"c1\", \"delimiter\": \"C\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2",
                         "type": "tool",
-                        "uuid": "8fd368d0-ef84-4414-9fc9-ef408947a080",
+                        "uuid": "0909fb62-c832-4d1d-9d95-5b8ebac25dae",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_scatter_plot",
-                                "uuid": "043f8530-e77a-4768-abdc-365ff91127fa"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_actual_vs_pred",
-                                "uuid": "3a0f039e-b4c4-466a-9be9-b7d9ceeb73e7"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "output_residual_plot",
-                                "uuid": "1ec7ae83-9fd7-4b98-b613-3cb3802211ee"
+                                "output_name": "out_file1",
+                                "uuid": "fd1c2370-a25e-41d3-8351-fb3aae79c394"
                             }
                         ]
                     }
                 ],
-                "parent_id": "statistics/age-prediction-with-ml",
-                "path": "topics/statistics/tutorials/age-prediction-with-ml/workflows/age-prediction-dnam.ga",
-                "tags": [
-                    "statistics"
-                ],
+                "parent_id": "statistics/gpu_jupyter_lab",
+                "path": "topics/statistics/tutorials/gpu_jupyter_lab/workflows/gpu_jupyterlab_as_jupytool.ga",
+                "tags": [],
                 "test_results": null,
                 "tests": false,
-                "title": "Age Prediction DNA Methylation",
+                "title": "gpu_jupytool",
                 "topic_id": "statistics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-age-prediction-with-ml/versions/age-prediction-dnam",
-                "tutorial_id": "age-prediction-with-ml",
-                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/age-prediction-with-ml/workflows/age-prediction-dnam.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/age-prediction-with-ml/workflows/age-prediction-dnam.html",
-                "version": 6,
-                "wfid": "statistics-age-prediction-with-ml",
-                "wfname": "age-prediction-dnam",
-                "workflow": "age-prediction-dnam.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-gpu_jupyter_lab/versions/gpu-jupyterlab-as-jupytool",
+                "tutorial_id": "gpu_jupyter_lab",
+                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/gpu_jupyter_lab/workflows/gpu_jupyterlab_as_jupytool.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/gpu_jupyter_lab/workflows/gpu_jupyterlab_as_jupytool.html",
+                "version": 1,
+                "wfid": "statistics-gpu_jupyter_lab",
+                "wfname": "gpu-jupyterlab-as-jupytool",
+                "workflow": "gpu_jupyterlab_as_jupytool.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.8.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.8.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1"
+                    "Cut1",
+                    "Filter1",
+                    "interactive_tool_ml_jupyter_notebook"
                 ],
-                "workflowhub_id": "1277"
+                "workflowhub_id": "1325"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/6091361"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "iwtomics_loadandplot",
+                    "owner": "iuc",
+                    "revisions": "ce633cc8f5f9",
+                    "tool_panel_section_label": "Statistics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "iwtomics_plotwithscale",
+                    "owner": "iuc",
+                    "revisions": "1bc9150ed125",
+                    "tool_panel_section_label": "Statistics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "iwtomics_testandplot",
+                    "owner": "iuc",
+                    "revisions": "94965e369be4",
+                    "tool_panel_section_label": "Statistics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: iwtomics_loadandplot\n  owner: iuc\n  revisions: ce633cc8f5f9\n  tool_panel_section_label: Statistics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: iwtomics_plotwithscale\n  owner: iuc\n  revisions: 1bc9150ed125\n  tool_panel_section_label: Statistics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: iwtomics_testandplot\n  owner: iuc\n  revisions: 94965e369be4\n  tool_panel_section_label: Statistics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/iwtomics/tutorial.json",
+        "contributors": [
+            {
+                "email": "mac78@psu.edu",
+                "id": "marziacremona",
+                "joined": "2018-02",
+                "name": "Marzia A Cremona",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/marziacremona/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/marziacremona.json"
             },
+            {
+                "email": "fabio.cumbo@gmail.com",
+                "id": "cumbof",
+                "joined": "2018-02",
+                "linkedin": "fabiocumbo",
+                "name": "Fabio Cumbo",
+                "orcid": "0000-0003-2920-5838",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/cumbof/",
+                "twitter": "cumbofabio",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/cumbof.json"
+            }
+        ],
+        "dir": "topics/statistics/tutorials/iwtomics",
+        "edam_operation": [
+            "Peak calling",
+            "Genome annotation",
+            "Differential gene expression analysis",
+            "Comparison",
+            "Differentially-methylated region identification"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "statistics/iwtomics",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "High-resolution omics data can be represented as curves along the genome",
+            "IWTomics permits to visualize these data",
+            "The Interval-Wise Testing detects statistically significant differences between pairs of genomic regions",
+            "The Interval-Wise Testing corrects p-values taking into consideration the ordered nature of measurements along the genome",
+            "Locations and scales do not need to be specified at the outset, indeed IWTomics permits to detect them"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": [
+            "Pre-process high-resolution omics data",
+            "Create pointwise boxplots corresponding to different groups of genomic regions",
+            "Perform the Interval-Wise Testing between two groups of genomic regions",
+            "Visualize and inspect test results",
+            "Detect relevant locations and scales"
+        ],
+        "pageviews": 454,
+        "pub_date": "2018-06-14",
+        "questions": [
+            "How to visualize high-resolution omics data in different groups of genomic regions?",
+            "How to evaluate differences in high-resolution omics data between groups of genomic regions?",
+            "How to detect locations and scales at which the significant effects unfold?"
+        ],
+        "requirements": null,
+        "short_id": "T00269",
+        "short_tools": [
+            "iwtomics_testandplot",
+            "iwtomics_loadandplot",
+            "iwtomics_plotwithscale"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "time_estimation": "1h",
+        "title": "Interval-Wise Testing for omics data",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_loadandplot/iwtomics_loadandplot/1.0.0.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_plotwithscale/iwtomics_plotwithscale/1.0.0.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_testandplot/iwtomics_testandplot/1.0.0.0"
+        ],
+        "topic_name": "statistics",
+        "topic_name_human": "Statistics and machine learning",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "iwtomics",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/iwtomics/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/iwtomics/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/iwtomics/tutorial.json"
+        },
+        "version": 17,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 192,
+        "visitors": 333,
+        "workflows": [
             {
                 "creators": [],
-                "description": "Age prediction using machine learning",
+                "description": "Interval-Wise Testing for omics data",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"Pipeline Builder\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[label=\"Hyperparameter Search\"]\n  0 -> 2 [label=\"outfile_params\"]\n  0 -> 2 [label=\"outfile\"]\n  1 -> 2 [label=\"output\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"Parallel Coordinates Plot\"]\n  2 -> 3 [label=\"outfile_result\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nETn_fixed.bed\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nControl.bed\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nfeatures_header.tabular\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nregions_header.tabular\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nRecombination_hotspots.txt\"]\n  5[label=\"IWTomics Load\"]\n  4 -> 5 [label=\"output\"]\n  2 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"output\"]\n  6[label=\"IWTomics Test\"]\n  5 -> 6 [label=\"outfeatures\"]\n  5 -> 6 [label=\"outrdata\"]\n  5 -> 6 [label=\"outregions\"]\n  7[label=\"IWTomics Plot with Threshold\"]\n  6 -> 7 [label=\"iwtomicsselectedfeatures\"]\n  6 -> 7 [label=\"iwtomicsrdata\"]\n  6 -> 7 [label=\"iwtomicstests\"]\n}",
                 "history": [
+                    {
+                        "hash": "b97fcf8dbc18d441d3e8e6eb7a2e4f01fda1cb14",
+                        "message": "Updating IWTomics data",
+                        "num": 6,
+                        "short_hash": "b97fcf8db",
+                        "unix": "1634825035"
+                    },
                     {
                         "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
                         "message": "annotation",
-                        "num": 8,
+                        "num": 5,
                         "short_hash": "667ff3de9",
                         "unix": "1579690769"
                     },
-                    {
-                        "hash": "f7f017f3329dac306d19ca406c5e28f75bbf4ef8",
-                        "message": "dna and rna capitals",
-                        "num": 7,
-                        "short_hash": "f7f017f33",
-                        "unix": "1579092000"
-                    },
                     {
                         "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
                         "message": "Workflow renaming",
-                        "num": 6,
+                        "num": 4,
                         "short_hash": "eb4d724e0",
                         "unix": "1579084895"
                     },
                     {
-                        "hash": "cad9f0a86642e5d5580ac0a3a2f7ffef6cd56311",
-                        "message": "Merge branch 'master' into ml_tools",
-                        "num": 5,
-                        "short_hash": "cad9f0a86",
-                        "unix": "1577658485"
-                    },
-                    {
-                        "hash": "0c8165c369cbc93a90c6f963d9fd5fcda86d4c5d",
-                        "message": "update workflow",
-                        "num": 4,
-                        "short_hash": "0c8165c36",
-                        "unix": "1577390920"
-                    },
-                    {
-                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
-                        "message": "unflatten workflows",
+                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
+                        "message": "Changed format of workflows",
                         "num": 3,
-                        "short_hash": "faf6d298a",
-                        "unix": "1576155753"
+                        "short_hash": "361236c41",
+                        "unix": "1554368414"
                     },
                     {
-                        "hash": "9d78b64348e1f3e59dc99c6860d4ae3c6a0619cc",
-                        "message": "Add workflows",
+                        "hash": "251bebcf11feffcbd9a103e1ac5898def74c861e",
+                        "message": "workflow fixed",
                         "num": 2,
-                        "short_hash": "9d78b6434",
-                        "unix": "1560616699"
+                        "short_hash": "251bebcf1",
+                        "unix": "1528895196"
                     },
                     {
-                        "hash": "17a20f8e6367994c2dae74c93846a738275b9ee6",
-                        "message": "Fine-tuning formatting",
+                        "hash": "5752bb6b95a47c674c4600c00537a015f6357967",
+                        "message": "IWTomics Workflow",
                         "num": 1,
-                        "short_hash": "17a20f8e6",
-                        "unix": "1548412498"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 295.9375,
-                            "top": 391.09375
-                        },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "7bcdbca8-beb1-4015-85f8-a289e0d5baa6",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "f68ac118-2beb-41f3-9a64-41c66162c474"
-                            }
-                        ]
+                        "short_hash": "5752bb6b9",
+                        "unix": "1528889546"
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"Pipeline Builder\"];\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Hyperparameter Search\"];\n  0 -->|outfile_params| 2;\n  0 -->|outfile| 2;\n  1 -->|output| 2;\n  1 -->|output| 2;\n  3[\"Parallel Coordinates Plot\"];\n  2 -->|outfile_result| 3;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Age Prediction RNA-Seq",
-                "outputs": [
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.8.1",
+                        "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "Pipeline Builder",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "zip"
-                            },
+                        "inputs": [
                             {
-                                "name": "outfile_params",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "ETn_fixed.bed"
                             }
                         ],
+                        "label": "ETn_fixed.bed",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 216.9140625,
-                            "top": 222.98828125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.8.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3f3c6dc38f3e",
-                            "name": "sklearn_build_pipeline",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 200,
+                            "top": 200
                         },
-                        "tool_state": "{\"final_estimator\": \"{\\\"estimator_selector\\\": {\\\"__current_case__\\\": 1, \\\"selected_estimator\\\": \\\"ElasticNet\\\", \\\"selected_module\\\": \\\"linear_model\\\", \\\"text_params\\\": \\\"random_state=42\\\"}}\", \"pipeline_component\": \"[{\\\"__index__\\\": 0, \\\"component_selector\\\": {\\\"__current_case__\\\": 2, \\\"component_type\\\": \\\"feature_selection\\\", \\\"fs_algorithm_selector\\\": {\\\"__current_case__\\\": 2, \\\"options\\\": {\\\"k\\\": \\\"10\\\"}, \\\"score_func\\\": \\\"f_regression\\\", \\\"selected_algorithm\\\": \\\"SelectKBest\\\"}}}]\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"get_params\": \"\\\"true\\\"\"}",
-                        "tool_version": "1.0.8.1",
-                        "type": "tool",
-                        "uuid": "26db8419-6a23-48d3-bf72-33ca0416e645",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile_params",
-                                "uuid": "551e9e48-ff1b-42ec-90b6-98e6b5058b04"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "2a7377ad-1474-4953-bd39-8bcdeccbc046"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"ETn_fixed.bed\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "7709e0ee-56fc-491d-afad-b10c18758c07",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
@@ -252579,182 +259723,138 @@
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": null,
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Control.bed"
+                            }
+                        ],
+                        "label": "Control.bed",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 295.9375,
-                            "top": 391.09375
+                            "left": 200,
+                            "top": 320
                         },
                         "tool_id": null,
-                        "tool_state": "{}",
+                        "tool_state": "{\"name\": \"Control.bed\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "7bcdbca8-beb1-4015-85f8-a289e0d5baa6",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "f68ac118-2beb-41f3-9a64-41c66162c474"
-                            }
-                        ]
+                        "uuid": "9c4be2e1-6f14-4ec4-a0e8-3ec4e21a6523",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1",
+                        "content_id": null,
                         "errors": null,
                         "id": 2,
-                        "input_connections": {
-                            "input_options|infile1": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "input_options|infile2": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "search_schemes|infile_estimator": {
-                                "id": 0,
-                                "output_name": "outfile"
-                            },
-                            "search_schemes|search_params_builder|infile_params": {
-                                "id": 0,
-                                "output_name": "outfile_params"
-                            }
-                        },
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Hyperparameter Search",
-                                "name": "search_schemes"
-                            },
-                            {
-                                "description": "runtime parameter for tool Hyperparameter Search",
-                                "name": "input_options"
-                            },
-                            {
-                                "description": "runtime parameter for tool Hyperparameter Search",
-                                "name": "input_options"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Hyperparameter Search",
-                        "outputs": [
-                            {
-                                "name": "outfile_result",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "outfile_object",
-                                "type": "zip"
+                                "description": "",
+                                "name": "features_header.tabular"
                             }
                         ],
+                        "label": "features_header.tabular",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 647.5,
-                            "top": 180.99609375
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionoutfile_object": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "outfile_object"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "c1ca24a1509d",
-                            "name": "sklearn_searchcv",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 200,
+                            "top": 680
                         },
-                        "tool_state": "{\"__page__\": null, \"search_schemes\": \"{\\\"__current_case__\\\": 0, \\\"infile_estimator\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"is_deep_learning\\\": \\\"false\\\", \\\"options\\\": {\\\"cv_selector\\\": {\\\"__current_case__\\\": 1, \\\"n_splits\\\": \\\"5\\\", \\\"random_state\\\": \\\"3111696\\\", \\\"selected_cv\\\": \\\"KFold\\\", \\\"shuffle\\\": \\\"true\\\"}, \\\"error_score\\\": \\\"false\\\", \\\"iid\\\": \\\"true\\\", \\\"return_train_score\\\": \\\"false\\\", \\\"scoring\\\": {\\\"__current_case__\\\": 26, \\\"primary_scoring\\\": \\\"r2\\\", \\\"secondary_scoring\\\": null}, \\\"verbose\\\": \\\"0\\\"}, \\\"search_params_builder\\\": {\\\"infile_params\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"param_set\\\": [{\\\"__index__\\\": 0, \\\"sp_list\\\": \\\"[5880, 5890, 5895, 5900]\\\", \\\"sp_name\\\": \\\"selectkbest__k\\\"}, {\\\"__index__\\\": 1, \\\"sp_list\\\": \\\"[True, False]\\\", \\\"sp_name\\\": \\\"elasticnet__normalize\\\"}, {\\\"__index__\\\": 2, \\\"sp_list\\\": \\\"[0.00001, 0.0001, 0.001]\\\", \\\"sp_name\\\": \\\"elasticnet__alpha\\\"}]}, \\\"selected_search_scheme\\\": \\\"GridSearchCV\\\"}\", \"__rerun_remap_job_id__\": null, \"save\": \"\\\"save_estimator\\\"\", \"input_options\": \"{\\\"__current_case__\\\": 0, \\\"column_selector_options_1\\\": {\\\"__current_case__\\\": 3, \\\"col1\\\": \\\"age\\\", \\\"selected_column_selector_option\\\": \\\"all_but_by_header_name\\\"}, \\\"column_selector_options_2\\\": {\\\"__current_case__\\\": 2, \\\"col2\\\": \\\"age\\\", \\\"selected_column_selector_option2\\\": \\\"by_header_name\\\"}, \\\"header1\\\": \\\"true\\\", \\\"header2\\\": \\\"true\\\", \\\"infile1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"infile2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"selected_input\\\": \\\"tabular\\\"}\", \"outer_split\": \"{\\\"__current_case__\\\": 0, \\\"split_mode\\\": \\\"no\\\"}\"}",
-                        "tool_version": "1.0.8.1",
-                        "type": "tool",
-                        "uuid": "4127ab12-dbd9-4888-bcda-b05748a05295",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile_result",
-                                "uuid": "cd5488b6-e604-411d-9032-8189d9b0205f"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"features_header.tabular\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "4a071a64-59d3-481d-8d84-f063c38ddac7",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1",
+                        "content_id": null,
                         "errors": null,
                         "id": 3,
-                        "input_connections": {
-                            "infile": {
-                                "id": 2,
-                                "output_name": "outfile_result"
-                            }
-                        },
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Parallel Coordinates Plot",
-                                "name": "infile"
+                                "description": "",
+                                "name": "regions_header.tabular"
                             }
                         ],
-                        "label": null,
-                        "name": "Parallel Coordinates Plot",
-                        "outputs": [
+                        "label": "regions_header.tabular",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 560
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"regions_header.tabular\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ac9cf2c6-9bbc-42b4-b4fb-f0fcf92dcee6",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "html"
+                                "description": "",
+                                "name": "Recombination_hotspots.txt"
                             }
                         ],
+                        "label": "Recombination_hotspots.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 961.0546875,
-                            "top": 252.05078125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "7b2455348edf",
-                            "name": "plotly_parallel_coordinates_plot",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 200,
+                            "top": 440
                         },
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"col_color\": \"\\\"3\\\"\", \"col_dimensions\": \"\\\"4, 5, 6\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "0.1",
-                        "type": "tool",
-                        "uuid": "a208b2c4-9a3f-40a9-a55c-c98a7b552bcb",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "0dc1b427-05f1-40d5-b28b-9b2e73ce4a29"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Recombination_hotspots.txt\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "946f863d-0ef4-42b1-bb87-25247e31d4d9",
+                        "workflow_outputs": []
                     }
                 ],
-                "parent_id": "statistics/age-prediction-with-ml",
-                "path": "topics/statistics/tutorials/age-prediction-with-ml/workflows/age-prediction-rna.ga",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nETn_fixed.bed\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nControl.bed\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nfeatures_header.tabular\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nregions_header.tabular\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nRecombination_hotspots.txt\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"IWTomics Load\"];\n  4 -->|output| 5;\n  2 -->|output| 5;\n  0 -->|output| 5;\n  1 -->|output| 5;\n  3 -->|output| 5;\n  6[\"IWTomics Test\"];\n  5 -->|outfeatures| 6;\n  5 -->|outrdata| 6;\n  5 -->|outregions| 6;\n  7[\"IWTomics Plot with Threshold\"];\n  6 -->|iwtomicsselectedfeatures| 7;\n  6 -->|iwtomicsrdata| 7;\n  6 -->|iwtomicstests| 7;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "Workflow Constructed From History 'IWTomics Workflow'",
+                "outputs": [],
+                "parent_id": "statistics/iwtomics",
+                "path": "topics/statistics/tutorials/iwtomics/workflows/IWTomics_Workflow.ga",
                 "tags": [
+                    "genomics",
+                    "iwtomics",
                     "statistics"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Age Prediction RNA-Seq",
+                "title": "Workflow Constructed From History 'IWTomics Workflow'",
                 "topic_id": "statistics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-age-prediction-with-ml/versions/age-prediction-rna",
-                "tutorial_id": "age-prediction-with-ml",
-                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/age-prediction-with-ml/workflows/age-prediction-rna.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/age-prediction-with-ml/workflows/age-prediction-rna.html",
-                "version": 6,
-                "wfid": "statistics-age-prediction-with-ml",
-                "wfname": "age-prediction-rna",
-                "workflow": "age-prediction-rna.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-iwtomics/versions/iwtomics-workflow",
+                "tutorial_id": "iwtomics",
+                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/iwtomics/workflows/IWTomics_Workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/iwtomics/workflows/IWTomics_Workflow.html",
+                "version": 5,
+                "wfid": "statistics-iwtomics",
+                "wfname": "iwtomics-workflow",
+                "workflow": "IWTomics_Workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.8.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.1"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_loadandplot/iwtomics_loadandplot/1.0.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_plotwithscale/iwtomics_plotwithscale/1.0.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_testandplot/iwtomics_testandplot/1.0.0.0"
                 ],
-                "workflowhub_id": "1280"
+                "workflowhub_id": "1317"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/2545213"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.5589610"
     },
     {
         "admin_install": {
@@ -252763,193 +259863,184 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "keras_model_builder",
-                    "owner": "bgruening",
-                    "revisions": "772e0e89fc68",
-                    "tool_panel_section_label": "Machine Learning",
+                    "name": "pancancer_alternative_genes_pathwaymapper",
+                    "owner": "vijay",
+                    "revisions": "c594c4333b76",
+                    "tool_panel_section_label": "Statistics and machine learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "keras_model_config",
-                    "owner": "bgruening",
-                    "revisions": "8a794e6d3388",
-                    "tool_panel_section_label": "Machine Learning",
+                    "name": "pancancer_apply_weights",
+                    "owner": "vijay",
+                    "revisions": "3543d3e66ecb",
+                    "tool_panel_section_label": "Statistics and machine learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "keras_train_and_eval",
-                    "owner": "bgruening",
-                    "revisions": "f1b9a42d6809",
-                    "tool_panel_section_label": "Machine Learning",
+                    "name": "pancancer_classifier",
+                    "owner": "vijay",
+                    "revisions": "20b049f5b3f5",
+                    "tool_panel_section_label": "Statistics and machine learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "keras_train_and_eval",
-                    "owner": "bgruening",
-                    "revisions": "b6ef6d0cb6b7",
-                    "tool_panel_section_label": "Machine Learning",
+                    "name": "pancancer_compare_within_models",
+                    "owner": "vijay",
+                    "revisions": "84ac2a86bde1",
+                    "tool_panel_section_label": "Statistics and machine learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ml_visualization_ex",
-                    "owner": "bgruening",
-                    "revisions": "05143043ca13",
-                    "tool_panel_section_label": "Machine Learning",
+                    "name": "pancancer_external_sample_status_prediction",
+                    "owner": "vijay",
+                    "revisions": "8f426aeccfe3",
+                    "tool_panel_section_label": "Statistics and machine learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ml_visualization_ex",
-                    "owner": "bgruening",
-                    "revisions": "947c2eacccb8",
-                    "tool_panel_section_label": "Machine Learning",
+                    "name": "pancancer_map_mutation_class",
+                    "owner": "vijay",
+                    "revisions": "54c85c40dce1",
+                    "tool_panel_section_label": "Statistics and machine learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "model_prediction",
-                    "owner": "bgruening",
-                    "revisions": "83228baae3c5",
-                    "tool_panel_section_label": "Machine Learning",
+                    "name": "pancancer_pathway_count_heatmaps",
+                    "owner": "vijay",
+                    "revisions": "dc1d71493ebf",
+                    "tool_panel_section_label": "Statistics and machine learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "model_prediction",
-                    "owner": "bgruening",
-                    "revisions": "1552b8cb4a94",
-                    "tool_panel_section_label": "Machine Learning",
+                    "name": "pancancer_targene_cell_line_predictions",
+                    "owner": "vijay",
+                    "revisions": "872aab514d37",
+                    "tool_panel_section_label": "Statistics and machine learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sklearn_to_categorical",
-                    "owner": "bgruening",
-                    "revisions": "ec69cbe34b73",
-                    "tool_panel_section_label": "Machine Learning",
+                    "name": "pancancer_targene_pharmacology",
+                    "owner": "vijay",
+                    "revisions": "aa5e0e353148",
+                    "tool_panel_section_label": "Statistics and machine learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "pancancer_targene_summary_figures",
+                    "owner": "vijay",
+                    "revisions": "d533f991e22e",
+                    "tool_panel_section_label": "Statistics and machine learning",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pancancer_visualize_decisions",
+                    "owner": "vijay",
+                    "revisions": "f6dd27775d28",
+                    "tool_panel_section_label": "Statistics and machine learning",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pancancer_within_disease_analysis",
+                    "owner": "vijay",
+                    "revisions": "99d944bfe9b3",
+                    "tool_panel_section_label": "Statistics and machine learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: keras_model_builder\n  owner: bgruening\n  revisions: 772e0e89fc68\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_model_config\n  owner: bgruening\n  revisions: 8a794e6d3388\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_train_and_eval\n  owner: bgruening\n  revisions: f1b9a42d6809\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_train_and_eval\n  owner: bgruening\n  revisions: b6ef6d0cb6b7\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ml_visualization_ex\n  owner: bgruening\n  revisions: 05143043ca13\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ml_visualization_ex\n  owner: bgruening\n  revisions: 947c2eacccb8\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: model_prediction\n  owner: bgruening\n  revisions: 83228baae3c5\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: model_prediction\n  owner: bgruening\n  revisions: 1552b8cb4a94\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_to_categorical\n  owner: bgruening\n  revisions: ec69cbe34b73\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/fruit_360/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: pancancer_alternative_genes_pathwaymapper\n  owner: vijay\n  revisions: c594c4333b76\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_apply_weights\n  owner: vijay\n  revisions: 3543d3e66ecb\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_classifier\n  owner: vijay\n  revisions: 20b049f5b3f5\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_compare_within_models\n  owner: vijay\n  revisions: 84ac2a86bde1\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_external_sample_status_prediction\n  owner: vijay\n  revisions: 8f426aeccfe3\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_map_mutation_class\n  owner: vijay\n  revisions: 54c85c40dce1\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_pathway_count_heatmaps\n  owner: vijay\n  revisions: dc1d71493ebf\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_targene_cell_line_predictions\n  owner: vijay\n  revisions: 872aab514d37\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_targene_pharmacology\n  owner: vijay\n  revisions: aa5e0e353148\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_targene_summary_figures\n  owner: vijay\n  revisions: d533f991e22e\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_visualize_decisions\n  owner: vijay\n  revisions: f6dd27775d28\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pancancer_within_disease_analysis\n  owner: vijay\n  revisions: 99d944bfe9b3\n  tool_panel_section_label: Statistics and machine learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.json",
         "contributors": [
             {
-                "email": "kxk302@gmail.com",
-                "id": "kxk302",
-                "joined": "2021-02",
-                "name": "Kaivan Kamali",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kxk302/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/kxk302.json"
+                "id": "nvk747",
+                "joined": "2018-07",
+                "name": "Vijay",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nvk747/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nvk747.json"
+            },
+            {
+                "id": "blankenberg",
+                "joined": "2018-07",
+                "name": "Daniel Blankenberg",
+                "orcid": "0000-0002-6833-9049",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankenberg/",
+                "twitter": "dblankenberg",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankenberg.json"
             }
         ],
-        "dir": "topics/statistics/tutorials/fruit_360",
+        "dir": "topics/statistics/tutorials/aberrant_pi3k_pathway_analysis",
         "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "statistics/fruit_360",
+        "id": "statistics/aberrant_pi3k_pathway_analysis",
         "inexact_supported_servers": [],
         "js_requirements": {
-            "mathjax": 24661,
+            "mathjax": null,
             "mermaid": false
         },
+        "key_points": [
+            "Machine learning based Aberrant pathway activity analysis can distinguish normal and tumor samples. Also can identify transcriptomic signature of tumors associated with oncogene or tumor suppressor gene mutations.",
+            "Correlations from classifier predictions and pharmacological responses determine drug sensitivity among cancer cell lines and can be useful in improving personalized medicine approaches.",
+            "Classifier models generated from the suite-papaa can identify potential biomarkers with in the transcriptomic signature of tumors."
+        ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-09",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Learn how to create a CNN using Galaxy's deep learning tools",
-            "Solve an image classification problem on fruit 360 dataset using CNN in Galaxy"
+            "Learn to predict aberrant pathway activity using RNA-Seq data, mutational status and copy number variation data from TCGA.",
+            "Apply logistic regression based machine learning algorithms on TCGA data."
         ],
-        "pageviews": 4097715,
-        "pub_date": "2021-12-01",
+        "pageviews": 1098,
+        "pub_date": "2021-05-06",
         "questions": [
-            "How to solve an image classification problem using convolutional neural network (CNN)?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "kxk302"
-                ],
-                "date": "2022-01-19",
-                "galaxy_version": "21.09",
-                "length": "1H",
-                "speakers": [
-                    "kxk302"
-                ],
-                "youtube_id": "EX8gZ1lxhNY"
-            }
-        ],
-        "requirements": [
-            {
-                "topic_name": "statistics",
-                "tutorials": [
-                    "CNN"
-                ],
-                "type": "internal"
-            }
+            "How to predict aberrant pathway activity in The Cancer Genome Atlas (TCGA) using Machine learning approaches?"
         ],
-        "short_id": "T00265",
+        "short_id": "T00260",
         "short_tools": [
-            "keras_model_builder",
-            "keras_model_config",
-            "tp_cut_tool",
-            "model_prediction",
-            "keras_train_and_eval",
-            "ml_visualization_ex",
-            "sklearn_to_categorical"
+            "pancancer_targene_pharmacology",
+            "pancancer_classifier",
+            "pancancer_map_mutation_class",
+            "pancancer_pathway_count_heatmaps",
+            "pancancer_targene_summary_figures",
+            "pancancer_within_disease_analysis",
+            "pancancer_targene_cell_line_predictions",
+            "pancancer_apply_weights",
+            "pancancer_external_sample_status_prediction",
+            "pancancer_compare_within_models",
+            "pancancer_visualize_decisions",
+            "pancancer_alternative_genes_pathwaymapper"
         ],
-        "slides": true,
+        "slides": false,
         "slides_recordings": false,
         "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
+            "exact": [],
             "inexact": []
         },
         "symlink": null,
-        "time_estimation": "2H",
-        "title": "Image classification in Galaxy with fruit 360 dataset",
+        "tags": [
+            "Machine learning",
+            "Pan-cancer",
+            "cancer biomarkers",
+            "oncogenes and tumor suppressor genes"
+        ],
+        "time_estimation": "1H30M",
+        "title": "PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/0.5.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/0.5.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.3",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.3",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.3",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_to_categorical/sklearn_to_categorical/1.0.8.3",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0"
+            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_alternative_genes_pathwaymapper/pancancer_alternative_genes_pathwaymapper/0.1.9",
+            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_apply_weights/pancancer_apply_weights/0.1.9",
+            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_classifier/pancancer_classifier/0.1.9",
+            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_compare_within_models/pancancer_compare_within_models/0.1.9",
+            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_external_sample_status_prediction/pancancer_external_sample_status_prediction/0.1.9",
+            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_map_mutation_class/pancancer_map_mutation_class/0.1.9",
+            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_pathway_count_heatmaps/pancancer_pathway_count_heatmaps/0.1.9",
+            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_targene_cell_line_predictions/pancancer_targene_cell_line_predictions/0.1.9",
+            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_targene_pharmacology/pancancer_targene_pharmacology/0.1.9",
+            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_targene_summary_figures/pancancer_targene_summary_figures/0.1.9",
+            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_visualize_decisions/pancancer_visualize_decisions/0.1.9",
+            "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_within_disease_analysis/pancancer_within_disease_analysis/0.1.9"
         ],
         "topic_name": "statistics",
         "topic_name_human": "Statistics and machine learning",
@@ -252959,70 +260050,65 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "fruit_360",
+        "tutorial_name": "aberrant_pi3k_pathway_analysis",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/fruit_360/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/fruit_360/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/fruit_360/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/tutorial.json"
         },
-        "version": 8,
+        "version": 7,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 195,
-        "visitors": 1577765,
+        "visit_duration": 211,
+        "visitors": 678,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "name": "Kaivan Kamali"
-                    }
-                ],
-                "description": "Image classification with fruit 360 dataset",
+                "creators": [],
+                "description": "PanCancer Aberrant Pathway Activity Analysis: PI3K example",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntest_y_10.tsv\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntrain_y_10.tsv\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntrain_X_10.tsv\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntest_X_10.tsv\"]\n  4[label=\"Create a deep learning model architecture\"]\n  5[label=\"Advanced Cut\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Advanced Cut\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"Create deep learning model\"]\n  4 -> 7 [label=\"outfile\"]\n  8[label=\"To categorical\"]\n  6 -> 8 [label=\"output\"]\n  9[label=\"Deep learning training and evaluation\"]\n  7 -> 9 [label=\"outfile\"]\n  2 -> 9 [label=\"output\"]\n  8 -> 9 [label=\"outfile\"]\n  10[label=\"Model Prediction\"]\n  9 -> 10 [label=\"outfile_object\"]\n  9 -> 10 [label=\"outfile_weights\"]\n  3 -> 10 [label=\"output\"]\n  11[label=\"Machine Learning Visualization Extension\"]\n  10 -> 11 [label=\"outfile_predict\"]\n  5 -> 11 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\npancan_rnaseq_freeze.tsv\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\npancan_mutation_freeze.tsv\"]\n  10[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSE69822_pi3k_sign.txt\"]\n  11[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGSE69822_pi3k_trans.csv\"]\n  12[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGDSC_CCLE_common_mut_cnv_binary.tsv.gz\"]\n  13[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nccle_rnaseq_genes_rpkm_20180929_mod.tsv.gz\"]\n  14[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGDSC_EXP_CCLE_converted_name.tsv.gz\"]\n  15[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCCLE_MUT_CNA_AMP_DEL_binary_Revealer.tsv\"]\n  16[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncompounds_of_interest.txt\"]\n  17[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncosmic_cancer_classification.tsv\"]\n  18[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\npath_rtk_ras_pi3k_genes.txt\"]\n  19[label=\"PAPAA: PanCancer classifier\"]\n  17 -> 19 [label=\"output\"]\n  3 -> 19 [label=\"output\"]\n  2 -> 19 [label=\"output\"]\n  1 -> 19 [label=\"output\"]\n  4 -> 19 [label=\"output\"]\n  5 -> 19 [label=\"output\"]\n  0 -> 19 [label=\"output\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncopy_number_loss_status.tsv\"]\n  20[label=\"PAPAA: PanCancer within disease analysis\"]\n  17 -> 20 [label=\"output\"]\n  3 -> 20 [label=\"output\"]\n  2 -> 20 [label=\"output\"]\n  1 -> 20 [label=\"output\"]\n  4 -> 20 [label=\"output\"]\n  5 -> 20 [label=\"output\"]\n  0 -> 20 [label=\"output\"]\n  21[label=\"PAPAA: PanCancer apply weights\"]\n  17 -> 21 [label=\"output\"]\n  3 -> 21 [label=\"output\"]\n  2 -> 21 [label=\"output\"]\n  1 -> 21 [label=\"output\"]\n  4 -> 21 [label=\"output\"]\n  5 -> 21 [label=\"output\"]\n  19 -> 21 [label=\"classifier_coefficients\"]\n  19 -> 21 [label=\"classifier_summary\"]\n  0 -> 21 [label=\"output\"]\n  22[label=\"PAPAA: PanCancer external sample status prediction\"]\n  19 -> 22 [label=\"classifier_summary\"]\n  11 -> 22 [label=\"output\"]\n  19 -> 22 [label=\"classifier_coefficients\"]\n  10 -> 22 [label=\"output\"]\n  23[label=\"PAPAA: PanCancer compare within models\"]\n  19 -> 23 [label=\"classifier_coefficients\"]\n  19 -> 23 [label=\"classifier_summary\"]\n  20 -> 23 [label=\"classifier_coefficients\"]\n  20 -> 23 [label=\"classifier_summary\"]\n  24[label=\"PAPAA: PanCancer visualize decisions\"]\n  21 -> 24 [label=\"classifier_decisions\"]\n  25[label=\"PAPAA: PanCancer alternative genes pathwaymapper\"]\n  21 -> 25 [label=\"classifier_decisions\"]\n  3 -> 25 [label=\"output\"]\n  2 -> 25 [label=\"output\"]\n  1 -> 25 [label=\"output\"]\n  5 -> 25 [label=\"output\"]\n  18 -> 25 [label=\"output\"]\n  26[label=\"PAPAA: PanCancer map mutation class\"]\n  21 -> 26 [label=\"classifier_decisions\"]\n  3 -> 26 [label=\"output\"]\n  2 -> 26 [label=\"output\"]\n  6 -> 26 [label=\"output\"]\n  18 -> 26 [label=\"output\"]\n  27[label=\"PAPAA: PanCancer pathway count heatmaps\"]\n  25 -> 27 [label=\"all_gene_metric_ranks\"]\n  21 -> 27 [label=\"classifier_decisions\"]\n  17 -> 27 [label=\"output\"]\n  3 -> 27 [label=\"output\"]\n  2 -> 27 [label=\"output\"]\n  1 -> 27 [label=\"output\"]\n  4 -> 27 [label=\"output\"]\n  5 -> 27 [label=\"output\"]\n  18 -> 27 [label=\"output\"]\n  25 -> 27 [label=\"pathway_metrics_pathwaymapper\"]\n  0 -> 27 [label=\"output\"]\n  28[label=\"PAPAA: PanCancer targene summary figures\"]\n  25 -> 28 [label=\"all_gene_metric_ranks\"]\n  19 -> 28 [label=\"classifier_summary\"]\n  26 -> 28 [label=\"mutation_classification_scores\"]\n  19 -> 28 [label=\"classifier_coefficients\"]\n  27 -> 28 [label=\"path_events_per_sample\"]\n  19 -> 28 [label=\"summary_counts\"]\n  29[label=\"PAPAA: PanCancer targene cell line predictions\"]\n  28 -> 29 [label=\"amino_acid_mutation_scores\"]\n  7 -> 29 [label=\"output\"]\n  15 -> 29 [label=\"output\"]\n  13 -> 29 [label=\"output\"]\n  19 -> 29 [label=\"classifier_summary\"]\n  8 -> 29 [label=\"output\"]\n  9 -> 29 [label=\"output\"]\n  12 -> 29 [label=\"output\"]\n  14 -> 29 [label=\"output\"]\n  28 -> 29 [label=\"nucleotide_mutation_scores\"]\n  19 -> 29 [label=\"classifier_coefficients\"]\n  18 -> 29 [label=\"output\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncopy_number_gain_status.tsv\"]\n  30[label=\"PAPAA: PanCancer targene pharmacology\"]\n  16 -> 30 [label=\"output\"]\n  29 -> 30 [label=\"gdsc1_ccle_targene_pharmacology_predictions\"]\n  29 -> 30 [label=\"gdsc1_targene_pharmacology_predictions\"]\n  29 -> 30 [label=\"gdsc2_ccle_targene_pharmacology_predictions\"]\n  29 -> 30 [label=\"gdsc2_targene_pharmacology_predictions\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmutation_burden_freeze.tsv\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nsample_freeze.tsv\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmc3.v0.2.8.PUBLIC.maf\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCCLE_DepMap_18Q1_maf_20180207.txt\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ngdsc1_ccle_pharm_fitted_dose_data.txt\"]\n  9[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ngdsc2_ccle_pharm_fitted_dose_data.txt\"]\n}",
                 "history": [
                     {
-                        "hash": "e5dd4d5746166c3bdb191f35b22435d1fe9627cc",
-                        "message": "Fixed an error in WF. Must cut test label data to get labels only",
+                        "hash": "7ea290c2bf6caf772265aa2a77f2b3c2ed976239",
+                        "message": "aberrant_pi3k_activity_tutorial update-18",
                         "num": 5,
-                        "short_hash": "e5dd4d574",
-                        "unix": "1639248119"
+                        "short_hash": "7ea290c2b",
+                        "unix": "1608318040"
                     },
                     {
-                        "hash": "4b60e0407fb5348216da2c52c8bed4f7e0d8191c",
-                        "message": "Added Creator section to WF",
+                        "hash": "34bebb50ba04a773e3548ca5648714a73baffb35",
+                        "message": "reformat workflow and add tags and annotation",
                         "num": 4,
-                        "short_hash": "4b60e0407",
-                        "unix": "1638371876"
+                        "short_hash": "34bebb50b",
+                        "unix": "1608304565"
                     },
                     {
-                        "hash": "6dd9ffea125cd0c6858b425ac786eb37e1e64f67",
-                        "message": "Adde title and tag to WF",
+                        "hash": "b0a2a036f47e662fcc522d0275deaf6579abf15b",
+                        "message": "aberrant_pi3k_activity_tutorial update-17",
                         "num": 3,
-                        "short_hash": "6dd9ffea1",
-                        "unix": "1637350965"
+                        "short_hash": "b0a2a036f",
+                        "unix": "1608220697"
                     },
                     {
-                        "hash": "d6c5afc6958f3deff1ac8b11c466e8dd35c9b3e5",
-                        "message": "Wrote parts of fruit image classification tutorial.",
+                        "hash": "d49e2046f964c70efc6eddffdcdde0b424444d6c",
+                        "message": "pi3k_aberrant_activity_tutorial update-12",
                         "num": 2,
-                        "short_hash": "d6c5afc69",
-                        "unix": "1637285151"
+                        "short_hash": "d49e2046f",
+                        "unix": "1608048752"
                     },
                     {
-                        "hash": "7d52835fb825a71e893a71304557c62c183cd929",
-                        "message": "Added the tutorial directory. Revising copied files now.",
+                        "hash": "5eeb04b8888e1cd2216696b70312102ecab548c5",
+                        "message": "pi3k_aberrant activity tutorial edit-8",
                         "num": 1,
-                        "short_hash": "7d52835fb",
-                        "unix": "1637156335"
+                        "short_hash": "5eeb04b88",
+                        "unix": "1607726416"
                     }
                 ],
                 "inputs": [
@@ -253035,34 +260121,22 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "test_y_10.tsv"
+                                "name": "pancan_rnaseq_freeze.tsv"
                             }
                         ],
-                        "label": "test_y_10.tsv",
+                        "label": "pancan_rnaseq_freeze.tsv",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 274,
-                            "height": 81,
-                            "left": 393,
-                            "right": 593,
-                            "top": 193,
-                            "width": 200,
-                            "x": 393,
-                            "y": 193
+                            "left": 155.9921875,
+                            "top": 100
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "af3547d0-573b-429a-8aa9-c653604221c1",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "24c728c7-3029-4732-ab49-fe4d3f8fb1b3"
-                            }
-                        ]
+                        "uuid": "a5f07814-0162-40f0-bc9f-33c4aae981bd",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
@@ -253073,778 +260147,509 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "train_y_10.tsv"
+                                "name": "pancan_mutation_freeze.tsv"
                             }
                         ],
-                        "label": "train_y_10.tsv",
+                        "label": "pancan_mutation_freeze.tsv",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 394,
-                            "height": 81,
-                            "left": 393,
-                            "right": 593,
-                            "top": 313,
-                            "width": 200,
-                            "x": 393,
-                            "y": 313
+                            "left": 155.9921875,
+                            "top": 154.5
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "a43671c9-f8b4-4308-a223-e940be9ef115",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "8da8be9c-8ed0-44ae-80af-5f3cc69a95e2"
-                            }
-                        ]
+                        "uuid": "085443c7-55ab-486a-9231-cbd7bf0f9f13",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 10,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "train_X_10.tsv"
+                                "name": "GSE69822_pi3k_sign.txt"
                             }
                         ],
-                        "label": "train_X_10.tsv",
+                        "label": "GSE69822_pi3k_sign.txt",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 514,
-                            "height": 81,
-                            "left": 393,
-                            "right": 593,
-                            "top": 433,
-                            "width": 200,
-                            "x": 393,
-                            "y": 433
+                            "left": 155.9921875,
+                            "top": 665
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "d52183d4-71b5-4750-804a-9c8bb31087c1",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "a65e5725-c11d-4eb4-b163-925399acbb40"
-                            }
-                        ]
+                        "uuid": "dc7daff3-f271-486a-873c-562122ae633f",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 11,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "test_X_10.tsv"
+                                "name": "GSE69822_pi3k_trans.csv"
                             }
                         ],
-                        "label": "test_X_10.tsv",
+                        "label": "GSE69822_pi3k_trans.csv",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 634,
-                            "height": 81,
-                            "left": 393,
-                            "right": 593,
-                            "top": 553,
-                            "width": 200,
-                            "x": 393,
-                            "y": 553
+                            "left": 155.9921875,
+                            "top": 719.5
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "21548965-7cd1-453c-8fab-039f51f2320a",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "fd40d525-f72b-4121-bafc-6e380f6128bc"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ntest_y_10.tsv\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ntrain_y_10.tsv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ntrain_X_10.tsv\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\ntest_X_10.tsv\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Create a deep learning model architecture\"];\n  5[\"Advanced Cut\"];\n  0 -->|output| 5;\n  6[\"Advanced Cut\"];\n  1 -->|output| 6;\n  7[\"Create deep learning model\"];\n  4 -->|outfile| 7;\n  8[\"To categorical\"];\n  6 -->|output| 8;\n  9[\"Deep learning training and evaluation\"];\n  7 -->|outfile| 9;\n  2 -->|output| 9;\n  8 -->|outfile| 9;\n  10[\"Model Prediction\"];\n  9 -->|outfile_object| 10;\n  9 -->|outfile_weights| 10;\n  3 -->|output| 10;\n  11[\"Machine Learning Visualization Extension\"];\n  10 -->|outfile_predict| 11;\n  5 -->|output| 11;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "fruit_360",
-                "outputs": [
+                        "uuid": "eb46a60a-e122-4d04-817a-a77518b35495",
+                        "workflow_outputs": []
+                    },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 12,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "test_y_10.tsv"
+                                "name": "GDSC_CCLE_common_mut_cnv_binary.tsv.gz"
                             }
                         ],
-                        "label": "test_y_10.tsv",
+                        "label": "GDSC_CCLE_common_mut_cnv_binary.tsv.gz",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 274,
-                            "height": 81,
-                            "left": 393,
-                            "right": 593,
-                            "top": 193,
-                            "width": 200,
-                            "x": 393,
-                            "y": 193
+                            "left": 155.9921875,
+                            "top": 774
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "af3547d0-573b-429a-8aa9-c653604221c1",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "24c728c7-3029-4732-ab49-fe4d3f8fb1b3"
-                            }
-                        ]
+                        "uuid": "255c456d-686d-4509-b420-1ba0831a9300",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 13,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "train_y_10.tsv"
+                                "name": "ccle_rnaseq_genes_rpkm_20180929_mod.tsv.gz"
                             }
                         ],
-                        "label": "train_y_10.tsv",
+                        "label": "ccle_rnaseq_genes_rpkm_20180929_mod.tsv.gz",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 394,
-                            "height": 81,
-                            "left": 393,
-                            "right": 593,
-                            "top": 313,
-                            "width": 200,
-                            "x": 393,
-                            "y": 313
+                            "left": 155.9921875,
+                            "top": 838.5
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "a43671c9-f8b4-4308-a223-e940be9ef115",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "8da8be9c-8ed0-44ae-80af-5f3cc69a95e2"
-                            }
-                        ]
+                        "uuid": "b4fae5c5-59ef-4c15-b796-8934c3988ace",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 14,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "train_X_10.tsv"
+                                "name": "GDSC_EXP_CCLE_converted_name.tsv.gz"
                             }
                         ],
-                        "label": "train_X_10.tsv",
+                        "label": "GDSC_EXP_CCLE_converted_name.tsv.gz",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 514,
-                            "height": 81,
-                            "left": 393,
-                            "right": 593,
-                            "top": 433,
-                            "width": 200,
-                            "x": 393,
-                            "y": 433
+                            "left": 155.9921875,
+                            "top": 903
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "d52183d4-71b5-4750-804a-9c8bb31087c1",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "a65e5725-c11d-4eb4-b163-925399acbb40"
-                            }
-                        ]
+                        "uuid": "a20c0bf6-07ee-47f3-9170-4fa80c792e70",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 15,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "test_X_10.tsv"
+                                "name": "CCLE_MUT_CNA_AMP_DEL_binary_Revealer.tsv"
                             }
                         ],
-                        "label": "test_X_10.tsv",
+                        "label": "CCLE_MUT_CNA_AMP_DEL_binary_Revealer.tsv",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 634,
-                            "height": 81,
-                            "left": 393,
-                            "right": 593,
-                            "top": 553,
-                            "width": 200,
-                            "x": 393,
-                            "y": 553
+                            "left": 155.9921875,
+                            "top": 967.5
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "21548965-7cd1-453c-8fab-039f51f2320a",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "fd40d525-f72b-4121-bafc-6e380f6128bc"
-                            }
-                        ]
+                        "uuid": "fb05135f-4178-44e4-bac6-05f00976098b",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/0.5.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 4,
+                        "id": 16,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "Create a deep learning model architecture",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "outfile",
-                                "type": "json"
+                                "description": "",
+                                "name": "compounds_of_interest.txt"
                             }
                         ],
+                        "label": "compounds_of_interest.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 794,
-                            "height": 121,
-                            "left": 393,
-                            "right": 593,
-                            "top": 673,
-                            "width": 200,
-                            "x": 393,
-                            "y": 673
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/0.5.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2b8d85927742",
-                            "name": "keras_model_config",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 155.9921875,
+                            "top": 1032
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"model_selection\": {\"model_type\": \"sequential\", \"__current_case__\": 0, \"input_shape\": \"(30000, )\", \"layers\": [{\"__index__\": 0, \"layer_selection\": {\"layer_type\": \"Reshape\", \"__current_case__\": 4, \"target_shape\": \"(100, 100, 3)\"}}, {\"__index__\": 1, \"layer_selection\": {\"layer_type\": \"Conv2D\", \"__current_case__\": 13, \"filters\": \"16\", \"kernel_size\": \"5\", \"activation\": \"relu\", \"kwargs\": \"input_shape=(100, 100, 3)\"}}, {\"__index__\": 2, \"layer_selection\": {\"layer_type\": \"MaxPooling2D\", \"__current_case__\": 30, \"pool_size\": \"(2, 2)\", \"strides\": \"\", \"kwargs\": \"\"}}, {\"__index__\": 3, \"layer_selection\": {\"layer_type\": \"Conv2D\", \"__current_case__\": 13, \"filters\": \"32\", \"kernel_size\": \"5\", \"activation\": \"relu\", \"kwargs\": \"\"}}, {\"__index__\": 4, \"layer_selection\": {\"layer_type\": \"MaxPooling2D\", \"__current_case__\": 30, \"pool_size\": \"(2, 2)\", \"strides\": \"\", \"kwargs\": \"\"}}, {\"__index__\": 5, \"layer_selection\": {\"layer_type\": \"Conv2D\", \"__current_case__\": 13, \"filters\": \"64\", \"kernel_size\": \"5\", \"activation\": \"relu\", \"kwargs\": \"\"}}, {\"__index__\": 6, \"layer_selection\": {\"layer_type\": \"MaxPooling2D\", \"__current_case__\": 30, \"pool_size\": \"(2, 2)\", \"strides\": \"\", \"kwargs\": \"\"}}, {\"__index__\": 7, \"layer_selection\": {\"layer_type\": \"Flatten\", \"__current_case__\": 3, \"data_format\": \"channels_last\"}}, {\"__index__\": 8, \"layer_selection\": {\"layer_type\": \"Dense\", \"__current_case__\": 0, \"units\": \"256\", \"activation\": \"relu\", \"kwargs\": \"\"}}, {\"__index__\": 9, \"layer_selection\": {\"layer_type\": \"Dense\", \"__current_case__\": 0, \"units\": \"10\", \"activation\": \"softmax\", \"kwargs\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "e88ed344-23fb-4122-9af5-d8a75df0f049",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "061ae4fe-aec2-42f7-ac20-cd19cd57c7dc"
-                            }
-                        ]
+                        "type": "data_input",
+                        "uuid": "9a2ce838-ed30-40c9-b7c8-1863ccbc020e",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "input": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
+                        "id": 17,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Advanced Cut",
-                                "name": "input"
+                                "description": "",
+                                "name": "cosmic_cancer_classification.tsv"
                             }
                         ],
-                        "label": null,
-                        "name": "Advanced Cut",
-                        "outputs": [
+                        "label": "cosmic_cancer_classification.tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 155.9921875,
+                            "top": 1086.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "4f425257-9b54-48c7-828c-72812aa6e8fa",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 18,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "path_rtk_ras_pi3k_genes.txt"
                             }
                         ],
+                        "label": "path_rtk_ras_pi3k_genes.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 213,
-                            "height": 112,
-                            "left": 972,
-                            "right": 1172,
-                            "top": 101,
-                            "width": 200,
-                            "x": 972,
-                            "y": 101
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f46f0e4f75c4",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 155.9921875,
+                            "top": 1151
                         },
-                        "tool_state": "{\"complement\": \"\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"list\": \"3\\n\"}, \"delimiter\": \"\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "c9066525-d9fb-4e8d-976c-0f9a3b030576",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "490b3818-84b5-4370-9b1f-34af163e1f9a"
-                            }
-                        ]
+                        "type": "data_input",
+                        "uuid": "87edb72c-ff8c-4b05-902d-e31a6bdcefc8",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "input": {
-                                "id": 1,
-                                "output_name": "output"
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "copy_number_loss_status.tsv"
                             }
+                        ],
+                        "label": "copy_number_loss_status.tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 155.9921875,
+                            "top": 209
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Advanced Cut",
-                        "outputs": [
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "e1e7ce2e-0dee-4cc7-bed0-428b1ef6045c",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "copy_number_gain_status.tsv"
                             }
                         ],
+                        "label": "copy_number_gain_status.tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 425,
-                            "height": 112,
-                            "left": 613,
-                            "right": 813,
-                            "top": 313,
-                            "width": 200,
-                            "x": 613,
-                            "y": 313
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f46f0e4f75c4",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 155.9921875,
+                            "top": 263.5
                         },
-                        "tool_state": "{\"__input_ext\": \"tsv\", \"__workflow_invocation_uuid__\": \"c39c89a6466311ec8344005056ba2773\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"complement\": \"\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"list\": [\"3\"]}, \"delimiter\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "9d569bfd-dfc6-4a0a-83ff-751385fb1881",
-                        "workflow_outputs": [
+                        "type": "data_input",
+                        "uuid": "237f24d7-f089-47db-9bdb-89b804d346cb",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "388b3201-c37d-412b-b610-3d52983c0365"
+                                "description": "",
+                                "name": "mutation_burden_freeze.tsv"
                             }
-                        ]
+                        ],
+                        "label": "mutation_burden_freeze.tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 155.9921875,
+                            "top": 318
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "297e1125-93e2-4dd6-ac9a-4728fef8862a",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/0.5.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "mode_selection|infile_json": {
-                                "id": 4,
-                                "output_name": "outfile"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Create deep learning model",
-                        "outputs": [
+                        "id": 5,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "outfile",
-                                "type": "zip"
+                                "description": "",
+                                "name": "sample_freeze.tsv"
                             }
                         ],
+                        "label": "sample_freeze.tsv",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 605,
-                            "height": 172,
-                            "left": 613,
-                            "right": 813,
-                            "top": 433,
-                            "width": 200,
-                            "x": 613,
-                            "y": 433
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/0.5.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "5b35833076f0",
-                            "name": "keras_model_builder",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 155.9921875,
+                            "top": 372.5
                         },
-                        "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"mode_selection\": {\"mode_type\": \"train_model\", \"__current_case__\": 0, \"infile_json\": {\"__class__\": \"ConnectedValue\"}, \"learning_type\": \"KerasGClassifier\", \"compile_params\": {\"loss\": \"categorical_crossentropy\", \"optimizer_selection\": {\"optimizer_type\": \"Adam\", \"__current_case__\": 4, \"optimizer_options\": {\"lr\": \"0.001\", \"decay\": \"0.0\", \"beta_1\": \"0.9\", \"beta_2\": \"0.999\", \"amsgrad\": \"false\"}}, \"metrics\": [\"acc\"]}, \"fit_params\": {\"epochs\": \"40\", \"batch_size\": \"50\", \"steps_per_epoch\": null, \"validation_steps\": null, \"callbacks\": [{\"__index__\": 0, \"callback_selection\": {\"callback_type\": \"None\", \"__current_case__\": 0}}]}, \"random_seed\": null, \"get_params\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "83b42cfe-b173-421f-999e-341f2891faa0",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "ea147ba5-e226-4529-bce2-3a6eadea74f0"
-                            }
-                        ]
+                        "type": "data_input",
+                        "uuid": "0cbc8b0f-1933-46a9-8645-2ddf805198cd",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_to_categorical/sklearn_to_categorical/1.0.8.3",
+                        "content_id": null,
                         "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "infile": {
-                                "id": 6,
-                                "output_name": "output"
-                            }
-                        },
+                        "id": 6,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool To categorical",
-                                "name": "infile"
-                            }
-                        ],
-                        "label": null,
-                        "name": "To categorical",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "mc3.v0.2.8.PUBLIC.maf"
                             }
                         ],
+                        "label": "mc3.v0.2.8.PUBLIC.maf",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 486,
-                            "height": 112,
-                            "left": 838,
-                            "right": 1038,
-                            "top": 374,
-                            "width": 200,
-                            "x": 838,
-                            "y": 374
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_to_categorical/sklearn_to_categorical/1.0.8.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "612ca26c197d",
-                            "name": "sklearn_to_categorical",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 155.9921875,
+                            "top": 417
                         },
-                        "tool_state": "{\"header0\": \"true\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"num_classes\": \"10\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "2daa2610-efc3-4e1e-9da3-532dfb960d62",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "9e1b61c9-cb6b-447c-aba7-376b69e38d6d"
-                            }
-                        ]
+                        "type": "data_input",
+                        "uuid": "9c34e447-97a8-4f2d-b485-c4ca627f4021",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.3",
+                        "content_id": null,
                         "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "experiment_schemes|infile_estimator": {
-                                "id": 7,
-                                "output_name": "outfile"
-                            },
-                            "input_options|infile1": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "input_options|infile2": {
-                                "id": 8,
-                                "output_name": "outfile"
-                            }
-                        },
+                        "id": 7,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Deep learning training and evaluation",
-                                "name": "experiment_schemes"
-                            },
-                            {
-                                "description": "runtime parameter for tool Deep learning training and evaluation",
-                                "name": "input_options"
-                            },
-                            {
-                                "description": "runtime parameter for tool Deep learning training and evaluation",
-                                "name": "input_options"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Deep learning training and evaluation",
-                        "outputs": [
-                            {
-                                "name": "outfile_result",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "outfile_object",
-                                "type": "zip"
-                            },
-                            {
-                                "name": "outfile_weights",
-                                "type": "h5"
+                                "description": "",
+                                "name": "CCLE_DepMap_18Q1_maf_20180207.txt"
                             }
                         ],
+                        "label": "CCLE_DepMap_18Q1_maf_20180207.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 945,
-                            "height": 462,
-                            "left": 1049,
-                            "right": 1249,
-                            "top": 483,
-                            "width": 200,
-                            "x": 1049,
-                            "y": 483
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "470aed90aa41",
-                            "name": "keras_train_and_eval",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 155.9921875,
+                            "top": 471.5
                         },
-                        "tool_state": "{\"experiment_schemes\": {\"selected_exp_scheme\": \"train_val\", \"__current_case__\": 0, \"infile_estimator\": {\"__class__\": \"RuntimeValue\"}, \"hyperparams_swapping\": {\"infile_params\": {\"__class__\": \"RuntimeValue\"}, \"param_set\": [{\"__index__\": 0, \"sp_name\": null, \"sp_value\": \"\"}]}, \"test_split\": {\"split_algos\": {\"shuffle\": \"simple\", \"__current_case__\": 1, \"test_size\": \"0.2\", \"random_state\": null}}, \"metrics\": {\"scoring\": {\"primary_scoring\": \"default\", \"__current_case__\": 0}}}, \"input_options\": {\"selected_input\": \"tabular\", \"__current_case__\": 0, \"infile1\": {\"__class__\": \"RuntimeValue\"}, \"header1\": \"false\", \"column_selector_options_1\": {\"selected_column_selector_option\": \"all_columns\", \"__current_case__\": 4}, \"infile2\": {\"__class__\": \"RuntimeValue\"}, \"header2\": \"false\", \"column_selector_options_2\": {\"selected_column_selector_option2\": \"all_columns\", \"__current_case__\": 4}}, \"save\": [\"save_estimator\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "caaf7c3c-b170-4cd7-b894-a4eecb898844",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile_result",
-                                "uuid": "2eb2e1bc-217d-4e93-a987-312934f9fc19"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "outfile_object",
-                                "uuid": "fb9d855c-754d-4d32-8e6a-182664fa1f92"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "outfile_weights",
-                                "uuid": "29e19193-b9b7-4ccc-b312-62409c2a7dcc"
-                            }
-                        ]
+                        "type": "data_input",
+                        "uuid": "e788af12-1a46-4b65-b714-6e4cea14b047",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.3",
+                        "content_id": null,
                         "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "infile_estimator": {
-                                "id": 9,
-                                "output_name": "outfile_object"
-                            },
-                            "infile_weights": {
-                                "id": 9,
-                                "output_name": "outfile_weights"
-                            },
-                            "input_options|infile1": {
-                                "id": 3,
-                                "output_name": "output"
-                            }
-                        },
+                        "id": 8,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Model Prediction",
-                                "name": "infile_estimator"
-                            },
-                            {
-                                "description": "runtime parameter for tool Model Prediction",
-                                "name": "infile_weights"
-                            },
-                            {
-                                "description": "runtime parameter for tool Model Prediction",
-                                "name": "input_options"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Model Prediction",
-                        "outputs": [
-                            {
-                                "name": "outfile_predict",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "gdsc1_ccle_pharm_fitted_dose_data.txt"
                             }
                         ],
+                        "label": "gdsc1_ccle_pharm_fitted_dose_data.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 877,
-                            "height": 252,
-                            "left": 1347,
-                            "right": 1547,
-                            "top": 625,
-                            "width": 200,
-                            "x": 1347,
-                            "y": 625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "1e088aa741eb",
-                            "name": "model_prediction",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 155.9921875,
+                            "top": 536
                         },
-                        "tool_state": "{\"infile_estimator\": {\"__class__\": \"RuntimeValue\"}, \"infile_weights\": {\"__class__\": \"RuntimeValue\"}, \"input_options\": {\"selected_input\": \"tabular\", \"__current_case__\": 0, \"infile1\": {\"__class__\": \"RuntimeValue\"}, \"header1\": \"false\", \"column_selector_options_1\": {\"selected_column_selector_option\": \"all_columns\", \"__current_case__\": 4}}, \"method\": \"predict\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "91789cf1-96a7-4e81-a989-4c60bed386b8",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile_predict",
-                                "uuid": "82004f35-b05d-4799-a082-1291e103c036"
-                            }
-                        ]
+                        "type": "data_input",
+                        "uuid": "f8953224-c89d-4980-8620-2f85e964bdea",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.3",
+                        "content_id": null,
                         "errors": null,
-                        "id": 11,
-                        "input_connections": {
-                            "plotting_selection|infile_predicted": {
-                                "id": 10,
-                                "output_name": "outfile_predict"
-                            },
-                            "plotting_selection|infile_true": {
-                                "id": 5,
-                                "output_name": "output"
-                            }
-                        },
+                        "id": 9,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Machine Learning Visualization Extension",
-                                "name": "plotting_selection"
-                            },
-                            {
-                                "description": "runtime parameter for tool Machine Learning Visualization Extension",
-                                "name": "plotting_selection"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Machine Learning Visualization Extension",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "html"
+                                "description": "",
+                                "name": "gdsc2_ccle_pharm_fitted_dose_data.txt"
                             }
                         ],
+                        "label": "gdsc2_ccle_pharm_fitted_dose_data.txt",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 567,
-                            "height": 242,
-                            "left": 1574,
-                            "right": 1774,
-                            "top": 325,
-                            "width": 200,
-                            "x": 1574,
-                            "y": 325
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.3",
-                        "tool_shed_repository": {
-                            "changeset_revision": "e88c782a127d",
-                            "name": "ml_visualization_ex",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 155.9921875,
+                            "top": 600.5
                         },
-                        "tool_state": "{\"plotting_selection\": {\"plot_type\": \"classification_confusion_matrix\", \"__current_case__\": 6, \"infile_true\": {\"__class__\": \"RuntimeValue\"}, \"header_true\": \"true\", \"column_selector_options_true\": {\"selected_column_selector_option\": \"all_columns\", \"__current_case__\": 4}, \"infile_predicted\": {\"__class__\": \"RuntimeValue\"}, \"header_predicted\": \"true\", \"title\": \"Confusion matrix between true and predicted labels\", \"plot_format\": \"png\", \"plot_color\": \"Greens\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "tool",
-                        "uuid": "429e06e9-c9d0-447b-a9ab-4b36869beaf8",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "73af0f64-43f7-4b5e-815a-1c0326875a3a"
-                            }
-                        ]
+                        "type": "data_input",
+                        "uuid": "562ae27c-b15d-4732-89ab-82d5b6135f88",
+                        "workflow_outputs": []
                     }
                 ],
-                "parent_id": "statistics/fruit_360",
-                "path": "topics/statistics/tutorials/fruit_360/workflows/fruit_360.ga",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\npancan_rnaseq_freeze.tsv\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\npancan_mutation_freeze.tsv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"\u2139\ufe0f Input Dataset\\nGSE69822_pi3k_sign.txt\"];\n  style 10 stroke:#2c3143,stroke-width:4px;\n  11[\"\u2139\ufe0f Input Dataset\\nGSE69822_pi3k_trans.csv\"];\n  style 11 stroke:#2c3143,stroke-width:4px;\n  12[\"\u2139\ufe0f Input Dataset\\nGDSC_CCLE_common_mut_cnv_binary.tsv.gz\"];\n  style 12 stroke:#2c3143,stroke-width:4px;\n  13[\"\u2139\ufe0f Input Dataset\\nccle_rnaseq_genes_rpkm_20180929_mod.tsv.gz\"];\n  style 13 stroke:#2c3143,stroke-width:4px;\n  14[\"\u2139\ufe0f Input Dataset\\nGDSC_EXP_CCLE_converted_name.tsv.gz\"];\n  style 14 stroke:#2c3143,stroke-width:4px;\n  15[\"\u2139\ufe0f Input Dataset\\nCCLE_MUT_CNA_AMP_DEL_binary_Revealer.tsv\"];\n  style 15 stroke:#2c3143,stroke-width:4px;\n  16[\"\u2139\ufe0f Input Dataset\\ncompounds_of_interest.txt\"];\n  style 16 stroke:#2c3143,stroke-width:4px;\n  17[\"\u2139\ufe0f Input Dataset\\ncosmic_cancer_classification.tsv\"];\n  style 17 stroke:#2c3143,stroke-width:4px;\n  18[\"\u2139\ufe0f Input Dataset\\npath_rtk_ras_pi3k_genes.txt\"];\n  style 18 stroke:#2c3143,stroke-width:4px;\n  19[\"PAPAA: PanCancer classifier\"];\n  17 -->|output| 19;\n  3 -->|output| 19;\n  2 -->|output| 19;\n  1 -->|output| 19;\n  4 -->|output| 19;\n  5 -->|output| 19;\n  0 -->|output| 19;\n  2[\"\u2139\ufe0f Input Dataset\\ncopy_number_loss_status.tsv\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  20[\"PAPAA: PanCancer within disease analysis\"];\n  17 -->|output| 20;\n  3 -->|output| 20;\n  2 -->|output| 20;\n  1 -->|output| 20;\n  4 -->|output| 20;\n  5 -->|output| 20;\n  0 -->|output| 20;\n  21[\"PAPAA: PanCancer apply weights\"];\n  17 -->|output| 21;\n  3 -->|output| 21;\n  2 -->|output| 21;\n  1 -->|output| 21;\n  4 -->|output| 21;\n  5 -->|output| 21;\n  19 -->|classifier_coefficients| 21;\n  19 -->|classifier_summary| 21;\n  0 -->|output| 21;\n  22[\"PAPAA: PanCancer external sample status prediction\"];\n  19 -->|classifier_summary| 22;\n  11 -->|output| 22;\n  19 -->|classifier_coefficients| 22;\n  10 -->|output| 22;\n  23[\"PAPAA: PanCancer compare within models\"];\n  19 -->|classifier_coefficients| 23;\n  19 -->|classifier_summary| 23;\n  20 -->|classifier_coefficients| 23;\n  20 -->|classifier_summary| 23;\n  24[\"PAPAA: PanCancer visualize decisions\"];\n  21 -->|classifier_decisions| 24;\n  25[\"PAPAA: PanCancer alternative genes pathwaymapper\"];\n  21 -->|classifier_decisions| 25;\n  3 -->|output| 25;\n  2 -->|output| 25;\n  1 -->|output| 25;\n  5 -->|output| 25;\n  18 -->|output| 25;\n  26[\"PAPAA: PanCancer map mutation class\"];\n  21 -->|classifier_decisions| 26;\n  3 -->|output| 26;\n  2 -->|output| 26;\n  6 -->|output| 26;\n  18 -->|output| 26;\n  27[\"PAPAA: PanCancer pathway count heatmaps\"];\n  25 -->|all_gene_metric_ranks| 27;\n  21 -->|classifier_decisions| 27;\n  17 -->|output| 27;\n  3 -->|output| 27;\n  2 -->|output| 27;\n  1 -->|output| 27;\n  4 -->|output| 27;\n  5 -->|output| 27;\n  18 -->|output| 27;\n  25 -->|pathway_metrics_pathwaymapper| 27;\n  0 -->|output| 27;\n  28[\"PAPAA: PanCancer targene summary figures\"];\n  25 -->|all_gene_metric_ranks| 28;\n  19 -->|classifier_summary| 28;\n  26 -->|mutation_classification_scores| 28;\n  19 -->|classifier_coefficients| 28;\n  27 -->|path_events_per_sample| 28;\n  19 -->|summary_counts| 28;\n  29[\"PAPAA: PanCancer targene cell line predictions\"];\n  28 -->|amino_acid_mutation_scores| 29;\n  7 -->|output| 29;\n  15 -->|output| 29;\n  13 -->|output| 29;\n  19 -->|classifier_summary| 29;\n  8 -->|output| 29;\n  9 -->|output| 29;\n  12 -->|output| 29;\n  14 -->|output| 29;\n  28 -->|nucleotide_mutation_scores| 29;\n  19 -->|classifier_coefficients| 29;\n  18 -->|output| 29;\n  3[\"\u2139\ufe0f Input Dataset\\ncopy_number_gain_status.tsv\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  30[\"PAPAA: PanCancer targene pharmacology\"];\n  16 -->|output| 30;\n  29 -->|gdsc1_ccle_targene_pharmacology_predictions| 30;\n  29 -->|gdsc1_targene_pharmacology_predictions| 30;\n  29 -->|gdsc2_ccle_targene_pharmacology_predictions| 30;\n  29 -->|gdsc2_targene_pharmacology_predictions| 30;\n  4[\"\u2139\ufe0f Input Dataset\\nmutation_burden_freeze.tsv\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nsample_freeze.tsv\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nmc3.v0.2.8.PUBLIC.maf\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nCCLE_DepMap_18Q1_maf_20180207.txt\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\ngdsc1_ccle_pharm_fitted_dose_data.txt\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"\u2139\ufe0f Input Dataset\\ngdsc2_ccle_pharm_fitted_dose_data.txt\"];\n  style 9 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "papaa@0.1.9_PI3K_OG_model_tutorial",
+                "outputs": [],
+                "parent_id": "statistics/aberrant_pi3k_pathway_analysis",
+                "path": "topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/workflows/main_workflow.ga",
                 "tags": [
-                    "statistics"
+                    "statistics",
+                    "classification",
+                    "ml",
+                    "cancer"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "fruit_360",
+                "title": "papaa@0.1.9_PI3K_OG_model_tutorial",
                 "topic_id": "statistics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-fruit_360/versions/fruit-360",
-                "tutorial_id": "fruit_360",
-                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/fruit_360/workflows/fruit_360.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/fruit_360/workflows/fruit_360.html",
-                "version": 2,
-                "wfid": "statistics-fruit_360",
-                "wfname": "fruit-360",
-                "workflow": "fruit_360.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-aberrant_pi3k_pathway_analysis/versions/main-workflow",
+                "tutorial_id": "aberrant_pi3k_pathway_analysis",
+                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/aberrant_pi3k_pathway_analysis/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "statistics-aberrant_pi3k_pathway_analysis",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/0.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/0.5.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.3",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.3",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.3",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_to_categorical/sklearn_to_categorical/1.0.8.3",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0"
+                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_alternative_genes_pathwaymapper/pancancer_alternative_genes_pathwaymapper/0.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_apply_weights/pancancer_apply_weights/0.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_classifier/pancancer_classifier/0.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_compare_within_models/pancancer_compare_within_models/0.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_external_sample_status_prediction/pancancer_external_sample_status_prediction/0.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_map_mutation_class/pancancer_map_mutation_class/0.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_pathway_count_heatmaps/pancancer_pathway_count_heatmaps/0.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_targene_cell_line_predictions/pancancer_targene_cell_line_predictions/0.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_targene_pharmacology/pancancer_targene_pharmacology/0.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_targene_summary_figures/pancancer_targene_summary_figures/0.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_visualize_decisions/pancancer_visualize_decisions/0.1.9",
+                    "toolshed.g2.bx.psu.edu/repos/vijay/pancancer_within_disease_analysis/pancancer_within_disease_analysis/0.1.9"
                 ],
-                "workflowhub_id": "1322"
+                "workflowhub_id": "1284"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/5702887"
+        "zenodo_link": "https://zenodo.org/record/4306639"
     },
     {
         "admin_install": {
@@ -253853,62 +260658,101 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "keras_model_builder",
+                    "name": "plotly_ml_performance_plots",
                     "owner": "bgruening",
-                    "revisions": "66d7efc06000",
+                    "revisions": "f234e2e59d76",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sklearn_build_pipeline",
+                    "owner": "bgruening",
+                    "revisions": "4c4ec859c31a",
                     "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "keras_model_config",
+                    "name": "sklearn_ensemble",
                     "owner": "bgruening",
-                    "revisions": "f22a9297440f",
+                    "revisions": "060ca94ac049",
                     "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "keras_train_and_eval",
+                    "name": "sklearn_generalized_linear",
                     "owner": "bgruening",
-                    "revisions": "2af1346e68c9",
+                    "revisions": "d4808d5b83da",
                     "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ml_visualization_ex",
+                    "name": "sklearn_nn_classifier",
                     "owner": "bgruening",
-                    "revisions": "8334dc98c48e",
+                    "revisions": "8b1b2b91f8d0",
                     "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "model_prediction",
+                    "name": "sklearn_searchcv",
                     "owner": "bgruening",
-                    "revisions": "25b46af53232",
+                    "revisions": "7626ea9c2e1b",
                     "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sklearn_to_categorical",
+                    "name": "sklearn_svm_classifier",
                     "owner": "bgruening",
-                    "revisions": "61634a87efc7",
+                    "revisions": "80852884053f",
                     "tool_panel_section_label": "Machine Learning",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: keras_model_builder\n  owner: bgruening\n  revisions: 66d7efc06000\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_model_config\n  owner: bgruening\n  revisions: f22a9297440f\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: keras_train_and_eval\n  owner: bgruening\n  revisions: 2af1346e68c9\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ml_visualization_ex\n  owner: bgruening\n  revisions: 8334dc98c48e\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: model_prediction\n  owner: bgruening\n  revisions: 25b46af53232\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_to_categorical\n  owner: bgruening\n  revisions: 61634a87efc7\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/CNN/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: plotly_ml_performance_plots\n  owner: bgruening\n  revisions: f234e2e59d76\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_build_pipeline\n  owner: bgruening\n  revisions: 4c4ec859c31a\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_ensemble\n  owner: bgruening\n  revisions: 060ca94ac049\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_generalized_linear\n  owner: bgruening\n  revisions: d4808d5b83da\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_nn_classifier\n  owner: bgruening\n  revisions: 8b1b2b91f8d0\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_searchcv\n  owner: bgruening\n  revisions: 7626ea9c2e1b\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sklearn_svm_classifier\n  owner: bgruening\n  revisions: 80852884053f\n  tool_panel_section_label: Machine Learning\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/classification_machinelearning/tutorial.json",
         "contributors": [
             {
-                "email": "kxk302@gmail.com",
-                "id": "kxk302",
-                "joined": "2021-02",
-                "name": "Kaivan Kamali",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kxk302/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/kxk302.json"
+                "email": "khanteymoori@gmail.com",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "khanteymoori",
+                "joined": "2019-07",
+                "name": "Alireza Khanteymoori",
+                "orcid": "0000-0001-6811-9196",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/khanteymoori/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/khanteymoori.json"
+            },
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "eurosciencegateway",
+                    "elixir-europe"
+                ],
+                "elixir_node": "de",
+                "email": "anup.rulez@gmail.com",
+                "id": "anuprulez",
+                "joined": "2018-08",
+                "name": "Anup Kumar",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/anuprulez/",
+                "twitter": "musafirtweetsz",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/anuprulez.json"
+            },
+            {
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "simonbray",
+                "joined": "2019-05",
+                "name": "Simon Bray",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/simonbray/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/simonbray.json"
             }
         ],
-        "dir": "topics/statistics/tutorials/CNN",
+        "dir": "topics/statistics/tutorials/classification_machinelearning",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -253919,64 +260763,76 @@
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "statistics/CNN",
+        "id": "statistics/classification_machinelearning",
         "inexact_supported_servers": [
-            "UseGalaxy.cz"
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.no"
         ],
         "js_requirements": {
-            "mathjax": 1168,
+            "mathjax": null,
             "mermaid": false
         },
+        "key_points": [
+            "Classification is a supervised approach in machine learning.",
+            "For classification tasks, data is divided into training and test sets.",
+            "Using classification, the samples are learned using the training set and predicted using the test set.",
+            "For each classification algorithm, it parameters should be optimised based on the dataset.",
+            "Machine learning algorithms can be applied to chemical datasets to predict important properties."
+        ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-09",
+        "mod_date": "2024-09-19",
         "objectives": [
-            "Understand the inspiration behind CNN and learn the CNN architecture",
-            "Learn the convolution operation and its parameters",
-            "Learn how to create a CNN using Galaxy's deep learning tools",
-            "Solve an image classification problem on MNIST digit classification dataset using CNN in Galaxy"
+            "Learn classification background",
+            "Learn what a quantitative structure-analysis relationship (QSAR) model is and how it can be constructed in Galaxy",
+            "Learn to apply logistic regression, k-nearest neighbors, support verctor machines, random forests and bagging algorithms",
+            "Learn how visualizations can be used to analyze the classification results"
         ],
-        "pageviews": 5193185,
-        "pub_date": "2021-04-19",
+        "pageviews": 3148,
+        "pub_date": "2020-04-30",
         "questions": [
-            "What is a convolutional neural network (CNN)?",
-            "What are some applications of CNN?"
+            "What is classification and how we can use classification techniques?"
         ],
         "recordings": [
             {
                 "captioners": [
-                    "FilipposZ"
+                    "anuprulez"
                 ],
                 "date": "2021-02-15",
                 "galaxy_version": "21.01",
-                "length": "1H",
+                "length": "1H50M",
                 "speakers": [
-                    "kxk302"
+                    "anuprulez"
                 ],
-                "youtube_id": "P1NVYOJrv_4"
-            }
-        ],
-        "requirements": [
+                "youtube_id": "Gz2OdRPS2Nk"
+            },
             {
-                "topic_name": "statistics",
-                "tutorials": [
-                    "intro_deep_learning",
-                    "FNN",
-                    "RNN"
+                "bot-timestamp": 1724930690,
+                "captioners": [
+                    "anuprulez"
                 ],
-                "type": "internal"
+                "date": "2024-08-29",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "1H7M",
+                "speakers": [
+                    "anuprulez"
+                ],
+                "youtube_id": "l4LCy6Zci4g"
             }
         ],
-        "short_id": "T00257",
+        "short_id": "T00262",
         "short_tools": [
-            "keras_model_builder",
-            "keras_model_config",
-            "model_prediction",
-            "keras_train_and_eval",
-            "ml_visualization_ex",
-            "sklearn_to_categorical"
+            "plotly_ml_performance_plots",
+            "sklearn_build_pipeline",
+            "sklearn_generalized_linear",
+            "sklearn_nn_classifier",
+            "sklearn_svm_classifier",
+            "sklearn_ensemble",
+            "Remove beginning1",
+            "sklearn_searchcv"
         ],
-        "slides": true,
+        "slides": false,
         "slides_recordings": false,
         "supported_servers": {
             "exact": [
@@ -253997,23 +260853,35 @@
                 }
             ],
             "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
                 }
             ]
         },
         "symlink": null,
         "time_estimation": "2H",
-        "title": "Deep Learning (Part 3) - Convolutional neural networks (CNN)",
+        "title": "Classification in Machine Learning",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/1.0.10.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/1.0.10.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.11.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.11.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.11.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_to_categorical/sklearn_to_categorical/1.0.10.0"
+            "Remove beginning1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.4",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.11.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_generalized_linear/sklearn_generalized_linear/1.0.11.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_nn_classifier/sklearn_nn_classifier/1.0.11.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.11.0"
         ],
         "topic_name": "statistics",
         "topic_name_human": "Statistics and machine learning",
@@ -254023,50 +260891,108 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "CNN",
+        "tutorial_name": "classification_machinelearning",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/CNN/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/classification_machinelearning/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/CNN/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/CNN/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/classification_machinelearning/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/classification_machinelearning/tutorial.json"
         },
-        "version": 17,
+        "version": 15,
         "video": false,
-        "video_versions": 1,
+        "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 204,
-        "visitors": 1917311,
+        "visit_duration": 116,
+        "visitors": 2078,
         "workflows": [
             {
                 "creators": [
                     {
-                        "class": "Person",
-                        "identifier": "0000-0001-6585-3619",
-                        "name": "Kaivan Kamali"
+                        "class": "Organization",
+                        "identifier": "https://orcid.org/0000-0002-2068-4695",
+                        "name": "Anup Kumar"
                     }
                 ],
-                "description": "",
+                "description": "Classification in Machine Learning",
                 "features": {
                     "comments": false,
                     "parameters": false,
-                    "report": null,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                    },
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nX_test\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nX_train\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ny_test\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ny_train\"]\n  4[label=\"Create a deep learning model architecture\"]\n  5[label=\"To categorical\"]\n  3 -> 5 [label=\"output\"]\n  6[label=\"Create deep learning model\"]\n  4 -> 6 [label=\"outfile\"]\n  7[label=\"Deep learning training and evaluation\"]\n  6 -> 7 [label=\"outfile\"]\n  1 -> 7 [label=\"output\"]\n  5 -> 7 [label=\"outfile\"]\n  8[label=\"Model Prediction\"]\n  7 -> 8 [label=\"outfile_object\"]\n  0 -> 8 [label=\"output\"]\n  9[label=\"Machine Learning Visualization Extension\"]\n  8 -> 9 [label=\"outfile_predict\"]\n  2 -> 9 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntrain_rows.csv\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntest_rows_labels.csv\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntest_rows.csv\"]\n  3[label=\"Pipeline Builder\"]\n  4[label=\"Generalized linear models\"]\n  0 -> 4 [label=\"output\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Nearest Neighbors Classification\"]\n  0 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Support vector machines SVMs\"]\n  0 -> 6 [label=\"output\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Ensemble methods\"]\n  0 -> 7 [label=\"output\"]\n  0 -> 7 [label=\"output\"]\n  8[label=\"Remove beginning\"]\n  1 -> 8 [label=\"output\"]\n  9[label=\"Hyperparameter Search\"]\n  3 -> 9 [label=\"outfile\"]\n  0 -> 9 [label=\"output\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"Generalized linear models\"]\n  2 -> 10 [label=\"output\"]\n  4 -> 10 [label=\"outfile_fit\"]\n  11[label=\"Nearest Neighbors Classification\"]\n  2 -> 11 [label=\"output\"]\n  5 -> 11 [label=\"outfile_fit\"]\n  12[label=\"Support vector machines SVMs\"]\n  2 -> 12 [label=\"output\"]\n  6 -> 12 [label=\"outfile_fit\"]\n  13[label=\"Ensemble methods\"]\n  2 -> 13 [label=\"output\"]\n  7 -> 13 [label=\"outfile_fit\"]\n  14[label=\"Ensemble methods\"]\n  2 -> 14 [label=\"output\"]\n  9 -> 14 [label=\"outfile_object\"]\n  15[label=\"Plot confusion matrix, precision, recall and ROC and AUC curves\"]\n  8 -> 15 [label=\"out_file1\"]\n  10 -> 15 [label=\"outfile_predict\"]\n  4 -> 15 [label=\"outfile_fit\"]\n  16[label=\"Plot confusion matrix, precision, recall and ROC and AUC curves\"]\n  1 -> 16 [label=\"output\"]\n  11 -> 16 [label=\"outfile_predict\"]\n  5 -> 16 [label=\"outfile_fit\"]\n  17[label=\"Plot confusion matrix, precision, recall and ROC and AUC curves\"]\n  1 -> 17 [label=\"output\"]\n  12 -> 17 [label=\"outfile_predict\"]\n  6 -> 17 [label=\"outfile_fit\"]\n  18[label=\"Plot confusion matrix, precision, recall and ROC and AUC curves\"]\n  1 -> 18 [label=\"output\"]\n  13 -> 18 [label=\"outfile_predict\"]\n  7 -> 18 [label=\"outfile_fit\"]\n  19[label=\"Plot confusion matrix, precision, recall and ROC and AUC curves\"]\n  1 -> 19 [label=\"output\"]\n  14 -> 19 [label=\"outfile_predict\"]\n  9 -> 19 [label=\"outfile_object\"]\n}",
                 "history": [
                     {
-                        "hash": "ce48b25d3253616efc9591ba44031331827b1f62",
-                        "message": "Fixed lint issues",
+                        "hash": "291c6262660a5b22f913321d85494bc45b4f803e",
+                        "message": "Add license",
+                        "num": 10,
+                        "short_hash": "291c62626",
+                        "unix": "1726129256"
+                    },
+                    {
+                        "hash": "328755cfaa711e1209d7217d55963746e5f3c7e3",
+                        "message": "Add files via upload",
+                        "num": 9,
+                        "short_hash": "328755cfa",
+                        "unix": "1726039775"
+                    },
+                    {
+                        "hash": "6439ff1d5b866f5eb249eff701851b538e0972f0",
+                        "message": "rename workflow file and add workflow test",
+                        "num": 8,
+                        "short_hash": "6439ff1d5",
+                        "unix": "1716281718"
+                    },
+                    {
+                        "hash": "502f6e6508564d450f0c1625e0324f11e36f14d0",
+                        "message": "rename workflow file and add workflow test",
+                        "num": 7,
+                        "short_hash": "502f6e650",
+                        "unix": "1716281168"
+                    },
+                    {
+                        "hash": "e6df909ee94fbedab4bfe0ad62927f8bbf2d5d4a",
+                        "message": "update workflows due to tool upgrade",
+                        "num": 6,
+                        "short_hash": "e6df909ee",
+                        "unix": "1715938213"
+                    },
+                    {
+                        "hash": "bdfa0296c91ec296d171375c5da00a304aa4e165",
+                        "message": "Update ml_classification.ga",
+                        "num": 5,
+                        "short_hash": "bdfa0296c",
+                        "unix": "1588252485"
+                    },
+                    {
+                        "hash": "2680ad593256d485316ebd30e52dbcf234f95211",
+                        "message": "some fixes",
+                        "num": 4,
+                        "short_hash": "2680ad593",
+                        "unix": "1588243701"
+                    },
+                    {
+                        "hash": "becca5c2776328e21e9acbb7da6601717fde7976",
+                        "message": "tags and annotation are added to workflow",
+                        "num": 3,
+                        "short_hash": "becca5c27",
+                        "unix": "1588181809"
+                    },
+                    {
+                        "hash": "0da8a889e86da886397ebb454a695e3286214eda",
+                        "message": "workflow format is changed",
                         "num": 2,
-                        "short_hash": "ce48b25d3",
-                        "unix": "1699469857"
+                        "short_hash": "0da8a889e",
+                        "unix": "1588180978"
                     },
                     {
-                        "hash": "0c206197dd1637890ad853b508f4c14009d1cd77",
-                        "message": "Renamed workflow and test yml file",
+                        "hash": "28d2cd66bda9c8aa8f5fb0d2f4685af2b4b85820",
+                        "message": "workflow is added",
                         "num": 1,
-                        "short_hash": "0c206197d",
-                        "unix": "1699461926"
+                        "short_hash": "28d2cd66b",
+                        "unix": "1588179550"
                     }
                 ],
                 "inputs": [
@@ -254079,21 +261005,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "X_test"
+                                "name": "train_rows.csv"
                             }
                         ],
-                        "label": "X_test",
+                        "label": "train_rows.csv",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 0
+                            "left": 21.98957654096855,
+                            "top": 374.77129070095475
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "67fe95aa-be8d-4ce8-89a3-844c55d4edf9",
+                        "uuid": "2b808085-c925-4327-8310-e45702344b59",
                         "when": null,
                         "workflow_outputs": []
                     },
@@ -254106,21 +261032,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "X_train"
+                                "name": "test_rows_labels.csv"
                             }
                         ],
-                        "label": "X_train",
+                        "label": "test_rows_labels.csv",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 120
+                            "left": 13.333333333333329,
+                            "top": 467.4453024769383
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "cf3a589c-9683-47d0-a4b3-f56046633552",
+                        "uuid": "b04a2c8d-d019-49cd-8ef3-f2565cc9a2d5",
                         "when": null,
                         "workflow_outputs": []
                     },
@@ -254133,207 +261059,64 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "y_test"
-                            }
-                        ],
-                        "label": "y_test",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 240
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "5d37d651-f5c9-4af6-9ff1-211d7a145a30",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "y_train"
+                                "name": "test_rows.csv"
                             }
                         ],
-                        "label": "y_train",
+                        "label": "test_rows.csv",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
                             "left": 0,
-                            "top": 360
+                            "top": 566.1119691436049
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "ec126ab6-12b4-4559-9ade-321d6e5f37dd",
+                        "uuid": "0c0a1583-9e8c-4382-af2b-feae2d1fc845",
                         "when": null,
                         "workflow_outputs": []
                     }
                 ],
-                "license": "CC-BY-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nX_test\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nX_train\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ny_test\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\ny_train\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Create a deep learning model architecture\"];\n  5[\"To categorical\"];\n  3 -->|output| 5;\n  6[\"Create deep learning model\"];\n  4 -->|outfile| 6;\n  7[\"Deep learning training and evaluation\"];\n  6 -->|outfile| 7;\n  1 -->|output| 7;\n  5 -->|outfile| 7;\n  8[\"Model Prediction\"];\n  7 -->|outfile_object| 8;\n  0 -->|output| 8;\n  9[\"Machine Learning Visualization Extension\"];\n  8 -->|outfile_predict| 9;\n  2 -->|output| 9;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Intro_To_CNN_v1.0.11.0",
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ntrain_rows.csv\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ntest_rows_labels.csv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ntest_rows.csv\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Pipeline Builder\"];\n  4[\"Generalized linear models\"];\n  0 -->|output| 4;\n  0 -->|output| 4;\n  5[\"Nearest Neighbors Classification\"];\n  0 -->|output| 5;\n  0 -->|output| 5;\n  6[\"Support vector machines SVMs\"];\n  0 -->|output| 6;\n  0 -->|output| 6;\n  7[\"Ensemble methods\"];\n  0 -->|output| 7;\n  0 -->|output| 7;\n  8[\"Remove beginning\"];\n  1 -->|output| 8;\n  9[\"Hyperparameter Search\"];\n  3 -->|outfile| 9;\n  0 -->|output| 9;\n  0 -->|output| 9;\n  10[\"Generalized linear models\"];\n  2 -->|output| 10;\n  4 -->|outfile_fit| 10;\n  11[\"Nearest Neighbors Classification\"];\n  2 -->|output| 11;\n  5 -->|outfile_fit| 11;\n  12[\"Support vector machines SVMs\"];\n  2 -->|output| 12;\n  6 -->|outfile_fit| 12;\n  13[\"Ensemble methods\"];\n  2 -->|output| 13;\n  7 -->|outfile_fit| 13;\n  14[\"Ensemble methods\"];\n  2 -->|output| 14;\n  9 -->|outfile_object| 14;\n  15[\"Plot confusion matrix, precision, recall and ROC and AUC curves\"];\n  8 -->|out_file1| 15;\n  10 -->|outfile_predict| 15;\n  4 -->|outfile_fit| 15;\n  16[\"Plot confusion matrix, precision, recall and ROC and AUC curves\"];\n  1 -->|output| 16;\n  11 -->|outfile_predict| 16;\n  5 -->|outfile_fit| 16;\n  17[\"Plot confusion matrix, precision, recall and ROC and AUC curves\"];\n  1 -->|output| 17;\n  12 -->|outfile_predict| 17;\n  6 -->|outfile_fit| 17;\n  18[\"Plot confusion matrix, precision, recall and ROC and AUC curves\"];\n  1 -->|output| 18;\n  13 -->|outfile_predict| 18;\n  7 -->|outfile_fit| 18;\n  19[\"Plot confusion matrix, precision, recall and ROC and AUC curves\"];\n  1 -->|output| 19;\n  14 -->|outfile_predict| 19;\n  9 -->|outfile_object| 19;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "ml_classification",
                 "outputs": [],
-                "parent_id": "statistics/CNN",
-                "path": "topics/statistics/tutorials/CNN/workflows/Intro_To_CNN_v1_0_11_0.ga",
-                "tags": [],
+                "parent_id": "statistics/classification_machinelearning",
+                "path": "topics/statistics/tutorials/classification_machinelearning/workflows/ml_classification.ga",
+                "tags": [
+                    "statistics",
+                    "classification",
+                    "ml",
+                    "cheminformatics"
+                ],
                 "test_results": null,
                 "tests": true,
-                "title": "Intro_To_CNN_v1.0.11.0",
+                "title": "ml_classification",
                 "topic_id": "statistics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-CNN/versions/intro-to-cnn-v1-0-11-0",
-                "tutorial_id": "CNN",
-                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/CNN/workflows/Intro_To_CNN_v1_0_11_0.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/CNN/workflows/Intro_To_CNN_v1_0_11_0.html",
-                "version": 1,
-                "wfid": "statistics-CNN",
-                "wfname": "intro-to-cnn-v1-0-11-0",
-                "workflow": "Intro_To_CNN_v1_0_11_0.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/statistics-classification_machinelearning/versions/ml-classification",
+                "tutorial_id": "classification_machinelearning",
+                "url": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/classification_machinelearning/workflows/ml_classification.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/statistics/tutorials/classification_machinelearning/workflows/ml_classification.html",
+                "version": 3,
+                "wfid": "statistics-classification_machinelearning",
+                "wfname": "ml-classification",
+                "workflow": "ml_classification.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/1.0.10.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/1.0.10.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.11.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.11.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.11.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_to_categorical/sklearn_to_categorical/1.0.10.0"
-                ],
-                "workflowhub_id": "1313"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/4697906"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/fine_tuning_protTrans/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "eurosciencegateway",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "email": "anup.rulez@gmail.com",
-                "id": "anuprulez",
-                "joined": "2018-08",
-                "name": "Anup Kumar",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/anuprulez/",
-                "twitter": "musafirtweetsz",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/anuprulez.json"
-            }
-        ],
-        "dir": "topics/statistics/tutorials/fine_tuning_protTrans",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "statistics/fine_tuning_protTrans",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-17",
-        "objectives": [
-            "Learn to load and use large protein models from HuggingFace",
-            "Learn to fine-tune them on specific tasks such as predicting dephosphorylation sites"
-        ],
-        "pageviews": 161,
-        "pub_date": "2024-06-17",
-        "questions": [
-            "How to load large protein AI models?",
-            "How to fine-tune such models on downstream tasks such as post-translational site prediction?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "jupyterlab"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "statistics",
-                "tutorials": [
-                    "gpu_jupyter_lab"
+                    "Remove beginning1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.4",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.11.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_generalized_linear/sklearn_generalized_linear/1.0.11.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_nn_classifier/sklearn_nn_classifier/1.0.11.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0.11.0"
                 ],
-                "type": "internal"
+                "workflowhub_id": "1331"
             }
         ],
-        "short_id": "T00442",
-        "short_tools": [
-            "interactive_tool_ml_jupyter_notebook"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "interactive-tools",
-            "machine-learning",
-            "deep-learning",
-            "jupyter-lab",
-            "fine-tuning",
-            "dephosphorylation-site-prediction"
-        ],
-        "time_estimation": "1H",
-        "title": "Fine tune large protein model (ProtTrans) using HuggingFace",
-        "tools": [
-            "interactive_tool_ml_jupyter_notebook"
-        ],
-        "topic_name": "statistics",
-        "topic_name_human": "Statistics and machine learning",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "fine_tuning_protTrans",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/fine_tuning_protTrans/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/fine_tuning_protTrans/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/fine_tuning_protTrans/tutorial.json"
-        },
-        "version": 1,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 95,
-        "visitors": 124,
-        "zenodo_link": "https://zenodo.org/records/10986248"
+        "zenodo_link": "https://zenodo.org/record/3738729"
     },
     {
         "admin_install": {
@@ -254431,7 +261214,7 @@
             "Interpret and visualize the results obtained from ML analyses on omics datasets",
             "Apply the ML techniques to analyse their own datasets"
         ],
-        "pageviews": 5178,
+        "pageviews": 5315,
         "pub_date": "2021-05-21",
         "questions": [
             "What are the main categories in Machine Learning algorithms?",
@@ -254530,8 +261313,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 68,
-        "visitors": 3311,
+        "visit_duration": 67,
+        "visitors": 3414,
         "zenodo_link": ""
     },
     {
@@ -254593,7 +261376,7 @@
             "Build a vector-symbolic architecture",
             "Use the architecture to build a classification model"
         ],
-        "pageviews": 388,
+        "pageviews": 408,
         "pub_date": "2023-04-28",
         "questions": [
             "How to encode data into vectors in a high-dimensional space?",
@@ -254643,10 +261426,148 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 33,
-        "visitors": 304,
+        "visit_duration": 32,
+        "visitors": 321,
         "zenodo_link": "https://doi.org/10.5281/zenodo.6467875"
     },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/fine_tuning_protTrans/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "eurosciencegateway",
+                    "elixir-europe"
+                ],
+                "elixir_node": "de",
+                "email": "anup.rulez@gmail.com",
+                "id": "anuprulez",
+                "joined": "2018-08",
+                "name": "Anup Kumar",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/anuprulez/",
+                "twitter": "musafirtweetsz",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/anuprulez.json"
+            }
+        ],
+        "dir": "topics/statistics/tutorials/fine_tuning_protTrans",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "statistics/fine_tuning_protTrans",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-19",
+        "objectives": [
+            "Learn to load and use large protein models from HuggingFace",
+            "Learn to fine-tune them on specific tasks such as predicting dephosphorylation sites"
+        ],
+        "pageviews": 317,
+        "pub_date": "2024-06-17",
+        "questions": [
+            "How to load large protein AI models?",
+            "How to fine-tune such models on downstream tasks such as post-translational site prediction?"
+        ],
+        "recordings": [
+            {
+                "bot-timestamp": 1724930837,
+                "captioners": [
+                    "anuprulez"
+                ],
+                "date": "2024-08-29",
+                "galaxy_version": " 24.1.2.dev0",
+                "length": "35M",
+                "speakers": [
+                    "anuprulez"
+                ],
+                "youtube_id": "QTXdcsYaLlE"
+            }
+        ],
+        "requirements": [
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "jupyterlab"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "statistics",
+                "tutorials": [
+                    "gpu_jupyter_lab"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00442",
+        "short_tools": [
+            "interactive_tool_ml_jupyter_notebook"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "interactive-tools",
+            "machine-learning",
+            "deep-learning",
+            "jupyter-lab",
+            "fine-tuning",
+            "dephosphorylation-site-prediction"
+        ],
+        "time_estimation": "1H",
+        "title": "Fine tune large protein model (ProtTrans) using HuggingFace",
+        "tools": [
+            "interactive_tool_ml_jupyter_notebook"
+        ],
+        "topic_name": "statistics",
+        "topic_name_human": "Statistics and machine learning",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "fine_tuning_protTrans",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/statistics/tutorials/fine_tuning_protTrans/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/fine_tuning_protTrans/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/statistics/tutorials/fine_tuning_protTrans/tutorial.json"
+        },
+        "version": 2,
+        "video": false,
+        "video_versions": 1,
+        "video_view": 0,
+        "visit_duration": 69,
+        "visitors": 247,
+        "zenodo_link": "https://zenodo.org/records/10986248"
+    },
     {
         "admin_install": {
             "install_repository_dependencies": true,
@@ -254789,7 +261710,7 @@
             "Define what data are required to run RetroSynthesis analysis.",
             "Understanding how to run the tools to search heterologous pathways."
         ],
-        "pageviews": 505,
+        "pageviews": 520,
         "pub_date": "2022-06-23",
         "questions": [
             "Which heterologous pathways are candidates to produce a compound in a chassis?"
@@ -254811,11 +261732,11 @@
         "short_id": "T00275",
         "short_tools": [
             "rpcompletion",
+            "retropath2",
+            "rrparser",
             "rpextractsink",
-            "rp2paths",
             "get_sbml_model",
-            "rrparser",
-            "retropath2"
+            "rp2paths"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -254854,7 +261775,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 144,
-        "visitors": 343,
+        "visitors": 356,
         "workflows": [
             {
                 "creators": [],
@@ -254924,7 +261845,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nTarget to produce\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"Pick SBML Model\"];\n  dc7acc73-6d5a-4cbb-a8a2-d10a8bd38914[\"Output\\nPick SBML Model - iML1515\"];\n  1 --> dc7acc73-6d5a-4cbb-a8a2-d10a8bd38914;\n  style dc7acc73-6d5a-4cbb-a8a2-d10a8bd38914 stroke:#2c3143,stroke-width:4px;\n  2[\"RRules Parser\"];\n  9fc1e94f-34ea-4173-bdb1-3ecbef49efe3[\"Output\\nRRules Parser(retro, d=['2', '4', '6', '8', '10', '12', '14', '16'])\"];\n  2 --> 9fc1e94f-34ea-4173-bdb1-3ecbef49efe3;\n  style 9fc1e94f-34ea-4173-bdb1-3ecbef49efe3 stroke:#2c3143,stroke-width:4px;\n  3[\"Sink from SBML\"];\n  1 -->|sbml_model| 3;\n  4[\"RetroPath2.0\"];\n  2 -->|out_rules| 4;\n  3 -->|sink| 4;\n  0 -->|output| 4;\n  5[\"RP2paths\"];\n  4 -->|Reaction_Network| 5;\n  6[\"Complete Reactions\"];\n  4 -->|Reaction_Network| 6;\n  5 -->|compounds| 6;\n  5 -->|master_pathways| 6;\n  3 -->|sink| 6;",
-                "modified": "2024-08-18 00:06:25 +0000",
+                "modified": "2024-10-02 12:08:10 +0000",
                 "name": "RetroSynthesis",
                 "outputs": [
                     {
@@ -255346,37 +262267,30 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "rpfba",
-                    "owner": "iuc",
-                    "revisions": "19be43e96154",
-                    "tool_panel_section_label": "Synthetic Biology",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "rpranker",
+                    "name": "dnabot",
                     "owner": "tduigou",
-                    "revisions": "bab690866445",
+                    "revisions": "ec9cef4b5b5a",
                     "tool_panel_section_label": "Synthetic Biology",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "rpscore",
+                    "name": "rpbasicdesign",
                     "owner": "tduigou",
-                    "revisions": "da8ae7fa5ed3",
+                    "revisions": "de9f53630349",
                     "tool_panel_section_label": "Synthetic Biology",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "rpthermo",
+                    "name": "selenzy",
                     "owner": "tduigou",
-                    "revisions": "21a900eee812",
+                    "revisions": "34a9d136a5bf",
                     "tool_panel_section_label": "Synthetic Biology",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: rpfba\n  owner: iuc\n  revisions: 19be43e96154\n  tool_panel_section_label: Synthetic Biology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rpranker\n  owner: tduigou\n  revisions: bab690866445\n  tool_panel_section_label: Synthetic Biology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rpscore\n  owner: tduigou\n  revisions: da8ae7fa5ed3\n  tool_panel_section_label: Synthetic Biology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rpthermo\n  owner: tduigou\n  revisions: 21a900eee812\n  tool_panel_section_label: Synthetic Biology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/synthetic-biology/tutorials/pathway_analysis/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: dnabot\n  owner: tduigou\n  revisions: ec9cef4b5b5a\n  tool_panel_section_label: Synthetic Biology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rpbasicdesign\n  owner: tduigou\n  revisions: de9f53630349\n  tool_panel_section_label: Synthetic Biology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: selenzy\n  owner: tduigou\n  revisions: 34a9d136a5bf\n  tool_panel_section_label: Synthetic Biology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/synthetic-biology/tutorials/basic_assembly_analysis/tutorial.json",
         "contributors": [
             {
                 "email": "kenza.bazi-kabbaj@inrae.fr",
@@ -255444,53 +262358,57 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/jfaulon.json"
             }
         ],
-        "dir": "topics/synthetic-biology/tutorials/pathway_analysis",
+        "dir": "topics/synthetic-biology/tutorials/basic_assembly_analysis",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "synthetic-biology/pathway_analysis",
+        "id": "synthetic-biology/basic_assembly_analysis",
         "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
+        "key_points": [
+            "Knowing the reaction is not sufficient to implement a pathway, one needs to find out which enzyme is capable of catalyzing the reactions. For this, Selenzyme is used to search for enzymes using reactions as query. As a result, UniProt IDs of enzymes are stored as annotation in SBML files.",
+            "Expressing pathways into cells involved not only gene encoding enzymes, but also additional genetic parts such as libraries of promoter(s), RBSs, terminators, ... From these, multiple combinations of parts are possible, and each one could produce different results. Several methods exist to assemble genetic parts together into plasmids, the BASIC Assembly approach is one of them. The BasicDesign tool generates combinations of the genetic parts that are compliant with the BASIC Assembly patterns.",
+            "Automatizing the construction of compound producing strains necessitate to translate protocols into instructions that could be understable by lab robots. To do this, DNA-Bot reads the list of constructs and the DNA parts information and generates python instructions for the automated build of the genetic constructs using OpenTrons liquid handling robots."
+        ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2024-06-14",
         "objectives": [
-            "Calculate the production flux of the lycopene target molecule using _Flux Balance Analysis_ tool.",
-            "Compute thermodynamics values to optimize the yield of the reaction producing the lycopene using _Thermo_ tool.",
-            "Compute the global score for the previous annotated pathways.",
-            "Rank the computed heterologous pathways depending on their score."
+            "Annotate the SBML pathway using Selenzy tool.",
+            "Design plasmids encoding predicted pathways using rpbasicdesign tool.",
+            "Generate dnabot scripts enabling the automatic build of plasmids."
         ],
-        "pageviews": 621,
-        "pub_date": "2022-09-26",
+        "pageviews": 1144,
+        "pub_date": "2022-05-12",
         "questions": [
-            "How to evaluate a set of heterologous pathways ?"
+            "How to design plasmids encoding predicted pathways using BASIC assembly method ?",
+            "How to generate scripts enabling the automatic build of plasmids ?"
         ],
         "recordings": [
             {
                 "captioners": [
                     "kenza12"
                 ],
-                "date": "2022-09-26",
-                "length": "5M",
+                "date": "2022-05-11",
+                "length": "3M",
                 "speakers": [
                     "breakthewall"
                 ],
                 "type": "Demo",
-                "youtube_id": "240oxe8unnU"
+                "youtube_id": "0ItpHuSM7t0"
             }
         ],
-        "short_id": "T00274",
+        "short_id": "T00273",
         "short_tools": [
-            "rpranker",
-            "rpscore",
-            "rpthermo",
-            "rpfba"
+            "dnabot",
+            "selenzy-wrapper",
+            "rpbasicdesign"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -255499,13 +262417,12 @@
             "inexact": []
         },
         "symlink": null,
-        "time_estimation": "20M",
-        "title": "Evaluating and ranking a set of pathways based on multiple metrics",
+        "time_estimation": "15M",
+        "title": "Designing plasmids encoding predicted pathways by using the BASIC assembly method",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/rpfba/rpfba/5.12.1",
-            "toolshed.g2.bx.psu.edu/repos/tduigou/rpranker/rpranker/5.12.1",
-            "toolshed.g2.bx.psu.edu/repos/tduigou/rpscore/rpscore/5.12.1",
-            "toolshed.g2.bx.psu.edu/repos/tduigou/rpthermo/rpthermo/5.12.1"
+            "toolshed.g2.bx.psu.edu/repos/tduigou/dnabot/dnabot/3.1.0",
+            "toolshed.g2.bx.psu.edu/repos/tduigou/rpbasicdesign/rpbasicdesign/0.3.4",
+            "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.2.0"
         ],
         "topic_name": "synthetic-biology",
         "topic_name_human": "Synthetic Biology",
@@ -255515,44 +262432,51 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "pathway_analysis",
+        "tutorial_name": "basic_assembly_analysis",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/synthetic-biology/tutorials/pathway_analysis/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/synthetic-biology/tutorials/basic_assembly_analysis/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/synthetic-biology/tutorials/pathway_analysis/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/synthetic-biology/tutorials/pathway_analysis/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/synthetic-biology/tutorials/basic_assembly_analysis/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/synthetic-biology/tutorials/basic_assembly_analysis/tutorial.json"
         },
-        "version": 7,
+        "version": 8,
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 188,
-        "visitors": 397,
+        "visit_duration": 146,
+        "visitors": 707,
         "workflows": [
             {
                 "creators": [],
-                "description": "Evaluating and ranking a set of pathways based on multiple metrics",
+                "description": "Design plasmids encoding predicted pathways by using the BASIC assembly method.",
                 "features": {
                     "comments": false,
                     "parameters": true,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nHeterologous pathways\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nChassis where to produce target from\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nCell compartment ID\"]\n  3[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nBiomass reaction ID\"]\n  4[label=\"Flux balance analysis\"]\n  3 -> 4 [label=\"output\"]\n  2 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Thermo\"]\n  4 -> 5 [label=\"pathway_with_fba\"]\n  6[label=\"Score Pathway\"]\n  5 -> 6 [label=\"pathway_with_thermo\"]\n  7[label=\"Rank Pathways\"]\n  6 -> 7 [label=\"scored_pathway\"]\n  k8111f52558454ac2a1d6c4bfd218cf3f[color=lightseagreen,label=\"Output\\nRanked Pathways\"]\n  7 -> k8111f52558454ac2a1d6c4bfd218cf3f\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPathway SBML\"]\n  1[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nHost taxon ID\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nEnzyme taxon IDs\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nLinkers and user parts\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDNA-Bot settings\"]\n  5[label=\"Selenzyme\"]\n  2 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  k54b833faec4f458ab08523211f4e56ca[color=lightseagreen,label=\"Output\\nUniprot IDs\"]\n  5 -> k54b833faec4f458ab08523211f4e56ca\n  6[label=\"BasicDesign\"]\n  3 -> 6 [label=\"output\"]\n  5 -> 6 [label=\"uniprot_ids\"]\n  7[label=\"DNA-Bot\"]\n  4 -> 7 [label=\"output\"]\n  6 -> 7 [label=\"Constructs\"]\n  6 -> 7 [label=\"User parts plate\"]\n  6 -> 7 [label=\"Biolegio plate\"]\n}",
                 "history": [
                     {
-                        "hash": "25d6ed2bc398ff3ab67a86136615e7597e929ae8",
-                        "message": "fix(main_workflow.ga): add tag and annotation",
+                        "hash": "ef543ff8fc3b4e277e4fea70716284dc64680159",
+                        "message": "add slides, more background and new contributors",
+                        "num": 3,
+                        "short_hash": "ef543ff8f",
+                        "unix": "1647522263"
+                    },
+                    {
+                        "hash": "002bde23969696132aacbc96d5f20e011d478acc",
+                        "message": "add tag synthetic biology",
                         "num": 2,
-                        "short_hash": "25d6ed2bc",
-                        "unix": "1663316015"
+                        "short_hash": "002bde239",
+                        "unix": "1646148305"
                     },
                     {
-                        "hash": "47a55fc0c8a916d8f494dbb6158659719a2b0872",
-                        "message": "feat(pathway_analysis): add pathway analysis tutorial",
+                        "hash": "e01203d3bc2a8e9de5f6e1253d1b5fd368e2ef9a",
+                        "message": "add new tutorial for synthetic biology: basic assembly analysis",
                         "num": 1,
-                        "short_hash": "47a55fc0c",
-                        "unix": "1660053898"
+                        "short_hash": "e01203d3b",
+                        "unix": "1645628230"
                     }
                 ],
                 "inputs": [
@@ -255565,27 +262489,27 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Heterologous pathways"
+                                "name": "Pathway (SBML)"
                             }
                         ],
-                        "label": "Heterologous pathways",
-                        "name": "Input dataset collection",
+                        "label": "Pathway (SBML)",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 335.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 192.5,
-                            "right": 392.5,
+                            "bottom": 314.8000030517578,
+                            "height": 61.80000305175781,
+                            "left": 239,
+                            "right": 439,
                             "top": 253,
                             "width": 200,
-                            "x": 192.5,
+                            "x": 239,
                             "y": 253
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "396a82be-e939-4c16-95d7-cfafb0e472bd",
+                        "type": "data_input",
+                        "uuid": "1adcdfe9-4e38-4d09-8d9f-ee7b8e089a26",
                         "workflow_outputs": []
                     },
                     {
@@ -255597,59 +262521,59 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Chassis where to produce target from"
+                                "name": "Host taxon ID"
                             }
                         ],
-                        "label": "Chassis where to produce target from",
-                        "name": "Input dataset",
+                        "label": "Host taxon ID",
+                        "name": "Input parameter",
                         "outputs": [],
                         "position": {
-                            "bottom": 449.6999969482422,
-                            "height": 82.19999694824219,
-                            "left": 190.5,
-                            "right": 390.5,
-                            "top": 367.5,
+                            "bottom": 404.8000030517578,
+                            "height": 61.80000305175781,
+                            "left": 241,
+                            "right": 441,
+                            "top": 343,
                             "width": 200,
-                            "x": 190.5,
-                            "y": 367.5
+                            "x": 241,
+                            "y": 343
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"default\": 83333, \"parameter_type\": \"integer\", \"optional\": true}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ca69a88b-c781-4d72-ab5c-92df2afc720a",
+                        "type": "parameter_input",
+                        "uuid": "59aef08a-be1d-4967-85fe-c497f948471c",
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "Comma separated values",
                         "content_id": null,
                         "errors": null,
                         "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "Cell compartment ID"
+                                "description": "Comma separated values",
+                                "name": "Enzyme taxon IDs"
                             }
                         ],
-                        "label": "Cell compartment ID",
+                        "label": "Enzyme taxon IDs",
                         "name": "Input parameter",
                         "outputs": [],
                         "position": {
-                            "bottom": 555.6999969482422,
+                            "bottom": 517.1999969482422,
                             "height": 82.19999694824219,
-                            "left": 192.5,
-                            "right": 392.5,
-                            "top": 473.5,
+                            "left": 241,
+                            "right": 441,
+                            "top": 435,
                             "width": 200,
-                            "x": 192.5,
-                            "y": 473.5
+                            "x": 241,
+                            "y": 435
                         },
                         "tool_id": null,
-                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
+                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": true}",
                         "tool_version": null,
                         "type": "parameter_input",
-                        "uuid": "d92f3120-93f4-4341-aab7-7432a889fd40",
+                        "uuid": "37fa5d18-c5dc-42f0-be7c-88bdd6205d74",
                         "workflow_outputs": []
                     },
                     {
@@ -255661,50 +262585,78 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Biomass reaction ID"
+                                "name": "Linkers and user parts"
                             }
                         ],
-                        "label": "Biomass reaction ID",
-                        "name": "Input parameter",
+                        "label": "Linkers and user parts",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 656.6999969482422,
+                            "bottom": 628.1999969482422,
                             "height": 82.19999694824219,
-                            "left": 191.5,
-                            "right": 391.5,
-                            "top": 574.5,
+                            "left": 243,
+                            "right": 443,
+                            "top": 546,
                             "width": 200,
-                            "x": 191.5,
-                            "y": 574.5
+                            "x": 243,
+                            "y": 546
                         },
                         "tool_id": null,
-                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "d2ebc0df-8d14-471a-a940-f9163d309d70",
+                        "type": "data_input",
+                        "uuid": "1e990d43-4095-4d45-a8e8-ccc1a905b283",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "DNA-Bot settings"
+                            }
+                        ],
+                        "label": "DNA-Bot settings",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 852.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 246,
+                            "right": 446,
+                            "top": 770,
+                            "width": 200,
+                            "x": 246,
+                            "y": 770
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": true}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "d797586c-cfd7-4c33-be64-28354ad76b22",
                         "workflow_outputs": []
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nHeterologous pathways\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nChassis where to produce target from\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nCell compartment ID\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nBiomass reaction ID\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"Flux balance analysis\"];\n  3 -->|output| 4;\n  2 -->|output| 4;\n  1 -->|output| 4;\n  0 -->|output| 4;\n  5[\"Thermo\"];\n  4 -->|pathway_with_fba| 5;\n  6[\"Score Pathway\"];\n  5 -->|pathway_with_thermo| 6;\n  7[\"Rank Pathways\"];\n  6 -->|scored_pathway| 7;\n  8111f525-5845-4ac2-a1d6-c4bfd218cf3f[\"Output\\nRanked Pathways\"];\n  7 --> 8111f525-5845-4ac2-a1d6-c4bfd218cf3f;\n  style 8111f525-5845-4ac2-a1d6-c4bfd218cf3f stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Pathway Analysis",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPathway SBML\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nHost taxon ID\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nEnzyme taxon IDs\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nLinkers and user parts\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nDNA-Bot settings\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Selenzyme\"];\n  2 -->|output| 5;\n  1 -->|output| 5;\n  0 -->|output| 5;\n  54b833fa-ec4f-458a-b085-23211f4e56ca[\"Output\\nUniprot IDs\"];\n  5 --> 54b833fa-ec4f-458a-b085-23211f4e56ca;\n  style 54b833fa-ec4f-458a-b085-23211f4e56ca stroke:#2c3143,stroke-width:4px;\n  6[\"BasicDesign\"];\n  3 -->|output| 6;\n  5 -->|uniprot_ids| 6;\n  7[\"DNA-Bot\"];\n  4 -->|output| 7;\n  6 -->|Constructs| 7;\n  6 -->|User parts plate| 7;\n  6 -->|Biolegio plate| 7;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "Genetic Design (BASIC Assembly)",
                 "outputs": [
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rpfba/rpfba/5.12.1",
+                        "annotation": "Performs enzyme selection from a reaction query.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.2.0",
                         "errors": null,
-                        "id": 4,
+                        "id": 5,
                         "input_connections": {
-                            "biomass_rxn_id": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "compartment_id": {
+                            "adv|enzyme_taxIDs": {
                                 "id": 2,
                                 "output_name": "output"
                             },
-                            "model": {
+                            "adv|host_taxID": {
                                 "id": 1,
                                 "output_name": "output"
                             },
@@ -255715,235 +262667,251 @@
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Flux balance analysis",
-                                "name": "model"
-                            },
-                            {
-                                "description": "runtime parameter for tool Flux balance analysis",
+                                "description": "runtime parameter for tool Selenzyme",
                                 "name": "pathway"
                             }
                         ],
-                        "label": null,
-                        "name": "Flux balance analysis",
+                        "label": "Selenzyme",
+                        "name": "Selenzyme",
                         "outputs": [
                             {
-                                "name": "pathway_with_fba",
-                                "type": "sbml"
+                                "name": "uniprot_ids",
+                                "type": "xml"
+                            },
+                            {
+                                "name": "uniprot_ids_csv",
+                                "type": "csv"
                             }
                         ],
                         "position": {
-                            "bottom": 542.8000030517578,
-                            "height": 204.8000030517578,
-                            "left": 447.5,
-                            "right": 647.5,
-                            "top": 338,
+                            "bottom": 508.1999969482422,
+                            "height": 225.1999969482422,
+                            "left": 553,
+                            "right": 753,
+                            "top": 283,
                             "width": 200,
-                            "x": 447.5,
-                            "y": 338
+                            "x": 553,
+                            "y": 283
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rpfba/rpfba/5.12.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.2.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "19be43e96154",
-                            "name": "rpfba",
-                            "owner": "iuc",
+                            "changeset_revision": "34a9d136a5bf",
+                            "name": "selenzy",
+                            "owner": "tduigou",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"merge\": \"false\", \"ignore_orphan_species\": \"true\"}, \"biomass_rxn_id\": {\"__class__\": \"ConnectedValue\"}, \"compartment_id\": {\"__class__\": \"ConnectedValue\"}, \"input_sim_type\": {\"sim_type\": \"fraction\", \"__current_case__\": 0, \"fraction_of\": \"0.75\"}, \"model\": {\"__class__\": \"RuntimeValue\"}, \"objective_rxn_id\": \"rxn_target\", \"pathway\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.12.1",
+                        "tool_state": "{\"adv\": {\"host_taxID\": {\"__class__\": \"ConnectedValue\"}, \"enzyme_taxIDs\": {\"__class__\": \"ConnectedValue\"}, \"nb_ids\": \"-1\", \"nb_targets\": \"500\", \"direction\": \"0.0\", \"NoMSA\": \"true\"}, \"pathway\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "84470349-6e9c-4810-b2c8-3d5fdae0cca4",
+                        "uuid": "2136d777-a9ec-4904-a88e-155e40aaf22a",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "pathway_with_fba",
-                                "uuid": "7ff9a6bb-52a0-4ea3-bd2e-4091f37a8a27"
+                                "output_name": "uniprot_ids_csv",
+                                "uuid": "33768258-3781-4bd1-802c-e4b14cdca234"
+                            },
+                            {
+                                "label": "Uniprot IDs",
+                                "output_name": "uniprot_ids",
+                                "uuid": "54b833fa-ec4f-458a-b085-23211f4e56ca"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpthermo/rpthermo/5.12.1",
+                        "annotation": "Extracts enzyme IDs from rpSBML files.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpbasicdesign/rpbasicdesign/0.3.4",
                         "errors": null,
-                        "id": 5,
+                        "id": 6,
                         "input_connections": {
-                            "input": {
-                                "id": 4,
-                                "output_name": "pathway_with_fba"
+                            "adv|parts_files": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "rpsbml_file": {
+                                "id": 5,
+                                "output_name": "uniprot_ids"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Thermo",
-                                "name": "input"
+                                "description": "runtime parameter for tool BasicDesign",
+                                "name": "adv"
+                            },
+                            {
+                                "description": "runtime parameter for tool BasicDesign",
+                                "name": "rpsbml_file"
                             }
                         ],
-                        "label": null,
-                        "name": "Thermo",
+                        "label": "BasicDesign",
+                        "name": "BasicDesign",
                         "outputs": [
                             {
-                                "name": "pathway_with_thermo",
-                                "type": "xml"
+                                "name": "sbol_dir",
+                                "type": "input"
+                            },
+                            {
+                                "name": "Constructs",
+                                "type": "csv"
+                            },
+                            {
+                                "name": "User parts plate",
+                                "type": "csv"
+                            },
+                            {
+                                "name": "Biolegio plate",
+                                "type": "csv"
                             }
                         ],
                         "position": {
-                            "bottom": 559.1000061035156,
-                            "height": 113.60000610351562,
-                            "left": 719.5,
-                            "right": 919.5,
-                            "top": 445.5,
+                            "bottom": 646.8000030517578,
+                            "height": 214.8000030517578,
+                            "left": 816,
+                            "right": 1016,
+                            "top": 432,
                             "width": 200,
-                            "x": 719.5,
-                            "y": 445.5
+                            "x": 816,
+                            "y": 432
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpthermo/rpthermo/5.12.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpbasicdesign/rpbasicdesign/0.3.4",
                         "tool_shed_repository": {
-                            "changeset_revision": "21a900eee812",
-                            "name": "rpthermo",
+                            "changeset_revision": "de9f53630349",
+                            "name": "rpbasicdesign",
                             "owner": "tduigou",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"ph\": \"7.5\", \"ionic_strength\": \"0.25\", \"pMg\": \"3.0\"}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.12.1",
+                        "tool_state": "{\"adv\": {\"parts_files\": {\"__class__\": \"RuntimeValue\"}, \"lms_id\": \"LMS\", \"lmp_id\": \"LMP\", \"cds_permutation\": \"true\"}, \"backbone_id\": \"BASIC_SEVA_37_CmR-p15A.1\", \"rpsbml_file\": {\"__class__\": \"RuntimeValue\"}, \"sample_size\": \"88\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "7b32553d-b992-4a54-a863-815f9b946581",
+                        "uuid": "7a2617aa-2e4a-4214-b497-1a8102b85f8b",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "pathway_with_thermo",
-                                "uuid": "bdcb02f8-c488-4098-a20a-b43e7c172847"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpscore/rpscore/5.12.1",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "pathway": {
-                                "id": 5,
-                                "output_name": "pathway_with_thermo"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Score Pathway",
-                        "outputs": [
+                                "output_name": "Constructs",
+                                "uuid": "afe416d0-ee9e-467b-81e0-b8a64f1251ac"
+                            },
                             {
-                                "name": "scored_pathway",
-                                "type": "xml"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 544.6999969482422,
-                            "height": 93.19999694824219,
-                            "left": 1078.5,
-                            "right": 1278.5,
-                            "top": 451.5,
-                            "width": 200,
-                            "x": 1078.5,
-                            "y": 451.5
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpscore/rpscore/5.12.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "da8ae7fa5ed3",
-                            "name": "rpscore",
-                            "owner": "tduigou",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adv\": {\"no_of_rxns_thres\": \"10\"}, \"pathway\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.12.1",
-                        "type": "tool",
-                        "uuid": "6b680491-6b40-4f44-943e-9026a9264b54",
-                        "workflow_outputs": [
+                                "label": null,
+                                "output_name": "User parts plate",
+                                "uuid": "2283c57e-2fa0-4177-95b9-64373f21d044"
+                            },
                             {
                                 "label": null,
-                                "output_name": "scored_pathway",
-                                "uuid": "b1227404-d3a1-4a4d-a832-e89bdda762fa"
+                                "output_name": "sbol_dir",
+                                "uuid": "81404f3f-327e-4c80-8ec7-c833ae5414fb"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "Biolegio plate",
+                                "uuid": "2d455fed-880e-4ab5-b15d-c1c7d789147a"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpranker/rpranker/5.12.1",
+                        "annotation": "DNA assembly using BASIC on OpenTrons.",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/dnabot/dnabot/3.1.0",
                         "errors": null,
                         "id": 7,
                         "input_connections": {
-                            "pathway_collection": {
+                            "adv|default_settings_file": {
+                                "id": 4,
+                                "output_name": "output"
+                            },
+                            "construct_file": {
                                 "id": 6,
-                                "output_name": "scored_pathway"
-                            }
+                                "output_name": "Constructs"
+                            },
+                            "plate_files": [
+                                {
+                                    "id": 6,
+                                    "output_name": "User parts plate"
+                                },
+                                {
+                                    "id": 6,
+                                    "output_name": "Biolegio plate"
+                                }
+                            ]
                         },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Rank Pathways",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool DNA-Bot",
+                                "name": "adv"
+                            },
+                            {
+                                "description": "runtime parameter for tool DNA-Bot",
+                                "name": "construct_file"
+                            },
+                            {
+                                "description": "runtime parameter for tool DNA-Bot",
+                                "name": "plate_files"
+                            }
+                        ],
+                        "label": "DNA-Bot",
+                        "name": "DNA-Bot",
                         "outputs": [
                             {
-                                "name": "sorted_pathways",
-                                "type": "csv"
+                                "name": "dnabot_scripts",
+                                "type": "tar"
                             }
                         ],
                         "position": {
-                            "bottom": 538.6999969482422,
-                            "height": 93.19999694824219,
-                            "left": 1343.5,
-                            "right": 1543.5,
-                            "top": 445.5,
+                            "bottom": 728.8000030517578,
+                            "height": 194.8000030517578,
+                            "left": 1073,
+                            "right": 1273,
+                            "top": 534,
                             "width": 200,
-                            "x": 1343.5,
-                            "y": 445.5
+                            "x": 1073,
+                            "y": 534
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpranker/rpranker/5.12.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/dnabot/dnabot/3.1.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "bab690866445",
-                            "name": "rpranker",
+                            "changeset_revision": "de6812daba39",
+                            "name": "dnabot",
                             "owner": "tduigou",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"pathway_collection\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.12.1",
+                        "tool_state": "{\"adv\": {\"default_settings_file\": {\"__class__\": \"RuntimeValue\"}, \"etoh_well\": \"A11\", \"soc_column\": \"1\"}, \"construct_file\": {\"__class__\": \"RuntimeValue\"}, \"plate_files\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": null,
                         "type": "tool",
-                        "uuid": "39986296-e23e-4af7-ac3d-e84de3cb1b4c",
+                        "uuid": "c09c99e4-5e0c-4c04-9f9b-3c30183d3816",
                         "workflow_outputs": [
                             {
-                                "label": "Ranked Pathways",
-                                "output_name": "sorted_pathways",
-                                "uuid": "8111f525-5845-4ac2-a1d6-c4bfd218cf3f"
+                                "label": null,
+                                "output_name": "dnabot_scripts",
+                                "uuid": "ce5be4f0-48fb-45f0-84ad-15348645c950"
                             }
                         ]
                     }
                 ],
-                "parent_id": "synthetic-biology/pathway_analysis",
-                "path": "topics/synthetic-biology/tutorials/pathway_analysis/workflows/main_workflow.ga",
+                "parent_id": "synthetic-biology/basic_assembly_analysis",
+                "path": "topics/synthetic-biology/tutorials/basic_assembly_analysis/workflows/Genetic_Design_BASIC_Assembly.ga",
                 "tags": [
                     "synthetic-biology"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Pathway Analysis",
+                "title": "Genetic Design (BASIC Assembly)",
                 "topic_id": "synthetic-biology",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/synthetic-biology-pathway_analysis/versions/main-workflow",
-                "tutorial_id": "pathway_analysis",
-                "url": "https://training.galaxyproject.org/training-material/topics/synthetic-biology/tutorials/pathway_analysis/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/synthetic-biology/tutorials/pathway_analysis/workflows/main_workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/synthetic-biology-basic_assembly_analysis/versions/genetic-design-basic-assembly",
+                "tutorial_id": "basic_assembly_analysis",
+                "url": "https://training.galaxyproject.org/training-material/topics/synthetic-biology/tutorials/basic_assembly_analysis/workflows/Genetic_Design_BASIC_Assembly.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/synthetic-biology/tutorials/basic_assembly_analysis/workflows/Genetic_Design_BASIC_Assembly.html",
                 "version": 1,
-                "wfid": "synthetic-biology-pathway_analysis",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "wfid": "synthetic-biology-basic_assembly_analysis",
+                "wfname": "genetic-design-basic-assembly",
+                "workflow": "Genetic_Design_BASIC_Assembly.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/rpfba/rpfba/5.12.1",
-                    "toolshed.g2.bx.psu.edu/repos/tduigou/rpranker/rpranker/5.12.1",
-                    "toolshed.g2.bx.psu.edu/repos/tduigou/rpscore/rpscore/5.12.1",
-                    "toolshed.g2.bx.psu.edu/repos/tduigou/rpthermo/rpthermo/5.12.1"
+                    "toolshed.g2.bx.psu.edu/repos/tduigou/dnabot/dnabot/3.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/tduigou/rpbasicdesign/rpbasicdesign/0.3.4",
+                    "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.2.0"
                 ],
-                "workflowhub_id": "1137"
+                "workflowhub_id": "1147"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/6628296"
+        "zenodo_link": "https://zenodo.org/record/6123887"
     },
     {
         "admin_install": {
@@ -255952,30 +262920,37 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "dnabot",
+                    "name": "rpfba",
+                    "owner": "iuc",
+                    "revisions": "19be43e96154",
+                    "tool_panel_section_label": "Synthetic Biology",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rpranker",
                     "owner": "tduigou",
-                    "revisions": "ec9cef4b5b5a",
+                    "revisions": "bab690866445",
                     "tool_panel_section_label": "Synthetic Biology",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "rpbasicdesign",
+                    "name": "rpscore",
                     "owner": "tduigou",
-                    "revisions": "de9f53630349",
+                    "revisions": "da8ae7fa5ed3",
                     "tool_panel_section_label": "Synthetic Biology",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "selenzy",
+                    "name": "rpthermo",
                     "owner": "tduigou",
-                    "revisions": "34a9d136a5bf",
+                    "revisions": "21a900eee812",
                     "tool_panel_section_label": "Synthetic Biology",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: dnabot\n  owner: tduigou\n  revisions: ec9cef4b5b5a\n  tool_panel_section_label: Synthetic Biology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rpbasicdesign\n  owner: tduigou\n  revisions: de9f53630349\n  tool_panel_section_label: Synthetic Biology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: selenzy\n  owner: tduigou\n  revisions: 34a9d136a5bf\n  tool_panel_section_label: Synthetic Biology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/synthetic-biology/tutorials/basic_assembly_analysis/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: rpfba\n  owner: iuc\n  revisions: 19be43e96154\n  tool_panel_section_label: Synthetic Biology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rpranker\n  owner: tduigou\n  revisions: bab690866445\n  tool_panel_section_label: Synthetic Biology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rpscore\n  owner: tduigou\n  revisions: da8ae7fa5ed3\n  tool_panel_section_label: Synthetic Biology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rpthermo\n  owner: tduigou\n  revisions: 21a900eee812\n  tool_panel_section_label: Synthetic Biology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/synthetic-biology/tutorials/pathway_analysis/tutorial.json",
         "contributors": [
             {
                 "email": "kenza.bazi-kabbaj@inrae.fr",
@@ -256043,57 +263018,53 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/jfaulon.json"
             }
         ],
-        "dir": "topics/synthetic-biology/tutorials/basic_assembly_analysis",
+        "dir": "topics/synthetic-biology/tutorials/pathway_analysis",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "synthetic-biology/basic_assembly_analysis",
+        "id": "synthetic-biology/pathway_analysis",
         "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
-        "key_points": [
-            "Knowing the reaction is not sufficient to implement a pathway, one needs to find out which enzyme is capable of catalyzing the reactions. For this, Selenzyme is used to search for enzymes using reactions as query. As a result, UniProt IDs of enzymes are stored as annotation in SBML files.",
-            "Expressing pathways into cells involved not only gene encoding enzymes, but also additional genetic parts such as libraries of promoter(s), RBSs, terminators, ... From these, multiple combinations of parts are possible, and each one could produce different results. Several methods exist to assemble genetic parts together into plasmids, the BASIC Assembly approach is one of them. The BasicDesign tool generates combinations of the genetic parts that are compliant with the BASIC Assembly patterns.",
-            "Automatizing the construction of compound producing strains necessitate to translate protocols into instructions that could be understable by lab robots. To do this, DNA-Bot reads the list of constructs and the DNA parts information and generates python instructions for the automated build of the genetic constructs using OpenTrons liquid handling robots."
-        ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2024-06-14",
         "objectives": [
-            "Annotate the SBML pathway using Selenzy tool.",
-            "Design plasmids encoding predicted pathways using rpbasicdesign tool.",
-            "Generate dnabot scripts enabling the automatic build of plasmids."
+            "Calculate the production flux of the lycopene target molecule using _Flux Balance Analysis_ tool.",
+            "Compute thermodynamics values to optimize the yield of the reaction producing the lycopene using _Thermo_ tool.",
+            "Compute the global score for the previous annotated pathways.",
+            "Rank the computed heterologous pathways depending on their score."
         ],
-        "pageviews": 1116,
-        "pub_date": "2022-05-12",
+        "pageviews": 635,
+        "pub_date": "2022-09-26",
         "questions": [
-            "How to design plasmids encoding predicted pathways using BASIC assembly method ?",
-            "How to generate scripts enabling the automatic build of plasmids ?"
+            "How to evaluate a set of heterologous pathways ?"
         ],
         "recordings": [
             {
                 "captioners": [
                     "kenza12"
                 ],
-                "date": "2022-05-11",
-                "length": "3M",
+                "date": "2022-09-26",
+                "length": "5M",
                 "speakers": [
                     "breakthewall"
                 ],
                 "type": "Demo",
-                "youtube_id": "0ItpHuSM7t0"
+                "youtube_id": "240oxe8unnU"
             }
         ],
-        "short_id": "T00273",
+        "short_id": "T00274",
         "short_tools": [
-            "dnabot",
-            "rpbasicdesign",
-            "selenzy-wrapper"
+            "rpranker",
+            "rpscore",
+            "rpthermo",
+            "rpfba"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -256102,12 +263073,13 @@
             "inexact": []
         },
         "symlink": null,
-        "time_estimation": "15M",
-        "title": "Designing plasmids encoding predicted pathways by using the BASIC assembly method",
+        "time_estimation": "20M",
+        "title": "Evaluating and ranking a set of pathways based on multiple metrics",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/tduigou/dnabot/dnabot/3.1.0",
-            "toolshed.g2.bx.psu.edu/repos/tduigou/rpbasicdesign/rpbasicdesign/0.3.4",
-            "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.2.0"
+            "toolshed.g2.bx.psu.edu/repos/iuc/rpfba/rpfba/5.12.1",
+            "toolshed.g2.bx.psu.edu/repos/tduigou/rpranker/rpranker/5.12.1",
+            "toolshed.g2.bx.psu.edu/repos/tduigou/rpscore/rpscore/5.12.1",
+            "toolshed.g2.bx.psu.edu/repos/tduigou/rpthermo/rpthermo/5.12.1"
         ],
         "topic_name": "synthetic-biology",
         "topic_name_human": "Synthetic Biology",
@@ -256117,51 +263089,44 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "basic_assembly_analysis",
+        "tutorial_name": "pathway_analysis",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/synthetic-biology/tutorials/basic_assembly_analysis/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/synthetic-biology/tutorials/pathway_analysis/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/synthetic-biology/tutorials/basic_assembly_analysis/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/synthetic-biology/tutorials/basic_assembly_analysis/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/synthetic-biology/tutorials/pathway_analysis/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/synthetic-biology/tutorials/pathway_analysis/tutorial.json"
         },
-        "version": 8,
+        "version": 7,
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 146,
-        "visitors": 685,
+        "visit_duration": 187,
+        "visitors": 407,
         "workflows": [
             {
                 "creators": [],
-                "description": "Design plasmids encoding predicted pathways by using the BASIC assembly method.",
+                "description": "Evaluating and ranking a set of pathways based on multiple metrics",
                 "features": {
                     "comments": false,
                     "parameters": true,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPathway SBML\"]\n  1[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nHost taxon ID\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nEnzyme taxon IDs\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nLinkers and user parts\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDNA-Bot settings\"]\n  5[label=\"Selenzyme\"]\n  2 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  k54b833faec4f458ab08523211f4e56ca[color=lightseagreen,label=\"Output\\nUniprot IDs\"]\n  5 -> k54b833faec4f458ab08523211f4e56ca\n  6[label=\"BasicDesign\"]\n  3 -> 6 [label=\"output\"]\n  5 -> 6 [label=\"uniprot_ids\"]\n  7[label=\"DNA-Bot\"]\n  4 -> 7 [label=\"output\"]\n  6 -> 7 [label=\"Constructs\"]\n  6 -> 7 [label=\"User parts plate\"]\n  6 -> 7 [label=\"Biolegio plate\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nHeterologous pathways\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nChassis where to produce target from\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nCell compartment ID\"]\n  3[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nBiomass reaction ID\"]\n  4[label=\"Flux balance analysis\"]\n  3 -> 4 [label=\"output\"]\n  2 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Thermo\"]\n  4 -> 5 [label=\"pathway_with_fba\"]\n  6[label=\"Score Pathway\"]\n  5 -> 6 [label=\"pathway_with_thermo\"]\n  7[label=\"Rank Pathways\"]\n  6 -> 7 [label=\"scored_pathway\"]\n  k8111f52558454ac2a1d6c4bfd218cf3f[color=lightseagreen,label=\"Output\\nRanked Pathways\"]\n  7 -> k8111f52558454ac2a1d6c4bfd218cf3f\n}",
                 "history": [
                     {
-                        "hash": "ef543ff8fc3b4e277e4fea70716284dc64680159",
-                        "message": "add slides, more background and new contributors",
-                        "num": 3,
-                        "short_hash": "ef543ff8f",
-                        "unix": "1647522263"
-                    },
-                    {
-                        "hash": "002bde23969696132aacbc96d5f20e011d478acc",
-                        "message": "add tag synthetic biology",
+                        "hash": "25d6ed2bc398ff3ab67a86136615e7597e929ae8",
+                        "message": "fix(main_workflow.ga): add tag and annotation",
                         "num": 2,
-                        "short_hash": "002bde239",
-                        "unix": "1646148305"
+                        "short_hash": "25d6ed2bc",
+                        "unix": "1663316015"
                     },
                     {
-                        "hash": "e01203d3bc2a8e9de5f6e1253d1b5fd368e2ef9a",
-                        "message": "add new tutorial for synthetic biology: basic assembly analysis",
+                        "hash": "47a55fc0c8a916d8f494dbb6158659719a2b0872",
+                        "message": "feat(pathway_analysis): add pathway analysis tutorial",
                         "num": 1,
-                        "short_hash": "e01203d3b",
-                        "unix": "1645628230"
+                        "short_hash": "47a55fc0c",
+                        "unix": "1660053898"
                     }
                 ],
                 "inputs": [
@@ -256174,27 +263139,27 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Pathway (SBML)"
+                                "name": "Heterologous pathways"
                             }
                         ],
-                        "label": "Pathway (SBML)",
-                        "name": "Input dataset",
+                        "label": "Heterologous pathways",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "bottom": 314.8000030517578,
-                            "height": 61.80000305175781,
-                            "left": 239,
-                            "right": 439,
+                            "bottom": 335.1999969482422,
+                            "height": 82.19999694824219,
+                            "left": 192.5,
+                            "right": 392.5,
                             "top": 253,
                             "width": 200,
-                            "x": 239,
+                            "x": 192.5,
                             "y": 253
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "1adcdfe9-4e38-4d09-8d9f-ee7b8e089a26",
+                        "type": "data_collection_input",
+                        "uuid": "396a82be-e939-4c16-95d7-cfafb0e472bd",
                         "workflow_outputs": []
                     },
                     {
@@ -256206,59 +263171,59 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Host taxon ID"
+                                "name": "Chassis where to produce target from"
                             }
                         ],
-                        "label": "Host taxon ID",
-                        "name": "Input parameter",
+                        "label": "Chassis where to produce target from",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 404.8000030517578,
-                            "height": 61.80000305175781,
-                            "left": 241,
-                            "right": 441,
-                            "top": 343,
+                            "bottom": 449.6999969482422,
+                            "height": 82.19999694824219,
+                            "left": 190.5,
+                            "right": 390.5,
+                            "top": 367.5,
                             "width": 200,
-                            "x": 241,
-                            "y": 343
+                            "x": 190.5,
+                            "y": 367.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"default\": 83333, \"parameter_type\": \"integer\", \"optional\": true}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "59aef08a-be1d-4967-85fe-c497f948471c",
+                        "type": "data_input",
+                        "uuid": "ca69a88b-c781-4d72-ab5c-92df2afc720a",
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "Comma separated values",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Comma separated values",
-                                "name": "Enzyme taxon IDs"
+                                "description": "",
+                                "name": "Cell compartment ID"
                             }
                         ],
-                        "label": "Enzyme taxon IDs",
+                        "label": "Cell compartment ID",
                         "name": "Input parameter",
                         "outputs": [],
                         "position": {
-                            "bottom": 517.1999969482422,
+                            "bottom": 555.6999969482422,
                             "height": 82.19999694824219,
-                            "left": 241,
-                            "right": 441,
-                            "top": 435,
+                            "left": 192.5,
+                            "right": 392.5,
+                            "top": 473.5,
                             "width": 200,
-                            "x": 241,
-                            "y": 435
+                            "x": 192.5,
+                            "y": 473.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
                         "tool_version": null,
                         "type": "parameter_input",
-                        "uuid": "37fa5d18-c5dc-42f0-be7c-88bdd6205d74",
+                        "uuid": "d92f3120-93f4-4341-aab7-7432a889fd40",
                         "workflow_outputs": []
                     },
                     {
@@ -256270,333 +263235,289 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Linkers and user parts"
+                                "name": "Biomass reaction ID"
                             }
                         ],
-                        "label": "Linkers and user parts",
-                        "name": "Input dataset",
+                        "label": "Biomass reaction ID",
+                        "name": "Input parameter",
                         "outputs": [],
                         "position": {
-                            "bottom": 628.1999969482422,
+                            "bottom": 656.6999969482422,
                             "height": 82.19999694824219,
-                            "left": 243,
-                            "right": 443,
-                            "top": 546,
+                            "left": 191.5,
+                            "right": 391.5,
+                            "top": 574.5,
                             "width": 200,
-                            "x": 243,
-                            "y": 546
+                            "x": 191.5,
+                            "y": 574.5
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "1e990d43-4095-4d45-a8e8-ccc1a905b283",
+                        "type": "parameter_input",
+                        "uuid": "d2ebc0df-8d14-471a-a940-f9163d309d70",
                         "workflow_outputs": []
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nHeterologous pathways\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nChassis where to produce target from\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nCell compartment ID\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nBiomass reaction ID\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"Flux balance analysis\"];\n  3 -->|output| 4;\n  2 -->|output| 4;\n  1 -->|output| 4;\n  0 -->|output| 4;\n  5[\"Thermo\"];\n  4 -->|pathway_with_fba| 5;\n  6[\"Score Pathway\"];\n  5 -->|pathway_with_thermo| 6;\n  7[\"Rank Pathways\"];\n  6 -->|scored_pathway| 7;\n  8111f525-5845-4ac2-a1d6-c4bfd218cf3f[\"Output\\nRanked Pathways\"];\n  7 --> 8111f525-5845-4ac2-a1d6-c4bfd218cf3f;\n  style 8111f525-5845-4ac2-a1d6-c4bfd218cf3f stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:10 +0000",
+                "name": "Pathway Analysis",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rpfba/rpfba/5.12.1",
                         "errors": null,
                         "id": 4,
-                        "input_connections": {},
+                        "input_connections": {
+                            "biomass_rxn_id": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "compartment_id": {
+                                "id": 2,
+                                "output_name": "output"
+                            },
+                            "model": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "pathway": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "DNA-Bot settings"
+                                "description": "runtime parameter for tool Flux balance analysis",
+                                "name": "model"
+                            },
+                            {
+                                "description": "runtime parameter for tool Flux balance analysis",
+                                "name": "pathway"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Flux balance analysis",
+                        "outputs": [
+                            {
+                                "name": "pathway_with_fba",
+                                "type": "sbml"
                             }
                         ],
-                        "label": "DNA-Bot settings",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 852.1999969482422,
-                            "height": 82.19999694824219,
-                            "left": 246,
-                            "right": 446,
-                            "top": 770,
+                            "bottom": 542.8000030517578,
+                            "height": 204.8000030517578,
+                            "left": 447.5,
+                            "right": 647.5,
+                            "top": 338,
                             "width": 200,
-                            "x": 246,
-                            "y": 770
+                            "x": 447.5,
+                            "y": 338
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rpfba/rpfba/5.12.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "19be43e96154",
+                            "name": "rpfba",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": true}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "d797586c-cfd7-4c33-be64-28354ad76b22",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPathway SBML\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nHost taxon ID\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nEnzyme taxon IDs\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nLinkers and user parts\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nDNA-Bot settings\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Selenzyme\"];\n  2 -->|output| 5;\n  1 -->|output| 5;\n  0 -->|output| 5;\n  54b833fa-ec4f-458a-b085-23211f4e56ca[\"Output\\nUniprot IDs\"];\n  5 --> 54b833fa-ec4f-458a-b085-23211f4e56ca;\n  style 54b833fa-ec4f-458a-b085-23211f4e56ca stroke:#2c3143,stroke-width:4px;\n  6[\"BasicDesign\"];\n  3 -->|output| 6;\n  5 -->|uniprot_ids| 6;\n  7[\"DNA-Bot\"];\n  4 -->|output| 7;\n  6 -->|Constructs| 7;\n  6 -->|User parts plate| 7;\n  6 -->|Biolegio plate| 7;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Genetic Design (BASIC Assembly)",
-                "outputs": [
+                        "tool_state": "{\"adv\": {\"merge\": \"false\", \"ignore_orphan_species\": \"true\"}, \"biomass_rxn_id\": {\"__class__\": \"ConnectedValue\"}, \"compartment_id\": {\"__class__\": \"ConnectedValue\"}, \"input_sim_type\": {\"sim_type\": \"fraction\", \"__current_case__\": 0, \"fraction_of\": \"0.75\"}, \"model\": {\"__class__\": \"RuntimeValue\"}, \"objective_rxn_id\": \"rxn_target\", \"pathway\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.12.1",
+                        "type": "tool",
+                        "uuid": "84470349-6e9c-4810-b2c8-3d5fdae0cca4",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "pathway_with_fba",
+                                "uuid": "7ff9a6bb-52a0-4ea3-bd2e-4091f37a8a27"
+                            }
+                        ]
+                    },
                     {
-                        "annotation": "Performs enzyme selection from a reaction query.",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.2.0",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpthermo/rpthermo/5.12.1",
                         "errors": null,
                         "id": 5,
                         "input_connections": {
-                            "adv|enzyme_taxIDs": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "adv|host_taxID": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "pathway": {
-                                "id": 0,
-                                "output_name": "output"
+                            "input": {
+                                "id": 4,
+                                "output_name": "pathway_with_fba"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Selenzyme",
-                                "name": "pathway"
+                                "description": "runtime parameter for tool Thermo",
+                                "name": "input"
                             }
                         ],
-                        "label": "Selenzyme",
-                        "name": "Selenzyme",
+                        "label": null,
+                        "name": "Thermo",
                         "outputs": [
                             {
-                                "name": "uniprot_ids",
+                                "name": "pathway_with_thermo",
                                 "type": "xml"
-                            },
-                            {
-                                "name": "uniprot_ids_csv",
-                                "type": "csv"
                             }
                         ],
                         "position": {
-                            "bottom": 508.1999969482422,
-                            "height": 225.1999969482422,
-                            "left": 553,
-                            "right": 753,
-                            "top": 283,
+                            "bottom": 559.1000061035156,
+                            "height": 113.60000610351562,
+                            "left": 719.5,
+                            "right": 919.5,
+                            "top": 445.5,
                             "width": 200,
-                            "x": 553,
-                            "y": 283
+                            "x": 719.5,
+                            "y": 445.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.2.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpthermo/rpthermo/5.12.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "34a9d136a5bf",
-                            "name": "selenzy",
+                            "changeset_revision": "21a900eee812",
+                            "name": "rpthermo",
                             "owner": "tduigou",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"host_taxID\": {\"__class__\": \"ConnectedValue\"}, \"enzyme_taxIDs\": {\"__class__\": \"ConnectedValue\"}, \"nb_ids\": \"-1\", \"nb_targets\": \"500\", \"direction\": \"0.0\", \"NoMSA\": \"true\"}, \"pathway\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"adv\": {\"ph\": \"7.5\", \"ionic_strength\": \"0.25\", \"pMg\": \"3.0\"}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.12.1",
                         "type": "tool",
-                        "uuid": "2136d777-a9ec-4904-a88e-155e40aaf22a",
+                        "uuid": "7b32553d-b992-4a54-a863-815f9b946581",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "uniprot_ids_csv",
-                                "uuid": "33768258-3781-4bd1-802c-e4b14cdca234"
-                            },
-                            {
-                                "label": "Uniprot IDs",
-                                "output_name": "uniprot_ids",
-                                "uuid": "54b833fa-ec4f-458a-b085-23211f4e56ca"
+                                "output_name": "pathway_with_thermo",
+                                "uuid": "bdcb02f8-c488-4098-a20a-b43e7c172847"
                             }
                         ]
                     },
                     {
-                        "annotation": "Extracts enzyme IDs from rpSBML files.",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpbasicdesign/rpbasicdesign/0.3.4",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpscore/rpscore/5.12.1",
                         "errors": null,
                         "id": 6,
                         "input_connections": {
-                            "adv|parts_files": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "rpsbml_file": {
+                            "pathway": {
                                 "id": 5,
-                                "output_name": "uniprot_ids"
+                                "output_name": "pathway_with_thermo"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool BasicDesign",
-                                "name": "adv"
-                            },
-                            {
-                                "description": "runtime parameter for tool BasicDesign",
-                                "name": "rpsbml_file"
-                            }
-                        ],
-                        "label": "BasicDesign",
-                        "name": "BasicDesign",
+                        "inputs": [],
+                        "label": null,
+                        "name": "Score Pathway",
                         "outputs": [
                             {
-                                "name": "sbol_dir",
-                                "type": "input"
-                            },
-                            {
-                                "name": "Constructs",
-                                "type": "csv"
-                            },
-                            {
-                                "name": "User parts plate",
-                                "type": "csv"
-                            },
-                            {
-                                "name": "Biolegio plate",
-                                "type": "csv"
+                                "name": "scored_pathway",
+                                "type": "xml"
                             }
                         ],
                         "position": {
-                            "bottom": 646.8000030517578,
-                            "height": 214.8000030517578,
-                            "left": 816,
-                            "right": 1016,
-                            "top": 432,
+                            "bottom": 544.6999969482422,
+                            "height": 93.19999694824219,
+                            "left": 1078.5,
+                            "right": 1278.5,
+                            "top": 451.5,
                             "width": 200,
-                            "x": 816,
-                            "y": 432
+                            "x": 1078.5,
+                            "y": 451.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpbasicdesign/rpbasicdesign/0.3.4",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpscore/rpscore/5.12.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "de9f53630349",
-                            "name": "rpbasicdesign",
+                            "changeset_revision": "da8ae7fa5ed3",
+                            "name": "rpscore",
                             "owner": "tduigou",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"parts_files\": {\"__class__\": \"RuntimeValue\"}, \"lms_id\": \"LMS\", \"lmp_id\": \"LMP\", \"cds_permutation\": \"true\"}, \"backbone_id\": \"BASIC_SEVA_37_CmR-p15A.1\", \"rpsbml_file\": {\"__class__\": \"RuntimeValue\"}, \"sample_size\": \"88\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"adv\": {\"no_of_rxns_thres\": \"10\"}, \"pathway\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.12.1",
                         "type": "tool",
-                        "uuid": "7a2617aa-2e4a-4214-b497-1a8102b85f8b",
+                        "uuid": "6b680491-6b40-4f44-943e-9026a9264b54",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "Constructs",
-                                "uuid": "afe416d0-ee9e-467b-81e0-b8a64f1251ac"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "User parts plate",
-                                "uuid": "2283c57e-2fa0-4177-95b9-64373f21d044"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "sbol_dir",
-                                "uuid": "81404f3f-327e-4c80-8ec7-c833ae5414fb"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "Biolegio plate",
-                                "uuid": "2d455fed-880e-4ab5-b15d-c1c7d789147a"
+                                "output_name": "scored_pathway",
+                                "uuid": "b1227404-d3a1-4a4d-a832-e89bdda762fa"
                             }
                         ]
                     },
                     {
-                        "annotation": "DNA assembly using BASIC on OpenTrons.",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/dnabot/dnabot/3.1.0",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpranker/rpranker/5.12.1",
                         "errors": null,
                         "id": 7,
                         "input_connections": {
-                            "adv|default_settings_file": {
-                                "id": 4,
-                                "output_name": "output"
-                            },
-                            "construct_file": {
+                            "pathway_collection": {
                                 "id": 6,
-                                "output_name": "Constructs"
-                            },
-                            "plate_files": [
-                                {
-                                    "id": 6,
-                                    "output_name": "User parts plate"
-                                },
-                                {
-                                    "id": 6,
-                                    "output_name": "Biolegio plate"
-                                }
-                            ]
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool DNA-Bot",
-                                "name": "adv"
-                            },
-                            {
-                                "description": "runtime parameter for tool DNA-Bot",
-                                "name": "construct_file"
-                            },
-                            {
-                                "description": "runtime parameter for tool DNA-Bot",
-                                "name": "plate_files"
+                                "output_name": "scored_pathway"
                             }
-                        ],
-                        "label": "DNA-Bot",
-                        "name": "DNA-Bot",
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Rank Pathways",
                         "outputs": [
                             {
-                                "name": "dnabot_scripts",
-                                "type": "tar"
+                                "name": "sorted_pathways",
+                                "type": "csv"
                             }
                         ],
                         "position": {
-                            "bottom": 728.8000030517578,
-                            "height": 194.8000030517578,
-                            "left": 1073,
-                            "right": 1273,
-                            "top": 534,
+                            "bottom": 538.6999969482422,
+                            "height": 93.19999694824219,
+                            "left": 1343.5,
+                            "right": 1543.5,
+                            "top": 445.5,
                             "width": 200,
-                            "x": 1073,
-                            "y": 534
+                            "x": 1343.5,
+                            "y": 445.5
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/dnabot/dnabot/3.1.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpranker/rpranker/5.12.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "de6812daba39",
-                            "name": "dnabot",
+                            "changeset_revision": "bab690866445",
+                            "name": "rpranker",
                             "owner": "tduigou",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"default_settings_file\": {\"__class__\": \"RuntimeValue\"}, \"etoh_well\": \"A11\", \"soc_column\": \"1\"}, \"construct_file\": {\"__class__\": \"RuntimeValue\"}, \"plate_files\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": null,
+                        "tool_state": "{\"pathway_collection\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.12.1",
                         "type": "tool",
-                        "uuid": "c09c99e4-5e0c-4c04-9f9b-3c30183d3816",
+                        "uuid": "39986296-e23e-4af7-ac3d-e84de3cb1b4c",
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "dnabot_scripts",
-                                "uuid": "ce5be4f0-48fb-45f0-84ad-15348645c950"
+                                "label": "Ranked Pathways",
+                                "output_name": "sorted_pathways",
+                                "uuid": "8111f525-5845-4ac2-a1d6-c4bfd218cf3f"
                             }
                         ]
                     }
                 ],
-                "parent_id": "synthetic-biology/basic_assembly_analysis",
-                "path": "topics/synthetic-biology/tutorials/basic_assembly_analysis/workflows/Genetic_Design_BASIC_Assembly.ga",
+                "parent_id": "synthetic-biology/pathway_analysis",
+                "path": "topics/synthetic-biology/tutorials/pathway_analysis/workflows/main_workflow.ga",
                 "tags": [
                     "synthetic-biology"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Genetic Design (BASIC Assembly)",
+                "title": "Pathway Analysis",
                 "topic_id": "synthetic-biology",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/synthetic-biology-basic_assembly_analysis/versions/genetic-design-basic-assembly",
-                "tutorial_id": "basic_assembly_analysis",
-                "url": "https://training.galaxyproject.org/training-material/topics/synthetic-biology/tutorials/basic_assembly_analysis/workflows/Genetic_Design_BASIC_Assembly.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/synthetic-biology/tutorials/basic_assembly_analysis/workflows/Genetic_Design_BASIC_Assembly.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/synthetic-biology-pathway_analysis/versions/main-workflow",
+                "tutorial_id": "pathway_analysis",
+                "url": "https://training.galaxyproject.org/training-material/topics/synthetic-biology/tutorials/pathway_analysis/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/synthetic-biology/tutorials/pathway_analysis/workflows/main_workflow.html",
                 "version": 1,
-                "wfid": "synthetic-biology-basic_assembly_analysis",
-                "wfname": "genetic-design-basic-assembly",
-                "workflow": "Genetic_Design_BASIC_Assembly.ga",
+                "wfid": "synthetic-biology-pathway_analysis",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/tduigou/dnabot/dnabot/3.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/tduigou/rpbasicdesign/rpbasicdesign/0.3.4",
-                    "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.2.0"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/rpfba/rpfba/5.12.1",
+                    "toolshed.g2.bx.psu.edu/repos/tduigou/rpranker/rpranker/5.12.1",
+                    "toolshed.g2.bx.psu.edu/repos/tduigou/rpscore/rpscore/5.12.1",
+                    "toolshed.g2.bx.psu.edu/repos/tduigou/rpthermo/rpthermo/5.12.1"
                 ],
-                "workflowhub_id": "1147"
+                "workflowhub_id": "1137"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/6123887"
+        "zenodo_link": "https://zenodo.org/record/6628296"
     },
     {
         "admin_install": {
@@ -256654,7 +263575,7 @@
         "license": "CC-BY-4.0",
         "logo": "GTN",
         "mod_date": "2024-02-20",
-        "pageviews": 5726884,
+        "pageviews": 5897564,
         "pub_date": "2019-06-04",
         "redirect_from": [
             "/topics/instructors/tutorials/workshop-intro/slides",
@@ -256691,7 +263612,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2063758
+        "visitors": 2133613
     },
     {
         "admin_install": {
@@ -256756,7 +263677,7 @@
         "license": "CC-BY-4.0",
         "logo": "GTN",
         "mod_date": "2024-08-08",
-        "pageviews": 2667600,
+        "pageviews": 2838280,
         "pub_date": "2022-09-23",
         "questions": [
             "How can I use the GTN for teaching?",
@@ -256791,8 +263712,8 @@
         "video": true,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 142,
-        "visitors": 1117114
+        "visit_duration": 143,
+        "visitors": 1186473
     },
     {
         "admin_install": {
@@ -256802,20 +263723,38 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/assessment/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "bebatut",
-                "fpsom",
-                "allegravia",
-                "ppalagi",
-                "elixir-goblet-ttt"
-            ],
-            "funding": [
-                "gallantries"
-            ]
-        },
+        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/setup-galaxy-for-training/tutorial.json",
         "contributors": [
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
             {
                 "affiliations": [
                     "gallantries",
@@ -256841,158 +263780,52 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
                 "twitter": "bebatut",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "elixir-europe"
-                ],
-                "elixir_node": "gr",
-                "email": "fpsom@certh.gr",
-                "id": "fpsom",
-                "joined": "2019-03",
-                "linkedin": "fpsom",
-                "matrix": "fpsom:matrix.org",
-                "name": "Fotis E. Psomopoulos",
-                "orcid": "0000-0002-0222-4273",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
-                "twitter": "fopsom",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
-            },
-            {
-                "id": "allegravia",
-                "joined": "2022-09",
-                "name": "Allegra Via",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/allegravia/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/allegravia.json"
-            },
-            {
-                "id": "ppalagi",
-                "joined": "2022-09",
-                "name": "Patricia Palagi",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ppalagi/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/ppalagi.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/elixir.png",
-                "github": false,
-                "id": "elixir-goblet-ttt",
-                "joined": "2022-09",
-                "name": "ELIXIR Goblet Train the Trainers",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-goblet-ttt/",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/elixir-goblet-ttt.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/teaching/tutorials/assessment",
+        "dir": "topics/teaching/tutorials/setup-galaxy-for-training",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "teaching/assessment",
+        "id": "teaching/setup-galaxy-for-training",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Formative assessment should be frequent",
-            "Feedback is hard"
+            "Technical requirements have been defined for all the training materials",
+            "Ephemeris can be used to automatically install these requirements to an existing Galaxy",
+            "Convenience scripts are provided in the training material repository allow for easy installation",
+            "Docker images can easily be created per topic"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2023-11-09",
         "objectives": [
-            "Describe the differences between formative and summative assessment",
-            "Explain why frequent feedback is important",
-            "Describe a few techniques for formative feedback",
-            "List a few techniques to cope with feedback on your teaching efforts"
+            "Use ephemeris to install the training requirements to a Galaxy instance",
+            "Create a docker image for a training topic"
         ],
-        "pageviews": 1039,
-        "pub_date": "2022-09-23",
+        "pageviews": 268,
+        "pub_date": "2018-06-04",
         "questions": [
-            "What are the different types of feedback?",
-            "When do get and receive feedback?",
-            "For which purpose do we need feedback?"
-        ],
-        "quiz": [
-            {
-                "contributors": [
-                    "bebatut"
-                ],
-                "id": "diagnostic_assessment.yaml",
-                "path": "topics/teaching/tutorials/assessment/quiz/diagnostic_assessment.yaml",
-                "title": "Diagnostic Assessment"
-            },
-            {
-                "contributors": [
-                    "bebatut"
-                ],
-                "id": "formative_assessment.yaml",
-                "path": "topics/teaching/tutorials/assessment/quiz/formative_assessment.yaml",
-                "title": "Collecting formative assessment"
-            },
-            {
-                "contributors": [
-                    "bebatut"
-                ],
-                "id": "frequency_formative_assessment.yaml",
-                "path": "topics/teaching/tutorials/assessment/quiz/frequency_formative_assessment.yaml",
-                "title": "How frequent should formative feedback be?"
-            },
-            {
-                "contributors": [
-                    "bebatut"
-                ],
-                "id": "integrate_formative_assessment.yaml",
-                "path": "topics/teaching/tutorials/assessment/quiz/integrate_formative_assessment.yaml",
-                "title": "How to integrate the result of formative assessment / feedback in your course?"
-            }
+            "How do I prepare my Galaxy instance to support a training module?",
+            "How can I generate a Docker Galaxy instance for my topic?"
         ],
-        "requirements": [
-            {
-                "topic_name": "contributing",
-                "tutorials": [
-                    "learning-principles",
-                    "design"
-                ],
-                "type": "internal"
-            }
+        "redirect_from": [
+            "/topics/instructors/tutorials/setup-galaxy-for-training/tutorial",
+            "/short/teaching/setup-galaxy-for-training",
+            "/short/T00285"
         ],
-        "short_id": "T00276",
+        "short_id": "T00285",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "pedagogy",
+        "subtopic": "prepare",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "3h30m",
-        "title": "Assessment and feedback in training and teachings",
+        "time_estimation": "2h",
+        "title": "Set up a Galaxy for Training",
         "tools": [],
         "topic_name": "teaching",
         "topic_name_human": "Teaching and Hosting Galaxy training",
@@ -257002,19 +263835,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "assessment",
+        "tutorial_name": "setup-galaxy-for-training",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/assessment/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/setup-galaxy-for-training/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/assessment/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/assessment/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/setup-galaxy-for-training/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/setup-galaxy-for-training/tutorial.json"
         },
-        "version": 10,
+        "version": 5,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 40,
-        "visitors": 879
+        "visit_duration": 198,
+        "visitors": 236
     },
     {
         "admin_install": {
@@ -257024,34 +263857,16 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/organize-workshop/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/gallantries-coursebuilder/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "hexylena"
+            ],
+            "funding": [
+                "gallantries"
+            ]
+        },
         "contributors": [
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
@@ -257080,157 +263895,6 @@
                 "orcid": "0000-0001-9760-8992",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            }
-        ],
-        "dir": "topics/teaching/tutorials/organize-workshop",
-        "edam_operation": [],
-        "edam_topic": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "teaching/organize-workshop",
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Running a workshop is not easy, there are many things to remember",
-            "This document is a non-exhaustive list, please add to it!"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": null,
-        "pageviews": 141,
-        "pub_date": "2018-11-15",
-        "questions": [
-            "What should we think about when we organize a workshop?",
-            "Have we done everything necessary for organising a great workshop?"
-        ],
-        "redirect_from": [
-            "/topics/instructors/tutorials/organize-workshop/tutorial",
-            "/short/teaching/organize-workshop",
-            "/short/T00283"
-        ],
-        "short_id": "T00283",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "prepare",
-        "supported_servers": [],
-        "symlink": null,
-        "time_estimation": "3H",
-        "title": "Organizing a workshop",
-        "tools": [],
-        "topic_name": "teaching",
-        "topic_name_human": "Teaching and Hosting Galaxy training",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "organize-workshop",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/organize-workshop/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/organize-workshop/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/organize-workshop/tutorial.json"
-        },
-        "version": 4,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 62,
-        "visitors": 125
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/motivation_demotivation/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "bebatut",
-                "fpsom",
-                "allegravia",
-                "ppalagi",
-                "elixir-goblet-ttt"
-            ],
-            "funding": [
-                "gallantries"
-            ]
-        },
-        "contributors": [
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "elixir-europe"
-                ],
-                "elixir_node": "gr",
-                "email": "fpsom@certh.gr",
-                "id": "fpsom",
-                "joined": "2019-03",
-                "linkedin": "fpsom",
-                "matrix": "fpsom:matrix.org",
-                "name": "Fotis E. Psomopoulos",
-                "orcid": "0000-0002-0222-4273",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
-                "twitter": "fopsom",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
-            },
-            {
-                "id": "allegravia",
-                "joined": "2022-09",
-                "name": "Allegra Via",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/allegravia/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/allegravia.json"
-            },
-            {
-                "id": "ppalagi",
-                "joined": "2022-09",
-                "name": "Patricia Palagi",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ppalagi/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/ppalagi.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/elixir.png",
-                "github": false,
-                "id": "elixir-goblet-ttt",
-                "joined": "2022-09",
-                "name": "ELIXIR Goblet Train the Trainers",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-goblet-ttt/",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/elixir-goblet-ttt.json"
             },
             {
                 "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
@@ -257259,187 +263923,49 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/teaching/tutorials/motivation_demotivation",
+        "dir": "topics/teaching/tutorials/gallantries-coursebuilder",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "teaching/motivation_demotivation",
+        "id": "teaching/gallantries-coursebuilder",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "To have fully MOTIVATED learners, it is important that learners see the value, learner self-efficacy is high and the environment is supportive"
+            "Can make hosting Gallantries/Sm\u00f6rg\u00e5sbord style courses easier"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2023-11-02",
         "objectives": [
-            "List factors of motivation and demotivation",
-            "Identify what instructors can do to motivate and avoid demotivating learners"
+            "Identify if it is appropriate"
         ],
-        "pageviews": 1615,
-        "pub_date": "2022-09-23",
+        "pageviews": 67,
+        "pub_date": "2023-11-02",
         "questions": [
-            "What is motivation and demotivation?",
-            "How do motivation and demotivation impact learning processes?",
-            "What can instructors do to motivate learners?"
-        ],
-        "quiz": [
-            {
-                "contributors": [
-                    "bebatut"
-                ],
-                "id": "demotivating_learning_experience.yaml",
-                "path": "topics/teaching/tutorials/motivation_demotivation/quiz/demotivating_learning_experience.yaml",
-                "title": "Recall a demotivating learning experience"
-            },
-            {
-                "contributors": [
-                    "bebatut"
-                ],
-                "id": "motivating_learning_experience.yaml",
-                "path": "topics/teaching/tutorials/motivation_demotivation/quiz/motivating_learning_experience.yaml",
-                "title": "Recall a motivating learning experience"
-            }
+            "Is this service appropriate for my event?"
         ],
         "requirements": [
             {
                 "topic_name": "contributing",
-                "tutorials": [
-                    "learning-principles"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00282",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "pedagogy",
-        "supported_servers": [],
-        "symlink": null,
-        "time_estimation": "60m",
-        "title": "Motivation and Demotivation",
-        "tools": [],
-        "topic_name": "teaching",
-        "topic_name_human": "Teaching and Hosting Galaxy training",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "motivation_demotivation",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/motivation_demotivation/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/motivation_demotivation/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/motivation_demotivation/tutorial.json"
-        },
-        "version": 10,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 40,
-        "visitors": 1370
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/galaxy-admin-training/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            }
-        ],
-        "dir": "topics/teaching/tutorials/galaxy-admin-training",
-        "edam_operation": [],
-        "edam_topic": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "teaching/galaxy-admin-training",
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Infrastructure is available for running GATs for free from UseGalaxy.eu",
-            "This can be very convenient and easy to use",
-            "EU provides appropriate DNS entries so you can run trainings with ITs."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Interact with the UseGalaxy.eu admins to arrange for infrastructure",
-            "Run a great training!"
-        ],
-        "pageviews": 103,
-        "pub_date": "2020-11-04",
-        "questions": [
-            "How do I organise a Galaxy Admin Training (GAT)",
-            "What do I need to set up?",
-            "What should I know during the training?"
-        ],
-        "redirect_from": [
-            "/topics/instructors/tutorials/galaxy-admin-training/tutorial",
-            "/short/teaching/galaxy-admin-training",
-            "/short/T00278"
-        ],
-        "requirements": [
-            {
-                "topic_name": "admin",
-                "tutorials": [
-                    "ansible",
-                    "terraform"
-                ],
                 "type": "internal"
             }
         ],
-        "short_id": "T00278",
+        "short_id": "T00372",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "prepare",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "60m",
-        "title": "Galaxy Admin Training",
+        "tags": [
+            "cyoa"
+        ],
+        "time_estimation": "10m",
+        "title": "Course Builder",
         "tools": [],
         "topic_name": "teaching",
         "topic_name_human": "Teaching and Hosting Galaxy training",
@@ -257449,19 +263975,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "galaxy-admin-training",
+        "tutorial_name": "gallantries-coursebuilder",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/galaxy-admin-training/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/gallantries-coursebuilder/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/galaxy-admin-training/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/galaxy-admin-training/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/gallantries-coursebuilder/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/gallantries-coursebuilder/tutorial.json"
         },
-        "version": 4,
+        "version": 1,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 205,
-        "visitors": 93
+        "visit_duration": 103,
+        "visitors": 55
     },
     {
         "admin_install": {
@@ -257471,38 +263997,8 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/setup-galaxy-for-training/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/live-coding/tutorial.json",
         "contributors": [
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
@@ -257528,52 +264024,75 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
                 "twitter": "bebatut",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "elixir-europe"
+                ],
+                "elixir_node": "gr",
+                "email": "fpsom@certh.gr",
+                "id": "fpsom",
+                "joined": "2019-03",
+                "linkedin": "fpsom",
+                "matrix": "fpsom:matrix.org",
+                "name": "Fotis E. Psomopoulos",
+                "orcid": "0000-0002-0222-4273",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
+                "twitter": "fopsom",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
+            },
+            {
+                "id": "carpentries",
+                "joined": "2021-09",
+                "name": "The Carpentries",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
+                "ror": "0356fgm10",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
             }
         ],
-        "dir": "topics/teaching/tutorials/setup-galaxy-for-training",
+        "dir": "topics/teaching/tutorials/live-coding",
+        "draft": true,
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "teaching/setup-galaxy-for-training",
+        "id": "teaching/live-coding",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Technical requirements have been defined for all the training materials",
-            "Ephemeris can be used to automatically install these requirements to an existing Galaxy",
-            "Convenience scripts are provided in the training material repository allow for easy installation",
-            "Docker images can easily be created per topic"
+            "Live coding forces the instructor to slow down.",
+            "Coding-along gives learners continuous practice and feedback.\\",
+            "Mistakes made during participatory live coding are valuable learning opportunities."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2023-11-09",
         "objectives": [
-            "Use ephemeris to install the training requirements to a Galaxy instance",
-            "Create a docker image for a training topic"
+            "Explain the advantages and limitations of participatory live coding.",
+            "Summarize the key dos and do nots of participatory live coding.",
+            "Demonstrate participatory live coding."
         ],
-        "pageviews": 256,
-        "pub_date": "2018-06-04",
+        "pageviews": 56,
+        "pub_date": "2022-09-23",
         "questions": [
-            "How do I prepare my Galaxy instance to support a training module?",
-            "How can I generate a Docker Galaxy instance for my topic?"
-        ],
-        "redirect_from": [
-            "/topics/instructors/tutorials/setup-galaxy-for-training/tutorial",
-            "/short/teaching/setup-galaxy-for-training",
-            "/short/T00285"
+            "Why do we teach programming using participatory live coding?"
         ],
-        "short_id": "T00285",
+        "short_id": "T00281",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "prepare",
+        "subtopic": "practises",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "2h",
-        "title": "Set up a Galaxy for Training",
+        "tags": [
+            "work-in-progress"
+        ],
+        "time_estimation": "1h",
+        "title": "Live Coding is a Skill",
         "tools": [],
         "topic_name": "teaching",
         "topic_name_human": "Teaching and Hosting Galaxy training",
@@ -257583,19 +264102,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "setup-galaxy-for-training",
+        "tutorial_name": "live-coding",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/setup-galaxy-for-training/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/live-coding/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/setup-galaxy-for-training/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/setup-galaxy-for-training/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/live-coding/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/live-coding/tutorial.json"
         },
-        "version": 5,
+        "version": 6,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 202,
-        "visitors": 227
+        "visit_duration": 0,
+        "visitors": 56
     },
     {
         "admin_install": {
@@ -257605,7 +264124,7 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/live-coding/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/organize-workshop/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
@@ -257636,71 +264155,72 @@
             {
                 "affiliations": [
                     "gallantries",
-                    "elixir-europe"
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
                 ],
-                "elixir_node": "gr",
-                "email": "fpsom@certh.gr",
-                "id": "fpsom",
-                "joined": "2019-03",
-                "linkedin": "fpsom",
-                "matrix": "fpsom:matrix.org",
-                "name": "Fotis E. Psomopoulos",
-                "orcid": "0000-0002-0222-4273",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
-                "twitter": "fopsom",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
-            },
-            {
-                "id": "carpentries",
-                "joined": "2021-09",
-                "name": "The Carpentries",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
-                "ror": "0356fgm10",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "dir": "topics/teaching/tutorials/live-coding",
-        "draft": true,
+        "dir": "topics/teaching/tutorials/organize-workshop",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "teaching/live-coding",
+        "id": "teaching/organize-workshop",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Live coding forces the instructor to slow down.",
-            "Coding-along gives learners continuous practice and feedback.\\",
-            "Mistakes made during participatory live coding are valuable learning opportunities."
+            "Running a workshop is not easy, there are many things to remember",
+            "This document is a non-exhaustive list, please add to it!"
         ],
         "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Explain the advantages and limitations of participatory live coding.",
-            "Summarize the key dos and do nots of participatory live coding.",
-            "Demonstrate participatory live coding."
-        ],
-        "pageviews": 55,
-        "pub_date": "2022-09-23",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": null,
+        "pageviews": 157,
+        "pub_date": "2018-11-15",
         "questions": [
-            "Why do we teach programming using participatory live coding?"
+            "What should we think about when we organize a workshop?",
+            "Have we done everything necessary for organising a great workshop?"
         ],
-        "short_id": "T00281",
+        "redirect_from": [
+            "/topics/instructors/tutorials/organize-workshop/tutorial",
+            "/short/teaching/organize-workshop",
+            "/short/T00283"
+        ],
+        "short_id": "T00283",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "practises",
+        "subtopic": "prepare",
         "supported_servers": [],
         "symlink": null,
-        "tags": [
-            "work-in-progress"
-        ],
-        "time_estimation": "1h",
-        "title": "Live Coding is a Skill",
+        "time_estimation": "3H",
+        "title": "Organizing a workshop",
         "tools": [],
         "topic_name": "teaching",
         "topic_name_human": "Teaching and Hosting Galaxy training",
@@ -257710,19 +264230,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "live-coding",
+        "tutorial_name": "organize-workshop",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/live-coding/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/organize-workshop/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/live-coding/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/live-coding/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/organize-workshop/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/organize-workshop/tutorial.json"
         },
-        "version": 6,
+        "version": 4,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 0,
-        "visitors": 55
+        "visit_duration": 62,
+        "visitors": 140
     },
     {
         "admin_install": {
@@ -257732,14 +264252,11 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/learner_participation_engagement/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/hybrid-training/tutorial.json",
         "contributions": {
             "authorship": [
                 "bebatut",
-                "fpsom",
-                "allegravia",
-                "ppalagi",
-                "elixir-goblet-ttt"
+                "fpsom"
             ],
             "funding": [
                 "gallantries"
@@ -257789,29 +264306,6 @@
                 "twitter": "fopsom",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
             },
-            {
-                "id": "allegravia",
-                "joined": "2022-09",
-                "name": "Allegra Via",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/allegravia/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/allegravia.json"
-            },
-            {
-                "id": "ppalagi",
-                "joined": "2022-09",
-                "name": "Patricia Palagi",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ppalagi/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/ppalagi.json"
-            },
-            {
-                "avatar": "/training-material/shared/images/elixir.png",
-                "github": false,
-                "id": "elixir-goblet-ttt",
-                "joined": "2022-09",
-                "name": "ELIXIR Goblet Train the Trainers",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-goblet-ttt/",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/elixir-goblet-ttt.json"
-            },
             {
                 "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
                 "end_date": "2023-09-30",
@@ -257839,98 +264333,48 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/teaching/tutorials/learner_participation_engagement",
+        "dir": "topics/teaching/tutorials/hybrid-training",
+        "draft": true,
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "teaching/learner_participation_engagement",
+        "id": "teaching/hybrid-training",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Select learning experiences according to the Training Goals, write the Learning Objectives and identify the corresponding Bloom's level",
-            "Select teaching practices (learning techniques) that will allow learners to achieve the LOs",
-            "Always remember that learning occurs BY DOING, which means that learners will be able to DESCRIBE something if and only if they will have the chance to practice it; they will be able to APPLY a rule only after having applied themselves the rule, and that, in order to successfully practice the APPLICATION of the rule, they must remember the rule, they must have understood it and how it can be used for applications, and they must have seen examples of how to apply it.",
-            "Be aware of other practices and behaviours supporting interactivity, a positive and engaging learning environment, active and collaborative learning, stimulating lessons, frequent feedback"
+            "With hybrid training events, remote instructors pair up with on-site helpers to deliver 1 training across multiple sites simultaneously",
+            "Hybrid training events reduce costs and improve accessibility"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-11",
+        "mod_date": "2024-06-25",
         "objectives": [
-            "Describe what makes training effective",
-            "Describe what makes a trainer effective",
-            "Identify some strategies that facilitate active, interactive and collaborative learning"
+            "Describe hybrid training",
+            "Organize an hybrid training event using Galaxy"
         ],
-        "pageviews": 1590,
+        "pageviews": 10,
         "pub_date": "2022-09-23",
         "questions": [
-            "What does make a training effective?",
-            "How can instructors enhance learner participation and engagement?"
-        ],
-        "quiz": [
-            {
-                "contributors": [
-                    "bebatut"
-                ],
-                "id": "active_learning_strategies.yaml",
-                "path": "topics/teaching/tutorials/learner_participation_engagement/quiz/active_learning_strategies.yaml",
-                "title": "Which strategies for active learning training did you use?"
-            },
-            {
-                "contributors": [
-                    "bebatut"
-                ],
-                "id": "active_learning_strategies_bloom_levels.yaml",
-                "path": "topics/teaching/tutorials/learner_participation_engagement/quiz/active_learning_strategies_bloom_levels.yaml",
-                "title": "What is the highest Bloom's level supported by each teaching technique?"
-            },
-            {
-                "contributors": [
-                    "bebatut"
-                ],
-                "id": "effective_training_trainer.yaml",
-                "path": "topics/teaching/tutorials/learner_participation_engagement/quiz/effective_training_trainer.yaml",
-                "title": "What makes training effective and a good trainer?"
-            },
-            {
-                "contributors": [
-                    "bebatut"
-                ],
-                "id": "mazur_interview.yaml",
-                "path": "topics/teaching/tutorials/learner_participation_engagement/quiz/mazur_interview.yaml",
-                "title": "Reflect on Mazur's interview"
-            },
-            {
-                "contributors": [
-                    "bebatut"
-                ],
-                "id": "trainer_skills.yaml",
-                "path": "topics/teaching/tutorials/learner_participation_engagement/quiz/trainer_skills.yaml",
-                "title": "Reflect on your skills as a trainer"
-            }
-        ],
-        "requirements": [
-            {
-                "topic_name": "contributing",
-                "tutorials": [
-                    "learning-principles",
-                    "design"
-                ],
-                "type": "internal"
-            }
+            "What is hybrid training?",
+            "How to deliver hybrid training using Galaxy?",
+            "What should be prepared for an hybrid training event?"
         ],
-        "short_id": "T00280",
+        "short_id": "T00279",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "pedagogy",
+        "subtopic": "practises",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "60m",
-        "title": "Training techniques to enhance learner participation and engagement",
+        "tags": [
+            "work-in-progress"
+        ],
+        "time_estimation": "1h",
+        "title": "Hybrid training",
         "tools": [],
         "topic_name": "teaching",
         "topic_name_human": "Teaching and Hosting Galaxy training",
@@ -257940,19 +264384,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "learner_participation_engagement",
+        "tutorial_name": "hybrid-training",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/learner_participation_engagement/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/hybrid-training/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/learner_participation_engagement/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/learner_participation_engagement/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/hybrid-training/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/hybrid-training/tutorial.json"
         },
-        "version": 13,
+        "version": 7,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 46,
-        "visitors": 1331
+        "visit_duration": 3,
+        "visitors": 8
     },
     {
         "admin_install": {
@@ -257962,11 +264406,14 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/hybrid-training/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/motivation_demotivation/tutorial.json",
         "contributions": {
             "authorship": [
                 "bebatut",
-                "fpsom"
+                "fpsom",
+                "allegravia",
+                "ppalagi",
+                "elixir-goblet-ttt"
             ],
             "funding": [
                 "gallantries"
@@ -258016,6 +264463,29 @@
                 "twitter": "fopsom",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
             },
+            {
+                "id": "allegravia",
+                "joined": "2022-09",
+                "name": "Allegra Via",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/allegravia/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/allegravia.json"
+            },
+            {
+                "id": "ppalagi",
+                "joined": "2022-09",
+                "name": "Patricia Palagi",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ppalagi/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/ppalagi.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/elixir.png",
+                "github": false,
+                "id": "elixir-goblet-ttt",
+                "joined": "2022-09",
+                "name": "ELIXIR Goblet Train the Trainers",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-goblet-ttt/",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/elixir-goblet-ttt.json"
+            },
             {
                 "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
                 "end_date": "2023-09-30",
@@ -258043,48 +264513,70 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/teaching/tutorials/hybrid-training",
-        "draft": true,
+        "dir": "topics/teaching/tutorials/motivation_demotivation",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "teaching/hybrid-training",
+        "id": "teaching/motivation_demotivation",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "With hybrid training events, remote instructors pair up with on-site helpers to deliver 1 training across multiple sites simultaneously",
-            "Hybrid training events reduce costs and improve accessibility"
+            "To have fully MOTIVATED learners, it is important that learners see the value, learner self-efficacy is high and the environment is supportive"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-25",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Describe hybrid training",
-            "Organize an hybrid training event using Galaxy"
+            "List factors of motivation and demotivation",
+            "Identify what instructors can do to motivate and avoid demotivating learners"
         ],
-        "pageviews": 10,
+        "pageviews": 1732,
         "pub_date": "2022-09-23",
         "questions": [
-            "What is hybrid training?",
-            "How to deliver hybrid training using Galaxy?",
-            "What should be prepared for an hybrid training event?"
+            "What is motivation and demotivation?",
+            "How do motivation and demotivation impact learning processes?",
+            "What can instructors do to motivate learners?"
         ],
-        "short_id": "T00279",
+        "quiz": [
+            {
+                "contributors": [
+                    "bebatut"
+                ],
+                "id": "demotivating_learning_experience.yaml",
+                "path": "topics/teaching/tutorials/motivation_demotivation/quiz/demotivating_learning_experience.yaml",
+                "title": "Recall a demotivating learning experience"
+            },
+            {
+                "contributors": [
+                    "bebatut"
+                ],
+                "id": "motivating_learning_experience.yaml",
+                "path": "topics/teaching/tutorials/motivation_demotivation/quiz/motivating_learning_experience.yaml",
+                "title": "Recall a motivating learning experience"
+            }
+        ],
+        "requirements": [
+            {
+                "topic_name": "contributing",
+                "tutorials": [
+                    "learning-principles"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00282",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "practises",
+        "subtopic": "pedagogy",
         "supported_servers": [],
         "symlink": null,
-        "tags": [
-            "work-in-progress"
-        ],
-        "time_estimation": "1h",
-        "title": "Hybrid training",
+        "time_estimation": "60m",
+        "title": "Motivation and Demotivation",
         "tools": [],
         "topic_name": "teaching",
         "topic_name_human": "Teaching and Hosting Galaxy training",
@@ -258094,19 +264586,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "hybrid-training",
+        "tutorial_name": "motivation_demotivation",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/hybrid-training/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/motivation_demotivation/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/hybrid-training/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/hybrid-training/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/motivation_demotivation/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/motivation_demotivation/tutorial.json"
         },
-        "version": 7,
+        "version": 10,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 3,
-        "visitors": 8
+        "visit_duration": 40,
+        "visitors": 1474
     },
     {
         "admin_install": {
@@ -258171,7 +264663,7 @@
             "Identify if it is appropriate",
             "Interact with the service administrators to arrange for infrastructure"
         ],
-        "pageviews": 308,
+        "pageviews": 323,
         "pub_date": "2018-11-15",
         "questions": [
             "Is this service appropriate for my event?"
@@ -258213,125 +264705,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 253,
-        "visitors": 131
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/experiences/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "elixir-europe"
-                ],
-                "elixir_node": "gr",
-                "email": "fpsom@certh.gr",
-                "id": "fpsom",
-                "joined": "2019-03",
-                "linkedin": "fpsom",
-                "matrix": "fpsom:matrix.org",
-                "name": "Fotis E. Psomopoulos",
-                "orcid": "0000-0002-0222-4273",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
-                "twitter": "fopsom",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
-            }
-        ],
-        "dir": "topics/teaching/tutorials/experiences",
-        "edam_operation": [],
-        "edam_topic": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "teaching/experiences",
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Every instructor has their prefered way to teach using Galaxy"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2022-09-23",
-        "objectives": [
-            "Learn how others teach using Galaxy"
-        ],
-        "pageviews": 396,
-        "pub_date": "2022-09-23",
-        "questions": [
-            "How to teach using Galaxy?",
-            "What are the different practises?"
-        ],
-        "redirect_from": [
-            "/topics/instructors/philosophies/",
-            "/short/teaching/experiences",
-            "/short/T00277"
-        ],
-        "short_id": "T00277",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "practises",
-        "supported_servers": [],
-        "symlink": null,
-        "time_estimation": "1h",
-        "title": "Teaching experiences",
-        "tools": [],
-        "topic_name": "teaching",
-        "topic_name_human": "Teaching and Hosting Galaxy training",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "experiences",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/experiences/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/experiences/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/experiences/tutorial.json"
-        },
-        "version": 1,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 192,
-        "visitors": 182
+        "visit_duration": 277,
+        "visitors": 140
     },
     {
         "admin_install": {
@@ -258341,7 +264716,7 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/workshop-final-exercise/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/assessment/tutorial.json",
         "contributions": {
             "authorship": [
                 "bebatut",
@@ -258448,32 +264823,70 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/teaching/tutorials/workshop-final-exercise",
+        "dir": "topics/teaching/tutorials/assessment",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "teaching/workshop-final-exercise",
+        "id": "teaching/assessment",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Feedback needs to be positive and be specific"
+            "Formative assessment should be frequent",
+            "Feedback is hard"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-10-23",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Create a 5 minute training",
-            "Deliver a 5 minute training",
-            "Deliver and receive feedback"
+            "Describe the differences between formative and summative assessment",
+            "Explain why frequent feedback is important",
+            "Describe a few techniques for formative feedback",
+            "List a few techniques to cope with feedback on your teaching efforts"
         ],
-        "pageviews": 47,
-        "pub_date": "2023-06-12",
+        "pageviews": 1112,
+        "pub_date": "2022-09-23",
         "questions": [
-            "How can we apply all pedagogical concepts together for training?"
+            "What are the different types of feedback?",
+            "When do get and receive feedback?",
+            "For which purpose do we need feedback?"
+        ],
+        "quiz": [
+            {
+                "contributors": [
+                    "bebatut"
+                ],
+                "id": "diagnostic_assessment.yaml",
+                "path": "topics/teaching/tutorials/assessment/quiz/diagnostic_assessment.yaml",
+                "title": "Diagnostic Assessment"
+            },
+            {
+                "contributors": [
+                    "bebatut"
+                ],
+                "id": "formative_assessment.yaml",
+                "path": "topics/teaching/tutorials/assessment/quiz/formative_assessment.yaml",
+                "title": "Collecting formative assessment"
+            },
+            {
+                "contributors": [
+                    "bebatut"
+                ],
+                "id": "frequency_formative_assessment.yaml",
+                "path": "topics/teaching/tutorials/assessment/quiz/frequency_formative_assessment.yaml",
+                "title": "How frequent should formative feedback be?"
+            },
+            {
+                "contributors": [
+                    "bebatut"
+                ],
+                "id": "integrate_formative_assessment.yaml",
+                "path": "topics/teaching/tutorials/assessment/quiz/integrate_formative_assessment.yaml",
+                "title": "How to integrate the result of formative assessment / feedback in your course?"
+            }
         ],
         "requirements": [
             {
@@ -258483,25 +264896,17 @@
                     "design"
                 ],
                 "type": "internal"
-            },
-            {
-                "topic_name": "teaching",
-                "tutorials": [
-                    "assessment",
-                    "motivation_demotivation"
-                ],
-                "type": "internal"
             }
         ],
-        "short_id": "T00354",
+        "short_id": "T00276",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "pedagogy",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "60m",
-        "title": "Train-the-Trainer: putting it all together",
+        "time_estimation": "3h30m",
+        "title": "Assessment and feedback in training and teachings",
         "tools": [],
         "topic_name": "teaching",
         "topic_name_human": "Teaching and Hosting Galaxy training",
@@ -258511,19 +264916,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "workshop-final-exercise",
+        "tutorial_name": "assessment",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/workshop-final-exercise/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/assessment/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/workshop-final-exercise/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/workshop-final-exercise/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/assessment/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/assessment/tutorial.json"
         },
-        "version": 2,
+        "version": 10,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 50,
-        "visitors": 40
+        "visit_duration": 43,
+        "visitors": 943
     },
     {
         "admin_install": {
@@ -258533,7 +264938,7 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/running-workshop/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/experiences/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
@@ -258561,133 +264966,64 @@
                 "twitter": "bebatut",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             },
-            {
-                "affiliations": [
-                    "eurosciencegateway",
-                    "eosc-life",
-                    "by-covid",
-                    "deNBI",
-                    "sfb992",
-                    "elixir-converge",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "de",
-                "email": "bjoern.gruening@gmail.com",
-                "fediverse": "https://fosstodon.org/@bgruening",
-                "fediverse_flavor": "mastodon",
-                "id": "bgruening",
-                "joined": "2017-09",
-                "linkedin": "bgruening",
-                "location": {
-                    "country": "DE",
-                    "lat": 47.997791,
-                    "lon": 7.842609
-                },
-                "matrix": "bgruening:matrix.org",
-                "name": "Bj\u00f6rn Gr\u00fcning",
-                "orcid": "0000-0002-3079-6586",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
-                "twitter": "bjoerngruening",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
             {
                 "affiliations": [
                     "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
+                    "elixir-europe"
                 ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+                "elixir_node": "gr",
+                "email": "fpsom@certh.gr",
+                "id": "fpsom",
+                "joined": "2019-03",
+                "linkedin": "fpsom",
+                "matrix": "fpsom:matrix.org",
+                "name": "Fotis E. Psomopoulos",
+                "orcid": "0000-0002-0222-4273",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
+                "twitter": "fopsom",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
             }
         ],
-        "dir": "topics/teaching/tutorials/running-workshop",
+        "dir": "topics/teaching/tutorials/experiences",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "teaching/running-workshop",
+        "id": "teaching/experiences",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "The take-home messages",
-            "They will appear at the end of the tutorial"
+            "Every instructor has their prefered way to teach using Galaxy"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": null,
-        "pageviews": 182,
-        "pub_date": "2018-11-15",
-        "questions": null,
+        "mod_date": "2022-09-23",
+        "objectives": [
+            "Learn how others teach using Galaxy"
+        ],
+        "pageviews": 406,
+        "pub_date": "2022-09-23",
+        "questions": [
+            "How to teach using Galaxy?",
+            "What are the different practises?"
+        ],
         "redirect_from": [
-            "/topics/instructors/tutorials/running-workshop/tutorial",
-            "/short/teaching/running-workshop",
-            "/short/T00284"
+            "/topics/instructors/philosophies/",
+            "/short/teaching/experiences",
+            "/short/T00277"
         ],
-        "short_id": "T00284",
+        "short_id": "T00277",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "prepare",
+        "subtopic": "practises",
         "supported_servers": [],
         "symlink": null,
-        "time_estimation": "3H",
-        "title": "Running a workshop as instructor",
+        "time_estimation": "1h",
+        "title": "Teaching experiences",
         "tools": [],
         "topic_name": "teaching",
         "topic_name_human": "Teaching and Hosting Galaxy training",
@@ -258697,19 +265033,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "running-workshop",
+        "tutorial_name": "experiences",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/running-workshop/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/experiences/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/running-workshop/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/running-workshop/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/experiences/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/experiences/tutorial.json"
         },
-        "version": 5,
+        "version": 1,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 54,
-        "visitors": 65
+        "visit_duration": 192,
+        "visitors": 192
     },
     {
         "admin_install": {
@@ -258719,10 +265055,11 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/gallantries-coursebuilder/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/teaching-online/tutorial.json",
         "contributions": {
             "authorship": [
-                "hexylena"
+                "bebatut",
+                "fpsom"
             ],
             "funding": [
                 "gallantries"
@@ -258732,31 +265069,45 @@
             {
                 "affiliations": [
                     "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
+                    "ifb",
+                    "elixir-europe"
                 ],
-                "id": "hexylena",
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
                 "joined": "2017-09",
+                "linkedin": "berenicebatut",
                 "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
                 },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "elixir-europe"
+                ],
+                "elixir_node": "gr",
+                "email": "fpsom@certh.gr",
+                "id": "fpsom",
+                "joined": "2019-03",
+                "linkedin": "fpsom",
+                "matrix": "fpsom:matrix.org",
+                "name": "Fotis E. Psomopoulos",
+                "orcid": "0000-0002-0222-4273",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
+                "twitter": "fopsom",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
             },
             {
                 "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
@@ -258785,49 +265136,46 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/teaching/tutorials/gallantries-coursebuilder",
+        "dir": "topics/teaching/tutorials/teaching-online",
+        "draft": true,
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "teaching/gallantries-coursebuilder",
+        "id": "teaching/teaching-online",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Can make hosting Gallantries/Sm\u00f6rg\u00e5sbord style courses easier"
+            "There are different ways of teaching online"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-02",
+        "mod_date": "2023-10-23",
         "objectives": [
-            "Identify if it is appropriate"
+            "List different ways to teach online",
+            "Use Galaxy to teach online"
         ],
-        "pageviews": 58,
-        "pub_date": "2023-11-02",
+        "pageviews": 13,
+        "pub_date": "2022-09-23",
         "questions": [
-            "Is this service appropriate for my event?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "contributing",
-                "type": "internal"
-            }
+            "What are the different ways of teaching online?",
+            "How Galaxy can be used to teach online?"
         ],
-        "short_id": "T00372",
+        "short_id": "T00287",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "prepare",
+        "subtopic": "practises",
         "supported_servers": [],
         "symlink": null,
         "tags": [
-            "cyoa"
+            "work-in-progress"
         ],
-        "time_estimation": "10m",
-        "title": "Course Builder",
+        "time_estimation": "1h",
+        "title": "Teaching online",
         "tools": [],
         "topic_name": "teaching",
         "topic_name_human": "Teaching and Hosting Galaxy training",
@@ -258837,19 +265185,19 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "gallantries-coursebuilder",
+        "tutorial_name": "teaching-online",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/gallantries-coursebuilder/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/teaching-online/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/gallantries-coursebuilder/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/gallantries-coursebuilder/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/teaching-online/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/teaching-online/tutorial.json"
         },
-        "version": 1,
+        "version": 4,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 103,
-        "visitors": 48
+        "visit_duration": 0,
+        "visitors": 13
     },
     {
         "admin_install": {
@@ -259045,11 +265393,14 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/teaching-online/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/learner_participation_engagement/tutorial.json",
         "contributions": {
             "authorship": [
                 "bebatut",
-                "fpsom"
+                "fpsom",
+                "allegravia",
+                "ppalagi",
+                "elixir-goblet-ttt"
             ],
             "funding": [
                 "gallantries"
@@ -259099,6 +265450,29 @@
                 "twitter": "fopsom",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
             },
+            {
+                "id": "allegravia",
+                "joined": "2022-09",
+                "name": "Allegra Via",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/allegravia/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/allegravia.json"
+            },
+            {
+                "id": "ppalagi",
+                "joined": "2022-09",
+                "name": "Patricia Palagi",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ppalagi/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/ppalagi.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/elixir.png",
+                "github": false,
+                "id": "elixir-goblet-ttt",
+                "joined": "2022-09",
+                "name": "ELIXIR Goblet Train the Trainers",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-goblet-ttt/",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/elixir-goblet-ttt.json"
+            },
             {
                 "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
                 "end_date": "2023-09-30",
@@ -259126,1288 +265500,616 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/teaching/tutorials/teaching-online",
-        "draft": true,
+        "dir": "topics/teaching/tutorials/learner_participation_engagement",
         "edam_operation": [],
         "edam_topic": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "teaching/teaching-online",
+        "id": "teaching/learner_participation_engagement",
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "There are different ways of teaching online"
+            "Select learning experiences according to the Training Goals, write the Learning Objectives and identify the corresponding Bloom's level",
+            "Select teaching practices (learning techniques) that will allow learners to achieve the LOs",
+            "Always remember that learning occurs BY DOING, which means that learners will be able to DESCRIBE something if and only if they will have the chance to practice it; they will be able to APPLY a rule only after having applied themselves the rule, and that, in order to successfully practice the APPLICATION of the rule, they must remember the rule, they must have understood it and how it can be used for applications, and they must have seen examples of how to apply it.",
+            "Be aware of other practices and behaviours supporting interactivity, a positive and engaging learning environment, active and collaborative learning, stimulating lessons, frequent feedback"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-10-23",
+        "mod_date": "2024-06-11",
         "objectives": [
-            "List different ways to teach online",
-            "Use Galaxy to teach online"
+            "Describe what makes training effective",
+            "Describe what makes a trainer effective",
+            "Identify some strategies that facilitate active, interactive and collaborative learning"
         ],
-        "pageviews": 13,
+        "pageviews": 1634,
         "pub_date": "2022-09-23",
         "questions": [
-            "What are the different ways of teaching online?",
-            "How Galaxy can be used to teach online?"
-        ],
-        "short_id": "T00287",
-        "short_tools": [],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "practises",
-        "supported_servers": [],
-        "symlink": null,
-        "tags": [
-            "work-in-progress"
+            "What does make a training effective?",
+            "How can instructors enhance learner participation and engagement?"
         ],
-        "time_estimation": "1h",
-        "title": "Teaching online",
-        "tools": [],
-        "topic_name": "teaching",
-        "topic_name_human": "Teaching and Hosting Galaxy training",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "teaching-online",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/teaching-online/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/teaching-online/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/teaching-online/tutorial.json"
-        },
-        "version": 4,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 0,
-        "visitors": 13
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "e7b2202befea",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "chira_collapse",
-                    "owner": "iuc",
-                    "revisions": "2b2bfeda00d0",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "chira_extract",
-                    "owner": "iuc",
-                    "revisions": "e7ee3aadf1a5",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "chira_map",
-                    "owner": "iuc",
-                    "revisions": "95ddee768b61",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "chira_merge",
-                    "owner": "iuc",
-                    "revisions": "6492560fe1b4",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "chira_quantify",
-                    "owner": "iuc",
-                    "revisions": "06ac35533793",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "query_tabular",
-                    "owner": "iuc",
-                    "revisions": "33d61c89fb8d",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "cutadapt",
-                    "owner": "lparsons",
-                    "revisions": "49370cb85f0f",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chira_collapse\n  owner: iuc\n  revisions: 2b2bfeda00d0\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chira_extract\n  owner: iuc\n  revisions: e7ee3aadf1a5\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chira_map\n  owner: iuc\n  revisions: 95ddee768b61\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chira_merge\n  owner: iuc\n  revisions: 6492560fe1b4\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chira_quantify\n  owner: iuc\n  revisions: 06ac35533793\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n  owner: iuc\n  revisions: 33d61c89fb8d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 49370cb85f0f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-interactome/tutorial.json",
-        "contributors": [
+        "quiz": [
             {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
+                "contributors": [
+                    "bebatut"
                 ],
-                "id": "pavanvidem",
-                "joined": "2017-09",
-                "name": "Pavankumar Videm",
-                "orcid": "0000-0002-5192-126X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
-            }
-        ],
-        "dir": "topics/transcriptomics/tutorials/rna-interactome",
-        "edam_operation": [
-            "Sequencing quality control",
-            "Primer removal",
-            "Sequence trimming",
-            "Sequence composition calculation",
-            "Read pre-processing",
-            "Statistical calculation"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "transcriptomics/rna-interactome",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.org.au"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Choosing the correct alignment parameters is one of the imporatant factor in the analysis.",
-            "For poorly annotated organisms use reference genome instead of trascriptome."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Quality control and data preparation",
-            "Mapping chimeric reads",
-            "Quantification of the mapped loci",
-            "Visualization and filtering of results"
-        ],
-        "pageviews": 1874,
-        "pub_date": "2020-03-23",
-        "questions": [
-            "What are the difficulties in mapping chimeric reads from RNA interactome data?",
-            "How multi mapping is a big problem in these datasets?",
-            "How to filter for meaningful results from large analysis output files?"
-        ],
-        "short_id": "T00296",
-        "short_tools": [
-            "chira_merge",
-            "chira_extract",
-            "fastqc",
-            "query_tabular",
-            "chira_map",
-            "cutadapt",
-            "chira_collapse",
-            "chira_quantify"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "time_estimation": "2H",
-        "title": "RNA-RNA interactome data analysis",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/chira_collapse/chira_collapse/1.4.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/chira_extract/chira_extract/1.4.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.4.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/chira_merge/chira_merge/1.4.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/chira_quantify/chira_quantify/1.4.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
-            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5"
+                "id": "active_learning_strategies.yaml",
+                "path": "topics/teaching/tutorials/learner_participation_engagement/quiz/active_learning_strategies.yaml",
+                "title": "Which strategies for active learning training did you use?"
+            },
+            {
+                "contributors": [
+                    "bebatut"
+                ],
+                "id": "active_learning_strategies_bloom_levels.yaml",
+                "path": "topics/teaching/tutorials/learner_participation_engagement/quiz/active_learning_strategies_bloom_levels.yaml",
+                "title": "What is the highest Bloom's level supported by each teaching technique?"
+            },
+            {
+                "contributors": [
+                    "bebatut"
+                ],
+                "id": "effective_training_trainer.yaml",
+                "path": "topics/teaching/tutorials/learner_participation_engagement/quiz/effective_training_trainer.yaml",
+                "title": "What makes training effective and a good trainer?"
+            },
+            {
+                "contributors": [
+                    "bebatut"
+                ],
+                "id": "mazur_interview.yaml",
+                "path": "topics/teaching/tutorials/learner_participation_engagement/quiz/mazur_interview.yaml",
+                "title": "Reflect on Mazur's interview"
+            },
+            {
+                "contributors": [
+                    "bebatut"
+                ],
+                "id": "trainer_skills.yaml",
+                "path": "topics/teaching/tutorials/learner_participation_engagement/quiz/trainer_skills.yaml",
+                "title": "Reflect on your skills as a trainer"
+            }
         ],
-        "topic_name": "transcriptomics",
-        "topic_name_human": "Transcriptomics",
+        "requirements": [
+            {
+                "topic_name": "contributing",
+                "tutorials": [
+                    "learning-principles",
+                    "design"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00280",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "pedagogy",
+        "supported_servers": [],
+        "symlink": null,
+        "time_estimation": "60m",
+        "title": "Training techniques to enhance learner participation and engagement",
+        "tools": [],
+        "topic_name": "teaching",
+        "topic_name_human": "Teaching and Hosting Galaxy training",
         "tours": false,
         "translations": {
             "slides": [],
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "rna-interactome",
+        "tutorial_name": "learner_participation_engagement",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-interactome/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/learner_participation_engagement/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-interactome/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-interactome/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/learner_participation_engagement/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/learner_participation_engagement/tutorial.json"
         },
-        "version": 12,
+        "version": 13,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 181,
-        "visitors": 1168,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "RNA-RNA interactome analysis using ChiRA tool suite",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreads_fastq\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreference1_fasta\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreference2_fasta\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nannotation_gtf\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ngenome_fasta\"]\n  5[label=\"FastQC\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Cutadapt\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"FastQC\"]\n  6 -> 7 [label=\"out1\"]\n  8[label=\"ChiRA collapse\"]\n  6 -> 8 [label=\"out1\"]\n  9[label=\"ChiRA map\"]\n  8 -> 9 [label=\"out\"]\n  1 -> 9 [label=\"output\"]\n  2 -> 9 [label=\"output\"]\n  10[label=\"ChiRA merge\"]\n  9 -> 10 [label=\"mapped_bed\"]\n  3 -> 10 [label=\"output\"]\n  1 -> 10 [label=\"output\"]\n  2 -> 10 [label=\"output\"]\n  11[label=\"ChiRA qauntify\"]\n  10 -> 11 [label=\"merged_bed\"]\n  10 -> 11 [label=\"segments_bed\"]\n  12[label=\"ChiRA extract\"]\n  4 -> 12 [label=\"output\"]\n  3 -> 12 [label=\"output\"]\n  11 -> 12 [label=\"loci\"]\n  1 -> 12 [label=\"output\"]\n  2 -> 12 [label=\"output\"]\n  k7182226db48a4ce1882e6bb41091a5d4[color=lightseagreen,label=\"Output\\ninteractions\"]\n  12 -> k7182226db48a4ce1882e6bb41091a5d4\n  k011f4c89d15a48779d490146773ce781[color=lightseagreen,label=\"Output\\nchimeric_reads\"]\n  12 -> k011f4c89d15a48779d490146773ce781\n  13[label=\"Query Tabular\"]\n  12 -> 13 [label=\"chimeras\"]\n  kf1315db211d14dee9014eafa1fc0f82f[color=lightseagreen,label=\"Output\\ndb\"]\n  13 -> kf1315db211d14dee9014eafa1fc0f82f\n}",
-                "history": [
-                    {
-                        "hash": "1dde32698b8894ce6ea44c28fcf48fe2b28d15b3",
-                        "message": "update rna-rna interactome workflow and add workflow test",
-                        "num": 2,
-                        "short_hash": "1dde32698",
-                        "unix": "1607121201"
-                    },
-                    {
-                        "hash": "922058fc64848a1fb74d005020896346a189d852",
-                        "message": "update rna-rna interactome workflow and add workflow test",
-                        "num": 1,
-                        "short_hash": "922058fc6",
-                        "unix": "1607121057"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "reads_fastq"
-                            }
-                        ],
-                        "label": "reads_fastq",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 250,
-                            "height": 61,
-                            "left": -969.5,
-                            "right": -769.5,
-                            "top": 189,
-                            "width": 200,
-                            "x": -969.5,
-                            "y": 189
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "36ae119e-7b4c-424e-902f-a1f37b525bd1",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "b7bf00b3-3646-44b5-b160-f9364c0e536c"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "reference1_fasta"
-                            }
-                        ],
-                        "label": "reference1_fasta",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 379,
-                            "height": 81,
-                            "left": -969.5,
-                            "right": -769.5,
-                            "top": 298,
-                            "width": 200,
-                            "x": -969.5,
-                            "y": 298
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "5481a3fd-b578-433a-bcdc-ef19c194f1cf",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "a641e20a-7835-4318-9387-ec98acef6bb6"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "reference2_fasta"
-                            }
-                        ],
-                        "label": "reference2_fasta",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 488,
-                            "height": 81,
-                            "left": -969.5,
-                            "right": -769.5,
-                            "top": 407,
-                            "width": 200,
-                            "x": -969.5,
-                            "y": 407
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "c6b92dfd-a636-48c9-8854-cf85c6704239",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "a375f37f-cd68-4847-bb2a-ef7b1a7c385d"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "annotation_gtf"
-                            }
-                        ],
-                        "label": "annotation_gtf",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 597,
-                            "height": 81,
-                            "left": -969.5,
-                            "right": -769.5,
-                            "top": 516,
-                            "width": 200,
-                            "x": -969.5,
-                            "y": 516
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "7b67eecd-1c75-407b-a684-96ed53c74f5c",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1b35e4cd-b9c7-4db1-9361-b74c127f3dbf"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "genome_fasta"
-                            }
-                        ],
-                        "label": "genome_fasta",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 706,
-                            "height": 81,
-                            "left": -969.5,
-                            "right": -769.5,
-                            "top": 625,
-                            "width": 200,
-                            "x": -969.5,
-                            "y": 625
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "100bac6e-c0b8-412c-bc71-e55028d1d70e",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "5396a7d8-957f-4858-8ce7-4c5131d2852d"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nreads_fastq\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nreference1_fasta\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nreference2_fasta\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nannotation_gtf\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\ngenome_fasta\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"FastQC\"];\n  0 -->|output| 5;\n  6[\"Cutadapt\"];\n  0 -->|output| 6;\n  7[\"FastQC\"];\n  6 -->|out1| 7;\n  8[\"ChiRA collapse\"];\n  6 -->|out1| 8;\n  9[\"ChiRA map\"];\n  8 -->|out| 9;\n  1 -->|output| 9;\n  2 -->|output| 9;\n  10[\"ChiRA merge\"];\n  9 -->|mapped_bed| 10;\n  3 -->|output| 10;\n  1 -->|output| 10;\n  2 -->|output| 10;\n  11[\"ChiRA qauntify\"];\n  10 -->|merged_bed| 11;\n  10 -->|segments_bed| 11;\n  12[\"ChiRA extract\"];\n  4 -->|output| 12;\n  3 -->|output| 12;\n  11 -->|loci| 12;\n  1 -->|output| 12;\n  2 -->|output| 12;\n  7182226d-b48a-4ce1-882e-6bb41091a5d4[\"Output\\ninteractions\"];\n  12 --> 7182226d-b48a-4ce1-882e-6bb41091a5d4;\n  style 7182226d-b48a-4ce1-882e-6bb41091a5d4 stroke:#2c3143,stroke-width:4px;\n  011f4c89-d15a-4877-9d49-0146773ce781[\"Output\\nchimeric_reads\"];\n  12 --> 011f4c89-d15a-4877-9d49-0146773ce781;\n  style 011f4c89-d15a-4877-9d49-0146773ce781 stroke:#2c3143,stroke-width:4px;\n  13[\"Query Tabular\"];\n  12 -->|chimeras| 13;\n  f1315db2-11d1-4dee-9014-eafa1fc0f82f[\"Output\\ndb\"];\n  13 --> f1315db2-11d1-4dee-9014-eafa1fc0f82f;\n  style f1315db2-11d1-4dee-9014-eafa1fc0f82f stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "RNA-RNA interactome data analysis - chira  v1.4.3",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "reads_fastq"
-                            }
-                        ],
-                        "label": "reads_fastq",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 250,
-                            "height": 61,
-                            "left": -969.5,
-                            "right": -769.5,
-                            "top": 189,
-                            "width": 200,
-                            "x": -969.5,
-                            "y": 189
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "36ae119e-7b4c-424e-902f-a1f37b525bd1",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "b7bf00b3-3646-44b5-b160-f9364c0e536c"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "reference1_fasta"
-                            }
-                        ],
-                        "label": "reference1_fasta",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 379,
-                            "height": 81,
-                            "left": -969.5,
-                            "right": -769.5,
-                            "top": 298,
-                            "width": 200,
-                            "x": -969.5,
-                            "y": 298
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "5481a3fd-b578-433a-bcdc-ef19c194f1cf",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "a641e20a-7835-4318-9387-ec98acef6bb6"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "reference2_fasta"
-                            }
-                        ],
-                        "label": "reference2_fasta",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 488,
-                            "height": 81,
-                            "left": -969.5,
-                            "right": -769.5,
-                            "top": 407,
-                            "width": 200,
-                            "x": -969.5,
-                            "y": 407
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "c6b92dfd-a636-48c9-8854-cf85c6704239",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "a375f37f-cd68-4847-bb2a-ef7b1a7c385d"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "annotation_gtf"
-                            }
-                        ],
-                        "label": "annotation_gtf",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 597,
-                            "height": 81,
-                            "left": -969.5,
-                            "right": -769.5,
-                            "top": 516,
-                            "width": 200,
-                            "x": -969.5,
-                            "y": 516
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "7b67eecd-1c75-407b-a684-96ed53c74f5c",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1b35e4cd-b9c7-4db1-9361-b74c127f3dbf"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "genome_fasta"
-                            }
-                        ],
-                        "label": "genome_fasta",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 706,
-                            "height": 81,
-                            "left": -969.5,
-                            "right": -769.5,
-                            "top": 625,
-                            "width": 200,
-                            "x": -969.5,
-                            "y": 625
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "100bac6e-c0b8-412c-bc71-e55028d1d70e",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "5396a7d8-957f-4858-8ce7-4c5131d2852d"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "FastQC",
-                        "outputs": [
-                            {
-                                "name": "html_file",
-                                "type": "html"
-                            },
-                            {
-                                "name": "text_file",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 481,
-                            "height": 292,
-                            "left": -683.5,
-                            "right": -483.5,
-                            "top": 189,
-                            "width": 200,
-                            "x": -683.5,
-                            "y": 189
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActiontext_file": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "text_file"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "e7b2202befea",
-                            "name": "fastqc",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"adapters\": null, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"contaminants\": null, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": null, \"min_length\": \"\", \"nogroup\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.72+galaxy1",
-                        "type": "tool",
-                        "uuid": "d9a7bf3f-f741-4c11-9f5b-fdca1ddea405",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "html_file",
-                                "uuid": "10d9a489-63d2-4f45-9a24-822093d4734e"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "library|input_1": {
-                                "id": 0,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cutadapt",
-                        "outputs": [
-                            {
-                                "name": "out1",
-                                "type": "fastqsanger"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 641,
-                            "height": 132,
-                            "left": -683.5,
-                            "right": -483.5,
-                            "top": 509,
-                            "width": 200,
-                            "x": -683.5,
-                            "y": 509
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
-                        "tool_shed_repository": {
-                            "changeset_revision": "49370cb85f0f",
-                            "name": "cutadapt",
-                            "owner": "lparsons",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"input\", \"adapter_options\": {\"error_rate\": \"0.1\", \"no_indels\": \"false\", \"count\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"no_trim\": \"false\", \"mask_adapter\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"discard\": \"false\", \"discard_untrimmed\": \"false\", \"min\": \"16\", \"max\": \"0\", \"max_n\": \"\", \"pair_filter\": \"any\"}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"\", \"adapter\": \"GTGTCAGTCACTTCCAGCGG\"}}], \"front_adapters\": [{\"__index__\": 0, \"front_adapter_source\": {\"front_adapter_source_list\": \"user\", \"__current_case__\": 0, \"front_adapter_name\": \"\", \"front_adapter\": \"GCATAGGGAGGACGATGCGG\"}}], \"anywhere_adapters\": [], \"cut\": \"0\"}}, \"output_options\": {\"report\": \"false\", \"info_file\": \"false\", \"rest_file\": \"false\", \"wildcard_file\": \"false\", \"too_short_file\": \"false\", \"too_long_file\": \"false\", \"untrimmed_file\": \"false\", \"multiple_output\": \"false\"}, \"read_mod_options\": {\"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"prefix\": \"\", \"suffix\": \"\", \"strip_suffix\": \"\", \"length\": \"0\", \"length_tag\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16.5",
-                        "type": "tool",
-                        "uuid": "004e566f-fa52-439e-9196-ba93bb401022",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out1",
-                                "uuid": "0a7b8f7a-fb0b-47c9-8ac4-ffdde708f13a"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 6,
-                                "output_name": "out1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "FastQC",
-                        "outputs": [
-                            {
-                                "name": "html_file",
-                                "type": "html"
-                            },
-                            {
-                                "name": "text_file",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 481,
-                            "height": 292,
-                            "left": -397.5,
-                            "right": -197.5,
-                            "top": 189,
-                            "width": 200,
-                            "x": -397.5,
-                            "y": 189
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActiontext_file": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "text_file"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "e7b2202befea",
-                            "name": "fastqc",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"adapters\": null, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"contaminants\": null, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": null, \"min_length\": \"\", \"nogroup\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.72+galaxy1",
-                        "type": "tool",
-                        "uuid": "3ce4fbbf-1e35-4c73-82d8-d78567dc7f98",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "html_file",
-                                "uuid": "16c57790-7c4d-474e-a094-c48e8573c249"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_collapse/chira_collapse/1.4.3+galaxy0",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "in": {
-                                "id": 6,
-                                "output_name": "out1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "ChiRA collapse",
-                        "outputs": [
-                            {
-                                "name": "out",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 641,
-                            "height": 132,
-                            "left": -397.5,
-                            "right": -197.5,
-                            "top": 509,
-                            "width": 200,
-                            "x": -397.5,
-                            "y": 509
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_collapse/chira_collapse/1.4.3+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2b2bfeda00d0",
-                            "name": "chira_collapse",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"in\": {\"__class__\": \"ConnectedValue\"}, \"umi_len\": \"5\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.4.3+galaxy0",
-                        "type": "tool",
-                        "uuid": "c1bc53ab-37cf-4302-9f60-3ab98337e68c",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out",
-                                "uuid": "4a8852b4-c52e-438d-b803-000e7e0c3ccb"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.4.3+galaxy0",
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {
-                            "query": {
-                                "id": 8,
-                                "output_name": "out"
-                            },
-                            "reference|ref_fasta1": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "reference|ref_fasta2": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "ChiRA map",
-                        "outputs": [
-                            {
-                                "name": "mapped_bed",
-                                "type": "bed"
-                            },
-                            {
-                                "name": "unmapped_fasta",
-                                "type": "fasta"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 431,
-                            "height": 242,
-                            "left": -111.5,
-                            "right": 88.5,
-                            "top": 189,
-                            "width": 200,
-                            "x": -111.5,
-                            "y": 189
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.4.3+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "92dbdc4d2722",
-                            "name": "chira_map",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"fasta\", \"alignment\": {\"aligner\": \"bwa\", \"__current_case__\": 0, \"stranded\": \"fw\", \"seed_length1\": \"12\", \"seed_length2\": \"16\", \"align_score1\": \"18\", \"align_score2\": \"16\", \"match1\": \"1\", \"mismatch1\": \"4\", \"match2\": \"1\", \"mismatch2\": \"6\", \"gapo1\": \"6\", \"gape1\": \"1\", \"gapo2\": \"100\", \"gape2\": \"100\", \"nhits1\": \"50\", \"nhits2\": \"100\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"query\": {\"__class__\": \"ConnectedValue\"}, \"reference\": {\"ref_type\": \"split\", \"__current_case__\": 0, \"ref_fasta1\": {\"__class__\": \"ConnectedValue\"}, \"ref_fasta2\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.4.3+galaxy0",
-                        "type": "tool",
-                        "uuid": "60e2db9d-f2ba-4293-9dab-343917d22702",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "mapped_bed",
-                                "uuid": "cc3b4775-520e-4c40-8a84-6dd4ac8c63c9"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "unmapped_fasta",
-                                "uuid": "c85cb34d-71c0-46d8-90e1-145e7a883b1f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_merge/chira_merge/1.4.3+galaxy0",
-                        "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "alignments": {
-                                "id": 9,
-                                "output_name": "mapped_bed"
-                            },
-                            "annotation|gtf": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "reference|ref_fasta1": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "reference|ref_fasta2": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "ChiRA merge",
-                        "outputs": [
-                            {
-                                "name": "segments_bed",
-                                "type": "bed"
-                            },
-                            {
-                                "name": "merged_bed",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 521,
-                            "height": 332,
-                            "left": 174.5,
-                            "right": 374.5,
-                            "top": 189,
-                            "width": 200,
-                            "x": 174.5,
-                            "y": 189
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_merge/chira_merge/1.4.3+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "bd57d16524fe",
-                            "name": "chira_merge",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"bed\", \"alignment_overlap\": \"0.7\", \"alignments\": {\"__class__\": \"ConnectedValue\"}, \"annotation\": {\"choice\": \"yes\", \"__current_case__\": 0, \"gtf\": {\"__class__\": \"ConnectedValue\"}}, \"chimeric_only\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"length_threshold\": \"0.9\", \"merge\": {\"mode\": \"overlap\", \"__current_case__\": 0, \"min_locus_size\": \"1\"}, \"reference\": {\"ref_type\": \"split\", \"__current_case__\": 0, \"ref_fasta1\": {\"__class__\": \"ConnectedValue\"}, \"ref_fasta2\": {\"__class__\": \"ConnectedValue\"}}, \"segment_overlap\": \"0.7\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.4.3+galaxy0",
-                        "type": "tool",
-                        "uuid": "bb4a876e-53c4-4231-8481-ff7f12b1f15f",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "merged_bed",
-                                "uuid": "9430b287-c1a4-489d-be0e-991e1eb77a7a"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "segments_bed",
-                                "uuid": "787ba9ae-d3db-461a-b48b-4834adf94c17"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_quantify/chira_quantify/1.4.3+galaxy0",
-                        "errors": null,
-                        "id": 11,
-                        "input_connections": {
-                            "merged": {
-                                "id": 10,
-                                "output_name": "merged_bed"
-                            },
-                            "segments": {
-                                "id": 10,
-                                "output_name": "segments_bed"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "ChiRA qauntify",
-                        "outputs": [
-                            {
-                                "name": "loci",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 391,
-                            "height": 202,
-                            "left": 460.5,
-                            "right": 660.5,
-                            "top": 189,
-                            "width": 200,
-                            "x": 460.5,
-                            "y": 189
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_quantify/chira_quantify/1.4.3+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "7fb3fc24be0e",
-                            "name": "chira_quantify",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"bed\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"crl\": \"true\", \"crl_share\": \"0.7\", \"em_threshold\": \"1e-05\", \"merged\": {\"__class__\": \"ConnectedValue\"}, \"min_locus_size\": \"10\", \"segments\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.4.3+galaxy0",
-                        "type": "tool",
-                        "uuid": "428b7bab-aef3-4c55-8a7b-4bd712f87340",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "loci",
-                                "uuid": "dce6af3f-130d-455b-9e20-c55ca20eab08"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_extract/chira_extract/1.4.3+galaxy0",
-                        "errors": null,
-                        "id": 12,
-                        "input_connections": {
-                            "annotation|fasta_source|fasta": {
-                                "id": 4,
-                                "output_name": "output"
-                            },
-                            "annotation|gtf": {
-                                "id": 3,
-                                "output_name": "output"
-                            },
-                            "loci": {
-                                "id": 11,
-                                "output_name": "loci"
-                            },
-                            "reference|ref_fasta1": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "reference|ref_fasta2": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool ChiRA extract",
-                                "name": "annotation"
-                            },
-                            {
-                                "description": "runtime parameter for tool ChiRA extract",
-                                "name": "loci"
-                            },
-                            {
-                                "description": "runtime parameter for tool ChiRA extract",
-                                "name": "reference"
-                            },
-                            {
-                                "description": "runtime parameter for tool ChiRA extract",
-                                "name": "reference"
-                            }
-                        ],
-                        "label": null,
-                        "name": "ChiRA extract",
-                        "outputs": [
-                            {
-                                "name": "chimeras",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "interactions",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 491,
-                            "height": 302,
-                            "left": 746.5,
-                            "right": 946.5,
-                            "top": 189,
-                            "width": 200,
-                            "x": 746.5,
-                            "y": 189
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_extract/chira_extract/1.4.3+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6977e9b7143d",
-                            "name": "chira_extract",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"acc_width\": \"150\", \"accessibility\": \"false\", \"annotation\": {\"annot_choice\": \"yes\", \"__current_case__\": 0, \"gtf\": {\"__class__\": \"RuntimeValue\"}, \"fasta_source\": {\"fasta_source_selector\": \"history\", \"__current_case__\": 0, \"fasta\": {\"__class__\": \"RuntimeValue\"}}}, \"chimeric_overlap\": \"2\", \"hybridize\": \"true\", \"intarna_mode\": \"H\", \"loci\": {\"__class__\": \"RuntimeValue\"}, \"reference\": {\"ref_type\": \"split\", \"__current_case__\": 0, \"ref_fasta1\": {\"__class__\": \"RuntimeValue\"}, \"ref_fasta2\": {\"__class__\": \"RuntimeValue\"}}, \"score_cutoff\": \"0.0\", \"seed_bp\": \"5\", \"seed_interaction\": \"true\", \"seed_min_pu\": \"0.0\", \"summarize\": \"true\", \"temperature\": \"37.0\", \"tpm_cutoff\": \"0.0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.4.3+galaxy0",
-                        "type": "tool",
-                        "uuid": "ef85dc12-e50c-47b5-ab65-43d1bf2a6352",
-                        "workflow_outputs": [
-                            {
-                                "label": "interactions",
-                                "output_name": "interactions",
-                                "uuid": "7182226d-b48a-4ce1-882e-6bb41091a5d4"
-                            },
-                            {
-                                "label": "chimeric_reads",
-                                "output_name": "chimeras",
-                                "uuid": "011f4c89-d15a-4877-9d49-0146773ce781"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
-                        "errors": null,
-                        "id": 13,
-                        "input_connections": {
-                            "tables_0|table": {
-                                "id": 12,
-                                "output_name": "chimeras"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Query Tabular",
-                                "name": "add_to_database"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Query Tabular",
-                        "outputs": [
-                            {
-                                "name": "sqlitedb",
-                                "type": "sqlite"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 351,
-                            "height": 162,
-                            "left": 1032.5,
-                            "right": 1232.5,
-                            "top": 189,
-                            "width": 200,
-                            "x": 1032.5,
-                            "y": 189
-                        },
-                        "post_job_actions": {
-                            "ChangeDatatypeActionsqlitedb": {
-                                "action_arguments": {
-                                    "newtype": "chira.sqlite"
-                                },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "sqlitedb"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "33d61c89fb8d",
-                            "name": "query_tabular",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"save_db\": \"true\", \"sqlquery\": \"\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"RuntimeValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"\", \"column_names_from_first_line\": \"true\", \"col_names\": \"\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "3.0.0",
-                        "type": "tool",
-                        "uuid": "fe30bba1-cda8-4926-924c-8dec7cd28222",
-                        "workflow_outputs": [
-                            {
-                                "label": "db",
-                                "output_name": "sqlitedb",
-                                "uuid": "f1315db2-11d1-4dee-9014-eafa1fc0f82f"
-                            }
-                        ]
-                    }
+        "visit_duration": 44,
+        "visitors": 1373
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/running-workshop/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
                 ],
-                "parent_id": "transcriptomics/rna-interactome",
-                "path": "topics/transcriptomics/tutorials/rna-interactome/workflows/rna-rna-interactome-data-analysis-chira.ga",
-                "tags": [
-                    "RNA",
-                    "transcriptomics"
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "affiliations": [
+                    "eurosciencegateway",
+                    "eosc-life",
+                    "by-covid",
+                    "deNBI",
+                    "sfb992",
+                    "elixir-converge",
+                    "uni-freiburg",
+                    "elixir-europe"
                 ],
-                "test_results": null,
-                "tests": true,
-                "title": "RNA-RNA interactome data analysis - chira  v1.4.3",
-                "topic_id": "transcriptomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-rna-interactome/versions/rna-rna-interactome-data-analysis-chira",
-                "tutorial_id": "rna-interactome",
-                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-interactome/workflows/rna-rna-interactome-data-analysis-chira.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-interactome/workflows/rna-rna-interactome-data-analysis-chira.html",
-                "version": 1,
-                "wfid": "transcriptomics-rna-interactome",
-                "wfname": "rna-rna-interactome-data-analysis-chira",
-                "workflow": "rna-rna-interactome-data-analysis-chira.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/chira_collapse/chira_collapse/1.4.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/chira_extract/chira_extract/1.4.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.4.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/chira_merge/chira_merge/1.4.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/chira_quantify/chira_quantify/1.4.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5"
+                "contact_for_training": true,
+                "elixir_node": "de",
+                "email": "bjoern.gruening@gmail.com",
+                "fediverse": "https://fosstodon.org/@bgruening",
+                "fediverse_flavor": "mastodon",
+                "id": "bgruening",
+                "joined": "2017-09",
+                "linkedin": "bgruening",
+                "location": {
+                    "country": "DE",
+                    "lat": 47.997791,
+                    "lon": 7.842609
+                },
+                "matrix": "bgruening:matrix.org",
+                "name": "Bj\u00f6rn Gr\u00fcning",
+                "orcid": "0000-0002-3079-6586",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/",
+                "twitter": "bjoerngruening",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bgruening.json"
+            },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
                 ],
-                "workflowhub_id": "1291"
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/3709188"
+        "dir": "topics/teaching/tutorials/running-workshop",
+        "edam_operation": [],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "teaching/running-workshop",
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "The take-home messages",
+            "They will appear at the end of the tutorial"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": null,
+        "pageviews": 192,
+        "pub_date": "2018-11-15",
+        "questions": null,
+        "redirect_from": [
+            "/topics/instructors/tutorials/running-workshop/tutorial",
+            "/short/teaching/running-workshop",
+            "/short/T00284"
+        ],
+        "short_id": "T00284",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "prepare",
+        "supported_servers": [],
+        "symlink": null,
+        "time_estimation": "3H",
+        "title": "Running a workshop as instructor",
+        "tools": [],
+        "topic_name": "teaching",
+        "topic_name_human": "Teaching and Hosting Galaxy training",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "running-workshop",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/running-workshop/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/running-workshop/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/running-workshop/tutorial.json"
+        },
+        "version": 5,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 54,
+        "visitors": 74
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/workshop-final-exercise/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "bebatut",
+                "fpsom",
+                "allegravia",
+                "ppalagi",
+                "elixir-goblet-ttt"
+            ],
+            "funding": [
+                "gallantries"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "elixir-europe"
+                ],
+                "elixir_node": "gr",
+                "email": "fpsom@certh.gr",
+                "id": "fpsom",
+                "joined": "2019-03",
+                "linkedin": "fpsom",
+                "matrix": "fpsom:matrix.org",
+                "name": "Fotis E. Psomopoulos",
+                "orcid": "0000-0002-0222-4273",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/fpsom/",
+                "twitter": "fopsom",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
+            },
+            {
+                "id": "allegravia",
+                "joined": "2022-09",
+                "name": "Allegra Via",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/allegravia/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/allegravia.json"
+            },
+            {
+                "id": "ppalagi",
+                "joined": "2022-09",
+                "name": "Patricia Palagi",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ppalagi/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/ppalagi.json"
+            },
+            {
+                "avatar": "/training-material/shared/images/elixir.png",
+                "github": false,
+                "id": "elixir-goblet-ttt",
+                "joined": "2022-09",
+                "name": "ELIXIR Goblet Train the Trainers",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-goblet-ttt/",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/elixir-goblet-ttt.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            }
+        ],
+        "dir": "topics/teaching/tutorials/workshop-final-exercise",
+        "edam_operation": [],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "teaching/workshop-final-exercise",
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Feedback needs to be positive and be specific"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-10-23",
+        "objectives": [
+            "Create a 5 minute training",
+            "Deliver a 5 minute training",
+            "Deliver and receive feedback"
+        ],
+        "pageviews": 50,
+        "pub_date": "2023-06-12",
+        "questions": [
+            "How can we apply all pedagogical concepts together for training?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "contributing",
+                "tutorials": [
+                    "learning-principles",
+                    "design"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "teaching",
+                "tutorials": [
+                    "assessment",
+                    "motivation_demotivation"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00354",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "pedagogy",
+        "supported_servers": [],
+        "symlink": null,
+        "time_estimation": "60m",
+        "title": "Train-the-Trainer: putting it all together",
+        "tools": [],
+        "topic_name": "teaching",
+        "topic_name_human": "Teaching and Hosting Galaxy training",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "workshop-final-exercise",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/workshop-final-exercise/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/workshop-final-exercise/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/workshop-final-exercise/tutorial.json"
+        },
+        "version": 2,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 50,
+        "visitors": 43
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/galaxy-admin-training/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            }
+        ],
+        "dir": "topics/teaching/tutorials/galaxy-admin-training",
+        "edam_operation": [],
+        "edam_topic": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "teaching/galaxy-admin-training",
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Infrastructure is available for running GATs for free from UseGalaxy.eu",
+            "This can be very convenient and easy to use",
+            "EU provides appropriate DNS entries so you can run trainings with ITs."
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Advanced",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-17",
+        "objectives": [
+            "Interact with the UseGalaxy.eu admins to arrange for infrastructure",
+            "Run a great training!"
+        ],
+        "pageviews": 108,
+        "pub_date": "2020-11-04",
+        "questions": [
+            "How do I organise a Galaxy Admin Training (GAT)",
+            "What do I need to set up?",
+            "What should I know during the training?"
+        ],
+        "redirect_from": [
+            "/topics/instructors/tutorials/galaxy-admin-training/tutorial",
+            "/short/teaching/galaxy-admin-training",
+            "/short/T00278"
+        ],
+        "requirements": [
+            {
+                "topic_name": "admin",
+                "tutorials": [
+                    "ansible",
+                    "terraform"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00278",
+        "short_tools": [],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "prepare",
+        "supported_servers": [],
+        "symlink": null,
+        "time_estimation": "60m",
+        "title": "Galaxy Admin Training",
+        "tools": [],
+        "topic_name": "teaching",
+        "topic_name_human": "Teaching and Hosting Galaxy training",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "galaxy-admin-training",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/teaching/tutorials/galaxy-admin-training/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/galaxy-admin-training/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/teaching/tutorials/galaxy-admin-training/tutorial.json"
+        },
+        "version": 5,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 205,
+        "visitors": 98
     },
     {
         "admin_install": {
@@ -260584,14 +266286,14 @@
         ],
         "dir": "topics/transcriptomics/tutorials/clipseq",
         "edam_operation": [
-            "Sequencing quality control",
-            "Primer removal",
+            "Statistical calculation",
             "Sequence alignment",
-            "Mapping",
+            "Sequence trimming",
+            "Sequencing quality control",
             "Sequence composition calculation",
+            "Mapping",
             "Read pre-processing",
-            "Sequence trimming",
-            "Statistical calculation"
+            "Primer removal"
         ],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -260600,6 +266302,7 @@
         "hands_on": true,
         "id": "transcriptomics/clipseq",
         "inexact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.no"
         ],
@@ -260625,7 +266328,7 @@
             "Analyse the peaks and find potential binding motifs and targets",
             "Check the quality of the peak calling"
         ],
-        "pageviews": 14663,
+        "pageviews": 14792,
         "pub_date": "2018-08-17",
         "questions": [
             "How is raw CLIP-Seq data processed and analysed?",
@@ -260633,32 +266336,37 @@
         ],
         "short_id": "T00288",
         "short_tools": [
-            "deeptools_plot_correlation",
-            "peakachu",
-            "bctools_extract_alignment_ends",
-            "tp_awk_tool",
-            "umi_tools_dedup",
+            "deeptools_plot_fingerprint",
             "rna_star",
+            "deeptools_multi_bam_summary",
+            "wig_to_bigWig",
             "__MERGE_COLLECTION__",
-            "__SORTLIST__",
             "meme_chip",
-            "rcas",
-            "wig_to_bigWig",
-            "deeptools_multi_bam_summary",
-            "sort1",
-            "bedtools_slopbed",
-            "cutadapt",
+            "deeptools_plot_correlation",
+            "tp_awk_tool",
+            "umi_tools_dedup",
+            "bctools_extract_alignment_ends",
             "umi_tools_extract",
-            "fastqc",
-            "deeptools_plot_fingerprint",
+            "peakachu",
             "Extract genomic DNA 1",
-            "bedtools_genomecoveragebed_bedgraph"
+            "fastqc",
+            "bedtools_slopbed",
+            "cutadapt",
+            "bedtools_genomecoveragebed_bedgraph",
+            "sort1",
+            "rcas",
+            "__SORTLIST__"
         ],
         "slides": false,
         "slides_recordings": false,
         "supported_servers": {
             "exact": [],
             "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -260715,8 +266423,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 117,
-        "visitors": 6953,
+        "visit_duration": 116,
+        "visitors": 7053,
         "workflows": [
             {
                 "creators": [],
@@ -260894,7 +266602,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nBackground\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nEnriched set as a paired-end reads collection\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nAnnotation Reference File for RCAS\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nGenome Chromosome Sizes\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"FastQC\"];\n  0 -->|output| 4;\n  5[\"Cutadapt\"];\n  0 -->|output| 5;\n  6[\"FastQC\"];\n  1 -->|output| 6;\n  7[\"Cutadapt\"];\n  1 -->|output| 7;\n  8[\"UMI-tools extract\"];\n  5 -->|out_pairs| 8;\n  9[\"UMI-tools extract\"];\n  7 -->|out_pairs| 9;\n  10[\"RNA STAR\"];\n  2 -->|output| 10;\n  8 -->|out_paired_collection| 10;\n  11[\"RNA STAR\"];\n  2 -->|output| 11;\n  9 -->|out_paired_collection| 11;\n  12[\"UMI-tools deduplicate\"];\n  10 -->|mapped_reads| 12;\n  13[\"UMI-tools deduplicate\"];\n  11 -->|mapped_reads| 13;\n  14[\"Extract alignment ends\"];\n  12 -->|output| 14;\n  15[\"FastQC\"];\n  12 -->|output| 15;\n  16[\"PEAKachu\"];\n  12 -->|output| 16;\n  13 -->|output| 16;\n  17[\"Merge collections\"];\n  12 -->|output| 17;\n  13 -->|output| 17;\n  18[\"Extract alignment ends\"];\n  13 -->|output| 18;\n  19[\"FastQC\"];\n  13 -->|output| 19;\n  20[\"Sort\"];\n  14 -->|alignment_ends| 20;\n  21[\"Text reformatting\"];\n  16 -->|peak_tables| 21;\n  22[\"Sort collection\"];\n  17 -->|output| 22;\n  23[\"Sort\"];\n  18 -->|alignment_ends| 23;\n  24[\"Create a BedGraph of genome coverage\"];\n  20 -->|out_file1| 24;\n  25[\"bedtools SlopBed\"];\n  3 -->|output| 25;\n  21 -->|outfile| 25;\n  26[\"plotFingerprint\"];\n  22 -->|output| 26;\n  27[\"multiBamSummary\"];\n  22 -->|output| 27;\n  28[\"Create a BedGraph of genome coverage\"];\n  23 -->|out_file1| 28;\n  29[\"Wig/BedGraph-to-bigWig\"];\n  24 -->|output| 29;\n  30[\"Extract Genomic DNA\"];\n  25 -->|output| 30;\n  31[\"Text reformatting\"];\n  25 -->|output| 31;\n  32[\"plotCorrelation\"];\n  27 -->|outFile| 32;\n  33[\"Wig/BedGraph-to-bigWig\"];\n  28 -->|output| 33;\n  34[\"MEME-ChIP\"];\n  30 -->|output| 34;\n  35[\"RCAS\"];\n  31 -->|outfile| 35;\n  2 -->|output| 35;",
-                "modified": "2024-08-18 00:06:25 +0000",
+                "modified": "2024-10-02 12:08:11 +0000",
                 "name": "Tutorial CLIPseq Explorer Demultiplexed PEAKachu eCLIP Hg38 ",
                 "outputs": [
                     {
@@ -261413,245 +267121,615 @@
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1",
+                        "errors": null,
+                        "id": 34,
+                        "input_connections": {
+                            "input": {
+                                "id": 30,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool MEME-ChIP",
+                                "name": "control"
+                            }
+                        ],
+                        "label": null,
+                        "name": "MEME-ChIP",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "html"
+                            }
+                        ],
+                        "position": {
+                            "left": 2521.9664633523466,
+                            "top": 1688.0055192125387
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "cc100e0f61f4",
+                            "name": "meme_chip",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"control\": {\"__class__\": \"RuntimeValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"non_commercial_use\": \"true\", \"options_type_cond\": {\"options_type\": \"advanced\", \"__current_case__\": 1, \"background_model_order\": \"1\", \"nmeme\": \"100\", \"subsampling_cond\": {\"subsampling\": \"yes\", \"__current_case__\": 0, \"seed\": \"123\"}, \"ccut\": \"0\", \"group_threash\": \"0.05\", \"group_weak\": \"0.0\", \"filter_thresh\": \"0.05\", \"search_given_strand\": \"true\", \"old_clustering\": \"false\", \"meme_mod\": \"zoops\", \"meme_minw\": \"5\", \"meme_maxw\": \"20\", \"meme_nmotifs\": \"20\", \"meme_minsites\": \"0\", \"meme_maxsites\": \"0\", \"meme_pal\": \"false\", \"dreme_e\": \"0.05\", \"dreme_m\": \"5\"}, \"sequence_alphabet\": \"-dna\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.11.2+galaxy1",
+                        "type": "tool",
+                        "uuid": "aee66596-2a91-413a-8587-4922d9db96bf",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "eb37ad5e-3b36-4f25-b6c2-d57d077ce3cc"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/rcas/rcas/1.5.4",
+                        "errors": null,
+                        "id": 35,
+                        "input_connections": {
+                            "analysis_type|single_bed_file": {
+                                "id": 31,
+                                "output_name": "outfile"
+                            },
+                            "input_gtf_file": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "RCAS",
+                        "outputs": [
+                            {
+                                "name": "report",
+                                "type": "html"
+                            },
+                            {
+                                "name": "summarizeQueryRegions",
+                                "type": "tsv"
+                            },
+                            {
+                                "name": "query_gene_types",
+                                "type": "tsv"
+                            },
+                            {
+                                "name": "transcriptBoundaryCoverage.fiveprime",
+                                "type": "tsv"
+                            },
+                            {
+                                "name": "transcriptBoundaryCoverage.threeprime",
+                                "type": "tsv"
+                            },
+                            {
+                                "name": "exonIntronBoundaryCoverage.fiveprime",
+                                "type": "tsv"
+                            },
+                            {
+                                "name": "exonIntronBoundaryCoverage.threeprime",
+                                "type": "tsv"
+                            },
+                            {
+                                "name": "coverageprofilelist",
+                                "type": "tsv"
+                            },
+                            {
+                                "name": "getTargetedGenesTable",
+                                "type": "tsv"
+                            },
+                            {
+                                "name": "goCC",
+                                "type": "tsv"
+                            },
+                            {
+                                "name": "goBP",
+                                "type": "tsv"
+                            },
+                            {
+                                "name": "goMF",
+                                "type": "tsv"
+                            }
+                        ],
+                        "position": {
+                            "left": 2521.9664633523466,
+                            "top": 702.0572039871533
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActioncoverageprofilelist": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "coverageprofilelist"
+                            },
+                            "HideDatasetActionexonIntronBoundaryCoverage.fiveprime": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "exonIntronBoundaryCoverage.fiveprime"
+                            },
+                            "HideDatasetActionexonIntronBoundaryCoverage.threeprime": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "exonIntronBoundaryCoverage.threeprime"
+                            },
+                            "HideDatasetActiongetTargetedGenesTable": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "getTargetedGenesTable"
+                            },
+                            "HideDatasetActiongoBP": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "goBP"
+                            },
+                            "HideDatasetActiongoCC": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "goCC"
+                            },
+                            "HideDatasetActiongoMF": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "goMF"
+                            },
+                            "HideDatasetActionquery_gene_types": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "query_gene_types"
+                            },
+                            "HideDatasetActionsummarizeQueryRegions": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "summarizeQueryRegions"
+                            },
+                            "HideDatasetActiontranscriptBoundaryCoverage.fiveprime": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "transcriptBoundaryCoverage.fiveprime"
+                            },
+                            "HideDatasetActiontranscriptBoundaryCoverage.threeprime": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "transcriptBoundaryCoverage.threeprime"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/rcas/rcas/1.5.4",
+                        "tool_shed_repository": {
+                            "changeset_revision": "7c7a2a381dfe",
+                            "name": "rcas",
+                            "owner": "rnateam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"single_set_analysis\", \"__current_case__\": 0, \"single_bed_file\": {\"__class__\": \"ConnectedValue\"}, \"run_go\": \"true\", \"gsea_set\": {\"run_gsea\": \"false\", \"__current_case__\": 0}, \"downsampling\": \"0\", \"output_raw_tables\": \"true\"}, \"genome_version\": \"hg38\", \"input_gtf_file\": {\"__class__\": \"ConnectedValue\"}, \"run_annot\": \"true\", \"run_motif\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.5.4",
+                        "type": "tool",
+                        "uuid": "264661e0-55b6-4e6b-89df-cf4eae0fedee",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "report",
+                                "uuid": "8b0f0c38-1413-452b-b6ea-bbbd8be70ed8"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "transcriptomics/clipseq",
+                "path": "topics/transcriptomics/tutorials/clipseq/workflows/init_workflow.ga",
+                "tags": [
+                    "transcriptomics"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Tutorial CLIPseq Explorer Demultiplexed PEAKachu eCLIP Hg38 ",
+                "topic_id": "transcriptomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-clipseq/versions/init-workflow",
+                "tutorial_id": "clipseq",
+                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/clipseq/workflows/init_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/clipseq/workflows/init_workflow.html",
+                "version": 8,
+                "wfid": "transcriptomics-clipseq",
+                "wfname": "init-workflow",
+                "workflow": "init_workflow.ga",
+                "workflow_tools": [
+                    "__MERGE_COLLECTION__",
+                    "__SORTLIST__",
+                    "sort1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.1.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.1.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.1.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bctools_extract_alignment_ends/bctools_extract_alignment_ends/0.2.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed_bedgraph/2.19.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/1.1.2+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/rnateam/peakachu/peakachu/0.1.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/rnateam/rcas/rcas/1.5.4",
+                    "wig_to_bigWig"
+                ],
+                "workflowhub_id": "1285"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/1327423"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "74a8bef53a00",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "merge_cols",
+                    "owner": "devteam",
+                    "revisions": "f2aac0c5c60d",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "annotatemyids",
+                    "owner": "iuc",
+                    "revisions": "1a125daea0d8",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "limma_voom",
+                    "owner": "iuc",
+                    "revisions": "d5a940112511",
+                    "tool_panel_section_label": "RNA Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 74a8bef53a00\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merge_cols\n  owner: devteam\n  revisions: f2aac0c5c60d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: annotatemyids\n  owner: iuc\n  revisions: 1a125daea0d8\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: limma_voom\n  owner: iuc\n  revisions: d5a940112511\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.json",
+        "contributors": [
+            {
+                "id": "mblue9",
+                "joined": "2018-09",
+                "name": "Maria Doyle",
+                "orcid": "0000-0003-4847-8436",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
+            },
+            {
+                "id": "bphipson",
+                "joined": "2018-09",
+                "name": "Belinda Phipson",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bphipson/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bphipson.json"
+            },
+            {
+                "id": "JovMaksimovic",
+                "joined": "2019-04",
+                "name": "Jovana Maksimovic",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/JovMaksimovic/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/JovMaksimovic.json"
+            },
+            {
+                "github": false,
+                "id": "annatrigos",
+                "joined": "2018-09",
+                "name": "Anna Trigos",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annatrigos/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/annatrigos.json"
+            },
+            {
+                "id": "mritchie",
+                "joined": "2018-09",
+                "name": "Matt Ritchie",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mritchie/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mritchie.json"
+            },
+            {
+                "id": "hdashnow",
+                "joined": "2018-09",
+                "name": "Harriet Dashnow",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hdashnow/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hdashnow.json"
+            },
+            {
+                "id": "Shians",
+                "joined": "2019-02",
+                "name": "Shian Su",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Shians/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Shians.json"
+            },
+            {
+                "id": "charitylaw",
+                "joined": "2018-09",
+                "name": "Charity Law",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/charitylaw/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/charitylaw.json"
+            }
+        ],
+        "dir": "topics/transcriptomics/tutorials/rna-seq-counts-to-genes",
+        "edam_operation": [
+            "RNA-Seq analysis",
+            "Annotation"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.eu"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "transcriptomics",
+                "tutorials": [
+                    "rna-seq-genes-to-pathways",
+                    "rna-seq-viz-with-heatmap2",
+                    "rna-seq-viz-with-volcanoplot",
+                    "rna-seq-analysis-with-askomics-it"
+                ],
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "transcriptomics/rna-seq-counts-to-genes",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.fr",
+            "UseGalaxy.org.au"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "The limma-voom tool can be used to perform differential expression and output useful plots",
+            "Multiple comparisons can be input and compared",
+            "Results can be interactively explored with limma-voom via Glimma"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-04-10",
+        "objectives": [
+            "Analysis of RNA-seq count data using limma-voom",
+            "QC of count data",
+            "Visualisation and interactive exploration of count data",
+            "Identification of differentially expressed genes"
+        ],
+        "pageviews": 65029,
+        "pub_date": "2018-12-31",
+        "questions": [
+            "What are the differentially expressed genes in the mammary gland of pregnant versus lactating mice?",
+            "How to analyze RNA count data using limma-voom?",
+            "How to perform quality control (QC) of RNA-seq count data?"
+        ],
+        "requirements": [
+            {
+                "topic_name": "transcriptomics",
+                "tutorials": [
+                    "rna-seq-reads-to-counts"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00298",
+        "short_tools": [
+            "limma_voom",
+            "annotatemyids",
+            "mergeCols1",
+            "tp_replace_in_line",
+            "tp_cut_tool"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "end-to-end",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "limma-voom",
+            "mouse",
+            "QC"
+        ],
+        "time_estimation": "2h",
+        "title": "2: RNA-seq counts to genes",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.9"
+        ],
+        "topic_name": "transcriptomics",
+        "topic_name_human": "Transcriptomics",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "rna-seq-counts-to-genes",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.json"
+        },
+        "version": 21,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 134,
+        "visitors": 36908,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "RNA-seq counts to genes",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nseqdata\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nsampleinfo\"]\n  2[label=\"Cut\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Merge Columns\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Replace Text\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Cut\"]\n  3 -> 5 [label=\"out_file1\"]\n  6[label=\"annotateMyIDs\"]\n  4 -> 6 [label=\"outfile\"]\n  7[label=\"limma\"]\n  4 -> 7 [label=\"outfile\"]\n  6 -> 7 [label=\"out_tab\"]\n  5 -> 7 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 3,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 2,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "0ea8c79012ba1b18d3f79be0ff2e2b826092f5e2",
+                        "message": "Rename tutorial and image folders to the updated titles",
+                        "num": 1,
+                        "short_hash": "0ea8c7901",
+                        "unix": "1546155649"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
                         "errors": null,
-                        "id": 34,
-                        "input_connections": {
-                            "input": {
-                                "id": 30,
-                                "output_name": "output"
-                            }
-                        },
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool MEME-ChIP",
-                                "name": "control"
-                            }
-                        ],
-                        "label": null,
-                        "name": "MEME-ChIP",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "html"
+                                "description": "",
+                                "name": "seqdata"
                             }
                         ],
+                        "label": "seqdata",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2521.9664633523466,
-                            "top": 1688.0055192125387
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "cc100e0f61f4",
-                            "name": "meme_chip",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 199.9921875,
+                            "top": 199.9921875
                         },
-                        "tool_state": "{\"control\": {\"__class__\": \"RuntimeValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"non_commercial_use\": \"true\", \"options_type_cond\": {\"options_type\": \"advanced\", \"__current_case__\": 1, \"background_model_order\": \"1\", \"nmeme\": \"100\", \"subsampling_cond\": {\"subsampling\": \"yes\", \"__current_case__\": 0, \"seed\": \"123\"}, \"ccut\": \"0\", \"group_threash\": \"0.05\", \"group_weak\": \"0.0\", \"filter_thresh\": \"0.05\", \"search_given_strand\": \"true\", \"old_clustering\": \"false\", \"meme_mod\": \"zoops\", \"meme_minw\": \"5\", \"meme_maxw\": \"20\", \"meme_nmotifs\": \"20\", \"meme_minsites\": \"0\", \"meme_maxsites\": \"0\", \"meme_pal\": \"false\", \"dreme_e\": \"0.05\", \"dreme_m\": \"5\"}, \"sequence_alphabet\": \"-dna\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.11.2+galaxy1",
-                        "type": "tool",
-                        "uuid": "aee66596-2a91-413a-8587-4922d9db96bf",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "eb37ad5e-3b36-4f25-b6c2-d57d077ce3cc"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"seqdata\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "8424dc54-041c-4fd4-880a-bc9d97fff0b0",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/rcas/rcas/1.5.4",
+                        "content_id": null,
                         "errors": null,
-                        "id": 35,
-                        "input_connections": {
-                            "analysis_type|single_bed_file": {
-                                "id": 31,
-                                "output_name": "outfile"
-                            },
-                            "input_gtf_file": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "RCAS",
-                        "outputs": [
-                            {
-                                "name": "report",
-                                "type": "html"
-                            },
-                            {
-                                "name": "summarizeQueryRegions",
-                                "type": "tsv"
-                            },
-                            {
-                                "name": "query_gene_types",
-                                "type": "tsv"
-                            },
-                            {
-                                "name": "transcriptBoundaryCoverage.fiveprime",
-                                "type": "tsv"
-                            },
-                            {
-                                "name": "transcriptBoundaryCoverage.threeprime",
-                                "type": "tsv"
-                            },
-                            {
-                                "name": "exonIntronBoundaryCoverage.fiveprime",
-                                "type": "tsv"
-                            },
-                            {
-                                "name": "exonIntronBoundaryCoverage.threeprime",
-                                "type": "tsv"
-                            },
-                            {
-                                "name": "coverageprofilelist",
-                                "type": "tsv"
-                            },
-                            {
-                                "name": "getTargetedGenesTable",
-                                "type": "tsv"
-                            },
-                            {
-                                "name": "goCC",
-                                "type": "tsv"
-                            },
-                            {
-                                "name": "goBP",
-                                "type": "tsv"
-                            },
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "goMF",
-                                "type": "tsv"
+                                "description": "",
+                                "name": "sampleinfo"
                             }
                         ],
+                        "label": "sampleinfo",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2521.9664633523466,
-                            "top": 702.0572039871533
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActioncoverageprofilelist": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "coverageprofilelist"
-                            },
-                            "HideDatasetActionexonIntronBoundaryCoverage.fiveprime": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "exonIntronBoundaryCoverage.fiveprime"
-                            },
-                            "HideDatasetActionexonIntronBoundaryCoverage.threeprime": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "exonIntronBoundaryCoverage.threeprime"
-                            },
-                            "HideDatasetActiongetTargetedGenesTable": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "getTargetedGenesTable"
-                            },
-                            "HideDatasetActiongoBP": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "goBP"
-                            },
-                            "HideDatasetActiongoCC": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "goCC"
-                            },
-                            "HideDatasetActiongoMF": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "goMF"
-                            },
-                            "HideDatasetActionquery_gene_types": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "query_gene_types"
-                            },
-                            "HideDatasetActionsummarizeQueryRegions": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "summarizeQueryRegions"
-                            },
-                            "HideDatasetActiontranscriptBoundaryCoverage.fiveprime": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "transcriptBoundaryCoverage.fiveprime"
-                            },
-                            "HideDatasetActiontranscriptBoundaryCoverage.threeprime": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "transcriptBoundaryCoverage.threeprime"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/rcas/rcas/1.5.4",
-                        "tool_shed_repository": {
-                            "changeset_revision": "7c7a2a381dfe",
-                            "name": "rcas",
-                            "owner": "rnateam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 199.9921875,
+                            "top": 290.015625
                         },
-                        "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"single_set_analysis\", \"__current_case__\": 0, \"single_bed_file\": {\"__class__\": \"ConnectedValue\"}, \"run_go\": \"true\", \"gsea_set\": {\"run_gsea\": \"false\", \"__current_case__\": 0}, \"downsampling\": \"0\", \"output_raw_tables\": \"true\"}, \"genome_version\": \"hg38\", \"input_gtf_file\": {\"__class__\": \"ConnectedValue\"}, \"run_annot\": \"true\", \"run_motif\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.5.4",
-                        "type": "tool",
-                        "uuid": "264661e0-55b6-4e6b-89df-cf4eae0fedee",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "report",
-                                "uuid": "8b0f0c38-1413-452b-b6ea-bbbd8be70ed8"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"sampleinfo\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "7f07c2d1-5ae3-4992-85e4-040a96852d22",
+                        "workflow_outputs": []
                     }
                 ],
-                "parent_id": "transcriptomics/clipseq",
-                "path": "topics/transcriptomics/tutorials/clipseq/workflows/init_workflow.ga",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nseqdata\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nsampleinfo\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Cut\"];\n  0 -->|output| 2;\n  3[\"Merge Columns\"];\n  1 -->|output| 3;\n  4[\"Replace Text\"];\n  2 -->|output| 4;\n  5[\"Cut\"];\n  3 -->|out_file1| 5;\n  6[\"annotateMyIDs\"];\n  4 -->|outfile| 6;\n  7[\"limma\"];\n  4 -->|outfile| 7;\n  6 -->|out_tab| 7;\n  5 -->|output| 7;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "RNA Seq Counts To Genes",
+                "outputs": [],
+                "parent_id": "transcriptomics/rna-seq-counts-to-genes",
+                "path": "topics/transcriptomics/tutorials/rna-seq-counts-to-genes/workflows/rna-seq-counts-to-genes.ga",
                 "tags": [
                     "transcriptomics"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Tutorial CLIPseq Explorer Demultiplexed PEAKachu eCLIP Hg38 ",
+                "title": "RNA Seq Counts To Genes",
                 "topic_id": "transcriptomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-clipseq/versions/init-workflow",
-                "tutorial_id": "clipseq",
-                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/clipseq/workflows/init_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/clipseq/workflows/init_workflow.html",
-                "version": 8,
-                "wfid": "transcriptomics-clipseq",
-                "wfname": "init-workflow",
-                "workflow": "init_workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-rna-seq-counts-to-genes/versions/rna-seq-counts-to-genes",
+                "tutorial_id": "rna-seq-counts-to-genes",
+                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/workflows/rna-seq-counts-to-genes.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/workflows/rna-seq-counts-to-genes.html",
+                "version": 3,
+                "wfid": "transcriptomics-rna-seq-counts-to-genes",
+                "wfname": "rna-seq-counts-to-genes",
+                "workflow": "rna-seq-counts-to-genes.ga",
                 "workflow_tools": [
-                    "__MERGE_COLLECTION__",
-                    "__SORTLIST__",
-                    "sort1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.5.1.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.5.1.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.5.1.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bctools_extract_alignment_ends/bctools_extract_alignment_ends/0.2.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed_bedgraph/2.19.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/1.1.2+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/rnateam/peakachu/peakachu/0.1.0.2",
-                    "toolshed.g2.bx.psu.edu/repos/rnateam/rcas/rcas/1.5.4",
-                    "wig_to_bigWig"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.9"
                 ],
-                "workflowhub_id": "1285"
+                "workflowhub_id": "1321"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/1327423"
+        "zenodo_link": "https://zenodo.org/record/4273218"
     },
     {
         "admin_install": {
@@ -261660,153 +267738,130 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "salmon",
+                    "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "53e9709776a0",
-                    "tool_panel_section_label": "RNA Analysis",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "trim_galore",
+                    "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "1bfc7254232e",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastq_manipulation",
-                    "owner": "devteam",
-                    "revisions": "bb07615a5b6a",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "3fdc1a74d866",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "samtool_filter2",
+                    "name": "column_maker",
                     "owner": "devteam",
-                    "revisions": "dc6ff68ea5e8",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "revisions": "02026300aa45",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bedtools",
+                    "name": "egsea",
                     "owner": "iuc",
-                    "revisions": "c78cf6fe3018",
-                    "tool_panel_section_label": "BED",
+                    "revisions": "fba1660fb717",
+                    "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "deseq2",
+                    "name": "fgsea",
                     "owner": "iuc",
-                    "revisions": "24a09ca67621",
-                    "tool_panel_section_label": "RNA Analysis",
+                    "revisions": "17eb1e0d711f",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "hisat2",
+                    "name": "goseq",
                     "owner": "iuc",
-                    "revisions": "1eb21dccc2fa",
-                    "tool_panel_section_label": "Mapping",
+                    "revisions": "ef2ad746b589",
+                    "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: salmon\n  owner: bgruening\n  revisions: 53e9709776a0\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trim_galore\n  owner: bgruening\n  revisions: 1bfc7254232e\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastq_manipulation\n  owner: devteam\n  revisions: bb07615a5b6a\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3fdc1a74d866\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtool_filter2\n  owner: devteam\n  revisions: dc6ff68ea5e8\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: c78cf6fe3018\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deseq2\n  owner: iuc\n  revisions: 24a09ca67621\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: hisat2\n  owner: iuc\n  revisions: 1eb21dccc2fa\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/srna/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 02026300aa45\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: egsea\n  owner: iuc\n  revisions: fba1660fb717\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fgsea\n  owner: iuc\n  revisions: 17eb1e0d711f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: goseq\n  owner: iuc\n  revisions: ef2ad746b589\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.json",
         "contributors": [
             {
-                "id": "malloryfreeberg",
-                "joined": "2017-09",
-                "name": "Mallory Freeberg",
-                "orcid": "0000-0003-2949-3921",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/malloryfreeberg/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/malloryfreeberg.json"
+                "id": "mblue9",
+                "joined": "2018-09",
+                "name": "Maria Doyle",
+                "orcid": "0000-0003-4847-8436",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
+            },
+            {
+                "id": "bphipson",
+                "joined": "2018-09",
+                "name": "Belinda Phipson",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bphipson/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bphipson.json"
             }
         ],
-        "dir": "topics/transcriptomics/tutorials/srna",
+        "dir": "topics/transcriptomics/tutorials/rna-seq-genes-to-pathways",
         "edam_operation": [
-            "Sequencing quality control",
-            "Primer removal",
-            "Sequence alignment",
-            "Sequence composition calculation",
-            "Read pre-processing",
-            "RNA-Seq quantification",
-            "Gene expression analysis",
-            "Sequence trimming",
-            "Differential gene expression analysis",
-            "RNA-Seq analysis",
-            "Statistical calculation"
+            "Gene-set enrichment analysis",
+            "Gene set testing",
+            "Gene functional annotation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.eu",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "transcriptomics/srna",
+        "id": "transcriptomics/rna-seq-genes-to-pathways",
         "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
+            "UseGalaxy.be",
+            "UseGalaxy.cz"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Analysis of small RNAs is complex due to the diversity of small RNA subclasses.",
-            "Both alignment to references and transcript quantification approaches are useful for small RNA-seq analyses."
+            "goseq can be used to identify enriched gene ontology categories and incorporate gene length bias",
+            "fgsea can be used to identify enriched gene sets, such as the MSigDB collections, and generate barcode plots",
+            "EGSEA can be used to identify enriched gene sets, such as MSigDB and KEGG, generating visualisations that include heatmaps and KEGG pathway diagrams",
+            "Multiple methods can be used to help identify differentially expressed pathways and to visualise results"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2023-11-09",
         "objectives": [
-            "Process small RNA-seq datasets to determine quality and reproducibility.",
-            "Filter out contaminants (e.g. rRNA reads) in small RNA-seq datasets.",
-            "Differentiate between subclasses of small RNAs based on their characteristics.",
-            "Identify differently abundant small RNAs and their targets."
+            "Identification of differentially expressed pathways"
         ],
-        "pageviews": 10966,
-        "pub_date": "2017-06-29",
+        "pageviews": 37169,
+        "pub_date": "2018-12-31",
         "questions": [
-            "What small RNAs are expressed?",
-            "What RNA features have significantly different numbers of small RNAs targeting them between two conditions?"
+            "What are the differentially expressed pathways in the mammary gland of pregnant versus lactating mice?"
         ],
-        "short_id": "T00307",
+        "short_id": "T00300",
         "short_tools": [
-            "hisat2",
-            "fastq_manipulation",
-            "bedtools_bamtofastq",
-            "samtool_filter2",
-            "fastqc",
-            "salmon",
-            "Filter1",
-            "deseq2",
-            "trim_galore"
+            "join1",
+            "tp_sort_header_tool",
+            "egsea",
+            "goseq",
+            "Add_a_column1",
+            "Cut1",
+            "fgsea",
+            "tp_cut_tool"
         ],
         "slides": false,
         "slides_recordings": false,
+        "subtopic": "end-to-end",
         "supported_servers": {
             "exact": [
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.no",
@@ -261823,21 +267878,35 @@
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
                 }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
             ]
         },
         "symlink": null,
-        "time_estimation": "3h",
-        "title": "Differential abundance testing of small RNAs",
+        "tags": [
+            "mouse"
+        ],
+        "time_estimation": "2h",
+        "title": "3: RNA-seq genes to pathways",
         "tools": [
-            "Filter1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.8.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.0.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.39",
-            "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3"
+            "Cut1",
+            "join1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
+            "toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.44.0+galaxy0"
         ],
         "topic_name": "transcriptomics",
         "topic_name_human": "Transcriptomics",
@@ -261847,638 +267916,1027 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "srna",
+        "tutorial_name": "rna-seq-genes-to-pathways",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/srna/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/srna/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/srna/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.json"
         },
-        "version": 26,
+        "version": 13,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 131,
-        "visitors": 5939,
+        "visit_duration": 112,
+        "visitors": 22384,
         "workflows": [
             {
                 "creators": [],
-                "description": "This workflow completes the first part of the small RNA-seq tutorial from read pre-processing to trimming.e",
+                "description": "RNA-seq genes to pathways",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nrRNA reference FASTA\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmiRNA hairpin reference FASTA\"]\n  3[label=\"FastQC\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Trim Galore!\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"FastQC\"]\n  4 -> 5 [label=\"trimmed_reads_single\"]\n  6[label=\"HISAT\"]\n  4 -> 6 [label=\"trimmed_reads_single\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"Filter SAM or BAM, output SAM or BAM\"]\n  6 -> 7 [label=\"output_alignments\"]\n  8[label=\"Convert from BAM to FastQ\"]\n  7 -> 8 [label=\"output1\"]\n  9[label=\"HISAT\"]\n  8 -> 9 [label=\"output\"]\n  2 -> 9 [label=\"output\"]\n  10[label=\"Filter SAM or BAM, output SAM or BAM\"]\n  9 -> 10 [label=\"output_alignments\"]\n  11[label=\"Convert from BAM to FastQ\"]\n  10 -> 11 [label=\"output1\"]\n  12[label=\"Manipulate FASTQ\"]\n  11 -> 12 [label=\"output\"]\n  13[label=\"Manipulate FASTQ\"]\n  11 -> 13 [label=\"output\"]\n  14[label=\"FastQC\"]\n  12 -> 14 [label=\"output_file\"]\n  15[label=\"FastQC\"]\n  13 -> 15 [label=\"output_file\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nseqdata\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nfactordata\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nDE table\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmouse_hallmark_sets\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlimma_filtered_counts\"]\n  5[label=\"Compute\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"Cut\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"Advanced Cut\"]\n  4 -> 7 [label=\"output\"]\n  8[label=\"Advanced Cut\"]\n  4 -> 8 [label=\"output\"]\n  9[label=\"Join two Datasets\"]\n  5 -> 9 [label=\"out_file1\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"Sort\"]\n  6 -> 10 [label=\"out_file1\"]\n  11[label=\"EGSEA\"]\n  8 -> 11 [label=\"output\"]\n  7 -> 11 [label=\"output\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"Cut\"]\n  9 -> 12 [label=\"out_file1\"]\n  13[label=\"Cut\"]\n  9 -> 13 [label=\"out_file1\"]\n  14[label=\"fgsea\"]\n  10 -> 14 [label=\"outfile\"]\n  3 -> 14 [label=\"output\"]\n  15[label=\"goseq\"]\n  12 -> 15 [label=\"out_file1\"]\n  13 -> 15 [label=\"out_file1\"]\n}",
                 "history": [
+                    {
+                        "hash": "d4c89b2dd1df9f664b50c12830c206c195ded1ba",
+                        "message": "Update workflow (#3198)",
+                        "num": 5,
+                        "short_hash": "d4c89b2dd",
+                        "unix": "1645817433"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 4,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
                     {
                         "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
                         "message": "Workflow renaming",
-                        "num": 2,
+                        "num": 3,
                         "short_hash": "eb4d724e0",
                         "unix": "1579084895"
                     },
                     {
-                        "hash": "6efea8d060e13f09bf9d0ea32b07c1eaf3a577d1",
-                        "message": "Move the srna tutorial to transcriptomics topic",
+                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
+                        "message": "Changed format of workflows",
+                        "num": 2,
+                        "short_hash": "361236c41",
+                        "unix": "1554368414"
+                    },
+                    {
+                        "hash": "0ea8c79012ba1b18d3f79be0ff2e2b826092f5e2",
+                        "message": "Rename tutorial and image folders to the updated titles",
                         "num": 1,
-                        "short_hash": "6efea8d06",
-                        "unix": "1498731718"
+                        "short_hash": "0ea8c7901",
+                        "unix": "1546155649"
                     }
                 ],
                 "inputs": [
                     {
                         "annotation": "",
                         "content_id": null,
+                        "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Input Dataset Collection"
+                                "name": "seqdata"
                             }
                         ],
-                        "label": null,
-                        "name": "Input dataset collection",
+                        "label": "seqdata",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 278,
-                            "top": 200.96875
+                            "bottom": 376.9375,
+                            "height": 61.78125,
+                            "left": 164.984375,
+                            "right": 364.984375,
+                            "top": 315.15625,
+                            "width": 200,
+                            "x": 164.984375,
+                            "y": 315.15625
                         },
-                        "tool_errors": null,
                         "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "5e34fb1f-fa44-4178-9d5e-953d69030004",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "12c8979f-7a43-4133-98ac-6b4c1b6d9e57"
-                            }
-                        ]
+                        "type": "data_input",
+                        "uuid": "530892fe-96db-4ac9-86da-57adf9dc569d",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
+                        "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "rRNA reference FASTA"
+                                "name": "factordata"
                             }
                         ],
-                        "label": "rRNA reference FASTA",
+                        "label": "factordata",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 842.5,
-                            "top": 239
+                            "bottom": 466.96875,
+                            "height": 61.78125,
+                            "left": 164.984375,
+                            "right": 364.984375,
+                            "top": 405.1875,
+                            "width": 200,
+                            "x": 164.984375,
+                            "y": 405.1875
                         },
-                        "tool_errors": null,
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"rRNA reference FASTA\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "01fce37f-1a11-4d1e-b039-6d53ba373064",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "6fafacef-3b18-425e-9f15-e717d0febbdc"
-                            }
-                        ]
+                        "uuid": "a7dfbd15-e384-4bbb-a30f-a8ff03b07784",
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "Be sure to use hairpin sequences, not just mature miRNA sequences.",
+                        "annotation": "",
                         "content_id": null,
+                        "errors": null,
                         "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Be sure to use hairpin sequences, not just mature miRNA sequences.",
-                                "name": "miRNA hairpin reference FASTA"
+                                "description": "",
+                                "name": "DE table"
                             }
                         ],
-                        "label": "miRNA hairpin reference FASTA",
-                        "name": "Input dataset",
+                        "label": "DE table",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 1159.5,
-                            "top": 232
+                            "bottom": 556.984375,
+                            "height": 61.78125,
+                            "left": 164.984375,
+                            "right": 364.984375,
+                            "top": 495.203125,
+                            "width": 200,
+                            "x": 164.984375,
+                            "y": 495.203125
                         },
-                        "tool_errors": null,
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"miRNA hairpin reference FASTA\"}",
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "cba8d787-dc52-4ed6-bc9a-d697db038495",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "c8ab4106-9b66-4c54-8d62-27b370fbff01"
-                            }
-                        ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nrRNA reference FASTA\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nmiRNA hairpin reference FASTA\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"FastQC\"];\n  0 -->|output| 3;\n  4[\"Trim Galore!\"];\n  0 -->|output| 4;\n  5[\"FastQC\"];\n  4 -->|trimmed_reads_single| 5;\n  6[\"HISAT\"];\n  4 -->|trimmed_reads_single| 6;\n  1 -->|output| 6;\n  7[\"Filter SAM or BAM, output SAM or BAM\"];\n  6 -->|output_alignments| 7;\n  8[\"Convert from BAM to FastQ\"];\n  7 -->|output1| 8;\n  9[\"HISAT\"];\n  8 -->|output| 9;\n  2 -->|output| 9;\n  10[\"Filter SAM or BAM, output SAM or BAM\"];\n  9 -->|output_alignments| 10;\n  11[\"Convert from BAM to FastQ\"];\n  10 -->|output1| 11;\n  12[\"Manipulate FASTQ\"];\n  11 -->|output| 12;\n  13[\"Manipulate FASTQ\"];\n  11 -->|output| 13;\n  14[\"FastQC\"];\n  12 -->|output_file| 14;\n  15[\"FastQC\"];\n  13 -->|output_file| 15;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "sRNA Seq Step 1: Read Pre Processing And Removal Of Artifacts (no Grooming)",
-                "outputs": [
+                        "type": "data_collection_input",
+                        "uuid": "e3e247b3-de91-4ae4-af20-41fe85400e05",
+                        "workflow_outputs": []
+                    },
                     {
                         "annotation": "",
                         "content_id": null,
-                        "id": 0,
+                        "errors": null,
+                        "id": 3,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Input Dataset Collection"
+                                "name": "mouse_hallmark_sets"
                             }
                         ],
-                        "label": null,
-                        "name": "Input dataset collection",
+                        "label": "mouse_hallmark_sets",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 278,
-                            "top": 200.96875
+                            "bottom": 667.421875,
+                            "height": 82.171875,
+                            "left": 164.984375,
+                            "right": 364.984375,
+                            "top": 585.25,
+                            "width": 200,
+                            "x": 164.984375,
+                            "y": 585.25
                         },
-                        "tool_errors": null,
                         "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "5e34fb1f-fa44-4178-9d5e-953d69030004",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "12c8979f-7a43-4133-98ac-6b4c1b6d9e57"
-                            }
-                        ]
+                        "type": "data_input",
+                        "uuid": "651a815a-cadf-4bdf-8d6e-d08379ed4684",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
-                        "id": 1,
+                        "errors": null,
+                        "id": 4,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "rRNA reference FASTA"
+                                "name": "limma_filtered_counts"
                             }
                         ],
-                        "label": "rRNA reference FASTA",
+                        "label": "limma_filtered_counts",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 842.5,
-                            "top": 239
+                            "bottom": 796.453125,
+                            "height": 82.171875,
+                            "left": 164.984375,
+                            "right": 364.984375,
+                            "top": 714.28125,
+                            "width": 200,
+                            "x": 164.984375,
+                            "y": 714.28125
                         },
-                        "tool_errors": null,
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"rRNA reference FASTA\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "01fce37f-1a11-4d1e-b039-6d53ba373064",
+                        "uuid": "9347a180-d878-4afe-95cb-9b6cfd383448",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nseqdata\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nfactordata\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nDE table\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nmouse_hallmark_sets\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nlimma_filtered_counts\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Compute\"];\n  2 -->|output| 5;\n  6[\"Cut\"];\n  2 -->|output| 6;\n  7[\"Advanced Cut\"];\n  4 -->|output| 7;\n  8[\"Advanced Cut\"];\n  4 -->|output| 8;\n  9[\"Join two Datasets\"];\n  5 -->|out_file1| 9;\n  0 -->|output| 9;\n  10[\"Sort\"];\n  6 -->|out_file1| 10;\n  11[\"EGSEA\"];\n  8 -->|output| 11;\n  7 -->|output| 11;\n  1 -->|output| 11;\n  12[\"Cut\"];\n  9 -->|out_file1| 12;\n  13[\"Cut\"];\n  9 -->|out_file1| 13;\n  14[\"fgsea\"];\n  10 -->|outfile| 14;\n  3 -->|output| 14;\n  15[\"goseq\"];\n  12 -->|out_file1| 15;\n  13 -->|out_file1| 15;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "RNA Seq Genes To Pathways (imported from uploaded file)",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "input": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Compute",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 408.328125,
+                            "height": 93.171875,
+                            "left": 477.015625,
+                            "right": 677.015625,
+                            "top": 315.15625,
+                            "width": 200,
+                            "x": 477.015625,
+                            "y": 315.15625
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
+                        "tool_shed_repository": {
+                            "changeset_revision": "02026300aa45",
+                            "name": "column_maker",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"avoid_scientific_notation\": \"false\", \"cond\": \"bool(c8<0.01) and bool(abs(c4)>0.58)\", \"header_lines_conditional\": {\"header_lines_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"round\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.6",
+                        "type": "tool",
+                        "uuid": "20efeeff-6096-48d2-9f1f-e3e776112b13",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "6fafacef-3b18-425e-9f15-e717d0febbdc"
+                                "output_name": "out_file1",
+                                "uuid": "52fae575-f107-4657-aec1-1f2b3d71ac95"
                             }
                         ]
                     },
                     {
-                        "annotation": "Be sure to use hairpin sequences, not just mature miRNA sequences.",
-                        "content_id": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
+                        "annotation": "",
+                        "content_id": "Cut1",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "input": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Cut",
+                        "outputs": [
                             {
-                                "description": "Be sure to use hairpin sequences, not just mature miRNA sequences.",
-                                "name": "miRNA hairpin reference FASTA"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "miRNA hairpin reference FASTA",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 1159.5,
-                            "top": 232
+                            "bottom": 534.359375,
+                            "height": 93.171875,
+                            "left": 477.015625,
+                            "right": 677.015625,
+                            "top": 441.1875,
+                            "width": 200,
+                            "x": 477.015625,
+                            "y": 441.1875
                         },
-                        "tool_errors": null,
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"miRNA hairpin reference FASTA\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "cba8d787-dc52-4ed6-bc9a-d697db038495",
+                        "post_job_actions": {},
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm10.len\", \"columnList\": \"c1,c6\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"limma-voom_luminalpregnant-luminallactate\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2",
+                        "type": "tool",
+                        "uuid": "a301610d-4e49-4dd6-b603-482674c9ec7f",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "c8ab4106-9b66-4c54-8d62-27b370fbff01"
+                                "output_name": "out_file1",
+                                "uuid": "b9d13636-4ef9-45a6-9563-b91005fa9d57"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2",
-                        "id": 4,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                        "errors": null,
+                        "id": 7,
                         "input_connections": {
-                            "singlePaired|input_singles": {
-                                "id": 0,
+                            "input": {
+                                "id": 4,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Advanced Cut",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool Trim Galore!",
-                                "name": "singlePaired"
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
+                        "position": {
+                            "bottom": 680.765625,
+                            "height": 113.5625,
+                            "left": 477.015625,
+                            "right": 677.015625,
+                            "top": 567.203125,
+                            "width": 200,
+                            "x": 477.015625,
+                            "y": 567.203125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"complement\": \"--complement\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"list\": \"2,3\"}, \"delimiter\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.0",
+                        "type": "tool",
+                        "uuid": "74f84dac-988e-436e-80cf-e45720a1ca6d",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "8cf43669-dd17-42be-bd0d-f1a8ca299db6"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "input": {
+                                "id": 4,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
                         "label": null,
-                        "name": "Trim Galore!",
+                        "name": "Advanced Cut",
                         "outputs": [
                             {
-                                "name": "trimmed_reads_paired_collection",
-                                "type": "input"
-                            },
-                            {
-                                "name": "trimmed_reads_unpaired_collection",
-                                "type": "input"
-                            },
-                            {
-                                "name": "trimmed_reads_single",
-                                "type": "fastqsanger"
-                            },
-                            {
-                                "name": "trimmed_reads_pair1",
-                                "type": "fastqsanger"
-                            },
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 800.8125,
+                            "height": 113.5625,
+                            "left": 477.015625,
+                            "right": 677.015625,
+                            "top": 687.25,
+                            "width": 200,
+                            "x": 477.015625,
+                            "y": 687.25
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"complement\": \"\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"list\": \"1,2\"}, \"delimiter\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.0",
+                        "type": "tool",
+                        "uuid": "e5c8206a-72d0-4faa-a19e-8d7ac0190316",
+                        "workflow_outputs": [
                             {
-                                "name": "trimmed_reads_pair2",
-                                "type": "fastqsanger"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "3ce059c1-68f7-49c1-a1fd-fd7d6e1c0bc8"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "join1",
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {
+                            "input1": {
+                                "id": 5,
+                                "output_name": "out_file1"
                             },
+                            "input2": {
+                                "id": 0,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Join two Datasets",
+                        "outputs": [
                             {
-                                "name": "unpaired_reads_1",
-                                "type": "fastqsanger"
-                            },
+                                "name": "out_file1",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 459.109375,
+                            "height": 143.953125,
+                            "left": 734.046875,
+                            "right": 934.046875,
+                            "top": 315.15625,
+                            "width": 200,
+                            "x": 734.046875,
+                            "y": 315.15625
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "join1",
+                        "tool_state": "{\"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm10.len\", \"field1\": \"1\", \"field2\": \"1\", \"fill_empty_columns\": {\"fill_empty_columns_switch\": \"no_fill\", \"__current_case__\": 0}, \"header\": \"\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input1|__identifier__\": \"limma-voom_luminalpregnant-luminallactate\", \"input2\": {\"__class__\": \"ConnectedValue\"}, \"partial\": \"\", \"unmatched\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.3",
+                        "type": "tool",
+                        "uuid": "2f81fad6-b41c-4c4b-b803-51a5ccd1c047",
+                        "workflow_outputs": [
                             {
-                                "name": "unpaired_reads_2",
-                                "type": "fastqsanger"
-                            },
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "49d52f1a-b5ce-4cde-a141-eb684154f8ad"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {
+                            "infile": {
+                                "id": 6,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Sort",
+                        "outputs": [
                             {
-                                "name": "report_file",
-                                "type": "txt"
+                                "name": "outfile",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 549.5,
-                            "top": 238
+                            "bottom": 562.359375,
+                            "height": 93.171875,
+                            "left": 734.046875,
+                            "right": 934.046875,
+                            "top": 469.1875,
+                            "width": 200,
+                            "x": 734.046875,
+                            "y": 469.1875
                         },
-                        "post_job_actions": {
-                            "HideDatasetActiontrimmed_reads_pair1": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "trimmed_reads_pair1"
-                            },
-                            "HideDatasetActiontrimmed_reads_pair2": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "trimmed_reads_pair2"
-                            },
-                            "HideDatasetActiontrimmed_reads_paired_collection": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "trimmed_reads_paired_collection"
-                            },
-                            "HideDatasetActiontrimmed_reads_unpaired_collection": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "trimmed_reads_unpaired_collection"
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm10.len\", \"header\": \"1\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"infile|__identifier__\": \"limma-voom_luminalpregnant-luminallactate\", \"sortkeys\": [{\"__index__\": 0, \"column\": \"2\", \"order\": \"r\", \"style\": \"n\"}], \"unique\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
+                        "type": "tool",
+                        "uuid": "ce9e6449-48c9-4857-b20a-e82f0a554685",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "304a128c-3da0-4a25-bd5b-52da23d9f850"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0",
+                        "errors": null,
+                        "id": 11,
+                        "input_connections": {
+                            "genes": {
+                                "id": 8,
+                                "output_name": "output"
                             },
-                            "HideDatasetActionunpaired_reads_1": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "unpaired_reads_1"
+                            "input|counts": {
+                                "id": 7,
+                                "output_name": "output"
                             },
-                            "HideDatasetActionunpaired_reads_2": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "unpaired_reads_2"
+                            "input|fact|finfo": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "EGSEA",
+                        "outputs": [
+                            {
+                                "name": "outTables",
+                                "type": "input"
                             },
-                            "RenameDatasetActiontrimmed_reads_single": {
-                                "action_arguments": {
-                                    "newname": "Trimmed reads"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "trimmed_reads_single"
+                            {
+                                "name": "outReport",
+                                "type": "html"
                             }
+                        ],
+                        "position": {
+                            "bottom": 820.34375,
+                            "height": 225.125,
+                            "left": 734.046875,
+                            "right": 934.046875,
+                            "top": 595.21875,
+                            "width": 200,
+                            "x": 734.046875,
+                            "y": 595.21875
                         },
-                        "tool_errors": null,
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "f1e71aeaa923",
-                            "name": "trim_galore",
-                            "owner": "bgruening",
+                            "changeset_revision": "fba1660fb717",
+                            "name": "egsea",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"params\": \"{\\\"min_length\\\": \\\"12\\\", \\\"stringency\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"retain_unpaired\\\": {\\\"retain_unpaired_select\\\": \\\"no_output\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 1, \\\"report\\\": \\\"true\\\", \\\"settingsType\\\": \\\"custom\\\", \\\"quality\\\": \\\"0\\\", \\\"clip_R1\\\": \\\"\\\", \\\"clip_R2\\\": \\\"\\\"}\", \"rrbs\": \"{\\\"settingsType\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"three_prime_clip_R1\\\": \\\"\\\", \\\"trimming\\\": {\\\"trimming_select\\\": \\\"\\\", \\\"__current_case__\\\": 0}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_singles\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\"}",
-                        "tool_version": "0.4.2",
+                        "tool_state": "{\"advanced\": {\"display_top\": \"5\", \"min_size\": \"2\", \"fdr_cutoff\": \"0.05\", \"combine_method\": \"wilkinson\", \"sort_method\": \"med.rank\", \"rscriptOpt\": \"false\", \"rdaOpt\": \"false\"}, \"base_methods\": [\"camera\", \"safe\", \"gage\", \"zscore\", \"gsva\", \"globaltest\", \"ora\", \"ssgsea\", \"padog\", \"plage\", \"fry\"], \"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm10.len\", \"genes\": {\"__class__\": \"ConnectedValue\"}, \"gsdb\": {\"gsdb_gsets\": null}, \"input\": {\"format\": \"matrix\", \"__current_case__\": 1, \"counts\": {\"__class__\": \"ConnectedValue\"}, \"fact\": {\"ffile\": \"yes\", \"__current_case__\": 0, \"finfo\": {\"__class__\": \"ConnectedValue\"}}}, \"keggdb\": {\"keggdb_gsets\": [\"keggmet\", \"keggsig\"], \"kegg_updated\": \"false\"}, \"msigdb\": {\"msigdb_gsets\": [\"h\"]}, \"non_commercial_use\": \"true\", \"rep_contrast\": [{\"__index__\": 0, \"contrast\": \"basalpregnant-basallactate\"}, {\"__index__\": 1, \"contrast\": \"luminalpregnant-luminallactate\"}], \"species\": \"mouse\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.20.0",
                         "type": "tool",
-                        "uuid": "21f6bafb-48bb-4f7d-8543-8b8b96345d1a",
+                        "uuid": "e9df8569-f438-4144-9f3a-ebb569ec2047",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "report_file",
-                                "uuid": "8d621eea-f61d-4780-b3d7-d1de6a7a9e12"
+                                "output_name": "outTables",
+                                "uuid": "778284eb-56d6-4079-badb-951d5714c8f8"
                             },
                             {
                                 "label": null,
-                                "output_name": "trimmed_reads_single",
-                                "uuid": "d148afd4-9b94-4ef6-9856-98963e71ef6d"
+                                "output_name": "outReport",
+                                "uuid": "86db0251-4d15-45b7-b471-2af7def64d39"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65",
-                        "id": 5,
+                        "content_id": "Cut1",
+                        "errors": null,
+                        "id": 12,
                         "input_connections": {
-                            "input_file": {
-                                "id": 4,
-                                "output_name": "trimmed_reads_single"
+                            "input": {
+                                "id": 9,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "contaminants"
-                            },
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "limits"
-                            },
-                            {
-                                "description": "runtime parameter for tool FastQC",
-                                "name": "input_file"
+                                "description": "runtime parameter for tool Cut",
+                                "name": "input"
                             }
                         ],
                         "label": null,
-                        "name": "FastQC",
+                        "name": "Cut",
                         "outputs": [
                             {
-                                "name": "html_file",
-                                "type": "html"
-                            },
-                            {
-                                "name": "text_file",
-                                "type": "txt"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 548.5,
-                            "top": 615
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActiontext_file": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "text_file"
-                            },
-                            "RenameDatasetActionhtml_file": {
-                                "action_arguments": {
-                                    "newname": "FastQC on Groomed and Trimmed data"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "html_file"
-                            }
-                        },
-                        "tool_errors": null,
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65",
-                        "tool_shed_repository": {
-                            "changeset_revision": "3fdc1a74d866",
-                            "name": "fastqc",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 408.328125,
+                            "height": 93.171875,
+                            "left": 1003.09375,
+                            "right": 1203.09375,
+                            "top": 315.15625,
+                            "width": 200,
+                            "x": 1003.09375,
+                            "y": 315.15625
                         },
-                        "tool_state": "{\"__page__\": 0, \"contaminants\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"limits\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "0.65",
+                        "post_job_actions": {},
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"columnList\": \"c1,c10\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2",
                         "type": "tool",
-                        "uuid": "972f64c0-14f5-460e-9d30-27faa6df86d4",
+                        "uuid": "af9206ae-98cc-4432-a81e-ee39bb2c2a8a",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "html_file",
-                                "uuid": "da777968-7f09-4ba1-8ff0-1c9358de161c"
+                                "output_name": "out_file1",
+                                "uuid": "fd382af4-5a99-4264-af9a-f8fdc6c134b7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0",
-                        "id": 8,
+                        "content_id": "Cut1",
+                        "errors": null,
+                        "id": 13,
                         "input_connections": {
                             "input": {
-                                "id": 7,
-                                "output_name": "output1"
+                                "id": 9,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Convert from BAM to FastQ",
+                                "description": "runtime parameter for tool Cut",
                                 "name": "input"
                             }
                         ],
                         "label": null,
-                        "name": "Convert from BAM to FastQ",
+                        "name": "Cut",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "fastq"
-                            },
-                            {
-                                "name": "output2",
-                                "type": "fastq2"
+                                "name": "out_file1",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 859,
-                            "top": 763
+                            "bottom": 534.359375,
+                            "height": 93.171875,
+                            "left": 1003.09375,
+                            "right": 1203.09375,
+                            "top": 441.1875,
+                            "width": 200,
+                            "x": 1003.09375,
+                            "y": 441.1875
                         },
-                        "post_job_actions": {
-                            "ChangeDatatypeActionoutput": {
-                                "action_arguments": {
-                                    "newtype": "fastqsanger"
-                                },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "output"
-                            },
-                            "HideDatasetActionoutput2": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output2"
+                        "post_job_actions": {},
+                        "tool_id": "Cut1",
+                        "tool_state": "{\"columnList\": \"c1,c12\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.2",
+                        "type": "tool",
+                        "uuid": "4a72bc30-2d4e-4480-875b-507b2a7274b4",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "655e9412-ca8c-4b0f-9dcc-fa8da9126e90"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1",
+                        "errors": null,
+                        "id": 14,
+                        "input_connections": {
+                            "rnk_file": {
+                                "id": 10,
+                                "output_name": "outfile"
                             },
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Non-rRNA reads (FASTQ)"
-                                },
-                                "action_type": "RenameDatasetAction",
+                            "sets_file": {
+                                "id": 3,
                                 "output_name": "output"
                             }
                         },
-                        "tool_errors": null,
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0",
+                        "inputs": [],
+                        "label": null,
+                        "name": "fgsea",
+                        "outputs": [
+                            {
+                                "name": "out_tab",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "out_pdf",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 782.328125,
+                            "height": 215.125,
+                            "left": 1003.09375,
+                            "right": 1203.09375,
+                            "top": 567.203125,
+                            "width": 200,
+                            "x": 1003.09375,
+                            "y": 567.203125
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "d25966c8ddeb",
-                            "name": "bedtools",
+                            "changeset_revision": "17eb1e0d711f",
+                            "name": "fgsea",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"fq2\": \"\\\"false\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"tags\": \"\\\"false\\\"\"}",
-                        "tool_version": "2.24.0",
+                        "tool_state": "{\"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm10.len\", \"header\": \"true\", \"max_size\": \"500\", \"min_size\": \"15\", \"n_perm\": \"1000\", \"plot_opt\": \"true\", \"rda_opt\": \"false\", \"rnk_file\": {\"__class__\": \"ConnectedValue\"}, \"rnk_file|__identifier__\": \"limma-voom_luminalpregnant-luminallactate\", \"sets_file\": {\"__class__\": \"ConnectedValue\"}, \"top_num\": \"10\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8.0+galaxy1",
                         "type": "tool",
-                        "uuid": "697122c3-2a2b-4e20-aae7-9179d7e8d4a6",
+                        "uuid": "8e1c5077-edf1-4dcf-9a07-3b521c49a76f",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "9ef5503f-5cfa-4195-9985-4f1743a556cc"
+                                "output_name": "out_pdf",
+                                "uuid": "d8219c05-bd0a-43e5-8f5c-f4bb77a22863"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "out_tab",
+                                "uuid": "8b684bd0-a210-42e8-8c32-16a143e20086"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0",
-                        "id": 11,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.44.0+galaxy0",
+                        "errors": null,
+                        "id": 15,
                         "input_connections": {
-                            "input": {
-                                "id": 10,
-                                "output_name": "output1"
+                            "dge_file": {
+                                "id": 12,
+                                "output_name": "out_file1"
+                            },
+                            "length_file": {
+                                "id": 13,
+                                "output_name": "out_file1"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Convert from BAM to FastQ",
-                                "name": "input"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Convert from BAM to FastQ",
+                        "name": "goseq",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "fastq"
+                                "name": "wallenius_tab",
+                                "type": "tabular"
                             },
                             {
-                                "name": "output2",
-                                "type": "fastq2"
+                                "name": "top_plot",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "left": 1156,
-                            "top": 769
-                        },
-                        "post_job_actions": {
-                            "ChangeDatatypeActionoutput": {
-                                "action_arguments": {
-                                    "newtype": "fastqsanger"
-                                },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "output"
-                            },
-                            "ChangeDatatypeActionoutput2": {
-                                "action_arguments": {
-                                    "newtype": "fastqsanger"
-                                },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "output2"
-                            },
-                            "HideDatasetActionoutput2": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output2"
-                            },
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Non-r/miRNA reads (FASTQ)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
-                            },
-                            "RenameDatasetActionoutput2": {
-                                "action_arguments": {
-                                    "newname": "Non-r/miRNA reads (FASTQ)"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output2"
-                            }
+                            "bottom": 611.84375,
+                            "height": 296.6875,
+                            "left": 1258.109375,
+                            "right": 1458.109375,
+                            "top": 315.15625,
+                            "width": 200,
+                            "x": 1258.109375,
+                            "y": 315.15625
                         },
-                        "tool_errors": null,
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.44.0+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "d25966c8ddeb",
-                            "name": "bedtools",
+                            "changeset_revision": "ef2ad746b589",
+                            "name": "goseq",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"fq2\": \"\\\"false\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"tags\": \"\\\"false\\\"\"}",
-                        "tool_version": "2.24.0",
+                        "tool_state": "{\"adv\": {\"p_adj_method\": \"BH\", \"use_genes_without_cat\": \"false\"}, \"categorySource\": {\"catSource\": \"getgo\", \"__current_case__\": 0, \"genome\": \"mm10\", \"gene_id\": \"knownGene\", \"fetchcats\": [\"GO:BP\"]}, \"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm10.len\", \"dge_file\": {\"__class__\": \"ConnectedValue\"}, \"dge_file|__identifier__\": \"limma-voom_luminalpregnant-luminallactate\", \"length_file\": {\"__class__\": \"ConnectedValue\"}, \"length_file|__identifier__\": \"limma-voom_luminalpregnant-luminallactate\", \"methods\": {\"wallenius\": \"true\", \"hypergeometric\": \"false\", \"repcnt\": \"0\"}, \"out\": {\"topgo_plot\": \"true\", \"make_plots\": \"false\", \"cat_genes\": \"false\", \"rdata_out\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.44.0+galaxy0",
                         "type": "tool",
-                        "uuid": "2af3a8c2-4056-4922-9353-c693d78230c9",
+                        "uuid": "cddd834a-87f6-470a-b4cd-3c7af7f75e50",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "cd5b8c93-9ea0-422b-8f0a-9643961b1ab4"
+                                "output_name": "top_plot",
+                                "uuid": "6aacfcb1-f009-4fc9-8607-b3725488fb1d"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "wallenius_tab",
+                                "uuid": "a473f119-2db7-451f-8ad5-3700df2ae19b"
                             }
                         ]
                     }
                 ],
-                "parent_id": "transcriptomics/srna",
-                "path": "topics/transcriptomics/tutorials/srna/workflows/sRNA_seq_Step_1_Read_preprocessing_and_removal_of_artifacts.ga",
+                "parent_id": "transcriptomics/rna-seq-genes-to-pathways",
+                "path": "topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/workflows/rna-seq-genes-to-pathways.ga",
                 "tags": [
                     "transcriptomics"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "sRNA Seq Step 1: Read Pre Processing And Removal Of Artifacts (no Grooming)",
+                "title": "RNA Seq Genes To Pathways (imported from uploaded file)",
                 "topic_id": "transcriptomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-srna/versions/srna-seq-step-1-read-preprocessing-and-removal-of-artifacts",
-                "tutorial_id": "srna",
-                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/srna/workflows/sRNA_seq_Step_1_Read_preprocessing_and_removal_of_artifacts.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/srna/workflows/sRNA_seq_Step_1_Read_preprocessing_and_removal_of_artifacts.html",
-                "version": 2,
-                "wfid": "transcriptomics-srna",
-                "wfname": "srna-seq-step-1-read-preprocessing-and-removal-of-artifacts",
-                "workflow": "sRNA_seq_Step_1_Read_preprocessing_and_removal_of_artifacts.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-rna-seq-genes-to-pathways/versions/rna-seq-genes-to-pathways",
+                "tutorial_id": "rna-seq-genes-to-pathways",
+                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/workflows/rna-seq-genes-to-pathways.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/workflows/rna-seq-genes-to-pathways.html",
+                "version": 5,
+                "wfid": "transcriptomics-rna-seq-genes-to-pathways",
+                "wfname": "rna-seq-genes-to-pathways",
+                "workflow": "rna-seq-genes-to-pathways.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3"
+                    "Cut1",
+                    "join1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.44.0+galaxy0"
                 ],
-                "workflowhub_id": "1281"
-            },
+                "workflowhub_id": "1316"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/2596382"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "datamash_transpose",
+                    "owner": "iuc",
+                    "revisions": "22c2a1ac7ae3",
+                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ggplot2_heatmap2",
+                    "owner": "iuc",
+                    "revisions": "4955e9bb96d1",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: datamash_transpose\n  owner: iuc\n  revisions: 22c2a1ac7ae3\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ggplot2_heatmap2\n  owner: iuc\n  revisions: 4955e9bb96d1\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.json",
+        "contributors": [
+            {
+                "id": "mblue9",
+                "joined": "2018-09",
+                "name": "Maria Doyle",
+                "orcid": "0000-0003-4847-8436",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
+            }
+        ],
+        "dir": "topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "transcriptomics/rna-seq-viz-with-heatmap2",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
+        ],
+        "js_requirements": {
+            "mathjax": 8185,
+            "mermaid": false
+        },
+        "key_points": [
+            "Heatmaps can be used to visualize the expression of genes in RNA-Seq samples"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": [
+            "Create heatmaps of RNA-seq data"
+        ],
+        "pageviews": 117773,
+        "pub_date": "2018-12-31",
+        "questions": [
+            "How to generate heatmaps from RNA-seq data?"
+        ],
+        "short_id": "T00303",
+        "short_tools": [
+            "ggplot2_heatmap2",
+            "join1",
+            "Cut1",
+            "datamash_transpose"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "visualisation",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "time_estimation": "1h",
+        "title": "Visualization of RNA-Seq results with heatmap2",
+        "tools": [
+            "Cut1",
+            "join1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1+galaxy1"
+        ],
+        "topic_name": "transcriptomics",
+        "topic_name_human": "Transcriptomics",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "rna-seq-viz-with-heatmap2",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.json"
+        },
+        "version": 13,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 83,
+        "visitors": 69038,
+        "workflows": [
             {
                 "creators": [],
-                "description": "This workflow completes the second part of the sRNA-seq tutorial from transcript quantification through differential abundance testing.",
+                "description": "Visualization of RNA-Seq results with heatmap2",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nDataset collection - Control\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDataset - Ref Txome\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nDataset collection - Case\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  4[label=\"Salmon\"]\n  1 -> 4 [label=\"output\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Salmon\"]\n  1 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Salmon\"]\n  1 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"Salmon\"]\n  1 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"DESeq2\"]\n  6 -> 8 [label=\"output_quant\"]\n  4 -> 8 [label=\"output_quant\"]\n  3 -> 8 [label=\"output\"]\n  9[label=\"DESeq2\"]\n  7 -> 9 [label=\"output_quant\"]\n  5 -> 9 [label=\"output_quant\"]\n  3 -> 9 [label=\"output\"]\n  10[label=\"Filter\"]\n  8 -> 10 [label=\"deseq_out\"]\n  11[label=\"Filter\"]\n  9 -> 11 [label=\"deseq_out\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nheatmap_genes\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nnormalized_counts\"]\n  2[label=\"Join two Datasets\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Cut\"]\n  2 -> 3 [label=\"out_file1\"]\n  4[label=\"Transpose\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"heatmap2\"]\n  4 -> 5 [label=\"out_file\"]\n  kb3f6352362fb46159a9cb6b36b340172[color=lightseagreen,label=\"Output\\nheatmap_pdf\"]\n  5 -> kb3f6352362fb46159a9cb6b36b340172\n}",
                 "history": [
+                    {
+                        "hash": "2e2cb42d8ac99927000d81734fb53c7943c0c4ba",
+                        "message": "add tests from workflow-testing for blockclust and rna-seq-viz-with-volcano-plot, edit workflows",
+                        "num": 5,
+                        "short_hash": "2e2cb42d8",
+                        "unix": "1601812751"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 4,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
                     {
                         "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
                         "message": "Workflow renaming",
@@ -262487,157 +268945,156 @@
                         "unix": "1579084895"
                     },
                     {
-                        "hash": "93d49854590788054c478350af91ebe28162c08f",
-                        "message": "Update Salmon calls",
+                        "hash": "08df9d7e1855e90a0c05708a3541d318a9bbe002",
+                        "message": "Start on workflow test for heatmap2",
                         "num": 2,
-                        "short_hash": "93d498545",
-                        "unix": "1499979115"
+                        "short_hash": "08df9d7e1",
+                        "unix": "1546157457"
                     },
                     {
-                        "hash": "6efea8d060e13f09bf9d0ea32b07c1eaf3a577d1",
-                        "message": "Move the srna tutorial to transcriptomics topic",
+                        "hash": "0ea8c79012ba1b18d3f79be0ff2e2b826092f5e2",
+                        "message": "Rename tutorial and image folders to the updated titles",
                         "num": 1,
-                        "short_hash": "6efea8d06",
-                        "unix": "1498731718"
+                        "short_hash": "0ea8c7901",
+                        "unix": "1546155649"
                     }
                 ],
                 "inputs": [
                     {
                         "annotation": "",
                         "content_id": null,
+                        "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Input Dataset Collection - Control RNAi sRNA reads"
+                                "name": "heatmap_genes"
                             }
                         ],
-                        "label": "Dataset collection - Control",
-                        "name": "Input dataset collection",
+                        "label": "heatmap_genes",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 217,
-                            "top": 436
+                            "left": 199.9921875,
+                            "top": 199.9921875
                         },
-                        "tool_errors": null,
                         "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection - Control RNAi sRNA reads\"}",
+                        "tool_state": "{\"name\": \"heatmap_genes\"}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "91427be9-059a-4e6c-89e9-b4cfea01639b",
+                        "type": "data_input",
+                        "uuid": "d9f7a901-a868-430e-8bca-32e6956c2cb5",
                         "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
+                        "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Input Dataset - Reference Transcriptome"
+                                "name": "normalized_counts"
                             }
                         ],
-                        "label": "Dataset - Ref Txome",
+                        "label": "normalized_counts",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 221.5,
-                            "top": 524
+                            "left": 199.9921875,
+                            "top": 290.015625
                         },
-                        "tool_errors": null,
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"Input Dataset - Reference Transcriptome\"}",
+                        "tool_state": "{\"name\": \"normalized_counts\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "52018b9a-9b80-445d-8a0b-6ce9d3b3b47c",
+                        "uuid": "59a5f2aa-972a-441c-93c1-9d2436a6b81f",
                         "workflow_outputs": []
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nheatmap_genes\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nnormalized_counts\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Join two Datasets\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Cut\"];\n  2 -->|out_file1| 3;\n  4[\"Transpose\"];\n  3 -->|out_file1| 4;\n  5[\"heatmap2\"];\n  4 -->|out_file| 5;\n  b3f63523-62fb-4615-9a9c-b6b36b340172[\"Output\\nheatmap_pdf\"];\n  5 --> b3f63523-62fb-4615-9a9c-b6b36b340172;\n  style b3f63523-62fb-4615-9a9c-b6b36b340172 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "Heatmap2 Workflow",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Input Dataset Collection - Case RNAi sRNA reads"
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1+galaxy1",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "input1": {
+                                "id": 4,
+                                "output_name": "out_file"
                             }
-                        ],
-                        "label": "Dataset collection - Case",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 223,
-                            "top": 612
                         },
-                        "tool_errors": null,
-                        "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection - Case RNAi sRNA reads\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "c26c73ec-cd58-4674-95be-90ca097afc20",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "Tab-delimited",
-                        "content_id": null,
-                        "id": 3,
-                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Tab-delimited",
-                                "name": "Tx2Gene reference"
+                                "description": "runtime parameter for tool heatmap2",
+                                "name": "input1"
                             }
                         ],
                         "label": null,
-                        "name": "Input dataset",
-                        "outputs": [],
+                        "name": "heatmap2",
+                        "outputs": [
+                            {
+                                "name": "output1",
+                                "type": "pdf"
+                            }
+                        ],
                         "position": {
-                            "left": 1104,
-                            "top": 512
+                            "left": 1254.1171875,
+                            "top": 199.9921875
                         },
-                        "tool_errors": null,
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Tx2Gene reference\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "dcb51b30-6cea-43c4-8399-b310f04fe8d9",
-                        "workflow_outputs": []
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "4955e9bb96d1",
+                            "name": "ggplot2_heatmap2",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"scale\": \"\\\"column\\\"\", \"colorscheme\": \"\\\"blwhre\\\"\", \"__rerun_remap_job_id__\": null, \"labels\": \"\\\"both\\\"\", \"transform\": \"\\\"none\\\"\", \"cluster\": \"\\\"false\\\"\", \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"key\": \"\\\"\\\"\", \"title\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm10.len\\\"\"}",
+                        "tool_version": "2.2.1+galaxy1",
+                        "type": "tool",
+                        "uuid": "94e37309-eafe-4a3e-bbcb-fcf1924b77f3",
+                        "workflow_outputs": [
+                            {
+                                "label": "heatmap_pdf",
+                                "output_name": "output1",
+                                "uuid": "b3f63523-62fb-4615-9a9c-b6b36b340172"
+                            }
+                        ]
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nDataset collection - Control\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nDataset - Ref Txome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nDataset collection - Case\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Salmon\"];\n  1 -->|output| 4;\n  0 -->|output| 4;\n  5[\"Salmon\"];\n  1 -->|output| 5;\n  0 -->|output| 5;\n  6[\"Salmon\"];\n  1 -->|output| 6;\n  2 -->|output| 6;\n  7[\"Salmon\"];\n  1 -->|output| 7;\n  2 -->|output| 7;\n  8[\"DESeq2\"];\n  6 -->|output_quant| 8;\n  4 -->|output_quant| 8;\n  3 -->|output| 8;\n  9[\"DESeq2\"];\n  7 -->|output_quant| 9;\n  5 -->|output_quant| 9;\n  3 -->|output| 9;\n  10[\"Filter\"];\n  8 -->|deseq_out| 10;\n  11[\"Filter\"];\n  9 -->|deseq_out| 11;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "sRNA Seq Step 2: Salmon And DESeq2",
-                "outputs": [],
-                "parent_id": "transcriptomics/srna",
-                "path": "topics/transcriptomics/tutorials/srna/workflows/sRNA_seq_Step_2_Salmon_and_DESeq2.ga",
+                "parent_id": "transcriptomics/rna-seq-viz-with-heatmap2",
+                "path": "topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/workflows/rna-seq-viz-with-heatmap2.ga",
                 "tags": [
                     "transcriptomics"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "sRNA Seq Step 2: Salmon And DESeq2",
+                "tests": true,
+                "title": "Heatmap2 Workflow",
                 "topic_id": "transcriptomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-srna/versions/srna-seq-step-2-salmon-and-deseq2",
-                "tutorial_id": "srna",
-                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/srna/workflows/sRNA_seq_Step_2_Salmon_and_DESeq2.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/srna/workflows/sRNA_seq_Step_2_Salmon_and_DESeq2.html",
-                "version": 3,
-                "wfid": "transcriptomics-srna",
-                "wfname": "srna-seq-step-2-salmon-and-deseq2",
-                "workflow": "sRNA_seq_Step_2_Salmon_and_DESeq2.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-rna-seq-viz-with-heatmap2/versions/rna-seq-viz-with-heatmap2",
+                "tutorial_id": "rna-seq-viz-with-heatmap2",
+                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/workflows/rna-seq-viz-with-heatmap2.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/workflows/rna-seq-viz-with-heatmap2.html",
+                "version": 4,
+                "wfid": "transcriptomics-rna-seq-viz-with-heatmap2",
+                "wfname": "rna-seq-viz-with-heatmap2",
+                "workflow": "rna-seq-viz-with-heatmap2.ga",
                 "workflow_tools": [
-                    "Filter1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.8.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.39"
+                    "Cut1",
+                    "join1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1+galaxy1"
                 ],
-                "workflowhub_id": "1279"
+                "workflowhub_id": "1311"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/826906"
+        "zenodo_link": "https://zenodo.org/record/2529926"
     },
     {
         "admin_install": {
@@ -262646,51 +269103,142 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "9da02be9c6cc",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "3d0c7bdf12f5",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "column_maker",
+                    "name": "picard",
                     "owner": "devteam",
-                    "revisions": "02026300aa45",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "revisions": "b9fbec5ac6b2",
+                    "tool_panel_section_label": "Picard",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "egsea",
+                    "name": "picard",
+                    "owner": "devteam",
+                    "revisions": "b502c227b5e6",
+                    "tool_panel_section_label": "Picard",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "samtools_idxstats",
+                    "owner": "devteam",
+                    "revisions": "811fc2d75ad4",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "samtools_idxstats",
+                    "owner": "devteam",
+                    "revisions": "7def34e6cf4d",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collection_column_join",
                     "owner": "iuc",
-                    "revisions": "fba1660fb717",
+                    "revisions": "3ddd99c7efee",
+                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "featurecounts",
+                    "owner": "iuc",
+                    "revisions": "1759d845181e",
                     "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fgsea",
+                    "name": "featurecounts",
                     "owner": "iuc",
-                    "revisions": "17eb1e0d711f",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "38b6d12edc68",
+                    "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "goseq",
+                    "name": "hisat2",
                     "owner": "iuc",
-                    "revisions": "ef2ad746b589",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "61ee47027bd3",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "hisat2",
+                    "owner": "iuc",
+                    "revisions": "6c19daec423d",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "9a913cdee30e",
+                    "tool_panel_section_label": "Quality Control",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "1c2db0054039",
+                    "tool_panel_section_label": "Quality Control",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "b2f1f75d49c4",
+                    "tool_panel_section_label": "Quality Control",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "cutadapt",
+                    "owner": "lparsons",
+                    "revisions": "660cffd8d92a",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "cutadapt",
+                    "owner": "lparsons",
+                    "revisions": "c5e2e5902201",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rseqc",
+                    "owner": "nilesh",
+                    "revisions": "dbedfc5f5a3c",
+                    "tool_panel_section_label": "RNA Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rseqc",
+                    "owner": "nilesh",
+                    "revisions": "dbedfc5f5a3c",
+                    "tool_panel_section_label": "RNA Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rseqc",
+                    "owner": "nilesh",
+                    "revisions": "dbedfc5f5a3c",
+                    "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 02026300aa45\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: egsea\n  owner: iuc\n  revisions: fba1660fb717\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fgsea\n  owner: iuc\n  revisions: 17eb1e0d711f\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: goseq\n  owner: iuc\n  revisions: ef2ad746b589\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastqc\n  owner: devteam\n  revisions: 9da02be9c6cc\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: b9fbec5ac6b2\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: b502c227b5e6\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_idxstats\n  owner: devteam\n  revisions: 811fc2d75ad4\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_idxstats\n  owner: devteam\n  revisions: 7def34e6cf4d\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_column_join\n  owner: iuc\n  revisions: 3ddd99c7efee\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: featurecounts\n  owner: iuc\n  revisions: 1759d845181e\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: featurecounts\n  owner: iuc\n  revisions: 38b6d12edc68\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: hisat2\n  owner: iuc\n  revisions: 61ee47027bd3\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: hisat2\n  owner: iuc\n  revisions: 6c19daec423d\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 9a913cdee30e\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 1c2db0054039\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: b2f1f75d49c4\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 660cffd8d92a\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: c5e2e5902201\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: dbedfc5f5a3c\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: dbedfc5f5a3c\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: dbedfc5f5a3c\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.json",
         "contributors": [
             {
                 "id": "mblue9",
@@ -262706,59 +269254,115 @@
                 "name": "Belinda Phipson",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bphipson/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/bphipson.json"
+            },
+            {
+                "id": "hdashnow",
+                "joined": "2018-09",
+                "name": "Harriet Dashnow",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hdashnow/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hdashnow.json"
             }
         ],
-        "dir": "topics/transcriptomics/tutorials/rna-seq-genes-to-pathways",
+        "dir": "topics/transcriptomics/tutorials/rna-seq-reads-to-counts",
         "edam_operation": [
-            "Gene-set enrichment analysis",
-            "Gene functional annotation",
-            "Gene set testing"
+            "Data handling",
+            "Sequence alignment",
+            "Sequence trimming",
+            "Sequencing quality control",
+            "Read summarisation",
+            "Statistical calculation",
+            "RNA-Seq quantification",
+            "Validation",
+            "Sequence composition calculation",
+            "Read pre-processing",
+            "Primer removal",
+            "Formatting"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "transcriptomics",
+                "tutorials": [
+                    "rna-seq-counts-to-genes"
+                ],
+                "type": "internal"
+            }
+        ],
         "hands_on": true,
-        "id": "transcriptomics/rna-seq-genes-to-pathways",
+        "id": "transcriptomics/rna-seq-reads-to-counts",
         "inexact_supported_servers": [
-            "UseGalaxy.cz"
+            "MISSISSIPPI",
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "goseq can be used to identify enriched gene ontology categories and incorporate gene length bias",
-            "fgsea can be used to identify enriched gene sets, such as the MSigDB collections, and generate barcode plots",
-            "EGSEA can be used to identify enriched gene sets, such as MSigDB and KEGG, generating visualisations that include heatmaps and KEGG pathway diagrams",
-            "Multiple methods can be used to help identify differentially expressed pathways and to visualise results"
+            "In RNA-seq, reads (FASTQs) are mapped to a reference genome with a spliced aligner (e.g HISAT2, STAR)",
+            "The aligned reads (BAMs) can then be converted to counts",
+            "Many QC steps can be performed to help check the quality of the data",
+            "MultiQC can be used to create a nice summary report of QC information",
+            "The Galaxy Rule-based Uploader, Collections and Workflows can help make analysis more efficient and easier"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-08-09",
         "objectives": [
-            "Identification of differentially expressed pathways"
+            "Learn how RNA-seq reads are converted into counts",
+            "Understand QC steps that can be performed on RNA-seq reads",
+            "Generate interactive reports to summarise QC information with MultiQC",
+            "Use the Galaxy Rule-based Uploader to import FASTQs from URLs",
+            "Make use of Galaxy Collections for a tidy analysis",
+            "Create a Galaxy Workflow that converts RNA-seq reads into counts"
         ],
-        "pageviews": 36629,
-        "pub_date": "2018-12-31",
+        "pageviews": 126626,
+        "pub_date": "2018-09-23",
         "questions": [
-            "What are the differentially expressed pathways in the mammary gland of pregnant versus lactating mice?"
+            "How to convert RNA-seq reads into counts?",
+            "How to perform quality control (QC) of RNA-seq reads?",
+            "How to do this analysis efficiently in Galaxy?"
         ],
-        "short_id": "T00300",
+        "requirements": [
+            {
+                "topic_name": "transcriptomics",
+                "tutorials": [
+                    "ref-based"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "collections",
+                    "upload-rules"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00301",
         "short_tools": [
-            "fgsea",
-            "egsea",
-            "tp_cut_tool",
-            "Cut1",
-            "tp_sort_header_tool",
-            "Add_a_column1",
-            "join1",
-            "goseq"
+            "hisat2",
+            "picard_MarkDuplicates",
+            "rseqc_geneBody_coverage",
+            "cutadapt",
+            "samtools_idxstats",
+            "multiqc",
+            "collection_column_join",
+            "rseqc_infer_experiment",
+            "rseqc_read_distribution",
+            "fastqc",
+            "featurecounts"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -262769,6 +269373,28 @@
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.no",
@@ -262785,30 +269411,36 @@
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
                 }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                }
             ]
         },
         "symlink": null,
         "tags": [
-            "mouse"
+            "collections",
+            "mouse",
+            "QC"
         ],
-        "time_estimation": "2h",
-        "title": "3: RNA-seq genes to pathways",
-        "tools": [
-            "Cut1",
-            "join1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
-            "toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.44.0+galaxy0"
+        "time_estimation": "3h",
+        "title": "1: RNA-Seq reads to counts",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4",
+            "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3",
+            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.7+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3",
+            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1",
+            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1"
         ],
         "topic_name": "transcriptomics",
         "topic_name_human": "Transcriptomics",
@@ -262818,65 +269450,58 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "rna-seq-genes-to-pathways",
+        "tutorial_name": "rna-seq-reads-to-counts",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.json"
         },
-        "version": 13,
+        "version": 33,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 112,
-        "visitors": 21972,
+        "visit_duration": 149,
+        "visitors": 66867,
         "workflows": [
             {
                 "creators": [],
-                "description": "RNA-seq genes to pathways",
+                "description": "rna-seq-reads-to-counts",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nseqdata\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nfactordata\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nDE table\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmouse_hallmark_sets\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nlimma_filtered_counts\"]\n  5[label=\"Compute\"]\n  2 -> 5 [label=\"output\"]\n  6[label=\"Cut\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"Advanced Cut\"]\n  4 -> 7 [label=\"output\"]\n  8[label=\"Advanced Cut\"]\n  4 -> 8 [label=\"output\"]\n  9[label=\"Join two Datasets\"]\n  5 -> 9 [label=\"out_file1\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"Sort\"]\n  6 -> 10 [label=\"out_file1\"]\n  11[label=\"EGSEA\"]\n  8 -> 11 [label=\"output\"]\n  7 -> 11 [label=\"output\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"Cut\"]\n  9 -> 12 [label=\"out_file1\"]\n  13[label=\"Cut\"]\n  9 -> 13 [label=\"out_file1\"]\n  14[label=\"fgsea\"]\n  10 -> 14 [label=\"outfile\"]\n  3 -> 14 [label=\"output\"]\n  15[label=\"goseq\"]\n  12 -> 15 [label=\"out_file1\"]\n  13 -> 15 [label=\"out_file1\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genes\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nBAM files\"]\n  2[label=\"Infer Experiment\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"MarkDuplicates\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Samtools idxstats\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"MultiQC\"]\n  2 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"metrics_file\"]\n  4 -> 5 [label=\"output\"]\n}",
                 "history": [
                     {
-                        "hash": "d4c89b2dd1df9f664b50c12830c206c195ded1ba",
-                        "message": "Update workflow (#3198)",
-                        "num": 5,
-                        "short_hash": "d4c89b2dd",
-                        "unix": "1645817433"
-                    },
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
+                        "hash": "e309846054da31a5946eaf34c1bf8b02771b054c",
+                        "message": "Update qc workflow",
                         "num": 4,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
+                        "short_hash": "e30984605",
+                        "unix": "1605438895"
                     },
                     {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
+                        "hash": "bf6f08b6a5db96726fa60f5b6cee040a4e40e51d",
+                        "message": "Fix tags attribute",
                         "num": 3,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
+                        "short_hash": "bf6f08b6a",
+                        "unix": "1605332237"
                     },
                     {
-                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
-                        "message": "Changed format of workflows",
+                        "hash": "d42f753afbda69d81cf63335037ef57ffe2487af",
+                        "message": "Fix workflow for failing travis test",
                         "num": 2,
-                        "short_hash": "361236c41",
-                        "unix": "1554368414"
+                        "short_hash": "d42f753af",
+                        "unix": "1605316521"
                     },
                     {
-                        "hash": "0ea8c79012ba1b18d3f79be0ff2e2b826092f5e2",
-                        "message": "Rename tutorial and image folders to the updated titles",
+                        "hash": "cea2aaab2718b8d92d77b9d0f84bdc8d325a46fc",
+                        "message": "Reconfiguration of some content",
                         "num": 1,
-                        "short_hash": "0ea8c7901",
-                        "unix": "1546155649"
+                        "short_hash": "cea2aaab2",
+                        "unix": "1605176495"
                     }
                 ],
                 "inputs": [
@@ -262889,778 +269514,381 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "seqdata"
+                                "name": "Reference genes"
                             }
                         ],
-                        "label": "seqdata",
+                        "label": "Reference genes",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 376.9375,
-                            "height": 61.78125,
-                            "left": 164.984375,
-                            "right": 364.984375,
-                            "top": 315.15625,
+                            "bottom": 272.4609375,
+                            "height": 80.95703125,
+                            "left": 658.4765625,
+                            "right": 858.4765625,
+                            "top": 191.50390625,
                             "width": 200,
-                            "x": 164.984375,
-                            "y": 315.15625
+                            "x": 658.4765625,
+                            "y": 191.50390625
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "530892fe-96db-4ac9-86da-57adf9dc569d",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "uuid": "cb0135e4-38e7-4c4d-9ce8-16edc02f6af9",
+                        "workflow_outputs": [
                             {
-                                "description": "",
-                                "name": "factordata"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "6268565d-6ad3-42ee-b55f-2184412e7468"
                             }
-                        ],
-                        "label": "factordata",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 466.96875,
-                            "height": 61.78125,
-                            "left": 164.984375,
-                            "right": 364.984375,
-                            "top": 405.1875,
-                            "width": 200,
-                            "x": 164.984375,
-                            "y": 405.1875
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "a7dfbd15-e384-4bbb-a30f-a8ff03b07784",
-                        "workflow_outputs": []
+                        ]
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "DE table"
+                                "name": "BAM files"
                             }
                         ],
-                        "label": "DE table",
+                        "label": "BAM files",
                         "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "bottom": 556.984375,
-                            "height": 61.78125,
-                            "left": 164.984375,
-                            "right": 364.984375,
-                            "top": 495.203125,
+                            "bottom": 490.44921875,
+                            "height": 60.95703125,
+                            "left": 658.4765625,
+                            "right": 858.4765625,
+                            "top": 429.4921875,
                             "width": 200,
-                            "x": 164.984375,
-                            "y": 495.203125
+                            "x": 658.4765625,
+                            "y": 429.4921875
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
                         "tool_version": null,
                         "type": "data_collection_input",
-                        "uuid": "e3e247b3-de91-4ae4-af20-41fe85400e05",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
+                        "uuid": "034877ee-f1be-43d8-a5cf-b0a973dc50a4",
+                        "workflow_outputs": [
                             {
-                                "description": "",
-                                "name": "mouse_hallmark_sets"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "2a973089-9bcd-49e0-8a37-e1ef0bdad4fd"
                             }
-                        ],
-                        "label": "mouse_hallmark_sets",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "bottom": 667.421875,
-                            "height": 82.171875,
-                            "left": 164.984375,
-                            "right": 364.984375,
-                            "top": 585.25,
-                            "width": 200,
-                            "x": 164.984375,
-                            "y": 585.25
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "651a815a-cadf-4bdf-8d6e-d08379ed4684",
-                        "workflow_outputs": []
-                    },
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nReference genes\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nBAM files\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Infer Experiment\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"MarkDuplicates\"];\n  1 -->|output| 3;\n  4[\"Samtools idxstats\"];\n  1 -->|output| 4;\n  5[\"MultiQC\"];\n  2 -->|output| 5;\n  3 -->|metrics_file| 5;\n  4 -->|output| 5;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "QC report",
+                "outputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 4,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "limma_filtered_counts"
+                                "name": "Reference genes"
                             }
                         ],
-                        "label": "limma_filtered_counts",
+                        "label": "Reference genes",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 796.453125,
-                            "height": 82.171875,
-                            "left": 164.984375,
-                            "right": 364.984375,
-                            "top": 714.28125,
+                            "bottom": 272.4609375,
+                            "height": 80.95703125,
+                            "left": 658.4765625,
+                            "right": 858.4765625,
+                            "top": 191.50390625,
                             "width": 200,
-                            "x": 164.984375,
-                            "y": 714.28125
+                            "x": 658.4765625,
+                            "y": 191.50390625
                         },
                         "tool_id": null,
                         "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "9347a180-d878-4afe-95cb-9b6cfd383448",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nseqdata\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nfactordata\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nDE table\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nmouse_hallmark_sets\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nlimma_filtered_counts\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Compute\"];\n  2 -->|output| 5;\n  6[\"Cut\"];\n  2 -->|output| 6;\n  7[\"Advanced Cut\"];\n  4 -->|output| 7;\n  8[\"Advanced Cut\"];\n  4 -->|output| 8;\n  9[\"Join two Datasets\"];\n  5 -->|out_file1| 9;\n  0 -->|output| 9;\n  10[\"Sort\"];\n  6 -->|out_file1| 10;\n  11[\"EGSEA\"];\n  8 -->|output| 11;\n  7 -->|output| 11;\n  1 -->|output| 11;\n  12[\"Cut\"];\n  9 -->|out_file1| 12;\n  13[\"Cut\"];\n  9 -->|out_file1| 13;\n  14[\"fgsea\"];\n  10 -->|outfile| 14;\n  3 -->|output| 14;\n  15[\"goseq\"];\n  12 -->|out_file1| 15;\n  13 -->|out_file1| 15;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "RNA Seq Genes To Pathways (imported from uploaded file)",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "input": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Compute",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 408.328125,
-                            "height": 93.171875,
-                            "left": 477.015625,
-                            "right": 677.015625,
-                            "top": 315.15625,
-                            "width": 200,
-                            "x": 477.015625,
-                            "y": 315.15625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
-                        "tool_shed_repository": {
-                            "changeset_revision": "02026300aa45",
-                            "name": "column_maker",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"avoid_scientific_notation\": \"false\", \"cond\": \"bool(c8<0.01) and bool(abs(c4)>0.58)\", \"header_lines_conditional\": {\"header_lines_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"round\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.6",
-                        "type": "tool",
-                        "uuid": "20efeeff-6096-48d2-9f1f-e3e776112b13",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "52fae575-f107-4657-aec1-1f2b3d71ac95"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "Cut1",
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "input": {
-                                "id": 2,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Cut",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 534.359375,
-                            "height": 93.171875,
-                            "left": 477.015625,
-                            "right": 677.015625,
-                            "top": 441.1875,
-                            "width": 200,
-                            "x": 477.015625,
-                            "y": 441.1875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm10.len\", \"columnList\": \"c1,c6\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input|__identifier__\": \"limma-voom_luminalpregnant-luminallactate\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2",
-                        "type": "tool",
-                        "uuid": "a301610d-4e49-4dd6-b603-482674c9ec7f",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "b9d13636-4ef9-45a6-9563-b91005fa9d57"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "input": {
-                                "id": 4,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Advanced Cut",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 680.765625,
-                            "height": 113.5625,
-                            "left": 477.015625,
-                            "right": 677.015625,
-                            "top": 567.203125,
-                            "width": 200,
-                            "x": 477.015625,
-                            "y": 567.203125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"complement\": \"--complement\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"list\": \"2,3\"}, \"delimiter\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.0",
-                        "type": "tool",
-                        "uuid": "74f84dac-988e-436e-80cf-e45720a1ca6d",
+                        "uuid": "cb0135e4-38e7-4c4d-9ce8-16edc02f6af9",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "8cf43669-dd17-42be-bd0d-f1a8ca299db6"
+                                "uuid": "6268565d-6ad3-42ee-b55f-2184412e7468"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "input": {
-                                "id": 4,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Advanced Cut",
-                        "outputs": [
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "description": "",
+                                "name": "BAM files"
                             }
                         ],
+                        "label": "BAM files",
+                        "name": "Input dataset collection",
+                        "outputs": [],
                         "position": {
-                            "bottom": 800.8125,
-                            "height": 113.5625,
-                            "left": 477.015625,
-                            "right": 677.015625,
-                            "top": 687.25,
+                            "bottom": 490.44921875,
+                            "height": 60.95703125,
+                            "left": 658.4765625,
+                            "right": 858.4765625,
+                            "top": 429.4921875,
                             "width": 200,
-                            "x": 477.015625,
-                            "y": 687.25
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "x": 658.4765625,
+                            "y": 429.4921875
                         },
-                        "tool_state": "{\"complement\": \"\", \"cut_type_options\": {\"cut_element\": \"-f\", \"__current_case__\": 0, \"list\": \"1,2\"}, \"delimiter\": \"\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.0",
-                        "type": "tool",
-                        "uuid": "e5c8206a-72d0-4faa-a19e-8d7ac0190316",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "034877ee-f1be-43d8-a5cf-b0a973dc50a4",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "3ce059c1-68f7-49c1-a1fd-fd7d6e1c0bc8"
+                                "uuid": "2a973089-9bcd-49e0-8a37-e1ef0bdad4fd"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "join1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
                         "errors": null,
-                        "id": 9,
+                        "id": 5,
                         "input_connections": {
-                            "input1": {
-                                "id": 5,
-                                "output_name": "out_file1"
+                            "results_0|software_cond|output_0|type|input": {
+                                "id": 2,
+                                "output_name": "output"
                             },
-                            "input2": {
-                                "id": 0,
+                            "results_1|software_cond|output_0|input": {
+                                "id": 3,
+                                "output_name": "metrics_file"
+                            },
+                            "results_2|software_cond|output_0|type|input": {
+                                "id": 4,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Join two Datasets",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 459.109375,
-                            "height": 143.953125,
-                            "left": 734.046875,
-                            "right": 934.046875,
-                            "top": 315.15625,
-                            "width": 200,
-                            "x": 734.046875,
-                            "y": 315.15625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "join1",
-                        "tool_state": "{\"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm10.len\", \"field1\": \"1\", \"field2\": \"1\", \"fill_empty_columns\": {\"fill_empty_columns_switch\": \"no_fill\", \"__current_case__\": 0}, \"header\": \"\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"input1|__identifier__\": \"limma-voom_luminalpregnant-luminallactate\", \"input2\": {\"__class__\": \"ConnectedValue\"}, \"partial\": \"\", \"unmatched\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.3",
-                        "type": "tool",
-                        "uuid": "2f81fad6-b41c-4c4b-b803-51a5ccd1c047",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "49d52f1a-b5ce-4cde-a141-eb684154f8ad"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-                        "errors": null,
-                        "id": 10,
-                        "input_connections": {
-                            "infile": {
-                                "id": 6,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Sort",
+                        "name": "MultiQC",
                         "outputs": [
                             {
-                                "name": "outfile",
+                                "name": "stats",
                                 "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 562.359375,
-                            "height": 93.171875,
-                            "left": 734.046875,
-                            "right": 934.046875,
-                            "top": 469.1875,
-                            "width": 200,
-                            "x": 734.046875,
-                            "y": 469.1875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm10.len\", \"header\": \"1\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"infile|__identifier__\": \"limma-voom_luminalpregnant-luminallactate\", \"sortkeys\": [{\"__index__\": 0, \"column\": \"2\", \"order\": \"r\", \"style\": \"n\"}], \"unique\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
-                        "type": "tool",
-                        "uuid": "ce9e6449-48c9-4857-b20a-e82f0a554685",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "304a128c-3da0-4a25-bd5b-52da23d9f850"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0",
-                        "errors": null,
-                        "id": 11,
-                        "input_connections": {
-                            "genes": {
-                                "id": 8,
-                                "output_name": "output"
-                            },
-                            "input|counts": {
-                                "id": 7,
-                                "output_name": "output"
                             },
-                            "input|fact|finfo": {
-                                "id": 1,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "EGSEA",
-                        "outputs": [
                             {
-                                "name": "outTables",
+                                "name": "plots",
                                 "type": "input"
                             },
                             {
-                                "name": "outReport",
+                                "name": "html_report",
                                 "type": "html"
                             }
                         ],
                         "position": {
-                            "bottom": 820.34375,
-                            "height": 225.125,
-                            "left": 734.046875,
-                            "right": 934.046875,
-                            "top": 595.21875,
+                            "bottom": 790.44921875,
+                            "height": 391.953125,
+                            "left": 1234.4921875,
+                            "right": 1434.4921875,
+                            "top": 398.49609375,
                             "width": 200,
-                            "x": 734.046875,
-                            "y": 595.21875
+                            "x": 1234.4921875,
+                            "y": 398.49609375
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0",
+                        "post_job_actions": {
+                            "HideDatasetActionplots": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "plots"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
                         "tool_shed_repository": {
-                            "changeset_revision": "fba1660fb717",
-                            "name": "egsea",
+                            "changeset_revision": "5e33b465d8d5",
+                            "name": "multiqc",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"advanced\": {\"display_top\": \"5\", \"min_size\": \"2\", \"fdr_cutoff\": \"0.05\", \"combine_method\": \"wilkinson\", \"sort_method\": \"med.rank\", \"rscriptOpt\": \"false\", \"rdaOpt\": \"false\"}, \"base_methods\": [\"camera\", \"safe\", \"gage\", \"zscore\", \"gsva\", \"globaltest\", \"ora\", \"ssgsea\", \"padog\", \"plage\", \"fry\"], \"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm10.len\", \"genes\": {\"__class__\": \"ConnectedValue\"}, \"gsdb\": {\"gsdb_gsets\": null}, \"input\": {\"format\": \"matrix\", \"__current_case__\": 1, \"counts\": {\"__class__\": \"ConnectedValue\"}, \"fact\": {\"ffile\": \"yes\", \"__current_case__\": 0, \"finfo\": {\"__class__\": \"ConnectedValue\"}}}, \"keggdb\": {\"keggdb_gsets\": [\"keggmet\", \"keggsig\"], \"kegg_updated\": \"false\"}, \"msigdb\": {\"msigdb_gsets\": [\"h\"]}, \"non_commercial_use\": \"true\", \"rep_contrast\": [{\"__index__\": 0, \"contrast\": \"basalpregnant-basallactate\"}, {\"__index__\": 1, \"contrast\": \"luminalpregnant-luminallactate\"}], \"species\": \"mouse\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.20.0",
+                        "tool_state": "{\"comment\": \"\", \"flat\": \"false\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"rseqc\", \"__current_case__\": 21, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"infer_experiment\", \"__current_case__\": 2, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"RuntimeValue\"}}]}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 23, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"idxstats\", \"__current_case__\": 2, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8+galaxy1",
                         "type": "tool",
-                        "uuid": "e9df8569-f438-4144-9f3a-ebb569ec2047",
+                        "uuid": "101e4661-c986-4bde-90c1-835d15c35898",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "outTables",
-                                "uuid": "778284eb-56d6-4079-badb-951d5714c8f8"
+                                "output_name": "stats",
+                                "uuid": "3fcde9be-0512-43a3-ac61-c34102116b38"
                             },
                             {
                                 "label": null,
-                                "output_name": "outReport",
-                                "uuid": "86db0251-4d15-45b7-b471-2af7def64d39"
+                                "output_name": "html_report",
+                                "uuid": "dd4f76fb-bf9c-4825-ba7b-8d6b06a648d9"
                             }
                         ]
+                    }
+                ],
+                "parent_id": "transcriptomics/rna-seq-reads-to-counts",
+                "path": "topics/transcriptomics/tutorials/rna-seq-reads-to-counts/workflows/qc_report.ga",
+                "tags": [
+                    "transcriptomics"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "QC report",
+                "topic_id": "transcriptomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-rna-seq-reads-to-counts/versions/qc-report",
+                "tutorial_id": "rna-seq-reads-to-counts",
+                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/workflows/qc_report.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/workflows/qc_report.html",
+                "version": 2,
+                "wfid": "transcriptomics-rna-seq-reads-to-counts",
+                "wfname": "qc-report",
+                "workflow": "qc_report.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1"
+                ],
+                "workflowhub_id": "1299"
+            },
+            {
+                "creators": [],
+                "description": "RNA-Seq reads to counts",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput FASTQs collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput Reference gene BED\"]\n  10[label=\"Infer Experiment\"]\n  5 -> 10 [label=\"output_alignments\"]\n  1 -> 10 [label=\"output\"]\n  11[label=\"Read Distribution\"]\n  5 -> 11 [label=\"output_alignments\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"Column Join\"]\n  6 -> 12 [label=\"output_short\"]\n  13[label=\"MultiQC\"]\n  4 -> 13 [label=\"text_file\"]\n  3 -> 13 [label=\"report\"]\n  10 -> 13 [label=\"output\"]\n  7 -> 13 [label=\"metrics_file\"]\n  8 -> 13 [label=\"output\"]\n  9 -> 13 [label=\"outputtxt\"]\n  11 -> 13 [label=\"output\"]\n  6 -> 13 [label=\"output_summary\"]\n  5 -> 13 [label=\"summary_file\"]\n  2[label=\"FastQC raw reads\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Cutadapt\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"FastQC post QC\"]\n  3 -> 4 [label=\"out1\"]\n  5[label=\"HISAT2\"]\n  3 -> 5 [label=\"out1\"]\n  6[label=\"featureCounts\"]\n  5 -> 6 [label=\"output_alignments\"]\n  7[label=\"MarkDuplicates\"]\n  5 -> 7 [label=\"output_alignments\"]\n  8[label=\"Samtools idxstats\"]\n  5 -> 8 [label=\"output_alignments\"]\n  9[label=\"Gene Body Coverage BAM\"]\n  5 -> 9 [label=\"output_alignments\"]\n  1 -> 9 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 4,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
                     },
                     {
-                        "annotation": "",
-                        "content_id": "Cut1",
-                        "errors": null,
-                        "id": 12,
-                        "input_connections": {
-                            "input": {
-                                "id": 9,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Cut",
-                                "name": "input"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Cut",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 408.328125,
-                            "height": 93.171875,
-                            "left": 1003.09375,
-                            "right": 1203.09375,
-                            "top": 315.15625,
-                            "width": 200,
-                            "x": 1003.09375,
-                            "y": 315.15625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"columnList\": \"c1,c10\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2",
-                        "type": "tool",
-                        "uuid": "af9206ae-98cc-4432-a81e-ee39bb2c2a8a",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "fd382af4-5a99-4264-af9a-f8fdc6c134b7"
-                            }
-                        ]
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 3,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
                     },
                     {
-                        "annotation": "",
-                        "content_id": "Cut1",
-                        "errors": null,
-                        "id": 13,
-                        "input_connections": {
-                            "input": {
-                                "id": 9,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Cut",
-                                "name": "input"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Cut",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "bottom": 534.359375,
-                            "height": 93.171875,
-                            "left": 1003.09375,
-                            "right": 1203.09375,
-                            "top": 441.1875,
-                            "width": 200,
-                            "x": 1003.09375,
-                            "y": 441.1875
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "Cut1",
-                        "tool_state": "{\"columnList\": \"c1,c12\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.2",
-                        "type": "tool",
-                        "uuid": "4a72bc30-2d4e-4480-875b-507b2a7274b4",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "655e9412-ca8c-4b0f-9dcc-fa8da9126e90"
-                            }
-                        ]
+                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
+                        "message": "Changed format of workflows",
+                        "num": 2,
+                        "short_hash": "361236c41",
+                        "unix": "1554368414"
                     },
+                    {
+                        "hash": "0ea8c79012ba1b18d3f79be0ff2e2b826092f5e2",
+                        "message": "Rename tutorial and image folders to the updated titles",
+                        "num": 1,
+                        "short_hash": "0ea8c7901",
+                        "unix": "1546155649"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 14,
-                        "input_connections": {
-                            "rnk_file": {
-                                "id": 10,
-                                "output_name": "outfile"
-                            },
-                            "sets_file": {
-                                "id": 3,
-                                "output_name": "output"
-                            }
-                        },
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [],
-                        "label": null,
-                        "name": "fgsea",
-                        "outputs": [
-                            {
-                                "name": "out_tab",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "out_pdf",
-                                "type": "pdf"
-                            }
-                        ],
+                        "label": "Input FASTQs collection",
+                        "name": "Input dataset collection",
+                        "outputs": [],
                         "position": {
-                            "bottom": 782.328125,
-                            "height": 215.125,
-                            "left": 1003.09375,
-                            "right": 1203.09375,
-                            "top": 567.203125,
-                            "width": 200,
-                            "x": 1003.09375,
-                            "y": 567.203125
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "17eb1e0d711f",
-                            "name": "fgsea",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 199.9921875,
+                            "top": 199.9921875
                         },
-                        "tool_state": "{\"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm10.len\", \"header\": \"true\", \"max_size\": \"500\", \"min_size\": \"15\", \"n_perm\": \"1000\", \"plot_opt\": \"true\", \"rda_opt\": \"false\", \"rnk_file\": {\"__class__\": \"ConnectedValue\"}, \"rnk_file|__identifier__\": \"limma-voom_luminalpregnant-luminallactate\", \"sets_file\": {\"__class__\": \"ConnectedValue\"}, \"top_num\": \"10\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8.0+galaxy1",
-                        "type": "tool",
-                        "uuid": "8e1c5077-edf1-4dcf-9a07-3b521c49a76f",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "out_pdf",
-                                "uuid": "d8219c05-bd0a-43e5-8f5c-f4bb77a22863"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "out_tab",
-                                "uuid": "8b684bd0-a210-42e8-8c32-16a143e20086"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{\"collection_type\": \"list\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "015f389e-94eb-40f2-82c8-267093ca8c8a",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.44.0+galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 15,
-                        "input_connections": {
-                            "dge_file": {
-                                "id": 12,
-                                "output_name": "out_file1"
-                            },
-                            "length_file": {
-                                "id": 13,
-                                "output_name": "out_file1"
-                            }
-                        },
+                        "id": 1,
+                        "input_connections": {},
                         "inputs": [],
-                        "label": null,
-                        "name": "goseq",
-                        "outputs": [
-                            {
-                                "name": "wallenius_tab",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "top_plot",
-                                "type": "pdf"
-                            }
-                        ],
+                        "label": "Input Reference gene BED",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "bottom": 611.84375,
-                            "height": 296.6875,
-                            "left": 1258.109375,
-                            "right": 1458.109375,
-                            "top": 315.15625,
-                            "width": 200,
-                            "x": 1258.109375,
-                            "y": 315.15625
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.44.0+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ef2ad746b589",
-                            "name": "goseq",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 199.9921875,
+                            "top": 290.015625
                         },
-                        "tool_state": "{\"adv\": {\"p_adj_method\": \"BH\", \"use_genes_without_cat\": \"false\"}, \"categorySource\": {\"catSource\": \"getgo\", \"__current_case__\": 0, \"genome\": \"mm10\", \"gene_id\": \"knownGene\", \"fetchcats\": [\"GO:BP\"]}, \"chromInfo\": \"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm10.len\", \"dge_file\": {\"__class__\": \"ConnectedValue\"}, \"dge_file|__identifier__\": \"limma-voom_luminalpregnant-luminallactate\", \"length_file\": {\"__class__\": \"ConnectedValue\"}, \"length_file|__identifier__\": \"limma-voom_luminalpregnant-luminallactate\", \"methods\": {\"wallenius\": \"true\", \"hypergeometric\": \"false\", \"repcnt\": \"0\"}, \"out\": {\"topgo_plot\": \"true\", \"make_plots\": \"false\", \"cat_genes\": \"false\", \"rdata_out\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.44.0+galaxy0",
-                        "type": "tool",
-                        "uuid": "cddd834a-87f6-470a-b4cd-3c7af7f75e50",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "top_plot",
-                                "uuid": "6aacfcb1-f009-4fc9-8607-b3725488fb1d"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "wallenius_tab",
-                                "uuid": "a473f119-2db7-451f-8ad5-3700df2ae19b"
-                            }
-                        ]
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "dc707df4-3c9d-4d76-98a8-53b60cc2f41d",
+                        "workflow_outputs": []
                     }
                 ],
-                "parent_id": "transcriptomics/rna-seq-genes-to-pathways",
-                "path": "topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/workflows/rna-seq-genes-to-pathways.ga",
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput FASTQs collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput Reference gene BED\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Infer Experiment\"];\n  5 -->|output_alignments| 10;\n  1 -->|output| 10;\n  11[\"Read Distribution\"];\n  5 -->|output_alignments| 11;\n  1 -->|output| 11;\n  12[\"Column Join\"];\n  6 -->|output_short| 12;\n  13[\"MultiQC\"];\n  4 -->|text_file| 13;\n  3 -->|report| 13;\n  10 -->|output| 13;\n  7 -->|metrics_file| 13;\n  8 -->|output| 13;\n  9 -->|outputtxt| 13;\n  11 -->|output| 13;\n  6 -->|output_summary| 13;\n  5 -->|summary_file| 13;\n  2[\"FastQC raw reads\"];\n  0 -->|output| 2;\n  3[\"Cutadapt\"];\n  0 -->|output| 3;\n  4[\"FastQC post QC\"];\n  3 -->|out1| 4;\n  5[\"HISAT2\"];\n  3 -->|out1| 5;\n  6[\"featureCounts\"];\n  5 -->|output_alignments| 6;\n  7[\"MarkDuplicates\"];\n  5 -->|output_alignments| 7;\n  8[\"Samtools idxstats\"];\n  5 -->|output_alignments| 8;\n  9[\"Gene Body Coverage BAM\"];\n  5 -->|output_alignments| 9;\n  1 -->|output| 9;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "RNA Seq Reads To Counts",
+                "outputs": [],
+                "parent_id": "transcriptomics/rna-seq-reads-to-counts",
+                "path": "topics/transcriptomics/tutorials/rna-seq-reads-to-counts/workflows/rna-seq-reads-to-counts.ga",
                 "tags": [
                     "transcriptomics"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "RNA Seq Genes To Pathways (imported from uploaded file)",
+                "title": "RNA Seq Reads To Counts",
                 "topic_id": "transcriptomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-rna-seq-genes-to-pathways/versions/rna-seq-genes-to-pathways",
-                "tutorial_id": "rna-seq-genes-to-pathways",
-                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/workflows/rna-seq-genes-to-pathways.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-genes-to-pathways/workflows/rna-seq-genes-to-pathways.html",
-                "version": 5,
-                "wfid": "transcriptomics-rna-seq-genes-to-pathways",
-                "wfname": "rna-seq-genes-to-pathways",
-                "workflow": "rna-seq-genes-to-pathways.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-rna-seq-reads-to-counts/versions/rna-seq-reads-to-counts",
+                "tutorial_id": "rna-seq-reads-to-counts",
+                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/workflows/rna-seq-reads-to-counts.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/workflows/rna-seq-reads-to-counts.html",
+                "version": 4,
+                "wfid": "transcriptomics-rna-seq-reads-to-counts",
+                "wfname": "rna-seq-reads-to-counts",
+                "workflow": "rna-seq-reads-to-counts.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "join1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.44.0+galaxy0"
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6",
+                    "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3",
+                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3",
+                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1",
+                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1"
                 ],
-                "workflowhub_id": "1316"
+                "workflowhub_id": "1295"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/2596382"
+        "zenodo_link": "https://zenodo.org/record/4249555"
     },
     {
         "abbreviations": {
@@ -263681,6 +269909,13 @@
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "cpat",
+                    "owner": "bgruening",
+                    "revisions": "7ccc6234b54e",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "pfamscan",
                     "owner": "bgruening",
@@ -263691,35 +269926,56 @@
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "d698c222f354",
+                    "revisions": "86755160afbf",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "d698c222f354",
+                    "revisions": "86755160afbf",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "d698c222f354",
+                    "revisions": "86755160afbf",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "d698c222f354",
+                    "revisions": "86755160afbf",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "add_value",
+                    "owner": "devteam",
+                    "revisions": "023f0a3760b3",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "column_maker",
+                    "owner": "devteam",
+                    "revisions": "6595517c2dd8",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "column_maker",
+                    "owner": "devteam",
+                    "revisions": "aff5135563c6",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "fastqc",
                     "owner": "devteam",
-                    "revisions": "3d0c7bdf12f5",
+                    "revisions": "2c64fded1286",
                     "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
@@ -263731,10 +269987,10 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "tabular_to_fasta",
+                    "name": "gffread",
                     "owner": "devteam",
-                    "revisions": "0a7799698fe5",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "3e436657dcd0",
+                    "tool_panel_section_label": "Convert Formats",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
@@ -263747,7 +270003,7 @@
                 {
                     "name": "fastp",
                     "owner": "iuc",
-                    "revisions": "65b93b623c77",
+                    "revisions": "d60c3f704da0",
                     "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
@@ -263765,13 +270021,6 @@
                     "tool_panel_section_label": "Convert Formats",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
-                {
-                    "name": "hisat2",
-                    "owner": "iuc",
-                    "revisions": "f4af63aaf57a",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
                 {
                     "name": "isoformswitchanalyzer",
                     "owner": "iuc",
@@ -263793,10 +270042,24 @@
                     "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "pygenometracks",
+                    "owner": "iuc",
+                    "revisions": "36b848d5f3ec",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "rgrnastar",
                     "owner": "iuc",
-                    "revisions": "3ea5a2a63fa2",
+                    "revisions": "b0f2be869d6d",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "rgrnastar",
+                    "owner": "iuc",
+                    "revisions": "4014de1b6daf",
                     "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
@@ -263817,97 +270080,62 @@
                 {
                     "name": "stringtie",
                     "owner": "iuc",
-                    "revisions": "ae618321f34a",
+                    "revisions": "cbf488da3b2c",
                     "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "stringtie",
-                    "owner": "iuc",
-                    "revisions": "ae618321f34a",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "rseqc",
-                    "owner": "nilesh",
-                    "revisions": "5968573462fa",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "rseqc",
-                    "owner": "nilesh",
-                    "revisions": "473382134e56",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "rseqc",
-                    "owner": "nilesh",
-                    "revisions": "5968573462fa",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "rseqc",
-                    "owner": "nilesh",
-                    "revisions": "473382134e56",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "rseqc",
-                    "owner": "nilesh",
-                    "revisions": "473382134e56",
+                    "owner": "iuc",
+                    "revisions": "cbf488da3b2c",
                     "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "rseqc",
                     "owner": "nilesh",
-                    "revisions": "5968573462fa",
+                    "revisions": "27e16a30667a",
                     "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "rseqc",
                     "owner": "nilesh",
-                    "revisions": "473382134e56",
+                    "revisions": "27e16a30667a",
                     "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "rseqc",
                     "owner": "nilesh",
-                    "revisions": "5968573462fa",
+                    "revisions": "27e16a30667a",
                     "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "rseqc",
                     "owner": "nilesh",
-                    "revisions": "473382134e56",
+                    "revisions": "27e16a30667a",
                     "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "rseqc",
                     "owner": "nilesh",
-                    "revisions": "5968573462fa",
+                    "revisions": "27e16a30667a",
                     "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "rseqc",
                     "owner": "nilesh",
-                    "revisions": "473382134e56",
+                    "revisions": "27e16a30667a",
                     "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: cpat\n  owner: bgruening\n  revisions: 8e9e228c54c4\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pfamscan\n  owner: bgruening\n  revisions: 15cff34c2005\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gffread\n  owner: devteam\n  revisions: 154d00cbbf2d\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tabular_to_fasta\n  owner: devteam\n  revisions: 0a7799698fe5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_element_identifiers\n  owner: iuc\n  revisions: d3c07d270a50\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gffcompare\n  owner: iuc\n  revisions: f99dd58de04f\n  tool_panel_section_label: Filter and Sort\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gtftobed12\n  owner: iuc\n  revisions: b026dae67fba\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: hisat2\n  owner: iuc\n  revisions: f4af63aaf57a\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: isoformswitchanalyzer\n  owner: iuc\n  revisions: 298d81e5e138\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: abfd8a6544d7\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pygenometracks\n  owner: iuc\n  revisions: 360df4999907\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n  owner: iuc\n  revisions: 3ea5a2a63fa2\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rnaquast\n  owner: iuc\n  revisions: 96f74538896e\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rnaquast\n  owner: iuc\n  revisions: 8e66f695d859\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stringtie\n  owner: iuc\n  revisions: ae618321f34a\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stringtie\n  owner: iuc\n  revisions: ae618321f34a\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 5968573462fa\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 473382134e56\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 5968573462fa\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 473382134e56\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 473382134e56\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 5968573462fa\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 473382134e56\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 5968573462fa\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 473382134e56\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 5968573462fa\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 473382134e56\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: cpat\n  owner: bgruening\n  revisions: 8e9e228c54c4\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cpat\n  owner: bgruening\n  revisions: 7ccc6234b54e\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pfamscan\n  owner: bgruening\n  revisions: 15cff34c2005\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: add_value\n  owner: devteam\n  revisions: 023f0a3760b3\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 6595517c2dd8\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: aff5135563c6\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 2c64fded1286\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gffread\n  owner: devteam\n  revisions: 154d00cbbf2d\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gffread\n  owner: devteam\n  revisions: 3e436657dcd0\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_element_identifiers\n  owner: iuc\n  revisions: d3c07d270a50\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: d60c3f704da0\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gffcompare\n  owner: iuc\n  revisions: f99dd58de04f\n  tool_panel_section_label: Filter and Sort\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gtftobed12\n  owner: iuc\n  revisions: b026dae67fba\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: isoformswitchanalyzer\n  owner: iuc\n  revisions: 298d81e5e138\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: abfd8a6544d7\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pygenometracks\n  owner: iuc\n  revisions: 360df4999907\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pygenometracks\n  owner: iuc\n  revisions: 36b848d5f3ec\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n  owner: iuc\n  revisions: b0f2be869d6d\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n  owner: iuc\n  revisions: 4014de1b6daf\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rnaquast\n  owner: iuc\n  revisions: 96f74538896e\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rnaquast\n  owner: iuc\n  revisions: 8e66f695d859\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stringtie\n  owner: iuc\n  revisions: cbf488da3b2c\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: stringtie\n  owner: iuc\n  revisions: cbf488da3b2c\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 27e16a30667a\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 27e16a30667a\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 27e16a30667a\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 27e16a30667a\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 27e16a30667a\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 27e16a30667a\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
         "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.json",
         "contributions": {
             "authorship": [
@@ -263968,33 +270196,33 @@
         "edam_operation": [
             "Visualisation",
             "Sequencing quality control",
-            "Sequence contamination filtering",
-            "De-novo assembly",
-            "Sequence alignment",
-            "Sequence comparison",
-            "Sequence analysis",
-            "Formatting",
+            "RNA-Seq analysis",
             "Sequence assembly validation",
+            "Statistical calculation",
+            "Validation",
             "Sequence composition calculation",
-            "Transcriptome assembly",
+            "Sequence comparison",
+            "Formatting",
             "Data handling",
+            "Sequence alignment",
+            "De-novo assembly",
+            "Sequence analysis",
+            "Sequence contamination filtering",
             "Sequence annotation",
-            "Validation",
-            "Protein sequence analysis",
-            "RNA-Seq analysis",
-            "Statistical calculation"
+            "Transcriptome assembly",
+            "Protein sequence analysis"
         ],
         "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
         "id": "transcriptomics/differential-isoform-expression",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.fr"
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.org.au"
         ],
         "js_requirements": {
             "mathjax": null,
@@ -264008,12 +270236,12 @@
         "layout": "tutorial_hands_on",
         "level": "Advanced",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-07",
+        "mod_date": "2024-09-27",
         "objectives": [
-            "Perform genome-wide isoform analysis in order to evaluate differences in expression profiles between cancer and healthy tissues",
+            "Perform genome-wide isoform analysis in order to evaluate differences in expression profiles between two conditions",
             "Evaluate the differential alternative splicing in specific genes"
         ],
-        "pageviews": 1628807,
+        "pageviews": 1799801,
         "pub_date": "2023-05-17",
         "questions": [
             "Are there statistically significant differences in gene splicing patterns between samples?",
@@ -264021,63 +270249,66 @@
         ],
         "short_id": "T00345",
         "short_tools": [
-            "gffread",
+            "rna_star",
+            "pygenomeTracks",
+            "gffcompare",
+            "collection_element_identifiers",
+            "rseqc_inner_distance",
+            "cpat",
+            "rna_quast",
+            "rseqc_junction_annotation",
             "tp_awk_tool",
-            "Cut1",
+            "gtftobed12",
+            "fastqc",
+            "rseqc_geneBody_coverage",
+            "tp_cat",
+            "Filter1",
             "isoformswitchanalyzer",
+            "multiqc",
+            "pfamscan",
+            "Cut1",
+            "rseqc_infer_experiment",
+            "gene2exon1",
             "rseqc_read_distribution",
-            "rna_star",
-            "gtftobed12",
+            "tp_uniq_tool",
             "Remove beginning1",
-            "stringtie",
-            "hisat2",
             "rseqc_junction_saturation",
-            "pfamscan",
-            "rseqc_inner_distance",
-            "CONVERTER_fasta_to_tabular",
-            "gffcompare",
-            "tp_sorted_uniq",
-            "pygenomeTracks",
-            "tab2fasta",
             "cat1",
-            "rseqc_infer_experiment",
-            "sort1",
-            "tp_cat",
             "stringtie_merge",
-            "rseqc_geneBody_coverage",
-            "collection_element_identifiers",
-            "rseqc_junction_annotation",
-            "param_value_from_file",
+            "addValue",
             "fastp",
-            "multiqc",
-            "rna_quast",
+            "sort1",
             "tp_grep_tool",
-            "__FILTER_FROM_FILE__",
-            "fastqc",
-            "gene2exon1",
+            "stringtie",
+            "Add_a_column1",
             "__FLATTEN__",
-            "cpat"
+            "gffread",
+            "__FILTER_FROM_FILE__"
         ],
         "slides": true,
         "slides_recordings": false,
         "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ],
+            "exact": [],
             "inexact": [
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.fr",
                     "url": "https://usegalaxy.fr/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ]
         },
@@ -264089,48 +270320,49 @@
         "time_estimation": "3H",
         "title": "Genome-wide alternative splicing analysis",
         "tools": [
-            "CONVERTER_fasta_to_tabular",
             "Cut1",
+            "Filter1",
             "Remove beginning1",
             "__FILTER_FROM_FILE__",
             "__FLATTEN__",
+            "addValue",
             "cat1",
             "gene2exon1",
-            "param_value_from_file",
             "sort1",
             "toolshed.g2.bx.psu.edu/repos/bgruening/cpat/cpat/3.0.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/cpat/cpat/3.0.5+galaxy1",
             "toolshed.g2.bx.psu.edu/repos/bgruening/pfamscan/pfamscan/1.6+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1",
             "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.2.1.4+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1",
             "toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.12.6+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357",
-            "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1",
             "toolshed.g2.bx.psu.edu/repos/iuc/isoformswitchanalyzer/isoformswitchanalyzer/1.20.0+galaxy5",
             "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
             "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1",
             "toolshed.g2.bx.psu.edu/repos/iuc/rnaquast/rna_quast/2.2.1",
             "toolshed.g2.bx.psu.edu/repos/iuc/rnaquast/rna_quast/2.2.3+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/5.0.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/5.0.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/5.0.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/5.0.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/5.0.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/5.0.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/5.0.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.1+galaxy2"
+            "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/5.0.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/5.0.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/5.0.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/5.0.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.3+galaxy0"
         ],
         "topic_name": "transcriptomics",
         "topic_name_human": "Transcriptomics",
@@ -264147,30 +270379,51 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.json"
         },
-        "version": 8,
+        "version": 10,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 271,
-        "visitors": 703404,
+        "visit_duration": 268,
+        "visitors": 772528,
         "workflows": [
             {
                 "creators": [
                     {
                         "class": "Person",
-                        "identifier": "0000-0002-5752-2155",
-                        "name": "Crist\u00f3bal Gallardo Alba"
+                        "identifier": "https://orcid.org/0000-0002-5752-2155",
+                        "name": "Cristobal Gallardo"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0002-1964-4960",
+                        "name": "Lucille Delisle"
                     }
                 ],
-                "description": "Training workflow",
+                "description": "Analyze differential isoform expression",
                 "features": {
-                    "comments": false,
-                    "parameters": true,
-                    "report": null,
+                    "comments": true,
+                    "parameters": false,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                    },
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nRNA-seq data collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genome\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenome annotation\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nControl IDs\"]\n  4[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nFactor 02\"]\n  5[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nFactor 01\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCPAT header\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nActive sites dataset\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPfam-A HMM Stockholm file\"]\n  9[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPfam-A HMM library\"]\n  10[label=\"fastp\"]\n  0 -> 10 [label=\"output\"]\n  11[label=\"Flatten collection\"]\n  0 -> 11 [label=\"output\"]\n  12[label=\"Search in textfiles\"]\n  2 -> 12 [label=\"output\"]\n  13[label=\"Search in textfiles\"]\n  2 -> 13 [label=\"output\"]\n  14[label=\"Convert GTF to BED12\"]\n  2 -> 14 [label=\"output\"]\n  15[label=\"FastQC\"]\n  11 -> 15 [label=\"output\"]\n  16[label=\"gffread\"]\n  12 -> 16 [label=\"output\"]\n  1 -> 16 [label=\"output\"]\n  ke34fd125e86048a29e58bed5c3600b8d[color=lightseagreen,label=\"Output\\nlncRNA sequences\"]\n  16 -> ke34fd125e86048a29e58bed5c3600b8d\n  17[label=\"gffread\"]\n  13 -> 17 [label=\"output\"]\n  1 -> 17 [label=\"output\"]\n  k836eeb38dc6742df93fa2fcd5bbe7a80[color=lightseagreen,label=\"Output\\nprotein coding sequences\"]\n  17 -> k836eeb38dc6742df93fa2fcd5bbe7a80\n  18[label=\"MultiQC\"]\n  15 -> 18 [label=\"text_file\"]\n  10 -> 18 [label=\"report_json\"]\n  19[label=\"Search in textfiles\"]\n  15 -> 19 [label=\"text_file\"]\n  20[label=\"Concatenate datasets\"]\n  19 -> 20 [label=\"output\"]\n  21[label=\"Search in textfiles\"]\n  20 -> 21 [label=\"out_file1\"]\n  22[label=\"Cut\"]\n  21 -> 22 [label=\"output\"]\n  23[label=\"Text reformatting\"]\n  22 -> 23 [label=\"out_file1\"]\n  24[label=\"Parse parameter value\"]\n  23 -> 24 [label=\"outfile\"]\n  25[label=\"RNA STAR\"]\n  2 -> 25 [label=\"output\"]\n  24 -> 25 [label=\"integer_param\"]\n  1 -> 25 [label=\"output\"]\n  10 -> 25 [label=\"output_paired_coll\"]\n  26[label=\"Concatenate datasets\"]\n  25 -> 26 [label=\"splice_junctions\"]\n  27[label=\"Text reformatting\"]\n  26 -> 27 [label=\"out_file1\"]\n  28[label=\"Cut\"]\n  27 -> 28 [label=\"outfile\"]\n  29[label=\"Sort\"]\n  28 -> 29 [label=\"out_file1\"]\n  30[label=\"Unique\"]\n  29 -> 30 [label=\"out_file1\"]\n  31[label=\"RNA STAR\"]\n  2 -> 31 [label=\"output\"]\n  24 -> 31 [label=\"integer_param\"]\n  1 -> 31 [label=\"output\"]\n  10 -> 31 [label=\"output_paired_coll\"]\n  30 -> 31 [label=\"outfile\"]\n  32[label=\"StringTie\"]\n  2 -> 32 [label=\"output\"]\n  31 -> 32 [label=\"mapped_reads\"]\n  33[label=\"Junction Annotation\"]\n  31 -> 33 [label=\"mapped_reads\"]\n  14 -> 33 [label=\"bed_file\"]\n  34[label=\"Junction Saturation\"]\n  31 -> 34 [label=\"mapped_reads\"]\n  14 -> 34 [label=\"bed_file\"]\n  35[label=\"Gene Body Coverage BAM\"]\n  31 -> 35 [label=\"mapped_reads\"]\n  14 -> 35 [label=\"bed_file\"]\n  36[label=\"Inner Distance\"]\n  31 -> 36 [label=\"mapped_reads\"]\n  14 -> 36 [label=\"bed_file\"]\n  37[label=\"Infer Experiment\"]\n  31 -> 37 [label=\"mapped_reads\"]\n  14 -> 37 [label=\"bed_file\"]\n  38[label=\"Read Distribution\"]\n  31 -> 38 [label=\"mapped_reads\"]\n  14 -> 38 [label=\"bed_file\"]\n  39[label=\"gffread\"]\n  32 -> 39 [label=\"output_gtf\"]\n  1 -> 39 [label=\"output\"]\n  40[label=\"StringTie merge\"]\n  2 -> 40 [label=\"output\"]\n  32 -> 40 [label=\"output_gtf\"]\n  41[label=\"MultiQC\"]\n  31 -> 41 [label=\"output_log\"]\n  37 -> 41 [label=\"output\"]\n  38 -> 41 [label=\"output\"]\n  34 -> 41 [label=\"outputr\"]\n  33 -> 41 [label=\"stats\"]\n  35 -> 41 [label=\"outputtxt\"]\n  36 -> 41 [label=\"outputfreqtxt\"]\n  42[label=\"rnaQUAST\"]\n  2 -> 42 [label=\"output\"]\n  1 -> 42 [label=\"output\"]\n  39 -> 42 [label=\"output_exons\"]\n  43[label=\"gffread\"]\n  40 -> 43 [label=\"out_gtf\"]\n  1 -> 43 [label=\"output\"]\n  44[label=\"StringTie\"]\n  40 -> 44 [label=\"out_gtf\"]\n  31 -> 44 [label=\"mapped_reads\"]\n  45[label=\"Filter collection\"]\n  3 -> 45 [label=\"output\"]\n  44 -> 45 [label=\"transcript_expression\"]\n  46[label=\"IsoformSwitchAnalyzeR\"]\n  2 -> 46 [label=\"output\"]\n  24 -> 46 [label=\"integer_param\"]\n  5 -> 46 [label=\"output\"]\n  45 -> 46 [label=\"output_filtered\"]\n  40 -> 46 [label=\"out_gtf\"]\n  4 -> 46 [label=\"output\"]\n  45 -> 46 [label=\"output_discarded\"]\n  43 -> 46 [label=\"output_exons\"]\n  47[label=\"IsoformSwitchAnalyzeR\"]\n  46 -> 47 [label=\"switchList\"]\n  48[label=\"CPAT\"]\n  17 -> 48 [label=\"output_exons\"]\n  47 -> 48 [label=\"isoformNT\"]\n  16 -> 48 [label=\"output_exons\"]\n  1 -> 48 [label=\"output\"]\n  49[label=\"PfamScan\"]\n  7 -> 49 [label=\"output\"]\n  47 -> 49 [label=\"isoformAA\"]\n  8 -> 49 [label=\"output\"]\n  9 -> 49 [label=\"output\"]\n  50[label=\"Remove beginning\"]\n  48 -> 50 [label=\"orf_seqs_prob_best\"]\n  51[label=\"Text reformatting\"]\n  50 -> 51 [label=\"out_file1\"]\n  52[label=\"Concatenate datasets\"]\n  6 -> 52 [label=\"output\"]\n  51 -> 52 [label=\"outfile\"]\n  53[label=\"IsoformSwitchAnalyzeR\"]\n  52 -> 53 [label=\"out_file1\"]\n  49 -> 53 [label=\"output\"]\n  47 -> 53 [label=\"switchList\"]\n  54[label=\"IsoformSwitchAnalyzeR\"]\n  52 -> 54 [label=\"out_file1\"]\n  49 -> 54 [label=\"output\"]\n  47 -> 54 [label=\"switchList\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nRNA-seq data collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenome annotation\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genome\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPfam-A HMM library\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPfam-A HMM Stockholm file\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nActive sites dataset\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nCPAT header\"]\n  7[label=\"Flatten collection\"]\n  0 -> 7 [label=\"output\"]\n  8[label=\"fastp\"]\n  0 -> 8 [label=\"output\"]\n  9[label=\"Convert GTF to BED12\"]\n  1 -> 9 [label=\"output\"]\n  10[label=\"Search in textfiles\"]\n  1 -> 10 [label=\"output\"]\n  11[label=\"Search in textfiles\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"FastQC\"]\n  7 -> 12 [label=\"output\"]\n  13[label=\"gather fastp reports\"]\n  8 -> 13 [label=\"report_json\"]\n  14[label=\"RNA STAR\"]\n  1 -> 14 [label=\"output\"]\n  2 -> 14 [label=\"output\"]\n  8 -> 14 [label=\"output_paired_coll\"]\n  15[label=\"Gene BED To Exon/Intron/Codon BED\"]\n  9 -> 15 [label=\"bed_file\"]\n  16[label=\"gffread\"]\n  10 -> 16 [label=\"output\"]\n  2 -> 16 [label=\"output\"]\n  17[label=\"gffread\"]\n  11 -> 17 [label=\"output\"]\n  2 -> 17 [label=\"output\"]\n  18[label=\"gather FastQC reports\"]\n  12 -> 18 [label=\"text_file\"]\n  19[label=\"Concatenate datasets\"]\n  14 -> 19 [label=\"splice_junctions\"]\n  20[label=\"Compute\"]\n  15 -> 20 [label=\"out_file1\"]\n  21[label=\"Filter\"]\n  19 -> 21 [label=\"out_file1\"]\n  22[label=\"Sort\"]\n  20 -> 22 [label=\"out_file1\"]\n  23[label=\"Cut\"]\n  21 -> 23 [label=\"out_file1\"]\n  24[label=\"Text reformatting\"]\n  22 -> 24 [label=\"out_file1\"]\n  25[label=\"Text reformatting\"]\n  22 -> 25 [label=\"out_file1\"]\n  26[label=\"Sort\"]\n  23 -> 26 [label=\"out_file1\"]\n  27[label=\"Unique lines\"]\n  26 -> 27 [label=\"out_file1\"]\n  28[label=\"RNA STAR\"]\n  1 -> 28 [label=\"output\"]\n  2 -> 28 [label=\"output\"]\n  8 -> 28 [label=\"output_paired_coll\"]\n  27 -> 28 [label=\"outfile\"]\n  29[label=\"StringTie\"]\n  1 -> 29 [label=\"output\"]\n  28 -> 29 [label=\"mapped_reads\"]\n  30[label=\"Infer Experiment\"]\n  28 -> 30 [label=\"mapped_reads\"]\n  9 -> 30 [label=\"bed_file\"]\n  31[label=\"Gene Body Coverage BAM\"]\n  28 -> 31 [label=\"mapped_reads\"]\n  9 -> 31 [label=\"bed_file\"]\n  32[label=\"Junction Saturation\"]\n  28 -> 32 [label=\"mapped_reads\"]\n  9 -> 32 [label=\"bed_file\"]\n  33[label=\"Junction Annotation\"]\n  28 -> 33 [label=\"mapped_reads\"]\n  9 -> 33 [label=\"bed_file\"]\n  34[label=\"Inner Distance\"]\n  28 -> 34 [label=\"mapped_reads\"]\n  9 -> 34 [label=\"bed_file\"]\n  35[label=\"Read Distribution\"]\n  28 -> 35 [label=\"mapped_reads\"]\n  9 -> 35 [label=\"bed_file\"]\n  36[label=\"StringTie merge\"]\n  1 -> 36 [label=\"output\"]\n  29 -> 36 [label=\"output_gtf\"]\n  37[label=\"gffread\"]\n  29 -> 37 [label=\"output_gtf\"]\n  2 -> 37 [label=\"output\"]\n  38[label=\"MultiQC\"]\n  28 -> 38 [label=\"output_log\"]\n  28 -> 38 [label=\"reads_per_gene\"]\n  30 -> 38 [label=\"output\"]\n  32 -> 38 [label=\"outputr\"]\n  31 -> 38 [label=\"outputtxt\"]\n  34 -> 38 [label=\"outputfreqtxt\"]\n  35 -> 38 [label=\"output\"]\n  33 -> 38 [label=\"stats\"]\n  39[label=\"StringTie\"]\n  36 -> 39 [label=\"out_gtf\"]\n  28 -> 39 [label=\"mapped_reads\"]\n  40[label=\"GffCompare\"]\n  1 -> 40 [label=\"output\"]\n  36 -> 40 [label=\"out_gtf\"]\n  41[label=\"Plot a transcript in intron\"]\n  28 -> 41 [label=\"signal_unique_str2\"]\n  28 -> 41 [label=\"signal_unique_str1\"]\n  36 -> 41 [label=\"out_gtf\"]\n  42[label=\"gffread\"]\n  36 -> 42 [label=\"out_gtf\"]\n  2 -> 42 [label=\"output\"]\n  43[label=\"Plot ADD3\"]\n  28 -> 43 [label=\"signal_unique_str2\"]\n  28 -> 43 [label=\"signal_unique_str1\"]\n  36 -> 43 [label=\"out_gtf\"]\n  44[label=\"Plot ADD3 zoomed\"]\n  28 -> 44 [label=\"signal_unique_str2\"]\n  28 -> 44 [label=\"signal_unique_str1\"]\n  36 -> 44 [label=\"out_gtf\"]\n  45[label=\"rnaQUAST\"]\n  1 -> 45 [label=\"output\"]\n  2 -> 45 [label=\"output\"]\n  37 -> 45 [label=\"output_exons\"]\n  46[label=\"Extract element identifiers\"]\n  39 -> 46 [label=\"transcript_expression\"]\n  47[label=\"Filter\"]\n  40 -> 47 [label=\"tmap_output\"]\n  48[label=\"Search in textfiles\"]\n  46 -> 48 [label=\"output\"]\n  49[label=\"Filter collection\"]\n  48 -> 49 [label=\"output\"]\n  39 -> 49 [label=\"transcript_expression\"]\n  50[label=\"IsoformSwitchAnalyzeR\"]\n  1 -> 50 [label=\"output\"]\n  49 -> 50 [label=\"output_discarded\"]\n  36 -> 50 [label=\"out_gtf\"]\n  49 -> 50 [label=\"output_filtered\"]\n  42 -> 50 [label=\"output_exons\"]\n  51[label=\"IsoformSwitchAnalyzeR\"]\n  50 -> 51 [label=\"switchList\"]\n  52[label=\"PfamScan\"]\n  5 -> 52 [label=\"output\"]\n  51 -> 52 [label=\"isoformAA\"]\n  4 -> 52 [label=\"output\"]\n  3 -> 52 [label=\"output\"]\n  53[label=\"CPAT\"]\n  16 -> 53 [label=\"output_exons\"]\n  51 -> 53 [label=\"isoformNT\"]\n  17 -> 53 [label=\"output_exons\"]\n  2 -> 53 [label=\"output\"]\n  54[label=\"Cut\"]\n  53 -> 54 [label=\"orf_seqs_prob_best\"]\n  55[label=\"Add column\"]\n  54 -> 55 [label=\"out_file1\"]\n  56[label=\"Remove beginning\"]\n  55 -> 56 [label=\"out_file1\"]\n  57[label=\"Concatenate datasets\"]\n  6 -> 57 [label=\"output\"]\n  56 -> 57 [label=\"out_file1\"]\n  58[label=\"IsoformSwitchAnalyzeR\"]\n  57 -> 58 [label=\"out_file1\"]\n  52 -> 58 [label=\"output\"]\n  51 -> 58 [label=\"switchList\"]\n  59[label=\"IsoformSwitchAnalyzeR\"]\n  57 -> 59 [label=\"out_file1\"]\n  52 -> 59 [label=\"output\"]\n  51 -> 59 [label=\"switchList\"]\n  kd2f0865b20ba43ef8ebcad9f517ec60d[color=lightseagreen,label=\"Output\\nconsequencesSummary\"]\n  59 -> kd2f0865b20ba43ef8ebcad9f517ec60d\n  k8dd909686ef648e1a104547cbeaa80c8[color=lightseagreen,label=\"Output\\nconsequencesEnrichment\"]\n  59 -> k8dd909686ef648e1a104547cbeaa80c8\n  k6b812e8d997d4a539c4fcb2aa3bb26bc[color=lightseagreen,label=\"Output\\nsplicingEnrichment\"]\n  59 -> k6b812e8d997d4a539c4fcb2aa3bb26bc\n  k9c8369e28f864984a47aa35415ecb9b9[color=lightseagreen,label=\"Output\\nmostSwitching\"]\n  59 -> k9c8369e28f864984a47aa35415ecb9b9\n  k292b9609061f49f794fc7831526bb48b[color=lightseagreen,label=\"Output\\nsplicingSummary\"]\n  59 -> k292b9609061f49f794fc7831526bb48b\n}",
                 "history": [
+                    {
+                        "hash": "21737f95da51da632f55ff695423aec671a3c49e",
+                        "message": "update slides - workflow - tutorial conclusion",
+                        "num": 16,
+                        "short_hash": "21737f95d",
+                        "unix": "1725612196"
+                    },
+                    {
+                        "hash": "a04d2d7a8458312602a5a688b3ce4acaa3a0be71",
+                        "message": "update end of tutorial + results",
+                        "num": 15,
+                        "short_hash": "a04d2d7a8",
+                        "unix": "1725540349"
+                    },
                     {
                         "hash": "e956757639b0d549bc129c0564d8c69914d4cdf4",
                         "message": "Update plots",
@@ -264263,671 +270516,2165 @@
                         "unix": "1683638438"
                     },
                     {
-                        "hash": "a021922f229a004fa6efbacf9fffc60e5736b223",
-                        "message": "Add_files",
+                        "hash": "a021922f229a004fa6efbacf9fffc60e5736b223",
+                        "message": "Add_files",
+                        "num": 1,
+                        "short_hash": "a021922f2",
+                        "unix": "1678376823"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "input fastqs",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "input fastqs",
+                                "name": "RNA-seq data collection"
+                            }
+                        ],
+                        "label": "RNA-seq data collection",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 450.8019651393007
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "c054b2bb-2db5-4cd2-baee-f28981ba61ca",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "gene annotation file",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "gene annotation file",
+                                "name": "Genome annotation"
+                            }
+                        ],
+                        "label": "Genome annotation",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 54.59111061414387,
+                            "top": 555.852577093315
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "c5b581ef-74f5-4609-b9a8-093c42e2650c",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "genome reference fasta file",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "genome reference fasta file",
+                                "name": "Reference genome"
+                            }
+                        ],
+                        "label": "Reference genome",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 78.44792118195437,
+                            "top": 770.009783538481
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0b1f9aae-b6de-487f-b54c-02ebf10d2c41",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "Pfam-A.hmm.gz from EMBL-EBI",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Pfam-A.hmm.gz from EMBL-EBI",
+                                "name": "Pfam-A HMM library"
+                            }
+                        ],
+                        "label": "Pfam-A HMM library",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 133.12557107829184,
+                            "top": 884.2188387929808
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0b4993cc-7bb4-4c9b-a3bd-50ead42ceb5b",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "Pfam-A.hmm.dat.gz from EMBL-EBI",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Pfam-A.hmm.dat.gz from EMBL-EBI",
+                                "name": "Pfam-A HMM Stockholm file"
+                            }
+                        ],
+                        "label": "Pfam-A HMM Stockholm file",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 175.92675244688508,
+                            "top": 1007.3573412539237
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "b839da27-1eff-4ddf-9aae-37548b500b8b",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "active_site.dat.gz from EMBL-EBI",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "active_site.dat.gz from EMBL-EBI",
+                                "name": "Active sites dataset"
+                            }
+                        ],
+                        "label": "Active sites dataset",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 243.74366243379598,
+                            "top": 1115.2799010380445
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "dd58472d-606c-48d0-98b8-b7211e9432f0",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "header",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "header",
+                                "name": "CPAT header"
+                            }
+                        ],
+                        "label": "CPAT header",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 288.25785051802495,
+                            "top": 1232.4319275334062
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "dc68fd90-51b8-4734-95c0-97e402044d0f",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nRNA-seq data collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGenome annotation\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nPfam-A HMM library\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nPfam-A HMM Stockholm file\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nActive sites dataset\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nCPAT header\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"Flatten collection\"];\n  0 -->|output| 7;\n  8[\"fastp\"];\n  0 -->|output| 8;\n  9[\"Convert GTF to BED12\"];\n  1 -->|output| 9;\n  10[\"Search in textfiles\"];\n  1 -->|output| 10;\n  11[\"Search in textfiles\"];\n  1 -->|output| 11;\n  12[\"FastQC\"];\n  7 -->|output| 12;\n  13[\"gather fastp reports\"];\n  8 -->|report_json| 13;\n  14[\"RNA STAR\"];\n  1 -->|output| 14;\n  2 -->|output| 14;\n  8 -->|output_paired_coll| 14;\n  15[\"Gene BED To Exon/Intron/Codon BED\"];\n  9 -->|bed_file| 15;\n  16[\"gffread\"];\n  10 -->|output| 16;\n  2 -->|output| 16;\n  17[\"gffread\"];\n  11 -->|output| 17;\n  2 -->|output| 17;\n  18[\"gather FastQC reports\"];\n  12 -->|text_file| 18;\n  19[\"Concatenate datasets\"];\n  14 -->|splice_junctions| 19;\n  20[\"Compute\"];\n  15 -->|out_file1| 20;\n  21[\"Filter\"];\n  19 -->|out_file1| 21;\n  22[\"Sort\"];\n  20 -->|out_file1| 22;\n  23[\"Cut\"];\n  21 -->|out_file1| 23;\n  24[\"Text reformatting\"];\n  22 -->|out_file1| 24;\n  25[\"Text reformatting\"];\n  22 -->|out_file1| 25;\n  26[\"Sort\"];\n  23 -->|out_file1| 26;\n  27[\"Unique lines\"];\n  26 -->|out_file1| 27;\n  28[\"RNA STAR\"];\n  1 -->|output| 28;\n  2 -->|output| 28;\n  8 -->|output_paired_coll| 28;\n  27 -->|outfile| 28;\n  29[\"StringTie\"];\n  1 -->|output| 29;\n  28 -->|mapped_reads| 29;\n  30[\"Infer Experiment\"];\n  28 -->|mapped_reads| 30;\n  9 -->|bed_file| 30;\n  31[\"Gene Body Coverage BAM\"];\n  28 -->|mapped_reads| 31;\n  9 -->|bed_file| 31;\n  32[\"Junction Saturation\"];\n  28 -->|mapped_reads| 32;\n  9 -->|bed_file| 32;\n  33[\"Junction Annotation\"];\n  28 -->|mapped_reads| 33;\n  9 -->|bed_file| 33;\n  34[\"Inner Distance\"];\n  28 -->|mapped_reads| 34;\n  9 -->|bed_file| 34;\n  35[\"Read Distribution\"];\n  28 -->|mapped_reads| 35;\n  9 -->|bed_file| 35;\n  36[\"StringTie merge\"];\n  1 -->|output| 36;\n  29 -->|output_gtf| 36;\n  37[\"gffread\"];\n  29 -->|output_gtf| 37;\n  2 -->|output| 37;\n  38[\"MultiQC\"];\n  28 -->|output_log| 38;\n  28 -->|reads_per_gene| 38;\n  30 -->|output| 38;\n  32 -->|outputr| 38;\n  31 -->|outputtxt| 38;\n  34 -->|outputfreqtxt| 38;\n  35 -->|output| 38;\n  33 -->|stats| 38;\n  39[\"StringTie\"];\n  36 -->|out_gtf| 39;\n  28 -->|mapped_reads| 39;\n  40[\"GffCompare\"];\n  1 -->|output| 40;\n  36 -->|out_gtf| 40;\n  41[\"Plot a transcript in intron\"];\n  28 -->|signal_unique_str2| 41;\n  28 -->|signal_unique_str1| 41;\n  36 -->|out_gtf| 41;\n  42[\"gffread\"];\n  36 -->|out_gtf| 42;\n  2 -->|output| 42;\n  43[\"Plot ADD3\"];\n  28 -->|signal_unique_str2| 43;\n  28 -->|signal_unique_str1| 43;\n  36 -->|out_gtf| 43;\n  44[\"Plot ADD3 zoomed\"];\n  28 -->|signal_unique_str2| 44;\n  28 -->|signal_unique_str1| 44;\n  36 -->|out_gtf| 44;\n  45[\"rnaQUAST\"];\n  1 -->|output| 45;\n  2 -->|output| 45;\n  37 -->|output_exons| 45;\n  46[\"Extract element identifiers\"];\n  39 -->|transcript_expression| 46;\n  47[\"Filter\"];\n  40 -->|tmap_output| 47;\n  48[\"Search in textfiles\"];\n  46 -->|output| 48;\n  49[\"Filter collection\"];\n  48 -->|output| 49;\n  39 -->|transcript_expression| 49;\n  50[\"IsoformSwitchAnalyzeR\"];\n  1 -->|output| 50;\n  49 -->|output_discarded| 50;\n  36 -->|out_gtf| 50;\n  49 -->|output_filtered| 50;\n  42 -->|output_exons| 50;\n  51[\"IsoformSwitchAnalyzeR\"];\n  50 -->|switchList| 51;\n  52[\"PfamScan\"];\n  5 -->|output| 52;\n  51 -->|isoformAA| 52;\n  4 -->|output| 52;\n  3 -->|output| 52;\n  53[\"CPAT\"];\n  16 -->|output_exons| 53;\n  51 -->|isoformNT| 53;\n  17 -->|output_exons| 53;\n  2 -->|output| 53;\n  54[\"Cut\"];\n  53 -->|orf_seqs_prob_best| 54;\n  55[\"Add column\"];\n  54 -->|out_file1| 55;\n  56[\"Remove beginning\"];\n  55 -->|out_file1| 56;\n  57[\"Concatenate datasets\"];\n  6 -->|output| 57;\n  56 -->|out_file1| 57;\n  58[\"IsoformSwitchAnalyzeR\"];\n  57 -->|out_file1| 58;\n  52 -->|output| 58;\n  51 -->|switchList| 58;\n  59[\"IsoformSwitchAnalyzeR\"];\n  57 -->|out_file1| 59;\n  52 -->|output| 59;\n  51 -->|switchList| 59;\n  d2f0865b-20ba-43ef-8ebc-ad9f517ec60d[\"Output\\nconsequencesSummary\"];\n  59 --> d2f0865b-20ba-43ef-8ebc-ad9f517ec60d;\n  style d2f0865b-20ba-43ef-8ebc-ad9f517ec60d stroke:#2c3143,stroke-width:4px;\n  8dd90968-6ef6-48e1-a104-547cbeaa80c8[\"Output\\nconsequencesEnrichment\"];\n  59 --> 8dd90968-6ef6-48e1-a104-547cbeaa80c8;\n  style 8dd90968-6ef6-48e1-a104-547cbeaa80c8 stroke:#2c3143,stroke-width:4px;\n  6b812e8d-997d-4a53-9c4f-cb2aa3bb26bc[\"Output\\nsplicingEnrichment\"];\n  59 --> 6b812e8d-997d-4a53-9c4f-cb2aa3bb26bc;\n  style 6b812e8d-997d-4a53-9c4f-cb2aa3bb26bc stroke:#2c3143,stroke-width:4px;\n  9c8369e2-8f86-4984-a47a-a35415ecb9b9[\"Output\\nmostSwitching\"];\n  59 --> 9c8369e2-8f86-4984-a47a-a35415ecb9b9;\n  style 9c8369e2-8f86-4984-a47a-a35415ecb9b9 stroke:#2c3143,stroke-width:4px;\n  292b9609-061f-49f7-94fc-7831526bb48b[\"Output\\nsplicingSummary\"];\n  59 --> 292b9609-061f-49f7-94fc-7831526bb48b;\n  style 292b9609-061f-49f7-94fc-7831526bb48b stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "GTN_differential_isoform_expression",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/isoformswitchanalyzer/isoformswitchanalyzer/1.20.0+galaxy5",
+                        "errors": null,
+                        "id": 59,
+                        "input_connections": {
+                            "functionMode|coding_potential|analyzeCPAT": {
+                                "id": 57,
+                                "output_name": "out_file1"
+                            },
+                            "functionMode|protein_domains|analyzePFAM": {
+                                "id": 52,
+                                "output_name": "output"
+                            },
+                            "functionMode|robject": {
+                                "id": 51,
+                                "output_name": "switchList"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool IsoformSwitchAnalyzeR",
+                                "name": "functionMode"
+                            }
+                        ],
+                        "label": null,
+                        "name": "IsoformSwitchAnalyzeR",
+                        "outputs": [
+                            {
+                                "name": "plots_summary",
+                                "type": "input"
+                            },
+                            {
+                                "name": "genes_consequences",
+                                "type": "input"
+                            },
+                            {
+                                "name": "genes_wo_consequences",
+                                "type": "input"
+                            },
+                            {
+                                "name": "switchList",
+                                "type": "rdata"
+                            },
+                            {
+                                "name": "mostSwitching",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "consequencesSummary",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "consequencesEnrichment",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "splicingSummary",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "splicingEnrichment",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "splicing_fulldata",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "consequences_fulldata",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "isoformFeatures",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 5576.086302167356,
+                            "top": 1406.0664696202693
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/isoformswitchanalyzer/isoformswitchanalyzer/1.20.0+galaxy5",
+                        "tool_shed_repository": {
+                            "changeset_revision": "298d81e5e138",
+                            "name": "isoformswitchanalyzer",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"rdata\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"functionMode\": {\"selector\": \"second_step\", \"__current_case__\": 2, \"robject\": {\"__class__\": \"ConnectedValue\"}, \"analysis_mode\": {\"selector\": \"top\", \"__current_case__\": 0, \"alpha\": \"0.05\", \"dIFcutoff\": \"0.1\", \"n\": \"10\", \"advanced_options\": {\"filterForConsequences\": false, \"sortByQvals\": true, \"onlySigIsoforms\": false, \"onlySwitchingGenes\": true, \"countGenes\": true, \"asFractionTotal\": false, \"plotGenes\": false, \"simplifyLocation\": true, \"removeEmptyConsequences\": false, \"analysisOppositeConsequence\": false}}, \"coding_potential\": {\"selector\": \"cpat\", \"__current_case__\": 1, \"analyzeCPAT\": {\"__class__\": \"ConnectedValue\"}, \"codingCutoff\": \"0.725\"}, \"protein_domains\": {\"selector\": \"enabled\", \"__current_case__\": 1, \"analyzePFAM\": {\"__class__\": \"ConnectedValue\"}}, \"signal_peptides\": {\"selector\": \"disabled\", \"__current_case__\": 0}, \"disordered_regions\": {\"selector\": \"disabled\", \"__current_case__\": 0}, \"analyzeSwitchConsequences\": {\"ntCutoff\": \"50\", \"ntFracCutoff\": null, \"ntJCsimCutoff\": \"0.8\", \"AaCutoff\": \"10\", \"AaFracCutoff\": \"0.5\", \"AaJCsimCutoff\": \"0.9\", \"removeNonConseqSwitches\": true}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.20.0+galaxy5",
+                        "type": "tool",
+                        "uuid": "001ed6b0-a597-4923-a049-b4993e0718f3",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "consequencesSummary",
+                                "output_name": "consequencesSummary",
+                                "uuid": "d2f0865b-20ba-43ef-8ebc-ad9f517ec60d"
+                            },
+                            {
+                                "label": "consequencesEnrichment",
+                                "output_name": "consequencesEnrichment",
+                                "uuid": "8dd90968-6ef6-48e1-a104-547cbeaa80c8"
+                            },
+                            {
+                                "label": "splicingEnrichment",
+                                "output_name": "splicingEnrichment",
+                                "uuid": "6b812e8d-997d-4a53-9c4f-cb2aa3bb26bc"
+                            },
+                            {
+                                "label": "mostSwitching",
+                                "output_name": "mostSwitching",
+                                "uuid": "9c8369e2-8f86-4984-a47a-a35415ecb9b9"
+                            },
+                            {
+                                "label": "splicingSummary",
+                                "output_name": "splicingSummary",
+                                "uuid": "292b9609-061f-49f7-94fc-7831526bb48b"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "transcriptomics/differential-isoform-expression",
+                "path": "topics/transcriptomics/tutorials/differential-isoform-expression/workflows/main_workflow.ga",
+                "tags": [],
+                "test_results": null,
+                "tests": true,
+                "title": "GTN_differential_isoform_expression",
+                "topic_id": "transcriptomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-differential-isoform-expression/versions/main-workflow",
+                "tutorial_id": "differential-isoform-expression",
+                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/differential-isoform-expression/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/differential-isoform-expression/workflows/main_workflow.html",
+                "version": 3,
+                "wfid": "transcriptomics-differential-isoform-expression",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
+                    "Cut1",
+                    "Filter1",
+                    "Remove beginning1",
+                    "__FILTER_FROM_FILE__",
+                    "__FLATTEN__",
+                    "cat1",
+                    "gene2exon1",
+                    "sort1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/cpat/cpat/3.0.5+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/pfamscan/pfamscan/1.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.12.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/isoformswitchanalyzer/isoformswitchanalyzer/1.20.0+galaxy5",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/rnaquast/rna_quast/2.2.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/5.0.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/5.0.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/5.0.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/5.0.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.3+galaxy0"
+                ],
+                "workflowhub_id": "1324"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/records/13692977"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "volcanoplot",
+                    "owner": "iuc",
+                    "revisions": "83c573f2e73c",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: volcanoplot\n  owner: iuc\n  revisions: 83c573f2e73c\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/tutorial.json",
+        "contributors": [
+            {
+                "id": "mblue9",
+                "joined": "2018-09",
+                "name": "Maria Doyle",
+                "orcid": "0000-0003-4847-8436",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
+            }
+        ],
+        "dir": "topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "Galaxy@AuBi",
+            "MISSISSIPPI",
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "follow_up_training": [
+            {
+                "topic_name": "transcriptomics",
+                "tutorials": [
+                    "rna-seq-viz-with-volcanoplot-r"
+                ],
+                "type": "internal"
+            }
+        ],
+        "hands_on": true,
+        "id": "transcriptomics/rna-seq-viz-with-volcanoplot",
+        "inexact_supported_servers": [
+            "GalaxyTrakr",
+            "UseGalaxy.be"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "A volcano plot can be used to quickly visualize significant genes in RNA-seq results"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Introductory",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-09-19",
+        "objectives": [
+            "Create a volcano plot of RNA-seq data to visualize significant genes"
+        ],
+        "pageviews": 228436,
+        "pub_date": "2018-12-31",
+        "questions": [
+            "How to generate a volcano plot from RNA-seq data?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "mblue9"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "10M",
+                "speakers": [
+                    "mblue9"
+                ],
+                "youtube_id": "uNGXIcEGZwA"
+            },
+            {
+                "bot-timestamp": 1725623696,
+                "captioners": [
+                    "SaimMomin12"
+                ],
+                "date": "2024-09-06",
+                "galaxy_version": " 24.1.2.dev0",
+                "length": "13M",
+                "speakers": [
+                    "SaimMomin12"
+                ],
+                "youtube_id": "ZnvAWAgk7Z4"
+            }
+        ],
+        "requirements": [
+            {
+                "topic_name": "transcriptomics",
+                "tutorials": [
+                    "rna-seq-counts-to-genes"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00304",
+        "short_tools": [
+            "volcanoplot"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "visualisation",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "time_estimation": "30m",
+        "title": "Visualization of RNA-Seq results with Volcano Plot",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5"
+        ],
+        "topic_name": "transcriptomics",
+        "topic_name_human": "Transcriptomics",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "rna-seq-viz-with-volcanoplot",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/tutorial.json"
+        },
+        "version": 15,
+        "video": false,
+        "video_versions": 2,
+        "video_view": 0,
+        "visit_duration": 82,
+        "visitors": 133762,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Visualization of RNA-Seq results with Volcano Plot",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDE results\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nVolcano genes\"]\n  2[label=\"Volcano plot highlighting significant\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Volcano plot labelling top 10\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Volcano plot labelling genes of interest\"]\n  0 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  k16aef53e11fd4defa7fb6cf9a98f0902[color=lightseagreen,label=\"Output\\nvolcano_pdf\"]\n  4 -> k16aef53e11fd4defa7fb6cf9a98f0902\n}",
+                "history": [
+                    {
+                        "hash": "470fa57969cc2fa659ec0bf0b00e69ca81367521",
+                        "message": "Fix name",
+                        "num": 8,
+                        "short_hash": "470fa5796",
+                        "unix": "1624047135"
+                    },
+                    {
+                        "hash": "086ac3f5016bee399d245984727bb0059be29c4c",
+                        "message": "Update workflow",
+                        "num": 7,
+                        "short_hash": "086ac3f50",
+                        "unix": "1624046952"
+                    },
+                    {
+                        "hash": "2e2cb42d8ac99927000d81734fb53c7943c0c4ba",
+                        "message": "add tests from workflow-testing for blockclust and rna-seq-viz-with-volcano-plot, edit workflows",
+                        "num": 6,
+                        "short_hash": "2e2cb42d8",
+                        "unix": "1601812751"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 5,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "f7f017f3329dac306d19ca406c5e28f75bbf4ef8",
+                        "message": "dna and rna capitals",
+                        "num": 4,
+                        "short_hash": "f7f017f33",
+                        "unix": "1579092000"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 3,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
+                        "message": "unflatten workflows",
+                        "num": 2,
+                        "short_hash": "faf6d298a",
+                        "unix": "1576155753"
+                    },
+                    {
+                        "hash": "47566efc6793de54afd1915977d5514b732f9ea8",
+                        "message": "Add workflow to volcanoplot tutorial",
+                        "num": 1,
+                        "short_hash": "47566efc6",
+                        "unix": "1562337491"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "DE results"
+                            }
+                        ],
+                        "label": "DE results",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 329.5,
+                            "height": 61,
+                            "left": 318,
+                            "right": 518,
+                            "top": 268.5,
+                            "width": 200,
+                            "x": 318,
+                            "y": 268.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "3adb32da-3a59-4e01-bbf1-f8501e8f4af4",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Volcano genes"
+                            }
+                        ],
+                        "label": "Volcano genes",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "bottom": 505.5,
+                            "height": 81,
+                            "left": 320,
+                            "right": 520,
+                            "top": 424.5,
+                            "width": 200,
+                            "x": 320,
+                            "y": 424.5
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "f49407c4-5995-446c-b28f-c39bbee8c6d9",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nDE results\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nVolcano genes\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Volcano plot highlighting significant\"];\n  0 -->|output| 2;\n  3[\"Volcano plot labelling top 10\"];\n  0 -->|output| 3;\n  4[\"Volcano plot labelling genes of interest\"];\n  0 -->|output| 4;\n  1 -->|output| 4;\n  16aef53e-11fd-4def-a7fb-6cf9a98f0902[\"Output\\nvolcano_pdf\"];\n  4 --> 16aef53e-11fd-4def-a7fb-6cf9a98f0902;\n  style 16aef53e-11fd-4def-a7fb-6cf9a98f0902 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "Visualization Of RNA-Seq Results With Volcano Plot",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5",
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {
+                            "input": {
+                                "id": 0,
+                                "output_name": "output"
+                            },
+                            "labels|label_file": {
+                                "id": 1,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Volcano plot labelling genes of interest",
+                        "name": "Volcano Plot",
+                        "outputs": [
+                            {
+                                "name": "plot",
+                                "type": "pdf"
+                            }
+                        ],
+                        "position": {
+                            "bottom": 531.5,
+                            "height": 142,
+                            "left": 595,
+                            "right": 795,
+                            "top": 389.5,
+                            "width": 200,
+                            "x": 595,
+                            "y": 389.5
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5",
+                        "tool_shed_repository": {
+                            "changeset_revision": "83c573f2e73c",
+                            "name": "volcanoplot",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"fdr_col\": \"8\", \"header\": \"auto\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"label_col\": \"2\", \"labels\": {\"label_select\": \"file\", \"__current_case__\": 1, \"label_file\": {\"__class__\": \"ConnectedValue\"}}, \"lfc_col\": \"4\", \"lfc_thresh\": \"0.58\", \"out_options\": {\"rscript_out\": \"false\"}, \"plot_options\": {\"boxes\": \"true\", \"title\": \"\", \"xlab\": \"\", \"ylab\": \"\", \"xmin\": null, \"xmax\": null, \"ymax\": null, \"legend\": \"\", \"legend_labs\": \"Down,Not Sig,Up\"}, \"pval_col\": \"7\", \"signif_thresh\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.0.5",
+                        "type": "tool",
+                        "uuid": "01bf8268-3e8a-4f99-b03c-05c5656ac96e",
+                        "workflow_outputs": [
+                            {
+                                "label": "volcano_pdf",
+                                "output_name": "plot",
+                                "uuid": "16aef53e-11fd-4def-a7fb-6cf9a98f0902"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "transcriptomics/rna-seq-viz-with-volcanoplot",
+                "path": "topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/workflows/rna-seq-viz-with-volcanoplot.ga",
+                "tags": [
+                    "transcriptomics"
+                ],
+                "test_results": null,
+                "tests": true,
+                "title": "Visualization Of RNA-Seq Results With Volcano Plot",
+                "topic_id": "transcriptomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-rna-seq-viz-with-volcanoplot/versions/rna-seq-viz-with-volcanoplot",
+                "tutorial_id": "rna-seq-viz-with-volcanoplot",
+                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/workflows/rna-seq-viz-with-volcanoplot.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/workflows/rna-seq-viz-with-volcanoplot.html",
+                "version": 6,
+                "wfid": "transcriptomics-rna-seq-viz-with-volcanoplot",
+                "wfname": "rna-seq-viz-with-volcanoplot",
+                "workflow": "rna-seq-viz-with-volcanoplot.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5"
+                ],
+                "workflowhub_id": "1335"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/2529117"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "goenrichment",
+                    "owner": "iuc",
+                    "revisions": "2c7c9646ccf0",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "goslimmer",
+                    "owner": "iuc",
+                    "revisions": "de3e053bd6a5",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: goenrichment\n  owner: iuc\n  revisions: 2c7c9646ccf0\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: goslimmer\n  owner: iuc\n  revisions: de3e053bd6a5\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/goenrichment/tutorial.json",
+        "contributors": [
+            {
+                "id": "igcbioinformatics",
+                "joined": "2018-12",
+                "name": "IGC Bioinformatics Unit",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/igcbioinformatics/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/igcbioinformatics.json"
+            },
+            {
+                "id": "mblue9",
+                "joined": "2018-09",
+                "name": "Maria Doyle",
+                "orcid": "0000-0003-4847-8436",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
+            }
+        ],
+        "dir": "topics/transcriptomics/tutorials/goenrichment",
+        "edam_operation": [
+            "Gene-set enrichment analysis"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "transcriptomics/goenrichment",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "The goenrichment tool can be used to perform GO Enrichment analysis",
+            "One needs to be careful when chosing the background population",
+            "There are several methods to simplify the output of the GO Enrichment analysis"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-03-05",
+        "objectives": [
+            "How to perform a GO Enrichment Analysis",
+            "How to interpret and simplify the results"
+        ],
+        "pageviews": 34415,
+        "pub_date": "2019-01-23",
+        "questions": [
+            "How can I functionally interpret a list of genes of interest that I obtained from my experiment?"
+        ],
+        "short_id": "T00291",
+        "short_tools": [
+            "Filter1",
+            "goslimmer",
+            "goenrichment"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "symlink": null,
+        "time_estimation": "1h",
+        "title": "GO Enrichment Analysis",
+        "tools": [
+            "Filter1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/goenrichment/goenrichment/2.0.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/goslimmer/goslimmer/1.0.1"
+        ],
+        "topic_name": "transcriptomics",
+        "topic_name_human": "Transcriptomics",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "goenrichment",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/goenrichment/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/goenrichment/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/goenrichment/tutorial.json"
+        },
+        "version": 12,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 77,
+        "visitors": 20487,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "GO Enrichment Analysis Tutorial",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGO annotations Drosophila melanogaster\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGO\"]\n  10[label=\"Filter\"]\n  2 -> 10 [label=\"output\"]\n  11[label=\"GOEnrichment\"]\n  3 -> 11 [label=\"output\"]\n  1 -> 11 [label=\"output\"]\n  4 -> 11 [label=\"output\"]\n  5 -> 11 [label=\"output\"]\n  12[label=\"GOEnrichment\"]\n  3 -> 12 [label=\"output\"]\n  1 -> 12 [label=\"output\"]\n  4 -> 12 [label=\"output\"]\n  5 -> 12 [label=\"output\"]\n  13[label=\"GOSlimmer\"]\n  3 -> 13 [label=\"output\"]\n  1 -> 13 [label=\"output\"]\n  6 -> 13 [label=\"output\"]\n  14[label=\"GOEnrichment\"]\n  3 -> 14 [label=\"output\"]\n  1 -> 14 [label=\"output\"]\n  4 -> 14 [label=\"output\"]\n  7 -> 14 [label=\"output\"]\n  15[label=\"GOEnrichment\"]\n  3 -> 15 [label=\"output\"]\n  1 -> 15 [label=\"output\"]\n  4 -> 15 [label=\"output\"]\n  8 -> 15 [label=\"output\"]\n  16[label=\"GOEnrichment\"]\n  0 -> 16 [label=\"output\"]\n  1 -> 16 [label=\"output\"]\n  2 -> 16 [label=\"output\"]\n  9 -> 16 [label=\"out_file1\"]\n  17[label=\"GOEnrichment\"]\n  0 -> 17 [label=\"output\"]\n  1 -> 17 [label=\"output\"]\n  10 -> 17 [label=\"out_file1\"]\n  9 -> 17 [label=\"out_file1\"]\n  18[label=\"GOEnrichment\"]\n  13 -> 18 [label=\"output\"]\n  6 -> 18 [label=\"output\"]\n  4 -> 18 [label=\"output\"]\n  5 -> 18 [label=\"output\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntrapnellPopulation.tab\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGO annotations Mus musculus\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMouse population\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMouse diff\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGO Slim\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmouseUnderexpressed.txt\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmouseOverexpressed.txt\"]\n  9[label=\"Filter\"]\n  2 -> 9 [label=\"output\"]\n}",
+                "history": [
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 3,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
+                        "message": "Changed format of workflows",
+                        "num": 2,
+                        "short_hash": "361236c41",
+                        "unix": "1554368414"
+                    },
+                    {
+                        "hash": "79f4dd991355ce9a98383d5425140fc9af718dd1",
+                        "message": "Create goenrichment-workflow.ga",
                         "num": 1,
-                        "short_hash": "a021922f2",
-                        "unix": "1678376823"
+                        "short_hash": "79f4dd991",
+                        "unix": "1550179581"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "Collection of paired-end RNA-seq datasets.",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Collection of paired-end RNA-seq datasets.",
-                                "name": "RNA-seq data collection"
+                                "description": "",
+                                "name": "GO annotations Drosophila melanogaster"
                             }
                         ],
-                        "label": "RNA-seq data collection",
-                        "name": "Input dataset collection",
+                        "label": "GO annotations Drosophila melanogaster",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 767
+                            "left": 200,
+                            "top": 200
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
+                        "tool_state": "{\"name\": \"GO annotations Drosophila melanogaster\"}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "b60e28c3-2fe1-4122-8808-71f1e033d21f",
-                        "when": null,
+                        "type": "data_input",
+                        "uuid": "44a4f678-6028-45fb-b5fc-59e6d6d30360",
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "Genome reference in FASTA format.",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Genome reference in FASTA format.",
-                                "name": "Reference genome"
+                                "description": "",
+                                "name": "GO"
                             }
                         ],
-                        "label": "Reference genome",
+                        "label": "GO",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 2240,
-                            "top": 451
+                            "left": 200,
+                            "top": 320
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"name\": \"GO\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "2e05fd1f-440d-4644-9b64-86da0ece0bc9",
-                        "when": null,
+                        "uuid": "ae9b3261-ca22-4018-8774-169358633422",
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "Reference genome annotation in GTF format.",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Reference genome annotation in GTF format.",
-                                "name": "Genome annotation"
+                                "description": "",
+                                "name": "trapnellPopulation.tab"
                             }
                         ],
-                        "label": "Genome annotation",
+                        "label": "trapnellPopulation.tab",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 2240,
-                            "top": 678
+                            "left": 200,
+                            "top": 440
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"name\": \"trapnellPopulation.tab\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "52d813b7-2387-4c82-a3aa-37320c40ae96",
-                        "when": null,
+                        "uuid": "b9332a9d-0dee-4a27-826c-1213b93c9c20",
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "IDs of control sequences, corresponding to filenames.",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 3,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "IDs of control sequences, corresponding to filenames.",
-                                "name": "Control IDs"
+                                "description": "",
+                                "name": "GO annotations Mus musculus"
                             }
                         ],
-                        "label": "Control IDs",
+                        "label": "GO annotations Mus musculus",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 5170,
-                            "top": 949
+                            "left": 200,
+                            "top": 560
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"name\": \"GO annotations Mus musculus\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "3089ebb6-7505-4113-a3d0-632437d7185f",
-                        "when": null,
+                        "uuid": "623b33b8-5edb-4f85-b377-127d0659504e",
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "Second factor name.",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 4,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Second factor name.",
-                                "name": "Factor 02"
+                                "description": "",
+                                "name": "Mouse population"
                             }
                         ],
-                        "label": "Factor 02",
-                        "name": "Input parameter",
+                        "label": "Mouse population",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 5470,
-                            "top": 1080
+                            "left": 200,
+                            "top": 680
                         },
                         "tool_id": null,
-                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
+                        "tool_state": "{\"name\": \"Mouse population\"}",
                         "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "b7327437-1d68-4878-a085-de89cdf28647",
-                        "when": null,
+                        "type": "data_input",
+                        "uuid": "ea004077-e2c7-4e92-a003-ec25f25df0a0",
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "First factor name.",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 5,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "First factor name.",
-                                "name": "Factor 01"
+                                "description": "",
+                                "name": "Mouse diff"
                             }
                         ],
-                        "label": "Factor 01",
-                        "name": "Input parameter",
+                        "label": "Mouse diff",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 5470,
-                            "top": 1183
+                            "left": 200,
+                            "top": 800
                         },
                         "tool_id": null,
-                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
+                        "tool_state": "{\"name\": \"Mouse diff\"}",
                         "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "d670477b-e0f1-4a11-9bf5-3f44ff1aca5b",
-                        "when": null,
+                        "type": "data_input",
+                        "uuid": "af1838d3-3af6-4e52-aa38-6ba38eae2c58",
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "Galaxy compatible CPAT header.",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 6,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Galaxy compatible CPAT header.",
-                                "name": "CPAT header"
+                                "description": "",
+                                "name": "GO Slim"
                             }
                         ],
-                        "label": "CPAT header",
+                        "label": "GO Slim",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 6910,
-                            "top": 193
+                            "left": 200,
+                            "top": 920
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"name\": \"GO Slim\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "b075a3c9-f558-435d-a9d8-6761c2eb63e8",
-                        "when": null,
+                        "uuid": "bc59fd06-ef94-46ea-a20b-b884f3b9a1b2",
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "Active sites dataset.",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 7,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Active sites dataset.",
-                                "name": "Active sites dataset"
+                                "description": "",
+                                "name": "mouseUnderexpressed.txt"
                             }
                         ],
-                        "label": "Active sites dataset",
+                        "label": "mouseUnderexpressed.txt",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 6910,
-                            "top": 316
+                            "left": 200,
+                            "top": 1040
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"name\": \"mouseUnderexpressed.txt\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "47b83b83-c888-4f4f-b0da-4582cd7ca8df",
-                        "when": null,
+                        "uuid": "3d85962e-96c5-4152-962d-0cbb1757e2ed",
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "Stockholm file.",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 8,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Stockholm file.",
-                                "name": "Pfam-A HMM Stockholm file"
+                                "description": "",
+                                "name": "mouseOverexpressed.txt"
                             }
                         ],
-                        "label": "Pfam-A HMM Stockholm file",
+                        "label": "mouseOverexpressed.txt",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 6910,
-                            "top": 439
+                            "left": 200,
+                            "top": 1160
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"name\": \"mouseOverexpressed.txt\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "22ffc661-6bd9-4678-91df-8644f3ea3018",
-                        "when": null,
+                        "uuid": "a81fec4d-a0b7-4e26-b1be-55ae410e5b58",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGO annotations Drosophila melanogaster\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGO\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Filter\"];\n  2 -->|output| 10;\n  11[\"GOEnrichment\"];\n  3 -->|output| 11;\n  1 -->|output| 11;\n  4 -->|output| 11;\n  5 -->|output| 11;\n  12[\"GOEnrichment\"];\n  3 -->|output| 12;\n  1 -->|output| 12;\n  4 -->|output| 12;\n  5 -->|output| 12;\n  13[\"GOSlimmer\"];\n  3 -->|output| 13;\n  1 -->|output| 13;\n  6 -->|output| 13;\n  14[\"GOEnrichment\"];\n  3 -->|output| 14;\n  1 -->|output| 14;\n  4 -->|output| 14;\n  7 -->|output| 14;\n  15[\"GOEnrichment\"];\n  3 -->|output| 15;\n  1 -->|output| 15;\n  4 -->|output| 15;\n  8 -->|output| 15;\n  16[\"GOEnrichment\"];\n  0 -->|output| 16;\n  1 -->|output| 16;\n  2 -->|output| 16;\n  9 -->|out_file1| 16;\n  17[\"GOEnrichment\"];\n  0 -->|output| 17;\n  1 -->|output| 17;\n  10 -->|out_file1| 17;\n  9 -->|out_file1| 17;\n  18[\"GOEnrichment\"];\n  13 -->|output| 18;\n  6 -->|output| 18;\n  4 -->|output| 18;\n  5 -->|output| 18;\n  2[\"\u2139\ufe0f Input Dataset\\ntrapnellPopulation.tab\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nGO annotations Mus musculus\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nMouse population\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nMouse diff\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nGO Slim\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nmouseUnderexpressed.txt\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nmouseOverexpressed.txt\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"Filter\"];\n  2 -->|output| 9;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "GO Enrichment Workflow",
+                "outputs": [],
+                "parent_id": "transcriptomics/goenrichment",
+                "path": "topics/transcriptomics/tutorials/goenrichment/workflows/goenrichment-workflow.ga",
+                "tags": [
+                    "transcriptomics"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "GO Enrichment Workflow",
+                "topic_id": "transcriptomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-goenrichment/versions/goenrichment-workflow",
+                "tutorial_id": "goenrichment",
+                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/goenrichment/workflows/goenrichment-workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/goenrichment/workflows/goenrichment-workflow.html",
+                "version": 3,
+                "wfid": "transcriptomics-goenrichment",
+                "wfname": "goenrichment-workflow",
+                "workflow": "goenrichment-workflow.ga",
+                "workflow_tools": [
+                    "Filter1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/goenrichment/goenrichment/2.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/goslimmer/goslimmer/1.0.1"
+                ],
+                "workflowhub_id": "1315"
+            }
+        ],
+        "zenodo_link": "https://zenodo.org/record/2565417"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "deseq2",
+                    "owner": "iuc",
+                    "revisions": "d9e5cadc7f0b",
+                    "tool_panel_section_label": "RNA Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "heinz",
+                    "owner": "iuc",
+                    "revisions": "2b80a2596064",
+                    "tool_panel_section_label": "RNA Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "heinz",
+                    "owner": "iuc",
+                    "revisions": "2b80a2596064",
+                    "tool_panel_section_label": "RNA Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "heinz",
+                    "owner": "iuc",
+                    "revisions": "2b80a2596064",
+                    "tool_panel_section_label": "RNA Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "heinz",
+                    "owner": "iuc",
+                    "revisions": "5f589c91566e",
+                    "tool_panel_section_label": "RNA Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: deseq2\n  owner: iuc\n  revisions: d9e5cadc7f0b\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: heinz\n  owner: iuc\n  revisions: 2b80a2596064\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: heinz\n  owner: iuc\n  revisions: 2b80a2596064\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: heinz\n  owner: iuc\n  revisions: 2b80a2596064\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: heinz\n  owner: iuc\n  revisions: 5f589c91566e\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.json",
+        "contributors": [
+            {
+                "id": "ChaoZhang123",
+                "joined": "2018-08",
+                "maintainer_contact": "https://hi-it.org",
+                "name": "Chao Zhang",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ChaoZhang123/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/ChaoZhang123.json"
+            }
+        ],
+        "dir": "topics/transcriptomics/tutorials/network-analysis-with-heinz",
+        "edam_operation": [
+            "Pathway or network analysis",
+            "RNA-Seq analysis",
+            "Differential gene expression analysis"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.eu"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "transcriptomics/network-analysis-with-heinz",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Using Heinz do the network analysis based on the metatranscriptomics or transcriptomics data.",
+            "Extracting the signals hidden in the p-value distribution of the differential expression analysis.",
+            "Visualizing the pinpointed subnetwork helps us understand the result better",
+            "Heinz helps narrow down the scope to find the key pathways",
+            "Multiple CPUs will accelerate the computation especially for the complex datasets"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-01-15",
+        "objectives": [
+            "Network Analysis of metatranscriptomics data using Heinz in Galaxy to pinpoint the optimal scoring subnetwork."
+        ],
+        "pageviews": 5900522,
+        "pub_date": "2018-10-11",
+        "questions": [
+            "Which pathways are potentially contributing to dental caries?"
+        ],
+        "short_id": "T00293",
+        "short_tools": [
+            "heinz",
+            "heinz_scoring",
+            "Cut1",
+            "deseq2",
+            "heinz_visualization",
+            "heinz_bum"
+        ],
+        "slides": true,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "metatranscriptomics",
+            "network analysis"
+        ],
+        "time_estimation": "1h30m",
+        "title": "Network analysis with Heinz",
+        "tools": [
+            "Cut1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz/1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_bum/1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_scoring/1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_visualization/0.1.0"
+        ],
+        "topic_name": "transcriptomics",
+        "topic_name_human": "Transcriptomics",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "network-analysis-with-heinz",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.json"
+        },
+        "version": 16,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 343,
+        "visitors": 2135469,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Network analysis with Heinz",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nEdge File\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  3[label=\"DESeq2\"]\n  1 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Cut\"]\n  3 -> 4 [label=\"deseq_out\"]\n  5[label=\"Cut\"]\n  3 -> 5 [label=\"deseq_out\"]\n  6[label=\"Fit a BUM model\"]\n  4 -> 6 [label=\"out_file1\"]\n  7[label=\"Calculate a Heinz score\"]\n  5 -> 7 [label=\"out_file1\"]\n  6 -> 7 [label=\"dist_params\"]\n  8[label=\"Identify optimal scoring subnetwork\"]\n  7 -> 8 [label=\"score\"]\n  0 -> 8 [label=\"output\"]\n  9[label=\"Visualize\"]\n  8 -> 9 [label=\"subnetwork\"]\n}",
+                "history": [
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 3,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 2,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "6a6b3b2cfd5007d26b1bbbcaf388fee819397d85",
+                        "message": "Renamed the folder, rewrote the key points; added tags; added a paragraph in the end to correspond to the research question in this tutorial.",
+                        "num": 1,
+                        "short_hash": "6a6b3b2cf",
+                        "unix": "1539171768"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "The background network",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "Edge File",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 202.4296875,
+                            "top": 238.03125
+                        },
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "3939e577-a385-4d04-8db9-5b692670fb00",
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "HMM library.",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 9,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "HMM library.",
-                                "name": "Pfam-A HMM library"
+                                "description": "",
+                                "name": "Input Dataset Collection"
                             }
                         ],
-                        "label": "Pfam-A HMM library",
-                        "name": "Input dataset",
+                        "label": null,
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 6910,
-                            "top": 563
+                            "left": 202.4296875,
+                            "top": 358.03125
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "494f5134-2496-481e-910a-8c640726fc07",
-                        "when": null,
+                        "type": "data_collection_input",
+                        "uuid": "c6808009-a8e5-447d-a62a-37003ef0bb96",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Input Dataset Collection"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 202.4296875,
+                            "top": 478.03125
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "76dd0c7b-e654-462f-810b-7c7f9c69e17b",
                         "workflow_outputs": []
                     }
                 ],
-                "license": "CC-BY-SA-4.0",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nRNA-seq data collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nGenome annotation\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nControl IDs\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nFactor 02\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Parameter\\nFactor 01\"];\n  style 5 fill:#ded,stroke:#393,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nCPAT header\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nActive sites dataset\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nPfam-A HMM Stockholm file\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"\u2139\ufe0f Input Dataset\\nPfam-A HMM library\"];\n  style 9 stroke:#2c3143,stroke-width:4px;\n  10[\"fastp\"];\n  0 -->|output| 10;\n  11[\"Flatten collection\"];\n  0 -->|output| 11;\n  12[\"Search in textfiles\"];\n  2 -->|output| 12;\n  13[\"Search in textfiles\"];\n  2 -->|output| 13;\n  14[\"Convert GTF to BED12\"];\n  2 -->|output| 14;\n  15[\"FastQC\"];\n  11 -->|output| 15;\n  16[\"gffread\"];\n  12 -->|output| 16;\n  1 -->|output| 16;\n  e34fd125-e860-48a2-9e58-bed5c3600b8d[\"Output\\nlncRNA sequences\"];\n  16 --> e34fd125-e860-48a2-9e58-bed5c3600b8d;\n  style e34fd125-e860-48a2-9e58-bed5c3600b8d stroke:#2c3143,stroke-width:4px;\n  17[\"gffread\"];\n  13 -->|output| 17;\n  1 -->|output| 17;\n  836eeb38-dc67-42df-93fa-2fcd5bbe7a80[\"Output\\nprotein coding sequences\"];\n  17 --> 836eeb38-dc67-42df-93fa-2fcd5bbe7a80;\n  style 836eeb38-dc67-42df-93fa-2fcd5bbe7a80 stroke:#2c3143,stroke-width:4px;\n  18[\"MultiQC\"];\n  15 -->|text_file| 18;\n  10 -->|report_json| 18;\n  19[\"Search in textfiles\"];\n  15 -->|text_file| 19;\n  20[\"Concatenate datasets\"];\n  19 -->|output| 20;\n  21[\"Search in textfiles\"];\n  20 -->|out_file1| 21;\n  22[\"Cut\"];\n  21 -->|output| 22;\n  23[\"Text reformatting\"];\n  22 -->|out_file1| 23;\n  24[\"Parse parameter value\"];\n  23 -->|outfile| 24;\n  25[\"RNA STAR\"];\n  2 -->|output| 25;\n  24 -->|integer_param| 25;\n  1 -->|output| 25;\n  10 -->|output_paired_coll| 25;\n  26[\"Concatenate datasets\"];\n  25 -->|splice_junctions| 26;\n  27[\"Text reformatting\"];\n  26 -->|out_file1| 27;\n  28[\"Cut\"];\n  27 -->|outfile| 28;\n  29[\"Sort\"];\n  28 -->|out_file1| 29;\n  30[\"Unique\"];\n  29 -->|out_file1| 30;\n  31[\"RNA STAR\"];\n  2 -->|output| 31;\n  24 -->|integer_param| 31;\n  1 -->|output| 31;\n  10 -->|output_paired_coll| 31;\n  30 -->|outfile| 31;\n  32[\"StringTie\"];\n  2 -->|output| 32;\n  31 -->|mapped_reads| 32;\n  33[\"Junction Annotation\"];\n  31 -->|mapped_reads| 33;\n  14 -->|bed_file| 33;\n  34[\"Junction Saturation\"];\n  31 -->|mapped_reads| 34;\n  14 -->|bed_file| 34;\n  35[\"Gene Body Coverage BAM\"];\n  31 -->|mapped_reads| 35;\n  14 -->|bed_file| 35;\n  36[\"Inner Distance\"];\n  31 -->|mapped_reads| 36;\n  14 -->|bed_file| 36;\n  37[\"Infer Experiment\"];\n  31 -->|mapped_reads| 37;\n  14 -->|bed_file| 37;\n  38[\"Read Distribution\"];\n  31 -->|mapped_reads| 38;\n  14 -->|bed_file| 38;\n  39[\"gffread\"];\n  32 -->|output_gtf| 39;\n  1 -->|output| 39;\n  40[\"StringTie merge\"];\n  2 -->|output| 40;\n  32 -->|output_gtf| 40;\n  41[\"MultiQC\"];\n  31 -->|output_log| 41;\n  37 -->|output| 41;\n  38 -->|output| 41;\n  34 -->|outputr| 41;\n  33 -->|stats| 41;\n  35 -->|outputtxt| 41;\n  36 -->|outputfreqtxt| 41;\n  42[\"rnaQUAST\"];\n  2 -->|output| 42;\n  1 -->|output| 42;\n  39 -->|output_exons| 42;\n  43[\"gffread\"];\n  40 -->|out_gtf| 43;\n  1 -->|output| 43;\n  44[\"StringTie\"];\n  40 -->|out_gtf| 44;\n  31 -->|mapped_reads| 44;\n  45[\"Filter collection\"];\n  3 -->|output| 45;\n  44 -->|transcript_expression| 45;\n  46[\"IsoformSwitchAnalyzeR\"];\n  2 -->|output| 46;\n  24 -->|integer_param| 46;\n  5 -->|output| 46;\n  45 -->|output_filtered| 46;\n  40 -->|out_gtf| 46;\n  4 -->|output| 46;\n  45 -->|output_discarded| 46;\n  43 -->|output_exons| 46;\n  47[\"IsoformSwitchAnalyzeR\"];\n  46 -->|switchList| 47;\n  48[\"CPAT\"];\n  17 -->|output_exons| 48;\n  47 -->|isoformNT| 48;\n  16 -->|output_exons| 48;\n  1 -->|output| 48;\n  49[\"PfamScan\"];\n  7 -->|output| 49;\n  47 -->|isoformAA| 49;\n  8 -->|output| 49;\n  9 -->|output| 49;\n  50[\"Remove beginning\"];\n  48 -->|orf_seqs_prob_best| 50;\n  51[\"Text reformatting\"];\n  50 -->|out_file1| 51;\n  52[\"Concatenate datasets\"];\n  6 -->|output| 52;\n  51 -->|outfile| 52;\n  53[\"IsoformSwitchAnalyzeR\"];\n  52 -->|out_file1| 53;\n  49 -->|output| 53;\n  47 -->|switchList| 53;\n  54[\"IsoformSwitchAnalyzeR\"];\n  52 -->|out_file1| 54;\n  49 -->|output| 54;\n  47 -->|switchList| 54;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "Genome-wide alternative splicing analysis: human",
-                "outputs": [
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nEdge File\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"DESeq2\"];\n  1 -->|output| 3;\n  2 -->|output| 3;\n  4[\"Cut\"];\n  3 -->|deseq_out| 4;\n  5[\"Cut\"];\n  3 -->|deseq_out| 5;\n  6[\"Fit a BUM model\"];\n  4 -->|out_file1| 6;\n  7[\"Calculate a Heinz score\"];\n  5 -->|out_file1| 7;\n  6 -->|dist_params| 7;\n  8[\"Identify optimal scoring subnetwork\"];\n  7 -->|score| 8;\n  0 -->|output| 8;\n  9[\"Visualize\"];\n  8 -->|subnetwork| 9;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "Workflow Constructed From History 'Heinz Workflow Trial Sep 11'",
+                "outputs": [],
+                "parent_id": "transcriptomics/network-analysis-with-heinz",
+                "path": "topics/transcriptomics/tutorials/network-analysis-with-heinz/workflows/Galaxy-Workflow-Heinz.ga",
+                "tags": [
+                    "transcriptomics"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Workflow Constructed From History 'Heinz Workflow Trial Sep 11'",
+                "topic_id": "transcriptomics",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-network-analysis-with-heinz/versions/galaxy-workflow-heinz",
+                "tutorial_id": "network-analysis-with-heinz",
+                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/network-analysis-with-heinz/workflows/Galaxy-Workflow-Heinz.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/network-analysis-with-heinz/workflows/Galaxy-Workflow-Heinz.html",
+                "version": 3,
+                "wfid": "transcriptomics-network-analysis-with-heinz",
+                "wfname": "galaxy-workflow-heinz",
+                "workflow": "Galaxy-Workflow-Heinz.ga",
+                "workflow_tools": [
+                    "Cut1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz/1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_bum/1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_scoring/1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_visualization/0.1.0"
+                ],
+                "workflowhub_id": "1303"
+            }
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.1344105"
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "samtools_sort",
+                    "owner": "devteam",
+                    "revisions": "f56bdb93ae58",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "blockbuster",
+                    "owner": "rnateam",
+                    "revisions": "7c7ff7a3503f",
+                    "tool_panel_section_label": "RNA Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "blockclust",
+                    "owner": "rnateam",
+                    "revisions": "aab6cf87b40a",
+                    "tool_panel_section_label": "RNA Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_sort\n  owner: devteam\n  revisions: f56bdb93ae58\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: blockbuster\n  owner: rnateam\n  revisions: 7c7ff7a3503f\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: blockclust\n  owner: rnateam\n  revisions: aab6cf87b40a\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/small_ncrna_clustering/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "pavanvidem",
+                "joined": "2017-09",
+                "name": "Pavankumar Videm",
+                "orcid": "0000-0002-5192-126X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
+            }
+        ],
+        "dir": "topics/transcriptomics/tutorials/small_ncrna_clustering",
+        "edam_operation": [],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.be",
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "transcriptomics/small_ncrna_clustering",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.no",
+            "UseGalaxy.org.au"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Small non-coding RNA read profiles are often associate with function",
+            "Clusters of read profiles correlate with the ncRNA classes"
+        ],
+        "layout": "tutorial_hands_on",
+        "license": "CC-BY-4.0",
+        "mod_date": "2023-11-09",
+        "objectives": [
+            "Difference between mRNA-seq and smallRNA-seq",
+            "Unsupervised grouping of the adjacent reads into read profiles",
+            "Look and learn what the shapes of the read profiles represent",
+            "Clustering of the read profiles by machine learning algorithm"
+        ],
+        "pageviews": 1205,
+        "pub_date": "2018-12-14",
+        "questions": [
+            "What do the read profiles of small non-coding RNAs represent?",
+            "How to cluster the read profiles based on some intrinsic features?"
+        ],
+        "short_id": "T00306",
+        "short_tools": [
+            "blockclust",
+            "samtools_sort",
+            "tp_sort_header_tool",
+            "blockbuster"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "symlink": null,
+        "time_estimation": "1H",
+        "title": "Small Non-coding RNA Clustering using BlockClust",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.2",
+            "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2",
+            "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0"
+        ],
+        "topic_name": "transcriptomics",
+        "topic_name_human": "Transcriptomics",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "small_ncrna_clustering",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/small_ncrna_clustering/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/small_ncrna_clustering/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/small_ncrna_clustering/tutorial.json"
+        },
+        "version": 8,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 175,
+        "visitors": 865,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Small Non-coding RNA Clustering using BlockClust",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nblockclust_input\"]\n  1[label=\"Samtools sort\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"BlockClust\"]\n  1 -> 2 [label=\"output1\"]\n  k39f8722a844442f88104f81201804c9c[color=lightseagreen,label=\"Output\\ntags_bed\"]\n  2 -> k39f8722a844442f88104f81201804c9c\n  3[label=\"Sort\"]\n  2 -> 3 [label=\"tags_bed\"]\n  4[label=\"blockbuster\"]\n  3 -> 4 [label=\"outfile\"]\n  k95c21ce9e98844b9978e10a27b74d18e[color=lightseagreen,label=\"Output\\nblockbuster_out\"]\n  4 -> k95c21ce9e98844b9978e10a27b74d18e\n  5[label=\"BlockClust\"]\n  4 -> 5 [label=\"output\"]\n  k241feec19ffd4d289b65e58850198c6d[color=lightseagreen,label=\"Output\\nmodel_based_pred_bed\"]\n  5 -> k241feec19ffd4d289b65e58850198c6d\n  k287b4bae55a14f38b1c362ae60b4d950[color=lightseagreen,label=\"Output\\nclusters_bed\"]\n  5 -> k287b4bae55a14f38b1c362ae60b4d950\n}",
+                "history": [
+                    {
+                        "hash": "2e2cb42d8ac99927000d81734fb53c7943c0c4ba",
+                        "message": "add tests from workflow-testing for blockclust and rna-seq-viz-with-volcano-plot, edit workflows",
+                        "num": 4,
+                        "short_hash": "2e2cb42d8",
+                        "unix": "1601812751"
+                    },
+                    {
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
+                        "num": 3,
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 2,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "0afe265cf142d3ad8b39a4010e0b2d0ca931677c",
+                        "message": "initial version of training material for small ncRNA clustering using blockclust",
+                        "num": 1,
+                        "short_hash": "0afe265cf",
+                        "unix": "1544604285"
+                    }
+                ],
+                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 16,
-                        "input_connections": {
-                            "input": {
-                                "id": 12,
-                                "output_name": "output"
-                            },
-                            "reference_genome|genome_fasta": {
-                                "id": 1,
-                                "output_name": "output"
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "blockclust_input"
                             }
+                        ],
+                        "label": "blockclust_input",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 212
                         },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "b6e23dd8-46ca-4bd6-87f3-2f6b741b459b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "64e45b5f-8e46-4ae9-96c1-c452601a3bfc"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nblockclust_input\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Samtools sort\"];\n  0 -->|output| 1;\n  2[\"BlockClust\"];\n  1 -->|output1| 2;\n  39f8722a-8444-42f8-8104-f81201804c9c[\"Output\\ntags_bed\"];\n  2 --> 39f8722a-8444-42f8-8104-f81201804c9c;\n  style 39f8722a-8444-42f8-8104-f81201804c9c stroke:#2c3143,stroke-width:4px;\n  3[\"Sort\"];\n  2 -->|tags_bed| 3;\n  4[\"blockbuster\"];\n  3 -->|outfile| 4;\n  95c21ce9-e988-44b9-978e-10a27b74d18e[\"Output\\nblockbuster_out\"];\n  4 --> 95c21ce9-e988-44b9-978e-10a27b74d18e;\n  style 95c21ce9-e988-44b9-978e-10a27b74d18e stroke:#2c3143,stroke-width:4px;\n  5[\"BlockClust\"];\n  4 -->|output| 5;\n  241feec1-9ffd-4d28-9b65-e58850198c6d[\"Output\\nmodel_based_pred_bed\"];\n  5 --> 241feec1-9ffd-4d28-9b65-e58850198c6d;\n  style 241feec1-9ffd-4d28-9b65-e58850198c6d stroke:#2c3143,stroke-width:4px;\n  287b4bae-55a1-4f38-b1c3-62ae60b4d950[\"Output\\nclusters_bed\"];\n  5 --> 287b4bae-55a1-4f38-b1c3-62ae60b4d950;\n  style 287b4bae-55a1-4f38-b1c3-62ae60b4d950 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "Blockclust 1.1.0 Clustering",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool gffread",
-                                "name": "chr_replace"
+                                "description": "",
+                                "name": "blockclust_input"
                             }
                         ],
+                        "label": "blockclust_input",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 212
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "b6e23dd8-46ca-4bd6-87f3-2f6b741b459b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "64e45b5f-8e46-4ae9-96c1-c452601a3bfc"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0",
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {
+                            "tool_mode|reads_bam": {
+                                "id": 1,
+                                "output_name": "output1"
+                            }
+                        },
+                        "inputs": [],
                         "label": null,
-                        "name": "gffread",
+                        "name": "BlockClust",
                         "outputs": [
                             {
-                                "name": "output_exons",
-                                "type": "fasta"
+                                "name": "tags_bed",
+                                "type": "bed"
                             }
                         ],
                         "position": {
-                            "left": 2820,
-                            "top": 0
-                        },
-                        "post_job_actions": {
-                            "TagDatasetActionoutput_exons": {
-                                "action_arguments": {
-                                    "tags": "#lncRNA"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "output_exons"
-                            }
+                            "left": 788,
+                            "top": 212
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "154d00cbbf2d",
-                            "name": "gffread",
-                            "owner": "devteam",
+                            "changeset_revision": "aab6cf87b40a",
+                            "name": "blockclust",
+                            "owner": "rnateam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"chr_replace\": {\"__class__\": \"RuntimeValue\"}, \"decode_url\": false, \"expose\": false, \"filtering\": null, \"full_gff_attribute_preservation\": false, \"gffs\": {\"gff_fmt\": \"none\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"maxintron\": null, \"merging\": {\"merge_sel\": \"none\", \"__current_case__\": 0}, \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 2, \"genome_fasta\": {\"__class__\": \"ConnectedValue\"}, \"ref_filtering\": null, \"fa_outputs\": [\"-w exons.fa\"]}, \"region\": {\"region_filter\": \"none\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.2.1.3+galaxy0",
+                        "tool_state": "{\"tool_mode\": {\"operation\": \"pre\", \"__current_case__\": 0, \"reads_bam\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.0",
                         "type": "tool",
-                        "uuid": "221894ea-cf04-4328-bf2e-ebdafa717b27",
-                        "when": null,
+                        "uuid": "fd3043d3-609e-4303-bcb5-448cb749a319",
                         "workflow_outputs": [
                             {
-                                "label": "lncRNA sequences",
-                                "output_name": "output_exons",
-                                "uuid": "e34fd125-e860-48a2-9e58-bed5c3600b8d"
+                                "label": "tags_bed",
+                                "output_name": "tags_bed",
+                                "uuid": "39f8722a-8444-42f8-8104-f81201804c9c"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2",
                         "errors": null,
-                        "id": 17,
+                        "id": 4,
                         "input_connections": {
                             "input": {
-                                "id": 13,
-                                "output_name": "output"
-                            },
-                            "reference_genome|genome_fasta": {
-                                "id": 1,
-                                "output_name": "output"
+                                "id": 3,
+                                "output_name": "outfile"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "blockbuster",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool gffread",
-                                "name": "chr_replace"
+                                "name": "output",
+                                "type": "bed"
                             }
                         ],
+                        "position": {
+                            "left": 1376,
+                            "top": 212
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "7c7ff7a3503f",
+                            "name": "blockbuster",
+                            "owner": "rnateam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"distance\": \"40\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"merge\": \"0\", \"minBlockHeight\": \"1.0\", \"minClusterHeight\": \"50.0\", \"print\": \"bbf_reads\", \"scale\": \"0.5\", \"tagFilter\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.1.2",
+                        "type": "tool",
+                        "uuid": "8a3db40c-ae03-49ca-b47c-559ac455d712",
+                        "workflow_outputs": [
+                            {
+                                "label": "blockbuster_out",
+                                "output_name": "output",
+                                "uuid": "95c21ce9-e988-44b9-978e-10a27b74d18e"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "tool_mode|input_bbo": {
+                                "id": 4,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
                         "label": null,
-                        "name": "gffread",
+                        "name": "BlockClust",
                         "outputs": [
                             {
-                                "name": "output_exons",
-                                "type": "fasta"
+                                "name": "hclust_plot",
+                                "type": "pdf"
+                            },
+                            {
+                                "name": "clusters",
+                                "type": "bed"
+                            },
+                            {
+                                "name": "model_based_pred_bed",
+                                "type": "bed"
+                            },
+                            {
+                                "name": "sim_tab_out",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 2820,
-                            "top": 256
+                            "left": 1694,
+                            "top": 212
                         },
                         "post_job_actions": {
-                            "TagDatasetActionoutput_exons": {
-                                "action_arguments": {
-                                    "tags": "#proteon_coding"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "output_exons"
+                            "HideDatasetActionhclust_plot": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "hclust_plot"
+                            },
+                            "HideDatasetActionsim_tab_out": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "sim_tab_out"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "154d00cbbf2d",
-                            "name": "gffread",
-                            "owner": "devteam",
+                            "changeset_revision": "aab6cf87b40a",
+                            "name": "blockclust",
+                            "owner": "rnateam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"chr_replace\": {\"__class__\": \"RuntimeValue\"}, \"decode_url\": false, \"expose\": false, \"filtering\": null, \"full_gff_attribute_preservation\": false, \"gffs\": {\"gff_fmt\": \"none\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"maxintron\": null, \"merging\": {\"merge_sel\": \"none\", \"__current_case__\": 0}, \"reference_genome\": {\"source\": \"history\", \"__current_case__\": 2, \"genome_fasta\": {\"__class__\": \"ConnectedValue\"}, \"ref_filtering\": null, \"fa_outputs\": [\"-w exons.fa\"]}, \"region\": {\"region_filter\": \"none\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.2.1.3+galaxy0",
+                        "tool_state": "{\"tool_mode\": {\"operation\": \"analysis\", \"__current_case__\": 1, \"input_bbo\": {\"__class__\": \"ConnectedValue\"}, \"reference\": \"hg19\", \"nochr\": \"false\", \"pred\": {\"enable_pred\": \"yes\", \"__current_case__\": 0, \"pred_mode\": \"MODEL\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.0",
                         "type": "tool",
-                        "uuid": "aeb74658-0173-4007-a1c3-e07f67c3338a",
-                        "when": null,
+                        "uuid": "e41a16eb-4edd-4f9e-b615-44d0c2988b63",
                         "workflow_outputs": [
                             {
-                                "label": "protein coding sequences",
-                                "output_name": "output_exons",
-                                "uuid": "836eeb38-dc67-42df-93fa-2fcd5bbe7a80"
+                                "label": "model_based_pred_bed",
+                                "output_name": "model_based_pred_bed",
+                                "uuid": "241feec1-9ffd-4d28-9b65-e58850198c6d"
+                            },
+                            {
+                                "label": "clusters_bed",
+                                "output_name": "clusters",
+                                "uuid": "287b4bae-55a1-4f38-b1c3-62ae60b4d950"
                             }
                         ]
                     }
                 ],
-                "parent_id": "transcriptomics/differential-isoform-expression",
-                "path": "topics/transcriptomics/tutorials/differential-isoform-expression/workflows/main_workflow.ga",
+                "parent_id": "transcriptomics/small_ncrna_clustering",
+                "path": "topics/transcriptomics/tutorials/small_ncrna_clustering/workflows/blockclust_clustering.ga",
                 "tags": [
-                    "name:alternative_splicing",
-                    "name:GTN",
-                    "name:transcriptomics"
+                    "transcriptomics"
                 ],
                 "test_results": null,
                 "tests": true,
-                "title": "Genome-wide alternative splicing analysis: human",
+                "title": "Blockclust 1.1.0 Clustering",
                 "topic_id": "transcriptomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-differential-isoform-expression/versions/main-workflow",
-                "tutorial_id": "differential-isoform-expression",
-                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/differential-isoform-expression/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/differential-isoform-expression/workflows/main_workflow.html",
-                "version": 2,
-                "wfid": "transcriptomics-differential-isoform-expression",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-small_ncrna_clustering/versions/blockclust-clustering",
+                "tutorial_id": "small_ncrna_clustering",
+                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/small_ncrna_clustering/workflows/blockclust_clustering.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/small_ncrna_clustering/workflows/blockclust_clustering.html",
+                "version": 4,
+                "wfid": "transcriptomics-small_ncrna_clustering",
+                "wfname": "blockclust-clustering",
+                "workflow": "blockclust_clustering.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "Remove beginning1",
-                    "__FILTER_FROM_FILE__",
-                    "__FLATTEN__",
-                    "param_value_from_file",
-                    "sort1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/cpat/cpat/3.0.4+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/pfamscan/pfamscan/1.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/isoformswitchanalyzer/isoformswitchanalyzer/1.20.0+galaxy5",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/rnaquast/rna_quast/2.2.3+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/5.0.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/5.0.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/5.0.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/5.0.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.1+galaxy2"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0"
                 ],
-                "workflowhub_id": "1324"
+                "workflowhub_id": "1333"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/7974884"
+        "zenodo_link": "https://zenodo.org/record/1491876"
     },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "9da02be9c6cc",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "3d0c7bdf12f5",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "picard",
-                    "owner": "devteam",
-                    "revisions": "b9fbec5ac6b2",
-                    "tool_panel_section_label": "Picard",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "picard",
-                    "owner": "devteam",
-                    "revisions": "b502c227b5e6",
-                    "tool_panel_section_label": "Picard",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_idxstats",
-                    "owner": "devteam",
-                    "revisions": "811fc2d75ad4",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_idxstats",
-                    "owner": "devteam",
-                    "revisions": "7def34e6cf4d",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collection_column_join",
-                    "owner": "iuc",
-                    "revisions": "3ddd99c7efee",
-                    "tool_panel_section_label": "Join, Subtract and Group",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "featurecounts",
-                    "owner": "iuc",
-                    "revisions": "1759d845181e",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "featurecounts",
-                    "owner": "iuc",
-                    "revisions": "38b6d12edc68",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "hisat2",
-                    "owner": "iuc",
-                    "revisions": "61ee47027bd3",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "hisat2",
-                    "owner": "iuc",
-                    "revisions": "6c19daec423d",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
                 {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "9a913cdee30e",
-                    "tool_panel_section_label": "Quality Control",
+                    "name": "salmon",
+                    "owner": "bgruening",
+                    "revisions": "53e9709776a0",
+                    "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "1c2db0054039",
-                    "tool_panel_section_label": "Quality Control",
+                    "name": "trim_galore",
+                    "owner": "bgruening",
+                    "revisions": "1bfc7254232e",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "b2f1f75d49c4",
-                    "tool_panel_section_label": "Quality Control",
+                    "name": "fastq_manipulation",
+                    "owner": "devteam",
+                    "revisions": "bb07615a5b6a",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cutadapt",
-                    "owner": "lparsons",
-                    "revisions": "660cffd8d92a",
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "3fdc1a74d866",
                     "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "cutadapt",
-                    "owner": "lparsons",
-                    "revisions": "c5e2e5902201",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "samtool_filter2",
+                    "owner": "devteam",
+                    "revisions": "dc6ff68ea5e8",
+                    "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "rseqc",
-                    "owner": "nilesh",
-                    "revisions": "dbedfc5f5a3c",
-                    "tool_panel_section_label": "RNA Analysis",
+                    "name": "bedtools",
+                    "owner": "iuc",
+                    "revisions": "c78cf6fe3018",
+                    "tool_panel_section_label": "BED",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "rseqc",
-                    "owner": "nilesh",
-                    "revisions": "dbedfc5f5a3c",
+                    "name": "deseq2",
+                    "owner": "iuc",
+                    "revisions": "24a09ca67621",
                     "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "rseqc",
-                    "owner": "nilesh",
-                    "revisions": "dbedfc5f5a3c",
-                    "tool_panel_section_label": "RNA Analysis",
+                    "name": "hisat2",
+                    "owner": "iuc",
+                    "revisions": "1eb21dccc2fa",
+                    "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastqc\n  owner: devteam\n  revisions: 9da02be9c6cc\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: b9fbec5ac6b2\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: b502c227b5e6\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_idxstats\n  owner: devteam\n  revisions: 811fc2d75ad4\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_idxstats\n  owner: devteam\n  revisions: 7def34e6cf4d\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_column_join\n  owner: iuc\n  revisions: 3ddd99c7efee\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: featurecounts\n  owner: iuc\n  revisions: 1759d845181e\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: featurecounts\n  owner: iuc\n  revisions: 38b6d12edc68\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: hisat2\n  owner: iuc\n  revisions: 61ee47027bd3\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: hisat2\n  owner: iuc\n  revisions: 6c19daec423d\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 9a913cdee30e\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 1c2db0054039\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: b2f1f75d49c4\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 660cffd8d92a\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: c5e2e5902201\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: dbedfc5f5a3c\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: dbedfc5f5a3c\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: dbedfc5f5a3c\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: salmon\n  owner: bgruening\n  revisions: 53e9709776a0\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trim_galore\n  owner: bgruening\n  revisions: 1bfc7254232e\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastq_manipulation\n  owner: devteam\n  revisions: bb07615a5b6a\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3fdc1a74d866\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtool_filter2\n  owner: devteam\n  revisions: dc6ff68ea5e8\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bedtools\n  owner: iuc\n  revisions: c78cf6fe3018\n  tool_panel_section_label: BED\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deseq2\n  owner: iuc\n  revisions: 24a09ca67621\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: hisat2\n  owner: iuc\n  revisions: 1eb21dccc2fa\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/srna/tutorial.json",
         "contributors": [
             {
-                "id": "mblue9",
-                "joined": "2018-09",
-                "name": "Maria Doyle",
-                "orcid": "0000-0003-4847-8436",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
-            },
-            {
-                "id": "bphipson",
-                "joined": "2018-09",
-                "name": "Belinda Phipson",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bphipson/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bphipson.json"
-            },
-            {
-                "id": "hdashnow",
-                "joined": "2018-09",
-                "name": "Harriet Dashnow",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hdashnow/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hdashnow.json"
+                "id": "malloryfreeberg",
+                "joined": "2017-09",
+                "name": "Mallory Freeberg",
+                "orcid": "0000-0003-2949-3921",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/malloryfreeberg/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/malloryfreeberg.json"
             }
         ],
-        "dir": "topics/transcriptomics/tutorials/rna-seq-reads-to-counts",
+        "dir": "topics/transcriptomics/tutorials/srna",
         "edam_operation": [
-            "Sequencing quality control",
-            "Primer removal",
             "Sequence alignment",
-            "Formatting",
+            "Sequence trimming",
+            "Differential gene expression analysis",
+            "Sequencing quality control",
+            "RNA-Seq analysis",
+            "Statistical calculation",
+            "Gene expression analysis",
+            "RNA-Seq quantification",
             "Sequence composition calculation",
-            "Read summarisation",
             "Read pre-processing",
-            "RNA-Seq quantification",
-            "Data handling",
-            "Validation",
-            "Sequence trimming",
-            "Statistical calculation"
+            "Primer removal"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "transcriptomics",
-                "tutorials": [
-                    "rna-seq-counts-to-genes"
-                ],
-                "type": "internal"
-            }
-        ],
         "hands_on": true,
-        "id": "transcriptomics/rna-seq-reads-to-counts",
+        "id": "transcriptomics/srna",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
@@ -264937,66 +272684,45 @@
             "mermaid": false
         },
         "key_points": [
-            "In RNA-seq, reads (FASTQs) are mapped to a reference genome with a spliced aligner (e.g HISAT2, STAR)",
-            "The aligned reads (BAMs) can then be converted to counts",
-            "Many QC steps can be performed to help check the quality of the data",
-            "MultiQC can be used to create a nice summary report of QC information",
-            "The Galaxy Rule-based Uploader, Collections and Workflows can help make analysis more efficient and easier"
+            "Analysis of small RNAs is complex due to the diversity of small RNA subclasses.",
+            "Both alignment to references and transcript quantification approaches are useful for small RNA-seq analyses."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-09",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Learn how RNA-seq reads are converted into counts",
-            "Understand QC steps that can be performed on RNA-seq reads",
-            "Generate interactive reports to summarise QC information with MultiQC",
-            "Use the Galaxy Rule-based Uploader to import FASTQs from URLs",
-            "Make use of Galaxy Collections for a tidy analysis",
-            "Create a Galaxy Workflow that converts RNA-seq reads into counts"
+            "Process small RNA-seq datasets to determine quality and reproducibility.",
+            "Filter out contaminants (e.g. rRNA reads) in small RNA-seq datasets.",
+            "Differentiate between subclasses of small RNAs based on their characteristics.",
+            "Identify differently abundant small RNAs and their targets."
         ],
-        "pageviews": 124667,
-        "pub_date": "2018-09-23",
+        "pageviews": 11082,
+        "pub_date": "2017-06-29",
         "questions": [
-            "How to convert RNA-seq reads into counts?",
-            "How to perform quality control (QC) of RNA-seq reads?",
-            "How to do this analysis efficiently in Galaxy?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "transcriptomics",
-                "tutorials": [
-                    "ref-based"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "collections",
-                    "upload-rules"
-                ],
-                "type": "internal"
-            }
+            "What small RNAs are expressed?",
+            "What RNA features have significantly different numbers of small RNAs targeting them between two conditions?"
         ],
-        "short_id": "T00301",
+        "short_id": "T00307",
         "short_tools": [
-            "picard_MarkDuplicates",
             "hisat2",
-            "multiqc",
-            "rseqc_infer_experiment",
-            "collection_column_join",
-            "featurecounts",
+            "samtool_filter2",
+            "Filter1",
+            "fastq_manipulation",
+            "deseq2",
             "fastqc",
-            "samtools_idxstats",
-            "rseqc_geneBody_coverage",
-            "rseqc_read_distribution",
-            "cutadapt"
+            "salmon",
+            "bedtools_bamtofastq",
+            "trim_galore"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "end-to-end",
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
@@ -265009,11 +272735,6 @@
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -265032,33 +272753,18 @@
             ]
         },
         "symlink": null,
-        "tags": [
-            "collections",
-            "mouse",
-            "QC"
-        ],
         "time_estimation": "3h",
-        "title": "1: RNA-Seq reads to counts",
+        "title": "Differential abundance testing of small RNAs",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4",
-            "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3",
-            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.7+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3",
-            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1",
-            "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1"
+            "Filter1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.8.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.0.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.39",
+            "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3"
         ],
         "topic_name": "transcriptomics",
         "topic_name_human": "Transcriptomics",
@@ -265068,340 +272774,638 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "rna-seq-reads-to-counts",
+        "tutorial_name": "srna",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/srna/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/srna/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/srna/tutorial.json"
         },
-        "version": 33,
+        "version": 26,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 149,
-        "visitors": 65434,
+        "visit_duration": 130,
+        "visitors": 6037,
         "workflows": [
             {
                 "creators": [],
-                "description": "rna-seq-reads-to-counts",
+                "description": "This workflow completes the first part of the small RNA-seq tutorial from read pre-processing to trimming.e",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference genes\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nBAM files\"]\n  2[label=\"Infer Experiment\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"MarkDuplicates\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Samtools idxstats\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"MultiQC\"]\n  2 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"metrics_file\"]\n  4 -> 5 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nrRNA reference FASTA\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmiRNA hairpin reference FASTA\"]\n  3[label=\"FastQC\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Trim Galore!\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"FastQC\"]\n  4 -> 5 [label=\"trimmed_reads_single\"]\n  6[label=\"HISAT\"]\n  4 -> 6 [label=\"trimmed_reads_single\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"Filter SAM or BAM, output SAM or BAM\"]\n  6 -> 7 [label=\"output_alignments\"]\n  8[label=\"Convert from BAM to FastQ\"]\n  7 -> 8 [label=\"output1\"]\n  9[label=\"HISAT\"]\n  8 -> 9 [label=\"output\"]\n  2 -> 9 [label=\"output\"]\n  10[label=\"Filter SAM or BAM, output SAM or BAM\"]\n  9 -> 10 [label=\"output_alignments\"]\n  11[label=\"Convert from BAM to FastQ\"]\n  10 -> 11 [label=\"output1\"]\n  12[label=\"Manipulate FASTQ\"]\n  11 -> 12 [label=\"output\"]\n  13[label=\"Manipulate FASTQ\"]\n  11 -> 13 [label=\"output\"]\n  14[label=\"FastQC\"]\n  12 -> 14 [label=\"output_file\"]\n  15[label=\"FastQC\"]\n  13 -> 15 [label=\"output_file\"]\n}",
                 "history": [
                     {
-                        "hash": "e309846054da31a5946eaf34c1bf8b02771b054c",
-                        "message": "Update qc workflow",
-                        "num": 4,
-                        "short_hash": "e30984605",
-                        "unix": "1605438895"
-                    },
-                    {
-                        "hash": "bf6f08b6a5db96726fa60f5b6cee040a4e40e51d",
-                        "message": "Fix tags attribute",
-                        "num": 3,
-                        "short_hash": "bf6f08b6a",
-                        "unix": "1605332237"
-                    },
-                    {
-                        "hash": "d42f753afbda69d81cf63335037ef57ffe2487af",
-                        "message": "Fix workflow for failing travis test",
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
                         "num": 2,
-                        "short_hash": "d42f753af",
-                        "unix": "1605316521"
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
                     },
                     {
-                        "hash": "cea2aaab2718b8d92d77b9d0f84bdc8d325a46fc",
-                        "message": "Reconfiguration of some content",
+                        "hash": "6efea8d060e13f09bf9d0ea32b07c1eaf3a577d1",
+                        "message": "Move the srna tutorial to transcriptomics topic",
                         "num": 1,
-                        "short_hash": "cea2aaab2",
-                        "unix": "1605176495"
+                        "short_hash": "6efea8d06",
+                        "unix": "1498731718"
                     }
                 ],
                 "inputs": [
                     {
                         "annotation": "",
                         "content_id": null,
-                        "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Reference genes"
+                                "name": "Input Dataset Collection"
                             }
                         ],
-                        "label": "Reference genes",
-                        "name": "Input dataset",
+                        "label": null,
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "bottom": 272.4609375,
-                            "height": 80.95703125,
-                            "left": 658.4765625,
-                            "right": 858.4765625,
-                            "top": 191.50390625,
-                            "width": 200,
-                            "x": 658.4765625,
-                            "y": 191.50390625
+                            "left": 278,
+                            "top": 200.96875
                         },
+                        "tool_errors": null,
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "cb0135e4-38e7-4c4d-9ce8-16edc02f6af9",
+                        "type": "data_collection_input",
+                        "uuid": "5e34fb1f-fa44-4178-9d5e-953d69030004",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "6268565d-6ad3-42ee-b55f-2184412e7468"
+                                "uuid": "12c8979f-7a43-4133-98ac-6b4c1b6d9e57"
                             }
                         ]
                     },
                     {
                         "annotation": "",
                         "content_id": null,
-                        "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "BAM files"
+                                "name": "rRNA reference FASTA"
                             }
                         ],
-                        "label": "BAM files",
-                        "name": "Input dataset collection",
+                        "label": "rRNA reference FASTA",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 490.44921875,
-                            "height": 60.95703125,
-                            "left": 658.4765625,
-                            "right": 858.4765625,
-                            "top": 429.4921875,
-                            "width": 200,
-                            "x": 658.4765625,
-                            "y": 429.4921875
+                            "left": 842.5,
+                            "top": 239
                         },
+                        "tool_errors": null,
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"name\": \"rRNA reference FASTA\"}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "034877ee-f1be-43d8-a5cf-b0a973dc50a4",
+                        "type": "data_input",
+                        "uuid": "01fce37f-1a11-4d1e-b039-6d53ba373064",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "2a973089-9bcd-49e0-8a37-e1ef0bdad4fd"
+                                "uuid": "6fafacef-3b18-425e-9f15-e717d0febbdc"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Be sure to use hairpin sequences, not just mature miRNA sequences.",
+                        "content_id": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Be sure to use hairpin sequences, not just mature miRNA sequences.",
+                                "name": "miRNA hairpin reference FASTA"
+                            }
+                        ],
+                        "label": "miRNA hairpin reference FASTA",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 1159.5,
+                            "top": 232
+                        },
+                        "tool_errors": null,
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"miRNA hairpin reference FASTA\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "cba8d787-dc52-4ed6-bc9a-d697db038495",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "c8ab4106-9b66-4c54-8d62-27b370fbff01"
                             }
                         ]
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nReference genes\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nBAM files\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Infer Experiment\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"MarkDuplicates\"];\n  1 -->|output| 3;\n  4[\"Samtools idxstats\"];\n  1 -->|output| 4;\n  5[\"MultiQC\"];\n  2 -->|output| 5;\n  3 -->|metrics_file| 5;\n  4 -->|output| 5;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "QC report",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nrRNA reference FASTA\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nmiRNA hairpin reference FASTA\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"FastQC\"];\n  0 -->|output| 3;\n  4[\"Trim Galore!\"];\n  0 -->|output| 4;\n  5[\"FastQC\"];\n  4 -->|trimmed_reads_single| 5;\n  6[\"HISAT\"];\n  4 -->|trimmed_reads_single| 6;\n  1 -->|output| 6;\n  7[\"Filter SAM or BAM, output SAM or BAM\"];\n  6 -->|output_alignments| 7;\n  8[\"Convert from BAM to FastQ\"];\n  7 -->|output1| 8;\n  9[\"HISAT\"];\n  8 -->|output| 9;\n  2 -->|output| 9;\n  10[\"Filter SAM or BAM, output SAM or BAM\"];\n  9 -->|output_alignments| 10;\n  11[\"Convert from BAM to FastQ\"];\n  10 -->|output1| 11;\n  12[\"Manipulate FASTQ\"];\n  11 -->|output| 12;\n  13[\"Manipulate FASTQ\"];\n  11 -->|output| 13;\n  14[\"FastQC\"];\n  12 -->|output_file| 14;\n  15[\"FastQC\"];\n  13 -->|output_file| 15;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "sRNA Seq Step 1: Read Pre Processing And Removal Of Artifacts (no Grooming)",
                 "outputs": [
                     {
                         "annotation": "",
                         "content_id": null,
-                        "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Reference genes"
+                                "name": "Input Dataset Collection"
                             }
                         ],
-                        "label": "Reference genes",
-                        "name": "Input dataset",
+                        "label": null,
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "bottom": 272.4609375,
-                            "height": 80.95703125,
-                            "left": 658.4765625,
-                            "right": 858.4765625,
-                            "top": 191.50390625,
-                            "width": 200,
-                            "x": 658.4765625,
-                            "y": 191.50390625
+                            "left": 278,
+                            "top": 200.96875
                         },
+                        "tool_errors": null,
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "cb0135e4-38e7-4c4d-9ce8-16edc02f6af9",
+                        "type": "data_collection_input",
+                        "uuid": "5e34fb1f-fa44-4178-9d5e-953d69030004",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "6268565d-6ad3-42ee-b55f-2184412e7468"
+                                "uuid": "12c8979f-7a43-4133-98ac-6b4c1b6d9e57"
                             }
                         ]
                     },
                     {
                         "annotation": "",
                         "content_id": null,
-                        "errors": null,
                         "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "BAM files"
+                                "name": "rRNA reference FASTA"
                             }
                         ],
-                        "label": "BAM files",
-                        "name": "Input dataset collection",
+                        "label": "rRNA reference FASTA",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "bottom": 490.44921875,
-                            "height": 60.95703125,
-                            "left": 658.4765625,
-                            "right": 858.4765625,
-                            "top": 429.4921875,
-                            "width": 200,
-                            "x": 658.4765625,
-                            "y": 429.4921875
+                            "left": 842.5,
+                            "top": 239
                         },
+                        "tool_errors": null,
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"name\": \"rRNA reference FASTA\"}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "034877ee-f1be-43d8-a5cf-b0a973dc50a4",
+                        "type": "data_input",
+                        "uuid": "01fce37f-1a11-4d1e-b039-6d53ba373064",
                         "workflow_outputs": [
                             {
                                 "label": null,
                                 "output_name": "output",
-                                "uuid": "2a973089-9bcd-49e0-8a37-e1ef0bdad4fd"
+                                "uuid": "6fafacef-3b18-425e-9f15-e717d0febbdc"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Be sure to use hairpin sequences, not just mature miRNA sequences.",
+                        "content_id": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Be sure to use hairpin sequences, not just mature miRNA sequences.",
+                                "name": "miRNA hairpin reference FASTA"
+                            }
+                        ],
+                        "label": "miRNA hairpin reference FASTA",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 1159.5,
+                            "top": 232
+                        },
+                        "tool_errors": null,
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"miRNA hairpin reference FASTA\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "cba8d787-dc52-4ed6-bc9a-d697db038495",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "c8ab4106-9b66-4c54-8d62-27b370fbff01"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-                        "errors": null,
-                        "id": 5,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2",
+                        "id": 4,
                         "input_connections": {
-                            "results_0|software_cond|output_0|type|input": {
-                                "id": 2,
-                                "output_name": "output"
-                            },
-                            "results_1|software_cond|output_0|input": {
-                                "id": 3,
-                                "output_name": "metrics_file"
-                            },
-                            "results_2|software_cond|output_0|type|input": {
-                                "id": 4,
+                            "singlePaired|input_singles": {
+                                "id": 0,
                                 "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Trim Galore!",
+                                "name": "singlePaired"
+                            }
+                        ],
                         "label": null,
-                        "name": "MultiQC",
+                        "name": "Trim Galore!",
                         "outputs": [
                             {
-                                "name": "stats",
+                                "name": "trimmed_reads_paired_collection",
                                 "type": "input"
                             },
                             {
-                                "name": "plots",
+                                "name": "trimmed_reads_unpaired_collection",
                                 "type": "input"
                             },
                             {
-                                "name": "html_report",
+                                "name": "trimmed_reads_single",
+                                "type": "fastqsanger"
+                            },
+                            {
+                                "name": "trimmed_reads_pair1",
+                                "type": "fastqsanger"
+                            },
+                            {
+                                "name": "trimmed_reads_pair2",
+                                "type": "fastqsanger"
+                            },
+                            {
+                                "name": "unpaired_reads_1",
+                                "type": "fastqsanger"
+                            },
+                            {
+                                "name": "unpaired_reads_2",
+                                "type": "fastqsanger"
+                            },
+                            {
+                                "name": "report_file",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 549.5,
+                            "top": 238
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActiontrimmed_reads_pair1": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "trimmed_reads_pair1"
+                            },
+                            "HideDatasetActiontrimmed_reads_pair2": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "trimmed_reads_pair2"
+                            },
+                            "HideDatasetActiontrimmed_reads_paired_collection": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "trimmed_reads_paired_collection"
+                            },
+                            "HideDatasetActiontrimmed_reads_unpaired_collection": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "trimmed_reads_unpaired_collection"
+                            },
+                            "HideDatasetActionunpaired_reads_1": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "unpaired_reads_1"
+                            },
+                            "HideDatasetActionunpaired_reads_2": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "unpaired_reads_2"
+                            },
+                            "RenameDatasetActiontrimmed_reads_single": {
+                                "action_arguments": {
+                                    "newname": "Trimmed reads"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "trimmed_reads_single"
+                            }
+                        },
+                        "tool_errors": null,
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f1e71aeaa923",
+                            "name": "trim_galore",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"params\": \"{\\\"min_length\\\": \\\"12\\\", \\\"stringency\\\": \\\"1\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"retain_unpaired\\\": {\\\"retain_unpaired_select\\\": \\\"no_output\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 1, \\\"report\\\": \\\"true\\\", \\\"settingsType\\\": \\\"custom\\\", \\\"quality\\\": \\\"0\\\", \\\"clip_R1\\\": \\\"\\\", \\\"clip_R2\\\": \\\"\\\"}\", \"rrbs\": \"{\\\"settingsType\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"three_prime_clip_R1\\\": \\\"\\\", \\\"trimming\\\": {\\\"trimming_select\\\": \\\"\\\", \\\"__current_case__\\\": 0}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_singles\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\"}",
+                        "tool_version": "0.4.2",
+                        "type": "tool",
+                        "uuid": "21f6bafb-48bb-4f7d-8543-8b8b96345d1a",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "report_file",
+                                "uuid": "8d621eea-f61d-4780-b3d7-d1de6a7a9e12"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "trimmed_reads_single",
+                                "uuid": "d148afd4-9b94-4ef6-9856-98963e71ef6d"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65",
+                        "id": 5,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 4,
+                                "output_name": "trimmed_reads_single"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "contaminants"
+                            },
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "limits"
+                            },
+                            {
+                                "description": "runtime parameter for tool FastQC",
+                                "name": "input_file"
+                            }
+                        ],
+                        "label": null,
+                        "name": "FastQC",
+                        "outputs": [
+                            {
+                                "name": "html_file",
                                 "type": "html"
+                            },
+                            {
+                                "name": "text_file",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 790.44921875,
-                            "height": 391.953125,
-                            "left": 1234.4921875,
-                            "right": 1434.4921875,
-                            "top": 398.49609375,
-                            "width": 200,
-                            "x": 1234.4921875,
-                            "y": 398.49609375
+                            "left": 548.5,
+                            "top": 615
                         },
                         "post_job_actions": {
-                            "HideDatasetActionplots": {
+                            "HideDatasetActiontext_file": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "plots"
+                                "output_name": "text_file"
+                            },
+                            "RenameDatasetActionhtml_file": {
+                                "action_arguments": {
+                                    "newname": "FastQC on Groomed and Trimmed data"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "html_file"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "tool_errors": null,
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65",
                         "tool_shed_repository": {
-                            "changeset_revision": "5e33b465d8d5",
-                            "name": "multiqc",
+                            "changeset_revision": "3fdc1a74d866",
+                            "name": "fastqc",
+                            "owner": "devteam",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": 0, \"contaminants\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"limits\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "0.65",
+                        "type": "tool",
+                        "uuid": "972f64c0-14f5-460e-9d30-27faa6df86d4",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "html_file",
+                                "uuid": "da777968-7f09-4ba1-8ff0-1c9358de161c"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0",
+                        "id": 8,
+                        "input_connections": {
+                            "input": {
+                                "id": 7,
+                                "output_name": "output1"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Convert from BAM to FastQ",
+                                "name": "input"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Convert from BAM to FastQ",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "fastq"
+                            },
+                            {
+                                "name": "output2",
+                                "type": "fastq2"
+                            }
+                        ],
+                        "position": {
+                            "left": 859,
+                            "top": 763
+                        },
+                        "post_job_actions": {
+                            "ChangeDatatypeActionoutput": {
+                                "action_arguments": {
+                                    "newtype": "fastqsanger"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "output"
+                            },
+                            "HideDatasetActionoutput2": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output2"
+                            },
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Non-rRNA reads (FASTQ)"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_errors": null,
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "d25966c8ddeb",
+                            "name": "bedtools",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"comment\": \"\", \"flat\": \"false\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"rseqc\", \"__current_case__\": 21, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"infer_experiment\", \"__current_case__\": 2, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"RuntimeValue\"}}]}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 23, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"idxstats\", \"__current_case__\": 2, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8+galaxy1",
+                        "tool_state": "{\"fq2\": \"\\\"false\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"tags\": \"\\\"false\\\"\"}",
+                        "tool_version": "2.24.0",
                         "type": "tool",
-                        "uuid": "101e4661-c986-4bde-90c1-835d15c35898",
+                        "uuid": "697122c3-2a2b-4e20-aae7-9179d7e8d4a6",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "stats",
-                                "uuid": "3fcde9be-0512-43a3-ac61-c34102116b38"
+                                "output_name": "output",
+                                "uuid": "9ef5503f-5cfa-4195-9985-4f1743a556cc"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0",
+                        "id": 11,
+                        "input_connections": {
+                            "input": {
+                                "id": 10,
+                                "output_name": "output1"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Convert from BAM to FastQ",
+                                "name": "input"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Convert from BAM to FastQ",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "fastq"
+                            },
+                            {
+                                "name": "output2",
+                                "type": "fastq2"
+                            }
+                        ],
+                        "position": {
+                            "left": 1156,
+                            "top": 769
+                        },
+                        "post_job_actions": {
+                            "ChangeDatatypeActionoutput": {
+                                "action_arguments": {
+                                    "newtype": "fastqsanger"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "output"
+                            },
+                            "ChangeDatatypeActionoutput2": {
+                                "action_arguments": {
+                                    "newtype": "fastqsanger"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "output2"
+                            },
+                            "HideDatasetActionoutput2": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output2"
                             },
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Non-r/miRNA reads (FASTQ)"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            },
+                            "RenameDatasetActionoutput2": {
+                                "action_arguments": {
+                                    "newname": "Non-r/miRNA reads (FASTQ)"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output2"
+                            }
+                        },
+                        "tool_errors": null,
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "d25966c8ddeb",
+                            "name": "bedtools",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"fq2\": \"\\\"false\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"tags\": \"\\\"false\\\"\"}",
+                        "tool_version": "2.24.0",
+                        "type": "tool",
+                        "uuid": "2af3a8c2-4056-4922-9353-c693d78230c9",
+                        "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "html_report",
-                                "uuid": "dd4f76fb-bf9c-4825-ba7b-8d6b06a648d9"
+                                "output_name": "output",
+                                "uuid": "cd5b8c93-9ea0-422b-8f0a-9643961b1ab4"
                             }
                         ]
                     }
                 ],
-                "parent_id": "transcriptomics/rna-seq-reads-to-counts",
-                "path": "topics/transcriptomics/tutorials/rna-seq-reads-to-counts/workflows/qc_report.ga",
+                "parent_id": "transcriptomics/srna",
+                "path": "topics/transcriptomics/tutorials/srna/workflows/sRNA_seq_Step_1_Read_preprocessing_and_removal_of_artifacts.ga",
                 "tags": [
                     "transcriptomics"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "QC report",
+                "title": "sRNA Seq Step 1: Read Pre Processing And Removal Of Artifacts (no Grooming)",
                 "topic_id": "transcriptomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-rna-seq-reads-to-counts/versions/qc-report",
-                "tutorial_id": "rna-seq-reads-to-counts",
-                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/workflows/qc_report.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/workflows/qc_report.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-srna/versions/srna-seq-step-1-read-preprocessing-and-removal-of-artifacts",
+                "tutorial_id": "srna",
+                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/srna/workflows/sRNA_seq_Step_1_Read_preprocessing_and_removal_of_artifacts.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/srna/workflows/sRNA_seq_Step_1_Read_preprocessing_and_removal_of_artifacts.html",
                 "version": 2,
-                "wfid": "transcriptomics-rna-seq-reads-to-counts",
-                "wfname": "qc-report",
-                "workflow": "qc_report.ga",
+                "wfid": "transcriptomics-srna",
+                "wfname": "srna-seq-step-1-read-preprocessing-and-removal-of-artifacts",
+                "workflow": "sRNA_seq_Step_1_Read_preprocessing_and_removal_of_artifacts.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3"
                 ],
-                "workflowhub_id": "1299"
+                "workflowhub_id": "1281"
             },
             {
                 "creators": [],
-                "description": "RNA-Seq reads to counts",
+                "description": "This workflow completes the second part of the sRNA-seq tutorial from transcript quantification through differential abundance testing.",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput FASTQs collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput Reference gene BED\"]\n  10[label=\"Infer Experiment\"]\n  5 -> 10 [label=\"output_alignments\"]\n  1 -> 10 [label=\"output\"]\n  11[label=\"Read Distribution\"]\n  5 -> 11 [label=\"output_alignments\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"Column Join\"]\n  6 -> 12 [label=\"output_short\"]\n  13[label=\"MultiQC\"]\n  4 -> 13 [label=\"text_file\"]\n  3 -> 13 [label=\"report\"]\n  10 -> 13 [label=\"output\"]\n  7 -> 13 [label=\"metrics_file\"]\n  8 -> 13 [label=\"output\"]\n  9 -> 13 [label=\"outputtxt\"]\n  11 -> 13 [label=\"output\"]\n  6 -> 13 [label=\"output_summary\"]\n  5 -> 13 [label=\"summary_file\"]\n  2[label=\"FastQC raw reads\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Cutadapt\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"FastQC post QC\"]\n  3 -> 4 [label=\"out1\"]\n  5[label=\"HISAT2\"]\n  3 -> 5 [label=\"out1\"]\n  6[label=\"featureCounts\"]\n  5 -> 6 [label=\"output_alignments\"]\n  7[label=\"MarkDuplicates\"]\n  5 -> 7 [label=\"output_alignments\"]\n  8[label=\"Samtools idxstats\"]\n  5 -> 8 [label=\"output_alignments\"]\n  9[label=\"Gene Body Coverage BAM\"]\n  5 -> 9 [label=\"output_alignments\"]\n  1 -> 9 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nDataset collection - Control\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDataset - Ref Txome\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nDataset collection - Case\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  4[label=\"Salmon\"]\n  1 -> 4 [label=\"output\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"Salmon\"]\n  1 -> 5 [label=\"output\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Salmon\"]\n  1 -> 6 [label=\"output\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"Salmon\"]\n  1 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  8[label=\"DESeq2\"]\n  6 -> 8 [label=\"output_quant\"]\n  4 -> 8 [label=\"output_quant\"]\n  3 -> 8 [label=\"output\"]\n  9[label=\"DESeq2\"]\n  7 -> 9 [label=\"output_quant\"]\n  5 -> 9 [label=\"output_quant\"]\n  3 -> 9 [label=\"output\"]\n  10[label=\"Filter\"]\n  8 -> 10 [label=\"deseq_out\"]\n  11[label=\"Filter\"]\n  9 -> 11 [label=\"deseq_out\"]\n}",
                 "history": [
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 4,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
                     {
                         "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
                         "message": "Workflow renaming",
@@ -265410,103 +273414,157 @@
                         "unix": "1579084895"
                     },
                     {
-                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
-                        "message": "Changed format of workflows",
+                        "hash": "93d49854590788054c478350af91ebe28162c08f",
+                        "message": "Update Salmon calls",
                         "num": 2,
-                        "short_hash": "361236c41",
-                        "unix": "1554368414"
+                        "short_hash": "93d498545",
+                        "unix": "1499979115"
                     },
                     {
-                        "hash": "0ea8c79012ba1b18d3f79be0ff2e2b826092f5e2",
-                        "message": "Rename tutorial and image folders to the updated titles",
+                        "hash": "6efea8d060e13f09bf9d0ea32b07c1eaf3a577d1",
+                        "message": "Move the srna tutorial to transcriptomics topic",
                         "num": 1,
-                        "short_hash": "0ea8c7901",
-                        "unix": "1546155649"
+                        "short_hash": "6efea8d06",
+                        "unix": "1498731718"
                     }
                 ],
                 "inputs": [
                     {
                         "annotation": "",
                         "content_id": null,
-                        "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "Input FASTQs collection",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Input Dataset Collection - Control RNAi sRNA reads"
+                            }
+                        ],
+                        "label": "Dataset collection - Control",
                         "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 199.9921875,
-                            "top": 199.9921875
+                            "left": 217,
+                            "top": 436
                         },
+                        "tool_errors": null,
                         "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list\"}",
+                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection - Control RNAi sRNA reads\"}",
                         "tool_version": null,
                         "type": "data_collection_input",
-                        "uuid": "015f389e-94eb-40f2-82c8-267093ca8c8a",
+                        "uuid": "91427be9-059a-4e6c-89e9-b4cfea01639b",
                         "workflow_outputs": []
                     },
                     {
                         "annotation": "",
                         "content_id": null,
-                        "errors": null,
                         "id": 1,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "Input Reference gene BED",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Input Dataset - Reference Transcriptome"
+                            }
+                        ],
+                        "label": "Dataset - Ref Txome",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 199.9921875,
-                            "top": 290.015625
+                            "left": 221.5,
+                            "top": 524
                         },
+                        "tool_errors": null,
                         "tool_id": null,
-                        "tool_state": "{}",
+                        "tool_state": "{\"name\": \"Input Dataset - Reference Transcriptome\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "dc707df4-3c9d-4d76-98a8-53b60cc2f41d",
+                        "uuid": "52018b9a-9b80-445d-8a0b-6ce9d3b3b47c",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Input Dataset Collection - Case RNAi sRNA reads"
+                            }
+                        ],
+                        "label": "Dataset collection - Case",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 223,
+                            "top": 612
+                        },
+                        "tool_errors": null,
+                        "tool_id": null,
+                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection - Case RNAi sRNA reads\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "c26c73ec-cd58-4674-95be-90ca097afc20",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "Tab-delimited",
+                        "content_id": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Tab-delimited",
+                                "name": "Tx2Gene reference"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 1104,
+                            "top": 512
+                        },
+                        "tool_errors": null,
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Tx2Gene reference\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "dcb51b30-6cea-43c4-8399-b310f04fe8d9",
                         "workflow_outputs": []
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput FASTQs collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput Reference gene BED\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Infer Experiment\"];\n  5 -->|output_alignments| 10;\n  1 -->|output| 10;\n  11[\"Read Distribution\"];\n  5 -->|output_alignments| 11;\n  1 -->|output| 11;\n  12[\"Column Join\"];\n  6 -->|output_short| 12;\n  13[\"MultiQC\"];\n  4 -->|text_file| 13;\n  3 -->|report| 13;\n  10 -->|output| 13;\n  7 -->|metrics_file| 13;\n  8 -->|output| 13;\n  9 -->|outputtxt| 13;\n  11 -->|output| 13;\n  6 -->|output_summary| 13;\n  5 -->|summary_file| 13;\n  2[\"FastQC raw reads\"];\n  0 -->|output| 2;\n  3[\"Cutadapt\"];\n  0 -->|output| 3;\n  4[\"FastQC post QC\"];\n  3 -->|out1| 4;\n  5[\"HISAT2\"];\n  3 -->|out1| 5;\n  6[\"featureCounts\"];\n  5 -->|output_alignments| 6;\n  7[\"MarkDuplicates\"];\n  5 -->|output_alignments| 7;\n  8[\"Samtools idxstats\"];\n  5 -->|output_alignments| 8;\n  9[\"Gene Body Coverage BAM\"];\n  5 -->|output_alignments| 9;\n  1 -->|output| 9;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "RNA Seq Reads To Counts",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nDataset collection - Control\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nDataset - Ref Txome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nDataset collection - Case\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Salmon\"];\n  1 -->|output| 4;\n  0 -->|output| 4;\n  5[\"Salmon\"];\n  1 -->|output| 5;\n  0 -->|output| 5;\n  6[\"Salmon\"];\n  1 -->|output| 6;\n  2 -->|output| 6;\n  7[\"Salmon\"];\n  1 -->|output| 7;\n  2 -->|output| 7;\n  8[\"DESeq2\"];\n  6 -->|output_quant| 8;\n  4 -->|output_quant| 8;\n  3 -->|output| 8;\n  9[\"DESeq2\"];\n  7 -->|output_quant| 9;\n  5 -->|output_quant| 9;\n  3 -->|output| 9;\n  10[\"Filter\"];\n  8 -->|deseq_out| 10;\n  11[\"Filter\"];\n  9 -->|deseq_out| 11;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "sRNA Seq Step 2: Salmon And DESeq2",
                 "outputs": [],
-                "parent_id": "transcriptomics/rna-seq-reads-to-counts",
-                "path": "topics/transcriptomics/tutorials/rna-seq-reads-to-counts/workflows/rna-seq-reads-to-counts.ga",
+                "parent_id": "transcriptomics/srna",
+                "path": "topics/transcriptomics/tutorials/srna/workflows/sRNA_seq_Step_2_Salmon_and_DESeq2.ga",
                 "tags": [
                     "transcriptomics"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "RNA Seq Reads To Counts",
+                "title": "sRNA Seq Step 2: Salmon And DESeq2",
                 "topic_id": "transcriptomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-rna-seq-reads-to-counts/versions/rna-seq-reads-to-counts",
-                "tutorial_id": "rna-seq-reads-to-counts",
-                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/workflows/rna-seq-reads-to-counts.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/workflows/rna-seq-reads-to-counts.html",
-                "version": 4,
-                "wfid": "transcriptomics-rna-seq-reads-to-counts",
-                "wfname": "rna-seq-reads-to-counts",
-                "workflow": "rna-seq-reads-to-counts.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-srna/versions/srna-seq-step-2-salmon-and-deseq2",
+                "tutorial_id": "srna",
+                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/srna/workflows/sRNA_seq_Step_2_Salmon_and_DESeq2.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/srna/workflows/sRNA_seq_Step_2_Salmon_and_DESeq2.html",
+                "version": 3,
+                "wfid": "transcriptomics-srna",
+                "wfname": "srna-seq-step-2-salmon-and-deseq2",
+                "workflow": "sRNA_seq_Step_2_Salmon_and_DESeq2.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6",
-                    "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3",
-                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3",
-                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1",
-                    "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1"
+                    "Filter1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.8.2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.39"
                 ],
-                "workflowhub_id": "1295"
+                "workflowhub_id": "1279"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/4249555"
+        "zenodo_link": "https://zenodo.org/record/826906"
     },
     {
         "admin_install": {
@@ -265683,14 +273741,14 @@
         "draft": true,
         "edam_operation": [
             "Sequencing quality control",
-            "De-novo assembly",
-            "Sequence composition calculation",
             "de Novo sequencing",
-            "Transcriptome assembly",
-            "Coding region prediction",
+            "De-novo assembly",
+            "Statistical calculation",
             "Validation",
+            "Transcriptome assembly",
+            "Sequence composition calculation",
             "Gene functional annotation",
-            "Statistical calculation"
+            "Coding region prediction"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -265701,6 +273759,7 @@
         "hands_on": true,
         "id": "transcriptomics/full-de-novo",
         "inexact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.no",
             "UseGalaxy.org.au"
@@ -265722,7 +273781,7 @@
             "They are single sentences describing what a learner should be able to do once they have completed the tutorial",
             "You can use Bloom's Taxonomy to write effective learning objectives"
         ],
-        "pageviews": 21493,
+        "pageviews": 21999,
         "pub_date": "2020-02-13",
         "questions": [
             "Which biological questions are addressed by the tutorial?",
@@ -265730,20 +273789,20 @@
         ],
         "short_id": "T00290",
         "short_tools": [
-            "trinity",
-            "trinity_analyze_diff_expr",
-            "multiqc",
+            "trinotate",
+            "transdecoder",
+            "trinity_abundance_estimates_to_matrix",
+            "describe_samples",
+            "trinity_run_de_analysis",
+            "trinity_samples_qccheck",
             "trinity_filter_low_expr_transcripts",
             "trinity_align_and_estimate_abundance",
+            "multiqc",
+            "trinity_analyze_diff_expr",
+            "trinity",
             "trinity_contig_exn50_statistic",
-            "trinity_samples_qccheck",
-            "trinity_run_de_analysis",
-            "describe_samples",
-            "transdecoder",
-            "fastqc",
-            "trinity_abundance_estimates_to_matrix",
             "trinity_define_clusters_by_cutting_tree",
-            "trinotate",
+            "fastqc",
             "trimmomatic"
         ],
         "slides": false,
@@ -265757,6 +273816,11 @@
                 }
             ],
             "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -265817,7 +273881,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 151,
-        "visitors": 10954,
+        "visitors": 11314,
         "workflows": [
             {
                 "creators": [],
@@ -265940,7 +274004,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  20[\"Trinotate\"];\n  18 -->|transdecoder_pep| 20;\n  21[\"Differential expression analysis\"];\n  19 -->|TPM_no_norm_gene| 21;\n  3 -->|output| 21;\n  22[\"Extract and cluster differentially expressed transcripts\"];\n  21 -->|DE_results| 22;\n  19 -->|norm_TMM| 22;\n  3 -->|output| 22;\n  23[\"Partition genes into expression clusters\"];\n  22 -->|rdata| 23;\n  1[\"\u2139\ufe0f Input Collection\\nCollection of R2 reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  0[\"\u2139\ufe0f Input Collection\\nCollection of R1 reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nSamples description\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  2[\"Describe samples\"];\n  5[\"FastQC\"];\n  1 -->|output| 5;\n  4[\"FastQC\"];\n  0 -->|output| 4;\n  7[\"MultiQC\"];\n  5 -->|text_file| 7;\n  4 -->|text_file| 7;\n  6[\"Trimmomatic\"];\n  0 -->|output| 6;\n  1 -->|output| 6;\n  9[\"FastQC\"];\n  6 -->|fastq_out_r2_paired| 9;\n  8[\"FastQC\"];\n  6 -->|fastq_out_r1_paired| 8;\n  11[\"MultiQC\"];\n  9 -->|text_file| 11;\n  8 -->|text_file| 11;\n  10[\"Trinity\"];\n  6 -->|fastq_out_r2_paired| 10;\n  6 -->|fastq_out_r1_paired| 10;\n  13[\"Build expression matrix\"];\n  12 -->|genes_counts_rsem| 13;\n  12[\"Align reads and estimate abundance\"];\n  10 -->|assembled_transcripts| 12;\n  6 -->|fastq_out_r2_paired| 12;\n  6 -->|fastq_out_r1_paired| 12;\n  15[\"Filter low expression transcripts\"];\n  10 -->|assembled_transcripts| 15;\n  13 -->|TPM_no_norm_gene| 15;\n  14[\"RNASeq samples quality check\"];\n  13 -->|trans_counts| 14;\n  3 -->|output| 14;\n  17[\"Align reads and estimate abundance\"];\n  15 -->|filtered| 17;\n  6 -->|fastq_out_r1_paired| 17;\n  6 -->|fastq_out_r2_paired| 17;\n  16[\"Compute contig Ex90N50 statistic and Ex90 transcript count\"];\n  10 -->|assembled_transcripts| 16;\n  13 -->|trans_counts| 16;\n  19[\"Build expression matrix\"];\n  17 -->|genes_counts_rsem| 19;\n  18[\"TransDecoder\"];\n  15 -->|filtered| 18;",
-                "modified": "2024-08-18 00:06:25 +0000",
+                "modified": "2024-10-02 12:08:11 +0000",
                 "name": "trinity NG",
                 "outputs": [
                     {
@@ -266593,20 +274657,6 @@
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
             "tools": [
-                {
-                    "name": "salmon",
-                    "owner": "bgruening",
-                    "revisions": "e3d32471da11",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "trim_galore",
-                    "owner": "bgruening",
-                    "revisions": "949f01671246",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
                 {
                     "name": "fastqc",
                     "owner": "devteam",
@@ -266615,79 +274665,59 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "filter_by_fasta_ids",
-                    "owner": "galaxyp",
-                    "revisions": "3c623e81be77",
-                    "tool_panel_section_label": "Proteomics",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "deseq2",
+                    "name": "chira_collapse",
                     "owner": "iuc",
-                    "revisions": "6a3a025714d3",
+                    "revisions": "2b2bfeda00d0",
                     "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "multiqc",
+                    "name": "chira_extract",
                     "owner": "iuc",
-                    "revisions": "b2f1f75d49c4",
-                    "tool_panel_section_label": "Quality Control",
+                    "revisions": "e7ee3aadf1a5",
+                    "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "multiqc",
+                    "name": "chira_map",
                     "owner": "iuc",
-                    "revisions": "5e33b465d8d5",
-                    "tool_panel_section_label": "Quality Control",
+                    "revisions": "95ddee768b61",
+                    "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sample_seqs",
-                    "owner": "peterjc",
-                    "revisions": "7c40a1fbc82e",
-                    "tool_panel_section_label": "Filter and Sort",
+                    "name": "chira_merge",
+                    "owner": "iuc",
+                    "revisions": "6492560fe1b4",
+                    "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mirdeep2_mapper",
-                    "owner": "rnateam",
-                    "revisions": "a8d24f4b6d95",
+                    "name": "chira_quantify",
+                    "owner": "iuc",
+                    "revisions": "06ac35533793",
                     "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mirdeep2_quantifier",
-                    "owner": "rnateam",
-                    "revisions": "d5ea61ff12eb",
-                    "tool_panel_section_label": "RNA Analysis",
+                    "name": "query_tabular",
+                    "owner": "iuc",
+                    "revisions": "33d61c89fb8d",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "targetfinder",
-                    "owner": "rnateam",
-                    "revisions": "c9d56748fbde",
-                    "tool_panel_section_label": "RNA Analysis",
+                    "name": "cutadapt",
+                    "owner": "lparsons",
+                    "revisions": "49370cb85f0f",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: salmon\n  owner: bgruening\n  revisions: e3d32471da11\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trim_galore\n  owner: bgruening\n  revisions: 949f01671246\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filter_by_fasta_ids\n  owner: galaxyp\n  revisions: 3c623e81be77\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deseq2\n  owner: iuc\n  revisions: 6a3a025714d3\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: b2f1f75d49c4\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 5e33b465d8d5\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sample_seqs\n  owner: peterjc\n  revisions: 7c40a1fbc82e\n  tool_panel_section_label: Filter and Sort\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mirdeep2_mapper\n  owner: rnateam\n  revisions: a8d24f4b6d95\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mirdeep2_quantifier\n  owner: rnateam\n  revisions: d5ea61ff12eb\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: targetfinder\n  owner: rnateam\n  revisions: c9d56748fbde\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chira_collapse\n  owner: iuc\n  revisions: 2b2bfeda00d0\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chira_extract\n  owner: iuc\n  revisions: e7ee3aadf1a5\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chira_map\n  owner: iuc\n  revisions: 95ddee768b61\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chira_merge\n  owner: iuc\n  revisions: 6492560fe1b4\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: chira_quantify\n  owner: iuc\n  revisions: 06ac35533793\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: query_tabular\n  owner: iuc\n  revisions: 33d61c89fb8d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 49370cb85f0f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-interactome/tutorial.json",
         "contributors": [
-            {
-                "elixir_node": "de",
-                "former_affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "gallardoalba",
-                "joined": "2020-11",
-                "name": "Crist\u00f3bal Gallardo",
-                "orcid": "0000-0002-5752-2155",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
-            },
             {
                 "affiliations": [
                     "uni-freiburg",
@@ -266699,139 +274729,84 @@
                 "orcid": "0000-0002-5192-126X",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
-            },
-            {
-                "email": "beatrizserrano.galaxy@gmail.com",
-                "id": "beatrizserrano",
-                "joined": "2020-07",
-                "linkedin": "beatriz-serrano",
-                "matrix": "beatrizserrano:matrix.org",
-                "name": "Beatriz Serrano-Solano",
-                "orcid": "0000-0002-5862-6132",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/beatrizserrano/",
-                "twitter": "BSerranoSolano",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/beatrizserrano.json"
             }
         ],
-        "dir": "topics/transcriptomics/tutorials/mirna-target-finder",
+        "dir": "topics/transcriptomics/tutorials/rna-interactome",
         "edam_operation": [
+            "Statistical calculation",
+            "Sequence trimming",
             "Sequencing quality control",
-            "Primer removal",
             "Sequence composition calculation",
             "Read pre-processing",
-            "RNA-Seq quantification",
-            "Gene expression analysis",
-            "Validation",
-            "Sequence trimming",
-            "Differential gene expression analysis",
-            "RNA-Seq analysis",
-            "Statistical calculation"
+            "Primer removal"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org.au"
+            "UseGalaxy.be",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "transcriptomics/mirna-target-finder",
+        "id": "transcriptomics/rna-interactome",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.no"
+            "UseGalaxy.eu",
+            "UseGalaxy.org.au"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "MiRDeep2 in combination with the PmiREN database allows to quantify miRNA expression in plants",
-            "The use of the Salmon tool and the AtRTD2 transcriptome allows rapid and accurate quantification of transcripts in _Arabidopsis_",
-            "The combination of differential expression analysis and the TargetFinder tool is an effective strategy for the identification of miRNA target genes"
+            "Choosing the correct alignment parameters is one of the imporatant factor in the analysis.",
+            "For poorly annotated organisms use reference genome instead of trascriptome."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-09",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Perform miRNA differential expression analysis",
-            "Understand the quasi-mapping-based Salmon method for quantifying the expression of transcripts using RNA-Seq data",
-            "Idenfity potential miRNAs involved in brassinosteroid-mediated regulation networks"
+            "Quality control and data preparation",
+            "Mapping chimeric reads",
+            "Quantification of the mapped loci",
+            "Visualization and filtering of results"
         ],
-        "pageviews": 5219864,
-        "pub_date": "2021-04-08",
+        "pageviews": 1935,
+        "pub_date": "2020-03-23",
         "questions": [
-            "Which miRNAs are upregulated in response to brassinosteroids?",
-            "Which genes are potential target of brassinosteroid-induced miRNAs?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "gallardoalba"
-                ],
-                "date": "2021-07-25",
-                "galaxy_version": "21.05",
-                "length": "1H10M",
-                "speakers": [
-                    "gallardoalba"
-                ],
-                "youtube_id": "wS1X_0Mgw7M"
-            }
+            "What are the difficulties in mapping chimeric reads from RNA interactome data?",
+            "How multi mapping is a big problem in these datasets?",
+            "How to filter for meaningful results from large analysis output files?"
         ],
-        "short_id": "T00292",
+        "short_id": "T00296",
         "short_tools": [
-            "cat1",
-            "multiqc",
-            "filter_by_fasta_ids",
-            "targetfinder",
-            "sort1",
-            "sample_seqs",
-            "Cut1",
+            "chira_merge",
+            "chira_quantify",
+            "query_tabular",
+            "cutadapt",
+            "chira_map",
+            "chira_collapse",
             "fastqc",
-            "salmon",
-            "Filter1",
-            "deseq2",
-            "rbc_mirdeep2_mapper",
-            "rbc_mirdeep2_quantifier",
-            "__MERGE_COLLECTION__",
-            "trim_galore"
-        ],
-        "slides": true,
-        "slides_recordings": [
-            {
-                "captioners": [
-                    "gallardoalba"
-                ],
-                "date": "2021-04-20",
-                "galaxy_version": "21.01",
-                "length": "10M",
-                "speakers": [
-                    "awspolly"
-                ],
-                "youtube_id": "FNmZoo2OXTU"
-            },
-            {
-                "captioners": [
-                    "gallardoalba"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "10M",
-                "speakers": [
-                    "awspolly"
-                ],
-                "youtube_id": "7t0Gr1Jklqs"
-            }
+            "chira_extract"
         ],
+        "slides": false,
+        "slides_recordings": false,
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 }
             ],
@@ -266842,37 +274817,29 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
-        "tags": [
-            "miRNA",
-            "plants",
-            "stress tolerance"
-        ],
         "time_estimation": "2H",
-        "title": "Whole transcriptome analysis of Arabidopsis thaliana",
+        "title": "RNA-RNA interactome data analysis",
         "tools": [
-            "Cut1",
-            "Filter1",
-            "__MERGE_COLLECTION__",
-            "cat1",
-            "sort1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.14.1.2+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1",
             "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.2.5",
-            "toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_mapper/rbc_mirdeep2_mapper/2.0.0",
-            "toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_quantifier/rbc_mirdeep2_quantifier/2.0.0",
-            "toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1"
+            "toolshed.g2.bx.psu.edu/repos/iuc/chira_collapse/chira_collapse/1.4.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/chira_extract/chira_extract/1.4.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.4.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/chira_merge/chira_merge/1.4.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/chira_quantify/chira_quantify/1.4.3+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+            "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5"
         ],
         "topic_name": "transcriptomics",
         "topic_name_human": "Transcriptomics",
@@ -266880,81 +274847,46 @@
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": true
+            "video": false
         },
-        "tutorial_name": "mirna-target-finder",
+        "tutorial_name": "rna-interactome",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-interactome/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-interactome/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-interactome/tutorial.json"
         },
-        "version": 17,
-        "video": true,
-        "video_versions": 1,
+        "version": 12,
+        "video": false,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 314,
-        "visitors": 1919285,
+        "visit_duration": 178,
+        "visitors": 1217,
         "workflows": [
             {
                 "creators": [],
-                "description": "Identify upregulated miRNAS and analyze potential targets in downregulated genes.",
+                "description": "RNA-RNA interactome analysis using ChiRA tool suite",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nControl miRNA FASTQ collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nTreated miRNA FASTQ collection\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nTreated mRNA FASTQ collection\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPrecursor miRNA sequences\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nControl mRNA FASTQ collection\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTranscriptome FASTA\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAnnotation GTF\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMature miRNA sequences\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nStar miRNA sequenes\"]\n  9[label=\"FastQC\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"Trim Galore!\"]\n  0 -> 10 [label=\"output\"]\n  11[label=\"FastQC\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"Trim Galore!\"]\n  1 -> 12 [label=\"output\"]\n  13[label=\"FastQC\"]\n  2 -> 13 [label=\"output\"]\n  14[label=\"FastQC\"]\n  4 -> 14 [label=\"output\"]\n  15[label=\"Salmon quant\"]\n  6 -> 15 [label=\"output\"]\n  2 -> 15 [label=\"output\"]\n  5 -> 15 [label=\"output\"]\n  16[label=\"Salmon quant\"]\n  6 -> 16 [label=\"output\"]\n  4 -> 16 [label=\"output\"]\n  5 -> 16 [label=\"output\"]\n  17[label=\"FastQC\"]\n  10 -> 17 [label=\"trimmed_reads_single\"]\n  18[label=\"MiRDeep2 Mapper\"]\n  10 -> 18 [label=\"trimmed_reads_single\"]\n  19[label=\"Merge collections\"]\n  11 -> 19 [label=\"text_file\"]\n  9 -> 19 [label=\"text_file\"]\n  20[label=\"FastQC\"]\n  12 -> 20 [label=\"trimmed_reads_single\"]\n  21[label=\"MiRDeep2 Mapper\"]\n  12 -> 21 [label=\"trimmed_reads_single\"]\n  22[label=\"Merge collections\"]\n  13 -> 22 [label=\"text_file\"]\n  14 -> 22 [label=\"text_file\"]\n  23[label=\"DESeq2\"]\n  15 -> 23 [label=\"output_gene_quant\"]\n  16 -> 23 [label=\"output_gene_quant\"]\n  6 -> 23 [label=\"output\"]\n  24[label=\"MiRDeep2 Quantifier\"]\n  7 -> 24 [label=\"output\"]\n  3 -> 24 [label=\"output\"]\n  18 -> 24 [label=\"output_reads_collapsed\"]\n  8 -> 24 [label=\"output\"]\n  25[label=\"MultiQC\"]\n  19 -> 25 [label=\"output\"]\n  26[label=\"Merge collections\"]\n  20 -> 26 [label=\"text_file\"]\n  17 -> 26 [label=\"text_file\"]\n  27[label=\"MiRDeep2 Quantifier\"]\n  7 -> 27 [label=\"output\"]\n  3 -> 27 [label=\"output\"]\n  21 -> 27 [label=\"output_reads_collapsed\"]\n  8 -> 27 [label=\"output\"]\n  28[label=\"MultiQC\"]\n  22 -> 28 [label=\"output\"]\n  29[label=\"Filter\"]\n  23 -> 29 [label=\"deseq_out\"]\n  30[label=\"Cut\"]\n  24 -> 30 [label=\"miRNAsExpressed\"]\n  31[label=\"MultiQC\"]\n  26 -> 31 [label=\"output\"]\n  32[label=\"Cut\"]\n  27 -> 32 [label=\"miRNAsExpressed\"]\n  33[label=\"Filter\"]\n  29 -> 33 [label=\"out_file1\"]\n  34[label=\"Filter\"]\n  29 -> 34 [label=\"out_file1\"]\n  35[label=\"DESeq2\"]\n  32 -> 35 [label=\"out_file1\"]\n  30 -> 35 [label=\"out_file1\"]\n  36[label=\"Cut\"]\n  34 -> 36 [label=\"out_file1\"]\n  37[label=\"Filter\"]\n  35 -> 37 [label=\"deseq_out\"]\n  38[label=\"Filter FASTA\"]\n  36 -> 38 [label=\"out_file1\"]\n  5 -> 38 [label=\"output\"]\n  39[label=\"Filter\"]\n  37 -> 39 [label=\"out_file1\"]\n  40[label=\"Filter\"]\n  37 -> 40 [label=\"out_file1\"]\n  41[label=\"Cut\"]\n  40 -> 41 [label=\"out_file1\"]\n  42[label=\"Filter FASTA\"]\n  41 -> 42 [label=\"out_file1\"]\n  8 -> 42 [label=\"output\"]\n  43[label=\"Filter FASTA\"]\n  41 -> 43 [label=\"out_file1\"]\n  7 -> 43 [label=\"output\"]\n  44[label=\"Concatenate datasets\"]\n  43 -> 44 [label=\"output\"]\n  42 -> 44 [label=\"output\"]\n  45[label=\"TargetFinder\"]\n  38 -> 45 [label=\"output\"]\n  44 -> 45 [label=\"out_file1\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreads_fastq\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreference1_fasta\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nreference2_fasta\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nannotation_gtf\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ngenome_fasta\"]\n  5[label=\"FastQC\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"Cutadapt\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"FastQC\"]\n  6 -> 7 [label=\"out1\"]\n  8[label=\"ChiRA collapse\"]\n  6 -> 8 [label=\"out1\"]\n  9[label=\"ChiRA map\"]\n  8 -> 9 [label=\"out\"]\n  1 -> 9 [label=\"output\"]\n  2 -> 9 [label=\"output\"]\n  10[label=\"ChiRA merge\"]\n  9 -> 10 [label=\"mapped_bed\"]\n  3 -> 10 [label=\"output\"]\n  1 -> 10 [label=\"output\"]\n  2 -> 10 [label=\"output\"]\n  11[label=\"ChiRA qauntify\"]\n  10 -> 11 [label=\"merged_bed\"]\n  10 -> 11 [label=\"segments_bed\"]\n  12[label=\"ChiRA extract\"]\n  4 -> 12 [label=\"output\"]\n  3 -> 12 [label=\"output\"]\n  11 -> 12 [label=\"loci\"]\n  1 -> 12 [label=\"output\"]\n  2 -> 12 [label=\"output\"]\n  k7182226db48a4ce1882e6bb41091a5d4[color=lightseagreen,label=\"Output\\ninteractions\"]\n  12 -> k7182226db48a4ce1882e6bb41091a5d4\n  k011f4c89d15a48779d490146773ce781[color=lightseagreen,label=\"Output\\nchimeric_reads\"]\n  12 -> k011f4c89d15a48779d490146773ce781\n  13[label=\"Query Tabular\"]\n  12 -> 13 [label=\"chimeras\"]\n  kf1315db211d14dee9014eafa1fc0f82f[color=lightseagreen,label=\"Output\\ndb\"]\n  13 -> kf1315db211d14dee9014eafa1fc0f82f\n}",
                 "history": [
                     {
-                        "hash": "87d458cc1fd8db170670ddd5c186c98295267d9e",
-                        "message": "Undo error",
-                        "num": 7,
-                        "short_hash": "87d458cc1",
-                        "unix": "1674149735"
-                    },
-                    {
-                        "hash": "edf36428b978d5519a494eaee576a8a17c6c948e",
-                        "message": "Fix tutorial",
-                        "num": 6,
-                        "short_hash": "edf36428b",
-                        "unix": "1669862549"
-                    },
-                    {
-                        "hash": "a6636e32469b78edc30efcc646f92e77c4bdb58b",
-                        "message": "add tags and annotation to the workflow",
-                        "num": 5,
-                        "short_hash": "a6636e324",
-                        "unix": "1617760834"
-                    },
-                    {
-                        "hash": "a5a1a7567b95fa539b493a98f5924d2482e16997",
-                        "message": "Update workflow for miRNA target identification in Arabidopsis",
-                        "num": 4,
-                        "short_hash": "a5a1a7567",
-                        "unix": "1617760351"
-                    },
-                    {
-                        "hash": "0eacaeef42cdfef3d6f60d4ec481a3ef84b72765",
-                        "message": "Update workflow and include downregulated miRNAS",
-                        "num": 3,
-                        "short_hash": "0eacaeef4",
-                        "unix": "1617194856"
-                    },
-                    {
-                        "hash": "bdbe72dd283efbb454cf60a91384a9d130f8b342",
-                        "message": "Fix tests workflow",
+                        "hash": "1dde32698b8894ce6ea44c28fcf48fe2b28d15b3",
+                        "message": "update rna-rna interactome workflow and add workflow test",
                         "num": 2,
-                        "short_hash": "bdbe72dd2",
-                        "unix": "1616702513"
+                        "short_hash": "1dde32698",
+                        "unix": "1607121201"
                     },
                     {
-                        "hash": "4b406638ca884e2ad7b58db02d9c4cc7eff0005d",
-                        "message": "New training: miRNA target finder",
+                        "hash": "922058fc64848a1fb74d005020896346a189d852",
+                        "message": "update rna-rna interactome workflow and add workflow test",
                         "num": 1,
-                        "short_hash": "4b406638c",
-                        "unix": "1616700503"
+                        "short_hash": "922058fc6",
+                        "unix": "1607121057"
                     }
                 ],
                 "inputs": [
@@ -266967,1486 +274899,983 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Control miRNA FASTQ collection"
+                                "name": "reads_fastq"
                             }
                         ],
-                        "label": "Control miRNA FASTQ collection",
-                        "name": "Input dataset collection",
+                        "label": "reads_fastq",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 1.984375
+                            "bottom": 250,
+                            "height": 61,
+                            "left": -969.5,
+                            "right": -769.5,
+                            "top": 189,
+                            "width": 200,
+                            "x": -969.5,
+                            "y": 189
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "286f34e3-d05b-40ba-b39e-2f0c7455ff23",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "type": "data_input",
+                        "uuid": "36ae119e-7b4c-424e-902f-a1f37b525bd1",
+                        "workflow_outputs": [
                             {
-                                "description": "",
-                                "name": "Treated miRNA FASTQ collection"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "b7bf00b3-3646-44b5-b160-f9364c0e536c"
                             }
-                        ],
-                        "label": "Treated miRNA FASTQ collection",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 331.984375
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "6ffd974f-fd40-4234-9bda-6edd9e65e702",
-                        "workflow_outputs": []
+                        ]
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Treated mRNA FASTQ collection"
+                                "name": "reference1_fasta"
                             }
                         ],
-                        "label": "Treated mRNA FASTQ collection",
-                        "name": "Input dataset collection",
+                        "label": "reference1_fasta",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 1161.984375,
-                            "top": 778.984375
+                            "bottom": 379,
+                            "height": 81,
+                            "left": -969.5,
+                            "right": -769.5,
+                            "top": 298,
+                            "width": 200,
+                            "x": -969.5,
+                            "y": 298
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "e2260dff-96ce-4345-902a-73958f9ac0cf",
-                        "workflow_outputs": []
+                        "type": "data_input",
+                        "uuid": "5481a3fd-b578-433a-bcdc-ef19c194f1cf",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "a641e20a-7835-4318-9387-ec98acef6bb6"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Precursor miRNA sequences"
+                                "name": "reference2_fasta"
                             }
                         ],
-                        "label": "Precursor miRNA sequences",
+                        "label": "reference2_fasta",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 575.984375,
-                            "top": 1461.984375
+                            "bottom": 488,
+                            "height": 81,
+                            "left": -969.5,
+                            "right": -769.5,
+                            "top": 407,
+                            "width": 200,
+                            "x": -969.5,
+                            "y": 407
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "7e8825d5-8e7f-4ec4-b0b4-f0efcc70e504",
-                        "workflow_outputs": []
+                        "uuid": "c6b92dfd-a636-48c9-8854-cf85c6704239",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "a375f37f-cd68-4847-bb2a-ef7b1a7c385d"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 4,
+                        "id": 3,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Control mRNA FASTQ collection"
+                                "name": "annotation_gtf"
                             }
                         ],
-                        "label": "Control mRNA FASTQ collection",
-                        "name": "Input dataset collection",
+                        "label": "annotation_gtf",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 1161.984375,
-                            "top": 1101.984375
+                            "bottom": 597,
+                            "height": 81,
+                            "left": -969.5,
+                            "right": -769.5,
+                            "top": 516,
+                            "width": 200,
+                            "x": -969.5,
+                            "y": 516
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "5f622114-e64d-4a96-9866-e519b583cd98",
-                        "workflow_outputs": []
+                        "type": "data_input",
+                        "uuid": "7b67eecd-1c75-407b-a684-96ed53c74f5c",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "1b35e4cd-b9c7-4db1-9361-b74c127f3dbf"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 5,
+                        "id": 4,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Transcriptome FASTA"
+                                "name": "genome_fasta"
                             }
                         ],
-                        "label": "Transcriptome FASTA",
+                        "label": "genome_fasta",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 1161.984375,
-                            "top": 1220.984375
+                            "bottom": 706,
+                            "height": 81,
+                            "left": -969.5,
+                            "right": -769.5,
+                            "top": 625,
+                            "width": 200,
+                            "x": -969.5,
+                            "y": 625
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "5bbd4e69-3b60-47e1-aecf-5d43ae6b54e5",
-                        "workflow_outputs": []
-                    },
+                        "uuid": "100bac6e-c0b8-412c-bc71-e55028d1d70e",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "5396a7d8-957f-4858-8ce7-4c5131d2852d"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nreads_fastq\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nreference1_fasta\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nreference2_fasta\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nannotation_gtf\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\ngenome_fasta\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"FastQC\"];\n  0 -->|output| 5;\n  6[\"Cutadapt\"];\n  0 -->|output| 6;\n  7[\"FastQC\"];\n  6 -->|out1| 7;\n  8[\"ChiRA collapse\"];\n  6 -->|out1| 8;\n  9[\"ChiRA map\"];\n  8 -->|out| 9;\n  1 -->|output| 9;\n  2 -->|output| 9;\n  10[\"ChiRA merge\"];\n  9 -->|mapped_bed| 10;\n  3 -->|output| 10;\n  1 -->|output| 10;\n  2 -->|output| 10;\n  11[\"ChiRA qauntify\"];\n  10 -->|merged_bed| 11;\n  10 -->|segments_bed| 11;\n  12[\"ChiRA extract\"];\n  4 -->|output| 12;\n  3 -->|output| 12;\n  11 -->|loci| 12;\n  1 -->|output| 12;\n  2 -->|output| 12;\n  7182226d-b48a-4ce1-882e-6bb41091a5d4[\"Output\\ninteractions\"];\n  12 --> 7182226d-b48a-4ce1-882e-6bb41091a5d4;\n  style 7182226d-b48a-4ce1-882e-6bb41091a5d4 stroke:#2c3143,stroke-width:4px;\n  011f4c89-d15a-4877-9d49-0146773ce781[\"Output\\nchimeric_reads\"];\n  12 --> 011f4c89-d15a-4877-9d49-0146773ce781;\n  style 011f4c89-d15a-4877-9d49-0146773ce781 stroke:#2c3143,stroke-width:4px;\n  13[\"Query Tabular\"];\n  12 -->|chimeras| 13;\n  f1315db2-11d1-4dee-9014-eafa1fc0f82f[\"Output\\ndb\"];\n  13 --> f1315db2-11d1-4dee-9014-eafa1fc0f82f;\n  style f1315db2-11d1-4dee-9014-eafa1fc0f82f stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "RNA-RNA interactome data analysis - chira  v1.4.3",
+                "outputs": [
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 6,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Annotation GTF"
+                                "name": "reads_fastq"
                             }
                         ],
-                        "label": "Annotation GTF",
+                        "label": "reads_fastq",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 1161.984375,
-                            "top": 1340
+                            "bottom": 250,
+                            "height": 61,
+                            "left": -969.5,
+                            "right": -769.5,
+                            "top": 189,
+                            "width": 200,
+                            "x": -969.5,
+                            "y": 189
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "570e8113-930a-4567-a380-fdb93fbcc60f",
-                        "workflow_outputs": []
+                        "uuid": "36ae119e-7b4c-424e-902f-a1f37b525bd1",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "b7bf00b3-3646-44b5-b160-f9364c0e536c"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 7,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Mature miRNA sequences"
+                                "name": "reference1_fasta"
                             }
                         ],
-                        "label": "Mature miRNA sequences",
+                        "label": "reference1_fasta",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 575.984375,
-                            "top": 1770.984375
+                            "bottom": 379,
+                            "height": 81,
+                            "left": -969.5,
+                            "right": -769.5,
+                            "top": 298,
+                            "width": 200,
+                            "x": -969.5,
+                            "y": 298
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "5d65f949-64bf-4f17-b242-f94d342b14a8",
-                        "workflow_outputs": []
+                        "uuid": "5481a3fd-b578-433a-bcdc-ef19c194f1cf",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "a641e20a-7835-4318-9387-ec98acef6bb6"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 8,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Star miRNA sequenes"
+                                "name": "reference2_fasta"
                             }
                         ],
-                        "label": "Star miRNA sequenes",
+                        "label": "reference2_fasta",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 575.984375,
-                            "top": 1890
+                            "bottom": 488,
+                            "height": 81,
+                            "left": -969.5,
+                            "right": -769.5,
+                            "top": 407,
+                            "width": 200,
+                            "x": -969.5,
+                            "y": 407
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "d11848be-2417-4393-b87f-5e4d9500b4ed",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nControl miRNA FASTQ collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nTreated miRNA FASTQ collection\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nTreated mRNA FASTQ collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nPrecursor miRNA sequences\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Collection\\nControl mRNA FASTQ collection\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nTranscriptome FASTA\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nAnnotation GTF\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nMature miRNA sequences\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nStar miRNA sequenes\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"FastQC\"];\n  0 -->|output| 9;\n  10[\"Trim Galore!\"];\n  0 -->|output| 10;\n  11[\"FastQC\"];\n  1 -->|output| 11;\n  12[\"Trim Galore!\"];\n  1 -->|output| 12;\n  13[\"FastQC\"];\n  2 -->|output| 13;\n  14[\"FastQC\"];\n  4 -->|output| 14;\n  15[\"Salmon quant\"];\n  6 -->|output| 15;\n  2 -->|output| 15;\n  5 -->|output| 15;\n  16[\"Salmon quant\"];\n  6 -->|output| 16;\n  4 -->|output| 16;\n  5 -->|output| 16;\n  17[\"FastQC\"];\n  10 -->|trimmed_reads_single| 17;\n  18[\"MiRDeep2 Mapper\"];\n  10 -->|trimmed_reads_single| 18;\n  19[\"Merge collections\"];\n  11 -->|text_file| 19;\n  9 -->|text_file| 19;\n  20[\"FastQC\"];\n  12 -->|trimmed_reads_single| 20;\n  21[\"MiRDeep2 Mapper\"];\n  12 -->|trimmed_reads_single| 21;\n  22[\"Merge collections\"];\n  13 -->|text_file| 22;\n  14 -->|text_file| 22;\n  23[\"DESeq2\"];\n  15 -->|output_gene_quant| 23;\n  16 -->|output_gene_quant| 23;\n  6 -->|output| 23;\n  24[\"MiRDeep2 Quantifier\"];\n  7 -->|output| 24;\n  3 -->|output| 24;\n  18 -->|output_reads_collapsed| 24;\n  8 -->|output| 24;\n  25[\"MultiQC\"];\n  19 -->|output| 25;\n  26[\"Merge collections\"];\n  20 -->|text_file| 26;\n  17 -->|text_file| 26;\n  27[\"MiRDeep2 Quantifier\"];\n  7 -->|output| 27;\n  3 -->|output| 27;\n  21 -->|output_reads_collapsed| 27;\n  8 -->|output| 27;\n  28[\"MultiQC\"];\n  22 -->|output| 28;\n  29[\"Filter\"];\n  23 -->|deseq_out| 29;\n  30[\"Cut\"];\n  24 -->|miRNAsExpressed| 30;\n  31[\"MultiQC\"];\n  26 -->|output| 31;\n  32[\"Cut\"];\n  27 -->|miRNAsExpressed| 32;\n  33[\"Filter\"];\n  29 -->|out_file1| 33;\n  34[\"Filter\"];\n  29 -->|out_file1| 34;\n  35[\"DESeq2\"];\n  32 -->|out_file1| 35;\n  30 -->|out_file1| 35;\n  36[\"Cut\"];\n  34 -->|out_file1| 36;\n  37[\"Filter\"];\n  35 -->|deseq_out| 37;\n  38[\"Filter FASTA\"];\n  36 -->|out_file1| 38;\n  5 -->|output| 38;\n  39[\"Filter\"];\n  37 -->|out_file1| 39;\n  40[\"Filter\"];\n  37 -->|out_file1| 40;\n  41[\"Cut\"];\n  40 -->|out_file1| 41;\n  42[\"Filter FASTA\"];\n  41 -->|out_file1| 42;\n  8 -->|output| 42;\n  43[\"Filter FASTA\"];\n  41 -->|out_file1| 43;\n  7 -->|output| 43;\n  44[\"Concatenate datasets\"];\n  43 -->|output| 44;\n  42 -->|output| 44;\n  45[\"TargetFinder\"];\n  38 -->|output| 45;\n  44 -->|out_file1| 45;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "Plant bulk RNA-Seq workflow",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
-                        "errors": null,
-                        "id": 23,
-                        "input_connections": {
-                            "select_data|rep_factorName_0|rep_factorLevel_0|countsFile": {
-                                "id": 15,
-                                "output_name": "output_gene_quant"
-                            },
-                            "select_data|rep_factorName_0|rep_factorLevel_1|countsFile": {
-                                "id": 16,
-                                "output_name": "output_gene_quant"
-                            },
-                            "tximport|mapping_format|gtf_file": {
-                                "id": 6,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool DESeq2",
-                                "name": "batch_factors"
-                            }
-                        ],
-                        "label": null,
-                        "name": "DESeq2",
-                        "outputs": [
-                            {
-                                "name": "deseq_out",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "plots",
-                                "type": "pdf"
-                            }
-                        ],
-                        "position": {
-                            "left": 1737.984375,
-                            "top": 1170.984375
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActiondeseq_out": {
-                                "action_arguments": {
-                                    "newname": "DESeq2 results mRNA"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "deseq_out"
-                            },
-                            "RenameDatasetActionplots": {
-                                "action_arguments": {
-                                    "newname": "DESeq2 plots mRNA"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "plots"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "6a3a025714d3",
-                            "name": "deseq2",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"auto_mean_filter_off\": \"false\", \"batch_factors\": {\"__class__\": \"RuntimeValue\"}, \"esf\": \"\", \"fit_type\": \"1\", \"header\": \"true\", \"many_contrasts\": \"false\", \"normCounts\": \"false\", \"normRLog\": \"false\", \"normVST\": \"false\", \"outlier_filter_off\": \"false\", \"outlier_replace_off\": \"false\", \"pdf\": \"true\", \"select_data\": {\"how\": \"datasets_per_level\", \"__current_case__\": 1, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": \"effects_brassinolide\", \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": \"brassinolide\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"factorLevel\": \"control\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"tximport\", \"__current_case__\": 0, \"txtype\": \"salmon\", \"mapping_format\": {\"mapping_format_selector\": \"gtf\", \"__current_case__\": 0, \"gtf_file\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.11.40.6+galaxy1",
-                        "type": "tool",
-                        "uuid": "db23fb5b-af4b-4fe1-8f8d-99a3176808e7",
+                        "uuid": "c6b92dfd-a636-48c9-8854-cf85c6704239",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "plots",
-                                "uuid": "6c720aa2-a057-45c4-a813-3065d95c6c7f"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "deseq_out",
-                                "uuid": "77e6746d-7bf9-400f-ac1e-106db58fbbbd"
+                                "output_name": "output",
+                                "uuid": "a375f37f-cd68-4847-bb2a-ef7b1a7c385d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "content_id": null,
                         "errors": null,
-                        "id": 25,
-                        "input_connections": {
-                            "results_0|software_cond|output_0|input": {
-                                "id": 19,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "MultiQC",
-                        "outputs": [
-                            {
-                                "name": "stats",
-                                "type": "input"
-                            },
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "html_report",
-                                "type": "html"
+                                "description": "",
+                                "name": "annotation_gtf"
                             }
                         ],
+                        "label": "annotation_gtf",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 883.984375,
-                            "top": 342.984375
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionstats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "stats"
-                            },
-                            "RenameDatasetActionhtml_report": {
-                                "action_arguments": {
-                                    "newname": "MultiQC unprocessed miRNA: Webpage"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "html_report"
-                            },
-                            "RenameDatasetActionstats": {
-                                "action_arguments": {
-                                    "newname": "MultiQC unprocessed miRNA: Stats"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "stats"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b2f1f75d49c4",
-                            "name": "multiqc",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 597,
+                            "height": 81,
+                            "left": -969.5,
+                            "right": -769.5,
+                            "top": 516,
+                            "width": 200,
+                            "x": -969.5,
+                            "y": 516
                         },
-                        "tool_state": "{\"comment\": \"\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": \"false\", \"title\": \"miRNA initial quality check\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7",
-                        "type": "tool",
-                        "uuid": "3e845cfd-ddd1-4f60-b1cb-ac16dc2c6d10",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "7b67eecd-1c75-407b-a684-96ed53c74f5c",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "html_report",
-                                "uuid": "7cd34a0f-1142-4965-afa2-5f77e9c79b9e"
+                                "output_name": "output",
+                                "uuid": "1b35e4cd-b9c7-4db1-9361-b74c127f3dbf"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "content_id": null,
                         "errors": null,
-                        "id": 28,
-                        "input_connections": {
-                            "results_0|software_cond|output_0|input": {
-                                "id": 22,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "MultiQC",
-                        "outputs": [
-                            {
-                                "name": "stats",
-                                "type": "input"
-                            },
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "html_report",
-                                "type": "html"
+                                "description": "",
+                                "name": "genome_fasta"
                             }
                         ],
+                        "label": "genome_fasta",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 2035.984375,
-                            "top": 1455
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionstats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "stats"
-                            },
-                            "RenameDatasetActionhtml_report": {
-                                "action_arguments": {
-                                    "newname": "MultiQC mRNA: Webpage"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "html_report"
-                            },
-                            "RenameDatasetActionstats": {
-                                "action_arguments": {
-                                    "newname": "MultiQC mRNA: Stats"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "stats"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-                        "tool_shed_repository": {
-                            "changeset_revision": "b2f1f75d49c4",
-                            "name": "multiqc",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "bottom": 706,
+                            "height": 81,
+                            "left": -969.5,
+                            "right": -769.5,
+                            "top": 625,
+                            "width": 200,
+                            "x": -969.5,
+                            "y": 625
                         },
-                        "tool_state": "{\"comment\": \"\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"RuntimeValue\"}}]}}], \"saveLog\": \"false\", \"title\": \"mRNA initial quality check\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7",
-                        "type": "tool",
-                        "uuid": "b7ffd734-4c99-4132-814f-47b75b4b5d63",
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "100bac6e-c0b8-412c-bc71-e55028d1d70e",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "html_report",
-                                "uuid": "7d5b5d84-d0b0-4639-9b42-61bf9f7e014d"
+                                "output_name": "output",
+                                "uuid": "5396a7d8-957f-4858-8ce7-4c5131d2852d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
                         "errors": null,
-                        "id": 31,
+                        "id": 5,
                         "input_connections": {
-                            "results_0|software_cond|output_0|input": {
-                                "id": 26,
+                            "input_file": {
+                                "id": 0,
                                 "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "MultiQC",
+                        "name": "FastQC",
                         "outputs": [
                             {
-                                "name": "stats",
-                                "type": "input"
+                                "name": "html_file",
+                                "type": "html"
                             },
                             {
-                                "name": "html_report",
-                                "type": "html"
+                                "name": "text_file",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 1161.984375,
-                            "top": 558.984375
+                            "bottom": 481,
+                            "height": 292,
+                            "left": -683.5,
+                            "right": -483.5,
+                            "top": 189,
+                            "width": 200,
+                            "x": -683.5,
+                            "y": 189
                         },
                         "post_job_actions": {
-                            "HideDatasetActionstats": {
+                            "HideDatasetActiontext_file": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
-                                "output_name": "stats"
-                            },
-                            "RenameDatasetActionhtml_report": {
-                                "action_arguments": {
-                                    "newname": "MultiQC processed miRNA: Webpage"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "html_report"
-                            },
-                            "RenameDatasetActionstats": {
-                                "action_arguments": {
-                                    "newname": "MultiQC processed miRNA: Stats"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "stats"
+                                "output_name": "text_file"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "b2f1f75d49c4",
-                            "name": "multiqc",
-                            "owner": "iuc",
+                            "changeset_revision": "e7b2202befea",
+                            "name": "fastqc",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"comment\": \"\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": \"false\", \"title\": \"miRNA trimmed quality check\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7",
+                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"adapters\": null, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"contaminants\": null, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": null, \"min_length\": \"\", \"nogroup\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.72+galaxy1",
                         "type": "tool",
-                        "uuid": "b8e44272-be04-47ad-8b06-aa0f7d51a38c",
+                        "uuid": "d9a7bf3f-f741-4c11-9f5b-fdca1ddea405",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "html_report",
-                                "uuid": "45f7bd2f-aafe-471c-b41e-431cbbe28781"
+                                "output_name": "html_file",
+                                "uuid": "10d9a489-63d2-4f45-9a24-822093d4734e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
                         "errors": null,
-                        "id": 35,
+                        "id": 6,
                         "input_connections": {
-                            "select_data|rep_factorName_0|rep_factorLevel_0|countsFile": {
-                                "id": 32,
-                                "output_name": "out_file1"
-                            },
-                            "select_data|rep_factorName_0|rep_factorLevel_1|countsFile": {
-                                "id": 30,
-                                "output_name": "out_file1"
+                            "library|input_1": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool DESeq2",
-                                "name": "batch_factors"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "DESeq2",
+                        "name": "Cutadapt",
                         "outputs": [
                             {
-                                "name": "deseq_out",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "plots",
-                                "type": "pdf"
+                                "name": "out1",
+                                "type": "fastqsanger"
                             }
                         ],
                         "position": {
-                            "left": 1460,
-                            "top": 1445.984375
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActiondeseq_out": {
-                                "action_arguments": {
-                                    "newname": "DESeq2 results miRNA"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "deseq_out"
-                            },
-                            "RenameDatasetActionplots": {
-                                "action_arguments": {
-                                    "newname": "DESeq2 plots miRNA"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "plots"
-                            }
+                            "bottom": 641,
+                            "height": 132,
+                            "left": -683.5,
+                            "right": -483.5,
+                            "top": 509,
+                            "width": 200,
+                            "x": -683.5,
+                            "y": 509
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5",
                         "tool_shed_repository": {
-                            "changeset_revision": "6a3a025714d3",
-                            "name": "deseq2",
-                            "owner": "iuc",
+                            "changeset_revision": "49370cb85f0f",
+                            "name": "cutadapt",
+                            "owner": "lparsons",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"auto_mean_filter_off\": \"false\", \"batch_factors\": {\"__class__\": \"RuntimeValue\"}, \"esf\": \"\", \"fit_type\": \"1\", \"header\": \"false\", \"many_contrasts\": \"false\", \"normCounts\": \"false\", \"normRLog\": \"false\", \"normVST\": \"false\", \"outlier_filter_off\": \"false\", \"outlier_replace_off\": \"false\", \"pdf\": \"true\", \"select_data\": {\"how\": \"datasets_per_level\", \"__current_case__\": 1, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": \"effects_brassinolide\", \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": \"brassinolide\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"factorLevel\": \"control\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"count\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.11.40.6+galaxy1",
+                        "tool_state": "{\"__input_ext\": \"input\", \"adapter_options\": {\"error_rate\": \"0.1\", \"no_indels\": \"false\", \"count\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"no_trim\": \"false\", \"mask_adapter\": \"false\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"filter_options\": {\"discard\": \"false\", \"discard_untrimmed\": \"false\", \"min\": \"16\", \"max\": \"0\", \"max_n\": \"\", \"pair_filter\": \"any\"}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"\", \"adapter\": \"GTGTCAGTCACTTCCAGCGG\"}}], \"front_adapters\": [{\"__index__\": 0, \"front_adapter_source\": {\"front_adapter_source_list\": \"user\", \"__current_case__\": 0, \"front_adapter_name\": \"\", \"front_adapter\": \"GCATAGGGAGGACGATGCGG\"}}], \"anywhere_adapters\": [], \"cut\": \"0\"}}, \"output_options\": {\"report\": \"false\", \"info_file\": \"false\", \"rest_file\": \"false\", \"wildcard_file\": \"false\", \"too_short_file\": \"false\", \"too_long_file\": \"false\", \"untrimmed_file\": \"false\", \"multiple_output\": \"false\"}, \"read_mod_options\": {\"quality_cutoff\": \"0\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"prefix\": \"\", \"suffix\": \"\", \"strip_suffix\": \"\", \"length\": \"0\", \"length_tag\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16.5",
                         "type": "tool",
-                        "uuid": "15632b70-0358-4ca6-918f-f236468dd8d5",
+                        "uuid": "004e566f-fa52-439e-9196-ba93bb401022",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "plots",
-                                "uuid": "b4252bda-8ee4-47f5-85e0-ccacb840c702"
-                            },
-                            {
-                                "label": null,
-                                "output_name": "deseq_out",
-                                "uuid": "55ea0b93-52e0-4d07-a64f-4db6e39f42ab"
+                                "output_name": "out1",
+                                "uuid": "0a7b8f7a-fb0b-47c9-8ac4-ffdde708f13a"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
                         "errors": null,
-                        "id": 38,
+                        "id": 7,
                         "input_connections": {
-                            "header_criteria|identifiers": {
-                                "id": 36,
-                                "output_name": "out_file1"
-                            },
-                            "input": {
-                                "id": 5,
-                                "output_name": "output"
+                            "input_file": {
+                                "id": 6,
+                                "output_name": "out1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Filter FASTA",
+                        "name": "FastQC",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "fasta"
+                                "name": "html_file",
+                                "type": "html"
+                            },
+                            {
+                                "name": "text_file",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 2880,
-                            "top": 1662.984375
+                            "bottom": 481,
+                            "height": 292,
+                            "left": -397.5,
+                            "right": -197.5,
+                            "top": 189,
+                            "width": 200,
+                            "x": -397.5,
+                            "y": 189
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Downregulated mRNA sequences"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
+                            "HideDatasetActiontext_file": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "text_file"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "3c623e81be77",
-                            "name": "filter_by_fasta_ids",
-                            "owner": "galaxyp",
+                            "changeset_revision": "e7b2202befea",
+                            "name": "fastqc",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"dedup\": \"false\", \"header_criteria\": {\"header_criteria_select\": \"id_list\", \"__current_case__\": 1, \"identifiers\": {\"__class__\": \"ConnectedValue\"}, \"id_regex\": {\"find\": \"pattern\", \"__current_case__\": 1, \"pattern\": \"GENE=(AT.{7})\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"output_discarded\": \"false\", \"sequence_criteria\": {\"sequence_criteria_select\": \"\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1",
-                        "type": "tool",
-                        "uuid": "4d1f1434-2cd7-4025-aa31-955646f26ae0",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "e8c830ca-388d-43e9-a30a-6ce4e1db2103"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "cat1",
-                        "errors": null,
-                        "id": 44,
-                        "input_connections": {
-                            "input1": {
-                                "id": 43,
-                                "output_name": "output"
-                            },
-                            "queries_0|input2": {
-                                "id": 42,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Concatenate datasets",
-                        "outputs": [
-                            {
-                                "name": "out_file1",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 2880,
-                            "top": 1882.984375
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Upregulated miRNA sequences"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "tool_id": "cat1",
-                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [{\"__index__\": 0, \"input2\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
+                        "tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"adapters\": null, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"contaminants\": null, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"kmers\": \"7\", \"limits\": null, \"min_length\": \"\", \"nogroup\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.72+galaxy1",
                         "type": "tool",
-                        "uuid": "97871054-6cba-4834-bc56-26a7f37be2b8",
+                        "uuid": "3ce4fbbf-1e35-4c73-82d8-d78567dc7f98",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "800ea133-2a03-469d-875e-24b0635c3cd2"
+                                "output_name": "html_file",
+                                "uuid": "16c57790-7c4d-474e-a094-c48e8573c249"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_collapse/chira_collapse/1.4.3+galaxy0",
                         "errors": null,
-                        "id": 45,
+                        "id": 8,
                         "input_connections": {
-                            "d": {
-                                "id": 38,
-                                "output_name": "output"
-                            },
-                            "f": {
-                                "id": 44,
-                                "output_name": "out_file1"
+                            "in": {
+                                "id": 6,
+                                "output_name": "out1"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "TargetFinder",
+                        "name": "ChiRA collapse",
                         "outputs": [
                             {
-                                "name": "output_file",
-                                "type": "txt"
+                                "name": "out",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 3157.984375,
-                            "top": 1712.984375
+                            "bottom": 641,
+                            "height": 132,
+                            "left": -397.5,
+                            "right": -197.5,
+                            "top": 509,
+                            "width": 200,
+                            "x": -397.5,
+                            "y": 509
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_collapse/chira_collapse/1.4.3+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "c9d56748fbde",
-                            "name": "targetfinder",
-                            "owner": "rnateam",
+                            "changeset_revision": "2b2bfeda00d0",
+                            "name": "chira_collapse",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"c\": \"4.0\", \"d\": {\"__class__\": \"ConnectedValue\"}, \"f\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"classic\", \"r\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.7.0+galaxy1",
+                        "tool_state": "{\"in\": {\"__class__\": \"ConnectedValue\"}, \"umi_len\": \"5\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.4.3+galaxy0",
                         "type": "tool",
-                        "uuid": "d81d9ea9-a085-478f-a148-0c31083f16fc",
+                        "uuid": "c1bc53ab-37cf-4302-9f60-3ab98337e68c",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output_file",
-                                "uuid": "2a3de11c-addc-4e1a-a156-f760f861ce64"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "transcriptomics/mirna-target-finder",
-                "path": "topics/transcriptomics/tutorials/mirna-target-finder/workflows/main_workflow.ga",
-                "tags": [
-                    "transcriptomics",
-                    "mirna",
-                    "arabidopsis"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Plant bulk RNA-Seq workflow",
-                "topic_id": "transcriptomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-mirna-target-finder/versions/main-workflow",
-                "tutorial_id": "mirna-target-finder",
-                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/mirna-target-finder/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/mirna-target-finder/workflows/main_workflow.html",
-                "version": 3,
-                "wfid": "transcriptomics-mirna-target-finder",
-                "wfname": "main-workflow",
-                "workflow": "main_workflow.ga",
-                "workflow_tools": [
-                    "Cut1",
-                    "Filter1",
-                    "__MERGE_COLLECTION__",
-                    "cat1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.14.1.2+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
-                    "toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_mapper/rbc_mirdeep2_mapper/2.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_quantifier/rbc_mirdeep2_quantifier/2.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1"
-                ],
-                "workflowhub_id": "1318"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/4710649"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "74a8bef53a00",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "merge_cols",
-                    "owner": "devteam",
-                    "revisions": "f2aac0c5c60d",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "annotatemyids",
-                    "owner": "iuc",
-                    "revisions": "1a125daea0d8",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "limma_voom",
-                    "owner": "iuc",
-                    "revisions": "d5a940112511",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 74a8bef53a00\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merge_cols\n  owner: devteam\n  revisions: f2aac0c5c60d\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: annotatemyids\n  owner: iuc\n  revisions: 1a125daea0d8\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: limma_voom\n  owner: iuc\n  revisions: d5a940112511\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.json",
-        "contributors": [
-            {
-                "id": "mblue9",
-                "joined": "2018-09",
-                "name": "Maria Doyle",
-                "orcid": "0000-0003-4847-8436",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
-            },
-            {
-                "id": "bphipson",
-                "joined": "2018-09",
-                "name": "Belinda Phipson",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bphipson/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bphipson.json"
-            },
-            {
-                "id": "JovMaksimovic",
-                "joined": "2019-04",
-                "name": "Jovana Maksimovic",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/JovMaksimovic/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/JovMaksimovic.json"
-            },
-            {
-                "github": false,
-                "id": "annatrigos",
-                "joined": "2018-09",
-                "name": "Anna Trigos",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/annatrigos/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/annatrigos.json"
-            },
-            {
-                "id": "mritchie",
-                "joined": "2018-09",
-                "name": "Matt Ritchie",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mritchie/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mritchie.json"
-            },
-            {
-                "id": "hdashnow",
-                "joined": "2018-09",
-                "name": "Harriet Dashnow",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hdashnow/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hdashnow.json"
-            },
-            {
-                "id": "Shians",
-                "joined": "2019-02",
-                "name": "Shian Su",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Shians/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/Shians.json"
-            },
-            {
-                "id": "charitylaw",
-                "joined": "2018-09",
-                "name": "Charity Law",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/charitylaw/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/charitylaw.json"
-            }
-        ],
-        "dir": "topics/transcriptomics/tutorials/rna-seq-counts-to-genes",
-        "edam_operation": [
-            "RNA-Seq analysis",
-            "Annotation"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "transcriptomics",
-                "tutorials": [
-                    "rna-seq-genes-to-pathways",
-                    "rna-seq-viz-with-heatmap2",
-                    "rna-seq-viz-with-volcanoplot",
-                    "rna-seq-analysis-with-askomics-it"
-                ],
-                "type": "internal"
-            }
-        ],
-        "hands_on": true,
-        "id": "transcriptomics/rna-seq-counts-to-genes",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.fr",
-            "UseGalaxy.org.au"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "The limma-voom tool can be used to perform differential expression and output useful plots",
-            "Multiple comparisons can be input and compared",
-            "Results can be interactively explored with limma-voom via Glimma"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-04-10",
-        "objectives": [
-            "Analysis of RNA-seq count data using limma-voom",
-            "QC of count data",
-            "Visualisation and interactive exploration of count data",
-            "Identification of differentially expressed genes"
-        ],
-        "pageviews": 64017,
-        "pub_date": "2018-12-31",
-        "questions": [
-            "What are the differentially expressed genes in the mammary gland of pregnant versus lactating mice?",
-            "How to analyze RNA count data using limma-voom?",
-            "How to perform quality control (QC) of RNA-seq count data?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "transcriptomics",
-                "tutorials": [
-                    "rna-seq-reads-to-counts"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00298",
-        "short_tools": [
-            "limma_voom",
-            "tp_cut_tool",
-            "tp_replace_in_line",
-            "annotatemyids",
-            "mergeCols1"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "end-to-end",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "limma-voom",
-            "mouse",
-            "QC"
-        ],
-        "time_estimation": "2h",
-        "title": "2: RNA-seq counts to genes",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.9"
-        ],
-        "topic_name": "transcriptomics",
-        "topic_name_human": "Transcriptomics",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "rna-seq-counts-to-genes",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.json"
-        },
-        "version": 21,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 135,
-        "visitors": 36104,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "RNA-seq counts to genes",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nseqdata\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nsampleinfo\"]\n  2[label=\"Cut\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Merge Columns\"]\n  1 -> 3 [label=\"output\"]\n  4[label=\"Replace Text\"]\n  2 -> 4 [label=\"output\"]\n  5[label=\"Cut\"]\n  3 -> 5 [label=\"out_file1\"]\n  6[label=\"annotateMyIDs\"]\n  4 -> 6 [label=\"outfile\"]\n  7[label=\"limma\"]\n  4 -> 7 [label=\"outfile\"]\n  6 -> 7 [label=\"out_tab\"]\n  5 -> 7 [label=\"output\"]\n}",
-                "history": [
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 3,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 2,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
+                                "output_name": "out",
+                                "uuid": "4a8852b4-c52e-438d-b803-000e7e0c3ccb"
+                            }
+                        ]
                     },
-                    {
-                        "hash": "0ea8c79012ba1b18d3f79be0ff2e2b826092f5e2",
-                        "message": "Rename tutorial and image folders to the updated titles",
-                        "num": 1,
-                        "short_hash": "0ea8c7901",
-                        "unix": "1546155649"
-                    }
-                ],
-                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.4.3+galaxy0",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 9,
+                        "input_connections": {
+                            "query": {
+                                "id": 8,
+                                "output_name": "out"
+                            },
+                            "reference|ref_fasta1": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "reference|ref_fasta2": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "ChiRA map",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "seqdata"
+                                "name": "mapped_bed",
+                                "type": "bed"
+                            },
+                            {
+                                "name": "unmapped_fasta",
+                                "type": "fasta"
                             }
                         ],
-                        "label": "seqdata",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 199.9921875,
-                            "top": 199.9921875
+                            "bottom": 431,
+                            "height": 242,
+                            "left": -111.5,
+                            "right": 88.5,
+                            "top": 189,
+                            "width": 200,
+                            "x": -111.5,
+                            "y": 189
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"seqdata\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "8424dc54-041c-4fd4-880a-bc9d97fff0b0",
-                        "workflow_outputs": []
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.4.3+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "92dbdc4d2722",
+                            "name": "chira_map",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"fasta\", \"alignment\": {\"aligner\": \"bwa\", \"__current_case__\": 0, \"stranded\": \"fw\", \"seed_length1\": \"12\", \"seed_length2\": \"16\", \"align_score1\": \"18\", \"align_score2\": \"16\", \"match1\": \"1\", \"mismatch1\": \"4\", \"match2\": \"1\", \"mismatch2\": \"6\", \"gapo1\": \"6\", \"gape1\": \"1\", \"gapo2\": \"100\", \"gape2\": \"100\", \"nhits1\": \"50\", \"nhits2\": \"100\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"query\": {\"__class__\": \"ConnectedValue\"}, \"reference\": {\"ref_type\": \"split\", \"__current_case__\": 0, \"ref_fasta1\": {\"__class__\": \"ConnectedValue\"}, \"ref_fasta2\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.4.3+galaxy0",
+                        "type": "tool",
+                        "uuid": "60e2db9d-f2ba-4293-9dab-343917d22702",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "mapped_bed",
+                                "uuid": "cc3b4775-520e-4c40-8a84-6dd4ac8c63c9"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "unmapped_fasta",
+                                "uuid": "c85cb34d-71c0-46d8-90e1-145e7a883b1f"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_merge/chira_merge/1.4.3+galaxy0",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 10,
+                        "input_connections": {
+                            "alignments": {
+                                "id": 9,
+                                "output_name": "mapped_bed"
+                            },
+                            "annotation|gtf": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "reference|ref_fasta1": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "reference|ref_fasta2": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "ChiRA merge",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "sampleinfo"
+                                "name": "segments_bed",
+                                "type": "bed"
+                            },
+                            {
+                                "name": "merged_bed",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "sampleinfo",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 199.9921875,
-                            "top": 290.015625
+                            "bottom": 521,
+                            "height": 332,
+                            "left": 174.5,
+                            "right": 374.5,
+                            "top": 189,
+                            "width": 200,
+                            "x": 174.5,
+                            "y": 189
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"sampleinfo\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "7f07c2d1-5ae3-4992-85e4-040a96852d22",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nseqdata\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nsampleinfo\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Cut\"];\n  0 -->|output| 2;\n  3[\"Merge Columns\"];\n  1 -->|output| 3;\n  4[\"Replace Text\"];\n  2 -->|output| 4;\n  5[\"Cut\"];\n  3 -->|out_file1| 5;\n  6[\"annotateMyIDs\"];\n  4 -->|outfile| 6;\n  7[\"limma\"];\n  4 -->|outfile| 7;\n  6 -->|out_tab| 7;\n  5 -->|output| 7;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "RNA Seq Counts To Genes",
-                "outputs": [],
-                "parent_id": "transcriptomics/rna-seq-counts-to-genes",
-                "path": "topics/transcriptomics/tutorials/rna-seq-counts-to-genes/workflows/rna-seq-counts-to-genes.ga",
-                "tags": [
-                    "transcriptomics"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "RNA Seq Counts To Genes",
-                "topic_id": "transcriptomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-rna-seq-counts-to-genes/versions/rna-seq-counts-to-genes",
-                "tutorial_id": "rna-seq-counts-to-genes",
-                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/workflows/rna-seq-counts-to-genes.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/workflows/rna-seq-counts-to-genes.html",
-                "version": 3,
-                "wfid": "transcriptomics-rna-seq-counts-to-genes",
-                "wfname": "rna-seq-counts-to-genes",
-                "workflow": "rna-seq-counts-to-genes.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.9"
-                ],
-                "workflowhub_id": "1321"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/4273218"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "datamash_transpose",
-                    "owner": "iuc",
-                    "revisions": "22c2a1ac7ae3",
-                    "tool_panel_section_label": "Join, Subtract and Group",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ggplot2_heatmap2",
-                    "owner": "iuc",
-                    "revisions": "4955e9bb96d1",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: datamash_transpose\n  owner: iuc\n  revisions: 22c2a1ac7ae3\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ggplot2_heatmap2\n  owner: iuc\n  revisions: 4955e9bb96d1\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.json",
-        "contributors": [
-            {
-                "id": "mblue9",
-                "joined": "2018-09",
-                "name": "Maria Doyle",
-                "orcid": "0000-0003-4847-8436",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
-            }
-        ],
-        "dir": "topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "transcriptomics/rna-seq-viz-with-heatmap2",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
-        ],
-        "js_requirements": {
-            "mathjax": 8185,
-            "mermaid": false
-        },
-        "key_points": [
-            "Heatmaps can be used to visualize the expression of genes in RNA-Seq samples"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Create heatmaps of RNA-seq data"
-        ],
-        "pageviews": 116209,
-        "pub_date": "2018-12-31",
-        "questions": [
-            "How to generate heatmaps from RNA-seq data?"
-        ],
-        "short_id": "T00303",
-        "short_tools": [
-            "Cut1",
-            "join1",
-            "ggplot2_heatmap2",
-            "datamash_transpose"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "visualisation",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "time_estimation": "1h",
-        "title": "Visualization of RNA-Seq results with heatmap2",
-        "tools": [
-            "Cut1",
-            "join1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1+galaxy1"
-        ],
-        "topic_name": "transcriptomics",
-        "topic_name_human": "Transcriptomics",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "rna-seq-viz-with-heatmap2",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/tutorial.json"
-        },
-        "version": 13,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 83,
-        "visitors": 67654,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Visualization of RNA-Seq results with heatmap2",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nheatmap_genes\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nnormalized_counts\"]\n  2[label=\"Join two Datasets\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Cut\"]\n  2 -> 3 [label=\"out_file1\"]\n  4[label=\"Transpose\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"heatmap2\"]\n  4 -> 5 [label=\"out_file\"]\n  k21dd5b7b6db441a3b246711f90f29e8c[color=lightseagreen,label=\"Output\\nheatmap_pdf\"]\n  5 -> k21dd5b7b6db441a3b246711f90f29e8c\n}",
-                "history": [
-                    {
-                        "hash": "2e2cb42d8ac99927000d81734fb53c7943c0c4ba",
-                        "message": "add tests from workflow-testing for blockclust and rna-seq-viz-with-volcano-plot, edit workflows",
-                        "num": 5,
-                        "short_hash": "2e2cb42d8",
-                        "unix": "1601812751"
-                    },
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 4,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 3,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "08df9d7e1855e90a0c05708a3541d318a9bbe002",
-                        "message": "Start on workflow test for heatmap2",
-                        "num": 2,
-                        "short_hash": "08df9d7e1",
-                        "unix": "1546157457"
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_merge/chira_merge/1.4.3+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "bd57d16524fe",
+                            "name": "chira_merge",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"bed\", \"alignment_overlap\": \"0.7\", \"alignments\": {\"__class__\": \"ConnectedValue\"}, \"annotation\": {\"choice\": \"yes\", \"__current_case__\": 0, \"gtf\": {\"__class__\": \"ConnectedValue\"}}, \"chimeric_only\": \"false\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"length_threshold\": \"0.9\", \"merge\": {\"mode\": \"overlap\", \"__current_case__\": 0, \"min_locus_size\": \"1\"}, \"reference\": {\"ref_type\": \"split\", \"__current_case__\": 0, \"ref_fasta1\": {\"__class__\": \"ConnectedValue\"}, \"ref_fasta2\": {\"__class__\": \"ConnectedValue\"}}, \"segment_overlap\": \"0.7\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.4.3+galaxy0",
+                        "type": "tool",
+                        "uuid": "bb4a876e-53c4-4231-8481-ff7f12b1f15f",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "merged_bed",
+                                "uuid": "9430b287-c1a4-489d-be0e-991e1eb77a7a"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "segments_bed",
+                                "uuid": "787ba9ae-d3db-461a-b48b-4834adf94c17"
+                            }
+                        ]
                     },
-                    {
-                        "hash": "0ea8c79012ba1b18d3f79be0ff2e2b826092f5e2",
-                        "message": "Rename tutorial and image folders to the updated titles",
-                        "num": 1,
-                        "short_hash": "0ea8c7901",
-                        "unix": "1546155649"
-                    }
-                ],
-                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_quantify/chira_quantify/1.4.3+galaxy0",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 11,
+                        "input_connections": {
+                            "merged": {
+                                "id": 10,
+                                "output_name": "merged_bed"
+                            },
+                            "segments": {
+                                "id": 10,
+                                "output_name": "segments_bed"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "ChiRA qauntify",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "heatmap_genes"
+                                "name": "loci",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "heatmap_genes",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 199.9921875,
-                            "top": 199.9921875
+                            "bottom": 391,
+                            "height": 202,
+                            "left": 460.5,
+                            "right": 660.5,
+                            "top": 189,
+                            "width": 200,
+                            "x": 460.5,
+                            "y": 189
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"heatmap_genes\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "d9f7a901-a868-430e-8bca-32e6956c2cb5",
-                        "workflow_outputs": []
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_quantify/chira_quantify/1.4.3+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "7fb3fc24be0e",
+                            "name": "chira_quantify",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__input_ext\": \"bed\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"crl\": \"true\", \"crl_share\": \"0.7\", \"em_threshold\": \"1e-05\", \"merged\": {\"__class__\": \"ConnectedValue\"}, \"min_locus_size\": \"10\", \"segments\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.4.3+galaxy0",
+                        "type": "tool",
+                        "uuid": "428b7bab-aef3-4c55-8a7b-4bd712f87340",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "loci",
+                                "uuid": "dce6af3f-130d-455b-9e20-c55ca20eab08"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_extract/chira_extract/1.4.3+galaxy0",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
+                        "id": 12,
+                        "input_connections": {
+                            "annotation|fasta_source|fasta": {
+                                "id": 4,
+                                "output_name": "output"
+                            },
+                            "annotation|gtf": {
+                                "id": 3,
+                                "output_name": "output"
+                            },
+                            "loci": {
+                                "id": 11,
+                                "output_name": "loci"
+                            },
+                            "reference|ref_fasta1": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "reference|ref_fasta2": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "normalized_counts"
+                                "description": "runtime parameter for tool ChiRA extract",
+                                "name": "annotation"
+                            },
+                            {
+                                "description": "runtime parameter for tool ChiRA extract",
+                                "name": "loci"
+                            },
+                            {
+                                "description": "runtime parameter for tool ChiRA extract",
+                                "name": "reference"
+                            },
+                            {
+                                "description": "runtime parameter for tool ChiRA extract",
+                                "name": "reference"
+                            }
+                        ],
+                        "label": null,
+                        "name": "ChiRA extract",
+                        "outputs": [
+                            {
+                                "name": "chimeras",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "interactions",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "normalized_counts",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 199.9921875,
-                            "top": 290.015625
+                            "bottom": 491,
+                            "height": 302,
+                            "left": 746.5,
+                            "right": 946.5,
+                            "top": 189,
+                            "width": 200,
+                            "x": 746.5,
+                            "y": 189
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"normalized_counts\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "59a5f2aa-972a-441c-93c1-9d2436a6b81f",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nheatmap_genes\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nnormalized_counts\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Join two Datasets\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Cut\"];\n  2 -->|out_file1| 3;\n  4[\"Transpose\"];\n  3 -->|out_file1| 4;\n  5[\"heatmap2\"];\n  4 -->|out_file| 5;\n  21dd5b7b-6db4-41a3-b246-711f90f29e8c[\"Output\\nheatmap_pdf\"];\n  5 --> 21dd5b7b-6db4-41a3-b246-711f90f29e8c;\n  style 21dd5b7b-6db4-41a3-b246-711f90f29e8c stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "Heatmap2 Workflow",
-                "outputs": [
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/chira_extract/chira_extract/1.4.3+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "6977e9b7143d",
+                            "name": "chira_extract",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"acc_width\": \"150\", \"accessibility\": \"false\", \"annotation\": {\"annot_choice\": \"yes\", \"__current_case__\": 0, \"gtf\": {\"__class__\": \"RuntimeValue\"}, \"fasta_source\": {\"fasta_source_selector\": \"history\", \"__current_case__\": 0, \"fasta\": {\"__class__\": \"RuntimeValue\"}}}, \"chimeric_overlap\": \"2\", \"hybridize\": \"true\", \"intarna_mode\": \"H\", \"loci\": {\"__class__\": \"RuntimeValue\"}, \"reference\": {\"ref_type\": \"split\", \"__current_case__\": 0, \"ref_fasta1\": {\"__class__\": \"RuntimeValue\"}, \"ref_fasta2\": {\"__class__\": \"RuntimeValue\"}}, \"score_cutoff\": \"0.0\", \"seed_bp\": \"5\", \"seed_interaction\": \"true\", \"seed_min_pu\": \"0.0\", \"summarize\": \"true\", \"temperature\": \"37.0\", \"tpm_cutoff\": \"0.0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.4.3+galaxy0",
+                        "type": "tool",
+                        "uuid": "ef85dc12-e50c-47b5-ab65-43d1bf2a6352",
+                        "workflow_outputs": [
+                            {
+                                "label": "interactions",
+                                "output_name": "interactions",
+                                "uuid": "7182226d-b48a-4ce1-882e-6bb41091a5d4"
+                            },
+                            {
+                                "label": "chimeric_reads",
+                                "output_name": "chimeras",
+                                "uuid": "011f4c89-d15a-4877-9d49-0146773ce781"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "errors": null,
-                        "id": 5,
+                        "id": 13,
                         "input_connections": {
-                            "input1": {
-                                "id": 4,
-                                "output_name": "out_file"
+                            "tables_0|table": {
+                                "id": 12,
+                                "output_name": "chimeras"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool heatmap2",
-                                "name": "input1"
+                                "description": "runtime parameter for tool Query Tabular",
+                                "name": "add_to_database"
                             }
                         ],
                         "label": null,
-                        "name": "heatmap2",
+                        "name": "Query Tabular",
                         "outputs": [
                             {
-                                "name": "output1",
-                                "type": "pdf"
+                                "name": "sqlitedb",
+                                "type": "sqlite"
                             }
                         ],
                         "position": {
-                            "left": 1254.1171875,
-                            "top": 199.9921875
+                            "bottom": 351,
+                            "height": 162,
+                            "left": 1032.5,
+                            "right": 1232.5,
+                            "top": 189,
+                            "width": 200,
+                            "x": 1032.5,
+                            "y": 189
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1+galaxy1",
+                        "post_job_actions": {
+                            "ChangeDatatypeActionsqlitedb": {
+                                "action_arguments": {
+                                    "newtype": "chira.sqlite"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "sqlitedb"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "4955e9bb96d1",
-                            "name": "ggplot2_heatmap2",
+                            "changeset_revision": "33d61c89fb8d",
+                            "name": "query_tabular",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"scale\": \"\\\"column\\\"\", \"colorscheme\": \"\\\"blwhre\\\"\", \"__rerun_remap_job_id__\": null, \"labels\": \"\\\"both\\\"\", \"transform\": \"\\\"none\\\"\", \"cluster\": \"\\\"false\\\"\", \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"key\": \"\\\"\\\"\", \"title\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm10.len\\\"\"}",
-                        "tool_version": "2.2.1+galaxy1",
+                        "tool_state": "{\"add_to_database\": {\"withdb\": {\"__class__\": \"RuntimeValue\"}}, \"addqueries\": {\"queries\": []}, \"modify_database\": {\"sql_stmts\": []}, \"query_result\": {\"header\": \"yes\", \"__current_case__\": 0, \"header_prefix\": \"35\"}, \"save_db\": \"true\", \"sqlquery\": \"\", \"tables\": [{\"__index__\": 0, \"table\": {\"__class__\": \"RuntimeValue\"}, \"input_opts\": {\"linefilters\": []}, \"tbl_opts\": {\"table_name\": \"\", \"column_names_from_first_line\": \"true\", \"col_names\": \"\", \"load_named_columns\": \"false\", \"pkey_autoincr\": \"\", \"indexes\": []}}], \"workdb\": \"workdb.sqlite\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "3.0.0",
                         "type": "tool",
-                        "uuid": "94e37309-eafe-4a3e-bbcb-fcf1924b77f3",
+                        "uuid": "fe30bba1-cda8-4926-924c-8dec7cd28222",
                         "workflow_outputs": [
                             {
-                                "label": "heatmap_pdf",
-                                "output_name": "output1",
-                                "uuid": "21dd5b7b-6db4-41a3-b246-711f90f29e8c"
+                                "label": "db",
+                                "output_name": "sqlitedb",
+                                "uuid": "f1315db2-11d1-4dee-9014-eafa1fc0f82f"
                             }
                         ]
                     }
                 ],
-                "parent_id": "transcriptomics/rna-seq-viz-with-heatmap2",
-                "path": "topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/workflows/rna-seq-viz-with-heatmap2.ga",
+                "parent_id": "transcriptomics/rna-interactome",
+                "path": "topics/transcriptomics/tutorials/rna-interactome/workflows/rna-rna-interactome-data-analysis-chira.ga",
                 "tags": [
+                    "RNA",
                     "transcriptomics"
                 ],
                 "test_results": null,
                 "tests": true,
-                "title": "Heatmap2 Workflow",
+                "title": "RNA-RNA interactome data analysis - chira  v1.4.3",
                 "topic_id": "transcriptomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-rna-seq-viz-with-heatmap2/versions/rna-seq-viz-with-heatmap2",
-                "tutorial_id": "rna-seq-viz-with-heatmap2",
-                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/workflows/rna-seq-viz-with-heatmap2.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-viz-with-heatmap2/workflows/rna-seq-viz-with-heatmap2.html",
-                "version": 4,
-                "wfid": "transcriptomics-rna-seq-viz-with-heatmap2",
-                "wfname": "rna-seq-viz-with-heatmap2",
-                "workflow": "rna-seq-viz-with-heatmap2.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-rna-interactome/versions/rna-rna-interactome-data-analysis-chira",
+                "tutorial_id": "rna-interactome",
+                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-interactome/workflows/rna-rna-interactome-data-analysis-chira.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-interactome/workflows/rna-rna-interactome-data-analysis-chira.html",
+                "version": 1,
+                "wfid": "transcriptomics-rna-interactome",
+                "wfname": "rna-rna-interactome-data-analysis-chira",
+                "workflow": "rna-rna-interactome-data-analysis-chira.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "join1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1+galaxy1"
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/chira_collapse/chira_collapse/1.4.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/chira_extract/chira_extract/1.4.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.4.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/chira_merge/chira_merge/1.4.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/chira_quantify/chira_quantify/1.4.3+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5"
                 ],
-                "workflowhub_id": "1311"
+                "workflowhub_id": "1291"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/2529926"
+        "zenodo_link": "https://zenodo.org/record/3709188"
     },
     {
         "admin_install": {
@@ -268455,129 +275884,285 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "goenrichment",
+                    "name": "salmon",
+                    "owner": "bgruening",
+                    "revisions": "e3d32471da11",
+                    "tool_panel_section_label": "RNA Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "trim_galore",
+                    "owner": "bgruening",
+                    "revisions": "949f01671246",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "e7b2202befea",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "filter_by_fasta_ids",
+                    "owner": "galaxyp",
+                    "revisions": "3c623e81be77",
+                    "tool_panel_section_label": "Proteomics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "deseq2",
                     "owner": "iuc",
-                    "revisions": "2c7c9646ccf0",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "6a3a025714d3",
+                    "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "goslimmer",
+                    "name": "multiqc",
                     "owner": "iuc",
-                    "revisions": "de3e053bd6a5",
-                    "tool_panel_section_label": "Annotation",
+                    "revisions": "b2f1f75d49c4",
+                    "tool_panel_section_label": "Quality Control",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "5e33b465d8d5",
+                    "tool_panel_section_label": "Quality Control",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sample_seqs",
+                    "owner": "peterjc",
+                    "revisions": "7c40a1fbc82e",
+                    "tool_panel_section_label": "Filter and Sort",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mirdeep2_mapper",
+                    "owner": "rnateam",
+                    "revisions": "a8d24f4b6d95",
+                    "tool_panel_section_label": "RNA Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mirdeep2_quantifier",
+                    "owner": "rnateam",
+                    "revisions": "d5ea61ff12eb",
+                    "tool_panel_section_label": "RNA Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "targetfinder",
+                    "owner": "rnateam",
+                    "revisions": "c9d56748fbde",
+                    "tool_panel_section_label": "RNA Analysis",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: goenrichment\n  owner: iuc\n  revisions: 2c7c9646ccf0\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: goslimmer\n  owner: iuc\n  revisions: de3e053bd6a5\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/goenrichment/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: salmon\n  owner: bgruening\n  revisions: e3d32471da11\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trim_galore\n  owner: bgruening\n  revisions: 949f01671246\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: filter_by_fasta_ids\n  owner: galaxyp\n  revisions: 3c623e81be77\n  tool_panel_section_label: Proteomics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deseq2\n  owner: iuc\n  revisions: 6a3a025714d3\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: b2f1f75d49c4\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 5e33b465d8d5\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sample_seqs\n  owner: peterjc\n  revisions: 7c40a1fbc82e\n  tool_panel_section_label: Filter and Sort\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mirdeep2_mapper\n  owner: rnateam\n  revisions: a8d24f4b6d95\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mirdeep2_quantifier\n  owner: rnateam\n  revisions: d5ea61ff12eb\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: targetfinder\n  owner: rnateam\n  revisions: c9d56748fbde\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.json",
         "contributors": [
             {
-                "id": "igcbioinformatics",
-                "joined": "2018-12",
-                "name": "IGC Bioinformatics Unit",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/igcbioinformatics/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/igcbioinformatics.json"
+                "elixir_node": "de",
+                "former_affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "gallardoalba",
+                "joined": "2020-11",
+                "name": "Crist\u00f3bal Gallardo",
+                "orcid": "0000-0002-5752-2155",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/gallardoalba.json"
             },
             {
-                "id": "mblue9",
-                "joined": "2018-09",
-                "name": "Maria Doyle",
-                "orcid": "0000-0003-4847-8436",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
+                "affiliations": [
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "id": "pavanvidem",
+                "joined": "2017-09",
+                "name": "Pavankumar Videm",
+                "orcid": "0000-0002-5192-126X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
+            },
+            {
+                "email": "beatrizserrano.galaxy@gmail.com",
+                "id": "beatrizserrano",
+                "joined": "2020-07",
+                "linkedin": "beatriz-serrano",
+                "matrix": "beatrizserrano:matrix.org",
+                "name": "Beatriz Serrano-Solano",
+                "orcid": "0000-0002-5862-6132",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/beatrizserrano/",
+                "twitter": "BSerranoSolano",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/beatrizserrano.json"
             }
         ],
-        "dir": "topics/transcriptomics/tutorials/goenrichment",
+        "dir": "topics/transcriptomics/tutorials/mirna-target-finder",
         "edam_operation": [
-            "Gene-set enrichment analysis"
+            "Sequence trimming",
+            "Differential gene expression analysis",
+            "Sequencing quality control",
+            "RNA-Seq analysis",
+            "Statistical calculation",
+            "Gene expression analysis",
+            "RNA-Seq quantification",
+            "Validation",
+            "Sequence composition calculation",
+            "Read pre-processing",
+            "Primer removal"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "transcriptomics/goenrichment",
-        "inexact_supported_servers": [],
+        "id": "transcriptomics/mirna-target-finder",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz",
+            "UseGalaxy.no"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "The goenrichment tool can be used to perform GO Enrichment analysis",
-            "One needs to be careful when chosing the background population",
-            "There are several methods to simplify the output of the GO Enrichment analysis"
+            "MiRDeep2 in combination with the PmiREN database allows to quantify miRNA expression in plants",
+            "The use of the Salmon tool and the AtRTD2 transcriptome allows rapid and accurate quantification of transcripts in _Arabidopsis_",
+            "The combination of differential expression analysis and the TargetFinder tool is an effective strategy for the identification of miRNA target genes"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-05",
+        "mod_date": "2024-08-09",
         "objectives": [
-            "How to perform a GO Enrichment Analysis",
-            "How to interpret and simplify the results"
+            "Perform miRNA differential expression analysis",
+            "Understand the quasi-mapping-based Salmon method for quantifying the expression of transcripts using RNA-Seq data",
+            "Idenfity potential miRNAs involved in brassinosteroid-mediated regulation networks"
         ],
-        "pageviews": 33923,
-        "pub_date": "2019-01-23",
+        "pageviews": 5390935,
+        "pub_date": "2021-04-08",
         "questions": [
-            "How can I functionally interpret a list of genes of interest that I obtained from my experiment?"
+            "Which miRNAs are upregulated in response to brassinosteroids?",
+            "Which genes are potential target of brassinosteroid-induced miRNAs?"
         ],
-        "short_id": "T00291",
+        "recordings": [
+            {
+                "captioners": [
+                    "gallardoalba"
+                ],
+                "date": "2021-07-25",
+                "galaxy_version": "21.05",
+                "length": "1H10M",
+                "speakers": [
+                    "gallardoalba"
+                ],
+                "youtube_id": "wS1X_0Mgw7M"
+            }
+        ],
+        "short_id": "T00292",
         "short_tools": [
-            "goenrichment",
-            "goslimmer",
-            "Filter1"
+            "filter_by_fasta_ids",
+            "targetfinder",
+            "sample_seqs",
+            "sort1",
+            "rbc_mirdeep2_mapper",
+            "Filter1",
+            "multiqc",
+            "rbc_mirdeep2_quantifier",
+            "Cut1",
+            "deseq2",
+            "fastqc",
+            "salmon",
+            "__MERGE_COLLECTION__",
+            "cat1",
+            "trim_galore"
+        ],
+        "slides": true,
+        "slides_recordings": [
+            {
+                "captioners": [
+                    "gallardoalba"
+                ],
+                "date": "2021-04-20",
+                "galaxy_version": "21.01",
+                "length": "10M",
+                "speakers": [
+                    "awspolly"
+                ],
+                "youtube_id": "FNmZoo2OXTU"
+            },
+            {
+                "captioners": [
+                    "gallardoalba"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "10M",
+                "speakers": [
+                    "awspolly"
+                ],
+                "youtube_id": "7t0Gr1Jklqs"
+            }
         ],
-        "slides": false,
-        "slides_recordings": false,
         "supported_servers": {
             "exact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
                 }
-            ],
-            "inexact": []
+            ]
         },
         "symlink": null,
-        "time_estimation": "1h",
-        "title": "GO Enrichment Analysis",
+        "tags": [
+            "miRNA",
+            "plants",
+            "stress tolerance"
+        ],
+        "time_estimation": "2H",
+        "title": "Whole transcriptome analysis of Arabidopsis thaliana",
         "tools": [
+            "Cut1",
             "Filter1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/goenrichment/goenrichment/2.0.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/goslimmer/goslimmer/1.0.1"
+            "__MERGE_COLLECTION__",
+            "cat1",
+            "sort1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.14.1.2+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.2.5",
+            "toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_mapper/rbc_mirdeep2_mapper/2.0.0",
+            "toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_quantifier/rbc_mirdeep2_quantifier/2.0.0",
+            "toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1"
         ],
         "topic_name": "transcriptomics",
         "topic_name_human": "Transcriptomics",
@@ -268585,53 +276170,81 @@
         "translations": {
             "slides": [],
             "tutorial": [],
-            "video": false
+            "video": true
         },
-        "tutorial_name": "goenrichment",
+        "tutorial_name": "mirna-target-finder",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/goenrichment/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/mirna-target-finder/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/goenrichment/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/goenrichment/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/mirna-target-finder/tutorial.json"
         },
-        "version": 12,
-        "video": false,
-        "video_versions": 0,
+        "version": 17,
+        "video": true,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 77,
-        "visitors": 20093,
+        "visit_duration": 313,
+        "visitors": 1988943,
         "workflows": [
             {
                 "creators": [],
-                "description": "GO Enrichment Analysis Tutorial",
+                "description": "Identify upregulated miRNAS and analyze potential targets in downregulated genes.",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGO annotations Drosophila melanogaster\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGO\"]\n  10[label=\"Filter\"]\n  2 -> 10 [label=\"output\"]\n  11[label=\"GOEnrichment\"]\n  3 -> 11 [label=\"output\"]\n  1 -> 11 [label=\"output\"]\n  4 -> 11 [label=\"output\"]\n  5 -> 11 [label=\"output\"]\n  12[label=\"GOEnrichment\"]\n  3 -> 12 [label=\"output\"]\n  1 -> 12 [label=\"output\"]\n  4 -> 12 [label=\"output\"]\n  5 -> 12 [label=\"output\"]\n  13[label=\"GOSlimmer\"]\n  3 -> 13 [label=\"output\"]\n  1 -> 13 [label=\"output\"]\n  6 -> 13 [label=\"output\"]\n  14[label=\"GOEnrichment\"]\n  3 -> 14 [label=\"output\"]\n  1 -> 14 [label=\"output\"]\n  4 -> 14 [label=\"output\"]\n  7 -> 14 [label=\"output\"]\n  15[label=\"GOEnrichment\"]\n  3 -> 15 [label=\"output\"]\n  1 -> 15 [label=\"output\"]\n  4 -> 15 [label=\"output\"]\n  8 -> 15 [label=\"output\"]\n  16[label=\"GOEnrichment\"]\n  0 -> 16 [label=\"output\"]\n  1 -> 16 [label=\"output\"]\n  2 -> 16 [label=\"output\"]\n  9 -> 16 [label=\"out_file1\"]\n  17[label=\"GOEnrichment\"]\n  0 -> 17 [label=\"output\"]\n  1 -> 17 [label=\"output\"]\n  10 -> 17 [label=\"out_file1\"]\n  9 -> 17 [label=\"out_file1\"]\n  18[label=\"GOEnrichment\"]\n  13 -> 18 [label=\"output\"]\n  6 -> 18 [label=\"output\"]\n  4 -> 18 [label=\"output\"]\n  5 -> 18 [label=\"output\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ntrapnellPopulation.tab\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGO annotations Mus musculus\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMouse population\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMouse diff\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGO Slim\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmouseUnderexpressed.txt\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nmouseOverexpressed.txt\"]\n  9[label=\"Filter\"]\n  2 -> 9 [label=\"output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nControl miRNA FASTQ collection\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nTreated miRNA FASTQ collection\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nTreated mRNA FASTQ collection\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPrecursor miRNA sequences\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nControl mRNA FASTQ collection\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nTranscriptome FASTA\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nAnnotation GTF\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nMature miRNA sequences\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nStar miRNA sequenes\"]\n  9[label=\"FastQC\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"Trim Galore!\"]\n  0 -> 10 [label=\"output\"]\n  11[label=\"FastQC\"]\n  1 -> 11 [label=\"output\"]\n  12[label=\"Trim Galore!\"]\n  1 -> 12 [label=\"output\"]\n  13[label=\"FastQC\"]\n  2 -> 13 [label=\"output\"]\n  14[label=\"FastQC\"]\n  4 -> 14 [label=\"output\"]\n  15[label=\"Salmon quant\"]\n  6 -> 15 [label=\"output\"]\n  2 -> 15 [label=\"output\"]\n  5 -> 15 [label=\"output\"]\n  16[label=\"Salmon quant\"]\n  6 -> 16 [label=\"output\"]\n  4 -> 16 [label=\"output\"]\n  5 -> 16 [label=\"output\"]\n  17[label=\"FastQC\"]\n  10 -> 17 [label=\"trimmed_reads_single\"]\n  18[label=\"MiRDeep2 Mapper\"]\n  10 -> 18 [label=\"trimmed_reads_single\"]\n  19[label=\"Merge collections\"]\n  11 -> 19 [label=\"text_file\"]\n  9 -> 19 [label=\"text_file\"]\n  20[label=\"FastQC\"]\n  12 -> 20 [label=\"trimmed_reads_single\"]\n  21[label=\"MiRDeep2 Mapper\"]\n  12 -> 21 [label=\"trimmed_reads_single\"]\n  22[label=\"Merge collections\"]\n  13 -> 22 [label=\"text_file\"]\n  14 -> 22 [label=\"text_file\"]\n  23[label=\"DESeq2\"]\n  15 -> 23 [label=\"output_gene_quant\"]\n  16 -> 23 [label=\"output_gene_quant\"]\n  6 -> 23 [label=\"output\"]\n  24[label=\"MiRDeep2 Quantifier\"]\n  7 -> 24 [label=\"output\"]\n  3 -> 24 [label=\"output\"]\n  18 -> 24 [label=\"output_reads_collapsed\"]\n  8 -> 24 [label=\"output\"]\n  25[label=\"MultiQC\"]\n  19 -> 25 [label=\"output\"]\n  26[label=\"Merge collections\"]\n  20 -> 26 [label=\"text_file\"]\n  17 -> 26 [label=\"text_file\"]\n  27[label=\"MiRDeep2 Quantifier\"]\n  7 -> 27 [label=\"output\"]\n  3 -> 27 [label=\"output\"]\n  21 -> 27 [label=\"output_reads_collapsed\"]\n  8 -> 27 [label=\"output\"]\n  28[label=\"MultiQC\"]\n  22 -> 28 [label=\"output\"]\n  29[label=\"Filter\"]\n  23 -> 29 [label=\"deseq_out\"]\n  30[label=\"Cut\"]\n  24 -> 30 [label=\"miRNAsExpressed\"]\n  31[label=\"MultiQC\"]\n  26 -> 31 [label=\"output\"]\n  32[label=\"Cut\"]\n  27 -> 32 [label=\"miRNAsExpressed\"]\n  33[label=\"Filter\"]\n  29 -> 33 [label=\"out_file1\"]\n  34[label=\"Filter\"]\n  29 -> 34 [label=\"out_file1\"]\n  35[label=\"DESeq2\"]\n  32 -> 35 [label=\"out_file1\"]\n  30 -> 35 [label=\"out_file1\"]\n  36[label=\"Cut\"]\n  34 -> 36 [label=\"out_file1\"]\n  37[label=\"Filter\"]\n  35 -> 37 [label=\"deseq_out\"]\n  38[label=\"Filter FASTA\"]\n  36 -> 38 [label=\"out_file1\"]\n  5 -> 38 [label=\"output\"]\n  39[label=\"Filter\"]\n  37 -> 39 [label=\"out_file1\"]\n  40[label=\"Filter\"]\n  37 -> 40 [label=\"out_file1\"]\n  41[label=\"Cut\"]\n  40 -> 41 [label=\"out_file1\"]\n  42[label=\"Filter FASTA\"]\n  41 -> 42 [label=\"out_file1\"]\n  8 -> 42 [label=\"output\"]\n  43[label=\"Filter FASTA\"]\n  41 -> 43 [label=\"out_file1\"]\n  7 -> 43 [label=\"output\"]\n  44[label=\"Concatenate datasets\"]\n  43 -> 44 [label=\"output\"]\n  42 -> 44 [label=\"output\"]\n  45[label=\"TargetFinder\"]\n  38 -> 45 [label=\"output\"]\n  44 -> 45 [label=\"out_file1\"]\n}",
                 "history": [
                     {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
+                        "hash": "87d458cc1fd8db170670ddd5c186c98295267d9e",
+                        "message": "Undo error",
+                        "num": 7,
+                        "short_hash": "87d458cc1",
+                        "unix": "1674149735"
+                    },
+                    {
+                        "hash": "edf36428b978d5519a494eaee576a8a17c6c948e",
+                        "message": "Fix tutorial",
+                        "num": 6,
+                        "short_hash": "edf36428b",
+                        "unix": "1669862549"
+                    },
+                    {
+                        "hash": "a6636e32469b78edc30efcc646f92e77c4bdb58b",
+                        "message": "add tags and annotation to the workflow",
+                        "num": 5,
+                        "short_hash": "a6636e324",
+                        "unix": "1617760834"
+                    },
+                    {
+                        "hash": "a5a1a7567b95fa539b493a98f5924d2482e16997",
+                        "message": "Update workflow for miRNA target identification in Arabidopsis",
+                        "num": 4,
+                        "short_hash": "a5a1a7567",
+                        "unix": "1617760351"
+                    },
+                    {
+                        "hash": "0eacaeef42cdfef3d6f60d4ec481a3ef84b72765",
+                        "message": "Update workflow and include downregulated miRNAS",
                         "num": 3,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
+                        "short_hash": "0eacaeef4",
+                        "unix": "1617194856"
                     },
                     {
-                        "hash": "361236c416497d2d9f2735d64f8c43050a5a5a4e",
-                        "message": "Changed format of workflows",
+                        "hash": "bdbe72dd283efbb454cf60a91384a9d130f8b342",
+                        "message": "Fix tests workflow",
                         "num": 2,
-                        "short_hash": "361236c41",
-                        "unix": "1554368414"
+                        "short_hash": "bdbe72dd2",
+                        "unix": "1616702513"
                     },
                     {
-                        "hash": "79f4dd991355ce9a98383d5425140fc9af718dd1",
-                        "message": "Create goenrichment-workflow.ga",
+                        "hash": "4b406638ca884e2ad7b58db02d9c4cc7eff0005d",
+                        "message": "New training: miRNA target finder",
                         "num": 1,
-                        "short_hash": "79f4dd991",
-                        "unix": "1550179581"
+                        "short_hash": "4b406638c",
+                        "unix": "1616700503"
                     }
                 ],
                 "inputs": [
@@ -268644,21 +276257,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "GO annotations Drosophila melanogaster"
+                                "name": "Control miRNA FASTQ collection"
                             }
                         ],
-                        "label": "GO annotations Drosophila melanogaster",
-                        "name": "Input dataset",
+                        "label": "Control miRNA FASTQ collection",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 200
+                            "left": 0,
+                            "top": 1.984375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"GO annotations Drosophila melanogaster\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "44a4f678-6028-45fb-b5fc-59e6d6d30360",
+                        "type": "data_collection_input",
+                        "uuid": "286f34e3-d05b-40ba-b39e-2f0c7455ff23",
                         "workflow_outputs": []
                     },
                     {
@@ -268670,21 +276283,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "GO"
+                                "name": "Treated miRNA FASTQ collection"
                             }
                         ],
-                        "label": "GO",
-                        "name": "Input dataset",
+                        "label": "Treated miRNA FASTQ collection",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 320
+                            "left": 0,
+                            "top": 331.984375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"GO\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ae9b3261-ca22-4018-8774-169358633422",
+                        "type": "data_collection_input",
+                        "uuid": "6ffd974f-fd40-4234-9bda-6edd9e65e702",
                         "workflow_outputs": []
                     },
                     {
@@ -268696,21 +276309,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "trapnellPopulation.tab"
+                                "name": "Treated mRNA FASTQ collection"
                             }
                         ],
-                        "label": "trapnellPopulation.tab",
-                        "name": "Input dataset",
+                        "label": "Treated mRNA FASTQ collection",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 440
+                            "left": 1161.984375,
+                            "top": 778.984375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"trapnellPopulation.tab\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "b9332a9d-0dee-4a27-826c-1213b93c9c20",
+                        "type": "data_collection_input",
+                        "uuid": "e2260dff-96ce-4345-902a-73958f9ac0cf",
                         "workflow_outputs": []
                     },
                     {
@@ -268722,21 +276335,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "GO annotations Mus musculus"
+                                "name": "Precursor miRNA sequences"
                             }
                         ],
-                        "label": "GO annotations Mus musculus",
+                        "label": "Precursor miRNA sequences",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 560
+                            "left": 575.984375,
+                            "top": 1461.984375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"GO annotations Mus musculus\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "623b33b8-5edb-4f85-b377-127d0659504e",
+                        "uuid": "7e8825d5-8e7f-4ec4-b0b4-f0efcc70e504",
                         "workflow_outputs": []
                     },
                     {
@@ -268748,21 +276361,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Mouse population"
+                                "name": "Control mRNA FASTQ collection"
                             }
                         ],
-                        "label": "Mouse population",
-                        "name": "Input dataset",
+                        "label": "Control mRNA FASTQ collection",
+                        "name": "Input dataset collection",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 680
+                            "left": 1161.984375,
+                            "top": 1101.984375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"Mouse population\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
                         "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ea004077-e2c7-4e92-a003-ec25f25df0a0",
+                        "type": "data_collection_input",
+                        "uuid": "5f622114-e64d-4a96-9866-e519b583cd98",
                         "workflow_outputs": []
                     },
                     {
@@ -268774,21 +276387,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "Mouse diff"
+                                "name": "Transcriptome FASTA"
                             }
                         ],
-                        "label": "Mouse diff",
+                        "label": "Transcriptome FASTA",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 800
+                            "left": 1161.984375,
+                            "top": 1220.984375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"Mouse diff\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "af1838d3-3af6-4e52-aa38-6ba38eae2c58",
+                        "uuid": "5bbd4e69-3b60-47e1-aecf-5d43ae6b54e5",
                         "workflow_outputs": []
                     },
                     {
@@ -268800,21 +276413,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "GO Slim"
+                                "name": "Annotation GTF"
                             }
                         ],
-                        "label": "GO Slim",
+                        "label": "Annotation GTF",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 920
+                            "left": 1161.984375,
+                            "top": 1340
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"GO Slim\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "bc59fd06-ef94-46ea-a20b-b884f3b9a1b2",
+                        "uuid": "570e8113-930a-4567-a380-fdb93fbcc60f",
                         "workflow_outputs": []
                     },
                     {
@@ -268826,21 +276439,21 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "mouseUnderexpressed.txt"
+                                "name": "Mature miRNA sequences"
                             }
                         ],
-                        "label": "mouseUnderexpressed.txt",
+                        "label": "Mature miRNA sequences",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 1040
+                            "left": 575.984375,
+                            "top": 1770.984375
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"mouseUnderexpressed.txt\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "3d85962e-96c5-4152-962d-0cbb1757e2ed",
+                        "uuid": "5d65f949-64bf-4f17-b242-f94d342b14a8",
                         "workflow_outputs": []
                     },
                     {
@@ -268852,1069 +276465,684 @@
                         "inputs": [
                             {
                                 "description": "",
-                                "name": "mouseOverexpressed.txt"
+                                "name": "Star miRNA sequenes"
                             }
                         ],
-                        "label": "mouseOverexpressed.txt",
+                        "label": "Star miRNA sequenes",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 1160
+                            "left": 575.984375,
+                            "top": 1890
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"mouseOverexpressed.txt\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "a81fec4d-a0b7-4e26-b1be-55ae410e5b58",
+                        "uuid": "d11848be-2417-4393-b87f-5e4d9500b4ed",
                         "workflow_outputs": []
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGO annotations Drosophila melanogaster\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGO\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Filter\"];\n  2 -->|output| 10;\n  11[\"GOEnrichment\"];\n  3 -->|output| 11;\n  1 -->|output| 11;\n  4 -->|output| 11;\n  5 -->|output| 11;\n  12[\"GOEnrichment\"];\n  3 -->|output| 12;\n  1 -->|output| 12;\n  4 -->|output| 12;\n  5 -->|output| 12;\n  13[\"GOSlimmer\"];\n  3 -->|output| 13;\n  1 -->|output| 13;\n  6 -->|output| 13;\n  14[\"GOEnrichment\"];\n  3 -->|output| 14;\n  1 -->|output| 14;\n  4 -->|output| 14;\n  7 -->|output| 14;\n  15[\"GOEnrichment\"];\n  3 -->|output| 15;\n  1 -->|output| 15;\n  4 -->|output| 15;\n  8 -->|output| 15;\n  16[\"GOEnrichment\"];\n  0 -->|output| 16;\n  1 -->|output| 16;\n  2 -->|output| 16;\n  9 -->|out_file1| 16;\n  17[\"GOEnrichment\"];\n  0 -->|output| 17;\n  1 -->|output| 17;\n  10 -->|out_file1| 17;\n  9 -->|out_file1| 17;\n  18[\"GOEnrichment\"];\n  13 -->|output| 18;\n  6 -->|output| 18;\n  4 -->|output| 18;\n  5 -->|output| 18;\n  2[\"\u2139\ufe0f Input Dataset\\ntrapnellPopulation.tab\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nGO annotations Mus musculus\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nMouse population\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nMouse diff\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nGO Slim\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nmouseUnderexpressed.txt\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nmouseOverexpressed.txt\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"Filter\"];\n  2 -->|output| 9;",
-                "modified": "2024-08-18 00:06:25 +0000",
-                "name": "GO Enrichment Workflow",
-                "outputs": [],
-                "parent_id": "transcriptomics/goenrichment",
-                "path": "topics/transcriptomics/tutorials/goenrichment/workflows/goenrichment-workflow.ga",
-                "tags": [
-                    "transcriptomics"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "GO Enrichment Workflow",
-                "topic_id": "transcriptomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-goenrichment/versions/goenrichment-workflow",
-                "tutorial_id": "goenrichment",
-                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/goenrichment/workflows/goenrichment-workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/goenrichment/workflows/goenrichment-workflow.html",
-                "version": 3,
-                "wfid": "transcriptomics-goenrichment",
-                "wfname": "goenrichment-workflow",
-                "workflow": "goenrichment-workflow.ga",
-                "workflow_tools": [
-                    "Filter1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/goenrichment/goenrichment/2.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/goslimmer/goslimmer/1.0.1"
-                ],
-                "workflowhub_id": "1315"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/2565417"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_sort",
-                    "owner": "devteam",
-                    "revisions": "f56bdb93ae58",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "blockbuster",
-                    "owner": "rnateam",
-                    "revisions": "7c7ff7a3503f",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "blockclust",
-                    "owner": "rnateam",
-                    "revisions": "aab6cf87b40a",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_sort\n  owner: devteam\n  revisions: f56bdb93ae58\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: blockbuster\n  owner: rnateam\n  revisions: 7c7ff7a3503f\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: blockclust\n  owner: rnateam\n  revisions: aab6cf87b40a\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/small_ncrna_clustering/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "id": "pavanvidem",
-                "joined": "2017-09",
-                "name": "Pavankumar Videm",
-                "orcid": "0000-0002-5192-126X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pavanvidem.json"
-            }
-        ],
-        "dir": "topics/transcriptomics/tutorials/small_ncrna_clustering",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "transcriptomics/small_ncrna_clustering",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Small non-coding RNA read profiles are often associate with function",
-            "Clusters of read profiles correlate with the ncRNA classes"
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Difference between mRNA-seq and smallRNA-seq",
-            "Unsupervised grouping of the adjacent reads into read profiles",
-            "Look and learn what the shapes of the read profiles represent",
-            "Clustering of the read profiles by machine learning algorithm"
-        ],
-        "pageviews": 1180,
-        "pub_date": "2018-12-14",
-        "questions": [
-            "What do the read profiles of small non-coding RNAs represent?",
-            "How to cluster the read profiles based on some intrinsic features?"
-        ],
-        "short_id": "T00306",
-        "short_tools": [
-            "blockclust",
-            "blockbuster",
-            "tp_sort_header_tool",
-            "samtools_sort"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ]
-        },
-        "symlink": null,
-        "time_estimation": "1H",
-        "title": "Small Non-coding RNA Clustering using BlockClust",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.2",
-            "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2",
-            "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0"
-        ],
-        "topic_name": "transcriptomics",
-        "topic_name_human": "Transcriptomics",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "small_ncrna_clustering",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/small_ncrna_clustering/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/small_ncrna_clustering/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/small_ncrna_clustering/tutorial.json"
-        },
-        "version": 8,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 177,
-        "visitors": 843,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Small Non-coding RNA Clustering using BlockClust",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nblockclust_input\"]\n  1[label=\"Samtools sort\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"BlockClust\"]\n  1 -> 2 [label=\"output1\"]\n  k39f8722a844442f88104f81201804c9c[color=lightseagreen,label=\"Output\\ntags_bed\"]\n  2 -> k39f8722a844442f88104f81201804c9c\n  3[label=\"Sort\"]\n  2 -> 3 [label=\"tags_bed\"]\n  4[label=\"blockbuster\"]\n  3 -> 4 [label=\"outfile\"]\n  k95c21ce9e98844b9978e10a27b74d18e[color=lightseagreen,label=\"Output\\nblockbuster_out\"]\n  4 -> k95c21ce9e98844b9978e10a27b74d18e\n  5[label=\"BlockClust\"]\n  4 -> 5 [label=\"output\"]\n  k241feec19ffd4d289b65e58850198c6d[color=lightseagreen,label=\"Output\\nmodel_based_pred_bed\"]\n  5 -> k241feec19ffd4d289b65e58850198c6d\n  k287b4bae55a14f38b1c362ae60b4d950[color=lightseagreen,label=\"Output\\nclusters_bed\"]\n  5 -> k287b4bae55a14f38b1c362ae60b4d950\n}",
-                "history": [
-                    {
-                        "hash": "2e2cb42d8ac99927000d81734fb53c7943c0c4ba",
-                        "message": "add tests from workflow-testing for blockclust and rna-seq-viz-with-volcano-plot, edit workflows",
-                        "num": 4,
-                        "short_hash": "2e2cb42d8",
-                        "unix": "1601812751"
-                    },
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 3,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 2,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "0afe265cf142d3ad8b39a4010e0b2d0ca931677c",
-                        "message": "initial version of training material for small ncRNA clustering using blockclust",
-                        "num": 1,
-                        "short_hash": "0afe265cf",
-                        "unix": "1544604285"
-                    }
-                ],
-                "inputs": [
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nControl miRNA FASTQ collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nTreated miRNA FASTQ collection\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nTreated mRNA FASTQ collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nPrecursor miRNA sequences\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Collection\\nControl mRNA FASTQ collection\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nTranscriptome FASTA\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nAnnotation GTF\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nMature miRNA sequences\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nStar miRNA sequenes\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"FastQC\"];\n  0 -->|output| 9;\n  10[\"Trim Galore!\"];\n  0 -->|output| 10;\n  11[\"FastQC\"];\n  1 -->|output| 11;\n  12[\"Trim Galore!\"];\n  1 -->|output| 12;\n  13[\"FastQC\"];\n  2 -->|output| 13;\n  14[\"FastQC\"];\n  4 -->|output| 14;\n  15[\"Salmon quant\"];\n  6 -->|output| 15;\n  2 -->|output| 15;\n  5 -->|output| 15;\n  16[\"Salmon quant\"];\n  6 -->|output| 16;\n  4 -->|output| 16;\n  5 -->|output| 16;\n  17[\"FastQC\"];\n  10 -->|trimmed_reads_single| 17;\n  18[\"MiRDeep2 Mapper\"];\n  10 -->|trimmed_reads_single| 18;\n  19[\"Merge collections\"];\n  11 -->|text_file| 19;\n  9 -->|text_file| 19;\n  20[\"FastQC\"];\n  12 -->|trimmed_reads_single| 20;\n  21[\"MiRDeep2 Mapper\"];\n  12 -->|trimmed_reads_single| 21;\n  22[\"Merge collections\"];\n  13 -->|text_file| 22;\n  14 -->|text_file| 22;\n  23[\"DESeq2\"];\n  15 -->|output_gene_quant| 23;\n  16 -->|output_gene_quant| 23;\n  6 -->|output| 23;\n  24[\"MiRDeep2 Quantifier\"];\n  7 -->|output| 24;\n  3 -->|output| 24;\n  18 -->|output_reads_collapsed| 24;\n  8 -->|output| 24;\n  25[\"MultiQC\"];\n  19 -->|output| 25;\n  26[\"Merge collections\"];\n  20 -->|text_file| 26;\n  17 -->|text_file| 26;\n  27[\"MiRDeep2 Quantifier\"];\n  7 -->|output| 27;\n  3 -->|output| 27;\n  21 -->|output_reads_collapsed| 27;\n  8 -->|output| 27;\n  28[\"MultiQC\"];\n  22 -->|output| 28;\n  29[\"Filter\"];\n  23 -->|deseq_out| 29;\n  30[\"Cut\"];\n  24 -->|miRNAsExpressed| 30;\n  31[\"MultiQC\"];\n  26 -->|output| 31;\n  32[\"Cut\"];\n  27 -->|miRNAsExpressed| 32;\n  33[\"Filter\"];\n  29 -->|out_file1| 33;\n  34[\"Filter\"];\n  29 -->|out_file1| 34;\n  35[\"DESeq2\"];\n  32 -->|out_file1| 35;\n  30 -->|out_file1| 35;\n  36[\"Cut\"];\n  34 -->|out_file1| 36;\n  37[\"Filter\"];\n  35 -->|deseq_out| 37;\n  38[\"Filter FASTA\"];\n  36 -->|out_file1| 38;\n  5 -->|output| 38;\n  39[\"Filter\"];\n  37 -->|out_file1| 39;\n  40[\"Filter\"];\n  37 -->|out_file1| 40;\n  41[\"Cut\"];\n  40 -->|out_file1| 41;\n  42[\"Filter FASTA\"];\n  41 -->|out_file1| 42;\n  8 -->|output| 42;\n  43[\"Filter FASTA\"];\n  41 -->|out_file1| 43;\n  7 -->|output| 43;\n  44[\"Concatenate datasets\"];\n  43 -->|output| 44;\n  42 -->|output| 44;\n  45[\"TargetFinder\"];\n  38 -->|output| 45;\n  44 -->|out_file1| 45;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "Plant bulk RNA-Seq workflow",
+                "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
+                        "id": 23,
+                        "input_connections": {
+                            "select_data|rep_factorName_0|rep_factorLevel_0|countsFile": {
+                                "id": 15,
+                                "output_name": "output_gene_quant"
+                            },
+                            "select_data|rep_factorName_0|rep_factorLevel_1|countsFile": {
+                                "id": 16,
+                                "output_name": "output_gene_quant"
+                            },
+                            "tximport|mapping_format|gtf_file": {
+                                "id": 6,
+                                "output_name": "output"
+                            }
+                        },
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "blockclust_input"
+                                "description": "runtime parameter for tool DESeq2",
+                                "name": "batch_factors"
+                            }
+                        ],
+                        "label": null,
+                        "name": "DESeq2",
+                        "outputs": [
+                            {
+                                "name": "deseq_out",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "plots",
+                                "type": "pdf"
                             }
                         ],
-                        "label": "blockclust_input",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 212
+                            "left": 1737.984375,
+                            "top": 1170.984375
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "b6e23dd8-46ca-4bd6-87f3-2f6b741b459b",
+                        "post_job_actions": {
+                            "RenameDatasetActiondeseq_out": {
+                                "action_arguments": {
+                                    "newname": "DESeq2 results mRNA"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "deseq_out"
+                            },
+                            "RenameDatasetActionplots": {
+                                "action_arguments": {
+                                    "newname": "DESeq2 plots mRNA"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "plots"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "6a3a025714d3",
+                            "name": "deseq2",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"auto_mean_filter_off\": \"false\", \"batch_factors\": {\"__class__\": \"RuntimeValue\"}, \"esf\": \"\", \"fit_type\": \"1\", \"header\": \"true\", \"many_contrasts\": \"false\", \"normCounts\": \"false\", \"normRLog\": \"false\", \"normVST\": \"false\", \"outlier_filter_off\": \"false\", \"outlier_replace_off\": \"false\", \"pdf\": \"true\", \"select_data\": {\"how\": \"datasets_per_level\", \"__current_case__\": 1, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": \"effects_brassinolide\", \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": \"brassinolide\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"factorLevel\": \"control\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"tximport\", \"__current_case__\": 0, \"txtype\": \"salmon\", \"mapping_format\": {\"mapping_format_selector\": \"gtf\", \"__current_case__\": 0, \"gtf_file\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.11.40.6+galaxy1",
+                        "type": "tool",
+                        "uuid": "db23fb5b-af4b-4fe1-8f8d-99a3176808e7",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "64e45b5f-8e46-4ae9-96c1-c452601a3bfc"
+                                "output_name": "plots",
+                                "uuid": "6c720aa2-a057-45c4-a813-3065d95c6c7f"
+                            },
+                            {
+                                "label": null,
+                                "output_name": "deseq_out",
+                                "uuid": "77e6746d-7bf9-400f-ac1e-106db58fbbbd"
                             }
                         ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nblockclust_input\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Samtools sort\"];\n  0 -->|output| 1;\n  2[\"BlockClust\"];\n  1 -->|output1| 2;\n  39f8722a-8444-42f8-8104-f81201804c9c[\"Output\\ntags_bed\"];\n  2 --> 39f8722a-8444-42f8-8104-f81201804c9c;\n  style 39f8722a-8444-42f8-8104-f81201804c9c stroke:#2c3143,stroke-width:4px;\n  3[\"Sort\"];\n  2 -->|tags_bed| 3;\n  4[\"blockbuster\"];\n  3 -->|outfile| 4;\n  95c21ce9-e988-44b9-978e-10a27b74d18e[\"Output\\nblockbuster_out\"];\n  4 --> 95c21ce9-e988-44b9-978e-10a27b74d18e;\n  style 95c21ce9-e988-44b9-978e-10a27b74d18e stroke:#2c3143,stroke-width:4px;\n  5[\"BlockClust\"];\n  4 -->|output| 5;\n  241feec1-9ffd-4d28-9b65-e58850198c6d[\"Output\\nmodel_based_pred_bed\"];\n  5 --> 241feec1-9ffd-4d28-9b65-e58850198c6d;\n  style 241feec1-9ffd-4d28-9b65-e58850198c6d stroke:#2c3143,stroke-width:4px;\n  287b4bae-55a1-4f38-b1c3-62ae60b4d950[\"Output\\nclusters_bed\"];\n  5 --> 287b4bae-55a1-4f38-b1c3-62ae60b4d950;\n  style 287b4bae-55a1-4f38-b1c3-62ae60b4d950 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "Blockclust 1.1.0 Clustering",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 25,
+                        "input_connections": {
+                            "results_0|software_cond|output_0|input": {
+                                "id": 19,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "MultiQC",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "blockclust_input"
+                                "name": "stats",
+                                "type": "input"
+                            },
+                            {
+                                "name": "html_report",
+                                "type": "html"
                             }
                         ],
-                        "label": "blockclust_input",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 200,
-                            "top": 212
+                            "left": 883.984375,
+                            "top": 342.984375
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "b6e23dd8-46ca-4bd6-87f3-2f6b741b459b",
+                        "post_job_actions": {
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "RenameDatasetActionhtml_report": {
+                                "action_arguments": {
+                                    "newname": "MultiQC unprocessed miRNA: Webpage"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "html_report"
+                            },
+                            "RenameDatasetActionstats": {
+                                "action_arguments": {
+                                    "newname": "MultiQC unprocessed miRNA: Stats"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "stats"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                        "tool_shed_repository": {
+                            "changeset_revision": "b2f1f75d49c4",
+                            "name": "multiqc",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"comment\": \"\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": \"false\", \"title\": \"miRNA initial quality check\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7",
+                        "type": "tool",
+                        "uuid": "3e845cfd-ddd1-4f60-b1cb-ac16dc2c6d10",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "output",
-                                "uuid": "64e45b5f-8e46-4ae9-96c1-c452601a3bfc"
+                                "output_name": "html_report",
+                                "uuid": "7cd34a0f-1142-4965-afa2-5f77e9c79b9e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
                         "errors": null,
-                        "id": 2,
+                        "id": 28,
                         "input_connections": {
-                            "tool_mode|reads_bam": {
-                                "id": 1,
-                                "output_name": "output1"
+                            "results_0|software_cond|output_0|input": {
+                                "id": 22,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "BlockClust",
+                        "name": "MultiQC",
                         "outputs": [
                             {
-                                "name": "tags_bed",
-                                "type": "bed"
+                                "name": "stats",
+                                "type": "input"
+                            },
+                            {
+                                "name": "html_report",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 788,
-                            "top": 212
+                            "left": 2035.984375,
+                            "top": 1455
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0",
+                        "post_job_actions": {
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "RenameDatasetActionhtml_report": {
+                                "action_arguments": {
+                                    "newname": "MultiQC mRNA: Webpage"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "html_report"
+                            },
+                            "RenameDatasetActionstats": {
+                                "action_arguments": {
+                                    "newname": "MultiQC mRNA: Stats"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "stats"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
                         "tool_shed_repository": {
-                            "changeset_revision": "aab6cf87b40a",
-                            "name": "blockclust",
-                            "owner": "rnateam",
+                            "changeset_revision": "b2f1f75d49c4",
+                            "name": "multiqc",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"tool_mode\": {\"operation\": \"pre\", \"__current_case__\": 0, \"reads_bam\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.0",
+                        "tool_state": "{\"comment\": \"\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"RuntimeValue\"}}]}}], \"saveLog\": \"false\", \"title\": \"mRNA initial quality check\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7",
                         "type": "tool",
-                        "uuid": "fd3043d3-609e-4303-bcb5-448cb749a319",
+                        "uuid": "b7ffd734-4c99-4132-814f-47b75b4b5d63",
                         "workflow_outputs": [
                             {
-                                "label": "tags_bed",
-                                "output_name": "tags_bed",
-                                "uuid": "39f8722a-8444-42f8-8104-f81201804c9c"
+                                "label": null,
+                                "output_name": "html_report",
+                                "uuid": "7d5b5d84-d0b0-4639-9b42-61bf9f7e014d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
                         "errors": null,
-                        "id": 4,
+                        "id": 31,
                         "input_connections": {
-                            "input": {
-                                "id": 3,
-                                "output_name": "outfile"
+                            "results_0|software_cond|output_0|input": {
+                                "id": 26,
+                                "output_name": "output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "blockbuster",
+                        "name": "MultiQC",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "bed"
+                                "name": "stats",
+                                "type": "input"
+                            },
+                            {
+                                "name": "html_report",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 1376,
-                            "top": 212
+                            "left": 1161.984375,
+                            "top": 558.984375
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2",
+                        "post_job_actions": {
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "RenameDatasetActionhtml_report": {
+                                "action_arguments": {
+                                    "newname": "MultiQC processed miRNA: Webpage"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "html_report"
+                            },
+                            "RenameDatasetActionstats": {
+                                "action_arguments": {
+                                    "newname": "MultiQC processed miRNA: Stats"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "stats"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
                         "tool_shed_repository": {
-                            "changeset_revision": "7c7ff7a3503f",
-                            "name": "blockbuster",
-                            "owner": "rnateam",
+                            "changeset_revision": "b2f1f75d49c4",
+                            "name": "multiqc",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"distance\": \"40\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"merge\": \"0\", \"minBlockHeight\": \"1.0\", \"minClusterHeight\": \"50.0\", \"print\": \"bbf_reads\", \"scale\": \"0.5\", \"tagFilter\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.1.2",
+                        "tool_state": "{\"comment\": \"\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": \"false\", \"title\": \"miRNA trimmed quality check\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7",
                         "type": "tool",
-                        "uuid": "8a3db40c-ae03-49ca-b47c-559ac455d712",
+                        "uuid": "b8e44272-be04-47ad-8b06-aa0f7d51a38c",
                         "workflow_outputs": [
                             {
-                                "label": "blockbuster_out",
-                                "output_name": "output",
-                                "uuid": "95c21ce9-e988-44b9-978e-10a27b74d18e"
+                                "label": null,
+                                "output_name": "html_report",
+                                "uuid": "45f7bd2f-aafe-471c-b41e-431cbbe28781"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
                         "errors": null,
-                        "id": 5,
+                        "id": 35,
                         "input_connections": {
-                            "tool_mode|input_bbo": {
-                                "id": 4,
-                                "output_name": "output"
+                            "select_data|rep_factorName_0|rep_factorLevel_0|countsFile": {
+                                "id": 32,
+                                "output_name": "out_file1"
+                            },
+                            "select_data|rep_factorName_0|rep_factorLevel_1|countsFile": {
+                                "id": 30,
+                                "output_name": "out_file1"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool DESeq2",
+                                "name": "batch_factors"
+                            }
+                        ],
                         "label": null,
-                        "name": "BlockClust",
+                        "name": "DESeq2",
                         "outputs": [
                             {
-                                "name": "hclust_plot",
-                                "type": "pdf"
-                            },
-                            {
-                                "name": "clusters",
-                                "type": "bed"
-                            },
-                            {
-                                "name": "model_based_pred_bed",
-                                "type": "bed"
+                                "name": "deseq_out",
+                                "type": "tabular"
                             },
                             {
-                                "name": "sim_tab_out",
-                                "type": "tabular"
+                                "name": "plots",
+                                "type": "pdf"
                             }
                         ],
                         "position": {
-                            "left": 1694,
-                            "top": 212
+                            "left": 1460,
+                            "top": 1445.984375
                         },
                         "post_job_actions": {
-                            "HideDatasetActionhclust_plot": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "hclust_plot"
+                            "RenameDatasetActiondeseq_out": {
+                                "action_arguments": {
+                                    "newname": "DESeq2 results miRNA"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "deseq_out"
                             },
-                            "HideDatasetActionsim_tab_out": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "sim_tab_out"
+                            "RenameDatasetActionplots": {
+                                "action_arguments": {
+                                    "newname": "DESeq2 plots miRNA"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "plots"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "aab6cf87b40a",
-                            "name": "blockclust",
-                            "owner": "rnateam",
+                            "changeset_revision": "6a3a025714d3",
+                            "name": "deseq2",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"tool_mode\": {\"operation\": \"analysis\", \"__current_case__\": 1, \"input_bbo\": {\"__class__\": \"ConnectedValue\"}, \"reference\": \"hg19\", \"nochr\": \"false\", \"pred\": {\"enable_pred\": \"yes\", \"__current_case__\": 0, \"pred_mode\": \"MODEL\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.0",
+                        "tool_state": "{\"auto_mean_filter_off\": \"false\", \"batch_factors\": {\"__class__\": \"RuntimeValue\"}, \"esf\": \"\", \"fit_type\": \"1\", \"header\": \"false\", \"many_contrasts\": \"false\", \"normCounts\": \"false\", \"normRLog\": \"false\", \"normVST\": \"false\", \"outlier_filter_off\": \"false\", \"outlier_replace_off\": \"false\", \"pdf\": \"true\", \"select_data\": {\"how\": \"datasets_per_level\", \"__current_case__\": 1, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": \"effects_brassinolide\", \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": \"brassinolide\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"factorLevel\": \"control\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"count\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.11.40.6+galaxy1",
                         "type": "tool",
-                        "uuid": "e41a16eb-4edd-4f9e-b615-44d0c2988b63",
+                        "uuid": "15632b70-0358-4ca6-918f-f236468dd8d5",
                         "workflow_outputs": [
                             {
-                                "label": "model_based_pred_bed",
-                                "output_name": "model_based_pred_bed",
-                                "uuid": "241feec1-9ffd-4d28-9b65-e58850198c6d"
+                                "label": null,
+                                "output_name": "plots",
+                                "uuid": "b4252bda-8ee4-47f5-85e0-ccacb840c702"
                             },
                             {
-                                "label": "clusters_bed",
-                                "output_name": "clusters",
-                                "uuid": "287b4bae-55a1-4f38-b1c3-62ae60b4d950"
+                                "label": null,
+                                "output_name": "deseq_out",
+                                "uuid": "55ea0b93-52e0-4d07-a64f-4db6e39f42ab"
                             }
                         ]
-                    }
-                ],
-                "parent_id": "transcriptomics/small_ncrna_clustering",
-                "path": "topics/transcriptomics/tutorials/small_ncrna_clustering/workflows/blockclust_clustering.ga",
-                "tags": [
-                    "transcriptomics"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "Blockclust 1.1.0 Clustering",
-                "topic_id": "transcriptomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-small_ncrna_clustering/versions/blockclust-clustering",
-                "tutorial_id": "small_ncrna_clustering",
-                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/small_ncrna_clustering/workflows/blockclust_clustering.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/small_ncrna_clustering/workflows/blockclust_clustering.html",
-                "version": 4,
-                "wfid": "transcriptomics-small_ncrna_clustering",
-                "wfname": "blockclust-clustering",
-                "workflow": "blockclust_clustering.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.2",
-                    "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0"
-                ],
-                "workflowhub_id": "1333"
-            }
-        ],
-        "zenodo_link": "https://zenodo.org/record/1491876"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "volcanoplot",
-                    "owner": "iuc",
-                    "revisions": "83c573f2e73c",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: volcanoplot\n  owner: iuc\n  revisions: 83c573f2e73c\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/tutorial.json",
-        "contributors": [
-            {
-                "id": "mblue9",
-                "joined": "2018-09",
-                "name": "Maria Doyle",
-                "orcid": "0000-0003-4847-8436",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mblue9.json"
-            }
-        ],
-        "dir": "topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "Galaxy@AuBi",
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "follow_up_training": [
-            {
-                "topic_name": "transcriptomics",
-                "tutorials": [
-                    "rna-seq-viz-with-volcanoplot-r"
-                ],
-                "type": "internal"
-            }
-        ],
-        "hands_on": true,
-        "id": "transcriptomics/rna-seq-viz-with-volcanoplot",
-        "inexact_supported_servers": [
-            "GalaxyTrakr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "A volcano plot can be used to quickly visualize significant genes in RNA-seq results"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Introductory",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
-        "objectives": [
-            "Create a volcano plot of RNA-seq data to visualize significant genes"
-        ],
-        "pageviews": 225119,
-        "pub_date": "2018-12-31",
-        "questions": [
-            "How to generate a volcano plot from RNA-seq data?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "mblue9"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "10M",
-                "speakers": [
-                    "mblue9"
-                ],
-                "youtube_id": "uNGXIcEGZwA"
-            }
-        ],
-        "requirements": [
-            {
-                "topic_name": "transcriptomics",
-                "tutorials": [
-                    "rna-seq-counts-to-genes"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00304",
-        "short_tools": [
-            "volcanoplot"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "visualisation",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "time_estimation": "30m",
-        "title": "Visualization of RNA-Seq results with Volcano Plot",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5"
-        ],
-        "topic_name": "transcriptomics",
-        "topic_name_human": "Transcriptomics",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "rna-seq-viz-with-volcanoplot",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/tutorial.json"
-        },
-        "version": 14,
-        "video": false,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 82,
-        "visitors": 131254,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Visualization of RNA-Seq results with Volcano Plot",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nDE results\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nVolcano genes\"]\n  2[label=\"Volcano plot highlighting significant\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Volcano plot labelling top 10\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Volcano plot labelling genes of interest\"]\n  0 -> 4 [label=\"output\"]\n  1 -> 4 [label=\"output\"]\n  k16aef53e11fd4defa7fb6cf9a98f0902[color=lightseagreen,label=\"Output\\nvolcano_pdf\"]\n  4 -> k16aef53e11fd4defa7fb6cf9a98f0902\n}",
-                "history": [
-                    {
-                        "hash": "470fa57969cc2fa659ec0bf0b00e69ca81367521",
-                        "message": "Fix name",
-                        "num": 8,
-                        "short_hash": "470fa5796",
-                        "unix": "1624047135"
-                    },
-                    {
-                        "hash": "086ac3f5016bee399d245984727bb0059be29c4c",
-                        "message": "Update workflow",
-                        "num": 7,
-                        "short_hash": "086ac3f50",
-                        "unix": "1624046952"
-                    },
-                    {
-                        "hash": "2e2cb42d8ac99927000d81734fb53c7943c0c4ba",
-                        "message": "add tests from workflow-testing for blockclust and rna-seq-viz-with-volcano-plot, edit workflows",
-                        "num": 6,
-                        "short_hash": "2e2cb42d8",
-                        "unix": "1601812751"
-                    },
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 5,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "f7f017f3329dac306d19ca406c5e28f75bbf4ef8",
-                        "message": "dna and rna capitals",
-                        "num": 4,
-                        "short_hash": "f7f017f33",
-                        "unix": "1579092000"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 3,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
-                        "message": "unflatten workflows",
-                        "num": 2,
-                        "short_hash": "faf6d298a",
-                        "unix": "1576155753"
                     },
-                    {
-                        "hash": "47566efc6793de54afd1915977d5514b732f9ea8",
-                        "message": "Add workflow to volcanoplot tutorial",
-                        "num": 1,
-                        "short_hash": "47566efc6",
-                        "unix": "1562337491"
-                    }
-                ],
-                "inputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "DE results"
+                        "id": 38,
+                        "input_connections": {
+                            "header_criteria|identifiers": {
+                                "id": 36,
+                                "output_name": "out_file1"
+                            },
+                            "input": {
+                                "id": 5,
+                                "output_name": "output"
                             }
-                        ],
-                        "label": "DE results",
-                        "name": "Input dataset",
-                        "outputs": [],
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Filter FASTA",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "fasta"
+                            }
+                        ],
                         "position": {
-                            "bottom": 329.5,
-                            "height": 61,
-                            "left": 318,
-                            "right": 518,
-                            "top": 268.5,
-                            "width": 200,
-                            "x": 318,
-                            "y": 268.5
+                            "left": 2880,
+                            "top": 1662.984375
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "3adb32da-3a59-4e01-bbf1-f8501e8f4af4",
-                        "workflow_outputs": []
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Downregulated mRNA sequences"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "3c623e81be77",
+                            "name": "filter_by_fasta_ids",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"dedup\": \"false\", \"header_criteria\": {\"header_criteria_select\": \"id_list\", \"__current_case__\": 1, \"identifiers\": {\"__class__\": \"ConnectedValue\"}, \"id_regex\": {\"find\": \"pattern\", \"__current_case__\": 1, \"pattern\": \"GENE=(AT.{7})\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"output_discarded\": \"false\", \"sequence_criteria\": {\"sequence_criteria_select\": \"\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1",
+                        "type": "tool",
+                        "uuid": "4d1f1434-2cd7-4025-aa31-955646f26ae0",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "e8c830ca-388d-43e9-a30a-6ce4e1db2103"
+                            }
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "cat1",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 44,
+                        "input_connections": {
+                            "input1": {
+                                "id": 43,
+                                "output_name": "output"
+                            },
+                            "queries_0|input2": {
+                                "id": 42,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Concatenate datasets",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "Volcano genes"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
-                        "label": "Volcano genes",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "bottom": 505.5,
-                            "height": 81,
-                            "left": 320,
-                            "right": 520,
-                            "top": 424.5,
-                            "width": 200,
-                            "x": 320,
-                            "y": 424.5
+                            "left": 2880,
+                            "top": 1882.984375
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "f49407c4-5995-446c-b28f-c39bbee8c6d9",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nDE results\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nVolcano genes\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Volcano plot highlighting significant\"];\n  0 -->|output| 2;\n  3[\"Volcano plot labelling top 10\"];\n  0 -->|output| 3;\n  4[\"Volcano plot labelling genes of interest\"];\n  0 -->|output| 4;\n  1 -->|output| 4;\n  16aef53e-11fd-4def-a7fb-6cf9a98f0902[\"Output\\nvolcano_pdf\"];\n  4 --> 16aef53e-11fd-4def-a7fb-6cf9a98f0902;\n  style 16aef53e-11fd-4def-a7fb-6cf9a98f0902 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "Visualization Of RNA-Seq Results With Volcano Plot",
-                "outputs": [
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Upregulated miRNA sequences"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "tool_id": "cat1",
+                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [{\"__index__\": 0, \"input2\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "97871054-6cba-4834-bc56-26a7f37be2b8",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "800ea133-2a03-469d-875e-24b0635c3cd2"
+                            }
+                        ]
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1",
                         "errors": null,
-                        "id": 4,
+                        "id": 45,
                         "input_connections": {
-                            "input": {
-                                "id": 0,
+                            "d": {
+                                "id": 38,
                                 "output_name": "output"
                             },
-                            "labels|label_file": {
-                                "id": 1,
-                                "output_name": "output"
+                            "f": {
+                                "id": 44,
+                                "output_name": "out_file1"
                             }
                         },
                         "inputs": [],
-                        "label": "Volcano plot labelling genes of interest",
-                        "name": "Volcano Plot",
+                        "label": null,
+                        "name": "TargetFinder",
                         "outputs": [
                             {
-                                "name": "plot",
-                                "type": "pdf"
+                                "name": "output_file",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "bottom": 531.5,
-                            "height": 142,
-                            "left": 595,
-                            "right": 795,
-                            "top": 389.5,
-                            "width": 200,
-                            "x": 595,
-                            "y": 389.5
+                            "left": 3157.984375,
+                            "top": 1712.984375
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "83c573f2e73c",
-                            "name": "volcanoplot",
-                            "owner": "iuc",
+                            "changeset_revision": "c9d56748fbde",
+                            "name": "targetfinder",
+                            "owner": "rnateam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"fdr_col\": \"8\", \"header\": \"auto\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"label_col\": \"2\", \"labels\": {\"label_select\": \"file\", \"__current_case__\": 1, \"label_file\": {\"__class__\": \"ConnectedValue\"}}, \"lfc_col\": \"4\", \"lfc_thresh\": \"0.58\", \"out_options\": {\"rscript_out\": \"false\"}, \"plot_options\": {\"boxes\": \"true\", \"title\": \"\", \"xlab\": \"\", \"ylab\": \"\", \"xmin\": null, \"xmax\": null, \"ymax\": null, \"legend\": \"\", \"legend_labs\": \"Down,Not Sig,Up\"}, \"pval_col\": \"7\", \"signif_thresh\": \"0.01\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.0.5",
+                        "tool_state": "{\"c\": \"4.0\", \"d\": {\"__class__\": \"ConnectedValue\"}, \"f\": {\"__class__\": \"ConnectedValue\"}, \"output_format\": \"classic\", \"r\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.7.0+galaxy1",
                         "type": "tool",
-                        "uuid": "01bf8268-3e8a-4f99-b03c-05c5656ac96e",
+                        "uuid": "d81d9ea9-a085-478f-a148-0c31083f16fc",
                         "workflow_outputs": [
                             {
-                                "label": "volcano_pdf",
-                                "output_name": "plot",
-                                "uuid": "16aef53e-11fd-4def-a7fb-6cf9a98f0902"
+                                "label": null,
+                                "output_name": "output_file",
+                                "uuid": "2a3de11c-addc-4e1a-a156-f760f861ce64"
                             }
                         ]
                     }
                 ],
-                "parent_id": "transcriptomics/rna-seq-viz-with-volcanoplot",
-                "path": "topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/workflows/rna-seq-viz-with-volcanoplot.ga",
+                "parent_id": "transcriptomics/mirna-target-finder",
+                "path": "topics/transcriptomics/tutorials/mirna-target-finder/workflows/main_workflow.ga",
                 "tags": [
-                    "transcriptomics"
+                    "transcriptomics",
+                    "mirna",
+                    "arabidopsis"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "Visualization Of RNA-Seq Results With Volcano Plot",
+                "tests": false,
+                "title": "Plant bulk RNA-Seq workflow",
                 "topic_id": "transcriptomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-rna-seq-viz-with-volcanoplot/versions/rna-seq-viz-with-volcanoplot",
-                "tutorial_id": "rna-seq-viz-with-volcanoplot",
-                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/workflows/rna-seq-viz-with-volcanoplot.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/workflows/rna-seq-viz-with-volcanoplot.html",
-                "version": 6,
-                "wfid": "transcriptomics-rna-seq-viz-with-volcanoplot",
-                "wfname": "rna-seq-viz-with-volcanoplot",
-                "workflow": "rna-seq-viz-with-volcanoplot.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-mirna-target-finder/versions/main-workflow",
+                "tutorial_id": "mirna-target-finder",
+                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/mirna-target-finder/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/mirna-target-finder/workflows/main_workflow.html",
+                "version": 3,
+                "wfid": "transcriptomics-mirna-target-finder",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5"
+                    "Cut1",
+                    "Filter1",
+                    "__MERGE_COLLECTION__",
+                    "cat1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.14.1.2+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7",
+                    "toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_mapper/rbc_mirdeep2_mapper/2.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_quantifier/rbc_mirdeep2_quantifier/2.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1"
                 ],
-                "workflowhub_id": "1335"
+                "workflowhub_id": "1318"
             }
         ],
-        "zenodo_link": "https://zenodo.org/record/2529117"
+        "zenodo_link": "https://zenodo.org/record/4710649"
     },
     {
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "deseq2",
-                    "owner": "iuc",
-                    "revisions": "d9e5cadc7f0b",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "heinz",
-                    "owner": "iuc",
-                    "revisions": "2b80a2596064",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "heinz",
-                    "owner": "iuc",
-                    "revisions": "2b80a2596064",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "heinz",
-                    "owner": "iuc",
-                    "revisions": "2b80a2596064",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "heinz",
-                    "owner": "iuc",
-                    "revisions": "5f589c91566e",
-                    "tool_panel_section_label": "RNA Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
+            "tools": []
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: deseq2\n  owner: iuc\n  revisions: d9e5cadc7f0b\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: heinz\n  owner: iuc\n  revisions: 2b80a2596064\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: heinz\n  owner: iuc\n  revisions: 2b80a2596064\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: heinz\n  owner: iuc\n  revisions: 2b80a2596064\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: heinz\n  owner: iuc\n  revisions: 5f589c91566e\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-viz-with-cummerbund/tutorial.json",
         "contributors": [
             {
-                "id": "ChaoZhang123",
-                "joined": "2018-08",
-                "maintainer_contact": "https://hi-it.org",
-                "name": "Chao Zhang",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/ChaoZhang123/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/ChaoZhang123.json"
+                "email": "andrea.bagnacani@gmail.com",
+                "id": "bagnacan",
+                "joined": "2017-10",
+                "name": "Andrea Bagnacani",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bagnacan/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bagnacan.json"
             }
         ],
-        "dir": "topics/transcriptomics/tutorials/network-analysis-with-heinz",
-        "edam_operation": [
-            "RNA-Seq analysis",
-            "Differential gene expression analysis",
-            "Pathway or network analysis"
-        ],
+        "dir": "topics/transcriptomics/tutorials/rna-seq-viz-with-cummerbund",
+        "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu"
-        ],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "transcriptomics/network-analysis-with-heinz",
+        "id": "transcriptomics/rna-seq-viz-with-cummerbund",
         "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Using Heinz do the network analysis based on the metatranscriptomics or transcriptomics data.",
-            "Extracting the signals hidden in the p-value distribution of the differential expression analysis.",
-            "Visualizing the pinpointed subnetwork helps us understand the result better",
-            "Heinz helps narrow down the scope to find the key pathways",
-            "Multiple CPUs will accelerate the computation especially for the complex datasets"
+            "Extract information from a SQLite CuffDiff database",
+            "Filter and sort results to highlight differential expressed genes of interest",
+            "Generate publication-ready visualizations of RNA-Seq analysis results"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-01-15",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Network Analysis of metatranscriptomics data using Heinz in Galaxy to pinpoint the optimal scoring subnetwork."
+            "Manage RNA-Seq results",
+            "Extract genes for producing differential gene expression analysis visualizations",
+            "Visualize meaningful information"
         ],
-        "pageviews": 5729787,
-        "pub_date": "2018-10-11",
+        "pageviews": 5901051,
+        "pub_date": "2017-10-16",
         "questions": [
-            "Which pathways are potentially contributing to dental caries?"
-        ],
-        "short_id": "T00293",
-        "short_tools": [
-            "heinz_scoring",
-            "heinz",
-            "heinz_bum",
-            "heinz_visualization",
-            "Cut1",
-            "deseq2"
+            "How are RNA-Seq results stored?",
+            "Why are visualization techniques needed?",
+            "How to select genes for visualizing meaningful results of differential gene expression analysis?"
         ],
+        "short_id": "T00302",
+        "short_tools": [],
         "slides": true,
         "slides_recordings": false,
+        "subtopic": "visualisation",
         "supported_servers": {
-            "exact": [
+            "exact": [],
+            "inexact": [
                 {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.org (Main)",
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 },
                 {
+                    "human": "Galaxy Australia",
+                    "id": "au",
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
-        "tags": [
-            "metatranscriptomics",
-            "network analysis"
-        ],
-        "time_estimation": "1h30m",
-        "title": "Network analysis with Heinz",
-        "tools": [
-            "Cut1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz/1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_bum/1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_scoring/1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_visualization/0.1.0"
-        ],
+        "time_estimation": "1h",
+        "title": "Visualization of RNA-Seq results with CummeRbund",
+        "tools": [],
         "topic_name": "transcriptomics",
         "topic_name_human": "Transcriptomics",
         "tours": false,
@@ -269923,162 +277151,20 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "network-analysis-with-heinz",
+        "tutorial_name": "rna-seq-viz-with-cummerbund",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-cummerbund/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-viz-with-cummerbund/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-viz-with-cummerbund/tutorial.json"
         },
         "version": 16,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 342,
-        "visitors": 2065570,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Network analysis with Heinz",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nEdge File\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nInput dataset collection\"]\n  3[label=\"DESeq2\"]\n  1 -> 3 [label=\"output\"]\n  2 -> 3 [label=\"output\"]\n  4[label=\"Cut\"]\n  3 -> 4 [label=\"deseq_out\"]\n  5[label=\"Cut\"]\n  3 -> 5 [label=\"deseq_out\"]\n  6[label=\"Fit a BUM model\"]\n  4 -> 6 [label=\"out_file1\"]\n  7[label=\"Calculate a Heinz score\"]\n  5 -> 7 [label=\"out_file1\"]\n  6 -> 7 [label=\"dist_params\"]\n  8[label=\"Identify optimal scoring subnetwork\"]\n  7 -> 8 [label=\"score\"]\n  0 -> 8 [label=\"output\"]\n  9[label=\"Visualize\"]\n  8 -> 9 [label=\"subnetwork\"]\n}",
-                "history": [
-                    {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 3,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
-                        "num": 2,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
-                    },
-                    {
-                        "hash": "6a6b3b2cfd5007d26b1bbbcaf388fee819397d85",
-                        "message": "Renamed the folder, rewrote the key points; added tags; added a paragraph in the end to correspond to the research question in this tutorial.",
-                        "num": 1,
-                        "short_hash": "6a6b3b2cf",
-                        "unix": "1539171768"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "The background network",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": "Edge File",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 202.4296875,
-                            "top": 238.03125
-                        },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "3939e577-a385-4d04-8db9-5b692670fb00",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Input Dataset Collection"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 202.4296875,
-                            "top": 358.03125
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "c6808009-a8e5-447d-a62a-37003ef0bb96",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Input Dataset Collection"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 202.4296875,
-                            "top": 478.03125
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "76dd0c7b-e654-462f-810b-7c7f9c69e17b",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nEdge File\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"DESeq2\"];\n  1 -->|output| 3;\n  2 -->|output| 3;\n  4[\"Cut\"];\n  3 -->|deseq_out| 4;\n  5[\"Cut\"];\n  3 -->|deseq_out| 5;\n  6[\"Fit a BUM model\"];\n  4 -->|out_file1| 6;\n  7[\"Calculate a Heinz score\"];\n  5 -->|out_file1| 7;\n  6 -->|dist_params| 7;\n  8[\"Identify optimal scoring subnetwork\"];\n  7 -->|score| 8;\n  0 -->|output| 8;\n  9[\"Visualize\"];\n  8 -->|subnetwork| 9;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "Workflow Constructed From History 'Heinz Workflow Trial Sep 11'",
-                "outputs": [],
-                "parent_id": "transcriptomics/network-analysis-with-heinz",
-                "path": "topics/transcriptomics/tutorials/network-analysis-with-heinz/workflows/Galaxy-Workflow-Heinz.ga",
-                "tags": [
-                    "transcriptomics"
-                ],
-                "test_results": null,
-                "tests": false,
-                "title": "Workflow Constructed From History 'Heinz Workflow Trial Sep 11'",
-                "topic_id": "transcriptomics",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/transcriptomics-network-analysis-with-heinz/versions/galaxy-workflow-heinz",
-                "tutorial_id": "network-analysis-with-heinz",
-                "url": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/network-analysis-with-heinz/workflows/Galaxy-Workflow-Heinz.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/network-analysis-with-heinz/workflows/Galaxy-Workflow-Heinz.html",
-                "version": 3,
-                "wfid": "transcriptomics-network-analysis-with-heinz",
-                "wfname": "galaxy-workflow-heinz",
-                "workflow": "Galaxy-Workflow-Heinz.ga",
-                "workflow_tools": [
-                    "Cut1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz/1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_bum/1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_scoring/1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_visualization/0.1.0"
-                ],
-                "workflowhub_id": "1303"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.1344105"
+        "visit_duration": 266,
+        "visitors": 2135823,
+        "zenodo_link": "https://zenodo.org/record/1001880"
     },
     {
         "admin_install": {
@@ -270183,7 +277269,7 @@
             "Create a complex query to get over-expressed genes, their location on the reference genome, and check if they are included in a known QTL",
             "Complete the query to get the human homologs and their location using neXtProt database"
         ],
-        "pageviews": 5727982,
+        "pageviews": 5898685,
         "pub_date": "2020-07-09",
         "questions": [
             "How to integrate RNA-Seq results with other datasets using AskOmics?",
@@ -270259,8 +277345,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 400,
-        "visitors": 2064588,
+        "visit_duration": 398,
+        "visitors": 2134460,
         "zenodo_link": "https://zenodo.org/record/3925863"
     },
     {
@@ -270344,7 +277430,7 @@
         "license": "CC-BY-4.0",
         "logo": "GTN",
         "mod_date": "2024-06-14",
-        "pageviews": 5726884,
+        "pageviews": 5897569,
         "priority": 1,
         "pub_date": "2016-10-05",
         "recordings": [
@@ -270442,7 +277528,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2063758
+        "visitors": 2133613
     },
     {
         "admin_install": {
@@ -270452,25 +277538,26 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-viz-with-cummerbund/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rb-rnaseq/tutorial.json",
         "contributors": [
             {
-                "email": "andrea.bagnacani@gmail.com",
-                "id": "bagnacan",
-                "joined": "2017-10",
-                "name": "Andrea Bagnacani",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bagnacan/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bagnacan.json"
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
+                "joined": "2017-09",
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
             }
         ],
-        "dir": "topics/transcriptomics/tutorials/rna-seq-viz-with-cummerbund",
+        "dir": "topics/transcriptomics/tutorials/rb-rnaseq",
+        "draft": true,
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "transcriptomics/rna-seq-viz-with-cummerbund",
+        "id": "transcriptomics/rb-rnaseq",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -270478,34 +277565,25 @@
             "UseGalaxy.fr"
         ],
         "js_requirements": {
-            "mathjax": null,
+            "mathjax": 26071,
             "mermaid": false
         },
-        "key_points": [
-            "Extract information from a SQLite CuffDiff database",
-            "Filter and sort results to highlight differential expressed genes of interest",
-            "Generate publication-ready visualizations of RNA-Seq analysis results"
-        ],
+        "key_points": null,
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2023-02-17",
         "objectives": [
-            "Manage RNA-Seq results",
-            "Extract genes for producing differential gene expression analysis visualizations",
-            "Visualize meaningful information"
+            "Learns basic concepts of RNAseq analysis"
         ],
-        "pageviews": 5730330,
-        "pub_date": "2017-10-16",
+        "pageviews": 32647,
+        "pub_date": "2017-02-22",
         "questions": [
-            "How are RNA-Seq results stored?",
-            "Why are visualization techniques needed?",
-            "How to select genes for visualizing meaningful results of differential gene expression analysis?"
+            "How to perform analysis of RNAseq data when reference genome is available?"
         ],
-        "short_id": "T00302",
+        "short_id": "T00294",
         "short_tools": [],
-        "slides": true,
+        "slides": false,
         "slides_recordings": false,
-        "subtopic": "visualisation",
         "supported_servers": {
             "exact": [],
             "inexact": [
@@ -270540,8 +277618,11 @@
             ]
         },
         "symlink": null,
+        "tags": [
+            "work-in-progress"
+        ],
         "time_estimation": "1h",
-        "title": "Visualization of RNA-Seq results with CummeRbund",
+        "title": "Reference-based RNAseq data analysis (long)",
         "tools": [],
         "topic_name": "transcriptomics",
         "topic_name_human": "Transcriptomics",
@@ -270551,20 +277632,20 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "rna-seq-viz-with-cummerbund",
+        "tutorial_name": "rb-rnaseq",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-viz-with-cummerbund/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rb-rnaseq/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-viz-with-cummerbund/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-viz-with-cummerbund/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rb-rnaseq/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rb-rnaseq/tutorial.json"
         },
-        "version": 16,
+        "version": 12,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 268,
-        "visitors": 2065934,
-        "zenodo_link": "https://zenodo.org/record/1001880"
+        "visit_duration": 132,
+        "visitors": 20622,
+        "zenodo_link": ""
     },
     {
         "admin_install": {
@@ -270574,33 +277655,30 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r/tutorial.json",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-bash-star-align/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "Sofokli5"
+            ],
+            "editing": [
+                "fpsom",
+                "shiltemann",
+                "hexylena",
+                "carpentries"
+            ],
+            "funding": [
+                "gallantries"
+            ]
+        },
         "contributors": [
             {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+                "email": "sofoskeisaris@gmail.com",
+                "id": "Sofokli5",
+                "joined": "2022-05",
+                "name": "Sofoklis Keisaris",
+                "orcid": "0000-0002-4833-4726",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Sofokli5/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/Sofokli5.json"
             },
             {
                 "affiliations": [
@@ -270620,14 +277698,71 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
             },
             {
-                "email": "tbyhdgs@gmail.com",
-                "id": "tobyhodges",
-                "joined": "2019-07",
-                "name": "Toby Hodges",
-                "orcid": "0000-0003-1766-456X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tobyhodges/",
-                "twitter": "tbyhdgs",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tobyhodges.json"
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "id": "carpentries",
+                "joined": "2021-09",
+                "name": "The Carpentries",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
+                "ror": "0356fgm10",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
             },
             {
                 "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
@@ -270656,171 +277791,14 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r",
-        "edam_operation": [],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "transcriptomics/rna-seq-counts-to-viz-in-r",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "When creating plots with `ggplot2`, think about the graphics in layers (aesthetics, geometry, statistics, scale transformation, and grouping)."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
-        "objectives": [
-            "Describe the role of data, aesthetics, geoms, and layers in `ggplot` functions.",
-            "Customize plot scales, titles, subtitles, themes, fonts, layout, and orientation."
-        ],
-        "pageviews": 4779,
-        "pub_date": "2019-10-08",
-        "questions": [
-            "How can I create neat visualizations of the data?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "hexylena",
-                    "shiltemann",
-                    "fpsom"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "30M",
-                "speakers": [
-                    "fpsom"
-                ],
-                "youtube_id": "rJWgnLgA2BE"
-            }
-        ],
-        "requirements": [
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "rstudio"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "data-science",
-                "tutorials": [
-                    "r-basics",
-                    "r-advanced"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "transcriptomics",
-                "tutorials": [
-                    "ref-based"
-                ],
-                "type": "internal"
-            }
-        ],
-        "short_id": "T00299",
-        "short_tools": [
-            "interactive_tool_rstudio"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "visualisation",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "interactive-tools"
-        ],
-        "time_estimation": "1H",
-        "title": "RNA Seq Counts to Viz in R",
-        "tools": [
-            "interactive_tool_rstudio"
-        ],
-        "topic_name": "transcriptomics",
-        "topic_name_human": "Transcriptomics",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "rna-seq-counts-to-viz-in-r",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r/tutorial.json"
-        },
-        "version": 20,
-        "video": false,
-        "video_versions": 1,
-        "video_view": 0,
-        "visit_duration": 112,
-        "visitors": 3668,
-        "zenodo_link": "https://zenodo.org/record/3477564/"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": []
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rb-rnaseq/tutorial.json",
-        "contributors": [
-            {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
-                "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
-            }
-        ],
-        "dir": "topics/transcriptomics/tutorials/rb-rnaseq",
-        "draft": true,
+        "dir": "topics/transcriptomics/tutorials/rna-seq-bash-star-align",
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "transcriptomics/rb-rnaseq",
+        "id": "transcriptomics/rna-seq-bash-star-align",
         "inexact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.org",
@@ -270828,22 +277806,30 @@
             "UseGalaxy.fr"
         ],
         "js_requirements": {
-            "mathjax": 26071,
+            "mathjax": null,
             "mermaid": false
         },
-        "key_points": null,
+        "key_points": [
+            "Bioinformatic command line tools are collections of commands that can be used to carry out bioinformatic analyses.",
+            "To use most powerful bioinformatic tools, you will need to use the command line.",
+            "There a few basic steps to follow in order to process the RNA sequences",
+            "Quality control, trimming and alignment to reference genome are the first part of the RNA-seq downstream analysis"
+        ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-02-17",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Learns basic concepts of RNAseq analysis"
+            "Learn the basics to process RNA sequences",
+            "Check the quality and trim the sequences with bash",
+            "Use command line STAR aligner to map the RNA sequences",
+            "Estimate the number of reads per gens"
         ],
-        "pageviews": 32285,
-        "pub_date": "2017-02-22",
+        "pageviews": 8439,
+        "pub_date": "2023-05-15",
         "questions": [
-            "How to perform analysis of RNAseq data when reference genome is available?"
+            "What are the first steps to process RNA-seq data?"
         ],
-        "short_id": "T00294",
+        "short_id": "T00346",
         "short_tools": [],
         "slides": false,
         "slides_recordings": false,
@@ -270881,11 +277867,8 @@
             ]
         },
         "symlink": null,
-        "tags": [
-            "work-in-progress"
-        ],
-        "time_estimation": "1h",
-        "title": "Reference-based RNAseq data analysis (long)",
+        "time_estimation": "90M",
+        "title": "RNA-seq Alignment with STAR",
         "tools": [],
         "topic_name": "transcriptomics",
         "topic_name_human": "Transcriptomics",
@@ -270895,20 +277878,20 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "rb-rnaseq",
+        "tutorial_name": "rna-seq-bash-star-align",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rb-rnaseq/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-bash-star-align/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rb-rnaseq/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rb-rnaseq/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-bash-star-align/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-bash-star-align/tutorial.json"
         },
-        "version": 12,
+        "version": 6,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 132,
-        "visitors": 20355,
-        "zenodo_link": ""
+        "visit_duration": 85,
+        "visitors": 6837,
+        "zenodo_link": "https://zenodo.org/record/6457007"
     },
     {
         "admin_install": {
@@ -270918,30 +277901,33 @@
             "tools": []
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-bash-star-align/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "Sofokli5"
-            ],
-            "editing": [
-                "fpsom",
-                "shiltemann",
-                "hexylena",
-                "carpentries"
-            ],
-            "funding": [
-                "gallantries"
-            ]
-        },
+        "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r/tutorial.json",
         "contributors": [
             {
-                "email": "sofoskeisaris@gmail.com",
-                "id": "Sofokli5",
-                "joined": "2022-05",
-                "name": "Sofoklis Keisaris",
-                "orcid": "0000-0002-4833-4726",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/Sofokli5/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/Sofokli5.json"
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
             },
             {
                 "affiliations": [
@@ -270961,71 +277947,14 @@
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/fpsom.json"
             },
             {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "id": "carpentries",
-                "joined": "2021-09",
-                "name": "The Carpentries",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
-                "ror": "0356fgm10",
-                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
+                "email": "tbyhdgs@gmail.com",
+                "id": "tobyhodges",
+                "joined": "2019-07",
+                "name": "Toby Hodges",
+                "orcid": "0000-0003-1766-456X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tobyhodges/",
+                "twitter": "tbyhdgs",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tobyhodges.json"
             },
             {
                 "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
@@ -271054,85 +277983,120 @@
                 "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/transcriptomics/tutorials/rna-seq-bash-star-align",
+        "dir": "topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r",
         "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "transcriptomics/rna-seq-bash-star-align",
-        "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
-        ],
+        "id": "transcriptomics/rna-seq-counts-to-viz-in-r",
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Bioinformatic command line tools are collections of commands that can be used to carry out bioinformatic analyses.",
-            "To use most powerful bioinformatic tools, you will need to use the command line.",
-            "There a few basic steps to follow in order to process the RNA sequences",
-            "Quality control, trimming and alignment to reference genome are the first part of the RNA-seq downstream analysis"
+            "When creating plots with `ggplot2`, think about the graphics in layers (aesthetics, geometry, statistics, scale transformation, and grouping)."
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2024-06-14",
         "objectives": [
-            "Learn the basics to process RNA sequences",
-            "Check the quality and trim the sequences with bash",
-            "Use command line STAR aligner to map the RNA sequences",
-            "Estimate the number of reads per gens"
+            "Describe the role of data, aesthetics, geoms, and layers in `ggplot` functions.",
+            "Customize plot scales, titles, subtitles, themes, fonts, layout, and orientation."
         ],
-        "pageviews": 7718,
-        "pub_date": "2023-05-15",
+        "pageviews": 4860,
+        "pub_date": "2019-10-08",
         "questions": [
-            "What are the first steps to process RNA-seq data?"
+            "How can I create neat visualizations of the data?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "hexylena",
+                    "shiltemann",
+                    "fpsom"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "30M",
+                "speakers": [
+                    "fpsom"
+                ],
+                "youtube_id": "rJWgnLgA2BE"
+            }
+        ],
+        "requirements": [
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "rstudio"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "data-science",
+                "tutorials": [
+                    "r-basics",
+                    "r-advanced"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "transcriptomics",
+                "tutorials": [
+                    "ref-based"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00299",
+        "short_tools": [
+            "interactive_tool_rstudio"
         ],
-        "short_id": "T00346",
-        "short_tools": [],
         "slides": false,
         "slides_recordings": false,
+        "subtopic": "visualisation",
         "supported_servers": {
-            "exact": [],
-            "inexact": [
+            "exact": [
                 {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
                 {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 },
                 {
-                    "human": "Galaxy Australia",
-                    "id": "au",
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
-                },
-                {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
                 }
-            ]
+            ],
+            "inexact": []
         },
         "symlink": null,
-        "time_estimation": "90M",
-        "title": "RNA-seq Alignment with STAR",
-        "tools": [],
+        "tags": [
+            "interactive-tools"
+        ],
+        "time_estimation": "1H",
+        "title": "RNA Seq Counts to Viz in R",
+        "tools": [
+            "interactive_tool_rstudio"
+        ],
         "topic_name": "transcriptomics",
         "topic_name_human": "Transcriptomics",
         "tours": false,
@@ -271141,20 +278105,20 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "rna-seq-bash-star-align",
+        "tutorial_name": "rna-seq-counts-to-viz-in-r",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-bash-star-align/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-bash-star-align/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-bash-star-align/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r/tutorial.json"
         },
-        "version": 6,
+        "version": 20,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 85,
-        "visitors": 6224,
-        "zenodo_link": "https://zenodo.org/record/6457007"
+        "visit_duration": 111,
+        "visitors": 3743,
+        "zenodo_link": "https://zenodo.org/record/3477564/"
     },
     {
         "admin_install": {
@@ -271212,7 +278176,7 @@
         "objectives": [
             "Learn how to use R to edit Volcano plot colours, points, labels and categories"
         ],
-        "pageviews": 39244,
+        "pageviews": 39714,
         "pub_date": "2021-06-14",
         "questions": [
             "How to customise Volcano plot output in R?"
@@ -271258,8 +278222,8 @@
         ],
         "short_id": "T00305",
         "short_tools": [
-            "interactive_tool_rstudio",
-            "volcanoplot"
+            "volcanoplot",
+            "interactive_tool_rstudio"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -271319,7 +278283,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 102,
-        "visitors": 28362,
+        "visitors": 28758,
         "zenodo_link": "https://zenodo.org/record/2529117"
     },
     {
@@ -271331,14 +278295,14 @@
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "fbf99087e067",
+                    "revisions": "86755160afbf",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "fbf99087e067",
+                    "revisions": "86755160afbf",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
@@ -271352,7 +278316,7 @@
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "fbf99087e067",
+                    "revisions": "86755160afbf",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
@@ -271366,7 +278330,7 @@
                 {
                     "name": "text_processing",
                     "owner": "bgruening",
-                    "revisions": "fbf99087e067",
+                    "revisions": "86755160afbf",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
@@ -271617,7 +278581,7 @@
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 6595517c2dd8\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: f9242e01365a\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: 3f254c5ced1d\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_idxstats\n  owner: devteam\n  revisions: 7def34e6cf4d\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_idxstats\n  owner: devteam\n  revisions: fa5d3e61e429\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_element_identifiers\n  owner: iuc\n  revisions: d3c07d270a50\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deg_annotate\n  owner: iuc\n  revisions: e98d4ab5b5bc\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deseq2\n  owner: iuc\n  revisions: 9a882d108833\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dexseq\n  owner: iuc\n  revisions: 62adf13b86ea\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dexseq\n  owner: iuc\n  revisions: 62adf13b86ea\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: featurecounts\n  owner: iuc\n  revisions: 6f66ae7c5f7a\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: featurecounts\n  owner: iuc\n  revisions: f9d49f5cb597\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ggplot2_heatmap2\n  owner: iuc\n  revisions: 374e9062d874\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: goseq\n  owner: iuc\n  revisions: 602de62d995b\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gtftobed12\n  owner: iuc\n  revisions: b026dae67fba\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: length_and_gc_content\n  owner: iuc\n  revisions: e3ba567abdf5\n  tool_panel_section_label: Extract Features\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: abfd8a6544d7\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pathview\n  owner: iuc\n  revisions: f1691de443a7\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pygenometracks\n  owner: iuc\n  revisions: 360df4999907\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pygenometracks\n  owner: iuc\n  revisions: 36b848d5f3ec\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n  owner: iuc\n  revisions: 3ea5a2a63fa2\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n  owner: iuc\n  revisions: b0f2be869d6d\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: 5826298f6a73\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: 6be888be75f9\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: table_compute\n  owner: iuc\n  revisions: 3bf5661c0280\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 135b80fb1ac2\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: fe74900d6dc7\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 473382134e56\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 27e16a30667a\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 473382134e56\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 27e16a30667a\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 473382134e56\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 27e16a30667a\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 6595517c2dd8\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: f9242e01365a\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: 3f254c5ced1d\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_idxstats\n  owner: devteam\n  revisions: 7def34e6cf4d\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_idxstats\n  owner: devteam\n  revisions: fa5d3e61e429\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collection_element_identifiers\n  owner: iuc\n  revisions: d3c07d270a50\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deg_annotate\n  owner: iuc\n  revisions: e98d4ab5b5bc\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: deseq2\n  owner: iuc\n  revisions: 9a882d108833\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dexseq\n  owner: iuc\n  revisions: 62adf13b86ea\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: dexseq\n  owner: iuc\n  revisions: 62adf13b86ea\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: featurecounts\n  owner: iuc\n  revisions: 6f66ae7c5f7a\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: featurecounts\n  owner: iuc\n  revisions: f9d49f5cb597\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ggplot2_heatmap2\n  owner: iuc\n  revisions: 374e9062d874\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: goseq\n  owner: iuc\n  revisions: 602de62d995b\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gtftobed12\n  owner: iuc\n  revisions: b026dae67fba\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: length_and_gc_content\n  owner: iuc\n  revisions: e3ba567abdf5\n  tool_panel_section_label: Extract Features\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: abfd8a6544d7\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pathview\n  owner: iuc\n  revisions: f1691de443a7\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pygenometracks\n  owner: iuc\n  revisions: 360df4999907\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pygenometracks\n  owner: iuc\n  revisions: 36b848d5f3ec\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n  owner: iuc\n  revisions: 3ea5a2a63fa2\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rgrnastar\n  owner: iuc\n  revisions: b0f2be869d6d\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: 5826298f6a73\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: 6be888be75f9\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: table_compute\n  owner: iuc\n  revisions: 3bf5661c0280\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: 135b80fb1ac2\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: cutadapt\n  owner: lparsons\n  revisions: fe74900d6dc7\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 473382134e56\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 27e16a30667a\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 473382134e56\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 27e16a30667a\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 473382134e56\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rseqc\n  owner: nilesh\n  revisions: 27e16a30667a\n  tool_panel_section_label: RNA Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
         "api": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/ref-based/tutorial.json",
         "contributions": {
             "authorship": [
@@ -271826,31 +278790,32 @@
         "dir": "topics/transcriptomics/tutorials/ref-based",
         "edam_operation": [
             "Visualisation",
-            "Primer removal",
-            "Sequencing quality control",
-            "Sequence alignment",
-            "Formatting",
-            "Sequence composition calculation",
-            "Gene functional annotation",
-            "Validation",
-            "Sequence trimming",
             "Differential gene expression analysis",
+            "Sequencing quality control",
+            "RNA-Seq analysis",
             "Statistical calculation",
+            "RNA-Seq quantification",
             "Pathway or network visualisation",
+            "Validation",
+            "Exonic splicing enhancer prediction",
+            "Sequence composition calculation",
+            "Formatting",
+            "Data handling",
+            "Sequence alignment",
+            "Sequence trimming",
             "Enrichment analysis",
             "Read summarisation",
-            "RNA-Seq analysis",
+            "Pathway or network analysis",
             "Read pre-processing",
-            "RNA-Seq quantification",
-            "Data handling",
-            "Exonic splicing enhancer prediction",
-            "Pathway or network analysis"
+            "Primer removal",
+            "Gene functional annotation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu",
             "UseGalaxy.fr",
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
@@ -271868,12 +278833,12 @@
         "hands_on": true,
         "id": "transcriptomics/ref-based",
         "inexact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
+            "UseGalaxy.no"
         ],
         "js_requirements": {
-            "mathjax": 81142,
+            "mathjax": 81127,
             "mermaid": false
         },
         "key_points": [
@@ -271883,7 +278848,7 @@
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-07-17",
+        "mod_date": "2024-09-18",
         "objectives": [
             "Check a sequence quality report generated by FastQC for RNA-Seq data",
             "Explain the principle and specificity of mapping of RNA-Seq data to an eukaryotic reference genome",
@@ -271897,7 +278862,7 @@
             "Perform a gene ontology enrichment analysis",
             "Perform and visualize an enrichment analysis for KEGG pathways"
         ],
-        "pageviews": 283706,
+        "pageviews": 289636,
         "priority": 2,
         "pub_date": "2016-10-05",
         "questions": [
@@ -271910,6 +278875,7 @@
                 "captioners": [
                     "lldelisle"
                 ],
+                "cyoa": true,
                 "date": "2023-05-15",
                 "galaxy_version": "23.01",
                 "length": "2H50M",
@@ -271934,44 +278900,44 @@
         ],
         "short_id": "T00295",
         "short_tools": [
-            "samtools_view",
-            "pathview",
-            "Cut1",
-            "rseqc_read_distribution",
             "rna_star",
-            "table_compute",
-            "gtftobed12",
+            "join1",
+            "picard_MarkDuplicates",
+            "ChangeCase",
+            "pygenomeTracks",
+            "length_and_gc_content",
+            "samtools_idxstats",
+            "collection_element_identifiers",
             "deseq2",
             "__MERGE_COLLECTION__",
-            "__EXTRACT_DATASET__",
-            "__TAG_FROM_FILE__",
+            "gtftobed12",
+            "fastqc",
+            "deg_annotate",
+            "dexseq",
             "Grouping1",
+            "__EXTRACT_DATASET__",
+            "pathview",
+            "table_compute",
+            "rseqc_geneBody_coverage",
+            "tp_cat",
+            "samtools_view",
+            "Filter1",
             "ggplot2_heatmap2",
-            "tp_tail_tool",
-            "featurecounts",
             "tp_sort_header_tool",
-            "ChangeCase",
-            "length_and_gc_content",
+            "cutadapt",
+            "multiqc",
             "goseq",
-            "dexseq",
-            "pygenomeTracks",
-            "cat1",
+            "Cut1",
+            "__TAG_FROM_FILE__",
             "rseqc_infer_experiment",
-            "tp_cat",
-            "deg_annotate",
-            "samtools_idxstats",
-            "rseqc_geneBody_coverage",
-            "Filter1",
-            "collection_element_identifiers",
+            "rseqc_read_distribution",
+            "tp_tail_tool",
+            "cat1",
             "tp_replace_in_line",
-            "cutadapt",
-            "join1",
-            "picard_MarkDuplicates",
-            "multiqc",
             "dexseq_count",
-            "fastqc",
             "Add_a_column1",
-            "__FLATTEN__"
+            "__FLATTEN__",
+            "featurecounts"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -271992,9 +278958,19 @@
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
             ],
             "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -272004,11 +278980,6 @@
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
                 }
             ]
         },
@@ -272091,12 +279062,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/ref-based/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/transcriptomics/tutorials/ref-based/tutorial.json"
         },
-        "version": 93,
+        "version": 94,
         "video": false,
         "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 177,
-        "visitors": 138622,
+        "visit_duration": 176,
+        "visitors": 142889,
         "workflows": [
             {
                 "creators": [
@@ -272441,7 +279412,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nDrosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nheader\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nKEGG pathways to plot\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Extract samples\u2019 name\"];\n  0 -->|output| 4;\n  5[\"Compute gene length\"];\n  1 -->|output| 5;\n  6[\"Extract groups\"];\n  4 -->|output| 6;\n  7[\"Change Case\"];\n  5 -->|length| 7;\n  8[\"Tag elements with groups\"];\n  0 -->|output| 8;\n  6 -->|outfile| 8;\n  9[\"Differential Analysis\"];\n  8 -->|output| 9;\n  c1ff3e9a-46d3-4862-adb6-076ea951be26[\"Output\\nDESeq2_plots\"];\n  9 --> c1ff3e9a-46d3-4862-adb6-076ea951be26;\n  style c1ff3e9a-46d3-4862-adb6-076ea951be26 stroke:#2c3143,stroke-width:4px;\n  b430e84e-cfa5-48e8-92a7-ef5630ced1e5[\"Output\\nDESeq2_normalized_counts\"];\n  9 --> b430e84e-cfa5-48e8-92a7-ef5630ced1e5;\n  style b430e84e-cfa5-48e8-92a7-ef5630ced1e5 stroke:#2c3143,stroke-width:4px;\n  10[\"Compute\"];\n  9 -->|deseq_out| 10;\n  11[\"Annotate DESeq2/DEXSeq output tables\"];\n  1 -->|output| 11;\n  9 -->|deseq_out| 11;\n  12[\"Table Compute\"];\n  9 -->|counts_out| 12;\n  13[\"Cut\"];\n  10 -->|out_file1| 13;\n  14[\"Concatenate datasets\"];\n  2 -->|output| 14;\n  11 -->|output| 14;\n  11f46837-7dbb-453b-962a-3c97cb0faad4[\"Output\\nDESeq2_annotated_results_with_header\"];\n  14 --> 11f46837-7dbb-453b-962a-3c97cb0faad4;\n  style 11f46837-7dbb-453b-962a-3c97cb0faad4 stroke:#2c3143,stroke-width:4px;\n  15[\"Table Compute\"];\n  9 -->|counts_out| 15;\n  12 -->|table| 15;\n  32004d23-7c99-4405-a65f-fd861b40c949[\"Output\\nz_score\"];\n  15 --> 32004d23-7c99-4405-a65f-fd861b40c949;\n  style 32004d23-7c99-4405-a65f-fd861b40c949 stroke:#2c3143,stroke-width:4px;\n  16[\"Change Case\"];\n  13 -->|out_file1| 16;\n  17[\"Filter\"];\n  14 -->|out_file1| 17;\n  18[\"goseq\"];\n  16 -->|out_file1| 18;\n  7 -->|out_file1| 18;\n  a0dd7397-7262-4336-abd6-a915ab6be36a[\"Output\\ngo_genes\"];\n  18 --> a0dd7397-7262-4336-abd6-a915ab6be36a;\n  style a0dd7397-7262-4336-abd6-a915ab6be36a stroke:#2c3143,stroke-width:4px;\n  659fec58-4ed5-4aee-9e50-7acce21113cb[\"Output\\ngo_plot\"];\n  18 --> 659fec58-4ed5-4aee-9e50-7acce21113cb;\n  style 659fec58-4ed5-4aee-9e50-7acce21113cb stroke:#2c3143,stroke-width:4px;\n  c06c58d4-ab5d-49da-b481-baf668c6fc29[\"Output\\ngo_terms\"];\n  18 --> c06c58d4-ab5d-49da-b481-baf668c6fc29;\n  style c06c58d4-ab5d-49da-b481-baf668c6fc29 stroke:#2c3143,stroke-width:4px;\n  19[\"goseq\"];\n  16 -->|out_file1| 19;\n  7 -->|out_file1| 19;\n  9872b017-9b39-4cd3-b232-a305979a782b[\"Output\\nkegg_genes\"];\n  19 --> 9872b017-9b39-4cd3-b232-a305979a782b;\n  style 9872b017-9b39-4cd3-b232-a305979a782b stroke:#2c3143,stroke-width:4px;\n  8d0ac5be-ac7d-4f10-85ac-d3461f561a50[\"Output\\nkegg_pathways\"];\n  19 --> 8d0ac5be-ac7d-4f10-85ac-d3461f561a50;\n  style 8d0ac5be-ac7d-4f10-85ac-d3461f561a50 stroke:#2c3143,stroke-width:4px;\n  20[\"Cut\"];\n  17 -->|out_file1| 20;\n  21[\"Filter\"];\n  17 -->|out_file1| 21;\n  22[\"Filter\"];\n  18 -->|wallenius_tab| 22;\n  ae762394-0e90-4b9a-a7b4-7cffeccc80a7[\"Output\\ngo_underrepresented\"];\n  22 --> ae762394-0e90-4b9a-a7b4-7cffeccc80a7;\n  style ae762394-0e90-4b9a-a7b4-7cffeccc80a7 stroke:#2c3143,stroke-width:4px;\n  23[\"Filter\"];\n  18 -->|wallenius_tab| 23;\n  b788d5b7-119c-418a-a12b-a97ef7ea5bf2[\"Output\\ngo_overrepresented\"];\n  23 --> b788d5b7-119c-418a-a12b-a97ef7ea5bf2;\n  style b788d5b7-119c-418a-a12b-a97ef7ea5bf2 stroke:#2c3143,stroke-width:4px;\n  24[\"Filter\"];\n  19 -->|wallenius_tab| 24;\n  69f80c89-fc7d-4bea-836f-34e68615abcd[\"Output\\nkegg_underrepresented\"];\n  24 --> 69f80c89-fc7d-4bea-836f-34e68615abcd;\n  style 69f80c89-fc7d-4bea-836f-34e68615abcd stroke:#2c3143,stroke-width:4px;\n  25[\"Filter\"];\n  19 -->|wallenius_tab| 25;\n  930f1461-0ade-4744-a83d-843108c4b597[\"Output\\nkegg_overrepresented\"];\n  25 --> 930f1461-0ade-4744-a83d-843108c4b597;\n  style 930f1461-0ade-4744-a83d-843108c4b597 stroke:#2c3143,stroke-width:4px;\n  26[\"Pathview\"];\n  20 -->|out_file1| 26;\n  3 -->|output| 26;\n  7cdd4475-6de3-4c02-be8d-d76e788980f6[\"Output\\npathview_plot\"];\n  26 --> 7cdd4475-6de3-4c02-be8d-d76e788980f6;\n  style 7cdd4475-6de3-4c02-be8d-d76e788980f6 stroke:#2c3143,stroke-width:4px;\n  27[\"Join two Datasets\"];\n  9 -->|counts_out| 27;\n  21 -->|out_file1| 27;\n  28[\"Group\"];\n  22 -->|out_file1| 28;\n  d1ae921d-2e2b-46d8-95a2-4443f5a1b3b4[\"Output\\ngo_underrepresented_categories\"];\n  28 --> d1ae921d-2e2b-46d8-95a2-4443f5a1b3b4;\n  style d1ae921d-2e2b-46d8-95a2-4443f5a1b3b4 stroke:#2c3143,stroke-width:4px;\n  29[\"Group\"];\n  23 -->|out_file1| 29;\n  4d2d01eb-15d2-4863-a522-9462c15eb51c[\"Output\\ngo_overrepresented_categories\"];\n  29 --> 4d2d01eb-15d2-4863-a522-9462c15eb51c;\n  style 4d2d01eb-15d2-4863-a522-9462c15eb51c stroke:#2c3143,stroke-width:4px;\n  30[\"Cut\"];\n  27 -->|out_file1| 30;\n  31[\"heatmap2\"];\n  30 -->|out_file1| 31;\n  42cb6b68-4ed6-4b6e-9312-744b9e0c1442[\"Output\\nheatmap_log\"];\n  31 --> 42cb6b68-4ed6-4b6e-9312-744b9e0c1442;\n  style 42cb6b68-4ed6-4b6e-9312-744b9e0c1442 stroke:#2c3143,stroke-width:4px;\n  32[\"heatmap2\"];\n  30 -->|out_file1| 32;\n  0ecef5aa-76ed-4fe7-9244-3b32d231e7f3[\"Output\\nheatmap_zscore\"];\n  32 --> 0ecef5aa-76ed-4fe7-9244-3b32d231e7f3;\n  style 0ecef5aa-76ed-4fe7-9244-3b32d231e7f3 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
+                "modified": "2024-10-02 12:08:11 +0000",
                 "name": "DEG Part - Ref Based RNA Seq - Transcriptomics - GTN",
                 "outputs": [
                     {
@@ -273451,7 +280422,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nsingle fastqs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\npaired fastqs\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nDrosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Cutadapt: remove bad quality bp\"];\n  0 -->|output| 3;\n  4[\"Flatten paired collection for FastQC\"];\n  1 -->|output| 4;\n  5[\"Cutadapt\"];\n  1 -->|output| 5;\n  6[\"Get gene length\"];\n  2 -->|output| 6;\n  077640cc-edbb-4185-9eb1-d11b522774af[\"Output\\nGene length\"];\n  6 --> 077640cc-edbb-4185-9eb1-d11b522774af;\n  style 077640cc-edbb-4185-9eb1-d11b522774af stroke:#2c3143,stroke-width:4px;\n  7[\"convert gtf to bed12\"];\n  2 -->|output| 7;\n  8[\"STAR: map single reads\"];\n  2 -->|output| 8;\n  3 -->|out1| 8;\n  9[\"Merge fastqs for FastQC\"];\n  4 -->|output| 9;\n  0 -->|output| 9;\n  10[\"Merge Cutadapt reports\"];\n  5 -->|report| 10;\n  3 -->|report| 10;\n  11[\"STAR: map paired reads\"];\n  2 -->|output| 11;\n  5 -->|out_pairs| 11;\n  12[\"count reads per gene for SR\"];\n  8 -->|mapped_reads| 12;\n  2 -->|output| 12;\n  13[\"FastQC check read qualities\"];\n  9 -->|output| 13;\n  14[\"Combine cutadapt results\"];\n  10 -->|output| 14;\n  cab760db-5c9d-4a3c-b768-998bfbac6b57[\"Output\\nmultiqc_cutadapt_html\"];\n  14 --> cab760db-5c9d-4a3c-b768-998bfbac6b57;\n  style cab760db-5c9d-4a3c-b768-998bfbac6b57 stroke:#2c3143,stroke-width:4px;\n  15[\"Merge STAR logs\"];\n  11 -->|output_log| 15;\n  8 -->|output_log| 15;\n  16[\"Merge STAR counts\"];\n  8 -->|reads_per_gene| 16;\n  11 -->|reads_per_gene| 16;\n  17[\"count fragments per gene for PE\"];\n  11 -->|mapped_reads| 17;\n  2 -->|output| 17;\n  1527b5d7-1681-4934-9d9e-3a5f86ae0fee[\"Output\\nfeatureCounts_gene_length\"];\n  17 --> 1527b5d7-1681-4934-9d9e-3a5f86ae0fee;\n  style 1527b5d7-1681-4934-9d9e-3a5f86ae0fee stroke:#2c3143,stroke-width:4px;\n  18[\"Merge STAR BAM\"];\n  11 -->|mapped_reads| 18;\n  8 -->|mapped_reads| 18;\n  802017f4-fb1a-4243-b50d-2ed46f746f11[\"Output\\nSTAR_BAM\"];\n  18 --> 802017f4-fb1a-4243-b50d-2ed46f746f11;\n  style 802017f4-fb1a-4243-b50d-2ed46f746f11 stroke:#2c3143,stroke-width:4px;\n  19[\"merge coverage unique strand 1\"];\n  8 -->|signal_unique_str1| 19;\n  11 -->|signal_unique_str1| 19;\n  20[\"merge coverage unique strand 2\"];\n  8 -->|signal_unique_str2| 20;\n  11 -->|signal_unique_str2| 20;\n  21[\"Combine FastQC results\"];\n  13 -->|text_file| 21;\n  8d0ce9ee-e4e4-4c0c-8261-420ce756ecfd[\"Output\\nmultiqc_fastqc_html\"];\n  21 --> 8d0ce9ee-e4e4-4c0c-8261-420ce756ecfd;\n  style 8d0ce9ee-e4e4-4c0c-8261-420ce756ecfd stroke:#2c3143,stroke-width:4px;\n  22[\"Combine STAR Results\"];\n  15 -->|output| 22;\n  204e3f6c-6f54-46f0-b07c-1f31113265e7[\"Output\\nmultiqc_star_html\"];\n  22 --> 204e3f6c-6f54-46f0-b07c-1f31113265e7;\n  style 204e3f6c-6f54-46f0-b07c-1f31113265e7 stroke:#2c3143,stroke-width:4px;\n  23[\"Remove statistics from STAR counts\"];\n  16 -->|output| 23;\n  24[\"Determine library strandness with STAR\"];\n  16 -->|output| 24;\n  fe7b84dd-4466-4fe7-94a8-408f4ac7ed1a[\"Output\\nmultiqc_star_counts_html\"];\n  24 --> fe7b84dd-4466-4fe7-94a8-408f4ac7ed1a;\n  style fe7b84dd-4466-4fe7-94a8-408f4ac7ed1a stroke:#2c3143,stroke-width:4px;\n  25[\"merge counts from featureCounts\"];\n  12 -->|output_short| 25;\n  17 -->|output_short| 25;\n  c82388f8-cb09-4fdf-8a0e-03cdad579f37[\"Output\\nfeatureCounts\"];\n  25 --> c82388f8-cb09-4fdf-8a0e-03cdad579f37;\n  style c82388f8-cb09-4fdf-8a0e-03cdad579f37 stroke:#2c3143,stroke-width:4px;\n  26[\"merge featureCounts summary\"];\n  12 -->|output_summary| 26;\n  17 -->|output_summary| 26;\n  27[\"Determine library strandness with Infer Experiment\"];\n  18 -->|output| 27;\n  7 -->|bed_file| 27;\n  940ec3ec-dd2e-4d50-bbc4-756945eb16b2[\"Output\\ninferexperiment\"];\n  27 --> 940ec3ec-dd2e-4d50-bbc4-756945eb16b2;\n  style 940ec3ec-dd2e-4d50-bbc4-756945eb16b2 stroke:#2c3143,stroke-width:4px;\n  28[\"Read Distribution\"];\n  18 -->|output| 28;\n  7 -->|bed_file| 28;\n  29[\"Compute read distribution statistics\"];\n  18 -->|output| 29;\n  7 -->|bed_file| 29;\n  30[\"sample BAM\"];\n  18 -->|output| 30;\n  31[\"Get reads number per chromosome\"];\n  18 -->|output| 31;\n  32[\"Remove duplicates\"];\n  18 -->|output| 32;\n  33[\"Determine library strandness with STAR coverage\"];\n  19 -->|output| 33;\n  20 -->|output| 33;\n  2 -->|output| 33;\n  89e1b053-03c2-467a-95a0-d2dc404670ec[\"Output\\npgt\"];\n  33 --> 89e1b053-03c2-467a-95a0-d2dc404670ec;\n  style 89e1b053-03c2-467a-95a0-d2dc404670ec stroke:#2c3143,stroke-width:4px;\n  34[\"Select unstranded counts\"];\n  23 -->|outfile| 34;\n  bce755be-ac3b-4346-9ac5-1128a287bf00[\"Output\\ncounts_from_star\"];\n  34 --> bce755be-ac3b-4346-9ac5-1128a287bf00;\n  style bce755be-ac3b-4346-9ac5-1128a287bf00 stroke:#2c3143,stroke-width:4px;\n  35[\"Sort counts to get gene with highest count on feature Counts\"];\n  25 -->|output| 35;\n  6aeb4dd1-445f-4c66-b1ce-4bb8faac53db[\"Output\\nfeatureCounts_sorted\"];\n  35 --> 6aeb4dd1-445f-4c66-b1ce-4bb8faac53db;\n  style 6aeb4dd1-445f-4c66-b1ce-4bb8faac53db stroke:#2c3143,stroke-width:4px;\n  36[\"Combine read asignments statistics\"];\n  26 -->|output| 36;\n  fc72242a-f23c-4ceb-9a8b-5280343ea5d6[\"Output\\nmultiqc_featureCounts_html\"];\n  36 --> fc72242a-f23c-4ceb-9a8b-5280343ea5d6;\n  style fc72242a-f23c-4ceb-9a8b-5280343ea5d6 stroke:#2c3143,stroke-width:4px;\n  37[\"Combine read distribution on known features\"];\n  29 -->|output| 37;\n  07dca732-0ac7-432e-9e61-2b77f921a23b[\"Output\\nmultiqc_read_distrib\"];\n  37 --> 07dca732-0ac7-432e-9e61-2b77f921a23b;\n  style 07dca732-0ac7-432e-9e61-2b77f921a23b stroke:#2c3143,stroke-width:4px;\n  38[\"Get gene body coverage\"];\n  30 -->|outputsam| 38;\n  7 -->|bed_file| 38;\n  39[\"Combine results on reads per chromosome\"];\n  31 -->|output| 39;\n  7bfa8ae7-8ffd-46a1-a56e-815ed2c9f1cf[\"Output\\nmultiqc_reads_per_chrom\"];\n  39 --> 7bfa8ae7-8ffd-46a1-a56e-815ed2c9f1cf;\n  style 7bfa8ae7-8ffd-46a1-a56e-815ed2c9f1cf stroke:#2c3143,stroke-width:4px;\n  40[\"Combine results of duplicate reads\"];\n  32 -->|metrics_file| 40;\n  66553d0f-e851-458b-82c2-f9b30e394bac[\"Output\\nmultiqc_dup\"];\n  40 --> 66553d0f-e851-458b-82c2-f9b30e394bac;\n  style 66553d0f-e851-458b-82c2-f9b30e394bac stroke:#2c3143,stroke-width:4px;\n  41[\"Sort counts to get gene with highest count on STAR\"];\n  34 -->|out_file1| 41;\n  383df008-0ccb-4d67-98dd-33fa5e2db81e[\"Output\\ncounts_from_star_sorted\"];\n  41 --> 383df008-0ccb-4d67-98dd-33fa5e2db81e;\n  style 383df008-0ccb-4d67-98dd-33fa5e2db81e stroke:#2c3143,stroke-width:4px;\n  42[\"Combine gene body coverage\"];\n  38 -->|outputtxt| 42;\n  8544ea5c-faf2-44c9-85d6-40658fc9b9eb[\"Output\\nmultiqc_gene_body_cov\"];\n  42 --> 8544ea5c-faf2-44c9-85d6-40658fc9b9eb;\n  style 8544ea5c-faf2-44c9-85d6-40658fc9b9eb stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
+                "modified": "2024-10-02 12:08:11 +0000",
                 "name": "QC + Mapping + Counting (single+paired) - Ref Based RNA Seq - Transcriptomics - GTN",
                 "outputs": [
                     {
@@ -274778,7 +281749,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nPaired list collection with PE fastqs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nDrosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\ud83d\udee0\ufe0f Subworkflow\\nFastQC\"];\n  style 2 fill:#edd,stroke:#900,stroke-width:4px;\n  0 -->|output| 2;\n  5f7652f1-e225-4ad1-8dbd-4d21544edb89[\"Output\\nmultiqc_fastqc_html\"];\n  2 --> 5f7652f1-e225-4ad1-8dbd-4d21544edb89;\n  style 5f7652f1-e225-4ad1-8dbd-4d21544edb89 stroke:#2c3143,stroke-width:4px;\n  3[\"\ud83d\udee0\ufe0f Subworkflow\\ncutadapt\"];\n  style 3 fill:#edd,stroke:#900,stroke-width:4px;\n  0 -->|output| 3;\n  41c7fbb5-655b-457c-8ba7-0e2eeab3d7ee[\"Output\\nmultiqc_cutadapt_html\"];\n  3 --> 41c7fbb5-655b-457c-8ba7-0e2eeab3d7ee;\n  style 41c7fbb5-655b-457c-8ba7-0e2eeab3d7ee stroke:#2c3143,stroke-width:4px;\n  4[\"\ud83d\udee0\ufe0f Subworkflow\\nSTAR + multiQC\"];\n  style 4 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 4;\n  3 -->|out_pairs| 4;\n  8aa5ef30-3f09-4a93-944d-0d89101c056a[\"Output\\nmultiqc_star_html\"];\n  4 --> 8aa5ef30-3f09-4a93-944d-0d89101c056a;\n  style 8aa5ef30-3f09-4a93-944d-0d89101c056a stroke:#2c3143,stroke-width:4px;\n  11af5c57-91b4-496c-9b0c-b02904963f81[\"Output\\nSTAR_BAM\"];\n  4 --> 11af5c57-91b4-496c-9b0c-b02904963f81;\n  style 11af5c57-91b4-496c-9b0c-b02904963f81 stroke:#2c3143,stroke-width:4px;\n  5[\"\ud83d\udee0\ufe0f Subworkflow\\nmore QC\"];\n  style 5 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 5;\n  4 -->|STAR_BAM| 5;\n  f2eed352-ca21-4d65-8810-f5a1d3c282b4[\"Output\\nmultiqc_read_distrib_html\"];\n  5 --> f2eed352-ca21-4d65-8810-f5a1d3c282b4;\n  style f2eed352-ca21-4d65-8810-f5a1d3c282b4 stroke:#2c3143,stroke-width:4px;\n  b306cb12-a275-4c6d-b609-47fdc208864b[\"Output\\nmultiqc_reads_per_chrom_html\"];\n  5 --> b306cb12-a275-4c6d-b609-47fdc208864b;\n  style b306cb12-a275-4c6d-b609-47fdc208864b stroke:#2c3143,stroke-width:4px;\n  3375d63c-cdc3-4fbb-8a55-6f504c934918[\"Output\\nmultiqc_gene_body_cov_html\"];\n  5 --> 3375d63c-cdc3-4fbb-8a55-6f504c934918;\n  style 3375d63c-cdc3-4fbb-8a55-6f504c934918 stroke:#2c3143,stroke-width:4px;\n  3ea82568-5698-49a7-88fe-91381070aac2[\"Output\\nmultiqc_dup_html\"];\n  5 --> 3ea82568-5698-49a7-88fe-91381070aac2;\n  style 3ea82568-5698-49a7-88fe-91381070aac2 stroke:#2c3143,stroke-width:4px;\n  6[\"\ud83d\udee0\ufe0f Subworkflow\\nDetermine strandness\"];\n  style 6 fill:#edd,stroke:#900,stroke-width:4px;\n  4 -->|STAR_BAM| 6;\n  1 -->|output| 6;\n  4 -->|signal_unique_str1| 6;\n  4 -->|signal_unique_str2| 6;\n  4 -->|reads_per_gene| 6;\n  fb810859-f2d0-43f8-ac7c-5c714c5c6805[\"Output\\ninferexperiment\"];\n  6 --> fb810859-f2d0-43f8-ac7c-5c714c5c6805;\n  style fb810859-f2d0-43f8-ac7c-5c714c5c6805 stroke:#2c3143,stroke-width:4px;\n  9727824a-3eb2-4430-92d1-b3c40c3041d1[\"Output\\npgt\"];\n  6 --> 9727824a-3eb2-4430-92d1-b3c40c3041d1;\n  style 9727824a-3eb2-4430-92d1-b3c40c3041d1 stroke:#2c3143,stroke-width:4px;\n  105313d8-e31a-405d-8fcd-cc5fd93275e2[\"Output\\nmultiqc_star_counts_html\"];\n  6 --> 105313d8-e31a-405d-8fcd-cc5fd93275e2;\n  style 105313d8-e31a-405d-8fcd-cc5fd93275e2 stroke:#2c3143,stroke-width:4px;\n  7[\"\ud83d\udee0\ufe0f Subworkflow\\ncount STAR\"];\n  style 7 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 7;\n  4 -->|reads_per_gene| 7;\n  5fee8aff-4023-43f1-a653-f5af5357d798[\"Output\\ncounts_from_star\"];\n  7 --> 5fee8aff-4023-43f1-a653-f5af5357d798;\n  style 5fee8aff-4023-43f1-a653-f5af5357d798 stroke:#2c3143,stroke-width:4px;\n  bd3388e6-5b45-4fdc-9780-3efd1c34ebf8[\"Output\\ncounts_from_star_sorted\"];\n  7 --> bd3388e6-5b45-4fdc-9780-3efd1c34ebf8;\n  style bd3388e6-5b45-4fdc-9780-3efd1c34ebf8 stroke:#2c3143,stroke-width:4px;\n  7b7c698b-4808-4b45-adf1-686f8d273d18[\"Output\\nGene length\"];\n  7 --> 7b7c698b-4808-4b45-adf1-686f8d273d18;\n  style 7b7c698b-4808-4b45-adf1-686f8d273d18 stroke:#2c3143,stroke-width:4px;\n  8[\"\ud83d\udee0\ufe0f Subworkflow\\ncount featureCount\"];\n  style 8 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 8;\n  4 -->|STAR_BAM| 8;\n  f0de4714-4df8-4506-90d9-384537ad663e[\"Output\\nfeatureCounts_sorted\"];\n  8 --> f0de4714-4df8-4506-90d9-384537ad663e;\n  style f0de4714-4df8-4506-90d9-384537ad663e stroke:#2c3143,stroke-width:4px;\n  8b9d6c76-6e82-4691-b8bc-9996d6ae1594[\"Output\\nfeatureCounts_gene_length\"];\n  8 --> 8b9d6c76-6e82-4691-b8bc-9996d6ae1594;\n  style 8b9d6c76-6e82-4691-b8bc-9996d6ae1594 stroke:#2c3143,stroke-width:4px;\n  152ba01e-d4f2-4227-8812-87648a1c19ea[\"Output\\nmultiqc_featureCounts_html\"];\n  8 --> 152ba01e-d4f2-4227-8812-87648a1c19ea;\n  style 152ba01e-d4f2-4227-8812-87648a1c19ea stroke:#2c3143,stroke-width:4px;\n  46c7a2e8-7819-4715-a028-7ad1de9ed605[\"Output\\nfeatureCounts\"];\n  8 --> 46c7a2e8-7819-4715-a028-7ad1de9ed605;\n  style 46c7a2e8-7819-4715-a028-7ad1de9ed605 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
+                "modified": "2024-10-02 12:08:11 +0000",
                 "name": "QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN - subworkflows",
                 "outputs": [
                     {
@@ -277697,20 +284668,20 @@
         ],
         "dir": "topics/transcriptomics/tutorials/minerva-pathways",
         "edam_operation": [
-            "Primer removal",
-            "Sequencing quality control",
+            "Data handling",
             "Sequence alignment",
-            "Sequence composition calculation",
+            "Sequence trimming",
+            "Sequencing quality control",
+            "RNA-Seq analysis",
             "Read summarisation",
-            "Read pre-processing",
+            "Statistical calculation",
             "RNA-Seq quantification",
-            "Gene functional annotation",
-            "Data handling",
             "Validation",
-            "Sequence trimming",
-            "Statistical calculation",
-            "RNA-Seq analysis",
-            "Annotation"
+            "Annotation",
+            "Sequence composition calculation",
+            "Read pre-processing",
+            "Primer removal",
+            "Gene functional annotation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -277722,6 +284693,7 @@
         "hands_on": true,
         "id": "transcriptomics/minerva-pathways",
         "inexact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.fr",
             "UseGalaxy.no",
@@ -277744,7 +284716,7 @@
             "Perform an analysis using a workflow from WorkflowHub",
             "Visualise and interpret the results with MINERVA"
         ],
-        "pageviews": 163,
+        "pageviews": 210,
         "priority": 2,
         "pub_date": "2024-03-28",
         "questions": [
@@ -277753,26 +284725,26 @@
         ],
         "short_id": "T00437",
         "short_tools": [
-            "Cut1",
-            "rseqc_read_distribution",
-            "__EXTRACT_DATASET__",
-            "Grep1",
-            "hisat2",
+            "limma_voom",
+            "join1",
             "collection_column_join",
-            "featurecounts",
-            "tp_sort_header_tool",
+            "hisat2",
+            "fastqc",
+            "annotatemyids",
+            "__EXTRACT_DATASET__",
             "tp_sorted_uniq",
-            "goseq",
             "rseqc_geneBody_coverage",
-            "tp_replace_in_line",
-            "annotatemyids",
-            "join1",
+            "tp_sort_header_tool",
             "cutadapt",
-            "limma_voom",
             "multiqc",
+            "goseq",
+            "Grep1",
+            "Cut1",
             "fasterq_dump",
-            "fastqc",
-            "Add_a_column1"
+            "rseqc_read_distribution",
+            "tp_replace_in_line",
+            "Add_a_column1",
+            "featurecounts"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -277791,6 +284763,11 @@
                 }
             ],
             "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -277863,8 +284840,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 176,
-        "visitors": 137,
+        "visit_duration": 126,
+        "visitors": 176,
         "workflows": [
             {
                 "creators": [
@@ -277922,7 +284899,7 @@
                 ],
                 "license": "AGPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSample Table\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Cut\"];\n  0 -->|output| 1;\n  2[\"Select\"];\n  1 -->|out_file1| 2;\n  3[\"Faster Download and Extract Reads in FASTQ\"];\n  2 -->|out_file1| 3;\n  b7c7e59d-6a78-41af-ae59-e52fcc1fe2f6[\"Output\\noutput_collection\"];\n  3 --> b7c7e59d-6a78-41af-ae59-e52fcc1fe2f6;\n  style b7c7e59d-6a78-41af-ae59-e52fcc1fe2f6 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
+                "modified": "2024-10-02 12:08:11 +0000",
                 "name": "BY-COVID: Data Download",
                 "outputs": [
                     {
@@ -278147,7 +285124,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nfeatureCounts: Counts\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nfactordata\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nfeatureCounts: Lengths\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Column join\"];\n  0 -->|output| 3;\n  4[\"Extract dataset\"];\n  2 -->|output| 4;\n  5[\"countdata\"];\n  3 -->|tabular_output| 5;\n  e8dcfaaf-0d8d-46eb-8cc9-ce2fbdfc45e5[\"Output\\ncount_data\"];\n  5 --> e8dcfaaf-0d8d-46eb-8cc9-ce2fbdfc45e5;\n  style e8dcfaaf-0d8d-46eb-8cc9-ce2fbdfc45e5 stroke:#2c3143,stroke-width:4px;\n  6[\"annodata\"];\n  3 -->|tabular_output| 6;\n  7[\"Replace Text\"];\n  5 -->|outfile| 7;\n  8[\"limma DEG analysis\"];\n  6 -->|out_tab| 8;\n  7 -->|outfile| 8;\n  1 -->|output| 8;\n  1c8d7950-1003-4c86-9986-c6ed1264cd8b[\"Output\\nlimma_report\"];\n  8 --> 1c8d7950-1003-4c86-9986-c6ed1264cd8b;\n  style 1c8d7950-1003-4c86-9986-c6ed1264cd8b stroke:#2c3143,stroke-width:4px;\n  9[\"Extract dataset\"];\n  8 -->|outTables| 9;\n  10[\"MINERVA Formatting\"];\n  9 -->|output| 10;\n  9ce4f48b-e742-4b7c-9bde-5d51f11068d3[\"Output\\nminerva_table\"];\n  10 --> 9ce4f48b-e742-4b7c-9bde-5d51f11068d3;\n  style 9ce4f48b-e742-4b7c-9bde-5d51f11068d3 stroke:#2c3143,stroke-width:4px;\n  11[\"Join two Datasets\"];\n  9 -->|output| 11;\n  4 -->|output| 11;\n  12[\"Compute\"];\n  11 -->|out_file1| 12;\n  13[\"Cut\"];\n  12 -->|out_file1| 13;\n  14[\"Unique\"];\n  13 -->|out_file1| 14;\n  15[\"Cut\"];\n  14 -->|outfile| 15;\n  16[\"Cut\"];\n  14 -->|outfile| 16;\n  17[\"goseq\"];\n  15 -->|out_file1| 17;\n  16 -->|out_file1| 17;",
-                "modified": "2024-08-18 00:06:26 +0000",
+                "modified": "2024-10-02 12:08:11 +0000",
                 "name": "mRNA-Seq BY-COVID Pipeline: Analysis",
                 "outputs": [
                     {
@@ -278436,7 +285413,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nmRNA-Seq Reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nUCSC Genome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"FastQC\"];\n  0 -->|output| 2;\n  3[\"Cutadapt\"];\n  0 -->|output| 3;\n  4[\"FastQC\"];\n  3 -->|out1| 4;\n  5[\"HISAT2\"];\n  3 -->|out1| 5;\n  6[\"featureCounts\"];\n  5 -->|output_alignments| 6;\n  5cb5bd5d-df81-4463-8002-e89551780f01[\"Output\\noutput_feature_lengths\"];\n  6 --> 5cb5bd5d-df81-4463-8002-e89551780f01;\n  style 5cb5bd5d-df81-4463-8002-e89551780f01 stroke:#2c3143,stroke-width:4px;\n  5dec13e1-0011-472c-a72d-6715fe55c23c[\"Output\\noutput_short\"];\n  6 --> 5dec13e1-0011-472c-a72d-6715fe55c23c;\n  style 5dec13e1-0011-472c-a72d-6715fe55c23c stroke:#2c3143,stroke-width:4px;\n  7[\"Read Distribution\"];\n  5 -->|output_alignments| 7;\n  1 -->|output| 7;\n  8[\"Gene Body Coverage BAM\"];\n  5 -->|output_alignments| 8;\n  1 -->|output| 8;\n  9[\"Multi QC raw reads\"];\n  2 -->|text_file| 9;\n  4 -->|text_file| 9;\n  3 -->|report| 9;\n  5 -->|summary_file| 9;\n  7 -->|output| 9;\n  8 -->|outputtxt| 9;\n  6 -->|output_summary| 9;\n  9217af4e-e34c-4a49-9d67-4b3df511ac2c[\"Output\\nhtml_report\"];\n  9 --> 9217af4e-e34c-4a49-9d67-4b3df511ac2c;\n  style 9217af4e-e34c-4a49-9d67-4b3df511ac2c stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
+                "modified": "2024-10-02 12:08:11 +0000",
                 "name": "mRNA-Seq BY-COVID Pipeline: Counts",
                 "outputs": [
                     {
@@ -278735,20 +285712,21 @@
         ],
         "dir": "topics/transcriptomics/tutorials/de-novo",
         "edam_operation": [
-            "Sequencing quality control",
             "Sequence alignment",
-            "Sequence composition calculation",
+            "Differential gene expression analysis",
+            "Sequencing quality control",
+            "RNA-Seq analysis",
             "Read summarisation",
+            "Statistical calculation",
             "RNA-Seq quantification",
-            "Transcriptome assembly",
             "Sequence annotation",
-            "Differential gene expression analysis",
-            "RNA-Seq analysis",
-            "Statistical calculation"
+            "Transcriptome assembly",
+            "Sequence composition calculation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
             "Galaxy@AuBi",
+            "UseGalaxy.be",
             "UseGalaxy.fr",
             "UseGalaxy.org (Main)"
         ],
@@ -278779,7 +285757,7 @@
             "Reconstruction of transcripts without reference transcriptome (de novo)",
             "Analysis of differentially expressed genes"
         ],
-        "pageviews": 23466,
+        "pageviews": 23998,
         "priority": 3,
         "pub_date": "2017-02-19",
         "questions": [
@@ -278803,15 +285781,15 @@
         "short_id": "T00289",
         "short_tools": [
             "hisat2",
-            "deeptools_bam_coverage",
-            "stringtie_merge",
-            "featurecounts",
-            "fastqc",
-            "Filter1",
             "gffcompare",
-            "deseq2",
+            "Filter1",
+            "fastqc",
             "stringtie",
-            "trimmomatic"
+            "deseq2",
+            "deeptools_bam_coverage",
+            "featurecounts",
+            "trimmomatic",
+            "stringtie_merge"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -278823,6 +285801,11 @@
                     "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.fr",
                     "url": "https://usegalaxy.fr/",
@@ -278891,8 +285874,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 150,
-        "visitors": 13032,
+        "visit_duration": 151,
+        "visitors": 13418,
         "workflows": [
             {
                 "creators": [],
@@ -279254,7 +286237,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nG1E_rep1_forward_read\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nG1E_rep1_reverse_read\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nG1E_rep2_forward_read\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nG1E_rep2_reverse_read\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_rep1_forward_read\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_rep1_reverse_read\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_rep2_forward_read\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_rep2_reverse_read\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nRefSeq_reference_GTF\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"FastQC\"];\n  0 -->|output| 9;\n  10[\"FastQC\"];\n  1 -->|output| 10;\n  11[\"Trimmomatic\"];\n  0 -->|output| 11;\n  1 -->|output| 11;\n  12[\"FastQC\"];\n  2 -->|output| 12;\n  13[\"FastQC\"];\n  3 -->|output| 13;\n  14[\"Trimmomatic\"];\n  2 -->|output| 14;\n  3 -->|output| 14;\n  15[\"FastQC\"];\n  4 -->|output| 15;\n  16[\"FastQC\"];\n  5 -->|output| 16;\n  17[\"Trimmomatic\"];\n  4 -->|output| 17;\n  5 -->|output| 17;\n  18[\"FastQC\"];\n  6 -->|output| 18;\n  19[\"FastQC\"];\n  7 -->|output| 19;\n  20[\"Trimmomatic\"];\n  6 -->|output| 20;\n  7 -->|output| 20;\n  21[\"HISAT2\"];\n  11 -->|fastq_out_r1_paired| 21;\n  11 -->|fastq_out_r2_paired| 21;\n  22[\"FastQC\"];\n  11 -->|fastq_out_r1_paired| 22;\n  23[\"FastQC\"];\n  11 -->|fastq_out_r2_paired| 23;\n  24[\"HISAT2\"];\n  14 -->|fastq_out_r1_paired| 24;\n  14 -->|fastq_out_r2_paired| 24;\n  25[\"FastQC\"];\n  14 -->|fastq_out_r1_paired| 25;\n  26[\"FastQC\"];\n  14 -->|fastq_out_r2_paired| 26;\n  27[\"HISAT2\"];\n  17 -->|fastq_out_r1_paired| 27;\n  17 -->|fastq_out_r2_paired| 27;\n  28[\"FastQC\"];\n  17 -->|fastq_out_r1_paired| 28;\n  29[\"FastQC\"];\n  17 -->|fastq_out_r2_paired| 29;\n  30[\"HISAT2\"];\n  20 -->|fastq_out_r1_paired| 30;\n  20 -->|fastq_out_r2_paired| 30;\n  31[\"FastQC\"];\n  20 -->|fastq_out_r1_paired| 31;\n  32[\"FastQC\"];\n  20 -->|fastq_out_r2_paired| 32;\n  33[\"StringTie\"];\n  21 -->|output_alignments| 33;\n  34[\"bamCoverage\"];\n  21 -->|output_alignments| 34;\n  35[\"bamCoverage\"];\n  21 -->|output_alignments| 35;\n  36[\"StringTie\"];\n  24 -->|output_alignments| 36;\n  37[\"bamCoverage\"];\n  24 -->|output_alignments| 37;\n  38[\"bamCoverage\"];\n  24 -->|output_alignments| 38;\n  39[\"StringTie\"];\n  27 -->|output_alignments| 39;\n  40[\"bamCoverage\"];\n  27 -->|output_alignments| 40;\n  41[\"bamCoverage\"];\n  27 -->|output_alignments| 41;\n  42[\"StringTie\"];\n  30 -->|output_alignments| 42;\n  43[\"bamCoverage\"];\n  30 -->|output_alignments| 43;\n  44[\"bamCoverage\"];\n  30 -->|output_alignments| 44;\n  45[\"StringTie merge\"];\n  8 -->|output| 45;\n  33 -->|output_gtf| 45;\n  36 -->|output_gtf| 45;\n  42 -->|output_gtf| 45;\n  39 -->|output_gtf| 45;\n  46[\"GffCompare\"];\n  8 -->|output| 46;\n  45 -->|out_gtf| 46;\n  47[\"featureCounts\"];\n  21 -->|output_alignments| 47;\n  46 -->|transcripts_annotated| 47;\n  48[\"featureCounts\"];\n  24 -->|output_alignments| 48;\n  46 -->|transcripts_annotated| 48;\n  49[\"featureCounts\"];\n  27 -->|output_alignments| 49;\n  46 -->|transcripts_annotated| 49;\n  50[\"featureCounts\"];\n  30 -->|output_alignments| 50;\n  46 -->|transcripts_annotated| 50;\n  51[\"DESeq2\"];\n  47 -->|output_short| 51;\n  48 -->|output_short| 51;\n  49 -->|output_short| 51;\n  50 -->|output_short| 51;\n  52[\"Filter\"];\n  51 -->|deseq_out| 52;\n  53[\"Filter\"];\n  52 -->|out_file1| 53;\n  54[\"Filter\"];\n  52 -->|out_file1| 54;",
-                "modified": "2024-08-18 00:06:25 +0000",
+                "modified": "2024-10-02 12:08:11 +0000",
                 "name": "De novo transcriptome reconstruction with RNA-Seq",
                 "outputs": [
                     {
@@ -281389,7 +288372,7 @@
         "license": "CC-BY-4.0",
         "logo": "GTN",
         "mod_date": "2023-03-05",
-        "pageviews": 5726884,
+        "pageviews": 5897569,
         "priority": 0,
         "pub_date": "2016-08-19",
         "redirect_from": [
@@ -281458,7 +288441,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2063758
+        "visitors": 2133613
     },
     {
         "admin_install": {
@@ -281576,17 +288559,17 @@
             "topic_0199"
         ],
         "edam_operation": [
-            "Sequencing quality control",
-            "Genome indexing",
+            "Data handling",
             "Sequence alignment",
-            "Formatting",
-            "Sequence composition calculation",
-            "Sequence alignment analysis",
             "Read mapping",
+            "Sequencing quality control",
+            "Sequence alignment analysis",
             "Generation",
-            "Data handling",
+            "Statistical calculation",
             "Variant calling",
-            "Statistical calculation"
+            "Sequence composition calculation",
+            "Formatting",
+            "Genome indexing"
         ],
         "edam_topic": [
             "Genomics",
@@ -281597,6 +288580,7 @@
             "Genetic variation"
         ],
         "exact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.eu",
             "UseGalaxy.fr",
             "UseGalaxy.no",
@@ -281626,29 +288610,34 @@
         "objectives": [
             "Using Galaxy's main site we will see how to call variants in bacteria, viruses, and organelles."
         ],
-        "pageviews": 13427,
+        "pageviews": 13577,
         "pub_date": "2017-02-16",
         "questions": [
             "How does frequency of mitochondrial polymorphisms change from mother to child?"
         ],
         "short_id": "T00314",
         "short_tools": [
+            "bwa_mem",
             "picard_MarkDuplicates",
-            "freebayes",
-            "vcf2tsv",
-            "picard_MergeSamFiles",
             "vcffilter2",
             "bamFilter",
+            "picard_MergeSamFiles",
             "Cut1",
-            "fastqc",
             "bamleftalign",
-            "bwa_mem"
+            "fastqc",
+            "vcf2tsv",
+            "freebayes"
         ],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "introduction",
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
@@ -281724,7 +288713,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 123,
-        "visitors": 7035,
+        "visitors": 7149,
         "workflows": [
             {
                 "creators": [],
@@ -281929,7 +288918,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nraw_child-ds-1.fq\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nraw_child-ds-2.fq\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nraw_mother-ds-1.fq\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nraw_mother-ds-2.fq\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"FastQC\"];\n  0 -->|output| 4;\n  5[\"FastQC\"];\n  1 -->|output| 5;\n  6[\"Map with BWA-MEM\"];\n  0 -->|output| 6;\n  1 -->|output| 6;\n  7[\"FastQC\"];\n  2 -->|output| 7;\n  8[\"FastQC\"];\n  3 -->|output| 8;\n  9[\"Map with BWA-MEM\"];\n  2 -->|output| 9;\n  3 -->|output| 9;\n  10[\"MergeSamFiles\"];\n  9 -->|bam_output| 10;\n  6 -->|bam_output| 10;\n  11[\"MarkDuplicates\"];\n  10 -->|outFile| 11;\n  12[\"BamLeftAlign\"];\n  11 -->|outFile| 12;\n  13[\"Filter\"];\n  12 -->|output_bam| 13;\n  14[\"FreeBayes\"];\n  13 -->|out_file1| 14;\n  15[\"VCFfilter:\"];\n  14 -->|output_vcf| 15;\n  16[\"VCFtoTab-delimited:\"];\n  15 -->|out_file1| 16;\n  17[\"Cut\"];\n  16 -->|out_file1| 17;\n  f2e84a79-a71f-4b5f-a526-55d8cd472a05[\"Output\\ncut_variants\"];\n  17 --> f2e84a79-a71f-4b5f-a526-55d8cd472a05;\n  style f2e84a79-a71f-4b5f-a526-55d8cd472a05 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
+                "modified": "2024-10-02 12:08:11 +0000",
                 "name": "Calling variants in non-diploid systems",
                 "outputs": [
                     {
@@ -282987,14 +289976,15 @@
         "draft": true,
         "edam_operation": [
             "Generation",
+            "Statistical calculation",
             "Sequence alignment",
-            "Genome indexing",
             "Variant calling",
             "Read mapping",
-            "Statistical calculation"
+            "Genome indexing"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
@@ -283017,7 +290007,7 @@
             "Processing raw duplex sequencing data into consensus sequences",
             "Find rare variants without relying on diploid assumptions"
         ],
-        "pageviews": 2460,
+        "pageviews": 2479,
         "pub_date": "2017-02-22",
         "questions": [
             "What frequency of variants is so low that it is obscured by sequencing error rate?",
@@ -283025,22 +290015,27 @@
         ],
         "short_id": "T00310",
         "short_tools": [
-            "allele_counts_1",
+            "bwa_mem",
+            "naive_variant_caller",
             "align_families",
+            "correct_barcodes",
             "dunovo",
-            "bamleftalign",
             "Filter1",
-            "make_families",
+            "allele_counts_1",
+            "bamleftalign",
             "sequence_content_trimmer",
-            "bwa_mem",
-            "correct_barcodes",
-            "naive_variant_caller"
+            "make_families"
         ],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "introduction",
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -283086,8 +290081,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 102,
-        "visitors": 1492,
+        "visit_duration": 101,
+        "visitors": 1509,
         "workflows": [
             {
                 "creators": [],
@@ -283190,7 +290185,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSRR1799908_forward\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSRR1799908_reverse\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Du Novo: Make families\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"Du Novo: Correct barcodes\"];\n  2 -->|output| 3;\n  4[\"Du Novo: Align families\"];\n  3 -->|output| 4;\n  5[\"Du Novo: Make consensus reads\"];\n  4 -->|output| 5;\n  6[\"DCS: Sequence Content Trimmer\"];\n  5 -->|dcs1| 6;\n  5 -->|dcs2| 6;\n  7[\"SSCS: Sequence Content Trimmer\"];\n  5 -->|sscs1| 7;\n  5 -->|sscs2| 7;\n  75dfe52d-711e-4826-ba9b-b4feed30f5bf[\"Output\\n\"];\n  7 --> 75dfe52d-711e-4826-ba9b-b4feed30f5bf;\n  style 75dfe52d-711e-4826-ba9b-b4feed30f5bf stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
+                "modified": "2024-10-02 12:08:11 +0000",
                 "name": "Du Novo GTN Tutorial - Make Consensus Sequences",
                 "outputs": [
                     {
@@ -283537,7 +290532,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nTrimmed reads mate 1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nTrimmed reads mate 2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Map with BWA-MEM\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"BamLeftAlign\"];\n  2 -->|bam_output| 3;\n  4[\"Naive Variant Caller NVC\"];\n  3 -->|output_bam| 4;\n  5[\"Variant Annotator\"];\n  4 -->|output_vcf| 5;\n  6[\"Filter\"];\n  5 -->|output| 6;",
-                "modified": "2024-08-18 00:06:26 +0000",
+                "modified": "2024-10-02 12:08:11 +0000",
                 "name": "Du Novo GTN Tutorial - Variant Calling",
                 "outputs": [
                     {
@@ -283581,156 +290576,1243 @@
                             "left": 201,
                             "top": 383
                         },
-                        "tool_id": null,
-                        "tool_state": "{}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "efc0fed6-846f-467f-82a3-45898dc3e0a4",
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "efc0fed6-846f-467f-82a3-45898dc3e0a4",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "347dcece-5ddc-40fb-a5ed-4ff05f2d2d3a"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/nick/allele_counts/allele_counts_1/1.2",
+                        "errors": null,
+                        "id": 5,
+                        "input_connections": {
+                            "input": {
+                                "id": 4,
+                                "output_name": "output_vcf"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Variant Annotator",
+                                "name": "input"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Variant Annotator",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 474,
+                            "top": 502
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "All variants"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nick/allele_counts/allele_counts_1/1.2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "411adeff1eec",
+                            "name": "allele_counts",
+                            "owner": "nick",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"stranded\": \"\\\"true\\\"\", \"covg\": \"\\\"10\\\"\", \"header\": \"\\\"true\\\"\", \"seed\": \"\\\"\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"freq\": \"\\\"0.0\\\"\", \"nofilt\": \"\\\"false\\\"\"}",
+                        "tool_version": "1.2",
+                        "type": "tool",
+                        "uuid": "b27aa8b9-adb8-43b4-9a70-53025ae1f9f1",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "ad99c585-39c1-4888-9726-28c30317ec21"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "Filter1",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "input": {
+                                "id": 5,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Filter",
+                                "name": "input"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Filter",
+                        "outputs": [
+                            {
+                                "name": "out_file1",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 765,
+                            "top": 503
+                        },
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Filtered variants"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"1\\\"\", \"cond\": \"\\\"c16 >= 0.01\\\"\", \"__page__\": null}",
+                        "tool_version": "1.1.0",
+                        "type": "tool",
+                        "uuid": "3ada37c0-11f6-4d2c-bf53-cf1e228ee91e",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "out_file1",
+                                "uuid": "dcdddac9-bd96-4f27-b585-bd3167fef38d"
+                            }
+                        ]
+                    }
+                ],
+                "parent_id": "variant-analysis/dunovo",
+                "path": "topics/variant-analysis/tutorials/dunovo/workflows/variant-calling.ga",
+                "tags": [
+                    "variant-analysis"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Du Novo GTN Tutorial - Variant Calling",
+                "topic_id": "variant-analysis",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-dunovo/versions/variant-calling",
+                "tutorial_id": "dunovo",
+                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/dunovo/workflows/variant-calling.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/dunovo/workflows/variant-calling.html",
+                "version": 3,
+                "wfid": "variant-analysis-dunovo",
+                "wfname": "variant-calling",
+                "workflow": "variant-calling.ga",
+                "workflow_tools": [
+                    "Filter1",
+                    "toolshed.g2.bx.psu.edu/repos/blankenberg/naive_variant_caller/naive_variant_caller/0.0.4",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.1.0.46-0",
+                    "toolshed.g2.bx.psu.edu/repos/nick/allele_counts/allele_counts_1/1.2"
+                ],
+                "workflowhub_id": "1089"
+            }
+        ],
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "86755160afbf",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "86755160afbf",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "emboss_5",
+                    "owner": "devteam",
+                    "revisions": "63dd26468588",
+                    "tool_panel_section_label": "EMBOSS",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "3d0c7bdf12f5",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "5ec9f6bceaee",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "samtools_stats",
+                    "owner": "devteam",
+                    "revisions": "541082d03bef",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bcftools_consensus",
+                    "owner": "iuc",
+                    "revisions": "da0bf365652d",
+                    "tool_panel_section_label": "Variant Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastp",
+                    "owner": "iuc",
+                    "revisions": "c59d48774d03",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "jbrowse",
+                    "owner": "iuc",
+                    "revisions": "a6e57ff585c0",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "jvarkit_wgscoverageplotter",
+                    "owner": "iuc",
+                    "revisions": "ac048a34cac3",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "kraken2",
+                    "owner": "iuc",
+                    "revisions": "20e2f64aa1fe",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mosdepth",
+                    "owner": "iuc",
+                    "revisions": "5854d0da92b4",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "multiqc",
+                    "owner": "iuc",
+                    "revisions": "abfd8a6544d7",
+                    "tool_panel_section_label": "Quality Control",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "qualimap_bamqc",
+                    "owner": "iuc",
+                    "revisions": "4a89c6f84425",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "snippy",
+                    "owner": "iuc",
+                    "revisions": "d220115f882b",
+                    "tool_panel_section_label": "Variant Calling",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "tb_variant_filter",
+                    "owner": "iuc",
+                    "revisions": "32f14a2723ec",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "tbprofiler",
+                    "owner": "iuc",
+                    "revisions": "4839e590cb26",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "tbvcfreport",
+                    "owner": "iuc",
+                    "revisions": "42818629ec4c",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "tbvcfreport",
+                    "owner": "iuc",
+                    "revisions": "9793bc5d741b",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: emboss_5\n  owner: devteam\n  revisions: 63dd26468588\n  tool_panel_section_label: EMBOSS\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 541082d03bef\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_consensus\n  owner: iuc\n  revisions: da0bf365652d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: c59d48774d03\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jvarkit_wgscoverageplotter\n  owner: iuc\n  revisions: ac048a34cac3\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: 20e2f64aa1fe\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mosdepth\n  owner: iuc\n  revisions: 5854d0da92b4\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: abfd8a6544d7\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qualimap_bamqc\n  owner: iuc\n  revisions: 4a89c6f84425\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snippy\n  owner: iuc\n  revisions: d220115f882b\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tb_variant_filter\n  owner: iuc\n  revisions: 32f14a2723ec\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbprofiler\n  owner: iuc\n  revisions: 4839e590cb26\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbvcfreport\n  owner: iuc\n  revisions: 42818629ec4c\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbvcfreport\n  owner: iuc\n  revisions: 9793bc5d741b\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.json",
+        "contributors": [
+            {
+                "bio": "Research at the South African National Bioinformatics Institute",
+                "id": "pvanheus",
+                "joined": "2017-09",
+                "name": "Peter van Heusden",
+                "orcid": "0000-0001-6553-5274",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/",
+                "twitter": "pvanheus",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/pvanheus.json"
+            },
+            {
+                "elixir_node": "au",
+                "email": "simon.gladman@unimelb.edu.au",
+                "id": "slugger70",
+                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
+                "joined": "2017-09",
+                "name": "Simon Gladman",
+                "orcid": "0000-0002-6100-4385",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
+            },
+            {
+                "id": "thobalose",
+                "joined": "2019-11",
+                "name": "Thoba Lose",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/thobalose/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/thobalose.json"
+            }
+        ],
+        "dir": "topics/variant-analysis/tutorials/tb-variant-analysis",
+        "edam_ontology": [
+            "topic_0622",
+            "topic_3301",
+            "topic_0196",
+            "topic_0199",
+            "topic_3305",
+            "topic_3324"
+        ],
+        "edam_operation": [
+            "Sequence alignment",
+            "Phylogenetic tree generation",
+            "Phylogenetic tree visualisation",
+            "Sequencing quality control",
+            "Sequence alignment analysis",
+            "Genome visualisation",
+            "Sequence analysis",
+            "Sequence contamination filtering",
+            "Variant calling",
+            "Global alignment",
+            "Statistical calculation",
+            "Taxonomic classification",
+            "Validation",
+            "Local alignment",
+            "Sequence composition calculation",
+            "Antimicrobial resistance prediction"
+        ],
+        "edam_topic": [
+            "Genomics",
+            "Microbiology",
+            "Sequence assembly",
+            "Genetic variation",
+            "Public health and epidemiology",
+            "Infectious disease"
+        ],
+        "exact_supported_servers": [],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "variant-analysis/tb-variant-analysis",
+        "inexact_supported_servers": [],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "variants in _M. tuberculosis_ sequencing data can be discovered using common microbial bioinformatics tools",
+            "it is not enough to just call variants, variant calling involves multiple quality control steps",
+            "the choice of reference genome and some quality control procedures are species-specific, and require knowledge of the organism in question",
+            "batches of samples can be processed using Galaxy dataset collections and workflows"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-07-26",
+        "objectives": [
+            "How should we filter those variants",
+            "How can we predict drug resistance from those variants",
+            "How do we annotate those variants"
+        ],
+        "pageviews": 9172,
+        "pub_date": "2020-07-25",
+        "questions": [
+            "How do we detect differences between a set of reads from _M. tuberculosis_ (Mtb) and the Mtb reference genome"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "pvanheus",
+                    "nagoue",
+                    "hexylena"
+                ],
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "40M",
+                "speakers": [
+                    "pvanheus"
+                ],
+                "youtube_id": "G1DmquX6Wh8"
+            },
+            {
+                "captioners": [
+                    "pvanheus"
+                ],
+                "date": "2024-06-11",
+                "galaxy_version": "24.0",
+                "length": "1H17M",
+                "speakers": [
+                    "pvanheus"
+                ],
+                "youtube_id": "-nJPngFk36c"
+            }
+        ],
+        "short_id": "T00319",
+        "short_tools": [
+            "tp_sed_tool",
+            "upload1",
+            "snippy",
+            "qualimap_bamqc",
+            "tb_variant_filter",
+            "EMBOSS: seqret84",
+            "tb_profiler_profile",
+            "mosdepth",
+            "jvarkit_wgscoverageplotter",
+            "tbvcfreport",
+            "tp_awk_tool",
+            "fastqc",
+            "jbrowse",
+            "samtools_stats",
+            "bcftools_consensus",
+            "multiqc",
+            "fastp",
+            "kraken2",
+            "EMBOSS:%20seqret84",
+            "__FLATTEN__"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "one-health",
+        "supported_servers": {
+            "exact": [],
+            "inexact": []
+        },
+        "symlink": null,
+        "tags": [
+            "prokaryote",
+            "one-health",
+            "microgalaxy",
+            "tuberculosis"
+        ],
+        "time_estimation": "2h",
+        "title": "M. tuberculosis Variant Analysis",
+        "tools": [
+            "__FLATTEN__",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: seqret84/5.0.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS:%20seqret84/5.0.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/jvarkit_wgscoverageplotter/jvarkit_wgscoverageplotter/20201223+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/mosdepth/mosdepth/0.3.8+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.4.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.2.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.1+galaxy0",
+            "upload1"
+        ],
+        "topic_name": "variant-analysis",
+        "topic_name_human": "Variant Analysis",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "tb-variant-analysis",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.json"
+        },
+        "version": 30,
+        "video": false,
+        "video_versions": 2,
+        "video_view": 0,
+        "visit_duration": 177,
+        "visitors": 5788,
+        "workflows": [
+            {
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0001-6553-5274",
+                        "name": "Peter van Heusden"
+                    }
+                ],
+                "description": "Predict variants and drug resistance from M. tuberculosis sequence samples (Illumina)",
+                "features": {
+                    "comments": false,
+                    "parameters": true,
+                    "report": {
+                        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+                    },
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nReads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference Genome\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMinimum depth of coverage\"]\n  3[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMinimum variant allele frequency\"]\n  4[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nAdditional BWA-MEM options\"]\n  5[label=\"fastp\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"seqret\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"snippy\"]\n  4 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  3 -> 7 [label=\"output\"]\n  5 -> 7 [label=\"output_paired_coll\"]\n  1 -> 7 [label=\"output\"]\n  8[label=\"Kraken2\"]\n  5 -> 8 [label=\"output_paired_coll\"]\n  kc7abf2bfed4c433ea6959eca61282bb5[color=lightseagreen,label=\"Output\\nreport_output\"]\n  8 -> kc7abf2bfed4c433ea6959eca61282bb5\n  k083a0e5177804c91a071dc0e4641d060[color=lightseagreen,label=\"Output\\noutput\"]\n  8 -> k083a0e5177804c91a071dc0e4641d060\n  9[label=\"QualiMap BamQC\"]\n  7 -> 9 [label=\"snpsbam\"]\n  10[label=\"mosdepth\"]\n  2 -> 10 [label=\"output\"]\n  7 -> 10 [label=\"snpsbam\"]\n  11[label=\"TB Variant Filter\"]\n  7 -> 11 [label=\"snpvcf\"]\n  12[label=\"TB-Profiler Profile\"]\n  7 -> 12 [label=\"snpsbam\"]\n  k335635b4a4de4980ad0268f0035daeaa[color=lightseagreen,label=\"Output\\noutput_txt\"]\n  12 -> k335635b4a4de4980ad0268f0035daeaa\n  13[label=\"TB Variant Filter\"]\n  7 -> 13 [label=\"snpvcf\"]\n  14[label=\"Flatten collection\"]\n  9 -> 14 [label=\"raw_data\"]\n  15[label=\"Text reformatting\"]\n  10 -> 15 [label=\"output_quantized_bed\"]\n  16[label=\"Text transformation\"]\n  11 -> 16 [label=\"output1\"]\n  k007df8c2bd13495f8904abf31d4594d0[color=lightseagreen,label=\"Output\\nFinal annotated VCF\"]\n  16 -> k007df8c2bd13495f8904abf31d4594d0\n  17[label=\"MultiQC\"]\n  5 -> 17 [label=\"report_json\"]\n  14 -> 17 [label=\"output\"]\n  k5952823575254ef9881036f1ed0f01f6[color=lightseagreen,label=\"Output\\nhtml_report\"]\n  17 -> k5952823575254ef9881036f1ed0f01f6\n  18[label=\"bcftools consensus\"]\n  13 -> 18 [label=\"output1\"]\n  6 -> 18 [label=\"out_file1\"]\n  15 -> 18 [label=\"outfile\"]\n  kc71b135d35f944d0a20ef25528e518af[color=lightseagreen,label=\"Output\\nconsensus_genome\"]\n  18 -> kc71b135d35f944d0a20ef25528e518af\n  19[label=\"TB Variant Report\"]\n  16 -> 19 [label=\"output\"]\n  12 -> 19 [label=\"results_json\"]\n  k959528d2f8f2444099cf44fddd6c5069[color=lightseagreen,label=\"Output\\ndrug_resistance_report_html\"]\n  19 -> k959528d2f8f2444099cf44fddd6c5069\n  k4d9636eb075b4fd2a1e41a7c37a17fc0[color=lightseagreen,label=\"Output\\nvariants_report_html\"]\n  19 -> k4d9636eb075b4fd2a1e41a7c37a17fc0\n}",
+                "history": [
+                    {
+                        "hash": "c0042e7f333bb9758580a564dbf559e83396a6d3",
+                        "message": "Update to address comments from wm",
+                        "num": 14,
+                        "short_hash": "c0042e7f3",
+                        "unix": "1718025591"
+                    },
+                    {
+                        "hash": "01cf3d5e27fb411603014ca3e0729b2daacc0a0d",
+                        "message": "Add snippers for running workflow from workflowhub.eu and jbrowse vis",
+                        "num": 13,
+                        "short_hash": "01cf3d5e2",
+                        "unix": "1717788409"
+                    },
+                    {
+                        "hash": "d3db4cd3e349677c907c71a761fde1b2935928d2",
+                        "message": "Update the M. tuberculosis variant analysis tutorial * Update all tools to latest versions * Change to fastp instead of Trimmomatic * Add section on running workflow * Update workflow and workflow test",
+                        "num": 12,
+                        "short_hash": "d3db4cd3e",
+                        "unix": "1717771237"
+                    },
+                    {
+                        "hash": "d61d5645fa6b21c25cd5d09f540c4e584b35f2c2",
+                        "message": "Update tb_variant_filter to v. 0.4.0",
+                        "num": 11,
+                        "short_hash": "d61d5645f",
+                        "unix": "1695643686"
+                    },
+                    {
+                        "hash": "c89f11fe32c66c1da9f058ec3fa522e8b18cba82",
+                        "message": "Update some tools in tuberculosis variant analysis tutorial (#4070)",
+                        "num": 10,
+                        "short_hash": "c89f11fe3",
+                        "unix": "1682624753"
+                    },
+                    {
+                        "hash": "fa9e9fb000ef9d2ab91acc67c4f338c213d641e2",
+                        "message": "New variant of tb_variant_filter and tbprofiler, more detail on tb_variant_filter",
+                        "num": 9,
+                        "short_hash": "fa9e9fb00",
+                        "unix": "1672566129"
+                    },
+                    {
+                        "hash": "6e9c1860b186754249a0a90d9957dbace653e9ac",
+                        "message": "Restore workflow indentation and fix WF step order",
+                        "num": 8,
+                        "short_hash": "6e9c1860b",
+                        "unix": "1648048765"
+                    },
+                    {
+                        "hash": "354e9edf1340c37133b7d1834cea608895acebc0",
+                        "message": "Use correct snippy wrapper version everywhere",
+                        "num": 7,
+                        "short_hash": "354e9edf1",
+                        "unix": "1648028595"
+                    },
+                    {
+                        "hash": "6f476a03271eeabffcf0877e8a402f7af815deba",
+                        "message": "Update snippy to 4.6.0",
+                        "num": 6,
+                        "short_hash": "6f476a032",
+                        "unix": "1647976648"
+                    },
+                    {
+                        "hash": "946f6f60f8e068a147f03d89f369f19e552793da",
+                        "message": "Generate cleaner intermediate diff",
+                        "num": 5,
+                        "short_hash": "946f6f60f",
+                        "unix": "1647938051"
+                    },
+                    {
+                        "hash": "8e46a42b5a664cf72ea7e2aae61739348f64dfea",
+                        "message": "Autoupdate workflow, change Kraken2 test",
+                        "num": 4,
+                        "short_hash": "8e46a42b5",
+                        "unix": "1647929062"
+                    },
+                    {
+                        "hash": "f98407ff47fe6ea903372a39b09530ae075d65b3",
+                        "message": "tb-variant-analysis: label workflow outputs and add test",
+                        "num": 3,
+                        "short_hash": "f98407ff4",
+                        "unix": "1595713523"
+                    },
+                    {
+                        "hash": "392830f9b51662e8028b8984f48f827be8a10aed",
+                        "message": "Reformat tb-variant-analysis workflow",
+                        "num": 2,
+                        "short_hash": "392830f9b",
+                        "unix": "1595707349"
+                    },
+                    {
+                        "hash": "2e73bb7aa538d3fb94e7f7ca21bfc6078d35e73f",
+                        "message": "Update M. tuberculosis variant analysis tutorial with new data and workflow",
+                        "num": 1,
+                        "short_hash": "2e73bb7aa",
+                        "unix": "1595705571"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "List of paired Illumina reads (set format to fastqsanger or fastqsanger.gz as appropriate)",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "List of paired Illumina reads (set format to fastqsanger or fastqsanger.gz as appropriate)",
+                                "name": "Reads"
+                            }
+                        ],
+                        "label": "Reads",
+                        "name": "Input dataset collection",
+                        "outputs": [],
+                        "position": {
+                            "left": 0,
+                            "top": 197.65334499942068
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
+                        "tool_version": null,
+                        "type": "data_collection_input",
+                        "uuid": "2bfdfb62-da85-4d2d-8609-8f5e6975b4b3",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "M. tuberculosis reference genome (must be in H37Rv coordinates. The M. tuberculosis inferred ancestral genome is recommended)",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "M. tuberculosis reference genome (must be in H37Rv coordinates. The M. tuberculosis inferred ancestral genome is recommended)",
+                                "name": "Reference Genome"
+                            }
+                        ],
+                        "label": "Reference Genome",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 1.2375059369900399,
+                            "top": 468.60335731890825
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false, \"format\": [\"genbank\"], \"tag\": null}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "023233a0-8cb1-4558-8861-cd246ab58bac",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "Minimum depth of coverage for a position on the genome",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Minimum depth of coverage for a position on the genome",
+                                "name": "Minimum depth of coverage"
+                            }
+                        ],
+                        "label": "Minimum depth of coverage",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 1.8793911063654463,
+                            "top": 625.941216238093
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"default\": 10, \"parameter_type\": \"integer\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "e31bf396-08b6-43ce-872a-545a5e4580c6",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "Minimum proportion of reads that must support a variant for it to be called",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Minimum proportion of reads that must support a variant for it to be called",
+                                "name": "Minimum variant allele frequency"
+                            }
+                        ],
+                        "label": "Minimum variant allele frequency",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 1.358958473709409,
+                            "top": 769.7667492120408
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"default\": 0.9, \"parameter_type\": \"float\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "d1814962-a30d-463a-a081-857a5141385b",
+                        "when": null,
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "Increasing the minimum seed length (-k) parameter can help eliminate matches from contaminants. If used this should be set to 2/3rds of the read length, i.e. the string \"-k 100\" should be used for 150 base pair reads",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "Increasing the minimum seed length (-k) parameter can help eliminate matches from contaminants. If used this should be set to 2/3rds of the read length, i.e. the string \"-k 100\" should be used for 150 base pair reads",
+                                "name": "Additional BWA-MEM options"
+                            }
+                        ],
+                        "label": "Additional BWA-MEM options",
+                        "name": "Input parameter",
+                        "outputs": [],
+                        "position": {
+                            "left": 7.8094297093662135,
+                            "top": 931.4341211532
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_version": null,
+                        "type": "parameter_input",
+                        "uuid": "40d47253-c7c5-471b-871c-9a19fbe60bfe",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "AGPL-3.0-or-later",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nReads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference Genome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nMinimum depth of coverage\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nMinimum variant allele frequency\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nAdditional BWA-MEM options\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"fastp\"];\n  0 -->|output| 5;\n  6[\"seqret\"];\n  1 -->|output| 6;\n  7[\"snippy\"];\n  4 -->|output| 7;\n  2 -->|output| 7;\n  3 -->|output| 7;\n  5 -->|output_paired_coll| 7;\n  1 -->|output| 7;\n  8[\"Kraken2\"];\n  5 -->|output_paired_coll| 8;\n  c7abf2bf-ed4c-433e-a695-9eca61282bb5[\"Output\\nreport_output\"];\n  8 --> c7abf2bf-ed4c-433e-a695-9eca61282bb5;\n  style c7abf2bf-ed4c-433e-a695-9eca61282bb5 stroke:#2c3143,stroke-width:4px;\n  083a0e51-7780-4c91-a071-dc0e4641d060[\"Output\\noutput\"];\n  8 --> 083a0e51-7780-4c91-a071-dc0e4641d060;\n  style 083a0e51-7780-4c91-a071-dc0e4641d060 stroke:#2c3143,stroke-width:4px;\n  9[\"QualiMap BamQC\"];\n  7 -->|snpsbam| 9;\n  10[\"mosdepth\"];\n  2 -->|output| 10;\n  7 -->|snpsbam| 10;\n  11[\"TB Variant Filter\"];\n  7 -->|snpvcf| 11;\n  12[\"TB-Profiler Profile\"];\n  7 -->|snpsbam| 12;\n  335635b4-a4de-4980-ad02-68f0035daeaa[\"Output\\noutput_txt\"];\n  12 --> 335635b4-a4de-4980-ad02-68f0035daeaa;\n  style 335635b4-a4de-4980-ad02-68f0035daeaa stroke:#2c3143,stroke-width:4px;\n  13[\"TB Variant Filter\"];\n  7 -->|snpvcf| 13;\n  14[\"Flatten collection\"];\n  9 -->|raw_data| 14;\n  15[\"Text reformatting\"];\n  10 -->|output_quantized_bed| 15;\n  16[\"Text transformation\"];\n  11 -->|output1| 16;\n  007df8c2-bd13-495f-8904-abf31d4594d0[\"Output\\nFinal annotated VCF\"];\n  16 --> 007df8c2-bd13-495f-8904-abf31d4594d0;\n  style 007df8c2-bd13-495f-8904-abf31d4594d0 stroke:#2c3143,stroke-width:4px;\n  17[\"MultiQC\"];\n  5 -->|report_json| 17;\n  14 -->|output| 17;\n  59528235-7525-4ef9-8810-36f1ed0f01f6[\"Output\\nhtml_report\"];\n  17 --> 59528235-7525-4ef9-8810-36f1ed0f01f6;\n  style 59528235-7525-4ef9-8810-36f1ed0f01f6 stroke:#2c3143,stroke-width:4px;\n  18[\"bcftools consensus\"];\n  13 -->|output1| 18;\n  6 -->|out_file1| 18;\n  15 -->|outfile| 18;\n  c71b135d-35f9-44d0-a20e-f25528e518af[\"Output\\nconsensus_genome\"];\n  18 --> c71b135d-35f9-44d0-a20e-f25528e518af;\n  style c71b135d-35f9-44d0-a20e-f25528e518af stroke:#2c3143,stroke-width:4px;\n  19[\"TB Variant Report\"];\n  16 -->|output| 19;\n  12 -->|results_json| 19;\n  959528d2-f8f2-4440-99cf-44fddd6c5069[\"Output\\ndrug_resistance_report_html\"];\n  19 --> 959528d2-f8f2-4440-99cf-44fddd6c5069;\n  style 959528d2-f8f2-4440-99cf-44fddd6c5069 stroke:#2c3143,stroke-width:4px;\n  4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0[\"Output\\nvariants_report_html\"];\n  19 --> 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0;\n  style 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "TB Variant Analysis v1.0",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "single_paired|input_pair": {
+                                "id": 5,
+                                "output_name": "output_paired_coll"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Kraken2",
+                                "name": "single_paired"
+                            }
+                        ],
+                        "label": null,
+                        "name": "Kraken2",
+                        "outputs": [
+                            {
+                                "name": "report_output",
+                                "type": "tabular"
+                            },
+                            {
+                                "name": "output",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 1605.1346167188794,
+                            "top": 0
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionoutput": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output"
+                            },
+                            "TagDatasetActionreport_output": {
+                                "action_arguments": {
+                                    "tags": "kraken_report"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "report_output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "20e2f64aa1fe",
+                            "name": "kraken2",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"confidence\": \"0.0\", \"kraken2_database\": \"pluspf2021-05\", \"min_base_quality\": \"0\", \"minimum_hit_groups\": \"2\", \"quick\": false, \"report\": {\"create_report\": true, \"use_mpa_style\": false, \"report_zero_counts\": false, \"report_minimizer_data\": false}, \"single_paired\": {\"single_paired_selector\": \"collection\", \"__current_case__\": 0, \"input_pair\": {\"__class__\": \"ConnectedValue\"}}, \"split_reads\": false, \"use_names\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.1+galaxy1",
+                        "type": "tool",
+                        "uuid": "60b17d56-0ef9-4829-829e-923f66de5e2f",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "report_output",
+                                "output_name": "report_output",
+                                "uuid": "c7abf2bf-ed4c-433e-a695-9eca61282bb5"
+                            },
+                            {
+                                "label": "output",
+                                "output_name": "output",
+                                "uuid": "083a0e51-7780-4c91-a071-dc0e4641d060"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.2.1+galaxy0",
+                        "errors": null,
+                        "id": 12,
+                        "input_connections": {
+                            "fastq_or_bam|bam_input": {
+                                "id": 7,
+                                "output_name": "snpsbam"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool TB-Profiler Profile",
+                                "name": "fastq_or_bam"
+                            }
+                        ],
+                        "label": null,
+                        "name": "TB-Profiler Profile",
+                        "outputs": [
+                            {
+                                "name": "results_json",
+                                "type": "json"
+                            },
+                            {
+                                "name": "output_vcf",
+                                "type": "vcf"
+                            },
+                            {
+                                "name": "output_txt",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 1132.7778271896836,
+                            "top": 615.3961147101202
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionoutput_vcf": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_vcf"
+                            },
+                            "HideDatasetActionresults_json": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "results_json"
+                            },
+                            "TagDatasetActionoutput_txt": {
+                                "action_arguments": {
+                                    "tags": "drug_resistance_report"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "output_txt"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.2.1+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "4839e590cb26",
+                            "name": "tbprofiler",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"advanced\": {\"options\": \"no\", \"__current_case__\": 0}, \"fastq_or_bam\": {\"input_select\": \"bam\", \"__current_case__\": 3, \"bam_input\": {\"__class__\": \"ConnectedValue\"}}, \"output_format\": \"txt\", \"platform\": \"illumina\", \"spoligotype\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "6.2.1+galaxy0",
+                        "type": "tool",
+                        "uuid": "22d89589-70a3-4e6e-8b95-68604a287052",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "output_txt",
+                                "output_name": "output_txt",
+                                "uuid": "335635b4-a4de-4980-ad02-68f0035daeaa"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
+                        "errors": null,
+                        "id": 16,
+                        "input_connections": {
+                            "infile": {
+                                "id": 11,
+                                "output_name": "output1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Text transformation",
+                        "outputs": [
+                            {
+                                "name": "output",
+                                "type": "input"
+                            }
+                        ],
+                        "position": {
+                            "left": 1379.287563641826,
+                            "top": 248.44083584414724
+                        },
+                        "post_job_actions": {
+                            "TagDatasetActionoutput": {
+                                "action_arguments": {
+                                    "tags": "annotated_vcf"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "fbf99087e067",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"s/GENE_//g\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "9.3+galaxy1",
+                        "type": "tool",
+                        "uuid": "c45f6679-0d38-4663-a783-775b0f522bcc",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Final annotated VCF",
+                                "output_name": "output",
+                                "uuid": "007df8c2-bd13-495f-8904-abf31d4594d0"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+                        "errors": null,
+                        "id": 17,
+                        "input_connections": {
+                            "results_0|software_cond|input": {
+                                "id": 5,
+                                "output_name": "report_json"
+                            },
+                            "results_1|software_cond|input": {
+                                "id": 14,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "MultiQC",
+                        "outputs": [
+                            {
+                                "name": "stats",
+                                "type": "input"
+                            },
+                            {
+                                "name": "html_report",
+                                "type": "html"
+                            }
+                        ],
+                        "position": {
+                            "left": 1604.2880860884582,
+                            "top": 202.3882167631859
+                        },
+                        "post_job_actions": {
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "TagDatasetActionhtml_report": {
+                                "action_arguments": {
+                                    "tags": "qc_report"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "html_report"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "abfd8a6544d7",
+                            "name": "multiqc",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"qualimap\", \"__current_case__\": 20, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.11+galaxy1",
+                        "type": "tool",
+                        "uuid": "6367e2a7-c3b0-4dc4-bbc2-e861e66eaeae",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "347dcece-5ddc-40fb-a5ed-4ff05f2d2d3a"
+                                "label": "html_report",
+                                "output_name": "html_report",
+                                "uuid": "59528235-7525-4ef9-8810-36f1ed0f01f6"
                             }
                         ]
                     },
                     {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/nick/allele_counts/allele_counts_1/1.2",
+                        "annotation": "Compute consensus genome with single nucleotide variants inserted, suitable for use in building a phylogeny",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
                         "errors": null,
-                        "id": 5,
+                        "id": 18,
                         "input_connections": {
-                            "input": {
-                                "id": 4,
-                                "output_name": "output_vcf"
+                            "input_file": {
+                                "id": 13,
+                                "output_name": "output1"
+                            },
+                            "reference_source|fasta_ref": {
+                                "id": 6,
+                                "output_name": "out_file1"
+                            },
+                            "sec_default|mask": {
+                                "id": 15,
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool Variant Annotator",
-                                "name": "input"
+                                "description": "runtime parameter for tool bcftools consensus",
+                                "name": "reference_source"
+                            },
+                            {
+                                "description": "runtime parameter for tool bcftools consensus",
+                                "name": "sec_default"
                             }
                         ],
                         "label": null,
-                        "name": "Variant Annotator",
+                        "name": "bcftools consensus",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "name": "output_file",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 474,
-                            "top": 502
+                            "left": 1601.1886936133394,
+                            "top": 1003.2778990479657
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput": {
+                            "TagDatasetActionoutput_file": {
                                 "action_arguments": {
-                                    "newname": "All variants"
+                                    "tags": "consensus_genome"
                                 },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
+                                "action_type": "TagDatasetAction",
+                                "output_name": "output_file"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/nick/allele_counts/allele_counts_1/1.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
                         "tool_shed_repository": {
-                            "changeset_revision": "411adeff1eec",
-                            "name": "allele_counts",
-                            "owner": "nick",
+                            "changeset_revision": "147de996e34f",
+                            "name": "bcftools_consensus",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"stranded\": \"\\\"true\\\"\", \"covg\": \"\\\"10\\\"\", \"header\": \"\\\"true\\\"\", \"seed\": \"\\\"\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"freq\": \"\\\"0.0\\\"\", \"nofilt\": \"\\\"false\\\"\"}",
-                        "tool_version": "1.2",
+                        "tool_state": "{\"absent\": \"\", \"chain\": false, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"ConnectedValue\"}}, \"rename\": false, \"sec_default\": {\"mask\": {\"__class__\": \"ConnectedValue\"}, \"iupac_codes\": false, \"sample\": null, \"select_haplotype\": null, \"mark_del\": \"\", \"mark_ins\": null, \"mark_snv\": null, \"conditional_mask\": {\"selector\": \"disabled\", \"__current_case__\": 0}}, \"sec_restrict\": {\"include\": null, \"exclude\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.15.1+galaxy3",
                         "type": "tool",
-                        "uuid": "b27aa8b9-adb8-43b4-9a70-53025ae1f9f1",
+                        "uuid": "2b226e0c-8e59-472d-8bcd-6d8d84dfddab",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "ad99c585-39c1-4888-9726-28c30317ec21"
+                                "label": "consensus_genome",
+                                "output_name": "output_file",
+                                "uuid": "c71b135d-35f9-44d0-a20e-f25528e518af"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Filter1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.0+galaxy0",
                         "errors": null,
-                        "id": 6,
+                        "id": 19,
                         "input_connections": {
-                            "input": {
-                                "id": 5,
+                            "input_vcf": {
+                                "id": 16,
                                 "output_name": "output"
+                            },
+                            "tbprofiler_json": {
+                                "id": 12,
+                                "output_name": "results_json"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Filter",
-                                "name": "input"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "Filter",
+                        "name": "TB Variant Report",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "name": "variants_report_html",
+                                "type": "html"
+                            },
+                            {
+                                "name": "variants_report_txt",
+                                "type": "txt"
+                            },
+                            {
+                                "name": "drug_resistance_report_html",
+                                "type": "html"
+                            },
+                            {
+                                "name": "drug_resistance_report_txt",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 765,
-                            "top": 503
+                            "left": 1591.762535768669,
+                            "top": 427.7783435581315
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
+                            "HideDatasetActiondrug_resistance_report_txt": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "drug_resistance_report_txt"
+                            },
+                            "HideDatasetActionvariants_report_txt": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "variants_report_txt"
+                            },
+                            "TagDatasetActiondrug_resistance_report_html": {
                                 "action_arguments": {
-                                    "newname": "Filtered variants"
+                                    "tags": "variant_report"
                                 },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
+                                "action_type": "TagDatasetAction",
+                                "output_name": "drug_resistance_report_html"
+                            },
+                            "TagDatasetActionvariants_report_html": {
+                                "action_arguments": {
+                                    "tags": "variant_report"
+                                },
+                                "action_type": "TagDatasetAction",
+                                "output_name": "variants_report_html"
                             }
                         },
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"1\\\"\", \"cond\": \"\\\"c16 >= 0.01\\\"\", \"__page__\": null}",
-                        "tool_version": "1.1.0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.0+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "42818629ec4c",
+                            "name": "tbvcfreport",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv\": {\"database_uri\": \"neodb.sanbi.ac.za\"}, \"filter_udi\": true, \"input_vcf\": {\"__class__\": \"ConnectedValue\"}, \"tbprofiler_json\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0+galaxy0",
                         "type": "tool",
-                        "uuid": "3ada37c0-11f6-4d2c-bf53-cf1e228ee91e",
+                        "uuid": "183d84e7-91ea-4e8f-950b-f65629b60b1b",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "out_file1",
-                                "uuid": "dcdddac9-bd96-4f27-b585-bd3167fef38d"
+                                "label": "drug_resistance_report_html",
+                                "output_name": "drug_resistance_report_html",
+                                "uuid": "959528d2-f8f2-4440-99cf-44fddd6c5069"
+                            },
+                            {
+                                "label": "variants_report_html",
+                                "output_name": "variants_report_html",
+                                "uuid": "4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0"
                             }
                         ]
                     }
                 ],
-                "parent_id": "variant-analysis/dunovo",
-                "path": "topics/variant-analysis/tutorials/dunovo/workflows/variant-calling.ga",
+                "parent_id": "variant-analysis/tb-variant-analysis",
+                "path": "topics/variant-analysis/tutorials/tb-variant-analysis/workflows/tb-variant-analysis.ga",
                 "tags": [
-                    "variant-analysis"
+                    "pathogen",
+                    "tuberculosis"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "Du Novo GTN Tutorial - Variant Calling",
+                "tests": true,
+                "title": "TB Variant Analysis v1.0",
                 "topic_id": "variant-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-dunovo/versions/variant-calling",
-                "tutorial_id": "dunovo",
-                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/dunovo/workflows/variant-calling.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/dunovo/workflows/variant-calling.html",
-                "version": 3,
-                "wfid": "variant-analysis-dunovo",
-                "wfname": "variant-calling",
-                "workflow": "variant-calling.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-tb-variant-analysis/versions/tb-variant-analysis",
+                "tutorial_id": "tb-variant-analysis",
+                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/tb-variant-analysis/workflows/tb-variant-analysis.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/tb-variant-analysis/workflows/tb-variant-analysis.html",
+                "version": 7,
+                "wfid": "variant-analysis-tb-variant-analysis",
+                "wfname": "tb-variant-analysis",
+                "workflow": "tb-variant-analysis.ga",
                 "workflow_tools": [
-                    "Filter1",
-                    "toolshed.g2.bx.psu.edu/repos/blankenberg/naive_variant_caller/naive_variant_caller/0.0.4",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.1.0.46-0",
-                    "toolshed.g2.bx.psu.edu/repos/nick/allele_counts/allele_counts_1/1.2"
+                    "__FLATTEN__",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: seqret84/5.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/mosdepth/mosdepth/0.3.8+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.4.0+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.2.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.0+galaxy0"
                 ],
-                "workflowhub_id": "1089"
+                "workflowhub_id": "1069"
             }
         ],
-        "zenodo_link": ""
+        "zenodo_link": "https://doi.org/10.5281/zenodo.3496437"
     },
     {
         "admin_install": {
@@ -283746,77 +291828,136 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "regex_find_replace",
-                    "owner": "galaxyp",
-                    "revisions": "ae8c4b2488e7",
-                    "tool_panel_section_label": "Text Manipulation",
+                    "name": "bwa",
+                    "owner": "devteam",
+                    "revisions": "3fe632431b68",
+                    "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bcftools_merge",
+                    "name": "picard",
+                    "owner": "devteam",
+                    "revisions": "a1f0b3f4b781",
+                    "tool_panel_section_label": "Picard",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "samtools_stats",
+                    "owner": "devteam",
+                    "revisions": "145f6d74ff5e",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastp",
                     "owner": "iuc",
-                    "revisions": "86296490704e",
-                    "tool_panel_section_label": "Variant Calling",
+                    "revisions": "dbf9c561ef29",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bcftools_norm",
+                    "name": "lofreq_call",
                     "owner": "iuc",
-                    "revisions": "da6fc9f4a367",
+                    "revisions": "65432c3abf6c",
                     "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ega_download_client",
+                    "name": "lofreq_indelqual",
                     "owner": "iuc",
-                    "revisions": "7d87a9d58aa1",
-                    "tool_panel_section_label": "Get Data",
+                    "revisions": "426d707dfc47",
+                    "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "gemini_inheritance",
+                    "name": "lofreq_viterbi",
                     "owner": "iuc",
-                    "revisions": "2c68e29c3527",
-                    "tool_panel_section_label": "Gemini",
+                    "revisions": "aa35ee7f3ab2",
+                    "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "gemini_load",
+                    "name": "multiqc",
                     "owner": "iuc",
-                    "revisions": "2270a8b83c12",
-                    "tool_panel_section_label": "Gemini",
+                    "revisions": "bf675f34b056",
+                    "tool_panel_section_label": "Quality Control",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "geneiobio",
+                    "name": "snpeff_sars_cov_2",
                     "owner": "iuc",
-                    "revisions": "c0af7b196a89",
-                    "tool_panel_section_label": "Graph/Display Data",
+                    "revisions": "2a3a00c1fa0a",
+                    "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "snpeff",
+                    "name": "snpsift",
                     "owner": "iuc",
-                    "revisions": "5c7b70713fb5",
+                    "revisions": "5fab4f81391d",
                     "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sra_tools",
+                    "owner": "iuc",
+                    "revisions": "494b2ec08162",
+                    "tool_panel_section_label": "Get Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "sra_tools",
+                    "owner": "iuc",
+                    "revisions": "4df8de2d0e48",
+                    "tool_panel_section_label": "Get Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: ae8c4b2488e7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_merge\n  owner: iuc\n  revisions: 86296490704e\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_norm\n  owner: iuc\n  revisions: da6fc9f4a367\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ega_download_client\n  owner: iuc\n  revisions: 7d87a9d58aa1\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_inheritance\n  owner: iuc\n  revisions: 2c68e29c3527\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_load\n  owner: iuc\n  revisions: 2270a8b83c12\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: geneiobio\n  owner: iuc\n  revisions: c0af7b196a89\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n  owner: iuc\n  revisions: 5c7b70713fb5\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/trio-analysis/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: 3fe632431b68\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: a1f0b3f4b781\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 145f6d74ff5e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: dbf9c561ef29\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lofreq_call\n  owner: iuc\n  revisions: 65432c3abf6c\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lofreq_indelqual\n  owner: iuc\n  revisions: 426d707dfc47\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lofreq_viterbi\n  owner: iuc\n  revisions: aa35ee7f3ab2\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: bf675f34b056\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff_sars_cov_2\n  owner: iuc\n  revisions: 2a3a00c1fa0a\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpsift\n  owner: iuc\n  revisions: 5fab4f81391d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: 494b2ec08162\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: 4df8de2d0e48\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "mvdbeek",
+                "tnabtaf",
+                "blankenberg",
+                "nekrut"
+            ],
+            "editing": [
+                "wm75"
+            ]
+        },
         "contributors": [
             {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "nl",
-                "email": "j.ouwerkerk.1@erasmusmc.nl",
-                "id": "JasperO98",
-                "joined": "2022-04",
-                "name": "Jasper Ouwerkerk",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/JasperO98/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/JasperO98.json"
+                "id": "mvdbeek",
+                "joined": "2018-06",
+                "name": "Marius van den Beek",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
+            },
+            {
+                "id": "tnabtaf",
+                "joined": "2017-09",
+                "name": "Dave Clements",
+                "orcid": "0000-0002-9970-6657",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
+            },
+            {
+                "id": "blankenberg",
+                "joined": "2018-07",
+                "name": "Daniel Blankenberg",
+                "orcid": "0000-0002-6833-9049",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankenberg/",
+                "twitter": "dblankenberg",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankenberg.json"
+            },
+            {
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
+                "joined": "2017-09",
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
             },
             {
                 "affiliations": [
@@ -283834,82 +291975,36 @@
                 "orcid": "0000-0002-9464-6640",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "by-covid",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "elixir-converge"
-                ],
-                "contact_for_training": false,
-                "elixir_node": "nl",
-                "former_affiliations": [
-                    "deNBI",
-                    "avans-atgm",
-                    "uni-freiburg"
-                ],
-                "id": "hexylena",
-                "joined": "2017-09",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.91,
-                    "lon": 4.46
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "hexylena:matrix.org",
-                "name": "Helena Rasche",
-                "orcid": "0000-0001-9760-8992",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
-            },
-            {
-                "affiliations": [
-                    "CINECA-Project",
-                    "gallantries",
-                    "erasmusmc",
-                    "elixir-europe",
-                    "uni-freiburg"
-                ],
-                "bio": "Researcher at Erasmus Medical Center",
-                "bluesky": "shiltemann.bsky.social",
-                "contact_for_training": true,
-                "elixir_node": "nl",
-                "email": "saskia.hiltemann@gmail.com",
-                "fediverse": "https://mstdn.science/@shiltemann",
-                "fediverse_flavor": "mastodon",
-                "id": "shiltemann",
-                "joined": "2017-09",
-                "linkedin": "shiltemann",
-                "location": {
-                    "country": "NL",
-                    "lat": 51.912,
-                    "lon": 4.462
-                },
-                "maintainer_contact": "gitter",
-                "matrix": "shiltemann:matrix.org",
-                "name": "Saskia Hiltemann",
-                "orcid": "0000-0003-3803-468X",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             }
         ],
-        "dir": "topics/variant-analysis/tutorials/trio-analysis",
+        "dir": "topics/variant-analysis/tutorials/sars-cov-2",
         "edam_operation": [
-            "Sequence analysis",
-            "Genetic variation analysis"
+            "Data handling",
+            "Sequence alignment",
+            "Read mapping",
+            "Sequencing quality control",
+            "Sequence contamination filtering",
+            "Generation",
+            "Validation",
+            "SNP detection",
+            "Formatting",
+            "Genome indexing"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "variant-analysis/trio-analysis",
+        "id": "variant-analysis/sars-cov-2",
         "inexact_supported_servers": [
+            "MISSISSIPPI",
+            "UseGalaxy.be",
             "UseGalaxy.cz",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
             "UseGalaxy.org.au"
         ],
         "js_requirements": {
@@ -283917,71 +292012,99 @@
             "mermaid": false
         },
         "key_points": [
-            "Downloading whole datasets with HTSGET is safe and easy with Galaxy.",
-            "Regex is a usefull tool for pre-processing VCF files.",
-            "Variant annotations allows us to strictly filter VCFs to find the causative variant."
+            "Sequence data in the SRA can be directly imported into Galaxy",
+            "Collections enable efficient/parallel processing of sequence data from whole batches of samples",
+            "Genomic mutations in SARS-CoV-2 viral isolates can be identified through a straightforward pipeline involving sequenced reads preprocessing, mapping to the SARS-CoV-2 reference genome, postprocessing of mapping results, and variant calling"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2024-06-14",
         "objectives": [
-            "Requesting DAC access and importing data from the EGA.",
-            "Pre-process VCFs using regular expressions.",
-            "Use annotations and phenotype information to find the causative variant(s)."
+            "Understand how Galaxy and the Sequence Read Archive interact",
+            "Be able to go from Galaxy to the Short Reach Archive, query SRA, use the SRA Run Selector to send selected metadata to Galaxy, and then import sequence data from SRA into Galaxy",
+            "Understand how collections enable processing of sequencing data in batches",
+            "Understand the analysis steps required to identify and annotate genomic mutations from sequencing data of SARS-CoV-2 samples"
         ],
-        "pageviews": 2739,
-        "pub_date": "2022-05-19",
+        "pageviews": 18702,
+        "pub_date": "2020-06-24",
         "questions": [
-            "How do you import data from the EGA?",
-            "How to download files with HTSGET in Galaxy?",
-            "How do you pre-process VCFs?",
-            "How do you identify causative variants?"
+            "How can you download public sequencing data deposited in the NCBI Sequence Read Archive (SRA) into a Galaxy history for analysis?",
+            "How can you process a batch of sequencing data from several samples efficiently/in parallel with Galaxy?",
+            "Starting from raw sequenced reads of whole-genome sequenced samples of SARS-CoV-2, how can you identify mutations in the genomes of these samples?"
         ],
         "recordings": [
             {
                 "captioners": [
-                    "JasperO98"
+                    "nekrut"
                 ],
-                "date": "2023-05-12",
-                "length": "40M",
+                "date": "2021-02-15",
+                "galaxy_version": "21.01",
+                "length": "15M",
                 "speakers": [
-                    "JasperO98"
+                    "nekrut"
                 ],
-                "youtube_id": "3OWXWOkJRqU"
+                "youtube_id": "9mIL0tIfZ_o"
             }
         ],
-        "short_id": "T00320",
+        "short_id": "T00315",
         "short_tools": [
-            "gemini_inheritance",
-            "gemini_load",
-            "bcftools_merge",
-            "bcftools_norm",
-            "tp_grep_tool",
-            "pyega3",
-            "CONVERTER_uncompressed_to_gz",
+            "bwa_mem",
+            "samtools_stats",
+            "picard_MarkDuplicates",
+            "fastp",
             "Filter1",
-            "regexColumn1",
-            "CONVERTER_gz_to_uncompressed",
-            "snpEff",
-            "gene_iobio_display_generation_iframe"
+            "lofreq_viterbi",
+            "snpeff_sars_cov_2",
+            "multiqc",
+            "lofreq_indelqual",
+            "Grep1",
+            "fasterq_dump",
+            "lofreq_call",
+            "tp_cut_tool",
+            "snpSift_extractFields"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "human-genetics-cancer",
+        "subtopic": "one-health",
         "supported_servers": {
             "exact": [
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 }
             ],
             "inexact": [
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
@@ -283991,23 +292114,28 @@
         },
         "symlink": null,
         "tags": [
-            "cyoa"
+            "covid19",
+            "virology",
+            "one-health"
         ],
-        "time_estimation": "2H",
-        "title": "Trio Analysis using Synthetic Datasets from RD-Connect GPAP",
+        "time_estimation": "1H",
+        "title": "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis",
         "tools": [
-            "CONVERTER_gz_to_uncompressed",
-            "CONVERTER_uncompressed_to_gz",
             "Filter1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/geneiobio/gene_iobio_display_generation_iframe/4.7.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1"
+            "Grep1",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.3+galaxy0"
         ],
         "topic_name": "variant-analysis",
         "topic_name_human": "Variant Analysis",
@@ -284017,631 +292145,358 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "trio-analysis",
+        "tutorial_name": "sars-cov-2",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/trio-analysis/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/sars-cov-2/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/trio-analysis/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/trio-analysis/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2/tutorial.json"
         },
-        "version": 12,
+        "version": 16,
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 244,
-        "visitors": 1385,
+        "visit_duration": 174,
+        "visitors": 12312,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0003-2556-2125",
-                        "name": "Jasper Ouwerkerk"
-                    }
-                ],
-                "description": "Trio Analysis using Synthetic Datasets from RD-Connect GPAP",
+                "creators": [],
+                "description": "Analysis of variation within individual COVID-19 samples (Paired End Illumina). Does not use paured",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"EGA Download Client\"]\n  k85672f3a155649b6be092e6c81721fb3[color=lightseagreen,label=\"Output\\nEGA Download Client: authorized datasets\"]\n  0 -> k85672f3a155649b6be092e6c81721fb3\n  1[label=\"EGA Download Client\"]\n  kacd2bcf04b9d47439034716e73d4824f[color=lightseagreen,label=\"Output\\nList of files in EGAD00001008392\"]\n  1 -> kacd2bcf04b9d47439034716e73d4824f\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\npedigree\"]\n  3[label=\"Search in textfiles\"]\n  1 -> 3 [label=\"dataset_file_list\"]\n  k6d5d135ea37349389374019a09f45a51[color=lightseagreen,label=\"Output\\nList of Case 5 VCFs\"]\n  3 -> k6d5d135ea37349389374019a09f45a51\n  4[label=\"EGA Download Client\"]\n  3 -> 4 [label=\"output\"]\n  kbdce7169390b4adb93055550d5d70a73[color=lightseagreen,label=\"Output\\nCase 5 VCFs.gz\"]\n  4 -> kbdce7169390b4adb93055550d5d70a73\n  5[label=\"Convert compressed file to uncompressed.\"]\n  4 -> 5 [label=\"downloaded_file_collection\"]\n  k82b71cdcd8134c778ff3fa59e1725709[color=lightseagreen,label=\"Output\\nCase 5 VCFs\"]\n  5 -> k82b71cdcd8134c778ff3fa59e1725709\n  6[label=\"Column Regex Find And Replace\"]\n  5 -> 6 [label=\"output1\"]\n  k5e1ff158cf8a4dc89c22b987a9f5ac27[color=lightseagreen,label=\"Output\\nCase 5 VCFs (Fixed Header and Chr)\"]\n  6 -> k5e1ff158cf8a4dc89c22b987a9f5ac27\n  7[label=\"bcftools norm\"]\n  6 -> 7 [label=\"out_file1\"]\n  k96b34c8dfa9248cbb01fc05364deba5d[color=lightseagreen,label=\"Output\\nCase 5 Normalized VCFs\"]\n  7 -> k96b34c8dfa9248cbb01fc05364deba5d\n  8[label=\"Filter\"]\n  7 -> 8 [label=\"output_file\"]\n  ka8539eb98bc3473ba27f201c3acf5539[color=lightseagreen,label=\"Output\\nCase 5 Normalized VCFs (Removed <NON_REF>)\"]\n  8 -> ka8539eb98bc3473ba27f201c3acf5539\n  9[label=\"bcftools merge\"]\n  8 -> 9 [label=\"out_file1\"]\n  kb5c479b2e58a4fe2b1cffc64476c8192[color=lightseagreen,label=\"Output\\nCase 5 Merged VCF\"]\n  9 -> kb5c479b2e58a4fe2b1cffc64476c8192\n  10[label=\"SnpEff eff:\"]\n  9 -> 10 [label=\"output_file\"]\n  kcd7b49414f4c46318ad53411e60fbbd9[color=lightseagreen,label=\"Output\\nCase 5 SnpEff Annotated vcf\"]\n  10 -> kcd7b49414f4c46318ad53411e60fbbd9\n  11[label=\"Convert uncompressed file to compressed\"]\n  10 -> 11 [label=\"snpeff_output\"]\n  k6e5e1084b5e14daf8f3bbd3868a52a25[color=lightseagreen,label=\"Output\\nSnpEff Annotated vcf_bgzip\"]\n  11 -> k6e5e1084b5e14daf8f3bbd3868a52a25\n  12[label=\"gene.iobio visualisation\"]\n  11 -> 12 [label=\"output1\"]\n  11 -> 12 [label=\"output1\"]\n  11 -> 12 [label=\"output1\"]\n  k0b30f4e0732844798a56bbf828fcfdba[color=lightseagreen,label=\"Output\\nCase 5 gene.iobio results\"]\n  12 -> k0b30f4e0732844798a56bbf828fcfdba\n  13[label=\"Case 5 GEMINI Database\"]\n  11 -> 13 [label=\"output1\"]\n  2 -> 13 [label=\"output\"]\n  k8a1964d9607c4dd3a2dc0f9a68dbb681[color=lightseagreen,label=\"Output\\nGEMINI Database\"]\n  13 -> k8a1964d9607c4dd3a2dc0f9a68dbb681\n  14[label=\"Case 5 GEMINI Inheritance pattern\"]\n  13 -> 14 [label=\"outfile\"]\n  k960ef978089c429281b5731965c72a0d[color=lightseagreen,label=\"Output\\nCase 5 GEMINI results\"]\n  14 -> k960ef978089c429281b5731965c72a0d\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nNC_045512.2 fasta file\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSRA Manifest\"]\n  2[label=\"Faster Download and Extract Reads in FASTQ\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"fastp\"]\n  2 -> 3 [label=\"list_paired\"]\n  4[label=\"Map with BWA-MEM\"]\n  3 -> 4 [label=\"output_paired_coll\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"MarkDuplicates\"]\n  4 -> 5 [label=\"bam_output\"]\n  6[label=\"Realign reads\"]\n  5 -> 6 [label=\"outFile\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Samtools stats\"]\n  5 -> 7 [label=\"outFile\"]\n  8[label=\"Insert indel qualities\"]\n  6 -> 8 [label=\"realigned\"]\n  0 -> 8 [label=\"output\"]\n  k2ca7c89b999f41dc8037e54e25959a7e[color=lightseagreen,label=\"Output\\nRealigned Alignments with Indel Qualities\"]\n  8 -> k2ca7c89b999f41dc8037e54e25959a7e\n  9[label=\"Call variants\"]\n  8 -> 9 [label=\"output\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"SnpEff eff:\"]\n  9 -> 10 [label=\"variants\"]\n  11[label=\"SnpSift Extract Fields\"]\n  10 -> 11 [label=\"snpeff_output\"]\n  k06259137eaa5404a923c70ee5f1d89d4[color=lightseagreen,label=\"Output\\nSnpSift tabular output\"]\n  11 -> k06259137eaa5404a923c70ee5f1d89d4\n  12[label=\"MultiQC\"]\n  3 -> 12 [label=\"report_json\"]\n  7 -> 12 [label=\"output\"]\n  5 -> 12 [label=\"metrics_file\"]\n  10 -> 12 [label=\"csvFile\"]\n  k758ffde57ddd482a88b21504f8335488[color=lightseagreen,label=\"Output\\nMultiQC Report PE\"]\n  12 -> k758ffde57ddd482a88b21504f8335488\n}",
                 "history": [
                     {
-                        "hash": "9623387f047fbfa77afe213505d4328e84075023",
-                        "message": "Add gene.iobio",
-                        "num": 22,
-                        "short_hash": "9623387f0",
-                        "unix": "1689082264"
-                    },
-                    {
-                        "hash": "c7df034841bfa97e3bae35a0fc124ce37d77ab9a",
-                        "message": "Add gene.iobio to workflow",
-                        "num": 21,
-                        "short_hash": "c7df03484",
-                        "unix": "1688999139"
-                    },
-                    {
-                        "hash": "a133ddbaf3b94a0da4f645047d9e48562bbff274",
-                        "message": "Add EGA download client authorized dataset",
-                        "num": 20,
-                        "short_hash": "a133ddbaf",
-                        "unix": "1684243281"
-                    },
-                    {
-                        "hash": "89798a1513ae26d2802470e9be2ce286a36e4ecf",
-                        "message": "Update PyEGA version in main_workflow.ga",
-                        "num": 19,
-                        "short_hash": "89798a151",
-                        "unix": "1684243121"
-                    },
-                    {
-                        "hash": "890e3ed491c20efb1e20c846851b29bf8af689e0",
-                        "message": "add orcid",
-                        "num": 18,
-                        "short_hash": "890e3ed49",
-                        "unix": "1679655504"
-                    },
-                    {
-                        "hash": "d20983843449c103e35d458f6988096ad6c1e4e1",
-                        "message": "fix reator and workflow_output labels",
-                        "num": 17,
-                        "short_hash": "d20983843",
-                        "unix": "1679655099"
-                    },
-                    {
-                        "hash": "588e52155ae2c1e3cf2a5fb1c53a9cb9dd552880",
-                        "message": "now really add license",
-                        "num": 16,
-                        "short_hash": "588e52155",
-                        "unix": "1679415213"
-                    },
-                    {
-                        "hash": "cdfd52652e3656e2f51226e181f5fd24dd00f115",
-                        "message": "properly add license",
-                        "num": 15,
-                        "short_hash": "cdfd52652",
-                        "unix": "1679414902"
-                    },
-                    {
-                        "hash": "49bda25d3f12d6589c3ab4b831d99a65ddd888ec",
-                        "message": "rename workflow",
-                        "num": 14,
-                        "short_hash": "49bda25d3",
-                        "unix": "1679414277"
-                    },
-                    {
-                        "hash": "79e4f95acbef417531b4d67eb2e860236a86eeb8",
-                        "message": "add test",
-                        "num": 13,
-                        "short_hash": "79e4f95ac",
-                        "unix": "1679414214"
-                    },
-                    {
-                        "hash": "9ba85fb0a7f7257bb6c27a9c8cc549552ba77f05",
-                        "message": "update PyEGA version & add creator/license",
-                        "num": 12,
-                        "short_hash": "9ba85fb0a",
-                        "unix": "1679413554"
-                    },
-                    {
-                        "hash": "b79cc70eadad03fe5c5b031e79e72e757f3a48a2",
-                        "message": "Update workflow with nice labels",
-                        "num": 11,
-                        "short_hash": "b79cc70ea",
-                        "unix": "1677684691"
-                    },
-                    {
-                        "hash": "4ed74364ae051c7deab6b239091eae03c1355177",
-                        "message": "Update workflow (<NON_REF> skip header)",
-                        "num": 10,
-                        "short_hash": "4ed74364a",
-                        "unix": "1652186595"
-                    },
-                    {
-                        "hash": "2726695af3b5bfe98b1a2906c1d5a330758c1fb2",
-                        "message": "add annotation and tag to workflow",
-                        "num": 9,
-                        "short_hash": "2726695af",
-                        "unix": "1651586250"
-                    },
-                    {
-                        "hash": "0816782f5e10f9b06a6fd96dccc51acca59bd54f",
-                        "message": "Update prefix pattern",
-                        "num": 8,
-                        "short_hash": "0816782f5",
-                        "unix": "1651568447"
-                    },
-                    {
-                        "hash": "4cb441ff692dad48e6e2b2e1ea5bd6883e905c69",
-                        "message": "Move decompress step",
+                        "hash": "18338ab9a1ef29b46dc8f2e8a7f7a4b055f16e3d",
+                        "message": "Use correct fasterqdump version",
                         "num": 7,
-                        "short_hash": "4cb441ff6",
-                        "unix": "1651564709"
+                        "short_hash": "18338ab9a",
+                        "unix": "1593005231"
                     },
                     {
-                        "hash": "e61e6713377e9e1a815ea31629471c7ec0d4cf2e",
-                        "message": "Replace AWK with Filter tool to remove <NON_REF> sites",
+                        "hash": "979d6cd2174d0f2ce10ad195d9d3cc4b29a1623a",
+                        "message": "Reformat workflow, bump lofreq to 2.1.5",
                         "num": 6,
-                        "short_hash": "e61e67133",
-                        "unix": "1651497677"
+                        "short_hash": "979d6cd21",
+                        "unix": "1593004337"
                     },
                     {
-                        "hash": "72a287e5e831cf4fe072285dd2109bccdd32aaff",
-                        "message": "update tutorial",
+                        "hash": "ced05a792b3048548fd31a9d0bde9a1bf634481f",
+                        "message": "Fix workflow connections",
                         "num": 5,
-                        "short_hash": "72a287e5e",
-                        "unix": "1651235598"
+                        "short_hash": "ced05a792",
+                        "unix": "1592944690"
                     },
                     {
-                        "hash": "0e98aba15d56063a4505c95578f36506c61489cf",
-                        "message": "change workflow",
+                        "hash": "1c38a3ed277eb7434c02927dce89f72e8a9c0c78",
+                        "message": "Use newer, simpler output",
                         "num": 4,
-                        "short_hash": "0e98aba15",
-                        "unix": "1650981994"
+                        "short_hash": "1c38a3ed2",
+                        "unix": "1592943019"
                     },
                     {
-                        "hash": "1eca39b5430f412c1e2047acfef461a4e6062377",
-                        "message": "Spelling check + testing workflow",
+                        "hash": "a58450027f50bbdb5e91ee3529c7deef7ee1cf4e",
+                        "message": "add topic tag to workflow",
                         "num": 3,
-                        "short_hash": "1eca39b54",
-                        "unix": "1650462724"
+                        "short_hash": "a58450027",
+                        "unix": "1592838416"
                     },
                     {
-                        "hash": "129023b5fcf34c1f2b13583b346ff5f684428ef3",
-                        "message": "initial tutorial",
+                        "hash": "e8eea07056121bf6ee287bec31c64cd69d2e6dcb",
+                        "message": "reformat workflow",
                         "num": 2,
-                        "short_hash": "129023b5f",
-                        "unix": "1650381596"
+                        "short_hash": "e8eea0705",
+                        "unix": "1592835884"
                     },
                     {
-                        "hash": "4b2ff311ba4c0a03301e4e796d804cce013a1678",
-                        "message": "initial commit",
+                        "hash": "a06c40264814dc80888f2a9ce28d4f06c2c3e687",
+                        "message": "Skeleton from PE sars-cov-2 workflow",
                         "num": 1,
-                        "short_hash": "4b2ff311b",
-                        "unix": "1649341437"
+                        "short_hash": "a06c40264",
+                        "unix": "1592389814"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "",
+                        "annotation": "Contains SARS-CoV-2 reference sequence",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "pedigree"
+                                "description": "Contains SARS-CoV-2 reference sequence",
+                                "name": "NC_045512.2 fasta file"
                             }
                         ],
-                        "label": "pedigree",
+                        "label": "NC_045512.2 fasta file",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 563.1557760665268,
-                            "top": 635.975477057033
+                            "left": 199.95736694335938,
+                            "top": 317.85511016845703
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
+                        "tool_state": "{\"optional\": false}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "e0eb82fb-bfa7-43fe-b5c7-690fc2e9ed95",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"EGA Download Client\"];\n  85672f3a-1556-49b6-be09-2e6c81721fb3[\"Output\\nEGA Download Client: authorized datasets\"];\n  0 --> 85672f3a-1556-49b6-be09-2e6c81721fb3;\n  style 85672f3a-1556-49b6-be09-2e6c81721fb3 stroke:#2c3143,stroke-width:4px;\n  1[\"EGA Download Client\"];\n  acd2bcf0-4b9d-4743-9034-716e73d4824f[\"Output\\nList of files in EGAD00001008392\"];\n  1 --> acd2bcf0-4b9d-4743-9034-716e73d4824f;\n  style acd2bcf0-4b9d-4743-9034-716e73d4824f stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\npedigree\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Search in textfiles\"];\n  1 -->|dataset_file_list| 3;\n  6d5d135e-a373-4938-9374-019a09f45a51[\"Output\\nList of Case 5 VCFs\"];\n  3 --> 6d5d135e-a373-4938-9374-019a09f45a51;\n  style 6d5d135e-a373-4938-9374-019a09f45a51 stroke:#2c3143,stroke-width:4px;\n  4[\"EGA Download Client\"];\n  3 -->|output| 4;\n  bdce7169-390b-4adb-9305-5550d5d70a73[\"Output\\nCase 5 VCFs.gz\"];\n  4 --> bdce7169-390b-4adb-9305-5550d5d70a73;\n  style bdce7169-390b-4adb-9305-5550d5d70a73 stroke:#2c3143,stroke-width:4px;\n  5[\"Convert compressed file to uncompressed.\"];\n  4 -->|downloaded_file_collection| 5;\n  82b71cdc-d813-4c77-8ff3-fa59e1725709[\"Output\\nCase 5 VCFs\"];\n  5 --> 82b71cdc-d813-4c77-8ff3-fa59e1725709;\n  style 82b71cdc-d813-4c77-8ff3-fa59e1725709 stroke:#2c3143,stroke-width:4px;\n  6[\"Column Regex Find And Replace\"];\n  5 -->|output1| 6;\n  5e1ff158-cf8a-4dc8-9c22-b987a9f5ac27[\"Output\\nCase 5 VCFs (Fixed Header and Chr)\"];\n  6 --> 5e1ff158-cf8a-4dc8-9c22-b987a9f5ac27;\n  style 5e1ff158-cf8a-4dc8-9c22-b987a9f5ac27 stroke:#2c3143,stroke-width:4px;\n  7[\"bcftools norm\"];\n  6 -->|out_file1| 7;\n  96b34c8d-fa92-48cb-b01f-c05364deba5d[\"Output\\nCase 5 Normalized VCFs\"];\n  7 --> 96b34c8d-fa92-48cb-b01f-c05364deba5d;\n  style 96b34c8d-fa92-48cb-b01f-c05364deba5d stroke:#2c3143,stroke-width:4px;\n  8[\"Filter\"];\n  7 -->|output_file| 8;\n  a8539eb9-8bc3-473b-a27f-201c3acf5539[\"Output\\nCase 5 Normalized VCFs (Removed <NON_REF>)\"];\n  8 --> a8539eb9-8bc3-473b-a27f-201c3acf5539;\n  style a8539eb9-8bc3-473b-a27f-201c3acf5539 stroke:#2c3143,stroke-width:4px;\n  9[\"bcftools merge\"];\n  8 -->|out_file1| 9;\n  b5c479b2-e58a-4fe2-b1cf-fc64476c8192[\"Output\\nCase 5 Merged VCF\"];\n  9 --> b5c479b2-e58a-4fe2-b1cf-fc64476c8192;\n  style b5c479b2-e58a-4fe2-b1cf-fc64476c8192 stroke:#2c3143,stroke-width:4px;\n  10[\"SnpEff eff:\"];\n  9 -->|output_file| 10;\n  cd7b4941-4f4c-4631-8ad5-3411e60fbbd9[\"Output\\nCase 5 SnpEff Annotated vcf\"];\n  10 --> cd7b4941-4f4c-4631-8ad5-3411e60fbbd9;\n  style cd7b4941-4f4c-4631-8ad5-3411e60fbbd9 stroke:#2c3143,stroke-width:4px;\n  11[\"Convert uncompressed file to compressed\"];\n  10 -->|snpeff_output| 11;\n  6e5e1084-b5e1-4daf-8f3b-bd3868a52a25[\"Output\\nSnpEff Annotated vcf_bgzip\"];\n  11 --> 6e5e1084-b5e1-4daf-8f3b-bd3868a52a25;\n  style 6e5e1084-b5e1-4daf-8f3b-bd3868a52a25 stroke:#2c3143,stroke-width:4px;\n  12[\"gene.iobio visualisation\"];\n  11 -->|output1| 12;\n  11 -->|output1| 12;\n  11 -->|output1| 12;\n  0b30f4e0-7328-4479-8a56-bbf828fcfdba[\"Output\\nCase 5 gene.iobio results\"];\n  12 --> 0b30f4e0-7328-4479-8a56-bbf828fcfdba;\n  style 0b30f4e0-7328-4479-8a56-bbf828fcfdba stroke:#2c3143,stroke-width:4px;\n  13[\"Case 5 GEMINI Database\"];\n  11 -->|output1| 13;\n  2 -->|output| 13;\n  8a1964d9-607c-4dd3-a2dc-0f9a68dbb681[\"Output\\nGEMINI Database\"];\n  13 --> 8a1964d9-607c-4dd3-a2dc-0f9a68dbb681;\n  style 8a1964d9-607c-4dd3-a2dc-0f9a68dbb681 stroke:#2c3143,stroke-width:4px;\n  14[\"Case 5 GEMINI Inheritance pattern\"];\n  13 -->|outfile| 14;\n  960ef978-089c-4292-81b5-731965c72a0d[\"Output\\nCase 5 GEMINI results\"];\n  14 --> 960ef978-089c-4292-81b5-731965c72a0d;\n  style 960ef978-089c-4292-81b5-731965c72a0d stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "Trio Analysis Tutorial",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0",
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "EGA Download Client",
-                        "outputs": [
-                            {
-                                "name": "authorized_datasets",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 4.293246161777436,
-                            "top": 0
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f9db47f68e5e",
-                            "name": "ega_download_client",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"action\": {\"action_type\": \"list_datasets\", \"__current_case__\": 1}, \"output_log\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.0.2+galaxy0",
-                        "type": "tool",
-                        "uuid": "5f03b99a-3f46-47d8-a5b1-31b6d3ae39ee",
-                        "when": null,
+                        "uuid": "0e91bcb8-fa43-4fc5-87f9-9e65784373e6",
                         "workflow_outputs": [
                             {
-                                "label": "EGA Download Client: authorized datasets",
-                                "output_name": "authorized_datasets",
-                                "uuid": "85672f3a-1556-49b6-be09-2e6c81721fb3"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "1dedf4c3-5fc4-4505-baa0-b13e4416d67d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0",
+                        "content_id": null,
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": null,
-                        "name": "EGA Download Client",
-                        "outputs": [
-                            {
-                                "name": "dataset_file_list",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 4.293246161777436,
-                            "top": 148.56248504578429
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f9db47f68e5e",
-                            "name": "ega_download_client",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"action\": {\"action_type\": \"list_dataset_files\", \"__current_case__\": 0, \"dataset_id\": \"EGAD00001008392\"}, \"output_log\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.0.2+galaxy0",
-                        "type": "tool",
-                        "uuid": "265bf049-ac9f-4a59-bba3-311c6c818121",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "List of files in EGAD00001008392",
-                                "output_name": "dataset_file_list",
-                                "uuid": "acd2bcf0-4b9d-4743-9034-716e73d4824f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {
-                            "infile": {
-                                "id": 1,
-                                "output_name": "dataset_file_list"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Search in textfiles",
-                        "outputs": [
+                        "inputs": [
                             {
-                                "name": "output",
-                                "type": "input"
+                                "description": "",
+                                "name": "SRA Manifest"
                             }
                         ],
+                        "label": "SRA Manifest",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 1.4413503643385859,
-                            "top": 307.6653714034882
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ddf54b12c295",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 199.95736694335938,
+                            "top": 372.3295364379883
                         },
-                        "tool_state": "{\"case_sensitive\": \"\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-E\", \"url_paste\": \"Case5.+17.+vcf.gz$\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
-                        "type": "tool",
-                        "uuid": "d55be511-416e-416b-99c5-da3023124c85",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "3c5adef0-7af6-435e-bb10-966361130b58",
                         "workflow_outputs": [
                             {
-                                "label": "List of Case 5 VCFs",
+                                "label": null,
                                 "output_name": "output",
-                                "uuid": "6d5d135e-a373-4938-9374-019a09f45a51"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0",
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {
-                            "action|id_table": {
-                                "id": 3,
-                                "output_name": "output"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "EGA Download Client",
-                        "outputs": [
-                            {
-                                "name": "downloaded_file_collection",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 1.4348650983573101,
-                            "top": 478.47790000624343
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "f9db47f68e5e",
-                            "name": "ega_download_client",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"action\": {\"action_type\": \"download_files\", \"__current_case__\": 3, \"id_table\": {\"__class__\": \"ConnectedValue\"}, \"id_column\": \"1\", \"range\": {\"reference_name\": \"\", \"start\": null, \"end\": null}}, \"output_log\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.0.2+galaxy0",
-                        "type": "tool",
-                        "uuid": "e9b6ed7b-4275-47a4-99cb-e6779a56ec4e",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Case 5 VCFs.gz",
-                                "output_name": "downloaded_file_collection",
-                                "uuid": "bdce7169-390b-4adb-9305-5550d5d70a73"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "CONVERTER_gz_to_uncompressed",
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {
-                            "input1": {
-                                "id": 4,
-                                "output_name": "downloaded_file_collection"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Convert compressed file to uncompressed.",
-                        "outputs": [
-                            {
-                                "name": "output1",
-                                "type": "auto"
-                            }
-                        ],
-                        "position": {
-                            "left": 0,
-                            "top": 620.6925527804436
-                        },
-                        "post_job_actions": {
-                            "ChangeDatatypeActionoutput1": {
-                                "action_arguments": {
-                                    "newtype": "vcf"
-                                },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "output1"
-                            }
-                        },
-                        "tool_id": "CONVERTER_gz_to_uncompressed",
-                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0",
-                        "type": "tool",
-                        "uuid": "51d1b3e4-6574-4784-b814-01ab3bd097a3",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Case 5 VCFs",
-                                "output_name": "output1",
-                                "uuid": "82b71cdc-d813-4c77-8ff3-fa59e1725709"
+                                "uuid": "fa458185-44d5-4d2d-ad69-20595c8ad337"
                             }
                         ]
-                    },
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nNC_045512.2 fasta file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSRA Manifest\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Faster Download and Extract Reads in FASTQ\"];\n  1 -->|output| 2;\n  3[\"fastp\"];\n  2 -->|list_paired| 3;\n  4[\"Map with BWA-MEM\"];\n  3 -->|output_paired_coll| 4;\n  0 -->|output| 4;\n  5[\"MarkDuplicates\"];\n  4 -->|bam_output| 5;\n  6[\"Realign reads\"];\n  5 -->|outFile| 6;\n  0 -->|output| 6;\n  7[\"Samtools stats\"];\n  5 -->|outFile| 7;\n  8[\"Insert indel qualities\"];\n  6 -->|realigned| 8;\n  0 -->|output| 8;\n  2ca7c89b-999f-41dc-8037-e54e25959a7e[\"Output\\nRealigned Alignments with Indel Qualities\"];\n  8 --> 2ca7c89b-999f-41dc-8037-e54e25959a7e;\n  style 2ca7c89b-999f-41dc-8037-e54e25959a7e stroke:#2c3143,stroke-width:4px;\n  9[\"Call variants\"];\n  8 -->|output| 9;\n  0 -->|output| 9;\n  10[\"SnpEff eff:\"];\n  9 -->|variants| 10;\n  11[\"SnpSift Extract Fields\"];\n  10 -->|snpeff_output| 11;\n  06259137-eaa5-404a-923c-70ee5f1d89d4[\"Output\\nSnpSift tabular output\"];\n  11 --> 06259137-eaa5-404a-923c-70ee5f1d89d4;\n  style 06259137-eaa5-404a-923c-70ee5f1d89d4 stroke:#2c3143,stroke-width:4px;\n  12[\"MultiQC\"];\n  3 -->|report_json| 12;\n  7 -->|output| 12;\n  5 -->|metrics_file| 12;\n  10 -->|csvFile| 12;\n  758ffde5-7ddd-482a-88b2-1504f8335488[\"Output\\nMultiQC Report PE\"];\n  12 --> 758ffde5-7ddd-482a-88b2-1504f8335488;\n  style 758ffde5-7ddd-482a-88b2-1504f8335488 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "Simple COVID-19 - PE Variation",
+                "outputs": [
                     {
-                        "annotation": "Add chr prefix",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
+                        "annotation": "Contains SARS-CoV-2 reference sequence",
+                        "content_id": null,
                         "errors": null,
-                        "id": 6,
-                        "input_connections": {
-                            "input": {
-                                "id": 5,
-                                "output_name": "output1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Column Regex Find And Replace",
-                        "outputs": [
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "input"
+                                "description": "Contains SARS-CoV-2 reference sequence",
+                                "name": "NC_045512.2 fasta file"
                             }
                         ],
+                        "label": "NC_045512.2 fasta file",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 285.74353593563336,
-                            "top": 0.3954410820455898
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ae8c4b2488e7",
-                            "name": "regex_find_replace",
-                            "owner": "galaxyp",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 199.95736694335938,
+                            "top": 317.85511016845703
                         },
-                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \"^([0-9MYX])\", \"replacement\": \"chr\\\\1\"}, {\"__index__\": 1, \"pattern\": \"^(##contig=<.*ID=)([0-9MYX].+)\", \"replacement\": \"\\\\1chr\\\\2\"}], \"field\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.1",
-                        "type": "tool",
-                        "uuid": "4a50616e-4b18-4fa9-9ffa-dfbcc8c32c44",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "0e91bcb8-fa43-4fc5-87f9-9e65784373e6",
                         "workflow_outputs": [
                             {
-                                "label": "Case 5 VCFs (Fixed Header and Chr)",
-                                "output_name": "out_file1",
-                                "uuid": "5e1ff158-cf8a-4dc8-9c22-b987a9f5ac27"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "1dedf4c3-5fc4-4505-baa0-b13e4416d67d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1",
+                        "content_id": null,
                         "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "input_file": {
-                                "id": 6,
-                                "output_name": "out_file1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "bcftools norm",
-                        "outputs": [
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "output_file",
-                                "type": "vcf"
+                                "description": "",
+                                "name": "SRA Manifest"
                             }
                         ],
+                        "label": "SRA Manifest",
+                        "name": "Input dataset",
+                        "outputs": [],
                         "position": {
-                            "left": 269.93026650504567,
-                            "top": 197.0992986309266
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "da6fc9f4a367",
-                            "name": "bcftools_norm",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                            "left": 199.95736694335938,
+                            "top": 372.3295364379883
                         },
-                        "tool_state": "{\"check_ref\": \"w\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"multiallelics\": {\"mode\": \"-\", \"__current_case__\": 1, \"multiallelic_types\": \"both\"}, \"normalize_indels\": true, \"output_type\": \"v\", \"reference_source\": {\"reference_source_selector\": \"cached\", \"__current_case__\": 0, \"fasta_ref\": \"hg19\"}, \"rm_dup\": \"\", \"sec_default\": {\"site_win\": \"1000\"}, \"sec_restrict\": {\"regions\": {\"regions_src\": \"__none__\", \"__current_case__\": 0}, \"targets\": {\"targets_src\": \"__none__\", \"__current_case__\": 0}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.9+galaxy1",
-                        "type": "tool",
-                        "uuid": "5dbde914-89fe-443b-b1f5-28182e971fca",
-                        "when": null,
+                        "tool_id": null,
+                        "tool_state": "{\"optional\": false}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "3c5adef0-7af6-435e-bb10-966361130b58",
                         "workflow_outputs": [
                             {
-                                "label": "Case 5 Normalized VCFs",
-                                "output_name": "output_file",
-                                "uuid": "96b34c8d-fa92-48cb-b01f-c05364deba5d"
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "fa458185-44d5-4d2d-ad69-20595c8ad337"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "Filter1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1",
                         "errors": null,
-                        "id": 8,
+                        "id": 2,
                         "input_connections": {
-                            "input": {
-                                "id": 7,
-                                "output_name": "output_file"
+                            "input|file_list": {
+                                "id": 1,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool Faster Download and Extract Reads in FASTQ",
+                                "name": "input"
+                            }
+                        ],
                         "label": null,
-                        "name": "Filter",
+                        "name": "Faster Download and Extract Reads in FASTQ",
                         "outputs": [
                             {
-                                "name": "out_file1",
+                                "name": "list_paired",
                                 "type": "input"
+                            },
+                            {
+                                "name": "output_collection",
+                                "type": "input"
+                            },
+                            {
+                                "name": "output_collection_other",
+                                "type": "input"
+                            },
+                            {
+                                "name": "log",
+                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 281.1327747391346,
-                            "top": 399.5494962135009
+                            "left": 342.9971618652344,
+                            "top": 317.85511016845703
                         },
-                        "post_job_actions": {},
-                        "tool_id": "Filter1",
-                        "tool_state": "{\"cond\": \"c5!='<NON_REF>'\", \"header_lines\": \"142\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.1.1",
+                        "post_job_actions": {
+                            "HideDatasetActionlog": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "log"
+                            },
+                            "HideDatasetActionoutput_collection": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_collection"
+                            },
+                            "HideDatasetActionoutput_collection_other": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "output_collection_other"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "248f85ff0733",
+                            "name": "sra_tools",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"adv\": {\"minlen\": \"\", \"split\": \"--split-3\", \"skip_technical\": \"true\"}, \"input\": {\"input_select\": \"file_list\", \"__current_case__\": 2, \"file_list\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.10.7+galaxy1",
                         "type": "tool",
-                        "uuid": "da21d9af-cbe0-4cd0-bf70-1c6f16aab26f",
-                        "when": null,
+                        "uuid": "3ce5b504-3641-4ea9-8d24-07f9bebaec23",
                         "workflow_outputs": [
                             {
-                                "label": "Case 5 Normalized VCFs (Removed <NON_REF>)",
-                                "output_name": "out_file1",
-                                "uuid": "a8539eb9-8bc3-473b-a27f-201c3acf5539"
+                                "label": null,
+                                "output_name": "list_paired",
+                                "uuid": "9e5c0368-e97c-4def-9704-1b902fbb2ed7"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
                         "errors": null,
-                        "id": 9,
+                        "id": 8,
                         "input_connections": {
-                            "input_files": {
-                                "id": 8,
-                                "output_name": "out_file1"
+                            "reads": {
+                                "id": 6,
+                                "output_name": "realigned"
+                            },
+                            "strategy|reference_source|ref": {
+                                "id": 0,
+                                "output_name": "output"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool bcftools merge",
-                                "name": "sec_header"
-                            }
-                        ],
+                        "inputs": [],
                         "label": null,
-                        "name": "bcftools merge",
+                        "name": "Insert indel qualities",
                         "outputs": [
                             {
-                                "name": "output_file",
-                                "type": "vcf"
+                                "name": "output",
+                                "type": "bam"
                             }
                         ],
                         "position": {
-                            "left": 287.16415974045077,
-                            "top": 590.7331216507386
+                            "left": 1057.5852355957031,
+                            "top": 317.85511016845703
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10",
+                        "post_job_actions": {
+                            "RenameDatasetActionoutput": {
+                                "action_arguments": {
+                                    "newname": "Realigned Alignments with Indel Qualities"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "86296490704e",
-                            "name": "bcftools_merge",
+                            "changeset_revision": "354b534eeab7",
+                            "name": "lofreq_indelqual",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input_files\": {\"__class__\": \"ConnectedValue\"}, \"output_type\": \"v\", \"sec_header\": {\"use_header\": {\"__class__\": \"RuntimeValue\"}, \"print_header\": false}, \"sec_merge\": {\"force_samples\": false, \"info_rules\": \"\", \"merge\": \"none\"}, \"sec_restrict\": {\"apply_filters\": \"\", \"regions\": {\"regions_src\": \"__none__\", \"__current_case__\": 0}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.10",
+                        "tool_state": "{\"reads\": {\"__class__\": \"ConnectedValue\"}, \"strategy\": {\"selector\": \"dindel\", \"__current_case__\": 1, \"reference_source\": {\"ref_selector\": \"history\", \"__current_case__\": 1, \"ref\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "2.1.5+galaxy0",
                         "type": "tool",
-                        "uuid": "3471d534-2877-4989-b13b-b7bb3aa20efc",
-                        "when": null,
+                        "uuid": "cbc7ee7f-5cfa-4d45-a83e-623efbf66068",
                         "workflow_outputs": [
                             {
-                                "label": "Case 5 Merged VCF",
-                                "output_name": "output_file",
-                                "uuid": "b5c479b2-e58a-4fe2-b1cf-fc64476c8192"
+                                "label": "Realigned Alignments with Indel Qualities",
+                                "output_name": "output",
+                                "uuid": "2ca7c89b-999f-41dc-8037-e54e25959a7e"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
                         "errors": null,
                         "id": 10,
                         "input_connections": {
                             "input": {
                                 "id": 9,
-                                "output_name": "output_file"
+                                "output_name": "variants"
                             }
                         },
                         "inputs": [
@@ -284664,273 +292519,215 @@
                             {
                                 "name": "statsFile",
                                 "type": "html"
+                            },
+                            {
+                                "name": "csvFile",
+                                "type": "csv"
                             }
                         ],
                         "position": {
-                            "left": 556.8129698338548,
-                            "top": 8.0719203679202
+                            "left": 1343.0823059082031,
+                            "top": 317.85511016845703
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1",
+                        "post_job_actions": {
+                            "HideDatasetActioncsvFile": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "csvFile"
+                            },
+                            "HideDatasetActionstatsFile": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "statsFile"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
                         "tool_shed_repository": {
-                            "changeset_revision": "cfcf33df7fc0",
-                            "name": "snpeff",
+                            "changeset_revision": "2a3a00c1fa0a",
+                            "name": "snpeff_sars_cov_2",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"annotations\": null, \"chr\": \"\", \"csvStats\": false, \"filter\": {\"specificEffects\": \"no\", \"__current_case__\": 0}, \"filterOut\": null, \"generate_stats\": true, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inputFormat\": \"vcf\", \"intervals\": {\"__class__\": \"RuntimeValue\"}, \"noLog\": true, \"offset\": \"default\", \"outputConditional\": {\"outputFormat\": \"vcf\", \"__current_case__\": 0}, \"snpDb\": {\"genomeSrc\": \"cached\", \"__current_case__\": 0, \"genomeVersion\": \"hg19\", \"reg_section\": {\"regulation\": null}}, \"spliceRegion\": {\"setSpliceRegions\": \"no\", \"__current_case__\": 0}, \"spliceSiteSize\": \"2\", \"transcripts\": {\"__class__\": \"RuntimeValue\"}, \"udLength\": \"5000\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.3+T.galaxy1",
+                        "tool_state": "{\"annotations\": [\"-formatEff\", \"-classic\"], \"chr\": \"\", \"csvStats\": \"true\", \"filter\": {\"specificEffects\": \"no\", \"__current_case__\": 0}, \"filterOut\": [\"-no-downstream\", \"-no-intergenic\", \"-no-upstream\", \"-no-utr\"], \"generate_stats\": \"true\", \"genome_version\": \"NC_045512.2\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inputFormat\": \"vcf\", \"intervals\": {\"__class__\": \"RuntimeValue\"}, \"noLog\": \"true\", \"offset\": \"default\", \"outputConditional\": {\"outputFormat\": \"vcf\", \"__current_case__\": 0}, \"transcripts\": {\"__class__\": \"RuntimeValue\"}, \"udLength\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.5covid19",
                         "type": "tool",
-                        "uuid": "73d85553-fe49-4a78-9a5c-ac90bc2a1e12",
-                        "when": null,
+                        "uuid": "8fb55fb1-4986-45f5-bb6b-45c1329842b2",
                         "workflow_outputs": [
                             {
                                 "label": null,
-                                "output_name": "statsFile",
-                                "uuid": "bb59ec32-10c8-4923-8f41-62e3ed1adf11"
-                            },
-                            {
-                                "label": "Case 5 SnpEff Annotated vcf",
                                 "output_name": "snpeff_output",
-                                "uuid": "cd7b4941-4f4c-4631-8ad5-3411e60fbbd9"
+                                "uuid": "d5bec60d-c853-4979-a191-e69f47539684"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "CONVERTER_uncompressed_to_gz",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
                         "errors": null,
                         "id": 11,
                         "input_connections": {
-                            "input1": {
+                            "input": {
                                 "id": 10,
                                 "output_name": "snpeff_output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Convert uncompressed file to compressed",
+                        "name": "SnpSift Extract Fields",
                         "outputs": [
                             {
-                                "name": "output1",
-                                "type": "auto"
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 552.4385400335957,
-                            "top": 373.4495808144635
+                            "left": 1486.0794982910156,
+                            "top": 317.85511016845703
                         },
                         "post_job_actions": {
-                            "ChangeDatatypeActionoutput1": {
+                            "RenameDatasetActionoutput": {
                                 "action_arguments": {
-                                    "newtype": "vcf_bgzip"
+                                    "newname": "SnpSift tabular output"
                                 },
-                                "action_type": "ChangeDatatypeAction",
-                                "output_name": "output1"
-                            }
-                        },
-                        "tool_id": "CONVERTER_uncompressed_to_gz",
-                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.16+galaxy0",
-                        "type": "tool",
-                        "uuid": "2c959f43-8264-48d7-adf1-c12d5a2b3394",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "SnpEff Annotated vcf_bgzip",
-                                "output_name": "output1",
-                                "uuid": "6e5e1084-b5e1-4daf-8f3b-bd3868a52a25"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/geneiobio/gene_iobio_display_generation_iframe/4.7.1",
-                        "errors": null,
-                        "id": 12,
-                        "input_connections": {
-                            "input_type|father|vcf": {
-                                "id": 11,
-                                "output_name": "output1"
-                            },
-                            "input_type|mother|vcf": {
-                                "id": 11,
-                                "output_name": "output1"
-                            },
-                            "proband_vcf": {
-                                "id": 11,
-                                "output_name": "output1"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool gene.iobio visualisation",
-                                "name": "proband_bam"
-                            }
-                        ],
-                        "label": null,
-                        "name": "gene.iobio visualisation",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "html"
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "output"
                             }
-                        ],
-                        "position": {
-                            "left": 866.6404599769689,
-                            "top": 23.224599201146997
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/geneiobio/gene_iobio_display_generation_iframe/4.7.1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "c0af7b196a89",
-                            "name": "geneiobio",
+                            "changeset_revision": "2b3e65a4252f",
+                            "name": "snpsift",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"genes\": \"\", \"input_type\": {\"input_type_selector\": \"trio\", \"__current_case__\": 0, \"father\": {\"vcf\": {\"__class__\": \"ConnectedValue\"}, \"bam\": {\"__class__\": \"RuntimeValue\"}, \"affected\": false, \"name\": \"Case6F\"}, \"mother\": {\"vcf\": {\"__class__\": \"ConnectedValue\"}, \"bam\": {\"__class__\": \"RuntimeValue\"}, \"affected\": true, \"name\": \"Case6M\"}}, \"proband_affected\": true, \"proband_bam\": {\"__class__\": \"RuntimeValue\"}, \"proband_name\": \"Case6C\", \"proband_sex\": \"female\", \"proband_vcf\": {\"__class__\": \"ConnectedValue\"}, \"refgen_version\": \"GRCh37\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.7.1",
+                        "tool_state": "{\"empty_text\": \".\", \"extract\": \"CHROM POS REF ALT QUAL DP AF SB DP4 EFF[*].IMPACT EFF[*].FUNCLASS EFF[*].EFFECT EFF[*].GENE EFF[*].CODON\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"one_effect_per_line\": \"false\", \"separator\": \",\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.3+t.galaxy0",
                         "type": "tool",
-                        "uuid": "63a20112-21fe-4046-9fdd-3b5e766b0d68",
-                        "when": null,
+                        "uuid": "33e13bce-928f-41d6-b418-bc0a9e53d83d",
                         "workflow_outputs": [
                             {
-                                "label": "Case 5 gene.iobio results",
-                                "output_name": "outfile",
-                                "uuid": "0b30f4e0-7328-4479-8a56-bbf828fcfdba"
+                                "label": "SnpSift tabular output",
+                                "output_name": "output",
+                                "uuid": "06259137-eaa5-404a-923c-70ee5f1d89d4"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
                         "errors": null,
-                        "id": 13,
+                        "id": 12,
                         "input_connections": {
-                            "infile": {
-                                "id": 11,
-                                "output_name": "output1"
+                            "results_0|software_cond|input": {
+                                "id": 3,
+                                "output_name": "report_json"
                             },
-                            "ped": {
-                                "id": 2,
+                            "results_1|software_cond|output_0|type|input": {
+                                "id": 7,
                                 "output_name": "output"
+                            },
+                            "results_2|software_cond|output_0|input": {
+                                "id": 5,
+                                "output_name": "metrics_file"
+                            },
+                            "results_3|software_cond|input": {
+                                "id": 10,
+                                "output_name": "csvFile"
                             }
                         },
                         "inputs": [],
-                        "label": "Case 5 GEMINI Database",
-                        "name": "GEMINI load",
+                        "label": null,
+                        "name": "MultiQC",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "gemini.sqlite"
-                            }
-                        ],
-                        "position": {
-                            "left": 867.1106984600971,
-                            "top": 518.7461949332695
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "45296e47d565",
-                            "name": "gemini_load",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"annotation_databases\": \"2019-01-12\", \"annotation_type\": \"snpEff\", \"has_genotypes\": true, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"opt_content\": [\"gerp_bp\", \"cadd\", \"gene_tables\", \"genotypes\", \"gt_pl\", \"info_string\"], \"ped\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.20.1+galaxy2",
-                        "type": "tool",
-                        "uuid": "f8d4a15e-b99a-455c-a788-2cbd8c7cb4cc",
-                        "when": null,
-                        "workflow_outputs": [
+                                "name": "stats",
+                                "type": "input"
+                            },
                             {
-                                "label": "GEMINI Database",
-                                "output_name": "outfile",
-                                "uuid": "8a1964d9-607c-4dd3-a2dc-0f9a68dbb681"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1",
-                        "errors": null,
-                        "id": 14,
-                        "input_connections": {
-                            "infile": {
-                                "id": 13,
-                                "output_name": "outfile"
-                            }
-                        },
-                        "inputs": [],
-                        "label": "Case 5 GEMINI Inheritance pattern",
-                        "name": "GEMINI inheritance pattern",
-                        "outputs": [
+                                "name": "plots",
+                                "type": "input"
+                            },
                             {
-                                "name": "outfile",
-                                "type": "tabular"
+                                "name": "html_report",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 1132.4996805716235,
-                            "top": 583.0393503253775
+                            "left": 1486.0794982910156,
+                            "top": 397.8408889770508
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1",
+                        "post_job_actions": {
+                            "HideDatasetActionplots": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "plots"
+                            },
+                            "HideDatasetActionstats": {
+                                "action_arguments": {},
+                                "action_type": "HideDatasetAction",
+                                "output_name": "stats"
+                            },
+                            "RenameDatasetActionhtml_report": {
+                                "action_arguments": {
+                                    "newname": "MultiQC Report PE"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "html_report"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "18d13111692b",
-                            "name": "gemini_inheritance",
+                            "changeset_revision": "bf675f34b056",
+                            "name": "multiqc",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"family_wise\": {\"min_kindreds\": \"1\", \"families\": \"\", \"per_variant_selection\": {\"enabled\": \"no\", \"__current_case__\": 0, \"min_dp\": \"0\", \"min_gq\": \"0\", \"max_pl\": \"-1\"}}, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"inheritance\": {\"pattern_type\": \"autosomal_dominant\", \"__current_case__\": 3, \"constraint\": [{\"__index__\": 0, \"filter\": \"impact_severity != 'LOW'\"}], \"lenient\": false, \"allow_unaffected\": false}, \"oformat\": {\"report\": {\"report_selector\": \"custom\", \"__current_case__\": 2, \"columns\": null, \"extra_cols\": \"chrom, start, ref, alt, impact, gene, clinvar_sig, clinvar_disease_name, clinvar_gene_phenotype, rs_ids\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.20.1",
+                        "tool_state": "{\"comment\": \"\", \"flat\": \"false\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 23, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"stats\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"snpeff\", \"__current_case__\": 25, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.8+galaxy0",
                         "type": "tool",
-                        "uuid": "11a2ec8f-6c18-4000-ba5d-468dc896f866",
-                        "when": null,
+                        "uuid": "8c98527f-d1db-4cc4-89f1-1e75c508b8e9",
                         "workflow_outputs": [
                             {
-                                "label": "Case 5 GEMINI results",
-                                "output_name": "outfile",
-                                "uuid": "960ef978-089c-4292-81b5-731965c72a0d"
+                                "label": "MultiQC Report PE",
+                                "output_name": "html_report",
+                                "uuid": "758ffde5-7ddd-482a-88b2-1504f8335488"
                             }
                         ]
                     }
                 ],
-                "parent_id": "variant-analysis/trio-analysis",
-                "path": "topics/variant-analysis/tutorials/trio-analysis/workflows/main_workflow.ga",
+                "parent_id": "variant-analysis/sars-cov-2",
+                "path": "topics/variant-analysis/tutorials/sars-cov-2/workflows/main_workflow.ga",
                 "tags": [
                     "variant-analysis"
                 ],
                 "test_results": null,
-                "tests": true,
-                "title": "Trio Analysis Tutorial",
+                "tests": false,
+                "title": "Simple COVID-19 - PE Variation",
                 "topic_id": "variant-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-trio-analysis/versions/main-workflow",
-                "tutorial_id": "trio-analysis",
-                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/trio-analysis/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/trio-analysis/workflows/main_workflow.html",
-                "version": 5,
-                "wfid": "variant-analysis-trio-analysis",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-sars-cov-2/versions/main-workflow",
+                "tutorial_id": "sars-cov-2",
+                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2/workflows/main_workflow.html",
+                "version": 1,
+                "wfid": "variant-analysis-sars-cov-2",
                 "wfname": "main-workflow",
                 "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "CONVERTER_gz_to_uncompressed",
-                    "CONVERTER_uncompressed_to_gz",
-                    "Filter1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/geneiobio/gene_iobio_display_generation_iframe/4.7.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1"
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1"
                 ],
-                "workflowhub_id": "1096"
+                "workflowhub_id": "1074"
             }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.6483454"
+        ]
     },
     {
         "admin_install": {
@@ -284939,132 +292736,114 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "bwa",
-                    "owner": "devteam",
-                    "revisions": "e188dc7a68e6",
-                    "tool_panel_section_label": "Mapping",
+                    "name": "column_arrange_by_header",
+                    "owner": "bgruening",
+                    "revisions": "6c6d26ff01ff",
+                    "tool_panel_section_label": "Filter and Sort",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "column_maker",
-                    "owner": "devteam",
-                    "revisions": "6595517c2dd8",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "0a8c6b61f0f4",
                     "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "emboss_5",
+                    "name": "bamtools_filter",
                     "owner": "devteam",
-                    "revisions": "63dd26468588",
-                    "tool_panel_section_label": "EMBOSS",
+                    "revisions": "cb20f99fd45b",
+                    "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fasta_compute_length",
+                    "name": "bwa",
                     "owner": "devteam",
-                    "revisions": "7d37cfda8e00",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "revisions": "3fe632431b68",
+                    "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "compose_text_param",
-                    "owner": "iuc",
-                    "revisions": "e188c9826e0f",
-                    "tool_panel_section_label": "Expression Tools",
+                    "name": "fastqc",
+                    "owner": "devteam",
+                    "revisions": "e7b2202befea",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "datamash_ops",
-                    "owner": "iuc",
-                    "revisions": "746e8e4bf929",
-                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "name": "freebayes",
+                    "owner": "devteam",
+                    "revisions": "57def2d7c093",
+                    "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fastp",
-                    "owner": "iuc",
-                    "revisions": "65b93b623c77",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "samtools_calmd",
+                    "owner": "devteam",
+                    "revisions": "06dc50b7b711",
+                    "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ivar_consensus",
-                    "owner": "iuc",
-                    "revisions": "40737febe339",
-                    "tool_panel_section_label": "Virology",
+                    "name": "samtools_rmdup",
+                    "owner": "devteam",
+                    "revisions": "586f9e1cdb2b",
+                    "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ivar_trim",
+                    "name": "gemini_annotate",
                     "owner": "iuc",
-                    "revisions": "86a20ae274fc",
-                    "tool_panel_section_label": "Virology",
+                    "revisions": "cf0f0f05ba9f",
+                    "tool_panel_section_label": "Gemini",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "qualimap_bamqc",
+                    "name": "gemini_load",
                     "owner": "iuc",
-                    "revisions": "19ece8afbaab",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "revisions": "2270a8b83c12",
+                    "tool_panel_section_label": "Gemini",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "samtools_merge",
+                    "name": "gemini_query",
                     "owner": "iuc",
-                    "revisions": "36677f429310",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "revisions": "da74170c55c7",
+                    "tool_panel_section_label": "Gemini",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "samtools_view",
+                    "name": "multiqc",
                     "owner": "iuc",
-                    "revisions": "5826298f6a73",
-                    "tool_panel_section_label": "SAM/BAM",
+                    "revisions": "bf675f34b056",
+                    "tool_panel_section_label": "Quality Control",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "ucsc_fatovcf",
+                    "name": "snpeff",
                     "owner": "iuc",
-                    "revisions": "78df8fc2b3ab",
+                    "revisions": "5c7b70713fb5",
                     "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fasta_regex_finder",
-                    "owner": "mbernt",
-                    "revisions": "9a811adb714f",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mafft",
-                    "owner": "rnateam",
-                    "revisions": "bf28a8cff401",
-                    "tool_panel_section_label": "Multiple Alignments",
+                    "name": "varscan_somatic",
+                    "owner": "iuc",
+                    "revisions": "cf8ffc79db67",
+                    "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mimodd_main",
-                    "owner": "wolma",
-                    "revisions": "f0f2795de2c7",
-                    "tool_panel_section_label": "MiModD",
+                    "name": "trimmomatic",
+                    "owner": "pjbriggs",
+                    "revisions": "dfa082f84068",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 6595517c2dd8\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: emboss_5\n  owner: devteam\n  revisions: 63dd26468588\n  tool_panel_section_label: EMBOSS\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_compute_length\n  owner: devteam\n  revisions: 7d37cfda8e00\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: compose_text_param\n  owner: iuc\n  revisions: e188c9826e0f\n  tool_panel_section_label: Expression Tools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 746e8e4bf929\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ivar_consensus\n  owner: iuc\n  revisions: 40737febe339\n  tool_panel_section_label: Virology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ivar_trim\n  owner: iuc\n  revisions: 86a20ae274fc\n  tool_panel_section_label: Virology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qualimap_bamqc\n  owner: iuc\n  revisions: 19ece8afbaab\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_merge\n  owner: iuc\n  revisions: 36677f429310\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: 5826298f6a73\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ucsc_fatovcf\n  owner: iuc\n  revisions: 78df8fc2b3ab\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_regex_finder\n  owner: mbernt\n  revisions: 9a811adb714f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mafft\n  owner: rnateam\n  revisions: bf28a8cff401\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mimodd_main\n  owner: wolma\n  revisions: f0f2795de2c7\n  tool_panel_section_label: MiModD\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "wm75",
-                "TKlingstrom"
-            ],
-            "funding": [
-                "by-covid",
-                "elixir-converge",
-                "h2020-defend"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: column_arrange_by_header\n  owner: bgruening\n  revisions: 6c6d26ff01ff\n  tool_panel_section_label: Filter and Sort\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 0a8c6b61f0f4\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_filter\n  owner: devteam\n  revisions: cb20f99fd45b\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: 3fe632431b68\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: freebayes\n  owner: devteam\n  revisions: 57def2d7c093\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_calmd\n  owner: devteam\n  revisions: 06dc50b7b711\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_rmdup\n  owner: devteam\n  revisions: 586f9e1cdb2b\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_annotate\n  owner: iuc\n  revisions: cf0f0f05ba9f\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_load\n  owner: iuc\n  revisions: 2270a8b83c12\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_query\n  owner: iuc\n  revisions: da74170c55c7\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: bf675f34b056\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n  owner: iuc\n  revisions: 5c7b70713fb5\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: varscan_somatic\n  owner: iuc\n  revisions: cf8ffc79db67\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n  owner: pjbriggs\n  revisions: dfa082f84068\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/somatic-variants/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
@@ -285082,210 +292861,145 @@
                 "orcid": "0000-0002-9464-6640",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
-            },
-            {
-                "affiliations": [
-                    "elixir-europe"
-                ],
-                "elixir_node": "se",
-                "email": "tomas.klingstrom@slu.se",
-                "id": "TKlingstrom",
-                "joined": "2018-11",
-                "matrix": "TKlingstrom:matrix.org",
-                "name": "Tomas Klingstr\u00f6m",
-                "orcid": "0000-0002-9504-1352",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/TKlingstrom/",
-                "twitter": "TKlingstrom",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/TKlingstrom.json"
-            },
-            {
-                "funder": true,
-                "funding_id": "101046203",
-                "funding_statement": "BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response.\n\nThis project has received funding from the European Union\u2019s Horizon Europe research and innovation programme under grant agreement \u2116 101046203 (BY-COVID)",
-                "funding_system": "cordis",
-                "id": "by-covid",
-                "joined": "2023-04",
-                "members": [
-                    "bgruening",
-                    "hexylena",
-                    "ilveroluca",
-                    "kikkomep",
-                    "mbaardwijk",
-                    "PapXis",
-                    "pauldg",
-                    "simleo",
-                    "stain",
-                    "wm75"
-                ],
-                "name": "BeYond-COVID",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/by-covid/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/by-covid.json"
-            },
-            {
-                "avatar": "https://elixir-europe.org/sites/default/files/styles/right-medium/public/images/converge_logo.png",
-                "funder": true,
-                "funding_id": "871075",
-                "funding_statement": "ELIXIR CONVERGE is connecting and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services. This project has received funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement \u2116 871075",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "elixir-converge",
-                "joined": "2023-01",
-                "members": [
-                    "bgruening",
-                    "hexylena"
-                ],
-                "name": "ELIXIR-CONVERGE",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-converge/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-converge.json"
-            },
-            {
-                "funder": true,
-                "funding_id": "773701",
-                "funding_statement": "DEFEND is Addressing the dual emerging threats of African Swine Fever and Lumpy Skin Disease in Europe.\n\nThis work has received funding from the DEFEND project (www.defend2020.eu) with funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement No 773701.",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "h2020-defend",
-                "joined": "2023-05",
-                "name": "Addressing the dual emerging threats of African Swine Fever and Lumpy Skin Disease in Europe",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/h2020-defend/",
-                "short_name": "DEFEND",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/h2020-defend.json"
             }
         ],
-        "dir": "topics/variant-analysis/tutorials/pox-tiled-amplicon",
+        "dir": "topics/variant-analysis/tutorials/somatic-variants",
         "edam_operation": [
-            "Global alignment",
-            "Sequencing quality control",
-            "Sequence contamination filtering",
-            "Genome indexing",
+            "Data handling",
             "Sequence alignment",
-            "Sequence analysis",
             "Read mapping",
+            "Sequencing quality control",
             "Sequence alignment analysis",
-            "Multiple sequence alignment",
             "Generation",
-            "Local alignment"
+            "Statistical calculation",
+            "Variant calling",
+            "Validation",
+            "Sequence composition calculation",
+            "Genome indexing"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.be",
+            "UseGalaxy.eu",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "variant-analysis/pox-tiled-amplicon",
+        "id": "variant-analysis/somatic-variants",
         "inexact_supported_servers": [
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.cz",
+            "UseGalaxy.fr"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Compared to other viruses, analysis of sequencing data from pox viruses is complicated by the rather large genome size and by the presence of inverted terminal repeats, but well-designed wet lab and bioinformatic workflows can handle these particularities.",
-            "Galaxy and its huge set of tools are flexible enough to handle half-genome sequencing data efficiently.",
-            "A mapping-based approach can result in high-quality consensus genome reconstructions from pox virus sequencing data and appears promising even when dealing with recombinant samples."
+            "Follow best practices for read mapping, quality control and mapped reads postprocessing to minimize false-positive variant calls.",
+            "Use a dedicated somatic variant caller to call variants and to classify them into somatic, germline and LOH event variants on statistical grounds.",
+            "Annotations and queries based on variant properties add relevance to variant and gene reports.",
+            "A framework like GEMINI is very helpful for managing, annotating and querying lists of variants in a flexible way.",
+            "Prefer public, free annotation sources to foster reproducibility and information sharing."
         ],
         "layout": "tutorial_hands_on",
-        "level": "Advanced",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-20",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Learn how to deal with pox virus genomes inverted terminal repeats through a combination of wet lab protocol and tailored bioinformatics",
-            "Construct a sample consensus genome from mapped reads",
-            "Explore a recombinant pox virus genome via a multiple-sequence alignment of consensus genome and references and through lists of mutations derived from it"
+            "Call variants and their somatic status from whole-exome sequencing data",
+            "Annotate variants with a wealth of human genetic and cancer-specific information extracted from public databases",
+            "Add gene-level annotations and generate reports of annotated somatic and germline variants, loss-of-heterozygosity (LOH) events, and affected genes, ready for interpretation by clinicians"
         ],
-        "pageviews": 594,
-        "pub_date": "2023-05-15",
+        "pageviews": 22023,
+        "pub_date": "2019-03-13",
         "questions": [
-            "Which special challenges does one encounter during sequence data analysis of pox viruses?",
-            "How can standard workflows for viral mutation calling and consensus generation be adapted to the particularities of pox viruses?",
-            "How can viral consensus sequences, multiple-sequence alignments and mutation calls be generated from each other and used to answer questions about the data?"
-        ],
-        "requirements": [
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "collections",
-                    "upload-rules"
-                ],
-                "type": "internal"
-            }
+            "What are the specific challenges in somatic variant calling that set it apart from regular diploid variant calling?",
+            "How can you call variants and classify them according to their presence/absence in/from tumor and normal tissue of the same individual?",
+            "How can you annotate variants and affected genes with prior knowledge from human genetic and cancer-specific databases to generate clinically relevant reports?"
         ],
-        "short_id": "T00347",
+        "short_id": "T00318",
         "short_tools": [
-            "samtools_view",
-            "rbc_mafft",
-            "Cut1",
-            "EMBOSS: maskseq51",
-            "ivar_consensus",
-            "Grep1",
-            "__APPLY_RULES__",
-            "datamash_ops",
-            "qualimap_bamqc",
-            "fatovcf",
-            "ivar_trim",
-            "__ZIP_COLLECTION__",
-            "fasta_regex_finder",
-            "fasta_compute_length",
             "bwa_mem",
-            "upload1",
-            "param_value_from_file",
-            "compose_text_param",
-            "fastp",
-            "mimodd_info",
-            "Add_a_column1",
-            "samtools_merge"
+            "tp_easyjoin_tool",
+            "snpEff",
+            "gemini_annotate",
+            "gemini_load",
+            "samtools_rmdup",
+            "bg_column_arrange_by_header",
+            "bamFilter",
+            "multiqc",
+            "varscan_somatic",
+            "bamleftalign",
+            "fastqc",
+            "trimmomatic",
+            "gemini_query",
+            "samtools_calmd"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "one-health",
+        "subtopic": "human-genetics-cancer",
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                }
-            ],
-            "inexact": [
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
                 }
             ]
         },
         "symlink": null,
-        "tags": [
-            "virology",
-            "one-health"
-        ],
-        "time_estimation": "4H",
-        "title": "Pox virus genome analysis from tiled-amplicon sequencing data",
+        "time_estimation": "7h",
+        "title": "Identification of somatic and germline variants from tumor and normal sample pairs",
         "tools": [
-            "Cut1",
-            "Grep1",
-            "__APPLY_RULES__",
-            "__ZIP_COLLECTION__",
-            "param_value_from_file",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_fatovcf/fatovcf/426+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/mbernt/fasta_regex_finder/fasta_regex_finder/0.1.0",
-            "toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.520+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_info/0.1.8_1",
-            "upload1"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/varscan_somatic/varscan_somatic/2.4.3.6",
+            "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5"
         ],
         "topic_name": "variant-analysis",
         "topic_name_human": "Variant Analysis",
@@ -285295,264 +293009,441 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "pox-tiled-amplicon",
+        "tutorial_name": "somatic-variants",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/somatic-variants/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/somatic-variants/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/somatic-variants/tutorial.json"
         },
-        "version": 4,
+        "version": 15,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 140,
-        "visitors": 497,
+        "visit_duration": 151,
+        "visitors": 11663,
         "workflows": [
             {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0001-6897-1215",
-                        "name": "Viktoria Isabel Schwarz"
-                    },
-                    {
-                        "class": "Person",
-                        "identifier": "https://orcid.org/0000-0002-9464-6640",
-                        "name": "Wolfgang Maier"
-                    }
-                ],
-                "description": "From a reference and a primer scheme generate two masked half-genome references for ITR-aware pox virus sequencing data analysis.",
+                "creators": [],
+                "description": "Identification of somatic and germline variants from tumor and normal sample pairs tutorial",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPrimer Scheme\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference FASTA\"]\n  2[label=\"Select pool1 primers\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Select pool2 primers\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Compute sequence length\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Datamash\"]\n  2 -> 5 [label=\"out_file1\"]\n  6[label=\"Datamash\"]\n  3 -> 6 [label=\"out_file1\"]\n  7[label=\"Cut\"]\n  4 -> 7 [label=\"output\"]\n  8[label=\"Compute\"]\n  5 -> 8 [label=\"out_file\"]\n  9[label=\"Get start position of Pool2\"]\n  6 -> 9 [label=\"out_file\"]\n  10[label=\"Get end position of sequence\"]\n  7 -> 10 [label=\"out_file1\"]\n  11[label=\"Get end position of Pool1\"]\n  8 -> 11 [label=\"out_file1\"]\n  12[label=\"Compose text parameter value\"]\n  9 -> 12 [label=\"text_param\"]\n  13[label=\"Compose text parameter value\"]\n  11 -> 13 [label=\"text_param\"]\n  10 -> 13 [label=\"text_param\"]\n  14[label=\"Mask Reference for Pool2\"]\n  1 -> 14 [label=\"output\"]\n  12 -> 14 [label=\"out1\"]\n  kaf755a5e2b2049bc9d5234781f937f48[color=lightseagreen,label=\"Output\\nmasked_ref_pool2\"]\n  14 -> kaf755a5e2b2049bc9d5234781f937f48\n  15[label=\"Mask Reference for Pool1\"]\n  1 -> 15 [label=\"output\"]\n  13 -> 15 [label=\"out1\"]\n  k0c3b5b20c426428ca08bc835a82477c1[color=lightseagreen,label=\"Output\\nmasked_ref_pool1\"]\n  15 -> k0c3b5b20c426428ca08bc835a82477c1\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSLGFSK-N_231335_r1_chr5_12_17.fastq\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSLGFSK-N_231335_r2_chr5_12_17.fastq\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSLGFSK-T_231336_r1_chr5_12_17.fastq\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSLGFSK-T_231336_r2_chr5_12_17.fastq\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhg19.chr5_12_17.fa\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhotspots.bed\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncgi_variant_positions.bed\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\n01-Feb-2019-CIVic.bed\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ndbsnp.b147.chr5_12_17.vcf.gz\"]\n  9[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nUniprot_Cancer_Genes.13Feb2019.txt\"]\n  10[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncgi_genes.txt\"]\n  11[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\n01-Feb-2019-GeneSummaries.tsv\"]\n  12[label=\"FastQC\"]\n  0 -> 12 [label=\"output\"]\n  13[label=\"FastQC\"]\n  1 -> 13 [label=\"output\"]\n  14[label=\"Trimmomatic\"]\n  0 -> 14 [label=\"output\"]\n  1 -> 14 [label=\"output\"]\n  15[label=\"FastQC\"]\n  2 -> 15 [label=\"output\"]\n  16[label=\"FastQC\"]\n  3 -> 16 [label=\"output\"]\n  17[label=\"Trimmomatic\"]\n  2 -> 17 [label=\"output\"]\n  3 -> 17 [label=\"output\"]\n  18[label=\"FastQC\"]\n  14 -> 18 [label=\"fastq_out_r2_paired\"]\n  19[label=\"FastQC\"]\n  14 -> 19 [label=\"fastq_out_r1_paired\"]\n  20[label=\"Map with BWA-MEM\"]\n  14 -> 20 [label=\"fastq_out_r1_paired\"]\n  14 -> 20 [label=\"fastq_out_r2_paired\"]\n  21[label=\"MultiQC\"]\n  13 -> 21 [label=\"text_file\"]\n  15 -> 21 [label=\"text_file\"]\n  16 -> 21 [label=\"text_file\"]\n  12 -> 21 [label=\"text_file\"]\n  22[label=\"FastQC\"]\n  17 -> 22 [label=\"fastq_out_r1_paired\"]\n  23[label=\"FastQC\"]\n  17 -> 23 [label=\"fastq_out_r2_paired\"]\n  24[label=\"Map with BWA-MEM\"]\n  17 -> 24 [label=\"fastq_out_r1_paired\"]\n  17 -> 24 [label=\"fastq_out_r2_paired\"]\n  25[label=\"Filter\"]\n  20 -> 25 [label=\"bam_output\"]\n  26[label=\"MultiQC\"]\n  19 -> 26 [label=\"text_file\"]\n  22 -> 26 [label=\"text_file\"]\n  23 -> 26 [label=\"text_file\"]\n  18 -> 26 [label=\"text_file\"]\n  27[label=\"Filter\"]\n  24 -> 27 [label=\"bam_output\"]\n  28[label=\"RmDup\"]\n  25 -> 28 [label=\"out_file1\"]\n  29[label=\"RmDup\"]\n  27 -> 29 [label=\"out_file1\"]\n  30[label=\"BamLeftAlign\"]\n  28 -> 30 [label=\"output1\"]\n  31[label=\"BamLeftAlign\"]\n  29 -> 31 [label=\"output1\"]\n  32[label=\"CalMD\"]\n  30 -> 32 [label=\"output_bam\"]\n  33[label=\"CalMD\"]\n  31 -> 33 [label=\"output_bam\"]\n  34[label=\"Filter\"]\n  32 -> 34 [label=\"calmd_output\"]\n  35[label=\"Filter\"]\n  33 -> 35 [label=\"calmd_output\"]\n  36[label=\"VarScan somatic\"]\n  34 -> 36 [label=\"out_file1\"]\n  35 -> 36 [label=\"out_file1\"]\n  37[label=\"SnpEff eff:\"]\n  36 -> 37 [label=\"output\"]\n  38[label=\"GEMINI load\"]\n  37 -> 38 [label=\"snpeff_output\"]\n  39[label=\"GEMINI annotate\"]\n  36 -> 39 [label=\"output\"]\n  38 -> 39 [label=\"outfile\"]\n  40[label=\"GEMINI annotate\"]\n  8 -> 40 [label=\"output\"]\n  39 -> 40 [label=\"outfile\"]\n  41[label=\"GEMINI annotate\"]\n  5 -> 41 [label=\"output\"]\n  40 -> 41 [label=\"outfile\"]\n  42[label=\"GEMINI annotate\"]\n  7 -> 42 [label=\"output\"]\n  41 -> 42 [label=\"outfile\"]\n  43[label=\"GEMINI annotate\"]\n  6 -> 43 [label=\"output\"]\n  42 -> 43 [label=\"outfile\"]\n  44[label=\"GEMINI query\"]\n  43 -> 44 [label=\"outfile\"]\n  45[label=\"GEMINI query\"]\n  43 -> 45 [label=\"outfile\"]\n  46[label=\"GEMINI query\"]\n  43 -> 46 [label=\"outfile\"]\n  47[label=\"GEMINI query\"]\n  43 -> 47 [label=\"outfile\"]\n  48[label=\"Join\"]\n  47 -> 48 [label=\"outfile\"]\n  9 -> 48 [label=\"output\"]\n  49[label=\"Join\"]\n  48 -> 49 [label=\"output\"]\n  10 -> 49 [label=\"output\"]\n  50[label=\"Join\"]\n  49 -> 50 [label=\"output\"]\n  11 -> 50 [label=\"output\"]\n  51[label=\"Column arrange\"]\n  50 -> 51 [label=\"output\"]\n  kfeb210a2c0954ebb944668fccaa0cce7[color=lightseagreen,label=\"Output\\ngene_report_output\"]\n  51 -> kfeb210a2c0954ebb944668fccaa0cce7\n}",
                 "history": [
                     {
-                        "hash": "79db81a7c1c23d9778536abaa9ca879f3b0bbda5",
-                        "message": "Update pox-virus-tiled-amplicon-ref-masking.ga",
-                        "num": 2,
-                        "short_hash": "79db81a7c",
-                        "unix": "1684740183"
+                        "hash": "caffacad4879c005f2c65ec0fce10bca42df9576",
+                        "message": "Somatic variants tutorial updates (#2054)",
+                        "num": 1,
+                        "short_hash": "caffacad4",
+                        "unix": "1602363051"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "SLGFSK-N_231335_r1_chr5_12_17.fastq"
+                            }
+                        ],
+                        "label": "SLGFSK-N_231335_r1_chr5_12_17.fastq",
+                        "name": "SLGFSK-N_231335_r1_chr5_12_17.fastq",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 200
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"SLGFSK-N_231335_r1_chr5_12_17.fastq\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "42e41cea-0eef-4411-8d05-3497e4305454",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "SLGFSK-N_231335_r2_chr5_12_17.fastq"
+                            }
+                        ],
+                        "label": "SLGFSK-N_231335_r2_chr5_12_17.fastq",
+                        "name": "SLGFSK-N_231335_r2_chr5_12_17.fastq",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 320
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"SLGFSK-N_231335_r2_chr5_12_17.fastq\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "c01c6659-b9cd-4463-a845-4a27e4734509",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "SLGFSK-T_231336_r1_chr5_12_17.fastq"
+                            }
+                        ],
+                        "label": "SLGFSK-T_231336_r1_chr5_12_17.fastq",
+                        "name": "SLGFSK-T_231336_r1_chr5_12_17.fastq",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 440
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"SLGFSK-T_231336_r1_chr5_12_17.fastq\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "44387739-ebc5-4ca9-9274-ca568f6981be",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 3,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "SLGFSK-T_231336_r2_chr5_12_17.fastq"
+                            }
+                        ],
+                        "label": "SLGFSK-T_231336_r2_chr5_12_17.fastq",
+                        "name": "SLGFSK-T_231336_r2_chr5_12_17.fastq",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 560
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"SLGFSK-T_231336_r2_chr5_12_17.fastq\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "cd735b71-4735-4613-88c2-585e9ae752cd",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 4,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "hg19.chr5_12_17.fa"
+                            }
+                        ],
+                        "label": "hg19.chr5_12_17.fa",
+                        "name": "hg19.chr5_12_17.fa",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 680
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"hg19.chr5_12_17.fa\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "3c81dd70-5abd-4c35-ae8c-cd0f2e4936fa",
+                        "workflow_outputs": []
                     },
                     {
-                        "hash": "314d08f56a2d904cbab620fa5400ed0dbfa9619a",
-                        "message": "Add some material for new pox virus tiled amplicon tutorial",
-                        "num": 1,
-                        "short_hash": "314d08f56",
-                        "unix": "1682289363"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "The workflow expects a primer scheme split into two separate sequencing pools. These pools must be denoted as pool1/pool2 in the BED score column. The pool ids may, optionally, be followed by indicators of the subpool for tiled PCR amplification (e.g., pool1a/pool1b/pool2a/pool2b)",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 5,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "The workflow expects a primer scheme split into two separate sequencing pools. These pools must be denoted as pool1/pool2 in the BED score column. The pool ids may, optionally, be followed by indicators of the subpool for tiled PCR amplification (e.g., pool1a/pool1b/pool2a/pool2b)",
-                                "name": "Primer Scheme (BED file with Pool identifiers)"
+                                "description": "",
+                                "name": "hotspots.bed"
                             }
                         ],
-                        "label": "Primer Scheme",
-                        "name": "Input dataset",
+                        "label": "hotspots.bed",
+                        "name": "hotspots.bed",
                         "outputs": [],
                         "position": {
-                            "left": 0,
-                            "top": 667.3406219482422
+                            "left": 200,
+                            "top": 800
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{\"name\": \"hotspots.bed\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "1829d4e0-ee74-4a94-8dc5-98a11d96b961",
-                        "when": null,
+                        "uuid": "90dd17da-34a9-4ed4-a1a0-b1389a795f4c",
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "The viral reference sequence to map sequenced reads against",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 6,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "The viral reference sequence to map sequenced reads against",
-                                "name": "Reference FASTA"
+                                "description": "",
+                                "name": "cgi_variant_positions.bed"
                             }
                         ],
-                        "label": "Reference FASTA",
-                        "name": "Input dataset",
+                        "label": "cgi_variant_positions.bed",
+                        "name": "cgi_variant_positions.bed",
                         "outputs": [],
                         "position": {
-                            "left": 251.7752034262281,
-                            "top": 650.9021921247038
+                            "left": 200,
+                            "top": 920
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+                        "tool_state": "{\"name\": \"cgi_variant_positions.bed\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "f17c7022-fc94-42b5-ae90-7b3ec3d70ffb",
-                        "when": null,
+                        "uuid": "4392884e-1b45-4c29-94c5-39c2c9ec1fb6",
                         "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPrimer Scheme\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference FASTA\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Select pool1 primers\"];\n  0 -->|output| 2;\n  3[\"Select pool2 primers\"];\n  0 -->|output| 3;\n  4[\"Compute sequence length\"];\n  1 -->|output| 4;\n  5[\"Datamash\"];\n  2 -->|out_file1| 5;\n  6[\"Datamash\"];\n  3 -->|out_file1| 6;\n  7[\"Cut\"];\n  4 -->|output| 7;\n  8[\"Compute\"];\n  5 -->|out_file| 8;\n  9[\"Get start position of Pool2\"];\n  6 -->|out_file| 9;\n  10[\"Get end position of sequence\"];\n  7 -->|out_file1| 10;\n  11[\"Get end position of Pool1\"];\n  8 -->|out_file1| 11;\n  12[\"Compose text parameter value\"];\n  9 -->|text_param| 12;\n  13[\"Compose text parameter value\"];\n  11 -->|text_param| 13;\n  10 -->|text_param| 13;\n  14[\"Mask Reference for Pool2\"];\n  1 -->|output| 14;\n  12 -->|out1| 14;\n  af755a5e-2b20-49bc-9d52-34781f937f48[\"Output\\nmasked_ref_pool2\"];\n  14 --> af755a5e-2b20-49bc-9d52-34781f937f48;\n  style af755a5e-2b20-49bc-9d52-34781f937f48 stroke:#2c3143,stroke-width:4px;\n  15[\"Mask Reference for Pool1\"];\n  1 -->|output| 15;\n  13 -->|out1| 15;\n  0c3b5b20-c426-428c-a08b-c835a82477c1[\"Output\\nmasked_ref_pool1\"];\n  15 --> 0c3b5b20-c426-428c-a08b-c835a82477c1;\n  style 0c3b5b20-c426-428c-a08b-c835a82477c1 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "pox-virus-tiled-amplicon-ref-masking",
-                "outputs": [
+                    },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 14,
-                        "input_connections": {
-                            "input1": {
-                                "id": 1,
-                                "output_name": "output"
-                            },
-                            "regions": {
-                                "id": 12,
-                                "output_name": "out1"
+                        "id": 7,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "01-Feb-2019-CIVic.bed"
                             }
+                        ],
+                        "label": "01-Feb-2019-CIVic.bed",
+                        "name": "01-Feb-2019-CIVic.bed",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 1040
                         },
-                        "inputs": [],
-                        "label": "Mask Reference for Pool2",
-                        "name": "maskseq",
-                        "outputs": [
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"01-Feb-2019-CIVic.bed\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "06b14682-2e30-4b72-82ec-07c2f08bfe4e",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "name": "out_file1",
-                                "type": "fasta"
+                                "description": "",
+                                "name": "dbsnp.b147.chr5_12_17.vcf.gz"
                             }
                         ],
+                        "label": "dbsnp.b147.chr5_12_17.vcf.gz",
+                        "name": "dbsnp.b147.chr5_12_17.vcf.gz",
+                        "outputs": [],
                         "position": {
-                            "left": 1438.15352300995,
-                            "top": 648.5794855890229
+                            "left": 200,
+                            "top": 1160
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Masked reference for mapping of pool2"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"dbsnp.b147.chr5_12_17.vcf.gz\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "ecbfe5d9-1585-488b-b47c-62f2927a47a7",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "Uniprot_Cancer_Genes.13Feb2019.txt"
                             }
+                        ],
+                        "label": "Uniprot_Cancer_Genes.13Feb2019.txt",
+                        "name": "Uniprot_Cancer_Genes.13Feb2019.txt",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 1280
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "ce385837c160",
-                            "name": "emboss_5",
-                            "owner": "devteam",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"maskchar\": \"N\", \"out_format1\": \"fasta\", \"regions\": {\"__class__\": \"ConnectedValue\"}, \"tolower\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.0.0",
-                        "type": "tool",
-                        "uuid": "140608b3-48b3-46f2-92e3-2b9c3fb9e3b2",
-                        "when": null,
-                        "workflow_outputs": [
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"Uniprot_Cancer_Genes.13Feb2019.txt\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "27376556-09b4-4841-ae6b-daf27961cb26",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 10,
+                        "input_connections": {},
+                        "inputs": [
                             {
-                                "label": "masked_ref_pool2",
-                                "output_name": "out_file1",
-                                "uuid": "af755a5e-2b20-49bc-9d52-34781f937f48"
+                                "description": "",
+                                "name": "cgi_genes.txt"
                             }
-                        ]
+                        ],
+                        "label": "cgi_genes.txt",
+                        "name": "cgi_genes.txt",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 1400
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"cgi_genes.txt\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "a1b1e2a4-d8a9-4b28-8438-d6cac706f9af",
+                        "workflow_outputs": []
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
+                        "content_id": null,
                         "errors": null,
-                        "id": 15,
+                        "id": 11,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "01-Feb-2019-GeneSummaries.tsv"
+                            }
+                        ],
+                        "label": "01-Feb-2019-GeneSummaries.tsv",
+                        "name": "01-Feb-2019-GeneSummaries.tsv",
+                        "outputs": [],
+                        "position": {
+                            "left": 200,
+                            "top": 1520
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"01-Feb-2019-GeneSummaries.tsv\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "af690aec-8006-41ad-b05c-6c388d74ad97",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSLGFSK-N_231335_r1_chr5_12_17.fastq\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSLGFSK-N_231335_r2_chr5_12_17.fastq\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nSLGFSK-T_231336_r1_chr5_12_17.fastq\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nSLGFSK-T_231336_r2_chr5_12_17.fastq\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nhg19.chr5_12_17.fa\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nhotspots.bed\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\ncgi_variant_positions.bed\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\n01-Feb-2019-CIVic.bed\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\ndbsnp.b147.chr5_12_17.vcf.gz\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"\u2139\ufe0f Input Dataset\\nUniprot_Cancer_Genes.13Feb2019.txt\"];\n  style 9 stroke:#2c3143,stroke-width:4px;\n  10[\"\u2139\ufe0f Input Dataset\\ncgi_genes.txt\"];\n  style 10 stroke:#2c3143,stroke-width:4px;\n  11[\"\u2139\ufe0f Input Dataset\\n01-Feb-2019-GeneSummaries.tsv\"];\n  style 11 stroke:#2c3143,stroke-width:4px;\n  12[\"FastQC\"];\n  0 -->|output| 12;\n  13[\"FastQC\"];\n  1 -->|output| 13;\n  14[\"Trimmomatic\"];\n  0 -->|output| 14;\n  1 -->|output| 14;\n  15[\"FastQC\"];\n  2 -->|output| 15;\n  16[\"FastQC\"];\n  3 -->|output| 16;\n  17[\"Trimmomatic\"];\n  2 -->|output| 17;\n  3 -->|output| 17;\n  18[\"FastQC\"];\n  14 -->|fastq_out_r2_paired| 18;\n  19[\"FastQC\"];\n  14 -->|fastq_out_r1_paired| 19;\n  20[\"Map with BWA-MEM\"];\n  14 -->|fastq_out_r1_paired| 20;\n  14 -->|fastq_out_r2_paired| 20;\n  21[\"MultiQC\"];\n  13 -->|text_file| 21;\n  15 -->|text_file| 21;\n  16 -->|text_file| 21;\n  12 -->|text_file| 21;\n  22[\"FastQC\"];\n  17 -->|fastq_out_r1_paired| 22;\n  23[\"FastQC\"];\n  17 -->|fastq_out_r2_paired| 23;\n  24[\"Map with BWA-MEM\"];\n  17 -->|fastq_out_r1_paired| 24;\n  17 -->|fastq_out_r2_paired| 24;\n  25[\"Filter\"];\n  20 -->|bam_output| 25;\n  26[\"MultiQC\"];\n  19 -->|text_file| 26;\n  22 -->|text_file| 26;\n  23 -->|text_file| 26;\n  18 -->|text_file| 26;\n  27[\"Filter\"];\n  24 -->|bam_output| 27;\n  28[\"RmDup\"];\n  25 -->|out_file1| 28;\n  29[\"RmDup\"];\n  27 -->|out_file1| 29;\n  30[\"BamLeftAlign\"];\n  28 -->|output1| 30;\n  31[\"BamLeftAlign\"];\n  29 -->|output1| 31;\n  32[\"CalMD\"];\n  30 -->|output_bam| 32;\n  33[\"CalMD\"];\n  31 -->|output_bam| 33;\n  34[\"Filter\"];\n  32 -->|calmd_output| 34;\n  35[\"Filter\"];\n  33 -->|calmd_output| 35;\n  36[\"VarScan somatic\"];\n  34 -->|out_file1| 36;\n  35 -->|out_file1| 36;\n  37[\"SnpEff eff:\"];\n  36 -->|output| 37;\n  38[\"GEMINI load\"];\n  37 -->|snpeff_output| 38;\n  39[\"GEMINI annotate\"];\n  36 -->|output| 39;\n  38 -->|outfile| 39;\n  40[\"GEMINI annotate\"];\n  8 -->|output| 40;\n  39 -->|outfile| 40;\n  41[\"GEMINI annotate\"];\n  5 -->|output| 41;\n  40 -->|outfile| 41;\n  42[\"GEMINI annotate\"];\n  7 -->|output| 42;\n  41 -->|outfile| 42;\n  43[\"GEMINI annotate\"];\n  6 -->|output| 43;\n  42 -->|outfile| 43;\n  44[\"GEMINI query\"];\n  43 -->|outfile| 44;\n  45[\"GEMINI query\"];\n  43 -->|outfile| 45;\n  46[\"GEMINI query\"];\n  43 -->|outfile| 46;\n  47[\"GEMINI query\"];\n  43 -->|outfile| 47;\n  48[\"Join\"];\n  47 -->|outfile| 48;\n  9 -->|output| 48;\n  49[\"Join\"];\n  48 -->|output| 49;\n  10 -->|output| 49;\n  50[\"Join\"];\n  49 -->|output| 50;\n  11 -->|output| 50;\n  51[\"Column arrange\"];\n  50 -->|output| 51;\n  feb210a2-c095-4ebb-9446-68fccaa0cce7[\"Output\\ngene_report_output\"];\n  51 --> feb210a2-c095-4ebb-9446-68fccaa0cce7;\n  style feb210a2-c095-4ebb-9446-68fccaa0cce7 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "Identification of somatic and germline variants from tumor and normal sample pairs tutorial",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2",
+                        "errors": null,
+                        "id": 51,
                         "input_connections": {
-                            "input1": {
-                                "id": 1,
+                            "param_input": {
+                                "id": 50,
                                 "output_name": "output"
-                            },
-                            "regions": {
-                                "id": 13,
-                                "output_name": "out1"
                             }
                         },
                         "inputs": [],
-                        "label": "Mask Reference for Pool1",
-                        "name": "maskseq",
+                        "label": null,
+                        "name": "Column arrange",
                         "outputs": [
                             {
-                                "name": "out_file1",
-                                "type": "fasta"
+                                "name": "output",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1452.6333312988281,
-                            "top": 223.50729370117188
-                        },
-                        "post_job_actions": {
-                            "RenameDatasetActionout_file1": {
-                                "action_arguments": {
-                                    "newname": "Masked reference for mapping of pool1"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "out_file1"
-                            }
+                            "left": 4600,
+                            "top": 200
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2",
                         "tool_shed_repository": {
-                            "changeset_revision": "ce385837c160",
-                            "name": "emboss_5",
-                            "owner": "devteam",
+                            "changeset_revision": "6c6d26ff01ff",
+                            "name": "column_arrange_by_header",
+                            "owner": "bgruening",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"maskchar\": \"N\", \"out_format1\": \"fasta\", \"regions\": {\"__class__\": \"ConnectedValue\"}, \"tolower\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "5.0.0",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/hg19.len\", \"discard_remaining\": \"true\", \"param_input\": {\"__class__\": \"ConnectedValue\"}, \"rep_param_columns\": [{\"__index__\": 0, \"param_column\": \"gene\"}, {\"__index__\": 1, \"param_column\": \"chrom\"}, {\"__index__\": 2, \"param_column\": \"synonym\"}, {\"__index__\": 3, \"param_column\": \"hgnc_id\"}, {\"__index__\": 4, \"param_column\": \"entrez_id\"}, {\"__index__\": 5, \"param_column\": \"rvis_pct\"}, {\"__index__\": 6, \"param_column\": \"is_OG\"}, {\"__index__\": 7, \"param_column\": \"is_TS\"}, {\"__index__\": 8, \"param_column\": \"in_cgi_biomarkers\"}, {\"__index__\": 9, \"param_column\": \"clinvar_gene_phenotype\"}, {\"__index__\": 10, \"param_column\": \"gene_civic_url\"}, {\"__index__\": 11, \"param_column\": \"description\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.2",
                         "type": "tool",
-                        "uuid": "3c8b86c1-7e53-4b72-b836-88a921a368ba",
-                        "when": null,
+                        "uuid": "96059b98-f7dd-4ce0-9000-7eea6282f629",
                         "workflow_outputs": [
                             {
-                                "label": "masked_ref_pool1",
-                                "output_name": "out_file1",
-                                "uuid": "0c3b5b20-c426-428c-a08b-c835a82477c1"
+                                "label": "gene_report_output",
+                                "output_name": "output",
+                                "uuid": "feb210a2-c095-4ebb-9446-68fccaa0cce7"
                             }
                         ]
                     }
                 ],
-                "parent_id": "variant-analysis/pox-tiled-amplicon",
-                "path": "topics/variant-analysis/tutorials/pox-tiled-amplicon/workflows/pox-virus-tiled-amplicon-ref-masking.ga",
+                "parent_id": "variant-analysis/somatic-variants",
+                "path": "topics/variant-analysis/tutorials/somatic-variants/workflows/somatic_variants_tutorial_workflow.ga",
                 "tags": [
-                    "GTN",
                     "variant-analysis"
                 ],
                 "test_results": null,
                 "tests": true,
-                "title": "pox-virus-tiled-amplicon-ref-masking",
+                "title": "Identification of somatic and germline variants from tumor and normal sample pairs tutorial",
                 "topic_id": "variant-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-pox-tiled-amplicon/versions/pox-virus-tiled-amplicon-ref-masking",
-                "tutorial_id": "pox-tiled-amplicon",
-                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/pox-tiled-amplicon/workflows/pox-virus-tiled-amplicon-ref-masking.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/pox-tiled-amplicon/workflows/pox-virus-tiled-amplicon-ref-masking.html",
-                "version": 2,
-                "wfid": "variant-analysis-pox-tiled-amplicon",
-                "wfname": "pox-virus-tiled-amplicon-ref-masking",
-                "workflow": "pox-virus-tiled-amplicon-ref-masking.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-somatic-variants/versions/somatic-variants-tutorial-workflow",
+                "tutorial_id": "somatic-variants",
+                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/somatic-variants/workflows/somatic_variants_tutorial_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/somatic-variants/workflows/somatic_variants_tutorial_workflow.html",
+                "version": 1,
+                "wfid": "variant-analysis-somatic-variants",
+                "wfname": "somatic-variants-tutorial-workflow",
+                "workflow": "somatic_variants_tutorial_workflow.ga",
                 "workflow_tools": [
-                    "Cut1",
-                    "Grep1",
-                    "param_value_from_file",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2"
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/varscan_somatic/varscan_somatic/2.4.3.6",
+                    "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5"
                 ],
-                "workflowhub_id": "1078"
+                "workflowhub_id": "1081"
             }
-        ]
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.2582555"
     },
     {
         "admin_install": {
@@ -285778,18 +293669,18 @@
         ],
         "dir": "topics/variant-analysis/tutorials/somatic-variant-discovery",
         "edam_operation": [
-            "Sequencing quality control",
-            "Genome alignment",
-            "Genome indexing",
+            "Copy number estimation",
             "Sequence alignment",
-            "Sequence composition calculation",
             "Sequence visualisation",
             "Read mapping",
+            "Sequencing quality control",
             "Generation",
-            "Copy number estimation",
-            "Validation",
             "Variant calling",
-            "Statistical calculation"
+            "Statistical calculation",
+            "Validation",
+            "Genome alignment",
+            "Sequence composition calculation",
+            "Genome indexing"
         ],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -285798,6 +293689,7 @@
         "hands_on": true,
         "id": "variant-analysis/somatic-variant-discovery",
         "inexact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.eu",
             "UseGalaxy.no",
@@ -285812,12 +293704,12 @@
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-26",
+        "mod_date": "2024-09-19",
         "objectives": [
             "Use Control-Freec for hCNV Identefication in tumor tissue.",
             "Visualise the detected hCNVs in specific chromosomes."
         ],
-        "pageviews": 1449,
+        "pageviews": 1535,
         "pub_date": "2022-10-05",
         "questions": [
             "What are the specific challenges in locating human Copy Number Variances (hCNVs)?",
@@ -285827,22 +293719,22 @@
         ],
         "short_id": "T00317",
         "short_tools": [
-            "Grep1",
-            "tp_text_file_with_recurring_lines",
-            "__BUILD_LIST__",
-            "multiqc",
-            "samtools_view",
-            "trimmomatic",
-            "samtools_calmd",
+            "bwa_mem",
+            "__EXTRACT_DATASET__",
             "circos",
+            "samtools_view",
             "samtools_rmdup",
-            "bamleftalign",
-            "fastqc",
-            "control_freec",
             "tp_replace_in_line",
             "__RELABEL_FROM_FILE__",
-            "bwa_mem",
-            "__EXTRACT_DATASET__"
+            "control_freec",
+            "multiqc",
+            "Grep1",
+            "__BUILD_LIST__",
+            "bamleftalign",
+            "tp_text_file_with_recurring_lines",
+            "fastqc",
+            "trimmomatic",
+            "samtools_calmd"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -285850,6 +293742,11 @@
         "supported_servers": {
             "exact": [],
             "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -285917,12 +293814,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/somatic-variant-discovery/tutorial.json"
         },
-        "version": 12,
+        "version": 13,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 126,
-        "visitors": 1095,
+        "visit_duration": 119,
+        "visitors": 1167,
         "workflows": [
             {
                 "creators": [
@@ -286112,7 +294009,7 @@
                 ],
                 "license": "AGPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nNormal_r1.fastq.gz\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nNormal_r2.fastq.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nTumor_r1.fastq.gz\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Create text file\"];\n  4[\"\u2139\ufe0f Input Dataset\\nTumor_r2.fastq.gz\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\ncapture_targets_chr5_12_17.bed\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"FastQC\"];\n  0 -->|output| 6;\n  7[\"Trimmomatic\"];\n  0 -->|output| 7;\n  1 -->|output| 7;\n  8[\"FastQC\"];\n  1 -->|output| 8;\n  9[\"FastQC\"];\n  2 -->|output| 9;\n  10[\"Trimmomatic\"];\n  2 -->|output| 10;\n  4 -->|output| 10;\n  11[\"FastQC\"];\n  4 -->|output| 11;\n  12[\"FastQC\"];\n  7 -->|fastq_out_r2_paired| 12;\n  13[\"Map with BWA-MEM\"];\n  7 -->|fastq_out_r1_paired| 13;\n  7 -->|fastq_out_r2_paired| 13;\n  14[\"FastQC\"];\n  7 -->|fastq_out_r1_paired| 14;\n  15[\"FastQC\"];\n  10 -->|fastq_out_r2_paired| 15;\n  16[\"Map with BWA-MEM\"];\n  10 -->|fastq_out_r1_paired| 16;\n  10 -->|fastq_out_r2_paired| 16;\n  17[\"FastQC\"];\n  10 -->|fastq_out_r1_paired| 17;\n  18[\"MultiQC\"];\n  9 -->|text_file| 18;\n  6 -->|text_file| 18;\n  8 -->|text_file| 18;\n  11 -->|text_file| 18;\n  19[\"Build list\"];\n  13 -->|bam_output| 19;\n  16 -->|bam_output| 19;\n  20[\"MultiQC\"];\n  12 -->|text_file| 20;\n  14 -->|text_file| 20;\n  15 -->|text_file| 20;\n  17 -->|text_file| 20;\n  21[\"Relabel identifiers\"];\n  3 -->|outfile| 21;\n  19 -->|output| 21;\n  22[\"Samtools view\"];\n  21 -->|output| 22;\n  23[\"RmDup\"];\n  22 -->|outputsam| 23;\n  24[\"BamLeftAlign\"];\n  23 -->|output1| 24;\n  25[\"Samtools calmd\"];\n  24 -->|output_bam| 25;\n  26[\"Samtools view\"];\n  25 -->|calmd_output| 26;\n  27[\"Samtools view\"];\n  25 -->|calmd_output| 27;\n  28[\"Select\"];\n  26 -->|outputsam| 28;\n  29[\"Replace Text\"];\n  28 -->|out_file1| 29;\n  30[\"Samtools view\"];\n  27 -->|outputsam| 30;\n  29 -->|outfile| 30;\n  31[\"Extract Tumor read\"];\n  30 -->|outputsam| 31;\n  32[\"Extract normal read\"];\n  30 -->|outputsam| 32;\n  33[\"Control-FREEC\"];\n  5 -->|output| 33;\n  32 -->|output| 33;\n  31 -->|output| 33;\n  2f4f45dd-d145-4078-aed9-5d832c51923b[\"Output\\nout_sample_info\"];\n  33 --> 2f4f45dd-d145-4078-aed9-5d832c51923b;\n  style 2f4f45dd-d145-4078-aed9-5d832c51923b stroke:#2c3143,stroke-width:4px;\n  13edcdd6-d7f6-4e0f-976e-1032084accf1[\"Output\\nout_sample_coord\"];\n  33 --> 13edcdd6-d7f6-4e0f-976e-1032084accf1;\n  style 13edcdd6-d7f6-4e0f-976e-1032084accf1 stroke:#2c3143,stroke-width:4px;\n  ac78da9a-8aa8-45ce-a2d1-3c366783fa60[\"Output\\nout_control_raw\"];\n  33 --> ac78da9a-8aa8-45ce-a2d1-3c366783fa60;\n  style ac78da9a-8aa8-45ce-a2d1-3c366783fa60 stroke:#2c3143,stroke-width:4px;\n  213ea0be-1ec6-469b-9556-69682bba69fe[\"Output\\nout_sample_raw\"];\n  33 --> 213ea0be-1ec6-469b-9556-69682bba69fe;\n  style 213ea0be-1ec6-469b-9556-69682bba69fe stroke:#2c3143,stroke-width:4px;\n  59a99e4f-01ef-4118-8777-63707e8b1696[\"Output\\nout_ratio_log2_circos\"];\n  33 --> 59a99e4f-01ef-4118-8777-63707e8b1696;\n  style 59a99e4f-01ef-4118-8777-63707e8b1696 stroke:#2c3143,stroke-width:4px;\n  75a0f2fc-e9a3-4537-8470-4c1efb5b7be5[\"Output\\nout_chr_sorted_circos\"];\n  33 --> 75a0f2fc-e9a3-4537-8470-4c1efb5b7be5;\n  style 75a0f2fc-e9a3-4537-8470-4c1efb5b7be5 stroke:#2c3143,stroke-width:4px;\n  662d214b-3d22-4f67-a4ef-a77b106d1535[\"Output\\nout_gc_profile\"];\n  33 --> 662d214b-3d22-4f67-a4ef-a77b106d1535;\n  style 662d214b-3d22-4f67-a4ef-a77b106d1535 stroke:#2c3143,stroke-width:4px;\n  02c14e20-cccd-4804-bbb6-13323afeda2e[\"Output\\nout_mg_log2_png\"];\n  33 --> 02c14e20-cccd-4804-bbb6-13323afeda2e;\n  style 02c14e20-cccd-4804-bbb6-13323afeda2e stroke:#2c3143,stroke-width:4px;\n  189dc4ef-a15f-49cc-9c6e-dff3dbd27ad7[\"Output\\nout_mg_png\"];\n  33 --> 189dc4ef-a15f-49cc-9c6e-dff3dbd27ad7;\n  style 189dc4ef-a15f-49cc-9c6e-dff3dbd27ad7 stroke:#2c3143,stroke-width:4px;\n  14aba5a4-1ade-477e-b937-7714038f3fd3[\"Output\\nout_sample_subclones\"];\n  33 --> 14aba5a4-1ade-477e-b937-7714038f3fd3;\n  style 14aba5a4-1ade-477e-b937-7714038f3fd3 stroke:#2c3143,stroke-width:4px;\n  61323e5f-7846-47e9-a0b3-d79f64ca2bd8[\"Output\\nout_sample_ratio\"];\n  33 --> 61323e5f-7846-47e9-a0b3-d79f64ca2bd8;\n  style 61323e5f-7846-47e9-a0b3-d79f64ca2bd8 stroke:#2c3143,stroke-width:4px;\n  34[\"Circos\"];\n  33 -->|out_chr_sorted_circos| 34;\n  33 -->|out_ratio_log2_circos| 34;\n  23ea7d87-b936-4879-bfaa-beb1e141834e[\"Output\\noutput_png\"];\n  34 --> 23ea7d87-b936-4879-bfaa-beb1e141834e;\n  style 23ea7d87-b936-4879-bfaa-beb1e141834e stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
+                "modified": "2024-10-02 12:08:11 +0000",
                 "name": "Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC",
                 "outputs": [
                     {
@@ -286247,815 +294144,105 @@
                                 "uuid": "189dc4ef-a15f-49cc-9c6e-dff3dbd27ad7"
                             },
                             {
-                                "label": "out_sample_subclones",
-                                "output_name": "out_sample_subclones",
-                                "uuid": "14aba5a4-1ade-477e-b937-7714038f3fd3"
-                            },
-                            {
-                                "label": "out_sample_ratio",
-                                "output_name": "out_sample_ratio",
-                                "uuid": "61323e5f-7846-47e9-a0b3-d79f64ca2bd8"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy9",
-                        "errors": null,
-                        "id": 34,
-                        "input_connections": {
-                            "reference_genome|ref|input_karyotype": {
-                                "id": 33,
-                                "output_name": "out_chr_sorted_circos"
-                            },
-                            "sec_tdd|data_0|plot_format|data_source": {
-                                "id": 33,
-                                "output_name": "out_ratio_log2_circos"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Circos",
-                        "outputs": [
-                            {
-                                "name": "output_png",
-                                "type": "png"
-                            }
-                        ],
-                        "position": {
-                            "left": 4219.874910965515,
-                            "top": 1517.9999724484023
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy9",
-                        "tool_shed_repository": {
-                            "changeset_revision": "31a35811dda6",
-                            "name": "circos",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/hg19.len\", \"ideogram\": {\"limit_chromosomes\": null, \"chromosomes_reverse\": null, \"units\": \"mb\", \"spacing\": \"3.0\", \"pairwise_spacing\": [], \"radius\": \"0.8\", \"thickness\": \"45.0\", \"angle_offset\": \"-90\", \"angle_orientation\": \"clockwise\", \"ideogram_labels\": {\"show_label\": true, \"radius_offset\": \"0.01\", \"size\": \"40\", \"parallel\": true}, \"bands\": {\"show_bands\": true, \"fill_bands\": true, \"band_transparency\": \"3\", \"band_stroke_thickness\": \"0\", \"band_stroke_color\": \"#000000\"}}, \"limits\": {\"max_ticks\": \"5000\", \"max_ideograms\": \"200\", \"max_links\": \"2500000\", \"max_points_per_track\": \"2500000\"}, \"outputs\": {\"png\": true, \"svg\": false, \"tar\": false}, \"plot_options\": {\"background\": {\"background_select\": \"color\", \"__current_case__\": 1, \"background_color\": \"#ffffff\"}, \"radius\": \"1500\", \"colour_profile\": null}, \"reference_genome\": {\"ref\": {\"ref_source\": \"karyotype\", \"__current_case__\": 3, \"input_karyotype\": {\"__class__\": \"ConnectedValue\"}}}, \"scaling\": {\"zooms\": []}, \"sec_links\": {\"data\": []}, \"sec_tdd\": {\"data\": [{\"__index__\": 0, \"r1\": \"0.95\", \"r0\": \"0.8\", \"zdepth\": \"0\", \"plot_format\": {\"plot_format_select\": \"scatter\", \"__current_case__\": 5, \"data_source\": {\"__class__\": \"ConnectedValue\"}, \"format_specific\": {\"glyph\": \"circle\", \"glyph_size\": \"4\", \"fill_color\": \"#919191\", \"fill_color_alpha\": \"1.0\", \"stroke_color\": \"#000000\", \"stroke_color_alpha\": \"1.0\", \"stroke_thickness\": \"0\"}}, \"orientation\": false, \"minsize\": \"0.0\", \"minmax\": {\"minmax_select\": \"no\", \"__current_case__\": 1}, \"sec_rule\": {\"rules\": [{\"__index__\": 0, \"conditions\": [{\"__index__\": 0, \"application\": {\"application_select\": \"value\", \"__current_case__\": 4, \"pos_gt\": \"0.0\", \"pos_lt\": null}}], \"actions\": [{\"__index__\": 0, \"action\": {\"action_select\": \"fill_color\", \"__current_case__\": 2, \"action_value\": \"#e41111\"}}], \"continue_flow\": false}, {\"__index__\": 1, \"conditions\": [{\"__index__\": 0, \"application\": {\"application_select\": \"value\", \"__current_case__\": 4, \"pos_gt\": null, \"pos_lt\": \"0.0\"}}], \"actions\": [{\"__index__\": 0, \"action\": {\"action_select\": \"fill_color\", \"__current_case__\": 2, \"action_value\": \"#3c19e6\"}}], \"continue_flow\": false}]}, \"sec_axes\": {\"axes\": [{\"__index__\": 0, \"radial_position\": {\"select\": \"data\", \"__current_case__\": 1, \"spacing\": \"1.0\"}, \"y0\": \"-4.0\", \"y1\": \"4.0\", \"color\": \"#bababa\", \"color_alpha\": \"1.0\", \"thickness\": \"2\"}], \"only_if_data\": \"always\"}, \"sec_bkgs\": {\"backgrounds\": [], \"only_if_data\": \"always\"}}]}, \"ticks\": {\"radius\": \"1.0\", \"skip_first_label\": false, \"skip_last_label\": false, \"tick_group\": []}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.69.8+galaxy9",
-                        "type": "tool",
-                        "uuid": "7f009ef4-16bc-40f2-a938-fc264f7bfcd6",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "output_png",
-                                "output_name": "output_png",
-                                "uuid": "23ea7d87-b936-4879-bfaa-beb1e141834e"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "variant-analysis/somatic-variant-discovery",
-                "path": "topics/variant-analysis/tutorials/somatic-variant-discovery/workflows/Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC.ga",
-                "tags": [
-                    "hCNV",
-                    "variant-analysis",
-                    "MIRACUM"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC",
-                "topic_id": "variant-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-somatic-variant-discovery/versions/somatic-variant-discovery-from-wes-data-using-control-freec",
-                "tutorial_id": "somatic-variant-discovery",
-                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/somatic-variant-discovery/workflows/Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/somatic-variant-discovery/workflows/Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC.html",
-                "version": 1,
-                "wfid": "variant-analysis-somatic-variant-discovery",
-                "wfname": "somatic-variant-discovery-from-wes-data-using-control-freec",
-                "workflow": "Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC.ga",
-                "workflow_tools": [
-                    "Grep1",
-                    "__BUILD_LIST__",
-                    "__EXTRACT_DATASET__",
-                    "__RELABEL_FROM_FILE__",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.3",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy9",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/control_freec/control_freec/11.6+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy0"
-                ],
-                "workflowhub_id": "1118"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.2582555"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "column_arrange_by_header",
-                    "owner": "bgruening",
-                    "revisions": "6c6d26ff01ff",
-                    "tool_panel_section_label": "Filter and Sort",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "0a8c6b61f0f4",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bamtools_filter",
-                    "owner": "devteam",
-                    "revisions": "cb20f99fd45b",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bwa",
-                    "owner": "devteam",
-                    "revisions": "3fe632431b68",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "e7b2202befea",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "freebayes",
-                    "owner": "devteam",
-                    "revisions": "57def2d7c093",
-                    "tool_panel_section_label": "Variant Calling",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_calmd",
-                    "owner": "devteam",
-                    "revisions": "06dc50b7b711",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_rmdup",
-                    "owner": "devteam",
-                    "revisions": "586f9e1cdb2b",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gemini_annotate",
-                    "owner": "iuc",
-                    "revisions": "cf0f0f05ba9f",
-                    "tool_panel_section_label": "Gemini",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gemini_load",
-                    "owner": "iuc",
-                    "revisions": "2270a8b83c12",
-                    "tool_panel_section_label": "Gemini",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "gemini_query",
-                    "owner": "iuc",
-                    "revisions": "da74170c55c7",
-                    "tool_panel_section_label": "Gemini",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "bf675f34b056",
-                    "tool_panel_section_label": "Quality Control",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "snpeff",
-                    "owner": "iuc",
-                    "revisions": "5c7b70713fb5",
-                    "tool_panel_section_label": "Variant Calling",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "varscan_somatic",
-                    "owner": "iuc",
-                    "revisions": "cf8ffc79db67",
-                    "tool_panel_section_label": "Variant Calling",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "trimmomatic",
-                    "owner": "pjbriggs",
-                    "revisions": "dfa082f84068",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: column_arrange_by_header\n  owner: bgruening\n  revisions: 6c6d26ff01ff\n  tool_panel_section_label: Filter and Sort\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 0a8c6b61f0f4\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_filter\n  owner: devteam\n  revisions: cb20f99fd45b\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: 3fe632431b68\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: e7b2202befea\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: freebayes\n  owner: devteam\n  revisions: 57def2d7c093\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_calmd\n  owner: devteam\n  revisions: 06dc50b7b711\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_rmdup\n  owner: devteam\n  revisions: 586f9e1cdb2b\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_annotate\n  owner: iuc\n  revisions: cf0f0f05ba9f\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_load\n  owner: iuc\n  revisions: 2270a8b83c12\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_query\n  owner: iuc\n  revisions: da74170c55c7\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: bf675f34b056\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n  owner: iuc\n  revisions: 5c7b70713fb5\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: varscan_somatic\n  owner: iuc\n  revisions: cf8ffc79db67\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n  owner: pjbriggs\n  revisions: dfa082f84068\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/somatic-variants/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "by-covid",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "fediverse": "https://scholar.social/@zerodivision",
-                "fediverse_flavor": "mastodon",
-                "id": "wm75",
-                "joined": "2017-09",
-                "matrix": "wm75:matrix.org",
-                "name": "Wolfgang Maier",
-                "orcid": "0000-0002-9464-6640",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
-            }
-        ],
-        "dir": "topics/variant-analysis/tutorials/somatic-variants",
-        "edam_operation": [
-            "Sequencing quality control",
-            "Genome indexing",
-            "Sequence alignment",
-            "Sequence composition calculation",
-            "Sequence alignment analysis",
-            "Read mapping",
-            "Generation",
-            "Data handling",
-            "Validation",
-            "Variant calling",
-            "Statistical calculation"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "variant-analysis/somatic-variants",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.fr"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Follow best practices for read mapping, quality control and mapped reads postprocessing to minimize false-positive variant calls.",
-            "Use a dedicated somatic variant caller to call variants and to classify them into somatic, germline and LOH event variants on statistical grounds.",
-            "Annotations and queries based on variant properties add relevance to variant and gene reports.",
-            "A framework like GEMINI is very helpful for managing, annotating and querying lists of variants in a flexible way.",
-            "Prefer public, free annotation sources to foster reproducibility and information sharing."
-        ],
-        "layout": "tutorial_hands_on",
-        "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
-        "objectives": [
-            "Call variants and their somatic status from whole-exome sequencing data",
-            "Annotate variants with a wealth of human genetic and cancer-specific information extracted from public databases",
-            "Add gene-level annotations and generate reports of annotated somatic and germline variants, loss-of-heterozygosity (LOH) events, and affected genes, ready for interpretation by clinicians"
-        ],
-        "pageviews": 21540,
-        "pub_date": "2019-03-13",
-        "questions": [
-            "What are the specific challenges in somatic variant calling that set it apart from regular diploid variant calling?",
-            "How can you call variants and classify them according to their presence/absence in/from tumor and normal tissue of the same individual?",
-            "How can you annotate variants and affected genes with prior knowledge from human genetic and cancer-specific databases to generate clinically relevant reports?"
-        ],
-        "short_id": "T00318",
-        "short_tools": [
-            "varscan_somatic",
-            "multiqc",
-            "gemini_load",
-            "trimmomatic",
-            "tp_easyjoin_tool",
-            "bamFilter",
-            "samtools_rmdup",
-            "bamleftalign",
-            "fastqc",
-            "bg_column_arrange_by_header",
-            "gemini_annotate",
-            "gemini_query",
-            "samtools_calmd",
-            "bwa_mem",
-            "snpEff"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "human-genetics-cancer",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "time_estimation": "7h",
-        "title": "Identification of somatic and germline variants from tumor and normal sample pairs",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/varscan_somatic/varscan_somatic/2.4.3.6",
-            "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5"
-        ],
-        "topic_name": "variant-analysis",
-        "topic_name_human": "Variant Analysis",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "somatic-variants",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/somatic-variants/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/somatic-variants/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/somatic-variants/tutorial.json"
-        },
-        "version": 15,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 11289,
-        "workflows": [
-            {
-                "creators": [],
-                "description": "Identification of somatic and germline variants from tumor and normal sample pairs tutorial",
-                "features": {
-                    "comments": false,
-                    "parameters": false,
-                    "report": null,
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSLGFSK-N_231335_r1_chr5_12_17.fastq\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSLGFSK-N_231335_r2_chr5_12_17.fastq\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSLGFSK-T_231336_r1_chr5_12_17.fastq\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSLGFSK-T_231336_r2_chr5_12_17.fastq\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhg19.chr5_12_17.fa\"]\n  5[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nhotspots.bed\"]\n  6[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncgi_variant_positions.bed\"]\n  7[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\n01-Feb-2019-CIVic.bed\"]\n  8[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ndbsnp.b147.chr5_12_17.vcf.gz\"]\n  9[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nUniprot_Cancer_Genes.13Feb2019.txt\"]\n  10[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ncgi_genes.txt\"]\n  11[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\n01-Feb-2019-GeneSummaries.tsv\"]\n  12[label=\"FastQC\"]\n  0 -> 12 [label=\"output\"]\n  13[label=\"FastQC\"]\n  1 -> 13 [label=\"output\"]\n  14[label=\"Trimmomatic\"]\n  0 -> 14 [label=\"output\"]\n  1 -> 14 [label=\"output\"]\n  15[label=\"FastQC\"]\n  2 -> 15 [label=\"output\"]\n  16[label=\"FastQC\"]\n  3 -> 16 [label=\"output\"]\n  17[label=\"Trimmomatic\"]\n  2 -> 17 [label=\"output\"]\n  3 -> 17 [label=\"output\"]\n  18[label=\"FastQC\"]\n  14 -> 18 [label=\"fastq_out_r2_paired\"]\n  19[label=\"FastQC\"]\n  14 -> 19 [label=\"fastq_out_r1_paired\"]\n  20[label=\"Map with BWA-MEM\"]\n  14 -> 20 [label=\"fastq_out_r1_paired\"]\n  14 -> 20 [label=\"fastq_out_r2_paired\"]\n  21[label=\"MultiQC\"]\n  13 -> 21 [label=\"text_file\"]\n  15 -> 21 [label=\"text_file\"]\n  16 -> 21 [label=\"text_file\"]\n  12 -> 21 [label=\"text_file\"]\n  22[label=\"FastQC\"]\n  17 -> 22 [label=\"fastq_out_r1_paired\"]\n  23[label=\"FastQC\"]\n  17 -> 23 [label=\"fastq_out_r2_paired\"]\n  24[label=\"Map with BWA-MEM\"]\n  17 -> 24 [label=\"fastq_out_r1_paired\"]\n  17 -> 24 [label=\"fastq_out_r2_paired\"]\n  25[label=\"Filter\"]\n  20 -> 25 [label=\"bam_output\"]\n  26[label=\"MultiQC\"]\n  19 -> 26 [label=\"text_file\"]\n  22 -> 26 [label=\"text_file\"]\n  23 -> 26 [label=\"text_file\"]\n  18 -> 26 [label=\"text_file\"]\n  27[label=\"Filter\"]\n  24 -> 27 [label=\"bam_output\"]\n  28[label=\"RmDup\"]\n  25 -> 28 [label=\"out_file1\"]\n  29[label=\"RmDup\"]\n  27 -> 29 [label=\"out_file1\"]\n  30[label=\"BamLeftAlign\"]\n  28 -> 30 [label=\"output1\"]\n  31[label=\"BamLeftAlign\"]\n  29 -> 31 [label=\"output1\"]\n  32[label=\"CalMD\"]\n  30 -> 32 [label=\"output_bam\"]\n  33[label=\"CalMD\"]\n  31 -> 33 [label=\"output_bam\"]\n  34[label=\"Filter\"]\n  32 -> 34 [label=\"calmd_output\"]\n  35[label=\"Filter\"]\n  33 -> 35 [label=\"calmd_output\"]\n  36[label=\"VarScan somatic\"]\n  34 -> 36 [label=\"out_file1\"]\n  35 -> 36 [label=\"out_file1\"]\n  37[label=\"SnpEff eff:\"]\n  36 -> 37 [label=\"output\"]\n  38[label=\"GEMINI load\"]\n  37 -> 38 [label=\"snpeff_output\"]\n  39[label=\"GEMINI annotate\"]\n  36 -> 39 [label=\"output\"]\n  38 -> 39 [label=\"outfile\"]\n  40[label=\"GEMINI annotate\"]\n  8 -> 40 [label=\"output\"]\n  39 -> 40 [label=\"outfile\"]\n  41[label=\"GEMINI annotate\"]\n  5 -> 41 [label=\"output\"]\n  40 -> 41 [label=\"outfile\"]\n  42[label=\"GEMINI annotate\"]\n  7 -> 42 [label=\"output\"]\n  41 -> 42 [label=\"outfile\"]\n  43[label=\"GEMINI annotate\"]\n  6 -> 43 [label=\"output\"]\n  42 -> 43 [label=\"outfile\"]\n  44[label=\"GEMINI query\"]\n  43 -> 44 [label=\"outfile\"]\n  45[label=\"GEMINI query\"]\n  43 -> 45 [label=\"outfile\"]\n  46[label=\"GEMINI query\"]\n  43 -> 46 [label=\"outfile\"]\n  47[label=\"GEMINI query\"]\n  43 -> 47 [label=\"outfile\"]\n  48[label=\"Join\"]\n  47 -> 48 [label=\"outfile\"]\n  9 -> 48 [label=\"output\"]\n  49[label=\"Join\"]\n  48 -> 49 [label=\"output\"]\n  10 -> 49 [label=\"output\"]\n  50[label=\"Join\"]\n  49 -> 50 [label=\"output\"]\n  11 -> 50 [label=\"output\"]\n  51[label=\"Column arrange\"]\n  50 -> 51 [label=\"output\"]\n  k0a9a947ea6c8480494ea779a1fc6a776[color=lightseagreen,label=\"Output\\ngene_report_output\"]\n  51 -> k0a9a947ea6c8480494ea779a1fc6a776\n}",
-                "history": [
-                    {
-                        "hash": "caffacad4879c005f2c65ec0fce10bca42df9576",
-                        "message": "Somatic variants tutorial updates (#2054)",
-                        "num": 1,
-                        "short_hash": "caffacad4",
-                        "unix": "1602363051"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "SLGFSK-N_231335_r1_chr5_12_17.fastq"
-                            }
-                        ],
-                        "label": "SLGFSK-N_231335_r1_chr5_12_17.fastq",
-                        "name": "SLGFSK-N_231335_r1_chr5_12_17.fastq",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 200
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"SLGFSK-N_231335_r1_chr5_12_17.fastq\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "42e41cea-0eef-4411-8d05-3497e4305454",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "SLGFSK-N_231335_r2_chr5_12_17.fastq"
-                            }
-                        ],
-                        "label": "SLGFSK-N_231335_r2_chr5_12_17.fastq",
-                        "name": "SLGFSK-N_231335_r2_chr5_12_17.fastq",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 320
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"SLGFSK-N_231335_r2_chr5_12_17.fastq\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "c01c6659-b9cd-4463-a845-4a27e4734509",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "SLGFSK-T_231336_r1_chr5_12_17.fastq"
-                            }
-                        ],
-                        "label": "SLGFSK-T_231336_r1_chr5_12_17.fastq",
-                        "name": "SLGFSK-T_231336_r1_chr5_12_17.fastq",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 440
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"SLGFSK-T_231336_r1_chr5_12_17.fastq\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "44387739-ebc5-4ca9-9274-ca568f6981be",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 3,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "SLGFSK-T_231336_r2_chr5_12_17.fastq"
-                            }
-                        ],
-                        "label": "SLGFSK-T_231336_r2_chr5_12_17.fastq",
-                        "name": "SLGFSK-T_231336_r2_chr5_12_17.fastq",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 560
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"SLGFSK-T_231336_r2_chr5_12_17.fastq\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "cd735b71-4735-4613-88c2-585e9ae752cd",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 4,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "hg19.chr5_12_17.fa"
-                            }
-                        ],
-                        "label": "hg19.chr5_12_17.fa",
-                        "name": "hg19.chr5_12_17.fa",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 680
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"hg19.chr5_12_17.fa\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "3c81dd70-5abd-4c35-ae8c-cd0f2e4936fa",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "hotspots.bed"
-                            }
-                        ],
-                        "label": "hotspots.bed",
-                        "name": "hotspots.bed",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 800
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"hotspots.bed\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "90dd17da-34a9-4ed4-a1a0-b1389a795f4c",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "cgi_variant_positions.bed"
-                            }
-                        ],
-                        "label": "cgi_variant_positions.bed",
-                        "name": "cgi_variant_positions.bed",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 920
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"cgi_variant_positions.bed\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "4392884e-1b45-4c29-94c5-39c2c9ec1fb6",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "01-Feb-2019-CIVic.bed"
-                            }
-                        ],
-                        "label": "01-Feb-2019-CIVic.bed",
-                        "name": "01-Feb-2019-CIVic.bed",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 1040
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"01-Feb-2019-CIVic.bed\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "06b14682-2e30-4b72-82ec-07c2f08bfe4e",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "dbsnp.b147.chr5_12_17.vcf.gz"
-                            }
-                        ],
-                        "label": "dbsnp.b147.chr5_12_17.vcf.gz",
-                        "name": "dbsnp.b147.chr5_12_17.vcf.gz",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 1160
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"dbsnp.b147.chr5_12_17.vcf.gz\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "ecbfe5d9-1585-488b-b47c-62f2927a47a7",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 9,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "Uniprot_Cancer_Genes.13Feb2019.txt"
-                            }
-                        ],
-                        "label": "Uniprot_Cancer_Genes.13Feb2019.txt",
-                        "name": "Uniprot_Cancer_Genes.13Feb2019.txt",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 1280
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"Uniprot_Cancer_Genes.13Feb2019.txt\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "27376556-09b4-4841-ae6b-daf27961cb26",
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 10,
-                        "input_connections": {},
-                        "inputs": [
+                                "label": "out_sample_subclones",
+                                "output_name": "out_sample_subclones",
+                                "uuid": "14aba5a4-1ade-477e-b937-7714038f3fd3"
+                            },
                             {
-                                "description": "",
-                                "name": "cgi_genes.txt"
+                                "label": "out_sample_ratio",
+                                "output_name": "out_sample_ratio",
+                                "uuid": "61323e5f-7846-47e9-a0b3-d79f64ca2bd8"
                             }
-                        ],
-                        "label": "cgi_genes.txt",
-                        "name": "cgi_genes.txt",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 1400
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"cgi_genes.txt\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "a1b1e2a4-d8a9-4b28-8438-d6cac706f9af",
-                        "workflow_outputs": []
+                        ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 11,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "01-Feb-2019-GeneSummaries.tsv"
-                            }
-                        ],
-                        "label": "01-Feb-2019-GeneSummaries.tsv",
-                        "name": "01-Feb-2019-GeneSummaries.tsv",
-                        "outputs": [],
-                        "position": {
-                            "left": 200,
-                            "top": 1520
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"01-Feb-2019-GeneSummaries.tsv\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "af690aec-8006-41ad-b05c-6c388d74ad97",
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSLGFSK-N_231335_r1_chr5_12_17.fastq\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSLGFSK-N_231335_r2_chr5_12_17.fastq\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nSLGFSK-T_231336_r1_chr5_12_17.fastq\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nSLGFSK-T_231336_r2_chr5_12_17.fastq\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nhg19.chr5_12_17.fa\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nhotspots.bed\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\ncgi_variant_positions.bed\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\n01-Feb-2019-CIVic.bed\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\ndbsnp.b147.chr5_12_17.vcf.gz\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"\u2139\ufe0f Input Dataset\\nUniprot_Cancer_Genes.13Feb2019.txt\"];\n  style 9 stroke:#2c3143,stroke-width:4px;\n  10[\"\u2139\ufe0f Input Dataset\\ncgi_genes.txt\"];\n  style 10 stroke:#2c3143,stroke-width:4px;\n  11[\"\u2139\ufe0f Input Dataset\\n01-Feb-2019-GeneSummaries.tsv\"];\n  style 11 stroke:#2c3143,stroke-width:4px;\n  12[\"FastQC\"];\n  0 -->|output| 12;\n  13[\"FastQC\"];\n  1 -->|output| 13;\n  14[\"Trimmomatic\"];\n  0 -->|output| 14;\n  1 -->|output| 14;\n  15[\"FastQC\"];\n  2 -->|output| 15;\n  16[\"FastQC\"];\n  3 -->|output| 16;\n  17[\"Trimmomatic\"];\n  2 -->|output| 17;\n  3 -->|output| 17;\n  18[\"FastQC\"];\n  14 -->|fastq_out_r2_paired| 18;\n  19[\"FastQC\"];\n  14 -->|fastq_out_r1_paired| 19;\n  20[\"Map with BWA-MEM\"];\n  14 -->|fastq_out_r1_paired| 20;\n  14 -->|fastq_out_r2_paired| 20;\n  21[\"MultiQC\"];\n  13 -->|text_file| 21;\n  15 -->|text_file| 21;\n  16 -->|text_file| 21;\n  12 -->|text_file| 21;\n  22[\"FastQC\"];\n  17 -->|fastq_out_r1_paired| 22;\n  23[\"FastQC\"];\n  17 -->|fastq_out_r2_paired| 23;\n  24[\"Map with BWA-MEM\"];\n  17 -->|fastq_out_r1_paired| 24;\n  17 -->|fastq_out_r2_paired| 24;\n  25[\"Filter\"];\n  20 -->|bam_output| 25;\n  26[\"MultiQC\"];\n  19 -->|text_file| 26;\n  22 -->|text_file| 26;\n  23 -->|text_file| 26;\n  18 -->|text_file| 26;\n  27[\"Filter\"];\n  24 -->|bam_output| 27;\n  28[\"RmDup\"];\n  25 -->|out_file1| 28;\n  29[\"RmDup\"];\n  27 -->|out_file1| 29;\n  30[\"BamLeftAlign\"];\n  28 -->|output1| 30;\n  31[\"BamLeftAlign\"];\n  29 -->|output1| 31;\n  32[\"CalMD\"];\n  30 -->|output_bam| 32;\n  33[\"CalMD\"];\n  31 -->|output_bam| 33;\n  34[\"Filter\"];\n  32 -->|calmd_output| 34;\n  35[\"Filter\"];\n  33 -->|calmd_output| 35;\n  36[\"VarScan somatic\"];\n  34 -->|out_file1| 36;\n  35 -->|out_file1| 36;\n  37[\"SnpEff eff:\"];\n  36 -->|output| 37;\n  38[\"GEMINI load\"];\n  37 -->|snpeff_output| 38;\n  39[\"GEMINI annotate\"];\n  36 -->|output| 39;\n  38 -->|outfile| 39;\n  40[\"GEMINI annotate\"];\n  8 -->|output| 40;\n  39 -->|outfile| 40;\n  41[\"GEMINI annotate\"];\n  5 -->|output| 41;\n  40 -->|outfile| 41;\n  42[\"GEMINI annotate\"];\n  7 -->|output| 42;\n  41 -->|outfile| 42;\n  43[\"GEMINI annotate\"];\n  6 -->|output| 43;\n  42 -->|outfile| 43;\n  44[\"GEMINI query\"];\n  43 -->|outfile| 44;\n  45[\"GEMINI query\"];\n  43 -->|outfile| 45;\n  46[\"GEMINI query\"];\n  43 -->|outfile| 46;\n  47[\"GEMINI query\"];\n  43 -->|outfile| 47;\n  48[\"Join\"];\n  47 -->|outfile| 48;\n  9 -->|output| 48;\n  49[\"Join\"];\n  48 -->|output| 49;\n  10 -->|output| 49;\n  50[\"Join\"];\n  49 -->|output| 50;\n  11 -->|output| 50;\n  51[\"Column arrange\"];\n  50 -->|output| 51;\n  0a9a947e-a6c8-4804-94ea-779a1fc6a776[\"Output\\ngene_report_output\"];\n  51 --> 0a9a947e-a6c8-4804-94ea-779a1fc6a776;\n  style 0a9a947e-a6c8-4804-94ea-779a1fc6a776 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "Identification of somatic and germline variants from tumor and normal sample pairs tutorial",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy9",
                         "errors": null,
-                        "id": 51,
+                        "id": 34,
                         "input_connections": {
-                            "param_input": {
-                                "id": 50,
-                                "output_name": "output"
+                            "reference_genome|ref|input_karyotype": {
+                                "id": 33,
+                                "output_name": "out_chr_sorted_circos"
+                            },
+                            "sec_tdd|data_0|plot_format|data_source": {
+                                "id": 33,
+                                "output_name": "out_ratio_log2_circos"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Column arrange",
+                        "name": "Circos",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "name": "output_png",
+                                "type": "png"
                             }
                         ],
                         "position": {
-                            "left": 4600,
-                            "top": 200
+                            "left": 4219.874910965515,
+                            "top": 1517.9999724484023
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy9",
                         "tool_shed_repository": {
-                            "changeset_revision": "6c6d26ff01ff",
-                            "name": "column_arrange_by_header",
-                            "owner": "bgruening",
+                            "changeset_revision": "31a35811dda6",
+                            "name": "circos",
+                            "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/hg19.len\", \"discard_remaining\": \"true\", \"param_input\": {\"__class__\": \"ConnectedValue\"}, \"rep_param_columns\": [{\"__index__\": 0, \"param_column\": \"gene\"}, {\"__index__\": 1, \"param_column\": \"chrom\"}, {\"__index__\": 2, \"param_column\": \"synonym\"}, {\"__index__\": 3, \"param_column\": \"hgnc_id\"}, {\"__index__\": 4, \"param_column\": \"entrez_id\"}, {\"__index__\": 5, \"param_column\": \"rvis_pct\"}, {\"__index__\": 6, \"param_column\": \"is_OG\"}, {\"__index__\": 7, \"param_column\": \"is_TS\"}, {\"__index__\": 8, \"param_column\": \"in_cgi_biomarkers\"}, {\"__index__\": 9, \"param_column\": \"clinvar_gene_phenotype\"}, {\"__index__\": 10, \"param_column\": \"gene_civic_url\"}, {\"__index__\": 11, \"param_column\": \"description\"}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.2",
+                        "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/hg19.len\", \"ideogram\": {\"limit_chromosomes\": null, \"chromosomes_reverse\": null, \"units\": \"mb\", \"spacing\": \"3.0\", \"pairwise_spacing\": [], \"radius\": \"0.8\", \"thickness\": \"45.0\", \"angle_offset\": \"-90\", \"angle_orientation\": \"clockwise\", \"ideogram_labels\": {\"show_label\": true, \"radius_offset\": \"0.01\", \"size\": \"40\", \"parallel\": true}, \"bands\": {\"show_bands\": true, \"fill_bands\": true, \"band_transparency\": \"3\", \"band_stroke_thickness\": \"0\", \"band_stroke_color\": \"#000000\"}}, \"limits\": {\"max_ticks\": \"5000\", \"max_ideograms\": \"200\", \"max_links\": \"2500000\", \"max_points_per_track\": \"2500000\"}, \"outputs\": {\"png\": true, \"svg\": false, \"tar\": false}, \"plot_options\": {\"background\": {\"background_select\": \"color\", \"__current_case__\": 1, \"background_color\": \"#ffffff\"}, \"radius\": \"1500\", \"colour_profile\": null}, \"reference_genome\": {\"ref\": {\"ref_source\": \"karyotype\", \"__current_case__\": 3, \"input_karyotype\": {\"__class__\": \"ConnectedValue\"}}}, \"scaling\": {\"zooms\": []}, \"sec_links\": {\"data\": []}, \"sec_tdd\": {\"data\": [{\"__index__\": 0, \"r1\": \"0.95\", \"r0\": \"0.8\", \"zdepth\": \"0\", \"plot_format\": {\"plot_format_select\": \"scatter\", \"__current_case__\": 5, \"data_source\": {\"__class__\": \"ConnectedValue\"}, \"format_specific\": {\"glyph\": \"circle\", \"glyph_size\": \"4\", \"fill_color\": \"#919191\", \"fill_color_alpha\": \"1.0\", \"stroke_color\": \"#000000\", \"stroke_color_alpha\": \"1.0\", \"stroke_thickness\": \"0\"}}, \"orientation\": false, \"minsize\": \"0.0\", \"minmax\": {\"minmax_select\": \"no\", \"__current_case__\": 1}, \"sec_rule\": {\"rules\": [{\"__index__\": 0, \"conditions\": [{\"__index__\": 0, \"application\": {\"application_select\": \"value\", \"__current_case__\": 4, \"pos_gt\": \"0.0\", \"pos_lt\": null}}], \"actions\": [{\"__index__\": 0, \"action\": {\"action_select\": \"fill_color\", \"__current_case__\": 2, \"action_value\": \"#e41111\"}}], \"continue_flow\": false}, {\"__index__\": 1, \"conditions\": [{\"__index__\": 0, \"application\": {\"application_select\": \"value\", \"__current_case__\": 4, \"pos_gt\": null, \"pos_lt\": \"0.0\"}}], \"actions\": [{\"__index__\": 0, \"action\": {\"action_select\": \"fill_color\", \"__current_case__\": 2, \"action_value\": \"#3c19e6\"}}], \"continue_flow\": false}]}, \"sec_axes\": {\"axes\": [{\"__index__\": 0, \"radial_position\": {\"select\": \"data\", \"__current_case__\": 1, \"spacing\": \"1.0\"}, \"y0\": \"-4.0\", \"y1\": \"4.0\", \"color\": \"#bababa\", \"color_alpha\": \"1.0\", \"thickness\": \"2\"}], \"only_if_data\": \"always\"}, \"sec_bkgs\": {\"backgrounds\": [], \"only_if_data\": \"always\"}}]}, \"ticks\": {\"radius\": \"1.0\", \"skip_first_label\": false, \"skip_last_label\": false, \"tick_group\": []}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.69.8+galaxy9",
                         "type": "tool",
-                        "uuid": "96059b98-f7dd-4ce0-9000-7eea6282f629",
+                        "uuid": "7f009ef4-16bc-40f2-a938-fc264f7bfcd6",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "gene_report_output",
-                                "output_name": "output",
-                                "uuid": "0a9a947e-a6c8-4804-94ea-779a1fc6a776"
+                                "label": "output_png",
+                                "output_name": "output_png",
+                                "uuid": "23ea7d87-b936-4879-bfaa-beb1e141834e"
                             }
                         ]
                     }
                 ],
-                "parent_id": "variant-analysis/somatic-variants",
-                "path": "topics/variant-analysis/tutorials/somatic-variants/workflows/somatic_variants_tutorial_workflow.ga",
+                "parent_id": "variant-analysis/somatic-variant-discovery",
+                "path": "topics/variant-analysis/tutorials/somatic-variant-discovery/workflows/Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC.ga",
                 "tags": [
-                    "variant-analysis"
+                    "hCNV",
+                    "variant-analysis",
+                    "MIRACUM"
                 ],
                 "test_results": null,
                 "tests": true,
-                "title": "Identification of somatic and germline variants from tumor and normal sample pairs tutorial",
+                "title": "Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC",
                 "topic_id": "variant-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-somatic-variants/versions/somatic-variants-tutorial-workflow",
-                "tutorial_id": "somatic-variants",
-                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/somatic-variants/workflows/somatic_variants_tutorial_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/somatic-variants/workflows/somatic_variants_tutorial_workflow.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-somatic-variant-discovery/versions/somatic-variant-discovery-from-wes-data-using-control-freec",
+                "tutorial_id": "somatic-variant-discovery",
+                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/somatic-variant-discovery/workflows/Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/somatic-variant-discovery/workflows/Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC.html",
                 "version": 1,
-                "wfid": "variant-analysis-somatic-variants",
-                "wfname": "somatic-variants-tutorial-workflow",
-                "workflow": "somatic_variants_tutorial_workflow.ga",
+                "wfid": "variant-analysis-somatic-variant-discovery",
+                "wfname": "somatic-variant-discovery-from-wes-data-using-control-freec",
+                "workflow": "Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2",
+                    "Grep1",
+                    "__BUILD_LIST__",
+                    "__EXTRACT_DATASET__",
+                    "__RELABEL_FROM_FILE__",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.3",
                     "toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/varscan_somatic/varscan_somatic/2.4.3.6",
-                    "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy9",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/control_freec/control_freec/11.6+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy0"
                 ],
-                "workflowhub_id": "1081"
+                "workflowhub_id": "1118"
             }
         ],
         "zenodo_link": "https://doi.org/10.5281/zenodo.2582555"
@@ -287074,136 +294261,77 @@
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "bwa",
-                    "owner": "devteam",
-                    "revisions": "3fe632431b68",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "picard",
-                    "owner": "devteam",
-                    "revisions": "a1f0b3f4b781",
-                    "tool_panel_section_label": "Picard",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_stats",
-                    "owner": "devteam",
-                    "revisions": "145f6d74ff5e",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastp",
-                    "owner": "iuc",
-                    "revisions": "dbf9c561ef29",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "lofreq_call",
-                    "owner": "iuc",
-                    "revisions": "65432c3abf6c",
-                    "tool_panel_section_label": "Variant Calling",
+                    "name": "regex_find_replace",
+                    "owner": "galaxyp",
+                    "revisions": "ae8c4b2488e7",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "lofreq_indelqual",
+                    "name": "bcftools_merge",
                     "owner": "iuc",
-                    "revisions": "426d707dfc47",
+                    "revisions": "86296490704e",
                     "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "lofreq_viterbi",
+                    "name": "bcftools_norm",
                     "owner": "iuc",
-                    "revisions": "aa35ee7f3ab2",
+                    "revisions": "da6fc9f4a367",
                     "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "multiqc",
+                    "name": "ega_download_client",
                     "owner": "iuc",
-                    "revisions": "bf675f34b056",
-                    "tool_panel_section_label": "Quality Control",
+                    "revisions": "7d87a9d58aa1",
+                    "tool_panel_section_label": "Get Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "snpeff_sars_cov_2",
+                    "name": "gemini_inheritance",
                     "owner": "iuc",
-                    "revisions": "2a3a00c1fa0a",
-                    "tool_panel_section_label": "Variant Calling",
+                    "revisions": "2c68e29c3527",
+                    "tool_panel_section_label": "Gemini",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "snpsift",
+                    "name": "gemini_load",
                     "owner": "iuc",
-                    "revisions": "5fab4f81391d",
-                    "tool_panel_section_label": "Variant Calling",
+                    "revisions": "2270a8b83c12",
+                    "tool_panel_section_label": "Gemini",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sra_tools",
+                    "name": "geneiobio",
                     "owner": "iuc",
-                    "revisions": "494b2ec08162",
-                    "tool_panel_section_label": "Get Data",
+                    "revisions": "c0af7b196a89",
+                    "tool_panel_section_label": "Graph/Display Data",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "sra_tools",
+                    "name": "snpeff",
                     "owner": "iuc",
-                    "revisions": "4df8de2d0e48",
-                    "tool_panel_section_label": "Get Data",
+                    "revisions": "5c7b70713fb5",
+                    "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: 3fe632431b68\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: picard\n  owner: devteam\n  revisions: a1f0b3f4b781\n  tool_panel_section_label: Picard\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 145f6d74ff5e\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: dbf9c561ef29\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lofreq_call\n  owner: iuc\n  revisions: 65432c3abf6c\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lofreq_indelqual\n  owner: iuc\n  revisions: 426d707dfc47\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: lofreq_viterbi\n  owner: iuc\n  revisions: aa35ee7f3ab2\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: bf675f34b056\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff_sars_cov_2\n  owner: iuc\n  revisions: 2a3a00c1fa0a\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpsift\n  owner: iuc\n  revisions: 5fab4f81391d\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: 494b2ec08162\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: sra_tools\n  owner: iuc\n  revisions: 4df8de2d0e48\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "mvdbeek",
-                "tnabtaf",
-                "blankenberg",
-                "nekrut"
-            ],
-            "editing": [
-                "wm75"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: regex_find_replace\n  owner: galaxyp\n  revisions: ae8c4b2488e7\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_merge\n  owner: iuc\n  revisions: 86296490704e\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_norm\n  owner: iuc\n  revisions: da6fc9f4a367\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ega_download_client\n  owner: iuc\n  revisions: 7d87a9d58aa1\n  tool_panel_section_label: Get Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_inheritance\n  owner: iuc\n  revisions: 2c68e29c3527\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_load\n  owner: iuc\n  revisions: 2270a8b83c12\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: geneiobio\n  owner: iuc\n  revisions: c0af7b196a89\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n  owner: iuc\n  revisions: 5c7b70713fb5\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/trio-analysis/tutorial.json",
         "contributors": [
             {
-                "id": "mvdbeek",
-                "joined": "2018-06",
-                "name": "Marius van den Beek",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/mvdbeek/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/mvdbeek.json"
-            },
-            {
-                "id": "tnabtaf",
-                "joined": "2017-09",
-                "name": "Dave Clements",
-                "orcid": "0000-0002-9970-6657",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tnabtaf/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/tnabtaf.json"
-            },
-            {
-                "id": "blankenberg",
-                "joined": "2018-07",
-                "name": "Daniel Blankenberg",
-                "orcid": "0000-0002-6833-9049",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/blankenberg/",
-                "twitter": "dblankenberg",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/blankenberg.json"
-            },
-            {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
-                "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "nl",
+                "email": "j.ouwerkerk.1@erasmusmc.nl",
+                "id": "JasperO98",
+                "joined": "2022-04",
+                "name": "Jasper Ouwerkerk",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/JasperO98/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/JasperO98.json"
             },
             {
                 "affiliations": [
@@ -287221,34 +294349,82 @@
                 "orcid": "0000-0002-9464-6640",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "affiliations": [
+                    "CINECA-Project",
+                    "gallantries",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "uni-freiburg"
+                ],
+                "bio": "Researcher at Erasmus Medical Center",
+                "bluesky": "shiltemann.bsky.social",
+                "contact_for_training": true,
+                "elixir_node": "nl",
+                "email": "saskia.hiltemann@gmail.com",
+                "fediverse": "https://mstdn.science/@shiltemann",
+                "fediverse_flavor": "mastodon",
+                "id": "shiltemann",
+                "joined": "2017-09",
+                "linkedin": "shiltemann",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.912,
+                    "lon": 4.462
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "shiltemann:matrix.org",
+                "name": "Saskia Hiltemann",
+                "orcid": "0000-0003-3803-468X",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
             }
         ],
-        "dir": "topics/variant-analysis/tutorials/sars-cov-2",
+        "dir": "topics/variant-analysis/tutorials/trio-analysis",
         "edam_operation": [
-            "Sequencing quality control",
-            "Sequence contamination filtering",
-            "Genome indexing",
-            "SNP detection",
-            "Sequence alignment",
-            "Formatting",
-            "Read mapping",
-            "Generation",
-            "Data handling",
-            "Validation"
+            "Genetic variation analysis",
+            "Sequence analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "variant-analysis/sars-cov-2",
+        "id": "variant-analysis/trio-analysis",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
             "UseGalaxy.org.au"
         ],
         "js_requirements": {
@@ -287256,71 +294432,64 @@
             "mermaid": false
         },
         "key_points": [
-            "Sequence data in the SRA can be directly imported into Galaxy",
-            "Collections enable efficient/parallel processing of sequence data from whole batches of samples",
-            "Genomic mutations in SARS-CoV-2 viral isolates can be identified through a straightforward pipeline involving sequenced reads preprocessing, mapping to the SARS-CoV-2 reference genome, postprocessing of mapping results, and variant calling"
+            "Downloading whole datasets with HTSGET is safe and easy with Galaxy.",
+            "Regex is a usefull tool for pre-processing VCF files.",
+            "Variant annotations allows us to strictly filter VCFs to find the causative variant."
         ],
         "layout": "tutorial_hands_on",
+        "level": "Advanced",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-09-17",
         "objectives": [
-            "Understand how Galaxy and the Sequence Read Archive interact",
-            "Be able to go from Galaxy to the Short Reach Archive, query SRA, use the SRA Run Selector to send selected metadata to Galaxy, and then import sequence data from SRA into Galaxy",
-            "Understand how collections enable processing of sequencing data in batches",
-            "Understand the analysis steps required to identify and annotate genomic mutations from sequencing data of SARS-CoV-2 samples"
+            "Requesting DAC access and importing data from the EGA.",
+            "Pre-process VCFs using regular expressions.",
+            "Use annotations and phenotype information to find the causative variant(s)."
         ],
-        "pageviews": 18450,
-        "pub_date": "2020-06-24",
+        "pageviews": 2787,
+        "pub_date": "2022-05-19",
         "questions": [
-            "How can you download public sequencing data deposited in the NCBI Sequence Read Archive (SRA) into a Galaxy history for analysis?",
-            "How can you process a batch of sequencing data from several samples efficiently/in parallel with Galaxy?",
-            "Starting from raw sequenced reads of whole-genome sequenced samples of SARS-CoV-2, how can you identify mutations in the genomes of these samples?"
+            "How do you import data from the EGA?",
+            "How to download files with HTSGET in Galaxy?",
+            "How do you pre-process VCFs?",
+            "How do you identify causative variants?"
         ],
         "recordings": [
             {
                 "captioners": [
-                    "nekrut"
+                    "JasperO98"
                 ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "15M",
+                "date": "2023-05-12",
+                "length": "40M",
                 "speakers": [
-                    "nekrut"
+                    "JasperO98"
                 ],
-                "youtube_id": "9mIL0tIfZ_o"
+                "youtube_id": "3OWXWOkJRqU"
             }
         ],
-        "short_id": "T00315",
+        "short_id": "T00320",
         "short_tools": [
-            "Grep1",
-            "picard_MarkDuplicates",
-            "samtools_stats",
-            "fastp",
-            "multiqc",
-            "tp_cut_tool",
-            "fasterq_dump",
-            "snpSift_extractFields",
+            "CONVERTER_uncompressed_to_gz",
             "Filter1",
-            "lofreq_call",
-            "lofreq_indelqual",
-            "lofreq_viterbi",
-            "bwa_mem",
-            "snpeff_sars_cov_2"
+            "gemini_load",
+            "pyega3",
+            "tp_grep_tool",
+            "bcftools_merge",
+            "gene_iobio_display_generation_iframe",
+            "gemini_inheritance",
+            "regexColumn1",
+            "CONVERTER_gz_to_uncompressed",
+            "snpEff",
+            "bcftools_norm"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "one-health",
+        "subtopic": "human-genetics-cancer",
         "supported_servers": {
             "exact": [
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
                 }
             ],
             "inexact": [
@@ -287329,16 +294498,6 @@
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
@@ -287348,28 +294507,23 @@
         },
         "symlink": null,
         "tags": [
-            "covid19",
-            "virology",
-            "one-health"
+            "cyoa"
         ],
-        "time_estimation": "1H",
-        "title": "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis",
+        "time_estimation": "2H",
+        "title": "Trio Analysis using Synthetic Datasets from RD-Connect GPAP",
         "tools": [
+            "CONVERTER_gz_to_uncompressed",
+            "CONVERTER_uncompressed_to_gz",
             "Filter1",
-            "Grep1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.3+galaxy0"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/geneiobio/gene_iobio_display_generation_iframe/4.7.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1"
         ],
         "topic_name": "variant-analysis",
         "topic_name_human": "Variant Analysis",
@@ -287379,358 +294533,631 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "sars-cov-2",
+        "tutorial_name": "trio-analysis",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/sars-cov-2/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/trio-analysis/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/trio-analysis/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/trio-analysis/tutorial.json"
         },
-        "version": 16,
+        "version": 13,
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 175,
-        "visitors": 12116,
+        "visit_duration": 242,
+        "visitors": 1424,
         "workflows": [
             {
-                "creators": [],
-                "description": "Analysis of variation within individual COVID-19 samples (Paired End Illumina). Does not use paured",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "0000-0003-2556-2125",
+                        "name": "Jasper Ouwerkerk"
+                    }
+                ],
+                "description": "Trio Analysis using Synthetic Datasets from RD-Connect GPAP",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nNC_045512.2 fasta file\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nSRA Manifest\"]\n  2[label=\"Faster Download and Extract Reads in FASTQ\"]\n  1 -> 2 [label=\"output\"]\n  3[label=\"fastp\"]\n  2 -> 3 [label=\"list_paired\"]\n  4[label=\"Map with BWA-MEM\"]\n  3 -> 4 [label=\"output_paired_coll\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"MarkDuplicates\"]\n  4 -> 5 [label=\"bam_output\"]\n  6[label=\"Realign reads\"]\n  5 -> 6 [label=\"outFile\"]\n  0 -> 6 [label=\"output\"]\n  7[label=\"Samtools stats\"]\n  5 -> 7 [label=\"outFile\"]\n  8[label=\"Insert indel qualities\"]\n  6 -> 8 [label=\"realigned\"]\n  0 -> 8 [label=\"output\"]\n  k2ca7c89b999f41dc8037e54e25959a7e[color=lightseagreen,label=\"Output\\nRealigned Alignments with Indel Qualities\"]\n  8 -> k2ca7c89b999f41dc8037e54e25959a7e\n  9[label=\"Call variants\"]\n  8 -> 9 [label=\"output\"]\n  0 -> 9 [label=\"output\"]\n  10[label=\"SnpEff eff:\"]\n  9 -> 10 [label=\"variants\"]\n  11[label=\"SnpSift Extract Fields\"]\n  10 -> 11 [label=\"snpeff_output\"]\n  k06259137eaa5404a923c70ee5f1d89d4[color=lightseagreen,label=\"Output\\nSnpSift tabular output\"]\n  11 -> k06259137eaa5404a923c70ee5f1d89d4\n  12[label=\"MultiQC\"]\n  3 -> 12 [label=\"report_json\"]\n  7 -> 12 [label=\"output\"]\n  5 -> 12 [label=\"metrics_file\"]\n  10 -> 12 [label=\"csvFile\"]\n  k758ffde57ddd482a88b21504f8335488[color=lightseagreen,label=\"Output\\nMultiQC Report PE\"]\n  12 -> k758ffde57ddd482a88b21504f8335488\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[label=\"EGA Download Client\"]\n  k85672f3a155649b6be092e6c81721fb3[color=lightseagreen,label=\"Output\\nEGA Download Client: authorized datasets\"]\n  0 -> k85672f3a155649b6be092e6c81721fb3\n  1[label=\"EGA Download Client\"]\n  kacd2bcf04b9d47439034716e73d4824f[color=lightseagreen,label=\"Output\\nList of files in EGAD00001008392\"]\n  1 -> kacd2bcf04b9d47439034716e73d4824f\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\npedigree\"]\n  3[label=\"Search in textfiles\"]\n  1 -> 3 [label=\"dataset_file_list\"]\n  k6d5d135ea37349389374019a09f45a51[color=lightseagreen,label=\"Output\\nList of Case 5 VCFs\"]\n  3 -> k6d5d135ea37349389374019a09f45a51\n  4[label=\"EGA Download Client\"]\n  3 -> 4 [label=\"output\"]\n  kbdce7169390b4adb93055550d5d70a73[color=lightseagreen,label=\"Output\\nCase 5 VCFs.gz\"]\n  4 -> kbdce7169390b4adb93055550d5d70a73\n  5[label=\"Convert compressed file to uncompressed.\"]\n  4 -> 5 [label=\"downloaded_file_collection\"]\n  k82b71cdcd8134c778ff3fa59e1725709[color=lightseagreen,label=\"Output\\nCase 5 VCFs\"]\n  5 -> k82b71cdcd8134c778ff3fa59e1725709\n  6[label=\"Column Regex Find And Replace\"]\n  5 -> 6 [label=\"output1\"]\n  k5e1ff158cf8a4dc89c22b987a9f5ac27[color=lightseagreen,label=\"Output\\nCase 5 VCFs (Fixed Header and Chr)\"]\n  6 -> k5e1ff158cf8a4dc89c22b987a9f5ac27\n  7[label=\"bcftools norm\"]\n  6 -> 7 [label=\"out_file1\"]\n  k96b34c8dfa9248cbb01fc05364deba5d[color=lightseagreen,label=\"Output\\nCase 5 Normalized VCFs\"]\n  7 -> k96b34c8dfa9248cbb01fc05364deba5d\n  8[label=\"Filter\"]\n  7 -> 8 [label=\"output_file\"]\n  ka8539eb98bc3473ba27f201c3acf5539[color=lightseagreen,label=\"Output\\nCase 5 Normalized VCFs (Removed <NON_REF>)\"]\n  8 -> ka8539eb98bc3473ba27f201c3acf5539\n  9[label=\"bcftools merge\"]\n  8 -> 9 [label=\"out_file1\"]\n  kb5c479b2e58a4fe2b1cffc64476c8192[color=lightseagreen,label=\"Output\\nCase 5 Merged VCF\"]\n  9 -> kb5c479b2e58a4fe2b1cffc64476c8192\n  10[label=\"SnpEff eff:\"]\n  9 -> 10 [label=\"output_file\"]\n  kcd7b49414f4c46318ad53411e60fbbd9[color=lightseagreen,label=\"Output\\nCase 5 SnpEff Annotated vcf\"]\n  10 -> kcd7b49414f4c46318ad53411e60fbbd9\n  11[label=\"Convert uncompressed file to compressed\"]\n  10 -> 11 [label=\"snpeff_output\"]\n  k6e5e1084b5e14daf8f3bbd3868a52a25[color=lightseagreen,label=\"Output\\nSnpEff Annotated vcf_bgzip\"]\n  11 -> k6e5e1084b5e14daf8f3bbd3868a52a25\n  12[label=\"gene.iobio visualisation\"]\n  11 -> 12 [label=\"output1\"]\n  11 -> 12 [label=\"output1\"]\n  11 -> 12 [label=\"output1\"]\n  k0b30f4e0732844798a56bbf828fcfdba[color=lightseagreen,label=\"Output\\nCase 5 gene.iobio results\"]\n  12 -> k0b30f4e0732844798a56bbf828fcfdba\n  13[label=\"Case 5 GEMINI Database\"]\n  11 -> 13 [label=\"output1\"]\n  2 -> 13 [label=\"output\"]\n  k8a1964d9607c4dd3a2dc0f9a68dbb681[color=lightseagreen,label=\"Output\\nGEMINI Database\"]\n  13 -> k8a1964d9607c4dd3a2dc0f9a68dbb681\n  14[label=\"Case 5 GEMINI Inheritance pattern\"]\n  13 -> 14 [label=\"outfile\"]\n  k960ef978089c429281b5731965c72a0d[color=lightseagreen,label=\"Output\\nCase 5 GEMINI results\"]\n  14 -> k960ef978089c429281b5731965c72a0d\n}",
                 "history": [
                     {
-                        "hash": "18338ab9a1ef29b46dc8f2e8a7f7a4b055f16e3d",
-                        "message": "Use correct fasterqdump version",
+                        "hash": "9623387f047fbfa77afe213505d4328e84075023",
+                        "message": "Add gene.iobio",
+                        "num": 22,
+                        "short_hash": "9623387f0",
+                        "unix": "1689082264"
+                    },
+                    {
+                        "hash": "c7df034841bfa97e3bae35a0fc124ce37d77ab9a",
+                        "message": "Add gene.iobio to workflow",
+                        "num": 21,
+                        "short_hash": "c7df03484",
+                        "unix": "1688999139"
+                    },
+                    {
+                        "hash": "a133ddbaf3b94a0da4f645047d9e48562bbff274",
+                        "message": "Add EGA download client authorized dataset",
+                        "num": 20,
+                        "short_hash": "a133ddbaf",
+                        "unix": "1684243281"
+                    },
+                    {
+                        "hash": "89798a1513ae26d2802470e9be2ce286a36e4ecf",
+                        "message": "Update PyEGA version in main_workflow.ga",
+                        "num": 19,
+                        "short_hash": "89798a151",
+                        "unix": "1684243121"
+                    },
+                    {
+                        "hash": "890e3ed491c20efb1e20c846851b29bf8af689e0",
+                        "message": "add orcid",
+                        "num": 18,
+                        "short_hash": "890e3ed49",
+                        "unix": "1679655504"
+                    },
+                    {
+                        "hash": "d20983843449c103e35d458f6988096ad6c1e4e1",
+                        "message": "fix reator and workflow_output labels",
+                        "num": 17,
+                        "short_hash": "d20983843",
+                        "unix": "1679655099"
+                    },
+                    {
+                        "hash": "588e52155ae2c1e3cf2a5fb1c53a9cb9dd552880",
+                        "message": "now really add license",
+                        "num": 16,
+                        "short_hash": "588e52155",
+                        "unix": "1679415213"
+                    },
+                    {
+                        "hash": "cdfd52652e3656e2f51226e181f5fd24dd00f115",
+                        "message": "properly add license",
+                        "num": 15,
+                        "short_hash": "cdfd52652",
+                        "unix": "1679414902"
+                    },
+                    {
+                        "hash": "49bda25d3f12d6589c3ab4b831d99a65ddd888ec",
+                        "message": "rename workflow",
+                        "num": 14,
+                        "short_hash": "49bda25d3",
+                        "unix": "1679414277"
+                    },
+                    {
+                        "hash": "79e4f95acbef417531b4d67eb2e860236a86eeb8",
+                        "message": "add test",
+                        "num": 13,
+                        "short_hash": "79e4f95ac",
+                        "unix": "1679414214"
+                    },
+                    {
+                        "hash": "9ba85fb0a7f7257bb6c27a9c8cc549552ba77f05",
+                        "message": "update PyEGA version & add creator/license",
+                        "num": 12,
+                        "short_hash": "9ba85fb0a",
+                        "unix": "1679413554"
+                    },
+                    {
+                        "hash": "b79cc70eadad03fe5c5b031e79e72e757f3a48a2",
+                        "message": "Update workflow with nice labels",
+                        "num": 11,
+                        "short_hash": "b79cc70ea",
+                        "unix": "1677684691"
+                    },
+                    {
+                        "hash": "4ed74364ae051c7deab6b239091eae03c1355177",
+                        "message": "Update workflow (<NON_REF> skip header)",
+                        "num": 10,
+                        "short_hash": "4ed74364a",
+                        "unix": "1652186595"
+                    },
+                    {
+                        "hash": "2726695af3b5bfe98b1a2906c1d5a330758c1fb2",
+                        "message": "add annotation and tag to workflow",
+                        "num": 9,
+                        "short_hash": "2726695af",
+                        "unix": "1651586250"
+                    },
+                    {
+                        "hash": "0816782f5e10f9b06a6fd96dccc51acca59bd54f",
+                        "message": "Update prefix pattern",
+                        "num": 8,
+                        "short_hash": "0816782f5",
+                        "unix": "1651568447"
+                    },
+                    {
+                        "hash": "4cb441ff692dad48e6e2b2e1ea5bd6883e905c69",
+                        "message": "Move decompress step",
                         "num": 7,
-                        "short_hash": "18338ab9a",
-                        "unix": "1593005231"
+                        "short_hash": "4cb441ff6",
+                        "unix": "1651564709"
                     },
                     {
-                        "hash": "979d6cd2174d0f2ce10ad195d9d3cc4b29a1623a",
-                        "message": "Reformat workflow, bump lofreq to 2.1.5",
+                        "hash": "e61e6713377e9e1a815ea31629471c7ec0d4cf2e",
+                        "message": "Replace AWK with Filter tool to remove <NON_REF> sites",
                         "num": 6,
-                        "short_hash": "979d6cd21",
-                        "unix": "1593004337"
+                        "short_hash": "e61e67133",
+                        "unix": "1651497677"
                     },
                     {
-                        "hash": "ced05a792b3048548fd31a9d0bde9a1bf634481f",
-                        "message": "Fix workflow connections",
+                        "hash": "72a287e5e831cf4fe072285dd2109bccdd32aaff",
+                        "message": "update tutorial",
                         "num": 5,
-                        "short_hash": "ced05a792",
-                        "unix": "1592944690"
+                        "short_hash": "72a287e5e",
+                        "unix": "1651235598"
                     },
                     {
-                        "hash": "1c38a3ed277eb7434c02927dce89f72e8a9c0c78",
-                        "message": "Use newer, simpler output",
+                        "hash": "0e98aba15d56063a4505c95578f36506c61489cf",
+                        "message": "change workflow",
                         "num": 4,
-                        "short_hash": "1c38a3ed2",
-                        "unix": "1592943019"
+                        "short_hash": "0e98aba15",
+                        "unix": "1650981994"
                     },
                     {
-                        "hash": "a58450027f50bbdb5e91ee3529c7deef7ee1cf4e",
-                        "message": "add topic tag to workflow",
+                        "hash": "1eca39b5430f412c1e2047acfef461a4e6062377",
+                        "message": "Spelling check + testing workflow",
                         "num": 3,
-                        "short_hash": "a58450027",
-                        "unix": "1592838416"
+                        "short_hash": "1eca39b54",
+                        "unix": "1650462724"
                     },
                     {
-                        "hash": "e8eea07056121bf6ee287bec31c64cd69d2e6dcb",
-                        "message": "reformat workflow",
+                        "hash": "129023b5fcf34c1f2b13583b346ff5f684428ef3",
+                        "message": "initial tutorial",
                         "num": 2,
-                        "short_hash": "e8eea0705",
-                        "unix": "1592835884"
+                        "short_hash": "129023b5f",
+                        "unix": "1650381596"
                     },
                     {
-                        "hash": "a06c40264814dc80888f2a9ce28d4f06c2c3e687",
-                        "message": "Skeleton from PE sars-cov-2 workflow",
+                        "hash": "4b2ff311ba4c0a03301e4e796d804cce013a1678",
+                        "message": "initial commit",
                         "num": 1,
-                        "short_hash": "a06c40264",
-                        "unix": "1592389814"
+                        "short_hash": "4b2ff311b",
+                        "unix": "1649341437"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "Contains SARS-CoV-2 reference sequence",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 0,
+                        "id": 2,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Contains SARS-CoV-2 reference sequence",
-                                "name": "NC_045512.2 fasta file"
+                                "description": "",
+                                "name": "pedigree"
                             }
                         ],
-                        "label": "NC_045512.2 fasta file",
+                        "label": "pedigree",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 199.95736694335938,
-                            "top": 317.85511016845703
+                            "left": 563.1557760665268,
+                            "top": 635.975477057033
                         },
                         "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "0e91bcb8-fa43-4fc5-87f9-9e65784373e6",
+                        "uuid": "e0eb82fb-bfa7-43fe-b5c7-690fc2e9ed95",
+                        "when": null,
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"EGA Download Client\"];\n  85672f3a-1556-49b6-be09-2e6c81721fb3[\"Output\\nEGA Download Client: authorized datasets\"];\n  0 --> 85672f3a-1556-49b6-be09-2e6c81721fb3;\n  style 85672f3a-1556-49b6-be09-2e6c81721fb3 stroke:#2c3143,stroke-width:4px;\n  1[\"EGA Download Client\"];\n  acd2bcf0-4b9d-4743-9034-716e73d4824f[\"Output\\nList of files in EGAD00001008392\"];\n  1 --> acd2bcf0-4b9d-4743-9034-716e73d4824f;\n  style acd2bcf0-4b9d-4743-9034-716e73d4824f stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\npedigree\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Search in textfiles\"];\n  1 -->|dataset_file_list| 3;\n  6d5d135e-a373-4938-9374-019a09f45a51[\"Output\\nList of Case 5 VCFs\"];\n  3 --> 6d5d135e-a373-4938-9374-019a09f45a51;\n  style 6d5d135e-a373-4938-9374-019a09f45a51 stroke:#2c3143,stroke-width:4px;\n  4[\"EGA Download Client\"];\n  3 -->|output| 4;\n  bdce7169-390b-4adb-9305-5550d5d70a73[\"Output\\nCase 5 VCFs.gz\"];\n  4 --> bdce7169-390b-4adb-9305-5550d5d70a73;\n  style bdce7169-390b-4adb-9305-5550d5d70a73 stroke:#2c3143,stroke-width:4px;\n  5[\"Convert compressed file to uncompressed.\"];\n  4 -->|downloaded_file_collection| 5;\n  82b71cdc-d813-4c77-8ff3-fa59e1725709[\"Output\\nCase 5 VCFs\"];\n  5 --> 82b71cdc-d813-4c77-8ff3-fa59e1725709;\n  style 82b71cdc-d813-4c77-8ff3-fa59e1725709 stroke:#2c3143,stroke-width:4px;\n  6[\"Column Regex Find And Replace\"];\n  5 -->|output1| 6;\n  5e1ff158-cf8a-4dc8-9c22-b987a9f5ac27[\"Output\\nCase 5 VCFs (Fixed Header and Chr)\"];\n  6 --> 5e1ff158-cf8a-4dc8-9c22-b987a9f5ac27;\n  style 5e1ff158-cf8a-4dc8-9c22-b987a9f5ac27 stroke:#2c3143,stroke-width:4px;\n  7[\"bcftools norm\"];\n  6 -->|out_file1| 7;\n  96b34c8d-fa92-48cb-b01f-c05364deba5d[\"Output\\nCase 5 Normalized VCFs\"];\n  7 --> 96b34c8d-fa92-48cb-b01f-c05364deba5d;\n  style 96b34c8d-fa92-48cb-b01f-c05364deba5d stroke:#2c3143,stroke-width:4px;\n  8[\"Filter\"];\n  7 -->|output_file| 8;\n  a8539eb9-8bc3-473b-a27f-201c3acf5539[\"Output\\nCase 5 Normalized VCFs (Removed <NON_REF>)\"];\n  8 --> a8539eb9-8bc3-473b-a27f-201c3acf5539;\n  style a8539eb9-8bc3-473b-a27f-201c3acf5539 stroke:#2c3143,stroke-width:4px;\n  9[\"bcftools merge\"];\n  8 -->|out_file1| 9;\n  b5c479b2-e58a-4fe2-b1cf-fc64476c8192[\"Output\\nCase 5 Merged VCF\"];\n  9 --> b5c479b2-e58a-4fe2-b1cf-fc64476c8192;\n  style b5c479b2-e58a-4fe2-b1cf-fc64476c8192 stroke:#2c3143,stroke-width:4px;\n  10[\"SnpEff eff:\"];\n  9 -->|output_file| 10;\n  cd7b4941-4f4c-4631-8ad5-3411e60fbbd9[\"Output\\nCase 5 SnpEff Annotated vcf\"];\n  10 --> cd7b4941-4f4c-4631-8ad5-3411e60fbbd9;\n  style cd7b4941-4f4c-4631-8ad5-3411e60fbbd9 stroke:#2c3143,stroke-width:4px;\n  11[\"Convert uncompressed file to compressed\"];\n  10 -->|snpeff_output| 11;\n  6e5e1084-b5e1-4daf-8f3b-bd3868a52a25[\"Output\\nSnpEff Annotated vcf_bgzip\"];\n  11 --> 6e5e1084-b5e1-4daf-8f3b-bd3868a52a25;\n  style 6e5e1084-b5e1-4daf-8f3b-bd3868a52a25 stroke:#2c3143,stroke-width:4px;\n  12[\"gene.iobio visualisation\"];\n  11 -->|output1| 12;\n  11 -->|output1| 12;\n  11 -->|output1| 12;\n  0b30f4e0-7328-4479-8a56-bbf828fcfdba[\"Output\\nCase 5 gene.iobio results\"];\n  12 --> 0b30f4e0-7328-4479-8a56-bbf828fcfdba;\n  style 0b30f4e0-7328-4479-8a56-bbf828fcfdba stroke:#2c3143,stroke-width:4px;\n  13[\"Case 5 GEMINI Database\"];\n  11 -->|output1| 13;\n  2 -->|output| 13;\n  8a1964d9-607c-4dd3-a2dc-0f9a68dbb681[\"Output\\nGEMINI Database\"];\n  13 --> 8a1964d9-607c-4dd3-a2dc-0f9a68dbb681;\n  style 8a1964d9-607c-4dd3-a2dc-0f9a68dbb681 stroke:#2c3143,stroke-width:4px;\n  14[\"Case 5 GEMINI Inheritance pattern\"];\n  13 -->|outfile| 14;\n  960ef978-089c-4292-81b5-731965c72a0d[\"Output\\nCase 5 GEMINI results\"];\n  14 --> 960ef978-089c-4292-81b5-731965c72a0d;\n  style 960ef978-089c-4292-81b5-731965c72a0d stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "Trio Analysis Tutorial",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0",
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": null,
+                        "name": "EGA Download Client",
+                        "outputs": [
+                            {
+                                "name": "authorized_datasets",
+                                "type": "txt"
+                            }
+                        ],
+                        "position": {
+                            "left": 4.293246161777436,
+                            "top": 0
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f9db47f68e5e",
+                            "name": "ega_download_client",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"action\": {\"action_type\": \"list_datasets\", \"__current_case__\": 1}, \"output_log\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.0.2+galaxy0",
+                        "type": "tool",
+                        "uuid": "5f03b99a-3f46-47d8-a5b1-31b6d3ae39ee",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "1dedf4c3-5fc4-4505-baa0-b13e4416d67d"
+                                "label": "EGA Download Client: authorized datasets",
+                                "output_name": "authorized_datasets",
+                                "uuid": "85672f3a-1556-49b6-be09-2e6c81721fb3"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0",
                         "errors": null,
                         "id": 1,
                         "input_connections": {},
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "EGA Download Client",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "SRA Manifest"
+                                "name": "dataset_file_list",
+                                "type": "tabular"
                             }
                         ],
-                        "label": "SRA Manifest",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 199.95736694335938,
-                            "top": 372.3295364379883
+                            "left": 4.293246161777436,
+                            "top": 148.56248504578429
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "3c5adef0-7af6-435e-bb10-966361130b58",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f9db47f68e5e",
+                            "name": "ega_download_client",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"action\": {\"action_type\": \"list_dataset_files\", \"__current_case__\": 0, \"dataset_id\": \"EGAD00001008392\"}, \"output_log\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.0.2+galaxy0",
+                        "type": "tool",
+                        "uuid": "265bf049-ac9f-4a59-bba3-311c6c818121",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "fa458185-44d5-4d2d-ad69-20595c8ad337"
+                                "label": "List of files in EGAD00001008392",
+                                "output_name": "dataset_file_list",
+                                "uuid": "acd2bcf0-4b9d-4743-9034-716e73d4824f"
                             }
                         ]
-                    }
-                ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nNC_045512.2 fasta file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSRA Manifest\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Faster Download and Extract Reads in FASTQ\"];\n  1 -->|output| 2;\n  3[\"fastp\"];\n  2 -->|list_paired| 3;\n  4[\"Map with BWA-MEM\"];\n  3 -->|output_paired_coll| 4;\n  0 -->|output| 4;\n  5[\"MarkDuplicates\"];\n  4 -->|bam_output| 5;\n  6[\"Realign reads\"];\n  5 -->|outFile| 6;\n  0 -->|output| 6;\n  7[\"Samtools stats\"];\n  5 -->|outFile| 7;\n  8[\"Insert indel qualities\"];\n  6 -->|realigned| 8;\n  0 -->|output| 8;\n  2ca7c89b-999f-41dc-8037-e54e25959a7e[\"Output\\nRealigned Alignments with Indel Qualities\"];\n  8 --> 2ca7c89b-999f-41dc-8037-e54e25959a7e;\n  style 2ca7c89b-999f-41dc-8037-e54e25959a7e stroke:#2c3143,stroke-width:4px;\n  9[\"Call variants\"];\n  8 -->|output| 9;\n  0 -->|output| 9;\n  10[\"SnpEff eff:\"];\n  9 -->|variants| 10;\n  11[\"SnpSift Extract Fields\"];\n  10 -->|snpeff_output| 11;\n  06259137-eaa5-404a-923c-70ee5f1d89d4[\"Output\\nSnpSift tabular output\"];\n  11 --> 06259137-eaa5-404a-923c-70ee5f1d89d4;\n  style 06259137-eaa5-404a-923c-70ee5f1d89d4 stroke:#2c3143,stroke-width:4px;\n  12[\"MultiQC\"];\n  3 -->|report_json| 12;\n  7 -->|output| 12;\n  5 -->|metrics_file| 12;\n  10 -->|csvFile| 12;\n  758ffde5-7ddd-482a-88b2-1504f8335488[\"Output\\nMultiQC Report PE\"];\n  12 --> 758ffde5-7ddd-482a-88b2-1504f8335488;\n  style 758ffde5-7ddd-482a-88b2-1504f8335488 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "Simple COVID-19 - PE Variation",
-                "outputs": [
+                    },
                     {
-                        "annotation": "Contains SARS-CoV-2 reference sequence",
-                        "content_id": null,
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
                         "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 3,
+                        "input_connections": {
+                            "infile": {
+                                "id": 1,
+                                "output_name": "dataset_file_list"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "Search in textfiles",
+                        "outputs": [
                             {
-                                "description": "Contains SARS-CoV-2 reference sequence",
-                                "name": "NC_045512.2 fasta file"
+                                "name": "output",
+                                "type": "input"
                             }
                         ],
-                        "label": "NC_045512.2 fasta file",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 199.95736694335938,
-                            "top": 317.85511016845703
+                            "left": 1.4413503643385859,
+                            "top": 307.6653714034882
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "0e91bcb8-fa43-4fc5-87f9-9e65784373e6",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ddf54b12c295",
+                            "name": "text_processing",
+                            "owner": "bgruening",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"case_sensitive\": \"\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-E\", \"url_paste\": \"Case5.+17.+vcf.gz$\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
+                        "type": "tool",
+                        "uuid": "d55be511-416e-416b-99c5-da3023124c85",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
+                                "label": "List of Case 5 VCFs",
                                 "output_name": "output",
-                                "uuid": "1dedf4c3-5fc4-4505-baa0-b13e4416d67d"
+                                "uuid": "6d5d135e-a373-4938-9374-019a09f45a51"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": null,
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0",
                         "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
+                        "id": 4,
+                        "input_connections": {
+                            "action|id_table": {
+                                "id": 3,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "EGA Download Client",
+                        "outputs": [
                             {
-                                "description": "",
-                                "name": "SRA Manifest"
+                                "name": "downloaded_file_collection",
+                                "type": "input"
                             }
                         ],
-                        "label": "SRA Manifest",
-                        "name": "Input dataset",
-                        "outputs": [],
                         "position": {
-                            "left": 199.95736694335938,
-                            "top": 372.3295364379883
+                            "left": 1.4348650983573101,
+                            "top": 478.47790000624343
                         },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "3c5adef0-7af6-435e-bb10-966361130b58",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "f9db47f68e5e",
+                            "name": "ega_download_client",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"action\": {\"action_type\": \"download_files\", \"__current_case__\": 3, \"id_table\": {\"__class__\": \"ConnectedValue\"}, \"id_column\": \"1\", \"range\": {\"reference_name\": \"\", \"start\": null, \"end\": null}}, \"output_log\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.0.2+galaxy0",
+                        "type": "tool",
+                        "uuid": "e9b6ed7b-4275-47a4-99cb-e6779a56ec4e",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "fa458185-44d5-4d2d-ad69-20595c8ad337"
+                                "label": "Case 5 VCFs.gz",
+                                "output_name": "downloaded_file_collection",
+                                "uuid": "bdce7169-390b-4adb-9305-5550d5d70a73"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1",
+                        "content_id": "CONVERTER_gz_to_uncompressed",
                         "errors": null,
-                        "id": 2,
+                        "id": 5,
                         "input_connections": {
-                            "input|file_list": {
-                                "id": 1,
-                                "output_name": "output"
+                            "input1": {
+                                "id": 4,
+                                "output_name": "downloaded_file_collection"
                             }
                         },
-                        "inputs": [
+                        "inputs": [],
+                        "label": null,
+                        "name": "Convert compressed file to uncompressed.",
+                        "outputs": [
                             {
-                                "description": "runtime parameter for tool Faster Download and Extract Reads in FASTQ",
-                                "name": "input"
+                                "name": "output1",
+                                "type": "auto"
                             }
                         ],
+                        "position": {
+                            "left": 0,
+                            "top": 620.6925527804436
+                        },
+                        "post_job_actions": {
+                            "ChangeDatatypeActionoutput1": {
+                                "action_arguments": {
+                                    "newtype": "vcf"
+                                },
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "output1"
+                            }
+                        },
+                        "tool_id": "CONVERTER_gz_to_uncompressed",
+                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.0",
+                        "type": "tool",
+                        "uuid": "51d1b3e4-6574-4784-b814-01ab3bd097a3",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Case 5 VCFs",
+                                "output_name": "output1",
+                                "uuid": "82b71cdc-d813-4c77-8ff3-fa59e1725709"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "Add chr prefix",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
+                        "errors": null,
+                        "id": 6,
+                        "input_connections": {
+                            "input": {
+                                "id": 5,
+                                "output_name": "output1"
+                            }
+                        },
+                        "inputs": [],
                         "label": null,
-                        "name": "Faster Download and Extract Reads in FASTQ",
+                        "name": "Column Regex Find And Replace",
                         "outputs": [
                             {
-                                "name": "list_paired",
-                                "type": "input"
-                            },
-                            {
-                                "name": "output_collection",
-                                "type": "input"
-                            },
-                            {
-                                "name": "output_collection_other",
+                                "name": "out_file1",
                                 "type": "input"
-                            },
-                            {
-                                "name": "log",
-                                "type": "txt"
                             }
                         ],
                         "position": {
-                            "left": 342.9971618652344,
-                            "top": 317.85511016845703
+                            "left": 285.74353593563336,
+                            "top": 0.3954410820455898
                         },
-                        "post_job_actions": {
-                            "HideDatasetActionlog": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "log"
-                            },
-                            "HideDatasetActionoutput_collection": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_collection"
-                            },
-                            "HideDatasetActionoutput_collection_other": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_collection_other"
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "ae8c4b2488e7",
+                            "name": "regex_find_replace",
+                            "owner": "galaxyp",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"checks\": [{\"__index__\": 0, \"pattern\": \"^([0-9MYX])\", \"replacement\": \"chr\\\\1\"}, {\"__index__\": 1, \"pattern\": \"^(##contig=<.*ID=)([0-9MYX].+)\", \"replacement\": \"\\\\1chr\\\\2\"}], \"field\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.0.1",
+                        "type": "tool",
+                        "uuid": "4a50616e-4b18-4fa9-9ffa-dfbcc8c32c44",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Case 5 VCFs (Fixed Header and Chr)",
+                                "output_name": "out_file1",
+                                "uuid": "5e1ff158-cf8a-4dc8-9c22-b987a9f5ac27"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "input_file": {
+                                "id": 6,
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "inputs": [],
+                        "label": null,
+                        "name": "bcftools norm",
+                        "outputs": [
+                            {
+                                "name": "output_file",
+                                "type": "vcf"
                             }
+                        ],
+                        "position": {
+                            "left": 269.93026650504567,
+                            "top": 197.0992986309266
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "248f85ff0733",
-                            "name": "sra_tools",
+                            "changeset_revision": "da6fc9f4a367",
+                            "name": "bcftools_norm",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"minlen\": \"\", \"split\": \"--split-3\", \"skip_technical\": \"true\"}, \"input\": {\"input_select\": \"file_list\", \"__current_case__\": 2, \"file_list\": {\"__class__\": \"RuntimeValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.10.7+galaxy1",
+                        "tool_state": "{\"check_ref\": \"w\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"multiallelics\": {\"mode\": \"-\", \"__current_case__\": 1, \"multiallelic_types\": \"both\"}, \"normalize_indels\": true, \"output_type\": \"v\", \"reference_source\": {\"reference_source_selector\": \"cached\", \"__current_case__\": 0, \"fasta_ref\": \"hg19\"}, \"rm_dup\": \"\", \"sec_default\": {\"site_win\": \"1000\"}, \"sec_restrict\": {\"regions\": {\"regions_src\": \"__none__\", \"__current_case__\": 0}, \"targets\": {\"targets_src\": \"__none__\", \"__current_case__\": 0}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.9+galaxy1",
                         "type": "tool",
-                        "uuid": "3ce5b504-3641-4ea9-8d24-07f9bebaec23",
+                        "uuid": "5dbde914-89fe-443b-b1f5-28182e971fca",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "list_paired",
-                                "uuid": "9e5c0368-e97c-4def-9704-1b902fbb2ed7"
+                                "label": "Case 5 Normalized VCFs",
+                                "output_name": "output_file",
+                                "uuid": "96b34c8d-fa92-48cb-b01f-c05364deba5d"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
+                        "content_id": "Filter1",
                         "errors": null,
                         "id": 8,
                         "input_connections": {
-                            "reads": {
-                                "id": 6,
-                                "output_name": "realigned"
-                            },
-                            "strategy|reference_source|ref": {
-                                "id": 0,
-                                "output_name": "output"
+                            "input": {
+                                "id": 7,
+                                "output_name": "output_file"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Insert indel qualities",
+                        "name": "Filter",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "bam"
+                                "name": "out_file1",
+                                "type": "input"
                             }
                         ],
                         "position": {
-                            "left": 1057.5852355957031,
-                            "top": 317.85511016845703
+                            "left": 281.1327747391346,
+                            "top": 399.5494962135009
                         },
-                        "post_job_actions": {
-                            "RenameDatasetActionoutput": {
-                                "action_arguments": {
-                                    "newname": "Realigned Alignments with Indel Qualities"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
+                        "post_job_actions": {},
+                        "tool_id": "Filter1",
+                        "tool_state": "{\"cond\": \"c5!='<NON_REF>'\", \"header_lines\": \"142\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.1.1",
+                        "type": "tool",
+                        "uuid": "da21d9af-cbe0-4cd0-bf70-1c6f16aab26f",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "Case 5 Normalized VCFs (Removed <NON_REF>)",
+                                "output_name": "out_file1",
+                                "uuid": "a8539eb9-8bc3-473b-a27f-201c3acf5539"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10",
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {
+                            "input_files": {
+                                "id": 8,
+                                "output_name": "out_file1"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool bcftools merge",
+                                "name": "sec_header"
+                            }
+                        ],
+                        "label": null,
+                        "name": "bcftools merge",
+                        "outputs": [
+                            {
+                                "name": "output_file",
+                                "type": "vcf"
+                            }
+                        ],
+                        "position": {
+                            "left": 287.16415974045077,
+                            "top": 590.7331216507386
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10",
                         "tool_shed_repository": {
-                            "changeset_revision": "354b534eeab7",
-                            "name": "lofreq_indelqual",
+                            "changeset_revision": "86296490704e",
+                            "name": "bcftools_merge",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"reads\": {\"__class__\": \"ConnectedValue\"}, \"strategy\": {\"selector\": \"dindel\", \"__current_case__\": 1, \"reference_source\": {\"ref_selector\": \"history\", \"__current_case__\": 1, \"ref\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.5+galaxy0",
+                        "tool_state": "{\"input_files\": {\"__class__\": \"ConnectedValue\"}, \"output_type\": \"v\", \"sec_header\": {\"use_header\": {\"__class__\": \"RuntimeValue\"}, \"print_header\": false}, \"sec_merge\": {\"force_samples\": false, \"info_rules\": \"\", \"merge\": \"none\"}, \"sec_restrict\": {\"apply_filters\": \"\", \"regions\": {\"regions_src\": \"__none__\", \"__current_case__\": 0}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.10",
                         "type": "tool",
-                        "uuid": "cbc7ee7f-5cfa-4d45-a83e-623efbf66068",
+                        "uuid": "3471d534-2877-4989-b13b-b7bb3aa20efc",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "Realigned Alignments with Indel Qualities",
-                                "output_name": "output",
-                                "uuid": "2ca7c89b-999f-41dc-8037-e54e25959a7e"
+                                "label": "Case 5 Merged VCF",
+                                "output_name": "output_file",
+                                "uuid": "b5c479b2-e58a-4fe2-b1cf-fc64476c8192"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1",
                         "errors": null,
                         "id": 10,
                         "input_connections": {
                             "input": {
                                 "id": 9,
-                                "output_name": "variants"
+                                "output_name": "output_file"
                             }
                         },
                         "inputs": [
@@ -287753,215 +295180,273 @@
                             {
                                 "name": "statsFile",
                                 "type": "html"
-                            },
-                            {
-                                "name": "csvFile",
-                                "type": "csv"
                             }
                         ],
                         "position": {
-                            "left": 1343.0823059082031,
-                            "top": 317.85511016845703
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActioncsvFile": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "csvFile"
-                            },
-                            "HideDatasetActionstatsFile": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "statsFile"
-                            }
+                            "left": 556.8129698338548,
+                            "top": 8.0719203679202
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "2a3a00c1fa0a",
-                            "name": "snpeff_sars_cov_2",
+                            "changeset_revision": "cfcf33df7fc0",
+                            "name": "snpeff",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"annotations\": [\"-formatEff\", \"-classic\"], \"chr\": \"\", \"csvStats\": \"true\", \"filter\": {\"specificEffects\": \"no\", \"__current_case__\": 0}, \"filterOut\": [\"-no-downstream\", \"-no-intergenic\", \"-no-upstream\", \"-no-utr\"], \"generate_stats\": \"true\", \"genome_version\": \"NC_045512.2\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"inputFormat\": \"vcf\", \"intervals\": {\"__class__\": \"RuntimeValue\"}, \"noLog\": \"true\", \"offset\": \"default\", \"outputConditional\": {\"outputFormat\": \"vcf\", \"__current_case__\": 0}, \"transcripts\": {\"__class__\": \"RuntimeValue\"}, \"udLength\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.5covid19",
+                        "tool_state": "{\"annotations\": null, \"chr\": \"\", \"csvStats\": false, \"filter\": {\"specificEffects\": \"no\", \"__current_case__\": 0}, \"filterOut\": null, \"generate_stats\": true, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inputFormat\": \"vcf\", \"intervals\": {\"__class__\": \"RuntimeValue\"}, \"noLog\": true, \"offset\": \"default\", \"outputConditional\": {\"outputFormat\": \"vcf\", \"__current_case__\": 0}, \"snpDb\": {\"genomeSrc\": \"cached\", \"__current_case__\": 0, \"genomeVersion\": \"hg19\", \"reg_section\": {\"regulation\": null}}, \"spliceRegion\": {\"setSpliceRegions\": \"no\", \"__current_case__\": 0}, \"spliceSiteSize\": \"2\", \"transcripts\": {\"__class__\": \"RuntimeValue\"}, \"udLength\": \"5000\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.3+T.galaxy1",
                         "type": "tool",
-                        "uuid": "8fb55fb1-4986-45f5-bb6b-45c1329842b2",
+                        "uuid": "73d85553-fe49-4a78-9a5c-ac90bc2a1e12",
+                        "when": null,
                         "workflow_outputs": [
                             {
                                 "label": null,
+                                "output_name": "statsFile",
+                                "uuid": "bb59ec32-10c8-4923-8f41-62e3ed1adf11"
+                            },
+                            {
+                                "label": "Case 5 SnpEff Annotated vcf",
                                 "output_name": "snpeff_output",
-                                "uuid": "d5bec60d-c853-4979-a191-e69f47539684"
+                                "uuid": "cd7b4941-4f4c-4631-8ad5-3411e60fbbd9"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
+                        "content_id": "CONVERTER_uncompressed_to_gz",
                         "errors": null,
                         "id": 11,
                         "input_connections": {
-                            "input": {
+                            "input1": {
                                 "id": 10,
                                 "output_name": "snpeff_output"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "SnpSift Extract Fields",
+                        "name": "Convert uncompressed file to compressed",
                         "outputs": [
                             {
-                                "name": "output",
-                                "type": "tabular"
+                                "name": "output1",
+                                "type": "auto"
                             }
                         ],
                         "position": {
-                            "left": 1486.0794982910156,
-                            "top": 317.85511016845703
+                            "left": 552.4385400335957,
+                            "top": 373.4495808144635
                         },
                         "post_job_actions": {
-                            "RenameDatasetActionoutput": {
+                            "ChangeDatatypeActionoutput1": {
                                 "action_arguments": {
-                                    "newname": "SnpSift tabular output"
+                                    "newtype": "vcf_bgzip"
                                 },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "output"
+                                "action_type": "ChangeDatatypeAction",
+                                "output_name": "output1"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "2b3e65a4252f",
-                            "name": "snpsift",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"empty_text\": \".\", \"extract\": \"CHROM POS REF ALT QUAL DP AF SB DP4 EFF[*].IMPACT EFF[*].FUNCLASS EFF[*].EFFECT EFF[*].GENE EFF[*].CODON\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"one_effect_per_line\": \"false\", \"separator\": \",\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.3+t.galaxy0",
+                        "tool_id": "CONVERTER_uncompressed_to_gz",
+                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "1.16+galaxy0",
                         "type": "tool",
-                        "uuid": "33e13bce-928f-41d6-b418-bc0a9e53d83d",
+                        "uuid": "2c959f43-8264-48d7-adf1-c12d5a2b3394",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "SnpSift tabular output",
-                                "output_name": "output",
-                                "uuid": "06259137-eaa5-404a-923c-70ee5f1d89d4"
+                                "label": "SnpEff Annotated vcf_bgzip",
+                                "output_name": "output1",
+                                "uuid": "6e5e1084-b5e1-4daf-8f3b-bd3868a52a25"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/geneiobio/gene_iobio_display_generation_iframe/4.7.1",
                         "errors": null,
                         "id": 12,
                         "input_connections": {
-                            "results_0|software_cond|input": {
-                                "id": 3,
-                                "output_name": "report_json"
-                            },
-                            "results_1|software_cond|output_0|type|input": {
-                                "id": 7,
-                                "output_name": "output"
+                            "input_type|father|vcf": {
+                                "id": 11,
+                                "output_name": "output1"
                             },
-                            "results_2|software_cond|output_0|input": {
-                                "id": 5,
-                                "output_name": "metrics_file"
+                            "input_type|mother|vcf": {
+                                "id": 11,
+                                "output_name": "output1"
                             },
-                            "results_3|software_cond|input": {
-                                "id": 10,
-                                "output_name": "csvFile"
+                            "proband_vcf": {
+                                "id": 11,
+                                "output_name": "output1"
                             }
                         },
-                        "inputs": [],
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool gene.iobio visualisation",
+                                "name": "proband_bam"
+                            }
+                        ],
                         "label": null,
-                        "name": "MultiQC",
+                        "name": "gene.iobio visualisation",
                         "outputs": [
                             {
-                                "name": "stats",
-                                "type": "input"
-                            },
+                                "name": "outfile",
+                                "type": "html"
+                            }
+                        ],
+                        "position": {
+                            "left": 866.6404599769689,
+                            "top": 23.224599201146997
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/geneiobio/gene_iobio_display_generation_iframe/4.7.1",
+                        "tool_shed_repository": {
+                            "changeset_revision": "c0af7b196a89",
+                            "name": "geneiobio",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"genes\": \"\", \"input_type\": {\"input_type_selector\": \"trio\", \"__current_case__\": 0, \"father\": {\"vcf\": {\"__class__\": \"ConnectedValue\"}, \"bam\": {\"__class__\": \"RuntimeValue\"}, \"affected\": false, \"name\": \"Case6F\"}, \"mother\": {\"vcf\": {\"__class__\": \"ConnectedValue\"}, \"bam\": {\"__class__\": \"RuntimeValue\"}, \"affected\": true, \"name\": \"Case6M\"}}, \"proband_affected\": true, \"proband_bam\": {\"__class__\": \"RuntimeValue\"}, \"proband_name\": \"Case6C\", \"proband_sex\": \"female\", \"proband_vcf\": {\"__class__\": \"ConnectedValue\"}, \"refgen_version\": \"GRCh37\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.7.1",
+                        "type": "tool",
+                        "uuid": "63a20112-21fe-4046-9fdd-3b5e766b0d68",
+                        "when": null,
+                        "workflow_outputs": [
                             {
-                                "name": "plots",
-                                "type": "input"
+                                "label": "Case 5 gene.iobio results",
+                                "output_name": "outfile",
+                                "uuid": "0b30f4e0-7328-4479-8a56-bbf828fcfdba"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2",
+                        "errors": null,
+                        "id": 13,
+                        "input_connections": {
+                            "infile": {
+                                "id": 11,
+                                "output_name": "output1"
                             },
+                            "ped": {
+                                "id": 2,
+                                "output_name": "output"
+                            }
+                        },
+                        "inputs": [],
+                        "label": "Case 5 GEMINI Database",
+                        "name": "GEMINI load",
+                        "outputs": [
                             {
-                                "name": "html_report",
-                                "type": "html"
+                                "name": "outfile",
+                                "type": "gemini.sqlite"
                             }
                         ],
                         "position": {
-                            "left": 1486.0794982910156,
-                            "top": 397.8408889770508
+                            "left": 867.1106984600971,
+                            "top": 518.7461949332695
                         },
-                        "post_job_actions": {
-                            "HideDatasetActionplots": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "plots"
-                            },
-                            "HideDatasetActionstats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "stats"
-                            },
-                            "RenameDatasetActionhtml_report": {
-                                "action_arguments": {
-                                    "newname": "MultiQC Report PE"
-                                },
-                                "action_type": "RenameDatasetAction",
-                                "output_name": "html_report"
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2",
+                        "tool_shed_repository": {
+                            "changeset_revision": "45296e47d565",
+                            "name": "gemini_load",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"annotation_databases\": \"2019-01-12\", \"annotation_type\": \"snpEff\", \"has_genotypes\": true, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"opt_content\": [\"gerp_bp\", \"cadd\", \"gene_tables\", \"genotypes\", \"gt_pl\", \"info_string\"], \"ped\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.20.1+galaxy2",
+                        "type": "tool",
+                        "uuid": "f8d4a15e-b99a-455c-a788-2cbd8c7cb4cc",
+                        "when": null,
+                        "workflow_outputs": [
+                            {
+                                "label": "GEMINI Database",
+                                "output_name": "outfile",
+                                "uuid": "8a1964d9-607c-4dd3-a2dc-0f9a68dbb681"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1",
+                        "errors": null,
+                        "id": 14,
+                        "input_connections": {
+                            "infile": {
+                                "id": 13,
+                                "output_name": "outfile"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
+                        "inputs": [],
+                        "label": "Case 5 GEMINI Inheritance pattern",
+                        "name": "GEMINI inheritance pattern",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 1132.4996805716235,
+                            "top": 583.0393503253775
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "bf675f34b056",
-                            "name": "multiqc",
+                            "changeset_revision": "18d13111692b",
+                            "name": "gemini_inheritance",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"comment\": \"\", \"flat\": \"false\", \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 23, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"stats\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"snpeff\", \"__current_case__\": 25, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.8+galaxy0",
+                        "tool_state": "{\"family_wise\": {\"min_kindreds\": \"1\", \"families\": \"\", \"per_variant_selection\": {\"enabled\": \"no\", \"__current_case__\": 0, \"min_dp\": \"0\", \"min_gq\": \"0\", \"max_pl\": \"-1\"}}, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"inheritance\": {\"pattern_type\": \"autosomal_dominant\", \"__current_case__\": 3, \"constraint\": [{\"__index__\": 0, \"filter\": \"impact_severity != 'LOW'\"}], \"lenient\": false, \"allow_unaffected\": false}, \"oformat\": {\"report\": {\"report_selector\": \"custom\", \"__current_case__\": 2, \"columns\": null, \"extra_cols\": \"chrom, start, ref, alt, impact, gene, clinvar_sig, clinvar_disease_name, clinvar_gene_phenotype, rs_ids\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.20.1",
                         "type": "tool",
-                        "uuid": "8c98527f-d1db-4cc4-89f1-1e75c508b8e9",
+                        "uuid": "11a2ec8f-6c18-4000-ba5d-468dc896f866",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "MultiQC Report PE",
-                                "output_name": "html_report",
-                                "uuid": "758ffde5-7ddd-482a-88b2-1504f8335488"
+                                "label": "Case 5 GEMINI results",
+                                "output_name": "outfile",
+                                "uuid": "960ef978-089c-4292-81b5-731965c72a0d"
                             }
                         ]
                     }
                 ],
-                "parent_id": "variant-analysis/sars-cov-2",
-                "path": "topics/variant-analysis/tutorials/sars-cov-2/workflows/main_workflow.ga",
+                "parent_id": "variant-analysis/trio-analysis",
+                "path": "topics/variant-analysis/tutorials/trio-analysis/workflows/main_workflow.ga",
                 "tags": [
                     "variant-analysis"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "Simple COVID-19 - PE Variation",
+                "tests": true,
+                "title": "Trio Analysis Tutorial",
                 "topic_id": "variant-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-sars-cov-2/versions/main-workflow",
-                "tutorial_id": "sars-cov-2",
-                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2/workflows/main_workflow.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2/workflows/main_workflow.html",
-                "version": 1,
-                "wfid": "variant-analysis-sars-cov-2",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-trio-analysis/versions/main-workflow",
+                "tutorial_id": "trio-analysis",
+                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/trio-analysis/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/trio-analysis/workflows/main_workflow.html",
+                "version": 5,
+                "wfid": "variant-analysis-trio-analysis",
                 "wfname": "main-workflow",
                 "workflow": "main_workflow.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1"
+                    "CONVERTER_gz_to_uncompressed",
+                    "CONVERTER_uncompressed_to_gz",
+                    "Filter1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/geneiobio/gene_iobio_display_generation_iframe/4.7.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1"
                 ],
-                "workflowhub_id": "1074"
+                "workflowhub_id": "1096"
             }
-        ]
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.6483454"
     },
     {
         "admin_install": {
@@ -287970,182 +295455,353 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "freebayes",
+                    "name": "bwa",
                     "owner": "devteam",
-                    "revisions": "156b60c1530f",
-                    "tool_panel_section_label": "Variant Calling",
+                    "revisions": "e188dc7a68e6",
+                    "tool_panel_section_label": "Mapping",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "vcfallelicprimitives",
+                    "name": "column_maker",
                     "owner": "devteam",
-                    "revisions": "f49b23b41a12",
-                    "tool_panel_section_label": "Variant Calling",
+                    "revisions": "6595517c2dd8",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "gemini_db_info",
+                    "name": "emboss_5",
+                    "owner": "devteam",
+                    "revisions": "63dd26468588",
+                    "tool_panel_section_label": "EMBOSS",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_compute_length",
+                    "owner": "devteam",
+                    "revisions": "7d37cfda8e00",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "compose_text_param",
                     "owner": "iuc",
-                    "revisions": "4c5f4e9b1931",
-                    "tool_panel_section_label": "Gemini",
+                    "revisions": "e188c9826e0f",
+                    "tool_panel_section_label": "Expression Tools",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "gemini_load",
+                    "name": "datamash_ops",
                     "owner": "iuc",
-                    "revisions": "cf61daf064fe",
-                    "tool_panel_section_label": "Gemini",
+                    "revisions": "746e8e4bf929",
+                    "tool_panel_section_label": "Join, Subtract and Group",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "gemini_query",
+                    "name": "fastp",
                     "owner": "iuc",
-                    "revisions": "666f60a9331a",
-                    "tool_panel_section_label": "Gemini",
+                    "revisions": "65b93b623c77",
+                    "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "snpeff",
+                    "name": "ivar_consensus",
                     "owner": "iuc",
-                    "revisions": "5c7b70713fb5",
-                    "tool_panel_section_label": "Variant Calling",
+                    "revisions": "40737febe339",
+                    "tool_panel_section_label": "Virology",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "snpeff",
+                    "name": "ivar_trim",
                     "owner": "iuc",
-                    "revisions": "68693743661e",
+                    "revisions": "86a20ae274fc",
+                    "tool_panel_section_label": "Virology",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "qualimap_bamqc",
+                    "owner": "iuc",
+                    "revisions": "19ece8afbaab",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "samtools_merge",
+                    "owner": "iuc",
+                    "revisions": "36677f429310",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "samtools_view",
+                    "owner": "iuc",
+                    "revisions": "5826298f6a73",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ucsc_fatovcf",
+                    "owner": "iuc",
+                    "revisions": "78df8fc2b3ab",
                     "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_regex_finder",
+                    "owner": "mbernt",
+                    "revisions": "9a811adb714f",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mafft",
+                    "owner": "rnateam",
+                    "revisions": "bf28a8cff401",
+                    "tool_panel_section_label": "Multiple Alignments",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mimodd_main",
+                    "owner": "wolma",
+                    "revisions": "f0f2795de2c7",
+                    "tool_panel_section_label": "MiModD",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: freebayes\n  owner: devteam\n  revisions: 156b60c1530f\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: vcfallelicprimitives\n  owner: devteam\n  revisions: f49b23b41a12\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_db_info\n  owner: iuc\n  revisions: 4c5f4e9b1931\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_load\n  owner: iuc\n  revisions: cf61daf064fe\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_query\n  owner: iuc\n  revisions: 666f60a9331a\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n  owner: iuc\n  revisions: 5c7b70713fb5\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n  owner: iuc\n  revisions: 68693743661e\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/dip/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: column_maker\n  owner: devteam\n  revisions: 6595517c2dd8\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: emboss_5\n  owner: devteam\n  revisions: 63dd26468588\n  tool_panel_section_label: EMBOSS\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_compute_length\n  owner: devteam\n  revisions: 7d37cfda8e00\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: compose_text_param\n  owner: iuc\n  revisions: e188c9826e0f\n  tool_panel_section_label: Expression Tools\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: datamash_ops\n  owner: iuc\n  revisions: 746e8e4bf929\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ivar_consensus\n  owner: iuc\n  revisions: 40737febe339\n  tool_panel_section_label: Virology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ivar_trim\n  owner: iuc\n  revisions: 86a20ae274fc\n  tool_panel_section_label: Virology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qualimap_bamqc\n  owner: iuc\n  revisions: 19ece8afbaab\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_merge\n  owner: iuc\n  revisions: 36677f429310\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: 5826298f6a73\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ucsc_fatovcf\n  owner: iuc\n  revisions: 78df8fc2b3ab\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_regex_finder\n  owner: mbernt\n  revisions: 9a811adb714f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mafft\n  owner: rnateam\n  revisions: bf28a8cff401\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mimodd_main\n  owner: wolma\n  revisions: f0f2795de2c7\n  tool_panel_section_label: MiModD\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "wm75",
+                "TKlingstrom"
+            ],
+            "funding": [
+                "by-covid",
+                "elixir-converge",
+                "h2020-defend"
+            ]
+        },
         "contributors": [
             {
-                "email": "anton@nekrut.org",
-                "id": "nekrut",
+                "affiliations": [
+                    "by-covid",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "elixir_node": "de",
+                "fediverse": "https://scholar.social/@zerodivision",
+                "fediverse_flavor": "mastodon",
+                "id": "wm75",
                 "joined": "2017-09",
-                "name": "Anton Nekrutenko",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+                "matrix": "wm75:matrix.org",
+                "name": "Wolfgang Maier",
+                "orcid": "0000-0002-9464-6640",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
             },
             {
                 "affiliations": [
-                    "earlham",
                     "elixir-europe"
                 ],
-                "elixir_node": "uk",
-                "fediverse": "https://mstdn.science/@nsoranzo",
-                "fediverse_flavor": "mastodon",
-                "id": "nsoranzo",
-                "joined": "2017-09",
-                "linkedin": "nicola-soranzo-7884125",
-                "matrix": "nsoranzo:matrix.org",
-                "name": "Nicola Soranzo",
-                "orcid": "0000-0003-3627-5340",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
-                "twitter": "NicolaSoranzo",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
+                "elixir_node": "se",
+                "email": "tomas.klingstrom@slu.se",
+                "id": "TKlingstrom",
+                "joined": "2018-11",
+                "matrix": "TKlingstrom:matrix.org",
+                "name": "Tomas Klingstr\u00f6m",
+                "orcid": "0000-0002-9504-1352",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/TKlingstrom/",
+                "twitter": "TKlingstrom",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/TKlingstrom.json"
+            },
+            {
+                "funder": true,
+                "funding_id": "101046203",
+                "funding_statement": "BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response.\n\nThis project has received funding from the European Union\u2019s Horizon Europe research and innovation programme under grant agreement \u2116 101046203 (BY-COVID)",
+                "funding_system": "cordis",
+                "id": "by-covid",
+                "joined": "2023-04",
+                "members": [
+                    "bgruening",
+                    "hexylena",
+                    "ilveroluca",
+                    "kikkomep",
+                    "mbaardwijk",
+                    "PapXis",
+                    "pauldg",
+                    "simleo",
+                    "stain",
+                    "wm75"
+                ],
+                "name": "BeYond-COVID",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/by-covid/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/by-covid.json"
+            },
+            {
+                "avatar": "https://elixir-europe.org/sites/default/files/styles/right-medium/public/images/converge_logo.png",
+                "funder": true,
+                "funding_id": "871075",
+                "funding_statement": "ELIXIR CONVERGE is connecting and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services. This project has received funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement \u2116 871075",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "elixir-converge",
+                "joined": "2023-01",
+                "members": [
+                    "bgruening",
+                    "hexylena"
+                ],
+                "name": "ELIXIR-CONVERGE",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-converge/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-converge.json"
+            },
+            {
+                "funder": true,
+                "funding_id": "773701",
+                "funding_statement": "DEFEND is Addressing the dual emerging threats of African Swine Fever and Lumpy Skin Disease in Europe.\n\nThis work has received funding from the DEFEND project (www.defend2020.eu) with funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement No 773701.",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "h2020-defend",
+                "joined": "2023-05",
+                "name": "Addressing the dual emerging threats of African Swine Fever and Lumpy Skin Disease in Europe",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/h2020-defend/",
+                "short_name": "DEFEND",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/h2020-defend.json"
             }
         ],
-        "dir": "topics/variant-analysis/tutorials/dip",
+        "dir": "topics/variant-analysis/tutorials/pox-tiled-amplicon",
         "edam_operation": [
-            "Variant calling",
+            "Sequence alignment",
+            "Read mapping",
+            "Sequencing quality control",
+            "Sequence alignment analysis",
             "Sequence analysis",
-            "Genetic variation analysis",
-            "Statistical calculation"
+            "Multiple sequence alignment",
+            "Sequence contamination filtering",
+            "Generation",
+            "Global alignment",
+            "Local alignment",
+            "Genome indexing"
         ],
         "edam_topic": [],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "variant-analysis/dip",
+        "id": "variant-analysis/pox-tiled-amplicon",
         "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org.au"
+            "UseGalaxy.org (Main)"
         ],
         "js_requirements": {
-            "mathjax": 3591,
+            "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Variants versus Genotypes",
-            "Bayesian approach to variant calling",
-            "Freebayes calls variant using haplotype windows",
-            "SNPEff allows functional annotation of variants",
-            "Gemini is a flexible system for analyzing variation patterns"
+            "Compared to other viruses, analysis of sequencing data from pox viruses is complicated by the rather large genome size and by the presence of inverted terminal repeats, but well-designed wet lab and bioinformatic workflows can handle these particularities.",
+            "Galaxy and its huge set of tools are flexible enough to handle half-genome sequencing data efficiently.",
+            "A mapping-based approach can result in high-quality consensus genome reconstructions from pox virus sequencing data and appears promising even when dealing with recombinant samples."
         ],
         "layout": "tutorial_hands_on",
+        "level": "Advanced",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-03-05",
+        "mod_date": "2024-03-20",
         "objectives": [
-            "Identification of genetic variations using variant calling"
+            "Learn how to deal with pox virus genomes inverted terminal repeats through a combination of wet lab protocol and tailored bioinformatics",
+            "Construct a sample consensus genome from mapped reads",
+            "Explore a recombinant pox virus genome via a multiple-sequence alignment of consensus genome and references and through lists of mutations derived from it"
         ],
-        "pageviews": 22267,
-        "pub_date": "2017-02-20",
+        "pageviews": 670,
+        "pub_date": "2023-05-15",
         "questions": [
-            "How to find variable sites in diploid genomes?"
+            "Which special challenges does one encounter during sequence data analysis of pox viruses?",
+            "How can standard workflows for viral mutation calling and consensus generation be adapted to the particularities of pox viruses?",
+            "How can viral consensus sequences, multiple-sequence alignments and mutation calls be generated from each other and used to answer questions about the data?"
         ],
-        "short_id": "T00309",
+        "requirements": [
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "collections",
+                    "upload-rules"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00347",
         "short_tools": [
-            "freebayes",
-            "gemini_db_info",
-            "gemini_load",
-            "gemini_query",
-            "snpEff_download",
-            "snpEff",
-            "vcfallelicprimitives"
+            "ivar_trim",
+            "upload1",
+            "compose_text_param",
+            "qualimap_bamqc",
+            "param_value_from_file",
+            "__ZIP_COLLECTION__",
+            "mimodd_info",
+            "datamash_ops",
+            "bwa_mem",
+            "ivar_consensus",
+            "fatovcf",
+            "EMBOSS: maskseq51",
+            "__APPLY_RULES__",
+            "samtools_view",
+            "rbc_mafft",
+            "Grep1",
+            "Cut1",
+            "fasta_regex_finder",
+            "samtools_merge",
+            "fastp",
+            "fasta_compute_length",
+            "Add_a_column1"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "introduction",
+        "subtopic": "one-health",
         "supported_servers": {
-            "exact": [],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                },
+            "exact": [
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
+                }
+            ],
+            "inexact": [
                 {
-                    "name": "UseGalaxy.org.au",
-                    "url": "https://usegalaxy.org.au",
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
-        "time_estimation": "3h",
-        "title": "Calling variants in diploid systems",
+        "tags": [
+            "virology",
+            "one-health"
+        ],
+        "time_estimation": "4H",
+        "title": "Pox virus genome analysis from tiled-amplicon sequencing data",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.1.0.46-0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/0.0.3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.18.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.18.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.18.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1"
+            "Cut1",
+            "Grep1",
+            "__APPLY_RULES__",
+            "__ZIP_COLLECTION__",
+            "param_value_from_file",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+            "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_fatovcf/fatovcf/426+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/mbernt/fasta_regex_finder/fasta_regex_finder/0.1.0",
+            "toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.520+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_info/0.1.8_1",
+            "upload1"
         ],
         "topic_name": "variant-analysis",
         "topic_name_human": "Variant Analysis",
@@ -288155,366 +295811,264 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "dip",
+        "tutorial_name": "pox-tiled-amplicon",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/dip/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/dip/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/dip/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/pox-tiled-amplicon/tutorial.json"
         },
-        "version": 16,
+        "version": 4,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 193,
-        "visitors": 12375,
+        "visit_duration": 145,
+        "visitors": 562,
         "workflows": [
             {
-                "creators": [],
-                "description": "Calling variants in diploid systems",
+                "creators": [
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0001-6897-1215",
+                        "name": "Viktoria Isabel Schwarz"
+                    },
+                    {
+                        "class": "Person",
+                        "identifier": "https://orcid.org/0000-0002-9464-6640",
+                        "name": "Wolfgang Maier"
+                    }
+                ],
+                "description": "From a reference and a primer scheme generate two masked half-genome references for ITR-aware pox virus sequencing data analysis.",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGIAB-Ashkenazim-Trio-hg19.bam\"]\n  1[label=\"SnpEff Download\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGIAB-Ashkenazim-Trio.tabular\"]\n  3[label=\"FreeBayes\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"VcfAllelicPrimitives:\"]\n  3 -> 4 [label=\"output_vcf\"]\n  5[label=\"SnpEff eff:\"]\n  4 -> 5 [label=\"out_file1\"]\n  1 -> 5 [label=\"snpeff_db\"]\n  6[label=\"GEMINI load\"]\n  5 -> 6 [label=\"snpeff_output\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"GEMINI_db_info\"]\n  6 -> 7 [label=\"outfile\"]\n  8[label=\"GEMINI_query2\"]\n  6 -> 8 [label=\"outfile\"]\n  9[label=\"GEMINI_query1\"]\n  6 -> 9 [label=\"outfile\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPrimer Scheme\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference FASTA\"]\n  2[label=\"Select pool1 primers\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Select pool2 primers\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Compute sequence length\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Datamash\"]\n  2 -> 5 [label=\"out_file1\"]\n  6[label=\"Datamash\"]\n  3 -> 6 [label=\"out_file1\"]\n  7[label=\"Cut\"]\n  4 -> 7 [label=\"output\"]\n  8[label=\"Compute\"]\n  5 -> 8 [label=\"out_file\"]\n  9[label=\"Get start position of Pool2\"]\n  6 -> 9 [label=\"out_file\"]\n  10[label=\"Get end position of sequence\"]\n  7 -> 10 [label=\"out_file1\"]\n  11[label=\"Get end position of Pool1\"]\n  8 -> 11 [label=\"out_file1\"]\n  12[label=\"Compose text parameter value\"]\n  9 -> 12 [label=\"text_param\"]\n  13[label=\"Compose text parameter value\"]\n  11 -> 13 [label=\"text_param\"]\n  10 -> 13 [label=\"text_param\"]\n  14[label=\"Mask Reference for Pool2\"]\n  1 -> 14 [label=\"output\"]\n  12 -> 14 [label=\"out1\"]\n  kaf755a5e2b2049bc9d5234781f937f48[color=lightseagreen,label=\"Output\\nmasked_ref_pool2\"]\n  14 -> kaf755a5e2b2049bc9d5234781f937f48\n  15[label=\"Mask Reference for Pool1\"]\n  1 -> 15 [label=\"output\"]\n  13 -> 15 [label=\"out1\"]\n  k0c3b5b20c426428ca08bc835a82477c1[color=lightseagreen,label=\"Output\\nmasked_ref_pool1\"]\n  15 -> k0c3b5b20c426428ca08bc835a82477c1\n}",
                 "history": [
                     {
-                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
-                        "message": "annotation",
-                        "num": 3,
-                        "short_hash": "667ff3de9",
-                        "unix": "1579690769"
-                    },
-                    {
-                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
-                        "message": "Workflow renaming",
+                        "hash": "79db81a7c1c23d9778536abaa9ca879f3b0bbda5",
+                        "message": "Update pox-virus-tiled-amplicon-ref-masking.ga",
                         "num": 2,
-                        "short_hash": "eb4d724e0",
-                        "unix": "1579084895"
+                        "short_hash": "79db81a7c",
+                        "unix": "1684740183"
                     },
                     {
-                        "hash": "a294ecfbb57eb17046ebbb47ccb2c877f2c0cf85",
-                        "message": "workflow for diploid",
+                        "hash": "314d08f56a2d904cbab620fa5400ed0dbfa9619a",
+                        "message": "Add some material for new pox virus tiled amplicon tutorial",
                         "num": 1,
-                        "short_hash": "a294ecfbb",
-                        "unix": "1544185856"
+                        "short_hash": "314d08f56",
+                        "unix": "1682289363"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "",
+                        "annotation": "The workflow expects a primer scheme split into two separate sequencing pools. These pools must be denoted as pool1/pool2 in the BED score column. The pool ids may, optionally, be followed by indicators of the subpool for tiled PCR amplification (e.g., pool1a/pool1b/pool2a/pool2b)",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "GIAB-Ashkenazim-Trio-hg19.bam"
+                                "description": "The workflow expects a primer scheme split into two separate sequencing pools. These pools must be denoted as pool1/pool2 in the BED score column. The pool ids may, optionally, be followed by indicators of the subpool for tiled PCR amplification (e.g., pool1a/pool1b/pool2a/pool2b)",
+                                "name": "Primer Scheme (BED file with Pool identifiers)"
                             }
                         ],
-                        "label": "GIAB-Ashkenazim-Trio-hg19.bam",
+                        "label": "Primer Scheme",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 229,
-                            "top": 204
+                            "left": 0,
+                            "top": 667.3406219482422
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"GIAB-Ashkenazim-Trio-hg19.bam\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "5bbfca3e-68d7-4c87-8976-724ccaab2eb3",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "bc2eeefe-9c1e-4db8-bf4c-83ed024d67a0"
-                            }
-                        ]
+                        "uuid": "1829d4e0-ee74-4a94-8dc5-98a11d96b961",
+                        "when": null,
+                        "workflow_outputs": []
                     },
                     {
-                        "annotation": "",
+                        "annotation": "The viral reference sequence to map sequenced reads against",
                         "content_id": null,
                         "errors": null,
-                        "id": 2,
+                        "id": 1,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "",
-                                "name": "GIAB-Ashkenazim-Trio.tabular"
+                                "description": "The viral reference sequence to map sequenced reads against",
+                                "name": "Reference FASTA"
                             }
                         ],
-                        "label": "GIAB-Ashkenazim-Trio.tabular",
+                        "label": "Reference FASTA",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 289,
-                            "top": 530
+                            "left": 251.7752034262281,
+                            "top": 650.9021921247038
                         },
                         "tool_id": null,
-                        "tool_state": "{\"name\": \"GIAB-Ashkenazim-Trio.tabular\"}",
+                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "4d40770f-b5f9-464b-b3e5-b99ae836fbf0",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "6f4a6fbd-e2a2-43dc-92ea-b99d4f32a20f"
-                            }
-                        ]
+                        "uuid": "f17c7022-fc94-42b5-ae90-7b3ec3d70ffb",
+                        "when": null,
+                        "workflow_outputs": []
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGIAB-Ashkenazim-Trio-hg19.bam\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"SnpEff Download\"];\n  2[\"\u2139\ufe0f Input Dataset\\nGIAB-Ashkenazim-Trio.tabular\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"FreeBayes\"];\n  0 -->|output| 3;\n  4[\"VcfAllelicPrimitives:\"];\n  3 -->|output_vcf| 4;\n  5[\"SnpEff eff:\"];\n  4 -->|out_file1| 5;\n  1 -->|snpeff_db| 5;\n  6[\"GEMINI load\"];\n  5 -->|snpeff_output| 6;\n  2 -->|output| 6;\n  7[\"GEMINI_db_info\"];\n  6 -->|outfile| 7;\n  8[\"GEMINI_query2\"];\n  6 -->|outfile| 8;\n  9[\"GEMINI_query1\"];\n  6 -->|outfile| 9;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "Diploid",
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPrimer Scheme\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference FASTA\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Select pool1 primers\"];\n  0 -->|output| 2;\n  3[\"Select pool2 primers\"];\n  0 -->|output| 3;\n  4[\"Compute sequence length\"];\n  1 -->|output| 4;\n  5[\"Datamash\"];\n  2 -->|out_file1| 5;\n  6[\"Datamash\"];\n  3 -->|out_file1| 6;\n  7[\"Cut\"];\n  4 -->|output| 7;\n  8[\"Compute\"];\n  5 -->|out_file| 8;\n  9[\"Get start position of Pool2\"];\n  6 -->|out_file| 9;\n  10[\"Get end position of sequence\"];\n  7 -->|out_file1| 10;\n  11[\"Get end position of Pool1\"];\n  8 -->|out_file1| 11;\n  12[\"Compose text parameter value\"];\n  9 -->|text_param| 12;\n  13[\"Compose text parameter value\"];\n  11 -->|text_param| 13;\n  10 -->|text_param| 13;\n  14[\"Mask Reference for Pool2\"];\n  1 -->|output| 14;\n  12 -->|out1| 14;\n  af755a5e-2b20-49bc-9d52-34781f937f48[\"Output\\nmasked_ref_pool2\"];\n  14 --> af755a5e-2b20-49bc-9d52-34781f937f48;\n  style af755a5e-2b20-49bc-9d52-34781f937f48 stroke:#2c3143,stroke-width:4px;\n  15[\"Mask Reference for Pool1\"];\n  1 -->|output| 15;\n  13 -->|out1| 15;\n  0c3b5b20-c426-428c-a08b-c835a82477c1[\"Output\\nmasked_ref_pool1\"];\n  15 --> 0c3b5b20-c426-428c-a08b-c835a82477c1;\n  style 0c3b5b20-c426-428c-a08b-c835a82477c1 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "pox-virus-tiled-amplicon-ref-masking",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "GIAB-Ashkenazim-Trio-hg19.bam"
-                            }
-                        ],
-                        "label": "GIAB-Ashkenazim-Trio-hg19.bam",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 229,
-                            "top": 204
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"GIAB-Ashkenazim-Trio-hg19.bam\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "5bbfca3e-68d7-4c87-8976-724ccaab2eb3",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "bc2eeefe-9c1e-4db8-bf4c-83ed024d67a0"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "",
-                                "name": "GIAB-Ashkenazim-Trio.tabular"
-                            }
-                        ],
-                        "label": "GIAB-Ashkenazim-Trio.tabular",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 289,
-                            "top": 530
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"name\": \"GIAB-Ashkenazim-Trio.tabular\"}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "4d40770f-b5f9-464b-b3e5-b99ae836fbf0",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "output",
-                                "uuid": "6f4a6fbd-e2a2-43dc-92ea-b99d4f32a20f"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.18.1.0",
-                        "errors": null,
-                        "id": 7,
-                        "input_connections": {
-                            "infile": {
-                                "id": 6,
-                                "output_name": "outfile"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool GEMINI db_info",
-                                "name": "infile"
-                            }
-                        ],
-                        "label": "GEMINI_db_info",
-                        "name": "GEMINI db_info",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 1559,
-                            "top": 197
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.18.1.0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "4c5f4e9b1931",
-                            "name": "gemini_db_info",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "0.18.1.0",
-                        "type": "tool",
-                        "uuid": "7f7f05f6-00b9-472b-8de9-044dc4feeb8c",
-                        "workflow_outputs": [
-                            {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "7e61f96f-fc5a-436b-8433-dc78b10e5cea"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.18.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
                         "errors": null,
-                        "id": 8,
+                        "id": 14,
                         "input_connections": {
-                            "infile": {
-                                "id": 6,
-                                "output_name": "outfile"
+                            "input1": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "regions": {
+                                "id": 12,
+                                "output_name": "out1"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool GEMINI query",
-                                "name": "infile"
-                            }
-                        ],
-                        "label": "GEMINI_query2",
-                        "name": "GEMINI query",
+                        "inputs": [],
+                        "label": "Mask Reference for Pool2",
+                        "name": "maskseq",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "tabular"
+                                "name": "out_file1",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 1502,
-                            "top": 478
+                            "left": 1438.15352300995,
+                            "top": 648.5794855890229
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.18.1.0",
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Masked reference for mapping of pool2"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "5596c2dc4218",
-                            "name": "gemini_query",
-                            "owner": "iuc",
+                            "changeset_revision": "ce385837c160",
+                            "name": "emboss_5",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"show_families\": \"\\\"false\\\"\", \"min_kindreds\": \"\\\"1\\\"\", \"sample_filter\": \"\\\"\\\"\", \"show_samples\": \"\\\"false\\\"\", \"__page__\": null, \"region\": \"\\\"\\\"\", \"gt_filter\": \"\\\"\\\"\", \"family_wise\": \"\\\"false\\\"\", \"q\": \"\\\"SELECT rs_ids, aaf_esp_ea, impact, clinvar_disease_name, clinvar_sig FROM variants WHERE filter is NULL and gene = 'POLRMT'\\\"\", \"header\": \"\\\"false\\\"\", \"dgidb\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"in\": \"\\\"all\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "0.18.1.0",
+                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"maskchar\": \"N\", \"out_format1\": \"fasta\", \"regions\": {\"__class__\": \"ConnectedValue\"}, \"tolower\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.0.0",
                         "type": "tool",
-                        "uuid": "7e13bb42-cf27-4251-85bb-9f695d711127",
+                        "uuid": "140608b3-48b3-46f2-92e3-2b9c3fb9e3b2",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "2ff2734e-c1c6-448b-95eb-e3f47329bc65"
+                                "label": "masked_ref_pool2",
+                                "output_name": "out_file1",
+                                "uuid": "af755a5e-2b20-49bc-9d52-34781f937f48"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.18.1.0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
                         "errors": null,
-                        "id": 9,
+                        "id": 15,
                         "input_connections": {
-                            "infile": {
-                                "id": 6,
-                                "output_name": "outfile"
+                            "input1": {
+                                "id": 1,
+                                "output_name": "output"
+                            },
+                            "regions": {
+                                "id": 13,
+                                "output_name": "out1"
                             }
                         },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool GEMINI query",
-                                "name": "infile"
-                            }
-                        ],
-                        "label": "GEMINI_query1",
-                        "name": "GEMINI query",
+                        "inputs": [],
+                        "label": "Mask Reference for Pool1",
+                        "name": "maskseq",
                         "outputs": [
                             {
-                                "name": "outfile",
-                                "type": "tabular"
+                                "name": "out_file1",
+                                "type": "fasta"
                             }
                         ],
                         "position": {
-                            "left": 1598,
-                            "top": 334
+                            "left": 1452.6333312988281,
+                            "top": 223.50729370117188
                         },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.18.1.0",
+                        "post_job_actions": {
+                            "RenameDatasetActionout_file1": {
+                                "action_arguments": {
+                                    "newname": "Masked reference for mapping of pool1"
+                                },
+                                "action_type": "RenameDatasetAction",
+                                "output_name": "out_file1"
+                            }
+                        },
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
                         "tool_shed_repository": {
-                            "changeset_revision": "5596c2dc4218",
-                            "name": "gemini_query",
-                            "owner": "iuc",
+                            "changeset_revision": "ce385837c160",
+                            "name": "emboss_5",
+                            "owner": "devteam",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"show_families\": \"\\\"false\\\"\", \"min_kindreds\": \"\\\"1\\\"\", \"sample_filter\": \"\\\"\\\"\", \"show_samples\": \"\\\"false\\\"\", \"__page__\": null, \"region\": \"\\\"\\\"\", \"gt_filter\": \"\\\"\\\"\", \"family_wise\": \"\\\"false\\\"\", \"q\": \"\\\"SELECT count(*) FROM variants WHERE in_dbsnp == 0\\\"\", \"header\": \"\\\"false\\\"\", \"dgidb\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"in\": \"\\\"all\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
-                        "tool_version": "0.18.1.0",
+                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"maskchar\": \"N\", \"out_format1\": \"fasta\", \"regions\": {\"__class__\": \"ConnectedValue\"}, \"tolower\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "5.0.0",
                         "type": "tool",
-                        "uuid": "00092a96-787b-444b-9b64-fe096588368b",
+                        "uuid": "3c8b86c1-7e53-4b72-b836-88a921a368ba",
+                        "when": null,
                         "workflow_outputs": [
                             {
-                                "label": null,
-                                "output_name": "outfile",
-                                "uuid": "2522c327-28ec-4e30-ac5f-cd751769e5ac"
+                                "label": "masked_ref_pool1",
+                                "output_name": "out_file1",
+                                "uuid": "0c3b5b20-c426-428c-a08b-c835a82477c1"
                             }
                         ]
                     }
                 ],
-                "parent_id": "variant-analysis/dip",
-                "path": "topics/variant-analysis/tutorials/dip/workflows/diploid.ga",
+                "parent_id": "variant-analysis/pox-tiled-amplicon",
+                "path": "topics/variant-analysis/tutorials/pox-tiled-amplicon/workflows/pox-virus-tiled-amplicon-ref-masking.ga",
                 "tags": [
+                    "GTN",
                     "variant-analysis"
                 ],
                 "test_results": null,
-                "tests": false,
-                "title": "Diploid",
+                "tests": true,
+                "title": "pox-virus-tiled-amplicon-ref-masking",
                 "topic_id": "variant-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-dip/versions/diploid",
-                "tutorial_id": "dip",
-                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/dip/workflows/diploid.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/dip/workflows/diploid.html",
-                "version": 3,
-                "wfid": "variant-analysis-dip",
-                "wfname": "diploid",
-                "workflow": "diploid.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-pox-tiled-amplicon/versions/pox-virus-tiled-amplicon-ref-masking",
+                "tutorial_id": "pox-tiled-amplicon",
+                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/pox-tiled-amplicon/workflows/pox-virus-tiled-amplicon-ref-masking.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/pox-tiled-amplicon/workflows/pox-virus-tiled-amplicon-ref-masking.html",
+                "version": 2,
+                "wfid": "variant-analysis-pox-tiled-amplicon",
+                "wfname": "pox-virus-tiled-amplicon-ref-masking",
+                "workflow": "pox-virus-tiled-amplicon-ref-masking.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.1.0.46-0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/0.0.3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.18.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.18.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.18.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1"
+                    "Cut1",
+                    "Grep1",
+                    "param_value_from_file",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2"
                 ],
-                "workflowhub_id": "1104"
+                "workflowhub_id": "1078"
             }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.60520"
+        ]
     },
     {
         "admin_install": {
@@ -288553,7 +296107,7 @@
                 {
                     "name": "bcftools_norm",
                     "owner": "iuc",
-                    "revisions": "1ca7418e46ee",
+                    "revisions": "aaac3ed89508",
                     "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
@@ -288588,14 +296142,14 @@
                 {
                     "name": "snpeff",
                     "owner": "iuc",
-                    "revisions": "9473cd297a76",
+                    "revisions": "6322be79bd8e",
                     "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "snpeff",
                     "owner": "iuc",
-                    "revisions": "9473cd297a76",
+                    "revisions": "6322be79bd8e",
                     "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
@@ -288608,7 +296162,7 @@
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: freebayes\n  owner: devteam\n  revisions: a5937157062f\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_rmdup\n  owner: devteam\n  revisions: 586f9e1cdb2b\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_norm\n  owner: iuc\n  revisions: 1ca7418e46ee\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_inheritance\n  owner: iuc\n  revisions: 2c68e29c3527\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_load\n  owner: iuc\n  revisions: 2270a8b83c12\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: abfd8a6544d7\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: 5826298f6a73\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n  owner: iuc\n  revisions: 9473cd297a76\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n  owner: iuc\n  revisions: 9473cd297a76\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n  owner: pjbriggs\n  revisions: d94aff5ee623\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: freebayes\n  owner: devteam\n  revisions: a5937157062f\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_rmdup\n  owner: devteam\n  revisions: 586f9e1cdb2b\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_norm\n  owner: iuc\n  revisions: aaac3ed89508\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_inheritance\n  owner: iuc\n  revisions: 2c68e29c3527\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_load\n  owner: iuc\n  revisions: 2270a8b83c12\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: abfd8a6544d7\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: 5826298f6a73\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n  owner: iuc\n  revisions: 6322be79bd8e\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n  owner: iuc\n  revisions: 6322be79bd8e\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: trimmomatic\n  owner: pjbriggs\n  revisions: d94aff5ee623\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
         "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/exome-seq/tutorial.json",
         "contributors": [
             {
@@ -288715,17 +296269,17 @@
         ],
         "dir": "topics/variant-analysis/tutorials/exome-seq",
         "edam_operation": [
-            "Sequencing quality control",
-            "Genetic variation analysis",
-            "Genome indexing",
-            "Sequence analysis",
             "Sequence alignment",
-            "Sequence composition calculation",
             "Read mapping",
+            "Sequencing quality control",
+            "Sequence analysis",
             "Generation",
-            "Validation",
+            "Statistical calculation",
             "Variant calling",
-            "Statistical calculation"
+            "Validation",
+            "Sequence composition calculation",
+            "Genetic variation analysis",
+            "Genome indexing"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -288739,6 +296293,7 @@
         "hands_on": true,
         "id": "variant-analysis/exome-seq",
         "inexact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.no",
             "UseGalaxy.org.au"
         ],
@@ -288758,7 +296313,7 @@
             "Jointly call variants and genotypes for a family trio from whole-exome sequencing data",
             "Use variant annotation and the observed inheritance pattern of a phenotype to identify candidate causative variants and to prioritize them"
         ],
-        "pageviews": 51237,
+        "pageviews": 52086,
         "pub_date": "2016-08-19",
         "questions": [
             "How do you identify genetic variants in samples based on exome sequencing data?",
@@ -288766,18 +296321,18 @@
         ],
         "short_id": "T00311",
         "short_tools": [
-            "gemini_inheritance",
-            "freebayes",
+            "bwa_mem",
+            "snpEff",
             "samtools_view",
-            "multiqc",
             "gemini_load",
-            "bcftools_norm",
-            "trimmomatic",
             "samtools_rmdup",
-            "fastqc",
-            "bwa_mem",
             "snpEff_download",
-            "snpEff"
+            "multiqc",
+            "gemini_inheritance",
+            "fastqc",
+            "trimmomatic",
+            "freebayes",
+            "bcftools_norm"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -288806,6 +296361,11 @@
                 }
             ],
             "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -288854,8 +296414,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 169,
-        "visitors": 26338,
+        "visit_duration": 168,
+        "visitors": 26968,
         "workflows": [
             {
                 "creators": [
@@ -289022,7 +296582,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nFather data\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nMother data\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nProband data\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nPEDigree data\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Samtools view\"];\n  0 -->|output| 4;\n  5[\"Samtools view\"];\n  1 -->|output| 5;\n  6[\"Samtools view\"];\n  2 -->|output| 6;\n  7[\"RmDup\"];\n  4 -->|outputsam| 7;\n  8[\"RmDup\"];\n  5 -->|outputsam| 8;\n  9[\"RmDup\"];\n  6 -->|outputsam| 9;\n  10[\"FreeBayes\"];\n  7 -->|output1| 10;\n  8 -->|output1| 10;\n  9 -->|output1| 10;\n  11[\"bcftools norm\"];\n  10 -->|output_vcf| 11;\n  12[\"SnpEff eff:\"];\n  11 -->|output_file| 12;\n  974b6b15-ccf7-4fe8-8a71-2b3fe8b45272[\"Output\\nsnpeff_variant_stats\"];\n  12 --> 974b6b15-ccf7-4fe8-8a71-2b3fe8b45272;\n  style 974b6b15-ccf7-4fe8-8a71-2b3fe8b45272 stroke:#2c3143,stroke-width:4px;\n  083b9686-5c6d-495f-9257-7243896e64d7[\"Output\\nnormalized_snpeff_annotated_variants\"];\n  12 --> 083b9686-5c6d-495f-9257-7243896e64d7;\n  style 083b9686-5c6d-495f-9257-7243896e64d7 stroke:#2c3143,stroke-width:4px;\n  13[\"GEMINI load\"];\n  12 -->|snpeff_output| 13;\n  3 -->|output| 13;\n  14[\"GEMINI inheritance pattern\"];\n  13 -->|outfile| 14;\n  c5a64822-3c68-495e-b2fd-4642b1aabb5a[\"Output\\ncandidate_mutations\"];\n  14 --> c5a64822-3c68-495e-b2fd-4642b1aabb5a;\n  style c5a64822-3c68-495e-b2fd-4642b1aabb5a stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
+                "modified": "2024-10-02 12:08:11 +0000",
                 "name": "Exome Seq Training Pre-Mapped W Cached Ref",
                 "outputs": [
                     {
@@ -289336,1132 +296896,110 @@
                                 "name": "proband_R1"
                             }
                         ],
-                        "label": "proband_R1",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 6.399993896484375,
-                            "top": 1085.474998474121
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "d085976e-0b16-4fc4-8cc1-d22d13276e95",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "reverse reads of the child/proband sample",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 5,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "reverse reads of the child/proband sample",
-                                "name": "proband_R2"
-                            }
-                        ],
-                        "label": "proband_R2",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 3.391101287840783,
-                            "top": 1193.4037194011914
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "e4b41228-d950-4b21-8293-76c80c54e1a8",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "Family tree with sex and phenotype information in PED format",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 6,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Family tree with sex and phenotype information in PED format",
-                                "name": "PEDigree data"
-                            }
-                        ],
-                        "label": "PEDigree data",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 1563.338553416431,
-                            "top": 1198.4751636451388
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "35c029e1-1165-4895-a6be-495d138d1e37",
-                        "when": null,
-                        "workflow_outputs": []
-                    }
-                ],
-                "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nfather_R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nfather_R2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nmother_R1\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nmother_R2\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nproband_R1\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nproband_R2\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nPEDigree data\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"FastQC\"];\n  0 -->|output| 7;\n  8[\"FastQC\"];\n  1 -->|output| 8;\n  9[\"Map with BWA-MEM\"];\n  0 -->|output| 9;\n  1 -->|output| 9;\n  10[\"FastQC\"];\n  2 -->|output| 10;\n  11[\"FastQC\"];\n  3 -->|output| 11;\n  12[\"Map with BWA-MEM\"];\n  2 -->|output| 12;\n  3 -->|output| 12;\n  13[\"FastQC\"];\n  4 -->|output| 13;\n  14[\"FastQC\"];\n  5 -->|output| 14;\n  15[\"Map with BWA-MEM\"];\n  4 -->|output| 15;\n  5 -->|output| 15;\n  16[\"Samtools view\"];\n  9 -->|bam_output| 16;\n  17[\"Samtools view\"];\n  12 -->|bam_output| 17;\n  18[\"MultiQC\"];\n  7 -->|text_file| 18;\n  8 -->|text_file| 18;\n  10 -->|text_file| 18;\n  11 -->|text_file| 18;\n  13 -->|text_file| 18;\n  14 -->|text_file| 18;\n  de867748-890a-454c-baf3-6a9313269975[\"Output\\nmultiqc_input_data\"];\n  18 --> de867748-890a-454c-baf3-6a9313269975;\n  style de867748-890a-454c-baf3-6a9313269975 stroke:#2c3143,stroke-width:4px;\n  19[\"Samtools view\"];\n  15 -->|bam_output| 19;\n  20[\"RmDup\"];\n  16 -->|outputsam| 20;\n  21[\"RmDup\"];\n  17 -->|outputsam| 21;\n  22[\"RmDup\"];\n  19 -->|outputsam| 22;\n  23[\"FreeBayes\"];\n  20 -->|output1| 23;\n  21 -->|output1| 23;\n  22 -->|output1| 23;\n  24[\"bcftools norm\"];\n  23 -->|output_vcf| 24;\n  25[\"SnpEff eff:\"];\n  24 -->|output_file| 25;\n  4aab5884-4099-4e41-a82d-c4e1ff19609f[\"Output\\nsnpeff_variant_stats\"];\n  25 --> 4aab5884-4099-4e41-a82d-c4e1ff19609f;\n  style 4aab5884-4099-4e41-a82d-c4e1ff19609f stroke:#2c3143,stroke-width:4px;\n  e5a2fbc7-acdd-4782-822a-91568cb8d5b8[\"Output\\nnormalized_snpeff_annotated_variants\"];\n  25 --> e5a2fbc7-acdd-4782-822a-91568cb8d5b8;\n  style e5a2fbc7-acdd-4782-822a-91568cb8d5b8 stroke:#2c3143,stroke-width:4px;\n  26[\"GEMINI load\"];\n  25 -->|snpeff_output| 26;\n  6 -->|output| 26;\n  27[\"GEMINI inheritance pattern\"];\n  26 -->|outfile| 27;\n  07bd4bba-e7d9-48a8-b812-5dc2b07712bd[\"Output\\ncandidate_mutations\"];\n  27 --> 07bd4bba-e7d9-48a8-b812-5dc2b07712bd;\n  style 07bd4bba-e7d9-48a8-b812-5dc2b07712bd stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "Exome Seq Training Full W Cached Ref",
-                "outputs": [
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
-                        "errors": null,
-                        "id": 18,
-                        "input_connections": {
-                            "results_0|software_cond|output_0|input": {
-                                "id": 7,
-                                "output_name": "text_file"
-                            },
-                            "results_0|software_cond|output_1|input": {
-                                "id": 8,
-                                "output_name": "text_file"
-                            },
-                            "results_0|software_cond|output_2|input": {
-                                "id": 10,
-                                "output_name": "text_file"
-                            },
-                            "results_0|software_cond|output_3|input": {
-                                "id": 11,
-                                "output_name": "text_file"
-                            },
-                            "results_0|software_cond|output_4|input": {
-                                "id": 13,
-                                "output_name": "text_file"
-                            },
-                            "results_0|software_cond|output_5|input": {
-                                "id": 14,
-                                "output_name": "text_file"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "MultiQC",
-                        "outputs": [
-                            {
-                                "name": "stats",
-                                "type": "input"
-                            },
-                            {
-                                "name": "html_report",
-                                "type": "html"
-                            }
-                        ],
-                        "position": {
-                            "left": 615.375,
-                            "top": 0.0
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionstats": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "stats"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "abfd8a6544d7",
-                            "name": "multiqc",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 3, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 4, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 5, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": false, \"title\": \"Input reads quality control\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.11+galaxy1",
-                        "type": "tool",
-                        "uuid": "13fa97d1-a167-4137-a68c-f066b50908b2",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "multiqc_input_data",
-                                "output_name": "html_report",
-                                "uuid": "de867748-890a-454c-baf3-6a9313269975"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2",
-                        "errors": null,
-                        "id": 25,
-                        "input_connections": {
-                            "input": {
-                                "id": 24,
-                                "output_name": "output_file"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool SnpEff eff:",
-                                "name": "intervals"
-                            },
-                            {
-                                "description": "runtime parameter for tool SnpEff eff:",
-                                "name": "transcripts"
-                            }
-                        ],
-                        "label": null,
-                        "name": "SnpEff eff:",
-                        "outputs": [
-                            {
-                                "name": "snpeff_output",
-                                "type": "vcf"
-                            },
-                            {
-                                "name": "statsFile",
-                                "type": "html"
-                            }
-                        ],
-                        "position": {
-                            "left": 1569.6792734462322,
-                            "top": 827.3970308639739
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2",
-                        "tool_shed_repository": {
-                            "changeset_revision": "5b80f544c67f",
-                            "name": "snpeff",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"annotations\": null, \"chr\": \"\", \"csvStats\": false, \"filter\": {\"specificEffects\": \"no\", \"__current_case__\": 0}, \"filterOut\": null, \"generate_stats\": true, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inputFormat\": \"vcf\", \"intervals\": {\"__class__\": \"RuntimeValue\"}, \"noLog\": true, \"offset\": \"default\", \"outputConditional\": {\"outputFormat\": \"vcf\", \"__current_case__\": 0}, \"snpDb\": {\"genomeSrc\": \"cached\", \"__current_case__\": 0, \"genomeVersion\": \"hg19\", \"reg_section\": {\"regulation\": null}}, \"spliceRegion\": {\"setSpliceRegions\": \"no\", \"__current_case__\": 0}, \"spliceSiteSize\": \"2\", \"transcripts\": {\"__class__\": \"RuntimeValue\"}, \"udLength\": \"5000\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "4.3+T.galaxy2",
-                        "type": "tool",
-                        "uuid": "02ce6c03-7a90-46c2-8d38-3fce5366eaab",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "snpeff_variant_stats",
-                                "output_name": "statsFile",
-                                "uuid": "4aab5884-4099-4e41-a82d-c4e1ff19609f"
-                            },
-                            {
-                                "label": "normalized_snpeff_annotated_variants",
-                                "output_name": "snpeff_output",
-                                "uuid": "e5a2fbc7-acdd-4782-822a-91568cb8d5b8"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1",
-                        "errors": null,
-                        "id": 27,
-                        "input_connections": {
-                            "infile": {
-                                "id": 26,
-                                "output_name": "outfile"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "GEMINI inheritance pattern",
-                        "outputs": [
-                            {
-                                "name": "outfile",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 2036.9508077255032,
-                            "top": 1034.4095449070464
-                        },
-                        "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "18d13111692b",
-                            "name": "gemini_inheritance",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/hg19.len\", \"family_wise\": {\"min_kindreds\": \"1\", \"families\": \"\", \"per_variant_selection\": {\"enabled\": \"no\", \"__current_case__\": 0, \"min_dp\": \"0\", \"min_gq\": \"0\", \"max_pl\": \"-1\"}}, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"inheritance\": {\"pattern_type\": \"autosomal_recessive\", \"__current_case__\": 2, \"constraint\": [{\"__index__\": 0, \"filter\": \"impact_severity != 'LOW'\"}], \"lenient\": false, \"allow_unaffected\": false}, \"oformat\": {\"report\": {\"report_selector\": \"custom\", \"__current_case__\": 2, \"columns\": [\"max_aaf_all\"], \"extra_cols\": \"chrom, start, ref, alt, impact, gene, clinvar_sig, clinvar_disease_name, clinvar_gene_phenotype, rs_ids\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "0.20.1",
-                        "type": "tool",
-                        "uuid": "eecc879f-93bc-4513-840e-b56704e5ed77",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "candidate_mutations",
-                                "output_name": "outfile",
-                                "uuid": "07bd4bba-e7d9-48a8-b812-5dc2b07712bd"
-                            }
-                        ]
-                    }
-                ],
-                "parent_id": "variant-analysis/exome-seq",
-                "path": "topics/variant-analysis/tutorials/exome-seq/workflows/workflow_exome_seq_full.ga",
-                "tags": [
-                    "variant-analysis"
-                ],
-                "test_results": null,
-                "tests": true,
-                "title": "Exome Seq Training Full W Cached Ref",
-                "topic_id": "variant-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-exome-seq/versions/workflow-exome-seq-full",
-                "tutorial_id": "exome-seq",
-                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/workflows/workflow_exome_seq_full.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/workflows/workflow_exome_seq_full.html",
-                "version": 5,
-                "wfid": "variant-analysis-exome-seq",
-                "wfname": "workflow-exome-seq-full",
-                "workflow": "workflow_exome_seq_full.ga",
-                "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2"
-                ],
-                "workflowhub_id": "1114"
-            }
-        ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.3054169"
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "fbf99087e067",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "fbf99087e067",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "emboss_5",
-                    "owner": "devteam",
-                    "revisions": "63dd26468588",
-                    "tool_panel_section_label": "EMBOSS",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "3d0c7bdf12f5",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastqc",
-                    "owner": "devteam",
-                    "revisions": "5ec9f6bceaee",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_stats",
-                    "owner": "devteam",
-                    "revisions": "fed4aa48ba09",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bcftools_consensus",
-                    "owner": "iuc",
-                    "revisions": "1171446da5db",
-                    "tool_panel_section_label": "Variant Calling",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastp",
-                    "owner": "iuc",
-                    "revisions": "c59d48774d03",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "jbrowse",
-                    "owner": "iuc",
-                    "revisions": "a6e57ff585c0",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "jvarkit_wgscoverageplotter",
-                    "owner": "iuc",
-                    "revisions": "ac048a34cac3",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "kraken2",
-                    "owner": "iuc",
-                    "revisions": "20e2f64aa1fe",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mosdepth",
-                    "owner": "iuc",
-                    "revisions": "5854d0da92b4",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "multiqc",
-                    "owner": "iuc",
-                    "revisions": "abfd8a6544d7",
-                    "tool_panel_section_label": "Quality Control",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "qualimap_bamqc",
-                    "owner": "iuc",
-                    "revisions": "4a89c6f84425",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "snippy",
-                    "owner": "iuc",
-                    "revisions": "d220115f882b",
-                    "tool_panel_section_label": "Variant Calling",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "tb_variant_filter",
-                    "owner": "iuc",
-                    "revisions": "32f14a2723ec",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "tbprofiler",
-                    "owner": "iuc",
-                    "revisions": "4839e590cb26",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "tbvcfreport",
-                    "owner": "iuc",
-                    "revisions": "42818629ec4c",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "tbvcfreport",
-                    "owner": "iuc",
-                    "revisions": "9793bc5d741b",
-                    "tool_panel_section_label": "Annotation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: emboss_5\n  owner: devteam\n  revisions: 63dd26468588\n  tool_panel_section_label: EMBOSS\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 3d0c7bdf12f5\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastqc\n  owner: devteam\n  revisions: 5ec9f6bceaee\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: fed4aa48ba09\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bcftools_consensus\n  owner: iuc\n  revisions: 1171446da5db\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: c59d48774d03\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jbrowse\n  owner: iuc\n  revisions: a6e57ff585c0\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: jvarkit_wgscoverageplotter\n  owner: iuc\n  revisions: ac048a34cac3\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: kraken2\n  owner: iuc\n  revisions: 20e2f64aa1fe\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mosdepth\n  owner: iuc\n  revisions: 5854d0da92b4\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: abfd8a6544d7\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qualimap_bamqc\n  owner: iuc\n  revisions: 4a89c6f84425\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snippy\n  owner: iuc\n  revisions: d220115f882b\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tb_variant_filter\n  owner: iuc\n  revisions: 32f14a2723ec\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbprofiler\n  owner: iuc\n  revisions: 4839e590cb26\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbvcfreport\n  owner: iuc\n  revisions: 42818629ec4c\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: tbvcfreport\n  owner: iuc\n  revisions: 9793bc5d741b\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.json",
-        "contributors": [
-            {
-                "bio": "Research at the South African National Bioinformatics Institute",
-                "id": "pvanheus",
-                "joined": "2017-09",
-                "name": "Peter van Heusden",
-                "orcid": "0000-0001-6553-5274",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/pvanheus/",
-                "twitter": "pvanheus",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/pvanheus.json"
-            },
-            {
-                "elixir_node": "au",
-                "email": "simon.gladman@unimelb.edu.au",
-                "id": "slugger70",
-                "in_memoriam": "<a href=\"https://www.biocommons.org.au/news/simon-gladman\">Simon Gladman, system administrator of UseGalaxy.org.au, passed away on November 26, 2022</a>\n\n<a href=\"https://galaxyproject.org/news/2022-11-28-simon-gladman/\">He was a fantastic teacher, tutorial author, system administrator, and warm and welcoming friend.</a> He contributed heavily to the Galaxy Training Network and especially the Galaxy Administration community over the years, we will miss him dearly. The GTN and GAT would not be what they are today, without him.\n\n\u201cHave I told you about my watch?\u201d",
-                "joined": "2017-09",
-                "name": "Simon Gladman",
-                "orcid": "0000-0002-6100-4385",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/slugger70/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/slugger70.json"
-            },
-            {
-                "id": "thobalose",
-                "joined": "2019-11",
-                "name": "Thoba Lose",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/thobalose/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/thobalose.json"
-            }
-        ],
-        "dir": "topics/variant-analysis/tutorials/tb-variant-analysis",
-        "edam_ontology": [
-            "topic_0622",
-            "topic_3301",
-            "topic_0196",
-            "topic_0199",
-            "topic_3305",
-            "topic_3324"
-        ],
-        "edam_operation": [
-            "Global alignment",
-            "Sequencing quality control",
-            "Sequence contamination filtering",
-            "Sequence alignment",
-            "Sequence analysis",
-            "Sequence composition calculation",
-            "Sequence alignment analysis",
-            "Taxonomic classification",
-            "Phylogenetic tree generation",
-            "Variant calling",
-            "Local alignment",
-            "Phylogenetic tree visualisation",
-            "Validation",
-            "Genome visualisation",
-            "Statistical calculation",
-            "Antimicrobial resistance prediction"
-        ],
-        "edam_topic": [
-            "Genomics",
-            "Microbiology",
-            "Sequence assembly",
-            "Genetic variation",
-            "Public health and epidemiology",
-            "Infectious disease"
-        ],
-        "exact_supported_servers": [],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "variant-analysis/tb-variant-analysis",
-        "inexact_supported_servers": [],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "variants in _M. tuberculosis_ sequencing data can be discovered using common microbial bioinformatics tools",
-            "it is not enough to just call variants, variant calling involves multiple quality control steps",
-            "the choice of reference genome and some quality control procedures are species-specific, and require knowledge of the organism in question",
-            "batches of samples can be processed using Galaxy dataset collections and workflows"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-07-26",
-        "objectives": [
-            "How should we filter those variants",
-            "How can we predict drug resistance from those variants",
-            "How do we annotate those variants"
-        ],
-        "pageviews": 8997,
-        "pub_date": "2020-07-25",
-        "questions": [
-            "How do we detect differences between a set of reads from _M. tuberculosis_ (Mtb) and the Mtb reference genome"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "pvanheus",
-                    "nagoue",
-                    "hexylena"
-                ],
-                "date": "2021-02-15",
-                "galaxy_version": "21.01",
-                "length": "40M",
-                "speakers": [
-                    "pvanheus"
-                ],
-                "youtube_id": "G1DmquX6Wh8"
-            },
-            {
-                "captioners": [
-                    "pvanheus"
-                ],
-                "date": "2024-06-11",
-                "galaxy_version": "24.0",
-                "length": "1H17M",
-                "speakers": [
-                    "pvanheus"
-                ],
-                "youtube_id": "-nJPngFk36c"
-            }
-        ],
-        "short_id": "T00319",
-        "short_tools": [
-            "tp_awk_tool",
-            "kraken2",
-            "bcftools_consensus",
-            "mosdepth",
-            "EMBOSS: seqret84",
-            "tb_profiler_profile",
-            "qualimap_bamqc",
-            "samtools_stats",
-            "tb_variant_filter",
-            "tp_sed_tool",
-            "EMBOSS:%20seqret84",
-            "upload1",
-            "tbvcfreport",
-            "fastp",
-            "jbrowse",
-            "multiqc",
-            "jvarkit_wgscoverageplotter",
-            "snippy",
-            "fastqc",
-            "__FLATTEN__"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "one-health",
-        "supported_servers": {
-            "exact": [],
-            "inexact": []
-        },
-        "symlink": null,
-        "tags": [
-            "prokaryote",
-            "one-health",
-            "microgalaxy",
-            "tuberculosis"
-        ],
-        "time_estimation": "2h",
-        "title": "M. tuberculosis Variant Analysis",
-        "tools": [
-            "__FLATTEN__",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: seqret84/5.0.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS:%20seqret84/5.0.0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/jvarkit_wgscoverageplotter/jvarkit_wgscoverageplotter/20201223+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/mosdepth/mosdepth/0.3.8+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.4.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.2.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.1+galaxy0",
-            "upload1"
-        ],
-        "topic_name": "variant-analysis",
-        "topic_name_human": "Variant Analysis",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "tb-variant-analysis",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.json"
-        },
-        "version": 30,
-        "video": false,
-        "video_versions": 2,
-        "video_view": 0,
-        "visit_duration": 177,
-        "visitors": 5641,
-        "workflows": [
-            {
-                "creators": [
-                    {
-                        "class": "Person",
-                        "identifier": "0000-0001-6553-5274",
-                        "name": "Peter van Heusden"
-                    }
-                ],
-                "description": "Predict variants and drug resistance from M. tuberculosis sequence samples (Illumina)",
-                "features": {
-                    "comments": false,
-                    "parameters": true,
-                    "report": {
-                        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
-                    },
-                    "subworkflows": false
-                },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Collection\\nReads\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nReference Genome\"]\n  2[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMinimum depth of coverage\"]\n  3[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nMinimum variant allele frequency\"]\n  4[color=lightgreen,label=\"\u2139\ufe0f Input Parameter\\nAdditional BWA-MEM options\"]\n  5[label=\"fastp\"]\n  0 -> 5 [label=\"output\"]\n  6[label=\"seqret\"]\n  1 -> 6 [label=\"output\"]\n  7[label=\"snippy\"]\n  4 -> 7 [label=\"output\"]\n  2 -> 7 [label=\"output\"]\n  3 -> 7 [label=\"output\"]\n  5 -> 7 [label=\"output_paired_coll\"]\n  1 -> 7 [label=\"output\"]\n  8[label=\"Kraken2\"]\n  5 -> 8 [label=\"output_paired_coll\"]\n  kc7abf2bfed4c433ea6959eca61282bb5[color=lightseagreen,label=\"Output\\nreport_output\"]\n  8 -> kc7abf2bfed4c433ea6959eca61282bb5\n  k083a0e5177804c91a071dc0e4641d060[color=lightseagreen,label=\"Output\\noutput\"]\n  8 -> k083a0e5177804c91a071dc0e4641d060\n  9[label=\"QualiMap BamQC\"]\n  7 -> 9 [label=\"snpsbam\"]\n  10[label=\"mosdepth\"]\n  2 -> 10 [label=\"output\"]\n  7 -> 10 [label=\"snpsbam\"]\n  11[label=\"TB Variant Filter\"]\n  7 -> 11 [label=\"snpvcf\"]\n  12[label=\"TB-Profiler Profile\"]\n  7 -> 12 [label=\"snpsbam\"]\n  k335635b4a4de4980ad0268f0035daeaa[color=lightseagreen,label=\"Output\\noutput_txt\"]\n  12 -> k335635b4a4de4980ad0268f0035daeaa\n  13[label=\"TB Variant Filter\"]\n  7 -> 13 [label=\"snpvcf\"]\n  14[label=\"Flatten collection\"]\n  9 -> 14 [label=\"raw_data\"]\n  15[label=\"Text reformatting\"]\n  10 -> 15 [label=\"output_quantized_bed\"]\n  16[label=\"Text transformation\"]\n  11 -> 16 [label=\"output1\"]\n  k007df8c2bd13495f8904abf31d4594d0[color=lightseagreen,label=\"Output\\nFinal annotated VCF\"]\n  16 -> k007df8c2bd13495f8904abf31d4594d0\n  17[label=\"MultiQC\"]\n  5 -> 17 [label=\"report_json\"]\n  14 -> 17 [label=\"output\"]\n  k5952823575254ef9881036f1ed0f01f6[color=lightseagreen,label=\"Output\\nhtml_report\"]\n  17 -> k5952823575254ef9881036f1ed0f01f6\n  18[label=\"bcftools consensus\"]\n  13 -> 18 [label=\"output1\"]\n  6 -> 18 [label=\"out_file1\"]\n  15 -> 18 [label=\"outfile\"]\n  kc71b135d35f944d0a20ef25528e518af[color=lightseagreen,label=\"Output\\nconsensus_genome\"]\n  18 -> kc71b135d35f944d0a20ef25528e518af\n  19[label=\"TB Variant Report\"]\n  16 -> 19 [label=\"output\"]\n  12 -> 19 [label=\"results_json\"]\n  k959528d2f8f2444099cf44fddd6c5069[color=lightseagreen,label=\"Output\\ndrug_resistance_report_html\"]\n  19 -> k959528d2f8f2444099cf44fddd6c5069\n  k4d9636eb075b4fd2a1e41a7c37a17fc0[color=lightseagreen,label=\"Output\\nvariants_report_html\"]\n  19 -> k4d9636eb075b4fd2a1e41a7c37a17fc0\n}",
-                "history": [
-                    {
-                        "hash": "c0042e7f333bb9758580a564dbf559e83396a6d3",
-                        "message": "Update to address comments from wm",
-                        "num": 14,
-                        "short_hash": "c0042e7f3",
-                        "unix": "1718025591"
-                    },
-                    {
-                        "hash": "01cf3d5e27fb411603014ca3e0729b2daacc0a0d",
-                        "message": "Add snippers for running workflow from workflowhub.eu and jbrowse vis",
-                        "num": 13,
-                        "short_hash": "01cf3d5e2",
-                        "unix": "1717788409"
-                    },
-                    {
-                        "hash": "d3db4cd3e349677c907c71a761fde1b2935928d2",
-                        "message": "Update the M. tuberculosis variant analysis tutorial * Update all tools to latest versions * Change to fastp instead of Trimmomatic * Add section on running workflow * Update workflow and workflow test",
-                        "num": 12,
-                        "short_hash": "d3db4cd3e",
-                        "unix": "1717771237"
-                    },
-                    {
-                        "hash": "d61d5645fa6b21c25cd5d09f540c4e584b35f2c2",
-                        "message": "Update tb_variant_filter to v. 0.4.0",
-                        "num": 11,
-                        "short_hash": "d61d5645f",
-                        "unix": "1695643686"
-                    },
-                    {
-                        "hash": "c89f11fe32c66c1da9f058ec3fa522e8b18cba82",
-                        "message": "Update some tools in tuberculosis variant analysis tutorial (#4070)",
-                        "num": 10,
-                        "short_hash": "c89f11fe3",
-                        "unix": "1682624753"
-                    },
-                    {
-                        "hash": "fa9e9fb000ef9d2ab91acc67c4f338c213d641e2",
-                        "message": "New variant of tb_variant_filter and tbprofiler, more detail on tb_variant_filter",
-                        "num": 9,
-                        "short_hash": "fa9e9fb00",
-                        "unix": "1672566129"
-                    },
-                    {
-                        "hash": "6e9c1860b186754249a0a90d9957dbace653e9ac",
-                        "message": "Restore workflow indentation and fix WF step order",
-                        "num": 8,
-                        "short_hash": "6e9c1860b",
-                        "unix": "1648048765"
-                    },
-                    {
-                        "hash": "354e9edf1340c37133b7d1834cea608895acebc0",
-                        "message": "Use correct snippy wrapper version everywhere",
-                        "num": 7,
-                        "short_hash": "354e9edf1",
-                        "unix": "1648028595"
-                    },
-                    {
-                        "hash": "6f476a03271eeabffcf0877e8a402f7af815deba",
-                        "message": "Update snippy to 4.6.0",
-                        "num": 6,
-                        "short_hash": "6f476a032",
-                        "unix": "1647976648"
-                    },
-                    {
-                        "hash": "946f6f60f8e068a147f03d89f369f19e552793da",
-                        "message": "Generate cleaner intermediate diff",
-                        "num": 5,
-                        "short_hash": "946f6f60f",
-                        "unix": "1647938051"
-                    },
-                    {
-                        "hash": "8e46a42b5a664cf72ea7e2aae61739348f64dfea",
-                        "message": "Autoupdate workflow, change Kraken2 test",
-                        "num": 4,
-                        "short_hash": "8e46a42b5",
-                        "unix": "1647929062"
-                    },
-                    {
-                        "hash": "f98407ff47fe6ea903372a39b09530ae075d65b3",
-                        "message": "tb-variant-analysis: label workflow outputs and add test",
-                        "num": 3,
-                        "short_hash": "f98407ff4",
-                        "unix": "1595713523"
-                    },
-                    {
-                        "hash": "392830f9b51662e8028b8984f48f827be8a10aed",
-                        "message": "Reformat tb-variant-analysis workflow",
-                        "num": 2,
-                        "short_hash": "392830f9b",
-                        "unix": "1595707349"
-                    },
-                    {
-                        "hash": "2e73bb7aa538d3fb94e7f7ca21bfc6078d35e73f",
-                        "message": "Update M. tuberculosis variant analysis tutorial with new data and workflow",
-                        "num": 1,
-                        "short_hash": "2e73bb7aa",
-                        "unix": "1595705571"
-                    }
-                ],
-                "inputs": [
-                    {
-                        "annotation": "List of paired Illumina reads (set format to fastqsanger or fastqsanger.gz as appropriate)",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 0,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "List of paired Illumina reads (set format to fastqsanger or fastqsanger.gz as appropriate)",
-                                "name": "Reads"
-                            }
-                        ],
-                        "label": "Reads",
-                        "name": "Input dataset collection",
-                        "outputs": [],
-                        "position": {
-                            "left": 0,
-                            "top": 197.65334499942068
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
-                        "tool_version": null,
-                        "type": "data_collection_input",
-                        "uuid": "2bfdfb62-da85-4d2d-8609-8f5e6975b4b3",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "M. tuberculosis reference genome (must be in H37Rv coordinates. The M. tuberculosis inferred ancestral genome is recommended)",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 1,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "M. tuberculosis reference genome (must be in H37Rv coordinates. The M. tuberculosis inferred ancestral genome is recommended)",
-                                "name": "Reference Genome"
-                            }
-                        ],
-                        "label": "Reference Genome",
-                        "name": "Input dataset",
-                        "outputs": [],
-                        "position": {
-                            "left": 1.2375059369900399,
-                            "top": 468.60335731890825
-                        },
-                        "tool_id": null,
-                        "tool_state": "{\"optional\": false, \"format\": [\"genbank\"], \"tag\": null}",
-                        "tool_version": null,
-                        "type": "data_input",
-                        "uuid": "023233a0-8cb1-4558-8861-cd246ab58bac",
-                        "when": null,
-                        "workflow_outputs": []
-                    },
-                    {
-                        "annotation": "Minimum depth of coverage for a position on the genome",
-                        "content_id": null,
-                        "errors": null,
-                        "id": 2,
-                        "input_connections": {},
-                        "inputs": [
-                            {
-                                "description": "Minimum depth of coverage for a position on the genome",
-                                "name": "Minimum depth of coverage"
-                            }
-                        ],
-                        "label": "Minimum depth of coverage",
-                        "name": "Input parameter",
+                        "label": "proband_R1",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 1.8793911063654463,
-                            "top": 625.941216238093
+                            "left": 6.399993896484375,
+                            "top": 1085.474998474121
                         },
                         "tool_id": null,
-                        "tool_state": "{\"default\": 10, \"parameter_type\": \"integer\", \"optional\": true}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "e31bf396-08b6-43ce-872a-545a5e4580c6",
+                        "type": "data_input",
+                        "uuid": "d085976e-0b16-4fc4-8cc1-d22d13276e95",
                         "when": null,
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "Minimum proportion of reads that must support a variant for it to be called",
+                        "annotation": "reverse reads of the child/proband sample",
                         "content_id": null,
                         "errors": null,
-                        "id": 3,
+                        "id": 5,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Minimum proportion of reads that must support a variant for it to be called",
-                                "name": "Minimum variant allele frequency"
+                                "description": "reverse reads of the child/proband sample",
+                                "name": "proband_R2"
                             }
                         ],
-                        "label": "Minimum variant allele frequency",
-                        "name": "Input parameter",
+                        "label": "proband_R2",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 1.358958473709409,
-                            "top": 769.7667492120408
+                            "left": 3.391101287840783,
+                            "top": 1193.4037194011914
                         },
                         "tool_id": null,
-                        "tool_state": "{\"default\": 0.9, \"parameter_type\": \"float\", \"optional\": true}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "d1814962-a30d-463a-a081-857a5141385b",
+                        "type": "data_input",
+                        "uuid": "e4b41228-d950-4b21-8293-76c80c54e1a8",
                         "when": null,
                         "workflow_outputs": []
                     },
                     {
-                        "annotation": "Increasing the minimum seed length (-k) parameter can help eliminate matches from contaminants. If used this should be set to 2/3rds of the read length, i.e. the string \"-k 100\" should be used for 150 base pair reads",
+                        "annotation": "Family tree with sex and phenotype information in PED format",
                         "content_id": null,
                         "errors": null,
-                        "id": 4,
+                        "id": 6,
                         "input_connections": {},
                         "inputs": [
                             {
-                                "description": "Increasing the minimum seed length (-k) parameter can help eliminate matches from contaminants. If used this should be set to 2/3rds of the read length, i.e. the string \"-k 100\" should be used for 150 base pair reads",
-                                "name": "Additional BWA-MEM options"
+                                "description": "Family tree with sex and phenotype information in PED format",
+                                "name": "PEDigree data"
                             }
                         ],
-                        "label": "Additional BWA-MEM options",
-                        "name": "Input parameter",
+                        "label": "PEDigree data",
+                        "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 7.8094297093662135,
-                            "top": 931.4341211532
+                            "left": 1563.338553416431,
+                            "top": 1198.4751636451388
                         },
                         "tool_id": null,
-                        "tool_state": "{\"parameter_type\": \"text\", \"optional\": true}",
+                        "tool_state": "{\"optional\": false, \"tag\": null}",
                         "tool_version": null,
-                        "type": "parameter_input",
-                        "uuid": "40d47253-c7c5-471b-871c-9a19fbe60bfe",
+                        "type": "data_input",
+                        "uuid": "35c029e1-1165-4895-a6be-495d138d1e37",
                         "when": null,
                         "workflow_outputs": []
                     }
                 ],
-                "license": "AGPL-3.0-or-later",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nReads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference Genome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nMinimum depth of coverage\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nMinimum variant allele frequency\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nAdditional BWA-MEM options\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"fastp\"];\n  0 -->|output| 5;\n  6[\"seqret\"];\n  1 -->|output| 6;\n  7[\"snippy\"];\n  4 -->|output| 7;\n  2 -->|output| 7;\n  3 -->|output| 7;\n  5 -->|output_paired_coll| 7;\n  1 -->|output| 7;\n  8[\"Kraken2\"];\n  5 -->|output_paired_coll| 8;\n  c7abf2bf-ed4c-433e-a695-9eca61282bb5[\"Output\\nreport_output\"];\n  8 --> c7abf2bf-ed4c-433e-a695-9eca61282bb5;\n  style c7abf2bf-ed4c-433e-a695-9eca61282bb5 stroke:#2c3143,stroke-width:4px;\n  083a0e51-7780-4c91-a071-dc0e4641d060[\"Output\\noutput\"];\n  8 --> 083a0e51-7780-4c91-a071-dc0e4641d060;\n  style 083a0e51-7780-4c91-a071-dc0e4641d060 stroke:#2c3143,stroke-width:4px;\n  9[\"QualiMap BamQC\"];\n  7 -->|snpsbam| 9;\n  10[\"mosdepth\"];\n  2 -->|output| 10;\n  7 -->|snpsbam| 10;\n  11[\"TB Variant Filter\"];\n  7 -->|snpvcf| 11;\n  12[\"TB-Profiler Profile\"];\n  7 -->|snpsbam| 12;\n  335635b4-a4de-4980-ad02-68f0035daeaa[\"Output\\noutput_txt\"];\n  12 --> 335635b4-a4de-4980-ad02-68f0035daeaa;\n  style 335635b4-a4de-4980-ad02-68f0035daeaa stroke:#2c3143,stroke-width:4px;\n  13[\"TB Variant Filter\"];\n  7 -->|snpvcf| 13;\n  14[\"Flatten collection\"];\n  9 -->|raw_data| 14;\n  15[\"Text reformatting\"];\n  10 -->|output_quantized_bed| 15;\n  16[\"Text transformation\"];\n  11 -->|output1| 16;\n  007df8c2-bd13-495f-8904-abf31d4594d0[\"Output\\nFinal annotated VCF\"];\n  16 --> 007df8c2-bd13-495f-8904-abf31d4594d0;\n  style 007df8c2-bd13-495f-8904-abf31d4594d0 stroke:#2c3143,stroke-width:4px;\n  17[\"MultiQC\"];\n  5 -->|report_json| 17;\n  14 -->|output| 17;\n  59528235-7525-4ef9-8810-36f1ed0f01f6[\"Output\\nhtml_report\"];\n  17 --> 59528235-7525-4ef9-8810-36f1ed0f01f6;\n  style 59528235-7525-4ef9-8810-36f1ed0f01f6 stroke:#2c3143,stroke-width:4px;\n  18[\"bcftools consensus\"];\n  13 -->|output1| 18;\n  6 -->|out_file1| 18;\n  15 -->|outfile| 18;\n  c71b135d-35f9-44d0-a20e-f25528e518af[\"Output\\nconsensus_genome\"];\n  18 --> c71b135d-35f9-44d0-a20e-f25528e518af;\n  style c71b135d-35f9-44d0-a20e-f25528e518af stroke:#2c3143,stroke-width:4px;\n  19[\"TB Variant Report\"];\n  16 -->|output| 19;\n  12 -->|results_json| 19;\n  959528d2-f8f2-4440-99cf-44fddd6c5069[\"Output\\ndrug_resistance_report_html\"];\n  19 --> 959528d2-f8f2-4440-99cf-44fddd6c5069;\n  style 959528d2-f8f2-4440-99cf-44fddd6c5069 stroke:#2c3143,stroke-width:4px;\n  4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0[\"Output\\nvariants_report_html\"];\n  19 --> 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0;\n  style 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "TB Variant Analysis v1.0",
+                "license": "MIT",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nfather_R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nfather_R2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nmother_R1\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nmother_R2\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nproband_R1\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nproband_R2\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nPEDigree data\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"FastQC\"];\n  0 -->|output| 7;\n  8[\"FastQC\"];\n  1 -->|output| 8;\n  9[\"Map with BWA-MEM\"];\n  0 -->|output| 9;\n  1 -->|output| 9;\n  10[\"FastQC\"];\n  2 -->|output| 10;\n  11[\"FastQC\"];\n  3 -->|output| 11;\n  12[\"Map with BWA-MEM\"];\n  2 -->|output| 12;\n  3 -->|output| 12;\n  13[\"FastQC\"];\n  4 -->|output| 13;\n  14[\"FastQC\"];\n  5 -->|output| 14;\n  15[\"Map with BWA-MEM\"];\n  4 -->|output| 15;\n  5 -->|output| 15;\n  16[\"Samtools view\"];\n  9 -->|bam_output| 16;\n  17[\"Samtools view\"];\n  12 -->|bam_output| 17;\n  18[\"MultiQC\"];\n  7 -->|text_file| 18;\n  8 -->|text_file| 18;\n  10 -->|text_file| 18;\n  11 -->|text_file| 18;\n  13 -->|text_file| 18;\n  14 -->|text_file| 18;\n  de867748-890a-454c-baf3-6a9313269975[\"Output\\nmultiqc_input_data\"];\n  18 --> de867748-890a-454c-baf3-6a9313269975;\n  style de867748-890a-454c-baf3-6a9313269975 stroke:#2c3143,stroke-width:4px;\n  19[\"Samtools view\"];\n  15 -->|bam_output| 19;\n  20[\"RmDup\"];\n  16 -->|outputsam| 20;\n  21[\"RmDup\"];\n  17 -->|outputsam| 21;\n  22[\"RmDup\"];\n  19 -->|outputsam| 22;\n  23[\"FreeBayes\"];\n  20 -->|output1| 23;\n  21 -->|output1| 23;\n  22 -->|output1| 23;\n  24[\"bcftools norm\"];\n  23 -->|output_vcf| 24;\n  25[\"SnpEff eff:\"];\n  24 -->|output_file| 25;\n  4aab5884-4099-4e41-a82d-c4e1ff19609f[\"Output\\nsnpeff_variant_stats\"];\n  25 --> 4aab5884-4099-4e41-a82d-c4e1ff19609f;\n  style 4aab5884-4099-4e41-a82d-c4e1ff19609f stroke:#2c3143,stroke-width:4px;\n  e5a2fbc7-acdd-4782-822a-91568cb8d5b8[\"Output\\nnormalized_snpeff_annotated_variants\"];\n  25 --> e5a2fbc7-acdd-4782-822a-91568cb8d5b8;\n  style e5a2fbc7-acdd-4782-822a-91568cb8d5b8 stroke:#2c3143,stroke-width:4px;\n  26[\"GEMINI load\"];\n  25 -->|snpeff_output| 26;\n  6 -->|output| 26;\n  27[\"GEMINI inheritance pattern\"];\n  26 -->|outfile| 27;\n  07bd4bba-e7d9-48a8-b812-5dc2b07712bd[\"Output\\ncandidate_mutations\"];\n  27 --> 07bd4bba-e7d9-48a8-b812-5dc2b07712bd;\n  style 07bd4bba-e7d9-48a8-b812-5dc2b07712bd stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "Exome Seq Training Full W Cached Ref",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
-                        "errors": null,
-                        "id": 8,
-                        "input_connections": {
-                            "single_paired|input_pair": {
-                                "id": 5,
-                                "output_name": "output_paired_coll"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool Kraken2",
-                                "name": "single_paired"
-                            }
-                        ],
-                        "label": null,
-                        "name": "Kraken2",
-                        "outputs": [
-                            {
-                                "name": "report_output",
-                                "type": "tabular"
-                            },
-                            {
-                                "name": "output",
-                                "type": "tabular"
-                            }
-                        ],
-                        "position": {
-                            "left": 1605.1346167188794,
-                            "top": 0
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionoutput": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output"
-                            },
-                            "TagDatasetActionreport_output": {
-                                "action_arguments": {
-                                    "tags": "kraken_report"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "report_output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "20e2f64aa1fe",
-                            "name": "kraken2",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"confidence\": \"0.0\", \"kraken2_database\": \"pluspf2021-05\", \"min_base_quality\": \"0\", \"minimum_hit_groups\": \"2\", \"quick\": false, \"report\": {\"create_report\": true, \"use_mpa_style\": false, \"report_zero_counts\": false, \"report_minimizer_data\": false}, \"single_paired\": {\"single_paired_selector\": \"collection\", \"__current_case__\": 0, \"input_pair\": {\"__class__\": \"ConnectedValue\"}}, \"split_reads\": false, \"use_names\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "2.1.1+galaxy1",
-                        "type": "tool",
-                        "uuid": "60b17d56-0ef9-4829-829e-923f66de5e2f",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "report_output",
-                                "output_name": "report_output",
-                                "uuid": "c7abf2bf-ed4c-433e-a695-9eca61282bb5"
-                            },
-                            {
-                                "label": "output",
-                                "output_name": "output",
-                                "uuid": "083a0e51-7780-4c91-a071-dc0e4641d060"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.2.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
                         "errors": null,
-                        "id": 12,
+                        "id": 18,
                         "input_connections": {
-                            "fastq_or_bam|bam_input": {
+                            "results_0|software_cond|output_0|input": {
                                 "id": 7,
-                                "output_name": "snpsbam"
-                            }
-                        },
-                        "inputs": [
-                            {
-                                "description": "runtime parameter for tool TB-Profiler Profile",
-                                "name": "fastq_or_bam"
-                            }
-                        ],
-                        "label": null,
-                        "name": "TB-Profiler Profile",
-                        "outputs": [
-                            {
-                                "name": "results_json",
-                                "type": "json"
-                            },
-                            {
-                                "name": "output_vcf",
-                                "type": "vcf"
+                                "output_name": "text_file"
                             },
-                            {
-                                "name": "output_txt",
-                                "type": "txt"
-                            }
-                        ],
-                        "position": {
-                            "left": 1132.7778271896836,
-                            "top": 615.3961147101202
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActionoutput_vcf": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "output_vcf"
+                            "results_0|software_cond|output_1|input": {
+                                "id": 8,
+                                "output_name": "text_file"
                             },
-                            "HideDatasetActionresults_json": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "results_json"
+                            "results_0|software_cond|output_2|input": {
+                                "id": 10,
+                                "output_name": "text_file"
                             },
-                            "TagDatasetActionoutput_txt": {
-                                "action_arguments": {
-                                    "tags": "drug_resistance_report"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "output_txt"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.2.1+galaxy0",
-                        "tool_shed_repository": {
-                            "changeset_revision": "4839e590cb26",
-                            "name": "tbprofiler",
-                            "owner": "iuc",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"advanced\": {\"options\": \"no\", \"__current_case__\": 0}, \"fastq_or_bam\": {\"input_select\": \"bam\", \"__current_case__\": 3, \"bam_input\": {\"__class__\": \"ConnectedValue\"}}, \"output_format\": \"txt\", \"platform\": \"illumina\", \"spoligotype\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "6.2.1+galaxy0",
-                        "type": "tool",
-                        "uuid": "22d89589-70a3-4e6e-8b95-68604a287052",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "output_txt",
-                                "output_name": "output_txt",
-                                "uuid": "335635b4-a4de-4980-ad02-68f0035daeaa"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
-                        "errors": null,
-                        "id": 16,
-                        "input_connections": {
-                            "infile": {
+                            "results_0|software_cond|output_3|input": {
                                 "id": 11,
-                                "output_name": "output1"
-                            }
-                        },
-                        "inputs": [],
-                        "label": null,
-                        "name": "Text transformation",
-                        "outputs": [
-                            {
-                                "name": "output",
-                                "type": "input"
-                            }
-                        ],
-                        "position": {
-                            "left": 1379.287563641826,
-                            "top": 248.44083584414724
-                        },
-                        "post_job_actions": {
-                            "TagDatasetActionoutput": {
-                                "action_arguments": {
-                                    "tags": "annotated_vcf"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "output"
-                            }
-                        },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
-                        "tool_shed_repository": {
-                            "changeset_revision": "fbf99087e067",
-                            "name": "text_processing",
-                            "owner": "bgruening",
-                            "tool_shed": "toolshed.g2.bx.psu.edu"
-                        },
-                        "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"s/GENE_//g\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "9.3+galaxy1",
-                        "type": "tool",
-                        "uuid": "c45f6679-0d38-4663-a783-775b0f522bcc",
-                        "when": null,
-                        "workflow_outputs": [
-                            {
-                                "label": "Final annotated VCF",
-                                "output_name": "output",
-                                "uuid": "007df8c2-bd13-495f-8904-abf31d4594d0"
-                            }
-                        ]
-                    },
-                    {
-                        "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
-                        "errors": null,
-                        "id": 17,
-                        "input_connections": {
-                            "results_0|software_cond|input": {
-                                "id": 5,
-                                "output_name": "report_json"
+                                "output_name": "text_file"
                             },
-                            "results_1|software_cond|input": {
+                            "results_0|software_cond|output_4|input": {
+                                "id": 13,
+                                "output_name": "text_file"
+                            },
+                            "results_0|software_cond|output_5|input": {
                                 "id": 14,
-                                "output_name": "output"
+                                "output_name": "text_file"
                             }
                         },
                         "inputs": [],
@@ -290478,21 +297016,14 @@
                             }
                         ],
                         "position": {
-                            "left": 1604.2880860884582,
-                            "top": 202.3882167631859
+                            "left": 615.375,
+                            "top": 0.0
                         },
                         "post_job_actions": {
                             "HideDatasetActionstats": {
                                 "action_arguments": {},
                                 "action_type": "HideDatasetAction",
                                 "output_name": "stats"
-                            },
-                            "TagDatasetActionhtml_report": {
-                                "action_arguments": {
-                                    "tags": "qc_report"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "html_report"
                             }
                         },
                         "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
@@ -290502,219 +297033,161 @@
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"qualimap\", \"__current_case__\": 20, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 3, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 4, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 5, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": false, \"title\": \"Input reads quality control\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                         "tool_version": "1.11+galaxy1",
                         "type": "tool",
-                        "uuid": "6367e2a7-c3b0-4dc4-bbc2-e861e66eaeae",
+                        "uuid": "13fa97d1-a167-4137-a68c-f066b50908b2",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "html_report",
+                                "label": "multiqc_input_data",
                                 "output_name": "html_report",
-                                "uuid": "59528235-7525-4ef9-8810-36f1ed0f01f6"
+                                "uuid": "de867748-890a-454c-baf3-6a9313269975"
                             }
                         ]
                     },
                     {
-                        "annotation": "Compute consensus genome with single nucleotide variants inserted, suitable for use in building a phylogeny",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2",
                         "errors": null,
-                        "id": 18,
+                        "id": 25,
                         "input_connections": {
-                            "input_file": {
-                                "id": 13,
-                                "output_name": "output1"
-                            },
-                            "reference_source|fasta_ref": {
-                                "id": 6,
-                                "output_name": "out_file1"
-                            },
-                            "sec_default|mask": {
-                                "id": 15,
-                                "output_name": "outfile"
+                            "input": {
+                                "id": 24,
+                                "output_name": "output_file"
                             }
                         },
                         "inputs": [
                             {
-                                "description": "runtime parameter for tool bcftools consensus",
-                                "name": "reference_source"
+                                "description": "runtime parameter for tool SnpEff eff:",
+                                "name": "intervals"
                             },
                             {
-                                "description": "runtime parameter for tool bcftools consensus",
-                                "name": "sec_default"
+                                "description": "runtime parameter for tool SnpEff eff:",
+                                "name": "transcripts"
                             }
                         ],
                         "label": null,
-                        "name": "bcftools consensus",
+                        "name": "SnpEff eff:",
                         "outputs": [
                             {
-                                "name": "output_file",
-                                "type": "fasta"
+                                "name": "snpeff_output",
+                                "type": "vcf"
+                            },
+                            {
+                                "name": "statsFile",
+                                "type": "html"
                             }
                         ],
                         "position": {
-                            "left": 1601.1886936133394,
-                            "top": 1003.2778990479657
-                        },
-                        "post_job_actions": {
-                            "TagDatasetActionoutput_file": {
-                                "action_arguments": {
-                                    "tags": "consensus_genome"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "output_file"
-                            }
+                            "left": 1569.6792734462322,
+                            "top": 827.3970308639739
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2",
                         "tool_shed_repository": {
-                            "changeset_revision": "147de996e34f",
-                            "name": "bcftools_consensus",
+                            "changeset_revision": "5b80f544c67f",
+                            "name": "snpeff",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"absent\": \"\", \"chain\": false, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"ConnectedValue\"}}, \"rename\": false, \"sec_default\": {\"mask\": {\"__class__\": \"ConnectedValue\"}, \"iupac_codes\": false, \"sample\": null, \"select_haplotype\": null, \"mark_del\": \"\", \"mark_ins\": null, \"mark_snv\": null, \"conditional_mask\": {\"selector\": \"disabled\", \"__current_case__\": 0}}, \"sec_restrict\": {\"include\": null, \"exclude\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.15.1+galaxy3",
+                        "tool_state": "{\"annotations\": null, \"chr\": \"\", \"csvStats\": false, \"filter\": {\"specificEffects\": \"no\", \"__current_case__\": 0}, \"filterOut\": null, \"generate_stats\": true, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inputFormat\": \"vcf\", \"intervals\": {\"__class__\": \"RuntimeValue\"}, \"noLog\": true, \"offset\": \"default\", \"outputConditional\": {\"outputFormat\": \"vcf\", \"__current_case__\": 0}, \"snpDb\": {\"genomeSrc\": \"cached\", \"__current_case__\": 0, \"genomeVersion\": \"hg19\", \"reg_section\": {\"regulation\": null}}, \"spliceRegion\": {\"setSpliceRegions\": \"no\", \"__current_case__\": 0}, \"spliceSiteSize\": \"2\", \"transcripts\": {\"__class__\": \"RuntimeValue\"}, \"udLength\": \"5000\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "4.3+T.galaxy2",
                         "type": "tool",
-                        "uuid": "2b226e0c-8e59-472d-8bcd-6d8d84dfddab",
+                        "uuid": "02ce6c03-7a90-46c2-8d38-3fce5366eaab",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "consensus_genome",
-                                "output_name": "output_file",
-                                "uuid": "c71b135d-35f9-44d0-a20e-f25528e518af"
+                                "label": "snpeff_variant_stats",
+                                "output_name": "statsFile",
+                                "uuid": "4aab5884-4099-4e41-a82d-c4e1ff19609f"
+                            },
+                            {
+                                "label": "normalized_snpeff_annotated_variants",
+                                "output_name": "snpeff_output",
+                                "uuid": "e5a2fbc7-acdd-4782-822a-91568cb8d5b8"
                             }
                         ]
                     },
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.0+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1",
                         "errors": null,
-                        "id": 19,
+                        "id": 27,
                         "input_connections": {
-                            "input_vcf": {
-                                "id": 16,
-                                "output_name": "output"
-                            },
-                            "tbprofiler_json": {
-                                "id": 12,
-                                "output_name": "results_json"
+                            "infile": {
+                                "id": 26,
+                                "output_name": "outfile"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "TB Variant Report",
+                        "name": "GEMINI inheritance pattern",
                         "outputs": [
                             {
-                                "name": "variants_report_html",
-                                "type": "html"
-                            },
-                            {
-                                "name": "variants_report_txt",
-                                "type": "txt"
-                            },
-                            {
-                                "name": "drug_resistance_report_html",
-                                "type": "html"
-                            },
-                            {
-                                "name": "drug_resistance_report_txt",
-                                "type": "txt"
+                                "name": "outfile",
+                                "type": "tabular"
                             }
                         ],
                         "position": {
-                            "left": 1591.762535768669,
-                            "top": 427.7783435581315
-                        },
-                        "post_job_actions": {
-                            "HideDatasetActiondrug_resistance_report_txt": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "drug_resistance_report_txt"
-                            },
-                            "HideDatasetActionvariants_report_txt": {
-                                "action_arguments": {},
-                                "action_type": "HideDatasetAction",
-                                "output_name": "variants_report_txt"
-                            },
-                            "TagDatasetActiondrug_resistance_report_html": {
-                                "action_arguments": {
-                                    "tags": "variant_report"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "drug_resistance_report_html"
-                            },
-                            "TagDatasetActionvariants_report_html": {
-                                "action_arguments": {
-                                    "tags": "variant_report"
-                                },
-                                "action_type": "TagDatasetAction",
-                                "output_name": "variants_report_html"
-                            }
+                            "left": 2036.9508077255032,
+                            "top": 1034.4095449070464
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.0+galaxy0",
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1",
                         "tool_shed_repository": {
-                            "changeset_revision": "42818629ec4c",
-                            "name": "tbvcfreport",
+                            "changeset_revision": "18d13111692b",
+                            "name": "gemini_inheritance",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
                         },
-                        "tool_state": "{\"adv\": {\"database_uri\": \"neodb.sanbi.ac.za\"}, \"filter_udi\": true, \"input_vcf\": {\"__class__\": \"ConnectedValue\"}, \"tbprofiler_json\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-                        "tool_version": "1.0.0+galaxy0",
+                        "tool_state": "{\"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/hg19.len\", \"family_wise\": {\"min_kindreds\": \"1\", \"families\": \"\", \"per_variant_selection\": {\"enabled\": \"no\", \"__current_case__\": 0, \"min_dp\": \"0\", \"min_gq\": \"0\", \"max_pl\": \"-1\"}}, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"inheritance\": {\"pattern_type\": \"autosomal_recessive\", \"__current_case__\": 2, \"constraint\": [{\"__index__\": 0, \"filter\": \"impact_severity != 'LOW'\"}], \"lenient\": false, \"allow_unaffected\": false}, \"oformat\": {\"report\": {\"report_selector\": \"custom\", \"__current_case__\": 2, \"columns\": [\"max_aaf_all\"], \"extra_cols\": \"chrom, start, ref, alt, impact, gene, clinvar_sig, clinvar_disease_name, clinvar_gene_phenotype, rs_ids\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+                        "tool_version": "0.20.1",
                         "type": "tool",
-                        "uuid": "183d84e7-91ea-4e8f-950b-f65629b60b1b",
+                        "uuid": "eecc879f-93bc-4513-840e-b56704e5ed77",
                         "when": null,
                         "workflow_outputs": [
                             {
-                                "label": "drug_resistance_report_html",
-                                "output_name": "drug_resistance_report_html",
-                                "uuid": "959528d2-f8f2-4440-99cf-44fddd6c5069"
-                            },
-                            {
-                                "label": "variants_report_html",
-                                "output_name": "variants_report_html",
-                                "uuid": "4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0"
+                                "label": "candidate_mutations",
+                                "output_name": "outfile",
+                                "uuid": "07bd4bba-e7d9-48a8-b812-5dc2b07712bd"
                             }
                         ]
                     }
                 ],
-                "parent_id": "variant-analysis/tb-variant-analysis",
-                "path": "topics/variant-analysis/tutorials/tb-variant-analysis/workflows/tb-variant-analysis.ga",
+                "parent_id": "variant-analysis/exome-seq",
+                "path": "topics/variant-analysis/tutorials/exome-seq/workflows/workflow_exome_seq_full.ga",
                 "tags": [
-                    "pathogen",
-                    "tuberculosis"
+                    "variant-analysis"
                 ],
                 "test_results": null,
                 "tests": true,
-                "title": "TB Variant Analysis v1.0",
+                "title": "Exome Seq Training Full W Cached Ref",
                 "topic_id": "variant-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-tb-variant-analysis/versions/tb-variant-analysis",
-                "tutorial_id": "tb-variant-analysis",
-                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/tb-variant-analysis/workflows/tb-variant-analysis.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/tb-variant-analysis/workflows/tb-variant-analysis.html",
-                "version": 7,
-                "wfid": "variant-analysis-tb-variant-analysis",
-                "wfname": "tb-variant-analysis",
-                "workflow": "tb-variant-analysis.ga",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-exome-seq/versions/workflow-exome-seq-full",
+                "tutorial_id": "exome-seq",
+                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/workflows/workflow_exome_seq_full.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/workflows/workflow_exome_seq_full.html",
+                "version": 5,
+                "wfid": "variant-analysis-exome-seq",
+                "wfname": "workflow-exome-seq-full",
+                "workflow": "workflow_exome_seq_full.ga",
                 "workflow_tools": [
-                    "__FLATTEN__",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: seqret84/5.0.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/mosdepth/mosdepth/0.3.8+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2",
                     "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c+galaxy1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.4.0+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.2.1+galaxy0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.0+galaxy0"
+                    "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2"
                 ],
-                "workflowhub_id": "1069"
+                "workflowhub_id": "1114"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.3496437"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.3054169"
     },
     {
         "admin_install": {
@@ -290723,47 +297196,65 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "datamash_ops",
-                    "owner": "iuc",
-                    "revisions": "4c07ddedc198",
-                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "a6f147a050a2",
+                    "tool_panel_section_label": "Text Manipulation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "nextclade",
+                    "name": "snpeff",
                     "owner": "iuc",
-                    "revisions": "4f6349228462",
-                    "tool_panel_section_label": "Phylogenetics",
+                    "revisions": "20f0429a4bfe",
+                    "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "pangolin",
+                    "name": "snpeff",
                     "owner": "iuc",
-                    "revisions": "03ed9524dcd1",
-                    "tool_panel_section_label": "Phylogenetics",
+                    "revisions": "20f0429a4bfe",
+                    "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "fasta_regex_finder",
-                    "owner": "mbernt",
-                    "revisions": "9a811adb714f",
-                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "name": "mimodd_main",
+                    "owner": "wolma",
+                    "revisions": "f0f2795de2c7",
+                    "tool_panel_section_label": "MiModD",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mimodd_main",
+                    "owner": "wolma",
+                    "revisions": "f0f2795de2c7",
+                    "tool_panel_section_label": "MiModD",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mimodd_main",
+                    "owner": "wolma",
+                    "revisions": "f0f2795de2c7",
+                    "tool_panel_section_label": "MiModD",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mimodd_main",
+                    "owner": "wolma",
+                    "revisions": "f0f2795de2c7",
+                    "tool_panel_section_label": "MiModD",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mimodd_main",
+                    "owner": "wolma",
+                    "revisions": "f0f2795de2c7",
+                    "tool_panel_section_label": "MiModD",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: datamash_ops\n  owner: iuc\n  revisions: 4c07ddedc198\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nextclade\n  owner: iuc\n  revisions: 4f6349228462\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pangolin\n  owner: iuc\n  revisions: 03ed9524dcd1\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_regex_finder\n  owner: mbernt\n  revisions: 9a811adb714f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.json",
-        "contributions": {
-            "authorship": [
-                "wm75",
-                "bebatut"
-            ],
-            "funding": [
-                "by-covid",
-                "elixir-converge"
-            ]
-        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: a6f147a050a2\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n  owner: iuc\n  revisions: 20f0429a4bfe\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n  owner: iuc\n  revisions: 20f0429a4bfe\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mimodd_main\n  owner: wolma\n  revisions: f0f2795de2c7\n  tool_panel_section_label: MiModD\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mimodd_main\n  owner: wolma\n  revisions: f0f2795de2c7\n  tool_panel_section_label: MiModD\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mimodd_main\n  owner: wolma\n  revisions: f0f2795de2c7\n  tool_panel_section_label: MiModD\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mimodd_main\n  owner: wolma\n  revisions: f0f2795de2c7\n  tool_panel_section_label: MiModD\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mimodd_main\n  owner: wolma\n  revisions: f0f2795de2c7\n  tool_panel_section_label: MiModD\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
@@ -290781,208 +297272,115 @@
                 "orcid": "0000-0002-9464-6640",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
-            },
-            {
-                "affiliations": [
-                    "gallantries",
-                    "ifb",
-                    "elixir-europe"
-                ],
-                "contact_for_training": true,
-                "elixir_node": "fr",
-                "email": "berenice.batut@gmail.com",
-                "fediverse": "https://piaille.fr/@bebatut",
-                "fediverse_flavor": "mastodon",
-                "id": "bebatut",
-                "joined": "2017-09",
-                "linkedin": "berenicebatut",
-                "location": {
-                    "country": "FR",
-                    "lat": 45.77,
-                    "lon": 3.08
-                },
-                "matrix": "bebatut:matrix.org",
-                "name": "B\u00e9r\u00e9nice Batut",
-                "orcid": "0000-0001-9852-1987",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
-                "twitter": "bebatut",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
-            },
-            {
-                "funder": true,
-                "funding_id": "101046203",
-                "funding_statement": "BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response.\n\nThis project has received funding from the European Union\u2019s Horizon Europe research and innovation programme under grant agreement \u2116 101046203 (BY-COVID)",
-                "funding_system": "cordis",
-                "id": "by-covid",
-                "joined": "2023-04",
-                "members": [
-                    "bgruening",
-                    "hexylena",
-                    "ilveroluca",
-                    "kikkomep",
-                    "mbaardwijk",
-                    "PapXis",
-                    "pauldg",
-                    "simleo",
-                    "stain",
-                    "wm75"
-                ],
-                "name": "BeYond-COVID",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/by-covid/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/by-covid.json"
-            },
-            {
-                "avatar": "https://elixir-europe.org/sites/default/files/styles/right-medium/public/images/converge_logo.png",
-                "funder": true,
-                "funding_id": "871075",
-                "funding_statement": "ELIXIR CONVERGE is connecting and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services. This project has received funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement \u2116 871075",
-                "funding_system": "cordis",
-                "github": false,
-                "id": "elixir-converge",
-                "joined": "2023-01",
-                "members": [
-                    "bgruening",
-                    "hexylena"
-                ],
-                "name": "ELIXIR-CONVERGE",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-converge/",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-converge.json"
             }
         ],
-        "dir": "topics/variant-analysis/tutorials/sars-cov-2-variant-discovery",
-        "edam_operation": [
-            "Variant calling",
-            "Methylation analysis",
-            "Variant classification",
-            "Tree-based sequence alignment"
-        ],
+        "dir": "topics/variant-analysis/tutorials/mapping-by-sequencing",
+        "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)"
+            "UseGalaxy.be",
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "variant-analysis/sars-cov-2-variant-discovery",
-        "inexact_supported_servers": [],
+        "id": "variant-analysis/mapping-by-sequencing",
+        "inexact_supported_servers": [
+            "GalaxyTrakr",
+            "UseGalaxy.cz",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "The Galaxy Covid-19 project has developed a flexible set of workflows for SARS-CoV-2 genome surveillance, which is freely available through public workflow registries.",
-            "The workflows enable processing of whole batches of samples with rather limited user interaction.",
-            "They provide a high-throughput and flexible analysis solution without compromising on accuracy, nor on the possibility to explore intermediate steps and outputs in detail."
+            "Mapping-by-sequencing is a powerful method for the molecular identification of mutations",
+            "The MiModD suite of tools bundles most of the functionality required to perform mapping-by-sequencing analyses with Galaxy"
         ],
         "layout": "tutorial_hands_on",
-        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2023-11-09",
         "objectives": [
-            "Discover and obtain recommended Galaxy workflows for SARS-CoV-2 sequence data analysis through public workflow registries",
-            "Choose and run a workflow to discover mutations in a batch of viral samples from sequencing data obtained through a range of different protocols and platforms",
-            "Run a workflow to summarize and visualize the mutation discovery results for a batch of samples",
-            "Run a workflow to construct viral consensus sequences for the samples in a batch",
-            "Know different SARS-CoV-2 lineage classification systems, and use pangolin and Nextclade to assign samples to predefined lineages",
-            "Combine information from different analysis steps to be able to draw appropriate conclusions about individual samples and batches of viral data"
+            "Use joint variant calling and extraction to facilitate variant comparison across samples",
+            "Perform variant linkage analyses for phenotypically selected recombinant progeny",
+            "Filter, annotate and report lists of variants"
         ],
-        "pageviews": 11912,
-        "pub_date": "2021-06-30",
+        "pageviews": 5499,
+        "pub_date": "2018-03-07",
         "questions": [
-            "How can a complete analysis, including viral consensus sequence reconstruction and lineage assignment be performed?",
-            "How can such an analysis be kept manageable for lots of samples, yet flexible enough to handle different types of input data?",
-            "What are key results beyond consensus genomes and lineage assignments that need to be understood to avoid inappropriate conclusions about samples?",
-            "How can the needs for high-throughput data analysis in an ongoing infectious disease outbreak/pandemic and the need for proper quality control and data inspection be balanced?"
-        ],
-        "recordings": [
-            {
-                "captioners": [
-                    "wm75"
-                ],
-                "date": "2023-05-10",
-                "length": "55M",
-                "speakers": [
-                    "wm75"
-                ],
-                "youtube_id": "hjlmCWQhBvI"
-            },
-            {
-                "captioners": [
-                    "hexylena"
-                ],
-                "date": "2021-08-09",
-                "length": "1H30M",
-                "speakers": [
-                    "wm75"
-                ],
-                "youtube_id": "vnFQ2fR_fzw"
-            }
-        ],
-        "requirements": [
-            {
-                "topic_name": "galaxy-interface",
-                "tutorials": [
-                    "collections"
-                ],
-                "type": "internal"
-            },
-            {
-                "topic_name": "variant-analysis",
-                "tutorials": [
-                    "sars-cov-2"
-                ],
-                "type": "internal"
-            }
+            "What is mapping-by-sequencing?",
+            "How can it help you identify the causative mutation in phenotypic mutants isolated from genetic screens?"
         ],
-        "short_id": "T00316",
+        "short_id": "T00312",
         "short_tools": [
-            "nextclade",
-            "datamash_ops",
-            "fasta_regex_finder",
-            "pangolin",
-            "Filter1",
-            "upload1"
+            "mimodd_map",
+            "mimodd_varcall",
+            "snpEff_download",
+            "tp_find_and_replace",
+            "mimodd_varextract",
+            "mimodd_varreport",
+            "snpEff",
+            "mimodd_vcf_filter"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "one-health",
+        "subtopic": "model-organisms",
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
                 }
-            ],
-            "inexact": []
+            ]
         },
         "symlink": null,
-        "tags": [
-            "covid19",
-            "virology",
-            "one-health"
-        ],
-        "time_estimation": "3H",
-        "title": "Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data",
+        "time_estimation": "2h",
+        "title": "Mapping and molecular identification of phenotype-causing mutations",
         "tools": [
-            "Filter1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/nextclade/nextclade/2.7.0+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/4.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/mbernt/fasta_regex_finder/fasta_regex_finder/0.1.0",
-            "upload1"
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.1.0",
+            "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_map/0.1.8_1",
+            "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varcall/0.1.8_1",
+            "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varextract/0.1.8_1",
+            "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varreport/0.1.8_1",
+            "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_vcf_filter/0.1.8_1"
         ],
         "topic_name": "variant-analysis",
         "topic_name_human": "Variant Analysis",
@@ -290992,20 +297390,154 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "sars-cov-2-variant-discovery",
+        "tutorial_name": "mapping-by-sequencing",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.json"
         },
-        "version": 15,
+        "version": 16,
         "video": false,
-        "video_versions": 2,
+        "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 207,
-        "visitors": 6391,
-        "zenodo_link": "https://zenodo.org/record/5036687"
+        "visit_duration": 179,
+        "visitors": 3602,
+        "workflows": [
+            {
+                "creators": [],
+                "description": "Reproduce the tutorial analysis at https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html",
+                "features": {
+                    "comments": false,
+                    "parameters": false,
+                    "report": null,
+                    "subworkflows": false
+                },
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nA. thaliana TAIR10 ref genome\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\naligned reads from outcrossed F2 pool\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\naligned reads from Ler mapping strain\"]\n  3[label=\"SnpEff Download\"]\n  4[label=\"Replace parts of text\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"MiModD Variant Calling\"]\n  4 -> 5 [label=\"outfile\"]\n  2 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"MiModD Extract Variant Sites\"]\n  5 -> 6 [label=\"ofile\"]\n  7[label=\"MiModD NacreousMap\"]\n  6 -> 7 [label=\"output_vcf\"]\n  8[label=\"MiModD VCF Filter\"]\n  6 -> 8 [label=\"output_vcf\"]\n  9[label=\"SnpEff\"]\n  8 -> 9 [label=\"outputfile\"]\n  3 -> 9 [label=\"snpeff_db\"]\n  10[label=\"MiModD Report Variants\"]\n  9 -> 10 [label=\"snpeff_output\"]\n}",
+                "history": [
+                    {
+                        "hash": "3f568e83cac25b4567e24d0c32cf75008e2330d2",
+                        "message": "Correct some ancient URLs",
+                        "num": 3,
+                        "short_hash": "3f568e83c",
+                        "unix": "1665080483"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 2,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "a14e0a4b74829330dd99f3f82a0d2320c756b0e9",
+                        "message": "mapping-by-sequencing tutorial: add workflow",
+                        "num": 1,
+                        "short_hash": "a14e0a4b7",
+                        "unix": "1520870838"
+                    }
+                ],
+                "inputs": [
+                    {
+                        "annotation": "can be obtained from https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "A. thaliana TAIR10 ref genome",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 169,
+                            "top": 200
+                        },
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "e1f007b9-4064-4085-a5f9-3f58db2dfe80",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "as obtained from\nhttps://zenodo.org/record/1098034/files/outcrossed_F2.bam",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 1,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "aligned reads from outcrossed F2 pool",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 174,
+                            "top": 524
+                        },
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "d8951962-720f-444f-9ba9-38eb5d3bc69d",
+                        "workflow_outputs": []
+                    },
+                    {
+                        "annotation": "as obtained from\nhttps://zenodo.org/record/1098034/files/Ler_mapping_strain.bam",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 2,
+                        "input_connections": {},
+                        "inputs": [],
+                        "label": "aligned reads from Ler mapping strain",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 172,
+                            "top": 687
+                        },
+                        "tool_id": null,
+                        "tool_state": "{}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "299b9599-74e4-45ac-b6db-cabedca6d396",
+                        "workflow_outputs": []
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nA. thaliana TAIR10 ref genome\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\naligned reads from outcrossed F2 pool\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\naligned reads from Ler mapping strain\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"SnpEff Download\"];\n  4[\"Replace parts of text\"];\n  0 -->|output| 4;\n  5[\"MiModD Variant Calling\"];\n  4 -->|outfile| 5;\n  2 -->|output| 5;\n  1 -->|output| 5;\n  6[\"MiModD Extract Variant Sites\"];\n  5 -->|ofile| 6;\n  7[\"MiModD NacreousMap\"];\n  6 -->|output_vcf| 7;\n  8[\"MiModD VCF Filter\"];\n  6 -->|output_vcf| 8;\n  9[\"SnpEff\"];\n  8 -->|outputfile| 9;\n  3 -->|snpeff_db| 9;\n  10[\"MiModD Report Variants\"];\n  9 -->|snpeff_output| 10;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "Mapping And Molecular Identification Of Phenotype Causing Mutations",
+                "outputs": [],
+                "parent_id": "variant-analysis/mapping-by-sequencing",
+                "path": "topics/variant-analysis/tutorials/mapping-by-sequencing/workflows/workflow-arabidopsis.ga",
+                "tags": [
+                    "variant-analysis"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "Mapping And Molecular Identification Of Phenotype Causing Mutations",
+                "topic_id": "variant-analysis",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-mapping-by-sequencing/versions/workflow-arabidopsis",
+                "tutorial_id": "mapping-by-sequencing",
+                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/mapping-by-sequencing/workflows/workflow-arabidopsis.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/mapping-by-sequencing/workflows/workflow-arabidopsis.html",
+                "version": 3,
+                "wfid": "variant-analysis-mapping-by-sequencing",
+                "wfname": "workflow-arabidopsis",
+                "workflow": "workflow-arabidopsis.ga",
+                "workflow_tools": [
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_map/0.1.8_1",
+                    "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varcall/0.1.8_1",
+                    "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varextract/0.1.8_1",
+                    "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varreport/0.1.8_1",
+                    "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_vcf_filter/0.1.8_1"
+                ],
+                "workflowhub_id": "1063"
+            }
+        ],
+        "zenodo_link": "https://doi.org/10.5281/zenodo.1098033"
     },
     {
         "admin_install": {
@@ -291014,154 +297546,165 @@
             "install_tool_dependencies": true,
             "tools": [
                 {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "a6f147a050a2",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "snpeff",
-                    "owner": "iuc",
-                    "revisions": "20f0429a4bfe",
+                    "name": "freebayes",
+                    "owner": "devteam",
+                    "revisions": "156b60c1530f",
                     "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "snpeff",
-                    "owner": "iuc",
-                    "revisions": "20f0429a4bfe",
+                    "name": "vcfallelicprimitives",
+                    "owner": "devteam",
+                    "revisions": "f49b23b41a12",
                     "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mimodd_main",
-                    "owner": "wolma",
-                    "revisions": "f0f2795de2c7",
-                    "tool_panel_section_label": "MiModD",
+                    "name": "gemini_db_info",
+                    "owner": "iuc",
+                    "revisions": "4c5f4e9b1931",
+                    "tool_panel_section_label": "Gemini",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mimodd_main",
-                    "owner": "wolma",
-                    "revisions": "f0f2795de2c7",
-                    "tool_panel_section_label": "MiModD",
+                    "name": "gemini_load",
+                    "owner": "iuc",
+                    "revisions": "cf61daf064fe",
+                    "tool_panel_section_label": "Gemini",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mimodd_main",
-                    "owner": "wolma",
-                    "revisions": "f0f2795de2c7",
-                    "tool_panel_section_label": "MiModD",
+                    "name": "gemini_query",
+                    "owner": "iuc",
+                    "revisions": "666f60a9331a",
+                    "tool_panel_section_label": "Gemini",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mimodd_main",
-                    "owner": "wolma",
-                    "revisions": "f0f2795de2c7",
-                    "tool_panel_section_label": "MiModD",
+                    "name": "snpeff",
+                    "owner": "iuc",
+                    "revisions": "5c7b70713fb5",
+                    "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
-                    "name": "mimodd_main",
-                    "owner": "wolma",
-                    "revisions": "f0f2795de2c7",
-                    "tool_panel_section_label": "MiModD",
+                    "name": "snpeff",
+                    "owner": "iuc",
+                    "revisions": "68693743661e",
+                    "tool_panel_section_label": "Variant Calling",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: a6f147a050a2\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n  owner: iuc\n  revisions: 20f0429a4bfe\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n  owner: iuc\n  revisions: 20f0429a4bfe\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mimodd_main\n  owner: wolma\n  revisions: f0f2795de2c7\n  tool_panel_section_label: MiModD\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mimodd_main\n  owner: wolma\n  revisions: f0f2795de2c7\n  tool_panel_section_label: MiModD\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mimodd_main\n  owner: wolma\n  revisions: f0f2795de2c7\n  tool_panel_section_label: MiModD\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mimodd_main\n  owner: wolma\n  revisions: f0f2795de2c7\n  tool_panel_section_label: MiModD\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mimodd_main\n  owner: wolma\n  revisions: f0f2795de2c7\n  tool_panel_section_label: MiModD\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: freebayes\n  owner: devteam\n  revisions: 156b60c1530f\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: vcfallelicprimitives\n  owner: devteam\n  revisions: f49b23b41a12\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_db_info\n  owner: iuc\n  revisions: 4c5f4e9b1931\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_load\n  owner: iuc\n  revisions: cf61daf064fe\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gemini_query\n  owner: iuc\n  revisions: 666f60a9331a\n  tool_panel_section_label: Gemini\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n  owner: iuc\n  revisions: 5c7b70713fb5\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: snpeff\n  owner: iuc\n  revisions: 68693743661e\n  tool_panel_section_label: Variant Calling\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/dip/tutorial.json",
         "contributors": [
             {
-                "affiliations": [
-                    "by-covid",
-                    "uni-freiburg",
+                "email": "anton@nekrut.org",
+                "id": "nekrut",
+                "joined": "2017-09",
+                "name": "Anton Nekrutenko",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nekrut/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nekrut.json"
+            },
+            {
+                "affiliations": [
+                    "earlham",
                     "elixir-europe"
                 ],
-                "elixir_node": "de",
-                "fediverse": "https://scholar.social/@zerodivision",
+                "elixir_node": "uk",
+                "fediverse": "https://mstdn.science/@nsoranzo",
                 "fediverse_flavor": "mastodon",
-                "id": "wm75",
+                "id": "nsoranzo",
                 "joined": "2017-09",
-                "matrix": "wm75:matrix.org",
-                "name": "Wolfgang Maier",
-                "orcid": "0000-0002-9464-6640",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
+                "linkedin": "nicola-soranzo-7884125",
+                "matrix": "nsoranzo:matrix.org",
+                "name": "Nicola Soranzo",
+                "orcid": "0000-0003-3627-5340",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/",
+                "twitter": "NicolaSoranzo",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/nsoranzo.json"
             }
         ],
-        "dir": "topics/variant-analysis/tutorials/mapping-by-sequencing",
-        "edam_operation": [],
+        "dir": "topics/variant-analysis/tutorials/dip",
+        "edam_operation": [
+            "Statistical calculation",
+            "Genetic variation analysis",
+            "Variant calling",
+            "Sequence analysis"
+        ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu"
+            "UseGalaxy.be"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
         "hands_on": true,
-        "id": "variant-analysis/mapping-by-sequencing",
+        "id": "variant-analysis/dip",
         "inexact_supported_servers": [
-            "GalaxyTrakr",
             "UseGalaxy.cz",
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
             "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
         "js_requirements": {
-            "mathjax": null,
+            "mathjax": 3591,
             "mermaid": false
         },
         "key_points": [
-            "Mapping-by-sequencing is a powerful method for the molecular identification of mutations",
-            "The MiModD suite of tools bundles most of the functionality required to perform mapping-by-sequencing analyses with Galaxy"
+            "Variants versus Genotypes",
+            "Bayesian approach to variant calling",
+            "Freebayes calls variant using haplotype windows",
+            "SNPEff allows functional annotation of variants",
+            "Gemini is a flexible system for analyzing variation patterns"
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2023-11-09",
+        "mod_date": "2023-03-05",
         "objectives": [
-            "Use joint variant calling and extraction to facilitate variant comparison across samples",
-            "Perform variant linkage analyses for phenotypically selected recombinant progeny",
-            "Filter, annotate and report lists of variants"
+            "Identification of genetic variations using variant calling"
         ],
-        "pageviews": 5430,
-        "pub_date": "2018-03-07",
+        "pageviews": 22534,
+        "pub_date": "2017-02-20",
         "questions": [
-            "What is mapping-by-sequencing?",
-            "How can it help you identify the causative mutation in phenotypic mutants isolated from genetic screens?"
+            "How to find variable sites in diploid genomes?"
         ],
-        "short_id": "T00312",
+        "short_id": "T00309",
         "short_tools": [
-            "mimodd_varextract",
-            "tp_find_and_replace",
-            "mimodd_vcf_filter",
-            "mimodd_varcall",
-            "mimodd_varreport",
-            "mimodd_map",
+            "snpEff",
+            "gemini_load",
             "snpEff_download",
-            "snpEff"
+            "gemini_db_info",
+            "vcfallelicprimitives",
+            "gemini_query",
+            "freebayes"
         ],
         "slides": false,
         "slides_recordings": false,
-        "subtopic": "model-organisms",
+        "subtopic": "introduction",
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
                 }
             ],
             "inexact": [
                 {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
                     "usegalaxy": false
                 },
                 {
@@ -291169,11 +297712,6 @@
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
@@ -291182,17 +297720,16 @@
             ]
         },
         "symlink": null,
-        "time_estimation": "2h",
-        "title": "Mapping and molecular identification of phenotype-causing mutations",
+        "time_estimation": "3h",
+        "title": "Calling variants in diploid systems",
         "tools": [
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.1.0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.1.0",
-            "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_map/0.1.8_1",
-            "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varcall/0.1.8_1",
-            "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varextract/0.1.8_1",
-            "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varreport/0.1.8_1",
-            "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_vcf_filter/0.1.8_1"
+            "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.1.0.46-0",
+            "toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/0.0.3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.18.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.18.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.18.1.0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1"
         ],
         "topic_name": "variant-analysis",
         "topic_name_human": "Variant Analysis",
@@ -291202,37 +297739,37 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "mapping-by-sequencing",
+        "tutorial_name": "dip",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/dip/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/dip/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/dip/tutorial.json"
         },
         "version": 16,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 180,
-        "visitors": 3533,
+        "visit_duration": 192,
+        "visitors": 12589,
         "workflows": [
             {
                 "creators": [],
-                "description": "Reproduce the tutorial analysis at https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html",
+                "description": "Calling variants in diploid systems",
                 "features": {
                     "comments": false,
                     "parameters": false,
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nA. thaliana TAIR10 ref genome\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\naligned reads from outcrossed F2 pool\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\naligned reads from Ler mapping strain\"]\n  3[label=\"SnpEff Download\"]\n  4[label=\"Replace parts of text\"]\n  0 -> 4 [label=\"output\"]\n  5[label=\"MiModD Variant Calling\"]\n  4 -> 5 [label=\"outfile\"]\n  2 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  6[label=\"MiModD Extract Variant Sites\"]\n  5 -> 6 [label=\"ofile\"]\n  7[label=\"MiModD NacreousMap\"]\n  6 -> 7 [label=\"output_vcf\"]\n  8[label=\"MiModD VCF Filter\"]\n  6 -> 8 [label=\"output_vcf\"]\n  9[label=\"SnpEff\"]\n  8 -> 9 [label=\"outputfile\"]\n  3 -> 9 [label=\"snpeff_db\"]\n  10[label=\"MiModD Report Variants\"]\n  9 -> 10 [label=\"snpeff_output\"]\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGIAB-Ashkenazim-Trio-hg19.bam\"]\n  1[label=\"SnpEff Download\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGIAB-Ashkenazim-Trio.tabular\"]\n  3[label=\"FreeBayes\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"VcfAllelicPrimitives:\"]\n  3 -> 4 [label=\"output_vcf\"]\n  5[label=\"SnpEff eff:\"]\n  4 -> 5 [label=\"out_file1\"]\n  1 -> 5 [label=\"snpeff_db\"]\n  6[label=\"GEMINI load\"]\n  5 -> 6 [label=\"snpeff_output\"]\n  2 -> 6 [label=\"output\"]\n  7[label=\"GEMINI_db_info\"]\n  6 -> 7 [label=\"outfile\"]\n  8[label=\"GEMINI_query2\"]\n  6 -> 8 [label=\"outfile\"]\n  9[label=\"GEMINI_query1\"]\n  6 -> 9 [label=\"outfile\"]\n}",
                 "history": [
                     {
-                        "hash": "3f568e83cac25b4567e24d0c32cf75008e2330d2",
-                        "message": "Correct some ancient URLs",
+                        "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
+                        "message": "annotation",
                         "num": 3,
-                        "short_hash": "3f568e83c",
-                        "unix": "1665080483"
+                        "short_hash": "667ff3de9",
+                        "unix": "1579690769"
                     },
                     {
                         "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
@@ -291242,114 +297779,326 @@
                         "unix": "1579084895"
                     },
                     {
-                        "hash": "a14e0a4b74829330dd99f3f82a0d2320c756b0e9",
-                        "message": "mapping-by-sequencing tutorial: add workflow",
+                        "hash": "a294ecfbb57eb17046ebbb47ccb2c877f2c0cf85",
+                        "message": "workflow for diploid",
                         "num": 1,
-                        "short_hash": "a14e0a4b7",
-                        "unix": "1520870838"
+                        "short_hash": "a294ecfbb",
+                        "unix": "1544185856"
                     }
                 ],
                 "inputs": [
                     {
-                        "annotation": "can be obtained from https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 0,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "A. thaliana TAIR10 ref genome",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "GIAB-Ashkenazim-Trio-hg19.bam"
+                            }
+                        ],
+                        "label": "GIAB-Ashkenazim-Trio-hg19.bam",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 169,
-                            "top": 200
+                            "left": 229,
+                            "top": 204
                         },
                         "tool_id": null,
-                        "tool_state": "{}",
+                        "tool_state": "{\"name\": \"GIAB-Ashkenazim-Trio-hg19.bam\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "e1f007b9-4064-4085-a5f9-3f58db2dfe80",
-                        "workflow_outputs": []
+                        "uuid": "5bbfca3e-68d7-4c87-8976-724ccaab2eb3",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "bc2eeefe-9c1e-4db8-bf4c-83ed024d67a0"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "as obtained from\nhttps://zenodo.org/record/1098034/files/outcrossed_F2.bam",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
-                        "id": 1,
+                        "id": 2,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "aligned reads from outcrossed F2 pool",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "GIAB-Ashkenazim-Trio.tabular"
+                            }
+                        ],
+                        "label": "GIAB-Ashkenazim-Trio.tabular",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 174,
-                            "top": 524
+                            "left": 289,
+                            "top": 530
                         },
                         "tool_id": null,
-                        "tool_state": "{}",
+                        "tool_state": "{\"name\": \"GIAB-Ashkenazim-Trio.tabular\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "d8951962-720f-444f-9ba9-38eb5d3bc69d",
-                        "workflow_outputs": []
+                        "uuid": "4d40770f-b5f9-464b-b3e5-b99ae836fbf0",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "6f4a6fbd-e2a2-43dc-92ea-b99d4f32a20f"
+                            }
+                        ]
+                    }
+                ],
+                "license": null,
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGIAB-Ashkenazim-Trio-hg19.bam\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"SnpEff Download\"];\n  2[\"\u2139\ufe0f Input Dataset\\nGIAB-Ashkenazim-Trio.tabular\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"FreeBayes\"];\n  0 -->|output| 3;\n  4[\"VcfAllelicPrimitives:\"];\n  3 -->|output_vcf| 4;\n  5[\"SnpEff eff:\"];\n  4 -->|out_file1| 5;\n  1 -->|snpeff_db| 5;\n  6[\"GEMINI load\"];\n  5 -->|snpeff_output| 6;\n  2 -->|output| 6;\n  7[\"GEMINI_db_info\"];\n  6 -->|outfile| 7;\n  8[\"GEMINI_query2\"];\n  6 -->|outfile| 8;\n  9[\"GEMINI_query1\"];\n  6 -->|outfile| 9;",
+                "modified": "2024-10-02 12:08:11 +0000",
+                "name": "Diploid",
+                "outputs": [
+                    {
+                        "annotation": "",
+                        "content_id": null,
+                        "errors": null,
+                        "id": 0,
+                        "input_connections": {},
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "GIAB-Ashkenazim-Trio-hg19.bam"
+                            }
+                        ],
+                        "label": "GIAB-Ashkenazim-Trio-hg19.bam",
+                        "name": "Input dataset",
+                        "outputs": [],
+                        "position": {
+                            "left": 229,
+                            "top": 204
+                        },
+                        "tool_id": null,
+                        "tool_state": "{\"name\": \"GIAB-Ashkenazim-Trio-hg19.bam\"}",
+                        "tool_version": null,
+                        "type": "data_input",
+                        "uuid": "5bbfca3e-68d7-4c87-8976-724ccaab2eb3",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "bc2eeefe-9c1e-4db8-bf4c-83ed024d67a0"
+                            }
+                        ]
                     },
                     {
-                        "annotation": "as obtained from\nhttps://zenodo.org/record/1098034/files/Ler_mapping_strain.bam",
+                        "annotation": "",
                         "content_id": null,
                         "errors": null,
                         "id": 2,
                         "input_connections": {},
-                        "inputs": [],
-                        "label": "aligned reads from Ler mapping strain",
+                        "inputs": [
+                            {
+                                "description": "",
+                                "name": "GIAB-Ashkenazim-Trio.tabular"
+                            }
+                        ],
+                        "label": "GIAB-Ashkenazim-Trio.tabular",
                         "name": "Input dataset",
                         "outputs": [],
                         "position": {
-                            "left": 172,
-                            "top": 687
+                            "left": 289,
+                            "top": 530
                         },
                         "tool_id": null,
-                        "tool_state": "{}",
+                        "tool_state": "{\"name\": \"GIAB-Ashkenazim-Trio.tabular\"}",
                         "tool_version": null,
                         "type": "data_input",
-                        "uuid": "299b9599-74e4-45ac-b6db-cabedca6d396",
-                        "workflow_outputs": []
+                        "uuid": "4d40770f-b5f9-464b-b3e5-b99ae836fbf0",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "output",
+                                "uuid": "6f4a6fbd-e2a2-43dc-92ea-b99d4f32a20f"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.18.1.0",
+                        "errors": null,
+                        "id": 7,
+                        "input_connections": {
+                            "infile": {
+                                "id": 6,
+                                "output_name": "outfile"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool GEMINI db_info",
+                                "name": "infile"
+                            }
+                        ],
+                        "label": "GEMINI_db_info",
+                        "name": "GEMINI db_info",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 1559,
+                            "top": 197
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.18.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "4c5f4e9b1931",
+                            "name": "gemini_db_info",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "0.18.1.0",
+                        "type": "tool",
+                        "uuid": "7f7f05f6-00b9-472b-8de9-044dc4feeb8c",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "7e61f96f-fc5a-436b-8433-dc78b10e5cea"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.18.1.0",
+                        "errors": null,
+                        "id": 8,
+                        "input_connections": {
+                            "infile": {
+                                "id": 6,
+                                "output_name": "outfile"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool GEMINI query",
+                                "name": "infile"
+                            }
+                        ],
+                        "label": "GEMINI_query2",
+                        "name": "GEMINI query",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 1502,
+                            "top": 478
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.18.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "5596c2dc4218",
+                            "name": "gemini_query",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"show_families\": \"\\\"false\\\"\", \"min_kindreds\": \"\\\"1\\\"\", \"sample_filter\": \"\\\"\\\"\", \"show_samples\": \"\\\"false\\\"\", \"__page__\": null, \"region\": \"\\\"\\\"\", \"gt_filter\": \"\\\"\\\"\", \"family_wise\": \"\\\"false\\\"\", \"q\": \"\\\"SELECT rs_ids, aaf_esp_ea, impact, clinvar_disease_name, clinvar_sig FROM variants WHERE filter is NULL and gene = 'POLRMT'\\\"\", \"header\": \"\\\"false\\\"\", \"dgidb\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"in\": \"\\\"all\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "0.18.1.0",
+                        "type": "tool",
+                        "uuid": "7e13bb42-cf27-4251-85bb-9f695d711127",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "2ff2734e-c1c6-448b-95eb-e3f47329bc65"
+                            }
+                        ]
+                    },
+                    {
+                        "annotation": "",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.18.1.0",
+                        "errors": null,
+                        "id": 9,
+                        "input_connections": {
+                            "infile": {
+                                "id": 6,
+                                "output_name": "outfile"
+                            }
+                        },
+                        "inputs": [
+                            {
+                                "description": "runtime parameter for tool GEMINI query",
+                                "name": "infile"
+                            }
+                        ],
+                        "label": "GEMINI_query1",
+                        "name": "GEMINI query",
+                        "outputs": [
+                            {
+                                "name": "outfile",
+                                "type": "tabular"
+                            }
+                        ],
+                        "position": {
+                            "left": 1598,
+                            "top": 334
+                        },
+                        "post_job_actions": {},
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.18.1.0",
+                        "tool_shed_repository": {
+                            "changeset_revision": "5596c2dc4218",
+                            "name": "gemini_query",
+                            "owner": "iuc",
+                            "tool_shed": "toolshed.g2.bx.psu.edu"
+                        },
+                        "tool_state": "{\"show_families\": \"\\\"false\\\"\", \"min_kindreds\": \"\\\"1\\\"\", \"sample_filter\": \"\\\"\\\"\", \"show_samples\": \"\\\"false\\\"\", \"__page__\": null, \"region\": \"\\\"\\\"\", \"gt_filter\": \"\\\"\\\"\", \"family_wise\": \"\\\"false\\\"\", \"q\": \"\\\"SELECT count(*) FROM variants WHERE in_dbsnp == 0\\\"\", \"header\": \"\\\"false\\\"\", \"dgidb\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"in\": \"\\\"all\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+                        "tool_version": "0.18.1.0",
+                        "type": "tool",
+                        "uuid": "00092a96-787b-444b-9b64-fe096588368b",
+                        "workflow_outputs": [
+                            {
+                                "label": null,
+                                "output_name": "outfile",
+                                "uuid": "2522c327-28ec-4e30-ac5f-cd751769e5ac"
+                            }
+                        ]
                     }
                 ],
-                "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nA. thaliana TAIR10 ref genome\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\naligned reads from outcrossed F2 pool\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\naligned reads from Ler mapping strain\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"SnpEff Download\"];\n  4[\"Replace parts of text\"];\n  0 -->|output| 4;\n  5[\"MiModD Variant Calling\"];\n  4 -->|outfile| 5;\n  2 -->|output| 5;\n  1 -->|output| 5;\n  6[\"MiModD Extract Variant Sites\"];\n  5 -->|ofile| 6;\n  7[\"MiModD NacreousMap\"];\n  6 -->|output_vcf| 7;\n  8[\"MiModD VCF Filter\"];\n  6 -->|output_vcf| 8;\n  9[\"SnpEff\"];\n  8 -->|outputfile| 9;\n  3 -->|snpeff_db| 9;\n  10[\"MiModD Report Variants\"];\n  9 -->|snpeff_output| 10;",
-                "modified": "2024-08-18 00:06:26 +0000",
-                "name": "Mapping And Molecular Identification Of Phenotype Causing Mutations",
-                "outputs": [],
-                "parent_id": "variant-analysis/mapping-by-sequencing",
-                "path": "topics/variant-analysis/tutorials/mapping-by-sequencing/workflows/workflow-arabidopsis.ga",
+                "parent_id": "variant-analysis/dip",
+                "path": "topics/variant-analysis/tutorials/dip/workflows/diploid.ga",
                 "tags": [
                     "variant-analysis"
                 ],
                 "test_results": null,
                 "tests": false,
-                "title": "Mapping And Molecular Identification Of Phenotype Causing Mutations",
+                "title": "Diploid",
                 "topic_id": "variant-analysis",
-                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-mapping-by-sequencing/versions/workflow-arabidopsis",
-                "tutorial_id": "mapping-by-sequencing",
-                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/mapping-by-sequencing/workflows/workflow-arabidopsis.ga",
-                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/mapping-by-sequencing/workflows/workflow-arabidopsis.html",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/variant-analysis-dip/versions/diploid",
+                "tutorial_id": "dip",
+                "url": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/dip/workflows/diploid.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/dip/workflows/diploid.html",
                 "version": 3,
-                "wfid": "variant-analysis-mapping-by-sequencing",
-                "wfname": "workflow-arabidopsis",
-                "workflow": "workflow-arabidopsis.ga",
+                "wfid": "variant-analysis-dip",
+                "wfname": "diploid",
+                "workflow": "diploid.ga",
                 "workflow_tools": [
-                    "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.1",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.1.0",
-                    "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_map/0.1.8_1",
-                    "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varcall/0.1.8_1",
-                    "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varextract/0.1.8_1",
-                    "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varreport/0.1.8_1",
-                    "toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_vcf_filter/0.1.8_1"
+                    "toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.1.0.46-0",
+                    "toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/0.0.3",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.18.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.18.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.18.1.0",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1",
+                    "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1"
                 ],
-                "workflowhub_id": "1063"
+                "workflowhub_id": "1104"
             }
         ],
-        "zenodo_link": "https://doi.org/10.5281/zenodo.1098033"
+        "zenodo_link": "https://doi.org/10.5281/zenodo.60520"
     },
     {
         "admin_install": {
@@ -291419,8 +298168,8 @@
         "edam_operation": [
             "Genome visualisation",
             "Variant calling",
-            "Phylogenetic tree generation",
-            "Phylogenetic tree visualisation"
+            "Phylogenetic tree visualisation",
+            "Phylogenetic tree generation"
         ],
         "edam_topic": [
             "Genomics",
@@ -291431,6 +298180,7 @@
             "Genetic variation"
         ],
         "exact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.eu",
             "UseGalaxy.org (Main)"
         ],
@@ -291463,7 +298213,7 @@
             "Determine the effect of those variants on genomic features",
             "Understand if the SNP is potentially affecting the phenotype"
         ],
-        "pageviews": 20322,
+        "pageviews": 20693,
         "pub_date": "2018-02-26",
         "questions": [
             "How do we detect differences between a set of reads from a microorganism and a reference genome"
@@ -291478,6 +298228,11 @@
         "subtopic": "introduction",
         "supported_servers": {
             "exact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
@@ -291549,8 +298304,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 120,
-        "visitors": 12166,
+        "visit_duration": 119,
+        "visitors": 12476,
         "workflows": [
             {
                 "creators": [],
@@ -291561,7 +298316,7 @@
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  5[label=\"snippy\"]\n  0 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"output\"]\n  k58cbabf03a3c4ec5b16a40d19fc82aae[color=lightseagreen,label=\"Output\\nsnippy_fasta\"]\n  5 -> k58cbabf03a3c4ec5b16a40d19fc82aae\n  k4002677b75f248f49d5332ab4dd44165[color=lightseagreen,label=\"Output\\nsnippy_tabular\"]\n  5 -> k4002677b75f248f49d5332ab4dd44165\n  6[label=\"JBrowse\"]\n  5 -> 6 [label=\"snpgff\"]\n  4 -> 6 [label=\"output\"]\n  5 -> 6 [label=\"snpsbam\"]\n  2 -> 6 [label=\"output\"]\n  kadfd738e00464e26a338254cdcb175af[color=lightseagreen,label=\"Output\\njbrowse_html\"]\n  6 -> kadfd738e00464e26a338254cdcb175af\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  2[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  3[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  4[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nInput dataset\"]\n  5[label=\"snippy\"]\n  0 -> 5 [label=\"output\"]\n  1 -> 5 [label=\"output\"]\n  3 -> 5 [label=\"output\"]\n  k419ad933d100406bbd61a70885eec0f8[color=lightseagreen,label=\"Output\\nsnippy_fasta\"]\n  5 -> k419ad933d100406bbd61a70885eec0f8\n  k47781ae9a68240a9aa61b972e5e5c9af[color=lightseagreen,label=\"Output\\nsnippy_tabular\"]\n  5 -> k47781ae9a68240a9aa61b972e5e5c9af\n  6[label=\"JBrowse\"]\n  5 -> 6 [label=\"snpgff\"]\n  4 -> 6 [label=\"output\"]\n  5 -> 6 [label=\"snpsbam\"]\n  2 -> 6 [label=\"output\"]\n  k6d6b366134ed417ab7b6394afe7a0edd[color=lightseagreen,label=\"Output\\njbrowse_html\"]\n  6 -> k6d6b366134ed417ab7b6394afe7a0edd\n}",
                 "history": [
                     {
                         "hash": "667ff3de9c4e13d341a6d864bd6dc826ef15ca04",
@@ -291732,8 +298487,8 @@
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"snippy\"];\n  0 -->|output| 5;\n  1 -->|output| 5;\n  3 -->|output| 5;\n  58cbabf0-3a3c-4ec5-b16a-40d19fc82aae[\"Output\\nsnippy_fasta\"];\n  5 --> 58cbabf0-3a3c-4ec5-b16a-40d19fc82aae;\n  style 58cbabf0-3a3c-4ec5-b16a-40d19fc82aae stroke:#2c3143,stroke-width:4px;\n  4002677b-75f2-48f4-9d53-32ab4dd44165[\"Output\\nsnippy_tabular\"];\n  5 --> 4002677b-75f2-48f4-9d53-32ab4dd44165;\n  style 4002677b-75f2-48f4-9d53-32ab4dd44165 stroke:#2c3143,stroke-width:4px;\n  6[\"JBrowse\"];\n  5 -->|snpgff| 6;\n  4 -->|output| 6;\n  5 -->|snpsbam| 6;\n  2 -->|output| 6;\n  adfd738e-0046-4e26-a338-254cdcb175af[\"Output\\njbrowse_html\"];\n  6 --> adfd738e-0046-4e26-a338-254cdcb175af;\n  style adfd738e-0046-4e26-a338-254cdcb175af stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-08-18 00:06:26 +0000",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"snippy\"];\n  0 -->|output| 5;\n  1 -->|output| 5;\n  3 -->|output| 5;\n  419ad933-d100-406b-bd61-a70885eec0f8[\"Output\\nsnippy_fasta\"];\n  5 --> 419ad933-d100-406b-bd61-a70885eec0f8;\n  style 419ad933-d100-406b-bd61-a70885eec0f8 stroke:#2c3143,stroke-width:4px;\n  47781ae9-a682-40a9-aa61-b972e5e5c9af[\"Output\\nsnippy_tabular\"];\n  5 --> 47781ae9-a682-40a9-aa61-b972e5e5c9af;\n  style 47781ae9-a682-40a9-aa61-b972e5e5c9af stroke:#2c3143,stroke-width:4px;\n  6[\"JBrowse\"];\n  5 -->|snpgff| 6;\n  4 -->|output| 6;\n  5 -->|snpsbam| 6;\n  2 -->|output| 6;\n  6d6b3661-34ed-417a-b7b6-394afe7a0edd[\"Output\\njbrowse_html\"];\n  6 --> 6d6b3661-34ed-417a-b7b6-394afe7a0edd;\n  style 6d6b3661-34ed-417a-b7b6-394afe7a0edd stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-02 12:08:11 +0000",
                 "name": "Microbial Variant Calling",
                 "outputs": [
                     {
@@ -291820,12 +298575,12 @@
                             {
                                 "label": "snippy_fasta",
                                 "output_name": "snpconsensus",
-                                "uuid": "58cbabf0-3a3c-4ec5-b16a-40d19fc82aae"
+                                "uuid": "419ad933-d100-406b-bd61-a70885eec0f8"
                             },
                             {
                                 "label": "snippy_tabular",
                                 "output_name": "snpsum",
-                                "uuid": "4002677b-75f2-48f4-9d53-32ab4dd44165"
+                                "uuid": "47781ae9-a682-40a9-aa61-b972e5e5c9af"
                             }
                         ]
                     },
@@ -291881,7 +298636,7 @@
                             {
                                 "label": "jbrowse_html",
                                 "output_name": "output",
-                                "uuid": "adfd738e-0046-4e26-a338-254cdcb175af"
+                                "uuid": "6d6b3661-34ed-417a-b7b6-394afe7a0edd"
                             }
                         ]
                     }
@@ -291912,6 +298667,570 @@
         ],
         "zenodo_link": "https://doi.org/10.5281/zenodo.582600"
     },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "datamash_ops",
+                    "owner": "iuc",
+                    "revisions": "4c07ddedc198",
+                    "tool_panel_section_label": "Join, Subtract and Group",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "nextclade",
+                    "owner": "iuc",
+                    "revisions": "4f6349228462",
+                    "tool_panel_section_label": "Phylogenetics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "pangolin",
+                    "owner": "iuc",
+                    "revisions": "8ad84c5753ea",
+                    "tool_panel_section_label": "Phylogenetics",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fasta_regex_finder",
+                    "owner": "mbernt",
+                    "revisions": "9a811adb714f",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: datamash_ops\n  owner: iuc\n  revisions: 4c07ddedc198\n  tool_panel_section_label: Join, Subtract and Group\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: nextclade\n  owner: iuc\n  revisions: 4f6349228462\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pangolin\n  owner: iuc\n  revisions: 8ad84c5753ea\n  tool_panel_section_label: Phylogenetics\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fasta_regex_finder\n  owner: mbernt\n  revisions: 9a811adb714f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.json",
+        "contributions": {
+            "authorship": [
+                "wm75",
+                "bebatut"
+            ],
+            "funding": [
+                "by-covid",
+                "elixir-converge"
+            ]
+        },
+        "contributors": [
+            {
+                "affiliations": [
+                    "by-covid",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "elixir_node": "de",
+                "fediverse": "https://scholar.social/@zerodivision",
+                "fediverse_flavor": "mastodon",
+                "id": "wm75",
+                "joined": "2017-09",
+                "matrix": "wm75:matrix.org",
+                "name": "Wolfgang Maier",
+                "orcid": "0000-0002-9464-6640",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "ifb",
+                    "elixir-europe"
+                ],
+                "contact_for_training": true,
+                "elixir_node": "fr",
+                "email": "berenice.batut@gmail.com",
+                "fediverse": "https://piaille.fr/@bebatut",
+                "fediverse_flavor": "mastodon",
+                "id": "bebatut",
+                "joined": "2017-09",
+                "linkedin": "berenicebatut",
+                "location": {
+                    "country": "FR",
+                    "lat": 45.77,
+                    "lon": 3.08
+                },
+                "matrix": "bebatut:matrix.org",
+                "name": "B\u00e9r\u00e9nice Batut",
+                "orcid": "0000-0001-9852-1987",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/",
+                "twitter": "bebatut",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bebatut.json"
+            },
+            {
+                "funder": true,
+                "funding_id": "101046203",
+                "funding_statement": "BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response.\n\nThis project has received funding from the European Union\u2019s Horizon Europe research and innovation programme under grant agreement \u2116 101046203 (BY-COVID)",
+                "funding_system": "cordis",
+                "id": "by-covid",
+                "joined": "2023-04",
+                "members": [
+                    "bgruening",
+                    "hexylena",
+                    "ilveroluca",
+                    "kikkomep",
+                    "mbaardwijk",
+                    "PapXis",
+                    "pauldg",
+                    "simleo",
+                    "stain",
+                    "wm75"
+                ],
+                "name": "BeYond-COVID",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/by-covid/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/by-covid.json"
+            },
+            {
+                "avatar": "https://elixir-europe.org/sites/default/files/styles/right-medium/public/images/converge_logo.png",
+                "funder": true,
+                "funding_id": "871075",
+                "funding_statement": "ELIXIR CONVERGE is connecting and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services. This project has received funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement \u2116 871075",
+                "funding_system": "cordis",
+                "github": false,
+                "id": "elixir-converge",
+                "joined": "2023-01",
+                "members": [
+                    "bgruening",
+                    "hexylena"
+                ],
+                "name": "ELIXIR-CONVERGE",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/elixir-converge/",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/elixir-converge.json"
+            }
+        ],
+        "dir": "topics/variant-analysis/tutorials/sars-cov-2-variant-discovery",
+        "edam_operation": [
+            "Tree-based sequence alignment",
+            "Variant calling",
+            "Variant classification",
+            "Methylation analysis"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "variant-analysis/sars-cov-2-variant-discovery",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "The Galaxy Covid-19 project has developed a flexible set of workflows for SARS-CoV-2 genome surveillance, which is freely available through public workflow registries.",
+            "The workflows enable processing of whole batches of samples with rather limited user interaction.",
+            "They provide a high-throughput and flexible analysis solution without compromising on accuracy, nor on the possibility to explore intermediate steps and outputs in detail."
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-10-01",
+        "objectives": [
+            "Discover and obtain recommended Galaxy workflows for SARS-CoV-2 sequence data analysis through public workflow registries",
+            "Choose and run a workflow to discover mutations in a batch of viral samples from sequencing data obtained through a range of different protocols and platforms",
+            "Run a workflow to summarize and visualize the mutation discovery results for a batch of samples",
+            "Run a workflow to construct viral consensus sequences for the samples in a batch",
+            "Know different SARS-CoV-2 lineage classification systems, and use pangolin and Nextclade to assign samples to predefined lineages",
+            "Combine information from different analysis steps to be able to draw appropriate conclusions about individual samples and batches of viral data"
+        ],
+        "pageviews": 12061,
+        "pub_date": "2021-06-30",
+        "questions": [
+            "How can a complete analysis, including viral consensus sequence reconstruction and lineage assignment be performed?",
+            "How can such an analysis be kept manageable for lots of samples, yet flexible enough to handle different types of input data?",
+            "What are key results beyond consensus genomes and lineage assignments that need to be understood to avoid inappropriate conclusions about samples?",
+            "How can the needs for high-throughput data analysis in an ongoing infectious disease outbreak/pandemic and the need for proper quality control and data inspection be balanced?"
+        ],
+        "recordings": [
+            {
+                "captioners": [
+                    "wm75"
+                ],
+                "date": "2023-05-10",
+                "length": "55M",
+                "speakers": [
+                    "wm75"
+                ],
+                "youtube_id": "hjlmCWQhBvI"
+            },
+            {
+                "captioners": [
+                    "hexylena"
+                ],
+                "date": "2021-08-09",
+                "length": "1H30M",
+                "speakers": [
+                    "wm75"
+                ],
+                "youtube_id": "vnFQ2fR_fzw"
+            },
+            {
+                "bot-timestamp": 1727459029,
+                "captioners": [
+                    "wm75"
+                ],
+                "date": "2024-09-27",
+                "galaxy_version": "24.1.2.dev0",
+                "length": "55M",
+                "speakers": [
+                    "wm75"
+                ],
+                "youtube_id": "-HQB1zyWWXM"
+            }
+        ],
+        "requirements": [
+            {
+                "topic_name": "galaxy-interface",
+                "tutorials": [
+                    "collections"
+                ],
+                "type": "internal"
+            },
+            {
+                "topic_name": "variant-analysis",
+                "tutorials": [
+                    "sars-cov-2"
+                ],
+                "type": "internal"
+            }
+        ],
+        "short_id": "T00316",
+        "short_tools": [
+            "pangolin",
+            "Filter1",
+            "upload1",
+            "fasta_regex_finder",
+            "nextclade",
+            "datamash_ops"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "one-health",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "covid19",
+            "virology",
+            "one-health"
+        ],
+        "time_estimation": "3H",
+        "title": "Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data",
+        "tools": [
+            "Filter1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/nextclade/nextclade/2.7.0+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/4.3+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/mbernt/fasta_regex_finder/fasta_regex_finder/0.1.0",
+            "upload1"
+        ],
+        "topic_name": "variant-analysis",
+        "topic_name_human": "Variant Analysis",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "sars-cov-2-variant-discovery",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.json"
+        },
+        "version": 17,
+        "video": false,
+        "video_versions": 3,
+        "video_view": 0,
+        "visit_duration": 208,
+        "visitors": 6502
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": [
+                {
+                    "name": "text_processing",
+                    "owner": "bgruening",
+                    "revisions": "d698c222f354",
+                    "tool_panel_section_label": "Text Manipulation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bwa",
+                    "owner": "devteam",
+                    "revisions": "e188dc7a68e6",
+                    "tool_panel_section_label": "Mapping",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "bamtools_split_ref",
+                    "owner": "iuc",
+                    "revisions": "9b520009db81",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "fastp",
+                    "owner": "iuc",
+                    "revisions": "65b93b623c77",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "iqtree",
+                    "owner": "iuc",
+                    "revisions": "24d024316465",
+                    "tool_panel_section_label": "Evolution",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "ivar_consensus",
+                    "owner": "iuc",
+                    "revisions": "40737febe339",
+                    "tool_panel_section_label": "Virology",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "qualimap_bamqc",
+                    "owner": "iuc",
+                    "revisions": "19ece8afbaab",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "samtools_view",
+                    "owner": "iuc",
+                    "revisions": "5826298f6a73",
+                    "tool_panel_section_label": "SAM/BAM",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "seqtk",
+                    "owner": "iuc",
+                    "revisions": "3da72230c066",
+                    "tool_panel_section_label": "FASTA/FASTQ",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "vapor",
+                    "owner": "iuc",
+                    "revisions": "244812f5bd1f",
+                    "tool_panel_section_label": "Metagenomic Analysis",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "collapse_collections",
+                    "owner": "nml",
+                    "revisions": "90981f86000f",
+                    "tool_panel_section_label": "Collection Operations",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
+                {
+                    "name": "mafft",
+                    "owner": "rnateam",
+                    "revisions": "bf28a8cff401",
+                    "tool_panel_section_label": "Multiple Alignments",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_split_ref\n  owner: iuc\n  revisions: 9b520009db81\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: iqtree\n  owner: iuc\n  revisions: 24d024316465\n  tool_panel_section_label: Evolution\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ivar_consensus\n  owner: iuc\n  revisions: 40737febe339\n  tool_panel_section_label: Virology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qualimap_bamqc\n  owner: iuc\n  revisions: 19ece8afbaab\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: 5826298f6a73\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: vapor\n  owner: iuc\n  revisions: 244812f5bd1f\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mafft\n  owner: rnateam\n  revisions: bf28a8cff401\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/aiv-analysis/tutorial.json",
+        "contributors": [
+            {
+                "affiliations": [
+                    "by-covid",
+                    "uni-freiburg",
+                    "elixir-europe"
+                ],
+                "elixir_node": "de",
+                "fediverse": "https://scholar.social/@zerodivision",
+                "fediverse_flavor": "mastodon",
+                "id": "wm75",
+                "joined": "2017-09",
+                "matrix": "wm75:matrix.org",
+                "name": "Wolfgang Maier",
+                "orcid": "0000-0002-9464-6640",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
+            }
+        ],
+        "dir": "topics/variant-analysis/tutorials/aiv-analysis",
+        "edam_operation": [
+            "Data handling",
+            "Sequence alignment",
+            "Read mapping",
+            "Sequencing quality control",
+            "De-novo assembly",
+            "Sequence alignment analysis",
+            "Phylogenetic analysis",
+            "Sequence contamination filtering",
+            "Sequence analysis",
+            "Multiple sequence alignment",
+            "Generation",
+            "Sequence file editing",
+            "Data retrieval",
+            "Genome indexing"
+        ],
+        "edam_topic": [],
+        "exact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org (Main)"
+        ],
+        "feedback_mean_note": null,
+        "feedback_number": 0,
+        "hands_on": true,
+        "id": "variant-analysis/aiv-analysis",
+        "inexact_supported_servers": [
+            "UseGalaxy.cz"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "Reassortment of gene segments makes reference-based mapping of influenza sequencing data challenging",
+            "An alternative to *de-novo* assembly can be mapping to a dynamically chosen reference genome",
+            "Variant calling and consensus genome construction can follow workflows used also for other viral sequence data",
+            "Standard phylogenetic tools can be used to find relationships between influenza samples but should be used on a per-segment basis"
+        ],
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
+        "license": "CC-BY-4.0",
+        "mod_date": "2024-03-20",
+        "objectives": [
+            "Determine how reassortment impacts reference-based mapping approaches",
+            "Use a collection of per-segment reference sequences to construct a hybrid reference genome that is sufficiently close to a sequenced sample to be useful as a reference for mapping",
+            "Construct a sample consensus genome from mapped reads",
+            "Generate per-segment phylogenetic trees of AIV consensus sequences"
+        ],
+        "pageviews": 1887,
+        "pub_date": "2022-11-21",
+        "questions": [
+            "With reassortment of gene segments being a common event in avian influenza virus (AIV) evolution, does it make sense to use a reference-based mapping approach for constructing consensus genome sequences for AIV samples?",
+            "Is it possible to reuse existing tools and workflows developed for the analysis of sequencing data from other viruses?",
+            "How can we obtain meaningful phylogenetic insight from AIV consensus sequences?"
+        ],
+        "short_id": "T00308",
+        "short_tools": [
+            "bwa_mem",
+            "fastp",
+            "samtools_view",
+            "vapor",
+            "upload1",
+            "Show beginning1",
+            "__RELABEL_FROM_FILE__",
+            "tp_find_and_replace",
+            "ivar_consensus",
+            "qualimap_bamqc",
+            "seqtk_subseq",
+            "Grep1",
+            "bamtools_split_ref",
+            "iqtree",
+            "rbc_mafft",
+            "collapse_dataset"
+        ],
+        "slides": false,
+        "slides_recordings": false,
+        "subtopic": "one-health",
+        "supported_servers": {
+            "exact": [
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "symlink": null,
+        "tags": [
+            "virology",
+            "one-health"
+        ],
+        "time_estimation": "4H",
+        "title": "Avian influenza viral strain analysis from gene segment sequencing data",
+        "tools": [
+            "Grep1",
+            "Show beginning1",
+            "__RELABEL_FROM_FILE__",
+            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4",
+            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_ref/bamtools_split_ref/2.5.2+galaxy1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.1.2+galaxy2",
+            "toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.2+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
+            "toolshed.g2.bx.psu.edu/repos/iuc/vapor/vapor/1.0.2+galaxy3",
+            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
+            "toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.520+galaxy0",
+            "upload1"
+        ],
+        "topic_name": "variant-analysis",
+        "topic_name_human": "Variant Analysis",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "aiv-analysis",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/aiv-analysis/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/aiv-analysis/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/aiv-analysis/tutorial.json"
+        },
+        "version": 9,
+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 163,
+        "visitors": 1279
+    },
     {
         "admin_install": {
             "install_repository_dependencies": true,
@@ -291935,6 +299254,19 @@
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/khaled196/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/khaled196.json"
             },
+            {
+                "affiliations": [
+                    "elixir-europe"
+                ],
+                "elixir_node": "uk",
+                "id": "kkamieniecka",
+                "joined": "2018-08",
+                "name": "Katarzyna Kamieniecka",
+                "orcid": "0009-0004-2454-5950",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/",
+                "twitter": "katemurat",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/kkamieniecka.json"
+            },
             {
                 "affiliations": [
                     "elixir-europe"
@@ -291951,8 +299283,8 @@
         ],
         "dir": "topics/variant-analysis/tutorials/beacon_cnv_query",
         "edam_operation": [
-            "Genetic variation analysis",
             "Service discovery",
+            "Genetic variation analysis",
             "Database search"
         ],
         "edam_topic": [],
@@ -291987,12 +299319,12 @@
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-06",
+        "mod_date": "2024-09-27",
         "objectives": [
             "Comprehend the concept of Beacon databases and their role in genomic research.",
             "Demonstrate proficiency in querying Beacon databases to identify and analyze specific Copy Number Variants (CNVs)."
         ],
-        "pageviews": 8,
+        "pageviews": 27,
         "priority": 1,
         "pub_date": "2024-08-06",
         "questions": [
@@ -292018,7 +299350,7 @@
         },
         "symlink": null,
         "time_estimation": "30M",
-        "title": "Querying a Beacon Database for Copy Number Variants (CNVs)",
+        "title": "Querying the University of Bradford GDC Beacon Database for Copy Number Variants (CNVs)",
         "tools": [
             "toolshed.g2.bx.psu.edu/repos/iuc/beacon2_cnv/beacon2_cnv/2.1.1+galaxy0"
         ],
@@ -292037,273 +299369,14 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/beacon_cnv_query/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/beacon_cnv_query/tutorial.json"
         },
-        "version": 1,
+        "version": 3,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 69,
-        "visitors": 6,
+        "visit_duration": 278,
+        "visitors": 22,
         "zenodo_link": "https://zenodo.org/records/10658688"
     },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "text_processing",
-                    "owner": "bgruening",
-                    "revisions": "d698c222f354",
-                    "tool_panel_section_label": "Text Manipulation",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bwa",
-                    "owner": "devteam",
-                    "revisions": "e188dc7a68e6",
-                    "tool_panel_section_label": "Mapping",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "bamtools_split_ref",
-                    "owner": "iuc",
-                    "revisions": "9b520009db81",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "fastp",
-                    "owner": "iuc",
-                    "revisions": "65b93b623c77",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "iqtree",
-                    "owner": "iuc",
-                    "revisions": "24d024316465",
-                    "tool_panel_section_label": "Evolution",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "ivar_consensus",
-                    "owner": "iuc",
-                    "revisions": "40737febe339",
-                    "tool_panel_section_label": "Virology",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "qualimap_bamqc",
-                    "owner": "iuc",
-                    "revisions": "19ece8afbaab",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "samtools_view",
-                    "owner": "iuc",
-                    "revisions": "5826298f6a73",
-                    "tool_panel_section_label": "SAM/BAM",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "seqtk",
-                    "owner": "iuc",
-                    "revisions": "3da72230c066",
-                    "tool_panel_section_label": "FASTA/FASTQ",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "vapor",
-                    "owner": "iuc",
-                    "revisions": "244812f5bd1f",
-                    "tool_panel_section_label": "Metagenomic Analysis",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "collapse_collections",
-                    "owner": "nml",
-                    "revisions": "90981f86000f",
-                    "tool_panel_section_label": "Collection Operations",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
-                {
-                    "name": "mafft",
-                    "owner": "rnateam",
-                    "revisions": "bf28a8cff401",
-                    "tool_panel_section_label": "Multiple Alignments",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
-        },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa\n  owner: devteam\n  revisions: e188dc7a68e6\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bamtools_split_ref\n  owner: iuc\n  revisions: 9b520009db81\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: fastp\n  owner: iuc\n  revisions: 65b93b623c77\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: iqtree\n  owner: iuc\n  revisions: 24d024316465\n  tool_panel_section_label: Evolution\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: ivar_consensus\n  owner: iuc\n  revisions: 40737febe339\n  tool_panel_section_label: Virology\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: qualimap_bamqc\n  owner: iuc\n  revisions: 19ece8afbaab\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_view\n  owner: iuc\n  revisions: 5826298f6a73\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: seqtk\n  owner: iuc\n  revisions: 3da72230c066\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: vapor\n  owner: iuc\n  revisions: 244812f5bd1f\n  tool_panel_section_label: Metagenomic Analysis\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: mafft\n  owner: rnateam\n  revisions: bf28a8cff401\n  tool_panel_section_label: Multiple Alignments\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/aiv-analysis/tutorial.json",
-        "contributors": [
-            {
-                "affiliations": [
-                    "by-covid",
-                    "uni-freiburg",
-                    "elixir-europe"
-                ],
-                "elixir_node": "de",
-                "fediverse": "https://scholar.social/@zerodivision",
-                "fediverse_flavor": "mastodon",
-                "id": "wm75",
-                "joined": "2017-09",
-                "matrix": "wm75:matrix.org",
-                "name": "Wolfgang Maier",
-                "orcid": "0000-0002-9464-6640",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/wm75/",
-                "url": "https://training.galaxyproject.org/training-material/api/contributors/wm75.json"
-            }
-        ],
-        "dir": "topics/variant-analysis/tutorials/aiv-analysis",
-        "edam_operation": [
-            "Sequencing quality control",
-            "Sequence contamination filtering",
-            "Genome indexing",
-            "Sequence file editing",
-            "De-novo assembly",
-            "Sequence analysis",
-            "Read mapping",
-            "Sequence alignment analysis",
-            "Phylogenetic analysis",
-            "Sequence alignment",
-            "Data retrieval",
-            "Multiple sequence alignment",
-            "Generation",
-            "Data handling"
-        ],
-        "edam_topic": [],
-        "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org (Main)"
-        ],
-        "feedback_mean_note": null,
-        "feedback_number": 0,
-        "hands_on": true,
-        "id": "variant-analysis/aiv-analysis",
-        "inexact_supported_servers": [
-            "UseGalaxy.cz"
-        ],
-        "js_requirements": {
-            "mathjax": null,
-            "mermaid": false
-        },
-        "key_points": [
-            "Reassortment of gene segments makes reference-based mapping of influenza sequencing data challenging",
-            "An alternative to *de-novo* assembly can be mapping to a dynamically chosen reference genome",
-            "Variant calling and consensus genome construction can follow workflows used also for other viral sequence data",
-            "Standard phylogenetic tools can be used to find relationships between influenza samples but should be used on a per-segment basis"
-        ],
-        "layout": "tutorial_hands_on",
-        "level": "Intermediate",
-        "license": "CC-BY-4.0",
-        "mod_date": "2024-03-20",
-        "objectives": [
-            "Determine how reassortment impacts reference-based mapping approaches",
-            "Use a collection of per-segment reference sequences to construct a hybrid reference genome that is sufficiently close to a sequenced sample to be useful as a reference for mapping",
-            "Construct a sample consensus genome from mapped reads",
-            "Generate per-segment phylogenetic trees of AIV consensus sequences"
-        ],
-        "pageviews": 1792,
-        "pub_date": "2022-11-21",
-        "questions": [
-            "With reassortment of gene segments being a common event in avian influenza virus (AIV) evolution, does it make sense to use a reference-based mapping approach for constructing consensus genome sequences for AIV samples?",
-            "Is it possible to reuse existing tools and workflows developed for the analysis of sequencing data from other viruses?",
-            "How can we obtain meaningful phylogenetic insight from AIV consensus sequences?"
-        ],
-        "short_id": "T00308",
-        "short_tools": [
-            "Grep1",
-            "fastp",
-            "upload1",
-            "samtools_view",
-            "bamtools_split_ref",
-            "tp_find_and_replace",
-            "rbc_mafft",
-            "seqtk_subseq",
-            "qualimap_bamqc",
-            "Show beginning1",
-            "vapor",
-            "iqtree",
-            "ivar_consensus",
-            "__RELABEL_FROM_FILE__",
-            "bwa_mem",
-            "collapse_dataset"
-        ],
-        "slides": false,
-        "slides_recordings": false,
-        "subtopic": "one-health",
-        "supported_servers": {
-            "exact": [
-                {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
-                    "url": "https://usegalaxy.org",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
-                }
-            ]
-        },
-        "symlink": null,
-        "tags": [
-            "virology",
-            "one-health"
-        ],
-        "time_estimation": "4H",
-        "title": "Avian influenza viral strain analysis from gene segment sequencing data",
-        "tools": [
-            "Grep1",
-            "Show beginning1",
-            "__RELABEL_FROM_FILE__",
-            "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4",
-            "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_ref/bamtools_split_ref/2.5.2+galaxy1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.1.2+galaxy2",
-            "toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.2+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0",
-            "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1",
-            "toolshed.g2.bx.psu.edu/repos/iuc/vapor/vapor/1.0.2+galaxy3",
-            "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
-            "toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.520+galaxy0",
-            "upload1"
-        ],
-        "topic_name": "variant-analysis",
-        "topic_name_human": "Variant Analysis",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "aiv-analysis",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/variant-analysis/tutorials/aiv-analysis/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/aiv-analysis/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/aiv-analysis/tutorial.json"
-        },
-        "version": 9,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 166,
-        "visitors": 1198
-    },
     {
         "admin_install": {
             "install_repository_dependencies": true,
@@ -292371,8 +299444,8 @@
         ],
         "dir": "topics/variant-analysis/tutorials/beaconise_1000hg",
         "edam_operation": [
-            "Service discovery",
             "Database search",
+            "Service discovery",
             "Genetic variation analysis"
         ],
         "edam_topic": [],
@@ -292398,7 +299471,7 @@
         "layout": "tutorial_hands_on",
         "level": "Advanced",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-08-07",
+        "mod_date": "2024-09-27",
         "objectives": [
             "Comprehend the fundamental concepts and applications of Beacons",
             "Apply skills in utilizing MongoDB to construct and manage Beacons",
@@ -292406,7 +299479,7 @@
             "Execute a step-by-step process to import data into Beacons",
             "Develop the ability to query Beacons for variants"
         ],
-        "pageviews": 8,
+        "pageviews": 31,
         "priority": 2,
         "pub_date": "2024-08-06",
         "questions": [
@@ -292437,10 +299510,10 @@
         ],
         "short_id": "T00449",
         "short_tools": [
-            "cnv_vcf2json",
-            "cnv_phenopacket",
             "beacon2_cnv",
-            "beacon2_import"
+            "cnv_phenopacket",
+            "beacon2_import",
+            "cnv_vcf2json"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -292480,12 +299553,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/beaconise_1000hg/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/variant-analysis/tutorials/beaconise_1000hg/tutorial.json"
         },
-        "version": 2,
+        "version": 3,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 0,
-        "visitors": 7,
+        "visit_duration": 71,
+        "visitors": 27,
         "zenodo_link": "https://zenodo.org/records/10658688"
     },
     {
@@ -292620,6 +299693,8 @@
         "hands_on": true,
         "id": "visualisation/circos-microbial",
         "inexact_supported_servers": [
+            "MISSISSIPPI",
+            "UseGalaxy.be",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
@@ -292633,13 +299708,14 @@
             "Not all customisations have to be done with rules, but they can be a useful method"
         ],
         "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-01-15",
+        "mod_date": "2024-09-17",
         "objectives": [
             "Plot an *E. coli* genome in Galaxy",
             "With tracks for the annotations, sequencing data, and variants."
         ],
-        "pageviews": 696,
+        "pageviews": 886,
         "pub_date": "2023-11-08",
         "questions": [
             "How can I visualise common genomic datasets like GFF3, BigWig, and VCF"
@@ -292655,14 +299731,14 @@
         ],
         "short_id": "T00373",
         "short_tools": [
+            "circos_interval_to_tile",
             "circos",
-            "deeptools_bam_coverage",
-            "Cut1",
             "circos_wiggle_to_scatter",
-            "circos_gc_skew",
-            "circos_interval_to_tile",
+            "gff2bed1",
+            "Cut1",
             "circos_interval_to_text",
-            "gff2bed1"
+            "deeptools_bam_coverage",
+            "circos_gc_skew"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -292685,6 +299761,16 @@
                 }
             ],
             "inexact": [
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -292730,12 +299816,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/circos-microbial/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/circos-microbial/tutorial.json"
         },
-        "version": 2,
+        "version": 3,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 81,
-        "visitors": 547,
+        "visit_duration": 108,
+        "visitors": 684,
         "workflows": [
             {
                 "creators": [
@@ -292928,7 +300014,7 @@
                 ],
                 "license": "AGPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGenome\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGenes\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Circos: bigWig to Scatter\"];\n  3 -->|output| 10;\n  11[\"Circos: bigWig to Scatter\"];\n  4 -->|output| 11;\n  12[\"Cut\"];\n  5 -->|output| 12;\n  13[\"Circos: bigWig to Scatter\"];\n  6 -->|output| 13;\n  14[\"Circos: Interval to Tiles\"];\n  8 -->|out_file1| 14;\n  15[\"Circos\"];\n  0 -->|output| 15;\n  10 -->|output| 15;\n  12 -->|out_file1| 15;\n  9 -->|output| 15;\n  11 -->|output| 15;\n  7 -->|output| 15;\n  14 -->|output| 15;\n  14 -->|output| 15;\n  13 -->|output| 15;\n  ad540557-b836-4f68-9d64-7132c059c53e[\"Output\\nplot\"];\n  15 --> ad540557-b836-4f68-9d64-7132c059c53e;\n  style ad540557-b836-4f68-9d64-7132c059c53e stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nRNA Seq Coverage 1\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nRNA Seq Coverage 2\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nDNA Sequencing Coverage\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nVariants\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"GC Skew\"];\n  0 -->|output| 6;\n  7[\"Circos: Interval to Circos Text Labels\"];\n  1 -->|output| 7;\n  8[\"GFF-to-BED\"];\n  1 -->|output| 8;\n  9[\"Circos: bigWig to Scatter\"];\n  2 -->|output| 9;",
-                "modified": "2024-08-18 00:06:26 +0000",
+                "modified": "2024-10-02 12:08:11 +0000",
                 "name": "Circos for E. Coli",
                 "outputs": [
                     {
@@ -293156,6 +300242,7 @@
         "edam_topic": [],
         "exact_supported_servers": [
             "Galaxy@Pasteur",
+            "MISSISSIPPI",
             "UseGalaxy.eu",
             "UseGalaxy.fr",
             "UseGalaxy.org (Main)"
@@ -293165,6 +300252,7 @@
         "hands_on": true,
         "id": "visualisation/circos",
         "inexact_supported_servers": [
+            "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.no"
         ],
@@ -293177,13 +300265,14 @@
             "Circos is often used for genomics, but can also be used for other types of data"
         ],
         "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-09-17",
         "objectives": [
             "Create a number of Circos plots using the Galaxy tool",
             "Familiarise yourself with the various different track types"
         ],
-        "pageviews": 5768253,
+        "pageviews": 5939927,
         "pub_date": "2020-01-10",
         "questions": [
             "What can the Circos Galaxy tool be used for?",
@@ -293208,12 +300297,12 @@
         ],
         "short_id": "T00321",
         "short_tools": [
-            "Grep1",
             "circos",
+            "upload1",
             "random_lines1",
+            "Grep1",
             "Cut1",
-            "Remove beginning1",
-            "upload1"
+            "Remove beginning1"
         ],
         "slides": true,
         "slides_recordings": [
@@ -293238,6 +300327,11 @@
                     "url": "https://galaxy.pasteur.fr/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
@@ -293255,6 +300349,11 @@
                 }
             ],
             "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -293293,12 +300392,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/circos/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/circos/tutorial.json"
         },
-        "version": 20,
+        "version": 21,
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 257,
-        "visitors": 2088447,
+        "visit_duration": 256,
+        "visitors": 2159100,
         "workflows": [
             {
                 "creators": [
@@ -293423,7 +300522,7 @@
                 ],
                 "license": "AGPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Remove beginning\"];\n  2[\"Remove beginning\"];\n  3[\"Select\"];\n  4[\"Circos\"];\n  5[\"Cut\"];\n  1 -->|out_file1| 5;\n  6[\"Select random lines\"];\n  2 -->|out_file1| 6;\n  7[\"Cut\"];\n  3 -->|out_file1| 7;\n  8[\"Select random lines\"];\n  5 -->|out_file1| 8;\n  9[\"Circos\"];\n  0 -->|output| 9;\n  7 -->|out_file1| 9;\n  10[\"Circos\"];\n  0 -->|output| 10;\n  7 -->|out_file1| 10;\n  11[\"Circos\"];\n  0 -->|output| 11;\n  7 -->|out_file1| 11;\n  8 -->|out_file1| 11;\n  12[\"Circos\"];\n  0 -->|output| 12;\n  7 -->|out_file1| 12;\n  8 -->|out_file1| 12;\n  13[\"Circos\"];\n  0 -->|output| 13;\n  7 -->|out_file1| 13;\n  8 -->|out_file1| 13;\n  14[\"Circos\"];\n  0 -->|output| 14;\n  7 -->|out_file1| 14;\n  8 -->|out_file1| 14;\n  15[\"Circos\"];\n  0 -->|output| 15;\n  7 -->|out_file1| 15;\n  8 -->|out_file1| 15;\n  6 -->|out_file1| 15;\n  16[\"Circos\"];\n  0 -->|output| 16;\n  7 -->|out_file1| 16;\n  8 -->|out_file1| 16;\n  6 -->|out_file1| 16;",
-                "modified": "2024-08-18 00:06:26 +0000",
+                "modified": "2024-10-02 12:08:11 +0000",
                 "name": "Circos tutorial",
                 "outputs": [],
                 "parent_id": "visualisation/circos",
@@ -293566,7 +300665,7 @@
                 ],
                 "license": "AGPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Circos\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  1 -->|output| 2;\n  1 -->|output| 2;\n  3[\"Circos\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  1 -->|output| 3;\n  1 -->|output| 3;",
-                "modified": "2024-08-18 00:06:26 +0000",
+                "modified": "2024-10-02 12:08:11 +0000",
                 "name": "Circos: Nature workflow",
                 "outputs": [],
                 "parent_id": "visualisation/circos",
@@ -293672,7 +300771,7 @@
         "license": "MIT",
         "logo": "GTN",
         "mod_date": "2023-11-20",
-        "pageviews": 1008582,
+        "pageviews": 1179269,
         "pub_date": "2023-11-20",
         "short_id": "S00112",
         "short_tools": [],
@@ -293734,7 +300833,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 149,
-        "visitors": 425897,
+        "visitors": 494809,
         "voice": {
             "id": "Brian",
             "lang": "en-GB",
@@ -293746,10 +300845,18 @@
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": []
+            "tools": [
+                {
+                    "name": "jbrowse",
+                    "owner": "iuc",
+                    "revisions": "17359b808b01",
+                    "tool_panel_section_label": "Graph/Display Data",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                }
+            ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/introduction/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: jbrowse\n  owner: iuc\n  revisions: 17359b808b01\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/jbrowse/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
@@ -293809,82 +300916,158 @@
                 "orcid": "0000-0003-3803-468X",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/visualisation/tutorials/introduction",
-        "edam_operation": [],
+        "dir": "topics/visualisation/tutorials/jbrowse",
+        "edam_operation": [
+            "Genome visualisation"
+        ],
         "edam_topic": [],
-        "exact_supported_servers": [],
+        "exact_supported_servers": [
+            "Galaxy@AuBi",
+            "UseGalaxy.be",
+            "UseGalaxy.eu",
+            "UseGalaxy.fr",
+            "UseGalaxy.no",
+            "UseGalaxy.org (Main)",
+            "UseGalaxy.org.au"
+        ],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": false,
-        "id": "visualisation/introduction",
+        "hands_on": true,
+        "id": "visualisation/jbrowse",
         "inexact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.org",
-            "UseGalaxy.org.au",
-            "UseGalaxy.fr"
+            "Galaxy@Pasteur",
+            "GalaxyTrakr",
+            "MISSISSIPPI",
+            "UseGalaxy.cz"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "Visualizations are vital for the interpretation of large datasets",
-            "Galaxy has numerous visualization options available"
+            "This tutorial can not exhaustively cover every data type, but maybe it provides inspiration for your own analyses",
+            "JBrowse is a great, workflow-compatible alternative to other genome browsers",
+            "You can build visualisations that summarise dozens of analyses in one visualisation"
         ],
-        "layout": "introduction_slides",
+        "layout": "tutorial_hands_on",
+        "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "logo": "GTN",
-        "mod_date": "2023-01-12",
-        "pageviews": 5726884,
-        "priority": 1,
+        "mod_date": "2024-09-17",
+        "objectives": [
+            "Build several visualisations in JBrowse",
+            "Have basic familiarity with moving around JBrowse, and loading several data tracks"
+        ],
+        "pageviews": 5902923,
         "pub_date": "2020-01-10",
-        "redirect_from": [
-            "/topics/visualisation/slides/introduction",
-            "/short/visualisation/introduction/slides",
-            "/short/S00101"
+        "questions": [
+            "How can I visualise features or blast data?",
+            "How can I visualise sequencing data in a workflow"
+        ],
+        "short_id": "T00322",
+        "short_tools": [
+            "jbrowse"
         ],
-        "short_id": "S00101",
-        "short_tools": [],
         "slides": true,
         "slides_recordings": false,
         "supported_servers": {
-            "exact": [],
-            "inexact": [
+            "exact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
-                    "human": "Galaxy Europe",
-                    "id": "eu",
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
                 {
-                    "human": "Galaxy Main",
-                    "id": "us",
-                    "name": "UseGalaxy.org",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 },
                 {
-                    "human": "Galaxy Australia",
-                    "id": "au",
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
                 },
                 {
-                    "human": "Galaxy France",
-                    "id": "fr",
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr",
-                    "usegalaxy": true
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
                 }
             ]
         },
         "symlink": null,
-        "title": "Visualisations in Galaxy",
-        "tools": [],
+        "tags": [
+            "gmod",
+            "jbrowse1"
+        ],
+        "time_estimation": "1h",
+        "title": "Genomic Data Visualisation with JBrowse",
+        "tools": [
+            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0"
+        ],
         "topic_name": "visualisation",
         "topic_name_human": "Visualisation",
         "tours": false,
@@ -293893,37 +301076,30 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "introduction",
+        "tutorial_name": "jbrowse",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/visualisation/tutorials/introduction/slides.html",
+        "url": "https://training.galaxyproject.org//topics/visualisation/tutorials/jbrowse/tutorial.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/introduction/slides.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/introduction/slides.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/jbrowse/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/jbrowse/tutorial.json"
         },
-        "version": 1,
+        "version": 16,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 152,
-        "visitors": 2063758
+        "visit_duration": 287,
+        "visitors": 2137540,
+        "zenodo_link": "https://doi.org/10.5281/zenodo.3591856"
     },
     {
         "admin_install": {
             "install_repository_dependencies": true,
             "install_resolver_dependencies": true,
             "install_tool_dependencies": true,
-            "tools": [
-                {
-                    "name": "jbrowse",
-                    "owner": "iuc",
-                    "revisions": "17359b808b01",
-                    "tool_panel_section_label": "Graph/Display Data",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                }
-            ]
+            "tools": []
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: jbrowse\n  owner: iuc\n  revisions: 17359b808b01\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
-        "api": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/jbrowse/tutorial.json",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/introduction/tutorial.json",
         "contributors": [
             {
                 "affiliations": [
@@ -293983,139 +301159,82 @@
                 "orcid": "0000-0003-3803-468X",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/shiltemann.json"
-            },
-            {
-                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
-                "end_date": "2023-09-30",
-                "funder": true,
-                "funder_name": "Erasmus+ Programme",
-                "funding_id": "2020-1-NL01-KA203-064717",
-                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
-                "funding_system": "erasmusplus",
-                "github": false,
-                "id": "gallantries",
-                "joined": "2020-09",
-                "members": [
-                    "abretaud",
-                    "bebatut",
-                    "colineroyaux",
-                    "fpsom",
-                    "hexylena",
-                    "shiltemann",
-                    "yvanlebras"
-                ],
-                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
-                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
-                "short_name": "Gallantries",
-                "start_date": "2020-09-01",
-                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
             }
         ],
-        "dir": "topics/visualisation/tutorials/jbrowse",
-        "edam_operation": [
-            "Genome visualisation"
-        ],
+        "dir": "topics/visualisation/tutorials/introduction",
+        "edam_operation": [],
         "edam_topic": [],
-        "exact_supported_servers": [
-            "Galaxy@AuBi",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr",
-            "UseGalaxy.no",
-            "UseGalaxy.org (Main)",
-            "UseGalaxy.org.au"
-        ],
+        "exact_supported_servers": [],
         "feedback_mean_note": null,
         "feedback_number": 0,
-        "hands_on": true,
-        "id": "visualisation/jbrowse",
+        "hands_on": false,
+        "id": "visualisation/introduction",
         "inexact_supported_servers": [
-            "GalaxyTrakr",
-            "UseGalaxy.cz"
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
         ],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
         },
         "key_points": [
-            "This tutorial can not exhaustively cover every data type, but maybe it provides inspiration for your own analyses",
-            "JBrowse is a great, workflow-compatible alternative to other genome browsers",
-            "You can build visualisations that summarise dozens of analyses in one visualisation"
+            "Visualizations are vital for the interpretation of large datasets",
+            "Galaxy has numerous visualization options available"
         ],
-        "layout": "tutorial_hands_on",
+        "layout": "introduction_slides",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-02-29",
-        "objectives": [
-            "Build several visualisations in JBrowse",
-            "Have basic familiarity with moving around JBrowse, and loading several data tracks"
-        ],
-        "pageviews": 5732004,
+        "logo": "GTN",
+        "mod_date": "2023-01-12",
+        "pageviews": 5897571,
+        "priority": 1,
         "pub_date": "2020-01-10",
-        "questions": [
-            "How can I visualise features or blast data?",
-            "How can I visualise sequencing data in a workflow"
-        ],
-        "short_id": "T00322",
-        "short_tools": [
-            "jbrowse"
+        "redirect_from": [
+            "/topics/visualisation/slides/introduction",
+            "/short/visualisation/introduction/slides",
+            "/short/S00101"
         ],
+        "short_id": "S00101",
+        "short_tools": [],
         "slides": true,
         "slides_recordings": false,
         "supported_servers": {
-            "exact": [
-                {
-                    "name": "Galaxy@AuBi",
-                    "url": "https://galaxy.mesocentre.uca.fr",
-                    "usegalaxy": false
-                },
+            "exact": [],
+            "inexact": [
                 {
+                    "human": "Galaxy Europe",
+                    "id": "eu",
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.no",
-                    "url": "https://usegalaxy.no/",
-                    "usegalaxy": false
-                },
-                {
-                    "name": "UseGalaxy.org (Main)",
+                    "human": "Galaxy Main",
+                    "id": "us",
+                    "name": "UseGalaxy.org",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
                 },
                 {
+                    "human": "Galaxy Australia",
+                    "id": "au",
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
-                }
-            ],
-            "inexact": [
-                {
-                    "name": "GalaxyTrakr",
-                    "url": "https://galaxytrakr.org/",
-                    "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.cz",
-                    "url": "https://usegalaxy.cz/",
-                    "usegalaxy": false
+                    "human": "Galaxy France",
+                    "id": "fr",
+                    "name": "UseGalaxy.fr",
+                    "url": "https://usegalaxy.fr",
+                    "usegalaxy": true
                 }
             ]
         },
         "symlink": null,
-        "tags": [
-            "gmod",
-            "jbrowse1"
-        ],
-        "time_estimation": "1h",
-        "title": "Genomic Data Visualisation with JBrowse",
-        "tools": [
-            "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0"
-        ],
+        "title": "Visualisations in Galaxy",
+        "tools": [],
         "topic_name": "visualisation",
         "topic_name_human": "Visualisation",
         "tours": false,
@@ -294124,19 +301243,18 @@
             "tutorial": [],
             "video": false
         },
-        "tutorial_name": "jbrowse",
+        "tutorial_name": "introduction",
         "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/visualisation/tutorials/jbrowse/tutorial.html",
+        "url": "https://training.galaxyproject.org//topics/visualisation/tutorials/introduction/slides.html",
         "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/jbrowse/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/jbrowse/tutorial.json"
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/introduction/slides.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/visualisation/tutorials/introduction/slides.json"
         },
-        "version": 15,
+        "version": 1,
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 287,
-        "visitors": 2067558,
-        "zenodo_link": "https://doi.org/10.5281/zenodo.3591856"
+        "visit_duration": 152,
+        "visitors": 2133613
     }
 ]
\ No newline at end of file
diff --git a/communities/assembly/resources/tools.html b/communities/assembly/resources/tools.html
index 4eaad265..0953ee76 100644
--- a/communities/assembly/resources/tools.html
+++ b/communities/assembly/resources/tools.html
@@ -88,10 +88,8 @@
       <th>Tools available on UseGalaxy.eu</th>
       <th>Tools available on UseGalaxy.fr</th>
       <th>Tools available on APOSTL</th>
-      <th>Tools available on BF2I-MAP</th>
-      <th>Tools available on BioBix</th>
+      <th>Tools available on ARGs-OAP</th>
       <th>Tools available on CIRM-CFBP</th>
-      <th>Tools available on Center for Phage Technology (CPT)</th>
       <th>Tools available on ChemFlow</th>
       <th>Tools available on Coloc-stats</th>
       <th>Tools available on CoralSNP</th>
@@ -114,7 +112,6 @@
       <th>Tools available on Oqtans</th>
       <th>Tools available on Palfinder</th>
       <th>Tools available on PepSimili</th>
-      <th>Tools available on PhagePromotor</th>
       <th>Tools available on UseGalaxy.be</th>
       <th>Tools available on UseGalaxy.cz</th>
       <th>Tools available on UseGalaxy.no</th>
@@ -183,9 +180,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -237,8 +231,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -258,7 +250,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -273,28 +264,26 @@
       <td>De novo genome sequence assembler using short reads.</td>
       <td>Genome assembly, De-novo assembly, Scaffolding</td>
       <td>Sequence assembly</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://www.bcgsc.ca/platform/bioinfo/software/abyss</td>
       <td>Assembly</td>
       <td>abyss</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss</td>
-      <td>2.3.7</td>
+      <td>2.3.9</td>
       <td>abyss</td>
-      <td>2.3.8</td>
+      <td>2.3.9</td>
       <td>Genome assembly, De-novo assembly, Scaffolding</td>
       <td>Sequence assembly</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -320,8 +309,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -387,9 +375,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -409,7 +394,7 @@
       <td>Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.</td>
       <td>Data handling, Genome annotation</td>
       <td>Genomics</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/NBISweden/AGAT</td>
       <td>Convert Formats, Statistics, Fasta Manipulation</td>
       <td>agat</td>
@@ -418,7 +403,7 @@
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/agat</td>
       <td>1.4.0</td>
       <td>agat</td>
-      <td>1.4.0</td>
+      <td>1.4.1</td>
       <td>Data handling, Genome annotation</td>
       <td>Genomics</td>
       <td>0</td>
@@ -455,9 +440,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -523,9 +505,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -596,9 +575,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -645,8 +621,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -666,7 +640,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -727,9 +700,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -800,9 +770,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -868,9 +835,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -936,9 +900,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -999,9 +960,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1067,9 +1025,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1121,8 +1076,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1137,7 +1090,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1188,8 +1140,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1210,7 +1160,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1257,8 +1206,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1278,7 +1225,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1324,8 +1270,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1346,7 +1290,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1393,8 +1336,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1414,7 +1355,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1475,9 +1415,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1528,8 +1465,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1545,7 +1480,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1595,8 +1529,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1613,7 +1545,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1664,8 +1595,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1686,7 +1615,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1747,9 +1675,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1778,7 +1703,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell</td>
       <td>0.0.7</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -1820,9 +1745,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1888,9 +1810,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1956,9 +1875,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1982,7 +1898,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants</td>
       <td>0.0.6</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -2005,8 +1921,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2026,7 +1940,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2050,7 +1963,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats</td>
       <td>0.1.0</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -2073,8 +1986,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2094,7 +2005,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2130,10 +2040,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -2156,8 +2064,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2209,8 +2116,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2224,8 +2129,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2296,9 +2200,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2337,8 +2238,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>107</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -2360,8 +2259,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>107</td>
       <td>107</td>
       <td>107</td>
       <td>0</td>
@@ -2381,14 +2279,14 @@
       <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
       <td></td>
       <td>Sequence analysis</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
       <td>Fasta Manipulation</td>
       <td>ucsc_fasplit</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit</td>
-      <td>377</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit</td>
+      <td>469</td>
       <td>ucsc-fasplit</td>
       <td>469</td>
       <td></td>
@@ -2413,8 +2311,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2428,8 +2324,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2463,13 +2358,11 @@
       <td></td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -2502,7 +2395,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2538,10 +2430,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -2564,8 +2454,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2594,7 +2483,7 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species</td>
       <td>0.0.1</td>
       <td>bx-python</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -2617,8 +2506,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2632,8 +2519,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2704,9 +2590,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2745,8 +2628,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -2768,8 +2649,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2810,10 +2690,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -2836,8 +2714,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -2889,8 +2766,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2904,8 +2779,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2957,8 +2831,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2972,8 +2844,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3014,10 +2885,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -3040,8 +2909,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3112,9 +2980,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -3153,8 +3018,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -3176,8 +3039,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3229,8 +3091,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3244,8 +3104,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3316,9 +3175,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -3354,10 +3210,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -3380,8 +3234,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3433,8 +3286,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3449,7 +3300,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3514,10 +3364,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3582,10 +3429,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3656,9 +3500,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -3712,16 +3553,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3771,8 +3609,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -3788,8 +3624,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3841,8 +3676,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3856,8 +3689,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3922,10 +3754,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3977,8 +3806,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3992,8 +3819,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4045,8 +3871,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4060,8 +3884,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4112,8 +3935,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4128,8 +3949,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4200,9 +4020,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -4252,8 +4069,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4264,8 +4079,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4306,8 +4120,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -4332,8 +4144,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4374,8 +4185,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -4400,8 +4209,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4460,16 +4268,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4534,10 +4339,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4578,10 +4380,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -4604,8 +4404,7 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4676,9 +4475,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -4717,8 +4513,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -4740,8 +4534,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4782,10 +4575,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -4808,8 +4599,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4853,8 +4643,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -4876,8 +4664,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4918,10 +4705,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -4944,8 +4729,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4989,8 +4773,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -5012,8 +4794,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5057,8 +4838,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -5080,8 +4859,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5125,8 +4903,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -5148,8 +4924,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5193,8 +4968,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -5216,8 +4989,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5261,8 +5033,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -5284,8 +5054,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5329,8 +5098,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -5352,8 +5119,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5424,9 +5190,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -5472,8 +5235,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5494,7 +5255,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -5548,8 +5308,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5557,7 +5315,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5609,8 +5366,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5630,7 +5385,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -5676,8 +5430,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5692,8 +5444,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5758,10 +5509,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -5813,8 +5561,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5828,8 +5574,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5849,14 +5594,14 @@
       <td>Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.</td>
       <td>Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly</td>
       <td>Sequence assembly, Metagenomics, Whole genome sequencing, Genomics</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/fenderglass/Flye/</td>
       <td>Assembly</td>
       <td>flye</td>
       <td>bgruening</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/flye</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/flye</td>
-      <td>2.9.4</td>
+      <td>2.9.5</td>
       <td>flye</td>
       <td>2.9.5</td>
       <td>Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly</td>
@@ -5880,8 +5625,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5896,8 +5639,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5941,9 +5683,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6036,9 +5775,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -6085,8 +5821,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6106,7 +5840,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -6167,9 +5900,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -6198,7 +5928,7 @@
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/graphmap</td>
       <td>0.5.2</td>
       <td>graphmap</td>
-      <td>0.6.3</td>
+      <td>0.6.4</td>
       <td>Sequence trimming, EST assembly, Read mapping</td>
       <td>Gene transcripts, RNA-Seq, RNA splicing</td>
       <td>0</td>
@@ -6221,8 +5951,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -6236,8 +5964,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -6289,8 +6016,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6310,7 +6035,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -6376,9 +6100,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -6439,9 +6160,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6493,8 +6211,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6509,7 +6225,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6561,8 +6276,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6581,7 +6294,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>228</td>
       <td></td>
     </tr>
@@ -6627,8 +6339,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -6644,8 +6354,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -6711,9 +6420,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6778,10 +6484,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -6847,9 +6550,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6901,8 +6601,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6917,7 +6615,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -6968,8 +6665,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -6984,8 +6679,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>8</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
@@ -7035,8 +6729,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7052,8 +6744,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7119,9 +6810,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7173,8 +6861,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7189,7 +6875,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7260,9 +6945,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -7307,8 +6989,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -7324,8 +7004,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7377,8 +7056,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7393,7 +7070,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7459,9 +7135,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7532,9 +7205,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -7600,9 +7270,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -7649,8 +7316,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7664,8 +7329,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7717,8 +7381,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7732,8 +7394,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7785,8 +7446,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7801,7 +7460,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7853,8 +7511,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7869,7 +7525,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7934,10 +7589,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7964,9 +7616,9 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc</td>
-      <td>1.11</td>
-      <td>multiqc</td>
       <td>1.24.1</td>
+      <td>multiqc</td>
+      <td>1.25.1</td>
       <td>Sequencing quality control</td>
       <td>Sequencing, Bioinformatics, Sequence analysis, Genomics</td>
       <td>1</td>
@@ -7981,8 +7633,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -8004,8 +7654,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8071,9 +7720,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8139,9 +7785,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8212,9 +7855,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -8261,8 +7901,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8276,8 +7914,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8328,8 +7965,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8350,7 +7985,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -8397,8 +8031,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8412,8 +8044,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>4</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
@@ -8484,9 +8115,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -8532,8 +8160,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8548,8 +8174,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8593,8 +8218,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -8622,7 +8245,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -8668,9 +8290,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8684,8 +8304,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8729,8 +8348,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>13</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -8753,8 +8370,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>13</td>
+      <td>6</td>
       <td>13</td>
       <td>0</td>
       <td>409</td>
@@ -8805,8 +8421,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8820,8 +8434,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8892,9 +8505,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -8955,9 +8565,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9007,12 +8614,9 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -9096,9 +8700,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -9137,8 +8738,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -9160,8 +8759,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -9228,9 +8826,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9281,8 +8876,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9297,7 +8890,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -9349,8 +8941,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9365,7 +8955,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9431,9 +9020,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -9498,10 +9084,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9553,8 +9136,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9568,8 +9149,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9640,9 +9220,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -9689,8 +9266,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9705,7 +9280,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -9734,7 +9308,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad</td>
       <td>0.0.5</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -9776,9 +9350,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -9802,7 +9373,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth</td>
       <td>0.0.3</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -9823,8 +9394,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -9840,8 +9409,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -9870,7 +9438,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats</td>
       <td>0.0.6</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -9882,8 +9450,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -9908,8 +9474,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -9961,8 +9526,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9977,7 +9540,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -10029,8 +9591,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10045,7 +9605,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -10097,8 +9656,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10118,7 +9675,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -10184,9 +9740,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -10233,8 +9786,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10250,7 +9801,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10301,8 +9851,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10322,7 +9870,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -10388,9 +9935,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -10437,8 +9981,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10458,7 +10000,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -10482,7 +10023,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta</td>
       <td>0.6.0</td>
       <td>shasta</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -10505,8 +10046,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10520,8 +10059,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10586,10 +10124,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -10639,8 +10174,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -10656,8 +10189,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -10716,16 +10248,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -10745,7 +10274,7 @@
       <td>Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568</td>
       <td>Sequence trimming, Genotyping, k-mer counting</td>
       <td>Sequence assembly, Genetic variation, Mathematics</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/KamilSJaron/smudgeplot</td>
       <td>Assembly</td>
       <td>smudgeplot</td>
@@ -10754,7 +10283,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot</td>
       <td>0.2.5</td>
       <td>smudgeplot</td>
-      <td>0.2.5</td>
+      <td>0.3.0</td>
       <td>Sequence trimming, Genotyping, k-mer counting</td>
       <td>Sequence assembly, Genetic variation, Mathematics</td>
       <td>1</td>
@@ -10791,9 +10320,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -10807,7 +10333,7 @@
       <td>spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades</td>
       <td>SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.</td>
       <td>spades</td>
-      <td>coronaspades, biosyntheticspades, metaplasmidspades, plasmidspades, metaspades, rnaspades, metaviralspades, rnaviralspades, spades</td>
+      <td>spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades</td>
       <td></td>
       <td>SPAdes</td>
       <td>St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.</td>
@@ -10837,8 +10363,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -10860,8 +10384,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>9</td>
       <td>3</td>
       <td>0</td>
@@ -10932,9 +10455,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -10981,8 +10501,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -11002,7 +10520,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -11047,8 +10564,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>3</td>
@@ -11064,8 +10579,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -11106,10 +10620,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11136,6 +10646,7 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>200</td>
       <td>7388</td>
@@ -11204,9 +10715,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -11251,8 +10759,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -11268,8 +10774,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -11335,9 +10840,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -11378,8 +10880,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11404,8 +10904,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -11446,10 +10945,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11472,8 +10969,7 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -11525,8 +11021,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -11541,7 +11035,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -11592,8 +11085,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -11608,8 +11099,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -11641,16 +11131,13 @@
       <td>1.0</td>
       <td></td>
       <td></td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11727,8 +11214,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -11744,8 +11229,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -11786,8 +11270,6 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11812,8 +11294,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -11842,19 +11323,16 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko</td>
       <td>1.3.1</td>
       <td>verkko</td>
-      <td>2.1</td>
+      <td>2.2</td>
       <td></td>
       <td></td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11933,8 +11411,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -11949,7 +11425,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -12020,9 +11495,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -12068,8 +11540,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -12090,7 +11560,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -12105,7 +11574,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/c-zhou/yahs</td>
       <td>Assembly</td>
       <td>yahs</td>
@@ -12114,7 +11583,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs</td>
       <td>1.2a.2</td>
       <td>yahs</td>
-      <td>1.2a.2</td>
+      <td>1.2.2</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -12151,9 +11620,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
diff --git a/communities/assembly/resources/tools.tsv b/communities/assembly/resources/tools.tsv
index 582f8393..95725e88 100644
--- a/communities/assembly/resources/tools.tsv
+++ b/communities/assembly/resources/tools.tsv
@@ -1,178 +1,178 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on BF2I-MAP	Tools available on BioBix	Tools available on CIRM-CFBP	Tools available on Center for Phage Technology (CPT)	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	42	False		
-abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	To update	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.7	abyss	2.3.8	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	391	4278	False		
-adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	37	217	False		
-agat	agat	GTF/GFF analysis toolkit	agat	agat		AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	Up-to-date	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.4.0	agat	1.4.0	Data handling, Genome annotation	Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	42	481	False		
-align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	329	False		
-assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-atactk_trim_adapters	atactk_trim_adapters	Trim adapters from paired-end HTS reads.								To update	https://github.com/ParkerLab/atactk/	Fastq Manipulation	atactk_trim_adapters	rnateam	https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters	https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters	0.1.6	atactk	0.1.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	26	257	False		
-bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-barcode_splitter	barcode_splitter	A utility to split sequence files using multiple sets of barcodes								To update	https://bitbucket.org/princeton_genomics/barcode_splitter/	Fastq Manipulation	barcode_splitter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter	0.18.4.0	barcode_splitter	0.18.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-berokka	berokka	Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.								Up-to-date	https://github.com/tseemann/berokka	Fasta Manipulation	berokka	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka	0.2.3	berokka	0.2.3			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	531	False		
-biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	3	False		
-blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	121	22499	False		
-blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blast_unmatched	blast_unmatched	Extract unmatched query sequences from blast								To update	http://artbio.fr	Fasta Manipulation	blast_unmatched	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	1.0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	685	False		
-cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	101	7766	False		
-cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	280	4474	False		
-cherry_pick_fasta	cherry_pick_fasta	Pick fasta sequence with specific header content								To update	http://artbio.fr	Fasta Manipulation	cherry_pick_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	4.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	269	False		
-clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-convert_solid_color2nuc	color2nuc	Convert Color Space to Nucleotides								To update		Fasta Manipulation	convert_solid_color2nuc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	5090	232004	False		
-disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	42	369	False		
-ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	107	107	107	107	107	0	0	0	0	107	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	0	0	107	107	0	1816	89530	False		
-fasplit	fasplit	faSplit is a tool to split a single FASTA file into several files	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://hgdownload.cse.ucsc.edu/admin/exe/	Fasta Manipulation	ucsc_fasplit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	377	ucsc-fasplit	469		Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	242	2644	False		
-fasta_clipping_histogram	cshl_fasta_clipping_histogram	Length Distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Graphics, Statistics	fasta_clipping_histogram	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram	0.0.14	fastx_toolkit	0.0.14			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fasta_compute_length	fasta_compute_length	Compute sequence length								To update		Fasta Manipulation	fasta_compute_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length	1.0.3	python				1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	380	7758	False		
-fasta_concatenate_by_species	fasta_concatenate0	Concatenate FASTA alignment by species								To update		Fasta Manipulation	fasta_concatenate_by_species	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.12.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	88	35793	False		
-fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fasta_filter_by_length	fasta_filter_by_length	Filter sequences by length								To update		Fasta Manipulation	fasta_filter_by_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length	1.2	python				1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	350	48649	False		
-fasta_formatter	cshl_fasta_formatter	FASTA Width formatter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_formatter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	68	2912	False		
-fasta_merge_files_and_filter_unique_sequences	fasta_merge_files_and_filter_unique_sequences	Concatenate FASTA database files together								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Fasta Manipulation	fasta_merge_files_and_filter_unique_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	1.2.0	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	461	29886	False		
-fasta_nucleotide_changer	cshl_fasta_nucleotides_changer	RNA/DNA converter.								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_nucleotide_changer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	29	774	False		
-fasta_to_tabular	fasta2tab	FASTA-to-Tabular converter								To update		Fasta Manipulation	fasta_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular	1.1.1	python				1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	622	105935	False		
-fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastq_combiner	fastq_combiner	Combine FASTA and QUAL into FASTQ								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation, Fasta Manipulation	fastq_combiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	66	8676	False		
-fastq_filter	fastq_filter	Filter FASTQ reads by quality score and length								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	266	14222	False		
-fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastq_groomer	fastq_groomer	Convert between various FASTQ quality formats.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_groomer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1028	94802	False		
-fastq_info	fastq_info	FASTQ info allows to validate single or paired fastq files								To update	https://github.com/nunofonseca/fastq_utils	Fastq Manipulation	fastq_info	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	0.25.1	fastq_utils	0.25.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	679	5765	False		
-fastq_manipulation	fastq_manipulation	Manipulate FASTQ reads on various attributes.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_manipulation	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	69	2503	False		
-fastq_masker_by_quality	fastq_masker_by_quality	FASTQ Masker by quality score								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_masker_by_quality	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	170	False		
-fastq_pair	fastq_pair	Paired-end fastq pairer								To update	https://github.com/linsalrob/fastq-pair	Fastq Manipulation	fastq_pair	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair	1.0+galaxy0	fastq-pair	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastq_paired_end_deinterlacer	fastq_paired_end_deinterlacer	FASTQ de-interlacer on paired end reads.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_deinterlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	122	8410	False		
-fastq_paired_end_interlacer	fastq_paired_end_interlacer	FASTQ interlacer on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_interlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1087	17024	False		
-fastq_paired_end_joiner	fastq_paired_end_joiner	FASTQ joiner on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_joiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	245	16635	False		
-fastq_paired_end_splitter	fastq_paired_end_splitter	FASTQ splitter on joined paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	196	3092	False		
-fastq_quality_boxplot	cshl_fastq_quality_boxplot	Draw quality score boxplot								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics, Statistics	fastq_quality_boxplot	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	51	1178	False		
-fastq_quality_converter	cshl_fastq_quality_converter	Quality format converter (ASCII-Numeric)								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_converter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	11	220	False		
-fastq_quality_filter	cshl_fastq_quality_filter	Filter by quality								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1509	15172	False		
-fastq_quality_trimmer	cshl_fastq_quality_trimmer	FASTQ trimmer based on quality								To update	https://github.com/agordon/fastx_toolkit	Fastq Manipulation	fastq_quality_trimmer	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer	0.0.14+galaxy0	fastx_toolkit	0.0.14			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastq_stats	fastq_stats	FASTQ Summary Statistics by column								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_stats	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	221	4246	False		
-fastq_to_fasta	cshl_fastq_to_fasta	FASTQ to FASTA converter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Convert Formats	fastq_to_fasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	419	13599	False		
-fastq_to_tabular	fastq_to_tabular	FASTQ to Tabular converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_to_tabular	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	93	12593	False		
-fastq_trimmer	fastq_trimmer	FASTQ Trimmer by quality								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	210	9757	False		
-fastq_trimmer_by_quality	fastq_quality_trimmer	FASTQ Quality Trimmer by sliding window								Up-to-date		Fastq Manipulation	fastq_trimmer_by_quality	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	459	5676	False		
-fastqc	fastqc	Read QC reports using FastQC	fastqc	fastqc		FastQC	This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	Fastq Manipulation	fastqc	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc	0.74+galaxy1	fastqc	0.12.1	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	1	1	1	1	1	1	1	1	0	1	1	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	1	1	0	0	1	1	0	17447	1556625	False		
-fastqsolexa_to_fasta_qual	fastqsolexa_to_fasta_qual	FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data								To update		Convert Formats, Fastq Manipulation	fastqsolexa_to_fasta_qual	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastqtofasta	fastq_to_fasta_python	FASTQ to FASTA converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastqtofasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	0	1	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1371	178178	False		
-fastx_artifacts_filter	cshl_fastx_artifacts_filter	Remove sequencing artifacts								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_artifacts_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	27	1810	False		
-fastx_barcode_splitter	cshl_fastx_barcode_splitter	Barcode Splitter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_barcode_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	128	16591	False		
-fastx_clipper	cshl_fastx_clipper	Clip adapter sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_clipper	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	96	3333	False		
-fastx_collapser	cshl_fastx_collapser	Collapse sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fastx_collapser	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	114	61218	False		
-fastx_nucleotides_distribution	cshl_fastx_nucleotides_distribution	Draw nucleotides distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics	fastx_nucleotides_distribution	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	25	249	False		
-fastx_quality_statistics	cshl_fastx_quality_statistics	Compute quality statistics								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Statistics	fastx_quality_statistics	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	63	2176	False		
-fastx_renamer	cshl_fastx_renamer	Rename sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_renamer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	68	2280	False		
-fastx_reverse_complement	cshl_fastx_reverse_complement	Reverse-Complement								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Fasta Manipulation	fastx_reverse_complement	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	156	10832	False		
-fastx_trimmer	cshl_fastx_trimmer	Trim sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	205	13149	False		
-fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fetch_fasta_from_ncbi	retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers								To update	http://artbio.fr	Fasta Manipulation, Data Source	fetch_fasta_from_ncbi	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	3.1.0	urllib3	1.12			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	426	26274	False		
-filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	617	30483	False		
-flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	14	331	False		
-flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	74	13759	False		
-flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	To update	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.4	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1499	20904	False		
-format_cd_hit_output	format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file								To update		Fasta Manipulation	format_cd_hit_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output	1.0.0+galaxy1					0	0	1	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	166	False		
-get_pairs	get_pairs	Separate paired and unpaired reads from two fastq files								To update		Fastq Manipulation	get_pairs	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	0.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-get_reference_fasta	get_fasta_reference	Obtain reference genome sequence.								To update	http://artbio.fr	Data Source, Fasta Manipulation	get_reference_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	0.3.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	18	495	False		
-graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.3	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	136	6651	False		
-guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	295	False		
-hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	1410	False		
-hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	False		
-hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	4183	299104	False		
-hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354	False		
-idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	69	1127	False		
-instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	139	False		
-jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138	False		
-khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	8	8	0	63	2022	False		
-length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	322	4090	False		
-lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	152	False		
-links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	77	405	False		
-make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	0	1	1	0	548	9530	False		
-megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	54	475	False		
-merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483	False		
-meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	109	2206	False		
-miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	178	11938	False		
-mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	66	881	False		
-mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	56	613	False		
-msaboot	msaboot	A multiple sequences alignment bootstrapping tool.								Up-to-date	https://github.com/phac-nml/msaboot	Fasta Manipulation	msaboot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot	0.1.2	msaboot	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	803	False		
-multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.11	multiqc	1.24.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	8320	162790	False		
-necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	95	667	False		
-nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268	False		
-nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	162	6384	False		
-oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	39	2654	False		
-pbtk	bam2fastx	Convert PacBio Bam File to fasta or fastq file								Up-to-date	https://github.com/PacificBiosciences/pbtk	Convert Formats, Fasta Manipulation, Fastq Manipulation	bam2fastx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk	3.1.1	pbtk	3.1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-pear	iuc_pear	PEAR evaluates all possible paired-end read overlaps	pear	pear		PEAR	Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.	Sequence merging	Sequence assembly	Up-to-date	https://cme.h-its.org/exelixis/web/software/pear/	Fastq Manipulation	pear	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear	0.9.6	pear	0.9.6	Sequence merging	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	150	4305	False		
-plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-porechop	porechop	Porechop - Finding and removing adapters from Oxford Nanopore reads								To update	https://github.com/rrwick/Porechop	Fasta Manipulation, Fastq Manipulation	porechop	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop	https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop		porechop	0.2.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1046	185468	False		
-poretools	poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot	A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	poretools	poretools		Poretools	Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	Nucleic acid sequence analysis	DNA, Sequencing	Up-to-date	https://poretools.readthedocs.io/en/latest/	Fasta Manipulation, Fastq Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools	0.6.1a1	poretools	0.6.1a1	Nucleic acid sequence analysis	DNA, Sequencing	13	13	13	0	13	13	13	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	13	0	409	18773	False		
-prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	70	7881	False		
-promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	167	16800	False		
-pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	350	21123	False		
-qfilt	qfilt	Filter sequencing data								To update	https://github.com/veg/qfilt	Fastq Manipulation	qfilt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt	1.0.0+galaxy1	qfilt	0.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	3567	51567	False		
-quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	False		
-ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	237	2833	False		
-raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	6902	False		
-rcorrector	rcorrector	Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.	rcorrector	rcorrector		Rcorrector	This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.	Sequencing error detection	RNA, RNA-Seq, Sequencing	To update	https://github.com/mourisl/Rcorrector	Fastq Manipulation	rcorrector	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector	1.0.3+galaxy1	rcorrector	1.0.7	Sequencing error detection	RNA, RNA-Seq	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	569	False		
-rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	109	1110	False		
-salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	454	False		
-samblaster	samblaster	samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files	samblaster	samblaster		SAMBLASTER	A tool to mark duplicates and extract discordant and split reads from SAM files.	Split read mapping	DNA, Sequencing, Mapping	To update	https://github.com/GregoryFaust/samblaster	SAM, Fastq Manipulation, Variant Analysis	samblaster	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster	https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster	0.1.24	samblaster	0.1.26	Split read mapping	DNA, Sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	3765	False		
-samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.20			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	296	4948	False		
-samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.20			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1450	48426	False		
-seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	306	25302	False		
-seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	82	3784	False		
-seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	False		
-seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-sequence_format_converter	sequence_format_converter	various fasta to tabular conversions								To update	http://artbio.fr	Convert Formats, Fasta Manipulation	sequence_format_converter	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter	https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter	2.2.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.12.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	154	763	False		
-short_reads_trim_seq	trim_reads	Select high quality segments								To update		Fastq Manipulation	short_reads_trim_seq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	21	220	False		
-shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1008	41600	False		
-sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	269	14982	False		
-smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	Up-to-date	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.2.5	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	22	203	False		
-spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	coronaspades, biosyntheticspades, metaplasmidspades, plasmidspades, metaspades, rnaspades, metaviralspades, rnaviralspades, spades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	1	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	0	0	9	3	0	3547	72953	False		
-spades_header_fixer	spades_header_fixer	Fixes Spades Fasta ids								To update	https://github.com/phac-nml/galaxy_tools	Fasta Manipulation	spades_fasta_header_fixer	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer	1.1.2+galaxy1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-split_paired_reads	split_paired_reads	Split paired end reads								To update		Fastq Manipulation	split_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-sra-tools	fasterq_dump, fastq_dump, sam_dump	NCBI Sequence Read Archive toolkit utilities	sra-tools	sra-tools		SRA Software Toolkit	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	Data handling	DNA, Genomics, Sequencing	Up-to-date	https://github.com/ncbi/sra-tools	Data Source, Fastq Manipulation	sra_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools	3.1.1	sra-tools	3.1.1	Data handling	DNA, Genomics, Sequencing	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	2	0	3	0	0	3	0	0	0	3	0	0	0	0	0	0	0	3	3	0	6247	350032	False		
-tabular_to_fastq	tabular_to_fastq	Tabular to FASTQ converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	tabular_to_fastq	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	200	7388	False		
-tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	0	1	1	0	1801	27426	False		
-tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	460	False		
-trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2334	238699	False		
-trimmomatic	trimmomatic	A flexible read trimming tool for Illumina NGS data								Up-to-date	http://www.usadellab.org/cms/?page=trimmomatic	Fastq Manipulation	trimmomatic	pjbriggs	https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic	0.39	trimmomatic	0.39			1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	0	0	1	1	0	5862	305866	False		
-trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942	False		
-unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1558	65732	False		
-validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	25	86	False		
-velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	2083	25420	False		
-velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	255	4741	False		
-verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	22	False		
-wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660	False		
-xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-yahs	yahs	Yet Another Hi-C scaffolding tool								Up-to-date	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2a.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	64	344	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
+TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	42	False		
+abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	391	4278	False		
+adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	37	217	False		
+agat	agat	GTF/GFF analysis toolkit	agat	agat		AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	To update	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.4.0	agat	1.4.1	Data handling, Genome annotation	Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	42	481	False		
+align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	329	False		
+assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+atactk_trim_adapters	atactk_trim_adapters	Trim adapters from paired-end HTS reads.								To update	https://github.com/ParkerLab/atactk/	Fastq Manipulation	atactk_trim_adapters	rnateam	https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters	https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters	0.1.6	atactk	0.1.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	26	257	False		
+bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+barcode_splitter	barcode_splitter	A utility to split sequence files using multiple sets of barcodes								To update	https://bitbucket.org/princeton_genomics/barcode_splitter/	Fastq Manipulation	barcode_splitter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter	0.18.4.0	barcode_splitter	0.18.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+berokka	berokka	Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.								Up-to-date	https://github.com/tseemann/berokka	Fasta Manipulation	berokka	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka	0.2.3	berokka	0.2.3			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	531	False		
+biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	3	False		
+blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	121	22499	False		
+blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+blast_unmatched	blast_unmatched	Extract unmatched query sequences from blast								To update	http://artbio.fr	Fasta Manipulation	blast_unmatched	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	1.0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	685	False		
+cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	101	7766	False		
+cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	280	4474	False		
+cherry_pick_fasta	cherry_pick_fasta	Pick fasta sequence with specific header content								To update	http://artbio.fr	Fasta Manipulation	cherry_pick_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	4.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	269	False		
+clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+convert_solid_color2nuc	color2nuc	Convert Color Space to Nucleotides								To update		Fasta Manipulation	convert_solid_color2nuc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	5090	232004	False		
+disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	42	369	False		
+ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	107	107	107	107	107	0	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	107	107	107	0	1816	89530	False		
+fasplit	fasplit	faSplit is a tool to split a single FASTA file into several files	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Fasta Manipulation	ucsc_fasplit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	469	ucsc-fasplit	469		Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	242	2644	False		
+fasta_clipping_histogram	cshl_fasta_clipping_histogram	Length Distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Graphics, Statistics	fasta_clipping_histogram	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram	0.0.14	fastx_toolkit	0.0.14			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+fasta_compute_length	fasta_compute_length	Compute sequence length								To update		Fasta Manipulation	fasta_compute_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length	1.0.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	380	7758	False		
+fasta_concatenate_by_species	fasta_concatenate0	Concatenate FASTA alignment by species								To update		Fasta Manipulation	fasta_concatenate_by_species	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	88	35793	False		
+fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fasta_filter_by_length	fasta_filter_by_length	Filter sequences by length								To update		Fasta Manipulation	fasta_filter_by_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length	1.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	350	48649	False		
+fasta_formatter	cshl_fasta_formatter	FASTA Width formatter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_formatter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	1	68	2912	False		
+fasta_merge_files_and_filter_unique_sequences	fasta_merge_files_and_filter_unique_sequences	Concatenate FASTA database files together								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Fasta Manipulation	fasta_merge_files_and_filter_unique_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	1.2.0	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	461	29886	False		
+fasta_nucleotide_changer	cshl_fasta_nucleotides_changer	RNA/DNA converter.								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_nucleotide_changer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	29	774	False		
+fasta_to_tabular	fasta2tab	FASTA-to-Tabular converter								To update		Fasta Manipulation	fasta_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular	1.1.1	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	622	105935	False		
+fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_combiner	fastq_combiner	Combine FASTA and QUAL into FASTQ								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation, Fasta Manipulation	fastq_combiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	66	8676	False		
+fastq_filter	fastq_filter	Filter FASTQ reads by quality score and length								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	266	14222	False		
+fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_groomer	fastq_groomer	Convert between various FASTQ quality formats.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_groomer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1028	94802	False		
+fastq_info	fastq_info	FASTQ info allows to validate single or paired fastq files								To update	https://github.com/nunofonseca/fastq_utils	Fastq Manipulation	fastq_info	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	0.25.1	fastq_utils	0.25.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	679	5765	False		
+fastq_manipulation	fastq_manipulation	Manipulate FASTQ reads on various attributes.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_manipulation	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	69	2503	False		
+fastq_masker_by_quality	fastq_masker_by_quality	FASTQ Masker by quality score								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_masker_by_quality	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	170	False		
+fastq_pair	fastq_pair	Paired-end fastq pairer								To update	https://github.com/linsalrob/fastq-pair	Fastq Manipulation	fastq_pair	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair	1.0+galaxy0	fastq-pair	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_paired_end_deinterlacer	fastq_paired_end_deinterlacer	FASTQ de-interlacer on paired end reads.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_deinterlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	122	8410	False		
+fastq_paired_end_interlacer	fastq_paired_end_interlacer	FASTQ interlacer on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_interlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1087	17024	False		
+fastq_paired_end_joiner	fastq_paired_end_joiner	FASTQ joiner on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_joiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	245	16635	False		
+fastq_paired_end_splitter	fastq_paired_end_splitter	FASTQ splitter on joined paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	196	3092	False		
+fastq_quality_boxplot	cshl_fastq_quality_boxplot	Draw quality score boxplot								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics, Statistics	fastq_quality_boxplot	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	51	1178	False		
+fastq_quality_converter	cshl_fastq_quality_converter	Quality format converter (ASCII-Numeric)								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_converter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	11	220	False		
+fastq_quality_filter	cshl_fastq_quality_filter	Filter by quality								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1509	15172	False		
+fastq_quality_trimmer	cshl_fastq_quality_trimmer	FASTQ trimmer based on quality								To update	https://github.com/agordon/fastx_toolkit	Fastq Manipulation	fastq_quality_trimmer	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer	0.0.14+galaxy0	fastx_toolkit	0.0.14			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_stats	fastq_stats	FASTQ Summary Statistics by column								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_stats	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	221	4246	False		
+fastq_to_fasta	cshl_fastq_to_fasta	FASTQ to FASTA converter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Convert Formats	fastq_to_fasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	419	13599	False		
+fastq_to_tabular	fastq_to_tabular	FASTQ to Tabular converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_to_tabular	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	93	12593	False		
+fastq_trimmer	fastq_trimmer	FASTQ Trimmer by quality								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	210	9757	False		
+fastq_trimmer_by_quality	fastq_quality_trimmer	FASTQ Quality Trimmer by sliding window								Up-to-date		Fastq Manipulation	fastq_trimmer_by_quality	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	459	5676	False		
+fastqc	fastqc	Read QC reports using FastQC	fastqc	fastqc		FastQC	This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	Fastq Manipulation	fastqc	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc	0.74+galaxy1	fastqc	0.12.1	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	1	1	1	1	1	0	17447	1556625	False		
+fastqsolexa_to_fasta_qual	fastqsolexa_to_fasta_qual	FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data								To update		Convert Formats, Fastq Manipulation	fastqsolexa_to_fasta_qual	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastqtofasta	fastq_to_fasta_python	FASTQ to FASTA converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastqtofasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1371	178178	False		
+fastx_artifacts_filter	cshl_fastx_artifacts_filter	Remove sequencing artifacts								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_artifacts_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	27	1810	False		
+fastx_barcode_splitter	cshl_fastx_barcode_splitter	Barcode Splitter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_barcode_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	128	16591	False		
+fastx_clipper	cshl_fastx_clipper	Clip adapter sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_clipper	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	96	3333	False		
+fastx_collapser	cshl_fastx_collapser	Collapse sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fastx_collapser	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	114	61218	False		
+fastx_nucleotides_distribution	cshl_fastx_nucleotides_distribution	Draw nucleotides distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics	fastx_nucleotides_distribution	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	25	249	False		
+fastx_quality_statistics	cshl_fastx_quality_statistics	Compute quality statistics								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Statistics	fastx_quality_statistics	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	63	2176	False		
+fastx_renamer	cshl_fastx_renamer	Rename sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_renamer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	68	2280	False		
+fastx_reverse_complement	cshl_fastx_reverse_complement	Reverse-Complement								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Fasta Manipulation	fastx_reverse_complement	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	156	10832	False		
+fastx_trimmer	cshl_fastx_trimmer	Trim sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	205	13149	False		
+fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fetch_fasta_from_ncbi	retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers								To update	http://artbio.fr	Fasta Manipulation, Data Source	fetch_fasta_from_ncbi	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	3.1.0	urllib3	1.12			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	426	26274	False		
+filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	617	30483	False		
+flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	14	331	False		
+flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	74	13759	False		
+flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	20904	False		
+format_cd_hit_output	format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file								To update		Fasta Manipulation	format_cd_hit_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output	1.0.0+galaxy1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	166	False		
+get_pairs	get_pairs	Separate paired and unpaired reads from two fastq files								To update		Fastq Manipulation	get_pairs	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	0.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+get_reference_fasta	get_fasta_reference	Obtain reference genome sequence.								To update	http://artbio.fr	Data Source, Fasta Manipulation	get_reference_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	0.3.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	18	495	False		
+graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	136	6651	False		
+guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	295	False		
+hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	1410	False		
+hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	False		
+hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	4183	299104	False		
+hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354	False		
+idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	69	1127	False		
+instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	139	False		
+jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138	False		
+khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	8	8	8	0	63	2022	False		
+length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	322	4090	False		
+lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	152	False		
+links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	77	405	False		
+make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	548	9530	False		
+megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	54	475	False		
+merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483	False		
+meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	109	2206	False		
+miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	178	11938	False		
+mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	66	881	False		
+mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	56	613	False		
+msaboot	msaboot	A multiple sequences alignment bootstrapping tool.								Up-to-date	https://github.com/phac-nml/msaboot	Fasta Manipulation	msaboot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot	0.1.2	msaboot	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34	803	False		
+multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	8320	162790	False		
+necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	95	667	False		
+nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268	False		
+nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	162	6384	False		
+oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	39	2654	False		
+pbtk	bam2fastx	Convert PacBio Bam File to fasta or fastq file								Up-to-date	https://github.com/PacificBiosciences/pbtk	Convert Formats, Fasta Manipulation, Fastq Manipulation	bam2fastx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk	3.1.1	pbtk	3.1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pear	iuc_pear	PEAR evaluates all possible paired-end read overlaps	pear	pear		PEAR	Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.	Sequence merging	Sequence assembly	Up-to-date	https://cme.h-its.org/exelixis/web/software/pear/	Fastq Manipulation	pear	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear	0.9.6	pear	0.9.6	Sequence merging	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	150	4305	False		
+plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+porechop	porechop	Porechop - Finding and removing adapters from Oxford Nanopore reads								To update	https://github.com/rrwick/Porechop	Fasta Manipulation, Fastq Manipulation	porechop	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop	https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop		porechop	0.2.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1046	185468	False		
+poretools	poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot	A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	poretools	poretools		Poretools	Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	Nucleic acid sequence analysis	DNA, Sequencing	Up-to-date	https://poretools.readthedocs.io/en/latest/	Fasta Manipulation, Fastq Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools	0.6.1a1	poretools	0.6.1a1	Nucleic acid sequence analysis	DNA, Sequencing	13	13	13	0	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	6	13	0	409	18773	False		
+prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	70	7881	False		
+promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	167	16800	False		
+pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	350	21123	False		
+qfilt	qfilt	Filter sequencing data								To update	https://github.com/veg/qfilt	Fastq Manipulation	qfilt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt	1.0.0+galaxy1	qfilt	0.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	3567	51567	False		
+quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	False		
+ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	237	2833	False		
+raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	6902	False		
+rcorrector	rcorrector	Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.	rcorrector	rcorrector		Rcorrector	This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.	Sequencing error detection	RNA, RNA-Seq, Sequencing	To update	https://github.com/mourisl/Rcorrector	Fastq Manipulation	rcorrector	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector	1.0.3+galaxy1	rcorrector	1.0.7	Sequencing error detection	RNA, RNA-Seq	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	569	False		
+rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	109	1110	False		
+salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	84	454	False		
+samblaster	samblaster	samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files	samblaster	samblaster		SAMBLASTER	A tool to mark duplicates and extract discordant and split reads from SAM files.	Split read mapping	DNA, Sequencing, Mapping	To update	https://github.com/GregoryFaust/samblaster	SAM, Fastq Manipulation, Variant Analysis	samblaster	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster	https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster	0.1.24	samblaster	0.1.26	Split read mapping	DNA, Sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	3765	False		
+samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	1	296	4948	False		
+samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1450	48426	False		
+seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	306	25302	False		
+seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	82	3784	False		
+seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	False		
+seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sequence_format_converter	sequence_format_converter	various fasta to tabular conversions								To update	http://artbio.fr	Convert Formats, Fasta Manipulation	sequence_format_converter	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter	https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter	2.2.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	154	763	False		
+short_reads_trim_seq	trim_reads	Select high quality segments								To update		Fastq Manipulation	short_reads_trim_seq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	21	220	False		
+shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1008	41600	False		
+sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	269	14982	False		
+smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	22	203	False		
+spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	3	9	3	0	3547	72953	False		
+spades_header_fixer	spades_header_fixer	Fixes Spades Fasta ids								To update	https://github.com/phac-nml/galaxy_tools	Fasta Manipulation	spades_fasta_header_fixer	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer	1.1.2+galaxy1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+split_paired_reads	split_paired_reads	Split paired end reads								To update		Fastq Manipulation	split_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sra-tools	fasterq_dump, fastq_dump, sam_dump	NCBI Sequence Read Archive toolkit utilities	sra-tools	sra-tools		SRA Software Toolkit	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	Data handling	DNA, Genomics, Sequencing	Up-to-date	https://github.com/ncbi/sra-tools	Data Source, Fastq Manipulation	sra_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools	3.1.1	sra-tools	3.1.1	Data handling	DNA, Genomics, Sequencing	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	2	0	3	0	0	3	0	0	0	3	0	0	0	0	0	3	3	3	0	6247	350032	False		
+tabular_to_fastq	tabular_to_fastq	Tabular to FASTQ converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	tabular_to_fastq	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	200	7388	False		
+tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	1801	27426	False		
+tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	460	False		
+trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	2334	238699	False		
+trimmomatic	trimmomatic	A flexible read trimming tool for Illumina NGS data								Up-to-date	http://www.usadellab.org/cms/?page=trimmomatic	Fastq Manipulation	trimmomatic	pjbriggs	https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic	0.39	trimmomatic	0.39			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	1	1	1	0	5862	305866	False		
+trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942	False		
+unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1558	65732	False		
+validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	25	86	False		
+velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	2083	25420	False		
+velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	4741	False		
+verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	22	False		
+wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660	False		
+xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	64	344	False		
diff --git a/communities/assembly/resources/tools_filtered_by_ts_categories.tsv b/communities/assembly/resources/tools_filtered_by_ts_categories.tsv
index 582f8393..95725e88 100644
--- a/communities/assembly/resources/tools_filtered_by_ts_categories.tsv
+++ b/communities/assembly/resources/tools_filtered_by_ts_categories.tsv
@@ -1,178 +1,178 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on BF2I-MAP	Tools available on BioBix	Tools available on CIRM-CFBP	Tools available on Center for Phage Technology (CPT)	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	42	False		
-abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	To update	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.7	abyss	2.3.8	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	391	4278	False		
-adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	37	217	False		
-agat	agat	GTF/GFF analysis toolkit	agat	agat		AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	Up-to-date	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.4.0	agat	1.4.0	Data handling, Genome annotation	Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	42	481	False		
-align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	329	False		
-assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-atactk_trim_adapters	atactk_trim_adapters	Trim adapters from paired-end HTS reads.								To update	https://github.com/ParkerLab/atactk/	Fastq Manipulation	atactk_trim_adapters	rnateam	https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters	https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters	0.1.6	atactk	0.1.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	26	257	False		
-bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-barcode_splitter	barcode_splitter	A utility to split sequence files using multiple sets of barcodes								To update	https://bitbucket.org/princeton_genomics/barcode_splitter/	Fastq Manipulation	barcode_splitter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter	0.18.4.0	barcode_splitter	0.18.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-berokka	berokka	Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.								Up-to-date	https://github.com/tseemann/berokka	Fasta Manipulation	berokka	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka	0.2.3	berokka	0.2.3			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	531	False		
-biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	3	False		
-blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	121	22499	False		
-blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blast_unmatched	blast_unmatched	Extract unmatched query sequences from blast								To update	http://artbio.fr	Fasta Manipulation	blast_unmatched	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	1.0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	685	False		
-cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	101	7766	False		
-cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	280	4474	False		
-cherry_pick_fasta	cherry_pick_fasta	Pick fasta sequence with specific header content								To update	http://artbio.fr	Fasta Manipulation	cherry_pick_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	4.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	269	False		
-clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-convert_solid_color2nuc	color2nuc	Convert Color Space to Nucleotides								To update		Fasta Manipulation	convert_solid_color2nuc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	5090	232004	False		
-disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	42	369	False		
-ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	107	107	107	107	107	0	0	0	0	107	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	0	0	107	107	0	1816	89530	False		
-fasplit	fasplit	faSplit is a tool to split a single FASTA file into several files	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://hgdownload.cse.ucsc.edu/admin/exe/	Fasta Manipulation	ucsc_fasplit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	377	ucsc-fasplit	469		Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	242	2644	False		
-fasta_clipping_histogram	cshl_fasta_clipping_histogram	Length Distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Graphics, Statistics	fasta_clipping_histogram	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram	0.0.14	fastx_toolkit	0.0.14			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fasta_compute_length	fasta_compute_length	Compute sequence length								To update		Fasta Manipulation	fasta_compute_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length	1.0.3	python				1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	380	7758	False		
-fasta_concatenate_by_species	fasta_concatenate0	Concatenate FASTA alignment by species								To update		Fasta Manipulation	fasta_concatenate_by_species	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.12.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	88	35793	False		
-fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fasta_filter_by_length	fasta_filter_by_length	Filter sequences by length								To update		Fasta Manipulation	fasta_filter_by_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length	1.2	python				1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	350	48649	False		
-fasta_formatter	cshl_fasta_formatter	FASTA Width formatter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_formatter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	68	2912	False		
-fasta_merge_files_and_filter_unique_sequences	fasta_merge_files_and_filter_unique_sequences	Concatenate FASTA database files together								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Fasta Manipulation	fasta_merge_files_and_filter_unique_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	1.2.0	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	461	29886	False		
-fasta_nucleotide_changer	cshl_fasta_nucleotides_changer	RNA/DNA converter.								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_nucleotide_changer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	29	774	False		
-fasta_to_tabular	fasta2tab	FASTA-to-Tabular converter								To update		Fasta Manipulation	fasta_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular	1.1.1	python				1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	622	105935	False		
-fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastq_combiner	fastq_combiner	Combine FASTA and QUAL into FASTQ								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation, Fasta Manipulation	fastq_combiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	66	8676	False		
-fastq_filter	fastq_filter	Filter FASTQ reads by quality score and length								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	266	14222	False		
-fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastq_groomer	fastq_groomer	Convert between various FASTQ quality formats.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_groomer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1028	94802	False		
-fastq_info	fastq_info	FASTQ info allows to validate single or paired fastq files								To update	https://github.com/nunofonseca/fastq_utils	Fastq Manipulation	fastq_info	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	0.25.1	fastq_utils	0.25.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	679	5765	False		
-fastq_manipulation	fastq_manipulation	Manipulate FASTQ reads on various attributes.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_manipulation	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	69	2503	False		
-fastq_masker_by_quality	fastq_masker_by_quality	FASTQ Masker by quality score								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_masker_by_quality	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	170	False		
-fastq_pair	fastq_pair	Paired-end fastq pairer								To update	https://github.com/linsalrob/fastq-pair	Fastq Manipulation	fastq_pair	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair	1.0+galaxy0	fastq-pair	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastq_paired_end_deinterlacer	fastq_paired_end_deinterlacer	FASTQ de-interlacer on paired end reads.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_deinterlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	122	8410	False		
-fastq_paired_end_interlacer	fastq_paired_end_interlacer	FASTQ interlacer on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_interlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1087	17024	False		
-fastq_paired_end_joiner	fastq_paired_end_joiner	FASTQ joiner on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_joiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	245	16635	False		
-fastq_paired_end_splitter	fastq_paired_end_splitter	FASTQ splitter on joined paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	196	3092	False		
-fastq_quality_boxplot	cshl_fastq_quality_boxplot	Draw quality score boxplot								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics, Statistics	fastq_quality_boxplot	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	51	1178	False		
-fastq_quality_converter	cshl_fastq_quality_converter	Quality format converter (ASCII-Numeric)								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_converter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	11	220	False		
-fastq_quality_filter	cshl_fastq_quality_filter	Filter by quality								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1509	15172	False		
-fastq_quality_trimmer	cshl_fastq_quality_trimmer	FASTQ trimmer based on quality								To update	https://github.com/agordon/fastx_toolkit	Fastq Manipulation	fastq_quality_trimmer	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer	0.0.14+galaxy0	fastx_toolkit	0.0.14			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastq_stats	fastq_stats	FASTQ Summary Statistics by column								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_stats	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	221	4246	False		
-fastq_to_fasta	cshl_fastq_to_fasta	FASTQ to FASTA converter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Convert Formats	fastq_to_fasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	419	13599	False		
-fastq_to_tabular	fastq_to_tabular	FASTQ to Tabular converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_to_tabular	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	93	12593	False		
-fastq_trimmer	fastq_trimmer	FASTQ Trimmer by quality								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	210	9757	False		
-fastq_trimmer_by_quality	fastq_quality_trimmer	FASTQ Quality Trimmer by sliding window								Up-to-date		Fastq Manipulation	fastq_trimmer_by_quality	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	459	5676	False		
-fastqc	fastqc	Read QC reports using FastQC	fastqc	fastqc		FastQC	This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	Fastq Manipulation	fastqc	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc	0.74+galaxy1	fastqc	0.12.1	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	1	1	1	1	1	1	1	1	0	1	1	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	1	1	0	0	1	1	0	17447	1556625	False		
-fastqsolexa_to_fasta_qual	fastqsolexa_to_fasta_qual	FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data								To update		Convert Formats, Fastq Manipulation	fastqsolexa_to_fasta_qual	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastqtofasta	fastq_to_fasta_python	FASTQ to FASTA converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastqtofasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	0	1	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1371	178178	False		
-fastx_artifacts_filter	cshl_fastx_artifacts_filter	Remove sequencing artifacts								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_artifacts_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	27	1810	False		
-fastx_barcode_splitter	cshl_fastx_barcode_splitter	Barcode Splitter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_barcode_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	128	16591	False		
-fastx_clipper	cshl_fastx_clipper	Clip adapter sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_clipper	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	96	3333	False		
-fastx_collapser	cshl_fastx_collapser	Collapse sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fastx_collapser	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	114	61218	False		
-fastx_nucleotides_distribution	cshl_fastx_nucleotides_distribution	Draw nucleotides distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics	fastx_nucleotides_distribution	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	25	249	False		
-fastx_quality_statistics	cshl_fastx_quality_statistics	Compute quality statistics								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Statistics	fastx_quality_statistics	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	63	2176	False		
-fastx_renamer	cshl_fastx_renamer	Rename sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_renamer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	68	2280	False		
-fastx_reverse_complement	cshl_fastx_reverse_complement	Reverse-Complement								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Fasta Manipulation	fastx_reverse_complement	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	156	10832	False		
-fastx_trimmer	cshl_fastx_trimmer	Trim sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	205	13149	False		
-fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fetch_fasta_from_ncbi	retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers								To update	http://artbio.fr	Fasta Manipulation, Data Source	fetch_fasta_from_ncbi	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	3.1.0	urllib3	1.12			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	426	26274	False		
-filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	617	30483	False		
-flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	14	331	False		
-flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	74	13759	False		
-flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	To update	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.4	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1499	20904	False		
-format_cd_hit_output	format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file								To update		Fasta Manipulation	format_cd_hit_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output	1.0.0+galaxy1					0	0	1	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	166	False		
-get_pairs	get_pairs	Separate paired and unpaired reads from two fastq files								To update		Fastq Manipulation	get_pairs	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	0.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-get_reference_fasta	get_fasta_reference	Obtain reference genome sequence.								To update	http://artbio.fr	Data Source, Fasta Manipulation	get_reference_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	0.3.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	18	495	False		
-graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.3	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	136	6651	False		
-guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	295	False		
-hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	1410	False		
-hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	False		
-hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	4183	299104	False		
-hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354	False		
-idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	69	1127	False		
-instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	139	False		
-jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138	False		
-khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	8	8	0	63	2022	False		
-length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	322	4090	False		
-lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	152	False		
-links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	77	405	False		
-make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	0	1	1	0	548	9530	False		
-megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	54	475	False		
-merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483	False		
-meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	109	2206	False		
-miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	178	11938	False		
-mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	66	881	False		
-mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	56	613	False		
-msaboot	msaboot	A multiple sequences alignment bootstrapping tool.								Up-to-date	https://github.com/phac-nml/msaboot	Fasta Manipulation	msaboot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot	0.1.2	msaboot	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	803	False		
-multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.11	multiqc	1.24.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	8320	162790	False		
-necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	95	667	False		
-nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268	False		
-nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	162	6384	False		
-oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	39	2654	False		
-pbtk	bam2fastx	Convert PacBio Bam File to fasta or fastq file								Up-to-date	https://github.com/PacificBiosciences/pbtk	Convert Formats, Fasta Manipulation, Fastq Manipulation	bam2fastx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk	3.1.1	pbtk	3.1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-pear	iuc_pear	PEAR evaluates all possible paired-end read overlaps	pear	pear		PEAR	Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.	Sequence merging	Sequence assembly	Up-to-date	https://cme.h-its.org/exelixis/web/software/pear/	Fastq Manipulation	pear	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear	0.9.6	pear	0.9.6	Sequence merging	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	150	4305	False		
-plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-porechop	porechop	Porechop - Finding and removing adapters from Oxford Nanopore reads								To update	https://github.com/rrwick/Porechop	Fasta Manipulation, Fastq Manipulation	porechop	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop	https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop		porechop	0.2.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1046	185468	False		
-poretools	poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot	A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	poretools	poretools		Poretools	Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	Nucleic acid sequence analysis	DNA, Sequencing	Up-to-date	https://poretools.readthedocs.io/en/latest/	Fasta Manipulation, Fastq Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools	0.6.1a1	poretools	0.6.1a1	Nucleic acid sequence analysis	DNA, Sequencing	13	13	13	0	13	13	13	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	13	0	409	18773	False		
-prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	70	7881	False		
-promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	167	16800	False		
-pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	350	21123	False		
-qfilt	qfilt	Filter sequencing data								To update	https://github.com/veg/qfilt	Fastq Manipulation	qfilt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt	1.0.0+galaxy1	qfilt	0.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	3567	51567	False		
-quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	False		
-ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	237	2833	False		
-raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	6902	False		
-rcorrector	rcorrector	Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.	rcorrector	rcorrector		Rcorrector	This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.	Sequencing error detection	RNA, RNA-Seq, Sequencing	To update	https://github.com/mourisl/Rcorrector	Fastq Manipulation	rcorrector	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector	1.0.3+galaxy1	rcorrector	1.0.7	Sequencing error detection	RNA, RNA-Seq	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	569	False		
-rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	109	1110	False		
-salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	454	False		
-samblaster	samblaster	samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files	samblaster	samblaster		SAMBLASTER	A tool to mark duplicates and extract discordant and split reads from SAM files.	Split read mapping	DNA, Sequencing, Mapping	To update	https://github.com/GregoryFaust/samblaster	SAM, Fastq Manipulation, Variant Analysis	samblaster	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster	https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster	0.1.24	samblaster	0.1.26	Split read mapping	DNA, Sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	3765	False		
-samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.20			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	296	4948	False		
-samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.20			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1450	48426	False		
-seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	306	25302	False		
-seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	82	3784	False		
-seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	False		
-seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-sequence_format_converter	sequence_format_converter	various fasta to tabular conversions								To update	http://artbio.fr	Convert Formats, Fasta Manipulation	sequence_format_converter	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter	https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter	2.2.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.12.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	154	763	False		
-short_reads_trim_seq	trim_reads	Select high quality segments								To update		Fastq Manipulation	short_reads_trim_seq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	21	220	False		
-shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1008	41600	False		
-sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	269	14982	False		
-smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	Up-to-date	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.2.5	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	22	203	False		
-spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	coronaspades, biosyntheticspades, metaplasmidspades, plasmidspades, metaspades, rnaspades, metaviralspades, rnaviralspades, spades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	1	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	0	0	9	3	0	3547	72953	False		
-spades_header_fixer	spades_header_fixer	Fixes Spades Fasta ids								To update	https://github.com/phac-nml/galaxy_tools	Fasta Manipulation	spades_fasta_header_fixer	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer	1.1.2+galaxy1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-split_paired_reads	split_paired_reads	Split paired end reads								To update		Fastq Manipulation	split_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-sra-tools	fasterq_dump, fastq_dump, sam_dump	NCBI Sequence Read Archive toolkit utilities	sra-tools	sra-tools		SRA Software Toolkit	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	Data handling	DNA, Genomics, Sequencing	Up-to-date	https://github.com/ncbi/sra-tools	Data Source, Fastq Manipulation	sra_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools	3.1.1	sra-tools	3.1.1	Data handling	DNA, Genomics, Sequencing	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	2	0	3	0	0	3	0	0	0	3	0	0	0	0	0	0	0	3	3	0	6247	350032	False		
-tabular_to_fastq	tabular_to_fastq	Tabular to FASTQ converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	tabular_to_fastq	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	200	7388	False		
-tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	0	1	1	0	1801	27426	False		
-tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	460	False		
-trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2334	238699	False		
-trimmomatic	trimmomatic	A flexible read trimming tool for Illumina NGS data								Up-to-date	http://www.usadellab.org/cms/?page=trimmomatic	Fastq Manipulation	trimmomatic	pjbriggs	https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic	0.39	trimmomatic	0.39			1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	0	0	1	1	0	5862	305866	False		
-trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942	False		
-unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1558	65732	False		
-validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	25	86	False		
-velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	2083	25420	False		
-velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	255	4741	False		
-verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	22	False		
-wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660	False		
-xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-yahs	yahs	Yet Another Hi-C scaffolding tool								Up-to-date	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2a.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	64	344	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
+TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	42	False		
+abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	391	4278	False		
+adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	37	217	False		
+agat	agat	GTF/GFF analysis toolkit	agat	agat		AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	To update	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.4.0	agat	1.4.1	Data handling, Genome annotation	Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	42	481	False		
+align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	329	False		
+assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+atactk_trim_adapters	atactk_trim_adapters	Trim adapters from paired-end HTS reads.								To update	https://github.com/ParkerLab/atactk/	Fastq Manipulation	atactk_trim_adapters	rnateam	https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters	https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters	0.1.6	atactk	0.1.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	26	257	False		
+bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+barcode_splitter	barcode_splitter	A utility to split sequence files using multiple sets of barcodes								To update	https://bitbucket.org/princeton_genomics/barcode_splitter/	Fastq Manipulation	barcode_splitter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter	0.18.4.0	barcode_splitter	0.18.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+berokka	berokka	Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.								Up-to-date	https://github.com/tseemann/berokka	Fasta Manipulation	berokka	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka	0.2.3	berokka	0.2.3			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	531	False		
+biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	3	False		
+blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	121	22499	False		
+blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+blast_unmatched	blast_unmatched	Extract unmatched query sequences from blast								To update	http://artbio.fr	Fasta Manipulation	blast_unmatched	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	1.0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	685	False		
+cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	101	7766	False		
+cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	280	4474	False		
+cherry_pick_fasta	cherry_pick_fasta	Pick fasta sequence with specific header content								To update	http://artbio.fr	Fasta Manipulation	cherry_pick_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	4.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	269	False		
+clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+convert_solid_color2nuc	color2nuc	Convert Color Space to Nucleotides								To update		Fasta Manipulation	convert_solid_color2nuc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	5090	232004	False		
+disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	42	369	False		
+ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	107	107	107	107	107	0	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	107	107	107	0	1816	89530	False		
+fasplit	fasplit	faSplit is a tool to split a single FASTA file into several files	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Fasta Manipulation	ucsc_fasplit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	469	ucsc-fasplit	469		Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	242	2644	False		
+fasta_clipping_histogram	cshl_fasta_clipping_histogram	Length Distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Graphics, Statistics	fasta_clipping_histogram	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram	0.0.14	fastx_toolkit	0.0.14			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+fasta_compute_length	fasta_compute_length	Compute sequence length								To update		Fasta Manipulation	fasta_compute_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length	1.0.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	380	7758	False		
+fasta_concatenate_by_species	fasta_concatenate0	Concatenate FASTA alignment by species								To update		Fasta Manipulation	fasta_concatenate_by_species	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	88	35793	False		
+fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fasta_filter_by_length	fasta_filter_by_length	Filter sequences by length								To update		Fasta Manipulation	fasta_filter_by_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length	1.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	350	48649	False		
+fasta_formatter	cshl_fasta_formatter	FASTA Width formatter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_formatter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	1	68	2912	False		
+fasta_merge_files_and_filter_unique_sequences	fasta_merge_files_and_filter_unique_sequences	Concatenate FASTA database files together								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Fasta Manipulation	fasta_merge_files_and_filter_unique_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	1.2.0	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	461	29886	False		
+fasta_nucleotide_changer	cshl_fasta_nucleotides_changer	RNA/DNA converter.								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_nucleotide_changer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	29	774	False		
+fasta_to_tabular	fasta2tab	FASTA-to-Tabular converter								To update		Fasta Manipulation	fasta_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular	1.1.1	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	622	105935	False		
+fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_combiner	fastq_combiner	Combine FASTA and QUAL into FASTQ								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation, Fasta Manipulation	fastq_combiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	66	8676	False		
+fastq_filter	fastq_filter	Filter FASTQ reads by quality score and length								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	266	14222	False		
+fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_groomer	fastq_groomer	Convert between various FASTQ quality formats.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_groomer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1028	94802	False		
+fastq_info	fastq_info	FASTQ info allows to validate single or paired fastq files								To update	https://github.com/nunofonseca/fastq_utils	Fastq Manipulation	fastq_info	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	0.25.1	fastq_utils	0.25.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	679	5765	False		
+fastq_manipulation	fastq_manipulation	Manipulate FASTQ reads on various attributes.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_manipulation	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	69	2503	False		
+fastq_masker_by_quality	fastq_masker_by_quality	FASTQ Masker by quality score								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_masker_by_quality	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	170	False		
+fastq_pair	fastq_pair	Paired-end fastq pairer								To update	https://github.com/linsalrob/fastq-pair	Fastq Manipulation	fastq_pair	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair	1.0+galaxy0	fastq-pair	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_paired_end_deinterlacer	fastq_paired_end_deinterlacer	FASTQ de-interlacer on paired end reads.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_deinterlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	122	8410	False		
+fastq_paired_end_interlacer	fastq_paired_end_interlacer	FASTQ interlacer on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_interlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1087	17024	False		
+fastq_paired_end_joiner	fastq_paired_end_joiner	FASTQ joiner on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_joiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	245	16635	False		
+fastq_paired_end_splitter	fastq_paired_end_splitter	FASTQ splitter on joined paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	196	3092	False		
+fastq_quality_boxplot	cshl_fastq_quality_boxplot	Draw quality score boxplot								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics, Statistics	fastq_quality_boxplot	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	51	1178	False		
+fastq_quality_converter	cshl_fastq_quality_converter	Quality format converter (ASCII-Numeric)								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_converter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	11	220	False		
+fastq_quality_filter	cshl_fastq_quality_filter	Filter by quality								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1509	15172	False		
+fastq_quality_trimmer	cshl_fastq_quality_trimmer	FASTQ trimmer based on quality								To update	https://github.com/agordon/fastx_toolkit	Fastq Manipulation	fastq_quality_trimmer	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer	0.0.14+galaxy0	fastx_toolkit	0.0.14			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_stats	fastq_stats	FASTQ Summary Statistics by column								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_stats	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	221	4246	False		
+fastq_to_fasta	cshl_fastq_to_fasta	FASTQ to FASTA converter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Convert Formats	fastq_to_fasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	419	13599	False		
+fastq_to_tabular	fastq_to_tabular	FASTQ to Tabular converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_to_tabular	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	93	12593	False		
+fastq_trimmer	fastq_trimmer	FASTQ Trimmer by quality								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	210	9757	False		
+fastq_trimmer_by_quality	fastq_quality_trimmer	FASTQ Quality Trimmer by sliding window								Up-to-date		Fastq Manipulation	fastq_trimmer_by_quality	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	459	5676	False		
+fastqc	fastqc	Read QC reports using FastQC	fastqc	fastqc		FastQC	This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	Fastq Manipulation	fastqc	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc	0.74+galaxy1	fastqc	0.12.1	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	1	1	1	1	1	0	17447	1556625	False		
+fastqsolexa_to_fasta_qual	fastqsolexa_to_fasta_qual	FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data								To update		Convert Formats, Fastq Manipulation	fastqsolexa_to_fasta_qual	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastqtofasta	fastq_to_fasta_python	FASTQ to FASTA converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastqtofasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1371	178178	False		
+fastx_artifacts_filter	cshl_fastx_artifacts_filter	Remove sequencing artifacts								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_artifacts_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	27	1810	False		
+fastx_barcode_splitter	cshl_fastx_barcode_splitter	Barcode Splitter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_barcode_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	128	16591	False		
+fastx_clipper	cshl_fastx_clipper	Clip adapter sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_clipper	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	96	3333	False		
+fastx_collapser	cshl_fastx_collapser	Collapse sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fastx_collapser	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	114	61218	False		
+fastx_nucleotides_distribution	cshl_fastx_nucleotides_distribution	Draw nucleotides distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics	fastx_nucleotides_distribution	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	25	249	False		
+fastx_quality_statistics	cshl_fastx_quality_statistics	Compute quality statistics								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Statistics	fastx_quality_statistics	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	63	2176	False		
+fastx_renamer	cshl_fastx_renamer	Rename sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_renamer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	68	2280	False		
+fastx_reverse_complement	cshl_fastx_reverse_complement	Reverse-Complement								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Fasta Manipulation	fastx_reverse_complement	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	156	10832	False		
+fastx_trimmer	cshl_fastx_trimmer	Trim sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	205	13149	False		
+fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fetch_fasta_from_ncbi	retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers								To update	http://artbio.fr	Fasta Manipulation, Data Source	fetch_fasta_from_ncbi	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	3.1.0	urllib3	1.12			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	426	26274	False		
+filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	617	30483	False		
+flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	14	331	False		
+flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	74	13759	False		
+flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	20904	False		
+format_cd_hit_output	format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file								To update		Fasta Manipulation	format_cd_hit_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output	1.0.0+galaxy1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	166	False		
+get_pairs	get_pairs	Separate paired and unpaired reads from two fastq files								To update		Fastq Manipulation	get_pairs	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	0.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+get_reference_fasta	get_fasta_reference	Obtain reference genome sequence.								To update	http://artbio.fr	Data Source, Fasta Manipulation	get_reference_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	0.3.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	18	495	False		
+graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	136	6651	False		
+guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	295	False		
+hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	1410	False		
+hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	False		
+hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	4183	299104	False		
+hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354	False		
+idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	69	1127	False		
+instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	139	False		
+jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138	False		
+khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	8	8	8	0	63	2022	False		
+length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	322	4090	False		
+lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	152	False		
+links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	77	405	False		
+make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	548	9530	False		
+megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	54	475	False		
+merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483	False		
+meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	109	2206	False		
+miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	178	11938	False		
+mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	66	881	False		
+mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	56	613	False		
+msaboot	msaboot	A multiple sequences alignment bootstrapping tool.								Up-to-date	https://github.com/phac-nml/msaboot	Fasta Manipulation	msaboot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot	0.1.2	msaboot	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34	803	False		
+multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	8320	162790	False		
+necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	95	667	False		
+nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268	False		
+nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	162	6384	False		
+oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	39	2654	False		
+pbtk	bam2fastx	Convert PacBio Bam File to fasta or fastq file								Up-to-date	https://github.com/PacificBiosciences/pbtk	Convert Formats, Fasta Manipulation, Fastq Manipulation	bam2fastx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk	3.1.1	pbtk	3.1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pear	iuc_pear	PEAR evaluates all possible paired-end read overlaps	pear	pear		PEAR	Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.	Sequence merging	Sequence assembly	Up-to-date	https://cme.h-its.org/exelixis/web/software/pear/	Fastq Manipulation	pear	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear	0.9.6	pear	0.9.6	Sequence merging	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	150	4305	False		
+plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+porechop	porechop	Porechop - Finding and removing adapters from Oxford Nanopore reads								To update	https://github.com/rrwick/Porechop	Fasta Manipulation, Fastq Manipulation	porechop	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop	https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop		porechop	0.2.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1046	185468	False		
+poretools	poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot	A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	poretools	poretools		Poretools	Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	Nucleic acid sequence analysis	DNA, Sequencing	Up-to-date	https://poretools.readthedocs.io/en/latest/	Fasta Manipulation, Fastq Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools	0.6.1a1	poretools	0.6.1a1	Nucleic acid sequence analysis	DNA, Sequencing	13	13	13	0	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	6	13	0	409	18773	False		
+prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	70	7881	False		
+promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	167	16800	False		
+pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	350	21123	False		
+qfilt	qfilt	Filter sequencing data								To update	https://github.com/veg/qfilt	Fastq Manipulation	qfilt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt	1.0.0+galaxy1	qfilt	0.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	3567	51567	False		
+quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	False		
+ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	237	2833	False		
+raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	6902	False		
+rcorrector	rcorrector	Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.	rcorrector	rcorrector		Rcorrector	This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.	Sequencing error detection	RNA, RNA-Seq, Sequencing	To update	https://github.com/mourisl/Rcorrector	Fastq Manipulation	rcorrector	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector	1.0.3+galaxy1	rcorrector	1.0.7	Sequencing error detection	RNA, RNA-Seq	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	569	False		
+rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	109	1110	False		
+salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	84	454	False		
+samblaster	samblaster	samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files	samblaster	samblaster		SAMBLASTER	A tool to mark duplicates and extract discordant and split reads from SAM files.	Split read mapping	DNA, Sequencing, Mapping	To update	https://github.com/GregoryFaust/samblaster	SAM, Fastq Manipulation, Variant Analysis	samblaster	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster	https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster	0.1.24	samblaster	0.1.26	Split read mapping	DNA, Sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	3765	False		
+samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	1	296	4948	False		
+samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1450	48426	False		
+seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	306	25302	False		
+seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	82	3784	False		
+seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	False		
+seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sequence_format_converter	sequence_format_converter	various fasta to tabular conversions								To update	http://artbio.fr	Convert Formats, Fasta Manipulation	sequence_format_converter	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter	https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter	2.2.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	154	763	False		
+short_reads_trim_seq	trim_reads	Select high quality segments								To update		Fastq Manipulation	short_reads_trim_seq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	21	220	False		
+shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1008	41600	False		
+sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	269	14982	False		
+smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	22	203	False		
+spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	3	9	3	0	3547	72953	False		
+spades_header_fixer	spades_header_fixer	Fixes Spades Fasta ids								To update	https://github.com/phac-nml/galaxy_tools	Fasta Manipulation	spades_fasta_header_fixer	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer	1.1.2+galaxy1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+split_paired_reads	split_paired_reads	Split paired end reads								To update		Fastq Manipulation	split_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sra-tools	fasterq_dump, fastq_dump, sam_dump	NCBI Sequence Read Archive toolkit utilities	sra-tools	sra-tools		SRA Software Toolkit	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	Data handling	DNA, Genomics, Sequencing	Up-to-date	https://github.com/ncbi/sra-tools	Data Source, Fastq Manipulation	sra_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools	3.1.1	sra-tools	3.1.1	Data handling	DNA, Genomics, Sequencing	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	2	0	3	0	0	3	0	0	0	3	0	0	0	0	0	3	3	3	0	6247	350032	False		
+tabular_to_fastq	tabular_to_fastq	Tabular to FASTQ converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	tabular_to_fastq	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	200	7388	False		
+tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	1801	27426	False		
+tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	460	False		
+trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	2334	238699	False		
+trimmomatic	trimmomatic	A flexible read trimming tool for Illumina NGS data								Up-to-date	http://www.usadellab.org/cms/?page=trimmomatic	Fastq Manipulation	trimmomatic	pjbriggs	https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic	0.39	trimmomatic	0.39			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	1	1	1	0	5862	305866	False		
+trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942	False		
+unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1558	65732	False		
+validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	25	86	False		
+velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	2083	25420	False		
+velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	4741	False		
+verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	22	False		
+wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660	False		
+xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	64	344	False		
diff --git a/communities/biodiversity/resources/tools.html b/communities/biodiversity/resources/tools.html
index 34a4c5b6..ce8795c7 100644
--- a/communities/biodiversity/resources/tools.html
+++ b/communities/biodiversity/resources/tools.html
@@ -88,10 +88,8 @@
       <th>Tools available on UseGalaxy.eu</th>
       <th>Tools available on UseGalaxy.fr</th>
       <th>Tools available on APOSTL</th>
-      <th>Tools available on BF2I-MAP</th>
-      <th>Tools available on BioBix</th>
+      <th>Tools available on ARGs-OAP</th>
       <th>Tools available on CIRM-CFBP</th>
-      <th>Tools available on Center for Phage Technology (CPT)</th>
       <th>Tools available on ChemFlow</th>
       <th>Tools available on Coloc-stats</th>
       <th>Tools available on CoralSNP</th>
@@ -114,7 +112,6 @@
       <th>Tools available on Oqtans</th>
       <th>Tools available on Palfinder</th>
       <th>Tools available on PepSimili</th>
-      <th>Tools available on PhagePromotor</th>
       <th>Tools available on UseGalaxy.be</th>
       <th>Tools available on UseGalaxy.cz</th>
       <th>Tools available on UseGalaxy.no</th>
@@ -128,7 +125,7 @@
     <tr>
       <td></td>
       <td>EMLassemblyline</td>
-      <td>eal_table_template, eal_templates, eml2eal, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template</td>
+      <td>annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template</td>
       <td>Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa</td>
       <td></td>
       <td></td>
@@ -144,22 +141,19 @@
       <td>ecology</td>
       <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline</td>
       <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline</td>
-      <td>0.1.1+galaxy0</td>
-      <td>r-emlassemblyline</td>
+      <td>0.1.0+galaxy0</td>
+      <td>r-base</td>
       <td></td>
       <td></td>
       <td></td>
       <td>0</td>
       <td>0</td>
-      <td>9</td>
+      <td>11</td>
       <td>9</td>
       <td>0</td>
       <td>0</td>
+      <td>11</td>
       <td>9</td>
-      <td>9</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -251,9 +245,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -324,9 +315,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -387,9 +375,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>4</td>
       <td>0</td>
@@ -455,9 +440,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -509,8 +491,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -530,7 +510,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -545,28 +524,26 @@
       <td>De novo genome sequence assembler using short reads.</td>
       <td>Genome assembly, De-novo assembly, Scaffolding</td>
       <td>Sequence assembly</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://www.bcgsc.ca/platform/bioinfo/software/abyss</td>
       <td>Assembly</td>
       <td>abyss</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss</td>
-      <td>2.3.7</td>
+      <td>2.3.9</td>
       <td>abyss</td>
-      <td>2.3.8</td>
+      <td>2.3.9</td>
       <td>Genome assembly, De-novo assembly, Scaffolding</td>
       <td>Sequence assembly</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -592,8 +569,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -645,8 +621,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -660,8 +634,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -732,9 +705,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -763,15 +733,12 @@
       <td></td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -868,9 +835,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -917,8 +881,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -938,7 +900,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1004,9 +965,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1072,9 +1030,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1135,9 +1090,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1208,9 +1160,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1271,9 +1220,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1324,8 +1270,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1346,7 +1290,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1392,8 +1335,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1414,7 +1355,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1461,8 +1401,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1482,7 +1420,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1543,9 +1480,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1610,10 +1544,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1679,9 +1610,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1732,8 +1660,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1749,7 +1675,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1815,9 +1740,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -1876,8 +1798,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1885,7 +1805,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1951,9 +1870,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1982,7 +1898,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell</td>
       <td>0.0.7</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -2024,9 +1940,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2092,9 +2005,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2118,7 +2028,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants</td>
       <td>0.0.6</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -2141,8 +2051,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2162,7 +2070,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2186,7 +2093,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats</td>
       <td>0.1.0</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -2209,8 +2116,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2230,7 +2135,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2291,9 +2195,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
       <td>0</td>
       <td>0</td>
@@ -2363,9 +2264,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td></td>
     </tr>
@@ -2413,8 +2311,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2428,8 +2324,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2500,9 +2395,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2568,6 +2460,68 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>evidencemodeler</td>
+      <td>evidencemodeler</td>
+      <td>EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.</td>
+      <td>EvidenceModeler</td>
+      <td>EvidenceModeler</td>
+      <td></td>
+      <td>EvidenceModeler</td>
+      <td>The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.</td>
+      <td>Gene prediction</td>
+      <td>Gene expression, Gene structure</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file</td>
+      <td>Genome annotation</td>
+      <td>evidencemodeler</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler</td>
+      <td>2.1.0</td>
+      <td>evidencemodeler</td>
+      <td>2.1.0</td>
+      <td>Gene prediction</td>
+      <td>Gene expression, Gene structure</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -2636,9 +2590,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2704,9 +2655,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2753,8 +2701,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2774,7 +2720,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2821,8 +2766,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2836,8 +2779,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2857,14 +2799,14 @@
       <td>Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.</td>
       <td>Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly</td>
       <td>Sequence assembly, Metagenomics, Whole genome sequencing, Genomics</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/fenderglass/Flye/</td>
       <td>Assembly</td>
       <td>flye</td>
       <td>bgruening</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/flye</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/flye</td>
-      <td>2.9.4</td>
+      <td>2.9.5</td>
       <td>flye</td>
       <td>2.9.5</td>
       <td>Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly</td>
@@ -2888,8 +2830,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2904,8 +2844,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2970,10 +2909,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -3039,9 +2975,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
@@ -3107,9 +3040,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -3161,8 +3091,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -3176,8 +3104,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -3206,7 +3133,7 @@
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/graphmap</td>
       <td>0.5.2</td>
       <td>graphmap</td>
-      <td>0.6.3</td>
+      <td>0.6.4</td>
       <td>Sequence trimming, EST assembly, Read mapping</td>
       <td>Gene transcripts, RNA-Seq, RNA splicing</td>
       <td>0</td>
@@ -3229,8 +3156,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -3244,8 +3169,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -3316,9 +3240,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -3379,9 +3300,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3447,9 +3365,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3501,8 +3416,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3517,7 +3430,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3544,7 +3456,7 @@
       <td>ecology</td>
       <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper</td>
       <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes</td>
-      <td>0.1.0</td>
+      <td>0.2.0</td>
       <td>r-base</td>
       <td></td>
       <td></td>
@@ -3588,9 +3500,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -3637,8 +3546,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3657,7 +3564,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>228</td>
       <td></td>
     </tr>
@@ -3703,8 +3609,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -3720,8 +3624,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3787,9 +3690,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3841,8 +3741,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3862,7 +3760,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -3922,10 +3819,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -3991,9 +3885,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4064,9 +3955,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -4113,8 +4001,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4129,7 +4015,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4180,8 +4065,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4196,8 +4079,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>8</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
@@ -4249,8 +4131,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4265,7 +4145,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4298,15 +4177,12 @@
       <td></td>
       <td></td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -4376,10 +4252,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -4472,9 +4345,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -4519,8 +4389,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4536,8 +4404,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4589,8 +4456,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4605,7 +4470,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4671,9 +4535,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4744,9 +4605,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -4806,10 +4664,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4861,8 +4716,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4876,8 +4729,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4929,8 +4781,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4944,8 +4794,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4997,8 +4846,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5013,7 +4860,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5065,8 +4911,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5081,7 +4925,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5152,9 +4995,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -5215,9 +5055,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5283,9 +5120,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5337,8 +5171,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5352,8 +5184,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5404,8 +5235,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5426,7 +5255,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -5487,9 +5315,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5559,9 +5384,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
       <td></td>
     </tr>
@@ -5628,9 +5450,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -5696,9 +5515,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -5745,8 +5561,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5761,7 +5575,6 @@
       <td>0</td>
       <td>1</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5805,8 +5618,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -5834,7 +5645,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -5862,15 +5672,13 @@
       <td>Genome annotation</td>
       <td>Genomics, Sequence analysis</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -5902,7 +5710,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -5968,9 +5775,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -6031,9 +5835,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6077,8 +5878,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6100,8 +5899,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -6168,9 +5966,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6221,8 +6016,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6237,7 +6030,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -6289,8 +6081,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6305,7 +6095,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6370,10 +6159,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>6</td>
       <td>7</td>
       <td>7</td>
       <td>0</td>
@@ -6443,9 +6229,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>16</td>
       <td></td>
     </tr>
@@ -6493,8 +6276,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6509,7 +6290,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6580,9 +6360,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -6642,10 +6419,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6697,8 +6471,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6712,8 +6484,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6765,8 +6536,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6781,7 +6550,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -6810,7 +6578,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad</td>
       <td>0.0.5</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -6852,9 +6620,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -6878,7 +6643,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth</td>
       <td>0.0.3</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -6899,8 +6664,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -6916,8 +6679,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -6946,7 +6708,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats</td>
       <td>0.0.6</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -6958,8 +6720,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6984,8 +6744,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7056,9 +6815,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -7105,8 +6861,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7121,7 +6875,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7192,9 +6945,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -7218,7 +6968,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta</td>
       <td>0.6.0</td>
       <td>shasta</td>
-      <td>0.12.0</td>
+      <td>0.13.0</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -7241,8 +6991,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7256,8 +7004,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7307,8 +7054,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -7324,8 +7069,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7345,7 +7089,7 @@
       <td>Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568</td>
       <td>Sequence trimming, Genotyping, k-mer counting</td>
       <td>Sequence assembly, Genetic variation, Mathematics</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/KamilSJaron/smudgeplot</td>
       <td>Assembly</td>
       <td>smudgeplot</td>
@@ -7354,7 +7098,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot</td>
       <td>0.2.5</td>
       <td>smudgeplot</td>
-      <td>0.2.5</td>
+      <td>0.3.0</td>
       <td>Sequence trimming, Genotyping, k-mer counting</td>
       <td>Sequence assembly, Genetic variation, Mathematics</td>
       <td>1</td>
@@ -7391,9 +7135,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7407,7 +7148,7 @@
       <td>spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades</td>
       <td>SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.</td>
       <td>spades</td>
-      <td>coronaspades, biosyntheticspades, metaplasmidspades, plasmidspades, metaspades, rnaspades, metaviralspades, rnaviralspades, spades</td>
+      <td>spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades</td>
       <td></td>
       <td>SPAdes</td>
       <td>St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.</td>
@@ -7437,8 +7178,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -7460,8 +7199,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>9</td>
       <td>3</td>
       <td>0</td>
@@ -7513,8 +7251,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -7528,8 +7264,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -7594,10 +7329,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7663,9 +7395,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>7</td>
       <td>0</td>
       <td>0</td>
@@ -7731,9 +7460,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -7785,8 +7511,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7806,7 +7530,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -7851,8 +7574,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -7868,8 +7589,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7940,9 +7660,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -8003,9 +7720,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8070,10 +7784,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -8125,8 +7836,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -8141,7 +7850,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -8161,14 +7869,14 @@
       <td>TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.</td>
       <td>Homology-based gene prediction, Alternative splicing prediction</td>
       <td>Gene expression, RNA-Seq, Gene transcripts, Model organisms</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/Gaius-Augustus/TSEBRA</td>
       <td>Genome annotation</td>
       <td></td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra</td>
-      <td>1.1.2.4</td>
+      <td>1.1.2.5</td>
       <td>tsebra</td>
       <td>1.1.2.5</td>
       <td>Homology-based gene prediction, Alternative splicing prediction</td>
@@ -8211,9 +7919,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td></td>
     </tr>
@@ -8260,8 +7965,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8276,8 +7979,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8327,8 +8029,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -8344,8 +8044,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -8386,8 +8085,6 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -8412,8 +8109,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8442,19 +8138,16 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko</td>
       <td>1.3.1</td>
       <td>verkko</td>
-      <td>2.1</td>
+      <td>2.2</td>
       <td></td>
       <td></td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -8547,9 +8240,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
@@ -8601,8 +8291,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8617,7 +8305,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8683,9 +8370,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
       <td>2</td>
       <td>0</td>
@@ -8705,7 +8389,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/c-zhou/yahs</td>
       <td>Assembly</td>
       <td>yahs</td>
@@ -8714,7 +8398,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs</td>
       <td>1.2a.2</td>
       <td>yahs</td>
-      <td>1.2a.2</td>
+      <td>1.2.2</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -8751,9 +8435,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8824,9 +8505,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
   </tbody>
diff --git a/communities/biodiversity/resources/tools.tsv b/communities/biodiversity/resources/tools.tsv
index 44c1fbd1..64b21831 100644
--- a/communities/biodiversity/resources/tools.tsv
+++ b/communities/biodiversity/resources/tools.tsv
@@ -1,131 +1,132 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on BF2I-MAP	Tools available on BioBix	Tools available on CIRM-CFBP	Tools available on Center for Phage Technology (CPT)	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-EMLassemblyline	eal_table_template, eal_templates, eml2eal, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.1+galaxy0	r-emlassemblyline				0	0	9	9	0	0	9	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	102	False		
-Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	82	False		
-Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	73	1004	False		
-TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	42	False		
-abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	To update	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.7	abyss	2.3.8	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	391	4278	False		
-annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1175	25975	False		
-aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	531	False		
-biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	3	False		
-blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	685	False		
-braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	17	109	False		
-braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	567	False		
-cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	101	7766	False		
-champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	19	174	False		
-chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	418	15690	False		
-circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	269	False		
-clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	146	658	False		
-deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	False		
-disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	42	369	False		
-dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	74	13759	False		
-flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	To update	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.4	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1499	20904	False		
-funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	900	5906	False		
-gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	8	0	0	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	10	1475	False		
-getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	18	495	False		
-goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	408	5484	False		
-graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.3	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	136	6651	False		
-hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	295	False		
-helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	93	False		
-hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	1410	False		
-hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	False		
-hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	4183	299104	False		
-hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354	False		
-icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	69	1127	False		
-instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	139	False		
-interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138	False		
-khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	8	8	0	63	2022	False		
-links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	77	405	False		
-marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	24	False		
-medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	0	1	1	0	548	9530	False		
-megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	54	475	False		
-merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483	False		
-meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	5.34c21f2	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	184	False		
-minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	109	2206	False		
-miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	178	11938	False		
-mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	66	881	False		
-mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	56	613	False		
-ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	95	667	False		
-nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268	False		
-novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	162	6384	False		
-oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	1	1	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	45	False		
-ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	False		
-ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
+EMLassemblyline	annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.0+galaxy0	r-base				0	0	11	9	0	0	11	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	102	False		
+Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	82	False		
+Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	73	1004	False		
+TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	42	False		
+abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	391	4278	False		
+annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1175	25975	False		
+aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	531	False		
+biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	3	False		
+blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	685	False		
+braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	17	109	False		
+braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	567	False		
+cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	101	7766	False		
+champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	19	174	False		
+chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	418	15690	False		
+circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	269	False		
+clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	146	658	False		
+deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	False		
+disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	42	369	False		
+dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+evidencemodeler	evidencemodeler	EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.	EvidenceModeler	EvidenceModeler		EvidenceModeler	The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.	Gene prediction	Gene expression, Gene structure	Up-to-date	https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file	Genome annotation	evidencemodeler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler	2.1.0	evidencemodeler	2.1.0	Gene prediction	Gene expression, Gene structure	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	74	13759	False		
+flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	20904	False		
+funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	0	900	5906	False		
+gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	8	0	0	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	10	1475	False		
+getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	18	495	False		
+goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	408	5484	False		
+graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	136	6651	False		
+hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	295	False		
+helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	93	False		
+hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	1410	False		
+hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.2.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	False		
+hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	4183	299104	False		
+hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354	False		
+icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	69	1127	False		
+instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	139	False		
+interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138	False		
+khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	8	8	8	0	63	2022	False		
+links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	77	405	False		
+marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	24	False		
+medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	548	9530	False		
+megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	54	475	False		
+merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483	False		
+meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	5.34c21f2	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	184	False		
+minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	109	2206	False		
+miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	178	11938	False		
+mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	66	881	False		
+mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	56	613	False		
+ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	95	667	False		
+nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268	False		
+novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	162	6384	False		
+oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	1	1	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	45	False		
+ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	False		
+ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
 pharokka	pharokka	rapid standardised annotation tool for bacteriophage genomes and metagenomes	pharokka	pharokka		Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.	Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	To update	https://github.com/gbouras13/pharokka	Genome annotation	pharokka	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	1.3.2	"
                 pharokka
-            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	74	2565	False		
-plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	167	16800	False		
-quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	3567	51567	False		
-quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	False		
-ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	237	2833	False		
-raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	6902	False		
-regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	22	526	False		
-repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	False		
-repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	217	1177	False		
-retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	109	1110	False		
-salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	454	False		
-sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	3765	False		
-samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.20			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	296	4948	False		
-samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.20			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1450	48426	False		
-sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	82	3784	False		
-seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.12.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	154	763	False		
-shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1008	41600	False		
-smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	Up-to-date	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.2.5	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	22	203	False		
-spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	coronaspades, biosyntheticspades, metaplasmidspades, plasmidspades, metaspades, rnaspades, metaviralspades, rnaviralspades, spades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	1	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	0	0	9	3	0	3547	72953	False		
-spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	34	446	False		
-spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	56	769	False		
-srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	7	4	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	21	225	False		
-stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	10	325	False		
-taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	0	1	1	0	1801	27426	False		
-telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	460	False		
-transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	84	907	False		
-trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942	False		
-tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	To update	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.4	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	False		
-unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1558	65732	False		
-velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	2083	25420	False		
-velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	255	4741	False		
-verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	22	False		
-vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	351	12203	False		
-wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660	False		
-xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	5	5	2	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	175	5876	False		
-yahs	yahs	Yet Another Hi-C scaffolding tool								Up-to-date	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2a.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	64	344	False		
-zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	74	2565	False		
+plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	167	16800	False		
+quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	3567	51567	False		
+quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	False		
+ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	237	2833	False		
+raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	6902	False		
+regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	7	7	0	22	526	False		
+repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	False		
+repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	217	1177	False		
+retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	109	1110	False		
+salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	84	454	False		
+sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	3765	False		
+samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	1	296	4948	False		
+samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1450	48426	False		
+sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	82	3784	False		
+seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	154	763	False		
+shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1008	41600	False		
+smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	22	203	False		
+spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	3	9	3	0	3547	72953	False		
+spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	34	446	False		
+spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	56	769	False		
+srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	7	4	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	21	225	False		
+stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	10	325	False		
+taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	1801	27426	False		
+telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	460	False		
+transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	0	84	907	False		
+trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942	False		
+tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	Up-to-date	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.5	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	False		
+unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1558	65732	False		
+velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	2083	25420	False		
+velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	4741	False		
+verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	22	False		
+vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	351	12203	False		
+wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660	False		
+xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	5	5	2	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	175	5876	False		
+yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	64	344	False		
+zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
diff --git a/communities/biodiversity/resources/tools_filtered_by_ts_categories.tsv b/communities/biodiversity/resources/tools_filtered_by_ts_categories.tsv
index 44c1fbd1..64b21831 100644
--- a/communities/biodiversity/resources/tools_filtered_by_ts_categories.tsv
+++ b/communities/biodiversity/resources/tools_filtered_by_ts_categories.tsv
@@ -1,131 +1,132 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on BF2I-MAP	Tools available on BioBix	Tools available on CIRM-CFBP	Tools available on Center for Phage Technology (CPT)	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-EMLassemblyline	eal_table_template, eal_templates, eml2eal, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.1+galaxy0	r-emlassemblyline				0	0	9	9	0	0	9	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	102	False		
-Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	82	False		
-Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	73	1004	False		
-TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	42	False		
-abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	To update	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.7	abyss	2.3.8	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	391	4278	False		
-annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1175	25975	False		
-aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	531	False		
-biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	3	False		
-blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	685	False		
-braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	17	109	False		
-braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	567	False		
-cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	101	7766	False		
-champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	19	174	False		
-chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	418	15690	False		
-circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	269	False		
-clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	146	658	False		
-deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	False		
-disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	42	369	False		
-dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	74	13759	False		
-flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	To update	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.4	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1499	20904	False		
-funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	900	5906	False		
-gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	8	0	0	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	10	1475	False		
-getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	18	495	False		
-goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	408	5484	False		
-graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.3	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	136	6651	False		
-hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	295	False		
-helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	93	False		
-hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	1410	False		
-hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	False		
-hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	4183	299104	False		
-hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354	False		
-icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	69	1127	False		
-instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	139	False		
-interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138	False		
-khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	8	8	0	63	2022	False		
-links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	77	405	False		
-marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	24	False		
-medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	0	1	1	0	548	9530	False		
-megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	54	475	False		
-merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483	False		
-meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	5.34c21f2	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	184	False		
-minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	109	2206	False		
-miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	178	11938	False		
-mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	66	881	False		
-mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	56	613	False		
-ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	95	667	False		
-nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268	False		
-novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	162	6384	False		
-oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	1	1	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	45	False		
-ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	False		
-ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
+EMLassemblyline	annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.0+galaxy0	r-base				0	0	11	9	0	0	11	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	102	False		
+Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	82	False		
+Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	73	1004	False		
+TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	42	False		
+abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	391	4278	False		
+annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1175	25975	False		
+aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	531	False		
+biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	3	False		
+blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	685	False		
+braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	17	109	False		
+braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	567	False		
+cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	101	7766	False		
+champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	19	174	False		
+chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	418	15690	False		
+circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	269	False		
+clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	146	658	False		
+deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	False		
+disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	42	369	False		
+dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+evidencemodeler	evidencemodeler	EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.	EvidenceModeler	EvidenceModeler		EvidenceModeler	The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.	Gene prediction	Gene expression, Gene structure	Up-to-date	https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file	Genome annotation	evidencemodeler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler	2.1.0	evidencemodeler	2.1.0	Gene prediction	Gene expression, Gene structure	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	74	13759	False		
+flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	20904	False		
+funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	0	900	5906	False		
+gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	8	0	0	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	10	1475	False		
+getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	18	495	False		
+goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	408	5484	False		
+graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	136	6651	False		
+hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	295	False		
+helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	93	False		
+hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	1410	False		
+hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.2.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	False		
+hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	4183	299104	False		
+hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354	False		
+icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	69	1127	False		
+instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	139	False		
+interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138	False		
+khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	8	8	8	0	63	2022	False		
+links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	77	405	False		
+marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	24	False		
+medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	548	9530	False		
+megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	54	475	False		
+merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483	False		
+meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	5.34c21f2	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	184	False		
+minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	109	2206	False		
+miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	178	11938	False		
+mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	66	881	False		
+mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	56	613	False		
+ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	95	667	False		
+nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268	False		
+novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	162	6384	False		
+oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
+obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	1	1	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	45	False		
+ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	False		
+ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
 pharokka	pharokka	rapid standardised annotation tool for bacteriophage genomes and metagenomes	pharokka	pharokka		Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.	Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	To update	https://github.com/gbouras13/pharokka	Genome annotation	pharokka	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	1.3.2	"
                 pharokka
-            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	74	2565	False		
-plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	167	16800	False		
-quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	3567	51567	False		
-quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	False		
-ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	237	2833	False		
-raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	6902	False		
-regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	22	526	False		
-repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	False		
-repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	217	1177	False		
-retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	109	1110	False		
-salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	454	False		
-sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	3765	False		
-samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.20			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	296	4948	False		
-samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.20			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1450	48426	False		
-sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	82	3784	False		
-seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.12.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	154	763	False		
-shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1008	41600	False		
-smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	Up-to-date	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.2.5	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	22	203	False		
-spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	coronaspades, biosyntheticspades, metaplasmidspades, plasmidspades, metaspades, rnaspades, metaviralspades, rnaviralspades, spades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	1	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	0	0	9	3	0	3547	72953	False		
-spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	34	446	False		
-spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	56	769	False		
-srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	7	4	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	21	225	False		
-stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	10	325	False		
-taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	0	1	1	0	1801	27426	False		
-telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	460	False		
-transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	84	907	False		
-trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942	False		
-tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	To update	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.4	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	False		
-unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1558	65732	False		
-velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	2083	25420	False		
-velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	255	4741	False		
-verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	22	False		
-vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	351	12203	False		
-wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660	False		
-xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	5	5	2	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	175	5876	False		
-yahs	yahs	Yet Another Hi-C scaffolding tool								Up-to-date	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2a.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	64	344	False		
-zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	74	2565	False		
+plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	167	16800	False		
+quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	3567	51567	False		
+quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	False		
+ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	237	2833	False		
+raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	6902	False		
+regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	7	7	0	22	526	False		
+repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	False		
+repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	217	1177	False		
+retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	109	1110	False		
+salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	84	454	False		
+sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	3765	False		
+samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	1	296	4948	False		
+samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1450	48426	False		
+sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	82	3784	False		
+seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	154	763	False		
+shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1008	41600	False		
+smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	22	203	False		
+spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	3	9	3	0	3547	72953	False		
+spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	34	446	False		
+spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	56	769	False		
+srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	7	4	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	21	225	False		
+stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	10	325	False		
+taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	1801	27426	False		
+telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	460	False		
+transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	0	84	907	False		
+trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942	False		
+tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	Up-to-date	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.5	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	False		
+unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1558	65732	False		
+velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	2083	25420	False		
+velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	4741	False		
+verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	22	False		
+vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	351	12203	False		
+wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660	False		
+xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	5	5	2	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	175	5876	False		
+yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	64	344	False		
+zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
diff --git a/communities/imaging/resources/tools.html b/communities/imaging/resources/tools.html
index 221396d6..22558511 100644
--- a/communities/imaging/resources/tools.html
+++ b/communities/imaging/resources/tools.html
@@ -88,10 +88,8 @@
       <th>Tools available on UseGalaxy.eu</th>
       <th>Tools available on UseGalaxy.fr</th>
       <th>Tools available on APOSTL</th>
-      <th>Tools available on BF2I-MAP</th>
-      <th>Tools available on BioBix</th>
+      <th>Tools available on ARGs-OAP</th>
       <th>Tools available on CIRM-CFBP</th>
-      <th>Tools available on Center for Phage Technology (CPT)</th>
       <th>Tools available on ChemFlow</th>
       <th>Tools available on Coloc-stats</th>
       <th>Tools available on CoralSNP</th>
@@ -114,7 +112,6 @@
       <th>Tools available on Oqtans</th>
       <th>Tools available on Palfinder</th>
       <th>Tools available on PepSimili</th>
-      <th>Tools available on PhagePromotor</th>
       <th>Tools available on UseGalaxy.be</th>
       <th>Tools available on UseGalaxy.cz</th>
       <th>Tools available on UseGalaxy.no</th>
@@ -182,10 +179,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -250,10 +244,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -318,10 +309,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -386,10 +374,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -454,10 +439,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -528,9 +510,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -591,9 +570,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -664,9 +640,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -726,10 +699,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -799,9 +769,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td></td>
     </tr>
@@ -862,10 +829,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -931,9 +895,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1003,9 +964,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>9</td>
       <td></td>
     </tr>
@@ -1028,7 +986,7 @@
       <td>bgruening</td>
       <td>https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging</td>
-      <td>2.3.1</td>
+      <td>2.4.0</td>
       <td>python</td>
       <td></td>
       <td></td>
@@ -1072,9 +1030,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1140,9 +1095,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1202,10 +1154,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>19</td>
       <td>23</td>
       <td>19</td>
       <td>0</td>
@@ -1257,8 +1206,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1273,7 +1220,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1339,9 +1285,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1412,9 +1355,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1475,9 +1415,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1543,9 +1480,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1610,10 +1544,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1679,9 +1610,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1747,9 +1675,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1776,7 +1701,7 @@
       <td>bgruening</td>
       <td>https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick</td>
-      <td>1.3.44</td>
+      <td>1.3.45</td>
       <td>graphicsmagick</td>
       <td>1.3.26</td>
       <td></td>
@@ -1814,10 +1739,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -1846,7 +1768,7 @@
       <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie</td>
       <td>20230328</td>
       <td>Fiji</td>
-      <td>20231211</td>
+      <td>20240614</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -1888,9 +1810,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1950,10 +1869,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2024,9 +1940,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2087,9 +2000,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2155,9 +2065,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2168,7 +2075,7 @@
     <tr>
       <td></td>
       <td>imagej2</td>
-      <td>imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary</td>
+      <td>imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary</td>
       <td>ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.</td>
       <td>imagej</td>
       <td>imagej</td>
@@ -2184,7 +2091,7 @@
       <td>imgteam</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2</td>
-      <td>20170530</td>
+      <td>20240614</td>
       <td></td>
       <td></td>
       <td>Image analysis, Image annotation, Visualisation</td>
@@ -2223,9 +2130,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>27</td>
       <td>27</td>
       <td>0</td>
@@ -2254,7 +2158,7 @@
       <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero</td>
       <td>20231221</td>
       <td>Fiji</td>
-      <td>20231211</td>
+      <td>20240614</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -2296,9 +2200,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2364,9 +2265,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2427,9 +2325,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2495,9 +2390,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2563,9 +2455,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2594,7 +2483,7 @@
       <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids</td>
       <td>20221216</td>
       <td>fiji</td>
-      <td>20231211</td>
+      <td>20240614</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -2636,9 +2525,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2699,9 +2585,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2772,16 +2655,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
       <td></td>
       <td>omero</td>
-      <td>omero_import, omero_metadata_import</td>
-      <td>Import images and metadata into an OMERO.server using omero-py</td>
+      <td>omero_import, omero_metadata_import, omero_roi_import</td>
+      <td>Import images, region of interest, metadata into an OMERO.server using omero-py</td>
       <td>omero</td>
       <td>omero</td>
       <td></td>
@@ -2840,9 +2720,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2866,7 +2743,7 @@
       <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables</td>
       <td>20230623</td>
       <td>fiji</td>
-      <td>20231211</td>
+      <td>20240614</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -2908,9 +2785,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2976,9 +2850,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -3002,7 +2873,7 @@
       <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images</td>
       <td>20240521</td>
       <td>fiji</td>
-      <td>20231211</td>
+      <td>20240614</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -3044,9 +2915,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -3070,7 +2938,7 @@
       <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid</td>
       <td>20230809</td>
       <td>fiji</td>
-      <td>20231211</td>
+      <td>20240614</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -3112,9 +2980,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -3138,7 +3003,7 @@
       <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements</td>
       <td>20240214</td>
       <td>fiji</td>
-      <td>20231211</td>
+      <td>20240614</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -3180,9 +3045,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -3248,9 +3110,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -3311,9 +3170,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3379,9 +3235,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3452,9 +3305,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -3476,18 +3326,15 @@
       <td>imgteam</td>
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/</td>
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage</td>
-      <td>0.2</td>
+      <td>0.3</td>
       <td>scikit-image</td>
       <td></td>
       <td>Image analysis</td>
       <td>Imaging, Bioinformatics</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -3544,8 +3391,8 @@
       <td>imgteam</td>
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/</td>
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage</td>
-      <td>0.3-2</td>
-      <td>numpy</td>
+      <td>0.4</td>
+      <td>scikit-image</td>
       <td></td>
       <td>Image analysis</td>
       <td>Imaging, Bioinformatics</td>
@@ -3583,9 +3430,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3651,9 +3495,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3719,9 +3560,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3787,9 +3625,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3816,7 +3651,7 @@
       <td>galaxyp</td>
       <td>hhttps://github.com/npinter/ROIsplitter</td>
       <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter</td>
-      <td>0.3.1</td>
+      <td>0.3.2</td>
       <td>geojson</td>
       <td></td>
       <td></td>
@@ -3855,9 +3690,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3928,9 +3760,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -3995,9 +3824,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>7</td>
       <td></td>
     </tr>
@@ -4059,9 +3885,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4127,9 +3950,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4195,9 +4015,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4263,9 +4080,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4292,9 +4106,9 @@
       <td>imgteam</td>
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/</td>
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d</td>
-      <td>0.0.3-2</td>
-      <td>imageio</td>
-      <td></td>
+      <td>0.1</td>
+      <td>giatools</td>
+      <td>0.3.1</td>
       <td>Image analysis</td>
       <td>Imaging, Bioinformatics</td>
       <td>0</td>
@@ -4331,9 +4145,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4398,10 +4209,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4430,7 +4238,7 @@
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm</td>
       <td>0.2.0</td>
       <td>superdsm</td>
-      <td>0.3.0</td>
+      <td>0.4.0</td>
       <td>Image analysis</td>
       <td></td>
       <td>0</td>
@@ -4467,9 +4275,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4540,9 +4345,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -4603,9 +4405,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4676,9 +4475,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -4744,9 +4540,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -4807,9 +4600,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
diff --git a/communities/imaging/resources/tools.tsv b/communities/imaging/resources/tools.tsv
index 16acb3d7..9fd99532 100644
--- a/communities/imaging/resources/tools.tsv
+++ b/communities/imaging/resources/tools.tsv
@@ -1,70 +1,70 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on BF2I-MAP	Tools available on BioBix	Tools available on CIRM-CFBP	Tools available on Center for Phage Technology (CPT)	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-2d_auto_threshold	ip_threshold	Automatic thresholding	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_auto_threshold	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	6541	False		
-2d_feature_extraction	ip_2d_feature_extraction	2D feature extraction	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_feature_extraction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	19	13760	False		
-2d_filter_segmentation_by_features	ip_2d_filter_segmentation_by_features	filter segmentation by rules	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	2d_filter_segmentation_by_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features	0.0.1-4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	6834	False		
-2d_histogram_equalization	ip_histogram_equalization	2d histogram equalization	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_histogram_equalization	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	656	False		
-2d_simple_filter	ip_filter_standard	2d simple filter			scipy					To update	https://github.com/bmcv	Imaging	2d_simple_filter	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter	1.12.0	scipy				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	35	6156	False		
-3d_tensor_feature_dimension_reduction	ip_3d_tensor_feature_dimension_reduction	Dimensionality reduction for features (channels) of 3D tensor data using UMAP								To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	3d_tensor_feature_dimension_reduction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction	0.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-anisotropic_diffusion	ip_anisotropic_diffusion	Anisotropic image diffusion								Up-to-date	https://github.com/bmcv	Imaging	anisotropic_diffusion	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion	0.4.0	medpy	0.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	40	False		
-background_removal	background_removal	Background removal filters using scikit-image								To update	https://github.com/bmcv	Imaging	background_removal	imgteam	https://github.com/BMCV/galaxy-image-analysis/tools/background_removal	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal	0.24.0	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bfconvert	ip_convertimage	Convert image			python-bioformats					Up-to-date	https://github.com/bmcv	Imaging, Convert Formats	bfconvert	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert	6.7.0	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	38	1523	False		
-bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	False		
-binary2labelimage	ip_binary_to_labelimage	Binary 2 label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binary2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage	0.5	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	1273	False		
-binaryimage2points	ip_binaryimage_to_points	Binary Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binaryimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points	0.1-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	29	False		
-bioformats2raw	bf2raw	Convert image to OME-Zarr								To update	https://github.com/Euro-BioImaging	Imaging, Convert Formats	bioformats2raw	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	0.7.0					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	False		
-bioimaging	bioimage_inference	Load model from BioImage.IO and make inferences	pytorch	pytorch	pytorch	PyTorch	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.		Machine learning, Computer science	To update	https://github.com/bgruening/galaxytools	Imaging	bioimage_inference	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging	https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging	2.3.1	python			Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.10	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-cellprofiler	cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	19	0	23	23	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	23	19	0	178	4614	False		
-cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update	https://github.com/CellProfiler/CellProfiler	Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.7					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	43	False		
-color-deconvolution	ip_color_deconvolution	Color-deconvolution methods	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	color_deconvolution	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution	0.8-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	16	False		
-colorize_labels	colorize_labels	Colorize label map								To update	https://github.com/bmcv	Imaging	colorize_labels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	3.2.1	networkx				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-concat_channels	ip_concat_channels	Concatenate images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	concat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels	0.3-1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	78	False		
-coordinates_of_roi	ip_coordinates_of_roi	Coordinates of ROI	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	coordinates_of_roi	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi	0.0.4-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	16546	False		
-count_objects	ip_count_objects	Count Objects	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	count_objects	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects	0.0.5-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	25	272	False		
-curve_fitting	ip_curve_fitting	Polynomial curve fitting to data points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	curve_fitting	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	12	False		
-detection_viz	ip_detection_viz	Detection Visualization	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	detection_viz	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	46	False		
-graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.44	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	43	2605	False		
-hyperstack_to_bleach_corrected_movie	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack								To update		Imaging	hyperstack_to_bleach_corrected_movie	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	20230328	Fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-image_info	ip_imageinfo	Extracts image metadata			python-bioformats					To update	https://github.com/bmcv	Imaging	image_info	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info	5.7.1	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	41	621	False		
-image_math	image_math	Process images using arithmetic expressions								To update	https://github.com/bmcv	Imaging	image_math	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	1.26.4	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-image_registration_affine	ip_image_registration	Intensity-based Image Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	image_registration_affine	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine	0.0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	12	False		
-imagecoordinates_flipaxis	imagecoordinates_flipaxis	Flip coordinate axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	imagecoordinates_flipaxis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis	0.1-2	pandas		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	21825	False		
-imagej2	imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	20170530			Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	0	26	1537	False		
-incucyte_stack_and_upload_omero	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server								To update		Imaging	incucyte_stack_and_upload_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	20231221	Fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-label_to_binary	label_to_binary	Convert label map to binary image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	label_to_binary	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-labelimage2points	ip_labelimage_to_points	Label Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	labelimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	36	False		
-landmark_registration	ip_landmark_registration	Landmark Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	landmark_registration	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration	0.1.0-2	scikit-image		Image analysis	Imaging, Bioinformatics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	857	False		
-mahotas-features	ip_mahotas_features	Compute image features using mahotas.			mahotas-feature-computation					To update	https://github.com/luispedro/mahotas	Imaging	mahotas_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features	0.7-2	mahotas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	37	False		
-measure_gastruloids	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index								To update		Imaging	measure_gastruloids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	20221216	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-mergeneighboursinlabelimage	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	mergeneighboursinlabelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	25	False		
-morphological_operations	morphological_operations	Apply morphological operations to images			scipy					To update	https://github.com/bmcv	Imaging	morphological_operations	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	1.12.0	scipy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero	omero_import, omero_metadata_import	Import images and metadata into an OMERO.server using omero-py	omero	omero		OMERO	Client-server Java software for visualisation, management and analysis of biological microscope images.	Image analysis	Imaging, Data visualisation	To update	https://github.com/ome/omero-py/	Imaging	omero_upload	ufz	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	5.18.0	omero-py	5.11.1	Image analysis	Imaging, Data visualisation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_clean_rois_tables	omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down								To update		Imaging	omero_clean_rois_tables	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	20230623	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_get_children_ids	omero_get_children_ids	Get omero id of children of an omero object id								To update		Imaging	omero_get_children_ids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	0.2.0	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_get_full_images	omero_get_full_images	Get full images from omero								To update		Imaging	omero_get_full_images	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	20240521	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_hyperstack_to_fluo_measurements_on_gastruloid	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels								To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	20230809	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_hyperstack_to_gastruloid_measurements	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements								To update		Imaging	omero_hyperstack_to_gastruloid_measurements	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	20240214	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-orientationpy	orientationpy	Compute image orientation			orientationj					Up-to-date	https://github.com/bmcv	Imaging	orientationpy	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	0.2.0.4	orientationpy	0.2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-overlay_images	ip_overlay_images	Overlay two images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	overlay_images	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images	0.0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	60	False		
-permutate_axis	ip_permutate_axis	Permutates axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	permutate_axis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	42	False		
-plantseg	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	plantseg	plantseg		PlantSeg	Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.	Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	To update	https://github.com/bmcv	Imaging	plantseg	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg	1.8.1	plant-seg		Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-points2binaryimage	ip_points_to_binaryimage	Points to Binary Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2binaryimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage	0.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	41	False		
-points2labelimage	ip_points_to_label	Points to label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage	0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	31	False		
-points_association_nn	ip_points_association_nn	Association of points in consecutive frames	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	points_association_nn	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	29	False		
-projective_transformation	ip_projective_transformation	Projective transformation	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation	0.1.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	85	False		
-projective_transformation_points	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation_points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points	0.1.1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	21343	False		
-qupath_roi_splitter	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type								To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter	0.3.1	geojson				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	59	False		
-repeat_channels	repeat_channels	Convert single-channel to multi-channel image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	repeat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-rfove	rfove	Perform segmentation region-based fitting of overlapping ellipses	rfove	rfove		RFOVE	RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.	Image analysis	Cell biology, Biomedical science, Imaging	To update	https://sites.google.com/site/costaspanagiotakis/research/cs	Imaging	rfove	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove	2023.11.12			Image analysis	Cell biology, Biomedical science, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	False		
-scale_image	ip_scale_image	Scale image	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	scale_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image	0.18.3	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	512	False		
-segmetrics	ip_segmetrics	Image segmentation and object detection performance measures	segmetrics	segmetrics	segmetrics	SegMetrics	Image segmentation and object detection performance measures	Image analysis		To update	https://github.com/bmcv	Imaging	segmetrics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics	1.4	segmetrics	1.5	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	3	False		
-slice_image	ip_slice_image	Slice image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image	0.3-4	scikit-image		Image analysis	Imaging, Bioinformatics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	102	False		
-split_labelmap	ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap	0.2-3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	42	False		
-spot_detection_2d	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d	0.0.3-2	imageio		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	16	False		
-spyboat	spyboat	Wavelet analysis for 3d-image stacks								To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	0.1.2	spyboat				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	67	False		
-superdsm	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	superdsm	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm	0.2.0	superdsm	0.3.0	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	16	False		
-upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server								To update		Imaging	upload_roi_and_measures_to_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	0.0.5	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-visceral-evaluatesegmentation	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool			evaluatesegmentation-tool					To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	0.5-2	visceral-evaluatesegmentation	2015.07.03			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	25	False		
-voronoi_tessellation	voronoi_tessellation	Compute Voronoi tesselation	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	voronoi_tesselation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation	0.22.0	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-wsi_extract_top_view	ip_wsi_extract_top_view	WSI Extract Top View								To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view	0.2-2	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	38	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
+2d_auto_threshold	ip_threshold	Automatic thresholding	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_auto_threshold	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39	6541	False		
+2d_feature_extraction	ip_2d_feature_extraction	2D feature extraction	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_feature_extraction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19	13760	False		
+2d_filter_segmentation_by_features	ip_2d_filter_segmentation_by_features	filter segmentation by rules	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	2d_filter_segmentation_by_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features	0.0.1-4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	6834	False		
+2d_histogram_equalization	ip_histogram_equalization	2d histogram equalization	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_histogram_equalization	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39	656	False		
+2d_simple_filter	ip_filter_standard	2d simple filter			scipy					To update	https://github.com/bmcv	Imaging	2d_simple_filter	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter	1.12.0	scipy				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	35	6156	False		
+3d_tensor_feature_dimension_reduction	ip_3d_tensor_feature_dimension_reduction	Dimensionality reduction for features (channels) of 3D tensor data using UMAP								To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	3d_tensor_feature_dimension_reduction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction	0.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+anisotropic_diffusion	ip_anisotropic_diffusion	Anisotropic image diffusion								Up-to-date	https://github.com/bmcv	Imaging	anisotropic_diffusion	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion	0.4.0	medpy	0.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	40	False		
+background_removal	background_removal	Background removal filters using scikit-image								To update	https://github.com/bmcv	Imaging	background_removal	imgteam	https://github.com/BMCV/galaxy-image-analysis/tools/background_removal	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal	0.24.0	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bfconvert	ip_convertimage	Convert image			python-bioformats					Up-to-date	https://github.com/bmcv	Imaging, Convert Formats	bfconvert	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert	6.7.0	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	38	1523	False		
+bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	False		
+binary2labelimage	ip_binary_to_labelimage	Binary 2 label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binary2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage	0.5	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34	1273	False		
+binaryimage2points	ip_binaryimage_to_points	Binary Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binaryimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points	0.1-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	29	False		
+bioformats2raw	bf2raw	Convert image to OME-Zarr								To update	https://github.com/Euro-BioImaging	Imaging, Convert Formats	bioformats2raw	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	0.7.0					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	False		
+bioimaging	bioimage_inference	Load model from BioImage.IO and make inferences	pytorch	pytorch	pytorch	PyTorch	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.		Machine learning, Computer science	To update	https://github.com/bgruening/galaxytools	Imaging	bioimage_inference	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging	https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging	2.4.0	python			Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.10	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cellprofiler	cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	19	0	23	23	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	23	19	0	178	4614	False		
+cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update	https://github.com/CellProfiler/CellProfiler	Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.7					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	43	False		
+color-deconvolution	ip_color_deconvolution	Color-deconvolution methods	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	color_deconvolution	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution	0.8-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	16	False		
+colorize_labels	colorize_labels	Colorize label map								To update	https://github.com/bmcv	Imaging	colorize_labels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	3.2.1	networkx				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+concat_channels	ip_concat_channels	Concatenate images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	concat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels	0.3-1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	78	False		
+coordinates_of_roi	ip_coordinates_of_roi	Coordinates of ROI	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	coordinates_of_roi	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi	0.0.4-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	16546	False		
+count_objects	ip_count_objects	Count Objects	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	count_objects	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects	0.0.5-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	25	272	False		
+curve_fitting	ip_curve_fitting	Polynomial curve fitting to data points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	curve_fitting	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	12	False		
+detection_viz	ip_detection_viz	Detection Visualization	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	detection_viz	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	46	False		
+graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.45	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	43	2605	False		
+hyperstack_to_bleach_corrected_movie	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack								To update		Imaging	hyperstack_to_bleach_corrected_movie	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	20230328	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+image_info	ip_imageinfo	Extracts image metadata			python-bioformats					To update	https://github.com/bmcv	Imaging	image_info	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info	5.7.1	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	41	621	False		
+image_math	image_math	Process images using arithmetic expressions								To update	https://github.com/bmcv	Imaging	image_math	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	1.26.4	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+image_registration_affine	ip_image_registration	Intensity-based Image Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	image_registration_affine	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine	0.0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	12	False		
+imagecoordinates_flipaxis	imagecoordinates_flipaxis	Flip coordinate axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	imagecoordinates_flipaxis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis	0.1-2	pandas		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	21825	False		
+imagej2	imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	20240614			Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	0	26	1537	False		
+incucyte_stack_and_upload_omero	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server								To update		Imaging	incucyte_stack_and_upload_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	20231221	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+label_to_binary	label_to_binary	Convert label map to binary image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	label_to_binary	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+labelimage2points	ip_labelimage_to_points	Label Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	labelimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	36	False		
+landmark_registration	ip_landmark_registration	Landmark Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	landmark_registration	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration	0.1.0-2	scikit-image		Image analysis	Imaging, Bioinformatics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	857	False		
+mahotas-features	ip_mahotas_features	Compute image features using mahotas.			mahotas-feature-computation					To update	https://github.com/luispedro/mahotas	Imaging	mahotas_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features	0.7-2	mahotas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	37	False		
+measure_gastruloids	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index								To update		Imaging	measure_gastruloids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	20221216	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mergeneighboursinlabelimage	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	mergeneighboursinlabelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	25	False		
+morphological_operations	morphological_operations	Apply morphological operations to images			scipy					To update	https://github.com/bmcv	Imaging	morphological_operations	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	1.12.0	scipy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero	omero_import, omero_metadata_import, omero_roi_import	Import images, region of interest, metadata into an OMERO.server using omero-py	omero	omero		OMERO	Client-server Java software for visualisation, management and analysis of biological microscope images.	Image analysis	Imaging, Data visualisation	To update	https://github.com/ome/omero-py/	Imaging	omero_upload	ufz	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	5.18.0	omero-py	5.11.1	Image analysis	Imaging, Data visualisation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_clean_rois_tables	omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down								To update		Imaging	omero_clean_rois_tables	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	20230623	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_get_children_ids	omero_get_children_ids	Get omero id of children of an omero object id								To update		Imaging	omero_get_children_ids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	0.2.0	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_get_full_images	omero_get_full_images	Get full images from omero								To update		Imaging	omero_get_full_images	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	20240521	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_hyperstack_to_fluo_measurements_on_gastruloid	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels								To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	20230809	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_hyperstack_to_gastruloid_measurements	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements								To update		Imaging	omero_hyperstack_to_gastruloid_measurements	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	20240214	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+orientationpy	orientationpy	Compute image orientation			orientationj					Up-to-date	https://github.com/bmcv	Imaging	orientationpy	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	0.2.0.4	orientationpy	0.2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+overlay_images	ip_overlay_images	Overlay two images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	overlay_images	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images	0.0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	60	False		
+permutate_axis	ip_permutate_axis	Permutates axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	permutate_axis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	42	False		
+plantseg	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	plantseg	plantseg		PlantSeg	Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.	Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	To update	https://github.com/bmcv	Imaging	plantseg	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg	1.8.1	plant-seg		Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+points2binaryimage	ip_points_to_binaryimage	Points to Binary Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2binaryimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage	0.3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	41	False		
+points2labelimage	ip_points_to_label	Points to label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage	0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	31	False		
+points_association_nn	ip_points_association_nn	Association of points in consecutive frames	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	points_association_nn	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	29	False		
+projective_transformation	ip_projective_transformation	Projective transformation	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation	0.1.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	85	False		
+projective_transformation_points	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation_points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points	0.1.1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	21343	False		
+qupath_roi_splitter	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type								To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter	0.3.2	geojson				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	59	False		
+repeat_channels	repeat_channels	Convert single-channel to multi-channel image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	repeat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rfove	rfove	Perform segmentation region-based fitting of overlapping ellipses	rfove	rfove		RFOVE	RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.	Image analysis	Cell biology, Biomedical science, Imaging	To update	https://sites.google.com/site/costaspanagiotakis/research/cs	Imaging	rfove	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove	2023.11.12			Image analysis	Cell biology, Biomedical science, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	False		
+scale_image	ip_scale_image	Scale image	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	scale_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image	0.18.3	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	512	False		
+segmetrics	ip_segmetrics	Image segmentation and object detection performance measures	segmetrics	segmetrics	segmetrics	SegMetrics	Image segmentation and object detection performance measures	Image analysis		To update	https://github.com/bmcv	Imaging	segmetrics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics	1.4	segmetrics	1.5	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	3	False		
+slice_image	ip_slice_image	Slice image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image	0.3-4	scikit-image		Image analysis	Imaging, Bioinformatics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	102	False		
+split_labelmap	ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap	0.2-3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	42	False		
+spot_detection_2d	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d	0.1	giatools	0.3.1	Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	16	False		
+spyboat	spyboat	Wavelet analysis for 3d-image stacks								To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	0.1.2	spyboat				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	67	False		
+superdsm	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	superdsm	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm	0.2.0	superdsm	0.4.0	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	16	False		
+upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server								To update		Imaging	upload_roi_and_measures_to_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	0.0.5	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+visceral-evaluatesegmentation	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool			evaluatesegmentation-tool					To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	0.5-2	visceral-evaluatesegmentation	2015.07.03			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	25	False		
+voronoi_tessellation	voronoi_tessellation	Compute Voronoi tesselation	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	voronoi_tesselation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation	0.22.0	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+wsi_extract_top_view	ip_wsi_extract_top_view	WSI Extract Top View								To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view	0.2-2	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	38	False		
diff --git a/communities/imaging/resources/tools_filtered_by_ts_categories.tsv b/communities/imaging/resources/tools_filtered_by_ts_categories.tsv
index 16acb3d7..9fd99532 100644
--- a/communities/imaging/resources/tools_filtered_by_ts_categories.tsv
+++ b/communities/imaging/resources/tools_filtered_by_ts_categories.tsv
@@ -1,70 +1,70 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on BF2I-MAP	Tools available on BioBix	Tools available on CIRM-CFBP	Tools available on Center for Phage Technology (CPT)	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-2d_auto_threshold	ip_threshold	Automatic thresholding	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_auto_threshold	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	6541	False		
-2d_feature_extraction	ip_2d_feature_extraction	2D feature extraction	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_feature_extraction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	19	13760	False		
-2d_filter_segmentation_by_features	ip_2d_filter_segmentation_by_features	filter segmentation by rules	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	2d_filter_segmentation_by_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features	0.0.1-4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	6834	False		
-2d_histogram_equalization	ip_histogram_equalization	2d histogram equalization	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_histogram_equalization	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	656	False		
-2d_simple_filter	ip_filter_standard	2d simple filter			scipy					To update	https://github.com/bmcv	Imaging	2d_simple_filter	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter	1.12.0	scipy				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	35	6156	False		
-3d_tensor_feature_dimension_reduction	ip_3d_tensor_feature_dimension_reduction	Dimensionality reduction for features (channels) of 3D tensor data using UMAP								To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	3d_tensor_feature_dimension_reduction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction	0.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-anisotropic_diffusion	ip_anisotropic_diffusion	Anisotropic image diffusion								Up-to-date	https://github.com/bmcv	Imaging	anisotropic_diffusion	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion	0.4.0	medpy	0.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	40	False		
-background_removal	background_removal	Background removal filters using scikit-image								To update	https://github.com/bmcv	Imaging	background_removal	imgteam	https://github.com/BMCV/galaxy-image-analysis/tools/background_removal	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal	0.24.0	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bfconvert	ip_convertimage	Convert image			python-bioformats					Up-to-date	https://github.com/bmcv	Imaging, Convert Formats	bfconvert	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert	6.7.0	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	38	1523	False		
-bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	False		
-binary2labelimage	ip_binary_to_labelimage	Binary 2 label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binary2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage	0.5	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	1273	False		
-binaryimage2points	ip_binaryimage_to_points	Binary Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binaryimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points	0.1-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	29	False		
-bioformats2raw	bf2raw	Convert image to OME-Zarr								To update	https://github.com/Euro-BioImaging	Imaging, Convert Formats	bioformats2raw	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	0.7.0					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	False		
-bioimaging	bioimage_inference	Load model from BioImage.IO and make inferences	pytorch	pytorch	pytorch	PyTorch	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.		Machine learning, Computer science	To update	https://github.com/bgruening/galaxytools	Imaging	bioimage_inference	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging	https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging	2.3.1	python			Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.10	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-cellprofiler	cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	19	0	23	23	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	23	19	0	178	4614	False		
-cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update	https://github.com/CellProfiler/CellProfiler	Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.7					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	43	False		
-color-deconvolution	ip_color_deconvolution	Color-deconvolution methods	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	color_deconvolution	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution	0.8-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	16	False		
-colorize_labels	colorize_labels	Colorize label map								To update	https://github.com/bmcv	Imaging	colorize_labels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	3.2.1	networkx				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-concat_channels	ip_concat_channels	Concatenate images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	concat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels	0.3-1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	78	False		
-coordinates_of_roi	ip_coordinates_of_roi	Coordinates of ROI	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	coordinates_of_roi	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi	0.0.4-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	16546	False		
-count_objects	ip_count_objects	Count Objects	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	count_objects	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects	0.0.5-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	25	272	False		
-curve_fitting	ip_curve_fitting	Polynomial curve fitting to data points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	curve_fitting	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	12	False		
-detection_viz	ip_detection_viz	Detection Visualization	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	detection_viz	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	46	False		
-graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.44	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	43	2605	False		
-hyperstack_to_bleach_corrected_movie	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack								To update		Imaging	hyperstack_to_bleach_corrected_movie	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	20230328	Fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-image_info	ip_imageinfo	Extracts image metadata			python-bioformats					To update	https://github.com/bmcv	Imaging	image_info	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info	5.7.1	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	41	621	False		
-image_math	image_math	Process images using arithmetic expressions								To update	https://github.com/bmcv	Imaging	image_math	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	1.26.4	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-image_registration_affine	ip_image_registration	Intensity-based Image Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	image_registration_affine	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine	0.0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	12	False		
-imagecoordinates_flipaxis	imagecoordinates_flipaxis	Flip coordinate axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	imagecoordinates_flipaxis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis	0.1-2	pandas		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	21825	False		
-imagej2	imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	20170530			Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	0	26	1537	False		
-incucyte_stack_and_upload_omero	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server								To update		Imaging	incucyte_stack_and_upload_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	20231221	Fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-label_to_binary	label_to_binary	Convert label map to binary image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	label_to_binary	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-labelimage2points	ip_labelimage_to_points	Label Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	labelimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	36	False		
-landmark_registration	ip_landmark_registration	Landmark Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	landmark_registration	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration	0.1.0-2	scikit-image		Image analysis	Imaging, Bioinformatics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	857	False		
-mahotas-features	ip_mahotas_features	Compute image features using mahotas.			mahotas-feature-computation					To update	https://github.com/luispedro/mahotas	Imaging	mahotas_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features	0.7-2	mahotas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	37	False		
-measure_gastruloids	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index								To update		Imaging	measure_gastruloids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	20221216	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-mergeneighboursinlabelimage	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	mergeneighboursinlabelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	25	False		
-morphological_operations	morphological_operations	Apply morphological operations to images			scipy					To update	https://github.com/bmcv	Imaging	morphological_operations	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	1.12.0	scipy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero	omero_import, omero_metadata_import	Import images and metadata into an OMERO.server using omero-py	omero	omero		OMERO	Client-server Java software for visualisation, management and analysis of biological microscope images.	Image analysis	Imaging, Data visualisation	To update	https://github.com/ome/omero-py/	Imaging	omero_upload	ufz	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	5.18.0	omero-py	5.11.1	Image analysis	Imaging, Data visualisation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_clean_rois_tables	omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down								To update		Imaging	omero_clean_rois_tables	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	20230623	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_get_children_ids	omero_get_children_ids	Get omero id of children of an omero object id								To update		Imaging	omero_get_children_ids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	0.2.0	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_get_full_images	omero_get_full_images	Get full images from omero								To update		Imaging	omero_get_full_images	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	20240521	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_hyperstack_to_fluo_measurements_on_gastruloid	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels								To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	20230809	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_hyperstack_to_gastruloid_measurements	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements								To update		Imaging	omero_hyperstack_to_gastruloid_measurements	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	20240214	fiji	20231211			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-orientationpy	orientationpy	Compute image orientation			orientationj					Up-to-date	https://github.com/bmcv	Imaging	orientationpy	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	0.2.0.4	orientationpy	0.2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-overlay_images	ip_overlay_images	Overlay two images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	overlay_images	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images	0.0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	60	False		
-permutate_axis	ip_permutate_axis	Permutates axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	permutate_axis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	42	False		
-plantseg	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	plantseg	plantseg		PlantSeg	Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.	Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	To update	https://github.com/bmcv	Imaging	plantseg	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg	1.8.1	plant-seg		Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-points2binaryimage	ip_points_to_binaryimage	Points to Binary Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2binaryimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage	0.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	41	False		
-points2labelimage	ip_points_to_label	Points to label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage	0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	31	False		
-points_association_nn	ip_points_association_nn	Association of points in consecutive frames	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	points_association_nn	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	29	False		
-projective_transformation	ip_projective_transformation	Projective transformation	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation	0.1.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	85	False		
-projective_transformation_points	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation_points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points	0.1.1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	21343	False		
-qupath_roi_splitter	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type								To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter	0.3.1	geojson				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	59	False		
-repeat_channels	repeat_channels	Convert single-channel to multi-channel image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	repeat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-rfove	rfove	Perform segmentation region-based fitting of overlapping ellipses	rfove	rfove		RFOVE	RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.	Image analysis	Cell biology, Biomedical science, Imaging	To update	https://sites.google.com/site/costaspanagiotakis/research/cs	Imaging	rfove	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove	2023.11.12			Image analysis	Cell biology, Biomedical science, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	False		
-scale_image	ip_scale_image	Scale image	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	scale_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image	0.18.3	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	512	False		
-segmetrics	ip_segmetrics	Image segmentation and object detection performance measures	segmetrics	segmetrics	segmetrics	SegMetrics	Image segmentation and object detection performance measures	Image analysis		To update	https://github.com/bmcv	Imaging	segmetrics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics	1.4	segmetrics	1.5	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	3	False		
-slice_image	ip_slice_image	Slice image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image	0.3-4	scikit-image		Image analysis	Imaging, Bioinformatics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	102	False		
-split_labelmap	ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap	0.2-3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	42	False		
-spot_detection_2d	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d	0.0.3-2	imageio		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	16	False		
-spyboat	spyboat	Wavelet analysis for 3d-image stacks								To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	0.1.2	spyboat				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	67	False		
-superdsm	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	superdsm	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm	0.2.0	superdsm	0.3.0	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	16	False		
-upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server								To update		Imaging	upload_roi_and_measures_to_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	0.0.5	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-visceral-evaluatesegmentation	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool			evaluatesegmentation-tool					To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	0.5-2	visceral-evaluatesegmentation	2015.07.03			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	25	False		
-voronoi_tessellation	voronoi_tessellation	Compute Voronoi tesselation	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	voronoi_tesselation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation	0.22.0	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-wsi_extract_top_view	ip_wsi_extract_top_view	WSI Extract Top View								To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view	0.2-2	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	38	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
+2d_auto_threshold	ip_threshold	Automatic thresholding	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_auto_threshold	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39	6541	False		
+2d_feature_extraction	ip_2d_feature_extraction	2D feature extraction	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_feature_extraction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19	13760	False		
+2d_filter_segmentation_by_features	ip_2d_filter_segmentation_by_features	filter segmentation by rules	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	2d_filter_segmentation_by_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features	0.0.1-4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	6834	False		
+2d_histogram_equalization	ip_histogram_equalization	2d histogram equalization	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_histogram_equalization	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39	656	False		
+2d_simple_filter	ip_filter_standard	2d simple filter			scipy					To update	https://github.com/bmcv	Imaging	2d_simple_filter	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter	1.12.0	scipy				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	35	6156	False		
+3d_tensor_feature_dimension_reduction	ip_3d_tensor_feature_dimension_reduction	Dimensionality reduction for features (channels) of 3D tensor data using UMAP								To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	3d_tensor_feature_dimension_reduction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction	0.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+anisotropic_diffusion	ip_anisotropic_diffusion	Anisotropic image diffusion								Up-to-date	https://github.com/bmcv	Imaging	anisotropic_diffusion	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion	0.4.0	medpy	0.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	40	False		
+background_removal	background_removal	Background removal filters using scikit-image								To update	https://github.com/bmcv	Imaging	background_removal	imgteam	https://github.com/BMCV/galaxy-image-analysis/tools/background_removal	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal	0.24.0	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bfconvert	ip_convertimage	Convert image			python-bioformats					Up-to-date	https://github.com/bmcv	Imaging, Convert Formats	bfconvert	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert	6.7.0	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	38	1523	False		
+bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	False		
+binary2labelimage	ip_binary_to_labelimage	Binary 2 label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binary2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage	0.5	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34	1273	False		
+binaryimage2points	ip_binaryimage_to_points	Binary Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binaryimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points	0.1-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	29	False		
+bioformats2raw	bf2raw	Convert image to OME-Zarr								To update	https://github.com/Euro-BioImaging	Imaging, Convert Formats	bioformats2raw	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	0.7.0					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	False		
+bioimaging	bioimage_inference	Load model from BioImage.IO and make inferences	pytorch	pytorch	pytorch	PyTorch	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.		Machine learning, Computer science	To update	https://github.com/bgruening/galaxytools	Imaging	bioimage_inference	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging	https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging	2.4.0	python			Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.10	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cellprofiler	cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	19	0	23	23	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	23	19	0	178	4614	False		
+cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update	https://github.com/CellProfiler/CellProfiler	Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.7					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	43	False		
+color-deconvolution	ip_color_deconvolution	Color-deconvolution methods	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	color_deconvolution	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution	0.8-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	16	False		
+colorize_labels	colorize_labels	Colorize label map								To update	https://github.com/bmcv	Imaging	colorize_labels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	3.2.1	networkx				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+concat_channels	ip_concat_channels	Concatenate images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	concat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels	0.3-1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	78	False		
+coordinates_of_roi	ip_coordinates_of_roi	Coordinates of ROI	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	coordinates_of_roi	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi	0.0.4-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	16546	False		
+count_objects	ip_count_objects	Count Objects	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	count_objects	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects	0.0.5-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	25	272	False		
+curve_fitting	ip_curve_fitting	Polynomial curve fitting to data points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	curve_fitting	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	12	False		
+detection_viz	ip_detection_viz	Detection Visualization	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	detection_viz	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	46	False		
+graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.45	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	43	2605	False		
+hyperstack_to_bleach_corrected_movie	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack								To update		Imaging	hyperstack_to_bleach_corrected_movie	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	20230328	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+image_info	ip_imageinfo	Extracts image metadata			python-bioformats					To update	https://github.com/bmcv	Imaging	image_info	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info	5.7.1	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	41	621	False		
+image_math	image_math	Process images using arithmetic expressions								To update	https://github.com/bmcv	Imaging	image_math	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	1.26.4	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+image_registration_affine	ip_image_registration	Intensity-based Image Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	image_registration_affine	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine	0.0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	12	False		
+imagecoordinates_flipaxis	imagecoordinates_flipaxis	Flip coordinate axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	imagecoordinates_flipaxis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis	0.1-2	pandas		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	21825	False		
+imagej2	imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	20240614			Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	0	26	1537	False		
+incucyte_stack_and_upload_omero	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server								To update		Imaging	incucyte_stack_and_upload_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	20231221	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+label_to_binary	label_to_binary	Convert label map to binary image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	label_to_binary	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+labelimage2points	ip_labelimage_to_points	Label Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	labelimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	36	False		
+landmark_registration	ip_landmark_registration	Landmark Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	landmark_registration	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration	0.1.0-2	scikit-image		Image analysis	Imaging, Bioinformatics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	857	False		
+mahotas-features	ip_mahotas_features	Compute image features using mahotas.			mahotas-feature-computation					To update	https://github.com/luispedro/mahotas	Imaging	mahotas_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features	0.7-2	mahotas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	37	False		
+measure_gastruloids	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index								To update		Imaging	measure_gastruloids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	20221216	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mergeneighboursinlabelimage	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	mergeneighboursinlabelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	25	False		
+morphological_operations	morphological_operations	Apply morphological operations to images			scipy					To update	https://github.com/bmcv	Imaging	morphological_operations	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	1.12.0	scipy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero	omero_import, omero_metadata_import, omero_roi_import	Import images, region of interest, metadata into an OMERO.server using omero-py	omero	omero		OMERO	Client-server Java software for visualisation, management and analysis of biological microscope images.	Image analysis	Imaging, Data visualisation	To update	https://github.com/ome/omero-py/	Imaging	omero_upload	ufz	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	5.18.0	omero-py	5.11.1	Image analysis	Imaging, Data visualisation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_clean_rois_tables	omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down								To update		Imaging	omero_clean_rois_tables	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	20230623	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_get_children_ids	omero_get_children_ids	Get omero id of children of an omero object id								To update		Imaging	omero_get_children_ids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	0.2.0	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_get_full_images	omero_get_full_images	Get full images from omero								To update		Imaging	omero_get_full_images	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	20240521	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_hyperstack_to_fluo_measurements_on_gastruloid	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels								To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	20230809	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_hyperstack_to_gastruloid_measurements	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements								To update		Imaging	omero_hyperstack_to_gastruloid_measurements	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	20240214	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+orientationpy	orientationpy	Compute image orientation			orientationj					Up-to-date	https://github.com/bmcv	Imaging	orientationpy	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	0.2.0.4	orientationpy	0.2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+overlay_images	ip_overlay_images	Overlay two images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	overlay_images	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images	0.0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	60	False		
+permutate_axis	ip_permutate_axis	Permutates axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	permutate_axis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	42	False		
+plantseg	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	plantseg	plantseg		PlantSeg	Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.	Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	To update	https://github.com/bmcv	Imaging	plantseg	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg	1.8.1	plant-seg		Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+points2binaryimage	ip_points_to_binaryimage	Points to Binary Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2binaryimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage	0.3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	41	False		
+points2labelimage	ip_points_to_label	Points to label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage	0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	31	False		
+points_association_nn	ip_points_association_nn	Association of points in consecutive frames	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	points_association_nn	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	29	False		
+projective_transformation	ip_projective_transformation	Projective transformation	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation	0.1.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	85	False		
+projective_transformation_points	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation_points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points	0.1.1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	21343	False		
+qupath_roi_splitter	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type								To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter	0.3.2	geojson				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	59	False		
+repeat_channels	repeat_channels	Convert single-channel to multi-channel image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	repeat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rfove	rfove	Perform segmentation region-based fitting of overlapping ellipses	rfove	rfove		RFOVE	RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.	Image analysis	Cell biology, Biomedical science, Imaging	To update	https://sites.google.com/site/costaspanagiotakis/research/cs	Imaging	rfove	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove	2023.11.12			Image analysis	Cell biology, Biomedical science, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	False		
+scale_image	ip_scale_image	Scale image	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	scale_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image	0.18.3	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	512	False		
+segmetrics	ip_segmetrics	Image segmentation and object detection performance measures	segmetrics	segmetrics	segmetrics	SegMetrics	Image segmentation and object detection performance measures	Image analysis		To update	https://github.com/bmcv	Imaging	segmetrics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics	1.4	segmetrics	1.5	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	3	False		
+slice_image	ip_slice_image	Slice image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image	0.3-4	scikit-image		Image analysis	Imaging, Bioinformatics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	102	False		
+split_labelmap	ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap	0.2-3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	42	False		
+spot_detection_2d	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d	0.1	giatools	0.3.1	Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	16	False		
+spyboat	spyboat	Wavelet analysis for 3d-image stacks								To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	0.1.2	spyboat				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	67	False		
+superdsm	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	superdsm	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm	0.2.0	superdsm	0.4.0	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	16	False		
+upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server								To update		Imaging	upload_roi_and_measures_to_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	0.0.5	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+visceral-evaluatesegmentation	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool			evaluatesegmentation-tool					To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	0.5-2	visceral-evaluatesegmentation	2015.07.03			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	25	False		
+voronoi_tessellation	voronoi_tessellation	Compute Voronoi tesselation	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	voronoi_tesselation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation	0.22.0	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+wsi_extract_top_view	ip_wsi_extract_top_view	WSI Extract Top View								To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view	0.2-2	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	38	False		
diff --git a/communities/machine-learning/resources/tools.html b/communities/machine-learning/resources/tools.html
index 70da80fe..f8ba0823 100644
--- a/communities/machine-learning/resources/tools.html
+++ b/communities/machine-learning/resources/tools.html
@@ -88,10 +88,8 @@
       <th>Tools available on UseGalaxy.eu</th>
       <th>Tools available on UseGalaxy.fr</th>
       <th>Tools available on APOSTL</th>
-      <th>Tools available on BF2I-MAP</th>
-      <th>Tools available on BioBix</th>
+      <th>Tools available on ARGs-OAP</th>
       <th>Tools available on CIRM-CFBP</th>
-      <th>Tools available on Center for Phage Technology (CPT)</th>
       <th>Tools available on ChemFlow</th>
       <th>Tools available on Coloc-stats</th>
       <th>Tools available on CoralSNP</th>
@@ -114,7 +112,6 @@
       <th>Tools available on Oqtans</th>
       <th>Tools available on Palfinder</th>
       <th>Tools available on PepSimili</th>
-      <th>Tools available on PhagePromotor</th>
       <th>Tools available on UseGalaxy.be</th>
       <th>Tools available on UseGalaxy.cz</th>
       <th>Tools available on UseGalaxy.no</th>
@@ -187,9 +184,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>13</td>
       <td></td>
     </tr>
@@ -256,9 +250,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -324,9 +315,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -387,9 +375,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -455,9 +440,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -528,9 +510,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -590,10 +569,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>29</td>
       <td>31</td>
       <td>27</td>
       <td>0</td>
@@ -658,10 +634,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -727,9 +700,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -800,9 +770,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td></td>
     </tr>
   </tbody>
diff --git a/communities/machine-learning/resources/tools.tsv b/communities/machine-learning/resources/tools.tsv
index 39af4e6f..a9ba70a9 100644
--- a/communities/machine-learning/resources/tools.tsv
+++ b/communities/machine-learning/resources/tools.tsv
@@ -1,12 +1,12 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on BF2I-MAP	Tools available on BioBix	Tools available on CIRM-CFBP	Tools available on Center for Phage Technology (CPT)	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-biomodelsML	biomodels_biomd0000001066, biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.								To update	https://www.ebi.ac.uk/biomodels/	Machine Learning	biomodels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML	1.1					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	False		
-chatgpt	chatgpt_openai_api	Using the OpenAI GPT models to generate text based on user input.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	Machine Learning	chatgpt_openai_api	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	2024	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-chopin2	chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing								To update	https://github.com/cumbof/chopin2	Machine Learning	chopin2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2	1.0.9.post1	chopin2				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-decontaminator	decontaminator	Deep Learning method for novel virus detection in sequencing data	decontaminator	decontaminator		decontaminator	Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.	Filtering	Metagenomics	To update	https://github.com/cbib/decontaminator	Machine Learning	decontaminator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator	1.0.0	numpy		Filtering	Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	99	False		
-deepmicro	deepmicro	Representation learning and classification framework	DeepMicro	DeepMicro		DeepMicro	Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.	Essential dynamics, Splitting, Community profiling	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	Up-to-date	https://github.com/paulzierep/DeepMicro	Machine Learning	deepmicro	iuc	https://github.com/paulzierep/DeepMicro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro	1.4	deepmicro	1.4	Essential dynamics, Splitting	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	501	False		
-flexynesis	flexynesis	This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.								Up-to-date	https://github.com/BIMSBbioinfo/flexynesis/tree/main	Machine Learning, Statistics, Systems Biology	flexynesis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis	https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis	0.2.10	flexynesis	0.2.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-jupyter_job	run_jupyter_job	Run jupyter notebook script in Galaxy								To update		Machine Learning	run_jupyter_job	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	0.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	30	True	False	False
-sklearn	sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split	Machine Learning tool suite from Scikit-learn								To update	http://scikit-learn.org	Machine Learning, Statistics	sklearn	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	1.0.11.0					30	14	31	16	30	14	31	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	27	0	958	113932	False		
-tool_recommendation_model	create_tool_recommendation_model	Create model to recommend tools								To update	https://github.com/bgruening/galaxytools	Machine Learning	create_tool_recommendation_model	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model	https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model	0.0.5	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	445	False		
-virhunter	virhunter	Deep Learning method for novel virus detection in sequencing data	virhunter	virhunter		VirHunter	VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).	Sequence classification	Virology	To update	https://github.com/cbib/virhunter	Machine Learning	virhunter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter	1.0.0	numpy		Sequence classification	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	234	False		
-whisper	whisper	Transcribe audio or video files to text using the OpenAI Whisper.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	Machine Learning	whisper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	20231117					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
+biomodelsML	biomodels_biomd0000001066, biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.								To update	https://www.ebi.ac.uk/biomodels/	Machine Learning	biomodels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML	1.1					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	False		
+chatgpt	chatgpt_openai_api	Using the OpenAI GPT models to generate text based on user input.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	Machine Learning	chatgpt_openai_api	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	2024	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+chopin2	chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing								To update	https://github.com/cumbof/chopin2	Machine Learning	chopin2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2	1.0.9.post1	chopin2				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+decontaminator	decontaminator	Deep Learning method for novel virus detection in sequencing data	decontaminator	decontaminator		decontaminator	Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.	Filtering	Metagenomics	To update	https://github.com/cbib/decontaminator	Machine Learning	decontaminator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator	1.0.0	numpy		Filtering	Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	99	False		
+deepmicro	deepmicro	Representation learning and classification framework	DeepMicro	DeepMicro		DeepMicro	Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.	Essential dynamics, Splitting, Community profiling	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	Up-to-date	https://github.com/paulzierep/DeepMicro	Machine Learning	deepmicro	iuc	https://github.com/paulzierep/DeepMicro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro	1.4	deepmicro	1.4	Essential dynamics, Splitting	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	501	False		
+flexynesis	flexynesis	This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.								Up-to-date	https://github.com/BIMSBbioinfo/flexynesis/tree/main	Machine Learning, Statistics, Systems Biology	flexynesis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis	https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis	0.2.10	flexynesis	0.2.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+jupyter_job	run_jupyter_job	Run jupyter notebook script in Galaxy								To update		Machine Learning	run_jupyter_job	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	0.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	30	True	False	False
+sklearn	sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split	Machine Learning tool suite from Scikit-learn								To update	http://scikit-learn.org	Machine Learning, Statistics	sklearn	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	1.0.11.0					30	14	31	16	30	14	31	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	29	31	27	0	958	113932	False		
+tool_recommendation_model	create_tool_recommendation_model	Create model to recommend tools								To update	https://github.com/bgruening/galaxytools	Machine Learning	create_tool_recommendation_model	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model	https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model	0.0.5	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15	445	False		
+virhunter	virhunter	Deep Learning method for novel virus detection in sequencing data	virhunter	virhunter		VirHunter	VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).	Sequence classification	Virology	To update	https://github.com/cbib/virhunter	Machine Learning	virhunter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter	1.0.0	numpy		Sequence classification	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	234	False		
+whisper	whisper	Transcribe audio or video files to text using the OpenAI Whisper.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	Machine Learning	whisper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	20231117					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
diff --git a/communities/machine-learning/resources/tools_filtered_by_ts_categories.tsv b/communities/machine-learning/resources/tools_filtered_by_ts_categories.tsv
index 39af4e6f..a9ba70a9 100644
--- a/communities/machine-learning/resources/tools_filtered_by_ts_categories.tsv
+++ b/communities/machine-learning/resources/tools_filtered_by_ts_categories.tsv
@@ -1,12 +1,12 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on BF2I-MAP	Tools available on BioBix	Tools available on CIRM-CFBP	Tools available on Center for Phage Technology (CPT)	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-biomodelsML	biomodels_biomd0000001066, biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.								To update	https://www.ebi.ac.uk/biomodels/	Machine Learning	biomodels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML	1.1					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	False		
-chatgpt	chatgpt_openai_api	Using the OpenAI GPT models to generate text based on user input.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	Machine Learning	chatgpt_openai_api	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	2024	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-chopin2	chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing								To update	https://github.com/cumbof/chopin2	Machine Learning	chopin2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2	1.0.9.post1	chopin2				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-decontaminator	decontaminator	Deep Learning method for novel virus detection in sequencing data	decontaminator	decontaminator		decontaminator	Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.	Filtering	Metagenomics	To update	https://github.com/cbib/decontaminator	Machine Learning	decontaminator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator	1.0.0	numpy		Filtering	Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	99	False		
-deepmicro	deepmicro	Representation learning and classification framework	DeepMicro	DeepMicro		DeepMicro	Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.	Essential dynamics, Splitting, Community profiling	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	Up-to-date	https://github.com/paulzierep/DeepMicro	Machine Learning	deepmicro	iuc	https://github.com/paulzierep/DeepMicro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro	1.4	deepmicro	1.4	Essential dynamics, Splitting	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	501	False		
-flexynesis	flexynesis	This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.								Up-to-date	https://github.com/BIMSBbioinfo/flexynesis/tree/main	Machine Learning, Statistics, Systems Biology	flexynesis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis	https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis	0.2.10	flexynesis	0.2.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-jupyter_job	run_jupyter_job	Run jupyter notebook script in Galaxy								To update		Machine Learning	run_jupyter_job	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	0.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	30	True	False	False
-sklearn	sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split	Machine Learning tool suite from Scikit-learn								To update	http://scikit-learn.org	Machine Learning, Statistics	sklearn	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	1.0.11.0					30	14	31	16	30	14	31	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	27	0	958	113932	False		
-tool_recommendation_model	create_tool_recommendation_model	Create model to recommend tools								To update	https://github.com/bgruening/galaxytools	Machine Learning	create_tool_recommendation_model	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model	https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model	0.0.5	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	445	False		
-virhunter	virhunter	Deep Learning method for novel virus detection in sequencing data	virhunter	virhunter		VirHunter	VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).	Sequence classification	Virology	To update	https://github.com/cbib/virhunter	Machine Learning	virhunter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter	1.0.0	numpy		Sequence classification	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	234	False		
-whisper	whisper	Transcribe audio or video files to text using the OpenAI Whisper.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	Machine Learning	whisper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	20231117					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
+biomodelsML	biomodels_biomd0000001066, biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.								To update	https://www.ebi.ac.uk/biomodels/	Machine Learning	biomodels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML	1.1					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	False		
+chatgpt	chatgpt_openai_api	Using the OpenAI GPT models to generate text based on user input.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	Machine Learning	chatgpt_openai_api	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	2024	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+chopin2	chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing								To update	https://github.com/cumbof/chopin2	Machine Learning	chopin2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2	1.0.9.post1	chopin2				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+decontaminator	decontaminator	Deep Learning method for novel virus detection in sequencing data	decontaminator	decontaminator		decontaminator	Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.	Filtering	Metagenomics	To update	https://github.com/cbib/decontaminator	Machine Learning	decontaminator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator	1.0.0	numpy		Filtering	Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	99	False		
+deepmicro	deepmicro	Representation learning and classification framework	DeepMicro	DeepMicro		DeepMicro	Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.	Essential dynamics, Splitting, Community profiling	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	Up-to-date	https://github.com/paulzierep/DeepMicro	Machine Learning	deepmicro	iuc	https://github.com/paulzierep/DeepMicro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro	1.4	deepmicro	1.4	Essential dynamics, Splitting	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	501	False		
+flexynesis	flexynesis	This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.								Up-to-date	https://github.com/BIMSBbioinfo/flexynesis/tree/main	Machine Learning, Statistics, Systems Biology	flexynesis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis	https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis	0.2.10	flexynesis	0.2.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+jupyter_job	run_jupyter_job	Run jupyter notebook script in Galaxy								To update		Machine Learning	run_jupyter_job	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	0.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	30	True	False	False
+sklearn	sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split	Machine Learning tool suite from Scikit-learn								To update	http://scikit-learn.org	Machine Learning, Statistics	sklearn	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	1.0.11.0					30	14	31	16	30	14	31	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	29	31	27	0	958	113932	False		
+tool_recommendation_model	create_tool_recommendation_model	Create model to recommend tools								To update	https://github.com/bgruening/galaxytools	Machine Learning	create_tool_recommendation_model	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model	https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model	0.0.5	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15	445	False		
+virhunter	virhunter	Deep Learning method for novel virus detection in sequencing data	virhunter	virhunter		VirHunter	VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).	Sequence classification	Virology	To update	https://github.com/cbib/virhunter	Machine Learning	virhunter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter	1.0.0	numpy		Sequence classification	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	234	False		
+whisper	whisper	Transcribe audio or video files to text using the OpenAI Whisper.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	Machine Learning	whisper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	20231117					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
diff --git a/communities/microgalaxy/resources/tools.html b/communities/microgalaxy/resources/tools.html
index ea2cf691..46ed2739 100644
--- a/communities/microgalaxy/resources/tools.html
+++ b/communities/microgalaxy/resources/tools.html
@@ -88,10 +88,8 @@
       <th>Tools available on UseGalaxy.eu</th>
       <th>Tools available on UseGalaxy.fr</th>
       <th>Tools available on APOSTL</th>
-      <th>Tools available on BF2I-MAP</th>
-      <th>Tools available on BioBix</th>
+      <th>Tools available on ARGs-OAP</th>
       <th>Tools available on CIRM-CFBP</th>
-      <th>Tools available on Center for Phage Technology (CPT)</th>
       <th>Tools available on ChemFlow</th>
       <th>Tools available on Coloc-stats</th>
       <th>Tools available on CoralSNP</th>
@@ -114,7 +112,6 @@
       <th>Tools available on Oqtans</th>
       <th>Tools available on Palfinder</th>
       <th>Tools available on PepSimili</th>
-      <th>Tools available on PhagePromotor</th>
       <th>Tools available on UseGalaxy.be</th>
       <th>Tools available on UseGalaxy.cz</th>
       <th>Tools available on UseGalaxy.no</th>
@@ -183,9 +180,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>4</td>
       <td>0</td>
@@ -237,8 +231,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -253,7 +245,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -305,8 +296,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -326,7 +315,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -371,8 +359,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>3</td>
@@ -388,8 +374,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -409,14 +394,14 @@
       <td>an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.</td>
       <td>Antimicrobial resistance prediction</td>
       <td>Microbiology, Public health and epidemiology, Infectious disease</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://zenodo.org/record/7370628</td>
       <td>Sequence Analysis</td>
       <td>abritamr</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr</td>
-      <td>1.0.14</td>
+      <td>1.0.19</td>
       <td>abritamr</td>
       <td>1.0.19</td>
       <td>Antimicrobial resistance prediction</td>
@@ -460,9 +445,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -477,28 +459,26 @@
       <td>De novo genome sequence assembler using short reads.</td>
       <td>Genome assembly, De-novo assembly, Scaffolding</td>
       <td>Sequence assembly</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://www.bcgsc.ca/platform/bioinfo/software/abyss</td>
       <td>Assembly</td>
       <td>abyss</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss</td>
-      <td>2.3.7</td>
+      <td>2.3.9</td>
       <td>abyss</td>
-      <td>2.3.8</td>
+      <td>2.3.9</td>
       <td>Genome assembly, De-novo assembly, Scaffolding</td>
       <td>Sequence assembly</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -524,8 +504,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -591,9 +570,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -659,9 +635,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -731,9 +704,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>591</td>
       <td>False</td>
     </tr>
@@ -795,9 +765,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -845,8 +812,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -865,7 +830,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -898,14 +862,12 @@
       <td>Sequence alignment</td>
       <td>Genomics</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
+      <td>2</td>
+      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -932,8 +894,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>2</td>
       <td>1</td>
       <td>0</td>
@@ -985,8 +946,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1006,7 +965,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -1021,28 +979,26 @@
       <td>Rapid &amp; standardized annotation of bacterial genomes, MAGs &amp; plasmids</td>
       <td>Genome annotation</td>
       <td>Genomics, Data submission, annotation and curation, Sequence analysis</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/oschwengers/bakta</td>
       <td>Sequence Analysis</td>
       <td>bakta</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta</td>
-      <td>1.9.3</td>
+      <td>1.9.4</td>
       <td>bakta</td>
       <td>1.9.4</td>
       <td>Genome annotation</td>
       <td>Genomics, Data submission, annotation and curation, Sequence analysis</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -1069,7 +1025,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1119,8 +1074,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1136,8 +1089,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1181,8 +1133,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -1204,8 +1154,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -1270,10 +1219,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1293,7 +1239,7 @@
       <td>BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.</td>
       <td>RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment</td>
       <td>Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://jgi.doe.gov/data-and-tools/bbtools/</td>
       <td>Sequence Analysis</td>
       <td>bbtools</td>
@@ -1302,15 +1248,15 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools</td>
       <td>39.08</td>
       <td>bbmap</td>
-      <td>39.08</td>
+      <td>39.09</td>
       <td>RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment</td>
       <td>RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq</td>
       <td>6</td>
-      <td>1</td>
+      <td>3</td>
       <td>5</td>
       <td>0</td>
       <td>6</td>
-      <td>1</td>
+      <td>3</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -1325,8 +1271,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -1341,7 +1285,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -1412,9 +1355,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -1461,8 +1401,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1477,7 +1415,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1548,9 +1485,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -1596,8 +1530,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1612,8 +1544,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1684,9 +1615,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -1722,9 +1650,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -1801,8 +1726,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1817,7 +1740,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1868,10 +1790,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -1935,8 +1854,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -1953,7 +1870,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2005,8 +1921,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2020,8 +1934,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2073,8 +1986,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -2088,8 +1999,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -2141,8 +2051,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2162,7 +2070,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -2207,8 +2114,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2225,7 +2130,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2291,9 +2195,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2313,28 +2214,26 @@
       <td>CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.</td>
       <td>Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation</td>
       <td>Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/Ecogenomics/CheckM</td>
       <td>Metagenomics</td>
       <td>checkm</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm</td>
-      <td>1.2.0</td>
+      <td>1.2.3</td>
       <td>checkm-genome</td>
       <td>1.2.3</td>
       <td>Sequence assembly validation, Sequence composition calculation, Statistical calculation</td>
       <td>Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management</td>
       <td>0</td>
-      <td>0</td>
       <td>10</td>
       <td>10</td>
-      <td>0</td>
+      <td>10</td>
       <td>0</td>
       <td>10</td>
       <td>10</td>
-      <td>0</td>
-      <td>0</td>
+      <td>10</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -2361,7 +2260,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>10</td>
       <td>0</td>
       <td>0</td>
@@ -2394,14 +2292,12 @@
       <td>Variant calling</td>
       <td>Molecular genetics</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -2429,7 +2325,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2500,9 +2395,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -2538,10 +2430,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -2564,8 +2454,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2631,9 +2520,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2698,10 +2584,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2767,9 +2650,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -2840,9 +2720,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -2903,9 +2780,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2971,9 +2845,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3006,15 +2877,13 @@
       <td>Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly</td>
       <td>Sequence assembly, Transcriptomics, Sequence analysis</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -3046,7 +2915,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -3107,9 +2975,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -3161,8 +3026,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -3177,7 +3040,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -3243,9 +3105,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3286,10 +3145,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -3312,8 +3169,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3363,8 +3219,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>10</td>
       <td>0</td>
       <td>10</td>
@@ -3380,8 +3234,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>10</td>
       <td>10</td>
       <td>10</td>
       <td>0</td>
@@ -3447,9 +3300,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -3490,10 +3340,8 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -3516,8 +3364,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3561,8 +3408,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>3</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -3585,7 +3430,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -3637,8 +3481,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3652,8 +3494,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3719,9 +3560,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -3773,8 +3611,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -3788,8 +3624,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -3841,8 +3676,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3857,7 +3690,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3928,9 +3760,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -3989,11 +3818,8 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>3</td>
       <td>1</td>
       <td>0</td>
@@ -4037,8 +3863,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>107</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -4060,8 +3884,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>107</td>
       <td>107</td>
       <td>107</td>
       <td>0</td>
@@ -4127,9 +3950,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>7</td>
       <td>7</td>
       <td>0</td>
@@ -4181,8 +4001,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4196,8 +4014,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4256,8 +4073,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4270,7 +4085,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -4317,8 +4131,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4332,8 +4144,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4385,8 +4196,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4400,8 +4209,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4472,9 +4280,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -4519,8 +4324,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4536,8 +4339,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4587,8 +4389,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4603,9 +4404,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4646,8 +4445,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -4672,8 +4469,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4717,8 +4513,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -4740,8 +4534,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4793,8 +4586,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4814,7 +4605,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -4860,8 +4650,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4876,8 +4664,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4942,10 +4729,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4965,14 +4749,14 @@
       <td>Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.</td>
       <td>Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly</td>
       <td>Sequence assembly, Metagenomics, Whole genome sequencing, Genomics</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/fenderglass/Flye/</td>
       <td>Assembly</td>
       <td>flye</td>
       <td>bgruening</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/flye</td>
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/flye</td>
-      <td>2.9.4</td>
+      <td>2.9.5</td>
       <td>flye</td>
       <td>2.9.5</td>
       <td>Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly</td>
@@ -4996,8 +4780,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5012,8 +4794,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5065,8 +4846,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5080,8 +4859,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5133,8 +4911,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5148,8 +4924,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5201,8 +4976,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -5217,7 +4990,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -5268,8 +5040,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>18</td>
       <td>18</td>
       <td>0</td>
@@ -5290,7 +5060,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -5350,10 +5119,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -5405,8 +5171,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5426,7 +5190,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -5471,8 +5234,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>5</td>
@@ -5488,8 +5249,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -5540,8 +5300,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5556,8 +5314,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5622,10 +5379,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>4</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -5696,9 +5450,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -5745,8 +5496,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -5760,8 +5509,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -5811,8 +5559,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5828,8 +5574,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5881,8 +5626,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -5896,8 +5639,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -5926,7 +5668,7 @@
       <td>https://github.com/bgruening/galaxytools/tree/master/tools/graphmap</td>
       <td>0.5.2</td>
       <td>graphmap</td>
-      <td>0.6.3</td>
+      <td>0.6.4</td>
       <td>Sequence trimming, EST assembly, Read mapping</td>
       <td>Gene transcripts, RNA-Seq, RNA splicing</td>
       <td>0</td>
@@ -5949,8 +5691,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -5964,8 +5704,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -5985,14 +5724,14 @@
       <td>a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).</td>
       <td>Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval</td>
       <td>Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/Ecogenomics/GTDBTk</td>
       <td>Metagenomics</td>
       <td>gtdbtk</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk</td>
-      <td>2.3.2</td>
+      <td>2.4.0</td>
       <td>gtdbtk</td>
       <td>2.4.0</td>
       <td>Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval</td>
@@ -6017,8 +5756,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6038,7 +5775,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -6085,8 +5821,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6100,8 +5834,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -6153,8 +5886,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -6169,7 +5900,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -6234,10 +5964,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -6303,9 +6030,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6360,8 +6084,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6378,7 +6100,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -6417,8 +6138,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>12</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6440,8 +6159,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>12</td>
       <td>12</td>
       <td>12</td>
       <td>0</td>
@@ -6452,7 +6170,7 @@
     <tr>
       <td></td>
       <td>humann</td>
-      <td>humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways</td>
+      <td>humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways</td>
       <td>HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution</td>
       <td>humann</td>
       <td>humann</td>
@@ -6461,30 +6179,26 @@
       <td>HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”</td>
       <td>Species frequency estimation, Taxonomic classification, Phylogenetic analysis</td>
       <td>Metagenomics, Phylogenomics</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://huttenhower.sph.harvard.edu/humann</td>
       <td>Metagenomics</td>
       <td>humann</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann</td>
-      <td>3.8</td>
+      <td>3.9</td>
       <td>humann</td>
       <td>3.9</td>
       <td>Species frequency estimation, Taxonomic classification, Phylogenetic analysis</td>
       <td>Metagenomics, Phylogenomics</td>
       <td>6</td>
-      <td>13</td>
-      <td>13</td>
-      <td>13</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
       <td>6</td>
-      <td>13</td>
-      <td>13</td>
-      <td>13</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6495,9 +6209,9 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>13</td>
       <td>0</td>
       <td>0</td>
+      <td>10</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6510,11 +6224,12 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>13</td>
-      <td>13</td>
+      <td>1</td>
+      <td>10</td>
+      <td>10</td>
       <td>0</td>
-      <td>1045</td>
-      <td>19521</td>
+      <td>1037</td>
+      <td>19490</td>
       <td>False</td>
     </tr>
     <tr>
@@ -6568,16 +6283,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>12</td>
       <td>17</td>
       <td>12</td>
       <td>0</td>
@@ -6643,9 +6355,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6697,8 +6406,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6718,7 +6425,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -6778,10 +6484,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -6847,9 +6550,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
       <td>6</td>
       <td>0</td>
@@ -6915,9 +6615,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -6949,16 +6646,14 @@
       <td>2.0.5</td>
       <td>Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation</td>
       <td>Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6985,7 +6680,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7026,10 +6720,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -7056,6 +6746,7 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>677</td>
       <td>35243</td>
@@ -7124,9 +6815,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -7171,8 +6859,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -7188,8 +6874,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7221,16 +6906,14 @@
       <td>1.7.2.1</td>
       <td>Structural variation detection</td>
       <td>Genomics, Sequence analysis, Genetic variation</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -7257,7 +6940,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7323,9 +7005,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7377,8 +7056,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -7392,8 +7069,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -7443,10 +7119,8 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -7460,8 +7134,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -7513,8 +7186,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7529,7 +7200,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7600,9 +7270,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -7662,10 +7329,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7716,8 +7380,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7732,8 +7394,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>8</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
@@ -7762,7 +7423,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate</td>
       <td>2.3.2</td>
       <td>kleborate</td>
-      <td>3.0.6</td>
+      <td>3.0.9</td>
       <td>Multilocus sequence typing, Genome assembly, Virulence prediction</td>
       <td>Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing</td>
       <td>0</td>
@@ -7785,8 +7446,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7801,7 +7460,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7866,10 +7524,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7917,8 +7572,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -7936,8 +7589,7 @@
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -7987,8 +7639,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -8004,8 +7654,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8055,8 +7704,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -8072,8 +7719,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8123,8 +7769,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8141,7 +7785,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8206,10 +7849,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8259,12 +7899,9 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>4</td>
       <td>6</td>
-      <td>0</td>
+      <td>6</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -8329,8 +7966,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8350,7 +7985,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -8410,10 +8044,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8479,9 +8110,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8547,9 +8175,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8614,10 +8239,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8683,9 +8305,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8751,9 +8370,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8818,10 +8434,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8891,9 +8504,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>False</td>
     </tr>
@@ -8909,14 +8519,14 @@
       <td>MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.</td>
       <td>Filtering, Statistical calculation, Standardisation and normalisation, Visualisation</td>
       <td>Metagenomics, Statistics and probability</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://huttenhower.sph.harvard.edu/maaslin</td>
       <td>Metagenomics</td>
       <td>maaslin2</td>
       <td>iuc</td>
       <td>https://github.com/biobakery/Maaslin2</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2</td>
-      <td>1.16.0</td>
+      <td>1.18.0</td>
       <td>bioconductor-maaslin2</td>
       <td>1.18.0</td>
       <td>Filtering, Standardisation and normalisation, Visualisation</td>
@@ -8955,9 +8565,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8998,10 +8605,8 @@
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -9024,8 +8629,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -9096,9 +8700,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -9145,8 +8746,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9160,8 +8759,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -9213,8 +8811,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9229,7 +8825,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9281,8 +8876,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -9296,8 +8889,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -9349,8 +8941,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9364,8 +8954,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -9416,8 +9005,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -9432,8 +9019,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -9499,9 +9085,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -9530,7 +9113,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka</td>
       <td>1.7.2</td>
       <td>medaka</td>
-      <td>1.11.3</td>
+      <td>2.0.0</td>
       <td>Base-calling, Variant calling, Sequence assembly</td>
       <td>Sequence assembly, Machine learning</td>
       <td>3</td>
@@ -9553,8 +9136,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -9568,8 +9149,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -9619,8 +9199,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -9636,8 +9214,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -9689,8 +9266,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9705,7 +9280,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -9771,9 +9345,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>7</td>
       <td>0</td>
       <td>0</td>
@@ -9844,9 +9415,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -9907,9 +9475,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9980,9 +9545,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -10029,8 +9591,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10045,7 +9605,6 @@
       <td>0</td>
       <td>1</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -10110,10 +9669,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -10163,8 +9719,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -10181,7 +9735,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -10233,8 +9786,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10248,8 +9799,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -10282,15 +9832,12 @@
       <td>Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis</td>
       <td>Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -10367,9 +9914,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
+      <td>2</td>
       <td>0</td>
       <td>4</td>
       <td>0</td>
@@ -10385,7 +9930,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
@@ -10450,10 +9994,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>6</td>
       <td>6</td>
       <td>6</td>
       <td>0</td>
@@ -10524,9 +10065,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -10573,8 +10111,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10588,8 +10124,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -10641,8 +10176,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10656,8 +10189,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -10709,8 +10241,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10725,7 +10255,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10791,9 +10320,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -10845,8 +10371,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10860,8 +10384,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>1</td>
       <td>0</td>
@@ -10913,8 +10436,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -10928,8 +10449,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -10981,8 +10501,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -10997,7 +10515,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -11038,8 +10555,6 @@
       <td>129</td>
       <td>129</td>
       <td>0</td>
-      <td>3</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11064,8 +10579,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>126</td>
       <td>129</td>
       <td>129</td>
       <td>0</td>
@@ -11116,8 +10630,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -11132,8 +10644,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11198,10 +10709,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -11267,9 +10775,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -11335,9 +10840,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -11364,9 +10866,9 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc</td>
-      <td>1.11</td>
-      <td>multiqc</td>
       <td>1.24.1</td>
+      <td>multiqc</td>
+      <td>1.25.1</td>
       <td>Sequencing quality control</td>
       <td>Sequencing, Bioinformatics, Sequence analysis, Genomics</td>
       <td>1</td>
@@ -11381,8 +10883,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11404,8 +10904,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -11476,9 +10975,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -11544,9 +11040,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -11606,10 +11099,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -11661,8 +11151,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -11676,8 +11164,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -11727,8 +11214,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -11744,8 +11229,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -11810,10 +11294,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -11854,10 +11335,8 @@
       <td>16</td>
       <td>16</td>
       <td>0</td>
-      <td>15</td>
       <td>0</td>
       <td>0</td>
-      <td>15</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11880,8 +11359,7 @@
       <td>0</td>
       <td>0</td>
       <td>16</td>
-      <td>0</td>
-      <td>0</td>
+      <td>16</td>
       <td>16</td>
       <td>15</td>
       <td>0</td>
@@ -11933,8 +11411,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -11954,7 +11430,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -12001,8 +11476,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -12016,8 +11489,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -12069,8 +11541,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -12085,7 +11555,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -12151,9 +11620,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -12205,8 +11671,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -12220,8 +11684,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -12287,9 +11750,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -12360,9 +11820,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -12423,9 +11880,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -12491,9 +11945,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>10</td>
       <td>10</td>
       <td>0</td>
@@ -12564,9 +12015,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -12627,9 +12075,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -12670,10 +12115,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -12699,6 +12140,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>239</td>
@@ -12726,7 +12168,7 @@
       <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker</td>
       <td></td>
       <td>searchgui</td>
-      <td>4.3.9</td>
+      <td>4.3.11</td>
       <td></td>
       <td></td>
       <td>4</td>
@@ -12762,10 +12204,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>4</td>
       <td>2</td>
       <td>0</td>
@@ -12831,9 +12270,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -12885,8 +12321,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -12901,7 +12335,6 @@
       <td>0</td>
       <td>1</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -12951,8 +12384,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -12969,7 +12400,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -13010,8 +12440,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -13036,8 +12464,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -13089,8 +12516,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
       <td>0</td>
       <td>0</td>
@@ -13105,7 +12530,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -13171,9 +12595,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>7</td>
       <td>0</td>
       <td>0</td>
@@ -13223,8 +12644,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -13240,8 +12659,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -13273,16 +12691,14 @@
       <td>2.1.6</td>
       <td>Genome assembly, Scaffolding, Multilocus sequence typing</td>
       <td>Whole genome sequencing, Sequence assembly, Mapping, Probes and primers</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -13309,7 +12725,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -13353,8 +12768,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -13382,7 +12795,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -13429,8 +12841,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -13445,7 +12855,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -13478,15 +12887,13 @@
       <td>Genome annotation</td>
       <td>Genomics, Sequence analysis</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -13518,7 +12925,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -13563,8 +12969,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -13580,8 +12984,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -13652,9 +13055,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -13701,8 +13101,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -13716,8 +13114,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -13767,12 +13164,9 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -13835,8 +13229,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -13852,8 +13244,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -13919,9 +13310,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -13971,8 +13359,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>31</td>
       <td>0</td>
       <td>1</td>
@@ -13989,7 +13375,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>31</td>
       <td>31</td>
       <td>0</td>
@@ -14041,8 +13426,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -14056,8 +13439,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>4</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
@@ -14101,8 +13483,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -14124,8 +13504,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -14192,9 +13571,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -14264,9 +13640,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -14313,8 +13686,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -14328,8 +13699,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -14400,9 +13770,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -14441,8 +13808,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -14464,8 +13829,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -14517,8 +13881,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -14533,7 +13895,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -14604,9 +13965,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -14628,9 +13986,9 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge</td>
-      <td>1.14.1</td>
+      <td>1.15.0</td>
       <td>recentrifuge</td>
-      <td>1.14.1</td>
+      <td>1.15.0</td>
       <td>Taxonomic classification, Expression analysis, Cross-assembly</td>
       <td>Metagenomics, Microbial ecology, Metagenomic sequencing</td>
       <td>1</td>
@@ -14651,8 +14009,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -14669,7 +14025,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -14739,9 +14094,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>16</td>
       <td>False</td>
     </tr>
@@ -14789,8 +14141,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -14804,8 +14154,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -14855,8 +14204,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>22</td>
       <td>0</td>
       <td>0</td>
@@ -14872,8 +14219,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>22</td>
       <td>22</td>
       <td>22</td>
       <td>0</td>
@@ -14924,8 +14270,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>1</td>
       <td>0</td>
@@ -14940,8 +14284,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -15006,10 +14349,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -15074,10 +14414,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -15115,9 +14452,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -15145,7 +14480,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -15211,9 +14545,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
       <td>0</td>
       <td>0</td>
@@ -15248,13 +14579,11 @@
       <td>0</td>
       <td>2</td>
       <td>5</td>
-      <td>2</td>
+      <td>3</td>
       <td>0</td>
       <td>2</td>
       <td>5</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -15281,7 +14610,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -15352,9 +14680,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -15419,9 +14744,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>12</td>
       <td>False</td>
     </tr>
@@ -15469,8 +14791,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -15490,7 +14810,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -15535,8 +14854,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -15552,8 +14869,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -15605,8 +14921,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -15621,7 +14935,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -15687,9 +15000,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -15741,8 +15051,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -15762,7 +15070,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -15822,10 +15129,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -15869,8 +15173,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -15892,8 +15194,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>2</td>
       <td>0</td>
@@ -15945,8 +15246,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -15961,7 +15260,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -16002,8 +15300,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -16028,8 +15324,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -16043,7 +15338,7 @@
       <td>spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades</td>
       <td>SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.</td>
       <td>spades</td>
-      <td>coronaspades, biosyntheticspades, metaplasmidspades, plasmidspades, metaspades, rnaspades, metaviralspades, rnaviralspades, spades</td>
+      <td>spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades</td>
       <td></td>
       <td>SPAdes</td>
       <td>St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.</td>
@@ -16073,8 +15368,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -16096,8 +15389,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>9</td>
       <td>3</td>
       <td>0</td>
@@ -16163,9 +15455,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -16216,8 +15505,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -16238,7 +15525,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -16285,8 +15571,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -16301,7 +15585,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -16330,7 +15613,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2</td>
       <td>0.2.0</td>
       <td>samtools</td>
-      <td>1.20</td>
+      <td>1.21</td>
       <td>Multilocus sequence typing</td>
       <td>Whole genome sequencing, Public health and epidemiology</td>
       <td>0</td>
@@ -16353,8 +15636,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -16369,7 +15650,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -16419,8 +15699,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -16436,8 +15714,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -16489,8 +15766,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -16510,7 +15785,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -16570,10 +15844,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -16639,9 +15910,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -16707,9 +15975,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -16775,9 +16040,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -16843,9 +16105,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -16911,9 +16170,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -16979,9 +16235,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
       <td>0</td>
       <td>0</td>
@@ -17015,15 +16268,12 @@
       <td></td>
       <td>21</td>
       <td>21</td>
+      <td>22</td>
       <td>21</td>
       <td>21</td>
       <td>21</td>
+      <td>22</td>
       <td>21</td>
-      <td>21</td>
-      <td>21</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -17115,9 +16365,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>12</td>
       <td>0</td>
       <td>0</td>
@@ -17183,9 +16430,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -17251,9 +16495,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>10</td>
       <td>0</td>
       <td>0</td>
@@ -17319,9 +16560,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>17</td>
       <td>0</td>
       <td>0</td>
@@ -17387,9 +16625,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -17455,9 +16690,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>11</td>
       <td>0</td>
       <td>0</td>
@@ -17523,9 +16755,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -17591,9 +16820,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>12</td>
       <td>0</td>
       <td>0</td>
@@ -17659,9 +16885,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>6</td>
       <td>0</td>
       <td>0</td>
@@ -17727,9 +16950,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -17800,9 +17020,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -17863,9 +17080,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>15</td>
       <td>0</td>
       <td>0</td>
@@ -17931,9 +17145,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -17999,9 +17210,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>8</td>
       <td>0</td>
       <td>0</td>
@@ -18072,9 +17280,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -18135,9 +17340,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -18189,8 +17391,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -18204,8 +17404,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -18257,8 +17456,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -18272,8 +17469,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -18314,9 +17510,6 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -18391,8 +17584,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -18408,8 +17599,7 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -18474,10 +17664,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -18504,9 +17691,9 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator</td>
-      <td>0.9</td>
+      <td>0.9.1</td>
       <td>tooldistillator</td>
-      <td>0.9</td>
+      <td>0.9.1</td>
       <td>Parsing</td>
       <td>Microbiology, Bioinformatics, Sequence analysis</td>
       <td>2</td>
@@ -18548,9 +17735,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -18610,10 +17794,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -18678,10 +17859,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -18722,8 +17900,6 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -18748,8 +17924,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -18801,8 +17976,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -18817,7 +17990,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -18868,8 +18040,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -18884,8 +18054,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -18935,8 +18104,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -18952,8 +18119,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -19019,9 +18185,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -19087,9 +18250,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -19141,8 +18301,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -19156,8 +18314,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -19212,8 +18369,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -19225,7 +18380,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -19245,7 +18399,7 @@
       <td>variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.</td>
       <td>PCR primer design</td>
       <td>Virology, Probes and primers</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/jonas-fuchs/varVAMP/</td>
       <td>Sequence Analysis</td>
       <td>varvamp</td>
@@ -19254,7 +18408,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp</td>
       <td>1.2.0</td>
       <td>varvamp</td>
-      <td>1.2.0</td>
+      <td>1.2.1</td>
       <td>PCR primer design</td>
       <td>Virology, Probes and primers</td>
       <td>0</td>
@@ -19296,9 +18450,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -19345,8 +18496,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -19360,8 +18509,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
@@ -19411,8 +18559,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -19428,8 +18574,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -19470,8 +18615,6 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -19496,8 +18639,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -19524,7 +18666,7 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot</td>
-      <td>1.0.1+galaxy0</td>
+      <td>1.1.0+galaxy0</td>
       <td>biopython</td>
       <td>1.70</td>
       <td>Sequence annotation, Sequence clustering, Sequence cluster visualisation</td>
@@ -19568,9 +18710,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -19594,7 +18733,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch</td>
       <td>2.8.3</td>
       <td>vsearch</td>
-      <td>2.28.1</td>
+      <td>2.29.0</td>
       <td>DNA mapping, Chimera detection</td>
       <td>Metagenomics, Sequence analysis</td>
       <td>8</td>
@@ -19616,8 +18755,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
@@ -19632,8 +18769,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>8</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
@@ -19685,8 +18821,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -19701,7 +18835,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
diff --git a/communities/microgalaxy/resources/tools.tsv b/communities/microgalaxy/resources/tools.tsv
index f6990275..9e964f17 100644
--- a/communities/microgalaxy/resources/tools.tsv
+++ b/communities/microgalaxy/resources/tools.tsv
@@ -1,291 +1,291 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on BF2I-MAP	Tools available on BioBix	Tools available on CIRM-CFBP	Tools available on Center for Phage Technology (CPT)	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	73	1004	True	False	True
-TreeBest	treebest_best	TreeBeST best	treebest	treebest		TreeBeST	TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	984	True	False	True
-abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-abricate	abricate, abricate_list, abricate_summary	Mass screening of contigs for antiobiotic resistance genes	ABRicate	ABRicate		ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.	Antimicrobial resistance prediction	Genomics, Microbiology	Up-to-date	https://github.com/tseemann/abricate	Sequence Analysis	abricate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate	1.0.1	abricate	1.0.1	Antimicrobial resistance prediction	Genomics, Microbiology	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	1764	496717	True	False	True
-abritamr	abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	abritamr	abritamr		abriTAMR	an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	To update	https://zenodo.org/record/7370628	Sequence Analysis	abritamr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr	1.0.14	abritamr	1.0.19	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	To update	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.7	abyss	2.3.8	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	391	4278	True	False	True
-aldex2	aldex2	Performs analysis Of differential abundance taking sample variation into account	aldex2	aldex2		ALDEx2	A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	Statistical inference	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	13	129	True	False	True
-amplican	amplican	AmpliCan is an analysis tool for genome editing.	amplican	amplican		amplican	It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	53	True	False	True
-amrfinderplus	amrfinderplus	"""AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms."	amrfinderplus	amrfinderplus		AMRFinderPlus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms"	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.12.8	ncbi-amrfinderplus	3.12.8	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	591	True	False	True
-ancombc	ancombc	Performs analysis of compositions of microbiomes with bias correction.	ancombc	ancombc		ANCOMBC	Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	7	True	False	True
-antismash	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash		antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	279	14596	True	False	True
-artic	artic_guppyplex, artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	artic	artic		ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	Sequence alignment	Genomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	1	0	123	8175	True	False	True
-assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-bakta	bakta	"""Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."""	bakta	bakta		Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	To update	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.3	bakta	1.9.4	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	151	2982	True	False	True
-bamtools	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	208	14021	True	False	True
-bandage	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	bandage	bandage		Bandage	GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	Sequence assembly visualisation	Genomics, Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	2	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	2	2	0	2016	44390	True	False	True
-bayescan	BayeScan	Detecting natural selection from population-based genetic data	bayescan	bayescan		BayeScan	BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	64	True	False	True
-bbtools	bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.	bbmap	bbtools, bbmap		BBMap	BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	Up-to-date	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.08	bbmap	39.08	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	6	1	5	0	6	1	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	0	4	0	0	420	6381	True	False	True
-bigscape	bigscape	Construct sequence similarity networks of BGCs and groups them into GCF	BiG-SCAPE	BiG-SCAPE		BiG-SCAPE	A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-binning_refiner	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	binning_refiner	binning_refiner		Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	81	True	False	True
-biohansel	biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-biom_format	biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	biomformat	biomformat		biomformat	"This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods."	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	Formatting	Laboratory information management, Sequence analysis	2	2	6	0	2	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	98	3906	True	False	True
-biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-blast2go	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe				0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	101	1232	True	False	True
-blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	121	22499	True	False	True
-blastxml_to_top_descr	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	159	264558	True	False	True
-bracken	est_abundance	Bayesian Reestimation of Abundance with KrakEN	bracken	bracken		Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	Statistical calculation	Metagenomics, Microbial ecology	Up-to-date	https://ccb.jhu.edu/software/bracken/	Sequence Analysis, Metagenomics	bracken	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken	3.0	bracken	3.0	Statistical calculation	Metagenomics, Microbial ecology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	326	18351	True	False	True
-busco	busco	BUSCO assess genome and annotation completeness	busco	busco		BUSCO	Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://gitlab.com/ezlab/busco/-/releases	Sequence Analysis	busco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco	5.7.1	busco	5.7.1	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1804	86180	True	False	True
-cat	cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	cat_bins		CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat	5.2.3	cat	5.3	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	5	2	5	0	5	2	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	268	2878	True	False	True
-cd_hit_dup	cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	280	4474	True	False	True
-cemitool	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.26.0	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	98	True	False	True
-checkm	checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	checkm	checkm		CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	To update	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.0	checkm-genome	1.2.3	Sequence assembly validation, Sequence composition calculation, Statistical calculation	Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	0	0	10	10	0	0	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	390	5165	True	False	True
-clair3	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	clair3	clair3		Clair3	Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	1.0.8	clair3	1.0.10	Variant calling	Molecular genetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	68	1856	True	False	True
-clinod	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-clustalw	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	clustal2	clustal2		Clustal 2 (Clustal W, Clustal X)	Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.	Multiple sequence alignment	Phylogeny, Sequence analysis	Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw	2.1	clustalw	2.1	Multiple sequence alignment	Phylogeny, Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	651	46793	True	False	True
-cmsearch_deoverlap	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	102	True	False	True
-codeml	codeml	Detects positive selection	paml	paml		PAML	Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml	4.9	paml	4.10.7	Probabilistic sequence generation	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	29	60901	True	False	True
-cojac	cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	cojac	cojac		COJAC	CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.2	cojac	0.9.2		Genetic variation	2	0	3	0	2	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	20	2757	True	False	True
-combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-combine_metaphlan_humann	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	147	True	False	True
-compare_humann2_output	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	332	True	False	True
-compleasm	compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	compleasm	compleasm		compleasm	"""Compleasm: a faster and more accurate reimplementation of BUSCO"""	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm	0.2.6	compleasm	0.2.6	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-concoct	concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	concoct	concoct		CONCOCT	A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct	1.1.0	concoct	1.1.0	Sequence clustering, Read binning	Metagenomics	0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	92	786	True	False	True
-coverm	coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm		CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	Local alignment	Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	72	529	True	False	True
-cryptogenotyper	CryptoGenotyper	CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	8518	True	False	True
-cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	5090	232004	True	False	True
-dada2	dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	dada2	dada2		dada2	This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	10	0	0	1	0	0	0	0	0	0	0	0	0	0	0	10	10	0	1263	66609	True	False	True
-das_tool	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	dastool		dastool	DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	Read binning	Metagenomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	24	706	True	False	True
-deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	4990	95752	True	False	True
-diamond	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	diamond		Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	Sequence alignment analysis	Sequence analysis, Proteins	3	3	3	3	3	3	3	3	0	0	0	0	3	0	0	0	0	0	0	0	3	3	3	0	0	0	1	0	0	0	0	0	0	0	0	0	0	3	3	0	963	49711	True	False	True
-disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	42	369	True	False	True
-dram	dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram		DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	Up-to-date	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.5.0	dram	1.5.0	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	39	6886	True	False	True
-drep	drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep		dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	Up-to-date	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.5.0	drep	3.5.0	Genome comparison	Metagenomics, Sequence analysis	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	46	646	True	False	True
-ectyper	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	9907	True	False	True
-effectiveT3	effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-eggnog_mapper	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2		eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3	1	0	510	30565	True	False	True
-emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	107	107	107	107	107	0	0	0	0	107	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	0	0	107	107	0	1816	89530	True	False	True
-ete	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete		ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	Phylogenetic tree editing	Phylogenetics	0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	45	899	True	False	True
-export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan		export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	Conversion	Taxonomy, Metabolomics, Biomarkers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	200	5265	True	False	True
-ez_histograms	ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-fargene	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fargene		fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	52	459	True	False	True
-fastani	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity	fastani	fastani		FastANI	FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	250	3498	True	False	True
-fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-fastp	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp		fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	Sequence contamination filtering	Probes and primers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	1	2803	1055760	True	False	True
-fastqe	fastqe	FASTQE	fastqe	fastqe		FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	Sequencing quality control	Sequence analysis, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1266	4333	True	False	True
-fasttree	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree		FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11		Phylogenetics	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	379	55434	True	False	True
-featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	4679	696399	True	False	True
-filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	617	30483	True	False	True
-flashlfq	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	Label-free quantification	Proteomics experiment, Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	17	645	True	False	True
-flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	To update	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.4	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1499	20904	True	False	True
-format_metaphlan2_output	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	166	5588	True	False	True
-fraggenescan	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan		FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	Gene prediction	Genetics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	68	1102	True	False	True
-freyja	freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja		Freyja	Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset	RNA-Seq quantification	Metagenomics	To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.1	RNA-Seq quantification	Metagenomics	2	0	4	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	55	20021	True	False	True
-frogs	FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis	frogs	frogs		FROGS	The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	To update	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	5.0.0	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	0	0	0	28	0	0	0	28	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	900	5906	True	False	True
-getmlst	getmlst	Download MLST datasets by species from pubmlst.org								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-ggplot2	ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2		ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		Visualisation	Data visualisation	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	5	0	0	0	0	0	0	3	0	0	0	0	0	0	0	5	5	0	1388	22148	True	False	True
-gi2taxonomy	Fetch Taxonomic Ranks	Fetch taxonomic representation	gi2taxonomy	gi2taxonomy		gi2taxonomy	The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	27	660	True	False	True
-glimmer	glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based	Glimmer makes gene predictions.	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	Sequence analysis, Genetic variation analysis	Sequence analysis	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	187	3965	True	False	True
-glimmer_hmm		GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	408	5484	True	False	True
-goseq	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq		GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	Gene functional annotation	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1210	19167	True	False	True
-graphlan	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	graphlan	graphlan		GraPhlAn	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	432	9277	True	False	True
-graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.3	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	136	6651	True	False	True
-gtdbtk	gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 	GTDB-Tk	GTDB-Tk		GTDB-Tk	a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	To update	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.3.2	gtdbtk	2.4.0	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-gubbins	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins		Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	145	3340	True	False	True
-hamronization	hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization		hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	117	4459	True	False	True
-hansel	bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	Biohansel		BioHansel	BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	339	True	False	True
-hifiasm_meta	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	hifiasm-meta		Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	Sequence assembly	Sequence assembly, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	137	True	False	True
-hivtrace	hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-hmmer3	hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	hmmer3	hmmer3		HMMER3	This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	0	12	12	12	0	12	12	12	0	0	0	0	12	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	0	439	33702	True	False	True
-humann	humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	humann	humann		humann	HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	To update	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.8	humann	3.9	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	6	13	13	13	6	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	13	0	1045	19521	True	False	True
-hyphy	hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy		HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.62	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	17	2	17	2	17	2	17	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	17	12	0	161	10370	True	False	True
-hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354	True	False	True
-icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	69	1127	True	False	True
-infernal	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	infernal		Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	67	100294	True	False	True
-instrain	instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	instrain	instrain		InStrain	InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	SNP detection, Genome comparison	Mapping, Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	94	True	False	True
-integron_finder	integron_finder	"""IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"""	integron_finder	integron_finder		Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.5	integron_finder	2.0.5	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	58	52965	True	False	True
-interproscan	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi		InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	677	35243	True	False	True
-iprscan5		Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-iqtree	iqtree	Efficient phylogenomic software by maximum likelihood	iqtree	iqtree		iqtree	A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time	Phylogenetic analysis, Sequence analysis	Phylogenetics	Up-to-date	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.3.6	iqtree	2.3.6	Phylogenetic analysis, Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	681	21598	True	False	True
-isescan	isescan	"""ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."""	ISEScan	ISEScan		ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	Structural variation detection	Genomics, Sequence analysis, Genetic variation	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	50	57581	True	False	True
-itsx	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	38	868	True	False	True
-ivar	ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing								Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.3	ivar	1.4.3			5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	4	0	0	0	4	0	0	0	0	0	0	0	5	5	0	1171	1224275	True	False	True
-jbrowse	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse		JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	Genome visualisation	Genomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	2	2	0	2346	18229	True	False	True
-jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138	True	False	True
-kat_filter	kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-kc-align	kc-align	Kc-Align custom tool	kc-align	kc-align		kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	Multiple sequence alignment	Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	19	363	True	False	True
-khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	8	8	0	63	2022	True	False	True
-kleborate	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	kleborate	kleborate		Kleborate	Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	To update	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	3.0.6	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	38	319	True	False	True
-kofamscan	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	kofamscan	kofamscan		kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	Sequence analysis, Gene functional annotation	Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	33	594	True	False	True
-kraken	kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	kraken	kraken		Kraken	System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	Taxonomic classification	Taxonomy, Metagenomics	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	5	0	1209	33778	True	False	True
-kraken2	kraken2	Kraken2 for taxonomic designation.	kraken2	kraken2		kraken2	Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	Up-to-date	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.3	kraken2	2.1.3	Taxonomic classification	Taxonomy, Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	0	1	1	0	2367	185308	True	False	True
-kraken2tax	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	481	14683	True	False	True
-kraken_biom	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)								Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	182	1444	True	False	True
-kraken_taxonomy_report	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report		Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	Visualisation, Classification	Metagenomics, Taxonomy	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	354	2527	True	False	True
-krakentools	krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	krakentools		KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	Visualisation, Aggregation	Taxonomy, Metagenomics	6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	1	4	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	703	16525	True	False	True
-krocus	krocus	Predict MLST directly from uncorrected long reads	krocus	krocus		krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	Multilocus sequence typing, k-mer counting	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-lca_wrapper	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	137	True	False	True
-legsta	legsta	Performs in silico Legionella pneumophila sequence based typing.	legsta	legsta		legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	Sequence analysis	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	55	True	False	True
-lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	152	True	False	True
-limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1012	20344	True	False	True
-lineagespot	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	lineagespot	lineagespot		lineagespot	Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	37	True	False	True
-lorikeet	lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet		lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	Sequence analysis, Genotyping	Genotype and phenotype	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	647	True	False	True
-lotus2	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2		lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	To update	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.34.1	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	114	936	True	False	True
-m6anet	m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet		m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	True	False	True
-maaslin2	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	maaslin2	maaslin2		MaAsLin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	To update	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	1.16.0	bioconductor-maaslin2	1.18.0	Filtering, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	188	True	False	True
-mafft	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.526	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	2	2	2	2	2	0	1	0	0	2	0	0	0	0	0	0	0	1	0	2	0	0	2	0	0	0	2	0	0	0	0	0	0	0	2	2	0	817	143045	True	False	True
-make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-maker	maker, maker_map_ids	MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	maker	maker		MAKER	Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	Genome annotation	Genomics, DNA, Sequence analysis	To update	http://www.yandell-lab.org/software/maker.html	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker	2.31.11	maker	3.01.03	Genome annotation	Genomics, DNA, Sequence analysis	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	554	5591	True	False	True
-mapseq	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	mapseq	mapseq		MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .	k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	To update	https://github.com/jfmrod/MAPseq	Metagenomics	mapseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq	2.1.1	perl		k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	167	True	False	True
-mash	mash_screen, mash_sketch	Fast genome and metagenome distance estimation using MinHash	mash	mash		Mash	Fast genome and metagenome distance estimation using MinHash.	Sequence distance matrix generation	Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	Up-to-date	https://github.com/marbl/Mash	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash	2.3	mash	2.3	Sequence distance matrix generation	Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	27	9763	True	False	True
-maxbin2	maxbin2	clusters metagenomic contigs into bins	maxbin	maxbin		MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	To update	https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html	Metagenomics	maxbin2	mbernt	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2		maxbin2	2.2.7	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	0	118	2059	True	False	True
-maxquant	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering	Proteomics experiment, Proteomics, Statistics and probability	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	415	6078	True	False	True
-mcl	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	mcl	mcl		MCL	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.	Clustering, Network analysis, Gene regulatory network analysis	Molecular interactions, pathways and networks	Up-to-date	https://micans.org/mcl/man/mcl.html	Sequence Analysis	mcl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/mcl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl	22.282	mcl	22.282	Clustering, Gene regulatory network analysis	Molecular interactions, pathways and networks	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	29	True	False	True
-medaka	medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	medaka	medaka		Medaka	medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	1.11.3	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	2	0	0	0	0	0	0	0	3	3	0	768	99863	True	False	True
-megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	0	1	1	0	548	9530	True	False	True
-megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	54	475	True	False	True
-megan	megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma	MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data.  MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).	megan	megan		MEGAN	Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Sequence analysis, Taxonomic classification	Sequence analysis	To update	https://github.com/husonlab/megan-ce	Sequence Analysis	megan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan	6.21.7	megan	6.25.9	Sequence analysis, Taxonomic classification	Sequence analysis	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	261	3610	True	False	True
-meningotype	meningotype	Assign sequence type to N. meningitidis genome assemblies	meningotype	meningotype		meningotype	In silico typing of Neisseria meningitidis contigs.	Genotyping, Multilocus sequence typing	Microbiology, Genotype and phenotype	Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype	0.8.5	meningotype	0.8.5	Multilocus sequence typing	Microbiology, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483	True	False	True
-meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-metabat2	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT_2		MetaBAT 2	"an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning"	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	To update	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.17	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	2	1	2	2	2	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	192	4329	True	False	True
-metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	5.34c21f2	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	184	True	False	True
-metagene_annotator	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	115	636	True	False	True
-metagenomeseq	metagenomeseq_normalizaton	metagenomeSeq Normalization	metagenomeseq	metagenomeseq		metagenomeSeq	Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	To update	https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html	Metagenomics	metagenomeseq_normalization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq	1.16.0-0.0.1	bioconductor-metagenomeseq	1.43.0	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	753	True	False	True
-metanovo	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	4181	True	False	True
-metaphlan	customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	metaphlan	metaphlan		MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.	Nucleic acid sequence analysis, Phylogenetic tree analysis	Metagenomics, Phylogenomics	Up-to-date	https://github.com/biobakery/MetaPhlAn	Metagenomics	metaphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan	4.1.1	metaphlan	4.1.1	Nucleic acid sequence analysis	Metagenomics, Phylogenomics	1	2	4	4	1	2	4	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	499	11069	True	False	True
-metaquantome	metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome		metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	104	2522	True	False	True
-metawrapmg	metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	metawrap	metawrap		MetaWRAP	MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	Up-to-date	https://github.com/bxlab/metaWRAP	Metagenomics	metawrapmg_binning	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg	1.3.0	metawrap-mg	1.3.0	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	109	2206	True	False	True
-miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	178	11938	True	False	True
-minipolish	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	185	True	False	True
-miniprot	miniprot, miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	miniprot	miniprot		miniprot	Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	Up-to-date	https://github.com/lh3/miniprot	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot	0.13	miniprot	0.13	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	30	842	True	False	True
-mitos	mitos, mitos2	de-novo annotation of metazoan mitochondrial genomes	mitos	mitos		MITOS	De novo metazoan mitochondrial genome annotation.	Genome annotation	Zoology, Whole genome sequencing	To update	http://mitos.bioinf.uni-leipzig.de/	Sequence Analysis	mitos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos	1.1.7	mitos	2.1.9	Genome annotation	Zoology, Whole genome sequencing	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	1	0	236	100920	True	False	True
-mlst	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst		MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	Multilocus sequence typing	Immunoproteins and antigens	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	635	9304	True	False	True
-mob_suite	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.9			0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	322	89021	True	False	True
-mothur	mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn	Mothur wrappers	mothur	mothur		mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	129	129	129	129	129	129	129	129	0	3	0	0	0	0	0	0	0	0	0	0	128	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	129	129	0	14353	302916	True	False	True
-mrbayes	mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-msconvert	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert		msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			Filtering, Formatting	Proteomics, Proteomics experiment	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	189	19958	True	False	True
-msstatstmt	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	726	True	False	True
-multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	53	True	False	True
-multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.11	multiqc	1.24.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	8320	162790	True	False	True
-mykrobe	mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe		Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-mykrobe_parser	mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-mz_to_sqlite	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	Conversion, Peptide database search	Proteomics, Biological databases	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	33	844	True	False	True
-nanocompore	nanocompore_db, nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Nanocompore	Nanocompore		Nanocompore	RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	3	836	True	False	True
-nanoplot	nanoplot	Plotting tool for long read sequencing data and alignments	nanoplot	nanoplot		NanoPlot	NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences	Scatter plot plotting, Box-Whisker plot plotting	Genomics	Up-to-date	https://github.com/wdecoster/NanoPlot	Visualization	nanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot	1.43.0	nanoplot	1.43.0	Scatter plot plotting, Box-Whisker plot plotting	Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	2195	63235	True	False	True
-nanopolishcomp	nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate	NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.	nanopolishcomp	nanopolishcomp		NanopolishComp	NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	To update	https://a-slide.github.io/NanopolishComp	Sequence Analysis	nanopolishcomp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp	0.6.11	nanopolishcomp	0.6.12	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	15	1074	True	False	True
-ncbi_blast_plus	blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper	NCBI BLAST+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	devteam	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	2.14.1	python				16	16	16	16	16	16	16	16	0	15	0	0	15	0	0	0	0	0	0	0	16	15	16	0	0	0	0	0	0	16	0	0	0	0	16	0	0	16	15	0	4066	365597	True	False	True
-ncbi_fcs_gx	ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).	ncbi_fcs	ncbi_fcs		NCBI fcs	The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	Up-to-date	https://github.com/ncbi/fcs-gx	Sequence Analysis	ncbi_fcs_gx	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	0.5.4	ncbi-fcs-gx	0.5.4	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-newick_utils	newick_display	Perform operations on Newick trees	newick_utilities	newick_utilities		Newick Utilities	The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.	Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction	Phylogeny, Genomics, Computer science	To update	http://cegg.unige.ch/newick_utils	Visualization, Metagenomics	newick_utils	iuc	https://github.com/tjunier/newick_utils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils	1.6+galaxy1	newick_utils	1.6		Phylogeny, Genomics, Computer science	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	448	25505	True	False	True
-nextclade	nextalign, nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	nextclade	nextclade		Nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.	Methylation analysis, Variant calling	Genomics, Sequence analysis, Cladistics	To update	https://github.com/nextstrain/nextclade	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade	2.7.0	nextalign	2.14.0	Methylation analysis, Variant calling	Genomics, Cladistics	1	1	2	2	1	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	0	0	0	1	0	0	0	0	0	0	0	2	0	0	210	4080	True	False	True
-nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268	True	False	True
-nonpareil	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil		nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.5.5	Operation		1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	142	True	False	True
-nucleosome_prediction	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	861	True	False	True
-nugen_nudup	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	1	1	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	45	True	False	True
-obitools	obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq	OBITools is a set of programs developed to simplify the manipulation of sequence files	obitools	obitools		OBITools	Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	Up-to-date	http://metabarcoding.org/obitools	Sequence Analysis	obitools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools	1.2.13	obitools	1.2.13	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	0	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	503	26251	True	False	True
-omark	omark	Proteome quality assessment software	omark	omark		OMArk	Proteome quality assessment software	Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	To update	https://github.com/DessimozLab/OMArk	Sequence Analysis	omark	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark	0.3.0			Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-orfipy	orfipy	Galaxy wrapper for ORFIPY	orfipy	orfipy		orfipy	A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	Up-to-date	https://github.com/urmi-21/orfipy	Sequence Analysis	orfipy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy	0.0.4	orfipy	0.0.4	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	774	True	False	True
-orthofinder	orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	OrthoFinder	OrthoFinder		OrthoFinder	OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.	Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis	Up-to-date	https://github.com/davidemms/OrthoFinder	Phylogenetics, Sequence Analysis	orthofinder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder	2.5.5	orthofinder	2.5.5	Genome comparison, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics	0	1	1	1	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	239	1333	True	False	True
-peptideshaker	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.9			4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	2	0	485	17477	True	False	True
-pfamscan	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	19	165	True	False	True
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
+PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	73	1004	True	False	True
+TreeBest	treebest_best	TreeBeST best	treebest	treebest		TreeBeST	TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	984	True	False	True
+abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+abricate	abricate, abricate_list, abricate_summary	Mass screening of contigs for antiobiotic resistance genes	ABRicate	ABRicate		ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.	Antimicrobial resistance prediction	Genomics, Microbiology	Up-to-date	https://github.com/tseemann/abricate	Sequence Analysis	abricate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate	1.0.1	abricate	1.0.1	Antimicrobial resistance prediction	Genomics, Microbiology	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	2	3	3	0	1764	496717	True	False	True
+abritamr	abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	abritamr	abritamr		abriTAMR	an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://zenodo.org/record/7370628	Sequence Analysis	abritamr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr	1.0.19	abritamr	1.0.19	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	391	4278	True	False	True
+aldex2	aldex2	Performs analysis Of differential abundance taking sample variation into account	aldex2	aldex2		ALDEx2	A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	Statistical inference	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	13	129	True	False	True
+amplican	amplican	AmpliCan is an analysis tool for genome editing.	amplican	amplican		amplican	It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	53	True	False	True
+amrfinderplus	amrfinderplus	"""AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms."	amrfinderplus	amrfinderplus		AMRFinderPlus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms"	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.12.8	ncbi-amrfinderplus	3.12.8	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	591	True	False	True
+ancombc	ancombc	Performs analysis of compositions of microbiomes with bias correction.	ancombc	ancombc		ANCOMBC	Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	7	True	False	True
+antismash	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash		antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	279	14596	True	False	True
+artic	artic_guppyplex, artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	artic	artic		ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	Sequence alignment	Genomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	2	1	0	123	8175	True	False	True
+assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+bakta	bakta	"""Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."""	bakta	bakta		Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	Up-to-date	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.4	bakta	1.9.4	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	151	2982	True	False	True
+bamtools	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	208	14021	True	False	True
+bandage	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	bandage	bandage		Bandage	GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	Sequence assembly visualisation	Genomics, Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	2	2	2	0	2016	44390	True	False	True
+bayescan	BayeScan	Detecting natural selection from population-based genetic data	bayescan	bayescan		BayeScan	BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8	64	True	False	True
+bbtools	bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.	bbmap	bbtools, bbmap		BBMap	BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	To update	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.08	bbmap	39.09	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	6	3	5	0	6	3	5	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	4	0	0	420	6381	True	False	True
+bigscape	bigscape	Construct sequence similarity networks of BGCs and groups them into GCF	BiG-SCAPE	BiG-SCAPE		BiG-SCAPE	A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+binning_refiner	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	binning_refiner	binning_refiner		Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	81	True	False	True
+biohansel	biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+biom_format	biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	biomformat	biomformat		biomformat	"This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods."	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	Formatting	Laboratory information management, Sequence analysis	2	2	6	0	2	2	6	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	98	3906	True	False	True
+biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+blast2go	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	101	1232	True	False	True
+blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	121	22499	True	False	True
+blastxml_to_top_descr	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	159	264558	True	False	True
+bracken	est_abundance	Bayesian Reestimation of Abundance with KrakEN	bracken	bracken		Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	Statistical calculation	Metagenomics, Microbial ecology	Up-to-date	https://ccb.jhu.edu/software/bracken/	Sequence Analysis, Metagenomics	bracken	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken	3.0	bracken	3.0	Statistical calculation	Metagenomics, Microbial ecology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	326	18351	True	False	True
+busco	busco	BUSCO assess genome and annotation completeness	busco	busco		BUSCO	Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://gitlab.com/ezlab/busco/-/releases	Sequence Analysis	busco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco	5.7.1	busco	5.7.1	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1804	86180	True	False	True
+cat	cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	cat_bins		CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat	5.2.3	cat	5.3	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	5	2	5	0	5	2	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	268	2878	True	False	True
+cd_hit_dup	cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	280	4474	True	False	True
+cemitool	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.26.0	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	98	True	False	True
+checkm	checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	checkm	checkm		CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	Up-to-date	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.3	checkm-genome	1.2.3	Sequence assembly validation, Sequence composition calculation, Statistical calculation	Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	0	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	390	5165	True	False	True
+clair3	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	clair3	clair3		Clair3	Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	1.0.8	clair3	1.0.10	Variant calling	Molecular genetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	68	1856	True	False	True
+clinod	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+clustalw	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	clustal2	clustal2		Clustal 2 (Clustal W, Clustal X)	Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.	Multiple sequence alignment	Phylogeny, Sequence analysis	Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw	2.1	clustalw	2.1	Multiple sequence alignment	Phylogeny, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	651	46793	True	False	True
+cmsearch_deoverlap	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	102	True	False	True
+codeml	codeml	Detects positive selection	paml	paml		PAML	Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml	4.9	paml	4.10.7	Probabilistic sequence generation	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	29	60901	True	False	True
+cojac	cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	cojac	cojac		COJAC	CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.2	cojac	0.9.2		Genetic variation	2	0	3	0	2	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	20	2757	True	False	True
+combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+combine_metaphlan_humann	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	147	True	False	True
+compare_humann2_output	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	332	True	False	True
+compleasm	compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	compleasm	compleasm		compleasm	"""Compleasm: a faster and more accurate reimplementation of BUSCO"""	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm	0.2.6	compleasm	0.2.6	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+concoct	concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	concoct	concoct		CONCOCT	A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct	1.1.0	concoct	1.1.0	Sequence clustering, Read binning	Metagenomics	0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	92	786	True	False	True
+coverm	coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm		CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	Local alignment	Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	72	529	True	False	True
+cryptogenotyper	CryptoGenotyper	CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	8518	True	False	True
+cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	5090	232004	True	False	True
+dada2	dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	dada2	dada2		dada2	This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	0	10	0	10	0	0	1	0	0	0	0	0	0	0	0	0	10	10	10	0	1263	66609	True	False	True
+das_tool	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	dastool		dastool	DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	Read binning	Metagenomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	24	706	True	False	True
+deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	4990	95752	True	False	True
+diamond	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	diamond		Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	Sequence alignment analysis	Sequence analysis, Proteins	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	3	3	3	0	0	0	1	0	0	0	0	0	0	0	0	0	3	3	0	963	49711	True	False	True
+disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	42	369	True	False	True
+dram	dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram		DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	Up-to-date	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.5.0	dram	1.5.0	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	39	6886	True	False	True
+drep	drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep		dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	Up-to-date	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.5.0	drep	3.5.0	Genome comparison	Metagenomics, Sequence analysis	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	46	646	True	False	True
+ectyper	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	9907	True	False	True
+effectiveT3	effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+eggnog_mapper	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2		eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	1	3	1	0	510	30565	True	False	True
+emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	107	107	107	107	107	0	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	107	107	107	0	1816	89530	True	False	True
+ete	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete		ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	Phylogenetic tree editing	Phylogenetics	0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	45	899	True	False	True
+export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan		export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	Conversion	Taxonomy, Metabolomics, Biomarkers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	200	5265	True	False	True
+ez_histograms	ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+fargene	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fargene		fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	52	459	True	False	True
+fastani	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity	fastani	fastani		FastANI	FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	250	3498	True	False	True
+fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+fastp	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp		fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	Sequence contamination filtering	Probes and primers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	2803	1055760	True	False	True
+fastqe	fastqe	FASTQE	fastqe	fastqe		FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	Sequencing quality control	Sequence analysis, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1266	4333	True	False	True
+fasttree	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree		FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11		Phylogenetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	379	55434	True	False	True
+featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	4679	696399	True	False	True
+filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	617	30483	True	False	True
+flashlfq	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	Label-free quantification	Proteomics experiment, Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	17	645	True	False	True
+flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	20904	True	False	True
+format_metaphlan2_output	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	166	5588	True	False	True
+fraggenescan	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan		FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	Gene prediction	Genetics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	68	1102	True	False	True
+freyja	freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja		Freyja	Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset	RNA-Seq quantification	Metagenomics	To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.1	RNA-Seq quantification	Metagenomics	2	0	4	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	55	20021	True	False	True
+frogs	FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis	frogs	frogs		FROGS	The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	To update	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	5.0.0	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	0	0	0	28	0	0	0	28	0	0	0	0	0	0	0	0	0	0	0	18	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	0	900	5906	True	False	True
+getmlst	getmlst	Download MLST datasets by species from pubmlst.org								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+ggplot2	ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2		ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		Visualisation	Data visualisation	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	5	0	0	0	0	0	0	3	0	0	0	0	0	5	5	5	0	1388	22148	True	False	True
+gi2taxonomy	Fetch Taxonomic Ranks	Fetch taxonomic representation	gi2taxonomy	gi2taxonomy		gi2taxonomy	The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	27	660	True	False	True
+glimmer	glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based	Glimmer makes gene predictions.	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	Sequence analysis, Genetic variation analysis	Sequence analysis	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	0	187	3965	True	False	True
+glimmer_hmm		GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	408	5484	True	False	True
+goseq	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq		GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	Gene functional annotation	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1210	19167	True	False	True
+graphlan	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	graphlan	graphlan		GraPhlAn	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	432	9277	True	False	True
+graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	136	6651	True	False	True
+gtdbtk	gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 	GTDB-Tk	GTDB-Tk		GTDB-Tk	a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	Up-to-date	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.4.0	gtdbtk	2.4.0	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+gubbins	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins		Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	145	3340	True	False	True
+hamronization	hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization		hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	117	4459	True	False	True
+hansel	bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	Biohansel		BioHansel	BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	339	True	False	True
+hifiasm_meta	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	hifiasm-meta		Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	Sequence assembly	Sequence assembly, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	137	True	False	True
+hivtrace	hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+hmmer3	hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	hmmer3	hmmer3		HMMER3	This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	0	12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	12	12	12	0	439	33702	True	False	True
+humann	humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	humann	humann		humann	HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	Up-to-date	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.9	humann	3.9	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	6	10	10	10	6	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	1037	19490	True	False	True
+hyphy	hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy		HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.62	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	17	2	17	2	17	2	17	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	12	17	12	0	161	10370	True	False	True
+hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354	True	False	True
+icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	69	1127	True	False	True
+infernal	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	infernal		Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	67	100294	True	False	True
+instrain	instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	instrain	instrain		InStrain	InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	SNP detection, Genome comparison	Mapping, Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	94	True	False	True
+integron_finder	integron_finder	"""IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"""	integron_finder	integron_finder		Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.5	integron_finder	2.0.5	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	58	52965	True	False	True
+interproscan	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi		InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	677	35243	True	False	True
+iprscan5		Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+iqtree	iqtree	Efficient phylogenomic software by maximum likelihood	iqtree	iqtree		iqtree	A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time	Phylogenetic analysis, Sequence analysis	Phylogenetics	Up-to-date	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.3.6	iqtree	2.3.6	Phylogenetic analysis, Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	681	21598	True	False	True
+isescan	isescan	"""ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."""	ISEScan	ISEScan		ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	Structural variation detection	Genomics, Sequence analysis, Genetic variation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	50	57581	True	False	True
+itsx	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	38	868	True	False	True
+ivar	ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing								Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.3	ivar	1.4.3			5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	4	0	0	0	4	0	0	0	0	0	5	5	5	0	1171	1224275	True	False	True
+jbrowse	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse		JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	Genome visualisation	Genomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	2	2	2	0	2346	18229	True	False	True
+jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138	True	False	True
+kat_filter	kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+kc-align	kc-align	Kc-Align custom tool	kc-align	kc-align		kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	Multiple sequence alignment	Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19	363	True	False	True
+khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	8	8	8	0	63	2022	True	False	True
+kleborate	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	kleborate	kleborate		Kleborate	Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	To update	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	3.0.9	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	38	319	True	False	True
+kofamscan	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	kofamscan	kofamscan		kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	Sequence analysis, Gene functional annotation	Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	33	594	True	False	True
+kraken	kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	kraken	kraken		Kraken	System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	Taxonomic classification	Taxonomy, Metagenomics	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	5	0	1209	33778	True	False	True
+kraken2	kraken2	Kraken2 for taxonomic designation.	kraken2	kraken2		kraken2	Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	Up-to-date	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.3	kraken2	2.1.3	Taxonomic classification	Taxonomy, Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	2367	185308	True	False	True
+kraken2tax	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	481	14683	True	False	True
+kraken_biom	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)								Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	182	1444	True	False	True
+kraken_taxonomy_report	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report		Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	Visualisation, Classification	Metagenomics, Taxonomy	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	354	2527	True	False	True
+krakentools	krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	krakentools		KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	Visualisation, Aggregation	Taxonomy, Metagenomics	6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	1	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	703	16525	True	False	True
+krocus	krocus	Predict MLST directly from uncorrected long reads	krocus	krocus		krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	Multilocus sequence typing, k-mer counting	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+lca_wrapper	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	137	True	False	True
+legsta	legsta	Performs in silico Legionella pneumophila sequence based typing.	legsta	legsta		legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	Sequence analysis	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	55	True	False	True
+lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	152	True	False	True
+limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1012	20344	True	False	True
+lineagespot	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	lineagespot	lineagespot		lineagespot	Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	37	True	False	True
+lorikeet	lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet		lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	Sequence analysis, Genotyping	Genotype and phenotype	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	647	True	False	True
+lotus2	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2		lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	To update	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.34.1	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	114	936	True	False	True
+m6anet	m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet		m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	True	False	True
+maaslin2	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	maaslin2	maaslin2		MaAsLin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	Up-to-date	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	1.18.0	bioconductor-maaslin2	1.18.0	Filtering, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	188	True	False	True
+mafft	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.526	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	2	0	0	0	2	0	0	0	0	0	2	2	2	0	817	143045	True	False	True
+make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+maker	maker, maker_map_ids	MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	maker	maker		MAKER	Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	Genome annotation	Genomics, DNA, Sequence analysis	To update	http://www.yandell-lab.org/software/maker.html	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker	2.31.11	maker	3.01.03	Genome annotation	Genomics, DNA, Sequence analysis	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	554	5591	True	False	True
+mapseq	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	mapseq	mapseq		MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .	k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	To update	https://github.com/jfmrod/MAPseq	Metagenomics	mapseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq	2.1.1	perl		k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	167	True	False	True
+mash	mash_screen, mash_sketch	Fast genome and metagenome distance estimation using MinHash	mash	mash		Mash	Fast genome and metagenome distance estimation using MinHash.	Sequence distance matrix generation	Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	Up-to-date	https://github.com/marbl/Mash	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash	2.3	mash	2.3	Sequence distance matrix generation	Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	27	9763	True	False	True
+maxbin2	maxbin2	clusters metagenomic contigs into bins	maxbin	maxbin		MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	To update	https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html	Metagenomics	maxbin2	mbernt	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2		maxbin2	2.2.7	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	118	2059	True	False	True
+maxquant	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering	Proteomics experiment, Proteomics, Statistics and probability	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	415	6078	True	False	True
+mcl	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	mcl	mcl		MCL	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.	Clustering, Network analysis, Gene regulatory network analysis	Molecular interactions, pathways and networks	Up-to-date	https://micans.org/mcl/man/mcl.html	Sequence Analysis	mcl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/mcl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl	22.282	mcl	22.282	Clustering, Gene regulatory network analysis	Molecular interactions, pathways and networks	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	29	True	False	True
+medaka	medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	medaka	medaka		Medaka	medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	2.0.0	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	2	0	0	0	0	0	3	3	3	0	768	99863	True	False	True
+megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	548	9530	True	False	True
+megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	54	475	True	False	True
+megan	megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma	MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data.  MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).	megan	megan		MEGAN	Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Sequence analysis, Taxonomic classification	Sequence analysis	To update	https://github.com/husonlab/megan-ce	Sequence Analysis	megan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan	6.21.7	megan	6.25.9	Sequence analysis, Taxonomic classification	Sequence analysis	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	261	3610	True	False	True
+meningotype	meningotype	Assign sequence type to N. meningitidis genome assemblies	meningotype	meningotype		meningotype	In silico typing of Neisseria meningitidis contigs.	Genotyping, Multilocus sequence typing	Microbiology, Genotype and phenotype	Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype	0.8.5	meningotype	0.8.5	Multilocus sequence typing	Microbiology, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483	True	False	True
+meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+metabat2	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT_2		MetaBAT 2	"an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning"	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	To update	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.17	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	2	1	2	2	2	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	192	4329	True	False	True
+metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	5.34c21f2	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	184	True	False	True
+metagene_annotator	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	115	636	True	False	True
+metagenomeseq	metagenomeseq_normalizaton	metagenomeSeq Normalization	metagenomeseq	metagenomeseq		metagenomeSeq	Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	To update	https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html	Metagenomics	metagenomeseq_normalization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq	1.16.0-0.0.1	bioconductor-metagenomeseq	1.43.0	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6	753	True	False	True
+metanovo	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	4181	True	False	True
+metaphlan	customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	metaphlan	metaphlan		MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.	Nucleic acid sequence analysis, Phylogenetic tree analysis	Metagenomics, Phylogenomics	Up-to-date	https://github.com/biobakery/MetaPhlAn	Metagenomics	metaphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan	4.1.1	metaphlan	4.1.1	Nucleic acid sequence analysis	Metagenomics, Phylogenomics	1	2	4	4	1	2	4	4	0	0	0	0	0	0	0	0	0	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	499	11069	True	False	True
+metaquantome	metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome		metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	104	2522	True	False	True
+metawrapmg	metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	metawrap	metawrap		MetaWRAP	MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	Up-to-date	https://github.com/bxlab/metaWRAP	Metagenomics	metawrapmg_binning	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg	1.3.0	metawrap-mg	1.3.0	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	109	2206	True	False	True
+miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	178	11938	True	False	True
+minipolish	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	185	True	False	True
+miniprot	miniprot, miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	miniprot	miniprot		miniprot	Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	Up-to-date	https://github.com/lh3/miniprot	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot	0.13	miniprot	0.13	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	30	842	True	False	True
+mitos	mitos, mitos2	de-novo annotation of metazoan mitochondrial genomes	mitos	mitos		MITOS	De novo metazoan mitochondrial genome annotation.	Genome annotation	Zoology, Whole genome sequencing	To update	http://mitos.bioinf.uni-leipzig.de/	Sequence Analysis	mitos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos	1.1.7	mitos	2.1.9	Genome annotation	Zoology, Whole genome sequencing	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	0	236	100920	True	False	True
+mlst	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst		MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	Multilocus sequence typing	Immunoproteins and antigens	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	635	9304	True	False	True
+mob_suite	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.9			0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	322	89021	True	False	True
+mothur	mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn	Mothur wrappers	mothur	mothur		mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	129	129	129	129	129	129	129	129	0	0	0	0	0	0	0	0	0	0	128	0	3	0	0	0	0	0	0	0	0	0	0	0	0	126	129	129	0	14353	302916	True	False	True
+mrbayes	mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	True	False	True
+msconvert	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert		msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			Filtering, Formatting	Proteomics, Proteomics experiment	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	189	19958	True	False	True
+msstatstmt	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	726	True	False	True
+multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	53	True	False	True
+multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	8320	162790	True	False	True
+mykrobe	mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe		Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+mykrobe_parser	mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+mz_to_sqlite	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	Conversion, Peptide database search	Proteomics, Biological databases	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33	844	True	False	True
+nanocompore	nanocompore_db, nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Nanocompore	Nanocompore		Nanocompore	RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	3	836	True	False	True
+nanoplot	nanoplot	Plotting tool for long read sequencing data and alignments	nanoplot	nanoplot		NanoPlot	NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences	Scatter plot plotting, Box-Whisker plot plotting	Genomics	Up-to-date	https://github.com/wdecoster/NanoPlot	Visualization	nanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot	1.43.0	nanoplot	1.43.0	Scatter plot plotting, Box-Whisker plot plotting	Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	2195	63235	True	False	True
+nanopolishcomp	nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate	NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.	nanopolishcomp	nanopolishcomp		NanopolishComp	NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	To update	https://a-slide.github.io/NanopolishComp	Sequence Analysis	nanopolishcomp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp	0.6.11	nanopolishcomp	0.6.12	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	15	1074	True	False	True
+ncbi_blast_plus	blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper	NCBI BLAST+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	devteam	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	2.14.1	python				16	16	16	16	16	16	16	16	0	0	0	0	0	0	0	0	0	0	16	15	16	0	0	0	0	0	0	16	0	0	0	0	16	16	16	15	0	4066	365597	True	False	True
+ncbi_fcs_gx	ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).	ncbi_fcs	ncbi_fcs		NCBI fcs	The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	Up-to-date	https://github.com/ncbi/fcs-gx	Sequence Analysis	ncbi_fcs_gx	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	0.5.4	ncbi-fcs-gx	0.5.4	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+newick_utils	newick_display	Perform operations on Newick trees	newick_utilities	newick_utilities		Newick Utilities	The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.	Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction	Phylogeny, Genomics, Computer science	To update	http://cegg.unige.ch/newick_utils	Visualization, Metagenomics	newick_utils	iuc	https://github.com/tjunier/newick_utils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils	1.6+galaxy1	newick_utils	1.6		Phylogeny, Genomics, Computer science	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	448	25505	True	False	True
+nextclade	nextalign, nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	nextclade	nextclade		Nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.	Methylation analysis, Variant calling	Genomics, Sequence analysis, Cladistics	To update	https://github.com/nextstrain/nextclade	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade	2.7.0	nextalign	2.14.0	Methylation analysis, Variant calling	Genomics, Cladistics	1	1	2	2	1	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	0	0	0	1	0	0	0	0	0	0	2	0	0	210	4080	True	False	True
+nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268	True	False	True
+nonpareil	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil		nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.5.5	Operation		1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	142	True	False	True
+nucleosome_prediction	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	861	True	False	True
+nugen_nudup	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	1	1	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	45	True	False	True
+obitools	obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq	OBITools is a set of programs developed to simplify the manipulation of sequence files	obitools	obitools		OBITools	Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	Up-to-date	http://metabarcoding.org/obitools	Sequence Analysis	obitools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools	1.2.13	obitools	1.2.13	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	0	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	503	26251	True	False	True
+omark	omark	Proteome quality assessment software	omark	omark		OMArk	Proteome quality assessment software	Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	To update	https://github.com/DessimozLab/OMArk	Sequence Analysis	omark	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark	0.3.0			Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+orfipy	orfipy	Galaxy wrapper for ORFIPY	orfipy	orfipy		orfipy	A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	Up-to-date	https://github.com/urmi-21/orfipy	Sequence Analysis	orfipy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy	0.0.4	orfipy	0.0.4	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	774	True	False	True
+orthofinder	orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	OrthoFinder	OrthoFinder		OrthoFinder	OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.	Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis	Up-to-date	https://github.com/davidemms/OrthoFinder	Phylogenetics, Sequence Analysis	orthofinder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder	2.5.5	orthofinder	2.5.5	Genome comparison, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	239	1333	True	False	True
+peptideshaker	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.11			4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	4	2	0	485	17477	True	False	True
+pfamscan	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	19	165	True	False	True
 pharokka	pharokka	rapid standardised annotation tool for bacteriophage genomes and metagenomes	pharokka	pharokka		Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.	Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	To update	https://github.com/gbouras13/pharokka	Genome annotation	pharokka	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	1.3.2	"
                 pharokka
-            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	74	2565	True	False	True
-phyloseq	phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	phyloseq	phyloseq		phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq	1.46.0	bioconductor-phyloseq	1.46.0	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	0	1	4	4	0	1	4	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	82	812	True	False	True
-phyml	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	phyml	phyml		PhyML	Phylogenetic estimation software using Maximum Likelihood	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Bioinformatics, Phylogenetics	Up-to-date	http://www.atgc-montpellier.fr/phyml/	Phylogenetics	phyml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml	3.3.20220408	phyml	3.3.20220408		Phylogenetics, Bioinformatics, Phylogenetics	0	1	1	1	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	104	1770	True	False	True
-picrust	picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes	PICRUSt wrappers	picrust	picrust		PICRUSt	PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust	1.1.1	picrust	1.1.4	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	0	6	5	6	0	6	5	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	45	1095	True	False	True
-picrust2	picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions	PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	picrust2	picrust2		PICRUSt2	PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	Up-to-date	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.3	picrust2	2.5.3	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	88	1000	True	False	True
-plasflow	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	plasflow	plasflow		PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.	Sequence analysis	Metagenomics	Up-to-date	https://github.com/smaegol/PlasFlow	Sequence Analysis	plasflow	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow	1.1.0	plasflow	1.1.0	Sequence analysis	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	278	22589	True	False	True
-plasmidfinder	plasmidfinder	"""PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"""	PlasmidFinder	PlasmidFinder		PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	Up-to-date	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	Sequence Analysis	plasmidfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder	2.1.6	plasmidfinder	2.1.6	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	22	True	False	True
-plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-polypolish	polypolish	"""Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."""	Polypolish	Polypolish		Polypolish	Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	To update	https://github.com/rrwick/Polypolish	Sequence Analysis	polypolish	iuc	https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish	0.5.0	polypolish	0.6.0	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	239	True	False	True
-prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-prokka	prokka	Rapid annotation of prokaryotic genomes	prokka	prokka		Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka	1.14.6	prokka	1.14.6	Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	0	1	1	0	3233	371445	True	False	True
-promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-proteinortho	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho		Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	To update	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.2	Sequence clustering, Sequence analysis	Comparative genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	200	3320	True	False	True
-pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	350	21123	True	False	True
-pygenometracks	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	pygenometracks	pygenometracks		pyGenomeTracks	reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	Visualisation, Formatting	Model organisms, Imaging, Workflows	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	377	11332	True	False	True
-qiime_add_on	qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_add_on, qiime_core		qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	68	1909	True	False	True
-qiime_core	qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file	QIIME to perform microbial community analysis	qiime_core	qiime_core		qiime_core	QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	32	32	0	0	32	32	0	0	0	0	0	0	0	0	0	0	0	0	31	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	0	1155	28681	True	False	True
-qualimap	qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq	Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.	qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	Up-to-date	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.3	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	1	4	4	4	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1	0	0	0	1	0	0	0	0	0	0	0	4	4	0	1328	664470	True	False	True
-quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	3567	51567	True	False	True
-quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	True	False	True
-rRNA	meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-racon	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	309	21353	True	False	True
-rasusa	rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa		rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	2.0.0	rasusa	2.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-raxml	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml		RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	Sequence analysis	Phylogenetics	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	383	6808	True	False	True
-read_it_and_keep	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep		read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	Filtering, Genome alignment	Pathology, Genomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	3370	True	False	True
-reago	reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-recentrifuge	recentrifuge	"""With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."""	Recentrifuge	Recentrifuge		Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.14.1	recentrifuge	1.14.1	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	48	331	True	False	True
-repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	True	False	True
-roary	roary	Roary the pangenome pipeline	roary	roary		Roary	A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary	3.13.0	roary	3.13.0	Genome assembly	DNA, Genomics, Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	656	12225	True	False	True
-rseqc	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	22	22	22	22	22	0	0	0	0	0	0	0	0	0	0	0	0	22	0	0	0	0	22	0	0	0	22	0	0	0	0	0	0	0	22	22	0	3206	133498	True	False	True
-salmon	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	2	3	1	2	2	3	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	2	0	0	0	0	0	0	0	3	3	0	969	61937	True	False	True
-sarscov2formatter	sarscov2formatter	sarscov2formatter custom script								Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	173	True	False	True
-sarscov2summary	sarscov2summary	sarscov2summary custom script								To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	140	True	False	True
-scoary	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	scoary	scoary		Scoary	Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	61	676	True	False	True
-semibin	semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	semibin	semibin		SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	0	0	6	1	0	0	6	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	39	542	True	False	True
-seqkit	seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit		seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	Up-to-date	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.8.2	seqkit	2.8.2	DNA transcription, Sequence trimming, DNA translation	Database management, Sequence analysis	0	2	5	2	0	2	5	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	129	1964	True	False	True
-seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-seqsero2	seqsero2	Salmonella serotype prediction from genome sequencing data	seqsero2	seqsero2		SeqSero2	"rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)"	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	True	False	True
-shorah	shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	shorah	shorah		ShoRAH	Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	To update	https://github.com/cbg-ethz/shorah/blob/master/README.md	Sequence Analysis	shorah_amplicon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah	1.1.3	shorah	1.99.2	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1008	41600	True	False	True
-sistr_cmd	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	133	2489	True	False	True
-smallgenomeutilities	smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe		V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.1	smallgenomeutilities	0.4.1	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	121	True	False	True
-smalt	smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-snap	snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap		SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	Gene prediction	DNA polymorphism, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	133	1349	True	False	True
-snippy	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy		snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	Phylogenetic tree visualisation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	3	3	3	3	3	3	3	3	0	0	0	0	2	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	2	0	1372	105708	True	False	True
-sonneityping	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping		sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	True	False	True
-sortmerna	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	376	18183	True	False	True
-spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	coronaspades, biosyntheticspades, metaplasmidspades, plasmidspades, metaspades, rnaspades, metaviralspades, rnaviralspades, spades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	1	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	0	0	9	3	0	3547	72953	True	False	True
-spotyping	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping		SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	1278	True	False	True
-sr_bowtie	bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-srst2	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	205	True	False	True
-srst2	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2		srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.20	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	205	True	False	True
-staramr	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	889	12673	True	False	True
-stringmlst	stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-structure	structure	for using multi-locus genotype data to investigate population structure.	structure	structure		Structure	The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Genetic variation analysis	Population genetics	Up-to-date	https://web.stanford.edu/group/pritchardlab/structure.html	Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	Genetic variation analysis	Population genetics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	59	2623	True	False	True
-suite_qiime2__alignment	qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	13	True	False	True
-suite_qiime2__composition	qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.5.0+q2galaxy.2024.5.0					4	4	4	2	4	4	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	2	5	True	False	True
-suite_qiime2__cutadapt	qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	5	67	True	False	True
-suite_qiime2__dada2	qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	31	202	True	False	True
-suite_qiime2__deblur	qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	9	73	True	False	True
-suite_qiime2__demux	qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	26	114	True	False	True
-suite_qiime2__diversity	qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.5.0+q2galaxy.2024.5.0					21	21	21	21	21	21	21	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	0	43	168	True	False	True
-suite_qiime2__diversity_lib	qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	4	4	True	False	True
-suite_qiime2__emperor	qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	2	6	True	False	True
-suite_qiime2__feature_classifier	qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.5.0+q2galaxy.2024.5.0					10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	48	263	True	False	True
-suite_qiime2__feature_table	qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.5.0+q2galaxy.2024.5.0					17	17	17	17	17	17	17	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	59	213	True	False	True
-suite_qiime2__fragment_insertion	qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	20	True	False	True
-suite_qiime2__longitudinal	qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.5.0+q2galaxy.2024.5.0					11	11	11	11	11	11	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	0	6	14	True	False	True
-suite_qiime2__metadata	qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	40	232	True	False	True
-suite_qiime2__phylogeny	qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	12	37	True	False	True
-suite_qiime2__quality_control	qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	True	False	True
-suite_qiime2__quality_filter	qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.5.0+q2galaxy.2024.5.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	13	True	False	True
-suite_qiime2__rescript	qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.5.0+q2galaxy.2024.5.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-suite_qiime2__sample_classifier	qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.5.0+q2galaxy.2024.5.0					15	15	15	15	15	15	15	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	0	0	1	1	True	False	True
-suite_qiime2__taxa	qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	22	172	True	False	True
-suite_qiime2__vsearch	qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.5.0+q2galaxy.2024.5.0					8	8	8	7	8	8	8	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	8	16	True	False	True
-suite_qiime2_core										To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-suite_qiime2_core__tools	qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.5.0+dist.he540b0b0					2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	124	7087	True	False	True
-t2ps	Draw_phylogram	Draw phylogeny	t2ps	t2ps		Draw phylogeny	"""Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper"	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	31	457	True	False	True
-t2t_report	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	26	947	True	False	True
-t_coffee	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b			0	0	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	70	8690	True	False	True
-taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	0	1	1	0	1801	27426	True	False	True
-tb-profiler	tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	6.2.1	tb-profiler	6.3.0	Antimicrobial resistance prediction		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	198	5161	True	False	True
-tooldistillator	tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator		ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.9	tooldistillator	0.9	Parsing	Microbiology, Bioinformatics, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	84	907	True	False	True
-transtermhp	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	transtermhp	transtermhp		TransTermHP	TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	229	True	False	True
-trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2334	238699	True	False	True
-trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942	True	False	True
-unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1558	65732	True	False	True
-unipept	unipept	Unipept retrieves metaproteomics information	unipept	unipept		Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	115	5005	True	False	True
-uniprotxml_downloader	uniprotxml_downloader	Download UniProt proteome in XML or fasta format								To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	79	1360	True	False	True
-usher	usher_matutils, usher	UShER toolkit wrappers	usher	usher		usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Cladistics, Genotype and phenotype, Phylogenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	1060	True	False	True
-valet	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	637	True	False	True
-vapor	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor		VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	94	3164	True	False	True
-varvamp	varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp		varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology, Probes and primers	Up-to-date	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.0	PCR primer design	Virology, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-vegan	vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	74	2020	True	False	True
-velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	2083	25420	True	False	True
-velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	255	4741	True	False	True
-virAnnot	virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers	virannot	virannot		virAnnot	"VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy."	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.0.1+galaxy0	biopython	1.70	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-vsearch	vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	vsearch	vsearch		VSEARCH	High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.28.1	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	8	8	8	8	8	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	0	0	0	0	0	8	0	0	0	0	0	0	0	8	8	0	182	8507	True	False	True
-wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660	True	False	True
+            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	74	2565	True	False	True
+phyloseq	phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	phyloseq	phyloseq		phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq	1.46.0	bioconductor-phyloseq	1.46.0	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	0	1	4	4	0	1	4	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	82	812	True	False	True
+phyml	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	phyml	phyml		PhyML	Phylogenetic estimation software using Maximum Likelihood	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Bioinformatics, Phylogenetics	Up-to-date	http://www.atgc-montpellier.fr/phyml/	Phylogenetics	phyml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml	3.3.20220408	phyml	3.3.20220408		Phylogenetics, Bioinformatics, Phylogenetics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	104	1770	True	False	True
+picrust	picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes	PICRUSt wrappers	picrust	picrust		PICRUSt	PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust	1.1.1	picrust	1.1.4	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	0	6	5	6	0	6	5	6	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	45	1095	True	False	True
+picrust2	picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions	PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	picrust2	picrust2		PICRUSt2	PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	Up-to-date	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.3	picrust2	2.5.3	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	88	1000	True	False	True
+plasflow	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	plasflow	plasflow		PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.	Sequence analysis	Metagenomics	Up-to-date	https://github.com/smaegol/PlasFlow	Sequence Analysis	plasflow	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow	1.1.0	plasflow	1.1.0	Sequence analysis	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	278	22589	True	False	True
+plasmidfinder	plasmidfinder	"""PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"""	PlasmidFinder	PlasmidFinder		PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	Up-to-date	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	Sequence Analysis	plasmidfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder	2.1.6	plasmidfinder	2.1.6	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	22	True	False	True
+plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+polypolish	polypolish	"""Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."""	Polypolish	Polypolish		Polypolish	Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	To update	https://github.com/rrwick/Polypolish	Sequence Analysis	polypolish	iuc	https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish	0.5.0	polypolish	0.6.0	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	239	True	False	True
+prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+prokka	prokka	Rapid annotation of prokaryotic genomes	prokka	prokka		Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka	1.14.6	prokka	1.14.6	Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	3233	371445	True	False	True
+promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+proteinortho	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho		Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	To update	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.2	Sequence clustering, Sequence analysis	Comparative genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	200	3320	True	False	True
+pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	350	21123	True	False	True
+pygenometracks	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	pygenometracks	pygenometracks		pyGenomeTracks	reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	Visualisation, Formatting	Model organisms, Imaging, Workflows	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	377	11332	True	False	True
+qiime_add_on	qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_add_on, qiime_core		qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	68	1909	True	False	True
+qiime_core	qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file	QIIME to perform microbial community analysis	qiime_core	qiime_core		qiime_core	QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	32	32	0	0	32	32	0	0	0	0	0	0	0	0	0	0	31	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	0	1155	28681	True	False	True
+qualimap	qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq	Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.	qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	Up-to-date	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.3	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	1	4	4	4	1	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1	0	0	0	1	0	0	0	0	0	4	4	4	0	1328	664470	True	False	True
+quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	3567	51567	True	False	True
+quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	True	False	True
+rRNA	meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+racon	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	309	21353	True	False	True
+rasusa	rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa		rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	2.0.0	rasusa	2.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+raxml	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml		RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	Sequence analysis	Phylogenetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	383	6808	True	False	True
+read_it_and_keep	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep		read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	Filtering, Genome alignment	Pathology, Genomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	3370	True	False	True
+reago	reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+recentrifuge	recentrifuge	"""With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."""	Recentrifuge	Recentrifuge		Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.15.0	recentrifuge	1.15.0	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	48	331	True	False	True
+repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	True	False	True
+roary	roary	Roary the pangenome pipeline	roary	roary		Roary	A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary	3.13.0	roary	3.13.0	Genome assembly	DNA, Genomics, Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	656	12225	True	False	True
+rseqc	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	22	22	22	22	22	0	0	0	0	0	0	0	0	0	0	22	0	0	0	0	22	0	0	0	22	0	0	0	0	0	22	22	22	0	3206	133498	True	False	True
+salmon	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	2	3	1	2	2	3	1	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	2	0	0	0	0	0	3	3	3	0	969	61937	True	False	True
+sarscov2formatter	sarscov2formatter	sarscov2formatter custom script								Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	173	True	False	True
+sarscov2summary	sarscov2summary	sarscov2summary custom script								To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	140	True	False	True
+scoary	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	scoary	scoary		Scoary	Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	61	676	True	False	True
+semibin	semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	semibin	semibin		SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	0	0	6	1	0	0	6	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	39	542	True	False	True
+seqkit	seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit		seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	Up-to-date	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.8.2	seqkit	2.8.2	DNA transcription, Sequence trimming, DNA translation	Database management, Sequence analysis	0	2	5	3	0	2	5	3	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	129	1964	True	False	True
+seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+seqsero2	seqsero2	Salmonella serotype prediction from genome sequencing data	seqsero2	seqsero2		SeqSero2	"rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)"	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	True	False	True
+shorah	shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	shorah	shorah		ShoRAH	Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	To update	https://github.com/cbg-ethz/shorah/blob/master/README.md	Sequence Analysis	shorah_amplicon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah	1.1.3	shorah	1.99.2	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1008	41600	True	False	True
+sistr_cmd	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	133	2489	True	False	True
+smallgenomeutilities	smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe		V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.1	smallgenomeutilities	0.4.1	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	121	True	False	True
+smalt	smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+snap	snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap		SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	Gene prediction	DNA polymorphism, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	133	1349	True	False	True
+snippy	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy		snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	Phylogenetic tree visualisation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	0	1372	105708	True	False	True
+sonneityping	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping		sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	True	False	True
+sortmerna	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	376	18183	True	False	True
+spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	3	9	3	0	3547	72953	True	False	True
+spotyping	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping		SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	1278	True	False	True
+sr_bowtie	bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+srst2	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	205	True	False	True
+srst2	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2		srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.21	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	205	True	False	True
+staramr	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	889	12673	True	False	True
+stringmlst	stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+structure	structure	for using multi-locus genotype data to investigate population structure.	structure	structure		Structure	The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Genetic variation analysis	Population genetics	Up-to-date	https://web.stanford.edu/group/pritchardlab/structure.html	Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	Genetic variation analysis	Population genetics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	59	2623	True	False	True
+suite_qiime2__alignment	qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	13	True	False	True
+suite_qiime2__composition	qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.5.0+q2galaxy.2024.5.0					4	4	4	2	4	4	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	2	5	True	False	True
+suite_qiime2__cutadapt	qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	5	67	True	False	True
+suite_qiime2__dada2	qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	31	202	True	False	True
+suite_qiime2__deblur	qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	9	73	True	False	True
+suite_qiime2__demux	qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	26	114	True	False	True
+suite_qiime2__diversity	qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.5.0+q2galaxy.2024.5.0					21	21	22	21	21	21	22	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	0	43	168	True	False	True
+suite_qiime2__diversity_lib	qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	4	4	True	False	True
+suite_qiime2__emperor	qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	2	6	True	False	True
+suite_qiime2__feature_classifier	qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.5.0+q2galaxy.2024.5.0					10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	48	263	True	False	True
+suite_qiime2__feature_table	qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.5.0+q2galaxy.2024.5.0					17	17	17	17	17	17	17	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	59	213	True	False	True
+suite_qiime2__fragment_insertion	qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	20	True	False	True
+suite_qiime2__longitudinal	qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.5.0+q2galaxy.2024.5.0					11	11	11	11	11	11	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	0	6	14	True	False	True
+suite_qiime2__metadata	qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	40	232	True	False	True
+suite_qiime2__phylogeny	qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	12	37	True	False	True
+suite_qiime2__quality_control	qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	True	False	True
+suite_qiime2__quality_filter	qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.5.0+q2galaxy.2024.5.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	13	True	False	True
+suite_qiime2__rescript	qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.5.0+q2galaxy.2024.5.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+suite_qiime2__sample_classifier	qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.5.0+q2galaxy.2024.5.0					15	15	15	15	15	15	15	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	0	0	1	1	True	False	True
+suite_qiime2__taxa	qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	22	172	True	False	True
+suite_qiime2__vsearch	qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.5.0+q2galaxy.2024.5.0					8	8	8	7	8	8	8	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	8	16	True	False	True
+suite_qiime2_core										To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+suite_qiime2_core__tools	qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.5.0+dist.he540b0b0					2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	124	7087	True	False	True
+t2ps	Draw_phylogram	Draw phylogeny	t2ps	t2ps		Draw phylogeny	"""Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper"	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	31	457	True	False	True
+t2t_report	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	26	947	True	False	True
+t_coffee	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	70	8690	True	False	True
+taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	1801	27426	True	False	True
+tb-profiler	tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	6.2.1	tb-profiler	6.3.0	Antimicrobial resistance prediction		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	198	5161	True	False	True
+tooldistillator	tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator		ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.9.1	tooldistillator	0.9.1	Parsing	Microbiology, Bioinformatics, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	0	84	907	True	False	True
+transtermhp	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	transtermhp	transtermhp		TransTermHP	TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	229	True	False	True
+trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	2334	238699	True	False	True
+trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942	True	False	True
+unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1558	65732	True	False	True
+unipept	unipept	Unipept retrieves metaproteomics information	unipept	unipept		Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	115	5005	True	False	True
+uniprotxml_downloader	uniprotxml_downloader	Download UniProt proteome in XML or fasta format								To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	79	1360	True	False	True
+usher	usher_matutils, usher	UShER toolkit wrappers	usher	usher		usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Cladistics, Genotype and phenotype, Phylogenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	1060	True	False	True
+valet	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20	637	True	False	True
+vapor	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor		VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	94	3164	True	False	True
+varvamp	varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp		varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology, Probes and primers	To update	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.1	PCR primer design	Virology, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+vegan	vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	74	2020	True	False	True
+velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	2083	25420	True	False	True
+velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	4741	True	False	True
+virAnnot	virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers	virannot	virannot		virAnnot	"VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy."	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.1.0+galaxy0	biopython	1.70	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+vsearch	vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	vsearch	vsearch		VSEARCH	High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.29.0	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	8	8	8	8	8	8	8	8	0	0	0	0	0	0	0	0	0	0	0	8	8	0	0	0	0	0	0	8	0	0	0	0	0	8	8	8	0	182	8507	True	False	True
+wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660	True	False	True
diff --git a/communities/microgalaxy/resources/tools_filtered_by_ts_categories.tsv b/communities/microgalaxy/resources/tools_filtered_by_ts_categories.tsv
index cf3a2d59..c54f0f36 100644
--- a/communities/microgalaxy/resources/tools_filtered_by_ts_categories.tsv
+++ b/communities/microgalaxy/resources/tools_filtered_by_ts_categories.tsv
@@ -1,825 +1,827 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on BF2I-MAP	Tools available on BioBix	Tools available on CIRM-CFBP	Tools available on Center for Phage Technology (CPT)	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-AggregateAlignments	graphclust_aggregate_alignments	Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.								Up-to-date		RNA	graphclust_aggregate_alignments	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments	0.6.0	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	116	True	False	False
-AlignCluster	graphclust_align_cluster	Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.								To update		RNA	graphclust_align_cluster	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster	0.1	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	10	3060	True	False	False
-CMFinder	cmFinder	Determines consensus motives for sequences.								To update		RNA	graphclust_cmfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	14	45191	True	False	False
-CollectResults	glob_report	Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.								To update		RNA	graphclust_postprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	14	1961	True	False	False
-CollectResultsNoAlign	graphclust_glob_report_no_align	Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.								To update		RNA	graphclust_postprocessing_no_align	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	108	True	False	False
-EMLassemblyline	eal_table_template, eal_templates, eml2eal, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.1+galaxy0	r-emlassemblyline				0	0	9	9	0	0	9	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	102	True	False	False
-Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	82	True	False	False
-GAFA	gafa	Gene Align and Family Aggregator								To update	http://aequatus.tgac.ac.uk	Visualization	gafa	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA	0.3.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	45	True	False	False
-GSPAN	gspan	Second step of GraphClust								To update		RNA	graphclust_fasta_to_gspan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	133	True	False	False
-Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-LocARNAGraphClust	locarna_best_subtree	MLocARNA computes a multiple sequence-structure alignment of RNA sequences.								To update		RNA	graphclust_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	45325	True	False	False
-NSPDK	NSPDK_candidateClust, nspdk_sparse	Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.								To update		RNA	graphclust_nspdk	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	9.2.3.1	graphclust-wrappers	0.6.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	28	62388	True	False	False
-PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	73	1004	True	False	True
-Plotting	motifFinderPlot	Plotting results for GraphClust								To update		RNA	graphclust_motif_finder_plot	rnateam	https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting	0.4	seaborn				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	68	True	False	False
-PrepareForMlocarna	preMloc	This tool prepares files for locarna step.								To update		RNA	graphclust_prepocessing_for_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	1932	True	False	False
-Preprocessing	preproc	Preprocessing input for GraphClust								To update		RNA	graphclust_preprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	1758	True	False	False
-Structure_GSPAN	structure_to_gspan	Convert RNA structure to GSPAN graphs								To update		RNA	structure_to_gspan	rnateam	https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	2925	True	False	False
-ThermoRawFileParser	thermo_raw_file_converter	Thermo RAW file converter								To update	https://github.com/compomics/ThermoRawFileParser	Proteomics	thermo_raw_file_converter	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	1.3.4	thermorawfileparser	1.4.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	2689	True	False	False
-TreeBest	treebest_best	TreeBeST best	treebest	treebest		TreeBeST	TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	984	True	False	True
-TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	42	True	False	False
-abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-abricate	abricate, abricate_list, abricate_summary	Mass screening of contigs for antiobiotic resistance genes	ABRicate	ABRicate		ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.	Antimicrobial resistance prediction	Genomics, Microbiology	Up-to-date	https://github.com/tseemann/abricate	Sequence Analysis	abricate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate	1.0.1	abricate	1.0.1	Antimicrobial resistance prediction	Genomics, Microbiology	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	1764	496717	True	False	True
-abritamr	abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	abritamr	abritamr		abriTAMR	an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	To update	https://zenodo.org/record/7370628	Sequence Analysis	abritamr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr	1.0.14	abritamr	1.0.19	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	To update	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.7	abyss	2.3.8	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	391	4278	True	False	True
-adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	37	217	True	False	False
-aegean	aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval	AEGeAn toolkit wrappers	gaeval	gaeval		GAEVAL	Gene Annotation EVAluation.	Sequence annotation	Sequence analysis, Gene structure	Up-to-date	https://github.com/BrendelGroup/AEGeAn	Transcriptomics, Sequence Analysis	aegean	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean	0.16.0	aegean	0.16.0	Sequence annotation	Sequence analysis, Gene structure	1	4	4	4	1	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	47	168	True	False	False
-aldex2	aldex2	Performs analysis Of differential abundance taking sample variation into account	aldex2	aldex2		ALDEx2	A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	Statistical inference	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	13	129	True	False	True
-align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	329	True	False	False
-amplican	amplican	AmpliCan is an analysis tool for genome editing.	amplican	amplican		amplican	It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	53	True	False	True
-ampvis2	ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn	ampvis2	ampvis	ampvis		ampvis	ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.	Analysis, Visualisation	Biodiversity	To update	https://github.com/MadsAlbertsen/ampvis2/	Metagenomics	ampvis2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2	2.8.9			Analysis, Visualisation	Biodiversity	0	0	19	0	0	0	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	42	267	True	False	False
-amrfinderplus	amrfinderplus	"""AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms."	amrfinderplus	amrfinderplus		AMRFinderPlus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms"	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.12.8	ncbi-amrfinderplus	3.12.8	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	591	True	False	True
-ancombc	ancombc	Performs analysis of compositions of microbiomes with bias correction.	ancombc	ancombc		ANCOMBC	Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	7	True	False	True
-anndata	anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Transcriptomics, Sequence Analysis	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.3	anndata	0.6.22.post1			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	625	35620	True	False	False
-annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1175	25975	True	False	False
-antarna	antarna	antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .								To update		RNA	antarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna	1.1	antarna	2.0.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	52	True	False	False
-antismash	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash		antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	279	14596	True	False	True
-aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-aresite2	AREsite2_REST	AREsite2 REST Interface								To update	http://rna.tbi.univie.ac.at/AREsite	RNA, Data Source, Sequence Analysis	aresite2	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	65	True	False	False
-argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-arriba	arriba, arriba_draw_fusions, arriba_get_filters	Arriba detects fusion genes in RNA-Seq data after running RNA-STAR								Up-to-date	https://github.com/suhrig/arriba	Sequence Analysis, Transcriptomics	arriba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba	2.4.0	arriba	2.4.0			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	38	3528	True	False	False
-art	art_454, art_illumina, art_solid	Simulator for Illumina, 454, and SOLiD sequencing data	art	art		ART	ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD	Conversion	Bioinformatics	To update	http://www.niehs.nih.gov/research/resources/software/biostatistics/art/	Sequence Analysis, Data Source	art	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/art	https://github.com/galaxyproject/tools-iuc/tree/main/tools/art	2014.11.03.0	art	2016.06.05	Conversion	Bioinformatics	0	0	3	0	0	0	3	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-artic	artic_guppyplex, artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	artic	artic		ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	Sequence alignment	Genomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	1	0	123	8175	True	False	True
-assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-astral	astral	Tool for estimating an unrooted species tree given a set of unrooted gene trees								Up-to-date	https://github.com/smirarab/ASTRAL	Phylogenetics	astral	iuc	https://github.com/usegalaxy-be/galaxytools/tree/main/astral	https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral	5.7.8	astral-tree	5.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-augustus	augustus	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.								To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	3.1.0	augustus	3.5.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	516	8864	True	False	False
-augustus	augustus, augustus_training	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.	augustus	augustus		AUGUSTUS	AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.	Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus	3.4.0	augustus	3.5.0	Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	685	11245	True	False	False
-b2btools	b2btools_single_sequence	This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.	b2btools	b2btools		b2bTools	The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA	Protein disorder prediction, Protein secondary structure prediction, Protein feature detection		To update	https://bio2byte.be	Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools	3.0.5+galaxy0	b2btools	3.0.7	Protein disorder prediction, Protein secondary structure prediction		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	345	True	False	False
-bakta	bakta	"""Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."""	bakta	bakta		Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	To update	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.3	bakta	1.9.4	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	151	2982	True	False	True
-bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-bamclipper	bamclipper	Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.								Up-to-date	https://github.com/tommyau/bamclipper	Sequence Analysis	bamclipper	nml	https://github.com/tommyau/bamclipper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper	1.0.0	bamclipper	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-bamhash	bamhash	Hash BAM and FASTQ files to verify data integrity								Up-to-date	https://github.com/DecodeGenetics/BamHash	Sequence Analysis	bamhash	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	1.1	bamhash	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	169	True	False	False
-bamparse	bamparse	Generates hit count lists from bam alignments.								To update	http://artbio.fr	RNA, Transcriptomics	bamparse	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	4.1.1	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-bamtools	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	208	14021	True	False	True
-bamtools_filter	bamFilter	Filter BAM datasets on various attributes using bamtools filter	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1195	114863	True	False	False
-bamtools_split	bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag	Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett.	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	197	4328	True	False	False
-bamutil	bamutil_clip_overlap, bamutil_diff	bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.								To update	https://github.com/statgen/bamUtil	Sequence Analysis	bamutil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil		bamutil	1.0.15			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	39	True	False	False
-bandage	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	bandage	bandage		Bandage	GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	Sequence assembly visualisation	Genomics, Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	2	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	2	2	0	2016	44390	True	False	True
-barcode_collapse	barcode_collapse	Paired End randomer aware duplicate removal algorithm								To update	https://github.com/YeoLab/gscripts	RNA, Sequence Analysis	barcode_collapse	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	0.1.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	71	True	False	False
-barrnap	barrnap	Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.	barrnap	barrnap		Barrnap	Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).	Gene prediction	Genomics, Model organisms, Model organisms	To update	https://github.com/tseemann/barrnap	Sequence Analysis	barrnap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap	1.2.2	barrnap	0.9	Gene prediction	Genomics, Model organisms, Model organisms	0	1	1	1	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	160	3938	True	False	False
-baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bax2bam	bax2bam	BAX to BAM converter								Up-to-date	https://github.com/pacificbiosciences/bax2bam/	Convert Formats, Sequence Analysis	bax2bam	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam	0.0.11	bax2bam	0.0.11			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	200	True	False	False
-bayescan	BayeScan	Detecting natural selection from population-based genetic data	bayescan	bayescan		BayeScan	BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	64	True	False	True
-bbtools	bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.	bbmap	bbtools, bbmap		BBMap	BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	Up-to-date	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.08	bbmap	39.08	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	6	1	5	0	6	1	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	0	4	0	0	420	6381	True	False	True
-bctools	bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events	bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0								Up-to-date	https://github.com/dmaticzka/bctools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools	0.2.2	bctools	0.2.2			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	87	2895	True	False	False
-bed_to_protein_map	bed_to_protein_map	Converts a BED file to a tabular list of exon locations								To update		Proteomics	bed_to_protein_map	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	49	385	True	False	False
-bellerophon	bellerophon	Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.								Up-to-date	https://github.com/davebx/bellerophon	Sequence Analysis	bellerophon	iuc	https://github.com/davebx/bellerophon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon	1.0	bellerophon	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	123	1194	True	False	False
-best_regression_subsets	BestSubsetsRegression1	Perform Best-subsets Regression								To update		Sequence Analysis, Variant Analysis	best_regression_subsets	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets	https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets	1.0.0	numpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	3	True	False	False
-bigscape	bigscape	Construct sequence similarity networks of BGCs and groups them into GCF	BiG-SCAPE	BiG-SCAPE		BiG-SCAPE	A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-bigwig_outlier_bed	bigwig_outlier_bed	pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files	bigtools	bigtools		bigtools	Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust.			To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	Sequence Analysis	bigwig_outlier_bed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-binning_refiner	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	binning_refiner	binning_refiner		Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	81	True	False	True
-biohansel	biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-bioinformatics_cafe	fasta_regex_finder	Miscellanea of scripts for bioinformatics								To update	https://github.com/dariober/bioinformatics-cafe/	Sequence Analysis	bioinformatics_cafe	mbernt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe	0.1.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	978	True	False	False
-biom_format	biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	biomformat	biomformat		biomformat	"This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods."	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	Formatting	Laboratory information management, Sequence analysis	2	2	6	0	2	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	98	3906	True	False	True
-bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	531	True	False	False
-bioperl	bp_genbank2gff3	Converts GenBank format files to GFF3	bioperl	bioperl		BioPerl	A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.  It provides software modules for many of the typical tasks of bioinformatics programming.	Data handling, Service invocation	Genomics, Software engineering, Data management	To update	https://bioperl.org/	Sequence Analysis	bp_genbank2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl	1.1	perl-bioperl	1.7.8	Data handling, Service invocation	Genomics, Software engineering	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	240	6736	True	False	False
-biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	3	True	False	False
-bismark	bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor	A tool to map bisulfite converted sequence reads and determine cytosine methylation states								To update	https://www.bioinformatics.babraham.ac.uk/projects/bismark/	Sequence Analysis, Next Gen Mappers	bismark	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	0.22.1	bismark	0.24.2			0	4	4	4	0	4	4	4	0	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	4	4	0	332	12876	True	False	False
-blast2go	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe				0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	101	1232	True	False	True
-blast_parser	blast_parser	Convert 12- or 24-column BLAST output into 3-column hcluster_sg input								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	blast_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	0.1.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	27	296	True	False	False
-blast_plus_remote_blastp	blast_plus_remote_blastp	NCBI BLAST+ with -remote option								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	blast_plus_remote_blastp	galaxyp	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp	2.6.0	blast	2.16.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	121	22499	True	False	True
-blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-blastxml_to_gapped_gff3	blastxml_to_gapped_gff3	BlastXML to gapped GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	Convert Formats, Sequence Analysis	blastxml_to_gapped_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3	1.1	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24	185	True	False	False
-blastxml_to_top_descr	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	159	264558	True	False	True
-blat_coverage_report	generate_coverage_report	Polymorphism of the Reads								To update		Next Gen Mappers, Sequence Analysis	blat_coverage_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-blat_mapping	blat2wig	Coverage of the Reads in wiggle format								To update		Next Gen Mappers, Sequence Analysis	blat_mapping	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	685	True	False	False
-blockbuster	blockbuster	Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.								To update	http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html	RNA, Sequence Analysis	blockbuster	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	0.1.2	blockbuster	0.0.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	34	3009	True	False	False
-blockclust	blockclust	BlockClust detects transcripts with similar processing patterns.								Up-to-date	https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust	RNA	blockclust	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	1.1.1	blockclust	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	15	1478	True	False	False
-bracken	est_abundance	Bayesian Reestimation of Abundance with KrakEN	bracken	bracken		Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	Statistical calculation	Metagenomics, Microbial ecology	Up-to-date	https://ccb.jhu.edu/software/bracken/	Sequence Analysis, Metagenomics	bracken	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken	3.0	bracken	3.0	Statistical calculation	Metagenomics, Microbial ecology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	326	18351	True	False	True
-braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	17	109	True	False	False
-braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	567	True	False	False
-brew3r_r	brew3r_r	Extend 3' end of a GTF using another GTF as a template	brew3r.r	brew3r.r		BREW3R.r	This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.	Genome annotation	Transcriptomics, Genomics	To update	https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html	Transcriptomics, RNA	brew3r_r	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r	https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r	1.0.2			Genome annotation	Transcriptomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bumbershoot	idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch									To update	http://proteowizard.sourceforge.net/	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot	3.0.21142	bumbershoot	3_0_21142_0e4f4a4			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	3	1348	True	False	False
-bundle_collections	bundle_collection	Tool to bundle up list collection into a single zip to be download								To update		Sequence Analysis	bundle_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections	1.3.0	perl-getopt-long	2.58			0	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-busco	busco	BUSCO assess genome and annotation completeness	busco	busco		BUSCO	Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://gitlab.com/ezlab/busco/-/releases	Sequence Analysis	busco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco	5.7.1	busco	5.7.1	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1804	86180	True	False	True
-bwameth	bwameth	Fast and accurate alignment of BS-seq reads								Up-to-date	https://github.com/brentp/bwa-meth	Sequence Analysis, Next Gen Mappers	bwameth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth	0.2.7	bwameth	0.2.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	201	10619	True	False	False
-cactus	cactus_cactus, cactus_export	Cactus is a reference-free whole-genome multiple alignment program	cactus	cactus		Cactus	Cactus is a reference-free whole-genome multiple alignment program.	Multiple sequence alignment, Genome alignment	Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics	To update	https://github.com/ComparativeGenomicsToolkit/cactus	Sequence Analysis	cactus	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	2.7.1			Multiple sequence alignment, Genome alignment	Genomics, Sequence assembly, Mapping, Phylogenetics	0	2	2	1	0	2	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	26	234	True	False	False
-calculate_contrast_threshold	calculate_contrast_threshold	Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.								To update	https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold	Visualization, Genomic Interval Operations, SAM	calculate_contrast_threshold	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold	1.0.0	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-calisp	calisp	Calgary approach to isotopes in proteomics								Up-to-date	https://github.com/kinestetika/Calisp/	Proteomics	calisp	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp	3.0.13	calisp	3.0.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	True	False	False
-cami_amber	biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert	Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments								Up-to-date	https://github.com/CAMI-challenge/AMBER	Metagenomics	cami_amber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber	2.0.6	cami-amber	2.0.6			0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	101	7766	True	False	False
-cardinal	cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots	Statistical and computational tools for analyzing mass spectrometry imaging datasets								Up-to-date	http://cardinalmsi.org	Proteomics, Metabolomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	3.4.3	bioconductor-cardinal	3.4.3			0	9	11	11	0	9	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	11	9	0	277	48705	True	False	False
-cat	cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	cat_bins		CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat	5.2.3	cat	5.3	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	5	2	5	0	5	2	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	268	2878	True	False	True
-cd_hit_dup	cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	280	4474	True	False	True
-cell-types-analysis	ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals	Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis								To update		Transcriptomics, RNA, Statistics	suite_cell_types_analysis	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis	1.1.1	cell-types-analysis	0.1.11			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	6	True	False	False
-cemitool	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.26.0	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	98	True	False	True
-champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	19	174	True	False	False
-charts	charts	Enables advanced visualization options in Galaxy Charts								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	Visualization	charts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts	1.0.1	r-getopt				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	287	3589	True	False	False
-checkm	checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	checkm	checkm		CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	To update	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.0	checkm-genome	1.2.3	Sequence assembly validation, Sequence composition calculation, Statistical calculation	Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	0	0	10	10	0	0	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	390	5165	True	False	True
-cherri	cherri_eval, cherri_train	Computational Help Evaluating RNA-RNA interactions	cherri	cherri		cherri	CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.		Molecular interactions, pathways and networks, Structure analysis, Machine learning	To update	https://github.com/BackofenLab/Cherri	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri	0.7	cherri	0.8		Molecular interactions, pathways and networks, Structure analysis, Machine learning	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	207	True	False	False
-chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	418	15690	True	False	False
-chira	chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify	Chimeric Read Annotator for RNA-RNA interactome data	chira	chira		ChiRA	ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.		RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	Up-to-date	https://github.com/pavanvidem/chira	RNA, Transcriptomics, Sequence Analysis	chira	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira	1.4.3	chira	1.4.3		Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	97	6418	True	False	False
-chromeister	chromeister	ultra-fast pairwise genome comparisons								Up-to-date	https://github.com/estebanpw/chromeister	Sequence Analysis	chromeister	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister	1.5.a	chromeister	1.5.a			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	182	2130	True	False	False
-chromosome_diagram	chromosome_diagram	Chromosome Diagrams using Biopython								To update		Graphics, Sequence Analysis, Visualization	chromosome_diagram	peterjc		https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-circexplorer	circexplorer	A combined strategy to identify circular RNAs (circRNAs and ciRNAs)								To update	https://github.com/YangLab/CIRCexplorer	Sequence Analysis, RNA	circexplorer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	1.1.9.0	circexplorer	1.1.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	251	True	False	False
-circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	269	True	False	False
-clair3	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	clair3	clair3		Clair3	Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	1.0.8	clair3	1.0.10	Variant calling	Molecular genetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	68	1856	True	False	True
-clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-climate-stripes	climate_stripes	Create climate stripes from a tabular input file								To update	https://www.climate-lab-book.ac.uk/2018/warming-stripes/	Climate Analysis, Visualization	climate_stripes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	1.0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	237	True	False	False
-clinod	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-clustalw	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	clustal2	clustal2		Clustal 2 (Clustal W, Clustal X)	Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.	Multiple sequence alignment	Phylogeny, Sequence analysis	Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw	2.1	clustalw	2.1	Multiple sequence alignment	Phylogeny, Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	651	46793	True	False	True
-cmsearch_deoverlap	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	102	True	False	True
-cmv	cmcv, cmv, hmmcv, hmmv	cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.								Up-to-date	https://github.com/eggzilla/cmv	RNA	cmv	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	1.0.8	cmv	1.0.8			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	1	108	True	False	False
-codeml	codeml	Detects positive selection	paml	paml		PAML	Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml	4.9	paml	4.10.7	Probabilistic sequence generation	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	29	60901	True	False	True
-cofold	cofold	Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.								To update	http://www.e-rna.org/cofold/	RNA	cofold	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	2.0.4.0	cofold	2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	342	True	False	False
-cojac	cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	cojac	cojac		COJAC	CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.2	cojac	0.9.2		Genetic variation	2	0	3	0	2	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	20	2757	True	False	True
-colabfold	colabfold_alphafold, colabfold_msa	Protein prediction based on AlphaFold2	Colabfold	Colabfold		ColabFold	ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.	Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	To update	https://github.com/sokrypton/ColabFold	Proteomics, Graphics	colabfold	iuc	https://github.com/sokrypton/ColabFold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold	1.5.5			Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-colibread	commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak	Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome								To update	https://colibread.inria.fr/	Sequence Analysis, Variant Analysis	colibread	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread	24.7.14+galaxy0	commet	24.7.14			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	251	True	False	False
-collapse_collection	collapse_dataset	Collection tool that collapses a list of files into a single datasset in order of appears in collection								To update		Sequence Analysis	collapse_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection	5.1.0	gawk				1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1583	33934	True	False	False
-combineJSON	combine_json	JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.								To update		Sequence Analysis	combine_json	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-combine_metaphlan_humann	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	147	True	False	True
-combine_tabular_collection	combine	Combine Tabular Collection into a single file								To update		Sequence Analysis	combine_tabular_collection	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-compalignp	compalignp	Compute fractional identity between trusted alignment and test alignment								Up-to-date		RNA, Sequence Analysis	compalignp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp	1.0	compalignp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	220	True	False	False
-compare_humann2_output	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	332	True	False	True
-compleasm	compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	compleasm	compleasm		compleasm	"""Compleasm: a faster and more accurate reimplementation of BUSCO"""	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm	0.2.6	compleasm	0.2.6	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-compute_motif_frequencies_for_all_motifs	compute_motif_frequencies_for_all_motifs	Compute Motif Frequencies For All Motifs, motif by motif.								To update		Sequence Analysis, Statistics	compute_motif_frequencies_for_all_motifs	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	94	True	False	False
-compute_motifs_frequency	compute_motifs_frequency	Compute Motif Frequencies in indel flanking regions.								To update		Sequence Analysis, Statistics	compute_motifs_frequency	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	65	True	False	False
-concoct	concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	concoct	concoct		CONCOCT	A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct	1.1.0	concoct	1.1.0	Sequence clustering, Read binning	Metagenomics	0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	92	786	True	False	True
-consensus_from_alignments	aligned_to_consensus	Tool to compute a consensus sequence from several aligned fasta sequences								To update		Sequence Analysis	consalign	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments	https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments	1.0.0	r-bioseq				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55	585	True	False	False
-consolidate_vcfs	consolidate_vcfs	Combines freebayes and mpileup files for use by vcf2snvalignment								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	consolidate_vcfs	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-coprarna	coprarna	Target prediction for prokaryotic trans-acting small RNAs								To update	https://github.com/PatrickRWright/CopraRNA	RNA, Sequence Analysis	coprarna	rnateam	https://github.com/PatrickRWright/CopraRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna	2.1.1	coprarna	2.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-count_gff_features	count_gff_features	Count GFF Features								To update		Sequence Analysis	count_gff_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features	https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features	0.2	galaxy-ops	1.1.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	49	271	True	False	False
-count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-coverage_report	CoverageReport2	Generate Detailed Coverage Report from BAM file								To update	https://github.com/galaxyproject/tools-iuc	Sequence Analysis	coverage_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report	0.0.4	perl-number-format	1.76			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-coverm	coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm		CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	Local alignment	Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	72	529	True	False	True
-crispr_studio	crispr_studio	CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.	crisprstudio	crisprstudio		CRISPRStudio	CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.	Visualisation	Sequence analysis, Genomics, Data visualisation	To update	https://github.com/moineaulab/CRISPRStudio	Sequence Analysis	crispr_studio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio	1+galaxy0	crispr_studio	1	Visualisation	Sequence analysis, Genomics, Data visualisation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	636	True	False	False
-crosscontamination_barcode_filter	crosscontamination_barcode_filter	Barcode contamination discovery tool								To update		Transcriptomics, Visualization	crosscontamination_barcode_filter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter	0.3	r-ggplot2	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	17	347	True	False	False
-crt	crispr_recognition_tool	CRISPR Recognition Tool								To update		Sequence Analysis	crispr_recognition_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/crt	https://github.com/bgruening/galaxytools/tree/master/tools/crt	1.2.0	crisper_recognition_tool	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	74	3389	True	False	False
-cryptogenotyper	CryptoGenotyper	CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	8518	True	False	True
-ctd_batch	ctdBatch_1	CTD analysis of chemicals, diseases, or genes								To update		Sequence Analysis	ctd_batch	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	203	True	False	False
-cummerbund	cummeRbund	Wrapper for the Bioconductor cummeRbund library								To update	https://bioconductor.org/packages/release/bioc/html/cummeRbund.html	RNA, Visualization	cummerbund	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund	2.16.0	fonts-conda-ecosystem				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	31	1782	True	False	False
-custom_pro_db	custom_pro_db	CustomProDB								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db	1.22.0	bioconductor-rgalaxy	1.37.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	57	1652	True	False	False
-custom_pro_db_annotation_data_manager		CustomProDB Annotation								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db_annotation_data_manager	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	5090	232004	True	False	True
-dada2	dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	dada2	dada2		dada2	This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	10	0	0	1	0	0	0	0	0	0	0	0	0	0	0	10	10	0	1263	66609	True	False	True
-das_tool	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	dastool		dastool	DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	Read binning	Metagenomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	24	706	True	False	True
-data-hca	hca_matrix_downloader	Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects								To update		Transcriptomics, Sequence Analysis	suite_human_cell_atlas_tools	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca	v0.0.4+galaxy0	hca-matrix-downloader	0.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	439	True	False	False
-data-scxa	retrieve_scxa	Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home								To update		Transcriptomics, Sequence Analysis	suite_ebi_expression_atlas	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa	v0.0.2+galaxy2	wget				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	99	799	True	False	False
-data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	146	658	True	False	False
-data_manager_eggnog_mapper		downloads eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-data_manager_eggnog_mapper_abspath		download eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper_abspath	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-dbbuilder	dbbuilder	Protein Database Downloader								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	Proteomics	dbbuilder	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	0.3.4	wget				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	161	4758	True	False	False
-decoyfasta		Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.								To update		Proteomics	decoyfasta	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	True	False	False
-delete_overlapping_indels	delete_overlapping_indels	Delete Overlapping Indels from a chromosome indels file								To update		Sequence Analysis	delete_overlapping_indels	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels	https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	39	True	False	False
-deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	4990	95752	True	False	True
-deseq2_normalization	deseq2_normalization	Normalizes gene hitlists								To update	http://artbio.fr	RNA, Transcriptomics, Sequence Analysis, Statistics	deseq2_normalization	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	1.40.2+galaxy0	bioconductor-deseq2	1.42.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-dewseq	dewseq	DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data								To update	https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers	Sequence Analysis, RNA, CLIP-seq	dewseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	0.1.0+galaxy0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11	72	True	False	False
-dexseq	dexseq, dexseq_count, plotdexseq	Inference of differential exon usage in RNA-Seq	dexseq	dexseq		DEXSeq	The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html	Transcriptomics, RNA, Statistics	dexseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq	1.48.0	bioconductor-dexseq	1.48.0	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	218	16064	True	False	False
-dia_umpire	dia_umpire_se	DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics								To update	http://diaumpire.sourceforge.net/	Proteomics	dia_umpire	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire	2.1.3	dia_umpire	2.1.6			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	33	True	False	False
-dialignr	dialignr	DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.								To update	https://github.com/shubham1637/DIAlignR	Proteomics	dialignr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	1.2.0	bioconductor-dialignr	2.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	40	True	False	False
-diamond	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	diamond		Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	Sequence alignment analysis	Sequence analysis, Proteins	3	3	3	3	3	3	3	3	0	0	0	0	3	0	0	0	0	0	0	0	3	3	3	0	0	0	1	0	0	0	0	0	0	0	0	0	0	3	3	0	963	49711	True	False	True
-diann	diann	DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.								To update	https://github.com/vdemichev/DiaNN	Proteomics	diann	galaxyp	https://github.com/vdemichev/DiaNN	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann	1.8.1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	15	True	False	False
-diapysef	diapysef	diapysef is a convenience package for working with DIA-PASEF data								To update	https://pypi.org/project/diapysef/	Proteomics	diapysef	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef	0.3.5.0	diapysef	1.0.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	245	True	False	False
-diffacto	diffacto	Diffacto comparative protein abundance estimation								To update	https://github.com/statisticalbiotechnology/diffacto	Proteomics	diffacto	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	1.0.6	diffacto	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	7	True	False	False
-disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	42	369	True	False	True
-divide_pg_snp	dividePgSnp	Separate pgSnp alleles into columns								To update		Sequence Analysis	divide_pg_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	32	True	False	False
-dorina	dorina_search	data source for RNA interactions in post-transcriptional regulation								To update		RNA, Data Source	dorina	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1576	True	False	False
-dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-dot2ct	rnastructure_dot2ct	Dot-Bracket to Connect Table (CT)								To update		Sequence Analysis, RNA	dot2ct	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	5.7.a	rnastructure	6.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-dotknot	dotknot	DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence								To update	http://dotknot.csse.uwa.edu.au/	RNA, Proteomics	dotknot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot	1.3.1	vienna_rna				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	83	True	False	False
-dram	dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram		DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	Up-to-date	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.5.0	dram	1.5.0	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	39	6886	True	False	True
-drep	drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep		dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	Up-to-date	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.5.0	drep	3.5.0	Genome comparison	Metagenomics, Sequence analysis	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	46	646	True	False	True
-droplet-barcode-plot	_dropletBarcodePlot	Make a cell barcode plot for droplet single-cell RNA-seq QC								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	droplet_barcode_plot	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot	1.6.1+galaxy2	scxa-plots	0.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	95	973	True	False	False
-dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Transcriptomics, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	126	3934	True	False	False
-dropletutils	dropletutils_empty_drops, dropletutils_read_10x	De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_dropletutils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils	1.0.4	dropletutils-scripts	0.0.5			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	201	1599	True	False	False
-ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ectyper	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	9907	True	False	True
-edger	edger	Perform RNA-Seq differential expression analysis using edgeR pipeline	edger	edger		edgeR	Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	To update	http://bioconductor.org/packages/release/bioc/html/edgeR.html	Transcriptomics, RNA, Statistics	edger	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger	https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger	3.36.0	bioconductor-edger	4.0.16	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	945	18117	True	False	False
-effectiveT3	effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-eggnog_mapper	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2		eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3	1	0	510	30565	True	False	True
-egsea	egsea	This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing	egsea	egsea		EGSEA	This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.	Gene set testing	Systems biology	To update	https://bioconductor.org/packages/release/bioc/html/EGSEA.html	Transcriptomics, RNA, Statistics	egsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea	1.20.0	bioconductor-egsea	1.28.0	Gene set testing	Systems biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	177	2524	True	False	False
-emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	107	107	107	107	107	0	0	0	0	107	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	0	0	107	107	0	1816	89530	True	False	True
-encyclopedia	encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut	Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis								To update	https://bitbucket.org/searleb/encyclopedia/wiki/Home	Proteomics	encyclopedia	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia	1.12.34	encyclopedia	2.12.30			2	4	7	0	2	4	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	48	706	True	False	False
-ete	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete		ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	Phylogenetic tree editing	Phylogenetics	0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	45	899	True	False	True
-exomedepth	exomedepth	ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data	exomedepth	exomedepth		ExomeDepth	Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases	To update	https://cran.r-project.org/package=ExomeDepth	Sequence Analysis, Variant Analysis	exomedepth	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth	1.1.0	r-exomedepth	1.1.16	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	29	410	True	False	False
-exonerate	exonerate	Exonerate is a generic tool for pairwise sequence comparison.	exonerate	exonerate		Exonerate	A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	Up-to-date	https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate	Sequence Analysis	exonerate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate	2.4.0	exonerate	2.4.0	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	59	988	True	False	False
-exparna	exparna	ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.								Up-to-date	http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp	RNA	exparna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	1.0.1	exparna	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan		export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	Conversion	Taxonomy, Metabolomics, Biomarkers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	200	5265	True	False	True
-express	express	Quantify the abundances of a set of target sequences from sampled subsequences								To update		RNA	express	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/express	https://github.com/galaxyproject/tools-devteam/tree/main/tools/express	1.1.1	eXpress	1.5.1			0	1	1	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	12	325	True	False	False
-ez_histograms	ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-falco	falco	A high throughput sequence QC analysis tool	falco	falco		Falco	A high-speed FastQC emulation for quality control of sequencing data.	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	To update	https://github.com/smithlabcode/falco/	Sequence Analysis	falco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco	https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco	1.2.2+galaxy1	falco	1.2.3	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fargene	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fargene		fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	52	459	True	False	True
-fasta2bed	fasta2bed	Convert multiple fasta file into tabular bed file format								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fasta2bed	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fasta_extract	fa-extract-sequence	extract single fasta from multiple fasta file								To update	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	Sequence Analysis	fasta_extract	nml	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	10	True	False	False
-fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fasta_nucleotide_color_plot	fasta_nucleotide_color_plot	Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot	Visualization	fasta_nucleotide_color_plot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	160	True	False	False
-fasta_stats	fasta-stats	Display summary statistics for a fasta file.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	Sequence Analysis	fasta_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats	2.0	numpy				1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1080	35336	True	False	False
-fastani	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity	fastani	fastani		FastANI	FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	250	3498	True	False	True
-fastg2protlib	fastg2protlib-peptides, fastg2protlib-validate	Generate FASTA from FASTG								To update	https://github.com/galaxyproteomics/fastg2protlib.git	Proteomics	fastg2protlib	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	1.0.2					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	28	True	False	False
-fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-fastp	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp		fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	Sequence contamination filtering	Probes and primers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	1	2803	1055760	True	False	True
-fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fastq_pair_names	fastq_pair_names	Extract FASTQ paired read names								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	Sequence Analysis	fastq_pair_names	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	0.0.5	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fastq_paired_unpaired	fastq_paired_unpaired	Divide FASTQ file into paired and unpaired reads								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	Sequence Analysis, Text Manipulation	fastq_paired_unpaired	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	0.1.5	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fastq_provider	fastq_provider	Retrieval and download of FASTQ files from ENA and other repositories such as HCA.								To update	https://github.com/ebi-gene-expression-group/atlas-fastq-provider	Data Source, RNA, Transcriptomics	atlas_fastq_provider	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider	0.4.4	atlas-fastq-provider	0.4.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fastq_utils	fastq_filter_n, fastq_trim_poly_at	Set of tools for handling fastq files								To update	https://github.com/nunofonseca/fastq_utils	Transcriptomics, RNA	fastq_utils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils	0.25.1+galaxy0	fastq_utils	0.25.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fastqc_stats	FastQC_Summary	Summary multiple FastQC into a single tabular line report								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fastqc_stats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats	1.2	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fastqe	fastqe	FASTQE	fastqe	fastqe		FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	Sequencing quality control	Sequence analysis, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1266	4333	True	False	True
-fasttree	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree		FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11		Phylogenetics	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	379	55434	True	False	True
-feature_alignment	feature_alignment	TRIC integrates information from all available runs via a graph-based alignment strategy								Up-to-date		Proteomics	feature_alignment	galaxyp	https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment	0.11.0	msproteomicstools	0.11.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	18	True	False	False
-featurecounter	featureCoverage1	Feature coverage								To update		Sequence Analysis, Variant Analysis	featurecounter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter	2.0.0	bx-python	0.12.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	22385	True	False	False
-featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	4679	696399	True	False	True
-feelnc	feelnc	Galaxy wrapper for FEELnc	feelnc	feelnc		FEELnc	A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.	Annotation, Classification	RNA-seq, Functional, regulatory and non-coding RNA	To update	https://github.com/tderrien/FEELnc	Sequence Analysis	feelnc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc	0.2.1	feelnc	0.2	Annotation, Classification	Functional, regulatory and non-coding RNA	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	46	1191	True	False	False
-feht	feht	Automatically identify makers predictive of groups.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	feht	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht	0.1.0	feht	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fgsea	fgsea	Perform gene set testing using fgsea	fgsea	fgsea		fgsea	The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.	Gene-set enrichment analysis	Genetics	To update	https://bioconductor.org/packages/release/bioc/html/fgsea.html	Visualization, Transcriptomics, Statistics	fgsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea	1.8.0+galaxy1	bioconductor-fgsea	1.28.0	Gene-set enrichment analysis	Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	307	5240	True	False	False
-filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	426	26274	True	False	False
-filter_density	filterdensity	Filter out position based on distance between SNVs								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_density	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-filter_stats	filterstat	SNVPhyl filter_stats								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_stats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-filter_transcripts_via_tracking	filter_combined_via_tracking	Filter Combined Transcripts								To update		RNA	filter_transcripts_via_tracking	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking	https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking	0.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	20	True	False	False
-filter_vcf	filtervcf	SNVPhyl filter_vcf								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_vcf	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	617	30483	True	False	True
-find_diag_hits	find_diag_hits	Find diagnostic hits								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	find_diag_hits	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits	1.0.0	taxonomy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	69	True	False	False
-find_repeats	findrepeat	Find repetitive regions on a reference genome using MUMMer								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	find_repeats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fisher_test	fishertest	Fisher's exact test on two-column hit lists.								To update	http://artbio.fr	RNA, Statistics	fishertest	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	2.32.0+galaxy0	bioconductor-qvalue	2.34.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	14	331	True	False	False
-flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	74	13759	True	False	False
-flashlfq	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	Label-free quantification	Proteomics experiment, Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	17	645	True	False	True
-flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	To update	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.4	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1499	20904	True	False	True
-format_metaphlan2_output	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	166	5588	True	False	True
-fraggenescan	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan		FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	Gene prediction	Genetics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	68	1102	True	False	True
-fragpipe	fragpipe	Data analysis for mass spectrometry-based proteomics.								Up-to-date	https://fragpipe.nesvilab.org/	Proteomics	fragpipe	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	20.0	fragpipe	20.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-freyja	freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja		Freyja	Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset	RNA-Seq quantification	Metagenomics	To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.1	RNA-Seq quantification	Metagenomics	2	0	4	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	55	20021	True	False	True
-frogs	FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis	frogs	frogs		FROGS	The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	To update	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	5.0.0	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	0	0	0	28	0	0	0	28	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	900	5906	True	False	True
-garnett	garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file	De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_garnett	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett	0.2.8	garnett-cli	0.0.5			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	27	True	False	False
-gblocks	gblocks	Gblocks								Up-to-date	http://molevol.cmima.csic.es/castresana/Gblocks.html	Sequence Analysis	gblocks	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	0.91b	gblocks	0.91b			0	1	0	1	0	1	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	8	0	0	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	10	1475	True	False	False
-gecko	gecko	Ungapped genome comparison								Up-to-date	https://github.com/otorreno/gecko	Sequence Analysis	gecko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko	1.2	gecko	1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	519	True	False	False
-gemini	gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@	GEMINI: a flexible framework for exploring genome variation	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://github.com/arq5x/gemini	Sequence Analysis, Next Gen Mappers	gemini	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini	0.20.1	gemini	0.30.2	Sequence analysis, Genetic variation analysis	Sequence analysis	1	2	2	2	1	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	662	4916	True	False	False
-geneiobio	gene_iobio_display_generation_iframe	Gene.iobio is an interactive tool for variant and trio analysis.								To update	https://github.com/iobio/gene.iobio	Sequence Analysis	geneiobio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio	4.7.1+galaxy1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	67	True	False	False
-generate_pc_lda_matrix	generate_matrix_for_pca_and_lda1	Generate a Matrix for using PC and LDA								To update		Sequence Analysis	generate_pc_lda_matrix	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix	https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix	1.0.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	12	119	True	False	False
-genomad	genomad_end_to_end	Identify virus and plasmid genomes from nucleotide sequences	genomad	genomad		geNomad	geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.	Sequence annotation, Taxonomic classification	Sequence analysis	Up-to-date	https://github.com/apcamargo/genomad/	Metagenomics	genomad	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/longorf/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad	1.8.0	genomad	1.8.0	Sequence annotation, Taxonomic classification	Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-genomic_super_signature	genomic_super_signature	Interpretation of RNAseq experiments through robust, efficient comparison to public databases	genomicsupersignature	genomicsupersignature		GenomicSuperSignature	GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	To update	https://github.com/shbrief/GenomicSuperSignature	Sequence Analysis, RNA, Transcriptomics	genomic_super_signature	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature	1.2.0	bioconductor-genomicsupersignature	1.10.0	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11	46	True	False	False
-get_orfs_or_cdss	get_orfs_or_cdss	Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	Sequence Analysis	get_orfs_or_cdss	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	0.2.3	biopython	1.70			0	1	1	1	0	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	15	186	True	False	False
-getindelrates_3way	indelRates_3way	Estimate Indel Rates for 3-way alignments								To update		Sequence Analysis, Variant Analysis	getindelrates_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way	1.0.0	bx-python	0.12.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-getindels_2way	getIndels_2way	Fetch Indels from pairwise alignments								To update		Sequence Analysis, Variant Analysis	getindels_2way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way	1.0.0	numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-getmlst	getmlst	Download MLST datasets by species from pubmlst.org								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	18	495	True	False	False
-gfastats	gfastats	Tool for generating sequence statistics and simultaneous genome assembly file manipulation.	gfastats	gfastats		gfastats	gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.	Data handling	Computational biology	Up-to-date	https://github.com/vgl-hub/gfastats	Sequence Analysis	gfastats	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	1.3.6	gfastats	1.3.6	Data handling	Computational biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	418	8159	True	False	False
-gff3_rebase	gff3.rebase	Rebase a GFF against a parent GFF (e.g. an original genome)								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	Sequence Analysis	gff3_rebase	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase	1.2	bcbiogff	0.6.6			1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	12	135	True	False	False
-gffread	gffread	gffread filters and/or converts GFF3/GTF2 records	gffread	gffread		gffread	program for filtering, converting and manipulating GFF files	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/	Sequence Analysis	gffread	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread	0.12.7	gffread	0.12.7	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	680	10995	True	False	False
-ggplot2	ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2		ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		Visualisation	Data visualisation	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	5	0	0	0	0	0	0	3	0	0	0	0	0	0	0	5	5	0	1388	22148	True	False	True
-gi2taxonomy	Fetch Taxonomic Ranks	Fetch taxonomic representation	gi2taxonomy	gi2taxonomy		gi2taxonomy	The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	27	660	True	False	True
-glimmer	glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based	Glimmer makes gene predictions.	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	Sequence analysis, Genetic variation analysis	Sequence analysis	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	187	3965	True	False	True
-glimmer_hmm		GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-gmaj	gmaj_1	GMAJ Multiple Alignment Viewer								To update		Visualization	gmaj	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj	https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj	2.0.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	11	True	False	False
-goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	408	5484	True	False	True
-goseq	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq		GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	Gene functional annotation	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1210	19167	True	False	True
-gotohscan	rbc_gotohscan	Find subsequences in db								To update		Sequence Analysis	gotohscan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	1.3.0	gotohscan	1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	71	True	False	False
-graphclust	graphclust	GraphClust can be used for structural clustering of RNA sequences.								To update	http://www.bioinf.uni-freiburg.de/Software/GraphClust/	RNA	graphclust	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	0.1	GraphClust				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	True	False	False
-graphlan	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	graphlan	graphlan		GraPhlAn	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	432	9277	True	False	True
-graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.3	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	136	6651	True	False	True
-graphprot	graphprot_predict_profile	GraphProt models binding preferences of RNA-binding proteins.								To update	https://github.com/dmaticzka/GraphProt	Sequence Analysis, RNA, CLIP-seq	graphprot	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	1.1.7+galaxy2	graphprot	1.1.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	474	True	False	False
-gsc_high_dimensions_visualisation	high_dimensions_visualisation	Generates PCA, t-SNE and HCPC visualisation								To update	http://artbio.fr	Transcriptomics, Visualization	gsc_high_dimensions_visualisation	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation	4.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-gtdb_to_taxdump	gtdb_to_taxdump	Convert GTDB taxonomy to NCBI taxdump format	gtdb_to_taxdump	gtdb_to_taxdump		gtdb_to_taxdump	Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI.	Data handling, Mapping, Generation	Computational biology	Up-to-date	https://github.com/nick-youngblut/gtdb_to_taxdump	Metagenomics	gtdb_to_taxdump	iuc	https://github.com/nick-youngblut/gtdb_to_taxdump	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump	0.1.9	gtdb_to_taxdump	0.1.9	Data handling, Mapping, Generation	Computational biology	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-gtdbtk	gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 	GTDB-Tk	GTDB-Tk		GTDB-Tk	a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	To update	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.3.2	gtdbtk	2.4.0	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-gtf-2-gene-list	_ensembl_gtf2gene_list	Utility to extract annotations from Ensembl GTF files.								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	gtf2gene_list	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list	1.52.0+galaxy0	atlas-gene-annotation-manipulation	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	155	1678	True	False	False
-gubbins	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins		Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	145	3340	True	False	True
-guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-gwastools	gwastools_manhattan_plot		gwastools	gwastools		GWASTools	Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.	Deposition, Analysis, Annotation	GWAS study	To update	https://bioconductor.org/packages/release/bioc/html/GWASTools.html	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools	0.1.0	bioconductor-gwastools	1.48.0	Deposition, Analysis, Annotation	GWAS study	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	True	False	False
-hamronization	hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization		hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	117	4459	True	False	True
-hansel	bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	Biohansel		BioHansel	BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	339	True	False	True
-hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	295	True	False	False
-hardklor	hardklor, kronik	Hardklör								To update		Proteomics	hardklor	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor	2.30.1+galaxy1	hardklor	2.3.2			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2	111	True	False	False
-hcluster_sg	hcluster_sg	Hierarchically clustering on a sparse graph								To update	https://github.com/douglasgscofield/hcluster	Phylogenetics	hcluster_sg	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	0.5.1.1	hcluster_sg	0.5.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	238	True	False	False
-hcluster_sg_parser	hcluster_sg_parser	Converts hcluster_sg 3-column output into lists of ids								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	hcluster_sg_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	0.2.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	290	True	False	False
-heatmap2	ggplot2_heatmap2	heatmap.2 function from the R gplots package								To update	https://github.com/cran/gplots	Visualization	ggplot2_heatmap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2	3.1.3.1	r-gplots	2.17.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1953	44240	True	False	False
-heinz	heinz_bum, heinz, heinz_scoring, heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	heinz	bionet, heinz		Heinz	Tool for single-species active module discovery.	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	To update	https://github.com/ls-cwi/heinz	Transcriptomics, Visualization, Statistics	heinz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz	1.0	bioconductor-bionet	1.62.0	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	242	1186	True	False	False
-helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	93	True	False	False
-hgv_fundo	hgv_funDo	FunDO human genes associated with disease terms								To update		Sequence Analysis	hgv_fundo	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	True	False	False
-hgv_hilbertvis	hgv_hilbertvis	HVIS visualization of genomic data with the Hilbert curve								To update	https://www.ebi.ac.uk/huber-srv/hilbert/	Graphics, Visualization	hgv_hilbertvis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis	1.0.0	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	True	False	False
-hicexplorer	hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations	HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.								Up-to-date	https://github.com/deeptools/HiCExplorer	Sequence Analysis, Visualization	hicexplorer	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer	3.7.5	hicexplorer	3.7.5			38	38	38	4	38	38	38	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	36	33	0	1085	66003	True	False	False
-hicstuff	hicstuff_pipeline	A toolkit to generate and manipulate Hi-C matrices								To update	https://github.com/koszullab/hicstuff	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff	3.1.5	hicstuff	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	1410	True	False	False
-hifiasm_meta	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	hifiasm-meta		Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	Sequence assembly	Sequence assembly, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	137	True	False	True
-high_dim_heatmap	high_dim_heatmap	gplot heatmap.2 function adapted for plotting large heatmaps								To update	https://github.com/cran/gplots	Visualization	high_dim_heatmap	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap	https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap	3.1.3+galaxy0	r-gplots	2.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	True	False	False
-hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	4183	299104	True	False	False
-hivtrace	hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-hmmer3	hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	hmmer3	hmmer3		HMMER3	This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	0	12	12	12	0	12	12	12	0	0	0	0	12	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	0	439	33702	True	False	True
-homer	homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide	HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.	homer	homer		homer	HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein).  It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other.  It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment.  HOMER also tries its best to account for sequenced bias in the dataset.  It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.	Sequence motif discovery		Up-to-date	http://homer.ucsd.edu/homer/index.html	Sequence Analysis	data_manager_homer_preparse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer	4.11	homer	4.11	Sequence motif discovery		0	0	5	4	0	0	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	5	0	0	394	6937	True	False	False
-homer		Software for motif discovery and next generation sequencing analysis.								To update	http://homer.salk.edu/homer/	Sequence Analysis	homer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/homer	https://github.com/bgruening/galaxytools/tree/master/tools/homer						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-htseq-clip	htseq_clip	htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets								To update	https://github.com/EMBL-Hentze-group/htseq-clip	Sequence Analysis, RNA, CLIP-seq	htseq_clip	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	0.1.0+galaxy0	htseq-clip	2.19.0b0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	77	True	False	False
-htseq_count	htseq_count	Count aligned reads (SAM/BAM) that overlap genomic features (GFF)	htseq	htseq		HTSeq	Python framework to process and analyse high-throughput sequencing (HTS) data	Nucleic acid sequence analysis	Sequence analysis	Up-to-date	https://readthedocs.org/projects/htseq/	Genomic Interval Operations, SAM, Sequence Analysis, RNA	htseq_count	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count	2.0.5	htseq	2.0.5	Nucleic acid sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1419	154533	True	False	False
-humann	humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	humann	humann		humann	HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	To update	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.8	humann	3.9	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	6	13	13	13	6	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	13	0	1045	19521	True	False	True
-hybpiper	hybpiper	Analyse targeted sequence capture data	HybPiper	HybPiper		HybPiper	Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	To update	https://github.com/mossmatters/HybPiper	Sequence Analysis, Phylogenetics	hybpiper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper	2.1.6	hybpiper	2.2.0	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-hyphy	hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy		HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.62	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	17	2	17	2	17	2	17	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	17	12	0	161	10370	True	False	True
-hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354	True	False	True
-icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	69	1127	True	False	True
-idconvert	idconvert	Convert mass spectrometry identification files on linux or MacOSX								To update		Proteomics	idconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert		proteowizard	3_0_9992			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	275	True	False	False
-idr	idr	Galaxy wrappers for the IDR package from Nathan Boleu								To update	https://github.com/nboley/idr	Sequence Analysis	idr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr	2.0.3	idr	2.0.4.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	30	2873	True	False	False
-iedb_api	iedb_api	Get epitope binding predictions from IEDB-API								To update	http://tools.immuneepitope.org/main/tools-api/	Data Source, Sequence Analysis	iedb_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api	2.15.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	12	1506	True	False	False
-illumina_methylation_analyser	illumina_methylation_analyser	Methylation analyzer for Illumina 450k DNA emthylation microarrays								To update	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	Sequence Analysis	illumina_methylation_analyser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	0.1	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-improviser	proteomics_improviser	Visualisation of PepXML files								To update	http://www.improviser.uni-freiburg.de/	Proteomics	proteomics_improviser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	1.1.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-indels_3way	indels_3way	Fetch Indels from 3-way alignments								To update		Sequence Analysis	indels_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way	1.0.3					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	22	True	False	False
-infernal	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	infernal		Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	67	100294	True	False	True
-inforna		INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.								To update	http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp	RNA	inforna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	139	True	False	False
-instrain	instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	instrain	instrain		InStrain	InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	SNP detection, Genome comparison	Mapping, Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	94	True	False	True
-intarna	intarna	Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.								Up-to-date	https://github.com/BackofenLab/IntaRNA	RNA	intarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	3.4.0	intarna	3.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	7569	True	False	False
-integron_finder	integron_finder	"""IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"""	integron_finder	integron_finder		Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.5	integron_finder	2.0.5	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	58	52965	True	False	True
-interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-interproscan	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi		InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	677	35243	True	False	True
-iprscan5		Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-iqtree	iqtree	Efficient phylogenomic software by maximum likelihood	iqtree	iqtree		iqtree	A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time	Phylogenetic analysis, Sequence analysis	Phylogenetics	Up-to-date	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.3.6	iqtree	2.3.6	Phylogenetic analysis, Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	681	21598	True	False	True
-isescan	isescan	"""ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."""	ISEScan	ISEScan		ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	Structural variation detection	Genomics, Sequence analysis, Genetic variation	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	50	57581	True	False	True
-isoformswitchanalyzer	isoformswitchanalyzer	Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.	IsoformSwitchAnalyzeR	IsoformSwitchAnalyzeR		IsoformSwitchAnalyzeR	Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	To update	https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html	Transcriptomics, RNA, Statistics	isoformswitchanalyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer	1.20.0	bioconductor-isoformswitchanalyzer	2.2.0	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	822	True	False	False
-isoplot	isoplot	Isoplot is a software for the visualisation of MS data from C13 labelling experiments								To update		Metabolomics, Visualization	isoplot	workflow4metabolomics	https://github.com/llegregam/Isoplot/tree/main	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot	1.3.0+galaxy1	isoplot	1.3.1			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	2	True	False	False
-itsx	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	38	868	True	False	True
-ivar	ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing								Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.3	ivar	1.4.3			5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	4	0	0	0	4	0	0	0	0	0	0	0	5	5	0	1171	1224275	True	False	True
-jbrowse	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse		JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	Genome visualisation	Genomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	2	2	0	2346	18229	True	False	True
-jbrowse2	jbrowse2	JBrowse2 Genome Browser integrated as a Galaxy Tool	jbrowse_2	jbrowse_2		JBrowse 2	Modular genome browser with views of synteny and structural variation.	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	To update	https://jbrowse.org	Sequence Analysis	jbrowse2	fubar	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2	https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2	2.13.1	jbrowse2	2.14.0	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-jcvi_gff_stats	jcvi_gff_stats	Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)								To update	https://github.com/tanghaibao/jcvi	Sequence Analysis	jcvi_gff_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats	0.8.4	jcvi	1.4.16			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	255	2469	True	False	False
-jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138	True	False	True
-kaptive	kaptive	Kaptive reports information about capsular (K) loci found in genome assemblies.								To update		Sequence Analysis	kaptive	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive	0.3.0	kaptive	3.0.0b5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-kat_filter	kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-kc-align	kc-align	Kc-Align custom tool	kc-align	kc-align		kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	Multiple sequence alignment	Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	19	363	True	False	True
-khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	8	8	0	63	2022	True	False	True
-kinwalker		Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.								To update	http://www.bioinf.uni-leipzig.de/Software/Kinwalker/	RNA	kinwalker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-kleborate	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	kleborate	kleborate		Kleborate	Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	To update	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	3.0.6	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	38	319	True	False	True
-kofamscan	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	kofamscan	kofamscan		kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	Sequence analysis, Gene functional annotation	Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	33	594	True	False	True
-kraken	kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	kraken	kraken		Kraken	System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	Taxonomic classification	Taxonomy, Metagenomics	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	5	0	1209	33778	True	False	True
-kraken2	kraken2	Kraken2 for taxonomic designation.	kraken2	kraken2		kraken2	Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	Up-to-date	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.3	kraken2	2.1.3	Taxonomic classification	Taxonomy, Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	0	1	1	0	2367	185308	True	False	True
-kraken2tax	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	481	14683	True	False	True
-kraken_biom	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)								Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	182	1444	True	False	True
-kraken_taxonomy_report	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report		Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	Visualisation, Classification	Metagenomics, Taxonomy	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	354	2527	True	False	True
-krakentools	krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	krakentools		KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	Visualisation, Aggregation	Taxonomy, Metagenomics	6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	1	4	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	703	16525	True	False	True
-krocus	krocus	Predict MLST directly from uncorrected long reads	krocus	krocus		krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	Multilocus sequence typing, k-mer counting	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-labels	bg_labels	remaps and annotates alignments								To update	https://github.com/bgruening/galaxytools/tree/master/tools/labels	Sequence Analysis	labels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/labels	https://github.com/bgruening/galaxytools/tree/master/tools/labels	1.0.5.0	labels				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-last	last_al, last_db, last_split, last_train, last_maf_convert	LAST finds similar regions between sequences.	last	last		LAST	Short read alignment program incorporating quality scores	Sequence alignment	Genomics, Comparative genomics	To update	http://last.cbrc.jp/	Sequence Analysis	last	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/last	https://github.com/galaxyproject/tools-iuc/tree/main/tools/last	1205	last	1574	Sequence alignment	Comparative genomics	0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	41	227	True	False	False
-lca_wrapper	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	137	True	False	True
-legsta	legsta	Performs in silico Legionella pneumophila sequence based typing.	legsta	legsta		legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	Sequence analysis	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	55	True	False	True
-length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	322	4090	True	False	False
-lfq_protein_quant	lfq_protein_quant	Enable protein summarisation and quantitation								To update	https://github.com/compomics/LFQ_galaxy_p	Proteomics	lfq_protein_quant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	1.0	bioconductor-msnbase	2.28.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	111	True	False	False
-lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	152	True	False	True
-limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1012	20344	True	False	True
-lineagespot	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	lineagespot	lineagespot		lineagespot	Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	37	True	False	True
-links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	77	405	True	False	False
-locarna	locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile	LocARNA - A suite for multiple alignment and folding of RNAs								Up-to-date	http://www.bioinf.uni-freiburg.de/Software/LocARNA/	RNA	locarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	2.0.1	locarna	2.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	339	True	False	False
-logistic_regression_vif	LogisticRegression	Perform Logistic Regression with vif								To update		Sequence Analysis, Variant Analysis, Statistics	logistic_regression_vif	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif	https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif	1.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-logol	logol_wrapper	Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence								Up-to-date	http://logol.genouest.org/web/app.php/logol	Sequence Analysis		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	1.7.8	logol	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-longorf	longORF	obtain longest ORF in six-frame translations								To update		Sequence Analysis	longorf	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf	0.3.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-lorikeet	lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet		lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	Sequence analysis, Genotyping	Genotype and phenotype	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	647	True	False	True
-lotus2	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2		lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	To update	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.34.1	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	114	936	True	False	True
-m6anet	m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet		m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	True	False	True
-maaslin2	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	maaslin2	maaslin2		MaAsLin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	To update	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	1.16.0	bioconductor-maaslin2	1.18.0	Filtering, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	188	True	False	True
-macs2	macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak	MACS - Model-based Analysis of ChIP-Seq	macs	macs		MACS	Model-based Analysis of ChIP-seq data.	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	Up-to-date	https://github.com/taoliu/MACS	Sequence Analysis, Statistics	macs2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2	2.2.9.1	macs2	2.2.9.1	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	9	9	9	9	9	9	9	9	0	9	0	0	0	0	0	0	0	0	0	0	9	9	0	0	0	0	0	0	0	9	0	0	0	0	0	0	0	9	9	0	1969	84521	True	False	False
-maf_cpg_filter	cpgFilter	Mask CpG/non-CpG sites from MAF file								To update		Sequence Analysis, Variant Analysis	maf_cpg_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter	1.0.0	bx-python	0.12.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-mafft	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.526	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	2	2	2	2	2	0	1	0	0	2	0	0	0	0	0	0	0	1	0	2	0	0	2	0	0	0	2	0	0	0	0	0	0	0	2	2	0	817	143045	True	False	True
-make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-maker	maker, maker_map_ids	MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	maker	maker		MAKER	Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	Genome annotation	Genomics, DNA, Sequence analysis	To update	http://www.yandell-lab.org/software/maker.html	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker	2.31.11	maker	3.01.03	Genome annotation	Genomics, DNA, Sequence analysis	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	554	5591	True	False	True
-maldiquant	maldi_quant_peak_detection, maldi_quant_preprocessing	MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.								To update	http://strimmerlab.org/software/maldiquant/	Proteomics	MALDIquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant	1.22.0	r-base				0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	25	3797	True	False	False
-map_peptides_to_bed	map_peptides_to_bed	Map peptides to a reference genome for display by a genome browser								To update		Proteomics	map_peptides_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	0.2	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	41	True	False	False
-mapping_quality_stats	mapqstatistics	Collects and shows the distribution of MAPQ values in a BAM alignment file								To update	http://artbio.fr	Sequence Analysis, Statistics	mapping_quality_stats	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	0.22.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-mapping_to_ucsc	mapToUCSC	Format mapping data as UCSC custom track								To update		Visualization, Convert Formats, Next Gen Mappers	mapping_to_ucsc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-mapseq	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	mapseq	mapseq		MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .	k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	To update	https://github.com/jfmrod/MAPseq	Metagenomics	mapseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq	2.1.1	perl		k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	167	True	False	True
-marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-mash	mash_screen, mash_sketch	Fast genome and metagenome distance estimation using MinHash	mash	mash		Mash	Fast genome and metagenome distance estimation using MinHash.	Sequence distance matrix generation	Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	Up-to-date	https://github.com/marbl/Mash	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash	2.3	mash	2.3	Sequence distance matrix generation	Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	27	9763	True	False	True
-mashmap	mashmap	Fast local alignment boundaries								Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	Sequence Analysis	mashmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap	3.1.3	mashmap	3.1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-masigpro	masigpro	Identify significantly differential expression profiles in time-course microarray experiments	masigpro	masigpro		maSigPro	Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.	Regression analysis	Gene expression, Molecular genetics, Microarray experiment, RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html	Transcriptomics, RNA, Statistics	masigpro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro	1.49.3	coreutils	8.25	Regression analysis	Gene expression, Microarray experiment, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	576	True	False	False
-mauve_contig_mover	mauve_contig_mover	Order a draft genome relative to a related reference genome								To update	https://github.com/phac-nml/mauve_contig_mover	Sequence Analysis	mauve_contig_mover	nml	https://github.com/phac-nml/mauve_contig_mover	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover	1.0.10	mauve	2.4.0.r4736			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-maxbin2	maxbin2	clusters metagenomic contigs into bins	maxbin	maxbin		MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	To update	https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html	Metagenomics	maxbin2	mbernt	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2		maxbin2	2.2.7	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	0	118	2059	True	False	True
-maxquant	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering	Proteomics experiment, Proteomics, Statistics and probability	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	415	6078	True	False	True
-mcl	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	mcl	mcl		MCL	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.	Clustering, Network analysis, Gene regulatory network analysis	Molecular interactions, pathways and networks	Up-to-date	https://micans.org/mcl/man/mcl.html	Sequence Analysis	mcl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/mcl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl	22.282	mcl	22.282	Clustering, Gene regulatory network analysis	Molecular interactions, pathways and networks	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	29	True	False	True
-mea	mea	Maximum expected accuracy prediction								To update	http://www.bioinf.uni-leipzig.de/Software/mea	RNA	mea	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	0.6.4.1	mea	0.6.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	85	True	False	False
-mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	24	True	False	False
-medaka	medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	medaka	medaka		Medaka	medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	1.11.3	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	2	0	0	0	0	0	0	0	3	3	0	768	99863	True	False	True
-medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	0	1	1	0	548	9530	True	False	True
-megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	54	475	True	False	True
-megan	megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma	MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data.  MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).	megan	megan		MEGAN	Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Sequence analysis, Taxonomic classification	Sequence analysis	To update	https://github.com/husonlab/megan-ce	Sequence Analysis	megan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan	6.21.7	megan	6.25.9	Sequence analysis, Taxonomic classification	Sequence analysis	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	261	3610	True	False	True
-meningotype	meningotype	Assign sequence type to N. meningitidis genome assemblies	meningotype	meningotype		meningotype	In silico typing of Neisseria meningitidis contigs.	Genotyping, Multilocus sequence typing	Microbiology, Genotype and phenotype	Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype	0.8.5	meningotype	0.8.5	Multilocus sequence typing	Microbiology, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483	True	False	True
-meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-meta_proteome_analyzer	meta_proteome_analyzer	MetaProteomeAnalyzer								Up-to-date	https://github.com/compomics/meta-proteome-analyzer/	Proteomics	meta_proteome_analyzer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	2.0.0	mpa-portable	2.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	123	True	False	False
-metabat2	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT_2		MetaBAT 2	"an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning"	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	To update	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.17	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	2	1	2	2	2	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	192	4329	True	False	True
-metabuli	metabuli_classify	Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences	metabuli	metabuli		metabuli	Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid	Taxonomic classification	Taxonomy	Up-to-date	https://github.com/steineggerlab/Metabuli	Sequence Analysis, Metagenomics	metabuli	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli	1.0.5	metabuli	1.0.5	Taxonomic classification	Taxonomy	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	5.34c21f2	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	184	True	False	True
-metagene_annotator	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	115	636	True	False	True
-metagenomeseq	metagenomeseq_normalizaton	metagenomeSeq Normalization	metagenomeseq	metagenomeseq		metagenomeSeq	Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	To update	https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html	Metagenomics	metagenomeseq_normalization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq	1.16.0-0.0.1	bioconductor-metagenomeseq	1.43.0	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	753	True	False	True
-metanovo	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	4181	True	False	True
-metaphlan	customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	metaphlan	metaphlan		MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.	Nucleic acid sequence analysis, Phylogenetic tree analysis	Metagenomics, Phylogenomics	Up-to-date	https://github.com/biobakery/MetaPhlAn	Metagenomics	metaphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan	4.1.1	metaphlan	4.1.1	Nucleic acid sequence analysis	Metagenomics, Phylogenomics	1	2	4	4	1	2	4	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	499	11069	True	False	True
-metaquantome	metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome		metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	104	2522	True	False	True
-metawrapmg	metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	metawrap	metawrap		MetaWRAP	MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	Up-to-date	https://github.com/bxlab/metaWRAP	Metagenomics	metawrapmg_binning	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg	1.3.0	metawrap-mg	1.3.0	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-methtools	methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling	tools for methylation analysis								To update	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	Sequence Analysis	methtools	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	0.1.1	methtools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5461	True	False	False
-methyldackel	pileometh	A tool for processing bisulfite sequencing alignments								To update	https://github.com/dpryan79/MethylDackel	Sequence Analysis	pileometh	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	0.5.2	methyldackel	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	200	16573	True	False	False
-metilene	metilene	Differential DNA methylation calling								To update		RNA, Statistics	metilene	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	0.2.6.1	metilene	0.2.8			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	103	3966	True	False	False
-mg_toolkit	mg_toolkit_bulk_download, mg_toolkit_original_metadata	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	mg-toolkit	mg-toolkit		mg-toolkit	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	Data retrieval	Metagenomics	Up-to-date	https://github.com/EBI-Metagenomics/emg-toolkit	Metagenomics	mg_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	0.10.4	mg-toolkit	0.10.4	Data retrieval	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-miclip	mi_clip	Identification of binding sites in CLIP-Seq data.								To update	https://cran.r-project.org/src/contrib/Archive/MiClip/	Sequence Analysis	miclip	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	1.2.0	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-microsatbed	microsatbed	Select microsatellites for a bed file								To update	https://github.com/lmdu/pytrf	Sequence Analysis	microsatbed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed	1.3.2	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-microsatellite_birthdeath	microsatellite_birthdeath	Identify microsatellite births and deaths								To update		Sequence Analysis	microsatellite_birthdeath	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-microsats_alignment_level	microsats_align1	Extract Orthologous Microsatellites from pair-wise alignments								To update		Sequence Analysis, Variant Analysis	microsats_alignment_level	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level	1.0.0	sputnik				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-microsats_mutability	microsats_mutability1	Estimate microsatellite mutability by specified attributes								To update		Sequence Analysis, Variant Analysis	microsats_mutability	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability	1.1.0	bx-python	0.12.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-migmap	migmap	mapper for full-length T- and B-cell repertoire sequencing	MiGMAP	MiGMAP		MiGMAP	Mapper for full-length T- and B-cell repertoire sequencing.	Sequence analysis, Read mapping	Immunoproteins, genes and antigens, Sequence analysis	Up-to-date	https://github.com/mikessh/migmap	RNA, Sequence Analysis	migmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap	1.0.3	migmap	1.0.3	Sequence analysis, Read mapping	Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	1226	True	False	False
-minced	minced	MinCED - Mining CRISPRs in Environmental Datasets								To update	http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README	Sequence Analysis	minced	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minced	https://github.com/bgruening/galaxytools/tree/master/tools/minced	0.2.0	minced	0.4.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	53	895	True	False	False
-minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	109	2206	True	False	True
-miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	178	11938	True	False	True
-minipolish	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	185	True	False	True
-miniprot	miniprot, miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	miniprot	miniprot		miniprot	Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	Up-to-date	https://github.com/lh3/miniprot	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot	0.13	miniprot	0.13	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	30	842	True	False	True
-miranda	miranda	Finds potential target sites for miRNAs in genomic sequences								To update	http://www.microrna.org/	RNA	miranda	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	3.3a+galaxy1	miranda	3.3a			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	41	6076	True	False	False
-mircounts	mircounts	Generates miRNA count lists from read alignments to mirBase.								To update	http://artbio.fr	RNA, Transcriptomics	mircounts	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts	https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts	1.6	tar				0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-mirmachine	mirmachine	Tool to detect miRNA in genome sequences								Up-to-date	https://github.com/sinanugur/MirMachine	Sequence Analysis	mirmachine	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine	0.2.13	mirmachine	0.2.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-mirnature	mirnature	Computational detection of canonical microRNAs								Up-to-date	https://github.com/Bierinformatik/miRNAture	RNA, Sequence Analysis	mirnature	iuc	https://github.com/Bierinformatik/miRNAture	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature	1.1	mirnature	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	10	True	False	False
-mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	66	881	True	False	False
-mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	56	613	True	False	False
-mitos	mitos, mitos2	de-novo annotation of metazoan mitochondrial genomes	mitos	mitos		MITOS	De novo metazoan mitochondrial genome annotation.	Genome annotation	Zoology, Whole genome sequencing	To update	http://mitos.bioinf.uni-leipzig.de/	Sequence Analysis	mitos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos	1.1.7	mitos	2.1.9	Genome annotation	Zoology, Whole genome sequencing	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	1	0	236	100920	True	False	True
-mlst	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst		MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	Multilocus sequence typing	Immunoproteins and antigens	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	635	9304	True	False	True
-moFF	proteomics_moff	moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.								Up-to-date	https://github.com/compomics/moFF	Proteomics	proteomics_moff	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	2.0.3	moff	2.0.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	759	True	False	False
-mob_suite	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.9			0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	322	89021	True	False	True
-monocle3	monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers	De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_monocle3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3	0.1.4	monocle3-cli	0.0.9			9	0	9	0	9	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	264	3266	True	False	False
-morpheus	morpheus	Morpheus MS Search Application	morpheus	morpheus		Morpheus	A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.	Peptide database search	Proteomics	To update	https://cwenger.github.io/Morpheus	Proteomics	morpheus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	288	morpheus	290	Peptide database search	Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	140	True	False	False
-mothur	mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn	Mothur wrappers	mothur	mothur		mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	129	129	129	129	129	129	129	129	0	3	0	0	0	0	0	0	0	0	0	0	128	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	129	129	0	14353	302916	True	False	True
-mqc	mqc	Ribosome profiling mapping quality control tool								To update	https://github.com/Biobix/mQC	Sequence Analysis	mqc	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc	1.9	mqc	1.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	76	True	False	False
-mqppep	mqppep_anova, mqppep_preproc	MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Proteomics	mqppep	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	0.1.19	bioconductor-preprocesscore	1.64.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	2	True	False	False
-mrbayes	mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-msconvert	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert		msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			Filtering, Formatting	Proteomics, Proteomics experiment	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	189	19958	True	False	True
-msgfplus	msgfplus	MSGF+								To update		Proteomics	msgfplus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	0.5	msgf_plus	2024.03.26			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	507	True	False	False
-msms_extractor	msms_extractor	Extract MS/MS scans from the mzML file(s) based on PSM report.								To update		Proteomics	msms_extractor	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor	1.0.0	proteowizard	3_0_9992			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	110	True	False	False
-msstats	msstats	MSstats tool for analyzing mass spectrometry proteomic datasets	msstatstmt	msstatstmt		MSstatsTMT	Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	To update	https://github.com/MeenaChoi/MSstats	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	4.0.0	bioconductor-msstats	4.10.0	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	144	2036	True	False	False
-msstatstmt	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	726	True	False	True
-mt2mq	mt2mq	Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome								To update		Proteomics	mt2mq	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq	1.1.0	r-tidyverse				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	19	270	True	False	False
-multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	53	True	False	True
-multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.11	multiqc	1.24.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	8320	162790	True	False	True
-multispecies_orthologous_microsats	multispecies_orthologous_microsats	Extract orthologous microsatellites								To update		Sequence Analysis, Variant Analysis	multispecies_orthologous_microsats	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats	https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats	1.0.0	bx-sputnik				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-mummer	mummerplot_wrapper	Draw dotplots using mummer, mucmer, or promer with mummerplot								To update	http://mummer.sourceforge.net/	Graphics, Sequence Analysis, Visualization	mummer	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	0.0.8	ghostscript	9.18			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	83	652	True	False	False
-mummer4	mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords	Mummer4 Tools	mummer4	mummer4						Up-to-date	https://github.com/mummer4/mummer	Sequence Analysis	mummer4	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4	4.0.0rc1	mummer4	4.0.0rc1			6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	6	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	669	18347	True	False	False
-mykrobe	mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe		Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-mykrobe_parser	mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-mz_to_sqlite	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	Conversion, Peptide database search	Proteomics, Biological databases	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	33	844	True	False	True
-mzml_validator	mzml_validator	mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.								To update	https://github.com/RECETOX/galaxytools	Metabolomics, Proteomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	0.1.0+galaxy2	lxml				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-naltorfs	bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs	nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)								Up-to-date	https://github.com/BlankenbergLab/nAltORFs	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs	0.1.2	naltorfs	0.1.2			3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-nanocompore	nanocompore_db, nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Nanocompore	Nanocompore		Nanocompore	RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	3	836	True	False	True
-nanoplot	nanoplot	Plotting tool for long read sequencing data and alignments	nanoplot	nanoplot		NanoPlot	NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences	Scatter plot plotting, Box-Whisker plot plotting	Genomics	Up-to-date	https://github.com/wdecoster/NanoPlot	Visualization	nanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot	1.43.0	nanoplot	1.43.0	Scatter plot plotting, Box-Whisker plot plotting	Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	2195	63235	True	False	True
-nanopolishcomp	nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate	NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.	nanopolishcomp	nanopolishcomp		NanopolishComp	NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	To update	https://a-slide.github.io/NanopolishComp	Sequence Analysis	nanopolishcomp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp	0.6.11	nanopolishcomp	0.6.12	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	15	1074	True	False	True
-nastiseq	nastiseq	A method to identify cis-NATs using ssRNA-seq								Up-to-date	https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/	RNA	nastiseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	1.0	r-nastiseq	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	40	True	False	False
-ncbi_blast_plus	blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper	NCBI BLAST+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	devteam	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	2.14.1	python				16	16	16	16	16	16	16	16	0	15	0	0	15	0	0	0	0	0	0	0	16	15	16	0	0	0	0	0	0	16	0	0	0	0	16	0	0	16	15	0	4066	365597	True	False	True
-ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ncbi_fcs_adaptor	ncbi_fcs_adaptor	FCS-adaptor detects adaptor and vector contamination in genome sequences.								To update	https://github.com/ncbi/fcs	Sequence Analysis	ncbi_fcs_adaptor	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	0.5.0					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-ncbi_fcs_gx	ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).	ncbi_fcs	ncbi_fcs		NCBI fcs	The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	Up-to-date	https://github.com/ncbi/fcs-gx	Sequence Analysis	ncbi_fcs_gx	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	0.5.4	ncbi-fcs-gx	0.5.4	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	95	667	True	False	False
-newick_utils	newick_display	Perform operations on Newick trees	newick_utilities	newick_utilities		Newick Utilities	The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.	Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction	Phylogeny, Genomics, Computer science	To update	http://cegg.unige.ch/newick_utils	Visualization, Metagenomics	newick_utils	iuc	https://github.com/tjunier/newick_utils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils	1.6+galaxy1	newick_utils	1.6		Phylogeny, Genomics, Computer science	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	448	25505	True	False	True
-nextclade	nextalign, nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	nextclade	nextclade		Nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.	Methylation analysis, Variant calling	Genomics, Sequence analysis, Cladistics	To update	https://github.com/nextstrain/nextclade	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade	2.7.0	nextalign	2.14.0	Methylation analysis, Variant calling	Genomics, Cladistics	1	1	2	2	1	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	0	0	0	1	0	0	0	0	0	0	0	2	0	0	210	4080	True	False	True
-nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268	True	False	True
-nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-nonpareil	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil		nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.5.5	Operation		1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	142	True	False	True
-novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	162	6384	True	False	False
-nucleosome_prediction	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	861	True	False	True
-nugen_nudup	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	1	1	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	45	True	False	True
-obitools	obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq	OBITools is a set of programs developed to simplify the manipulation of sequence files	obitools	obitools		OBITools	Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	Up-to-date	http://metabarcoding.org/obitools	Sequence Analysis	obitools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools	1.2.13	obitools	1.2.13	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	0	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	503	26251	True	False	True
-ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	True	False	False
-odgi	odgi_build, odgi_viz	Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.								To update	https://github.com/vgteam/odgi	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi	0.3	odgi	0.8.6			0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2	25	True	False	False
-ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-omark	omark	Proteome quality assessment software	omark	omark		OMArk	Proteome quality assessment software	Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	To update	https://github.com/DessimozLab/OMArk	Sequence Analysis	omark	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark	0.3.0			Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	39	2654	True	False	False
-openms	AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter	OpenMS in version 2.1.								To update		Proteomics	openms	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/openms	https://github.com/bgruening/galaxytools/tree/master/tools/openms	2.1.0	openms	3.1.0			7	34	135	0	7	34	135	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	135	134	0	916	105743	True	False	False
-openms	AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter	OpenMS Suite for LC/MS data management and analyses								To update	https://www.openms.de/	Proteomics	openms	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	3.1	openms	3.1.0			8	34	144	0	8	34	144	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	141	124	0	886	105432	True	False	False
-optitype	optitype	Precision HLA typing from NGS data								Up-to-date	https://github.com/FRED-2/OptiType	Sequence Analysis	optitype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype	1.3.5	optitype	1.3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	321	True	False	False
-orfipy	orfipy	Galaxy wrapper for ORFIPY	orfipy	orfipy		orfipy	A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	Up-to-date	https://github.com/urmi-21/orfipy	Sequence Analysis	orfipy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy	0.0.4	orfipy	0.0.4	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	774	True	False	True
-orthofinder	orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	OrthoFinder	OrthoFinder		OrthoFinder	OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.	Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis	Up-to-date	https://github.com/davidemms/OrthoFinder	Phylogenetics, Sequence Analysis	orthofinder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder	2.5.5	orthofinder	2.5.5	Genome comparison, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics	0	1	1	1	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	239	1333	True	False	True
-pacu	pacu_map, pacu_snp	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.	pacu	pacu		PACU	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads).	Clustering	Phylogenetics, Sequence analysis	Up-to-date	https://github.com/BioinformaticsPlatformWIV-ISP/PACU	Sequence Analysis, Phylogenetics	pacu	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu	0.0.5	pacu_snp	0.0.5	Clustering	Phylogenetics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-pairtools	pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats	Flexible tools for Hi-C data processing								Up-to-date	https://pairtools.readthedocs.io	Sequence Analysis	pairtools	iuc	https://github.com/open2c/pairtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools	1.1.0	pairtools	1.1.0			5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-pangolin	pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages								To update	https://github.com/hCoV-2019/pangolin	Sequence Analysis	pangolin	nml	https://github.com/hCoV-2019/pangolin	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin	1.1.14	pangolin	4.3			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	259	7276	True	False	False
-pangolin	pangolin	Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.	pangolin_cov-lineages	pangolin_cov-lineages		pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages	Tree-based sequence alignment, Variant classification	Virology	Up-to-date	https://github.com/cov-lineages/pangolin	Sequence Analysis	pangolin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin	4.3	pangolin	4.3	Tree-based sequence alignment, Variant classification	Virology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	259	7276	True	False	False
-paralyzer	paralyzer	A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.								Up-to-date	https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/	RNA	paralyzer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	1.5	paralyzer	1.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	299	True	False	False
-parse_mito_blast	parse_mito_blast	Filtering blast out from querying assembly against mitochondrial database.								Up-to-date	https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py	Sequence Analysis	parse_mito_blast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast	1.0.2	parse_mito_blast	1.0.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	31	90	True	False	False
-pathview	pathview	Pathview is a tool set for pathway based data integration and visualization.	pathview	pathview		pathview	Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	To update	https://bioconductor.org/packages/release/bioc/html/pathview.html	Statistics, RNA, Micro-array Analysis	pathview	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview	1.34.0	bioconductor-pathview	1.42.0	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	565	5260	True	False	False
-pathwaymatcher	reactome_pathwaymatcher	Reactome Pathway Matcher								To update	https://github.com/LuisFranciscoHS/PathwayMatcher	Proteomics	reactome_pathwaymatcher	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher		pathwaymatcher	1.9.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	238	True	False	False
-patrist	patrist	Extract Patristic Distance From a Tree								To update	https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02	Phylogenetics	patrist	nml	https://github.com/phac-nml/patrist	https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist	0.1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-peakachu	peakachu	PEAKachu is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	peakachu	rnateam	https://github.com/tbischler/PEAKachu	https://github.com/bgruening/galaxytools/tree/master/tools/peakachu	0.2.0+galaxy1	peakachu	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	78	3109	True	False	False
-pep_pointer	pep_pointer	PepPointer categorizes peptides by their genomic coordinates.								To update		Genomic Interval Operations, Proteomics	pep_pointer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	0.1.3+galaxy1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	498	True	False	False
-pepquery	pepquery	A peptide-centric MS search engine for novel peptide identification and validation.								To update	https://pepquery.org	Proteomics	pepquery	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	1.6.2	pepquery	2.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	4862	True	False	False
-pepquery2	pepquery2, pepquery2_index, pepquery2_show_sets	PepQuery2 peptide-centric MS search for peptide identification and validation								Up-to-date	https://pepquery.org	Proteomics	pepquery2	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	2.0.2	pepquery	2.0.2			0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	13	717	True	False	False
-peptide_genomic_coordinate	peptide_genomic_coordinate	Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files								To update		Proteomics	peptide_genomic_coordinate	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate	1.0.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	468	True	False	False
-peptideshaker	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.9			4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	2	0	485	17477	True	False	True
-peptimapper	peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag	Proteogenomics workflow for the expert annotation of eukaryotic genomes								To update	https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9	Proteomics		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	2.1					0	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-pepxml_to_xls		Convert PepXML to Tabular								To update		Proteomics	pepxml_to_xls	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-percolator	batched_set_list_creator, percolator, percolator_input_converters, pout2mzid	Percolator								To update		Proteomics	percolator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator	3.5	percolator	3.6.5			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	5	368	True	False	False
-pfamscan	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	19	165	True	False	True
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
+AggregateAlignments	graphclust_aggregate_alignments	Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.								Up-to-date		RNA	graphclust_aggregate_alignments	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments	0.6.0	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	116	True	False	False
+AlignCluster	graphclust_align_cluster	Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.								To update		RNA	graphclust_align_cluster	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster	0.1	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	10	3060	True	False	False
+CMFinder	cmFinder	Determines consensus motives for sequences.								To update		RNA	graphclust_cmfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	14	45191	True	False	False
+CollectResults	glob_report	Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.								To update		RNA	graphclust_postprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	14	1961	True	False	False
+CollectResultsNoAlign	graphclust_glob_report_no_align	Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.								To update		RNA	graphclust_postprocessing_no_align	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	108	True	False	False
+EMLassemblyline	annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.0+galaxy0	r-base				0	0	11	9	0	0	11	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	102	True	False	False
+Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	82	True	False	False
+GAFA	gafa	Gene Align and Family Aggregator								To update	http://aequatus.tgac.ac.uk	Visualization	gafa	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA	0.3.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	45	True	False	False
+GSPAN	gspan	Second step of GraphClust								To update		RNA	graphclust_fasta_to_gspan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	133	True	False	False
+Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+LocARNAGraphClust	locarna_best_subtree	MLocARNA computes a multiple sequence-structure alignment of RNA sequences.								To update		RNA	graphclust_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	45325	True	False	False
+NSPDK	NSPDK_candidateClust, nspdk_sparse	Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.								To update		RNA	graphclust_nspdk	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	9.2.3.1	graphclust-wrappers	0.6.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	28	62388	True	False	False
+PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	73	1004	True	False	True
+Plotting	motifFinderPlot	Plotting results for GraphClust								To update		RNA	graphclust_motif_finder_plot	rnateam	https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting	0.4	seaborn				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	68	True	False	False
+PrepareForMlocarna	preMloc	This tool prepares files for locarna step.								To update		RNA	graphclust_prepocessing_for_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	1932	True	False	False
+Preprocessing	preproc	Preprocessing input for GraphClust								To update		RNA	graphclust_preprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	1758	True	False	False
+Structure_GSPAN	structure_to_gspan	Convert RNA structure to GSPAN graphs								To update		RNA	structure_to_gspan	rnateam	https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	2925	True	False	False
+ThermoRawFileParser	thermo_raw_file_converter	Thermo RAW file converter								To update	https://github.com/compomics/ThermoRawFileParser	Proteomics	thermo_raw_file_converter	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	1.3.4	thermorawfileparser	1.4.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	2689	True	False	False
+TreeBest	treebest_best	TreeBeST best	treebest	treebest		TreeBeST	TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	984	True	False	True
+TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	42	True	False	False
+abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+abricate	abricate, abricate_list, abricate_summary	Mass screening of contigs for antiobiotic resistance genes	ABRicate	ABRicate		ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.	Antimicrobial resistance prediction	Genomics, Microbiology	Up-to-date	https://github.com/tseemann/abricate	Sequence Analysis	abricate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate	1.0.1	abricate	1.0.1	Antimicrobial resistance prediction	Genomics, Microbiology	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	2	3	3	0	1764	496717	True	False	True
+abritamr	abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	abritamr	abritamr		abriTAMR	an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://zenodo.org/record/7370628	Sequence Analysis	abritamr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr	1.0.19	abritamr	1.0.19	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	391	4278	True	False	True
+adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	37	217	True	False	False
+aegean	aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval	AEGeAn toolkit wrappers	gaeval	gaeval		GAEVAL	Gene Annotation EVAluation.	Sequence annotation	Sequence analysis, Gene structure	Up-to-date	https://github.com/BrendelGroup/AEGeAn	Transcriptomics, Sequence Analysis	aegean	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean	0.16.0	aegean	0.16.0	Sequence annotation	Sequence analysis, Gene structure	1	4	4	4	1	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	47	168	True	False	False
+aldex2	aldex2	Performs analysis Of differential abundance taking sample variation into account	aldex2	aldex2		ALDEx2	A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	Statistical inference	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	13	129	True	False	True
+align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	329	True	False	False
+amplican	amplican	AmpliCan is an analysis tool for genome editing.	amplican	amplican		amplican	It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	53	True	False	True
+ampvis2	ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn	ampvis2	ampvis	ampvis		ampvis	ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.	Analysis, Visualisation	Biodiversity	To update	https://github.com/MadsAlbertsen/ampvis2/	Metagenomics	ampvis2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2	2.8.9			Analysis, Visualisation	Biodiversity	0	0	19	0	0	0	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	42	267	True	False	False
+amrfinderplus	amrfinderplus	"""AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms."	amrfinderplus	amrfinderplus		AMRFinderPlus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms"	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.12.8	ncbi-amrfinderplus	3.12.8	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	591	True	False	True
+ancombc	ancombc	Performs analysis of compositions of microbiomes with bias correction.	ancombc	ancombc		ANCOMBC	Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	7	True	False	True
+annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1175	25975	True	False	False
+antarna	antarna	antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .								To update		RNA	antarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna	1.1	antarna	2.0.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	52	True	False	False
+antismash	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash		antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	279	14596	True	False	True
+aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+aresite2	AREsite2_REST	AREsite2 REST Interface								To update	http://rna.tbi.univie.ac.at/AREsite	RNA, Data Source, Sequence Analysis	aresite2	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	65	True	False	False
+argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+arriba	arriba, arriba_draw_fusions, arriba_get_filters	Arriba detects fusion genes in RNA-Seq data after running RNA-STAR								Up-to-date	https://github.com/suhrig/arriba	Sequence Analysis, Transcriptomics	arriba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba	2.4.0	arriba	2.4.0			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	38	3528	True	False	False
+art	art_454, art_illumina, art_solid	Simulator for Illumina, 454, and SOLiD sequencing data	art	art		ART	ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD	Conversion	Bioinformatics	To update	http://www.niehs.nih.gov/research/resources/software/biostatistics/art/	Sequence Analysis, Data Source	art	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/art	https://github.com/galaxyproject/tools-iuc/tree/main/tools/art	2014.11.03.0	art	2016.06.05	Conversion	Bioinformatics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+artic	artic_guppyplex, artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	artic	artic		ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	Sequence alignment	Genomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	2	1	0	123	8175	True	False	True
+assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+astral	astral	Tool for estimating an unrooted species tree given a set of unrooted gene trees								Up-to-date	https://github.com/smirarab/ASTRAL	Phylogenetics	astral	iuc	https://github.com/usegalaxy-be/galaxytools/tree/main/astral	https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral	5.7.8	astral-tree	5.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	False		
+augustus	augustus, augustus_training	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.	augustus	augustus		AUGUSTUS	AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.	Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus	3.4.0	augustus	3.5.0	Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	685	11245	True	False	False
+augustus	augustus	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.								To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	3.1.0	augustus	3.5.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	516	8864	True	False	False
+b2btools	b2btools_single_sequence	This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.	b2btools	b2btools		b2bTools	The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA	Protein disorder prediction, Protein secondary structure prediction, Protein feature detection		To update	https://bio2byte.be	Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools	3.0.5+galaxy0	b2btools	3.0.7	Protein disorder prediction, Protein secondary structure prediction		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	12	345	True	False	False
+bakta	bakta	"""Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."""	bakta	bakta		Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	Up-to-date	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.4	bakta	1.9.4	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	151	2982	True	False	True
+bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+bamclipper	bamclipper	Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.								Up-to-date	https://github.com/tommyau/bamclipper	Sequence Analysis	bamclipper	nml	https://github.com/tommyau/bamclipper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper	1.0.0	bamclipper	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+bamhash	bamhash	Hash BAM and FASTQ files to verify data integrity								Up-to-date	https://github.com/DecodeGenetics/BamHash	Sequence Analysis	bamhash	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	1.1	bamhash	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	169	True	False	False
+bamparse	bamparse	Generates hit count lists from bam alignments.								To update	http://artbio.fr	RNA, Transcriptomics	bamparse	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	4.1.1	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+bamtools	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	208	14021	True	False	True
+bamtools_filter	bamFilter	Filter BAM datasets on various attributes using bamtools filter	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1195	114863	True	False	False
+bamtools_split	bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag	Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett.	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	197	4328	True	False	False
+bamutil	bamutil_clip_overlap, bamutil_diff	bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.								To update	https://github.com/statgen/bamUtil	Sequence Analysis	bamutil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil		bamutil	1.0.15			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	39	True	False	False
+bandage	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	bandage	bandage		Bandage	GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	Sequence assembly visualisation	Genomics, Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	2	2	2	0	2016	44390	True	False	True
+barcode_collapse	barcode_collapse	Paired End randomer aware duplicate removal algorithm								To update	https://github.com/YeoLab/gscripts	RNA, Sequence Analysis	barcode_collapse	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	0.1.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Single Cell, Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	71	True	False	False
+barrnap	barrnap	Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.	barrnap	barrnap		Barrnap	Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).	Gene prediction	Genomics, Model organisms, Model organisms	To update	https://github.com/tseemann/barrnap	Sequence Analysis	barrnap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap	1.2.2	barrnap	0.9	Gene prediction	Genomics, Model organisms, Model organisms	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	160	3938	True	False	False
+baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bax2bam	bax2bam	BAX to BAM converter								Up-to-date	https://github.com/pacificbiosciences/bax2bam/	Convert Formats, Sequence Analysis	bax2bam	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam	0.0.11	bax2bam	0.0.11			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8	200	True	False	False
+bayescan	BayeScan	Detecting natural selection from population-based genetic data	bayescan	bayescan		BayeScan	BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8	64	True	False	True
+bbtools	bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.	bbmap	bbtools, bbmap		BBMap	BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	To update	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.08	bbmap	39.09	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	6	3	5	0	6	3	5	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	4	0	0	420	6381	True	False	True
+bctools	bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events	bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0								Up-to-date	https://github.com/dmaticzka/bctools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools	0.2.2	bctools	0.2.2			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	7	7	0	87	2895	True	False	False
+bed_to_protein_map	bed_to_protein_map	Converts a BED file to a tabular list of exon locations								To update		Proteomics	bed_to_protein_map	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	49	385	True	False	False
+bellerophon	bellerophon	Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.								Up-to-date	https://github.com/davebx/bellerophon	Sequence Analysis	bellerophon	iuc	https://github.com/davebx/bellerophon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon	1.0	bellerophon	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	123	1194	True	False	False
+best_regression_subsets	BestSubsetsRegression1	Perform Best-subsets Regression								To update		Sequence Analysis, Variant Analysis	best_regression_subsets	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets	https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets	1.0.0	numpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	3	True	False	False
+bigscape	bigscape	Construct sequence similarity networks of BGCs and groups them into GCF	BiG-SCAPE	BiG-SCAPE		BiG-SCAPE	A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+bigwig_outlier_bed	bigwig_outlier_bed	pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files	bigtools	bigtools		bigtools	Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust.			To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	Sequence Analysis	bigwig_outlier_bed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed	0.2.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+binning_refiner	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	binning_refiner	binning_refiner		Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	81	True	False	True
+biohansel	biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+bioinformatics_cafe	fasta_regex_finder	Miscellanea of scripts for bioinformatics								To update	https://github.com/dariober/bioinformatics-cafe/	Sequence Analysis	bioinformatics_cafe	mbernt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe	0.1.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	978	True	False	False
+biom_format	biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	biomformat	biomformat		biomformat	"This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods."	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	Formatting	Laboratory information management, Sequence analysis	2	2	6	0	2	2	6	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	98	3906	True	False	True
+bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	531	True	False	False
+bioperl	bp_genbank2gff3	Converts GenBank format files to GFF3	bioperl	bioperl		BioPerl	A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.  It provides software modules for many of the typical tasks of bioinformatics programming.	Data handling, Service invocation	Genomics, Software engineering, Data management	To update	https://bioperl.org/	Sequence Analysis	bp_genbank2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl	1.1	perl-bioperl	1.7.8	Data handling, Service invocation	Genomics, Software engineering	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	240	6736	True	False	False
+biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	3	True	False	False
+bismark	bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor	A tool to map bisulfite converted sequence reads and determine cytosine methylation states								To update	https://www.bioinformatics.babraham.ac.uk/projects/bismark/	Sequence Analysis, Next Gen Mappers	bismark	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	0.22.1	bismark	0.24.2			0	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	4	0	0	0	0	0	0	0	0	0	4	4	4	0	332	12876	True	False	False
+blast2go	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	101	1232	True	False	True
+blast_parser	blast_parser	Convert 12- or 24-column BLAST output into 3-column hcluster_sg input								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	blast_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	0.1.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	27	296	True	False	False
+blast_plus_remote_blastp	blast_plus_remote_blastp	NCBI BLAST+ with -remote option								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	blast_plus_remote_blastp	galaxyp	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp	2.6.0	blast	2.16.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	121	22499	True	False	True
+blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+blastxml_to_gapped_gff3	blastxml_to_gapped_gff3	BlastXML to gapped GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	Convert Formats, Sequence Analysis	blastxml_to_gapped_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3	1.1	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24	185	True	False	False
+blastxml_to_top_descr	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	159	264558	True	False	True
+blat_coverage_report	generate_coverage_report	Polymorphism of the Reads								To update		Next Gen Mappers, Sequence Analysis	blat_coverage_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+blat_mapping	blat2wig	Coverage of the Reads in wiggle format								To update		Next Gen Mappers, Sequence Analysis	blat_mapping	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	685	True	False	False
+blockbuster	blockbuster	Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.								To update	http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html	RNA, Sequence Analysis	blockbuster	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	0.1.2	blockbuster	0.0.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	34	3009	True	False	False
+blockclust	blockclust	BlockClust detects transcripts with similar processing patterns.								Up-to-date	https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust	RNA	blockclust	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	1.1.1	blockclust	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	15	1478	True	False	False
+bracken	est_abundance	Bayesian Reestimation of Abundance with KrakEN	bracken	bracken		Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	Statistical calculation	Metagenomics, Microbial ecology	Up-to-date	https://ccb.jhu.edu/software/bracken/	Sequence Analysis, Metagenomics	bracken	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken	3.0	bracken	3.0	Statistical calculation	Metagenomics, Microbial ecology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	326	18351	True	False	True
+braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	17	109	True	False	False
+braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	567	True	False	False
+brew3r_r	brew3r_r	Extend 3' end of a GTF using another GTF as a template	brew3r.r	brew3r.r		BREW3R.r	This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.	Genome annotation	Transcriptomics, Genomics	To update	https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html	Transcriptomics, RNA	brew3r_r	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r	https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r	1.0.2			Genome annotation	Transcriptomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bumbershoot	idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch									To update	http://proteowizard.sourceforge.net/	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot	3.0.21142	bumbershoot	3_0_21142_0e4f4a4			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	3	1348	True	False	False
+bundle_collections	bundle_collection	Tool to bundle up list collection into a single zip to be download								To update		Sequence Analysis	bundle_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections	1.3.0	perl-getopt-long	2.58			0	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+busco	busco	BUSCO assess genome and annotation completeness	busco	busco		BUSCO	Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://gitlab.com/ezlab/busco/-/releases	Sequence Analysis	busco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco	5.7.1	busco	5.7.1	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1804	86180	True	False	True
+bwameth	bwameth	Fast and accurate alignment of BS-seq reads								Up-to-date	https://github.com/brentp/bwa-meth	Sequence Analysis, Next Gen Mappers	bwameth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth	0.2.7	bwameth	0.2.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	201	10619	True	False	False
+cactus	cactus_cactus, cactus_export	Cactus is a reference-free whole-genome multiple alignment program	cactus	cactus		Cactus	Cactus is a reference-free whole-genome multiple alignment program.	Multiple sequence alignment, Genome alignment	Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics	To update	https://github.com/ComparativeGenomicsToolkit/cactus	Sequence Analysis	cactus	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	2.7.1			Multiple sequence alignment, Genome alignment	Genomics, Sequence assembly, Mapping, Phylogenetics	0	2	2	1	0	2	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	26	234	True	False	False
+calculate_contrast_threshold	calculate_contrast_threshold	Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.								To update	https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold	Visualization, Genomic Interval Operations, SAM	calculate_contrast_threshold	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold	1.0.0	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+calisp	calisp	Calgary approach to isotopes in proteomics								Up-to-date	https://github.com/kinestetika/Calisp/	Proteomics	calisp	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp	3.0.13	calisp	3.0.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	True	False	False
+cami_amber	biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert	Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments								Up-to-date	https://github.com/CAMI-challenge/AMBER	Metagenomics	cami_amber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber	2.0.7	cami-amber	2.0.7			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	101	7766	True	False	False
+cardinal	cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots	Statistical and computational tools for analyzing mass spectrometry imaging datasets								Up-to-date	http://cardinalmsi.org	Proteomics, Metabolomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	3.4.3	bioconductor-cardinal	3.4.3			0	9	11	11	0	9	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	0	0	0	0	0	0	0	9	11	9	0	277	48705	True	False	False
+cat	cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	cat_bins		CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat	5.2.3	cat	5.3	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	5	2	5	0	5	2	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	268	2878	True	False	True
+cd_hit_dup	cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	280	4474	True	False	True
+cell-types-analysis	ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals	Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis								To update		Transcriptomics, RNA, Statistics	suite_cell_types_analysis	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis	1.1.1	cell-types-analysis	0.1.11			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	6	True	False	False
+cemitool	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.26.0	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	98	True	False	True
+champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	19	174	True	False	False
+charts	charts	Enables advanced visualization options in Galaxy Charts								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	Visualization	charts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts	1.0.1	r-getopt				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	287	3589	True	False	False
+checkm	checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	checkm	checkm		CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	Up-to-date	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.3	checkm-genome	1.2.3	Sequence assembly validation, Sequence composition calculation, Statistical calculation	Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	0	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	390	5165	True	False	True
+checkv	checkv_end_to_end	Assess quality of single-contig viral genomes	checkv	checkv		CheckV	CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	Up-to-date	https://bitbucket.org/berkeleylab/checkv/	Metagenomics	checkv	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv	1.0.3	checkv	1.0.3	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cherri	cherri_eval, cherri_train	Computational Help Evaluating RNA-RNA interactions	cherri	cherri		cherri	CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.		Molecular interactions, pathways and networks, Structure analysis, Machine learning	To update	https://github.com/BackofenLab/Cherri	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri	0.7	cherri	0.8		Molecular interactions, pathways and networks, Structure analysis, Machine learning	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	207	True	False	False
+chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	418	15690	True	False	False
+chira	chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify	Chimeric Read Annotator for RNA-RNA interactome data	chira	chira		ChiRA	ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.		RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	Up-to-date	https://github.com/pavanvidem/chira	RNA, Transcriptomics, Sequence Analysis	chira	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira	1.4.3	chira	1.4.3		Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	97	6418	True	False	False
+chromeister	chromeister	ultra-fast pairwise genome comparisons								Up-to-date	https://github.com/estebanpw/chromeister	Sequence Analysis	chromeister	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister	1.5.a	chromeister	1.5.a			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	182	2130	True	False	False
+chromosome_diagram	chromosome_diagram	Chromosome Diagrams using Biopython								To update		Graphics, Sequence Analysis, Visualization	chromosome_diagram	peterjc		https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+circexplorer	circexplorer	A combined strategy to identify circular RNAs (circRNAs and ciRNAs)								To update	https://github.com/YangLab/CIRCexplorer	Sequence Analysis, RNA	circexplorer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	1.1.9.0	circexplorer	1.1.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	251	True	False	False
+circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	269	True	False	False
+cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	To update	https://github.com/Hoohm/CITE-seq-Count	Single Cell, Transcriptomics, Proteomics	cite_seq_count	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	1.4.4	cite-seq-count	1.4.5	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	18	False		
+clair3	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	clair3	clair3		Clair3	Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	1.0.8	clair3	1.0.10	Variant calling	Molecular genetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	68	1856	True	False	True
+clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+climate-stripes	climate_stripes	Create climate stripes from a tabular input file								To update	https://www.climate-lab-book.ac.uk/2018/warming-stripes/	Climate Analysis, Visualization	climate_stripes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	1.0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	237	True	False	False
+clinod	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+clustalw	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	clustal2	clustal2		Clustal 2 (Clustal W, Clustal X)	Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.	Multiple sequence alignment	Phylogeny, Sequence analysis	Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw	2.1	clustalw	2.1	Multiple sequence alignment	Phylogeny, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	651	46793	True	False	True
+cmsearch_deoverlap	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	102	True	False	True
+cmv	cmcv, cmv, hmmcv, hmmv	cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.								Up-to-date	https://github.com/eggzilla/cmv	RNA	cmv	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	1.0.8	cmv	1.0.8			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	1	108	True	False	False
+codeml	codeml	Detects positive selection	paml	paml		PAML	Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml	4.9	paml	4.10.7	Probabilistic sequence generation	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	29	60901	True	False	True
+cofold	cofold	Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.								To update	http://www.e-rna.org/cofold/	RNA	cofold	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	2.0.4.0	cofold	2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	342	True	False	False
+cojac	cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	cojac	cojac		COJAC	CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.2	cojac	0.9.2		Genetic variation	2	0	3	0	2	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	20	2757	True	False	True
+colabfold	colabfold_alphafold, colabfold_msa	Protein prediction based on AlphaFold2	Colabfold	Colabfold		ColabFold	ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.	Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	To update	https://github.com/sokrypton/ColabFold	Proteomics, Graphics	colabfold	iuc	https://github.com/sokrypton/ColabFold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold	1.5.5			Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+colibread	commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak	Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome								To update	https://colibread.inria.fr/	Sequence Analysis, Variant Analysis	colibread	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread	24.7.14+galaxy0	commet	24.7.14			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	251	True	False	False
+collapse_collection	collapse_dataset	Collection tool that collapses a list of files into a single datasset in order of appears in collection								To update		Sequence Analysis	collapse_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection	5.1.0	gawk				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1583	33934	True	False	False
+combineJSON	combine_json	JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.								To update		Sequence Analysis	combine_json	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+combine_metaphlan_humann	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	147	True	False	True
+combine_tabular_collection	combine	Combine Tabular Collection into a single file								To update		Sequence Analysis	combine_tabular_collection	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+compalignp	compalignp	Compute fractional identity between trusted alignment and test alignment								Up-to-date		RNA, Sequence Analysis	compalignp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp	1.0	compalignp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	220	True	False	False
+compare_humann2_output	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	332	True	False	True
+compleasm	compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	compleasm	compleasm		compleasm	"""Compleasm: a faster and more accurate reimplementation of BUSCO"""	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm	0.2.6	compleasm	0.2.6	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+compute_motif_frequencies_for_all_motifs	compute_motif_frequencies_for_all_motifs	Compute Motif Frequencies For All Motifs, motif by motif.								To update		Sequence Analysis, Statistics	compute_motif_frequencies_for_all_motifs	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	94	True	False	False
+compute_motifs_frequency	compute_motifs_frequency	Compute Motif Frequencies in indel flanking regions.								To update		Sequence Analysis, Statistics	compute_motifs_frequency	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	65	True	False	False
+concoct	concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	concoct	concoct		CONCOCT	A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct	1.1.0	concoct	1.1.0	Sequence clustering, Read binning	Metagenomics	0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	92	786	True	False	True
+consensus_from_alignments	aligned_to_consensus	Tool to compute a consensus sequence from several aligned fasta sequences								To update		Sequence Analysis	consalign	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments	https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments	1.0.0	r-bioseq				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55	585	True	False	False
+consolidate_vcfs	consolidate_vcfs	Combines freebayes and mpileup files for use by vcf2snvalignment								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	consolidate_vcfs	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+coprarna	coprarna	Target prediction for prokaryotic trans-acting small RNAs								To update	https://github.com/PatrickRWright/CopraRNA	RNA, Sequence Analysis	coprarna	rnateam	https://github.com/PatrickRWright/CopraRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna	2.1.1	coprarna	2.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis, Single Cell	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+count_gff_features	count_gff_features	Count GFF Features								To update		Sequence Analysis	count_gff_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features	https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features	0.2	galaxy-ops	1.1.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	49	271	True	False	False
+count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+coverage_report	CoverageReport2	Generate Detailed Coverage Report from BAM file								To update	https://github.com/galaxyproject/tools-iuc	Sequence Analysis	coverage_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report	0.0.4	perl-number-format	1.76			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+coverm	coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm		CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	Local alignment	Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	72	529	True	False	True
+crispr_studio	crispr_studio	CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.	crisprstudio	crisprstudio		CRISPRStudio	CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.	Visualisation	Sequence analysis, Genomics, Data visualisation	To update	https://github.com/moineaulab/CRISPRStudio	Sequence Analysis	crispr_studio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio	1+galaxy0	crispr_studio	1	Visualisation	Sequence analysis, Genomics, Data visualisation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	30	636	True	False	False
+crosscontamination_barcode_filter	crosscontamination_barcode_filter	Barcode contamination discovery tool								To update		Transcriptomics, Visualization	crosscontamination_barcode_filter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter	0.3	r-ggplot2	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	17	347	True	False	False
+crt	crispr_recognition_tool	CRISPR Recognition Tool								To update		Sequence Analysis	crispr_recognition_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/crt	https://github.com/bgruening/galaxytools/tree/master/tools/crt	1.2.0	crisper_recognition_tool	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	74	3389	True	False	False
+cryptogenotyper	CryptoGenotyper	CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	8518	True	False	True
+ctd_batch	ctdBatch_1	CTD analysis of chemicals, diseases, or genes								To update		Sequence Analysis	ctd_batch	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13	203	True	False	False
+cummerbund	cummeRbund	Wrapper for the Bioconductor cummeRbund library								To update	https://bioconductor.org/packages/release/bioc/html/cummeRbund.html	RNA, Visualization	cummerbund	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund	2.16.0	fonts-conda-ecosystem				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	31	1782	True	False	False
+custom_pro_db	custom_pro_db	CustomProDB								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db	1.22.0	bioconductor-rgalaxy	1.37.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	57	1652	True	False	False
+custom_pro_db_annotation_data_manager		CustomProDB Annotation								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db_annotation_data_manager	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	5090	232004	True	False	True
+dada2	dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	dada2	dada2		dada2	This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	0	10	0	10	0	0	1	0	0	0	0	0	0	0	0	0	10	10	10	0	1263	66609	True	False	True
+das_tool	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	dastool		dastool	DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	Read binning	Metagenomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	24	706	True	False	True
+data-hca	hca_matrix_downloader	Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects								To update		Transcriptomics, Sequence Analysis	suite_human_cell_atlas_tools	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca	v0.0.4+galaxy0	hca-matrix-downloader	0.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	439	True	False	False
+data-scxa	retrieve_scxa	Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home								To update		Transcriptomics, Sequence Analysis	suite_ebi_expression_atlas	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa	v0.0.2+galaxy2	wget				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	99	799	True	False	False
+data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	146	658	True	False	False
+data_manager_eggnog_mapper		downloads eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+data_manager_eggnog_mapper_abspath		download eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper_abspath	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+dbbuilder	dbbuilder	Protein Database Downloader								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	Proteomics	dbbuilder	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	0.3.4	wget				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	161	4758	True	False	False
+decoyfasta		Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.								To update		Proteomics	decoyfasta	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	True	False	False
+delete_overlapping_indels	delete_overlapping_indels	Delete Overlapping Indels from a chromosome indels file								To update		Sequence Analysis	delete_overlapping_indels	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels	https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	39	True	False	False
+deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	4990	95752	True	False	True
+deseq2_normalization	deseq2_normalization	Normalizes gene hitlists								To update	http://artbio.fr	RNA, Transcriptomics, Sequence Analysis, Statistics	deseq2_normalization	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	1.40.2+galaxy0	bioconductor-deseq2	1.42.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+dewseq	dewseq	DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data								To update	https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers	Sequence Analysis, RNA, CLIP-seq	dewseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	0.1.0+galaxy0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11	72	True	False	False
+dexseq	dexseq, dexseq_count, plotdexseq	Inference of differential exon usage in RNA-Seq	dexseq	dexseq		DEXSeq	The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html	Transcriptomics, RNA, Statistics	dexseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq	1.48.0	bioconductor-dexseq	1.48.0	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	218	16064	True	False	False
+dia_umpire	dia_umpire_se	DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics								To update	http://diaumpire.sourceforge.net/	Proteomics	dia_umpire	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire	2.1.3	dia_umpire	2.1.6			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	33	True	False	False
+dialignr	dialignr	DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.								To update	https://github.com/shubham1637/DIAlignR	Proteomics	dialignr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	1.2.0	bioconductor-dialignr	2.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	40	True	False	False
+diamond	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	diamond		Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	Sequence alignment analysis	Sequence analysis, Proteins	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	3	3	3	0	0	0	1	0	0	0	0	0	0	0	0	0	3	3	0	963	49711	True	False	True
+diann	diann	DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.								To update	https://github.com/vdemichev/DiaNN	Proteomics	diann	galaxyp	https://github.com/vdemichev/DiaNN	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann	1.8.1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	15	True	False	False
+diapysef	diapysef	diapysef is a convenience package for working with DIA-PASEF data								To update	https://pypi.org/project/diapysef/	Proteomics	diapysef	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef	0.3.5.0	diapysef	1.0.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	11	245	True	False	False
+diffacto	diffacto	Diffacto comparative protein abundance estimation								To update	https://github.com/statisticalbiotechnology/diffacto	Proteomics	diffacto	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	1.0.6	diffacto	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	7	True	False	False
+disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	42	369	True	False	True
+divide_pg_snp	dividePgSnp	Separate pgSnp alleles into columns								To update		Sequence Analysis	divide_pg_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	32	True	False	False
+dorina	dorina_search	data source for RNA interactions in post-transcriptional regulation								To update		RNA, Data Source	dorina	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1576	True	False	False
+dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dot2ct	rnastructure_dot2ct	Dot-Bracket to Connect Table (CT)								To update		Sequence Analysis, RNA	dot2ct	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	5.7.a	rnastructure	6.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+dotknot	dotknot	DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence								To update	http://dotknot.csse.uwa.edu.au/	RNA, Proteomics	dotknot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot	1.3.1	vienna_rna				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	83	True	False	False
+dram	dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram		DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	Up-to-date	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.5.0	dram	1.5.0	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	39	6886	True	False	True
+drep	drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep		dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	Up-to-date	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.5.0	drep	3.5.0	Genome comparison	Metagenomics, Sequence analysis	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	46	646	True	False	True
+droplet-barcode-plot	_dropletBarcodePlot	Make a cell barcode plot for droplet single-cell RNA-seq QC								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	droplet_barcode_plot	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot	1.6.1+galaxy2	scxa-plots	0.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	95	973	True	False	False
+dropletutils	dropletutils_empty_drops, dropletutils_read_10x	De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_dropletutils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils	1.0.4	dropletutils-scripts	0.0.5			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	201	1599	True	False	False
+dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Single Cell, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	126	3934	True	False	False
+ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ectyper	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	9907	True	False	True
+edger	edger	Perform RNA-Seq differential expression analysis using edgeR pipeline	edger	edger		edgeR	Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	To update	http://bioconductor.org/packages/release/bioc/html/edgeR.html	Transcriptomics, RNA, Statistics	edger	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger	https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger	3.36.0	bioconductor-edger	4.0.16	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	945	18117	True	False	False
+effectiveT3	effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+eggnog_mapper	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2		eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	1	3	1	0	510	30565	True	False	True
+egsea	egsea	This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing	egsea	egsea		EGSEA	This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.	Gene set testing	Systems biology	To update	https://bioconductor.org/packages/release/bioc/html/EGSEA.html	Transcriptomics, RNA, Statistics	egsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea	1.20.0	bioconductor-egsea	1.28.0	Gene set testing	Systems biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	177	2524	True	False	False
+emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	107	107	107	107	107	0	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	107	107	107	0	1816	89530	True	False	True
+encyclopedia	encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut	Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis								To update	https://bitbucket.org/searleb/encyclopedia/wiki/Home	Proteomics	encyclopedia	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia	1.12.34	encyclopedia	2.12.30			2	4	7	0	2	4	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	48	706	True	False	False
+ete	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete		ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	Phylogenetic tree editing	Phylogenetics	0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	45	899	True	False	True
+evidencemodeler	evidencemodeler	EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.	EvidenceModeler	EvidenceModeler		EvidenceModeler	The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.	Gene prediction	Gene expression, Gene structure	Up-to-date	https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file	Genome annotation	evidencemodeler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler	2.1.0	evidencemodeler	2.1.0	Gene prediction	Gene expression, Gene structure	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+exomedepth	exomedepth	ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data	exomedepth	exomedepth		ExomeDepth	Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases	To update	https://cran.r-project.org/package=ExomeDepth	Sequence Analysis, Variant Analysis	exomedepth	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth	1.1.0	r-exomedepth	1.1.16	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	29	410	True	False	False
+exonerate	exonerate	Exonerate is a generic tool for pairwise sequence comparison.	exonerate	exonerate		Exonerate	A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	Up-to-date	https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate	Sequence Analysis	exonerate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate	2.4.0	exonerate	2.4.0	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	59	988	True	False	False
+exparna	exparna	ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.								Up-to-date	http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp	RNA	exparna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	1.0.1	exparna	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan		export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	Conversion	Taxonomy, Metabolomics, Biomarkers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	200	5265	True	False	True
+express	express	Quantify the abundances of a set of target sequences from sampled subsequences								To update		RNA	express	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/express	https://github.com/galaxyproject/tools-devteam/tree/main/tools/express	1.1.1	eXpress	1.5.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	325	True	False	False
+ez_histograms	ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+falco	falco	A high throughput sequence QC analysis tool	falco	falco		Falco	A high-speed FastQC emulation for quality control of sequencing data.	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	Up-to-date	https://github.com/smithlabcode/falco/	Sequence Analysis	falco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco	https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco	1.2.4	falco	1.2.4	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fargene	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fargene		fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	52	459	True	False	True
+fasta2bed	fasta2bed	Convert multiple fasta file into tabular bed file format								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fasta2bed	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fasta_extract	fa-extract-sequence	extract single fasta from multiple fasta file								To update	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	Sequence Analysis	fasta_extract	nml	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	10	True	False	False
+fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fasta_nucleotide_color_plot	fasta_nucleotide_color_plot	Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot	Visualization	fasta_nucleotide_color_plot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15	160	True	False	False
+fasta_stats	fasta-stats	Display summary statistics for a fasta file.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	Sequence Analysis	fasta_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats	2.0	numpy				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1080	35336	True	False	False
+fastani	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity	fastani	fastani		FastANI	FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	250	3498	True	False	True
+fastg2protlib	fastg2protlib-peptides, fastg2protlib-validate	Generate FASTA from FASTG								To update	https://github.com/galaxyproteomics/fastg2protlib.git	Proteomics	fastg2protlib	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	1.0.2					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	28	True	False	False
+fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+fastp	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp		fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	Sequence contamination filtering	Probes and primers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	2803	1055760	True	False	True
+fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fastq_pair_names	fastq_pair_names	Extract FASTQ paired read names								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	Sequence Analysis	fastq_pair_names	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	0.0.5	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fastq_paired_unpaired	fastq_paired_unpaired	Divide FASTQ file into paired and unpaired reads								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	Sequence Analysis, Text Manipulation	fastq_paired_unpaired	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	0.1.5	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fastq_provider	fastq_provider	Retrieval and download of FASTQ files from ENA and other repositories such as HCA.								To update	https://github.com/ebi-gene-expression-group/atlas-fastq-provider	Data Source, RNA, Transcriptomics	atlas_fastq_provider	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider	0.4.4	atlas-fastq-provider	0.4.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fastq_utils	fastq_filter_n, fastq_trim_poly_at	Set of tools for handling fastq files								To update	https://github.com/nunofonseca/fastq_utils	Transcriptomics, RNA	fastq_utils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils	0.25.1+galaxy0	fastq_utils	0.25.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fastqc_stats	FastQC_Summary	Summary multiple FastQC into a single tabular line report								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fastqc_stats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats	1.2	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fastqe	fastqe	FASTQE	fastqe	fastqe		FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	Sequencing quality control	Sequence analysis, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1266	4333	True	False	True
+fasttree	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree		FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11		Phylogenetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	379	55434	True	False	True
+feature_alignment	feature_alignment	TRIC integrates information from all available runs via a graph-based alignment strategy								Up-to-date		Proteomics	feature_alignment	galaxyp	https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment	0.11.0	msproteomicstools	0.11.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	18	True	False	False
+featurecounter	featureCoverage1	Feature coverage								To update		Sequence Analysis, Variant Analysis	featurecounter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter	2.0.0	bx-python	0.13.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6	22385	True	False	False
+featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	4679	696399	True	False	True
+feelnc	feelnc	Galaxy wrapper for FEELnc	feelnc	feelnc		FEELnc	A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.	Annotation, Classification	RNA-seq, Functional, regulatory and non-coding RNA	To update	https://github.com/tderrien/FEELnc	Sequence Analysis	feelnc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc	0.2.1	feelnc	0.2	Annotation, Classification	Functional, regulatory and non-coding RNA	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	46	1191	True	False	False
+feht	feht	Automatically identify makers predictive of groups.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	feht	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht	0.1.0	feht	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fgsea	fgsea	Perform gene set testing using fgsea	fgsea	fgsea		fgsea	The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.	Gene-set enrichment analysis	Genetics	To update	https://bioconductor.org/packages/release/bioc/html/fgsea.html	Visualization, Transcriptomics, Statistics	fgsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea	1.8.0+galaxy1	bioconductor-fgsea	1.28.0	Gene-set enrichment analysis	Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	307	5240	True	False	False
+filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	426	26274	True	False	False
+filter_density	filterdensity	Filter out position based on distance between SNVs								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_density	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+filter_stats	filterstat	SNVPhyl filter_stats								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_stats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+filter_transcripts_via_tracking	filter_combined_via_tracking	Filter Combined Transcripts								To update		RNA	filter_transcripts_via_tracking	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking	https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking	0.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	20	True	False	False
+filter_vcf	filtervcf	SNVPhyl filter_vcf								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_vcf	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	617	30483	True	False	True
+find_diag_hits	find_diag_hits	Find diagnostic hits								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	find_diag_hits	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	69	True	False	False
+find_repeats	findrepeat	Find repetitive regions on a reference genome using MUMMer								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	find_repeats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fisher_test	fishertest	Fisher's exact test on two-column hit lists.								To update	http://artbio.fr	RNA, Statistics	fishertest	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	2.32.0+galaxy0	bioconductor-qvalue	2.34.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	14	331	True	False	False
+flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	74	13759	True	False	False
+flashlfq	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	Label-free quantification	Proteomics experiment, Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	17	645	True	False	True
+flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	20904	True	False	True
+format_metaphlan2_output	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	166	5588	True	False	True
+fraggenescan	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan		FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	Gene prediction	Genetics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	68	1102	True	False	True
+fragpipe	fragpipe	Data analysis for mass spectrometry-based proteomics.								Up-to-date	https://fragpipe.nesvilab.org/	Proteomics	fragpipe	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	20.0	fragpipe	20.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+freyja	freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja		Freyja	Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset	RNA-Seq quantification	Metagenomics	To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.1	RNA-Seq quantification	Metagenomics	2	0	4	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	55	20021	True	False	True
+frogs	FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis	frogs	frogs		FROGS	The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	To update	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	5.0.0	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	0	0	0	28	0	0	0	28	0	0	0	0	0	0	0	0	0	0	0	18	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	0	900	5906	True	False	True
+garnett	garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file	De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_garnett	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett	0.2.8	garnett-cli	0.0.5			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	27	True	False	False
+gblocks	gblocks	Gblocks								Up-to-date	http://molevol.cmima.csic.es/castresana/Gblocks.html	Sequence Analysis	gblocks	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	0.91b	gblocks	0.91b			0	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	True	False	False
+gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	8	0	0	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	10	1475	True	False	False
+gecko	gecko	Ungapped genome comparison								Up-to-date	https://github.com/otorreno/gecko	Sequence Analysis	gecko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko	1.2	gecko	1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	112	519	True	False	False
+gemini	gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@	GEMINI: a flexible framework for exploring genome variation	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://github.com/arq5x/gemini	Sequence Analysis, Next Gen Mappers	gemini	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini	0.20.1	gemini	0.30.2	Sequence analysis, Genetic variation analysis	Sequence analysis	1	2	2	2	1	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	662	4916	True	False	False
+geneiobio	gene_iobio_display_generation_iframe	Gene.iobio is an interactive tool for variant and trio analysis.								To update	https://github.com/iobio/gene.iobio	Sequence Analysis	geneiobio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio	4.7.1+galaxy1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	67	True	False	False
+generate_pc_lda_matrix	generate_matrix_for_pca_and_lda1	Generate a Matrix for using PC and LDA								To update		Sequence Analysis	generate_pc_lda_matrix	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix	https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix	1.0.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	119	True	False	False
+genomad	genomad_end_to_end	Identify virus and plasmid genomes from nucleotide sequences	genomad	genomad		geNomad	geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.	Sequence annotation, Taxonomic classification	Sequence analysis	Up-to-date	https://github.com/apcamargo/genomad/	Metagenomics	genomad	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad	1.8.0	genomad	1.8.0	Sequence annotation, Taxonomic classification	Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+genomic_super_signature	genomic_super_signature	Interpretation of RNAseq experiments through robust, efficient comparison to public databases	genomicsupersignature	genomicsupersignature		GenomicSuperSignature	GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	To update	https://github.com/shbrief/GenomicSuperSignature	Sequence Analysis, RNA, Transcriptomics	genomic_super_signature	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature	1.2.0	bioconductor-genomicsupersignature	1.10.0	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11	46	True	False	False
+get_orfs_or_cdss	get_orfs_or_cdss	Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	Sequence Analysis	get_orfs_or_cdss	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	0.2.3	biopython	1.70			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	0	0	15	186	True	False	False
+getindelrates_3way	indelRates_3way	Estimate Indel Rates for 3-way alignments								To update		Sequence Analysis, Variant Analysis	getindelrates_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+getindels_2way	getIndels_2way	Fetch Indels from pairwise alignments								To update		Sequence Analysis, Variant Analysis	getindels_2way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way	1.0.0	numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+getmlst	getmlst	Download MLST datasets by species from pubmlst.org								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	18	495	True	False	False
+gfastats	gfastats	Tool for generating sequence statistics and simultaneous genome assembly file manipulation.	gfastats	gfastats		gfastats	gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.	Data handling	Computational biology	To update	https://github.com/vgl-hub/gfastats	Sequence Analysis	gfastats	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	1.3.6	gfastats	1.3.7	Data handling	Computational biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	418	8159	True	False	False
+gff3_rebase	gff3.rebase	Rebase a GFF against a parent GFF (e.g. an original genome)								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	Sequence Analysis	gff3_rebase	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase	1.2	bcbiogff	0.6.6			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	135	True	False	False
+gffread	gffread	gffread filters and/or converts GFF3/GTF2 records	gffread	gffread		gffread	program for filtering, converting and manipulating GFF files	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/	Sequence Analysis	gffread	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread	0.12.7	gffread	0.12.7	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	680	10995	True	False	False
+ggplot2	ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2		ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		Visualisation	Data visualisation	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	5	0	0	0	0	0	0	3	0	0	0	0	0	5	5	5	0	1388	22148	True	False	True
+gi2taxonomy	Fetch Taxonomic Ranks	Fetch taxonomic representation	gi2taxonomy	gi2taxonomy		gi2taxonomy	The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	27	660	True	False	True
+glimmer	glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based	Glimmer makes gene predictions.	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	Sequence analysis, Genetic variation analysis	Sequence analysis	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	0	187	3965	True	False	True
+glimmer_hmm		GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+gmaj	gmaj_1	GMAJ Multiple Alignment Viewer								To update		Visualization	gmaj	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj	https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj	2.0.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4	11	True	False	False
+goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	408	5484	True	False	True
+goseq	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq		GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	Gene functional annotation	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1210	19167	True	False	True
+gotohscan	rbc_gotohscan	Find subsequences in db								To update		Sequence Analysis	gotohscan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	1.3.0	gotohscan	1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	71	True	False	False
+graphclust	graphclust	GraphClust can be used for structural clustering of RNA sequences.								To update	http://www.bioinf.uni-freiburg.de/Software/GraphClust/	RNA	graphclust	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	0.1	GraphClust				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	True	False	False
+graphlan	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	graphlan	graphlan		GraPhlAn	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	432	9277	True	False	True
+graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	136	6651	True	False	True
+graphprot	graphprot_predict_profile	GraphProt models binding preferences of RNA-binding proteins.								To update	https://github.com/dmaticzka/GraphProt	Sequence Analysis, RNA, CLIP-seq	graphprot	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	1.1.7+galaxy2	graphprot	1.1.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	474	True	False	False
+gsc_high_dimensions_visualisation	high_dimensions_visualisation	Generates PCA, t-SNE and HCPC visualisation								To update	http://artbio.fr	Transcriptomics, Visualization	gsc_high_dimensions_visualisation	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation	4.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+gtdb_to_taxdump	gtdb_to_taxdump	Convert GTDB taxonomy to NCBI taxdump format	gtdb_to_taxdump	gtdb_to_taxdump		gtdb_to_taxdump	Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI.	Data handling, Mapping, Generation	Computational biology	Up-to-date	https://github.com/nick-youngblut/gtdb_to_taxdump	Metagenomics	gtdb_to_taxdump	iuc	https://github.com/nick-youngblut/gtdb_to_taxdump	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump	0.1.9	gtdb_to_taxdump	0.1.9	Data handling, Mapping, Generation	Computational biology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gtdbtk	gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 	GTDB-Tk	GTDB-Tk		GTDB-Tk	a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	Up-to-date	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.4.0	gtdbtk	2.4.0	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+gtf-2-gene-list	_ensembl_gtf2gene_list	Utility to extract annotations from Ensembl GTF files.								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	gtf2gene_list	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list	1.52.0+galaxy0	atlas-gene-annotation-manipulation	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	155	1678	True	False	False
+gubbins	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins		Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	145	3340	True	False	True
+guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+gwastools	gwastools_manhattan_plot		gwastools	gwastools		GWASTools	Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.	Deposition, Analysis, Annotation	GWAS study	To update	https://bioconductor.org/packages/release/bioc/html/GWASTools.html	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools	0.1.0	bioconductor-gwastools	1.48.0	Deposition, Analysis, Annotation	GWAS study	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	True	False	False
+hamronization	hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization		hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	117	4459	True	False	True
+hansel	bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	Biohansel		BioHansel	BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	339	True	False	True
+hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	295	True	False	False
+hardklor	hardklor, kronik	Hardklör								To update		Proteomics	hardklor	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor	2.30.1+galaxy1	hardklor	2.3.2			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2	111	True	False	False
+hcluster_sg	hcluster_sg	Hierarchically clustering on a sparse graph								To update	https://github.com/douglasgscofield/hcluster	Phylogenetics	hcluster_sg	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	0.5.1.1	hcluster_sg	0.5.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	238	True	False	False
+hcluster_sg_parser	hcluster_sg_parser	Converts hcluster_sg 3-column output into lists of ids								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	hcluster_sg_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	0.2.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	290	True	False	False
+heatmap2	ggplot2_heatmap2	heatmap.2 function from the R gplots package								To update	https://github.com/cran/gplots	Visualization	ggplot2_heatmap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2	3.1.3.1	r-gplots	2.17.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1953	44240	True	False	False
+heinz	heinz_bum, heinz, heinz_scoring, heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	heinz	heinz, bionet		Heinz	Tool for single-species active module discovery.	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	To update	https://github.com/ls-cwi/heinz	Transcriptomics, Visualization, Statistics	heinz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz	1.0	bioconductor-bionet	1.62.0	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	242	1186	True	False	False
+helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	93	True	False	False
+hgv_fundo	hgv_funDo	FunDO human genes associated with disease terms								To update		Sequence Analysis	hgv_fundo	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	True	False	False
+hgv_hilbertvis	hgv_hilbertvis	HVIS visualization of genomic data with the Hilbert curve								To update	https://www.ebi.ac.uk/huber-srv/hilbert/	Graphics, Visualization	hgv_hilbertvis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis	1.0.0	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	True	False	False
+hicexplorer	hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations	HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.								Up-to-date	https://github.com/deeptools/HiCExplorer	Sequence Analysis, Visualization	hicexplorer	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer	3.7.5	hicexplorer	3.7.5			38	38	38	4	38	38	38	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	33	36	33	0	1085	66003	True	False	False
+hicstuff	hicstuff_pipeline	A toolkit to generate and manipulate Hi-C matrices								To update	https://github.com/koszullab/hicstuff	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff	3.1.5	hicstuff	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	1410	True	False	False
+hifiasm_meta	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	hifiasm-meta		Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	Sequence assembly	Sequence assembly, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	137	True	False	True
+high_dim_heatmap	high_dim_heatmap	gplot heatmap.2 function adapted for plotting large heatmaps								To update	https://github.com/cran/gplots	Visualization	high_dim_heatmap	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap	https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap	3.1.3+galaxy0	r-gplots	2.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.2.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	True	False	False
+hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	4183	299104	True	False	False
+hivtrace	hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+hmmer3	hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	hmmer3	hmmer3		HMMER3	This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	0	12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	12	12	12	0	439	33702	True	False	True
+homer	homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide	HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.	homer	homer		homer	HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein).  It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other.  It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment.  HOMER also tries its best to account for sequenced bias in the dataset.  It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.	Sequence motif discovery		Up-to-date	http://homer.ucsd.edu/homer/index.html	Sequence Analysis	data_manager_homer_preparse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer	4.11	homer	4.11	Sequence motif discovery		0	0	5	4	0	0	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	5	0	0	394	6937	True	False	False
+homer		Software for motif discovery and next generation sequencing analysis.								To update	http://homer.salk.edu/homer/	Sequence Analysis	homer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/homer	https://github.com/bgruening/galaxytools/tree/master/tools/homer						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+htseq-clip	htseq_clip	htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets								To update	https://github.com/EMBL-Hentze-group/htseq-clip	Sequence Analysis, RNA, CLIP-seq	htseq_clip	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	0.1.0+galaxy0	htseq-clip	2.19.0b0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	77	True	False	False
+htseq_count	htseq_count	Count aligned reads (SAM/BAM) that overlap genomic features (GFF)	htseq	htseq		HTSeq	Python framework to process and analyse high-throughput sequencing (HTS) data	Nucleic acid sequence analysis	Sequence analysis	Up-to-date	https://readthedocs.org/projects/htseq/	Genomic Interval Operations, SAM, Sequence Analysis, RNA	htseq_count	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count	2.0.5	htseq	2.0.5	Nucleic acid sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1419	154533	True	False	False
+humann	humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	humann	humann		humann	HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	Up-to-date	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.9	humann	3.9	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	6	10	10	10	6	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	1037	19490	True	False	True
+hybpiper	hybpiper	Analyse targeted sequence capture data	HybPiper	HybPiper		HybPiper	Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	To update	https://github.com/mossmatters/HybPiper	Sequence Analysis, Phylogenetics	hybpiper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper	2.1.6	hybpiper	2.3.0	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+hyphy	hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy		HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.62	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	17	2	17	2	17	2	17	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	12	17	12	0	161	10370	True	False	True
+hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354	True	False	True
+icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	69	1127	True	False	True
+idconvert	idconvert	Convert mass spectrometry identification files on linux or MacOSX								To update		Proteomics	idconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert		proteowizard	3_0_9992			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	275	True	False	False
+idr	idr	Galaxy wrappers for the IDR package from Nathan Boleu								To update	https://github.com/nboley/idr	Sequence Analysis	idr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr	2.0.3	idr	2.0.4.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	30	2873	True	False	False
+iedb_api	iedb_api	Get epitope binding predictions from IEDB-API								To update	http://tools.immuneepitope.org/main/tools-api/	Data Source, Sequence Analysis	iedb_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api	2.15.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	1506	True	False	False
+illumina_methylation_analyser	illumina_methylation_analyser	Methylation analyzer for Illumina 450k DNA emthylation microarrays								To update	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	Sequence Analysis	illumina_methylation_analyser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	0.1	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+improviser	proteomics_improviser	Visualisation of PepXML files								To update	http://www.improviser.uni-freiburg.de/	Proteomics	proteomics_improviser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	1.1.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+indels_3way	indels_3way	Fetch Indels from 3-way alignments								To update		Sequence Analysis	indels_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way	1.0.3					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	22	True	False	False
+infernal	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	infernal		Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	67	100294	True	False	True
+inforna		INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.								To update	http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp	RNA	inforna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	139	True	False	False
+instrain	instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	instrain	instrain		InStrain	InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	SNP detection, Genome comparison	Mapping, Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	94	True	False	True
+intarna	intarna	Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.								Up-to-date	https://github.com/BackofenLab/IntaRNA	RNA	intarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	3.4.1	intarna	3.4.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	7569	True	False	False
+integron_finder	integron_finder	"""IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"""	integron_finder	integron_finder		Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.5	integron_finder	2.0.5	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	58	52965	True	False	True
+interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+interproscan	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi		InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	677	35243	True	False	True
+iprscan5		Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+iqtree	iqtree	Efficient phylogenomic software by maximum likelihood	iqtree	iqtree		iqtree	A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time	Phylogenetic analysis, Sequence analysis	Phylogenetics	Up-to-date	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.3.6	iqtree	2.3.6	Phylogenetic analysis, Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	681	21598	True	False	True
+isescan	isescan	"""ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."""	ISEScan	ISEScan		ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	Structural variation detection	Genomics, Sequence analysis, Genetic variation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	50	57581	True	False	True
+isoformswitchanalyzer	isoformswitchanalyzer	Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.	IsoformSwitchAnalyzeR	IsoformSwitchAnalyzeR		IsoformSwitchAnalyzeR	Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	To update	https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html	Transcriptomics, RNA, Statistics	isoformswitchanalyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer	1.20.0	bioconductor-isoformswitchanalyzer	2.2.0	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	822	True	False	False
+isoplot	isoplot	Isoplot is a software for the visualisation of MS data from C13 labelling experiments								To update		Metabolomics, Visualization	isoplot	workflow4metabolomics	https://github.com/llegregam/Isoplot/tree/main	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot	1.3.0+galaxy1	isoplot	1.3.1			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	2	True	False	False
+itsx	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	38	868	True	False	True
+ivar	ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing								Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.3	ivar	1.4.3			5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	4	0	0	0	4	0	0	0	0	0	5	5	5	0	1171	1224275	True	False	True
+jbrowse	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse		JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	Genome visualisation	Genomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	2	2	2	0	2346	18229	True	False	True
+jbrowse2	jbrowse2	JBrowse2 Genome Browser integrated as a Galaxy Tool	jbrowse_2	jbrowse_2		JBrowse 2	Modular genome browser with views of synteny and structural variation.	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse2	fubar	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2	https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2	2.15.4	jbrowse2	2.15.4	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+jcvi_gff_stats	jcvi_gff_stats	Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)								To update	https://github.com/tanghaibao/jcvi	Sequence Analysis	jcvi_gff_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats	0.8.4	jcvi	1.4.16			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	2469	True	False	False
+jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138	True	False	True
+kaptive	kaptive	Kaptive reports information about capsular (K) loci found in genome assemblies.								To update		Sequence Analysis	kaptive	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive	0.3.0	kaptive	3.0.0b5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+kat_filter	kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+kc-align	kc-align	Kc-Align custom tool	kc-align	kc-align		kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	Multiple sequence alignment	Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19	363	True	False	True
+khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	8	8	8	0	63	2022	True	False	True
+kinwalker		Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.								To update	http://www.bioinf.uni-leipzig.de/Software/Kinwalker/	RNA	kinwalker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+kleborate	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	kleborate	kleborate		Kleborate	Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	To update	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	3.0.9	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	38	319	True	False	True
+kofamscan	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	kofamscan	kofamscan		kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	Sequence analysis, Gene functional annotation	Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	33	594	True	False	True
+kraken	kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	kraken	kraken		Kraken	System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	Taxonomic classification	Taxonomy, Metagenomics	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	5	0	1209	33778	True	False	True
+kraken2	kraken2	Kraken2 for taxonomic designation.	kraken2	kraken2		kraken2	Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	Up-to-date	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.3	kraken2	2.1.3	Taxonomic classification	Taxonomy, Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	2367	185308	True	False	True
+kraken2tax	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	481	14683	True	False	True
+kraken_biom	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)								Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	182	1444	True	False	True
+kraken_taxonomy_report	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report		Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	Visualisation, Classification	Metagenomics, Taxonomy	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	354	2527	True	False	True
+krakentools	krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	krakentools		KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	Visualisation, Aggregation	Taxonomy, Metagenomics	6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	1	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	703	16525	True	False	True
+krocus	krocus	Predict MLST directly from uncorrected long reads	krocus	krocus		krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	Multilocus sequence typing, k-mer counting	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+labels	bg_labels	remaps and annotates alignments								To update	https://github.com/bgruening/galaxytools/tree/master/tools/labels	Sequence Analysis	labels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/labels	https://github.com/bgruening/galaxytools/tree/master/tools/labels	1.0.5.0	labels				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+last	last_al, last_db, last_split, last_train, last_maf_convert	LAST finds similar regions between sequences.	last	last		LAST	Short read alignment program incorporating quality scores	Sequence alignment	Genomics, Comparative genomics	To update	http://last.cbrc.jp/	Sequence Analysis	last	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/last	https://github.com/galaxyproject/tools-iuc/tree/main/tools/last	1205	last	1584	Sequence alignment	Comparative genomics	0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	41	227	True	False	False
+lca_wrapper	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	137	True	False	True
+legsta	legsta	Performs in silico Legionella pneumophila sequence based typing.	legsta	legsta		legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	Sequence analysis	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	55	True	False	True
+length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	322	4090	True	False	False
+lfq_protein_quant	lfq_protein_quant	Enable protein summarisation and quantitation								To update	https://github.com/compomics/LFQ_galaxy_p	Proteomics	lfq_protein_quant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	1.0	bioconductor-msnbase	2.28.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	111	True	False	False
+lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	152	True	False	True
+limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1012	20344	True	False	True
+lineagespot	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	lineagespot	lineagespot		lineagespot	Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	37	True	False	True
+links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	77	405	True	False	False
+locarna	locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile	LocARNA - A suite for multiple alignment and folding of RNAs								Up-to-date	http://www.bioinf.uni-freiburg.de/Software/LocARNA/	RNA	locarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	2.0.1	locarna	2.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	339	True	False	False
+logistic_regression_vif	LogisticRegression	Perform Logistic Regression with vif								To update		Sequence Analysis, Variant Analysis, Statistics	logistic_regression_vif	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif	https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif	1.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+logol	logol_wrapper	Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence								Up-to-date	http://logol.genouest.org/web/app.php/logol	Sequence Analysis		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	1.7.8	logol	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+longorf	longORF	obtain longest ORF in six-frame translations								To update		Sequence Analysis	longorf	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf	0.3.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+lorikeet	lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet		lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	Sequence analysis, Genotyping	Genotype and phenotype	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	647	True	False	True
+lotus2	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2		lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	To update	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.34.1	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	114	936	True	False	True
+m6anet	m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet		m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	True	False	True
+maaslin2	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	maaslin2	maaslin2		MaAsLin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	Up-to-date	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	1.18.0	bioconductor-maaslin2	1.18.0	Filtering, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	188	True	False	True
+macs2	macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak	MACS - Model-based Analysis of ChIP-Seq	macs	macs		MACS	Model-based Analysis of ChIP-seq data.	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	Up-to-date	https://github.com/taoliu/MACS	Sequence Analysis, Statistics	macs2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2	2.2.9.1	macs2	2.2.9.1	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	0	9	9	0	0	0	0	0	0	0	9	0	0	0	0	0	9	9	9	0	1969	84521	True	False	False
+maf_cpg_filter	cpgFilter	Mask CpG/non-CpG sites from MAF file								To update		Sequence Analysis, Variant Analysis	maf_cpg_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+mafft	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.526	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	2	0	0	0	2	0	0	0	0	0	2	2	2	0	817	143045	True	False	True
+make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+maker	maker, maker_map_ids	MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	maker	maker		MAKER	Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	Genome annotation	Genomics, DNA, Sequence analysis	To update	http://www.yandell-lab.org/software/maker.html	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker	2.31.11	maker	3.01.03	Genome annotation	Genomics, DNA, Sequence analysis	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	554	5591	True	False	True
+maldiquant	maldi_quant_peak_detection, maldi_quant_preprocessing	MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.								To update	http://strimmerlab.org/software/maldiquant/	Proteomics	MALDIquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant	1.22.0	r-base				0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	2	2	0	25	3797	True	False	False
+map_peptides_to_bed	map_peptides_to_bed	Map peptides to a reference genome for display by a genome browser								To update		Proteomics	map_peptides_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	0.2	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	41	True	False	False
+mapping_quality_stats	mapqstatistics	Collects and shows the distribution of MAPQ values in a BAM alignment file								To update	http://artbio.fr	Sequence Analysis, Statistics	mapping_quality_stats	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	0.22.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+mapping_to_ucsc	mapToUCSC	Format mapping data as UCSC custom track								To update		Visualization, Convert Formats, Next Gen Mappers	mapping_to_ucsc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+mapseq	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	mapseq	mapseq		MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .	k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	To update	https://github.com/jfmrod/MAPseq	Metagenomics	mapseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq	2.1.1	perl		k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	167	True	False	True
+marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mash	mash_screen, mash_sketch	Fast genome and metagenome distance estimation using MinHash	mash	mash		Mash	Fast genome and metagenome distance estimation using MinHash.	Sequence distance matrix generation	Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	Up-to-date	https://github.com/marbl/Mash	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash	2.3	mash	2.3	Sequence distance matrix generation	Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	27	9763	True	False	True
+mashmap	mashmap	Fast local alignment boundaries								Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	Sequence Analysis	mashmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap	3.1.3	mashmap	3.1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+masigpro	masigpro	Identify significantly differential expression profiles in time-course microarray experiments	masigpro	masigpro		maSigPro	Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.	Regression analysis	Gene expression, Molecular genetics, Microarray experiment, RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html	Transcriptomics, RNA, Statistics	masigpro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro	1.49.3	coreutils	8.25	Regression analysis	Gene expression, Microarray experiment, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13	576	True	False	False
+mauve_contig_mover	mauve_contig_mover	Order a draft genome relative to a related reference genome								To update	https://github.com/phac-nml/mauve_contig_mover	Sequence Analysis	mauve_contig_mover	nml	https://github.com/phac-nml/mauve_contig_mover	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover	1.0.10	mauve	2.4.0.r4736			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+maxbin2	maxbin2	clusters metagenomic contigs into bins	maxbin	maxbin		MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	To update	https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html	Metagenomics	maxbin2	mbernt	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2		maxbin2	2.2.7	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	118	2059	True	False	True
+maxquant	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering	Proteomics experiment, Proteomics, Statistics and probability	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	415	6078	True	False	True
+mcl	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	mcl	mcl		MCL	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.	Clustering, Network analysis, Gene regulatory network analysis	Molecular interactions, pathways and networks	Up-to-date	https://micans.org/mcl/man/mcl.html	Sequence Analysis	mcl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/mcl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl	22.282	mcl	22.282	Clustering, Gene regulatory network analysis	Molecular interactions, pathways and networks	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	29	True	False	True
+mea	mea	Maximum expected accuracy prediction								To update	http://www.bioinf.uni-leipzig.de/Software/mea	RNA	mea	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	0.6.4.1	mea	0.6.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	85	True	False	False
+mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	24	True	False	False
+medaka	medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	medaka	medaka		Medaka	medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	2.0.0	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	2	0	0	0	0	0	3	3	3	0	768	99863	True	False	True
+medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	548	9530	True	False	True
+megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	54	475	True	False	True
+megan	megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma	MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data.  MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).	megan	megan		MEGAN	Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Sequence analysis, Taxonomic classification	Sequence analysis	To update	https://github.com/husonlab/megan-ce	Sequence Analysis	megan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan	6.21.7	megan	6.25.9	Sequence analysis, Taxonomic classification	Sequence analysis	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	261	3610	True	False	True
+meningotype	meningotype	Assign sequence type to N. meningitidis genome assemblies	meningotype	meningotype		meningotype	In silico typing of Neisseria meningitidis contigs.	Genotyping, Multilocus sequence typing	Microbiology, Genotype and phenotype	Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype	0.8.5	meningotype	0.8.5	Multilocus sequence typing	Microbiology, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483	True	False	True
+meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+meta_proteome_analyzer	meta_proteome_analyzer	MetaProteomeAnalyzer								Up-to-date	https://github.com/compomics/meta-proteome-analyzer/	Proteomics	meta_proteome_analyzer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	2.0.0	mpa-portable	2.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	123	True	False	False
+metabat2	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT_2		MetaBAT 2	"an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning"	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	To update	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.17	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	2	1	2	2	2	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	192	4329	True	False	True
+metabuli	metabuli_classify	Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences	metabuli	metabuli		metabuli	Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid	Taxonomic classification	Taxonomy	To update	https://github.com/steineggerlab/Metabuli	Sequence Analysis, Metagenomics	metabuli	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli	1.0.5	metabuli	1.0.8	Taxonomic classification	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	5.34c21f2	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	184	True	False	True
+metagene_annotator	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	115	636	True	False	True
+metagenomeseq	metagenomeseq_normalizaton	metagenomeSeq Normalization	metagenomeseq	metagenomeseq		metagenomeSeq	Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	To update	https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html	Metagenomics	metagenomeseq_normalization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq	1.16.0-0.0.1	bioconductor-metagenomeseq	1.43.0	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6	753	True	False	True
+metanovo	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	4181	True	False	True
+metaphlan	customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	metaphlan	metaphlan		MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.	Nucleic acid sequence analysis, Phylogenetic tree analysis	Metagenomics, Phylogenomics	Up-to-date	https://github.com/biobakery/MetaPhlAn	Metagenomics	metaphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan	4.1.1	metaphlan	4.1.1	Nucleic acid sequence analysis	Metagenomics, Phylogenomics	1	2	4	4	1	2	4	4	0	0	0	0	0	0	0	0	0	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	499	11069	True	False	True
+metaquantome	metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome		metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	104	2522	True	False	True
+metawrapmg	metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	metawrap	metawrap		MetaWRAP	MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	Up-to-date	https://github.com/bxlab/metaWRAP	Metagenomics	metawrapmg_binning	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg	1.3.0	metawrap-mg	1.3.0	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+methtools	methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling	tools for methylation analysis								To update	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	Sequence Analysis	methtools	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	0.1.1	methtools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5461	True	False	False
+methyldackel	pileometh	A tool for processing bisulfite sequencing alignments								To update	https://github.com/dpryan79/MethylDackel	Sequence Analysis	pileometh	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	0.5.2	methyldackel	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	200	16573	True	False	False
+metilene	metilene	Differential DNA methylation calling								To update		RNA, Statistics	metilene	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	0.2.6.1	metilene	0.2.8			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	103	3966	True	False	False
+mg_toolkit	mg_toolkit_bulk_download, mg_toolkit_original_metadata	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	mg-toolkit	mg-toolkit		mg-toolkit	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	Data retrieval	Metagenomics	Up-to-date	https://github.com/EBI-Metagenomics/emg-toolkit	Metagenomics	mg_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	0.10.4	mg-toolkit	0.10.4	Data retrieval	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+miclip	mi_clip	Identification of binding sites in CLIP-Seq data.								To update	https://cran.r-project.org/src/contrib/Archive/MiClip/	Sequence Analysis	miclip	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	1.2.0	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+microsatbed	microsatbed	Select microsatellites for a bed file								To update	https://github.com/lmdu/pytrf	Sequence Analysis	microsatbed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed	1.3.3	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+microsatellite_birthdeath	microsatellite_birthdeath	Identify microsatellite births and deaths								To update		Sequence Analysis	microsatellite_birthdeath	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+microsats_alignment_level	microsats_align1	Extract Orthologous Microsatellites from pair-wise alignments								To update		Sequence Analysis, Variant Analysis	microsats_alignment_level	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level	1.0.0	sputnik				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+microsats_mutability	microsats_mutability1	Estimate microsatellite mutability by specified attributes								To update		Sequence Analysis, Variant Analysis	microsats_mutability	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability	1.1.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+migmap	migmap	mapper for full-length T- and B-cell repertoire sequencing	MiGMAP	MiGMAP		MiGMAP	Mapper for full-length T- and B-cell repertoire sequencing.	Sequence analysis, Read mapping	Immunoproteins, genes and antigens, Sequence analysis	Up-to-date	https://github.com/mikessh/migmap	RNA, Sequence Analysis	migmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap	1.0.3	migmap	1.0.3	Sequence analysis, Read mapping	Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	1226	True	False	False
+minced	minced	MinCED - Mining CRISPRs in Environmental Datasets								To update	http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README	Sequence Analysis	minced	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minced	https://github.com/bgruening/galaxytools/tree/master/tools/minced	0.2.0	minced	0.4.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	53	895	True	False	False
+minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	109	2206	True	False	True
+miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	178	11938	True	False	True
+minipolish	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	185	True	False	True
+miniprot	miniprot, miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	miniprot	miniprot		miniprot	Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	Up-to-date	https://github.com/lh3/miniprot	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot	0.13	miniprot	0.13	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	30	842	True	False	True
+miranda	miranda	Finds potential target sites for miRNAs in genomic sequences								To update	http://www.microrna.org/	RNA	miranda	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	3.3a+galaxy1	miranda	3.3a			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	41	6076	True	False	False
+mircounts	mircounts	Generates miRNA count lists from read alignments to mirBase.								To update	http://artbio.fr	RNA, Transcriptomics	mircounts	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts	https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts	1.6	tar				0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+mirmachine	mirmachine	Tool to detect miRNA in genome sequences								Up-to-date	https://github.com/sinanugur/MirMachine	Sequence Analysis	mirmachine	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine	0.2.13	mirmachine	0.2.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+mirnature	mirnature	Computational detection of canonical microRNAs								Up-to-date	https://github.com/Bierinformatik/miRNAture	RNA, Sequence Analysis	mirnature	iuc	https://github.com/Bierinformatik/miRNAture	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature	1.1	mirnature	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	10	True	False	False
+mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	66	881	True	False	False
+mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	56	613	True	False	False
+mitos	mitos, mitos2	de-novo annotation of metazoan mitochondrial genomes	mitos	mitos		MITOS	De novo metazoan mitochondrial genome annotation.	Genome annotation	Zoology, Whole genome sequencing	To update	http://mitos.bioinf.uni-leipzig.de/	Sequence Analysis	mitos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos	1.1.7	mitos	2.1.9	Genome annotation	Zoology, Whole genome sequencing	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	0	236	100920	True	False	True
+mlst	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst		MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	Multilocus sequence typing	Immunoproteins and antigens	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	635	9304	True	False	True
+moFF	proteomics_moff	moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.								Up-to-date	https://github.com/compomics/moFF	Proteomics	proteomics_moff	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	2.0.3	moff	2.0.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	759	True	False	False
+mob_suite	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.9			0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	322	89021	True	False	True
+monocle3	monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers	De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_monocle3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3	0.1.4	monocle3-cli	0.0.9			9	0	9	0	9	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	264	3266	True	False	False
+morpheus	morpheus	Morpheus MS Search Application	morpheus	morpheus		Morpheus	A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.	Peptide database search	Proteomics	To update	https://cwenger.github.io/Morpheus	Proteomics	morpheus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	288	morpheus	290	Peptide database search	Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	140	True	False	False
+mothur	mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn	Mothur wrappers	mothur	mothur		mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	129	129	129	129	129	129	129	129	0	0	0	0	0	0	0	0	0	0	128	0	3	0	0	0	0	0	0	0	0	0	0	0	0	126	129	129	0	14353	302916	True	False	True
+motus	mereg_mOTUs_tables, motus_profiler	Tool for profiling the abundance of microbial taxa.	mOTUs	mOTUs		Metagenomic operational taxonomic units (mOTUs)	Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/motu-tool/mOTUs	Metagenomics	motus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs	https://github.com/bgruening/galaxytools/tree/master/tools/motus	3.1.0	motus	3.1.0	Taxonomic classification	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mqc	mqc	Ribosome profiling mapping quality control tool								To update	https://github.com/Biobix/mQC	Sequence Analysis	mqc	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc	1.9	mqc	1.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	76	True	False	False
+mqppep	mqppep_anova, mqppep_preproc	MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Proteomics	mqppep	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	0.1.19	bioconductor-preprocesscore	1.64.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	2	True	False	False
+mrbayes	mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	True	False	True
+msconvert	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert		msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			Filtering, Formatting	Proteomics, Proteomics experiment	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	189	19958	True	False	True
+msgfplus	msgfplus	MSGF+								To update		Proteomics	msgfplus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	0.5	msgf_plus	2024.03.26			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	507	True	False	False
+msms_extractor	msms_extractor	Extract MS/MS scans from the mzML file(s) based on PSM report.								To update		Proteomics	msms_extractor	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor	1.0.0	proteowizard	3_0_9992			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	110	True	False	False
+msstats	msstats	MSstats tool for analyzing mass spectrometry proteomic datasets	msstatstmt	msstatstmt		MSstatsTMT	Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	To update	https://github.com/MeenaChoi/MSstats	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	4.0.0	bioconductor-msstats	4.10.0	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	144	2036	True	False	False
+msstatstmt	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	726	True	False	True
+mt2mq	mt2mq	Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome								To update		Proteomics	mt2mq	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq	1.1.0	r-tidyverse				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	19	270	True	False	False
+multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	53	True	False	True
+multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	8320	162790	True	False	True
+multispecies_orthologous_microsats	multispecies_orthologous_microsats	Extract orthologous microsatellites								To update		Sequence Analysis, Variant Analysis	multispecies_orthologous_microsats	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats	https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats	1.0.0	bx-sputnik				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+mummer	mummerplot_wrapper	Draw dotplots using mummer, mucmer, or promer with mummerplot								To update	http://mummer.sourceforge.net/	Graphics, Sequence Analysis, Visualization	mummer	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	0.0.8	ghostscript	9.18			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	83	652	True	False	False
+mummer4	mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords	Mummer4 Tools	mummer4	mummer4						Up-to-date	https://github.com/mummer4/mummer	Sequence Analysis	mummer4	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4	4.0.0rc1	mummer4	4.0.0rc1			6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	6	3	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	669	18347	True	False	False
+mykrobe	mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe		Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+mykrobe_parser	mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+mz_to_sqlite	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	Conversion, Peptide database search	Proteomics, Biological databases	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33	844	True	False	True
+mzml_validator	mzml_validator	mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.								To update	https://github.com/RECETOX/galaxytools	Metabolomics, Proteomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	0.1.0+galaxy2	lxml				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+naltorfs	bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs	nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)								Up-to-date	https://github.com/BlankenbergLab/nAltORFs	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs	0.1.2	naltorfs	0.1.2			3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+nanocompore	nanocompore_db, nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Nanocompore	Nanocompore		Nanocompore	RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	3	836	True	False	True
+nanoplot	nanoplot	Plotting tool for long read sequencing data and alignments	nanoplot	nanoplot		NanoPlot	NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences	Scatter plot plotting, Box-Whisker plot plotting	Genomics	Up-to-date	https://github.com/wdecoster/NanoPlot	Visualization	nanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot	1.43.0	nanoplot	1.43.0	Scatter plot plotting, Box-Whisker plot plotting	Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	2195	63235	True	False	True
+nanopolishcomp	nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate	NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.	nanopolishcomp	nanopolishcomp		NanopolishComp	NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	To update	https://a-slide.github.io/NanopolishComp	Sequence Analysis	nanopolishcomp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp	0.6.11	nanopolishcomp	0.6.12	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	15	1074	True	False	True
+nastiseq	nastiseq	A method to identify cis-NATs using ssRNA-seq								Up-to-date	https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/	RNA	nastiseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	1.0	r-nastiseq	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	40	True	False	False
+ncbi_blast_plus	blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper	NCBI BLAST+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	devteam	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	2.14.1	python				16	16	16	16	16	16	16	16	0	0	0	0	0	0	0	0	0	0	16	15	16	0	0	0	0	0	0	16	0	0	0	0	16	16	16	15	0	4066	365597	True	False	True
+ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ncbi_fcs_adaptor	ncbi_fcs_adaptor	FCS-adaptor detects adaptor and vector contamination in genome sequences.								To update	https://github.com/ncbi/fcs	Sequence Analysis	ncbi_fcs_adaptor	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	0.5.0					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+ncbi_fcs_gx	ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).	ncbi_fcs	ncbi_fcs		NCBI fcs	The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	Up-to-date	https://github.com/ncbi/fcs-gx	Sequence Analysis	ncbi_fcs_gx	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	0.5.4	ncbi-fcs-gx	0.5.4	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	95	667	True	False	False
+newick_utils	newick_display	Perform operations on Newick trees	newick_utilities	newick_utilities		Newick Utilities	The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.	Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction	Phylogeny, Genomics, Computer science	To update	http://cegg.unige.ch/newick_utils	Visualization, Metagenomics	newick_utils	iuc	https://github.com/tjunier/newick_utils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils	1.6+galaxy1	newick_utils	1.6		Phylogeny, Genomics, Computer science	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	448	25505	True	False	True
+nextclade	nextalign, nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	nextclade	nextclade		Nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.	Methylation analysis, Variant calling	Genomics, Sequence analysis, Cladistics	To update	https://github.com/nextstrain/nextclade	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade	2.7.0	nextalign	2.14.0	Methylation analysis, Variant calling	Genomics, Cladistics	1	1	2	2	1	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	0	0	0	1	0	0	0	0	0	0	2	0	0	210	4080	True	False	True
+nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268	True	False	True
+nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+nonpareil	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil		nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.5.5	Operation		1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	142	True	False	True
+novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	162	6384	True	False	False
+nucleosome_prediction	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	861	True	False	True
+nugen_nudup	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	1	1	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	45	True	False	True
+obitools	obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq	OBITools is a set of programs developed to simplify the manipulation of sequence files	obitools	obitools		OBITools	Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	Up-to-date	http://metabarcoding.org/obitools	Sequence Analysis	obitools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools	1.2.13	obitools	1.2.13	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	0	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	503	26251	True	False	True
+ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	True	False	False
+odgi	odgi_build, odgi_viz	Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.								To update	https://github.com/vgteam/odgi	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi	0.3	odgi	0.8.6			0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	2	25	True	False	False
+ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+omark	omark	Proteome quality assessment software	omark	omark		OMArk	Proteome quality assessment software	Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	To update	https://github.com/DessimozLab/OMArk	Sequence Analysis	omark	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark	0.3.0			Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	39	2654	True	False	False
+openms	AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter	OpenMS Suite for LC/MS data management and analyses								To update	https://www.openms.de/	Proteomics	openms	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	3.1	openms	3.2.0			8	34	144	0	8	34	144	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	141	124	0	886	105432	True	False	False
+openms	AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter	OpenMS in version 2.1.								To update		Proteomics	openms	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/openms	https://github.com/bgruening/galaxytools/tree/master/tools/openms	2.1.0	openms	3.2.0			7	34	135	0	7	34	135	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	135	134	0	916	105743	True	False	False
+optitype	optitype	Precision HLA typing from NGS data								Up-to-date	https://github.com/FRED-2/OptiType	Sequence Analysis	optitype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype	1.3.5	optitype	1.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	321	True	False	False
+orfipy	orfipy	Galaxy wrapper for ORFIPY	orfipy	orfipy		orfipy	A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	Up-to-date	https://github.com/urmi-21/orfipy	Sequence Analysis	orfipy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy	0.0.4	orfipy	0.0.4	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	774	True	False	True
+orthofinder	orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	OrthoFinder	OrthoFinder		OrthoFinder	OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.	Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis	Up-to-date	https://github.com/davidemms/OrthoFinder	Phylogenetics, Sequence Analysis	orthofinder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder	2.5.5	orthofinder	2.5.5	Genome comparison, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	239	1333	True	False	True
+pacu	pacu_map, pacu_snp	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.	pacu	pacu		PACU	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads).	Clustering	Phylogenetics, Sequence analysis	Up-to-date	https://github.com/BioinformaticsPlatformWIV-ISP/PACU	Sequence Analysis, Phylogenetics	pacu	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu	0.0.5	pacu_snp	0.0.5	Clustering	Phylogenetics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pairtools	pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats	Flexible tools for Hi-C data processing								Up-to-date	https://pairtools.readthedocs.io	Sequence Analysis	pairtools	iuc	https://github.com/open2c/pairtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools	1.1.0	pairtools	1.1.0			5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+pangolin	pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages								To update	https://github.com/hCoV-2019/pangolin	Sequence Analysis	pangolin	nml	https://github.com/hCoV-2019/pangolin	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin	1.1.14	pangolin	4.3			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	0	0	259	7276	True	False	False
+pangolin	pangolin	Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.	pangolin_cov-lineages	pangolin_cov-lineages		pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages	Tree-based sequence alignment, Variant classification	Virology	Up-to-date	https://github.com/cov-lineages/pangolin	Sequence Analysis	pangolin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin	4.3	pangolin	4.3	Tree-based sequence alignment, Variant classification	Virology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	0	0	259	7276	True	False	False
+paralyzer	paralyzer	A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.								Up-to-date	https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/	RNA	paralyzer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	1.5	paralyzer	1.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	299	True	False	False
+parse_mito_blast	parse_mito_blast	Filtering blast out from querying assembly against mitochondrial database.								Up-to-date	https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py	Sequence Analysis	parse_mito_blast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast	1.0.2	parse_mito_blast	1.0.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	31	90	True	False	False
+pathview	pathview	Pathview is a tool set for pathway based data integration and visualization.	pathview	pathview		pathview	Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	To update	https://bioconductor.org/packages/release/bioc/html/pathview.html	Statistics, RNA, Micro-array Analysis	pathview	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview	1.34.0	bioconductor-pathview	1.42.0	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	565	5260	True	False	False
+pathwaymatcher	reactome_pathwaymatcher	Reactome Pathway Matcher								To update	https://github.com/LuisFranciscoHS/PathwayMatcher	Proteomics	reactome_pathwaymatcher	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher		pathwaymatcher	1.9.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	238	True	False	False
+patrist	patrist	Extract Patristic Distance From a Tree								To update	https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02	Phylogenetics	patrist	nml	https://github.com/phac-nml/patrist	https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist	0.1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+peakachu	peakachu	PEAKachu is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	peakachu	rnateam	https://github.com/tbischler/PEAKachu	https://github.com/bgruening/galaxytools/tree/master/tools/peakachu	0.2.0+galaxy1	peakachu	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	78	3109	True	False	False
+pep_pointer	pep_pointer	PepPointer categorizes peptides by their genomic coordinates.								To update		Genomic Interval Operations, Proteomics	pep_pointer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	0.1.3+galaxy1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9	498	True	False	False
+pepquery	pepquery	A peptide-centric MS search engine for novel peptide identification and validation.								To update	https://pepquery.org	Proteomics	pepquery	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	1.6.2	pepquery	2.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	4862	True	False	False
+pepquery2	pepquery2, pepquery2_index, pepquery2_show_sets	PepQuery2 peptide-centric MS search for peptide identification and validation								Up-to-date	https://pepquery.org	Proteomics	pepquery2	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	2.0.2	pepquery	2.0.2			0	1	3	0	0	1	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	13	717	True	False	False
+peptide_genomic_coordinate	peptide_genomic_coordinate	Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files								To update		Proteomics	peptide_genomic_coordinate	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate	1.0.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9	468	True	False	False
+peptideshaker	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.11			4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	4	2	0	485	17477	True	False	True
+peptimapper	peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag	Proteogenomics workflow for the expert annotation of eukaryotic genomes								To update	https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9	Proteomics		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	2.1					0	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+pepxml_to_xls		Convert PepXML to Tabular								To update		Proteomics	pepxml_to_xls	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+percolator	batched_set_list_creator, percolator, percolator_input_converters, pout2mzid	Percolator								To update		Proteomics	percolator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator	3.5	percolator	3.7.1			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	5	368	True	False	False
+pfamscan	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	19	165	True	False	True
 pharokka	pharokka	rapid standardised annotation tool for bacteriophage genomes and metagenomes	pharokka	pharokka		Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.	Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	To update	https://github.com/gbouras13/pharokka	Genome annotation	pharokka	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	1.3.2	"
                 pharokka
-            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	74	2565	True	False	True
-phyloseq	phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	phyloseq	phyloseq		phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq	1.46.0	bioconductor-phyloseq	1.46.0	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	0	1	4	4	0	1	4	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	82	812	True	False	True
-phyml	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	phyml	phyml		PhyML	Phylogenetic estimation software using Maximum Likelihood	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Bioinformatics, Phylogenetics	Up-to-date	http://www.atgc-montpellier.fr/phyml/	Phylogenetics	phyml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml	3.3.20220408	phyml	3.3.20220408		Phylogenetics, Bioinformatics, Phylogenetics	0	1	1	1	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	104	1770	True	False	True
-pi_db_tools	calc_delta_pi, pi_db_split, pi_dbspec_align	HiRIEF tools								To update		Proteomics	hirieftools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools	1.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-picrust	picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes	PICRUSt wrappers	picrust	picrust		PICRUSt	PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust	1.1.1	picrust	1.1.4	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	0	6	5	6	0	6	5	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	45	1095	True	False	True
-picrust2	picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions	PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	picrust2	picrust2		PICRUSt2	PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	Up-to-date	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.3	picrust2	2.5.3	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	88	1000	True	False	True
-pipmir	pipmir	A method to identify novel plant miRNA.								To update	https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/	RNA	pipmir	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	0.1.0	pipmir	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	21	275	True	False	False
-piranha	piranha	Piranha is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	piranha	rnateam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha	https://github.com/bgruening/galaxytools/tree/master/tools/piranha	1.2.1.0	piranha	1.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	1809	True	False	False
-plasflow	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	plasflow	plasflow		PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.	Sequence analysis	Metagenomics	Up-to-date	https://github.com/smaegol/PlasFlow	Sequence Analysis	plasflow	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow	1.1.0	plasflow	1.1.0	Sequence analysis	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	278	22589	True	False	True
-plasmid_profiler_suite		Plasmid Profiler suite defining all dependencies for Plasmid Profiler								To update		Sequence Analysis	suite_plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-plasmidfinder	plasmidfinder	"""PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"""	PlasmidFinder	PlasmidFinder		PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	Up-to-date	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	Sequence Analysis	plasmidfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder	2.1.6	plasmidfinder	2.1.6	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	22	True	False	True
-plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-platypus	bg_platypus	efficient and accurate variant-detection in high-throughput sequencing data								To update	http://www.well.ox.ac.uk/platypus	Sequence Analysis	platypus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	0.0.11	platypus				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-plotly_ml_performance_plots	plotly_ml_performance_plots	performance plots for machine learning problems								To update	http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics	Visualization	plotly_ml_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	0.4	galaxy-ml	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	71	1323	True	False	False
-plotly_parallel_coordinates_plot	plotly_parallel_coordinates_plot	parallel coordinates plot produced with plotly								To update	https://plot.ly/python/parallel-coordinates-plot/	Visualization	plotly_parallel_coordinates_plot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	37	652	True	False	False
-plotly_regression_performance_plots	plotly_regression_performance_plots	performance plots for regression problems								To update	http://scikit-learn.org/stable/supervised_learning.html#supervised-learning	Visualization	plotly_regression_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	0.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	79	843	True	False	False
-pmd_fdr	pmd_fdr	Calculate Precursor Mass Discrepancy (PMD) for MS/MS								To update	https://github.com/slhubler/PMD-FDR-for-Galaxy-P	Proteomics	pmd_fdr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	1.4.0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-poisson2test	poisson2test	Poisson two-sample test								To update	https://bitbucket.org/natefoo/taxonomy	Statistics, Metagenomics	poisson2test	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test	1.0.0	taxonomy	0.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	116	True	False	False
-polypolish	polypolish	"""Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."""	Polypolish	Polypolish		Polypolish	Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	To update	https://github.com/rrwick/Polypolish	Sequence Analysis	polypolish	iuc	https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish	0.5.0	polypolish	0.6.0	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	239	True	False	True
-predictnls	predictnls	Python reimplementation of predictNLS for Galaxy								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	Sequence Analysis	predictnls	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	0.0.10					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-presto	presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3	pRESTO toolkit for immune repertoire analysis.	presto	presto		pRESTO	Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	To update	https://presto.readthedocs.io/	Sequence Analysis	presto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto	0.6.2	presto	0.7.2	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-pretext	pretext_graph, pretext_map, pretext_snapshot	Process genome contacts maps processing images.								Up-to-date	https://github.com/wtsi-hpag/PretextSnapshot	Sequence Analysis	suite_pretext	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext	0.0.6	pretextgraph	0.0.6			3	2	3	0	3	2	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	254	2350	True	False	False
-prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	70	7881	True	False	False
-probecoverage	probecoverage	computes and plots read coverage of genomic regions by sequencing datasets								To update	http://artbio.fr	Sequence Analysis, Genomic Interval Operations, Graphics, Statistics	probecoverage	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	0.22.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-progressivemauve	progressivemauve, xmfa2gff3	Mauve/ProgressiveMauve Multiple Sequence Aligner								To update	http://darlinglab.org/mauve/user-guide/progressivemauve.html	Sequence Analysis	progressivemauve	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve	https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve		progressivemauve	snapshot_2015_02_13			2	0	2	0	2	0	2	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	286	1734	True	False	False
-prokka	prokka	Rapid annotation of prokaryotic genomes	prokka	prokka		Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka	1.14.6	prokka	1.14.6	Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	0	1	1	0	3233	371445	True	False	True
-promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-prot-scriber	prot_scriber	Protein annotation of short human readable descriptions								Up-to-date	https://github.com/usadellab/prot-scriber	Proteomics	prot_scriber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber	0.1.6	prot-scriber	0.1.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	5	True	False	False
-protease_prediction	eden_protease_prediction	This tool can learn the cleavage specificity of a given class of proteases.								To update	https://github.com/fabriziocosta/eden	Sequence Analysis, Proteomics	protease_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	0.9	eden	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	154	True	False	False
-protein_analysis	promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort	TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	Sequence Analysis	tmhmm_and_signalp	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	0.0.13	promoter				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	451	6428	True	False	False
-protein_properties	bg_protein_properties	Calculation of various properties from given protein sequences								To update		Sequence Analysis	protein_properties	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	604	True	False	False
-proteinortho	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho		Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	To update	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.2	Sequence clustering, Sequence analysis	Comparative genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	200	3320	True	False	True
-proteomiqon_joinquantpepionswithproteins	proteomiqon_joinquantpepionswithproteins	The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.								To update	https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html	Proteomics	proteomiqon_joinquantpepionswithproteins	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	0.0.1	proteomiqon-joinquantpepionswithproteins	0.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	366	True	False	False
-proteomiqon_labeledproteinquantification	proteomiqon_labeledproteinquantification	The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html	Proteomics	proteomiqon_labeledproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	0.0.1	proteomiqon-labeledproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	14	True	False	False
-proteomiqon_labelfreeproteinquantification	proteomiqon_labelfreeproteinquantification	The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html	Proteomics	proteomiqon_labelfreeproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	0.0.1	proteomiqon-labelfreeproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	6	True	False	False
-proteomiqon_mzmltomzlite	proteomiqon_mzmltomzlite	The tool MzMLToMzLite allows to convert mzML files to mzLite files.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html	Proteomics	proteomiqon_mzmltomzlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite	0.0.8	proteomiqon-mzmltomzlite	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	721	True	False	False
-proteomiqon_peptidedb	proteomiqon_peptidedb	The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html	Proteomics	proteomiqon_peptidedb	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	0.0.7	proteomiqon-peptidedb	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	96	True	False	False
-proteomiqon_peptidespectrummatching	proteomiqon_peptidespectrummatching	Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html	Proteomics	proteomiqon_peptidespectrummatching	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	0.0.7	proteomiqon-peptidespectrummatching	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	686	True	False	False
-proteomiqon_proteininference	proteomiqon_proteininference	MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html	Proteomics	proteomiqon_proteininference	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	0.0.7	proteomiqon-proteininference	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	89	True	False	False
-proteomiqon_psmbasedquantification	proteomiqon_psmbasedquantification	The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.								To update	https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html	Proteomics	proteomiqon_psmbasedquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	0.0.8	proteomiqon-psmbasedquantification	0.0.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	604	True	False	False
-proteomiqon_psmstatistics	proteomiqon_psmstatistics	The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html	Proteomics	proteomiqon_psmstatistics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	0.0.8	proteomiqon-psmstatistics	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	694	True	False	False
-proteore_venn_diagram	proteore_venn_diagram	ProteoRE JVenn Diagram								To update		Proteomics	proteore_venn_diagram	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram	2021.06.08	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	True	False	False
-pseudogenome	pseudogenome	Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	pseudogenome	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-psm2sam	PSMtoSAM	PSM to SAM								To update	https://bioconductor.org/packages/release/bioc/html/proBAMr.html	Proteomics	psm_to_sam	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam	1.3.2.1	r-base				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-psm_validation	psmvalidator	Validate PSM from Ion Fragmentation								To update	https://github.com/galaxyproteomics/psm_fragments.git	Proteomics	psm_validation	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	1.0.3					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	20	True	False	False
-psy-maps	psy_maps	Visualization of regular geographical data on a map with psyplot								To update	https://github.com/Chilipp/psy-maps	Visualization, Climate Analysis	psy_maps	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	1.2.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	46	469	True	False	False
-pureclip	pureclip	PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data								To update	https://github.com/skrakau/PureCLIP	Sequence Analysis, RNA, CLIP-seq	pureclip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip	1.0.4	pureclip	1.3.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	1423	True	False	False
-purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	167	16800	True	False	False
-pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	350	21123	True	False	True
-pygenometracks	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	pygenometracks	pygenometracks		pyGenomeTracks	reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	Visualisation, Formatting	Model organisms, Imaging, Workflows	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	377	11332	True	False	True
-pyprophet	pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample	Semi-supervised learning and scoring of OpenSWATH results.								To update	https://github.com/PyProphet/pyprophet	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	2.1.4	pyprophet	2.2.5			0	5	6	0	0	5	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	33	2509	True	False	False
-pyscenic	pyscenic_aucell, pyscenic_ctx, pyscenic_grn	PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/								To update		Transcriptomics, RNA, Sequence Analysis	suite_pyscenic	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic	0.12.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-pysradb	pysradb_search	pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.	pysradb	pysradb		pysradb	Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	To update	https://github.com/saketkc/pysradb	Sequence Analysis	pysradb_search	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb	1.4.2	pysradb	2.2.1	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	26	144	True	False	False
-pyteomics	mztab2tsv	Tools using the pyteomics library	pyteomics	pyteomics		Pyteomics	Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.	Protein identification	Proteomics, Proteomics experiment	To update	https://pyteomics.readthedocs.io/en/latest/	Proteomics, Metabolomics	pyteomics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	4.4.1	pyteomics	4.7.3	Protein identification	Proteomics, Proteomics experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	81	True	False	False
-qiime_add_on	qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_add_on, qiime_core		qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	68	1909	True	False	True
-qiime_core	qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file	QIIME to perform microbial community analysis	qiime_core	qiime_core		qiime_core	QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	32	32	0	0	32	32	0	0	0	0	0	0	0	0	0	0	0	0	31	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	0	1155	28681	True	False	True
-qiime_extract_viz	qiime_extract_viz	Extract vizualization from QIIME artifacts								To update	http://www.qiime.org	Metagenomics	qiime_extract_viz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz	0.1.0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-qq_tools	qq_manhattan									To update	https://CRAN.R-project.org/package=qqman	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools	0.1.0	r-qqman	0.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-qualimap	qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq	Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.	qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	Up-to-date	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.3	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	1	4	4	4	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1	0	0	0	1	0	0	0	0	0	0	0	4	4	0	1328	664470	True	False	True
-quality_filter	qualityFilter	Filter nucleotides based on quality scores								To update		Sequence Analysis, Variant Analysis	quality_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter	1.0.1	bx-python	0.12.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-quantp	quantp	Correlation between protein and transcript abundance								To update		Proteomics	quantp	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp	1.1.2	r-data.table	1.11.6			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	230	True	False	False
-quantwiz_iq	quantwiz_iq	Isobaric Quantitation using QuantWiz-IQ								Up-to-date	https://sourceforge.net/projects/quantwiz/	Proteomics	quantwiz_iq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	2.0	quantwiz-iq	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	32	True	False	False
-quasitools	aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality	A collection of tools for analysing Viral Quasispecies								Up-to-date	https://github.com/phac-nml/quasitools	Sequence Analysis	quasitools	nml	https://github.com/phac-nml/quasitools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools	0.7.0	quasitools	0.7.0			0	12	0	12	0	12	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	3567	51567	True	False	True
-quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	True	False	True
-rRNA	meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-racon	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	309	21353	True	False	True
-ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	237	2833	True	False	False
-rapidnj	rapidnj	Galaxy wrapper for the RapidNJ tool	rapidnj	rapidnj		RapidNJ	A tool for fast canonical neighbor-joining tree construction.	Phylogenetic tree generation	Phylogeny	Up-to-date	https://birc.au.dk/software/rapidnj/	Phylogenetics	rapidnj	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj	2.3.2	rapidnj	2.3.2		Phylogeny	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	176	True	False	False
-rasusa	rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa		rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	2.0.0	rasusa	2.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	6902	True	False	False
-rawtools	rawtools	Raw Tools								To update	https://github.com/kevinkovalchik/RawTools	Proteomics	rawtools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools		rawtools	2.0.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	14	175	True	False	False
-raxml	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml		RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	Sequence analysis	Phylogenetics	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	383	6808	True	False	True
-rbpbench	rbpbench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs	rbpbench	rbpbench		RBPBench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	To update	https://github.com/michauhl/RBPBench	Sequence Analysis, RNA, CLIP-seq	rbpbench	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	0.8.1	rbpbench	0.9		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	36	True	False	False
-rcas	rcas	RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments								To update	https://github.com/BIMSBbioinfo/RCAS	RNA	rcas	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas	1.5.4	bioconductor-rcas	1.28.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	38	1226	True	False	False
-rcve	rcve1	Compute RCVE								To update		Sequence Analysis, Variant Analysis	rcve	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-read_it_and_keep	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep		read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	Filtering, Genome alignment	Pathology, Genomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	3370	True	False	True
-reago	reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-recentrifuge	recentrifuge	"""With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."""	Recentrifuge	Recentrifuge		Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.14.1	recentrifuge	1.14.1	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	48	331	True	False	True
-red	red	Red (REpeat Detector)	red	red		RED	This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	Up-to-date	https://github.com/BioinformaticsToolsmith/Red	Sequence Analysis	red	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/red	https://github.com/galaxyproject/tools-iuc/tree/main/tools/red	2018.09.10	red	2018.09.10	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	88	578	True	False	False
-refseq_masher	refseq_masher_contains, refseq_masher_matches	Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.								Up-to-date	https://github.com/phac-nml/refseq_masher	Sequence Analysis	refseq_masher	nml	https://github.com/phac-nml/refseq_masher	https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher	0.1.2	refseq_masher	0.1.2			2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	22	526	True	False	False
-remurna	remurna	remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation								To update	https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna	RNA	remurna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	1.0.0	remurna	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	42	True	False	False
-repeat_masker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.								To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	0.1.2	RepeatMasker	4.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	248	3750	True	False	False
-repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	True	False	True
-repeatmasker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.	repeatmasker	repeatmasker		RepeatMasker	A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).	Genome annotation	Sequence analysis, Sequence composition, complexity and repeats	Up-to-date	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker	4.1.5	repeatmasker	4.1.5	Genome annotation	Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	248	3750	True	False	False
-repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	217	1177	True	False	False
-retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-revoluzer	revoluzer_crex, revoluzer_distmat	revoluzer wrappers	revoluzer	revoluzer		revoluzer	Various tools for genome rearrangement analysis. CREx, TreeREx, etc	Structural variation detection	Molecular evolution, Phylogeny	Up-to-date	https://gitlab.com/Bernt/revoluzer/	Phylogenetics	revoluzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer	0.1.6	revoluzer	0.1.6	Structural variation detection	Molecular evolution, Phylogeny	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-ribotaper	ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling	A method for defining traslated ORFs using Ribosome Profiling data.	ribotaper	ribotaper		RiboTaper	New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.	Gene expression profiling	Functional genomics	To update	https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/	RNA	ribotaper	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper	1.3.1a	ribotaper	1.3.1	Gene expression profiling	Functional genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	44	628	True	False	False
-ribowaltz	ribowaltz_process, ribowaltz_plot	Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data	riboWaltz	riboWaltz		riboWaltz	riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.		Computational biology	To update	https://github.com/LabTranslationalArchitectomics/riboWaltz	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz	1.2.0	ribowaltz	2.0		Computational biology	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	14	161	True	False	False
-rna_shapes	RNAshapes	Compute secondary structures of RNA								To update		RNA	rnashapes	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	3.3.0	@EXECUTABLE@				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	129	True	False	False
-rnabob	rbc_rnabob	Fast pattern searching for RNA structural motifs								To update	http://eddylab.org/software.html	RNA	rnabob	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	2.2.1.0	rnabob	2.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	164	True	False	False
-rnacode	rbc_rnacode	Analyze the protein coding potential in MSA								To update		RNA	rnacode	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	0.3.2	rnacode	0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	1358	True	False	False
-rnacommender	rbc_rnacommender	RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.								To update	https://github.com/gianlucacorrado/RNAcommender	RNA	rnacommender	rnateam	https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender	0.1.1	sam	3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	1074	True	False	False
-rnaformer	infer_rnaformer	RNAformer: RNA secondary structure prediction								To update	https://github.com/automl/RNAformer	RNA	rnaformer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	1.0.0	rnaformer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-rnalien	RNAlien	RNAlien unsupervized RNA family model construction								To update	http://rna.tbi.univie.ac.at/rnalien/	RNA, Sequence Analysis	rnalien	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	1.3.6	rnalien	1.8.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	33	True	False	False
-rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	109	1110	True	False	False
-rnasnp	rnasnp	RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs								To update	http://rth.dk/resources/rnasnp/	RNA	rnasnp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp	1.2.0	rnasnp	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	86	True	False	False
-rnaz	rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window	RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.								Up-to-date	https://www.tbi.univie.ac.at/~wash/RNAz/	RNA	rnaz	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz	2.1.1	rnaz	2.1.1			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	28	43279	True	False	False
-roary	roary	Roary the pangenome pipeline	roary	roary		Roary	A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary	3.13.0	roary	3.13.0	Genome assembly	DNA, Genomics, Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	656	12225	True	False	True
-rsem	extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie	transcript quantification from RNA-Seq data								To update	https://github.com/deweylab/RSEM	Transcriptomics, RNA	rsem	artbio	https://github.com/artbio/tools-artbio/tree/master/tools/rsem	https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem		rsem	1.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	1	1	0	67	377	True	False	False
-rseqc	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	22	22	22	22	22	0	0	0	0	0	0	0	0	0	0	0	0	22	0	0	0	0	22	0	0	0	22	0	0	0	0	0	0	0	22	22	0	3206	133498	True	False	True
-ruvseq	ruvseq	Remove Unwanted Variation from RNA-Seq Data	ruvseq	ruvseq		RUVSeq	This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.	Differential gene expression analysis	Gene expression, RNA-seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	ruvseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq	1.26.0	bioconductor-ruvseq	1.36.0	Differential gene expression analysis	Gene expression	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	76	1236	True	False	False
-sailfish	sailfish	Sailfish is a tool for transcript quantification from RNA-seq data								To update	http://www.cs.cmu.edu/~ckingsf/software/sailfish/	Sequence Analysis, RNA	sailfish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	0.10.1.1	bzip2				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	55	4024	True	False	False
-salmon	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	2	3	1	2	2	3	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	2	0	0	0	0	0	0	0	3	3	0	969	61937	True	False	True
-salmon-kallisto-mtx-to-10x	_salmon_kallisto_mtx_to_10x	Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	salmon_kallisto_mtx_to_10x	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x	0.0.1+galaxy6	scipy				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	86	561	True	False	False
-salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	454	True	False	False
-sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	3765	True	False	False
-samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.20			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	296	4948	True	False	False
-samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.20			1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1450	48426	True	False	False
-sarscov2formatter	sarscov2formatter	sarscov2formatter custom script								Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	173	True	False	True
-sarscov2summary	sarscov2summary	sarscov2summary custom script								To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	140	True	False	True
-sashimi_plot	sashimi_plot	Generates a sashimi plot from bam files.								To update	http://artbio.fr	RNA, Transcriptomics, Graphics, Visualization	sashimi_plot	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot	https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot	0.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-sc3	sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare	De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_sc3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3	1.8.0	sc3-scripts	0.0.6			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	9	True	False	False
-scanpy	anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data	scanpy-scripts, command-line wrapper scripts around Scanpy.								To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis, RNA	scanpy_scripts	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy	1.9.3	scanpy-scripts	1.9.301			27	27	27	0	27	27	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	13	0	2185	39356	True	False	False
-scanpy	scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	scanpy	scanpy		SCANPY	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.9.6	scanpy	1.7.2	Differential gene expression analysis	Gene expression, Cell biology, Genetics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	766	51978	True	False	False
-scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Transcriptomics, RNA, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	77	1365	True	False	False
-scater	scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results	De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scater	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater	1.10.0	scater-scripts	0.0.5			1	2	6	0	1	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	16	387	True	False	False
-schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	0	23	779	True	False	False
-scikit-bio	scikit_bio_diversity_beta_diversity	scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics								Up-to-date	http://scikit-bio.org/	Sequence Analysis	scikit_bio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio	0.4.2	scikit-bio	0.4.2			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	True	False	False
-scmap	scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features	De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scmap	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap	1.6.4	scmap-cli	0.1.0			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	13	83	True	False	False
-scoary	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	scoary	scoary		Scoary	Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	61	676	True	False	True
-scpipe	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	scpipe	scpipe		scPipe	A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, RNA, Statistics	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	628	True	False	False
-scpred	scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model	De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scpred	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred	1.0.2	scpred-cli	0.1.0			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	25	True	False	False
-sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-selectsequencesfrommsa	selectsequencesfrommsa	SelectSequences - selects representative entries from a multiple sequence alignment in clustal format								Up-to-date	https://github.com/eggzilla/SelectSequences	RNA, Sequence Analysis	selectsequencesfrommsa	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	1.0.5	selectsequencesfrommsa	1.0.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	27	457	True	False	False
-semibin	semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	semibin	semibin		SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	0	0	6	1	0	0	6	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	39	542	True	False	True
-seq2hla	seq2hla	Precision HLA typing and expression from RNAseq data	seq2hla	seq2hla		Seq2HLA	seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	Up-to-date	https://github.com/TRON-Bioinformatics/seq2HLA	Sequence Analysis	seq2hla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla	2.3	seq2hla	2.3	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	288	True	False	False
-seq_composition	seq_composition	Sequence composition								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	Sequence Analysis	seq_composition	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	0.0.5	biopython	1.70			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	71	874	True	False	False
-seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	306	25302	True	False	False
-seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	82	3784	True	False	False
-seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	True	False	False
-seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-seqcomplexity	seqcomplexity	Sequence complexity for raw reads								Up-to-date	https://github.com/stevenweaver/seqcomplexity	Sequence Analysis		iuc	https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity	0.1.2	seqcomplexity	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	68	True	False	False
-seqkit	seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit		seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	Up-to-date	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.8.2	seqkit	2.8.2	DNA transcription, Sequence trimming, DNA translation	Database management, Sequence analysis	0	2	5	2	0	2	5	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	129	1964	True	False	True
-seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-seqsero2	seqsero2	Salmonella serotype prediction from genome sequencing data	seqsero2	seqsero2		SeqSero2	"rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)"	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	True	False	True
-seqtk	seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq	Toolkit for processing sequences in FASTA/Q formats	seqtk	seqtk		seqtk	A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.	Data handling, Sequence file editing	Data management	Up-to-date	https://github.com/lh3/seqtk	Sequence Analysis	seqtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk	1.4	seqtk	1.4	Data handling, Sequence file editing		15	15	15	15	15	15	15	15	0	0	0	0	14	0	0	0	0	0	0	0	14	0	14	0	0	14	0	0	0	15	0	0	0	0	0	0	0	14	14	14	753	59668	True	False	False
-seqtk_nml	seqtk_nml_sample	Tool to downsample fastq reads								To update	https://github.com/lh3/seqtk	Sequence Analysis	seqtk_nml	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml	1.0.1	seqtk	1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-seqwish	seqwish	Alignment to variation graph inducer								To update	https://github.com/ekg/seqwish	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish	0.7.5	seqwish	0.7.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	271	True	False	False
-seurat	seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features	De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1								Up-to-date	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	Transcriptomics, RNA, Statistics, Sequence Analysis	suite_seurat	ebi-gxa		https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat	4.0.0	seurat-scripts	4.0.0			14	14	14	11	14	14	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	0	0	0	0	0	0	0	0	181	1966	True	False	False
-seurat	seurat	A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data								To update	https://github.com/satijalab/seurat	Transcriptomics, RNA, Statistics	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	4.3.0.1	r-seurat	3.0.2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	66	1543	True	False	False
-shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.12.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	154	763	True	False	False
-shorah	shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	shorah	shorah		ShoRAH	Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	To update	https://github.com/cbg-ethz/shorah/blob/master/README.md	Sequence Analysis	shorah_amplicon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah	1.1.3	shorah	1.99.2	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-short_reads_figure_high_quality_length	hist_high_quality_score	Histogram of high quality score reads								To update		Sequence Analysis, Graphics	short_reads_figure_high_quality_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length	1.0.0	rpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-short_reads_figure_score	quality_score_distribution	Build base quality distribution								To update		Sequence Analysis, Graphics	short_reads_figure_score	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score	1.0.2	fontconfig				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	163	True	False	False
-shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1008	41600	True	False	True
-sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	269	14982	True	False	False
-sina	sina	SINA reference based multiple sequence alignment	sina	sina		SINA	Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	Up-to-date	https://sina.readthedocs.io/en/latest/	Sequence Analysis	sina	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina	1.7.2	sina	1.7.2	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	1	0	1	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	42	1128	True	False	False
-sinto	sinto_barcode, sinto_fragments	Sinto single-cell analysis tools								To update	https://github.com/timoast/sinto	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto	0.9.0	sinto	0.10.1			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	17	91	True	False	False
-sistr_cmd	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	133	2489	True	False	True
-sixgill	sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge	Six-frame Genome-Inferred Libraries for LC-MS/MS								Up-to-date		Proteomics, MetaProteomics	sixgill	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	0.2.4	sixgill	0.2.4			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	24	293	True	False	False
-slamdunk	alleyoop, slamdunk	Slamdunk maps and quantifies SLAMseq reads								Up-to-date	http://t-neumann.github.io/slamdunk	RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers	slamdunk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk	0.4.3	slamdunk	0.4.3			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2	361	True	False	False
-sleuth	sleuth	Sleuth is a program for differential analysis of RNA-Seq data.	sleuth	sleuth		sleuth	A statistical model and software application for RNA-seq differential expression analysis.	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	RNA-seq, Gene expression, Statistics and probability	Up-to-date	https://github.com/pachterlab/sleuth	Transcriptomics, RNA, Statistics	sleuth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth	0.30.1	r-sleuth	0.30.1	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	64	True	False	False
-small_rna_clusters	small_rna_clusters	clusters small rna reads in alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_clusters	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters	1.3.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-small_rna_maps	small_rna_maps	Generates small read maps from alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_maps	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps	3.1.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-small_rna_signatures	overlapping_reads, signature	Computes the tendency of small RNAs to overlap with each other.								To update	http://artbio.fr	RNA	small_rna_signatures	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures	3.4.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-smallgenomeutilities	smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe		V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.1	smallgenomeutilities	0.4.1	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	121	True	False	True
-smalt	smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-smart_domains	smart_domains	SMART domains								To update	http://smart.embl.de/	Sequence Analysis	smart_domains	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	0.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	Up-to-date	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.2.5	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	22	203	True	False	False
-snap	snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap		SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	Gene prediction	DNA polymorphism, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	133	1349	True	False	True
-snapatac2	snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing	SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis								To update	https://kzhang.org/SnapATAC2/	Epigenetics, Sequence Analysis	snapatac2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2	2.6.4					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-sniffles	sniffles	Galaxy wrapper for sniffles	sniffles	sniffles		Sniffles	An algorithm for structural variation detection from third generation sequencing alignment.	Sequence analysis, Structural variation detection	DNA structural variation, Sequencing	To update	https://github.com/fritzsedlazeck/Sniffles	Sequence Analysis	sniffles	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles	1.0.12	sniffles	2.4	Sequence analysis, Structural variation detection	Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	58	919	True	False	False
-snipit	snipit	Summarise snps relative to a reference sequence	snipit	snipit		snipit	Summarise snps relative to a reference sequence	Base position variability plotting	Virology	Up-to-date	https://github.com/aineniamh/snipit	Variant Analysis, Sequence Analysis	snipit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	1.2	snipit	1.2	Base position variability plotting	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	669	True	False	False
-snippy	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy		snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	Phylogenetic tree visualisation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	3	3	3	3	3	3	3	3	0	0	0	0	2	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	2	0	1372	105708	True	False	True
-snv_matrix	snvmatrix	Generate matrix of SNV distances								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	snv_matrix	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-socru	socru	Order and orientation of complete bacterial genomes								To update	https://github.com/quadram-institute-bioscience/socru	Sequence Analysis	socru	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru	https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru	2.1.7	socru	2.2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	621	True	False	False
-sonneityping	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping		sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	True	False	True
-sortmerna	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	376	18183	True	False	True
-spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	coronaspades, biosyntheticspades, metaplasmidspades, plasmidspades, metaspades, rnaspades, metaviralspades, rnaviralspades, spades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	1	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	0	0	9	3	0	3547	72953	True	False	True
-spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	34	446	True	False	False
-spapros	spapros, spapros	Select and evaluate probe sets for targeted spatial transcriptomics.								Up-to-date	https://github.com/theislab/spapros	Transcriptomics, Sequence Analysis	spapros	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros	0.1.5	spapros	0.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-spatyper	spatyper	Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.								Up-to-date	https://github.com/HCGB-IGTP/spaTyper	Sequence Analysis	spatyper	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	0.3.3	spatyper	0.3.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-spectrast2spectrast_irt	gp_spectrast2spectrast_irt	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2spectrast_irt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-spectrast2tsv	gp_spectrast2tsv	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2tsv	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	56	769	True	False	False
-spolpred	spolpred	A program for predicting the spoligotype from raw sequence reads								To update		Sequence Analysis	spolpred	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred	1.0.1	spolpred				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-spotyping	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping		SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	1278	True	False	True
-sr_bowtie	bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-sr_bowtie_dataset_annotation	sr_bowtie_dataset_annotation	Maps iteratively small RNA sequencing datasets to reference sequences.								To update	http://artbio.fr	RNA	sr_bowtie_dataset_annotation	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation	2.8	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	7	4	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	21	225	True	False	False
-srst2	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	205	True	False	True
-srst2	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2		srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.20	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	205	True	False	True
-sshmm	sshmm	ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data								Up-to-date	https://github.molgen.mpg.de/heller/ssHMM	Sequence Analysis, RNA	sshmm	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm	1.0.7	sshmm	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	223	True	False	False
-stacks	stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq	stacks	stacks		Stacks	Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.	Data handling	Mapping, Population genetics	To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis	stacks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks		stacks	2.65	Data handling	Mapping, Population genetics	0	13	13	12	0	13	13	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	13	0	152	11635	True	False	False
-stacks2	stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq								To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2	2.55	stacks	2.65			0	12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	0	238	7292	True	False	False
-star_fusion	star_fusion	STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR								To update	https://github.com/STAR-Fusion/STAR-Fusion	Sequence Analysis, Transcriptomics	star_fusion	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion	https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion	0.5.4-3+galaxy1	star-fusion	1.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	35	1212	True	False	False
-staramr	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	889	12673	True	False	True
-stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	10	325	True	False	False
-stringmlst	stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-structure	structure	for using multi-locus genotype data to investigate population structure.	structure	structure		Structure	The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Genetic variation analysis	Population genetics	Up-to-date	https://web.stanford.edu/group/pritchardlab/structure.html	Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	Genetic variation analysis	Population genetics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	59	2623	True	False	True
-structureharvester	structureharvester	for parsing STRUCTURE outputs and for performing the Evanno method								Up-to-date	http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/	Phylogenetics, Variant Analysis	structureharvester	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester	0.6.94	structureharvester	0.6.94			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-substitution_rates	subRate1	Estimate substitution rates for non-coding regions								To update		Sequence Analysis, Variant Analysis	substitution_rates	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-substitutions	substitutions1	Fetch substitutions from pairwise alignments								To update		Sequence Analysis, Variant Analysis	substitutions	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions	1.0.1	bx-python	0.12.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-suite_qiime2__alignment	qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	13	True	False	True
-suite_qiime2__composition	qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.5.0+q2galaxy.2024.5.0					4	4	4	2	4	4	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	2	5	True	False	True
-suite_qiime2__cutadapt	qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	5	67	True	False	True
-suite_qiime2__dada2	qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	31	202	True	False	True
-suite_qiime2__deblur	qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	9	73	True	False	True
-suite_qiime2__demux	qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	26	114	True	False	True
-suite_qiime2__diversity	qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.5.0+q2galaxy.2024.5.0					21	21	21	21	21	21	21	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	0	43	168	True	False	True
-suite_qiime2__diversity_lib	qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	4	4	True	False	True
-suite_qiime2__emperor	qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	2	6	True	False	True
-suite_qiime2__feature_classifier	qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.5.0+q2galaxy.2024.5.0					10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	48	263	True	False	True
-suite_qiime2__feature_table	qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.5.0+q2galaxy.2024.5.0					17	17	17	17	17	17	17	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	59	213	True	False	True
-suite_qiime2__fragment_insertion	qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	20	True	False	True
-suite_qiime2__longitudinal	qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.5.0+q2galaxy.2024.5.0					11	11	11	11	11	11	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	0	6	14	True	False	True
-suite_qiime2__metadata	qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	40	232	True	False	True
-suite_qiime2__phylogeny	qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	12	37	True	False	True
-suite_qiime2__quality_control	qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	True	False	True
-suite_qiime2__quality_filter	qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.5.0+q2galaxy.2024.5.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	13	True	False	True
-suite_qiime2__rescript	qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.5.0+q2galaxy.2024.5.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-suite_qiime2__sample_classifier	qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.5.0+q2galaxy.2024.5.0					15	15	15	15	15	15	15	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	0	0	1	1	True	False	True
-suite_qiime2__taxa	qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	22	172	True	False	True
-suite_qiime2__vsearch	qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.5.0+q2galaxy.2024.5.0					8	8	8	7	8	8	8	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	8	16	True	False	True
-suite_qiime2_core										To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-suite_qiime2_core__tools	qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.5.0+dist.he540b0b0					2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	124	7087	True	False	True
-suite_snvphyl		SNVPhyl suite defining all dependencies for SNVPhyl								To update		Sequence Analysis	suite_snvphyl_1_2_3	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-syndiva	syndiva	SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.								To update		Proteomics	syndiva	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA	https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva	1.0	clustalo	1.2.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	30	True	False	False
-t2ps	Draw_phylogram	Draw phylogeny	t2ps	t2ps		Draw phylogeny	"""Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper"	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	31	457	True	False	True
-t2t_report	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	26	947	True	False	True
-t_coffee	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b			0	0	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	70	8690	True	False	True
-tapscan	tapscan_classify	Search for transcription associated proteins (TAPs)								To update	https://plantcode.cup.uni-freiburg.de/tapscan/	Proteomics	tapscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	4.76+galaxy0	hmmer	3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-targetfinder	targetfinder	Plant small RNA target prediction tool								Up-to-date	https://github.com/carringtonlab/TargetFinder.git	RNA	targetfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder	1.7	targetfinder	1.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	37	713	True	False	False
-tasmanian_mismatch	tasmanian_mismatch	Analysis of positional mismatches								Up-to-date	https://github.com/nebiolabs/tasmanian-mismatch	Sequence Analysis	tasmanian_mismatch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch	1.0.7	tasmanian-mismatch	1.0.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-taxonkit	name2taxid, profile2cami	TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit	taxonkit	taxonkit		TaxonKit	TaxonKit is a practical and efficient NCBI taxonomy toolkit.	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	Up-to-date	https://bioinf.shenwei.me/taxonkit/	Metagenomics	taxonkit	iuc	https://github.com/shenwei356/taxonkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit	0.17.0	taxonkit	0.17.0	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	0	1	1	0	1801	27426	True	False	True
-taxpasta	taxpasta	standardise taxonomic profiles	taxpasta	taxpasta		taxpasta	TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table.	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	Up-to-date	https://taxpasta.readthedocs.io/en/latest/	Sequence Analysis	taxpasta	iuc	https://github.com/taxprofiler/taxpasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta	0.7.0	taxpasta	0.7.0	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-tb-profiler	tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	6.2.1	tb-profiler	6.3.0	Antimicrobial resistance prediction		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	198	5161	True	False	True
-tbl2gff3	tbl2gff3	Table to GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	Convert Formats, Sequence Analysis	tbl2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3	1.2	bcbiogff	0.6.6			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	229	1584	True	False	False
-te_finder	te_finder	Transposable element insertions finder	tefinder	tefinder		TEfinder	A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	To update	https://github.com/VistaSohrab/TEfinder	Sequence Analysis	te_finder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder	1.0.1	samtools	1.20	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	81	True	False	False
-telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-tetoolkit	tetoolkit_tetranscripts	The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.								Up-to-date	http://hammelllab.labsites.cshl.edu/software/	Sequence Analysis	tetoolkit	iuc	https://github.com/mhammell-laboratory/TEtranscripts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit	2.2.3	tetranscripts	2.2.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	33	871	True	False	False
-tetyper	tetyper	Type a specific transposable element (TE) of interest from paired-end sequencing data.								Up-to-date	https://github.com/aesheppard/TETyper	Sequence Analysis	tetyper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper	1.1	tetyper	1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	69	True	False	False
-tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	460	True	False	False
-tiara	tiara	Tool for identification of eukaryotic sequences in the metagenomic datasets.	Tiara	Tiara		TIARA	Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).	Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism, DNA structural variation	To update	https://github.com/ibe-uw/tiara	Metagenomics, Sequence Analysis	tiara	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	1.0.3	tiara		Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-tn93	tn93_readreduce, tn93, tn93_cluster, tn93_filter	Compute distances between sequences								To update	https://github.com/veg/tn93/	Sequence Analysis	tn93	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93	1.0.6	tn93	1.0.14			4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	4	0	0	17	1881	True	False	False
-tooldistillator	tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator		ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.9	tooldistillator	0.9	Parsing	Microbiology, Bioinformatics, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-tophat	tophat	Tophat for Illumina								To update		RNA, Next Gen Mappers	tophat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat	1.5.0	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	True	False	False
-tophat2	tophat2	Tophat - fast splice junction mapper for RNA-Seq reads								To update	http://ccb.jhu.edu/software/tophat/index.shtml	RNA, Next Gen Mappers	tophat2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2	2.1.1	bowtie2	2.5.4			1	1	1	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	1	0	312	24167	True	False	False
-transdecoder	transdecoder	TransDecoder finds coding regions within transcripts	TransDecoder	TransDecoder		TransDecoder	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	To update	https://transdecoder.github.io/	Transcriptomics, RNA	transdecoder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder	5.5.0	transdecoder	5.7.1	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	348	5468	True	False	False
-transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	84	907	True	False	True
-translate_bed	translate_bed	Translate BED transcript CDS or cDNA in 3 frames								To update	http://rest.ensembl.org/	Proteomics	translate_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	0.1.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	49	643	True	False	False
-translate_bed_sequences	translate_bed_sequences	Perform 3 frame translation of BED file augmented with a sequence column								To update		Proteomics	translate_bed_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	57	True	False	False
-transtermhp	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	transtermhp	transtermhp		TransTermHP	TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	229	True	False	True
-trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2334	238699	True	False	True
-trinity	trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats	Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq	trinity	trinity		Trinity	Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.	Transcriptome assembly	Transcriptomics, Gene expression, Gene transcripts	To update	https://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity	2.15.1	trinity	2.15.2	Transcriptome assembly	Transcriptomics, Gene transcripts	9	13	13	13	9	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	1	2	1	0	0	0	0	0	0	11	0	0	1	0	0	0	0	13	12	0	1762	31951	True	False	False
-trinotate	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	trinotate	trinotate		Trinotate	Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.	Gene functional annotation	Gene expression, Transcriptomics	To update	https://trinotate.github.io/	Transcriptomics, RNA	trinotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate	3.2.2	trinotate	4.0.2	Gene functional annotation	Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	151	1796	True	False	False
-trna_prediction	aragorn_trna, trnascan	Aragorn predicts tRNA and tmRNA in nucleotide sequences.								To update	http://mbioserv2.mbioekol.lu.se/ARAGORN/	RNA	trna_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	0.6	aragorn	1.2.41			0	2	2	0	0	2	2	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	2	2	0	236	2935	True	False	False
-trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942	True	False	True
-tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	To update	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.4	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	True	False	False
-ucsc_axtchain	ucsc_axtchain	Chain together genome alignments	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_axtchain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain	455	ucsc-axtchain	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ucsc_blat	ucsc_blat	Standalone blat sequence search command line tool	blat	blat		BLAT	Fast, accurate spliced alignment of DNA sequences.	Sequence alignment	Sequence analysis	To update	http://genome.ucsc.edu/goldenPath/help/blatSpec.html	Sequence Analysis	ucsc_blat	yating-l	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat	377	ucsc-blat	469	Sequence alignment	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-ucsc_chainnet	ucsc_chainnet	Make alignment nets out of chains	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainnet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	469	ucsc-chainnet	469		Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ucsc_chainprenet	ucsc_chainprenet	Remove chains that don't have a chance of being netted	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainprenet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainprenet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet	377	ucsc-chainprenet	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ucsc_chainsort	ucsc_chainsort	Sort chains. By default sorts by score.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainsort	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort	455	ucsc-chainsort	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ucsc_custom_track	build_ucsc_custom_track_1	Build custom track for UCSC genome browser								To update		Sequence Analysis	ucsc_custom_track	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	1.0.1	python				1	0	1	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	45	394	True	False	False
-umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	To update	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.2	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	0	0	5	5	0	379	61618	True	False	False
-unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1558	65732	True	False	True
-unipept	unipept	Unipept retrieves metaproteomics information	unipept	unipept		Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	115	5005	True	False	True
-uniprot_rest_interface	uniprot	UniProt ID mapping and sequence retrieval								To update	https://github.com/jdrudolph/uniprot	Proteomics, Sequence Analysis	uniprot_rest_interface	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	0.6	requests				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	132	2406	True	False	False
-uniprotxml_downloader	uniprotxml_downloader	Download UniProt proteome in XML or fasta format								To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	79	1360	True	False	True
-usher	usher_matutils, usher	UShER toolkit wrappers	usher	usher		usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Cladistics, Genotype and phenotype, Phylogenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	1060	True	False	True
-valet	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	637	True	False	True
-validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	25	86	True	False	False
-vapor	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor		VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	94	3164	True	False	True
-varvamp	varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp		varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology, Probes and primers	Up-to-date	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.0	PCR primer design	Virology, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-vcf2snvalignment	vcf2snvalignment	Generates multiple alignment of variant calls								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	vcf2snvalignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-vegan	vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	74	2020	True	False	True
-velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	2083	25420	True	False	True
-velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	255	4741	True	False	True
-venn_list	venn_list	Draw Venn Diagram (PDF) from lists, FASTA files, etc								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	Graphics, Sequence Analysis, Visualization	venn_list	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	0.1.2	galaxy_sequence_utils	1.1.5			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	248	5067	True	False	False
-verify_map	verify_map	Checks the mapping quality of all BAM(s)								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	verify_map	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	22	True	False	False
-vg	vg_convert, vg_deconstruct, vg_view	Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods								To update	https://github.com/vgteam/vg	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg	1.23.0	vg	1.56.0			0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	3	477	True	False	False
-vienna_rna	viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup	ViennaRNA - Prediction and comparison of RNA secondary structures								To update	http://www.tbi.univie.ac.at/RNA/	RNA	viennarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	2.2.10	viennarna	2.6.4			0	0	21	0	0	0	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	21	0	123	7864	True	False	False
-vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	351	12203	True	False	False
-virAnnot	virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers	virannot	virannot		virAnnot	"VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy."	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.0.1+galaxy0	biopython	1.70	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-virheat	virheat	generates a heatmap of allele frequencies from vcf files	virheat	virheat		virHEAT	VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists.  The tool provides a condensed look at variant frequencies after mapping  raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time.			Up-to-date	https://github.com/jonas-fuchs/virHEAT	Visualization, Variant Analysis	virheat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat	0.7.1	virheat	0.7.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-virsorter	virsorter	VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.	virsorter	virsorter		virsorter	Identify DNA and RNA virus sequences.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/jiarong/VirSorter2/	Metagenomics	virsorter	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter	2.2.4	virsorter	2.2.4	Taxonomic classification	Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-volcanoplot	volcanoplot	Tool to create a Volcano Plot								To update	https://ggplot2.tidyverse.org/	Visualization, Transcriptomics, Statistics	volcanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot	0.0.6	r-ggplot2	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	1749	30946	True	False	False
-vsearch	vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	vsearch	vsearch		VSEARCH	High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.28.1	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	8	8	8	8	8	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	0	0	0	0	0	8	0	0	0	0	0	0	0	8	8	0	182	8507	True	False	True
-vsnp	vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics	The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.								To update	https://github.com/USDA-VS/vSNP	Sequence Analysis	vsnp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp	3.0.6	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-vt	vt_@BINARY@, vt_@BINARY@	A tool set for short variant discovery in genetic sequence data.								To update		Sequence Analysis, Variant Analysis	vt	bgruening	https://github.com/atks/vt	https://github.com/bgruening/galaxytools/tree/master/tools/vt	0.2	vt	2015.11.10			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-wade	wade	identify regions of interest								To update	https://github.com/phac-nml/wade	Sequence Analysis	wade	nml	https://github.com/phac-nml/wade	https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade	0.2.5+galaxy1	wade	0.2.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-weather_app	simple_weather	provides simple weather in text format								To update	http://wttr.in/	Visualization, Web Services	simpleweather	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app	0.1.2	curl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-weightedaverage	wtavg	Assign weighted-average of the values of features overlapping an interval								To update		Sequence Analysis, Variant Analysis	weightedaverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage	https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage	1.0.1	galaxy-ops	1.1.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-windowmasker	windowmasker_mkcounts, windowmasker_ustat	Identify repetitive regions using WindowMasker								To update	https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/	Sequence Analysis	windowmasker	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker	1.0	blast	2.16.0			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	85	True	False	False
-windowsplitter	winSplitter	Make windows								To update		Sequence Analysis, Variant Analysis	windowsplitter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter	1.0.1	bx-python	0.12.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	True	False	False
-wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660	True	False	True
-xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	5	5	2	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	175	5876	True	False	False
-xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-yahs	yahs	Yet Another Hi-C scaffolding tool								Up-to-date	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2a.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	64	344	True	False	False
-zeiss_lmd_converter	ZeissLMDconverter	Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	2.0.4	shapely				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	74	2565	True	False	True
+phyloseq	phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	phyloseq	phyloseq		phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq	1.46.0	bioconductor-phyloseq	1.46.0	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	0	1	4	4	0	1	4	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	82	812	True	False	True
+phyml	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	phyml	phyml		PhyML	Phylogenetic estimation software using Maximum Likelihood	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Bioinformatics, Phylogenetics	Up-to-date	http://www.atgc-montpellier.fr/phyml/	Phylogenetics	phyml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml	3.3.20220408	phyml	3.3.20220408		Phylogenetics, Bioinformatics, Phylogenetics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	104	1770	True	False	True
+pi_db_tools	calc_delta_pi, pi_db_split, pi_dbspec_align	HiRIEF tools								To update		Proteomics	hirieftools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools	1.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+picrust	picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes	PICRUSt wrappers	picrust	picrust		PICRUSt	PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust	1.1.1	picrust	1.1.4	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	0	6	5	6	0	6	5	6	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	45	1095	True	False	True
+picrust2	picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions	PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	picrust2	picrust2		PICRUSt2	PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	Up-to-date	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.3	picrust2	2.5.3	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	88	1000	True	False	True
+pipmir	pipmir	A method to identify novel plant miRNA.								To update	https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/	RNA	pipmir	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	0.1.0	pipmir	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	21	275	True	False	False
+piranha	piranha	Piranha is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	piranha	rnateam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha	https://github.com/bgruening/galaxytools/tree/master/tools/piranha	1.2.1.0	piranha	1.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	1809	True	False	False
+plasflow	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	plasflow	plasflow		PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.	Sequence analysis	Metagenomics	Up-to-date	https://github.com/smaegol/PlasFlow	Sequence Analysis	plasflow	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow	1.1.0	plasflow	1.1.0	Sequence analysis	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	278	22589	True	False	True
+plasmid_profiler_suite		Plasmid Profiler suite defining all dependencies for Plasmid Profiler								To update		Sequence Analysis	suite_plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+plasmidfinder	plasmidfinder	"""PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"""	PlasmidFinder	PlasmidFinder		PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	Up-to-date	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	Sequence Analysis	plasmidfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder	2.1.6	plasmidfinder	2.1.6	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	22	True	False	True
+plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+platypus	bg_platypus	efficient and accurate variant-detection in high-throughput sequencing data								To update	http://www.well.ox.ac.uk/platypus	Sequence Analysis	platypus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	0.0.11	platypus				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+plotly_ml_performance_plots	plotly_ml_performance_plots	performance plots for machine learning problems								To update	http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics	Visualization	plotly_ml_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	0.4	galaxy-ml	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	71	1323	True	False	False
+plotly_parallel_coordinates_plot	plotly_parallel_coordinates_plot	parallel coordinates plot produced with plotly								To update	https://plot.ly/python/parallel-coordinates-plot/	Visualization	plotly_parallel_coordinates_plot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37	652	True	False	False
+plotly_regression_performance_plots	plotly_regression_performance_plots	performance plots for regression problems								To update	http://scikit-learn.org/stable/supervised_learning.html#supervised-learning	Visualization	plotly_regression_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	0.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	79	843	True	False	False
+pmd_fdr	pmd_fdr	Calculate Precursor Mass Discrepancy (PMD) for MS/MS								To update	https://github.com/slhubler/PMD-FDR-for-Galaxy-P	Proteomics	pmd_fdr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	1.4.0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+poisson2test	poisson2test	Poisson two-sample test								To update	https://bitbucket.org/natefoo/taxonomy	Statistics, Metagenomics	poisson2test	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test	1.0.0	taxonomy	0.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6	116	True	False	False
+polypolish	polypolish	"""Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."""	Polypolish	Polypolish		Polypolish	Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	To update	https://github.com/rrwick/Polypolish	Sequence Analysis	polypolish	iuc	https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish	0.5.0	polypolish	0.6.0	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	239	True	False	True
+predictnls	predictnls	Python reimplementation of predictNLS for Galaxy								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	Sequence Analysis	predictnls	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	0.0.10					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+presto	presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3	pRESTO toolkit for immune repertoire analysis.	presto	presto		pRESTO	Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	To update	https://presto.readthedocs.io/	Sequence Analysis	presto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto	0.6.2	presto	0.7.2	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+pretext	pretext_graph, pretext_map, pretext_snapshot	Process genome contacts maps processing images.								Up-to-date	https://github.com/wtsi-hpag/PretextSnapshot	Sequence Analysis	suite_pretext	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext	0.0.6	pretextgraph	0.0.6			3	2	3	0	3	2	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	254	2350	True	False	False
+prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	70	7881	True	False	False
+probecoverage	probecoverage	computes and plots read coverage of genomic regions by sequencing datasets								To update	http://artbio.fr	Sequence Analysis, Genomic Interval Operations, Graphics, Statistics	probecoverage	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	0.22.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+progressivemauve	progressivemauve, xmfa2gff3	Mauve/ProgressiveMauve Multiple Sequence Aligner								To update	http://darlinglab.org/mauve/user-guide/progressivemauve.html	Sequence Analysis	progressivemauve	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve	https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve		progressivemauve	snapshot_2015_02_13			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	286	1734	True	False	False
+prokka	prokka	Rapid annotation of prokaryotic genomes	prokka	prokka		Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka	1.14.6	prokka	1.14.6	Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	3233	371445	True	False	True
+promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+prot-scriber	prot_scriber	Protein annotation of short human readable descriptions								Up-to-date	https://github.com/usadellab/prot-scriber	Proteomics	prot_scriber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber	0.1.6	prot-scriber	0.1.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	5	True	False	False
+protease_prediction	eden_protease_prediction	This tool can learn the cleavage specificity of a given class of proteases.								To update	https://github.com/fabriziocosta/eden	Sequence Analysis, Proteomics	protease_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	0.9	eden	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	154	True	False	False
+protein_analysis	promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort	TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	Sequence Analysis	tmhmm_and_signalp	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	0.0.13	promoter				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	451	6428	True	False	False
+protein_properties	bg_protein_properties	Calculation of various properties from given protein sequences								To update		Sequence Analysis	protein_properties	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	604	True	False	False
+proteinortho	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho		Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	To update	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.2	Sequence clustering, Sequence analysis	Comparative genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	200	3320	True	False	True
+proteomiqon_joinquantpepionswithproteins	proteomiqon_joinquantpepionswithproteins	The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.								To update	https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html	Proteomics	proteomiqon_joinquantpepionswithproteins	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	0.0.1	proteomiqon-joinquantpepionswithproteins	0.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	366	True	False	False
+proteomiqon_labeledproteinquantification	proteomiqon_labeledproteinquantification	The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html	Proteomics	proteomiqon_labeledproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	0.0.1	proteomiqon-labeledproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	14	True	False	False
+proteomiqon_labelfreeproteinquantification	proteomiqon_labelfreeproteinquantification	The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html	Proteomics	proteomiqon_labelfreeproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	0.0.1	proteomiqon-labelfreeproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	6	True	False	False
+proteomiqon_mzmltomzlite	proteomiqon_mzmltomzlite	The tool MzMLToMzLite allows to convert mzML files to mzLite files.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html	Proteomics	proteomiqon_mzmltomzlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite	0.0.8	proteomiqon-mzmltomzlite	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	721	True	False	False
+proteomiqon_peptidedb	proteomiqon_peptidedb	The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html	Proteomics	proteomiqon_peptidedb	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	0.0.7	proteomiqon-peptidedb	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	96	True	False	False
+proteomiqon_peptidespectrummatching	proteomiqon_peptidespectrummatching	Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html	Proteomics	proteomiqon_peptidespectrummatching	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	0.0.7	proteomiqon-peptidespectrummatching	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	686	True	False	False
+proteomiqon_proteininference	proteomiqon_proteininference	MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html	Proteomics	proteomiqon_proteininference	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	0.0.7	proteomiqon-proteininference	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	89	True	False	False
+proteomiqon_psmbasedquantification	proteomiqon_psmbasedquantification	The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.								To update	https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html	Proteomics	proteomiqon_psmbasedquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	0.0.8	proteomiqon-psmbasedquantification	0.0.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	604	True	False	False
+proteomiqon_psmstatistics	proteomiqon_psmstatistics	The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html	Proteomics	proteomiqon_psmstatistics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	0.0.8	proteomiqon-psmstatistics	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	694	True	False	False
+proteore_venn_diagram	proteore_venn_diagram	ProteoRE JVenn Diagram								To update		Proteomics	proteore_venn_diagram	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram	2021.06.08	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	True	False	False
+pseudogenome	pseudogenome	Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	pseudogenome	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+psm2sam	PSMtoSAM	PSM to SAM								To update	https://bioconductor.org/packages/release/bioc/html/proBAMr.html	Proteomics	psm_to_sam	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam	1.3.2.1	r-base				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+psm_validation	psmvalidator	Validate PSM from Ion Fragmentation								To update	https://github.com/galaxyproteomics/psm_fragments.git	Proteomics	psm_validation	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	1.0.3					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	20	True	False	False
+psy-maps	psy_maps	Visualization of regular geographical data on a map with psyplot								To update	https://github.com/Chilipp/psy-maps	Visualization, Climate Analysis	psy_maps	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	1.3.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	46	469	True	False	False
+pureclip	pureclip	PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data								To update	https://github.com/skrakau/PureCLIP	Sequence Analysis, RNA, CLIP-seq	pureclip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip	1.0.4	pureclip	1.3.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	1423	True	False	False
+purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	167	16800	True	False	False
+pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	350	21123	True	False	True
+pygenometracks	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	pygenometracks	pygenometracks		pyGenomeTracks	reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	Visualisation, Formatting	Model organisms, Imaging, Workflows	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	377	11332	True	False	True
+pyprophet	pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample	Semi-supervised learning and scoring of OpenSWATH results.								To update	https://github.com/PyProphet/pyprophet	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	2.1.4	pyprophet	2.2.5			0	5	6	0	0	5	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	6	6	0	33	2509	True	False	False
+pyscenic	pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn	PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/								To update		Transcriptomics, RNA, Sequence Analysis	suite_pyscenic	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic	0.12.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pysradb	pysradb_search	pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.	pysradb	pysradb		pysradb	Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	To update	https://github.com/saketkc/pysradb	Sequence Analysis	pysradb_search	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb	1.4.2	pysradb	2.2.1	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	26	144	True	False	False
+pyteomics	mztab2tsv	Tools using the pyteomics library	pyteomics	pyteomics		Pyteomics	Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.	Protein identification	Proteomics, Proteomics experiment	To update	https://pyteomics.readthedocs.io/en/latest/	Proteomics, Metabolomics	pyteomics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	4.4.1	pyteomics	4.7.4	Protein identification	Proteomics, Proteomics experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	81	True	False	False
+qiime_add_on	qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_add_on, qiime_core		qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	68	1909	True	False	True
+qiime_core	qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file	QIIME to perform microbial community analysis	qiime_core	qiime_core		qiime_core	QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	32	32	0	0	32	32	0	0	0	0	0	0	0	0	0	0	31	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	0	1155	28681	True	False	True
+qiime_extract_viz	qiime_extract_viz	Extract vizualization from QIIME artifacts								To update	http://www.qiime.org	Metagenomics	qiime_extract_viz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz	0.1.0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+qq_tools	qq_manhattan									To update	https://CRAN.R-project.org/package=qqman	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools	0.1.0	r-qqman	0.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+qualimap	qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq	Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.	qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	Up-to-date	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.3	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	1	4	4	4	1	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1	0	0	0	1	0	0	0	0	0	4	4	4	0	1328	664470	True	False	True
+quality_filter	qualityFilter	Filter nucleotides based on quality scores								To update		Sequence Analysis, Variant Analysis	quality_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter	1.0.1	bx-python	0.13.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+quantp	quantp	Correlation between protein and transcript abundance								To update		Proteomics	quantp	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp	1.1.2	r-data.table	1.11.6			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	230	True	False	False
+quantwiz_iq	quantwiz_iq	Isobaric Quantitation using QuantWiz-IQ								Up-to-date	https://sourceforge.net/projects/quantwiz/	Proteomics	quantwiz_iq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	2.0	quantwiz-iq	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	32	True	False	False
+quasitools	aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality	A collection of tools for analysing Viral Quasispecies								Up-to-date	https://github.com/phac-nml/quasitools	Sequence Analysis	quasitools	nml	https://github.com/phac-nml/quasitools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools	0.7.0	quasitools	0.7.0			0	12	0	12	0	12	0	12	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	3567	51567	True	False	True
+quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	True	False	True
+rRNA	meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+racon	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	309	21353	True	False	True
+ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	237	2833	True	False	False
+rapidnj	rapidnj	Galaxy wrapper for the RapidNJ tool	rapidnj	rapidnj		RapidNJ	A tool for fast canonical neighbor-joining tree construction.	Phylogenetic tree generation	Phylogeny	Up-to-date	https://birc.au.dk/software/rapidnj/	Phylogenetics	rapidnj	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj	2.3.2	rapidnj	2.3.2		Phylogeny	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	176	True	False	False
+rasusa	rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa		rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	2.0.0	rasusa	2.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	6902	True	False	False
+rawtools	rawtools	Raw Tools								To update	https://github.com/kevinkovalchik/RawTools	Proteomics	rawtools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools		rawtools	2.0.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	14	175	True	False	False
+raxml	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml		RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	Sequence analysis	Phylogenetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	383	6808	True	False	True
+rbpbench	rbpbench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs	rbpbench	rbpbench		RBPBench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	To update	https://github.com/michauhl/RBPBench	Sequence Analysis, RNA, CLIP-seq	rbpbench	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	0.8.1	rbpbench	1.0		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	36	True	False	False
+rcas	rcas	RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments								To update	https://github.com/BIMSBbioinfo/RCAS	RNA	rcas	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas	1.5.4	bioconductor-rcas	1.28.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	38	1226	True	False	False
+rcve	rcve1	Compute RCVE								To update		Sequence Analysis, Variant Analysis	rcve	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+read_it_and_keep	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep		read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	Filtering, Genome alignment	Pathology, Genomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	3370	True	False	True
+reago	reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+recentrifuge	recentrifuge	"""With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."""	Recentrifuge	Recentrifuge		Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.15.0	recentrifuge	1.15.0	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	48	331	True	False	True
+red	red	Red (REpeat Detector)	red	red		RED	This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	Up-to-date	https://github.com/BioinformaticsToolsmith/Red	Sequence Analysis	red	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/red	https://github.com/galaxyproject/tools-iuc/tree/main/tools/red	2018.09.10	red	2018.09.10	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	88	578	True	False	False
+refseq_masher	refseq_masher_contains, refseq_masher_matches	Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.								Up-to-date	https://github.com/phac-nml/refseq_masher	Sequence Analysis	refseq_masher	nml	https://github.com/phac-nml/refseq_masher	https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher	0.1.2	refseq_masher	0.1.2			2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	7	7	0	22	526	True	False	False
+remurna	remurna	remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation								To update	https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna	RNA	remurna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	1.0.0	remurna	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	42	True	False	False
+repeat_masker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.								To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	0.1.2	RepeatMasker	4.0.9_p2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	248	3750	True	False	False
+repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	True	False	True
+repeatmasker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.	repeatmasker	repeatmasker		RepeatMasker	A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).	Genome annotation	Sequence analysis, Sequence composition, complexity and repeats	To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker	4.1.5	repeatmasker	4.0.9_p2	Genome annotation	Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	248	3750	True	False	False
+repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	217	1177	True	False	False
+retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+revoluzer	revoluzer_crex, revoluzer_distmat	revoluzer wrappers	revoluzer	revoluzer		revoluzer	Various tools for genome rearrangement analysis. CREx, TreeREx, etc	Structural variation detection	Molecular evolution, Phylogeny	Up-to-date	https://gitlab.com/Bernt/revoluzer/	Phylogenetics	revoluzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer	0.1.6	revoluzer	0.1.6	Structural variation detection	Molecular evolution, Phylogeny	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+ribotaper	ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling	A method for defining traslated ORFs using Ribosome Profiling data.	ribotaper	ribotaper		RiboTaper	New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.	Gene expression profiling	Functional genomics	To update	https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/	RNA	ribotaper	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper	1.3.1a	ribotaper	1.3.1	Gene expression profiling	Functional genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	44	628	True	False	False
+ribowaltz	ribowaltz_process, ribowaltz_plot	Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data	riboWaltz	riboWaltz		riboWaltz	riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.		Computational biology	To update	https://github.com/LabTranslationalArchitectomics/riboWaltz	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz	1.2.0	ribowaltz	2.0		Computational biology	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	14	161	True	False	False
+rna_shapes	RNAshapes	Compute secondary structures of RNA								To update		RNA	rnashapes	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	3.3.0	@EXECUTABLE@				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	129	True	False	False
+rnabob	rbc_rnabob	Fast pattern searching for RNA structural motifs								To update	http://eddylab.org/software.html	RNA	rnabob	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	2.2.1.0	rnabob	2.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	164	True	False	False
+rnacode	rbc_rnacode	Analyze the protein coding potential in MSA								To update		RNA	rnacode	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	0.3.2	rnacode	0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	1358	True	False	False
+rnacommender	rbc_rnacommender	RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.								To update	https://github.com/gianlucacorrado/RNAcommender	RNA	rnacommender	rnateam	https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender	0.1.1	sam	3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	1074	True	False	False
+rnaformer	infer_rnaformer	RNAformer: RNA secondary structure prediction								To update	https://github.com/automl/RNAformer	RNA	rnaformer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	1.0.0	rnaformer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rnalien	RNAlien	RNAlien unsupervized RNA family model construction								To update	http://rna.tbi.univie.ac.at/rnalien/	RNA, Sequence Analysis	rnalien	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	1.3.6	rnalien	1.8.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	33	True	False	False
+rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	109	1110	True	False	False
+rnasnp	rnasnp	RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs								To update	http://rth.dk/resources/rnasnp/	RNA	rnasnp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp	1.2.0	rnasnp	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	86	True	False	False
+rnaz	rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window	RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.								Up-to-date	https://www.tbi.univie.ac.at/~wash/RNAz/	RNA	rnaz	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz	2.1.1	rnaz	2.1.1			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	28	43279	True	False	False
+roary	roary	Roary the pangenome pipeline	roary	roary		Roary	A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary	3.13.0	roary	3.13.0	Genome assembly	DNA, Genomics, Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	656	12225	True	False	True
+rsem	extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie	transcript quantification from RNA-Seq data								To update	https://github.com/deweylab/RSEM	Transcriptomics, RNA	rsem	artbio	https://github.com/artbio/tools-artbio/tree/master/tools/rsem	https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem		rsem	1.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	1	1	0	67	377	True	False	False
+rseqc	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	22	22	22	22	22	0	0	0	0	0	0	0	0	0	0	22	0	0	0	0	22	0	0	0	22	0	0	0	0	0	22	22	22	0	3206	133498	True	False	True
+ruvseq	ruvseq	Remove Unwanted Variation from RNA-Seq Data	ruvseq	ruvseq		RUVSeq	This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.	Differential gene expression analysis	Gene expression, RNA-seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	ruvseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq	1.26.0	bioconductor-ruvseq	1.36.0	Differential gene expression analysis	Gene expression	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	76	1236	True	False	False
+sailfish	sailfish	Sailfish is a tool for transcript quantification from RNA-seq data								To update	http://www.cs.cmu.edu/~ckingsf/software/sailfish/	Sequence Analysis, RNA	sailfish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	0.10.1.1	bzip2				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	55	4024	True	False	False
+salmon	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	2	3	1	2	2	3	1	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	2	0	0	0	0	0	3	3	3	0	969	61937	True	False	True
+salmon-kallisto-mtx-to-10x	_salmon_kallisto_mtx_to_10x	Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	salmon_kallisto_mtx_to_10x	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x	0.0.1+galaxy6	scipy				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	86	561	True	False	False
+salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	84	454	True	False	False
+sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	3765	True	False	False
+samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	1	296	4948	True	False	False
+samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1450	48426	True	False	False
+sarscov2formatter	sarscov2formatter	sarscov2formatter custom script								Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	173	True	False	True
+sarscov2summary	sarscov2summary	sarscov2summary custom script								To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	140	True	False	True
+sashimi_plot	sashimi_plot	Generates a sashimi plot from bam files.								To update	http://artbio.fr	RNA, Transcriptomics, Graphics, Visualization	sashimi_plot	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot	https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot	0.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+sc3	sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare	De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_sc3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3	1.8.0	sc3-scripts	0.0.6			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	9	True	False	False
+scanpy	anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data	scanpy-scripts, command-line wrapper scripts around Scanpy.								To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis, RNA	scanpy_scripts	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy	1.9.3	scanpy-scripts	1.9.301			27	27	27	0	27	27	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	13	0	2185	39356	True	False	False
+scater	scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results	De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scater	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater	1.10.0	scater-scripts	0.0.5			1	2	6	0	1	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	16	387	True	False	False
+scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Single Cell, Transcriptomics, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	77	1365	True	False	False
+schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization, Single Cell	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	16	0	23	779	True	False	False
+scikit-bio	scikit_bio_diversity_beta_diversity	scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics								Up-to-date	http://scikit-bio.org/	Sequence Analysis	scikit_bio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio	0.4.2	scikit-bio	0.4.2			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	True	False	False
+scmap	scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features	De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scmap	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap	1.6.4	scmap-cli	0.1.0			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	13	83	True	False	False
+scoary	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	scoary	scoary		Scoary	Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	61	676	True	False	True
+scpred	scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model	De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scpred	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred	1.0.2	scpred-cli	0.1.0			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	25	True	False	False
+sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+selectsequencesfrommsa	selectsequencesfrommsa	SelectSequences - selects representative entries from a multiple sequence alignment in clustal format								Up-to-date	https://github.com/eggzilla/SelectSequences	RNA, Sequence Analysis	selectsequencesfrommsa	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	1.0.5	selectsequencesfrommsa	1.0.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	27	457	True	False	False
+semibin	semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	semibin	semibin		SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	0	0	6	1	0	0	6	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	39	542	True	False	True
+seq2hla	seq2hla	Precision HLA typing and expression from RNAseq data	seq2hla	seq2hla		Seq2HLA	seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	Up-to-date	https://github.com/TRON-Bioinformatics/seq2HLA	Sequence Analysis	seq2hla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla	2.3	seq2hla	2.3	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	288	True	False	False
+seq_composition	seq_composition	Sequence composition								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	Sequence Analysis	seq_composition	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	0.0.5	biopython	1.70			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	71	874	True	False	False
+seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	306	25302	True	False	False
+seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	82	3784	True	False	False
+seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	True	False	False
+seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+seqcomplexity	seqcomplexity	Sequence complexity for raw reads								Up-to-date	https://github.com/stevenweaver/seqcomplexity	Sequence Analysis		iuc	https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity	0.1.2	seqcomplexity	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	16	68	True	False	False
+seqkit	seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit		seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	Up-to-date	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.8.2	seqkit	2.8.2	DNA transcription, Sequence trimming, DNA translation	Database management, Sequence analysis	0	2	5	3	0	2	5	3	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	129	1964	True	False	True
+seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+seqsero2	seqsero2	Salmonella serotype prediction from genome sequencing data	seqsero2	seqsero2		SeqSero2	"rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)"	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	True	False	True
+seqtk	seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq	Toolkit for processing sequences in FASTA/Q formats	seqtk	seqtk		seqtk	A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.	Data handling, Sequence file editing	Data management	Up-to-date	https://github.com/lh3/seqtk	Sequence Analysis	seqtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk	1.4	seqtk	1.4	Data handling, Sequence file editing		15	15	15	15	15	15	15	15	0	0	0	0	0	0	0	0	0	0	14	0	14	0	0	14	0	0	0	15	0	0	0	0	0	14	14	14	14	753	59668	True	False	False
+seqtk_nml	seqtk_nml_sample	Tool to downsample fastq reads								To update	https://github.com/lh3/seqtk	Sequence Analysis	seqtk_nml	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml	1.0.1	seqtk	1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+seqwish	seqwish	Alignment to variation graph inducer								To update	https://github.com/ekg/seqwish	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish	0.7.5	seqwish	0.7.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	271	True	False	False
+seurat	seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features	De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	Transcriptomics, RNA, Statistics, Sequence Analysis	suite_seurat	ebi-gxa		https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat	4.0.0	seurat-scripts	4.4.0			14	14	14	11	14	14	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	0	0	0	0	0	0	0	181	1966	True	False	False
+seurat	seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension	Seurat - R toolkit for single cell genomics								To update	https://satijalab.org/seurat/	Single Cell, Transcriptomics, Sequence Analysis	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	5.0	r-seurat	3.0.2			1	1	7	1	1	1	7	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	154	763	True	False	False
+shorah	shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	shorah	shorah		ShoRAH	Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	To update	https://github.com/cbg-ethz/shorah/blob/master/README.md	Sequence Analysis	shorah_amplicon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah	1.1.3	shorah	1.99.2	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+short_reads_figure_high_quality_length	hist_high_quality_score	Histogram of high quality score reads								To update		Sequence Analysis, Graphics	short_reads_figure_high_quality_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length	1.0.0	rpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+short_reads_figure_score	quality_score_distribution	Build base quality distribution								To update		Sequence Analysis, Graphics	short_reads_figure_score	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score	1.0.2	fontconfig				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	163	True	False	False
+shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1008	41600	True	False	True
+sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	269	14982	True	False	False
+sina	sina	SINA reference based multiple sequence alignment	sina	sina		SINA	Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	Up-to-date	https://sina.readthedocs.io/en/latest/	Sequence Analysis	sina	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina	1.7.2	sina	1.7.2	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	42	1128	True	False	False
+sistr_cmd	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	133	2489	True	False	True
+sixgill	sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge	Six-frame Genome-Inferred Libraries for LC-MS/MS								Up-to-date		Proteomics, MetaProteomics	sixgill	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	0.2.4	sixgill	0.2.4			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	24	293	True	False	False
+slamdunk	alleyoop, slamdunk	Slamdunk maps and quantifies SLAMseq reads								Up-to-date	http://t-neumann.github.io/slamdunk	RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers	slamdunk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk	0.4.3	slamdunk	0.4.3			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	2	361	True	False	False
+sleuth	sleuth	Sleuth is a program for differential analysis of RNA-Seq data.	sleuth	sleuth		sleuth	A statistical model and software application for RNA-seq differential expression analysis.	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	RNA-seq, Gene expression, Statistics and probability	Up-to-date	https://github.com/pachterlab/sleuth	Transcriptomics, RNA, Statistics	sleuth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth	0.30.1	r-sleuth	0.30.1	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	64	True	False	False
+small_rna_clusters	small_rna_clusters	clusters small rna reads in alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_clusters	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters	1.3.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+small_rna_maps	small_rna_maps	Generates small read maps from alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_maps	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps	3.1.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+small_rna_signatures	overlapping_reads, signature	Computes the tendency of small RNAs to overlap with each other.								To update	http://artbio.fr	RNA	small_rna_signatures	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures	3.4.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+smallgenomeutilities	smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe		V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.1	smallgenomeutilities	0.4.1	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	121	True	False	True
+smalt	smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+smart_domains	smart_domains	SMART domains								To update	http://smart.embl.de/	Sequence Analysis	smart_domains	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	0.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	22	203	True	False	False
+snap	snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap		SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	Gene prediction	DNA polymorphism, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	133	1349	True	False	True
+sniffles	sniffles	Galaxy wrapper for sniffles	sniffles	sniffles		Sniffles	An algorithm for structural variation detection from third generation sequencing alignment.	Sequence analysis, Structural variation detection	DNA structural variation, Sequencing	Up-to-date	https://github.com/fritzsedlazeck/Sniffles	Sequence Analysis	sniffles	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles	2.4	sniffles	2.4	Sequence analysis, Structural variation detection	Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	58	919	True	False	False
+snipit	snipit	Summarise snps relative to a reference sequence	snipit	snipit		snipit	Summarise snps relative to a reference sequence	Base position variability plotting	Virology	Up-to-date	https://github.com/aineniamh/snipit	Variant Analysis, Sequence Analysis	snipit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	1.2	snipit	1.2	Base position variability plotting	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	22	669	True	False	False
+snippy	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy		snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	Phylogenetic tree visualisation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	0	1372	105708	True	False	True
+snv_matrix	snvmatrix	Generate matrix of SNV distances								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	snv_matrix	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+socru	socru	Order and orientation of complete bacterial genomes								To update	https://github.com/quadram-institute-bioscience/socru	Sequence Analysis	socru	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru	https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru	2.1.7	socru	2.2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13	621	True	False	False
+sonneityping	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping		sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	True	False	True
+sortmerna	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	376	18183	True	False	True
+spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	3	9	3	0	3547	72953	True	False	True
+spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	34	446	True	False	False
+spapros	spapros_evaluation, spapros_selection	Select and evaluate probe sets for targeted spatial transcriptomics.								Up-to-date	https://github.com/theislab/spapros	Single Cell, Transcriptomics, Sequence Analysis	spapros	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros	0.1.5	spapros	0.1.5			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spatyper	spatyper	Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.								Up-to-date	https://github.com/HCGB-IGTP/spaTyper	Sequence Analysis	spatyper	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	0.3.3	spatyper	0.3.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+spectrast2spectrast_irt	gp_spectrast2spectrast_irt	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2spectrast_irt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+spectrast2tsv	gp_spectrast2tsv	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2tsv	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	56	769	True	False	False
+spolpred	spolpred	A program for predicting the spoligotype from raw sequence reads								To update		Sequence Analysis	spolpred	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred	1.0.1	spolpred				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+spotyping	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping		SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	1278	True	False	True
+sr_bowtie	bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+sr_bowtie_dataset_annotation	sr_bowtie_dataset_annotation	Maps iteratively small RNA sequencing datasets to reference sequences.								To update	http://artbio.fr	RNA	sr_bowtie_dataset_annotation	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation	2.8	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	7	4	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	21	225	True	False	False
+srst2	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2		srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.21	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	205	True	False	True
+srst2	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	205	True	False	True
+sshmm	sshmm	ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data								Up-to-date	https://github.molgen.mpg.de/heller/ssHMM	Sequence Analysis, RNA	sshmm	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm	1.0.7	sshmm	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	223	True	False	False
+stacks	stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq	stacks	stacks		Stacks	Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.	Data handling	Mapping, Population genetics	To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis	stacks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks		stacks	2.65	Data handling	Mapping, Population genetics	0	13	13	12	0	13	13	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	13	13	0	152	11635	True	False	False
+stacks2	stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq								To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2	2.55	stacks	2.65			0	12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	0	238	7292	True	False	False
+star_fusion	star_fusion	STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR								To update	https://github.com/STAR-Fusion/STAR-Fusion	Sequence Analysis, Transcriptomics	star_fusion	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion	https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion	0.5.4-3+galaxy1	star-fusion	1.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	35	1212	True	False	False
+staramr	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	889	12673	True	False	True
+stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	10	325	True	False	False
+stringmlst	stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+structure	structure	for using multi-locus genotype data to investigate population structure.	structure	structure		Structure	The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Genetic variation analysis	Population genetics	Up-to-date	https://web.stanford.edu/group/pritchardlab/structure.html	Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	Genetic variation analysis	Population genetics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	59	2623	True	False	True
+structureharvester	structureharvester	for parsing STRUCTURE outputs and for performing the Evanno method								Up-to-date	http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/	Phylogenetics, Variant Analysis	structureharvester	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester	0.6.94	structureharvester	0.6.94			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+substitution_rates	subRate1	Estimate substitution rates for non-coding regions								To update		Sequence Analysis, Variant Analysis	substitution_rates	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+substitutions	substitutions1	Fetch substitutions from pairwise alignments								To update		Sequence Analysis, Variant Analysis	substitutions	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+suite_qiime2__alignment	qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	13	True	False	True
+suite_qiime2__composition	qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.5.0+q2galaxy.2024.5.0					4	4	4	2	4	4	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	2	5	True	False	True
+suite_qiime2__cutadapt	qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	5	67	True	False	True
+suite_qiime2__dada2	qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	31	202	True	False	True
+suite_qiime2__deblur	qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	9	73	True	False	True
+suite_qiime2__demux	qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	26	114	True	False	True
+suite_qiime2__diversity	qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.5.0+q2galaxy.2024.5.0					21	21	22	21	21	21	22	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	0	43	168	True	False	True
+suite_qiime2__diversity_lib	qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	4	4	True	False	True
+suite_qiime2__emperor	qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	2	6	True	False	True
+suite_qiime2__feature_classifier	qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.5.0+q2galaxy.2024.5.0					10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	48	263	True	False	True
+suite_qiime2__feature_table	qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.5.0+q2galaxy.2024.5.0					17	17	17	17	17	17	17	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	59	213	True	False	True
+suite_qiime2__fragment_insertion	qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	20	True	False	True
+suite_qiime2__longitudinal	qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.5.0+q2galaxy.2024.5.0					11	11	11	11	11	11	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	0	6	14	True	False	True
+suite_qiime2__metadata	qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	40	232	True	False	True
+suite_qiime2__phylogeny	qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	12	37	True	False	True
+suite_qiime2__quality_control	qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	True	False	True
+suite_qiime2__quality_filter	qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.5.0+q2galaxy.2024.5.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	13	True	False	True
+suite_qiime2__rescript	qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.5.0+q2galaxy.2024.5.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+suite_qiime2__sample_classifier	qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.5.0+q2galaxy.2024.5.0					15	15	15	15	15	15	15	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	0	0	1	1	True	False	True
+suite_qiime2__taxa	qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	22	172	True	False	True
+suite_qiime2__vsearch	qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.5.0+q2galaxy.2024.5.0					8	8	8	7	8	8	8	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	8	16	True	False	True
+suite_qiime2_core										To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+suite_qiime2_core__tools	qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.5.0+dist.he540b0b0					2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	124	7087	True	False	True
+suite_snvphyl		SNVPhyl suite defining all dependencies for SNVPhyl								To update		Sequence Analysis	suite_snvphyl_1_2_3	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+syndiva	syndiva	SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.								To update		Proteomics	syndiva	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA	https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva	1.0	clustalo	1.2.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	30	True	False	False
+t2ps	Draw_phylogram	Draw phylogeny	t2ps	t2ps		Draw phylogeny	"""Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper"	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	31	457	True	False	True
+t2t_report	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	26	947	True	False	True
+t_coffee	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	70	8690	True	False	True
+tapscan	tapscan_classify	Search for transcription associated proteins (TAPs)								To update	https://plantcode.cup.uni-freiburg.de/tapscan/	Proteomics	tapscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	4.76+galaxy0	hmmer	3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+targetfinder	targetfinder	Plant small RNA target prediction tool								Up-to-date	https://github.com/carringtonlab/TargetFinder.git	RNA	targetfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder	1.7	targetfinder	1.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	37	713	True	False	False
+tasmanian_mismatch	tasmanian_mismatch	Analysis of positional mismatches								Up-to-date	https://github.com/nebiolabs/tasmanian-mismatch	Sequence Analysis	tasmanian_mismatch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch	1.0.7	tasmanian-mismatch	1.0.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+taxonkit	name2taxid, profile2cami	TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit	taxonkit	taxonkit		TaxonKit	TaxonKit is a practical and efficient NCBI taxonomy toolkit.	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	Up-to-date	https://bioinf.shenwei.me/taxonkit/	Metagenomics	taxonkit	iuc	https://github.com/shenwei356/taxonkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit	0.17.0	taxonkit	0.17.0	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	1801	27426	True	False	True
+taxpasta	taxpasta	standardise taxonomic profiles	taxpasta	taxpasta		taxpasta	TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table.	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	Up-to-date	https://taxpasta.readthedocs.io/en/latest/	Sequence Analysis	taxpasta	iuc	https://github.com/taxprofiler/taxpasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta	0.7.0	taxpasta	0.7.0	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+tb-profiler	tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	6.2.1	tb-profiler	6.3.0	Antimicrobial resistance prediction		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	198	5161	True	False	True
+tbl2gff3	tbl2gff3	Table to GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	Convert Formats, Sequence Analysis	tbl2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3	1.2	bcbiogff	0.6.6			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	229	1584	True	False	False
+te_finder	te_finder	Transposable element insertions finder	tefinder	tefinder		TEfinder	A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	To update	https://github.com/VistaSohrab/TEfinder	Sequence Analysis	te_finder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder	1.0.1	samtools	1.21	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	81	True	False	False
+telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+tetoolkit	tetoolkit_tetranscripts	The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.								Up-to-date	http://hammelllab.labsites.cshl.edu/software/	Sequence Analysis	tetoolkit	iuc	https://github.com/mhammell-laboratory/TEtranscripts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit	2.2.3	tetranscripts	2.2.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33	871	True	False	False
+tetyper	tetyper	Type a specific transposable element (TE) of interest from paired-end sequencing data.								Up-to-date	https://github.com/aesheppard/TETyper	Sequence Analysis	tetyper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper	1.1	tetyper	1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8	69	True	False	False
+tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	460	True	False	False
+tiara	tiara	Tool for identification of eukaryotic sequences in the metagenomic datasets.	Tiara	Tiara		TIARA	Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).	Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism, DNA structural variation	To update	https://github.com/ibe-uw/tiara	Metagenomics, Sequence Analysis	tiara	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	1.0.3	tiara		Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+tn93	tn93_readreduce, tn93, tn93_cluster, tn93_filter	Compute distances between sequences								Up-to-date	https://github.com/veg/tn93/	Sequence Analysis	tn93	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93	1.0.14	tn93	1.0.14			4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	4	0	0	17	1881	True	False	False
+tooldistillator	tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator		ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.9.1	tooldistillator	0.9.1	Parsing	Microbiology, Bioinformatics, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+tophat	tophat	Tophat for Illumina								To update		RNA, Next Gen Mappers	tophat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat	1.5.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	True	False	False
+tophat2	tophat2	Tophat - fast splice junction mapper for RNA-Seq reads								To update	http://ccb.jhu.edu/software/tophat/index.shtml	RNA, Next Gen Mappers	tophat2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2	2.1.1	bowtie2	2.5.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	1	1	1	0	312	24167	True	False	False
+transdecoder	transdecoder	TransDecoder finds coding regions within transcripts	TransDecoder	TransDecoder		TransDecoder	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	To update	https://transdecoder.github.io/	Transcriptomics, RNA	transdecoder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder	5.5.0	transdecoder	5.7.1	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	348	5468	True	False	False
+transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	0	84	907	True	False	True
+translate_bed	translate_bed	Translate BED transcript CDS or cDNA in 3 frames								To update	http://rest.ensembl.org/	Proteomics	translate_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	0.1.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	49	643	True	False	False
+translate_bed_sequences	translate_bed_sequences	Perform 3 frame translation of BED file augmented with a sequence column								To update		Proteomics	translate_bed_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	57	True	False	False
+transtermhp	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	transtermhp	transtermhp		TransTermHP	TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	229	True	False	True
+trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	2334	238699	True	False	True
+trinity	trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats	Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq	trinity	trinity		Trinity	Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.	Transcriptome assembly	Transcriptomics, Gene expression, Gene transcripts	To update	https://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity	2.15.1	trinity	2.15.2	Transcriptome assembly	Transcriptomics, Gene transcripts	9	13	13	13	9	13	13	13	0	0	0	0	0	0	0	0	0	0	1	2	1	0	0	0	0	0	0	11	0	0	1	0	0	11	13	12	0	1762	31951	True	False	False
+trinotate	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	trinotate	trinotate		Trinotate	Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.	Gene functional annotation	Gene expression, Transcriptomics	To update	https://trinotate.github.io/	Transcriptomics, RNA	trinotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate	3.2.2	trinotate	4.0.2	Gene functional annotation	Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	151	1796	True	False	False
+trna_prediction	aragorn_trna, trnascan	Aragorn predicts tRNA and tmRNA in nucleotide sequences.								To update	http://mbioserv2.mbioekol.lu.se/ARAGORN/	RNA	trna_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	0.6	aragorn	1.2.41			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	0	236	2935	True	False	False
+trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942	True	False	True
+tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	Up-to-date	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.5	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	True	False	False
+ucsc_axtchain	ucsc_axtchain	Chain together genome alignments	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_axtchain	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain	469	ucsc-axtchain	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_blat	ucsc_blat	Standalone blat sequence search command line tool	blat	blat		BLAT	Fast, accurate spliced alignment of DNA sequences.	Sequence alignment	Sequence analysis	Up-to-date	http://genome.ucsc.edu/goldenPath/help/blatSpec.html	Sequence Analysis	ucsc_blat	yating-l	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat	469	ucsc-blat	469	Sequence alignment	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+ucsc_chainnet	ucsc_chainnet	Make alignment nets out of chains	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainnet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	469	ucsc-chainnet	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_chainprenet	ucsc_chainprenet	Remove chains that don't have a chance of being netted	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainprenet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet	469	ucsc-chainprenet	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_chainsort	ucsc_chainsort	Sort chains. By default sorts by score.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainsort	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort	469	ucsc-chainsort	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_custom_track	build_ucsc_custom_track_1	Build custom track for UCSC genome browser								To update		Sequence Analysis	ucsc_custom_track	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	45	394	True	False	False
+ucsc_netfilter	ucsc_netfilter	Filter out parts of net	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netfilter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter	469	ucsc-netfilter	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_netsyntenic	ucsc_netsyntenic	Add synteny info to a net dataset	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netsyntenic	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic	469	ucsc-netsyntenic	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	Up-to-date	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics, Single Cell		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.5	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	3	5	5	0	379	61618	True	False	False
+unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1558	65732	True	False	True
+unipept	unipept	Unipept retrieves metaproteomics information	unipept	unipept		Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	115	5005	True	False	True
+uniprot_rest_interface	uniprot	UniProt ID mapping and sequence retrieval								To update	https://github.com/jdrudolph/uniprot	Proteomics, Sequence Analysis	uniprot_rest_interface	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	0.6	requests				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	132	2406	True	False	False
+uniprotxml_downloader	uniprotxml_downloader	Download UniProt proteome in XML or fasta format								To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	79	1360	True	False	True
+usher	usher_matutils, usher	UShER toolkit wrappers	usher	usher		usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Cladistics, Genotype and phenotype, Phylogenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	1060	True	False	True
+valet	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20	637	True	False	True
+validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	25	86	True	False	False
+vapor	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor		VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	94	3164	True	False	True
+varvamp	varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp		varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology, Probes and primers	To update	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.1	PCR primer design	Virology, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+vcf2snvalignment	vcf2snvalignment	Generates multiple alignment of variant calls								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	vcf2snvalignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+vegan	vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	74	2020	True	False	True
+velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	2083	25420	True	False	True
+velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	4741	True	False	True
+venn_list	venn_list	Draw Venn Diagram (PDF) from lists, FASTA files, etc								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	Graphics, Sequence Analysis, Visualization	venn_list	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	0.1.2	galaxy_sequence_utils	1.1.5			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	248	5067	True	False	False
+verify_map	verify_map	Checks the mapping quality of all BAM(s)								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	verify_map	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	22	True	False	False
+vg	vg_convert, vg_deconstruct, vg_view	Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods								To update	https://github.com/vgteam/vg	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg	1.23.0	vg	1.59.0			0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	3	477	True	False	False
+vibrant	vibrant	Virus Identification By iteRative ANnoTation	VIBRANT	VIBRANT		VIBRANT	Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	Up-to-date	https://github.com/AnantharamanLab/VIBRANT	Metagenomics	vibrant	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant	1.2.1	vibrant	1.2.1	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+vienna_rna	viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup	ViennaRNA - Prediction and comparison of RNA secondary structures								To update	http://www.tbi.univie.ac.at/RNA/	RNA	viennarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	2.2.10	viennarna	2.6.4			0	0	21	0	0	0	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	21	0	123	7864	True	False	False
+vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	351	12203	True	False	False
+virAnnot	virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers	virannot	virannot		virAnnot	"VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy."	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.1.0+galaxy0	biopython	1.70	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+virheat	virheat	generates a heatmap of allele frequencies from vcf files	virheat	virheat		virHEAT	VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists.  The tool provides a condensed look at variant frequencies after mapping  raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time.			Up-to-date	https://github.com/jonas-fuchs/virHEAT	Visualization, Variant Analysis	virheat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat	0.7.1	virheat	0.7.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+virsorter	virsorter	VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.	virsorter	virsorter		virsorter	Identify DNA and RNA virus sequences.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/jiarong/VirSorter2/	Metagenomics	virsorter	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter	2.2.4	virsorter	2.2.4	Taxonomic classification	Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+volcanoplot	volcanoplot	Tool to create a Volcano Plot								To update	https://ggplot2.tidyverse.org/	Visualization, Transcriptomics, Statistics	volcanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot	0.0.6	r-ggplot2	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1749	30946	True	False	False
+vsearch	vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	vsearch	vsearch		VSEARCH	High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.29.0	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	8	8	8	8	8	8	8	8	0	0	0	0	0	0	0	0	0	0	0	8	8	0	0	0	0	0	0	8	0	0	0	0	0	8	8	8	0	182	8507	True	False	True
+vsnp	vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics	The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.								To update	https://github.com/USDA-VS/vSNP	Sequence Analysis	vsnp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp	3.0.6	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+vt	vt_@BINARY@, vt_@BINARY@	A tool set for short variant discovery in genetic sequence data.								To update		Sequence Analysis, Variant Analysis	vt	bgruening	https://github.com/atks/vt	https://github.com/bgruening/galaxytools/tree/master/tools/vt	0.2	vt	2015.11.10			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+wade	wade	identify regions of interest								To update	https://github.com/phac-nml/wade	Sequence Analysis	wade	nml	https://github.com/phac-nml/wade	https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade	0.2.5+galaxy1	wade	0.2.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+weather_app	simple_weather	provides simple weather in text format								To update	http://wttr.in/	Visualization, Web Services	simpleweather	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app	0.1.2	curl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+weightedaverage	wtavg	Assign weighted-average of the values of features overlapping an interval								To update		Sequence Analysis, Variant Analysis	weightedaverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage	https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage	1.0.1	galaxy-ops	1.1.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+windowmasker	windowmasker_mkcounts, windowmasker_ustat	Identify repetitive regions using WindowMasker								To update	https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/	Sequence Analysis	windowmasker	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker	1.0	blast	2.16.0			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	85	True	False	False
+windowsplitter	winSplitter	Make windows								To update		Sequence Analysis, Variant Analysis	windowsplitter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	True	False	False
+wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660	True	False	True
+xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	5	5	2	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	175	5876	True	False	False
+xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	64	344	True	False	False
+zeiss_lmd_converter	ZeissLMDconverter	Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	2.0.4	shapely				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
diff --git a/communities/microgalaxy/resources/tools_wordcloud.png b/communities/microgalaxy/resources/tools_wordcloud.png
index ec4ceee2df2db52e0f4a9f15157d030778d22d3b..6e436d5c71e86e6c366ed475a07827ebbba7b2ef 100644
GIT binary patch
literal 324410
zcmce-g<F(c)He)>l$3yiFqG0F(jC$aDWP<CcXtRP-3`LPAOeFhgmei*hbY6)9a7Q_
z@2%&Y?|Yv24|uO@xEO|+ec!Y9+H3t{?daF4@&tI4cxY&71YiXj4K%d-WN2vU$2eHP
zE6TftzQ8Xb4_O@#O=l|)Z&No*G!;`17YAn#2U{~bFH1LfTW2R84j~S1b~+mm4;Odg
zmoFXvzc+9=yIH@aSG|V<2Elbv&~-;cBQpK-gZ@dP)D{gL4Gk<KspXTqb7P%oXq!Fd
zeY>zS+Bjb<puiA-&a&TB-dga4&^l6@`xCY8lT;$v*M%nE_Sk9*yv)Om9~I)j!jcti
z8Sm$PqG$au%q2D_HZh+nz~Vzkx>ePHXun#TRYtq7`RNz;r(b8}?=W1BW>@z5a|A~N
zV-qzL$z;|4=YuBX)OA0kh~>lococxxK7RUNuMFJNM3?=)KA4He!uCHu_2IBX>y`Td
z8ax#nit*upy{AZ&^U-Uq|9JysYoTQ!MgQaK!25}m?~^_HUzhVW`G0#$PiW5w|C<3?
z`Qz?Hsv8d1Z0?-rXo-qocTp*FN<O3|NL~TAJdN#!&cuD}nKMd(VJ2MMcaX_hPl3TS
zd5q{DUV3=RcJ1{;(_~^MR-p+7XI)U$<aoq+W`fb*X<AE>{qK9GCgc?`@ZLP6x}j0e
zUZ!Mn%_d>MZSF>oggz|A4QG*2>^G~Hd5N#H?^*Vhqb${6ulCav2Om=UDeiJ+x`frV
z(r@LI@;rVBOIL#VK)m$ak>K01P+|pEuqK!dZrsE~obt*%TQT`~62VZ0DWpq?DfKG3
zFDC&vF~t&%SB3N9StN{}@f-L<;R9ZkM+B^Y*6gsq=)c7qKsZ?oE+Pab&kqmT;Eke@
z(1YoDesX<+wxDyCZkAPlWR*sZqZ_oR$16ph?4eTsa}oV-wgbu>Y7+Q17v_iQvYj<T
zJbZ(x+om>@8PhL#>4Dp2P{CbZHM!F0ikl;xD;#yQ?=Wap5ZVt3k+bfrt9%?~RqhiH
zPF55S=V~n+UDkSn;Qyi$UYEx|7drY~`3XHHIQjdpI0emqhq_n9JrS;5sAujG>RtNU
z4MI&i)=hfn6r(MFqiVpv^#A`Js^l0-g9FKu8a33*yt1TW^%A`a<{m1qy$tZuduE2k
z4xv2`9BRn3C$jWqshLgj=9vl%7%l|&2FJ!_(q(a!6?5+&QePz&Cvz%N#NJzGpifF}
zoeW_BXO%r>S$Bva-r4cu!jIEqmAB^XJ@))8o4^1DYk(m<GDu!t6_ZU$Xl2To!*Y-!
z@qG_0^CFf`BJ<?qJpaPKp?3IN^W@Rr-7=e&dKhm^`^`_>hIYLv*iaOIV~h_U+6vmB
z^uP8okK1k~3<9O_yqLG!aV?pEIy8eg-Uu4Nev@x&qbQCAdH9A4HL{vAo+*>yr2|i&
zXby(GuZKa@o<?JYGGS(q5lgwqZ^$H_I2?E5(ARXVysHyiW>{;Sh!PYvhG_i$T8*UN
z*AWeJ2$i$$ST~BIi{&J^H_DHi+OGMzGfs8+Ls5uu_^nPhtLBghovC}(pjWvX8{=X8
z7wA6|-mRu^Qsw-2|L&PhQH{^<CcWJF0wVQJ&O0&k%(-`&hyG5HW{}@ibUUze!>Bm5
z*!9C0W;RUxd7uRF2N*8|YEQelef05K(2O|p9E|^Jye4`gl|==7c14UQ*;zBj7pJt#
zbbrvQ@OAMvb_7@|l}Ru%v~oKoRxYl^()9gK(-ai}^Y%de=nuYMuqfg%-ZTT0!}qNO
zl${5w4`F)A1T7X0Jtsk2quxV$OmgR)BzJbV_#PwXK@+m<SIC<A_j8>T6F>T!`4Q>R
zPh<wbI=T{%(_&q3)3$|f>jbQAnWr9cz#M~CH}wD6$=ZdA`F}H3WBFLZChz5DBw@%}
zrf%70Pz87%Uj~dDS(3t(%%D1UTrsOT!FR3xs)4JcRvFU-CHMFXNumrcjw^Ajq{|oa
zL<R6^T{C85acZ9y2?F<Kl6a7-+VH^yH{mH)Jjr(kF+nUe!}i8J2Z<UD9acuy%#T|b
z^t`-cR7La?yo0lYw<3b|f<u@4wpY@8n8p1svVu|)9NuANL+N>4dG5Km8F)XKox2QR
zW$b6rvC9+&=O#m0r;Bsn+F)c2goi#w{laW2oICMxg3(&Afs+|#1n4&#qHxfiIy*Vz
zc0>asK;7Ra2^dn2@Za};Nxe~P?^)#vnK;P`-*{^%AcCD@$xF{N?d@dFAAD!@4hmb+
z!76D9C#K|nr`Tx;lJSTVPm_vud;(0KE!&g(5AToCtCB<py)U$<Xp&>2R+dJ<RU8I8
zX76aY3EW`C5_n?~AKwm`ehOv(yDb7R{;L$;e7~+7jO|VIuxzvM?<*@IzTg)RVYrzR
zkJ}UCgum~3#)I!~?&Vy|^7Fx0p_~DaBuVRUrzcqP)=A%3!MSEaSU8>YagQU*R#qJp
ze~M<q#_b8Bi!vELfHk9c^?q0ldM_YC)$B_Lz3(nYbws(l3rXGC3o;S41m6WMtt&e}
z@<6!_hcJ8;KGb0}!MHZ#IF;{BaC17Q9B`T({i1o79F+rS)pD1S9Qq=_g!eR=K^B@U
z#VFslQ|;?WR9vhxyz<CUS;>0r3Ca1xP8J3gcu2_>C7Gg-n{38df<j6vZ_?B}!}$fF
zhGLkj45&xORN1~cW;b)FN_Ap-k8>xXKSOjjR~oj;y>lfK6ah?=2f^HrGUZ3O*T3Ue
zz@%WZ-UvyVP5IjTW}o}m%+^OY64ydaFxSgQ$PmqE&Ch|N;Zm5h>L0E@UL?0G+Nk2_
zWS3b;&i31vM(0RQIUK_Iv*tzL<zlv+Wtftj&yEJq679`TH@kA;*__FPbSpFmgfiJ6
zZ~sJosv66`^?WVAI5qZC+%@$}>!gWQS?{q~niE8=UCd(T7l+Y&&oByeC6V*}dq~7!
zRi&vA(`e8Qy8<{H3anFacZdmSY26WD(|U@E^zz{?%j%Dba-I189_=b?N%27wXShmX
zGDK(CoZ^z2ao9GSL>?E?rbgDQOJ<$Sx|x7cM8`yd-Esj}BD42h*M{n}f05;k-}H_g
zqRlt+vixuoqkj%bGy#1_?V|tg<B{L2zpOBv>K&XZE-S7^L3M^TKd<42X9~umT51Lh
zHIK;3edmJ??CR$@#aVVw5%fw3D_tN4E_)n#4bA-uKeQk?;~7-9_^)^ygloN<$p(bF
zIxKdtA9vqont*D8Tyx4U@XAXwbVS<wKkctP0?7pyjCYiZYs*dW6>+xh`Xn=0{-A}s
z`bKpSv8K9D!NA!JvDoNPOOS<Q5NI#G`r_jnvfVDLUa(K=e)WR+L3&6L6LSXgMZz3D
z&3wSlEh5>nk4Cp*MP(pYBL2|rZ=OvxPWu;*xfyrQzYmhHflq#OeX;)b*YS*WJ#6=2
znrOs*Ct7-_Qh6x>LrP+BRpf4f&qHNpt17?$?bE`ACnT3#{#1@`ve+|qV;*s*P6?Ie
z%|jeNf8%jD-yPzul|5ba3q5*iSi-NpzN#7Za4%1c#F7oX6495Cs9}~Vj3Jp_9E+`M
zGD<7oatS$Nr_QtVD;)SKAYilax#caVlQPt9@9ap7^$-}Q?twlKDN(9J@P_gAU1KBD
z+uyuW9s2Dp%GJrG1}{0`1_;_q17CCMs?DNpVdvYOrz@r*%8WlzB-u<;M$YsR9}Ql*
zT*P^TkWha8whgpYUe&F=ldnNe;oBPmzSj>*Im6gpSa~H$N)3V><GK^rxq}5~&H#Wh
zP<9`fi)tW1?b@W;cDVSA8~-dvAso4Kt)z|HOP>&YKxUh5X(VSF0mb#uY|rvMqwlXl
zW4;Gwz($2+pB`W%od_7_Z>J2?n+M(Z<tKRAH8-X-sHKtn%@zL^zyGjnBQq<b^UX3h
zMkm}@LMgDVD~N(o+e7H~8y<p2LdLOvC`|yl)gXVIeebf8-f6_DJ;@{++Hx6ww5mh{
z+y?`4)Un3bGQ;czk%C=HY!ibjfOUp6;z-q~twfLEZmVqxrkmcWI2%edg|ta8{eNt*
z0rB4Z1s^MqemkRni~sU?T3W7^E3%9SZm?n<d`MY2N5h;is_a>h`O3N~Y8NGXxTDUF
zD5{$)Y(+vAD1kyCKf<y6$N;PL;mv7c>oEUl;EFl}C^fvntI6j+IRZYek|)i)!S&+a
z4E)InqUHF;9mp`sFSJ<Ry6+3Wg7Rzkp0dYFv`JO*Ee;nLGH4%vaR?vqK(E>)md6Dr
zn+Y+M<{JT1Fiwy+cY+0VoOKnwI)L?<!#5*)4-iDAnOGW%cxxb|PRpe}eCWjzRx@m`
z{v09U_pVMZLz4I~Yh^IkFn=YclrZ?y%*|Kd_-J#>8&-+iv9f<={^~!RH=D6*QPQlQ
zns(l+o}3o)i_)mGbI=+U**%}B9<00=rEB8C&F53Fg37Fy1oi4}l@>m{|B#OJ#l7wp
z-R}-UOc%*fD=6KMT;Tn_O;V|kRKl0VWWt2zayMMEn#}Pem%H>3$yc0&;FMIB*e68y
zlxI2)cKTms?PS>I*fjMieqp{L@idg)#9+{E?<$H}(Zhr!3M&4VN7t}o9JoS2sD!hb
zICmY`>TPp;?q?iySdURdwkXpbi>NM}t>C*7$l;j?$%tLOK3+zAGmmE?##h@(Wfr3N
zIN=rY5Zj#1CNIPR8UuqMj1MKxEaI&m2D9(uwfsRvi^(Lx9z+J8-*IzomUITW*nI9P
z^jnjjneUcD@@mb<{LK{N1pl(MRDTkw-?IWVjA_Zn0UHEGbiMtk;%FH<;%qFbL@4X-
z9L+6@Xy(&^=Z46O>wVFlk0Q%y?LIlEHQ_%AvH1&ul!*wF(|qHLdk3vrb5QWWbkB>+
zIr@T|VdnQ;nd@F>CYRNi*)!BeH=Q$o(t%gw$jnP4dSj2W(F|Q-VI}`61W;bpo_HZP
zn|gVS#iSRbQt}!brPs<ZexkTv2JOGNR`2-8V|LJo4<Gb2LUOp+gWgPF#@lmk;y>|-
z1O-_nmG%7c7rvwG%MeqQ2#(!$cK$xUYt^Yc`0@1tCwt!bUM6kum1WZ~didUZd1Jx&
z5RrIhJo8h2y_EjRhWtebVz7M`LhbJS4Nc$@W{kYmUbXgLoWU|sCGuZYgDIY1Fc%mx
z8lS#W%)jb|q;9_p->G9z#OcnILUn(^|8rr60mbx$T-~lO_`E8Rw%46*FFyPPrIkI6
zw_bTvv$%Au5y<^XYIGokFK(m#gr%+#PijK&bc&uh@umMxg}@UJxrSYH*lOWc*ywfd
z3I#NNjbaM+&S_Kh_JXvyj6p>sKG(2oP$;!DMyDRgvZ>qm*?1U1qgJ<lymgJ-JcFLe
zf|3)MPV=TtmLEp1*H=>Q-c>}LH$t$*POnX0kuZOA?V4R;&CMMqH5Qf4R^&B&U9mpy
znHRtsrOXJBmmUa@?%g*nx0M0HIk~&|m1<DRR>}0Ro7D_mn(%}23821RtB08W0?OjI
z;*F0hDA7yQ$~Sc>vfdvXgLJ?}FY8yTQ^@AVK8^J1Vy&-UWWx?t$!Y21&DaseT7$t1
z$jra{6Cjku{}Qp;H*Kp)FMY9ttCTYcZ+Co7sRyfab0s#JKWz!{EGpJvl;|y)G+qY0
zon|Ys@M<Jf=00E|^-vS9^ZT-M{mX;jhcOL1+{Eck-V2~~3tb$WCh9_qoPO!l_y5Xb
z{LUb&=rmIh$dlrD4_mS=OY3QEPPgP|)#zVC!z<z*X168_6Eb0aHN<DgRzIt)ddK3j
zZ_mH(zyzudV=e>UX;g-!>Mr#9Q;*InQmZt#^4Ih018C18xb{omZ4}HNz>`2l`Iys?
zsxjzr)j&fOlG1!sH^CbRN#IC<vfAdh*$2!2qg|{abN(&LhoKL{D)tw{Iqv8*17#l*
ziyo|+#*5bn%w+HyN>9{=hZMu+=Fik@yj7P28+JuMVe9f!L>UCEQL4@_T{w%Ww(S&B
z>3-QWOxSR078DxMrxtHj0QGvGS_UK_;O#*-(lmYl%yCh`;eQyJHq)Dm_b@1Z&UnO4
zx#N23Y@?OEd@C%Vzx&i-wk6zEX>31SkcO2JD98+8BE{<9NA16k(h`hPnIgbp5US1T
zRvsmRNW)9@juveI^E=#(%%HI{nr4qZxCcAU0df4ubaQY2ehX&ZiZJhW9iqegBt*lv
z(ORXc2xiyxD;$026b|X3)P%7OYySa?2{E6o{}G2S5~t#OfQ5SewzN!@T;g|szZ4Gi
z@#i59BrW@l=EaY`NLp|h1M~@g^!L@a!S=7-;lb`Vpq!MB<yQQa#0PU?x3~HdYf|24
z_fSatR{knp{&UDlL*oy}mi-e<*P$M#@b<Iy1VQA5$*Ia;jCv;jpUgtGMk<GK!?NmD
z)n738RpB|sg7<}WX~sof+64RRAlZ<}mCZkzRtx#(Ro#E69d&W43|Ntj8PipnjJa4N
zxtLr3Rfsq%*CbzP;WkBfq&cNc_E+bvGFrKvlc<ypJ7scr9D0R`R8!)IjJT$`%G_g_
z6>26=uwb?(l)}^ZQUyx6sjNu9ak(aw^m6rEbf~bwSBO(21)GR7Bjd}qzoth+acj?X
zZb3b`fZ~KNmCV4XI&pKswV54hyQ$L@Z=G{h`n&T=-;L+lXo6W+|8_Do+2T&;v;nf6
z85wD<i|PQ)>$7@iD;Dw6zc(uqWK>KJcgIBuO~`l!)%I_j*-)mJr6_=(YF;x43!cg-
z0*o!2u!(7m_!tr*17%1tCy{#1>F7~d_&_p~Nyav;;2Sm~T_KvD_b|o8<f*3Djrevr
zA$gO(sF8687d~jN<A=u(SYljIg`($S6Y;7FmD0p`&+s;nDxBL4>}7ZiNi+q`i_&V)
z>^KXfj8$yNl%LNm^w-gp;NGzG8I|^LTiOZ3Op~92L+Sd{ZO^4ivdnPea!pO`E<1^f
z=%Oj)mO6zs7+_Azn@p(eM#qInbp>HxQR~e2{TC|CqiGtz7ZU339mAYnokF;Nqr>Cm
zB?zTUVr?1&o{Vx5rEC6C8`t*!(<axblX=$$RAXXh2#i|X!k>%05PnuL!a0aRilLaV
zG{RrDDi%MYl~wiFcfF4!Emw(ef6jfb%3xu+{k-6oufB}OaOh~^j=4RdY`Zq<S=-H_
zFULNw?{+T-g!5^v*?>@nUgyg3GQP2(XXc8#W~ykEcTCbdS1Gu}>Pej=Y~Rx-FfiuS
zL>VGsMkWVj9$wxLFqLt4!B)=hr7bpNarcNK`xU+Y%JvmMc()&Xu)#PeXV<GB&Z|HW
zJmwj<rIEkl?x{MWb`U3@kfO**up)N<MGCm%q?8;f*xrax(iYgncWz^X!nocHz=aLh
zHXY)e#l3PB=X?0)XC%C%O#4n+3ERK6jI8Z4k=Ik=Ux#!Gie`Q`JO$wa_u(nnEZQwq
z_YE@WzVj{cw2NM1s!8gprm_m;Q7mf~Ves}UTv<ryL;7%g(<xI9goYqkA@kc*(@4Aj
z4y)B1hNe@#z>G)*!SuDwHf1(3MfS%fBHe*E=T!2vqZqcXeRp1KZ|Wn(>gB{DUHfvi
zSIaJ+$}4%kjp0M{>b=+IzJejKU|9Mj_B>eh)bg>LEVR|(&~JkF@ND!Z!WHzegw=QA
zse)6wTEfcvV84q;lq>YRCd!F&TI>nI8=Iuc&Ay*iy(+7Sgs)SSsyJh%!x)$p%v4iL
z&#!mbApPbW!XgH=wHFgq<fx;lA^-b9{%a54KH&S667;@Gpy7gC+xVFx{G*4!;YHUh
zn{lRoi9=&U>)RlbqhN#J6m?LNV!yGl2cEvbIdg_l;iK5iDDfZ?c<Rd||L4}32Y6&J
zutPE^sjeY0FRL{^nQUQ+tcbfiCG`YkRdImCbX5N)qUQfpbi#8<ncQL@*hxOmk3D(C
zek1s3U&1C)z~c=zEk$pvxof)R0lo0I)(Q;*>t*sp>O&%5<1dm3@KJlms9nPI5vq(S
zhclgp?XgXwC-PjTsdUV~8tTd4skS`i#qUWh%E4o-bt^`G>`}c|X3`Ci%(a|wto8Gd
zGdF6i@3%)bptcEYh!8TaQoQ}gR8bGX*_MNb^R@?daCz3*XPe9=7NFh=0g>y2a`Gvg
z6B`0KhkF0mutZbhWGG!ytTdRo2mhKlOVO+8o?qLjyL^U_s3GHi%ateR?|ZOa&-1l4
zPYx9fmsa&x-mBKAfNZ(!Q}9IUsYwI}rev<k=JdUjz*LRzPc9t1FRyo&DajkC9O|!T
zZM+U3nREj+=Rnq)U@x!bqev=FmezcfFVYmj)4$VFprtr@D*WfRHoN$MeKfUA08GXE
z<OmkknhNP8OY_rSbQO0Q;vR>(D~jy+K4~-PH(RN>{sRTi$V$@!K^336#(u@ZE-9Fd
z1fGjW_~=Ll=lg&#hNY8r{uPaHsX5GPsBIuAMa8@!B>(Jy-;9I#Qh;AjJs)c24|*|K
z%@?kvNK-xxPkjz7`od%U!6%QI2PX_@J#fD77?h+OO%wL=Ueik^e@T4KwV$>rFRl{&
zZO`Y`OZ=%LZ2Y2-nq9Zg+|n;Wq=TvCR02M=!t$0RuR(~1$V*4nH_)sTyiF<d-eFC5
zx7ZYxLApnjgBRQgB~6ETKLu7_c%Agm5o%1b(mB!5(Tc=@R96!BIwZ!TU3*W~06WGQ
zu>)aqi=!S;9K&pZ`y++o-t<`$-yib5Kl0Xk3)7t8cTB5ieu0pOixZ%zdW$YbUt++G
zLc8CwF%A|wH0oq$d%*rE(ED<K>tw3h3)VI2gk9{Cy^}h9+B?r|pXT6Mi0gY=nXmP@
zm)PFdWvLDh-c$AjU#ow1Ru4C0ks*S<J$Ig8tc=k&Fm&eRd9yqw^$6+fjB?vY+zNf2
z-~7FP$$z(lsN%+ZhK8vdUGDg+m|G-YotP_?es?L8s*)q#R^!k>*>Gd%`%tsfOH~ay
z$!}?Mk2m<eF1ia^B`FXJxb<20dGQT737<tuepB`C=-FkO=m90LtHS9%2wI)0HF_JB
zL+Dn&d!+=Q-x$*|cS?t5rV55TX5yHDWKph|5B*!|0ox*GaC<6J66M~9VmecNH!ESB
zS2#NQ5_W{B%HODro2!V`#o<Mdw|$D~A#Xn2{cuBoYUd=9%rHk|BoJw`7L;}5<lRw@
zY&efvxMP%-VE8~90c5#ITN?#j4Jmt0s1Su~kbS}feH9uJUPLvDvMwyD(B4~2`)UTP
z**}xh+!ElJ5_}EOCTxSMC{Cyt4l4GRSS(^6BTyzOCvs7ZiVu;zx<;%iRTd>3&)=~H
z+g?0`oy^Qqc%5fxFNm@*(#X+IIOVqoY(AvyOq?4J3HG_&C@vNiY0cebMjhm_sU6kz
ztQhR^HGa20bVkmvzb@=DaLTrZrUPyfYx2ucTCqOGmNzIbU#E3q?W-5dyp6lL`xnw)
za)D^7Y1Zf8yB-=jJGocSEDoO%R+@ZU|1u~TulwT1`L1-r7oL%Uio1;mFEwgFBR|&B
zD44mny9pQcggeRC2{r2tc?;=7S`X-&_dN0@(sYB&FBt4^_%r+nZWFehU7NTc^z8WQ
z4P@vJWuQ^W&`ZoUs!q_lRW~E5&BXjwLdshocMCEolR#s9jWP|F%o;i;KdB{t1NPm;
z^(>n{goC_^;1;!}EoAVCCKtjP2SCnrH^!04^{gYj_P6^Ne`wobxyE0Qa!vEOiU$A7
zeG?rlfXM5+a5AB1?inQ*!PP9Gv1^$+FwZ03KYqjVJ^W8%JAfD`Na%Y~NpPASczcMX
zl|@Qi(wM!=9TsSF!5ghpAiaR;TGAG4DRv1iVQ;_==L9&o;>{kHGmdbK9%h+GWwLIt
ze&u%~dA*Zx&(FNzL@wib^9woCKJ5{ZY1!MLMaTHA#JfEaiS9aO)gk1?Ko*4kr=l|X
z5%!gbYjbDGF4Nt5NyC$<ha!3CcZ<#Ki|)+Y=k^7@$FM*gC84MizvxkrNQ611PkR4W
ziSB3Lj50Gqdkw6eC@v(G;~#lM!dO_|dzA-YD#&d~_{Ozk;qq`|)nS`Mzb`VZLO{61
zFEA$fGDX{#2tm=*i(1pA(al_kBZ$<GLHH`qVo4`+s9^%a*IV}FD2J284o;kXs&BYO
znQgScB?8XK4W^yOs4j-I6^GJ~u1_^fKRt5OI^s~kDT>&R<8KGh6M2=x7)`wI$tBa>
zNkeeo!ugK5D7@*tS3+!`;BZ*;-LDL1SJ(2;)Zd$j?DAH20S8HM@L+M)ISQ=Nn&4od
zI>fZnJI_xQ8ucBd@yI{PMwfo5;qHbVu4WgHpd+-wl&+5w8-RBA?9l*#bLZmTGB0Bi
z>!X?G%3|ag?=Mxt(J#ausVU~(v!zQ!M1Ie2KMOCtpJ&LaGC|>BPB_KC<;3_%9n1Ny
z_hN(t2qGXFi+CB+Y~P9p47y~L1Z3T<{y3@t@Ir(0O+=WjdyVMu1NSKAwFTjrMsCJI
zNi>+LnH|=O;L{{lv=xTs-BXU>YR~)f0$|I5-cM2GIb<)Wz;D-E_;<$e5L%82cjrHj
z*w+TpfHJUsL+I@7wG}D;lHZBAM3-pjox#J=7T*{4Qr(jTc24n4DOayXO8-!{Yhm?&
zqP8%Nfi;QNQuj@EN9}MpdspA6U&mHtB-FY+OdUtTLt1`<FIlhzxoPhIINi}?8tW>B
zB+Rw%lLS=fC7tEz3THHFvS48&s<)P)r6_7wZ<E&a^|mCK)z&i-(=-f*yUf4{)`$hy
zzs*+sY)ORRvaO4faXmfJQp7ie=#7|CQZ~UJ%HejacdV;soD4tqA4V6bpCLOWggGuZ
zKGx`Rf~#d)-ERj!t$q<$LqkoE*{%MHxHtBiSOupzLJ-Wd3UW*FERMDiBt+Stx;mr?
zs=9!VO!OlQHLKQH*Qr5>mS<?S1+RoDv1^+lV5@8fuqK{RRKN&RJZTq;DJLFripz{h
zgL{LCZMI^ssSHHIqCAD#UTDM3$~K*65I&T8xSGdKmt<M??zmUna+Gm@8bGe^?4mXH
zI{m8{%Pg8FHhz1g$v?IhY~~#_tNf<Lg^i=Z>dJm^kW;X|8UfT2pw0}6sJw-;9V5_%
zX1<L%8$qOSlnqOl8%3K$qs%G4{@GzqfF0(?l|isWOe}{hJIb`L)8ey+RTeSgGUR3b
zYQ&Zn|7jzV@9X%l>dDP7Kex<n!g3v5{an`<b02}Iq>%s`aT_Vz{JZNoRj2H%C1qz?
z&LrghS3=^vfW$D|&+n1G&8Rx0=I-SiZ#Q3(JjiVrE(qO3#dg0Br9C`S+6DmJhQQgB
z-PvYr0GrSm3^&6yIW5iE`;zxkm(#IOZ~6E;zIBFmzX(6flCEEI5_=`26|gJk(F~C+
zjr>Px7*wXhPgvaC1K#Ie?@umqmZf5M8?qb9cYn0=S5_Gaa?Uq*dLr$nbb8!rKiqja
zPu}l%<##nLbbc#DLCk<z4>QN%c@Q!^-}(IlY<t2<xFwIiYciBCVc{)Gr%Z~8AwP;W
z_3H81giQVZ)jd<;P&M;pKB0o=g%9EwRKRsNl2V6@%3mYFowZMT(N_dpZnjg7l6I>?
zOSV#9oSA$azE!uAGO<H_q5G?l%v1d%v(e~vvY1@`;)t{bk~UA&FYM0N);OjmK?d!S
zr02e0eWNO$ixk@`7A7N}TZM)L;&Ee9%&uMvT5&uSxA%stkhXAJ_>$q{!&nTzVf5g`
zyDOTsEN(=;p5?{r)5hl1b#eT*tCa@;X6X}R%Dc^+?<h6!NFs?`NnE(-H3vzE4!7Uj
z=G0C<6K>@)CDUYUx=sT$m)7i3Ef*AO+jUniW&e87(JLpgH>j_VD6@doedjl?wHiBd
zFYevo-7QZS3lmt=?_NPkBVO>DK>kOgesf)6XQQd*={P25!`WVLzVBM!f5rOT_IHb(
zo#VOYavn-^7|)mkD!i=??~HUjO!=UTM_$OwC)@0{Gt8A7wsYv*cIEfjBVO}Tx?oha
zall=z;tLY=r4_lBQ3Weht5K%45HZdDf~4X;mR@EU%+$;J{M&ytzmtpLSU)T$n;6AO
zinOZMTfQ();r@A+`QtOLWM`f4WgkZHm3~2wAL1j4N=G$Hn5RV4eGTKT+dFt9VZ_+F
z6}7hP6)rGYFVxB_EwnLTz1O1`eYa{qN_~CfbY+zzjM(@E%7@iVZvO6_CS35}=FX|4
z>9=6%ZDlB19bIVZ(iiYb)X*65WuH{M#y0kitl60NY6D;$us2KmvN*v$Ytu}3+eAh|
z$Rl?r^9+gLZMK=+3hWhwl8$|G_w1K>;$fDX4VKo^kt5?M$`iAA>v)bs@7oO~`#3^@
zY(t~gws+S00b5CL9Ck;7ZwYS_Tj$XvhG5PirP|~dmCS0()9b@%G`j01LK_+*ji9{p
z1Jp{?D+^=$Iz;gj08c`U=CMDnC2U5RLvuj@1b!C~E&UD;coKZK3irlcuw3RfMeg&&
zVlaH!NC0rkgcG6sXuN5#o_pfA{pX)_Y78#b`$o>O!dcK5UIZ&J_hHSYI-Z#X(^d{2
zX={(pAMVVYA$gPm(kW<^Zw8VN@ZSY>3$8X(k!Kx!ut}*$Kf8P!Z82b9sX}?1h%!h5
zYG`(t?UDTU#@0LWpyWE*FP`DPRek%kL8&WithYJH;11H0`|GVFk7mrdXyF>44%6O2
z0vr#f#Ll$;GD_pPe-uWdJl?b&qlFS6M%)7vr0QO^?a-GLHzUnAE@`^=aDvIk>;dV0
z1n9$1SjG&daM>#*7d%~MOUokRPK#K1KVp<{kY<QKvv{6Tj^Fgm$zZCu?X|2824pn}
zn(R{(FBm)Sc~iJomIl?WUrI`|g;ng1?<NRU3&+sPwH#kkR-Pv21rSNR&&*=`JxluB
z<H|gYbA6-AU}aqML23-gS~9{c_wam67G~f)Mtd2sb+Mu~AT%ILj^wM>46kZ&3FB1(
zYxJkpVPz8=G}T90QvP_}7>>!N63#rz0W_I7?0HCb#Z*;sy&1HAq6-~Cr5v#jznPle
zei+H+oV#EV1U>FR?|FyfHom)N{jRkfg`y+x9{U>58fyNekL)||+PJ3D&}b@+jYwp^
zifBF4lMD^T?3;%#jpr7J4%sbVKA4`{P4;Qeh=$pM@+x_ZS*ex9+HSH3Z+CQ<22Z$o
zN-zK+$eI@_fcLd_&cYMwhYTqqUJgA|A`QE+O9GN_2q*YAL~zhfWzCRV7G5!SVwF*;
zIvMU<_ICNlGJbv1edGPpR){?%!phzw${b%s1ZTc=B1mo)U=zTW!70kr7+LG@exRIj
znAzl|-@8z`F#uP#^G#@UO9FZtHVFXU-`Fy-dc>@~*CaN>%kou~pCxifqix>i=yIB0
z4aQ;e>vGQcEGI|oyg4;l9pqLBNBog!W>&<bm3@QOiKFlyt+zgXGh<Ht?mDKt%6dcA
zhJE8XAelUN*S+h|QjApZv#)&73;wqLDT;$vT%ci~R{s@gSW`;(xC)@<dJDWf@UqS@
zFJb+q8vl8hgn?_=<lFY}i+LMIIREBvNM8AnuPotO`43QnP*q53vVh)9Z8#Uu1cx7q
zlayxva<%5w+}_twTGdnJcl`82%k`G0JWly^(I}d;i~bQ${KBNCjbkYDfnoO|(RZmR
z;?%40cP8`CzvBkLj<W-TkGO><%)Dor(+=xjHNQ#}*zHHlkXB&5Kq42Gqs#8EyE6{d
z5B?0=HVGE%Hk*H5o%@njx#aC%-A^0x*K-)?mRFn>F$5lz0(yN~MO(VKyB~R0r*pP#
zvgJ4l8xJo%57$6FcKKV<o`8Yse0NQ<Rz{*aBB=;ojPf}3tL2}W${&6<N{gU9->DRM
za?<-%2wO3QPL3_QC_*dD_6ZU1yHoRLaGG$Xqeqmx=op;?8gaKB8yhc;Av3fSHUtMZ
z?|T~Y)N*x;P&8j!XI6}F`^$$^GKi&K4~f`Fxh(gwo2HIsDQk}?<~gSmi+kCjM+o9@
z)(Jmza;VeQt&n8gmW1L0f^)90FydM{x-RZ<Ro-A^1=&&5!|aZF{CL{@^_?<V{(6y?
zK-(Nzz_B;KyG4)cm%R77a+T#VD1tb)7xghl)qAMdD{AdRF`bJEQ=afAt&d0(z(n;`
z*rl1@o9Tr=tg3Y6(&jLGf(3=CM0!{td#Wg1CiyzuT8Ff_ykFz_3Dlc%8V+ba_epgp
zY^@%p!_l$#_zf{`EyyQ+{c@EMs>y7tNWqM~_NnDr!}B~$GVkVl*(oGTD7VmOJU`i|
zyc3R|_Hi={=!q#Cwr{%>hdUOt4tKsU_kYpFK<}(CS|g~!xKXsQZ;*v0)uF{D50@w!
zr~1B=@O6AAc@`2e!|ibx|4u9mt99Y%V3<k-Nbo7}8g5@hQtZ%5e`*M37q6xLk8U-y
zrlri9-NU#Z(jR%C`x8a$K7gKcZLuMY28EKAvSt%wqxU$7;Q|EJF<3?f1ULBfJFaI%
zi<*c)vfs;<fRuHqa*{u%n?|U+Yn<S7y;3F<(8XEBD}Vx>Y`zl*sK_y-LdJ*782B&y
zu!;STmEMnowK>emxcNzGd}__U0DBqv6#S)KsQYO;E6kL8WgT}S0;oQ;PKG_-3GnFw
zrCie~Uit#he}&#P+hnV^6KK70(1YjWDM<D?bRGRPib<DPA3o&=2na5<zJLopkG_!&
z0INo7S+WRA@g@v@@m;LV3#+NT)PTDK)I%(|<J}$&+M^l93I;9e3^o*>lMQ9QDUF4%
z`1_kz4a8@6^9d^qR~?8krqG+5l9lmQdt0{Z7b|qX?>K{fO8$sH-v4eCX?dHlv<W32
z*^J%tX22B#`dmQ4mpI`giFFMEER%S;?X4GVE1j9Waw+6NXS&OrR<lQ}T27}=XByiO
zmorqNcQa~m7mvq-Tn8U$O8gG$Z{If-W!#_o?ECBJ(PK4^k5sfbCdp?~6PWqdOH)kH
zvK03h%Yx`1C#VW>JA3T?XQzI-+<qqnXIq7n|B^ivx-y*1$L-3Lv+rmJcr4tuA#%jX
zKLmz5Ae(TU&d!4vsd@B56EVgI-Ik3Y2EbG@Z%;M;W2-?QSRC=9FjEuL@9@p~liAU!
z1fQ!zeu?V~O9KRh3S-=9NUptlp9trc$hlDiM9mLP+}+|KD`W8Wuls<YkFq&C?`*Um
zN`KJe;`R>0^M+7O8{qkuRiM{DbSfT~t<kdE+cjlcTYm16D@Sw?HO|`vbE3=A?d$kV
zR!-Ey+dRusTj1RW!Jt1FExstcW^>CdKh1Bgty8>jpuj!8$DyRd$oW<3?1i5U7#ITx
zbu*BRLI+$Weq@rhX+OV*jrd255ZfI4N(~<c9JMzGXP@Hsz>6Q&9tADMorngz?y*TU
ze(8OVtUr%&*9J7$rSUbPd_hsQ%0+dTy_;6JMAn5uS?`9mHc`zsUV0o8CS_Q=$7WKv
zDf`ux{g&V4j9b?vfvUEZZ&6!E%E^7ecd-%noe;(e%aU4Y+_D7zLoD_2K`0~#yK}3>
z7Rby!8g0s{ObmY<m&h?rzMGF8ml6_Jjo@~<XpY(n?PBHr9R76Z(N)xFvVyOB@Vk!5
z*zlX-oX6JoN7wE7x9gHjrI_q02tH*XVSfjwL&Z>5D7P%72f2DxbOWp^?h19uEA}yn
zi=iF7O9o<QrjmhdVxP$VTJ6Ps@hd7FjnbJXN3C}^pz?Ch+w!Www4$^?!9#&~an+}c
zTNc55^j~=IU8NgE7i8%!d3dIO@U-^YZ#@r^soK|M_1Bqfb%q3;F29)+&<|MOdX}oh
zQDSy_Gq-;guphP27~q&dmE(AOBjFQz(RgUcJpUZn5(C|;{|KT{8e}~T>W?Xo<i%Yn
z=ryBlbI9y3*i$%TfyO)LjYS{+$~;1V!HiKqoFlPtJtCZl`t{9Jxt;GLa%aMsh{7Y1
zS3nPq%<ev~;YXF4@-TG;cZjTIeeCXh;J|LTRP#yiRk{O(G_snV8mR5-)ay|A5HrB%
zR;lgMW|(vEk}Stscorvj6Kp-@F(s8tav^U=xQ?a2GqgVIW>;Y}O|@K9=<nP%QN5hQ
zrRT)Ip*zyFC=)sx*7D!D)X$@zYf~fc9s2QLGjha)?Bljxy5zBV1H6E>*5D;zLjuSe
zkVgG)=yP^y!s&qcqijXr9_BbodwL&f^*QsIwf-43huglR)!Gn|@bEOhr@`}PnltR^
zS$mg(+iE~`hj12&fJl3BB|)T&Tap)kY;cFN6RRktnc*2^=NvMy!Epu}3XJjsKHtvo
zsnT6n<51UppKL;l8~<sSpwLwKt>EI%ZGFH1=oeb29&LP+tT;(!C=97cSPH^DYc&d{
z$Bcxzx|vd{;CMBMR}@$g*G$@w_Hz9-NA2z>Tqq{hY`i`+_>do{Py7Zg9hSmV;h&D2
z7Y427ot~*HV|^qW@~^_KSz>^>o&jVuCbVSXZn|RXjL7Cu#TB+IJoGtby#LwmtmD21
zJ&PbeGr85L$2Ci;kx)}xVWFe>{YEU#we^GW_pT(|l$h^v>>8BqINAnpyKY8jM0Two
zd-<6=In=rs9<`zONX-`-4V%yOI^O%}0q83I)n1TjS{YrY6+>9?AI5vZ@cLi1=UGW{
z9SRDc8C2BsH@9GecM@sJs*1a(#=JB%9iujF=C8ZJE71$pZo3lBYo%#MQnBY{TH94)
zb#x`^=3ibyTF&#3Q-(9r6MU1Sj$dw1v22rTTpZ%J)-EL%IaM^gkW?+_rBw&B&SKH6
zuWtm^5La*eM3mn=7*Zh@@^pw_I6vH)X$!KC&Lh?(>h#b!476Xg41^Dl7!|nnuN+Lo
zi2AvO?%$k?4v!=nEwnr41rbmD!jE2#U;qP(k^=5pauk1K^<?dt1c+W$gTrVBGC{3g
zzIuM`F5mCVzi`)o|MDKKL}n^a%vpOLLVI0ENFvUhq9q_OX20DxYp<_V4CEeIm2$s;
zH;$Qb)ZGKx`$sVKg!cZp!ex2tqI_>V^xg+1A%ql;WHL0iYcoF(hyJ-r+x+GifO`(q
z5di32WDdQxI)Sz)7HHiBzn@4w=RjZf$4!Y)r<hMa*vQ1X=x=Myxp8<cja=k-v>Bax
z99TftcG1}Z=<Iiw3)hRGr~C0Yapt|I9tpo~<VY!v{VdW_jwZB@XchujNC4}>mQarO
z^4Yx3f+T5JuKB_007gR9(81JzsCBxPOJ$Tu%7rQ4o9DkPtMY};ue$Y4pO;t&;_Ebz
zFPFYFGWCMWRJ-gC^}-X_(H?k<<`1F*_AVgbz={p~=Aw&dt$(yX(b#`XY2Qs8`b@pg
zniY>ejcC7zP|#zho10Py4<@i{WW6Ab!fh%v7h-}sayARA*q3+fOEkW!PDj+@s|KF}
zZ(Lq=$iJB+WdKW6zx~K>ymY*wy1Y&eG<fXl+B8KnvbUWhB_3#)0b;nf#X(^5j{%{_
z8_xkNOTXFhcI)my35|Ww#J6yu%i)5~ew>>CYL9Y>Y<*i0d>~)Nsrj;|<u!c)JbERy
zpe^8CHLaUxCAgf24!lZ@vH@fa3ao&A#KwU^4A4e|DtlVsf65ZcM4@^~JwH5^FooJa
zSl+g8@imPB1Vy0m$^s>t@a0dzS{;a%i%#})9ttdg><t#&zUp>o&(5RAAcP9v*<q#^
z9vvq!zO}Y*aWQ-MAjf~l<Eo{)O&WlLJRo=5=FYdxqZgH8fCcUf^tU;Sxsr_Xa~)$p
zAX8Xncz%q|e5`l@layd(1YqU1zvJ!s&lrc=rdllXCddH;8Vlh2_|EjQ+uKM<lXBuc
zyIcu5u{!HKUDKu`-puw|Xl&+wr%&{T^yzlOxp@7CE)&dByu<x|T5k6dB11O|HkOM?
z(l9Ls+o=Z>x`Xaa0q31B<9mlG59~!7g-4UJD2>GfBkorz3?B#@Wf!>=uz&N0>s0`L
zpx~SQBD-MTeaX1VkXE^Z2N~WtVHAesv2yfuKBr}mKBs|B?D8{=^daM*vF!vf6UuW`
z+&9xsNWN_K5N>Q_X<ypy9B{*~UB!2Pn=o>;lM=<6A$l3k)dVZFrMwAMYvx()S~JWK
z{>51yRr=|Tn@xj-fBen+m<;c!`Q4hCO~^K-(5RIuY-q=0s~)_pp*SztAXzHHq@qdq
z0;#L}dG0K;Bz1PmVPZD{Wsk3;3#+ctG8e?3n%_PEF29sSdZbk@6m%K$91zjI)=w^~
zwckDFnP7aI{#h9rqx|y$T5a>Qk-UY~Unf}M>V3`uC-`g0{`$WUf+Q#C-k*1>ad3m8
zB21M*rC(wFDG3~!9KL4+W`A032IN)#t+DaMVFvx(!y>C}Lik7NHC&nq4`ragzVAk3
zaz|+`i=?qg-o89e+l5OxZ`y2kvC-(jO4r!;vj@`Ap0Xm>=&6bZP!KB-%iX<4I~DDD
zuq7d;lA;(>n@p%`$*MYA6QD!X+2vdL_r>iJqQM+B*uOTUiS93a+7P9h;Ra^uX~ajp
z(@YpSA=bm=DD)jqt`i3lnB#ns<+D&LkwK#!f?kl(=jtYdQWRw(G`YpvdachQ%P!vW
zHLK;#^BYd9hH(VZQ})4+0>6pktvNo7^GY_ZCY@D;&&NuOeB<PG&_vX$fMyuL-~F97
z=4!$s`bH1|b$!Z0qX&(wfb2{)%wd}A*1c!8NeQ8|5TN)nzXNzLfcq%w?GY_3^kF{S
zSO9#vm=(Gu5|%J6!Xz{Z9__AFEqI_$aJxMFrs-J$-3I`n=3COF+BT<y=lg3gJyjq)
zAov8e=<8PpBe;VC;Si!<bLjyasdh8GndM|-%;;lhUDe9J-px`^e0E-#AGXY}vs@pL
z4Pya>Zv&JgM2+c{x12bHu1JK^-Lh0Rl_56lJ&?><eF@WyT|ayw4*R^@d6gjF_7dW%
z0O4D_?s4p5Db#V<I+bH6voLMLe^s_vQ~lG_y*!*&Mn*k7x~1i{ERJN^s+)QFaL=Gf
zz^+olm<@r?#fj&-^<ad$6r8WaQyGLPo}q#_&MmDWkvc{d+ya_X>F~4Sn<ZvRVpqr3
z&Jm{sIs5mfHmM&tghq?>`j>=t69oascqOrNmm_WxZH7NHpG|zs_3TpIKTaHp%+XTh
zVE>5&iSY98+uq>+gggXda8flx&b`Bh;>*nDy)Zo#Bw%nfjYZL>KFZ*0i!_99^__LX
zViS?xTLRbI!_yM#011GvxF)~u6N&AmZ^Yj5E&oHAXdnG2UrUkdoQnB{&ygt1mfBJ_
zy2W=V&=l!BUwkxsW+=tX8wwL^>68g^4mu#yu)4u*|2@lP<g<>GUdAI}2=o;ZwTIbK
zZe}kEv;|ORDW0ypma-7raUy`>php%S=o<@lH?$q&(2dnPWLJ-2DxAN(gFDYXUVWIt
zOxfg>Sf<6+lnWeBKuQFEK$V&CuSz00J>nX-zDx4wb8WrR<?s_d`(~Oi+#D;EHFC9o
zJ;GDWou`~KNqDM_gx@Cq)QBGyb5GsK7tB?eom(jAkKd(5w${71&s*;o<Ay>X&;Tvh
zL*LnrMf_9eSw4z^{#xZ-Ug5NP?fI5fo|mca9HSuJW&H%&;EyLtxc4Li7CYHiIE(hL
z`uZdG!|WHhFc}p|Zack$JKqgs>F?6ig&_vCvhFs^M{8ccsDAxI)z1kdWkHkG*F7*N
z1LkzNoEGOjM>NRUhdS;2w&Jj0b{XV?r03XAEoOZtL8qG19At>(9T39aNasE@clW$4
zXg_;o=Sw~s<Q%ASR=PPa?y-LBp|Xf#8l~1>&w8eG{c~dkAYnB#)V~o`MvEsWjw6mc
zhtt#i0Oln*A7)l{v9diC+nwo_!+79sdE0C3n=a@63eLAE5*!p?xl0I~Gu(~qUvs!^
zZNC-mc2y|lS)B>K#5&Q-Pg|qRW*Xz&rDJ(pwQgIBg^xgQZ5xdSHl4Uusm7tsf(^WN
z29nth-&mR=LfIc*+$M1RUK`C@ygNkZi)@mY+f%CN0_lF-Bd#)!BlvW~d4l$GRW!yq
zXpMLB%0|*f;HP4KcNFw|np_P)lKqVjX0At^#YeseSSCCA9{GPX8a^6+S-=F=;4qx?
zN21H_ll8D>z;;}gH`&|IGV<v*P?^yDlaGN4gPp+Pv{Yl`e-6=#*6w-U^K7Sj-p$RT
zmf<2wHNn3pLbrV5aAis#@pU&+cfw;xze^An#ItxvCop-1@NYNC@h({6y+W6z$83U`
z>I#pDU|G-ZPU^kyZ(B&_`!sXbjw|64f3b+Z(CoO;ncpC>Xyq1!AE@D1e)Qwl)3p{Q
zfCx`+j?rQp%-hx&yp;HTsmZz(8xYyqs?_Ps_gh*oyut&;j}JIr^@qP)DaNxbl<K2U
zZsikiXmoQ;Ek8@~?I*PlMl7={C1Z26)~kdU*_;2Gw#Zbgcivq(Z`1v7CGB3sP$+`;
ze%b#%*?r5=PWTJJ;8umxa|e-`Zu;WwMHN)m-A(5-5&G5d*GUl$j``l6bJtq}XEK2%
z55N;7Z=gI@tq9n>Iw>ScJaRY`qC)WZ`93yZc#88Z5)z{7tqkX*izPAg-^Mac<;<?-
znz{?}a3Do;q2_l<<ZzW9JX&TboEc1iB$YUd(n$|BwbNbSFr0S=T4My?yD)FNQ*YM~
zP2JenOZ<L9crTe@?c4a1bt}cGbXWbYWB<C~JPd5wicDy{>E>orq~nt*?~5-=K+C2<
zQ+}FxJA(EZwCtcS+82aajcX79AU4pUQ2lcYY<1Fo;|~7AEKdG8tvgWq!7}H^Iveeo
z)Ai*;R8>Exr8v;b5O2Ax!&D&Qnb|$@1~}@eX4I<S&$-_9Haz7>6T9_p{sl)K(1qr#
z;0&7OpF7JtZJ&G+huX3zS%Fz{8V)V+k6A88?RZ@BUP)sGp>;r_*3Z9hy-EMI#xCfE
zXo4?9Nq!S-8jMJ7c6kwQH{Z<-2M@a@f2Rh9AY>+OTN4XEv}FU@3f4_zh#4DHI_Ioy
zC^dUTWs$wyp2?hy@6GsU#GoI9K7ViBXuSM_L*FOz*cV|2(<n}MXBFfJj2}NpNQ2YP
z*poQg^SWRPT+Fp(rNTr@e9Fj3%U|DIALBcCM>_1EY<kGYB9<iAtpV$fv!DA|G{#_L
z{g)o;#1A1ai%0--ZJzeZsD}Z{y&pQEJo<{OOi6CHdu8+KjIt)UT+D)(5H-JbaIF~y
z0HSA1q;m@sCx8;X5_oTgsBIFPN#-<kWJAI|_9(;qe9t(y+mju-egE<LfDg<Qx&Qa@
z=f&4g{~l#;=axna1qQ^ksJ>s0P(0Ayes%^n%>w*3jCf1BP`VG%$^L4FL8XF!9Wl)w
zP!O5<6X8q4FuHC!v(_vX`}ti0g_7d8zkRNMi{9U`TDQrCo~ygfaFPy=9aJ=9TbwdR
zua=Yx__zn2g`Vn@VrU`-`SqE>njDS-zW(M3oT}%&DD$baz7J^{hm&#C^YadzgphEW
zkKPdbFzFM#QEJ2Wjf_duHqnKIv8a5%dnW56PKotJ#rf(ijx{dcI4#967JA>YC1IlK
z9eAin)gxqeW)?>cXAXhP#oU6=&SD)8J~d**=m>zQReMM4GdUo=&j+)b06wgH5*HR8
z1SKj0fB+GO*QwtzcBf&+IB%!ci_ux-tc?PrwUY+^uO5~e?FUz*R!@qF5|bP#DI;Ol
zV)QHQ+toj5#<t>}^quZ>x;f>76sq8b_Q2R&Vs93sd6Zf%PMN|BN7am52C9GB#?$2A
zzOMgUi}$1cYqftq!Rwk>cnp5T2oxiRSThpVe$-q3fZj29eoD%#g&?6~S~>h)^t>cB
zGG?3(uHj}Y^m(OhML_)4&!a(}>J6pG_@oQ<3zLOdfaHLHA93Cp-%P++!9?(~_yW4f
z@@~mKFis^`zeC7-wQQ(@3UF|*M1!OU#pNAo?!?>7d)bXW?M#oEP0aq|1JHB{tjShv
zFVI6dYvY-vdYCG<VUmbz(K+c#;p*DluLp5o!2fa+SV1lpKm60zJTOO{80ao=@oX6O
z;2QN{O>o@QX*kYM(gZ(UD;5=IiiL-=rnM-Ij2PuKrz0aD-df!8CY`9(dfb?p3<vej
z-1-6?ovp4w?`29ci3*OvpwFn-5sl*6`!n5i)y7N}%J`yl6FoTb;#99>Gv+9qWz}(d
zmmWSLt0;R$_m!DRjCe(`aDr;Wf#As%ect?gIe!HX>y@U*Fmp5A-cGcPalzGIE0O0C
zllSW#t!@m_XSe~n0TSUJZhWARABCQyPi<Exnx?_Ox)v1uA>Mp>3M+_sd=DQry)_05
ziSLZX^^Q1&+fI_AcZct4s@|3J+W@cUcP$b*SN_<~5>~u~wsn!4dZ#qYs(P<H{LPzM
zAGXns+Y!NOqM@OV*4z6Y^4MY;^bbz=iQ4}<pi$BPE_@N%Zf9nJLCeU`IewrKibtM2
zi}jICMLLV`h@`D68>4Hon`wC`V7HxHO9Z90&J#-`1-Xo^3olJ3Ea{);fw1V?zj}nr
zIsffq0_9Y~Mc?#CmJ}z)=o1(j&#VXE#$;^b2LeYX$F#Ek^kBano=qRuaig|)qZ;O*
zD|A$j6ae&*?ukcu*@48rV^dP|oC*pIbXE}Lu%rJ&(^o)6*?nIdNH<7HcXy|R<j~#H
z-Q7wfF?4rIcXu~PcMcuWUEkyT`+u`sE^s-+<;FQ@@4L@_rW25$UjuF&1L<c@WWZ&y
zjSRlduXyF%$vH%q8!t<f9-b~g|H-r+C%R`{w%JX9i}-&^#_QgsrK4*ANjx$t=g2dF
z*t8kXuVk!r)@-WRPcFf}=d2rE5cJNs=RA6~aQeBCrnv8FcKFQKK#=ZQNkamnDj@jn
z*7vwYlrLvwR;O9#_;~%Om*(`PHGO5VzaI2YrD#|VVmMPAZiaaev>M?Cq3zqAT)s3`
zoCi3mA4d9IM)i})u&Fp^on$}0U|uqo(kbh-)$}e$V!c6x9$A#6*=6nbcKBrwR5LxF
zQ2~5KE(HjHc<^V7Rcjm%Ub`el=nvMu+<QOqRXX{!_a~Hk0efVh(b@@kQwYi&&(qL{
zOe0p+(W~c~QXOrp^S2k6jsAvOi(3g~d55EWpbHsEWRsf`0LPO;e({mz$Zz*3eiPV&
zPU%b?_S?E(E8D^dRR1;cEYl~_PWMB+f>;?$3eB$glaFyJ#iUkTT6L{PuXCL~364{{
z4`ynbdS%tz>ZT`V!jnQTS57(|EfTE)eRoEtMd4-iK)`lHrlHt)t>tR!m^U^m?alIi
zV<<fO6h)M=buhx7X?B6~x<G^;%#vub`Gi)GJ9_rE`wwgry@r?l!vkkO|L-zB!HUmj
z{tH3W_`)zB7SEt(wx9+endNL<`X1VyOy<N<DDwdR4nCXAG8SC3!K=KqmntBSK%d7W
zs5q+!M9o7>Sf3UKYC+Drq6<)pvFQD9<FBFOev($qA{hRb>yU6T{@zZ{?8m!FHkXVd
zF#V<k3!uYz+Yh%>9&S~+To?Z8P_$y!$d%7`iH4_wpH!J807(Cu`TUIvb7E>40Og|L
z5icPAUp2ou?@jhQU(=6vqURqa4@LLqE)>84>WbQhFP8-~rOp!Xg}k3=FFwXQ!;>U4
zU~_Y-?*rmN2ZK`KTA}T2wSd>fePBPeS()wA%N-&P)`b{>bd8$TNcR_YmMo?_<xyui
z5l1pdxrq3>SH5VX+F^>9akM<IByALKE@D#l8ocwD8ur1Vs)Htb^c|9GoCGdXHb^Mq
zA_lI~kb1cHmi5y9bwg0{tc(=;Sosr6!$Oix{ra?OMXk68SY)v*DLOp&V4Ze*sA}9u
zzcwG_GR*x>6j+tQZMR7S1O^?q{SpA&gMCjGH4ebYOyhGCANb>X{(h;AZwo9bC7<uD
zI<MHBYAN2y5oQ@V2p-#LSME9x#8FK!IvJb%8l0q$bvmV|))-Z0^n^KkXs~fSTBLVk
zqwu8Kn~Jn1mM%C^EZwUD1=#sMu-|Ci>ItbbZE|B3T2!^&e{Xko5lH*+HeQ)NOgVCl
z7i9x<=}d7O`%cHHFL0<OT0YNnO&H?vHkec~s|#}5j<P2M!x@{A;0DN9;!tW#9mmXX
z#Rp0>9+I06MQR>9_xJ(AUyBd6J+S5+qokL5nVmZ>AL7WRepQ&YOA+vmb~$IjWGVb7
z<0ks_f3OtL)(BSWt>tQ+|KSjxXudPv(w3rGvb_VgSX0MBPOO{I{Euy4j~(CUVzV^b
z?0Y!k81_d|fZPI94r9Sgl3_V!GZ{z%2-Lw2tTa#KtQE98NhwO1W?)7ZZCd{GTaYNE
zc&@)J-mRz~Wm2C^mdfXoi7P?Bh1$_?IANN7X62EKX5|p7?$VV!_23G~lD(%xFyO?o
zVKs9EHkXSUu9bza=<Py*g#<dF0!|U12KRz6=zzW8>uW)P+ke(_CIWjDgx{?)2J{#l
zJdv!$Oq#ZiMye(0>va4Cx~@b}DTm2tWFTP)JeEQDP6;3WA%XYboLE)wfF5DxQLi=^
zqa@(icyVus*y*<(pGUk%b#dtvMVi;VcrEDzA10B<wNw73Rg!#&{-9OpZ~?p>fNn-o
zGg$b`Bk|Zo(CHa<?wP95&AfV3F1TP7v2Q8yrwwk~`RY`_pc;zonwvnB&GsT?=fh1c
z446Q(`HII(o}ukna4E6-NH^1~bkc8cu{(=y7a!2SOpAP?p^$RCquI8<!b1~Lpyu|z
zs2x0OCD6sDA5+&z?)1u@u0gb%<F7w@@%zhvvzYVb`!erT{x7beu>Jo91(#1a7&;tb
z5d8q^0lSl{#~X%;^0SKtp*!k1|HtYlW;!qAEFM=_RQ#+`C*N9OyPX-rsEfQ%ZmA2h
zupFx$f^eXL$dhC+teF?c2=?wRBO>*I7lgq<K=(m~&gN_nd*{oJRL9i-1rUjvtLBo8
zdnr^L8RyzY!yah<%?BU=D+8$_dzP(L%gI8R1YCZZMbSF|VnzVD8{;OmzgLVUG}fEH
zBpi&I^Eml~4<<}Ca%mYUIE9ulEiL0}LGeZeG-rOh&9&(|$$QJTX+mCCtgUPB`7#6#
zji>*57YqR;s)U)9_f<6n=zQ?16<%L=U${Z|-k_A7?!;5i+z+Vln_5=36OOe3QaAO5
z#21q+#yv5}%uF+gPWiK`^d~~i)V-5wdbZtXVWKfNt&)V{B`jd;M5=)SW%hCaS}(CN
zz8JZMbi8rF&ObH7M6CuxwGQ1C5bpq)=~z6%!FJqJ=8XmVAPpDi%Ic!!hEs~jM2^}h
ziz?mbBJGp>zp`VU&c!Sb(45oMWz9MJ6!}E2%@V;#!WE>8wr?s9djZO8C`C}ZbbkCn
z>i2539@fYJUk3yH+NBc{lT0a*RB4@2;|3*Spfhh;o(B#;(80gLVoV(Y=>0QFfm!M7
zSQ%hJLewP--7ZsXH&J46Hy5dz!Tm$@g!mFYx3o<DJNf0e^mM$MUmx{QFo`)SLORfA
z)@B8fwS|R{7w}zbu8al?20DmLR2P5d2be)_IiPh6fFg0u=<zXqVa64ypBQfM8mGPh
zz%>j6ctr7>DGfIRBS!77gMkEG4rn*l`gtccrs^!&RyQo{^_T`6Dn;d{omLtZ6Lq5i
zN>_jalrSx6N)#S;!nr4TabO+>$w(FS{Q+7u@)9Q%CwPEe!p*8|)S%O3^L6NBiq4?P
zq(Nc&e)TIp0Q`VI2I;62a2_j#J4^rmC#SkuPO1-hosOF_F#EvNB$*1krnsth_rrL1
zG__n<9MojPxpjC#G3(%dp+-tcv>QDT7y#PIuvtyKM>u$^HH#}_*AsV;{qW&^d3UI(
zpIB_+fk<Aun?^~ZW=T>?C8ng(a2JZl_BlU5KMg<7nEs7Xqz~+xb#a#HWkC`*5L>Ti
zMhaM8EMmjQ=!264mVvwQr&S8Q$}bfJLO{8$a>+R06THh^C`_^MXldZ-`08{mE(mNT
zw@L}rJ}BY7Rh<;?iJZi{WSZR+25idxiGgH9J4HcX5o6o{p2?1V)+i&x)L_r?|3pbX
z=$F1^x4@V2@<3++G~`F;ot-cLApxa_l}{46l>6lnslLZGY?eTC&)dCO=l9YzGfc5Q
z2Y(~nXZ_AgOyvUpdJ(mjg#)CAA|dyL`R^dR9pENc=7zQNY4xy-YWe%voqi`MJ^vsz
zdx<E{jsEor0qkhrGA6=soa18a6ViEinpLI1pm=TFu;N4Okt90vS@3Ph03^D<@w|;+
zslTzkZ5q&d)vCX94oY~iRGY^YWAS?(_{?a><#F{Wmq@Xv#qaC>b7qtcU;p>j<t`GV
z4adX!andl)Qs8>~-%tz$W$(iiS|+{qY`*JZKy$m5Jn^R}^)6a6*mp?ZYfCYcw*|H<
zZK3gDqBP0;Iyi#rec!%3{nbe|#cj(+PHh2SPhTY6QCso5#;aWkaI_N$AOQRxX1Eql
zk%2PfpGHre;rw6(zbMHp*$X9rFCIJqb0eSYhM@3#@XYZ#^Y*I$PQl*#b#&te9SB+J
z$(?={`(A4kFc0!=FmNs2s4J}-u7YC=`+CPwxq<5XZQ`vQ`ExkuyLRcOp3~Up!t<rx
z*Xxrmxq5v6u5CTeR6GNLyNW?_kk7O6kY3dQ_221mEvUn2W&(^Nl46jg<exu(0;6&?
z4|@7gDS7e&%RMm1@I2Z<6VwpAZ_Y6$n-Kw_f2qG?iqX%@c<=3ybi6&9w1{Q_wP38u
z<!z)clz+k@JeVNUj2RgRn#Av7Pc>?C;bA*P6=<?^<^A|fy>~s$9%5F)4rBC4mL=rz
z@FBb&y~2jHVCURAVKS4y&$U(F4*z_57YG}Cu+-vGi3azxG5=y=HzyMQD6yF~rob0j
z4DY`&p96moOEX8N6$A)l&Ja92UrzJh7-n`p%oY8i)RY03y2Hfbl2l5-Ywh319$6<u
znr5vJ?eAkR;NFuoSp1uHyN$&>zH5)mp$~b?Kx);akW!9iH>sU7YUCo1!032BK!dLk
zwPMbl`*M+?&gf{|0L_Z9>U(=nqGn19v+}SM#L;ol=b%<d2MniIXU(E|>f};;GTpEx
zz9`*^#v^N8sw&Hv$V@@l7k0((&yCa}naPiMBjOCuUxpkDLSo4o5~*o%SZoqdVAW43
z8l&mDa8$}v&PY@|r9$#y=<GZTMy0|Z!G)?nP-%LHull=ri75fa<yMXbM?QWu(i8Q2
zI8-u|U#NKB{irKv+UG5B@Ja_wVFQwxLunG)^;b5Psqkw!Y^UI1l2f~9=E%%Z48raz
zkB@<P4{-h*|K;KbSSgyAe5k`@ht(o%u0?$Pd~6PL=(LD9LP)-R@*_Dbr5u^__*c=v
zd0j*U0}JGDPVnkX3bp&ing~C-rkt4Js0S=KgE&*;IV&bqn(LMT;n0|RxFnqRsbEW?
zBGV4Q`{1v|$OH9BYo#tPPT(}bW8EX!fUwwlJrBP&#R7q&Ptkb7DHg@#@JOsnq$kT@
z9-R{?;nJGD6<ASdDse8h3Sdp}#W4j!c8ghOcAp6Z(A7;#bk=Qw;M{ma8onK<h*~pu
z#HLMiIXl%K(2dYoLG%?{^Q(hN;Yc3cmCBXwy2i?0LTQ?N!?%fs<Wj69^IKGrDh;No
zFAsed(zLbfApk0wu#X@T2V|>bYVbgD(LV8`l#d~?Xk>|9LDtBl#c|M;o#gk9F0j-v
zyHjBLaRsJ5!F;;o1#moiiu3>km4+nA@9t|{JUWd5JK|Sq$4~n?u!7#J^`xu>F@-ky
z_@q+rexmX!SrUIz0(wX(MYv%Nax8WO-Wg*lT>q&%95y1cSpEQ|v@DrI94O!s1&;U0
z24N{g)YwR8v7csJp#LT@A)>)>768XXq_StAZUa(?BAFwkC>hWlJ<<$^``Zdsh4Cr+
z9Oj`#W;m?*=(5&28A+ag^wuDfGZO~oTez-`3_Bb5jun3TQs`SH>xY?}#_L~(ogII<
z={ZOB!Xp%Q?3x~U@~CSYq0QYgteil$>NXwupA|!v<$q-RCE73JF7Ce<kO88a<I3t&
zeTsx7=ASB*ODc*xJ9nUTQ?5eAqgubad05+bACMw@9|kqXh2*-+49qo&t2P&h*pF>o
zUk3=^PCH*{PP;>6_s_NEv$lc$bs240%Wq&$8U)AB0wL@Pbx&lEWJEtq?fN3yk%0qh
zQZ%zaXs1slTbqN4a6_7Dlxy)%t86KFEO3wv-C%(#hIYY#!3l__5Hl>hjUEMi(f$_l
zU0U3T152rLweE9fU^8lLQ6e_MiRK@$#Ry>@dF;0EZ!_A`qD(XZ@M7-$o-bvb#ngi9
za$9|e%!VJ@LQS;Nwg&W7J!x>oniHQdPK@s=TCV;_0~|JdsOMw9SD7B-ZMzpU{qCm0
z=vW_zbin=WZRPFK=-FY&?>fuxg*f`^m_9;}?A-4i$luQsNjFP0^aCrwI~w9Jh|Jet
zCIT|}`eah`%;jcNHz%Tz)ZQ7~nxYsyvBu%lzF(N9ZZt0+-r~9S$bPN&)MS2zjblGW
z4`PZT=hL{of>nfqGPuW6Lar)fLLJ1GiXGLM-=C_ZB{IQ3J>}wT^0Wxif4*mZ$nD*B
zjI4aw(=?@0_N~-kgIx9#w49PC&ro#S-$=YWe+jjF8%_GdE?m5Q(Z^OwOyPGg?<-!!
zk-tHJArAN8-+NSzoB6iNf=rb0ezSaG{^7RMJ**dSgJj6CO1i^A`WVZ-CG@<aZ{%4K
zc*An1|M@rf|GZECw^?GMSt%$CoV;Un-*~klbl2O^!o1$+E+GHNcVS~S7wBKHDLwKW
zwGUHJKgb5K%hGrvQ(+eY40F0sjGK+4Tw?Kl2%0a>drhqGsQrtDKTV8<2=VC<nm+5K
z0YN}w@8}(jvMmQmO%6h8Fy|pfC@O3p`Ijp-(iJ9>^{Z>s(LdFo00&ewF_yd5jL*g?
z0Wi4yBCBYDsG$L^hShKR+L>p7e1eLuUyxJC<&XSyO1#Cf2rAW<ZllvNi&g5^5o?7A
zOU>u*k=O?EpG4^QEc`=<2}|cB8(<u89*pNmB@D~Mq=-2WyUj29UVF*ZzweeAQhq+>
zTQ7;s&>lP@rmB5{Dn5xTBtSfdjfG-p7N(UT7Olaih8C%LXCi{t<!q-Z4~Kg2$Zla7
zL#{40V>4anCR2PPQKU4EMz5BVX+`{_3oJR4rY_59r<_G=zcr2&D@Ldj=a63ITQ2O=
zGBkzZq>+dWs|FrtCJes!ov(G}hHdipO#^(d2#t#e97fzR(Z8`&m^mDceNaqBg1U6P
z_3}OQW~xDHAm4A{!l5ETmx`wZ<l4DSKY$Endy|WH%DmfuyKDVD0mP%0Ol8O2)Y5PJ
zr+_H3nmwRxOQHHw@;lB`+iJ&%W5q;``o4%?xC1`waG*+|xrh-3m+VB<Fs`OHpe%E&
z?)(-%K+X!ZH)h(_9?T7WL2jrhWb;!2%ts8yviS<zS4>QcgCR=?!GK)-Vi3)CLS(_k
zSrmy{3Ap=l$^K8|PV^H~Dn3}};3Xa5C2I!REjpiQsKrS<tff7W#J0UU6^d{s{=pI;
z8XfSJ7tm6_zN47TQM+zxTI#AEJ29O^0r)=nI9Agixn{~tyUFF4?vIP;`uw%<s}Y?U
z8;eG@OBqlnfBmka`_BlCas1mLZxtp=_BP7_ECCK*X-yi&Tg3tcHw8?DI^qi9N<M*$
zhaLQOr^xU#iwW^XX(^cW*T3Tg-fc{f+owuP#T)O=HWD7UZdl7sbm@XG;vDjBI|6>k
zt^~BjLE3G6;x0{Wy$<F(PwptZE1&M85RMs-AM(@RU=lvTAi&maW*Xp=$+}6+U`f>k
zp<;=|qxF0=AdNBCGO0O1V=sUA0|YZv7h-__4Hitk6tMHipdEW+#`kyT8kgM$zL(n{
zl~YL?5yEY;+;!I(0D6+dmHhx-m+;g}R67DqCg6ZYwIbh-x4+uxSIU0Aa76aI2m4Cn
z48Ty_D8}2Lju7_8j)qC>v5Z?^-tBjK!^>ir$K3@j=<7lFHhd!|{ch0KA506a@OGu6
zfNy4nQ?4XPV&H@py~1@nWymqatHC7BuX{&HD6Ext&xGUlU)k`PBYgbH_fXV2x^mTf
z=NKxGT$?#p^S<-ad$`c5WyZ&=ac^enypeSBypbc=MrN^3)I!{F1_TvTzgs~2d0gP`
zrNd{&d;-H%PrAA3nc+O$O99RtV=bRM1n+PVY;Tlt6ui0D@6K-584Ad8f~<Az&i5vn
zu2SsMO)PVM*_tDI8fmo(6z<b;1I|+#XAdv>uooSf|0*7D@Bc(<yJUaBcx`h}Xj}vP
zhu_A%pfMQ6`%@6LSptJ{Qpj0_W6=u)74gsuje;GL;-Mr)71^!g%PpK8t{8mq#jnNR
zEA<3LLcg8!b&lE2azqv@MfI|AOwdm{Iv9aR0R_t|(Mvq>FErSHg&`JIfC^R#1$}R}
z*5Y>L@k+Y(#{2Be<uZ`EP*oY9Pz2D+{M`RV-5tP6GTKOENt0~K6HeB?zw(?o04xLG
zh?%>OuW5cSqV%GJ^&p_;ESpf#Or`ZBe#*7N3n?mvG8nsA<Mg}UehBzJ4QlRkrg{51
zXmf<;G)HPzel`uDDha<=R<>RKq9jv|R9a;QeslYsTXgsCUM{FDJ<m0kjVH*$6gyJy
ztT{)pric3kB`hgOdB4&3jONzWv+Z>R4}d_-p<%g!5UPD{SIf*tm91?02W+8^zPZs>
zG2w_mP{BDfmdHc91mx$BqgHJXM|e`PfT<<Kp-*{|XzP5+!m|EZ_wM3oSGPiUokEs;
z&NGuLlV@zw*FA<V$yIVYp86NubMmC$E~ZoX=aM^($)Xrk%EB8c)>FW-l^6uYnVKju
z@-DQA<FfQP{Hwpv>jL>Oqk|)oZrV54w2OnR81fZzi;pwj_zvgqLw~p--lF!1!g3u0
z7ikBc1SDnPqbj203aiDa?#m<0RMfVcWu&h_t`1Q<9%E1gG8ub<^NMK48<ibu5a8>V
z`vs3rn_vKPZb~G6y4RepNnKl|^D^|2GWgHKD8eLqfhJv4X|Jx9a27(lto0gs(MnTr
zzrWsYCB2Y57ycCDQ`>y=MAXJs<6hRbq;F#E;e~`Y6B%kc4TF=>tntE`V?*0moiZuK
z?xQ`n=)rS+!KC3aWumD<W4Olhc$SGUx<hs6a9o0FW;sFslnwq`zU6LpoxC>lg<50B
zS$L~2&RveJZV%x8s)!Tt!;k{7W_7sYtS|%Y27w9$8chTv&{qso4A4q);{M(Pi{=vd
z5XpIlNQXhRU}aGw@&dB*=2Eu1y}XO2%=i({FOdPs<(_peGl?vEF0%pu`Go`tn~W-m
zuT@S(0dPOxh5WCNf++WegdSqtwReF2^7|Wo?@A(?IZh9`o!a>|I!~VDRC*64R<LQz
zP++_<x&k6>9Lr0SEUA(8c)|DCs=AdT=)1x9rv~$Eim|d%>rAbuQQoE_pZ+r!5|su3
zq7-d4;KdmCJqh*00w;|Jr_<aA;PPvo`MBKth*vRoQ;RanLV<2)NFKTwC$$UchbW==
z^>-Zo+aRk(CM^-Y+lmM2m*8y)mWE<wroEbz4i(^zVLMTn4iKTKyQY#C$3(h>V#KPD
zqQ-&5L$ta9iUjI|=mK>UC&C=*r%9k)-v9@XV$z^Nsf!hnf7Ccft*=&=on(jyE1_*v
zr+&!R?FUhx{iw$n50*%1t6h;=A14yv`Ar|^IAPEdPbD|Kq8H-U>H0m{IduA+(6BUw
z!`bro1Mj2p_GvFe6gua;c2g#h!<~%E!z$oRvFX_F9wljTBSl&=(9*cHBvTR&!4hbZ
z?SesuX-fT~=Kj<XODm_<&FiE|jZ>5+w^EL5+(d(L9YisGz+XTQr#a_id?^p@+zQM#
z&_-OzmpgY*+qy=P<rbP}9BY7u5m8$+dqJJQKrmx{ec{NNVEIaR3b|7p3ND$geGSWH
z$L)xvN}JUo{cMZ%6_Yb{k3<ZOq~<;SD*EPp9V>bkcMEJFaolj-K@a)6;=HhJa&B|^
z8ss}Rth<oNcLz%wCJ}!e4<6}JAVQiPvf0OYGqn^0dG?M-GSe!o0?Mg6bpBnF6*)J@
zvLNL_2L^W8O>nK1YN4BN*A8&)YUYz~K+ZEfQ19|lbmkALd&~IOFEj8kI|ZV0jny0&
z%52;_vQun>JBT6b%j#298#te4D88|RK8Q<6k}7L;|IlMM?JiejtrcvVFcwI(-IV(f
z6lF_L22*40q~2)nj3L7|jLR8ix^;lHTvQcjL`%`zBpUw+b%^s$G+E{J6Z^wdJQ|Fz
z7|;ps77W<vc7d4@30B5OQaE(8>aL>mEq;M0a)?+?9+qzSA09XlA`a?9B4FOXOU*Rd
z{~%_NZgPBt*I;ER2aSERLKghO0(fu&XYe#R&{y(6!dXjno0wEeX}Z;W@;`9h9&)B{
z2B7RLR$<;kj8n(zw^2U-uy+-iMTX-SyD381hT}@?$1wUBp)1mUcN7+4^km{vMDk3l
z)f0{LZcR07+u>&FDdm_NDHX9J@xX5OyYqV@q{1p<cJ4m&-5Vn)P)&99VicQlx^Le<
z(~%2JqZpGX(B{8)>aGXezWw&yI_<Tk&Zi!D-?IG9(i&y$1i4`nyG6=}I`0aoYTFQ-
zi8N3f6PP>gj}+#ml-A3_K9i0rpmr7Srj%hOrcD;_;0ro!qfQd&x7hgT^R|v)PnP9c
zeUOTITk(F`G=%|d%tH$48VT-%Tl=ImPud%5H}=Q=aCEqvCNQN7dY{ufBxOdq#l@aW
zA5Q|L!p`<4_B(gauuhNrGbQHIWFiNl<~yUe`gHBz_B)G+X~ztg-$I!DAc#Ol;?ihs
z8N3;7txNs*L1??t@6DpnOy=bD+Win)9Y7(TVL`jJ6=t=rE@0uw!5jM5jLsVm0C+_n
z%R;}<4>9~0%+lMcrmD5dpCNSkTkoP({@$*mW#BSrS@`gGh1ESIl<0Y>xlDy42)o0X
z6+sW)eJh;m;RIWb_~+UwW734(%;GT%J~X~o#`X+nY!CaSVXB#}huFK)#%F;~e7k!N
z$7dR@m%pq1CrIdzX}0g-4bDjmJ@8~Jb1al$S>P~p9V9FsZ1&m5ec=e!G<xbXn<?@x
zwsI}-<OLc>Zs@$c@4$Kz()I%38?P@##gmxtH9FUgo!a~DQO|pl<Sv_;vW(dg-EaD>
zp3lAPHuBnT)<$oH%&S2-{qNsS9>E9VWIAiPMBuRLK+Q(~QZpjx1khRbEVmsuEL6bI
zV5TvaR_f296?ac8)YCyD#%nHIs{d-OPrd!9yq&f8_zS_U&+_UWA$e)>WB7jd2UnQo
zX~&fs9<OT&OqZVfyl;?%vsgB3HOHCfiS62^mLM8I-9}c$qpR?}#wB1S9}isK9o>=w
z?|h5Q^THt#F8sS!FHn)S(Nlxi0?c)%b7bY~Yb|J8{jd8mhVjoHz=z|CNxz6Q?nb!Y
zI*!ZNHRY;Ohe}pyHC?tk7P9=n;O`(=tVXQwNE0u>8!0F<gCj3k6#)sPv$M9p-{GJ1
zgV2v>AeUzlcHXaR(^tsVdV6!O+!me25&WZ_v*j1$4S+8~q5$IRKtdKB_hN#D;@xQT
z%ouN}N;!{CyS?_|CD4OJA%bB({T24Kf(r*|$9F)zx*Z@qj${N-f1pDI(LlOprb(gB
zS6Bya%At1tMaS)^PK!sNQAs5G&`oZ({ig8i!dYjATkFpu!)P}~GO@%pw^D5|&C13~
zXGQxl!Hd_%gcs1Lj&b@Y@>bF~ktF5ib@&T~VKQEnRqhwwLW|87tl&(OY*#+AR4*Ub
zhL*PbS~|>8!aReoMI6}*_EYSU+;RslgE)oa)jPm-YLt;;$qqAO2DcpG&ssjt`NfI>
zq-@3y545U4)x4W5e{5%IUC~|lw#n#~DAE+*4LD6Uj{AkdsK01x*BD}gd(BJM(8&8P
z`Hc13qcA~<`u)nrBmKKX1A9w@BZ2rXzw>p06;*pS48=Ccom+*(2g+1x1DtSkEeoX{
z>sTbWW*2R@<6?M=8d=(v<h_*PItxg}sISJ3vHN6@leTqPBlp`LbU?>sHrJk+P}|V6
zQUXTNo&!I^3MX}v6FY)W5Aj6QIxDrh<Ibh#pH2-&+-re>yl8}d&afUF-G#-rsa&OT
zqa_rHsyYnhrCUCn)QK|XJr#>Et6qXs;kO3sE=6>7dFX%#3o#}_AfQ)d5>%po5S`)H
zN*<g>tUz=H0D}muV{kyRiRRjj9GnbW6?*_dXD>HgGy9_HM7ce8mTWs`&_tW|H*CCG
zxu6@xkGke<Yir**ghbb9e6OjFMB`(pk+}{B$KBe_{G6=^^A#=^^{kljpa4@^{7Dh6
zzn6j}HT1eOtPX8u=^jENw#mE=aqVZ=bUcN7bk^k@VLi#-!v&nmxvaWC4`#PL$O-VZ
z*94p`(`s25jAFa#0B`8Sep<Fs4$~w{oWhnMRe*fQ`R!%|Y*myPv1xEBVlF4mux=tM
zy+@J8En$waoPYwZRbpgO9vneH>qe;D=d1kU9f|#l7|AfRl!#u`N!Evx;@+`DKcB}g
zAN13t5w|=6Xoq9SdWL>Vj+I8kPh0Z?@mn+5g=i(#0~qIJGQ3tFJ+BAesI*USmmX=B
z3?a7W<WeK%INx!2#Rb1G8f)-A_y^dU!}uUq>aIijv-AoT>?LF4<;>zgSyS#hKLvlx
zQgiAu$9Ft9$GnnJMN|gPthdm1PqQpz`bxfnGf=qu`hk2(B&&CPh%Z+E8Eo8JO}-q_
zJr04yb2~#!YL#|90@cJ|Vg3+t=TXbvNzR}ZKES4`r5JPi*5wD5Cb_!5ByhNL@<JJa
zF#FnGFJ16j1@`tv&0D%0K=2evI_o?*o(0GLB1`>OH6&~WQqlZj$`$%cMpk*U)dy%n
zEHky=bnf<^nhN1S$`UJC#BXSn1^|<x4Z%t@Wj4X~C~5iiH9Kc2OdMu3GVTX;BoH$V
zPG;ajb`aCrJZf)(8J(l{%q)U^fDLsX7u~kCZN4X*=sD#~lgv2U%*#|?QN?L#@6!~*
z=nO=|r3X|z6FP~d5r;D7!8^D0eC)_3{>8$-n8jCzaMaQ?QYIo)%O>&8LJcqWI^iNq
zkkce+;CTloC83Zd;87{jtaLnbaVJ2XJ2N7kdnfZsf>6c>NOS9dgRoO{E4Dm2x482a
zCKS_XSn3r_%-X|*;14-rc8pL~SWrBvP1~`%tDH@-O2+_tNUzM-dS4v4&1uf~Pp0D?
zN*=4$^o?t|9b(nOT+NY$YZhd&k4m(YVbp#AkmS$%oi99JbK!((Yd3UPdLDnUmdB$=
z#6L#F61M;DW`4c5r5CbJEo2eUh9Vyq&)Rrwr%K6MrMFBCE<}L;mb68jtu;Bbc*=GF
z2HX$-fGz&s0H@dw|6<R|3h_yh&B>(WI&uaecL0Z5=}ieY>qez<r{`Jz&KLEpz3B&=
z*WtHo(br9(`wxZ1PKVE&4(T;jDiFF2UQwgQ$!0EFX2P{*!rk@2p}a4e#4&f=l0(e$
zq$a$>plA2>Qg+#MAR}(4OyW~S%><Nvo0(;apieGeWA%9eG@X7=Z?9=ElQ*`*zgz^u
zcN2Ku`u%RSiJ?-5D(rwqili&iw!(bWl*`aHK2(U*S?{hBT=pwmI4$!TkpF_+^k>7^
zXO=t>t~kCCNm{BPAMN%5CaJTR84lPCl@t6UZEkFTj9??@o)KRrk{er&`IWQ`yGMh^
z0xiav;qLdXgbKezRXGRv#@`@3mp>GxxQxDwh>Kp!9u?Ama+ohtn=$|Nu`mN&KgA=y
z<mT}4JH4a?B7}3z9IUwNcSq$dsYDYN7r)g794mI+(RHVQ<ayhqFG+6Am-Cbsw8i7`
z8a~E9kM|p!F87dfnN9yHWKapZ`IC37g#30>r`~tJt~F^`NCmv{=~ueykbZpz3v(fu
zT8aE-HT#ziBmTEFhI(eHKmmM&3qe2g_N&=pl%KvoZQ-^=<s5U*_bN&kwQ(67v4z(D
zq<5RNesTUs2cMwbqXG1<JO0$6F&7xnJ%U*EK*~ir!#T%G#Nk#+Zc^Lvwq9bG1);<C
z5ig(tJu@-Z6k5;5SLc=-KwTL=%Aqy>{>!l}=X|Or%`G{^fgAC_RXjrceQ~@ux(sk7
zpsBXyg#vB*{^Pz8fp;xY9W|yd{I|QGnMO;LGqnY+6*90tO{~Vo5;j}}Dy+6zh$h9X
zwApA<2tyo|f$5Fi&B@C_K$2)2N<&tq8<e(96+X#BK;o(g8YgiZLAwO+1!dTx<F@Ec
zMvX=oO|O1^n}^Re_B4kDjT75(<A@a5Vh`aq#>*jO{7T8<ml&KOC_Eum<@5Vvb^&;@
z1|vckt0SVly+tK}hk4lMP0o5#AW&Os-FA;te_h~!Hv#w0S<v2m0BoBKaO00Y?V-pk
zrqD*y885W}?$gvD%Aei%dg}%kL+lB~AK1cGM{Yjobr-U#zJt>17B56+vIBm}0xdzW
z$_bN&fC>xl^<J)1T>xt@r2OA<`8$KiU-$?c*^^>9f?m<sHPr<*A05I8-e{|zoz40!
zS_XO?kz^OBb=P;9UQZaF9bCr{WK<K8=kCX_<)TMd{*|q($6PqbKCk^kuecRviu4{4
zgCx!A<Cj}Bwq^BA_O@}hZh<DaOJcf%ee8B9@Nn;2auh4}xL*!P6MhZqKQC#=kMQ_H
z+_E-rk`}n{29TD^yM@J<2S4us*4MxC%x2==_O_Td+?v@6MDL!L%W;iqV!363BlE3t
z!qOM(eR5A1JL2o(CBmI9I4_01N%i%GOy6g6@KS0v>~`^@GHwKXCz{_L$%(C}3*ma*
ztOb%%sZfh#CtDA*OCq3e<Ivx##*W&!O@Bz>o%DMd156<<$7s*ky?(n68aaj7BIjxg
za;Dvctxt+$GS@3S{D=YpvG5`LKfCae5Gm<cc5<mR>yipt=o0giKnaf!gH;ni)%6ev
zgL(BSsq%F|b0h)3pk`3L(}fe^vYB$S!#+ZSP`A$&WV$Eac3uz{AweP)YqICglcuvi
z;5rsS+`mMHQeCG+C9CYLJ6MAV-1qg)7OOb%U!{-%6W-$@3z(m$88fC93LeTN-LyT8
za8068(X?cmNTwEcbLjvNJ)%w!=s2&JaK9cFZOTlL704<ZbQrTf_>t=k@1wAr&n1p@
z`}%hBvJa-vOf3o%*vD5^*YB)Y6D?Iqs41x_X>q=DmJd(KSeiorIKh~h{qFwfJK<=J
z56>TAKR_iBNqz|5{p)BJ!q?)}Qq)@1QqtNYmITT`i^(C=2``n+>P0d2?G;!R=vnJ!
zBW0b*{3`C=vS#H9N;fj?yy`e(I=D1ABdnIYe_ni0WZyPuxYCrdJMBL%3v$b9$>w&l
z#5Y2`tEh}FOx3C#y9Wi#t3Z5hCcy}BJ*$-jkD9H}@W4yZ0@L46SXj7wF!X($)E!9s
z^U&&4v-@|(MN*kkq-nuZ_ua5oFG8+Nv#Xwcxro=dhon6Tp{#ahj>je2c(&d+3H$9?
zZYsIcDEp=Du?L!o^sHq!o*&NSlQvco#V0^0kC2}i?`#E3kjYk*6cnns+PS||oY)t%
zcGWFxChXykj4<@&_zVxc7%b;}sT7=ZHv2K){&`eM$K#k&%L)&oYB>&Hzc+X$_Ld(R
z`ftSWgkTW`dTMIw`(&16AAMA@iyfURm^I^!Pj6)C1Olgpn7|AFS9rbVglf^lQQws&
zd54OIe0T9v+<<sppP~Iru>^G@9iiUR?)WesP7SQhvHgJbr+=?3BzWQK?Ck7KBayWD
zS#opqx+Ml`EG5J4fPBh+`IdXBBn6Z#&wS~B^JP$--y`C41X31cM9)CY7x1r>&-WQq
z=KO)Klsz=U|8EeOnEVm{8!9)kDO2lWNOWqT1`Ii`_*qO#i;qo+?wzY(6no8}#iVOZ
zp#bjTb<=ViHrOiyWw}9RuuKBsIu^;WePsxy=6K+Hl!+fot$xVTx`S>U%-Wt}!`*Ke
zA?pnJ$3>!Gh{ei5(V*UfqDSJ>l^(vC7r50YYp262{)V4!e>?j$)TK+y9V|S(?zXxy
z;^MyQ<CQp=(M~<Rg8<BCrcK}jch=&+i52{YV+4B>ZLn;@(<BxD*hfh&8A47;F8xtN
zfOrb+Ct-A|F*)itUgGK3s2k0m?gWZ~bX;rAWwTN*vcT*^(1mvG+f^Gf<O01=G}t0!
z?wm0of85hONdcyhml)*3PBVaGefS;ji@GXxDKCdtx`SENuet9%0x_M4{5--eENH&V
zW&$k|LhIj?Zx05n#FnW*A$`0eak;X;FySdM6YZ-4MWs|}w2}B#O{N9D%~?)67ozg}
zqInwCBz230AWm}z<cmfl18;>o{2@GDm}HH9L=s>eXWJ$xw6t1JNJGCTgRR&jZhwD(
z_CCF&tuK&o^6I9N7$qh+`6y7YrhE4<xOw_%xMH`0_9Ak)Q)b*&u{t%xb|rI#9ZpE&
zCCOS`#u-viK<Yh{V!X^Zcy+_1*hqD&JLr2I$0@XN|8aSWHN&0Y9R+5?_5Jp}om1iE
zWyc0^Ae|u`SOH%U<B-?f8Cp9)$zKj7^P`(;0x5J$)Z%{4<y&&3ILj+4ag@w24qn!r
z6bU@%4@$d-`%as(>5QfCxk%>wu;UpaMmZ}^55y(3*%*PEsEW0a2GW<PcyX(+m(2|c
z{>XD4_J6S!L%6rdvTft!orpn}h}o3ZkR(rZw$Be?5TGsjSwuT~3U_qNO`%$33nn^h
z5dwKB$Nh;)Ivh+Z3v9fI1C~oRKcKDsy^>^pmAwg^c1wIYw9zdhhgC%Jv?l)HmgJen
z3f6J7@AO{z_}fs%RtV4la)PCw_N=W^22BB&dm)7YOXlr&<ClwFIVH2qmnhqG1!^gB
zFTUWAp6_kEt8&=axlt{YG2>D8#g$nH2eUsk1Iy*St%~(>3}pc}Sf-eM9~KoV8#p%j
zR&KQJTv)sU0R~;T#<n>9sW0Zqg7dExDZyruuIB~iPr^Up^A|IOy>${yn!wLRj72_m
z#}zs~)dDl<n95*Bix60>CW$yUJi^EQrD0SNdaI7$E0&W4jY-?b2``(HX&EL<EI(PC
z`3{I@PL$_I_K3iR*QoZ!5CRiq8mU-w1mdQ$SH+cAjcPCdFFXuNpyg;NC@9#&k`nv@
zb7|n{k^B)g1cu{dNC0d#;bp4%se|{A1~jE%VUp9KKR0+pWT2GSEh44{Zzno$s)Rr-
zh||a!=0Urg(Cx+n37c3sgy@BWIfSN9rtA&ZRr#_~bH6o^@NO}42$dSOBy%p4_D=dW
ze?erjmZjm?22hWGEQ*oy8Yf@l6cVWQXglYs0_SYp++?L0Zi<qGgGQP<zp5%IoPl6O
zEue%$Txw3zS*$mcn1jWnG>Sq8|4?8)TtjH7Prk)kEc`l7HrN6zS2xCdIwj93(PLI;
z7YJ`2XK!}j9kcRovlu?H4kbe+sU7DD$R|xK_q!Fl6so;;FSlf${6%eM%+>tU=s$63
zfd8IqaK@zfp(9uOo=P6eIrll*$0cmeo3Eh<m5#J2yp2$Ai^Kk8ftHoFG=!D{MjIAs
z{<F204*2=JQ>?zcL!_~?5vYcBj1o<=Ck`d9;i+?^EG$S~@ban(8ej%nT%$`X-fnrX
z>)1%p$u+R8I5iN?(06PQrs*TsaRTz%VxskGwP(v53<;DP*=B&~QdJPnkeQwm%z_t5
z2?|-#NVEPErhX_^3j7|plmyEc(v<Ki$&yb?edCGQ)R+y<4kmCCiI=ZB1&1Iu$->_n
zvW5iP#jF&nqVUJn0|h5|!<4C{1bcBzcL#l?^q&@R$q76!pkoMQ4?-259>ju!N@=;L
z^DH@Vxoz-n$zg>xIeu%&>Zl6CAza}2&tqwCpD5Y;Om^_?jiD9>7=5-=imTbtHxkgw
zCSW?#z&d)5?m|3M91_WAQW{)3l6)z%WEM%nNm7k`*njLHq`UL?oVB-Zlz3^Z|K`M(
zB&a7Axq==tg5K^P5X|;%#v-qZTH9qr?PE|RuZR$bIWV$-{0!Z}3q0ZFB8*CANnYSs
zWVmy5h6FuTP;rtphMW<2K50uDyUGqj*i@HVZaHXtf#?ha#Et$<Jm6F750C?zM6+QK
z<K))mjiy(#C(x0lH8gq(4LR(M!+>aIE3Z(Em(M$qMVHDw{YBRID_Z@(Lvc>82>a{b
zF@fp(4xH&#T)n*zt2aDX6<*fX*Vp`*_Up2XxSI_Vfwoa;cP~uMM%kW~iwu=JVY4Yc
zt1SZ7G~AyI1X>gLW~G&m4VSc3qmz)|z26K710|nUalN|)-e?hCRj~rVp-O(&xsO#1
zRN?_)Vdo@4a&04tyiZa0gbnsI#qgEj7wFo8tMt+iUt<gc8}wJh(~TM&9mwrDfI{<(
zTIZ(a_gt<lNWFOeVx++atfL{-eWtiGqkBu2YZKvG8iINes9-XxaiNgvduKjKXMKZ2
z0(Dg&^E`0kCq9!|Xgx>Ny0&H<Fm4``Rq-ZxJf+K-+b?meD->D#BF(9RboP$;^7jaf
zS?d0=zCp(|KGi7G_b@7D1SU=r-(|?l1d0Zntz*F*20BK}k?{&(HU9L$*f1z8%%v+D
znOI{>twI060b3G?(fcKp7Z3AxET-~8^G(Lg`ILK>XGQeT3+|Oy`+<kiVj)k2UN%bT
z7-&Z%#2P4Pj$Y@4uwfL|lxuP6#cgBzc=|<$W1IM_o-eh1%!kvF^RBbhde@cJ_^UfG
zR&T6eX%s?V#_3Sv(~tgh=Mx87#Y>Pece97>dwn3Y3eVy3IX{sSoWIPy5sh}s0+U|D
z;P-3brLPY-wCk3BA+5bA&HMTkQ)mMRAyESFs^LPfvYw>)I%|JT38=w_QPBY>c|!Hy
zXAR3lR_^2C24(-ZMamTZw?#s}(*;RgIqTwp<CqC*&=?%8?g>k~Z4&<_$-h5yCH~f4
zxd_dZthq<71l%1`*@y@jkEIw4@WE{3td=9K;&=3lHw~S3w>ocgcwX=d^A4@}+$YtY
ziUhHwF5)24a6#Km4S&jUaEoFw+oK+*7+3D7iC^?L!xk+e1G2}+B{jhX@MM6p;Krqh
zMA+-^lP$lWDlc9~>x1Hoguw<<`_)>!pcd!t&w@v9={NR2=gzSL$Zpo27JTx3crWl4
zp6se|8PJY@u$TqIospkkaL-u90l!5R);i?xd9R|e^Y0h_Z<o}$;Y&1T$z`Voww{Vg
zb7T@BrVvrAt(Fu0{k=^B-V0jcWwNOYlCk&(U0iXDFS1m6ySL{8N^yT2_uVUQ3+ShB
zl4r7oki?eFl3m}6GU=Idw2jWK%LCDGn@T_lgJ@gN=C3{r<*_zhx6Qh(U&z%QSF-CQ
z^WO=A$5h;Jdjuu&f-A;7K7IAClbQ%;4p!&Lr{)RNH(+z}hN}mXCl-p?k05IeWZT%V
zQ2C0$e>JUecQ-Xuzd!I2t@^x6%5xwSBz%UU7+2|Vy&sL_ae}$c;4mxiwR*#J<-0%G
z#MgEi-SC%z^5pZ+>?t6zeeCS@_xtpIEGg4ynlFg`NJA;n7HNHVV$;VKd7bBb{NTET
zM<*=2taQFI@DBz&O<@!|@9=JCb7oLK!L++J$jEyEjjd6+JW>9rjw`(Ix1=m7*$0wf
zVuC8d_1%|=J56A)$p_W*HZs`qs=u|$2P?+s<vE*=_4iJ1-850oF3ufH!8g`VUg5Lk
zh_OI5INqKUF6Pj3$uqFZgX!36G+Lb<Nm!7zanL!wa(Wh<+8gQ!GZ-C~#42x=5aNxv
zE*-F7?(f`{(GAnK@Sv>L%Li^^bR~Lgk9wKsIi*S~3%WCJb^>{sSulq&;1d>QZWP5Z
z1DQdeCc{0_>Lu$+_%6g5GAAJDQ{`0kE#HTeG%L~^EldQ*DL=JE1UAt9zR6EtZsjf2
zFWo^Oo(J!aD5U&YXo{sbzc(a<$YHWmnorMjsPWdX#Y070!q70buGiBYg|G9?cXi=S
zjrLB@=d|OrYu+O^#C9fN{*we7=F0Nx1n0V)munUi0Epbt{}0Q(M}xIg3&+@%c^>K8
z;Qr&rp8Dmbk=5v@vCkl@dSbCAgPfXPelA{!RXD0j*`CpyKASnCn_r**8=76?TOcss
z3%%{cG6D43NVIAM5{VKhrPauxF3A$CL0%myR_sZwLZ%c=L6u%QCGEp?ZhJ$g>xT1u
zV3t(vfIDWCFp=uOI0SA@BpM29`ooA{eRr`)J<ea5mKNOzgn2hJCfuaL6h&C{eUT;b
z`3)suhf|J9BU-7rHGK^>CJQJF)5>bmR}DGZ+O3)ybo6kaIHTxuqTCU(F6H)JF5wLf
zg?eTuE%gcofIYNV^u_Nhmmb*?S&NFnR*9n?)oe@FbSkow!HI7cx}<5F6R5d}kZziZ
z1&zqn52#pSbpF038!Q`DcF-vTN!zsXT!rJTb;&iaP0oN%i;{CHGp4pW%)RqzzwDda
zQbdwR^954s#C6O{J2n^0S=E7G9~0Lb@Bzbv(IN7v#?bVdk<t{_@l{f?@pCbt#}tcM
z!tDqO>j^bIlR{_CGocV67z5t#Y<k;#qi+mpQ<ohJ-x}IM{1r>(tM_^AC2l;RmJ}A{
znudM10Ou}g`|yp{JN*mq7dn3ZH+0C~VI2+ncR2Y3#`#V2Z#**HF6+zB;0GUTDvna1
zwo*~Skl~fgVZEwzj$Wue6(o0DwFhoz6a9}Pnw{8B!ak<S(HJ=8+<pS4A-%M%;cVX!
zV;al_1n!AZvXlIL%eK{Lti&o5mJ|;n5-7HHo}=5HoX#g==<&5J6W@l1r`0cd!(?K2
ztF)@6VMVMnRCH%WDatOUDj4}6{p%))E#hkYp!SPLWYVd1dFOe@o(v-7aXKRl_NvR{
zS`#g1%y3?D6H~jL^dvTWawdo8uSTXaH)5{|rCNSibw;4B92*WmO=(jv^;Az1S*-o5
z96}0EG5<kQWMMTizli4P{*OL-aW&|xtGnljOQYpQCBSOd`ag$!g}wZ6EP+A6ih-N;
z?TuH)!*k0uUtzJQz!JPQ0uR8IniAz2OYRzWbP7WPpiFBK5RNwOU+@|p7@Bhq|B7<Z
zXGMRn4qz^&`qX%pmufv!AmjGt2T%~86XZ^5^z@H}H@21pQs_vRq;`T#4S&aKlH7w7
zK)Cs*F_6o|r<yERH&|iqnDn$MbRa(#w%3M83uD3p)n5g@fC|4HD3HMOdb_<}mIiZX
z9ap+0nAcFZHB~@PN>wm%c1|9l8V&$k007wCq&ziGnI(tqiuug1IxzmWhF;bf2yeq4
z78a_U_4SF&fo0m)_LhwYojl4B8OU5zx>(PpWl)W-H@d*tGEi=$vN!SAVLUB{zvVQ_
zq0T}yUsS%gVB!kb7`McVnr1`tUCtw5sNK{bx6IkIEdzg{i9bmGdZ&qGSGx%q&+08H
z&!S1jSN+x)CkUoXNppguU@clKubU<&h(4gMR6f`@rS4rd&}8{Lp<JsK61BPXi+(v2
zOB30y25)^p9;TI2(R#~3CaFb$#WAXKZvef)SppK3<q9`VlHradbPDhQkHdSCup9tD
zHC;ilRjSoiIlUO8NQH!5zUIdrzzUrLV>1xY!3op;ASE?NT}(@%nzseo9$_^pjR|vX
z&c-<+>CKPJ3J}b2PwDF;quOS8CU?@)LpjR{<gLo41{Cu0W&;xQ_Z?XXH_=GVeOk^i
zw|_WnwwNIqy@`KgC}RUr^NueZn3EM#g61|keU~>9Ms({3Y8(b9(jjcv58}3|#_uVK
z$VB~}lau1jG1Bafr5jAF8&$)rE#z7D#xBVzyAfHWT0&7x;xm8n*S<SB=^p(tZ&UZ%
z5EOyxY8$~JmW|r;;biJQR~DA?Cx44JvDCClgp`6M{?G8SJf=HqdA%ZR=fpEZQl)nB
zSjO+#`(3bKNvoL6(c2Mm>M}>wh@t$c%*s@O`gtku|91b+q7wHK>CqIvKl{pY_EzVN
zKmYcA?Dk4@E?#1oP|-IX5qM##bM*rr`|$cGx9`=AJ1obqS+F~CZh6JTa++aK;k<=*
zs1yto#*X#@S+>vbOS?~XW4L<jdI5r?_&4-&J`lIVyd%uhEY9c??SC&BT|+o?ZY>ru
z*wdxt67&rR_y&{NWJfc`^LTIlvgJU1#E0iVYFj1n9ZFc&KcTUue^|h!)McDo=g&_G
z{yrjbGbI0Qd9c<JfR$d1>OFhbyBwCTR`DOy?4JSF!)i*`x8(vx^BUyKpwVM8!Z$vA
ziI7e$G??y&CZAC47B;GRq)DY`7F`FVa?|0?2`%@K=F4xCt8uLj9tz7-@TFTeK;(<F
z*75l9OSQ;C{_5dk!?Y*GY=CdHSHBPG7$`aeR-VmYHfnGgX8gY9kKtRYr`Yd>O_N|-
z>U&!YFUvoz;&t@GWDxPsc5`AdTX|PpxD2d$03<<es7!MbnFA*hGpH39D#EM8KQba%
zT?5W8COO$DK^@l#MIYvKP0~{%-v%(nA6qV<y}l`NW>^64?_hsbw^)or$)I0G|0;C!
z7V+tg_N=Z`2C$W$N(k-~(;<3}E!e~Z7=U=M5AuSU%-0qGvU5PcgxvTwLhhojxph6l
zY7^9Xw0(kt1s<Z|aC$A>lj_frH}qfjogqlU7W+TtjVB;yZm;Q*Pe9#)GAkH1^0d*5
zTL=UKa1-D2_sQKTT8ErR=!z2l2H|N4tjsbwP@Vy&yU(+(%Boq+vEz}qwg90`<&9QO
zaO={(#>zYS8Yuc|(ASO0w6;Cpu$$Ao`g9ISsYWIRVx*XjNOSLLzmu4J{uzKts1!wZ
z9^FG67+2pHh+`cg6&gD#srhXfT3W6q0Xd`a*nH+ae!e|wj}huKiIy96v;JViUd)lf
zWE{<a7!JmF(AV4~I7n&Vuq^#C;z$HZP$Z^o7ivFI&fGg0Sp!KlZVk&!QnDO?ZiVFj
zxAg^Q$UVD=J0ylvyA@HeL!+*VU!%v`Pp!O^Y6l0*(c|nVJ9|Rbh<5)b-hH7_1nqv<
z4m$b*a;Ks$UM4#dH@OKODVeBqi(;zt4X;0E6w-VX_^?Jb-5n**bWa4VCR>6!zzOl#
zc+tV{Iz`%<DxyPEw#CJ(Bv=wE9+pfum}kC#t9x>-=eX5<A^~zz@(CdPtohHUF)gwH
zc97UYS&4&RmFG`0-~EHnHC^0hhm}qDV6W~Q{Ff=x7x%c?K1oafy|Vrta{@RgRjUX9
zEE}s{{Z3okU&ImCocqU12$;6jLRn-b^7)YqOMa2HH2hb^h`%uyV*J&xg$toMV=o$I
zawxe(k6SO+arRoQkG)wd;RybJES&{VmEZUEe=5=<0@B^3G$M7C?oKJ`?rx<o-Ce>(
zq`OO6S{g3h4blzo;roAQbjG<e@Gy9ubM{{Qv({mp^)kOJt6X1NPC9@LQ{Iz?v^H^h
zMM)r~mo%e}eN+mlU<;B!0`gyT%{AHVyf}Yd;DGk^^QuKr6X`7iR}*{Hz{<(rxSrzk
zMxJq^woG%Yu=3<7Qy#@e5r}+|RfA)FVe?*7R1Q&D1*pAf>LvNUthBecz$^yihaG?1
z@QyEP_AGo%w|?`(vm&9^yYi0TaF{c*5C|D-J<IRLtW7uzB9C`YKW`xoCcHmZTC)tc
zc{B|i-$+WflmF*+ul{Rmr%y@aHWSG(+oY~Mpi`ap0a4u(vhn3{3t{K0IJ}vgVW9mL
zc!U8-PQd-2y~k|Bv-TcGw!-e)>c6zc@0x`_=q}Y1o79-W$NAMC+1G}NBN=l^9p>v;
zY18PLG`W7Za7-N73kj@SZ5aDGg=AgeyKa%q{oXA%8>f@Rg^qjDe-xX&Cp36%KY>qX
zXh2RAS{A)4Yq8N5#EN0>5k;*dk|vm#9>ibuiHOX)gFp3nWds7hg6*K{-%<2jX-x5J
z_E%HLPD_rzQfdj=@_HsM_Z-m>v8zvK^$g>An#InCXL!fS22M{sl<t2;cssVS=je9E
z^QhU2M~}J3KCgn|w&QHp_`I(9#}@pOrR=IDTY<B*+dV}8Pcg~gK0Dw^tCfqtVOdqy
z`V0RWauy9%Feo|s$uCft%{dM-HdU@gGmCto{we=68X!^aNF;qbnQbobn0JYnEOCT|
z^C3qR3mg0A3#%3K$x#a-YwJ^)jknaO(r};^S490=1<KJInx8G>oClJJ*GZ#d;7hQv
z4ac5!R!jd1cC#p>FYu#_nmrX?mY}61T6v!Kr`hCZL=j^;y+E(mH5QN~$UaG6Bgg1u
zVbCy6tysVgMNP2QtBB{9FaF(=6a+p0P9*^9p!Cw_!EX50N13H_mAC3@zkbmgt8Voy
zmlWd~H7YA;qaCix^*zgs7LR1bIR7Ts+%eSN)HEhdQ52)0q`E1U^z`C^{Sd<_sDh?<
zZmhj$HfEJz4_P?$9qIcMfj?@6r{o7lT!%TvcSyTEeO?Z0B0CMuVrvaAO0+h6?dCJ`
zcVwbO3ST~298zbJ5Xnjvzp!}?`9$vi<M=HsCJTN$p@@kL7XG^oQ=rX&SC!bTQVQG;
z(H(8fsOJB9%;aNzOwvI;3q2t_(xJ~7?UcUH(v1~~FX$P!AriBN94nb$OP$!tMm<^C
ztJnjna3a@6zdD?yCr{Q}DOYLHAH#Gt>xhpGs|m2^rbjKX428O0Oe>p2zFi;ne<SG;
z#o8)WbC&c>VqA61>816J#0o|DOU~c0PpN3}uiM0`aJIPZJxHwmv=s)$8m*cH^}PtR
zGDM+>DcShBvROP0DS1L^nC1UXsFn?X{I_FfvZj(Rd_uv~n)*xIwf^!f&n|ifJ?>?-
zWOPT5q9OeXdx$NS0=;IB;wx(Ipa61BDw%0}RWusyc;+9n;oNMW8-w2M#UBuSTF=s>
z;i7<xsO&3KH_FpBhtu>o;1pCCy;QHsy!d{jfjmy})b#bWiA7(yOrS6q5x(+_Et7k&
zwwS^fmyM}_36H0&62<u@)xnom7KXD9HAr{9`82mrKFFt>4?9+#tj1jS;=Tt;+NTQx
zhj_p9rYQ!UMYDTjZOzrq<pZ5f48+baZg}Dz!KL1s|Ln_E4J~fZQ#T)dtMPnf`_)$N
zG>`aMKD6~+?-ETM9OtWfI$+i{z;79f+DYz^D8rc4{3S1OmeOx-8~%7#bHm4s$M}Xm
z<Ua^Pv~Q>9@tbQ5-Lr$i!CrdiGpN0@`aQ7fz)VSS{~@HQbKsUxKfSEA-D-zl&+7gy
z@s40E-@EAiP||}yUK)KMR?Zzjeq>n*maDL)$ai=dua+4O<R(x?(}RswK}a7ZSkLN#
zB5l<BQrlm@uPu^>Iq{x|Gh;_MQRm7D)aS{^!(clkl5x*}?LA}#J;`Tep$zQ4RDZlK
zb+rBqDh|*;m`H7rHqoxoz4Gtd^*&U@ZZwEs+sW|RkKeyV=2va+t3uDDMvN%gJWgl%
zI{3e6n8({L&eiYgThtBG7Tl6!dBxm0q+i3u3J5b#8GW|nXww3YRkgKN;aS4{YytM=
zC8r@TA|)f8-+YhQYK~-kX74~W?fz26kL?+`#5o~;gz=EVMJtq|efwDfX?FZ8;^srg
zr)}&r!+%l`oz%rApVwMbiXFzu%mxy6lL!S+Rxk{$%o(dK&Xx7UjHS0W6{0|Swbh^<
z9xf>>VIkBwDy~r}(k&<%T^zG5sKld@gMetTKr{Lxs88TiWT?NXuL0HqmBcj4xU<w0
zPHpkV%UTG@8)U5xeJjeuyFDQElNeAMu^556slTwbvw4Np%3B;Ijm?zXaXQ|Z^1ya3
zlY$Ec^j=(+s}&d0$oAnZtk=ACs5e^9QiY9FO32^%jX9=P9+(*14Dc7k^NEb!kiEq;
zc5)yJ2vnhSFh4+^W>1Op7|1a0;S--NgdA7%)i1dUA5`IJ4@A(pTr9AeCW7TequPyi
zVR)`1-dLSJJ1+q{`}QNAV)P9->kWrj_Am)^M``uBnyUcEBV+)YAc7-iP-wXoI#>;t
zip##`GUFX(1Olc$d_Xy-t^}{W+BFfJ?uXoX2f5Yq`pOkO$xInrQe~2m#rYU`spP+L
zQt9>x{`)3OoH{Uqkc-bEOSvRYEICzEdqq2c?R~@qh2sCr&@rLTBI(MEV=RD@)sH}W
zaK*eOvNPRq%y8KXWRrMWgbP2!<fJw*q~Q-mb1wYPF!}_eKvy(Pu%`>ZYC%UgHzKNU
zJg(;OYxrw=gy+^+vFq=pB67QCo_#T<3JCk%=OY&VGYlU)ZrA35NRhH>x?nKmB@&fT
zt;G#4m}Yws|No;+G%Z=~iZqkUpDL|7_fk^!x6_VgfO#6Ljv@Y%Flt&Qm%Nn+j5p2u
z)wnZapEdF9Ck-sH-B7^0imxEQ6OCbZGsugS66(p!-UPw4|MRK*6kR+PVY^&l&u>Xs
zpGAqc!_5oTxb&6m^v(?RCZuULgoeADu%@J~pSQCRP-p0bnKnO3{Gsm_dVQdEFwm;x
zt;m2D)v8CDPxm(`!@z@V>cs?o-apL(6#9VQZ&KcfEP&g73@EEOD5=JLDCh;Lww(ew
z37!ioWe71w@!X&Yso6~sYsRmxl)YoXQ9dNtl*0R{>Aq5*=52R!`CA_jDiu8RxP_e{
zP$xT9p7Be~L<yi6NJk~|iFan^nAFUK;JS+J&|bs3fFAbOTRkmaLmcQQCSZYBHc;tU
z07bvZmQ}CyOok^WpH_dgt^bSL(KCB4VbpGLUZxylkd-vxaW#of5*iLZU^k8u+E+TJ
z6Hx1vUifq*a|jQlyv)p~I5i)uHU-1f^A~)qN8&?-U{smtG^;CQ93}yDM`xuLSEqw~
zf@f4o`$#Bb&koE2C#dla1>2`#pODjd8idoCqhYQUCFArTB@5Lh$BlE=5tW#8hoVa)
zE|{IKA8K-BC1T&NXR(>JK&Sk@3O=U^cK!=?8!nP)a?f^IXp52zP`Fx=cg#(E$$#t~
zpZ-Vsj=$ODzmmsZ=|5dx9*4oIr+He!DJ$aN7D6ApQoVbZ0g5^oa;z#A2P|uzdemD9
zd+kp#VhR%-ri2nUs|;?)I7W<3-1g!h;vZH+%Y|%&!!*pAFA;nyg<wrG@vYye_GT)B
z2piT387~<6r}*{ZJu$Da1Vjqy$Rf@v^s}?9#v;_fKyDRjm+*P@ye9Z>QxNBroDHii
z<TxB2mz{D&4F%<6WAFYShVxm^E7gvEO4tQvf+5KvdpEtCR0tMw7-uU=$LBw&Vy17x
z#NT35aC~ggxb3Jw5seaN(aa|@^>%eNivKz$(CxIdUx8|;>KUHM0an?fqV)SwwxX2`
zFQrvGZ`WuSb8+baxcJeVl}Wpw^(wcNZ;P%6Wj4*?DskqYCVgKv{}c<F45Z|`gf!Ym
z36X;$go=xe%n97S)fhusnJiwoSOy#pqLk(hj@9!7jB0BYmIsnQ%3;EyT=>6$axqt-
zofg1)ep-o~^$sBvTuMp4Q$83$G5{aN(&t_Oa^wz5;K9WAUX-GuG<zxoz8S^CF0|-U
zibBX}G`%sE{Tk<O|N9Z0({+)$&=Y`<ojbwv9Bqy_EEZd{MA$&(fmrLp=Utc@4!6`4
zTNlFU$jRBRqO^j;a|TPE3(;`sDVyRdoW(%X(Vavzf}%^QN<#66+QXhi%%saj`iE}_
z41^8OWS)+VW99JoK+2QH`JMy&Nst_^-z;Ha5Km7PnDMrG3Xy_ZtXHHltWVEqT)SCu
zOc*)vGj<+{!2;FP3#Uw*Snr>HIRPc9^egLuRaLx}QasoG34^3BPEm}trv6Rv)D}|&
z`cw4nBSG9pI&ZOH-a+O`Ga}n0&d;jg{xqrr7kKV~Sx~V~qEDJM*xl+7N)_kl*Fw@F
zzl2_~o5kfsES`G4l*gse4zR0==U5Qmi(r;oV^dzqQwVQzoY>FTk)LFh@wk$-P1-wA
zTY6W-`}X{*hh@&*2pU^>NcftQ5OVNl=YQ5`KeXY(0<a{j=v}vwi9fN0Y#SNvig~7D
z;eX8<k3Dqj9Oxp?=!?YE_GC%rz1hG2{`yN3Pz-%KYz_sI__QP)P7*n}RMS>>)#L#%
zi-?UpUeZSmWQrIu18F=<7Ii%*-OP=uBq7GYr%|h#GimrDdX0RJA()PR`(edZDIu@F
zwY5P`t0+%KK}@`d&S!bL8ORZU<VJ70rI8k4Jc}@OajXROc+YF`o8X|$dT47}UPx_;
zuRHnK7h5tzqxa}jVnXX?Ef(ma9D24Fv(4u`Q?sL6%;#=2#!nOwh7bik*zNiC5lRV7
zF_(UlEx}d<<!4ic$wS64d@5u4CPc6L7!41%=rxtCf{yfA=~oQ;7^OTAc2HA|lFWN_
zcSyOmo`0?!%y>A`hqBjNu&O_tH@6O59C>@p0`(B>$V6y|8>o)I05j4ZlV`Z_^Bswl
zn)L|h;DksQobK-neoavU!*j-}BC{jQj&NOW)J$%r2r5-<W1X(;x2wy9iKmE4at;%M
z?*c&^q`a8YEBC`on;kow59m)#iL)I)U>0tLe%>-*`W|`qPsKS(@T-K3Nc`o3j1zzI
zuNgpYoRl3<gquth<C-#+Ef<~`);?T;Hj@U>*t!c(Z6<g-mz3Q+w1LQz(>&knf*#b>
z1?tDCoF<^cC}gelx=X61X6wt7?0Jyv7#t~baB(rjpj@~eUY+Fz3<d6Pp^Q_2iGzee
z4hi-P1{BD`l{bKva_&jMRP;%<O6h0P7`qM-9Vg|sc57q%r|&)9Uk9UaS~A$;2wWbu
zcB{=yc>=Q1yj-$Afq!J8YH?K4SOyiGs52BW?0eN}^<ialMXo$IK2WY1QLHtsFnUYD
z3`BDOcSREV<4$_SZ`<E%j%(z|^rd#Ny}@^BUbmUlA--Jvgi1uiAMf-gr!V00r8d`h
z%+N;1H#GdribIsN5K;7TQh!(#6Z;>0*<Zn4GxwvJIo)gJZ{CC9X7qN;%YX@(2=DKh
z4Z~CW`A`V}2gYFh8yBp=fI59L$SKBegr3rO;zSG&Q932o#*34eilYGm<+k>oCv*gl
zUr-Yk{HY)DOGxuKpG_w#8Km$R9nUdr)Skp%Rbdp%k@!nGXgdHFnv_^5ibM&`vs~dz
zU?SRLxNrz2BQDLAW!EAWSOz5PrDI4`V}kdvmhpAuKg2pkRQhL{lCE;HLOH^e0@RDb
z2+k_dLN1qI^h5qiN?iSFR81zA_!j?-EKH{#=_K<%ngm3v6w@wNg#C5!eYVfRdxnM(
z$vEn;Rj+W%Ux#?aCgVC~I0Xyv_+wH%IMhB@EPe?_`wA7QKw?O};4EcSRy#N4H#lCl
z_Doi2ToOEdxYyU~%i1th2Qsea|7ls7sK%a=l>&8ZuC>1mps0}+F?lDN$T4}os{7b;
zf+-E?wax0M@!K*MUNin_xw|}tV%?c@v<N5&Z-4gdk$Bhc2#THtMiD@E*d^fnSKQU-
z&;QwM$?Mmt5A;gWh9KlRo#)0vrD*Y9a51ngxMe)CVqc7+opxx55X=*~34f-10unwR
zfihM`Lx^RrxZj#78|p@!_+}3D7r7{bQDUg6jGyF(=*pnq1ESsjXrXV5pg6lJZaX9}
z>mX0$&;m&b*^UwJ$7N_81DE8Y>-qO3YvCu#%ylvg8@azQGQZGMEKuN`5;k^Pw8AaS
zqz)yRN?PS~Z@r$O;7evt>t*|^vu{3?*C}MV2!4f=zY}_y=t(C@9>xa~^=AV(M$pd7
zz`|P1zei#hsPq|^p4y?=vy#QFPS@O&PT~QA=ud$_rh#jtA-U=8D9`2vDb;DXk=&5Q
zqiL`Fm`gbK<@i6@i}?I_Vx5k;x)uSQN6q@Sx1dC={J*xv6r)d<<>6M~jJSK~u<H7M
zZ+E`RCynJp*-|I=b>t6N0muNzf$5vJY?88a!ukI6WLcR)Lr#VQ$<q+EI6Q?9xglM}
z?=~MsjGh~}S4FXTJMCiMJR&mmVmhRAK44N1$KMnGibMVw$uEKs_l`tc(}PwF)ev2A
z7dx*hB0iHA4x<j<Zz_PEG#2oQvNBMs7P<d2>!tf#EbPbWXug0Z&Er;hQ6ZuNA8S{8
zucToXx6eCVfq^o<Vk)Tgh1^bcgF{dHL{h1Wj;E}WIWl3Hwr%Dv*DKbBC6`?|8AIch
z&1hueQv)1%f?t)Nawf;VlDQ5PB7W6Qfz4PZ&mYRN+u~lAzIV@D%a~819tPSZ8(i+@
zykqB}e#vC_ha>e57uMBN+bVIisY`eHO9l@e=#h1fv9uV5yhQ>QC5*ax+aJI&9wq*N
zXMwU&RUV(-T2!oD<w$<r{rxPcUHSxf!sNqBLOMEIv23B=p-_NWJqe~_Ve_YDV-f0L
zqmNB(*|o&=+GVA{N9p<&h?zJ4PMJysrAw{<v_0n6{JV=;{C8N`M+6j?oNUR$VVdym
z=78UaN3&zzR>6yFv|Q$bD-|D<=$ZA&ZdEIt$p)ESaTpxbac0zZf=2j-jPg(fjcKGZ
zjhW4J1G?iqQKe^!gIu?}_s-&mVzBQoJj*_V#mV!E;3tVuu^5eHhf@f7n!>L+?0A(|
zd><UI>nU%X3THJes+=5OX87=rAj@0ug$(WkT21BoKrO+AS0j-CoJq&RP?dI5E0;S@
zvcDX!+|BXjfZ~5R%fA_ZEqR-#x#deTBCrY8JcjpF5x1&VV3_v~-0k#33~B0zJgV(r
z=U`Q`HAb-+Tiu39?D6;W`cH)+D|WlIz4R30hY&L`PZ&0ekkM)0kF@0YX0iu6HOk7Q
z=Sf2T%D<$<!^z4p#BlGg!nj<J2Vkkw1!o2?MgZnaKS{#Z8M$H(!}O7yxqmJQUnRFv
znp_0YfZRvmDsNYNg6ewD^fa+)$~YPg`+#!(b?L}lsqvT)^rS@obywG$WJ*<E(hFKU
zx_9xCFNOh2i(z$frYR=%UCZUFL(eBdz3m+9{Ft#$u)cTX@yZ&vjD=(Wy4s{y0l0H8
zc!dwWtN&!(hmjpyJ}&Qt%YMi@#CU2ESO0te<XKzE-k?)?L2iMG{u?A5Q|RAjnf7n{
z(D%A_Wd5_K8_GF$F!3Rqm43Q32cDJ8-!Y3na-`WgLZV&ge4oZvG>;y-dN!A>C?bb`
zT6q?L#<ZB}=vICkU#`&6frX*;>kg74`Vu7!4E3H~;w-DfJt=VAPn9Z(BP1YIq>vpb
zX(W%~)DIv1*p=iy>js}|LOJ;vZ^7V{*=l9Xj<%xvxRD<M>S%vQjTZ@uDc=`DkSq!W
znE0hiZ#6df9oq!=Z8BR7&&kE11_J!6DQw5r%xs~goY}C>05Hr^Gvif0Ta#7moCBi!
z+3G9aW4Le?(A~gf<`5kM!?RVW>;0(Zo{-4b8}5pG98Eae+YWDWwrO$2D|w|mxt3R^
zz1lxg>Uh5O!EA`T-AG8=vGH?@>PE+&sY2rO7m(ZBI!!&e2wf^q=qPmawC$L2vH~@+
zgtURAfZDv!earJ`d|{ho{{|)*T8UHUeM^ImdG^A_*DgwbM4VA_Tbx?4W2^Oo-*EgD
zSiAMcNOLvOQhsbOsF)PA66ZO-Q}Edbq`MQoqY69klsU5bHI|2a7LEGaE@)U4XFj1!
zCjOGEZ)%)#q2XJ^3@ZW1<C<%-0A$E=$pgxlbTqoKJ+8TDzuWLpP7qMF8AX5?GK~_l
z21q^vb|6ZN?kCS&`MNd7%VETYVN3>UTd!m0+WU3%mxt520~X`fD4g<XF>$uKeDWxP
zcY{C05AH4K0=pEA0sZ&N^8{M^Yh#e~OT2^=K-cWN|4ARdDq9a+a;1!+*UyE?E@Wog
z$g>^}j@!}xQwc1b>_~iHYsVgJuK(kN^F0F&H-`Ex1n}$7ETRS+ev;bhhIurKJxz<M
zo!oI6r$*>TD-=^TQqAz3z$lBJlYv=V)daBQnv+>(afBBtn}59icn;FN%Q@7i-12VU
zUz^WwnSR&RId^f!CNH5d=;^Ni{#XTEOQ`@#0f5--j1eG8raj?s0$yZVi$he!Yj>K=
zv(7sB=rI_8%d32|*qKO*7$O@_Q2z^SOe6PzM7pW!6?QNik+gN`!z!YZBw?Jh?%j##
zp|0k#c-t+<`&N5g3WS5n_l{fnDZE_m4eD|~m;>AG_WYaXukF55%i&*mt&)?XSPT{1
zP}Swu&_c0FTb$!2J&DlaPuU?3%$vjV{+Q^E!i(1r!A@#?@q5OI8P6WbVQh+>W<y<G
zXmb_dPNYw%FcF`C%D0heqK9HWGQNht&+BX}+#CZV@-RLuHg#t6b-7r_mn8Fy!d-ot
zwG>H;FmK*uoC7oWa1(G3j<mUd540R8Uew8N8OwtgKj}j4rvI58t`NWv6^WII%X{S$
za6tcMO_jKpR+h`Wu%eibF1-W+@Uujqls1u0N`9x~VKBEC<x&mEoThn#R$&85xp-Zp
z);r3oysb=^@l2lDGrM^4&F`LMG*$qWAK_|iZ|Jv_ua;HP(ClBPK<EaR51-a+FqzgJ
z)+urYrR3TnN@h`8U$N_V$s_8-at;at=$~9n@nZ#{!(XKh=a*IYl@GHNY@@<^NQ4W*
zL}VGIl<U;B=fvg?Br<**UdJf4XKS5`G~kBFsf2gLj8pheKq<%KEFGMd=AhYUx&5{@
zmOGPiT%Oydi-`aqiZKG9hhr6Yy*E^j!LK3QF%w@yoFy8?545Ctcq-3i(9A1ln+{%P
z=~9Ola`gnl@p!<d0D6fvF76yr+<VJ;(q?f$MmbVq9)^V-IX{H+`Cm4S-LnCxeon^S
zv^<inM2Ar_6?Qk<c7x^=8{37Vcgv(_aC1hjB#Ee#6_Lly;<JHOwe{0nW<sG>h#@c|
z%t;8@=QPVFjZ=;d@lZ!+eQ{D0Yz#?@Vp$`PJxo#a!#5qYMXn#Vtuda~SK0kho1AG)
z=cZKf(cSB%d@jD8?vbocd|AWFVaOfi;gv_)3vS%GyX{LKG0(h#JeKs4$P700CPB36
zME5<<qvNQyYhWwiB?!Rbq_t2Xq-i~_YaQ%3H(q=ge|@#Nbd5UV{Xkr6Y8n&%dNxac
z#B_5XXQ%+tW_Ba5OfY!q^%dUZ^wQdJ!pr^|tjFy(U?m_VYpak0N<x+BQ|;m9S3wfy
zFxh=>6;D$zq1{3L8TGponQiDFU7pGSHRozJo|EOsLNYo)N5I$I3WcHxDFwVXb-!fc
zNX>W(MiZeINLB<$_Z12RCX%2Va(?E`CMv5UoTr`W)G=2vRs|EIr}4RCURXGv<3#aP
z45iXgZ5vu9X@Mjug%rY9;s9ddLQPmIjqK6pK<)5S6;mTIg7l2%RLFo#1QsCb$Gu(A
zpx{Jm8tF~6yReEFLbc4gFtJL|<2j_~H<US)A&bh{bFGoJsyUdYZYt~A7E-tyEI%J)
zP~Z{ze#R;mRjMjI!&BKsK5Hb<*vq=Z{vU^M^PM3`0|^wV=t14fyw9Je6TMuC!9F6k
zxg+OwHlwN5?2aa(9z{|GyVhLK5GJ%H6&sH(Of51@Z2F5_r;cx*C6>%+z+p|Jbojs<
zzwyGFj#$iTs<B#~uS<V$feB6Xi@oPJxgmO<g(A0^NYN5iQN}<y&K1^<BP3172nw*N
z+?^3FoRiXJW#tR%b~2e_D=JAcGdCBC7p$(haVK~{zZCJpvpD507qb40RC310)@KeC
z;B7V>4_hzZ_i-@}v6rME)>NRXDOwa{FLQ{G?xCRywyPA8Zd7*md?6c9N^fE9hD*Kn
z#b2q%l{$zdc4v(>*n74^{{}Y~i}zZ+H$6E2Be4rn)OhW?-3w|i%jbrmdg*Ts>>#U+
zICvd{WIj+u$Yvmkq;(kSFh)xwajVIw)apC3Drm-;Hp&i&a<vX{K?xcH_92R#s_yDu
zoG)Eb@Rf!MiWbI1;IAvrKmGJZn|vu8{{*wfy~7K#i_z%!n3XapBOoGwu%e%b%2#I7
z|DoKtz={Gr&i1oZ9K%75S=+kYfCNyQVNRNbw~y%PW#zH`iIvlh)jz7G=B1TD!gsvG
zC<O)<=MY-sGH3*|ko{w=fNbsXiqB}m%Pf+B==c&|<Dy}w9ds5>pFsL^0OJ9u#Q(1C
z66#dG*97b!V#0#^ci-fyJDhfy$3hGVh#HB!aczssYwP>)d{4O^#vpfy31Y^ak&M!-
z^|%pzHxf>Ba;X*_`hPATC-utzjbd$hptRv(qCfvRBE!a=L2Aa=nK^RPfp}T^9xE7S
zpia%P*QBq@D{NOoZMyNJVlRX7@N{B{-2jGpx+uTU)Rv#mAF{jYCF6^E&NlFJ_f7Oc
zU!ZwK!Lz6vY*CFr;+A=>iB28b{JY5V{=IaybjLm7eaxR&;)WP>0LlP5ng3qejyFPf
zCuayssLaxew(;~yB(QlciT}JhLkI11@hTaBj~7S&Y$dd4{zzdw`4v7eMkge&JhhyZ
zdn5)ICqGt6sG1xB^Va9tNyQa}^It#Kix~*@qyv%jRK|VF#i}W(m_vfQe(@0n-t~=~
z3&nVHxu#<2M^^E8nEJ7ERIG(v;T@_FvJ$pq%Of_qv}p#T&TriJX`_@yE6!7XX~-0(
zAt3?MHD&Av8IbtBwJ&aAa?OJd{}eBt8==24O)caap54WZ7K%*`aOHk{0fm~)aGb@x
z0yv2j5_o=t!Y#Yh%*Z+#=_gg-_IT$;zVnfb%^w!m@;B{&TPSIK#K1iW5W|^p+)M5E
zf!$#dWo&yH;;4OVp%Mj>$Tg1@AuqF35LSN#Puh8Lom5MP)W|1eaO5v|M_UjwFm?64
zaysKcfC&HjV$*-phl~9T(=T;0$AHV_U8r*xxj6tZ4Y0pDUZn=fW2q+;%({2|s~r%@
z-RZUj1H}SKh1FReTdA3uv0MYLljE=ThVIc9=Dkd0VP=4q1_Hq?$ciZ8edW3OiDAp&
z?5K11GpXK^tgH+W$kr*m>z1paG$eo&NV%3ee+y73%~wZH^p^;H>1{zX&OG>Kx431*
z7OoZc$`_SzGY#q_uS`F*Pa`8zJl?e3yztorXU{bnM{fLPaKz_~$@g`T`e0)wIqlT7
zp(URTPj%dSZ};!itt_nq7JM5XQ0TS2$*>G4F#eUa-7>i|;C^45y}JK)VS%^aNvFAZ
zJ^s4h(f#{rS>|R}-be6Vy5B)qzcW`N3nPFeJGmps9I+Ef);o;yx!iJ^^6)yf^-bv}
z8bIib#%psx>2-8T8GUL?8vm~?A@8xu`)u^6R(M#uv?L!h6V?>~Y-b7oc%3Z`&OEKL
z68$YX_ZbL>IX~%Y+<FshcBsDXaQgO{3KN{g1df~08Zh1t`6eq7SLE?$aO#Qu+r7om
zf4jYV;FDSOqaTtnLNVLPU6FrbU9?^Dp2a~Q3g+U{8Qa*UcC=pEenm+N;)vizL5Yp{
zhe5QW!=3vwzMK^wU>m#b!Xz)r_!Cp(b({M=+|pdC<MCcii}cV<2+O6amzTHWtN9Ui
z(f<C5PYt{f<Psh#CC79M>5s?%o_xlKg+G!>>R7`NC4y%XZ)HMrddwR8c)`S=#%dtN
zy<b3dAmc?OX?OWXVQOl?48m)efp_8?_xry4$fCaP=`}2x*xT+q$;<n6%(nr>l;vzc
z{kdNN>!?uVu{o<T!N-K7mESghyLgY9;Js=in?}EJYn>R1zP!J(?Zw=+YL2LmD(e4b
z`ny3r)JpqU<rRcv9}9<ygjE7gHh}*I_TsL(sf;3uX&}DjroHDQ1t~#^ce?inHn!tm
zM?N>b@{m`@<7P{yEb6l=C8kZbf|4)=;5sxe`aCeW+K&YgBOGm0jxRm(V35;UE&PFj
zL#9b%tbOD7rD$(e0XI|gS;AKR^&-jQ&G@BeQ{Cr0MR4yQ|LtGlMl~#&Gd^Lb!V2QB
zDJTC$v8a9n=;G$R{i@>JasT@WDB<}r_`|47*Hfn*WXGR2lqW|^f5?%NuPltyHQ!SC
zN4%}RZ#GGOHQp+gr~BxdUQ4lXG0Ut{8_k$umGx)c$LyA|_IFKJ_sgGd<3v!}$(JvX
zTq~@)9rgG}ntXjyK)p4zfdQT~xq0ZR3hJ5sq$e-%6@meJz-O6QSl8=8VqG8K?-xDa
z^zH|;I?qYVzByYMaOZk9kKGM4b6?C!{LsJ<T$NXUfPi}0ViZ-@H0URX^g>DwjL<3W
zZR7EYZpo(95pYMfc9xAil>Pd$R$uuXAK^I-G41^L!~p}K9X`RlWm=hOj7Qr#tajXo
z)!M$%5W`0)eOoV<PQC8;yc}<`l$0Vyr3<le{rrcbX=x3jtsF)kzn%Z%_BG%1{a#cV
z{Nt$XuC5qyS`*C%xLp|vip4aibkmXumwxUHK0}n;B)w+_`}Cjr(7*tJoI~yoQGh6G
z|7!j2g=pzWz<KZX0&)O`Uj^){mg%Vi_RKbQ|B1#eM%acIcvXVZ$Q0#yO-If)-~JG1
zRrHV_RN^l3ebNz#z*J2ivt0zblDzbxD))Cs6L|{nr*1#9SfPMBtFQ0dJJ5cmjJYrF
z-CdU&Bg(QYE?+DQ0AIsA2j!_bc_4sT(;^^!J(0#OMkHRRf8+0RD{&Wq#NQ&`_wu{Q
zs2y#Jojmz#yE1GEtCd47=_!0!Gp|^~(CYneqT)cb?GXv5OZlm?llz)Wlrc9@!wT&^
z_r32@&lDOEL_wyVSAMdkHjjJRZe-clT*m3dbyQ$9@HG!YE3+-YR4y?gw%Q~uewQ>)
z44U;g$_MhmF0bewx7to6%v%I?*E%foudm74y2m2k;+B<>t8&L^79Qg8lhtNafU-#~
z;q~JxBU9b<weQ2x1K<CwrdPYm_{9r0SK=>xNr_y7weNShe2(dkP99#D{+-)DU5SFM
zHa+em4Q6JU+ze8;-CVZvvg@Sqew1^qkv7d6AiMvtv=;ohncsZPS2mt*L2TxmXj@j{
zWtp&{Rm6YUjdr&Sx#B&=Gu3RZ>2JGfyBD;5m;%9|T4iL{=}-ITiCgWG4`A~zs8J0|
zb##O*tC&R1j~8kEeL|+hLpWJYdI!QpfZDFDN-)_{DWWzofG^-NiYG)F@d-%#NkoR6
z6&QcTsG{SINYvF_CQswU3{Zko1-`!{ZafA@X%}yHF+lNON%O#HN%ItE$8ur2Gh=g9
zyBnisam#chcQ9ed>~hcYmS&R-H&bZ@E!$`$GVqsJT!{E+yG&DisWE6dgKjPIUr2Zx
z({2$7OU1h0miESE{zONxA#lxZ3m^zGFca@=I%AW`D~!Ud#0Jn~FR<lZhgWw<YhNQq
z_%NE!JpWFU?)?&U2|i;~mG_3Ti>y1qdE^cI^TQb_*E(DhvoaD>b?l7&Igz<_f{vSu
zXstLE@ar<FVQaa;XyI?qYj7946O4z|^gMZG`N=a2|CZ;MuP?^w_`^B{9#NGS2^goQ
zx_*xfxGK>D>wM#}jXGSzRPnsU=!Lv0fLINqAX=BpF4co#)xZ4}{S(UzG{GzFwJgc}
z{deMUt72$s@e%FRF^mp4YPdUI4hmC-L9CGx@CvKk`g=S+)eER*^8UUg^En#Zw;n!~
z6i1F(($WUj24}z(kmi!v?$7A?(@qF0k>p0`H_Y|M`avx=6ujl6QlQRyt$)r6P|{=l
z6=G){mAmvjNhw|`Ne#C-q@EplCrBCE`hT9Q`4yq+zBaA<vjyH=kTi4lg7@?9*=q(`
z(;hp1&t4Z8O$r1eOx&fJA;KWe^@gR{Cvj(78R$&kK5K@iR4MahMr^?6p|{1m$&gm>
zS9zaBgYbOMMGG^fEp5U-`0hE&wb}XYjAKhA==g$dvqtSL#Ss~qF+<Omme+x8Gt`*L
zYDE8H9|zP7QZ0jyOKzDdcw5Pt7C+)e7{4Fza?({D*N@S2*ynWT*$R%#&zdu9u{m4#
zDNS~|SpAfjC0${B%8Z~^enJ(pKKYSv`d=PW{LlEn>$664og{HS5*ALKU<Hj7;aTJv
zBLj2c6i;SxI3-bl0#Bic+9Rvr-xsCa3^Ameo6kuj86jU;?b?vrL`EGpfuUT?4M{8U
zf5M$9ITkh1^g;{3Xj^MnVQl_deCNR0<I3N}0t?YRO&^{|R(7g;3por~r7tLUnY#G(
zLaULp*qr$K%KU>o`ZI9q0ZFugJvCn92*+ot(-XhaiEEDEzh)+!V)8iiyq~=aX{#c)
zDx3{q1-J_!F5|dMc_#1^%K6{>zqH;`<^h@kIq(lcqwD8)L7wj+^jd3*kXfUT^`CD-
zwprpz<7nUXpesx<1Te;k*isq2?B#vI?;|jjANs9OKx~q<Q`z`VC3k4pu#$LQgq)4G
zn_no|?dh#tG3u!PbQmhMOGh+M+}sH=6TS{|YNp<goA2Rb_0@a&MVOgSS9Xb@kH61w
z3ydw?RNQY6*jHpr`CUi)9!yteouiy#z4d&-`HV;|Wl2INaW=Oyh-PtP^4!p~{n5Fh
z`_?(AnkI_v!N==U^RC#?N{1`3-M-5gn}ri7nhXTD*%)iSzKyz_^=7zM5%>Bs))Omh
zae?4$nf`fxkwStf7pj!i)rD_Z-!j@$gM&TU|HHx;mBEfbc-r@1<95#F-Tn!V<Cbak
z^|#ZGB$gBKcXO`wF}(4-YC}VXB&_Ulh$T1T2T?$CU3qw0b<b&5Q<p|VfT0#&ZQMtu
zq?9(+sw!Eje+^}VZMJC<Y<Chi<@F82@}({E156w`rC`2tvqivSJkkc9adH1(#wV1`
z+<mqq>9f^#CEZl}>>u3sg!c>4W}&Bi<daC!Tg0mM!)nfbVhur=jt+<?DdM$H82tEu
z(-yDi4C>mgXH0nZ#Av+>vk~e^O$eW>_b#>Q^#N|ka}M1|%r=scm7&w^N#xtRL#80(
zb5=kN%(uWt*XJdd@TAvY30d$<7jY;&;mt6M+4Ij@4Z#8~fuAS5s!T<eYk$}ynK!r|
zZxGDM)DvE(Z#I)i^KkADdgZMQ{)^c0jm<Ye3m=uBV9+vbB38?q#Jdn*=|g4VZXE`O
zTi`7?(wLIw25TOG_`qyp-0F4AP~%`5fC=On8rS^CE)Y*}L3SG`9rsbUZTx|BZ>6R8
z%QWC_i8U9e6(n+Zx-4hLx|QW?<wn&4a`G8fRQ&bfa}>yVv@3`Ig!xrBw9mH{OH*+m
z2NgKlTVjt%o{heTRvH8WqN&>A$V3$VW-UR~E7&ZwHn|oxSK4c7UK5W5MJop+1C7Uw
z|2uN^{T=Qa$#66=ZnjEQ5%5GX7d8h_2^?OlyD+~Vdj_l|rDqR*pT{<Z4$$NU0<}<p
zO>%3S24JO<h?1V-gst4EVD6l&todYKUemQba7zhX5eLx$_`p^_P&9?l!qqA_o+<c`
zw`%`+aBQKX8n9_39mLU8VAKn^MKubv^Cv~lUrbOVH1-PF1#0=b3UXkKd?u`TbAEl_
zou!XfBmK$ihfl1nY+Lh4U6m;;STx-tZVakkH9`W|ma1^>zRc+eOe}E^jgAid`kKWa
zrPzWmZ>1%f8O#%_4C5?@gqoz|VVnar@q<dP_w=+}gt_{~N;yVz=(!<8duewk7nCeR
zvTT|~c9oMbfiv^hF9>PyrfYxk%sPr&pu2wH)sRwhCSfe~r=j7R&NG^uk;2MnsE|7@
z*C4w>&q3Cb>W>t#SkrH)Z5VEZtoz;umaQ<LX)){`9vlA=G4E%MygqHJ3vupW@;Njv
z7RYoAmX!H`e%+a-{&CvsxF~;^OpEA=TuAv(5~jn<qb@mSj5O5eLoIp5JJ}`Ke<hMY
zJu1;~DJ_fJw?Pp=J@w3T<sAYg2m7pYxO;WM=VT0gT5FF!LJ-_SelQv}4SHz$B3da8
zdVTP#21k6_iojiUFqHsnHcWIOvp<)v@~oBo04q<pT80&$Q4NiyOrJim1NXhNXKYtj
zao~qz6)tSZE0tn4ZB;~sm<x~qanr}!2?Kz`*{UjN!5H01Naa-vz8E5yt6lM8OV&Q9
zx*G-0Q^8l`s8p<4;^)Tn;d}!o)gfn-k=0uh)WCfoxJ(68;7mu6stkqG2^^Q3<#KH4
zV(W+htacv803le62UxCka8h$f(Mo>qp!F?g&QanUX_m!ol6Sy3&L-p1Ht0K#T&tUE
zMe4LR3@_N}v5Z%ZVA~pfgVGDH<>wj#5hO)&*}<^69&|(YimIgIH97%eRrrTgdlng8
z2Z|{QV3r5IDF5nP1>wYE9d4nSuS(%NIp?TCZpg<w^yqDqt~#0qjZTR`AE)NKwJ|Wb
ztL_EfY%QMn5)T_62Y#D0I1ENh!=@=!OjjhHs`5rCr##ti3uUbR{b#nYbU95F8;U@K
zem;=5QwODwBKw}6N*y-wal3{AA+u1Ss>keOm57H#;}B=Z*O~A{daYORV|L?7{@889
zaEdWt){6j6sLtwOpHCVUfzpzbzy(5VA*5e))L1AYsd_xV82P7n0_L=uP%LIW)~UK7
ztiz|}{b52_&2P?W4P=^JDyQT$;bDF6KQf-pSpRN+`=(c4nt7nKZ(+?xN{CK34`wk@
zN3bX$SuI)hB@N#8NPLaIY3f-5nR=tR8)ac;D^6bJ8CuPTf5#(6>laBDy*<cWzG|Y0
z3Y8-eWAkUt!3&^gP*h?KH$cx8F|muSPn|IH@cGl?k`z~h__kNS1x)Y)obLYzi7cqc
z&>c6y4@9sR`hfgQc=|OD+f?={FFk`;M;><&&*Yh3NJM+I55A(kbv*yoX(U?^tL$-H
zvJFlpJMrHLKPv-yM&cCF>Kn<ylkBKISwiL9f*Fi=WdS7<+l~7H&lXsz**qrnh)Tu#
zD&HXU{umKz>pdSvtdMJ%v{tUL<~LS!WM5&IQBFh@NJR85b>+qsva70+oOH2^7ag*n
zLHFVoCX+WFiKvjXe}|^dn5v5cftn*dtB@OY=d*~E9<sMj;0ncDK=%r=mw}BddiJ)k
zXBw|Do<lPxSm>`f|HC%3KEZIPOilmii_b<JR9teAoNmL)t-GME;AH%Ez@<RLusT=t
z!EEO-^IncOzL+;pnD7fepc=ipnhqeqFl6-FpY|)2Ht>O1>zY5%zVZZvj`nMKTKLD)
zJEzm7=v`zQoPtrXy|!}QXRU3<Xx7rN{6Q`4SJDi?j8}EU5nuo;4z3>YBhfrTb7xk`
z!-rfXdut_N4&ahg*A*q#JYzZ4-QsgvH8wbiOAV;`hg*l(wtQaECNz|pV-dlj=YyiI
zdey%Bm^9IajDYxSF3!vIrtL~(QpyXzl=)QqKo$^^u83qt&XjecDc!W|Non8)SGQnb
z&ns+^)QKb;s8z;}vak$<Z#BTvJVX6&DPlPHC3)RBr(7rx;(7pRP8oTIU-g=<mH<69
z;B^yZ8L+^Ba*(HK6hjeRAnjG2)aHcG0zyoC?;icz^~op|lr%V$t0&$yNVmC_Ln$mi
z;UDd!zQ0!9B`~?K{OuuxMsAA~-OcVoOsT%`f1^M{Rul_ml#<N_#*lTy#M76s^z}IE
z8%SvA<nlE<se$hfxPdS_tE<-X=Hxx^oYr20FTXO6!XwnngBA8x9%z8@D-5tFe6l-c
zqeP;Km7e@yF9N-6T3T|X+;cc$so&BQ&E`?QCI<Ec{!MUs3MUAOX^_<lZkmqZb8Lp+
zsoq$o0V7uLmk&8Fm9S59&wYEDB5X+tY%Q=7JJYoH9@DdI9v(==So}cd1;E%H^U#Pl
z;H7hMG9LLLCWVjo1r~M%&ivPoHkt91O__}iFQvm}>T8kTS*3Tci-Xa!Qnp3D73vt&
zPOOHNNOSJ9=OHO&O7E_WyaxW$Icxx4ldkzBV}QvQO08YWi5!{d?Q5Z8;SQ%i2P?M|
z`?%nFvt0{s*o7}B$G~|(qSo2u?*2W)F9!=()|1e7E*ZBA1?_;8tfY86it^{Ksuc}N
zTs*zxEb+}<-v-ePxE2c48okt-O_zZ~xr|-yy}gA&IIAQ<z#AcCKhBk=q%vg}>;BqK
z&#-}T_5M3RAi3G<r{vj09ZLnCw?`B05#0@MWo~t8_@~yLreFF;H>K&Qc|6^UHz<Ow
zMS7=^*Hg~3eX`O+2&s1syZoSr92@Z1%i=q@;}OSkPP@eG9NGOj>hW?8LNm$$ow5pg
zW-BvtGX1{!k9MBi>@Y%i77NS27QPSLBF_|4!ExN?aYH;(M{6Iy>VK}<>UhiR>S0~|
zJ%W5$sH!{AB&=*O<2eHO=;3OLYf(#YQ_M3i3QpuzU(rLPT$Nt<;re7=@?n2b*5?v#
z{5~?m5WN@!DcwBMK1Xfq!-)3k7f=63yER6phyOvKC~*O0!x@|EoAUOJqg|>goX4Gk
ze9bM5U1QlvHR}0y8C$xWt1~?LyF>D$87<k%aq|D^`_E@nQ^IlrSi{{P51K?2{nRUG
zwU4OsmQVF~qt^BhSB1Wb*#EdN2C)x0!tvEH66is(77BG$&sU8n*Bv9;x{^6Q-1rO;
zZf*3GDc9wL^8;3n@3`q!ar_R1JB+DHfXFhc0nYuD(J;wL!d|TRWzZ#|xJ|BV^hoBF
zKUhlhS<alaGyoy|c&d4pGxL$E05(+bh^6HLwE0@^*FWbuG$Y<qn0=%J-_bh9Ndlk`
zyhUsD(i8iAiX>e>Il_t<RZ6BXz7NH0D7LT!tTfzAM++&|d<n+t%p^gOf&&xdN&ifp
zyX7h5FqC>!tcu|MiO<$8;5<?<a6r7!(<vHmctoUW77h%(&`4n30H<A+(@s|rKqwE)
z2q>sCi|xQ%5jPkUC(vL%!_+bAi^*)QGDz8w0ZJ8cpBlyZc*4XXGmB5TL%JZJ$Qxv(
z0HfnAj-{`0j4~J!0qmbo7k+F|D%<bihAp1(Yi<qj-3n?o;<#r^225CvmRjN|8)e|r
zr1wwhE<YA^SnLJ9ESC%&fuJz^O9YTTK<zMMX~J|uE^+G==X{91Xe!X$D^~w08>vaK
zjZVnOul(?<%xgoh@Wn3V*MGmR=L@OhNW@n^?G&ipEO1|$Vt=F?8^GhlNg#n7saK}4
z3`gi74WfxF@xXC7f-M(W4|1?|&U#y&`xYdT*)&Ju#5QuZ2f~SrcGkt`;wn{5=QGxn
z&YvQLPCWAXz5sUZ>er<*{20si{&mXvdypgrKnklBK~4wWQMLjo0qlv6hRkLY*)Hb`
z+#DmGZb*Zeim7K>X(VNplTYqDyi;~6VgSv1+q_;BCD%Z)wQsy@C@#%WopW7)!`$QV
zNkC<!?g7z%*DPJQMzVoWtCW}pjFSyxqLFY{tzmSZo#)fHZ8OTndS|xLse^ZhAX;cl
zpy6nya?%w^GR>#5Z>XIQ6#O$GiOA>2_#EC!5>8UlV%j?koiS53%8C65Wt=02x85;P
zx2i>w<0%FlU*Pr+9PO8cs+Q<l9_jRY9Wi-yyodR;G=E<RZa;j)5*;GV-xyX@<4V0a
z+rD0AMRW&vrE`acTUrF@&+hfgA3n7`FAtEGR3&iTI_1rqt<vqQ{Ro-uh%%hI6%NuD
zNuB1<J~-DrdVQRW-?XmeQ0cT@xaVNe3>^)kmo4DMP#yWP50_EtR}l!l_-mT;W%JG`
ztoF!|sk`T|sp0lG8l^6TOMcQ3IWB-za{CI@c%xPC<RZE71K!+|8&!;VR$)BA-vwrG
zB)GS7NiNuHZoBS?zwzC;a|~~wv4{*a)s#snx|=*5*?Kd~KxR{{R7)bLp_jMg5x;Mh
zK9BBY<2rYj$AM?oNLs4`wjcacDS8U1(hzwh!-n-;hU3WSi4>>6YjI8FuZ`Lpc~Ax^
z7u-p=#>I8@O*szLQUymHYCmu{F~L>3bvT<YV{QPks8A{TZSgCl0P_y8*X3C7Ss@7D
zQLlKq+Wz|hq;mYuLP$3D4f1l`hz{jwstvwF(VPj@zmJNR;gkeGq|6k20`&gj%rN>C
zv*q3#7-%*3ekQvBGCrBed~>TGTadCTZG)p_#P2Bg^HbCEgO)LHi6gySBE&V@n)9@}
zzl1wUCBt!&<xs<RC^b8$N8B?z;xlRmlT@YAB!i|iNE5mcBFZ4jrtYF8p91sC?47{_
zEGmGs^C?ec1UJ!fr<)TF=UU26?%M<BkMiQf>-+!ZXW8RTic<u9`jLDlXCNIM<pH4@
zdsZ=fcxVpVPZ0HaV-GBDgcQ_<!{|NS^@RbS4*r@A*0u$kM@fM9%NRZ?rG`ED7y{O(
zNwvgyrb$Nzq`Kmd8WBj1%nZUH94cw|q~={!xz3XjX<wh-7@o4Z2ba-s^v{<p+4v^u
zHp~4A4v}g7jOzUL^v4>xw5-akbSj4^i{=~!Js}vGW7XOf{GxqZ^c^Q<hJ28e<zDN6
z+r%jn0gGY1)tQj&$(aP_i=Yw+3eoBPNmMo}4_7Int%x+6!KT+Yje9;f+&Oirl<_xW
z8pMM*fE=2s4o|S>{2B4XVdtQk`EdSGT91RaD;ZNJWYjvG-XDdv12ImN)i-t=R@rLF
zrq%e3X~1jdR`I=rb(9fD^_ns7F={7lz)f)K=P*B)CAxS5#~Xv*50!1Nf<Q{7%#)jQ
zs`Dk_8POizdi2pQxFw)$A#mh5&d%Mvd7X#(Ts^^jMj3d-Vo{WiH%m{6(xRIlf&r_?
zJfkkT%l6I`_xqm!w6*63Bi>Lakgv&|^YW&T7T8IjVinhlnUVZnpoMAy7Xi}%ApS#~
z{)km4%kvv)MO2SC*l}>+gyDjY5tNCraxsS9IX3r$Rgjvru4l?t-vdH6PMt<F4AW?=
zqze0Y`Ul)IdU8k0>7XD$DKW6==1{B}WESO_%VY0Fr%no?pi!(Jwx;Drxvr{$vc~K0
z{gZRcr!oaHV&tt()MDu?Xl+H3ChBWAvZ1w;b?XBmyJS-1i0W7(_zdQGU<c`5rn1@@
zbD}NKpyi8-BEEDKj_D=7ta3nj1`OnwKLw>`29sDuoqi^>=ok#9{4mc4RXkS0k#g;Z
zz?><11vJFzw}D**%_A?Flh4&}w?v>of+cMu`&Bxa`U8m*bGJ%~R8g#GMWCb~S#R-q
zkQKTY+~-p=HS&t0gOyaRXw^R3^sfpy5oR6(O>d6XoLjAIw=?}Lw@>=A25#Ir>RJLj
zbPByAL?8bREeiG|yAtx$%?qp&(1{grn^{ZL(2f$)P{(ma0rkQxS99+bei<?Ut~%=H
z&U3SRQqx`8hx_vZr{ZsALs{*L7HJ>D*N0}Ykr5PA1(=GF1nU~pnz@~qjQZpa;QGJw
zD(vMZQzvxrqzjqv`5<&~Gx(1v9KW(G9{=-Cp)N%#n_g9-eU+MoXKp@Tv9{^_Rcjpj
zsq7(CaubB<wzbL3#_#9tQ%??W*onT&M^p1Jr5d$<F|_}?g@jh;X6YQW^zo8d3K_Iw
zjfx@MK_l`bKuKR9JAvqUCwbmu^fbFIuYsVuf5-oc%<|tg^3mgx6SBo&%Gw3^jsu(-
zC)=Aon9m_U$4MP_2N5<x2OL=jV}7P?<Z<_~O5q8<SIU^gRe6mZnDP1dm`BvH*hRUM
zqrHCv6!A1JSlV?y<PeO<fY*x-M*GtuV$?yNbtiLnI-_#gOr?YkXlG2=j|`W019w(y
zkp1hix;O7Yx+_3TK1W*UPn8Gw=T_o4`2!0ph!+BxvYqo#o}q`KT)T_XQFlA)P!!Y5
zl(CO;iFyFGki7bYqs5}TmRmjG=bIpT#0l))i5y`x#PQYQ2gKCY;JpJ)J}6y^UkDu-
zhKog`B&{9t(@7;=b#Ic5M<$UK9Rve+Es|`Xl%1u#a%{~uX~vN1`%9m25aQHGS6)ZS
zE_-p3w9A9HN#*ARrj*YGmJ@pF0EbLE`!B~NYOMhEG;gasplX2JNSfX~|5O0DwWG<(
z9<?l7n3^_?UQ!qx-W_7^fI%f`493ahUCg&HRbRkJ4j6WVB!i=FAahj$LT(ZtzpweE
zQ8x&sdWodYlgrw~inRT9&=oHnm*9Gl<!28JR?7v9PpsWMVe^1z#?jGk6ELDX1%rsv
zG=Epc4k6UA&_aDlQ<V<=A`{~rDg$h+J=P*;DPD&JS(&>Ek^QNCT;NNO;7+Yn-GU1$
zI{Lt=CWL*eFKnZMH{8-_c)gH4)M^RDJ*FnJlEfy{hbax_j*ZW6w`VJM_!Oh~si!WP
zv^qg;s)4Fu7+veiyo8<vnmgtjvXy@Jx2pMvGV3u{8(uOp_%Ka`ZIkNsj2GBj-rlBj
z)S-@((+w)VaXZaF*A>lq#{okIJ#o~ewyUl;YyjYUNS5sb(thN?WeK6IXJ}<%lm)j%
zuA?w#Rs{WC6R;Z8KpN#zhdDt^iM?qi*hS_#FC*tS<)4>DW^7#FK)sXrqU_uk!FeJ|
ztZCBT)@a&)1@hrQlPS1=A5vM!b~vbSJ6Xte`AQaa$;rqN63pFVNb};IGw>mT3`&Rf
z`*}(tGEUcEvdU$>4XOXf(^&^q{XTEsph3E%I}hD0-5t{1-5pAIcS?7|Ar2vRXpnA@
zmIjfo=l%K4Z=M<dz)=`r_P+1kYp;Fn9ZMob&bMoGt?L%cHs{a`2+yHq5DnH-+j$>=
zzhgby?0ua)KOz0S4{hUB4J47bYz>2j)05?n5Pmy9L(@6^C*wZG!;){(Az<9GMma-J
zi?%q;6;8GAymw$=n?D}oHdk{4{~S}$J8WA&ZC?z<Q!4n0Kj7;0vp49F{e`t?_vtw;
z!^pVGaN7_v(7NzRSX+MpKeIxMmuvIKVTAR^>TdGp$;+8IKA1pEx8ml}-mXWId|;t)
z)BH3Ac}`v1z{}%!Gwo-Vw1*A548*z6=-tbca+b^4du)rR`z8kv{S_$Y$TiL7qUT#S
z!GKurc<U70MIFoao9`2?22q5DoqZ**s)Mn-WFpo2kw<$|2eeix=WSeB+}to@Ruh*a
zt$U;Vztn}~ztqJU1>bBr)?cl-QinM`RU2(yj?FxHz4jH(PP8D*B;w{5?IL}ADrX+M
zV)@|8Bd^Dr**cTR-!hw(Xtk9ge0)?f#|?c-MXrUa3~6|hsZ<KN*_r0t(k9M6s)b_W
z_O{ij*~k+Mxw;SwS-3zM$YJy5XBAh6&~Isz!WPpeHChCc46Et=Xl6T9lS}o^_F-zS
zsh!5ifY{A(VBTB>2&+vC6QmT#@mTcOxWTe_RN1L>X%PF+7?j!DDeN_UY=zm{iua<4
zw;XMkss^J9U*v$%tm5aPmwU=bc1qZsPN69P00o#ElX-oA#23)a>a3Qbv&%!2_yL1=
zsAO{6oU$KKZ48uj57aJW0=QeZs%K1qH-mK^H6i#15uotsPJw_IJfsY;{cG1LidkdM
z@|t9N&d~HFE8zwtOP7|=Oi88#!?JFDbU&5-d?b!%rjjs`O2++<C_Y$AGyd1BbpZy<
zA{8n=0l4$oQF#>eaA`d;En34#ij->vE}-2?0^DbSE0lLO;E#-@LMWT?Y70icqz<h~
zOHfwdcQ&Elzw6qk+2yo(XUzbav_>4rLG1b*J_s$(c+GV^OXNCs4<hw<T~w*kze~A6
zBt8t-o#A3kK&HpeuVUTLqoFPZMwerF{!pI?2xl0KBUT<I1hy>{5Fc5H!7-4AG|@41
zpZWSG7E4(>0Noeh_HADHs`IbD8NfDWuGdQn5OAbKenCN)75+|QERUwwZq4piMRtZ|
z8}xN+lY+yVfo(U>qRu~w{_dZ3P(m~&ZXL*_=%3&RS(eQa8b8l}8x#5#b{{B|fQHNG
zG+-+-KH*8CV^=z<U3cvyNy_=r3{^zI?Va^#IWl#VRgd3*#|L7JBN#nx-mx7Co1LGQ
zL^#!>?E>RKiOOSWb^mSLEBkJSD*DPIK|)%4c67Zk?z4ejBO-?h+f9^0<_61bABhJa
zDSV0~7C~ft!OnRM3D_NRHjq1swx&z)`@56?S~f(0hB^W}{X$pyA6mrb0%iAneFR1d
zp|4UaMHJtJKB|@q?$SQTchsUsN16~J1x8PnfI2~HWk5B$>O|$b>F_|JT!-q%p^J@g
zt`xmIh9j_*tS3$Yg>DUZcL9Lhvl%iKo8xX9ToXaZNN&{9eTj5&=WZCLCly%dDpXlI
zfHOL(3%dlS6X52!*{!t6Ar8>Ki>QGY52i9H(kMJ=cOQ61-L%{20S^PzH@S8#+9dy0
zP=GvO1n81D_Kt^HrkhZOjl@-h!3{a5M2T6V*&78I4^|+0Fa5h<1#Pdies$crGzKOX
zLiMq9MJ^r-#5tI+^!gU6O%4au9z<zzJ|4qnMH;W18m#nm_Zt6$DGv`yZ)k?g4!XtJ
z*n;If5_ZN#39kLTHV<p#{QQF+9^-Qw%RyD?<8P<48QzV217FKY^L>$3s{J$=P%nDj
zBKC*4k+&Yc9UA8D?p3;gsQD(S^4Y>SSqJwxI@6LvQiFR)$-ik3_T0tT(NP0AtRQW9
zw#GQK*H``;@YA~9nM%F6*uhz;B9Xi*W5;rOzXu3vOT7pYU+q5aYu0tmveu&O;8wHv
zRJ#WFjcfpP9C2%PX4Lb2q8Phg=g&-z@pg`3<;9=`!Vs@Z(&H(c^WJxYrR*VC=dwM#
zo2E>i@)Z$)3!`rOk06(KuW!tgY9m4H3WvYPUnf)f3<+svNtGIHMLDgw>(-^Ka2z0g
z=sG+E-qI2b`3P?t5!A-7Mc$<k4!~`2_YCmF0eYv$Toc}iV;5LDuPb1Y37e~W2+$$`
zeUl3q%30=+b8CT}lPrHP`wx%q3D*AbD|(Tr)~<32O$M9qCtj~qg8&-U{vC-UKIo~9
zW%u>-(ec}enloTv65i802s9Wg*Q9Vqo6;~e>3JpsJ9lvTXQ1(mc$-I`rZ+U*aot@3
z#hoeOk-9&a-#UDmD!2~3djk695Gy@3EDi;;a5NznKQq~gaE{TXvR7^ZVfD%HSo=Hz
z?Ec_?!c*xv3{3US$#dT-aBM^iI-OYX{+O~y%&A(~8G_aW^IQyG;TLmJUr8X7)BFQe
z<{Zb@_2(~%)Ilk670Lt59OsMoe&s!VC2K$Sg>^@!iV_(0D+2QU2F3yWP50p;82SPa
zJN%MZL8}F(1Q>J#BuCj>@n6`F@^;b=+WwojtXd#2c$1Us@g(OcpYgc~tF2S@JOxlh
zw_d%ve%F)!0%FdVrm=IoifXlN=Bl1FELcr1PuG+Dz#o<grGvGu-ihXFg{5l$mz^x)
zHNF*F%NdWwE2&{Zv;Q8uG3TG=9b-Jox%>8Rv0L4qS(C;xJgc8S@g1ZA$4Q@v(8}f4
zu0UIT^YTUG0UED?(*YJZS=-9&BJgVr_J=Skxw)tJ@MsN77#U)$nsp7I7x{FY{_?Q&
z3_e)e9o~ihz#_0@-~!H(zQvWYp>N*UM~u`VzyCi(K!nvBboVhm+~9RPjK#TZwaE6u
z{RXn42c#e&B061TWKq0&4lZ@vqC=iCaVA3-jky0FUIZ@OY9Y|}uO@Z+<$&*M!xEeN
zK2W0fkh0|WEV7$~=tM1Hb=SW!*;63}om)yJt_%N`Z=}?~TAa}%n)p&}8?;PYEo-hZ
z7}Zz@o#phMgIPG2WFeIrFSvCB8@H=Hs?z5|A9M*&tyc$RRg`}8)H_ataEEt)wVP{d
z0-R~H;2D`eB;KDQjR2svXx6d(1E1S?jr=IR_zVF+n@8-;N7y>hjH@M|YG6E&pf6%j
zhJlZx0s>EY_zVJ*+PL3<jTSDyGpf5+wY0eYhk)&Y0t}ieuJnbsWCCSPmy$ab)suD%
zF|xS5hsTU&I$6z~%}b=58TNzEsv$&2YzF+}^-6D8bvHp!HRn8ww*zroV&Ux17lKSy
z>3D=j<Hh3g^EJ5p5$)5+s?t@s;3rLVZmBzrrdV`TvZP~}5gTEL1VJ%?U}VxSFbV+Q
z0M(D3=g}!nO$Q6hZJur(9xTC^fXxqtp6uPfo-ze#T?o4NGQeV*Y8M#xKf-K-znF;!
zK#Y#WW-r|n_olM~k{j9HHMayG)wF@8zQn+POE|`Ty;-VR%3mm@eUV@^tA|4Uf`OOP
zhOb!xV&$xHgnyCnK{}mR(<jPE-D30NmG5NRAU#Bn=*AZV0pN{gx+}-4H5+J_*|uKp
zT}fI9Rr}8y0S%(1hv#LVE<||g)j@vpc{ac<`5rJ?`I{ZjcvOd>YtL@G#np3cPpP*;
z+xfgRfGOws6P4BeQh*$&6PN_l4sp(G2?|1ng-w<T0F_3+s&_QhEqG<tM^JOa<0VEg
z`#cafzst0k?5%tGY9)lMO?p16`y|`R=uULePS&S4exFTv7m1u##|g89eyiIpM8l3o
z&O$5VBj?>(CP5r2?X#=J_cpBz=hS{>%<~)mE@7eJ2TNpmnX&Xq`&OkQF60;Hw;KVG
zL-X#wQQZ*a$*ZJ7g}ED<mNL?aXIGCTCG5-odu;W6B)sh1C-7I<(Icr8Q6iT~y+br7
zgQ1?3s2cTs29A9s7Ud~5u>BO5?)oW^tcblnp=}bJjb}aL1D^`~8+I887IqrFpsxHR
zIJi9Yz3_3JOLbeHC9io|%i4m==*5+)R~#gS`_u5Qnpt*+o*QQ#X4K;PX}w#w)z#vo
zP$)X^v3lD^1X8qY5#lp`?Wa0Bwjk5koTaZv9sw<E5mkj1ttJ-D(`1p6$=Kt`?O;jB
zp*jmBvMW65o&K7sP4~Fvv{k33xScpYwZQR$wF9tBY(LKMHP@<vDQqTu!L#5>3YOjr
zuZqR{FP)8Q`lo|^NobxA0MZ@7OhQGN?W4=%tB$F-){Q)PUw9Sx{+8)Fu2w^W9@v=z
zY^VX4hX9!ipahffd9dj9n)kRTRV|nUj4zy(NSVY;XY+G2DTl5trN$fD`a3Gs<*`yn
zMb@u9BS&NMfMnEcdiQ`FQ$4o)aOIthK%O}=2L~^Epp{eVjw&<x@|X&_a~ltr`r=rY
zcvdZel-6MsBM5uOwptdds2S^0_efB9ZpL~qTOb2pYzO@@1F6fXbxUlW9Q&jPG686S
zCSw8v9mjx^MwH^(eLMoExeeH$K0<>p;^w=^EtQJV^gZ=vcy-AttCsUlJq-_E`M`DH
z6S87-!L2mcLQ`iX+6m-=tGWB);AJ2g)dMmV>c*a6ozHjcqK5>y#eqNuoQEYeeV@jG
zO*(@T0(X==Vxx8U@RGQVwF%?IOWo8&L`UrV`9+QwZ##bIU<Ix0DJl;EJ15zNKhP7D
zWKY93=FJ)DHqyHp3_Q%J2|IlT`y=44%3?Iw0~WvlWhb>y7uP`O$fN#TJ}}n+EY_ea
zyi9qmkm$edfdtsE5a^U7Ms{uJJRnDWz94EYwO4~;a)*N~ZfqpHMQpf>g?Zo^0k%2v
zL^{-Z8OJwj+IM;Xsrq8B0nHIw7z!8{;;^FuCQ{0$5|z*+XK90-buIffp0+zPS(+bK
zcVjh<RT2EgOvBx4X$#DG%z5I7IU41IG$R+1F1HgMW?f76Ja%iFV`q2YYF|4%(D1zu
zKD$}+8U^Hare*D)4F|sL(7jkdzTH<$6Ne9^lddL|oshT1<bD}voN*R{363+CNiAEJ
z+mS_{ZfXdH`4}|=2vt1%Io|1M<y?f>b;I_h>1i~W!JWHm9z>wZ_656L-RQED{X@=y
z=F?|4W|M4ZK+x{gFHMHXezlJnb+yPSjKK~r(=+YTu&mOzaQQ_k(}YR9icdr@8&_6i
z57meoRSWY78tD$q;7s7YNfjHbLG5O0K8#>;8$Y|_q^4TM$1GO$iSCkECk>l?u}Z29
z0C@4d{Qr~5L+|$=4SL${F=!bSd-&YGznyllm?87|^2)|Sl}%rjMV<h>?)$gn0|Cxc
z%<Hs+o)eUCj1BPg=p2?t70GljuXJ(=h?!_Ib*K^B8<mT`qo*N0IeCeBf^DN}rb^RV
zLry~;wcHBY?&%aad7fw#bd9NQrkSjve%k~OAQL!txeU8`r&%Mf1~Qwhnj02N1rRcc
z>p8fzh8jg4;1COFK-+4qM4R|epMZ52wgsiX`2pSq^&2qAo)_2@Rd6foE>ZHL8XC;R
zZZeS044~1=oA}K<tfIq(hHAXH-DEY>l1AvfyXa_vH%~KbEC0=CHa;C#{LsPX9pl&q
z1qk~<4-0kieZP5KaUH|141lv19mp@)R`~B2YF4K~F!Ug+Tn7{87>Tk^QKfMX<&JUJ
zw%1=fH2knc&aPB1tbk1si^Z_~Gq#S2tP?Pl?uKn+&?J(4&~^n-wt_4)r%#l7WF{Sn
zW9X=WwNHcNaZcA_F90hcrY0f=P<k41H%$^ffrHZ_D;3)JBQ&g>!MiCr2crL9;}Gng
zA1)L{DKBumzEA_K$4RO6jYKn5$l*M~czh$E*OOVHh^?onP4V6jnkd&)SdV8CBmj@&
z>Gdj_vq$U#Hk=LbIGi`!Gw(1!HkWxC<mWLWhlK$<HvqVEBETD*U!~Rt1(;L7#*Txo
z>#V{^hPcP`VGjiZ9jJ>?&)zdF6-^PI)35k+z=x%S)TA4B=1pClVoM<=G?=L{xQy9G
zq%&5>qFHL9tky^Xzz2XQ6~KI_YI1Ni^3uR0&!tVfG(CT)=j<H<+FhP4{b$?2SmUSF
znK2psPdDgcVVIsYsnwVs)k7tI(cv6Jm49PWHR75yx7<MdN+l}oMHB!1C^h2T#gbb6
zYXJHja3<}P3;B-1HKIymae|$lH32x&b|t}eX$;^+$aGZ(gzm;r0e*1sgl4Dx8L7du
z4KOiEiNn+;wJ|keXRF2i`BX-rTEI^Rm^N4R%a&hY0SGJqIUFXvvpieG1awKVv~6ae
z*V~KzoayU*_zosiTA>xXW`L%pFl0;OLz?y<xyUHzKIh>@#27#Zv8;@oM0);@=$;}I
z5$Y?G9dk@S`iCSpjtdv~?ShYi<ygR2GC+r?m74|@inUk8QlFak`w+gJ@BqE2Q}kn9
z!z`A`{NFc~E2<9S_(QfkbYbs~<Hw!yx(DkEgr{E`*NkPuS{+P{kotmN|Khp5SN-vq
z;LjpB(w!Pcv3~GvTYk&5TCSLSU*`1r%x(JW#EMy^>2~T%$1kEog#eT|6Zxez%$rk(
zr`xm#^)5a?S81Dy{U72LSn1EGiscF$w|}IBla!*|qyIPP#Ko`rvuMk5qE-b=1kFPd
zCE!q?e5Q&aYbz}=$)M92wvtl^C^sel@kjH~yLn59;RUxcErBH2luy96ffs6wIGVM}
zOVBQ0y<3i^oZ~9beIpfh(@L^2l{iicN~Fp@(5Ch>6}}(H{FdYseWESl5{;RyRV=pR
zCS^lCz<O}711I*S`1opOgKKg1<09na4%JX2Q!2LmqcG2TZSx`tS*dZCD!C$;DE?ek
z1_pbK_jAiMid<5+JwWBQ?2fU=lK>;di-7X3U4VQ5?YypGk+5lbQ)k*5ut{ptUyU8<
zj5*%2rWwS1kmr>tR_QnC=M$CWs;uA#79q*N1J8g0yz6&_riy6L*v~R50MrEVq>3|k
zvo{F3?S&m%;`+XgkeE|rN}E$y(ujS2ZjtVFciAJ#%Jycgqe=MFL^sMnU7eouZu0jS
z`+p<BYomX!0eKz(KX=F!NJ?|(P3)O9i%>;kl@Tlm#ay5b;EP08wsXq?4o@_1l=E^;
zo&G`z9Qpq>ZRD)76qK4*jf(M5b&j28E8003NvPMv5z{*Ckl^K)fk~-4&~_yQ7bNWI
zS7dKQGtLX>IxA>o_E)Lu{8>~|Cg1rKKr939w;2oB9uZ8vP5`2j&J2Wo)qi`OcB;lu
z8;9{jl5v5Qo&_9eb<+0bKtuR^YF8F5(v{5xx6%^h=);GYJc}c*ohnQ`+XAaq0Z28f
z6>vRTCWwH)52qNP5Sb^1q4v|+Zv(vufM%xJtc#LDl5{J*^Xpa(PH)CVPCHctN4_1v
zY)3ErRM!NCCFGYo8vBQPS%U3Bs#4!K#1JJ%tJGR`L;qWJBMk?NiemM_-k>Ak$I}EI
zscE&UuKF)b=|dfkgqq$yo3XBv?Y-FfFQff&M8(gk+4a>MrtpjUsx5;pr^A`|dEH-N
z!z3rpIBsEqOD&Hzuqb+$cR5}BmtsTgKqimWKu*aqCt#$=@`-W3vsd@xsQ!MGMhp-<
zD~pli@1E*Hu%kOUqR;`ke9qM>N*d#MbfjA+8f3bFK?42<AV21>u{EXBJtgu8Qxr*n
zEbrd*q~87o_gk5e<XqN@n}}DNIxqwSNCcZ4RU1hp9)70g1a3qKg+SpJ0u*V$9LVj{
zt@Zk-LH&3CuGaQVBU6rJbuH#Vf?4I@B$IJ+FzR~3Ad3zc;K5K0%-7-{X5}GRV^?2g
zA6(f?aM+G-`k=1~O~GN%x^66zY|BSGeHM0<&2aI`2T<eo3)ffFWHKD&Y}~52+u0DP
z(?*DN*8ABZRcd`5z$vGy*7_{ytKEd|4W<lTrvBw1sbQHkiPqZ#^P7%~oyP}XuW}O2
zF6Q0X?dDyGw1c#e@nRDxSY!ENI9yhOmY|8`Hp*RYj$Rc^#2HTb!X=icqK29?!^+dy
zf-sw@U9Nw`yh|TbuaIxWbn0f+AgaShB{dfnkY7E`N{N%s`^QZOD91zo=L*IuB8~W0
z^i4ia_JDEHKx|b@bT1}O_L=j5Mazjzf#iJTYprjp9O_qLZR3F2Vfc&9{k<&2GAjZ)
z`Ta^<c!_UK*tl6Ha@n@A=x;%{uN*Q>rwY?B1#WeoOk&mZRSb;sKdQco;e3<g$=>)w
zlQT)qXWt}S=VBSlx%PQ?>U{M)VWm~m%#Irj23vB7wA*nr@-}13n^5JLBXbjeLhnTS
zVw1+t!7eWC-F{m=#rL%9D<P$EETLto)kmuRKJ4=3F5hqCCHkUk>xo^5F`4j@f&e8i
zZ~}stL4Wv>#!fQuc7`i^BT=ec8N1xOF2qc)hO5(_+posHl^*Yd5=g-qMMBnBJgt&5
z-eTjc_k`6adQd(?@1r)DxIFrzpt~RP_3Qn1NA(J6^ErCFV#3w@I!px32?Tbi`?Q5@
zp?hW9NJ+5CWh>3ZF71nPcmn-*1FD9Y`R=TUPI_{f;b@i(m#kK;45>Ed?o5cq_bx0c
zd$6B^W;9G)+}W5A6VF{d69@Im`=@{BPxVJMgf<0%USVdXY)XqXbcfG=%=026ye({W
zc`u$`RB&SE4v9VxvCTTxZPNCOn@uEg7+h|w*Y`bq*KJO|8~7oMjQAV<O=#q`;@XQJ
z7`kH<eZH7Y)ONRgs2;gqFbbgC^-pdH4WkA@yTgWsQVWpjK_9BW7~@oMAfp+6gue}1
zy14D;fhLv_jHjOpK6&Z|)cJQQBwjmr>um`mQ&IcHCJRAJf+FM3n|oU0^t+<jE{9Ue
zM{xr5w@ey4qQ9u1jd_2MIXh*6_QhSCD1CRcD@7DjDF9*Y4ZRrbZiCS#)U+XT;G^Fo
z0kzjkYfa(8Daa4yq~1d54fOn6`E~wb<%~u?bY_qzZl?U|z}@@|uh1}B;!Oub8mA`(
zZwu~S?mY8vluTXl_FTAPr%GLW$Z7Dp!{vQbFQSt<aK_=q2|f~(!qe`_iQ^kg>F|oF
zGcu~>r*QaY_dhxmO4JXoxu)8dj;P3+ML&mr`8+8QXD37cFuQD${-_uT_DCxpLWE=3
zE?z{U9xgxLZvc6fL=dy>y#I`YEgkDE5m|VlGJ1tjvnCY#Wz+SlRIx-YwF83KmKto;
z>zv4`SrXNMO-wZ0-=n-AY`5nB@K5v|h@O}KD?Cit&&gGF*ymL|<-$~e=yYOkn@H(q
zW}SzFZ(B-~o;oi-Kr8Z5wrbh_&inA0y&P5P?{RYkFQi=wzZB#I&Z@%k3elGm)E8Vk
z_*%dRb%VFOhjK{UpiyY$5WgNJIOY*O=!j-<SL*g<Vt<b~B-(cYx7M|G>Tg)H>oM*^
zP}5UWKcKB8Q&m#PsTFY!H4WAkSvPMK<58!&k>s0UwWD^^U9%7mjyC)t%cR?HbW(L!
zPAwuWeg1u_nce-q9Iq_1GL_DoL=6GXWz4o&eADZS7<maivzo}D*j!LLGqo@_$UtZ$
zGS#IW$Cm0UT<6d@Z*8K73%gZ}?X9i$3)xKAaPxQnD(>`zvKq@?R^8_5=O;Rh{^4Ju
z)EO#A6!grxP9f<MFF~Oeq*7zDB>|Z;4$~~mYbOqm8;PdW2`2*gd>K?qs&XmN=s+Ix
zUomt`e_OzvUDq#eAff_O`?9f#J~sZznjhLZbQscz&@VlIu(16X>m5wK`LmIYK(yl(
z>p6b^m6m`0w?^u^2k6O`ReSO}?Q%qAgQ~%2+RJs4*fjqj<g%%jL*gIPeBXOjgxWiJ
z*f@H&`#Qo-dyV1<`kqb9anX5uf0s|Zb6hQGz+-Dw8NLb(w78F4bL({d_VA342dVxy
zn`k*(Y<`$|TTR5Qpx%jwHiSVbby~gymrJMIM0~dr?W=!kpV%fu^NdMA$1lvXfM$v~
zs@6N2wuw82PmwpP00)zv^FWJwQLU6-F4MAl_Q4Js5d8b_I*o*F2QO<T?<Nuh4a0&n
zu44M}hy3PkgTw)&DWYi6f(n=W6LR{>bpo~*8b}sXGTTye@JlCe{Ll~5lrjc8TJF0P
zN7{-s$Mt{d$UJRmiW<n)X20YpEws!*d+UY#M^I1K9>|jll?2#P9_hn$8G5^Se4NAR
zOzD%llw6;A=@+(3e3t#?^Du1xi>SZUNGYj?_$IPZ4zhnYYuDoMOgN!bRJI?#hdIPu
zlugO0ei1ZY9uL8!rthXJ6N>yJjaa$Z?irTrJOf3irq2_VsN!@f`V+=h8z{q~ginRI
zpPOK}X7BOnJ`fq0i?WtW{o1gc`6MwDK>N=c!t-NeT6n1@linJQ!q-H>3Y|>`lSp1|
z6n3z(2uo_PvcHuH<=1Bkdr#j13d`F(Roz`a?mX6heCu2Bc!fm-A}g<)r8Zq6qH49v
zi}j{V>mle5X_2@K+wF!BGCQxTCm-nZvq1*D75<nSOv(oU_pp*3JN4>=vYA1dkCMz=
zx`lYe`GnF*K0{WhJ-Y47t(u9BhMAp1JS$O{N-^U1Pk@{;Mo$A8gI(<t`#y~hZX?ps
z?pq60h@(VhcDeTCoXzcwF2|qH`Etg+=wMFOe*zeBt=zQv%_BJeH72ZCi_wNWgDws&
z?CxMc6hH=**-f=h{C%h&iVZ|$-Wf@rWx|0a-n5ss)7>uybtX^U0J#Oh{EPJ#5na2M
zz^<d8y$E|CG-+M^KQ+I;V&tesu%QVaskkBEFII$k4TdCd$lG;?vmvVCqEmc{oDN!^
zK@~$F%7P82FFvAT+rA9!$8QLe9Qs7JDxBY9Lu;}qYr+|&<^31R_v>BdA|yDD_9)PM
zFmjrqICuw$y(A^ftBZ`OzlLU6qd#OuKOul3igp`6-#C{@(njG|{NuJ`<=hnxz)^R7
zhCCK=w)xpRxHk~X3SY2ssqgo%XmT&Eb^Tp+>H68%L~=f)_EUJPOrTZkyi0@e@ct1m
z-o?fzrn-8m@~f-DVl+`^mGFFH+;YOZ=pN~ryG#(?AL-GCq36+#@0~phd&78js^jqU
zfB6iB`Ms8|WHF4#WjnXgR6D<OznF;5P+W8eQzIo<Ui$r7ZD`skoH=vz>F#steda{I
zK>}0jIC=O4xx|gSzOVg6%3Ny|Eh7K7uayf`dC~i3P_*Z1#-ff#*V>E@mZbD&`OF!I
zD)Z&P=e?e@&-iev2=?PZ(1Eh333~z^lUNli_dYV$^H|@BPZ4EWHqRZN{)L++%{BpR
zNs--q`-G6@c4wFB2;km`#Rp$twxiyN<=g2gZuWHc2mQUl<73q#U(os9LOQe}(PxnQ
zYfZJ_ZF+^r+s!TNj)3vb9Yk!ymc{tDExs369rzjsVP=tdZ-R5_8g%9<&#Ff9yfeFc
z{5QoZNTv|mcqRGTiG@ALJ{m9RfgY@t!@0QHbybU&DZoDZeK(~-BZ-PW#4(Z$Zf&I=
zeN%ta(ynxL*vYU^V_cn>g^gRC{B%hF)jBF8aNh<sH&co+4&8VSH{NcSSLe$IcE2w@
ze`na^tvG}Y_Ct7>n>-z2Rwz?Ac~(LBdiyy+FPdX!u$vE?d_>bw7yEP;r+4V6rhkXt
z*~l_?2jzv7TYB#=<(t^GN}2^szvgCsAOYQY4tCFd#fYmIP$oRoL2R>;Fko<u@6_A-
zViL?&FEJU=C3lWdV1d%TDI!s6A$U>EJ4H`)c)v?BPg$HX2tvyq<QM%sDYaa9hbUi>
z*Z-sM7lNO*+Ky~a_c`u|?`+{0^+wB|y!dpoP5T+ylX+wDuYSiOMN>)%!oaB9xz4``
zp7By?(2u`(S}rnE)wOi2uN2jrV%9pYjoE)IHH@+3H0J+G<CT-zGQl(PYx&gm>X|^!
zMt}NXbqDu^k!eT!`@K5}#kohGUq&-ijBDTFZ+C~bAwJUe5KM=`>7mWtoUkZo^^?<G
z%j&hmGsf}U?5v;Zi`_>fp%QXv(|obBH}+8BX4*FmbycSba`juLSj`b1)I3&o%G;t)
zUGkr9_OAIM=)n@DoPHk<jxC__K4AU;!8J<=&q(Z&0sLBWY{uVMoNMb8dJK^$Gg+h_
z>8WvDA83rvUvV5W0hGp)y<gsGyoxTM7{gSuFylHy%N|3MqFm__d!g@kX0oz<URk8o
z4J+r3o9BfQ$Af(h#JbV;SzU+8ZU)e3ABGNrYO2`x7ATc7C3nW#?{qffXMK%2cO5b|
z?!sRGrB*`mF}vf~=)oY0(2y>1wT2Z<NnzjOJB>D34?Ml}MBd1?&`&Q#i8S<Qwan_s
z9>-V~U><(&@8WjV@|cXEHB;Ndsej-3)#0JQHTal^E^?t-hf@)sfv$$4cVO&V7=I{G
z!{StoDe2ZcP>F|DsHRxH0`wKyR?688sp!1#eG<mBlm2RBm>`B?XoLHveU`zkenQd+
z2MJ2ajNa~gSxlnKF*c4K|AqegHlh|T&k^{Mb8!vdp-Jm7IN@ZaLc>Co&hO631Z9|b
z<2Yy)bjy9;&^;2h11guhMo7Y8<_vFZV{xGqk*yVGpo?!0Y9TRJh~X4UP?K+;n#1St
zULWu+fdLPM8c87aiDf%CaSn+UhEu~BRj~X<6_Pu=){Kr<uGlG@O#Q9mg7S4${7U?w
zGoVQ@%xdM|T;_`Ze!iHgR4l%WpOn{UASS73LMY}sF!OkeKBFPbg$5E7$8I{9O|2+t
z&36nv#j#nNEh9kwC1<YaN96`QaeprUlz00rZQlW|8-E<L1}C6}-MeQ%NH9i(-CkY|
zK@h2L1B+Pt+0<Aeoei=<e7Sw&0gZt@9`d`+!jwTrtqXY9eF4?|<}Jt*E`~re=2L=R
z!!1DP5Sa`^{=r^;hfimlOf}mOJLOKlY)ldw&1XMeBw+tE<%8N|#-TOAVZhY5Zk@DQ
zWHAF~mo)v&kN-n!#6&MygC5RBZqqBP2HVE{iK>!DLCs#CU7d+dok@*x&vOZ@eTAFR
zry$EV>INu>$^jqf6q#MpB9yF@?84$$a;uddmgGSX=FvZWR51NEU(hMHR((Mt2cMo@
z0NJc&joD5GAB!>+8M=DCI`tS)CF^pSUQM{$5ukf>4*LH7S4pRMY8|;fB1HnVuu;Lx
zOOe{-54@!Dr`SmiAg~&UV+^g{!PyU+nu4K&`f*V!1n&ZSV({AcqWkJDwo%RIG^5kL
zjgvApw=Nc~ovPR2VSK3CrDhEmWifT_i7yy`{uHwySZcf2Q=oW`Kr{`2JJkqkn|l>W
z@dsR(xYKjKk)dJ%fxP5}Ur?=@11eM-IyU{d<&`LgB5t@|2!Bj_XEhIdNvDn2=2Pzz
zw#9eJRrbQ5+4e=?sQGj21N_(CIBF`Eg&-Gf3rZ3aXeeE4yj*?JJiBgNpG1P6b^`X6
z>t%`J3L@(_Mkn`GLG`>114o*#CNy8)H(m0Eh*EfF;D{N^$C#BO+8PS0Q*Z7Q2$~K?
zLO6if#lK3tU!(0+sF~fCj171t-r%%Mv=l{-kT=72RHa+jx%Ku5E-rOZ(xTzhuGsMO
zOK0Nqbj=<;Vz(&*ersxcjF@z#9f2M(rhLYhj{m-}?Tm^OiWhSj*DhFCKooN~r{I2T
zX(I^gKaoLT^EUPlrHup|Ez(z?YwwtUkx0~V2?#c`N>X1mH*FmJ^$khL;Eq(6+;rpP
z7J@#cDQ@cNTXb*iFVEvo6Xzbx>V_!YU&l!z^fex_f&D(d?h{@#ZxANZ4K>4CqJJqm
zufrr7L_8CfXhmOFqqZJFDi#s+N?Xy*!b6(|3@inTEuYa#s}W2nLqn_-6NS=C=&(#>
zlKRQj#R-bsKZ{5Igf>>mVEk~8Fm(NHc@IZ@p`&m2VJp86Ka7S(RZnJnXYJY<PqKEF
zSZzZpOZWrf8bh&SB-_f(U^1*e1Wu*}7>EJPh8Cu+@zj5fWkDp}us>5Ida#|JS733c
zYh7>8s_kpJ`Mh1j%MAqwp?|p<G-c>-t9j!@OQYSKj7l39caV)lTA$Rw+F*N!E(wRC
z3Bs+%Z{Fz5fQk^a<(-`sV%FCB@ede|vyET>!8(gm7Pz)r!2AOq7f#b&0TE_axXb!B
zf1ln4?zB5w;!hyC-rHnAlGyF2W$!MSqsFD&#<hII^eU-UDr^fPcP>$!WK!{L?sqY1
zyWchzGBw)5C?IXwq>2v;=gtEJfZ?eP`yaQ-d9rr}AFW(*P{O;;;&pR@S~v3lp2|@4
z`R<qP_m;c@>9&(!s6z)#%@)Q@w$vo48$$O~8spy`{7qY9!1f}+4*ogRM5Sv7l20D@
z(+M`ubv=3}06&?p52EgbE?7obvQTM8&mpUay7U7=41^T39I2EGOzmPH6Q!2lb*Rb+
z^Ue6pEx%AG5`Pde&ar?_b<jpG*V3U-4at8P>Sk|QMeV;tez>{LUl(WM15xxspZSBz
zE2vYPjn=+tJ(FO{Z<1Rn^=_$=4pzAIr&&#A>G=nqIC;VWDTp*r?8>>tSc8Tgh~60#
zQ*^<mHKzKn*?db+=#r~500=XJJYl}+{rd@g!djAAQJH3*FP~DpKTeZ76I(_+{SheG
zJo2~NT75~h6fuYJkSXD~WW#>aQBxV);1w1K3@k85r?qeKYk?>4rn7W_i~~`vR;pv$
z;^GkFI<<8;ek8z+wg17aRB*`TT_ky5=6k4hXrhd&R2GdKkIU(2d|VvTg_>(^dSy;~
zrrW&JX1aUkI)`0tT(cp;2wJ<?45U4w47tAYh4J|Bc2;MTJ-e(1^g9slItx{ngAoYo
z>K73??UnOWgw;zTKb{(kPBkjIg>x@egg$TjClr|9t1Dg}U72|Wrlrm`goj~rQ&uK5
z!FGDU7Y)8(`^vbxii=hHAx-~FpBMc-&y?hX|IflGhW%XSOZvbI5^89sNwu>8BXpEV
zZSQBNYJ-vovV&<$-nS^Wl0jSI5NI+iNL>Qy7mef*N#m+S*8A1Ll7W8Xq8tPmFlfU<
zkU`IoOXeT9&h|{=AEuTlRw?q(5Qj0H+gMpP$eK-Z1rrKlF)M+yP()M*!5SfPE;w#i
zcb-Ph`#a=B+*&7@EJ$4R;!qGbUNMOU7G~hYwh)^&$Q@I}8Gw*ptq`aIbynWNH!8VH
zHxi&1wB+`s;X+72M*epvDhK?q43?xvmrUJna;7Mvcr#P5T+g4~M^r2~O`>U0)alB=
zDYJv$ym_u)mJ?h8BF3~a#=!_kBnUutk5Ryk8N~$RF2WtN7Cb^fNp<A^iHUi_Mt>*`
zyiHRZ(0?k&k1V+iS1IckFr&5UEXyP*frxs7I)*!xQvQn%{(^`=wh2QK`YvU%f^W9S
z-A-W807TvZ%Bfc*?l^SdtqW@|w{Ca)&bj()`S{%L%%y4O{K{$TIg^K3zj%T4^6qtR
z>tIzYCg|<lXS1_uLaTh5ObIAO7Q}wm3;6}_&YAh|?-lC#z8V-hHMB46`H>o0wyv0T
zZxqiEql8cchefiin)-DtW196Vqnq)wWm?%{_JzN5R6_dV!=`k`gVFPWU6<?5ySKk_
zXzdN1qr>BbC_58gj!pW%C;B<3NpcSe%M(<`HvIKl*{CXaqz~&{9W7FTLPoBc=LaEl
zPcXuk{P+9>%oeX(YWX2eRuy)mW1|}>i__&m^VbJ7Qp24;8hLL6Mz3&NPxtIjMmh&K
z*GoX5A2myaU+rq#)o<i?!v|!wWef%RA}R0HN*}C!LJABzr_iPhEt==bXO4FHaQUXU
zSHeE$3-L~}6bScw(+7<Qn-;GfDsMu5u6<4K=xm&9m5On%$b9NsVFaWqoY%g)&DFd7
z4&5v#;h<n6A-7odW~_JC8`N@mY%~%`2|okk>AHWC1xC1@w>8!>c&P^pDNKPBTr5p&
zdmrvDi}UF4GU@QV&-VHPE>>(FHuVGp9{xP{EUDK%INRj4YL)Gow?8Y?4r-K+Y)26o
z3A-4#3pGAHZbvDs)cj+OdqFi5;nzI;qY<#RbzrO0D4$dF<8_qq0{A9!v-8Ln9^E*H
z>yK#hWae>`bo*M%oNL)o;Jy!%A<jvvZIB-ltuoz)9eI>EU!L;mS1XlmX#j`jUxcKC
zc!|~@DbgAFDfLf1vDDY=^mI}=k%q4EbOzK~gnPM^C1ujIzHWb}>8@&IiK?Tkxn<n3
z%&@^AjM9_PBd(T?HjT4s0nxtQkt4o|25RkdL<YiMMS16ds)>S!JQfStF(^<sW{K}k
z5D{z{93UGBbUa<?e#U3`c=vbo?%f`ea7XYo&)Z{l+xqRYdsySqSWn}+?I|>K!?zLN
zw=#A*mLHP@KECA=6hZ13sIYmP^>54`>aaR$eAkLWNdi+#NOk3By)g;mloDjs<dI(J
z=CR8IRIzn||0xOu6n7jSJ=-jTIvYoNJ0D4U`QEVMqq)jLX005<ndH=fqUUw^qGyy$
zNoUj1&AJGBb;L%-DCp<`Op-$mJK8%Xr#yH$b<Aqojb0wkcNnZPc(ffnNBo$}50L>0
zi#uF2w+To*c2;rUe)~CH4HaKM-^wee+-(Gm)exsn37);~y&&i6ZS3vXeq2lTzgiZ=
zkHj2Gi-RN8H`<-`4e2^O|J=N+c@f|qkaywl9o5FnGD9GtkouR1s6P3cs7M2NdZuda
zXOAPE8+_B=MwfcNbSD<O$EYBi{lFW_HCoy0eOpvsKEDM9;J?PRBvwqIIk_~CcI+#@
z8U;OK_1w;z^gPa!L**az&UZsh6>iZX3ujl;LC?a6UwJy3Hh<)z@d|5}yL+cgSjY`k
z=KwO9pTDz1T<`N32T^{7D&yX5fONpp_HS>TB``0)rd8$4&aqSqT3x-1y>D!zX}&nt
zLcm4ko_~IJPDwhN=NnCE9QAeRsK-0~0Q^$D5?{h!g2xhD#2;S?2R5%xI>w)FyWX_4
z)&8D-KME)W1%ukD@!^=(kGlnSSLkUrj|5#HOR;Q_p($nN=H}PwjHHgiHoU}sYK`$h
zTVw|@r1Lo-`wEMrM#4|hbSA0}r(~3{{bT`$GAk+Qha??uGL8w>oLWt)l@;_0W;N(<
zJl+c<yC51$*E}yNT%aLWs58^U8M}S2@0YCY@GD`OGBgaEnePrixaK~y0#1z=yPJhv
zVlh6i)$+|>!leJM=LLgtTrs`Q;Yt9Y@uHHD^ga<5ka_m@vLipQ+_gcvq{oN}-yqLg
zx7e5$9vgR(G%DRUPeTr`!aGSWUA*!`ObwjN6dG)2?qB*)D<G1VZf5fZm!Vc>C~^kk
zCtO8;KD9U+yJLlj{U)=3T@#MBnB4JYDe@pJtz*Z3#*k`r-Z*s0<={Q%;HlL+;m*4a
zO7VFsyb5tLU5jWuQ;&qu@ub`b^k3@Hd3-`|KSv%o6AXw6_=VpcH)~gNl(zla^2?S(
z-7W{a0li;xY}71y{oVU_?_?!JH85whrN&$YFXRzazl=RGa@uTs22=LNEZWhva-QZQ
zj82_#iydH4Bw+i1o><d!2b&I)nwsi)GdJu!RBZF8Ug>ptehs|U&wI@N13~|>(U`N|
z^9)`kBz8YK3?KL!QDi(-54^kx8k7eKOC642Pzn=E!2)8nFs1$l*F*6M>6N=jbXA5K
z16{zuyr|9<^Y-NUIMA`OS_3X{l~Joc96YTynbd>bQjdPBeL&hb8)#YUc89~r6AiUn
zi_N&6&>Gi3em{n<`;usg-MDdby|`~t_3&+xY|!ge4|lDFZLo5u{}@;Azs$>|EA?>s
zAAWl3zy3@u5py7dfjZ&3I>$S{TMvfIoT+jNtovUtLMz9?Uj8r8eoNW^aAO*{^wr4%
zGTD))SZ8m4Jzkz*D(f>IOz|a|0lX8+!@{D<vRAPepfsUiE;&b6xI)-4dwK~SvQyAP
zBFd>#pM*zi{egf^g9v;FBK%$+Z3Yh`8hN9x-yeL#46)~cy2ZXtXXV@(sC)2Gr`0Zn
zs>0TLE-LKw6jHB&=PyvBDEC@6^&sTLP9YtcD7)fnHmT!<X}T_@_2-kH)d5op0xJzP
z6Th@=hK7R_d*DsbmPATmiq@zt)VR#|aB*3n`|Xeq>5jc;diCMZak=T+>`I4J7OJk~
zDNIr3hFI&D90WaYnJj4p<l2<e?OBO|=}BoMw5S+t<`3}b+UybNn8O4E>0Z}d^K=|P
z0TH9hcwA7<tN8{IO&+Fw5q}j$W-e|5?j5o`c7sJ=#kc1NQmQ!(x7SmKLlML6fxEh^
zlb~C^`&b-ouVvM%jU~Umjow4Frp+hG$d^UZ1Y3wQfk4!<*eOv8?e4qS2Wnfx_ZHZb
z?ZcMqW#)%;0(|j!Ru|(>XR0X=jZ!5?7O9;I*a7gRS~Ir9GVjsG35Gp*8qUm?r$k#E
z6U#E9`b9)5KfNpAiW-=Nl{BO1zf1@prw2W~6WeP%OW|R9l1(+FjP6lR?oz(BXbWFk
zF;bb(SYxZ~43}fUqP<9>A}zk5VKC^=M38w$NbV1+&d0g0;RD$bjAs+z-k)zG<<N(S
z167Ue6xOiQk9p1HJwd2@-@gd?P6QpXF(kEA=UfN-LskSda#x<pPjR1r+z_}tr<~rO
zz}a;2D!BKU)a900$<Dd09}TleyzA%{JGgmrj+(_T{RGCAA#Zfr#Ss8%X(OWlJ0XL*
zGfEVuwJOSLq1ORTW_)k6Nj`yht%p~{gz}bXQr)a35P{!8H)w$cmO($;HX$S58yO;K
zZX@QN&+Vp@7~)Q}wZ+ake(*pq`};os*BN_z9Tu@HUD?j7X6$l3efP@Lg?*=nBKXP^
zw4DKH%Uy+c`c<ELubvTKuh2HP3*PPxHhF{MG;9KoDhJ*H2rq!>JaU4E``~Sp2V_3E
z<p(qmwRi>njWq^bU-4;c+NLhw?o*Z?t{$qNUoM_gjeH*wg08Ds);$ID9XJf=|Kb@6
zPhP`YHSJ1h?RekpiB2&)T?W14ZS9;fGKRX01wG_g1Vc`DU;d`VEIs^wBp@|3+MW1r
z6L>PD{=68YtU3ulVuBwvo4w`#N)`0@3j6vb@`BiVmx9IzY3U2PAq^nzDF2ytr>``n
zfHD`4lh!pY1%U_V4}K<%^4AmTE#Dx8DD2aQEq^snrATP`AoxUAsauZqN*^yIPJi!F
z;@^};MwzcM;h2etFk6@n{h?YWT?76@eJC?eGv<DEYNKyQBm}aRwmrj&+9eQ|<M96|
zt#x_&xrt+|TgYD)L*>@+M^3I;=@XW|UG8Z{{X+>$5qfa08@_{Dy1-keghNs`x8&Ww
z0bW)>h*RYxFaXJ`)gD~*TvAF<_*AuggPzj(j2H6UrYK|^(g0!F`<9@3lxA|}a45L@
zQKykj5f7uEHhxQDjDNNYZNWQ%)NGZmb;5I3MEZmYg$;iw?xkV0D~$uzBpWO{2Z$3`
zVL`EnZ%ASNThOMmZ@-mtJ^&|T3riAUSl$c8M!n~H9wuNI)GX7|5Ngqdg>iYtjd%O7
z1W^!vgNy{E$idY@vc%XPjN6$*EEG}FVhGKL45CsOOho@Krp&xkQ@XU7<nDsBkF}oR
zUbnKRlzu?I87pu4FXi(0#Q(36eUFkf)U{4bPL|<z)kQnq27pJ!Q@9RJEXMdq?UdP6
zkfN}4eoBi>1uGWmmAoBv+gmPy_n53whUI+9;K|hxcBo1h&{Q9%j=%!2wQ|D9h08XF
z^Q&Yrd{sULroU$p%{oK8?*ilq>+CtToo;?Xovn+eMpqD#^4sb^Ia<{;w_>L3n;yI@
zAI~D2`7iZYJX!zd2X0U{t%)=BKcCGqtFZrsW2E_iNi6|6az&}9P3B);>I$T{t$`f5
zRaaScm{I0pKDutkU0Is}`FdtudS-Qo4VoD6AAt8G_wXDpM27s<=i7?fIj*c%zd`OA
zOy{WuZ7M7ZLRKZ?JPowO`}TeNK-_I4Mw^uJIK|39d4Ds_`|sG?P<;EO@;`Yr3&i@>
z@l4}74bd}nc9_c3zefm}tmBD__k<FdVzeoKHXd86uPR1O1(t_v*QOl59Ob1?d{Qqy
z*_(J@;v5kz^_`7gj294-bUj+4k|-junV}^zM5#g{+-!AR;ne51&VV#$6~d`G*l2on
zjGKQUs0uq&z2Q-J3!plpu}{Cb)Q2(>ozm)NRYWkfBM;7?&Di3Y?G&0ip^j%uo`y<i
zA(Zm4b;hYJ&G>#Sl((J>=n`m*i9zQpsR?etSk_*YSabw2lIg?THc)p&s4<otQMYUo
zRN=E=4T}t1_e5K4yyj+w8Qnzf0=;2UQw73t{%@&V_J;@`NXZ4in8>j4OXO&QC*5Jk
zv!P%#bEN(Ngc6YH8vJF5Q`1r+pW-y8<d)<Ks+c#>kOA4fAJ6VS<0U?{VfWY>U}T_?
zoB3q6C}6O-W^iC<(N6`4dlrc$_+~&x4xXTSAlwMVwcLjwz^vkTn&5&c!`53Jj-=Q=
zd`}JTI{6V>D1<QD!5k0Jq7*PHTWBsUf|^TykkbC!O)U~xFGEL34%M(@5KUARi<yAv
z*)(7Hm|ZLvNhDQ(@MjxAAC?M<?jd)zlv1(n|5sdyhhnFWy%)XQ`^+l<9s=$-K0%${
zN==}97kj9}2-EUNK55vVv)Pr=eKFUjVwdhF45SunNIM!c$5uzPUOSf(d536IC^#uR
zi!7yNhaG^qp;atiOQZyAQ)W%R_26`thH=fop5DjSGnnIAou{>&FI|$F)Y-WU@JS5(
zcQ5NUi#PKaPjq@j%CcR0B76H`h_Px-%q3u!F-k7#8q_)3W0mS8xBEvr7=K-C>uBi=
z!wv>gkc{|=UH=^^c_dN3Lk@MOtNBwHAWKQxKjWU<d?!B^5ol(qAjAGoa&^WYI;t7_
zklA&|K8sDN$C%rJc5|6BTgOB31QPW7ur!aD%Lg;1Vk4HG%@_bZbvpG+V1o;)5S&Qw
zz4C#ZBI*$ukDsNoYkiXV0T&+VnkDLMvE?gdhcsNJ?ykJMf`#pqPFN-3vz8uch5~zM
z&Ye%IkHfX|+EL&({(863H@$E<vQ~D%n=jBsG90Z$yBC6%PM7g9-`6(1+je8vM>wF(
zCrm{Df!>NCB6B+KO6-gdhqg^Q?|v`u0!Pk(HfoC;<qe$`L3PkmY4>UC=Uvce`V(`b
z#86&<6Yvn}c-T9X$qg;}CKma3cjFWOBk7{^ItP9VnFYy`58`<K5IEt}T8xA7H??Ys
znLGS{Z`3a9L=3nrSmAG|!#+TM&_0l^*5U~K)v;}1%_YCjqkw$m#i9g6A%V&YEZy};
z;p~o7TZ-x@{mn}oo*(yAs}PE=y$F-e_5I}hLU&XUYfC&5o!qtkoY8wT!=*ce^nkpJ
z(WOe;&P&I}Q`^qN1tgnVqQA0kSv)t4KVaV)dcn_|z87**EkmDGpN4^u$_;XK2zfW$
z^qJ)V<7cZBmb@I%xM`U#m7E&0qdkWvv)VrcZhoO1&g<j+%G41*)O?4=*)gOX_~EL1
zz<?pUC?M3&yFECMf7>8%@KVZEMD?Fko}cF-aYnr6$x=c%6zU@OpEu)xkDHJCKe6A1
z^ncQ=KkCeX;*yEbcRUGt7_3sF(w~t16EX849(g3p(qE4U5fx{KBcAos$}IX;#dBuW
zYvmjWQR<4hWudZTWJ-U+T@JokwpTYbr(Ofb4=26Y=8{3c^}F~qAFoTu4GGxMP-TL-
zuWR<BbYmRj3-S_p;Weq<C{4Y-%FR(8j;F4~b8Ykg#2&T<=$dxumYYc?6J$!BIJsyc
zmLerwkrmj%8^$?nLb$MX0~)1~c575}jf=-SeB488{)=dG2UZ!06<n!~A5haZ*RFk$
zpn)JX=kXVAQiu9xZfgz|o@%?{XF((UoZ^H15dmexzMxQv->&tV=@X<^O6KqB+t#%D
z0-|%>yx)w%V$i4Z*$~dVkFV)*Fo)u;wo<gPABIF32ikgW-gg^@o~*X4ecYj=Hu|R`
zhc!&Ubq}@i-`d`KnSoHrdcK_AQ9_61{r4GZ>C!&xFIn1EkMEBYc3m%O2JTJ^OV_3!
z7Ncd@c)_8-u^By#A$D#=UIZSRB^Unf)}O+VL_G5x;R)JBY1REcp0Q}d{p1cIulIkz
z&p-TiBKf=*Ctp+FdXF4*MV+3}=JRqB11x}KQ0yhWnxAXV<>!;HUMQdW<9d5)TV}}f
z%MmRzuh#W3i_g-knm2wDDwX4QsKw{ynRb1sb@gH|(Co$q9gZOq5e|F7zwqke^b8&d
zqt_a6SUvg{<nbc?Zn=L)!zMpVKaMi&XqdZ4&qP6n_x|I~J=0IJeSC00sOi;(sZL7P
zs?$=)^pHz_e^VKoZw{|d3f(ieS8ubgJ3>;i%Kdcs*#WK?Hby@o815psO%O=Jx8As7
z&&kcB=$_9VlbdF`1sugsxOE*+*7}=eZMWX2^)F%uc3a)*Y2M)h%d3^XIgk#x7>>;E
zY2kRc-$^8V*lN_NNYknK+E8j<s8zUvrsD|CV!)$&B$?Z%IAbkZAyv5)gp(cXSWx`H
zqkbYMzau02o0s$HW9s5^dYF}7J9r3Q{sba7Y#H>Wc&(gJazb-Fmydr4vZMukr9Z=n
zJ!ZQC+>DdleA5;^S~N;H|Bt1!4vYHxy7pH@T3T8Vq#Fq-K|nxSLOKMb8>Cx68kBA%
zMsh%62I*#`1*93eYv_*m_<P>};JS!``J8k1+3Q|whX}XBxTu;RkWW%)<$#{ZFwrkn
zX03~^seCO{>~<YBn*5O+w*ZIeOZ`juFzdg=Bwby~1t2ibF_wjyn!_4UF3&^TJZa{{
zNRfrVKMQ(jiHj8~CKhw5d)1Guckb)}AppsmPiFzej~wls9yn<seOlqLBsS!bo4WR=
zpGRq>vC24vUiF2=hlvV~Gni-~F{1i_hMK<GV~bZ|WPM_9N*c>>wxeP2d+2|Y@Nd%j
zvGn6q?$Kzw!!ik$d(SEyObw3Wt}PXUQB!Zf!RkV76n#>)k1?foN&S_{l1vQ*W2P@F
zB#kY!`Kb;}-IDE)%(nvdTc?-OVdiTtQA3-SrwWW5(hKH%hur=1tkw&nk<@KfeQnuK
zB+m6at_5&6#cY;r@;A>JG6p4V^52z6zYVs~Ll2e#?Q`!TN9!JZn^J2bpHNe2;-UfW
zzb?p3C#mF7#z-@_f>=etaedlhw}YG8FaxNdBIOKJLZLijg%lz{5%QI|pIA4AG4<Tp
zDD&CI{3pK{zAhKV1lESVf9PaM$EGp^3#1LsWsk_$A2gjNn_$s8)u*nVs5N+)Ak2i9
zXiq#q!8zOE&UMqqWO7iox7$o`B|>SgYh*XFBd1m7t*w*sNtFH=R}dp46bj{Dde(lN
zwJXem1F7znrAId~FcM#Aci$`jGZn3C<WN;VA_d8?i#A}*X3`Efl`eX<I0M57Sj3Yo
zlh~UG8XqSMkxJO}6#Hmbmg!HY5w<e}{y+z4H>{hhcC=WF<O??YIItG4Tc$z>xnt#0
z9bfw1k8@CK*?Idd<c)8ycnkIStMv3l3CD#^d|_4GI+adf?5<vQrqdkNIu2SM43|T4
zsCyix@7P*{G&?cMuT){r9qeshnLd(zSXj6vTWkFAb)RU8VE76R9ei*9wgNYl)q<;T
zpE7CQizcMyx%AZ3*-|5?#e)YaPd-fJPT7X(>Qa#8oeF)q;D+<1S2~iR)zoB3YB7mk
zS71-KHa0GCcxp>XT<U5h92*{0$PD%0ZM`9?(pWVN*H~0PFq#RmccuQ8UDKeBhvkQv
zG~$&KhMEdhP!uP9{5CyI;EO_3`?~|=?woD4ZvX-gj++s=v1qd^mj>U~k^$ONc&~k4
zz7|mrTeGPc%v^!<TO_H3h!8}u#X*y26$pCGtO1+nBj5%y|38$L;_&yO(RJ`&^gXHH
zr%<wcB%NQb8^?6{20yN*-_{h`@hOhTFw=&}r_MB}YVLi1>)p_+%GoMTzsYr}>(-bh
zS~^=tPA|!Zg4qfcl+i*_Qd471r0-N~bN7T=Srff1(IofxPt-DR7R6;s>)!cLE0Ge#
zAC7vIj4kFG`-IC)v9!o$-j2c8jMK&6BKu!`8HuGh{D8&w)4q3IE|XxPv8VNd#p!3u
zjG0|c$j0>FZP^@e$KcAFBeuBgw4T$mdklkF|GO>88zQ>EpItDH%$vIV;nwbs_RO*T
z#_X@KWU@fi{h2&KNH4NmFR55^GL|+EOZ@x8z;h<JcpivSsW3t=_jS9ALLVsF++-=$
z)4VHL_rC0x7jd@EA~$Yv&okZ94_VuJ+;WPVH}_}asE{>H&@)<n#r%UqSvC2RBXFhv
z@Af0bwcFNNM%ArzhPy?R*6!uC#}Ym$(GV%+Qh`&S;LC^RSpgn7lPv*Jk-bO5Oa}rV
zH?GY_HXy0^hqoxEP}2^b7N3OvR3Y7lJE9qi(s7!=6{nUje0oc#*>&X8^ZSQqv(Xp9
zGW9gPB6?<j;%x+cnl9I$_%uiCOj7yXrsgiEf*)-+3D?!LVPN#zvttqQ@QZS@()r~a
z5WBX<d|s|h;=Fr7Dj%nc_6H^3bbQ7D)z0;t*Zb%JZ}9c^-h+{d`}@Q}AQ<FBmEaX+
zueC{MD>A**V%JwzN%mejRr<U0C}3w;vNiMM=2ut^aWIF2YAS(qzHtBXcxTgOQwL<9
zDzN%YC@;#}Vt2o!CmuhRk4WKY$Z@A)rzK(~;K5W`+#Mr##kEC}J}tNBapANTxY8h8
zM0abYsmGpTlo!tJAL>RBYs3LufRFgkn-Ky&X2##QYqKq=<2W%bN;LaV*M3cKsd@Ji
zx##F!abZ@oh6|2nsW^XeMKquzd8Q@E{Kb0k3ApK8xk#rm4rnQoil@eF3pt<ZqSdE#
z>o&hm_yI!Nm#Rc_%nM@MJ?%B1BCYT+CiI$QVka=R1*bi7%SC(ENZTOW-`wq7`6!-(
zZ@K-VTl^S2ks@aD7J121)FC@F1iP@4O|PFFlRyc~Oii8IJptnKKb5N>(H&n^iw#o(
z?y#gwwgct9Wo@~}p+nQa>hsR!RoDt8aw&bAJWnoElWLswhw6=WVhKaP$UVGgPti^^
zB*N!#qMHT6f4u#M4PZZFLKU~pYCB<VOsGctbBs_0AB2CjhOFDB&KBPJV5>^w*|4U{
zU_wnh+}4_;KqZv)L5C~R@?ov0ow;@QLwJD%l$CJ;$3HsUu~~kpG|AGtS$4>?WI?9w
zbt5%#H``@fH=JpoB@Q~FXP-z~cjqT3J}n?LW7yi%JDRLg$aJ|psYblol=;^?{!!wS
znt-d7Xt19uLV~0LT({&hv-d!u{9+Ml=anO4UeljyEY?z4Y|SeJ%b<e)nKu>d`Dokz
zrU2HmcDh?|p8CtnG1-j{`V6x8`>;e=3O}8gTU8+$JjRrGjxA)h2L2N|27V|px*9)d
z`-D%pVf#jx7d8Uc#;e6?St`2V>3qh@?%8v37_Q`ZurDa#W%W&1RpiqrFo>EEtwTzh
zqUUB+p8TuEPiJSaU?oo6?u8&pUM(Rjy1H<hIIhMog^~H=R0sQwlV4?EH{%?cUFtXt
zV)DE8tr~+a+kf!_4=_<bVdHC?BMLn%ic|2y$>@lcBn`H<;~MNX4H5aTjg2auLmL)&
z;MnoD$&4nSbfJl6RH*l{;IDC{VZU=g0K94G8XwMujYi&|(53$4W`VMjqEycFuF8?5
z?@ZXb>#0xy{^WHgo|bZXjkLia*TIIR@w&6=Hn*Kutu<0+XFVs>?CZqTJ6X?{Yp`fS
zZ_ctW8nN;(=G8*VpNb;x{F{%PYY6c*$egn_6vl8_-6MqqsG%=M8e%O58K5>a8wbwF
zd6Hug%flJ-zL?B)N<#x1O;t5klLH-H)gwEDo&2jA1|oq1FLJb8Kn&DG;E|Wc;&yTz
zdt7t97^eTo0WUh1%x(Nd3X{TU(kL%QH_U;(p3@q&*+s#hOq{dwwR9k$*ci*>)o<J!
zrF>G2x1s+jy=Cr~{STm!I5`Ndl3z~tXg|4d4J^rIhPejboydC#09ldX|71ne>N5k1
z6Z264JEy*l8f`@z>{X*tS4lg827iDYK|r6um$vn6*9Ba|x4Un<)ApauIAq?{5=p-s
z#01a&i9TNlBfaXl<7Xtk7=a$Z*r%!gTNIg&9cAgX@c?%6X@c;rL9totfc=lbyn0gV
z1P1WEa7RWX96v>oc!->xuv=Dw+j-p=)UE-T4$<&X!vTxad*d_1ZmCkW`&?PavE28t
zBw1dfnUilX!kMBzI_QgW_<VYKG($l(5@bm;s)T~3L2E5-U<%NLBK=;ZYpt*3xyQ@G
zvByL(v|!X6X<R`P^Lrdm;n^I29mgig>xJRT&cTgH%L2r-XXRl};048OmGJ2tS_)Hc
z#OHiIJv)@I6ORTsW)72||Fs2Y$1_cY(d=?8onhO5u~2TFCO<3$jP~l>VZ+evtdq(3
z{?1!SNR&ocpr@qBitWAYTQ=*LnB`ERX<fU5Bzlz-6_k_Ub(Umf2f<w@q8wVAmc`D`
zud{McrBDhJSG389m6)t_0Kl=-;=bL;#0+5=o0X*Dy4u}=QA2h_RV2f3t5<}pNcf7r
zVM}d$a`aBq`49uf)Xc8yde}o@`0KfL(PhWCY|cj1{oiy`y4;~iySG_|0-3Lj?++gV
zkIgX+oZ85KHeW(}N+*je8O?72f~5VoqIOIIqx1#i2^lo?engp#AgZ_ugZ$<@j~#D~
z1a?V@RD`Nbt6OE&`$k8FB(FxikG$#VKQxX&ba7ZyYku+}zG<<G7{27_5{-*ZGMno2
zJC<#qD-%5;8jWZ)+~ho7Ka=&bL8r)J=W%}aatIgp{36A-;7{LU++ai)AHdG}9#t=d
zlfExU5~dg=#!kyc{Kr;ijSOI1X@2SGhglQ2V52lYYg~2SSg@3`^uF#s0DI}#n*fR|
zvv=E6HdlN$KEaIOf0EPgk|WzEt}*egI)+core96<!Oezgi}v*Gxhr?3@O-~k{qK(@
zKT+J}K-QYrb~f{g*_#iFrhZ&21PZ$P8DXVa2ki_8V^IMmkps#GRlxt+>Jp+0i@S7k
z7!c$JuG0EGhSu23Wh=Zl#}h;LYXq@A@j&Hz_Q22iOP;v?#VOeTM)Z6?_5bcYyi3pW
zCLdoCEL?qMRb<ooJm5JD^F9j;S;fue$rUnx@!t4{D#>3Q5w!F5^se~S$;;lbojQ9F
z|0!@aBaa^hG2}=3A#}M$9|@Umw$sh8n+R4we=V#j&>^<2l9S(rr-oPCw8`+7MF)SI
zhi99oWWyWiSM$<p$tTVwBkRlCWI96d67nOO^zxNPf>wu>lMcoY7mG8ZR;d%01$C0^
zI>R&zo+LIgre$J_K<Af~Xno6eAS|v9(z|{+e2;nk?xY#{+1!qBbocRoNwGDSdV`Gb
z0iqD-{Z!8z_3GF#12L46y#J0sO0=66bl3DfuX7f_w9KPXvh092d5cTBdIxIt6d-Y!
zZSZuQ`9H|#;Tg+JZI-U{n(51rn|jQIK!TZ8vde017~)4*mApSvj(eiFu>EHTp{4jh
zWFhbCIZC{kC_c76#QZNp>68A$hP`%@@y`~@Xa4?M$pti$B7<eEpNJ7vUp0=FQ{#Sm
zS&%Gvg7YiZbH1r#ygySJ0Icy(P%TH-H1Zkj+NqhGMotH7l{t$g{KtNm9Ecihfp1}{
zg(cDuDg?|q>o)9MSW)DB1m}L2?k+-LJWE)xbK$bFRk4bc5O{sm@}<~h5<UhqhH3m9
zmV|>hb|}}ct<lNI!mXfl;X<vor~NqzjToPx)=+!Di9`<s*N#T?MY~$Sr{D>X+*A{h
zz7xab$X+!T%JU=0V;tFBpXT4anq#2v(7hws^0sW81@FABh@0E-uqM}NeRBlc(u%|H
z-k0t<I;dRPQqeGO(@sxe1LUI=@bH{)F)aFnrh#}q8b<4E@0XQOI2I<KP5$L(Clf|U
zT4W?~Ws67FGiOi?Mu&!^eVknJ_Jps*U8i{KD~`VT#;BGe`Kj2ffqiv&utj+UpH=ul
z&L`)>FsJ(8OA?Mf4z+yBUhyv}r_;*2J)I7f`_QE4XHkM2<;h-0w9lXDSAJvMcso|Z
z3X9b4w;n@mN_=^cMk*sJjxll|JSQfNzIxOez0(}AA|XS1$ERo{U&8e1mn_X~L;#A8
z!Qv^xA7|1Z8z2EIS)Uufc=-oRUE2lhx8bq;Kx}>COEzrVs#i!7VugZF)CQFgmfQ7k
z?%ol)5KOj|Q(Q#0MrK-|*Xd7^e6j%sL$~%s4<-sevo8OyKiK)jbTR<<d2XIG`l~{P
z8zn*1ml7ViqpNlF0L~Oi(hY%OtU$z*{emXG=(2$tu6vL<Gut@j?3^vWHz6TpMNk_q
z2EI1hK&6m$V3Gs9BE-(1P=D-coE@Nb%LNcc2%wj^>=UYz6tR^Ja+7Pnbg{R4>8@%w
z7_PKqXozG`6$G5wVR}^_!GQA*k12iX#}Cbugn+hk_DoZa6&jh4q%GMs`#7;TrtG}J
z>W6+le?;;6Lm>2flIx_G=@gT@t~Qnbe8SPaHjY8AQwLfwYQt)-pKLjClj>Efw6K2H
z<BJS;dpb}dB_^qWcrS2ZPu-tj?eMek8AV1As@9FV;E!bxANChgXd}f5?{E2682${b
z=DJU7ZRD1a<g{jZZ>sVoBWgU>S=+0)jzkEcj}=O>3X*tLr)<xxJ!KN!@KJQValv_-
zM#ZxvB2+T^$%hEE8asq>Io=Y>k`|p{@a^pfRoR+qy}Kc$IC(Clt<MS>Vb^^B$UELu
zFh199M6t%t-L81<MX}b(BYYD6Ct0rosw+}q<5$5-wM7>NFw;|?5CL^Pu_@l5E*H+)
z2T*~rW5F9!G260{0vJ-}@e|`73fmRg&rR|)KSD#ibbk(z(kSG!raV+!qp8mi)I7kN
zd)KL^nwl>5u1LQhrP&r968bQ_N3W?`)|>+u$x3<~Zu~Cvwr`zRIii3wtw8rvRd{#j
zEL(7`5a@=0gHLEuj7D6%eb+B``jRSV<HPj%k8L%xZWxEbr&;<qbN;$_Rsngc^$D|e
zd(MPzyIlg3{<jSO90L%CD9EBF2dlpJI?EJF{?iOS)Ks@`J~AVFbz|Kl{uCw@9<Tf?
z>^l;l5|5#R%W>(NyS_<2fmK__KsV*115~BRZRLg;@?H1jn+9lMavCGMJUHQS(KqTD
zFdF>fm1g5Njjx`moc_r$l|0X%bES!X=B%KpQZ~M^9Oe!-i)YTPWas35bb{WqR-=`?
zPyez`Nr>#MYwMWfAsHD3qg*O)(xRy{%E!HjS?D<(3q=<mix{4%?{*`tC~G=Cyv@jB
zdOxX<=vKH*tp9SP^g(eR6~Bdia~e{T@x1n~8B8xNr|O|;bHAoQQnEiG2eWf0p4PT}
znV9x?P&<#VQJB?M{o}H!_=yvO<(vyue*ur>)6@UNc2NCHD)|xn6Tj4^jd_s&2~D|P
zUD&rs2cqfC&Hwe&zeKK-M+gfVSp13Kbbk)|#mva_Kd0V#83e+wBzrScD{6ob>;CRc
zO;}LuAH5Ewud=ZXAnCtRP)uWNlu*fKj$`uP`c0!yD%{xAE~ca7b$mpu6e~0~&Hw;h
zXnRod9=@cw?-R)5?zR;k|3k`k1iPo9XIi15Q|(2n<YkakbKtiPd}Z?>DVk$sJa^5+
zHbdBANj-MJ@ns_EEp?QZpmLY-{5~O5y7wtKM`2LQ31&JLQ1Jfa(>Bj~>+yqk7D1dQ
zY_y``=wyy`+%OIm;FTV2XYfxhwyo*^Kd=$Wn=goUdFD$_!N>+ry4mKJ_ugL|cxtc@
zAq0LSK)xv_;ba-je{iXZw3-DQjqHL2VG%%LWJm;o-;$DNkCfCr$#!LmU$-G*R3(P?
zJ3xIMRO5B?tOcwxsX0##&Tr?Xl77NR)_2$3fk8y<y)1`H)<=cCoy@1kfg3oO8{09H
zIQD|qpRU2OHEKCrOI-CQhg72-exP7|@MkLwbPXxG{WeaI#r^FwLflTnn|E3d>?>+7
zZUb-3ubLxRmBCf2ljVo^r5#I}nE23l>O-FUa1@EW9{tZTDqi33Lr%B*9Dl*J3$hru
zGpTsI7kG`oXBlreR8Tc<`6r%r5@)(lLvr2oZfH_ZI0F(9aI-HMaD=P@R!^IZOR|8|
z%wgw?zj$_&b@d)LA@TD-QZ=xK*w}k`ok2RquOZKABwvNQW9Bx6g_zSwh<cBC!*p@H
z&Tug=7m+)hCU(wiqoVa${lPLXF)MGxu^zy=*pl5yl|<%!uh|vyizkl6{Vj781q0>t
zGBq-QZlGu6Nc;s`EjxXsWX#R0#m(eV39s_S<}K5*u&G&fSFnt^vTCZ6DECUDg(8F|
z@W9t;bZYmgy>YVm?-7lJ(B=2=#W-cvltaJpXz~d?1Bb);#z|+INC$%pDWUe_r1crI
z5D3HpF4X9EoH_hL<bA$&zuV;zM&Ly_>R|G|rwohjUEe_`T@Jz;XdoT00+K51YMejB
z;F3@18rU5>-3=Oe<*3wW6^v1S5F<Orbsx$xTDqwh)E@+)!<USfy~y)(EDhER;6{EH
zqo+S(X=9T)R<t4P<s8F5JoJ2R#kWu-DR=eVU5}Md<8|C%v26KRUeR)*SD?pm`jL3X
z=luF2yM~EbR`*!#oxpgF{!JvQEiOH~uJ+^pQi8-%BSKn0xcyL~X>Jb*?bn^aOA!p&
z@P7<7=o&eXT=9IH;Hi+{$@fDxp-Ca33ERu-&dzIo^7qC))uIckdv;hNg-{pXtyTZ?
z`Xw7WJV{xH_O5U&0-&p0|Nkb56Q-<ET|dvPLb|7&TXjf0?qfPhad+IM%QhS>zYg37
zE;i71*MdO<os`RitE)dv(`MyqD?qUY>lhWdQPf!4qDI1oj`)GN*fH@AM)~`J&@!Q&
zJ?@>o@?=Xy(c15i*_v)704N1ywBjMRd1fi;Wq)PX^n1gWfF&xI(ugrqHb!}tohH9e
z!5jFhz<#xNY-WFg0jxDQA*fbao*4BR!Xn_cma|c*Ax|ib3Op<DJfxvEz&Q#?sXaHj
zxhf<5^5d`cYbfD?j){L9K?U@1X_N|(Z{YB+|Jjg^T*gg<>ZCzaghj;K)5C0fqAnXH
zY_T5vd&$%${@^8lN{{u3_pIQw`ZA-jI88P-PP_s^E771R;J094)3{3e6f~-m0Ehwh
zmEYK*&cFYX#N#{QMQR)F3ru05D*gK?WcW~SyNl?}0m@nI4al!jX@B<Q?d?5nYJEaS
z-bH5F&P&!QLr9&y0%F=ce{w36ENTvTuRe^A)F&E-=^?Gh><O$rF!1t28OJ^8{zUj%
zB1ixps@L>u2)B~feCaoO1?pYtDn%ye(j`9J;?OSeP&R4kvjVq&6PPY?OvkzOOX#wZ
zlr)_BdG5LJ-2e^heiz3j%XNLN)4p8ba&fRMU0O`>-)dGZQ)^i~KANnCuR8j^Hm~W7
zzgvB{PN4Q*y6s_f>!$=oXxq$@P%|KmCF=(|zC{{AR-jmDsFZdZF<A)&>;;oH3nLy~
z0Ploq-g;OnzB>E0--epRM}J5!>h?JIpod^svt&)g$380kl8T@I{pYOcIX7eA1F$^<
zZQN%Z345gUD61m{HkGpJ=fCTd%Dh({(4;w)7BA0uoxAd<cS-PRIVmTr89`wze%+jk
zW*l&dRg{}kpo=FAy03;q=1Z@i_9xtoFZe$~qzG5U(tJtRg@1H?f%_^gr{o>$)xhv1
zB{k1-gAgV`EWeQP>Xxx`-r|Zke(NFia6WA4@0*hKzO~2mKF8ZFw_>*g;^r%QY0*rN
z;_OJ|*)S;R`X`K_tA`IUXZwcsKoWY&_jf0JRQNPB=4K4I_N=7hsyP{XhC_UO0iE0C
z2(hEg1-}$lMeu&Y5{lj(IF^+9C;3e<J3Zq59Mmi;YAzkKwJ?jLoB<;!xDdcK?<wr$
zV{`O38onVa*pwuc1-{=Mih^&hIK%fA_5d_7evKuGo7n#Jin-4;^T<8nf-9yzcVSia
z?VlmRw!Y8$bL2mFWxTG+icfG9p@b}`ugn`GK8cK%gu$_--s1PERpn|{8cPbRHD}lV
zitSrIpqF15ezOg0{}6p^dC)_lk;oLNm&<Fa&1{F8C@tYpuzTHoYHts^4b^ZFdh|8L
zxWmZNpQl^BQ{-&uB9nRl5YQet;}P5(<V~b1&a<eF`ImIdE)*=*XX&LeY>0x!k7&r(
z*kbv1PfCt;5mBR!^f0y`?6NJ#?Xs>pN<;3BBR(8hhMD;&i@nB93&)q7!&Ph>ei$y*
zm4v_CVptS`XOkvGcnOfQlA?jh06Zb@L9dWuLb+L2_w>uJi}3Nwfm9g>u><_ItYIbj
z^`C`rs5{4FnMZhSyjzSdD~#96itt|;aUnm(JY{AZ4EP;BIk6eA+#Z1VG(+*L!KL$<
z2h|9WR#xcwp23it*X5?)M8}@)&E_0~0a7B?k#3<1n<lf<%^l$5i?BpYN}ebC6g}0R
zNWjUMNCX58dJs&`FN6ENby|{9pLf!iYuH#)5=;~kB$pX5Vf@kOt>%CR^|yG&7%QGW
zYlh@%N{_9s5&zZ&cg`s9T)!dNFW3sDn`h7Av;H&L51IqS?H~7{5l}%T>f0cOCskic
z*@t0=hSZZ)9%H#R=i#7|SIGb40}6M6Kl&tL*lYSZVb4iOIYdB5h!R8hExm}dJ<c2L
zKRDNXgHZ0Beii)etd=4Nini0IKh|vxZ>%5LD6A92Co)HU+B{BWjyhd)=m=2$>M7!4
z8TV{s#P;MOaltpS-%2OVn4(|*40xy`*(}L=id9m)&JpDG7l$vljGDH<FLQT-kABro
z5wh1KHpg>GnsYajB*4UvPvr6PySaP8!7*zn+S)S;!{|;J{!Ry|f;b00zV|(+yT~^m
z%m)s@GbOc%k6U=|IW(oG_SFp=?HoSI&&Je2G!++Ciyjhi({>lAffGmDtR5;{D}PIg
z&YkExQ*07&dGK`deaULEmg~Uq0+t8`HOC8hku383sj4JD=EsFYZM)Z%zAHEIu}6Gj
z1{NN0pIL_|QFl*G?ipK9yswN*eHyA!C}}MF+2xb1dSBzoh}ma`p$GN#--UnmQ+s~4
zAnghL2pv1ucsG|x)BKWgO~_z+Z)6xJDjm|hm!hPQ5Fb%M2Si2<?W%G;ag-p<hK>C-
z)-u@=hr$sN+BGdAFteFh?0U_77Pn2>Bimy_-Ige{Ym>X@(}-<yDCa<ri^)wGJF5h%
zuS~il`h`W{*v$8scB-84eNT<e0K~V_-Mij-H?Cekq~I1Wg^T>!U7@%yP(q6Taf^Nx
zx>V&Os=isAv>ik*TjulPL}ptCk|cYyc;Tp52I`3cqTl!5yFg;CkjB}Ej0{0mIbvVE
z*KNR5g+eCU>zG^PA7!$4+hxOtsVygXGZZ*2zM7_<n23a%)YeP=AM1R2ICCuC0Do=y
zWFLHgk<330E#bqWuO`D$vLyGQzmU95mJE63>vbk!I^d+x4%C+f6W=r8`^(Da>K#w7
zM$AqpakrStEb&mG^^}qU=^!pflUME$04P|jY(AT-h+m3RuXRwM>2FYyI>m6^w7Rex
zrtS1p{l@yZ^F&$6(w1<z>O8D<7g)CVjMxtDZ+QYXay0oKr6;Uu_bDjhsPZVgx_V?S
z1Z-`Y`s7G`MgG>)*cUrHR~&M~HVkh)JtbGyFZe`u-jw(k=;$?jOME(ow#jdxiG`C9
zqtO(Ji=y&icwh6TJn7BkPp{f9=N!#KsbY^C6qL(R1-j4Ls<^a;W^NA8CC&b)+g$c3
z$%7-;UZ5eJC%5JB@-k=836LzAgWQ#^zE2QvaJg1zzev}3@xJM9=t&_dUI(Klc`Qz3
zF8dg+``yg_iO$6Vw5;iNB^p?W5V`3q<4)p_urdsc?oNSln!*M2j2=16{uC`ll(jqR
z&M1Yc_lcjO<gxz1lN*1DdYe*R1IOhCvc#JAVE;X}-%ey2Wwh|E2^slfIB)I)0s<@?
zTI#c+zkc?jXgPeni>vvhGym>ZQY+n*VgxCtUa}5q)w_-R@mveLnod|*X4CB$2dBxx
zy4wAPf6FzL0Na(j^}4R5FAsFPUh%;^pEnXf%)H{f-+7G2pd6O2-R-FPmdB*}sCpC$
zM>|<@-xZ&TDyl9ETkRh?hVeOQHAL_&{p46wjWB&MHbffU5M5vNX_F9IH?mEYhTb)J
z&eU_FzRk|w9Hr48)Z?O>$a7;QJVaSo?%H_#b>vm8<B`n`JA_82j|%ROgOHG=xsM6B
zr^`QmVS3^4c@8y)nAxwSxb}Yjo{9}U#eKz13xt@ATf#<6OSPY&e6^y_zn=uYj^Xq3
zvUoCCB~s7JcSD{2^6E+mWum{-UqryC&bC-zFxnSkA}+UZMU;!pkj(ooo$?oHLfcXG
znLJ*_fTN{Gfi;s6e3`8ILl8$c=b^4BD|9L<^CCrlr1yE)8-|~uviX{3iTkA_v3!hj
zd9iZT&DTE(b!lC7(Q)6u$*+NH8tBGDu_*D0F+wN`9>>{fa$c&f4x}+LiKw~qV0%hO
zAPeheoA;-MroJ{Ry>w&y<^Nw8A=*7zci-%i$e9C4wC6-!&0Oajyh-mOb61Y)&jnpv
zH#aNO(=QR#z^A(?5jTtcI$it18@1m`Z;qG32_(k^E_;r~s^jd$H&`dUuouUMGi<hg
zSN4d9+E;r<78}iG1_=e2J#UkH5)!0`I?rinX7i1E-9Es-jC_$wddIbqM$4nlwLwuy
z?ra1MTDk`=U-D>4U<^fZ${L&(Z|T+bQDoMx!TrJ0Ge&X(%K=ljgV*@{xPl#0%2hOf
zrZx#r%`1#%+D>VFvI%*$Y#)KAGDfJewBwop{nw!vTj3PB8yn==@A}4;C^@UB307r7
zjb$IzGkZz<KqTe;<23}bjt;@5p0wyK<V*KAc>)hZk2Q^Onr}L@qKRLxihn-4%3tGs
z0=tTE#K`tgD-#=&hIF3S^H5nx#?~}DL@^GsV^CfR7rtJ4(dH<njulMz>sM!Z3$HSe
zy7nhM-{VMq9Ukfp3GkbhE}uwOkxF1qnpkz^j=R=7QSG0JE&9>tx6~a%D%l-=P85%Z
zOK-?2g3T<og8{4-$~$w`JS~^!A7bQ6ERtrr(jt`eyk4Sftd4knl<mM!baLHr%Vkih
z%pafORbKO$9g(rHsBVlQq}7=C;xJU#aNi3rI}x?<3Cmtg3YYbe=tpx5b^coYrMBmR
zh`8meGtA|=y{6~<3-ajGcW1ofeqxc0-wLAwD9jCr`xAguZ!|+#{g<jG^lKr`t1SC@
zY*|u`#eG#AnWVy#PW0ibFB6!0&WS=9yo%qng-Wv7RkGN*EA5vW@nL3hW<xSKQl5n0
z3UMA7>d)jGVil7;YzT?)D*n&Y9(Ms&(`ora);x<nK}((DOUDTYQH8mw!F07gH8JE}
z-v?eGGL_pW_|=Rf+&O*3o=P%ju95)8-N31|#_4h>)Yr-yy3{bSe``&qm^{dRnd7Du
z+z~;PEBMb1q9)Kt``)&#?*j=vdR%S#$u=0`Ef^K0+3{hs=%G-7gLWqu{<`G>7rBzI
z)*M5mf*z&)l45FpB7%%8t`@sc%}hfhai5Hmo`a%Clzv2}`^z(qclai#!dE_9{~1iJ
z?k#?MLMmBux%mmhzPwJsOg3*5EV4R#B8tQ5kMjPPxI*;)2BANl_q+?S2&K*XiKV?(
zn{^0-M!Bjn^W>@fswYs+CCJyvqK1BV`<9crJmduBufxpj+=>@3-%r11QLJA8UTx#m
zsrE?!9kC|fp1e!Zt)Io_3iXZqYAu0X!^1=M6UR?~kZ&vV{Eh4gMcpnnp7;`>?oV(a
zik3X!#wBvOE3Ve;97Ly^&?6V_QP%48YWjZqwsHxTiwuu%G}TL(@%nbU#vB`q4}d8b
z#j=r3I8!$geR;`q=|KyANPu!H^<&(qm+x%WmomHbp6RwMt~~N(rhOwM!S)DmwySpH
zCEHdaBV>&7yQAj2Ip1QBmZ7kGwY<$5XXh9Jb%5Aht}FzGJKc`>HXRn=o?H{PUQwrS
zE54N~q1nB94brmo2Ln8^!flUyrSuaNnbb&`YT?(7Tl2Yotr{7;%2=J~$+qmtG%fcB
z%pYl=Xy6=q$CI!WiMYf&T*ZGLxg83j4}F700NVU~z)|-$A^vwoE?W=aMtJEJB%~qH
zZOzlZAC2&y6wb+&fDwe!rJ`cS6?GkHX~F>jE$+(34Y(o;Q}Nv-U^{2~cJ9>weN>6D
zceeBMTC+>z;lA^+$Lrr{8WU4&SkeQ{Pt3wm2r77yQj9t)vMsGW$3G;ybo%airStOD
zu04yYhBkZ#bix*DT$H?*-v9+oE9${N&zvwvIa?T&D#dh)Y(3%bOwCDWS~3(r`ExvK
z#;Zc6v|1tc)RKGw*6Yh{nlQQ_=69a0^jAqFM^v~wZ;J|K^&$5QYMBpcTCRs=d-}a|
zUWv*Sy!y~MEB{}27DBf^C<)E{Srp04ZN&bw<+hK>jPDH%oHY8bS09p3_9hk&I5Nj*
z*76C%W$6#VMP?i-1h;VcP@RF)#BLwZ#U6%LadFuBt9oiQ*N|-`L&-3T_jPHoBfjhi
z0VfB?K5gpArCpcR{|HMG6<g8`QJqNl&o837?{MHh({pId>s#B$=W!}yCF5U25zMAe
z#bkuCoAJ+EerFKsbZ8Owz%ck26%+u%<LAsuT2)7SkEKsZ%a)ik)e|!`^EOw1>ygpb
z@r)=oXdz$3{*vX`I)ELLyFfZEYX`OG%)U$aG|xB~c+v^+#Pb|1G@Wb+Yi61ba6Aio
zwgD;#@7wE*Zz<1cx*8>9<m1%LW^-kkx*~`?<@$(ogr(IS5{oUC=Ov}EFo#9rNT)-(
z3RZn8yAe=#jpIdVcU@zu-&c<T`w2g*=4ChXp%X@;GjnZVRBe{@q4O>NZD2BEdG$Jb
z%tSbX{MV-pf8+ZhL~Z7)A&`~@^5Z6aUUGI(Y@SP}R5~6WicMZ@X4`>uxP`0cy0nb4
z7eac>G+mx5-KT!xE5ids;n+$#LYKGq3p*6%KtMYV?-B8Hwe%by=v#~4LHABgZSg{{
zDtZJ((jE*AR{$*BY&t<k9+5t^vSp>0pvV=E5~DEJHL&@{bD^xdSI1&)@8P{+rL*;^
z1CuJZmND5jrz9Qc7_&$Cd}Q=pu$MUvX1wx0nQ{_#dC<HQYTAcuA|A6db3L=YA4(@I
zemo~m=l`o~T#4GSzBZWfb4hw%3ufo(xDZ`SV75mM_-*3umT`x@qfaNqmjnKEVw3D_
zSR35S%3={nUbu%Iyd49MmyjfaO^-X;xa&tW8zP0ARhn3uTTe7#Z(GmL6~-CTaZt2>
z{X5#-hY1l>5bd{#H56lDK*KAVYeu+RDCg<a2W6lYJb$0Md45l%51n%nllIb`pphn>
zVk>2Xy`{J__`Jviz{y?zzvDh6kP4zNfr>P@K?2SH&G}04sSM};GtM$-XjScnytN}^
zi^i&Y3Dq@KP8Bd>#Ji6WzN74Uliph3|3P@(SLQb{+zk(s@(0k;R}WIk&3hH>H&}m;
zMVkK?J7E;+Ovn&8Jo}5Jhho09Ns%WeaybdA9j|56a=7e*rx&~nt(n}yW6(#MvZRwL
zk4JSyE?>zdrmAuAifONhaFnqES#0qJ<{lH=S>rxI^>hN>NRv~-r_KE_OwZv3%%380
z-H(RjII@l_y2OV~lLRmiL(i2p0**!)6sdt*U=HSvKm0enGzDafPVJv~qn2?_U2`IB
zC2-lbs2~DP*^R1_iWf?)C!A%m_)a;^L%K}3PnsIwgPNEuB7Bm;e1tvNlara8PB841
z&;`FWwuF;)lx3DB`@kC;xc;k_`+W<XV5P<S7@eb9U;2Inhk!L)L|R2Et&bIGqQ+;8
zy!7fKiEaO*g!x8Pj#5@^Ye@l<jq%}=swXei<q|1m`S%I8vnQTQm6N~|@gF`}?%%bv
z*ywG@wp1uDQNVuR^*XGOS@tn5+F+p!|NcAo{!r2U^iL7)2@13Bijt4FApU6mELN{F
zCUOtI|4wDb*YNN&Ouzl~RE)nvM=_BxLsjezmb2k?1%C;EPqn{wbORqZt&M15X{3YN
zlCEZ_)^Duf^O9&%kg$a}=+$=hJvyN6^YWhM54w*%K8Q-Uu7Y+78Db7m=pC<@%(9nI
zn8s`W>X?;}1XA^%Q=i~Bs*@3$8C(P>!sruW|FO6zwo-%mn<+SB>=TzHVtH(cZJdT+
zyn{hfsR+g`=lhpB2We>~i#|f5381s52onbtT>y_XBue1D79x6pj>^ieAVl$rdKw*u
zcd&(0)LPKt){z5Co<|eLq;@80|AX*&RnWQ{C1$KL^M?(N_fs=QGMF3`kK>X?y|kw)
zH_daBr~Fl2t3voIJ#gjSIKY(c%D5)94Z74DW>cETp@IroOnEFWQ5#~qDZe#RDD_hq
zZHtr85mi-t)FgPW#qY`|aARW0fl-0eXx8k~Cq%j(K`@8>K>6xMxt0&0F`TnA@3k5#
z25<8CQc~eSC<VJfe@f@M70w@FRXt-{=cQd7ed;Jk&{q0(vC#$oZYbSuEuN^axc8Xp
zgJ-x?y-7|0s>muNJq}n`ze!_OPaa_{pe$zPa1B^?SDRVobgFY(?-iCem^w4nxPGA#
zm*<WPrS3XZd*C}IYRIJ711UZcxA95V;xhY0&ep%_dn8@^bGK91_OUb2`m{M14-GyL
z<6%p${*E&BA6@kyJt5ZTGFOgCg5^yvL4SU$4o!LzT5L8Tr0<l-NM|OdW*YIrJ(rJy
zR1um#+TS&z#`ohT=Ps;%5^e>}WOdI5D_!I7pN3e6I>JuA-4i0p#D6Jp%>r7VjM2LO
z=p0@+2cq^2p1mRJ7v=RECR2od`$4XdaL!x2w6Nw(N2>1`P8%n`Z*%L}Nuj&2Kl=3J
z-VkWJyCi^URCsbW$z)xlJ*-B0CGNJ<i%G4N6g1iQpIH)G;m9wzrxlZJ;+riqS~MmW
zjBM2)_n&WU3wxYhr$~QL2&T{EJ!qzmJPqFX1Li_%sSkm?wI9g%FI-b>gO0zSDOMFe
zQ`G=zsRhWQv~%aDnY^k%`c5k>ck;CHz)W|LC#{*W*5v-UkqF|E>gb4=wj^M7AX16)
z?pE9ON?08f$)-sqoa8#xNzo#JB&~AIVO6lHy#@_<Et{s{9Bcos2>*Y&XpS{wf=gxJ
z=!a}2BvX`XT!ul<H;;9zUptyv-Wnfi?GjeH9}2AC_fcp-H#cc#D0-0WMT+5D1h*88
zHgpD4q<c3Kt%BxliQHD~2-Z&zX-o@ZdWaLAhlyO-zUJ6+hPFmAapLnGm(WFLtr4OR
zwHSQO#!Ry^5q_Ic*!U<SyK4hP77VW<$?Huua!N=r4zJUXIz&!OoJ=TXiiuNvxVT|;
z`;BYfT~@izP%gVCoZ)J!sN+F$ja|6#ICInu@_xnS_YLlOPJ1`+Bi+||q|V#*k5t9^
zb73WJGDZyr696MyyzO&(m0ME1TOM?Af{Xd{j8sDv#61_~i1E_&srLJkp$m!_AYmF)
zY;o_m9~oc6tS*i!CH!YU=Q}9fv@H$3<aW7Rc_K79`xg<F#352)tiN#u!>GJp6bChh
z%h8q|8NMakfY?QFe~pRo?_{N&rqjg!o3g+w41PC3<6B7LRLUE+K>+VnBR8vH)AVsp
zM(^-2`6kKhF3tllxXFhqT(71d^(6<nGKE_xB<Q+0xI_~yv<_XyYkS>6WN2>RL^~4x
z`bQa=+?1Ito7~pCyjX0uyD_=n2^?H9PXu(20we>3D>foGW|CDpc$Xyac1(UqXcuY>
zYDr#xMofY{P>klZafriRx1@LWm2NOk;2wIiA}yk--qj_xpM26AwI{2ZowKreXp<w#
z-#TpI+7(bM1mqp;6+mUA<(4NLXCqskgna+@c>`xl6_cdjISx2gnr=?e5@8JdEAc{K
z?ZQ=Gd?)hs_Pu663NQ*@<ANQrrb*Nzilkd_kz^wn@g>$Fx9hlC;g{5XZr)!I%>e>}
z3G&PzzjwqiH+v?Fg^TdVHzg-zkf-s#ui)yGzPPw^Lc@2t!Pl?+ek#;FfB#k+E3q>_
zjgncOBh=X$$@B3p#5IQZ=3#Bido)-qp@kvp$?HF;`<gt&3Xb~8!_b3ouJ%(5bBMH|
zKN-Msa-rs&Rb(T0UuTV6oKK3v*7uC)xDVp<cl1)(zo60YY(3?ZON0q=RGTeRR9q8Z
zb}Y14TcS)2I$zZiB=q0PGajn_X$a<X0O<$Volf+jFXw(d?xH9l>|jd0j!xpZKYiu2
zqH1lfJ7YhxhtP_C5WMmZ&#zYKB6v_&WVjWTWl=M}60OGdvjqu0+F0#iEEzp1K&Ssu
zhBWtYM0}eT9e$emDDf6Ly#=JR7#$pOf9I$hUQ%AVkBKUfreR%3TgONDh068aWl@x|
z{?eKz<^i(&?ZqAB3Ak4%Pbz|MX(aJ!F?ZYk!x;X<7NqYUon2bM#r(lB4+7HEv+x~w
zs&8MtFepkowmFwJL|8VCv5ZIA@*$Lp$iQIUYOtW5sJpuH`GEL??QJ3IL2d&mZ8I-D
zIcp)QxTk%}sa&|0Mc$WNUV2m@yyG=6qBH(eSclO|)I-_xtv9~Dt>yDdQR?M(&hw3Z
z7gjF+SOfYqw0muzIJ;K<xua_#Z}f8-dz-54+WM*H9-pbUx)+-Bjx$!zXDq8)J3>tm
zb#v4NrqT>ybIq4ZvH96&5$;hBd~9;xB4^~~s5>D;WFZ2~TG-)H?maiu4){G36Btk7
z`Ls@sMl4!viX7|5?|-;5<v<55Yg~L|jwQWu*&$sn-?i|uIzs~_8FJ4L!pWDxc2haW
zE72;o&hwWF{wnY)lzmCRPJt!TV|?&=fXfuMEdz44ZhB$w)W09;SoO-}w7FY`Pite(
zAfD-KU5OsD;;X6NGP7i7GrCA>NjkfHyb95(A(ep<Tu9W~VY3z!n2JV7H2s#=I%!@>
z#Dbc-LMnxnG+KfsHv=+@4c1$B0M9bmQ|O_)qE<nd58aKuE(rr~u2F=Dmy(N0O2n(;
zpG|-Du0`AFc76@YK13)e68_5a4hZIH_Q<+?cuIXONuvqL*ytMLZ)ylg03H*ei5cKR
zw5h|;qu2acstyqdSX>r9Ygu{zhD^hC`7fTn-TdA3lYHK#-SGY??H@OIo#>&9CvLb+
zH+_6$__3x2uAdxQ9?$McAOpH!FlLa~H#~hB^z;q3O9GIh&v`f#2@F-AW-&&QV5lFp
z<$NcIw!3{i@5HsNglV8#9;U+XNNXZmJNBST^}nBx(=J^G)J2K@1ZmDWdk@~bEsKOz
z^B9`~cLH+^5G-Ut+n*t)PjYcrnSaWxaP#2Y@__Rzn5&e<ka}+is)Rqbk02EU58vmP
zm%aXIE7PCRUCn%W>-6EBH4@EmasBhM<A*Fa9Qx0u+sDKp`-79A$GW*a&h<|<{xhfx
z%?736xdo>kO@9W1=9vT1U9B*y%SCn3hbM0w^uNqMVZIF_H226FdMrJKrQT89^R4>J
zN=wj+cvzD8+$&07ltjZ@y>5blr?V1oY3>D-S|^~UdF0g{rLjp5G*t1EAq1Fg==`U|
zkBiiJV!mlC;@~d0MJy-9TBcSh(hgTm+n;UWn`uDmf7U9L3hV&?JPUi$v4rL+19%6T
ze-14BBnm4~R<4>B%MIkzpQ$xaJ{;T+s)^p=RMxJ7toGT4bi=@O4ch3k$5A4=(nC*G
z-xSIWZ*o4K`G`qmSL{go5vOzinOu6NzxX3(cXyzv=`HMQaICSe`>h@<XT|a#qdA^S
zQ|-~(#p3H|Q{m+&X}0t~Q?@?G(0e=h2h$g^IGSMQ`Pm6LA#wk$Tb7)^tQy&mim<Aq
zGhg7CG=K(IYQyB#4}W+fnKwt<H=$JDNy_4gy~5b%G&rjGI-;Ns$Sy?4)vAmS-l+O)
z1<B1V`$*c!rXTHe?)}d8Mj!*#V)JwH-^NNaV7*s%&79VAz}wK@vH$W)|1jwD${rc1
zC-;ZRYn37R#O3uypfn49q*e#0`Hu|!Q#6y=3~i8y`H4mXT&|b)9%Ylbhi=>uvxC?3
zcF$=g#T;nk9G39tB;?PZo<~V-3CYbjvWyPP6l;(*sx&B^bcr*9nACTaUrI=o9#q&J
zZ}Vh#xpUpEf#VJ~PG&&;)NnXYNc(?J{YjrXaDlb3_3G*;__c4Wj@2Zwi`?zCUQm|x
z&o<o;nVkh~&xjx2Na53Eu8vn`FCyzIs^OzuS6v~g4hjH)QxsGyA$7j&5WNM>FLF~6
z;>oI#xF^DX9}}J<m@h}|5NtY*IUiVcTtRXHT077X1F!y>z@Xi0(MF?hKt~PeAC_=M
zn0DK7mQlR&ht2n#!XCC6U@I8aasy-$U6XIDl%yOaV_P@)GE5X;LmS{_d@w7`VseZB
z#Wb5OVQ27^Os9@*Rs2VfV!G{HY7A55tdD!wC?nk;`h70TZRn92j0zc$?s+)X{Z`G?
z!s;os=4N}<4eNXINpbz7Blxi89Q}x`Fx$<l{~fT(C#_%+fyNd^!5<$=-Oe-$5Yc0Y
zGkJ>!cl&I(Ul*C5ODON;%Cp3vH!|Gmq6(5EzUIHp2v8<vi?P9<{lOLb`*GbdL!4W}
zv-6F2w#lI62FX^;j7knImu^E7{#ZX163>HC1%DM&BJ8iQzR5>0#Q9RqN+@ujZxH3<
zbm^Xn_q?%2)~_`L=h@DESVhOc?7w{>Z6s5e`Um7@_*f&QBFc?S6eVYWWC80R(HZ^C
zTrMJki8H;ia+pO^LKN&K1zA?rk(%!50!D9k9IEpxVv}V5MP4AjO?2X_5=-;GR0pK#
zkdXl*d3qJ-ZPvBdhQ>C$dLY+$-Rpjo-KF%M*rRT(s_AWd$af7eE{~^XeEV>y+d}jf
z3#c=qVsiPUC8Kp&q=abt&0oQijY+QQSgW_A2G{DX6X}Wy2Td*vu#6)U1aKkLaK$3g
z>wrGfx5%Nc_mWYO%L6^^VxDQpKT7oIIy!ZHJwHdbU6nyR<Fzmdy^j0#f?5ZZ?z{L?
zw&%YZCKy!(<t=wWDu5HA`R|-DkAx~N@0FYY7FJZR*mDp#egA)DyGG)X=?=sDx-OHP
zdw#=hV-`L(yCrS1(&bzRc9uqRUlHZXBrE|82LYy{pf^Xcy*!U6ZQsWBkR@b2eV2U$
zTG>@$u^dnRfEnI=`0*r5`mhS$*5n~4dGPDZ7bM29Z>(gaXPLz93cSr%*vmrj<C2=h
zTYg^amp?%YEQ29%lqjdlAU+z-iDI7zbdHsy5m$ek#6c6zxmdS#?dm~3Yu-Zi<%s8S
z!jGuK-WTM<P+)g@8Mxzp^MSG8z8pk0Mm<k-54eUDIon6~x-L~ou*Uv+mCd-E-SZ-L
zQyZ!aZu@80XyL6FI;|1f=?TwGPKeMfH+KF9$<w!2zfk)PJR$Y6Wk>k1Dh7yaTzWm#
z*3Z}I(=u6f!WS({5~xGTYm<8ng?u(0*Xs^z;7QiPzv!vVU4og2D$qbE96Xv6!+y`y
z7)|z^(i}ZP#r5?A*iU&_Tg2NZMWB~9)N?cgLI~9S72Tw=OM?nvLn+T6uDq|`0BoW&
zZxbCKMt?QXpoTqvli!RmE*MSC?N>ESuj3Z2v#q^~@}?WE0-QDA2tZQ>x*y~rnXiRa
zoZ^~<`(VxN_sz$!8}p`xLy!mE>jH+41V`2XF<P4LqhEJ5=j3+uV<z2=^GBPN2wiDG
zXYABo&t6ClA#DHI?NRhB#kIy@^=VxYA(_;H72gf}r8J#6>C31D*W&H|$8{th^xQ52
zo=*A`ng8XzS@j5J#?LvIH9QyjJZD02#h<Zs#e|lA$%Ye1A!Po57BYGtS8gQSQ@#Fc
zyugL!as3~?wRoNRWizXE9R!$zEZV6AyWADtg}+465cGP?Z8T5dEEqSmjn88&WWDN-
zJfblvew9{dI&o)IsC&i32lCQFZ|CF5q~Es5^o5iBM$=o`{qrgI@(`zpKxOZ0>#Ab#
zBlK71qCH-gC~t2gxz5FA9~FrCOf#F8XH&7cFbLRQWV9)b94qhERRny6e`qZIMHlS3
z^V7TK$)WGzWET)a58B%qH~B9%qg1mg;C^y>*O=<P{#$@#91RGk^id=!lLj%#ZUcXn
zSfMTsxJo$2Vr~?IC%(#KyVv9wLx1qmjYVN?A7QUc1%R8;%|2iyy2xXA2@LFUwRfcH
zPskD#?$sHh>2bH;HO)I+4OYNcnH-TT_ym94pD>lu1!9bQ6t$x3O{GsZ8+ey%hKs)o
zFJsFu8qijJBE+({33;HTdojx7^ax!$#Tl-tJjce}k&_~T{-o~Lb;hEcZ_Eyv(~Rv%
zy$jzN=lPHPJT9(UzNzIi<1maV9N*fN2V?cF>zBfXsd6C1Pj9=<8bNPDVF1P$<nOQP
zZq=#FxwXLBOZrxy#;ayn0~2EgdnhSsl!P6JN<+4DT7b3O-uqm>e^`<mCC{rS>JFk@
z{BMeS`!LGF-WA%u2o?&605Tv6qG&5K<oVM9cd`nAI|*;p+16ehUq~slp`I6hAE$gK
z>tUocHW0{m07fCn;aI~lf5oZLqmcfD1QAIIS5t$NzYX`>;ahmPpTw3p>&$J}C%Amm
zU;N28>{VaCOOmM5Pu&pnYLUs?T)2H)ryowL8)4+sO+*l9ZUBCeWDKPTsRq~jJH@fB
z@DmKZzFk$U&klRV#E-HAewFP8(tx}+h{^|VJ<O<}w=7^DPjHkc%lBNZ>XgI(q=J&p
z*JZo|ySu1`m^vDAJq(>F@HOkhPnD_**BE#`h7Er1)i-h%#Qdl<)5dV%_RP#;r(^j0
z-u}964^c3K7h@@?ziKN9AqqdCJ20jf^AP%A{wn|3@8;PvBg_>FS25$jPI*?uJY8rK
zfgzadG;a19Lh)`0vlBnlzM5sDo?`NQY@@G3BZ&r%Eks=33hmp|FcY@cd%veFQ9!JI
z`bF3~F4oQ}*f7U#rSaNeKuIL<<%JDO*bwnU14x=^rQLHaRXS&(Hf!Q9ahVtLe%|wA
zi$}Jy&}jOZnHbru#3f|Q`^8cCXUdC@2#>CZ&9Dh|U^u-T)^Lf^%6`G$e&M(ivHB%`
z9N&}p8_IuAs(YQd7ukh@(J43eoG(f<S%G~&7I#RavOAYE+uZFBh*r5YkvMkWHqL2t
z{jWXj3`5eebs&}5F|Y<LU0$>3)d$N8xx6%3A{gGyp)@NKvh+W@m|C<W@!{PW`|RP{
zJmKXtkRK<%p#u&%4AcKd)K><z`99J9XlZem;#P{g7cK7YQY>h3cW7~U*CK%e#WlDF
z_u>*<i@V>q|9fZdFnoXsA&_UE-96{**`BGOEsc@S#ZY+zy%n><sU1dEQuDg0ouEs`
zHqYJvDnaKnx0Ra<__?6E)kB;+^swClf+{?~Eh4YIb8uTHf|K@ibv>XjoHivRf&+N;
zah~B9IZ+7anY<BS<msYqqc@$o{apeYuw)2|R2ATu(pv{=bKE@X&sTm+4}UXBB%M$A
zE4`_abweg<=LP?=`&d8`@I<?lY~q2W4MYrmgQF})6trxjxRpJb7g0g1?mJG|oi&ZE
z681@tlFu^ux@_?~(Xv3#*uTJe;M(7rq`|c7pjRE&c}={AXz8d9aP`{zzeHAygi5{3
z!Vk%*p)EN}?F!FUoU0tA6^x@I|Ei-!BnNta;n?KXgB)U$xI8<<!jrv>p_E@<pWiHt
zQl+Ct+6I4Z+!9Xc_$*}08WI?W8yIs97>n{`5t9PTh=jF#w|7sW1bR*~0_a`=J}DK|
z6YhUXawLlM@}s*`09F}zqT$L3o%lTouk6SV@l63Q6d4*eVkwT0Rb#u!jc*=V_SiGB
zRHi8f>^fqb`aB)SD&(;s79*2NmEzr<+OWWh?tT$9>*AkBP1gOCG1bb9NJulm?%3G$
zlE2l}Dpa9A>xTs`F!_2XhMH{UDwT}|{<M*3vi>}LudpNUIo;zOJ;0E4ugFFtn!%#B
z9p6Lis0>TnxPMOkrudDk{Fz6af7uqjMdDkLim%#&D(P=@{`#%>6#p!Dk|||S;}%?v
z9FnHoZ_T-rBDY;jE+)i<X{u`5H_QEXwugqXfm^EQz822r$gw`KJq9orphntippr(9
zc5!kFI(7%T9*}u^|FmAxp3>Nq)wQmk9S5f_)WuF~PVX*PobuG^YMsxz?0)?T`Jdv0
z<vkM%HyiZ-ijGefmIO9m77W&QOJFbYTuKfMrf|SYr;dlc&a*yp7Z7R?SALQd)3u(h
z^xGEMQLP2gPwWS4u>w3fn@yox;@J9X33ukfMf6;A_47AxM)LPP72rcQUh!*+nzwpi
z+5yHC7>8tS_rw(~=J}2LmP!6>x->)qT!co8uB0+*jtmBp9J_!a)Wc3L1VKH62&7|Z
z`!m_%WPPDy?#iFl)Xh2zsD%12j#EqkU@SR@<Q?th`3rR0g)50HKl1+ifdBIT9D!&#
zoHpoH#OIZeS~oS<+H~Txw$c1azU1NXXc-H$-kTWv|5pEd|E-#{E{YQJep-qtW;=aK
zW{KcF%z}FCE=WorJx!z;%D%jaHL}{zQp1`4gT(c1%!$;|G>4mo)dp5&m2j9yrL>up
zg#_?nrm5AN*H~GJe#^M>9O(kP^gBHw=Glu(db$~6trc1Yt&xL9Ax+MYB^kYIm&5No
z7G7Ed5axTM3CZiD&1K3Y<6K;}MhECCL7M`%oyw=TdfjyydA~N-@EC5`p11_1fqGR(
z>R+!(M0t^FIq&#uaYxzPBUYgp5Bmp*pp|)|W_Tg;y}=QWS3Z01kZDeVHApT<fqqzv
zW&J8tY~{JyHYpI(OJ0SxXc>thk4e33MI>3$Mo}atOl-P)O;`;PS!*q`8uqqV>2p9C
zo>OWKzN;>w>)p$eBK`w&>Vq9mudr%r!Y|Z``ZLs|46zW|s=iV+QvJ+PGeUKLYdW)?
z<<Eb|JT1woQm~4V#;PX}D!40MGuvhjECh(E3DF5qMXH$5kW&?>oYPsgGF+ns)w9e>
zR69%|>1w8=xJeK2wI4NT89vTLYS6dHN{B?<{c7m;o&?pvOojHR6shKV$wU(|&Dc#+
zMHFZl`ja6C^`LamP|5E4jI+pOyRb#E5W>#UXruAvBSm6ZJ-g(ZyG7&*_+g7cY^M`K
zr7l#DE~7~-4z*J4;n>66+z1fhu9qB~fpc+Um_e?%y!@<1sG90rQP)4V2JBUQO}-5p
zbbVQ_-~8_phabvhZ9HtC6HtKA9=5<;aXrbZjblj|F&<u*oV98<7etn}bbk(u6$dgU
z5C$SKz$GEUn8+lK{(NEE+m%XVK9X<Sipv!Cxl?TQI^#y3T5ihG51K8;(kv6f9J9JA
zxZkQFH+3XEs-&4g#CrMgh=SS^Y!5705HbdAua+?mZp4;WzmHXrHJVQ!giu?*e?!zj
z^(@*4)k-Tp=MY28tPt)Gl&>N;(S;r-Z*5%jXdNh3ZwGaLOHf|NW8RCnu~pQN5{XdV
z7f(YO%4gdpc)v?I0kOB~T86a;t07l}rhN8zYTM%E_P?1o>JYH<H>#gQoetJ0e_V6$
zs78GYt45#2_PllfZbBd`RfZR#*6U-O2gr1F2wfMD5ty!)U6bOqNHB}(Bh=un+ge#B
zsxNGUt<`ESTui1})oKKZDkn13f<lk>jzdBr0!S$V^A{aS9S9qr@hk0AneRR7k$3lI
z7a{D))4g3$%SX9czc~a{DaZbN1Q*-?Zj{|jh9se#JmnWsm>ftYiA_POe)1j9rr%s>
z8Ojp~8VU6`tPxcd4J>ZrN?vZ+sr#udW}HoJ@9iidLPhCvq6RNw9b1$)b9V^v)eTeV
zs~&0`9%n*NmzwkoMQBjPH;LmqzRowESjUk8Liiv;q<?#{Xy5~Dj}v}HTkuf~t6`^{
zC&lRdF6e;-$j(gtQnjJG9tb@|p@Aw=1%D>3UW}KP-!^6n4V%YBlycB2$6StQH7)2I
z$6Fxxa@{a5D<^N}wO!f?f2(kTw0o_)EZXLezP|M5S$61{FTso^6*Zub%Qn6)_s9Vq
zz9A{1X%vcsu7>x;p%&YjZIbnQ+bLq?^>ggnRhKX$pQsk~^|U?KGsqB58^3UzTi>@Z
z3Hle$4e_;Qy`4CGVY7IeK8Dq2^c1buJoZ6c)zn&2G@X+s_TY78e31fM$RE<U*Zsdy
zf?u<?!8OXt#3ltCJxn`3N4${5)!hN&sFg#zI=ma%`X#*n+Wabu#w49z8%nfAI_8K#
zSkseYQDFj)06f14B8NjUn?oggue~~i$523=*(}_i`Rqa0h+=E1ll&AjcKksiG@AMg
zyGYZvNg8&XS`Uxu&|dAJtHf|aY?r#$F?T^@=Kb0~r<0Ly?cM(6*Bol<p;{q4p|Bk}
zpQP8VxK{%8L7|Q^@(*wBrvK3AmMUHd>>2g?zIi9f{yQ-xEV+a?Q20nR&4KCbM(-Sd
z+A^_gQn)K!<zC>~+Lj^AX{G!LgPH;KMN9x4^Vz`6SDon?Ikq_2GqiuvIjE#O>EFK~
zN}aZJ;lwY_ufip+gprp=2lm%_;|gB3%=5YZ-85k9ci(n7#bL$AuD*8>gT?_)&;1?W
zM`)6M_RL$Q&cNq;zQg&OyOpV`p)|!Wk$Q*rbZy&(H5XdCXYx*Dsky&NyYez-XT){0
z7irCW*<_UYEZ}jairwfp*|!Ykz}rTx`_8r(OIyhx@y7&3Z^;fmw@4$QbFPV5j5Pmm
z>F+~oCtQs9238=lPX(>ggKW%idj+5FAC*O(gdKR&?te9m3%`r=xw~Jid+IIe>`K<|
z;f%X+EdSw;eVH`&Zf#9(Bd0=>rGbZ_=-ghja@vb+HI^XY*6+WcX;R<6P~YEw3hr7M
zSC8}<e<zMe(rY@+$Z?$JW$qh$FP8G*kTcnKZ}8Ed_VH_~dtd)E8+nb|)si$Ld{B5=
zhoiglxPwjW00!V1*iiE(3E|FrEryahcf+wpFw4gd#(u!|249~vkqNLJ=wnACxm=f?
zQo^jAK43SzItOHk4_A>w9%Hi6|0YkA(LVljlp7cf)-NKwhWs(K>|vZ%2Kl!^x~6|B
z_7Cgt7q@YEpmV;rR>(Hz3%y_GDcCR-#rz2FVxxA-<{;>^@)POAQKUs*jD0iLyY{2J
zsmP4;FX!%>4PTzMWU_f%N6p}4h348fmO4RPLv(M$>FqdXFO&=_BL6kI5zlf+G^Ur^
z*a)Z&cl0rf=Ts1t`DSV5uia(g^}9;9tlwcm9N-iEwp#Vo#DjbaE?W$;B6g7#ou5e(
zRu!MM2@B13#z&OZKF!DSVVl#VJmUigvf<}|fPVS!cV8>rc@`0Ut`hIM8C!i;djn1c
z%`6^$6GFogYvI+2f^~<-?4v3iyVA9dml$Up{YbXXR}Hz4D{z7x+02ke(xnbC|L_P%
zFRqH;=6op@&BU}MY^SCoY3#h2Zu``cN8=g>J+KjtTdPj2CcHTSvlENPiDt6NY=zyZ
z$u$&^hQ-~X2@)Oi73Dz%hhkOcRH_#+D!3znBH>Lc0&pAIRrBv(Xt`wc`$x_Glurgr
zzqks_(}oWCzjXRYZdHb3ipA4OGNL2arps2<>(^-3-(WB%h^btWLJuX0X5Rn|2Sqrc
z4XzVYQiVG?{e|nM0(~u)a*;*`bddTwQn}&p)Gs_82Y0~GrjB+1Q2MM<EX|}6n-i{5
zn{xgof6$52jQk>aZe1Ut##IP6RxKhJN*+xKzsg7bxd;BcRwT93f}YJ@MDaVz385}V
zzCSc0VI8c%<#BA)<vr=M?gYU@-~WWQD15sb1T2ZO$98F`8`7KHsi?rScWrE*8aoz=
z<-d2@^E2M_hvfO%gvayAdz^ANwJiTeZ}By`ptc;2LD2fSI(FPd)}eV}ax$i8(*t;W
zAOW^3wJpt(1k?uJ9@b6Myy}s&{r`6FazS2ioAB#(qV#|t<H^RRMZu9?n@}e9)}gP|
zu&1rT3EUUp3G}_7QQ}Nw8hNHkp;1UQk^b*HlwDDQUR5uNPLfXneoa?c0lSB~pZikd
ztIvX7d3`Z?fA696850U6yi=x!y%|Gi53$;ARn6_flwKWKqxGk^mA7*k*^_BvDmA_|
ztH_pew-`!ofWp=!wVJ422fgv2gffVWOld*xoBNO29rjb+3;P5==xZtPHv2GPH0q-1
z3#w-n+IrzCrp;DMGLlsjx`p8l6Q*)G6%94(Ta40AH7jSiXM^E&N1dxBd65o^yHBX=
zZFHJL6?^G9PLk<$PmUes(L@$oqy&)Y^vUWBa|i>f?)<^6!+Mj&S?@KN@(4S}i}azS
z?+q>ZPZRIEcQxy^6udNx+llZV-OscP4@lVuO;g|N1FgRq@7Z8HwtVJ7Ptoo+%zTvv
zov{SNKUGdc_@$G3p(szvHR-#Cxz)v4a>0RGy}>RDnt`=nftCo6kV~WC0f{lH_r#db
zz~D{NV%pXh<n9dTpyrf|irI2_-JW{wUF9@kz(vfr1_~4#IQ`4KhB3u>2*8HH#GSv5
zuVjEXB*}acWYL^0JpG7!-(9?A)%Z^0Y(F=cF$ldbWVtlpA$ESrsjIX32~_ExX>e*U
z^oNJbi@VRL(s0Y!GKu^*>sf&R_0i~ua=xAwX`&WpLa^NV*4Vq3<FVWOb7+q^?Y^jC
z&W8cG&VWmyHG7tSCsL&O&MOjcFCtTO?X$9J$~5ZZ)4`_nlNl(1H*2IxAC8=Jagz12
zVwb~#JB>Yf+qHBYC5Etr$0HZ0F>dNF$zIpx^IZeY$Eo7)Zfp>l>e1movLcCZV{rD`
zF<#uf#QdCa=UVsnh`RncAhodP-87`dWt=}>oClT0CX*roxSr%);rY&-n-_ngOHrE`
z5yQK9hYACb5TB>%HlJ*RX(`O26t??##Cs2&HXlzVeyW(6xLoQJe0S+SGHWO9&c-~n
z;+nF@vYj$9a%8tjz4df}WI<E*)auX?BxaJKWoQTHE~czeKq3(I@edtlGry><f$REU
z^tpF)m<JYc34L3>C`}T>HMZY?(DvLe|FgSoMBT=>7<!+kbk5h(`!QuIQhXYrUK;k<
z;*c6^o?r20QCegZ$mdbda|0Y-<E?X0+NOY+jIsRwsG-+`S))yfQul59pg0sTSI)8U
zJWIs|^tQ@zCkPM7zr?R6fYAqp4IeDg`+Blh=tWEJihmb%?STkvIJ?@KKU5Z~|M~0G
z#a<+$2TBo%G?Tohvcef`JYGiiooj@do+HHww#oHTPQ8bEwIY|46`ziu$0>CcpInlK
zz+A3omb`lHh*N72rhVJ)8>nkN#}6@fAWR%`W}&$*2sfq^`{tbQ)M9$lXaE~R$oaHp
z!+gP774X<Kgr`m*_%&mPF=>KCPX%{7rTo~e>+x9f#cYS!9#{xQ#KjK&@sZi^SI)Ya
zS12soC#Aq`xp99S#-~P~#$Wz4bwT`ef9UgcDtt+t&8p~B%-5Z@%<Jj%h%aJgn4h+N
zuxUP0Xz}5G`tF^uh`YU!sMFrvp(Pe$kll;tj$-BY9OREK;e)MZbSqwQJ44mn#97Gs
zWi~hMW!aNS!)s^D3#qUbt5d#UFD%{9T3cmB_txll`^3M`loN)$($RCqI@a@@h^W>;
z(*iYq*{*<_De{D0$wukEsZ|q#os4uRzb!crYjJHa5u&Q<h#GY;mg|!QaVI$K7*dt{
zuRLp<A}_(#hSu5n)GL1P`g7dgTaRk3Y{jLnZA%3NF|KMpSo76?x%m7wd)?M45!iY}
z1hS9lVH<ju6}**-zAGXCO7dJfcc`M+U)qm;Eo{NtdnI|M)66xK4o;=*<37vfGL)W;
zJY(~gtZc{HH%x^MyJ|i;vp;)*dmzy*Ajt{l!NwevvB)3f-<KuQAqw7P7gF!9CG(>o
zFOLrK&njWKZH#}pztA*<8EofNq=+}o3WZlVeo6oIbSW>g8v;cQIJ&xgjEwkCf9m_|
z!!U7M2c%CxpHV{B8(7>?jem7_a)?ILjy*9~e7Cf6|F#?~Y@a#x9cT?-T+csNdNegp
zFBS>?E_>wb>w8wws}Z!CQKS;Kt+<?CV6v2R^FQw6#ASL+(1YEG8=E4=iMA+|%@OvU
zevh4^b`2EiNd^iilGM);lou|4r97g@D_PHuXKj9?dABlucS^-FJD(J1^4esqf8nPX
zTt2+LY}F^+7Or?b96n;YUS_({t1nPy0fckGzJJ!%JMZ?xo;*Q6TvFIy<}&u^GkI>R
z<(k$7eDCX&RWBU0S?3sqjh=hFzL}FRbKGUjkMCmSgl=;xD;9D$S2i3G@A))^43|tO
zI_*ll9pM1V;q4<xT<3ClAxHop=pQX66x8yVV1U{jpQPyA^91R9GI2{3hnNVlE;yjm
zGXg{J=*j9CALW^+o%*5gTO3O27*LG2Z0&TkDATDSm&H)+v5c!!-kFsaz)-w48fIib
z0|SH#BSjj{8K1pglP%;klbPc3NMBJUXIe|dI?v<D*7f$NbTjD>-(ie!xtHJm2N)s!
zO1B<ss$4Vn!HhSHEC8ujGxMuTtlnlYeSkn_O)+T!(~gyuZ%!`d{hl>n(u-FXmUb=2
zv$y|x0?_C&#ddp&n_O(n-2Ev&4ZUpUc}!d-hZfV>(S)Hf1dtnv7@M?)SnB@qi<9c6
zRZx4`f0l36Ou~bKxA|-_-t2zEJA7F?+RfO6|1{If{@XxdhH!|juRKqxZKkE)d*SoN
zZQ@}x#_~uJe_;x$BUlnhvPZM~V9HhM?dKcprUymfLbz*yXnS^eznSOr{9E+HJ{u)D
zpzVofB*+eky+u<N=VAuX$3s(O*@Ee}13aaGvB2*$_al6mfnQq1uP`x}O0JYgW|W|c
zW@$#UGX!}DM@Z}N!6sj)-=RFN0>TgDQF?WcrQadU-Un-sPQ`d*zXrZdiWMGMVl_Qv
z1$zW9x+TS@{FE%?Fz7X{ob2LtfUye5c70pe^l<Qxvsrc1bIPmDiSh%OJy){9g;)ez
ziLWoF*M4d#=ijza5rpKS4CVqSm(n8+7dJPGmAAarA>Gm1g={M~?kkquR!-%eLvqby
z{TECDd)s?X;E;QE-6vo}ptUhIU94w;Ok%Q$_M235W3ukTeOdAUTtXN`GaVbbpke`8
zN+cXRDPCn9<8{}Bksca#e+B;o9J3U&WUE|_A6L+e%_-1i8-Tg^{R(&mg%s=PG#T}G
zRK2xiFU4sGE0aRaThP3+X#Y${NPBlymONK4+yQ$8TY_9fVRTa#qt5iYjSE(Xi3zcX
z@B0d%ng%NCJX<Emiq`%cb`)gMR7`kTmj6E9WgN^jr-$)eiP*a@wd$)5idFUdEZaOe
zf_`MJGVA3zJ~C|&*smdHSL3^S#ATI~<0#yl)3i~=ng}OazZk+B7r5qeEsGryP%^>u
zWb9J}$IwW?oDAHz+5-0~c99u_3PmuZ@9r?Es@Ncxp0Z(qrxj~FY0Ftpj?ehZs?~e>
z+es9vUMM~S=tHh+@1K|M1l9c`oSM?ZG}7O5;`q?U84Q@Z*S0*qmJBeGr0VUs6YF%l
z(0KxYVl*HBbo@f4WX++vb#f@6>z=op-*l2x0n6>o?jmRuA8Q;mZhg1lTOZry00`-G
z3zvHwUUo;+B<s#-k$NUCH7v39X8aUyxMlW?%!;X_P=$&4OBJdF^0$?iGX$(cldS6T
zVMHlRab=oaoHwE3xTDV#Q>*dVW4W+pqR31=aS=J0>FC-$iWG^T)(GA9j5X$is}x{`
z(iIUO0)vlX6<rx>t)ibp1-*^Oh4QpL37}kh4RG;LKCx{Rew$UYtai~8&2nzBFLfea
z?3e6afG@ukyHn;AvRLXeX<4p(a`A7E$E$*L>X9>rBnf(c6PffP32V7xZqY>SV)~{=
zed=C@HNFwV#9((!>=MFMN?A>^mWGv+M23_&qG&<BUyI~yhAs1IKfmEso4r_(97Ve>
zpc9t{YYDE;8DHkZ_bb@U_2QRmUCo3??dTFIC4{OM;N4nF39VVLnsOda%Zuk$<!lGT
zjC;x*<KLD@%|y2h>NuCS2L32A=FetPGDeP=Qz5V|s4uql;=3?(QbW^^sk)g17H#*n
zR=k6*a&WhHEpAd*nwZEZg@^*nGDpDU$Z4&Nu8DA+eAgt+=5odIL(cS>=)gTtz*NPv
zYONZlk=evhf>l{RsaJ=0eWQ>btScr!__MwTmxjCbJF|m4?lYIEQ*}SW@hAKTMW7%D
zDMftlRO)sOGx314G0D<eDak?ouQ?CLCH)iARhI9h;daj4n^+Sy50q?{SoH>!@5Y}N
zESx6Id?o?D8jxP`^rC~5GB!)-n*Vj|V=^iv=Y2o9nOGcf-XmFOvWsY!2y<n;)~j)m
z8d{BBDA+|(j||q6d4G)bi)lflzi+iPlClBX3Kf?pzj+^8v95!<Ei0i8{m?w~$Pw~N
z;NBk<F}8U2r)Joa^6*i9Hz_r_H<4C#R*_QPwrC)Hqa_ft`+Ureo#K@L0GF4=H*}!p
zH{sLK;F|&juy4Tg9LP@jdHm1~-<!FE%PkTIy!4}+D~=e<-A=uk_w|ADluP@r`+->v
zEL;=Whu~D&(A}VvL|(yqHgfslZs$Hq5S9+*jT5+6rZ5L8QRPIIB(o!pXIKvhbjXHR
zxE%*OASVG)uy+Y`KN<b-G<&G{5-<<jjTr-**lZ;A&nhK_7)CYx9MQHIKL?O1u+?XB
zeVwWBt&j4Y5AE@{{+@1h)F<uwyflnY6|Xz2!l|;wZ1Rh!j|dNB-<%yF0WMoY9j)#`
zrxmLdzK9c(1EP!WUUt6zMz9@PtP!4Sro4%OYr<MC(90E{4+>*{{%?;SreZ>mdk=Y$
zVOp#c{yn4LIUDm9BCV&js}xiU>hD#fry)DN210qpgUM8KYHHwW)FA4S{r8lwH)9y=
zMcZKYnbG;OKgeF-ue9Mh_8z78EFI>m=U?@L;w=Kc+Yxv+_V)>kEveQV&sQIR@Sr^o
zW`he-K$25h!#+%>DIs?I)-fO_fPq|JRI~|cJ%)N)DPQ!gaLJ}l#o^fY8e@LKwIhb{
zls=Lbn*i7aZ<C&DPrMf9G}6aIf8l&CeP;FRul8I`R`1}(y1&<L#R!5|ToT@p%xq_r
zws||W&o9rP)|z?YGRGk`)h>^tcya49o?HSsg~dZF?#a(w&k52BwTa<;3UcY}a%sTP
zU>5n{&P~m~V`TWqLtdYDx3>GKqth$GpXi)C=jqKF+*YvyBT#bN5h+EKFmgU!j7Iqu
zbEIjHqs1+fcJt4Ei~G_f9{<TUnDphop|c3@_FN&WGvH*;tCD}BUV9lYw_%P6z42~q
zhxdLQD&4lMw;rH#N69*`e3>#d!FHgf<G~1gvnUBZm;oRk0UgS$!?f&signIeFOD3i
ziYBS})tfFm+PC-!`qT`)oJ>mi1N50q0`;kZ%pElkEMvc<d+9IYL@tjMe7K=G7sv8-
z??b3&BO887PPx+SB50qmqGmqrrM(J81<~l)ynNUTh~Vr;8pox*@jc12{kkPRR{qoq
z=Jo7s?*oof)!po3npdU!CS6!pIF`ul|JrBVTpKJ@Q~Q;bQA>+QEJV@#b(JbV{`bEG
z{;tHMUR2}C6Itav4v|=~#1e$ov-$q?KkJQLu=LX{-medmE>j9_Q!^cSGPG9wtp>0$
z0S)d!4L@%ed|PodE3CS1=j@%!bSyhm`Y{7_%mMbGsY%PT4kB^!{VYZL(~Otr*zKGH
zRq)-yJ4vt$=#n=}-oV=7A}K~P_3=1N?!yb8>UKWiG4*yug*kRgR>1^5LpIYK8H8Uf
zslXLOeJ-KkJ19rmMzYxZJ}8E5aH5#DNz9_J8!)*G%h!;z!GE-4Y2v-B1Iq*Ov`B&}
z)pkltgc=h@OIuw-4>_~%pmxaw`@si~@*pW+{`k<oOHvEKo|$mOZ{UiJX|H#_3g@bK
zAk{kgmmt^S34VVLTP4s@1Ao$4Va&VAdS0Y3JW=I09VSl21~4>EpJ^=90h<rOxQO(V
zatSnqQM_4zBd|iUqaVVu@Lj?XI}?M}59_8}ZMW6gGXA}|<JRoy%-ghiz=2#faZ`^b
zHpNFe%^<7xsCw!chlakc!S^YFVT?lQg5hLCh-D0So+lGnH;`^&>+UT>nO>S=jewOy
zv4Te$_m&d1YeCvp^FH0x^ERcIK^9FySB?>JasPUe3?A6LV_GLdF@r3Qn7mLbH&M>8
z46N@aubw-0Dul#1=mXVhK|aEk5}4&*?u5tE6VImiR+Y%4XIn%w8tPT<JD$0zRJWMF
zbl=PK@NHBmZ$n(CtlD@Z3Y4hFvwQ&2$N2t~PYRV82ngk3JlJwupWI{*Z#IJaD>Xx*
zF~4u6Q!HUsqduXJ$AUuHYzJO1kYb42-CAV7JMd>SMYA8xmkNBch0OCdZs2->okAH`
zx#t4$$=y>4Jw~YciM_e;C#`@RjTECg8`~+hmaI|Mb#2(U$Dta_4TvRdbEMK?wqWW(
zQ$VL4{$x<5=fjBW5xDSY^22hf*G`dNTEllKkj+@SI+TC?cACHHuK|kQZ}?@;Q1P)5
zMjYCe;au1|<8g=hU(pVg9n!35_rF?u(h{GVQwkp+!m+ykB{O(Ri4*RIcA<6X7>%BI
z2{8rO%(>vH6bJVdih0q|7%vc%>vTI+&e1UKDgfudF~!isQL%vfc$Ji{u!jTzU?kYr
zR#C^n;IS|;9s-ac(ERNmm}-X4P+fE&Q(G}(p8yp4)W+X`<!U<Jp~}D#T6G3gaA$Wy
zQSPG!oE3=E>79D5-A0uLTdNhbARE?zmA`^t+ExuVdXL=>V<#?S2zR42i~Q?PRgTQ)
z=y))DdblSN%$XByQ&tzc6VmTWB`F+HLE0*9bBo)+Z+kI2FQk>?`-~W3!TI;{W{x3;
zZ`0H*u;u6!iJs_u8$^KJx$pb}PRjQ8#;1HIn~jZTYVY5yKp@!hXjE{Kd?LX3%RTmC
zWxlyTz~h)1K*McAg9aMOF@hZQvYF%jzQOmCPIG;fzl><19zuM;N?X(KW1|)uXXl|j
zWu$8fRa|AcFt`S+A03r7GaUYk;H&Fhj&Cv$uL{eFx38<-kR;D3Xv=8`rd`{|84}FI
zL2FRog1J;Pse&QPJy~VZK*X>I7j3rs*4N5r7o%<l`)9L-Z*EA8ZFQo{QpT$p%S4bI
zI;$Zja)Ep>tA%YN8qtC%Ajf{peX;)`vEkzSyq#+i0{GV^J1+hzd))g6kHq*#)xH~w
zK>^qLf)4{`{0=Uu93QwZhn|*~ANax$LopSa@ph5jls=rI?Ij@Qmgi8bAgLj01@Tx7
zy54;M4^wgW;vdLD(z|r)XPOteNU9ZR$Ks|1K;%eGqfrg&3J}fVM~xdzro4F~%lq+%
zFyBet?cQ+?T9mCmhGnz>I07@TLD?}D%+lo9eBJ^FzHFvgoYLfq<~$$mBLfwZBCN4r
ztw(tV4NpGslLE+CL%=I_muMFdDaSNb=D%u(>E!OVli1c_xp}n+jsQI-?Gt<C<K5hZ
zCpUn!OgURag@Bi1)$hjvj{pCsI@n~HrXh3Ua$;;JsD&b5m37U7f_L*gL3_ole(O5`
z|DRT^Zm(A0J;+`ykpEQ&TlG^q@M_a7vxo?|Wy&9;`JX-rFx}{rXI0~y(~~#OL8ceC
zEgZ54J1=Tbhe0XMrR_r^omZeW>&of{hk$Q=eF9V47~P#d$INS1EI5|*tXvl9j9TR0
zIiXA+`#*ax-pb5K25$Qm(QW8hCiIy9Iea>hLOw&y0vf%-*8YI=skr8)Mc>W-J^^b<
zIPxO)*PGqPmBWU+Yn%x|_HLz*WYO_&dXw93gUSs893m!sPndXx4R#*`o_O|*_=o;P
z)U4vpZPARXWts%cliP<$Fuu(0<eiPrA)ne;VVf%}fm{A7e&VPLVc4=afd${tX5{(a
za)^p-ZbM{+J#Bt8`FqC5wSOV`^mO!k=;Qm$YqXp30mI%&K|_ug?fzv~nm}yrV`w((
z*hL*q9>nr9T(Uu!f;E%6bFFIOp-=t$Zu=~kMK^cG7s2H|c14B``6(y9#b2gb?^S_~
zP{*7`RTtAkgcJ^779SSt;(hC}u`#<uuC2|hc1oXt5XyH(t)A%M3pvRFF1Dg=iS|HT
z?2-7VI77c5T<QzO36IimG$+Ih@0a>rnu{aoKM^UmuV418;NGb4h4?DuH|!pL7&pnf
z*RgHWDcbc>(3JDqDVXCz77mSnn!B9%52ACR=XJff2<+f+Ycp}WeKrg>TXUGKK2_9R
z%QxoNsCbiPpQ40aopWV902f<-W9Ng9xcl_J4$#5YpKjrMvN4KAmA7-N<*3%70K9_0
z<SCBxh6}XZsgkdsc$s%0_R-+9LbcJ?qK)B=C@+!@p{>g_`A3<Ll{a(MMMDu{K}jJ_
zJcTTJjB`CajNLpX$T+Tv-&2gU*h~6?)ggONKql~QbV{{p=LUlAb^BRlJL8aPLSxqx
z>>nDrbByE!A(ykMyynp%;DSrPD9dJ6Jb8%!M?C^fOC7RphES$zoYo2eMzS4fVq7(o
zuy0o3d`z+E!wDhFR6iBw{RS))Q)PjP9DDZJC96Gp_X;u*?b86ge%i<}n*Ft&nTOzl
zJbb0KS}n<NYLp#8@3-u>6gnB4Kqhm>L!9D+d`Wgi!~7<ESIE@rCK$>DP;PO0M_0F{
zv0R~ciJHq`<0Zb(j3z-;hZ~brOtkjW9+Ph{liQELSbPB-V-O3DAy(D^E!_!x^~%2e
zr7ENHdn1$<pFpSBNM<y_nI2wX?a}sIcN1f|AGp{*zPyRdY2=qI#)}wEy4++cOoR4G
z->u#F(ingI3z824DyTmsd4cBYHSJ*>C$MuH4zqU^;;yMCgUG4u5yr380LO^Sl$E(f
zDo@o+<S+6_8g<)?i4Cj2@!Nmm!~C-7e1;Z9+Y+g6!xKnGj@UhR!b2?jsuCr8G5I5L
z=Y;IGaWqNQqY|NsT)`vOEk-SqLOxtmDxL;)I-PEWtOc2WCQ`Jld3vpnTfyICm)>AT
zFgd0_Tsb!<d2d`R?>Gj1e(h@!WKN1G5$YOqzQ`ZOG4F$@2HuCI@WCR)0etkfX})>M
znnMO7KqOww7@a)QE(1j{l`S;I@UJ23?Acn<a+Vn+z$o=ZPiy5>0h5a)FZ76X;oBYc
z%xUOV3#E19lr`Fdjvc4Rx9ILKwe5?aVozTEEcLJ~kwl4(A0LwS1&oK<rpLLqD+lsV
zb!@K@isZ1sUjNBr(%N3XWt!=#yLb$n%QPfVzaYVUGcZbi;B7+YnP?pY7!5@}wW}(K
zc(>(z5)1c9O!^_Txhiq6&XV1l<`zm8?okjLxS<55`ff+0qj#cZyGCynhj)8q|8UnQ
zF*s2Zc(5{~)cV+hNdU;0*NM?rsVOuG6XcwYy8Y&nBu9Wa!&vnuE@EG${$f)NmhHd5
zxC&X-?X+BIP4TUfJD`T!Qp!k7iQ6j>c%y}#Q-gQS7E)ve(Kvq7vGHG^J@$0OTe@w#
z=^V2!iwu7&AIB%uxxOmlLet3`$ywj&FN8)+6Uh_(Ii}jO&#2wmAmqt4f!#jt7sEYo
zK$eunf#^H6g)O0NL$Wl?QENRtNk@<K#8S3bCGsleR{@uTkOV-79YH0_v2^@Bj-`S_
zKpm{&==s|FX_{&4NnJhf>co#hW;2>j#$(wcE@;O;>t6%C$EbbkRqcVAGy{I0N1C@6
zrCySLGos-2sgLdJnX^yO$g!gT>#h%Q=%=D%=L*~)?Xm?Nxm6Qqsy@Iu9(nAjGF}?R
zXYh5~C7GBl$pG|WSCKN5CUld>^^vRl_H}<8$gM?yw%)(mKj|{1W&o4LnHY^)7uwkj
z<eg>1t-?9z#|mXC0v8lPO~S3k2izpX2$vo9vRG*^x(>bRuEa#@k<iixIDmU*Byt4L
zm@)5PKzFgDo^L*WqGm<of2xb~mq<3hnhwv)5{?21KG_X684<oL2kB?arvfxW&OCIF
z{4<`QaziXo?*W>&&(pP%BfAHO)aJ|me!&wjbby*|Q=;af`6^x-aGw2%4RrE3KnvkL
zDRd<f49dh+44Y8QHHNaf<a3M{X%}pIDm1^d?d@ZC7Fkwc<d>C*rva)+;1Ze(WC2nv
zpk|HP@eflG%Dj7OZ^#0Kp-&GHK$Dqf)r^6@M07r+o<(<=^19Bwb~lG$;P3O}^-$zl
zJom9j{VD8qKkb)tYR&2Zt&9YNIU`a0iqmLkYeSERR@G(Btc@+{`NIw&KHl<<M(KF7
z{!i1^Xow_9??R5}3{fBxkT!dmOxz|5@ely!08l@)IJv@HRFJzl8)U~*Zf}u&r`Z7+
zO8iwTWsso+E{)*plC^iv_gllx2(A+&r;K0GqWEafUr$MW&}yGUppWd~*s1!Yl@$&(
zi^n+BND~vv8%p{`a==%Yd*p^&b(Xv7rKz7qxW}cMCOZ8t-|7Wn&U2(!?t<8Zf6iji
zL-H!MuAUca5SB2GkSe0_#MX(&J7h;ZOc8?;k8AL5FXoP^sq1luA7vxo06o{Vuw6^o
zr$H)y*?1oexunQrlgP(_uv}~PMnQN?bEIXbJQuJm#fR!g>%ni;iUpj3T)W;5IWFMR
zw#?~r)uv12-58VQ^SXw6lMvG=&i+zCs~r|-HZ}m8$$)+T=<arQUcVLo%XB_>gZ47E
z8RydaV+pB)%l`+;j`cV`?WJR;-{cosBmm9-PsG-6=U+o!eguP@?sZ(Y#cE1<2Fn7Q
zr~Q}yDa>*S>O)^Bq-@4k3}V!2p>+79scHHPsgPx{^Ix1WIh(mT0o$er1EU4%F<iN0
z(*IsYEhpI5_?o#l9G6uAC0a?^F2?T<3^)p_SceHE#SJ<b-oBQ{L?)^6bp4BJL4bm1
zLOFYlyS^ifN&U))GODRjM{lL4QIP>J4j^-CU2US=eYzGe)iufnF3-FhW{R>T06_e_
zx@Cl0fgyDSFs6u20uxz|paGRqh{>lF^b&cuZ?OaE+UvyfX<i;SDdjn1LYlF+AkM?2
z!)TGVYq<H=F&{%#Js!>FEr(q1RGfaIy<s#W`yT~6>sfP^g=@goHhT^zM*(<i`|+r$
zdCr=wWwR1c{7kR;{<X81Z&d^&DQ9apL{ZYXLX_mT#A43HD?q?pUMw)7HFW_obMkO!
z@#1(OgR{)W2L3^!WrrkgESID0xrpvIZ@I$AA%kN`mSz5NzmDw6)6XSg_UA~0(&gZ_
zKJwl9E>#8Jx@&1SaNZ9|#+ZcFg*X~Qy1pP1i^nFIjZiNlSGr+EAPfr4N49KT8h}C%
z#C8%GaT`Lft49E7o-{tLP2<3XLXJg;4%oeK!q4CjX<p)vU`;-^N$SP!E{AF=hfI=C
z&#-?ob6DBd`Qe=)z+2RXZ~)kR!GTJ{SHT%5JE~x>7;*$<KO2^s8eU*QhLL!r)|$n$
zfnVmVXj)A5KpYP~Fs9P{fH}awof`>^Z|O5?-~a84NcedNf7z{Ec{z2&d-GHQSt@8)
z{Df?ZU-|oduk-e!0jz-EaCh%zx10cao+s{<Iu$FfmV#wTFaON*Pb7A8==L!5%s8q*
zd9Ij+GV4^_h7G)`MX{6ubM?lrg1vpIG`ZHhdx4m}vQ2HsmL;Z5c~CENZ|o^~Q-Gxv
z>+A;v1<d<3lgq`#(pRB)OKRJ<4-m2Ih0eIRx62LTa{^B<0ndQ5bZ=CiK+xW@E3iJ6
zuiY}*led_QE}eySZXAeMp@^0lLqFI~5pJ9Bw@~UawxXiHpZSVq7v278OKa}#OD3?X
zkv`4ms{-n<B-R`OAUPP!6ltBY6|G<C#0)wAPzPxyGW8}WmdZucsQrNGg-nbpJh>u9
zB7_hLmvWj(@8s5;cMq&7{WtF9bal!W&?#Xmo5bD<kJz{=9K=<eCuKX}=R0FDTwyHx
z7UoLeG3+`M-%t&R#t6*VBZhwoNPfF%#{-LPYc}r5C2{?wa%&w_tM0!r&Kg<8D`46w
zyy3|4?260MzRx(10(v%pE3Z2>Jgx74tI%u?bYAAPZjYFw_io6$Ndlon?3-H_|BuW<
zh35jqQZaAd!SYqAYmR;2Kl4FR^lavM_?ar|J&%GU6RAJ87fR|-cy44sK$y6MnZ>uj
zq|%nXleWs}%mEkhCXzSK-#_c0PAQ9RGHs>Qc;z~bo{53b=h+e-M{DW92W}tn9k>BA
zeMw}=w1@}}(AFpX51I8%2!glMvVy0cWpr9WEajpe6EL~d-g=|mBbN{9^vM}#Hx8hT
zD|rP^$#G4nl_Z==rgM3dqPvW032_*_^(e-i!?fbf_yx*OQ=e?QIe^uEr-WOc%xno0
z{Q*h`DlwdXhX3id<fUa4PWmXLo_QjM-4Un;K7U`8J!_k_IR|hv`|C#Q{*8n=N-P~U
zwR)1=vgmVHw?vrWH6cTz{5dAgy};&m4q1W+jeb+%_X@hav5r4$#zOm87WAdVvDA$K
zJXni&1DRchCMQPvIYf>4|MfkU!w9c4r=}6}lu@M^(h5(Ea~xHtILWDDT}1!1yy0s7
ziqKm4vwm00A?uE^Zzpi)Ou;TOY8I*ZNxBvKRF7RAeY9GE(BV*$;<Ccbq5b=8_P`~(
zD%PoZ#nTZb{lB+2^%OAro9o1I_iXJzNNB<`I!Sl!hEgEcM$9huWj}-5(WBNv^xd{j
zJ7h>7cJDX=E25l|13~bE?7P6c4ixYTqqFxH4sECyzYKf`)N-bjsno!Tb;(Do%)&%k
zV`P2f5S99D!T-vI$3hO__ZUIh<<T2NbK>M45yQa407WQp2S8R9;f+7;=LfB^fwk8>
zNY0A3K9Hb_UyLi;pACPQIRC?0x1dDkY?6u5Si%+z1h6Ht`k%j>LSIp1S31i@k-OEC
zZnfOzqME8CS+mnS_O2~0XjSx*N(Cu(<%Z0_%?<*Nne=KYKKTCFJj5TJFOZuMVv?^;
zF5y;;*j8%Fypnw)nzw{YP3C7VI(&XDUUTA8eZcVuG%9n4ql7>9{1V>}udBd{c8;1A
zs@{Y9KG#IuBeItwl?<>d8Fh{dE88L0aiR}4UMgol(E9u}bN!nK^9LNw9=!#N8km`o
zEl3t;zFNf!NSN%wZF>SOIpXL*xcxS=Tyyvv`Xm@G+Z1TIq->iu5ROI8`%fE+6NJeo
zpl<F`HxNUd#l&KlMBl%n5CcpS+P>dsn0Z=k5&>YR&X<M{)pl=ZRv4EQl{Lux1oY0I
zuZe%ZC$;U}cEO?bFpAQUV~w~=)AsLcU1m)00kVN;@3~hyWKe3M@Y|!W(<ZLvtu>`w
zQgp*C4~{xs@!q%5(YgKlHyy95jJCfUJS=C(=f%t6{g19(e9a$7K9p^R$+4v%`dgp8
znV2iNt8RemO$sEx8jztDhT@4eh4F`CYS_iW`0h~y_O4JA@Z@ea-jURk=jHvQt#SZZ
z#oo0EUDK_Z^j#|+am{e7Py_d{8UQulN9_Q@<$2iWL}~o(%|nI!(V1CU|GlU3Q9On}
zBp4I*amSPeX23K7Ku(;y*h;<?UNGDWXg+6g;7S9;_+j{X>J<yIZ(oL5VY^3ld-n*+
z0c84Qb4&c6WYhLT0wUDl#J*D=S&=3Pe7E+DCQJL6OQM8t)5gy;0VMrYAnD^R_Y-NY
z2s3n8ZxP|Yo~u^@sLo{+@Jy_%&*9}cG#glq29Lc(H$Yf*VCIlCro`k*<Z>B4A95Oa
z9{kDeJbse1F1rZZ%l~er`#$vEvywAH&5Ykd0KIwI`a*f_`Npq;2L2v$HoQR6>AXor
z8_7)++i7ENLiVuKB2pZWtB{ojweYGG9%DUR(XUC9XlrdB2Dr6;!>GMOPK5wDTG@^V
z#)(T#qeoQP>`gxWSQ`_)_nfpuPvasFL=DjAkZFo2Ybnx~<7o`G;I@INW5^-BzxBfo
zXw?$#HW>DomWWu*IJ!+=L^XNNb>{4c;X;H~eIhVxRZ}E8<m`lT_Eiu)GF5(zg#t^0
z!G!Tpt--f>f(JoYLI7#<`$y(OB{+Ekv*~R!ljw%(92DOmnj;hc)l5gmY=&6S;EMdY
zty5suvm#*cPGUQwC>D%4ddFS7a_D!f`(I@}pHc3vf>U5#mS?Ct$GWp+h={IN)~z1O
z)4?z>L-C!kb2y`CJNL>0F4@lE*1^R;=z|UIeMspZx?ML&-o^7P>FR)V^!I-q8WL3=
z63>}mR_PG(v#3NWJq_(}^2kX|1c)d`4S9e)gMiTlquu4C4^TOsfqzt3eG!QvbV2c9
zFllk>yEaU^u9hyqHA?3nOExOD_puEY;&KF(RCNu{ejmY<bSXk#J_37<MmzIL4;W+<
zu|p1W2@kjWI2C|uuq2WjNCgX_=Uuw(InQ)@=s5NXoICG{&^1HqdskCLD^1RA{UYnY
z@00wo^fNJV$K7uVjTaSE%%H4*>M8XR<L2FHsMPf;bwM6<;pV)){BR@MQ6%PmXcwEe
zRln8FEUcefAu@Grk4EXj)h%#lhaYdbmp9IXBC~0oIQdv`n@Teh=*FBBqfRRgCYHC+
zb<Z;x#^gHd^!;3lSAM#NGst1e==SmKs&M=VU#u!_6Z7TgpZ`Ab%Q#hGOoZp5qf&m>
zxBr(GCX_~9YIQ&>%zyPG&Z_?|C??yc(dQs&wsG-9fzsP*Ag)D`28xE@X2KiY{ibup
zNA<M8$9cG_ebdijtro&3a;#u(fKhI?cBtdnpIk1P^`f=f$ylP^V*s`NN#C)B0M%w6
z_b5o<!v#ZW+c1nhG-WeYe8^cwLkbvyIv;5bd?`Vrgg5N&ZZDj5-D|D0O?uElT86xC
zC4NE`oXNM?0bxC|h!)$DcFuPDcb=NO-cVrA(rUuRs!B!<-2O^0i&v0NpB`gYU~B%`
zf9naY&VwgX6d+^cqo|j*Q7qsnFp<prvMz@*UyY86{24v6SiYBqDwtvv8^8cu{I|ON
zM#YK58@I^f<9cn}Uwo7Hqcgvn{ZGjN%v?S*^<lq%H<QnG_0<(EDpY;b*&{^;T)!!t
zAQz7~oT|J5mmA+IDoEAjaHdFGCG#h<#QO-)5EJY3TG7H0n}mHnU7Jv^L(vG`GfUs0
zw0$?T$gAiB7=~i}D~;}S_!Pbj#!5?-ZeLu;)1G=gH!mr?3sjo|8#reW`1sZx5D9T<
zP4H=xmDoaB^Gvw+&(avR7m*Qw8})U2^MiHsJHcMlcp8HP+cRL&!QcMyZ^u!iU6Q&b
z^q?N$ss&CA`P=myqle*lYyQ3Fp!OhNRG>E09N3FWDrr{9F)nuGnu7A6$~E?;6)S<{
zwqyb~SCj41I=v2cfiV*@FU)lU$laZ-9TE6CA6}B+!Qs6S(8(;ZBSqeO<NebBo;(0O
zc?*W&I?FeuwVUT#7Js1OVaPQRy7|%UummJ^_FeqD#cpe0utoQzX;IK@e|-G@{GR|<
z?=BuD{75Bv`7-2tZ$s0_9=D<S1C@<!XW{H2fjt~1c0g8nJ?i8;ilt0ZX>w6co4X6H
z(e<}DyaK@t$IgE(vAlL4?0q)U-8kMIPSDTeuKwe23EicljnZrb;Xg_X@)w&MqtoJC
z3vW)N$Ms&Aiu{A`WhkvfAC1&WXUtZZFK+W*NG#>h##3)Uyot?Pt=FE}6mttinT?1u
zZ;i`(_E)BVm;1VY9^$~Sz=vmOWAM}T-V?fJe)95~2agcj8zu|$=pZY~a!vX~)Ak{Z
z3U*d;`+4^i@N7+g@$V}WkLNxglU3L-MaGDE!}W$Uk8Z_!Xw~v-9)36bOeBEy9ybT9
zUxV0CWfmiS09AVJjw%<qL&#>c{;q@*iMULQY*)h?|A!GypN?ArRlOQ4x8_*~s_%(A
z?0dY9MUn*^fP{7a@yNE{55SOvxO)C4GF=@n_w}1GpDV|)K+2&uV;+RjhM4{R52OD%
zwnE@sF{}<O+j5`|Kxn58_y?aTQJ!fglJ{=fw2`~BVG9+x1{ljL`wrVk;|RVdy?=Yd
zu>x}bHR;0mna6M@$!tPeQiTyo(HK=#SpD>tyF|Et2op8B`VL88<lcA<2I16CUboMm
z7|i36Xo&_vWru?t{hQ8FuZOq(GT`k^e*DeY)Wftq0nv8vQ^n(761s`BHNZ;o(RP|!
z>Zi2_G(aA983IUNP4=Cr0o2S^%8#e;#ZUjJ2p3nLrP3yWn$RhkIBa5cHY2libq4yc
z`;5!W6S|$OP)z0WG`Ee7`FT6}sNy2Hi;QPTm?hx+a{&EK_o5tVp7xl{iVGOUbm#gn
z_H^SIm<C#d8G=e-pVi9iDB-yWwisvj?jBaWik~^gLD^$#ae?NXUw@rp<h{Is>9=-w
zcATF~V(d9`8;m@o2Q+#{OvFy86Fme7S^cC54xt?Wn|6|2N~7n?VL}V|3IXa@&oT}u
z>$vcB&0|9j%Pd>S_MXMKGq`<dZ0#l?)d<78t*ISaHEQIm;KR4syl;OCxfp*#%c?Mw
zUUu^G)n*K+pcA2l%AM{H3sCCEsmLI|st|~F!B|y}Zz!OL_w3;Dql;U?k}g?BZ@!sA
zrX5#MAs6u+P5KoLXgqf3G!?uY=AjvzxOsNj0V}OO6nZvlLSGJoH6*{-%bgIS!N1qD
z3AB9+R=3qPi?5uCaZsr*t}#cVL}l6lg$KpeNnFclU{Io>nt(=-OVL&MyHh{m5@tlQ
z1&3f_S6t4$DD)5JTV?zb9^3Z|bWLh;fgAX>nQ^ZppMYI-Bx7QNh#-%D8=j-gA;$<v
zIsn!6-Ou*Ep-lonO8?0a;LE?hhBxUqspz?sv5ntfjDo7}gubSCVbi=WJz(iO<vCOZ
zbaAG9Hs~$pxe{N=C%nEppX07{n-8xI{$NwWr=8hH2)I>F8$+wq*+@2-cDx-(#btI;
zK)9pJ1Bz3w>8xA;mYm$*tCA87RL~%uM|Z*N>3Bd!R-`}lPOH81=X|s`6I!E+9-uF)
z-7#4Kp-}Lt5)|UyX5113<<Duu2T#8ve%dGyK-I(Q*4hHOKB>{KashI<v#}{|kG^oy
zf5XRdAzGGS%8A()>97Xq^>g4DiS2sm`dyfc2Zn)>?m4YIIyrV=%QevekFKG8e)4YL
z6FU+gRn^(im6$yXPpLKv?vnsRA$;F?A-L<L`lCm>7zZl8c{~j;NRE%d44hs|e;rke
ze{;*o#X%nx1G#7fej?K-x4xg@0v3!z);=k6*1v}}IicK~{5^9TFCY|CsV5mvMqkct
zf$>w%_-BObcVQ=Llz%KK(Xx$0su~Q|Uc#Yp#tr`N)FktaSX!>PXM!eu%`52X=Y;~C
zOJD>)>nd@7QjBDK^Y3q?4O6%54+9qTdN=us;5Za{B3$NfU^J|L^E&`r8GB8BcHLKc
z@q;p<@sHvH)%fd=N-i-11VI_AWaNv%DJ&7qZGV&ZwDR1!Rmv`98m~I#Pr;ZPws8yU
z06bho8U_GK0<wK_o#F+52DEl~Ha7r+YLql>!mP>@EL^y`4^82L!BJI!sagm*&f}sq
z;>B<m#585^Xr_%vcp_c<ZlUTi&%J)mEW_Ja3i^}0#uJnTmALN+EMQhdE*39RqjEdF
zqZo~~069Nd75tVgdxK57{e!HhFHu-beiGC2D+g)5t3t9JPAN~#;r3de9_1)fQDbu}
zo|iO1v}PLJGBlngmCkqsIpQ#(3@(+az*XTl|3YmriLk!~1C3_)<SU=i1jSb{F{?^-
zF&kI_^>@^ut4wkOCV`9zNJoIaRoUOBo<>;}2GD?qmFoofngZRJiMIQ)52}_K`p=3A
zlo_s!*(}i_H<vA@k7j!82bww<0)X;x<<LQei<Haz|8R88VRgQJd|}lx&a#)SwQP5C
z%gZ|1#<Fd@mTlW!wza&p^gh4$pRV&q*XeYw`+n~4{UL5kJkp_T0OO`L<4pK7uChZD
z$6$kYKVf)waP03tfHLtQDbgUMucm0VwP0*64*P3+D5acor3Q+YImhSmVbC)?JRn{^
z>vUF5Qeq*pf}GbnkA1w2Y|NeXSQbX~v(!@k1AX|TH(3OjV1`pw4vh^m0rvr*CrN3e
zr{TypFhcyI*Gx>DrZq1sy31e^E6z2C51a!M>%IS}Lu#*vLLzk9TBio*6LfwoZ=-d;
z3OFWwhxLEIkI_3S&+!gt?)FM{-O>Z9$$*Z+u1ozjD*H@jT&gP~cx6Og9~+>k2JI>k
z-7`EBcDpU+Etd{G(K<$>sNbSLQVj4Zw)Oy)`KE%OIA=iCCug@O%)&l<Qt6ab;;Ni7
zZzxOXi3{}GpO`HwL@bND4#Q!4IiH=g>7ACvjgLApSMK@%0;=+hMZJR0>B^6^nkDlp
z9B?Wzpz%neas$TP$%v>l$(veC1YmdvdM874C157aOGK_`XU&z19&ZomU(Ahmqzreb
zF0Z?NF2*yNmS}zbKht6M2CDBPVNu(o1iZhzUOJkj!u}(@G19$_8XT`c^T_nBs<o|q
z3hmx}ES~hL?E@a}`{nFMc4&}npLJEjly2`s_cr^HGXf;SqHFgre=tlx2`A^y3}X_r
z?_SSXqPe|?sB^zgFi=lj%B}q9s2j>9$h|8kdG=We?ww!w^mZK~I2~sAwfgvN`C)fH
zMmhaZ3%=;W7mk_P>UuK+DU<Kp=*x*GeTs`)tw;J1-GkQMA5uYsUiE^Og=Z?^Rj~rQ
zD8yt2%wjpVEMWN)7DUd`u3b|m%Fmd?jpC>2>hrcucwN)~&O}Oeb^cJuQ;6pylxU4%
zVjX@@n4Nc(R*2Un`Au`%>);Z-FrxzAR@s$l7vGt%032I6kG$2(e!47yN4Br{myndz
zl^Qi;r#*0G(N5VXie+tA=jq#ZBrEvoctb3P;6Il-uP`s(RgTXUJfC)!8DP7^^+2@|
z`yp`3P!PPki9<bg%f5$Gd$5<q;aDgQ2mv3ay_33ETP7|UUt)bd4l)wKF~Bi!B}br*
z4~!~+i?4O@huJ!#V;<k+mcTVP{?s`Wlq~)P4!&v#<2Ya%0&bl?K7ffAI2|HwS10hl
zhMO{B`!4Gqf+7C5MPV@XY+I0xUBTz8m{^frd~CCDEMOM%Kgi|yJ0Dxriw$TD&nfih
zD($*B`j7CBP#Xxil+3SUm|ig7Pye|-_8ywNJuTQOH6j71XYuQ56|)iZr;{Qm^)^co
zIOM3D`thz+-JC0D>O&b&9tr;+iUR`}8b6~c^7wvOE%k4k-5Bd<?7+N%Vh_}^Oq>(5
zA0q`H!?VuseYP6k?kuPO3AlTy6*$a)BZ(==)E?`vJ%N|@-JTwiheC+MWgwhDzD?2P
z^^jD2|3}$%UtX5I6iuZ6w0__f2f%Xs9~FZ1YCW_LT_1#~;^VHMtic?HP!F1}xu9L>
z&fu5~%?~u3oh;``BA2@@)b`$Q>xTEuw{I5ezb1L~+;U|U4RGCRNc}4V2%f$mg#%<F
zUUy#sA*MecMX^4Q6d5ti=ArpN$W2dSSN~kt7d3yT41*kbLSo1YkU|0Qj`AQ&RqIQv
zth}u!Im_tb!BYxgJm;|=@o;-=y4UWs_L|Sf3IQ=5%|JZAym<fwK^KR6IH0EqBPQTI
zxdHHbfIX27;2eb!3nOAH3ag8hC!AB*4XL^zzJ8pQIpQQ=*}V2!j2)o0PrT^?8uui~
z-MR$&0q3A8k_lq*>vF$=j~0-caQQwMV$Kn?+e?N%d51dL$f@M^?%73#66sxbsFGC6
zvJ5EG!F;5h_x4|6M-19)jeggdq=Bg^$`lH<68~@`8?Z|)g{ekp+}TaS$(a3}|JtBd
zXz>%$vd*o-$a*~iSBjszOb%{#p-2CWSj5iJ`m1!A+ZH$w-Jk26MkEh0RoqhN`aw)p
zO8xlZL2(us#*;r-=h5ZgbnFXhvlLKe@jDi|Bn45@9LmKs`y`eP7|pSaS%tCLFOnh4
z;(!}&-^l=a%Zd2e*bldfZu$vD_tzluTqy8(htr&>d^@z^(u^HMfW@J&*QuDWD`Syg
zxUapeS&jo(_uVv3@o|$_30x7Do#cl{Aw<~VSXG9Yx`SH0yI^5P@kkh|gz@Cz);Z9b
zQixa)pz8$~C0b-;GDSdvXgXK!P{%Tb)Cfcbr1iJP<g`%A0h;0Is4M^|?AT}%&nyB|
zD>W&91deF3a9n@?AqNOT_Ce|J#St~LflyvN{@SP(W_Q_QQ^sS=a%5SlV)2hlEbeBW
zX^`%|RPFW8Ak@BCOi>viY7(7lKzgV&ji<=J|C^5;;73d??q$a@lVTT7rj-$Y(4hPH
zP_WJW7anNv6Oc}iH?f$OqZU8~%8mfY4$xtc*sP0KrryZDtjtj&)27j@aw+{{-BWi-
znKfUPmWrhUF%q0X)vrRzLh}=c+`@WE^OsOY6GbSXD<2$FJrk#4RCL4aAKXj>kcua*
zYU9=Gh?H_NuE!^E%GTe1d9qLfT7{KVk$7`w8jPl#A=u&HHyuRqzz{zsF~jRXa0gho
z%+3-faOm3^sdG5K4;L7=16SYK@cxZ~n|{0c=BPyfO7owrVCGH|__WTWrTkgZdj$d`
z8^7wwANo~_Ph#RAQ7M3yh}7FD9pfS}$Ppu|%3`gSngR%kEH2>WRbbHy7~{|^8&M8Q
zB+n^UN#__HnTydI0eB&#1nU2CZU*euzwYjY_66F$^=eDe0(~Gvk6k|Bj2$cGK!5m$
z(XcoWVgbJuZv@!AQ9(zMBPfIstI&=nb)HKi$p`S+!5A*|vJcrs(gipLaG;K;CithR
zAKfQ>M{ga@Gx~kMZcxNRn?5h5iIhd-Z)NliPwUScyKTl|`(A~P5JzAD?Q33C%s{+2
z_{3-wx=M2x)JiFr*!XFlDtcCk)ZUmF!R-a>XgGot4eA;k!mPk2SNs_%fa=}nz}n{S
zn<hS@QFMb_o=ZHyANzRUe-2M>m#k<v%Mw+RM|>Jtf&%9I7dVsgBUOV;K^+gH<GU7c
zg&}4Z+hJm=Q+bE7;3Up4vqLdQ82v-IGf-q`pv>{Z!X=JN)*dB-wmR5X(#~*G2HCk}
z1n_y&UjQnRp$)`CsA)bx7&0B5wO4sgP!aN<f{{E4Sf$e=^EH-gekC$0nRN13ccn+P
zS`P|Y&4t2)_fIzi^Bo$3;`XC^61G_}tK$_x)|g3#GGVqYz?lJjcHkD$p(rTrowJ?V
zju+Gt`FJ(}%uDuq9O)V+9gU3xrpwf0%5+T;U*wv0p+1iHqNCZYJ7m2K-M+tVT(Yq1
z9;S3V#d#D7B^HX=i=+b?Xd+}e&cE>^hZB`EX$MJs_J{!EabKEr)%vo2JOB1X7;8RP
z(E?s>ousb@U<OSwWoA?VRmWj|E9{x{Ej@xOcr@Y;&&T<Ved2SOXY#DpZSOrDy>Lj$
z7*^tWfY}t(m<ifa<FdwCtQg*!wl@%k2?ndOFz&_CJzhwVr!uOhdX2Cow_k&SZ_%mH
z;*0QG=M?H%70KP+r=DauV3}iupj9OP77`4LnH04*nb~1ZuC5^>62OJKfjUhonZ8+l
ze4*ZyX(Z80<Cg7byi#*~nt`<79}i({>9qBkQOjS&vp;W}05!o-rK>%$-;p)@T?Jy$
z3$)i1kf6C#Y_6QF<IOA*6u<|kg?hWK|3KBYOmhlomodeDjk&`u>c&lqK3=?ByKyuN
zUb-(gA9ddspS>Q?HubHFWk3T!Z_bdJ#Y9%div|fgaQGCe@6xj$as4RswOV_H4A#l%
zzU^{T71MWIt){_jHP^KaetX|$q`UL{7^pTU2@&65nw5iT8|{3!CXIOdRsU1sR{4DU
z+$)|-;^We<I=n8?vM+Ea_%dd|23pvbq{*6zvQ=t2x|(1e_%W0ho~YXfu4qFbmC@E9
zfA7*MkT<+<oqfduE+c}PMHV^2c%NRKlH|P-)SU1tRl*k;ur|wSl44I|4|*SHG;e?Z
zxm7)PT&@FCw>Hv?X-Qzn5^ushb7Ang)pc3mJnlYz%&wXM^j&}+G0JqV@=6sFu2D2V
zCyxBSmjURURBB&ghMfTb+Up#a8qw(GzLZ(1mY;9Wjj9+iIN*HgiI-YXA(0YbuQ0o%
zF}uTlk89LPkB0qft>?PgzFuLL=N}($R2iV_|61Wm2XcKpSJB)5cBo4^VF+NSvknh|
z&FiC?Te&<xw#}%S;(tYo717+74QA2Fh)VJG4*{zG<QQPqtv5>jZQ`ew;hpC8*t%zh
zRmqNQgiK2Thq=^HQzSmx(XHrCtz``jCqm2z`7i$jMqy~gYXB>T5rwc{2ogmG8;lOf
z3-S*L%d`r0uhX(B?2K58l>c(E{up)!Cn|$uzSBHC$r+b0wk_Zzo3Y;>Abkvxcy+_%
zZ(Ou$hLfVjwM=Yj%p^FA`5NB93zeZAQeD<Y0-bs#1BlMeEa!pYAIQo1R6Q`iKnqZ^
zm!Cc_ub7Uyj5rZ<DK}j()8H2m#9<dh^pVT?tk(uyCUzn(uLZ6EY&^fUn`BgJw4X2Y
zOPV}^$Zp!A-S(aNLOJi2oB%@YafE0nG|#sZ`3Kf<K}4;i&9HNteYIxi!em?E77dO7
zvbhrVJjgAtO<&l~xdzx7{W-WBe&Lo!0*sOwz0m_o<%|{-UYM3-DRJ5ba7!)zw|s~!
zLO9LJvzs6p>P2o;teB_2sxZOeI|~GUMWjl~KP@0f*N(Xl?DgIe9Zt)!9mD<Qg;GKX
zx|y{gL#7tsEOW08|NL|NHdV7eMghD0Yk45ls*bZ3F|1BNygZs7slRYzxcNOzepZXf
zomYnbA0$F7Xn-!)Fv>_8O*D0wfW=HoJ}bl6tE_J#ECA-ckc`XS#ozE`^U{m=G~Pmd
zl4&-wZT(O69{yrBt9>e^l^Bufe1RN3u^{wPg%J%rt(BGLKq7Hd1!*8*6Hj%%YB=M#
zlmY5|;;m<?<!@GTs4($F>&sGPRUXRktw(v5i?cL@UoJapqY$%E@hB{D`v%zwQs;(y
zMB)skNtVp@5z)eeNO8ElzjjHsI7RW0N;#1TXOmka92wndPhB9)$BPKmVD-hreQg&y
zud-+&n!Pd@q2K41iOD-yjBT~!JoxVVjvYdR9s(1HD~dn@QLRNj>cUz<DfuhpD@+DE
zzqupM>8cTgFnp;^6OxpTW#jH@l~%+!1Kpo4%r{Wjxri4VZ$gi-qyL|kNbumlpAUfF
zpl}qh)+Cfgs?yUnwOcxPF7Ip{<p>TQW%CB%7o%PV)~qIv`o5gy3_3d4|C;~Q(m1mp
z^Zwc{rc`%k@_0I4@>mHpDJ=^mT&}5x6EpL%5C1a_;h22vqc>~u^3EDxT0%Q1dC*5J
zo^))42&iO`E8)plT0ss^jGsHUV&l6V|A}+V*m;eG;BuH(+Ve-qENoe0Ts8%WHt!Q+
zlfmxE`=vYbvG+wA%-MNWeBq15VaTBEjx^I6Uc5J#5*~Fi9}Xe73egn#8|t4gQcv^|
z5V`{cjt2!)`^95sbtI70G{aTAwc7#=SJI7##<fFZxuUnRWSp-Qhs^5L_FX(aTQ1&}
zU)UCk2wu2LSNj^7VvWZOPw<Tn-eKptmic@KN{~bmy13lqk51>&d~S!OHtx8!iFs=n
z&q*7CT?pso@`oGDzC;H&boS8exd)f%@r#1Qtg0Gneq=aQ3e}z(X&zobg%SFjS*W}W
zjhfM{NtR0}8|$3D{A|49S^8If`!r;0U;M~sVrlj5YS$j!lppgmu%1h!pK@=B7W*t2
zkT;KxsC`55F8L@O|7bi+yMTS}&!z=xA_@d_4{>~6i-1Um=CyC1=0e#AX?;4J(|kMs
zdQV{&->VuG@$4PyXJG|}8Ew25kjGAZ?&>&V{$O(E5)0mFMM&p|4&S`yCF~OX?tY+O
zY^%^CW1z%BO{-P^cqrSduy^(P`HbW98E9-W*o7jVSAlRV)41x&(eoa%`VO6|#Iv!H
zlK)k5Hoa&^z;T%R5qD6m5|HDRs<me^Dugdg?1`C_8;?GNEZ@-z?F}E7sEw2_uhH{V
zQz-s%Y7M(Bif<dV{S-+&jTPGx8{-Lfe`|4d0s>LP|6@nH5Xc;Q$5?<3BS-GfL59}^
zyB1tKOt42<#mEVHfX?Rq7GNMFlwcYz&%Dj->yQ*tLfvX-5&uRig3vp7tJ1Iv;}3}Q
z<cfCl5_y`+ctvFj$uP(t$o`-iZn~NI6)j+|RRZpDcbW?uG{4wC$wwrA@nHR>tC7uh
z`aSeDy#cJ|PNXTry#;K&oSe|iOL8fv7wd`Y6aP6pnxmALc#-vS=nrYoK-^)TR>)T%
zX31j&Jvd+_@$kPSm+j+)8t37?)*%k@ad*SA#tUP!9KQa2K-8MH7=jIAuLK4O0Mj4K
z?GIERSS^7TPRMnFSK(wa#+&xQpP^aU@E%rp$bG1Whh_=t1*8V8A_sn#?_9L0oO?Dq
ze!ZH{tWsEgMu;x>*KSgKi9iV8L9<O=S4)tIHaLga>~tR&$U#$-alGl9s9g>J6C$>q
zfz2Mortp2Jw#dDZK0}P{Os^-Ali*qo{Nz^NoHQk+Iw0Ye;Io>q@zxhtHiB&6(D#mv
zDNV20kG^PRKRP}f|I}?+>Av@@4zY2PPH<9KlrQFx&b%4JnX=#gqpNhaGA6B@g;JhT
z#;46a3V;oOD{^p{Wt{$ROgut)BNZxETP0KmJusq>N89e<{7|#8uJfo5OY~P>IQl)$
z4&;hMHr{!sF2{jnBoHoX@LMqX1M&v@U1e`9C(6+YzX1(&*w?@O6N3Ytd-Y!HmdFo#
z7iR}=&rY6cYkLP?)Av48G2_gwDZxNOgE;-gmmvMVQbLQq_jw5$?gfc*PRI>0<c3qm
z8Z*Q<*kFPziWZ%dRB;7vE_Gs%jbEtLI{tAjb+I1z&`fcKF>#ebw)$KxgKj|_UnO->
zyf9M)D<RM~n(8Cy_yZY%#{Cg`9c-%ciClvg^*A=V6p;4ifqMu+zNOGAG2d|SalxEB
z<~28LkQXwOD)57JM#hTwh?P>&wTq{B$fkFo@O(jiL+MKu8nZ{f1!*-(=U?V4^}iC4
zM!AE}+yg82w<1=_WtkI-Qbyt*l=4H-DGOPnVx5t1k?FL*$O;OT6Q|=kg&Sn|vP_d2
zdmFE@@2U(RhZ5P-fFZGT;`yMkF?xEoN?Oe+!0vu<haGXoIF*Gvj6+&PfnWqsVYYf&
z`C9iaz((PcXO$a0ncuUrayoH>sRJu9w3$y{BX5ddoE$GVqrEez=(IHrxp)F2{jge|
z8@2Mtvjw5Q*NnQL$bu$_5^&F*FMb&3yozXTj%NkQ#t>}PJv2ZB5f5v;pJ<4GHW?^3
zc7&L-^Wlc|#1E0Zs&S+#huG}!hl1&`pBdAY-bcm(bpJN#Q-=|z3kgn>!Hud(=Ah5>
z%(yuzV6`atd6z4>asBXlp>ax)XCU@_AWLl|Uc6P57-)355D-+(3lUEl0hm$RRrK)9
zZp#%o0-yL0gSi1ev@Vgx^RIL{MobKs{ECjX{oRH*HdD27PK9#CBUjbnX(g3?qTTKb
zN6a(Nm!MoLUT}-}Vfcclg~?6fniZ}~p34KZ?I=gE;Sw!JdcNjh+c+vY+U9rwTf<`i
z!A+$(C{6yR$%G<J{^C<FOCUGM*#U}f;gj&92|HjMu5c`SB#%Xs#)JvJT-gxtI1V#I
zo!65q?x+telVts6xPGT!*+@meWQ!01rlz@BJk9zFEvnwuufXT?_k#ReRYe@7#a7PW
zKS2=r%+A;MAanrSu1Y6%9MfT#yta6y9a}tST_=rdnbXcQAQ4tnP4}TTb}Sm4j8RKX
zEmx^<`*qDWzQp->JPEj2@p4M%QUOQ)XA&A3fzY+Bc_K0bS6>WhSnSV7=DM+HnCxh}
zhkICP>{$w+tsilpavMzPPj3O3UmjB*A%L~H<H+?5B60>LV;xUbePoz@5l3a4|C_3~
z>jOE?MEze(I0d8BqgfuYa+LV1tuKKg1_GkVmAP}}6tm43eIJq88iOI(k_c!9>Ozu*
z*D*8yxq$DmgYBXF`Pjh}4~i?~n*T5$FGhhhAJQ4LhwEJ17THvrJg!_S$kRh9-h8@p
zcs`ON8xcb$$b!PqKQ>q-6g5ljkrd2n|0ECd4K>LA$Uekks#GS9`ToHv{j%D^aFv-f
z3J-ZFfMvE!JXx1A%2y<r@$eZ0Y;AU_TMD>annrodSA<G!b0R;~pC8B~aO)<dvhl7V
zMot6KTp(fmdc1o#OG~^cDy4AQb7$RO(>EE^IiA}$%7}BS*CD=7#O!;Yvw66uy5A1h
z8rq-)A5K*=v#m*CCngs|6C!;CMJ%HrGU?i{9dcU4)B1fJ6u!?(x+_1nQgnI89Tldp
zc9OmVbz;5MZ@Z2_N^FdYc1%W=*xI5?4#%WRzct~o;e{B?JYQEbGL))S${dDv6{-lL
zA0tZiO?_MNV2e6e1KG{aJq%$#mlKk6@#j+vdXP%e_5C8^H_ys1%)A%aZq8Q8H(1%|
zX9U>QQPV&+g3rE53OtcdUF%4xvb7%6TC7RoU+FqqEb3;2-ES<$FvC0{AY!zoe70R_
zqdt0vI*kHjl1#TJX)=t|KH!?X$U^yMcf8>=hM~Yj5TX6@Cise^`?7-Mb?9jJbi4J8
z(J8MB@!ktCf$NNAewjmZwIm*nw$<{o*`>IB4h{Q|Cf~B@8*y%)2244@0JS;Y;F<jC
zfn)Dt)H``~+`}!vrftxrp|8T%4;X9$Dn!|}w$B&8x#it|rP`Q(DSU#5EtAa`QO?>O
zgH}-Y39kDp(feyoesMWG`RUg)P@+Q@haYP-pj!E9C=(0psgUQ?ht}ki1Ew@K7Sqfr
z;~%|E(#zFXvyXg^;0TYrw0U!Ns~fS5+S;bp_U%!=0&M^9a36#h`$3#l3@m4Qd<_T(
z?ws@W&H@if5iQwK=YKjke-m%-ysAQiRf58P@a7T`_V20}>-By`6@<e5`{ga;eJMvj
z70yWIdsWv1r&8*+2P#(m*C_$skTKB4;?MWX_gjUhqW5D*zT49TyvG~Jj+Sc_KnQSv
zA0~e-H;eLP!)aRu6EQif1E+kT`r%QDK>u&*%+=SHSO;iY0^CEq{N77Uc<+urL9ujd
zbdAE3&#FycfnVvYF4b8paYpMhj88uAUZKSe5eB;>R{!m$%t08D+9kPEgVLIsHb`~V
z?dFJnca1xIsfoYh-@S^d{lmO&#_Ri2O%7c^1XPomGuWUjQtGVgkx=vS-h2JdRQ!q$
zyb~E;VMW5w7CfxYjxSsv&_rj)GBN*H<jc37k;?H#rgbNke@VLD9fuTg2!W*vW>vuS
zCZHX*d)XpZa}i0_B|uCTeshnMR&A2O@0MPE$9XJz2M#=s-#I|yNK6v7WuU-r*kB@X
zm&S9AFy~N8&L5#~Ok8YVaE71#g^jS6cyPx_pF!jifY2Wc=9HO`SEc!UgICQpB^8fc
znWuA80}ha<7Lu{|`W(KW<UJP)^2+eP)K7<-PcRTzt0tBVKmjhtq)`wFnB713FhwBf
zB^KILRKT=lLDB`SAmaxa<=g+F6c|A9j+}Pb62TCJ&J`Ty3`V=>4V#oqbLKSBU2sd}
zJn8=vMu=D+A`J0XNE%X7G6y1}v$**FviZO4)S0g&T0Nw82kZ^U#s_QXn)7NX#}f(%
zo>O6z2Tb{mBN+TlPIVwOKvX_37-Iz+5!Pz6vhQ*!Y851sfA?5QS>T{ZzJ7cyKrGH`
z?i}B1wsTV*n1NqPgey*L=OhLGWE4JPY}#povp+hfUl2M|>8j8f@_6dcFRGeRTmp4q
z*5e>I@suIe&y_+bzIzn%()lqZCL8f^fMdaAt@DU$#7QFm3ul3LAziVl0$GqB<qy94
zNLsXSCyA%2VnKmrfDd_SUMuc6)n}3XJFASD)gZl;fnpQ>&mLAUs}nL-C_l14UTYFz
zJ;xsuYlmpH0J@CD%3wjY!k#TFzahU;U09S?b2$D2=A(G!SA#{-*k<)%I*JL8zjNn1
zmOtngDU@*~+mH&=$ip$y&xi<@`kEf19r?C~n2BG!SLfDU=S0uEpnLg5)|wa7eZCcP
zsu}+KjXQ_#)bw1jzHAJ<R=JJ(ft0K3DTEnAMNOP!^~hTpWbFY7#nM8E8`oJ=ijgWx
zl#6-l!@UiHLn(P2a1G-_e)>8D3kK?m`=;N2sKwQ#cbn;*2=#aE8N!HRkd+~5N}fW6
zi#J%nU>u_-G1etyRDLI@<TdC2aDhzEfsr2=`?b(&zj7A$$#e9gov0`sA&uPl6InUJ
ziV$L$np~om_?iA=>+N$jIwd+Wsmof-ZLLDGx~*x%)4f#4Gq2Fuhmqj3T4A@RH$)sV
zr2adEhUnR{AT@28#;+h#71gGoMgExrNB4n}g#Yd~en99I3c*%=+V$86<hsD}4Y}~-
zsJVYVv2jF9nd$q#!2yC#7w}$o-bp0g%{}j@mp*A`Q}V33^yGm;w3GiNQYc1Q<VN?!
z@P=76bs+{)e#(fnB%Mj>K(A&>vOQ76bf*{oe?-J&J&tKhYs+B9B_qowjq+7YGqjb-
zjA`E1E^qk~kTh>K=-wDWNui>f=9pxkO&0?gb=LE|qru}ncUFao<|y`wu_in?ozY54
z>ll%@PA0b+i9bZ8toF=B{3s~_+Z<Q1#rF}xwSd*xON#mQKN#I>st_BO<`o1FfSg7I
zo@s^?jEY|Vb2exIr~wca!Fwt!KmwYRIlZ6h@{vr5`xYG&8Ep3JOP4Q+y_azsIT#a8
zNrW@giq;(!;Cwy~rYBIZttyl~b)vTv2U(}WN=jKMe3#$^f#$6Oz}8Tl#Y+8brnm#P
z1>c2Mo>yzwc0awo2o3^?B7_Obl|s%PPF6&il7p;ZrbQ}TSEPrI<kM8rGlznAZ0Z-Y
zr@rN_P4+a0%q5W`_VjD$`b}}&idW1k2GWr85#BZ0G-s<5eW`%KH+bYaROTh0kFst3
z4+m!+Mfc@Go66qx@2H(l5eM5}5KV*Pzjt5yAl#hl{}c<-nCndvU%dw4RWUmKG2V81
z58`A%=h4(LdAiFPOctWM)%>*ZepUZ_I69jp12UL&!G>j%Wd9H=P$Qzxi_Km#{M5(H
zFUb|EscnA4{C?>x)u^=p65-Ajytk6-Ye6cIXLMWgNgF?rF~$eKmTkE>30dlUu!u^n
z*QtEmf0+fRzs*`SvWqT25?CpoTtbQ<)L`z2Sb<iOVt5f~GOdp^Y6#Eo$bp}@`Yl8V
zAQL@V0$FuGIn2;S-z8W<FEdJA8!*jSd8+I&(DC!4aS9*4q7%zlLx&(s&0}afM44ad
zp?;KvsZ4Jb%;&CsKk5!aPCD?3rRxN9JZ|g=1fU<R7dTK%Mm~brcq}CO&?~?GKP>qA
z;(qJ`x6<_ax0SCRE9)fN+vK;cyoJuJ%<@D-pzl+wUN+wJ<v^k8>TTgW;o5#tL_MFU
zO)&k^qIomS97Tc7eT{WO;~i($C1FG=g1hs`<RD{skPb_S<IKi+h)#Fo==gLNm-)45
zf+tq*P4473btWJ!gAJ+kzs`fxDuU^|3+ziPX235c@XaUuHp#w=(-Ug+4T?zyvddK+
zdxeC`+~tu@A<xPfFsLo(Pb#pO7tM;ygkfi8k}q;4ME1`H92fF|$kI7`IgQ}e4KBnW
zc}9U8h?*tk_ezQ&qqq%1bZ)*X#hCoRSm?<xN%mYWUo@O4i_5rli;7=JaY8kOV{M`w
zBPfcNI&5B>Vud{Wl~4IGlCGT?r3j?``ZH*f^OCtriTU5MC{hr6g0sx#o^5OOGE;rf
z7*<9x?Fe;Xw6ZsBza(?ztg+aMbN)V?%&^ps5&rjhr_Z!Vq{tHI&pF7+*2)CT_D_=;
z>o0a`jX_k9_&hf8^upg%V=?@(A8*3a09PSk#2K^8L_w%y60eW8OmwMs9d=}1<CUl_
z>~~Dcp;q?xsk;l|3XZW=<<k4dQ0(M@HW1Kv7`)?CDuZhbOe?-W#mIwtT{`^d@QNGI
zzU@%JW@`#t4k}+^ME^~@nVOqkHKrq5_>^pCA5{?Mdr&t0CyaF}GpEmmv7(*tliA?|
zVwRR=8${^l!<j#6MC<Ag{<*H)uaNk-0a{3=;R;-mL|jUjm*0tsQM0H_1C^Ze-!ED<
zkv~5*_oWOm|Hl`w04DY^dFF6R6f1~w6CYJ38|C;UKhJwxG;{DCQ>Ex~skz!3&BFTS
zr0a_-v!)A5WtkLru)&WWmg$6nEzxo&*YL21D$A`bo-1cs0t8KQGkS9)8(hA5Xrldv
zXfDsCFE^+CnOT<c<Z{e;zm<t+47>d~ily?qp@}xzyG8t2W+>bdCYS*DK&T9_kTvG~
z6?jQtvjS~^)^84kojS2%f+PvU#Y}+Q;sarVs3G)tl_DO>@s%Y{c}oo~+uGX3W@uS_
z%yEuiDc)_bp<JWrJph3WC>w$BYP3%QffS=P=U%ZExWh+zp}}gNHN0+<^iMa=l1gK0
z^bcS7Q2#+DEM^XX#9ts}qY&@@I`}hVcARHFZRIf~D^S9dlp7!hSY>la1jB4smxrLN
zISj&M-P>&%4*|6+?MF*`M!46#b63v5o_L4m$xAo%_9QsT6*O&pN!<%SPlrIi9pNaV
z5Xz|=N7|9OFG1}HWWTuIYKyFVbsmewH)!=kU*R&Iu}o<zxhRO$9L^EWc)vHxph?x4
z1hP2HTkpi1(u<8c>zwu3-MbAG<oXFG)+`X%IT{g&%7oka{2?mpd{DXqXSD5+u(6yZ
z2qU_izb~vISCeZMI7=0`(QHVD324Fh56C_(J?GtF4LN}E=f49tj6*GgBGBv9&mels
z-_+y3sp*D~dL2Ia>r4P2u1mKrO@350oVLQ?*J!^D_4~9u7ZMAyM=L*Se4p_U@3e<g
zz~mcmC;)_gKYT5@{$S*q=^)v5`Qwl@EF57D)pF-M!_KZ$j&56&*lq+}NN0Upolxo>
zWJuOcA}*X&*t14B|8~(zG*u(S>S43jg#l4K<oe{ai*dTj_0rpw{d7j5;8~s~P;)}7
zVX{SA;BOZK?NtP7lTlvc5E}~MtQ@_aS0xzSc+O449BzyoGN0Q~qSayo^bK7zkA<!W
zVbs-_PC}CIGPSEBfEu?ERm*Uz+hRk~=w~c~rZ7G`f+h^mz5bv%98hHk4>lh`6iHP2
z_pfH7B~1Cud_#2X#Gr9+Dg!0ZE_kU6x3X!bZ+xvB7;m0QkqaxnL_rEG@>L0z32JCq
zZZ4p+4jE@HkQo2G$k3NdX-;d`M{y$?9b?f>81Oz_!|DOOq4sS5U%%;lDh-6DFNlCW
zTZxw4=i|`_LH_yJ7X_d5`oibQOpB;Fcif?=pB>w)8p)$6zK49$@#j>$?a?2PjYwE1
zArk4P?dPk!#-b!ydsj*m4Tl8dDL|OmNV6K#ZPH1}Bbt0?50Lf?Xg}9?KJd+_1L@YA
z_lTEPjJKZOHjDA@O1b|t1uy`h<)x-;x+&1<E1eL@HT8J>N(q2fbe;^G7V!foHlDlo
z`qBaZ5R&#-S5;)%Yq>Kr;_Vzl&OQO8&c&*bRRh*Q{U$|jWyHq>p+T24W>vR($cK>f
zk;v~7%wfw2{{WtDD0@0HzEIYwzgz5NowFx#K__q)nZzJxBD_g~Kp6p_G6zRt@(O4+
zw-6^G<5C;<dsb>9GDSQvLNV}gh($0^wiAdk6AYmeM?@1<Rpik>W_y;t+}G2lGCg}a
z+<K-P|Hiqj3piSBFsqLhGkyWs6KF8}eR(bS$9%pqH;0bxR&BB+NZJ`py^?FFAn?~E
zGLJOv7kbg{ScT18VT#RVm!u)fMRwuNgk#>z$0`@Sk`x>J(q|ac&WMSBI3I#n#;EY{
zO2b=KD0E_MX5<%X(@+jy%~G$K97>=0Js=TMcbA)$-WUjF_n=9)xU<f0ZcYCjBYCMc
zQJD$?`+9`<#Nb6i0~|}dF9$hY^|sVQ)9+C@Em!O7+1;-fm9~zJ&3)3oyFxpH-|<pB
z$HBy8J^go9KCiz2>RY-3AP0<-(Pp=Q%S&uY9P#O*$n{<hj?z*)eKQ_IF^0o9OoiRV
z0^aeH7~`k}g+tkz%m1Rf{@{q@gQX;VVbb(SSbkirX<Ox5ls1_6!Z+9#rnmoVCN@jr
z7tIpMy}r9OEjT@u9YH?FmDc>NME%(HtvYpa9`|q_cZdNUW3W2GguYdAbjDNZqLLJ+
zE*!+E^)R}d@wfggb#WZ`P?O>LVEr3+rv%5N?QDOtWj|M#L1wQ*H_wXz(ANEz<^Ri^
zMb>;6N}Y#5Do(x3I*^~LlkI4%b=&!Yv2c4W<o=o+1%@nlo3{`mL0D1<8Pca=ATBq{
z{#hEvW*>iD+1(a+w31p}xD~Uqe#*-Jz0=I)pTUfIl@ll6=Fg<#{4dfv;!bmDW0z%}
z!dF98YY(5wOx9?5Zu`8_1hAwAEYdOmHoO1POh%bhroe_=%k69mUHLWJc8?3tof;As
zAkYW(a1|%tN^YRtenK|qLNrL9k<0fc;JFA9Qmo7LrvIL8OxT}q=qYKVvIJ;e$>AU(
zMhdlI1F>Iq&Q3ZG;QS!JgGKU%N{R6>MWc!9h(FKA7N+Gdpt;%FqiogMg9A>q!cJEA
zNUm1r_-YW}=A$L@oFmb(;l$baKTxCxQfNyQTpOnqJoW%L&qA_V6lv#*z;lg9arp7t
zs|Y5a(LtVI*1iBc6r||})CK|8pr9|_7Wc?$GA+NKpp<cO`||bGt|Kv{|E@%0FNfO9
zDQH(nHY=JNe(m{22b#do)+AShGFUX????;rH)i|?K|-ftBmb%oxgrZkrbTYrrDV%u
zxybB^YbJRsV!4{^Fkv3?SU>KT?yXSb0Ql7bz_QvfD&d5L@^>DvFO&RY&%!kE=FHcw
z2wFNRVO;Dx6Qd(-f(K2|RVnp-qjyT6daVc&0tEfwliWrTq$oFpjGyc{#lNDGP?2@Y
ze_!6!RIE{wGw%!n!is7orQ|s|n6bqjYUrRuReVaY3VETvwLMZ2ZLvZm*?x_(-p{kO
ziL9(##kOW5AF*iVbPjolwabasT`D)b-=3D#-VTG(?;0tQ(7j6HCD+I7t<DRYNIWOe
zj=UZ#4fq(pBxR@OXWU}Hy;a=gYbh*}V0VnQ=kI|X><8;Yq2$T8jzaP34B;=2i>HLa
z_HgL9Lm-hyDNW%K9(Uf_lnB$QC6)>Io<5gu0c6qZ5Z!P%k>!39<U-bnSjs{|f+iSQ
z^pD85<of!lM<49BT?$!I^M68ov7JJxpt26W2RmSrUGVuD+Y}geCsTuw2xv=Uhg69X
z`lYQNQe0rvZ|=>p$ST^kl7LeMz>N+UlKX~O<Vp8o^~s_>F+7_jT0pt4wIoKpu!k!w
z;rb3B{Fm^KD$N|GaoqfPIA&t{N(ZE?1T5kM>zi8}zuini9l_6NL!jdVgnik8vB}8A
z6CGwCRR^wZ+@OxcJha9d=HxcMx`x3JvHLfGyJTZ?v-RG-gjbFOFv3X-oa`#!vwcmm
zeRJ-U3-TKd1J1v$O81N#-Fo@#f|$P^UbyRJ-&ol<@ePF;Mgg&vE$b^l3Nof%PG`$y
zo7}j*VO_ksV{tgpi>r)?EXu~KM~!R*K6@<FE{si85Gtz?+YhVG*$w$4oIVrQ|0U#5
zitHB;agc(+xZ~tq^m<d7pFHNAtPO$b(Gn`mcxv8$a!6$!Tru!1i<u$sHY>IXVuDC8
zgqdh0AY;2~8EER9iuiQd{V7bD|1@C5msm(-BHx^H6?rBC7z0t-LX^qEf0Fu8<A5q7
zBKbgqcrI1b2Oe<%ef)d0vocl&66n@JrucClUrXmtH;T$?3n=Y+YCaO%-TPUgCNRqA
z5!|l8dXb%Ls^D1pz>{$eon@R*)EnXy?`-&0f1R5f^n418;3I7er~>+o9pScWBTnIB
z@h6F-XIJuP1cf|9v7DvhS5b%xDZX%96`PyX21*=f2>P*&?$xi1r}qr?Z{omNfj{Ze
z(MNh-L%cBn!d6aQo}*k~4X7ADxIlwQL^#FE+1zcJ(Cbp&!-3t+t|QsR>m|mo@CvPA
zhZMQ)(6w@B-A7h2&_%9ZEX|@{o->)iKmz4cQkptihs51{Y}BvG7RM1GY@qS7lm}$q
zaJVQ*KcLjN?*+4mYQMtVmf6<wUU;j(E{VqrDMEn904x@*Z*Q0fT2Mw6fz~4-h)k+!
z|KaWF=6}7X-wUb)Wp5MpfvPSBg8MI=$xV0}WxLpfeB)ep8+7wlOwD$D8LMu1OXw^N
zx^Ah{maEl<tJN2p0?p~PyV!62&rFu7C6}eOIQfwcIsFYeYp)sVFP;xu@Mr7%zF7H@
zP681JUM^cE_iNF6uTjr7)OzyJn8VKp-g+rRxW$d{jw_vK_5l95`rzE3+RGB{azT90
z{qJJwvN^k-i5(~;`)_X$hf>+DT_HytS+MhcCoVArN`*qh&+XUzuJoC<*7e)jw~I=S
zYA?~-;0z`dHubg#oU#(;zy1pdy}M%)bl-z(EQ{IG=y=$~q*jQ&UZpRIIk=Ugb-UPQ
zFq4nG?PGTgR1!(2<y$INb^4`_l!zE3u$O_B32&_BSj8u?;&H|E(O+c{|J<!dPl7-H
z&l_WYG1={@9GT0V&Q^2n1$)2~%O5u!pE;3ibm-gY>3<NQ$)#a;yGJH8AXWrWH@_%o
z2IX6(0+Q$vH1}MHI9V1~$I)jpD`cfn_`jaf(sId_1%ZNfdE9U=)>A>-rKPNeAO_C0
z5cxA75HguPGS-rtn{5j<Ugei~tB-QwY8b*d#O`<2ek`q#AmW(AMV?(H1P?OVrN#gJ
zWM{H#6iRhRN5A9}pEBOJ%W)6)EM=Kf0X=Zn<?9p(P`Wd-UJCZJ(@pS7#V*hF$8#3f
zxOd$nQP5GT_0HJN_Hptt#HIMiBFijt>1DkTxe$Ivi9@1Flcz}q=KQOAtal?0i{s{B
zA>#|K^VyEDm;uwOU45;)W+4f2oJ~6hhy*6l*LS7wPcxpsm+x#rQaS}c$ryC2UJ=8h
zrBnkctqW`H3Y#;q&j~)uf7ac$oqQ+xrIC=@2Xt1e&x#Vn^$|fI?d>-XskB;8c~>b$
zH$0y1BY`GENK~rU*C~!A(I^pKIWSSl`-H)*$?(4^U6(<vUH!Q@bF0VO*n|vg1I(>0
zT~Q_k6#X>>YmK;0qCius4s&iuQl!j*A6HhTK(f(p3-(}H%p&?<(ararube5(t&d}n
zG9ya-`30B<cKiV=hW~hW!s#Jq&q8UL<(OOVMWD%!1sP`M<!X9!kcGl5JIl<fO(yS8
zoEWWADtZuWA9{Nbw0$c2N7fxu3EChv{O)~&R5+zXeQv7Y&Ij(?CHxs{6c)y?^Ho)R
zaV-KOf89WJCwo4m>f^&?=``{v6}XL9J9JiOL*#L8E;q=)o*6r?UH$y7SEcYut2h5_
zk4STr(99JdkmlJIQ+@WH(<vAc$1pzsQnS_i+~|G1(Ql;3M$Sf0Z+X7zSz4uAT;^%&
zAt5@23`arg$2=Dx^a-7WLJEX%BK-4%{{Xr_DI&~N?6#eh{qp2y+0tr#nZtBsXyih_
zt1El+>%{{hzm8)BB|rK47d~=6wm&dsymK$Bjh0JO{Nt`&?+>)3N%7_9REVi|4vBwo
zs{cVE`-52XxQ4Px(fb`#ti@RH(<LadIA56D`}^jCBf5XUWty7xtg59fO;0*DGpmA1
z7;GC#K|gY3aH$@J1HXm-`hKgCEMI=ER1N=-2*Wq)iUD|`DUVh`x162ALZFgFS#GQG
z9%s}ll_a`)%5M)!#g^tg=`&Ib0kqUbzop3h&<jf^;_W_cMF2u?uil;9v4gt!qa%g=
z^H>7rn?$O3TA%bQE=w5gZ>)DX<LZ+$PJ|o!-QT~-n5ZGOQ;J^xA-{APV_<aUYv8A?
z^U);_%-z<QPz^s$*RNa<ML?|(+(dz9;XwIeehg0u)J~(X#ukn>9SqcX$zVN^<vo%=
zI5Bg+2oKCHIBRMDc<~X!-y-;p{qb6*#1lnsO|-97NY<f6E4wb?&QqDLk41vL?q($Z
zUYg|a*#I%(ljly}@bB{{&o^E<%1zRNI#8SUlBI6onHmi@R(rOY1$E#y6pgkD+G{%*
z7<rPyY+Xq@Wnx3{3?hsmJV?iP!zE`9=1ro$@sq=pCZrrNi07W*7sq@S|G9+*vAwf%
z;G_{RS?PCRKvtoSR)*uxnY#b!Gdv#Jk<U)|MeRl&V&4rkW<ooB455iUX@;Xoa!-8V
z-DE*m?#EA-qE?czEFT|IPAE7s9Zhk0cv6v>y>xr*{OPmy<w^wDYz}fSJ|p)Y1S5;^
z_L;HFEz4Ddiw;QrztaS{#nVS-TX$IuX0AgEj8z@@kN;WOIw5qRQ?lngQApP^B>1fL
zvowI^!bFPGWa`)OXKenC99Zwth|hDht-*BY3RUkZl^xdph?t29^AB|?_(raI07V@}
zUlbY-Dyo|yBOCD3&Y&rh@J~6C4wNa9N}5;<5Y4guVV>IG8l@UeDmN2^Yu$ka6+9zh
zDMbbwz-4GXV^XEq#~C@>MyQW2c`PDIXO{X<ER{&;O}zf;Nv4njjMYIwC8P4fb=aat
zgcWYYhcQ%M#Y+4MYB^XKQ>Mz5K<CWHgedvv`OF>=>bG=uJJCitl~m&T1Desc;mOTD
z;nM3)x6}<pt<&1rJ0bR|D0dA-QQ7|f4@ZeSSc!&<fzf&odHw=*4)({=$EOZCf$naO
zo=(x&Z`LmyrtHU9d?MDV!m|kQe|KZ^4Fv5l>5BRuzBv65ormp=&WQ`}IY3i4Z|3(o
zYtIoEBqb5IUlMxYi$lr9XTA~fRK4lY3nDkfJ-jtU`PWozCg2vM)V2}^?ctil7jyk5
zH!*($4amPok}P&VKSq|JwXtccLD|FdQ-l8`hkzIybXSUOG@2Vm7;TR)9;i%P<;*IZ
zDmKjr`aagO{`8brySS_Hb`bN}DENq}_jJBwk2J*}q1^u)&C1Ig9XXFbK2%0!bWS-z
zq}RaZS917X;NTz?7S=~9s&F*#_k^B@FPk2gaYn<Zgo4>|$s1ME?U$Q}N$Q6ZOSf#I
z9|oxvsYMRAenI>XCH}AayO9<gPWe>+t-0l8Jj0994C5ch<;yl(wbupg-3lT}cc)am
z@&5bn!FTZZw(I-Kx6nR?scszR>N*d{2oY{cqsGA^y>(o7&|x@}HvL)yXWPq#;4{yl
zRyK$9r`OmXBvxdijpf&;l+yjI?oJV0vBa{E$<>v6XwY4^G2KJ|D&cJ3&ncrb(<RLP
z>1{W5C(L5(PZz#CdXw;)8Kn-HR~DS$Z>Z(a+cGMbeV%bfS!-;0>&5JTDUXRQ9dH2C
zB~X^BP+AS|FBW|_jZr}L=8`Qe-QRP?hFISnH~yQ*N`;0cX~q^7!Yo;L^9|d>IeZ$k
z^$kAs$N*A9ZGGNFqcgJ)ms>Trx20Pf)naI*(@H@#a(l!X6#+k$!&OTs-d}~LI|M0|
z=fa>nxPYgdvP^h#zf;#wRZPLK)>R8-7Dj*)gSPrnV$qHqAIc?XkCGs<ZSUURt6C+L
zNTtyhZG@}QCY)NV(bo5ygM&;_h#K%L2TGxaY0Cit_W3v=R`3E<26aS_FHgH)-)2{q
zQtk9AdWKn1afSkSabp6Z|Jj@3dp7Zj&o;0I4kb-dQH~o3sGANkDzTiyyR4QbQiOGk
zyK(U<kAaI)i!sS^wI-p$lNPW^bhU)%VT((Rcn|$hOl4@(E1}w`ekD3mgi(ZJ*)VY0
z5hZw33X$0w3G6V{z!B1`{#U>}xM(d8vQP!5oaorAcW24(&m+Kf%<Gua<6g;_q{lZt
zi>b;;H}9diqJAEakegFA<fS^ZwB}<LA-am*ji^N8<C7|)P&;{BV1#D)G3?e0(r!ym
zsuGym%aD?8o96h#iVBxLlS*?S%^QE`661=qgx+IJtI%7UeG}a+gflG&dwN1nPlJ;x
zT4d<2jG;`qa@MymzRBf2n@50Gs+diqoWW$2KEy9LJTLDC7i`kIa`g8Z>eWZ6dGAX|
zS+)aZh{3Uy^_?Q3sVSR@VK>Q~`Cq#q30jpsyOoSDq*T#ZR%-(s&NAXDq>(2s-ZGRp
zOO3ylkRJG!{ww!{ZO|eXMpr2{9$l27^#C5bg2tZh3Iet}TvS=n3e9Kp7AT?lo=FEX
zw5!%=TQSEjFgi;E&W!(FN$IP>6s?&-XIfw|Xhyfj{z8~5)TeI#PrXOEuo)0@(QL2t
zoZa*|^li%i@5BU_?^J~UscP6>^+auJgIsq;DRLv(Y*Xi~uuNE1eGMVjaAPbaJU%DW
zUT$h>#wqIHjG%$D-R<=QEUxHaCc3}QDCKw$#(p@H&F1LbW{K>+Y&#Z9IQaD!0luWX
z0+u9emPC%vn$gTO=lhxCXTl{@%c7u!dL=}LC2~E7(#gcy5P^&IDg!Ml`Av!W#@UWp
z7ALDEk#8Ih;wi0r2~wp}2_Rmx4J>?<R2~&1=X{pD`Qurg%h+Pt*QSt!@u@RxB8D|m
zxjN4x0yuWbvkBr1{lnz}QPE$C%8yEs%CYrw@v4|5w8eP^paE$aa!O@X`X(o$HIBNa
z1dw+KtV%ekj8q|o^nAtpJgoaLc_fyHZm2arZkxmuXPAm~CdGj0*OFogSF&HJC9G1P
zM9K7Ilr=ULU7{l=R?&;25?zyM4oNi=#yD&#$bCMajRI+06q+?Do*>JbM`^^2%5)}Z
zsPUfjl}0S@@pPT_FPYLZDhwv&3hrNSr7DLCRfE!{-dSf;hmVM+i-H~Pjc`Jn4H^Va
ztY5Rz_Y5IC&eW20l)8jQkX4m6LgKxH-c&`xy*x$HR_AZ1Qc1>SdIp^8LyO3Zuf&e6
zm_WW(IMe+cnMptp#JJQ5m^ZlaP}%Tg#BqS-;RK^~Zl&yTI<U`@c(9EyIOIYyKU10r
zTz|mTBv;pW&NBU<{H^g6z%+<tT*=k5F`_`=Y}WMRVVXlY2<)i=?S1*x8qOOCwrl;p
z`T=Syom>0~sw+a74lW>;OD3!@uxJntLPwjdvsx*P4ag%n!!TW|j%vG+T$8(v`0$h|
zrT4Qi?>fop)n{~Dej<ARs#~#LQxeKoj_1b=f4~j)?L+j6d=)|X^;yTmM+ld?qKU^`
z#LmYj-T&4pA?0J5%=N*Q<=D%f@@LZT9AKttFOgxlCMlILLb_Ka#OCeT@wFCi0{g9(
zJ<SHW^D4HUUQ%PDg7HPu6pkd^;Hg<7XT*;oYUBMxnCJ$n+W=m)<_(-rG({R(tHtxz
zS1+L=y<{o%so8Y%XHON?uBmC2ij{}I77!mMWaBA{*6uVlSAgH+b|?%lHZj1~*5(KP
zZJQ-CPtTtad@CClJY*4Ii#~Q?+W&M}E7%~eX<R8#b)Zcq#E&9YN{pw7xA-bqy02V*
zfW{DbIS&l0%bUk`cb#kIZNUb|nz83sm$%eZdUPVSY)WF^oHn0lhXI63%plU{SR-1x
zdoOB4bbOQ#YF^BAx=HncZx1*KlZ|dJ(5h!_J;e+%-Dx+!A7(Q1taL8I+Vl>Mt}R!|
z<z@Cy@#n^<rA-@E9kX!j70v%K`7R#tb0$VnMyU#iHrX-p>|<tTk~J<bp1nrJ{>)$A
zqUyFh170c_KSD%yCzavRmE|hwQZ0Rtys3MM5MAD(IyooNFLKI-${NA)-o+F59=u=f
zo7)DI;-8p{G1qEGJ`*wwixsbUOt3f?NB>UM`o;S7{rG3QFnXMfIIx@ILCldOye`Q+
zM1ccg6M>Y<@%4;l>7<bfajC{7TPN^jO7WP3Cp6}BY)&1d`Ljf^jtqqJJ&oW#uDr{T
zK>H^5JP7_*#*nH{{xqi6?c>Z<OfaODl&8Qh)a-RCh;9C+uGC)^y&@7POo&nRsZ3+&
zH-{l*>&DrYeR=PwgG=|;hL#b!ByReY`eAfb*#I!^NnveTT5aRP)jyFF1Q16X><+R<
z8~FRnu4!`x_r{5Y(O1G17vC<l7JRYYlqv=>M);d_+KB|QqLTb~7NP}-VHD8<<)!AZ
zFaXbK%%hPm&-`f=Z!vq$SAp61faQIq`yT<rc&^$MfYrg1J^rD;oscvA<Th!Vb9aYI
zU(R^i$cJ?YElnp$i45<jO80h1O#(D)XYz6ODr~ilE)Woa7b6%dt!@w3zCBU<zRMEo
zxv?n_|1kG@IQ|$78q=|`y%J>f9wA}!9+?GFO-~f@%Fv9`<`CdG`k>bGBztSz8`;JM
z1@1nc-d_|kCPVE0JW>F6)?n5rFHXCR<lc3!L-7@BU<LW_X)H(kRSAB|d#q!)$PvJ#
z4VxQQq#<Vs>bh*$KZ+u{TzJ)MB9~W*cdDND@h2y{^s)xi5Tk=wv>C562Ki1DudU2i
zVBaAkp?N8PWNZB5#;~PVbI;!~M3z(kaeQb~!+-N!PtN&V)m1-|)NBit_CJoUIx5Py
ziHagEEg%ij-3==ZD-8l7A>G}Lba!{{A|N0w-7H;8NOwzjfA8=6kHcYi5AQxR&&=FA
z_cHyOBR+k4xh{FUR9-c9Y7ezrnnz*Lyzn_Z@mr7RpLxok|L1(MLtt<>Wa$Ii*|lF;
z>m8H_u1Lt%z~(O%2btc%F*<<yps!PDT%ghL;qF?v5nwu~O%_zo^xaS^<z(*I?Pn!N
zQifOCCi&<)U6>i~i6a}_ZlEft@7llYa2=(F?MnM>GnbsThUYzREmV?pT9>l|AH{4S
z+A~U$<>O<T!vIcCXE~3t&)%GZyiZMS5OlR-`Z(JEYVGFv$sRY%ai^R<l%&Odc_l|`
zFYT?}N<W7yarsy6sWWG1{2?}|rNh~0ddpw+Ukz-&FVI<LZd|?LOUu%I`Hl*~ucfEE
z`^P`FzGE94aMg#@VD0#rA_z2MG)iAvYcfm8$^NTlE7R|2hcs|JaO|J&9!Byqca}(C
zAV*&bJW>!y*}Y{v@41`;zI<GiywOdloJf~QVwB<T@9`Fa#bC8qgPlWAOB$sM2wjS&
zN#X2=B}cklYaUIVU%HEH{m8??e!W{hG3@@kyoq`!-c=M63kSblT!SjMZ5!r<eU9hY
zRLXWNE9>{`MPKQ}klz*d92y7@FKiGjA0ea~8|ffHbo}-xGH_hHmr(#Y1k*r<otqAy
zgl)61Lu*Ag7KKSHYCk{MhzK=u7|*SRXA&@yYj=AVn48VKRUI*bd}1`;Os4}q?h&Xa
za(!d2uA6}#z9r2m!`O`vT#VsMEx2f7&)ppwB1lVX)K342-HXaUo8@z{fvPmFg#B5b
zh~C36c~m^l*x$&C_{(C~G&krh3J>0E2^PlCJ}{+nC(+MSv=2z@RoF$l+zbZ>7Q5C-
zq|9H!{G!kzHgsJB6HVc9l1`!W{Ai2|1joK^a%zmwrPl^|ASD)BKhn)UPAIg<n%Ljx
zf(fnfBu8Z2r=aekFOIXHoRbb8=E2|w@DYWxek00@Tsm_9EF;AmTcO#y0_O_I&o3N*
z4DRH5$0SWS%p)MCRifr1TVs#7bwQAnBwaRRBU`GywETEmozHbb(K8XAlx#O%vV7I#
zU>D1ia*4b?5O*q18Bmt9Y0*BERub#jwwRBD@fYpBjymt1zeRo}jURDQa-qe74^(J8
z<bVfHiTv~86VCh0&Ke98rU+{Bs;m^%Ep*Hvzwi_3x`qdQG&`tGtxGP?@Fu*Y&Yw?Z
zNfmxX_>~gC);<H^RGj;$8so7aZtX*A;=ID@Lo~ETk*P(yKcTw$@Kyf6^lK+MN_<lE
zx4-I}lby%px}NIzh;t#-LMcu}fhmyClXM6uN)cZ=lKLC4G}1M}<r)ax{&3SgP5>@V
z@EZJ$LAP5@1kFt$E@MgmzDqb?5q!R{zZmQ86n!EqrOI```W>5#DA+?k96OLBI;`p~
z2GTrtG*Ou!jvPd0-3%a{5^G=6?-I)=PVL`HsRkx~4M1f2NZd_H&X~`0tox0q7mIXt
z`cz;XJz~Sf<VTTZppV#L?dEL~l`cDXFm`eod!zZr(}c@AU?d@^Nv}u)mp%OBNuo$N
zZC)<9VeowcNolNqaDLjHiBwcr(zaQlAbEJYqsM8Z2`}ldU{vWHvE2%tyjmd#P?oYN
z^l?sxk|1AYaH(P^vG4x2!J~bDBy&O@Cj-H6E?6hvnhY>CKXG@uW`KCg;{4Qr{;4BP
z0_s;OafQmg@9ACyN@f6y^ew^Im`WCtdfE0QPmEec=Td~c!Xl-X!vLXPnL4DPMisD`
zgm@tg^VOWJrzcy5B<vP`8<<W4GoC~KwP?_N-V4puYs8-KxY^@8k>&JDfBU6RGQ^0Q
zRyA?zLei|9Hc}9|i=$Y|EK-`W*1z0PV4gBu<<nq2r%Q|!c=nqpDV*lSq)bY@L4HFv
zLt?UiM0L<5xj5J{u=FrpMkagPCaKj{tZ`C<a)S4rB%H&QOpCwf3{e_1cC4OGBN;^@
zO^+s5Y%(=kgl>D;NVa-lho8t4k!SK89+8Z(k<Otwe~R=s^hX6r#*_wp-~(N(U3~FZ
z|7FxSIzPq_@}sDDV)4O67kliArUOLCG5<{sC8@BrGspO$%DA89snv&4A0l$%W!G<Y
zV~lHg0YYcNiL{HCSiKYG94F)UN%9pM!d>g=Je)gQSa^8k5<bt%Ir<B+7KC#47|xU8
z^IUJNJ6Peoe{jzseLYAS+&QDjreSs)Cw5``?Dix?Q8x<+Z7S*%z>WsSE2ZJ-uAj3j
z6wbh=kteLJ;L))-f_f~;L~tPG1|g_TDY2MTkgsbahP9b2jw3Q7n+bt8J3GWO*8LId
z&6Wf8nSck*@F(v2`4#u(6B!`|Sj(FbYN=8p$T9C%tis{o!7ofrpigr-gs~o?HgXV?
zrg_?E<3gJ4lsm>^wZ|h!R%-)Ck9q8<pOpya$BYen&T0ito}8L(jKMVXA0zCOoa4s(
z&VOdD|6xb4FVsF47HN-idv7RFpASY|V2SW)IpkVm8GjXO%I-@UE)O=8p>bRIihH!6
zLlQ7E!v`&eA0hp!sIRTrC=_O4Zsm5{%j~~&$)J%(?Fs%UYc;=f<O}$=8xs(c2sC88
z?L_@ycks8N3s4x&cyURNA73o8jw%cmkmts|5ZiJh5XZh)@&1gGui><R6;w^^80{;`
z@8Wla)qWW<7Y9r$21@s%A6G3eUPI$%@22eAuOl{X=e8Q32j|4j?)T?n&0etG?+vLC
ztDc7}^`BDU#XV)EJSn<<hjfc1Ig{QY0i_>Z58$S;zK0^2ekBsd^aK0Ab;jlGbDn$Q
zf7D`cB2FzYL@jL%H?@MB>OTx+cvqfGm&*!V9VB?`XNhV0uRRUDCxa3k3}_f>yNguB
z<z|_h3pG1e0qF-zWL%O{q~vvR^X5SjK8u2;fS{gn?MzXkdqiS#wyn|L&DgsXwJox!
zDA^KuwFo*y3O3vLMpm=3w`dL0EA?FGir`NUUJXi2v}Ej`DEGX&Cio`{_7;Evu|f)Z
zn7zoCiP+bLJRhD*B$)ahV%{An#oCWi?1Ia?uEzKb(lh82&_2UGy`58}<Ws%L&O--v
z+Xsvq6_cTtMJVcX>7#`6cZMe~vr)@@jm@kCEv$%vlo6a#G9o())*{a2o7Eh2_y$hB
zj+wM+A%j0}#tE}0*)oZa@Bd~-P*N%3Avwy$n?!kj;~&V1Tj@G@CvmSokn%0-)-af&
z|1b1MrFD8}|KLZw?DQ&QA|b9XzwF(JFsMoCtqYxN-;Z^0xpNrk1Z-;CG$KDn`9G;c
z52V{K=YRRgf>VzALD0Z|coejV#PhyhZDQkRMmYu<LNYY)Ny-{Y5dzk*#C??pT^Cz>
z^dSN8DKd_%vVzeflKI#;LgZ*YCLzc<S&i``paxSw)HWIxM%QcnKnZ44RVGqPEF)r{
z@14+9ST96>_<`80h6b|Dm-}7E)yy&3`^<+o9gn|cU&b3yx$Iqq&-t`Q&+y*yg@+Mr
zXS)AK%9!iy6(#ncRB;f>S39@#N_?Ex3qb*E>V?!`NHJj;Ae!!256?FNWLsbpE^O1#
z^wAV9$d<ZxcyUb+<>On`W~od*dDA$#mJkYm#DK~a#+Hr{Y~z~kuLXQx`Ug!fGW5MW
zN3pcD1-KPm%Y4Qi=T<sK^GQVD)>#>hNfc!vIu!`Hgld&r={Xgr!W|bvvBqlUrp4bO
ziJL8}zClKl1whA_qFb!t?$u`~Sd^U6sLN(f1=%=<%y{2hO3vMG5GuzG^zx*jC`J!u
zqzvtRZmu-Oz_T}HLhTNwQMx<r+4gSl>6J>DpC1ahz<#}<9lPU6udKw$uSJFz?JmwJ
zZQi2XGP!$1q1*3hi)NZO?tA#&gsI8XG9^SEu2G`jp4f+cHH?-Lavv^B(Q^0@hPJZ2
z(ost{C4+hr$X!K2d$|d)%!JM3rhja(P5stjcDS#9>qL7)ZZO+YrQE@cze8EDPb`6V
zqdT61e!J!R5BbU{)@*!}eWh(kryK_0IOQ<tiRjZrv}ib9rfA%@Oqd_Gp#^b?*&&O9
zM$JTmcxN0NtCM%RGz|TZhfAh_{Qd(~Xk}4>s*8=yNA>$QU*ix4V5~X6F(8#;#Thn%
z2sSl-lpW5hLlUbZ&+()))XDq9Zx_2N<VKhEU=65o4|1VKzBkH<FN>DD3|k3@H@$91
z4H;J0Mei*wwwcdn(PGpg$i(j1#4C%H>~p(CHaC!Fk{;v8aJl#sI%rQJ{CRRHd9_MW
z0q?W?s3R~5y_1NDy83qm{4}UbzR1zfy~{~XVw}288={s0i{(c_eN1O)<|bN*6{N;@
z|80yxUW_W9nXf{lrdE?JiW9l)*Qr@P?o|{;D0QoveWdV?zI5BjPKv?G>w3Yh9F*yC
zOcYCjh^WFQ<l-&HZ_h8#uCm)ZiRz;GeUG@(nrts0C=IcN;7SRoC7qKJnr4);RJi#C
zF#~v#7T)C3GaQRWYNP8rEM+sKDOR}*3h5c;Yt1_)bgXCaz?PWn8}!oYkF~m7Tt2dI
znw%X79^;=xsldVk5_7CPTY8Ai&AZwvy-uIXs4)^`@$NZ(T860*6Yzkx9^|+n>(5lj
z@`9smvWdl64DUY%XE44`2%t__l;a&BkL1iHk_a$1!y6IDhhGJG4=hVIF1`@OGqlo}
z!B3ov7EQVb!O_KPq=0vVZ{)0rT1fA{kg8J_jcvY0VEk)s1Y8W;$eM?&Xi<E37@R?1
z>^+%N-!CHxuzW`rBwuMn^Vp|SP50R}Gv!(=#M%QpQaY{sckmR4OQdv|#0oi1=uMGY
zlR90?;;JE0b4kt1i6>4@tb1I|Z?(bd-zqJ;UstI#j{BFZj<PTA>)&N6o>Urt_iG0?
zWw-45x)<rQi=2xwKr9{*<TF!VWqN6XZ|i~z-CANf<RjqtpjcV`E@>Ef2tDcab{&Z?
zUux#kqs9ASPR3+i{ik!wM1l3|8P~ETh%a7b8zqebu3G5??~l^MEmpiu`8G%LK$_9V
zqBaKfQx9wx){pu_l^5C_`%flo;vFx3HTFhsCy`=}-?`gVU~VINu!$0Jnq$gub4%XG
z^le(gKezO{X-w<qA%}0}GD^`ECFxJJzY>*T3z$K{3R5fsT=KMf?7di<3ChmN#WrsD
z9z9&=MM>|y{LGTRXCPJD#!ltFpZIr2!$q5dJ3KM?ZaAx!$0DkoVu~wf-E1(2Jqz=5
z&65C~U-;-38AP<9%AjYW!_rnu$A;_g%Fi}%y`yHnbcd76O~4<{nai8w?L3RGw!CUJ
zXdaf=a>#9d-sfFuo>(2zO@ti9S#X<3je(aLLvG*Z8I-b3fG%r2fBgQmuPVF0DX#MZ
zo?ekZE<CzD@=+4{-_$|o3B}*x@k-Wj1#6{w%$uU>bd)`tE`gC>lQ>&{U@A+ivAIa9
z)2OS<Re{bb#3s#KTQh#OC=RBde@MLgFghNO88gfZ|HRKFak8}k!3;Vyof~LAYBo{w
z0n-Dpf6^zNisB9lDzKdXM=E>%K6Z<VlvShps!cRAMJHEc(9pKNZzqOz#n(Dve;y5{
ztZ1BZUt%=*V%f6^B@d!jJx|!mrlCp|#r;4T7MxZ3-r-6}t*@AiMwN;n-w+ofN`qP&
zDK3u~m@W9`=j2%;zMgi#r?POnR+IopT6H~csK;+usmA<H&!$6UDs)->o;_H4^66dY
zCp=8?N2&-LDo7Z%klGB+#@c;k+J{VRpc0@&RAsvJs7L6m(i0hU*`7pyAw(!0d5i=E
zzCspwo*1Z;QT1`nZBt8jjeeq%d}c4w2*;)~^m(I~Tpj&3@D@$YGfr&qGfD(?>i&-}
zI3g%du`pSC{oUR>PlDsm6MF3pKjtn}J6`T~yKgj^1lupS)sZ(?+ln-Yc5T~F`|xg_
zY+tryuE_;Fts?R0=}+#m{9c)SNrpZeyzH?zHO!dQ3a@P}@t8vo9;^J1nDPIaALcw1
z9Y*QuEN*r9?@H34dlHnHKKHCXB5^}DidI{(9&h7TA#F38-Y+ZsO_#HZmF?bHJo5YQ
zB4R!lNU*W78V9fYN&05=myHtpi!`mu+Sz?hbtWfAw@Ck!^1R*Yts*>M3PR>1HhcDp
zbAy*hJ%X$wWO9B3M#nn+^_TNDdvzx<y-m;ROnQScQ36ia^s|F%%dug`4H~j5gw%uz
zW2Ny~PFFHLyvGA;dTv~W&byEBj7$xSuYXd8?u!PUa#!yjnTzy3!Uy>7rZfTv@TdA!
zsLCt@4ScU?QUasY(1xdFBl^sD=mf;RNEc2Z=20GIzKP4zHQ2yf?HGArKE!&oQ|}YG
zNWp!9bzB^de94W)^#B=0<rRm(h&Jzx6&Tuosi4umkF_>6<-Xv>_?Wb_cuoJAm{qaF
zWPy}@TIEwZ-O?WKgp>@CNEwSl0d^)4MDUwg(nt7v(qR+NB2gVuL~*G`!rvY(5tauZ
zJ8%k6$^T*2_!p~99^EbJSmE|DS~5A3COJ)-*60hw=WOTbmAGv=13m;X`bqCPVCVTU
zdHqE-j(Qebicy(4C3d@jcDvy$t7ALYlYGdm?*z{eLyM7-FMxTL)l+~@n_T;MxSi)8
z!6=DI&$S1b$2EtWT#au-H5oO?H~2Mss&7Nk=VB%aYR=#oNLoBo*A$u@?xP8wp0>8m
z54+ZI4b;#bY^W_@P8Nf<;NXEWWvljHm1B1z8IwWnJ>D?FvPVR-?~lOiwGi7fngoR#
zy>pg<M86YOthos(961#x$}hgjXdHEDXzs<jq?_Nd=@^fGjH}g-%CvwmoCo+!={~cI
zmHxC2jNG1xlXNM-Ddwb1AACRfL3yrM4+UK^PX_lBlL}M+H2v=wIF03-iLmi#;<VG%
zAcf@@0Rl9@&rsuCknC3579@}%I*bZqoG;yU>&H*)t&6drBe(M7X-_0|$ibbW|9r8$
zjx1AIvAV-!DW<O9c!`G-_KD2K&fpnAX0~ODq-#%bXc;G!h@>+yQR9L<?cg+vOFxxT
z9GtG@q|0b%9PhOe#KlSB?<5xVKaJH8Nu4n;K3a<7W#CRty;IPmSE{89&pD0FDa$D|
z=0+(hX}3HT$+slV<6`41@1AmXQH)_4Kh|#~y3b+vX?#lbTtxyJO1j~<y2B%7A7xyp
zUZFt_m&hFSU2M(DrO(IOU?)Cx1?EE%cL8oR*y*96rX~n%j)|qD#*Ew)+9@$y4VEgH
zMaa3k^3{2YS=DkT(LIqsrmiviGtABTwOGaB&+Wo%C<GKQ=j@87#h>9+lQSodduHez
zlWiE2SVBHK`V}h9Y3^)g_*xOq$Hh3O7FOcGnncm&>$~?3Ij3@b>YUI2p@(^7B$*NG
zvum;%%Lv8DSSj^Gc2*<F<ND2N(ef2)QE-ISkEq?9+nK6dh_(O`E}JIf=OBWY(U`{D
z{Q9x7InOm;HIo*N4ldVh{sUQoubG{*pS**^QlXaFg8bemyZwx5Al(Ap!5Gv&NhC=N
z?S<zyaPm<2qc#*vlubeSmlsH!3ddsWl98oN!RESD$6S@EfMi*Mkf1>misKWY#wdM=
za&#(GO{(HPW^DNuQAoc=oaI5|m%2qak^X0ic)qU}exc=ajOn#lt+`U*$E~ixJglJ7
z{q%*LYxdwzgo3#9bV~g4Q}2=^e^=lIgkmqGtB6p_LH6#cm>2a{^mKbjQfc&7EfQ;4
z^fQ38!M=g$UcyQ&VN9o0Om@cr+3Ul33*T@lRT}hab!usoz++3TekD;5LE5a@JH6{L
ziY_(CT73Ckdki%Dap{K|<;*5y?#+#0Bu~PCM&Xo=q(*{mFP$S87t~7OmpS1YqidIK
z^3q!UXL;jZGl@ao@>0}GT#6kdLMC{l>k~gO%UrSUa9ml~^m6e%`jjXDwb1VVRv8X{
z+s4ruhx;f{aP&~bb<KGlmayD;+TotrQ%jyzdpE!752Ztd(U+%(wnvQ@-S*zs>5n*?
zxxHTGA-7P!`fbhS8Ur3PZC5KK489DEr&KyEOjp9jrd2jT1@#l<5k#Z*rQv7N{bmVL
zf*JePD;k%lWdJS`&kG;u=uTMY_oNUG{nGOI2~go9QVk|T8Z7S0Zw6vP1=#V$jJXtN
zo9=ehh`)H7FP|6|sR#oly4IKGKPcs8nmJLUzjkm_RTN`0VY(Zp(31i8tv=-NJJ{g$
zOb~hCkbKj7hJk$3Ivy7DObvmB4Tct~FOeYq=3YP!+HXaB!=s@8u-<d!Ct&nxiw2ER
z`})CJ_`GS^zWT4dV^gg-J0>9Qvzjf|mvO#T1p4=U!azGJgQe&%ZkEZ8a}JfBU-3t)
zmY9tD7<jq<gNRrtRZ|M(jox343OEBz1jef$P*X_i{ZAfkqkU;;Hb1t7#~?vzbUby}
zG$~8lr-n3U6gXzWzct!-k0w!4UUFBbhY=>-lo902^UWp;_#?_}*|mvSF+4}{LwsU<
z9}0dNA6!uO)7&RXFiMx7s5-E;`yC6A<dFL%Q>GMZI>?g9vok&NTqvSV5q;wq_?Bx@
zpdwC4EDi7Wi_|xA@0l){l>Wh>O(zHH#9EbspKI^%ybdA^W%ZEx%UR_QSoX@R{@U?;
zvNreJMNYe$&udfmZBW>QxqR~-x}tWbFVUCd@{JDaY08iX%1+0YQ4^~11gi`ku`uUO
zDh~*lyo2Ig_GKfC#jmyhUM=b6uHzmDYRlE8Lh=@s%uU0Yt!hk>`x_f>KWga+i!Ly$
zdb!v%a4MhNFsr?4WxojN0c<K)^;`OcKbN~a#=l&+`v-x??t)*R{+0|MVRx*0vZ_cg
z+FQ_$D-C7)OF(E|lFptc)1IrwsK$7w1@ccDKK!P;Xd^b;1YEGDJ?Sbw@>Ic{br>we
zogA({pdmLW7u&g-Fm34NX8hulW<&fmqG!*LMX0FD^LF8|MnyOsB9IQ5cTa=DrI?1K
z31LH-g+#b<4W@<G87|NHCI7%(nzdnv+N2=05^aayEIFEsMRQo%ixzm&%DF~mD!M0p
ze`XeC82b`@LZVVWh=Hm<4c0McVmcAo!O=ty+;S859ct%_3E%om>+EvRz!VxZvEL;T
zzyx%E^N`K`zSh&M(jbVuWC)>_ki?_Q{LK*@1R<2y_>_&QLc>6-!ZfI#Bnp`9O2B5B
z({*qpFIDA=!SPHoW%#8=)bk$`^#bc8sgaABJ|&$0tm)7;D<1VLuL&Md_<5u^d|GFC
zZyTtAQ2GyJ)mX$4?V89vA60w>;AjPD07|)1$;Ek*)3+R>t+<N?$|5W+K(>!4BzvoI
zRFXd6M95<pL^o0Y+LAb_j2y}rSE`&CLLMW}{HLgU{>;R80Zg}8FW_XA>9<(4dIZe8
zRk6AEZnFhI<0HO?w8pJIz_)Z-l&)n)m%&D${WEp&-EJjv1V9I2P}plgqH&BoO2=px
z3#s|Ovj@mp^ikroO2W8YhK}1v`~c)eb)b6w5LCkKUCkLzUHQxY?0Slr3`D7rNT{~Y
z7)-hQPtVgf3+WnfL>fb{<ey)SC==v1ih1s<oooMtr*U+(Z0l`#ASXF`Xn`tIOY3t#
zr+yQMa$>P|gS?o1oDcd*ztTZwr6uXO7DFZ`Mg5$+V(P-X)%!=w<kxzH*<wP2OBx|@
zl~s5$s2vye7s=@Jo(k&p^0dR{i!7}6aV!4EzyrNqm=C%;H+d6rs6BlcGU=gOzQg!F
zJ7MWrK7ncQ+bC_bYN!2J-sTC#14dp2#eBVp&jPDcC6{!z8M$YgaMq*6CS8Y^`_3S{
zNwj20prv}PZXJM(Hhhc|#}&Iae;DK|MY9N*J556JHO|n!{{1E6!Ca~OGTbCh$%71J
zoA?tUKIIA3g~t2iaVt&X2MlsaRT_pYOzFcUE6E=bbl^`=-P9opx)|c$utVa_^$Fe>
zJoTAhhz!vYiNOtozbE%Ws%m$J;@qcy&yjtW=8cvQ;it&0YB>O3k*yIxh0Vp>mAg0K
zK@#6pT-sgdm~RNHVi4jP<crl_-))ij#Yr^juSIn@CPW#CNw0+fyJ`TRpgOZed(cp)
zABe%hvy>#+yObpK#})%0QRYdS3mf6n@w+i=M8DoqAkc|Ly;$Q)Lx@u%sAb1TM1C(h
zN2k4Mqugjqd8d>6(j7N!9L?Du74cvHC;<h))<2H6NoGZ1n>s|$SX1I`0barLWju-e
zSL}lr1B6Zh>zkhOD`w*ZtAe5|W|AQVU(<@k^`18sJ>fydOPsNjO#?U)3_xezKUG}F
zqDmvE^B(@4u?U#mK1VDdAiYBQ&GH5me!JZgwdG6@S^z(K%TiVEK#F%1;FkU|qY$+#
zK{q4NGHwdy)<p9u|3Ci(6M$JcMChF67#;S}Ui&{2$0*g(8YvxnfGbJ)S0{q;#@S*I
z#c+)nk0E7k?+Z&sxCWyvdPiubAW=8f7o61GucY`Ro;GdK6=^sq_=y=yX>!SNkd!}J
zYjR(tW`rcWvi<k25G^I>(XJI4(DE%7wqo?$euczNusB^4##;r@ktTy*g<Qw??sHxv
zD_Q{P2pv!CG_yjg(M}mHbSQ){SD|!X(4}B9<~56AiIHHdPF4ZQTfko_J+q;tvzlI-
zT3BwsKqI>H{Y1Txq0a}1k?!H^NSJ)^i%a+C<KPTYTNEnn=1#ZTyB|=?z0laB%yg*Z
zcjsVEeT9EC^MPxxj&R-kknQ!&t${neLUB(zSX{xmHYlmK>1>^gu-zeXeiKjmhPq$C
zMWx5-%#Wyg@(4!?wdqY=81aAK>|bVp=<qp`Cj|qEs?pA_+M~Ryw>RhQ#<WX>L|2n6
zX?2pHU>b8RhXw-ypw7>IZStXGcJKG(KS!I&P}_X~b$E2y&NWU}``hrtbel2Fd8q<E
z(c3lp7jaF94yZp{C|Fgi2pnvZ>SHifvsF9-z!#2`DZLXs02Ukjy!S(&^5>%95R@CE
z%#)|!Hs6>>kA&R|lgbGy-?!qw7Gz`}TnHh|Z~{F{7@zNqR92l3RC47!bhphF;Ja%C
zEPNbH<rqZidrI7VE#6f(_#w~74w3jZ`ka@mT*IE+`+T4YXP3E~iwYz&^=jAgS(oo6
z`)_3%@S!ONU6un*n9eEknLl92qpmE96lIQi$L>m|aWuBnrl1S;X{+Ef-r{q|Us~9t
zx;p=&qHT=1yZwWKMW~)S3_u5DFzz9xCsO$Vel|I7?{GLo?D)rfF)zKG6r<qQvLhi+
z;?_}u9R(=<iq(uI9Dzse!A67^$<CO_16f7?IfHJINr{15$Uud$89lI3S<JBp0Kzg8
zn_i7w2ETlxH6rJABN!Y1luV6Y$)u4CE4E*SaEsXJtnA<Zs;s~5imSp6;gnCrA*|BR
z-sSh-oS}bO_>>xdyS(~{aTE)?>SMhRihriu+DjnDtACAN%L_)1k7mIpWu4xG{by*p
z%iNMA;4WFHeJ<p(8PC0~fZ9yx5fsmpQe4_S`ZXOome%fscA>uJdTlAWJeDLEL3LSx
z=3p=NtqgxS2$TNvRf$iCch^e9fg3*H(FIy~IAcrClo{j6aJXpknrBSOPnMl~AyJ#}
z;~Y;YCZVYjr@cWYy6>Xt?ii7SZ0zjtsb(e?Cjy*-$gz?rjcV5*?rqe{x<+j>mpgv`
z71*@P*c`NUp~-g<R|J!1Js%YrboWX+xL_{A^y5cZ*qNm9D~8Oj0L?wo6Z8+8*y7<M
z-VbmLdUNhtmEEWgKb%G0>VMw5uJsv1csT~0zisZ}z7!zac(9|TZ<6)5QAb`lk#Y2y
zE~goZzM4g5=w`a4biQ~8VZLRc(WH0>JLhMV9}tqQcUh<<pV%?wG=}QF_0A{?sRGnJ
zj=rA621Kwp5v?{fw&^odni@7Dr(rr}Fr_?=AyH9)fRZe@m0oKQg$Y6$TFH4T;bjNx
zI82v$TBV58A9UTCSxPuG3v^|!ngVh&Gly!87aA;tlJJT8f8-31aMK~mh&>sE;UGRg
zV!%vYa^B11&MZ?dk;c>(B28LiaX)rqrIyD+nm*+e9R##M0?pzpb$j$w>*VkG)fjaO
zltF$zSbagA`gt8W`xSZpbrN|l6s0VwW`F|?%jn<bHGP!ese~c=6x+frI<Pbc-FHlU
zi2y<w8#iQpvMdIrS3j&X^2lj}v2W!ixG(>ndi`zwLB%7HA%-Un#pcUQmBk}a3y~UR
z%5=b{#!}9YTRM42_WHf>#PJE?NuW2XXxEo9jNA|3+0;0Sa**$hlJX40UjolzpeONA
zRWM!ydUMspcuaqH$zc{u8~FFKco^q9r_?*`@h&BugX>OMoG}uBZPC-HB|>pSbAv)F
z3#?y%o*Vp15NoM2+(gveP?D_Un3h*g*yr*Xkh+W4i)xr1&G!%3oZ-V5s#K)iO{^Um
z8NbI_WmQu567L1KNG_t2dt_IlD(LObG+F8%et(e30B<l9tX_p1qYpQ`?`wKVe5Rx#
zTJ8~0w7eF*H<SWlpl*zK$s(jy8XpMFWJ`86lx}5<F8Ayr@V4&oq_{l3Vvjv5{O2E$
z+-o_c<X&QJ^!M5|GB(KigTmH@#llKkV9F3~ptrc&su19}QjFLWfDf7eSwWl`YD=u$
ztTb6Y_?6CcxO>{Y>h`bTji!A7A?#LFAsHI%*uB`O)zt0^vlmmM1sUiT{1ZyYDpe`l
zB4ry<BFkL0hb)^`z-hzP&l?6KyljaaXe=;AfZ`E`g_;zs!Gw>dKF7hEV>L!=o;7{Z
zBzfWcs#rsJ<*yO845Fh%*WmqH5*}}~XyvFKPlM$pQm|#Db!IYI)}2*E_SNZWW)5F1
zoZc-6C@f^gYg?;Cbwb6g;wmlGTv#ylD7>9wtIhx4K{nWO2pd3Vh$n0=_uPEw=%TX4
zgeAr7Pl&;4^}6l6&Ih@34S`~5!X(*M3ZUdirY##L+BD7aHwg7pcBq+=cH^=DP3RO*
z4hP8cS3bpR0D(C{jqK;03zfa|*^)7o;RK<1;&wR%y>&)+=jE=;0FXs$P8d(4k5jGD
zjnw4(s+4RZd<obBZGg>_@@$q&#0=K`U9YtOB#`3%gE;o&;r-)j6+0dhXMKc`rqFS^
z&#t=x>~Bx7PqaC@9*WKKcRDSgvf_JO$z4ff8Z_#V{^(JSFLX3uUcI`ICQ)r8II=se
z-Gh4eq}<jiVSyB?NvGKOAsEzGuisNImIT>}J?ota&et5MUOB$F9{m!?P#~iFDL1{$
z$>^X@>jxBEL*}t`47eOGn8ZuTLH;aQI{eb!Hre0zm(@$2a3LHPP)f9$!t$3J0|aEm
zdi;_*n^WJlzCw8QN?uA_!(B4`$-Y(oKPIj8wPBFj@Anvg$(ivfB1TsNUI1n3%zCA`
zN{Vy;`{OESL$}Ba?xZCP8)sYREKrL}3h*~Eb`<PmA~l~IdTg2oeCm5|^u0qubVA@s
zaW@#nY8%p=p!Vv43YjQol6M4Iw$0*l>=={M1eaQFWap`UQk>)agT&}FT&n`k*^!58
zgQ8x~h403Tuz$IFJ#Nf$f&REfrMRVSYnn@?j-^J8q(=Fi{l#f_J0L14Ir!URW3w9P
zM|8Hnfb_B*=QkK<zvQ>(_;#@{)&0)@3Elxa^Kw1mx57HTM>uTE`o+pO;c|qR^}PCI
zZcxId>htd+YF!k+lQQ~ly<S>OTW`0hUNQBXUN?_8)6ZS!=?gXkkZW|5Gu-EDno~hf
z5>#9)$wb@6v6TjdOv4Om!xP;yW%2gi*F}}cR#R0sGP)?w747s*kG3IuJ%JcoVhitV
zN#?hPiRWki1Sb{0E-t<e+gu_4a`OUWBO9!s*Tac{7CY(#>6M~_SzmBxXJxKkY5>91
zHv#fwSBC&JE(+amTV~E#-(m>9Jt2H+Lx^dYr9Qb;zX^<g+4H}J%j%zKDUomIy=<=b
zOkYW!Jv?o1A3hHAuNp#@H&gaepKn(0km%{H@olp5R&{o!?g=`ybq(v6`=X50AV2?L
zUS$t!DU)sfyF^?S^FNsIp$O21K3;U(eMp;Y)V6Z<aJ9>H=1zK~@H@=HziJy*f4O1@
zt;K=<beq|CRs)vt6j{5gF9*AV^<jR33TnW&yV6?UyZG7K#>JbZUI<YhoLo$l*~tZD
z$sU)|PogL1_X%H>rpsITK$3t{{q=-wEGN=`5l#RWPb?l8(=63E2a5ZcN^799GdyTv
zlX3HAl`{rnyJWlP>Dz*6T;GiCEQublxmRD|EjK)FpuHBO70V&`l_nC`2SgXE9vomd
zZq9-7RmX};RIlHaqMiF<?}V+%$@dMMN5Iu)Bf`Dbuf2Ytqv`6{w+hpJBq{u8qUSTU
zUqk%>uyf*H@Agg|&KZU#9YL*t*R1-9AJYQJ$+Mde<yyDbk4<58mM}-~8cbm{`K%4)
zEsZJ|pEgX#_MA%+<p&#2EMeKLe4V+3Dx);><zGxup#o*#=C11z{!7ng3O}hO^FXwW
zUNW}i|1{$!sQSyu>b?@pEFGTwM!^?TuROl7BbbIJ#dlg@`|dks=d>#n{B}h^?6cr*
zEIxi-s=OJ~`=bf-?!mLZ{kOBodej+(D)=nc%0G;i(Wnp^$QDH+Oh*idxrw~U6a_>o
zH#8*yU7%7DW5zSM$v6SVI5ApZ=A1Dzk;utsPs4l-D89|LC|i~N+4=#U{j&bLW^JEU
zOBe+VQF4azlX3{K2Sn;ohb#shoyW0qb3y$oF4e!^wnHgkHdjcGxA(S{Ha2HxGC}%8
zlV@*$+d!mFMec3526c)uP<-Br0mCW05RqMTC@^Y3i)-+i<c$$fygTu`6D!YQJE^ky
zJ$bk(ok8tX!fWsL0L%@K+F>#Me6WKr&+EJTkgdOev8qESL-N0W9r*&z&i;wh%juZO
zI^d3<CXCiza<zre><R2ZIsE&_0#HU*N>sA-J!)d&6d*LW&)bK^YUcpY$i`cYY}FjQ
zzvranFF8|RJB0xd+pH`4I-4zdo*^MtALc|vN_T}1dS8w!ux>qy2CpijrT!sPEmP7c
z(K;q#`g8YD4*9{Kf9GiGrj=*C^V{xyZ6M-@ILAZ5V5S0|ME}Uw;`=<hNKvzN@O$BS
zYR?-{J`kiK#RLgYrcQ}uP(<BG-_{K4Gt0_yR&QO%T^A-)Qg;K*??94+<-5I^t$qG9
z%Y&j(Hqt5OWe%oVKIbYvO}4j$R+2UUX6JqEFwCr(Jgoh*45g5H9EI^)Vu}#^Vu4}-
zE|J9Kwa+8NP8F!VE6h4eciHB&++5ko&g^`m4%YJU_U%7+n9?#Y^~qJv6G!3E-Q%Hw
zU#D7m&(RUz=nq+J7)E!xhJ3L`FPQR+0u!wte(mgW&D61zQ(-?4(p5RagD(58-l)QE
zHU7h@idDb~bh!NH>pQGa^I=3kg~r2^G9@2uBgTDts=<%Ax)2S(W^Bj|8G)!jo`J}3
zwwog#qU|6DV4rhmPYfi%o5?&WJej^$^{<cdLjN$mWwy4}g>6k&)AQHp6W85sLO!=V
zN=Jh+c@VAj)81EIOgN(g^t#s>4v^YGLi#w-%UiOq-ql-$`@~O`c{%h+KmRdum`9sq
zDWaG;OV73*=dRW!HLOHQ2&u-Wn2}pasMfs4*z2RJUZNP(;;}VbntG!?sfr7cz^Fhn
zLQ~J92isxO@nfwG!2*7*a=65RSJr!dTh{XkBvcE+A;mU=TMBq&Kl1u%z($AO=%m6Z
zC<Vp`Nyu(uwtp<E^U9S|XcG5-im<m-_HcVKyalN6!smH6kXDEPN+Q)>wesPxa*|)}
zUK#gbl=FrZR-G?96{19JGFpqv2~5z9=IL`FgXEr!NCT1r6=qp^OMgb$?W=x^4*0Pf
zYv)>gK#FB_Tj61fIlf1*WzRoCMwFLmhH)C3b3P_zHO~Kgr)|@~5eD(f*e#b}3Qr79
zCHy^4@|*Wmd&%x%lp8h~>>*I_({jru>JA)HNnv6#7SFKo@7-w_q)r*H!CLj#7BH_v
zTdWroXV{5S=3`6+<CG-cq|WUjQKj)W$Ux#fg%>-ufL}7|<2#!6nAgKM-O5L;FW~sL
zB#l0Q!jU2PK<J)E^}W|zAmb@8w0JE!SB>!w)+)IK)DCL${3!F}9z@OkUX8Nzt^&fM
zKTP*5L_9{Uy~P?E7kysNc>(YXgyE=&r-$OyAV_`e7Cx4<TTB=XT=YPNI_MY<UoIEG
z&j42w2D=3Q`nSS!SwO7(5v+!!YWB7ORlF^JT*C`%zrDQD+ky~THSzc4C`w<9U0&QQ
zpL`0ibEpeP<ZeleNWOLKo*AVZK4QyS7LzSAg?@hfPi=jI;e8&jmw2aD%dmm3Ptd4c
zUM$60dWP@BG68{mqbw+PKaA>dSxlZOgJBDGqhzrv=4`+F|FdLB@6AUx|2lB(<Yvl+
zGY^SqrNQzVzuzIR*$xx(y=TY86}ry@a}_0oG}iFO?ef|ou=tR;xzg|}Qc6u0t6i~?
zX?>q;nwFs7D|t6HMmsiMMuJ=skGJ31w00IRcCTIj=}%L<=G4K?jH8SmN+G=q?CIAD
z6Hu_=d&m~y?Hkd351+n~#ss!)zgr3A<p^}U?Og<2JtcgP$sf=9_Swhznr4g*bs+4m
zAMV9)1+6AB7X74qk4@zW3EssYtXn^cKSVdl(I_mN0?_J!wbPX(!gsNj-#-Y|cekO>
zDo0htR*(Q})irv~AewFpx<vj!u?3FLkJ7<nm)(ow<H-#2@%<nBW(*%<-hXAhuh2jA
zG#Ek;kpe$&^~9-yCs8G0XPA7pw_bNVEC>Q<KOLIqBLkFB21ssQ<AiB<+ecpl1$KZ_
z<bM{#Ke$Ms-uL<~%xev=AOI*S8||ykUv8hV_TOf_kTdKs(T<HPon_p80N&@|P9!o~
z&gL4K2U$#up9Dze&`O~6bkc&%+Wl#5@4Kq7?G{+qZtGt4-lR4V;2Sro{xsuyx*6<8
zbUsJ1y0);x2WoCl_e4a(dFfkyjJD4f90T2Vo0EGyXPY`%74~;)fhA3+9jGeT44xkK
zR=$1RMb@%Ey3m@ZcnvD9UReirbr<KkeOKd7%R62?$Na9>v&OM{bXsI#E#m3L_%>0i
z4<nvq3d#;%H8Qljg~^2^!L6>|A#wbf{~h#u03Viq9L{SS?rY+GZd`p{$Q5DFd(T59
z0OFPxy8JAnU*%*~)89AGSmv2lYJ{MOlC1XY=H91ua?70G?qYp`jtul2vb-%jM+h`o
z{`cGb=?wqO;K}P)t1Tlyb@i*>n<!JJ&-E@W&p*bvo~wk;`mZEc$!=JN*T~JCg{}2v
zYpW2br*S+F`u#-T*K|KadCmXPyF=cIa6cW~m*;cK`Cla4uMSJSGo4!py|}l_w#CD|
z!j<z%&2v4&aLRMYU(QF}PYa2t5IbDgF@Q2aH$A8Dp8$&D#Mv9R3fuF^1v-DvZKO8J
zEg9#mm**oa;A4|sP8SVIP8rb?7MY(9h7|o=Y!eno`EaEttMA(8#+|)t#+vp~ZQz~L
zR|$D`&Kzs^vwX})<o2wU4sKqFC%OWXtS@VP0B(5m-`!)P0tWn$9g|I{$aOTwT%Qh*
zP<|>Ca8}4-ae*0eY2_&j6qbG%XL&Q|H@%@kbdO2`mfFFt-=CFIGmgGvJ)$gfxxI^+
zXNE3Q8{`N%auB*v&}E0EeULT`+?5unl=rQXtKRya-p^1$0wG(_8%X=mj6KpUZRLh3
zX;Ex-^0q67VNIu`i;yl(WX9S@O^R#XtFg&`oLe3KQyY`Ji8}PJuS9l=$PL0fDhwV~
zniM^?`TptMSLnHJr3c1@7^SMH^Wx%6(&;pHK>_;sPQP@!_}nN~Qq(RBu}kx97F$+|
z^oh)9zL9PcA<+)^bCP4nU%Zxll?n|?VEwdvLCcgXIbXx5)3TaHhya~%a4}vD{;4*h
zEP*61H7OzzRm}m+ToH~WvB6i=z?efjbWBPNb|`Bm2;v@`FGU4cN)9%lhS8=s)75CW
zGkUsP=1|7&BT;3wAsptA(^n8Lu#wxxUx`!vvN;7#Tg4A$Cfd--v!)Qi*g0n1^sF6=
z3W>pLMxkrDNdeV?Nvw}_QG)k|(R5PK;{{^_Ji3gw;lV+sUGtLLsk4tjffm#H!F}j+
zhr>S<Q<!1fqOtQHiD&KPhDRH?_C(d`NDq}0u;60jxbz+*hu|M`Xm46>?qz(4Oj&xf
z+tD|a^cIy)vST<zCj+>+*va$EE7gpk8Z`E%XtR-r01!NrJ$!UTK(dSgv_Js$$8)h*
z@RUIiv*`_Hu_tLbm8yqVS*&%20{*$e`-_p}NEVIHTSp_@j=KVLH4YeWzRm3;u5;+p
z0x$YAZy~B8_$TPfE)QraHNe2#0OT*->>Q(Z9pDp*7|oa~C9&x-x<v$s3wcj7*wZ|G
z4MR(fo`2ZtV;nJqZ*WZH0dQwlR6k$Bq}YgeSHuC+;cr55Vgm(-Iun;3%juo*#fTP|
zv^14Fge<VeI!<GNxkqgoNOo6t6zX%97$VpkKWL6hKEyl+Ks2+oq0>%+N(vfH0>Y!f
z^K{-;+wm^5)X)v%kpD@j3y$qM%N$oI?Hr6ChC{kbptz>d=0SwDjUP56uy1ixld+LF
z?ZyhVU2Z2=b=Pl8<=dYtv<7xhRQ$2d*VRA8(-q~1$g+Mr78_rVszYvj=Ajw@m%Hi}
z&5)~<Z@DWjEgW8DGt2^w$jScSpmW|OLFFnEV80Zi;*y@r$SrKJ-PTAjzp$6sk6X%o
z`39rr!{+yV^cdqlrrIXzO2ZA>$pMjPRf|w^dw#9k<LZmB8XlaQ>wS9E6F#l4H`hBj
zs2@r<_vrBKa*aa{=)sz9?N!OX-6lAS=@!&srugBBw1KxD!N>N6QD`E?Qu~yY<lKrX
zjG^m<adU+KuG=-hLWZ3wI|Osz78Tl^&I-_%N4o-~z~F|q@)G5qo4-VtUyt3=9WJuV
zX46MN9$gpIM!RBWwqu=>?}k!?{?qFCeMRW*WpaSz314X(QYo-NBDb9bX#{Uj#{R`X
z;^`TYFpPfcio<hC9qeneY=2l__POhQ-6_}AjJNAptOMN;8c9Z5`ny1Wm%`d8<kLF8
zX3<u2s4M?&IQ3;?=pB#*aUqtPO157g+1pQvfnh{;j@S7?;&MDVgadI^$UBjr!0c`(
zW0}u=IRSa2VfSM5Flx!7?$63!Ai732+@iSE@xs7{jX?6U_c6AA&k=`S%4N_oPL{KI
z^|AKxy012G?{K)XN1;g$6s>LP?rHCtQ}G<I?S_m92sx2fe8GHM@F!@TB4^hb-I=KQ
zdg5{wJhlzIHDMgtx>>C>HvMH#e8tN5y048%Q>`Sk&7!G`WcUuP`s*a-u@?|L*`GVd
zU#<yHs1e7<m6o|L$!i#woI^CwKw#jO>Pw3qzxYNtZUPx|FW6cDqN>%;By?0i??!X>
z>*1yL;Uz%ySX?|BdAX#e!Ed~OL(sTbtj4L%c3M$Oe|sMB5op|QNZpmavp+P#ICC-B
zkE1=KVS#EB`?r_g2%{C`j){rAjOO|oU5=~-_IwN}dZhe^t!*?=LgdHMdtM~@;3AS%
zogC9{Ho)pJBJ${bG(%nESJ>yGwAsZ=B!t~qWy7WVLmU~@xik_5O>~7BauCE0q=Gif
zCv3y(-TKsJOS(8R6m%lAL*a9CL7L+)gqkPZ-{W0?M-JskC^Z3?o)9d}@IplRG^3W2
zi}1==7R66GfT7nj?PBIk+b-goY`~Xl8RC6`bSQ;D(b%Z{uQ9^~O`$1lyv4$DVrO%V
zfH{awANT04O>lW@SY7t(fEKw#XfeQG*1zR0M#GWlnV^&Zg2mXjo^*9d7}`HjV&@Mm
z*2hcT&~P6kt1)J_%l2Go9|HoYDGc*`NlhY^p0FxLuzG`UT#A02K0c=wOCq-dFdtKE
z1P(KIz0hc93Fj$rhC?TQ?&^XYdNOp#)ZsvNa9ClBCixy#f&gYT%3!RfW^7tKZhe36
zGoiCvdnHJKma^*>qx{-kF4pS7CNJ{ee8pcj^t&N=(;rypk$9AW9qT5&v2qEl&!uz#
zbh}hen)g%W^3TVffEWeTWYG_-?BClKJLqrM?OcN5WmY!<YEg>Y4!Vz{U1TjB&&SL!
z)an^Eri$XVA_@>k{7MwNa`lfB#`IC1{{<9_tvir%3j#);1NiM(x%F6<YCFYPRKRC*
zFC7Lo?b9@v8+yAj1`o?~f=>tC#{Qw$-z|vqgoVZlV@E+QMI(GJ?at2_ue-+W*a}{O
zBJb`txSFAy-~9M4ZreI1cvZYV$|3^biF(q1rTu6>pLq7fb)aggFc#%|vYt*}#X=g$
z5%SW?v54A?Kz~p*oSc13@oYvNM&2w~h8|-e>YSKud8VahmyZt&)qzf|5T9ilVA^$K
zq1t>r>?oo^C)QcA!#bkxC)(U!hgS;`85>|@NUDX(cV^P1XO-jjp)Oa-CJrQceN0Ae
z6DY>PIEAMtTGo<z$w7eg^4lfoL*wPZRGH?Sarw;d<>a6@v0ipDpi@<?Xe`CR1UY81
z*W7CkwLHK_8>?*DjB|c-UMW4tW#Qf?3|TGeKu_Enq<;fuq|U&FqUH!tCNP#J7CX^@
zJDvo_&J5pLl>1W_nzRxHz<@vuNw9@Z>THGOLV<c^OoCxaFvLbMn@!Q7v|c=_4JWc%
zVSgZ*w`#a~)p&}Pw7Kk>w+c3uACo2(hhfu9l4|ErqfxT6MP5*;#-NrQ85X+j`>6n+
z#I=-6Q_vuOM>(oi=zte^IfHJt?d0$k$BW2rZ{-2-K(6$6DAJL;m@HSgvCa==W)uz{
z@fk-)j5qADvTpDFNa2^F&4!u;U%|Cg9j%r|`$FQl+~Gx{i{Dxq_GGC1i1A8pa3jBU
z1$<k!RZ6>t3W1`3yX16lGT^`Gd1F7GMWRe13_Tm|1kg!&8d%gN>_>rRGHDjKx+^&L
zLM4#aJR{tQd~sk0d!NH_HmVT0tgMXzI!OUksE-8+FTgAssDuvgNRQPuDl(dt#<((A
z2}?z~-6wh90acEM6J}}w9v!1TQSH<LE@@}>iKU^lX;#W%79apR(M#{wA>hMR^J$KU
z^gqDJye!^-&qrd82jDY9BRyGqD3#PVcueb;A^aE^f*5}@jE`KMXo6osLbtow0)OF)
zfD=_!W`cI!OT(aBf4^ENV^^;nRWBSD-~)TF-#Uy5oo*QW;TOvV=<nvZN_U+V($KKT
zV8H=R;D~uAgm3)eQ^^`kvqGXeS3R7uqSjliNi~O4SCWqmW^HiedN}Z}<LB7;H5T=g
z1L+kL%~;}$HVB);y;!D+xX?0?K>_>qm|nW^-8G;6%Lbi%Vqs{DSDV21<&*RJeZZ7H
z?9L~I;+Mg07zzKMWqZzj{Oc`v-Jj;sm~A8j&nHCp69jMZUgedh2-Cf6u}p|AwA6$n
zTrN!52ci~RI>?20wIO=Y4+|-<euRT=on!_?17^7~^Dm_lqMmF4solFdVE#OMI2G#?
z$g@&QxaEHy($RB5;cYwDu^-x>;aoeyJ}rj_@RyUB+>;CM#pA1tMZN$4h|li8SHC*P
zq!eEou{V#~L%a=-VuWRIiw%bqtEZU*Ucc)4I(yu*?>dkDOZ&16JuWtz_%e35(t+4Q
zp>FPi%e5b70dC&dUw=VGKq@YXT>Rc6s#754(Z@EVXdBIcccf|3<l$LgAO(#**3l)X
z(A3ejWpLjr2R%vMLIN8yZ_gcW-0&t3NVe}`hC&8JP|yA)n??Y4`K}WO=@%Kf-QTgD
zMOtRLJ*do@BV!8a;BmdY(_6wTG-)OsOyRuwTF9oVYh|m#!MgSjNU*-25^SyX_ifJ7
znCJFj-de(O3F5Dk`bfFAskyf|KAKy9ZMIJp`u3X@K<u)iSYQ6wT-VUdax^)QFmq=#
z@5w)w-UNDy!F*^hG`T4_cR6`tY7RN{m^i+%)zmE)kOb@6+r))W^q>Ivvvb`Tf5(kr
zc5BShl5l_19X&b`i#CCC3a&KFuh>45l9@k;VM{=b6*z&o5Jvt69UBVoGt}%tTU94g
zx2-0pbh^ji`DNoH<N3)(K;L=omIc(u`q+*@$7Y`k>f0X_O6u$RBJY&Go{j`NoQb|&
z?a}$Qr#&5d<XE%_i^H?y)ydBAapZrShqw!+2O5n-N##KR8H%NF@+lm;(HDkQ>s%#R
z9Rth{_Wzh4p(8iwE_!PMbjuC0*u4OEWK9<19)YW^$1O!6>`pgC8={>V3)#<RnRR^k
zrWF7E;=Jpe5@TOy+}`yYg1LsKhPpmL`j3CLgBR?g1Sy1HoCSt^{EWm1Om|z{9GY<j
z$bURMHjBlYquj#Z1b>s^vxo1y_}Z=5VFz<sG7UBnTv`42===pu@W*v{@U|?~mqft!
zeM`qZ%595#eJf);ZBkmM>zH=RaBAKcx5jx~ahS3SHF+c%+FY3cJ^uj?1Z1oJN7Gpb
z#o0tzI6{Iu1b26L8Qk67ArRahg1fuBySonV65QP#f|Gr}-P)?juT;S>^LF>`d(L^T
zL-3$X^?*>f5D8{&Gh$C)kq?gcf6EE@0r;gR-pR)z{AYSG85`s@0aM*Z;x5@SfVZOm
z>)V>ks`rmy@x)0X@yLqxkxHMX2KUby@*+w=?i@`M0~>SqR(*BDwm8Mm6`LPYeOJNc
zK=km*e!>&yOlIE!aQfs~Xi_y^)g8dk1Q`@9;n9UAj`4TkJ+bm4g2Gnrzr*dyxSO0{
zCnsxy8o|GluTYDi(`TTXoTj&~MEhoig2E4CS!6EF&|d8&RvgMe#7Jk1U^X~llz0`^
zvC#QSjw;n4P#C27ATxy3Ipgg?5BE{{<qZ5cq28!QlmQ_whdJrIL1?y_YFSh0uHera
z&ltTdD#;g93V{Q`D#}pQRUgL6Zp;@Io*xgLuYczI@#dG8T)&Q_r74L+31$}G_s8Bd
z(NSi9%O@<}IKJDIuQmdJmhM+`7jH)~ES~2#eAKeKCFX0Go~6H5o;ysB0kv3GmPAJB
z#ZbZtN;Uh0(XN>5dKv%83bB(GlPo+`S(2JeG95V>;LBOFxzb(v0;F#r7eJP7YwR90
ztC6?dZfM--gC*&tG^$q0&z`pL)GN{(VN$1$Z<+XtOb<ZL&9T1$$~eBRHM1711vlA}
z;o9BJZmJI^GAYB)w5zgFY#}Iqtu>RX`JW9-Kv#4y#wamSCJ9Ccz2Q1nYZEBB{Vmh?
zkdm3Qq5j*4gZOD99^O-3ECqTncHxD*7=)y_P7BAArTc0%?|6>2!~(Nu7t_X*RuK4p
z{SCm-%_gYZJicvsw6!-blI%FUJA{lNDRai8NDDEh7MBv-idnY0cRSixOB|=KHa3O!
zp`b|1sK6g_Rfk!{i&>*td)xl0e)9KAK4qRB4M1upt+q7GctNcoDpGp0d;i`7Nf-DV
zHpwCy{g<$9MVINo)S*;IcegMmc5txadIwF;0F@;1?A?n-zt6}HHV~}`gyRBaIE}{_
zPq}}(H{729f9q^uu8A3S(2?R{_dI@!a1NsO+4{M4!_MQQb2L`VNS#p9i4K!;6dxLu
z(zn9;fJ8hXc~oXaQWRsXE26B~bKiIwgar60>R16-X6%4OTgw)m1ghG1yiQV|N(DT>
z+{5-p|KF}0i(J|@%JmH*!)iz~Fkb1|AxO1M$9tIM!O2B0WJ=M|z;{At`<r0+I6b)R
z1XEa4n*wSX_nfwzxu;KljeIc72tKGCm7n<yzLV34UEOHR+a6j}oTF^n;Ou+wjO4=R
z54CWs0^oo0aUfL!Uv;1cvziadkb9Q3%<5XAa`5%Otr!MllII;(y_c0;A=J73Ngx=2
z)&=3lF{T$Q)>>18=VnX7CKx7G)d@~hzl*Mkg;rKNBMp%--!l^58?R2{U%i!v*qEC?
zA}cE2El?1n!RwOPYQMr<vp55}4gmY1M0Q_*_ZoT>qv)2QBqAy0xNUFUFxoU}4LrE!
zo}Z&W0FOslyo`57d89_<oRh|G=i@XF&@p5?x?Y^4UQN$E3$gn90!XV~t<91vO=Ye0
zfM)LBFz+lQD@=oKhg{&v-%Qc|Rd?J=@zL16$@t9Rlv}EgF#J+crbmX8OR+$2B*sg&
z1rmR<Tf6|Yy*K$C5X$$tz25&Y$;mF-$tHveA;@Z^ss7me%Q^G`5J~ivQj`1kox=JE
z`<vl6-OqlsbxtmIKfolNW(5K8>e8R<C@4WG0}vK6w5arnB~<B%^i8Enj-1VsW!u*&
zwmuWPr|kMZ7f%v^Eb#@Pf~DN4gxjz~xgmeybo5APlmc|3>4>nsfQ(XrWf;@_k6((a
z`+f2b?KUk(uH&eov3}C`9n?7rdVba49hjw%CR3q&W6d{N_453n)lUb|;zHijCd7;?
z)8`JCdFjgYtgNz($KML@{^F=}06vlKo3o?33vfa!$56n{#WTyqet74C2GI)O!Nx*(
zng+cQ`93~bzHQb;B+^0damhfCh6jVTCnwk5Qc`@U#teK9);<9q-SlaB{FQ`!Q6j%k
zPEE2Tyk3!|(}K}9VnN=3ok=FRAGhdgod{XxwjYY`oVx)R&dJ}cn@MuYn|efB%Feue
zT(UK!P^f^SSa|#;u}ml07LP}6v|g}x<z;_FT#Aa34Ssy)dAP>sdl?$=Oi78BqeUA=
z@)E@)(M+IAi&&&ntp<rry*WLQam_<GhtRG(!vmmMe*JzAKjmy7Hz%KT8fekKU}HRe
zC7T4`NDsEwy<%*qa}JWm{>*pGgcvNGIW*00>u<R|&bV=Rm)64Vm6gjIQQhoemZ7yH
zwF(d3H(-W2$@13!dG^6fXZMO3;U(VN_w!>3`Mgj@9Lh!S^}*R}X}HNzlcDKW|4C5R
z<k1d9>QBx}3l=~nzJrZHjTaW86cQu<7!4tCG%e`U*KG^K5Dl~!N;S(cmJ-}#2ZkEN
zXCM~@7tg{H0~KsR%Okv^@KP!j`t#P?YEA9>DNxVs)Ku&IY}+`vefjauI22*@aor`&
z3GOXeI{eAWq<G+&!zI7cM712kfOPyUXmGsR4S_6Vve}o8M2Th?kB{yDstKN9qpk+~
zUPmzi-f>5u`xvrh1EgUN!3(l)oaCXXANK_n%fVB=cM*@A9DJiU9zk3G&cFTQO1UL@
zGY7H*KAo*Bhrk}5PCmmLptK??B?&-+rRWos$z%XRt2Vo4Eai9mf%G0>G?N5|$IoOE
zLQrtR6i2-#RlRX1FqEljlu=Nk-V&5@Dlo?$YT?#t+|AYo>D=7}$ibtf_s@j0k3zWP
z1}^0?W!u1T#A?gg^~?E_7f5ENIi!iBvHOHjx8uGqn%9BB1`HW}h_`eJN;|K!p{eUY
z2d<bZIIjWd%q=}UR;FSDF+y(jLL5kdLDbl9Fnv%PC!=}V(zd#?3tr@|SvnfQ`SGHA
z8ebBnQ4C?xA5!I9-N>PN!!6=)#RG0O1FF*>FzAPO2YhiCU%txjBlQbF!7A6}t9+5j
zKBzVO#mz<`PJ(&<%*R7DjiVQH;FF=Wu$cl0q=4MVvHy<e+W+KOVTYr3#mnHhg3w;?
zI<q>$_lW_la7w>Yu_u)ow7nLQgmOtF;()w`ObE0nm^hv)s<+^<bw7xW`$N<p(?(0S
z?Hl_WzWU?n)#Gj~VhcyBLYkS4x!`r>ssJ%roy>FV{C2@2H*haB&rE$0K{A?NL4)+i
zOL}i`vq3x8=F95(dDJt&(gS)8VsE6DLJ9jpmZK0^e3CHz@YnY{8@4tQnB7If#t0N?
zeh&#mQFrHF$T@J<G=igzu_uxuIEy7Wn*o1dwZ(S2rg?atCD5fXzvpB3eCOLpz>D}a
zJ_Cf<#SiwZr+=1f5ZY=w1^gC7Yv8-a6k)>I;18~zM<h9<F$FeEPQ9Al)S(iaN^hNW
zbuyTB$Ifj#(7b1m67L@yBMvAcMyEcfGDfQ{@^{8Uy^;QAz!^vgxANC(Rc}Jg_7lvD
z;mE935b6W<kr{by6px`0U=5}G&kKXAJWp0!ES>3X`qyum65uqou2|ku(4=t2(<s+9
zT*o8~LLc5GL3XPzu}QgyOlRqDuZLMgPc8y72@{*Dkhy=w68o|ZJP?Db(Mv7S8O2*S
z5fv!gR-kUDT~`&$avZl}YflV^OdziUNK{u(XF4{v*CEmb`6_BC9-Rt<i}00viSeqH
zxb7DTMN$^T7B&x|1&NeWt@nM*0EjWkv67Z8Y|jZ$Xb6#n7|(vp{<fXU-rqRHCTL>+
zd#_i9c0sw#pjPcr*3{?wHn?@@miHon*k9r&h+B8*`YaE6LaxvY>ErMEOtH>evtZVy
zk+CCUZz}~WyFYu+TQ)0Jj<n<zC1R5>X6-~5)9Xeap{dTnrCQ!_=)3~=x7s{b>c++R
zTNzr3G^!`%%_g4bMG^j^oY!heykfdTMT=}|F{#q+%K+_~-*67S{tiw91*dYhm*JHk
zIm8jQGJvklvDw^Q^32E^&Y{!CdLXm?a|BW}du~K3WSTVS?dg1x-n6Jj;Wu-e#hgY6
z2ELgIUsXWHDW0CVVwOFiH25`r73Yw6S#7D6Z0;QzmdO~pvUz^n0QzUJ)Z_a~;1hOg
za#J_WV5)}QNsx3X$5p2U<HxD853Vwc0KFb#|GR@EXjmO}QI1Zg&de&md(8n1e@zp0
z9?l|vF5hlpp6+6*Z#T!d397Am)v&zij+DmRGP9~ti>UZO`xiy3)i&(U4bn@%lg;{q
zPhiX1+PtzqsXhJ{z(IfexYar`>+x+3lVQ9_De%U)ahO&6(d0rA6zjZxCl+6v#&Kdy
zT^bQBJ6p%arb!YPAB|z>ZX6+PsSSvh&g|`)cH@&~5!#bKu4t=(qf_p-=j{c9ONlOS
ztwePQlYwD~Z%I15GLdut^uU>Yk!Jv`EC1Q+A>$}Dvwf*U{*ya+*U8?$;ee`m!|GPa
zLt>O=eI@UQ5Yix(?-K_BfT{?}oIE=^1d<#TEiI|#=)eo0)22`ITb|*`NdIJ3Ck#j3
z<>ce^7cfnjd6-1-y?=kS*M${cI)3;H^mXqcKVSJYPK<fr{4Tg-i=G1MNrn|!918(o
z9B8w1bZycU2=dVnly+VlKDo+!XEVs+zYd%Qm$9%Zlf$6qGYV$s2ulTBq@qP2*k}6m
zYuiVHVTm9_=XY9SI)#YIfbd8s=cXf)7z2VPzSC1pb@w1m5>>b3KCS9F*-!qi(cd`(
zR!@9BwJrgOT4$ATtM`wR<g4v{Cvy;6JRW|M6g@{jb>PM;W!|B}(THT6s{F}yAP!lS
z6Axq~8V)2kEvqkHyO!GF-&haNSSZ9!C*BQ!fz|fc`DM5Gkm*RR!J<6p^#_k!dX;lg
zLaTZ5v<I+Nb~Az7Nn@m0GvdPMJSyU!fxmN5jkA|c1`susFXv%-R!<)Je_3CHA2R;S
z@F0cAU)&9Ga&iU>t~djzEm5&$=l9sd-h$J1^VjRcHHJ6NVvN97VuJ6AGHZ`<)HDgS
zJX3i@U>ES)sAS-8O9I*iVC0_zgCDlIyjZ)qg%k&r#9w3?ph-ptI-_uwRdB#PKf*oD
z{m<a^AeWP~*(pl_#poQ><`DLuz+RKh)mP_{<ZqpCxtpM85B}8fz8>;w|M(0iTd=(h
z=*NJ{c6e`+wICN`sSSw3-f@7OK^XmPXPuB~dK=SouX*0@rkO1v$+4_IB2P?4#{e6T
z`UUVfdqP=hU8+f425Mh?Q=*zvK^cJd!3DXHZf;yC5;PCbD?0<e138&L%cl?jsnGhH
zdIv5QvZ<sxTdRjLn?3ymUYEq;mjA^ex(wGHy9xoiD+g4YHvm(rz;O$(5+eV-#P1my
zwqtX&5tv(rBg6U4Y#oKAZEmE*f&s8#`VrjDK0H)5O!ENIFu!VO8(I$Fj~>-Ro{j<V
ztS<q-S5{z>;xm$zajzejSo?Zop0;nPi}C|3PFb5@Aq*o`YU?+PHy%Dw9$pNSqmiVc
zj0I{){qS6aU_Oj)m?`L4sF}{%cyQKTDpk1!S|ONbI|xeD_jy+mxJB~LD4?M}z$MDB
zowKLp830W&Eww5-)+Jl&&q^eN`r&f%J<6bW<(9NQSHOg9P$=}PqJfDiWw-))qi_z+
z203U&XCFgb+A8ED`>QEo0|ccu!Y~YaH)Gqi0%-9yE~!<Lbq8TSn<a*gDEk6pZdMj3
z4PeZYncH(Dw}Q8ZrHSdAI0OYIr%dq$B4t+r2LnX4O)ND)H#`yf9KcD8*L;WZ%z@PF
zRXt(V9ax1U!o1?RdWXPo!|`9L%=86Qi3+ATs0d4#V4K3WK+5zZt4`)7A@yv7+?Gx4
zY5pJvYk+8!bKyDYw=s4i?oqXh`Ed|3AV#m)yQSNN3uZDxfoGTRYuVfOvW~<xVXT^|
zl7b>ILsAuJ6CD$Oxw8t37v7?7-ALvDHu{rqhCgDTLUU`gn2#tWkH2YhH<Po5M|)HL
zapoDAYnmiCjE^46WSEk>Nm3Rkc>ZuJgz~(#oDDHFzgu8-gqfO_shhiGR;P0Cu8;&l
zodh9ES0SV$y>)TWM+cfST+iGMNB}UX-~sUO%#bKHo(m@Y_+5KyWT^1wAV;Xx0+*$A
z;Ir-M5|9#&B@L8xFgQ6$N8&8*i_|n}*VtdbC!Opb79pBe^A#un<pQ23*Vi{M`!vAw
zz-JR<e2z8!&jM$!jWAlN8Ru(scB+9#^Teq`1na2Rht86S6dQ3N1Qt~s<>;hd!rJ?V
zBBXmaGq`3d+kOA2>-mEY7+16H3S{w;CfRMfdnC|Go(%gv)zzplbf&UW#pZK0oLb!s
zvl~i&0vO_-d7mIDb%Dq93?rKHnuRTiz0#f2-pPn{r*jRdRmXwg%n^m^`JbLQ@QZ$Y
zd3tDL!DU!1TWRC-T<_A$@IBs2QX-Wci?Ymk(hH5Rt?!gYqv&+7$DhXq?J~fyLb%T#
zE*(wTk?QaK`<T+NKXrcWEGYX8Kwjk8z4({)_97BsJC)LQAER{(jXDx5DL6DQhtoXH
zeB0lV)p@kv%-??mkP=JHd&h+V$H_j3^B)bM0_GjIzG^v9A0(6`T=e~uNL&}AMpS?@
zWY+!IGCXB@eKU&*iMO~D^NxP@O3Oc)i3srC2=c+b$?>`Vs#h_2jdS<&DXNV&^GI;B
z%ovvzPS%)Roj87lc)zL&9d~2f^~aRGNly4II5hv@zc-%IK;aIsVpMH?&BF6!mf>FB
zwl+Utr&NodUM8S@j6dKU+nAprA%ZU;^{^Ybk8l6meE+O&Lt1hGi5Q>Tr|?LoY`)^~
zZ}bzgJL_y)t@Yiaee7v9iP^tS4Cn7=SOpnE?PTw=En5lfsY757@hh^dtmxX<0f<WL
z;+;AR9~9`l;nBjz>FL7vO%<5c-FW#P{g6g+Rsp0${+!PI{o2XtWBw^cY38ptyXV(r
zZ9Jti$~FYR0`%uLhC`j7QliM*lYfJ-H-=@Q*ciLBn{imi-Ii=;yox?z@~`rlui5xF
zau|BR335eOa~E=@Up)H=m5_MN6iSi@J+QI+IjQLmoT>Fe31Q!_R596nv?t2MHSTqM
zUV8?~>VXgV>dF$A+xx=8sOO7HN=mn2Aq;R{D3K~K0<9jq_$E(Y4F{5<=vFs3`#<n8
z7CONkQ@FzsM&uFSJ}x>^j-NgQH4A3ojq>|B6TdEI13Uv2z<$=ZtF;Okkv)F&&s(J%
z{a*U&VXMtis>L;xNUrFr2-%dEvRi;e5ziU-hsK@TJ4eNAAPf7Y_M8;W60Ez+D6#zO
zJ~W@!v{A(&t-A*9RT4ln*2w~VAn`fOptn6#CLa_Mq)hq+F8#C}Cky}GnQb42z}*4~
zLfNHS+JvxCV#Q;?z_oxK>*NxDu4k1rIUb1Tc$J>DXHqv+(S!v&B3dnNM~)IjP{2Hc
zVsQMbNh$3V%fXM*W%_CxC06UoyqJ<aixv9QT3P@q!3!q_H6N&li&6+(H3RsqYY!gX
zJL>w&mx|Cmc%y^Ohv=Ad7=Rg2K=ZiK_KPfX!We$K-E0%H6uC)YzTgjNLcgw(G7vp0
zQLS?V&@kQ`r2en2E-F_N;D7<T%Xbk~rV#!sI&p1YX`O~~ER}{M(d;i-5SsTg%`7z%
zMIy|!3rg`SQp9QT)RKwC1I%}ja3(^;%EW07l?p`wVZr*b=#oIG2#9+rN!}I@>hR+j
z1H|fNo)3f0*tI*JcgYn8w=VwSvD^k*A>_-aM*4@f&J7L0|F|k#%vJ^N;C%BH%=BoW
z1NTVD9K5N<OcaL#in@u%1e(u)<vnit!Y3m}3y1b$%_?M5I4395aOe0t`nVy>@qEnV
z&pO7Tc_4wFN_|+?icm!aT|0Lf+aS~Y^7Yp<?zh*I#Hk`?8raU2<?m?XmPwHKJfXyZ
zN4@UinWVqSd=0lk9bZa>-<Gmy#yKl24W`-BDD^S<$J%AWhISd6eL7&p2J{g-8;@N-
zlApw6OY9kdwUpF>!d&4<qf2PeyE~A09l8)(&`-rRF$GZwFi3!7fnp@e##detM520L
z8+mFd)t;5&oEN3k<f>Aq88mA=Q5ZZrbg28$j3T;(NXf<CCM**Vf>WZ}6{%l5v2UoG
zq+v-wyuVJ8vM-q31*(p8vmyL;a*fiYGK{~?{N5f&XjYc@JU|R>{1K2vlJl;#;=2l3
z&qIg^s%_@}KFU#ECaPSu@SUayTbQS&vsX4Mz9RTz8ApP7{G)GF4A;KTH<*5507kZW
zZ2Z<+qQFib`}LUQdrph{10SXLmJzc(*!omOn(Ov5;46uYFiBE)R297?PL|?IUt0qU
zq!i_gVB}e9CJ)=Y3dWz{Vy2THPlpp!KBlLf!>}>x-0y^`#nBe0I&K#u$4vm)-qa!$
zfgHX4W0x*i-|SB&F4_2wE5_8F^iOyFz+HqwC9idhYx|Nu{Te-EAkE&++h^INS?nkZ
ztkY60di1p-11-$-U@9k+q&TH6%3PcvR{zgS9kT52{I(n^09~Vj_n7y_wG+7UIilWq
zxfn%f*8LldRUs;~+SB-1xBtb^0ajwfNQ7DGM$_aCnusxQ+sZxO2G_1>e%V#1^NY>n
z8W3`NzImY|&*JUj_YE!>q!zz51sZS;!2q4F&IwP~yij<TF^&q5mW!wWN2|Qi8*4H8
z3m{hW+@6Si4j?reCzz40uix~w+hx-$lToZY(l^iPrSQW}UfsO>KdG-%EvE?G?d{<d
zo*Z!CQndWkjsb_aCmgl>n7Y|yJh$l43y*!E0OF{?3#8K{I_U6pd#@OcUQWADlSw77
zzz6_EvYO@%M--Szo7Uo{2@y1JJSyFF)w&RR*0lig-BlY1xi>J&c#O_2k9#tP-DWoC
zaf>6`{+hA_A=-jbpKczO#KyLzt#i|$fM*-X4Ui-e|HIrL(mOPhGBufzw^=8bQ~pto
zsCH(J$osK7=Df(=HEY@A6+KNqq3D#Y8@p0q2TDt#Y5i?r)a?I}*jcAs=4R^-uaKEm
zd6#R$Acgwzca;uMG;q5PQ@_^`q<MdYGv16cMyr@YXk$`5t}o#c9O40~jEu=2>g>&}
zv&);x3~9*vR4;Z709YwIRN^<KBy@tz=VA*Z74)W@gV0Y7$zh%tSoB3kRr5g0J4PiE
z|8P>I3{8EpWh9Nfg!~M#krcSM&u6r_`<fcxXJEBYRXDOBUchF53;gXtBu|#|j$pkd
zj#|5UVSMuPRl2@N<-eH8;K5nt=7KsO43D5>%sl=cDVc;38jNh{&iB8tZ7JMCj{ob>
zM*a?sb7q}SscZ;@0;7~-2dEClC|sSn?R(Rgc7|~{phJFr{T;D@<zsxgP6DclZ5VB1
z_k9D$Xsn&qwrw2A`+9{LZ5r06m&A^fJ3e=U-zvAy^tl2OQHlt2S^%?lr;a0}6jkz)
zmV6=aI;>OP%~j?bE^u4)X>XGNU|qC}K$cu44-s-C<Z+S3<|dDNkTLY8EA(-zE9y!V
z>NB&dj9e0vjQ4rLlfMv#KZ7h@k=YRtQRp$JweQ&SsdS{uMfdP(?V7sqft6+%$@oz`
z!x#)Rn3Xk=wK0p=q@7vpCMiM*WRWCd`8A<M7F^uB*vGfHJhC~+59^wSar~VW``P7)
z7k;bUORDCmxG2nt=iXG_h3QvJD%4wjn4G{&8VFpcjyAq?k|t95HabD8bJ#n56`zLN
zcTI%XjHm967E&Y%ks3q`Qi<0<fEG`}nz$-Ocm3!<4GOdvYarG`#Bp)CeYGE9Xi)=B
zKou$SbyX#*6`1dV%+D%`*=y-jjoRDl#WDE`Z-7Rh&*#x_87x6=6@m|1(b&%#qK>wS
z=a`HOSHoBx>E4ds<s!o?F98F$7h`V4+M}}>q~-Q05cj*L+4=;^wu5KF8PEa)e-WO4
z+We`vBT+Qa^R%)iQ3eza|K4nUhi*KQ)Q^g}04?L3I}sPMj5JIIaJdPh!AqNWK-f>%
z>hq4PP)*C6%$k-57w0MbXT}CxZ`faBA{vwd6b;!hkxacpK#NVyEf8Mn>2?T6#sDlw
zH4`#+hA#1Y4`X@P+G~Qi<ZtH;{G|BFxYcwvI}gGiYyZxtsZ<>Hr7!tl-|uojedl#y
z!ymk|CV`6?5#zKrEx?S_PCe5+t>S%7$|6h=WOa7zb*sjw@$n@K1m>+>z@Vg;mc0+y
zVK;rc!#O_-6VnaH{R*qv{KOFcbn~#*nk+h1|6gLl5)0TrF$V7oLLXC>+5n@wye<9g
zvFAQ*g5dpeTQrcEzJGaJb7h#tb?ani8B}4K24FlUOfklot;v$qs)zGukU+k0{a5qz
zo%B-cf)!DcQMJzQxr+A|5iw8Cyje{QxrkaG3dLJS3uv1~-0XRwfg+9ikmaFjtlt%I
zOA!RM7LN)wc~MG=3X%)C`#NVO$zdojacb2#07mz|DeBJeh9f|7<t)m&+xLX~Y$MW*
zM~lu8(D+BgP8}KgmIAjIo-O)G4{Z6n!<00s?*6@ofQ|q}pgvz)uS{8}rI}-AG(qjf
zx3{NN;w79lovmN-5@D9<Pd5c?#;K&0&7Q!bxBTzk{&tRr8sw#BmNUJlMP6+|Jj(m%
zDJU?0*VewWUsJul4FolJRhV_Dug50#^Hxo;_OAD?BXf;;l_jVEw3rWvKym!aGxg!j
zQC}-Vne1mDl-X#n<SzDroqP<m1i76!@~KY;{?c8UB`f$dkHm1g0Fo>Y@Gmkb;-ZA7
zlQY6)Wm@Kak`>51Hds5%<_E^23m}nWipj)FIO%#)4`d)|!Zg#f+8}DR21`;Pq`HKs
zwnw)?3e7G=g`k8hQN@eQU43&4pha$AS1eQ-%{%j?slea67KG|c)FzCJ2bS&%oQG4v
zZ@ETLOgCO2Gg+jUR-EtlQoH&-e1t{I2ym=UB~ox|m0rH$Y7)dIv0Iw_f+{LATyd1}
zpKhRZ?j~@iKr|u3EK96>_1seJ#;J=RkPKY%Z7<4<lhJ>P|1oGM4w`g1BuO(8<L3UN
z&cPG{aT$T2J3nIagCd-*-F{@cCHZ*p^Nlfinp9D!%2@FhXq(2H5wOo}Oxf3QgA=t4
zkV0A^w|6*)`ha(xHp(5qXw<BNo5b%6<kr?;fq8ih;bjL7Dvk(cN~C3ldys&xzu*!B
z92tVRcY}N4l-!=m)hRkSORN^2{1KDv?w06&m`MhZlKq5{Za>|lGNP>2c)HHhYGtNm
z7P+)&uG;O?z|7l}k`13Qm@~4oe3Yp~$6>F72NH07au!@{O)MH36k7^@Fgs`YTW=`m
zx8oEh0@Rtnk1TtEc?clei{|-x@YiK_+eR3yJiA_Nu_W8o9PAgsLIq_03JAo2usd0b
z=E*%c^ih4Wt-EQ`p+cJ2RP9u!!tPhS*k~QWaZ*{Zh<a+FrqPA&qXPWvwhv}hKLtt}
zUd#IF%uT>7-+EgP5YETub|3Gg$kGly$4}ACC}@J|BFx8usC0e>oWf?sDgsLo?rQ+D
zuia3B0SY+mvS>2k`8UlOH7As7>1?d{w2CmLM}bek)--Ev4X=~Zuv*8YS;u6NW>*V{
z=Z~>J6c%1Q1NmUUZoIG7AX;!`h{MfN^yOzUc`g1d{bk4}YOWA1esQ*=IYi-I6<`xX
zRpv;gM?Zd9ai(l42$wkyB6{$;Y@>O?hY(&WYh^dgte?HOyBy=rGW?_fGzEilaRPyu
z$@cBg4<M8Umk%Yqlvb0>$)ZY7UhGOhk~sE7ewWk~X=4k&;b+?!WLilP_9`_gbj8Jl
zt7@p#TDoBeD=Ylk%&6uf-}G-J{}rW0e5vRtg5iO(eeeQ&p^A!5h8_|?ymOMR<+}zb
zBtG_@L1MPQ^DH!iv#T@{#BG&Im`Oeus%&q77+EK$VX;c?K@vcS8eIeaeEeXr$wl4l
z<CB4Nz?t@%)!*-_?L$DWp{*<oquInK@+jax9#DTh967m^PDlOJ?FD%^0WcF)s5eMG
zX1zp7rBR4L_!uyUX)bm}u1myC9E?f)A^D2l{dB6R2jZA+TGMXy<d2feNz)3Gnmzb4
z8>V<H)pFF(xxQQT?=SPgKal4?Jd@$%Eq9}w1b$mR+c6xpPVcK7z(5{%UW`>Ag6lAn
zrWq|F1yiL~5UWNrIrNKNr~^kU45w}`*oZYx^Fn4~%5FGTcuSUj)W)Uf(&zjL9>0?&
zkz*<2Ufg%T3KmV_6O6!T#4BfSl22%-n;GuRwuhsR-AAvlJ`L>2RU}9g=TvtS^PVpI
z%ik0xN@i4o4w}dZy~6+Cjn!UZ2;$yo6TFcf;Z!^+4y3)@8pNhG?p-D<{JUMLVRDDu
z9c+fD9p9$W_jFLkPC+tK&w7IHm7oSQTzJOUA6)-k<^8w!%yGh>D|KD)n;IeqZ)1G)
z7NW;v`-DHu2Y@|#NMHd78kI1#WEUuPDdLsw0)=&~aH&~`r%4iq+lwIBw{ciozFYS5
z-OXGW!C9#rSkD;LG1Ayd6RrT1pBJc$zTJ$hlYTluu1grLe{_x<Dqa*hEVPk&$HDVn
zrn^Y;XySEjS#rk-v#txMF{luXs$&UtGPhI_zIQ{Ao%YVr$!GRes|MYh`wUY$GRdAc
zjjah*#Ao%%T-Sd#5xVWn35JJ*pErZXbt>4N_a3KjqY$UajH?Ea&fDWVKoZzvoH9Qg
z-iAtYO5*LC*Q+6_E0?%>>Zb_0T(JQHH^3#_MioKULsGnYxb8QxFFt~FGwk)f?bsUl
z!%C|Qo<sHRNHkO!<vgducv=kuM;={SZ55QlpnB3kyc@)gz6(pNFo4!Eg*WXGvL*tk
z>Y^jno`MpFpJssrtAg!mUik?4M@;2@eq|0;r%N7fn^^f#&<59YyPklHgCo=>?29GB
zbTvU|?_nRbL_hs^+Ej?~RS`u@3GmVv1S;rQxM*D6KOy?QA~LZ$+wnWA_Fbm*;$za^
z9FV+@uC&m%5@1(fgFFv3Kh}Dl_)Ajaug(@=)t`2XRtDzE<gdkUhMeP&ROgF$dp_n^
zO2hmA?YMpf8f5$hCJY#q%>tlOu^9@`tNz>&TdO?+NA(?LG?Q~wfUs$|n;U^XpS}6G
zaU0HU^PrzpSkLo4Q@8hDlq10FZ_%X5v$X^KBK8f)`+rPqNf?iEH*=dEC3?PSlqJeu
zA2WL8S@aJ!F}68ff8<dyICNsdI1Yy%jxob_Z*2h^z5GQ+cfl%4a=bDujgF4)5yQ03
z06eij<*Jvht8OQw$QR%SE;fAt`pDYfWOs&_mX@&AUP_}h;bP~W_=z}WMg5A=`ymBQ
zv~5X&aJO2dNnf+1Ve9(bH(2rZa9}y=brI|-BNb{g;lwmu)AI&*_dq^g#lFSkYr1w+
za}-k9(&6=bKIqwwuPSQzPa#a6U>RJ~eT}xF8?;M*`MD!-H-;*Zcm_U6YAa=?J}U4J
zs+Am^^rmc|jG-mB4chj@_%pU(%@)=sUU|6z6ehjtNHN`*Xh@{BQ5tu9G4YFo_q42+
zT=+LgRn=G&UI4I|fA+N;G7tj03jd;6x?uw>shP@AcnJM@Iwvzv$BPk!sY>bPVgeF(
z0I%C_uMX()(s(lr-1!UU$~DXmItvH>-jkQREavr{$b<4DR{480mRdd}RWmra$X#Md
zBXaArK7&sO!I(wQm_T>)T=za<BApuU;jQEp6B~H{h8V~EJ0p5CrW#p{M&hz&{Yfy^
zjf(nw@`t9QxVyc1I-=z`Yd}cGOiRQoIJjLr&M4Oj^}Sw8FrPQhAp@}`2AWlrs3613
z{q2)&1{JrT{NxofufX#iIFL}04Wyj5-8M!l4hvpRk1nQMF6X~SzX&Gi`IanC%>F}K
zxp->RA&!AyW4c=^ZeBV}sBZOS&f%Suk~;iln%%Fg0<%2aI6ZNmDwxGW%mHg|EpsAy
zp6ah^_;T>j!UOl!&pDln1&cO(*(Cy%=0e$kMpNeGaXTlc&@>;({fmB$!bGR{-@kyI
zLKC$ih-)b(zPExgJVBrjM+lghmR_9^h)W5Rp04rfI6WK(LL)uA1->Y*oI3K73e`4Y
z#(^2pY%76D_HQE0a{JJ)4&hZ+RHgEbq63e>cZCF%9utT9SmXNCqY;UqG9&yWdOseV
z@R}sGjB!ggf66)msQl8aZ?vel#s73gm52)hYgLnc%m;?rRM2U4Npk9Kq<KqZ15S*x
z8Sqx7W!gqg29rdf&tBXNnfVu0(Y2Rq*`rHh_l}Q|AcMynbz&MV=58)4-x^t?99DPQ
z`1ba#BZ|y2qOay3zOEBWSV`=<37n>-2Ul4Z$|lTu1=sIg-~XW$7Z0(A+sj73!I`e}
z8rvQ0QkF2F%{iF+mDGGS{};s{&IBdBs5~`Yifd2dW8|x}O$@wrJn9|^XYgzfJ`XLM
zcB76jQfjlJ5`Ww@Q~bD{gF|8f*c5lZ^Gv7iz@xIcT}P_|9<9&^4S7(qH;X_lAU9J(
z%4Dlw@M3EzJs(bG_|rin3*i7q?M+uoCRz?xZAfCCy?xVIQ4==aGy$d5XE<3h<8+fs
zQfD7|Ah1@(#HvaZT41f3VO<KFla4DI?`Glh{yX|;@B2>ghnet+WjS_mb$k<DFf#%f
z#URW49xf*J4(1R=|E(!T3_^z$7+97_$L(XsZhkV0-8+wPfBbt159+PBo)jf$?vI1{
z^CB%Ex_mTmH+Zt(K?6n~iwoP7$yRo$*#yLa1}3E99eX?OpB2%z^uMfL5at2oIP1Kz
zjH~H<OX_eBU1O@>UGqtJL}<Qdx14%j{~(4nPN!&As&QtloXXUB{tJ0eR?nBZ0@u3Z
z5lpR|%8kKcoY#6X^2|csgN34T9qWbT;67tnYHHGeD&c1$eo%7^gDfuLPu|>;C^-9f
z#L%J`qzv`k0CPV^t*_6=(4rDh8GLEPHfTzZy2+k&t9cv>gXg<90Z3nT6;TJn6_B9%
zId9-)Exw<U{N43RRS*%%{`j+RsFdFKe8_D>LKs;vT#q;#DAd>ZJT^d-O&jGv31W4d
zTtu5|7u4dg2VZyloAHk#5ue03sbUq5ZsIn&9>Fsb+JDd4IwX#*Is<}{aHeyOd^sSH
zcXq{@^HfzOlfEq(s>RkBDlUxXIH`4d<o+BkK9*5?>QCYvGSl_!LZyW>Ynl?gzsV7q
znb^iIT~p@l;0lZyW_??fQ8VVh5W)2pLk?KkS=rkM-pc0{XiR^2Vq(@A3s2fIgml=m
z$ouH>Wa|<Kyyp^eT5Uw3V5l+(J9+$Seo^nS2)lZ31qhrZWVe^cH_4L2az#fW%))<}
z3m%1p9naL$GOXSlfEC`=P;yX0%R;L;Ujxt9!7yB832hBEk;OUj=4iEWT(@^%h4tIt
zxgrnU^wzwKCC(!>;l#Jw2G7eczOUX0Pb_7;Wg|_folPtN4?m*BNT~z4=&0n)Shq!V
zB-~B^1Zg;NYr9^_F=?PSl4uLM+;V$xw*Axn2cHZEY^S%iUy@o#lgrQC)_XA0?4!Vx
zCi%BvGt!iU=M(5+X?ML%js=hl^uX5}KLISA3`xn$!@F2Y?}WQ-`IXK_*YHM*+8U*O
zdHJlLZ3|{~vqKjtsoL$?v8TnO-Fdrs^E04d14_H!h~(uW9e_P9G0)M)J*uUeu6D+J
z_71h4J*S?sSgEtsHU8`Wp3e;J<u=p-TQDfcFZ@xP7d7Idq*6OL$fK#0;WxJJL3rTY
z#fuI0*qUR~@Noz3!J-A~EpBhW1G9`EF%(L&I1}20IIHv<ujHC6&IuEyVc>{QKASsk
zOVygwFAr~})BI(QExf|YFd@U3DTydml9GPWoz5)-<s1*wTxlBLL<^*U<sxHhTXgo7
zUrU(SE>I00>m$S?bcJq)(ZY!tWuuH{`|M?~qv(^%5=K`wI525Kn8`x{$2DoPq{Urm
z7MbO8<-L|Go%3d|s~%`NZG61-V=>`9B|CFxkm4^RcRZMpH8~l_i5tHf$Ik8_V*$xC
zo^-|>Yf#TS>@?~VvZ2%2Sj?y3F~n?2y5IH`Ef<MZRk<{-kE=KDu?I!pyQ*V~E6~Cb
zg7c6?<0<3KS1$v05<clFx)<~Isc=sN<>%Wa;H=ov*b{QRsLPOxDXNz#bbPz*PM9zW
zmnpg{Y=UISLFy;8_C@duCT34a5Ns4fQ&&ukS;R1xZx^tThtZzrRMp+x(s$2c+$`e7
z7avfXgZ(PEq{g|XaUf7Ff;6aOq56D(tcS3F1v=ig5BvnI+;OmH>S*%Q1+1-Od-nv7
z<z39=L)jyGsITRgGA>Qz_1H)@UBWhvOM018cKO-{*@bPt1pB1#14p+I5?NrRG3Mib
zNKpm#zZG>*3<i05a$?@2v|9_vl#w;5)95Ct0P_2$wGSGFX?PtjB{sUK;6;ePhDW?f
zPP0wT;+$&Izj=AD9}G~?yQBhyKgqg(?LE^5B~C`X7DM%$Cm2x@5vnQ$M>oI|2#Z3=
zMZ!1K=<MG?KH9vt+Cu88GO|VGO^9a%cKY?auP3}sgn^$FMXL3StEpkIRCn$|9&hKm
zsn!XpB<05DP~)|fAuQ(4QwS^8(m$uB4;>+19R#I8e{4$2gY4GmbV-WN_LW`L%n(fH
z(3IFwgK&K?;nCvk_(H{0(dLT%iYx=_FY3I4{~a-STVJndQysL(VEquvEu)r~iF9x?
z36;OfArIZ_PG`e^x+SwUL((a#fT05S&crKpqCdjXTw1K|P{UADRSk%oTEHB#eq#Ga
zeYeqa5_l#-Jf{_8_)00fxFdU!Mu~;ipqZWi#;TYYn}_3Ffb>NbDzSTOtLu9&uawnO
zicKjJ$k8Ae!;Jj-Wquec-_1^@9I3QiXqA!C85mmEtj<IMk+a$pQc^PX{G2e1-`W*i
zyo>27zp$xK#iTi6@9-;<F`UC2gfk{CEQ=O^<C88gALVG`6k3A|#G@X4=r+W3sdEX~
zRSk=E_Jg_-Mtycg+}n0E+i%QNb<{Oi+oM-nFqX5JE_Z!ur71sBg#bb`P(y}Xg+TZO
zUWLHL>?`~+`Lu<=`^%@M#;BFw{4qaN?s(5u*?Z~St#W|}n7HPax~`(ub>pk53M@&h
z#mfX!<RT^PwMF}lPv9Aa1<13@KqR=UPll~o@2TbN$Gsiz4mWc8O=!}Ro3%`;@Y)Lr
z2R2mD2M?d8H=wjtm6>GmM3Ik!#mIl6LLjdS!=$eaibIM*F$aegLn)<C6`3U^ni0nR
z@lHv;+8N#v7lXqLmy%)u+@~S8!snxCTzZ&!08nQ#OKMGdCXrdl9Ez6kyHO$BtcpV7
zAG)zYad_!@Ce<kLGm#1rr?$S~<b}e6N2}uXG7?9J#P{uRq*g_Ng$oDSixR`38w#a|
zW~Q<UtRKzAcOv#^!ipBp^v*rv;75Mu!Tc}#lW5=O&1jPjMC=m-+F-u1G?BIKn}2r)
z%jvD<eSh_yqbWLric8dM)<Fb?kE9;{PV`s@QXfDH%iC8E+5bf8!*4Yg$}d0MZ_ctL
z7s_7SIjM}|!z>6-!WEqu`pQmbubDrB;3wSA`HZ(s_S(F{bxA9$hS++nty#J)e82}R
zD?5_ik!Z37r#!z5QdwQ(hmZ_oBe%<0(q$-DzN^Wnp;9r-g|W`%hq&HlSN#XmUOS71
zDtZiMQ%M>T78aWyRPKx^8Iv0xb9L`S!U!MVwzCns=NW|LpJ@&6B|v~~B|OaTbo*%M
zYg$<d=fMMujI*1XXc)`9eDmst(b0;^-_18gj}Ik?G*{~C{@xU!)6qWlM<z|JVR+Xo
zO8@BqBQ0Gn5ep;3va`ttUUx+Y8)XO?Xd~?3UpQ+N=P6Ebz3rDo$4jPZEFMb!8yagl
z3IayFB~XyhvZ9M3izv!e958d}8+%m>P&?ZO1Pp&hX<gSk(khwqT=>?WC(m&IJhx2r
z*ChOWT5Xxqqx7|F03^jR8x-yWX<<fgOa?Qrg(0h+wgMVBbwF*wFwjDj>%Ii4pQ2NZ
z=BX{v8}DTAfoDX@Q{NoAo_3mP-dgL`{UW3vF@)*(j)r~UbkyY@OTjB<^L#0f9y^i3
zz=K~>B7U6{^q#W{Sx9v>A%4Q}YQq6E&>rX1!`zuZn!dxhJ8Jz?xyx6a?F@=m2qY}X
z*oVugG`zW7CH^*l*kJ5Qb&d)B@g#`+MS9_BuuFahPDd_z_~~+&th>i4h^>W1<Bvxo
zqe@gtNQrwj^QgQGKDn)itIBZ-Z3r|)PeGC9*#>^a1p*`u8LMa>4n(KBb#{<g#8C+a
zWsy>jgo6b}$MT?fh+OMfx@#Om^qX+~3ls;2#$!J>&7~$k%YBdO2)EPtSzYAy?holM
zMDt*2v`Ib!OCe+fb*JtKU9ZmTn@f8a`>j}%enN76I{_#Je0*c)BFP$@Tnnk)EJ_2`
zqyth^&h)xb8m2@hbQ<u!u8=VM_A^nFS;|$9Gcs5r(!h3Lwu=OJl|`mtwn**D!PF&6
zXK|<*9s(&CIhz1^I9_Je$cfc;YxB2~)afL?<pMiFwsx;%nh9<M@V%cn@gAm}o~O|!
zxZqccDF0muhTZt?+h&*T7^Rx*A-mWmM=Y4aGz?piNE;F;g(kv$_*l~&gAp`gBE_qS
z+hNQo9e)T{u=fp(EbiYCEP^4qkYeI1zj%k67g6A`K3%MmvmBZ@m9|ATUivP06=l4O
z9RtUb_Cbr)+cu%ztt6Mw&MBZyCArMWZ$~BFI0!lT92iNP-DwC<{=(x9Z(~K1jIZQ!
z;$e$A2#-c4OsiW6H?pcPfQ|#RA9MJ!WnNNU8p*@e&FJ&{Ya8=bHADR$Ylr5#v0pW^
zG}riH*fO7*ixU=QVTvb1vxt6btx2W-BPB_WH`_KWr&d1UMU_Jk%%9jA>o`mB$GMX1
z*a|_LM4MJ4cenM9JJ5>&K7wC*DO18Qe6#35m4<a3%0~Ll1LoA=gd(Qk3tFrVk*@JO
z8e0vxk~yAVxFGGSyT$b{sBN@9Xg3?M>fei8x43-Mz+hAU6!+`fCEar)3<7!DNB%-|
z+5&2B!}GmiJf}giTqLQO@V1<MF7U!%OE-HQDiWcS0;nX(BX=3Hs60+Ldsv2Fb*I_J
zgM88qm5y!ie9SLU7FGU5hYEp1;hxDwn~<%F0To$2#aOiQvmug}!kk)ZdMX8Y)pdV7
zbJ!lg*!<b{x?`|wWVWahTEqk^;BS3O77yZ#zVZBQGd=A1wV&{2NQDi3jfqJHZ+_AB
zNCtSIy^T^7-k1Us<0-?T1E8j1Yn8v37c;VElED~fHnveE7MXK%rb~)(KtlMDGL^_$
za8I#&&-OFsAAQfv(Ut8aZk$Z`Ek!h$#|L(5=dZA&<LBj*FH0S=r$rMrIHoR6bK`N-
z>m8A}?B+u+3jEatUN?$r0kw*;TPxCX^4dFPnynqoEvN?5tU!{ZefBWy)hX%Ananb*
z)-Jj10P?#7OnSIVcb@nCg>XtlY1`d(?9%hDWzV|gnd`a<*+EEX<4daAavnSva${!m
z?SfOSo?L=MjQ01Q@_8MOuqcQzjW#wF@SmtQ1W?zUFW2!^@?z(l>f0qB=`WB3#5g1^
z2&^?PhHh}mhq7hjfG1O7D3V9By0P5bG*@7TI21J}nY33FXrMM#%bQw@nm?2Y1WJs6
z_w`L<CoD>-MOg;(yn-mC_keB;;NA-=D_?`L@KBJzLK(#Cyyi7j8T^BY6bK733uAFc
zhE|_3H81{6R*_N@L3Dh_%|4Kb2V8W>Z4Ww^f?|5|VgImtqTe`q^*b9Tf7zNI>In;1
zh8uH7N7*X$H+)pp<qEb6iTv1pUvmLYwW?ohmzJMc^WtYG{bFXoLXm}lUrQ*Kg)aDl
zb%SwR$e54ny{pgn)CE{`m4-HJAHwMViDta_#%uKKFR`Oe_@HP?O)7e}CFots8;#rc
zK<4fXHjkyV24DEi^$^bXzS^vvusKQwIN3Uow%Oe1)`EiXS52_dh*SbgCEfcZd(V;#
zO8(UxM^z&aaJL(T7uKpC#%Z_%`m7^b<Td)b-4q1<8HQ!t7IcbW8`rqu*(gDnXL^3F
zSS1umuImR+6^V?Y=BpZAtEhJ0DAPx{<n+M^?ZyCA+^R@om3BjTVM#^C$J#^PLey&H
zaU_rpNubc|dPF`IX1FkB$9?|yicK!9J`}-q(}j-TI8C8ZNEQ;ThV_TpCCC$~Lww~Q
zra~vgrjdDtc9c8Ay4*Y1z#hHY$1J%1-{MlU^@k9zuxqiZi&8lt48Lwh#%@#wphB`6
z&u8{~ZFs}+l#x&Y`@s0jg8B0~oAxKY*u+5`>=pljtmct@YZY111vJ)o57o_p_(-L(
zZd)s6IpOs!_PuVz-2j`PG$M-e`_<*z4EwrUj}Ho|y0^|49RI({9Dn}M)VH?3IQ1~X
zrQNw5Od4=&`}Z%(r(cOpMpcwBv~VEm%Q_`tC<$C%zOAEO{B&_DKF#gKtfW$Mw1rjo
zJxp5^GqEJOvHk6+MY4K&rMk8gH-891^z|<6>(h3C`)QQTKR<ilEKRh*w-r}@5mgA^
zv!B@q53V(}&70)WWD6cCk8%ulyCV=ua{=y_z#fnI6SV!lO8hgO#>>o&K>QZ`-!<m_
zVEpazNU!67B^(LZ`;QzfqgoaZ-As>nN{O6AcL*|{-~@54D@4@Lzo;sXfXt<?;79&S
zj{W<4kh5lz?L(1T9$bKf=?Y!ZhH*Zg{4|~YaogMaWHW<iD*o7miu9WvO)hzeOA+&c
zW-sJ85I?K;NX9z}*oNEWvWoOFlCSF4EoaZR#`O|QO$#{1)KygSNV~Js#l$$M(h#t~
zCbUVWr2oAPeVa22D}O<sBxELtTO8t&+%PqIW3KWm4K=j(dEUP%|CZXVdUBJ^RDqCB
z8v3t}ph1PS_=ZonwFiD-uIOTq*dPa9RlUX=7i7&)-dhVALxD>9FmZ7H=;*SfJ~kGU
z14?YS!9fKXh0Y0aD#4L9Ojbo@%LrWaW+PGsG-JO7mJ%<pPC=C6X5m}BFDQa&JGKq$
z+V}9_EV_P97wmF{*17VV%a<=;m+wtI+w-u(mwywP(31Y0HGm{B#YNUCXHkgVtNCrb
zL;ZV|SoN^7cY^XPd<+kvvAcndj!RYBX!4@=k9FO$^(+E!xn9cVHg;FHc^))+(-lGI
ztUlrz7IW~Z8})c<g7L(t1EY4|EWA>Bbe_4S);XVy0)hz*a2f7o<(=GUw^l_?4R=`z
zB9v7GE}P9q^LBiz-P5yiL<sQeoK3AS0;JcrxbDaxn5)tFeg)P0kFM?rd4x{J-CM0B
zkk=KQ?`_|Tc)h&x{1ZjbUyfyEYTo#FZzZBQN+DBT=XhWdyVUlJoMJf*?gp%0p^hVc
zi=u$hzoKA~UhIr$3_w@&_z5M8Azl$XC$;=5+n;IlWQgN>k6s?#C#;g+pO_U*1<AkU
zzGpCL3en=*IPUm6E&3T@`HVs!0u)eZ1;-1aejo3e2hKl=h@Q|q&Qc-qjo=a|v|$~c
zirbAl^`{iy_bD)ckbscbJBROG1uq}lUxj7{<I(;DRk<Gbw3cqy=%i<Anme{#etY&2
za^!adN?B94`jP!^!)V@ykc1p=2}8;b621Gb>gipbB$>q_xin6!vu+5c3$vJogYRwr
z0j4LMX<2v4nH}|F4YLQ=VUkYoi$^+LtHp{J3b<oN>Da|h9WzZ4lgngizUPE?xGaiP
z!Ap?MN@IefmEH~K+CmI4=HKbn*Vr1n`#<Fd3eR?Slql2-p(@)x9J}+kH@AVA;j_Gk
z$g`S5jU_7%;wM)zgT+>FW?7R4i@vw##m_}S%6a|m{Itf7N&S=2$y$I^R59`>1Tk@<
z(@&#6$t8)cWzvm$IBy+^BHZ{~5`$|^W963R%g7mf@-Kx)&o#BKb(%mV9?V30Uxh$_
zfw}J0Le;aGUrtyV)r`$0k!I#Gv?^liC`}u~SU8WC%wh70bZH|4ET~E*%W^F7V+wa3
ztR8$*x_SooK3PRY<Szn!l(T5x#+lttU_&I<el(XOe!-Pe3(rq`!*X=cC{HdGCD@@Z
zN<=p7ltWX8&L_)n^%LleF-yn^I!?La*P|&3vs18o@xk3FGzgY3i4VWnFZIxEHx!tE
zyxv7(fZ?E$N&0wR6ais1<%C+6Qd>;+&N*4BmKYRCSbYBmCbwPY^mg8sqmFEWRaI=R
zlJWWzi}FT!>IriiXfG0qsiCwUrGO@+P>(OS6&E`~UuBRc*E&?{jjOxT#;+|UDI<dP
zsNp!BupmByZTwYKM~uUsHNZcO@-)3$nr)-t)a68szp9T78`-ARDy~#WP%xK<I=GzN
zq{Sj(4sJ{>y#7F;9(PEYi&b=Ym`=s;GxuXXltC%=_tRwPnMdFq&7dc_9%00xn1z1}
zmxIw>f;^pg^*e^#0ZKz?QbXMNzg~+x8{+li((~V;hhwnA(z%XfDollfA0%&M3NC^L
z3@8!OYmq21%LC|XNtq>?D00zhkw*=3b({*w4bM>|dq8rEf~BRH=HWraDl&t8Djcv_
zDyrfb?BNPbXpm>cOW&}|8BvrJnG}n{%FHgyCN$$GyxV=QN2<k%280!lhU@`8N2af9
z^2(ibrq3CS`V{^DkaU(oaW&l*4haOe0KwfQ$Utxj?(QBeI0Sciad-D%g9UeYcXxMp
z8T6ifw~C)LHB-as?!EVV)@mhv%c-JzjB5o|g;|PG`Y1{R{Y2bA^mc5t&!j+6$gR8I
z87i3oi`0bVA0k#Zvr*x<j*7ju2!`IKp@JjJW$t%IGG;h(@?z5!ol!wj?s*W#tCRcE
zOAFnMo?A3TR&(%~L~^}?8uH1Pm}<D2bE=nKXtn-t%iLjA`)WSVj$z93k2YG&*o-`H
z)x1_gyV;Yc0KotQi=q<0650Sk$JdN|;$*d99D<YblB@Xt4Jwhs$WpS3S7%Hq6z-aJ
zY|3uNATtq#_Lxu5qw6xE#kXrS&_G`DlAYU4&yw~aHz{;BcT;lc7H^NRrlYLMy;kDY
z6mOK#mw~vx0&btXwwl)KX(+Lviwyz0PtE0V)kuH_IOECL;45MeZWp4yeZ0NY<7cgo
z-sw~PQ2lg9h3)5;8Uyvc<DnA@MLY9k0D0rRza_)%neJetrGMdVoZj<nL6213ag#;)
z(sT7sDP41keLi#R(ZiTl@I`y!<#IIMZF^1q(RWhlz#OFaqxUDoU1=BjM332+0M|G3
z7c(e<X70x_{4B9QqyeI!Ri76uzN8X^Vm$c-qG^QJue$?kuU%_j<=LMic-m}vE}D`b
z)*jb`Lp7w9eS`CGfvVK}k<kWod(D6Q(m-%H23P<E^ZIrLH=o);Ptk+8Jn6A`eMDtH
zV>#yExq|Hl1m_n$zb&Ull^vm4cNJi>YdkQ<&IeV_64a;d<>??Xt6)hhLpW^PCNvmF
zHoV>_@|KX4q+XaQBKVuy(^^~;B&O%bo+U`y^;6QGVi{<xV?qp8g@@531ImpRnSa1h
zTpLNyA+YrwQ!`qcb&Du}L5xj76F9dkha3PET~J(ixOOjyBrp2Q$N*D<Y|JP!^4*kf
zbPUaa3!WY3jJY$U?R`U^#lt(*5<3aD0zipnkVn`jWeI61eTk>7TcGtMfOgucV5rIE
zSJUm*$LFX>*4ON43X4|QlxS%0!6$pbb~wof<NJd{#ZmZEoW0owqWO1s#}!5lk6~!R
z!EUQW8AiZMm@sVKnl<rcAD&=@BJ#aC7Pu9Gi`GuQKo-P>-!pqy%jZWzcKIbX0$hr;
z0uemAjw~vxOUc$Xb=QZPVV`7+^qdl$!TKoB`yl*LKu9&g*IFoVK4<P!k)fc<%3o!<
z_YB6>=10R0mC1VNpa|63B+&@ufYBKRkgXZ(VW5CQgS^QA<scZhzDDxP75f}iFgW-(
zgMWwn&d0JS>4CeUe3`H&%nIJR<l-qZC8=fW<it6u14agGJVTiXY)B{*VWEa&<tS{t
z79vzrgzN(HV~=gyK=8p=O>NtoXP+lV158$(p+6_6-j)&+XOrYfEJkuRD|!;40-poy
zUOJ_Qp0vUtBc-FdI)XE*{O>mtHrIom3?$E#En?Nflti(hs{t&q_3zy!To43PJZs5+
z;Z8%_>hk_!eEP(l*y-jR&Ns@0peN=zWRJC>l}<r10k($jG5=@V^8Q^z`Q*`)tKN^i
zC2}~j7n1FQgL@ErlIetTYH7`hPIL2c9R$xen<iIW+&)1XH_O`sL3klX>G~Yj;qPCz
zCU$+oTj{00V~Y}5>UyiuXnxEQkj);qB=z*sG2msnCv-b`Zue(|h8J1JETvi}m*dY1
z8d^4!=dQ-n^PK}ny;F8U!?<GN*Qj0}N=gypk9hytmz|3|7=udeYnes5YKbwlp0;Rh
zzV}g-Mqdd*eB`u<-D#d1G1&b+Qz=jUp{0r&6_@%(Kul;zk-lH3gDSm{GJGI`JA`wP
zoW(CV1#zWca=CK-p^gRI8R31EisAXxnFSP0qHsZ=Xzy6&I6l9|KKloc4`$thaLBqt
z3ia8dA@cLxcGMb1b9}+&i=6JEp|h-in-9!jMtXVk!}8u1#lK*Tc%V)xVFq4#MrHFl
z#~2w!pL11qC@o)EXL(%UCCfAY-ty;KjgoIq*xxNgWdW%gTD-%7%kt7CVG<~4Bb`0?
z^%f3>mqg2THTFlf)iregqKl$ec<<<<WTY7HU-~n>)UPlK;!G7Wg4mJ{HmmIBlhS8P
z3CG(7#M=)Q{u&=T^XAe}g&E4Vd0{nRUn=W&@UL3~>t>l~Obd2|o!L6GGyJy)|4FH=
z98gIOOJp^8yF#g|4(?j*o0gh24<C46a|Y$)Su4&Hh{x3>eg!J5WvO^<euohIj?<R<
z`Tgl7(dz;>skV`APb^W2<37Z~uQ)^#4v)Ri7cYloC-mRCNxG|@P7@?s_TuO{Bjhh$
z9@@eOVE-+c^N?O6rd<3d;K<hky7|zHSRtkE20{(69F>WoHn%}ag7^~H*BZ~505MN~
zv&rVi1oCBDjLk&PL;PIpRn^BCWl7W9&UhJ8ny&=LWj)*WpB9i~B$Cw9jHju35*ff%
zto|8|`s}7OS^_jX=WyF03Syr+YGDNn_o{!pB_a}!8Z3oIWDQuoB#kd&236m3^QZdx
z=h7|6^14**OgbhGYY@#$(?;(d)$x^QY3~9*|K)2i>*g9QT+W~3z367#=<n=<?al)`
zqmY7KmnviHHrbjvqqb#(_jOVP7+3)~O<h~NqiZ^P%QC^EXyO3JW+HLa=$w#V1S6aF
z{yEE&zkk^=qJ>qv?u0W`az_^{!yCC9#)mD!_YyzbA*F#QPawuM>=;Hc0c2)%y5ssf
zV6}^BhffGin0yO`>xUqnp}6WuS-o~t#1e(izRF2pBftf47L(aOPc$CZoDfHH{$=Pt
zi6<non1CM`RL$E~N~c!Pe_R#AZ8Rv86g!ONx|C|XzL$4Kw@7?>FAs^)`0PdL=SLM+
z-Ha?yrV$h{O&!5!h#NZ}%$%TICY>J<8hV+_9*0A_;~kFa*e8VbIn5BM{%C-Y?1<dN
zvB!=!MXI^Ob_&%#^fC|S>~~<AOJD|nP%#*t!dex}OF<52<Ua-XfUCP+cT(W(Vi=!4
zIt{cJ+ArrMta}nchsNCvO2Bxje}6ZM#K(5EZQt+a1bW^QvZsfGvw@P5+?XmEP|{G>
zmWNN4B<)o<MZvs+%lVTJPDs8yj>}<C_<x-Wpk7eF!i|^HHZ@}G?NuJimryz+B?~C!
zu}!gWt&MlTo#~)Un1LaNRJ5K3wVLoh1z@LK&@Bwj|HKaba&^C`lUiYS)B|&D`ORv;
z*s*zZtMGx@>vzB>YARsrb_RxIUQixQ{2L{J%>Oo|wpGdi2Uef*O+t_Zj}VQs79$Xz
zR=Px~Es;Zm(2hT8ey^chVzkU%0!C6Q@)9sMDHg1mCv6ra+_1QfI}ZC5Ew>^%6IXp`
zGhk$1-aqP#UJdzgFOZvdfMPFYc4394#P1@oC@rjhPekF1cpUI5r((H=9du|?a52VX
zsNb~9r(Bv}2F{t&3SVcYfysp7GIyI^=dqH1Vjs7X5PPzaR1pwymmOn*%@d_7WQXn2
z>si>9c+YK$Pwyy9EPw#{Q!f$GtB9OM6LqzB)#I`@Zh4`*HM(cg{<cR=`%Bq)h8-AR
z7t~R`p97~4<N!s<?fk=?7^<qG>)zg{zvcC24Z69UzszW)2}THk6i=+KWC4!^=as!<
z&qS{oEO(pEMTsb-E(6c}O7hI?9}3J$j@|!RX5tMXlDoV{h}h>e^($5MHOBk=^eF;1
zl?S~R39mL;JDQd=$0701innF@UPTbj#^w8BUypw-9H<HN=<nE}3T|kxvrPMqhwYSk
z3vgsPSA7b}O>xf~XdxcGB7QkbcDq_?1D2Z4Yd@v;0qXkpW;^LG@UTvEbw5O!UZ<&k
z{C#^tK)N8Kh{xw5dVTwLi4uhf$HbUsWKbbV*>qo1*Ye862SQ1=hZHCz)M|A*R8~K-
z?4HiC-rPOaWAu{wen^epd2JEz^CI6N%b%SaBX5w#tzMz(_TbOu4LO;(S)K7fgVXam
z1L)58+n(rvSt1wvguj>os1=%BsZco^Y{bnN%DM5x4hW-w*l>98+o%X-r?`+a?zuR9
zuq{R6sa5@%kRnd4GN2q>ImbJZ>_ezMmIohxGbT_-SRTjPUkp(%c2~dLK}kw8n&s|N
zd2*B5NBU6qGZ4^U7q}}>dGX{iy|XX^vo~hd1kR_!En0P77aV(>R*M7~$dTp@qHn&C
z-`fS9k$<S|Q5|n+A1m=la<26A3nOy`W&p-l>NKeyKqDe>K8a|VQSuJ;{T%_2b%9A7
zI86}aGnY|@!3j<LxI>CmT8T?w(|P)+%LZv25u7iT6^cp6Xowe*I6bwuF)I4U!IWq!
zEHCV6j&4r5ubMVwR{)x5dB)hY#8zK!bnzo`<P1%Es5sCBNp|mX@p4Vz5}ho}L&Prn
zZ&fz)IeNdYp^o8Ew-G0imqLE+7fJ`F<mC;MK0evG7LhM*l#>@-3zvF-;KMUmKCkUU
zF7xi*eOvj*W1JEUp3#!hJZPT12!Q46w(fSvpwu1DM7XK`?jj&)&KYff5~^W<co-C9
zW0vtUN{W)1v7cDM-{te*^VXol`+Wd^gMX}7CeW1M;lb^E?f2I0$20JVy7#$xkeGu%
zjPlGhm!qfOP#ac%p|t1YJwv2cuvVS0QCs8zjK8+1)KGCl1zEsmxWEnO0%HZp!;VrB
zh0gE#H_DnqXm<!_6s;O4!_%A?IJHk68`nO_E->4c+{XV`LQCLn?{{orserO>aVrt2
zxfmr`&h&Wb<Tan9O~B1RG`o(_j-6|cP#O+gKu?+M!pso4RrN7(iojBOY(VdCWjO2r
zV@_i@51FLP7<w<drCxCOm@0#+xGLtdZ!~_OKWSHH5&u$j#)PR=byT2<+3xh$wJdo8
z>H-@f3Q9+C@fL)%J=yU`W_fT)7@=~hM4WwRek+%BKMQ<!iWRryx|XJ`A|q#mW8(t?
zluTjxs0)5Z$v0rcOq!=1QDD!3oENvFfA(GT@H>~XKA6y*U>rHNrEFnaH%d_|W+-fN
zdhUBb$*IKTsGKm|)C2lbUtV`mnjjp@;130ry`UfQx}K|~n7-x~31KLR;ZEzW&j{XV
z(-s~Cs{%61l1RHJk&F_O{H8|QPn~jPne`HdvT0+COO8VM1bl46QnX{Io{0sCRL$iq
ze5w@b^|V-o&1)hC8n%v2pq75i3VrB5bN2Ahq(8HWsZ18UC6-wv3y>J3<y(EM{2lv+
zJOb#K6bWWfc=x%HzcznU0$57inp%n+*8|eQ<GjPLz`R5>I73`OIY#T_SG_<09>p|?
zaSt5ou;dJusN!G68nEWU^Z``^B_2^3{DMQPE9!90#qP;0iEPT_H@zScb*t(pnt5ck
z4?){89R2XyMD=M0o|ah}>)f0A4~$ATrYs4V^{G8dH4=s@1`5pJO52noi|*V%KrWd1
zOJn$tu1GwuZhI_Qmf{pxg+SmFabz=ps9Tl1sY>nZUH4M}BX~7L<2!UVgUtc!{bpM-
zG#Ty*GPHo{LhL!<n=#yy-4_V>SNog9Yv27Bn*dN)Kor8IxB`1~c;-M*pC5ieEgw)3
zPyNFq;dW9;!a|;Q)My2ju?%UsYHFp1CyR{<uInSq=|t>g(E1+@a*5V89&9}Ly>W8x
zUylG<8<o79vws6FKL$9b6WX(Xj@(@Kz-h~O*CWXm>_Gw)Gx8HH@zP2vr!A-}njqe;
z2_)9I#G&%rnSW?e;&9N%$wT2xV1>sFfWj(p;cAQ~&4YQ4At{d3G=lZ4H6Sk$kkMrJ
zu@L$(lhRC<-C`BoQ>5@n<3!0-aq{o9`A$dn`HlC(agOJ`q{nd%e%_Dd*Ot8=!+aDq
zL(&wlOkfC`tePXh^@3C7<(BV-?V6e*ZTG&$8PhZ5V9^|9&1idQpFeqWTp@xerFAPL
zc~XWOoD?meWuxO88OkbGDO0IbV+L3M9p!OM)Af8<9~o@uJ`{<i3DeXz|6_r$<R?rp
zK=Nbi$$%wHsBnkUWWqqkQ<&`TGx(lrVe;BDk|u&CVJ5&p29pZ06}X8;LozTh7miI<
zR5ign^<n<zhbX!Pd=0ib2FRgotX()S1uWOHl&5%B*}iP}X0hF(N5eI{pbhQa`D7n&
z$R*33Ei{ACciZ2d*uJq%{rl`EHiv-=RYy2at}!=eB&J&r5GXke=?AEbz`WFq`y@Ey
zgap+t!jl<H(LbdK<}1Byjub!BKSx>TnjinzQ=;RB78C*K%w|E*=FLaU9G#04A~aCa
z=(swIY$kP7ge@Jmrk1t+-Y|mPu<K7DMRY%a=&-@O9&18fN~VpSmqGXyCP8)Wv?RZ9
zmm5QWMrT_#apmpgn_+MhzaxG=gydti87}j=3m5~GyQFrsN}2qPd0_-hg=OH$uw10}
zcKnHfes&B$B^#}+7CWDXSezg0j8m4CZJg`ZkX#x=)~&ie7NNM&`l&4K<*HaA#&V3(
z>;45I!R5us-LuF8+shUnPv;roNAQ_-e%;#T0x}w0L3UbWp9_SUg>%BnN%q4lRKME7
z;@Ha4(24bA{famLl9&>@<HNld0m;)b?#eVS@weYc!*r(O)LFH{i45{Y*%X=V7+6Ma
z{v`;*1#D@~uR5mFUjseE#PY;RlWzql1ZtA^=BRw`lMBt*JZ{~g^j}U5z*J$t)|FW<
z-nI_ltyAZ&DwdhDXK_j>gCZNKv|kArgii!`I@!J>yh0u22~ijUih%N*$-1Wg=8t;b
z$}1c>6P)EHg*_-}1QQ4SILs36|42eSTJ@iGDOdo(43Lx4mZ>od!m%5QG=hQi8IX{5
zY&wR44JUBjLj;s>d@dVBeP0x;&J_b8gRRylNZ^#-mW_AOmLBYi;FlU}84jFxVXw2>
z$<lO|ubK2pzM7S!+xPCzEPSpQ@Q0p3P6_L&bix#_dyd!W0_p+jGIfl1W?UuqhdlbP
z&4yJ>H<|=xqjTe^xbm6CfNJoUKa6bF`=gV@fc}pCv&ZR#cdY+X#ZMY`o5i114@8J<
zs2Wa8l>=_@k<ZGgfQtAngiP*R8FSLu>6fr<l3oz$<^G8*0xkXkbEOk9Q^=t!zg|Lq
zzL-)Rh^<@W+CRJ|VVYJh0@dh*JIxSH1YR(OqMw!IF0EX;=D@&=PIIJp`g^nBfB4X~
zyd470auPzi%CVqdZEFQb?g^Qg<})G-D#vR?Z6v)4iTRmfUG}As;G)@PzFdu5IKkoB
z3k{1`#UJXdMcvS(AqDa{4MTX(66SecPWL-A^JhN?o6A*d>Ud2YHa6eI?FGI+LKM#F
zSJwAKyduz_7p?V~QdvJaLDUu{BC{ki17?S;FCOf=0cM()^>s7HC<}kn*-H#81?(8c
z_77l$Ia%Z}1=`5nL3NN0S6e0dF*oVYiyXz%gf4xb2ZlI`zZ6j>KImjsjDk|l*3o(k
zu)F`IoY=yMq7(45NHS1Xbht+u(vA(f`dX^bhjzow$P9|KWdG$&kw^BHyGI{L&-NP1
z5dMAd&jq}D*&V-UvXapME|Ci8>D9iTm<36(o3ipInL0If6*x%O9`j{Hh?>**8yv%l
zBHe$3_7`Y*G&V|BSnbm#^<|E#RL#WbV?i;-*wf*;96WLMak?F6Mn)D@ee8b_pg7Uk
z1+kyhp#Zb2;c1qq_(9`9DosT@B`O0<^dOdfl#<2#gp8J2p=B1g?ZJK6#bK@Rh4t3a
zU5!}J`>tUOm7L3hE8z%m^{A6&YrT8o1*2}hS%HR2%ZHbt)nHGTBeF0BKv7&{{z<32
z>uQjYox&-zPlOqEcgIfL?j0IlxUZR7T3xM>*F2p+cew5Bm2^=0GSKn3Va>JplK6f|
z&-)OV*N~9lqRnUv{Aj4&j<JXr6IUIO3h!7?O5wcatxWX^ySr1eaP@^RKB({zskC7Y
z--@^65o1L2>83H(>(Yayl#beN;+L9>Eob0*%d0(o&nzbIS1uXtjp|Ha;%#T%x8V1u
zXmgd7musI#lYOQ#`@K~%Y=IQv8C9x#l&j(j{-Ir81HJcq^YRSM-P`nJ$pfVXafg@L
z4ewMTO5yUy80w%e<+?h*?q9xKc)x$Vvq%@KlRXR;**cpM@;O%5-=_9~6v%dH>)QY$
z{i`=i>>@@E&D4r13rDz@fJqn7*CU;<yoqsUe&wy9WE9@%%30=+$IH8sQC+RARgap#
zOdOXULnSu#hcQg1uID%6xLFJ!ugm*_cOI`cL8Uhy7lYKLn~@Cnoi8H`CAZu}254Kx
zR?}|jMiXZyp5Sf_rt|mSfRCa8Vm7xkgb^<zn?RFHAR|1$_MKpW0*S0&?0WWCw|q?X
z%Kror`Q*g<Ytk_RAE#Kk0LjFj74S@Ny!B!KUi%Lii|D_PpCF-{aJjoicrpfZWaMf5
z=4|vysd(+h@b};hqmUc!l*3h7SOMUZaA{<2KA#`qE*|{!rDfuJczJMvEY#sYE>|xp
zj@rjWw0t-z%i~hMUwkb48LE2mv1IZ`ce4+?_E<az_(?Ai-m#CW0Bh*5=To56c*+N8
zV)nO?T4&v>T-vYX_wd#Ii=8!SjTLb}C1vO}z*`eHh7b<P6At&bP}vpO%WagAbJ~)1
ztY$?l*_7K{?y;Z6@)YYUH?<h$Ge}8hfu$L?Z!jZmsOU7I?}iz?0?2z^&zBYr!Nlua
zZgtquo|Tm{1OvRRbv2SJEstg-lx(`d-MnaGEF1hD@Un`JbJ$ti-N)P)Obje>W1F9$
zlGQ8$d_ONv4!AY4x;_+K;vXn23a6%J&99-6lTyu68*r#??tJ*j5AeYyXbBmZ6?%=s
zo^6sieVkyqWj2iq$DyUKi4p$TRL1+I*yT!+JOsF9%zy`=k0q~(A*mcW&UKAs^V&Uf
z$>I|S+~d>GPX4z~${wR&XQ5npSm|$h@c6XCeutzG`19=nyd>+Gae)5&DH%%EIkb#}
zO2atxl_2Z+R?v|g-XAi&;fl8=(QiOIAoKNGE>4fk{?LTi@dpDOa-c*E`QeucD#D>V
zI_>iIpxE28+7M9O+Pn(&PRGjl8)#$Z2|38>XNzy&TvS#TQH(G@V$dnA{(W{0W~cjz
zLO^KZzJVqLmrDaykTSx-6V7wfd+Sz|Yi~sDk?<t?E=zeS+)X3Y|8t4EIp^xM5C!cs
zx{zeagrlyBtD~t^uk)4b4vWX}>9$?qVQD*N4q89D9%e4xM-BwdQ+A0Hs-RrMQf&;u
zKAo^BsiZ7?w1GJ02y<thZe~M6PI<;mG$=iRb)wjWQ%#}5rBkSdIp~L)Cp>9M91%y|
zY_$~=lQPLd%j(8yoL2GvIN+q8bEiJ)b@@O!V?d|78M=*AXd%tu479!Y0ER6!V-5i*
z2<ikDaBl3hW7KXiR|bBrRl!9lMp#dZ%|PDT;dGI+nF^1iHlrdAxk$hzbeWcmbS~{>
z&o>hXMNDOVOKY+)Ka$;lW8N%n<E>%3lM&f&60#^myg7C~CK7}OxuPVy+ziJS{<eBx
z*0RfL^J6nG<7HNGn_sgQ%a{SaCu9jx`mau@J!F(@WMN*jwYmRgPxS-$7!k&Ekb+7e
zeIa&AOYQKoVdh*Q_g&prVD3!P`zTC_nMY#i)ig9$6Q1GalGHRp59|lN*ho=z?dwzs
zWWeB9fBa_wlGOl3lnvkGvPC>Zx-`S*9dGOoB~lBv;pEOsiQ?`%R?qCDBUZx+Yki?m
zeN49$pXWx!uR7tp`Tf%tb)eoGPGm)N)M7MvC$gC1nFXe^h$xwA(K7s3wrpqG(ss^I
z?kDxS&EJw8F7%A<yT1V6ZSt=(Tx$$XnE5<+3O%5nPg%DBXDMc|17~W$pif2u(MsSc
zeL@}$Q39SV!>CBCeBntB%|DpsKxwfaN~p3@p>Rf0;!SQrSXtGcD_!N?LrdFs#=(nC
zl@bYKLU{re{>eDP<k)zcJy9yiarwBSmD)ON2S*ifgcA<1*eQK(F0a<Jc7P1irIjnK
zF%$XZ7qH}B1cU$3`H@8Z-a&)P-yQd$u?fhTedTK2!XtqV+eU`Tp;%T)qEJu_T<2Jn
zU(QEF6qZEqw-Hz@c-PA@EMB6R++`GdaS5h~;1fDBFxR}r_auasf@PNy|I}I}IoA?_
z?ZTd`{P`^=4rk~LTd`h<!b|ALH{sR3D{`yEuWWx36JL8w;CIuFRh`_LQx)4;y+yGe
zTIH-2OYDS=WqMmy^a%{ZH;(wY`d~O!)f56I!&_?Ghj5yxBOu>aH(G827y}^bQf61h
z!x)Gv*xvts1t#g#CiogbVx-AW8u#%marGyFu-)w4X<rjrPIbIkPF%Tu4$2w<3Z|7C
z_}q|2VobpO5S2qsNAN|6C5%!J4NZilB$tG;(cs6*jrpw(NNqa0UME_sA(%wcBZ;b(
z7xjbm0#MfxPMGGbi=5aNVh6YiN(}#|<$4umO<fHJgVDv%37I+(g-;*n&2@3apbcc|
z=KCKo5+B7>ealNzlH`_I>@q~qoAM4cpG2yp89qVd1udh#x^BJ!KyM>fafE37;bsd|
zJ3heBmgHJ_<ZwnA0aErE1ln7qJ)>WWPh+XEymS{~Av=2>*=VDT4rC8Q?N)y8@QM9N
zT~(DmHr?6BvxAiGzY{DeA-G}Tg>3bszkG|}61oQ7qv<A0x#fI~A&QC(1=?S?585==
zS*(3t(joXOt~++X{?U?^tLym@@CKZ3m!thxY!Lw3H*|<Zj8uKf!v%_a)<}~qx+s>k
zVLKX**1edQKI&hbZpLv9{H<bbb9u|BAf-`-(E``)Nob3W4g>ETF*FggwBbpG&oh&*
zuVd0G!?;nz>5D399!w$KDRo-usN)R3k54}qPB7)3;PG*!Mo7YE5l^2$K21AN|3T<#
zmq~qp4Q2XWQa_lemUzLWpL^_5+^kFS2R;yhpFS-iz&Z%Gvatzkaa?Hr{H4JyYy{(|
zYc#RNl1sDS!@+oyx#1D7LpwI<>dW-<QlpKBalyqKl)LU04NB7C{4U<GcOCqG>LEjf
z1LoD*?8HzOF%W4uvwLgPY|WA{Pg%d6T<tt`3>Bi3El&V1+#Nabw!dC%{5<bQK&-KR
zaBLlOPZoH?u88}_neV_p0~=IaRtMR<lMWCRabuWR?ZXNa*3^3$w$po_r~Ng-bi?z$
zyW)9v(P}SVu<D<yd2t=-bN6Ze{RG&k4(KL4@0n+U#W?NlQQOMJOV{_b-}l957qn`R
zb@iTx?e2;24-Q#bF@tR~YqQ)=5Ny337>L{5Qgx;bjyvJ@VhMtZF+}4mv6E9<8b=%6
zU(;3kuWy@)n0)r2J)-$NzmM?<a1Ou<H1{^Vjp^rE&;?2b`OC}14)KssBC4xvHdgm{
zJX8A&4I0NTYlWK%c<h!R_)wQO0JUS|?H2F*>HFKjhh1rN6n-wz@)R)+6}5c}hOx4n
zH33(A9&7viGfnUP3$HM0z2$d>@wq&|1Mx?}Twq)rDc$<C45LD+>4ef9q7O-D`u+0)
zO*x(tfWd(YbjRD;!ckMG;qPC~qi<fqKrDe#8h2H~%Q<mtA0&JPcyh#O$Gcv8PS@gT
zcBjoTdKBD_mc0JSvhOF^FO(J?3A|C1`cE(D?T<_3K%bhWzI&LXsP{Z2+72<jP^K%m
zdWEAlS)b>8HTZ!(R8xlKs$-$nG^t_gKlO4viyoEiTptZEUzxu%5zB0M%uM)sUQj0k
zBq=`0eSeD~Iky&U9s1@OP4NkI9Yh^?NDq6FbnND0wZ5^os>-972$XEZ?Co8MdmR%p
zPgrbyhGQ+A07u=sy74j7FRToUE9Dh5a4q04Q;Kix&I~$f*zk;=87V!jNU&)sV2<Ky
zsP0!`=_s=v*V8`O-cx<M5_knV?S~&{E%?>A={~opK1l!#BAj@Jo~7M&C&bU$F_=y~
zdOd!`r3BoUVCKuzVV_bw^^taE)5BJ8vwQCQzgNTu52U8jT+L+jM7bwd_3VVuL}7rM
z7V_qufX$46+%0JEt<A~MGk_$_?4I|U7ExJVDw*Cq_z1roMppH=Os40sm@0HsF>BJu
z<Y5!wYuC{$H8i6O4x;A-3wG64I!0azMOEnpLEPir7Ya^bf$kHJFS-5z=xBq*=@{6x
z*gP1q)fa{e8K@9KQC-HXUA-qLBs9#}uDaovA{tZQ&Fc8(=T~0ViQD>Kgd!n<?%65<
zTRBM2zk*z!cG)I)>w=Z8)Pyz#H^rS=%`)|vqjUBpPeS?p>70e5oU3k97CA($ozgCR
zZur!`S~#XN7Dohvt)gjATVtF78_Jv$Aang&E<ybQX}c#L@T6<!xly@r;Cr={jHS~(
zH-Q@qQvR&)^A=Z5fQoae`j*cISOB6XB2POE>>b+3i#5y%)*8?LYn?w;vUcVYXpt)2
znLdKdrs-M<8#xz`Z>5sn%O^E)x5(AZNvmi#VFu+?H3NG2-#5C!*E)Sgn5EjW^<oe>
zr%LYxz|CPF^yCNQL7Gq?<j89jq!M;+E%+ih0MY_AOHRpbiIUo2l1QpGD5nW_NhmT~
zpW^#Lo$vjY)i$*P3z<`hZ;Fc;NLUxZQ`kdvXnSG{AFRyfGMF}W%dkaRY(1aZAof8_
z@6(7fgg7~Danfq-+agfz+kIX*;Gjg1LY+2sU0S&Tk6%?Pf&m)(XY`A9_o%yqelJ<X
zK(tdn?(tCUhpiT<WPrYf+<v4-{O-xLStIbwmRQBxvm=^T$5?ZatdUweW#b5N_^Qgz
zx4tQVKlB4|3h~R~mooR{VY94cpKJJj@CZ=H1Q-OY+`+fT)Y$6piTglEf$H=#dS4Dh
zy~D|mXJBK^cc9I3-}{hcq(oy{Nq|vzLF#5~je0VI?0wPkPVdRIJDRS}`80aQ=i>Y^
z>qJ@G+U`EH)bp|51lU6F35a%@CWv!*;|40@5@&yv2?O^kHoTqb?>Kt_TPtirumezj
zHN`n-+s?u^tpgR_?@#=mJD`i#O<st78Xv5<+c}~*Es6<?^(R%;!+IU9I~1Qco{E2;
z0w^hr*_wY8hJe<yDKGY62Z5Fno3X62dfC{%b#U-^l+L^uoQ9r_{o6D`X4J^Bd$<%=
z&!ZVpkHS(*q0pi_{(d!kYHeV7@h6{E`3}$jFvJI7>0dw6U=r9b8ACKfdP}x9-wc9+
zstFc3crV2hzJRI2%wC_rW!Jb}HMJ3Nv4x$$EGBiG);X=ay)TnfQe)=C%p;@h(I<?~
zQXSh+BsT4sUcgo%g&Ly5V95e(-5jb3eDSlxhkU^2kgV|3_)qxmQ>sak3UY1~BTpHa
zl1leebVdnno}9nVuO%y8hq->@<RaJnv#3CckVA$hGA%w_<RkOB#PGuxCJV)zifuEK
z`jTcjI0b)=AZU()b}gx|(qmsF1>jxa)g>(Ve3e)tybN*k=pV3k>U~p{d=qkRQeRn%
z8d5u(1aq|rrEG0=Vl?Wcayi$l`i53WqZ-sqH|Ti<HgEeVfo-ZVdu?J-Axdcemlcip
zFaRS3?!fj-Xi`-r<TLD4A-S(G<_EZEH%gChm0c{sVK=f=0`u`Y=U|ueZ`D3U0oI3X
z?u;X2><)FG&1e4X=HrZ*9>NUaR7^=rmHG;1yS^Um3J79OU3smNoYMPrA`8ziXSQ=I
zDP1%-cKwou+e3+e;*2`F`?&6An?&4Zm&$tZ)x1u3**dzYB12cxdJBRM41P*-D@~h6
zM;#$qgApx)QlZ2gq44N}`X*)hk|#4f_0hVgAAerNvN#IwjIO9_=v!P;zaPW$-VH<1
z<-s5br*^%1k{fsIx;o|buNGj9w>kydtQ7F39i&bW8dyz~338+2KY*B)&OK~BH{@hI
zoQHaKS3~|u*DHQGW|&BcGV81Px(b1v3K!nEs_DA>$tMiu?1yepfRtuNT`-!wzaUwN
z^s8U$ulma0vW7#aPio5Fkc7#j;^W$2;Y}2=0&9&x{BhLDRc`OMyv^kxR!t(LbD%4T
zXQ#!Q<~e?-oZ3q&V>6*2TbF@EU335!&dHguq27K%dx>GS)hBEPKoJ>2Ji&#Fi~8iM
z-BphT&fkV{*^riOL&FWUKzvMe4td6U_eHbjFmS2Ay*e#rs!+-MyN3rSJSo7F40#Fj
zJ~xqz7z8AOCS@am9tpFb_ok@_DH?ldS2@Gu9nWUrVEftOmRqvvcbtvq#lf~5Q2OZ&
z>|7tgOlzhOYh+RDb9WA^m|tcwOH7lrWo4s<@nv@+4(=*z$7v|T2H|Eh8foE`fY;+9
z2p>r^lSW+L53Rpe{Ivu6!ZWc4U#pMjpEr<!X%a95`=UO<Xb*s3{|M@T6`xrUccXp}
zN$$cG=fk-wqgP{RaE1PMaWX2%>1TipY2TU639w^qGlN&||CKra3aYk&ey;0VqV`9`
ziJYQzSRj|({_f?=!FpT&$_CE}KyQl`N=L{fE{QGNFA7R&=vYiz-O*qXL=oZ{<#u#?
zzior+#IPq2&Fge1;-t8Q3p`D)Wj;`6r!=3mtEw8<=ML`bt|!ZB6SNF<%(HzT&(L44
zx-2{UX~bg6ZN!}E_DBaUDI*h5f<q%j9tWk=@2VK=Tp3ob(SR0Kg#>RDZKKkM;84^o
zN3BzU#jtZ|!f>~)YF-ubc?G#3TI9=642d(w_gn>q$;!EpQEK3QT~U(HL{V`83bV|L
zfm08j31(6t{t)9I3_ae%HwgRI%QOLD;QSEd|FG-ewuwrZ(S$_Rl~XJ}!@w}v%piSb
z4u}L(Ohl2~$AHAtWr#!y8Vgl^a;ERsJU{$d-(Nm)<p<JxXl&yZUK)Rr7tuw;k+e$J
zSQ2F5ZZG;O-pi^=q(1$L(1Pn~FGeUSLHZhKyRL@W_X(t`n%D)2*am_HV5we9;wY$W
zU4yM1_wd8}o5B3ILnR{H!K8`|Qz|gZ3(U_(<o^r;PH2_6r3e-q_u|T`Ks&crhqn{R
z00vLl^QD!G&p2sX)dJF-^g_rsj;tcwj_Z$2^DvNv?R<i9OIjR5t*e31SBnzAIa}$O
zJ2Wzg4h|)B-3KI9(TiwhRnb2We1x{VmWmX>)-ax-y$k%G{SROo&<Z2}i03UC-7j-1
z$BPD#EwZW_7Rsb>_^Asmkw)<zYV(McEU5dP8)EYW=Y*0q7st|r0fGkdmfb4No(&8-
zWVA1$AsqTnc9<BCq&LaxoUi*>?eCE;7<cE!v8m)n`2_KL2j@}_J<~32A6>4D!lQxU
zXl!B_pv_uxPP84*?2r7^{kD0ybdA|jc`(%C{T8WQlhIr`DDQLb8h7g%Z!5xb@Dm3w
z+ij0zP47p`nc)gII45>o12v<u6{<$y$J=%xYMwdW%uXM^S~!dldV?zMOQWzNw0PEf
zPnD@D=i}@xxvbF|LURsFollC+#)9yi%HIS@bI#y}8#~a~y)BWc&oM)VgII(Vn;uYW
zNz!WS2I&Q8E24!*(<M%DFENhmzdSe4(yH8u!%6@en+VM~@(!hL?mmeQ{sX;<;gV$P
zksA4LS@kNy_}I`dYe^$@h$D|So%LVh&oS=qz6!j|JOJy~V3}M0?a5)309TlULqJVM
zwo5MEbKf)z%oevZ9ek7FVf$5887GzTPTI`2&tJzDAQKuoJd*Y-Rr3SnUw7kAd047U
zG&^$X2z<PWNnD>jOjBEG!{Y1Qw);N)^nM|V6@o({#M!@|Q*DQoDQECEuxX_D?%KOT
z0$*ihF=3?+b$Rg?EueI(hH!TP!&iIVrT*<Jy3_UkE;7IGLhL*}k|u29yqmw}8SzwT
ziKI|%+&`M+ckT37k7ic2RaPA{uXH_)JnZkk^SH5BHgfj$NeiRnIjEMBAp{;X*}n$4
z2ao!*D;K?zT`b?fe$bU<F%amB@d^lYi^*V-qtUJI=R8RB8E@Lp&Vfgit-`5~zE#e)
z1=M-2j92*m7F)aGS3U+x>GhP;!Ym@{JmedtJ)gcXkF<x9ju|FcdB^;`d-$+^BtVll
zYgl@7zFd0sh>7D_M+BE&)lf&pfSlLWZ}LPY5Y1}cJ)i3wbeikOkHV!H%Ge>Bs~>R(
z41eYJPWV71WrSO-1=@Tyq}F+zBDM0Q+vauxsUMhGV|CKi_vax~9_qBaN|@EOSv)L#
ziIyiB9nHf$ru&EYo`$rz#N(_=<JZdBTwwq*(!SC)%jUhkC}@aFZZxDGO)WW;mV3F|
zOCv58cWn&+(p%+!SmH+p-EsdCA4=<+kT3g5RS{>xl(vu%h+kt$%l$)x(41T8QzU}Z
zM-$e0nho4mo<@2c?^hBRQ$Ew@DO7p?YHLIbS)z^tq~D}+pjY|QH{{HqE3As?eLqC*
zZ+Rbjg&q}!awj=?vS3$ua;098wbxyc_-&{+{pu-Qy=bAu^Qqud5f2-KQeY^U8*bKE
zP_+3&@AZ}z)amvBMxkCuZy)MD^S8`?_w*)d`j?ycf$X0tctEdlmZA|A3NHS%1*`$8
z_H$j-4dhFANh!yc^}Y9-?Dyy0tcdf|Kzg(n*!Q6YqR_EPM&~Qe?Hvy7<v#LYX!o3G
zV)4Z^IW!Sy5sIvFdu_TR8Ywk1`am|#f$m20-xhdyLjRc@xq3_FElEe@f6LSm;{I0k
zOqqaMZJ+t~Kl+65Pz1#V;y0;B>d!(7G^T@ztT<rj5jT(714Ts<5c6b3gQy~Ob1`W_
zZ>1C93Oq`Np*A-ga-z0X5<8_(QN^Vp-l2hyZTfB|gz{07gm$RIAyjdC{ci8G%|hXd
z{nhG!G!dVDDSU~m+oumpnc^km60UQ+n0&FT>oo>WAT(h@Capi}Q`WDW6)*+eD8zFz
z(2B~mf`Rwjhkr=J=Xc#$(B6dk`)$syMKbLMsD?b>n_)U5W0XK127v`jP9IjY<O}!6
zi0zBFd;HL1#x#&rs{s@yqJ%Pjo-@fT&CkFL6R}v(=c$n-TiWh%lP1wVsJ7-cL2L<i
z)t-lFVSHQ}mq{sAMrCtNEqafhes@??NfV#d#5@1BjSQ1bhHhVwpe_LayJA2P9TMp2
zlH{jI0N$BgG-Ba?j7jj-@C*)_D1~qYO(c~J(sx-YdX(w-ntslp<4v=@7BKONR9FPN
zUva+OHVB;7rFN5F`!PzZ>o{3a+u|!JG^GQv-YiuN-;Z4Q@B}p>Y)RU-u%NPi+`8y3
zQEQ>29E4BGl17$&y}_E24mZa^j0_0<6gDd2>I`fK|7g=WB)~g{<=@I8i01NKGVq7^
z@}s%6*<|}O5WkRMml<)J2PY8Gs8zP}8Oj?o=bte{NwSdHIn2aO25{HrlqMjWFY6Mo
z%nq4Y1&wH4Yo^<?WYPpR*hRr?E`GlI6}=QlH-Hj>(jRnIK2g_)SJ3KjeblHoXi+wH
zYM5v^o|7W|;_RW<*)8S&Yen?qy)Xq97AfF({jXEmh9<Dq(fSV>v_$$s1^SxW^YJi+
zrzjjtqZl&>#)>4Tbnbtvi}#TWE65iFFPPG)(CBw7<ORJ)*}=$^<UjhGZ6Xbi@wB<V
zh$)V`mkBqV*joObvAPG=nE%g;%tLytoV-v>bFXIN(cC|D>_KTh`NzG^n=|ly?gqek
zF=8=QTUx&$A85!GC77;<@Y!K*)~AnLuBHsloilGPbo1)xb7zi$?iE10N#g>4%}ld=
z`y{IT)97^a?y4<@ruF=8#nPh}Q1;d-qvD@mqkQc?u9o`*a{#ucY%4&PZ(00IG1e)H
zg}{V7QMqV7ed*CF5%d>{B~F_)kG-b~8DR;Nya0*zWFBg+zmqnMvd%quVWY8?*1+)>
zxcg?}Jc2p{&Cgz7%OzQ6l|SG=pkAH+nnOwq@XM7-{Zx0^3ee3tcls+bL`5Z_%cbz=
zH#O8xYQrRn^$IF54atv4VjN{Q{Z;w(>$xjZ!*A9D6p2+frBo3;I1M{j<D~~FfR?bw
ziujj_9iZCXt&=-ZVY3qaCn#>>g4xX;+@YjvP5}J^I9>tQYmumJ5SrhxnKv3Ips&<;
zmbnjHYzmfhOdxBtHj6c!ZQXgkZDxDfu4LbNz#BZ<-N8!pA}H@V&_)puw4HbmW1p@m
z8~l1|ChTpiEn9HbY;GOxc&qS<o_L!c@!V49hv|G0N)&iL*w`AHAT)Y9q!3o#i(bW6
zMyCs|)^FPJ(5gcjNlu33z3;2?KT9*+K=j+WVvJb>&}4X+te)O86+osmcpm4?vbt4M
zSn1S=9j+@66fwrP23dpeV=Xo}VmKwjecU2_+>R>`zwQ(Pc<dRJy*AHI46Qq1S~j!y
zZ$Jid_rJ4AZnajH<av3;&VK7f4@*i_@%4lx_Ape`HFE3k_2#h15oP|IaE0FqvOj16
za)Wc)dPM9-J6`t@m;~BfNMda3Ju*6~hvmKYX`aEu!0d)`qU>fXkn%0M<H|(rS?bjX
z0$XwO)&#SkWD%iezbK5_Lwq~$OuxF~ln>{taDLvAq0+K?yyQG^PZ7DCP+f8-J#cZS
zh1!z>i1usi_aRZgN`cC7O>skBR3oKisOU!2uQ3!`)$SIajdDy3a+B9-4}>Z1b1!f^
z0rq$Obl&Q{XTaL7d0dxrGW#ztswNRgwb}`AxER0o7w~#d+K^6V@PpNpXqjp`ah^}c
zf2cQ#RpCD~#1<(3H>R>vhl4gMCa}Srj`Vz?5kXhD@p$c8T!ZCOWB@Llep_o;C(Q&6
zajR_{a(9i2gz_0ty7Li3$;e_omkNR4|H5I2?#hi4ZfjIms+g87@2?h^bknShSix;d
zXY+RtlH-heXOIB7eJpS*k42<^vY*;SaV<A44)gv4ml|KwW_dzL=x<cZvov=r-ZriK
zO@|}KQ~)i@W@Ybr!!?=S^y?H-qOiQI!)_{HLoHXB;YX(3IRWorpu609d3G>smf|*b
zcsx4trmdZl?@xTW)As~?QB4J3Yzxr`ShDbuUaFC#JB&1|Q$fsDggJ14Q|aW%Md!*Z
z=Hy$HA#h}1ikbxtV=$c#*w;6dZC#NiR&|T(O}~@4W`uNmbjdZeu&M1z`yABl2HWR@
z?#b^=SMl&Ey3RJLuwvVEg$}Z`s)bh~3U&?aq}H4?%^Te8jRQhg%O=K?4z8B#EOp8j
zG_C3$3oxj0<O+vUUDP7^hb<wa*K`7DnFoD*7>oT#VDMHjsUFVNnL{!cug<=7@I}^#
z>@kgqs9m=sh*#|jQ9JSWzlMFs9m<y&VA;#D(Sq#a8lT~!Z0S#To7AxaBaG}^FPO`*
z?YEBUl8OPYgf*UWy13WKp>FvX@K><Bz2S9ZJzXrK&(RX2q4MZ0g0`*?dVJmVF0Tr<
zlV3k)jXov{*)dl1>Ctu&?_Zgw4B`2EuP6NH4=wI;mnvJ|FSa|kdKpW1I3U0#|GPhs
zNHR}28vF1oJc3IT@NUth+>@KH0H&_&r{nmD3En3(tbm`6$6Jp(7eF!y?Em)3ub}48
z0*j&?65B-yk{FgGcT3uBwaM==s;Z43{XR+D1p9GtZHqlA3r{lWN@v8xdYKS)0a-!C
zWB}tJNez#IfuoUIof0n3w*%*u{m!Ol8nchZ25tH--o7ZkYAbvvr5_ARm4_A)P}#GS
zY{we<@4;EUUtF*Rjug!zH)_?#^JBwF6<f=A)59<G`Q=CNkPE7}NPt2qoH<q`8e(Nv
zHZZPslupkh$yL4hecq<I{<N-{R)-?IBT99T%;NPs!D@<BU4ptj@FSxqbMVSl5nt}k
z8qFuk;j|0SY`PK<^WUV`KED>`um`U;Ny(1W^j`YANw_9MJZg^zcp-o-8RPMayN?g&
zOoA2+DWP-W8^FgH<&3&&Mbnk;P7HW7JFfwTNwY2fj`KD((iKj8lp0c@D_0?YAv#>)
zXBz$<#yd_DAqUQRh_5^Gb`d4T`5^XxDjum2jRY=+_|<<g2}*|GQNczPOc6)zHscnM
zn=XgbXaaB(fG_4-kdy?)v+8W`gUZ>8*Xofgk*Nf&=7qDSO+%AX1*<ZR6{MXxO7qB(
zv#ohJ6=-E@ZHe7RK01^djzxdA%w)t~n1`(T;!@db0uhKoC)La6m)NFEaq`woip%xL
z2oOvllVS4gv9Vmf0ecgcbgex4fD+oM@B|$iy&M~*{h3qF3d9Ro1bc$BzO*SX!s$qA
zevZ$B@nbeLDDaI30r>3I7C}-0IoePa3~3fNs6%G}bi2Er5Hqn{v^*XK@zx;~`Epsk
z)~70p&eMMQMKW8#`7kitObSnTY!VS$F(7K!-R+@GNJ^6W79IdCqMm%&K8A{@tH`Jd
ztE>C~g6{k{;k)T^oZlbP0nS?w^NVyS73Q!Sg7O?k+dA^A@0>E)K#>sOdG;pw=vQm=
z2OdimZk2|>3WFVUgAO1gEFbD6@cLMCB988(UGj1fNo<$R$ROkF_eTR$n@+-WlL10f
zGqBl~kBoNjyrOn86h?-$KrmRX&AqLtB$G@%cJGjm_z^J>7ZqKm<pD^DQsmKkNMvZn
z2rg<h{dS17d}!Q5KS;&k2o=z~#kR=`5bcfl>Cnjn(Zt^Qh8ER^zbXX{u|N3)#0ma^
zqEo8BXe7Rjorc9kqci-Of`&2hJ%CvuVIc2|H8wHv|1UR{*cd2qi85P;ugkVGEFElN
z@E|yTsC9E*(u_Y|2o48-%m5D$5z%Sc8g=2$ZTpd;r>BWfdM9!_Mc{oM*HL$`u;Us!
zDJRD~9ab@MdcL^u<cv|Em2HH$-6QB>KiS4jR~>MGnS1X+s38TW@~1NXE>~5;<%gFy
z9amh#Ms6yyTW!P{2gpn!7t}iG^<99{Nv+S{>7dU!y!&R5@l7hLlwP*|LHy$P{#og)
znzrYDp}ajHFL)l8%A-slv-@cY3G_OTii-u%hWP>RAv(hD%VyL_H+-z06=z${yv7Vu
zvdAMW&SD>{R99y63G{%F65YK=#OIV0TtnlhbEvQQ2P$*?O98njPZ|8*Ck{2Ts;;(m
zH#SZnY{!IePr=xWE<XcaVa2}qZIY)vv{*;`JZpEzm(F)R2%XkSuFA&+22?(8U384^
zq5g8a(Z0B<+j#jR?|qJw=Ml`2$g7@w@*@A<;1hlExz|9ZW!=DP15W=nlIiN)MUKVC
zAXcRxymG9lZ4>hitf&$wS2Hjo@XWyUcFX#KK}TyJ|NVBtjt3w|&>l%)v(`sO1Re-1
zZ&XXdzpp>mxWsKTspizH6oNFj9Xf6i;)DB{mG=pw590sJFuCH0CM36}fR4}M^X`#X
zRRj{gs&``KDR&b8nowGp%eGh}+>Q;JC>yh~?-&I_;i7sO62);5*#mJG(mEWSH^SV6
z(bDSkt|ytLt&njni@Nh3uEpR0L;gN&J>FgyeSrxN(|t*v&mR3@o>zUsKueA(YG6e(
zpg=pKz%^p~RwmD)G)|TfAd~oCacQ(~+T#wYtTHaqIB@!J%s-D5u=OMYM!Zvv4x)ZS
zzarp<;gAC4*zfl{;!b4$B5KeO9*jo645bKU@r~`NC8AnN?;_!A&j41#*Ch}W>IIN-
zB11vBktQ$@TxT-QvG6a&M4`QVBZa@++@t1<yP{(Jx@WJ{Q79XT)Y2o$+6MweKJ4=#
zdp`_6Ln{X02WD9QRj8UK7)QODUnU4sc=UkHHlfq~**kuDJWa`1SJGPL{taD<1_AIE
z0Y&fLjggBw*G5Rm!X7|?6YIUkK;$q~;XdN#e0aayO-}i3j}z7(t@aCuCfRN~-u@5T
zGneyUc2ag0cbq3<6vW5p(F=%i>hcV<Jj1iJNlshXE7;<DS@t!pREc!nyh%np;L_IL
z10V+tsp{swH=R_bDB{iE-iKKoHR8TNxqmJ3M!xi*mgB>bJNHV+d*S5x`a!8##12cC
zCjcxPQ{5hN@*0!%tlnFV3=;XWxv1YanJuC`Ai?mFVr<+N0~$L9T4D(XH%|JUDvdp`
zBx>D6K))N2zxQE7RMEcZ7%u6G3=O02`~1l}+K6kC&OQfmAMHvXHC*&Yhz)i$rG<C2
zMn8?vrWqBG-7;SsJB>u=jJL<g&jPe~IU8^GBjET%A5!R&G@QUfLJVQ`__$q~br#Bq
zAAigd>I;-<!BgLzX8eD2T4V84B|t063_O@OHGpT2O8j<kAEPUE4xDjfWPf{+T4F~-
zD`wDS0|Kf=>9>2r^v)qI6|sMQqF-hSK{ZJ7n7COq>k9R)xW2?ny5<0=8bAi9vAvV7
zQ1o@0bL0gSU&u($nxm=s6ggB75*h01zWQQM7u8o17)c8$N}0`b*FLR(m+L1}ml3F~
zc3hjJQ2_xkOevMQ8c!oRf4{ICiWdP;I~nLxQh&&yNdb#t_5&Vkz@cu%`2BK41=IIm
z@B#>qQEGS@CJp@M&Oa!ZMo21>B*eTy2Z>zq8(t8*f{-H*zX2xTR0QW3+$z`jljP3W
z0qKIOs+A0c9r9otvFeM+v(>*U77IMH>iCVi(K57Si|vZ;XGEFq!E@e~QD}ZsUgV9s
zsPw>9Plh!JZK(7n_O}JXl0TGiSbe;qMygT-8YCRbBoBiV`ok&}Os=LutOL|jvXROH
zoE#F0`kC5=%^K257N}8i<6O1)glxJyuNU4S@eXh=Xbop9-aiwrKIQ!#Er<F)j;;cz
zjjoFpO7Rv;aVJpRt!QyC?pEC0y|}x(yA>#I#oe7C#a)9-`S<&0GRX`x>}ImN_uY5y
z5&NrkI)KL9l-0U(wT4PV3HY{6Zj%dT1+iA&d-f}_o^s3XL8DAqI|Kw{NyK(#vA9sf
zi;B!4AnVM0=WVyuTb~VGE%H;lp-A%jl94UxU_JD|A!N{rebScRk0P?Fdk>e)O(m2D
zAh16b-5KWv14G^7+3ZKyh^7f+Mv0jw7LJb%Z@#K4)=A|4q!I331~7sVVb4QmmiS*n
zLhEitF&buV=Wh70wW@_S>lS>^aViP`yNCnz#WL46fU~)TX5L1eK|bBws!@2;37xm;
z@C!6%m&>M(vL{S5ZIGa{Dd4A~Jp!DA1H<NUa9W#G4rUuUbeO;<M=yt+l~F47sHv<P
zB{?eQMX1iYB8r$Kf`CBV^fahUI8I7CO09l83g@erN4iyHBe-8y+F5Sz$S5&Q8$F`B
zNe0j(+jfOqga&R_M)Y3Vr|58sJ#q?k3C1v^M*FadjO$evlp}BHVpHD%W140+bLjFF
zOg;?_7^Bl3iA#qvg;=-@SGub^)@w7C;Da-4Zsi%RE$A{m-UmSDWXE%-vP*5-L|>mr
z6;w@G#oF>?2`I4{daxJ7G}n#oO8SLMN7|MKVugDNa`5Vs0MtTyLCONY&ov~;^sg8h
z))8NZLfQ#CKsiq;ajI+m{^iEQ#26k7(5R#<M-7`tG9YAD8o1ijly?2%o4=NAuGa@-
zP&F+El{Bp<NK;0je1+OUbwyilX&0OtF1&o|>7qxK*y?MXOFSHE>z@GIKXuR=b$_%l
zpi!mz&k|6U3w1e_As;DN4_5)&29(x>#poUup!l|a4+Q+H$av*8ehIQ#<wJxNlO!xA
zJmkZ6;1xS!ihYrR^k}^Natdnc4CV}q2m(^Lk~=uW&v?z@1++QdSPL~b$w9Cp05%7T
z7ZsgBcIfzy%Oql)S5fG;EDwWTCQU4t*^f3!Y61t}?~u){C8ml@ZP<*qKG6Ap-aSz~
z-!yov6Wf=t04cam<&*M)do$0JIjzKqBj+QTZLl<%Tyb1i4!c{X(n7TH*SUE>?%qpH
zT(x!q&PtM^vQZo_ZL%KUxee<OMBIDIV^);v4|ME^tsGh%`jAgjXYUeig`@r-c7oIW
zj}YOzto`<Yv59B<fgqxAMWviK*Edzw60~R~;?Bk*g+ahQ4PaeDShF^ea8o8Pjr|8!
zI688sj)k*TR>}2O3EjcZ<;egS0VsX%SU-ebOP<%zwcW3CDqmpL!YhIr++DJTDZPe7
zpPp}P+99sH9|ebbe?1YHz69oy{30T_>_A_-b?`DUysV`u`w&VRrJ+-0R4VKE2y*b7
z5nobuYz0LWqe?TH(AOy=X;xWE8`=|tO;mGme$}s$W;gz_dH)K3F(O_Vc>*73bNu>_
zauZEM*MbVd?t&^(2)WhNvy2;A)<}uTfKbP8dY|4V!_zfX_SYG2|Hak+$D6yi-L9S{
z*gf3J#RMbe@fweV_M=$t`|DqNSJM-vd*_WUX!i?p9Js#wIa^r;$4bZZf_B1^Kvi}5
zxu3nF#D42+?9|H<O>K31{UVDT8Ef0>d<_<8bgGg@5_5S6H@@8c642iZyvW_+eS3Q5
zds`?4XcS1NK8_jkey?KKOpI(^o-y4oXX-4<@DyIOZhSeJWH4N)kAtmFzh8@zo;vqT
zdb#&ouN=DS{RI1t*!{fk=ovQ6?DD@gF7?Hd$9($e@Jj_BJwk432W={=2PF~7c^$f(
zIHfFG4A8<gPFx=+_r^pWqVg-M?mc&96CG&>6nNyi<f+>Xh8x8L+fEG2XvfYtC1^i)
zwYV|eU0&*j3jn9ze}uC0$1+ElyAywalx%aOe*M&D;!v!2;8;C)Z)TR*uibL+x`xzN
z@WYbUZk#cW^P{+vg_;&oMonZ*h1-o@yS{Z)wyel|AncNL#6+2!#t9NJoNYTcajyd!
z`cH}d*yluF-KbIB7+!!VqHf{J2h2spM(0_cus_o*{NZfeO#_kzI5pVehXFFrP^7!>
zpL@OTZ>1*`3Dc^xF(X@@eTQ5c#@2aiC-#7AYWKq=UPkrF)YragcYqjjnpqC)5xD-a
za>S4j9jrZ4$|_U120~J%=_39PZ?OP>+?;WA(jCc1OjPI!BvHHS<k8$gFVPZTEA=zv
zLIo;^j&%)N#_07)XwG}GG7nwfw^5qaty}brB-2Z46HE!V;X~|(v+9oqw5}QTdw+*8
zpxJ{&o2gtj^=;t<U;5XalBED)3*ZwMV;Z+8_kBqnfEE7hna~k4d}H5kZta+tEPhSf
z7?!W<0<i;wSn8`BzHi4g|Cr?c(i4jvB1|pk((<<2$D6ElPUg!!b^rB*PsMT27bU$c
zdTst!3Ux{+gAz;4^=d(LpObMyN>)-CY*zKxPwHl^u7q5|b29}7r>6M)-)+<~UTa_Y
zgg$-`j7X-c%%tAFqWAG7#2B*KZV4_Y5mOzSnRk4<XYkxW3)|rlE^;`nB?}TEterjn
z$5`_Q-*o%IxSM^2Q;>hz6g_7MZ4xVF>Dyr1;0Wa0?0p4mM1k4i-9OlJD%c=uEwZTn
zna0<$)ny7EiuMPv!GHQ8BC_}ghyM13uZx|GdZ2_k23b|3iIcyF;aXR=eX*XE5{)Z+
z5I>(!z~W_ME#TtF6k~IJzVekS6h$^_7f{_dbZwYAwDt@u#3=dMr%hN-wVSsi7N%7?
zss8JJyH*8kFPe(cq$ObVyge^Sk)C#t0atB?Y*_)Z_L<_QS#nfz6;&ZVFu55H5+B#!
zUcfy@zk<R@DnEftTb3=XbB&5!mqOinTJGaY5__eMXJ4~trj9`8pH{b8z`^Pd#I#^1
zkX&6F+M61~=I4=|{D|*&i(uz)Jr|0bPJ8=$oA5rm5VscRvQN+_7O)QS|Jf-q<Z(QQ
zFms-#<%@2NLi64C7`@cjIei6XtmCfwKD;39b?D15b^_FctpFfRIA8^@y>|~5cPOZ7
zYpI{qY9HIXrERQ{>4X$69s!Yt#H3qj$|3&c6&h`Wl8hpgO=&bZ0EGu{#MEAv=oSWX
zpur3~J-3pTFRO6f6{vHU<x_;c%<OSMKt?NP`((0A<*-J=#0nt~pLAW)e&>Bn{8Z_3
zL+SX0w-uqx2H+89fS!MXpUPDI7Xc&p-#FO|X+hhDsYk02XaM!&9`Hl{W`Dd4eDrr)
zd$NqQT{1K0jx;dG4H@;im@J@0uJztWU#W`Tu~yr0J=VpqWQd^nz#3c>JE>aloZ0C`
zI|p6=x#}3${h+=n;|+F6-mA3w**{Vow$slBu&mN(u-2!4&0?n{mchM?OE^}_)`OV1
zdm=*W6hT4;+@YrCDmW)WdSQt&EcK<rJQv`-1{$o1=}S+6iCgR@qxHEfXYX9gS_#Pg
ziaPyuA_Cg=1oWWXwS62EiCQ}M-cAGvr<}iGk1_aRfe-i!Y<_D?R-*ZrIwdGiPpL=<
zJ)gzwWZu1P{mNPr4r?CK8!sKqbOsr+E);5n?8Q#z?Cl*{=w+q7`}P@Dd+9O!Jp#8@
zxqbD_kNk!0DJES*_DnfIs`WFe26{5ZCo-=touj3hztz^!`0Ec=UtgvGiOfjq-TB_7
z&*{N;?yp}5fxwxSJ=N75`DzFdy&84UK#0#MINe0z27=P~?$~uk838dFmm&Y;0daz6
zrv78P8Bze4Sxg!oIjs#Kyi1iv$-(_-#+i0`50uG?UF^soi4-43KZIf-3~>c-mjk4f
zHR<)%U-N&f-Auna*~Ys*w_$G9vzwNTp{h1DRXjQbSI`2!F}ZK!1|?s{UiR)Mf3>X|
zn^cQ|1`%OI0FIz+@>d7zfYRKo0u||t!+-{YYV>|NLZ5&thj$_)vzJp_5-x^#d5GCw
zy1jM?#B`mUpXnyzTsmikltF_^D=-#!%s(o5@YV~8J<93=iY+xNa)4QBTE>z|jj~xC
z#JEQJpxgUo%D+goo!|+Oi!<GXH);Ioz{8YUm&XoZ&5-K(HG<!KC!_~rU9$LV4)4Vp
z>|a{&PF(pbT!2+JJl;BC7J&p8cM=JC^T3_jI;T@Myv#b4pZ6JispS|VW-vL}H^CNk
zip{@H5i||pOR5qI$tMD_O7KB5uz7ivSftKD%!&&JMW|r~9Hj8VMK^~x|H7EHL@{Uz
zTEsz13dw{Cvqbk!okZ||NkItHVJ29Dd=j{N1Dt}96#_YXr|s??b^metW0u{2l##Qz
z#+XErNFc&!_K_FkK@vJ@xp?TS*bi^Kd#OuST(4q+aoYyh9J8%g4R!VtXPK8u*Y7T`
zxBiGopBJ&TN`fM4aHh>~ff+EmDA1h|^fE}33w&S3MbBsw>dMLoq(K#K01Z7Lu`z+!
zze|fH!m$1W0>s08|AC;Q`VUHYK^V6*ANP*Nb~~9t?hjz<tkx+5qBKzwmKvr1too?o
zv5Ev!QSm9pz^2^a;^?9C2RfCA;IQZdC@U)3;>)hx_2cgI+{ff?z#@h-tT3(E>LeWb
zR~BAUa+_{09Y9!jxBP@B!>&7UZ>xG^3n$+15Oone{P5&9ZPO}hU^rggpWs@^Yu-){
zCkzA+gcRs;*>Evr$B%$9zN%}PY#rkl#}fiPvV_TEc$$&U7>Ra(1JuiU+sIj*PY4JM
zXpMqH_wUQ_@PqT|`x3=M1|w9|GwF3S_j(bWqGUfOGNa0!h4%FWc?wI=^6F;XOvXee
zlk;!|)PgY5h%y&lo*emx0|y|91)w=bTB%xQ6F1t%T9!tVh_@JQmJ#_I9RlgB)mBmL
zkX>a?hNZ&QBc-z&+zHAe!^tLv<THX(ySzEq@+F?Am_48#yFvzBYD2%5M+B76-n0og
z5E}8qSEr!-S+zvbRerKK&TOVDE^6C=|KZ&si96`bOWdjV4KxtWq%$>iPodQ$lOLC)
zT3g+G<jTh`m%nm4W82!Vq(uMU!5yAyGf2alZqU~*FZSRwKhAWEUwl|MO&!!qTv*|l
zeFUW&X8b`zw+{L^qJ3`Ug0e6V&nZj;|8~)gjmhRU$B6*fHoK`uI1u=JsTX6`*JEg;
zR6&PKqx<DIy*L{l>uX*jX-r-44{$b>9i-^ygz_!iQWpSyX+@RJD*=~DX)eUFR$F0b
zEBulQrC&BBP><jLp1XV=S>=|9tmTiI4Zzu^^7%l*;KwDC;<**pKh|?sH;@9`AYLT@
z{0eGeg|pkk;H76aGPsfoR%epuRstXfB)<aihR)x4u4>{PW>53nt~3`c`Vcn+69PDF
zG&QDLVlL*h3S@Pk9TX@1ZYKtmDCeHQXM_SSt?6*F9VLUc%utha#8)$jjdimwb}9k8
zHos@*iH`<|a_Tp;cL%=&!j>8<QvWQw3zmb|&hxg$_9Izmjy#V|zLoS_dhU(<SxjgF
zBH@s1&P=mZ=psk5Axrru{I97ZOPC3YgHms5)ZD;~cI&bSgLZG60fjp*sk%KU*5WV|
zbm+#b7Wd%ro=Zn4FRzS8xJ=XmZ6we~9dl&j!yN3>7CjnT1p49YV;s+eI{L^7<!Hjc
zWi9DmZhRGDSso8y3fa{5DkkjFw|Nt2#@XG}dcCz@xXCT?{%ui!Js(v%uX*)g&;@^B
zDYi#}<E{t=gvyJwyS9kIr}Z0O*PH7P^KE}6r0d>ZmL`$K0hbCE6(FtkGfI#Gd_lwp
zk_1QS$<kX_K8FrkCNz8--{7|>h=Jm_R1s?2tOO=nO<?=E1oh95iX?PliipMV9sD}$
z{EEHxZz;NKI0CJOg}SGRAh?o(tAV<}n}VMun-s<AX%*jlekl&zA^LO4Ph4*eQ2IWW
z<`}rv4OZIe_M?&OF#Vkm78`wJm$;{Tzr-A&sc%P7Y+Nm9kiDX8YPfyg0|Viq61$wQ
zLu%tHvfWq<*3Lz*ZJf1FNz4@(M(cVMXuwH%9C|x+!^<rPm}>xAFMzZFa(XpTD>wug
zWbt)`+|1Fb?^^*D6)n2C)A9+7sisR7OYM^2$cB@S*H<TFXgQd2VUb3yzNmq-^?FEx
zCBu<E=dD+9F%>_{%Pqz4O4~0XZu=F5frekTZjNfDpwB5+a5P7x(EIKnXG2tD7uh1`
zaSda#gKaFCE%IdsNL%#!6mz}%Na-xn=k|WGTX5*Q(M1jCIO=<<eLbi8)H*&c9C(X{
zKNnCsKfL+f{o@_3VHcc&%iWo{W$b*9NlXnIRafU~&ot&(F;=#A6bqj<m!JqXG-Z!i
zo{ll3awVs_+l*e1PG4VH4o9kXHT|6sk`y2g(*AAPbWy>mUq<VmD0xwHKa~5rvnEUG
z@BEHcv8>|R+4(cF2eid&?cTS0^LdrA=FGr_5ZmrQ?Y09^EGhcqVRR;#jYUOQoDDFs
zG_fZSHLyH1y$LA6qb-y`c$j747vUi};C*}f0!pp$z8RE@5#$wOwGl>?X%I^>jjUo&
z8AdC9-0QxjJ<t;v9X9rb*zh5OrNAlEkF9pPKde1}zTLiEUp)RDT6)~A*3NpHWpNa-
zU~T1ATMAET!J$=&lrycZy}W<R)Zd}&zNXKpIc-k>(sX|<T3=lVbo8DX29J%MaO)-E
zdT@Cgcv-HulMj0rFSe72`PyWVLs7nze&yHstDgH+N=JDnIkcTC*dUA=Ig5`&xOlDi
zzTiaQniK^O|GU$_6{HNgNM=+#ARDhmVSllj1OJvWFi<L?+=f;_xJ;E7oB(e&8BIoq
zS!@_6T`b3A<9PajK46%r*3h$N9d9fQbe|K)($TJCRM{*u&L1>WsFO2LKb3I5ox)|O
z$W_{0Xk_Ea3`p)L>i9fUO<3N@nggzfk<kbh)NV$1v#=*nO2<CDoX2B}$u8G~+?Oqg
zikcOB<-{w4DEe@$F&S!lch`8`K`c5P*+L^v%}zX?G)1Li+iz0a3n+$6I$Eb7l4|s<
zq*(k(F=pgNhsb)<2tK?Sa<H6`VlvpUVpM^=?(FZ>HJ@6B+`ohS&5I8Sk}5nzASpxc
z_~je9@pLLAj<)lL5~(o<YB!$W>+J<GjAK!yO8qLI{mX!rSgdNp<rhKBfnp>5zwV2!
zNCLRS2;oLZFtagx`kGSD9rwvfWXhRnkCofLW(5azBg9xXQJ8PgnQ`nJxwt@=AIxc_
zD0+~$vrTw<Fs5CXVBeuaM!Y|04$C8oD4>lv#jtfCTH9(FBAe!;X0MAj=BTMvtvozH
zvrAG{fhuC|X1$L?=j~_`zoaKH_>C;QW+YQ;%dW!*kc>Uf%FLNpbezCxNJ>%%$wrxR
zyEum7<Ya?QEyEK2ta&5ps*ji&n)7ztH?3l;+f_0982|LQX>vPgd}2S<p3kmy7eY}~
zh#%k<I?R{SgcI6UL=7>lAN)yNYTg(x7N2Lfv-1IlZk>u{?~-ches#5|f{j>4k$D>x
zAL(BvO82kyZ)f+I8C;^nolBHJBne2d;7DtpC^Ez<v9-2BAr(ZmZDBjVq<PMM=}FT=
zrkFPF**vfmQYuCB<TJME8w-EKebyqf5eB8hDt*|L%a*__fU^-ilzX}P_xAhhYRZ<?
z%_lj0M+8-VKV5+LNph_9WdrrrG17h1_+^>YNCGX-(k`@*5)nCqFXV(_%OeuKEod1|
z2t!CAz6h3d8$rzapzjbmDwR;z9eAeG>&mzty2roN@EJ+O>!TpG!HVDjR2>lsV*nKJ
z%S+28R{%1D1A0Ck75}V)$W9a)OFLEsdM~0j4NiyQ?}-<+h3xJ>r&7pZrWZ-IE^e^4
zeDd5d3_uU2DT@dq6>TV}A?V~L-W_kCMvVGY%vHI4Uc7o(-=?-XW47NQZUF9+5%dfB
zK4)lBL#P_Du4CeoPpAqRCeO$>+*Gb}#uZHt1Jp;mJnEa>fd@};oxidlwJX^xi4YC`
z4bs+}<sUiL(kgE621^Z=BD7rYVTHCuBM9M!IBRnz8wQg29K26CuQKX)p^EvKZ+=}8
zsw26(vcJrz2H8JG06ZpCX`)PVGlp51F&o2ZGGu+ZCs6eH#rO>Dp|h|Po}rO;YodU)
z<LPoMi{8tVh4+-1O@4i0-m(n@_}2&MrbmN11O8tRfeFh@wa&l;_lKH41b$a688xKR
z<n{FN!)YB)GE<_4H~r$;V$PlNIk>%H7QZcZM=M>VtvIl4Ys83ieqKBuhK$nH<{BB(
zP5~#EvZZz@6UZSLn?x&({~WIWy4gLrDjZzQd!i!4aJ+Z7KXy4-Rf93-e%H98C>hi0
z1?z$vqERE!y1q3#i_f(vO}}uwra>oRGf~rCn^J<10(q8@Y{C0}H8M+kGJ!o{nwc6C
z#gaY6nk3Da)SYpGpwrzXT)1K2Q{8iO)l;^YZqCK^qV_@Y8&{It*4Nb7L`iW&!%7Q9
znr03CN{K+OsW0)<@h0)H0$D~bjUgtjvfn?)eGb<uCVE7LhnWz^fyD3;N&xEuosAX)
zU4?f7ocK^ZoY0@=i**Cj62w2{Y!Ea!C4Q!Hbd8R>-h03MQtl?1%GH>=1?UlbyN=fZ
zm6JNQW+t8ES$5{U%t!oU?ACZx5eaxnw31(|oH%~&NQ#){I0RJ_)e;7D&!Ql>kWvJp
zpV}l7jz^{H>FpigDp$qPKj=L!q7*rX+q^e8KbMd24}XbyZaA}8uI#<)i|cXEN*x-!
z416b|8eT~&Z5Q{^jZUSheIq4PE`{LZcEzYM&jj!qSWu;3TCbu-^KY}6I|>hFfRvnZ
zgE>CF<}4mPR|XRAKj~RDYg%x!d=AdCaI9BYw)XJ-u|#6T@8wXcv$q4Nf<B>Ljt`?3
zOnV6;iEL!+?`n`O;egz}p~F#0)E8mGzh8k1Z~0DMlD}r;cU1=X5qHiM&m7JkEkmBx
z1<oEi@3TD%BhTE;D}I|?Pdo78PcTN1Q``%ebH?c2v<slW$}S~MeD|le9}@%d%POy*
z@*sJIuLz;nx2WtbX1gdM1zJ;y)0dD*8P*C5@}$&*ZM)o-yj)QVz;R(m%S}V0mf5nS
zqRK_or=syJ6YCY-aB!lS#~8*l{b&qeArTC$prGM^n4b@l2O%_cySKPlSEx-FSG>&|
zLve*S?idDhnatp#b7v1Dmy}ku<N?>{gaw0Yh;ZuXn9^%hJS5DBNu~C|FUg;4<`-$S
zZAM)Y(93vq8F$6a+n!O{*}&;lrjCqkqD%J=fxILV`N^X9Cln*}O#4IVA1w6SV!>fi
zLvt_J4>UDuOD%KMMx&PCe~7T%%#MU2YPiwG!0X79*pJVP##0cnu&wdRJ!3{ABB)I;
zpQFYc_1FP8PnibMzrT|bl87^pppXuB=1CRuu?<so`JC31N*(VVcp>zHqfrW!2q!Kz
z&5q8P0x`o^f5eDi)yrQH@guymNX@rApugMS@^MCIML~18PwE(OpM}E6WD1ujDFf_t
zT<@o@0+D?c;9vNcoZb+?7HQ1C?K^=S?r8db|DkUE`$xms|B7ZLDXMuJ=hDfEu?m*5
z8e(r;V!2R>XTY|tWI|YhWF}j=0WM{*XHNH5FNFBkrd771)N>g<UqVhTInMLM;I+Gk
zs+g0x<7G(Gst@)EDp;yWj@IhqHceveMu$}Oe9>IJqRR)i8W!f1bqBu>Fkms^Igm4(
z<%(Al=K?b-(5z*WFkLRXG1)xht*ew{6Q}^qMUzkxT#m;rZosmY$D9|W&~}|z5j2Au
z{0B|Z#boS<PJ$RnbudiK*F5xg+Io?<YBKe4#f=H$0p>_2D{)E=QywpK!N&mC&`pQ-
z#0A?dVy&ybf7CkM=wMJm<*_EOY}EJ~DaXSlW9>(RR;!dp_2k-ZGBweXN;(h6_!Sh3
z4?4;o$#z1W5r8ol*KC2&%n&MFH^RHw9@Q>4JtLlZy>NeF{rG(PEdf~Jidb3FhHV~K
zE{$_u6!15ptu7YvXnvl73y-YpddZqRxujfa+r_oHra;d)$0U2^eu{SN4Ix#Qj2lmT
z>9y+`J{yblzBCHwT}rV~S^b@fT|rfNB&|}HCU5_;f&@QQZywTCnA5Vwp?;w?o@(X&
zwu*{_lcHI+NaDfUOo7^S``#9ZZd}z;N1K5>0=AwyAu@Bu-bUZ13$}}dl}oz_;!wuL
zQ&u6%NBr?ljK*>y*%(6+RPb9<uuadY^`XSirgR4YHZA7cGv9A{3-}*Au65K2x1W*T
z@wM{_<|#!~jEhP2I~3fR2>smJa-Kiexv>3|B_Ynro}pW#t7&M`O58|umWKy!Z~$wH
zE*Mu-sz#tt&IZPR>%8h*A<87USU0^IL<W|h0Rp<;Cq%|#;^<*;1O6aj&+b|0Z{?Mw
zUeO8Xio{=2XpWo!7OS3goWBD#(ngkr1b}5o|NIf{I?$$N_OgH(a<nIk#hN178|%J8
zF5Y9EkUlx@lwNKrl`0F7Zi@qRC9F936`ieGdj(XGzyUKE90`fSn_ayVBV&0?TcoFz
z7{hkCx;e6v3Rx3?RK_Y?3@M&JvX1Z&!kzs^uN4!x^Q_XYi{JSNwA1x2DZAz*deO4h
z?BidAo)WpAIB-e4L~5CG&SD1a$=k&<imNewjtzLKv>SfnB(t4f<!T47!6yHDQuTm*
zIxr4fxeG%?HTGLB*G6Oqf9!YS(Kf-8u!27i_90hWs8d<o8p?i~Xk{u8_RK}ICLR_<
z5uK^nQ*RwK5p{GigNDwPdfm}v&bFGoa@JsPSg{z<p*);6c%ab`Htzn#Qn%wN5R`X<
z>`(Gz#qEn2pWqLZ>dENL%9od^Z1T+T!gAIwlE0pc#cd_)>)1=T<th+KCD8O|HWk99
zLKR!ZY8U2@pQq5mhFnl7D$Li)*YUxIqi`X7lIU%c0Wsto&*!h^OLb&))CI#T<bAS*
zz50xLU#c_A6QaO~nKm5;h(uFcW+x4xcAJXtp)m(aPHhhcAlA=`s)iAxmdzssRt;6o
z_`d<4_5*;Qs#@9?mfnx#t)eK5Ee00)hAj#gpJNh)X!x5?Sxu@OzH~Nl%{J+AV|HQ!
zDVrJfF+p&^=~1!B2iMXr2pm1A<n8l->&NPszUTU0GXb&pohG^mBbT_W8s79yR65PE
zYie%QM$boY(p??XmL*FfIbj~(-y{`aI|wl&A}os-CC;Eb72EjUG3`YvHrGJk&$t<l
zgm8EKyOsPqux2`)!|OKRV?KLe?94(FtM>L{u^6B?A09coFmro<-#fv1|GZ);kw>2A
z^mb3IO8tG?lP%~$W3oLcAEl)~$}Ybg2VDXE1C}N+87hOfT{xqixNo>5q9LJBoSW{{
zVsZd@@9LF9$BtNpKq&r;r)r<i6Ca<CP~B8c(6=!cbU1&uBQpBUzK?u7U6EL)Qw`L3
zbKwN|eh=%BRq9$*AcB{fdqFCUIlR#?oLKL6SfY;#-$$Vqd#SR`TwE+Qn|uKtP#p^l
zE{^fEL9KF(&Y<<7>_^PhS|+Eh)8&|g9Wx|FkOD_A)7!C!p6@Ga_Z3>#qKwT)PPznR
zP4b-8u73U$=7-~E#>?xe+@2;v%p=@mPJe7KvJvttz+CLj&NsUI*6(3Z<h912B0e;{
zhV-4I_;&7#+Z#sCi4m2jZybNg_m5EhSHXYZ?KZ{6y*e^;fN9%gC+h^$>m6Nx0({->
z-QY#+*!{mtU0a>3QZ?)ANMJhad)2H*70(*KTitMFfV<r)5VLnJ_^-Kp>h$)rfF~6G
zaf`k5!b*^YU+ITE{aCo!7fw1NxaAwpdFRg)3b=%0*W;CQFSDEO>COUI-y$4K;=u8&
zk0f1CdE$yukp!`AsrN1bh^3j#4c%6Z$t5{B@PmrI=)p3J`Z^?l4f`AUMKnGgd$;2#
zV&V}_B@oFv{*xIhXtEW=??)28fn^w(;k5m|Lf3A6pwu{N-8$O+v?7LW<+7M*V|{Or
z(3(S{aH8?D;gx$CXvOxDTI-iy?j1t$_}a-#S23>M?TfFPj1&+jsv`mt>w3*(D!7AB
zWa@GTA;wc8bspe3@2}xrZEz%w4M~;C4N^Hu7PK6FY1u-6pQ&4W@Fve^V@^6n3WxP%
zda!h)1-OSPY-U3RmTZdO)QZf1p1AA0*nb+kb|tFBWy$V-)PIBbCwWI!08;gG&xs|T
z1C-ACukzjg2ktFRk@HXkRhJLNON*)FgDhAQ4`1F+NysJdA4HMk71|wq)1(sD>_e1m
zvq*DdW;x!r{NC=F&s&>ONr-msUUR!Tk3w-n6lYs7mPTSt5np~n^?4gSYNhuvvmR%W
zsN`cY<%bm5O@>}snyzxK+8H^<$l(~PYa6Z`axvh9K+<uNmoJCZz&@UTDssdb|EFN9
zZ}xzAVD7}!&cnZwP%_c`@-`dj-S)OAX=HiD%iz&mR53BT_hwAW4zqUU)d82SeWS*%
zTI)E8PS?03dC!qQ4E&BmjB&%uz(nR+jmm?u%jf2U&<F1F3A9LXgn7NJfN26t;pkdX
z&25v2=XUv+54knqj(%$rQS76I!554OoB4Ugb#5<lEHdjWhcJ1*)732OS&ZCYgsN&T
zd%|2h-<>sV1ADIX@#L~ao(^||1nI_!iFA(19DK@TcJdYJcTy<@$3q*Uh0~eNEv{D4
z!i?YfN)*do&6{mfmMn`B;M0G%?(w%M*%<K>bJ<oqII~V!)e-{P$>0BN#?s>k1%%)@
zBVGM^F|>PS&3HHr0Q$$5)qcFSKSM|bUTQ;5kGVA+;WQHWnu_SS%-b(JPWl6A?_YA%
zE2p7C?0ds(s@S5FW)j>P<68(qQx#yXQ2L1e&&kX|SmnZCT4eH4wm^QF2z1RPM5M2&
zM1yf4QK7#JJxF@gQP)dUQ`RfCA}KTdp-_@>3zh_rY^-uVJ=_~)W^y6cO1$CDi1AeT
zK@U!@UVTAF-v+2~vN1?;^>kQ4G~Um7zwuC$p^|rF4k+$R5+xos_Q(DXdP)ll15?f3
zKl<5K<V-DEB}-p_6u)#@Yy8yU$MAfwh|ZlcVlB{@aMdk?`;W8WSEo;6O;<!o*2QC_
z?E}*gI^0L}!o1Hyl!-4)6g`S@7gysTu2;-^ttnktVV&Mzk@WHf6;m^*!B2d&uWY4L
zUDK3!A`z=u?KuE|1O7~;yphW_`Hj>6%w2_m$S_2jj9_T~vth`n0;3R>h3I=PnhcMH
z`9OXS{v|Vu#=*;P$bAZ}9%e*ijx6VFr@C5|$~BD+>r)cJ+v1Kc^jGHPZUtc52)o#J
zq5yClk-K+;zEsjMT50oZdIb&0bHV4nb~DTZmnC|htkf-4&9aI~9cV?J1$zE!a3Zs>
zlw?>J?on4%VVZN%XW77GM9|u)sh@`wjN)2%#}af!*VD7Gy8I#*2_VhOq-`rtkQ97!
z{IC4@K{#V_Tcf!f^a-cTiZ}iqOUKjEos1{ZCP9d*e8R#j!1<$?AqAqn#lXG@v8^li
z%)^-o2Lg4w@ki;6^Bn4h`UvP~^q>jDV>&pCZKxhH8{wz_mLktDv>4^@A&KiSBky5X
z)fp<B`OPes-1`l4ZeGD_p@ZNc#x=K$P<2_fV7D{C1GJlm5kk62Q6f?8Z2)Gr^=`Qj
z{i86lkEx-HAQtZidJ&TX>n^|QC9Li6q#7ehrA!Yxw)=kaTw35i_<r6suO*f&h0}zy
zw7b!8y20jYwBF`%&$DLbcWzQxV8=}ytK{H9B#3D5o!hDvUARJDKx%JmZ$BsRz-w3`
zEr7k_od2_&x?lCPW)%F47E{y!n#gvAwD25m*gzN!vV)uvcRXp0_<eO0###2eevXg%
zUnD>E?_`nSlNX<qC5TS4r%#$nS>jWK!)f-B=2sN4e-umLR;4CIgr$*#RKd*x3KxS@
zD}IODt&a~EVxR)#zYF3hOo%fkco3-hvg<|5jdqW~N1%V|TrOH)(T5z(g^`N(NC178
z1#5N<!OD4%LUogcn>9#mu)b68{`)Vx6Czz@X4GJ%R<YLA61CV0&tyHX`T|ik;gWL0
z8!A^(7M@M64IyvAZ}DQrV*L($tDV!Sa&NQDZDwCQ?}Y@z=)+Z9?nnN;izWSK(e4xk
z*ZB=G4vt7}{IX0H@FnDnb6>Nsn)s9S(O8kZ_QFQ_$1w6B@lJZDZx@;I#`D3vPjk_)
zr4XI^)#ZQZ7oQ49S%37$!#U_f%tmSViABB$p%0(!xJw2|>dgFw8hm-1wpIxh$C`%3
zBE0@NP%9R0v{F3&O+ogQBcq1-VK89?Kv^+K2s3XM;eS$R{IUHP3`<Hb)&3kS)BF7-
z95H}OXu2O|@v`HCu?0ZUy<gn)8@%;ke+n?n<;VEoPeu_A4qLNKG56rqo!ZjbN2D-~
zcpYEK6=dm6KO(c8{9Mk#n{+}1-+(lW6ljDMyxvy-DJW*|ax&D-eQQPPdWC!QaV)ls
zt6esFuL(7Pu91_@>Q<zd`xyFY;?pW_(KvZ!HYj<3*{;5PyV_cu;}^f+a=A9;+WT;j
zTw($}$X)w8k?ygPsqJ0%E-opbEiQ~DM-F3&U8y8y4GV@Y`_oA@r<?TWMS`;lxWh9<
z|E9BRUORo`+j({gWV{e%DOs0;_RCBA3{l~WM~Abn?ChAnvrH>vCkLw1Yx9hbS}&-p
zVe7Qj7~}yOD7fkS6+qQ>mNu<N&Y`4BGL*K-W8Nl?3Gv1Wh3Tk5xUBlM&`sa_cHrI=
zjtBpPrs~1E+Dge<;!DZxbpIPwZ_=IGyLG`nb}4Dl{QepFWqYO&!gwHhE~Lm=eA2<r
zGb&T)#$V<8yw<9Fe?sDSB*Xjf)L;=>R+bP%HTH73PqdveYERqa*&w%GuOR9WX=a@J
zC3MGqd`+`-7W(;>o*WsrfINPz-^(U$W;4`a*t1Tk-6&By-8@5<uf*nxYb~-ooG>PF
zf1=rL#u~7J{ggp#7vUG41}tK1>~Y}rOwrXeaKzB<#PQWuK1g@$KY+$E`ctELs#9s<
z2`!ws1gmV!fd&(YRKH7GN~CRB`zNq&cg$X@hV?5=LY@(=;&T}}l@zrE@sWma3Q{jR
z*QG~o%O9=g#uGCaseNrMGiH<9a@22+d{}TWfG+KfoZ3|<_U&vZR>Q8b48keJk%0^O
zh9Ra$h_~*dbTRkm7TbPJ#<^`%41Fi<>1248`qYYjvvlh2W;5pLbR-0(ixe>}p*Ju7
z&sFEJS-;!;p4rXTf*3Zi6em)#=<e<AzB?-Nzd(5TyH22TOoVR}X(k_~G~Az#J4sk3
zuf$gZeNvZClp8`9^>6qRiUH@Jnv=bH-3oCM+vwzu^!QdD<dgHAhau9my080L-&eHJ
zo!LgEG$(hrvinYFzL!QuWfA{(rmpu??8{<PzMgFzt9rq2t-d<`7`c6^qUVw~c?w`#
z=}M@xxv46fB!;0I@8N2lmah_!DB{6dBD6ZqqWVEIK>-~8@#ExO0rEh~nY~kWzhPs~
zeeF7c;z85|Lw=rltkI@C?nJ6TR^v>v#LHc@@UQ4Z8P6Uz-kkf&bI2wi8NDy7h^mrA
zQz5b)(lgLOgWen9CP-%n356A$Z%E&ZnbN0&5k)ribVL(P978Y~wLie<r)RBMoA_p3
zoEr$d70IrldGVWtzz+kC|Fj(ROT{ydQpfng?olJw8QvYazK`IQ%Z=aGsgDE5w}XMc
z8M&W1`EHt?pD7YOMi)5uqzN=J<0<27_LQm{H8ra8tdJM{!3R?@2KN;RsVS8~2J<C;
z#;o#uB{S#Ck_mqf?c2EUekV4Qv1?=BdWIGk(<V!!j5*@rNlTC*_tf*zL)OVHk@=)w
z6T+ye!SjXYN-05}sOad5+~zQSai4v?o?zRG;+7`(>7E2WiVA(hpaf8~y1O!kBsdrm
zwI{=Eto}OPHk;6G$LLYd_iVP-t3_+_xFPdxx+SxCU7Q@j-ttyoMK@iv{BCN}`h-&?
zFb23I_{2ar>_OBe9@B~q^0}{b|3P9XOkpn)qC%wkhj5NJ1<lG{8?WQlDlOh#$tb0R
z(<*o(%94Z5tGb~CPA4jsL>WYx&TBuJjkmi}>W9RXO=3v!;K&0nMrH`xYV7y>FH=$(
zr7(ejs=TwycSq32KTbZtjU~U)HL>db_${T}lC}0_Thm!&AgmmiY9H@mFBoD`)KG-O
z64d1z;64^sGpV-vn1ri!M!rLhF%2jA(QcO;D1uHd$fcU1KuLp%eev9yPu<Uv9A#l|
z>l{}YOwS}29Y4*ny?TC@W`N6@6vd`o_21nkT^N4S*en-$7Z_*QFcAu+d)Yp+2vJ7b
zC4v)~TYEcgsTke8&dqVFB1J@7R=DwqtFqXJhp`)<5UajS5nFO$0R=A&4$<^~GF1{j
zY7`h!`7HPJq8|APytBJam2;td<V@4FT7;Snd=FFiA2PR6xnBZLo-_b^`^6s5Fu1$Y
z=#MNchygi*R^Tb5fN%M6q9CyhITW#QK5McyRBMZ7n+yhC<S|DddPpBy!H+(GdwlUB
ztl;O)W4|oWZ+8tKXsA*embC3X0`rU}EIHxj7>PoY_~Yf_`k)#b#S@pQA(aGC!;%Pk
z38Y_bRE2leI(G@A1;b)UVzT+tc<eM|;;=VDg<+Ue`=2<`5A!hKV5HD-!_TJtnx+DS
z3_wb|tsC!&_-l4Vrj}ODd43;fhiciDn%H$UyJ=&OSQEN@5yJT8lUrqRx%vQixl6S~
zj36aT7ES~5*q+-+63C_a|H_EuzhIl)XqyN?&V}J?C10e(*K;3Onsv6e8^x}VaM@5O
zM;kfcMw;~p=T+4f2|AumfsjJBf$o?4i|Nzl4*R=HTjv7m%VhN!8(spouPJ+wP45)h
zdj0TA4`60d|DMJdO5z>u>g3k9_sYte{3Sj7YIZ7@DmxZ>(EZHT_56Hsd8OUV{Z?$$
zuT0gJZ|Fi;)ijZ9HCDx-me$@HQbHF+NOL*S{Ysnu{xbd4=@OWDcHgg}pn`W05xqNF
zq?e-MTN0?zl~sLTSLU*a@OBppcltR#i^V9B-D?}zdy`HXGxo6+io9G6RC*s2R#tIl
zxc3AyaP7H<dM<5W&*Ep$I~g)>=IZ|oU`CIO=aP%@xvk99%qMu;kn|EjEOGh@Y~wmO
z1!5jPAc5oI{Go*+K?W+x^mhT7yG+CX1a0VR=hHHoj8+)`eX0)4{SZJZ?NPJTK2M;_
zu6ph<)*Bzrhh?Oh^Od&=4@5PFxnrcM=euRTD?x{tX=ub_a!vAfSBWmZ<y1iZV}-Gv
zT4|Wl{VpA8-s_Yc*voD0UXjgvi4LmFg43BFp8XES;%_5JNh8R~$cAD*-SF9eU{@sr
z?>2Y6l1tZGzK+!rLT>mr8<4eB(1p{R+9l^&<;tHK-&G`;uwG>%z8aY4hW5MgsU3{1
zJ(%Zcr(!q1SnrQw=HM`U*#x`J89JEy=#QcHp;y`{YuWsA_lnjk53Zog@_D3wUkJfz
z34<+SC(>23_sTbabp!b9Do<|L0?&qh_k~+pDyQvi0ue3Uc+Y9&@l*X@ITiC%Y?P~h
zUwRR<7$8=VV{tWZ{COrDA0dVjLT~EOSdS!^0q^i6tda0}=foRh$f>9CeT}jriPAS^
zH7Y1$P5crXr<y*HPVPF?W68VrWQ?I1EldTwIdl)3ar-HNn%VXDpZRhO@mP@L0oLIw
za&;-D;yYzkZh^R+gBba`4QoXUx2wRP!16^^Z=sigZ^V~LPQVsl{E8AjO&}^g^M?h8
z>nn#&-n=a|HPuexLI77BJ>>5b%-Ahe-~!JOf+K_g>+W%l40*<bT+kG8M9(_HTt9BK
zLwu>g0)k4lU3R~$@*wobvLTppEc0l}CkHjzGE=GbQ6Z;Mo}y`I#@rQvF*Q<#=0#(i
zN7q36qKe;AiY9UlVd5z9Zo9V24zZbjNV?U&YITY<Sg^2WmBd9B-UW4k<b-WJr+j)0
z{Jcd#Gh9HuhIL0tdgQhlz7UEehblt)2PMPZ01!t|ZS{)yPF+C1QW-;uJZ<WP0ppI#
z_riIKHdydv0C@ce?HA9aKq}t$DluR(snr^6TCp3dl;v|Z922lTNW-UJd6j*#Bx$Ai
zunZ48y=&9Vbt1ms?~kDD)Bj&k6wxnxe`d@HVZ$ANXA=9K#2p`XUeP|Gvd_j+GUU|Z
z=^K#=6*I*KOnSo(5HcHT3#jvGF-Jf7I>`r|>2*AL|66{@iOnY9y)?;ncTI>dhedaM
z?ennpW}jL>Gp%d?6mynu$y!0Bj61=~ow7H4WT5xF2StrBVZnMbD=^uP44Y<~735_d
zj`t3UL>Z%20{y*-o*R0cy@8W}YVHyxgaiK7$o=feD8R@bEbGh3CSPcE!TplKpe}WY
zug`n+<Hz9KpYL4;u}>>rf^*$!PlVtBwagXi=-&p`7It@mKeY!~gWao`s09ob7f<MG
z7n?h|yi<PBry7=v)h&NZpw#oUb&O<gzVh|}jV5CQ*LG(Jz7XkZ$Q>Rj!2Zw0Ul@bK
zEqJ-LJbw~#BC-Pe=IVAok_+f%kaGrhaWZ~n^HLoHSDVC*E!M4crf2cQwe`^!Hl3*9
zziH8!a4eCIr)a0Nt85?iK6C(vf~vDMr^^<HSGrYyP?0j^NjyV|@aaOo`7j{hMgA_N
z%1{y+7S<O1$NhLvq*`QUBL~$Ep5f@Eo-R3T)7ceM7nD<Xta#n!VG>PH2px_mrBADP
zMds(Zt;NFO+(APa#vCxkPt5XmP52HOtXq@2D2mQQQB_u8$Lmw^5@2|RT$#aWVuoAL
z`n`=Y{b(glAO)DX3DN2C^7}CH$Km)>QJ?aqF`FZkZ3MZrD-5Yem9?+7;66pJi)Gj*
z#%yj0Kf#uCG!*xTHlo#eM<#|Rrqzd&*?hL=@kQWrmKq)D3U|+aZ&Ez7yS>edBOco1
zp2Oq&2hxC&MM!OL`RkI#b_*wVpqSPPx;NF4mlk$Hm_E+NnIMi1$1b;`B=*1!K*%(^
zSY@4zVWmi1<~#5<*Ml<LzC;ivEKE_o2m{345KWO>foBml$`GpSj(^%r&}*iwd_9Y~
zsz%KWn(KXi-`=%o)sQbxkoatrJld&UK7S?*TTT4<U>YBbC@}EKVMTXqDPh;#&m4-K
zan&K*lt|s%;Qiq&AQSMdgNf?yF<_dc=WYe3f*M1eJtPWTQk54mQ%->lOIbPaE8Uoj
z;K5kuOK!~Ep+;E1H!`dtsLu;2X=)5c2-$!oiimO;-ZL5oa3w566DV1O;nI6caqMRf
z?9o5K2!Xz;4P#(>ES4wSEGLKG7mi}W(u$057pr+m2-R&g0xChctvSsz4D{){)%i92
zkInu#=e8_=gNbbqF@t)rG00FwU}3fNB5O7&$pl-i#_rz(5c_(QgAN+x4sezuMJ>4d
zCiE>qR7F)>5xmXvQ3{j9)BfTarsiPI7Sdu1%0R!V65{N55tR~E1cRjdPd`xdsh}9<
z%Jnk$qri5M<{7L2>tz*tMiqy4W>+!UbQ2MPD~Bli_(A&iZQZ3n-;^p{001)gF~v+Q
zUIB!}{cx`h_)BY@n0|nR6B>*Q1<(RSB>VV*K%|&erY;h>LstfbDHMA`v?(;imv@_J
zVG)pC^90L2WhKn`qG58W6j63LA=ToE=cl>5Dt>z4d!Pw>ce}0WkW8Un^5v3-`C>oJ
zKs|T3G4Enx?VF#}&<i*{6+xW2u?ZlLz){DWPn1%S(6RMM>Ihtxj}#>=%o#n$-0W6F
z3F+KR0K>wgNtBkr$enen{Gjx%F&37zlGRk_OLin1U-D3x*wXQL2t_!#@)2s&!4`ZE
zK*9m4d(Pl7PCsLjeC|JO^IV^J6=zJE?41#R2B&bgYSxR?{jYeZ0w_05OoTf!I5A2V
zzh^+{#^c{eJ<%6{k>ga2gICw^R420>8J6H$_R(CaeC`l9pX6VEC@FFlG4UTq{*Bg#
zmNPTjGsa?50zpKi;wj(ip~!R`7~(R48{t^s0rQ0NP?q+`2?X5)=`HdSg&MYw$osh_
z1_vWA+1AY3LY&(HB13@{a=L6(`3NCJpM~$ggYWUu=|#k>b)5_K8oG9u`;cZ0oeF#C
z-P67&I|JsY9f!cWc=q?fV5Uy{p!^;XmeGpHDs)P4;d|<WX{2DccOdT`a%3ZX_w$BC
znzXUr!2^sf)9uRD3xCSu0V$%0c@up^F_jaFiJF>K?j6;whp4m1JC5;fco$J23e@*i
zdGlE3;GB7^$~hNvc6x!<4q%7hliiBBCmpFaR-ktB*Ha+oghD3%hxsA$NRbe$1+zd#
zew@7haX&iN&e!_%Wq;LFUo~@12Fu$|Zl*F-H4DJ-5qP(7BgB^j4$<r2qchZZ|K3|r
zRIzA7R2y7ES1-zAf*EO1qy)br8|AKJW)1H9M%MF<3^+Ks44Rv@i?SG(>UAH@#@iN0
zikS>*^a1zn8d(4N_Tavga4W~}RDv!A&i}|d#j<(KurOxt**syq&N_t@^{UT4(nUO1
zAlK~w4f9G`HpXB7I2a87xK1M#u;Mq6s8ZeVrb%Ij1V{vvCAvJGa3pO~K_L7wEguBT
zi=JQrE2ahU$VPF1x(Cc+xN|~Jo*#t5NPp5x<3>c44DT9J(TIG>WyX`HVpjR!U)`Xb
z$z~JV7>po+8v<uAY}qN+SFd5$RPM&m79%rPUwDin2wVYl0DWNB6i+mnE%`31OanGV
z1#g2tepF4!8P!}OMYVu@x~&nbTPazrJ8ZMP$$k>By?7JC#e@?|@}@={P6(rq01!!l
ztO-hQDFJq0m>HwrSXnpy@bA2gT$_Q?<I-L=pV<j*k{P<P=R+I1FU0%HEQ(opLR~_e
zRv|5`j3+xNg@;d3Zp;pOPNGbNHwZg;uHw{Ef#{}Ke&mUf8LO}3L$hmO&=EcNK*Em@
z<}_uF3ybGO4N*b@E54{eC35Cl$=_Lsd})nz$GfROuwD|u7BiOm3*79kKPXUGQ|z{a
zi8IPD(ElO`lqQrah$Ta+A<O>J1T7Ew@;WhWc$xiis2~<h6=~P-);mHnGQC4Z2ipEU
zZYj!<@_w4EKU?BZcrwL-94zkLdBUB2?h@zb#?~D->aUan6@coVR-<d6j73^}B2Kk|
zy_3pn5x;Vg78Z7@D5ob5RYkFQud%F^!&HlH+||^=Q%<1F=bM&PqLR|?0$;{&C`+5G
z5v6pbF11}I$m@I@_h2&05Pvj<-Dv5y)z>NcF_=}ork1%|p=9GwsTwH9BvViaewd-F
zLYVTMx_YfrtutnUl)d?I1FA2M{YJcY+PERyF+)SCIGQ?DjyrewD3Qq%?+}`st*4-M
z^k`$(_SUHjjqrPpk-(!WQG(3p<eDVADyq6SBp}E?RXXS3e(=gWK6!C2M2QSLREmIy
zE9tns{I}GRgdrtkd?K}#qv3m{&DoQtuJS{%KA#MEP2mYLi)t}??A6NybHF>Ir5$qt
z8R5vThUiglx%jm45;PBafj2k<6_4dJ9{%{!NRw9fOzi5WXp>f8W5c5xsy1fWxeP{h
z_3Lxy&mCJzp;6UZ>*#bfhcL=uO2mS2@xD8q9tvpFkOY?TeEkbdbXn=F8b$Os!;M5x
zcd@d#1)TE&Rt6IQT2v}@I6s`)yz_XVuT?+DK(Z5q(o(;@OSo>nNW-?iYolnru6&Wl
z8E6@I3|1I{oGk>H9CXsKzb(WmJG17l7VK?lC8Oin<nP}ju^!=miTRi?MTtu+ZL_+(
z7HiU)M8_b|^?P_$+GWUw-@`jh`Af)1(S-bZA3rLEofp7=)u>XSZKejM*VSC+jW(7*
zfEfTCI9fDPV9eBYPFQ+wq9F#BY4_g0hg1CHdag$0+V&}eywHj@B)^~na|sikMVS(N
z4oDo`E)f?<CC!aZl*I*IBY~yX?y@@kys_m8jFF}K^<W<jwBEG{{TWF9tftMdf5Op0
zN@|6h#RzIqqjjuS+0Gn_Nt|`N`*AvV02S6(IE9K{dKILU3?pu@gUu8{%r42{2Fc-D
zL<zs|dQ3BA?d;d<ZBne{7#V6EJUpUrO*0=IqnmbS9RU1J0u+?<%QSADqXb2Bkd@{;
z>i*2<4~poXHlf<VDvI14sd=yGU(g##;b3A&nAOYcm8=|1iiee|zZb6?G|u$8^3yN%
zp^3nKQ#Z!U5EoWYA2y)|8)o5-JDGA@mPel8Cs32ygbn8wST>NQz<1(gIkxv1Hcs9y
zkVBJs7Geg3i^Yc=j<^|hhk8&7EHT9r;wX`H<7bSKlvVL0`y~(YMatm<!?{I9B-5l1
z@f~!dyVQf^NIJgMUEJq13*m0N!vK^@Xfi$tLygjDb~CU`Z#tWHUEBCdoJYr6K_4HR
zzPrP69gb@z0go&9CHy~KOWx?LsnSWQ&*T$7OPviM{i7RCsnpTY$e#!3>*k6V;@iIt
z5U3NvXvaX?RR1ICDx;$6y08KYA`Q~*NDhsFq;xCYAua9DjkI)0mvl*YOSd!#Lns}R
zL+5vVzqR}$E<|VDd(N|;+9XpSn3DdSe)0>oN&T9g%jjSqXS`R}IFX7!ie>*Iil;zQ
zP4;?3jR*}b55s%RYJeJ}QV?4)7FW`btc<L7k+8s2#kth!j@9xNIEl3UdMh~;#NK^s
zbI+(>DcEy`A%(Oi(&y*Ja6gm$;zc6w5{hk2MT<^bZ|_*@9WH7cqiph((J`!kZd2tB
z&u4orL|Cz6aN?J;iX6IntH7J-vlg{<bj>u)XI-D0b+_iHYZQ75WSA`h&YnMq673P;
z;-;|E<2=DtSF`lA1qUB<B(vHQQ=&aA9~Si3_A|^RJuiJxU8&XCGvh)eeIv5L?oT7O
zM#|l+ee1xq1eRj_{5Zb1$d7t`R(<W&c;@idtJyMJIBNiP4+04a&)3;|^l4*(v+y0p
z+Rfwnh|p|iYz%(h^5<g+aPKbPd`R5m)o8jL?5e-{jUwDAyp;JH>C@dN6LJs=U?XBi
z!CqRm-pj_a!%U)a8|~Ze!nv!#G+x)c?~rF+h%?7@q1Qv9CIQi{Kl`&)EFF*6-0yc$
zH32&Ldp)l<`8()&JVRKZkpw<RDim@13r%r2`<IntYs^bCsere#ILZ>Cp*AIkwkI(*
zi_zWei|OpoZ$H1A%huUbDz4YkDOa|4($+7lF|bi8b=5W~`_p`1zxv>E>GR_(tyHh0
z$)o5d*OIg2vTjPy*XSe^EsQK@#I?iMz5k|5^n`iEEtsn?_>GTEOh6h>v>cZIxHy5S
z8e^nb3DJ;4<=CG{Pb;TIF}ZxgaAx)U-4IP}y^_jmofStCAL6$-OUNw4`R|hIJP#N{
z8>N`cPOj(1J^|PGyaI-L0*+^V`o*%VE!@nqsn7842>sBPuVIb9<7^bM?g)!}cBhI<
za7f9E=KtAlE??si>>9;uFrRJmE*$7GCh2!?M7I_B#h2*%P(D-ddY1tVs66;<msO(g
z6tFq@<LD^oCSJQ6&QczKm9=9JUGya4SI}G8YTJ1A&w87tsJCJP`Nyc2Ck@|Tji!0I
z8&|V2oL`CkoACv4+Y!0)dd+oRT>Zf$WFw!vs^2auVW0jX38Xn3Wp(f_>oL@87A>=$
zsI{>fiw>k4TOlYG`$6A>tp}aU{e=%BkQGaK6&(L8c<NcZ_a6-D6B0U)glGS#xP<q0
zC(Ib)q=}<x4O>@ku!P}Z>+i31v@%21uG-K?28gV3Q*BMi7hySfEDZwC8B&?J0Ym**
zj@Lnf1;>u`1$<nBKbWQaIMkk8sS*(A)^}&9B=Fjg!o14{&g$?IJ;#KDY03}naVb4#
zS@<%e*HE>h;0V6GN;O;RFfp~>nbL!)7Xa08roMw&F^oy@jLNH;07_8Rlhb@il=$Rl
zhNOAei+0a5LV$Lq=DJRDW^w0ME?EyVTOR52Ub70+lX)lQ42+p?D!&R1EP(lVec2I9
zv=?#=3oOsM(7DXyruls(ywc*5mS%0{<Ftl_IlR2+^N`835b5|D4T*fLa8KgK#iXnU
z+kWI5GrDRM#+KC6tLs6=C_)F_9v%^lD{M_W2iv-Vi}K~=YKnrA7#`>QLEiSRoj=`F
z7?fy8#3laafA5R1#J2faIn+fHUWziZ_P>c2?Cw8{h9M^raj{ifRX9|+#J={7Oq}b&
zvUx}M&H?HZk*b<&nsj-8eQ_ms&#cg22ylyz!Smq;H}50oRflxmA^VsZeABNO09DPc
z-S%zUKT_5`iQL2lSjlRQiOtmDM@(+Lp>_-hB*2jL_LY-tp-ocLRC~AdS#)xkB1aK+
zoW@k`Eun2io7soNxg2x}WgPIw;=|U*k)8G*<mjpy>~UGCf;@7&yHtYICVwgLwOtM(
z@!FN2^!r}ZoCTjLQQBn^fgyx+nE5q`0mah?Urr8B$z0Sq0IRHzLq@c)_HT>B#e%l}
z57q*}P&hh^G@3Yi8jJL>vjTFIbiTU@tXZ!h%G740t?V2_GW>(Zor29?7e0(=v6{OU
zCZwx7oiIV4)2Y3$LoBo5inC#u3;RX<BZ!=LxMOF}{2$FdKWd})pme*pSmvsFFM-3~
zD4Le)9ZKzl_RO-$aUf@~YT6gjJKaiSh^E)7>-(-2ZWjRp1oDcciq8)}|3zP*2r1t<
zk@h`#oZ=J#gvXWpnJqrf6pIfZN-HYNTA<KGs-5=xJeW{cP%l#wE8EFz3m2GLieESL
zMG;-m3DdNMcnFnz*3&OVoVRch2X{Gc(Kmkb@t^a(AIa?S-3($p5oheedD=(WCSxYz
zCi<gJB^19&@Szv<#EvcdV#5(RRwJ2~@((E!TjBo!1uf$0u9(=j_^u)ez*)j?1X>9r
zHIl9pn1agzBlk?Tdz`?D#lz1xc_^$>vuvg|y=c`EmOxf230$~NdPMfoBnPADjgS6%
zQYP#7=NoCaiZn>TT|NnB9V;-&Z7nIBcvQOyu@yEsM9xUXV{auj)$6QpdZZMXN&7EQ
z+MwHiUbFvO5jjmbPLQIY(C^Y#6lqH>J;W}vy^CLJ2ge!RWPUwMYRk$}c6>a^1mtZ(
zCg)r4D9)~rMwe~A$iM9$#7r4D6`4zPz)2vJGhoW<U6i9r9Q-R&I-jDB$Cs~T1X$We
z&+sVVy(cc%<zEtUQw#;#vD@^m=dqBK@Zb#9GH@4Sg&q=F`jnCUP)qP*tLM=KwXAEk
z%6P9n8U>{o2c@Vy=|{K<8FnupqP9ox1#C$5ixZ&ejiHJuDAJ)Bv6EQvC4dk?7rSZQ
zglW5qNkQ%F9!Np)IuzfNs{h>5SR@gz(&)3#1%CocXfnAt?h6S~NHzqF2V!E)21(Qr
zNbhtEthxN=(V^)-XsDa*!^BKuDDjN12;-<}XpQCQNL~kg{!G?b+e(;2y&58H_uCki
zr`~?e@gg-|l0=nLmXT3m5P~6YzQ9%6#`E}ba}gMSQj7k4`I&gPaCy^6-XDX}`r~DO
z-gtgM%2fk2$)k-dsN!_Nduvl(ucb+@X|ivrpajNdBY<uXkbV@%-HGr9mopa$!G6^X
zg>BGrxrQxfYOm-$bg$k#UMlZCk$a&`(8#4}{E=N&cn&*ofo<XqT@26Za^9cWn>;EM
z0$p1tZ922lQpNM|E!4$!Ra4uxPN2{?O%{N0p2yW*{t)3VCP83I0D8DR-pUYPU;545
zAUaV(uY5l5T`#6;ul1F^E??3zgB3Sxk9sTF1e(t5>D$0_;m(atW{g%F>iry;FZ84P
zILpbD%3P_Ms}E(3wOJGQ9W2UwZpBi-K#`KdBIQCBeYEJQm-Dl9U@WdaayHR3`^}B#
z#rrM%fv~_sRLEoq*)2X&;#Rf{ZFeY2Dn#hWXFiK)2O*gaZaH@-VCs-P$Yp=E86Tc$
zzB`%OiiVk)2ldvG60PXa9wB4s|4CWPRlu?!rWz7d3H5-(nwpz`K3oPgBr|Ik*HS$^
z$uXMehNh)twGOAmKK>bvb)4mUX2vZ^mu=0k8eeh0-ORe75%RDyCj1-Zgt&T7{Di*W
zvgfTe-mY(wA1-RI3J_JCWO<*NWs;Ds-foZMBT5kgG9Pccu~{7fYHu*d>KHBD^BB>z
z0>8fa|G+LEJt{*KVyP=(bOFV)d(3VO;d$uWWm7B%hn?T|dgI`^gH2)vTSIcO4d#Sy
zX9Ik`YrPiWwtPF}#kpmN6I^Q(LZz4W=e<Z10OYF$?3aAQde-$?*7a^{=j0te_uO0k
z!Ix=l8PbF(T{wx>n6sp1$P3}`Q(^`L9HVz1DdVsckZfcQSt{d9NK!~D(TcvC<nhKO
zGeDjo(mr5Sb+p#AH$Z)hOHge^s2FiuwyHud&W-aV_QLuQdHk3kW3M|R#UwEByB4#T
z{hjAWV>QuVPHEe5?{pOLmmNbmU&Vh<jg*iTT_iwm8^4)eX--oN-$)?MB&su6ZdY9|
zbG1Vppw>j|GoGD$azR-&-8b@cF|Z(mX1U{44*9)?-Vf-9?Y<#!*Rbd|Y@p@C&o9?R
zu0B_IZx9%|mjNmtDyt8lt(XR-Zp~a{GE9T=@g`YaiQYUgimZm^7V)ZI-=^LqZ|P=@
z5ypLc`HcU`ntYnC#m$S>Z{j%DGN=S2t9+Dz==Z&^SpHzy)LeMhDf$6Clp80WzNc8?
z0gU%tXVwae>m+26Olvl9GxvO{!kg2~8$f9R#{c23?;UQwO8mm(=atdn-(}JTxcV-&
z><qKUF!Kj6^Re7Z4`|W52<5-Wv;>i1gCd>6F^i=3Z@(<w`-5W#{sS8sf-;#JN-O83
zqD_~-tI$&u`1f9pIt(d{mg9BY%Xn@Q*1Tlh@^KqoF9*jIAmkILcFph5IPCDPiSGzm
zu;{P!I|%t4w!Lqx*D)>E%QvIC4e%^p_~9UUa!iarPtgC=AuXHpJ(38TRxxi=ZEfF0
z#pn?Tux+?(jraX7Kb)$yy<d;F29H;_C&ve9hAD%y8}fAIP!Bls-R<pSvz9Uof7wti
zT)T+HN@P-y39BLQ97@Hj<~I#HZg5@Y)Co(^#7k43dm8a%LCYqqZGG;#NTM*;`8bk&
zsXy#c&+S|agQT1<;-DY=43l=SLp*SrJrH{{N!z|&mXyCR7(K#56`;hgy6^87-(ZM!
zWh(l$tXTklEkRO2eMen=|BjR_X{{(nPGi)8+vn@fFQ;0ls2J{x6CEE!FeRQkM*6!f
zx>702F74OhOeIj~#3H^IadHk*yvKkDvOD^Hj^6el#1!l7Cxi3UExSSTyO*AhZQ7YJ
z@*KiagXO;ag0-qvMIferm>SKp9_n+lsb~OXE`Ye}W{vFHN7C$9%-g2DZWB%`ZIXsH
zlTy+L9Cz2*cfN)~Mf5ur-s6*<(})ts@i;9+i4Xf6E$;KP@`i5|vaauPiFQbAJ&&Yv
zIrisKzlk>pqJ8^?bqn`NO8*P|0O}vk$jfefgh>^w91Tj#Q-z1$j$1!F<d1gT#ACZ}
z^yaqScHstxsQ!xTU+~B%KRbOEHd@dN_zwFH-tJMjHQ+5O>zgjTQ;WhRXbWJcAN@N0
z?jl7p^E4Z2!_vu!zise={V>aaPOkYA50Brkc%yzM3YKPHZy%Z53KxA)IILlgE!377
zv@*G3t)>R1PkBzRQO;cRuuwObu?;t$^+*uU*a`G2XR77r0a-W|tKWRFhgrqUm!bog
zN*-foIv^-H^QSDu9RLbX4Z1Kff<~G%ywACTO)ZoG%E{gOhn<+aLTr7m2hj0t9fb|9
z8!I+pwA;+2MX&sy^zx;*M|~I+{hceX&Xf-Jvz(%3Po*$^7OZ^0smrx%pb{lE_7qM^
z)X=uC<rColLK_OK8`TVyL&yShFqft#gH?K7ixft6mooEsl*ieip_`g|*&?`Y0*ieA
zP)h54W$$|j_(mA5^mEX|e2l!<5^0ML0*in!Nij~zT1?MhI5=2XhN4dhhh3n=*!(pc
z=W4nLcq9@r8QTEo?Y{saYb{Ie6ed$#6u)A<ryDq`-_jCC<;n)5?H5B;np#>K8bkd*
z(}ucQczWJ6RYi+dc=MzAv)nW)l}%OJ&}~g7mxu}5sq8sfYQ68UnDE)*Z)x};-Cm*m
zHX4EsuJ+d?aej;`kgq7n3y<(OQE>Fd<ESOoU$$8@pdlk6Ra+(EnxIH3;h;PgIkI$T
zY4#zKR2pC)d3yR-qouU=jz^>Np}sE$hwbQ-I1$_F5fV1M0R};(|CHm5S0@}2*qALp
zcPK?8*S7!Sq9|@9vi!x960J60!{+K*l1e-ZA{<HFoy-p}I+A4CHIY~(5}=wDEL?9g
z0j<uIz{6bXY;GQo(&_z26iGS9?2xkIPe2Qm;hVANS_eV8Y9+RK&nQyb(dx-Chx?u*
zsRX~vwXT``c<%rGK=^%g`LJBupi;Hr+5FaEZV6{|flWL3#PA#YUwXbg-L!m(rr%mA
zKb+BxZTt4e*AV3%2w5<tvcO(<5QW{}(!D3sq!i@_hJTi@&4Gx1(@eiIym_O3c+Yxj
zkjxwH{OO|29qx@GwqTnUPBj+)juZpCV8Gm%FG{*>*}X(3vzxsK=2dcrHD_OT@~0mG
zhX3pFejECn3Z-9vt-{(1r3HAM^=V?+i5Va=bP?WnKbQ8XBl_H0oZ4)kKJ^f8r^0(G
zdU^*MK^<Jb*G#!HhSExNlGtf7c{NsxO@(H@BGT04(<NSC{P38A;7E{47OzR<D+|W_
z>AB{MD?g>IyMx20WF4NoM=X#0SOCN0jTQdyoY(Zvl!o7IxX-q*G`GvE%qqP~i8{nn
zot80O3`ld7+|(@5Yi*Yyma-fpdKc+%@Qc0U+R*|{{1b2;Uaj0msFaO9x9Gdj+azn)
zx*V40ZLF=Ww=m0rhOMvBsa|2IHbJi%L+OUMO8|P`;h*?yl)t>LF&01GV)2bAkcNsC
zTBBw??vPU%Lob@YWL7-;`{ABQ#JFrC$825z-8hFDuxnsY1<af@YISmne{sndv0ChZ
z6pRh<QUH=MBXR#P!{QT~@4WEaj*bVq6`ykqBqaK$jv;sl%7;3)6TQr>?$%N76KCtm
zZ*Fi=h=&V+Nw47f8x^VPf&%6?h&nB9-?5jKez?wD&M%u9wX&&Na;v5NAPZ4|I)W-P
z1iL=+yZ^rV<t#M2tLSsFAAY+&3k5=`rjeGW>16QFV?XkjJCKxQQI$E~DPwq|BHX1(
zwY*ZR4E)C?VT-nH<~%3}5w8cl!zFD~c3cx^Jb!J;l!)8IWC7c{fp9@^P7DwC&uDDb
zFZ~0(CLgN<p`qL@JS_d$zdkxTw)I%$O6FSIHa#WP5BI(J^I|rQWpn8DCX+Mi(pbnh
z;$WKanWxNW8M=+A_#DBip&@wFPir5m$c5>a=`PwVug720Kk8X0j^Bh#9a}nBv7(#q
zJPQzExg(H`K?_AP#B=bkDXzK99vd4H$z4_ZBFiBr22oycRg#mDnLDf=*Z&RZKwe$m
zD(|$YIU^-1Qzfc(uU*0BJg#rpIJ4qmF0sBXm-ZynsBcIGhD>eZ8gIAb9|1>VlY8Uk
zF%rNm8wm@Ek2Pq^x%gsCKe7j9OW)Kr8(27(y=$6Wp1K*Y)??MzUtJHS(U_CEsyXx-
z*-u$T?x2^aO{H@@9eA|!Rg}qce1{*L@R}86<2!seC)(*5Y=}PH28Q*uk2f-Xx3q}!
zMI`-xGeHDYq+Mv3O0Tu2N(}2Ra|mzlqDdRdmFezK=Hz`1+;33%*7IF%6BCjJ3RJj5
zm2I?3e;-T`NCtLuy|A1P_#vb}UW`ytLezZVmeh!NsRcz;;%(kunKa8pP85__P_AyZ
z%Q$G|uC1Zb#Ux>-?)qhDXty{c9xOv`h&qKm#w?T_t?KW9VWr02xQ%2zamzE4Orj$&
zXM^{ANaS9+LKVuRt!ph|+5i5TD9#BGJ{vu}Q$(&1(Nz?OZ+{Z`eViO+C#W@`tvL+2
zY>zhc<f{+g6Iz7v@d*9c!S5zct+p3{_B()}FG%llle|3t7S#I`$atQQ8`xOD2B&Nd
zE2Ey*)d8~a1i9YP*0iAJ(#f{^IHe{@_q(-CnHNv|z!vLMk#z``)tPF7Sx_j(zHv7#
z4T{^la$-rk5Kieo^J+io;!b7CWx%$Ot)+2VfxiZCXw;sgw>gDk!T>~(ld<N3b$m-{
zCrjVk<yFZeTw<=N9y8403mFE|X2@CyP44D$+2EtZHRCs|sxRjm^fgt9S@Xa*u9`b_
zyXvQi(Y>RsZ`o<uy8$ojNP_hut5kvwTz%o01eeTI5Hv_4Vh!2-X*}#{91Jftm^PH5
zI&euID|5)X*rhq0l!;xpT*c0{vCW`w|J8W2&)YU@m}8klH@}|hapZid?w%P?9l)6|
z<&bXM3mBl}k^I44#i(^ojC?#(g@8^|a>YbI_lx47b>R%3eLR(@548zaDFqx}P=ZJN
zHIKR}*l^VlX11J~V!=QnP1tL2wzf9rvV=KP^^Ypt@Nm@SP{yIQB__b*C~&X@?ybp!
zpC35=ikXPR{1@Qw{TMdpF_HMA#QR-}bqNzRlIqtgmu)7h$#v>Sb#fKwoImPdS&CaQ
zBv9M#67P0~7LdI_se6}{H46PysFy#xW5-N~{#KasWfuDzo|u=`sS##zrY3YS#a^X^
zQSVw{oInr{Lx3@qAkEh9dqQ!o090)cZYMtn17B->UGqa;m1aIUl$Jto#uDxV3>yFB
z22CqBpUSm2rE++M!N8el9APo3usI3A6gpu@$g!#f%2f;HnSt3+-)pcVMf*F?k(cij
zv1hrS_}gzLEm>)-Eja&N<+TC=K6GSUgZ(BKYA>HFq{hqm2hv%BkqY30)S_5b$8^Qa
zSH+NtR~d|sOz0-Zxz>hBr;6CU)EHWI8h{rB+Cpud6rq_v`?rHx#sx_NQJO-@VQvVr
zx*9L@Q!`~LB4>ywZLT?xQfuR)#Efy2B@<wdUXE~ZJSm$HC{7=VMdzhMiXniIfQT-9
zS0d-_i+w_(9Rq$JCx@r))~ZR;e+IBII81Vu>W>3(is=tBgx`qKP+2(fDe{};oEr?4
z*70murA3Qq=jqrU&Nu&ce_U#fS*~Yj?o!_4aa`V?#DE@wQOLNC7ZGU=R6_i4%N~Un
z@MGY-^5W?P2$xwi38v?(X;d|_4SE+kowG9i{!R_K@dxc+p-IRdA%_wdqCW4LZt-v2
zcL$~vNNomcp*N+31|-wlJOb1^*b3<hn0-Ab&(CkrX?c$mn)BnWFmM3GEQzDIkrPO+
zZpS`8X$m;}@C!VleEhH9(ouBR3+c`EJ9|U>dl5+F{k<?R!Lj~&Awdy-Kvv%A*H~6n
zYgp_*b3?b2Cib|@RvgZdek(z!NZ#=@@S_T$q+D*CL>zZuNKpY+cTB<zsUyP7d~1k1
zb;<j=NpLy4l1$uiuPmLjR0yE^#73ssF<!{xJq!5Pb*vZtu0MOJiZL-2XsTcoxe7Yj
zynwMK?yD5nxo_QRgSHQJ0{1U#&dLAxpUZ0!0$t#8d^rlh^a0wzJU`2#JeAE&*p!+(
zB871nuNrC>1~1=}-YO=0lKCb|8t9ljEX|4XZ4;dcf7DD%VE2f}cZbL>TnJdz{mQFe
z{{3^t44h<9nIx~`-+$Y6UD@eomrJThNY(T9O>817{i<PIOGcPlj`N-b6r(=vt4?ob
z4`Q%2d_#<6K>Te8FQAIA1cDn#1JX<w*>>6l%q$p+*-Oqmr5~Ktqne{l8F$4Tg#=fm
zu_Po6zs=YCeNz4K)$_4Y)E-cB{i$igsO9lCtit8my5F+;6_=(RV(1S`;(VK^)?$9`
zem=cj@a<O}IaGiN5(~i<SFHqV0<n2Iq$Pb$-aPgehX1q2wSXK+7{jrO5mLjPPKt^X
zhP&?!JsDs5dz`@5`(0V%;O3NVFSa;{gM-xvc$O{BxkMH7u(h7P_SU9{d;geR&KEj)
zue){SpV64dGi%a3@XxNgJ~+XxFzcvNX32Z?HpyWZ9-#xB`fhr8>zkEhX-EmfbGMtH
zNGmNKX~AZ;Y;T_-g+Y#oCSX4!F;0dpqH-BeGG*IAm4iFw^8|ihpPi>7t->`XDo(^*
z`T4JbWNVO?NnKE!yxUnfVVg(saJu<7Y9<ai?h<AH{VhIgT_EZc8*|C9r}KR}g?TQS
zMbq8UJQJLp1?r%y?|08c!LRB^j~_jfl@L|?kXdW=f&9}8bDTivT<Y!pO;)9zwT&!6
z2T|3W!`);oNBiAh%M%WK#n=n46tIZ<{b@9-!6x9U<m>v*S6=<g1$Uw*DVc>%bw7b9
zOL{1X!g86a7j_&h-6O3_CC!KHC`8!gX=TOND$cs>StFt!{q?Z5Lt9<xa7lBuNGhte
zAFuCLe0=Rv1^U6vww`$P{c0p)QQL*ixe%5HPs#Sx6f63Q$;P;`A{IBtvSfv7uC^M<
zEjW3au2zURiCpx`H*^=Rmbzjve!d#x0EUjQ3jXZB3-hxaTAaz$)kr3!cytR~jTgNt
zR|V<%8e`g9?gR0jg|*Poz=XXs5$P*uj@aRAZooMaz0&xu;>%OTguw!n+t~)g4_?sj
zU)vhi(E}~RTPwGnEqX0g)og4%^H+G8hmQMwyNNOAlCgZgF6kCoBx|LH!hQ>$#Vgbp
z;(#qpDu>$AB^}T)B$nDXs`kLzkmZ%{1ZmNbDioH4c>5<A4N_8n&w=IwlV#f~z(QM(
z&Sq;Fd1X$#PBFaMtZ6*x))buw4Lr68HlM9gp(m2scyEC7z+?(pkFVpVZ5sx1^iB(q
zcKMkp(Tevtzi*rFP#-r58C5M+fk?r@2;tSA_vOA;{y9_&d_Iw92Wc|??-WRK%?;@=
zgsQI{lmDRkL%+$~RNP0>EsBGa_0LJdD|7P;Dl6dqD9-Cdj47Vn*5E5BZi1YOebb6v
z$kvrpGb^us1xJU{rhu<YtX!R9+j85X<KxV&qYRO|N{cqcPR+5822(@h>zY3BQHoZb
z9(6i{?0M?KCWnBxRkEL0Txb<^FfS@+0L_N2-B!>fNz;1TiXtqZ5Qvr9Y_A)AOcGq+
z1)eKhwqD%BDXQJr8_2DKy6b(?h}%CRH;?HvGuAa9ep&-7`8J^_?vHxCO}p<W0uSAW
zDh6c}?QHJ%3%zd&#-cd9T`<&RaPw?YdfD?9>evZVz8l57J`m<2B*ok;eN8xP1#wEK
z%H|G(&<^8S(GgO}|1&O<k9D7Uts5x!$Z;^C4L~qeo|#Og7FoA^PfBBOfN-WZcSX)S
zv##j<$+w^*8KD1?q78H$b9mSI3ym=6<r~w?!3pS&X{~o;Vy{ONiL;p{I&u@rj8sVZ
zeyl7>a&xox@h@N3?Ha>>_AhVT__|R!<||yUx!~ur5ar)vJ|00)8^F6inEZ~;@?`gl
z5sxDyIosj<7yBeu{yy1^4e&6C-2Ud|YWad%&ER0<m295@N+Z^~3Gk{Yk~~FnsE<ar
zan|O!yLV8)VbL9Jzr0fyFML`qf(HmQUc1rbi7s^T#v&W%ygkLc8;X5qAjJPOsepc<
zSHVer-t|{7lWasm{Ox8CSA>O%o*~Q0&7rTDE17b|Uh`KS+xx$hn3*IL>uDD6$$RXO
zJ~_6HBqW@T%8lOur!+`T`JSF>5|8B(zk4-K2|HK7eHHAv-%THa-s<3#p15DBVsBgm
zlC6>gAMiJ*F|In#NQ8B?jIveW8XzVX>(#Yx-|m*F8t^0v(-Z&~h8v8B*jKo!N|${*
zCg~)UAGkBtL*^_R+ci9X*ZANl*}4KQ@tJz!<#`a7?$fd8Fd~#iJvPM6p?8;u<4uyf
z-$%oavk^vvbn=aamnM*iCFZ!pJAK7Ow~Yb5_$KZ#MGQno+Zhd4KDz$aCox-LMPM|m
zn=-3cGplPyd^pmg=`YSkx@m3OC)1AkH!G#K_1)B6G|jXJK?nH!0-!^JS?)eu#a9Ub
zrL;Ptf7CIAD3f9fOhyW8ozJ*MzxekVJX}phMC55}l>lFXt7475uDw!)v_T{pc?J_Z
zM<$53G{0pfl2+fag||$~#;-}EUhS>;_#NIIG0oYRA2epZ>-Vda%$<0Z7HYID=lh`&
zJL-i4#;diSy0Vo9aN8h8LT&NC-TaMU2#tu!qZ(WptJd3%WKFHVKxpASiF+0RUbf=F
z+n09x%V-knNuHtav*_X&jJMHCXpOefGor-*K6~~J{wL@kgQ6o8z`7+{)PIEhT%?wP
zxPmsE130R@zWgcLyRH?$61g5c^9~OM-$=~VaXq}1LOuq&o@O5mjLI&(u_}D=3U^A0
zPgv;3uaChmRo%@GzFr>Xz7cM3z5HCc-RSALEX;UIoj0+4vW)6_xr|*g`SEW@x12JB
zTX8dJtALnl^wa%cH>X961TBT7(~GZWu(@DoZ9-hhpov(F0A$7}1^09Tfv~;HS^=K_
zvJt(Y@}+ixaKFBLT_Vbhwd&Bt;&Vb1XM?bIPnDpPxX~wQxW|f6&jqs2wFMPyZIyga
z{srj5{7Bn>I<E{?)D73Xnk8gvtnc>}X&jm!H0morrPR`#bG*ukX5-8lJsCBjA2%cE
zzqmBDjbz@FEKib);Nvf0sM4^i*0A~@Kw05?MZlr&{g$DQ0vjI6^kle>$KHp%Thoxg
zFSd%@HF0Q~R9`NEFvuo7xj35%4}>_X76&M^d3oNyaxyNE!wKY0B`heX4MhSv)yDa*
z`4dE06Kx!XlRsHXHMc8Bo;QhvLgsiR6xT^nbU{jHf67AOzY~Mzksa~)r|$zrjTaXM
zc`>siLcStLxu0S^YUEq?#_Pxd`a~dsBxnR?L1-Fj%KE{ul>lpkO9&XXtTOi7jzF-F
zDjLR}wGkAGE5%jptyyD>(agya&{&=$L(6>j6bw_Fa<9oBK8+^4oZ!xz-8ng4Wh#v%
zT(ZS8cqMB}jk|UEA!>_W`c2%JpqjcqK|3|hl$vp>+??|SLFl1=i(>wi``d5Fz^V7Q
z&nmXD066T7*={#r^D;tMUHi;-am{@o%A4}%F=xTCR{muU!>QM+7hgI*(uMB3E0|8D
zB?#WU$h_#5D*ERF1OJ$XpXauQB&rtBjMbn}<-VHOkJs#9{68~1i^z*74ilS$HPsmy
z=TGF#FYUIF;615>&XMZr=&X@hM8!_m^>f-{bu)Z1Ynxb|^+@@Ng_OlK3@EO`5Oh6a
zDs%RPUl%C7eQ$JSdf3&1YO@iW`)?NNyY-sR)zpy4A&PMGI$UjB8~T%Q|Ig4+FhM@W
zt6CZspaPkrfg%!Ml#js~ZUFu%fl3mUVB(3~&xvFBq7^f5DCd$>M_||M?8SLiWuGfy
zWf<6nmi4y5A(Kulu9~6~)r%~~tHHi=$2+2QeKo{zv?Q`U74;OSh4txB8sW>2Sh9FW
zt}?%m?;gRU>U*p8Fzyg%LKK8RkJ8}&DiM3Eup3LK+A#p)0V7`A9P)8JqwE1~IA40a
z^)+RBL=5A}vE?D{Xv%O_WzWOH`E~|sTIy^WSyP(eFA+=yXkUzEkkR}jj$-_DGRno9
zCXFqd<SeNY{yZAY>-_yTuBK2rnRu8}IMKW4f<hSw$1K#eiy9Q6<SAn4=fj<~^h?*=
zAMblk=4a7S$&a0BYnK5eVB}IBSR?=Y&r|<LVbIvYo`Eg=bm2E6>uym15s4>K8K@EU
z8l)XyZ5ih;6zJK}$RkA-NY<FekM&JZoy^aaxE6iq#X(VWPLNnwtp51}`-nVx-g<as
z1!Ri#g6U5%qAcFH8^!4qhkln?ymj-_0Y}=XI_FhSy}vPz*itoPy#SPFH_sUvjz})n
zV00C@6#Ye}DbZiE1pDX$wSkMPuA`##MiP1spMR`{ZfY{sdK?~>?@iT_liEJl52r(W
zK7YCS<~x(?9g(`ERHE4KC~F)fPBsN_8B~GXaF;PGns3Wtfo9rxKsN&g2vRljUDMk-
ztV628?vq<PIY1zuCwkG+txz*UHRc_$(b6ai`R;9b#Ncaj-7Dn#5E<^;=;WBPa-F|5
zkZ)p&N0+Y?o}d!oi`Y6u$X8^TH&(h1cW-RG{>O#Pe%vQsG-BZN-P=H<Q&AXuP+y?&
zjNw)@aK^nm0jZ^wA@j?Q``&0RTS2e1AKfbZPT&RD1W>#aF8X66`Kj-P{20v0E70*J
za<sm;gBSal5>sb>zB4dQoGdR+B4<78iUDx@k>5f%Axu$Rlk$PEdiG<Dp7jA=ny0zx
zXCgYO(7gr1wLbx336S78SWbFpK>if|kB5^XMRV6@Cs!La^o{JoBaZmp(Lx^;)A$XA
zd1Q-cXbLQEH#W%N8j?Q~tpVF{e?B~hH&;(3b4b*G;cnpqn>uu)mzsR`@9QV|x%fc3
ziS}wW0o-uGC7exY_-caY-ro0kO+Ua(I9yMc@gyMgMW;)TT7npDpA*fn>A^(w#=9?H
zFg_x$*WD)0nl|puFpyvBh<Hyj1`uVXt)7AtT&mi0w-!lhp!aHXZwsiocQFp`zGGjC
zycITPk_xYOliq*ZH$JNp6)b?ApEBfjlh{G#K->f#%q|K!sVJM1rOWBG&ytpYw7T0p
z-+H<;h3aJaNK#?a$zIhtQETu1YaXYf0;M>PDdk4l-sZmZvb%k-LtW(BfzTk^Fl|M<
z(^o^EJMt-M*9P?kwlFBn%OfUN8hyLDE5UmB7IY<NGSR>SblSQP@9*IwKNEP{5a(jb
zkUr^})_X+Z)m23%-4y;NWr5C-(LkQ!BxC$bRplTU@rjJFMh)S!u+RulJv#W~qxmr7
z>^|SLJPYgn=~HIJD<{>Bw1<f#w|&i@@k2e8Ev%zDX%F{Vw^**_tcd&Q3T5KKPv;xC
z*x!f0n%y7N5M8?2Mn25ximbWufEpb=mKRrj6PEX#j%-I3D=iWuYHxh42$XTOn0YO0
zSs=1+J1QKiXa6dFuVqkQ_-bv-uTQk{JmyvGPAF0wq`Det+ig;%CP#mFltH7Vsh))s
zgCdXf#T$D8$`$W5(v+{jiRKjsiY#$Zq@JoQrs{6}6icyLfMAF*oneh-QmzeXVZo1M
zU-{KJAnR)?VSk92`%g&RsiCJCKPN}|?N;)3=3w%eTuclv3}h+=uFY+}4d4Zrs|@tX
z(qmvK(nw>>AzpSAc?;)lGCLm-l)~%#khZH87P$EYIDcsIoN2vqBKt!$pWHbimN=n+
z-hWYC+fWf9i004!&v}%h@?!3yfdX2fm@(lLhX8)^{M9e0O0TP8aqd>98T98i?ymA}
zp9r&|6*=eb4o-C=W9!Q{P$cfz=>|3V6*E90`%AyUBO}cy`>ZEDYI@IR@ND7pJUj0-
zO;v(_7XLv4*cTPgrAB$s)rLBR2<7(oHAd8yh*BpJ%H#SiNAI#gNSL4i&*{M4X~1V-
z0Mu|fz78)&2g=EobjUzoM1MQaGjZ_R@J9`Q;uo!3TH@Njs{ws{+|7iJ8>C4|b3Avt
zhxBAzZZ2MKHO;5r=J~K+<#jjlWrD4?ea9vNd2xN20fmt!rrS*M_;2t+8G^h;0_3KY
zQiM6*vXULvK@KhUP$W1`9x<=u3$gW5ph$|PvZT3eA!6O`A;2(b+y7@*CpK|^+*!{_
zvQO>BPYg^P)!eXqVejj|(bToa{)GCjPw0#OJjEmpbTdke@OgYpQ-TjPGX&D?+}>hi
zQ<%vi#i<D~6X->NtzO~)<Ad79v1HY#D^L=@3p-k&=xYLIK1ipnC12%u3iy_QQ4jd}
z2nm^|$pk`LmgITxb7S5gUC+IDJn6v!ELDz;eJ@PO<}xU3bxnPWzdqdd4X8SI5|?bW
zPh+-rKG4(6hSyJECcG?^CLtchc~3eJR@+3e<Aua!q{Pg#b8zGxmLo$$xb~4we1_D#
zT?6?ynRMZs1hx+YoYjztI{oq`0~1)CRE-Hfml}%bx7lr#@3kMfTNX3fCaQ9dsOAvQ
z4oKKgjAU|OJo)v=so8E!lVgEb1T9$~I<><eftjz(2ny(R0C{CI*FFBiiN#7Wx+@r|
zxn7<WUooBoGeM<Jv2d?a=ez1a-ymevhh07^<iGm^l}4Yf*)QWAcGaY%k}K4oow|%P
zFwj$@WV?jCj+;IrlPcjYZNWqxrh>j`Tu%!f0tx$zG}(P5VuO?`e<(_wqyU6|C0P<s
z|2#(po3j+ujRfO!EayY$80-Ss!5qh_y68@YfW;r%gw?zZ@C>dH!~k4V*E$+=-P3A_
z)U&n=TQQvA=@vpFA`M~%IxH!rQ^D{0D3Xe?p~btRu1=IpWGhQnZM{Hbcgon04>2j}
zlHu<h%tiuU5Y%Q&AO&y$*4van3h^1+0?o~DtS*7J87fl!PwvX3x}q<iZXhCfLd!PN
zsg_>z5*d}&|GEDUz{Ibif;sb2^eBapfcGcK3N`}|{GZ`om&J~(4`sspch@ERapB^e
ztx1Rf@|~jax4_HpE^hTGDl$my;sZi_Zet)>xcsFot!Sm|OoU|#c@`ygT2mT%8xdIu
zO9Ce&0p7?6;rw9GON{K9>W_z${!13jEd54h6RY$M7Qif0T-%bTn4vcUu_gsMY|u{l
zJ}cx0HVcU2Zj`N|INy$U9q+k`qN1U7--%#@{2)wlc9sl;Q-a&D57(26Pfo(6`P^;3
zh}|ErXi`c11|b|3#`vsOSO7JH$ZLPvw^h@oMpa!W4w&{y)D@l}c}gzA|AV&!hNZ8`
zt7}OWl+ni#a)$MrpR#_#n9hmY#JZa6EhzsPjozx_$1>O3T6c^GQR{7?7F_Mv7}E?V
zP`qZTq*rdd#KlMy_$SdWIk12uQ4SB!0p|Qd1kLSko4W)GLfc`q6IQx<ZEbQ*vve5Z
zVBR1Wt6R=iu~sc}P1a`;CuT9k>m9&X4l9pj|FV$OqQQ;jN{(H6k%1<5>Lb*k)_LaD
z7d-hrfpk$Ds%r0?dw$Mt>IBGIsWtvNkUgRj#Tj=_uo=qJvUDi4RJM1PeTCtW!Z#!y
z_y^pY|03U^pMSUsiVs==7o6C<ovJf`tzO!9N)uP+WwbHuqK4+%Vc!R=;Bq|P*H)3N
zWl@U7vzy)4;cB}Rf9F52b|z)Pbqo$Jg(=`0n;xOMdm9vYlYn(t?Ycy3cBrH~&7nTo
zoq%ymuJ-YW5}}IX1oLH%>2e`j%GYLc;{mc4J}QCuZU5m*l|5d(WSG;KwX~VC(>~N`
z6=)d<k8h!`J|NO2h;_x4BGXSZF1=H$kNX=8xC7S2t3PKXVBiS2KDJ3U6!1;;y8W$-
zhbc*8vYSptw&_wel3}Y;9>BgHpRXR#|IvE;e4)9b{JZjE_L4TilXeHMu;**tX`#-j
zl6tCFLGjX8osj}91vI{dXyOd@3%65LZKIKOll1`nOaCqY^VsLlv~t|_)IJGeAdUXq
z8Ze&#pyc<kYF)t|<HkSb@bW<-W2d;QT_*;B<Hy>G0~@PA?EoR8zwRA!J<dO~$X>=r
z37xu_PttV<><BSSfiUB&DtDvz!qo?(l*6UQ(Ya^}8X_)PvZsphoaMU9Hf*-zzuWA-
zYfX+>=jP`-h?Gvu)JD;8|0|{_!~S#mK$IdCI*;GaZg|snT=c;t5(TPn^oQYGr;wC!
z5=uFQqapu0T3F-Qpwr}UUf(<Se?F(0Y8{bjXCaKkR^D!U%|w^<<W{15qIJYxhld|m
zp)|YVepM+RGE(}FUQE4K_SCyciG*Y?J|6OFXttFcx25+3F=Jppe6RJQyHtxJ1cdu5
z?oPM}q`0u5(p+lX;=T2Ht)9>T)(TKD)pj+-vSlE%?%lC$2ZVx$?e`Btz-%Cc_b?-G
zXwFU;!d?O)_}qxAh?LgcwQ`xT1xBbkdYs_5#DOTHU-oYD@MA*|poO;6%ikpa3AKl2
ztc0IqzjQL?SOB#R>)Lv(XjH_;)d^y1q9qi9$EBWXn}*HG#{N2SBf)~c$-xs-8Apa5
zgHD<=P2&-eTn8pCO1|Wd6}|@<s~R?*lC9?Ua3(oZHDvX#Uxs(v0|lm(WP6<jMSj49
zY^1wjLS5{Tw215hJPo!=V}bVs{fJ_hoW#DR1rx+E@!I^fpJpc-5=J2&bOy_w+QyR-
zBrcnl@+X$Edkk=hWnU4?(_?!D+jA93s*}j|r7$Ko+@-Hw0jRwY6|jXWv$|GCYhB%H
zUF`rUto-GkGw<oQ{GUX3*^dHZq<BlrSsI$*?IX|Ls?5E)j`8EaktE0^O7)Y7P_g#R
zX2Zx{I8fRHmNM#867PY->itHw7D8Ki=X_r&ZjNjyfJU9BYBZl>w#sQ`BP^!!&Ql2Q
zxNDYexD1OOTeRk@@O1Db|0Tp~7$<}8QyM9Gn9`E0Fc-ZwWW7kYQ_1U4_qnbd10s1C
z!6(v_OL+PrI+<EMfngmF`;uWFRWX4hQiyJ}3kQDuDWe+`??%w5i4t?T04JIw^<5kX
z#%^M8IRm$C$WN?n9q;SYc}h_w5Cqp}qRzot{S(3y_YF~LKw7?4Q>zE+{#?F$wIq45
z{v1#WGacgNW^0Vpt;~^$h%y~8TT3pGYuG!mCc}Q-!8@y?YhPKv{6QpkDzx$ErB-m&
z1O{>tgZ|Y-z_r-oc<!F=*ZrZ{Glt`Cd;)b6^@J)GqPcT4e+B~3j6phsHKP)sQx$4g
zlIKvxG81}X{~%?t*v1eiqr>|<GYbt3w9qYc^9r1!JSI@4jprWdi5TtnwQp&KgsxBO
zjtxhi*?GCFAyP?$8b6l!LqpRJ=?k&}E9Zk_XP_8dUcIze32jOap0vIpQhxDFJ5HwO
zwaPQ(nu}!ww`<I)yT=ZwbU25gFuA0~&Ey<tk;`wAjK4Ip6?r!HNLtE~_(IbQLx_(V
z#fBqs>DzK0AWZXY1zLoO`fFr=Vh~{owgSU?6!s=#gTU!uI99rG%@jT!zf(P~VlIkt
ztO@d)cbG4*MrWaB+y9b!Frz1K<Bq-OUWt2{Rv93QM^j)OUB^N)MNP!zqSse9L+d=e
zYTxEWseW&R7FNFnf;BxVWujBd2IPr74A~d+RYud|Crn^1$BtN(gQvw|dYyUNnR$5B
z{)eJnar<Gb+`)ZglDQRaF;J@)AK)If+0d~`g{mL>Mu2}n*L4%yYyN#|)^h4bZtn|_
zw7I3Q;|!)nz}bYmPv0JJ!C1UBa8L#|@JzX2ke!KxkD-C@gvp}4($2?^G4zd$1zQeX
zwpcoVgQLDB^nqr4pI=L(W5d0JI80%dJ9!{4ciri&<|>#oBXG5|z~yD}u&qL=IPx0>
zM9*o^guZ_xn1?)b_5OVxVAiD9Ts^RGeb4kL%hSal@FZC>bqUb$2&}>s;xW$Gv1{iF
zFhiF45RmvRR?{8%ne^|ZzI*;7c2Kb6crMe#fp)H@z(dgLT}HwIslB@Jw{IIV3=@s8
zY2uu36yJNto`ULtOdiIv=^{-X6w%KNVOshj%!i}wzK)R|b)&^w1)yL;!R6Bp`?y_y
zHoPhp0t=TM8`R5u*y8myTY=ZW7KBEwTs55*ujQ2|FVCMZ4AA^i#NftEU=tA;?XpU^
zU>%K@?*{}##34K3;nbGV_P?hn=<{cyYqbm>d5WNVB21OO?$5Z6hfbT>UU6z(zAq%;
zn3Z7mu*$6i>mnq0RmGKo59{RkSN2FHFe8f10o5Qiv2Cqhkm;<v*SIdYC4f;wPnDs^
zq=)-VX)=nJT|MZJnz5!4BS!Y*LA9E-gUwq>ub#(zKV<l2>!y}478<jn)~c639t+s}
z_RPmVHpnD>X-gVH*F}L+epsVaHnFV(zt_V<k(!h}IUcyYWEXo)?eUmIrtkdw@*Y3s
z^BMl!6oQi5Ps_PyQN13yZ6-=_OtKKCNH4F$eK&$019jV>FM&Hc{R_$wo;o1&uCb@M
z+|D(&v2jKby#eZAUS2`_pE?p??Fcvc?Rx<CD8()N+gQl1{&NwuFP2Q@R5*c;E3){d
z=8l2s9SRbqAvFJdOYy6>zdlv?pLE)OcWDN6<4ZJg0@?N6L5{Fd9!&r@7I?}J*RCG}
zPz-))Pc61?wYhsn%{xT;Nnr4zZU4dw7~~_F`h9xz!$eOWX|VB~AYt80p`ohRP6?Nk
zVpMMh%W<RkgmP~}I+99DB8(V3qk8q{x`lpkO>c#=V>C53f;B!*P|7Qkid<RlZ-<<L
zVN!4EqX3pIJbR5#z#!?rQ_`>KObr)b#y^afE;J+_&40Rdec?u!ELiz@ky+CSn_AJ_
z#W@EN3NhIz=bKo#%8s*^4OApc{*#x-m!RI=LMDdUJqi%JSkh!jqDC|2;*gT&0_eJj
z{d~^7e#-%O{8a{rNixha@O$dhK=IOdD8!^=4yUJRd*Lta3=LM_-}k;B#4h{<jpn^y
zeF+3Q(9b{C>hLw5h%RTpb)`ZCV~3lCU-3CtcJ3k<-4fbfYZCi)@2Ic+ADXeYCE=E-
zvGW!$SpwNU=K?85f@&C`!4LO!JD94**8W@E@cf@AD5ic(sS3{LbNWr8_y(T}RBbw~
zPKc}6jO9-5uI^LU%jU=^r~+jwR2+>FKq$q;+#VzSeup+>A_91Qw?|D|@6m;UlVo;G
zL@x75wg#PLwL~Ac(z%v&uC=P2D<7#jm9_U(<KPF*C}`;Ap8!$z@<UZ%PrTfuXpSO#
z(uo%9n#nXg@qJ14oc+}Q^O=-&e+-T?!9c%aTyU`0mz8|*xnTq(H{aMGq{uvl?~i=!
zSm4<UI|opPAr&WE(uHgkQX9zEezk<W@~KMl+l)A-OirHf5G#ss_?}sLMPmI~bD&IM
z=0L$40lfUuG*7R>=y0-2uU3MTh<@kDAUW=Nj%2y<dUBhwwYuE+TH6q?R?AKFGtuQ&
zT?*2d0TBhNJ!(&6|F)T*vMTo@s)V9TOZQ}Qz7#V7W-;fN6#}HFSm2$<g3aa9IKe%y
zBlF7b(Zl96<y!?B2IeP3^~MS(>b9FHqYfRdijF?zKf0hsQ&tMI6ZCkIS~5V~+*~+r
zLCO@IO*<TIJ_>+MD$^lJ@TPlbd*o$D(TL_AbY>3??W+#OE%o})E`KoTlU8*B!VH6=
z*{SpNovE!IdK57UQBgc@0uIS9(vS|cK%>SA&u?3(TJ`c(i#_$OM7ul-vWO-W<g0c3
zGk^J4n0@`#(JxFLaB3HL5YNq^*7j*&7x;j=31|Vp*jK8$U;xQiTBf`i$Qu@MjnUJE
z0PMqG>%l4!@33)vh=APFif9{-pdjnH@M3NAChI>R$N0w+5DV}h{WuH(<x^KqpqF?f
zP9{wkrI#fOQye<h{XBQ;JJr*)jBzo0y|`)ayu$S+nlL1ATaz+9$$Uq(C!D4KUy%py
z=j89k157#8zn?tT7x9p3x{;|7L`zK^&2R`RZ@CK(1gp6$R6Nn?qr(dZFbeUxZEt?y
zo5`2)@XpBzT#xs@P6)Lj^(N}*40xOHN~NIP;)UrHm`(+v_3JniWdYg+En=WU<EsvK
z{noYUfL_y(Romc2`O@Y_F-H_(wHIRXctG&sGhQ1uIvml|q_I#nqeUPAGW*q4-D$;<
zvoB-Vxg&&h&d65^r*}W>fAZd!s+uuxSAkEQ3Rr#wzBNzu>1cT|O%jDyTDAa1op>*R
z_Y2gF{JVOyI<6k)n_I)jNWw;Bm^v%c1v<wlvcyDC#zs-ma)~xOP16Bye0h<j^{c$!
z&~uaEaD?@!bCDB=Ghz71_qKQL^R}Ret4nOb{?Tm48<oCirv_>9#51`^xnx`nae;fN
ztq!K?FPktBGyLIo{D5_9$P^h?;=HC5(bL-e7YTW|Br<^Oy(_a;-q-Tl8Q=?&NdH<+
zBTpN5babC}5w8H2I7AyrmKNcqvL0%i#mM%{2=$?)LBav~Q}}7;>amZZ(qclSmDl6s
zfdbD=-B{GbUuiN+Zat9}Say|5g=0j1<sD&byf{yuNGjyWKapFyI2KQPyrwQ8`t+PI
zd3JUe$};z9>BHEMQqTqSEe4Vli5pJg<=1Hk>KWc;5Q}-D*e?d;sn{Y0H}bt-y(=y0
zNixjXTtCi6UV17Sb1a^<aX?zC0dqvMVdD9TNU^|j(kDxAWtX+%8y&kp!Ixux&DzG*
z4cg3}iGPA7y(|oQ<6@USHTFK1?48KbO{7j5Sg3O5fWLxGoJL8Vu;i1|w&#A^xiP%R
zkaYRcIU#Cm6;<>r=7&^_-nHATj&o-zyg~8#IpAxd`%g5?mg9WG(#Mse>?A9-Gs=!h
z8cJX71LhCc?-ZpMrm_&rj|?Hd&@tNLVEW=quM#emLFdAT3#xC3w;CigubiUUK9wPC
z;*oW9XVV_)uX0q+K<vL#U*FQ<%&BK)5&sFeG8@|eSx=eZgEI*Of$lYpDuv;CWk@V|
zF8oZ>W7YgYD+~uFXrE&Fa}n@arBvJ%72j9+b7MKB9Puz=pbYhLDLN;bICL)3T#G8M
zd~I@jL4Y*Ix>`YHj<UE8Vf0ID%!Q@?{YxL5ahTq6hW`4{3IB$M1^fq|ECKL~0t-W@
z1drk>hmbr~aLjf){v0=fa!-;(TyPZKaA2UD&)e?m6c#Y;Jr+S@tP{|Br^exSXxc5c
zJso+*d6hf}sNo1p5UxH0nFiuI0l+_j?3+$MpwHl8fjQJM9GINJ?`}UcO+KOF6xN)P
z?q~?l`CQx2CG*Hh(f#}5LTa=xIgK~&I8rl&(Vt{}K_96}+VU6Wv+rXH#bW)=RYKV6
zapR^bCPC0p@uJEDP|G26DvV?7Zq~evPD2w$+@F~95RCcIb0;(kMtG0hmWprq;+n(*
z^y6w*RjOfBgh1FUJkXgJv`h;eeKcAwUcA_|M7Mt8V=8NG43%betyH(B`5humQ4vmb
zjUs`a+j{P%uh^1Jie79JLDcRN2A&?EcMHym<DeMJ2IN{ufwgpUP)llileF~(%26HE
zmj&@uavU(PFVk54z1T>gQ$*}{P%JJh(Hyuma#Nu7TW3AJ;_w;pL^1vML>Ub+;U7Z*
zn|O+T6xd5Td<J+sfooC5I0;tsgH%E<9MA_OOervaW+V6s9D*mTj76!?_{bE7IJcr5
zSRD1Y3!PBc?qjd!a!+dPk-TyQ8PU%Vp2C`%;Vtz$PmBg4>+ry?G;q^GO;QNr=eaw)
z4){Q%fT%CnGiOhT(dPY;7iM>nqG!``9+-OsplC>z-P8q4A=moo5?iANVxHsp)>QdI
z)t37P#a1P;4Le59y+JlUJng-=(qP}kzMC+x@%rBVlm>+XS^{}<d(}N^tlhr1K%wh3
zVF+PQsUibDi6V5srUlXz<b3;rXG9ztxZ#rIi&*a84vT<(0V{D<OQdLU;SP2UHX#X8
z@u0h;DOU9U8euWm2drm#VBe*RHM?%f2|bnJ|7iNkptjns>z3kDEJ$%E?$8vM;%-5T
zQ{3I1;_mKFfdZvKumHtfL($^yR$Tg>`+4V^$&bt=GdYuUoh@sxwf5TgZ%T(GZ=x0m
z#q{xzG;{#>NNh#LSR77Fr019O9}$47+O}cSGJAEDZuPZ{kqWK;X@GE;WD2MMT2~$*
z7kb~?9{v}&Vn};$fnnzaV6f5(r#2-9+)E5|iK)F&J(&F;{6x^uF09*QW{*d`j7im0
z)%u9V_DkgW0ZKg1%`J@m^AaFEzxnW$JmCo7b5R~qJbue8kETVl$_}QDL43sd`<7%9
z1F+&s|7_#iS%487R5g+-z@^CUI~8maMCt>6{!eBcHeGM!o5v<MfD%<aRLbrAG9daO
zm3{_lz3C<!_d$`v1GY%@EKDQ3R}Ui(T&p**DWeBAnk)jw$VP$_>kBss-zX9Pd{6bZ
zHcJfz<oZt>lrWWE=>6lQ@Z==nuD7rAg(_Rz>E7yXjSPQndz{n*MU4N={{Zq79BrHV
zAAZ=Pn8aKuk2lIfjDVxuQJY{m+febHWUv4r<S%E6z>D7W60u)ixhNOWt2##k1g{CT
zlZ8wXo(B(NK}RTKAWxO>2H^zg)(y;w0$U32-Dvq;m^vIV?iGDF=T7tR9E_gzW%{@b
z1OT8%4Xx$MjQwCR1mF;tfBH}XV=a3MKjI+|J3n_ZoEc~yIg-=z^<7Fr-NhEE=Us-Q
zzgOfk{^p&?QQS>!!Bub&bnEoUYi+Xp2dsC}U5eU#U-prVPYBQx;;IvfU?4>Ul7i=>
z4}P4@efnk6z9^4~Qh4`A974UV(_+A4gVYMfNJdPF+Pbu_-$srAz6RiSwF(oC*zxhY
zZ7KsQ1|YC@dAxuD&KJkpL!uGCXEM+~qel?~(w417(0>x$l7nwjvgwkkhTkTUNl(5-
zd@UdTmY~MZh%QcRbyn}+#$F;E?!<J%47xSx{n9!4(gJIn&}+c(+u28SW~-uV7D|ZU
zx}>aK+5EfyYE8)X3BEce;xF<B065J4x@L}`)>4)UjTT4IW)2nOB0-N+00YvprPX;v
zXb}^T8B-<vR94Zxej8=Th*PWf^r6{Ld5<bSH%~fywBk=*tua%mD*J^PJ=(?T%!-<t
ztuBN%GFK(9d>6cbM@aoz=cCf6A&QST3GuJ8%Q=Oz0JGnX*4M$Wr1d3uJqkc0Smj=)
zEDTv9yvW9X*RoqB%-g7*{w+Q>P!0clg5f{rx!xYN%Xl3pB|Sp2(lmc-{$9~si91D}
z`ot@SLnVpur$4Jmc1zZDMo5;vVcMjeNH|up+&dGOPM%~Yyz~ojE4E)DPH8X1tyZ_$
zj#rKN$M|2YJfGg~Z}><$B)v<@!fn;KuVZC--@9_waT<`}+I96WkTSj8*h=T4O)&&g
zHuMfT3et%1FG_j;zH-p!$514{v|(T)&k@zNbvP;OBX8Cy`TIJe>HZX=-3XyTOr(D5
z_8t`)0kuyb_P4Bb=+MOrF`~*&{yC&FOMxnGJNReJv^1N~PJW4hv00+XIkwQGb<W14
z8}<*&QpTA<>v;_45whk98|-K?w1Ffyv%ZZ_RbyOjZH=rQuHl(NF-U#p8%QwC_Qy7m
zcS#p3Icr!wNor8E2_xH5%g?p`vcL2z#HC9TO{(hWNFk%#8A}j@ymQIwp9Cx~TF_xW
z;qMhZ?3<9s6V$fUh49X^fqe+3?sb8-#CZws09st<;Qh|WRXy$Uqljhn)>>=TpY{`q
z39f#AZs+er1kaSZ3#+)7=?B4#Sizo<vdA;}mNDH5C1sVkX$<ksz<U9f6ZZG~5ykdu
z9`+;g5+C<Cxz7oIf5cKxS=MMiecq#bWianyr?YDPuKhmR&A|6qj;a2-i`rMJ<jlEb
zdOJgz!n{qtbd#^~ISAO?F8Xvw(<FmhLvra?jBKimxDOFZDqSDHUR5GyU@V&|9ji(y
zxM22M_-=)#txKS^;KhiD+%{%BBm~h7`c&lMK7R9*_`;4C^BPm4B(eF%d^3=NM?J`3
zzQ;Q@s7{7XGui_nS$XVTobu842Zz*JKYmdt;VkRU{1`3S8|&N0+>`vMcfc0<3I5Rq
zDdLZW55aP6*okhe!&aTwqz|#%tCgEpI_9zsZ@1uAqVc!-sv7e3*9DM}i||i0Q8S6s
zEy~KHrV5_6?~$lbM9Mq~gUtRx-WY+xXf&AuW-Q<9oAzY&Yw`onjf6+Hsw&yf_XxyI
zmu@9Nl-~`Ef1h#hZsUq`?xgbRP^{hBN2a8{ykQ2FC29lr%vx7Gl2ykGn*&xkvZO>w
zOD_^*hhFGA>{iw%S@}z&b!ZS!(8f@93|{-BNUtql^EAPN3iLaMm*;oydCzi7w1%9m
z8hbc$1xAvlaSgNbOhgB_#K^V=Z|lJRgmP&#K9XWwig>W|7lP=vRPBeC7~?j2u7Y1a
z6d5^jg#UW6*EVX7uJqTeR&PH9dV3_-kqHjvL}06W4~R!l<>>PZ>6T63dfo2gDb&1`
zVo(5s!S>7R#MFrI`7;*fqt<**qyl_QlbUPCuZ&)LG9uxr)kjz_*MgK-FrAHGvRM-E
z2|9hArpPs;AA^S=*|&mu>ZqJb<Xc=Yl89sM?9|Nc2`hG){^9u6aUM&B`2wrQrNoLD
z2w)B$g%hmH6k&g;QYtPa_o3+1JgvMresc!l+(mC@l+D*-TQx6naw6Za5H#l{%gS5w
z(5WA0NJyEwQCUyCxa}}3dmdgEkS9gSLVWj~_C@`Z6D0~Y;!d)}1y^u0MH*O6$IyD(
z>cnA8NFaIdmm5-RNZ3Fx4UXc1sU&kbrSBVTrMS2sQ6QIpRrm!|5LEh0r08_1Tv}pC
z$qCBSyy%?>+u9ltz;jl4=(CpmhJc8tWCe=F6FaP5H|R}Y49JMOUflBT2&D(p5SWRX
zGR}bMwYbC%OOOdl2wX8G8m7XOv+4V+WBFmnSc^y!V$MUgoTapm+GD%S`;g6kT%_KB
zV~z1Vpp9OrT5n(bA|9!zx^Q-q6q2*kVORa<FO6@i2V8{|f*P7Sd&xiR6=xK<gT(&*
z`-e5VtLaVj4yvB^g!w-wr8W(R_#_>6U#|16KHqy;$FbOwj%kgKX+$fgqWhl85z)zM
zsr{%>SP7)idbJ|NlcKT0D~rnA#cQzqZ=(c6)4mZXJy>a7#n;@}1Dr!Y0Oab}vlm=w
zbc^e4V&)iEJik1qtu+^NHuZibG4Hi?&Pq2(?U)4%aLVSBtH;Vq!7s^d8<1pD8Lq$o
z-M}!cgFII#ub+Y^kpi+4%n6+a8)lL%qfc<T$F<tL`&vj8z7Rg4O+9(!`k~P;a8w4m
zx%6gjL2q#1))lUp7X7%HQEh#RrtuFI+}fVLL#;w+Ag`#jRkEX*zD#}zmE(xCdVJjm
zdZc*Z*&Z%R?ZIwX52aN~qNxt`U=7h=N~WcY#dphkHjK2>pS}{`q@`AdMDvqM%*!UT
zdh@9<`HPYkXott!AMR(<5{HW0#jB-gOrJjLv?Swf=Y22Zj>U8M&SQ1$XE8XUH%TO(
zSju!}sJp(Pc+!doQYT2N!cnMBPA-&{(~vD@1+{nSqlkr`oeAB9*qMA&{Xtp1^yFM`
z|7O(hvUx#Xtcw!w4+GA*!zF)=JbyFCt#TzqhoAubjtf{DOD0tkRI=Du%)>7nL7i{(
zu4fk93HA+A<Gnf+5fo7#ALm+gC{n<ZnIF#arQB{JVcnz?wj1wP5elB&vw8tX$*VFx
z$R${4RJ^k<EHakQv9^3`K=S<|rp4#==h23B13FnD8UkZke2HwvLLyIOl=4kyaoz|&
zs8>M3Hnj@KKps83zo>`tWQsx7lo?`CGx?~PuA45R+K7XS$#mNxAQyRDZo)BNqKfFu
z4FaK{QZw@NNG<Q~FECQFvbuWPhiFZjmcidE{?zGOIW+3vEGCj3<6X+k9#E;KTjk>(
zB$auq>S9+)2Srx*z32#+6VIgeBV_M8ShqM1NbBXq*(mr`UujQ~^VpUy^IkKWQR(jB
zT57exXtSj3w|xP_t9h{Z&M#0MS?2D}VkJX+QM2)ZfT-v3)Ld7Wo0-GW-Um2-ZdU%n
z!|ldWh&rjg#NP23qNSxnhXqs@c&$F%wj^1?S{j(1NF%V1Ev_ihlu}eAVQH7c-z|rF
zlQicJVa-1jSGltocXdu~_Pt)0*Pi+AFIRjWkE+!B*VRyTty4+$S$_KJO%ES+Y;p~{
z=Q6h}{QC-jEdJEuPkmW<s>S4cR8tsd4-XcYslgmGy<zo`8WE%)Q#BSE9)MFM*Gk7Z
zAa^6AB=4rQsf~=Vk3wDWM}KSA244wXf4PtQ=R70G(I}T;Pn)cuHSk+sgLD;5YP8c|
z=gmfy)EiY=MvB_@eryxi7f<S-@FH`2*aI9F6!vP6hjNtRR!vQQ`UnM440e_B)o-;J
z;(WW~)5zp>0I4WWOA^Pc;OZz<5w<gt$2Txb37Z`8-Z19;7*|Ij)N+0HnZANg1n+WV
z1ieW={=zT6xal^JVDv@k<lAuRhf(Pt^6zymmqcWfE!J8K{;HMgpBa3@N9OPN)Xiv$
zo<jOOs<_ag4IPhLrE8NT4Wp?eayENg2I+D0oI{WZ|1;s_1~&VQC^sfOwe|dfVCwN&
zhWBo9KuI}mfM1_%W#0WvUI_2eb}n$)W@=|uOPo2)dz<#4!YIfG6dxDIsmJE*VG-PK
z5fQ^e`m{fSMVM`0TRTrF4~<C<1@hQ6w#Y_1;Kj4_2a|!p=BdAd!3jkUnxK$dnsqx<
zk-IWsU_r?7D5?z#LGQPmmbe(v&AS@4eL8KYtY5HOyY(I%l;P(Q8CkpE-21kj-@&t|
zBDlmplX8o|)Zh6Tj_vJbn3uO{WgnW5@fqddnu1`^7^=TH+qb~E<4x4ZTt@n+e^5Jv
z+7`P=H&Q<OP4m|brpM5yKodl@9?#XT;3Df-kgL94t?52V;06XmL$nVXkjEM%?}H@<
zG4{Qw=hKfC(z|7;6}}~;q=sD+e$F`hqi^rx;t|WI<o(#A)amv>^`VIyh&H9`x@5%F
zQ~Q4pd|qRa+DF$am92AX4O^zgMD<|5e-MkL|A-#1RFnH&i6GuOv7yG2In$PR;eoMj
zY&wQ0DorKPPPH+9(`sud0@eKD8K<sG(CCvv$^!I4qxzS<!l2LpFQt5MDWaj~iK9Bc
z?E6fhxF7wxKf3QH%$Y6FKD#0xsfEZ3B*5~wf&{N(a|tLYMB^LcW4jB2%`Zl_Y1>k>
zICezz_tGH5GwX%EWO}aC{vlM?=gA_B{Vl@d-#*3@-TnaQ{Nx|;`4I|C_xcS&akl>o
z)#jtT&gT54gAcs#_@<D1THEG6l(_uvzk*6CkzUd|8WbFCtj1~24xLAZo7qbHbXjEb
z#GN*bPWh|0gD472$s{WF7eb&t6@mA8tOVb7bN$=7R`tJ|k}QNP57#p-5JGFWq;N~Z
z$l|T1un-=^BuB5J;3z09j8u{M!3!nRw?kR<&dHp-kliV(uxVI3LqMS5Nw~{8o#o+D
zCqv3vxGwdemB{TB0be^m&j<M4vnXf3{l7ph*_l)*rIUS0_v6(lYqLP(v#(_!Z-{Mt
zT!M>_P3$maqmp<ea1M9#{(CC%Pu^{NjCruN4@Ir@7b_A1-s<!M*4^pb1&S@WV(P%(
z%^>qSIfk440TI_$HJ68m>Dubl;>Bx5J|1W#J_D0;_GSdv#4ih)cznb~TH|)2sY7oo
zU60y{Mf&Vi#xm3rzDIn9h4gsJ0dTvBacW#byWtPbEY!u1^=A>XNlGTAmE!YsZR{w&
zNAc!)oLJwe&wp!v^b+gyqElI2eIy)tmP932(nc+!4vVM91S^(u4pn{j^z4k=O7+UX
zZ_@DvNcfXG38d%OLyVEdUh@TM<)i)zz401~snUqnvMh(|bQI`A*6aigp#_K`Xa9_|
z*E}s;Vee$nzEa{o;L7DDikM7G*X}2BtO|CMRxlCq@-Qy)xbASjYQx#SEn>cKNQEF)
zs^m(SGK--`k-1@J&-6{ZWX|*?zvX9}Z0k}KJvEViW3X=}F7q~C&R`$-B$bElH<jX>
zr@oR5x9PH|n!QAuf9<j1LTmqZZi2-@9{VM!n_)AE45M2hrHIj!k7O%U<e9CfL|F_O
z;q-KJ*$yoFrSiC^DX&jGj+WHFnq|Bsd`QDH5)l~uBO8``{TC&zNj(0i=~*kv#xu?*
zwt|xM$&15o>mI&c>5l#g3>Lp1KgK*c3`-Vo_s?borJ3%mtkXtqNuTZxm0nIW40l)t
z-?|j)N(aVbRL~<mywy}Luf4#ii09--E%aXE3-6X>n(SlORp!Mt8!Q(&A8R)n4M;8z
zm4lrXn+V8$^G)B6z!mN2{B;)SlrJjedC|F7k!<VgRN7<o?@0j$2;BeL`0CnKZApkU
z$iA*%7|6e|5Nfs(PlmHfk0BT*pL;xWuMAZbgg$kY80}dZo9u-Ny#^(gt1|KB3JXOM
zNxD5JO3zEki%mB%?S8LeZoc+N@M#~M?C{DIpP&)_rnQ2ZSe16UO`em|U~1R+2y?YI
zKGH9qwV<i~Qm)m5LBr1R9lq~1D@egXF#&U7@s5B@l&3aiy<^+J)U^owdx0fj_-lTG
zq9`?x2XS$wL{+>9gQy4%Gf5^1r;MCpfRH|3z1Ygr9tKGv4!@x#d4C#XY(qSd(iP7F
z3c$hbZ?|RQ#Ufu`s^b(4t8UL_B{Lp2DtiY#p!1I>dg}^xi@w#PgvYl({#cFm=ooxT
z(<H3@K5g%dXcz>+7VUn%%!t35$r(Jo_vb*rcMSL|0cdk~DLY^8JC=^gamCjwL?|0q
zi;0>q;36F9h7$NWw<gV<3QAVmGt{cDi=s1K-X_jBckQXlPb&yC79(Ff5tKoyEaHmQ
zx)YI?RJlnmUxoV)CX(ZR8Xwl>-t|>lt>Gv{llwiQ#<SvY&-Dj3WDWW9P9UJgf2Khk
zmkzsDc^Lz*?7YNFWjTcoVQ|V5gi8kh@;!5}uW$cD(t`~ta(b;WF2|2{6v5!JGaFc@
zOh)peO%#zO{lflD>rbt{5udy?kBlZ|$3cG@d5CWQq$h{IX%l=))c;BoJ!Cynrh5i_
zOwRmViZhGOzbnn0o4a5%8njX<2e>Hn?Vbt;@^s-FSZJopwR9{LlrGk{uIUCQmm*H5
zWN9p*m4QZ2*m;lGUQPrlovrOnmrs(#Rmb^ZV8LNt6-vuC{XYWO$MbeSNDv9_YXd8;
z|8^vL48AXD;KH(ZDuMDYr<X4VP@6-^<(bm8^k}0@EPg)qSpopH#u(=P-;2`YcOv7Z
z%>4@DTF-<E0U^;@B__MvMQVW_x&yq`NAr5ZtDT&aX**b@i7+2Kk}?qK2?fTHeX>Ro
z7J{BlnUH9EW03tmNIwU^p-FEG(Yd;3ksCZP;$2$@*4B1(wJ+=b`ZaO-@c!=;4$_@*
zEM<SGb(?$bC^H4V2n-7Qy$buWT1*-0=jI<Kk)p{etWXk2VTWH_Dv|1en(SW6S$}N@
zD?y8h$m$sGarNkgT6XIS8qMEijLnFPyiU0HRZZ+;vi{jVtZ9&;oen&N!e0w*w5CD_
zd|Je&hf?NUUlEJ%S&m~5S@T!<n5)d^^r0Dwu8Y2$PHK17clV@y^s!H1jFsC2T_>*Y
zB6Kgfx$B9kQ8_8SQSki<iAGSgcBb`=4$YLL<I|;35XfcfknSgz!WVFDHQn#|_1i^H
zGcx6d6=)|vIq?N1^Tj2KlL`&~N~AYF++v`pP4Ar{b2Fx*=*j;wWSLS_$hZB~j=nV=
zGlwcFN^``fP9c>(w^mWr4?%7+5s5uBTbjxQs!soND&(06^jkzj96c#Y_2F#*M|ruL
zi(UDM)Bt*W9qnUdv78)`Hu-rXq*-9#58cvrlkL12Kade>h@?ZE#Zy<;O1L%AIil~K
zjI#iE$H?~p6i!d6qY4INslzE46=kUz7v|Ex-3gW0>Tp*L-lP>(lAuOEl0on*n2eK;
zAALMbJ{bE|E^cg&2#B`0m{v#cc<?-HGsq(;E5!m*{Rk&y`hT7!&||XMx#}~K6XrCf
z@0>XMR0`=6`JPAj@?tm^1SRR#R4BYX*3ckdm{ka8`RZ{AHa#|`M7yOg$j$&|M#G$U
z{&sm_nUy=3ky;L7r@n?qFn?rF%xLWLz2#b@&%S4`9JRGIua_s6S|XnuQicl8w3scy
zb*s$eCtE2k6kNC*j?fT7eGP=kBNnV|g94a6#EBKC9VW34?x~Gaf6VN2@*2|bX+Pa<
zky=3@ZfrnvNE|Y!WspLwyNhGJPtpX5|80?=HCeHOjk-n5gd{B5hf!>2B8@%+?kG`p
z{GjRMT+(4~562J>=Co*?HZI-AV?YaMFTl7ERHHCnqEXDw)P1Ma_R4B=qi<)Nc`|RR
zlvrPZ!rJu~*?I5dkz7jYL2dQ9n^N&v%89b!ByQ>J06f*HE57VFHZ~Hqn4D)RL-v9q
zlk{6RJPvddfjAM-hZ}yvy4rd-e{y?H4_ruMADUclu{9po!e^er4|0A-uJE|y79Q3-
zhw84AHlQ|B#E?iqe8bV-zBcSYZ%;|cM4R3SL`JIq8Z^VN>xBV+N8VdE;7WN}jaX{T
z)belHO=9g0W;6L6mWxOwjTOrR+YP+{B6j)diFQDR<}zHW-{pSbuN;V(6fB2zf;Rr^
z0FvCG_+UKbF-PT`JaY+SO>?A_n@Ke!KCz~000rmT8<S=kDT5f6<!OwQr*49cy+-{x
z!Ew6Olk@SEyK%iJ=f#<>F)V(KEhD$=23sROA%;$YC5Os5iC{>;W6kZ|Q@2j1_wJp4
z!6TI&{8y7AtHgV?<;kiF`RR){PX<s+(b3Gda8r`T=P%1*-zlXUg#*|6Ul@nu$14nq
z7B1dsEg8J5tp(-)zj0^WcygidVox89^wPZc#0=k|;U9&a0dy>NpN^m}s^s?jc+1>F
zd#uHb)XG0YryV#7&%($utMC|@Ms3+HYr{-)K$kquxl^|iowq3pe;=qh^0Lc$Acc^L
z`o=%vOkqda+Xfi$S+w3vsz|h6Vy3?Ix)RDhuK-D6sZwhm;<{9QMfJU1aYBbgPc|2C
z76q|5nqoe>czhlbe=rjxkwL)ChI_i!GR)5>eOf;LLN_U_j6N@aQnIGyqiSs&A+*YU
zj;HPK!|R>m82fiEr|{-LVs5jcpl&%k*I?s*$Bli$qIdX}&*TNdtmv6FX?HUR5~cFg
zVZXQ=4!eSFFADsw+*6ktxrXhm;}zo(bRI9u=QpP-r`fO_;Zr{p^LUjhY2($CyS1mM
z8W1lUGnM$riR-9{WB=vq?fu}LB-_4DY0yg%%%;CPTzt={LHJT=OZ?D)XWu|d%XpsR
z-qWb`o!faJkq&*JXobTfgUJaZLTcy;LC=?_k44aEvtQ|lqEg?~jDExStc*}1>>!Ai
z#@1`VMWsI`S<8O%X0=|OD{trZyPG4J=yJ`&I5T88ry-l)44cPRBj<or?cVR7RQp{v
z9FYkNDtI^kx>F2ufR`*^w758Y4H&FgyT0$?op9Qp1v&a{Vg9Z^(F=8F;^*QPPcDC2
z4Z|R-)f&p#ooiKj1@Fh(rC1hMT11i6NREmU%taG$&e04^lG}Tg?lu)Fa@<4wljFY%
z6ub1D&-VxNfjorp*(6k#wy*c03NUx2_m)|+zIZL3s@bJX<Q#vvJ61W8!POQDH>#>2
z8o`d`aOqWUYq}Sx{fZiJ;NNT-K)L<W7i_u+5LQz8%Ed&K_;pE#lLNyFj|ILr0*0~G
zmYT|*Y!a1<jU7LJcDuF85)WeM%|P!B4*#1uY)Wp}r(~9EXuaDwnZe)J8JKf-DUWJV
z;Z`7K$kJ|~6!%Ikzf*gf4bDo1c&YV``@}TYO}dt>mabl%-piKa5N8iWU63%)+bDjH
zPR&L6?DHtrcO8c1CY%#@dV?U%%ulvlxQFCr*f(Q?!Gx4euVZMNQXU;3TDpui1s<N3
z_&B4HM9Y-t@Tr*+ry}}>N~m!9)N*s%rsr!GZdKX$WLnhsJS4(4@4Z=B+7}(5kKeyH
zabd+VDqDLBNmqHh#LG1kC6+VUl9IorAnvcn5?BecST6Z}^OMw85JPPL25<>XpzS0$
zC179@!-3oR-id`$N^V~f7Nvr9{e3zBt4Hf5Vdfn&b!jF+<$|w;Rn#gdVI&&+Z@uYp
za#q-)a~<9XDQ}-0NFHy|lzu7QhcLBl+qqUJlOkK6CHvx~r6EYn8~^CC*ODD=XMu(O
z;-ag}_eXC2%w%m=5J!f}@A<jZF?@<H<j_S)-pfOvpOPdh9E2R5sv*@^iDE_&jg8-5
zzZ~857tM`Xcog-MkmSYTZsr%!$eBouvX<-+P_iT)ZHOEa&{!K_`ueWa)-~$1v`Mea
zXxJdd=Vonev$&?pU~EUfwT)3??+i>yy1+|ueNQIp8x$}(cosHGKl*)azBM2qtB`WW
z{+cP(fYtI*PN596!bv*l=tUuhxAlkckTLAb?D$D*VdlI7W3qvNK--ja6Ip!zVCrtC
z->yXXum2_%Z!n(e&+J&8+JwZEdAUl>m_H9BHY+EpY;K#8k^pm{9W4~7bq(fLXp=Hg
zU;$D#pOUrjOQ(kTu3}2Pc)kNpvR#88N370?ThxsX__?uAVYqu59Yu!4@A{6q)AK-J
zkMQ%|VBia(Sn28erE-|BYf_eck|A+YGvXyK@|(8QSOOPGxnQD|_O5dI`ni+oi)R@h
z$4NZz<<ex=7Ogcywc{}AqrBDp=<{V<NoOszdys=JuRq$6a6*Bh(K=<|ZH?m7nuVSl
z6B9pSm)`@ik)U&?u1K?e&eaKcnL;#Rk0fP_&Lw_0VvmU5$0-(wjXoulOVSaPo&I5O
zK4|V*NZ*}5AwbMDgXZ^+fa11(8UaAp3{#A?+`ri-H^sdj_wY!WKS9#(sGpd`s&WKQ
z{W3<2pMM<i#q`Q80eTDtrPcd$<OX$3Khf={9Rg_?^wj9L_$5*#H6px(hb^_kvUHP&
zJ`pjWKezgr=FLw`6dm!;fazjQo~Wd4Tv(o7QN`n@&o8mE^Xll>x_+sO7QdK?xB|KG
zw9((+ZQ{8$yw@0E=a-?{;rx30A!f6Z>{bFQLnEspUj?yPVIKc68TTTPBoFP8%jaoJ
zCCjN*8(VD8k8NpMY`3i(Pxn2;55u{QO!E}&RR6Jj6`V@n_7jD|j!E9!faZV)zXn@B
zo<1=<h&=pGEj5w;fP9Wb<xT%-HR3IaQcC-3#TFkm=4}9tRuL*P(**n!(eN0zlsbR}
zx8l*W0P5!&!a~WGSRQR^X?dUXuiBAYM6Z9?yy~e*h46m3z($drZ0Bwi<?gcCaOu+V
zEi4i{&?U?9--OED_R7)hyzbMC(KAB2y+g-~$0m5kr9+uv?B*b0Ztm3UPh#@tigLzd
z<HH7=;AsAzM|*pJ5%@cPSRPSwZwLG@#+r>yxE6y49^;ULX{9qr2;kk*+#I<fVa#>0
ze~x;8%(s*eE0*<@{f@Jz#7+rKQ+8Zq=?vzxsQkUCMeCz4UpsEs)Hg0|tJnQ=3q@bY
z_IR{S6a#3j2dq}<BJl!TPUuD3>swB)W;CYvA9IZi_h!xFlCRFi!-^Cvs?FQPhJ0=f
z|E19?wRTQ#-`&Bn&Aj!QYkSQqe?4BAEY}C{qUs#{z3C7rBSmCw7E~!iABZu@_D=|W
z+H-U^HqTSWabPJF2%kvOO<VJMX5|=HhB)ULeEwBlX=3tyXj?nVV!78{QI|Y{PnlCG
z?>&m`*tkYkR+ZDqt^m~B>2e=2o4%6Q7dYT$!AfP@kRkJ$A>f$n+9!nV(1*d4vYD&s
zhzuq}Wh&)Z)hiO4p-Xwja1=GC<0<Vqn-%PRU)&n40$w9QMO!LWWMf6sbx{qry{Xdm
zp>C3USe&^PaQMPt<G^L~>;@TpHGh{YA`)hsW0g%Sr~Y6l+c9nGP(A{D+DVz{sx)_G
z5L-XfdH)H^`$kPZskHq{oAhT_pSAdhV|AXZ%$aq?`&Ssx0&(9WB<=2DBKB%(a9Wgs
z(S2WiVeqyxc;kz;Ktq@j($8qAS4?9O=sr_mECV>Ihbo9bhd~W?ka7$5_)v!0o5|>d
zp7QTaz3wvgwsQ)nJZf-eN9`FQYLyn@$WKDMbvh9-67DTUZX3<pniJ^!g%z(45F}$K
zHQwdae$j1)>6Ot>1L-9;sz>mau6Kst%_iFDS<tAwe$K+QwcqpKvmop;4L{d^YhU=t
z1uNv=v1{F`=NMC1p^fPCt8t)DK>Tl9_hy)s5MTMLC-3fo^y}=ztgL@uaCl7i@`pUM
z+m!p=IZr>_#iXP{iPi_XoRd$zN0v`cyvF@6ZN{?boBU2YH&_G68m3RMAmwm>uE*y_
zn$Rz_XC|ZqbrVYU00+3c2i@7F&ZrCl#%WRm-;u3(kUfHzmZncS_bzp6nlxnBe6TVO
ze5edfP@dpsYQOPs7LCLgF#H5!c>KBMK#^kzg8zMDIOJ-x-d)+hZe6sxXdsRG4sEWZ
zSyj9d(Wt(B=+3HncFwRx;66fu&vId5DWNCR+OEu(7HYTwWu!ckWwr1aCs<Lv7u?A9
z6;9?AdY~4J6AUy|M#jXJXl2l(s0i^tHk71@t#@Luoh;NWM-vdkwkwZVVqONOK`+>i
zRbeuA0_8*_zUF<XLgjv<>xYXeFc{O{3ErILBJa^4syhz1x*l@W*0a}<$MWmL#2N)p
zf#t{?3)n@r8zib6!mcsB9~ePU3$y&t?D(2@+ionRqL-YDosSWq;9^_RlkvOR_hIoM
z0jaAYQ#P3l1f{h++4S;gKDmbIfr`fFe&<V#<0u}9uO5d!3$${OV#dV`*9tZ^zj1LY
zC@ZJIcz^O-XPjpV75(}9DpM&JDU@cXJuddLPxBu)8L2y!&R71juxVbk@aLG&4L-QU
zuuyWioNsSKk7mlYHEP0xd_~Uql%n8nlgoJ#nBH3dA=MPJi*8Ks-gdd)x%OE{Lzs}@
zt5vFgcz^;3X?c6fYNwNT-8i{PsIE~EkSN3wU0M0U?B%NVk*ERKCD`kXg_=PDX<|b8
zoS{I!d}rm+OB6LLfd*(lczh_DVC{R$=hlNCu{yo(Uh$H$vDehPde<obh~xW%EkUS9
z-XrsrPu{y;wunZU&9=I>d!fOUuFFQKXRjq_AbrW6{^FM(Z+lOMQnmAl489KL#6Y$7
zWE3DQx$h_lm4!$(>~R@6;+Cn@GE-e?#NB-seM~&lZyC6bL!Rd0#SI7SGgJQc&#$fD
zdBrWtA5f#rX06S&Ud7~g!Nz(ZDe8mt$kg;$!JG;>Qf8}PWZuqw<Mnw0f}BX6LlDmS
zNDRslcGW95xD0-McbdSiI<^dR@kv)<=fIc31#%}JviH1+dq;0v7&1{^&CKol0b40~
zsR*yD%+`|t`|nzkuL3VSRL)_M%9DFT`f<}X`S)egHx#Enla&y!fFbPFwy{6Qs2usZ
ztGdT4w_m;IH)re7YFG64o)h-0!H;BuLK7^O7F^?dR}1fc^3uwQcTv7w&M$aPHomPI
z5Nq*FGHRIOI-Zj{Miy~t+R`@M!T(Jn{5W<ids{!n!#Ah<!hlvT`b=g&+bko@$2b0L
z5V1Suj2=%skz--u_Tsrchbs2qaiddl#Qb$W!e`eh);LMJzxddqi=x#9w90auh;S~>
zG2ecn-dSfC!Vaj6V-6{sQiklf+2NNskCMSO*DKi5ZoU0{8gsu*T}%n7My?<WZbrL7
zx&Zk^Y}^L%q*mK=BK2dp6G&wHt8CIZD*+~pLOto25UI*S-N;8JdWC+JXm)e}CCqY!
zej{)>-XUcEQnPH@G0&iw?9b)T&d-CwY)&R2gTG0UAS%Uk<>Ox>_VJ86+ckf=3R=-$
z&a1Y{^KN{v1v+iko>&0ZM06f2A#8t_Jz!U+*zZ17_6JHwqdB$j?FWMmur#Po))Z=c
zoGAVZ46;<If&hnaq_$x%*d(<S=tjW81&rR@n)34I6uGu}?4oTxDGBLw+N~<>P4tK|
zw(oPZNw%D7<ZISXm%hB5y2r;6eoJ?aO(1+%M=<?Su5$m&GIAJ9sy<OOIzEALsGSf<
zV#IW^Oip&DwuJuhK(0OAmiQ>scc@vKUyj;J_1&hyVyhqdIW?)hcW}yrC8!-uiAmJ)
z%}dkilt{w|rbC*<+UWm281IgP=u#Elrk8zyjH}0*Z1VMUI^<<xD}HviPtl(!)}6SC
zdGA^x>73kzk>*OquU!JbmVZ7PK!%oqQjjY49qI5)LBVX_T%u(Pt=vTjU?egGmqPs-
z{^bvov1}Y#MQqKx)L61|aDEP#!kqLPjhb+=8J2p^rxf#2ua?8A@4+H;R|bA=?h2Ke
zeD+kKY4&dhOxe!7d$}8`JgGfy=wr7+4FORqW~^`r{sK9AWN{{A06IZ5g8pFN(hhCT
zo_V*G4dp~$M~e#Y>2#bgUt0*vhw1TI4+akr^tMXlOo0FnTFg^6R8F=x436-sTOjM*
z3b7*}1h*9x9gzfx!b*}aJbGw1P<S0VvpCKVXTjy=xO8Y3Cp<()r24iz{E(WrK*L&q
zmOm-D0I&e45o<dGiGo%V8x$?7>Fln$-$Vn@v+WVqgtCfV+2bjaJQFa3P1noww>AB?
z{WJYE*WAR4WSHl-GkQx)+gE!Mn8z3Ni&)}ZQO9ki7+vbXwVO*xrk>?wOG-j@I3J&`
zF}R?2_G7Y@Z;@@s@?IWk3|UQ_>bpiGVaGMgk9(UkXxZtln|8NROh~+kN+a>(7%8T{
zHe-}@X!A!(hyG_#cMJ}v_-eVFYgSiv0T0ykJS4New-X*1zh>PHbF<bzPv&o)TM-QU
zHFlTbWWDlyI=@?A)8YIjOBXol$}l*pqpFzgKjBH*SisL82MK|4W@)}vj?ZZ3(Zx(R
zVsA}VU>{6~UAuS)X?RbTOWtbgol~GBAj{ApY-U~zefAXz@X9rf82EWY9QnOMMbTbZ
z#Bekeu2hxwN6WU_FWw#@{Fv>ckj9#kQAGH(Q)_}x(;|0_n^ud-n8eh2a*$2t#t@|T
zQ#q3ro*+W&*cor1DQhh9w=@mHB`%xl^Y<zZf@}OUlwAQ;2T;IlHT+>=RTzYNdQ##^
zq2<NPls%=kd4WRJ6dNb=PnW4fsrGcW=T2`D9Of&g_fNc&LJ<U<6D(%Sahrxn`J;V!
zw458CW7v4v-i&e`GzmW$I;rp_n3IC!+2fkt#x*I^myYNqIEom-KbEG3ib?tvP>oT^
z-KDU6<})DO+P1<n&c1UVYi-gL(bn03bW9it1t8=WC2S_Dh!)ha%p~p+>djBPvPZ~N
zgC8kA&yy^p69K&*Fu3aa+jAjYb0?p+nRgVEtEa!xV7?khPZw`}-ugzTY3W&9BEZN0
zD|GK_l!L5fdtv)@3(mX!Vpq<w=7?i%LqfN_+EjnNg8DkW_CJanz}7e~Vd32myM=bK
zf|s8zWHP+`9kPq<Asz)?Uu7n^-;KAEQIhURcML<SeJ5S<(k??3cq2Dc3q-xmR9HqH
zjQg<JjrJ@$S}jNYaH16zpDaavGF%l{fSP_8YHx@t##XQe*d3WqOei|J{Ja_3D;1yE
z92>T-+W8}qHFlQz_nUPy3C`^y%c6bT_Q^iBbFMvlr9`+L9wHa%^(q`qjQFQi<^U}-
zT^mck`=X<BWkU~<bON`H@MBboJQ8h{0{kD3Jd?}rJ4Js4rQM)VK6`vRmi?cxptk@E
z{~Mw6lH?bvusHVW(vkOag5VCvl2LA`Gp2fuII0}Z+9z}(rR}LEZgi<^4^>IVv_e&@
z9;p;_5H8beYm&lH1k8Lah7kstN&voSeIwe55@VE4S>HBiYywj}t+a}c_E@f1#>l_R
zE(68J?=o$B?qRnXo^f?8P_0CWqcI^y$y<fn14}J?d0wec@RiJ+rbJVQ%h&wsJ4Vfz
z99K88|L^sEn-iHJXGizzo58`>i^oxY!LB})m+kieOi|9G`I;&oFF0UmJZ6+tU#~=a
ze6894&$Ro?K#XPUqRrLX%l04{YetgzdG{eYN1V!ehDyh;Z-R~GB$ta{7#ZJsvnN8n
zpbi86jsX9w>3SFX+cd5-Vde10^ih$VSa-lv)(=Lx^PbF{IQr3=2~&=<09op(vh{VV
zv~;5LiMW3I2qmRS%hr{hnL}h?V!>Bluc-#!?zTJq5I_dMd3r>TZliZ*+e-513&XJr
z!HGBBdJl7Tb=DJ`PN10+5UzCqGq%1(8kF9;e_(fKs&|X4bV-6z+OaS)BUR^7jGnx`
z&X?(iQqUxt`KCf7<-`ZETcE3ji))K|)*M#eB1d@?lx#Il-c6k+x9FUPLmvPd!Ps9u
zV3d46i1VVPZt2$;X@Ayf?o_ddc5%)hQz;)gBa+QIz0<KbC$s2CdGm1+UVriDGLh0b
zefes;`b~4sO!4=A=XSGeY87Op*<N;IJp5|Guoca&e(^5lL?LgLRvEFR#HvKb%J*SW
z^cb?nuSqJSWz$rWJ>+I6AllmDwDO022gun&AsWqWgAB1ms=A?-lZB|ChL5k^qLPNb
zs=lLD(2Fq4_26t&1M46{QlsT&=(EQf@{~p^$On0x$WtDnVt=GTbZ$P~T2u=u(oFll
z)cLm{Ay8RiVzYDZio5vV$JaIKyr_E1?Gw1KWs9hB`j`h)o@)FBWqXBn20cI{{8d|0
z?688FqX)b1jZQ9e>4ljbt+A8wLBVs<87ix-ZxMX#v6bdgVTm3MlMgN!U6h;xY6Bk4
zT?w;g+p4X>ME!n^og>#;_)4<!>EjypLrFH*od&8B;eJd1QEl^C0J3rlbHCpFZZo+?
zqfh~@()~->QEnE=o~tW7p<^PR^2eXU^SLH(hgrRZ4j2k`+4d2`+l_4Ge;d6RAym17
zYgWVztUSw4qW_-Q0-kq>?tYt4NWeu*uYM;eSAhTmG$lvf3a|bkkDK%rd-#jjiy*^*
zt%mE{K(|vowzE~zRa(uz@W{Z&2^qhiu!(;T$F>XMUte;g=)-F-9{ylDCtqI7EI}uA
z&Td*@T6_OTQ3AWZPa8Bm)2#r`IkIS*%bP&T;AH5Q<vh{-&0xk|_YP^}^9c)1Xi%5e
z4I&3+=4MmKhXit*odx8GJ!wkYcfMl92y;)apjd19-DCJ_F7;#R7uAlooM$cJ4oUSP
zhgD%w6aNkcP{2)Sx@DL~*^}2ZUfz&I*QjYbg`3X){6zu2nDe@}(k^o4d(PKrjCjB4
z)r27g@VA``Retg}^T081UivkIZBoeDWKAW8oAixB09Ty2v`S@HngWhJxgkZAHTO>e
zvIF1$hoWeY&Sc=zt>Qcm&s^d|cvB|cwt><@YxOg-NC#C!&_t^B7*ezA@p0n%De?Dj
zo(**?{_wAR54t%%&#S|~pQTfhhoiXDE>B@qq~juxlu$MCY-X_i*+4$D@dwzo8p5U6
zuq7&Yd*++P&mBIG?e#b*Qr<bU*>Pqxl$?V?kOPmf;p0ycy(1F+a<L@v@3QOBlzvZ|
zF=3ZU6Qhx*jn&YoWckv`g^<B8tAs~q)x!XSS{@^1Ct=y=e)kV{_0~E2GVpoF(d6i1
zYT0|pGWx&qY3nAy0OC|;T;O@8qWv?lOcQDPvUSgLr#9wRCJXfTltsTeHPJ<*y#oWX
zC=FZXj$RYk`-Z)WhK?(?4iUW_cQH1P`#sSy&~2RTQnI@3n^C(Vg}cV*?shKHBwVw;
z=+~|^2@poK9o&cY=q<|!DSd^FbJt~XGv;^zYIuq1`<C*r9SO(-9h}=WwpaT41{Fl1
z%RUa)5P&xMHcrc#q9J;M$GwU_<MUg^jZ9=9*+TtS<rzr5UPhZm)&aI7hhm&5sjnc_
z;uCubt#Re=^2OVOyVn3?(&rfJEg`S0Jg05rKBPx)NW6m2jQC^v<U(eTJ^6!@KKu*q
z-s(nEv)(2xovcZx>jg8gR|cPMxHF>OEhMP9j_tgch4=1Dz`HXMUKU{ZRZ%hEb+QhQ
zkdc|9pbpw`pxC)~CRwMuKE9S^t%>|ZgHuXd%1p1=o;f3x!ETr<JfFzk)|j;4SJ`~6
zPYo_^RAA7R#HUZ!`ot6l5-1-_`Ie~BPs>cKQO(4vBZ*EPMx)p+X^kz>7DDPSCm#%9
zg2<L~a&4b3HHIH^K!6qXYiT<n2tAD6%qIi#OeAq4C-E|%GZpQn#1-nWb#3EdMx`HT
z=mu6&!WJvI(F0e;2h_-#QQ2eEQVvt6$I181wKxn)#cm<ACsb2Eu63UH=#+UQlhYLU
zKM*%c5KWs=D5Y~Xp%t5j(Vm!%%H@=fgmmBIL4fqFo<l32o=78;?6W`f3H6P^ZlWL0
z8;TM03>!M$^IflV=hd?aR(2jVDB8|~V=-g*mH309B#sCcwv-cjh~Gr9hTHzBYGoEJ
z(^tR-cNbYMnOj5)cIHY+sQ2MrgY=!>HGx}E36^+h^uWs^1pr+oLC(t@^UO^=Lg96k
z^hPlE)q1j!ORKN*T>;snd%O4RG8tCC+r2u19^?V1tOHL!7paJgEap1@6Oej@gVL^{
zBhUTHRe{r^2yq`;2d7!l3cV)Nzl7#Bae#|0|FV=tR0%Z15q`-37gfvUrJfjzHU$6<
zMNJ_w9g}EBz3c?Hx4i?2`h1f3TZonC%^E~LiCHSO6e#(C#CMs8@%aGx@pE|>K-<qX
z=QbR>YJH<V>+3(){_N|JnhZ9tfp2x>D9rj&a45!8qljnHn-c<CSkZ9hvCM+HAJ?8z
zXrq67WZX-~T#X(9$VhG$#hSCXAZ`U(2i5kUP3C9L(l2@%`Vq+~Q9j~k#<-VUNLk~z
z1axTQos%lH6R!RpQGt|VL$l!M_;HQ<?#j*f?wJO$*(^ZT2;SKOc*Bl9IsTNQ(f7Rx
z?7)=gr+(q41+{Q?YQii4Sa!m}bedV8@=KYXIX4e|LI6|lYli~$6w?GYMjMC=z_xNL
zlU#I;Ob#_8HR=ZHjjd{4{tv<v8m*sJp+A=rx<9${4q6n03_;VEeyg24lK>O2?~!=m
zM=Owk{;OHN0t2F0j;<d?0%^}Kfj?$UlO=Y0<q<vMv3obb#0rNcApjOnBSnQmQ-q94
z^P55Kb-)ZF2ts@(_eM&-Se#5v3RN!iMpi?zs(9>{<zy;m{zoI8@(hh8SGW_Wc|PBD
z)Qm{dVUdQ%o050*Z9l}sQr!+1NHcYDvB;S)@zU<Y(5Si0-x`?JNcBQ@D`FB6;Ip15
z5$~kXE_enX1At+jMRnJf(pBQK3{|GPOrm%q{4AFkAR%sfM8Pin6p3Yx5lpC1cc;t=
zs1YmCBa^X`8^v<LvS|_Y`j|D+soyPm$PNS`3n4q&Rx}YHp6sEbVT1s;EJlO(%15-;
zL}fk8#|WTst=^fvsU{Lg8zT>81}ZBKUK!1&6@0!6>vC-;#*7t%`#m4Sp%I%H&d7p0
zOHe<WKSv*SaRv7<P3W(mnELa@+HU6|`(O74z?z}PJw4)Y26=83RYBrk(DC8m%FG>M
zon41-@dVCSgmr#9h$Z-R@wxenHlE?EjZ*NBhEJQgiVAxptw_a;<)mJ2dKBVj^IbMI
zL$lo^6^6o*Deb>6VXJ3Xk3<t|)Yb~rQ=zo-CXlkb5Cx)!GcovG+7?52@MhxV|FB=z
zuu5Ctj6T(H!1@aEx_SWC!P<?taqfS&y0xXP+sOY~3J^AIU7=Wd_=mVzyN3XxnE#jv
znU0M*)}95j!N>Gl{Rmz64>3Sg<&<k_Gh|ql2J0OCwfZakQXTjxGo~T$cfBAsp{T;C
z&cvPUN(oU7m0mL~nYS!j+?<im`>hN#F8{S#<f4Vyu3qjA*=y^6O}hqZHNBk23IbfR
z5;C;zPYPg@X05;6T8Cob_=+G5GD=Ew@L6&oCWj(NwAGFO%laRr3645P%{qsON^8HD
zDOQF-8E2H$)Pxv%q%|S`*h<J(mGpUSyC!SjTj&U~+8D4RgSAQE=~R&NB918D#j0_n
z8l{|3;6|e2jb})r1CEQe`+o#AQc^Y%9i9KKwrPdVGF!vtZQy+x{5VV)YQ7KS)Y&?N
zU7-JaVmNd0FY%sqoe}f7>GFGg^K$&8`Er_5um$j}foHE>S0=X{5S)zo@)F%|C2%+c
zVCSBQ{h;sgf2_-&jRR+$k6h1>Ui1z>ffCPhukNy>nzz|vy8uKtU!L7?UzSn0j~bc?
z4rY<GPJp<FYfJszbk~C2Mr!`byhcbmPZVcR!|kw2Blw5S54kgEo};ey><R%P*BX|*
zGo)4&q-7q6IRdv1NISj$Ot~R@k)d<kCG{RAE+5Qp$66yRYS=p)y&Z=}vy)Ovo#7iO
zSw&-~)AMm)DojbZ<<p`-pWP`I*qGW&sQN2)LIgchynQkDcQ6I*JPT4yyiCR8_8Zhq
zzMT||QC9Yk1$S)`e-yM#D^AbhAb=$hR+EM8E&>WlOkN@OVg5Nh`OL1W$xJ7&B?}ix
z42G0S-d%j$Y()DuCd1Xyv7%9=A&z5IG5rsl)`p6vidJs``p0Kdo@vu8j?tik(qA&Q
z7O(G0BiBeWgCKOFtM89xROK*UCuNa!GOZltok6ppNJi~<V6or%6Y5}qi)Nm!Ejhc9
zfj{%_q-OP+mRx?}ag|kck3Z?0(f8dd>`Bc1l_@DIRv5P^N*OIkIlKV}Ql;sdOKbk<
zK$Zd+m#)XhtaSk=w7eWOsz&zsNL<RR<q#I9zhjs?NeE%dF)b&Z7h?;=|DNmq4G15t
zoC+`@#_~yUIS*Ne{IB>jRwrw~%G=s1(brum++1peeOa!m3n0dAYJ+wCP#nZYu9+d^
zU+$X&zzQosgma+f+d$dx790d91IBpu^p~w>E<)J2rn%hc<&owDI{a(2!C<*zC?A(v
z32CUEoA2M?{ru=LNv32z<JRBQ@{nk#)G{_P%kDdlZ7z3mh54y6$+uN6P-bAuJsmea
zlNcHP09s9_%IKBO(M^kv<1{d@(sNvw!W9FV9tdnuXcm9##`G19weo(=#(}TmD<+%F
zEbYPuD3Sow9ci@ZBNi|YnY$L-$#2n&^Im?Ghe&1iNy^F3V_Q9TYkl1FE0G$+hIWX}
zh5q7k1KJrbJ+?FJcIR$rCNt69Q_;KCHUSk7?`fsJ`ln1<un)yE)pkf20Z*I1K)|Pd
z_aPnn_$*B!hfc>Kyj0#bUt$Je@BsWBA&CLR+-p{9XXYn|0DiU<kaz-jh_>Hf4ks06
z&3R2}KEKh|$B5rA6qnyzGgwGdJrtXq+FZx+WA31S`b2$VaiJ~#qt$h~I8FtVTsB@G
znt^B`X{cXg<4FH+tXfBK^9?~zw5_^}9RLCr3)gBL-o3_}EWr;IL>B$q8@Y4y62>bW
znUt#_I)=-D1i|Ymm8lXBO?;E&Fx43gRD4h^1S;93P`M1MlXV6qJc3uzj3>s{bapk7
zAY?|ds?BcOQN5EfIg;dW$Jnx^vs|SL#WX;*nAnJ#{MLA>UnRSgS-MyaM_pU@H8rg~
zU0-FwEGAI8sJ#1{T4;@6kRf>ya^o%4yagwv&1P=$jM@-PDrbrrRU(OdNzvIzd@NS|
zj-(T9Yh$iCo%1_7tE{`1O-1%=?Xba_f^+Vvbz0RYlOvR*ORe@&96a?LnzYwB6fpob
zew(uq_fyd@SvZf!vWuJDmaNA_8WQ-@jK(yY{;KZ)3|U|-+8`dBmc*q7v)cQp{@yRt
z2&TW}8;}EM$z+&^a&DlhXbUT0N(?$<0`m=z!NJ=z(fSOa41~<)_>;s@O!y0(--LJ!
znp(GBYcN9{2i@5$%9&x7C#>b=)+3klF-_NR^J)u}=np3MI_Z#a-!y+FaJVH~{y6Ox
zm5SFp`!0_aKLRb?7Q)ybJFemEN+`a%NNs)~kP>DoS{X2u$T0pN6Ymeu00V<Y*M{lM
znI&XO_V0GfTA9pJID=2qtug!D3Xvk*JUzfb`oe@lZ@wOjoFn?YBonY%0O}$PmZR@b
z-{o+j*j-n@tG~`Ke^W+tjda$UZy6=&)1RNBdUNy1_Dae$33KcZJ5EyULc~-@O+JuL
zDNtv!5&%LmfK3lGH?biJuLaO&wOlg<8#4G`KLCLd2sr<BSk2&^pnc{Il!-)IJkWrQ
z4_Nx6UmQxsf4gTg5-<w#K#kY4k#|3F#?7Si$zAkB#u+A*@3{tehg>@(0GlKS50TX8
zD_h<MZj7M~#M}$}s)(D-9iUVZyu5rCQORZ&5c_4)&`^UzQNiS#`CrZ29PoL(HPtTW
zKpuCH6L^*eey#mKlCA<M%J1#^Lt08eKzgOSmM%rQTN+`hrMpAAySqW81f)y4yE~Td
z?)YB+-wY1pjJ&M7_ul6`=Q-!x;b?X?9%*c@2VjHsOE=44^(g%Lg_ola<PEsE8Q7z-
zgaQ4JvGzHayb2(|K5cpa4=`5SkqB{f_qc+_T-l-vfs31$vBl<^yhd3}XVPyUm!oFI
zUEQ3+e6DLSp+|O`4&2B{YK8pamFbDO3jW>%vA=M2NAreAEnawKHOY%3^HAa)W7@P>
zizfoU^zex=v`8_u$P4QgXHSQ!*eD9V4a1dTU^mPpm*kUlJlLSp@d{wu1wR|1`-*3{
zOB#GPM{u;%@k)r}m0{7Nl6|Dy_++q1CCMi$g^xwcL{+Jv$iBPRXF<RooLvW8H%~2;
zE@Uu<Dq_@`V_=q2^d$rSR?r9FyezD^4pwOBso_NJ2K%xZ0jAK^o`IyAsYKaxzD4R6
zuEaYSfpT90p93!r9jUk9=PAlMtD|3~qIAf9t_otrAh7f(3!3+6-51pGyyp*G7Hl;+
zNk?q)n&cnh8<w#_1%FDK+WB1N;NC8U9+|rJIh3AM+C1z0ZgcIsAy_1+v$IS;e!8mX
ze-|4%Q~_b<=I<N{<Qu}o!Ub7ux7tDcMOF<BTmBRqP+%HbwRTBlGYVa!_DC;mUzO0k
zz+A>o@0KZ*bXwawu2cgH3#mD#J~%#4>ED~D@NG{BY)?E!-wMC$n~MQ?{PSvG=zI!T
z-(HZqNE#4+7>(96tAkoii8o2b6-_^qZcNex=clEvM0{$cVMb9wNoO=*?aOPHn-9nJ
z1N!fa&MlrbK8Fmzgce?ovGS<ed_3dv2R*aOFsl7EaqfO0QmpNHf@-!|(2oRhv_yH@
zL(^%=yg0q^Gv=>0Yqg6)Z8fVe8Cb<*CL%>-rk(TKGkn}mkw6nf&=f>%twt*il3cj*
z9B$#vr_6-~!`nT5W>Z4-&6R3%-o#=VlV{WFHxM=<7+OIF*icHFbkD;c7=ZJ(eeNds
z%UnFb4=+)brw{*m<4$0}UHOvj?L?}_tzI;@w2H8KbsBCSKTW>t<6%`cC|t=uMsS^Y
zMtc21ta5to_P7XFmuuP<@2|PRvrwiOv402h#$BPHZYt_vKq_)Ic8&ue+EX-{XZ4!R
zX{tm?f~Z&k(5UZV8DjllH><)4DGwOeaJ!T8Pe}35KBH`Pjl6%sgu(;XEsUn$F@~3S
z^CKhPe%a1asx7rIM~QLnuBp~7A{;H^3j!gfYQct^9DZ1ejC|AL@0K$#>(MnADUl(I
zB-!cjoB&DS1?EqT1%}yKenuv4O&#k=b4&)@Y%URGjBSgu2P^Le@AtZrjwR<(%_(AE
zP+YyXkSS(QetCfDs$@xY=VFvCiE`>fm4Ti|qO!f->UJp<MI@vn#fBWwI_qs>?+V-o
zNu|<nD(WyRJ)gOUAd%ioOZT@~0z#p?5{#99Ts%jR$VPAi*z{eG&(woQy<;iqyjYB&
zjXm28r2z_{m~H0^xAew^_q~0nW##qII_E5-R-g;;c|P^-wR!2aAWk9qGPPCgE&TMS
zy&X`K;QmvSI1Cw;d|s{Q0c%l_2FP`nEY=08bg0W*y5DYC3!%w%aXQJ%PxA<J_D)pA
zmj7zk!#a@~+It@7jLb-AakdRorDLv~kwTo&<qs5eRchJw#ZrJRrWb@!${}yImh<@!
zGYrq718~H&sMpQOIxGX4W8tx8PgnRiPP6&NY;-&LoAr0IMe<`l?{##K6v_ap>U^KI
zt{4Q@-z<g25`E%qPMMA7sevZxGxGLpTw6ew0gae*zvD7k8ZX%)*2^H>wJjgi00qAw
zmrP`H8E)Gk6q$AQV<)Nwd=kT<PWx?*bHZLJMna^rQ&r2J21bhh9Ea!%tPNy3Fk@;T
z76$ovU?dhc9oR9oRj*4lnJbNTJV1;d8~c48imxhRlKLVxUj82mJ}kn*aYU5yuG3RZ
z(5_a3G{$8(94Yx8WoX`MAn?)Hk~rui^o$%@0kS0TsxQSb!E5szP%4<q@WWYLjQXCH
z++CqG2nj!xb>;as0p&BcZoJtdhM(cDJx4DA7WYpeV*mbTexLfUk5vu3hWxnfq<CNF
zQc^2yw-*;HvfBSFcUH+g=!Jx*-tQmdNX04JT+RP<SunfGa+gdnK1d1bmE=@t%m9?B
z&PS7gCd>0~0#5jL8>ULnJ4l6JIL$%PL{}J+51&XMfGa7N2kkoVi~)_o{qN%s2Z{!7
z<m&}~`!L{eeab(5N-0ziPO5k4nd`DOul_f42fEERS*Gm7-e~+wV#4y@Ku`$v;~_lr
zk2rv=h6TGmucN*0WI6z2w(V%)HqnfNM|DsmNznB8c5&C5>>F4hTrsu9(=kh1Cm_qr
zcXLr_#i^$-P2>6C58ToA<R+w{v7sQ;*zLlsV_du9H7@v=l`j>VyZ>mf9bbbM6`^)7
z{JhA0he?*TE9~j&Ye5t#c)7N`B_pxR!@)Va_Rz@y95(>|raY+0y!j=mc{v*E(C6m1
zby|JmBLWmJA|{B%hhMYrt!u5{{hC#x-vKF4makcKl7B3S#vA#FvDN0dWWoNQ5_#&V
zm-iV_<j2;*S(5O6dh+lcOT6)%Y4Ts7ZRGJ#yvE6UF38PC;1Qoe0YL;9QdxApy<x;@
zL_jYk(~Wth6yV<4m;KZiZP#Y3Otc~#O;=bQ<xlpq#V&j|LG_fIawkjvgRZzUMDzP-
zd2AjQ9KE>rVVb!>=R7F6hIY&90P}1hB0k}eo13R?ks8@hR>i|a6etwIhiRTKwO@f-
z21m7pXF~F}d|_+iHGPq81Gheou{eFyyzZ_p8#d7*&9L+4_FIfyAw5s}{n1<4^*2l<
z+WF;-%2QhVn@3O^*|~?$oltUR*}1mQ_9eksO7do{Leid#mpxVRfkv#km5p*qFxtlp
zS2T&!uUXn$t^0!&BO4Q_|1ixcQ-v)6+Ag#*X{G9}wU*GMpo+g`<>jL6+|4tlR3Hf?
zNGfB9-C|3I;Or%ra};X?y%c}0;~I{5RUQ1Va~kH(8c-KaYnPBsB+Lp@z_Cyv1+d8G
zqXv}8ZZHxevX%Jl^fd8_I#(;}v<#?y>uL@R$?@5CO;ni<z5>b`=TP#&9`FMF6ZY23
zU?VJvc)-nAr9WB$W_cpI%bg8gMqSgYnGIkBH_|3Cba^XKrHowHscSMwWkN3oh$Zc3
zSJiQ>R{Qsr0ZxO5KfVz01@K9#FX>jyX&3D0qinzd7z{v&{uCcp1=#y?Cs0Sp2UtQ#
zmsejFJ}a^o{jL>Qas4Rf2hs)DWl*Na(=a?CYG{j`5$>mV`UCqg9xW%uDpv^y(l><l
zi}9RW&*9dh>bg0K$nZ&wF>^F*wVk>{q+xHyuzUPQ_9VT(&GC+5HadG{_VgeEqDk>z
zyj!GM3Nz$A^)n}z1A)dBdfE`L{Kvn8wIGEk%ZyKTB9oh7kUX~52B8umP5~QDm<les
z>2BbPc*&k3^R^lI5mTUELP;clVfWzL31e7wK+w1D5s0Y(!AC)qiRf7QwYPUh_%_~l
z^B1zm9+{r5{slV%^(+j*L!oprLD_P;d0EHIc7KxoTHIwUsTE&VLG8>x#IU1i4%5Z5
zM_#4p$@6U@z4yh<2aI9$)U2{2kD<HghUT|N2Yv4t*UBh32Nt-aRw-!p9&EEBxAA7q
zKW)bf)Rqj!FE4`thv+}G>=>sAvVGD(>>{!Q5Y6JSL4P{NQZ>0hdHuDM$D4LT1nuRU
zJ);SOvG-*yKCf~qJGcF=Sji@zY!d2TnzIDMZc+A{w~k98mZTi)+MgpMGj$ypbK2<Z
zuOC}n0!?@nYMlu=*)^Wb@{K<;RRz=*7~BKOjel}ld<?Q2v(u5!UNxOpL@a<Fc%IhB
z_5^N@n^5!d)T;c@!>+mEzV#rj;D8Tce}T{j%706qzT&wXNhWomq1V?u6-b;>QGpC|
zYdtNw2yJ!_^0l&llA82Iz6?2RI5y>#?9QUcPhn2JTMX?YCL-F9v@(*RT(bbv4J_eh
z3-fdhaR9L+;ed^&%+Vd*E~B+QSR;#ou_g^ziX0vFqZ$83Cm*<*zeL94vV@VjVH*@X
zz57pDGQriEfxHmQOawB`_eDNh^HR7YNeozkrE@2T3a&Q%dU(=`T$m<w!ye;7Ep$9@
z_9k-;NqXaY48kutWDAej+4MwCHW6FaFdJ>5fedrA1f?J75{c2OxOZnpEWV@_l~p+1
z<qN;WT;eB{aJxsh9)Ub$e&HGrPGJZ(RgD#nVjuVCf4nZy6hm!7KWd|LGon-|S6>HK
z7%7-A1eS0ei9wc;UaU2+(X{im+_b+YIstBpJtc+K?x35pv@{b5HSA5R_up)vS2#e*
zdnEgzukpjxWy53d4rSkyi2pnM<omlP><JZlm$rYn1x)v`WJhXhw4#Nia&7s$m0(TI
z{o+_=0hd-cxOS;x+QTP0K67(M_jS~}xIs<B?gVhuJWW|#@e4J!j4ZH_wnBJMy<g$T
zUhde7^@WEgI5_@QxEPx5e@MIJGg^1v9HzVjP}7p5NsOu%b~X<Xzs(+iA4nO>Pt@}q
zGKwTYtWJ@B#<4YMCiGOj;cowYtZ8LzaV{TOaO=?bT!HKlAg<y5A+*Z{nLxxSD;yHo
zDuc3$@pUStJmF^phQ5HnkWHOF;9dcQNTbR%Ut3SBmQThpKk<3TpzuKPy7Qz$nW>6$
z4a^BEpvuliWf!F>`I~$Z_!q;G33Q8iRDHdik!9u%(WQ3<SimweuKPF2zf%`Esf|P&
z$>K&{I^Pd`AK4a+FLvc;rs$Q1-9r~TDB|QOXCi*mBy^Y0rZ=qO$S7{l445AxwsfMV
z#eq|ecPM8|t64gB*`^nj7mzancyH+v>MlgaQVtL<4mGQTaL#@|#K)E{RF=zz*}$Q>
zP#}iJCY2}X3+Jw~vlVJxk528d<f`#6)tvQto*?;&Iy+esm8qLnYT0<Wq4B#y{HXKZ
zjkiw+3o1ZEPDJ_3X8hpM^6K%*FNRi1auQe9<g|E`4_N=9%2{9Y)u?3<0Nhr*#RCkp
zd8d}O6f&sql>V?}73uQ`424g@JYmxlnb}Xcz$+;^99F;BOY5Am07m=+F9K-Tnbn-Z
zuKjbz=KO^+JpvKT!D^yo?C~&TG~Ilyf!HF{u_fNtC*Tgp?!;1yr_A<qY8Z^F_cn)$
z2^sS69P@g1jM-rC6q()X;{U>2XWSnz5sMN=WDqPqE`}4Aw-GaC1qOwv`MqG3j7`NG
z1NNSJANRz}Wn=5%x%*aO*KELW0p;uHcHL)N8;LQEg-G-cG~%7M`oy>43;j;~Mi;Uf
zK-TURc;AEAeos`%Ca7j$p7%7rR8_aSJy^^6vU1u!RC{>XJy1hM-I>EtxOp-6GPrv`
znw`DtA>7hX8mc24a<{$=M|4dp{4(&N?V=DOE2qxmZ1lR=o9I`#O-&R@3e<1==U&7t
zvh%qYno5=O9a=o%CZ=e>M8>DrJ+Q{_{m=Iscx$a#@}Wd7@zzQkDCzbz|8_#L-^fB~
z^&v3I{ly!sB@}Ftw#5|hK9-+!x*qsmk2tmfmG1AjBS1=yvZt0Or4YDMkdhD;e%JON
zEbyR8j)MT4ThX9GU;9^7Uk<E$K$QRs6p$MObiwBL#6*J8S|AA)<o&x2@+%6Q)oMqJ
z&_aupCh<`)9Y2QKl2KVqew+gV3tmcT65afcy2zDYP2;faGRMb(W<b+IK$Ad{?!E@0
zJjH<TiHXb##_!SYR7oom^~YUTrE_#k&oSGZZyI&|7w1GUvJG@AxoHl(tjgY>$`6{w
zkgKTt@GQg0qfqh)RHigeZ|IsauJxj$$P`cA0_>=1sY^s+LM5AkEWWrF<Bhb`9E|~E
zzs-)=VIuo#)$Zx7tUA!i%`;R)kzwoS4l%ItfgwGh5u9{N%Ni4}SKvktjb|)$zkCL!
zfO%GIn)J2}Nho17G`*~KQe?7IjO)gg+oB**YD+>y6X6bLS;o0eR;O-?kO^oSwuDrY
zUej36W{_vYP3O{kk?+VZnDsk&%4R8A*7`|;MyJ26GDSLyxZ-G#H+50M4zHOF2pnD}
zQM1T={X{x?!GCm%gXjx^vzAAG@A_@ph!C(evNQBIcSQWvA6I`c({;D0(wySge_Jo`
z5A!UnPU>O}3xzp;%W6VJ?g}7}K<RWX{c2cq@FMkX4+X?p*rpb#!{tD$>a6F346=)t
zrb@0|v52Ge`u!c|29jZ50_gXyf8zT-J6X%2&mj_}l1mvmgM5gHNmOw(-XtrbBhNIC
z{7c219YXI<*~$MWZl^+qTy<2X9ZS>;HJj#ca%9)1X3(mXe%Qb6B4J2O92C&=C*OJM
zF$TOwb6}mhZgwX$$S&K-&Mr|9n^MBK<*lZM<;6fCRfVp;DYVf^Lgr=X;)dgo9Sv7~
z2fGsn*)O~OL3#=bH^PyZDDSX+@;x)}+%L^A4!*Qvz~{#qYDJV%6l9gY*VIiwStY#3
zvHbJ|By7py+QnguX%>f(8D&EWdKnqHG}iX)fhWyXRN@4&d9f4_m_kwkGe#c46xVp&
zeg#TPj9wqjnMmH*0*-4i+Wj9OVk+2^-Y%j{?RH%<P+!0)KzruO1r?+I(b-Dx9e2;b
zF3KF(R?Z&?S{YT}uv)#Oc5zJ#)kcptJc}+q|G1}|mma60vcR}^>|e#t|LJ56qjkk4
z?fJ>mv$7~jEy^1hd(k2q;4Pp3xBT38dREtb*zA$CdRr8{EmIT!5A4>D60hCQ6Srh%
z-pB+F!UuX0w%2nvJw5tdSw&@J!sd4|l+sB$Tmz>2`=fudaMR6%H3UlFKLw#J*aTqB
z*L9@p3k-UYEgLzNx56wsSxs73w_mT<e3IYRsOh=eB~^Og!>hy_|4Lj5?<cxuCL+>Z
zb>Af<^ZxS}V6`?MC+f07(~{Jdkqn-e-RP-92fP20e+t7EU;&=@wPuB8RqW9yt)Q%|
zE(S0W2U-yk1O-_c`y4(RLG6Ssp{$2dSVe3V*7m=6<b+W)Z<lb<cXP#hAi;gWCuY1~
zP~x70RZW-oJlgJ-J`pS6v;R$RV>%QiiiD&Od?jH%wT$b=pZSA40#IMe{Pdhf&e!gg
z#S*=04e8m&TRA!LLv0q!cF!N0RK~IR{n{W;O{n=+=|=N!og>=H_Mxx~Ft}tnLt1;W
z?VGbiJ$b##e*RIV70cab8}Ln!?{7z=5_O-9+2W|5A#w3A3s^(P`r==2BqJlYgHN=S
z<zUIbq@NuK@7^`e1LhvY*AtE~FnekS-a7TeRjJftU@N*m|5&@{wt>wf0yphQL`QIN
zYVK@>N{LHc$jT>FF+KZc=PIX$G*nFh#sk0z0FVR#NC&PA85}fEubts)^_Gk)(%y6}
z*;{VHRK${CvjfHl7pZ&9gzQF=z5fF&uu)BRF+spp<h7_2oTdgDt`LkpmQ))I97PC-
zkzI(NPm2U`VAhDw8x3e14(N-c4(!rbewQJV8A2>sX&8!pk(+&T@&m8e4wg1F`Ij%;
zmhIl$GW-zMZ|e=*;XBleo|>`qhTae~O=p$-YI&^UeCK_L-|ViNQS|g^K~{C(RDwjh
zCSaQ}HG_gy)f|>$8p<!^ul@R{dM41$O=EMp$UUk|%AovnhpeedkxpzJ6Ig=0w_V{G
z-mtrW{{h*W{cHD&JIaxyKK|2{zn5R*GTjvhMA!lLtmSn>AkrjTdBE86&yT~j26^?5
zl!c!qzu;0)N=ajN-+d9SC;F{)I(dx1SPs_IKgEV$3J;8e*q;5RWodW)A^d#OS5|hy
z=zc<_srIe&K78ov@$FI&&&q>WTtT;#x)mUAnOHxi9A)I61bYaC)?oPY$eaCnU}ULx
zo|z>HLh*U=58raY<DC<o;smF9*(l?frHQURWyWesnJwo0l8oPbDDOiTEd9iZ78y@N
zZAXlA40;aa&gM7#(0|C4RAjnZA&;UmMfTussma%q*Hwa}0<_sREt8A)9HEAUBSOM=
z=TywPdIpYQ1uGyuglH>6J3Cf6br+IW)a`%Dh=!BLgR}EQj>F<9Jornva9sx2sdpN&
z`(D_%_;^I%G_OS~o8S7BskJih7Cwv1^^>aad!*Dy_~z@m#O6j&*VOx9J0lMjvtGx&
zh`{^%AdW9L#wX+`xTFu3%d^1dofoe5lFcI`R5p2xFESmQxbC=gj6ARUv>hkYxOI~H
zCP7VJT0S!czR>m5KOL+MkWh=~wLk=d`K{aQvH*jH6}@qCNho_1WPP5x&dM^d&e9vm
zkK1s2e=QzuQlroevjZT=N|w(UuavYe^uY6(foA{uZQEt*JCBPjvfvSjwLAOaXrrfb
zBEXwkk8(S=Mu64szHn(K6ods9B7UnV-{7NeYzc(!?WJ{tIsbGt(nwW1Eba&q_n|y{
zOA_?ld5hNLW8J-vRL|C9$=MCObyZwF-$!MYC6P=1b13-aEtysjQjAN$VbmX^{ja;s
zc284^ch@lO&=y6#her_Wxqd+h=PGeY?<w~Y6y!O>nCBkm-0JU1)5dwTgo8}XHH`dK
zS<V}0n@9VOFC90z`Yt3U3hK&pT)Ay3M=yi9S!}BsJ1WWCeJjU^zo^*HZ7yF*<|(%c
z`ou;bl<FLUd16=`@^rf9catWIN7OYsa`;$27SOD%KGdf+m7w@iZ#jS%g=J_9CF5~d
z#(7>2Hjcy(EAUEq!lZD-xSmF|x>aY%lGWILmCZEH9n`cb?#9<MbGVsBOzhL!vraJ=
zkYhj+l#xL-?s7e|5c_ezqJ&RTahCV~T%SPfRi8u30ysVjRMe3ot@K;(kQK^#^qb=A
zCKC(s3~nm>OD|AqDM-d;mRc(pn$-!UF-5;iRv$;&6se8-2a|_1-};KId%QOwm^w!I
zvq)+|lqstiO17LtQ<$S+3&70`{fEG*mfMYy;!i+@8V=sYn>TYj_Ye6#-nsh-gpXjs
z`=fUA;1qYVg2LF(!Cu1=#kBISkEU}ck9Q_9fd*z8NxsJBnh5z2!#%>JLWnkEQ-yJP
zL{JcfXn0r^NMV%|(h=J*iP6xjx8sagr2~To4!P1?8xE_m;JU`?wyfkyv;W?HRaZZ?
zWLk*=s{yeQr)@rvQupiiW!gZ$5lO0G=>A?>kg~Z<&gD~?$e%UL^Jm~HL1_K6?E1+)
zEduYHk#mus@xJV-%6!+PeR%2ItcHd;cEEcBEK{ajyR>5k19jiMNB?K&?{>hgH$T%D
zE+dDRoaT8ouvr(K?jQE8kB#-J3~(QzJL(!Pnd}T%9RTS&YE+M#`yZznao>$*sVAWP
z7mPU@0t-mpKUjAScV6ax<Nh2Io~+*B3Pqqph>tf8b4!<ADAce;WEx+`j9OA(DqcBH
z$*#n~6s>+VAS4WI=^@G%?sRW`ltm6pkC>^xJRQJ^N2b%zvbL(dI1Qqdg1UGvW_mE_
z)%wO{I5446@b>{KRcsse;a*X@>O-d$%&EbfR{0u*O4xhX_f2jVNAX1q4g0gA9k6;q
z8M-XqaDRa2=lmxh0+hPcl=`I4*yO(pLR+j@1r4HA*oLk)Nn0Cy#*ValexA)NetXlf
zklhZe1u_%mQFY9%fDJH;nN(SG;G}ur6rvXPhI$z;I9yGyMDDWp?mzL&T$h!uiyGmV
zA4I$O_xts0yVv^OsbfBe#=RyIY-LB-5B@&4D$FlOs0LV&M(TU}s0U?#5vo3$=SrVQ
zy;2D;!1C(78_cK=P*e9*Eza5X?a!pedcuR<xoj92X*({jr)wtL4}?<^y?}M3rDANk
z1lo%^>v}#!^B?j9Xzj&xt*~~rXln000$ZSTl>XhJevyFsr*HOmQ)@3mhvDd2hgO@c
zy{zbM=k-2O2coHitUtf^e>Gg9X30w3CVMi)17N}H4~B1ZlBCKg;jn<j89a+a60n>R
z4$)iwAV-xac{M!Jx-L0>BktclEhB5s>H3@F9ZE&TgR1n*_bp=eL;}6dUObyTxpVLC
zPB2Gne$Th`4V}!6y?qR8_O4$8CU%!!pFWQtBczg%!hw){Y#v}JzQj+KX?*(k7j|I?
zNK>vnU)ZE^w3M>RDs<QFT@Zv(>VHMN^mec~u)dz*Gy$v$cl-G#>5dEOboc!Fe57S+
zskqHzI-m#qWK8{i&H8Ozqt)_*{N$34JeM{LnR`50YIyRuy9w=Y)iKe&Z)%|1v8!C6
ze|VuOBs2;p`l$IvGTpeFvuzHCr$-JSlr8V0P1Q!@7WPqp*TXbG>wk}sU+>o*3EMAi
zR(Hx>Dyphhy=Ylxz-nb>e*m}aTG}#^YpLbE6191$``s6rB;~WkU5xV`{3w8F%4;1`
zzoZE*lJY(Vpxi?wIx27Y?HJSVhH1~EZIj)jGJ9u->;~9!y#)VWx9|G{1}o+kAAjN3
z)?1C1w$ae!UE52pqLP}b=}&Sh2MkOV-YxywJ{J>^N{5?00uG7Z+wX?}D8KrDP=1D!
zef`~El<F-@Ev|$EEg=GSA{E>%Ovs{xPyUpzDvYi0OV7{m7F<ok7=e1r#qYT!)%eaT
zWa#z~F5I)Mm&ND;sh#Z8!s+C2!<?s0I5i->sl78R9ro^yFw*j$fgp71BRez$YxH6?
zXwEwll{EOx)jDcj^F8)pDkev}p>@xGtOh68R5XPUw8Ad8@gJbV*FL<;!xD~?LgcQT
z<45<Sq*kXhp4$1WW5V@ni7+K_$b*1HV*_*Ydh-5EOzkh-K~Q-(wYoQMbw!X~n)@;J
zi(B(5RVa=kY6&!@&Nsf^?t%+YQxMZBlCZ$=NYEHcbyhXX{?&=~cO1C%*fcirm0Q0Z
zG}Cg|F89Ii;JL*Dslk4uK<}lm9N-Es@K^zva(c<6js=b@h$8+&OGUKw2ktSJIO_d>
z*i6xKl^E}W3&})+$Nr~y93?PZI3NF@q}j6pN!p5CX;4r|N=;*Qu(eKDH2be>yuT5T
z_jUj^EPYeH5`Xeou<=?5t=@Xi<<=`zDWkSl*bg!0XM!Ga&Kq5`Zu(X#?-EBD4c8Pr
zF}ZjkHUbEbXtA{q12~sVJ(l_Fmts}wppF`{Nvt5YXYbGT_(xh`uQ-9DwgffhqDSl`
zM9uYn01CnSde5IivfDgJ#@>bIt@zAoCyryDr}5V#Fao*^=Kz3u;qkP^m5cYU2sDi>
z`{iNS(w&NLg4_i^G@Yt%iPg6cLGi(Cwh=(Zsi6SR@#(m}B1YD7eG?k=G&=rbYy@fj
znns^?sJp{bX<b_>jFANSha$c@|8oT0t14n1J}oTzbccK8fj=pOkd`$^lSZ+NKuUx)
zTTC^imbMkw@5>u{LNvEWV!2bCi)d39<Zkln`!Tt_Ba&Syp(3)wshdze+N`bo8=7u<
z>f&u4Js#<iU$H*}!dGOTUM9)TTy|clgD-*+hcq`mZ{cj_e0qO!c2>$g)2r3^RbZBO
z1swtIx8LIy=fH(WB-V~;jJNy|i_Dz-W4q>4+GF?UgXpVk8k@lk+#0u!EduNVKJEwC
zxj79o0azK{mpm|s{0yH%_QHwIS%^2wdM{1*)gr0<>c-s5rGDq(!?Hko|K|2gxpS}Q
z0@XKr*W+Y;!~FyLrrgWgHBWz>O0q_XZl-wh-*;}nX<HJJ+`oor2nzTPDH&LN;?tYk
z-5UzNd$4Kkcrf(eE-igpdcDEqxxdfP@O(yYt?L7pq5d;cyCkHxr`OQ`b<OAUvE?if
zLj1U#OLNhPe(xCTAZK4O!1B5Y#Q@?tvY#%=u;7=13yx^gNsaZrF9|ArPRJ!NqjL`z
z<Y1DV5>|iy9%wy=swbj1iWOj|DMf#*A8gRwH1YALm6KG`Nc$2dBD4ixg0()6Sm|{_
z?tmnoqHoDc#)a&cDR>#=*%Yh1&O_aPSBvj@-}AQ2%27klx~gr$%Wx?N8W(Gxwe}D>
z$7}Bzv5-m+9ITs2{2n<%P%Z`}i+nfl?Q~OK*Y5%0-_-9-+n>Mkk@%3e2sdXuZ@#|}
z3nqKoKmyP5Su)l)+^vpyWVu{Uq5|5(v#C?hi}^#xcU;+zjq%Z~K*F2Q$p243(i?w!
zWB*=fvah@P#4!pk0uSsn8|M$_wI{fpOZr0sDTqhNj0Kl-$Zqc&o>6!OCG=Q;e?5+z
zK0mqHGYQohDI{`%iZOZX_=M-*Q@B?3HQw~e&cjqk=(!&+;idXJmX}Fhf^cql>P%{m
zm|$jI>wzGTXgW^&rhz}&M$4o5QUl4<I|Nm_^y=z#=|2-H<w-WnXWU+%YoqUMAt=I8
zch_Hw=~D2btOd4R&OL40&C_TjpcS>OjF}f2@97YdAj%{x5DmWb@3w9GUUxa$^o8S&
z=tFF@(aFCZZUhgHxjf2%cDkWKwtgYMbpmt-CnB83u8#O`<!lxjt5=lAQll7Py}t)4
zc9xDCPcGZm#QbvbE=GhhBTs?!`3use=iPbdSG90Kj2Y>u{Ss8++Z{If%nU>K>Imob
zdb8R%Q%6dlHJDZZ3&aAEL;izs=viEd{Lw_DCtp=|AXGr4zGugcbvMlnCgy#}t+zXw
zsMhxQ{0``GJbh>xz10_fss2F+y7Z@!_6G!J9led>Q=Q$xnOd)MLN4Iu@6pZOHph%E
zBnh{TY23gT^q)*NL#FTTw8>Y8WfKhtdg{<C*5=oj``+oa)&XbX5hQctWE{~z_<@`e
zHHS}0gv0Tr_%&VMVE=({h?{E<{2;0%i%nI=%(Yi1a6tuFpjFBQUQ&wrxQ-5h__O~h
zyA=>n#WH$<@O8*6ftz43GrBA^2PO3LcWM7LHJHW=ZDCF~aI)OrAUt(T#8$tbJ;%nB
zsY!7%`I+)TODWwY?bN>2$N$?P3kb_HfatD7ArE`j&&luun{_l~P`ktj0f=<xO^Cp5
za^=Cyqw!S^1H91STpW|P%yc<sCcXO)x`^Gt#UaHgnY5o#zpVbQ9#i`)92TM`oj~pK
zhvTDiR}8iU_X#Ux&2nzVQ!as$GJRF-ZKy`rFk}deu&yFsCUomOetG(Ps~+)24_gjv
zfjICCr)8=$+Ul_qG6_nkw5Rq^67DApIehGI+|}uYR&@$=VlkAWP!Sf4fsfQl(@L~?
zV8HVe$DfpL70iFPjOJ#ed~MPnR(?3VCBu{UWuW^0J~cl<&VwO@N-eCbhaO0m&Fo<)
za}{(fnLzcDl_Nq8iw>3kkV^*Q422Sr!>3gk@a@zgUZt<Winym%0LjBgKKa$rPMwoa
z7&t)dSUE!zigVTB;P@3{)a19V0skDM*Q|hDyv&oGdMHCzBA-Ba)UoakbX1^j^_(y)
zKh}tapDvoZ7N#8(8#hwJ(f$cQo5G5o3AD(-F?HTEhY9fT1L$RMxahW+!n(GuiaU4i
zWxp!35`#-Xfk2vLH&lfGrp^<{@17d&6w>4M_#v{ob5P4!fD6`sF2_Cd`VhzM1s6Q?
zJVqQ;k-JM-*#ZteOmSQk%8ZJRfm@4q-X3Zq;(GpMHI$?HyCf11ILI`kNJ$}<Wg)nl
zP3J{xTQ%~H2?!HF#2>}XQ_i+f!Rp=y(uDfMef%%cIi&r~pxljl>KSv4q3L?+D0={T
zvfn+iwEVrkl+ht$`du~o3C%E%JP&{pPJn?Yc_I{B1xbR;Bb~msb5wzleT!rCf0Wes
zVN%#!(JMASAO79XYqq)*TOOB?Zw%QKN_0)*1U0?=&;|5b03ns&{QN!ysUn^I@24gw
z8Z-|jGE7ta4FIgldA0MBv+uz9c)N>aYzEPn()Y#}?k{xSaG1excujKNb#48x$E~Na
zv|_8^d*Qa5aN_>t)X_Cw3hp&4yOP?`*X@;4<tm+*aQwBc&$$uhL{B$?E)CPG>-oL(
znXIC@wCP+l^qlf)y>}xNrX`Cfv(?Il8s|+wzwYYe6^hA~q<QO6=BDch2FY?%w!dH6
zRyB^OR3O^`zP(>^vt$`ym1|glUf5J*!PfL2Q$!0}6hH3zxZTLe?#if^@!N=}8~l}S
z?`m&*0)69m0?P8AE^--sPA2)pJ{}$7jY?v-*f`^jgB`&`*~HC0z<*=v73<^vQv5Wg
zcPF5q#v>_=abHl?>yiw}DW>wsBxrFd>V{I{cjqv(cNB96QxBe7wZ)H!U(bf|KhB3h
z%pXXyW8MrVb>$i+a?|YGolL4dQSOL1pwqz{Tex06^AIGB_KOD25D_^ZkW5li?FCyh
zav|53$O8#Rq2y;GlU7evT+at55+zBd7mAUoFco62ZF1q)xz(0yKDwVQoEqtC-*@J5
zXF}P1_Q||qQGJ}x3+c-Q7f(Qc3e-^oB9BNLFW@M>if7Pitn0<}_DpqN>RQWJSJh1h
zByt%7LIWi@@t*gQ5Fl_2V2T*#qi4dvY3U$Sh32-M8i^RuZhDX`1XuIJbM6yCQE|=t
zo15Wx?naanCEz}w+ikh+kYm;-QDxwI{Ij^4RR*&Tz%o-d)aL6w6L=Ul)Z{DHPuZET
zLTP(Q!~uxfJAYtW4a~txEi(J`+7452Q8DzNFYKboGS?kgNd7u8IX;grYLC4;e>SZV
zIkyh@p**pXScAlK*$D<(yIF2N&)4AO26wN_LvAj!+Q-z&10j$x-YN$-_u!UmXic#x
zkGG{?Xejnfb$H9jJ0)&#ZxMY2favyR`jqy|6)Rs)d|oTf%A9zdor98B1$yUvo@e@2
z>yD{i{x@ao$~WqF7}<F<lRynqkEBJXI}jsO@@GZYyuw3?!}9$c*38gq{mdBfcf!&S
z+$|$8$vEjpj$WU{64*V-*jsM*1pdCD->cvW@8_2#fiu>(flJBu%(FR`TybvT6&RT_
zHgG`@ETblFiSLsBtJYCbZXUI!uFzx;=+pY5DMq>HpusQdGlmI8SDPW$xRa5c9@w{r
ziS})cy)=<(t6G`GAMXO75&1+K^p_eJn<1S40($q9t0zy-@OR`l_j)PZUg-*fdg@d;
zR=>+)U(qJQaphXe)iod;8Mpm?P@5aY0DCGL(pK-7$Z*VeYQ?xgqgidRP_1O7mOjUa
zPUtH!@rOr`blag8idM2x6RDJ@CdLI9J#@_H*0t$g+|e|bPh_GNUQ{#{{dLjcGdJq}
zXy*rYdJ=Jx<m!D(ZMhUR_EiQ$>*~~|pE9B4A2pj7$VES++cdZUbEY_2lb20)nQ!U<
z&8*qb5Mb~z;7bT_jgss)Rwj~m{IeGqVQM+$rV$}ud_&&)HX>j0Z}z`+aN3D%?^_Q8
zzI1o%MCuF_Dz3PRe9|8UD1-a3@VV=|yFUE?#?dneT~XwcBV^TSRUIhpI{Sp1kPQ`c
zc{Ga@2UId?Pv`oshuK}e!-H~^2UghE+uzCI5cBa!7amzZ-dPinFxi5o?i2NeWC*PF
zGd~rs_e^of3W@W`Gn=vrsc&hoxt_OKIf?w;5=~9rAEc<<^#&BPU|$#kpxdjWfB<5`
z#*7~ER+(bhl)0NLP@VACk$~hb?7jhY!ab9o@FFQkxvx`H6%b%o0Ae2IW`Mb#Qu$Cs
zJtV83{xhLwwq?YsAziEdhcb{RHY;;m{?m@w-+rN|X-qCpIV@2RQ#fib5H!{E$@uXF
zhvk7BZRg(|km5D3zsa^aLMvo`B@#b;MK(q4iF`rywm;?cnXysAtUkPlRcnIG2>c8?
zcGi9017o{!&Vxu&U>7ZtkO_ydD>SfD{|mEeO`PVJl*3~`q>s^3e_v>U4P<(alzp0Y
z8YwHE;j~*RdvJ1g4^W1_Qg23)r2}H^Vg)&2JD<tt_2K>f;k57RC~xLvOV$0m&--vP
zxb@o?KJl~ZbylN!pUCuSXdeG=TQ$gE?YYdiBs-_bqopQRRi`N#RL(*gnC|_qPrJov
z$<I#{8MRfCpsUBj+taNPYB;grK5`5|n!sv7BujZC>5|+-0Oey0O}cFtz6EqmJZ_$G
zGqqg60C4L3yd{P_Wd9Llmw*LW5_7`X<ZN{Hw{x1srG2?1$LpBhb^+P4Buk?eWPyJ1
zBoN;CbFEPO0R!iv!EV=3<$;A?@+}aL+73JZyOkX_t7g0;2tc|Q8L#hH1)+Vceia}?
z?T-Q78UQy-<7)CdjQo0E1QIT34@|z(Inp!iE;GT;M~YB`_sdhtBb_Y?cFF@&E1_im
z^oP4}Ck^eMAja6moCx<QLpp?q{=kiEiEW2?e4ko7mtWXf?L!i#`@X~_>2%nLN=gMf
zKXJO<3`z7(UTb{%kGn}uxzN?YJ_@L8JBn3dATm#!_k}2te_;UDulREaTn?6&2@`Eh
zLUFO{mKafk$0{BWtX4~)elpso26pv%*Y@G?2YOY@<hS?ONz*`bhJjZqdi&V6bEZWm
zB1hvV{Zzhy5@>(0C1}laZRGE+bn&RL;48<2UBKrvi(tKVpqi%YoJWmKheOm`ncE%q
z-vYgA9uWdDZ9?kMHv*T-0IALq>-f@4#F4)+X$yaSKHChOZ9;@8_jN8k%Zdp!fwp$X
z$T+COZ^aE)H{7r0WmnBQP#fFwsdeBKNj-q4VSo^`L<*^URKNK%qRtfSHYE_2JYyP3
zDSzhv-|5Q&Z$(z~z~qb?z#1-!WLoDB4WHBLJr>sR07?R~i{kd@x3WurnRr}DPBFf`
z|F2N%zxus#3y-HG1t30iDfxc0vSsk93I%oMNu7V@nRZTEBT5YV=kJ3^=B153;@=Ve
zma|^Fs8;)sMtl?6nXob)?QP7Lf$ZEjU0|NeLL6cN!OK)!Tzvt-uJB^h8!y2c4mA_g
zUo9^OFNkXiGR)g?L$6P#uTO0iNL=M)brQ(F)@B(3Yy&_&^xPhS0orl^ZvK;O)z$(+
zV{~BKWsyys2E!YO67-4!VR&#u)3(I#mbg-gS(M5fBBB#{>^%Jz&3wC%`VhH~FjwV4
z@HJCvCdH*K4}%>N-t8sII#$z~hqszXf9@YTx-fBZnN<4NonGSGpSLCSc8h&g>4eNj
zrlMLrda<r^hN|btWp67CEmWq3c(@0beU<cHmq7=S%)m>j(9<=|U)^4ebkbsqcJ9kR
z4Gb{wI}LuT#E&EIq&p;<-x6s>lpxJqn8zX6$)rrrCo7lqk&H!&o-ZY+u99iY#`6Uk
z_|reC5U@K+<Jf#Gmk3;A*EIdPMDWov5DP#Qz!$MFpM2@@g!#4GYnPk)+#=wn7<~{=
zmY*x0IWRpQQ1UA>HY|V;;f7-r=5-y(1};ka;`Gt{Ytv(61)7{IKLFeRZS1i@<1<Io
z62z_fwjtTFf?`(-$Oy!N6f*V*sV!%$<*e@60mHK)1|~pM0Svr=d9F1#&PNyzRm5ib
zXU3_1t;9&*&o*g%6f?y48Db?Vp*1~uBOCs;<)?$L-7pIWOAB5^>s7)<Y(Oy^@GpWd
z%L6FiGy2<o*V#Fkzu>t$`EYIsXi#a+aL9zO$r{k)%!mg^KtJwZ1bo_FyeQ#>(FtnI
zJ!@|qwjA;4C}~jp?&4>JVfMGEEVv46Pz6gSno@JLhSlbd+Epj!+X`c*C}@8HM+d+;
z{qXn^`Q2Y;We7M$Iu$(I>d#w!$@vB&IOJGPF6|y6Li;-3DatPWBgxneqgXd09C%#z
zVi!ws3e6BmeZW4k!YyvT>8*G;*1qlbcVc>E*&B*g?!j{#&l>x{wWZ0crqiQ#zu0>#
zN!)$&c+GCr>IIOT=-3LyCt9X<2PYk0I+vwZGg4rcq;9b#I(9?f6fx)z7M1?eL~_0i
z(Ad=M+-e-SxVm`7<`*hOC5e+Bcp*v20=1qd`zhg;J83UK$VPVfe0$()i+Xx))5yrC
zMC1qW$4w6%%L>>5;_LbqK94f7L4{&(jMj}H4cnS-%V6UJ>c4Mevv~KfdY;kx{8w-s
zF0~PBquc74oRxi*WI`h)7X+1&Bi}9DcchXiGfG)5UwX0IJ+3KcpGezXj&YXrS=dj6
znxbX+Q5%*kV14h6hk##EWQ1;N?IOYr22u+upL%!Qo|E<S)^5h-&{wAI-eDxAA1`IU
z?hFBpnyC6VR!@L;H`#0W=}J7fbe|AOUheYtWz2_!uIA&-rlf(4>(kI{Prc;kmT&n$
z5#(Z~{Q^;m;63KAsRHVOM4gP5$RerLr<rdk&mm@5>f{9gKB>|@Y#SnBH{xG3`0I1s
zC0y{)Rdm0VyT2*nDKVeLzCd-mCl&=DD*%iTk7L})dZ`uxqvYoT61$`1XJ)HFg#=Hr
zfc7QVg24ZPwQD?vUq9{!mkyp~x;JDpfi;wjmKvim5I1g24Kwy9?zi?!fhml~vIi#d
zvgg`BIy~Yi;>px3z>0~|M)sbDPAVg=VE;4mz>E4p64~nU2h}E_pD8od&ulovHPW2A
z9(7uoki^O8uTPYpq*ZWHzj4#0Gh>IS4u;K%$JJUyYw=<ingw}1QHtlLI1lal+pSg4
zQA^{5iF0u&8sYp+Cqbv0>X>y*%MGS;vTu^&aTOrBQ#ur>p0>#)Kje#j$Z??RkP+ci
z`Wv9qJ?YrOv*qa#D09p?s#-))WiQKD==I*;z9Q84pym9YB0woajRu3h2*$H=akE;M
zu)K^9ma|ryX^aBIK-&L-Fh8m73nn%-gVcpqToJwz^-R9J9s#pH#(l5V(C1a|+u=op
zOs~erSr2Z)l{abRD4*A<?F(WhBlqkgEJK05blaBassnb8jpH2AMRuf+Z_Cr0X4lUV
z^<IJ^%82<>ZOj`<tj}-Jui93;cppo=1_bqe`hPVo@wyy(G(X;yljSc&@@Y1zsn4d5
zJ-!N$jjSb$yC$(7!YQ&R(Gtqsw!ZMQ$rAm^ADS-5(a?fkG$s6I)i*II`g<T9Nh?jg
zxpCK)RRlYo8S&eTT&rrS*7zC^r#pA?N*Y=pl)Lgx?CJ|omR!{V2;*l+CcE)qz5zY0
z{5>3S0U%0EOaLw&Wu1xA_&e1R)Rl%{St{dv0V%`TfFLF&lXAYgq~a3yCW#4JWp-(J
z=x3e_b;dn}q$32!T#CQ~ql7asrov@P{SF-wcesSxx|B$nVVJwG9n`3Z9Xm1NB@5g5
zeb$a#r_M!tG?M8@CA<wYuEdE4j>(qIQz0ZeKOI@LsesEBM6y55uI-IqCs=t^%g#2B
zu!r<g^XzO4zs6AO9M@|ysPbt2I$s|CbRtyVFO?K$bWmrGASbE*&Uj}9PGXYKsjq9c
zVlAxqEr00uLd7B+gezDKiO=5*2OCUEn68wnI6qp$yv2o{Lwa~CwS%=U&Nd&*G=6H;
zN;>`P#q3_du|c*=`ck*%V1~+i;RCxx52}pbe$nxtt~Z6aYYPp3t;cs)cJS7;c%A#C
zC&?qLlp{^e-wEiZ@9t|0VE3Kg#h03%$MaOeMdo?%ooIg~Q{YBjc!!w(nIyg%y5=}q
zd=#C4O-EJ3;DT3W5w2z)?q&hq3r6GnD!W8}Rp~JhseRoNH#A{7ccVKt7~0c(5?>^>
zqkh^Vd|kMxJI7%>*otLJXLDlx8-^Kj1J&d#*s=(>n3fP~OfvqiiHLAIp`c+TJ%Ql~
zkYcjEp$9oKk$F&MR=G~#uh>lnJombi9D!K(HcBf_Y}ZeE1l?@j*a|20b>1~JR&mCn
zP-$*7scKwbauO7zDC_Tsd{jf9MwRox`8e=DmH18LjFDr*87pF6r=s(e)-}Z^s((v7
zZuH#??XhD@GNkP6wrz^P;V>~UB7?{SpDSZm5?`IkcZ+ChcuP-nGzxq=p-79<%g+ha
zmKgl-P?3y6;OY@}OSIUf3Q<iFiam%Vx(tUc*q=vc;oSoz{Z|}z%t#d!Z|td1&pgHs
zh08T21j&m-@08wntR`{RzZ{H~BRND!l$v4r>G4qs&Re^O(eTDo9dUfe^EC1}os7n_
z%sKsn<wP4XL(g~?dguy1jyQS`v`ns+sb{oG`99X^N-ghFr3b3t2ty49K1sV3&=2d=
z7^ECw7m&PhG=NBA$`NcW?8m8!85Njy0=YhN%bsOWyjW}qvMH|7$A}XKKUJ|isrWA~
zax(&8w=tggi*@Lh5lUg#yUEh6e>)G*X58P`vu1wIWZ#}Ld=TZ`uIfwT3SQ|V)@r^7
z=|;TR^bV7?joF%PHfoFuMtz8~|6{vFoqxt@n)t!gZS6XOEuf>4`GsA&WI6d<oJAZy
zYR9(7F=(oAsvcS9KF-a<DK<Zlq8>#7W;OG(`iL>Im*SwVeT_jG*%9=S`hBuH)5{du
zE0OclfBux4!tOf^0xH_;fe({jobB`oAHynHNOr!>$?u}{Ju()f40z)_z|p3=kS0ii
ze)5y9X$Xl^5L_tnf47*2Y~y`7B?p5h0t)a0pYCU=Uczs^yJvsP%-G)}jlBvKm(~z7
zjV#x#NhO^tStMgFHS6qg-Ax{$jtw&c8+cNVG#t_fZXTA-9rk%XADh2M@^pd0y}k_K
z^A=SPl)aX#$_3Aer0Q$(J82`M{jIW(M5zD!df7@gi53hzX|HEPkmR;J;+bC9?D)*i
zBe_@{ZYM*f`|gj7PmydY`!)!h5~clhB3Q?|o_EbWmM#!Pb=mW2O~^e$U%)d!<`{1`
zP3~pys4xC^QWDuZ0iW8^hVav5GA~<v^!rgR!j{I`fo#2|5Ndc+6Vv+{7>%ntbM_S!
zNho>I>Sb$Llk3q7jcz{><j=Ene~%zPXL@f@tWYy?Xji_po$Yh?pHf;L$`=TaXnfr6
zF8<xY0U-+u(|MQ0w*?Z61tN^Qn+ZrpYUbN@&(eYRR$E`qG05oUUGD~kS+>KM_YEcN
zY@=~H<ES1yX#*{~14~-P0^mA-0Ca4RNExrR=oT0@4le{ssjb(3Nl)8mgLr^Dg#c1V
zxqTo`+hmsc2bLw;VoQ}vVD)y4$;Z?BdP%h)QQJI$;OyR(wbiX}$=N%u&?K@GJ);RG
z$QZ$s*)6sK;pO5J8&@z%1v(${f2}<0mM*~@+XyC>(PXE(z#}hIjSUQQV}3H;(#w6?
zk`(ZXL#bhwn#?89?VU0G{fE8$4BLCrFy;iSNSFP?TR+yri6~|za1vXAKb`L4#0S4W
zUl(+`W=v^Ulso1X>h^kx7<tBGe}=5Ad!cQ-iL>@h<RQW~eye=_9cMlpN$+`fO5plJ
z$x%07F;zWTA@u^v_5rt8U{(iz@y!ic87bx8<Hx2qR)4Z6WuW4M0xP{!Hh6!*f28O%
z84haLEET~z#3KdPi7^ni{U4@32I@}FB64!y8?hM>+Br2yESzavA0V}F>~wu5swDtM
zL@SZuEo;jreWx|bKW)oYVGE0JLxJ|p_N#qeVTJpQO=8md^!5I$KI43+b>*Q|bqToW
z7Rnn0rgZzdCZ3nSaD3r{q=rxRAAV#XTm8mIbA>vm!nQxke={vvT5a24E*Wg#+8akk
zr2Rg6uHhJNR*&$oMWEa@>ljwlLmo=d%eF$BLliiTA*oogz&sSl9+dES;*V>utd#RE
zl3Y%5=Go)CTT>c9yWHQ#F038i$w}({VmSx4kdtr^9VUs~oGn0Ez7+0C#a$IScG9U7
z2?)e7Zu__DqLrL4E)sqi>Ya2FnA)<Xsw7aS$0z0X5Cn9>22o?fSj8yc_()b47K-*U
zp^wZTmQ30d*BkE<Zk~W;J-TFMGr!tUSV<B<so7geD*PqQ_)e-*ft$N=89H(0<wpq`
zVJGYYF%+^_mX~kzv1PJunWht!snHX^GcQXV0^ZmB>(Um&3R!9b4}<PN_3)`0CyYdf
z=$=;hmgs?>wbvp(!L7f8^FJ2QR~~s*Ij8*E-X2mA^b}@OMrH)&RlXpnq*m0l7<g!B
z*taiq4SZ%(;g{?DpuaJE#X}Cm8VG|$k<{=8Y2#r*#0(>b7JQMmfAz+TiIB=%KWs7@
z&z<I?NW~cw)9t{<qxqJ=o&Pn(xHd_pP+LCg3UpD9Du*?3{_+bzDDKWvF_|d`em)Hg
z*YTY~y{(gf)3y><mgRqv_!yF8h1dy$iu8rqmiZ|0nulQi4x|7m4W{dqDcwhzt4*d&
z%OBJDSY~FO-(xIyL9zA7VN!V5MVU(c&ayF%$YPkGUuO8ivcYCS_>D0Cf!z#|g`Pih
z1-JyWs+%eQD*#sM?Av&~{tp_3M~Ec9J7ySrqw&m*hy`B;ti-%lPxT-RB}$y{rpq=d
zzi*3om_2>}WPNv96+0Hm83lRg`JX6MmIdW5$0L%n-h0gNQ;3d+N*KA^-Q`I5lcP(f
zJnorRZf9j#=9a2cQm0@Y?^;L+bhudzH7M}>O_m7kvb14!wM@|nhA&}CK2ROHSJb~$
zce*1*A+GlYnlup!_p&z_taI$LCjrt=)7_D&ak&WthL(`=!VeE`5}4A%pn!8w%lXVh
zXQexVPxr%Q_=V4}q?*&;WhTvx?u9zjOS`AaAxe1-Q6MUB!nI`lvAd@SDG?5Wi_GhH
zM~H7NSAf!k%`#FUfQR`rnxQE-pNNme`!aRR{acajy-2)C*w8T-jmbd^pmNqKi7+KZ
z?v`tBwM(14@{*r6xhsV9u@!8MG3#yx&s9ufz%?02x>3^3>Lv#X8<nn^w$81%G<We-
zuHVm2K!B^_QYfG96Nk!f-NA3OS>=>y-IYW~?EXFEzlLS#Ww5ERVe?us$z55};8lLe
zwYAIS3u9ov{^9?TbQM5Rc3)o+kZx(|&ZWCSauF5~Nu|46U{SieySr16?(XjH?&f>m
z|2M-h!?J9!&%O7YUmd3;Cm}So!HAhH&tmpRyY|La+=P$r#EipJK>^yIIe9fxbIf<W
zHw~PWGE_LXO^>tmEZ~Q9;Y5NKkUy$|UD&Hu<i!^!Fm%j^7p1~+k8n_lv^XLWu>Na&
ziu2`X9RHd(?DxLcORPNprX*)qv?iJ09U7X`!%x(OM(S9<FDXnt)jOep6*mzK|Ipox
zfdl^N$?30UKg87dDZXXU@D2IPY0HTzjZv3d=EXi9qK+n=UUZS~avZx+;;}M&e4$34
zskD0FlrWiX9Rb6x@~yXnsDF-Hl(+;o&5I$C%IaxjT45yUB&H~lGX!ypB^U*qSejfx
zF<~aH?wZ<`YCW-wJs<WJI8xsyAqA`CA4{-a9P~=CpgXhWj)tmjp4?JD+KI;YOb^4P
zTN}uw4f%X#xoyyJEH)LlH>#AUJe&xAWLi{nEQ+F+;vvB@LUeFWqLbh6Y5WmJL*?L1
zphbue+4Jy1riZ<9_R}a)=)qT;S_wd)dZ)#4Us*Twb~18y(RIRDE1oeU9%o{V>uLl&
z`J>_kE@E>JIoo)NexKsQLfYWs*3dYTzGh-DPbq`-9~T!h!52)kx!OYJ*FJ&rIx|!A
zY-!_zo-D8ru`g8J$y+c=FJWC}Tj5m+HU{O2{QCLaHAH%8Q<1jU=K3a0%-KJv+PhmR
zEqIBCJb6SS`LwYQPd(LY;ny2>x$~mwULbezF+q6!Nh{&+w1r(YWG~^{*K^=O<CiB5
z1hrFv4l0&-jPv1#=Z=N;iQ~Obgm5mNl&gP7LpZTP8N|3KQOgjRmpWk{7i{pgltclX
zW4VyaKq+&|>iPGyDU|l)()!(ieN`Y#{VyRDumsY8ewOG+qi~g>8NbC2doqsY-4hdT
zu<GXkR@O35puy_$Y9|LuHs{7dqZ>oLXUfNmJs@sUnO<Hou6pCr;|Ajh8l#$*m?K(a
z=Cqk(vUC>qD$f=u@o3l2%0xmtzz#jTOi@(`2tK$B^NUeMNiZpve=fC)(<7`pxdSHh
zEZANaOFFFxs8JMZkPvloC;W0JW}elsA3}IPWbMZ~Gsio(Lao428Z~}!K-0oIf2X2u
z*sam|<5c_SLfN^!r<d0Tt8lPbwLDq<e)k-mBr+WYWrVuFNt@uA8ahcvZR2Jwm2h6e
zt<Sl!iZDj*XXn#0d19i4P2=x4e+i_|lLuY08NS!iv_yf5C*FKH8NFM>1e%^$+LWS9
zUZX+b&=yP|CK`gel=__adbldHI?tRm5Hl8hBvc*qzsY{|PW9g0E!`%GzO~uHP19fU
zkLj`gkaPLV%5WSib8DkyO@uz;I1+uWL8xh_uwp%iun97Ct&16>sKiYm1$a!aQjc7A
z=&ZsMRc_r?)eQ>e&8$GJFAe4^bndL_@&apO(U;t{PwQMO8b@ZJDNr1&FwNvoZvPzo
z<HxKi`%jf2LyQC*-0(V0%D-8-ILYm=&e{twQ7({nKaUwl?*v6|eKKaCRIov({2SFI
zWWI&9PO$suH7Igy`DjzIde`Z6XvzNi42or!H@Dk0i-yM!J`5j<`d^2s%JlKdAzqcw
zXt0bfE~*HF+%ebnn&wf3<SQpRuWI?bal{WOYqTRcHdZ!zhl`R*vEn}u9>KGp49IPd
z5j{kxa@GQl&LBDCpV*4}3EP}=bo?N}hOz#|Lmoc_yS81e{OQ1rlh!JrE4d1TI>K^2
zLI0U;H@}zf-!1z-_{#>0R$@C2#AaJIeV=UqB}vZw6{)_w=1^@SuREGwN{G}43AWri
zTZxI6T5v@_QF3@eDw`?K*v+*msANx1q};lCJAUETeP8xeg!zksnggf5rmb8oipew|
zps^>OMdJF_%-~e=TU3dYDSr8qimEr3(CHs&ku|JSIE(Sq)Q+v5f3}{U(1e&BOprgl
zj$AKN{5NrI+;rg(2m#D_Xk$=7Hp_`%qLho0VXlU6tea>ExwfMon*t$^jhKv}C+<6N
z5`vF%We8t2%b-?1*TuG4@PD>A$LRZXdbmUXaL)IybcSDfY6s>8hj2opOHqZ;FFpij
z`|>JIggtA>4mKMw4dE!K0^SIV>FAgHm8}AW#x&Z8Qz4_lRs`~M&JfA3vTFVmHb1PT
zKM1aDGTx{(uL=&uuWddI>gmT-6W4xsHW~NpZCm^m6TJakbM-#l5E;Q0<AEYJ1KcDR
zhSV``GhZRy^3Qz}Os_YyDZ`6Kj`CeoR`7Q1J+IurUfKEKe$bE(-fkEaZYK3!I#`X$
z+a+1c!|Mu5Ir&oHYfES8)z5}^C+{s#AbI;=$N{J7nM3)~x_HAtwYvT+%lY6llG;#~
zC7)~404S(&+2YdVXs>bdY<cOiCKO6+m$%kAi=r57V(Kr9*93mOAC$I4`}aJWq<%{0
zzj|-#)-2f7tYtXxuc26&95w(L?~w1berd0|a9J44Is5eab>d^iRqrVOzmDH)!WV)S
zqh%KkApxW#@C6EP{d8EHmUuexQQ6NLXQQ!W^bmx@@}bhbi^EH#7rIUDnt`>qoVC7j
zDpuxQ5`F#J<E~%U7WWd93Q-JxUsiv$ESzl-&^YM+5hG>`q^N%s(u9JF?t&&`Eml|x
z4r_+p;2i0T_|VpPJrYIk?<rST7V=G(Qj?3W!n&jj7b7wXQgL9kI83D_SZ-Z-=a%3v
z*LvHQU+~pyT(g`5r3wbURURx|ZrKW~Ki!uwekHwkfg@(v#%1MEv=>&>ASSve!<<i6
z9I@w9(RerC5VD208?koX7Lj1gr<>ezP)9Ii(0j?NoSZ>Lyk@oea4<;mRUKFMOZGxc
zXvrLCgzs?nV8Fu2;8Q;%Uk|e<qg&nCNd-O5i)#${Z6sy(2N!zHek-hYL}2sl=yCmA
zI#sp8#OeKfykeCpb|1Z2a+DF0Cl!wFlIi<k`vs}FOT;Wdr1amMpJF4tsbP@_>#>3f
zVx_XbiTUAXrhxYer{MVXhW?WkE*=B=36I%e>{#;uc1>owJRlU+T`%Dz6FkDC#3tyw
zo*&yuB!t<wFK#e9xFn(<$8Mvp^gH9rzIYeDU!n{-EysWX|HN<8X$B$_dKfX*+X<<F
zw9GJa&iZFuwHn(oj;FEV;j5#7(aLq)11a*AJ1<F&>xb1{Dcw|^O;<O6gS@1#R{qEO
z4FeB~J~e4V*-SfzjiWXs?%@VIgf-y-)J`bO6$+N{z{o2D5z$XwtYzujd5-|n=hr|;
z^c)g$cBSl|pi8V6orJftgq`Du5vyP^iPox3=g`DHWDyc@HqYSc30Jute~xn1diM|$
zZA7rP^0!@Jgn4ydqd<Qlm2U1KZbpR(Pi{(Moc`(3&LW}a1YS8_@tNnVnu*4BuqxBu
zABHH>*kzR&+5yelmopVmM%GWEry?t_!7U%iL+%2QjlSe-<}EB&hZ-HL9<TnLc_jd&
z%>G}9OMQczi%H6zi_5+*`3c#(b)OZT)~2Q}vAbmx@#Rz3p05J}HrPh=VyQ}XpJxY+
zjD;d<Gt?Ou{X62UQ{Hw@cnBmhp{cgb++A7reoaS;omGNU-CST|%C{9ZuCU@Q!T6$v
zM^l)a#zR7BWQT^Z7{@H-I;6jguWeC!$>%LMA@{Q4?A4eTC@~4U@t5z=4K!zXcgx!j
z<n$1%RQ2LmOZr8Sv+ViIn@RGf!3L=xKeKKhy?64FzD}FvTD=u(o&8GqlvYCI*L9(x
z#`Am!uAu)Tx?##?d{SVo89|L4s5M%H|4_fy^hz5>HFCedj2l<oHPKa*`ma)gxPVwl
zn-+W}cS|*5>f+ygbIJwGd8tM*S4+quoiIgn-I13**A59ua2}{$zIwTwfd@4CwMxbg
zB@#9m)to<iuhN?t#_4}p=6i3((m!Ds0d0CraVRK+fQr1{SU&>3!@s{p4;BV2W0{nq
zbp(Ml1iO_u#zX3Y0Vh-!OMZUXbL8bWtgj6dzQiN@DY*<?U&V=6#1pWjIR;`WWGLC=
zFiU*(2qE82g-H9V)pwT|X$u!v++Tl-G(KYDH8GF65PFO+c0>{aMii<iS~L+$=jZ=+
zy!sd6PgBNa-#6-dBvQ*q$s653Msld?Jf!<she?ZqUPe2xHHz=)*GF1VS1qhL6!ceZ
zPPT<3oj2-h4G?iqv9-o*!r;2}XPM6xtTr58Z1D={yEu18TEM`)fx3!UH+`cq2`;^S
z#ES-IuZx1HZr}*AdXXiOfCU6mxsA4xbEg|AIi;o0z>(nOO;g!vhm)k9-n~~?sf^%h
zRi~HAW~b7}dcCIWUbiEgoPh?+HB?~b4s16!`io7}(xu#bx;3mWaeLy>^UT7?>v8-V
zrXE<79N_NS|A3;=!;MDCCTfb{=!>86Mvh%kp!_$EM*GsHicIYTnM7uoe){zO3qNE(
zr@<)arjTehCkrt}p@(jA;DdT=nH`+8KMpR;70XgmFlj`v;9tg_mX*)`%Bdf}(AlD-
z73}UNUfB~Nf#sNV3QRSz-z48jOwnn4TSa1qqw86<Z4YpFx4e03%&>_r5bM+Et+_&u
zxl2xlM-nza2DWp5yUrR1htgO%K#1=@{YAK!--m9uYegp+`kRG%Y<Q$f>6}h;j+BmB
z2RI*^;u{hdn_lOUOdv9r;OfoM<vVv^tX{Nl#)<WK5KMN|jLe8L-?wz&(`AX+b9-RI
z(4R)N+p?H@bB%Glu7ny`*W&!mxD!lbpKYmHTi`qAih4^Za!X9UYd`XuR7%QTAbc16
zN@nO#0tPN~-4t>#_9ic7I5v<r6ftI{!mx;g#2s!hetNInIJ;e>B98!@P{B=yd)a1V
z<udMsIy9-VW(gSLm_`#Y^cN2WcS3qpm4N1e)VP#Ft)_jWlelSo+;=;YN8sVTYrTD-
z0=+^}&E{-U17jlOBW%U&*Qg?tylI(c47xaSKVmly`z80*mUEanQuCzH-d<hqx2YU2
zIQnkGAE%$>r;7Mk!t-mk<L=iy4^o~_8yg<ZSeu8ut}e!0p~fKqlnU1%Gf+#q_#hCd
z<JBGqO;Mo7ZNX}*bc{{jsb0fGjY&ja0jl@rvlCZ;*_qK7m>=m{dUZ;>Z_m9M|1l$P
z&nIo$JP|@61u3Ptj64sw`;bdjtMnVO^i#LisrDJv>8PhLsRu{5e~mp6F6EbFEX@-6
zI3jJ1v1`Jwf)&GM!nXILdwz=e=ZXd?Dl`07)*J0R;UlBArul=c>HJL<nTfP*-X@;*
zc53evn!vso!+da-;I^~wD}^1t@P<b#f3rb9YoBN{6>cl-E>U;b53f{1^A}Igwns>9
z?zdL!P2COKao-)~nSM!;<ZtCu=>2>98aT;3SsDQhBEld31<<O3zT;*nZwMl-futF<
z3Oon?6)Ls5os;TxiDMrki{H=jzoAc-eq^9l7DCa`%er>~)$%7_|DAmpldTc1w+rO8
z%2M^UNblteSFY8CB~x_KID5r2WPpi_EM%!~?bY6}nLyR0m0`(|jo>80C~)7eh7qS6
z`K6j>qihE~Wm$4NAWv_h=b`u=ZFJ@J*xT?$SlvK}FJqp=@KwvbR&z(Gaadjb8!fif
zJ60AZ`+VV$A~RD+He$zE+2_r;oln(K2^A0|tL-4uBmS_BNL_rTdP}+do;9x>MoQ8z
zek?oS7)1zzdHGO{!`1T$$JeN^TjhjBaOZBK7(N>UrLF)pweB)zVRsG9bM{FGdiLyI
zE8%4?qRAZl(0i$@-Ib{?1hraM0gx9DVD1=en{D9AmkiRkYYKOFPwlx}ZTp2~YX_^G
z9$f>`ngtVH6g$fg;21&AUrAqTA|Mz&h=8+prA1giL@nL(7hi+kVF0I=#32XVw}g^Z
zzB*qc#hnEDA58h`*Rk{skz?_@n_Xcu3XiA}v;KcyXC^RAd1}uR#ifg?+6Ml@obL8r
zYOQftAF1VhOw!VlBB?Dl-~8++n$UP}*TmnazB_k6ar<fZ<LA}}yQn!_bOVbouNb!o
zCL@mYY|?$v>ghWqaSh*0Z#E;-^fDrr{yFBXw>HFhK_8k+a)^cnq;yMJvk*HX>MJe*
z>Y#1Dxw}H6ph#1ZB$~pW;{mRr-&-r!n2*y32*YM(xm%pJa#;&VYSv_+9A)q1?BE#w
z%ACX@hh2`^)V$Qcl!{u!wuf{7&_h}JspM~O+6PmTkDZ))4&z3%b`ExUpuFzMYvniy
zH`4k*1@qFh^oB^zA=i69Wj|wX_8yX6OlUN~sfAmQhlu0+3@Z-gB1e$^<j(VrBD^8P
z&`oLVZzq>Bfo$|f-^DihU&GzFUZfsS&_xWa^prF<viFTxfG$q;cATx#hp~Rf=olty
z87x7e6c3la>#aauunpE1NL+wm=-r!c*oi@072iG}Z}-05ja{M|Iu$6~Jl&pg*Ru~(
zMYRiy$$850W3h1S$ruOK!LfgeHUwLGqK*lM6*2GXuOj>jH%X;X6OP2BQGYL+s4a!?
z0o>GmKq5z-xX9F0N`dkH@e+I#)!EB6mZ=KEKrO>U?gx(4CLblt9qfx{qyv@+Nxd`v
zAK*_ZRo-WwnhB_o2yYeVM?3A!vUyU0G#^LSkR_(9Q(!9{U+Q<P4YhkRp4jA&^4<D^
zV1wExYg39b`wZo(7LFzmKXAJXIR{7(OPEwCW$KGO4z!F>o`C-2q!J~0R$_YZHa&NP
z021gjF|x>4%p;EO2rD1VWCgE+OOGF5ZPC-J4op4L5J1m~%3DgO7M%!T#mdvc;*t!*
z8ba<R^k>pHs|%tQE!rP9y*1-}#Lxed^^-D>EEodp`n-xV(pj33Pb}8fb!IO9*S~}p
z=}hx9?SL8gjC0Agni7+oT~|z;^dJ;eodk58K%h0>OZs2EO)0ue0lU2RM1q<e8_OJ^
zzWc3ciRFx^;qT(vd4!0EPw@`$DURpC$qBJ5Pt2go<%ba?a*x=`c=)&wZU13k>Jr{-
zLWNd3@qI;phCT3#&o__@1IV!+fIkB+<MXK%r}FDX4>M~5b)Io22Z#|M_1Kar>NU^m
ze6aR`VqE}tNH1gFX3lKL>@OMoWhcXdZ(sQRMHN;m&pzw$1_-_~*@9WqX=@*HVDxaa
z_G|NecH?wg!Ib@cPIb#$t9>s!oM-J0K}@8V8mO%#PE#;~H3M!5@z#TIGC6`%e6I}Y
zILRwR)a);4sTEX!1z<66vda9^oIj<DgsyNwk)$xk?E1^V7Ql?XlaNalPof&4sYroH
z;OSS7j)>VrV?eVt3&;SOp((sD@NON#1Lz&dw+aM^w2y1=A9lK!+#1h}OW8Y_s7b6G
zv@bYcpOZTxt??l)+S~o^3<_80g$hN@3@(l*D<?H!lfDlBDFMAyNmqmoVF%P4HS$ki
z;hUH!tYu@FG*}G|<P8~eH$BpduR?fUbbx^^+)if|VBI4>5pp>mf^O360gCumndrI+
z!#~~+6#3tzWBit8a|YNQR&By{We;FQs1#lBCC@NTtbE5WhE2}5YEU-O&xcJWeC2tb
z*@Cst|1LS_3pOqvFc!vczO3j7TOVK8u<EYMP*>z?Gpe5t_swN*##9O&+ht9qE=#l_
z5MM93SA+_|i}1xvw9{%0=|I&<Mq8o36q>2es@EdAz8_pE=Ih^j^X&VYnEBc$H~h#o
zCGO&w74C3|(8s8t^pjm^p25?JDvC|ph}iGm!|y#ZWDuwC$(n4F7~l=gn|T)rQDWNN
zdP-X%DNtkq38;u7Aao`w^7JDMf0+XYop8#!9j%n0_+yUD{;p`Y5B*ivzGxoS@+BiA
z;coxhLry9sZihiHQLre9M<xB;|7!KG_`ru$LiAim`Sl8Fk#c6EyNk~1)eeAQYi@@_
zu8%qHiF}%)AAUmbmbENV{ylf(q2p6w0?LhGGeE7)uh&lW50IgDmRyy1%rE9Wy|Wr?
z04~XnX-??TyhHQU@}}j#j{mq}*R0lVpoVw`w_TYOJ3LE|LF3*oUq~H_<~B)N-uO%W
zkV<-*g|zVqlLn<q#IWqDmU1l@fg0s`cfy3U(Ig8JT;hYaCxH5TA#DR-coV*v<^uO-
z!)NJUPwUOCQ5BOMb#Ce9%*PGgd(kaFWs2E_%}?x_AzMfC0f<vLB0;ji%)b_^*{2oR
zO0j4o95C`2Xy11u_woFsh1r{G*VT#U4$EpcJsC=P<x>VM9;hEcRlAhyNG3!VpV($i
zbw?6<z09lZQ)b;-x}&R175!sr8ZTETdGr*vJcYOj5wB!o!^6so12HKVc{Kp7@<W@?
zJA>+8Hq~8XP<aR2n->hA+Y*U+f1AWcoDY2815%G{`9Cnwrhj7m#iu&N)R7rhJg#=u
zK?%kQl}<0^TeD=ct`$`yqm^%TBK0X4`@?R4v2n$?=I#f%UrI>G>JO<HI9QjrRXY92
z(!SO8J7oqjgb=zBQXEbV{09#2c1a|3m6W!TA&?gcA*hDN-A6<cAxM-~p**YKURlYA
zj4IhNs#EM|CL$g^(4d5z)}{d``(XXZKoY;xU6aTblqs|rWe*uHc=z=a5ILc%slDyk
zG76M2ofA%$5^Y6~_p)1>Z9@TNI?;U!u}#=|sh4RP>3ISO`%jp5(GXi^=!Ty`tRPVz
z`+W{+^Vfn5WL%;!mJcGE_i|}d0lTg@MG|zGD_0K*K!6&RilIht&j?L^mYr)>@1jSX
zx535j19*~2BF6iath>q)dfG@i{4HcS_R_++WMb=|O&V<|Rx~HIEC(91s@uUf(vEjm
zdj#6@sCow9aMjM^=Lnt=oVUZ92>g5U_@b$Uk3d2~N1aSfD4>YiQU7X?!tZtOb0-@e
z%c+9mlh|nf=ZEVBew?>YxvX$&Q<rg0U)~6fKMeqk3Lv;W?!$cjoL;c-dGZ+T;r@{2
zv2e3Q0D-sp`__=jY+;;sC*6j-O?m+j3V}Z$&}Y}WxIg3wD8eDu7I+(ZSieMDdsyJx
zEs=86nLK@%mSf>CiogqJ1;?jcuA6omcD(SHw}xiLMWTy&E9F|EyrQVY)2Gl{Ka_|f
zg%!VW!d+p+mqr!`QW4qKy-A~Np_<=b@w9C9Z)iY|);tNu>VVh`0J>8*DICM;XO~Jg
zgw-4VNNNQ{P(K_p_KnvHcDO;yea!$NaclcVoi9kPzZyknj_wz?S^Q2t-kn(l0K#vz
z#|YR1+z?{VEGiIFtzebTEAQs{M5z8`HC@PVJ4>&`zfQg%17Wj@U#0+bQ%hYWVL$sn
zj(m3Z_biU@A`9Q|BcFTxJQzQcV8M8N{{de1I*8`h7Xt?+giq_D^B8Mnd{4Y!0Qdu@
zqN*cwYdM$l1vEgk$*Yq_J;2U#rzxp1Xbt+=!5j)J^&gu~!*=w-4Up(uOVnx^icV5I
zNb|Q(sb`!r)i_|8Y|bo9lmp+74MBS(2Hpfqo~5u-Vy98FC?5QJGJwTp%XC_ixaJ7`
z@3@t6)v<EF_$vt*A$bEsn&aHj$9Nsv2r)i?3h~Jj{Ub56nlcjMYos*}1f;+nAQYU>
zg>@~Siy>*|jpO!iiYzDyxLm*!PJpXQEEyw@exMMQPlW+5Z3{spsBzMQBjs0&vqyhh
z#8&XEoxG6<(tql(RVmC|M0Iy7Tx2QjmE2GFC^3N`Spcf=pPondzs`>2m9LC-{^>UD
z>Mu0P&JEx4@siFH1WRT&jNL!q9l;tsPCL*fc|bywIYc;TbRPOrY*uXv9AOtR@(7$L
zR{m5+IjY_`r#E*9L6Xu)?rVq9s;EIzG-CFcV4Mk~Ak~}qe^k-7P*nf;V`#GQhkNT;
z3j^*nlR><XDpMe?uuC1y=+9m4Y$(N}9Z)ZE1Y_+4f}b~tHwwfYt+aLG8D)AA$10Dg
zp3~j3!K9MfD`r~(Y)O!Ny-?Dg(zE&jRRVB~_Nw^=0jw$#+R?wyglX^74XVG7F_up<
z8Q_0O{Z}7gM8F&0kyl3JpRbn!Uv32?QSQy%jXTNKtxxWwfE)+v($MP7Kq~eZU5U<X
zdxOr58Ti=VWWjb!J~u09{^cun0%AC8H;Hi&;Q0<7$T_GZZqm3{^!gV){D4@ReUyjC
zD`_^TuvZY39AuKyphAdjg#DKPgQZGe4S4b8ciESOtGV06GTcZ=<<cp~lx-0%F}zr}
zV#(OUjZm=^Uf=YB*&Xm?VJ&F+<(R#Q>h+q9E#VLppJwrsMQb9JIT~@j5}xfAWUas)
zC0nLnT^K{-^t`*R>BA8MMZtknER8V^{*ZzFH6#_r97JUBeC{CafWKjGCOdnyEJAXg
z8pgKpg)BFjimdRdl9@0Ytz~W{$WU+kTj|FB71aWUbPDC@Z3Yl_qmX(ds}{Qy^$x&i
zoZJvN*|8>vX-9uuXNM$e5{N9o+6y3QmH0$v!iIB)l+D=Qe1d$!Fwq%x(tJ{Uhl|YJ
z(>Zc?2Lu6LF;y#oJ5`<Ue)%eQE?Xilv6ly6BGM%gS2I-@$3hhP;8fBP{{NgOOU8JP
zi^FDeH)6S4YMz?kyg9LWZZKKfjC=S5HM`lST(DlKwR7@$+m>J32Jo=go0*8lNt-J%
zivU$4Rpx-ElZz!<-F3;l(K%c+paDtlIL~rKid6_{bG|o2$-*=t5SedM;6W?;j@DM~
z99&>=^^Q0B&k5mkMaC2V5;Vih?m}qP`4(7~mp)}QNf1+U2q$xJ{s7SUITS<oh8#+!
zPu%5apK<|WU&srDboX1q2vC!4>WsyR{xppSc;mKe`=ij)y@+KvX}fIpuBt(lvhf0A
zf$NySk{52EcQ66{>>~w*Qhr0C*6wPbbPP|hP_;_9fqq2&Q$R$_ItMI(y+h>ZpIb=o
zuV}!lrb3dDW@gs%5tfYydOugI0}Qd`&|+l+Al`lw%#bfsq(rC=3!Ps!8ojv}FwxC5
z=aV$+1YmDx{BblGer3@SJ3vnNX(@}4pO{6BMy(?m!!0s;XB8)(!+HV=9ON-G{9@6z
zRZE*byJ&!tZdxb8d0z#j0N7zH5?xSKl();a&p7Kz`g5*3FnJ%9iC++m_KqBVNH_ZM
z%szVkF-gs}d|Q^OjmeqK-LB`lACP*!#{y=SaVe@ewTcbBsdO6pP+6>2<_T~FicrXL
zgKGKYZW&{T6HHOweCbxG)zaKgQBs8&fF5c<xqU`A<t{~l>PKY!-idKUnQ;U#=+E9N
z-p1<zN1#kNB@FHD_@B+yp-O=3!!==xUccqS*4az1`u%FkUSs8ip;7tppe5YzRZ#BA
z)xk&13PI06n`YNkuh%`PPF_8|{J<h$t{Mw`nnudr+KZpb!u(O?!u}<z*FAX?i-uO=
z<!c^uJ&-51w2k*eaP(q_|KEx5nfCm4+Y67#7La8lSZ+l8H%)G$rC{qD5)d!0p3dLx
zlC3TJvYVi25A}@jy4s2uh}F+Oz7%M?_(XP>?Y@;`!TImQ>is&ysEm?t^QRdQCv>Z>
zK%+F_Z|%%~3;1~hU3gu-;2Q?Toy30+b3Pme$70FN>tYqL_7-yY-$r7~<fDgwbvP9O
z)FNE<DMG-n@6X<jtzKt&eq`znFf(|Aj0;w_x({no`8YF>6LW$@=-XUf+(cHlA!l#W
zv2{T;!eZ4D(Qvs8>!uG4h2IO3s&q3kn@7suD7_scc!@A*P_cF>*?2Wx1QIn7!Sj~a
zZ#W_gUl4qFkD?06)sD;tcM-oKw>f(~#UI<2z0o>uA^Q%HybEs?T@dVuzGG%88zj>x
z*mw(VSvRTeY{0~qH2e5Yg7I>BSfqU%Y1<(D2zxI$G!%!PIrnc{@f1;oPuvdSPIZW$
z>C@<nqDpFkpqT<(54}q3PY)w#SkuV_f<J(Q>jy6ReCsYeaav_Q2bi97KnxAVx*8sa
zVO%|#!TL0`;o3O5CUj-=E<Dbh>2J@|Di1kqa%`z9H77Y;67C6zOiqP8ZX>jlUQx}s
zXo<u>*27|l7XaQB0RraM`bK78!gqUaR`F_QK}|DjtcC;m34Q_aHu|kQa(z99S{uKY
z=Al{oXU7-Y$%V2@cMdR$d@5-<m}msum`RZSsCxr5{wu{lO=(X`$qls}2;{tw;@v+4
zO`{i+DDt|962wdo0BV`imyw6LO%ekvtOn+qZ-qb22)*7GDpuxDnlRj`mxpSG?w-@f
zK5SXsei_RF<{*ZNM@I!@5*CRXe4G+A-P^VJ5w05}4uEgCEfk~;cL-ClVPXjcOIgMO
zK(w{?c8s_}bpHz#jRIDEfG2z2If_s64glhv%B;5-*0GiF7YdsG#P4%+MN(j(RSxEr
ze<*D1YgYfcz&H^>N!SrNqK8g>SxGtun#eP3RMMX#1q2@DHv-pN7}7kK@dp!bjdK?k
z0@r|kJcgnFtB*pDAwxFNbEE<)rg&cjYn0(<q+N%7N>)mpcp1YW&LfV%Rf!_lC0=h9
z#>7RzCME+@j_Xd+9Mxb^EGl(b^g?G|1c`65Mj0TD0@7A+@(tqDi1PekEWL^_GeFl9
z+&fCgE&Pc6Rr!Z>;uvkg`sQ++NyTJc8s!;bte$Qjx7;XGR?GzB+{cC0&a6b%1|Rf8
zD+@BrsBJ}Afg3AsYgI6UzV>hUTa9!Fn?`yW=v?BlE7HCrYdsN&>8nDqR3WY7Hp#qn
zUI)otnhOuLgE$9sZa1CBGMdjaPh4kPkU<bR;-&U+E=TaDCVV~{5=0)d=$X+lW);ft
zmkMw84q+2kl?4<&!4>9h065I!vs4(H5XkqhJ%I*bjtXwB6Uc^@$ob|7ocxMw1uIuT
z^-%UL;f}=`6Bx=UlFNZW*M#d2^+e$&Nx{_#i8e7Xjo{8auc4@b9}TQ|-?A^r^~9%b
z5CyWD2xF<-d&AL6>6zG7HuN=%0gUTzcU-xkpedGruMvooH0iCrIPiAdWP|*<-KBrq
z64lX*e><NG``i;M0~4Z27Ik2om$92VKnsSEr7G;<dJC){F!GomFFrjRB9j}gZd#^E
z#-OF0OQ2{NHl8z!W+FP&mR-0igVM=~CDly>NFkhPTL<!Y9;?<ZxP#QRUw;W_!d!&7
zo+u>Q)Bf+E{sC%jvJI?YA#N%#GD(B+x*0$C$D&@NV_rWLG?@0{a0+-Lc2_8_tfTM_
zUEajrW(VzB>+GMyhk!+K6fm}YC7fD1Y+r5vPsW9E6TaiTuBYp+`IJbR!6rpev)Haw
zuxl<MTtQcTo4Kli=9dIi@NM;C&qix4?8*7B>W*#EV9AvQdaX?aa$_VNZRh&;b!>5r
zT(&N%bObMe%7ICdjIpO8US*<?qo;}U`!r;n_kDNkn~yHeWDpF%5$B%%#lL*y?mPRm
zz3Kx56&;}?Ou^E_aajbiZ~@ltVjN>>gS^O)p%-34w>^aG320aZ;|LCEy|ZkbKCpN~
zBs4c7Kev4qM1t~ZBuOPiOXM*ey`YW!jQGY2+f60=Yk86RtV*{Wb9)J4(luKDrBInF
z*Iaby4NbN_00%7zDYCP3R-LVm?;WRxcmj27Fuo+|2CaJGWeD$MR#fKqo@t6~#{jw&
zO2s>jPSH#N<F^~h6qOG23E=hrMmqv8d4O9)sDPE72a4>JK=7O#jmyyZ9Qp8u%Wn|$
zV7-(CXu{G47%SZ!w|?)dB(L9d;`?Ksw2nEKNSB;V9izSnamu!6<0JmYO{Ot(4tVZa
z!o&Ax%P(j9!3?42{oP)LqCF&u&=GfnD{vz0Dbmet!8A9dy=2C5owJNRJ|LB%-9Hs5
zP2z{Nk4~A*n+0(Mp`yOWA;t#FJwkyK)@3=|VC|oDX)F-0PV=Of{Mfw*l7ncrkgs`O
z2?9CRN&F+H7&<Y-YRJo(wEFv4HnkBDB)Rgickns0M&O}0Vcd5i<zeM!jkdffAd0XP
z;|wyn?`uPh^Gp&2y0?{~M|W1_k}Qh+xKei$-(Nj+l?<uOWkgyBH818g&Y|g4M3q9%
z!YAh+v^^2ke~3o`*S-G*ywj8X-$$4rLabc(T)jY((x{?9;NUZPNHi=u2j_xh)Vfd4
z`w9(XKvv{_P<1g(9B9)JXrcRSy~aiBNa_>AyQQu+LmpQjz3L#E&%k-eR3<mT+q-kx
z);?>Z!Th}VM?4+!fS-%^!?^Da^Xk+BC-ft!K!W_oB@Ljkp<@3G2dEm21}OpVb$r!)
zH3Lwa3NR~3<Qy;ljSngZn{eJ4EHGY*xE)dl`v(;rcv#%b=W^ZSB}7CQhjOY=F;J=z
z#OG5El-w|ZrLn#1^gqdxWJiWeY6tzCU}W2J6;w+}QFX%wBdeG{pTvymg-!PSNc%yq
zW<Kd(s`MN%*6IyGl9;+g5`+Drr7eMtB@yHL>-FdD88M$kF-{WXd2vJKdk)fU#t-3P
z#w*4cIrZNfeL4Dz&pru*rsCQ1vJ;h}+s^L+%?0M#I2v7lNdOo5{f-1JD3@C<eN}`>
zf4EW62VLu5MlnxpcV{F#<IWpgq<xFID9|6;Qw<_IGI=I-)xCY#(wq{kq!zhrV#-2H
zpsagytbXo}g2-@gkb`(tU)DllJ6_lf;YJ+!zCDeJnl`F$@(#+#*rQ928^KAGY$c6l
z4l#(!psBxMb80jf0DBSp&M45V0tBqbV9-@Wx?G1|qweOoc-YpEQ|pbrH5&y+jJfD<
z-jT!-+=nt7L6M~M;<)9MUR0#Osn`U?vhz9<G+<bdnduzk39L*9_>VFV1?=!Q<YOoJ
z(lbZiR&8l|sTu()MU}%(=n@Go%cEW9FG4_JmTjV3;VS6l`iCQ6_u*9l@8H_=c^{bZ
zClb0~b`umWC~B;IqQUBJnoJd};+!n>Oh-P1BXB~Z7p+u*^Sv;x5**frtk&vb9HyQ=
z2uH<N{Dp~k&QGGFWA8M?U$igQsCZW8_`aeBuQ>=p(B$}?{+a!@P)js(Yacmw7(4as
znMGVCcCfM*Nq&_lvXe>$vmNz}0Ng}wCtcPHtqvm(!M_~U0V7F8TE-Yl$n{R7#Pb*i
zMceuE9&ONS#g1$(M{LN%)-^6ZQAS(-E~tPs{OF!EKHVw>1OHFO{}p1Vf9#|dpfiR*
zvJwq_ety=#(TobZ!_romSG>`+9Q`CGWiZyS&l&my9o1p1u?LlqV5$)s@k|O*kK`tQ
z446C|vDnO?(SI4=>C7p~MH#s<a#GkV9iV*p1(m5=|9S9h)f=Y(R#_p3r@cmjxT~G}
z>h4il&@B^G>tQQ$`-Sjq?A}H!HIv=1{72jACTE&p>2?D6wUu)yLVoU2<F$(XY3p~<
z!7%@vSMlJiQ`d1dH~*R3$<nIeZYBa8fFR^{6CnQLfw~-x-r(MM3X@9#{BQl7^>PE7
z+ESACSDx}V!$q91<}!^?T^`AF$&=F<ENdB5X&!5>vBY4fGmc$Uul`Zn^P+m(UD-h_
z`8Icq$oB48b+mg6l4$)QpVxGQm8>*+5f}dC@rmt~5}aJngpKRps_Px1*QeE`e1HzJ
z7Z6LXWZP#~$Oh!)Bn;^W5ay;>ZDgI8>wt#~Ge{^T;!`jV*Q4htsstyP%nv{bkiup2
z)&UERY;rb^Z%(}qSguxPQ<@FxdUr*G;dW@3YHyY^u&ev=J*T^bH)x}O6Xky}#7wrp
z1@|*msMo(|kTH-j{&Jqry+<TF8LEd-)w)Czj9q?O3v?t#<=$Cl_j<!X6qLCm{XC7j
zvnKEp0AMZzCwv`jd^o$je?DsJt{DlE8jR__Imbx)n3lOW<1^VgX-tRDxIfv_N}RLf
zo34H)k3IIiV`49oXa2U(Q+#^b6vA>R1$elPh52X)WNaQidRGGssxJL`BEP=wEU7Ou
zq3l^rgP$D($X2>yjkFC2RN^OgY6ooxV*~ytP}m`ntzoiZZq8dQ#gi;;_&1y&s6Exq
zan{1To!*ePo9&bDRZkHq5<0(dc)mrNy4S->s&``hdCBd*?@1#I$MNMi@4)4^EM>Sw
z2s0iwPUXU3G`-YB)j%~0JuC-x0`CZLveid@bcD6*)WYL--MhrCNYymRf~@y@gsq(Z
zZc)q#NdX@kMMPVu*edAf{jHztWk)5R`kB8UT@-o>q6)^2W};M4sstMcvj82aUaAr^
zziWMv0ih$j*s8adZO~LKFL;2xhb++a#*-mE%z!|(nRQn5kc|8Sy7pEmIa`&n1vPak
zqG_JHSw_eE2Oh1zqd6!BnD3-Z4WJ5NHM5*}^j4!A{f2}?9Fi2>H<QLK^5XjW-5j^u
z>pfP$ZVA&c4)6)qOl-8h#$<%{CVB5PvX2pK{MVxPwvS2i{B9VvI`7D{istO$M#VLj
zD;<tMTg+#KP5qwKGtQ;!^~Ub?I8`HQ2gvgToecl9T_BI?r@)7uuD73f0C5kg!kl+O
zV?&bwD#LldKe$wS=IplB1q{ECoU4<a*-hk?JwTOsJ^x6Wi757O@2YMu{9OKraF210
zL=8_a56VMLM*7avnRf2Vjoa=%Oxxw58SonJ^(4!-fo|HW^=*`ztb*9{u^)yt{kySK
z>t#^Ho*k76qTQ^)th-<E3uk(3txcY1K1H-;zxl=7MW_+66?E;!&&+@dCLe(_b`YOt
zX@9a~)_7uDY^rGv6T#9mo$hGjzwV=DU@dyWg6oKY*fX4HP@rF?U)5Xugi-tSv0^Hs
zBDy#-+R58(&*IK8{J#}>_TSF-m3S*SpG<N72;CNpEk8#$|4lb5-iXTV^(zkoFtAl+
z>V9EnS@cn+MQ+5&4(vlU5;(bh#Khw?>NV`2WB89u78tQZFy=|dMuuVlBeI*8q0`Iw
zory`UXa+gaUokb;(CkaH@wK~K<ZmOQzvX^<=2Uk4#i1}$<4Q=sgfgfUWutMHxY-mw
z&vD33g))td{TGj;!@mDfQdthC7ZCX9cJx-GGA#i?GaB)jef05GK!|utd4$mszJK^u
zvZ0yoL?RWvT`K#2Kx_$1xB=7}dwi2~XXJ_qft+rhhG>MPDPQ>}e1h<vv+2X5m@jEh
z?V~Uw0G+3g^qkN@W5?>f9=ZuXjnRzYC`a$A1t9o~4Ue%{V$jly#a1qyf*FWdExCfC
zeOpN<(8ZrY8+8R}*wplA+KahA_r4sd-}1Z0cUTTcAOO^qM{U*6!~<c#Zn1}>72ec%
z<s1sjNv)~lRV0SzbiJcfLs*f8$HVqw_u4)b-^&HStpRiVY^F5h^?@{I8XcJewl^ou
zX!Ss~frx~JoMX{OxVH<jPJuZe4r)m93Hu%{pfb>!Iy+jt&z+knu=`9>8}_tvOS>`$
z0{;iR`>>?=oZ{6BOVCSk;7^87)&~e_>WPY=EnESfDY?j9;l!fBz$r)juw;lt43_*9
z9RYW_9_Yw57M#+w#dd~kEw}b62zpJ|IjuAEmtb+ya_ow<Cf@!drST;?EJAtxkS1LZ
z!fqAcg2lD8A(<y!JiGD+CA&kseXMnh7M^;+cP~!2;4y`l0E8Ki*}wI$z~UJ|7fAZh
zAFp6>9Wk<@AD4Vm{jF5t`KJgvAb$-L?qXcw_PGyH%cApb=j3d?9M<y&kz$LJaI&k|
zn>l`L_O$j<v2XxVl^`t&@kYSzobh^19Hz-~ng(Q&T9=F^jFmzdn^fgl%#y374lfeU
zbT_9Li3?_TzY~W^li@KZ92!B7Qdlbmwfv({Wm=9ehAPr26xpkp8jy?Pw9Tm_?pUpX
zwi<nT^e2`1Dk4~}_4Qeq6AZb$%-u5yXHv3fRxBI2Jo7w)3uhV0lpT1xPiXVa+R<aQ
zpEd$Up8F*o&8)-q>07l94i%^u;;snVHGMP8KdzoS-AIJDxcZdN*VMnM5Jaa~6rZY$
z+~ALaD{{B2>`g}#dgW|BG+u=JxtQmEJxx1h=j`>dglXmu{q-q3@=dqfkl{;~DXa}3
zjnI>^nVyJdKWp{R8OuWE!8?*!AbjO(vK`M0fzU(nncUW>DBniq^rCXDSe)MAl7eN`
ze$&gl_OjP=`-oD?xm%*P^^xfo;OUT2OJbwJhz$sS=@1OfnUM|q?F|k5a*lhlPpK41
zm*EXX82jEcu{WSqe~C00?Uu@Wbfx^%){Q~p&r}7u=MD~~JE`1iQxs|S%^RuYcm`T?
zn0NKxOlI8(Byi7U&;Rq>bo_5Sp)!ld>}LD-@;;qlD-k~3DB3s}Bun6rDV92Z=_wcQ
zXF=%kw=Seyb}&55B)Ks&aVO4FjQA@IZ#0tu#+O=8QW3>-g_z`{RR@@(Fe=$WTMYZ#
zE^sjioMm6Gs`I#07@Yzz2L}{-P#-|n?xX-rM>xRp!rx*3$4)9^T$DXUh$Rge4>$iJ
zhFfg@h1ZLW?52lc8#ci@KCZl5ivaLDo>rE5V6usxDKH_zD3}u*l;gVr%AFzpDF9!e
z_7+1$uN(^^-aXoP^0e%0w-a_78qT2rbFf(R*eUqzBw?xF@$W;hdJ)}M-Y3*+nL>bJ
zU@X>Lb|Zp4=f}Myucqyf&r#Idg~41zbxK5<tDTO}60x3|D9Gg9l?BSrl9?P*UsLhw
zmD8#@qRZzfDQ~)sXJg=T+2Q)OC!K-)*X-86bei#<_M$nYmU)*!%30t86D1GTnyDjj
z4ohVfx}t^DQ2@Id1Sy@bIgqAD2d>91r4AAd8e$~rV%mW;^wh8IS-MArK@*HYhVJtw
ziQU(mksxq?Y_i}wA*5^4(Gpx>xuD9N;%!#7{i$dP?i-TPCQ}}8lfp-^oFh4i%kxLd
zpMOzdH1NHfyJEaeY-TP{9B)7sHvSdsnN!%7PeRU;`Ku)~GT`OHxmQf2Xiy2MTKUn*
zpF%BIk9Y#@gR}n!&5aJTUMS&I7)<h?2$r)J?@LAA<nS^g^s+(wP{PkY@^S2v)j!c{
z^wx<1Zozf!f)2p##c|%aY{e!+@o2}=30Q6uX&TRV3iFmDvF1QYL=PGy3~EUZ$ixia
zz6@M*=f{U|8&nLAiCe13VTQHFK$C4-r+#{lZ<q+ASU!0=zX-d(0`EF-((qa+R@D+P
zSAq6$cvVu278sSQErb32OcK8*b0gki=8#c<SKZggy7=o^CryfDDMsxh=3XG7aO;P=
z-9MZxE8a(D0of~J#1kRnfONQK_3Rw#kYFW}F>e;|eqdh{#PvabD$z;%Q1K7nT#gpH
z26HTZB2BpQPjg@jL{76c?UPrRNm6(zY5ALg!5C>J*KrjdiY(e+brZRXFp0&ih%%AX
zK3qPex?l6STn*V4gtY2+=)Wy){VlnhN=MX-5`@B;=dQ|q#o9?<)<1Yhy=$C11@H=u
zl!|Iq)+!~&C}RTu@(Ch;*ZK}f%kU&>l3RS10RjIHx5wSzt<fe|&lg74QuI<KJc2(3
zqF2efBlNR*8&6scdh00*&_}?d2SG&Po=o=P4-b10pZ}I$I9qa{E4e-PZ_410$kw3n
z5q3=v`2`jJVr-&0D=KCe@!I(ZRJUYm!bwP&`>+QrVoj(r?4PhqB#?IXIQ4vnl^7~`
ziM!RmoZ(U}yrV}kzjcs_`r0d_m#I|Sg)US5KIpPY^Xmq|5Pmf;7TZV1&WMW`D{n`1
zsbC!7qIue%?BT+#swE)i3Na}i4;#b&;-1+)YfPUkT~(){P{z)O`{zpsucSz8XZjm_
zKGT+I4b!LAAPBwPEUk>o`IHWmhEbv=y8`!nI(!S&(t>ec4kxj6_8n~Y{|xL=*PVg7
z_<*bRETc_f3H?6f?YTr!cJSA~uA_uG#7$qkZ+LbnK2$0woA~l(_{sjnLXM`8N#e)n
z<3k#_A!0Qlw1v|fv+ID;*+Klv4$_`#)hH_ZSF-Hya%?E5<Z!a7)s3s$n~k5#b*;~*
z9U3#{1BgB=inJ(L<+l@6{K)*qYP&g2p+&^}Yvng%!fm0dw%n%#WRnJZ9IJHC3lOPS
zrC80xUY>e5hBW=j?C+Zra5R;XS)*L^vB-EtPArg|{)cx|%c4SOwTsiK_2r0l9bJO|
zgj~e^g`$at?_nCk(gYO_ro5%bGtAUwIX^t;>MrU;r}S4IR{S>x)H)n~+QjJ<z`Qmb
zU=snhF;&5of;rstW5J(!-y92Zh#Atm4lVtl7*z|$_P>nc>lzu#RwK>HGsxF0oy~4N
zjgb`79lwvhJOIVNT5wJX2XS)A<Y#}*UlOxKI<3yTpgR54MN2|LpsOGItYL^D`MlmW
zbnFyx?Sn!7(<pyfzAqkAR3y;e;7V?z{x<sszZ)~`XM2V=-;jHlm9XW>B#M7`&R~Jv
zx=itOcg;ob$6Y%4pc+8`Bi0_iMk>_JCTm0TG4gLyN03~a!H(dkr-V60Nd58C>uaq<
zh6|zAb4<kAZdjVdN0vK*uWg-co`*)Y(yq$+au@&U``+%JMEGoz)OXb%%CN@(8iqpc
zsbg_MCC}7PxNLmSyaLR4y@2mXtCpMa%METE5Jr4?U&R02^o5qRt>?}5wMEwZx@-L`
z^#SXx;~>En^}`8yh>Ad$F!1Ho>K25YMuYc{nHzqkS>NjVbCay;XPtsbuRRr~D=r3)
zju~BnudmDfLL;2?8ji?-0lc-vIn~4j*X@^adH`j^s)%y@<;o3mbK}1Oms!^Tkk@Em
zUU}NJJ_Vzgv(0UHUYU84YreVFEkGx@4}rM$Z7)2+uudo3yM(9f^*XcdIN4b+Ij_j#
zc+GoE2v6}imtO$f@7tWa2u+I=FShtOsn-GCL!1O{Rozk7CDo9rzXbGcGvL|MB&~r+
zi$^UjpR($-*WEg@*VjxzB>eB>5t-lmSh;TdtP_A;^Lz`xcpipX(-z`J^!bGoO6xTH
zQ3s%hZY#$gGbIGB8yAm&mkfv`96Nt<UO3n`UF}x(c|E^)B|SX|<+?k~*xyU9J%Wut
zpJfHb-VNEegi4<GRd@xGcE<{akjY_)pD#K{^ESl>d`Z<zG4O2YB7NJJU{dL;L-7|=
z=%~A|t4P-~s=rja-2*6z@B!AgU&*bc0Pw9Nc>YosJ*2Q;q?hmOma&4aBK#SLUZ9H<
z%gD<7wq|&qRS9&t7vOx&w$vp;tB_L5p22xFpxPPw0u!=2$7U$ZvO)}v&~=Q`^#E!Z
zkP)IvJZPArpu~&S#_bDOkdPdYn7M55;P4ETte<!sBPxM}4aWc7J-f%N{dknay&HwT
z)jy<+&C_s;%o!g03ZEpWOtr1@151aOOq54QH~nc$i6IHLO~<PuoaQ7&h@b#yZ$<yV
z<3ifMC)W|lJo;Gs@;jVV(Reb3scZ7e+^=a5QmLSz(>2X$*_C-bpZM$b1C_MZC?rsp
zf7ROS_q*L-5~s1e?RiSflh==(O<8&x@W3|#_?~E=a<c~?)#NNQtUk6PRl!`GTswaN
zAwbb`6p#p}CYqW)xPy6Y`Ms#{$9^VH)jp^b_Pu2}j~VwP%H#W{tc@qkkuT_dBU;&v
z9DdEkwi$ms;^_(9Jyr8T3Smq`TBTRt_L}p0YaNOEay73inYR9nb`^xt^b}Hm$D(#?
z4>H(k^_NXXx6Q=>6en5I!*R$DOs%9?)bwWYS+YS?6`TtP*8l($yf;qZuf1S4L2^HD
z3`J%M)6DIn@+zF<3d*wB*Mz1KBzI3<y;Py5MO#emqh91Bo`N!ernuJ2PE-ZP#IB6K
zqlYt^8~vcEq`hD@b^MfT=5Imp5$(PYJ->zS=N#!d5OfnJ7LjpU>d-i6+_Gkr*nMYY
zT8_V96hZP_(RQ;N(7#$JZo`Dqt??+TE}xI1mpqB)>HOUBXUJ2N+1ZD;X$xB0^&12p
zINeGW*HybzGzj?u%Kf~{T;9TK=rV5-Daq+gUe;bfDh-qv*?`L(9coJoSdaV%x;{m~
z+g*=qmU6^Rpm;21jm=h$^;pLMPLF?KR`vcu02R5I_4OAiNfeK6PNs~sO-t1Ps|tY+
z@20dC?h0Kl0g79Ft7r#^)U5|k+s1|@#KNo5Ey>{o9uQ~2+d0l{eO4zjp~HgPkm&}v
zR>gl}`8WW91Gu9WlKg_k_00$$-=B=5hp;}H5E{|@@EW`Dk~K;V<B0-|U>J--pM()W
zbh;H(^~C9>@Ho%%t(gJZS8S65oi^#l%w%vlj|{fItZxQYb4$Yj8JeA=Pn>vCSDtw~
z<SjD1=F@fzUkh({gn_fq`xoBq&-cf067aI!r<FjA*1?wzp_h0d-6|Zdyby{pS%v>X
zKq&IJe!!Btq8zyse`vVO(iekRBQ;BR)Tcu(9T?G(&d;8)6tGVSz(%%A;Y_1Se?z=B
zTkOZ30f|Asewczzh2Uq7S12Mmzzo(GO$Eaz7Jcb)B)xBnhJds#Dn~q;w^rF7=rM+4
z1r>Dqs!-(8!TC5oRECL?*U`WEN&?B9I+=PS3G=5XdgzW><jo{Ky*U9_Z>Ic7>vJfn
zIxLI?uFUjry=p0uR`FsFoM63X+5Aau;#evD2}&7f#3`DUeV8W4%fb6vR63?Ie$0D&
z@~=PpC#^bHoH$WVMrFqynmBW90h^AmXj@k`Opud=)E2<klAx-H*$rX`K!Q)KBX-*h
z*zhMWB)qqGxx;tl5LM>*xV0o=qItmp&?q&eU*z%fQ8@-iYmQz3w<)&UtoPTyp@BvM
zMb=@+|MB#dK~;9&+m8r}faD=1q`SMjySux)OS%st-QCh9E#2K6hwkopZ-4)p_oFii
z3}@}V*Sgjfju{bE+azU=d=9v1g&@7IJe|uF?Llp(ZibBwsj(hMSwy_dJ_c8eBp~5$
z9(}%w4TyVJDY}Tn$ZVVdoKT0Y2QJ|-09WB`+S=B&-D3WZzc~beNP3~+pgz>b*2Uv6
zF@JPCnIdrjUAYOVt&Yany*21(pwU#9qb$z^(Kk{wctQ=m3Pl>u-*~C7qktd6=dQ8r
zd7IK7g~x5qmQfUv)v`frXFm-SE>^ch-CBLe?b$fmxx}Yx9B5Pd{}f{b$Vi?+I<9uc
z)|FfofF{O>olU?xSTsuYIeY9+leHwlM`YQqs|+#mxk7dZV&~lf>SboYgihgKql(~M
z>-x_h(kti&Fpfvn;W&x}y^$~0-03Ir9ujoY?fLw1NB+Ft`5T8!?BxvT+v)9PXL*N7
zugwc%rrZ$^19ZgYV9Q~Kh%YlcH7#a*@NZ$)=hyL>);_b#V?o{>)#Kp{l1zOecJWR3
zjSqF!`<_iTvipSah|i1|f|WPiFBZ>K<snS(E6JUVS0&D5_ibTgvZqy=!}n}-SD4?D
zAEIKUMchkHTGUY!9V=%xeTuun#_;q~bd9z`i0Z&$0;{v&=Ms-;zL{@|0?ao{xHkZM
z&@pNH%g49FC3g>J_aNuYe)2c9VyUTE;WwviCjO<4{$0B$V8b+Q?>%8`{Zt^fACG?w
zoKgRWJET9WwgBm)DWX`pQrU$zva+v}`~CzkIh}Gp(SJbw*j?u={(JDBs?+Fm$-@#j
zFB|lqxeuBUrlcZe#<g_l!Pm-)pujE`O3oT4@6B2vhSE)3ZRi3jWA1}$J{#wb&K~Pq
zG!>cT_G<AZ2a0sMO1oc_eGD-kRqf-A8@uXB*@ZdU&50AfpAvcfAZUVJJVH34^-umX
z<Xqfk6f$w$y+7%)I-<>gBb(Z?#nYy3al7Qz{Sb)DgU6IES7MXTQR!w_!m08Cm<;k1
z|93E;w1l%8&*RO2XE91qZ84@ZR<p<gA@t?3Svn&vyHL+z=@_Yb`N+YJyy}dCn{D8T
z73X8N|Kr)fC`e~73MNZmbF>|Sz#(jg#n`-VOy18SOIe=Y5Nu{`kH9{~5}{pvg>h)u
zyDgP?B(t7ZUCSn1HwAh2zxx2TR-{<sc|D<0Lc3|<ODvNvJR)QjY~FUd8YMF4U)_0i
zuT-k={EeSwYHAxQXZ?5HE1eqCT~SIg^HPJGX~Y3}+Vbn<*RO=6A-`nPOc9<SzCJ%c
zzTW_^l>Xy%>5$C>a~LLoT>i3Fq~sVahS{U`q=GC4F=P)V<ATe1+Sw*-ni)`zv$QhJ
zOSOa+u9NguCOKKuNu^NpNPsBjQIKv~zRKR5mnZ6(vIC9H%w|>l6X;gSj^XX7lr>>^
zV*d{+(}+{7i15gYGG@8xn|SAikzR<!frSz>DYhVJAIMD%<z*7=Of*rcxNarr92+?0
zU0+@?v0fyWLAsOm0s#!S$L2oaKmGd)_Se@!#8}nLC;W^?L_0_|z~chQZvpeIN11M1
ztpItzp(p>|Z}j?B^et$H-pGpUiMVCSlnQh8e+6u8o*C6XkGCR101X3Bh5c&l#@}zr
zH@56?{X-$UI6%V8RpTW2C3AZm@BajjfacL1XXWJ@{``6-)AcT}OZZ)Fe=c?fP(}fS
zoejQ6o-paT2#Om?*y&&Zt?<KLn^H3zhRFU_0$BazW6}Ttmw8vzDoI?ishP{hNFs)_
zI3bMqOHA$73HRIAIvyFy;j1swvN}~H(JJ^?^RdDh8K{kB-;rI6vgJ;cnQUZAAy#C9
z00!}~qxBXAZ0FR*AU;(+75shp3fe%|3KlvI*`p<-@X(V`An8{Lf-<FB558m4_7NE%
zdzQ}RkiM=aPn?eW2;fpfwE0m3H5J+h)~qbYoF~gRZw18AkAIbjrW|fXSuBY|h5*Kw
z*-0`o#5+g{HkU9YfO6!AP%?g!8eYX~l>ROtLrPfr=iZaW0c~J`1CHY-nd42S7!%X8
zgIbx4m_|^ZA(KiGP^hJS;m9Qr>&<WMs)_hhcwCV0wy~5qzz~To!f1x9RL`f$9hnel
zG$bfBltb`~47>Z&%&eqxNCGM&oZi$e4-Kg_dP6Evh*6e~TIHVt%i+h^CUM9oMz7fK
zU?rW2A~kxV!d^FoqdHQyO18_-D51G%A(B}?GI!o|iVF90X(an!j8gR$zJpO^fK-yv
zmEW?;6DygzXd@l(pfMh7uJ5o$+Xtba%|A4n8fbA9)?O=^hqKDox&;wT$z1NK!4-l?
z2eM8E)}YABV9XO9GP(|)sJz|qlbof~Q<a(-JRmKyx{wPW+uBi|LJm#0lXTZ(FP)X0
zhv_l&PY|`CAcTW~V=EXw?H+voB_M&#F8(@mFJQop+Nhr1SijdXr^n;fc%rUV^*3ye
zT`O+YsEp5Q5w6TnvIohR-tY*9N_-3eHR47%TW;id%feBToAxJdR_%+qg?Of0;6wk4
zhO$K@8dln-*gfqhYe_gkc%H?J4SaN1MzSx&Mg(Z#*H3q<fQpMn_#Hd~{})gV{*BAP
zwLWW3Ca_K@iZ{kbEBMmtmz{k=0#FOSHM}xie)Ut~iO4>T0m2!8PVXsaWa$o{f4!q$
zZ?bbNPoR^qolD+kd}4*;Cna`BXRxKyCbo(I^-V6kV%p{MHX)!L%}{>m9f&K97DQcB
zw!TXkNVWmNHSpO?MSWCTrGi<5!uuo{4hpo}iI4ld335T3w1daHjt^I3Au$GhF9MPF
zbWOW(#mOh^<{7PB4Hkg2#axWD<#<SjQF+F?-4KitQOy|B{nBBIW%}CAK5|P4Nrf_(
z@{M+~dq&kE2db3nxTr+R?d;<hNJ@;|Fv!y1la8Ub)bL-$sZyv4ed+Tvg@OXC1FZUt
zU7NiY&IK!u0OCrq(kVr-02*6bea&quHyw3I0A2EB^op>Lok&mrY*w^DI$(i!G64v!
zuX+hXHouX_<_#)az%*l-Ti_Td)K~HIMEkF^Qa&8h^CTj9Foopqf6VW5ihEQFsKV1u
z=NSY@gN*9rBTk=-9s8DojFvuizOn0znObeDQWR`n)NuAsh(WCCXhxdMHMz{Qbi1yv
zj8ju-mC7+WoP6G%Jbwntd52d@&m%5yx;YV670l4$E*SZhGGYI)OdI93-5Z(Rm*RPS
zv7*C@__i!N&9kc|6;LE;#SBx%YOkc|-g#ov@EFhU5yh_8`8QG8JAMJ?VpTef)6pux
z|NYz#?^T)Y-S4OIl%2$IyQ0N2$#KVw*BwOeuq%=$<R&}QJM8?oK43{eoA+EI1^Qv0
z0z!x{+f~9U?Bi<Tl+u;83<F%B0GCd76wG_=*!*v}<)atN+lD%jw~zx$eIFUweQoLi
z02uN2c{F|@>Bw)&%C%ff8wc!$(oPx9F(_~_l4dUvf<$(+T*nL~r~ypCvX=7zhz0q$
z@THldZt6TR@ck+%`+^+|7}eKFBRyJN4{vSoJ|o(n+FrRCAA|F-c91SwW<5GOB-Y$C
zX%a46(3EF@AJ{`8f9Y3M)1${wfU<gWjvd=A@OIej{;;4vv32xmNVqbzEs^|`xjk`A
zFuBPMhJUeb)T?u(Kc~(f=LQh#o_S>ao~Ohy%TlTO1{l@?J15+mMfgtupy9btwySn9
z69M(sNzgvz%nbkXy5ISfqNXeRSg$Arm{{}2z|O!bTd~JD2eRxfSNHY3(FL*WG$Hwh
z<QW=UvcDGru8!9;{icYRfLLvGU`<voIk_YiMsK54V2#S5r7fHY^HXQtE8taOVEu{z
zAS2%l{o!tV#<M9-$#Wolmh2fq&Ujv538W=dni($QIAvS=jGQ}pR);B3ZN#o)&@Uif
zE1fc|2qw#RjvaerawzK=%~b>-KSxFYd7GVA!;E^qkFfsFO?u78&9kf#MMDGCzW>@9
zWv73fKXODu=$51?17qf^Z~lY#(kLJy0}Cy^L((}}bPd4s)zkSlRORtqx#>4V@P2`z
zzU@k(RMK>-;u!uVrQa@DXlQS;h7(wBf<IAuiU$cuec9>WIg?BN8_VHjl;t!h%wAdS
z1x1`ICkx$m>Gd5G!Cr(iB!T#Yn$E_#Jd=PEZxmWF2C`DM+aI~j0UO&!&i6|U#RO#X
z*t-wz{P;T_XSclfb!X3Ov8}Wlus(jZ&M{5jR&)+s&$M*&;3a`*7o9Su{eKHU&#Lfz
zY>&`5b+IoIguA^j>ja)eVBV2Wj=gu)^5k$9(84%f$X|dvm*E^#&5{|G%=pr`3pjHC
z?wl{)$UkOih=)=Asy##64LmlT0F@x%@&eeofQ10^g^lkA<5{OWNt7QI-$q+uvQjlS
zU-#}rC~8@JK^%&CHp?`BM6DWyyXsSFbN~^&fyScNx|(^kaHZJ70Yii(v@pQF1@7v$
znmRdlxC6Y&!16)ghxMhE?Q(c)T>1&Xu1lEPzMY}~{i$tbar=dWWA{6aEX1O;A4phg
zFiIpYgoByMGto+MGV%YpcQ_#U>*8dTD3fASsc8t%&q}wmtx=@d<l}vUwhXK|j9nGJ
zm3)%9H@2QM#@fFh1pIE!IztnH-+Mk%6%n2KH#!xdo6u}xfEyVqM~|l=mQnUn1R|h3
z0gdFYUOII<8zxtb<bM+tCQ^X3R0Q)^`70uGqcmXr@W8Q`0p<UCpd6eZImw*|0?06s
z`^T;MxsRCFF7fmeRSFEFVP-*!3^H(`w<6GvJaE7Q_z(kZ_LEX{>>o+pJYPX0tt(Qy
zFd2GKVHzC9k`GMdf9GX&#!SZ2v0Z5kMpsDlXbi~@azFrzw?<XHnV{)HrI9wy5CM2C
z&9`Bzt>SnKB1tnJhzP@l#+0XXqyZeZ)Ec<O>F;saNoF~cr(o3yKfrX(-9ZdL3T#Fc
zLZXVDI!s2p3NM%Xs7QS;$ZrZUM_?I(Fp#H_P$rL`PTJirtsF9P>jOh7hnJI~zIBFK
z{zMMu<oRPlIleS?gYP^S(E5-^021uoh+RQwdPXbl_GhQR!k#W2hM7t^Ylbm~Sar?o
zc}mwBdaeuzr$t?VZ`Uv=K&>mf2}&6}bs~jF_<v5?GxCm&AU*jCE*^J%!oTsd3OA4}
zS)bc3pJ2xQ+io4$Z?NN==zBQo_r>%_<xN)rz<3{t-nW-KhL$a?ox4Mv$UzM0O<$X*
z7m%9HN1B4wkFc)pl8UsOlH>S!_ElNF=^QpZRyRnqz!`Y9uuTMNkJ5fFT1~XC#D!49
zTbmr6c@_drr?JB0?rH8IP<9plMPdjmIMLj$jO&qP))rH_bq4Qb9Yx5%3g_A`0FZ%d
zoCBtvidigH8nbxGz=vC{R&oKT=>P>DD|Zw9pM_KXQ-E!D9<3F_eRKX(X)RV5AidPA
zp954}owbMF{u;>9g&oMDaAR++A7kNZ?PGE>EYI3b$P#Hshf8o3Eq<Owiu>zJsADhp
znC;umk>`uzvk!|^G9C#^(9X;ylMgE240jFZ$(q|aUQ-1D?bt=s$6hyu|NgsjmlP3H
z84-VYnnszIYX0LyK24L4DgLtCZ~Eo~Ap&|YM=V^83XjqSz`zibTbAVUG4%5@p4LU=
z%iYlawH?@7qXX{=xY!-V1#2wQUWRkyX*@}f!0sE*^#l;f8g23*0y3*#M7&S71dk)W
zC{$AjrMd7C<(fG;W}a9=BfiY&i)me2hM{UKB9uT~rfvO*deya33usX_m@AhR=@2cJ
zDPv*_wcQ!KcNnSwOgS}gow~{h!fv+zGba(Vd&K)iQ;7Er`ubVD$$>TK*Oo$)lXuGZ
zC`VUjd3XG<@wJO{AA|zf>2P4M74=L}$~WOiQObV!v7FYG#@<t=Zah`$Gi?4m^{bcC
zoPTk%dx@6M<C#jHx3fPtzYdp^al+4iVO}r0A_hbIm==IqGXHsQ%KXoH(?^j4WHZjw
z8d)UGLV1^|iA!9txi|##AB%3Db#|wwmu@mBk_~MAs|efq74_S~+1kvx<MtRk-P9=p
zWg;$ydKnF!Du3ds8HHa<-S{`|<Cn*$zE(BD3Uq2*+PMd9@+@FCS+|K^&H7P!Mr_X9
zT^y<oEI#L^aXCyJTM)dq^@C%CB8}|&jQsw}ODV-Y%H(Jr7xYR}g!aiDodigf%Tpf?
z!oi>Z*hIH0++?j!t@dzBTzohHY*_}?F&8vw6Ev@+JVGNVS#{R_wvAk#4YX<JSaH4(
z=s#irU}MPp*~yB|StHiTHQo>~f)X^`r!3t)Gzb^tM<SR1Ah6em=<9f7t2vlY^y>5a
z04g!(m;N~B1ex@1UbWe!mT}-{skJfr-(FC@T{pe`x&}5PE!ku3cTsPt>qz=p`nxW!
zNuADnq{BtBUDXU{UFvFZf>R8hfOczQcArzF?844Co&V3xR=~OCC%*T&XZwF$%$QTI
zk33rOv*9rpaCZLkuEpQ^MBQ@3?*3Hoq5UHYtgbQIw?CdPRKPmDj{$45(+B%0@Oa&B
zXIHdqC~=>D|9qLnb`%<0(yu95sE)c<lz}Mc-_5K*%w$B^%g__I%>!N@%@*~oF)sD^
zrO_#J%g+NPVW+i)+h=a`h}s0|o=?Tn(kisEhF;eup%vH}l=M^KPcLr`*)_ZFsdZ6p
z3fetWGDfb>=yt>>b%*X8D{Fb!cT0ENFRL$-G?tSwzH~SDe-<}H(NMLSJt}L5LpRJ)
zM6i?w=3R!1gsHhau1=$VSYrE}ek<1GWD#y~bMNxookX~nM$hu{L!ZeQhW-D=XE^B+
zq5g;c+Jg`p{QQVN3r7ez9O*6$*7}e=Msay8ty<JH&6s)?y2*cR2?IhwS(Gzu**O+0
zCnEwsCeH<%^t*8=0+v@#MDh!JsjfV@YaTgjwg547C?w#rW7gJw+UoQmRxo>V|A(V0
z=BhSpu~MYK%sCayp^%XkkP5mH|Km~<aAAeFiz_zY1N`MC#%O9cF;cu?1M5q72mA^&
z^0$yY-OK{S7*^GNaAx4bY!F*akO<e<lq2mxwTuUjxho`GIi_>dEO4QHhetGk4}G-?
z#hUuJVi4*CLk(+Y+3tmoFA5>_!c*o13Fk}HOX@mx%TM6_Dh0lH4wFOY_j+;)=UD-T
zc60R$AbA3e?RzT90d9i>fp;*4bn~KZE$0c~PBNVIDsVWT_S532{j^*OPJ4#&%*h6d
zp^(ke*Ix%&NccN8S*ynr6gK0%TGQi$LQ^Cxbj#qbV1U6m9ixO00wv`)#K<<=wW%@R
zGuh^nk}qGy<43gs7$P~WtiUty8cWxThQl;XF*|9vB!v!rrf*8dg%Th;1}f(oMN=h*
z{7t}dc8ka}gdCXB8Aa;2RAJFwyL}O7ro?7bogr4l2Hf?eGV`_!U;!^Pa&N0)aqdrF
zds5__1(16IVq6W8l9XblM{`&UGQwxVHwGia(m+NWOm;W#hn}BO6+bMku!`i2o5VN8
zdlk73Lmhe1Rv1fXd4dO{kcQD?om?eKPnfVy&Y8c7erX3!I3NS7WUx8dCc$Z&qp)UX
ztd*2W6uDP|@`4B6A1kf^yY8Cww_?fm+8r$%S{_C28m>&4)C>s>p@S}bm4$pD`M;Ib
z(p8@iSN1<k-GT7?jgH|4>aR8<29~=srE)TfL^5c=Ch;@i(%KHG6`k1ucCuGvbH*<(
zS5uOOOFcGgR6Hd1zbWMri)I;U!#Z7GmK2q@dc>1|?H@(`28{qo0suShb7+XojW;N|
zz14eQ?IU30;AR|;q|FVOx+3Y=t<zo^`NrvMad!<#z5d-j3k5-mFFdx&w~xj)Rb2vi
zhS~vy-{`zo`;o}M=w525UV~QcA${OqsdtleeFoeQfM@?V#L+VWwPWKp!2}!N$q_WT
zc{<w%sbi{94vJ^ny^5O6`z1ws28%rqj_abj5~z1D`s0XZ(N)Gw?{qdhd=lmRGRpD$
z;zzm02O$Z)bZ)t^8!|)kXIfjy%;I6``~t5K5W9McmeM}EnqJDwdD@{OGp}5N-8&+>
zYkFbgu<d;c^Db%S%EZod&5@rMZF|fbzW*Kl#@_altyT;l5J-^#FpN6hPK#5uOMnFH
z`;C_FB_#F-@AnaVX6|fq8vpl+_5J*Nwuif_&c824AtAeP{%`i{5a9neHgS<C3MEkj
z?^5?vJiO0w6`#NU^SmA6!`40Db~`(LUF+J`EHgDQ^WyN|j}`xS;2Qd}b^aPmArTG<
zjxuj@<cTWI(%yyKFC4o1zRhnua*bFs188XTamVSI%aWG;rTzP+>^6t!(J#0B*dj?e
z{<?1XD%{=2<XE1Y2?Jmfy8k!q|ErIQa0;o5FqG51A9e%pD%JtO-iyvn`{e24r_aG?
z|BZ6PASRc+9OWwGQmK;7*&@vm+`w;AvhL38_aE;m>Ikx{&8pFc8Si2P*-6cJ>m3_&
zZU=SDCmXCGk9xpDyy>oS5&sTJM+~mZDtD9~k83FU)GzNm4%t&7wa}904@^gmQv!jF
z-s7xxcIROBVSB9-#r23ac`0}H33JHt0Jm}LOX3{F1_8*9bthkUXacT_%lUP(i3Lnb
ztk~q7MKE10?+YbZPdEp~)K^Bccb-b60wSWBJ=S$h!34sV#86;JDp`>?v?7HLWH_A!
z(@jQII+Z-oLIVK`Arz-^B|l{PU|9+n!fWZI3J<19mA^zrtDYaHXssvl^4;stZZr)!
zQcmua2wjFQkiGLhE}ZTg0#>DZDLwNDJAb?sPdZOLe3b%l;1ln+E&XEsM?|F@XUemS
zvR$hnb**z-z^5(8Ti3nqgg(N?aX&@I|8n;47SL3q{BukFd)8I|q-N`H9S|TgImOxi
zootM0n_}x90G^f`F#OTw>=rAEG~HaEE4b(jTO})bCw9}BaOw7@*SzdpBKbHCVTgfu
zT?{1c|2}%gGMAJ3Fq*2di=zd3ln}<X@t@f*o4D{Js`KDcC92kY9dy8GH$lAT-$%du
z#e@e|;#c(F*q>Twtrkn4o2tvEXe`srL<|G%EDq8{*z42R^Am_7W~OSX*vSaUMMr!-
ztuS2w#d-|qDV??W&V(!G=^d4jlH{k&bsJM)DVAgwY#5#J=y=%DScPetMEQ#ZuU%Yr
zc?<fn5isu$1uqVaIK6a`3|)LC%)I+)w_rYr1RIpH^*wK)eTiOnft5wpAmvH;+veHR
zN5D)5XsWw!HhWKCss=Bw5cJdZ``g5`djV~&MD#~kpl4api@iSW?}*3+wwvfr*%CfD
z8|ghPTL6i!AFtb4rnF`g-4h6v$a@^>BLK$z$&zI{`iTl4_2iuSTFGbDCoTK%_4^Ob
zroYtJ<q0y+xoh^)MSTGL@={K1E?&C!{CS$?h0uJ(JJ^z`8G`^*&<5Gw+4cfcrNa22
zyI(%-&l7G|4ImqqNw`~tUneC73P*6+sGm!=OG6+TQR$#}>4%(0fbF~aXsf;utRyv;
ze1coV458t?AYjpb17M~FRQ+@NfLgLNQo}*Ne`o7~hmQ`{(c56NU60wc$FQ%$aL}7z
zC7Sv(0bBO2Yb6L+`Df1mSUW}Bc#FY&xUwey?;?z_M^GYZ-8=E-p|!nD&DgOya+V|q
zwg+(VHRl(cF{LA0A4ql4i6S1@$3_%F5H@~2dh7hE*Jb9`5nX8=Y$&rSPE$3$iH^7K
zzYo`Lx0Q8gi)+5~j8a%TlHB2h@MFwc_U)FSO|qObXW{lTl5JVo-69LPGhP`0VwQ}j
z&}A6PdAo0-|AYU#@jT*KHQ>bRf5F}P<M{O5pe$iK|DOHfqTSW+Jo_bl!EXy>o~60f
zpwAIvse8|gb0h3`)#IG;Y!L;&-?+4N1~lMlbebB!8MyWLRyv<>Z<~pn^VMR)WU=~L
zzWKh<zdvvEFt`E;;bVH|EBZVl!78f9?litS{pscVqxgoYXG8yj-y4YDe;14Sc7*^@
zYmCpn-7(^Rqq!e=``j8^b3nlN*UL0CEbV6Zf7Cpx6SZPy_x5jp-b1I$SlKh@?+__x
z&6zuxvHL199qs?N(LPS_cFoQZoo+uy51>iFX}gm4zlE`R-tv&hJZAZavQ6;=Ve>!L
z@m}UH%{@*1cAZZP*-eLwyDpt#1aYt0W1^nP<Q{;q2}FL!LdS%{`tBbDwz`GhKblG@
zSvzX0`vGKalyjXIrh1i{xpAaPE%y3#Yy|L%Ad;}VUwzKIu=Fju4-{d5`~mor9*unO
z3g^wCvne&YfDJ!zJUW{E9QF0btzQu{DRNK{N|zDAcMl#IMZ@MPHqP}o<ti0u99rlB
zU}T(@YKl}g`q_8$d{g4aSN4dy59vMG4kZfRbNdun(kd14BvgA+?;EJ5zAaO#;AFob
zt1S+KhIdLZ-$=$QE~fW;q)G@b<s0hCoBYz3^`XRE%6kB-P{Jb>;h&-qb*>WM9H6Nf
z+r&7D_<IPrCaagHxMM$;%H-A}BoK{&95b$p->>k1^+iOU2}^F};*y0j&9X_VkksX5
z&#|m@u|hpI0#pGR;H<O4I`vf&$Glh3Oa3_&iV~&{-c(A}U5Udgg)3?VxFBkqX2!HT
ziou-9MLtFUQ+Q=56p)e6Ik$2*A7DZ=78T|nHzA#=eEPPKrqjBdQ?no}Az0($JDHzg
z^lBA<T7hW)dc!m(mc7N$?KmpAE8YY_`}D>B<$y;VJYk&16%xp68RKCwKt`IDKmine
zvxi-}-vl{W*+ut^8*Odz)N%Jpk53?#T9JygDKm^lS*N{i;AxHw_^wxjDqQ#x)sKvg
zX};YITjcya14GQx7Ft<qyp`Ztmk7%v&<LVsQd}?PtKJVKxGD>X=e%tI=Wbclz7~?{
zW-?_WJVpSpBA0d&SPaVl1~`C_R`vc?{<D9V2V8n32{h@oyU}G_c9@7viQW-~nqoz@
z$Fx58lJszvVSGU(Tny2o@qu$jsVxxRn;Sz}0C>nT;~rhcKMp!8UcP#^y!u};B?O9A
z4Mv}?vqrr7VSjEI<-#v_mv99CW9(Um@U2nwI^q)uI=&q4+K#KrXlB)$QYmfQ2(Y(=
zf_}-E23w|+zz?bf6XB_L9CCPN)_R7Q2c7>a`A<B%YkC-~_CHt_LxVvmB`gXhnu=hu
z-*G7qeJ@!&R4kOmbEf}6Aqb0G5!ru`t5hcjw+5;dAw#+7<|Pn;e;wP7Qy~dr-v}oJ
zQbb#_KGmoB`tT2v&x8QZb_HbkrDwFk0v1q&*BBnM-(s6#C`7SVpF1dF6akv}g8%2b
zDXxCOm>I*v1j=mQe_QJWa%4j2Mq7mnbPi9mh*$tH*nY%&YX5JA(GG1oVR*%h|IHv?
zdf$DDW$0)bp*UMlY^FiddN$VI1B|rZ-hcmg`k97KU6WU3zqb?yL75!Ec-{A!>RA0-
z+xr=-p5HCSZsbUuu`>w2Hpe23OK)oLp%ezVLbg`L)9cedLh-lIqT98dt5>lADgkQ>
z80I?BEKkEzGDCSv(Im5%K6k#&e>dZne#Y)WgeOKaRR&KxG*MNw4@4aE4^VGSeqIsw
z??=vyjYF5p@MwaLIyD-l7yz?9Ee7BJD$IWB_=)Fwl`0H8T3hQ@7vNo?m!s05yXk|>
zln8{+0Q!;2Rl<{8D^5?V-|Bf*+}R$jK)TV{KSvqnvV_I`02>-UQBA2|rYY{#8h_BV
zd-#BbayJX7!r)9uf9eq~^?Fa$6@HYwv|a=x5gVXD5xG{=c0)#sZ&TOdTYhGgj@RgT
zup~bJM;(IN?!ktcd;cf_c;#R(Jn2#;^|W0N%{1`SLZeb5&{RZMsM<YgmkD`IvGSe0
z+*@>u!F}boHIzV7&u%VVYd4@Vv}RqmeKjta)S!MRs^kk3AVxZ#oGc6?`>K)zUM?gc
z*t)ITQ`=}~M6&L_QmlHP`c9#yBQs*)-YUH*USeb7zcs*e|J3V9=apV0mt^Mo%_T`2
zuFz7fiPyxwNj!=2U)-d5HJ)YG`scUxo792yV|qFs1yzcb-Iis!i5rgr$ASa0-V|L)
z!pITWGrM4{8bKyC6s>+gMGJIlnC8}LE6U}q@C-sqHze<tf%=N0T7lfnfaB9ky4O~M
zt5tY+ydU1>3L!79Iq-kT?XyOGu6Ks+hu+^kxd0!WIkr<Xq?y@=!VSPpGxE^wlh5%+
zyZZv;@}bA+?ef{kiO=s=ykzZ#g}Vk@M_lENgGo!Ia0phw_Z#AQb?povt3V~vy7ELt
zDXHNBVJeEE0-mlNc(!csTaIt#v}X3U4wo-H<Z`j3P)m5wf+C&!j@M6AV`8zz<Fbl)
z)CNnRgh*`1za0Z_yLZxK^H;t1ZObfg$53<q6vB8`l*sR3l8JVPo+GKK_jCRS#3=Z$
zZ?ET_Bl-`g^sD4oc+f3HS1(cGUxLD^F)^F{T!HQtAR!sMuW9rvUYWQ%R`#D%xXNYV
z8+#Q6+J1BQ<Y^3Lw?1!kjkjCbjj77mx~0$9>pf(wT{3xwXk3lfiEE^+Y`)*WKPp%1
zY7&A;A@Te*b7eY}dxN{SfrsG$06lE<afJ=*##d|r9+#VQIJKDUY#mcrc%kXu*+-#`
zV%y0#Ge);<>APg?>vk_A++J6#tkiHZiu6piimm)YDMeCmtip#{wu9Q~^Aj!6JW4oo
zDOED2u>A$LvmFl2l8c^1&W8sfFuxjKCF2@WnL^4qMv2CFZu@`<nLLScy)G4PVZ!el
zu85QeN_g`1bu_u@8@ow(_38#V;`!^vWmxK00yIe^&)C}Ko2r?MN+v5_`R~s(w;i#C
zK$a+mCCqj{Vd0LEbI6iikU#f5A=pfT4e#yVe8XVpNAEFf)5z`JC;vYlsb8C<=Z3Eu
zB9whxw`T)>zcV01N$nz_DU-@&W^S&r+dFKnX<oskHzZ<!jdRMNRFzA>yOgSR9GdYP
z@5TJx^{zJJ#frxYcw@N~fim+2Ouryw=X!>wrTzTR1n;1=Sp`slDR#o}Pz_=ato!D5
zG2jS9Ee)tCtsnftO%HFp`HIKo9JWWX<mU4l=l7odeIg1UxnjJM-RdTuq@o&jG3eWz
zXqxrc!~RPhN|6~;xm#`A`2$O{V&K@=fBu?(K6C8#;5T?VV=O~Zp-{OuBaoDkFz`b~
zK}OOuu*N2nSe)9#8AC}5WA7Lwo%)<~-S)%HS|ER&7*?prjB4j<UafD{V6(1q*~qk6
zvY2(VcR`Hv`i4Y4Grh%{mpI>344ADn<NYQeM}?+dYde(X$lC(h-^<IoXXBXa*yj~N
zAq{gFyL~kD9X=<OyWI?VGx(D>HwX2)S-x8oyH<A{Y$tjP#<qoh!%Aqf%ABrd8Fdpf
zPFFV%^Gr%oRK%LKp71Nvz!pNMwJnhQA|mXRs?pY9MRGSEInZxHc<$Go^8h12?WZCR
zBS(dH?3L=2UbuJDrL#}Tph&20xUnW8g+c8SUkR(qT&+#;=UDEL9&uihY(pjqH0pCg
zB#Aa9zXFWFofP<b6lDk&QqDe$lAy<9zg{48IfY90IZc90i}PguOUsfrk3A0`h{+sR
ziXi#vD|842r8{I)j*h?@Mj%KLA7-u8-^*lxY&UsjAIA(v7SWwwMY_l%vzrw;6V{a1
z`fW^fxZP))w@4iQ*+cQ0?BWj*^m$`FMt6_dHa>Q4){b_U#5P05t)0h_Vm;34+k4^c
zLcb`2-|HqF3p)~xy@xM@0Tu5Ii=go<m@wi2Dw@&xl8T0Sw!N${Mg$oZ5X=fAWfF6A
z^seP>3#{nRAyPHY$GjlZ!^K9yN`v^3mHKqwc{MGKMzG~!v>XTvo1SF5H9^F1wBIY;
ztxlc=!4I(ZjhSPE#EW(_2uVfkhuHjXJap9!{4S)3&O>kF+t8PDZp=;AEcENbCIzR_
zILDfbDJdlhY)GcY|ClH2$G;**RF6|6h9%Y$Il@;~=5Tewkr=n?dnZ6iNtumsD8op)
z`-LpN#^Y#}C0=}ZwWVg9o4+N%7Tf1d+Wbt*&ara5?;75v6+clbiQaGbL^puyo3*Xq
zOTM*>*2j$KK1}~@%d(YlqofLD3NsEjBbG0MsVg~(=hNqpCbgfr8P!-rl+DRCGOCm-
zO`4yknAX2<n)@G$&T{X?R;XpOclyUP%(0b~T|8mRIiB>svS&xZyRLg4e>(fSKR89D
z|F+D$a+VKCNsz(@XW|$Gmu0t4j9Q(1X-40W&lNkrAIPynHUI3Zn{K7aGLJSs_w0}@
zaF=~ig{_Yjgw{B7O*wCL19>yG2oBX#VqwgG@IGCW9ID5j*g>3Qzlh(1;LN<{_#mK1
zhUWd6LKsd8!VGa~{IVMvH|m}qZO+GgI^IgCK!G(7ZWMdl1>@C)6PhOcT_G4;L~@TG
zcVp?XVDVUY)AMy4<o8t+YiG=urTzFf!nz@UVGARn;HqKG{YR^HQmb`zt}fIy2hS8L
z-oAuu&&@ALM3T+1ahFh?FWOZo0}=Fj3efu-9ewQYn`;$et3t4R_fL{~9=jY$h#@y)
z#UG(qWJSYGnmcc}^+}VQtg%1z_Ee*ZqEnPf)g)}uzmBUnwPCTNNNxL<P{0ZOjWb4n
zg8;&C?T#3Cx+YB>24^E^QIfZa;&HG&Zw)e$=k<)dd>+C=>q4U~1~y0v(R@Pox~}tS
zdj5@U#K)~OSxJe{wjj_*YB)X`xund%<@etknUH4fZ?ng`IJfvq86kXa0YEvgwl#*9
z!NQ4#4V9vf<H>*Gr7xH}Knq6cAh<fU*ZVt!wL*sKZ8tbA<a-c7blHwP0gtGo5Nxu+
z=8J=gc{I!ROJvt(e7Ou2_r|AEU$@UW-WDsHMrpA~Y6kD29>+INLTTgRN_^u1=r$Rm
zpXu{6?|wAw&a2%P?!!FzJ!rs2#zk9teEeiseR>Qvcu2<i&p2;(qB`a0udDAqI<?9J
z_ZH7*;5B1#kut-m$+la#QA++X2;rF7*6W?)G>r&avxh?^P6IZ82pZUs?>4W%MM_va
z<FB3Sc}EW&&freG;x>BuXE#=w3}TCOq&-u*^a-Mq!BGj7PzVhu)WYT(S(^^;Y1%YI
z=k6#5OX+0;c!b`p;CF|56qi23UatU+PbJ+2CRrjVR4u;*b8_IK0v$oJ8XQLyWkyC+
zo=nRWMOvGeT-QqYm>|)dRcHCq!z14XPg&*r-BR0>=RZl|ue9XBe;M36306lYF2)z`
zTW!<3=!#OG5`Ye-@_(NY+UOqdaIZ=nTJgZ2i!PpqTSVY=$|wte^NRmn<^IRZ5_@fu
zB9U1JkCOQ8;`;jar&)eyqQ;B&`%T!hm%k_q@RaS_(c9tmcA!fmnrEk)oXvk~h(SEI
zKFw8^c5<FRZPDrY6Mh~Bf{V~dqhHl0+;08=oLi1aO-;Ki`nP0)6Kie+;l6tzpZCrC
zOT+Mj0=9#h4M7E!;2aCh9Rzr4TX(rfkaLyh3m)4|)4N}+MU%F&H3jL^z)!c;JKnU`
zdLDDvplvm#%dNO6naHA;D=f;$?0KNANJnx;d~Tr*&aqjZz2UP_E}@HySbU(g_M}TA
zr%WS1e{M#G5;kFsrV)iaR2~l=#hcu=@)p4NE5h|pJtt)jx7FO<m$`z=T<wlGA{|P!
zCX^bod?(i=B%7lO<~%iO?vXqF)mgVb=!~4}ZnQ7#eDoe9MU__(MR6ZvS5i{K=bv6O
zl9GZWmy0n@;o5j$Kd<SS-y0*)ffQd&<bI>FF1Jm>IHI9v_kc*7b3BjEzUrS{HDWq<
z7+fp!-}9suop>4(LQ4)ipIs;gi}%B|-Sy499DH8T(6_vV5a{gpsmChPnQLlW*VHSR
zJLZnp(c^B-rjo>YwYIWR3L>^<_V>g4Jd$UNQ5a1~wwF=L$R!V%;Kw?|Gk{CIU-76x
z=!97APM{fvqy%}+UnFyFXNW-UMzv$uZsczv9)$1##&Jl#Z4|vxL~Rr#k;Z`>WYNY%
z*l7JIaS0+!MFh|{P}vN8tHG%3aM;0H;41Ubz->c#-^QZ2nK5BZI)Y&NW8ldJhQA_X
ziZE~MN?5`5YKQtvYQI&Azfo>{pOt}20$+}owafn9oL`d7-Vkf~qk42}&A{9^tyl#d
zWIo?pavUk?5L$P9PcA27N6WRHT^vh1V+fDC`aEi?2CC30bm$PZ(b+?<3wViQ<^Hwh
z1wY5MRm7Ztwnq?|k-s(I_$gS>D0tQC?#s*1%ORqCNQC=#rcrJl90IW<Asa#rgj~GZ
z2GU^=?~Njmo6yC8I3Yb)>rzI{dF7cdRx$FT6N6SP9$`A&qEqF1x%xwivgbwyMs-aO
zR#g?IM?y>9W?=JSND)DKgV|6HWxMk3QXYqrG>Bo*5h}CZ<uK(LmP$g>Q|G4=sx&7E
z0>u@O?9uzUuHfUOdD3u>n*Bn1Nr?leKp2+*_|{OIqhxQVd<Tc`8j3p$V2KAi)<d2x
zA|pM+ZELj8i9s&A@pU{8G%<&MiwG-<{GnF3!m3klSlVAA{-fsijAJF;l_ZaE7&N)R
z|G}Qb*zO=86P<vnJLNzeo3<gM?n2YotMKawCOQl~Vz^0gE*5N@j<axTLDsQ5&*BB-
zzkt6AE?k1iYLi{DJv&}h#LI%o3Sz-bLj8ns(F!3_GSQfi7LlQ3Dl&bG?lAd=z!I(T
z+*e*w@^ME3rY|7@#DtBeIp%mZ$^kUE>z>zS{O{ECabuc*!a`Op35TL=vpE^;^s;l{
z+i9=)3Fs{=^)>q#Smm<ti@DN@6;@Yt-l|&<5tQ?7%sAbQ5(GE)U)}8-pH4Uou`ahh
z!~g3LksY>gu;|;pe8f>$;#o_hcNAD*$c>$jMxp1XR<qc-wL_Oy+Q~xw@og~)!ZoB?
zIy#MSBai_~TmQg!je-JP5aTaFkVAzgz<un$Pqt^=u)Q?&P5cf<o08~m|5_az^wWi2
z543frgjYljS5$`o)S#>kLQs9~JwoG`Hg3U;M7D?wEVZ%-JJF^_PKj*H&w<@6M2`e|
zATA+n#~R<S>~3GSf1og5qODyVx%A*i1)=x<rfRg>E@6XzMPD{dru4@BAkxe7f}zwO
zoq`S`{E4cz`jti0bhT{yLi>g|S#FUuTsTcIJ#<3|CD3iM5cBRZ)c49ORB*?syh&h=
zMtSlY*R^O;<f)pAbhl27%UDKIQZSsP@N`ret=F*krQ)lax>j$^&eNP~H-p)cM2Hb(
zP<(UeEub6be4T|RXycZyI=(!MwZB@8Vg`k6k*&!3Ksd+{j9F+)ZFoj~<CUClJkZ@Y
zogqh54KZ}^&a8Gi+J$<@Os)k&&1uBxb?&Q4Qmg}|b!csmuh#Y2AOCe(Rc(Gw<+|Rj
zzR`Ip6yUH@?-g}kt;T>nir$)n6}(OFFz$%>!HTksQ)E~fRZ)3rkTSmWwjs>QZa>$^
zD<Z$1u0g|wsqdt5=|a&r509zw{U?YNviJi~`^RMpq1h8XiBG}ECFyUvK0HEe=B_gL
zLJqA*?+ih1Y#Y?23agJe=b|Wr_1By!zkXdk5Ed3--a4wJ8;`S4pM6@Z{w&Z(!Dty<
zyIlzp!%r*CrJ@SWt2>)h2#Kt;*lD0CvSKhw(sVzzd2lVtWE8@#VbL%~ZVqPJF?z-^
z%^ytQ73;B|`r@5ouWL41#$={?5Jp#%piw5vegYZzAfEAM+T}VSVFJH22l(MoBzpb>
z^3l~D%iZ_F^9#$sT-L1<qqA;gR3<`aZkxWEF}8%u%O^!<J!N&*>|q!H{3WN*@-51k
zWURhDAxlZ(N^eu3fS5JWcEJ&2nV%+@<g}&=fIi;G8<mojDM>`pXMhAj0HOTtEc++G
z;5_)(!51tY)YMNJ7<TmMoHKLkO7$w4?}PS)D0`+L#Eakn?u*BZAWt)J3<H<mqLuf0
zhKv1~F^DYCh|M~;j2kvmZJLd?umBj^&YvIj2G!ysNiMD0dQzShf09T}w8{>C6&3Z3
z4#ZMYIuk+ERtciWBlzSqs{zS>!g)V>>dTE??}@nD26wJ$YWnPx6JB0$>o8K|KE0j>
zQ-M@OId6u$#z2;$6f0@x1SHwFjK05-d*+XHD=)n>gDBnWJl_zz|BDboF?!%FLza}J
ziO0Aa+udvo|NR9<6n1ti`Au)*(#hf@vb1D$uSz|wbs&}`Xr$u&fjj-N@8V4Yec0i}
zy(&1d=Wm`#X43+B^XsExXz5m(Lerbyq>Y_838dmPZQu@{D9VuMOUb=xO>{&-Z!FRF
z7UN9lfF#<=$|ec=bdPb&>Qhs2D|pH*MT%*>iQhf!a#MiFkvKLm$#@#yxUy4(`-BK+
zM0Pm0WgN;o1!zb;d7}aY>0H>_aMJSPrf|!|BHFTms?)eXst=^wzcR-X!B2kqrftl#
zpf9A(68S{QB1#<oalQ=)hF4s00;nbtrhXL!Ex~j@4vyLLp9u*G^5B01yW|If8I|#N
zj-Ds4&*a9J<LT^*s$I)gQNRP`0a)!jFs;DbJqE_aGd^A|WbIvvOSjzyS<{TMKb*Pq
zZQsnGnJ|%smd+fv0H6YURTV(`PP78+Kg=bkWYBFibbJrL)X5fWk2)8H7L+JoGPle{
z6e#93ux;oAMl+2haHTa+F1E)BR7<u^mpiFnSY(0Yp4#3l*LhyUplxizGJ)CYlvH#1
zQaMnpH1=yO^`%!n8}gKh?)TDj{JWwN`y0K(UFwhtH$tM^O5uuYv#W8YP*;)8(B=Ny
zOL@ZZy?wIjw`j0sG#GPH<NTtXzgZ@K-uP~ht54|@;oo~90B1@V)|AV_7M{U>J+x~Z
z;9WD6MNm>gg!;nL{()a772*yA8(Y<hjW{2Mya~%{fPP)`mVY}a<3i|Hm<p~{9V(=T
zGsK-i@}*;)=bviSBHV;Hv4MW@Wk3@Y9o!YfTJqeuylDJfC1+cU;`lFaPqI5oXgOeH
z<7uk1=<F_a81!gut_PWm!={@}ZeG=bjNNkXdCNWp$Ws`@g^CWjJX|e0g7>L>{7$f*
zJ!O!4QQq&bH}<rwGn?&#Iv-EeAD?zCnbL-Is=8VmVAgfAjT<%$T_*{}h>%ri!ceG3
zu6HFnc-#V&L)JcW8IkNCOOM{-yg1k<0Z2d*dk&@-@Xl8p;f^Gxx?H`??qHK;LP5sQ
z?iG<nV%hip0KX4`?kgiBV@uu@w>jTLYBvRa0{OjO7e396Rz?;5CB0q8fKC%Ih3I4R
z52=&OU0U73V!ytPXC$51@>pDt_w$UrvZ*g0*SCE*{Yx5741xwUZmi4+vSABi<{XIx
zTOn7oxxCeDAW-tEYFmr^cVVWo7|dt)FM~mYyJqembf*-8p|;)r=2Ti7NGWj`P<_%I
z+sYqj-BAd>F+%#%rskJL0rqHh3~-z5ny1Mc&g_liUAOd+;65PwAUqXelCiE_RNxaT
z`M*x#duoAJl3>Rs1Dj&b3_kLMq^bn)4^~~VnWj#YlCr=&Sh)-wQAHSF4B6J0F1i2X
z=!(8JImr_8Jsj9j%MFOKvz!>Vp10q$&>dUbj(4(4ABYDVid5~_FsOgbnQ_$Aw!2(k
zX_|CJ*Hs?cp#e&(ttALp4&bC_3>|m`{6*5#vq23-NwQ_&RbFaLd|vluk<FYjC!b_Z
zG|NX4XrJF*-Zf>>6;(y|;YShh)=l<V?{B=tvo8RNes>9pFCGZ*P8q?(v}}0N>8uUR
zWK>KjppsDhb<bB)-0Hoy7}8UGOBvg5#%ke3fdu{zcIf#*P%(Zz{)D=a#ybDGU6*>1
zjoN9rD5m1j#O0&(9BQuQ+++etPWOCh|D|x3Bs!F?Y7>>JR@TUJ&dBawf3BKVN#vqy
zH#QQr8y_9wb7odB<66{MS<zV1c~6Fq^j$~4wY$n_;YkchsfzZgy9Tz)1tc6OOGWCD
z*m<+&sS3x2cDbH!Hjm0|uOC>e#KmSxpFi4+ZCW&nEXlMLyQ8|0D%^YhM&zQo(`ISo
zv)$PBYVD7ai)mutYo67~KfAT?`e=k&HI<YNjTy7d`AM<*wIyu7_b6v%IA<&t@F_iD
z1-`EE>^5G+1>0Vg>&a1M?9{M~tN5BY1CGb6w(ui-%+V)&*Q$x<22wt&irQIwMzeja
z1}D(h^yo%s^&!9T?UY2pbZX(Qd$VFWZU@gY2C2T`p9>Wt4y{2zBNs3*2K+W`z&X${
z?m1=Lu%1Nn{bcx8tqCCzsP8j3#l)TSnuHA6=wIxJd^RHA6~ea2HP;BmLp7wJuz$`l
z!9uI%%c#kU2m)n{yi<=*roaIDDBi#r8fYZujKw(8tNlS1O8?V$QuO?A%+KKhg6b|R
zxeAPtH+dh*4oJUD5}|;CIB@xPB&+@bUZP5ZjHIM6SWl*<3V1`8Kr7{QE>EYpaj<P7
zLsle};b{hEn=ArMZrR?a&;XQbWYab%j)?)#GKqi=Eb91^h@lLb^_GbYI2(6sP$mSE
z&ppBB>@1y%lC+!}pwgNr0m%Hd_DaXXG5`T5Vi5TL`Ey(6)3pcKnp_|4%iFcuM*a$(
z;JM#Mz+BIUT=kJ=L`ydR+C6DrySGJCRsHu`cswmpf^o~Q&a~P8c>2aPZL~>lhKVT3
z(AmciY2tG8b=RN~^Z44~%&fl^xjT1X#PeU%$Y-bT`M>Tn{_EdgFJ*Pu1yog?IHPRl
z^E8HV!x=~=M&I4js-^yZ6%N$pSyj4=B8i4@+x08sqq8Gu9=bpJx83t5dEsewwC<m4
zq>0I~d%B*$&Mfhe!=sZid%_j<sgT7MT4Ft4AhgeyT^iaZ`ty4~DwN;4i1sP4K5gB_
zzd5AHy*Qep4R~vi@KDKjr<{dp*y+(Dsw+TW<XbExnF-G^%(`5?Gk7=-0+siCOUe~6
z@a}Nv{YUXfWeJdfuFVQ-BE#)a>d9-?`jyHoRC-JmP=Km?`raITT*AH)$}SX4_jfwQ
zt88HZGphw-*92o9Ibdz4#MsDpaE9{)`glH%@z4_@{c<_X$`$ar#}zwLtgHGG@>6cp
zsiA$`l=AUynO3h-?)qs^(eL@DJmu&P$&DZ((J!6g_u97px=-wq9iH%%hwlzWCyz52
zvwVi5>`fxE-VgWkwL$yE;Fj#&>`d52bXTHi(En=oTgIq*>QKU&wm*sSUdz{xI+w)v
zt?BzSFInY;Esk^%M;U4d&BG>5A*a%Y{@~30id)XNd1rlY7Qv}08nH3BiQS3y*JTI(
z@m=|IdtD&~Rw<R3=`;9c_xHN)wUH6Skdw@npFmf<M1&3kX6;5~A>hK>Hut~e)bo6W
z?!e5of}3GRpY@fY3r0>!8du&YOU<CWT*j1}I)ChSl);q-Aj26DlV-dOPy)jSnp{dx
z&{L?9gE`>{@yakvsm#&x7(balkwCdFAVBG=HwhWIEjQYXZy)o&^Hlk6fimy@Q&pu*
z!eg=Zj?KuNj~~+FakY!Qj38>y67Sq6^@~-?JETf00*(!^V$oR_+aTohiudUfWCzl-
z=sN?BKY7>*;0|aTast!hm8iFV-o73Ml#OgYX32^i729j-9n(%S6Z9c!i26@Qv^ftL
zLYv?}8^+gQeJCP<fG|%bT2f@R0oiR27*WcAYLvVOjrEd#Cd&}`8PvXykk8c4ZFP-<
zz)FGt#$AUl|64S-<~kPtaH>&agbcVWvuoa^wk4qA=%6gH;^_H`?3JT@L58)oWF<nO
z|3T5^pfG4^Qrup7hl}Rlbxbdq0qfgJ%D_+M^uX8JprM@>>L{RUCXZ8-@Zi{sv|#7h
z&@jG0KEaSl>C^~hnOVX1s=+`i>@w}?bn?D=wdw0`k3P{tUo;<~MC(?5aKGwl(5AUb
z)3K~lWMqDsQ?7C#QYS3d212`$#eqeLPE`aQsEA3l|75lC_y`(*L$|#vn@)d!puy9K
zk~53?x*=i)cO<D)16xK^`USzXH*pW=x}9u8=TEOqlOXv8M-r`b3qyBZVFWLK&^DOg
zeOr`}Un_feZJEfw-Xm3QlPQ(*Vn4RC*LnBLIEFYQx~=}kGdHbcO-(njID5a^d;a~E
zYcXxSYMf_)xsY)@k!<jA@6OOmXiK7TP`Qs$?^|lFl_@0-n>ie@2`ifT%oKW}hSVy>
zrjc`^b|%+`W`|VI`L&^O2z3Q3Q`)#okxLE|l1i=<mp6iV!}&#2yZ5X6*-Sfr`aMzb
zpYyIcw~^CcU8C*X);9p)@lh&phX*d=zk54WWa((Yf(orz8aDSsI+WscLSl-XI4q06
z_b;LBaBx5CU)9R6sZ{sD8)zg$b|_8eU2y4g21;Hcj%c6&A{r;pFr9TnuObN=Zwc%i
z3T)_Qhje_znOROxuajJVf3%)SEbK96rl$ix!E~bEmWQoyd7ncB3`&<P(bVW8Vef9P
ze+fw7R-g`ylw5Hle@fq%cH$$g;BUg)fHGMXg@s?#VdFfvBY*E(%`#f0^gvX$HT{v`
zYobG(^g(EdXcj6g)8pBp06p@vC{4V})o}&Rc_sbS*EZV;#SbNs-NEq?licq80dtQ^
zrg0TE|L=RR1fSC+US8d#)DR&g8JpF+)!fv3h>-TI0s!pP7TU<wrzi2lJ%7j%{;wqu
zx2)t*lRW8HgWzX=#K*!^XC7tT{lX(qnFQYgqXSTm64WCr$JaEsE5OSS_@yYY;p&yh
z)NHV<0<A+4zkn20le3TC4c0^w8Aba4W9cfO!T$dCn40b}HQm!~y1N<1w8`max|wdK
zySq(yPB+ut&3pa+uY=<p_2u6CiRXDf&t;D<LLn0H)3z$d=wZTLZYk#m*G1<L-M8p!
zZJ4>Gfe5I`(<f6m{JuBBE{}0AF-=(S!0Hz$K(=N+SX&QIox&`gnz_$u3#zMt%_1=9
z5ftLo&Ik7vRN!~_%<uQ5warSItadoLmm(x7<);_CpbgPI?H*S3@R{J=mN~IIx3_iY
zZqp=ZF|Pk}Y2+TM-g+liayY8SCZxb<k;e?3PA|*2g;}VH3!-z()Chfhk2B7k5;H+a
zz-xiB2ldI^Dq&hM5UIY;KCfSJrI|`dfl10Vq>cgN<aaz**s3hRu`YkX11yJHn9OFW
z6M-*l=NY%|j;4v-KQj$NC<iepSDFr1<P4^X+na>>_79sMqvBu4A|=7!=sid|h`*o&
z!cf_hnZ<C*G5QGn#uY`7RSQ3!1=~bTk~fabNLp1uZZrtbK4JL$!0x*zN#>5o9C43^
z-BXS%q5@i?_>;-gW3SKAV6mKtECW9T@d{O<RR(mw{f^Wl^d^$C1)@`s>WcuXI0BTf
z_3!<$%mQ)6tLl#)ITpmR%)fmsqJqL<Y-->{;4(>LY2ZRRbzt^LMWV(Z*xwjmx36u6
z7S8ck%20@Z*WAyZLgFoB=eRxFhve7MT2izh*rxz@p1hpz%iC5d7!MC*(&+2z!MauM
z**VQ=BnOlpY40tfcxa}(?b44~VNRkv3A-gwewVrNjg785QDmfJzRz~)IufHJzY@$S
zYae;vfhs*+8EYSMO2w;+zgf6}({6kD<-Exyfif2|brj?~>@U0QcfZ@Z>l4b)uX`a6
ztRi)}?w87DfAY-#h+$oBf7xfSW7RUIQI_z#Uf&VMfKN6)b^neYfMu{4?EW-v;xfLi
zJLW0CajM|osmp!G1(yEQzj9McpUQ&o9HT`c{hw)Fn9rJ)wEFGlmic2!BSHyM)8oIt
zAQXyX@E~L_jIXSZmb%z^#NU{O0uGX&B8-$Kpv&v|GQl~Mxu?+m%Dd&WKWbu;<LpTZ
zBKPCNUF2<7kF@(=ZSrhf_wR>LUR#&Nsr_*S``c}0bl`MwYT=0D5}M04K7`aH9X{^&
zBj%s0KHG0`S1)r*Ke5{_Qy8&yA#4@C^}wb<HDoh6fd<J~3HjHh6)`!vk%W>9j&!6(
zon+BF40N<gQPd?7^h_$;9Q&vO3CPX@L42Jard0tncAXz+-pE3fA!=xyV*8&IYsBzx
z6#g;`HEtSz3GiDdfh16k4X~_6mkf&itUpiOh$iQvqC!mdfjxd<`Pv~kXAfx?hEFk-
z?81`cPQugCt1CJd9e0G(=sm8}ufHGR760M}xk=2!xGdty^~z?QlB#TyL$NDzBJ9Ft
zVu+i6#Kcs5ll!wnFbF>gRZ!v_tFCoyX;XmCfZIE;Ui`s%a0O5Sv?E9#R=&-`ml@oV
zFsM;-Mbj$OrRGeY{G^%d)H_(yLr@rHG&H2V7Zl(*MP9xb3l(zJ`(ax8M}88p1k~gN
zt464VWgkD1*LXPL5ZdrV3XU?OsQz_F$EmCWxh#+X;wIFr2o=W^e@xZ%R<d7<<FwGt
z13W<Pca8m(Ed7a^Bzt%nZs@^0-!@;Tg1SBv<F2F1$&+!ExB6u9MK&brMig2?7>i!p
zteJqPO{a-C6ZF89rMm3=8L(<nm;hDqFFXxeR1^*oyfGoh&##qUxqM=cN9(B6_D`Ul
z0__E}*_Pu{L>elbJvkbt0d?b&_9h5^9J3~XL##?3ke5wg?-?XhmV?lmzM<DJb5l99
zvdaIYBBPpZI#+@sZ1~989oqS}{n%ZtsP>io`1;DfNevQo3;c|I8*oN2AiqhdS0l9g
zz$cW*xozG(N&ejh`CYaP%!*dx{TGEn#1;<4IQSwZy|wmm61on`un!V@dT{<4h%tzY
zznHsG%1QnF^CB{T;jWnWNbHg3@+`$)Mqd>a2xaPXaq_6}cPoJ*qKWgbKAfEj)38=r
z!9GL%4FL*8-Di+CHGWpczifzd5c*4Jt~hl_FIPn-<a|hid?E!3fFl3!XN4eI0kZ%g
zhf9$?*hu~QiH%;+BKz0TBqh5D4moY)=lKZ$W`AY05B9)T`lrbAV#*9X=9pC{|1r<A
zEJJkXxqao)3Mw3SpNFU7Z&ch3Pa-X=;?nC~%y4hH+nh|}e!XslKpe>~JjM@)hopA}
z64b#)G6uKfrdm*7M9#<MG!so89YZc%`Hp7c6J#6-6sRu#J`uio>d#-l`hNeUXM4A@
z^U#pCBctbMLn$ujb<3o6Setk>^KJu9Rq+R_ud+Xyan;sWuQ4UI*QoJz2PUA18BSQU
zZ75t0Nu0$Ii3lJ`Thm`IT;1LFXh4-RIDO5nEayF@n*WLp<(nB@JJ21Adh7XTeGD`3
zY;X*{IgoZYx%+^{(xsBuq04v03?47~?wina8j9v|oBNViPprUtgv$O$_;-%)dL_Zj
z9c$F+C|LXessgEZqSTpG(Ds%eWK%XAuaY{($FgW#WHw!VejxK}Q-sC8%U0E&_tpCu
zLMAqwR~hy`*yz1?NFE_^#AlNEE|jvjGy#tA3Ni8DbHh;UH#eZ}6=LbKXvpo4sEW>a
z)BWYS1Bz@}bvMMC+cue_Vgd9stLYH2C2dGlp+p{!lyhi+!$6#cE@b$t>jF|yKruf$
zq(@e_yBSJ4m}C&nA(rYEmD){Y0t?dt^Y4V=(*(WH2|bvV3{l!%aWo-@THtG$&eCh}
z&;1^#^z@+{Ep!?C$RlSa?@*58v_V5RyVmzM2j%m%92N~o1oKY6|M-q0_@s#@zBODL
zV2&FgZ_{0b``X&^$}|Q-;4bsVdO#Pry~TF3%n~kAaF6b_f8DMNC(PRxM2R-24T=(r
zH{b6*`I_#)_Y_*BGwpnfcFj-$b8ta%%U5m^Z?YXDid+`?xd<tkckDyY`9#XlXuF~;
z_PjN{>kXC<s+e~_M*VXLEtG*!R=hEy$buLAQ;}#3KkSHy*!gqb%6GGIxkuuwA`?~|
z|ChGWro}DY5l;ciQxHL4`gYoS2i)V(XqyeDw{+l$f3T+ErF{Uc9OR4ZHSdrwd$Pi9
zt-;t?+*!=9p|l1Hnn2AS#DkulKd3m&kB~H<f7YE$B6xsPM-)Iup2>-H-xU}d88a;;
z1rC39^nX=HhjFnVlLf~NI!gDPFjb0t0(3~UsNy*lNnk95;u2Z>lV0scnl~*vaf!%p
z%=z^(EP;<kGITuMHr5RmoFzhtK}L~OR#`MgehPYX>_}3R`t<aE5{ngt(5h4_N5kny
z7Rwzbm5atCF^g&nvCJfe#z&+^D7YMGA@R->Sw0F78DtuwWIJ)=XhPDO^EPOSa4LQk
zzibe45^AKB#RR2|wa!jIpGGl@4Px8W2;naaDfUUU_3Gz9F{LV425=q%31co<ESgf0
zQ*#{=sv^Gf4GiL>l%F^tjQ0U8a&4nZ6-ytO^*x4dSa?3bb9d^hRX77~8_8~Vzd}Lk
zkt%1?%@9RV;SidS-uj0r{n&q@K!XA+q*WM`(@judhzM0=B7*+HM+9+bFVJo{1Jj=T
zyTfvE=c*FhFb@>{y9T`=qLVS2E)~#Eob^NCSmCURK|~ua5{%4Eod1(!*X2;LJa8hx
zokD2&{NziDyD3IY#HK#~14B?53sP%(-~ju}NW;M#FBN+5dw;rX%^LRvf6th@lPq{>
zaW*QPnF#tlo-$=A7{zlg%_Ao+U0q{PhnShCS?x}sxIgMOC@~@$h34cmM{Y(%gO>X{
z*?%qfv6$4ytdrK@veB4YFRKIcKbF}ioZ#9nbIEDk#bvVPGTxX;(lG2`Bcfk^6Cau!
zp?)%IQo`+=`Gks0(C9S;?IXU`@k3&!h=1GUYi+P^VpB4U;&8)%ppo3$cuoblvpI*x
zEuBDqorci?p`?&n**HJ@;7!quHEu;`=p2#hu`Jy3Y}3A9XWY+gy2P8v5=7I^1b)zd
zB7b1}opG1%p%rZ5u5dD6z8Wr(M8pRWhJNU$dS@A|7Faq-n0eFJy-vrROnE7&m_Ht;
z=%@d707?T3J|ZvsI7(^15ACU=Z|2ft`#T?w4*q`%Dn1I!`3(j8sYw5i5vC2kIiDTy
zWK=h0Yz!alu6`z-)HF<65xU|G`o-kO?@?l05r||6^tx;4k_!=Pn(yEL?z6~uF~th`
zZ|NB$8nsuyG21!E-GU)#q8asfPG=>ULX2_rjGjSp(e<lgZ;^7HQx*KH;%3_L0<yAb
z_tlD;MK=0~*ZH7D!7)buD9{&4+QNumru;|g3KpJk5))c_3JnpuXPh*)`9yf+XkCn$
zU%R=swmmA=UN~|!qq!piG%sXYuD2c`Bmg10{ivNqbZgO+8^F9Bcu)`I5MG<wNr!LY
zLNdb|XLNSt)vZqD%iD#Ah}QbhAPW+4i_`)P=F#KxHccs-vQUQ-o!GGp+&s)y3~c!U
z3KMNB@V{*Tb$0<1_uzo4QxFX|da#?fN#R#j2u=ulfG4CXHL|ZZO!paW!9G>UkA4k)
z?=m?E_`Ea3env@GHOgO;J%2NVl=~o}9n4w&rRfU7;fWe5#CBFFq04OICv%6O;<DDB
zzaxknLtdy5s?_HKHXHHn9u2}>c&C8q4w&sjLP#ufb;|W&M3urCaeu4o1)mv<CI#*1
zoh3&arxZO*_m+%Fh?*qF*Z3JzXs+wp5h)XM;?honD=jFtDl$t2RSFk3k|Z~h=7DM-
z^LMt{7}>$>7}8tKsxHI5MO~8+)VbugVkayC{?ji`516tKnOa44q-WGIh@ESd=$Keg
z$yN1~#$=m0(Hk+d8qo&9WU)-1Eq1CPl}D5j?Q*UF7Jg28k_)9+-#Vt~h;iF+!cRz~
z<%rSGX86i6Eqd!m8LuPNA}H#9WUH>SF>dKOqxaeKi!dA4EgE`^FS4N?C<64mVZIFG
zNP#-{<2aVT4W;xn-(!u2ER~y1J~?WC(CyE$t}Y4?JDxAxW^Geu7l|RgKm8TA((_cX
z&$RNGA)!9o-1YXm=8T6@Jm(2fU{obAiu5?$fJ3_n?F%&yJBFOMlNo56HQnbldX?CE
z(|E@)`>1fP%MKPCQv%|=K`pTN2sf1kiR9IRqGnw=ZjRo|#IKpMrBOCK;O;PX<!>Xy
zaeC`y_r7sXJNKv=fZ$be>$IDc)G5f&%Ou5krb431pmzU}{d3DR<zs~ME84upBL1Ja
zW$CrPqsd;9bHOf<!j5ZxinX_dk>z35mLsz)6UM)|(DLHAn$q%0VE$NW%vwhwRn(tJ
z!)0%2yLiNOH6?L`DS2@CY+b=2nkF$=`mU0sTTSY>EnKdq(qN|gH)bX`e2g0v(M-by
zaD#i*);I#>qh%4?LfcTST7U0vd5%-Y>1N6Vp<OsdF{a}i3G{uO0oES@hQn5oDOsLO
zg}h`iDt=0DqKKZgASE9vW6@PIa@<ARJ=%6nZdSyJfiipyzDEZKTwr8F(%w8a)dda?
zNK0i?ynnHKVFhvJR^mR(4T&hY^F~{*Uz>0(8QFfqNj^DY+C~xHh{LL$Jg8VYz`wVl
zPC{1Y@hvR62}Vj0Vcu42{v%T-L1(12>mV?jGP2n^bHY6P9kmCxy-$7tRFo1@@vfHa
zFd+X5sjL2dOS3B7mh!E1b#vyEYJO3)Hjj7-BKgH1=u}uy<ya3mljtAs*Y6nTdF6@3
zmX<MxZ(Nx%EMi#8iucRjbq0EuS=E_Rb|w+|57eKZHk{PFq?89TOGSqo*_Im>E~Fda
z^`i0p00_vLw!g^`2I~_9=x+~>kPt-;hDVw7b_UG0-$n|Db%#TWl^`;x<vAB}kGR(l
zJk*NLEPs-<?$E-s>z0T>_Mmdo@}eSb%ItHBFR$d@WekFpn^#Sz2|G)WZ<AT6sPj=j
z&N*s+T;DKaCyWUU1+WD*tmJ<?<gmlDScovkRb+F0D4p=o7OR`-#G1~ovTg7t!30<Y
zglwIL_GReP#PG9jKH!yd>*3qwv7T!<*{0E{+!pRBKOWa!+%Ec&h;+d>dpT?hTh$yq
z=8v^STzB~N$nEqllWZPkEDv?v8GR_~b*2y(<52LQvpH{BIyimqWgb)Sy}68aS6I=~
z-Eg<`*Fi<)rDy|JPm#r8bg{Rj@dXpCW^Z3R6@)+BD*F56QQ?FnJ1bdMe`OlDYg%Rh
z1FP3KyAHlj>j)-1GP9|Bk`-8T&>Bo>Th1gNu%2l3Mv}C(^8y3HyZb2Re@F)%Ett*T
zW8sdz^Kvn@f+q^2zLb_SH=%ei!;T*wCpsN;h<JpiM-QK*A37pQlhcRp7MQKehS3gx
z$V3{3rc$d?YhJ6}AM5FxbI0dp!&PQ~!|4TA!0=%t9SIvE$F$*9RLmH*MCbqVU^Ms6
zTQxBnmy1q!(h!3LT<U?9^?^wdYS?^ZU{SvtX73UHK@udS;1Chxs;tsDxh;|EQFI>1
zx6E0xAW{p}9n(4)M?9M&IrxB)g0!vjR9FA(dFFs3lH7m(=VUKylQ#`3Iwp;)ooWsM
zgFBOQxc6=$aS%0{9Jq*4Hn|-!VE9(ZZSIepS9JDJy#uO`4JYfCKKFX>yn+^u^d+_<
zm&(}<R}<f+*?b}j6nL+TxzHAFTfd^Xc}0QnsG7$=GbcIV#XbJknaC>_d_aTRmEWNs
zng3@a;^oMzwV5Ac#oX;$n#{m>5edlQXBcrDs=~OwSg7*<rF^MQqnKU1>dW%C;wXym
zO47$N;Y?aYmaO7W_;4`nkX+LOD@lueX!?u1`-uPM+3mLaDcyH56VAKP)Q~l;#Om1D
zk-Zh7egO$aQ3A6Mmf1KZPJULC?Gpz(a?96CMO3oBUWJ;kJwA?WmFw3;p?1!8kE)sA
zLfd`ht+>kA8u#}cybW*gsWF6KrUglO>)mh0AE7wrOVZg@!wv2xBUJU#ckc<!eLtxu
zgHm4ny%u|nc(Zq3U@exJ)r-RQjU?U_tRN&?{g{6^)<T=px7l3JHM`u(QO$O721Li$
zAnCl3Gk09&Y2@6kdmT*TaZK_;k>&N)PK_$Q-H8_{npPltna3T+b4F}=!w>f^`|0Zx
z-pbE7Pq*1YsbE8galNi1$ly1|DDCxx6fU=lR4K@$YA~{jL54E?@N++!Ssf+xRzaRC
z_C=QU`ibY?wJ(y!#1oji*Zf>Y0@akI#2Rx-F3yrT5bxZ?*<1Js2i=vohte>oz3%Q2
zoVT-a{7bHl0CF5NuEbcWGMcfeYVTCWCXD5^lQjbILA(CXBHjhv&7wV|b>CPj@c8Na
zDM1k_0HsjN9H!Z*clGkLQ$gf^DV!0&|2yHoRwF}j5*`TlV#mk?@z1swcw>@yz0QWg
zc~Ikz|2uf{X*p}F`EfXEDiHnBMge~)f$9tL%SEnJG}#6LRPa!^!@gApe`@ofxxtjX
zmHocK$|Njhk_hNB=#=Mqmjl{MD>!B)(TTwSD8$I1uvy;oS{POQ()TAQQU|om5i%rF
zR;;LmezD2e1_X1==@fi9tZTHe;8hEbP0mtaJfhdFay!co(&~bR1F$%`tW$^o0?o_$
zf{W(!pHepleA%4~1C|oRV$*ukSf*Jmw&&?^6x>=CSnN?SYINQ_JIb<Xh2MYgxB=Gv
z3FLwE2M+#?(3n1;be&tsUM(uWZhl<3LRhkxb!w#`7{I!HoI^|f?DyOE8;gCvf=Wo9
ztX<#<F#~+#oW`c%`sR(owePQKG1#fUK{?&*taQSZ2ZtUEHpR+)Dr}xxyVV`neJt_O
zD6ar^8N{zCS+Np2tf~1rhigWzcv{M7|71aq(_Lu7liBzn@)jmn`@YqKKnUy7F{VY!
zwI1TSB4uXF^iL6b{M|10bXvy4qm|><=h?Mi+A4npThqCB_w>R8gb{3x#2<vukHZJp
z4C;~NNFKe1_%EAVL^h4Bqv2L*OtgF2E=8PmN51{v=HNX|@SMe1`j2g`=i#;0U<s@o
z_T56NUo%98*niCR7K<;DDClo)IN}>;ifjriN0rKjmkAVV@q1J8+no>T^74pt*7%3N
z8Z949oNIS-iotP4G1$@RZrtrd{i^YLHZ_W<6^u+?6ej_+j*s5i-5GAgc1Q_|>#&oS
zc1ij9pI-RZ@tv2e^^^i3K~+r8r+<y5QrQ=^SjIfERyF$tLd4kzA~s>!crD!QvOTs`
ziP%IIbk&n5wxwT$2fP2dQ>ZtXFA_q3RUFud(M{r(o2a?1&eh`iw0QmXd97Cz+l_v^
znZAwHC9Fly>Q0dm6Ucrpqr1BqBXFH;QKowv8)ajX@bg1e%j(TU7VU4LZA2DtZk;$7
z&V(F%GCsS)<hU1jL@NQ{=hI)c+nGnUvRZZ=UgK#v{asnEqyZZ;t>5gsmRg0ZtCr{k
ziT+lhfDhd0Tg$C`ACYI5rO+EG<hmGy?1|5`_?;2F&VJ{+Y^;`KI0Yc!bAt5AIViQ|
z);vlei*wC*l?k_=!i~g^5ZRn6N~zk|ch9opTt?&iOz#L8!e#hs_$@H|K&D~?2@}*Y
zHoGesuO-WSFhvZ0*xI(JRW07*%-+s8)>URNTQrk(IsG|EvjDmOeQd>GY8uj+n6?E-
zqWMX<ZHU^j6Mq~S(=@u+#>u(1$(eA-QR|XZ`|q*2Iw@#8c2t6&7c<RiwpxU(*QS8q
zxu{-F>~g~IhH>)^G2&Itmd--=xaywDe>^cc=nj>$hINZ;&9odzM>7zwfeFZ$5Jf*<
z?vJ}MVTOmqt()YHo(p;e4~?)r|2RXxXoZO=0=-j?A-9&07UGhr^^a<;9k13a2!Mfy
zptdkMh9%I7SFk;0`WSUrggi?dP*$j<)t#Iv+W9-w_r2I}iMxC3BkHE`$_myK6)hTG
zH1K`J&o-RXwkoqL*4lK<?`=<M?++h^d6}Qm{g|)Cc@xwm+GYHA)Y5-Mf|_epqgRDZ
zr!AkL`TZ^3b;{%XAQC`s19z@BuYQ8+nSATxe;Vc3F~qZqG)quq7#GV;*}dDq5mu}(
zB7(%t29OuX)%ux>`mL*Y$@#*Ic8Y#$jhUu9V#GV<#U<Cxf0y|N$7|ZmOgPnXg`;Jh
z*_Q}G4g>Ff8P}xj42skGLWMRmsh_p;2Vn7NLH&UvtXH*t-M<UdcVT3qN|}wfWICI4
zP}8t5_fahC_xL$%fzbNiBvnzBhues!A{I18xQSFYfTD;>hcS-VjJ8G5-s72Tl?M0O
zl8dETkkBB@UQNTAMurBiv+3beW^&ocpi%}LOSd9VFdFK2kDh)bOmkAM#LuhtU(eb0
z6lIDAs(cqO16)x!9XuYN>;s&xfd`$3>MyxKy5@;rJ#%8)*f^T;X&LlQZWb*VC%O7u
zVRK3J-e)@Ow4K}BvaF(iCeT-Vy5N`>81jmkk_JvR*xpM^PT74qc1k>ArAo%$ukdi@
z-`U!>3CisbB?b4H0PN1Qg1JwrJiI=Q#3Sf+cg7en$C!}B$S>&Df3F4TPHV@Gz6X{p
zRce1iWo=Hb2frY_Eso}vC>r?0@)bE>NvS7Y9P8^DNRWM5Kw(!q%?c`)Bcd!%nbVAR
zZp~ndv#8UA0YS#5vaVOCzIF3tH)PPhuEQ_J;O~HE$#Z*N5p&c4)9QE22UpZSx|;<$
z`;=iPO+$ybnZdC4qb?dMqJJt8lhYvH@(U<qRb4-G6D(2X?4baDQRG$VmsS%^8e}*;
zB9|6Af@OvH`A$aEfI@kru#;+`k1WxO1i1G4lvte$8HEJQn$#)pNSUWGMsTU8N{kkA
z3Sq!ANv<se$XH$Tz+FL?B$^3#WG!ifGar6h+;y#h8otjC3n*4fZPS4059pmZIJOf9
zF*&vHdj|HXguHeIikNuB)mU80cm@9xgnX)3+Y{$QXvJ2>t@ztKdtwSh-qkx}50feX
z(ZI^l44A1c>?<%v<bvmKSkT;gS|E9!OdHHkHt<>e6<IV1{!dnVH(bHRbXTf8b`GrU
zc3*CJWK0m;9rmI6&PC6gf^+w@Vsc-0FA=l?HY;QQwnBJa$iKXip1SMVlz%(m_q2#G
zdw2eq$@Ac{8h<2?F>pmJKK_=EU;rD}>AZ!BudDaB_>|KfPx%vOK$ee0*v=D`e(mZO
zsNu~^k)F%TUl3hLlM)|WIof-q+7ToGTeBK|yD~|q%G0&_vN1*qkkK>Um)pg}qTUJj
zD1$rZd2vK^MgO(@h}0Z26K5}jq?99=tFKCM3^TJ03ngdyq4k`}wC7VS`J7rG0J~t&
zIdHP;?Z9A#18APITC<YN=HWU#cNJX&hw&}3;!%X@cRIK!8zPyH3iQe;EedJBEw~=5
zX-_thMVEnX!@ts6Xk#9v_$GSK^*Lo;-L!Ar1BXc!G=c42nRSEH#^GMJTOMi;1T(P9
zeS--{I_aOnQAN;J)7#rTZ~|g$coW)Rt}{-1g0mm*rpD|@bV<zd+l)HoFcCvJdW{=q
zN^I;B)Ry?awhY8=b9+5(mD>P{^%0^ofdt6p9z6_>;oq~zf5E%ttE6F9h0`J87XqoS
zeC3gS=xH=!==nK3^l^TJzO3HdU2lV`Jd!|CDEOK)(3ca$scpBRYIkdwcn<aLU8oho
zlfgRPV1xUQ+Ll%o<FZAa?c6S@4Dy7Vdw>X-?ZyGw>27_HcU3oe3(qdWsYGTe2e=l3
zwr+Glf6D*`gEkpEgNUbdL@jN8^m<2-jC?h@ee`aD#_OPm!KO%IU8Bu@cd>4d=Kz}c
z?d;B9dxzC^I_oe30}8DT6k~={(34cEglDb)hWFP2c<9^v%t$<cK-s(>ig^v|<&pTZ
z#{_&3=S@B3!@Sap^?(HOYWNW>UCQ=sP2`RsKFy>W-lB)mP5ji6k9QAc<A(>$`xSqu
z@f@n%^U$UD(Dz-d8^}R`hhvOzuCMEVxDtIWkPxnno>zwW$7J#@C64au@-7zhbvIR>
zDLnCQGAoC}9m8Mtm#xna`gGRD2t1C<4ov6m$Nf6hd*x3R?cxx^v7V2X0^QBe;M?6U
zKI4ycsDN<(>1jNF4+*E%F6;}J=UG3C_V>~=acOmwe{-+>6Yr=0L3k!G#85O~82m>T
zoJS(bzA5*Ykq%t=A7>Rb$C|}r{BY=sig4U*;zM@z-IV_S0xqu3NdMW#fF?CuFe6pZ
z7UW4f3;VCjMX?J00;-s-Q8{}nxbA4Z5cFfRyiWGMkK=uEBm;XCpO;~wd^6|NoL~_<
ze}TL}jEb1`h66E><AnGO!rud&8E1+idAW>#JO~`8*+DvMmWzoPl9HJIB`8hZ%-at`
z)k_u}z-new4p~{1Nd@VvVnCdTlx>O8Mih20nlEF{`+JaZracpYh>~fy`mg!K^=Hkt
z6qRVPNJ6n+6G*^70-(x`a&}Y;EAlvfV7p6?AeHpsfuG8m%s{as5fIE*G8)rml+Brk
zNA{p#_poHf0p?{j4(oQIpW_n?XyHL`5f$ra(+$w0TO7X{8RPRB-pCR#$?t24p=&@r
zk8^oj(KguL><~QF15ZAcXSlE%;;LT!1<)ii5ktn!uBhS-dJWTgZh5SoN%~ir_45<<
z5$^}XkZ28fp09UI8BV|KIoxI6nQL281lK}$QDh%*CIcBXypMpGh>g<35`ue^_n1_B
z7l4<=uh_~s%>OR^`Kp>HZYK&@*}X=4UlCMJI(Axpsl1V3_aqE|X7t8Qu0v5YfW?43
z-k{g-p5J3%_cNOuYixk41ht1LQ>GW}klkB8yEF>Wae@Okj`UdS@d>BCc*E6O{^@5i
zc18`;a(Jp0@O<>d+z=mN<NL5cMQ5-1=xpgNw`P;uD7eB1AgsJ(cVq|A<)+?i$P7=M
ziaAU0nLly8FtTIIMIEaVg)-?e{_x@#q9FlSmGui0^kZ0Jhlmk*C!8<?F5~Nw*kyL$
z>kEbaA5Za@OZxp6u}%k^<jz4E(#g33f61sCUM@qh>dM)GA&5D(-_&grmPb?bK#058
zG9+wG3FPHFQkx~0izUrpL5~0i=gACU6o1lSTFCC$>-l}p@7U>!0QV_BYE0HTk-Srx
z;EXRm^{48N6jFmBz`mDVV*HKajF|OJW1h~2l|X#x2buD}y$u}s_kGmKunDMT@BG7z
zU&U-PswQo-AHztoALw7{QZ<{7Vp0~W^YtQ3=mCda)3R=PnbfQ;6ph1rjXkG^ag97P
zquY%+8{4K@@=sbty?EJupr4K}s{U&Y;CehOl&>}uftl=0S+>l&TiV}!_GF@%c%+}0
zq+-D!nj{z1|N5I?()a<WO`eO{FGo&i8>q61^}JV)R8kAQV2(rcv4@4>bY>rNRW}_-
z^o@oG&h5m<0In=$oIoS!5=fLmBo3zb<BOQ|O%$-0h6S)=Wf1ryPz4wecVP(G>g7Qs
z&ER)^NViPrI&!<*{IO`xIHt?}K;q!UXfc27R9XT0yC=OZ#GgLD^?3{(e0}tySY!}Y
zMc>nS;-ht=eO=9ee_wLdeA)GF_T90do;kPC)OPL!HD=}^Rj+{U5(C>z<K$9@0+31d
z;n-CT{|hm^%Bj_gmN|vZ9MiAwSpfSu+@XbWNsX$8E$w{~hO?ps2b}3csNXsz0~O&|
zLKO3NkBDVLV70Fy0oJIcxvjhTKsxo48cuC>YH?W91R}ods#y|pfKcUoe=VOMee$Dv
z4DeAM*8EqE;^>$xO@COn6pd{~#f}cYb{?fQC<fvAKV}b|FoSe#c?bvEDhg&Uiqs_q
zMAewV-;6oO*I<(I%Wj>sxr28A#~gcs@S8DpiUJLGA~yEK6Lx;=vqB3lNj!ZAe2C`s
zE?=sDN426WUv-7v(=bHJDb=!okkAE-Z)W=}2Jv-uQ^~;hN-(lf&OnRU`tJbq@xT6k
z7=+~+Z-fx}{X{F^<V&T63=W8E0dxvh{MQ+nug?~H*x8N&Xgpnw=Qz+^ofAmRu1XNA
z2p-tYmNUzQCnfag-Dhn=ndvl<=Ryvt*^L{0D`p74re)Jh!&u^|6_}3*iU(S$8hc->
zf*2MVx%V`{TLQPT8WV{YE#805wO|5|?{Y5?0?8V%8ih!-r=js9#RgMu@FAY4RWrNa
zK742@tDM>0NaR-P)VZIYun1N!VhPja`oyk&dpw9_<+!hf0u>q{3T#HM23S(5!_KFJ
zm9-u!-uwI`-roM~$GO%t3D6w5ZCV+V5bYC-Q;=>zeO=(<!JQfUDH^u6&(<i9Mby*r
zo?7l74gN^{P3`l@(P|CD-1h^2R4S!&42*ovboz@|!RWPSN%QB|tOj&T?q$s33b79n
ze~gpe&k1?Tb>C3hsYY;$metPMWdAxyLt4?yFjzi1m$69=Gq$)BOfKqW7){+QyylEa
zBJrwn5BJxJiSrB;{735jj;Ak2d95}o+uh}n4AijLu1Ho6AE;6cZU(r(v^JQmr220H
z?!3El<^)VtPM*SsapHPjb+g<mf=Pf2;Pvv4V9H!p5p2Q7?#tJTEN`n(+j{yo@cqg^
zey`^X8N>58T6{cu_?zNrXP+;Kl@)QTfhWSxT&qAvxn$Yg*uP7Bcu!;>Nv*+c5TRhP
zLEKyAx}gbn$oxncP#;T=C(hr1Dd(V}c&C-0z7;n?{rqsjkE3>dc=Fvf3}21M1)vkb
zk-sGTdU1kd2f8_<qd$h!Ati9q(aG-A%YE((iknA=X#L6?#tywWG~!@YchFK_$$BY@
zE<siqtEH0`{0rMcOOk8bkSmJeVm93ql(!$=?-#pkXl0I3l4>jklb}P~mVds0_hR)5
z=l|03M~Ad(+_G}v#5Oz4?;Ukl@Z2_6i;K1psQcc)+JupOwANTu6Xc_Uyj}SF4!{F1
zBW|nNo6S7%tBUy5OuHA$xmqo)bwQa$I3WQf(E}DWjjc9*9G54Dw<~pR2^dNE@(E&h
z;mTu5RThWyLr^yTO4cUwO}-+^n4X(|?NVvfz8u_uh-!K=8ILa=%s~3-ulfWQma=MK
zh9nbyej-);W#Dw-4WXd2Dzz4JyX_;c&WEJ6r*JGE&TV(gtB#u^NrEZ22~7X!?-%N$
zZQZbVLys%92$yv(6+p^q|2Csm5XJJAO9gA|6T|Swi0D8$w-%Funxw()yQ`QT=Q`#(
zEY>p{Qi+8JFa3KcqoM6~{ug0a@AiZ1o42nzvF+wk5d~~`xVpy!be@pg2s@IMqK#oQ
z$(s&O!a=V1Kf#6Y)wD?L$)Clfz94>GOu&idHH=QB4Yy;~ePzmQUNO$qr<CbjaDB_f
zrH57k=mG(TnXu~*VTGem$^6gZA__9JPFV0q5o0G%d;;`hY28VO%m7MKJfL(hF+^;@
z{@POh+}$NQrje#R3||lfKA?!n%*5#_t$VY&fAwi;%+lk=*xonQDwEm?k0)%=rH$J&
zgvDQRiK<(v_On)nDltg0t6UE*&yVjS1#!L=eE>PbYUdasK@nBP1RgVtrA6tp4@U{z
zN{bU~;B4Mwg~O7H>g!3~yuARrS}Lp|;_RdcLNGuIEPImvYt>vfg8m)F4~Jn>itTl&
zVJlA`7fr%#<_L*=91ozE3Q;h1e*5Sq^8_uas;Pbkf<%Q1JsMdWU2@hh4jCCyVUnbi
zntoi#H!_pPI1uR4)8LW`MILE2d73}$Jt-1WRZW6w{Bw8{IW$7DMQ4aHc5zG=vXs%b
zeedpCp=@LXTE1QnP=?SzvCNZDA{eF9grjydA(gkAe-sYOX-@j_@YB&249=*=Z8rXU
zlEWTqP@G&T<r5*<60H6bXJ*d5Lt_96LolMV$|7Qn8h{A*{Q<>MfHiZ?^r1L*Va!q9
z=t6=T$UilXX)O+askGvLtf&m7+)Y1`Bx%AQ!E(vu{u3;el&Z%ZNBxUqhRC%QrJ6vz
zO7vc@gJo-iY`ow-rT#T?J82XOui7seztFsq`3*SvI5AFTe7)RNawoXwB>D5imC)D$
zhg*QF=;5E~RCbm+Znlx_f1~=#FGZgFu@E_}{~xD1;igJvrwYYOr5mM{<=81Nu%3e3
zOa%4T>pj{|UaET(Q8Hx{%YhOk9GG#Y8HC9~aEP+dNpK57OJ(khp(8(1eXJDO2`JJ!
z-&!9yQVIQ_;kW&Guz*Ai#kEY9pAvRReEYedJ2XHR+zc^zc;alKhQ^)zr*ZN&eP|Kf
z-@S)YGm;X|)@K*zK|l1v4S!^=UiaVj`Bc(ITRrV7Ry8H?ACbpvqf&yHoCVZzD~lT2
zn#FP}jG%i7N&{YU0?fo3dk(kF{EsNzN?FKLNEZPE4EUdi?Ag6$U9pH?_2T0C;q6aP
z*3o#bw@(?m&orBI@p~5DCWG0xHvL{tn<w82K8Q|bv0oZN39516*hPo*AB=qP+6jEo
zD;83e8c3jsJX@6aLe4CJeYRhmv8P~5Ykydnz58a6WIg(I3uULQYRQ~`hM3eXlNP=_
zoM2t1a?tDH`NrAHBZ+n-{4=dHVL-GI=!iGU`CnkhV#Pr_lPwn?({t{v{)-nrz6fBk
zkfLxA|KJ~e5%>XQ;9<CaQUUN=&^5N-ZM?s$?n!yPC?;C#naH%LFWr0G4>oZI<3#){
zb{|yXTB!c{??b&eqlJC;Yz7Yiw!y7i#tZk$zjHTtr|<FgGutSvlG<;??Z`n~`)A#9
z>QCQ39OKVCn_T<WEyK-4sqa$mUXLUq+^8zdMD9Y{DD`E#^~9#F&UQ^T2FzIQ@3QKq
zbB|{5KjFtWz3ex1{WC4=FGySGce!?GtLGg$S-t&Hyl@)Rc_AFnzF?XxRQroKOuw^_
zm4FwlAXvkgkN@d^_+o%kXN>5x^hyON=A4rJ4vK_E8Sip8<)=`da_AKl75#p1xq%{2
zi%$%CYJ)@WGtZ@r)PfGZYPOlliP_ZrWsIAPeMojA30r++W&s%gkmIOJH_HIjWg@mo
z2x&oxPp;YHS!XzprcexH3`-A<>X06@TeGbQBugV?au$AwO&cm?PPamgSx-hPAF#Xv
zy;-AzmY(G}7`f-cv{6*X1ni_nTX%Jw4bW^J?^)Lpu}8)*m9*R^C9#02@h+w(h0aln
z?uJ{7&kH5Aj7p<u^kUjZ4to%wC2JaOHCyFLEHb@m+LQ4&i4|Y2fXfvssq$m*fJx&-
z*~Re!`bZ|q#%2&Iq^u&BYQaZxoTA>8;){|?p5}Xm<M&?`sgtqCV#T<U8O|`KC^@6)
zt^CJLLk2Y{#3yPhRgrGc#?qcDT#$>YIFtVzY_f!Le;JG)(XJn;HMSIAZG8GoO9MzJ
z@ha#xUYAr1|8qtSK~X_QeG_V&ZMDz`!3(m8z1CYrKc2_o`Q*`pn5~3}&pn{LeO*F*
zj&~u>bLQnVQ1L}}c^XC(>i^8a6DU$y2L}^5p$<915i_d9na~>G6iJEAy0}?J)p|xE
z)!zhLC}Z~7!>){9M2aKBOTS7wCGSe2{>Q9I0=-kdiJbLAa#;aLNn-?`t9M*O@<z(j
z+#PjKsQuRb_q)r6Qt4DUzcehXk>>uBvh%I=bdu&&@mmuimUQ$mvT)Ts@ldd!Fp@Vs
z598sI!=?cs=59!5&;18q#_n*R%=cQ8nggfpZnCxAr!PI@2T~SKpC#KqC9^ZAP&$`!
zk1B7W4ZkhfUA&yX4=&u~RmUZbW&&041PY{Pn>5vCDK=Z9wCeCS4!KXN0Gechz(CF2
zWH(cKX~aeE?eN!_%MvT*ZNq_Gm>G7G!ptHq%OfHVaB#sql#=Qv_L+i455s0jRz&+>
z!YISby*HyrZM0MZWPQsDwGX@ngwV2z02xrM!<WMxyjAQDyi!fpiT+JPE_^b&JT~Aq
zCJ6l3I+c@nUk}$%b_}l;u6TPFq@Zdv&34F<LY0MPx>EvWL7^Ee;jfBdW=w594(`|W
zVijFayCOHU%E&v|=nF1rSae=?d8UC=A-_9Jqfv1-vPjnbe1>Q=wc=_D3?R(7FlF(?
zr%sA-r1{kM+kD6zH$gQc`>0oe#_Yl`ta!JVq+Ehj3b&$)3Ghff3WF9Gx^He#PE%7(
zEJ-seYyb)v%2sY+WgeI{kt67To8l{`tTGxehEvG`^3+*Ykn|w;a!2zH@0)8IS#)88
zo{>3pVyJ+u<7Q3X5QBTGpM}My$@jt9+5GhXP0<<B#Ta~o3d#CSMvpyk5GA5$?ZvS|
zZ759*{C5c?#_b)7dmiPEF&*kLIyW_}ED?T%EwUf{x39Qx{A7sg0bifvt}j7-cfxlI
zVgB@~-Tsg|;$Mi&@|4t*Byk`y9^k*uKD%bh&)xvi5}fNz<K{n_?b1_r0A8t^)bQ1-
zRZ()u`Atoe7mbtpUM4i_d(;$CUKMnaV*tnrAh>Xmo|#v%B1unApfsS{T^xLhW&##K
zc(*kkkvB658b?lz^Hvp0)>D@-THjZ#Fs*_S^0K1YWU875?AgbH(q4l<V4wijgEjO=
zsg~aEe#9~|(EFYA@^#%hS)H*0BfW*{gNQqJE*OUMd;iKkHahwO+zBv{Ux+R>j%y1W
z-@+(HCw>r-3@Ix7zALpsYgY6jFWS!qbC^uUlsP8fbOC=XA#ngJX_PQ5aE@YvQTuhG
z0g6yPg$+<-0P@wg1~zJhfJ^!)BlGCXDMp~yWyDG#J%x*#w;eHun_e8jVr;_orC`a1
z(9B8RHSoo<>231LHw`Ao2X-kec;)$=kXuF3y0kgW)@E;Ue$Y`9zLJuE&FwPVIstk$
zBKvFsV{hS!9GWNkr=nm1cN94$T9@Fn(4U%qJPMbt1v4)&JWp-`{b|_)GulWhuhn6N
ze}Ctynln#H>e+seg2<xebhYiK)e>V}R@G=};H=#9tX!!swRDrPhlzeQcdMDT1rWn@
z6-y^SN>vSjNAeM6;dn|WX)i%W7dRZXEWGN3CNwEKjf0#nUEMSG%uP0?J3E5E{J6<y
zv+GW5fTY19f55%I2cWo)zjFGUyDmCHg@B+z6-#`2B5)ZZc&FlzN}0e!MPmQIq~U*s
z3%EK3Vc93dbY(L<?k~P6T0*U;J_Z;@I-dK-upYhu2t~O);(zX2I-G&H<^O!c=6T#d
zg>MrQ>F;%{XLr^K`JRCexSfcpV$qO-iP9q|@kmO~NRG17^BI)#i_V=0X6ER8?U9u$
zE^S@&i|w0oo4ahIrZkB5r}hW<Evb0-KaB?-O<xl{SM#+;e}BJ;TwN+f;&XP2xHuWh
z{7&O_$Nx;?pCwFTPH+q%0nUSqkjo>XJQx7X;nf2N5m@m-Pc78>9K{I10R>;_z!%Qc
zfA1h1oCN0WL6`!NR+rsbppQNd<+NuIS*)-sCZcGUiYhRE)ZwtP|9mD_ZPA;Ck0ED;
z<80@A<dkwSEyBD$iib_=7#+gB{;yyT`QQmscGakIiV!~H6A+x0ejhM&;KU^YMT%^S
z!5w<vIeC#IjI0I2Ppg0x{E-A?qjo|prjl>Ws+KtTIZCzon8ZNPKJy?c;Pc)eG3z55
z1K=A~F)B4=dmXE5S@TnXB3hABc$5)XK4=}S!UhA=6t==DIx+TS37<%sc-bCDFta0T
zT@mMw*K?*uQ^tZRI212DUjte;6KPec_>r8L)ieC1$L|AG)L*W>Po_NQN@@o2u)i$l
z=yL(kHRyGSbzdhVZ)fsSyHj>T7OkLbGiFK_eCL@vmt+is8Y8BImW@&MVCgrC+59f!
zdZy9^+$L}FO%~3)6chq>qv6thA=O+n%8YD~0FZ=xVYvq5g_n<}@c1x;1NQdsf8YaT
zW1<So2ZCZGY~c%-F6c6!*rX)`QuKkFfZV-U89Y@u_`H#zG`+v0i2RGkjAtBxKnGrR
zwEK*R^mpaids?e(TwR8LN5Kvc{?UdKC9jIfTqn7Db><64Y`AdU^0w4C!@u!^zdlSK
zQ@=4i>(e!x=qwmaN9Y<?`1=sqT0{e!PXtjXt&rdzgE*T!N^)cU1VySR^6OS85~}OK
z_`+B67&aSNJ|!U>F|Fy>5kDZ78{1^D14Dn3E|6$Kr?h<;&p8|hx&=bNi$3fO8f0AN
z;lrgoTx@){-1o#h%ieNPbNh<jOyK!6%z{5aVBxU5Ic)4On>4vj8BB=Tl*JfB%N#=s
zX+geehN6gj`Q0oWgY4nf-X%8Q8-TDcIUIW(4Nfvd{(T-Yz(Cq$qDw&qQFJR5L!7_2
z)RlJ}D{k|Sx$j~t@~Kt!t5Hd+flcc`hcxe}n-tWi9L2@m9~bxBFI%g3kee|*4>}p?
zg^Zu8?Luq|Q`d`iy#gFfe&*3q?JsA{16yNzZD6alKG`E0fnTb>c*9@tA%l*Y?~9>L
zrd;v7*CGGI>mQ%t_#aM6zJ;+pW!v>&W0fC^zKRsol}HuBNPw}-Iagjna3j9-^uBVj
zDnpRaShx8t3J2Vo59;DLwXr1>su<Hj>8F4)z5RjP9wlI;VSB5S8y22Lc2t|@9Y`e7
zASf})G@uECcSI=hgYK>L?0BFmbs5p5-RBlY;A<772VeZ&uf@&-4b=aUanw8b%rk$~
zCHRot<Hv@^&f7jyMY__tdPMqfQ5=o_qzbuPx?sV%KRPJf2^{|Pckfag=50nodK&TO
z;d4@OR-)r<53_@Xv{%m2A~H2Ok&ceBL+eN!UU4c9&w!o0Y}DA7f<=`E0vJymfYLFt
zDXkS|5BSz-_wxR7KoKJ1fFC$`D2`tW*N|FxeghOIyRg+BZlH(&o=8?m4fZy{q3^N3
z|8;vjBl>D+(bCbc;k`#{RP`kWfoQn8X;R;_tT&<U9CI^9G$glKE6ItwFE<wWr2~sg
z>vk94yZH~aL$c4iDLc4ej+jeT-=aza+@IO{efr0XYxK(uJ9o>&X3DLn1ZEGgYwb3S
zVv(1h{Eo8g2v+gy^7+?8$FIN<)^1Ez8FwIRAn~If_;vm$+fkL>H^TAQc(H@HVq)hl
zXIm_W;8uADK>5Z9{?|H!2pKOT7<3YV*z`#eRc{WaDDQUx{Jw$;x6A}_eDueNU1$i)
zF<DLcz|z)Vev_|;L~JU=K~YeOVekEcCkgR4R45CW36ZWkTG1s()1h4$fXw-)3{(xc
zBC)+g2CNmNAU>Md+4z_uVwVzGd|oCTbTC=Srk+tcPMNrVLGakR9=UIyFzM5ANA~7@
zgQozKx$^KFsKnp<u{OO${Mz*a9!E(kO9Nd54VVJ5N5N%jOdh)-@)B{t#l*XaX3jfc
zcyonO8Cj}`5{DSTw8>}lbRY=X%jR-pVt(ac+n<C1TCw2;LrY)83|T=YawGm*&+Y}W
zz_=@RU>DcfNctlX1}9+P0PhO9G-9Z+I)=y7_}{oZBOK|65xyQD4=NuLfzpYs8KLl#
zms{>SqaWwHaPwgU5Zexxp|Q~)!*HA-j>?8AgPAd=yB9SU#fD`de_~4I2~(c_?8Z|^
zgU<|$sX!wG_GD*_!LVjSPL(Q11X%C11T~5jqEFsZPXs^+>ET=Yd;2q=Z7d@;hZxF?
z9K=i@%BT{#;!wtuM#XkB8{;U;(rv}p2CX?dlyF-FsykI2&moT?>^W+0TUjcs?yfcR
z0RuL71`$O}F)>@th(GscDdy^G&L>A&soX4bZQoWYsgCdYtX^%Lu6wx;4lKbX8+O%f
z+8iBqNK$c!d^05Pd=k~F$8tlZwf@kz;jOt4$3@{E&HNN=?SnlT(Zl%=p9`XkQjsB*
zdKD*bj7%?Cguy-@0Wj1F{J!UG)d99zQYwwjrE^?@E)PVb$BE9XtRO%6KdcIbPCDTK
zESKH2xZ3n{(JrdeaC?usH!}RkWfG}m+#oSF6I%-ekyT0M!a)|iKj1BfHkDg=`TU9e
z?cFmP9b+;Qx&9O?CEb7P;3<}VwB{%~oz-<si#EF8PxFGc+&!vYI(nl}K?fuFGqdP1
zJfXc~>z=#a>x#4!xKNU6ruQY}N1ku(8OUs(gW1!IgW{I@x?%l%|GWZ3pP%tN=R^7F
z`Xnh`p(JI0IU1B!1=O(~sj~QRPHVF%In@a^=l6HhA)ru%oz`qD8+(;XWoNGvajC6T
z-?n*JdK+5{tkh|Ichs=7k5Y=RM2v{QZmd+wKY@PiDQ^oR5-VYE9xi2r%St4jhBPlF
z{5+e#rg8Z>BZbys#rdA9PfU8)vZkQcjgEs`M)h397FmcQj#`jx&kZ6k4;iC||G^uM
zn)*SHKVgWB*v-lHZKP)Fkk@T>r1M=P?qJWbpv8(u%h~z6h%uEUT{8u`W8I&wD*Dte
zH-jX2rG(*D8APe={&|IoO@n8_@EOgNu{|nmMP>nBx4G>VSQ}fWlBXjU^>STA3U<x-
zLux-*-*Uinu4-&6*@f$Jo+Ex40cKOc<wpk-csu~xHGV|rGFI=hf);fx8D0gX(2FZ_
zmCPS>>Vj{qFi*q%rSS(aT?{U9*y;oGs9H3VjDa$&Y_@xb75q21uM0GBtD1t#ia_a#
z&`L2S=UtVwZm(y!s#_dq7O%wBHGD?1dRq@%%I_X~y)IoSC_)R0qIut_K<Pf+v&0sE
z;XZ;GWw#u3QzRIP8Trzm;gx<ctM(<a_zcf$-C;0}t|-rf_IxEYj6C7fr>eFYiWnxB
zBZPcT*Agj@?4fB|+Q(!5Ct`+HcSKqBD5dj8^~j4mhBRZB%7ID!H2#NCao_?99>lm>
zzIr-;_TqL+*DFb%sf*)f`2l$MZ%JWKN#)OigeZ@^hsE#;+b9RbMoSkTGzj+FR|@q0
zwFwI>?=VBw{#0JVl02kPK_3#)ns4)B95?8mEm=C7zXK~`gO2zkM<wT5N|+%_qzYF4
zK8;#$7PqRghn25YvAAWSAdbkbRsXIGG^L4w(Xeo-3a<`T6q`(ZGlBj)^?f`Q0?K#P
z@4C8`r72<*_(OIPh0#f<_n`T(cqFx3CoH}dyy6?`cx;;Kp&|h5A5|3xCUywIR<$3%
zNDR=LNl;X)QqQBf!|3(XZW=i2fiaCS@cI!E*9QMyPXLgW+Ag3uEpGh;1Xh~ay;E^C
z+^`H(_j=u8#es$9hV;HsLh-4VK0il0vUl!Namv?Vh>zO(T#G{s&BL(mENUJkbM<ki
z>^x?)K3CNRXBLKGRw2&dvAVrA77Lln>y^qD#_0jHGRXBd_$)fZ%+X`N#xx{FBZ~BK
zKLq6I<8u3l`B#S9c!As`QGPOUjLhlv9ZeMtN^iJw556c_Wdv#Ir)Kt0pn7}-{ab#x
zqz?>=G@P6ff;eJ`OFs{)4@ydEzi3<i8q?fulFE(!Q;8%69oQ2`5pJBpC{@&v6FV#u
zH((@7rwogJ_Oejwpv@pbhnfRIrW~k$lDP9SL6pk_IL0ES1p^(2Y27`P-Z@`o82B~O
z4s^EjfiF6!aD#Uu9rmq1A5XcJ%x|KWR^@2@1Vj~BPmr(PZ3IaS{)13i!$6^hV0m?e
zNd#aJ%Q&XL<60ICJlAyAw>dE4fmAO4krb2K^w#4(N}lHjb&BL0WgU(vvbdnUBE3Rx
z+>vj5W+bG)Bw!SOl~Bq-jV>{cEUP(K*_#7~i!<W;y|0L@+%VNOpI8@-xG03IG7}<}
zDB4^^gok`{%lCbpfOx+G-nB$HVg*(2qQXQqTRGFFkRzO%)-fvy;GeeE2r=Ix%5EMt
zpeaE;VIL<}Dvm0GlgH;iLbjRs?;Lw30C@PJ1)zPjIzgyt`I|HKVGY?`tnWN5Vym8;
z3OErcr9=IHJ*eF8^l8<wb#ZfNEX}w{#hFadCU<&0qunE&BZ6psSR*dgDC<yhq;5X_
z>i7};gr1IN)^y#USP<tdbnJ6a(gaOhnD0HDP=>K7W|2#}=Mkoa<Qi<rXjwIP^XQe6
z_4(jfTmM`o8eJc6tdyuK93245BGUgkXLegO51_<vyV$uzm5<=B&bCm+GsX{`%Q(c|
z%&GyUp>8^#nC1A6@euSoN_cWP%xI`xtF;T?9xgD|!?&aXg82~`5QvdV)aAKARHXYq
zn!Ylw$@hI*5Gg4E$&r$Rbf<KURyw3XN}7=h2-4jR0#YL;Al-~k>1H(I=#J<1`};qy
z*b6p3?7pruj`KK=1E7Qec2JTV@~}?zVNkFc+ahO{n92&D{_f9f{08Xp=sqE!c*7UA
zzPtI1PUT#H6O{YG`llkdn_<*nJTW85&EK*wjo*iFq;2_7s=oK$?kDpX>=-vd)0Bnn
z)EYUTUc-2!l52^11?)#S4s(X$KcZj(SD+@z;ioVA>>@bnR4mXTOS*5Ntc}m(rK)NR
zDXf0L+YZ?V3s!VoR{b?+aQmul%w(g#@DJP!dMmYZpt;I?ZoHIj0E6FY1<TuiMuxfj
zP`4jH=j4{iP*Aq@LI(<8J1?UGq2g)J>+~v#5umU&GZc9$_`$KT8-Jy(b4fb8D48i6
zI`l_6nsk)P>|=`}H}ca%AtQ&8NrB`MW?>pv)b(^OB*%g`IX{mDt1u1O>XBU+E$~$E
z#Y<If1n1o#+q)tCVPi2jLG?s@PR`@?Eh`c6RIVtju5Y;ygHxbvXxvB|ewnc&V01C1
zAaCnI6px&fO|P&xX}xq_+7fRh4U)}@`VK5M5&zqd4l;vnyW3s)1A8$6pve<sYaY2W
z&lII*K*Hqry@V8q@#Tq0ENu({X29XxX;PGIOA<qJ6tFvw#XOdljcC20cOs@|1g=NM
z?5n6(0Du~9^tCKm?#W}o`YS*$cX&|i^5)7V3A8x223J&8YUc0oc=|e-y||PPZSzDR
zqYN<B#_A?hegESfOeh8gusV{NPOAKEM~60_741mL60vqjW31jnBFX_*kLCefie~?}
zWH&(fA8HRMcaur+?1_j9NDsKMSUGgDSQA|Noo?_uIq`XK?f!l>-BSn1*t4l}w0lGw
z3B&iss1&C7aTYrU^xgNxGwk2U7Z1spmIX5wQi69*(lS!OXdYB@pGm(eZu%ox!ycPS
zWq?Kl*v>aAqtIV|t4lamAw~8H_I~F!(oHWzjTjCvRt<-i8|!Nw@x_UrNh{SeCvXRV
zP~!yO6uUzB<fN#asw{uCVw7Mk%gyizd%0(QjV7TPsnQ$}1?ysGWm8)<8GK*aI}Jmc
z<j+%%|H0$pdkF{MF(SqMiYi7L3oVSYOt)GoRgzBeT-b#rOtuwtw_WZ(C(DP;j*W8h
zYRR$$`IL+auC__D+Gr0hwD{a$mL+({%GG?I**jgvcXqKZ8=T|l+VI+TK7yYL0@q4N
zzv4*H#OJBX)VHF|upzhMx=bU--#>8C4dDwDIJHfkjr%ML&*j>LAnxki_H9$<(B;k6
zbE}WR|L{yFGQt6GZ>JwZ{~-E&+j%i#YBQcp8~RKc-QVJ4N3<~jjVE#DvJYL*5Eo!r
zja^O<KQn$$K4zIdye+I<cCyq@CO5Tm$;=GMWEh&~Pi<!>%Vo3yP9Y7Wb;sbCRC#7$
z9Tt~bz3tXItB3QtNWfMGKwchC&Z`n8Jis2L`QJ9BdW&vE*jn*+W_5owKc#>InqXgK
zcN_Qt05QFPlgxu>cr#K=m#WZqUKA?&j9t6LVDQLZ@{v%Atj6Skt3hvP#xJ^X>Lrd$
zVO+!YR&D_G)VQ9BJxuf9$VRedu<CI`#nK_T^q9V?-8<`5qSZ<>*Vw7L`f(TU)MhQ9
zQx4oV#+#?Pt`qC2Z4c}&?0Xkt&?UWp?aAt0QEKUQGmr%}(LlMSCns*a?misLIdGc5
zN1hV(sN*`$tYx=A9YGQH%DSr&(>qXORJfUKQY1Oh65DbgtKk@1{mk0BJ7=Uglwd9{
zOFF%kgeRN|%M)SiFIz&!tqGpB=(!vr;)*3d^d35}e$OZ{e;qzv#QK_Cb*FIqwX5D?
zjvzarvH%E4CL)<j-cAn!$_a~JrFP;e7>-G1Tm$$sPPM>-BIZ-qrf_;-mQsk<N>-AE
z>IB;8r9-IY)UJ!w7qk%Ml_{IsuPfl+9Z6wI6(tmzAZwc@H?9UI%+`iJb43C60u5g~
zeB1NtrSQ6YSFR?>0U<?9l&|KY;67PR>M;vIUpc{*>_7IU@}Py97n#;NdZ*6G8m*#1
zlwiD;77`z`fT6_#*55J7&u+|Y&-5}1K*gzl0R$9+-X9TpD+fe<;dXaSPbKpZjMI$A
z)vfxofV4NGv!PNyhQ@%<T<B=L))%gby&H-4%fE6yIghsVDIp!Wy8^crD+cgUgEUV(
zQTxO<RxGik>E|Thy1bDd;tUxDYrFDVR;*-9F4*SeFyZBImMx6*H=2Ana*dR7n0)cy
z{37T>QCPc^z^fL(#;J9AXIi4%3+!du7iu8Y_VVjt4gT-o*Cruxwu4+zR^EB%>ld%P
z2MUT=9716rl29m*&T#F-{>C#pf6k8Qi5;I^Iqb-de$;)l2rso4DwYyX1@}A3Fz@K?
zW<=zdl4bOD`PkcwKZDcTP_oY~UYUiImJ1cD%?Oacu>{Z?P8@P?l=^(<Y-dy{ZVT=s
z8T5ea!?dLV<*FfH`ynH!GqCRq)QrHs5(WxQMb)QP{hf_I3d-OI4RB}_G*OV9PwoSd
z{ecbFy3WrBBO)}@Gv4-A@zDXXTPCEE*jQFk&>!J>KbYzDdtEURLP}MhJl(W;he|!6
zpJR|NrS*N+(fmNR-cl}<=RDfO2;VI!f1NlF;=QJKB1_=KVd8mVk<PBzSQ%F>Y=``c
zg6q|xQ0D<KHt#+`asUYPLL5hq4v46hrvr7Y*er$uZih_H9AmtzcD(5$>vDAU_4ke?
zAaog^8(hd6>s_EYJtT3i;;3CgYP#K?1=C_xXb^)`;WO^VZqKY;pV5=MmFeaGI#B#h
z)}-9WEi7Wp6v3bm-`tPp2NGZ5log+9FVOjcQ~HINQi@<dCqG!Vs{SX5`2J<t7P}d-
zcK<?D?541U_Ora1T_6k)!nuLB&&6-<0C_kQx!gmEE!EmK252r9mlB@}FvsZZor&!O
zrg2v#q^vJ5b_RZwzAnyR*AtnK3b&xN1U*H(VC(q~_R|xWtoiw);kIH%1e9ALHr~w!
zDD(3J?lY{O8fZO=XdhmS2rn<({Mm9R0(`lNUjj<>0Gs7o5ku7fgo;@*1So^4oyZ7!
z1}<aiiGgcbYAdUiKot?@L<}_I03UJo4Npen78~1VO;LrwGy!97s))YMn|FOR3^C>+
z*$lWoyhcUSe*j}4!#Be&>{vnHOlAvb&ySYkbYQW?r9km%bpQ-UqZsbsmogtIjnPnt
zlom?gzgLphX^9J1wHUtyz}69Yd^x4A5m(6bSzNues)-+${g&YUbLuu49s$iBE<OU^
zy>QoGriA1wINI=mG+Tp{)|JDi&6A69dD?%S7)<?tNS4@k3&j4*^T_g+=IW4Qmd!Vb
z@_}zxcp4ZwxMHqJopWv4Cd@0RdhuTo(|I5Fqj7?xPwQaJD7Lsp0my9pMt%G0aa+xS
zIa#gAUHqdkX@ZWTX^)4)>!FJJ=Ch|XoZr$|Ukd5GIWf%jjd5j4_m0}+F)Wz1-l)od
zEsL>6M~qJAG*(o<^cLnW5>1UM<m#EQ|1RBPj2Z>6YJ^+q?^3{WaT)HjIN9om@0N{=
zMe9wsCV>PBEzL~;kOsDNy=$Bri{r&<b2)wOIMy9o(40bAUEZ)|jk*gDFR};gJ_o0q
z8n$Ib&}+Qx95}{i?i*_HrayLHVqcg8Rk`t6h;{E8BLv@%;uBRQo@1hn(d0f!@Yj{)
zvCFL3OlR5g-umrMUmLNwS6)VNH)%hHBUg6yrOWn?1z74qEW!Y~hW}R@cHnZX>vVb5
zf_rFjY@0Y#dI_}~yPyXZxHorR$h$cF8QrTNZS~2uAMGe&poOg1z>YS;_cyvfiHIZG
z(cv}a-KZO<ThqJFcXh__hsxw<|F+8TR|B7OVuyz!%~)PD4gppm08_f?20eA3($D@v
zWHr6LlQ&uO;o`uwmx3wTISg&Z)Nni3<mPij3h5l#S-6!Ln11$?d$2~I(VX5^S06U{
z^4jB3BZGr&%~W4xmw0S58lXDhMQVKwr)h;x%SYEEacQg>67GwCP=u~?iBkdWP8}br
zJE4tJfV261qO3WAO6Qn0qGOz2z8qr2nKw^O%P3SYRg?wDy8uqR6&cJ?3_#B)v~t@S
zf()y0`U%|X>x$?yOn2j6zS^_p&uW4-klhR8nU7S;a$(A>FYw*E&z7w1-<BW`?E~Ac
z_Wz+VSF@{rl1i-&?g3jRrXQ@!&NS9(GJCX69;W4hjiTlJX=zsECx}xtZA3a~{+_oz
z{52Z0>q~Ri@Ni9y(0sul(m`P2O+h1Z^&)HVeM3Sj3R9LC!qe$MYSsFdkG`~nB*^Te
zdzUk{ugif=qS|B^M<TO^*FDq~?$vWps1PsnXnG#Axf5)z{q}D4Va<4Z=i}0^`p^UP
zBsTq=0M7_O!CDC769pKq0bVe<ez)|q9982#&aW;5kEjtuaxv6ZCylde8thhSX|GQv
z!k+&Y6uFBGyn8Ayf7)_&!VPF{7io=5?EL~nt-A~*TmE@={c`$@Q~;}|ri*B8Cy(X!
zc!E~~y;6{OVfa8)pv43X-GWSSD`$VqHo1!g8(%6ZD*<36*AYr*L)$S*Ss6j-i?8Mh
z==YKBH-x>D>u4|kjk3j@{(l-*CXjO%&;2SNx#gLe>$A@g1GTUP@S-E^V6G(|TkVjw
z-aV`sUFEZ|_xer*Cy4oHW#oWPobg!6%%Ph_;i#U(P^1FWC->|volIw=79U;4SzC@F
zO6HjH%cntR{D?|}VEojXtF0ZUhH-2lJ(v|OZ)G>i^_>XwgtpmK4*^O})u7;Ggaydo
zI%81wMM$2;h$DGdAZY29!(5Ml20x*!lBSBicFu0<%xFJY;&y~sC*;HLf$HCfT&s5f
zra}Ot&T(8FEk7)6!GDSWMJAC(zC*_K>akmAbuGW$Y^zsGLg30ndXmFenWefVjs9jg
zssSxjxmKI`^@EIzpLeXTHk#g|AOC)K9x*`xx%S|m+8I2e!S@DW`ll4*61|sM$WahH
zf;5SB9p^u8wJNd#3RpwScsqhRz)+r`V>Tx11AC&C>)c=k_7_q)rG9mS>dAvieE&O^
z4O?hP<>8(F{*8o3!`Nl&_OI%i2%4`z9Sdx93%!5Myp9iO$@X4pru{Vb%JBPD)92a{
zOpmr|n6>3z+I1{_-F6<vv+e31{G77fsH_qo7&xdRrjPf`L_JBgRTsLO+s1%7bH?IM
z^K*c@?-7>c(EMCeOL>WFEmN@SWMzTJ?T`dW>l3)Z<ehuN@`oN?y4krSF&yaWq{#k#
zgFt`(4ib{(^w&2l_njE$cO=s^LW*o+uW`32<C`=63pC$W1~CR~3lU?|_b-HETxNH4
zSq64qe=BGXkyq93-*FI={Ju=ZFzsO$b?}U=DZ-HvX+bX1SRog<Hg#}o2$)x*&DFP+
z2huN%p0kjE_};G%Rb>}U?87vH(sM;xc|g0QkEZERAG7nfV!Se4FinVqNy+ylL$f!x
z#$(nsnL#`i9O^SgPa-rLQkuOi1gk>40`R|?vB5N)Ofduli`fPbJ?Ih!uSX8H@GzvQ
zI7%Fxc3%0F<Vc7D)+d&*hGidq<KBU^e=6MykB^7<HgQ&akU7Z1Dq^g0<-6dPe;pE?
z!uAQ;TU0(;tU*msM8<r+yuo4LXy2cTGpPfni=j|+)gD=J1-;Hf_<VlP#PBylDb1g>
zQolm&_!hk0dt47zoIzT}FP8ClwkrqAD#|JZ-g;c#$`Cj0uOLphN5sbbhx4&UCEDI{
z?5z2aOb>_^xl*{p9D)Jg5$!S1##%lW`hA?%{HshimK2^soZg?C*Znni?#A6*?mXm~
z>DPogsTV`;4#9i#^y=ciabJ6}HIp>hA)C)Ru7ko3(}-25$HW6eSit4N2}1cI@rCb3
zKP;kKNvh=Ua`R`SM;p(YTSI$D+uTFb=jk<*K5b2+x6!!V)Ce;%ozB%O5i?h?&*~f6
zMTIu7L=^am{rFr^z%uyibrcarD@yr@fMGVZsjzQQOQIU%-QO+B3NMjAXr_F0-XG~k
zHYfRUS@TyYkDN{YBd^U-So3*t=KfwZYC0dCZLkNPmckU*lDFQsUEDMpGyc|YWVafV
zqe<Rj!nzy9H(jSBg+?hGcsbEeE#|PqR|qWn?VNZ>czDM@O(sOvN5_E~loGyg$wGVo
zth3_fq}#aG+z??g{Ix{=C>>Q>@3h>qC;j20NTNwfv1A_QRZD$MAH+X0;$Q;5`{#Fu
zBsSY9r<Sh-yBVR}gVj@Y?yq+o1QZ;{ZR!@c!^#DZ!9?0qpQ3((|IUoqHnnji9&1Ku
zvexC>HN@yrTBSvC#7p=*1jn?lkb_#zuO4_!oTw1Xf;0HAvBk^#YMCz|gC$Jc1B4H8
zf7spiZCHTb=m;C9gU+i$q=;)K?O+QB8r2Ti7p?GRzAzabU#ijB$zj=9uIp<VxR7!B
zrn{Bv>^Zsoi&n0+^AY}f4DpPIxL3VAIS?ecTy58_a(T^{P4Jh-YS*MkOlp~*%Q2T^
zvv)|)VU%g06zFt+`!y$YY0bJs&T-C$;H#hgHAQi;8<#1CX#<sJ*3tHih_j>fr$+s5
z0$?pChLc9D&w@xhs|;MwX-f#{YH%_^)B(%lTZ>hb&x6H9B39nSCj^k4Fza%<RxW?2
zoTalccxN2T$xglf4w7I|gw4oIb(N^7<Udy;3_3wXzdxxT`QjI!RfHOW&vPWxB%aF^
z0Zf18VPTHsn>+$Re0g(wcvxL&W(1SA=M(3Air%*k3DBY`|85q#D53%ud0SMOS(cYP
zOGf3fmqZNQm7X-d?^0er0sKW@igB2(eiz5?bHA0y{u^i1*XaiS4pvb?=&juN@?>mh
zG3<T9;e6wklhN;HQ8aqs%n55;Hd|B365{D?zW*ji6!dh;H&Elq=})qFTW+p}?;F^x
z?|y5_;$uy#7qi-k>&EXtP&il{&gYSH-LrlRJrH7wvEUI-Zb!N{aR7do85YdNmn$*$
z+=8aoP7i<a6+GwaJ5M=5i>Hm!F3fsj+yTSq?AtAdiy$0SsL6bfhpJjmI--AqwN^h&
zNa-q45|Y@ks>gKm#IOdqN@5@1z17qt-g>d6@WTEO4{F6@`Z@|#f%fYMo>Y{{6&05R
zE=-w+<?@{$=QklPQBXSo*Q}hiAuE!R{n#o|*%^1O^`+n-O1Y|o7nj5-lbEWHJ5|u$
z?_koSODOxsb~k9&89MbGb%Q|(#vm`q-p#dPUzJ<PPgbkPakSZm^Sr358Sl=K-4W*E
zpLpQ>hIbb?Jm_0=(VHku(~4jl67QQG>Oe`3;~X5-ozhbM0tPzp#!uax@gKja+r6)Z
zBw?SvVR3d_GIa-@cag%2CYlHs6gOnGJjD4_kMMKv(4b~(WK551;WiU;3(kL?L6X5V
z3hzL%1K<=Jo9)ReB#Q=%e36}KXW5SRwl`0@($I~(|1NkL(LfUzDim+|Cer(zPd3f7
z_%bMbRpOdV3WOlv#_(*FP!84XKlco7ciYD@NfYg`n6@(lSXSpQDS7r}pnlTyk?jcu
zsU_b%bP1|e1=JWbEl;CSonj#)_GJ$u=RJ|o?W6GYYZvnS;5MgJip9H8!>aF{s*CGY
zRH7p#)}#<mpPWA|h0bB6c49i&U4ZyW$_O&YH+oAgQnEQ9ywM>?eRvo_u?<B~^t}Kq
z3g~AIaG&Jl8gGI<5`e3eVT}`$G9|m9axw*r1aZCxR-xS*^%2UjhYtIIQhkJZVc+!)
ziE7|CCbY*$nEL7FCXTxL=myyyS7G*AH3ym%yzqlC*oT}i{=$?0{C*of&`$}gHJ}6e
z(42at(Aljn=@sHSQ8?S2+<4{uxcfdqcGBU}d;bp*`0K0L?5hn12}8LLJ#&$FM}*F;
zur6&Ik{>BBv4D>;*5zXheN2z{k9SWugy^E^a{~T6foVVEQ?>A+SEt)?y<T9_b#^!&
zdz|*d?7}pjx;h!lD%Khv-^aOrh^=z<Z|s|<G(5XS87lWsqs}%jNI>*|!D_p{k2Gqk
z4|gQTxsOwu-8s#b7~L?sj;G=%@cTs`I+_mO228Lco$uxi@2<jhCvdaZY4h|3kG|%L
z$}km5ENKvLA!MErzm(IY))Y;5C2VB#C77(pku8P<b#oO6lhv;L9mkhua!YryHcaSu
zq2Y0S_x>ewGlqwvB8G4O+3`h(P4lcx<+L?VYHv-{PmCO<Z(Ei6eW<o)7{7h}1w_Ri
zWOhE)f#*;AItRRDX8FNGwAyD}REZ2~-@3@s8T4Ypk3YNqx>P0#8m87aD^|RnNbXCt
z^w_2umvnxexO|Fyd8sp><w$lp;`+4zZ@hm|IG^^3312>PA@<}$#&|y&$!Q}hJmO_U
zJugL{TjbjhloYp(R(u{*i{lEN)$YH#w)0e0>Pwr*!K#$bfy_hhRaNKN-;+X=z-~gD
z2IZYx*sODS%!5S3R?mqqy~VNUj=+&vvk2RoAp11C$KUH*RMi`|g<o*()+C}VfO9Wj
zr81=M8$7yo0(zaqIyd^`a`ABXt4qq7d7I)C%^$YBU*fy4CA-N;R6Z2Q(7IyHaLq<#
zMUN;sJ(Y;%szv`0JU)pqkbssbJh8^>+3$Zas8@O>$Hp8}C`Yy9E2^@0Bbpr6KMur;
znNJlb!PQ(*;oaXpvUXcCHrTsX3RC=b{gfXxj+T<_G{naTHtq&9=wz)~PD!*YnRAQB
z+tg;rU~;Lx!ev(@8UOmhz7Y5;1KUQ{OwYZYC~&+Sg8fF<`#Z6)g;S+hdTU00Mh6iH
z)hqSECO&(UnWMdcj1|YZQH!vN#+WahQ>*oLjVwLh>s?<>@<}yj6)lo$rT4E3kw~lf
zUa5h%(=s_N0y^3Y|HV<|-=aDHN|Hey9Hv@wbgBN2<uXa%59hs@M4T^uXw8}z0ggLx
zns^NRkMSjLv4G!@FBzIOk%X&3Tqiv2F2aD~;%C^yFVI9R{mh~<x|wVegVEBGb>m6_
zX~^BiJP|0JWs2(NEa<bK?u-`|;$X<$Xl|~66b+P~w#{av-m-HF9ZfAAO%*;bMf7L}
ztzPc^ZVn0P-!y;O{Z6te315Dt9^&&c1yS@GHh-JCdI$$J-bIgG+=ETXYF~I<(~Pxu
zS`bb7o$s<L$Ee8rUak4^V531jM2)Dd@JB7#C4^ybA)uob!%k0O%^b2+EjW*v@A%Hg
za<$HSc(=O9moc4oxO}^csA8C9Rw?*+b931LRx2Z86sGM4?10fgm;KfnjqIl(juz1@
zYCr&IW+TdCSN}w7x-?d#;RI_mdKE*6mzA;jQe(*4fm&2}$b#7h+4%R*yDzW?aU{M>
zM&=vrWYDN1x$a(=3YX@<34Xu<thxTh&5J`H(vltCDm%YD-Q3<b_$OjxQom~(HO*Dq
z<36v|^-Wk<x`f7Z-SCd2$6edbty`|R5}`_lp`#Ae;nOjEHjUGUm6Rrcwl8nzblZ!w
z+S@fHxMYXM$A1eUHHD_l`>fa+TkP^KKKEiBc+z*jOPhJ*G?NsPiVncrJnSiv?x84;
zHwsk<1Ew519!zQMn5U?&^{NAIfG`!Cp+~@FSe4l>g%n8plktgKhNI>YsJMV#foafa
z8G6ducKhliMzvKi?@yy%A-F7EI%Y&Ic65AaY^6<67-2>(l6gq2-3SUTej&>}(ixYU
zs&jQbi9PKQ%Ay7ov7gV<OoV(sXE`R;&~SXHodPVv_owunT_3_yUEJ_OOWhudhK8xr
zH--W5KlOdmWn>}cu+^z|=yh95J*eAKByp>XO0xSP^B}9-@x;?HaoQv-GTLz)24QN!
z0U`p}M;~}Syf|2nWQ<QZ4+yjVWM6hQlLvo9D6Do)L^s!BIFmAC1%TWNm&qhadR{Ek
zD)J^PG?~3!ruj2y%^}S3a<<udj9(RV5ZYV?R{5Ngi_SqbIe8y^O%FBufpnxLL$5HJ
z&l8F-(HN<5wR##zKoG{QnT8j@^3H7z`Zcqrv{K+(V#rfwn|TvQEkk<(^cSIaahx_&
z4?kU`OXj;>!93S|S0Dwf%0oP-QF6(dg}<L36m*3yHl>)hht3wCvd_{Rp4mEk9bupZ
zL)D4pWzDjnnQrMu6@LfE7Y+{Q?9Oawn}61e{yZ?wpnOyBG!y3{?N%PWWw5DCjw;E3
zP2V&kQE!9rCg~1%3j%0&vh{20mLTk8_86OJLne7Muw$K6JMV|_b5^x&Zbzc2-=&Ux
z<evV6+Rs9m;s_1u@LFd+-^fRTJG)039jbm$@JY301j{D$xXya8sgokf+3)SJLh0^T
z;v81q)3o@%{e7DN1QDnGlIZ_p$vFQBv>QyP&?>k#lI#ICF4+~C3zZtJ;pUI7aEz~E
z2X*Jo9GotU@YmLV&9?{dz>;`5q%nC?lm^^{^;m0`Y+bF&`(y=znb4-LLHdhbeC~tf
zu`L!ByCS*`2TKn1tW9_|;55!6lvoxeK%~HMncBXRLvGBfe9^+5Sfj$4SBzVd_wVK9
zIK!2HZl84~Ta~HJ%{W7P%TO<ksT^kKo;p?FZ2KH@cn>~(0Z^wB@j#=Y$TN;R?`8HY
zDOmz}hVY(oezDn`Ipg5P^bGm=bHLC3;UJ#u{3ZJWM{c_4HyU`wrO5BFrvkUeD=RB&
zZ`=C8Ok=bWLPjhW2O`2leUlyz%fEIur_q$AXeRN4k1eu0c4DjAPBq}ah<<?qi$-Tv
z=P>sxupp*qwCP~R%+nH9d-^y2o|o6HtN2e1Ithd+40!jf`t%cMyvzt-0T!aTm^!Ww
zReZbkHzD0|mVAeTXELruI8DV9b{C2pKN;mpR;<nk(Ou|k91=f}(Gn?cr1e=-a_$r#
zG6a3=z%Q+8=qC{my~jy$)LON5J+HJHoRVwFQgJK)x}_HqplILRU45XvYP*h)DlJKG
zI>N)PYkj=Q-ju)WMXg*V{=v6S%CS<Zoi}fmdVJ|)aL9rW5gY~_f$p|gNzAz>eP+|q
zI5w+YzMCFRFg=|qbpo4pTG|`4g$5I67h-Kg=Sj!2-8zgOm!Ly^Z}PB_B8o$wRH29o
zcU)G+=x9$LP-Osx-iXLj%g-1mTeN_r`lsQE#<P_gBmPI6pZyaG>zTTx-nunM9_qc$
z`|&TB$^OU{h$vu*{Y8pLvqprmgN4|vZ;P<Y>*U7yIbpdPcvdu4ESN6+y_-<}sbR$;
zPmVIQ+gakW$NMw<FkK@BYOzbvMBw*#jxI-3ND|NXk0maXR)W{$gHhOP#s~cNBS;WS
zADJq0DIe>LjXwVH&!$|KD3@A+l3dBYPB_Uxa;>{zFrS5GNjRbzsPeAxSN$RdSM|3}
zCP^MQY5dZIPhXZ5g>fd{R^N^erCvuOjXziw_Ljbyx=VcAN)22HJJT-0!c`FbD{8xC
zW(AHM8>U)w@JLt{IY$fhyeCYh^a%LXHtbV1G@_O{+c49Y*cxcPP5^{9Ak8TOD(A#r
z7_;9)0?0Ptb}1ROhqFS-11tQho|1!5!5s6}S77r{7YguvJh})C@gE|grW#~k9u0s>
z5wK2ub{cJJmPEkcgL)mR1X$HyzE$3*d}FXkB`vwR$C+ie|27$UAEt}a**WzbQ}xw_
zOk9GLm!ezqkWJvBeyDhE>cgD}4+Nj{;M38tSff_xhHOsi!<omORL5!i8L{q)-o{C}
zp!d3NZs)PXcB~VZmu19tp*DCl6>=|1dX@WlAi3@Qh-~ZnGWEV*=fF0!gPXm8iyo)T
zKU>$oaG=gj@OrpPOs1W8?Kbf4^<p{h%^_XxLvqQyQQ7hKC5O2%lO{opyG!(-`<D}N
zyi==!RdLVr_B&!{|3|{1)EVKEs}1NOMt7XO^BcF_Kd7<(+i08*>uj{^9eer?v-F8x
zjV=MnLNW0j%z+PB;Ken=$G?m-srCBJ^>SAAiiFJU#(KTS?4Yp~k7akn1eT8q>mJ{&
zk!bs1`6?tV_c2<1y{wZKICz8VpRrk91NGB}!&Ju#e9@!R|I;f7T~C{G9F=M}<ZWnh
z@d5D?{&w-l5?xDTS@#Tafz<jv0Usa~`-+Yju&Zsl@ZimBZRgkS6SD3BYir9Wb=I-8
zQA&Twd`?}s&twd;>7sRV)x56OUP_>^An(AA#8;eHq;M{8SJxC)PL+9&`9GJoH&1n%
zset8S`KqDC#Y~`FsYQIM(A)Y{<EL9(K%4F9=i4D+v*5Sap^4-2_@}xxi|jm#&*?ep
z$M1=K&Z{${Vc7ULd2dlq+EkVb!ZnM(D_W%1fIY301D5QX@)jwoJ^dr41hakcKj@*S
zSP&|3f1%;|gS*Fni-UoZEgu`;rO1V2>r{sojG1qTsLDMwC}bC)T2`cScB(tVkjQ|V
z>4{`O<9m*Uw5yGg@jY0{>4XoqG_GeTDFmpN6i*K8(A^FFn?}y?KO=xd7_K?jY<$4A
zd);qoBWhRb(Jm@G#UEs*n7{xYPUZq<OU<eSn*gDQ2AH(i^gf3u%iEuwV7b<IOjsGv
z^~<LenTKaBh>&e-pEnyUbl8OxPbi|*3d79y8C-&(_L#i)PgHG1=7S=W{xmt=QZ>E!
z$}PB}{|b|SgNsRtp}2_GEiVEwuUFq09eIGGVD(2!na|kbc#f~$!d!SS=~8NJXOePA
z&+~@=5(A|vKXIV>7dd4<7PO^qc(Mprr^?xFFPgEblDb!!!<fn54Uz59MXL<s2&2<X
z`Y?~q6K}UVlE|Bu(m6OiqFD;Lahn*K8wUM|8EWQiYYQPj6|`8#mnH}@>U?E-0tD)e
zMdO=gy7Q5XU$Hh^I0GbNOx6*Wk<>24ZijatGgR3a%?Q@5sJ3Il=FP=}(09ag*94l#
zxqs*KmHixLt$V=N>7fHV`ELa72gWI!6|N_V@HC@}I94B;10Lh8?#>xphvl`%$S?)%
z1x8ZJMfSSPyMek$BfA-4-Nj8fC0k2tYiE&s^yBU(5r{oWUc12gRYy~$Zov~KvDm=7
zC7T)#gt!$ta-1JmWp+NCMVVHaut0O>^j=m8On*uGU9j)=iy{+FfvxUpUo5XG(XSj;
zfAPaGplo@ooD~&Z99t{&?CSpWf=^;)vPkesT=W*jp+TzI>P|L|Y4=YY9$`{d^{0?x
ztM66=pA%ik&iqE(-JgZf8V-IS6X8+XtwRS&pE+pnNTfZc>d_sim{jvhQQHbykFBE0
z4Fy)%i^Xz}dR+>K%HQ)w(0GOc<5qOl#f}jnqW}w5T&HK;jR{}342=A?D4xt0C^%Mz
z7h{cz1x7^|InFpcAgr^DQA!w;epCt0n^czEw&)k~#lwf1`5G4a1PpgWW0F3do}kCr
z<i{4vQWnP`=Gj|e%Ah{GJx^8@XqMSHRRJXhOrhA;;U`vTC-mTgR!bRGa&s~8>UE`0
zs?-=WCjCh-j_Jd>I*+hvf!@eTtE7K$<unuUB?v{;7)Q2W;J3ZCD&xXqsizcgyI2iK
zG-p(RydJwS0P?NSC%@3Wr!U#zo0)+}*o*dW_9-hh*BUx3a>cs7Ab5wH-nU)aIFCaw
zk7@+~+FNjrdQAcyHc{yP=hdsRcG<S9_2$4kkxGLwHJJLY!Z4`fq{#G<frwY`$wN2N
zkF@)DdIo1~P-xIAn{DBT9#o)QI@!W?GMV3;Mz#e@_(abL8h|9k;UxhN+<3V;7DAX;
zQ-SyXsFL)+L>*w|hcR7EKc2b0E5`mWNuSUatkeMLM3O=bK^&|1=8!Np5hO_JTT;TF
zOkz?=<S;0ML3h;Lmj;;=I2bmib`aES^aV?>+q|vcx*ZT>Pkh|#q6AK+ku$%yy>GCL
zJ!4K<7PYz+`uNvA0B*M9n-E3`60&YwHlG~Q@ay=#bKh@>_kMQqWmW|)h6C=+uoZGy
zk|RE0p<3OBkNid|qJHRSs#V=$G1Zlk)9+n{Tej@`A8tH&>VAJ2c;XeY)>%X~r}%*y
zx!Cb!DV4gL3wJ4Mg!J*EM6n>`#Qlqu&0CA|k@TI|qF@~~#F}aGnpu>xC%$C;+g<fn
zL|D?ad|wXd-&rgB?FpLF>JENrB>DQ0L~&Mq1C5o@B?~>;Yw(YUHhg5xZ+kYU7m1Nn
zf_=8&zvAQK<vixV-L0J~iThpLv5>3lC$76Vt|iZ)4o>LAl}+bx{(z=+jsTtpwg1MG
z=Wv^TVlm~!XF$JM$oIbECl1p#+n%rzRtA~XMz3u~C_#`=%+vulw$FfU4Eo$IS+Nwc
z{BBcdrbn7VMMBR2^q`(blMLo=7roc}+VskPug89ozf_IXPSB_2bb(Nsh@CojJ6xTr
zXpwsS0LS|{))dj74v{!bX8yu=3agn`O7&eAa$*{Ba_1GOx1cN9yyg_|+pl{A%`sd*
zZNI?b#VFg1SgD+}!I}>m+OxqwzKKl5y#Kb-_9?Wkhyvh+#h({ZEMGhcTys0w3kHes
zt5}rFl+SEYwqL%IxGY!auG7c|Q0Ipu26ew1AvLCvnPE$+mb=53goNpeIroj)AR&qF
z8`tPQolKhhY2h*$BM=ww7FKWlZupf5Ia+IE$$GMUuPI{111-hK6g7$EAZMljMlKO2
zinR_zf;(DSEaMAKL^pKXEQJh)gBx2$QT{18tb>KJ-}ulH>l|uRMnY1}I5KUR5_d9(
zbmw<H?5>^yGX!AFpvIioJd1&yA~X84+8xlt!~)!Wohad4E2*Cg?8z)E-H#HP(881W
z!kz+CRM`BIczGESYbid4yE7%3o22lN8neRlPFfs&q{rS@6e*BJOpqjvXO5XxEfwCD
zimb1t(|(40@A2P3S$=T#AQ+2v>zDJN>{$!fHlBxDqYE7kX2W3(7Ms#x;sKHt@!4mS
zdt<&1rh<Iiv8u5&r>^);r8V6nB85B_19^g$<BL>A9O|T{qbW|}Tnq3kp(id1G*e5|
z;!e&qQ3(Uh@8tE}pUej}>_7%AZ7{r$rx)<aCkK_(UC5N;gE^>D+h+Vg^IXi=RJR|M
zf~A!WTsYb0j6>_ZZa});&vb0NuA|ZZVF_Q1(;~!?F&eY}*an91#G0*OJII?2|Mm<2
zKv3N}V+lOQQw1hxUx_zJfj7bX?%X4jzxj(v2G5#hHiYu0_KDzF!O&c4ZGHtp6`w;o
zO2GphAC#zC4%ML#zz5c3P}yjrGKivVYhLX9_Dk<Bv2lS3e4(jroCMl$OjV5^mM;ng
zFer;~4t)S0YSA}^I>d6C5`4e2)Bg9ojUxAr($(*}5{<m~c*<u5^qQ)>PDIOFjw>4=
zH!88bjY6G0M%VYwekClDW{@E!dxNak>f^YmCi8mvMCcA@qOx9RSHD9(bPaLkvVHog
zw=G|;#CCLjui|`~+|8^vOuBk{OzZ#{FBG@1YbK1Jg|*bzp?B=<Z;B6<bu(-$*s}ro
z^s+9uu$Kpr&ovaRg7GW*Dx3Upj)$@1y&R+ocRnm(-u8AiPiYU>{3D+Ff}YCS4f%}P
zDHj&T%&PkG6KwQhX4yXd()*a-n2XzVo=VJ;n7w7Teig}imA$yQ16d&-_Y(wyl<DJb
z?#_PW`+&>#2i~QMksfe-)x*Wu_}t&>x|#1n@r8Wp7?ZTN35o`F9IY2?Gc}lBtSC2?
zsi)KFkpgX{lp-dhovvUUL->#g;`0ZKa#i3;4mQ3N(51Y)G9-=DD(>v=<#FmmrK@HS
z26q;T_#zS2#*yhy-!D}pUKpOS<H*2iLUC?T4u<#x9!>p-mdCl?1kZS4Ec5*Uzf>fg
z{`(e~)O5@KhgByjOy(U-Il4DOTyQy&uA9eC8?4@b7u0XniQPBaGghsCCg06*F}if^
z?cJcO1|eW&6kJdh`4US5Cw2@=KxkA`xpVLP|4PJt=8l?M84#Q7l(~?H@jczq3f^qL
zf2<aY05idDcJL-HIIG2XfxULQ>5&h%A^>Q&$)1^I7k!C<b4!7^ztIcaP=#uS5CqLT
z<TN@wK>Yy?llgt(3<AD;x>O4OCldOr=7U389<9KRQbMv?X67=<j(ui@hv;pS8gDvC
z3dFna<A8s2Rv3p|X&D6|#2r#RO%L8A5UI-Si|+%LQlND>_u@UZ6d@54R@igK+L=PZ
zc^zPf8%^Yo@5#BzqPJeLBRw#xQ1$D$@fCkGStatCAw`|rfwZq8yKjZ7@Hdvc>ht#~
z5>Kt%W#A(V4wV7~(w`2Ou<u6!)WvG<lspRE{JJ|%YK#Wgfg3ruR+(_#YMYUAAxwqq
z1z9_ee&pP;2C*;ZX^graZQ_KfkD(OOTFw-UVf*||DqKAf@)XEv``btQ>b@#u!GI``
z;DacW_H(P^Z8oC-xAYGDOOK_0^<<&k|2?+Y5Fi8k7xqp!qzIjsB8I8bnG6R%E2@-p
zwEJWS*jGQg)LvG*RV6YIvL+g55^?P}*1`TP3u<Z=-;Ydo#I@K<SCSpd5^dxxDmBo-
zr)2q6qlUm<_5PO^p7m~v(YKC^&G&N&;<Ka;lCJ8aD4d@4uv6r17NQk86_b6sU~lL(
zDbE<@<>a-K!RYJ2Ohw^$uzg$dlB;d00+<R<9bo{dzK|A+#Yd5Pv+qPnN~Uct3Dwg`
z7iinSxlZu83F#MFn|Uy#u^BZ&)EWi}xafFcV$eQd-45@S$NiGW4f;SS;x^wUbfBuN
z#C)`eCUL(0c~(Hz?nVYj6>&Y^3%oB5y(1?h%Zfm*r4A^M`veX@^xJ3J1EVf_=lQ*Z
zq@Sb<Th`GH4gaRg3tj`K4g#_EX~Wj1XiCzYI9KIc<ylq0-FHw+V&-y>2JN+N97E7r
zj2FMtgaW6i>_9vLr8k#kiswQ+S`YF#FmdY*;ZcY1j7`8vz4tg*tbJPtk{fjUQ+bKm
z^r8Q?sX!E6C7*OWA0SyWY{gfgKARX*<LqaN3NJj19ltPzW{)&`3x^H9`;w?mwV5dC
zwLOy~mr*lscQJ*(esRqGyY-?O2-9=;{hP*k*;!k^VPOE?cwQ-xEgxtKFZ(wg5c%y)
z@!u&>cxy%<mRL8STf5uT_i2p?ovz*{k<}X{2K$_JBA#5VgcU&GatKHXKc+f=vZ#})
zoPQNzUQ3?&k#%UyZ-eY~N{+-@*>^?$O(p-_oYU!kV<z8%|Ho+R>>PCvb6T+)H&Tn$
z`s$83hUfhVui*QoQ@yrZM7fb^>G4UX%H2|l`q9^&*i+I~->}RBTn^(^`Y7}7AzGal
z0Zsh?sv-t)&C%*?wl`Fw2d3kxD=nQ{2Zk;FkmP)t7oprl$?S>AAj#WOB0d9ucJ075
z)t%`gM}d!yChgVIt@9=Gf2aOl+bLz`YrnB7P2urd2b!fHn`zJ$sw~uR8zGfGVW}qV
zoyq^+LPb$Y?ZSSU^{4zGh_m%m#H;7;bNn4#X59`99XX7a*Xm9M=gYk2Ke|tZ04zP=
zUmjK`z5cBomR?~wV0EzyFl2t8gc&&tUM1R-a`WLD3IbEGdb2nfdxB<MJtZJi8>dDF
zge@~$iZSrm@!cO(;Kv4;?_-mWJ7|<F@s8Ohccb!9_2Im6_Sd{4Yyx=#5EfFLmJD>I
z<9d2{vVV(x1AOb&=Jy~?4=YdKIdre>;8FK-<IMO_t&}>~Oe2rSOzu%2i*$mor(&$6
zMUU)mWe8cX>nutd7b;E<GiPbMqxtCi7X==-V4O#-(~J+xy$t}+@N3@g_z`l?2zr$r
z)9OYonpljOkln34tc~M5>RQ@(dhwk_Quu-P`{JKd<l`+8z`Kh}rz$)?iDixjp4&xC
zgVM8x>Q2l50V&A4)kgr3oZyS*yj$P}zj;U9lK8?u39Hf5B6Hg_?D2@x^t)L4&M-3`
zFH9p}tnTvm_^=rN9gB{ek@uDesY&B#BTa0v<Bl<2R@!?1JS0oB*rS~is62&odc7X6
zJnCl+Tdup=aBla)@Eb0_0===O1n57qfE<K@(M6hA_H3~kMsl(Rnm0#hK3##ue^07#
z_{oKvy>-r1XPv4Bumoh?eI%l1K8L%ebaLfs4Sz61-=@-*XgDy2E?4|J<xZ<5l9*&S
zF8~gW)x3YMK_T2yc&GzEy<&6R1NT0r0_N$}(dU^NIV-52^@dy0cw_%WAajw*AR9$9
zi-0*n&AERZUx{$Qoj<G?nCM{;AlN$|xYqiVv%R2BpZ0E;>@(ja$kK;|LZ2tdy8b;8
zIaqWI;_~@WI=`S3Nm=dzeKWg@iy9ix-+><=E{iD@NT6ZwnO?RnL@1y1oH`VWd>xs{
zgNw>h#V_P#mF)vl_gW*8$C4uB#-XRElrSTUeOj|6jc&YXyiE$nqO8N4O=*DKPEx3p
z;{q_$y%ZO99sx7fz1drigHHy4W(n%p^?*9sSO!U>CW$F0rfttt!ndSBQFg^Batr~)
zUldCO)qjz{j)7|@!a)70{maY;qrcs8v=MqWK}>w3s>2$T7eExPNB7^*TsypA*D(f^
z=9ujbyo-B7GUxfFZah(0ggG!y<Z^Pd=#<R`ZtQZqb+}|{`wjM*G!x?Z-zdin9cv{^
z{c2ywHg^{b!?pq#JqOyj9Q+@FT<sVL3~vegu$q|SqIkR&ta_k8No`zPEY9(26;L>s
zB`>f8z!ly<7>HRNVn(!pZ&sPRO;70h(v777S}ZV$xsw8f3Fe^TU<OU%*b+L!lrL6+
zzhF<MkhdYSH&+up#U`D<%V`$wms(dbl|nkCzqP{rR`E3_>C_fvm55a5=K93Gopo~z
z2@ufZro1c{u7$)-%H|jibi2G^vQ_~QpFCvY9z}{Hmw%pezMnm2v{fcZL|g%~LH$Jv
zrQSlT!ZKZwCwwa{O-F>^ms!QdwLV1Hr&Y%$0`c(eS}XJ^yksDi$I_L97o+?q<-H5O
z!W7SVv^!U#lPyS$d#Hy>oZDFvk8?)@2Nog~f|#f6;Pb%VV#kP4*UlNXSU{h8Zj}W#
zSU9wHaDPQ*g786#+m`+V&^IwlDRh7rEU{$iiUKM1zaTEr$h$=v9*=6}wgj~^BOzfp
zQLgAcw87Z^;tD`1l66PloX&`rgVjm;eFTbH;GK<xML`M;G@ty7`VMw<fk>GiE(W0A
z0qJ`mb3U>*+xxbk*3p~<&q9HP*wU0*P)3!;Yj0a=4d+Y9&LBEzl{5WkxZ3bZ?Bhc!
zi>2|>VzGrX>vf@XTkj%3XzgzIiFBpwmSvS8W+ryyh|Nxuo8s$Y+4ik6DO&lX?R*aG
z0YPHmF=Izvyb9y|jz&3t4}&6)f4tg9qNhccbH=7@NYctS({nkr>@R-s``)e9*{2o9
zI8vOUqo`+R>^xqyKTeAe)jVbfUaO88>z7QOr)R$Aku?5pbf%aPV(r^uzvEQfvLgFL
z@^rxB&ZhkVwWuZ1Y6ZJKL~}Us(pPe=s}9!$Vjn&x;T4h?Rw7i(B~>D6384G{DcP}p
z-?+F8(sp&{(snd}0Ka!byoC}3t#s^owOtVIa8w-+E)Hc$h;+L%!fRv_dtAD>zFn=b
z>Dv9oaQBr7IMvNTOsUgs^yHT|2X#Jq?7p78rr~Vq6g_v`u7x~|mNH*0bxFk}uNZd7
zC=bZD4;fSq(HJ*&jHpEd<#3(JLh~mwg$`SD*rA4}5m4($@Os4o6?|^C<hOvuka^#)
z(p~}4&l5uq17dXrXT7c5l63`iO7U+UVo@WXSP9~`B~zuAFxlw!lU@%mp+wZnth9+n
zy4fs-CjmTgQb7*DXKlok!x$K&7p~(^$Qfk#|I*k7&_sZyXGy2K84GRemh|5<1h!RE
zu60eXJtFFZ?b9xo)Y%y|6OOWz4*;h#h|3oGK`V#hJ#{OW;#1}fwbA;43<2gLBG8-n
z-qs&ec&Aw-8nR_T%q`a^{0@t2n?#XD5)I0ZFgYt8_2vm1kJ8aU=EAtvyA&e^sn)Gw
zR+N^mc(BO#DNv_Lr!zevKBcv=pA_PEX5XOp!|X}vS#Nk;7A@EDGk;pWrI9q)wm!|(
z8ud&5xLxIMd+Aof;zT$kP%IJ6B=PI*dz&jlsz(eybW=DtNjlrzE3iMRs^#AaR74E!
zA8J1FfB>;{pWpQ6l7|eQ4^2A(f9G~aPem64#*dfU{shNZj2W-g=NiKs5fYVhK=Mga
zm<qeJcrOREK(ACWzhrvo2?-B%!k)jgo?2%ECIFpm$Ux?ID&%;h@2~#wD)d`Xfre<K
z%+;uKHs-!yJ=`^u+IofgJx<$;`Fb8hKX35bkfvv|(=z^wQIa?SGE>mcET4d~{yT6y
zvd!<Sj#vMAvWNmn8BnfzCE7OiaR&b71F9dQEr$gF3>#K`2|2t|ZF|^w23@UK*F(<@
zxcStS60&uU4kQ766MKze2*~8e37e^Rl=%uHV*WpBl1%}yT$k*z(pZ1p5u=w2*=8w;
z9i?To6pxIuLFl2oy2m7&r<4yZ`W+~w0!Mhyg(`;vgSe2znhOWAvw&`Rj#m<+c6ydB
zHwwzkkMqFnO8c5lC^(yGWV~YT2vY?yTZ&T-@r^6ockWk8WG*_Ihz2IID0^=Y)0=uf
z2*DDcML+~c=v4?widBr7YI<n`5V)hJ`pim%cw@SkI4lx^;tCU<wl^|7#l6Q`U$Hm=
z%S)vEiYpgiw5gbT7T}sec|VVpCFO(fxF-^07RUX@nn(Dgo)?cvV%Hw#cIs$L@eIEH
zr-xWOoqbGoj5}%)g<X`2iE6pyH!#Kh&~@H#Kw<^&ZGyY6XFJ*#w&zx=aRZ1zi;)$<
z*DIGOf)92gkRdaP)Dl}!StV)d+8qI80}T~HMqlX(8Z2E*A@b#oW<M<sR-$)SubrJp
zF;w%XF?N0T_tehiLUyqjLUfmoKILFwn6d^pYORj>H!rC4$#wGmW<?2vbf;arnS%Tm
zS9GDJ7NSg)<+xq6=0cc4J|9Vjxb+*`RGD_TxM9dCzmS2&2fwS!S5{zp44gtXobGbs
zR?fgY6uCvQ&jd`tM}(oCY`)GVmj_RmZFbKC>fL;wIIY(FT1;uS&%OnX1;iqx4$9K<
zftF7p_`lH>OKcKA^(stbi5hp09t4M%_P!>1KJBhJNG+A`rGoi`m=}oXK=cjsS|)ho
zjy|mZ@_K?&#mKbsc&3-1#6}sx9+hnsOO>|SFU^lj|JNlo>DZw*rx)L(SuK#Dwr1M=
z!lcOlRTFf5foV+A<y-oISQC^^)}X9~OS=o7zU{hO#lfLr!1|9%eVA-*+qAU@tk<&;
zzTuEggi&&}NrZ9ibP&i-hVBhjDxBV_J7xQIaUVz}<mQ0Rpf|H}PogUGDz)zVB9>$7
z5LbWoqnr1-PN*p{GjO1jqnTtRH~-Y=$55rMT>&deJX*?lobPt={r)u;F+}XztM92-
z_HpzUKe_?3DQB`dQ*i669t4Kxc~O#9t&lcTYR&bObNk4NPcUtif;h{TF+8y1o&T;w
zkC2)oA+VY1YZB|;5!=I$BR2JY-<mqj>dc8jNgAZ$ZY(o}Mm|MvVZgqP-BTF8D_WI(
zY0g~Tn8sO)DJH?~KW2qsFe{o3&?PeTVxk}0!5-dO1AClwvMmFZBC4dhMNzmUSOxH&
z%MgOfLFnNh)?P6R#iXl^zeJr<dph^P^>zv^v<OzWKp$cLkFRdran3&4?i0NJAu!lR
z0zApSL!kIJh=3_CzW*nhP9B{?r#YQFTHmiMy}_Rqke`fiV{!x=dB6Rd4G0-m7?V>Z
zk3n4*MK++LTKq(!vA%Np+DiCVfoR+Np2dkP%4r;bl_}Ma5che=m$eyRJqm9ev)KFZ
zW@jO?=w4z~uN12WMm^d6v1QoI_O)#{{*pY?lE0jb#S{A#RtZ3K1!86YSC)TwSei2j
z$P2S823^SO9?jwXWL)=Gt#;yfS11z4k?O6Sx08IGiOf5~F5dgl9anP7+0sv++N4X6
zZtMFZV>!mON}JG}fa3i46~Dig?~a6obUS%Gx>(Gc0R#DhTk6^PUMz{*;TPBto2+aM
zJFeFU^FW=<n+Un-j`M*9vgM^I0#AN(VT9sINi6sjC@8p)ww}(5Og1s2M}4B@K>cAx
zyn5+ffx$PF%d&&nMP@ujhW?_?+G|#z**|y0AdE$=+A*<luM7HQCkAMFEg5m^FT&`~
zJ##B;x_2pz^cOaO&JYkJm>)njz1!qgzHSbiv}|?H8=ZJc#9qY@1YUqePy<Gwr03tl
zYJn}xqD~@p_BDtX27yR6U1p}^_O`NjVa|v9fVb^58m}Q_NNo*2`||FsA<8UaUiBL9
z0}+Ps%@M)W8urAg5}VajfB!k#jJ2zI2-I|84gX;}@@}b0ynEgTFM$E;fwqSR4Lnxl
zztvQUa%i1vV$**n9nKQb=<0+!B{2SzPjr~eJ*2Ujb5}tdT=-ZbtMrtW2>Y*1%^9nc
zz+<j$SI2J~%tXhx-Mq2u870RRh$lFO_70wp7;!HW(pc=`0joXNKosL4@lTRa2=Qkr
z@9>$m%#Z<ra1g!K+nIorihCTh7FB|(sq;WS?0zXSXG9vDMJQKpmZwK4%-|7Na(>xm
z8Od;56QwV9z@7ua9#ULI-gYkXp$E!moyCVJk|(%HD2+a#6-&qwR8}wFiYHjUmHwPW
zm*Wu;bSua1PuTeoDt_L5%6Ai}mgOG*|C;;iueR2p-4-a;;1ms7v{(pEkwS1SRB%dg
zin|p`(Nf&qrKL!5mqKv2;_kuSDR*<u`M&$Z{Rb{<FBU5#JIUVj&O7rw&&;67kw=!L
zGZ={nSb}A~W(*Fq0GqM2`>+48KFt#8l2nuH-)PI$Uux1qzkgc4W0id}O1K@WY#Ol?
zpKp;U8EMZU(q(MT1~?{P2(`)c{Jtk}C43nxD_62hIzNe5_#N%?k^qYB=i_4AZ9oQS
zLhVyUAfA1WN-sK;X5N0*5YnNT19HPY$QC1z1D3{|(ZfZ^&_{Q>4Hu*vo}<c8;>6im
z6Ae{uod#ZrQj5zCdF4#NAt3T=pzlZwgGIjncY)l6ZK6&K5`)xTF<E6yUTfwMc|vKV
zhwHZ$f0pp5(7~f{tnns^R~4eK6y%FXR{uB()Rk9yY5XQOaL$o#c-f8zv=&3)NqTr?
zEYs3rW>-qhEAx!u5AR)LJ}xnWhx$(Lo#P{hOZRvYFXS2Synk<)rpP=`Q}KGq$|!+9
zvV&v6Td$<N9=vK?sS>ic$0-}3vg|$~$Y%3tUoG@N)~Nv&Ew$oKq85uU&268WX)$A-
zR$1A!crgvgkj+nn&oMDwJs-P}5up)C;1ft=)n^f)bNfm7?Bs72SWv*k+b?qLBLzS?
zYVnM2=>gW1wFe0Q$qe3EKGt|1un?c334KsPRZ<eyDjqBwk}r}3Q<&1W&f1~4%9gDW
zmHWOi7za_NQl4aqt$39@|FMB7&;sHKWHN59kQ;>jBVQI9XlO}<?<ekf?hq#3+)%8Q
zcS^;+mL$Xee)#Bt{9j7u>(P_#>_cI%LSyL=Tj=UcK<XFn?nZMX|22k0O`TbZBJmmx
zB~1_+*)4XrWX-!A#UPrU8*T({9qz-7!quhlPw3W+$gv;?6)O~7$RC!4Jz+OOhq2N5
z2gG8*%as$y<)a_Riv{2_*^e@+c%1qQ9QA*NEHKGmlX;LUyS0~x#A4koDLdW7m|y#$
ze92kJluv;>J?j$m=gc3?61(QDKU_iulRRj4S!j5ly?($os96C)1#om_2;H_GDCH)7
z^?X9?YRtnw9jZ*6hbn%Jcr-RnkfW(ybMVIY{4(UADMp1`-*$Kxbm$kk45@#{5EJUb
z(Tm}Ne*zA17=g9O^2g?5fnbyv2QG40d+DmS%$Zx-#E$!-ire7X%t*(s$K5aY(4NfB
z)1_45em+Ae7THt-a2}A2VYOi{MqtW59=Fe5qhdBs7EZU!vhal{VAP?(KWP|L&0biz
zjxFU|rVu+)CwuQqHHc=&6sktcEi^ZF&L&Lm+dpw-Gp4#m_%JAtIeC4oqE=ThHO1b_
zfpcm6vdOlfsNi`bG9-i98t}BxExn`thm<HL{rmUZryj`mrL^*u*<XM#@XfCaO&v@7
ztzm|0>(b_hwYj=?oFDYN?3MEKj|ElWll2I=T+_np@w&1vt+98r<S&8TSt=+vaLT1V
z9Ux9sYTYZu20cKC2GnoBk|x`B5{3b_+<spoc4l~Wyxwc1^bZpE7_%$&833O5+$AXB
z3QA~Rg?{OcsSXv;$XD-y3S2B>vtZK!bXlF>yT1V5cYAq66v0I+%ZQXDs@xW>7SQSM
zPe{^Yar|3lg1rvPxasI}QO>VD@!Xmo0^j$f^{e{4>WZ)#rudX1bzU0guCPD!+@Cgd
z$6p?&FY)=NNKk=tmc@Pv5Qk`9v&T#?D%>l-@;sym?2GFYm14%HC2vCV6<I~JBXq)y
z>>Cp+qjXyREWS(rv%eXykDD7SWRC}*uI+A;$xI@j*aGk3S9Hf)T_!hjhjO<BMr=Xj
zb{D}1G_+BGiG$&dUrJ0^JX`!N`tds{c`+7qCvGm<^=ZDmnuHS1aV;f%mr07^db8t&
z(<Rt=Apb{g)R0U+JNe2PIzdFHz1+&i`hXk<{i~B=q4@yC@fIzeowa_ti$)UY-TuA_
zk<sGz#W7(L$Zv>Gs3S5G8B^>_m8iysj}Tw~(k|h(98EOiu?-B)HZZUH4ax6gZ#5;L
z3@p$Bod}L@K73BwVRII4qKk=Re|TwzBR38eVwemUHZxE6`H<9hw~lI(pOsW3oKvN=
zd}K}5b}lo~6^VzM|3V1eTMh^r*98(Z=dF&~dxQX-wl=(utpS=wl9E2RVinA+I`Dl+
zd`Y;@CHY8b7o&0p_VW*Wx)~2&+~)Ql<r2NwHW#I62Do!o&zdpyP(`<~l`ri^XP7ku
zayadKhFJI6&MZ5}<o--Cpy(OQ8mWy7{zxYL=FJnpoaXl<3kpO!R_6TzRy0>`2*QnM
z^Nii=WbmZ`6d*>Gldua5uy{gdi=p-|nh(a7g#%YlEj^o6&;TcTd0w-)e2UaEHB-Dj
z4APJ%47R2mrxg8I#fgCXz_&ExTQ}YZ8IK<vPmQpC>i}&I{(1xv(5Sbhq0z2+g4tAr
zIQbwLhfe;5S=?*wJ^zMmQ@y)XFTS`wqteIA5yC&aixegl`DiFOPxXwsE9Kj%P*q0%
zW{OEPDmWf$<UD5ag*#Dw31k8@9Dlj_;!nHK9uZIOpD?w5M+u5zj)D;i{T}^JKxW?7
zIchfIkAca%Ob?`Vlr$nBxn6(B0(}%+zL+0AKME?WkUmoChy-5wrDUD^EQvP;ALk9*
zb4c)tbuQ?_%S-Qs46y8MnnsDC&p5EYy!FWmE#BqBGWV<pgQ5}oR{{E|Xb&`1yLe(x
zPe2cljg?NX0)Uo<)>T5EP0}X0ilE}}Xm_;0sf7@&f#o`qbfXbUw8|OOhjjYfODP$D
z>spN2e?i7>2bdwk8hqer6RZ?uKF4NOE{+L={YMjd@8aK6_NzQ&+0exu&`3;YUz%bn
zu^vU@0Pud77w3U7nQ%!A`r|v=m4T2#-4-nbuk*E^Pb<WrVLAucr<t*2@syxygA06d
zT4R;=sy*rptEW*(mF(A#z4n0d%B$08ev!0a4@E*GTNx7^BcTJ`DWzi$hT>nz!qFYJ
z>Sdz+orEnWa`7XF8m3%h*$%{HxH-LW5s3^@#?bTH{^{~iQN_wtK@Mq>9OPiyppT#m
zzU1oyV{%+ry<Uc(JV4ay4(88R?cY!Yw<W5$3R28vk0C+BPB^nY_<_iyDs9wqA&fqL
zEI-~^CqWQ5N1D|{{vzI}RYyeRY>P{N0Z)Zy)+9M}3%5Y&8HD4mWL<2AK^=F@o_Ul8
zN1a<HB7%fKSW>e=A=Q?&j~d?CLEGq)6*ue;i{%~m=fQ^bVjRdS<boo5A{mebohc02
zcs?cTrDrcB6Xgh<I9_TejC|%>I#<$*vT+@{;1|NiRPZmA-T5{fSPw*ZkB)w{Wbw~L
zVC5+F-YNfFNcyc$XCx}`c!<;HmIl%98t&8Vx&2Y36DP{{U=S+*8APZ&(4Sy$->0si
zsc#tgGt7ksa3$cFRI?llU!eP5hW92|;Qe-DV5j(PgjnCLQxr1z*6jr+%0!JYnuL=E
z4Fb>KM}2`YL)p{Q*+Z=AeT43W#O(8@`Qo4-0-mmM`}?(Z3u{Boj_GH6`~j(m&qo=b
zz5r0C0&B$%I6;FF;0#v8lK2BljwnC42i9;Em#JBv9P224+U(K*LccEl9uuoU>XhZ*
zR!JYOlXz+e=NYSk(-;ed<YRqvPZ*Q^4nX*JyEk~+1i4xnO=<?iyg2M^ch6WdfHEVt
z<r{*06FY;lwi)f1vorp1OG0UGNz}=zVgDrz@kYr8QCiSSgF-`$RC(EmsYzbXF))8M
z&w51=?%k|}FIB0H%FjR3ZZBC??<ptUAi8wC9;Q}G=+6Y<rCJSV9e629{o(IXRpqI0
zZG#hdw5UwIXEn(TSH1AUZSRayNoj3NKMWCBS4W>;P*L@V4$~0GMd4ZP2KaV=Zz)Iz
zf0Z@9?JC1by?{p!JXg$>=rCl3WvzLI`hKm!gd37OuB8n{xr!lVZtg=0R3SQ-i{U6X
z7V#@hzmz1o-25O5?W1Na_2MDc)VU+~MA^CW(M}gNG+9RE747AIM7Geh8*A`t_n?HY
z(iZwJf_BPXw8s}BG-$~XAG9RU!FDUHf4E6MLFdlpNSM>%Qv!Hnu#^GC7y!&?a)*|z
zYJH#XNsooLkAFYt9c`q6u^DPU(cM8)o68lt6jmF}6uNYLv7j+>8u9x4*MoATEF0z9
z!_L+9o*wRAECG-p+ugkC3qRATu9s`Y4Q=ruT0K!zXA^$BZp3I7=*jrLhJ%bLWe2@K
zEuF6cSMdC+A$Z5{u8hs!AUicrT~YC)K=rJy-i#@{-rs(<a*O3#LCrO<&YkDED%xmp
zZO&t=<b1XMI=2$%Ng*47diG*|movx4nAq2rr&BhkTW6@@G|7hLslZ#5aiDhb11PmR
ztA|@j)sCC1QfvkLVEl-47ywsavF#8$aB2;arvZ&Wo4hbpfDdj^CfU3cj$Zt#Y|H-8
zAddFy*l+a_z*V99@hWl!GpfakeYZe9BK@2Q$Y8h6IQPyCCeJRQBqt|~(QC9kJkkzA
z7<2{>(4izAN8%7_LQVaW1K~l4lAwbzbU>fj7ovngh}0H-C5tKOVug*Ubq2%nc@lAv
zXP@HZKh~7+L0+cdK4VP)WUpVuPx0wFio>%L4Mz|VUXdYcGxc}{a_wTVc<a|`-D*@g
zuU-&~y+FwB^W)ND?^8l=eh`^&X_F{sv{$Lno5)!nDnrkSwpR8D?_MTpCka{*v=;&)
z^jH?NJr(Pn*Fo2)8RU#LyEeRJ9f?7Dm{Y0xGmCUs+9p=$GBaj`yOKVWs0Y{jUb@Jf
zLNNm|&Su`$%1;vM(EUn3i?T74+VpEQ$s=IO75IeAel(v(Ka-|W9>187Q91Xt=jBk2
z<&#_`xm;DUU(2!rSlQ3~A;@bkBg&^_9?ujr=t2dMK?k9|<w2K6(0H*hpzc5`0x+L%
z$8<my_dj+N9~;fqH)|}KA{dXUOmD3HVv-UK2%M*joPjG9&iS5oZO&eZdzW}TZ+$r2
z$bkI1<k*6h5#Z%Ef7#%pji}OQ0+mJ6MXm$@!Q@fW@jYGG-(uJJRPL76(7m|TB}dT~
ze`)?Xs`c9d%v_VH5+g&h8NE$6$DEE1OUjFWr#Y?t&W~vTZKyp@H<YTi<TylS;!+Ob
zH1du_21`<0@;Fsf>gju|qBG;EzIh;M=HkEdzHo}gm$4}A|HFs<<e+3p6X<59I~Y1S
zkM(yx{j7$_X~x~kO#Q6z*L>z;%d;hjvfpO9s9as_^43U!-c3>l7mt93q{0sY58b-@
zx}B>eBz=T<bLmdmY{fdbYwf6u^guYAA*%6eLpizlubY<gnA-*t)fj5wqE+|F5?T*F
zn<6&6aNiTj-$5CwNX+1JG$?bJwBHRPE6$0S7z;Qr!<`VlMl;BKN(y6(su1siG)j6M
zc9D5J84}@s(bqJ2Q4pA?O4K<E%3(AVdWGj`u4&#zaUrZU?<ro*9c0~)&*%(llAFD!
z3s(9t8E%i?CF0L{oHIGPukrSpf-3H3j?p%ec}~y3K<fts<k(so>9Bu*jj`PTqFtUy
zUe5E9ULBnQnz{5T-uD8)8_>nIWe7*lK8tLxl0}zMe^0%V1{I?*FqF%RH@-5vgx#96
zrp<^D*KS~089kowfnqMg8!l`|kyDt4K+I%jKahhLhkPh&VTqvlH?tFqcd?PR45R*)
z-XdQ-ZDjLPj&2ij3X7jiZgjSYt12eR^X=mLyv#03VxxT4@4;^tF#tfM8vufJ50n?S
zuP6l@VK8GM5`i!}ZHIC^S@h!owSBaRlWKcV9#(5G;*FGi+eil%fAwsUZB?*QkCaf~
zTRz1a(qZ!p0K^pl*kx0u<I`(Tv%6SqYO{zTyQ@x;v-c7A=NHXGSy$L06^y=+{CRQ*
z6Za5+e~~GSSX)?qLdaU@;h6GgfN5Iov%F`ld(DS8ao`f`<BAO7*0VSYagP&pRB_|_
z=+&(+SW07nJ_3l|(-tCAc9eUcL@010G+Iv4_PrExXf_00m@qShL~Gb;U-<v#J-91;
zH$y}4?MZ}Lx>)T_UDNf8{Y^n9J-ge>Q@vK*3$d8K3*pJMu4DHEvveV;yxXOs$|iG3
z2-4(=vTN`dIgR>AuwG)?o}2d%+rC;37DkugZ%O36Aa=Ax?S`6_(U+pTQ<j_|ldRJZ
z^8#<wCi{%j%!JH2!#$pF@5VAdtyJrzy_g@u?Go&l%2$wl1SO~Xo`$PRAgs=`w#GbC
zg^~$3H#t6k>b7B_<Q16q$fEU*p8UoFZRW?l5sC6#vdUgEbJCzPok_n+gsfg)mZcCH
zQ#JRH)4n*Y*WYO>M2d(yP+!Ub1x1f7vPN9F(<4>zYT&5sW1F&Hfp&cAiAcEnr#UvY
zXajR0rzqGD9qtDz38r*M{N_R05D)a3uTswcDa1Zz03hVUct_xnzYv4M1(TeKEcJef
zxSp|nwG^G}j_G)r@`E5ng~Z$$9l#t9WnmmEnuPuYfON&G&%iYMcdrN0j#z8{g<@v~
z&~{7E**F;xFck240Ptn@#ICxfDbQ&>i^kWd$SmrNJy61N$l65D(<$8jkxkJ!fNk0=
zGKVwX!GB-B$C%_!O7E_yeBWYg&<_PE!I*(6%su{u65I0Tz0ezOY>t7C73_XRW-(`0
z;90O)z)ZXZr;+2aT=HGb{Fa*KDH#YQTd)=4<fLZ=0d3)-01nDYIdWji^-Qf{KK)HJ
z&0!*bB-Po^xrmn-UlQ{@Gx9E4I1EyQFKs5~ccyytK-FFctvq-$&Bc^TCgs3^r!R3;
zFx|6F)YkDQJd|cq8a)k^uTL$$kt};Y)mFTRsl==Hd-!}``sKnP)y+t*05+s;u#2F6
zW1jDpQ4YnIq5Y3;<x7+?6e49V`0lne3*-zt@co8La4cw*E_ryQiq$DAC%D0H9>r{2
z@n~Vxi<FyX!I4~<xa;u)^Cx}9qV`z&;l3HMCfI8xvL0Rh-T01`^Huz|Gex(txuer1
zh&GgU4ZQLF+wCza&FYq69LzCJ?{U20!g_!iZVnazX)pisc8e0=EIM3?_!VhyjV%=P
zeTe;V&IrS8_mchoG~=@<&YIV6G&_U*_WSFDPw}?5OZ2vSx~uCo@wMfZKz7uxOp=uG
z;&}G+>Km(xmqkSa(;rXI=YUyIUB-+-2SE>?qvo?y62JxeNysr7z2Pu*yKQIBxL@PW
zFLVbOZRkaJ=onusKtKW!hi$V{(&8P0=BVLwtta^;zdcn*Kob3ssJGANAoWtWq4VVM
zvsvh6?@;PGa_p&ym+6-WdJ<Ucf44D6gQJ}cUFkMoch|G`#|nB`1?Gehk#!=>9(jY2
z^)mbo_mA?j8%YV}C4D>Z`c`%%(gv1Ex*WUgPVX>|9~-WyrRN4p5i-#UTq`Cf%eS(>
zhMZ{rJk<oQvl?}Bq-PlV12`5N@#71P1M-?AZQtiF?OIY7i5y|ipLOf)96CmM`Z9LE
zP)mE`ECsp)_5M0fQ>$W|>K`>8z`A(o`4tMmq3VMI@`1#Xje>Zd#?wwhdvFAlS~1pU
zXPr6kfhhp0wJiJi!r9*oc^LQ>nH@}jurtZ&31Fi<4SJkzd32>p4Qt`BWR_<DMx8cJ
z<W6jr>+d`uqtTIP;PUi=GCv~ViGWOD^y71!NHMR=5=VeqYMjU%p|*2uk|)d8O3b%d
znqeYZKm7zP>A+j8{bFHGe8L&DQE1%63;APyQ2=NfjszA>y$T1eT~a<xv{ntMRjXYW
z%B9M+K};J)@^t$l?|P1OK6r%(JK*+>yHe@=0${*1t!eYoy{k%3STw_4nt6(FFelPN
ztjm-siFG}RgVa^;`MTdo1j^s}(TF7b5D^_Axz19cvu^*qVq&`!f=>LWo|)s+vMsw<
znC0yns*VJ>3~C-d!U4?>D@^e;-4&H%H}YkmRiHOaipNYz4lZo4ICw=U45!rF+G=}6
z<f}gpNKnw<H7G1}t5tr(M8m?`D}}Ke>CVFoTKcyQ;wl0v-0DM^c&!FxNQJSmym!aK
zJOu0g3djYMdBoD$nhMR$m4sr<C1DEY{y4($AerH%p3#_C4n7O5e{O$#??1?>*n8dC
zwIiYmS5bYAriSBwfOi3C<Uwl18X@Y$*5YO2M;Tr&u05Ht4wKLz(w`5MH?WY-HC5>G
zSFHz>p8-Mkf}@Z!k!EshRL2Whl0uR0RpyQTt5kg7j%jE}#bJAoCl|(H$7aOAm0N}A
z5?~NqEmcxr=2RhmM8DJ*!@&+n<<Zdv23?p-MwoUGK#uD+R`+O#eGZfy?5NL)6<(b-
zZmeYR<Z^E5q6|xk6-fxS_FB4Qi;Ja^y+!uUrg9A0|AhGEP?G)dS<%mC$RfIGtn><V
zo!PlPzFn=oB}Vxs->+UX=pQ3ZgrdVUywGu>$Zq7JhWDBHEn4t*PtD|jSNOe=@25J4
zK}v8#3zC7%j*dY_dU8M1Cl!xS2$P1fUZTmrGB-7swN8eIsEpG^VM${0zEMQ|28Abr
zEYNVEGU&3dcI-iNGMB+aRr}6PS*u&P@upc%sT3>77+@vmCHBzID6ju<Ytruj)#b7r
zRJcq@)3YYld2&9F;`QT?H;v{y5Z$GXCD<!foH(>Q^-RddU7_=HlWXla`YOxjbJ9Dj
z_-T)8Av4iY$lLte;`N_R2ndIRicduQMH=rM@(S3nE(iNG+^&i#0h!*Ru4n3A?T1<K
z1aUpD5H6*R_7P?5_=}}Dz_tFM#JRejnH6~ljKG~)b9cQHrIheHuxXKFXY}P2Oyq+S
z570LQZ5fs583!`uUs|0=9ob*oXGlQNjIWy+X_X|ek9=MSR_5@F7q$2^@hT1EQu9tJ
zRcn$L9U32DZ8Qnp3L22zFfcUExjoS{za8!8qK%S*nkHUqCI{0wVVhE`UdS0sif^xm
zms0_CPXNW__AfNSQWI<<DQX^O<4pvDXFkQzslkl-DktNXL)h%^Pm3jQ?EAeT_v9sG
zA%eq@+{he##=P8&YuoRUYz2WNJ~MaUopX795ECyULvZY6PRa*G9(iL)E{f8*4`vf-
zv}UGASr}n-LwNCqzz+-#TvI3A`Ob+VSH8Eaca<^4(>vc$)n9b5lTT(RE;f7u(}ok}
zf=zV8)dep+Dd2=e?F5Q<!lXJo>=)aOW7^CLh7;%<P++R7L&1!emFQld=7lG(ub6X-
zEc=+gW&JROFU{zR6%=)@=lQ)!BDOu1Majql>HJ|&fUJ`MPRO(Rj3wMR9wC@Zd0m8?
z3|e`_+B)jQKEL!j|62i43JMId&7{IDb&e5~C+oC`P}UI;j818v0I`eSz2lIhpJ|O8
zfTyVNqG1K*!!6K5lCa4UlB5)2nX1pXh#0xygk!;hvBjVgoAN!^$HM_KBgeomHZWv)
zEzxOo$(5e5OsRHmI+y&^{b%FXyu9^-gLs-C-GhlpIbJ%!$b!%z%cjL_BAg?q6gYSk
z7efjvLqze64c0Rl`fJCp<cnn@5Ef6AA|^`xa#9$8Ne03lx|6)&8%*|2L}sUFcq?Dy
zykl&5b4jmOl??RE`#l+ZUC?3XcxO!vc?@#&$*n$T5>Lg00VANNvlU+B2(oa!IE-eI
zubo=>JrOGU0V6QKV$^mx<WsUlMw-xBVE&tGXurufGD(`xY1KhgAHDI0O20-6dMSr8
zF=_0A$PrAo^+l(Y>}T7+VGN?w5zyQb=po}@AE_E5yLr07tWL<J=209FUOa0qX#}j=
zAS!xtxCMy>VQ9-F?<hM=rvm6Ll@+=rqj#;A;XVGH%EitZ;|<S|Q^IS1OsV8Af-jt@
z+fjl4*-W(#gK}fdw-V`b7?P8N%|go=12Q)zgH8Hlc>?kZ{s#Y((%SsfzwTT19Fqe5
zf{k824c_6ZPh(Q+A1bC@D6qhpx9xwYbPPM)GURRu9L4zfEr4mUq9ZjZHZh~|hwQjz
zr+pKI6@k!v@9ju{Orq4MmcQ3qi^63}hcP~3%lyv@<vL!hFh5T54old!J$idYT(Qp}
za9s#8`aD^tJY&M?Y-^Y2N%V#%skBdN##L3|&H~ueA(+T>FAxmz>9<`h<eQdu;n*(j
zBReXh*@eYlY)#$YH!dy(CO>R^Gz(GOQ>O5aC_)-oqGOalOK0aguIn*Us<(KBbTEra
zsQz{2S6q1doJQHaHc)=L_b_7cRwNxxz>Ia@(#JK5jd7bneQ)x@1zokq&He<s<HtWx
zI;26GzSeV0|7aj{DDNEogN}FDx_+9J!ngP?|Csdynj5fmUk>HfZBUBsp@&ftd5xR^
zxSZQOhBnFJ_;&Mqb9ZjccM<HyGs%pndwk8!9^og&e1xok5{^hEyv6hK4Y)^TiJT<i
zWy-Dj4Mm!r-1Ds?6;Hp-!l0y+Z=XC@=?U#{Ld@7O?3`jIci3)s`{lh|Hr`&JMOzr0
zEb879h?j634T+!80Cr}6K(|x%4EORbPb1jGx4`1|yX=R|pWh$%Cs<AjO=_<i<hRXa
zcBF)*I6bG46}TE-BM?&)Y9EV3y{ShJ(NA*WU8CF~z1+Bdl0T0kK?s;}ZXX5zeFu_@
zd*@l_<Bma=mj`JR=o$?=TarMzO}fnyWsq1a^Ut8}lzp$xfH@9{QQV-$3C)#=_(g-h
z1868P$J?$Rf|wo!w?OaFs^h8sVj*8q{_cfoY{~vj|K-<+JY3l@;j9vH&+|rA&LtY*
z2}GO_1znx_4Mp+o9!(;3EyG9!xa?`)<Wb?e)w!hUuc7*qGDSED3bZD*vEO@NIdfJ{
zx_z%|z0T|?JY!@ZFzD?$xowB17g94+4AF_!4<CW>U}T!f9lkGvGSGPaNX{}PSYX&P
z)LyZyTidu6T9t|;FVw4hG3m%UQTc;XDiQo?KSDAt6LT#2HU|m&{8h%EpzZyD4gBK%
zis978c~=|3(_31}OQdHGgfNAkZ;Q9hZ(#bCO)5R?$HqtY<$=jEB@apdLEyjos$MEX
za#SRa1v^nT!<{RGQJ}p~36iYsH#69z2aPN_JZG9LdC*^vNlucfi15x$PGEa^n_q&^
zp`xXAc~?aG`)_|e>iYr=j$6Us5vU9XNG2@=tj#Uy+q)%gTa(E$`OJ?A7J*d4Y8gNE
zvJJ$91-g@&64^HeT@0dk1S~;;kL!w*>k{d9fXU8)-VgwjOqzORiV+w3P2ViG0CDQT
zoN<(c_viKAbT}L{t;Kzbe8HxqTxj<&00}fe>W3^F_fX(U_dU0re}UBPjs@Cbn!N~N
zAOyNs7M8WeFD?&sVn0oSb{)rj^1enBxWV~5aF!sXle+2#|5lUCR$JcztQ}+SH*`RU
zL}I(Fs?N!H{q-2&4tLab9XiESNrV6gaEITNRiv^Gmh<hFPS_qjb&OD}hOQ~40B3M&
zqg!041!g*<#<E9vgYBAhRxe6g`d8PVi19dsRBL`*>DioqY}Ec>Sf{Z`x-l3&)Hk9`
z!t*Shh06hWyS^&Q+cd<GV^u}RhmsEly{y1O`#kIwR=f;G2)2)cgrkP)HeRH|9iif3
zJlMS=m1=1F4JirJ6fTbh-=wY^!vh=Z8gls+3>U0QAO~@mo?T*3bCX;d`*IA;M*k+?
z)S_#=)Dh9r&m=h2-2QWQdn#`_hw`LvUER~K7#>7p^I`ohJW!rFquJCcMD;!1iLrYW
zBv@wJQdGZS-oSEd{p?y<jL+UJRjrQ38+=@qr$OHSxC{HuC&mjwp)op%Xl^Tqz_3Cc
zh8)m>3U4kIF0kdvO)uOy9~!%VVeWkj9#B2*NFu^SlOQ~4DrRF)KR!NpPA>pwS}lIe
zh?MKOnt1W-WuGn09q3W=FpCbg)>yuQ`)zOAYAUk7e8KkQt@{_VLJS}X0D^&zLG|)Q
z&%#G^1`}z3=l>`{rECt^>4=_TlBv$GQw>bRjOWwO(d4za!M#9hno@Zp3Sr>`Cr$!J
zx*dcw(;k+COnlw~A%cO!J-*?b?N$Ec1(oq--5YSIhtR|=g`fE=b|aOw@HddBWNnuP
zX3h_^PH#}~|Ev<1z?3a*?fvA)P?|+n0TsE?ly|JM>%CYHJ>)pk_d^w<ZjOB5;M_6k
zFDm1T31fOd07M?gY>CMbt=X&Qp4-k1hIS4*ki?s|QFWo`-tg*z=Q~H(mG(w1kD47F
z^*K!i8(*(?*>aW5Zyj%Ryvu*#?m*6r!xBh<D*lk_otZ|wH~ZaMhYfIgulpNn2mdM%
zat!<)1*wplVMUV-l?o;nA4|EX3)NI^#%_kff$89-m6f`0VMf-&*#xIrG?grxoYkgw
zyy5{_$lJeR8l}#_3=yRC<0pNq#&GmEV^MO~Q9~Q0h`d3j&nHV2BJWd~ZG}@Uivb@4
z><2T;kvtt*f%e_BxSIX3LXoUIJ0w^!iIhzgo5_~o9_2?C=i2kY=z)qJQd5;9-E~^`
zv2__+O7UPI?8sccxV)O?S>3VOL1$z`Os{}9Wm^AqDW3SthtkLzE2k8}SGx$BSTZTE
zi8;a~i0zsh!ip(#3<}Rnded?k@+q%$_iWTCU3zplPxOOh0+0>y%8`}6kGoFZh`bT<
zDL^9M8YG2YG-X(p(#?qIYyXaTULQ47q_HOD{S7q<I}nH${c2L!-tOr<c7=@<2x~cI
zg(;?JTq^^v1PH*2aCi+_4}>>7qku?;+m_!(y_`qnoz@z%_c4<U<GLDQ1eDMDR**uR
zq$jasx9I~0io|s9Ylt2@N1B`1SD3yndqg=TC6!}A)aoY{ZjzmYh-iJu%vSw=V-T3;
zNmxbTz^DBF)jW68Ci;m6H@uO6z`_Q=aL1KE1GEx`7X0K0N;8stnA&JHZj?=)Nx!@t
z^LF@xrvwZ!%FYnU<FFRWp1wR1aqSP43TKjgS<i#}db?g_qI+d)@Ulr3^GlA<Ww7eY
zT_5~*Ad<{Em~?x^Fcy6pqyT#d01(9gR!$PHt611_ac`@mhk9Hmwf!EWvN;zh<qOG<
zLrf?E+*nRcZ|s{q15@&Ln6O$z7(5I(&X!5SO=BWMZvwF%&;N*^s+>Bs1jRg(&~BRw
z_R!tq1TvR)^BIc>>y}`A6s(4D<w(;5G<!Mb-EySBS7XVJ7jq}K-lOTBw~ro#*JlU%
z1{TGwb$ynN9{WtqG=%=#fmv`ZbfP@=b;-b%n?I^{$A`SkxXLTS8yFr|mUkqi+LpHl
zJ1_hMe@`e^2U6WKtR(e5zEu-%AgW_k$nV=ZGg&a7TT^|%u+}1SXA&OnF()yDI8rbR
zksx+p5NP#Jdu}HD2;Bc3u=~&D$0P%^9Gin={O?|N1>X|qsb&0T6&QlxUg_H<Nq{41
z>lTXDo_YX=3|U|6Vyp$`>kTPWuX?5=)Db*c4HfYDnU-f|CYv`QG_(8&wxyXYF;P0k
zt~s!D6^xK$SX``c8&b;1BtN~{?=;a*6z(l(>u<nSS={<_>9?){cxzTI>ieT*)z!J@
zeM7{;s&S-3(J6D!x@USq=MMPH(NP%)HEMon0z-Y7w7PTi?%y$Y(c)hHorqII+J3~x
zXng-+1Mt{vX&m5r<3#@=yqVN)Rd^Um#|>i?ntcDuJskZ+k+z|s^tzqY{r=0j$sL1O
zYd2sk>Z+pDO#XszSFvb3+T$Q1E-kVhRSUyxHR=!|sfatWJU!pJ_GZ&!6cazHJ8E$a
zOp{|ByWnIMiWcG(<A;$Mhk{xlCnu`~7lDvOhx{Ki@1jT6JmeNn@KIP@#pWJ6j^~`$
z9XldrMID$^)IvQcKbn7XSqb3vR8!!MYW5V<@Ia?)|6%sid#6eN0T_w(dh>6lUKhs6
zOVWr`BN-Yr5`MxHVl=h30-~7tF_auqK#nH=HBiR;?MIOV<<%}Ra)e16C)|=L-<0+X
zB)B_?I&fGhS+9MJN@TuuLP=7T0*E`a;O6M$^XqQ=v_vk!MayMNDiIZKK2Dd|zCZQW
z-1ZGTQm=FPjDJI&j>&`mWw;a5x_J&^Z4f2}LMLUQpG!aytg}K0qGMX0+~wSlSA@nL
zk9Ehwk>izPAM^Yw_^32IWDn<~w{0w6uen^%D<TSS!sQ6`vfstI`Dv?jto7rv(>5>3
zT_`95hr3{^v{ZzK7Q*$zqoDV!T`-C0v@G6L>)sKE8f(Y#gM)MHeQ*pDuM?fjv_3L2
z>eQg4mUw&=M}@>xhCGf^L{BT1^a(El_~M2$11&djcIY0?6i$#irpE}raxK}+d=puK
z97befPJcr~4I|Aq1<(MyV5h;?6@|OG^Cj#vy8SEbsr9OBsL<F(-L?dHKKB`DxC4kG
zM5S2lKh1O>m3?)}9I$Tv*)(_{@yid$L9sC!{{UqKPegP?eTwr?&CpP~AhH^p;X4Y~
zeAP0Ow|<<Pe`LBoCmd};YfwC1Mqr`Em&zGCu(=6p%Y4%*JV0Y`?YNVwZ)P2(V^^Q6
zw^^0;|4q!Ku0R+SD%P*o3i}6z5dWX74ZwoJH*xo`bfMc?KjvM=JT{F8dwOoOj)YAL
z?KA>o$l?UV-wE^m70CVaHI24a<#&4}NKDP$s!_M&#lE|h;{vhc!g$G^=nFu{KFOCZ
z!gv2>`d(imOHlsDjp%{}kU#Ae-nOLQIpdnLO(pkyC~iT#+;h%W;~Ge__*15|6$m3t
zG6>5*!i}+;gi3zZlZZ&`THosnP3MuKxbzsd4;i`doSmr}&{3RIA*wMeTeuVPDNF)l
zs3oq6!4nswxND`)<3qNuCY%z_zFmk^V*n04C*_nr<5g!7D7l}`P8RXn1;ZJwljV^I
z7oH=I6J4iCt82aJ;RJ3_5w7+p*Av3eJHIP#!%&Bowwc)OOlMx6g@?9yMZM%8a{0^Q
z8pgUPv_C7l<qY{M`4Pd%W&Obj$QfFMkKC>18I%m$1hYvoTuqo4W~#&g;-flK^ZQ&w
z{HJc5G3TCrC0^NQJRrqvT&#9YpLD<Q3;1UTs7v`Th!NX!?(?{xoeKKi^h@XFa#T9G
z?imC3{IG0&1B?+1`RJLvaDT^$GAN6vH*sg)df{Uc5H4`*{{@UmzynALuXe}n0U+W5
z-_qT;f^NpyI}_=R3C0$bk6PO0=oooU!Do76c&Oq%AJU%0lW%YL=9-6Ku+l`<G3=YU
ztv}OX7xN%ghy1>c(t#ZSaAc1luQ?n}(f~k+QeAA*WTDHZ;y!cC^k3Ab$8_QLTs-<;
zhE&s*%2vQS-U;{nqahDb{D)K_=>@xeN|DAf?_UxfgJR>Z5j5YY^Go2%6c#QY*%`w!
zhb+%bOq*6<81MM#N_k^obuY@4E+;yr)4@18kAc03VfDy=^A0mQ(Hm@F*|}Bqkxrh6
zebKzc06VR&A3?Rb*S_V+7>|`^S6k@xkLMy@*Z)_jt#)ql%V!`hV(*#$+=Y>+_2&$_
zXju-nqwfQwp!`&krtVFdn!p02F(@Py9>cv``Br@lz-=^YG-)conn<!U?%6>GFTa`i
zW=H{-LlY^G=<*aisBBjb8JL`0$fv>uqV&WQ1!ARyR14see0v`Vgz1Iz9Oe0lF#Rwf
z7nu$Mv7i{^r1&D$%b}INVj99aYsx`?Btqi6{eH&eS(#8@^U*%i;ptAoHJLT4(_l85
z0=B@O<a19C<>_Skj=|TZy3oLZ5A6gx2;52G*;IC=Rm_vD>gEi~NWRn{?4J~phzT5M
zptSAVzv<onXA&V>)r50FbpF4`d2!8{0ilmajm&~m0fuO#fw@J4f5AvB@@_aFFps=8
zP}+A*#x_L?Km`dq3F?m)nlEs&c$U|`MknU!UpGbbSvlnUeb>R`Th{((Gl;-Dqx5|!
z!2slR@0j~EHmFyJG!{1^-Y?La2?9Iuq3#*}kOtnHG9K{YySmY0hq{U$anH?^oG;W&
z6*f^Z0T#S;Te6SY?wA&5YURYSFI&W}3fE*~Tt3@u@G3S@+^>w*T)hlR->mDE0KW2S
z-V>4ejm5=JaremU2)W2LP)c;#a!rJHeDq!z^X-0+nI?EZ`RF3tE3ifP<q*yMCqDqg
z)*<FdSQNPxk#&s0i#u~|K-6K;Cmr55AL0NIM2q*K784Eqk~5biCUEmjULt<ce2UlD
zR=gD;{TqGXx7yO*s4-KKvC_1=Nx^RV0wfD_IydTMqvdUt%<u23+WBO3hmvj+EkHF$
zY_{lpFE?3w*&r(hAO$9Woz|6`%e>QRgXI_ic+<Wf0$d=PMb~)4>2tx<!t%s|((%Hh
z&)$1@z|>(`0io2C-*ZMDR|w#~xA0z&aoOl^e9*n-*FwMt*^cW9Rz=jb$?&Qlt~;@G
zUE06?;M;N3Dv}@gX6B9*L+|k5A3d}wcAp)AEJcQw-Mq1Nc(!C<Yb<{3X2OCV$r1?y
zdc8pLQu^mqmf)Tg-1z()tgzK9*8F)9jEZ*~O{0P@In8Fkz3(1UXY(LfZtRo?#iL{=
z2aET)BqtrnH-HBPUpxa8g%x?o+p~`EKm-J~9ph8NH7NuzBUS(ii<Ap4K-Sjx_-b@g
z;jCyKDy&*5Y1DM<aAu^7v>{j6t4$pQHP&sZ+~Q%=*ji)gGD*P48ae(kMgGFYW%BJ(
z&@u&6i~W|+PnYmUqyZ+CG7-2>HHz}dwt|c49M8d9c)UEbc<(kqH*NrqW3beo*H2X$
z44>do=bb;|SBMXy<87`#WEiu7-<}Oo;<i9M<0Zh5(C127Mmy+F#-uSJd{ifNC>fD9
zH3sgfFZzL!JA@!ZJeIm7u&kWRa|k`dvXT2c&H(h3ks>VfQa6+IicAuLKeMI%ZA8pA
z?I6qQnc`Sa3g^{G?vZDiQ`+-7ET99P6r2Khlma&->A1ui=;jElh&h$+rh3>z1`5pU
zXwPjqmg|fOUp%Q^89A>Uq4D`TqN{xwsTA8ZQfyz<&~d=k)Yho6LX&Y7p!3EVzKE*e
z5{N~<g0Nq}qc_n$1vB6cGR-GRS<P9Fmi@EddSyfZWvBqYf-VYmB{wW90e|Yi*|HM-
za{xozxLIkKwA1nk_?9slXdo`Hy9%jyvqdO-6P7sfUp=@{77jaz4wX3P7w@$b1+QT7
z`m0XV8lDVRo>h{|^{X!X(>pvW_qRB!UrmQMAIz|+yXBx<Yi#*-b?<kka61M8`$dy~
z$O$zu?Em~~Yy>YW5#jXn(3+zhfEmcLe8RiD-<ul)Wr`9j+od=0DGBra0>zQ>l^PRy
z<)ehT;`|8Y<tv37DTQ|QqCQ?W!DJ;jB9<F?s((P>6G>EZqCV>6Qi3)~QlWNLNTG5#
z6Zr*wMwmnjkh1!*7%#AKuab23VF95WIbz}LvgxfXOjGOysxNO8?tYTfF=%zExz7Wj
zAdX9^%SHZiSU~q6g*cIaZpv{~e0L;JQY2xQ9)9nou)wuU7E~IB+JNG2Kgz7czlA~i
zb%mnD8T(6kESAJ4BKc4wup}m`v1IW*#uhzn<j&n6zg<2<`~IRVO#1lT3?F61_&2Rc
zM1cnP85SCU*)9~s1xHpSdOVvH_G9vPAoo&NXl`*1P~5}$yR=~$TLc=j`EoxH%mrQF
z=vr?$Sl4KeQ0O^nI8qaIeOTaXu^4LP53(=7dUCOx*o^`OEsUfcb6zc=%|*$R_HpXn
zI|Cx1A(4QRb*vTVz>z1qCuArw-iQ3*?qsu??fe@fQs}dZ7_=kkfPS%BEW)~f<fuiJ
zY!bhXNyVeRTs0arW<-dqHp<Z2wLY$T9c{-h-chNuWM_k-$YU4kq<y@nv9?N0c2k?t
z@~^?&{TKbQ&{#_vd<6%_%T79MX`?I8iC(?$^<i0P<BQ0h_HUDF$7fUq^d&_6YNJws
z*5rv(u@9$+6Nh;3>&nrt)6+UZBq5_SyBCSPzY<DYZg^lofhrxA93hta0{QH%4_A;u
zTMqzy2o_!6J;=0y<G}ZSd>wb@a}&APajfijuMneVt{hod7_*w0G{7Ql3@}TlkMdF~
zRuXq3dIV$3dTRT@voh2IpCTA+`0*X6$(P_)lw5`su1r$&GyI<iK&$$PlOHettI>S8
z$a^3x?o({?9V}4Ow};w^xiaHWYj(qKPIVbF4=mQPP#M;kqX|Hdg$Z88PcF6DlijNA
zR0B1EeDa2}gTcYzh2C&t++dJ=ZbViBL<+Z6)rL0Y-?zzbq#1ur^3QD*V`3o0VgTyX
z&JR6bLA@u&nYw3&=HGi4h51G~oMMbJUwp`DtZ3maDwscc5a>J{SCD^2AAm}SX-$y*
zYv|W#{u-13TK@n}hlZ7a8kBD}o>M+6d$Th)|L;rwIm5$w&Xxa6|MR8)`%Em~%5DFn
z75}}?!0+DXf4kiM?^Ci_Zu0+8AO7!CzGd(J7mNPihyH&&(f#M|*>Rh%7YxCVfFF5j
L6{!+Q1K<Ax6A(Tr

literal 342126
zcmc$_1y@{Kuq}*3fP_YZ1a}GU(zv@z2!Y@ZL4vymcL*NbohBi;Hcs&1?(PoX&dE9V
zy?6h>HwFxv-Q8=iU8`2roU>|$sVGUmM16w_0|WC?Rz^Y%1_lua1_t&51qryKaG2u`
z{NZz!)Nxj~H*<D1bToxgG<5!CWAAKZX+-8?>gZ%?Z^yyR%gn(@X5sAo$%&tZ#rA(b
zz-;em&H~-iQ3nQj@k!>L6ATQ7;h$gFV&Ni77+4q>SqV`Mw~T{F_gE8IpXD&`g-2os
zX|s*YcdnY+my3de9D;bP_#hbAIG7Yanea)qh9;>vcG*M=_6gzm)S;VDiPS@1Yfl+H
z;<rpGoQ(FTFtBiFACcgPKK?ZKxD(oIJsXJ>So?5PDXcG{F`fBtaZ2;UW_H8gK)BoJ
zVz#g^%ewda^}Tm6WP0rrFVU;euGRnZ=Uzl;5B7gwjAnVIq~iR)uip2*2>*Y-{3_IV
znOAh|{~GR}_YVkZ>G=QGeWJbB5hVYgI|CoBvCsIn^MB^@ckrtyY#ieMbsuP}LqP8T
zJ?%g5|K|DsbCTD^$SZ%Re(HWQa>UT)bZGoE5T?zioBE`8w-D~}5Ljn_c6poU<+OUU
zJ-+=_G`U)6hh4i|<+3YuX?gYvcLv#3$jVOT6s<hbx|zSO(^<!3$6MfEy9pWS1^s>E
z=%RqPEi}(}1NS!4kE0c%c39{3RX%;RhZVp-Y^uo)jWhY#z1i}<0uI>`iyxjW9^rg{
zeon>ECA_HHaN3>!cXdv0*C_t8YnF%>vh7pHEYB^Wd26px$<?oWPund}(f;|38e1Qh
zS{|uK_P;9-EgksZa)3WuSnm|Q*zaO~-$gR2G^~CFFShH@+SH{qY0l3W_ePOLQASZp
z^tO3Hr!xTy<TbvOpG|}QIlKnf|C=h^7>YdOqG)^F^!O;&oNRZ`(JSe<6GJ!yI7!MZ
z^1s9GY$OGZG7bIXx7Dx2qO}QS$af0a_5+zSImKXlb=C4-BuV#RxZ7FzcUw?oIu^`q
zJZ|v=23(r`Ac+dw?p4znwucTAHl}xUI4++cOJztWSlC5@*24h#1|#y8pq6cCTrPx)
zGOl_pSR*i&a+4k|$u|Q%QF=@_e1MkgE;=B$CK<5uB4=SHIxGk!JZsb@XDDuz{`KO2
z=G*=BuLnjKMGxUmhY&w~yd)C-{iE-BE7;zto?j8)!^{2<Y;R+*n$(MWNVVozCCfol
ztx|sC+V=1^QNpkNOkhT6Rn9);(lABBT!!4;_6k%rT)DtT@hg5t<KbIlhcNj19~Zja
zd%*0>g>F?3#&B1ibPW#zwqdMRt8~g|ANF-S<MJx`v0#06UuJ%r-x4eV+K<%7<#<o$
zRL?%lamnXlIRt#Mt@(o4Twq>r|ND*WjL;fXU<T$UHF%w<YJ|*B|IIn@-Ns+Dn^tXz
zB9x4$a>l90jM-_EAM_5t-#$*&HP7f3WlF#hRdMrbrf<%~v;?udHlos5!Z3abJaBjL
z(JRt=?&@iZ;EyF5>-*=@ng4C#Q^bz{LPQoS0-UnUG%_*5Nz;t*)+hJy=N_l!4HMgt
zc)W#r2rV^>63bbcbQUdFnh3*yz8{wRi#-FuGorW=nJB6E@+?uezCI7)r9OQul^Fy)
zfwWW=CVh<~xNV+?*omNrs;p;RXz9zsK#Ha@zw=DuC+B_kHpiP;S?Beb?^S0bM{n?&
z1SSJ0V46<-%)l$h%{R8dJ!+DDeRhdma$&6>xnB!!d@@aI^Ei`lhB#$99ojxUtZvhU
zuud3a!s?Ma|CqLSXlNOhk1~ClE17}OIdr{gnNrrFpHUV2$e3|x<5XGKWx#v4W@00}
z*f@eb{8E3<#;F+GV^s5#MRiPPP}#LIuVU5LaZS^#ll`?YSuBaV;ps%S$-fa0x*hO8
zyGpbCC4V=+F=TmF!8;3&P@d;SFbo_WLw2xH5?&#m{oJx{M334zTB2Ye4jdZiI(d4R
zP=(1CNOH@WE(eKYPTk<8XnK!PQVQW94wy9TBjtWA_GROez4`^*R)i+P$_q)_Fbi5t
zIR>(ra?WYTpF&V)6|ol`ZB2LNEu4iZG>MO~;dq~Fxd-jQ?b_j#NtXInjEkI4O6(>)
zB&?GJb;0aaBjqq4nI2Yo3u^I(JfU9QIa!H(j%aOjHy0}szp@tGKt@9z5|v9dM%=Rd
zEMK&napOuAvxZm!m6R5cK}ldnFO<ZZ>2@q_Y#9cNJga>DZ)Q1lUi&X2C?n44Qe>Wv
zGPj5W?g+%p^2B|OmXiisL3%#*Z1dY!C4=q)^v{pM*|nIPyCYe#`MuTHmtoE!)Kw)G
z71YxNzReDCt}fcQy$@{BnuHn;AlQ5<r<Ucdxo^XJ-@2BcPn7B0pNdK0Q7AIwcF+wN
zw$NVJvjvTdM^V5H`t*^>6YM40WJ}Qzs>Uq3wF8kPs+!Zi<p43GbQmi=QoiK_40|4*
zW_o5M+D95jhupc3Z}-$ygv|Gx?)PRA!rLwvcz#SSZZ7NH#+tEr8{I}o>u<P0I(Fke
z-kQYvM^!guKcl0l!k?bJbo@8ElW_l+x=uC7q<mW;pE4T7QZGeQ0BcSdhIMVyi+w(a
zQc!ny51FuJavBNjjVXoTB#zE(MSm<WNa*!)J$#^JKa{G1a|1%6wt4b9Qs;Ms&b-UB
zW;r?qJGYYoa9qOq2Z+r=u0flQwiHsR<h-hx9Vy{<xRk*nFH%V(KnXH^r*zj>HiuDP
zdQZRhTJ}$=`ZhUacl5;~I_4!G7LV%HbY93<5SbAOs2<ZKB>5y)V`K2DrWdR&Gxsg+
z6Gb8pWq$yR3PkM`u?a8y98xjI79G=#fUssg5jrt|0=#Eznz6rsA1<;x-@1A^?ZWB-
zpZP)L%QzK-YAGe%?te>f;PoE_ST7Mp?O-A0?=q?x@Vy%${Z!KwQHA3ajOxFT9?l>I
zH$jZhL$#*cCdneN!#s7fDL%?RNlzHa>}yb(eua<bYmoMCwJOsq>iObud0V%w=f2`I
z+@|W8ms#fmfd>QQnUj2xo1q6L^_fRt@77p+3uEDYl=Pv4_{%0VBTiIfrc|zcDZn^n
zu_%QB6t=#7)78>EQM7SUfsCfczc)8iO#!EYX$TSI4iOBQjY8?OdsFxNvKSGuP|EJt
z+?#qXeDvNeu|jSn+abkHoBnfp_s`Lqg#;$_>8dGhkI-i#1BNFG7Nv#>UCIIpIe#`D
z3Dp9-{KDne>B>(!R10s<-Wap>M$Tb+-VqEh7UAN)oUZ>h%Qt@0ME4ns{B2&tes-<x
z-{=tyh5rv<xiR2N=g5+OWzo77VDU*8p8e5%tp6O8X0Re-8g87_>pkC3d0<9hMtX8J
z!r*&cv7EPatMjo^$E;AL)wnH3?Ez}8zis0g;p?#bf!%mVndwvc+{*2)<de;tQ~S#1
zQQ^iL^+~!rl^6ZXUPpvDNxsmUg-ad(-Rkb|xY4JfW!pDLbM9uHSO#f)-OoEGbwtd{
zswyO-$}DF`M{j(8x)Z<{FzA2PUu(Pr7fD+V&ApjMB7W)*&W?{n=!wTW>Ab)io!(A;
z6(PaDeyu%vX6F<Y^FF<spRz8bq8J)C!0G#Ra<1_R0!(*)-8QN<*@f+hC3qWkYuwD~
zoj0;xO?tkRo?<aH^Yufqf3OdW(d7VlsPYhp;Ct$5bujg*c#J3ujXbApd>jn{|3o=a
zIyH*)?s}@Ib=No2iMibxAKR2X+HKXWwei`PW?R-nOw%Qk5p<W9h?1}}`58Uu23;7f
zk+Clw<K_rP|Ds_x_WxjjGM%wHitPkgUs0xf_$37+uCaQg;;9KHNXJ@bT>4w}SJlM#
z%#|nzxB|1<WcGLO$XFNj+U%R3qg)Q6u7vU~#shz$$OBNRaBZ`5I_``!MNV-GO%bjn
zHm`;Wr!1p<MCA%DKmb2DXdn+4hgZw?S9mD!a^==d>`cu#l`^TMzX5Ucbo_!H06B0S
zY9+m_@~JFZ^ih!?;dTM61y)ZtjivdGkl&~7AV?oa3Ei#5tJbSjKY5USl<?bB%Z$fU
zITeR1v6Hj*sj2C{`zFq!h>{dayD779QGAQ2G;Q{dxE_cqu<}zFe5&b&g(_J;^hbkC
zfj9V;XLC}dbUwD~7&dAY?E%xGoO+`y7d~KKqeEHu#+d1~J!hfpkcp5l;^z7bHojhU
z2w(CbPwsU+H>axy3jGOK7NRd<9->cc#4AI0Vcal1kB}o>p!<<mrjI>vgwryYZSLbx
zRB<=3puc0-ddK(CE$yz0r{w9BYnx_8<@~qbcIL*Q2nK<&9i!w#$YXT~{SUWU(1KT1
za*gZ|@(E}m+cVki@iY6~X=C?r)Tjy8n%_P;S8Q9(1T0X|#Argks(M;o)QPSfhaC_t
zv-IA75xnnH6*im1&_SQx8xwltFBbl>KBh-k@b+C;=MKIdfVPZd`@$TCw|%q!V*VQ8
zpq9p8G5=7KXj%kgj>utrvw0M9)mo8K<lB7{^jgJ`S?-Bd4w==sRB}__I1#P>1CYPO
zi)=k2{~A_9n-DBRW`f`N$~duNacSh$MZCmtl72WOMr+>~V~eFJ=(ci)4zYTcW_mxr
zu=hTkcImxe4D*EeR?QquZ!KOC$6P8wSxL4l4#VCrwW(*jT5apkFWNtRxAUwrCc2)T
zJ3MWAUW2-2<?6h;-TSVbP?#38+$v{W8NTi5^}O6B-T0=~(HVDCo37wQJgJD~ZGS2r
zhAQ1=?#{fgM;4^4iHMI)+WPzG6x#d50a!AN!z=n^_<<=3gU8tkjiPXboac7yN!=)}
zCX-#LNk3_qj34|-S9TAE?-uM_y-6V#)`Cbl99+zh3oCcWZxmZ3lpHz_sAJApA)RW+
z@5IT2ZxV>~V(8)ssMM$ygoZV4x#8rUzwr&YV<}?z`sPPi^X~m|I!s6<VdcZgd$2dh
zQgFoCIof|C*m}CvDv2`X9D=OX+2?zH;~QhkJ-t9+uzw$ff|I(ND*<Z|)noc^bUgj>
zALDTo+byt0zkF3=r>^qSs>6_Cu`^!vJSKjRM4XHZKL4azD`AH@HSBk^5Shwrh9&km
zJ3|}xuyC=Bdl)w(n?CYbF{5&+dFL1vRjSyeW+vYk)K~T^r|&3(e&m52_N`s#?T+tV
z=Z-7qkIx~G4eshuy`GVqb^OtRM91ckmoT`_g<+vD7N=u*m1Y<B;=2j5ia>DT1+gWm
zsOe=)<&X?FmoPg|neSX8>4aigYVoWWsqfR$B$#PrLlWcnG~(16MH;o*@gqjiy-H0P
zFmnUWqA3t`(qZAq<z*meeztG!b`jYpXgCCWG27-|otgxT3`cuh$zC$6x@6M5r@lCQ
zVxP!5NJzyMyP;E+3fI$s<XZsN{F=JvdZJ0}uWaUFQm9DlgB<Ht+kJD|@!Rdf)F1l$
z%z~%{g)B%S9X9ND4xaCq224czREG;Ao+rN=93fmecs?|%v_R^czl_xl=U*Wpnl@49
zcwDhE?zfPb8wx_$?#J?8j0hRFQWo<B@XIk>wF#)v?<nD%o#B-*xWx<p5&{ZUnN`Z*
z+^X*&8B{A&+p|abcVhFALsC?Q5fCJUWV&K{)I!m*bjh$4%+c`m2tQB&*##S=Dr@w3
zKPfrFKmtxU?536fopb7?b<@s}N+mAA1$I0Yr99WWG&D^)+0I<$7S){Ps1tY$^0S$;
zORNGpnG#(Q6g#;jpA&eLIL9~SlXQqW6jL}WPLxvTWMi($I`$y*bSe)t>j_nyT$+ny
zmE1%$&*|84qu38QDP9V*y(p`OHl(&#k%}^xuhfv}-gTs?qfmv-il)O(7b?8ght|Cg
zI&l(JIsT<6Btdqn@lsg>M%2jVRN@8opoKuR2V;%|CcRi9<462hD|r^d2ySt&Df|K+
z>yTXrT)}V;q5z1SA!6SvUY@@soCNV-w74E7Nf9Kbi($<{u~?XG2TFexw?u4930Np{
zcqd<*bw}`WnvCsHPX>QVbWok(CE`0MHe$GbpihIO(a(G{KP*^8t|(emzn%oidPRJb
zboYV$2tmh#K&y&Amd88mNVIc=oKQ$|!YGq+J&iTvK*CKc^x+H##;~J^O?&euRkHHK
zZ;CJu7=}v<=qO_jxIbszX^2HxaZXE)BL6E&QnnD`^2cFj{`*+YCn2#BKNL(9@bl~D
z71LMDUtfUVK^dYz?pD>*c^kx(DjY#e6ptI=nq4DXDXTO(%q;^d6vXK+ZTB?iSz+#<
z$?9HwlKS(kc`Gby{cl<`-bgZwC4MN%&Jsrnrez3ngjJr#pV7Q9C03p$FiSa4H1j~P
zdS#%*HpFab6Ap2|gU}A*G)u18B+$(Vsb)flu3~TK-sKWyNbs${`3FX|g8s*0N!YN?
z!2?eeIVJ1;ApcMtlAN^8IrKv)ep!tLoMsOmHR=*)PPx%99c!t$NF;i%M06CB*Yt4g
z90(#Wgku!mOzA2df=uD7!L@T?%5OXe4TSr=mUOWl>_7BC5lg5F<j6_)i$ykgtxl)c
zzfY@OboRUW$I~gRmAsZ&1B=z@zEz_`ZnW6hK8ELkJiarsO_ZiVCGBfZi~E7QxN{+b
zBE}U;D~Hg)Rw`Tkq6HDG+LQ8G4B|)oRwsRR-ZC-@hSdax{A3d+t9-40Z%21TB^N;_
zA4MhCFHw?x9=h{&AxRgr_#OD2cs~VT$3u8ET$S8Nte&`c@*$ESk8`)&fEu=B9BZzu
zQgTT@T5BCHZu?qnLv>W)V*?y1`pJKN&~?Gy<{!gl=`c>~2EovK!D*V!KJRsZT1{pu
zL2_?_5GGyQ;Rzmee>AGHXTjE<eaO@+mmT)2*zpFdwx^h;96b;iRo@;6e{`wrP@uTT
zkBzYnC;_cCn7WnS@Z4T!r3flJ+;l&*%(s|kkG=|o2!deMGU4V4UWBo^^B;F$imAO&
zTE3WDvVMioYPIk?YXRczc@nBKAx1{$7D{&)s+t=Ka&*j8nyW*y=9udjz)$xT1r_sI
zEs=|H@r3ENa*Q4kC<~P!K95`{hzzT2;qcHbJMKSr|D*6g*JJ)=<Zfam$kOzlXgZv7
zI435%+?cCoLKOwQ!^iZP<0#7HDkzi0!3xlhF)gP`U;kW2R&34_Q$J8_8ag!<maLUJ
zLc9u6H;vSLMb+11S_x@55!77tgs0qfhJlTru2e~<v4g})#bNMU{Ml^VbDOt8jwDC!
zFG+A5QnF#GASauuiQhWZA*!6Ki$S9PAd=V5lO#O5Fdh0u*UB7OO)W=35`Vq-%MazN
ze^w^aEmmW^<^EvPL5BRLW~R#2HRRAIFYu^gF;hQ9OjTv#-fE`C7d<4?Eu~hQB9WYW
zlnmrtCzPe)CKfk`9@b5#Xkx^kU|3GhMK6x6sv*gqJ|_2Gqj@|}D4!PHA7mO-OlI=J
zP>xKb6fvm$?A;5C>n5{czhCL|zMd4WR##J#;sm3j-<|$}$ER-piM&!e)-|~K3(xS!
zOWx(f&)%_*#L<C9<pt?iJNd-AvJtbNaE)IcLjYj}R#NlZ&TAF1oD&ocKZ$Ard$zui
zi&~-O)Mo-KpVzx;ilkU<YQvbt!tgnWWo(6kpd@KQ)_;l6D8k=Vzh2U#3uMP$d}lKY
zp8IaqfdesO0NW_%)-{{0+?ZFq^jYzTn55>+zlrUpKOdYxM`o+YB&mz|+!+wVg=>7q
zA0oP=9Ml`bY**bdWoBFy!R8*-mF@e;8Bqt3=Em#QVXtt1e&8=lXS(YO+SLu~ikKkM
z&nVP;Fq#ye>^(`qs2a1mp0&EdghS04&Aw0FrVqlHF`UyGWR+{I|JkK1{L^RoFosc)
zW4ZX#*$HFTPi^m?>6jwLV(n@w<csyvMp)=b)KsnLbbTOt95p&4;)FRIY8>h+88Y~C
z2>NFUo_)-81mi<v%aOC5ZX?@ph;8JO)Bspc#oSzVi7hs!sQ7C>K^O0OlYLgfe9Up9
zE!zdJw{uo-DuYwh-Zp3FBU|(vWm`EjcCS=}>(pTtG4ePWayI<P;b$GjISbA=#xG5)
zA|>Ky(Usj$$iFxT;b1Ad;S1cgkWJ<j+iQ%I*AdKZ9hz_-w~?XAke~aMkF<U1TpL_4
zu>f=XlhqNZ_4WVATsa1iaWwSxe=9;0#!;)0AVELFVmo2`5(QPLM@=LLAM_HtJXmau
zHjE>lH&5e54epv@=iC&rN9GrgJO%3_XmHFl9S(dxP9qE-7P+7SxheCTmdDf2J||a_
zJ`Ww5;|i1oE2(+sF<L71A$0vW>))AAp!Od=8aEAcK(}rht1^sAbssuW!lmA~-uJ!}
z`uU^Zb6X1&&TP-r=c#NI><ma0@>Qhg>ll@129H~$i>~*==XaL+-Y&s;@=<{=!o^gy
zsPjQMn*LL({Es$%v|!Xyk)F5emjg27q9`8kV)Unt2eK(*h5XS)+Q|sVhkr`&_Znq>
zIwgpWc!w*)>XF3gj=kB2Kv%n=7=)s-bSe!V5WuD-7{2oJJ*o2Tp1PbC{BAob|4?9X
zhh^aNbYe_PC*~s@@p<SMI=wm)**K;@x{BDUJgF^LO&HtshHy;K^<?4AxHLtWqC&A4
zPPpB44>pOUCKcNYm>hIkI3v-`%8i;ZSp{|m7S{ZHIXZ(Jsq1GMX>9VkjihQFq*=0K
zX}S;(8M45zzZxxcJ^XK&JDoI&+$<6XL%)%(Ba;BT!6DJe$0Jy`rSC!^DQ2l<;8QGX
z8>gggsYIjJMuKZq4n&k*wv7-V(#H=w6#NtUvc0s&ABuEPzZ#^i?e#EeRUMp|`>qd8
z77fPS#U2l^j{K-?7@WGKDNDB<SEy@UT#dSBK2O4n2CLPaM+A_?m{cT-C2v`w=OuDZ
zpyviPCC+(~fmctx9^b)G#V4%|^g(8~EJwt0f`+82R#Y4iZ7-?D<;bMQG?G)R<D`}O
z*iJc&zCbXiFJMSZqGNl65g2`LZ1efgijm#4^Am4cjapTyl{mY2$>rE<6?_Z#uMM$N
zzr+ZTs%uDw>&NW}?#qy;q89Ezy|FSurLi*7^%LAVsI+1^B4j};c_Y$!Uks8Wd^awo
zp=-v%`^Kyq8m1IamSwbY!D=!%sLCFkpA&{H5>$fmt$&BPp5%wp3Q`cqeGT%NF4~%*
z^EBP+a<|fds{4l@#&G<FZ&39JNV1Z(NEJ3FE_j>@9?ddi>{v<%ez<~Uj5SB&6`iIS
z*kJrvl1epvn|@rwI4Wm`AOOaivCBsx%>-b`PEGPoO#-r+K6;p*Pubh8TXCP%<Wi8D
z>=9avzGhaQjF*@qImo4Lbt+_-bj$W$#_8N!#)_#CguTR-kL%3BT=1zZXIQwJbDQt{
zuyjvhSYe7^gm0`WxArz{`%rl8ypC8tlFPe%*Dned!&<!^KyPbfk=DX=^eFH#=FubS
zRX7B_^bYayCTSh4ITI1T?Jh|#S&t)XLb8rvzvUZ!L%tb@Vv|hks-?%9ynq+{mi}4R
zMvP88y!1=Qx2VD*Pkhh1Z@fyz(^}Z67Fbi(ed>kC9)2Q#@#7iD3z}tv4on5r62|-a
zfno53#09D92x`Iz_6(UNP=j&CCDH%zjP)Am-vWbM>DXK>4S^J)ToPQcQTwD#s-0*1
zZH$&|0=n=CN~d3H<D1Z!QHRR~8i&Ma3c}a=D>>jWF5D<dnLf4QMhq?5v6z@98f_H8
zXhuaR3x~8#2+jK@!B<QQryK_S9U7YvEd1UiD6kO6zVEHh0rssP;88Ec@?gjzxAsi>
zL(%i_aZT%@cRjo}T%)sh=o719sji7xsY2e9MQ&61uF(aJlmU|Cs*ZaR4C^dk5K5fY
zX<X!?PmsSfzT1QSbJ6lhO673Mr!-5U)*l_$K3>tj7w?6Ay7LxD<>-tE^CrMn)dxxM
zm>B_Q<+luVYH>=a-;|)G!-@LVVOJ|pd#ErM<{ZT0m8e42j@QV_M>;|oL^jQas7aPc
z?vPldAkCk<%2Vw2S}RXeuC&|8FfQUT;-Xe>XGkFgH?3Bign<6FtZleNt&UDN9`oYt
z9{?01{69`AqEdoOpCpzXGqQqAl2wHgAtakv<NU*a1YHb;0YY&pML<tYoAsV1OwHL$
zB}+oaU(Ipj#wL#a*<CMt3}3#6NNBICg;q@l)gL<A>JpF;YDOUSBFZC-Qhp*)KIZy2
zDPC_}2E{XSJC!EqiC|~@^H84PHFnPhl{7!KY%iJIO&8BdP0jpfFm^=q&CnSoHcoJc
zSQv=j`gcukBw5N9quPj2yu)E=|J`DpR0U!gqv#58@yK=_RV*x24hlnq8I&`0Y*->I
ztI(;(D{Vr7H0u}K3HQ26Y`6-u&yU_0Rp4$^rwgzn%f8}}u36waz(a8y)#OB8NDfy4
zR~YmW4ek&a$T$eZIZPP7=58bbn5FQ6eoxe!LMwXs0|Et)x%)z!zvCaw^RE=UZYd>F
zphZS^13vFW6$|eV%ve<CJeUq`5{H_dUo$04uDoxYd5WP_LxtNt-Afg3_SjO5+3Gj+
z+A9FL4HU5XOjD&6E)t&sP{PsO7Ef6=d22t$2COz+-4GrdC0G?5#7pRZvPzS4dMdSH
z%6pnGA$MCGTF2tGTc@Fy#!DZwPXXsX#~zaUDI|v^H^`{qhuH9_b@x(<ouL_rQD&2V
zie~C<Cm2z)FAuko{P!qpowUSA$t@QE#V#$p$3uJA4ZfN;{_uKlaP;)2tR2mQ^*{cQ
z7=YL22==u|#yBC{&Uz$@mX@m%TxmJqzd$<8BN-s!<ZpuE?wmu|%!WnpKly(8uzeDM
z=g$(tdo8)G<!>jHVa}Z)NkNPG<=RPINSA*gXN{b(aW{^(8UBT@aa|HnwO(D5i2SE0
zv>p-pUwWblB4b>*H9YfC4bHxLO#i-kT^NnrF?@_YNT&2|`6xC&dt_&;4r+7=GIoi*
z0>Sj!7#@yEgDZ<d1r`GZ-A|-R4eo9ZstQ*#gL)n0{zhWuH%I%b|6oTF@>`CoPq{PV
z#wPC$-6(c1LNZ!v`^n@;E>*6`K)FE>dMSh6G~#kg<6-7$sUI=Re_2o#!hcoy7##n^
zO2_FgF%-908yDz$6a=^8WyMh}+KkJWHJoK%z1(&xwGkuD00^<O3nq;41JZ!N*%#>6
zU-|HKcI9sY1dMB8yYtFuTp<sV1G>A(%GEfj!HtBV=LIPcvfHxuDn%*>^-1zAtGmgm
zp$O*3_9^F35deh(5G_F}TYhTCn}`~o>$g&cjB;{`SZ;EdH>mW8YG1tbrIx>_)lcU}
zQ7dx9D<tH5jBmRUD$9bEvD`>Rzo{Uz%HhWdOoU`=ky;<Ov~0`58K^QNxGk+yOcSBk
zY!iJQ)01+LD|~60W@sbCvhK7?FT3LDCWnQzgx9Hpd}fSqK=`gumLsqRsp8NUNpyWZ
zQ4Q;kB#V~zRV#+$k6xW|g#<JH<M)K+5d6CD%VVDz9HpJ9&p#h{q86BtNPDD=R6x+z
zaVnVR@awtpjlaZ4MlCWo9ST_%s>-oPs-<PZTEEZq#LyMV)1o+mLLX-{&B+nIV2w}L
zIFjU5!F+qzmNH{<J$_5ls1>9BBO*r`-wmO)Gg4xbZshDfpDlq8H^Kci4jjg)`c2F!
zmvu$K{OIxZx^a>ktAOT6+sE1M+h4uaiwDYE<S1wBmC2pn5Vlsk`jMFgwp%Xaa>JP8
z=?&K*x5qpE))4sR^zy%Dmn`nTg{o+1K&DIf^NjE_>~^J{lWj}CYwI2QXtv%Oi`TX!
zlB!q}-f5HY%@^x^MP|L_!YP8SfOJS=IC+v<UmbLd@8`mbxxPS$bA>`9KKR59Nww3i
zX%xU)Lzlzc+m$wByVB0cY+ZDcD0B!yJpsyW7w<AE*p`bOof|vQXz?r+lD<|ZAI-;r
z;FKAH`hr^z&9bjYD$bS~xrBJzl#1}ib}>%9V}4!p*76RIZ6dK`>8?$gV~iCqx5c#J
z8#mVe99({Cdr}`iSo*vj&8T#Gmiqb$+IGVbidTd&Il3P3rtvMjgo9ie&j!FH*3b5s
zNiz(Jcp`zspL48AAHq01<9?fJ8ePTd_E?aI@PxOXr<P`^^?gq7XX{|WzJQmbdxVy2
z-<F*##kXk0ShX>8_sWq2=U^6L->*O(;A>z%Z}+|qVZ*DmJ6~$ltSskh{A3HH&z$)f
z83^n*kXvE|Y?4vmKqn5zglQHZJ9IbioN-8lKE$<3)jV?ZUbwaWPAPOhor&Akv%X1u
zx<Nofc7Rn5b_WBy^?Kdup?@Ba25xr|)V_Q#(AHZvTDjmlk1W|o(ERa@o9RXPn$Pa_
zapwE==j;39lc!rQ7@yO9^FL40e6?VxyGTC6Gv{?oyUpwSIemDMq+$ey{)|OEd3%3|
zr_}2_X*~nXK6t9^phU`@%KebH?2(|%Y=1UFTLz;r6aKLLtn8b#tLv}~_o0dKwC$<w
z!5A13rYhsz>cyD*Q?I?3_wx27U{ULNVxOB4Np4pU8?JMAMd>xS6?!j&vErm+?eHNk
z2C$QJR?jR$RR*8LjwiO^+@IteT@=RBTl7!!0QgkLIxIdCKwtu2X6>$kpWn6^Zr2A4
zDO#@X_v_XN^~g3np6DU&^%U)_BRemR5ULmVCP-<T9nFG)1f2IJ<x%o9in2newZ3Cc
zD^z~Q^~WdgP_yk2R%~hl%QW(!kKfb+M4zhpzF;+^2~NB6D`=v*Wto)f{<LRsVn&jg
zTO?1Jak&MEm!tdVlrloa>4rJ<^+dyrt++5b!-@i)NXyTm=xagZ=juT6X1B^#6{NuU
zE-EX^9zG&l2gW*^_UrLU1kuha#+k(gFixR+U;>C5L~@W9p@Bt@Fkc~bcoge8T6xwH
z{J9}rklW>Fx205?shb=dJ`L5okP*%qp7$nmpDYZ+u|v&B=jo`dnX>hkjGT%F@3&`u
zTV4IOyqx{L%l-w6|M3gsgoSM!JD#?ucnsClLH(VC!@!<dx^+5}zM#_=N4DQHHM;52
zo<5&^GN&rIk2624-<d@$x@1?FW%KrbNdT9EKJLgObp<Jb*oX*9Y!0t>u8gCZc-%IJ
z20l>kMM9c=4Wr8T6<y}xe?EROOdQ{p#J9Gab0I2tG3&j}JP|UF`)KY5K{@~#Hvqjh
zV>)LJ498Rh0uD3Y5N^O^PptiU$GYAP>E7I~O%MI=@fv@Qtp%d(+i-b0-(v<EvWLZT
zPXmMMSif7|t*)6^Eig}}#|`k5@)KfMqcX-Xzz(%rR_BqNI6}5&Y7qrn8uR`%U)*nw
zz6Z?k!`V9puwrfN#A+wRmcQkzzOWf+^Smlbls=4>+97`INb0}^ss5+<R^eL|1nHC_
zzIs+cJ0eyctZJm7(J1~(e&47dFF#ys^`H~cNk8ZMQ5luYdee3qzaje-?*4h~)gAMe
zBGNw6V}##sljh+NMKXzE@$VJz)=a;JVxxQ25mfuGgPWK8*}jhbehDJWn2iLu5P0gZ
z=9=aB>JH{RsnB6y8RXaAR_E%RR{HW|2lQcQaquF<;c1I$7$Y}GH1QXa<o=&)4@m}3
zSSVjBlR%wIP73Svzj|4}V71<F@d-6ok0=W@yM!7y)g*9-@XFS-E0qb)ZVipOTWwNE
z<2F{2_VH?ZI(?UR1)XC&4-*1*XPn?UOgBs8oYITHs<f?lyI<eeTefl7x&fO<Gm*gs
z&&@QWc~PgPSN<aImXMXJBHgz1?G;MAJRwu)H6#yHci|QoVp1a3QMoY5Ds}tZ(vQ47
zbGzMkeI-N1#WQSg#J)zAHxcurcA6+NfqB_&lUF*K&`nLK!EQnLX@%i9>%(S~eMZlL
zqJ7o_i*)*F+VIX5C5+II>XCs59B48j(R-`Nanoa#_V;I8x6;CVqoH`y?&~dYdG1=e
zz)|YCo`GKv1!o3a%An`8xb9EgYm11I#_s!h)_TpY;>nAQWJ|KVSl>x*h<~VBtr&hh
zp9|YXrW&(1KJ=?;C&2L~-XtcCS<9-hu>Ea$4eXRprWM`7k1g4?KWAyeC+1y->&?6c
z@T`OzoBL~$kbqV<2RDZ_))Upr*d0ZD>&Bl;8_SQU$PYW2g9r8Y<^Atxf=LP_pt8Np
z@GyYdB3hwGHi1O0q=X<Dftc=pXdLFx04K>jK&_MRces(ufop^DR!&BfD9nT43&<Ke
z^DzxApb)tezO20g7P0nKAzC*XL!J<$SmJrj*H^#Er(e~~N~7>ase~T!l1?|A3E5z5
z5Q&Yz!ZX65fUqga10@3$L5>Whe|2fyzX@8I@08Whx<b<PyYd@zM&e9EUKtC!&$8?2
zB?ug7e-yv%x0PA*A~GEZMw$Aw6eNXI4stm}D)t&W;K^?~uY{+*mP5*IU4hMBS<VAI
zFx5mFkiNbIr@jfrEu?#W=Dell+MaYtqdlFbr@u%o%OzWQ+r=~L_;kk&)qXSiw#U1m
z?QxaR9EisIUe6V1*d3B`q9veDcfY}P>ZWfXSOrFY5D+!}q7MnN)6*WVLwuZBh`RI^
z?`IPigMgkNO6zTRU9RW4j#ya&HSMQK1V91`@(+!V-=bsKLbf-^pNIg`-H3kwgf8A2
zE`7eb&WIua5@ds_S%J)U!{f_W)xljln4C{=s1Gddwf&;1%wuz-hhaq7_ILa%%7^wm
zHUm?uLdO-C+BgTO?|qf81Wu7#*2dr{sd=lascBAh{B4H);g!zv(I07ZoREsjvbV`x
zTXr1$^LX39HzYW9Pn>sLdGyRHO3T#`q(UF0F-Sg2lxke6Wn@?=Rs&k`4Cfu*!EjuC
ztca<snb?~k?6%=*x(H=k_C9Ack7hYZ!aK4j`jbGMw7=gbWb2!F3sh<I3Vg^>W%<L7
zfZ?XpzHD#CIX#MsH3{TT5j&pFy{cG>jml&$iWxbFq(m=GsPvpuJvX&IoulV&gnYDe
ziaU$Ct~z0P3jOZiytD$?#O*ZIG)uVAZS)jvWvB*mQoMx2g4GO}-1=sf<>QbpGlOnm
zV%^5rhig3B1Pv!(GKXd{$8Deem4uBfD|_Wf899In>7uI2DYYuxo+4|{E*y>@NtN4v
z-npQ7x+HCd)<N<9NRA#T(Ayr9X1gV?XH;Rgdx{pH$YXjf+&!XqR-a59(n_o_mlNEw
zjPMJ9`~#qu%xOPJ1^50uv0RTIAS^s=If5FZl$J6V?klEHF#YJrC5R(B_T>FyK;$2*
z3xk!GJJM)yPvm?F$Qk@%WS4vPY|Eo!tq5{(*=An{(NUPdTQ}60IZ<i6YOn8~N$Hrw
z-)#%HFlgU9UyyHaD1<NMc%w{c6RG3_bJMqi7`X&TNZw*z?LnN-62tI-802d1KmG?|
zC?o&F_o9o4DwxK|a_Z)3-%t%PP7^p&Hq6We71q`&3tLxuO;j8?^2IBVHItg0M<%&!
zB4)Bzu1~-S{}AIO-5Jo-<tLhmRg|VAoD16ES_b^LZ`>vdP|LAJYi5bnnDFTE;C{Az
zabZy|S+KfdogUvqe*uoMx;^R?O}6|Q_%&k2^=4-cX+F;z-k^r}eV*#u(}yrgv!cPF
z$@96$=`F5XAgeF2(p<b&&A==osGE2_(DOL#&z7uV4FH88e`w7nff8xvdMf34Iimt5
z5=j=;K?5?U0KAK?w-(R5p6;S4KJ@|Ty_cI$W=|>u;7Y5WdzE8f*Jrxg*HiPHcv|oP
zt#-uE1M;KFLD&W;+vf#ME5(pq0Mgt=#hB&2B~&L~!^t~OvO;gAJBQ%U23@mZRwz@I
zyXaL)k!n$}2RWVIF$+|HiCt~WhW~`_!$xsVD{8Q^kV{D($0hsV`R8cnQI)rN7L)QB
zLj0r76@8sHQEF^tCpfC{DM%I#_rNxpL50oMn<EM<#7vn<n`8*~zMS2A)mWQ6s_u)w
zPT!w%%P*~M=5{)%#!Qzi4yLZb{Tb*+L5C}zy?Es(N59dx#)-zkwIR5rf!a|*>4a}=
zhd`w(pJ7#L-#|N0Pn}ws#M`j20>Fu5PxK_CPoqA<FX0e#!!;1ey5>lxrO4o}(#>rn
z0oK$8R#B_2W$iiB%fwS+W}7KiVTwWMG3>PS6tM@XGa~_Z4CI^uP{fG-QZDGmYyEW;
z4?C9o+}NC>ZA%Z3)V0jN#0LN~0=A!0`OqhT#AsCTvfaLsqVM80HY*)cDjU^+$UyYI
z>ArfGRi(aokC--<SKOZHP}&3``GuG?^Q+zrk9;prrdtmMcxBzRf$6(mZ`AHAef+Yz
z7S833^?Q+UvYt8SX-?_Ki+0WqDfhH`75DBO;suMCnu(#|eSNZOo${#j>;srG9#I6H
ziT?X)_;SmS!?;@Zu|;<OXo{A9&o!JTCd^F7Q#tg0iUoA9ccrtl7U$<}SJdH~vB!Y^
zV97Z7^+Tz8DK4-jMtpySLz2bFSJK-aD6CUlZ~95ShgPxACkqF%J@iyF2$@h|+iv8|
zZ|>xwHv?$WC*Hv#3n&fMCsEqbafNBmYdmdGC?1bH0NYhF#*SXOZzpIfk*044C%DEe
z%^#xQ03mTB>bmmesga9Og&uK8N%JP%cQ+mE>g9i%s+&dQ{ytG!-}BcT_>fhWt0185
z*jdh&k$;3Pg({*>^9kem+`#CkR<16pp>u}OWNS^beTzrH@#78ndD-`}$cE?sB81KN
zq?dL`DTU9;3#b##!8bO^(bJ5@#=zI1eGX_}5By#Ul71mTNDQceBtJ4aCrotJFVUK>
z9t@xIo>#1gCI^FBf9~eo0SjBJa6Y)~75%(r@DwY2*YD2l`m@}w0e}`~z|*Rh;gAf{
z^_a)7e6n#5!G6mzq^SMXT0`3UwVkdw>o_)JRhw7jIgkXJo;U3k_j+2KTwX7$Kg_uv
zEpG$<lkMXiMK`jqtfU$7aL3Zz2~ceX=ATPB%MVq0zrIXFnwj?j{!{YFRXmw3X?z$-
zetL_-%|RKp8MJaAu15Z?RoU=jb%lINmaOwDNivE8jE8sP)6cg32_1R+SQQj+t4+A)
z!M3wHqW6}pADA5XTVNRtJa_T`FdX6MnYJ#wCgty>=UuMM0HN?%-7m77l)rz<U6-Yq
zN^>32-#*jD_LFOD@9(O6IDTF?_{Q3b9BucKr^-OU!N<-83E%jfKiu>9GS^Qfw0ibl
zr|yL#t_`8JOI#<sS9xp53B#@D?EOc|SPq$*0MMrDz}Zb2{$h+ROAG}LQ@K8(Dv}dI
znRboG%hgPYFK{aDX*6(Q7fMF9q{Pp#E0h|DHfcpl%e6?s8L$Z4-pIz-c9V}djdU;k
zI!#E8hCfn83X`<G{nKxJy7RYZ5xl8$R{x$w<;LF#fJaq=-Php!coh1x&g)EaUBXB<
z6Uz{o+DTSUHasC+<6p#B$#5IyI%Q=VD7^J5+o_aJM8ceb$0hTKRjMtV`yCOqDQvxG
zN3#oD8ia#eb}>D(bD1&TRF2LbnD(u{!G~rT@+6p_ol81g^?gIu-*QZr^>}{GT5wZD
zRZ*kZ?8y7AM3S`$;PgUk>hK)j^teb6*@1-;Zqd!%AoOM_X0&eVU=uofaC%yxSXf$s
zjD>S9M3UXtq-5Q`mqhGbNUt41<ZYHUchNyq0d<o*?JS`N1~e_zr8=2BloF&+u3*B0
zA0bLN$ESWc!VscS;;84=)1NQUVq%>sKB&{$+y)R8>xoWQnK~l^w)Xyef)w0(T&sfE
zRFBl8V0vyBejsxI62s3xi{(dMYuXMaweW@J&Ou6{>&k+3`8UzICZ}IZaZw(dq$icG
zeyrcGe<>4azW(yk`D{H&2QI%H4l2TIG=-V3yAo~OiY#Bpr9_-+?D7-LKHO;PBfVXZ
ze+O(Lug3!8W~VEDQvKf|gz~PS)79Y5`e4WbLJ#KjQt<?Xq`vu-wj)+eGoHiwbM>?u
zQ?NVV^81-Ilvpd+w^Y+tn7NVEh#V5d?jqzSFUSeq2iQmBB3w~}5U8{avM++mDT71D
zV8xioG~vnhkufPY7{`4HniJdw#jX3IG$};LOuS9{;>l=i4SG@e_@gawWC>w}0HMv-
z!355@ozU+D)6v7|$;dW2W`^c=|BnRfR{HNjED;f%6SmZxmI>N0HB`@T(NS$GRsFX$
zI;b@|&Fz%3?C~;AkK?#<a&l8}j-(;4?h7<d_&&Qu8xL}n4=FD?y{AV2vhO0*7hsQQ
zwEK9av@rIH6_K6-qR?Cmd2CY@iGIe`XtPh+YzeAib(=wonj8sd`|-^g`Y2Imk=oD%
z{&5h{2X>;9QE|Gt9dj}*Ju_>yHAX2=Aq1#$rv>I19p<r)PsO{Rk;)C`5x)tkZ=Hm>
zPr_F+jV6FSZT$1(Uou>SH1ZRJ{5LjM-$g<mItb0fCiH&(Y#7VcXF9u!fRb3CV?^lb
z1&A=16<uo^tD%TG;Piawd|x0O>2$pzs^I&zh)vhio|2MWf;r>ZT`_%u4UGR{?t0FE
z{<b^(y~~*|VyAfNKoJ)2ws~puC#$d$xj3;;+ZIaX2(4Acny6m8jp8;C4=*=E_>XG#
zmwjr1rh6FRXxbO_-6X55c)bY<+t>Qk$GhQ7LEk`2hhT(nW|*aHKBnW)mqi<t2{S?E
z$Fs~;o)+=n3DR#+An2U2bU_&e1Z70xUmjfJ<JW!cdX9FToFfavWQFk`1*(!PBx9u|
zOM!+Ce_ev%K{sIs`SgX=&wscRxZ*!v9=_>kT!h!J7RBanD^cE~BVUs!-Q{&Zqn~Nh
z2Hp62z4W8~$|JqX=l)$lKqx4n8njT8jSLjOHukHC%<V{lG7Yf3eibjvd~cW@CzX=0
z^niLZ0^)@sfQDSkV%U(D)tkM{f`NQc{i~SbnBvHLn#dp(P{?k*Utj?6s7mO&SOu0+
zZUTVVM)c<>WG}Z_=R%dSOr7V&<LL@o1U{O#biG~X?FX_gvfZG1{I)XVl6E4AlZj;-
z>jjEe581%>^_)k9Bb%3vUbQe<Vj}0BX?PxgkS<{@<8$6*%ZCc{B8Ch;{!wTOx20<+
zpp`vLUoUMxBr*9M3a}{d4GCtN>>LpNMvxCV%j)k*LpCui9016~)n$(q+lBk)?CT}L
zCjLeq^bnwxcW$GMg~)q_4J_*>cQzEq7os{4Y%NgliMd^6bAJ7NdJUkzu0P6KiS7$!
z?>A!y)85C^(@QhdDk4Z#j^fSdFl=FVCTsZKzt~Vf>U}GNx57*cYH7jvmy{U48vZFB
z|BK2==&42NPQ5UyzZXovYFIU@h7#k&!hu)?Q)Uw0YNOrcT&ETh+_gd%oKwYqv>9mo
zXGe&5_SbiOZTcdD3&>MPWK#PJC*pD)dU;|ky4{|1uc}=O)n1h(q1~6Zd@b4v!4c2?
zbqy%-bV`=jAr?-b*5jd=quK!QmwI0gsZaMFr}F&PkPn(HLzL@z3|ll@0SX2<Vx;z8
zV++%kShIM2g`*>bM^1GC+C0uk8P36O`>XdGBz1C)vv-_?j|n4$XXv$~amf3;bUX8(
zS{uIy&@biud6fVu6VTqKb#cwChm?|1(?_cEjCO!ZGo~7t6FU)#2D?FDB~?W!!Bv%j
z?9TZWtP?dWw!)^#w8Z7;&Z34o5bS5vQ3SdHbegnHrES@}k29kQA@T9R_68JUKuqr9
z1rR@=N@G(~tH#%|3rjZQuxrw*(IW==yF!<vT+M~&7h4sVo-!kAjttB%o^0QKbN>FF
zv{><<ZL#=oi(vcj?6oJz(1DC9j@YN24RA!L`AI-1Wpl7U^vp{i@5l#*9L4MN`$rMu
zgAa(3)=Y!~9~#nI`mN>UqFK1UE}P%&nD=ND^l8}oa={gV5VCUh>D8)m!(4t|gv#nG
zs|phY7!_!loc`iG+#+)&w|{xWjJ}LakH~R(*0;0u6lsm6q%9Aq@*Km9VXgv!P=2wo
z&OXHE9#8X`-*(sU7Of@@p+FzS6D!TIf*ncXj%@hZ;i1lvYoc@t;n1kY%~JaIuend&
zb;DDaxY{%Cn@^u!<C>LbfWc601K!Tn9!q`CBT(xxxv=Ks3?5>b28YQV|GPVyWPJJ}
z82>Y+oQ)EAh!z9FkV4Y6?bi*@a5;LDpZb90Dj#oZbL0{hFCc9tY>UvkwqHduIQ&ki
zaRf4q+eNpzSZCerYWI?wnk7?z>tv17!2O98Aph08>P?4(41YBnmw!+He0-)s^8Ah_
zPP!~?vC;das;2TYw7<Khx4|GpRjQfxOz{g?_r#8?mIODehz7EK6bfooRl;|3-#~A4
zvP?7qf7`nH&4%B7VE1{q!HI)xv@I}hpcNCL)%DwFDi99plf*YAHSY<2cfIQA+Npz@
z#`$%OWnKWbq#SBxySU0^nEWFQS{T!Q#!SM(K@*zR&E=(@2s!W*tB;R2!aqszy_MH{
zXMNV|nZoC48Ua)XWRu7CUfte|Bh3$!Y#Q}FpA?bSfwj#|eZo^l8P&^higCK211LLn
z)FP#(;OEal83We)u*enm41Ma(-pYq>J>0?BtwmB>N&yOlxm4o&v>RI|1b}b?5Uo?5
z=W(9fv8I$ia$BadmTaA#MH|p&Fr3MZS9Qp$&Z1g{>weTt@%H>P04nm-P)UD3>{(Kb
zu=_YaG0eOtX13+Jb*jo({bU?oqPF^?^$Ivny}tYJ(M-3G&7nj!<iYLNlj8CT^&*8_
z?_9(c`YDN9M!6OV9Q~z;Sv}<GQzJ|$V!DUe&vm4K5eG4jp(DQ-W9^^decJ;dT<i^}
z&t%As9o?6&-N?oc4UHou3A^T8LL+8eZl07!>gEZ4?MnWUtgx1~>8MXz9(2#ZvLH8v
ztWNwvr7~sTuS7S$^Knqf-ES{Y&!Yeev^5qDH@El&ppyLJE@|GN0HYnJhhONl7{h8+
zug~xD>*9ZDXWv7vPB2kcH&w%y9L{t<!&t>s|M1NR6$h4oI6LRSZ7v@^e!2Ccktfpq
zmuDsjjv4`tL({BqfJ#=X0H?NbK9A=MP{nEy6)VDX@UBx_c`FwT=K47wLx<~?Y_^{m
z4ja5u$8vc}Wf*CiH?h7Bv0eJ%mc&B(-mp>^DQo(!^be3WS^c+a+W<7&CVCZP*i0{F
zt<ZOG8!%ac!{INjr74%|))USw1S)gB7Ni-`ulx$*D}@M5;m(s{u(u@>a)~=FPe83*
z01<b1k@@-9_eor+`G=A{h|;fJ{ZEMrXe-?6F;D)QUI|D9bSa%<b0c^+N_C^c58v(2
z#(F-Fd|34P#&(lsV%j=l|FHJ<VPF(2ZIAzlqBsE(*>SeP`kY6CXd=K@06Df}b}-%R
zdf16b_v;#7t4mr{n_~u0HW8W+b7!QZ$QKKTo92X#NQ@wRg?noQdoFSv(h@Mg4zUw{
z8wtrSH7id9z)$OAlDgOW6!stfHFRq|pV3r1jIrDb)c9ho37O(G63oP(R;0~upOl$T
zVtn?Y592&po3qB}4`<)A1Wxcom9Y_**Jt#-ql0yWw?4|8GBa=f0g^XHe@}n9$><39
z{A!GQRes3~BH!#R7P)(xuWblq6D+sPX*La_gNL1d)$vM1L(2Au#i&y^f=v-7pAq)S
zzxN`4#T`|7k=M?e36N0tMrWA#Tz^j?%jL;S-;0o};@|9rg(cH#qYW`B=5R!5#8b(U
z{t(Is=&EtO=#i68MKI@7LZ2W|BVJnH^!qtaaB?)O2~=V(kl1>4Ua=@S*fe(Rvk;pC
z=|3l!zI0Q}ZpBHSQxm6%jv9m<=|jk2Cr=+IJ?IfHwsXF4iU@QVCYxF7&07Fbp|N!~
zcb4GS-mBeL6w}`YnlHz=3QHw}{3s(P?%9cNjXrj~VlyMGU?ErWYd0yAIYt=}0MFU^
zo>xMsi5Cg4JPUg-*(wm}&wlzNhyQwn`vxH&Cec$Ns#*q9EUtORQ%1b(Bx}=3JA|F#
z)&;6Xfc^rATR;lT$oFzK%;c5jb2mwD+(nJL>xgs_Vqv!BX{?>d)gPjS3$>JkfYe^W
zzfzo;J;eA?4H00olB+j!FYP_kc#Y;9%C^np%3H?^wSf#-m5C>sp(iBTP;K4GVVS2<
z4WbCzW8L~X`h?u-2LHM~X#pGEO&cgT?%2Wv*08~01R<pR$D)AChpR2hhy5PRsjc!x
z-=fMR;g@sevB=|0_xcSZdZ&M9k?`yJXd47FT*AY+Mw16T!EO96r8o$DuU^*6b#OGi
z17CSk&AlwWuNgT@gKl1Z)!TJ`1An-9KW5PqJyIEGN{StR{B6?l33j%g%?!Il%Wti?
zO(5oQ%LiSzDoSXDg~D{RkZm!BFuSAe2Wc;2<EeZ#RHGLzkdFE`V}G-tghuh2mM(hK
zK7Qkpl&SIDi5XvT!{0|~lF&2=<U9|*W++y~N2W-ku>k?1N9l0uxV00HlRS<&_C$QU
zHp0{TWsRkGQx_?4e4**^sk?fsaXsQ;)?RQhB}-7@)~9lsTUqv@e0)PNDdL<(ur7l~
zm|buV&_j^zy*hzn(e6vEaYo~!#qAg$$1I}`+I~*?ItZ<tN_|7%h!A<yGpHasP{m|7
z6d~APfs*bBqvEA(eAEEp!aW>m_8=n%&^ZCfuUlfrK8pVzPiGlbW%osUm5`K>?t|13
zq`SMML8QA=y1To(J#-2PNF#BO?(XjHz7OyJ-aCd4zjzGTd#|<E{LQ(w+i3FD`5AJ0
z?vo%&xPUyt`J1sPC5LB_QTlcMvi<)1?dCaE^U>Qb8V0n};kj>>wsl+p89+Ni;%)`k
z<5E?5ak6}us*GH#Mz^rUFJW4wo>p0{P-bu5+|&Np_ugne)<V`4@9c=B_wIUcgKTwu
zn*QZh;^dt4Y0z>~8g!z&V$?iiTDD-Cny-eOBrI4fkk5uUUYyvW(WE%2`!r8GICE`i
zQ^>?lHSr~%4pbgv?E8yfIFZrWw~h&V&14cv3A&61f#1Ci22E3`F~gE{!kbOJL&?tk
z8*k93F!?J#-yK<=U7-erSA8ZB=!ZR*d3ACkU&|R&PdXKpHLm8v&o_yFSfgr$h5!h}
zO;hKO4yZ<w6KMa&<xc~?$J*l*s4|*F(KUze5W@%uGD>m{{84zxdcZf3iJ-Z6K~U_u
z$dTw*52Sg=l#FL+NPz@8UuYusdJ|$~)cwOj0D8DN#xh4uhIH$VYKe@HH+s+QR#8Q+
zH2o&&h9&&Ns5>smKQ8yK=b4cnmX5V_@X!r!a{h;#Q%K|9$jw_|=KX8w*x?V};`g6y
zR55B6H{`EK00202%3Kwi4KOeR12%fE8aV<}nIRR|<F67Wyn6k$?8!qWIb^5c<1Q;x
zD}!pFnvy~R#6TKokV(tTlI0lI7n8ogD~2n@i&u1qb+NQKTBHg8c!_bH#{<xruHCi9
z7xsP1&%h|71oNQENqx!c0_}M!W_Ixi7|o*%R{=D@V_H?#^I}vi3DtBVf}+G7!^Ry0
zjGoMUQ0XRy`a`?RbubfQ^Ad0P1^>_7x>%F+V=|KlK0!i}5<p~9UYePI;Z>Ag#AGuE
z+ILo#z`svBMN7mr)eBx`b)W!2U~<2;)8-le3Vl?y{0MB||I=^#au(7pC2os;@!mGG
zKoxwxUQ!Uk94!A;Kx%dm?Jgn&N3HZbIOHwd%0N5W8P*8>&{>1`u@hagQ0Dn@ol_us
zi<5DZZ4TFP^&ET^k^1@}^aF5K-TknRm_V+5gjzD3@|<K95cYUp-GY{z+vGg(&MK58
z_IeT9AD-u=U^iNsP~u&foZtA$HRBP2#02RF0mmS^Fi4?Mj|MAXlUR^kENsv!&zh7n
z{MO!YR6we9=AR6*VKc<*k#`;=sv1W6uO&?*DWJjwTFFi4e-Nr2TKN=2WrGU(`&<QI
zU8tl}QZka!#Prg^UkQ2B{2wCJD!~{R;PV5EBj+O+3nQ4m2m-X)3IohL%LkV|>YjPL
ziW$Xzk$!IBz)fLYZi`wNqe$d7{0V3(yD;Ot&tgpXJPGtSV__Kkf}~=fa=4Yxq^iTD
z9K8aPA`xPtcKMOMH7qZfv>R^9-p``MR|(S)1**pGa)H&rI?<TcyF*6q<j!<t)4c|F
zOn8}Q0;n<uoa~)%!t;Qc`)zkV8&pxciX~I@20rhmqt_&=U=E*AoA%w*gAHj9AWmi$
zwZ$lXE-Q$&*wXvZik87T;pon!L6{g1bjL|be(qPxon^#D9EEq>?rO(Vh5?X{o8m-a
zKy?Rh@hr;5?g6Qs#N&r32r#yoU^n!?s+&PyY)|newD=LG#S<Qi>oEL%&&X^S8_=MP
z(&qK=%Lk{{_|tQlf^7s07-b~KQ7j!KHufyyRzVqN#8{MDvL-Ck!bC;+B~*(cWXptM
zh1($Y1zND8KFQMDC?%4gL>Wu2D*fmrOpQ!!(^Mf(D3#^0-F@d<0N_!oNUKOxORHqk
zrk7(TjjWRd(ZG@@Apn>^OpXoKM1%n^Wl0JWQAXA_u&Ocu5<Xq=lJ5iCeqftHs^s=(
z<9;E)a(Jhac0Eei*neUh3H>kzI1|BX<_1IP;0Q>69svkR5@S7#TNST736H1SV6<MM
zuz|5KCJ8&AM&CM|-TL>k*aEu}*2Sc0%_9pjIQg<|tnIZ4`tv{NHrhkaI%Vy&0pn*N
zx>(Jnc77&A?Vj!Ta%Zab`tD7vJ&Ay8Tvz}M{<Nst!a%z^u7_<yI$d)hlcv$0y69ci
zr!5q_$5x)}ga|M8mt<lzgntlC*xXU~ELJb%5lvXZ{#e#0u=zbkw#$0Gcl>RPLy_Vd
zurlN9;Yt6EqcNFqkme0r`e1+c!7soWb9chD!w*~$Es15YFTKD6>A6)x?>(d33joC@
zAwRu=zX>|15@urB0j#0M{HE;odReAR*R@UZn~VkEE_E|fF}5d`5K^C3!VJIzM+ZWW
z5x!XOz?5T*#-_Dh87mKgJ34%w>uXTI1?jrAfQtjz?Dg)vxd$5`K!62!D%oxg-=rXJ
zi4=mEB)!}yP#<$--7Pt8(v9X$wSdg5^$nMgb;d48oaVSd;{!O51OV@ZrKK*q$}U3?
zD{M%lTog7iMwB@am7p5%iuMz34=rPJaE{K{S#9zpJ#r+7A3llT3<*up&A4#4csM5k
zx;qWdaTb(6lEwRe%n1O>5<Emo@J?R=lBC`N^#(Nrnm~@|Uc3RQO^WcYGI&L|rTur)
zKyyyHH~sN}5)zK7WhN)<z(7&Te-iN#ia17F-(Oh=e(FT5!0cYFx<SV~C@v}v9u-)i
zwFYY2dcjl>r`~VlBiX8=R}cIvQ^6^>Jv;Je8((Mc&I&9ahjKi!SRx!~!04M8g>I7&
z`CP0mMl!C^E9%p&cWOgqPkWne)`PpqLyWk47`M;NB><qHiS@{W$77V*5>XA-8!e1s
zC;n}nu+R3}e4|7xv7B5iO{FSc*Jru7a&Lq37od6d;>J;Ll)TQDNHC`@BF)#`P<c;a
zrw@G*#@t;JmFN^L;7V{5_jhSf)j^`zpaBGR@qYFE%=wAZ&I>sMM>nhzvubBwre>Ez
ziGFUSWQS@+xxC3vnsG{8>>vaQ_%Hs1{wB|U&%;kv8*bE!%XT$~<7T>yg+bE?5Hsn3
z*l*|mq-1p#TY{BB&RRY}F86xR&h}O%!NuRgTRh#<&={<Mi6P|xYf2@@-O-89zY*^{
ziU^i(NO?ZGOnrDPVT0)YFkC9SE%j0H{wI#`D$;Aj69N@OkbZzgd)#duaJ<Key<y|g
z1~8zzUV5ZGp)~bkP(Im!%rTU}U1c9F`8?A&9gV&mxTU+^4I*tB{OHw4g5m+n?sY$o
zt(U74xy)7}2sOHD@RSqI_dffl63U(g;=G#1l0L~@iqY+ImMkX}!_(HwF$#^LJR$#H
z5Db~#K4|6$1%6wt@|G7NBEDsxW46iC-d4#yFe>{DD{1!w%^D0CHE6Ise^PuJKsn$c
zo^J(iyl6`xZ-$LfhHkoX<ntQr$e_xz$ItoPfz_X8PQ5-@8x{>To6g*(&B(2LgxfRy
zIr>vhoFasG4t+>zY#U2&`3{EX_3-p_-}<XPE?^mm4oo`>uSF*cH2}PlEf5`0!Izv?
zD2B|OLNc41dL(c;K2XqTSdKw!mJSv1#GFo2WC#HS)wxVQ-aH>YF`U2cgs;9G70v*w
zkJd(mWgf5c@V6N%`RAb66tpjx?%^&~RiDrkuop<gTYS6{EI^w<Nn*n`hYBd3!*oMS
ze{4fDX3qc8bNLmSh?@_=DYXVydkLR(lWbt2c6KQvODg{T?tqu^*1v-%nEgmmyXT{;
zJ%RkN5>k6$HIuZ;dHvaFVc1{aA@MXq4FArAb4BRu3Pt?i2-M?ebzuZL9PbIExGugJ
zN_`(Grh|}TiE#^G&~;ETnJE1`X)d<X3^+Xu;WfA3F>=u~HbGzFWk^m*%NKRwegf&C
ztuL}l<?r(8qM?S@m!D36XbIxiKMz6r3sZD5Q+)^%&qoaMsvH_>Yb3xo{Z^V-y#Jvn
z${PbuKyRua#E_$-?@-jcZG&q~_njmCaT!fud)7WcX?I1^Yx$F>+M5h&lesuG%p&~k
z#Kwc8w=z`pRczHb07R)5g9jE@svd$%TPE9{7mvvCbWJ*zRJcquvT5q<>vDJ>UAUM*
z;@+U57_oIBw`Vyx10<U8C)EFD0tS}}LE=e(mPTp0S!6%bxTx%L3^aesT+QhbX~L^+
z@m&$hXjpli*&G9?>U-O$spUBV^~A2>8jXUPMilDe%^a_^5UK&7a~g)Y@f@4}7N1bL
zn24zagci2n><@CXiyksZ%dvGw9}4{CL8kyMNe|00eR%ul!f>$X6!5haEfuk0VgZbG
z0oJzvy5D%##q&D>+;0<uvF1bDaxto=f<CDV^wELRb{A?;A1SxyP_FE7o~TV7MKhd;
zYIs@#GQ!*CKAvMpg%DvB^;UlE1M!V>Z3<zal?xdAU8iFB{^qh^oA>*!z$}xT2L2YP
z4Rw{&4p^#AYZZ_jA#8SxHf_|4ThFI&Zs6YzPJV41;4q|i?t0jnew9$}?z$is2|4X&
zjVyrNKviy2_sSCkP!S^_7z&vNA7ohXCoMjCwj@*C1ZYlI5o_}V&=dgPC5vlGmZ(I3
zixR;#oSVzuC?2URsG6##w!5MX8;YBqv7a<ZuR$R9BV~6QRO729-o<u-<>Xhm!T~Yw
zAJ0fp(s4rZ#~Tr$T1GR_+$emnyx5h1-%OHeFLGBZF!Hh=??dprZ4=VINUxPiG7SgL
zI(#ctFQ0Nl6$2qYLGs;+EjRccBzf5!E+osThKKcK*_&_)BV`rV`~KCx;=U3=|G6MG
zNDve$5On_Tet~~_A+erTw1^|~B(C6a_$$A7e)R~8%npif3pxMr5mt9)f!RZ#d%27h
zB(0XQnD>NLG1E6*o8RZ5_Hn~a0ufn&hgqRfQ-HznlHlpt=WBAdM2VQ^3pVcwmh^CJ
zA!$@SYHW>vB3tBK{{lul^;y@=p-PbM-LwP1&L~wh{&33B5!hC0>GHWoYyS$-S)XE|
z9hCcSCX+-159ERU<SY=7!4pLUX3JI$?f@WlTh@L~P!uzCF&KCEAZ`gb2ZBka)qqjR
zW9v(A`_5psn;fa;DzJNmS2x_^0pxaR*jM0oj2gi1X6KLc>HzBMZaPKo^n4F{n;;1$
zEY+}_xUo|l>^{=f$dt@FMNvXEbiE_^^yd}viN`a1ExmtSy)vp=Ju{Q;c!TCH&O_z_
zR&1tW{&DpPSxegzxJBueZ=J4V0o!=3J5Qb9Y8)mC#4*+vx{*QJ$x<OzW5wEV-Vx00
zFoE56zmC!NG7Sf8-F1qM*GoDeQTSYEj4*R(7br69(El}uZq;ei>#VG0#Z);s8*Kx^
z0viVTO$2-JNt;`=&vmnav3H>~@O1(hp>4u%`&;A_SLE4BG?ZcMi8NAki+grw_w2Zp
zC#Qhi3*YsaeSLTa2gtsGFTQbgwaVCSmy7z#t}o2M#U0q2D-UbET7R0lMp~TX#al%y
zlmuf$BcF@w^?<Rrhr6Hq7x{{$&4b(waY<0gJ)BZPUIk@rc()n6y6_Z3Za&2{*zXb{
z-ypTX3}srQ5-sC$B6X)o^&IPvPM@1DFEBSj+zN%qs+Vtg5(oJB=jA13kDz}uRf6c$
z;Fl>|@0fx+?pGuN5U}@?$lI!R(JnOnea<J4wU*4P>z9NMcx!Glsz`RWCTIbvf%M<j
zoJIsm8dlUnShTMEcqGNpKjv13o6A;7u<P0+CeT`gLqs9&zfL@B0EBg9Zb0)@9-Av+
zR-VF?Dhx|V1XvKDux$e<A9@dBl0ocBj-z)@6DgE{`w8?i=W`QcW(aV=oNk=$^=L!#
zir}Ec@V}ec7?f^L{U#hSk6KGsfY(%rPy_(97Ie9K#<l`d^j#-uD7oqwMSw}h^%NU-
zSEy1dPo;-6;Dy1hcQ!{OpVlC5^E~9r)=oF9)-f*PSbe#8BAtl9wCHKBS`mt`nL9pP
zIPvbB8?qj@wYtze@$43E?T?^E&eTX<>t0-L{D}2vTFo1vS2gN#z@R8L=3{f2-2FY|
zjmH3g135TE_dN<u02UnVGhe+6U>WQ6{vVF92m^YIbGVSRQ6+~}8jc}~rQI~|wwH%p
zN6pWKUdWLdqk@niGuw*NG5epB6)f<<We6D2_j9ckIlMs{d6SCynF~DJfv2$+I9tRL
zrCi-KrHmXQ7%qD|=%HUmWyVtq=*UyM!j+EEhi28QdGDKp6ZvDwyK&`Jnn<&$OTLF^
za`Q^~q>di+0`1b1ekW8e#72M|g}2b9N#<JwFuku!=IjGDH6WYSPvuP!1F{KVPRW08
z{R2l6$Pe7``g`6O(g71lS82cz3e*8c%x+-10W4U+0tHx_n5~PGMS#T*tn2P|nX7F7
z947dRF92DyhiVu(43UWJgA1UT07!S9qi3TWnqgo(aW+gn1I(>fJs|5(%r6_XVkLNt
zE5!<4zPm*u0n*@njSnTsNSF5*fTb9)FT^4LKKe_6>DZhkQKZw<_SF{MF!EK29_?fW
zY%hSswy4Y+7N5x32cXy#6OD}{vzw-w+dMc=P=M?JP{1v~ki64b9q*=+j70+mV|(_0
zx;f^_TF|KL*fYFn@$t^G5$Mk<S%A^YXb@<VgXk3MfPVs`Sd=o&F90{r>0?c}qD(i4
z#o5N(6=b;p6r8tB0ii%8eWKAXnxd9t29QLRuW&&9*_4!$0xY@aPylxWq_G(e4V0f)
zV9F@>IDm@*WVi=GVNSt{_>sSJv>6Em#Q?(qRokC>cO@Ms4bBvmLWLyCWIW!hBjDXr
zVkRhF3-{|t(hdb}%5ir`{uDRuLK4XumASukiWJSQ`1=u4{<9L~EHHmP1PGPP{TNx-
z&0Uao$%K~}i&7J4!mP(}T#fD2S6*2B7?$crD~#}N1i*Ilb-)0zClznr-}B1Y*4c*^
zVFhsJEk$v9I7I*+Bi0GGO;fJTxea7Mt#35FZ(s`6&#ajs__eUN;%Uq1CVEg8g;SPM
z(Z_F|+^$Lo=&|WVv&dYH95mpxQtXmsVS=l3;)gHTo+hv2dwoa2l(w^`SFl~bYHdox
zC)kNA%sP8N)&aOKTFYiDwg*5}<f@;{)%o(nsg;fE=B6iFYsIA*aESwaBkKgPJOMLD
zBGTI)e*p}v4T_k@qie%q-KD~Xh=0HHbiUNEYHk1}#-!-j(=!GpLiw8xe~aW=@;|4r
zTvZhH^6zdY`oVklaibUF20zJ9d8Peg>VEt;)=t|~@-t*n#`26A#3R_ktTT|@1>;y?
z%P{~g>buA~-ge#*$HqXVcnc;Y<5GAWoc(Ww(s0swF+LM)0>hDie30CqiI207x}OfL
zkw6OTQcMXzEJk$i`~M;ldifB~9&!67yiq-DGnD8-TjSa{mrp5YPbqy%DHmu1LZ@|o
z57J*CljpKWOC>p(?|Rm&R?gEy62AtnVd~!^bF_YhU1>2DSk5P9!(W)C?zqTlKAYba
zvrTNfp#V}5cG~Yzs`y;+Do_DG%z78{fzkZvo<z&tbCOqsQ!Lgv5L=Owt-f7niWZmu
zKLT-%R@2kfZlmoXo0oMUZ3Fr7F301nt?uK*ATV%zba}Z(<!}1+mrPm$Lp+_P&EbAt
zwYC@d5wqNkvZ?sRuL!}@cK!3y;275{IdOizm-Iw>x$_SYOXNt>w=5Y*H-PGRG2(qv
z)N;3+^iX(km%SdO9O3ztwDGt<(i++nvs$-6@~dfX`{g?3B~%qqVa<NhP)^-f()Yib
zv|1f3A2UwcVzAy7Py~&3-C*?yca(J1X7aO-*gkgB%FNirL~Etx7&w=90^MNfdLrP(
z0S=%F8+zUqRM6_k(;@P!#0|LSZf91!PO=wP>R)yReB~H^PDK2vFEUy2PR*`7z5gn4
zcby`CcD}du-uaZjg;N$N+X2Xym+*)g&Dy{f&6#0+eE*pE=8RVgbh`G-L?>}Bl$)q(
z(7v2^Ky|SorRT7lFZ^@vdWfgfHs_Jizoh366-I(4C}JbjwZVe~pLPCOsjc;tU{i36
zJ3er4@9U*l255Dh<^N2(G^c{$-z~3EC>}%T5A2s%UW*_A!}g5sT;WEazmlU2J{QeE
zOLV(L>gl-Rrk+~y%9wa>nP!`|*_~iwo16TpA6viixkU82g#zpe$rrpHuvF>T_I2X=
zGTGXV_bpTVO;^kX*Ei;znNjLXzE|M9)jbnf25UQQ_WRLK_u1>a<E$^Wx=){9Ze5nw
zhnBI|Su@H@fK7S)C#Q&_K)B=8-1zDu<nY;{*3!0>v*=&WAVlntDwP^vRNKmZB~nf0
z=}wWWa=ce}=SKo;bNHbR@}$j2P9VJ|l}*B;=+h`=iQ_rw0rdx2Z~j`=-n0V6xuiI>
z+Ba=igNne<u`yNb=W7OU!<rFW&$}RbH?03aGp+xrLW==}7{ngRUN<+Zw1Ie2$x0lp
z&bHSpBSmF%tj9asiMw{%|1xwv&XxV44kbXaAklf*igz4v3Il$)S05iRsk(Pgp^*!l
z;1&CZB(&-gC`A8jXmS9Ur_&9px&ebL<k~4O?4qi~cYx^Uus%wszkAm3JkHVR>J>6j
z)~uyz%M_{{Z08S%*~<SRDwRK6Oa7+h2y_EfbceD_<d69QPA5Aea7vNywxZ+%+txqX
zul5f96hpt%oOzy_kxXJ>fRU&~av_(SYjTN2T%&l<t1}Bg5az`bX!<7D`3it}WRynO
zrvX%8n&kPkWk@$PrJ%HY^ZDOzkhBtD5Nmou;0u3Tyjj$Um~zWk`;S&oZIvk^Tv8l;
ztDuAlPvUdDzyP$%#@@Hb#_aVxR_q>*?ut637zh#vj{1erPMIV?_q`pj4N1$QSN?)s
zoD@L=9yReX{3d;xv=akFUOc|K#6Sx}`~ft5pD+^^-R220W-zZPk_;p(lmPqR=H(a{
z0O|1h7{md0&YXRnZLm}$-npf~4Q3U;M<@s2U<J+w=Q4pXstM@2hlPqfW4;DGBagO8
zrAFR<2!-mWz}&14bJ6Z*mc@5spLHbrkasCWoW&J`N{Ge&nkxwB0tp8AKqzY(%51a;
zYr<P#E7|bsIn1t^8N<udRHCLM==C!wBA;I?mz^DD2}Bbb0&@P8wBH1f`*P5J|LxVv
zb+Sm1!LuZVRfiWg27E!?3p&yaku$lO2l_tUrMKq*`CTURSvuX<yUTjwH^{XkY<W?C
z^BdRtZu#eq#YNAuh`W1tTGURt>|B#|ABH1Z9Np7i31pz^9I3`UGlC}I{Q!?DmT(T>
zqy%iKZhL^igr{1vRY}jLsl`@NL0YH)>zwrYt_p||TDw=Zta0{uN@bnMpVyOFt~#eE
z7%f7-2R?V<ak9<|3@!n*EO@7+@5DXeubQj@Iqx3i^iAB%fk;9+EDJN&gsNeA;XVgC
z0&~LZ0J{7=#38;RY0fe6XW1x~$U>wb&Ut!174##C(x$GnWS&AN;Z;K1e4x-YB{Pg_
zI5lE-6wUeBqh&^1I;Rh67`4~$p;0QzS};KrJDBoYPYN7!Ml`tvHcubHeBtCHK80JL
zg#{+-ob>}u-s#rUC&bqT{<EI{2_4l8HrUJ8jVYYF-e}V!e}Q}C`vV`_zt8fTi8@G9
z1$YWoI8=4}rCR|4zPH)whbOOu5CzKh&4HX$7}9_A&%be2V4|xc4YJg<_AJ;%-B3iW
zZz1zxx&+!TK#%C}1SHUJ(WL46#`@v&d_>=n{UqwN^qN!+oSQnwwW1o+km~I96XDeg
z@!<9HSpH2^dC6nkhj$@Q5UHnc2PuCAE)iSNah5J(zEzWLJBC(x%=1_E1;Fi4TB>`)
z$crvl3#It`xf82^vc6qC)Dyyd?}816OZlFWswms4pNV-3AUqxCT2Z+2UmUCoUUzqk
zZ35xjk8yW$AC}PkPiPZcFi>4-8!^H+dz8NdI0d;hGkr30px=neDCK~CSCZ1-k)R9_
zme)~mnW-vg(_*d)!arsah^m1}sc<3Nl>J)vObuRI5dfMi(8H-nzttQf`5y5FU|qZP
zg$1M?@-zr}bun(kfhr9s_W-%lc0JAnKw7~6?|JeDl}-Ai&(<JPNJ=4agQT^T4cG5*
z9{tqEn#La3Cb3FOaK#MdYxFb{)FvSXb-;iS^83YDGYHRQ?kGQdOA6iPPsb8O)o+BB
z^UjZ^An8gnXCSwQjpd6c;L9@KFQ|Q$3W9}9?uL^pT_H_M_!rC_U^yT+#>t9<PSsLN
z0E|Bdu)IVuB^&J4E)5P@2M(gTCz~D&vYr1M0ZtXJ`kMB6?+un!;?3nBr0-S+f^Hu&
zS2}J0hUK(B4I2np0n$f-8?;}QeZw&;uE#)+X9XWnHXyX9ZC3>!Rl?mqKX^i<Ygq;l
zjFXWQ!=JT%qNKnGB008g_WqU`vixmYgAhUwjOGe{#rPss%dDG&hsHC-M!X-uVGSIs
zfCrLXBIRNQ)v&zIh#kZNj@$b<i%#j8AN#3Vk!6zavbe3feovGLHuTCjTp)-bY`{>T
znMs5$Sr8{wR@A~EUjeTSfA>Qhf`V|=_&y&m2KvF<c@sR8C94#hrU8Ss-J^uJcdkyP
z0b*nbR+1K&N*^J8Vk48?G;5y%jfy=a?d^Ug9LLV53gVzctb(l^wHl5;{`+6N`v#)u
zY_mG|e{W&fkw&sXQlSA{zn7~k6p5>><W(YzHaGLE+mDLU3OPclU#<aO!0x@L!tke?
z^LdAj`+(`_=g9iBKLN~@gvk;}vP5|&%*TtqWG)3)i4><7tlvTBW_ff2mMu}Ag39YY
z3E57D3_{v?3$C+1bCW!9?wjg5=v{E(@!Wj2bC|C}Z$!{Uc<P1z>e0xU>0`Nj+;X6$
z-e6(pNFRf4`V$(4Y!U8^UD$(0NX1BxLaO(A^->qbNVqvIHgR-No|?0F!Xhqd`mJoA
zpc&I(nd!nR3Z<pcrpWb3pkDM{dkjS#h!jGee=|YYoSQXoXN6p}3`a<ZZ0SS2-I?4M
zS2)LQh}2CFQQse&U47~)7B4`j5jYXRRX(p6lq5<t$ZVpcvbMBzwY*^t8}l^Y#>@T(
z$71Nf1WjrDV^-0Vf)qf>0x!QEHX1g3PLMB5-g|JA?CpJdZ2a8U?h^sj)A9WeiqhvC
z-W!CE)GvQ$&S?xC44;mp=yCkRERQ(}F1*d}J$7t~oLZ{510OcYZkErgDa@S>`O+3n
z>Kf<dbu{f;9Dm-5YY(2;#Vlo<bi0y7F(n|V@?;P2-P|x4zPB$BzgZr;s^$2+sMgi9
z+)P2maW%#svr1q3Igd{1vfrxLGM}n2x4+S)y3UHa48<wNdwx5p#P*jKuO9=_A=QBv
zzGoymVm1n=7Pl;e<=B7*5k22m6J^!+JCfG^?BFabm&qbv@fue_zZ3W*AGs!FxhC!G
z>q3fcsz85;b$9GvMBLRQCcE)i=eIwMgh&^Gi^;Q35yk6J1@_zg7=$gJQA)yMB?;Cr
zfiu0i4_-pr6hVS~Z`lh6x!1M&d1&GOzu^NeA#UF5lPmIMZlbWF>i$@mx}|*q$IBAs
zyx;oc)gw6EXNSe##bd@#Zlb05shC-gPGf$yJtwOpM#VEi1k%{E6N?o^3yJw8MV`q7
zoN=e1G9<Yymf}I<Vm7J1lu5yUQel!@DwQ9L?S4c55p`^qKsUUBK$BWn>o4$Md(dKq
z(UTwh&V0#O(p7nh#7LzI{W~dShYZH1<ADT4EDP4QMdWdV{J)aO*;xoy-`W|al_zeM
z*7^tylB$y(F9oUMAZ{$M<6Q<)QNv=y^6S7=?YwcAs+V&T94DtvFDJXL$2*-T7l)9a
zn9ts2aT++d(?Q@_^6SUKEHut|%Koi2>Jy!iW&&wU%7_HL_adjj#>P>;n{~~dFg72i
zD$>4q>Cy&ZEl^_mbMPRIpmIAG<3Trl#PRd2)_^V@0Yt;QYKJX>5&2$7IxLZBcIif+
z5v)!I+Y|D`rWbJPf0m0=mz9D`cv$@tO~lx^423<1w)G>Q<DJ5U7Ef>McWxYfm*#gk
z(}@(7Tv1LuISD&ch*jEjqMBN&T549LBeDV_ZL=|RDgK&%ltJ;0=T8mQnNEAm{wgcn
zSGF#dBYE>rMtUlPijAonfBQiA_KuxgFj6`n4`sfvo2q}Jz*;8%0i}jM3_m_S(C?Tm
zhy$~KibhQ1V?TK|f;m-&Xw!RN;-!O|@EORQV5CxNP;8?w*wYhVL4h*yG}LK1=WlEp
zESPe>(1`slY-_nx{)1V<dc+$rR#&;p1V40Hy|{jwIaIm6$!odE^(k5x(1N99l7L3Z
z^~}$*;`N-{So>eHjjQD1mp6|(XbEUFBUy}_>)I?Nm^5NNX!s`JdmJGq6&?Eiy~OyP
z4JqJV2}NPd&td|yjB5MdetE;8vd~C6(7#U(^f&3i(-@xS+vt=dMY-qP(ohX|b!I7;
zFRmoh!ifd2%qu3j%Df=N0)t`}Ovqk7hUL=-O~sfrVRQ0A<LOv@5r(J>ugO0;2_{~%
zz#9>1OhgrO5a7sG4$qEZIG^`#Wi_GR|F{P{2eB`t&y1GFM!^lq`T%wV<*9tco#{4n
zSC`?I){c}Fw_ui2*-;Q4|N6<o+YYnQRJ<e(CM&|JO+l2Kk{Msw8!;d+3x(Pc=Ct5v
zt|#!Ra+W4_AW?ltZV^(g(gvc5k0`Bhjm=T6>QJC|lP<$W-%Fe|Qh9oZv%A7v-)c$2
z0;Ju4%~w`RuxnxFvCI474y1El*0_=zWS`g=lpAx?VeBR5$)zQHTdd96Fc(Jn8@9iA
zRCVI8^1e~)d<Bs{ZP!lXjd7K@$w%%pW9d?V>UZ;d>?Ki%#$h_sPz@2qZ&EVd3NDC7
zem{%Ri{D|}B2l(TdAQ{p`m?30q2ce+FO~O^9mJ=n+Dzvkk0`|&pVC!_p*M}l{EDRZ
zs{Ft&jub@w*wXe1KB#HWAsCZHtO})bJp-M&*nL9f3BT}>OX=g7H2Wy~r&|2@7P$>h
zB$isRIpz)<S&+Qcw`w)#%YE4g$zwWy&D=TC(*)$1+vb<eo8v#@x_nLD7a=&V&!dmp
z3vMclBvD7+U~VAn1o?jh6Or{rp6{Fw)0E3k3AHjq-|m9i&z-i>MieX;vz=KBYbOj{
zAVUIoBR(NQE|P|M!wgS#w&#oA(Y9+Ir7RPMihDitgnd$f5nm}nG~{5iFpV2IY5qab
z4)o(1g@Y8p-Yrg93SbjtV-sXIi)l3XlsyUzk*ssv=r-U@9E^WjKNd-@-8^pGNl-b$
zpKCjkbRyJDfmcQHnPm-FQ<`NzdkYG=0nzuh!88LjZv4P|GC_NAO;X)*jt*aXfmaO5
zuX$)dRN&GmVMI#UA)`=gthU6*A1p2>SNYwzz>uym;9d3D<#?)so5~}fQ`IleNgc!3
z0y29c1-0T^IHdlf&7gAB`EII$T{y@;`2kYfY)DQI>&DxaOo6_>ecrsw+3+UM#W^xy
zzJKmo*u-e(R52}r32B^PA#UulaNhV!(Zf6qHg4}2VaU$Q5IuxGWeo4l4O1;Brlbic
z=_me5xD+?Yqa4Sd5K3#(-8@<<bFAI1uRiKg6XC%J28jlDeZyP4PF_Zgc@=rPaD#!y
zs?u&*%`{(KJ#Icnj<Xg$Vzzm<kQ~46`7yHMhuXw%QG0qAb-nrB32yyAmU7_eD8E4t
zzopR<rB9MzAp|$|?w|4+l3o>b+HseDP%HHgC|y}K+jEoF!8Sxy{>z(<qCmq+VCnQM
zmW+ZPD%C3PE7v5#GAAsUJ#WR9_ZbvqK&9550!M*l&60Sj&`BK&f?9ljzT6z3G^`D~
z`^qj|jT0L7OZ9ADEq7gh>9;)1iPpjQH+2SnECUyh)B-QqfbQPUtm?v3-q55qZ^1v9
za9#3idOX75cQqD_PvVD@SGN1i@qdW7tK?y21J}(k_VV*{?;xqg>3PGjLQY91-~J}G
zopi(0&J$^NLG6O!*)CDl%lN?i<K_&g721PJOROAbE!UxJcaDBC^FK^@ZpvwO8*V)m
zOrcz?nTIdoI@!YP*f?<r>>+$j<}wEMem|5NqIjR`QntrJp&ABRZ<CkII(|%sFkn{?
z18)#9VdIpzzMaYyELR2|-T6cp1x=P9Ah(%(gxRIQ$mpVfrm>!#<#pmz_{<?4n_Ho8
zI4hFDOFWZ+DKCkc71b?_ER3GMXv`u%6zrWm`W2!WZmZ*BQ><JH*=>{KrWgn3osU5f
zx{rz_7$PK2j1#y`;)a3Sw<vc(E^l-qA+S1CdC8dYtB1{~ynfdiP5&Zxq6Xe}$)83)
zc+5lpE6O`GV&3h%2sy;vHNntSbg`FvuP#jERp^h|ES00m++uCzQSC9TZNbW8=W|I`
z3N#QUQ<IOK6jOX`>D@+-6Rt|OHgth<^S=S9VOIk2==ik5@_J$w+~W!H=O`uKadlL)
zWMan`+XSyZLy3S&Vk(<%4gg+LhY5QlmC>u-fD}Z7{qEh%9>(qoR@94F^f9I|dg!8S
zzU0;Q4F=XXw{zQ^SSja5xQMjWk~e`hl5=HI%k_aZt{K%*ea)>o3$%jUd&2?c0r*o+
zgI50a1je4g&MPj(`sTFG=w(Tm*QAbu1*xHO;fD6PemjdkSqdAyNi9jf9k0d?mg*;y
z0^gF%r}nBU5X~sH)h~dgSw3*=Cw6u`J=*~-7V-bcg^=#)D{X$yjdx2XIlopNu8UIA
z1Sa*4N1p*O7*$#_Kha9UiyXLZigJsQnPEw*$OtAHYaJeA?j?FB|EOE(KOjbu5&|P-
z_m1^r`CS4}f7Pg!D_wdP`ma-<Hf-aj(yE%liZz)JnoOED*9N=+UVZ9kC#y>b9=R$R
z3shnv#!5qac{zM?iKQ@iUq*ax8>tJy!7r(;`EB(@{1O2L-ro1^uQ!O81Fc>D5<}Yd
zDW*l&Hb=wGCss$U&dtu^<A>A3*EBzJHE1x&eBUzSy@51)Xq1g7eJf!Rp`BTIT8mRp
z`=(yntTE{L2rVu8-1QVO!pF<ENb0k)V@H!QT>M3YanA??!TSWdpq4H!&LQ#56R{~4
zf)3M1b{<ELja227ftL=QnBpRM_LZ%QAq{C>L#(vP&0jy7rb>`YPUs;Rc)}4PDiA`2
zC<LZwQ7eXXqz_<;FVrvEDiPlaS9(}u7I1230*l{d;UJ#PD!ecPGLve5-i+-l>>G?%
zhuQnvAEfD>lB6FYq65e9K^^~hsv{DX%zL5F@XjJJB6CQ|lXuW<v3$Kv5B!s37};ok
z<#q|ibH&S_tdd=0C{$TQ5)L2BQPPc^9_ky9dSc_Hct*~1`wC}_i%M#6@0xq%1(3|%
zi?FxSmj&SHV_v8<_D2Z?ObKO}evWv6My?0a4mdqOdZgT@wBM{h*lVqX&1uBF>{q>T
zPE7GmDQz#)M!KyibYFH_nvFxp`^`Fq7B}oKmdY=Fng710v;BSB{xTt8;?;cN*LG9&
zcu0LWs4T(7t9d85a?>Rq)!D$W1U@6hd?(eDUO0HUyRzp~>u$%P{@5DHw?)*pRpcS@
z^y8+z#8L*QMrL!u!3DiX2G=2XHE3Xfbbs+UP^m=zQsAz?LCxCnmPg<k94-4zy*!Ek
zup|nf#boe(znTIO@N4Q#nAMo^zCzN`6qVexfk9<pR`qe~x`^KV(8j(wvRr1qj_+CV
z`N-7JBq?LG%R+!W7L_xMOt7MF!QLiHM5IlgR38xa&mmZFjB0iZBdBLa;E?w28;=Nj
zuZ$_ut=+tI7E3wnq$rr1%O^1~{dsW=l}MIa(!hiTt|k}};k+=4iXu3X^$C>KA<u`$
zmeqB4{?CUAl}W0V1a876+uxW4!=!O^S@@%Wql}%)oDMsgrP^dBO0>=4*L)noIY*|z
zU=XX-k|1updXcDjL$MmZ5mN<}Mw31`5etPHHD56It5j?^9a?&*V)Ln1VPMG~0xVqD
z-$4r*E;tLhY??5)bg`P?sDi!QPitc_pO8#6Fu1S_k~A=dXz|8TTbJ~*)QcpCf4R`I
zLgL0+L2MSzB(jnpOv?hLJO>t)R=OF(B=We;eTM_HK9v=PW%3Ad?^Q}^&T1{?n>A(9
z4#(4o4fPqCbF=ZpR4iqi#L|cnQKPYeue}jE%^F&51|K4n5UbA>K9hssF=63@2Md|R
zKT{}zlnUN{H0RkgBQ{8seiMYw-Sn@6ct%lBIQ24Y@{RT%N&VcgEWv_6GV`}3dOru~
z-nsQQG9mT-*>JXFdHWc^?+w{BA-L*=hZ`DVSBx#>#x3PqTntG>xIk~zU9(-WU+>7_
zUk!Cp*WjI{xv4!|N_NY=nO9CKJqo0iN-FH|38YnhFC^K@k;`+553e{6W_o^pT{FG0
z)w!I&l3_ae7$hBix1mheS}Wa_X>4Nmj@r_P?1V3&kL74vQu5>*EQj@zi<0;TMczl(
z+4N!Msm3L&u`J_j`zBVd(#Ht5y0&35q&KOK_A=b+rOqZZkhAHV#w*MRn+61li=@lG
zc4^nTw)zvVLKe5u<Or<u`Xj%~!j>(xUu*$Ir4A36YA(rTT#a4_z`ac!KfG{2tMK>3
zMV3=Ox=eG=(j7J`?$)xFfRJ5db5C*#mH9SmMxzYAa-lvDs-`c_u)fcsEV;wd@V$7s
zX@$&s&AYX+lT5A*-O@Q3kygUkg*0^Gnyn*lvAc4{kh_6C)}8gkPv6Y7)qSd3n>gT{
zf@nU}KjeBb?rpm4Xw*79Bril@MPil<%udUS%q%<Y_N2ZSi9@H<Cf`b+;17qD<=!0^
z!$?5KD0?G2_sNITj~pc9PVrf^1VJpZ5@LM(=Y!x+gU<W_TwDD<=BB}1b9QM;8uG_K
zAACCmk&wZWJj1dyh&Sjo*M-DBv1Ur%htb+WKkKGUX0H%}LBS;e%l_U*IC8?X*E1jg
z7E~7X0Y*TEbUOOKZ&>30|ArN1a}VYzvpnwlJQ6kKDVA?DmM@ewEz4gw-7UI%Pz9})
zgsHeT=SaVKyDPjQV{Sk5BAvpl?K85Aw!yA|d){#~Cq>7<>*WY`voLtBKbmV^T-v_2
zNlrlcVB9|#E!vyqeE2g?bsi7$x$j|Zx_}kL^(~bgU&^Ctbo96y?b`leQ7MO;&4LuS
z*`ayDdF6zER%nJIWaqO=xH|vCW<U@^>vtIuQ|FpfKV%_NiO&2kr5hK8&#+j9s-3Z1
zyj~HJOd(WO8qb=X?x-RI`WBQw^G7URVi=7+h-~k{?o|K&TsxN|_%lz%eu4X)RH|cW
z0!Rw;7w@f?m6yLrV@?t2myI4xlul#EH9hl>vl>APs3)8a<<+4TD~$zzlm=r5)E-x!
zm*ss{vBN)Z5#2=wT{B^h!TOJjVpKK!9q>8lj=G}S+GBlF%B*a#HhCDr*TZCZ4D68A
zsRAc=ol|{zV_;ht@~c4o*MVQ5E%Kb|gw&SG*>o)f7~LMsCG9g!!l7Pay*E7BWh?4f
ze7k(4j>yM5UdP=5RwF_ucQ(njtO1%US3(mpCzsE|+5J!#mSrIakE%s$UG+ktf@0-I
zUrk)NT*CR@%Kn2c!ID6ly}VE<Qp)^Z_f$v4&jjBnB`8E`3=}?F%SSKlk|(G#m!^us
z0n6-Abz!;Y1ET&orHs31X$+|?NX%VMa^*WFwMe2QdZ*+}>%t<!Nt1RH)fj7n$ix;}
zi=E=cW^Wa_ys!R&T6EZ!22BA%D>?}7%md32*w8$ebH^XdF5w50Fa8wz8K$wi!?^1R
zj$BB^UxFekrBGx)ov3YUXS5g=plN>KoS~Ew&ZN<RL1T#A{lM4B35qm~r>MJ%Rnpt%
zF054SYvc?Tg0?+rWf#J}cMK*OxMKf!N9Q&}ZkUGh7%T46(Sa7Wp2{h;;L8T?Yi7qE
z$WM1T;T$3U$q5QKtmpO$)|XuQO1qC)Fq+>z$ws7H6hE+v$DN!<%Bi!0hIbE|sZTee
zO9=CXUyz|a<Iv!1VeE`iIzW__q!TGhmD)*jIYKM&;!+G}4BtcXY7&Xb#?62DBo)i-
z#hFqqTT?GJ=JX2%Rd$)A6ccJkz|MY(2Mf|cw=;(fZ(VT*knvS%X;f{%fijMktq%yB
zppAE6l%oK&41)jaYR3QFd!)wB_es5xcl?4KyM-=V;M;(3bWG*#H(`l5ZU?Zrr$3{9
zW9#6hYP{7xlns`BLf1A74}XFcT71L$Ge4#<?R{ke`Y4($I@K5dKeDNpzf=eaHg}cr
zm?fzH$fP<V#KXf~P^A9`R<r1mW<I9x8I!ce^DicufOC~NYM;$GFM)<-$jmQX@s_$4
zV5EBX<@vNO;_-;|0k)TlmMEk2T%t;Mz3#xW#oH@OAAJ=LqbE`Xd~kYL4ae_h<p;#W
z>l5Dl5ufX4j$U}SIh=6=U(psv<Des(9C6!!j0kbUtEt=*Jw$cF$vLj;SP~Y-!-G>c
zgtUs`5ta)ruEs$=k4d)Y7bDpla}bBj?2OIMeRiKmDCM&HTs{{b^C=8-vea<3>-Frr
zA``0H^Ms;m6k_e>3$e})G_xx{?}H$YKTUJ1M_aN@I)dmuMpgkDpn<h8W`V0s@Q0cH
z!EZ?Kb?g^sZS3q?hkb4|bvGstVFg|exo|8gTNu}My*98bZ5!0gf#_z~8P?P?tlP!C
zuFSNIO~A*RN-BKiN<=-`45QOhGZ^tb+0EKK>be8Ma#}4*Jj2YzA<zeWKly#O5m*X%
zE1jBiXD{9@w^aXaV4$<J^8(UFW!=36U3O3CFJ7J@CvV>CR(`Xmf4K(U1Xigz{$Fo}
zMr0^t_j)cYQ!c6ITsx<%JiR=FmsgLi85(~Mtfz4e^Lixi^@KeT=te&7{$wm%IK0@O
zS;=b~GqG&+JAupX7@CtAOfDHp;(9t%Tr7`j8BqRFfMu6>`bgRajnMT9xZ9W*B&j$X
zjNun<m@5K4KF={SQF&u#>k`(92ZFU3E@aj=GN>PfjAV5W5g)>(MU%4Zx@W#Df2;qV
zVO3SPTlb#A&Og@Q6D(4{YQNssrBa9_L$6{>_zB6-`-#*mNUk+xE7fz`G<$Q_Fy#76
zZR4VzL*sDH^ZiA)oqwg}<KoIadD0$cy=AmNA(m9;>GVa)-F%f#%Dzlk*c`LKBd&m7
z{SG{J*vC#rgS&O^g)-U7*4FTun=|-lGg9BI>K|Ij)Rrs`j`8E7*>@k6@e12)%LA^Z
z;%O>d>twttdd3&Z95uaKgaqR$QtSOP>e6`l#f(e;^%Z@991tiqKS8%4gUg0;;GTn%
zav=J7;uyuwD!>Z59#(r{v>2kyviBZHToq(DB%a+T5@%{{i#bSD+rG8m$#dx7qLOYB
z6c*5erl4YCE7X$`!c`wu{@H0azta2Zzc7tq25aYlwH*)N_^Vkigv`cII`o@hs-tA+
zEFaQxkL-iQmbi~y{h;pcSnu7Msr+gP#w*5>(C}pk4dy2hW!E+7ppfuqj`f$xD6!r=
zRiQOH+}JVKKSrlOEXRzeu_lZH4U!2tT7icw(9<wFhpAzz`Bg4DIkw4kx}>bZJXO8n
zPkaI;q(>oNj?=T&$@kT)aq=R9$A&%x$<bML;AtcZJNHOV^@qZgbq_si@=uD0Uo~a-
zm)`o^Pk&QQx1NWINmGiZkvoN?ssf%Ao>d;)WV35{tp%%7mXXZ7#KzWf_u7e_D8d8J
zqo@Hoj(Nur{&cF6Etb?^xp)c`|Jdmc2p4ePRbBk+#L~yIGpZ3DuC__rF{?+K*3@49
zQ~mcMCB^(YxSXA5Q#-=nk_m+z*blb57vo9T(*(r#IvqQ5q}#WSSM_eeii0N2y~rsk
zZfpI_xT+1}<Uggr8SoKsilXQ}E!8bTBWS4%xVLkr!wR%UCELs{i)9thu`a6YZfE`W
z`;@bXKP?F&K9+Rgi82jDvHP4ujhD5S1rbtdaXDGf{!)<97R(-Bt6MtX4ehKL6^xlc
zro<*FlC*-;l(HG4!{P&xEf=hu?=y9m)~SI2;5Ci3Ad55h1uQTu+>A+S>L)|>$!4!)
zLTimDkP-rpr7?4|pW*VddYr?dio#Q9rXe&EpJiL0xvi7r^;mZa6F@PucDjR}w1`%5
z>FpH0u?d&_EENg~1eUz1x8uLTwXg>qEEkRJ5bc<Ijfj~xC%>ryLb@zn!%_U7iR7C7
zzg#VXyG(adc~!&^{%vX}D!pGG1t-;8W%=9@_?$Ad4IAe0^~}kWY=n_=ix@(N?#J0z
z9uhbt473CE@W{}O2Jk=Rq;2gsy2<f5-3kf;sH{@Bw}+$`q(^f^*JLm2n~j!MQQZ_M
z`eS}#A~kX%^@XG?rYp;4zd9X&m*w`@4Z5_Qf42PI@IxyC5<~yvaxBQPDzd(;an5A#
z=-cz^_jVzo9=zmX2VL)YtG_+Yw)H7uLWAQxd-f8fX*;tJWY0C+?4>LgK|Iml4b55}
zmO+-bRj2bD!xNThyDq%%1c;8lhgkik{N8VWpY~~xG{<CL0b6!r^usOt67fRJX)yoy
z6^%7$5Sz}^g^QV$GoE8`w_W6s#-=p>u=hHiLvK;4P9|A`i}T070-uF@1MIKv*}u}F
za`VLq59et)a=F-V^TlM4n6BP|hNj;vjNc%J^HjYT60KzuoY_=U@GM4P)ene;kYN!g
z3dh$IOZ54wp(@%%GSr8CL<3*4X5qu2OX?SX=@X7GKJ9Q~HIG9tFu*q<_(wi*A(we8
z+J_E~T)JtWS%h67edkq?2~izha^SLEWjVYH^yVx@!G?qo#>+wE>r;_Jm&vS;l9*AO
zG2U@Uk@%5f+=J$RM(FR0>dUmV<kuzfOWHHz6k1~jVJM=H&F_=vci0cA1a=E1#0!l;
zCJxuo-es1{R;M@nAR~ffm42FYh$J0G2I&(t?~L5IKPw}tW@snw|N1@E$?ilnq1UDa
zOBQNCZ#!vz6{59V%yJ5|pT)1s>2ldIz2isvOUu^5x~xyU`Rj5Wm=mX<{Oed9;zl4)
zr?=cQOl&*c%f8}K4<;kaB%L=PhI^E_yhm6a7l#4i4b}Qurrj!bYt#<7Xa0aJ|6D!-
zTAJR%&qS3;WBIdQq4l-e9Q$8%nwmPl>$bxR4p(z3(JJ@P&KAl+IE=~`cA(A~z+)q;
z7Hxmi?xY-Lm4^R>@*s3+Gpx=#Cjgn;k2F6sol1<f`_)5)(8mwa%&*^TsV%JUs|K(*
zBuIi%t8i}MLR(1>tzLjbqUXx``SvP8)XpEve`DesQl%K>&Ny+Q^~p)Ojp7NatEq9q
zoyA))Z0#1W@UkZ(ZD0p0tF(HGD46E2bXWe#`^(lhU^w7Wy+ns&Kl0y(1iSNp&fS0t
zERY&m^{e-FBWuU^aRC+XHmLo<5XFN;5q-@Aq=@$s1!n)?OZ|+-;-6p7mC*0f7=Xk0
zhT)m$tjvFkHe(h)Vc!w4FalQR-}x4*&I8nK`F5DHvc)@KVuWOi;R#nDZJBp@BVGG#
z>$Go05><+h`Z|ysue)(&t0O4wmjIM4_Mn-YQ+WQ20one#cdgg46#TRLbeEstTS4vD
zXg(>(47wY@mIy@O4TcV`A+l<JLNO#b_`;rYpylZl)@Z1l`LJo%cA4WHo%V@Cvok+Y
zhP0IV(7jx1Ie!Ho-F3}|61C&L&N`XF`fyp0ra-N=CM=^4tTI7(&MBwX-X?2VD}qT4
z^b%>jDzY1)61QExuYY6CldexjMH2ke^_wo{f1AXGX!5!7zYS`%Pih($H=#jJ^zGgO
z4msSz$^xDyH&1Aby<zJfKIc>`cLCqs_AG6gc0atOQE`wVE+x;`8@(#7V!NAI@q9bL
z<a$<Sdm5zcnmqEf$dVd;=0!`R)2LXqgnxeXypPL>N(_d(7D1p?LTYLSr6kw8ttC;m
zJwjp_dFobj%4crWfQU|0Ad3W--^)LNRH5m<_pLIH+P@bGh)<ZxZ<zCKyFf|Xbb0I-
zb_72`@*qTn54hflU?u&kZQl33Sog)kw2jupetPr|lw|k?+_al!o)T612iVNe#bLV9
z`~bmaI~$(o2mzXwr*-Vg99`4nS&Ad~lqA{=&ohSCLvL+Mz$fFiw<6BiOcL;UKf%QL
zaL81zO6ZsYQ>m-gH8ihM6j3ZXcJjgPEM}$S7mCcnYEo4@u$MO`blv^SY%3IWZS|W?
zH1xf^qeh+&6B4N-fU|OPMw69;XOO5ekMJHw-O;h$qg;D#m9YJZ_s$-N#}LTqU%RA>
z@p?WKseX`5Tu-vJ#A0EmHl=zkji<Bgtd(iu3%RovH;pZ0tL;xiRpYy;=4iabRW^Bv
z26-Bb9Lrh-9Vyw83jq+$?J*JM)b!}KA{H_!td+Ju-5DJ0w+$=aQ3VxLFULU~Ts+?m
zYhqhBv=}O88Wn9FY`nuwV}{Nq<g=hmmvML~M}88m6Fcp9Ljw8*W7}7R2Q9TVeU41M
zaee(Z2M$=&<#pVTH!o|1R`tz+c7wVP>$RDg*{eWkL9@PAm=deIh|Q$tV~o$EcBKvb
ztwj5a?DIM`X+fqP*d!BXp@d_BFTM5cNS4Ot<{)hQX_!N*hI{mP>4FDa>j<Bx3Se#Z
zBfabsRw?)#au)4a7=5|$!k%&V{P=R!ptDs_R(8poGm^#MiI&CJSu3&AH@|(%+eNeX
zIM2S)^dsu!ZlUTdW5p{WrK&PIuy^tWgUnQuw~28mtx+nTg3qwk(J4p>{nyfwp&3CA
zpI54(GB!?W!*~7T(5{u7mCe_B@8I(P?(tt8MY{UtiM))mM`J=Esf?ka8-X;Tf9&jt
zyO`D5>#r)IF_7O=bN1snwY~ff@t#~F<~45+gawSQ`{4(0XVd|6=Kj=|8nKkEuY@Xv
z5k|<zODlq4c)l25*Hw8w5y#W$Z%al2qqIL<Ay)r~sk02q^83ENfFLO?2uMkTbf<)L
zNJ_Vagmi~=celh%NJ)2hr*wDU(hdLP_xHSbW_-ao%smWT=UjWQ^;vsQQ2vGWU@~@x
zNIB+rPiNBwI{y74VPDk+nN6(s@`?b}ge6PYg<-;e57MtHN_M&Tkyr;7A2b)=t$3}o
zX1GO#l`~d2c;U(=$&MC~r(yVN)5=gmF(g>JS{2&(WVNouxwtdLqjakjfMz#$Et%u*
z)FM;&r>!9*BxiAtZ4aU=F`pyT8o%7~`-^l%&7}VEf!ZApl5lJKc8o$6>6gK1`maul
z-S@};ZaH1|A3~_fJp4Z9Z~OUfz65x6A0)_?wbl&(sY`?@9F6C`>*w$JMoeu11`Csw
z9>2!Z)5w`6j-1gj*s+N)iXw5NIrb)b8KQ(51hd?#&@yjYyaEwItZ$tpO{=hd7Z*|~
z?u}t*)gaIM%M7h6*>L4+qgs0fS|`oULIkg3Iz}IoRL*ZJzkN+&+LwyyHm3(vU%pRk
zXn?gH5J%o+GKe99z40&a(*-Jeiw|luY1;Lb!Z>~LVQ*O@r5G*j_ZQwg`Y3Q3VTvOu
z;>3;R+m|F(Sz0=Sxq&xcVywu_$!T;k1M2m)!nuD6R*p9BF>P}sRXUA16v&`!ygRSn
zd>k*kR@bxs-7?clxT3dEXl<69IGR%MhBh9`V7-Jyw)NpDn2%`*=P1vq$%VRS<c+l4
z5`X@b0OVbLBxAbDZ@kb)GF1Ya5Jq@X=YU>^jHa>UR{`Tuh|NDdc+%9&(s;8;umY&I
z2VfO(s+_FSz@Mo#y{8&AP#_C@S&{l)%Z65dYeFtUAAfS;L@BNO^RI0Uy-EzFNhs=+
zJ($lkEt1e4HF@6V%ZzAlSv#e&Q$!BY%(Og(;orb{sk=~XHBTi?3o9f`-}tKIUGdTC
zpVm+#?Wwha_f-t?@r66Ad%4K$5F91RW@f`$ZT*%%5WWkb_&5ZvSQ(`>ig(m#q|<;a
zhdk?3+*$4F?fV+(1(P!K8-s3>0tF1px`?_Y8mZquB+%t-?M!?_JWN*S^2-eNdBID&
zixd>-`2rW_7YGb9gH4;3&i5spyq2}@h-ArhJKTb*>o%og6E)YzUv#F%*#}|<SatDj
zjhcGCRdpqdAnfiGjHCZv`J89K3B-%^jI_Miks~$9lVLVltR4DK)|PeVS3#D}uS(c?
z8PsH;#Xq_K!U2(JMoWMfE(!<-*&*cA`P79wY;(OMhe_O0>ghC<Gj#UGm7UTpBWeX>
z2@wck*bp6IMQI;ej^VU?<hj61Vo@+qLS0<*HdTPs!}MP>?-l(PCG_7dan8uX0N2Ip
za?ud?s`Y8dnaO|$;k(!FMiYV1UlGpl(<$18tSrhKNzYM25+LBD_ySacb7toWdiMz4
z7v-%zps*J~2FnENT+f0=my|!NAoE5r`kh1{?#|w9DG2tm30)y(-KJ1iSlVCjkVYEb
z9g`VgV18nezj}jSs2H#k5q9|S)ON%BWu;!2h?@U0fQ|opoBDQIK`_$bZ4+%iuqDBj
z;eFQjm{g*(xKZ;x-SqSV^@&v9u*_FwANz68AqJQ}(P~PZTnk$=8ct_|pa5d8<&|ZU
z2Tyih%d&xc%|Q3?2(k}_{G6`EBw<K6MAK)`!Pa?EC8z#j0gbWEDWg|B4Ky?A`~pLI
z_urq$=Y7NSp=~J#>~7VE0yAZnv9#RWJooKsx*S**dN&7z&36&!+8$p+rW8oFFW4k*
zdfJ|`xi#GD7Fhp^1bRm4-3PS|@iFPHZ_vv$pB{&a2@hYyER;pfOT0^<IVcrON~*nC
zv6yXWo$N*z@!E~jGj;maf20zlAmr#Dam?8EnD9k;T|j;hto;&T>5B4xLXG>w|L8LY
z*ln!~1ei=bEHTU}Z1~oj6lMHIaSZW?)7e#%suiQAiTCnYRCGMVLTnOb&<$P$@4I7^
z602&B)dSFGeAm<59k53k9*gh)YW1|0w%brKV{F?hQocJu_%fYa$;c~TtR{W?ILxBi
z(>$ZpEs8W8DL0wvx&J-G=og#(Q0)fYUH5XP3RUR(D@<Yh^8kg6wTn~QodOw~q-g)3
zfx#N9)+?y)#-jHF)#c@tXX&OfLudlSbK3J$(n`Y58{s(O`&W5=C@kNypImaV0;VZ~
z<VV0|jPD=-lm=v@e=-vNcZT!P>#}jHD_eWc6kk!$fHcgn#|b^*&*wB*=&&5!R@XK$
zWM;1SH@NafJe^$2*jI_x{V_cqMonq1x{szuHsmau<?%2{d~dotki>?*b^q%#>b)Rh
zG9M54uy&F=e=ji{adbz$ftbQ8Am~wAXyLoR{6O}Sr_V4adOIe7HeSgAftc`^xCZVQ
z5}I7sI6H70Pwq0Q^XcQOUMFTx9ih)3Tp(@Ul$9=tAQDZj6=d=E7?Xj0RLtKp5@M&S
zI5sE@AThP7<u#2IbUra_j$d;-_~_HB5s1UEDdk7xZ9tJyv~gT|p|MC|^p@Y#__fSz
zL#5*Gfr%efyLohCfb|4Mb-OWsF2AFy?~Thr|B)aIW_yinq?{Tz2b(a^K(uy~<_<1g
zHt%@<l(_3}Tz2J55S}ee5~LjyE5_P5S;tC%QCnQzP3T1cso#b*HL>v6*&=T{Z>cj!
z<8QUMMbbgup$oXS%KY#6`*r?53pI*6%JYgM%KHSTCuFHLQLo4X=NHeY*BQ4|$xVy*
zm8rvlj_ys@tOhsBNaw)5d!)eLEe;(*AF<9_#aQ~*MU@1LH4AQ1YWK)|5p|wYzm~OK
zEO+Tylb2UQ7?YkTZO^nwK-MFnp0QnatQzh~gR@=bn?LhddQTR5YyYZoz1wF`zb~y%
zua{?jC_HX$COa+c@Udu_Sn%ND@I??W(tp@dkgc+xs%}}xtC-jU9Xx(wWSPbEtfpmo
z?bYxH1B(XXrWN>~tg8BkwbjK6H1K|9Nh@=)p~+Q!R4lTO?SrCR7Dnm_4LM;>LF{uG
zp}q3CeRW>fl(lN9>X8Fc&k4KScGkpP(4WT*r!#11T)Thwv%Gv4JW__r^-PZs-mH+W
z6+C^(qShPDAzYBqRf$((RveA7Wq3WJw&x(=2A8GxuunZu|0eP4+8n}E9K6@QX_j~q
zJNMeL%po(f?Et?4ravY)`mPrjL<*T{eYFlmi+M_;r2eF#hMDd=_(K+QjJk^(5<>2w
z^F`#hC4OZxc{m;i1Mf?$t6euA=*9#*{f&YwwyHQs_pS@32siG@qOwx@YS3hrsW($;
z;AayF+4)5Ca2`67GD)SdfYLA|v#8xtF=DSklDl$*`3Xtru}6X#HA2m_J>n0Q-u;a0
z)7cn*L~cZ}N^kR6@J03{xMmSRRdflliWFc~aAl1$Pcx^tcmHTrChK?+4g7Ubm3dr8
z>2?ui^vMg^<1CMJ+nGdOIYpH}Uxk(Et>$yb>~>>^z4VeaY8m13zW$m@Xr)$W&FWq)
z{`FV;Y2O<&Yp0v4RWBc<4+=p4EGmd1g*2N!0ibok1HNl|PJ6*{{OtxB|C_N<wuWf6
zUqX4y-6|}74zv=Z7313-IR%XH+u;#xXIhtCh|dCuX(EX1v;zxNa6<a{`F}>8i<?V~
z-|Y;#o<&A{C1OZKfq|bTH!VQF@})7s_vf+_^Vt?pvsnBPuQYx3R(@>ecX-q4*@u}y
zR9_4q{id|Q_?wB2fxWkj#<eQ#HK^519`edPL=x0P{NDS#Ee7qAYS>V+u%5a}Vi(Z*
zn_#?DZv@Di6qTK`w~f*ucX~$FhQ)W?{CSeI(ZM$bCe{ku|4D5ub!=~NK+}HiQ@M#k
z<3C6Jt9h2?F+**Wro$F>7>+S>lRI1J?^I|mbH0khgyV5-!66By|Br!N<e;%p1Kyoh
zb^{*P{_>GT9#D(sTa6c8tG6^twXrS9skScG_85d)@5z!BvGC~0J-+>(=J&BprtniN
z1?bSgKk)V%jB^dG;s5thO*>Yq^o`k@#xKE{)xSKT0tTv{Rm=d73mi$26uapAFT>Fv
z@(^})#|jn?a%0(Rcp|axGGKI93)Dw|$P*|KrORg}wIWRWsbIeE@E(zNQa?d!;mjY0
z>$|S1=ItiBr-SIC6?8>Im&?&Xxo=>p1&!yg2zcEWf2j-hMeM8Lc5n-vH>z3e7A}(V
z#{r7}Iy&4I%^qnacA!qwIQj&XR2S@C6Iq)pGE--4+^Xb6<gR4)F)(W~plt-Jjh14#
zlRx(_IJgmCnq)DDVj?=oZOkFurpqx}7^U1<)7uhJ%l<*W5$-l=>FbnD37Ahi_L9m;
zPVdL=K?>jqn%~EgxS|MwR%_71D`WG7x+Wd%ogX;}%+&E-xDmIKC=M5Vr~|FMKvXu~
zq~+y)_*3SPW_|9rG?XN+xo;Ov0=0r=d0FQepTd<eQ-{e{M29Mr$fQ3Z8jy8gOZ*;u
z)gj+>^7{}I!JNKwJ9REHV44y+xHH(0qfRR%^+RK~!Egds5|ST{oK2)5Lth@RR!+lw
zcFi9tI9-Me*_CW<`X9cK^WuvpQD1{#X`IwD#T3Q~3v~P|e%Yb+5gzxhdT2;S#cypC
z+8*l{!D-IFwGY=lsZsiQcC5c{Wc1?Z)~f16Ug^YQtgbt2(0;<`5wq=NMh%e|>J5QS
zFo|V5!xCG5D8bo3X_!jn$roO!VRk%jSKG`$t8@^ML!+umt#{1K$j)lzGOt;a54&Eb
zY2@4vM}fWb0-`&q{A=q8PL7CXi{tYM{@{|Y;AsaVrE`*J+TS;JC8MJVg_~Uj`YZaD
zN&VuvZl@b+0q-s`LBDK^ZYhx#E`1Dt=pp}qvem1A|GA0i@f3=dfaOmVKGh}mz7A0e
zJqN#J>nn8)i_@hk2_CnPv37OP(^uYiZ+4l!|E|{F6}nGg0>k}slm>~I4}zki&A;t#
zc?1MtPdS4)!$^|tIcKd!MazP*r+M0pT9B8iWd7Ppl~Nve%w_|)#6xb+mhqb5Z1L@%
z+`nkFRKm0a+e)6lHh3G~IlXF{LOD#;<n?SaugX`88Y%nYp_)3i6rNZ&M)`NYe%l%m
z{@8H}ia1=Pkm~#momx1UEGn>at&;ebtd?qh2dpBRKWALKZ>UQ?SWQ@8Fn{>xSq`e4
z?(pa714U+Jq*~{qbeE~Z%`tAjhc2wZ6rAJECS(NlrrLoB@E2c%ldj>P3d6=JZdi7@
z^edEov(GX0G1+Ae8y@peX0hHiC;<DqjPuc}9Yv&Ux$qqNyvJe5hDK;seP3TIRTP~c
zmlVeMJTN9Sl!iBZQ}BGXXiO9*YLDCc@IFdkt5+au_g<Kb-E#4#+JM0kfY8BKg{q#K
zZC>!Y(aa!A#i4<}Z5AzBtE^aFzmxVmPnx~`v-+1AJQdnwnzHg+&RX|EWi+sN9oNAd
zRyi(VzW2(>cSlXcOyOLJIUL&OL?TO>Kkq6&(aH|3vFUl)&6=umvHRmtREWF?%(j0x
z?OC=rEJ`g<A7F8}oPH{@F0((_e@|g6f<<i}kd0&3Xnb-*Q6*uK?zMwR|Ao`_K7ii%
z>~&y~atb3$&FAeD5?2b`Q7|0-nu?-G9r{K)A2ov}e6J1xb*RoAuT|@%Z?jQc4fOaE
zea|v{WeYH}t0s^Bc0vd(9q)lB3hX1&(9^D98u{Q@e;<;(f%a?RURK)rQGs33fVoT6
zB~04u$+vFRuZWQYEZ(YAj_S}O!JL(SVljIE!vNzm6#ayzkf2d~rq#Y?_jQ?-l8sd!
z#!FjS(>2T<X!*~*Pnef0KbRvcP&1@Q-@*S~db>DYw4;q`RsPe(JG1(~>dMxXfd)V<
zJ8<t2-}5tVJtW9c(ai@@)5NL`9J^F5?{6%#f+^V<d5h=Z@yCEYIp=*A6(+19AWZc7
z@|{j@_O~VW5X*#|r|~!F6cp9={Pnd`H>zmC=MjU}p_eNZiq(WV2+J2#%vv@B5ev#t
zH8gVn_DVG51fr3V*S7dm3n!m5>GE3Dwiy}>4~967T&oXTs@-hXs#+FE|BAB9DWx(1
z5n_duG*YRfVwOO^=?$GCkod$5(rd%DdaVt2M)|+lf8B{vu)Uao2TCsQCGqOh<Cpr2
z1;-V)Cst+f*wSg3M9CY@7k%Gp*{eZtNPV1^sW=3>%a-%=e%5l=tkT5N0TzNeeDq}d
z^<=a!$;)`(%aPX+Y9x!(Jp6i)XlIw*v%A(`f;zLwDGa_CDxq)HxE2s$@XD?2%*sT_
zOre1e61E;|(BC-bj^A;XFBlfX@Zmj{+`<nU#TgHy$9MqMY)Z^mt#y3FyI+AF39BvL
zgQ}38Mtzu1USUO8A9>n}@Y+L&bey?H!$E_5CVyhf{oEWi=kVeYYCtFv9S+~~E)@G#
z@n?vS!HVpc$j;=_ZG^zDzg?VOQ(GK|dWax@&Kv5ozPDOni4Ilyroz&4?oQ_a5h;L-
za^6=4R7O-#{e|~>+O*@*_bR3LxZ7@ENvK<re2YweG?}vOSk#pOT{{Vm>qoOeze;;z
z4J#)X_pf1J%1SHe_bVn2a->3x2)2k&8nB5elw^XE%1bwbCf*f4Ud7f*3HiUm3Vqyd
zxu0|Lseh~1Yxc;eP3jq6o@Tv##i#yzrT2L8$xGJyzjppF{(tR!12x}@E8o&WW!2QL
z>Z!^4D%3oMN$0Y!0zzO--Pz8qY9yn)%~}7}9!CZJ$#FG2#II11UPY5EPqJ?{ZM@0e
zuRAk~Qffi1<=R9F(Z({aZ)|kR3{8FU=&0#bVYk#NAR>bd-W+#vZ+rPR1g`efpia)B
zQJf0;Gwn{NZ^i-5bNa+&q1Rg4q>b%oYWy1UU7(5CmP`s?KG!M=1PiomW#|UAYq3pZ
zzZAMS`@bkhwR1<BTREPJZ-U;vvIn&>8{)g+ltdvF@xYaI=&u`WVg}6opEw=Nq#@YN
zim^r06jJHq3kN_C+#VngEQOx$U@0*-eC{C$1Xl=6x##9PHAbtyrK_IsiyQ-QbTV(U
z*%;E(SC$!z20US*!dY_V8OWhDd(MFue4<{PB;En9Xq|CjMT96&R{(0a3e~#vdpur4
zKTTGXj(FJvGao)uWTZSi62FJ$!K)MXMEbboD5pegS`=TEE+9CP<+TfYT-J9>Pl$uU
z7?9p#k%aLH$(9JZKyxJf<y%pZ7JiS|#Bq7SqSHN*qfV}hP0<@RNti6pEBr{K6GrGg
zCeZte;w!->AHmCMOghNX$sw$*(DjMXZ<>S`u*zA~0y9%MJC8#&q&{$jAA2%|_U*hJ
z5;CvRLQj$=w&W!{N2Dv$HjfitI?aJ01MW{p5BEDn&aGY6dM7*0g3=#mw~Iu+`57Du
z6?_uzUYO*Z_wA~Xn2NvABFQ1TaK@h(TB3a+kw;uvbIS@ekFRO>eJ<^rx}d_FfYi*(
z!`0F8oF%ZccaI7h3$y$YSY@kFVz8>YL1$_ik@@n)4Bg`_vM2jn$i87_iXHJRyUhn|
z<=MZT!2p`+wzbpq%~`T<0n49x`i0R|tv3^)us-!eroXJ8Pq<wwmMy4VZe}H&4Wai-
z<u?u2snDORK7cs`vNiMnc$4d`8fP_^$75VeEoxvRmBN%68R8T88MF`N#(6wp_uclQ
zBxx*KPFbP>E(YG?v>^_(Mj^gQx_TRflbqoGsBB)@>eY-h3ZhCb+~Rh02u)gT9+k=U
zU!w_q>jIPIbwCreOK-__SMt54!OoLVN8xd9A%iR`Gjls8j!jIlQy<?3NUWu!(cwlQ
zzp0T-d)htk`o?6)c&TYM549zF^`<2We2{HyWYW-_$3DvL--l@3)y;&u#M9<#)-o>X
z!iRN*tUR?5Hnv+EY?uHXvp^@k5AnX$0&aa4OvvwHnYO%$t1MEx2j=$fnu<%5kVTl5
z<aVazJXKiip{^FGve*y^kt-g8*!%Y`MM&x4Jr^4<eMl;5mcUtXD}|APmS6^A%J-Vs
zWvAZRm}7NKpCSm(j+H~Kyje@%4C83;L@F5ay$bpYoUOAk?`P_p?kIsyAmq1RHZlDx
zmh2lkoV}iLb?+9^JT6x~(gNbxfVQ%Y;=QgBitSp$7mnvb*1`M{rq*J^*y@{oLX(@~
zN~pD2{I>x2JC0Vo+9tSz7D0pfH3`h)*1r9D0%gdOXd47e1g!cb4>x=|;==<H7LFaG
zC=;*`vn{}{jIdbF>z=;+<gSD>Re)}rA?v=|cJLFIRZ>=eRpm;~{K2`Fo@;<K%aD<&
zNlGRItHy|8@s^o$VD$oA>zV2I)6QZUep{!=fe?QCS2zAAYYPZKpZ(qXCtC>h=FjTQ
z$%#b}x@roIDUYXRs{HqUr`*2p4=Y1WZHD%2l;8e<wp*+HLGW+0hY&zQHiDA&?^neK
ziSk=NcHAP#dYX(Wu^e|mvAencc7~ae2VroAzK{`;?R6s{v&8z7%XTA*&@tq)?#jvg
z%*398EKhm8Yg5_>(?RNzGPAa7v@e0#*&f9hM*)X}S+lg-F`kdnX^7t(NumRRwgoG}
zAO~0x^^Wh*Gzxv96QsIm{*Kkn1%3=4>5qGJy|zS~I2!j;BoFc}aM)E}>68boKJ+FU
z+1>4THK7Zx9J@Y}rk9LV3;0a0y7!R$h>oQRE-L556d70l4#Vthm^u)!XeA>k+sVED
z2cnwU=8yr^ZS;X00(E&y=s83|d63)q9g4C-z<x&JmYR3J&~p{u?a!fQ<T8P8dT&tu
zqD{WL^j&SgbMnB$T}wsSF7b1E1tS2~RKsQ65FZbD3jGxLEBQJ3PHwg58hcT8G2QtA
zgRq5cs;B9m%x!&y(_Bt^P~+7uvDM_i6U;{S^?y}Q=EW<)v`a?NZUyRgABcyg43KM>
zSJckuD}f<C2-9hv;8f>l#}rmC+gRmB>;_HK@i-AXqtK3XpiN0e^l_vJBF*M?v$Gr0
zO2)n%Los(mu;gI4^UP9n@4r(E0-qMhD24T@n9bO=B|(jX%A7k4=P2;w#hoD6jOH}e
z*)<Lhna)@^$A;MCz8h*Fj8=s8g3@7trKO`JR?meo3>mxuepTf}FY`qZBMmH9*5B3D
zoI0B<E)S7BTxaMuf+BzW{c>lkD-@^cDDbD*7QF^2fq>UNAn9Of?Ktj$Mr~oRK$X%g
zlN~EM#R15-nq|o6k!-^KHZ;*(^^xpVvi-?wG*Cc&4z-+sG)$Omif71nK&Fm1(LEBG
ztT6&uI+#KIi^CRVK_tl6^u6_!0T0!!UE)7uiPZM<6y>(&Q(0>mG=W>{Z&&i@co+J6
z0IA}Wq#xb>9G1g-i|V)BC5_l`VmbIJDP;h*VOV}H6r3~l{K&5di0$l?#x^=hD$*KM
zgBo;@;giF}BIUs*hT%jOw0B+O<9SP^BCKc`9y2Bewc*(Xy99Dgw7yHcb??~aHq2r}
z>=M_R^@~@QOEqUCHo}bvL0x825DJ>MCfNG2A@;nr?4uT_!b<`XGm39Nqz!ZCM2gaM
zjim!92D_rluzIv|e<rY7_MnuJGTRQbnRSwv60pPgkc;b+;y*G5r;%&KULfXBvZsiK
z62YR-V&P!IN@*^hVE0<wOmO&*V@l#688rKVP{9FNf)9B|R2gPZnxsL6vR^`^9;v*W
z<T`105EK6DK#s^aRx}A$l5vOIkHjI)qS1FBkZD2NZLqpnT73~jBJkWOMqA70dC&s0
zoUKrkXwVqH+3k=JZnct_L)2@2XBS&|fA!fzeJgz$9aDcTXxiQRwfcNEuy!tkeoopX
zEA<LD`AHb!_c;h;F-J<N9L&0oJFfw%^E!wI!pt7=prcev@+PrNc_7~_*nnvDOM57Z
zIA}aNX>f65-d<<==3tnAqTMh_yO3za_4p5>r2d~NdonQkX)<M#4agZl6XbTZ3>B^V
zTBf_2KXG7x>6QVu{`7L(Lb5yqpV|xN3H~0oU1KFECF<SwD8MiaDR(kE$P*Qv=4SD=
zKzHs>tL*umoL>Jhv1ljU{W52L;d<UlU?11Ro+mbYQ!$odVp7>YY3Db)s<9r`_QW~H
z-x?fmK6tb%=;|w>Fjm<-v+=O)*m}9~HS&Y}XWEq(wAl)@r^%$O1*-|y#|&J~L!A}w
zHtC`@rC}Z#_<zdgEt5xRsdy6b2v%=%XG3z5tI&D4MJYp>gFj!#5EOp~B0GL~H=1Z)
zwc|=@|1~LMOuii9P9ZOAu+nPVeSKr(CPnF%3|3w?L@?U@SCeI*;Z;9H#3kpkTU3A4
z9{YWX_5!KiAhTm(Xub?`0z*E;h!>%QS$}&H0es0rC6&ImlQ9i<`WiQYPj)yVC7Is-
ztmr*zlc=VaPUds&Y{S(R^6K4klDgi4$?YV9%<dQ0tto1-#Pe^`<YzdmXRno_Nt}<_
zshj=tJWrF}r*SH#C))3v|F*U?M6IIB>U429Cf0(503tJ$%nrxdL>%6?rkSm!*)`Es
zwCU;VM<FR`8>cXbPZ4crDQQf<7Hh2K;?nszy5{4|w-=AgQQqv*KP>A#WiQ)aG1`qU
zU7hXiYY+<vxNA)vzV1Vx<@Ty~>YEiR<KB4>F8-GY2F+6OmPhUa@{RtdR9$PTs8*>B
zlinzZIe8s5$8EwTnlJD*(P%5@dZol>$%7M%wx8eRw{jEg|7<BW+MAN)_D)DE9fgJP
z=eQWD2)M>HoIS(I<&#lbls>;^YW_i@D?L>>v3EaaWEMA!^E~#0RDOYh>**SCU7xV;
z_r-fN^6T;I<-XV8Ef1|V?lX{O#=_cMTj!s4Nd|(4bd^jl*UPmVhXDKYxGkOgkE>my
z?WR>zrWpSIP<xDlQid7ni^mtVFAqx@%k}hjB}fFkW*y5cr+M0H14LM2#%#Vh!5+R&
zm=R#oH!qf&MM2DU;j+C`Q%iftSoR&eCp6v2wqC8nD~tYFS|f<<JkI0%VbW}IHo1K1
z(cpV7*BXGjFPdKrjdOGG33GT~AAX{x$S;Gm=1ODsvQ*sZ3+?`^8E<Kr|I=9Q^}w~~
zD66cns3PYXUr+bfFIc>)@6IGB8}IMEo_ick=&2u~=xl#PW;_&uH2eX<`By-!7^XPO
zm$L8n$Gx2S*=!dgYBO4rA8;{oi*91ZKoUgyr&7l!N#Um57z*UB@uGOvxx`2u*u}|-
zJPO1dcQ?dOw!`Bnu20*=-65Uh9Er1Os4W;eGR0*7cE3?(Ibx8P`c}$jFo&MZ-<?|r
z=OhEjaZiFm%Fh0IS%j$PrEc)-HB$3M;P8O@R%nXniY63K2^myhthdvj+ZGR|%r8zX
zmi6(+myR$HF!PO+er;c?p1!Re?Y2Z3V%e{`b4V4?)OrWrOK--8fo2Hli=`Tu%P{0n
zaBmvg0V8ZF!_u5TOB<LnP?-!}UxYNj6?*|brDWUn$i9FZ_+(wCCa#ZKc&_J7c>A39
zmfEWulNPfnJW9Fh%S_B$(kavEvhBZj6<5uoCY6OWE90`w=kkS}_prrSu%y_}2tAmN
zPWs@y5}zJ*5225Jo{ZN&%2%!a`0YIZH1Z&l@<fD|;81`2n9e?Kj47A+!iwUGV6U=K
zuMpc%#lU6i%c(VSU?68mksRDY>oyiHMlYe*DW`C?bjx#jG`T?E%hPX~rG*|F+~Sy6
zJ&WB^amOn{?{O(Su{d7hf>hFGbzo3XMg@)R7LNm!XLS9!`|j3C+pi<%Fbv;xs}r>{
zM+D+hpI3#CeOj>?-7HLcTI)3sN8dd^^go(~@ra$tcB2sJtLCc40j(iIVEl{J)I+tG
zuHgVfTdu3MIkJtG7d`wXl;6?iByvM9mf|I5v&}7nFwW_`a+uj!e)&Er;=Gw-Lp@lv
zD-K8dGuEC5Jfu51fo;o7pJvxDWFv|UBWLvc18P11%AY|6nJA^?sF)%m&VR%y3*fvS
z*BfXEUI0Y|CLaSE<Uwb(kClB;15Y##)h~F65RD22I_4MH;+5e13*nLZvvkZ)YXnRX
zd)zS^_@8C>NcJ+2jKv{@iZZawAUsoALQ&QmfBfXNxnp4S>F7aOg$pE}%=>VpLpRBK
zGAuS5&&CtdA@hCdXS99rhQEpX$D*~^v4tNZQxsP;kS~ZnMrnwXzwr`i9OPohc=6p*
zU5XAh7vwpR%^C=W@uv>moA0iW=@gB%!^HXI_DfamaxdXEX1m|1HkhY=oZarXd0byL
zrc&(uy^HBWW{bZ%;mw3h{@@b@g%=YJkB434u&ug!Wfw!8C)v|9v71gsR1h-E*TG#^
ziJiHLE(+LF+xVY{1Od`-hFUZ}nI-c=G+~A~C9yu${V7=7n=rosXkX|b?FBcADYa&8
z+Ag5QE**_qUr5G_P$Ca;(#mZ)Psu@F8L51A**YS!#j(FR;#b74@-WW;>|=E;Z;9^8
zPwto|xzEEp@9Ze?$S7Axf3_^YM^##Pr8e8k{XqqvpT8M^>4lG}KJjWL^O{slQ5K6n
zmaiIWo+{Qv32_>hcm)yJF#dtVs8oN{O@c@^g)D4KO(wN`_FU&(+sKeTGzbHIi%G3x
z_~*U6=0(dc=EjaIDJ~~&$eEN%me^(RCYb<qv1tg=AabGnJDSDYbKP+?G-@N|j1SoG
zTqMKu*9Hn_!teb_p>y2%J}(+YvrN8Aj-fMiSaI<)hHl0L*Y(iLSWwVeMLd#@71wwm
zFrlU}7;AiY)G&9budj`uqD)9n)6I$@9*9`^0eIQ4!$s{?>zE4E{4kzK1=Wg^jkcm6
z07!>%aWFtuo}CbfaRPlCAX2z$wZPN?W2-RfnXlPO&7~aLw4c%`C~^-)Ad`s)q@f|=
zySHM?)w_~d9BznYPK%Mwot7_H6GL<+Qs{QnEu7RBtnD1DIs$5}1~rmOtRPvqp)~U9
z*40z9VAMH#gi`N%_w>u{qh%{N2AzU<NAO?PL^hsHJ*P#;0%NPYOpVG&(B$6CwSvVl
zWB2Eb%&*g}Hp$FV0p_CLn%4b8TgU?UpO25i9)&~q8D7@4p}Y5fmL`+fxEZ~Nx|6^o
z6$v#mQp89j#v*DF^ef)XJRLVQtc)%>)moMF^xrhO4JSjt|F7s;VT&|k(V+(gl%aKF
zKhxt8ThVo-Wbv$%Y&`_WObNpuQ_(>g1GMq8E4taU*C}PV|H>ySL?d07OM)(gdUvvu
zTe7rE>qf8i-wn&cw1tV4<_E?4@wE?Yi#A4(jzPCDrH<`!%M?>$y{+4%@=6WpasF86
zNc9jpEcjLK{wYq=c6~&UAkpF;hqHMU&j7r`CORzegIINdSJC%@o1|acQFM2hI#QA3
z?SY=F{aXmm%6Q+K86SK34gVSotrFdN{mnbhL@TAj9d&-TI(k_V&5lYN!%*1{ve!n8
zt<BwM5VQw_{w<G``P>=-)d1i5_Z+ZHYk)+-`K1BNBqk|bw#RCp7iiwrbbweSWk;D5
z5I4ntw<JYyXay^j)4IYt4z;-2qfo?;8(0M71mSF5!_^G360%9;^vWNi6(;{5-$p5e
z4Ux<2`>txDVDa>tItKq(sU_8h<Su^d$u%|QadJuwN!fr4=`#|<XHV&wrb60`h(R|@
z9W7B2!!L~#>uo_Kr6T)?Y41*VQ988pl#25@(F;*Ijf#bLIR43kJ%vP-s+aU->M$1d
zyN!CEY`OJhRVtKc%BIpOI&nle+IKIV>*Vn5y=maJh8z!y<<ywIGrN0)hG;INrj~nM
zXbz&uoq?^%pyqd--5E5A`(u)Hr7y{ml^t)Z6jLFzwW0aWV(ZY&<Ck<5mp)|vwta^V
zqF))kP4X~pdi$6(b{<r&1M&k;tUP@ilBKe=oBC-889sd`1$~oFahZ6Z2e}^#vb<9z
z@bZ&sj8E{Jm4|tU6Hv70Ep5zOM$eP1KaVuVS2611OdX)RnmWd1?i#)2ZM#_7<aaVl
zZ8ln_BBqo+9jsC170oh;7Mwflj2<G~pL?OTEV$6PR+s7hZjqV!vbs`mR~@`E;wu^7
zT2MRkUp74sWqHL@qmTU+dI<Xdw}qa**~2jb`yX8{N12rU4;uf$^@S7vrpWm(lgAk*
zu}-q#ulS~d*-Z!9zFh^9^|6)4K|qJiuC@*WLagoj%#|ukgPja17hfpUM%K^!?^G70
zMS+N`&{;@qb?NFjJ8IDsiZU5%u9ib5j4n|Oo8{+Fby`M;Swz+0fd}@$@d^JtLbMQ7
zksKVa^gA))fthg$;&S9q@!ivYf{`Zr7F4?Fy5;Ih)RN>PxNN~9ofMr>qTifgM87%Y
zlD%D~%GF@^CHBHv?;%UmC1iTd^CjKr>-g684pvrqMve)d{#JsyWQII9g{-0PL_Km(
z_V7z#tO=wb963B0f<5OVUJ{UFxqh`-eEct{YHG=5#W8AXh0yhbuy{nL>cDWN!;!&q
zsGZYMyN?3#Js3LL{B(u9t%LvrOviMJYF;?tGEjt&BW_e<nLEG`d_w9nXitDxX#%^N
z@B^6GQ2Dusox_*8bu(_1S$gl%Q;ka#a2SBCWcV<9`Vh?wMk^0Z?qBiO5(p&Drd}Wv
z35^Gh9Q=`EY_9Aco{&msXoA%N6@zYnFVG_OS_7f*b7egbA?B5z@NNauvY@1ppPxsR
zQs`J&zR1(RtZM{mHV$ya3P-+Nscr`d`_Eqg^THVP7DywpzMbQmM9uuxvDc$3GS~xD
zjx6vZaez5kUE4?l=}%z8`PJYl%xDhD`}b0`x|qa>2oK1pU}ku%-2`3Pom&`%qIxX=
z_?;JXt{IC}c%cTs<3GZtmeOQ#4|1>s)I5&%>x|T|#|Kmq5wCak8l|zQap-s$W|yd4
zj#aRMU025e(7jmhY!&*W^LURrf8Z`7+R9<eiJL?E3o9>XJpU@{AG`UTm+P7yyFGqP
z^O0RKamyCj_AJCFwl|$FJfT1=$L>9JnfSU<FBQ*@kMJF%m=T=%@$qW%MuuD!v9Wsu
zkz|TNLZm?VUuxpde?TO92B>2gy%v%NMh8JG)d!Dq@_S~LKeETLiiy1(aA_?+`btMn
zcCd^=4D)4~FGWe&oBxV5qQa_#XaD)Vg?YkY7U{~Ya*%x(bfM|#HX^vNr(IVk{g~^E
z;ag&5SE#wA+=u=z0|_YVC9^347Z9-pKH&yF=rwpXveO;at(-#Qw&1XFoJZ#a%UHh9
z{skGbN7A*<1x^E;s+ptlBeV&Q5Ry+f2I1M}Kxi|r)t<XVZ&oHn`B7w!qmu@%NogFd
zW8$<7!I38nq0rOL>HM$RnmLJM{}`<lrKfg_STR~%9Zl1!<*q35P8zCUBhE!nfO?Xm
zInSSfZQcu-3-5BJWOWKshkhdYd<CFdPc`p%@+?YetV}+~;6LI)5l&HV&L7>^D*hZ}
zi|?CK2Iw~?7pV0E#w@n0hPBZNies-lOKU;|ZUgaIilmtX7lUr;Tv7ME?2rqXAV&C}
z@UE5eyvEgBJXaUnU@8hFWCX<@WbA`#iMm^uR4lOgy)ce#eTlQe*>m`{wD^n~%lYq6
zgH^(**gGji$gln=e81Oe=Juo!3iqqN(}W1~R!EC$xa~iMs<L8HV;fSMA$TGvew1J{
zLlB^d&DoFr`FA6lG{m{@Z(OiEx4zLFmBpN~BRKt2r=R_$zVTHHTCP)LF53hbr>Wbe
z=Lwh$qr?8s41lJ{_8I~}5fTrXEk7rGUZ=z{ckgPLssehJYpqMLHYXa#KDx(B<L_Q@
ziZeYQFqCr-dWU4Rv>R)s%ArQ7yr4wZLKrRl#Sm`j=J!MBaTGoe2Q2jc=er1=AF*)O
z@%gX+jkG6nBO_eYd0JCg-B_^8NVue0^;pNk{zF6^C0og@XYehj{qhe2*G#H*iy{f6
zQJVD{@yw;o^{^?)tfcN=PlZwWkt%D&p+`}~y{Qi{pxcLSkK}%%(J5UVnGe}h@dcq^
z9daI3k?flkA;F#$)2Oq9*|Dmc$u;z+o>|wEAqAyOhNE*vpkZFtywSU@`CjQ|h4O<f
zi+d2zQu@hmsoVmcKvO)&O)mj8nzq*?Z-%&A9O(QM(~6JI1=5p?e>Y5aAKqJ*b0YZ#
zZ-`}j@Ps-2_?tw5gs0moj?)XWbb!23OqXnlyQ)Q{v=u4mn8S7UGx(i`>S^Jgi2=Jj
z-k-$gaUc_Q4&u3^GvDHb9xtJlfL;K>RuH{G$3cb@G6o@7fcUnfxNZcE{v?Dd7}Do)
zeFJ8Avk?nw4f{T8BvkX&mBH_G4Q-D{gw?yjL-xZKxUSGaY@W!>49eRdq8Pn2q}hkw
z8Lijv9`<;pU5mI3COan46$hUB_7+|Sat3_O>_%s*TzT@&8NgEF&MO*q_fDE5v=dDO
z2VN2SDD%QW<16_!{q+YLX#?^aB%*Unf94|RXP(d>Dh#sB)fy%;&v<z@(W!nG0)8aA
z##QH0^%|Fj{R>$}oj1kr_4-)Q;b>n1hkWILH1B84^8DlNM#?R^tJ8gqNOXl9u~xcC
ze*7+1mbc%(Dq4Hd1TsMuYzWHR0g*%yCqM1ljjZ_m;cStqIfO*K>9~UgCorEyb@=ps
z6!GT#=J~_S`F9%tejd)w0>c+6Cpg?namdug*dUcj;NQ{23adF2=wTlkr#02_dZ@t0
zZ|rTmohb(8dPVgzMJP51%9Uxaots91tKwgzWwqi=KpxBM8dBHLtk`B0spY;lLF}?r
zSa<#Ck*(Q1PO)7w)SZceOZGA$U8bYv#$D)^h)Gv>r)OyBU(UT$KI>|{ixX9QXzl2M
zVt0q?_GrJ0K_#rIbE}0}qH||V$UU*(u<9Z0d&?k5(19``!p-8^C53UPaEtA}RiXT{
zPW>(C++SX?_Xdp8hT6-9E2S7kDtprb#*TAa2|HNuT|G0X&D<L{PO$X3RqHh%uUe9+
z=0#xlZ1os0%DZgSZ&=$KIBU{nVPt{eMO3-(OoPu@W};ZDjap<hIL%0-h6IKa#e_<!
zh%lWM&AX1`n9N`BI!G0x%N4P0;{?YBUmAo7ExV+pD(f%M8X}_UNXn)N_RD=PsZKhL
zi#8x)-HfNfuT#s50`2jA%>O7Oce}ee9A#|Re5$kQL6)|QDh1`@9h-M?Z4Yb;QT(sh
z2PAfQ94(Q@&<(aSlE&t_ujIx$EN3>#AC{^pq{#w)s@PPB=d7D%3G}9HPQB0SuFjE*
z+n<`M8F}4MGO`|koaN#XW5*(j-vbgE((p+lqhzQ?@<bUqO0rsxXBugJ@?)$zLu`Di
zo#T}M$V+?|7*QsQ&1Cg_c}}BsZmLwAhe0MU0%6U!)L-2U8nH!;2nd39=+tuuS^GGP
zR5||fqw~wJ(6PBp*_=H>$D=^Z{lWW5;W^QRQo^wj5f)a+aC?&1Vzw42rm`euwjlV<
z|JY+6|IL{T$6F{_h-F0KaS$D#dmtRPU5dw8)iSfS*!GNE)4<wT2BLvl#d1I}Eo-X^
zO{;RfXu#&b&yBLVS$eR-MHR_6pubg06yX^Hd6-zS7<!Zbq$=YuE+)wU44}9cG2p_O
zSvuffdCK!wNVdib*o;c$)ZYwZ6@THJ*R_bH|7ugk*`S0l#ma02w~BHaBzP#}$XWJ%
zYRQt#*)n!Bie#fZ4#bFF>ESf-1Sve+<i3yM{tqf~T}OW2^uGL_octk<z5t3F!1BcW
zbC!4w4K_8+>emz{6}l?-{lKR288qvsnHfQu`FIG(eEek9f$S}i(6V4o9*l!jYw=3%
zBJs+Xv)g2JEEvhNEA(}OsF*^S=$|US@kM$$*<+C&h#Y65cv2+_7}Prc%%2AfR_<$J
ze%F)qdEkhqk;ylHq{B$P>&%=TQyO{}ko9~`Te&2KTz9#NzrY@88<?SX$o{$OZA&=<
zBI``tTrX1P74>yEWc;h+^a=kP91;XrpKVPrbtKxCI~1v<+KLT%Rm=1Tu;VgI6^FSW
zx;Lq5z7mC=EVt!W)%M_#@bqp5nF32;I38syW3h$k-IV^X<V_*BD+U3kpU_v`A>@k4
z%2U5lBXSNukC@uXW-tlbg%?B(pZ=Rju{GQ+SRs$x0l@Ku^r6!tI-Wjqi?q4k4Enl%
z_;5Gb=&-_>sA&{y%-Cm#V?Jc3T7#c514)_OpH|WLP{F!CFk;3*u4|e@dk8c^JvGDk
zyw}t~T}6VFbXn4l={<I`q55Gk$<j}-)7r`c(uvY^(b<ZGlRe_OYs}N9m1Ifrb2Iiy
zKeQs2?}krZTB@VM73f(K)btNGM%0KBs(DJ%>?wDKJL%J#6O$wlwe_iE;D&v=!^?W-
zidnD{1q-I0fM{@6`}|Z4m`()WMM<ps`p&lBKcO$4w{aRnitb<;f7(1q6tyUh>s@7|
zoY%#Vij(WP3*KZUQ!-_Psl)N82T$FM)M%QYZ!i9CVED9$iD2PSvWX51M^BV4hjs?8
z<{Ia99_7#WPNEWxh+)Udb8n?-;q84QM*hv7A(>+Am?l>~M0zy=5!ZDt)Z{6<<gDO`
zi@SZx+02<?BS}z2IUz~^QRv(3Tc9<&Is;+|^c+iZ(zK!whx7gKwoyOq4(6s$R;i1x
z-&Dwo?p~bk!|A1^F|u&!G#>8?V^lOOcd@f0^91$WBD2Nycn;OSQo+>B9~GnQ6Wh)w
znTip0=5iMTiSV-WFITePsgq5hf-cDbN(X*_S7zVuUHjWhLUs8Aj>6BNp;-9y!5>FG
zvSaC#_Kmzen`7afPYoZGQg0Mw;9Y?VjCDhnq}wtIbO5z-OT{z=`m+t1?23u})pv%e
zKvT;!ieh92_sN3gE$0VPTnBjh8S*%1_15W*YBc0+hFS~56S;7l|7K|<r;fVAdDn3)
zw8(rb{5LSb8RTUg*@3!^La!ma*zUyeU;y%SbGlaK91Tt7yHN^?zqX-sZ%POW0MJOp
zD<ET3)iopSC*RU{n^aa&TOE;BHLyjL!`w@FbD`;{Xd^>VqMS*$#3sAfLcUG&NyjJN
z+-^I__Gl@LCfuCk4%JQ2;BQAkeq;k*t{JYZC$Vyy^VgIb35=J)aj%u??>m*8n5&Uc
ztu`W!_BC-I1%Kf>mio&h9TK0jRTBiN!9_0F4_^~Pl<s}jN!tknaimXt-k_`|1y2)n
z4lLmOx}CP}oKXx}_%iWiJuabY0p6kW4N@<#5-@(@Ga(17igegG!_knIa%&a7(I|Wa
z<*m&&2crNhitdY}1ynu=J8p%fi@Df-%)^o`GBQU1BWGAPe{(B#hQW1G<iB;AAP*sP
z1dm%1mykUS&iR{^ba9BGfi#+qne!9zBt;_?k2d}4tOpb&AvCl$TY0cCz7pCxDH|7S
z8r357r%(xzLDaM|+FcJTIRFFbfkp)JB>E)A4rw`W$pVb=;a#NK!<9u4_xwdESgml?
zSQ?|_M^L}A$%xnWzkS^pO+hD2sQSXhfl&FicxC|EH)`%r(hPD6J?=$uf2=_9j_5<{
zh@9_NtTCraz&?%MvK;(I&aA181Xehng56IraN5QZMfre2Q$*ewF_sZlcwktGoec*S
zPseOe>Al4q_!a`+;Og;@ks`K&-!d@%zk?Be8w_3mE*EUnJZ{#RmJ{1T4^={@pkn;8
zstq1OUtbZ*p^bfw$n>;b39o%+K$CcW=pvy=En7F?@H&M)Q<Rpz_I_Gqve}OK3dXF&
zs=et&QkpH4#Rc*6fr7S+mqGGlN431G$Agvp8pa@Z3glhmFvc)b(+alxPa<SLIlpA{
zDtG>N$RQQ^7CZkQ#FkNBjcLSroKce)0U|dgy=w<NleuFv(sA7K*a07g+U?{(_iJ!^
z!2me<)1oXlUlAU6Jz~EoL1*8oF{1U;vCOUB9!K4W142vfa-cf@c5=i9Y$lO?-Nsq>
zW*CvDL+1P49jN-_&F^uJ5Xhmwtw<H$7DzsOoLm^#MP9}<jzgXKS6p2~<a2?@3#M$L
zhf^q`-U)hNNqj%cDA!vPdS3Mm8Q9+l5-1H4FH0snpCb<%9eyu%pn7=uc+EgV+)etr
zeqwbapclUO@wNB)oI>mbiI-`|a{Zi^(IWJ>pruW%O|X5B=)JCYZc8`hgl=`gE2uJM
zQ_MP$B-10Dc6TRkSd7xc{{92F-CT-XQ?MH}UVr@t=2x3r9_Q`~@a#Cr?-Wc0!MCqa
zY`KkZx<?d~w#W01B}T<ed>|T`liOKwAF(ADLPKOHE1Ktd;NHj>rHcU+K2-@3igiG2
z%G=VU{0L}xl`}tNl1@u54<;yV9*NPBtA1(uBO*=8TVkenofERMMN!@2J?YBxa$e%g
zvMHI)^oSpm2yofL@Pa(t@4>@|oT^L28V<+0Ai*@@2@G@e-v4<W62wJP`PAoI_MA1}
zB1`W5++hHdL}eoV(EWT?g&#ONA+eK^Ol#CYrQmUb6INiteR*Nvt7wrNS5YL3TR0p~
zqf)6pdhA2~(XAj*<Y#p1))I9j=F>6>y#C4FbYag!%ZO(m>ayJw-5}_-#I0I8L#W^E
zgSkQ>BGSUOYa2W7BGWT+*)`_mbOj~TQT&3fE!wvX6AD^gA{&h2K<xRzA!Gx_YFH`h
zA8cjseF!8MU+aT^STnZ$SCA>wf{W#r>e54fCl@C>`sFtf_7o>@?|{InyGs2QK7KDS
z&|q(CNMleLo^FcL4uabIZl^Rpr(&Kg1pC+2Cw3iC$${Y*0{PL7QS}lgD_{$b1Bzq1
z;vF`hkwFs`wmt4Iwoij`@a&I|xIrMc#^M;O$P1*uAd9#E%A)pb*qO4~w-=A@O#I|6
z2Fi%to=9y*g8VP3c<$}ZSfk41A~bXR5XqQjGkS74;$g2}Z8b4P8g9@Cf5S?k@E5-G
zd=tdN#aN<PxRuOjYeU`DBwnQWQ7o1J-XNJOeuN=$dSIUu_wXvTAypN>rqMcACgO8X
z6Rr_oo}rv(MbmnLRnfkkQ7Z|C$WO8>fsd-vK0ivV?J2Yf12PcL0wZW0Wslbu9j)|4
zDgz-%-<-Vaj(JSE)%mQZoAw>=cPsf`;n=Z%AXAE|{I>n#Q#=KCV@R=95!Z%wPYD2V
zjlaWNxxF(xDf;y%pnC@O^;asyxL|e4Ei^pQhaW0hQE$&#{-dzZ;YLe8#JyTpr*1Ng
ztKVe3houvL3W9D^J?>1+Pc)zWZH-n_e3x2G#7)9+ckiAtCJ_Jzz-ZarLcISf*R@<7
zMFDW{a`F*#`3$Nhr8mp&SKz%xr10F|z!z@M%;&q_60NkhV@Z5_5wbYr{TY_Y*dEfc
zR6#4x-zr(QN4~Xkv8@&LJsI3$<qxw$-fJ$U$BaHCN=3N8*?u-q)!Yu2{k<h!vU2CN
zo<{Ox-=n<T@E-`Ei$hTbBXW`>2+`b*VL<7gXr&*ad4;~vcD=9*-L6-F|AhT{F0j|Q
zMsoC4zu4)dceK{M>&G^I8fxRpV|f@kF{QrO^hvEZ#;7VfHmy}?O4ifwg3}lSD74wY
zEZxgEaw=+=Z2K6UX<FVqT3W#LT8&6pa~ttUi|cW)P4yRn>W7dt@3w{~uzhOu{+OYv
zYSi!D7??HU0uyMC5rDaDf{x*@+rGHk(%(6d@(RohA|_p`m220ntIa5t5-+N)`;cV4
z^K?+r6yEaz{e#m^MOENjmE{N{G56?eloSGvCdp;!WLO~T=34F7yy*17F-6v@i}zW=
z4$tTsy&mlIJWh6jBPpFnO$4IIJ~#v@DfbpVLT0b)h+{bT6h>N`5+;QEPK9^jM9tEN
zg|>oT{=)$z|HA=p@y9QMC@54)hJDJt?H}o8-9KceY37;n;*|P{k~U_K{jrW)ZMdS+
z)8+3nN@%)ATZynLAFHvB`y>2H`P;+X5>oZ6dRj%AK*fHpnewxT9ki#N6a_{5*RNM@
z#y^KH-{Zn4ElQz!3P~dR;k`i95klyE@ltA17!hgj<rA0it@;&uZm=Sq$l#=zyr4dr
zzj&;}3!gbpw-U1Mk#ES5#`Z|_r%|BxeJpwb3CwjJ&QU=X%e^FdFt3INST336ak=EW
zYwFC7%L$ZnOW_z`Km_C9vi1Y$8jEt{b6RIi#?SkcSm)kib6HF+9kA}X&6R<%tp39O
z=5Ng!#kkm0wR8dn(7{Nq`F|sE$IlV{l9>^mg~seYc<W1_zb51&00=bI?%-a2V7~d5
zOi`T?e(w#y%f!qYmu7Q_5ir4bs7Lz5RoK|Srjx?I@PK8aKqkk6*s#61wR6g<zq2;`
zms7vTPYopL0h>*uYvj&IvJ*`qIFFHi+gxAvYN6>{t)^&=idmOW(Oe67+zCR1@j8@h
zn5pB;5UD&R+vQ2w<~dXRdt-LO07DGdxzqqgM_-DM*jPGy{!)#Rr5gTHVud0^=5f)?
z!2;SN;&{9ng+Yw$4Ca_chyfya1QpU#{A`VBYJ~tA#v5&`8SMQQ_C-%KXZ9Ty0*m)O
z$pd#yQQ8%n0si@djLdXhqh(p$Z48sZ;DzM^F<}5pmvH;@g+i-z_TE|6!{u1+VJvg-
z?cMB(iB-eErNyF|5;=#D6(RrW5oV^#4s)3WdG!Up=P6%Oy>02}mV-~PQxt?=%cbi@
z*EEl#Q{rYp0gu~8hll^G448idYcZy*uGHP^-%^{t&(q)DAh@0En5A<za{WDGQEH)0
zVmUzqFJbHu*1Uc;#Wt1`^{b(oTYt#ny!gwrzd9vq+>i8=&sAX$OGnfbVh4KH5v5!j
z*P7bU?=a?vJ0VM`VJQTrXDH1pt>WPHAO(SAW5+7=sy%;oCr#^n3>(o|;1D(>*Yf_|
zsB@xgRf|7f5QB+D`UuH}!+LIlF%VY&&G+P|`A=LW(Z_-Wt9Itkg7o;H+Rp2`3d4)G
zChQ`A-97u7#h-Ysbp;y+SW`&+wSfYba^7pO<PcJ|&_=E`={n)$=DPo*=`Ew;?3$+0
z5D2b=ySux)4jSCu-Q5F(5Zv7zf?M$5?he7--6h|3Kj%Gb@n_azV5Il%?&_{8wc*DQ
z9$DBo)Z`+m`L_IZ4da`uul-;^w`!D3Y)>?;tSABmEoSx=3=<{{LWe0UiUm=jCiZ8-
zYKy?~V<Ji~(EmgYjw!LGnGIc}unxNU8XELvIDQyb%!+0o5*o}VQI0I@K6Ag@fiJ2|
z2^WmLgY+43tdIBwNV+DJ;g?}h1~RUdas&hAFkch$K*`YAh>$OU8eO%tHCcFO6I=-F
zCc@QAxd=69Prn;nF-AzWbm@%g^zBhI^xhb*{90bq!T>%LEZheR1)@p)7ixR-R2a>}
zCxbtEhv&^c)ZkSM`!wsLAZ{7e>|Giu-11MWwkUH>DU(5>O0)JzY1;D<y};${{$?yg
zFksb2LGxQiA5hlu#N@gJ@L4G3C<4j~Ta|#lio=c`D?^X(kEtIOB(h|F+jG$`jeSfp
z7Wokzdm<23wd^+Sqij*%5lv!cl;)UUXHeM{6B)zn!l{6GPl%)PJc*CVg?a*u%nX-~
zq(>+vNgRpw$$fUqhy13oOe$-_FtJ>vS6>tn_wpOlcU*tvSqc~!zi6bMPcZdB1WU-$
zu2w;$PS#u>Pvru$Be6eDIJ0(lD|(KX8nhR2{a~FHVZLz62ov8*IsZzzhK;`ZpY14o
zd{v~Uwv2wl6j!s4*kVPS<}G}-XU|mKYnWkiAcdtLfI1^(TRA|gR!Ia_h1TAjFT)ji
zwp1LEn2}}FzOlj={&r8`@1e25KqW=B^J4r)(JS}aj4VQJd^Ar{@aRIrjxM>Dt!&o@
zE1ccBHZnI<@3>02!4cXDi7ZyGlQYJmbR-(&?P)O`>(@3Dr%*Fta_~`E^&gWEh~HSc
z{|nwXo&x+AKi6|QV~}e-Pq4tBhP~EuNu#XhhuUM$aDX4)4=@vLf#oU=zde63O2&ku
zNEJrJT>=$FROuyDw(xn2_(BRbQo97NY@W97WMtqIsEws*U@>kL%BVn%4tnsK>NEP-
z2U!MJL>y)BmU@C&HpK>@d;H@ooyeR8%Q$;bG%6LiLl&n?5hI5>@s;0dwcWA!ya@);
zhsah=mmw?7#H3_+&?R*unTpx(Ug02Sk;jeAzBFPt&A?Y=>kH5Z07_I#JkR~47FcuV
zv4v^p_gLqE!j0{4>|2=S4`|jJ|5q{+V0CQFk-_z89x?Z=PTK2U7u$Ntcbq647`tTy
zVqN<q0t@B64wW~e62{}e;@3UCd$WeF-*c+4TzQK093}qJ=`X!?Gn+1W%wXf=j{6<V
z)qA2a*_4TW==*yv;T!DS;?4V~RmU!w1PWMEpxXifKY)3Y<@Yw-UU9I}GtUVq3KD-e
zV@&Krr<BD#1PpM#%GNcjS-wj_2I6dN@`>clLQR0%Wd*Hf5Ld_BRgc7^(GxB?H;b^5
z(mhLOZTcww5UJDn)Cs?6OOV@{!iPj%#IdWGzIsfX;`lx}|Jgnxh_NuW#WFZ6RO{{F
z52NCInF;#u`GgO{_}UECCbn3LBUGi9EXB@K_PDp#`~B(GF<EJQXS)b*8;<_5H6I_R
zEsUl(c$UPOrClrgZ<+LsnIXyxO_MLOi3pB0Y~5PsHqD`|K37I*cuIjMIN$TPe`AS>
zRL&fF2E2a(#EepNx_hw$-u`x7R?z(LKKGRq__!krJWdskHa>!-{b3qbBKWjY@O1(x
zg0DJ1CGDJ*#uOe~FFZ$3$8PNry|tUnIo|rcfBqNQXSikNkmBu0cJE4#lyM|o9<&te
z_eQbD%;*<WkS+>8BHVSw4@|#L`z&;taA5Q<s#F^g-p+Ro#XbQ@`9G(RO$ZiiY~H=a
z;bY`~7ROV(N#*DLD$~d?9jhI^iN&S@8a&@fIZDnzi5~G$4h=$f^*am1UVxVW|93FR
z{&z4?f>VUe{FnE2N=1d?r;Gbz$$Kfb=Mp267{b3<-+I^rRZh6W7Fu~I57?`KPi~|3
zIFty#k4U$Vs4YnX+)D!QRU|NBS0Yk?G4{^o$hG9%S*Q356kvJGXrq`?k!{SXX@L{g
zF}J#>(;^D6FY2BXF%&Yh(hbHvKgZV87*a;<>eu8m)^xWMiV|F}PvGB)<r-svDsVKp
zy)8^~vW$&w`8HRz3edftoF$4tZlvA?d}AcCoxwno`R+X2-Tpvj3__!TQ&P7qUuH^F
zj7e?L{Jmj|RvAhIhD}Jbw7FF~NBq7_tTl5N-m&mkgf@(cQc2@*`N0QxO$FF5p<wy6
zeu7DLo&;vqdcEcjqQGXK^nzofQ@-p!Lkmcw8sB%r=y-2E(EXBWc6dZ>KGQm)Ou&Zx
z81#t*L|9#p7byLhjmT6jKKeNvwzoWP!h=zHi{|6lVpY(<vlQUwI5Dy?NisITrpiB|
z2u$D@EkN@c6qDo~N`pGI1QCI%U33TTrW3=kcFBul65B^*3oSzFw^|iYsU+Qp0(WFL
zD@0P!9bZ^y2R!~_vPbtK4Of&`&KNFD)`xc!H}$C-1@!YQuqts%Vz^<Kb?j#=9*;PD
z5MhM2b4IxWaq9idBV`$<&bHwY=ZvNwS9I(F=0FA$0Itce0epJk4RLc|DNT?RQ$(OA
zD7W7cev$mrRt{kApiq(s%q}2@`rYg^q?ned^X!y#ZswhCqlh2GDioaJiNQkq=NeD-
zc_<VCsu|hoedtyyATLsI0>RtIV?;HWLHy9CQvp@-ua%ZS9gld4il5T15QEz1(=nvx
zMV-ga7*r!!NZOtSyElqYP?!xe%y{(&_Gnbs)t5Fe(ia+PVA47cbkz)=wrCNOFp^Ts
zPr)@`3V%vR|J0^XhC}KGDnP{inMmlulj0yJwWhS0EH(Lg`y|;;LSukZ!kd;os!sab
z(kR9HXfKk<6#+9NnuvZ0pMj`SdGo^MxR)<Hb}=oT`7#Dy60VXPuQ9_PZ%q&oKf{OC
zYp<7VO^}@9oM*(0&R|M6{H2mfXOw20wlL}C3$VB0`ueGVh=YpDw4Rmm&d%3Lzv4*g
zux2@wO3+F+ADL*Oe6+J(Dqa<*ms*GW8`$aX6dz!goP*{R)3qN<U|c7i%Cx+Jk(3@P
zEO1qULr5ZU`h~KcM0$q5ax_>KmAACbm+N>VmN%SxrZq<LWDG>9lB%$3`ksDj{6=)^
zko;}iXjqWc+GdFUC7Ao1T(l}~V4m~iBULD*_*Bi6Y2j~sU>fKDs<r@@|1mxNVDAco
ziX9R!?F>qfQHF7`)~8KTCC4p)!b0%&?bwv|oJMnI^u&?G!0x0K90Mx<%QvqbbAR{5
zd?P!IK^39r#>8@StVQ3cI2`VDIvP92?+p;bb_S~O2}U$|5-M3TX<2@Jo@{A;S{&pA
zjwDgdxQR^kFXQ;UqcEXOoo=bLqVu9^hn-lzeo*n%&JWE~dXBg4>N2fHy94$wMVUkM
z90nT(#{ScU>TeWj8H09I-M+UQh~Mpe{lD>);J+Xi1bwqct7PM(9!hq|PHonJO-$P^
z+i~d~0frO(L`uUf5!TP*2DZP*(0;d#wBBH3_7O2Vtmg@WIK!2PS>Q+TsCfGdE|8u^
zqY(%ulWDY>G7VA_j$LRpO_+2^hR(m4Bv3pRVrk(tb(RE5(q6#`0V)()U5!0}+*Fyw
z_JJKB61iouS@Q=WIL<q?J`Rw(196I!LzLl={%Sl=M=kbCy7_7&k}xk_V~JW26ep>6
zhb;CRHeEVq{3-dTky><Gmxc)0R~(Vh5@M-QHWdw(d=;dxU=|%A$c~oAokfpS1K;7o
zTs|qT%QI+5Kn}AXkdjUZEgaADGa!EF;A#i<wt;>=pBPP=`^x}Ll$P#liPmIEK5ZKX
z@~-md#@<HNe`0f7Un79sR)wWB?O$wXuWma230i1hJRQ2#;Q{J)4&C%6BCxY9VJv|o
z0V~4Jfv8GN6p>iQ5kwVZGTJ2YKfOGPyI%e6Sr&J@r6MlXUi?sw7QV8_66yjuB)KI(
zJr!WSXJ8Oy|2n(aM0q{Xq#an)i5#?egjfWniAm2v#aLW6V_}aI7=WhXe67Ut;Lsyv
z{=xFz;Hk@yvW5kdy6a6)X}|^l96n}(zcN9QZg6%F{}ykK>W#Ro;G#nO%=G;UEF+AU
z2NzMeVs;PMooq){xOuAZ3`Kb}pJ`d|-Egtrn(ItJ*wQOt#i#*@KZ9Y-ZNyZTkxdC~
ztu0Jl+h3z+pO8vy?pnJL3h?r(6_DPGT~c&WlxV*s&PmE9GqiP4&)lcnii>^2h5`1}
zltJ<AdQtICEveZLM&%>xFm(KYcu0BSG0F$3%_!4NdIbC1^8x-Z<Wsv>{g^`wSapes
zu4DdV8>}yVl8JaK!^&j#KI<6eP|V23l0>-cWR;t5T`2%W6)7<d2Sf8`7O^CoEkXro
z-$GRG3P>9ql7DUI5nuheeob~+EY5Q0Wz%kb>;)i*|F*RI{zEPg#3is3z|=#A{O@oX
zA3@Qgv5t;R*FLV%Q%c0fW2gCWBY^=Ayr5#hb>_ospKNozW3nL;!Afk)3cB0xMq6*)
zsC;cNdXTTX{f;Z}cAOdreDksG_RJ+Tv8yraoDEC@Munk8#DI@0avIQvwSE5i^`q_y
zm-cZB#M9Xwnvk~cmY8p5Wj3@SzJZDTbk7WukMW;llW5``!NJAap_kgR?yfs{!z}(u
z%hFh<uBM2}%(n^l+};Hwh6xhWG&|%rw>6=Z682Quo7`;Qm}X(KvD4eq%G7dSNFrLL
zTlCw~r|tAz8VuVIrbFFKJ49a~&ofUFDJ7m`_}TA+N=neE;BwRX#<%s-Pdll&U+ljt
z_cIguM*$znU~OOJJ!ioAj@;Y3v`{3m^e+^?x9M?Z;5Fy%m`#WE$Kf@5T+!BdE$*y!
zKf*iu9g+b%Z$MFslLF{9BDRSGH5(vEiP%O2PP&@Mo^n1|DFpbd>z?cnPVrg?rBYpA
zxgAXqcRBLNL!*tcWE@vGin4keg(e(|DB)Sq#Kf0S;^Bk%qTa9yuLP9cFn7$0e&yRn
z!fJm4%_hkaN^LWz{3`Ge*Oh|X@fFkGKvD{Lz$mG5{n)4Eixz6OE&kAT((U!c37ucc
z>{n*HfnO8Ws7~6p40vw%wP|%Vx-_+GVP8b$eb$N&2-g+pUmCAMe=kpDHlId{ruj)c
ze5uII0Z@Ra0$(XJ*7Vz|gkl9fKU14F1Qbr*BiQP7|5n`k0yGZ?XLI4{yaJ+?8~d>z
zhlc<r?G+NV8#}&xK)}@5^_KInna#oh9^~@A*dqm2UYDA6v|gkSXGLfS7Fsk~ovn9+
z7hT<8);MVJp7jm6#gF7y)JH9hx&8L5CX3gXLi#r`xexw=seZ9tl!+<F!^3}azHrKL
zh?IdONZPS-K#t(5kZ4QiYG-ez;@Fc}o_|mikHNiVDO13F+Ot%;>b%r5c5fY-NmOmj
zfPB%<O>YIwu^;!Pc=-NVlnUSc=gI7PGtLnB8u*T`m7-X4dQENU{oXv<PZ)}tRuWUP
zsZTN&Dy7k&eNxqMz`1gjA<vH)b9nH;h#hV{tiC1r3aWx+-b=3O?3v$ziVe6JhdhVW
zWiQv34Dh%}lmN?f<J~OWYd#%nc8}JbA%5vwUr!0Cpz<8X2O8@eDO)(H?vc-;MJ6dP
znewZWldX|jvw!0749f(2GqX?qOivX^6kI-f_X_1#ieWPT{RfEvI!*7x(udW?K!Zt|
zQerHdUB90f>%hhz9F85v@dkn9D6)RqFzZ+t<dCMZGEj)%q;K=PO?0Gw1n)m@Em{BM
zwoPetknR%jxY>auEYFPh=%yr(GK|DhXE`I7w#lEn^_?Y;7#es|Ph<HqZbc#QdB?^b
z4Dh#G^9NkI6~>5XufiqhNR{Cuj7W9KMC)c96Itc;*7s@+HZU#O+9F6PDaU$Ht($sT
zkdMP4;$_QxAy<RLnJC?Bl&G(8`$cswOO~tbI+iy|OxhXtWRn=fqa3D@1u`~*zHeGK
zZIa4@fP2W`2)!~iGa2n?ma$45dlDnIcW&=Y?I9o-vV-DRRGn`P3QX$9e?c3tiSgs@
zTTvn~y*^|3Uf%6UiYNw)+TyzjSJy)3;%FYxGhwl|o}2J95Sp8i6I1qBMw=89WuT06
z6<3|}0+T}e^hY+LZk^>{&v0wpc?-EDsvB#OQIFK#GRCQi6##m4IO0jqOfD+1XW`YP
z0%IsAkrbP~d_Bq4syJ|B!$NN;UjO=ejCI;AdQ~1SiA>Xt74QU+IPv7+G$e&33q{?7
zXHxy&E?fc)0GmIaOX@4pqtGXocNaKVX~l?IlldF=&9gFw0CHL?iE2~`dq0^}5|gN0
za5V4^wk_-vXa+}CaZ-Bz&fvY2Rj}$h)n##z^67u9qxZA=1FZFkeCxEf?*vWc7yl52
zy%H!$;Z1e!iPjglf)|rvIm+|bK~O~q_KyT*2+?qr5@kEe2saAwQplQ~wMBLKe`~Sb
z$1Y=9=emA50QP&$d{`($9aB8j1AFojBtMSa1vOIf`<>;@$-?dN+j|t0aduxxbFlNQ
zzl};@DI`)vm@GfexFPlNJZ06B7i>m1W*g4L3a%QX=(7J%>!8QGcvE!46U@M`Qchc(
zxEB{TyM4iO`1q(2^%!)376d}xN(B<bAWH+@(#?0%^W~hC@zt3lG3z33!TuY?!NQ{Y
zr#GJdBtGxHVv_?8e$fgKh|bCxd~Xg7_1;kRKa1n*txdf`rv{0|Jy>f2;r88qDuIc=
z9N5p3q<4xYUus91H;v7;EK#4Kz{ABGcp<}<gN%g{cYNnBMv3>vi3`Sr!pQMrE?o`s
z3!|!pO|F{?9R4jdnDPB`Wkq0+BWV+FC<9rO_UviM4+;ZON<p>R&te|c_#!aIWae-Z
zT>6hhuJVEzkO^MogsM%VVR>R0BUb)|p`tcx317C!B!teFjocVrV^6E^TxGwGSm0@-
z&P#8*^i(e(;1t>tVdqapRR<G|_ezzcCP{;83e-@N8-sb)u@F%;@G7WnVbfvc)#{}P
zx)L2)oTevAMbZjS8-49nKaEmHEX`G;aemq_zAWE~CyXYr&rCKDAMGteDCR>(!Uv!y
zf7buVhR>)YxLnOS@UXajP#B#o3N(6`p4umzt&8^4om+*`I+hh4-z(0^P|0hAu@z+G
z%T-<L$!F|jTr#!pj2gvb4ffc#%|?!>KGW#p{?uUh7rdH&NubZ><Ng555G~`(v~$)Y
z-Y+_p+B{Gg*~nBZQx^5B_J0tCq2Zv0=zl_Bz^V-kCjPWb4L@zAw+b3W84H^++HwhI
zH4!~RTTVYd27YoD7Z!@mZ7_AbLu~_33<A7};`!Lg*xA@CMwN6uB)y(|FNORsTMq*j
zT@&Y;)Q#la)5$IQwN$R;=BRmfb$1PO{UHrklJs-CAD2tv65T!tZ&^6`T1Ta*J*6ll
zQMe^Gay+*q9D4iu2WOpwC|K`lj2Kk^Xj)rV5V@z@E@@qGc~`Iv8VcQEKpJ4#BUYYM
zHB>1~E-gK;M_%se9<zN}Gw+`=1xH|fme$75&xK%aC`3-$T|rb(qd~$33Su*V=Mb77
zKfd9NH9N5*qlbUzeL3S8$`KqMGYrhI>)8y?ZeV0{Iz6=g=X-BSD!}k+(KNj9-s+vc
z_OFW{n5E{tjL)2JO8XcXeQLFRqp1;WE)Eu8_CJqk)LRKsGkN6?C(2#^*x1rKZnIAg
zzmX@x-4LRn1tUxaY(G6*nzDyPO&}Ja_pR<w)dW7yyPpp43DSvwi4hW%tUdzPc%A)U
z^}2^G13rKmgZs`j%O~mFtdnAC!}qnrfa`Q!qTJWcl9O|$$V?=_=P3%EpqR)z{T8b^
zp)K{G;urJMgITsNDbnZQQavJig4VUqp8CYKos*{y<+dLi(!?mB=Wj|(mw;&FSY&3$
z^T`*2rGs+I((CGL@92WiTKw%cu4>C&9xUfy)-8~eIXY%mMKTsI7MZcxVui;iaW>0F
zf@Q4fxV>#*;TLbMlpFtMj@=T@Ge&>#M5POM%2@yQnq%|)2BElc_{5$1k4*hjq?)?G
zg{GJF7EV{2zt>_k%_`s)9+UnTHdVLsEfOK{J1ev<O%5Hg85MtT@VI)t`7+}UeR!=U
z3^^KN`#>YoU>>WU71Omeg0OjOJD4Bth=O!%T|ua9>V_UY*JPPdxsko2KHz5yHxt{E
zHZ>RPD$e3JX!LZ50RNjgGe#6jj7>eS?3D*RxgO|<MHx~pgcAYfjDyHNrLWDdzfT~N
zbTfm>UXgaTICr+zmead`?h8cj{!7kDmd!4^MM`)g0N+{2(q$lT1p&j%Pon`u=EMUd
zZ=4r4VJ2->or?4Cs%~yE6ao0zb|w8}Xx8_VLX;?yz%NPbuxmY_%bYrgGC=T`!_VNL
zqlMQL?z;B(piGa*+Q5mov}BWw@<lb4IK6F(R5*undbeO2cJr5n#b8IYb;rg`CiGwC
zx#J&^Nqi~)uKX~!yfIa9Mvdwc#N(H&c>eF_48Dwe(AghH@_nONiO#VHH^M5-AN-pn
z5zGk`sjMSpgKjD&%3gx}S!^muWL1zfuee1Sy)MGteWpv&#QuJ>Gt?NbN4sbRSRThz
z$96va$l9mPBWuXbYEc$9QI-fYq)!v#N{)%f)%7xs7Ikw+jB_Vp$^F0FGL}_ToZsyo
zStuzZ7XNOXpD)rZGa-%b%iAY=5SYmHnVlHNeXL*OOzfo(WAUcdTn$|JiB$Nw6%XX)
zN|L0FC)2bFCAN|s+McR~aMjdIY|A89usPCbu8Xn5d)2f_*m3NxkQt`)^y-ujz+{e5
zEI}#nF{IYX2OFmGMKDtS>uzwox`k16YUJt9%QY3CVM%Aak(-NUjaPu7ZI*{y?(l#A
zV_mu@U$W(T)`|-~DA&ocO@nkYUB0707m@2el3KqftKAXRfHKn0__sp8g$&cPA*XYF
z$(Pqd3^tCWni9sdt=hKBW%scKIs#x!L-OXl_C}n3R5L{Eu6m`reeyjw@}^$f)On1i
z*bDhqjL~I^P7Q}URKUh3!n%8ofcL9;V-<OKriFH(16xn-X8n}4E1u?Wr2E75l~Gh{
z4wOY;eD@$uz!P?<md>(S;p)yE%q_<W;m4Nnds2QpS#mG|b#9iK-HwfR6)KCXRT_`1
z*E=<~*EPGe*N1AjQ)gwrczG(Uuz-%4vqMPW^}iQa2Hkx0zTk9Hfqx(0zF{OpxzK89
z-*}`rBtWCD|ELS;E7!E2axg&vXR$b&CFMi5-yWm?8R?}6JiMAJUWDqbr8nd?OOhMB
ziG!tL5AieKqy0>{t)E!`u^(Rw>)!uEb5IpoMaH0vV7smtLWtiDB){51yQ&TUaGw|=
z2Ae}mY%#7x-F~xpU%?r%_0=J%+i$DE%{}R1Nd8-;ot`!O1<Dp3zAlXrr&AVs7<d)@
z+dukcbU+gsQjut(lH$3w?(q2T$4J#lP*k#yc*@zCdom3QMq329;>awA$19BI4Fc?j
zXL=&Y#tH=@fhH_)r&sS9A>h`O(F<dBj!p85{QYWq<b`aChtru}@z$Iii)U(sGbdI1
zea05GOM#&~GV`Cbk#Gtqre!^5Fbyf;O0eLfW%`=7vD)NLr{XJzs3Sl4rSl1cuQe)$
zIsYtC>*Db1gR6{s>jYMFGkSb~sZ1|-L|fo@#RHbM4OKm=&U?oK1(-tHqbIgmKx666
z-A!Oqm2Jb1c>SS~0)b+t+$}eOUU0$clrM~o!l(@g-9#dYb-|#$jm8&!?EP;{%l{5w
z{r`Ue6GKCFRFL@Wpa@g=k$%QVPkPY!;?g;MX91^;CSO%0<vAr4;7c>O<3WLeBeIOh
zAIfK3xBe#~L6kYu2jOA3v)_uWsvMf|EhoHy5_8pRwKFau58EptI?F(;L1EFwN*b-H
zR*uuE0j<$mf;K;`d8YKt0_VY1et$MN8e>ZaL9S%OWYtQ*+?huBj}&u9F<#?{HZmpk
zxz}bz1GcRK;~A=LG$ST?z$z_6v!IQ!=c{kC%AS2H;9F)T1tF}}F>KO4nU`98<dw9J
zXwKay(foT|N>0`;{e@x!fndqPsbhT0Ym?ks*i_E=_o=zZZv*CCyHu4+%!}fQM@Y&q
zF~usBr5H~!O^)B7bfS?fBRLEBLpSechB`&?73S$(Q^kxBPL(wtH$kVi3Rs8S%YUsB
z`!h^<`$k=|S>$C*CVI$c9z1;)v!fJ}jv67W^>io`-Ej$-P4#zukDigg*yG?cH*_s-
z-Gr&@O%2`>QkB90{)*ac+4IW=gH)PVSL{s9uBo0Dj^CzLxp4PECuzff&xA8CDc4`U
ziOc)B>MGHr&$WJc$zhZ<Bi}Gh6;`>U_((!`^3&r-vNfC+d!66FxRP`Gd;Z<zE$2N*
z#l3aBK(TA8I@_b+Z*8x(WMdzu@C+;^7>PaqZI1%7ep;pC>yiL<DiFMtX=c!)l6g)D
zHc5_37WFS@53@q{A3X_xpRkl4+mDCD$RwDMyw~WGxoQ<+@@LxM)n-OM$5e;Rv~<?Y
zC2TcH@JDQrBX@-?RvM9oj+072OXR3YTKk+|8o4z{cPxmQ#oOSKvj_Q(eT1-rbvy{N
zsbV%Lkh_#tX~N>XQR&`cj5r1x!8<53BMhV7aM=u>dXOij9CPLIvl&3rj%eYV(nGG+
zuVEp7AheI{4eR%VvoCa`SWjgdf?1I+B%U5-fJ~wnDU`n~O&p6lL1WgrwiD=e=-c=o
z7wefhR%l4AdR(G;*sno~@$5!v^R>r=?kF*tb+kIRlA#UUuhTN{?`^vh2N7R1JQuLh
zNgayaqC?Qsmfr^^y4!yK(SbLMExgKj2NKqyg#)4*{0d#p`{Em$S{6-nMTrvfW<LpN
zk*`-~aO;~xayb1Qw?A*{cKpf9EUq*yLXEPFBw$9q^|8o7h^G7Zo*9TNGFb2J;q*=X
z86L<mKru{QN7Q(oEJ=@C7rNs}6bNBD`>=tmy|!O>1AD2S>TT;EoU8~*shSHmTv<C2
z6J50?zN?qtmwjt0oVq?(6{x8mzd_0U_*^%mXQ%e8guOv^l&r0EI96WaayA_z*yDd!
zH)Tv4VM|*e(XeuKv$!wW<+MY>yXn98HoB@3-EgT#idfJd*cvP35$yBVIKNZW45Vl7
zEFgS6T=R&3ecyd|=24c!)!FEs4Dt~BsSEAre;`Ng^?W<@L?5`zUVd0%zh1;NWk&e1
zy7}?;z}G^>+AJdx{HM95`c*ZTe=ssvsJ^PJ8=Z`>0c*alSYc$O4rIrIitX?MxJ?2p
zJuR3)tTb!A_39_|{08~zwyeH3Id$TFPp#|E^Y=imO88=;PY&M&NhLK*5c6+LhBK@&
z=3&(33zfF?sid19vh@TBpmIy+$<-z~{T5i5s7)fGL#@0>nssI<K1v$O0LhhBTlz~^
z>Xb9#Dmmw}Kumj1khph^ROHm1ujwChwq6fKBy7C24vbU%KT4H}qK!DVR0nEp3ivK@
zP?sD*R{|Y!<{_G(q4<7Bf0b-#ba{T_m$vA@pNsS&-;zvaZ1K2XTjEbXiA6)eNpVkK
z^Y&hFg9|*57ytRPv|pnj|M(_MjT|7e{Gm?*MInZ4$~%>pW%+f{6oA@)5DXSoNM?`c
zC-Np7aWubvDRMuGIV_D8dO6zFxq}-JdhrScs+631FAJw{TGahgj;XNpq-i6Xz)g(T
z=o?yK#HM@ZzesA!A7$nuAjtB)l7SE0KhsMBDHui;M2^XfsKAy?zfCh>Rr04Sx39%+
z)Zu$6^dQd2p0y+?q`~)uUG}}h;XB!1!h&oHMd*#JdxWw5RxwyG>BAUTNdt+=$|uGm
z<g)4^)%84a^s3kOUZXoJJ#aeCKNvCN6>CGymZyw^vd$Cg>=?>b%nMca>{6$qCbwuK
z3wCeMws=AeQW8#0?`LtdbLeK&v4&*Dah5;)`826mGb}K6XfsKfhZ;h5?V#7~V+$de
z$MRAKQhtguk1;D`o3ZKoJYkCv`wN&X%Wm^>t>Q4y;?f>mWxvw<{-x)zwNJ6A>{m9-
zUmn^Jg9~%yW#CAi(MeP_$oPmf8m8Z9@bPChUV}HSv@dY2lz8=^vmy17$g6T{y%)@4
zqN}D4*#Ps`dU^;z<%JfV?Oi2@kTZ@xOpJDLAQ9>`aZOBMRW_WO$!Y5eBeB8plV)3B
zk7)o8=?aUxlK%*WE~<xGL1K*xeQ#9C%fgOx`9vBnTGS^`egms7H7XkVt7x=i?duaQ
z>GHr4-C$A9`Y7K|mmHCD+_-18;vb()SeR7I(0q81^4Z~NBQ#n~k0KQhX0E;E>!;~y
zq4zsN>thSgsC|o9_Bnp__v09wrYn)|q4K4le`(>6DR>moqB;Dc0=js4pS@<_6AEL^
z>;%~$><7S`3w{TVMT|7sG|3wW*}yx43KClLKUJj#Z%-U_Q@2Q<TBi^~aueN)cR^iy
z<t=i@F`por*Ye2<4QGK!LnV!r;fzsJr8$KaL;m~lcK6?n`uE5G-KgXN$c8I#C*$ZX
z4D15RL<bVyPbE|M%72tnYQDPoS=>PS`JX^R8a$+|#fe=tz{G6cI7$wgvU$2j#I;g+
zT&I>eBJcjj%Ee7@-Q5g)W*Q@AG~nd+Ozv05>Snurdf4pd@;-|h>t=Ba!v2nI_b;IK
z>$cH$Mec-G^B=E=hlY6=7s`(d)7-9It_R3!LF(h!g9l97PSL{U4{t}m_2#wO&g1r`
z{G}Ltu6Jc(90OmbS(IvCq9s2M%^#<MUKm3o8b5z!LW{LFoA>~uF*I+Q4KF?01uR!=
z&4}J?U+MenEvGqm6mG*;{;Gubhi9ktOO(Sl&tl1$$=bgwX6$yxatO3gvNAsvJq%HQ
z>h{=t4wfp69t6EMtaWAYMEya-(ry6=CH0Bqg&n%gA^8UOY=Iu}xo_8*h)T$DHG5w*
zD%2VYB$uOU5cg<Mu+eP(b#gm&P*;DnMZRtiKK^kB)(7jAHq)hQjGUAo&=?-sdD1tb
z*tpTXZzhRCmTEZqkB|rFeFFmXvPx^SQc-O{)#MB6vQPFk{~`z-sUjxhLWLF7L#RF(
z8^0P3xflQkcIhI-2@S})1jV`JZ~-!)5HMc<wk^)w;KYYQlrncVJz*{-vO&+0nl(*m
z<oUZ_oA44PZ6!ym_CdT2BJiA(H#n(A4-dk0*uvBPb;rk~xH~Z?#jS%6-O%xpp%bjQ
zGbX(Q<((H_hf<<Vf1pMR>Hj!O|1WA{39>Cj2uepuidB?~EjlCBzS#k#0XiuAg>b-F
zzLYRw!k2~;*jZbvtF?<%<d+dlW<yp+MVDq>_W<_GLPf`q=1Bq`HdHBvX<1gk>RZ=x
zv`;=i9;SCUN);}abOD?bPQDp0To~@%uSCPF0?NilMSswl3CS`ahxZ%=%hr&3Nd!GF
zJAHDRit!o_HOm|uj~hR?ouiV9X#cd^=o{lhj7h;EVg{ahu&k<TR?js0;gvMwwh94A
z8W*q7RYqpcbL-gs;yP;loN>>Ttsz1{3HU@N6dexLoAZ5bW_*hZIbBH#hc~+=3Uf)R
zJB9${+jdn$w3@}VQMytIBv_*zf>0AYmiMD0Z#(R0;bY780Goktiv7L&oYh&n#`eyM
z6c_Xuj|fq$z?+>-c3(`f0l*S%!|EA_FY}9;Zfk&h5V|{gf&|db$(CHAn9~E*;ys~@
zB(d<W3el)4?r0*jWjZh4&s_Jb$1QDlZW&VN<O%cv$i|(ZsQpg`(sUQGGv%xq8nXv#
z?-*jR492eYP6USMQy`;gW5!?CeG89eJl^#w;gtl?`eja;U_sMiOm>0i6?8j>r7|Y_
zS$lWhr+$v9z;oKkPWOlxAJfgYR%?4J?)G1di(2~2X6E^_4I9O6Dy8a|sBYxF4oO`I
zKC-r?P%)V)Ub@YaU3<Hh1OU$}OeMvx$JEavPK;O1{C80Od>55`D8sJV2j6G_{8g)?
zdFGW5(RXh|dlC|4Lr8SeDpNs~vybo^zLz+jC*z7~)k2zA3gGTkEA;#e6CASd|K&4r
zwqEbie1q~3a0Z}AtErU|pFTU^QK6F0!;S_pP%@YwBM<$N90sMlg1~nW;JZovN9u^F
z!reKX^`o%up!0uZquyQE-)^sQZycR}zCL#y6~-!ogoKn*g<hUud*Xi<?6My1J0-8W
zKgz+0Za7D{)f3j%FIg?}yZILVNOitqLyn%n`XtIv0S2*rB^aKu51+48=yeE9`bMGX
zlWi`UfD@Y6Qk}-L7`h%uF)N{bQ%8YNz+zz@5K=3hw}G7Ap=3@IySq}R>!pfo%0k8X
zZpYcCC)CjYR?Ios$v^aWKpijB{sdoP$6jn^V2mdT#ubP}930x67v$u80mwqhp8$W&
z^qfc3%a)2Kg7bcYE7KN<O9MYE;1wQ--0>XUd<}bjaT@p}$`LGqj;OI|ujuGxK73oG
zBoz#pdPGF*D_5qNcHvQ*%kOstI0;&F4jyoPXzPkH_MPCuMT_ejA6Xg=T{X?q#!QF_
zA8N|I8d8iziBgJu`DE^ZLBRHtPB(N%BnH6Yc0^JDlQXKr9ZUWCFWuNGaYQwp8Wna(
z^Mw=u7RYBT@2BwdCC8!Clfb<It}pGk=f7}Kd64Z6O?Db^w6K_}>^H^RMg1EldI!|?
zmNtYeP|(F-T?P=-v*hyqY!{vizoT-O#%>}H;sD-BXHt#2nl<Ook(Iv~7ybiI?aLM0
zSIk{I!7Z2|Xf$JPDllk=XC)`D{_Kv=Lom~iH6&LKZXkI3GjK+0@#E=VFh;fOy-|jm
zMh*l+JN(lxJH_CGDKX5s87DY9r;_4^`Muk5#eol@lyLT!`*Jyjsy1yppOE11UDKKw
z3aS!ZZirw?hDL9e#{(>`MLfG|&bg6(U0M}Kh$W?0n1P=8Q8W50DmFOJIX?bQqZB<>
z@o6~KDH;2(DHJiFBo$b1%b#=+oMX4@y$<pi8=V4fMny8!X+oNwuKM<!D7!5AYe?1$
zd~W=tz*nVlz^$FWY2@7{Te)HE->TTKL3$JlwVqb=$P{$9AqOXkFs6(ln|}9{><Vbp
zyLjhXREay24E>Q|^*7|h3YZ*lKX2?d8u2gC!GPV)|79uz*p)tRVq=P#geImOWS|zN
z&Te6BCrVtBo0lI#q+NP*@U;uX;{BNMfvie}hz1tBGR~?Vnb7}=kuG>m4WW^Ip6fX}
zanFf9_VA&d_j%7am%p3;))FWTm;Z-HhI0|Ye5EJgSi!CShw&*<ZJZ6BIpODD{3(IL
zc6RsnEiak{*at<v{;_wD1_DY&tb=*cJ;&P2jjN<7#kIaEsJfRNrk_mXR5ofa+_JeH
zRE2^(<p5X^^na*?QQ6^kY8TT$HJqg3O2;z&Eho+%<TOa%FEFNf#eET*J54}fw13;U
zVyww+>-XZHF&;A)AtnC<n&@aO*TWQFn^q|1-2(LJ#qa5fyZy@JZ_nyy8^1bES9q#B
z&r|Q5#odc1|J`lA*Np4ynR{3JtX+0K6(_#!|2v43CnhG>{H^V75=9!rQRDxJaoOz=
z(ft&{?Hj@r(kj{NT)A<KWMPvP7zjbSh5zpXvm`e9>dZ3crm6dl%ybU2h2yrH(I@o4
z^Wzr3<G!$=<MHH60g2S9ZVTY~{LKN1L#v~sIr}A@(TjkGV|?mu5JBL%yicBhVAUI+
zh_#obq;6*C{xWyF7Y0F3py|(mYNQ)K+Tf7^HP&o<{F)1*GHR**JF+0#=L6<yG3ITx
zIFFz9YbG~WsH)OZUdLmxtXzVB;;E^KWQLX+=2WI^8WgCbaG1<SmLDKhskv<I@tTn3
zG=UraZ&CAx$;S>|=Ba`Pwym0`4OBKwXV*pWvfq1qsrT-yB~iLd&%K?{<9(^u3%m65
zsG-lr495-=s>+?3lBci?AL}os#ovAw5uO1qIV}NB-|zSNvNht6$G1+J0y9sAA~@kt
z!{D+tGBnx*y6g0}S{D#Wp@7BQ_y~ArziS?t7{uEhY$b<o?gtPkn4S>;<%eZ|xPNm5
zu)vUxu|KcAn_l5_js^#>n|?6aXJ>d-h}b+{CQ<)(g<ms|izbod?s6C<+hxkc6JX@2
zKKoswZ0?|ZETCxXR-Z4o-yJ2w@O+G81nyt@r}qSt8RB_=m!ZZ%%yGF|sDi^Ig-Vnj
zDr0h}^$JKoPDD3@$4%g|c)r2ge8b*6C^qzpnMu#*PpCcDNDX{e`uMSOOW%2ToPEvx
zZ)WOtCD%70z8qrSVXO=Z$lyGWJp#fXbB}4=zemGVBiAI3)VUM*mxC$pV(fjG)lyH_
zHd1siA$-ij>nVV52#0|FdcG8y-QO;$oV*VM#--giR+vQ#=n8pbA$&_2u%3Q@ID)<i
zlbn1A@%hx0(!2?c1|XUX2cHMP<qyW$_@vs#ssu`Pu9Clq{2-GhR7%XggpW`o7u@W_
z7!0MjPEImYL+?~VXF-y$kC@5qJjaMTS)ObrSHnXjxAbh()M1Y6x9sT;0`$I4QB}^T
zu6k;zS&pF5s!g}~uqHNMd))1d<T3wL+9LI`0J0B*Lvlu2*^h@f1jDQxX-d?UN&W8j
zy)0BS8Fqt|F`S~P+dNn)lyymDU=HQ1iZDjGgg{uECm^j-<SEfS%nXqSq3-Ck5PWI`
zvrzTK#ijkwYH?CSlk>tsth+!x;Y+zw?(G4kpX0X3aL-VYv69Bn8I2@m$-1R}<*p44
z$KaCnvO+KZ_ro{aAcT>f#@oMi^V;t1mt1ukM0|pJQxmjv)|RC{n>VrWX-TeTCU8H`
za%hMvm6z1&M~*rL*W%YX87K2Z%|uujHOhdjfh?Qw)Ps^h#1$1x0bbDZT<un@9D8xe
zzQ!MJVx(L;0VZPq9r*V<vWCMHIKJ)47)?hJQ^YhH3wPth7DL|HGbBZ!*IOl%l|@GN
zc->_(w~ePBT#KoytCJRCBkyWi9El?{ONy&SySkof`!5U=8qXiZ-F*i>iO0L90{>b~
zmoF~V$N+_w_{^{Rz}l*FG6FF}ZI_DW#b0>*)9A)V*V4nC>a}l-<b05MNK(?jnCw7q
z<U03E`}qVgF;Oh8c2V2cAk(=J8e7MCV4eh}EKePE^qo~(y3n`bu|0SZFB=E2%QIN<
z3?H<}bf7NknkiUEJmP5Q;97%P|6$SDQ1xVI*9_!-AhaD`KVm9bp&R;6Z$(LBIKc@e
zhZmYMw9a~`%@hg=R=p%Uv*nUN$L)9ZLb<4U@@w1?c+I7UR^bw>_Ri6dJ561#fL8MU
zGhI#KKaNA;w8NWpb1D=Rc5fQWWlwY}7wUeh{7i`s!^~ndcc9s3WV9>iQBM1#iR@%6
zSvym{!xI6zL!P=#Ve{mUlS%rzJX@0JW<_b=IHNm<#jPM&Vlzw8q%{rQu1Q&2Jh=iF
zb<x>Uz~9|oz1d>syNUR{-wMw;(}Q3d{P}w)+t3ZSZ=-z^t?IDTQ#$TjR`~fUPSprj
zLz2Sram*)(PoKaNqH5BzQIm-Aj2mHotjC<bEsy6|eCKf*4VfE-{Cj&`OPTYPj2mw=
z+8T%4Y2A&3Z^ezWB*?qjKY1Oy5xBcxSdJ*xYm&nz?z~ryTu!RS5Th`jo4Vh>(1}08
z6l|;`g<j1Dq0AG}Z9&1}?+awpp@u1dI<vp$9Z`Y(hzd`S%#cY(X-+?>D3H&yj0%ZX
zXm#{mE%tZTZ&li8WRIh{cY{H>V#Dn;W6^_0bYQ=aRTS0a9d`&iIGvVYTeXK?K+vDR
z{R-*_BCI9M<`;QvQyptvAIdq{*I)x;U7K#k8$a%)-GMRNd3?g8BrAKF#*&$%oi;9X
zQ%b(|I2zemr-}_hA?|L#i?mS(0?=;gP@(>*g6YR~YD62RR=_<7l1bmtRe`V9PIcfe
zSc~@A^sMux8+sR=e4H7Q#`YJhixql+ivmwmQLqt$*7Gy%$cjTiOoJ5tB?|loJ<4C~
z;(O}Z%K6|G@=ht*<bLtf9Op$L;E=7Cpx11d38Y*pk5aNi#5*LU;fQ}@Wfh|-Y7O|b
zZ?2k4Z;F^=isnYncm9c%av+#sMGSh$6P6DxTSFG>6D;jaM9)1&z+$n0THYLdt$w>^
zjM;E%ed8%1m&R#3k(qxMsvB8FCDP7S1;|XUZpA+Qze9IH+%W)D)i$RSzN_C^t$z<_
zSl{dvyXSn2qt$y8AFu04`8JL7s^fLt_cdhsoWc`#IX`#J7b&NK+!m4>8NA%f2S+SR
zMrd0PPYPdy6*(dnIZg?&m};&cVyCW0TZD|<of91#AKrpnL^ID_xqKbIFz>RkDIcgB
z`e*Gb5$FA-Pi$dm+P%47Bb~`$Q5?(eqaa;;$$=hnPD1sVQ~5V>Ph~5Y$uOZ_?$`*F
z1CxU`A<<1#*%qEd6!OF<&?@kD((4j5c!{8VWmG_-*ck{nzo$X-fSW_&l0-=q2;(VN
z2h*ltl>}8s{e$w<*lBxWW24{G^x2BJ*pII3Lwxy|Fj=+?^;jG@PB$X5&68%~*Gad-
z?20Y2waH(BbD8Ki{rAPcRb6cPIJ8`rdgiGsBzBJ9KoE2Tk*EayBf13Bvs{u9i~m%H
z)B#N6&@<&NFYNKYNpEUiqA35@BH~qiI@*dmguiR5`J<V$wWUkX6euM&U$U39bSvsw
z7rjXA+sg_080%^PeqTpNPKm*xVAsRxlq%kEzK533zds}dfA%$w2OpbsjPuXX0m|Gk
zh!lcPNX~@GI00ZHMNs(gD@dl8YF$JgKQ6F{VFWQawbx%k$>X~s%~;-noPR@YKVH-g
z;F*4NTi4WtcVk`hqY4d+6XK`DP_6d}Po$xON?c`u-M&j`ysU9_Ul%l~{--Y!ya-Kb
zn5|W(pJ^}q2A$i7KQ-{T7aB-*^|+}X)J5yaW!!Chu0+j@<r=zfA!+3!E;XUJ8cTR?
z?SL`t+_97!A8D0GkV=Bs26^he6G5Z{cW*OhjwQMzoR~;mT>iqztlbwgHl}32WT5Ab
zkb3bI=rptQ|Cb4cM9WSacQI4=Ye>T+R|KI4NrFVUf4Jd`_v+oY!{+m7zu3AZy6aqn
z?zh;)XxJWPYM|In^55Z&YD0%~9`%cAdE(yb@V9ZfzOnC}v6`%#vkOd_Js_z4HKlQG
zI(wMjg_))Xxw$NaP{hpjn-{B{2$Fq)?HP|?&3U;~R_t_+po#L{Dej};SFpMB`H;<h
z9k6Ux=Z|qLMDNR|rV^eBW&kd8pwog{ziOM>rP+QAc=gTlb&P4aoItx&9zEYlcE@Yt
z>V8-1>ah&`02_R)?zX&N9Jkb5op1VPa|e2*oXGks$;~nQu}t0QC7bY$jT~BdUCU8F
z*sVWCR@Ju(KP>^gomL>$ce~VGA0zY7*#fPj9pBc7Z?OZfsFb?gek4v!0N$kj-~6T!
z&H_lF5ck+Z!D6(#yMO!a-ZO=H#{T<nox(nu4gh|HwtM%C_J|=5u3@N+l}0cxCd!dD
z5RPLTbUGdf9d2aq{#OjHXxYv>c))sY$vu+9QDo>e4ODJ^#CZm~<aiqJPR&qLKff5h
zV>H`trdCkQ!cCO*r5RFLKD#Bvi428;=T$$Icu>TG264m)SvR#wWM)UA)^LlUMCB`2
z_N6z4`=pvA%d<q`BkCz~-+P^Jyf5?5Vkj{r`Q<ilz)==-?D89{VBF(A@%EKs4f~Dz
z?2;y9@9I&M?q_7jk1K}MDW<t)tJ05|SXfAMNh%bi?ZXa1)$&bZsJ}g~cU?<N;dNP{
z(Ex(NQ;Hd1ifi12Cl2rvv{cLV2xjjje8DTD*{f$=)?wYdp_KNJ=wB+tqm=ujZ@%4N
z4_8Ew2BfA)cSqkEy@u@9_TxmJd)~!WR1Y#Pjg#YhW~g0ual7ipRu_v1kIs;D9f5~g
z<Bq7vbDjA`JQ-Twk@K69qzADLaa(cLOV!Gjx+Ei$jwpNDUKa2WN{(cCQt<-3*6K+(
z{E?e@QbLj(Zb>P0oETuYw(=|79DIPy^`pSe#N3M|ww~g20c$XgXd4Fvg`Bd=Y*6HX
zcReGO`}M3a*8j6Ts4?PGaQ|SuWKk_Ej@UYhJe~wN(V;&0ES*=nO@X_*peUSDKu>$w
zpd?eR&O9ZG^IH@{)J%VgWKkxtxtk&{2i9@HN=$>L6qwako}p)4v-VDpwnPjurQD$*
zH5?_Izb{5v`4-s3QSexIx)SR%{vd+}&Dvyh%U4rj(b;#PlQ>qIs`a~3YI(iA$B%##
zu$*JcHZVDOqM=8?2QZTwRahH)EubZTc!S3l(gSL#Rd<%bbyR59lEv-6ueW=0xQYVo
zVY%+a5h~8MUstTZFibf*y;RZb@wShjwPNbrBd<>ulB!mRu^zYDF7mnQKwv8|0vzK+
zSKgOB3Lw?BehXA0G^M1BF=sWPMWxP&I^9}_6kV~00V)v<Z0^UqjC0dV(&9gDJ>qo>
zN3&&3&s$BAS^tcJ!^Ui(){o+KRgU`Y!iDttI-&l|$D@_RMBRa$F6~9iiuzj!^sMLN
z(Tp)n<s=o`%KSkFd93|ZC7EulICjS5KL6T}+asusq}DbD)^kwGQ3dwsf*PUN*x=%0
ztf?WY8(VT4UX8Daz5wv7mo8=Vak8NS@TQVo$Fc%!Q=TJ%cJYLNV$0iT7)#*$(3myO
zfDlg#3Z9r22?G>v6vJmYF*DTqP}Ej~-WxWl8e=zfd!~3;V$yIlmrt~M4#@WLL48dU
z*>RXf87Gv?mm3<Q!(_7=7v<zF_$XRSn>A9V@~|z+c$-mPhntvK)@xtVpyWNV*IGF<
znmlv}O-bO%Y;2JjsP7x~b^jK1ZR8o)&;GSD<^Op<pg^$M<H2BaiqsJ$*Okz|-$uXB
zkYk&8O(-x$m3uq9FHnSmV?VsF$MSX9TT2!s3C4R#vtsKCF{dTajUV%dg-}k~@<moD
z9tF>#o2k*2Cuo9O^=E)>wJ<+fp;76ooAbihScsQU6Jq}}dKvf!ju^VHE-|0-6eQ?%
zD5g2Tc_qp$)tTWPfhagLW<H~@Ozo7zH_MMTo6M2Qa5<?*{Pa!ehYAIUD0V0o%@rN|
z^o{D5Sc5VzXeV)e-`Ru<MJ4dFgQ1k&;Svt~JOc#Ogh8$uf1q(Pia~cjOpT$*E<}=g
znCSR3$^kA8V*;bu)8D0Bioj@TbsUL~o2p0e#{~oc6dcWQ3`9`Ixt+W8`;qj`REf~&
zWtoQe^}r}2JeXnzh|(+Re=kEF?}ZKH=YN*}DU(KU0s+1?+G-x~R`vK?6?ny|D8N4v
zVOerv9dxV(Kcv#(b@V_P;qTXxm(+iKb}E~LUGvNJAe;UzJn(~XG1d09nqeKMuXrw!
zVM@K##UXw3t=;h8nVEoE_v(^1h`LaZt!vD$UA6$-#yGP443)jrSZ{&+f{4`^Ju^*4
z8VVfb_`LV)uRWw`K~Bx`mQ%3&VzKh&?0Lzk%{s!AH;!*%H0d<j*g74)aY*YV9!x_a
z!7!q5Xw@YmfYdiEwpQuz&1B@EUq=Vtnof2KPaU@q{q=Qf!6Be^*&6{9JZ@7j3;X<*
zIpvw<+raODJ_72CH#FlzC2+wbi%&9-pP)iWbBXWX?(lsj8kQI)+L9MK-K+E8vrVy;
zDZ|7KzwWPs-Tjq^qo~2wPWsk&_QpOrKlqz;u2I=wU=i01w#MHTE*P^6x94rKzc%+;
zi4zPW6628Qj<a|^FaVMwVXS~~!Y9j(jwGM<#8pj1#Ux%QyC{6(Suxlcf{y3(T6gJ<
z6YZvAiO>xRr>V#fjWGiLtQ=SS@dq~kbwy%elJEP!vGB6xG8_8F%L<M{oE<0~3)+7j
zs?`xm#SNuy)gL>!UtLmm5{*Ee#8D|<VO;Ojx3S<$QEi#m&@t7iuC7UqVW}s6(E9l$
zaToVcItn)Lb3fF+Y)a2|Zw$1%bJ7*@zx&wXeZhcZZUe79$e!$iHDoPaSxkN1oUp@<
z+{5s|8>aId>iv-3<OVsMD({#5K46NX0@jIUT1e)r@jLa$s`<6)Pw5*pFm~$qh_bPx
z`Eg+BnC|vY65kJJjCyO?eT$c>$b18o&~<e$P91d@*x-WWX7R4u+|9kawT8yP-7i$g
z$gEtPwUzgNY8S~u56H6#zq_K<zU862JdcBFJ_cw5Ua*N(Hm%P2*{*d$Mf*qpLJL3b
zdTM1<-HZk9HauwqriZ0;@|#uP`<|5t*)bI{sIQZvO9|}i0_P1?WY{#I4ZWX6yX{9@
z2R(5J>FZi&3Y6#OZS7_E86ZP=^_G0B$`55_>POdz`iVzlSkKNeMH{$}8pZLN9uz32
z25}N-w%2nF_Odl6Z!apbAJ$*<1oXD1M_36S6S@7`S58-?MoFE7Lg=NzJCRV)|Ikb`
zaONb34#8${W4Jp$%%b?Dbb`sI5WuR~y2uc=GO!Jxyi)l8XgbTND!Z-=3jzWnE#2MS
zDIwj`-QC?C0*7uXX^@aSba$uJp;NlMzT4*=-!B~wMfB`gd#-EFg{4DsS(cVJRNN8M
zB7$xp%FF+E9XCb+YuejHQYXn8wG25h-cYo@s%Vs27M|Bxak8FA0iKUE$MwR6=zWAF
z@Y9<cs_&`@IIg1g^MOAh$W8+IkUC{2yi~HHrroRkfm@&-<#6NS@}AZ6WZk`XEGBo|
zKI0#3uy#J|Lw++oC=`bJE3NOC%pu{BN=b93H^Iv`0}2K_mQW*68ip+eKu*xkw=hhU
zZ1XIug);p5WNdZ>2}g{XgQ;4m=s_zAfmlAazx<drwSHZ6x7H!WVFIObH(?ZBJy+Y!
zBPHE?-v1U=b<B!bpR#EA8YvPPAaiz18(X<&N0(qD+zoMGxG!qjph_adjB^zQ5%^CO
zH7@~@OUS52s^ztL7BPqQA1aHrj3VWu_`WiSiT5bTe^b^Pb)Xt<u+G|?bLcH*(XZkV
zL0o-&o6k>Iz~v-IOxW#?x!WxeYjN_!@L)SBgk!M}*q9}R&KItSnVx&uOOpCCUfdK;
zc<HXMAzplyfy}Qn>{7Ju$NjB@V38kEy3V!9Qs4AKD9EO!JMazZNNWni7%Oug_xF-5
zS~bG|dLhT!<S|HhY_JNbw3W5Jhya}h#y{?mOLudAR-aB1q<sD1t3Ml`rG8gFN@PZt
zV0mtTumBe7Dg6^%5yeCP<dh{sLtOCKEfM$QyEV|Yw>n8JO~y$ILmURzTS?9@X3--~
zQ)ickAXG$gI8wm8)k7f<vMNaO0v#C2^_;xdJDr<9f@Bu!x02MtCk&<|r*rXX9aD;~
z`|}@g;+kC3Ni29wA*1GpCifPKJt3#VWHaO?Q6>}gq_5spCKovh;4>d3(wpP_D6Qr*
zphPrjlY1PC>EStXfCnNz%K}<3rDz+e?L*N#2=!OW?Cvg~TUObgP96Y+oA|^34kPMw
zHCV-zrfDR7gtW31jTw>9X&fU|DHuczEJxEET_anc=41j@B+t0J#Db)?kE%aIN2}jB
zLe?-!iL7{2p6EnN{X}T|XMQ#S=96FaZdF-&dpBp<dt>}{uG-!2i5EX)!)MofUI7WB
zoO}XL%_h&+%nBEecM7xia47Ocs_T~16&~q=jdFQeX1>-NK?dOiIKd=alE68&{?yyZ
z`*NFdogM&V1Tr#d=nlBwU*GFz&NX$*8yFS7x);;%xxJVUs>ReFFn6gOJ~WOAxDobE
zQg5$28}75IVe1qzsT(JLYt`_44h!);ERQ?!T(U<;yAyb=>JQsPtUKZC;CrNieVYCd
ziBk~iI%HivfEt2X0fCj%?H{J5;;9;(j+D5a6G36`=a@%mD3v!>IRoF>q@@qXvh1BG
z@V<~t+q;+9)!Wl~t!dhvJG>s`I^DMOGG%L1c$Katd4!+PNKnxu#ih}r><jM|4xN5f
z2^$I`c$WZW6oSA?)it&2j>2Uo9L7r6bK7|Y+xiSO;)O<93(wgSeQU2r-Pkdi>;|*l
z_GRvc-L*FKz(2R|X;+og6LNWoYIoSzeK$S)9IKso4A4klxm+w~Vaf6*&I-2cJi`Lo
zTKoPI#R_}GlPk&xNl||+Oq3%aQh3qw(T|YGEH4@9+MWHV%iBJ6<sc7yF88>NY42A5
z0o?@ub#6>@zg%O6a0ld|2bEb!$>8aq$RWbO(F#-@GJ$O&j7W%Hy=>4v{By7>J(u>H
zT0nNDF10k0GUjZl2Te*XPfq``OtvU(Z=Y$HC@o<q<G6#$?*^+mew-xt@Q<*$(~)fb
zYaZ74jHy^Qb6nbePQlyDWBU4vkySQ)k9BDarB$2<^<wDR#eG<#K!+^uAVjQ@L-n*?
z4AA*pO0a2D*$L8#`fhCVS@w<(D1+_AF^dr#!6wRdW>q$j-cZ)+4qZvQ;ibF%QYHgV
ze{AT&MBo_!s7*+U$&La(5MgQRAAqcSlfrj2%6W)?qKA7<9clhLgSXT+xj9G;Y;NF1
zd$Jdl{0^d?40o9f=K^SiPJ*r2D@o`D<K7X=-bpE8G1pn){IWe9RBGWB47O|>8fM2|
zcEM(TchNTQHP`%i1xnU)%w8{-<rh}$Nnm!O0Wnk3iX~#7|DG3n(nTq?ulBQO@!h(*
zp(vpDi-=?P&2d9qe?Y}(XAYP@wFKs@9&1cRrt^0OA1#9>k=WR@ifhG21KR_0-Dp4U
z;p7rEouLw&AW2tP{o$|2Yo&j=t7FQ@ir&^gL%XluXu{gf6UbP3mH*AnC)iQ4-YnXh
z@i_dIUsYTO+~Z^iCxK|{%;Y~$p5#(P@Nq$Yv@{IU@QaN+fz=kxnz~qHrk?iroHi+P
zl26B3Jr^K2v!9J6GMjlGKLGy<pM{<MMN6gz_3y6EAwlpAuD=*OxFc^0C=<tSAp$SI
z(WCk-p$S*GGI-$0mMZ}*P)53zH*MKG)4Q^F$Px`AJ(@#&ef0%Ci2OI4a&oo+uT6lw
zedubs0(}!xvf1sk44$~Vbr2vzXqe`k(YJw;gr0mhjjJq5tbJ&~VpNIZ0JY1b@E0rw
zeC~?~R*lfE`40H#N%p<Q*I&YXX|HNDa*qn5STq0Llfe_y($ij034{(gb3X7uk%8<B
zl3-n(VNHG*&RAq5r_@tCa=jpw6)U-apnXHC1OOWnWdHBeM>J1bp$sJAMAJv)_{J=x
z=}j8yt6hITbx92Awu~{JGF!>#U2ltbd-#m>VM*W9r6Z?ap$`d&ntDUN&u|>w6YzC>
zpU%Xo>m63uBsE1a6Gph;b#;cy22e)jJA5h5AXRdBWjLd|0eC0xHn|Tb%YvMy&^?k%
ziiS&v#nl33J2x#6`2JNO%;`v~SaddCX1`m3KIxc$H~nV8e<GA5j1FC|&hu{ZTjvv7
zYj4U&o3_`aD{&*yg0;=dezn*foC4M1%Ykxi9%tWV=9jT;f{OtbxU~SE)Q=WvO|DLy
z@;0MBV+2HdE(Ss(dFjYZ>ZwQ1J0C1~o;Jx&+@;DAi)N7{d+u9A_9D*4uU;V<n);<^
zw{XRhiXc`__My3Jl07WKCW-dm5tSI>`|JhauK^j;$}S~xWJ0Y!%|EFEB0M*LsF7UN
zhRgLmP43gBG-A7BVuavBr=wZ+xOMbhfOmpD|H`YbROHbzfdK0SAaLnF&mcslFcbxG
z_)`B32e^tceqr9pR$*Sn5>CabrH3y=mcYwIRx@?0uWlCT_Zpq{jL5GisQ?H=aa^49
z^8sy+{{u@=w?Ims?~gA8)MGgYd&m4PZI9U~2tw&4xbE(5NI<VOk@;TW=5kYyu~7%d
zu2ci^d=TK7LT{0#l~cKP)e?$ILy3dO%+98@*;n^XRRR$tr&@}%d%=#Z&qc{wh)$b;
zQ!EVudaZznmL{ZYYE?C|TPF*AvvTE5Pt}2~n==QLz+b}Z=bOv|Dn-JcaW05(6v3v`
zl0a7Fxt+sQcFhenHvS8KZ_ZqC`a_99y%t1Ns#Ln8G~Y|yw+QZEoO>50bDQVjQ!*6^
za1+nh{KU0dc4%<Z6LXQ!Z6L9ltlbN2WHvrEBh&nzzd?u@ZIV_baVIpYadXk$MMag~
zGGzKft$l#X2bA$wYvub^e_HRp3Jogv0RNea9m$(Tz~$LTdlsl9=jn09mZwm?bF;2@
zYF~@S5jlP;{UR79J=|B>W3JI+$x+!9c3PGPhHqsIu31IY(p~JU#muot8s=kQ{?p`W
zpCQ^kSi2*JJ4a7COydD*wdG@%8(uPqYO$wor;1^P44(BaFgqQNj{@=|a`y501O1Fg
zL8cSH!>~>H+*&v@^~)d+)_I45z7kLZCtwL7&;gjovazk;T-3Fx7SNzXGT!28KJl|`
z#hM))p!o#61lJ^C`7$I2Ef64`Axa@MN7BhI(6k>!<gej{@Z|zo0f<40z&DM;8@r(V
z3p{+`5Ak1C_6r}>Z=FK%NUUFcK+-JUk=0i|LykC*H@9Rr__E?gwa@|AFAF}9EXv5=
zg`3Q^E9BI<Tk3RQ%?QQdiKib=TnS;svxUhbg}z*;rdVfjgcbp{J;mWGtMomU!~z&$
zrd0$UTO48Zi4BH{uQ_m<p29on=fz}o7IyW@e!{$T=ok<YUC&Y+Jzf6SG=YK-1qPlM
zR7>2t`wH(Q_Hg-07)4$c=f@&F@yNgZT@d&mv*~vXuYy>N{3#z}e997SG!a<y`~DBO
zuKB!In`F&xajfBu`mIAIit?8(otF&nqOb6MpEA$bIFsmL^#;vvXYfkaGWY-ei2)SV
zYKH#1ju)ukzHf4q8@&B4%tSl)!>n7HB_l<B=RR+z)NOb33<ht1_LuN5=x7l_(&@1m
zJfCi4fe-n<q4SXzF5*fR&RG*&sC50XyY3lOSb`~w-n$!J{`}e*kb)7X=y<<qKcah!
z42&#^prN$lZiR$o*iKtK{)O*6*U2^a^^U((iuI)pG1JRtb@$6GP*h;!;_NEvc*N<v
zW9}RT6gEJvTbXu`VI4EjE?PZCcNGO{NFenhB>~#x+xzFo^;c*>S(ORlt%W5XRbOm(
z$9exj5%h114yU19MZAs1HJxt??62o`794JA1KYm)<`_cfc#HVk?~G%AJ#%|bN8|5`
z*tz_naEa&PE;+zx?3AUU06mPP;Sw1}NR1=G$I%)U;=CN{Lez~Wu2d6XhIW{9IL|!r
z{2)a#4t5_J>4CG6<@5)Rl8n}-A8^~pmyUhPJ-M%gxxkB-O{{=&B*Y3r!~rOGEC89<
z$3A=KhrG>VWagA~_6)Qk*Uh$WuWOY5iR}dbw$KX!_mt|Q@NB#&%yj{yt?FskZMUnl
zFe1rx#%GQ#p_s`Zt_XMp#<rOWc7`x8lHq1761JCls=~IHht{49Wn(`6Ozyg{t%c2{
zm<GwEep6HDHg>!C3V=tRPlNkBR}&1QSNM10h4^;=V20ecQ=8{!hxW1i>+F;~uu>b3
zBMj}1{F?ufNXU5U*9q_QyHSN|tcn_3yTlqc%Yp+cs1^+wTNX%Rz5<6$x!ao86`K)i
z$$mvv(JC^0Fnox#8qm2~#%bX*t@*Yq<CD>EpVHgxByp?EB3tr#YS9)LH`Fn0Zq_jp
z_j)Wi(as&9!8Yy005>QzMnJrKzKx+8{!wlWsaOOvHsw)+uK9#KP3Y+xF>mE3Z5!9b
zUvt|uq_K&r4LWBmKwF`R{s>?*c;C7OPRy(A`Zv9~26K74HZ(7c2=XOSFp~QANrb+l
zcOYaVi7t}ps=&!Y<H<q8;ONQzi4>P|gCBjs9Px)MqiTLBY>7$!yz(qefnY#+{A#3l
z&;%g;ceDsJ0#(Q<Zod>L4iYl-SnNWtI6P$Ruxdkr2%c9ir*k}~bGv%|UU7N8n>U>}
zcvoo)^u#sq%y$6cOBOka_F;W($q9oAe8*mvmOq60Az+&PBlh>;GgQgnH*@hibc&xW
zK?pu(TY80@tC^UO@Lq=hF}9fhbzvVDNnsv><4_GjBuL-tE^8v$GXG%N(3f)@>ebIz
zRL#NnDzo8QwCaLa5iL32YsUl*$y+u;w*XeWNH)pX7~{ap%%ysa*sk>C(q%g0%f3{y
z_uAuu3KpZPe&w?!f89ly40O%RnkDL{ce}<&!t&!zbk*{Cs<QWVM(dN#c%p9p@U7a<
zeRC;#dSr1jNi2*Ho*qVI9~|&JZngsKifql9ADW})K*BobWgsk`=S3L4X<%=4*dYAD
z0zczT1~h#saOeDPR=(m5Y;iH_L7t0aj-|GUqxEG&VT&gKuzlbA6<L@|0aF~{pTyD6
z<W9b=Th=tMQAi_=Ec>YGp;Lz%jqS3_{u9Cnm}YImq(&zYcaZ?yU@#|Zr)wIGDBuFs
ze_&Pluvkg(+k4r~>oySB78=Bg1i~t<;wY`;Zj|0Wbk3%U@~HU1I#BIumMu5GdznGW
z0Fil5PvqEaLbabT?4=rhdV1x~4dl+&?+QMAF~1@b+XlvTd^+JN-A)RxmONbj<Uij%
z*#uM}1Kk)VS-$o^$Q9*oN0|Coe^ZxvPnKRU*v2h#4Y2U2n>yA@HCiYdAyqKio!&RQ
zF&<{xF=c5Ns&)EQCt)U%HU?6DUi%c9PtNF^8o_w?Z6mA;i;I<Yz%p@7IIL~gM#kp-
zGAfMI@9QNo!O)-Oj5tUwcSN7zwVfjD(bw3d_LPAUiNOjo#oR}POn_zjKqlpI<fNDR
zxgz9<7bzACHxq9I*gpgT-cdo*WEkur3up(eL9FKdS(QBTK*3krqWZq71B3r0-k5T9
zO7kG~B`^*@)KSD7jV*dQ)3P1eJR$j6rfJPYIlh>dzbrfMhv?Fv@<bg#7{)g?)}V<R
zgQ9B{p$RK?&=Ih-9j@U=I7#;Cv=%=GixgA#_MC>bB9W+uK|T!ekhqjt6r2_ojZrb0
zaRJkQ$?|91bl^8h=TKFUNh=F*>aGf%NHIlY3@gMmC+gBo(Xvfhic{ex`fk>Q4%WEL
z&T^rRNJBI24TQYI{1PqeSv65;OPT+%M^m4Sowcx^n5^&qU59l4DfHJh<nT~S718m*
z?(}``Gq|3E3hf#BG)8_63OEB5ObZVaxov})zx83NQq8_P$(3Lz{ce=5H}b8``t{xW
zGbW(XEPCROrdmnzE8GvGOgKM=cm>=4=qO_tPLVCgj1tne0ZCh^6tEb1)c{kDPR?AO
zYY@zlKP621@F+Z{N1MpIRd$~}Lp0!9(4-4%Z2KiRPpSu%FQ-Pt&fpUst6x$&@63?1
z2`sL=R>fpOrBX0D?+tu^-02f;_Hr}LRummfdxS|#_tWpE{?3ed*Ui+O-sgThP2+i3
zk&`(+-k6f2yr20kFgkX@s{gcR#aC%4*%5do%L$zCKk>;@y1;k0H*<@&b&g)y#Qs-$
z6CK=*HfLO;U>ts>O_$Ddj@+k*5}Zt;E~iStn*(}vXUq}a;<(sqfyVBhBF@*exBc9I
zTjP;Qr4eWck1Uz_KfPTHKHmh~y8wXlB0q@$;NRB%x2Osf2{$y}$|sW;3o+PzZhXgf
z1b{E(ym1b%*x{QFl*spKZ#(z^g2aF8vLfo%tYFtZe7OSGi(!Vi3qc8ojc<>EW-ZWV
z$Wz*ye)2<r`M{Qxyv;V=6lr3ctmK-AEJJfS|7S*{jN(J_hccv{?<O%S!79A1epU9n
z?9V@chV~_KQD1%odA-lFn@CW8ie5ws;rV2)<#4%)pZ0L~_6)JDSPiO2b9_FqiWOk(
zW`3S88BSxn*P^CGYvg0TgBn!_I6Q!<RS@ESKkyTy_t80qeqY`5?$4Dbcx&T=)pmdT
zjUa8FLsZ?dE&!j<064+(lXyY)fn`QxSfu79h@!lKwZ#e6(1TB~p+CN8&#o|0?0Un8
zGMF?Q3^)rbqPNK;>XIRML@Qv;qJI8HeL}D#rS;`IfoKf*AE;zM^ieOgyl`oRZb)~x
zvru%cf}xKA>G3lupO7Sad!rs)b}<JE=}Ad-`)@$7p(Vx1ZI3YVgdgPlzU$AVM(zFv
zLuepM4Q!U8{ZX9a(9&~n+NEA8H`GzU3nag47C<C`cM?bf!ey{fMhQ|{v2{(?S>EZr
zlJ(u)H31>5z3o^6>W#|zMF9H^;N$Q?glcCaa&Zf8im;vNmE~B<8oU^!^4!XJe@zi%
z`9A5}=cpp2hH)<0kD0dWkcE^L*wydel`#q`y)XUEbeWlqTbfrh7P0vZ(utN6+4?;z
z>G))@Vg;}r&vlB`wYnB&Wdr?J^hn5`aR?^9>Dg4bsTQmv^0IJt&5e;b<u`l!hXEC8
zedSNjIiPvN#>d(9ckW$(&`NBwnGU5|mBlw)CdbQWtBDTw(UG3L32xusQ<RuA&#fXc
zq?ojGZ<*O_aPKG&CcTz<Y+S9US9U|r)|SH50BQs)ez`mhbZb5LZ)%en%%1)wI^oAz
zkFu(HkI%aA0j8ggM|-Qh^HCsz2;ai6Fz`g%M_Zza@CU`aG8*+-V55!v7M$$=_VM{%
zalK>~(OnKKt~|D<9pZ8}o<M&O0K8)SL?Aqjq8yb_ND`EcIa>a@SrdkJC2}^6gmjPv
zWJe%Ewj94Na&N;Cmv$H2xZ*F7m$iF8`@!?{YLLg(IScTpfdAx#iP#ED!qCv-5HRK^
z?_3!KL|qY&U9BlHpIZCr93}#7-{gqPEMF#<K?^m@#Cppacxb{rpM`sCB@02zbMcFJ
z9XEfasw?+P(W5|@8N&)8($WJ;AL=oh<!S6sO3b8dwHiy1<&v@+xU811#8h;xO)LkY
zK4x?B@fBvmxF(%X`>3ozi*N(6WN&cMbw|LKrD#mQc5dVF{adC;xVJb9Ov*!2sW5c{
z)G+F6f2R|-mYX_OxU!k2^R5IV-Ssu_vL~j<w*`?!%?ZG<8M7-8hl(3YVCpbjqCXUQ
zMKHq`Ix|^lMB1LXQeT(f{Oi{h8qg;8Ds+P<b%C#`yVVtZMK`f6bVDVjhv$u_d+&xJ
zR{fGa*EuZ$$RwC5p9}HUkky*6++l_Y5~Xd==y6^c_#VhmgQQiQRZZiq3mb{Q{^QZ_
zNR`VTXGlz8DQz7)qnxY-cg@N*=yD1p7i|f9ZDp)~Nry6AR@1wIQ6*R#B+{-l)XO+q
z1YDe<X(@r5<W!Anw~ojuF`gp4W)oUEUrW0@=|+!%68Ld@87nMHk^6hR3=8mvuUj*!
zo6bwWg5M5puuc-4px$2c%!x6fujeY`_RL?ZXtV-DYiGx+bSu73MREl$f&Afp-P#;6
z($3D{65y6HDiG!a03o4Uq~^8{(1@_P1=NH0$7zaWVO{Z$pO?X+@u`gTlw}Lc|I9%+
z<l;XjRxDkm>#2}Te#9`1=XgENGLLQWV6EB@ar?i0(jK=-I)j1lo{~z)eUqKMjOe`L
z``79#a-p}hD@EE{)O4unSSI-^0Rp9YZn8^)Um}Ur1`pJ6a2TDB%jW25JEP~UNMQgu
z^tg-wcoVow(&#s`;o#9<^kBz*BceN&`Aixr^(O{4H^Za=Q0Qafzsmipfau!954W@~
z-?frPp{JTJJPbDq|05;-)QWa>IR<5H7x?Zj<gPn;UA>U$oDc5^cAS4y1l)vs*E)3-
zjP|GLN^-{Xb!(f?AFdW-0fFY*LEtsA_-JZaAeYFaV&kImk0QsX&@H>_uPyfAR@F>9
zTUq6?drxqG(VtJjG<#i!X#6otetnhg?1hQI^QY~+KS|(esepio?YXN_i)bu~{@!=b
zBKM0{BFb7*o6XF+WiOy{0A(uB;P!hugEC6|waQ3pC80-_9T?bri>IM&Logn<d1a~Q
zCJK*<ScEy7LHn+LI?FCc7GX;N3XBktQp|4<%_Cz+#3qwJ7t(o(6dsG5aa2JX2E+vv
znxGfleJ#6cfNw=xe=2DF>z;4(2&F+9N|Je(F2K{L5pV(vl#t3qBf`mGJHY~WuQ<6i
z6I<(zJX;TH)Shl<ecvuf^}COw{#!xz`{9+v7`yWnERkCmAL>4Dk|)QhdIVJAVK_Gs
zJnDlfQOQtteDauyKZz@gHq385r*Nh&9LmL{p@~kNhN^Pw;27GL0*D!WaC(qRDha5$
zwz~TZZS=l&R%@Gt&=H$Z#ZqZwO^UH8$)tJv`0*Cpg=2yOs?+HV9R@ii+^CjJzufOF
zIyJ&UryhWt8u1Qk7^g}qptRL7;;`l73k5y}N3?Gvw}4$)=;Ci2@*}X41p%3f)ZqL9
zSi{vU8oRl#>u;8=D>62{ldm(g0=GL9z2vaPD9BD*kqEEnclv`kVt`@@o;J5E4K$<m
zT{p6=9rJORtgWve?tHdbAGosBorHT&UeJGJaVI@^C?nHx-!KSVMYR6=>(A*8f8b<>
z^&?#)0eu*_<i*y!w%IZ&fQWaqtuJB6LKiyxp1z>Tx1L$kvuXM=rQyr1G==k5MP}#Q
z)n+|r<|0GG`k{Y#+{-bm?%8}!q({gRgdo8D$De*Y03TbQW^+oeuB{fyOEmjFBWQOg
zAucke*m*^I_PPTN_$NG$58yW*ksnmT4W52?4qcR#4DG%|XbZtB(O7sMFIm05zCCC>
zyu6*=c^ySqSl#(DdjzAbH;s(|*x|zxH7*|WY7N0$I+Iha47+C-Nk_1aydAxu^V)ub
z@AFIRDJ+~+{oXO4$6(L@4MnT6OSsehAtJ@Poi7A^C=R4}2Ar@e2nhD4`R{5yAGfbQ
z-9eA46Zm*Xv48+a;ngkuJ|KmiS`(&CGHmm3?P-kL!G2q|RBv%3BgDuIb%~)|mj2Q`
zQN6fi$XHqevn><~#pe_uuD9NyK)s?)3I1J^o}O7*%hTDt-{BhkEO?)A+Tj;oamn)|
zm&E2lQ?zDLi`+rjTNsR=*I?vV<UdM6!n_?%|M(meaD4@6A7+O`LvBK2{~1I>_Lt>i
zQnd6dw>6`Nr_u2nxLjm2LCBwnECeOsuEv-bG&Redto*ZirYRyfXIA*$<$9fxbl8|^
zMV&r;SEt@N-c`e^45XQF1H82=-TOAVf(dYPGLbEL4hsi>%(*&xUnNhqUEQQ2DHC+Y
zi<DZ2=`2(b@^IqV^UsCwpX@D3?C~{khn<)6OHEd4BCg8U@9|bj(Fz=^8R@q3{da`L
z$jC*MB746`25}tq_|?J}qf{tI6SfN&#?%mk(?zEhKM2B&q%btMNpc;rv8n;>YrvZ6
z#GpI5w>a$N?B$TTf~Mm5Tyx>-1@&MIXGTkftV)Bj1BgSy+lDLzf<oc(&=7S1mS}E^
z*oP#4aE?<Is84~`rLmYn@A6?NtF?=s`4Vf}-FrpYlI^H5Docrr$EbokvYrOjR*RXk
z`CJvuTF+IFr<ZT&L1f(+!WvE^)8uI#RJ3#$+eYyFYfa)mbp#Nnj2-JkRqxE(0)9&g
ziha&#8|=#?1qyK`y($-=x0vW@fmo%$|5M$L)yE&UY=;n`KN<b|45loS43@VwTF_q)
zZ2M@&{Rq&J(#T^|YEKQLbB@@A3yrBjp=Z;=guM|jqVTr!&IN+G0w{s`0p&&ejtv>m
z*J6cuftJ~xyFAVOFL}Tu*Phs*^R$Ub>Zo@3M9;Bv!Vya8@C4IRqPtQsbJ{)tULE4J
z7B)dzRj6<81Z1Kfk^%7Na(Xv)^~1haRi8DVCm0oY0;>Y?Wf@x2-*kD{Beij-K{|qB
zMVLr2Dd|FdJ=Zm?65c|SPi3pbX0}Th6zy;J-EI{p2x%-b-!Wo}R1yadZ^F<ktvtw8
zto3Y}$-_wC$+yH!AnGlk#J+Z=IGdM5J&5<;q+ntT920K~le5zkMhEwznT;}vX~7<)
z5<jo?0XGI`+%)4g6Q_o7%tRShG0Z^#`)pk}yFoH#XNpu99<UuKQXQH)gz1YcUP3<C
z!?&Z~5(fa`dVbOqh4c=|zgFU(7E?v9lcT{!L-$-&HhH%PPx)~|L{yLDq5oc}RXpCt
zpaSZF)B9`-eF4v#eQa~jy|4^^{{Z0hihQ5aYX4;6zggDmKUhl<aC8;``!|6F@e(%f
zZL9OO$8DWnt@b(l?L_0Or9(0(Igp-(Ma9%`XKnmv3MKHg0hBVJ1Hmv}b;d)Aqf#_w
zGC9fO_4ieVkWmM~YnsYuc7f1gU7H!Zb=_ch=Bda$2=e_!Zu{h+{b(obKRv_YIh&cy
z%@c>&<V-sA6gIVz24(kQPJ`IOvh5!PSf9x+AOY8s9Z&px!S4!z`f%n+{1Fv#kS~z(
z!_bq#7lEyr$vDL1WC2djk&7A;W4m+P=-{_$UiSy%@PuKu+_(OcS&~x8(3&!+j{E4z
z^KFOr$*q(d9l9a=h?Iv<Y+7j))0z^i&cRY->F4wm5*UZ+8OJQZ;K01nuXfhTPvAVp
zC#amu>fJvU3G?BH-bp0ifng<eCD>MtqEVE&e|Gus|IAlWtDJt8k%9^Cv;1Y0q$FA4
zVS}^4vXyeDw{#VQDr(q@HR<<?BmAVHZ+y9d3O2bJ?h}+K$43uktyE|_G2mlWT|vGt
zpNDWP>mlOCfzFivqD3huJ9^bbv68@okg+ZZK0*>1H1OwiphAimwAPE_-K;#sf>}tv
zZzWH0vG8ejEoso665HXZoT<{@-kzqaOnp*e?gu7sXWQekSn42_cnBh?Ib&W41zf(M
z(C!Gl&j0QNdGwomRZhgMw}{i8xflWyo@&r>CpU#(FYtXYiVE7U=Qt!vil)~6ZU{aM
zjHpK83Je-MajFS2F*v9&nd9Kop@y;=VY)avzpMOI{)Z}+(#f{rEY}L)ZmXyM3tWRL
zz^nIaZ0Umhft?2?j(QzB4X}Nssw<LQttZ?rn9qAHZNTnw#{_(gJF*_gm`(WLRK`y`
zI2jeyY@I<0?m|CRWt=yL;6n=fee8SZy#d`#e?Ww;hFs+vb+~!Ee3K+%e?R@vn4Tu!
zNIsD%D`V&fyofxPeH0iUA{>coM9pj<1s~w5ZTrV+SX1|ZRs5dwsP{#u%<^-H&AUJc
z`eU`QXDyg^CLAKZK|EU2-<k8}@lA|fTSLACqnfU!)%@9bztkDW2cC$t(OHzqi&;`<
z6ptLhsS|`>{{7D$h~4QK?8{nbu}Oai4N=~a5&9+>Ze<J35Nrf3k(Q+Q{b2dNsB5QG
zVLH6yAdlppSTDYqdJyP%G%-PgElXG77k}wXUO!FI?wDkgE3P6FE*T9VOPEwUmqdK5
zo*m;74bpaXVpLb>-|b{+qTItrE6wJ6>+9PxLpkzq-Ept|zjB>jTuus1{M&LI>Y`dc
zY1V6lYHdFD2`Mo^+j@hKtHWXzfsBC?p&(QN6)lwY><?B34&7znrW4k@bv+;Hs(s&~
zdD6IfL@uqF6XDlZeDnc?RhF$M2Yo~HwjS9yMW@3V#0K*Sm9-LWhi^9S4<jEXY4_T4
zmMa46&pt2X{4nYgE$Gg;;mjc<EZOm)(B7sAWBi=WBk?X)1%mjZfC=PQi=cmV6=a}A
zNP>~1)ulg4vdvCQl9b3Gpl4@Gr<UdjNvR)OJXu0<4gM}sH`?cz0I=Y+!}pHBQ0U${
z@pN?rQ{7;eyxC8@u7>g5&R7tYF#;Sz0frd_V`p6K1?iN^92<7FcnjCkz$4A%=p|L<
z@=swE(NMs3zr)6qV{_&qy8}erSpLO`0@h{VbgbCK{KEajmKGCtxque#pvHt`l+tq(
zP)<`vM!Jf&z0a)x?Hb;}rK7Z50qdzt3QD+<JEYTg4UjHRTiO6(14z2;5K|7tgg{Zr
z(ALME9X?sq=Rpwf<dnbZm9YXYy9v$?WBwpBY2Y?wV`Z1JB59<yTlxsd1j&@R!aPz_
zG466S0PC%__|Mn_m~*Ne3?ylSNvAXWykmH@%#OsvE_P2GOtVVv92JH17wMjA3t@)A
zhZ6W={NGuQ9YmG2q5ut?IybZXD*K5JfrGm`pw-WwPS#F1Bz!;?P``~zK>4iUJTjJZ
z%br^MsiFA;Qy~7u9x|I|oEa4(1fG$eCF)gU6Qr6*R$Dz;+Pu<GaXqmSX<8ag-z`lH
zNra*t#>iTg^$qia=quEhx8(SHI>D;ESS8WC>G~w59OoMMbhwHb(&@)MuQ(Z6AkdR2
zV3Q;%B77M8jtR3O?x?0oeS2gEZutxAk@DCBWOC4)TJF7H{oah|=OT*1V&i!mM!ZTU
z=x*=IeihCJuC6bw_-Nq>t0a5J$B6dK;`UbU-H+xU7r>h9wl&r2C4`}-ejj{@h2w+~
zSq7#e$<(#wg>-dHYL&#LGuG~;gDWW-?7w5iHxM2Zl`Y1YXe)~g{xzl#W2C$xDg4_4
z3Ejeyh(H7(uXbedMWMHd^qqgn@nvfGLWkvxH~{fCgNLF&`m`m^&Z?51ey1$Mra4h`
zc9O$5JO6ma8+VaVo^((I-T15zfU!=3w~~`(|0O4p8j}A#CuZ*G$3LoT)6;9(_JBP{
zA$o$IRHgE)5P0nRh;Iuq-r7J7n_0tI+?U0LlZgJVR~l1@$y3$f5t#}!$z_3B-=)$?
zV_mqCvr;00<@;#>q^tRE&+DYM#61gy6!?yN`@F#*AgAWwC8??zcA@Se1MqzRV_zo%
zs_Uxp-ytzfsy|F~uW!<K-a@~+{i2i}@WKlj@N5)PS2<p1o05zX$8RwTRY52HIe$1)
zUcC*Zh2WUnKh_N@KRL2&d2#{$Nhg3<Miv$dsy$WA_NWZld_n3ejswluMYP?7)KRob
z@d7!iMa^{oEODM!><lxk!rFpj^UfJVNQSauCAL)0L4F!-?!TPEwN=H)RJJg>G5QCG
zHMx`YL<{ry#wED31<(#)V*Juf?>;~UZFs)ElXOmk|B1($?(jRIfvw5fVjeAX71?E+
zFCxm!c_KtZGgeNO$I}@!>Gwh_@U|I-=7*keqbKu#RAtA?rD+H}9}gvxv<pU$FX0|4
zB91hXFkN<h(|D$lFzcj9Jx@Zk2y|ElwW+pw#hrS>9^AO_2@flgW89^1iq2R}II3(e
zwzg*vZV57Z=3RSn*8N<usE9w{{KOyhOzoE|>uWybtGmHtFJk)`!{>5?M_<X6Q<P4Z
zGQ^L}3)z%13-q4ay?(?qO8gnK$)Cn_x%B><uf6qSi`~jeSy6JA8>7De?S?$eMMIpx
zs0uL7zT^6Gn&1CSVKL(OsnFx1#(!tf^dL1{<g{%#;V+TQn4jaDJ%-j(0nt^_@0`KW
zl|&PAVAWt<){yNJdC7%;?&H?-*!UxU(@P=nEPG!EitQ(3M%gWIetKN40o1TzH}jLb
zV2WvR5jnSp?!z7`Z|tMd&%OXTm3+pYyeA?;H+=3H8I(ZQoUd4ddwlQ7X>A9zvGZpU
zt3FCgO~!np8bCFa3uPs(sWO5GK)<@Ug1&YiAOEZbOZfu)Yk#h>%7u3-4!_4a%=}Bt
zT2b(0ZCC*>`G_NwO@vj7cIJ_kH$>gi4onSQ&jpZS_qhA1g=-4Hqm=g3&Y94!HYf>v
zfOVy5;bdh(#k9?}M|Y~K31$3TRbMKZ&7lg@-Mw-i8~OVKg5<JkavZ(h52qxB8IiT0
zN-M#@@ujd>$^`&+a+Ca=@W#%t0fYOu{xvsQ*ix8OYN}+@mhJ@dC@|7;4YTG`lkcD@
zVZq6oC_``dTT`g)gM;V3PaV=XLZ?6qfJ*UOav~&;9$bk-xBopclqG65kfO-(q`VvZ
z#QwVqQL2hnsAiUugU3NQtJ9>u@ev&a@uL$%*sAPhSf<*X-!Tz%wU60|79<a&BuJfd
zvS8VYJnZL2%RTt(niE1&x;){vY9yiw68<W(^6zI}R_;5a(|L<}#;*e|=ekcVp?fxI
z>;oITSj*}4;$GNC>nC?WMV<uuA41`4{4*vGHzJgek??8kTm-J2;gTyy>%-M&nb<d_
zWcm@6WH@KfjCN(o`wp?H>ej+};3DFP@2#E7c_>{1hvhnXs7hFIgo@N}!)!xHBWG&|
zfsz&oJ~^>o>YgV179mOV=~PivnRfVZ5R?RpDj=}cc$#GwwzCHejW<x8b^1rDx4XF2
zyM0nYcZ%Uz5<h~={ws#wE}hSfGxo+Um5?a*f_!@epA>py9>EfO5X$Ocpe-dR?w9sp
z9aFJy>@HF)Am@o2K`rd|Jz@AVHjPyq0A?XFeY$Jpu^85Wuw<ms?Rf591$wuOe5f$#
zdtu=uqgy-X>*wnavmsRd^rRWXpIlmmCXbHxYs6(#b}O&7tPqB)HCC`gjfa^M>YS5L
z(9<Aw9QoyC3)~99l>cl*3}bfH&C>%oy_Yjoe{QG-iSenEoQOvJTEEWs@lhfO9IVVX
ztVf!tFEftlhto{or+%GxBEre@ylloL3NV7BC2ngUmVCb#n?!OK01{`e@jc?C81hEm
z7K5FbtgO+u+2rQ}Cz|?2+;~UxOxK5e2c<2uQ7liz7z3vX2&&RyMO0Di)`>6MgYVRQ
z-{VIUq~&xONo1gQc!|kt0Tv2()SS)W=jU)$enP5CF0DZ$nxtJhx0rGJ2$0$KU0b+@
zHY1-?XyuOG(}qXz{<5cs@()DPAt7;;CB~JJ$L*HMzVXR(Ku)0fA4Ml7@%H)hFR)6`
z+#?$XG`I|Kg-29RZx52b4)!LX?6a077Xk}nom_N!oX7N|kTJHu<x)Nn0n}M;b_!=E
ztLtDPoiTvZL(<_OTC@5W(4(}h|Lm=H`o2ddz}>vSMiJupI@zAjrn_;VNSvo^GrLNf
zhZD}~T{k|Xo6=oFMvjqkL?i_l!iwfpD^an4N|Ve$_7y9r2bKJBH9T_z!o@B|*~3FB
z!(mb+AcIIC>*VT+N~%I;(<wqHO||a?@NOd^{C9{a?qou~+ibu^r@-HLWe0Q(BM+ct
zLLThGu3nJRN5q;rPW;o#r9!e>LRTReQ3d)42E3q$-MJ?fsVH}MNIAX3SzIKHMhlE`
z+F6x9ilP_hu|Q(Z$S)1(c36lyP%tYB2m*6kf$MFf-D@I8UmPBA-_jC4n|`rHUv}!^
zZ@2>ZPoBigpOzN9iJ4s*{KSh-sr`;rquQ<g)~#Xa!5PLGAw}(sl3+r>W5?@hoE$PZ
zczeBiH!Uf?@`#;o3g!9<*ja@y1m79%W|RCbYG{LLBoKp+G@HQvO1yrrnlfx$nj|3f
zWK2`<oT~l(`LYJS=RFM|H)lRy+oldYO|}j3eRwFqF_~IE&nU5=F`a$7V^<`kn1-W-
z{Z?QGC#&U*dq=*LYngXEm|%?wc|m+9Y94Qm+4RRRK5&hq;>~0#M(4N6;$m0;NGZv1
zPB1A7dWa7>)=c@<54}KHlqAgXm!@&oBrq)lLz00j6Uo8_WPUaF$7U`>we0?RiiH<K
zI)gyz5Fp@khgf{q$yn<feb9c<4Di&%*w>P9e!j<spuEgJ;7FxMhIc!hHDYOZCKZ`*
zc1r#_A!9J2lWl8<v}}pR?`B+ydvOK)HtxuSJ}b7ua)u~yTnWRWa+*E*Y^+#v{J+fX
zIuF`$G#I{Oyn4&8q&3rh5(TJIq`(F_RfqIt8wiRx2;(aQ9}QW13N)=_VUHRX?r68h
zt^4rM39!;XM*v@)8X>Y_O~^jDzF=dhUbnlEK)}psU4*gv57-<N6%fB0v#Pz#l*kxG
zhD+zFc?*bq6RQTM<Y(exG_*huu*jw!RbyW9s45#4*@EP?46;W2^HnWOK-&BMil88h
zicE5)JI5<aVC;=w8U?J#*yZy;Y$Vu5nP`mN`=|3d<vI$$Sr6WikyJHaK>?1$U-R=o
z;0HHuPE(GYB8G!qSKu^_7FoLudT8~c{O}evLTchpvMeSwg~YcpPpPVa-^Y^ENk_}3
z&Si8<R~`ztmX%iXkU6g9`a{A(N?JEjILVKe*{R?GWzj^6g_QZTUv@c3RDEa8ye2^8
zPSOh1l91Ybq16QLDCNBLV}>(OdWWuX_X_H0lfck-(|s-xRbL%8;8yc3nykD|f9jBD
zI$PBknrJ6sMaVQtDpE*^`qtH`i|C%ZO0abOyjZ{eoo2dz%d$0~F3nLl)0k4SCXrm@
z`p);|;3nY2XGr3>cQ_2+2n2;uP~gFG!3$aw=VLai*oJpH3*rQ3**R=tWVa7AvNhf?
zwCp)c*GrJ#(3m0Qr%OzNd)1?+gPz?T!;_7lwAgi<f5lFi={m=KDRUP_1rmJ`0J4~H
zZBqq}N+@nx?MsOnai1ZWN<)vO^4ftPNvg#SBCg$0fr<O%onkoQG_=eGX9)vka{?Tj
z1F2Cg((x)Pj(QTcS~B|HlP75wr|rf^f{kA(@JyyGjS0y@`%;J!kfr5<8ME~bWOWzb
zW+d)XBjel69<2|Agy{a2TfWDr_~RMNh-Y>Tm+eJYSq>G`-=Xs<^8R|Ot}qzj@%Pkh
zu^15Yhqr~-e@sgEp4$z0TPChqwmJ{+Iz7tzRe3(~2>rWq+*o#acm_V;X39lCpJ*G!
zVtxPQ5L#H1PjP9SC57?oj`)ed#6Q94Z9WQxc0;9Z#KuPB{&fZx3*z?6D6?%>#o4!m
z%L#;0gx103|6IkqBs)%5!j<-r)clRX{cx;-3o0Zrs<&B0AywjjWr#F~2&d$Dtr-L7
zAe5NdU`N$1Be!b2cCHH8T`kfehb2?Shy&fQVcUeX2y@STfdNmjC*(%Yy5eeck1YV~
z7{03zQl!u>d1@^K{`U?3pglj>#5H&REW{}g<K4B2Xou8L8ZEBm&i*9BS(r>=FtTx)
z5RtEf?h_%th6R?%xpRK^E4k0zT?z|d49JXazYv=G<-zl^m*S&B6FZ6Ics)GqcUGWA
zG<J3W@x#OXSqJ#Yj5$}UXR?LB&ltUGNuJb~zy{6^x^OJPDTiX3G2axIQdY3GCJxfA
zQf8n_4R1Awu$nWu(R*pM$~aK`A)QYEw9nt#vX+vFIf9!^dBMhYGmdPO4mczfL%tA1
z0~*g_?4NG~C$C-rX;O;`BzO#Z4+@o*jXa!!5x`1|sfzUfMkVaykE&)7eCCc|^x#Ij
z`nf@u2D+>X{mO4&XPL^Q%;PkA7A_)Qu(q2*oMUDOc%76O%z(J;&6asF^3N&pri{6X
z*#)Qd@NQBS+j<F+Uw-M=F~p)E8A%T}$G9P)kYp7Bx8y%0lg5lFo{zP=Pa_ZpwTw;f
zSpIxD<m-1<c{x|CB;9vNR2dPTSXoe~5ug@)`#)-)r}q?@G04B$d@?{b>`Fr{oZ3{g
zN6dC%U;JuGMfPfH1Kt-L87}`kN;i$6xTm6xygw%i3_iNN{`>dSuQsBGCsux=nn-Cm
z(bD%wWjwnwPv}*yyvh6{z80z8x)wdcfs`}92qk%>NE1Y-LHHcN6w*~#XZ6@YL`A_v
zy~Bby!hdzdMNN-N>x6SjcR<G_(`Yu_k;uPf-0!&)suFyp^FJ2Uf3vLrLZd`bM3H03
zV1&}R;Z{bkLvz1>y$rJp(;L1)NK9wHQS)zej!dx+@hFexC<r7EBTZeV&AU4ZtMfI#
z-(W=Om!fW~5sKgnkNFux&PY}JHN1_Xk|#e&ysgDMEX6(vwCh;UQonj@GaV(irk}f?
zeF%MK&rrQ$Wf<5SCIZ%<ALrQs*1Gj#aZ>2m&IcZSf{tC;XO)5xU!Nr5Y~in*ma~!M
z18lH`s1({sIAX>e^x1H5y{=Ugc|9A9lOoiyJZd_7Hw{{Ay16FpkOB1If-q9_q+diP
zm67s2Dds5$y1Z&8Ydy1ezX2tWE6yJ$YH0O~RM62`wx}}Q5;=l<M_jDUw%JO%Ad2Ao
z+w89RU%98;-DJnKnEb6uG}_>Q@t=Es&tns+KNj%1dQ&ZCv(q34Y&z?$tLuc53Lz%7
zOh9fT-Ed3GvY}m>`>YX`U@xugCsH$HQh{XE!o!k??e1G;32KlfEa{oPmMDDC`Zs%1
z-OO%Z_w`SnvLU>5y<s-NUhZ(C(ijH?EL4a<fZGqpY<f>qXCf78q5%JJV@eOjr#8Z4
zQrK7<jIawP_^(p#Kb;joRCBBrN6{SHOkmZyd@gM5Q2`wxsR8e6>tb;r7YPWBpk&lN
zSSz$%3a-V>sOSZ{O`yAHmKTs1Rgw@f(R_RPKf^OD|7fUiU%K#@rQs9rr)(bMvOlJ5
z2I7d_#^oXdU|g<dLO~0UD4>IEYz{vd@Z|*xBN1jD7D;q3p*D1*;0q01s3V#+ya}Em
zbi7&oXChb0lYuKk5a|&=4K1&?A^f0vQ*783Jo?xjXXv|al9Livs&^Q{2Zmep6y3R(
zEC~HJlcVFJP#4o_6l>6{g<|wptbjLZ2;Y1P7Z~VUIO@BPm^n?AT{v$0gpL=&g%C2q
z0<J%xB4ksK4c0T|)m(1O83iO7{(p8sA*@9_fw4wzuK<(CH{S=rWK^UFuUM=>8h%{e
zqI8Ep88!}=?ruTs4QgDyTtJGyXR+ffk~cl#L-!0UTpI)ME2iKf>&D^CqpN4jT{7$+
zM`MlFNKd>uxak`@t5o#aQ~@21;mVy|vSQ!38`x)lEG(F_!a);W*_tIrWp*nk0x9g+
zct>r`LW8<C7zVtUwsA(xlvIs!exIg5&>fw=K@0O$=L&8?Wwsec!jl-g%I`!8uLhP0
z((u&$TfAWnmN>S7{ngDecp0v+*gwGMpuT@!_b_{(+N)aCx7oAdP9n{CT#M`K*~%A(
z8r<;nYy8TOF5m<NuBywIqN``qUADpKUSPNha9zQ|0JFK4-GIAjqH#g<2#j;-jIw)E
z#_GC-Dyem!nvG1C<mm&^d7n~=e%4OVw1P%P`A%<A;v}InP8HhfL;>5FA1kMmf9tQk
z#H^_9i^p9`ko1^fnt%f%wmZ2xmb=EK?NZc?VJrX@wHH4hD%i0W7HL9`;xDW0)(_Ys
zSuHDTl9#D8e+x1L)mIZ%1_0ll#VV~Vl3_YD9f6mPhS`*k?Pf)OJ!urKoHqGp!G%_m
z7*|g3{c&-*j~y4Ml<#LU6(ABmM>UsokDTek%4=%fB^cc5%G*2=VjnPc#hW23G&H<_
z#pn)0ZOZxD$QbF~5^p3)x4%dMq}A5Ne6?22B!5uG;?JybKgyz!+bBOeQ6hpR!@xMg
z3F}Ef&bhQNKdfPhG;1ah=ACf=87?h*PE_m{B7yNYzU^e2J|bg<W}Z={>?~Y?pk~E>
zCdLHB%D{z>^w2Dr>oK<H?m$@ct#GpK9ii`scz7G=gSK~|;|K69kWYal5c)$r9p3d5
zkVRn~e`I=sQp6Yx+K;~=pzHTxZhXBj;J&aBPI$FOLe1N?BD&>$qR7v#UxHuYg$TqH
z5Kuk8ho=a#XIn4BI7(matAHC7=cAZ{a^f2JCUmq(7f~yT<1VR0mfZ&n4w-!XYts3@
zgZ_&#M<vfrrc25F+KgARvzZVl$G8KLZ#c-z1R)HSHg6$P>~(+kw_``mJb9ahV@m&Q
z%Ei$<tvKJ}8&G@r+h4*YD0uqW#iDR)G)-v&sMl41_nrmrBqr{)GoY~rm?SKyTWFzZ
zhw?QKn@q(&V)~okle}e$O|os6UnIi<pm3MO;$Cjs%l=rS&2x8(2X8tv`{6$Bc`c;Q
zx32P&!h-sP0dr@x!;*kr#s;y#trry=<)!;F?fife|KcundD=s^tiwgY?nj_nyL2^6
zG-8$<ZeOGS>uQ&wq0Y3a&1HZiI2Pb@S$Cfr^M@W`O@#)$jT+RIGH)ka`i<;XK=y?1
zGjs3TY1wa<r1JQh<2BYm&61p`RSMvlkyEdXvRPCXQ;g*%EjsQ!we@zsOiUW~6AgAz
zbc-fB!#51LH1u%<y1Jj=@ji9as}U>=xZSCLB`cEqW7eu!w7qn{w2BtBERKU-=-9+n
z=k!r@ik=eEEOX(%xT`?_Q_JR?j>D<u9~i6U6Cfm|HZ0SxKA1<1>w^=>gqEP_uQ(de
z&z)=@=No6)DZ4<^9Tk<9=8lSNpqhS+9TgDb%c8UB{q8&<DJ{~DU%g^kyKL#?YZ~9S
zAgj^_3uK>wh;Vj%{p<&OCQ`!WYrnn~Z`;C4C(7fkp3TNg=DTGw9-JG#cJ|bH9B#YP
z;~?P$K_f**CWzknzj=OvcTC>8c;Ack**ObGQJR~wzk}fn509DE`DdHOWOh3f?q{;>
zoke+GaChPRgVvRgL9t8Ue}JCMsMtQ|(8*u<+odW=LXMVD_8w$tM(hzJ3wI|kx%$48
zU?~4~v*hBdhd^D`sR3+1$@ho;&TEFE%U<PvX^IZ#=0#o8G95E;T~Da+P-M?_)ja!#
zg_pZ$7Izx<K_6Og1_A8gl8ZKl&N;86DU3s0&s0?i0!vG5By-RhdHUj$oq*D!=0iX-
z-KrF-^E>g_7cSNrN#ZA{@@_VpZn{(@80oYd!;}WcFeyn>)zl&J_FNYpaL9UH-4s>#
zXQt?ESoN0CzCNBAQc@A;fKBuN?@r!pl1w20C%J4kT=^<iE<Wy_l7C=^FQp%W0lQ(8
zYmZ!qDC6Pfz#{=rWkjDWgIgRv)?%*#YaHk5BgFvA{=$$Z*D3`S>yHE7jA^-`tX;O9
zT^c^2pjbc>l%ihbhRKtHp&YcBn{?q3mKt!b_FhM5kX*Xqjc1&V5}TM)*E|7ho^X{l
zWt<4DIF}6T+9X*|?Uix^lNC@SF5iRhy%<OvQ$WB~q}@22(1ZHBLf5!x*0ic2sC-U7
z)VLHQm_iMjM@HG5-IQ^kPjv1YTDzW=V!$>jhTE9_o`Q=u<D07hUHgrm50T2Ou}il0
zk%$<=aA2nVT|<dF#}|6!nGG12Rf>F!k`NgkI*DiBUvs{Jp@C-73_3;qwmwbSt5q_z
zk-Nvo4Td0z%yjo!(L%`muV6|)h79!ayA^~Mer!icAY>@pz51xo5`daVw6b)L0~%I~
z2_^cpfq8UA6i)fdD)DXvd`{v8_|@~)+gey)l{r4Wd~pXwxfSaSb<|?YU?;hTRS^><
zl^JBwUzNx<m0T(2nSD65u_3@%={&hLa*cEET?KxAXCv-H2qM6_sYKbSRj?vNS{cEA
z6Z4-v%xHPv2Z<W+;cYBaZZ0mzx5Oxr4|e#RV0;#WO2h>`^p-wpIn<Xmv|8E$;G}o!
zN3t8GF~N7Rb1!5`va-*2#%-5|IdR51tR48rJ4{OOx>hFAUyV63jXv5Td5x}fueB^&
zBEd-(-}#&7LsEMV#4+GBr2D-q#aao`!!E$a>}pZM_s(jx;9n$2_(n<j*$_9LI7Uh>
z$bfnx3tFkZ)@zPJ3vJ}~lIh3)Bk3xG+U&Y*u@XF3i#x@=xCeK4C{V1p6)O(G-QC@-
zxVwi!ad(Ql+s*sk$-m6x$z-x+owe85YduiKG5w3A7F%&3D`_Ln%KD|INlY6#G#=yp
zXauh`h0qp$UrFbU=pp=`Hmzj*wvCyAC)Fl6*t&5nWvzc0p9+RokTf0DZNA$)FNk>!
zhZ4xc!?2CD{YsiF4U5$<!7R}vTjG|x$&#C@fb24P;2{`_ng^5SKMtbhu*48|+L3LI
zs8>Okr_+&NBn`%<6kvxy%``+=q^b`Z)oTT16`$6WX?}0lmI!qq>(T#L1jA+kkA#W#
zP0CPHvXqb#$Hc+IWn?HuSubODq7`n*B6ziP@mUGEG<5_Urv1tc&sh3`UDIUfSjsw5
zBQMwsJ$FO1YeSDOh8pK@>zK>R9aBi<>9oQ;)P0Rd%Wy~A7_id%O^`~O|LzFg`xiBp
z#|pIFK+}Vnv;1Lf>mQTAXKGlFkivhRk`SlIt3^z%e&$mi)7dHegkpxZFUO)0(0*|J
zHiWg2>YdZ=w%s7W&ola25<~b;58iO2gZ^`z(#uM8(9RM+1w~^R($A=%`Is`P6ui3}
zN_!<$*O;qP*MT4X&~*$)vL*}TeASZ|?vKf`NzMD8bjrC$dAL;KV}B^jyWmZjd02Vj
zP*a7?cL+9vtEjqcIhs`{Lrt!-+pE+&9MgVYF#QN3PvPcjt&bDRAu7_gZ!Bx#?`UqB
z_(85jy|bhH=_=SS1}eL{a`6B8(8U3Us(bKj>*jO6rqV2^nGsN6bw*ng52#?nUrI!V
zeFy{!S=RP+uGK(|TLyw4?c!}w;%rC4iqnr!Mk7kGr(G+#rK3r-aS3L#Z|q}@VJe~#
zYtB})&@<|M7D;9d^lEPMjL{o*ncs*miO#r5Q{xcGBJe-Uz@wD33Diw#>nR$yGlV##
zF!@kQgCmtJ#Tjz0<|eK`%RmXFV{0^mTjt~<+E3nz@s=7Qm360xN{PrbLL!4Qh%*)h
z&OZ~f^py0QnaSOq9Kd8@9=^6gyF#5V_BN#l{Qub%%mmUEaE=mvc>+r3<o&0~8^(b}
zKZw3N;;ruD{+L;@lTAotdLMz@1yv%${&&MH1|fjTyi22iSn6j&>PF`aSCK?cytA{^
zw2}5P-Fs8A?O?CMnxKD=mfqfsV1he&ZBZXB;YNKkBJmJjV(bdIkgK?axrIa(@Nt#V
z<9YuNA~}3tp)bq*$EDlSaj5B1qqQ!|OcNoh$FPZj+CcI`hMN6rW+TxTb_snm%tP>_
zX4J3Q&cjrJZv@oS>DRX!ka?}g_sl0u8d*wc5mv<c`;PwHnjt-|M{dpQW%fe5VSrQV
zn(<O1XV0;3xa;ni3dIb@EK_lPWYOxhj}A#>yeoSaG>X8xJ`eWf&Z>taD$G-!-Lf(G
zbB)grXEVItbUMYMjpgbOYV@{0omQdhGlhmW-Q~N*xo{xk_}#J4Mf0TNLJ5<7d%2<K
zJ<$ab>ZSAtDp4#dAej^uCxujI*rSL_FXpf`0iF359BkyM{eCcoBpXE;xmhqeJQ9!$
z28gjQC=hbL{CswFl_XRnY<Dh5dN*2GSv~=MG5%e1lTdeA=o~(AK4bH&>3p-s{CE7u
z)Eo%JV!}!U0DDUHsp6{)syw?lFOa4RdaD*5vU1@hJlhm&qd?QzQpTt|eH;C%()BZ}
z6HfEPbmM{K*8OZH<|Q%_@kv{ut9X&lg=VeSd<AUBJBf{3sYP$G*nf$CC+h2-!~Q87
z{JoPZiKmL!V5{p;kn{jkw}?{o4_BeHkz7V_nF^;U6lspFlF(!=bjG#L&aY7nKED0Z
zcv+bXV-h*=d)&lLUA0JVE#$<*GlpVY#M!h>fe9JUthw!VuHYh$(W9E1Yqkobof-oX
zeb{6&kVv*z+E!FSV%B9BX;5nOKHL=iC%`1k91k5ogUx^S+aUoBjPo_q{6g^T5#}}G
za^x`YArDP7+$<bL1MxSVw5811-LHYm1_-ODSDDwHE|HCi^I8(x2Mh$eLbSL=z*#-E
zX`!Gxp7!8|ip7@@qXkD-1PkWv3D_1Ki<G*hds-V(a=Y8lxK0F^LNTb>qUHT7Cp|FK
zU!I#&Pu${;P(eB3lEN@{#1;#6k8TdGxF^VvBtMZ6J`jm`Y5&MY1faF^YLqtw{}oRE
z5e8zb^r2$cBCfZAOgEJOCdlTIWbfiVV%7q9#0tvkO^aB3@iZDHqY%GfWao)cE^*l7
z&1?lvcAws}n7S}4lJ|!sxE@0(;ZUZo5DqyWXM}^HO=LSl2MQ`x;WOWy3v2FghLCMq
z$Gwm@0y^P=)@mgaSCbdw!k2TZBk5P@R!WJZ2EX8tvTWB+w6%Ml&<E&spxA{vi-`mP
zfKH$CqRDR^!9syRH|72HgX3QXO1rCgS{;F$DFV~>TICzl<l@BQaQFhz%2MUdRd+ts
zgD$@uxW%`I*s)a|1C(IDfVbgu066otst7?i^A}@dxQ6S_A&4&du!XTU2OG>_Ejl~u
zxDJpKmb3;MUla4W3>?PBW2adLKvz^eKj4&*Di?Psqsx1zKG(328=l}MBGT>*DIpy>
zHQI{*2}4qr1A76fyuLcgX5<H9W6$Lf&W8q-tUa3%Zm8wG+3Jq+O#biW*+g18%cD?{
zF$IkcSK>=?1OZ|1RFpu@bzQ^Fxw-L<lH?X1{hh}{%1pb-nd)dZ6_`BL4B44y!BDxM
zJ=Yxk&v;4m4lVPNup8g_raU{%DzB+mWu=?8obM1+k$2&~LN;27v5I!9al&E4uwYbw
zh^VFt6%h)rLgE5{CdNg%5pUHZ6;a=6Mxr;r$8n#XE7QSJ(?#~e=;*|2kwjGSTrJ3L
zX^6{?tyHTeLdmsGsRFjy06%4htC>HcpmZ5%l+)gjW3LF5#QzeX3BB{0uWCenrt@$$
zxTFI7vHEDzz9}+B07)hrQvbCrcxDC{-4}_MRFSa<F}f&5bTgEEEfryqC?T<bb0sVc
z!GSfYqB$h3>&J!?=2VI#ovJ5@F!s&HsbT38l9PmA&`EJ=xB9jF$fy!w>LT4TXOYDe
zfV6ySoZ)>A+p~<FXQ|)ZZbWF#I<S_M)sg1H!U22euURW(9Msl_sVZAJdy{|e!|vn`
zXuxD;K`XlYt7w_T(A?pACxPf!OGj`zi1j>NS#S)bMc8n&QO>F)0z`;|P5}~1bKkGE
z*b3fBnO{^2pNZI?tR!3wdd#~cIJ92h48oN>ttoG@M>gq9F9d3x>53-111Gy8Oh(Mh
zF?b0r437ThlEO`QTtBj+q+Sa51sPsFe<sN24wmsHwwMP}h_=Nk#V3b2>=QM)6DPdU
zLp0$vR)cEA;gvo-MN{qj^xijD(L7EB2(#>Y=s$MZXN>z{)huq5<7v9junb5TihYmW
zTCiK?qHc-X(0s%!eh`8%Z%wc-3T=w~0H2VV685o>1(GX5{7=XhTT)0?8^&xqKb@r0
z?2k3qE|G5AEMVtLD`8a>jBMgNh$UtYj-mrKyvI(Ly@YFyqa4cFAXVQZxNG+a7q^)*
zTlHU~KaukRmSCErQL~3ebz*J773)#$?kp!kBAG@3N)-Q}R5sxHL<o>!Qi;?%UK6PH
z*Nud6av05ghc8c^JJt`jt|0AAvTXa?mcsKb)Rus0gR&HH+PvLaFFt)cSn;R1Y<>7<
zMB<m}t>~IE5&Cq|6OE*v+6lUes`6YhnTVxQi0><<Z?s!mgqQUtk+62x0EQOx<?9~G
ztcx^9=wrfg_I4Nq#^+@-jW|YFHGO#H`h{g`{!tD3{sMF7;opiBmP<P~ByuDA%1d|8
zY?jHKT^bBwh=1Xubca<^Y^D|DVq%uOi^nZM3yO2IV|W(~x1>A!{dXb6(0j$`IHDI9
zq{I2L!Ru&@!F^F5l%e&^_P2WrQY5;RulGPLH*{T!Xs)FKH=th+vHR~Wm<siwFN~7*
zP@$fC<{p-smy<(6lVIIIzxb2YHv!ksiZvlsXnvVgQO<@ZaHw_sJYm&++#?ZYjaa^+
zxVB11!>G$pu^#%m(kK|iB5$c<c*fyb+pwobnyr>fjojepOa~j3%mJu#Q{8;hq&~f1
zZ8S<xx*;lXN@{!&Fh``G7)JBZakA~4+M8n@f5kjVnYX0I3@J(P=&qGzLVhrOpZ#o4
zr{${+1m*s|(L}jid#@(7xQSrX8n(uP0A(hZ_P3<AiGSmoaF}bO>qw{kOA(aZOFeW5
zcR);{=m}GE<~i{8C@DVvy^M4qtWN>pq)}Y6;;-M3wuKB%V?lV++aOl!gKeG9RNQ^B
z*j14I?kwlu1wS_WR=_y3dZR+Yb=nTpBOe_AdHb0A=~~Rm=l-Fh5VG4etF(+2j=(<_
z#)P-qRSrB0*Hm(s1bhETjq1<c`xItHb0k~hXsRc0Yb%UAS2Z;dOCOZT0}tpaenvWr
z$=~rCwYy*0oIAK8=>?3w*Dm`K4-i1A-20}hb5Gd!F1m+Xg+TKDw7s|VPL8<bC2?CQ
zWW{IYXr59?u0c*ON^Awb!3}bNII^3akqffWkC3XJF_e~VG=W0`iW`$8_De_83mgz}
zhuJtpe`w!Voc9T_<w}gyo$?5v6SB!jR>7Jhp%0ZFO_A?%1D_1BzrF{C>w5zn1Z^()
z_BP)&;`WZal*n`ew^Ygx*2P|kYF!~RzPK5_r1(NHvOZyJF3NY$ZFi<-yicT#gAA!B
z_Z4Q;AmR@oAgo2Q<Gz6FjY?7Ni&?<_2DDJXl5(H_Mf&2-<NiRoi1cOgvpU?Ftf+fE
z+oacwsd)(1cGVAfOte$}^5$~nW?!W66)!h_o<+vBCC9XKap0nQtIb*h*0<Z;atEB9
zlV}(^bg9FM{kNC4<|aKE!!a*fOXIA9pUIlQhD`L<ulgk!CD2x<wNTAUkFvl0arh|9
zHX%C*2oIW$#sU?2IPTLTCVcv995wi}=a*15?DzS{^(zVUosT8ye={v71#e*1Bv-JB
z|Dc=HusT6PE>?#x@W=<dXbRUg`0q{#_hUf?;$R%(B2BMQhu9(nkFL(C#Z$6EvhYCL
zr2Om2k41H}{l`TW>kPw`%Hbk(=0`}XfbXYCQ>vjW)eX2RE=QTpKlW&lT(9-OdFxH`
z&x*D4anVj=-;YJ=23lZ-s!eP@Qxj%1TyHbCqhz>Z(&E4*V}(%1UebKo(vgv22s<32
z+sQA~h)A`Z<q??M-nPOh4G3WXJsOMAivq0*+ZuufX>e5muw|`$y2HFu45hXoTNFZ~
zh-qF)YzV1!e^B76w7~=MEa+^*mL*l_z#_-Tr|Y!NB&e!=|9S;7UK7E>F|yKp#tCif
z&$(Wd;TGBtWa;L>Q@OHhP1>s1=fZWI{Et>7_yUL!t=PqF1J=)ij#OA+K0j1Lk&#DR
zE-0GW$<|&*JNaNy{r$>*OaE|O{MHiu!_UU^Hc77Tj$V}nR9Zl0r<9HCU9W16*0aaM
z-M7DSA3oSlg;V$ThIQmeqcCS&18i7u7(9l?Y-MOCg%XkEN2TqtYi&=ol=q&LxC|7)
z{XpO`X&b6u$LV<O>30csVo?c01YR_X%c8C$TFoZ!w01(crl+VJu~M;6+r&%|6@W8F
zU8)uU&b*fuUjl`4y`j^4c{J)=g=@8c+(YDXMk_)0OI>!}T<`4t<zjeAUoC(k4bH5o
z-lGF@xEGm+GqG$>NVQyHReODA0GT?V&kBIfzJq*7Ypg98oa(($^s*~(5{H3LJgOv>
z^VmG?kqy?1FNoh@EFs1b+%Qpq>?IYQf0_N8xyV0nZa>*^Y^orim#|#S*%jCKBGX@n
zI~J>EJ|DEX%nNT+uo;LA=Pch}!;=cj0|t?VFqJ{TiVxIOy3*MvM4LaIlM^Nn`D;25
z245A4T)PBTPIyetN2*vp!~OwbjuP7cRi>xdGn5YEEG#Z84zv{$leNaj<sH(2@7i@M
z@sGy|fKqnic-Lun0)x{fhx;a7tq#%W%sB_o<DVa2tx2!$o+yHtpbaT!DOq_{q!RW!
z?!|D7fWKpMpYAuE)(Ou}>bFs;np&Q->-{IrNDcvR@6^AO_=WBdfjk#1?~18FKu`tb
z8q&SgX%fievv@(5>!~Ld7Ai77O(BW=`bSQCxIgpfZ@0Y+)%Ze^JbTq2$mBfy+|J`y
z+@x8_@x$gdEN-QplSbb^p8~(zTQG;iZBwmYKQ_&?ofP5d3A|U1(@w$$wMtrQBHcQ|
zizZe7ijn0yP|N1{Tk;b>EE_c5=~*EdF5Tz1(?AUN`-L;D_#NFfUBJ;jy5bm4vQ_DN
zU6xi@p0+47;lkf@QAieG)}yX{fRVCcCP+$g0iTT(pHi$Oj0OHqMOm0EohR**u)2q5
zF=8XBaQY2x-GEfEcE&Y~N(HlsQ=4(v>e`KywF#o4JH981VM43~nGh|y3VyAVQqeuj
zm<v^I0B}aE=96(Oof}`L)ID-z=7-Ies9a9DCv6M%Y8*~`XL?}ZdlTcnQqeyijx|)L
z_c(pjpQ_lT?Hsc%xkFK*t8Y3PEb2m?t5)C3bDLIm#ufjZ^rB;WLB#$7g@(|2O>cJj
zsoD!$tt-av1?}DYCZT1U)8>&&;xd?qYP`9}`?31Y*DZ>~s9|I1lYJl|W&adKV2W~M
zw|l?K!30Iqi(lW%hQnSv55Guh;K+qs&)q_4Y{N({!Zh*>THLf2&}l3oT+e7yBePYc
z>yGr-xyUsPq$7qy4Y0N)+9~t$YR<aj8^o~Dvt%8*iC}s`CAwq(=&A+Ic9tkQc{zY$
z%HdD;6gH#<klcJ0PgS7Z-_g~Q<F;Rt&;wI~Pk+L;D?VmNsNx$H{hMV?W#ted1l`d!
zE&ty4HamGA+9>UzXGmfJ1iOQ1M>{$2H4_5^h}DgnAP6hojtzt?%3m6{f_2OoMV9wF
zSS1a!0!U8AiI7G&Qgwe*a~LXVk{_M9xf6(#$J0v#TZhauow|Q|2FsA9L|1+2Fa_Rz
z4R%Qma*Qdsg*0vOBcc?LjB6Ol)5xbPrE|wBAX+m;&+>UK>KO}?I{MU(rOh*1Wkfr6
zkF>CAo7o`4mO&qvk9~GVT~t&^JoNI<KS5wUZ6}7*BjEk%*1k3!?J+P2<FRiw%z(66
z94I|%v3yNb<;L?jeMc|i;6aM?Ew*{#GhNkQP4;77b+cP{TzWv!PZ2w`C^A#N^0<G`
z+64cOb<a2M&JpPYq{9GA);O*rmfZ4#r1Nz=WBG-Q_tnL*%__7)V}Sh4GpxQW$|<?X
zCD}w2k?$vdeT=c6&dKQK$~2uzS03!wpn9yn;-3)}JQk_p(ZcN5fajnk^DHXVmbUqw
zEC#s_7t1(hhUm$k<xY1}aG+o8dvTV3#Qd-Vq!9#``1)$)xn)>J3)ouWj4F+7hB65=
zX&Uf@7-$pXUH`0O=RJ_+feVW%*3S+1t=cA9r#ThpF|KB2mjrDsly~({Twc$~5f0j|
z2Xr~KDmEGujx_;WG;zDbr=9IE-0*Bsf2PR#NkxNMV7L>8u*BiOW|Sv8TVx_Z(Bf_K
zq3i3SnZEA_8PkiIFZc|zqVV{+4$OmTMf4&&y*;f&dR^y%BC#Wzk9s4T8z)@s?y!00
zPyn)M)*XGUMYZ61u;Pg}_D@da5I1H8buj2=Z;k$iqR9(Ut1FBH1sZ~RIcviOopAci
z6p9-?NuNc&3XXn$=NXw-u+<_fQQk_ybV|>EfA3k6uz6yMeWLxBuzE?b+I-x0A-izG
z?a&kvdkufvy|2-d--{+xOaU6fS3mt+yLA3tlJtATg8vMIl0=_tx5^f(y$g$HT`+PB
zk1jbU!X(+g(W)`Coimexg}S+E(?z+Hk&Tn88Y`{ZvS^g_uS*Hq+hT6tU7;*ZDr_$=
zHgX)A2XQjhbg{-SF2vh@;|0ti*0#vju8h}fwD?`Eg%3V`+uE`rKd;$}8o3|xZAT7L
zW?(AP?u)I1F*zJxgYTv!UG@_`f<(BLpa|)}-P=lSv?Y%3)K4_d(XmC*ToxM2slR`~
zFCYy@^;uhYY8z_MK?v!~lr7Pz6wLGaq^yXSjr(M|c9&bG7FQR0R~Wae$7;D{v$>WF
zfj{%Xu6P`T3$0vdn8$w5{WDH{tK1E@r<>*M*Jx3H6vIUhIzT^_P3P=4Lko*BA9kmn
z5lG2y*a9zh)i~jYHOUDvu+dqEzE7^N)TuB(I6}8QQ=ik5ukwb_RbhB8fj{6xV;v9S
zwGT;JteuYgK~$H=0N#c_{H0JFbG=7BOJyPg&S>{$U%qlgEgLK%tqKFkW3T3&EZqL8
zJ=j$V3ZchpaQ5rZ=I5D2UW@YS>SG{z{sa18IVq!a&4mRqu*Nv>wUx?_GR<RT+V<+t
zt~WTXX?=V+Xz5o;G}n7S@bpjIhDnJ&qmc!|fO0NG@m3ygAD^F%v9V#nciHjvd!9!5
zfeC+Y<c-J!jyzdDIOOk(vB$a#_hY&lIC*Qa@~l*;r@`*Z&t(&mi-Re}ZLk#K4A0Kk
z7e|$J)s;TGY&J0gDLzi$6#aFDLFC~cSb}-}tnkx<haVbqwd0#Z0M3wEn%E~tE&)JI
zvkoj~DW!BCX1;%e!HHykBcW&a$chl$*=w6C&-uX*t=c`QH?bv2cqK~H<76uo@~_eG
zWjPl<C4kxro`!#~1VQWbSA)F6x<Wm?QiWepEK?>Dc{+k5?PS{qLw(qawIag`C6PyS
zrDbe;7k4AaGnFmVMM3=1u@o?fdz3GcIYt4etp5wf{|={(fff&U+aBv@%vUumof4L4
zEE7cLTy{YFgmQgtxf<!Pq-xcS^Y;^5JJbzb9w{*?uiH(N-~HfP)x$&xJF~OT`7&b1
zUjuOpXhqyBN-KcZOBBe-;FnYgc^P|La5s6SFJM2oyd#R6;U*HZlUqM!x{8_VoS1PJ
z;g5VA6^pU2h(5ukOQTDZBUnjRMCr&Ev)ws#=Rmg5A;I|Z5p$AwHkObaJO0$0;v8}Q
znyr=d2VL2*!%9!~jL!No)8+EA#(%<-K$!^aC_40o<@@`m2RwQl>UfbSR-jxol{nUg
zG7<pM%#L+%o!<n6tWHLX#4_F~LSI+K_o(O)t%nm1`jPm9LLw9hYu&&!ntm_&i2)O<
z{0pa`f~6WV|5cG(4jGRK!>E>!b9j_!PL&rnDfRYu%0#ngF54GKjzFIq166?Z$B98(
zcD>qUj2}l}%~;^-@Mu9NSv+PCJwV;hm4KRxV+$3{`(AeI8I6vr4wdIGPv6hQ?d>0N
z>C2vn-)O=;oXn%o4cZ6Drg*2bDQ2FqeKgL{K#=@xVgFSw+$T(bX<)rZSx31~ODU9a
zRN|V)bowYhu^+1r27KROar!8|C8P_n!5F`_$lJaf<3j*x#CV-kw+I*Jh>sjjsv29U
zDUAtAFET82BAB6I`jE_$+i9TL`DcPg;PYa3RsoeP8?JlLp_}+;H+HS}$87_+=i3tq
z4&Gp)h*=s2Rd*T+Rf<_maAsBVB{@fv05q0Gs8_1ZvP_srXC^~t15?vVd%aG^7e4=G
z){?Z2REWlbJ!X`pEzakQn;qcWJ#vql#fcn?d@LR8ZRu|hWN`CX#g@OgxcG6C{v~yj
zB(E^HS}Z$5Xkrn^%kz?Q{gC-8M#w9z;gpxp7?ckyYe83;r&Wj=9y#96Y$)iS-caQc
zaPfv64iZra(Z_drq&fJuZ)%b*3B;BebmB54KXvx04eq~OoiL7uTE_GdzJ?U{5eyR$
zcd@z!K$%jhKn<VUz6_%3MjrKRB>$pDeS)g%`6t-VA;+0N<elqzC-Zb8Bx{Q(mFe)i
z8y%vX+fayVlvFT41bh^lFscAqYwhu2#uB*d$Tp~Q#O~>$>Md-pX}%uw{cnh`ID>p@
znAOidu(H+nDz^D}z5XPX6e!2@mw{c8vxIjgyZ!tq3tC_MTBh!kSy+kZQlpN){sbql
zb6acgqef(=Xn7Mf;>3T3nxUS|<|*v$!!H=?i&|-7N`sd2fA2^Ie07A_KG~e&=ChBi
zGjTx`xD!p-MWhcd6uWEjx#-p>Xa}-narKH=0t&h4>SHL~wyhO6(^<w@y^8@eMZ2y5
z>O^MWAKx<W;a(jj(?2K9tD=bU-KJuE(xi*pJITYRdfs_;72eG3H69ro2f*t#F$gw`
zjPdat)1cF{FdPRbb({M+2Winq{EHLp%245xGe=oJHZ)T%1gknvR_!=+u)4&j-@RpH
zTt6j(uqsk_8cjC6-t%e^%JBcrH2?a|cL41YvU2I4z;RyyIK$CX0<mwCl7voL^@&x`
zPD-sw9*10g&EUq91^r+CRW-1aG_ani=^CE?nN*#re_7Nw#DERRrPv`cW6?z;#Et@y
zm6wE9Y<mjef423(AX^=}uZ^31&Rt>LC4!*!p!Vwbjvh|NpQ7=k1f1^ZcdK%I>6(4q
zk6+H%%!K2H<sL{r=)HaEIsqz4f8w#Ia7ZQHo*1mM-U!)Q!-quEV<_y%fOz%FXxzFm
zyps~eN4P*-j(7BsJMZuJ%s%6u-PKu2TFrq+c=NS`o{53)&G*kOXkKLv#@B7mmbX6b
z(983Roclc5P55bE4K}T1CWWy8_^F@K(+rY~g$DaOT&KBBgXe~EX#o?7L{$nL#GHrl
zP~3IUjN2>E+FKC$|BzQ!8jH!p@{V?rY#VX>vqyLP0AeRDG?+8tWD*WbzfHpL>65tV
zC?a+&=zXV`<<UL=v-{>YRtTIB=lnF}{T6cn9{Sll+6GIH^hWC;w|invCFQYY^s|MM
zLkF7#Lx&K@7qAh1`IcV|iC5%C_Z`f+OUlFEbqzZyxBIWL6vW;6i~c0JN;68$1~$WN
z;X!AP5Z>6Y)7<!%{6yWJr*J-}+k{Zog&lj2SKazA687)J$nk*dKn)0nW-I%VQ|bJ+
zbHi|2lpW`TE01Oartf>_`3w>^6qG1(nL|r_7AtuJHMB_}GNfovN<y=oV^SwOjn91p
z(eC&$730_V%d1;=KQtvxpcVd0m4exUWZ9$J=cyeBD*DZcYZ@pUG(x#kc1zpa7ElM(
zpGuT2Yp3iW0x-CL_3;g_U4-Rd9W75Pb&B@sSd7Zc*rB3JRo=h}JLLd<+>j-#na+aa
zErM`3<1bpHike>T*8xZes6%FnT-42!k>hM!77OzI!yh^whn9^7XjxLN=LPfJZPOf8
zt`_|*3xEBLnKrIvre=b`1n}@|v0#w{B>Y?uhR^|t@Z_|oe5$j`RNCC2&A;oUNmR%D
zd9~E9-zScbKWk5gWZFzLq`K-%J_)P~h%0Ek`iK0aUH>AEIi8xpd9HQh&>{S=nLP8e
z<xPI9Azpw%M~`&IX6S1M5{=@<J5oEEHe)MOEBm*t7YF}?5)#Vzc2XijYv|lMY40+2
za5`3+4z^5NZn)5_t|pI>)DwV~-=8&;K}rt}Ae5CKOnyfO{|U8aAZ&VDxfBWenumGB
z+Q+=3-IEq0;_CMqdPZwM`CwhWdBWE+8&VOfiCbI$dV5%7h+?<qiM`()!<pjk9;I_d
z{Wp?6BCZ~p#KT>a9TLUBA_E7nq4Q)nBnvB!NS^+d;{0mG-~K>+e%t2SbX9)?&cAQc
zFDB|}42iPQRw)W49y@JR&$K03{+)`o`lQbXy~DwKoKTa!V{;7*Nhq6S=+~tF+sfo&
ze6(9Eq0YZ*HuDUREdWXdhGTo>L&paF{w*@EMX~q4<X(&(v9yK-g-$#hRz;p5mJFe3
z5rkfLcRWf;#QC^X_iNmAvEgZ@kPV-+n7VlMN2rEy{e<~K)Hg^pE-#2mJv@j1jWMSA
z-~n4ICzsfUrNJJ7P1x-PpTvIhvglFG%lT3a8oAvrj|TRS6!1{uk!2!lGp$U_%km8e
zdcd4@EprBZOBa+qL_K(_&?mWduW3f*fe#S(?B6Uah2-!&QI!z<^*ZdK)9tM?lZO@M
zmw$jVGh550!%kegP{xK8vQ;ZiPnH;N4!nL`+7Vddg?hYZuGiT<hnd`>s{(xX7Zdae
zZ(I3}E=BD<)Qmrs`AJ*)-1N{vn#><pPaL!V5#<tp$@x%j@=gv0MewDaZfE9IV_;XH
z85V{h7M(G-{@t1rY}ep+y-rNB8PKbU_}!nXi8md+jY#tKdsOdwP;)BKeQJd1U@T50
z-7J#WXf3u<Af(Yd@{~>E-2>!(!ll<CSojBAKUBADfuF(IHmH&41xD<1^XE|(_lLSz
z$?X;yx24sx<0Yg7hj<&VB3U|SJ3f*W=}3)#A)`Ctj699Q{Y)<rZlrDs$P1k%XLpX9
zsfLBobuA52$}<gUG2mULggqt-;>;|aa;)SU=g2bYSZVKj4n#<dZ8>_quibLk<&uh6
zsmQsmG-Z{4TqpGrso^(w?UL!{H|H67NXzkzb3Nz<w@AbL|M}_yqNz+s%j`>T|0b*)
zPRi?*=)C3<K3L&(`A3DK>hUZ|ZZ=>uPDa-EYc8-JQXrU^u-Y}Cp<Z4mb)bctAEoF6
zHQ%6PQ7-O|rv28NhJop{UI8?~(DMN^d>cw44LHfQ@<qV!8nKNT)Q9ph(7U)eTG`j8
zrW&x!H<q!4dz<7&j(hw(&XWo07zk!XUBBPlu%?MMd@_JrF6>KtxH@eaZ*!gB7SQqF
zJm#X4g}aXco~;lsCr=A4+0hl-M(o*#xFrsuX^-&(sOZUtbda}M=F7UJ9uzc{Zmam9
zD6sZs$Nf;!7M$i4Dg0X0m`PeW!@w?SrdWy-H!Cm2SzJJ1q3b*`gcdMHs)Q`6T(uE~
zg}$KsHSm}vp$*-m-uc5Zkqhzq1y(A$HBp7z!^sI-v<5jHY-r)W(adfc1O}a&Ns-$k
z6&X9&O!16y{Ls%QJMN#KIq>r3##r%d2``Y_jgjGxDm&o<?_8#&oJ=!b!&j18)-zA0
zI2@uf7bvB&y;LSfRMu=6vJ#t+<hFJBgp)=mqb}VoeTa)+#0kj#1pXb6>YDmsJGVSB
z7^R2EJ=cVVd$BreyuZ!2FyyWI7c+=6aUN)`v<#i<MbDMEmpeNgG@Wu-@tJa2U7XAs
z7Z)&VNeTXvkhMe$YMg~TuXu2`jvm%+facETc;nnITPra<EVWn3LQAH|{N*%1Ml(Ov
zc|E+lT3xdoIk?|5zq(MY+mQTB7T=@BVSWv#vR)40ug;xx#UJ592c_^&_=<FT+hFGJ
z>X`4%wB7KTzq2JW)5NkBRpd#8iu(lIgaNG-m{4O?<8i4Y*2w)e#dS4euB7g1tK`^<
zLtIQMBOGw>R!V*!(@uZ1c;OWB2f}FnWQB4+3;wyXaNJ4dm*k`q%w+I$RQWyM@sse2
z8l>UJb#nR$2t?&+11H~l1Hl+r4ZF-1bb4Qs+3LapX3{NanD&)LBd9u>s-J>+&~*%n
zXO5%l=1-TS`!t@rGNjV_<Cfz0Y&umRrMTfcPd};xbXDZ}!+!)%@7E!yQn<;PLQQ_;
zf=Rs__Y2m$GRR=TLcxD5fW6qbWp4Nx-Qmg&xOqGSX%d+Rpb<EL3lLub%_;gcdO=Bj
zpQn9uJT;=((X~$Zp0!j=+9m%g(Z-z}f?s*Mb#mdK6L7pptI$ojO7zgQa(Z&^!ek1!
zt1oePwuMij3z!yN^;hmt<8M^|y?ckv=kiLsf(wN=XKeU%N*7^)I02N6TvArHU0$0v
z$@X?xD_xJAKv@aAFE1r5Z#PXFIhK=GIo&rLE7k9m*EA2?FGz1QCM<Px9+q6y*EBJL
zgHt4)R?b;vtXn^wgM~e}m-LpKS|<%U<S`bOp&<W1?v81twa%>FgZlm7i;R!y+pa>+
zSx41MrwG6C1WT6BWiia?-S6JO6Z3f&X@iiLnZuMO20W9RgOk7L{-6l>9Ve&15)pU|
z_moHvB+FDHh*;hjWy9?nw34cM;9SG~fBN}_i%mF}KK%r4DP{9OFmhuN>O#rS&xx*a
zeT?MFw9}Hu=&*aEh3)D&MaAQ}+I=msCeDcf*P5RXskuqwRK`7{t#rx1#JV0K9@&CE
zv5%UsaY`8X_Kac9bVDBbtlTJx=24nX>3x;4NuL3`L?HNGSIlF{O{!!}h#BB!c%NGX
zinaarevgBe_o~i{CgU47+U^L{jI&Dkhj}zJjOo32$Z07#zH=Jx5z2KB>wg{IdH`Bv
zScEkr@jA|{-~>}jmBguD+&B-rA5<~$Aj*bC9o_Qx>1ZKvp1$gsXPVLJ9W;M>3tcLm
zR9`H_pA9_+h3R8}qPbUIrW+X|!vkD#E|tw~zC7T70tLXbKIr&9$@$N24to+dZ%kaz
z;S`c1_+X)^aNkd5QxpL!n3|tXu)e%Qr9Rzovfxaqg?B!7cNk28Mzf_ONf$9CzBZTD
zGl{Ne)F_OJI3c`Y=#qvJM-Pp9g(A(HxAuEdSi|Jgxi}Ds=*Ox24Bw2-za%kto}K|n
zB)I>Zv^Xxxx~?&KH~x+P9`bcN%6nZLY27j7Ue<W6Wuw#Hg2AKJfbC|@?s&eD^i1y2
z9QNj0j0-Ffly4g9OkG5%woE=`hS9F^Po&^>9ajRPd-Z#flUIvR&Pw*lBfLz#`i>mc
z{d(22_|)Zv1xyCGMWdcl760J@Wb*W*fKI2FhoQQ?c|qf!DbO*askHHsbe?616w)5e
zID<66KR#fm!FFHQMRCFfI{lOG%cZCwaYb>HEXAOdIC%w1_-S(dm>z0P6d|Qjz6KwW
zsm{|=*AEz%v!-BCV--eXk|q#+W5T&5+Yc&Ji<EaA|7k)CS6uKh?3X)oymIgWeQ~iB
zE%|5_X{LRn1zXYHOp(UCRtTg1F+0f~nGw&(KUb;5qGqwh(?*L5qm=eE!Z_(=(X4|K
z2oPC;j5CUiJPz~qyLdju4f9-f6zi^gyBI?_Z6&p8cpu)n_P5=WS=730RKqVV!i)b{
zmaiyn-fU~>Ksh3V!coA<@{<K@ThLeFk$4iBSNla5mYz>2$ATZ$?thZ7;GA3fLEA6i
zGvO@Sg?jeLMMwBlA;#10L3>z2gHMVMMhgzrdbXuu${Z&$<nGNt*jZEnss7$7AEZjt
z&|6?#3EKM{`*))RdZ7@Iy;cKsKC=5P34vF|q>JhpSDi$14G_t#!;6%oTm6Sgh9ioI
zjC+!${Chs`pq&OM>Uuq6NH<s_8rWAND7>j0&dx%2<utY9OAarZtD*;0-%u&!oqh#~
z5(z{*ib3@bI7r(hFXYt75}}R=sz0oL5xh#5B&<VC;U^kNqVrF`0ZT1mIR`a4JxceR
z8Mj185yTtCHQu5(B@v#6cknBUKm|N&0)EcXefWv7+>5CKHqzwN?77v)w0U&;qmxP3
z^Sbkz9~oJ0b@cyfBGuP6v5Qzs;2?U^^RCw_w`4Te-~_Zq^Zw-l8Osqxr-#=;*cpex
z>>}svt8~*aVd$wf201_7EzH7D);JZL_y<Tcw#GH(!ovElcKo6?aV(fkB1mDWRY@di
zgb|(4$?X-iyE!Upu-6DSf%&Il;;(q$+b=K=KEO4FIPZA!WqbMq8_Os3w)FiQ7=+e-
z?dY!Ww{ByXqd{CM3eEgu(ZH$Oy&a^58!44=uoj*g4$-~FG=<yn*sF+M`s*Xu&`MtN
zp_9Ulj`$+yWx9L&s<xeF<t0qa;^98$0jt3=OZ!yF)+u16-?+|nw`r<Hzkrppul?x9
zIVJp8e$JywJvrEOcs1SNHMXp@HR3?5@W;a5g&09dk!VUC9o{DdRcWiIUIU9m9t(kq
z#fm~{dKv3B$;4H@)UX>FP&6fUTPPSg_Fnpp4ii`!TGZR_*TWkTO#!+!>ZACw$YjU8
z+1{(_lX5KZgqMuJq2m#w7UiMHjV^GqZ}Xkk&{!LtH=PJN4cX-yUjLbMEOI%^A;mWT
zJ<?2IY;-1IuSn=rF$(fCYltK}#LQS)3Lmm=P;W!_Rm~Wio>Y<!p1~uA;Skv+3+P?G
z-n*Rgi{fJIlbC}i#-H>}(Si>Re$bKH{)WUyLlH2GKi|i8ssZ~TICd_plpvd4+nL<F
z4^RTaesf~4ef6MIth8VRIPlN+COdA)jqHgHplTFy5N^<)ZrySPyXbN*Q5sEogMaq+
za*9BJFW}FxF&G-GC7b-&VJ`#Vf-_ri{U5Wdg#4d6D&}h@2TyxI)i>pQdJg3ya1QTE
z@4veQ<O3qe?FYRygpCyuNGp+r=iJHGx=iY8uu|xa<zmrVPP7}pd<Wahu-BjG(q8L0
zsyrL43d@Oo#;5*>C7?(qSp0Hbu)VUbuz*PItbTWiz{vzJBVQIAR8c@uRH63wRPg-W
zF0O=Hr_JqLmJZ&L34~a#YHE}ERfedE-t4ycB1ne<S<z#oza0!jrUq3u;AydPS*N1;
z79o*fo<z&P6bi~jHB=smsa}T~#3Uh0BS}<#&!^utWdH-gaYJ}=Is~8EOoIDSLrnfC
zjn)U~Vy)+juls0q@%7;8d5o?bBm`X`TymGvW|`SIP1toV2+;wNKwmGgX-zT>;JGi5
zS@LBD2PmUpo73boHP-!GS=_qLzI270A^|zMumZCP$@DSwqs6{yz4N1JSMr|!EjT3*
z5D&`72ul+y?dM6^(uW=a{Aj;P!B0`>w;X01i>)|q+--Aa68eS4_UfE-d-S)q$0)2{
zw5U6eY&zOpGDB|J9`9pCqjAE7s|o3u^<7Z$7s-`B%rL0Z+#f<S2ooFR7$8MN4W0g)
zy}^Z_aEs2y9eq$aWy!xm!pUI<VfG}aIN<!-bZy9J4|JxKe<YC=4qhDk_bN)Mny#35
z;XIsUu6;JOc_v*Y#t=E3z#ifqEFK<f?tsc<GT(3?N8#R5)(KL!AEJuttT-H-nK_T5
zi{Nk1;Wtv>uPme#`d6I`7C|1ZV9<gxlY7#yy_n$zqGP2gXG_=e^fC=uK*?;X-;fF-
z1el@Qy7_0Sy?xl77qj2#pwV`gJq-%7Sk6KK?MbSgPtwxA3Glz1&Afgdxn{h$^bkUN
z7mnYk09$EUNj2`WV*-CbQ>R6EA1hH|$5a3H&jqPWK4-tdAZCVf?|qElNR-~s{&m;%
zr}eCfgKy>kkgf5O53>P-Yr!UhW59Z~vOKCqyQEJYp~}OelKdn)fnQk9_VqV9Am94n
zNxdK9E#8N>CNwfTA{(Gf&!Y;u%v!S?cg|@sok+yTYb>j`#rv@%K-;U5?<)avbxYiA
zkIfF|n2QF6?kwFq`|;fG(cI5b;~y2lp_{x^uo=FD39nFvBX(&5&(g<cw&@=|)h5^H
zMnm1OO%cjcvC|8fM|i9K;N5I8cp$|rlIhK`qdC4swKDoU;?EhW5lgU8nDa^`k`0Dl
zHr&Fk=?|X%EcK-3RTMqQ){q;vs#Aax-~Y0dOJ6k2_cNHH{8gfmFFH|8+8c*FK4h&e
zB!J=_E|WMvu%uNh(8T)F=uo%3`m@9?nvV_!qOR-_#qMBQLE>|vxwN_n6{ph`XhX{e
zsxfjvKb9p5KAo8*)y{zbZE^IQ&ok!-ZFqcR(OdPb59~j2q%u0BLW;z(5&?c+G-2tR
zc9S;ienA>}25L(s?l5ceP1;jg2?~PxD}kZPJkx|e#(3P%b#~m6C;a_w@iWEJRJxJ_
z<w463ek&-{VzuJil`@}VCu}5fRkQOG-vpc34E>C7k+ptUy^;IjVZG2fBKND44Jt)9
zKS&q2yul0*iHmx@K2e0zGhqrm3l&)LRn<U|@FsNGJN+}o@kvUI`Q8&Mb|C@F4<fNZ
zNGUW)WAdP**{&m<oS`%Zo_1Nbmvi7@4aMB3>=L!tzu*(HzyshDM<}8}yroucF};!t
zel)5+jNOSC4?T4&osVCE_=pY=Cg4xX&xkMVUYP#dy@|iq?cvEVC~hqrdQldy1i0S0
zB<|m}lWOgW3VN`En1E=7LP3CRk)tWUQs<r4(lLigiAuh3s0!$ca%|l<IyOXPQmbr4
zEVDI$^K<WA+_cj639kO-5wYIs1R_tv2Uov>56HEYnXSk+@>qBi570<4i$wxH)pBA|
z&XS8?q}euAs*L6gmF>*kLACUx%8Q&pwYOhAo6?SZ9#COB#{#fd4XTn=f4Q|vLqy4o
z&fTsFYz=2x?@6{dnlT*y#6o!^11|NLE0ue7IiGiQ1-KGpW{Q^n9l02HTb=q5Ti-QX
z!f8Mg3EMZ;JkNVBg+jImR?pl_h>983^9WGF?XX!_r>0=QyT(){5r?AZ8#a4$#$~_3
z*4ge4V98L;TVOL!`$v!g4RKa)>sE57O{_*a{rwuP*vQKr{r3T5O!%&A^`z<t)lkQ|
zQ7k>E0Tw^s+|ypNEfSYGzbLtQWa+FBM8}X|6S+Etm>#I25lr+jW$=v-d1H8)WS;q{
zi5%!;rPg(R@@M>xuA-^+=z%NRc;^MZb|2a7@{6bkW<~U~K?ELMh8}cj%2l~HdMp{p
z(5Y(*?8iMA^0?a;vo^of&EFXt)wo+ku8iy*f>o2@c<saWc1pBcEUroam6~RYS#K+|
zSF=kQJ;b@V?epC`(b}UfaF&40(ffR%hz>3AER}sDi;pH2nVM=yw{S*W6`Nk-%1^Lw
zMrB_R=e~~ySy@-rS`t3*{3DOnHmw6!|1z}tVKQI9jYRpM3-<6uxD1sDVq=ZKdti{W
zV9PtyI3!KwV8z2ZW{69~B<70)w)zKvyG=%>l8Y<yzj+UsNWnPZyf4vkR<{7Ub1y~+
z-%x?q!c_N~(T=_>IpB_`EG3y*t^ku^2h&n#CW$VK*1T(7L=d)n(r%N<qd4w}jS>Ao
zvgOKF-vhmbW#`!gYZZ?iL$j!8n8ckw>v(JIUhr~PQtzqRWP`hEgjVZY-!{+*8Bp<-
z!@@-E{*h*vM%=y&lLt#nC?p8uZbYl~Qt%&=gz0#R@QN7~I*k>;n}AC_1oYrmnkre^
z4|v5(Jl{S6CipIdG?c>OhVkEY2Znk{XkMT;sYB&`HJjmX6`P4fhUJ2HJ9(4n0fWi*
z6eqZb@k)`{FrfrkC@Wauuw|tEZA5vb!%3u@C+uAB%%NXKcwg|S`_trXA`J_nQ$;2B
z_kj>)aw^mQ6zIZ6a#kbe%@cYEGueqosceoTrQwX-!b@Qb)E+5BIa|7UeyeijchCo6
za)xr5T?!`r${6V*Ouj#Q^L40gCSc&eEwBo=o*+frgsn)FJ_nV#+%d=*U5y~KBKuvI
zjP!!)7TRjj{#SBI^n)Aab`QIIacY#!g+)eE>)qk#j-_1^3op4Ht7ACFcXtd$%L50Z
z-lGiH(C}{G84CI2@w^c}SZhJ6u>NBLAX5+Vt11LI=MzTuMD)Sz^5f%!R!3ef;ns-q
z5szxl7eyZ=aX%(us;Mr2y7j^5C^H^z5$O6CKGB(%jBEfCOG3;${(SZG-s*>(Pux<#
zSAfdtXK&9_zNLp8qj6_EXUq?DB`Uor@Y4&*PdM}Xg^b@yq<vE;-o+eDB-h?ibId=*
z{(i%tbpZf(m%8&N-T@}n>J5_!y224NC1F<GU}u9$9V*gSwXrJ$n@8ruf9DA$-7q3R
z@3fY;bM*sDk?glG#a<|C9U=F2HhBS4z#&5^M5VR+@m{_V7dx%7nsuI?D7gh5Plsf<
z(@q4iO*5%Aaev3=<T%Rj_)tYA<7y2WWo(K8wK?iC0~6EaKlQ=laVtW3Hs7>Z&iG#h
zJBWL!;U|c*zwe767E#Tgt)nm!e%9}-?fcQvUU=k_UH6sb;+uUM4d3+y4Vn<Q?~Om=
zdnNOYc3WE)%~S&|aw+Hc;sd=5>Zv%Ppn`$cNS>QOWb(c-F~>L&;?<P9`5T;hT=9Ar
zrR+#-`C8HuTN!iYUlPdf+s7((!=Yx8$T+(2g<M6o2zjeM^@Y=sWpk9Ds$FzC=J#&3
zARPP)+Yh7o`TR-zJ2dK=pV}gW?~BE|@QXOK5ANju++F{79jfcs4Sd}E%UO_f&+wma
zwXc7w-T_)2;WEA`dL1W7IonJEmsn)8`g<7bFeDvTD@g~e1-=1H!XFkkp3rPGiJ^#p
zAj#gDqwLF#$;g9}df_yUk@n%ox8||#D29#ufs9O8m(uis4R;~DOom?O%~kp@uW0gb
zwqOB~#m5@p6Fm1@HWt2DT<$Bp`O6fPMP7U{%QWaob55!;B*YYm3HL?*kCyv5^p2JB
zR>9A;V(#lF^NtItbTEkf*Yd3o&8Tka+|h(o_5-rU^L6P1joad{0Mu;Cla~!B@af!U
zc@|XqlVrbLvxk=l)eu^Ae4u(_izPm5j6Yf@Qy$Hcknlyt_eOyJVy163fE!MwFX00b
z+`9s*#Nz*km8Vm@{ZQg<G851_Bm;3w7$LmSKMPt~C5%Vv0~i^As=2>~=LIJ5@6@_3
zr@CTh<4c5m(*uVsekgg8kLL1!zq}%-D&uox%IDpyu*wV!lB-DV%Y{?0Xp%W)27RPS
z-4xxyzSzy##72b5W5Uq0L80(!-^52O)i0=IC&~ASK;ju3CF`{A6~mzwR42R{EGj9+
zlV*uN$ixCsl*4Jb@|X0`yCkQ4px<#$pNM@(4xToVi4dAPLh06fsMA=`dbUsK=c|E3
z!ht}71LSU|_V9*d9&T9FA!f2a@Y7oUSO-IikN4gqkp^&DMyFWN55_u!d$GG(UBPt1
zphFI6sOb2kYz~-qIPrXI)em|~tLYOb7te}<_^XzXsnf0uSJ27HKXMg&VVuW(BHzQ|
zdtnUqV}H*RX4!I{dn$2+JTp8w-+Tf!0d{g=i6D1u`;?Wf!AaNaF}vt+wP<@r#;Egr
zj6h2XtdD>mZ7KWA{6cXC87z1nA`i=!+ImI%Ovj&X3Y5r}1LP21S!*5AVt8FlD+w%k
zQ;E^JTOp1~K1aM<Fq!h(bJl$8noqC?gq8vD`+FVtZo!^Q*Hc;oHVE@Wh+`1OxdZk5
z9*(QHZgpNDyhn^_Tn>^e9=EwZvu2L2(+Xw$->-exE7c{96yb2`Sp@x}vT<um*qC0U
zn`599#<eWNxa4>dy6;7fJjmA5AVJpK$Q-7S^{3FYqjlNr<0`OuNpK=8IoGT<Z06ni
zCE*wfmFiaj&i#ugeIAl&-_M^|2dKIO;GBBpDkKtOocY+L0F0*v=mA|<_S1~ZhwS4_
zvgvHV;{1-<i9wNF)f%Jk3R9wTVl`C*{_FRik%xhUD9_jZCM5Du3I$aZx+}aYYBS3Y
zq`@qJ#LmB}C@#6e^G^lrdsc02OYA$0s?zA<YG9}PDIguZE`a%F9uu}rXROEv!_TCO
zt8N~wDu^XJlckb05dP`k-_n1>u}|_EaqL6FCb%OXK@f`D(aEu-)8?Yst%K<om-jHC
zLB#}XPpcxnU|FA!mYRNR3Z-iwc#p@Wno;S3_yVe5J+n>YZS54{KRFQ?yt{c*N86C^
z&LbHi)%#b!^3T=V)&z7+IY721%raX;N4sE}P_91kxnr6l=J7qSo7dIB`k>C-hIigH
zmzS3zWVZTYvz406&CKypi2Q--E4OA<z&>6LyYm%T*ih>9qY~LJj3FD2KuGnwi}=M?
z5V1K;fMRe?4UU`GolSY9IQ*3T^W?tZ{%;z=Tb;rm6uXh6$1QpG34j-O5#p=UM5Y1r
zZsQW`n>T|6vT{(`2O7e+b!;RMaeo?hM*s(6pVjKpg>7;Jz@@&;4q;qtzU8JDcBw^N
zS~L-U*HW}Wtw8WE6|p&^zP{P7E(st4eBRwo<_tTD`9Eb_5(OOsX5SWRuCdV}gkw3u
z0NPCsmTWS@&ygYc5uddjMV!kOcbHE+p&B4#BM`0P#fWI=hrHt0Be~K|%dr<vY41$d
zH@ZT;sMUWCOJ~*1hpgHS;&`Mq<*y!OJvcS2W8Gnm6+G?X$_j;iva}d}e;$Ur$%)^5
zNB(Zy5sPe1rdFM9>F2OM;uqc&cNRe5J7<J;yE+{?F{F~>Mx}4}fML5%DeX1yUWrX^
zGg!O9kL`0<UrMNzFS;MQZ&d!f;ddzd&jcYT<<Bw73d>}_=~Ws)zkC~wdN@P%WfMQq
zr=0KO#uk3%t3qTayf(O!vK0G^q0|W1(nAVTehrY?_bS+ycV&1PLH?4@`04=qWEf!L
zU<J;ra8LTUw#$dc2z+T1rdP+I7TOWH8torLm~nSz%0X<5Hy_1y)ldS%KY&$|ulM&P
zAS^Z4d&4o#wQGf#A=(Gh5%J^J239K49MJ&1@Jgty%DP3@8WlP$EOnU_d7dVJb-(Q$
zhqSY#hawZI`}zNobdJH5cFh`|XePGJiEU48+qP}nnAo=MOst7*CllK`&-<OK{MePs
zu8pj<x>xsoU%kd;r=xM;R2n-I{e=H|BN0^TjZ)3bVMeJVYWt(eG+B5$e-$B4NzCAf
z^PO9T4|eFG$l9)13mIw%A_Z;uo_~4!PZI-RILVR5*j%#9oI+1!!-)Lr?UCtDZOC8r
zoM<n9FzsWSvr4d~ls7MI{-zSkCNu0z6Sid{Dv03}IbmfFyhxqw)a*QCe`0-I-kxI@
z0u^ogJ~wv64xH1Cn7gJAN5kKU9WL!Z^c*`aZsa}kE?uv*=sP!S?kM7ah0va080qTp
zPiyiWC>!MrIcFzZ|1pXIBdzdkwH+b9yneaRkCv0)f+@O&m=<C-X4Nz4RzDtFLLuem
z(aLrjbokYXg#zw7M?E3AK^HEqguRsdqo~jeMhGW`((Yl3q_W8D40j}vGv|z_rSyV=
zGQ8>NVv%gvWUP!rTxM*~U7Q3qJr<?^dNy|jr9d((xl|yxClw9^8|{mO>htEq68{^M
zJ1*Awm6OJ)(&*Cm>Wx?a5v1nVtgIffaAw|1>tnM_X8<#xBvz|Gu_L_4GQNiG_*6qW
zCA79W+#~0+@rWpRha5-n-jRF(QC&!2Pp<PKs}K#*TXD%$zV}eRf8nOb@Z0qIzD2LR
zoCiB4XpjDU+GBI)tG&#A`Saf7pPK`ME|6bM_+8Tta}`kNTlNgOr_H9@%;Z=wU>9kB
z+9!~d9)+JVKA6Hz$q^rF1R&;tg~Wp@VQ%>xf+|V^r#nH90~CO;C*U7_z4c!Vp<AY_
z$^+HI_hARoU=JP)@9vreBJ<_{1kAyPLPu9bkP5HLBA+(ekJ!TNFxVHE<WANvd?Jr<
z8=-o6Ge7|C{wiR$rob=G0!voe3hq%l<ApfmNL2-s3|J6LIJIY$Qkzs5Lq`n6G5X7z
zrSn8N;dtcfWdc`BFwhQbL<eN0)|bbRBif2Zy+M@Q<;t0$!Tm{BYRsdZ2$S}%NJex9
z=PI}NdWtEvFZAc5epk2SdN)%+$wOQ5dVYs^l4sM~%DnkXQUDSSaPQBl-!>SVFqE*%
zzMLH6mtu)wo?&7@6!M5kg;b0uglY6KOaSWr=BVYij;&*QpOcWuk7~FPj$?N}gAgSr
zrT2fUC_rrGptsd1MGE7-G;7fqSpm1gOI`L{7`RTrgyn}u6wEh)qa{g-77sTE7fXxH
z5uW&fl6K^1Dw~Jr4|1R!F7_u;R%+F$T?%(UKOre9%o4Ecs`NqA7#kOiYcA&NZbq7v
zy=Y;J4^VFE4_B(jnrqP4PB|~Xe8y)yEv=$^_*WY<I_yOP0*{xw`>(uRtH$I^6!lQ#
z7m4t%vN*-G%ILf0@(}v`MV4IH`Hzo4BTBDaTi*znfvW;xaSE#}pgPx)Q;hX&A2Me`
zQ+m~y)H9&?h_5-w66g`T%rD2x@vF)kQ{2+?egcB4PXQ>LCqn^^=%K2K_C8`byqo?7
ziK@H(?v7Z>Y9eN`h)2o+K&&<Ho?Ll?Jp~9fvrE@TD60E*%TB`Qu!jM;fMj%Y5t|v8
zH3QzoWbB^rA1*NqxREm_-0I0|=Qqr&$J$$gFKkKiE8eaFFGY)xIj>HH$R;2tczFtQ
z95Vo|jxdVyf5CW7D?RIc*oRfM@a?W9*)-G~zCbI3s(71jP4j>(l~22<m91;Pp;f4g
z81N~~%|Jo-QEwtJob&3_&Vu|ngY)!|G@upBpv6CvcB<eNp^nCPe_jO7g$IZREAMgN
zfE#GRUT)>MtDPGHRIqq_-@LB1{(pj}{zrW2Lh`m+;Mfx_mBpmO&c+^@#y4gW2SS)4
z<({UnRYw4HjUI^ttuU29p;F;eIH$K|EaAd|#@L!+9FXd|pE{NP;T#@_KCC=rS!0#u
zcL`3mI*Wd#Jl^i<zX#~VFWq4wo0lJ~ec(@E|CN8^XuZ>`2gBl&8#z?c4@~1nABuf`
zMM2i49z*Y%!GP$+Zj7vnNPFOyoBD@G+H?g--&cmJ>_lxK@8tiY=(Sc6qzFeET>R_~
zs4bKHnYGS!=S%|P`O$c>WBb~8Ge=S162+><cvL{ntDybV*M1q&=pf4$cNO{(mHFA}
z@%_WBAt2E#-m!)2hnuej+Hf7${a|cjV!5ZFE$pVl_$xy(L#RCUtHt;$1sOfuFlSRD
z1yQ_Wd@xADWA8ErJ!TQ-ewVQe$I-ZF?ws=QZZd*l9%><vSrSH($QZ*U*6|SSnfPGK
z8<HTRrHFyP2Me)$<cq5jQ~WAufZP=;omfGFxnQ%>*wW^O0Hg@vS&}I*(TM)0H;9-m
z8uSQ3?ndC^w&v*|t8i56dp9Eh)QC}qy?q382p~;_F2$9Mv{`_8LI7GrCi!AHN1cj<
zHX>dnefQc%jRPLM{^ruUy2H6{ezj;v*d89~q~4x->t7Q71B?{tn5a>FeVXNG(_^&L
zBKy!CLnfl8$#cc#NH*)M)7H7o=Om||q48l#rz{l1NlSGZ2s8cEqhcnqwlJY4qCz9$
zME@|1YKnDI6!j?O)dvh0$e1CPI86(_4{I=KDQX5eq%5Gb+<!{5ZO~RZ!A>OUGMcgy
z=vN6q3YfxVIe{x~IuQOWW}n!eaGy*<S4xvH`r4G1)}Sf5B^=!J^*4_po0bY4h^C>X
zfbr8-jMRxpm9fy!I(_pm_3}?i43)K?Vr+pxj_80vU=17K5F?i?Q#m}YW-w&Cc^Wb{
zyqX95@*VGsu|E{^YIs_~BNdz?Tu`vnFjo6^EH%3*fY@iVb)oe(5kLT@ZTG_0dbb}H
z^Npr2`$|Wvm;|9Ax?i2E8I$a=MkqV$4itn^m<+M4l~9C;j7uI|;TLMyLI&drN9m|!
zWEbf)^lg>?3?2$OQFi)wMG5CTcJiFz0azj*^I1_uU9NG);wJz-q<V$MUqT}_;GTBT
z(Qiuas3p(Un}ePq&g-tX1jXm`KRI7?J`&T7u3sk96uNdSD@N;0!D_qGnRW#2R(}$~
zE+*nnKe*!QJ?q>BlcZMCDjWCc%@Z=0H<KbBf1!lb-T?TV?k#+7;7{}JjVN4<CtTSe
z7qT+Bsi)u>hO98X(Ci0edIJ!NreY}?ul6=3$@XwA##d$ADGqQI;o==r7(O)$*68ab
z<hj5ygD<mxz-UUYHK*m>ig}-2gUl7^m-8QtYsNLvq}wdWD>5xt>{FSDl%mhqkU1wN
z88O>f=F^XKEnPIO;M6VPG;9zsjXPBlIPK!%=APJl`bIA9ritP<aADT3;LON1YAwx<
zqhzgL{K(^<dTu7@nKb%Q@={(pJrhn&Z}u&0s4ZHdUAng|n3%99$kDzQQQY_tWo?>Y
zKR%aa_D9|2qp#$H>R%Lk{NqXfSM%w&E>GW(C*AJR_k{BGig;+NF`Kbb)W1V6Tne|p
z=EauPzIS~L+`+ziAt-P>uJDlaJB8y^%SlN#juXD2FU8uYjZb}Jn>;2z9mLtG)5hzC
z7SG9k^;p|Qvb2oM%zX*Lb8vX(J=z=LoPAa>Etm%<23ji*@5FX4elaKiNL_dbf(ES@
zjH#*`GagRRjC6Imr}Nu{WWu^yd;@eDOSE7uAY6(NfsURfS3!*tYT!bZlS!9k?|tyW
ze)Yg06(FZiP|iH;JYu69LI5ph?po~}G+aBpH8;7VeN}xzmZT7DUKDfo`u9tPY-q7)
zgH9gRcc<Opv^NvP*3^+H6KT|6fz!}D6th(bO8f9^<tpZ+CeGWj46!Hc@_@#{+v}^J
zhnn;05zQ{w9zkAEQH^n1+cz7g5CX{cL}jjcmGg3sy%%(jN8++cmq51L+~GSzlG1kO
zA<Sw3zc1y|m(b3ZH=kXAxct~OO4BDZ!JI-2Ie13{+M0+6Lh+Mq6WA|zxlz0i27Vug
zMd5MVp9e9`uya{gxt)W8c7LXMp0KbL#8J;<8z`y|H|DS%^3rRT%?EdVZg^XV8@x?o
zs0nCqX0_BthdJ-WO49jee##04qpr*~w5;r}e;u*ryv;WLCCENn_#LL9bAGe_b<lag
zECvLXp6ihu(-}O6i~h*g(=oWpsBRrEPrD(_9@*A^N*#%^Ge_b!exMJ)y~_1}yUUu$
z7;lV5vBkkP#`)Q;68Qj`C=;^&t$~V&R1kkKqf&jHT+R=LQtx|yy(v=p5w%>uk9991
zBxlrbD9PNxB!WcvPy8J)g(9v1<&lI_hUFi(pyjfl@$g?c^hW3|{m*BRNJP}Pvuh@|
zH~bKZmct7wWQ*)C#Sx~5N-s=HG|%8>ADCS4xQc86LH~9d)jNgRUc<D>QE9nektK6Y
z>7i^3ZdKN}Qn;8lf6~L93GqWhSJWl7o$_!T3n>93XaDrM{x+Jo`EDWVm-Qk$E_19*
zJ@%5!x+G>qS6$;|*fOBZd(=Pv8hdu$l#76&*50sXRL}p5GN3+I6LTh<B+&Bb%{+9#
zuSkDYcUUq|#m4Bw<ce0!y_^=kY^^g~^dMv+O}3eaSk%_1y6D9C0rF#WnMFuJnS?9f
zl&7^JG`@d;9J7`m?wkh_A<39Z(%tq5F#<ZgS(NvW^UBs~yqjKU6S+u&GAN$8DSS&h
z=R(iPs|p3H49ROELUn)sA<O4yi#hAZw_3LVR6{d`Q5*g00c@`U-kzkMkv#1`Ttc>D
zMI}<y9Knc@K-wnjo^^5!9;2W0_r9IUH@QEWLMPOPEZ<UIX&zTRhcF3_i90V-&ycqF
zkL1z3S+P8+MVK%kxO`S9lE>7l<M54o*dyNDLrzItaMqCBF2%y#5x*b<WHIMyR{QK4
zn7tCc>IXreSM_N<Fn_e)Ih<}*PpdY1@8}0ZOAEj32vM`^WXY@MAyXiWOsTA`Uw^m;
za)mGhN=)&XviDm{E<u<f>xG}JoD&xR2`L22HN-pr3cpEzKSz=jk6kuRkI}@fo!q+4
z{*_lmsxW);p|tN$vHCWc$e8kQ$airP`n1{sCWxlk0oZ*f^8~o9k<JmV3zD8<RV4TP
z3vRdOG`IehyP#w_!Fo|{E`n?>?(&8;h`+zU6p?GIHQ-<5^&DT2N&*hlyS`T{9JfZ)
zr`GUkO{tE<=K=XQUjbFcl<!KOXy&LtShOTuV(}y;svIz_*q14xgH-3J<B|q7uJSFS
zMId>0uPHD2&#?+(XT*S_=dNeqjW5x!@AS``qp=7$j2LxCfIN*v`F*5Ia+baxu#`t1
zjU(6}zOB5YW$AoJ3gl9NDC6O{AHlLXRH6&^OR2sOBLpu!E~%R`s3L*CFDZ3b^hmM8
zS9tKSpe?S?w46~zwo44yRM4!hgi0ocW+~jDo<CC%w}1_)2bbKnPa3}c?1!!#K#H53
zo{=UlvD7WMttw`pqKNKOpO7w$t)L14t&SIzSKap5wgp&a0AeNK@vTN|w?t-k&0d;*
zvaM^WP$#N9gs7PzZx9e+qfqE|D@O%Rx?Bbikefvq#wbQIECH8t;OrQmo3UP&*PJyc
zTgZfJ7L`r{7pFx6&G{PNPx6pR3T`Sn6({3#^vpQ{vw_b}E2NR^ryz`GiE)L)vvkfI
zoy)S$a@twhB1bnuOIQzV^}L#e<Ef|c|MeX=`j~t=8|o6~e|;7XDj_SuYqss>UZfsU
zg;A`k_Fp+4Y>F(@VCPsxS%$yQk+FsU#()QaCn$f02GH*&%lt8jRAVF-47bRVqAsu<
z_@S^jzhX<wDjZB$0m+lQMK0_tWIuj%6OJe^&KXh|us~in6m~E)(PQEWjm8tC9G1Xd
zyiV!UpZc@p3!MmCoKptT2ZG2<-f}A!Lrvb;PaP>%CSKx@z{7~MG2SJ~7ukwVKaw5M
z5#Js>K`sjAZ(fiY<KfxCDnd=J9Ij&S{n&ix3t9-Fa^x>+&_iyh3M#1_n<dH^6CVyy
z)m$=xU+T&1)RaibbXCr?iVoHtG6pp5jOHg3iTi}VAnguxVZc;>7y&;^Vw7Ul2>yU)
zt8?neW7Cv>xx<I9+EwB%aIp`Q2wV<7{Vp5t!Ghig9g>ulHx3!;=Y%}*np4>T-tN1e
zqA)mcDlsaSjWg+cDY8eiIE8TmlBqq?JeqMGuheSov&03#@qY3|DUY+qkn3P6L@LeQ
ztwr`HP_<;Rhb1v>cRK?)B4|l!0Gwr3BH;Df;b};6s4<4#{0{<Gr9C=p_m%f+hbten
z0{pc5Y98?FUcmXLoV|#k&$rf30n(iNTWa9U5sdV&+*jjN^h)?8yl~Hwj%RQ4&b99t
zvk^;SBMLO;f(D%X3&9&i4MwVtG5$NV1lo7#XBYBCqzkxkYkK{O^Xe$2Ry(VVk1>;}
zG1U^&LGrssot*(AwAt82TGP3s%R5))D(A3icF0Yp^PSW;;f8t%3O-14BB)|e)Qh}f
z=aoFXg}ODQN`HrRJ5SP@W1*!eq6ldAt7p}Cc_pNIh2Mu&BQr&SfkFYPU1xYDtWsWC
z(2*kj_G#8sv%$|$<K15+>Wp+lb~=>;{?S`3ZEj8n51D-T5>f<9UiG-8=8VM!jP|}o
zPK}IAp(vujpJ5?cu-@_u51Z>BkWs*5KF)VSgRDSPg6A(}UYw%|4gXxf>&CU1bk4fo
zeWfx|nt|W9Ox*qC4XbjA{+>?HI08tgzO2&}j)1B(794ZNMKA{xCLD8>gK$C#4Xueq
zT{Ge_?rIw$B&(!UpuACZ@hF^$LHykBUIxm|E!yBJkRS3la`j)ugST8S<fQ_Wf<z9k
zAX;64uzJSxbEB;#p1taS_Qs#;hH%<$d4IhX>APSOUHLHqh_&0SOA3=TG;_)b&`Gfg
ztDT)+l>zmx^CKG^Vt!c#$z1{R;FzYI78;7mOF~PWrv~9ws7KunlKhipVn~x5q_FoT
z{2qCv77B?+WRrt&33FXLK|?B2wZME4l3;&XWTQ%n_lMcEDjLe@VjZa&NfZkaLLV%9
z3)&J-e7mZ~1sudMkY<Le*V~+#t5~I!Hz9OSuq-EBOLofY;yU15vVHt0{6#W!DR^Xx
z;F89>(7xOFh@Ml+y1BEG4z^zN_Ix+OPR?13EKZru%@fiLZ-%F+<5zMb|C@z4;{w|n
zynSQnjwp$!9$I5^S;8i=#+nB?*`6>b)16w@Uhh9svwIPdaFFJm-w#1GUmte81`vmR
zKZu&a-i=mwwTM5zt^9$u5RaP8fY8ZES?ecCue8W@$gCW4aPILiveC8$BAP&XAbG?C
zrTurJn(3~QhhEr?=k&Q!TY0wE{g?G;RBkzYXk3L`7{t^+p^1`vANY27&cS23MA3fe
zdXGfkLgH<_!%9W8zufX4F<P^tVwfyKo<h1lnG#MpB<}n=58umi9w~)`7(R_SdY~^w
z4+F{d+)C#-R%~xEdakPob_gp_&8`wisS(CYW1rKRDf93{tgkurUj9n-Jg+d~+BWXr
z6`I8=X+||KQLo@OS@CIHVDvs$<+6UydN>1@yeV!ZZ_x|Oe!5%zE$06DO!PU}7)Mh4
z3rYg{`+A~uE?bhVG=HzZL;I6FDmLX~Z<TPQzr1VsBFz$-vFYk`PgJllfpC--?`kk2
zc>dn~@34~^_?IcW-gc|xz5YYihNhicu?bubuF3n20fhJ!XeG_5Zl932t@iQeC~7as
z*lg~V-LX{Jxpa%X7NS825J}fMx}o;Kews!`_j$`TxilU~$e94qtq?tngybC5wlOtD
z=t=2&%;L$kSlPWSkqH0eQojJ;NTBtJO8>{G`HDy{^F^jl@_W_M;2MBezKvvAdq=3+
zhll1II^S90R{O+WRln<iXUtF5&Mn*xR>%~+v!YD=oOb=h?cT%Q*824NJCwVtf6J16
zjTumd6p0-WTV83w$9|XkVt@U1A34Fp{{i!NMD82n=npY<DR6q(+zLoE$YQn4&(ZV!
z^@<JL)>jbQGTi2S$v<XmBN54dIn!daf-mOI+?_+=A<o^mX>+&|C7kT)2Zg)DxtV-I
zLL=Oom@JxOM|pPi6t{^mS9FL&eKpaKWQiRWH`Z?!U$(*puI|I332H6gA7(iN>Ry|6
z(!Z)*-=6NZ_@BewbldGGc%9gRLKsuJU!0^2ciHc<ZhrP8#6itFqY+u+Vq*smeXgF~
z&&(5w<K!zJalrqyBF8xFPF%-;%g;J;ul<{00oIdpi9`4EGVFdytceTC02L8DvVldM
zvND1u$Z000=64K?=O&T^GN26PxjAP9&^)B*<ZUR1!O@7bsaHbJ=_{l#D)&m_F2TfK
zd^J2_l+y-LsYr&<`Ei0|wtpV_YK$gX>!LD2LYO|8s9q(C_@E50#y7nB2q!ggqJe_D
z#{Tm;s@jq#%|qz>(b*Leg-9N0{*pN*``hrtzv1HnH@>b>N58?@a#fXl<^v4=FB(PY
zt&Wc1`jmckK6UNg`gW|I*JohzrvUxr^O4svRuPtl#q(XRSEwhZqHQR?XMvN@iMy>u
z%;9G|Lh5o_#n4|iD?XSzwh<0#r%(+616n(sw(+54m(T86A9(*OANL4(>S&iNEp3r+
zavUSn7&T0PouXZ69)DE9jl8F0<Qmp!^!9E2^A&)U*W9{ImtQ9+?-{xGq-BYyxbZ%w
z#I5l(gCypxx60W0+@1Zm3K+29fk99UvWZtQSkF^*Y~X=7+=YU{kgQ(wj;w=tlh-OL
zn%yp1phRn}m#UjxS;A!}TB#_VQa876?Rb6pEjA-l>oAChX4~9E#>L8At+5HJiK-2E
zdHtNNSZ#_bB6jeKRtEksEW_=S)4v&3SX#xxasFm#E&e69Eo@rTBX89*EBzQm$ZNc*
z4_PPFhJ_a@S~K_f;+lbnnJOqk5TeR{dRd3ZS)MxYV-u5`zWJ~l)#;>5pG%B&oa*(0
zD?TI<r@#gt#SBeY=|;5vU|EAApTZ}sxlo?7sG}>UsFh!%6SRIF3`mU8Qdxb1!U?Y1
z$RF_GMhzjtGie21gaps8$`|%89$djCV~Mc*ok>)TX9O6eOyp@mcPh+gR{;ARUkei#
zM%kndB~pIy&qNu+O(F$$K0lI0(iV~=NJ!%t@n&)5AGC#*T6_u|s<eU{LXZ+g84LHH
zuL+mm1tIrrU^h_Ew)86ymhs%|dSYAXFepTdYN%h5R1tJ=>Sucl(j7dSpnnmvmQ%Lz
z=o*ln8D)3dwEJjBiDS2V>Tf}r7^ru&OeH8ax@o)acR_>C(m`@wrBal!yZXg(oz*Qh
z*gGUs6I5@suz1qjbAaXp?zAGod;FgnSx!YI#;kZwJ*~PBhvF%sLdezW4o~z+Lkb!{
z)%7y6Vqt>YYQ*7$WKz%%JS4cL0JX!MgKRgJ4e}XIq=ONSq(o5?psgg>ibv--lPY>T
z)Aqxz%g=ifzsywM;tY$Q&yyt_pjWe)i~`uY(SP8+U2vz+J&_jR0aWEx!7`H3oksBw
zVU>t`{Yv#fNt+csGiNc%<)ycS;@YNvrC0%q!J3SlGniHyct;0^)jnkox{1kT*_!=p
z6e0`-3@HtDG|oSQCHI2!SafgHHKoeXG$m`QpAzPtvVF)BuPp~6|5^_tIqbYGo)so-
zaTNX@lwL&PY90(*-#q$(Z_K&*UpjCSJ6r`nf@xL1RKG#s=v^YziLMyeFJtg$&0N|p
z3)xae7jxUzh#*bVx6^D<cDnY%y+(ovs;C5wrGCmbF)|<a=jkBSCC-0$0l>I1v#VEd
zS>m_-{4pt%I0>@sN`Hp)wYJE`ePI@OK@?0H&pPfH?UbTwpD51;QeT^mu9v2+xQ0}W
z15DROgp^$GrKJ2&#r1n9q>_I><$p(ycI%zyp?(?I_6AeJ#`k+%;l=O!G%U2i*wS0M
z>tOz&*>!!$%(A{t?UOY@ISKl4?<O&UAQ3pSD((fpD3IjMa8QvHScGp=LUajnLSf|N
zVjtzG1Sv<6LPyd{Bx#WZ8J`RXT)LN%?<ZKd&Ofk=Cw&;;K!AV}B2_=N)8?~wNscD?
z%+xz+c5D+UVoQka);<*!?2rPap_OOHSedv#nw$fR760zXpKI%`=ae(EuCFwXnB|~l
zd7VL%Puc3>Kjj%z7mmVRb-PBm>GJg+H$AWC*BF)bqr2dtlyA!Y)i?&++g+U<f9<lr
z0H7sX!d#V!Q833;z3Oq#rjH^t_T*ryO<2a|S~vwfhqre|JD5!Y=}z`CJs`gqF`$qV
zLjB>)<&r2Wj2Z^}gHl8nXvqJ?JD0B%)9!AHbh3VZF}2v8*CtPfk3$Vc<X9CL{Vs6k
z7dO@uHrX3Rt2^Azs_g;7CRi-2m=Mk!zC#(z6&vX{ti}|vB;+y0x({iDhoRa5EVC{j
z6DZo^C%md~ku%)+7;FvQ>)k!7!hzNl6K-6EJdewj{If-270#RDMY;=3X=L+~Q>X`u
zyrz_L&p;=8kLr=~7mKOC)9#51lt95%6?s<D5MGW|f=bY#9;kR8y|0+b&P9_X+5_|W
z@N%oAx{0DbK%zeWLvvdw?BD{H<9hysVj$D8_RWy0JZqxP9WLIAPwop}HH9OCV1}!u
zV}E<@@=D4J2J#%)m3|JOFyB#u#6!FYg5u4@*xvE;S^ZBXbPd7*+m~Nsh1neATid=Y
zUfoB=VQ1!tv^_OAG?}63A#vet#S`m7Z1@ykCk0pZ1Qlz6945j7YDA9E#Cl}}_dHyd
zOP1#zq8fcwop*C*C2vac?#D7ckOf^INU3o+dxsW%`j7kA1x*~Mv^m>G{Fg7S-Rdu&
zNsw`R8>SS-O*&ma!|vKloRbFd1;(>t&mOOew=3WFQ62@O@;wv7Ll*iI)4S>%E@|O7
zylfzw)GI~2JuVjy)aU3Cw}L@)AE{qBIrs0Yr#cxt^P)GlUR~<D!pRw9Y3*&eFu#kP
zY`O|r+|lKBcWNB}H!mZ>ID>%unk9r1NpJ?LyF-)E{NHnnjZKS{vne)s{xEjunc^-D
zt^3u36wgh+Lufan1g{{UF#XmLwN=;MI0QOfE#sO{+x&%o7T~ieLIhW=PpVeh78-9v
z4J_x_{ks4g(wt@PQU;OJlqPYh%<E_eG}A_M`J^>8qi-ZCC875;+pyeGd>@k#d@2If
zz9njg&q0%sg~iGmRE|YcKq+WCJ`eu=nQj{+VsWzU;otiaYF4)Fx2Z=z9>)x<*3w@9
z_j{V?!HDCDdB>5kSJ##n717;_c=dKs#<8Y>%9G=`1wSlU^KNxstV>LfRe)&<TDQ|Z
z1}yt$SgEG7CF3v`yeuo{%ob<F>(PL@DAF`8@94PxD8mHxVtxUZNS2nSkx$a?%e)xY
zF~o6-DyNtJuonweGZyGwHv+wramA3)-F#NsN!<p)4YyrxAwEP?Vp?h}fhe_vTau$e
z^F;fh%BjL=L^^yfC&$RE``<N+hl)X3n@SN7Glaj_v$xm;G&R?cizc#@GB+z5ETu;!
zCkx0mF5R9?3z42^OScljrp%$He<!T$zVQ`_z{u#31NgS6`*{<D_GA?Ax&Q7tZD!U<
zw(dA*XFrc|_@os_WqzM&b*I$)4#FWTTW)pZ-Rk2IvYnVb_%oM6vCC~=L50=nksY(N
zA!}h@J92S-$T>h<iuW_v(#$9G=>o9aP$np|5ZI>;fTNs~vnl3CaT{8zicfOoZ|IzS
z+Sa|`+K0}?)=g0l(~v2e7vNPR){xYMG;y)UW@V7zV08XO&337xdu(@g2!XkxoyoC%
zMhxwQg>F~lI70)4NnL*amt6_;v7gX~3rNFa<=*l#9xuKhf&#meOH(uH+!{I3Fjwi)
z4j6KvNe#&Lv0vr0Hxt<Q1;$SW<A|y2hc6`{l-q7h5v52on*xLQl0=#l1f8}mFR1J^
zA_OD+|H1>jZ*f%3VT1*-o8RyXWDu=^!Sjv)A}T4qDQK<c>Vg6)+=|G7_D@nM&w4h0
zB_(Yo46kbHYgH{Q<o-@RVkBSNXkE*~{-zrJoEFZO6Xt}fx*1dv!rlowfZ5)$B@8B<
z1!<JXZd6Jki9v7vlPZV4#6$<3sDBl}(HXE5nV#82yBSL4)I3n6Dnnx<ZMy9|DLva}
zkX^lP=Q~xsy-96*8D@8(XXnk&LWwLPBi2^2p#<IDzVJZ&hI3;<Lf}*G7&s&5Pr~k<
zx{kXq>6l59V4e@9(p1=b5+q#48sJEpKt9ektQ^F03^ZCvlxSuD%GiANFi)<vJSkLD
zsiA`kR+oi<Xi^sZvbXMtsdr_j<$?k$_{BI5)6j6RaL%H(<VAD;n(X5b2H}ub9s+V!
z$e2Ce>D{3)pgw}5hK`8=;$cBi{jdZgqQT1!9z?S(oq#TwSDc3q(eyifZl$71)2VI#
zU{5nHxv#8&4%wV6-EJ`gZ1UATIx&%BW-#Dq+ob!&esq6Iw9L3+2Q27mN2pV*>C6t)
z)W$VWrhecD07S~t*OONlI)N=@5`)S$UZfuuC$cyVHb__G5YiFJY}Cckl^Gx|ED^F?
zb6cQ^?e_$o<&dHQOKHF-xUY5S;)_C#jQbw-m)r(^7;jA=5HYYHTTw|ri%b!FA7G(a
zK(O||F<`p>A)J0W+7o-9CU}qUy?d9tURdbEOO=}dz)ypIH{*79tE+|Y&C}iv+v_ZS
z;0VwSw=wfff`lg+7?8%<9~b57j`Jq8KFJGJ`Wu)6ZRC4QlAxc@^xgq>A7{(%Pm57r
zYj1D0dV2)#{C+{bHw0fAe0Tj0no3V<M2#r7UB))$(^nsB6W&kTJt8TWOGtAhkzhTa
z$NbYb+{v2I5rid8mBvFqie5Swj|0nJbIIpMu5KYO;bUC;-|H#qdQz`4nlv>2F=886
zX`cZlS{AO(k4f<C9Z0bH!Ii2z(<e2L+Al5P3K`1|=fJ|up0FpF82wnInCYA0*WMjg
zHO1xmEL-mwrODcj<quzMB=MM@31kMMF3StxF5iB?iwu*x<l0@snDV6CIcWFMcy;IG
z_dqQ@$>$!YYDJUEuX(g+=l93%eR`Wn%8j4Xf!sXb9KuCY059s$oJ~yWidVWAO@w9O
z`g`sE-6rdl%kuMF!ahs?k1|XQ?)NX-<<-gKH~)=fK+u^Us2&2TFK_Ce+<WMTu3K0_
z(!=yb+WrtMQ~H|isD(WCjTSXPIaByR_nn>}?%DnsKUEaNz3>TIX7kA0F>qSOC*b7Y
zR8JWKG`pVR1I5lnF6XX9|2j=;KrO!yI+e?QIv8_SMrKVH+^&7;(Ebmz`XwS#bIJt4
z>+{*5OyNf*v7_#%a>dO3?pi+IMEdNTh!LFe4Y0}YPBC1-DcsQKD59y7b8Pe3zrd`1
zR`E+XATg0Xmv?sv>yZlzAL5hqb1#B~$Ll=LE)!AwL}l*Bde6e!YT*y+Z6CQFUq#O5
zzemPDkJT?2$|pyqhgVDv*lKwW2wY*vpGge?DPtYIx_Bq-cvAhC1q4(zp#d!cvZRa@
zIqXEVE~jY>NXQ)?J{c)IW-8~%StD-kbV10Vx>PTwlS`LquXH**4uD1vVmdr^$D;)Q
zU@A5`&5RtZA8Y5(ex%37^-viu3jVc>ruY`T^^s+<$&k&jX?NEwRC*HJdc|S|;PK-B
z!_5od_2FE~G4%QN8`P`JwF&1#Cj9fED@LTiLaNlzd$fidj;Tccx0xI)3DnwFj;<p#
zVsq1<D5v%}ksLi#=X9`cPg}PE%k6W&9G?WDMUyW>5X~{JhGw0!NzB#PCAYS>UxESu
z=I><<vy#4zUHBhy(=$1%?Ojk6Os*OvbEWbHP+F0ZNo^k;Phb)xhMqM;$xah>Qi8LZ
zQaQ<4UdL2a@jN$sP+YqTpjh*eM~pT1lz*p)LWosuY9kf1PruOOSbJ29Q>;L-l-9B~
z;LA@=aBA2C4#Y1!z!Nia1fwpLP{GpeyFNuSc8QP|%lmCt8t{52J8}-qFB+rARjQ~X
zl(R*z&7UuP<^WLzZ#mm5BG(Kq58uG+xV>C3@t@mfmo1+MVi*iHAPdT=;b%ZoR}G2q
zzH-~z1HwRJ%$<*f+m=6hDfIA95>`&BRW7zu27;^VX%cqPPp#Gq+>qvTJ*%te&KI3a
zR(k_&^!KQ^Ekf4Tp3)2hY4Yfo{&xrLJ{QGBj){<6<PcVN<sXa6;T8P?#N`pj{>X_6
z>5LRgs*QY*a>w9;`M{?pg2Pi<o;77y1joP7k7S~2&(IZskvW0JKS%TMIyZ)E(qhd)
zG-Un@UKZYklbWEYt+u0j_KzF93_{Z8mD9G01RU}>LU81Pa44oeGqJUz73`1~FWY&M
zt>#LNN}>7U=n8y}Q<<=J#n{I&xwSr$VJa_p5MUZGV|R#>n-jUaqvN1>H~gpZTfxX8
zpsP=N9Mu`CUxN)$rZMxeq&hHXlBvaXpuJ$K;bOFUsXKjEcQmWxfd7e?1Wl1;z>0G%
z`h=`DY?W0u8HkA5QlwVmPj57}`2cd1C+<=0l_2jfxNq4ZN(u%bNS#-%v&+_#&^I;d
zKwH5*?LQ!z>b;9t094aXc{$i<c2|3aNwczZL0Yf-(U6Tqe9ZmWq~8@V0Z@m#<+Hnf
z;i&SSPB%kq0>*ADXvNXhb~{#Uy5OnQft|)-KgYGxrfu0MYiDc69`iVvRuLR%p{$Ld
z?!*|2ks)L6N=T*}=m?yI=EyrQxy4>y&r6Y|^DgYJq<iFepO6OWc3274)4-Y-JRkLX
zWKR&#-Yp!<&X_N<<&r(!b=*Z9Fr3G5er<vFJ|grEohs&f$DIzokSJyO?lFYPO)1)K
zl{>2vi3DjrZ?J9iK6_QoN~ZBMh0JwcfpZ`8GHkyWI{EKMV8}AyWSh|WdXKoQX^pR0
zN;9)|bCZ>zMvi3g`;HtMF7Ay@O>a5017%KCdvmq7oSj|bXcqD*+=I1{Mc&#@dyAOG
zAwGg`pp1idaq?;^dHvBp?B&cds@~Nw)%!BCZDdm4T5C+~ZfIr9gg#tZg$7nr%*XpG
zJ+N)`+wCEnk%H-SLanFIlC9&g6ToIpHJQCgn|*#4talD=?M$V}CX3H7NG~Yfi#S3e
zK1>eFt`m?E0~eg9SF9<vsyYHoiWgQ?6OJt?Mu}ZAWvdM3n_98VcV=$!l;ApU(Xnjo
z)uMHy;QK4hA=LYikx7WjtMKXHLr-I8acjps>Ay*@O;_(aFpC$4t^?lH-lqq)aKY_X
zhs@l*n2~yvmRKp<pD1?L>yJgJLGJe(T&}lYZk?r7ZHHI1+nXYVI32PSLf`;z*+4lK
zFz%buWz<Nnl27kIJrew<rSs_<hA~wKP?1Txe5M9nvNB@0vL(PtOjGh7Y)|twG14~y
zG%!dab6_m#YK9Oq8SCn)mXV5C@Wclh#tJjNOY{41OJ3bFuOE0`{6Wj$ZW{FIg0nFB
z{h@6;ZG_!#7Im(Pv&v<6FQ0@fnjG>a5I`T9K7}iF;=kxT*!y)5$CT@yJk_~LMhCz2
z^0)`l@sg&SaMPOefi35JWViaL$#?XyXw}v38Y4A8M|~1cz-yn_d;5HBt9}{N46&u&
zIb8Pl<cRY4&5DQJDZIU?4<Utq*I(Vj_v9WX%Ul+$E-^+O7vcFK%C0dbX0)0}5up0t
zM3v^6QAwI_3vjlhyowAPa_y+`d1l+@Fwr<gH%p7K>ZbAbM=^_WZ2hxt+3(knvD5a*
zwb}<+($Ex;Ca<`;BhNKpt3jdsYQxG5)Z=@?)}%5mz^<*;F`~s`reTg{E#X*A+arh1
z%~$b|ri*@~iT?4v7Sf8D!WqIkD9Mb${`{geJqN#!!?lFMqaNHKQD7FKjN?PlwH185
zOAjw}qL{^8bO<`Je>E48L#%wEV{`nR4)%W1`)*Pz4^(TrotJIY+n31jOyAkRj{T;j
z^n9`~dT%*?#7b|fK;PKb_weYytZ{wq^?v=t;8!<3IepFXo-#(WzJ1AcPn`aGMiFj>
zGrR$4OY<i2K2cTg->j6_I)<2Iz91CrZ|UNWE*ZS)CikcD4%d5MxPmS(jXJ99->);T
zX7vc1-p>VMdD*7#-#=fxWEljsVLU#i%-XI$K@}r;QJjEtAi4MJEz9GT!tb@#J3VNm
z#6o8AO3BKAMf|^Ps`tyP_Ihao1K4<?30JZYoftsAREC*ov1X9%y7P5E!N`gxBMFc$
zisaRS)dfq2DwAzrz!%mBw9ZZA^WyI#k)$+Ihn(^DaV5p08?&mWk;Es5cA*;;qU0;$
zy15*zMZ1=K(igo$Z0q4UnidvZew(e+JF;+o|8saFvh}ZfJn#JXde&UBG=!3LSYy}B
z3k_>`r`KKKY?wF8d;A<)k?CK_mcIedh^#utg}Y(6;Rv_NXIMvtLF#56&2K{6EgO|t
zC_2aXj=}Q}%+evuG$t_GQnlB+J0CKNj@HA2R6iA1dzju(Sb~1oW!lrLOTTq(YaN}G
z3%OODcVO97=@r+79+$@PB`%v9&@PMe(#3UXW4m&0>lLP!(v*?_a$wtTxuTSu!6#Qe
z5V2Dm_yufS=?orjr*Kh3r14HaRm*($jt`DvYD#N~0z*(N9)>x<rA+W&+3+n;6mg!7
zvyf^1exd9vO*lk_Q$w6uJPrCx-K^3v5;b5)evU{1gyc5~Qc=l@w2n1budFRxfU@vh
zrbB59A!6hLs(HEshY(3PyIGiEIr|fqq)!mS^km&s0?q*US(G+r6(fyPQG8Ls&TZMm
zp+V}<jsHdpdzDcZ2`dE5KFHNm3KlAN5h+)%w<&B8@$uvXL@c{4?bitg7Qh_~HJPd#
z{fACT@SvtKF`U^)-%VVs=WZwm*(b@hvEgRh6=z~9$)t3v;D@$fa+x9D#dhi7Fk@n{
zQCf$-@68|#$U;~%8>5Fc0IZ;0Eqy~qoP<n(@C>yglT{nfDX4wX))tRjs+dkz(1W#f
z?<nANRIq7v?(sJk8gsYVIM()C?2VR@IH5_Wboe9op(4vt0(@se{=W$2g)4#vkjG6A
z^W6y^NkBnY2^Ez%)Cz<ZCtogo5%sJFak&@=W|f@omqoL@-o|SrfXdQ|n^@P^D;eMf
z0AwC!I)}5Vc}c>yN;!=f&w1cd8kn9|LN&VTyL0ViTV5Z?6KczD7es9V6i}S*-k~Jq
zW}ME3rf$0kQ~I0VjNULCWi6I(Or}9Q!<g<q1iRB2{K|wdA-sOtbW{q}=x81S$yEX1
zKL}h>#(Rkmbou#gEMPITp#A$%I!Ls0IFEa6{^2BR|MUf|Nww=~O{D7P$=9kvH~DhY
z%VI6GzoV7yzdKfEt?ohhGX2f$x>^^)nNP(+l3<{dibvsf#Sqg2zR$UBytby4Ev$ux
zewL7wUBWzc;rin-Uv)ermqE<JGgYp<Ie^5L5kp-f^jF;x;wVB~P!<;=kCqW71Uuy-
zRv=Oo2Q9DgeIM!NX|RV#9l-!5>xE3tDw1R&cy=ks95GC3e;G+FMY4*Tj?P~kyMA2a
zBnzqDnSci_L~Bs1La7MbGJiM8)l@KI)ho`|Qa4i<uT9KA-G4VWuoMM07!$^nk`f%#
z?}nUO2LtaMU~-3iD5lvz^s}mCt0Gh30_3I{g3Psh1r2+fjeY&OeonEnCOIOvSWm>g
zEF<NkOkSR|tk&AZ$U|pwOK4SQyYk|q*0DLo#4`T{)TAlJ<)<&sdWVOD5@T(2=es0<
zgc}9F<fs7`I=GIkvs%^Qy?6zU`1Hg%P5vB}j1G8l=TRVL?39h=Yr;^1&pX7lw+S#u
zi&HWFwS5DYsrva*GkoCRBh(tw#P#(C0Qb}V|2G`>5}zywlKq%VvXXu-W`o}&T47yw
zM1cci-ve51es$^ovCQ5Fd;;v9d<;aYMALHFMR-4R;;T~DHIa?8569hOU<yryo2MGH
z_nVvrs{&6&8oGnuO@U!~DRD1vS3bD_1Nqv|bGI~23j01XsrPN_37A*;;}(dd0IXy`
zWR>LosMyW@Yw{4Ul^>1F`(nldh;)CO6>`6Jw0a%a9~YcQcQrF}`5$n<=6~=X941r0
zx9Yu#^z=F>d>u{N%~5x0G9*P_(diuM<@g1C-52vu-H3)|z<by{Km(-Qml1-Vag3w5
z8}+j(i?;P$AgBfbQ}c8)ILBcc#oS$A5qI=nLmGn>cl~v9ZUzpe-dpWHh`w&5^p0QB
zNu2xB)KqJ(Z^uo1_vg3)uJn!C^j6uZHs+Iu&jYsK-D>Ua!2$?z`3j@}ER|exzozf;
z_}jbv3-nj&7r)mR7O94-*-JpLSFUf(fKb#zMUyZH#OAL;9COA^-U>HUPuC2g8i#fx
z7CMXfe%3--{_~nu-&IzvLfZC5A$T*+14!A%MQN#TaB!&dWrAoGRFzcCka)XmA17W<
z19#V`Na<J!6%7@8P5IPwAKk}tTW(kFK<tguE53Yf3muDFuC=dU-^uO%qU!a%b~p-?
z9P{DffrPczFx~Ju4VAm%Ck?eP@0@P@klp&Y!YUbL#_M@q&pminx_j^an(mduz2M{J
zkV3<uw&{8K!GGxGcl$H<^N^hL^%*z!ZPAQEl}Gz(i`z2WH22{UUGJ+~jq~oVGK;%g
zJjM8&h}0$c1kA<vjsF#yJeSix%=p+!ez3?AY?&+2W(uVgV}?t>Dkcd(zK;$n;4R=)
zIYe-*m`k@{^B?oS3tbiHI%kKVukEk>>F0ZT{vkjry*JVO0&3gW*A}!r&-ds+E>202
z!V8a|yO%D9cUZdZ6DM$m{yVbu7wS*o9Srh+_P!(0`|hFwul*<0?+gO^shszu<-2uN
z%ggIk_joZg_4|ABoq6$P1@9^?ONO$UHq?>^6x&HDkxHld!3e4}#xYwm@p2(bi1vkx
zyO~jpKqAA@OIF$9%fUJ5k`JL4zhzy~*u;LRquvcILOaoii4=-fMiz}urgn}qwJ_CT
za?BH!+jthuv_nhhU&1K&DkibbPy6yM+YkmAkIp-%oEn}9r$sr2Ls_G7A^|6zFN38_
zv+-;J_z@aO>QBoH`sc0T*602~dc_u3HK_XLO$|E`BK`hsVg)GB=Z)vof5kd<kJE>i
zLe=eDZT&Dt^f!AerQh0^+6H^IUVSW=R_dJD)ktf?D!px9mpQdLLWy8~+irAx=iZ4j
zZ+?a{U^QOV<bDb0#}CuMae<#eNTv*U=V!nWDGy5l+~vlkW%k<mQ|(a(aU;o;i6XT<
z$zBoqh<}4bF0H>NZ%zh@(AM`?>p7>~*jHiSye)4LTW;(rVi)s9v|>y?HxK8tuB;tv
zy3^k*PtO#W>@>+0DH9}5NIi0o1l^oCJm4YbO?%W2F^*-g58I8hDr5{V12(Qqcwa4m
zsf=@yTvZ}CO^IwGjeqQ>e9-oZ9(NyaZu<E0+v2>2Q`*~UY0=-gY7BO<*+LmanT6NQ
z9%^1vtjm#FB@Lu4<QcLOJnokqmvQtV4XpJ>ob8J^HO*QZIlD<q&>-4EC01QAoqTWy
z29?moCX5C(m@MyW`AsGGtXxaCSGo8Txu>6@i6}DIR7Q%eJCkTr6Aulgz_hS|CzhZJ
zWX#MG;TYJd!@t9`jtnGzw-ShZl&37aG(5-)>tmx9NEJoB{`*YR7{YW^hf>=#6_XTZ
z!UX)9K`PxoO4%l^z`_W6tVwOJ{uH&=hUW5_iDsP+ZN1pgYvAms=+VwMhm?AxM-7Bm
z8o0IhzM<UxOtz9F;NRo?J6_q$%_aJ+%}v|R{lnlnoAzt!)j5P^^7$Z@;JCkYLYuP{
z@I4xr6E8uT`T8aU`!On&EiI!`p&BDSt8x!RClZaI_n+bF_ZAx>*Z|Z(8l^I6q!CI1
zeqv}8%`=^j3y{eed?^fea~tRO>r1AX2V32}u90;u@xF*s433)xP%-@6V&w<7O>{|I
z8l&&ULP_wW$}q)m6pI8I9{d{tT}hxoo_D)Kqe;2-v3kf`UEBOqhIy*DQM`1uw0X9W
zPsPB~AbL$0s&+@d;x(-#z(6uOAFErHN-jY;gH*!l&^#kSn9`ykJTQ$^R$?#7{@INq
z94ZJCk>|5tV7$5iN8(OrTv$*-=~^GxwC@o|sa~h>Ox&aNl0~t^UUbwI?Yza&#h(@9
zh_QC;hjJ$0*<ww4!?m9&Ci<&C4b$2x6h%@f`w8u&`hBIX8pV2X0Cj#|{ZeuL*6yAc
zbrX({a*1s_!CZV26@Ia1fZ^)?`$;kHTeINSv_lam^fN^o9oc-TAv(jO{3UJ?W#tFH
zSVepHgkdY#0TI&MN^G@n$x`&|c&pVD1gKUTE~V^#ricARkrt5x<y0NQmx90Da~I1a
zlcM<4)3m*VJ^nTY!||k2y`_6-m|#7YjlGGz17=+Tk~n%0^&pj?MRJ^q>+W4EgxJxd
zMoLq{0ckPoeYv!XB>x3*aFL<f4V>S-HOJgoke;(3xrGu-)XH3mp^8IM5a)dadvORY
zUeeU){YNXEd;AJ<M_ke=DoxmsuT@dB4pfJSM%~i=JZ3R#DU}lJTpIPqPlc2{EOfaA
zQ}Yp!i6Hovzm<zM@S4uQ!=<-7vOD#F{hrNn;6;tmK4*37>lNgb4X3Ff?upUM?|8l7
zK`}p`H}Rx8H7_N&Wf^;y{DOi?`@;=`w0tf@xfs~LK{U8ji9X%~<bZJhS-dRn>Bih3
zSAJu}Cx{HrR8(?s)1VSXx!#*<sal1F-7VU+amtoa{7%tuyNN<$YP54Y@jFZiw$ulF
zT`THHXUMn66q&JclS`3_d}D5*_TE9pzXs(le2t5df|?G0p48|!c3O!-@=l*gknQPL
z6k}{d!8#-c%TEvBK7T7h9@O3arkM0xAy<fms!h9UO{eERdc{<1z=C(Z2c^`2-?t4Y
zFxjrl)l%b{jWorbi4|fS0NK{$a~sg_M@_8Q-&|z8+~0>H0$=n*8i?<@e)&!6Fn)VD
z$?JgvYMj1zyQ)H$t8+N1Hs!GM4;7_RMV8mgzkZDAw-f8|&+)dN7(HjFhVgh(2hqd>
zV?$sG*0SyZ&sjpx)aGj)9&$@PadEvuYrA+Z`qLmI%j4s(G>xzSc|Djj?iEs3A5F=$
zD0ISCUKNOJp78BE0ymMoIIx4@b2Esb4Y$1ZZ?_gzuxoPk%x?C+V{B^~TwZgO=5UYZ
z@6RibL`hG^8FZqz7#Xg6tg5q-S~jqd;2s1Up#FsQL~=-*v4MkpW9%aY0xt?IF;@(J
zwyJ-;hb4WukKm1wKd_rhOytYln{ap&d0WWhQMRR0*)%%3##UQvnK;$<uZ<dU`8Wqw
zgd<)Ge*>TLZ0(uMOc_3VkkTS?*7p9N8>nWc5AeoH>z8)#&oC@%+$`8%JJ){9Cq>Js
zq;WEc`c(Aqg*<eUpoaWOL2qfYhsDtoA5W3%a~AvE-6@b%%rX#9e)^lEWK6LZ<~*!J
zJ1$d*s^;s;R$qK9p#S;bw#)J5T4na*zCwVRJCBx6z+HDE;M^(BW}(zL-1Rx#!NM<>
zv>3$6y6j?AOp>r@z^_h#_gSq)fZKp`?B$A}lrBmV5)inQD3=e`2q%J*G=<XAZ9HcT
zmYAi=Z!(O3pnwHq8&}1WS|K4GMf~2<q+m?(xOL>6hv>oWkjEj~*W^)HFTU#N0QWmN
zPpE`d@xbO+30jz>k@iWmdttk93987*k+Df+E_*7+yoT9uEn;Of^@pl$`~9~o0hjE_
z`9<9*{+@d_HBZ`_$MvTR_Qc&s9HF>(uxgha{7ix89oP}YR=+70Xc2n6_!C&IHTC`i
z{i75k&s^z^5wJi1MMR$sP(go6h+CqkI8wtTOj?Lm*|_h}DU(@xyS?6@scCn1uy_o?
zxCvff!*D^5>$%@NG9}j6lYdJR*%x_C?60rIG+fvh@eF@Gp!5p9e6JM_AcBCnD`foL
z6BiaHICjXa=M$;8XlB?luJ^Hf=B%}j!s-SA2P^}1oxdNiutKp5wt|qsxTlR_TW};-
zv(ouYG8x9k7NUv9Pq>Np*UzY81iAZapHt-NY1Lap=-~Q>qfFmLU^zuE^V5iif?%TC
z@L+{*%k{jo42Skdw!Opj5fcX81lA~IN>`0$VA}6Lp;JtV;UX-?wQpQ}po@A+&{rha
zmo$&@Jv0j&HeLm&W5!V>5xy!}d}oRNi4~27NwGG>bqduV7_6h~JvW<qd`(in|2wnW
z{upKv7U-WFf?G<}?E2h%Vua<q{e~t;SbG+4-L2Osov*T0QY0aoLb=D#UQK-Ci5Y6_
zT{6!9Jlzu+AIKs7ysOvaqh?b;NRBF(j9}lzg7Ay`q#l=zB5kWiDkrLCpwBT`O${TW
z!5Veu$$VCYfCu%p#iuMRBn#a0o|vGBp=`~FN5?0JoJx*a{7oB*?&d1x%fFZHjlEo5
zr3RL+9=isy%%5J?I|RxsQ9Q)k>jS4MRB9u8_20#`@Z$e*bQM5tbxpK}lmf-wiv@Qt
z6o(L?xE3u?+=>Kkad&qOPH}gK;1qX<;_mRj@1J2{5|TGBx%aM|J!iL^5(C)8y`{V&
z_d?2)@J=e@c=mtS)G=itjCa{*GA-Ds(GR40ijO1rxDknTcQ0)>o<Kym%70I_s`I(O
z*T(mxG))q~y&T?Gea9Jnf5*2mxPW>f8tLtIO!s*In+|GfMRq~<M&2ecykaa;o%L*2
zV`XzU+=M64Cj`kqUNq4Z=hPdxB@g>+`gX@hs8#otv%M^CNtl`I&ls|{b@u(g^I@sE
zb$1i);F~k0|8LF6&sN<XoTW>zJbsj05+f!nbLIY`a36Tv{cX7XeKfXt<GJETc<pkU
zF7}(B$0DxvoK8B6<az9jzUV-ZX;QfKxBE+qZV^4b4ht;qGA4*kF1Q-i^7f=QOS-cP
zq_sHZjZmLy!Wr;j0Dk+sgOj;9B9NCFqjn~bVKMffA^F3vmX<$X&y)DS((Os7d7A~t
zm&o%Z=(yCjmYw?2&o$@ldUdd&{fjk0&rDmd#7Af6VTxa3EdLydXkdVBDN*PdMX%;T
zYsx_4=@21z@@HK0U}f4_6&75*RUW6&>~BK&BcDujtyh?gSw`H5pEgi&1Vj4$$>Zf4
z(U)TxTY|RPfFs%Q)l|C8Wuu*OKBP!Rb{AJ4Ciq_MThxo=l@cB6Am)oK1Q4|^S3TW?
zyDL3}(r#oafL5Il##Vv08LiUc85N{DWXeYnF9xOz*p7hi`Qq?TBqs8OD1i!bd{jYP
zZd?9kHDp>-5)8dK4s$m{*#qKtTu`SVV9M4TYOTJ>Eb(dQB7v2{(#aSp;j=C_RcTA*
zGWI~S-J(%8|DHMJZ_E9T)lPqC7<L@&*hP?JsBqb39-yG}Q&)NOHz}IEHL<iXu7RHc
zlPLYC185PzG&W9)aanDvo&!HEnH-}8-x8ozwM}HMv)1uH;zopDpS}smre3si{>UP<
z-H-|NQOf(CfUH(g!rmG9UUJGbTeF)R!eq{Nq5;xjiK2^G4B#hOO-fQ$W+P=X{}o$;
z=Q$;X3@o;z7p@9{_-h#jRXoT;n~JHnrMCS5U???!d=}Q)d7j1ThG-M;8TDHcf8!tT
zL5GUG9t<qwOD6hzSx6L3DZ0Z!q2}`KicGDT$$R`}`Oz9)*ZSJgN{93q&x7Z5N>r=Y
z+$CX_4LHMZD#7D>*@~OX>FKEmR1el?!sY${nbgS7#dXp#CN-PCMk>ZkxeS(=F^c1+
z%G73jSCCpm7Y$?w{d79G<q@@p{cYaL5v7$vUO{*Nr25ST$jTlwzt)P1g#sBsvihUJ
z71h{`Sy9-?D<~4TvUxcHMvQnb(MkPG<C0}1;q^W(rg237v{&jZFJAH$oP=KO#v?4k
zkVAvs7)6#foNsadi+OLhvS$r>I&~K>^W)Q2mFE%ydPb7z^B%Q*oZWq`+~amT)M=KI
zITGtJr#n<%sJEc)k&o45ed}9%`!b5okPv7aiK84-%z&S^I*|4@eD#T>{bkjAxBPvt
z=i#R47jP%=CdqugtxL<q1`p@>o%_H|GF;`;`9H$Fo2(>8*9M;zYgiGIc3MFmSn-LB
zO_M9w(G9?^EjK?8PKH82jSEL#?XQJp&y}PEQSJcsXoN;z@@0tYB=xYen>l1;^vJ-6
z>7+zUjAI}s8!S61Z-f=E<l-4OBf*gSefz0!I*YgJr7~d4u#^K>zG4oBI_Vq^M6C>*
zl`zD|_56BhoiM!miXYM3hlYlG@sl!PvU;3#qNWKDz4|1V<Tc4kOgPXBQ*aZ05wyPO
zmuu&xu1DiSS*1Vyen)6AL!d0vmo7V#gNvvYd1C8DET@Sxg0);Dw@lWLfvC;M!Qr*?
zOlanQQb|@G^AE>AC!Q<G4tBe-#fnw3EdS>3p+MU@=Pq*vf$q9lS!T`z&IlFK)2Crq
zM+lz^6QTy$T;p99+kr;X)gS+*$F5=fl(S#qh5hTw>BUEeD8aUKf2}eT`#x@@%%D+c
zWB7c^7YLMd!b4(K&UdZiky{1{VPvZL?>t=-iRd+ViHKY*kS6{SAe-_EPAov@&?r20
zbqXooRARFZQ5Tk-l%ra){o~j;yA{dO*6q;Vt=-_+QdDCK9bccWWuz~=`$+D6SLa8y
zb+qdv!h7#B&#<f}*fQ0&wYW-$ePjRW8dz|TLqjl-{@z(4W#*9vKGvT+Qrzrd$M7ve
z)t`_U@%e!W<@4c%mwUP%))^B1>V{crD8!9ML5-GQX=Jc9-z(6TDLoq(i7WSYc;VO>
z5B{C)%H3;ho8Ry22h7aSPs}sxO}+I=^gD16ZF$ZmOlH{vL4$~jkt23lUvs&ZBEQ+X
z6X>07&u{7;*WN;ngD;llpSOn0YXV}9>`H|?V{1XCj~p51j>SBKtHSrFe{6Kur7aUH
z^MIYC9Dg>y-_3+m?7o0BAlJ%lc-lLkJA7}_R`2keyi~V`{hZKgtODw0mC~Khj-JqW
z-SXsl_=%M=PUxw~7&1CTA1CB>?aTRJmTacq8;C}E&QZ84;^N~=2fIC-%`h~AIjjyy
z<a7Dz4g3SAelSyqZX_cxsF5QiNgcl@40x}MLNZH5&_gX7aI)Aq_BCevHP)LAzV0ei
z$P@*tabBEjTkC-*j@TMLX@oF)zns1YYWp5Qy;y18#X1AdnU^Sd@Un}b{pzDgzy8z2
zLCeDe%}k;WH2LupGUdAqX<FCw{BEI}dF)|QB573ds1_gjqK$Rjw9h5fD)E@#F;9N7
zRFc*4>852HG?6esHi=v^mQ=N;BE&{{h+CSf27WsrEV9iJTtXd;fE}|^*|fgtqsq8o
z-{G&|Ys$5z>J(#xWna6xV^#Nik_gTwqbildA=I5?)l9-XJs)-tEa*v{I$$KgpEQ1(
z%LA52o2)>9nt8!~V2l{9%7iaR)H1IL6ND^yR`J9>6g-#|*99`8u^^%$nnRNEla#6a
zD8MQ{OxcMN5I4z?gzh|@o)|<)OWW8LchULMQ^u)weq}S!W0k#B1PgUN=R<H{u0M9%
zFo*J%S0IclFwa$Lz8LlCBTZyt=J!q!nK*xF4iAw=6JLPbV5wb$Yn-f0N{p5ia%WzO
z*nvmR3cK#VYrg7ZA>0xlN=Qbr5d3TdB!>HjNJSH8m`bfgfLf656p~5kl91xWJa{Lw
zPQdLRX7B#S41a7o*DpQeo45>#`I)XKneC5Iy9!m~;j2ni<9;(Q%Tgm0-zJ?klU+7!
zoAuu{Xjq+<=X|0m=UqKQ_yTA|6X6LMz;3ty)3Iw7VV9+8T>jN?iFqv*&jjAf6Bd0w
z8-vx)<|?*hoRqt5?^RbhFvgR3JGfwSzkkgTa#b-_a-ea$eJopC2fvl?FRr0dA1t(B
z9L|}zy_#HO(6-DdO<Snk;+Kh0+OMOePKf(dn`cY_MbJ-iXq@ijpuUJlX)`e-eh8j;
z7^qaFKi)L{C@!Phy>)lSzhcF7ag^_fV;$&Y?pUF@T$$(0d}v=jW$@{6B3RraqW?Tg
zyp&^u$@p48q?;m~e|0_&7wIy9vnp7*WmenxYiW$R{|t2Bsk7<~^+P`!dtTlT0Vt9-
zGKo3c&MjZSZ_0N87$i(HcBrx5&|{|=Uty($tXH#a{9g+>*6~j6Tha<4Un{J<n(Y0<
z3l&8Mv1j|1sc;uR4gW)?tU&WM|I-tS{o(N}-$nDV{;Rf16^TW}*x5Os$}@Mh?eDDb
z{7GGNJGl;@drk==6Z=6a=mlfXaW+_(W+0TpIToZ)wVcBVTCeM~AL8K7!%lk?nnWfQ
zt{K70=GSH6Wah=rN8;CPhDlh9m8YRBbQxM}x3L##t`=nGOa15GW$(NFc1$DX@MpC6
zxFU{{{0x1pcVE*g#bJkNn>VHZq95{HtWw34d|z%xnNJ<8!nD}Kh32;WYLUnOGx2!y
z@#A7d@2#r;r^vAwlaQO$21q@r(D?bb=b<q#hWN{f!}M-ZVuan@Fhjajri~y43U<{c
zrkiwd+9Q*?&<;AlTcnGuwEG^jAn_c*6DBk_$SBZ|QEMi~u2G#|>W9X1qX9}{aeU_c
zaJ^OD@?101qXp(g*E)8p%<o~B7qFL!I#vX_+2?aBB}@h(N@xvDD5nDuWDsy*e?ct4
zb>bqy`vvSy{p3Yxg7yPab7q_*2C{EgtG)`XnwBb?KAsm^M^wf2dJ*T+gHm`B-O7}P
zj<P2S)E0A%nj1qPUj)&ANW3oNBUqS`0T$ITAuOnmy}#i2w)=AHA(DBrhg(-6KC|Jd
z3RY1lxcN8zY>@?tZF`ihcbK`|1uc>N0e#WFT>gB_)v;a+1I0AjN9+4!a?|?7^6^O^
zf`jHiAyfSiu_TTjV0E&cpCw*CzYGoX<)*L6k_59be42C&+P<!zE#Rc{<)!*jgAIo~
zQ2F&s9ST*OfiXke)I4jcJVboD<(mYwL?iBH+(z-%7p8{=?4lxyzgCz~3!D9kBY5d>
zHVus$V6o1Q96HGAK0wdO!b71>+&qvkAMF&;BAcCjs254@geplOh5UX$duTd(o#9sp
zl3_#5z2|ph!Uq3=QNq7;CvGOUUT2VJ?w*jklf9N;*c7Yp{HV@aMYfU@cU$YP;$d?9
z4(0PX4p%^iPe2qe^+$4s@Uu*jr(O>h$A&{Zt%L^*Fe;_1n^i!6iOMHiG0;08Lqgyv
zJC#pWgpjQj-7}RNM#zjd>16G=KH`sg@!tp#Kf``4HQbO9-2ooHj`SJ6+aB}KuS@5|
zo8N;qYYO{k^SgNSOv1@+YwD8(8B6u{Q8mJ9&FwNaYj~Z>a`uwR5G(sSF2B~(zwmzg
zp29;n@`nbExMGBir%U^tNC?nDd_(`Ge)aqQBqBVKM`Z6?^XmZ0WD%iGppvp4>V2ez
z7ong`?+&dP@bp96;On)A?BMkUZN`-(5<hM|n9*wpSr|*2;`e<8S5~gjko5G}gGut=
z`6k)WW$B*Te-2gd{Y26OJa)G1xYP~TzrQl8By}9ik5>dpRMKRrz0S-l_h-<ymt7HQ
zksO8!PmdM~v|tUpyM<L~a$@^A^~;6#lM_p8d)M8R9QkE=_*xTQyjyhpP39v9kSW>k
zZE?YzHaY424BWC6{*aC@&82RKf~X~@a!up+7T!|DM-^Jlc2X)M(>}gYj8Ign`-UFJ
zh{Gg!qBHp9@}v+{g;N7d_p|c*%yOe0){KAx>rUF7;COR5XVAyGPKa0H%cAjM&C^AO
ztrwhQu2M%j<3lEz@IXf-79qnAdY56yu2IOgkJtFulKmLR4%PRqKSQ12WQ2Ilj8(u}
z0I2C<FkWKb8e#&5p#?C9=1%VBm^<choON_@UZ1Utb=FAdpX!{V5nC_K>r@|a{kH$;
zJ1L-9eCF-(@8Z#ACi3ojl7F;jmS2x>7brsBO}~xg)GxInzBt4iiyX5r78ukX-%a0P
zu(h)BwxutFnjCQ$CODLGcy*ujFc^Nai24_%*_*bn*MWhUv2V|>*~7WC^wB-=n_x3Q
zFO~A0){6`|-~iGnQ)6FhI3G9rZ}TnYTZ=!553&K2V-Usaub@pW7sBVp$Vi<3qQWIi
zZOi-gUv?N1D|<?*#b24+H6x%J)mUyx5smTMu74h8EYZIFI^ZXOwJ^p<U_hZ|G-yKS
zeG`yaO2b-Da?<Xec@vR=sF*Gmq31fU7dO{g!dy6M8-Dkg?Y3yFxnx}aV@oB35#8qD
z0jo1<lk*raiB<ii;fQz!*Qoz#@x55k=X^zCF(YK>+9M!VvZ2iXvOpVO`37cw`X4IP
z8%nI};o@I{KeOl36^Iv8VZDkPyr~TtnJ$!1fIi;&0(8)k%ijWCgWXl+!zD{qs8+LG
z7uNU7QS@LbP?feN3XMyW^74>MNxT#h)@-!{ZoajV7Gi{P#8508H_~XZm(8Y3pn((u
z?_umXquXT<uzmtIB~TN%PhYIJf0*m{^}~4c&J}@}68s<R3mH}g&7uI2B-pl4^O0iB
zjc1b+7o8;4XvZMEyTFtnmEKTLuq8Cm0&X<FdU2A+kQ;kxj~bft?G2Y(q9`t#syh|^
z91mwN7R_QO`-SSPI?iN-m}%(tld@oz!Mu<XT+U)7+bo;<qbX>SWt43xXXo~vme};D
zTml*;fAIkX3at$`P6EnNyumVYRFV@Bz{CaZPY)@e_BbRH0z~N{V<>+uS0U=r?;RBW
z=nVoyI>y-V+DcX5gg$+oIb|kRkrA4rRU(WqGy)s1hFX(%B+#v1yRR#_1iB6kZos1A
zm;%lIaVCiYmU#0^<q+VyArHMuch7p)=9XG=L^u%FCSh^d-w1$x`!5R~v$$f~Zvys>
z(W0IJ1=l6tm<8r<DU@&F>@a&)NQ*@qLNCDea0*#Azm94qL|HM`2sRUzB>Rz;v1D}L
zl<Uk5&qM5xhX&?zKSg=RvhF^I&}v)VonS>$lj8v#SgT{84SaSZVNo@O2_8^&=)T%M
z63-)s@=pbqWVP*&iT8cm+?<!4OuSK4-(xep0NUQ_ylBE~e)`=y#q7Xw7{BDB8PZK<
zq%^A6L@y)X<G<AhE_fm@^dy|oW7FF+zGQdyz3=UM$@)9ZI?-CawdBM|`;Fwc9`}rj
z1|Q+U<a1*oOT-fwRwxLG;aBKSdO_y0K!o4`p{0fU8Fp=dIFJFcp$6+$1kjAk1POsO
zJTczna~W?+{==qWf;U*I<(s4e^()F9^hn2zeW=$<`wPqNik8v%2NBoW4Q52Chud2K
zf<iHgWPO?W!1QflYrKf?`BA^MYueGWN9lgtH`5OXr$jjNvv<(g)6f)&x5aOVk#>^@
zN(@yxa9lr%`*WELO{tVTi8=fJ%v_juVe_6OE>o(H)276sc6<N4x^L6&33kX9O?GA`
zzW@ptqr)n@%eb~^@sCV-O%s_L!6QZ<NDHR<!R==(@@fr8n+JfdahQqah=jO#IE(S-
z8C*&QR(|Nj>IJ9UT?hbYArMUr8A5q``Ij=IWDH0tfZe&6QPAv<69X`R#a_L@?|7Z9
z`0*dChw3<qGHpN0)zu{19Z)j>^q??K?$TeekS3=%bs1-yi_h@9LjmZV2|?A|K81hQ
zkHxSDVSF9t88=T@h$Kp#e6JIG{*rn^Yh)zr|E(0BeH_N6nBE<{rSx!ov-)pAv8yCf
zJP5E{eHN)k)BR^w;Aul7)&I5-(+C?xwn)9h*&4AmD*wU~pdcYc2sHxb!Q}n7n?Ja;
ziZxqXUVq8n*i6)ATFhI0KM)hfrS>DA9U^O81xWx+^3g;X0rsE<ZOfD8;i1A9etJ)y
z<{I6JPTM{!jw1E`JMc{iX9=sV&npU&2=T}^PwckxmfKxD5&`N#$NeYV911AK)-NvV
z%_&@3(-NWUB~joHiMvt8kml?5Eu-d{x8zapUwd_S*2x2Y7QJ8Pdoq<ACj{P6gQ`15
ziyCWq>eo?)svsmBda~GHLpDk!p-_=$E|tIlQ8Cim@dQn<#0ddz{=EH8S|3(BvAI0U
zYQI0spfOtJaCb;#A6F11{DUB%hj|W|{2n&8HCy)e`nY97Sopk9F&=t7)t@9Hq~Ms_
zzbL{#7Vl`O`?-B|D8BFQdpxW+O#ML9|MW(2Y@w%fB>??oB1z9tW?jQyTC5`%L!mXZ
zEM={|eq0QQat-MI5=dXhr<w$_SZ+<c5IzojxT1BnunJINXzuJXgU9p}GN7GYx!kz#
zJ>1fFa6_!j*HSi<ZYG>%Ut#On$N4RXAwpB`oqkC8E^+Fcbfc6LXEK1O!Hg^)@nnCB
z!8oweH)K-Z7ql7E!?U%+la+&2LCX0-@kDnj>faLgm4nSpVS&%jjVTjA@)futeEt8d
zsP1brRj_i3B`L75s#letKXgas$%1iup!`2EHt*4U!N0j=gS-7^r10ZGx~qMRO>^b6
z;VMld!g9N_$w|cBtWA6CCwa0%S;R5apjL&B;ZA$VR952*rQC&9lpThlHtlvLm3D~|
zR*^|6eSTx6@dNW}l6`&0Z?P+JEr({c5RV@s2zS|CHK;KBJ_lvkUe@KSGVGd&=qf*)
zV>GxTYZyDfjwG@u%#D7!Kgz_9?Kg25Le1#-cVtM9wEzdqWDS=DV6~Wze{iW?HC8cc
z@p052EEbzLcJm6ear{EiQ~zzI29*|efz|mDOQ-*&0k1ALQ8e(0z?=YQh(&Kg6s0o@
z9}AIPHZ3}zP&REln_7!(r;6LRWtzp>pBI@jD&UJuusIR1IV#SxaHqKJKJchGa>MZd
zrMVqb0M*I}A)e5dk35*}{7A55I!?jzmFs0ZR25~WMrxaYIG+X0*R$33Bp=@KE;rvJ
z`kd%R_ST@HsyM98;lx&R`(ZR7AoW*A1yJuvN*Ib^6##?;S!Gq2((E_#TI<a7mwKnN
zJjx3P*JL^!IS?E3TXQgKcSjYPRezr58DVDmSKy}{*X~JhQFrNML&nJMPrV`S^5b%e
z=__k+yayJWJm*5X;nxUb!xR@5$yEW{Ry_%C40d+Cu7zCu9UFsrL;y<xsS7owznWrm
zW|~LI_0to{Srb&XK%j*&-uCKtPV5Kt*bh+z6{&l8jIB(wudrIxQsx(rsq#vgp#0g}
z04CX(VWU&!7{I{>a{=`JLze^EYxlc5_Ya)ytOziZmGJ=0I@!vY*rN~9bkL1n@xQd-
zF!?war=>TA;rPiJ<eR5OI!Irw43Ed(ZK~jgtwXu}f790M&KIA%M(yel#T4DK*SuMr
zU#>7cAbk>Tw>(BV?r&_>GP$Mja@3CpuxAuh5c{hGVa9y_0nc5}shoeVms3B8vk6MV
z*yLnYrD)}CR^I0027}G%NIB9gB{x$yW~_}n>p*kR%<cP?l^N^<9Xuji{ckOiI%0c)
z-`p!BKjI=TN7-0*v_Fuy`5!H`JWiV>C6%ow>Mn%q*(|iKtk>GM`WnhSuXsNLr<+H!
zt)X*h8w~<C_}9Vrp}(MTMviM%u;ry%?s0EyWo@ecoT)mHE?GoCa{S}I%NwACU8*;~
zb!D5mQ{sKXNdk4q5P3dn3*Sx(8~e-muww#&ukk*+wEsHN{(<IwE#gVO$OAotD}E(o
z+`v7K?6N5l61NN&GhU%Jw*rzFGVR?EozIt%|D;7IN7RF2LgQNXyQ;~X4et&HL-lS+
z-PS)A;k1RAK#Yfqh>x2gR|9`(VQFIEo1M%yL-HC^#rL_&L)rEFPX}D|@z^iT%#x&N
zaVKU*XP?*ZHMVB>r@`2lp9IQ;@mKW?_q!0oYtb1sc=qewE~I|GU;afsBo3~7M6h1$
zVRL*_{Pp@21syQqVD3zyln>-3oIFY!<3;<J>=YNF>{QCaK|FgqHeDms>p`b;>uvK=
z^eY?950$pF`k8uyS<8F&>&rCi<y=2(E;ZX~L~U;s4r<@V&=Y<mFXNgV2o|5>I9Ih;
z%u+qG_e>QV%vHWP3t@?^R%5t&1DF_2q<=VaEYoL`1LBHcsD5VlBBgiTUml}Ng@Hw4
zUsLyvlczI9erMO1*nU_t$ryaXHV^{xp;*^hb&n)}yd`-V^u9HL(ZX+BsTV7!Bb=LF
zx9auuxZ3w)WKNy1UL29PjKNvS3{8uN{(dJkM~({+dAZj~Yi<}-^m2}FzanNmopcOL
zB4CYt<RwS6X^>WXZlTZL=R&ICX$ER((bK)OWg}#ai9Gu*;%@1`0PG_eJ7zD%b{{X;
zW)aUnM=;HU0KOPi#38LPqMXU#cw3n~@!g+bC9<N~-QkkNytO3m;b2uiJ47pTp%f7<
zMK*G}qBDAfDU;CqynJjGZ)H(;*Q%s*7av`z>d)0h&FG-U<u%Wa!ow4Nt7TmU+2!p*
z<|8)Igu$W<QYd$XTHoCty~ljPyn$n5@`u}sjh~M3FZX397pBI^y<YB%H_~9^$5_@!
z9;ey%Z02`!VJS7S=qJu&N<5*%(5Y8*lSVVCZ5Mv)PTsc6P|xNj5%iUQg*goXWvi<o
z!EWDL!y{?&fzOQ>e0@7oi@vO$IU^M*O4s9ju~_u=Iw`57vTlw7#c1Xa4{)$3`w)O=
zlU1OhO*~%@@SQ#b!SL{Syzp9{qY)NEks-BUqAI3bWd?_}E!47b-7*5{!NTGBD=Snu
z0gvlVB>5`G!$@2JBsa_u?3jRtga9o{C2}@phJQg8#VTmj?uhEK4~cp+Tl>p0uftbL
zAwciuje(iT)Qm&@y%)I)5@ioPzsdosoNQDK1er-^g-4>B=cCdkDw8o0s60Mo+qdNx
z^*3sn71*8^-eB4L-U*76*9gvsc*<bm;q|mx5quqQ%Od*^Jd+pz$z0yE3NjuElq@&s
z0T6)No`VTfJ@@r}Le~fzb%L?s0;1PMr@b`*SDTau?F!x^;PYFFlOZhC2`L}89W|H`
z=QYy2cFFC!xc1w=n(b%Zru+uP5WD@zNbIdMzxWg!r;Xxb^5=sfe~J8-s0afrB*YDx
z8!i4iKy+vOYS2(<@cXOnKc^bee5B_LJbLK{#*ySz%I8<;+?Mx#7$f;!s-C6#^X5Bo
z&fl++H^2T3)duj5XfE$nH7psG>h&yUe@;y<IzN|_PR=Y-Vrux5PXcy)oWq%nN^7kM
zuudiqqB}>sDU5z$u7znjvzI;UrGDnhSj|29MXeCr6~_mb3fV2&HIR#M$dBM=juo39
zS&Yh&cWUv|A6SfQR^zg575sA8h{h4sFqvb7e=&~M^Epwd06c+=*Z}K2(<Xh`v1`gs
zx%d52jB~^XV6oKzweQ&FeU%@DTu@b<Dku*_a}o%PEFz>Q95m_Giv)$8>ML^p?fRlK
zzMu4?2nXN?0KVnv5^klY9a8pTBD^BC?(V_D>aPLli8OG-y06(r%@Am>?w}L7oY)OY
z8F%sw0OgO+8<>n|XVL=YOVJd7Zz5p=710Bsf})Ti<_2<a;cP&OwcK2}PPdOFGUteG
z->ahkTB%XE+0*NA;vyFN$K8dBfmLDgQ(?G%&$#KD`q8g9M)5I6IIcA3(WexoSv6e=
z(9;C7hGAC~!33ezn)`@{YJi1;{@}MEZ1Vv=3TOVd+R50cO6Pzp1@sk~5%`(vDKJ8|
zPC<k&!S&4cdVvcK2->}xWpN~sL8l=sHk7P4Aazfa_!bGv@ek&uHRffzi;$e3T%6@j
zZ6p4hDopyiaCpw<qdQ36YE}#!omhcp_OkxW{Y$GjXcGs{@s%isk4BzT6;?^=%cRm{
zAF#V9Ly7E5V7bSRhq}@7eY}#4D4B1;)^h}98HXdYb+<3k->3weCYl#n_mWg!0QtCO
zSbmPm6E{TYDSF-DQoXySOuvDLZHSY?<qzJpcDAgvP80Mr)!QbfJ?9TOiRC+5@egO~
zF7tcMm>*(XL~QT9EIl_D&c$nUW<cQn?lI~&??2^kp~BNTISMc|t-h5B(Wpchq1!wA
zdtDM`T)hh@MVrO1XZC*P`$YZ~^`!nlnAeYF8CxeGikdj-250#~5iRJESwJX=kh*V_
zUi8+O*XmoY^ddeo4v~{ezamO-%W+0an{i={*oSas6qTiv!XY`u`fK?^nM121>Eb`j
zsXDR9P&W0pnURP3TAQ}V8OI*9MK*tSfj|paz4Fz-gGl=W65SV)koEQ|$fw@XEq}xq
zF1Y79#CMq?ifNG~-fIOV(unR3(P_@9c!l}Gsk>nYZ|6H%cb%uJd|<4uwmC#4hda-l
zhbpIB#4|-`@L{lj=lu7j6PRaUx)<=^5)F8;iYXd`qMiUbz4lB&^3B@KmS>mvrfUUd
z@Wg???l&8U`zPECHxKk#cIhFG0lLRxlg#r?G8m=p=}w%o-NqhH0M6rWE!C*}c7?WO
z74hGxyJbrmsPE@a-(MJS`r+^lMq_f)NKv2?ZK(2Ex4RDq(FDHg)NU2}s;Ny814amt
zG&j9|H!4F@&E~rMW-9ZvF-<`wqKP+)#4W4ZyWt}y+Dcy-$;RcWa+tbt-i*}%a7!SV
zo3@oIGf8vJ)dYCP9`&v9fi-2%UMpqbNkkwNqT|`6KvG3`1+{)+kn=@9sh<V7x<5Cf
zoJpe4R!eB$z1)zYi0(WMqansK56_5sF~Ze~Q>G6(DY=%{Yzs?e#)APT{cLhtWIr3n
z=eKr8aDl@e`h*wGHXsL{ic>Y|(F!pkND|v1!fP`D>b|CrX}?mL<M?%nj2HfcEl0<t
z6+>E{Vo*!oldZ9P#+8rhWsrN{K9aCRvTx(wZEcB0sP~=8e~=^U);q2JI?fFDzl4or
zP@a=j(}*O!?^qV23g~w#@%)<yMq3;ru5>~|)RHNUnZN_9pCyzH?mZ7(R!nX!G(Wq=
zH*sCVoLBq%k^Vc?$0%U)6iaI#FTbHnG~X7RYDLFd`ItOv`>sB4Dt*Jw>ufc>zRQ`9
zV^wa@*j-`o5K-3ej`{K_dAz7Ob#~T>H`;G!EI<B7Ep~N_rXB^{Nrvk_eYG^LUCYC+
zer?O&t)X5tT~=1nOOL?n6Xxp1m3$ucjw%PIp&5fAC*}>{bmM+NI#9I~j$b%#DLcmJ
zO3}lb402~eV2((HouLKV5PfC)h60o4{5Pe5s7q$$P{F1!!h&J?z7iZ<6{po6!pw|l
z?nfgJkWYX?Fd$H>3qBv)fB@<wdLp9jlw4{}ESj5atfoITgIIJ<O;-$$vZm%_XS{IT
zC4r+UeTo{x40ZJ}rjX+<b!RFj^~pHlBaQO?k20BQ6lGVL_2?q92xw5{#%eyXS0o!W
zkxOUn30=1Ewmrm{tcSyN&wsT5|LIjYm5O!O7HYW@&Z1C{>zPY%3}=mx$m{fMCooJ9
zCp{6w$GZKZ?%B0P%2E591V^SCjpTqp@`kfv#=b`Vr%yXIL;;&-H<|wB#D3T}sSn4z
zP9dgjg6NUbzD_1h&onpDh_L$hdTMURkmO+P+qc+A0jl`Zk!kWN+54YUuZzH-6k+`|
zkLZwZJ)9)ZN0Tn*z2CS}@(t3xi0oQ^MyYIzdlWxY>+5^^Z`-{s<33P|9Vr|+n|$4u
z&LAD?n0D~Z<g=9#*jI+;a_X1jbf(d0>Xw0FK>gybYl&w9MQA|!QkY`c=h5{IChq3p
z#uYWMiZev8cwDdU9xKQGOwtwYZG7^Wa;>fBA8*U2f>LRD-ELUoJK$nD`)^ae^m=%0
z@b5f<o=^YP6MTn$?V<>!Pa)G!f9CRK%1gb5HhX4#?bYnc%0xt_yj>VJ`>G9mtd`kU
z8D2sISzn6KAhj-5MemgN1${~1cFaa@8vg3%B>$9ElPcyE7JO#nT;ao32-hG!Ikng%
zHEp%$8dqq7@H>I4f^?ZV^g#AMoKf??n9HYanKzijZl4c!&qz}fGd~LvG3kDs<-z>o
zg0aqzS8hCUh>9Wh_0&2>B0H|D4wWNcCML|N)03jj`{wN~OL=wE%6fRF{-9i;f7U!Y
z0XgF-AWbp0X$m>eeC*Y46))k;T11nL2~(cf2HJfRoMdRN4>zhkkFL4~OIdb^Jm8D0
zO|g=0kN>t$Df3bo)uuhV{sjd3B_ho|a%1EhDy$@i4mm;$P+=Ft^xkb++m==t7!Hh*
z-{FT(uv>J$!thGP7;)-ny}SK8CG!_nkL&Npxs7jYW?EdF<4r9)hO|@hGx!I(mI#hU
zf8C6hpZk($ZaZcQ|31+4IA}hpY?(2wp4il97}=5tHV&lY^DyvHo>+Gm5rFqHrnb17
z`nNw@j@fUmy^F<ecISQNaUpn8RWq3*5+pO_v9W%UDct#2B00I}DQ2=&4EZ+=GtVY^
zcp?1m84KwVw9^{=t&H3R<n6r9q?8hYSgw@dP&vJI@gXpo#p86#GKa&5YyBf@+sOV5
zk%)FH*P)<^pLscvvUui%hXCiz=L1?yOHq6knYPxS5h?$b5N?lh#~d2C`iyI3DaeQM
znNop*v1$Fsspd@0j}J^A1s<RM>-kpax0L_LM$zUm0KB33acx7(bGf(a)Om@>L=(SC
zT6qGZJY4pL%9Be5^)dtofJ=E9UK5lX8VaKlBXb2SdzkH$m@N={c%Gpy^W|jrNoa||
zoQ_56xhZ+mq9(qine=RtIUP|;P&F)B8V4C-_;a!4i%!%epUaUj&q582GVa9u>H17<
zqO;w-Pk{)_<>B#Xz*r<DT3e%Q#QQ%TfDYt@%saxjcVU20cq#?Bp;ay6{ukGs0^Y}K
ztL))Uqj2xbEwiL1Nus;lSNXVxDTk$BsOiu=rxsu{0YXRfoVs}!KX59C7NaC+mcT8T
zf$uvhc3NjyHe7iC<Y=h&%{s*nlJ~uoo}n?J$2orH0Hb-x!+QF|zrRCguU@};B`YDS
z+JO0g3y(}`V38f+m_FD7U_9TG#gYKO2D9^UFU*RXE0+X1d>za;Wccbgsi$bsy9474
za#SxWmzNq=S)2YAFw*CP)KQWG^0?H$5XB^mWB;Xf@P_?!#hk6T*A=8=4}3_VC5*4^
z@|6`KWsr1R#xR%JpwC}?zvtwuWK?8A{E3Q7zDl>Vkn4K9!uvo-7?7w@4%WajrJxRp
z!#`-=<}evXEpTm+rBi2NUePCwp3;=d1p4(`%!$5A=j-6K_UI-n{#g30o<v8&u~bZ8
zP$2b;BmH}9{u=62sXVLsq~apA0IeEk2x>kqtb*My7-Vg=ZzPvUaiCoHuZO{CDY@I&
zCH-~T8|B&n8oXEXF)YT(oCH;3DP<pndwGf$C`NeLzY~^W|E*{tNH-iHDzb>lgY(T8
zVt}-zyR+hj@>P(LR3f&sK>}3prtigaY0SB@ul#4;E4va@1x&uymX;Xgw{rBlg<_U*
za!iXI*fo$*K>R8&yChMND6LSHI-}J5PBD#ke?Rn-8sbgKA#rV@gBcmre~aQ#`mLQC
zB=gfI+gVukG5atX^`#roEKw_gl1F9Kz@^G5_JPhz#-piuxGu74;9?c!c&zW3Weswi
z`woR{zC{p@^obxrWJ>x)$pzU+8-Xk<JgJ9ihya1-+cCTS{I@e*w18!V*<Bo!SS=pj
zE9~XJ6_EY7N<cS2#j}BDQu3u3_rTDXEff<OoDc~LPb(!(7%G)!R!+w%PBL9WFc?k+
zjAo8Xf{zobVOC8J?hV0rN~Fh@?^3y1XuN|z1B^9mV#$v3q$e(cyG!aVm6Yd7u`dAA
z?N{TJavsgtqor19_3(ZpvC<X|1HGLgezNqX%4ZMs%20|kLKelK{dxb|Fm6Kt4-AS?
zU2pErs$lwrjLig8lgf+EiH=_TQuH}q>`E|(n<U@exYN&jX#xf8X9^?FYPe>ZjMFe(
zh)UdyZsS6S6Vs4n;)v<Te6IMAeglk8)VeJ#gOd)S;Zl)&gF!idQq^Ooxr*iu5hwFu
z(?IIkg$@x|juMTE%A1!VOa}G-a|?ur%7-8zu`^Ax-d=O(*zxt(&+ok*|MyOHi0rw7
z)sFGUIYs<4Afk956pK3kJ=v5kNRt?`Nek9fheop4Q6~?kNmQQbbt;X1GkIYJG~s5Y
z2vLst=GJF3^1Hm;MN`W<QiviShp#U9E@%$TgMjjv#P(4LQE~T8RUHjY7guG#YzG((
z9N}y1RZ&b;#_h{x$i3%K*V+kCjQD2fw;cXJ0lv+&atdU3yY^K&bxy2=m6WI6w{|f>
z^fUQT`#-M$GLMn0Y=irUt>!+8aC1pYTkZrP!8}(t_V4vdoz8OacdC~m|EX~Q3Md7M
zZ&9lcRsl(9@e%uGBLCOYo&3{}YXTN!!D@YO<Gad#1}%w0|5NzET1C?U*)oNh&0ODU
zd-6=Kl+i&$c_4_oj1LeN&P^Ib(F*CMdQp%*MNVEdii|0W1x9%hO@zGhs&e*M$5|u5
zQ|s@=LJa@WF`3ofIJ$$j2#)Vc*eSnPC#U8pdta6QUQ)C?#|2`kb1v`;bndlXDi|)c
zDMRev$J?T#9$&`HGp}hgp?hLLfCzvx4rO0b7-INF{)oaF9Gv3~1h!5$9dGV}Zq5w<
z&+8QwBZ^Uc8LIB!4z4yy_1J(bMr@7G!n5RR-vFwwL4To)l^WYL(PR;xUZ9az71P^v
zTgUZVE&u~{Y~-d0w+vsw_ddYRT@}82T(^F>DQSPWd+;3K?O^5mO9$3%s!$-=-BQA#
zO-lGZ#KjIWhuNih{33b>O|CxBhK$Y7CoBc7yvO@8c)pjnUh$JN@kRfLci^WK4EKqP
zN{KKUEYk$aFjR3wX(Uo2Xqn+t<Rq)WbS|7n_@@xOxor;oKKm8}eT5>)sI@uWm+6pw
z<H)nwE9hoJBS1BQS@^tH9e?_Urg}85xl8oLo?+%TV>H-IBmjd}^bxTf8s_t0p0g#C
zY=K2<CQ~i%7ZsNHOqnH9g+|o+5-fTtPzQ~I)G7(&so(1SNH-YZfUyUI`Z2qDY8BSC
z3(k#aJ_Eoj@M^>}Mf>4yWYoM%dUyTowHApuJp+t(S>9X3j3=&gZqfM%lP|eH$tlZ6
zUZpsosw5P->QjQpjCv$3dfUT|$>yi{ZyT~P>$M_N{IrHACWZ8qTz`)=jDQ;k$(g-E
zcP$F+it$8=l&cvZ!|zznaz`>98{3C#Gzv@;_o(@!cL?y>xnCq#_I1~euK8ih_XDX?
zZzF2%YUjstYfL#U&NM9lI25&`ZdtVC?4Q*pkF61+k2G}G&v*|JmvM#(;<^p~`YP$+
z{HSH&Oen35!<?C-)|F82Ezg+lLXcTVB5B_1_IGW5LDp^mmt$)QeVJYU$e&RUo0?I<
z^b0Eq=9Lq@JS$v~ws1fcM8Np*>W;M%k6SY`#l!K6?(ZR%bm#{HF%HxCyOBoytn|zO
z{^5S4M$#=s@q_MjUex3L;qJr_ZTm!#Z_mQJZW^vt4q+4@%xS(w;NmA;&=oB<-ZO%g
z+tSkwt*hbprmPyYZz8OfnW1r^EXHc&aIPOtNRNlhB}`?t$(iMteecT@zD(4g>82*1
zaVVu>(SQPX|MArgQiMT|(ixe`>xvRQbr*XanE`vo7Scdo(Z6?;#VvGo%cOsMDVva>
zquWw7$lK<a!lVLGR739a!<H_%J>ONVY@0WR=Jx{dvgMDmO6FL;QM$)I3k0{PD0nEE
z!16EO3#T13%fH143+ewwk;=^aD(Plmc7mS9$+JhImx7l=4SL+=iLVkMc?{azn*~c-
zy}mlf_-A7}Q$DvJE*3S5*~04Iz3KwgQ#f~L8-CVy+In0O_St~9J@2rkPd!toua3t{
zTyMsSfP1VFc>QwfA}m+5x29K6?D02f=i>*i6t+;pJV2%`VfYajEg`Oj?Q@_dk?Nrb
zmB1(mi<9=>)<B(odrporO|qK1z74JC!DbN{HWKyC7s!^d>-(3(Ck?=&RdMW{PW#6W
z;|u}y?%9ex+6hk~pY+P5lhdIEljnZUKla(xjh}wkX?)k7k~0E$#?j<udOPv8@W-wt
zcCVW)x<XBsYfpuK|Hp50$VeV$cO);Dt(g^nPcVci{LPASOGG09F?76MXupNZ<9%m8
zJJ~O(vs?$y<C_cMdTz4AFT3gF_N5#OBJ!@#e-xZv$#Si<2cj>d#88Ro!Z0Z=iXmr;
z>inK)THM86_PQH=67x-&R8|Eqw@a<kjcoSO(UY1?j|=M+w`~%-4E`^FNGm+d-!4|t
zt9xcV4Zo+TSGYTF_XNPBD^D?d^2O7=>%1F##UDMSct{724feoy2(5Dqd+TqG_c-|3
z*0Mn1s&?!$2-3noa^V(xm>Paj?-5()UAJuTqVV7#!X_jBd=+myDT~;{ux`uj5$x*^
zdIdK52<ItMeTptnP5IuVG?X8D5I01|SzVir>2WMdnGaAKbWdK>)4IG4hY{Y)BMX)y
zSZl8kByi0I3Ge~zLMzm0Bnj65$q7I{7n-w=S>k89)Sp1>)I5-+)`5W~M+9kBV^Ciy
zS`AkTlRC56l`i$e=Ua7;)mv!!l<X?#Disa7p}4l547c@XHp#@G72}gxe~XoGJZTlq
z*D4mnJh}H2y1q+E6dxNPg$ok;GKKz(TE@9?i4p;Q*Dv5V15$F!5Pc*Po4ad|{eWyp
zQ6XyS2WTzL{Z3!~#vyxSyjM_I-mK`{c5*Rzevt8zY~=NynG~-DDs{|C6t?_u8qyF`
zTydc#4Fy)Txv&K$e@oP=781T8BdYkXm0;CUEXk?<D8%rF5&iPEu1SM%pa(#mb4>BK
zp?J@(tYqiA`+t%1VcJ|9=!)tQ8w5OMd8xMITVA}4$#vmkm}v3dZ#t8{bz)$tq^KTJ
zB@gWty!Dvs<|cXPlgXn9?1Xr`*jVRaes7cubb$0fmcwXmWp0RqExpiVq`8yB2^cU9
zo>i%6LzGzHmGq&NdHk2$emVQ=sdtXssbt%R`*oIc-DA2|$%%OG0rJx<K;W1iV%|fl
z-i0>PP3v8GF8<C(lja9kydi}z4whU}Tv=BIwL9Z2!_9H*hIVsS9Bmku#C*XTKhEbs
z`oV^(Nvbdhk;NQaW1Yr}q=O_Gke21oO2}I{$Nsgrz-IzKcEh+5Jh&wOSS>v&Gy5c$
zuXNm3F4RHS)?Xs3Yx8x#O~4z}`BP{W5Z@9x`Fr0WJyz;4tQ@|4^)u0}1O29jFP0-k
zn^UMhNmA8{7(I=}m0Xu3OY8MhT)FdPYjd<$+LSjqTTR!du4TZRr?1epV9BXP=Z%V_
zx!Tt!#ovgUhHbnBQPrYyXU>G{pkf_#86rJET-W|Mv&dKHzdP@7?%y33dQAW0$hRZ+
zZ^SVIn9+xet`lND9wgv*eJslkdWYMeO&E}7%Mx1{rpkzD??btTB*kzY6C}k4^w_vz
zIH{f8@5S6lzZT*Zr?3mtB?QQ*39XqUb{(_$V*pCgz0Gd*>0`EQ6afBf%&=Va?O?5H
z3jo~gYR2sZ(D!2~<2$8<<%wN(x)=cu+q*Z*d>gi8&=m1}A{uz3?U+U>hk*Tni027i
znoU_1(PfaDTmRKN137GdpqGJ`9!hJX*FWQ0P)7OKl8f4^^!~ljz^-(*7U9oZeb&b`
zRgl6oEfDXGht(J4iToSyRz9Kl4~ImabY0|dD(J}5=x7-Hqhc<ZgOxWxO4H3m!tbq5
z#*{rFq$FIqIX6;)`WOSR&J=u41W1JcJWrc**=+?kw!EPpbUo<bwIOIeF(%h>{pn8g
z&_IVe8I^C~OK#O7Nw=?3B{ZbIUXI+mxUNmKhMq}W?}d33hsxkL7c2**4^kWY$h%_1
zY{5Q2<z@e`7c+YgeM+dLwhPVlQZ{CC|6SO0D2cED)Os~=kdFL^IXVF8MGw(j3|1KD
zmw!;l*vep&oEibNWnG+BO|r*~o5bh=G-vtpITtuBA=@f7&eA*E+f(l~d~dYSN2>@~
zS85~_Xp_1mkojvU+9Tq~T2U_i<Rk;kaEj)qG#yT!N%^CHyzZ-QN66xgBg;|^<XWVL
zteBLTbA{V88Dll7sWWjYIZ&>$mPJ*CnTO^6{F25z8R-=QviwCcsP2fHTl$8G5`wBF
zg$|GPuL$_f0CJb7TOE`>Rubd2=8##utmY|K>fju@mD<n#=of1!>%dEjDra*30LMXe
zY8IP6mqux(2yK|try4e5GXGi&zq{dJy;A(ymEVaH4F39KNF7rrr6z`@+%OVs)@%0w
zK3H0$4?ROga%mt9?jTFZqGlM8?VvPoz_J0945<EQe18wm+4#1vF{l*tx%}9vkHaS1
zg26zV2Lv)=xgc$_k;2f)kR}yEG@d#S<=0Gx26C|y1-WeaDg>Hc!-EXwYci=n=UDu-
zBt+1D6ntj6PLwue0UYl%OC;(6n&H-NSHr~SOl=u4qOlfi0Kmi?xD7j9#(jfEyn@WZ
zV1&S!lNg40>>yLGHsUhj2<!C)TCjPH>I6AMpBw_vj;7m%*<*|-z)Pq}F`5#g*T?rW
zwUGSO7qDmoD2I;*8M~=<NzlGznM+<4AbJ$FSV65@eK$3SM`rlE&C|UYsbo30h)#Hf
zyTRr;^qp+f8O^x#bx)oN)P%kiu<2t?^$Sp<5YvIS-Dvt`C+4hA)A*g!s+W8Z{m&gQ
zu^`=S*UQs)ZMGL0tDg9;7CHFse_F^uyer63Bf)}A_&>^|^YgLT&&3y+{V-f%y%sZ@
zM$NLNRZ8uau-ntmV|B;d>Lhlxs~ZoD_*x$yB<d+j93oqnENvM@XL*@9@`F^t#g{=O
zvH^8?DDooV(E8fGQhivW#1As7Nq{VjXg*AwD%VnHA3w`$bDX(d5zucS_bJm44|;DU
z%uoA%lCS<R;llQJFt*7)8g&99pv9TLMkF=_W*qI(YoSZR2^H#A9_)e3NX_jw!*{jN
zn=WmXoo(cU0N488U~mGCdc<>7OPsC*cdVWMs_o5s6QsDk7SE>Vxp#ngWmBfeOXcJB
z%74Jr$Ai0lYRo^jOb&Tm0T>k=dy^5}%_}DWzlbchjDAijT)Xm{MTAI7$BNHnhzw2c
zvj*>xHJY>*x`t@?=JuxGGb|1ZUZ=??;D4muW7y>`(hT7X0_5I?+K94g5kA@g12gq(
z?;3m!FfmCIOiq{R(07Z64i;ynv&!O;VXX|<HpvAgNbLE)U!mjE@vrJ^irJ!3W?8ul
zeG?3_<@<Csp^jux!r6Q!W|SmQr-NFBp8nmJb6LZ@hjFpZ1;7_d9V$-WnOLS3bN{A<
z<gv-BL0~FaxRdaOcUqBBH9cuAX>Xr58>%Y0SyxE?>?%hPNDkPP@sb%{`UfVi>y?v6
zC@YHy7@tY4j7??0O<9~x6E3pV+*Za3#V-dkT6x%yG|B&RuG9;pbZ^?5mo*#-*hpgv
zltofp%kJ=X$<kn?e>m4!*pA3x0%!FnA;@j`s-;w%Ht7i7DY^d8HnzJrY<X3Z!iB#)
z0=&A4&SrPp{V2~P8ja_2{aPW6Apv8nX)otrN22JGontLI*96gMAm(h_Gv;*5(Y(e~
z$_ujiDoLtG905_?qON`Tw0dh_4BaGFlDo~$_3WG~q)L^Goul7AbB)cCZ5D)20ob~m
zR@+O8?z9bBaEQWW0j5hKI&Rvlqr5;GNKJqjQ59h=eTr~|A^XvEawzSYeB`R$ElPQ`
z{x0(yHFS7~vjE;A$L-b>k}ZUs41EhCZbT3htZg4R0B4(VWyHL{zv75z^vrLN60^>y
z=&t2jFN<44itUHK*p+-PP4F~@F_I*aZ{9|O+Rl6XrB-Dr8(QYpCgbJ3&Vjy`76@KP
ziJ7p8!zl|ihpq?o=U)jXY<jF%e(&Lyjc@Gf;zH0bIMuu!>V-uys2`_Z?j9a%|9pm5
zD>APM)F11i0D;(pQQs#jd+S`eX6&VkC3OoY9FxP}i3{92W){N`HP`dMBxYlO?2o&M
zY}-8ji-I{a@3tx*UVPm<awh?|4&y4+6h2VG{zb<SNKg%TUr|VcSs}hIH%G;-B0qe0
z)ZY3trCnR7doqjjT(pG{7UyBOgDlPH1R%scVfrwmW+-ta*@EGvxzuamz?|LpQQ6wC
zOavk3*36vz(OUx&1Y}B^JHeZ`X4=FpvwFLk?Jq=Sd~^1M!D~g8gy`{o|8Zy06D<BN
zzmYt+cgdw4#$vfiNjtFm56#in`z+2$Wc5khhlvtJ`FY-5WSy=S^bE&u^D$m}5JX>V
zhU4F!E#Q`4>b%>(=GYaYnOjf9SFq30+zwvAF)mk}_$l>d91x3|tp1;P*{;KMZr7ur
z(_(z{r)4~2E8fWZ)j~?#OHYpwt2|l5pLeJKg$cvEyR7AHV=f6}#^6DNz=t)ZK(Px2
z$M72+K<3@F$+a-}k6Q6BtRB<75<C~iBkLqpiZy!4LgC-TD^!k}V24KM9e8XfTFvz-
zSY?C0)0w#?2kw|DD2ipqtBMY@2PX)<GoJPI*sB0UYsTd69pOjy1Vz$h+{lz{17`Yv
z>VLB5i!Os={)MTU+`_~SWoT2xtG-%>2isS#IgC{+i_YX@vSORP2J5GW;~;zF4mWU)
zy?$Y*U3z;fmF%M>h4S_{^^|$WK&i19H-$Ro<~5U=dx(#c=&@LBt&YsP0ig<kLm0&A
zeasYcbcqW@OM2)HtkhTGwPaix4V*`Gz;M2bpD7bBZ(hLA4G|PVKP`QbD##_6DPD%H
zJWUH81&VIxN7N@VMd(8z(hRcV37B1CMX!Bt<&~$qc+P(jihG>~J0*_}s6u$HC*_I!
ziWN)WV3Dr6_)pk;<@$`(4Cy>YRvVr_#--4hQ!ArFnCgzf)3)?s+VVL07Znxb3TPZJ
zi{?$@Mq|%eF7eqVgd46PiICMcV-u8EkV}}%_G_9GCsrerSUrIbUQz%mIRCr5?wru=
zgq4o27KRsLSh*%|OzcA5v`N5|u|EDkp1wLNs_y&SK)R&6ySp2uySr1m8&qPXyGy#e
zVG!vC0YP%;W*EBTz0Y^8-@BH7j@~=tIs5GMsjcE)9hMD{ZnG)@pN@tCxOI?#8;Bv)
zgJ+Aco5!p-zmGU6v_XNOJOQBY4$wo*N>_!ftA1w~7dYY)T2bOZC{kNATI}{RW2-;`
zLrmE3R%b`qHk@`tXdLC`w>(}0+ehyUuUdz;tLyR8>f(?cx9A`?Jkq0<cZ1&*324DS
zHn=0WQ7vCo-u$ZsFayNt7DhD1Zm03z95fmVTLQaB?$ITH7Rn}na2K!EA+a<{s<*(%
zy&@jh-U}Xlf1^z@JitM-t3ei}!5Gkw$rsvSkl38U$**Y*P*YH!bl-<aKbE=nK|g#g
z1v03LL>oS^(S@FaCuE8g+wfx`yc!A$pYa)KLn-!vPZQMP6V~A~-tk3DjCZn|Kz=SA
zd7NJW?!N@<C;*MUb*yFK1v-gP9oyfjRcNS;ky`+rS778R=;M}aBHqVC6FtsKRP*-I
zgBLj*Bd$5%@A6Ey1ZwJtc2~-Zu-=D2OIS&=#*dHZxd>;G7&{}OEanyKn;LDsfTLf_
ziJc-<%C%l^+tn{-T8Z4IR&CSOKBjVeGkf6&>ik!yj1*S<k^;M>3A{0Iqdy~kT|}Ne
zCs1wzG`vsoGIa*@hXSCy0D!B&kJR>2q%>gypP2=x3e4m7HB%}xIaQtx{El|Kmv<sj
zIgw6ROP<mdEt+#!_I-L6tI4_%jZ!jkpIXX7HJq`?+!kOZx(r9w1QJh-Tj}!C9!LT2
zQCsSu0^Eo3y@q9+_<yB$0|W1{O}>RorEZ<+Iiv55H3M-2fR8t0TeH;|=sW@&`i_1o
za--{=?hj<VqXScYI9`Z?b#D}T2a(-ea?4p3vJ55-)k^u2@!Fx`ccB6Gsm&2)gG`GT
zmFfi3(Ifz}7AjO4wEAL%d2>j7F6tHSA&ulb9%dvw8EJx*A|&}0NhM!A*^$iLgJUfG
zZu8m!XT-*gl{C;X1c`7c1!$LcAF=kVGp&$3KeC0CWji+F<N(vD{l6lbbL>sHg0J4O
z$G_5H-DA>R@srP_?Qz|5HBU-s3<c0EA;-S-yuCoraS;bOO>M7C7kR=lEQgAdHsUa*
z<@E8;RowLeSi#3q7@z@=JEUGxu)b;E)h9_Jjrzf3Sj2lrUARNy=1)i(Ogx@3q)UvG
zqq>;^0u2<(maa4-ghVkOr*yM#8Vr+vl;WfudAORx3$4DCgrRG9g;_49)KDFpC*KO;
zzdb_*4Ud5`FUvAqzu4hqtH<{k1%)fwB2s2}ACoXmoO|vHC@=$;c9-gx3?*isEc-T<
zK_>T~9Nk6!bhkE*fXcpv&<Alg!KJP{E%{z(`x1NF4ea?<uVjEp=8d>hjtqs|Xu00!
zp%bp_%p)hH!CcshL&)E1tYnqgU9(UC0vI$y)6D4CC}e$nC#q2Oa+yj#tBR1(x8Xv5
zhYZNZwr>7lH1?ZTKmAbqT+FoV!tzALeJZf6lB#&amF<=dyq0gq2{OF`Lgw{Qg|PO`
zY|`o~{BAzfDHntGn=iei@!XehONUJJjl;|SpgGv?ruZ-0^Bqf%2^HPU90ow~gA<so
zFj};+;+q${&>_W%Xle4i^m)qE$kwex@Iu<L1%V`kc)J82-Q!Mzw1zk2AvS-1bg^~x
zoH|)aRmb=6UYfeZ7C-?5_<-Y_Gx%YM7UJg;sX1KQFp*0i9QJiIk_+lAQM9z5nr{No
zEnjf+DPlaX%P})btpclm*vkQ6WnIW45B4^#N#G5IN0YYE%Fc?oZ$5K08eY2LPjf&?
zxP~O?X%>@N!L<H*F34uOWM$pbPrSth)BuCEuN{X>vKY!|x`4WtIoi+tMn~|DK2Lby
z#PfR7XpZ!(yrn3hH|-)|YQ@lQd6J`Kpp7Moh2CjE$NovWPp86082$cy*&5>FQZKTY
zSIPVaFw_fl{B|J;{BApJdp?;vN-JqntJh#`gMur@$vI7-d>3*AJ5%uppFGI2crxi@
zat74BK$_Wq!94i7>-1yJETXB1By&51ksp3}Z{V;iv#8a3)BS5(HX7#0WY)@H)>1RL
z1bpk_D|%K9>lUmBGhL$y&a4NCOoROR(-%vb{Yw6WGdDNL$|f)V1uGl-v8hgEp`|HG
zexHAFh2-@3?GQ$#i83K|<DybBqALd51`4Qm<8jTaTKdZm_@qtE$x}VpPsEu1+T~qm
z7GwIiAL<|6I{OnQ>pIylqY}pqSkli;9Gr%&;arQ2_CI-981~HZInu?R7qG?yT3eZ<
z^w{b4WWU`dR;f@Gv5+7A@snHkHw-vlUkb!J_Y8JRVDx!nU%Q9Tnt}pFfX*S<@l2h>
z7`m-KL~%U(BTfD~mXu0UFNY;4Nf36&YU+H8T^sb>ZF{|+i|*~H)&1*N`xx^PuI-W#
za?Zb^xH<Ue)tU@JHQ<2++LXA1h;<pn=%`zV_Jwm1-|(25jp-jrO#tIN`YclG^^TGx
zjH6wLjTJ=um&jB!-u~~~NXjaloOHK|BE3D4chUamK59Y|#~ixi$i$3M8I6rzH)px~
znS5m*rP<{)<Ir%E$VK4oK>!)!*6I;Ch49wUAkcYh3B2liutFVPZ067M;TQ}FOdlST
zJwr>^cfks$8j*T|Zuub1W-vqx>Sb(xI(&2a!h_n4@#=a1NFe3j=$X*}LV_I2s}xkb
z`1u##B_R%zX=&gOLKhKwYET4ByDNqf)x-%bU8o7DT}YZBaCw^v_Ji3q+&QO41klTx
zv%_;+IWL)crpvxX%Nz!BtG*g_P3xDJ0#oY=wrz#%S7?E$G-CZg8iGo#nKP|1z$**7
zBo!WBZY^3`_5Vx*suB0;?2i?tF0axxH<MZb4QO5foLo7SOZR&B90(}fK#rz{`h973
zfEtx=#S7eU)aBpP!l(1?h)@(Sn^LA65kBRLjO1S>h2xP$b5D;wm-?l2W5E6fR4O!X
zNr^Q5kIM--DClv3HIwf3K>RK|@!|52eh(11W1;!xDfjx^J&h0F4|sqMu8R_F&1QUL
z>_=tMl{vVzH!Fts{@4{`-u;So%D&5+1XS&t4cl`7L4nFB;P3l=^c+h*Ytz4t+>;<;
z=XYT4>jo?Yo$->(YkVxZa88SpTbq#ecJ>k^06fZm=gWfo=pZ5d`O}eZ9#st1cM8D%
z!!q|%ZzR6AK{@y^IvzU=DO57dDSI(3GoN~R;L<VpIXxf1LW@%l3PQF4E&cxcYB67&
zl^GDAxGWc9Lm1O8#>{~j5o@c9u-Lh?w~B-B@Y1^`Nz*HY$U>gaGy~l)D1al_)%#;%
z%Lh#&9G2d7(H9cnQZe`A-GUE=?<sv6g7M47mLUN9&8TiU;W({b-#^lu>|{Qm0&Th5
zZFwC2?~LtB&!Du|tHbF__NiY}stdIVtHpT7v>#1P1M>l?3HSAqk+u*1FgAKWvw@pL
z2JK2*nPb;~yo8^-W5jp+1`pKv(@h2JxwOFGJ-Ji)a$M}w=cbK&2IKtrt;<V_nJ8(%
zBJJYH;#RP-c=L>x=nuqS^sz!N{0aJgQ@Aj<$qhGZ6D5L$3)I}tQP5|37LA<U&bw(<
z!~%X?ES^E|{9d;JE|xz<;y;{lkse2!4igb8cSiNSzr94Id+J15dIqx-Nq--|dr#EL
z<R@z(YGS&3S|Mse_>l5V3H=`;CjE(gtvrkwCZ{DW{d}o9aQ|UaNR2<-%Dz*&Yu-xY
zVPVLBt$AC?sLW!n#?x*7<2TgByoR?yLC#Z#pD^ae7!_fz)m)v!h^t0obxBhZ&9>)1
z7kLUtw7NkeTB!6_^`t6VRE2)HrR+%$A1M{zoyh8nsR(QIHq~s8;#h~p6xNX8Gk9Jw
zTQ?7dI%8s#>_7Raz`e0lzPv*-MF-u-4nrCyx)J|_Y#}DB(F{@PnQBoSk99CfJJ&;-
zZ9dU6)Zia#6ssjk474(e$Kj_I1|y1`{_h0bFxNlDa+_Z{68d^M#`N~CNWJ%#^WP!Z
zE141gv*|(eyF!<x=7@brNC~{ctV-~1ROzhw`xqKZNuzl>weP^{h-vkaw=2fQKZS+7
zWS&FfQ_^9KB%Vf#f*(@zZjqPCivwy9`nb(U^GK&2K_BBcI)hAcvvGB@8G~^8JS^iE
z021))FsTxCr5;lvA^d925E})z>IV)NMwVNpG%tmj#7w6Q4>>dINqcZ9ca|Iex+`JR
zILVc*voBj$|GGCCg6uL0ixO;cK?{nd?Oc;Y>Qfox0$mYvMxwmnz;kBmXkiJB+EwqU
zUA6PCbiX{}-}rl;IkVpK<(t9v&^OrC4)h;8uCc=B^wG#%`HjePEbQ%nwSFBt>P(#-
z;Svd}duz1yO7Dk9apT)CT)v(AN1i`S-7Y+x)Qlf~6J|og-y3p%d`9>t+dvw$SYIqT
zGnJ~Kz{rvr;4G#DXD`K#EU<3xh;l!2tFF;toJX3!?JCGVvx-uTiAW<m=GDitt7acV
zp-hHIS=d51m*q`zwztPcEE!@bU+!W6T+#pY<Nucsv-bF@gdpPkU*mk+;r%<v*asj~
z450n^n-L;4jG%4$Xq|xYKH22Fw%Spn<X}LZjHmIvxrHKt`3r5wg_t7RODmx6h^D@U
zg~e}O-!q7c1K677unf;epl$MXy{awfQoEHTE@h~EnJmxGfl41O@-&czO*Uxh$;Ul9
zKYP7n!3*2&*<@rZ+zUN7>%)auzs?VXiU+$N_&4VVK&I*wfy9qMS1=ym0qt8;(`TeA
z^W>KDZ?sBA{hN_v=45pwd)(Wq>RjE42n#9)bZ?=>!_3*RdK^dBh8`*IQ$Wt6_PISm
zy4O`uU+DK{AB$<0e_r9Clj02=fz?NGC-At>zxAE@p{}Pg`Ve3+gH*;KxbYs{HXzyv
zZ9&F5f?FjQxT%_Ey}+To(0IHIpa=L;v!Us9aOrJNr<($a1#=3Wi-1Q0S5PNw-(!0k
zz_uca_o28RkqUML#sHhYGiH|Bwt|016C@;`uQmuMma@eFWzr=C&NTNPXImw_(QjYI
zm->sFSN)V}?Mv8heXo1HWcBRIL$j!k*g$e>|I^Uwe)-ahut0;tLFwCdqi06^2WId}
z#|WSe)skAesu0E{V<z9xyrvh>$S5)Mzf~U3s?6XxE^<M}NbLLhMOA~tMLZ)&iy~aL
z_nxNv0Oa}IWj1yF4UfVH-<vrta2@49kwele2j|GL5gLSED^!^M3DIn<hB|zQJuO5|
z9ECB1%q>lPm_0^RW{F9oLE&lsNOkcCATfxyx>FL<6dkSh*}vKM<_PcI-t7mkcTbqs
z{8H%kOq9a1`FQz4!>%eadH+I%{~$~+@=hsW8@M^lO%=&=!M3-<S;nyoO@p?vMp-9T
z!ZBGU<{8qBN}VNjf^*Kz9c0PjqFN^l6jDQ;nsk>?;h%=ihwEcNWolY>5Qmz}V24~8
zp2b9>{PXdgN~MdEB};*!HH<PPN`L~t=%P2>A<qvEPc;j$KX?Y>V1QV<^XF8Q6@}2Z
zK>X-##RDq4(gck0s|&rrtkn?v<?N0m&zUU#Ivuz+P`3!s2hC0L{tCWE4T1i_{(B?G
zAgRK@SM*h&%j?f@jOi41G`U+KAX1k-zxPW}voq1}9_SIeZA!fEodkkiF5BY8`cvA1
z+#mcMhm<?z$u)^mCf-?k$NC7{Mru!Zw9s>g`x%}qwJq(h8tVGJc$7JJOaQ^}+<+TA
z{w-E&Bd~e_@UxH`UO&uMh=o8iOkb%`W9l{yvGIoq*M<kSV6P3brR?r+yvVzz1wwfH
zPt{loX{v<ev2+?pi3;t1Obc_b<h{leE#p1f1)4(NsbEMWX-MIElm>*4hia#NM_ZP!
zb<Xx0miMfMcPtC~9z4MR&t&_483~n=(1$5Qm;pDyUV{4QEHt*Qok!1{))C<N7=2Lx
z)h9|d;_=<fZ|8nYbfu5aGa<TA*{5=8opSf8S4kMmm^E9i_&H<6@L)gUzgV1&>RLRR
zxP_XZ?~6A&#WeY;q&i#~VwbzUU*iEp1i`sh2D+xa_*>TxQJ@{#Qd*CfSv`=jPPvtH
z^l$c|wu0SSnQjA7fN!&Ry+;Uv8WkqrxS=7ednO`U{3ix<X<^5-WyF8B4mLmX6Y1|L
zy71ut!+>)b$CL^zxZZT(bqqvvi%d-%U$XHGf<%x3{o)Wysk-c$t6~EgucPrc2l1a6
zUAcLXWyB)C5nT>bez~}0H5Q9Kdh&Pksce#pi@d7b!u$`5vm~jk(|*_~)d9?2Nm6RS
z8NoVbsfePuN7}7brd5N5+XWDfxFgy>YQX`orH$HFz2xxa1gEVql+y9<;-BZ4%;mNd
zRb?Q<2q=t~v%Bv-EUntkzF{LWS!3+;$^Rjj4b)qiLHNd?Xb<<6U1<`_iZN584V+H~
z*Bk-l$g$mKx19hxJpNM830d)UwQU8h^`Sq{+^w8vXoo|uDE-szJf}v1;G7A7he{Uy
zjeBlPo|n(7R<?u`7TU2dUcj>1wd}O%IR_3&(;Ys&2V(7Ej5EtP7ioDN3J%L|zNX_z
z<ZxnN{_PjtJc-Dm&W7;=!n-vCOTRy~-G@fRQvWe3b{$g%8fdq8JI86cQ#OCCc#Y_#
zHwoFSt46-Gf8#yrS*yUXHGmIKlEoRi5`G&z8pJSf^?2uM*~5R!DN(3Vi@E^FGqT*`
zlXpKHd1rQN+ORs##B>2cFV?({uD{v_8fHmwt0ZPt{rJ8JuI{Xz(n9P_2RI#p{}fGU
zv}spY)ad#8(JzY|V`jNkp*bTt-p4F=$%}22mCXw|hsLxzNHA}9ZkRHMvo4@EiqujP
zK0G(s=OT8?uId#k1q4mnOx_<aI}QCD-awS$0SNIjG&bMEzCMbX75z?=1*h~34Fs44
zYTE`>vz2EHNS;)XqMlhc)=sT~3T`2|2!M-)j(Fw5){gdol%uKpbC$Y~=M?`|5m@8}
zr?s7u%REf4#E7W+!r)T$SJw-CvU9AyOAh`Qdd@Hsra~MC^W<PWjRxci|Ls8gix0rJ
z@+ymIidFl|v&~i}oPM`G2*a)*SgH4|_Do3H)#NZr>r*Cj1KkSi>Y))Sb@Br1@VD!Z
z=*K9-ebXYfHZ@(MK8e5##Lt#k;~B*p;5$j!R1wmoE0?(hx4{zLz-4(KH>t?n=B{wc
zR-9nGc*1(R)Lu!S_hB0CC<aj*(=bG8=8ExD%Dg*1NJ52Sxpj0i^cHXIykP*;Od5oV
zIF~YM_PcBkk0WeDR#BH+?&!ScXY*d5Z76g10&BXUdhSNU^4}mr$F9;rsfMv)-Qxdz
z+;?%w@&VswvwX500QKa_;xz8>iX%AHIOTQS3$t1^I(5G<*D7{0Z-KPAEf!Kzm`SiH
zaw4`y8-=_^%_3^R#6wBf@=Jf8Ec7ApZ(csaw;G&N6Qc9b`RE+y+QyGJZLGEmq1dTN
zKm?~g17vwi8pE1ovUt*>zE2`tuWx|cC`AX5rCgw=*}O@!)?f*M>;B<g1lrBuucj{k
z%|RxUu_q>`^j~uh4-oSm5GwY+Di?iy@_Cgcz5K>X=0NU{3DMc3ZqInh3$ks1?tSl&
zA<q_DkH9t65IXx|8I!Ewf$C-Ec^R-!IDso^th#|qHP&~Qt&sM!G9$w31|mLze_dl4
z##@nNn}%tc%sfD@A=hrqIse|T-`w+-6OYMyvlH_n2It$8b2-PX7q;Vdz;X+tG})Fg
zN1kqP$f1;WYxPMD@w+DmLQjTrkzXMNb)4I=+=p5pr3#w?*8JD62PT)6>C50-<U^;i
z=(j^qCe!Q}n*0iJc_0uC%&BCKKA&^1$TLC(tU$W;72jk)sW8|p1pFPhc8;bZkRCtb
z8U468(2$@hW<5<6m~JJA_c!xLNbFQNTGHQd4y`;LGp`pXqn7JY#%rVRed#l|IKD<~
z`tjdO8J)1tO-luPoHmiLv!40hQ$%niNEf=(uI>mQyPRDv_~C_my;$9YM6?CRZ0Yhk
z`;EOE?072T<h-~P0@j9QiIE3wn&r4nXh%93Zt5O^M2q;KlMj#3173iCZZ`!Yj+Gb%
zjcU|AZcVTP+Wy#0wGbP1e$EJcqoPCaYvFj57YYQ}Zq5<_nX~%Do{^`2$k$L(7J%r+
ztu@kFOXL1xi!KrdolNEwSQUKtDc(r)5I5_CJ-8;thx;VCGDb4%XEUTpW0F@HJ>?5d
zb*}aUlwl`C@Rcr7V*;1?uC#l*eJ^zA{}x|(6BG^NRC6A%zg~<DTKRRW6b<BniVNIR
zAw<ouI4e?ca0qA%4Sg4vt<)s3*W|eH28Jb9QB0WF{sxAxfM55lo8jv=zP8hW1fLdJ
zdY;K&XH77?$jRM+Kp=8#f<EAsbO#GeSMvj|gnV<_XhD-K`VlDz)C4Fs#a0jZCsXLq
zz|jk!>P2b)CWQYE<mAmKI9AOmz6XBgPJ0RF!!`A{8I0i$i#aUh0Am`(c$;P3xsXL2
zuCI|w8TK<BT@Q(PWoI)>B&?XwM<2~2f27lRPY#$ZZ(Lx3FS{~lhxa6(<(7WisXNl#
z>BLye3amIL;BF+tZIkY-XL1}EVK+r=yG&{+xJaSJIoUp*<5Of|>2Sj`gEZbtCy57)
zC-Hy?G@0ZU9#V%%IK<itD79-Vl&Z3mVpicu69B1)Haw&@oVlLAQ+tWltRzOSfbHYa
z%prUg)8(zsYVX?U`4#2aI;~%s?M64leOS$ay4{UV!$G<H!HNl(#T4ae_mYkN`s=1g
zPnM_98jI8g#d_3pXudb#&W6w<9TKV`$Fu-fySYtx>l{(z!HAehlu(%=hbE`>sZuj#
zYP>mh3bT&@{w^b<uP^04VG0gk+*Jho(&M_|B&;Y#i?%-~del>@uyDrjpOxKY{a<?i
zvMI$;G!}bHBz(o?b{V%%H|x(Y3|OSehbc<5G(uE!gcVWpUP_e~e1)I+iUyrRH}t}<
zlHk)3%FbiEA4~lHC)l&VAO6`=np=%s@%FjdW6m2nrCKPD#cZUTmKp*$G?+I9EpXQ)
zvQXe?tA^USd&;1+OmsT$v(AYc#)MP-?2>w$1K<>$LsTxlR)kSNlMbH9bcCqq4*z%(
z!wuDA+nXs6Yw9h|4st#{nV8!eMt7T4DXRkC*y4M&IGFw-fJT?8$~-ca08&KP>RDd`
zqID!G;&^y5r)W!(8}XD%L6eKPb*)TJY&5_~uC5FDrDRSO#`y(B$$WF<$%v>A%+7st
zAHe9M+h46(NQFh3Snhjuf>Gi)vbmFhLl<`i=mKqVWFI~14rrC7=F8IgT+~3BeT6ov
z+XQ5-t0r_kx{jZ84@+2^b&ANoOPDF9>%$I6=TFQR%JN$e%b@BBqYKZxHma5;wnz!4
zj~SmnfBGVk^1-jGbk6Cv5(hr5p0hZdIa+UabS3CiW%tV5UKSQea{tIU$0)f#41K-6
zEtlzSy-ogx17BJXnobB84GdN?k9`n!OPh(MUU&>L>K{l-Qo&Jg%mEd0X&NLmeilYL
zq+QW2EKLxIkX&+ST(fog)wm1fdV-$E9;JWmn17Fw;rZF}-hPvS&N43Ec6sr3!@3Qd
z#eRbbFVEgw(URCawLC_W2q1y_SO$BP7Y9^0!iw#dQdrUptz8slRJ4XHdL{#)UU+<I
z0vffN%_L*}$2Sb+)&JK_Ar>nDde_^PWAK{MXyghhPAZ^<E!q`A2}kDLze%Msymg-e
z0@SiS1yq_NyoI_bvEM!=4X<t@2~CRGCz&tzhru?Bws2w3xjpgmWdFMyINAdS(82Rr
zk+LxapQo4T<Y|CihB<>rGa>Wph+`_QCAk6KYg?xu5n1fdKHYP?0m}cJ@`IxcR5+~~
z&~YQ6bUe6~_3l<&0LJ1z%p?_|udbmxrTXPc%xqU_9Yoc0$_RiiZUT4$!c&FQVez}(
z<Wy<^0Qv7g(OVPKp219-WmV{Hqez^%-xkpoo;sYO-71i^(92nAbu7g-Ppik`Ia30;
z{dX7=CPo_8m&ngEx&O}J^4!M?<ta|S;s{&R$pe$Mw9lGabLy3ub&BYVPK;i>MaOHU
z$NYD~Wt!ug)@HCTIM+R92)$J5vh<s+X?KID73rg}&#3U}p|NAxh+5$OQ57CwqEPG3
zSykhV{MABkUHtIWyY+h9x_@RPFuTo-9g^z@gOiP#KDA#nlq}GTW}A!pr-ur$<u)kJ
z<{`8))*$^@^+wS*W44cfT&o(Xa)AcnnZA4}dBS&?jNvVoO;D$OXjSN~{ipG(S$N_Z
zszf5pO0fpy86j!JNJ<tZ0B>Vzmr2axo-FqGS}8hc{%X&1Xa;%Tn{b$-)2IS?vlO!&
zhoS)=?xa<!N@Fht^v|@=$~)gTS?5fXzNt;!|6oUL@i=*#Z5U7Z8M8y}p}Hkh+ch^n
zdL%iUp0~KQJqQ^1d3)gvrdw*8j8TpLx{r<FN@Y)@v*I?aog!3k+C~~}t4#O)?Y$I<
zI@JNAOOU57pe-ST2A)W74E^t9B6~s(dJ0b+U4#L-kTOvYv|EMR#DY;^nBo}I>Yke+
zd?1ajmc>jlK1=lTe3n(8=<jNuoI?G<9*mtQJm4j3d}9?u+w6vq9fuUD8!5G(b0jeN
z^7M!J$CNrzl)7XIn#%Og$op|_WiC!}yPM_No!q?6P7eT66!8GlguD!Ha-z?OM_+%b
zot7JFeiX0dVBSv)WsZH)GBYg({abcc0UgTF>hZxBLq{3irI<83I$*RI#l!<cYQd;H
z)$rN*Bvli{t#Sbegrd6pZvlK;pN#U%-?11H&2P9)H}g+}o_RsQH0y!XX0=GE6XEpU
z$7Jcr65<#H()&;p4Ei>j5|9w$yYm|7halxf-3crvn0x1?^ztbD8|<mKrEAhpTUX*g
zsp^#X>~V67du_lY7H49Lp-lkI33%(Or7UoFwGsM9i?Vn>k5+n&gd}xx51)uOKa!_;
zd-9LSucG5WxXi}r+6`9muNGA(s4>J)ZgyV>y93|V4|<<@9k0$)sZ}kqp<q90Be0Ph
z3!n*yA_(KSB>ly>9|HYP-*}WfR{dE<su)9@4V$c2Wkzoef@R}r21ouEj1GhJc+)HS
ze#VQM54aiWA_G1(7q%-2iv8IJeT;&-gM}Jwxm@@$f$=E7cpphDZaJ3|OIrhMYr<p6
z_)f#$>y~=?j5OBcyAl;+GZz9b{5sBZvMMbWet&i`*ulV1p6N>rmEiB1^YSJn`8{>}
zcP3}*U1H=d`}>j<6Ij4}px3>p>?cPLH(9Qa8;U@Z=hg`)9T;nYb!^rpg4M~<QR?GI
z8%k)o^knT8L6^g0ym<HT^D+>gNET`M=lFLYd*WqL0Qcqan^F#d7WVrNLy!F`0a#XO
z=Ze1IMmA=c5dBe=4xC%t3-B$A_=Nb@U?Y2qfrWy2>h~Jk)hCJ!@8JyBN<UB#D1S)<
z+8&`?IJ^39yVQxP1^}KslSLS-PPH;T9XfEK*J7CcJ>xpxB3XuThDb|pyM(-faXTO8
zfFXmc+}$4MNxx2C;V3}tF}XLI6dYF0Vl^`~Ow=ozw10mHv3wu~;v+eX_P}mN{Sdcx
zT0zRgY;+)rHTepF-)&Y)Eb!~=h<6-tsy06_6pkAm_9&KObGdsBru9*?drY-!wojTA
zbnNlFv&(5q(XW}Yf(O3%Mgr`Z<U&z?Yh<HXWL(7i0we3h0}kD|gD{TcxhUPGAGI1B
z%t`_%6OVu`rYWUHNMm)4f>qbZ4hy&GBl~|VYKWO<i}riL1)Z*Xc-WGeZ*6j76mpH4
zRAN#>WlHcu0kGFG>NW_(_Pbm-PA52F`Btl$!@S-wP#chT)jaC6@G}3y4oN#-i+*6~
zt6n&@^}o>HCUu=;HAOBDPr>WS{QkAhjLWB9RfclfN;L2tW2(#&s8BeIsauE{uu<Gy
z<GdR=wX9lYE4z#sS^gL#R>CoM!s(~S+9eKdpaS|tH`{N+WBK4?i2@_EPDx??eT`Qq
zzU`8nVnw0>CK|2x8mT+#+CtPbSxUt~KwW|tp_S7@pCV8#6`$J(efBah<1`zGytS+#
z%qdd`rD#C0Vcz@ze1clruoxaF0_vM;_n9VT8d?mAiAni})ZB-qXbXjki?h3qx4dHu
z1Sl_zd(X*#PoUWRU4rSzpXrx?pMGM#x65-@+2EY0;0W6$hzj>-Yl^3|S5Si2<!DZ|
zbi$1rYCQ0K0-wEd;Y$)Wk#Jia&cP|@E9q@C^!9#Xpa0d1ebIew?M4K8Mgju|znmDq
zJ`FB?HJP2L+g7{oAjz@hHrX<|wFRWk-OYm((1fEOpN6T!gT7OZ10nuZeI8sc;f4A|
zHp(82Pe_$FG#`pOt1chR0gX{j-E{({v8ABEFi>LFisk9oD8?@K_a6eZ(CABAbPy90
z6B7<`sGa5%4XR~z>(SCZy7M=QK2$EiaYNL<Eb!0<BuS?du}`zP)*B5rv0$Zg8Z(ID
zpn0%I>Z1j$RGPK|4a>IkTSG`!-=hr<OE%|lPhFTCeWc#0&yOa@;jVE`rK7lz>Cs+c
zN!0Fs(*9K)We?HsEVP|$*1j$)AbN+nVg<L>ZpkcX-N6s~V}R;59`LKjgB1gP?nQ=~
zw<jKORi0m$9-Al>8=t@!Pq`j}Jr1jj>8t6>jg_4!-S4`8QYKL#e#HFzy*MJpktTTn
z#5vawj$N8~%!suavf|@rw<MaB<4GhTWYnO6hePD?e@he#aX753u3WV=g$38u?N5ZR
z2XIqSQ*m=~yH`xy5rx;r9sh&5i3hJf2kt+HtS|nRKzelSyEbWl@tYZ%cIzXMuI3i2
zbU6b>>vqgT3i40!8~+;RPsdJQc0~HIr3|ZIKqTh+KOSZTFYKq+sA3|D9J)7k{U|en
z5C(A9>2*%$@*L578i<NLoudJvX+SQSE!!kVh<Oq*Ih*AQUKu-iUHU$f*rNa?j_JFd
z-NMgc>9MCUOo6^3;)JMf9-1+WK9;F|u~SMM5IeMDbR>qXIPVC^rpWoL=qbdsLP$rk
z4olUcC>Nq-3f=h|;Nsh_#YIaKS1%_ouiWYKtALXy8NHiF7d;h9fk7&;v$xL-N+LxK
z#M})s1%rn3u*0&n_GMdy|Ip?ie6|u|m*?$^NixR>#pwqPLLz7C;TYE0yKwTTUR&PZ
zEXfBr4zo7TFch4nDvC$j4Ls_K$qs+6{Z5ir<ufbx`H_rv?`Mvuuz`(er`N%+JXr$E
zKXkMUL9Io&&OYKhGW*7@+q>$KtCAxlb#*+^NKH>qPBPH~vzFWjB($aXm0`3{SvKy!
zbkqw$3;l-GSK`(sA+fP%Q)JqIg5sPd7Lv2?91b|HYCcwvsAk-<?<0S#`c8WSVw&b5
z=&K%=tszfZ+c(PH@a1Ij`$s2TlnC6bX2zFSPhXPeU%Z^J#oDLIP%CDNj=S<(Wb^NI
zkQo0`YohkMANw~B`M=_kw**U2Fa6A4gOMdC^H#|J;PIS;PhjpmJ|`;su6w5S*3iG`
z;(6QOd{RlF(9(O0SLfkh`@#!h)n@EW#xL@T)ALj``pQ_*6|EC_ny4)9+dsg7;S=O0
z^lRT(;ckrk_Um+><jHTdkFGRy>>wFw`tFrd`&$<77d*=wo*}-J6HX5H^hkdTiwAvr
z`Y>gg;(%&Uo8F1>ZvO(tX@Cna-S}|+C@cM&)@@vpLrpc@u_*y5xj=0xBERCV4bvAv
zp1!f@__WTR>%0E@`-0|=Z{G3H<09NPv522KFRV7jvKo!u2*8J8@ok@yXi6qFm+CWU
zBRU40EzNaAJnBnPACXoPxu+Cv`GVl}MbHDSHQiS&Yl07GIkU~vcM?(@BY$HhsbDo=
z-^4+EKz2jsCNIGw`w=4Z!c%13pROG%A~@B&jWlvUu1VVftn&<^_=>@hCLTGo`m*G3
z4y=)DF>%c($o65pHw~Hg)2Sj`UL4YJ^ny71@|_^t4hkqjhs3?RWiY?i$hK&G=^rdD
z;qU4@(+r~xDZiY<jZG$btlU4!k1RK7ZYATz!o9f=u3FE#z-xtHGeIh<i_wcl_O8(9
z&qvu#Of6L5!0o03Db2-k3!g;AH25xj4ja7qzYQiw$*6bwJ~_b2UcC{;Q5G0mtFqj$
zi7pl}Pt_sBw!1dOtJCM?>;=$3#8-_8CPaxDJpAXAg$QYwun0`GdT`KNW?%w*T_x#N
zI~U!p8mgBVAxetujL_;OCA)Tt@7Um|R3Sq1l3DwVv3W_)Ai^Xuu>G#vMTKtU=m&&o
z7m(J9r&D}<nbLVFo=Urk02WcEM}_-P!%G3KYf9RNr>3}n@^nnX?|^Gp2SY?RmxttD
z8*)<HxVpY$$`<tc3z7hogasrb=`UOlOC~Pu_;1?+$Q$t>JM675xQVC9=udfM9~#h?
zQ1S02pXwO&tbcJ{`((PSavz)e7C-YQu`U!DKAkVWg7iRE#UMH>aT3&mQ;(`!#k9x#
zStb6=TXwgOtCIbT@ME|D^FP$rIn3`N4#A-8+}rk<p!iR)TLU4c((a}X{xxco_l7f6
zRnNpvgEu|JsgBsz&$8$VBcTjBc68Z+voDOMgs<5X_xOT_0*g0W>h+6{87(hpFYf#6
zzy*bxcFV0d`2*f}U9yS^0ZvZfpljoQ;WV7VGMt&+fLtBiu20$}=K7|lzIg3DD+W4U
zz|@*6F-lZks;MVB3EZdqfF^<5`IQ|g5+xs9NZbl+#4Xn7XFjek-O<MgUp~byg?t*V
zRTqf3xY#Gmls~Xheu0jKjH`hARKVWVU&aPL{oUrpB8_#lXJI^d$_~!@6D2JMS=tIL
z847RMZo(5lHP2Fu?~`8t_9Qu4dI^VPX+3QHl!2?0OJh^C4$(vg6aO<@Veuw@y3B^b
zQ0|1$Gu}ofkv^!{ACz)-pUh}Z?xWx`#SMo99-=&1c_g~j83}u?0J&ACy!X#5<QJf5
z^2>GO=Z}D@v`(k&ZtRLs1-A;!#~1WzxMTSLZwrE-q_R)^u#o)tqvO@Xzqi_%@^CJ(
z(-+LZFpxU7?$A22UlXF#@682F1*GTMJeV@3^TUNiXQ?irstb2*uiF@R4?VAbM(cYk
zuUqt2LX-x?wcR~(6+~x)>%Q9sD_-C6iRr_(6yNkZe^`BPBTgeC*Wwe<+FU!TZ6G^6
ziyq?5k_XAmzI|Wo=}Ky=75rBL=zPSUPY&2&9qUuu;)qwZ7mSPp5?etW5j(|TRfga7
ztF5V?9Sizf2DXtcuD~3;Z+t|GdMQp0S1aatGviWy?-kf@Uf9}a_oUqNve$4I9)zD7
z{gS<xx3xG@%S0^oU@+IBCMkZjO!r|u#8Qvswf9rnWDH5-BdKa|W8>Z2r<YV3tGg(I
zhdOS>USFlOxS+X%X^_P4>fT%0z#lA9sCp2Sxm)cSU79OQ(fu@nmXxkr6Q|}Vv2{I`
zVSHQ?KR{O>#btIfD_}$@av+WD8`CBOx$c8p0p^H0(rW!leZCibRNZQd*sQT<mRr@M
zScMA160eB<fd9xJ3|q4saV>#U=X{Bcu{VaDzLj6G_*y;HLw{!&b!1g}1=xFR^t1{m
z4D9S4(wVn}kYeVrf(3!}d-AvMzLg<^O<tHX1>1K9%??Ufmk-f}&yVt^jR-fYs5Bw=
zEazvzf^(2e$q<nc_8+Q55h5o5ey})}rgyw<#ce<{=1*`{?!uDz*ezd>Fw&cAn0%C>
z2P%3KwTdnaY>kxaWgzHBi@tfz2{@KI)}FuWG<K_|9*hK{0_SRx2#%jx0%3V)Kg;dw
zNvYSYIVL<|!xR)d&7V9u%U3H8HX^I)9or}tYn599(FXp71Dfmi&&ISJs)a7Nm*=!O
zGooe$e^N57)Y6DBMk>Gk%dhvS6SeinS#-le%`YR~bmA)#c8u_`D-)(xo$A`38&7r9
zvBt6C)EYnw6{T7$%jT2$w8KGDmFw6<X)NaS8rBrfPvEoP5dNsafP0DjJuLNwS0lIn
zBcw2SL0*XmIq+P|UJEPuHqS}U^HVi-r+u>C?M?Y28ekqSVC3tVfBdT1TLq`{A_86)
zJ!%Rhuc1Ho(^CQ~1-PPvFy%zFe<#1q8yk+Nh0eeZzAbZeGrFb4=Lav4EpitZ1(ko(
zb(<lQMwHJP{M#>v*7uFxP@%Bt{rl}W;tI|IA<^<TaAx&yoJjAVcg@X^B8%eE?c|kZ
zGD<-@qs21GrT+OLkhxDn<=*~UdKy@Ie7aw_cY0$u`3+W@w-WBY&aO-lJm@3qD~Kz@
z_vBa2ls#jOuhH@Hn@wD2qK&mHh;oLX{NK5^ddSm0S8?g)kvtz9K%RM^5dGchk{P?q
z*CQ~Z5GponSV!_iKW35D+|UOoZK!w&ef$-1v?R>#ajMNsYu|iT;dRSUtA>N4#VA6P
z!C=Bpj^POk?srx>J8_j_$lG9ZFY1(LjYjoDzQkw?88vkd8KH-M7TM)E)$y$fjBqRK
z3)Ae?=1Z&BJE`#~Yn$@d6ZZunnCVG9@NfqHP&`%b{8FTU=yI+KdqVQ*Jm#4LChfpA
znZ#ZW`T^+=rh<24*7VK|guHh}2g4Xo&%ZD3j_!yDgf_i>a>ex?DN$Z<dic)i6cjXa
zFZK<|>zCI7YW;p_XCHXDjRXVa^_x-adp4Z?Ojl;#BfI1T?%u0%xIlimB;9dSQYB2X
zlah<MT=6Yi;n%oQNZ-jaBvEWV=P8~6P+%M#*qgVyl8=?SF4pBXPvxG<g4gfJ49{nO
zK~w4(S9tfH6#wSv53LEZYyt?ez<5vrUlHv>e>Tuk9h6QcHqMy+@XF8s_Zp@$Tf8^L
zwVf-S`Ly7llCDY#N82Uy#bRj9&wC3uYjh1M8z-qzRAnj8Y)n{MGL>;@n|ceIAR*T{
z?SWi9{@>y4GD6zv`T<yxd1=pMe*LGJwi<>UDoGO5I^g?y)+0Om8rvL_;<GByDc=8z
zbX_8|T^1exSN1YR{XtjmFT>j_>rcf2j)UVy4zDTMYZ!}>x^HAEDzpQ#3VDZ8e28QL
z)emX;h$XNA{J}E9HBGo|794T~04PT2VbkHVHZICBl#ua5cnzat`GJzWEu`6nII`GE
zyF$=o;sZWmQ<<CgS5~mP!o5xNCsC7a9azwVy)A}d!Hkj9EA8<nFa=(h&}Y9M`b2il
z@hndAxYpb|zhHWye$1|i;zHKhEsD62am~I_g+*Hx!77?k53hqn`P{55st@ewr9VFK
zWYI*r4>&cPHsDJPUdb`V3QaNR*B|jK;ug$CB5J96^-O<r1XU2~H0zmwB5b#MJBL>z
zsW+E<3i4DU?FI;-&T)fRc;OjjizD$qUD~mmJ4KC`9D2WyKX+u2k$Pw@F=B}fQ97~u
zuOdwlKV%(VRTVr`Jn1&OA;Z<fpb_t8C4be(TDqcSzPrOI^1?8S1>ul#7<ZsItf=3u
zd9iCOcB<=Spz2mHY)4Yda*9Xu)E*d#aaSqVTS);gW*muh`MI`P8EE^n`ShTsWx|LF
z-vbjld!}qNuP!*gdSiK10pE0|N7vh^nbXcvP4#YBxrI&vga1%nYJ>4Hviv6tBLc*I
zxNZ8A!-M`s23wXYUd4jd!@0o$Lv-C_-nLQ4Q22$wD=a=_f_{?KyYMj`sZ6G6239`<
zJ8P<;b*#uh83PN7jjwEbJhg<6|6Tq1J1Ib}XS);h%kKHIFgAa9@GR?obdO40uWJxN
z*a6`|J&h#2<LAV>kWYA1NrSA3fO?-4Qgn?kNN(8Z81nAo{yN?}xVM^rFh{&U)9kI+
zn|r2|-|j3xl$qpAK*qlTZ1BMUI$^t_!&1t~U*bq987V3Y^xQ;|#Xkd2j1{VMW_Q0F
z^XVG4>7Tl|3uWxZj_C&n9bMwoypdfNct4-R+2Nwid?<F<zk)ys_wB+J-U(*Q+06om
z^)C}Bn-0@}QiO?7dmPtxiuPEYJ#`pXfHsfu1#;-3-Vlw$LT;${J{*{D;zIhy3oag0
zRS2xzEm5uMXn!8OEu_2BwiH7|y)O67Y$1OGrA7CCK9V1>OJK|!`Hz*@At1t8cl{3E
z63Hj;8psIZAxB?#XEf~n20saqI(_fRs(%x!n7}V2P$R;{UAU&kQ^zYXMD@b$9&iwJ
z>L(9EhM$UGT<ptM0>pHs&J_;Fl{(7=bOV`hU9idGJU>e99Tk5IS(7?LHV3e;7T>ya
z($=C>QEaWR*JpGgzwX)Zt}A+`n|)3TG#!iy&kXLXSgtQGCNz5;QlM_7U`^l3FzW8a
zD0QTO_+=VhHR~L7lag#+J?Q#I(E<k0bDXI6+wnYC_m@HQ-I;t-?>A->m+2DPxi;$O
zBeWK&-|hW`G1<qaIAFw=Y5QJ1^%6`1YuAcyS7u-IL7$kG1=vNLhk1LRXH1{F_|zJ9
zA)(S5io~L4=rMB2O3Z5o0Q*&n_GRis`aX!r^1#{&s9(VvuhK;4LwVC5zH^83XSh$h
zc07F!)E-Fw;CP5WyM-IE>fp1`BT+348T%!8!DVz36a(?f^=<;fE3Vo7njX-iQtQx$
zX8U7bfOdNqQU?Baho0;CT9{TB1?+hf#-PY7VPPuqd5T1x7@XgJ^#f}jnSZ92o0FV?
z_U4`BWF~3OZBbi8uJfha@i5DcSm8&P6H08SLyg8Sfwd1X&eJK4ma=ngH=Y|%a*R2q
zPN6h};gu=YD%6zc1z<OLh4ze|3Ef+AAGv}pk6@b$uO(_vL_AfS*NL~TlG+RgmQM;$
z{)$Cxt&>Q}{PpV|UV_qVeGTkOg?mNdX%^JrNrXx9anUabf9Ogw9qS3%fSZ!ptY|pv
zsms3${jT_|Z(|;!;K^KwY(O4u+*SEva-i3f5912<{kzSBdn?Yr4qvX;>WN7cGgIVl
zfuHojK05VGXxZ+aHe_3zNRRKb#2w;8SI5IBc&f>0t)whtN)KWhDkez4Q#C`?*DzP~
zst$<rl3`c&_H*r7B=C6;$<zbd0DWl7-RTjUn7yN0cgyD#(e@MWdBWpo^yh2gKrPe#
zX&o01;*|TozwcZY_VgIE&dBNs9yxqx9`-*Ii^oUT)Q`vWot_OV=AWJ3AdiZgq-Y>2
zw2rs!v7P<HGcm7K3$A`c=AxE(Gqsp~)hM>sJe*-XsE(ed);`;-30nEtkvF+$6`3Er
zPd!UxZP_uU+Vl94c-+fzxKQZaH7}0dR}knOe!>0Op`-+TjFK)|{8Z-W*Er%b)-ii_
zs%Te?t<&%14IliiF0C?$b;7+Qscs5pB0s7WK@Fv+vJb($NI<py#1Ns+!_Xymx0yz$
zY{8|GOU87_Pr%m?f2^MCy==KaYzxWXxV{iXPHTe+v~Am%khz5oXJI8Z8vk@eNU45f
zXfW{Lyb*(wB;PhB#W8ri+mwS|S|KzjeY?*HD%@Saj!5C-Hi@-|or6IGc}Zso;wPuN
zCM97~=yX81Gkh*+WPsT*tnHS8`NF;JoyW^(;C#wKG9f2$T~{s0O3ccD+7W&O+UhZE
zU4%~(><$gfJu1vgrCUlGTA%=1GB`ycB|qB>EVm*-T<};1_hd{+Fi!D>nG%+bu@PbY
z$F+h~$2obQn{r%D>?T}RU>%coI7uP?4I;xILVfgn^~I-RPuEp#?=k&Ez+-rhToGqq
zVkj_MRz5c259Cy_yVl;_{6u|u`4_<_n7BG_(43?!q8)e;;K5&`8UOF1o+3#1Ls?jO
z8M0DG*?(`4x#7ifxaz|~STrgpThdRw3H^p)`BIpBkTHJ-e|c{0uOD5=8zDqR$)$t<
ziPT*p@<lrR^#WrOE-M#o%3%cewg>Pl?MmJ{TJjuHKwC2%e|qtqsfZXLTfTrN4@#VX
z%l{vx)*oIW(|mwrAWV3AsSmeuN~@MB@V6NA4Na<5RLdD2fwVxQ?TGwfuH6Sqp6=%G
zW|~_6D~*e3EdTeoIiJ*9hcjJO-CAA43wimNw10`Cwt99z?ggJGVy5hCRWN|sM05_%
zYkT@_+%do9(T;2uZ&oqeGwC7EZD*7UXqKA7nc;K@RdLC_teY>;P6#m^CS>BM;vs6;
z^SngRR!1(_aVtgdRbWQ>t3CJ=bSJMMj?x!?Px{d-b#)FE!H}OouQphG?z;WBB&NQD
za!#@mACMMX#i9^5USW}{LsAg-iFnfcFSU}UzkQ$`IWfRK^|6>!pVZGfabc&ZYiuwP
zJ6-)mUG5Www>bZNoR9DHB*GNKc{Ljr8w@gataEK@>Guz*`y4~T?j>eieeuOBs%>~5
zk!4@bBBeiJ`WYwhf?(nKLt1>DNTv7vHyC4Zul1MU7!%>*l~YUoq+osvhnC(u$MA+o
z{1xsyxcCTcsdHM1LQQ9%e;pcv0yDE_2Q;Eb@}S9b$x-C;<<AP<U%MR&iL5!tpIQC&
zf3V`Z=(4-Fas+I^O%UkCdoM<1KZ*s+CP+1Is5bmvfdeuvOYQDE@`vBv&dAK#u&z>)
zVMZZzPY}N+R?mep+?EO(W^6)_KIa&lNOsLAbXJEM77GpfNf4-5Xe>OeJQcdd!W>_6
zT$F<2#!Ei@;=P`-Tkp6M_4yu{z<3#>OFd?hk^mrCx+~Fv_D|Q3!TX;-6;cOxK7*>m
z`EN@~rtZ_*)$T}KbbCJcR=TF7V|*LHBQqs=bxI59=y>%8b6qeiDNALw03cHOKp0s6
zo^A_q;25*jRge@s#`wxb#I5GNJ2nCO#{3@W+>I&%b1OwBO&wpWMBkD{#_1!8Tc3V>
zZ>4f}WyZ037(C+2xnpsD2^_Hd&<2-HISjvnV?_!?_+Ynf;P^Aud_&F`@;euzZ9&>7
z98=(^dgi@r2-bK3uGyK?t@1zX{c4`HRS;b2NoyKOSv6G`zUIh5tyzIvFGKSf@NU=C
zN#cTB$rsTN`SoOwRet$Pt#1JH-d6hhw&}(1op!JswCOhhqfU_kk2`R|2=&&m6$K9>
z#KK@m5m<=D34zv6J_5!g+T|BNf_BHg%KLol;k(Sgh#qS5Ydd%1>mN+4tW9;^R~THt
z_z!Sv_1!I4e$tP?;`^Yzi2}r-q|V|aRbM0y{|1L-y4l91LdvSc+w{=tVE5oeN7u4j
z%ChhOOxpis{~h?7%=@74WBPUJu+L%QF}*?{S@stOG=llP(V<5P7tQ$X0>uuVaD>A(
zsgPS3&O2FsmK3IVw@<_GDF?8r`ARSY@Gj!tFB53gU|cr?NoksVY2f^oyW~(>+`Pty
z`1^L!ii``zr|#(dZJ#-Q0NDy@d}7S!;k%zpB|iBi>VJDKNM4v<vib#9zi1CIB>5bN
zxOcL3A*qU~NG8PD!6)9o9G@@sfl~|F2{oj{4V3T9b|D^kfj#?PVMx^4t(0fz^(D7w
zOsb);{q}A;fg{?k%=pFeSk`yedX{uQeNq)j4_wc9yj8<!H_iXW)BkkOcpBKL;?XsE
z7|osX<#Q$W=c#TX5WWZ)1Vb_j%)yLef2)z)fXl0o;iGrx!g;83E0?R8d~SY>r`V0w
z%sJu93xu@=<$c$X3*7w~Hl};#sZ^aDR7LvC0!Z20A^PTi5=WxS43rr+L*;_jB8T;)
zy!tw1D{je2xR|I|`JmD}AAjP&SreKdiK8-RXyOqkUq{xQ*$pGNp?rJ^gf71|{fDR2
z@8@xU&D;jE1$#QuEtUei`y#9hgnJ>fuu5Z^i(x_^W+1uI!X<a5o7c#mdta5Ly=TJ8
zN@h-xn#4YKYQ`3~-z=%dF4DV``{9ve!>TWHU+avh7CG)@oZ*wnOZmui-V_dmV)i-c
zEdv0-#(8#V+z&~&2<m=i!o=`jCASv;&S{(VmxjT-p)0{OJH}+0DtMrH4qL>SfTz`!
zVQCvcW%Uu+wn;Sb{0Jf}U(^+1G;%?SCj$<Dx93Hz3YmkLZs2T@UDTSt$U4u}i(-W{
zi>iF6duQ{B0ewcPRqr%p%wf0goh&sDr~t3VGsG-Lit}`0&w6SKHIHTIn=yu4d{B-D
zl3z$IsBJL@Z}jxM5KSvHOIUg`x5R2bZnbrWPX-7NX1vA0kB0q;;g|QJ^(dvY>3C)Q
z#pFH&Zn*7Y=Xj^RWpvK^WeT;HY3J|!$9O~JNLo^xr^~R;ws<wvCbAl<N4Z~p`Mju#
z&ln0Gc<;Ag1FAIRq6+GE%*VDlloyX~>r09c1Zaea7Y{Rx*F(6}q%5NQ$LT!YF$7TM
z`PkIIZiiuE>5`r@^Fz~poA}0;W(htV`;LCkk?vTrMc|c09?fncr0ecyb|J&_fz5?}
zAyhO|95mean1Hw5i?(F(A#wy6J2$sg$OiE}u1N>IqIUeV2uO%{0x6O=Ejs;~)?iB=
zW)zHnnR;S*+-LAz{2!fI1jH{d#rX%iTnp(E6A$>qM0tAHKA7eS^*dMs`f#QcCz#%;
zLxai>FQq{?^~R_P|2fBDVZTp(W{`lM^(7-G*X?vg#~NT{kQAWZ5+-I{Kw-;P^rG9V
zG`hctq}YTDaQm-!8;P-@cW#_r-_r4kO~OUh0bQgw0cnM8Zm}zCyl@;aRrgMgZdimR
zlKc#EefU`Hcrsfz3l%q^4=z!J_pGI8rAJNoz?YEhGPFpmA!6Iv8jX69)*`xhdQjNc
z|3}kVheiE;U0V?a3_u#`ZV^F1T6*XXMLMNBhLDoZp}Ubz>F!3lyQGGp8{YH%J=goc
zm!h6?K6|gd*1a)G2O#a4%#Y&E{+I7&AdXHe5Pe<OE8hTDFcHjce)~4Q6Vr%+NYR(K
z*-^lf6-%(K7Ryf9nSVYr^$ZLzG2`(n<W4Hh>}zGS3ySL+lf0}2RZ}UIP>q}3g*3mx
zgYIjYv#z0rK+1wSpwe$b2?c(Rd*tk!;2x8oJMe0g#x{L<&?nTOp<Pl=dEa#LH>b_!
zRw(wfx_j~zf`@4Akbl9#FGTW0WdVi1E}gpY!Xd4Wp*RYkc+*du%kqs>QTpBH0dfR}
z#0@B|zznehv*|>|i}w>-b8)|1lN7(^%4uSLu*x9==(Yr-o5i$~4D9m|FZ8C@zV4Vn
z1*~b3vp>XVYZn2X#LXpHZk)U!KV~)>9UIQDT<i(+QSFYC_p&qoP<&BV@pgInQnS4f
z^m?gmP~(ggPwq{cKf#bAj+(QpjO%;;SEPyk;4Td%u=@*$hCNbJmJet#-oI2e*^au=
zLJRr)NI7h1zG4yuACsyb!_bJlW2Q_`F(GD7{pkE?5dQcXKaU}~8C`WWpWK265=wK5
zd`ov<tt7lk@A!|+%s?_!V3G=M`@x-+UvBdy*S><|f|kPeH+%f+o<-NZy8ya#xHD-r
z=Rfa{(o)_r0hh}#cZ`Z0;B4eFuOe9ec52gH->skDPR8Of6gJIy$W2K~9YiM1EY3p}
z3=D9oMa)j`p2)a8f9Wf_Eb;jl-IAa@5t!t;5^VaBSV-^-SXv#^4bEsB)?8T9`M1U5
ztt9Y|^1@DKP;w2FEopfuM)YY@*m_bJPun@1-9kipMvBtw9{C*(M>tn*X9VfcVPmsP
zVXv%*(lLYSW&{4Km3}gjyvN(ApIBIZbluRg&$UY%Xe+bk{h=7K(6llXHb}R`*1}`!
zuP$wJ5&Jdv5a}rN`}&W4JZHCkcdyg$R*o}ubDEik&rzQ)*oJg3zhJs&$!mJ&y>+U%
zKdmfiOhb(ye0sNBV0~<@=GkUEx%&99+q$Zv7yR4{>l>q+=8%*Z%xy6*-e1N|)y+(l
zX^D)Q${%zvno6+a!}E08KaR<{%P*R%<@;aKYmoBVCL52h`EJX;j2m4rh<7Qoz5h9V
z=$}u#T&Sg6qO)TR9QchlA`eSRl;v7*B@HBruPy_6peq_6+DKMT&(_DM|9VSv(qeag
zoB#MyutaAIL(Qu%-Rdrd3`n?_HOqs8b0y@LmTU}%)uZBdBCKI9x$ePS13L*Pq$7_<
zuASg)f_D9qT4}p$D0dtmDD7l}nDeSnPanjB)!s<YLOtn*cpS!GlsF^{sitWXrqD1G
z?<!XQFr+1-`SI>`K~TR;usB(L&I$4;I!$BGPS3;3PtF(ZL}ct=`#HH#ygxKjM5VB3
z=~1|BRRl87FdH}9TZlWC`-vDwzr7~e$Aod3(k!?XCeR%VJUMqs{kC*@8FMW{ishJj
zg${=4cJe&|lA(ff1lgK<UL9^O;FznL1glHy<mvLKNhoGWX_OA<H2&ly9HuVA`CvM4
z=9}sg_6I?W4JU@bQp<y~f*-b~=kqt0)3=>6C*~fDiTQ?ymlSf2G6{}<M{Tffb95oe
zmHgf%7Xib}=K{3T6xJ%9mYAkak3vZSV#BAd_IAHi%-zg7+-jwxck`7HX3}CA2O?-`
zL#7>cI9YFv7@E)E{0Qz<`j9LSmkilr_IZeCA=%+OPO#{k1oKxkH)QN<HoNb167_JM
zqe*hb4{!GTp4|X8v!u7;43L!Qyd>pUpNMyM<skUMs(JTV@kKBPSc3TCPA^f&;@;$S
z)f7=REKu9cMuDpB&o*B2J)qI8l^lOwCQXOt?4Lp|M<;qhI6X;URE+#LAGoa*T*tsG
ztDHMJpvtE~s9DCf+TMI>VRKHK%WyBg{8Omhu1;DM_NFF_hm2D&b3G=}j!yAXF&tfQ
zE?9VOM;+{?o6KW!@vhq8^*pX(;r`qXYe&nx!U7jFUg}k`KX37`g<}7O$ql^H>VjTN
z9y2oE%sm`UM1I0~4<Rr48Q?8_${zxaxcH<lRdE$|ZQZnHmhQDAa%#0a(;)?B3e(WI
z43GPG%c;iZaHoD9qgu@?E#{F3chY^xt1(|~ymi#%$s7*YNFRG;?8OswYMkdj!QXY~
zNj8LS!@;#m7hC*Sib;>5Q}0j(ion0(>}zV=Br>OF(A~fNPF5pj5C<vtU95eAFAqXk
zhPRVpQj!*CW22PsAOV_QDOLWO?ptuCFlFJ7NAe00J1&3Re}PggO0I6=yUD^2EP4!I
zLQGk<!<-P#o2bF~G_JF8&JysnQp=;6$0Xcv_cHi*sn(;!u<(yF8)-~uk5SX+#n+Vk
zUk;&mFWM{XqdDs^6t-u`rZo&oXDQtjQ?kB72RG^kT7^7*1-cnE(XG4W7lj%+dUVM+
z2~v3^;;oH7zH|Pek3(%`EUgl`XI1Em)4W)j1jgT!j%f)mX&D&7U_$BwInJGPO(+o(
z<S5E&`PLYk&Mr0UQYkc-=JL<)3YzKX&!PpC@0!90RI$E^pzLA^-lfbv8M`Kqzo#hj
zcnFk-%!n2jN}HSjepI4)e$6SvoSQjW-E?Z|ABdD!HaQYaAvs4zmP!4zgZJ_Uui?+U
zRf(?{1RkJ%=9)5BPxa#T>4JSM4OS%19a743x)i4~TVu^+1!dDvgHn?2mX5gV@uW9N
z-2+G?#z5>UDuQm1<J=fSS}KNS>??LJVToG0RCjMB&XQFO^xBQ{P);(*j9EH5*DWIW
z*i6?2kI!iBO~*H^RB)LT<CGjd+{}jD%7%?w2gPS8`YS!U6cTd%?$OgZxEN;9t*4Di
z2juhu|Nm#?^UF{+YMyMufTr5!f!<+Rc=bND+YvMn%Lnk4q+=n=#ls)rxQLPs53+ui
z;n!kCKQVo*e$aoTk#h3(#9Nmn+VMOh=*eK0O)|`Zh{wSX=~6v7OFKaY{J#!?Q7)>r
z86oQw%~^DB`LHw}0hI2FxA4tEu3d!MIi>o*&ei<pLd@Zl{U_(YSa876*Ga$r2paHX
z*7(+5@!3`IvMXg*`04i)9lLEYTgQx^bk7&L&ueav)(W`jM)tvkh8Yy?rDn&s<*dOZ
z?4IJAB5dn{HoUrkN9;Ym{PA$XsO>=d`bzP`PxDlx>5kNAm+BQEP1*vzf(-~V#C?hL
zb)92?{DL$!50wb}Ryf<1+I6$?%DTRp_h&C3GD|Pf91NYc0~0p$HO@!(-Nxdx+J7c*
z)fw^W7oLhSsRLYFdUwl6GlQVj${MKCA{Lylmac(%tcDiT7*IXTe<lT5)Hlne+MCei
zBj8pWXbdyAxJ+`G5Rjq=L8F>yAh%<D_pTLuPa&68C3487G~X=5LjFOU(k<3LY@}wJ
zl8v&xP)iKv{}OY4kuYt-qsRWWBkp~!!A*&TZ(9`H8(B=w#N?Up_NYM6T~>$c^WbR$
z?2!)k>wC{>W2%N``C~diAjFDUMuy+j+2qPkrRfhcA3^v@X*r>VAEfkK$as9CcVv!e
zgksCNzq!DUO)^f1DTf+>vV7AZQaRYELeB6NcfctunBSJUmBvrEhgZ5V+oQz`=<9AS
zFtelA&(l2mx?w&-AJ@|K7gM1YG#4MfYXWILn3FE36F*u(r6cQi;r~X2uG6=*;-mGF
zm$Rrx2y3+mGBC97ukT0(ioy8LI*+>oG2J=j?z?(iBL*o{THgTaXipWeuF!$3TSHKK
z?sem>`&jrhy|{7N4TI)1J|ksYzDbH+?7ZvaMQKlBT)h~?1B$dpT$dxW6itM9cJHW{
zZF1|)(f73ue}<Uo;!>`we;c@ayx(JJT=xeUh<iJ1i%kSPnJFrm1ImU|I-j&UKUglW
zXl~(uW4har_Zkpy6%pjU`u-3RFJM$Ku~{qM`b!0aEcqnocE@Z32*eWIPLmt3ZQ954
z#+6*$08x~)_%e%!wOpOG;bX!UZr8n_Kiyb(*6NqPY{hxD-F7%Zh?L<7aT&@jWp?Or
zUA6M~9JSoSd=zJG(cJ#7`EgjsLzqRd-2@jnMPB_HqP7TV&3U^-F<5$XZtI^<OFt)2
zYDfR=InvhHsPK)ZXo6+*9{O`>_9N++aq+hoBnWbXhmt)U+nnK*lv^NHhzf@M?IHIk
zS6Kep$F#u^uiTFFxaGg1*HNPICj_dLO~Kmhnd^`gjf-G1D6`A^(3xQGb$ZX1-{s{7
zw+<CnL0`~*{kqBI{`kw^AbG)%K*wmNp&S6;{<tHrP>s|gaLsA0%6hV|oNhvqz=xRq
zZp6M5ae5w9>r!Qx<}^MStG#K|(_*KIO8a|OjM(hhS>7vT$P_rSl&u_fh*m7MHrz}S
zlb2M%RQhUqlK0tEW)&T`1QEN2t2Dt%X*maK^jvUK@kQ-t5}A#{M(jL2XspUrU6Uq1
zkW61&tBqjq$4usAiz@zaGeX-5_<kN^&|BXWgMpH1-nV)rYy2DqoD#-xcfS6I$R-j-
zZ@B*#Y$N{h+sJ<TSMtgv?mip8G7Q7Q?#|Nu-MFVc-W~G<Ete_0Rw2~kPs^V`+{6g4
zNjeK28@#SShn(Gu_*IW}HOT*N6m6)Lkfn^&=*TpjLTpx@W(5CwN_u&9h=wdy^y@NV
zU>AC+Szd^Y5+mQ+AkV%`zBH51O8QdGUuf$HHNwrx8Rb}#qCZskw<K53>oj&&(oAkX
zxa%X<lXKHB$x8_emUprV=Nh{@*|2HNH$WKZNwAYwv^QqZP<^R(p2_@noq5A#p9yr^
z{PkJP8^+lqyc72F{wmC~=*phQf2(KdrDxrQk>z=VX3=kZzoLJ&<;M$FwQwyT7U2rh
z+~Y*6l6Zxur1Vkk%|9oquO$L{34ag8=%vT@dnfn5*VOWYz3mh>XznO8f51B3@m=xi
zc@KvRi{8;Rs4ts_l3jxaO}T{yP5u1r=A|_tNythbxt0yx7WW>?`7*Rh4tvx|`TYM+
zi!0_jGu05*!|I4CxK-eSbfFM05E-y*70MvG3zUbDbLnmboHeeDnZP@E^oYLc#%Tbf
z*&dNqqQ9+csp@t1vN$<r)|5l&ulp&ux9iG?^J-GcSd$O+HYv6UcNeTP#rxzE*h@kC
zD%~8ytQy4WG&9#{UH004Z9N~%*S(f;n?kYT-Br6TnPVlpsb^u?_JwR8Q6S*Jm5Wd}
zX>rN1^zVyxGms0K@ZY_)g67&ic;8m#ewtrVM4b269^GF58Nnjsv<4d2e`X7JgFSnh
zC0Iu@Q4c{91mAo0zUR$XNJMH~f0N+T1NBS>3PmZq8pMIhXL)Q9*p8(0Zr<>-35K^m
zD!pfBM~?>-nX*o+z6-jNGSw1)uILG9D+$k5S57nVhn50kq3Zh1k4Fm5{e5ZIdyi<O
zZ;()n#|>ak5k6}gQVue7mXV3RbnNqnewsTKVx>Xhm;o|ESR_ZMB1<#c9E#I)(-gb>
zTXRbE%x2iX#|>C%`Or`7b^te8Q4*=h?=+Cq3q@qLXx-cB1Y>Uk|2dL(*~{K-Y=#%N
zP11B7|48qUR`lr>pU0HDsNe6l<r)3%8@hLK{-4cD?RJJia|1LW6ljz`;O?ZaX%G3Z
z-7qm<1i%^-rx#5RFpcI+v54{+YLniKsHTU{uhd%fXpu<|KyP>?VvIPl1cFAw`Dcsc
zsW~<tDg>%t#dYTBw8ibUZS3Zw?ca0S#-T*>S=0q8`Pj|T$tlf~$j(QAt#jlyebsq0
zA%R&qMi42n2yz<)f3g$}d9ZS{+Kng@4=HXZ#~!4$&re-<=uHA5_)hoGxTP)~?$P3>
zDaC}Qd02zWe4B~Z{r`{R=hvMz0ndES0`_ZNouNkQ(W>O-xtn%I(X4W*>q<uJvx6xS
zliIJFizV)!WcqGt;0y@7!p|c}X5PTJ7ks4Pdz{ngNm;$_0hPSZ7qs|^?v;%7l-^p}
zzZeN0R8rVu4xWdmQ^>s!$PWkAuynI*PYM>yD%Q;Tz<X=WHL>9hl2YpUXcl&dDYA&T
zc(K9yGaOmat35t!Kk9uba0O{G$xBJu$_VaBacrZdUbQDiw7Kzr3VMqi#(B<Nd_U~}
z9sWw)ApZj^t61K6d`$3#Y@RX)@LKNXg?+)gMH7Hx)_W!L$Yt&R>yw1Y%H)W^Q}GOG
z*SxfETHzFEq$mYJL5`0?(M;3#9yBwT9R#w!F-YxO7?rAjNM@!L=yQE~>#?*{`<DU}
zx$vwnlOmwKR>}n>atxR`O;UTc5m(G@ynZVD?PFl_bgUZmpVy{t>i*|t@=9)UO&^@%
znu;X4tEhUM#dGe)9#k#x5q1z_A=6rSK=6o}AGGAOl;E`1*u4A3I3QR05K$S*Tk?Y4
zKbvJ!;5~5x{rr2Fc2w$b3I6$HycGx)+(GG`V!Cz`CNb6La$F~k1CGA%C|&zlv8iKC
zdX<0FZ};y<(nh~QBxj}OLK_^S1EcS4R2jn!Y#$D&P2?i7|McJQ%cMP6F1#$Do>0cc
zbZw)cq>E&hW)sjRA2dcR?l?cN?c%x=advtg&&OZya4qlPFEHJLY)_1N2}_Sw`b2jC
zRZF_VBcElH>Bi0n0=vpf)@kcgLH8SM5Kj0TdfA#UgCgc>0H<vA*mhhl99}Qjx%`SE
z35&7f-P~DuB%s)889%>1h23p?olTicHemCWxwMq+Ve@hLVa`&v#R<eAAVUv7-~Lny
zI2)JED*p0ASWB}<Rh9WO{}o?W>f)E=*S@r4B*=Jag_yf|^VBK_Ri;Y%OYH<<oD4y5
z-9e<dGqfrmsXB1#EHs5)icz(E$)oy+t@jrdr?haj=-u*Dv|tnpcC==PXO>u@W8jy?
z48_JS8K!E~R^$Y*ysE2|;`&ZCMv_$=M3EoG_vsf)2=X+JFlsf#jBYTeL8AE7p4PuZ
z*`Tg4m}#&&n%9u$T}s3v`>48sAuZ*=e9WOTH}GE!VpPn>@y-#Z#&ej^iUj-eYkbTG
zfEuSsL-rp(`=!f6)DRjBMXXq_X}S8i2vH#79E68wx)DPgzeo$wA_CWH6sLi|m?Qel
zjb?yTr3mj*Ub@r297jqLtljrP;eTnVNbhQCiNe&us1QeotazNS-Q<OmhHr*%end)+
zfD7|ehpKI5Q-8umnj<d~jEO;v`S-Q7eS=PExs@Wxp_5&=liWUhF=C_!Ck`$0`)wTN
zVWia?-K|{odKBILMeq%wm;NjyJ*l6uNFwgA8_j&hD?huzH;>roG8S2>iJSUCLi`h(
z-gLI9DsXMl|9<JM+JkjLYE+5i6TEK_N-@Gw!c8rs94$kp(Nky5OwxIUCrs`S90vun
z%L2lpL?S6hK%A@TeD7J|W-*9!{(JOmnMW~AvJz?xrp&b%XD3{sgHbRoX38ogRybrZ
zwm*P}lmfY?q+Ic~<HN5dy>HhZrn5So&bBlxq4#$U+#&7tO!Mz|q&EVhUEhfSAa+6M
z<^R_%&^yZIJ!}39L3xW7f6VOC9;dC~wpHt_>%01}%B1PHDCFr1*1be%ikSSOmP2hE
z^B!0mxSBYw<Zm~5MQ5$a%8*su{^N*s?%$)2Rl`W#<qPHIZ#V}j3NjAK$%lfJQxx;m
zlN;u<A9cr}utNl+;`F-Ip&;$F<=)t*YKWvmgqwR<uzgarNARCzdBhZTJd;;QArzg)
z-KypxQoG?x!eL}0DvcIxGgl&7OJC?Gt*OSxY?>*LX{aF8z*j@sO}i~YQFLLtnhuQL
z66sj86Dq0pK>OpoIT{ZvtHOQ2`hZHU{IK(z2cP?U3J3`qW5qQJW~44=60RV%VLhFA
z09u@2z(#YA(&gyC++<VO-(Y-*OuXjftFv+71B-CYJ*h3IFZ%#*zGyQb=)mKwQLvz6
z0iSNQd4r+%6zCr!<sGEB4(<PVBo`en5WEJ2=@da*-N2DSR7;MaptNUVX@oMB;TKBw
zmoy81WjKMs=vaG$cXGqgY5l%vjn2hY7tN8J;Veh*12xZlzOWnKUs@>nwb6$z9v+3Y
z-+ulyBx&c>pV)Ux?Z%ccH99^!tq;EQ3tW6<sYJQtMGm=548ZgykA<l(_4?xkC-F*8
zC9Z>+tNZNDtLYA~{`qQIsGwDc(Beb&xaHSfPU-sy#STgZBW)J1M0S5BFq+NQRgK)X
zVywpTDcrA^+P5p3Tir-yX@JN~ozwH6+jloJb}wNsXIfv}+o*IXk|(gL%m&>6ZS2yc
zlx@*!CK2%x@S6GH%|^5EEh|_A5s_gpu?E=YC~V{-hjpyy;c;aBERoG!L#J0YIAkkG
z;(d|FUv>CR6#QmE<Z)m^LU&H9R8GkWU2WzatY|7);-EHvN>Kh45UJ}govYcZCj!0h
zcIE4r=k;?J=4(rEd}@14t~)l7TA>$VI}NQ)RD&Nov}Gpc(PbRqj_@NB51)AK|D8)M
zRijcw(QKt8DE!z_R><AWi6!D}Rm^f6lED8s4(Fj^kV*jHuYElQwDdQ*<!|Zb@LQjw
z?j6%zO>-ON4_u$<(6O`4=Ma3n+2thTdiX2`C3V@6w5;{(jd|phUJ^8@dVIPw*y=C+
z{6lp#&EB!2T&yRF^cBa(H;#?uoQBbbKaa!|)IElaaQ6Ul_tc8b4&C*|e8QC+-C-N6
zJFcgJm3YoPEA5I#7Mh~T$lvf#C#lm4qyD`Yo{dSJ2(6EY$V#%;iw#51`yzUnV(sZE
zt~bup5!r_rU})+BdM}?tZ2EW=6KdMrSckcwuf=`~T1U*V#LzPNmf@l;_Q{kJcF35g
zfZmG-!}L@v8w0!bJlOQL*oORUxEk=Un$a#mqjit`g<j+IFAD`3hE0;zGfH@~O>Ue&
z8?2N^a1*$E6Od?;mq(iaH#)+G-pPh;T1N1Bh2K2z8GeWzLHKQpk<<O-{h<r#h(vg%
z-~p`dbmEfr1u~ZOd<v7c-n3vZu%|d>se&LBFyT%}e+y81Y6=@0op+yqVE8YPGX5Y?
z7SjSK_r1c1fiyH{E{Mi%wTt<W7c|IZR+g_zVJU7OUQ}`zIM&PMPnrBE4bG(&e#tlb
z1@#L-4?T@y9CZ+T4i573OG)fo3c|>Lp{<K`9;=)n&qO&!*ve^-cb*WhQOv%l7||_f
zpit@BwDAS4T|G~Z%3JX34YK70tNDM44=1eSl6vVF3zQ?mt0w-kznezG0SqfSm^hXw
zpsHA3`9BNz+?!|a&gVQwR%M9xk$1y&t=7qetz8BB{;kk8`xGXUk{dXrGxohYW0_((
z+`2?xGdN@O_`0lB%CRXB8eyVe;FhJp*Y5eBti`~*s~By6Ho?NdaOiT}c4$Gk`fcMU
z1^e3qbOwzH?!rFtNB(Mv(9fa)jSi8>cxiK(Vx>GRF%mqU1wl`|^M7pCZn!JaC^$@f
z(qAH#(dvGt&YfG1TFj7B9_R>NrI|r7kaPePuwzv?*_>QF!~q{u=Ej=RU(6WG%DF{0
z<<G7OFM)xiW4h?2jY<%MAcoQ|wfUmy{Zqwh$|0w}v?6FkD}@w(lvDgzOTDqGQX_l|
zYZ9WGuz*CIkz1G_PhNv^PVB{1xnszrAr4AASCAY~eW}cpBNmD;oE3zX9D|$G1cpNe
zJ#)xY<IyfpC1QR*Q<je)YGGU(SoI!ApwOIv>;otD;z5f9)pABE{QH=yZ>9RT21$x2
z4f=w}j*eJ?xblh|-%s?(Djni_nSgxrj-UFgJfe=E8vx0f%pRGA$>CJQeIAeDRWg_4
zo733OEv|J}=-F<(plqR>Zqt3k4>TyB#`(~Mj|FCa3kld~Svprw!srzTRrxT~WK&oF
z^_A&~b*JT6gelu^|DMIh>0}HF0;3RA<e(sw;6+mh%bglzG+=O4s|+LgjH41eNj<r!
zskNK!2ZUF!KxUYpy4;e_D2lL(uAYDJV?%1>jaq<sbI8VAU8(<}Mh@f`+h4Quiqt!6
zNc1{4p64pkws%ez<_DeM<%^b-{@jQgEjTB`!uus^+H%rV8K0Emuke~#bZB+-hWe8?
zxCS6@B({(n-*Y?ZP_zWZehv7i#8(5{18(|Kb<o({h^F-Kj}O!Vu6dshsd=h%G$|1*
zw|{fCQP%#?5%oICRF)U5{_DzWezLTMe=7eyb)N^^#22efHQ&|4B8lN~_t##oo9UOR
z_%vziitsUlp41ADw7^TS%{nGps-*2o=6UPCL&9&RUSRXa|BfwP9czq@jZu(_Llk|C
zT}4hrmoN-PP?Ealb-9?gsB_f#3%znbUrx3pWJ@glrS0q<K~N-CLn1Z08l;OC3~9GZ
ziw1nj6*_Wthn4IB@YnjUtU6ndE+pOdNY!F@Lb~=J^`J}PFP2x?9<Qirpx&aFrf&jO
z3^<H#alAiO?94L3HT^KFVKmhcg^u>9t)|z1334hcRDX7ny3Fuv{n(D(`#geYl4!%I
zWx2El8=*|E#zzBVrfv=4EQOd<B;3Zf9drEa*gdA9Ygp4)0pIgLR#sNV9EE3;){m}H
z8Y-y_5A#EhH$m}j5Irzp!zmu{sAVSr?jqkquWtP#D&PisHi+4q>e`cHHiEaDV<G=x
zTSmFMr##nJ^bop6g!TNsc=*v_=TVejlMW(3fD``ex{KT6{eX8m4l<JZ^{oEmV78FH
zbi_)+Ljdr>K5Ox4Vquv3<nH>YYD+;~`m!9I{#aI4xVZD#RERuwT)Ay->yf{wMrkUk
z{hnQ+!T2*QlGt*D%1;-$;*V#q1md){P?`1E4^s^WcstEw%dmDyK~vbhtjgIbR_f>}
zm2iGhaQKNZ3VwRpL#7Ou0g;{UlD#ta-IN`aLFd^6=Q*_7yZ(}W)TsR0w35a1ujbRx
zyMut4psW~<;n{f$c1~@>2bHk>^y0DE-O8#tTKWc@VAAf&-Y%6yrMcc3+<}J2Kdf(?
z6qEB{qAC^<R_`#HD30_A9uTRq=1l^eom+dGRO$VoBzT;eB0Dy--;cUHCJ(KDY9jrq
z<&$$%x)n>stl7bJQ#{QgeDYeb_4d2x&d~l{*hJadw+n2lz3`i!N4|`=m)C1IB%GbT
z9=j|IAeIw>n{YyTJ{rR9`6RC4%|rj6^ivaauKMZ4dHjcUhU6LZi8~aNG6b*53b~8V
zy*)wA22W~E2o0`Sk<f4fh)cYS3ctRaCF(;_5L8U~JNx7G(CgSBCq`pr`Eay_XK>{~
zqV<>>V+}d|3wWyOT%L3-d3D{t%yla0`1LXBJ1mdhd|Y}O;y@%3SHQC~W_UIs8wd4z
zP{3}caK+NV4t0(HM_WYj@ipkP#GrWIv9QcS8D7n<1Gh-RA#x4cZq@p)ESEtRQU8`p
z4?kuVd($8hYYv2Uig~8!k6yb}_xfWZ`FE(Jo4jOq888}2&q%9=fDkh~b-iX)z82D!
zQspb)ul=7Q>S4_HISmh4->`!<3flMCSDcd2KCi;>RCMaIuq5&B2A`1X)L@c@L=i|;
zRKrsFjry^~#{M%o#4;Sc#)U@PI->*AX7R`HGeuv&rOr}cQHf__{r!%1T7ABsqT?wK
z#Iw+erFGj(fyd~R$+mz|Q|}WBn-`3Ww^p2I6nx}uv{P>@;1Mywqd)lQ_1<7v9o>6~
z6nFN@`L8re1UkB8SPGL?uG!h#%}j{EbyCoga?+Z8&X6$z8a-W*B7JwFa()nnTK}F`
z2B!RZvsCe>5w&Vj!Tp1JT6Wm@;8*5LL8Bht0IF9*@xh_40;k;{rGmd~h3Mre%%2ud
z%tz8PK%z65{rA6yhT$XJiAJju6W(Lg^rPOQK~lC?1lOT38XVP`om1E;s60(dW|mLu
zpMvck&g#~YgfO~=8-J>z$&>vR@G)m3J1Dj-sTX6a_e#3Yru4$-gB0nce(n@+9afvo
zO^4H*7^K=YHh1b+Ew<}kjZd0^F2C}S|KxVNT!nuKYu>iYu2zf=d^{-PnP3rO)RqC?
zK|2*ng<D$5{q0@0?&p{n+5r*J0QR18LZ|w<`88H9t13r%-IqVHuvRL8DuHpX;f|@@
z_23%S6T$fl6wu%&{!dk~IB&e|6Qx1+wmfxnO!C<(pE{!KhIuTM=XR(C7j9(xwdwxu
z1sg17Io|19s~lhvjp4;9NVr{Akc24F=<3%5tJ|Q^j5@b+eOC9dLvipKWtKzj#z%Fg
z*%PrYYZrXxMQH$Mc|MhmHjNORH$>g6Xq^w3L+{A}TG3Q}U*fn9#Tb9m@f*>5GQn|y
zR~H<@k^)wD_8rAf+Y;9SHbY0`<tu3y<Z0v}I9BqAB)_SQRDu<iKR^8ro?(N00vyw*
zMA6JN&%mw!#dCAKm3R4XSGdEKE5LG@&&mmFGJ4xV2aiTRVE3tHv3EcQClpPL0vQ*I
z^v!M5U(t)Vz#c?8&rM^sYi1_rqR~H@#Ic4x;$e><(LfI(n-|GC^{cRnF{=9|&mVG@
z@!tq<?oml=xMJnYUBvy)V)&}cID!*w(ptx+B1_6qYC!VVI5h>w<5wjCV4!VL9Z~4M
z`9;4UMT}{2{O^NkgM7+ix-LVeO^#QW-8r3e<!c`KBEe&44?W;ch%Q#FG$$~q(|SPS
z9b*h>F8VLOws8E??A?(otyn{^-6OVf^C_}gkhH<kYvCC5fG06npY;-qU0OscHrYOZ
z&s1Xh`Bc#6_mRVIYi9_^{Y^<;>wY7tlSY6H5f~hq@E#mei9VT!bhS3y<4Q0Z-(eZ`
ziUr-P+&6o({YuFRbQnl4TUu{E#1*jQ*L1{ftHVbSoyNOZLt}|bNU}JVl%>*4hm~p}
zb#AHh$;m1t>8D$^!P6Nkcc?L4@N5oW!JMAIp;UOhZ#>JLLSnUH;6-lrfDiXl;><uT
zAFjhL>A#}m_HLBD*D}si=&4P)d(Q+{vml<NgU-9lKRz)OubMPND0-wGl`NAFTom<@
z<O0!cN6O%8dL!1ih5o<r6PYCkD7x2oz~sxpez(msCKAUop6L&vMM2$#-&FLI=L?yJ
zjW{eQ1vu}9)v7xI5}=v6D-N&a<gd7Lg;c%K_%psslF>XK#q~d|DcPK=wDfM!7ZDo*
zt;?x&E>12N?0eY6M6Vfar?<ZDdu75($02e3GNCkDZo4nAA8>n?W^4?DtQvZTFUZCr
zYN%B&Y^SquS2Ew~7zkWVefhX~ESvDmJi0B3+RRa7|31N~GLXhy30tY$*me@^V)$Gc
zT7BY#E@DKiny0%JOehiiyYDpgb3CX=?i}`8`^hAcEHv{Dm=zq~KXJ7?OMnJxH?&7^
zKA4l!<uk%vdlsctQtU1Kjz|}-x!Yl4WAC!JhbnLnStv$ir1+OJEFuKUiLcEvVl8Y-
zPTAe&mhoAF)`tgX5>Hv#_P@7zwr%cxAb1U#7F64sI1TT_O@2n!-%E|uSu9O8$M-?@
zO3bh5Whn2fgDxi5ImD9}B205V>NJcO+486nuaq`}wO1I|CF4a`XjneNFn1%>D*c6&
zTwV$kqGal-COF_L*d4v9=S&g@05VI`1#7~STWPulvdFc5N^Ce%O<k+cjl%N>@+UjC
z_>5R26Ox>P=bp;9*i8fq8lj)raf)BsKhV7Ee<3*kaQ_7{yPakkf14hi^j{{pqVAEs
zj8AP<TBlJa=||`^y>u9DLz#9Woh*9}=3@OHf6F7peC%_n*e8QZ7~N6wF3&ypCyN#>
ztgCRHK&<BCs(njpHPo6_XQTO0)zjdC5|jl3f^4HXIvJ)%sz|l4K+u;#3}6xOi2jS(
zG^eU2DSBF~3TOCrDF&;UcRWKa?)3&al*1FQ(Wdt90p!Q{%NA+g@Qbibah!2k?1zZf
zD^4H{&lD=BuuLVKgrqR49Ww)RSemzw*5`Or*%TvSjBYR+a+)<_KTwKr(=xXLi(Ysj
zGSF39uC?d41G;2*iEIwAK=WZ1a5*n$tdy!r3d2Xi9|hJ&o#xsWmda0^Ctifq4Rm}K
zeLf>a*#H^R&mSpqN=-f_@vOED7%mra!KmlzQqLa+P9Qw>x!=878c>i9(hMb&meewW
z{R{PU;!}GE#1XG^TCycrTQgD62(aQ^wR#|S>Ydk=H4OQci8laO<MHIY>_g^DdYrNt
z){kUE(R(-&b2utbHeUr@zBeZI<LJLPTe)q|r<bOf(q<b!NVIJ^uWdo(pzk85EB@DV
zlAnyTV#tRX^x3r{SFE6Flb0LmAy%H&Fn@e49o3PiI~;n4^1UdSH0By?sJdB9cuj#^
z%4`5hADX;~A=`n~Y66{?YA`0n-&;Le2=&!B9D+-2s&Z0KVMc#{8vfu5zUhq6A!XI#
zFNp<h!Ws1Q_CLYxLx~zxmbxGoGe?)cqJkY)+9z36%JniEe4t-bsu;!8z@Gg`uAuz0
zJq~OyQQ{`31RCY*@HO4edtm=?DHLiitR!LWd>@;|Ntjw4o{#jBk5|~XZv5RoIONTv
zf-<P>evNH@yb(<I5=vfX*(h7}$M%?gCufuHO7vY%jmmmVKf?Gq(XjR-wdcE<s0$gt
z)x{K7v~POV&JX_`PCBc)u>V3&X%`_Z;Z|2DR5+nX_NG~Cp&z~UbsAx&sWggCY&lBq
zoO7(}uMhj%jAA62e)mGS?Y>c$@~lf`FDr6H#@<0Qq`slLW(1E#vW_J5%8U=mNO4(`
z{yTN?@kPujiG_HJg|cWdudNOswJ?6%(V_mt2JB3u_jSpiOsR<^8cHp`DH1Ymj*ffp
zxm=|%<1~-0^!|9hPH*I1>9@lRt>Jx1T#$fxmBJKeUq5b0cd%vFdO#yqlTA9z4XQrS
z|Fp>6JeR6ThJH_OqWz64Q4NcfPfFG*u}0V$fSh`W1Lna8_|{6l3@MV`qMyE;13g|a
zE~ZTdU%OOUw|Hw+z&}VBt?Z}TdB>U;y;>2sKv}Noc%Nppp@~;h7f?P<c>Y_SD`+mf
z!Qukwl>#%#3!<7ll)tqKem5+$`LS&ol^s&+GaXdoI@#t>mRo?!RHvRn7!X=7pxSHl
zLx{d%V8Ec@MZ6E`xjZ*H4iPBx0hnnGSRU><=D2R`)(8I6n1M?uhI`R-`}cpjIkSlL
zp!Ta>6NV*f0Z!quC*TKQ7ih|HlMH|FMAUndECH^3^hWd#{)P)FwWsn8)U^G$!Q&#q
z*#YHq;aLhNrd)10;Ny3BCHjIclbLQd0vJ-C`?Pha;%bxKqO>i4>}}+VZhzA&(4G9}
z(PC81IRxp%tB89?JU!GF4L)bL=;1h8_G}eCs+D{pD0p+JlXz7&t7Ff3w-OOa{i{2+
z;?dBH*GZ4_3M>2Mh<{;eNewN4y*so2V0nZ1;j(^Qr*Y>9T1#ZlN<9AyoMM#}hP-BW
z=JV2M+e?2wwzt6FWs}pJaB3kv^eIX5@=~@?H}VR<siPWt6Lp!M5U6nZ&xAz()X?4N
zVttj({ci5hWdO_KGhb097}g%#AYR>Rf|h7(U0TEk)EgjaojgW)|6S^<!D|o@w^#$=
zc&}e9iy=O$Mg#oA`c94!4V3H*wb0fsUEqRCgDhCADVF1iK|`&kb9fb~-+_Up7}HW7
zX_?}meA~%vSKBvwp~fX%zQd-rD<<H;9;UjkT5ELl;K5sh0>5DIk@g$BDClY!6?aJX
ztXYXa*y=vDCG)^i=*R-eo%8<IPK=rdn*IB4)U@yTA9)}ot8KcKx9jEV@1It^`ecm%
zBVugNJ@JZ5{`>Zy3Wn0!n%S3)XXE!Xo<BJL%S>bZ^l~~}TBQ4i`Z5mibu#7p&)RfN
z70lhN(>)C?_<-}QeqLh-wvD%-XT5Sni~{PUPh6|5Zl~tJq)+>JHb071btZ&V026Jh
zts1!HEov*h?($@sg+5Fz-tOf4Xqa@__Q-R_i=QSbDx=W+RYG+)(u4T7NB)qlF7i5g
zY<xU1=sxCFez(Deue~N^xvha~#;WwlH++0LJogH;xoa5sg2wd=#8EI-Y^`0eEn3^S
zFElUKiT*c8K}t~KnkySE-|W$N-W}?UFYaPqUS6oyo}Z+GI0wOhjvT*6CIggPe_})!
zibd^c_xjVvTY4|vtC`R-Q!FqF8ApjEi$f6Dv%VR(JSszNx=dO0YD7t`koZhS=Yj{?
zBvEZv^_c^=4M~TtRJdy41;^>b)}rVGp=+xV?H97b1nk)k*NlkCdyvzZ3x!AWKX=T+
z40UHZ>h7~g6v!|k*EnGCSqGt;^(05gAfqp=$kl4@>(KG5wKneHdou#;(B{T;#KqlG
zhUTtLFW&pI*j64?8&{t-W{ft3SiNZ&+g2)|e5Ec0OIa$#xupZrz)ofDiQid%iXF3`
z5J7tk^p^}Bm9TA~+`MjuGj5rRJF_s`kekB<?XY2pRl`j3RIGrQc_^C+-u_dX(Ks8M
zskQ^J83bT-u`g5Gk%b))gy%|Lf^7eSh)U~_izht0H)70w`X|eGKHSxBG~?8B+0>lk
z5f5)A>e7iX?gUDAZfpdN7B*Be2aZy`lAUYSud4necWKs?Av?vxJ`?zI{*^VT?x(v9
zIA5+KLR<&Aw(xlT3W-H)FzYgYToqm0;CU}C`96lut`%Z*dblO83IAhClGQP9Z_)UO
zAl@k5KY|Nx-jB1tU^sccgK|D<MNh%4`r9s-v$J-a^`km{_U5s`t#-_V>yM4zS1u;*
z-eofBYYw)dUiP;l`uBFT<BK60bZ3rz0mJf7e5pt*%r=-JLb|J-T+-mxsuA6tHIlJ;
zxTUa{4P{O)TbfUdF2CPH9wh@U8a5w3!HbS+nAkds%zNV4e9`1*p-_1nq@U5MRF2pd
zYmu1YI2a&o_sZIi)-_cU=)6y59w=Riu_JwBeg#+-$U6PTGKf+05ZZ-5Tlj!#_yc$X
z#iivL5JH<qNhsA^><mHSFJN7FcYF+3>QBPY$}uEo!W~6<=V(72XaDIG5|;w_3PP5s
z7HZPqG{z5W?^g>u(msCo)nodamBA?55Fft{gC>xuKav(#whF#19P(q2aEy@p#7;=G
z_TNktgy0zpUr!XIZ)bJ<9U&j$S%iDk?Nn(`>(exi6s$T1PtSVX31Rdg8qllW4;#X)
z=E=vMA!y!R%3{FiRLTD!BuFDY&pp1g++BI6*({O+jbMxW2*7dTb&?7EpVv35{C744
zc)GGfTeF3-%Kbu^Ja~jV_(QZsjAl>IJk`rdv~sVQUd5N^Y{s8|dZ#E^JmFzh*2u=}
z%l8_|y9j5(GfF4<^I-BHO}v-5;2mP%U65augbPFZ-7|&9oPfy0?3ny4y*Wl@p9<Ro
z<CV0eMJ^)7|2#o7MQByhpN3i~kShM)J3Fz(PT~w9T}V(q^GJNJtBIZW3g5Yuw!l4d
z&w9vTK@q-!W2(1x1NuFz$A9MB@4#m<Xe6*IzB6uHyNfn2*{Oc4IZRZk+TJ`c`unE)
zF~`8-ibPGt(%Od3;x_1mHqLSh?|d3f>=!<x8GZgg4c6s7Ik1iyWg^Z|Zgx;96fqRk
zQdYOb+Zn-b9*Z?u&a4FsQRkmps#9RbGX8+pTs&MRdsi~nb-ydT*%fcor#yA3efmO{
z%TfV&%nHvGprA()+((%0<b#n6TE8-?;agNB)gIM{meB^YXQ33+6iEkBlH&npy>+}2
zOiO}q&GUJIY(M(#xR!na+ockra2xIrL6qvOd7y2?`_<Dd+KgnE-IzD!rCkUJZ%9yO
zQ4H}E|C+g;2=nUr7OP`IQFr&cXIwk95p>M{0PB(<dWm+fAZ8Ni5Wmo@bJDy2$PY*~
zwFwULZ;<-ZNU4LRyPeDZJ5h#@cC`I`Pv-(>u8rmm+r6GMP;ZQM#v7aDEbg_8-i93=
z%7^1~mc@F-`me@PC04~Bq5;Iz0_QYEtsB{g!*pPXIaXa0S{d)u{kyo=)C))g7QKU`
z-o5*$-aA_YH->tWGQzCpAT{^55zm--cddw0iMWL0$V>#SzkZzikNwkD9{ae*-J3>t
zm6cVKZ_*K>2Qe1$Y%@D#T5bV@!0DWr&|7tKJJx;Dr3?ugURcA7`Ehq7@JM9g|GlNk
zE;Zen<rq)^&VPI9bnNKqVl=&3Nle(WDChw=0Gqrsm#u&7UxHQ|5u7XEn%gDL9R;i`
zwnf+2I#uyNw_!b$wj*VkWId#vVbSO^;JL28XHxIww9y}${?p6lGnrsIS$c03^H*C*
zUIEX?vC)@V%(Mgga?ek@G-bf9XzaK9hBz{Af^{t-mW3Td1-8cW@;0pM55<KIatQYg
zKQNfG_io%?YOk^yK+}FAnF;>Ii@nk&yDSbVf4)v~YUupx0;n9SAmwK;!d&A(N}y!J
zs+5`m+0C`2Tp~kOkqI5zIodg-j?@@$SMOe2u%5}8*PRWTu~D@#6drp`n+#G|c8|(6
z*+va!_GFsZ)Z{Oa3#j;+*CG=QMWYRAX~y}%jF8!k-B=KEB;{Qej9lo)qBZ^{5@(a9
zEDByly3`Rx3gRdcDtYEIq*h~6HFXoWk#3a_<B>saeM3-SP%geLJ}V2mnb8fbB;8+=
zjZ5Xb`_VBt;Y-GusFiFX`m2{G2R4nSlGw(G{TpjNaH}6!_zT-|put1b#lN`3(+OV#
z`QEs?4;&0X%?QX5PWYKEy277jj6{f}BM;>v@$P!xs$}nB0VRmpR6GAlb@5O+NlwH`
z1#U~Pmjr+g#z-cy+<G@h;0v&r6#Hv{aGU&JOcSyhSAP6rIS3beA_+rMzX92K2{&q<
zch_U@I4a;(*kzTAj{xpe^vu7|ebp1R{Qz<>d7E&Kn3jgcdE)R1UXBsl#$8rWs3YMX
zzN@j3nAzwoG&$X;HDqZLW1k~lOg~aWO9O7Ko)>zAqboV8sNUH)xV^oKct<iov+!^S
zZUHe-j*UoB6JIZmc>=$_ew=SoNQ3RlcmQ?9L;rCjzFsL=?|omasW9rtl7jlD|8eey
z{nan3^~PBN-{N@cn8i<$;_dhc_=~H7_2K!~;VMAJ2V<!vj*(8OaX)%#h=aH>$K3na
z#Sc?zlr}F0IOXSDe4oSwZzvMvu(m3t8cws?=c#0`^QEa5ThFC1&HSTg1IIcsLzD~h
zFPANqnsS;@FD@GWhH8p1NzZg?$(+@?wF?W22D!y(gYlKTrpk99xw5JM2A}cIBX7oI
z4n?A~B8bwr9_GR}2m}GDQWfxS+f)?5TWf1%@vB}qG3$`rkD%aPz!#R@r!>eqNj%-)
zaesXB*lXgSn9<ciJ_SXUn0FcI#KU7_tB^y)NGLuJct2@T#wD>FxL_{pkf+&F0f{rL
z^KJ}KIYWx?uiu056=S=<0I|)qRb)CB3Oz^w7bDO>`%B;`R7NO5OmhQ+I*vmrUf!&e
zo*|X|X|SId-Wr#?CM58){|G0YN{@``MGwFoqltGXP25BO68VKM-LoGf%%F;os^6E$
z3)^<P#HXg!pKi2S6}ag9E9VSShaH!kkF5^TJW-xJ+x`DxL<i8wRkM=+i1$w=LeQ#6
z(`&q>5*!JN1lohje@1@-{3}4V`j^KN?M-K%c9x77+)l3`VPQW^Z-4s`74y}6O%}xG
z|3fe}b1Vm4t_vUA#}u;(SlmBXoTec;v;N)4d{H_s&%0<RxM~jbN)G1tX6YsS@mLT9
z?mD1PRAQGMo89)NFlep0uK`Q!Ah!g_2q8(&0uw$~i|V`xJrYRK0CPV^?ZYR)FV#uC
z!XR)qwoNGr_+cI6e^yCb+d%f@gE82Pm)a9|sqTOp1rz^d5?))lvfkVS{=!Eu8^4@d
zZOGS8+y(-&7U=Ko{hkzP1ON)8XZf`ts7sXOr!U;$MOX$SIQYToR0<N(_2?>uzCiDi
zlxgbS|G>`R+(0%iOQdoLiD3`(@Eh=UYZ{Sq2}|dC@N+sbl;#mMcd>$JKdX*r@%;KI
zQr)l6u^l@e|9e(Bw6Th+@n^u7A4*?$(f`xDo+dUq>udkXPq-KnaI~HX@XyAniMfN%
zaRoZ|9A2QS6D4a|S|FA$7{lu1`S&KmsVGy?Q5ge*H*8B)3~1?(V|ORCN@eUSKDPgD
zGLg(;1OqIoyNlhKtHX&hlG$Gyv|9ds&}!30cgt<!RvwSIA=6S$fVcW{rE8L!Tw=-D
zfzGR!{y|!tp<&+CA`x3TTuH{|Db0dG4=bBGJ^LEI3)DRvQr4%Xu&hjaSJ$gp{aw3E
z4h#$4h3Pe}7?iAR8=EHsTcT5kK+*l8b2)AR2P}|!Fwjvv>ogMEyDjeJXeEON=kr0m
zObw%X){lqrSF!!i^L(*(oD0s=IM?nq57T`S+#5UY^*y0F>r4|Sby|s=!ba{ZSM5S|
zOcgiWAZh)0QDRNH@DNVacw1nIdmJ;E3dahPGtDQ_K4$%}8@{u7_SEC%c+}c{qtocg
zUNTEViGbG)t7j;F-B4Ph(C@|&zA6*itFTAJEBT!^IYc7JySe!6pwAoT(5}1PN^opA
zE)za3p)hi!(aiUA@*a~+cM|z&CW{87FnM~PcEgC^RenNP8b%=aejFRLvbNNdJ{~wD
z5ge%XybgTPE3nIyD)Q+ya0@SRz!DVy5FETft);l#7zc$yToa0=VhF4GTO)oqvk(9d
zGO@%WA*t~2iT=I;LhWEGCAmU_^Cl@5uG#?cm7$Yy%V+qufpfS=A4)&PRuE*C@A$PJ
zZ`cqdN_(GGI?#Cq;k*a&$PfEt0vWHbxGB1pHUL@Wd1|%5jSS2-`}938*rH&V3`h}K
zs@=-nW5H&|<K6>|z$sV|4v`TZd$-}fc9`8d`w|!i<E3@}$6;R2<tO7>f3sdZN>=(%
z3m9$S!7zd%N%LrE<WL*Z=E5d-a{#b~$9#;1rysolQl1;a!cQGNlyf^ErK93f*jL9p
z8gJe@90rFj!ad6+zE4Wk2027nmpx+O6tjWZ9xhZr<KZ-lQr*{>RxCM2h0d=*I^`Vv
zrov0P@ik5iIL-h^#pl3#`s8hYiq~5j9Pos2b}T?kCHkHzU}2v$hk1#Qy(2=7mD!NQ
zP=8(@pBi~ROIBSQ|0l>XU9D0!!4bvMN~wmfPU-q4(2!q>=vmQF_c|}f#;|wm#^IQc
zM4<uT&8)24r2_;G5S;<*%SQDl-K#+F9}aaHV{%R!5mw_;HJWH;*hbFySSO;&At4|m
zV`1}L{)Ggc1@dgin(#3Rc$#dgZkN*{8qHu`U3a@Zf|)<$*>-fmV`yvS`S6;s02C{-
zz$`la4`7~C-I{<NPT`kDE-e{FSK>6$W5VgMS%+9$lz19OF;(Bun*2ut!+K-ji4JZ7
zkMdQa&{$zuOm&>iiw&(ed_L@1#S#gQyLq7A=B<YP$MJO1d@BSeNsO2~?XES;=M`-b
zR6-X-Z=aQ3@N4j;3(>HP{Ob9dy5EK@E(Tx;f@=nurXVeBP^*makM-|H5){9du;7BP
zSQYaREAQyT13D4-+~Y(Sd?n^5X7EHeTizX(iS)+VI5*vo7iOKiLeFa@p3)(gHWmFm
zWqBo`sX}5MF|)csx}tELw6bPbDe{h<mlXb!18QlJq>+C%;Vld_hSbbI6vJndMx*5C
znrL8~T3pOkTv)zctbX?eBF0g-F|0nBo4E_7I_(*Ev-7*x?&#`zd(r>x8g%ulf`reA
z9sUBx^0Mt120hs~@QUM$DBSgpOuBOe<M)K)Q~&X3)h^YM%$MB*E>VdS*OZ7Whs5hs
zWqO(@sdW_eMw;M11=%c;X{%cu|98EepM9;F3yNnOt#4H_)^{_5rJ4q*RYI6FO@<P^
zria~jDg4^rlHx*x0c{8n!YHRfED@^mf>(uUY6B4ext|wx<Un6aY*7b(La0m2+Qqj?
zJN+~H4h)X>)nfV=Sb-R@!h-@zKoN9T&4IxW7#_`Y7pQ4_qB$$jcX{po8Uo(Q%wmyX
z?FYIw^~g01I8}G(A2C*-vjJonNWlS*$JhQ5Y&skY^)Ir}9SyjLRK#}L-$XD+0l{V3
z?43^q+{!pAMlqX-doBvoGoum1e$+hr9p6{M4W_z(Kp6F_J_R%@a6mYs&-q2=bD&*3
z)ITm0PHMn@gCB6>a71~I$PfMKr<oHnoFLBzjG-v^%qMoLMZY*1GU3fQep#5VdoH@M
zpTE@!(^;0|vP_JA_1#~>+!v^TPslkVRH7<Bjnwf5lm&zIwoWa*6715xm<s$ug4YL(
zaU9}3r{_)^FT+a$%&g}~0dN^4%Cm}jO;?s2hPwQy%_Qk8SNnl14P>1j<>yGMfI`Gb
zCnzgZOvPiC`eDBuyJUN2H^ZX<V)y(^B-BHqA+!<LYV&uEWkF800*--7A)5mQWJgh|
z<($3Zx5nR*ibOLQpZSPk8k2xUIpC8E2BQs{_M<-Hq?D@)DykrP&Wv293)$&2Tl`E|
zkZ?Tm-<1EN6wc5oD<c{$zIf0i0e;X=Y(`Klomd+`5Ow&W4?^sqbx=Ao;4w4cFy_<D
z*prDESc00J=F;J;&8<irb!3bIh3VW7+-Oczm5M|g{FCS0CP_lE2-UaWZs;==Iw*-S
zkDH5SSuH`=07`W!E^|0xKqTEa6t%=8_Q5)K2`=;KL>zD8*~r&N2R?c#Lm%FLefjBT
zGGmOE=q(%xk|ok$hW&{itvcq7c-ueT`tL&8uNhz5Hb{SZqs&Wv(l%*ELrv40ZQ3}L
zfyN$@DRJUE&w1zQO^j)1JY&1;fj`o_KQ<p1e?oeZx<tWir@)ZuY{_*uwKj{dva~pA
zPuo|b{>xh^8}BvT)h_<~kd59Z+;;i!&z;sQJEmGKmQU3db(g#Wk8+;Ot_c&XS{Mh?
ze1jcT%md*8Y|nU6EhCl4bA`;=Z@$HuRdZ^@btK$*HU2-2t~xBLzKIGV-QBss64C;a
z(k$H#N=vhJgM@S~-QCg%(nxnocb9aReE0pHhkv*%%d&fCeluszoKqE&h)Z+o*EAoA
zL-KVbO8hJlR`4PNMeW~c;S~=^RL=Imr9G?le%i19zIo3?VQTe3hzM?e0{ubw)3z*<
zJhRX)hIk~V|0xlR$Tqi(yaSu2G9bE9Lj}N?DA|It_*JZzN+%BaQ!>m2UdiC)nZzF`
z7SAKLGLb$GFP+|ViUPmc@GAkz`&Nd!f6mQ0;kxc?39$E8?ea70bW-U!=nYZrexKjG
z&B;N?<r>kojM!{;p$@4jfEvO9z1ZRl^Ph<&;C7feISmcc^k}Y-a$hc(A})|&KTdY^
zsCaxoj&H;`gTmK(R_~^KxDV{`rWNT_)-81cHw@_zAfhO-YF_4^wEM55mBHaD=4(Sc
zi|;tW`qs!#|JS@F)rNkLg3Awp?jhos$=SB>-YcRayNz?n6Ha7%tb3Ahq~Xcr!SBKk
zIoBw*o0ryyfXJ0!P(>wG9nM-FW%Y?e7aFSmuTi9G0FxXiTnF3^UxTIV#C(*kd{bS4
z-c$eLGB-5T*Cz%0mtgXx^9v}f5YYGmP#6m9adO}<0BV)1Z{_DCR)L;3eQ57XzFX(*
zUZrpq(+F8oH6Vvgs0RMOr9$<|Lt7Rwk#tAwh-h8z&(-vj6k74dG$i0SHrzN)=o|<Z
ze3gaM0N#+F&*rR$)3S2_Zp+vfdXM3n0zRszs9xi)y1PBIpACC&VDaqyoOJjatiSrX
zj&jX}(MU}6+ozBT((II{1F=c7UIx<-ZMDZ~E)%Y4^_;Cs#+dEW^bsiT0HFDdS@NvS
zv}6j%q-=w!=vmQ8=~@38QkI0rKwLVAReqKr|G-6*0Afp)7bvj+u?Lk|pWhsMJ%pGf
z&0aIOylOfN-86p;fiTWSuPKtx9qwhIoues>k?A#`D&H#aVVn*R533V7<LivXk5K<t
z5%qEAzC4&gu*NR_6z@>vT?H(~>WDJAMzy;emlsg`OtZz&X=bdcmcz1L7F&lPu7}tC
zJ21@q8oeo-V>H(VW9wjrrSmh=4FXie_n5aqiV8wHUm*vD7ziAjnWWf+-@V#m#IV{5
z(ZI$t6H9N`7ZI3PS*?Iq{hJa4V0XOf(Ckfm$7)RVDEI)c{OimBY0hX@gP5TgD%U<$
zWN^upB-FBsT=}8D>(VL9jd5qX&r0tkE-6W%+910~4W-6Ts+wrZKJ@tkON8c}qT_K^
zz84ZP_dWcA76O|(mRkAM3`r(2Y8H~n+t_--+Nbgf#3N@6#x`Tv4w?hhN@6)80Y}l&
zkD5m8p9Rh-zHD~$T<ynLJYDLlT4!$@0(*=?zvJ^1<$g%;c9UJ#GZ005?uTLa6L+(+
zvn)o~t2+~xenbm$`oVC#`GGaQdQMu`vJf-lf_<|BwTcy8i|NCdSrCWKj2ysUi^7JD
z6n*X!*yyvkcdDcGlS{mjRS4rmWCCeg#&ngdH8NP0=u7IR*tbZ`rWGBH!tWqN4e1>D
z%QCKRsvWZEbW2eWDkuQX7kAb1sbFn$;-L4!!?*YZ-l+cPm$V_h=(3qXOU-xW){nXX
z_%C5PzXL&)noY|ynfM~_-vDc%ct1Uo?olWE!`o#>APo{PuG+}Rq>G1t5_-k#y+|D_
zNg9uYLk-l70)iK)Kzf(<(QfC>yf=&G$s_nRO$Ue+|KO@x$(i;%ZvrI)gdz_L?S~+h
zB*MH7LF0Kd_atSk4Gx1t^_qSiWI%4;BLu}VTjlPeM?cn40Sk*B0C#|MHIU`4h}A1U
zyUl8m?9^BOt&fdSH?k--;yWT<0PUeL4x}q9SP7i9x3(oiU1nHOI#Ba(UCdAhkF1al
zO=iH)ry`=nhz*OM1_4z{OtUKl5W_ZRG%^=%g8++7iJYgj@s#o8YTd<V(Ey(m0GkT#
ze~O88*dG2Tg^$atI#&>H3v?=nmRZ7^0v~tdg?W_uHB=X;h3hUI_*jkcbm-aeMfuWq
z9Hb+Ib={Tk$9k~sI+#^e%mFiov`Zy*XNz-<&G@Cz!6$%lat^5EA|n7xz+QD7q2yc#
zbgP1Pn_J8|+`q|2@Au0V5&+kdrNdjgyQ|3W0Nz<1ob@?jScc&!`vNv|MBcDY7eyoE
z@oU&}yt6maJsog6`KC!)wx^bbZDA;2^;UjC!P^qzB3bxkE5ky}6LT#+;x&{TNX^Xz
z;9RVmj(PXZ-w;)R31Mx_;3&h-Z%$r}<4OI-b46u*HD=is>vE02*ol9d{sYr$180qj
zql!2Me;zLbqXOOPI?<_{&N7bxRy10QtO6hl13<qxIs}dRMQ}L8Qy3XKT>jY<bG$V8
zV;<XGXFOYqM;D~w;WB73X%J{307(O@EUW{-3=>d(trHH%MRMQbSg<Y?pwN?~&Q19V
zNWlV#ql$IsXoL6nu5y3_i`a$B=DRA55;-IGjpJl;WJyvtb`-<|b7fdj$N#|$NM^Gy
zzY4DG8vr&UapvhKCzxXvRLg2S8N$z9n=6YbQE-(QF{Z{$kaX+D#wC|loGKgR!OpV<
z!Wf&p#N7F)!yA(=en!F>P{AxJWF~5M7BL}#o>ksh7Ynmg;5T=0b89ZjUsWWmC%az(
zzn&a&-pS%OHl(=>SRqGBo=t{j1od46<s}C1FSpzxOnm%r8bnUw32zx$QF&HRvbN!J
z&O1jvRhMvDgU5bl|MEIOmb9L`#|ji(yxkek9#8(oUuJ<sD{Lf|fgiNVvfVk5=ntn&
z81VePgJ9KyrDbevT=}5bHL>QSwuj}lU~Bx5$7J@|RMb3h5%3E#b}oCa7=27((ogs+
zDgP&dK+B5?T6V3;9ONPy%`k<dt-o$sb|(*LGUl_AeFIW?rCHD&nZG2vO^jSr#4Z1R
zL}&LyH<5JkmMZ79j}<-Hk86>wgxj2iBZK$b;8?W2YR9|-^+pO}h37dyw2{!LU~haz
ziC6c;U%b$Jp?lYM^D2|M%~Kpq2`7#WG^bJ(a*Np;T6ezoZfgZ8Kc{ppIduK;`&2vT
z7(-}lm`6P<0S(|F#}uT_fE_;v$Fggw;<kF8EsVKteM!~3JOce@OS2H&S8~AOgaQBn
zvY97G^q#a%bMP;5*@r52tGR%orl1iJwRCehSpI%@henh~8E-7n902W%q68jb8cF5Z
zAUxVkfE?kL1js`ICn6iY4f<ySCS6k=O0M30DX}j}z)~ywoFAa<9ezi)zN>Ubx5ZD2
zO%z+cHj=<gamaa+MNy_i8IBwjzvMXH*_G&>9;j(tcE_o`EJ_;<6Z<+<(4_e$xdGsj
zmjnu%`^$vj<LduvQ+*(vS<?kv!#ck{qbyIMzOecZK7BG8)M@Nby8vWNF4ps{m2pdl
z>6F91n_6`nei==pnL!!3#7iF{On-@}M>-i(mnt6zo&EVox;_3p*jblbUhuRz5(7lP
zwR~tfcThDTdqOie^>y=PD!z&S&Ny=~tG06(fD3+chhm#()a9h7+AkHx+kQa<mf_&T
zW4<yj0|-I@DQhprGC-=4+(&H%W&$7>(DEX7S^>lbH431Yk-4k>d5)N-1ovCog^a#Z
z$WvI)xa^e)Z(OJrQx~HegAlC(3_Um5tZ@;T<rEKu%~3<=$d`D5-6WT?SI(CPiO=qr
z8r~H`DmijK6@z-O3~I6rD<KlgdxHT*{}^Tebe!2rN3NW{;F|IzJA#)?C0jySe1V)m
zV2S!U2^fjOj)DU}@ao;K`)8)xPk-UoGXtI$&`A8kf+cp!*g?4_O^xE35`Exi6vIm3
z?xhU{_!!)Ma<2kvI-`$7r2{s$l9Bk82DQzUYrQbGMwi1vS0ESpb~-OKueleY4Aw<O
z-w?L@DRffRx6c^66%X&q&kTx9O6F}$AMc-Su~c9Lzgc$&CkX|16{+2zz!NQNxd_l?
zWZ3cY(W{{*;sS~YTm19@Ne(}81WpbjB0>H~KD6y0sEKS)v-M*h|MeG2J4+XPMn{E-
zq7pF$W*PudYwl*6OOh$2o9lT`OTm3k%KsZBhT{LlIM`&>lBK0D^Od<IkdJ9Gp<zaG
zuE)kUnD4MquuVNfDz5X>1QNjc&o*B3kItF*&pA05&wDcZ>)SPUs*L=HSiJ~s6tNne
zD8Vr}w!$gjX{i;Mx35*a!g2qjSHm+#2?aXAl_zYO$5GE}^gzN(`gAOPe>plM(`iAO
zG2JhtSxBaF;>M8JPZVP|CVc4W9LML8k7w$Q#rJ!E{3CFA%fbO?!Wnt8=O6z%&v!36
z<)PYYrMxJSt9NOR6PIIUudLcDG|<A>Cm1eiEb2!UZ9~?Mp1@aB2aOJC#>#riwPKv=
znX&YSgp;<y;hplpw)M(3bjT7yc_52#gjP}nu-{e=#PIJFDfkM7Dbi*2Y*&1p?qX|Y
z;JG`Mg^da*tDz-#I9Ux!bO3qv5yZei21YOZZ;Rr+FmQqcU>&D-`poZR&(^;viGUV>
zuV!H`Grne0$LZe-D<8FU4Io@2Iz^sxfH@5&gILa_B9akQSM;ukXQ&H(wHw9;%y!H;
z?{?~jqXeB5JWD8>DR2QbXh3?m=@7kr&x>kCt_fJSLn_bt_Z7DyxI0-S=DbuOA@Kyl
zu=>v81ugLhsivj%&Y@<5wP)Fqd{h@RC(DF-T54{R{S+hvsJf?=j({a+pe2`-p>yaO
zEd(3y-l=W^PBbysOp8CosHZ{Or|{pH0g7_-Yd&kt=}7EbdVBzQ0BkYXQaT1LTtb!f
zEa~(Lv;Iy(jsc^>vhf#eZndbPk@r{rwmzEONtE>7nJ~=)vv~mHR&6K;An=8)3!hvd
zS^AX?0&3bDAMcp}vl)vv2=^lCeerGR5>Qv|4^xn!%ca|lKI{YeH}M2TZjM-PDc1M&
zOKP?qwCK^5Em33wNUwluZ!H0PJw+up#<Qe))=pX1bT=+$%r#ga52)X+{?S|8QwD3e
z7E8M^0RKbdfHHo>-G=VE3|jfHO;L5t#^>UcpE_sj`P|5G$Nw#N147gVyyz?+c}OCB
zG6kpm;zc?%^G%eobqMy_(114;@J%zXaN7ukaxWHARy#M|Gnn39Z!8U#O$~jUKm6ei
zr!PQUuo$i_Gu-Sq*T49I@aNQjDXjuE6J?EBg&=C`Pr(OtMD2IKn7iUd(#8?zXgH`0
zKp#*5_X%7BiY?i*PhN8*;6z^l>w^1WNl0(oFobEBQGyCKz8Epf7%d$2*gw}qF+~UN
zx7oD4#Mj|~MDk#<!_#kek*={yYL=r}i+2=uYCf9eD?JekztDPhsTBJcyEB4yQ^>MD
zqbCN4{Qk21L{l>i2*0M?u%Z9J2LU5|r8XGVTa`NN=A7bjj;{bk;@zvJS{7g?VziW>
z#S1hy<3wxXSUwEVQveu={@Arn@~FP%U3GU8Zo27(*=U0!doGj_9*$cClPQ=ob*}Fl
zS4x?kWzb)?o0}su5E6~v2A{H?Vk5B4%6+O|lz>1g2<m>$8hf|)6pe5L$qUG7KI?fp
z*WeT(@_B|Bbpt+sW&Yn+NTxhZEqs&t{h9s|Ix><1CUgcxX4<K@7UA^(kxloIUA?wK
zBa5`krR$UJ);GIA&~Ueps)|6N0LA^hbkLJA;CP<qP$D68Xe#=}fC9-&SC;+Q`R5H&
z_T?{wmadGXdB?(+!AL;W=XcQmJ#xZLbXvB`a5XKHp?CO7e{n4AfD!^$<W7Jo9_B-D
z;Gr|!mxS~*i*A0j>JmD3&H#`BveH|D0QNIG&rCBjQ#&c|rhcaytr7jMLb_byXh_Z|
za2MZ=9)<Mi0=3d3tNGHLVP!_a!}43+qTQoxSx__7KQ`+tN=V43z3?zFH9MIDupWMk
zD`IipT7{bGI6)oq0gN`BeT<^>yZpa#mUfXa2ryiD=(#6p@YO-J8AAQWypP(^0La4u
zADaDAuK6q?y&TRET(F6lrlaO3fGKXR9E~g`<0V6j+f+dK!dh&L#6R6l2C9Z^a&3-p
z4+jKl4h4lz3w$fbHgDcH^}@<Kkj;q@9s-2!Q@Mc=J*CVex;hpdKA}{_aHc;KqXHuR
znz_w0jw=h6$N(x@8NT`vPZc_{hCT5bgbe@3(HGiGs#tud3CV>NdO+EwdN>GS&){1{
zGy~vQ)Ix^;K8K{!t<&PK)krG0V(u^?fAj@R|G_|$de{qqZ$edE3S-|3_y1)AGH1f+
zp_q;g)Ws-zNWy{n7T<ZTPpnyi@{1~zf$A}n$r#{IB&;0@<Iw>Pr8fgRr{6e-P?Mal
zXI!`@!?2euzMXfdxLRJqpKv75LVIxjd-As5!8K;l>J7}mB3}RMJ0Hz1U|y+p70uaD
z5T;>6ZoUZ)F+J%NMWeaUfKw&_>u>W97i93(6e%yS6=(f9#6qqGjPe*L9-2__i6iS0
z*clSDpmM+(w@s$i*$VaMoQRXRdL>Q(%qiBg;JqR1=FWVvFbXm%G$gRxq%J^1a=|`(
z10^>&a*9{LIn{|x<%$6y=wp|1b-4b5_?LfxB;(LCA%gjN<>V5Dp0hKl^eNpEp1K|i
zuF}?J1RJ&yrOg7?q`;3Fe^F4&yTu*T%DEN$vcC`yzWK7bJ%q}=_7G21f(w{UdKY>p
z(g9}=0#MzdTDe}k)3c%mab0c)I3%UsOvL`NaMU*T!e+YV_fWf=3jIcJC&#62#>mi5
zh?&(O#$7fAIg)IV0R(cF;^GcL>>QLh7pVFz{LI8F?2Jr68hn-q+<Sb9%r5T=d?K9Y
z{W-C)p+&KbZw*MOgQ+PJ(L#0IIo!A#CR=Y^wQoM6BTkvg=E*9`aq;_0z`n>Lc$RZ8
zV-SWtEn&*$siaP|8t2pPd=UcrFFP)^gq=I$TD~r``|Ol-vkjT%`T2+3MhuBBr!O(Y
z2)hg2{mE?EtZ_&D)h)H<&6nJ(zrRSMfw5>QS&d`+J1Q<OlGt4<o_&=8ANtsCHR7y?
z_VVNB7R>^V@>XF6%$KYckL>_w-wAI|nDsPB8-oy)EyixMnYYT4uBi8l9JLRhrmGIr
zmmhkp2bMQkL>*B5Ri)U>b8kp<?wg@DRA6w4^QmG(tqj4VO88v4Ax928f<j4wcu-`x
zRHn#i$BoW*gemSPw2Re-<ju2{HD#j5N`d~}<(@LAHx8rCC@+f#qQFHQ^zfv_Vi(AH
zT}Qb+E@_{3-YZ`^_6f@5SOnPisn@^*bDt(){4dk@-xPxpm7W#8LVPUEvRn9VKmmOD
zE$c{o?BFS<yC^eyx>8+_mPhDA8sMIGSJiQrorngiVs$D$Cq(Qy8E-XU_D}Mg+jHBu
zGywaiS)EO92sUeL(&^=;d}vmA9HxZHQd9nN@+N+?O0Z}Xkqun?^5NNR0_Q)|-3h>S
zS8xRHshM!%<&a3PI5|mE7YwICpi%H{5_NS(xZGO?YH9h)MzH6DQ?rFU-AA7BCBOXl
zm5_AkTyoE0)@hpgT`oZj8Sxv8sZV(gRX^k?NJs>>tag{OsGj>q!bW9vliuND56GEG
z3%Pgt<wSZ<2){bxtIDL<XCcT1js|;1!33OVJYPII$(77<Ha%|D|7x<F8-rs+&{Ne2
z)rZxl8Jag=+_pQtjqecd_Rf=Aw=<5buk4RWbEt%SqCR%hc)Qd7qTjFG5i)&*b3+tg
zY5w4DKLB@(?mTyx(TGoln&-joB$t+{X0jxNC?xw@?0>f%S3bYx|GM|u%e|ZM>=66f
z@B34N;3m;yQ1jQ5yKj>p0rBiU@sy<}=rv8S;dSlHh?H$}m+ju4_a}=Kzs|SO>^Ocm
zh4%KXRv9j=>fiaZ+ifTH5s><Z9*W15`NRx8ugX884HLgJkAiH2-CHRi{XW&7sWmF_
zczQ2fZ=6)#k%LqV6BjcMVDA7!WaxrG#-m3cr|1D&J`0!fcoDFVs#JPIPDqBawz#x0
zxq#DOzv$iaPoQc*ueB%1I*T9T;o}vUS!H^BSNwx8evpOWQZ6lMuHaK3S@0h(-^=2d
zvQr<K)2LsIPkPBPp^vP7-nXAucu0s&tv0PBGm7%Z&NUuV93ECfA2J1Pg~!E?YlZ#q
zYSyi&=A5s^Y81J~QU~10FV@ylni}`kmei(-`E7H|^X@QLbCtB1O3-`+Z|kE|Q|%XI
z<?9kWh>^LU3#p;ZPvrJ1roe*&sns+F(s*L0Q5#FWM!@+krmFhO(5R>5CjRh41lRGV
z&n9fnsQOH6jdmFRLGK;HnXbV0e@w^P#kH97!VwD|$=hp&^v4`#Vq1t|ea6R70b}Qh
zMo3_9DyK5L?P{IkYvZ;p%}ptRWM-*^R0cyu;@Lx{!#`lJ8F>cu<C-0}53VkiIZ-{S
zS+-}LxZK8-vu9|fUIO<@?ha$+S1g_@xO^M`52y9oaP~m6;pdcwaKp}Z9fv9FyLkHe
z#Y0?f?%l+%IBHIgE<8ve<iM^!8u99kCBJ+;@dhsVz05LAID_nL7H$t5bLi+6H+dnj
z^TETiO_Pz09N*^!IvQDVJ+TC($*o-1;5I!;ag&i{vpn|@w*^w{Q(pTWmAeWAXaG3u
zD=db{6VyAJ>O2@EHSMnNu-Qi$T3PVc;U%~!!(kGuwV{Vl89&>C*ZGa&vm;)m!*?c<
zRG649%bUX&JP@2Qt{(_>$oJXBBu8asz}K{z$RabiRZYXeM@tenkq1R(;iJ@gmaNCC
z?DyB=nGmvsn075cd{xsGex;tz#;fhU8haq4m7Z{culW!qlEvCsGD@5L8gH&kF|DM=
zyD|uar)yx(?M$m5JBnPn5{|=rQzh;3JKndQcq@Y?Wc=4ib<dE3=lC?V*I)9-?zcTM
zVn6KY7%==Guw@n9*3$$mq(Ev~-`<Ex<EIcq|EEu~0bs}t{oQIdR_*7eJAz)EliX0e
z$KGCrv|S`Mb_ZoyKcTO;NIgBj?9UJfu)bmq*2Ww|a}5fq5Pmc)@jS7?z;S#o`TPt~
z>huN75HpRW#^cRU8YBEXIoxzs)#21&=%_`Byw>~_0f{QMj)Qx1gYNcJ8FV-qvNq{1
zEDA)<PrbLIF<}V^>Z%<0AyLI@C%56S)O;&y6nK>L{%O*5T4xI<bXDxIgy5fUNSd(0
zBT`{e>M+_saJPo0i*Ej!GtRqj?%GW?JQx!3wI47f=HB4I#q)n_Jf3zUU#gP%%|rby
zn+m(XOxbpgBTgzlB8diqn@PQ+*Zy09#vd(j;Xv@(C&yx4Dru(iqgWUSRbkf|_`jk%
zg7TOf$Wz?4`9AV$8UGodJP-_qDi9CsxKQZgLWAP+t>XAFlF8oZgMO=+vDs^t-5F+Q
zX7$cBcr)-eK_zw{9CM(eOcPV>8v-IJY(MH7bj*E!4khFWNqT}t4(^p+$3p$xBLhcE
zMPfnV1K3c5XA}rBjc*|a2^!d1VUsEa4JwezAeL_h*YSq1G9!mA$l*ZZIEu(EU{bhd
zPQ%D8sU(FQ`ewVhFmOpDU!W``LpCWXUkTO={Mz&euB!1^bKS^il~3g020I?k9)mr6
zRovXLrQFf`Tf33Lj|gItI2zp`Sv#sfI2x)Yg)ych?=Iy+z$o!j1iC7Sn&|yijpjS#
z5xF#|YSv@W8D4r<9~D>@bC2T3P`0!((Ung>nW*E`r3WkMK8cU4x6t=05MY?8{#HXx
zg}9Z*t$e4^4YT$V;pBu-8?*Fn-Xz33M;#-bZ#5gIyGjq!SaB66(#yf;gFw|W)M%)>
zMMBSMUU(>U)N9l8d~_*%oaiAw<DiTW-zB%s_3#`<r5b~VSO_wxIi`3>3_CSl+0ajW
z$oz@iUi_)3uvR=Qk@;1rXt1q9-*@v%;(d^_PU8<pfdzySi{8S0OGOZsYd14jr76L8
zED+IO+xyfEj*owzS*k30R1k)mY->8mP;5&h8ZdF$POD^+50cv_;u~Yr%5vQT?d5*B
zi;tPQy_gB|6^ByYeIsKTkvJLp^7Di5;gh$0d~(#u2jtfPwx%H5c(T2g=_=kLDw0IS
zFy?|sxb)woAN=F}7UUB0Oo?1W%PqW@?KFED51-@yt(dOgO?{dEqnZ%GJ212|Q8<9p
zc;_2hiD0GE?JMd?ms38Uf9kFxnTE2xnb>@4N+lYNycJMBU%cxML<h7W_!`g0n;s%g
z-Y01+i7%oPc=hs04P>S(j(x|5bD19|y`DFByp2fH!n%zJ_kO^<eN~K5s^6Jc41Y6}
zQ-76`M6t-kT*toQz>CsweLzFg_B}m#g<}U;0xHnW$gC<D!3Fj_9jbnCCjXo?OUukV
z^NP6j$+^nV=NFSDF4-|wng{IF2(2*!`Av%BWD-D<sv9dyh$M>URdF)d@4CTzTNVWB
zn#4aVHy;pG71kzeU6YEpu?J9~FqPrLLW{oP+@Z_!G|B-K;I)-anN+SC7soNu<Sn^|
zZCyX54=zS65Y{gWrL#`C7#KBoC``4@niTG~*t&WB_$gq<6B3b>clhfoY*d3yz6aW@
z<)Bup(AeU;W}w?Mr>UX3W8MCZN*c&KrCDO}pqA`dF!Bz1R+3f*M+}oWI-A{`j-5Nd
z1{-bUmM~t#5Oo=M4D62xJtZq5L(pA)*ZCt((aWD%!QWTnY#p7$BkTryS$tIq>}Ik7
zQx~yw_F}joX2EAlcch4u%7Y|?H0X90bsvwh<;R!CEq^j5<7Dv!blYax{MDLOI7C8P
zJ`Jnw{%?r}VZzq`P>sn~_#43`*?oagG>ZypGP1B#5A1tt)GfQ^<ap=S;f|4|XzP$R
zfx3NODc7icfyN3uKCgi#=M3P|aa&XT(%X<A5e1aCOqibAbvHxCsXf+J6ilzLFnqpA
ziOQ9!UcQJ89pvq|LyJsH!t~Q<adE!b))Yke@EhvhxJ-!FL~cr!|6hm+(jdb(|M-1U
zmDWy;4Buz6*CFCxEei|gR|-Qsn-ISJo{yfb+2px?vfUFHz$#m&h_W#t0$KPSPHrYf
zOSgCc6H`zaTbHvd2~(BAfD40t-B7PcP<KM8RTi|Rqs@&VB^m0D6n-9*A#w#l#PM9Y
z>Ow#w2I5oELfxPxW2(6E_bE>{y}jf$7I!PRZqCbQvEhgRem2Lp*C>Nex3g(baUZ*|
zCQz0=p#B^41$Bo;<|D2BC$LQsTVz=sr+ApinA0n{{U75cAG7->jtgwr&%|$NxsuiT
z<7`1<o7Q*cl42%nUgY{rXG`^9*_~Nv@24H7Cn@RcAPq#y2oz3ZTy!JJyAsCXK~HK1
zIUxb#B#b*$DOc+QG&}}MvA-BEl%nW=+Atk>tBU0)W*>9$PepEPV=2BO{dWmCn!XpV
zPMIDv!YR#fzof8TY|XFj%sRBaOvc_dciuom?lN-BY^$R3SM|zGZJ4E-yS}Nx@u8=&
z6YzI7_w81a=6vK)7De{hJaSb~{H=kHsV%n?m3Xjx<YLu~@*Sqcyh2?_6&we`S4gmK
zQvSKTZ5c~RD~CI`Y-kbb+3!5}UY-jAZ;VeDNm~cn3dI>2BRq4kRUIY<!+K|}vrG#B
zLma6+xp!RU-3pu&UM2DqS3}1F!t49(H;VaSnhG1A%>ywuTl<TD{e*t_oEFRfeGdeW
zX`a^p!hwC~I6vgz2`&N@Kkr&KOXgu5OeHNO%r_=EzUQ4n^d^;M&(qX1I(z?WsF|eB
zJI=$V60@R`H%Hhf;HOq7U-CRQ!XTLd%H)j@Z>ynFbZjAl6=%+^>e}ATt|pLyVwIII
zgDU11j&9=-zTpVcmzTGTw6Jo2X04e!${oVx?t50;opzTd@3Uo{{dGA<TkU&HF-O$o
zD8SZ17B`e;CQqpBf1%2N6${-e>$z)N_w_Nj_)@fbR~OAejTW<{e5&?p%YJ{VRgC7H
z*d;2vOnJ%+#jQIsK-|!|Wn%p(+CU7n4@_$s;%z4qo=unkGGf_LxYYMlxztV@?YtdD
z&)Xj#2e6EZoj2PF)_hJ#*B_TE&y;kN?=yf8b`LYk@&5ikHaA3682jBfx?5<!qW8Hw
z3S24R-nvQ`hP-lKy`DT7CW!Fi&_wKL$Y@G>klC|Qz2Ji?UBzB1uciA+H2kmx2oEk@
zEMuPR42b-i%4MCu)w$tIjX#gx%ffztJQX99hSt50Tfe${T0r`X7xDB9%Ql7Gaz}`y
zXfWNG(y&fdl7jDajkdPqb0Nfc#6wjtVkI&ip?09f8%2GXCX!UQD3A;6Ta$!p`iS#r
zoKX4ut>5x@y#y{|H9~#zABmXg;}}fxT2+(ibCbR31SfCOQ#beOLhE>gSebc(c-~D$
z3jm_xyr~OvB)%#pQ&{>9L5eNLS;?JBaUKoN7+P6ZU-QG6({-FsAaSZvK@q&M%%rxz
zv>o$ryQ&#U5=#zB^DjP`1Ac&8Vbqv9N7~IxhTGN-7@CP?Plgdk1d=qfpDAlgCW|zZ
zW>B84#bXtlAc?jWTr)%)rAE|r$Eh%B1qDIJUvv5;KXwO)85&Kn8Os=lOdNtZVp5y>
zRi#LD;~Z&oj1KBH=TKk`AQfCm*2UbyMV-2Dtg@1j(U#>eGj?iob-fS;x&zF&$a3Y;
zm8pph8nxJroJu=W=dC=?Y+`Ng(`;(fbvkuoTAWbY9IeT|Sn)tmJ{kW3EP}19$IV?L
zRJHw+7H@d?VF(*W=ZKF5x_onOHw7a~g;Ekn%=F}&F$Ow+4$(vq<Uoc}>7e$n22(jN
z{rgCovU{lP>KS@>0B#$9SM1wNu;$z2{Neb&_|sqBT+}=YMA04jg}P0a;N6Di;9-NU
zc^hq2R4S2}onsS%Q&WNWLe#|yX}rsY+OG9I*{DVT_X#36NAXzA61kqUEh!o(ZbJNx
zn2x+LzoQLOd#lm>@_G*0!`+{Gs|?fRC(UG}yHr{^Vp#w3SVfO1RUJdk4w=QNdmtWy
zi!c=<GPcyWA=}#lCj$O()68rc)ApgG+2~Newmq$kE-Z(Nwd7tGmFi(!C@gnaO;1aR
zdTxb-m|0>A^jm{KK~pTjVL>Krs|zL!`6_riNyb8+$j$-_7DCouVB1W(LuQA_cJ5~p
z2GGJoU`F*Vv;{+4<(W!GTL^*R{9{iZiWD#ec^iQ}DlDIvPnN)U?UN@X3T-*7u@y7?
zMhK4ZdddD%+4S_4Dk!{od*dAq=SHa2q6-Z4wN61=6Qv-v@wjfqR{iAmqTpJ{;qEpj
zAvpVNJ7lxVUx7Nx6iAKfF_C1!gRo#)xgHVJd}8(}$LF}1eLP8MxeGQzOZJ4cAib)&
z>ZhdLZ|nHMs*?Ef-nVCC$U)dm`_R(|Gy`Ava25x4HGR9STVZ(it{RLVnc;?mlQx1H
z4Dx1?gkF39hRg0QE`A3Iai6(n*y*DxE(x-p+duiF+Ier-AsEM{W`1uwK~ILgBS?F~
zB3(MZ&!;vSk>Y`#<yK-{Ry{#|luzG%OXT^(6B1Q~7s4q<JY{|DxEjDOci<*0^s04S
zn!^(;7Q7$AYOqKhfvY6K6>=TVJUG(_XSh^pq>0FjdMA*wT8v6B)=wVw^j)+SW9Ws0
zrB}@c>8);Jyn9q1UT*20s+75mlz{-l5+#|dVJvmjkflrS?_YA{Q6X*Ay=dak9Qj{K
z!t!Ow2f|GBjETN;27;+0O{^<nAXymyN)s)lXWP%<bl!JG^cJPhcZGYpkR=J_ia(J0
zLi}bu0mu`^-TWfR_@3vXQVP9-V-C~T^9M4D>HkQL{_OW1QGFSbaymjTxe`?tQ`A;u
zj55XlgJM+v502&K&O`8@00c&j#vJ;$goH2VFEX;MstRM;Ps;75j81v2vU3k$va+K;
z!W?6kleb%arFMhWJm>pX^fVz3cvcJUSZJ4*i7eRO3)s+pbzUirCb~HY!KiZioPYGW
zAfF;Pe+)`{*X*(@S9dRYF|P|<+ijowjMGaA#f3w`>xVLo;VsBLd_#0vb`(zmxYO(J
z{X#WMhRf9@a6x8bJ5L#B)W}SEm;N7bayYD#aj<_at!~J<CskK=D6qSrB)}OLFFjxW
zQ75l0;g2I3h=yl#O@7FV^amIa6PL1n*)tEG&-{g(fT>4_!!*j{^HqU=P((6)MXIeA
z2Aiwa!^|$#G^&?Jys|Vee{$9yH(jiwkYG>|@vqv6JKpszcJ0rb&IOj|v^gn9M2_7J
z3a2wkGeWSO{pNTc15g;9Ru(C{#`=EIk*BpE*&Fq_2isj7r9BJJLdO7%rr#q!ul}_0
zDs~QdpByWsnHNWKt>v!n3(7xV?f_4cF%bC{cnKbPk0P(n2h~u8W>r4|dd~GVj|8{L
z0T@PhWo8?_#;#ZmAlfjezkf&AIaa@`?&G$DQ#^*M*g107wDvm^zK!2(#I9!dCy>n{
zvZ*}7&pFC3yveq?Vbc=FHjI}Zm44w(>Dr!6%>km+4(6&`i^CA59g7EzLty!oI@lzN
z2uY~ZHD)A>V9nl$EZLSAHaxUK{@S<sxmoND3T=i_Lg$)KD3Q(nqEp5-T@KwXXrOM!
z$Mc8;)!NHpZN$}gQZ9$_ZfX9FJ^p!8(OLb%vRQ5CH&B>t;2_%UT`0@1*RhMvq41Tz
z!Wh)YzM;;*zK#PACw^Mz%>muu)7xsKKn50_^!`>Grp+{NwQe2kPYDijn#+EAd>TlO
z?NgHY?-ZnHBDNE202?H5@vaxpX8@(tAId!T?k{gTUMkHslG=<n5a3W8b2SQ6A?jAG
z9kF=9Kbizt=g4f`rq%v(L}0^Nstmt$ce^5pbxrd;iq#zdi%3X~R!RZd4&bXuIugK5
zJS)C4%a^JN<i$(jh#^=Z%``6^)hr!Nx(VY$Oq!>pKXuKyCD?t>&mBQ^V6B8J<KkqX
zfo$ydnd`+w;sw7A<jLFh(rEPsi4~q9vGVC(2Q>)&ndXs%1G3+oUe+IP=!WVcB8}pJ
zdBIE(xn=2sJ5_p%aO~JF>FZVJGaYHhdw7RC$rXT;uWzTtR?Y40gWEIx@#Qa2O~tHQ
z#6B$yC=*G7q>*O%u<+n%>0P%@sh&~3gToaR2qs-ZE{25Kvt=r#_LGRJYZ|9>jeKhY
zhGXd-eRC?K315%gJHn3<p0QrHMY}jO3aRiqiQ$X~;2Rw$5Vm7U8#6cKpHa{ut$h`>
z)^lMn5ADG;qF@B$D578k-HNHBk3w9c*$jCsToGVgMwGGa9<Kt4pR?QHbTeNgqPCF^
z$^%(ZdAu>pSreu-y{eSS8O>Z=WySZn5$jxf)@-Om(-s)<@1PS4*^{wfk%oo|`funy
zS?Aly=^}`k@LqvE>2I<*cUkfFI7Rp#W6KV%dS1Soe24M&(S@)VFJn<U(&7#{=g@~y
zbn{b(QP7H`b4Ie3gY!EgpVcKPaN=byKZ9h+^Fh=QweH`rnae%>31fY8-Co#;juVb<
zn`UipILYM^LJs&vKou7|q1+5#m7b1haF8!-ID&Tsujn&f)Y~mkZ|oB||2r+|S2aY#
zQS>Ke1xX-TM%?pDxdLOBDOvdMnSF6it!hOjqX~%(x;#U~V5T!niMdi_+D^_F*8OGq
zHWlC4Kx=iC_mnK;q|Es8OVN^(b;(lrx%_wBhjQiMDa=Qn7dHQ&{}^y_k+`<M=65&f
zZt@k2jsec54nI2k!;HT4m0g<L2wRM)Mx>9GX3OBHyKa5{(Gf-VAjIdC9%y1L%iKO_
zK2~-$n?y7P3ek1Omr4Y%h~o9WSor>E+}C4?PD%Fb0|eiW_6LS?kTWe`B#jl%Gp4`e
zOEps|Zw`sDgw#mU(a*tc6U&h5>h|F<)m$=xH@~0(G&avANS%W~Rnj)2x4}(knaar$
zMe;76e@o3W#FC|?^eHRvbtl<UUCS8+3Wg5ujx*PRFBBd??`}@5>Y9SU$S#2*DFQ6d
zHII~8lba4o{@)izk?FkPAZ@kX&6D~iyLb293yUr_)N&s2u{2gXPS(8tfNHBE6`Vh+
zU=bW>ePMP1jsW8@008Gi$Sv3UqDQ1MeoU_1T@H2AmWF2mG~`3ccc$a#?V!(+xJ7Wa
zTM61TSIAp`+`&q?0KO?_;%B~Pr2)yqyY}pC@3py+7cvwO(clHLQ@bK~&F1r4py*;(
z78(1whPbZhpOu+TQ<0kao?M#ZhlX-m($nYYHKj-Z5Z;Urzi_ExMUL9HWmTjo|0+e3
zg&h_chX_NLZN@V#AZHD2^%9gb`Sb}lc=MkI#H1x|Tb?miWjr-3uuGrixRrsV4t#mN
za?K_V&G>@8g)D|WXifS(pE{g2M}$9=8aYab1YPqth6G5A+#{X7t+q`LyH7}jJDlen
zK5C2D5OP*sKu1sv7`?x(?l1F6zOW_K#AULG5?f5>xK>0c)gi&x-8y_A$>*2GrVcYf
zKydmlJ#gb;>glT8xs={-s=nRBy?QzVGS1zK3g1eND$XC~`YhlXoNq-N3Ex<yHg3kx
zDFTBv1+~)9tj?iHM2UG`(IuFUrl3Vxo=`9?x%Y29u^9MWk-o&p6aU?XxV^2k4o&H}
zWiWM4`VU`wBHk!aLp!N}O>4Irmug7Y>m(}?OY<BFYb77KER8D@<SkeU0u@s4;ge`1
zXlAVW`tEVjdv(wF6TT!mM1oY~muD^Ck2hQ(Q|))EnV`1z8tHYkILU9;tupIq{GDwf
ztdX+$pQL9vG(x6)jwrG~C}(U{bP>yuCGdf7>OcT=?aQ7!<q9AnwSig8_z?b&+!2*F
z#NG>Yf43Qto`SbTPRSb8y0zq5WxLyRkp&`36Exj2#76QXSj$rdqv~krpQLYs?p81%
zaq*xul&b?_hXfD~6xT%VBbO7LCeNKLR6Z%yitNl@HXAppi7$4o-2un2ZjwGS-_6}z
zUx{Md@BI{ksx*$d(*AyULMqFuX8$$3sdRkF2-BhyH#&r-+6-LI8$n$FLDj7818z2=
z<q_aEgP(TVYO}u3*`$tacTIlM|8ZTxddtVZuDiD{O|>8J;XC~?0#sJisd>^!JVnFL
z;+oTfi*6?oU9&m_uYDltlv&?CGT&NV1E6noM*{~;{*PUc7MD!Fo!VXA2P}Di#aX*4
z6bgh~ifhjj*J#UO#{cS=FyZikPpfC=M#lo$-Zp<;FqIDA4$*k%Y=krghHw5ckl7~$
zTE}avaeXc897>)CRa*e<Tm*Ou)$30?CjAE)Vj2E;<(@N`Hn&1L0oP?v%0viMf#skU
zs56|8fwSE-M8b^V?Nu??5zsGfx~Fl<5YM0`Hn1w~;3VWmaQTsMNUup8+NjT|2P$z6
zG9$v%78m05(g5!Z5S|8yRX7Y&HK0qs$@A7s8$$__hV8OTD37W%t|X}#R`{P!g1Bl<
zW*Owuk|F93o^s`if(P|Se{`L#8v-f&!0&rHQjQ-jW)53#Zf+m42FLQ{nH~75)#jWM
zf3hkk#bDSWxY5GN;<os;c(p2)QwJ24O9t@<L!-!~8de*wlM#S^X#<gyo;G)gZ*VVW
zKLJ#>pG_s@Vax-X!JSsqmcoyhil>f&200$2B*f*)m8B~Zie~2#bO%VTNNdg4d~lTw
zMENV6M=`RNj*80H7VKu9!sp`jT?q!d7RvEjC%NVPG{uwpe#ZfV(>^s}_3zy6<Bd-<
zzimd5P0xhgt8Lj-FNS#W<)UzBN<>zkcuQ9zw+n+im?4tHdBS<2-<H#V<e?uTzI;=9
zlWEvVR{Orcp6}63-?w%CpC;4h!dG*Z7z)_z2f5@S7n-JHXKy>f?0S-cjuZEvMAkNn
zT5Jy39&ivJ%Xi^3uFY=t;r8|JbRH+B9+m!u*witmnH|d5h35CrOlssZ#eni**}CB3
zA&yj?)8MmEpv#%Lizh%a)K<|zfyO%B@<*TqBF|$W_aOJE0M|9!T_a#1ly6ix(l{MN
zF!bT0Ms{W~>^KlqhD^%r;g*nV=!^aY)-=~2YPp=L<@rA`zH+bt`_jW;FZSi2jHO0r
zQJ}AZz?T<O%hT4;o_r1xmBL1VlS)$6AQ_Pxa8IxLvLE$Z_<H8;z{R4D&F0gl@@liF
zLYO!y{Lif06%=o)EoWF<e6%si?QQ;sUc1D=#iVB1zpnJcwUZLFyf?*1revgeMJ_%#
zy`0C<m~W0Y(wLFqzn2$o=PTt{@KH!e2JP3qAt!#H&ob=WOLwxp9rhyVNhPXT>NVf|
z$1@)2sH9wvWL7h&$ar2TN0gGzY}>+#kkBO)uIXa!4>ks9I8kWfTS~diweDSZ(eb3y
z)|>AK@HH|L7Ii6EC{2cCM@lpNVhKvVgTwG=Ss9({WyRC84X2z&Qwd@$Ef=oS!zkhz
z<;%7-aV14`MaJ8bm>~)fx@x_suVqNGJ;#%`-Wo5wEu|dBi67&$NN|hjyt3cU@!S7(
zE^Fr^Z%Fyc+Gvs=fm&P`uc-iZ6T0+4;6Kf4>)qk-pS}#UUe%k%I=44LR*xMg)4$AC
z)=wIi6q=`TL?rS&5pHjLOQlL0997jE^75}6ZHbCLvye}WtF(=YFh;2@S*GFqfLr`3
z%QrY0x;Rfi%YXx#%Mv*IS>>EpFBAoe{Z_H6nGe!LxA(?h!#eWIXv#o)Zhv5RWEG62
zVe0YSNov<@#*+@8h!y!>Sy)l^@q+}Up2_B;SDrkhBk|PbovY!x&1X??AphQa+an@b
z7Mn5o44MzV>W=?SFQeKz3GiWxwVydw8kL+Oc^LPu`#-CiL3Uoo-YZD`p5w{R%8`l(
z<@4{ozHE)S2<5!a5Q&Vi$g>Ffp9oN_(}kHlgLh`GoXN?UoPTNTJ?{~I?sN>V+ArBL
z#fQ3?WY#Bale4Bwo~csYLc5UC%FlkD@GhDkl1@-AWF@BJhBvLxk9D@J{%eAInMCnJ
zPKV^r-G1d<5xx8Np!O|I+;4t@{^HjCDr;OUUX9)?{gdyV9o0^&^}K*><)5(aRwSAS
zqpmqQil*cEUX;LJ$~!9<`Cyd_w`P}3j5Tk|wAo#ON((B@grOzGSW(x2#Rr`1r{@b{
zd4hG|hw?;o_X(mNX%aI1_s#5Cn>%S%mm&H&hn2}a%}puyvHt%U(6o6UX4icJ=?3~g
zI=h`FPxM2(mmOH0Ui6aYjXLD&*9zvZ&fDKe#dC0z7Hof%Gta13Cja8r(f!BvF!{xn
zF2V#}bSs3)z|5+4SkS?!WX9>hjRMAh(>|gjP=NPQdceu&P<tH4ZZWv)aHAHr9o)1I
zJT`Bbh21Dm&u-?p<;{X_(4}mQrHF50S~Ko|vf>E<ecqQz)~{{1yC)yGw)=`-(Bx7z
zyL7XyFZ;l$V%O~O$c}5VX0r*$^kOJ~6-5u<B39Q1mjjCWl9W2_tlIiOro3=V{wbZ2
zWF7gVj1CpvaKN-JmA;^&t+OGV7Ls^^p3p}g_{LW>_xSObQH{-oE0t*TLTAF=1zt1&
z>;-GCluE4X7azTcVXJGD3|2f9DMNAbdYPJC%j&xuJ_a%mf6W(<lLXrDv&O0ur4RTB
zg<=<anV@@U7!?u%G%PGY2s|4N`Cis!MY<GC@W4Z&DoHrQ5yHc<jfk#G#@vn|ws7Il
z@)_n)bEe_Neg?)$#*XX#GsAX+zR0UYh-4=#+O(?W`Q;Nj-)O2GeUF%TCg7C4I@w26
zdQo-5OFWAfMMmE%rn?zL4S{_t`5Z-KrGdoU2eUY9R+frW3+esx?$SbNv;%W1%>M7C
z+zC948oH3(o2Wrtx@YZ|kv{L0>ldK$k+c`5jv8Y)B!t3lovaQVPXcBP5jzYC<41Ov
zotTR4d1|R@f;M&dsQ@+Tlw2Bg`M+7j5=AC8fV)%T%D})TR?M+c(NmW~OI0I3rQfP+
zrVU!?+W#!QqY(MXCqazBL;m039<%L?G-gDtzVGm2Dz6SIkV98;j12E06l-(CFd)OS
zbM5klUwbft`?{gw)_$Klav=oW^ojs8Gn?jGA|Fh9P1j9L8$k=t4#J%23=R4eA4^Kr
zIP^N6gR-KN^_u&%bZj|9Eo9-1{;wv8q*0Uw1^&+Zn-{yUnblGD(J&TEB25h5*4G+w
zM<NhZ9AB~*T0VELnpohQ83#g{ud>fOMvc}Zn!n)WCWV1;?`g7PdP45Bt$3djWo-NV
zuQa6Hm;Hl{gZB|#mM~w8%AMMDF*>e1jIpQAJb^16M7SYMxP3R)DV3GH)$Kk>Ku?_2
z7*sy=wMCp*nnR^?uG~<F-OQrOSH9Jak{g+JE}6{0!#~M=&7e^0Wb4`&U$a<a93Bug
zU&7$AHq7UcPDB7b%#oSf6!i6bMa~<wb?-?>S`>uR%I~1@B~C``r8F6J_CM<3X=;MC
zZBdKblct}332*V!pwk(7{ljgqiUdbw`j|yr3~jw<zQ|}=)^V6Fb!`R~$A`Zr`*8OB
z?kVst*9oGgJ(sBZTrqvf-$3fy&7oOSULKV;HMpl(TpVe}wIq`-u!>32>I2QHNZ|#*
zW2e5oT1L#3ixoJ%F_AIp*vPYLnh1DPJWqy_NN?CPG;_lnZnhHhXC>y1S4vkbav-u)
zyb6A}T3@lsD2G6@j25U@n9$mQFSl_vPwQmTO7L2MO`FZGrem)6PC~#g<@J7+PxW@e
z&qYW%FV*;TV~|3#|7jtb0~2NIjl^`Qbsq<cDy=yf@eRj^cMx2XG2H`eQsSl)-vy|U
z6UkdC+@S;Jgd%bPQ?@=dpouU=P5xFqDA8%9uC8i^gMHo|rzfb%DwqH3Z0AZn;J<c5
z^rF;T-qv&8qv_$j!bce`5@SixfXYPwKZ;MXwM3q{7%<r9iqBiokLLgS4m$^asTP(l
zxrm2WtbXWdx$HiDK{t|B+L^(i&`^a#5Xj?Z^$wvJ&IFPC`@4tI7u|X0vy2Q56jB&j
zeYiTASiM&l$ZIptuN!ESk|f8@<BLgRNDFVW)lzxSs=Ggt{JD_e+R-FOvt<0?)>VZ2
z5}AANl<VJ<6#TUW5d=GpN8aG*$0Q0s#k0iz_0v{|u;{m>hXWAYxBu}1{=*RW<nfd*
z>kE{*EDGr}vbr|q+;86EMDRs8J4CtK^Ifa}<-%9@bDJpGPDk~z-AZLO6*43cg#7$>
zGpNUD!hN1k*P6FkuiCVXnJzgbZ_vy&i9JU^sr{^G?(p1le_Wjl!|(VnN!1@~gYr3`
z_sia|SFzzRDf-77NImI7k*xRr-^ENUw>J2T%~I9XfrrREDaOCsf|8HIBI&r%cTmzg
zR#nmo=Yvslc=%N<taX$FSMtoN$o>0kJ>RyD(3u-YFE&-;c=YCPJB{IEPqM&-`upX@
zEh+B1Z&8mMzfG{-LNk?m{bALe895nPa`wH@(dBA(+6Z{1_3e##C?+{`E|@Fh_<fau
z-u^0Iwe#UKX*$EzP6?(uWv%EW=h?do7S}Z|-}uhQN5Ol)!5xM8v}UfNx~y`ON6Inj
zoDrhA12+R+zNOJoZ|_qUNY~+0+v^&z=IY=-IA=iymnzENeQ)+HzLq?Y8hw~M;|Ckx
z!HtlH;+kee`|5rqnx>KGh0_u*dm&f4`M(Y1q6kIUC)fJ1?pej`*R^+}QQwVAg)SFZ
zAGR=JPkdL%w)p#9-~LN^eeeW2+rhd)|9_ufgbKDj3k82ffFRvTk;j?dHsRIJ?Ccle
zC0I^>cR<|ryN1EDx9&&Ya3{$<SL=ck(?6MsCaR~-o`Q`fd2P6O<M%h>RXfhnVmUZ9
zyVMGi>U^82K#=tEr%NpM3#xysk%M);1+f!Odl${dN2ez>%~M<5-Ym~+o&QAYST9!g
zW3Co+gqtH(Rz&XjBMuuV#&h&H$L6ap)&%8Ume>IBkD<U=SHMz)bKoK&!K|KvL|y{B
z@$G~?PyYJVFBiY)|1#3n?E7Rwn_u<;`$fiv*<|O{e)}2TjetBBmh<H`PXc#QY?R8%
z1G-}4D>px&eI)4Si+Cz`;HQC{5I~Jt`jviVp%29{AH)#VLuSkkZ>C70nB@7qv6DOc
z(eBBjUZP^3%cus3@?G2S@tN-mACLv@<lk6GqaKPhbB5vuB<V%YdXZ@+-#+x_!2dTo
zy$>Hqg{J27jwO0B-x%WKD;)Y|p@?S3A>bIQ0h2wuPSI<-W$8?i2b38?^bSX#Gjum=
zUvD0$UF8VA2~Nfe0W-BVTcbTahai8a10r4bqqa5KA>icPyVx>zl0zK5em8^emFe)=
zas>>O%cOoONq$L@Sp?&RnA|xe?bVl?5!o`h^w0cetCc{JI||GZ#R9Y@_x1dPY}yq?
zL?4NbcIvk@&MMX=r$K+W7p-_#7}#yIw%g}uGwc(ZM~P?lkmw2kMBT+NyDr&Of&HAQ
zg59~YX}pPdZKFnbNX+KB<Mxi@Ng%98th_#ep?o1C92^D|B<!=}^}8R=Dk}Nts&&Xm
z#vSw8B?S*ISiC5u5^-=2FrT?xA?++fzwn^A+fsM#hN8%gXVp9##qP_z-=R@>2tGG2
zXu!zOFnRIs&B23+uA)qeIy_U!@xfcC$!QH~+{l=-0v0Y3%|3vHCsn-v^rK<9t+u6~
zv6z8mVhN}d7Q<0^Aba{LRRErwTz*;BOoEvdK^)Ny)DQmGz1#miHgZ0t=0h|$o@pit
zRgX$ys}TW=RyB>)WcPn0U2|OB-~S)7ZFjS6^QP@)w_MA1ZP~clww7I6wz0gdWplsx
z=llDkf7ZR#y^r13d7h_UoFuRP?+d=`Qlps`(9=ek7O>OCnr_p-y5PvRilA?zIzE&A
z&lP~j+xGC(3xD>{@8yO{uaQ0mALC3yv-}t-B!MKo%1N$wi|+m9mwFGj$emS6@J}~C
zG!mjct$-cGs}K|mSyC+9YKvU4hZZrjOWkC0-*e&RtdX_vNNt^upXuIgm{2#oUx@<W
z$;HN9$GsgL0JtDBLq)rgUZdvL+uGV^aCQXWo<%t{Y53tuYxB>mhZe9*$K@`<%VM8V
z_`c2bV~?D`Z9+7buUNmEYVC^TuNAjg35>et**_CYwU<HXIi=e5X+rG1Z2w|DebEuD
zU@aw!u@`UIxuOer;8cv_>3&<_L+A@P87WY&gCzOEE_O*mrMZ>&hwBhQ;N95}o|M#M
zfCw{tL;KpyufiW-AHtN%_bx4)?RvP7Yk2g`QW9ry-p0W2;Z4Ty<(G_R$_e0@J@h2&
zQ%^8Y@UB+uSU7k*&#`>;j#++03b-d14zs8C@ec6U#()7%?8}G`bmZy#z^f|L=+GDL
z8SGb2cp)o(Sk*SNySgJ@a?1V|!4Neh${}Zs9%9=tV`^9YtLNYPLAiaCHSbdr6K}C|
zN_6pzy#T*ooR+_5Isg=|juo{Yhy$LjEe@Ct2hRrB!B`wzjEQqJC~D?!)AW^NZos_x
z<>aTNwxc#hDv@Nb(LgRNJlbz&Oi*+O`FSnn?U&p0vLT?!n+Za+s!$qKf1EJ#j5cAV
zF=Au0udAQguD%}QxBo^i{X%Et4}C0OU1joBA7;?uhM3M(Z^^ws&Fd=?P=QQPqkYhm
zmiTkC_FG)Nu4D5$<yS=dOylecZ!=x5$V(fvL3LI&K`nV()W4waKQ|H`Q6NR0B5%7{
zq6VYb@xJfwG$<s{1adDl|H``boH-mAOpg$K3=5;Wm&0IfW|qy;5<w0Ru<t2L1*A6#
zu-0kfM9^tO)etSQ8+K4~;W7gX*u1XiSIH8HcFWTpPABPySx|inwTcPebLN9na5VwI
z;!os-v6k=7D=CDp!@Gh3B{BNYs~5EG?O>`MxQ68Y0Qp8)UQWewxarYT9I?h;f*+9>
zT)FP1D}gVQREHZhuAI+skBs>}3u>%B#bp@-nQ?h=`YGvws>e$(<J<z%u!a~(FV@(N
z2bWJTFaVO51g_x|d2(~-s`o;{LC$;dA=L!qmV;Jsq`d32QC-S75J~Ag{I-u%lUIJ2
z-&V~x?wt(+FopxAC7P_BtONAV9SRhQ3gW%B>{Fo~#`1G+I@ZPJlZEbZd<c#~7>W@d
zurdgJ3m2|=EnP&+QB=((fVD`sMsD57il4Q)1j4BdGYi_>0f!{JXT~1PxQjHmiztMC
z&q*F3795gew7vBP+yk)(T=shN&VGZo#2W3__w<oe8RhxuL|$iEj@_j07;+pcY#MBW
z264$u#5Y1`@W=N;l##Q$TlA3;1;G>u5pd>91D$P_X}xho;H*D4`o45OkIv4BHMBmX
z!gATX^(PwNf9#0Q=Z1)<(0uqV#E8x#Wp3LYXiO~iub&^Ry6q$97|R?fMa8ND<%adi
z6NJF+t*#y|UQ&$9lEIMKIqb+`&i<5@!h*q4mC-=?DB;K1xQwvF--JQvYro|3jXOk$
zR)f#s(@V2hD#$uSA`8@K_Lm=Qbwdh>3zaAI&~WEeA8$5<4^|nH`DRYQdEcI&M}Nf8
z%ien}IY@^*e<Fg1-(034#7!(>yXslifHZ}C)NB9+DUWC8u;g1K)z|A8G#lU%g<R(B
zjW}hA;@23id@-#ClME?Mr3kn?2L{Ov-gQnD(1(KBLLLx;!eg570JQW~j}-Vkj!$aw
zJNr^8E0X?YB7&J3AJ+h|&4&Lg5wVSOGq2t*^1f)kCpkv&{Gx@cFpw^!5yYRXy8o^3
zz$Mgk&o9<RM%B!_%6%e&BUA8s_%q?e#+AxNP<-(T&wpU7_qo!HIYxiO41h%`)rIs}
z#3x4{8}<UsthQTTl*A`2jJU*25A28ouF>%mnMz7{Z5JDiDw~#mP2ha1Q!u^#COQCk
zo^-iT*M_a4Q4wY{>)JN<R~8r#HuWT+{Wpf048{ja&H_Q+U5b^<2VE_x@ck8iqpGAr
zHtZZazXuq>(C};?0@5kt<&_^IT5Jw~ysYWR5_YhCQk3GN_vvxC?oYj#qNu`L%yr+Y
zccKxw#?)!UsLuR)9wp?v7EHamevMj0W!Yg2a1_x0t#<%u1~CL{4}*#rGU6t*uD6Y^
zhjBzuiu_2V_M)vJ!S7l5dAq|*Z3ddkkK-F03>D0U8^1n18)~FwP!%#fbI*N3zUw*i
z1M~y}Q}2XNal*alM$f$G+_jgl)gIH*u!=K}z<(3c!5b=bma+8S_rR#~V146of?_3D
zB8N@WB-f|(k(71lN~9uZ)4Wae@;zM5mjbQ_1R5Sil@Z6EL<j%8E<XtX>{}ksWD%sK
z;NYRUZOWys0oX6pEl+p2BlEt!2%rIWTlPh#BGyoJ2Kpmjd_>t~k_Z=&U*@EG`T<9Q
zuiGsRkzs~t37Byz>C;8|71&}NNpW)V<NapgK+tYGVYl<yefm`NrP&dEN>zXrnSKF9
z0Rom$&J)hqE6ZCLazHdOEPuk(T(RkWCpj2{!~8V=#!Y47%P>(cnZU%tnP5QI<K#uV
zXO&}o7L*WbgdPY`kUQQ9Vn%)ufavj7d;Ye;{)dM81fUNu;?Vt%y6<Ykulx*_&?5`J
zUZ;;zzbubNb*}6FNq&MggY?F8zwyZhWScHqztdbHWwq6)<4%^^qv~<qCSWr(+E%Dm
z=?b9MX_@&Xf|&@)Kk>1372I`=3Cw|x(aAC<DJAl0Ero*n2sM6@J*=p6((Xl%T+Sfb
zoT6=ZwEqMc3yYSq+H64y!=;fUK{>fmU>Z5-cS_H>J>KnAz8sJ2lnsVu_0bh|N2O<h
zX)UqfFhdfU)7SdOo=@&XbV<W3DnC{3IQtc=RGv~GT-*m-C#DU?X)&;h69i`kJR+rT
z8tzt~cek8)xX_iPiHS_i8F`~H1q4LB7aQTfdJuk0U^aT@+oZYp_<^nS)N(9QruzY1
zbZkDKxO>E(VD{3_J4XzJfLtOm!;J~Xf1i?RX9ku|kfv=|rd-xO7b-vMJb=`3M*l89
z@)JYQuHqXZA|li%{z7o%BuvhR5&?((+)KgJIpcvLlK{2Gkj9k2!KAUiYG)m*auW>d
zw<T577%4+CB*2p8FvNkJ3q2SQZz%{gv0Z-b_TR!HUD`=(m;>a@L0g}5m9~%4klp!o
z>)70^egJsc0v|o=lD+nd635pSypu}h4Zmx_<OJqpDHNU0Jn7NZ4b3Zg3x69N&7($+
zs6w{So~e}0@$40UhDk`*o?PA$M?LuWA8O}(67>k)DW!D~(oq?S)eBfUf9||_p-I69
zD%FQe#XPd4<c2<L9HpG{DDRhBqC=SV`o5&&_XH%29AQ1hZMhr`5f*?PkH@*eSr>ih
z27gu-Sa4+a>pqR2mSe2lopb=KNc99SaQmVyQ3T8m4v)4C8wdAqVgVBX!7_#X5ccoJ
zg+!QhFu`<3YA!oC7`Q8XZ9U^Z-tlc1UmoKby^dD;9&^cgJ*D@dzrN6wMhd^p3$wlb
z`2ftV6E-7rSLUGy>9_wVRmql}dH@2BhPVL)Dgd(78ummKi+V2c9WE#Jtodgw1MWb%
z{~qVE_<17i%lc$+hb|wlYdZ(qJW{;&LKJ=P^$xTRtS>y?-ncr1C%94uXRs4V){Q+1
zh#4I^+r@hh66)MUpIu6)-S$$RdF)oJ5wAR?40#^br(Q|#u0&T1tJ>C0oSSBLV(wFa
za1vR5Qo8mCc*HK3RK<vQ$H<i1mlfbw+j{uLVd#4eY?~X*yk8m)3;*)RTFgcT7;uAM
zChN~hJLAG4{$o$b5wdF(t2fMz>l8dbTg;yN@cZS~&5#sQ>yY`F!9j4scY<#x@G|vC
z@oJakp)e4fAI#bR#kkZ4T$8_E+?6c~a_ga;8|hP{%u+;vRM?f18{#HSEV-4qXkdKB
zik6REZgrEZb?JDf@L<h!w&x?jks&CATz-TAHN7I6__ca$V2qgF`766HZ^nSz#|)OR
zQc<UGS5oX_D$wAc$l6`?zaCTBuKTCN6s!v_^2w-gq_T3x#*BOtd)0G-K22RO&&cts
z@rz@G$p?lrGHTazkO%{o$zev?>qP=EG*n9IkVaa<Oo`30KSvS=MhR>>NU*geD;o0R
zKiqcg!#sj4?G%j<mnA3=V#rIt7x@u4_uKxklIku%#B9lkLa?Zjv1nMvqIG`7bHhlh
zL-t3uA@%iO!*vmfX_;g;W#R8EnMwpS+z<&YY1u~MI9xQ2f&(W>a`|}abe#rCoiWM?
zESZJ<gqQaPAX)6Wyhyb+0d7cs)!vMBIzwSJ)o^QF&)BEWcz}hCDqISwVxsOZcSV^m
zMQ#$;qu1c=2bc7^eBIC3xWLcu;d}%uR7`~D$R(RG|N7%<Peyko{{_9a4=0d9`~wY7
z)E8uOZzHC_{>0)PlIBt?I0G{YT520W&6K_U;Gcz+iq82Z0R~e_RUlF9XSB|itG#`h
ztWv};VuhY8lPf)!T+5YCjgbF@8mdu}M%vI<Z?>gd_e_?(jVEt997svtN?*}m3N$sS
zb`re}AC7Nx3FlXHPZ#r;lAU-6E<h${#I`8vB*#zR>A&p^j5Qj>rJOjIshd!xo>f|v
z90%d!*HWW=0Ir&p?>pIdRhtHrbxC!gKzarF7A|a*hPFW`klv(iVSD{n*$mQ;OkJ}`
zth84@zJKkZLASwnhqn3f8NH59weKxWb}WDCUiFitfkaBNdNC(E#y=;3q1E?sNVhpi
z(P?jOKJf^(`%E%bid620l21q!GD9MEzdGgg+RLc5*{0I5NOSR_fTH(@8>dbpb=(wS
zqJn;m8~<{8fwcPf&eO+^R4n=(yGAlJv%;H3A`ghkaSQFDpz5iCu@1dOZ~b%kG>O?z
z>eP8?5EFx$7KmOcexg(Jc8FkM<)q~lES|eqSB4fBH=|abqRBCtqcL%&+PJBMd)0Aj
z_%eZarOhNK_GE^PK6;&E_cewEEhUPC9uEM~%0qi!t2wMPdAVzm5((%KoC4W3xc$E&
zn(<nipbz&Od>8sCNtwwvg0BPvqd!zSbBHa2zLe)|QvVYmgzDP$OEpg~QUk68)f#9R
zsdX&&M|Y8Fiz8zi<sNrcTsv4}yyGasr`<y8B81y()*xNJ9j_tA(r%SfJ?GR2pPBV`
zky@Up?C<ru<MXxaF)$9@L;yS}9c1H3evc-BK|nfI$C1*<u0eFmsu-maNYS*_s&l$n
zb+6rS*yr-m)nMz-7NlOlbjc$Lgb4hqm|NORVqij>xYvx2>!;7ut+6a=0I9k3hKA0&
zS=<$tFedyZes_~V{z%Mzc=Xc_d@~m~Y&98Xy;8`z)9EqZX^Iq1u}g0D(A{hNKnM%)
zYn`&#Mf6Ne>K&sFjC#&z>;-MBO25m^HPBcbjFw|*Yk4F?PuhFSx#nC2(Q3O~LjX0c
zy#{69aQnwU2X%wL7p$9?>j*(TiqMCAh6`AU*4oSHgD`&kpEd_I4V@c*X1DRWy5nj_
zeNTPPA;al7F0^v{a??EKo@iibvrjEMk^B&qq7CYbL29*Z*be*<L2Z${9s~zFlw;HD
zkt&D$YT#3@IGMiDtwpYG!_Z^p3E*08)ijH^R7jz|rcUGY!}qy)$HBogNi_5Gr(mUa
z8uVA$+niQ;OI#e>f2I^s3_*j`kO4-vPTvq<U@Ajatr|2=9rtgzOFt=H4v#R1gQ87R
zw1~2LS|`V9S&Q~0>*d?bFhe=^pdl<r6n5B=1~n`T50&R#aR+dqBJ?fi858%CVBz>}
zDP5$7=9%r=7Q8lJH|#0&1Zhl-<PmdJGaZm=MW1upUNT&2t^Ji&fFGHZ8arz8j@*!S
z^Aj`c0>7{0Za!Az(p2rmX~6wQG!eo3E$m3(SYJ4JHu6eHoFdu#Tl(qJc5j}vCB0!V
zt>I3kOH@yo`=x>5WSjt3R?fxuBy;oNHI)s}JB=~0JShXNr`fo)(gx?%U{$f`!q<Z%
zv-bMu*GS>DEAkwhJ<}Qn^t3#9z+1?smJW|zkOqdYyrtLIE$a>vO$=on8bm`bTqIKy
zDF5u4Xt9NSF&)r;L?o)mxKC$@<L((->+&mQb_>m7@h4y}>!|GSyT7VnnnmiS7-e}n
zFHLDcwxsRva_-m=Bz0%2EYf-=JOtLxKi=F<o_wJL9&JzHm53qRqJ?y7@1UDONs*_3
zRC?v&u`Zj4^R_>33G7<}5&&}bY90RWwM#tTXo&CEmR93sBC;~JB4%fV{3jQ=2kkO}
z%<7%+8ihC!C|d7pMko`i0-c_5KRO;>*lxd=_crs~qbo+n91mdl6fzhkOl&hDlLFVu
zv7xm6(AX2w!kfkwxRpSbnpBGB%AUd;<X9q7?shs-IG&S#dTx{a-e$7ZOe0Rt2MSVM
zR9PCh{lKjusR82FAWUkbz0b0Eflwlu));A<AN4X4FL^w7rO-vW68UYTCwyMBuJA9l
zyi)lz9VQ?U3x5ujpj>zaRWR+EWlp_Te{$YRW|B4@KTdXgvV-45rjOmH|AhB=Q!6&I
z`-{UOR^{)CNA=Rd?H<oI2*~3NR-vfGSD@j7dl5fqu96mjxc;1Ad3R5#HcY5CfN|)?
zQ<3_hM`H_uh6I3}taZ_9`r0oxPW|_xtCxpg5b&D6wP-B?@czg*w%7vOKr@YDSEq_^
z`S31nd<6jJiVH*q6h*<?`*;=1963$accj3Dz|cr%@8*F%r2?(=82mv3r<fN9dh>Jd
zHSk?Zv8jc<LkGZXyDz?@RCc!Gd+xvNqv;wNyavVn`j2H_Q3yKsy*8jNiHeTi^8_Fs
zaGz%9Bx*0A80i4VWFOuOXT*>}lJba=s7>48H8o`+N`)H(PQHM5&MVRO?hfg%?IJ}g
zUl=84lkUA~lXg4^toy`(&_bgs%9zBcGm4uD5M|av{Z4@gA!(3k&$;KSnL|{C#E$?G
z_GfE`(zyG?<(3t=suMM_CeFzK^dbOJ8Im0|p74+enH8xsxxx$6fGKwzbgqV16qaF|
znPNBwXz8+DLsz$q+09Y}gDqvIAH{Y7)Jt?r_6`_&gLDqr9spRoZKA#X3SWBe^0yx*
zk&9;VKCKXt2!NY0Gs|MUdBVi)BD<YI3e5wi5%GNxMfjnsfuX1A_n5Dl6S`saD)BT4
z_M4^_oj?DYB`l9@$A9j`2b7CZ*~GmV+5^^V$Z$q<^4tJGz&Le&JMZ)a9=wB`D=ese
zsPwzSqqSaruhy_t9zz<yP&Eu$qMQ<KR{8W-q=+&S^0<vQXLwyd<iwl_=H%$hVP$Ww
zx>cRX(P968*441uUjBO?WqKJ*CAYLMQKBupT$(ca^N7!O-F6VmA*3b=0g>?K%^Y6B
z2fQ#|bJ4tw1w46imV}<bc3wU4Xf9>GTxuB|jP=|Qgh=QttsbO!-M?!1-{O-O>o?Nl
zvIJ5{;=o42BD?(&04B5|liS-md3XOoj?f@}z#Vr6ty;C4j(*kUlU`J3fKyDsg@+jI
zw;i~bWuxwh0)>~<f4kSa4M&W7d_C7>lN4UI<Sk+J5r>2^r2$9GrDA?4OsU3uSAqxr
zp5K$lPWTN{8^m0QHc<~-o;xoVwCa%Yj2=!8{O6T>*g&98&7NVv<0sdkHm*~c)I?HG
zfkne%zx$s**Q>+JVGAqKA|jXACyN8fD!q;{8YsO3%=m>)={?$Bk2%d8X32mfwXZD4
za{j>)d`r$}h65|YbZr!HC$J5Y#T(elQz3bf7=aE`?-WWqWw3WCtK*>f9nPeH%6lgf
zKi0QT?j&NTRYcMw{LUDhA{XdyaA^oabk#L6vu4a-rbhgbo0Yybe|Y$r1CY=|3%*n!
zjmD*aJ(oymKvj||UT{i~{(cleb!&kxhA_jkN6q8eqa`iTpWK4CtlimjQ3fwF=Av`r
znm)33mNvL{C)`P2AbfG?tIcn;UU0@QEFj=!G>QemBFtn^BN%bopBqAaiRV|LP{A-q
z)WNKCCfpTKpwQ5vayTr5O3P{ph^pq}Kk!Qo*CiksOqmuhSX9pyAGKx?kr$tO>z6O^
z^N1=4n5yzl%onnQ%kG}iDtdS3un!~0fxEqC?WaDci0xqP!b0r~g{A8{bzC|Gejx#g
z)oV}xEy2unRtVIaT=UtlX8srlMdUWJfitaMlAt)5sJX=1!Z%uNhgxaBo<3**VE~5#
zWzxDkt)~!uah;-amc<xX$e4h!B)w!f%sBc4wnKQ34DM<GC8hd$>R+ajnOocBm{{j{
zQ)Q-pTkB+RF{-Q7z$B6I?KtKBK9jFA#+@VAY<%)NC=57-UHSC;$P!4!F&oGXy%IH@
zil?rMZ=Uf%C{RqYx^oR1$gzWs#|K=-%&rMb4n(#2*Wp7b#91A#BIwXdXxi<<kPkG|
z(%Ck*i(A|E4`Nblw*}t=%Dw32jf6t7p5M3B+NIX!A2L}W97SGuw73mkGnph9bqU(c
zsrZR>^%g<E<)BAw$7tGefAsu=VuT9N2V@~;hCX|YOSN`RKw2_3H)CaQ<mkq4!*h=j
z&`*F&_-;BO8W~xadBCYfuHu2#(fu6vHNZpCZ%An8mvNR9Lzq|RD@pa~zStBh*V!ie
zg*VfZ^D0S6s5QJK_PjD9k7*c+wL~AlYZJy8d7i;!FcuDDrFaG42^7#fJ`KaX3wViX
zDdY8N^$)KZwdHBg>ZzZ!8nN)M`c^RvDhhtceOnN+su&l0_Q{pe0BwV|)}w4}7lmHl
za=UsRUazpn*C}6QFwLY#c9q`v^$cSMHjs$V@Ya6}9ldnvF`Sx`-~TW4PmWN7uUhFb
zV&*E#qytRcTrLh}+|}7oe~nn|>9e9pOqt|#61Fb{NHzGJ9638z$;trKg83CQi!K9B
zra5g6%4fj2CUn;MsFC~`*Q-_VxLx!#w(nRsaiW?R0AMAf+!=l=24S)daboo8XhGrr
zo29GQ!%Vbui86nqWl89E>*2D)2=E+*VEpCnibd6fl1ddGYNn2h-PE~~o1g8!RgD7U
zMSqzV{N;93&?!kAiUEh|Eo*94;u{5}0b?DXDEki4fmOMDm~xG;y>X{*5#g}kOW+V>
zE5jS-lh0PTA#`C#;Dp0fno+CK+(gG3pO`7~S}gXD6S-!Hs2c$Oo3$Ldo}JG|4)smy
zrjOf1?xKCY9g1f4a2e$ZEV{0GeidU)Tag|F(z{GL&Os76t1ipB6&!+mfk1+8?JKtD
z`|tRla~ShC55`^%ffyzrHP9WZ-L3#0T_ChTQb$*A^|<v8LO?*g8YuzpaN!@|b&d>S
z91SODN7ywsUA_3X@0=z?>6VH$O>>&_ES0Lx4c^!@Z_rY>a@YH_RZ&Dn3xY_082l?#
znNz(QFJwqizkD*|tbgnm7HIsL6P5ELr<2fc%E}Y7TcNT@Zd}FZk-Os+Rz;?LWe@~p
zdD8C`eG(>Lz|O7~r@F2APD*XI=omzpB3XL$=iP@(cgIkAG{kIIF@`qeBOamwj`oVY
z4a?E$^QRjjv~>&gdns<WPtah042*sbLxO@a&PWg?;s=Ax(&HO~7M2435^}imFe8#g
zh&l`<%aZO<<Iw|IMv`uVG&qnv1oVw{><}u90z;TH^%MEWp4V_eIOQ0>u{gnyG?<8;
zDvGKCgiVKNPw->rWcEsU`&r&OOhP-dBo8PEJi9w8@v&E2L6gCPm?KJQTogDGG}ljD
z^82swfuR|%nURq@@Z2!?@4r{o7&9V;QUMOQCd1sCb3m(z1W}<6G7M6b8zj#4j{%8o
zIDedmnWOl3p-`-i3T9IqU0oGYnPJuTKNL~3)BncQlYcoS|9bpJ5g8uzuBm+|e(tsr
z^z{D6D_QI5xyLOH`rrHxzbg93d*8S7U}i;m=<u#Orh(R>yYP7QAYfgpj=B3bZRG@*
zGHS5d1=I?(>xb8I)F~+_!maxf`6(j{I>???2ts8+fCVaN>U2Y6<j<4BY-mw#$58_q
zit#`RIKW1zM)Ll0d^Z-TJlG&;VTcUo_B;d3#OJW`&P2|2q}qufM3qhQyB*H&MOp9O
zzk3IkmQZ&`knQX`=cl}wyKG5lyNtc)N-BygB+y8WC=6b)2m^(VT0Pa^!@So>6q~)j
zzN>SUGXL7#pR7m>xUd#AiOsGD<3B4wgDJwTTApm}n;}i=3tIF#Rz78_&my^oOCcbZ
z7$YN_t3{h7_uCOx&~%jtVxN^K^EoxeQj2255G~TYjR=%K-|(cadvW(L0+Hg@B(|4e
z3GuhK1Lgx|O0^oj#gD&wh+<;lR_N-n#u#;gDP#MQhveWcXB8PhjpqAKBs*SPLp8x-
zEHj}BGX)DyKL90~8QSDJIJ%6k9%*;Tm{Oj=p#hkx7XNY>PR^b@>l@j`H=thWe1za2
z^oHl`G#J_yGIB1+;%g+xV_A8S>e_{QH+*tTeT#vHQy@A~qrXoG%#gw~cV%eGUl|f5
zgZnT2=}Q3=HvqLcqZSv_xH884UpB~!7ETNn7xkiJ&BFSrzvVLtdwYl4EZOL{cE%oT
z0<Dp*Utk~@4-Gw@QK}q$5vJI_S0f*zV|UqI-5h<(7CUTho0lux9#{A__k5;|))r(}
zXGc(=<KBL8)w=LfS`52N3Lk4T*`o!Vt&->?b@VGl=0!UQyEJpp|IH`{`-f9R`d*Uz
z#ZD9x^*pn^#n(MzR!N3d7ZbHbPRwsP<-BYc_B-`zy`2X{oIe1qD5W#z#~1uPPew1j
zIfJhb0p}vTcrD?*X>y`|Sv#M|_aDXl(qn8ifZ_OoO?&~@|1{SxA~;yHsqbXdGjmWD
zTPOLb`Ki?}&gf~X`{zvpB3f3u43|c8DI+)wO<a{nymzn{@7(vF-^Sa?y-r(uY(=HI
z)-j2%ZS07Ysqo#S8gpmY@Y27YO&SzQNwK22!>jq!$^X6pYr7)8=3~^qOTCxDfLp~Z
z-+lW3eh%=5e62+7zRC5^i3svwJ@LbUaq91wu<2ar>}}!OD9Zb-l!^N`vSmb7x|Ws{
zUgQt$;lIQIzUIR=V##^7-!D^v??oQ~iFpV)%(L@{hxN@XsSqi%gO9UaVkWto=;g=4
zJ?~CWzjUos&EJ3BA7|^RNtkiPra^CXgn>V6a9^_QzM%Uy3C4bES|~ht8io%4wZarb
zxD1RR|I@V%%RmT<{18i?hk{V*zDW~{4aAHtKahw~s9^Qdmz=|nt6$+X+{@WERgm)5
zYFRJ&czUF@uCrl%DV{4i6RdI<9N%?LLcunGE+4wJEq-+_)0Rxd#miK#cojum+R|=|
zW>#o59==wLs&ZdBR8>g14g5A?7?&1&WSfF0G}hYGf%9Xpom)RlOG|6`s~}e!$<nIw
zN{-yp{YV*Oa|Ne~?gOM>wNz$R(GU4N^|LPl5aGF1!RJE&*eK7pco@bExY8lH$FpQu
z;80K)+^rjN0=g-j^VH26R(IGodgLt~MRP^?<FMBV=GJ^$_EED-cIxMCor+W~1aqZu
zU`8$4Hvx;>ktbPb7FLUnlx4%J^1WN8kC+P9O3u)IEvvJ)Z<3m63uD3=Y(6<ATuW|i
zs6?<BKOY!xhWoL5PCLvl7F(FD^<Z{0x;UYZ8=%;NjiYxS{v)(lJ6ix7wEq6B79Rio
z9ac9vAn2i8Kd8aG+p#fWWt6=8AQ2zxCTz7_M~`&a9u10+hIo^GCoeeiNtJE4|90|#
zQJNwan!lz>N;HHBn820Qez?GWC&!ZEaLUU2%2`jPwr&M*J&{xiY&vFDN&J8Bg_{@k
z%$P|hJ`dw__4S`DobW(loI_BSJ0tAr9}MLQWC5g6m|>{b5GFf&>HDGD8+{4Y@rkSu
z+Y4Cmv!{#Oa<0a_3Y?l%^3i9Qa95C@lSEkpLPJ6h`Ufk$v<DkHw5CVEKfo6i7iTy3
z?R!TR4-j3$Gb*XzI#hO^xEZvcs%tv}XF=*@?d3th&5B419g3+w--|fRZI>jDOl)>q
zzsuZc1@Np2+UxPsxVo;`=@TDrA_KfyjgbRo3yZNNCY`@k{$pJI_ma9XqQ(R>r>(xP
zQyZPNcfdvZ1TJ`Ms5JPWu@n^MN+(Dz?$gXsTUJM_Lh%=fjl0)Qm%0De934Nqh9m}z
zph#R(b>nXP%vnS8!b%gHa&jG)hY`iG9BcNEp^oZnoP`fzRbE$L@nn9N`rch${0MM6
z-T7$j%ROY7E7ChwYp^%bQmaO9R<_WgoiaHu{e9*X`r$o{6MNo9u`f|o;Q8fQb_RWX
z6DqS}>C*M#oqqS@`aOqha_;M2#4E3lOogS!$WVD!n+vX7k;zNyosK&|AtzK*22UpK
zt?|@v+DFj~d#awk0)MJB;QKj2wq?~oeEl}kx1&U!-T%W4m@NSBJ>M|I@9R#cp*4+y
z%VlGN%Pf!OzeVmJ%O4q0*r?A6#$xUAPY$x&XSXGVV3pVMc%AB<Pp^C}BxEej6^boj
zs50Eh+jJU<+kco(&COdqoIU67e5-D$L&BqO*yEPq&E0YdI3R3~Ap_!id&o90_CLRK
zS?ieVp6x&k%3U5~VEy07eN)Q&cC=xm`r^pNXK)+IzXBj~>UAaYw+u3u4Fv<%+z{>K
ztk@eNlz;HlOW*H=sG`OZc%}-V-_5ik!B39Y`&!4W=mtgA8XDXB2U`Z5j^syP_JuMl
zkW8pRW}LG~U|IlsO(#@h9dp*HCHX<!DFFk9(jOz=`sy<{MFqt~pN~K#@AW$o<t=s$
zLLkAMdKkzLXFwVfEk?0M1Ma{5AU`|HC58Z`jWm+OmVR)4rf9Vn$B=#Sm#$uv!GVn>
zAzPjMH|*pGWSTuT4f3_e9S{EuI~EjMU;QAh0UX{O{ut0ER96GShvv1<TA*(=#W{k;
zt<S!K2KY<2mt7bJS|b*2ffR$+AAk$Mt_$2_Cm33U2dlThyJPAF;QuAmcyq*8UhHP{
zkL5%lLeKG6E1Y7!6$%su61nuz<yMKGuA*_()*iP#s~c}S6@NR)`#-t?Z4E8KQq0wh
zM|Z+xA_B@7vW-60gcT=Yoqp!HYFg|(xNPBvHwKezb|zmLGpH!Xup&VP!{wW$C8Oi9
zIESrdnK7*GjOZih@Ra=(m8dDK)tGYV5(|_?ue0bMV8jza^%=7332JWU&O0s=BwNAO
zR;k4mIBr2sW3*tbLFUZn^SYJO&m(5T^hnsvG39F&D>`S5+9$4_zQQa+Q}m3L>u5k<
z2)Nv%6hD-?NzaTYrj)MK%hEKv{ba4aHY_4SKV^zsG@g-`CL%CjZ6xgh5}Z#D<D@jh
zjaYyn@lH8K9xI}*YQPeGaz}=;0;D!cFkCRKU-vW3j>Bjid+><LMph%8Y4>rvt}jUm
zTLbFpY!Mk<@umDI&1`=1f{#o9tobQ1-yG7v$c>hSw2MkA7MTDz)d!`qU<Mm>M$^?{
zGd8J{Uyqg<p8UU+3@44lGYKhSS@HTbuD1MB0l2%Euc@H-bMt_Y!9an`Tzti@=UShy
z)y~@CPnbHNkmuR@tA~Ss3iu=2=?)zoVJ5xf-(8%5D|ohs?!`ZAdQ0g-jy4G2vlkeW
zSwP^t&3he#a`aUXu~A?71%Kdv?QIaJvYOw%K%2>Tue1tlHQx^0r9t38^CN&x3_b3(
zlQ!-zc469$BHTxdbH42r>?Y?7uu8HY%HO=!F{+^s{}2KVN#+3zJC*p0j#=-fF57(l
zaWynNuiB_VU?O$gP>yQvI1j^)LAo4)@p=7p?<Og?!hz8yqU1}GHc2?ZZdxeUuwi=Z
zjf(Z-dcWp;>h#&RidWmnnt};y`6VLhZ|A3wJNS^2k!a;zhPdCqn}2Qh;&C;Ye-M*~
z(g?HdZa-H7Zv(>5?|r7@<Hbw;hMO)>yw`W1>2+`v@s_ikrWl*rf^a!g?h+mpkv;%v
z3E4qs;5*e8aUo2Zp7!5LnB<{90jn~AX2At%qw*=HbaZN0|5%q=D@K(jlGwS9Md;%3
z74h6Pdj|S0OL15IvYK2cbF%ik#!jjXba(2o=Ndc6CSs*HEIBntPIZ}ExCE(bGL8PV
zadq6$p$<|O`aF1@1yfoN2ll7GAgTjROWNf|kDq?=JCchD{?7y~{=+W&qYJK~=Oa>e
zY+t`N8GttTl>vs&hoW**<sx$1Ouh`^qfFp=7zi{R**M0`o5};^sEP{)Ms<U(@s~Vr
zCuE@fTQhTWWfj56GYN3klkK!F4?ht;`I-1%T=i^G!yS!j;lN5mNC@ufg1Gs=nYDg+
zN%->Fq~6ylS#v=Ws5-=!+5c23K?%XxaW$x?i8?C8PNItnS6#8k3g1b4RGaIAl9nFK
zuGu!!wGQ;>bD-$aMPLIx4Zz&Sg<uS8)Q{)p7~8Z>0>>*5oi^qk`o-1I*t{~olnKmf
z4}fncOlP51_+YX4XP!&$h}U~wllW!t-_2=0-HiK#M8`_L!O67U-H#}|y>hC^5_V2C
z;KR*}SBXP+1>ny^_M>=-qucLuTom8toQ_&Zb(?rI6*YjHztIS%n`c(c01MuRwVIIw
zyOUM4RNO>>m9-<E6d+pPekk-d*0LIVr2?xK2cE!s8m2ulfvE~WSm^R??n8tsUr6Z0
zab%RF0JXuFO$j{wD{uZ@3efg9?-Po+ZOc~O<~W6QdXJuONXh-!zegp)C@X7Vuh%Hz
z4D~~LpJb6CIQ+g=NnHx$AH)il?sc@Qw!Pn*77F-^DRo6U!`0w#xBZI$>AL>T>B~Eo
z2rMTobXwM#3&Gp9##5oGAvZrk(p3M=p=J{lsr=R3Lw5sBP2!KH4wy0tNB1JUyeny;
zq0C@F@hd4u8%sX3jBixqiO1lg_wS$yhQ|uz2QuZL-BXN(UjZHt)F{-%_DQ{TK^jnE
z-x&7ag3FixZl<g`xTUTfo~IyKSag{6Wd);Di2_j(RfwSBg2->;S^XW&%V09veweyA
z&~W%)|K>B{&CFHz7MEuy84|jiXEI|P?2RH`-F2%Ot6Kp-UnsxIMW5BfziQ1?g-OW-
z^Uj~<4a<A8&dIj2ee>$JQc_SjGPlU!Vw?VCm?6|Mk0%^EY%o@+`P_Y!dv)KUvq)2|
zCjtO`*<-`u?9_@}O}6APB}h=mnoY5K`Dtk-@L;amRaE8<9~fp9kbSe*%{VJnXO$H~
z+YWB0okhN?<bDDiTJ%Uz3JRp7g&KM55qpB6o4|JlDd~-NHN3~%BKOoRgQLWPUORVp
z?;s?Je6C3nUuJo6bf_v%Is)yaDQRAslcNJ2ckG!m;EKml7mj_MT8wNpmjr}(>P{@7
z^aUeWArciGKVEAo*6Jn#DS$o|65oT%k8JU@pvDZe?B>K2`$)c=hSlO}z?*GRn952*
zi1a9FvE-wZQfxd8CXl`H*<fM(c^WS~g<QVW?%8trW23veS*(X^fR}U*9IcE~7QO#p
zRO3J8W>Ge3AsH@PL>|)jxz6^ZhT6s2H`!{%+LJA>Uv~Hv_L^CC<VGnnfZ)BTl?f8B
zUMbc-<`hlX)OhL?IkTSknXj~t=&-g1+|2czKEl{Th%vfEc{3-iRV+)0FX78U)U7H+
z-{#8P;7#9$u!n~iq%9ObO<VfjdXob1Vy~r}{J$7kO5fhSmVmP}6r^(Kp?{o7TEk|W
zz>@JX`H14XH-<_<S^1|w%@pruIVujGfVrGtmhcmO?)o7dQAQ_WcuyHX<?f4LOuJ+n
zX8PPdL`RGN2?N9#E1qWr$qXD(&XkVRH<(M=-_dp_fN?S{O-1DF40Z?G3q{TAOVin_
zI0g)}9$hNmFh1w}i9toC-IE_VS0NP`NssvSW<^Q0XXI%4%1%TyESaL{RggEKRK0l^
z|7_xVb@Vum&`#T;Ck`jHhFwf!`}CTr%C6bko#e^>IQwh5VB0TY9SpcBe+`QwtIM18
z$4uye!*9%W#K^L|aHNu#%geg8p&|1BmumntwQx%tmz|!UHg&N}x1Z2|^S;&P3$JP&
zrp))ITiQLSOvBz6J;B(M>nj_r%hzyhIXZW*j2qJ2FL~bt`L&GQE2J@`Z8e1SyP89c
z=>htIkZ`1~dm;b)fw`8qwe!bF{v&45_couNb5yM$J4HE+yw&UYV%7yf2;Wuw^D^M3
zxtKu??zvq-8%td*t63z>B;F!_8|zW_D&T+VqDNvV=Y<vv>#XtcUy|e=D`bnk2KbSJ
zQ$BO21NJX)3Vrk*e8oUoQ;2d_&Db7a?WM=RRilH8WiM$+(dys2?jOGvTJR$R!}qQ$
zk3a~+TF$$03}$-~RLA08v^Jcf)z}a3-|{-Cz*tXqVFCX({~-?42?w0?ylK#)$K<cE
zz_PqAJ#c>88+-W^XDHjk9j=x;q$DcU{U381Y3e2Vnwh(6^pE^a#NqYU=jBQ4nF@Yt
zoN`2LgDf~6E7+ma&5vIkIS>PkRmYrNRZR^vw~o0<L!_7Hl2kU)y$;qmv%fDLrUpE6
zD99jdBm*jbBCr%B2mdpx-uPsaj)Bd4!~v5~%^_p+;_oLRtwHaK>;l)&CDF)<_R>qy
z>)ID7IzKvLhGIepI7CzWoIbuCcbw1J-hS3dFBRpOx-Ax5N<GOE=7`|1y6<gbG{#As
zICkwI)6*l}xA>0*1RPpEIiG3|=Bxw}#7j>w2M}w!yTuz8hDHzhRemmNhBd@Zpn+#S
zCRuj)MVoX}`@&?s?$p9&xc9n8>$l)^mJoHz3PKsJ9}-froP!c{(}MNS4SJL8WE-8#
zBq%9=A^Ma-V`+hJ$NjImo4idLtR&kU29r%JBn_?*OoSx_$2*yZv7;fFkc-`YPpjue
z0|kS_LBsLl@t*UqEE)bW4A<`}%HAXDZ3x=$I{p*{26tNUa1bY+*xigYsj>oMnEmf9
zg?ka%Mnv1<Z;TZ{PXOG`0MIN}99&L8iO4A-e6fUO9>@<;F;R!m&{9Q9DKP{w3kz!;
z!pqbiT%M8}zH6lkH?}VRPF`dl6k5Wr+1S>pTDap0XirwZOzf+MJvKXgH7lb^<afE?
z+M-n^Ipbm8!)UKrP5%{CN@}p>?x<Q=8ILJ}nOtZROx%0%Yw@`~rcE{MNr7IFb8Ztz
zOMohii|bjI%tej9)Gh2P6i)8RX50V49zd+12hx06CvJl2DCS&JVkqT8Xk({%T@+oS
z+~D@YPi8ahhw!3C9liiE=gOYgf-%+w7+p$<pPD?K^t+i_wLg|mFljCgLy*Kc!vnv$
zhkZ-4gF4inHj5CbVO{*{G7=lkRKX+nJ>ggIe2$UX=HH*o6^l)ufureVSjK&zbm(@E
zadBWv03q%q!jgH}x-X@%rSg?Wn*k@Vcl8($FTXmZ+b1AgSKj9)_DiW*@_Y<SJ#5St
zky394a<%+^agrk|YKV04PnilIRpl}63}GNV>9&)9Zqf;BSZwP(-J%Y9JaW97`VRch
z=5x-I=4~+KRX2N2r_xd;xpD<$EB73?UU|Cjt6kLjR!M|~L#yQbrUslU^85k&rq_A4
zIh5Z5Fd5P13I%#4k~bEN3g6wl|4M9U=<~+8P|a&0OP$GA*Fd|Mz?^BL3`l4pQ71{V
zw$agpqb4!IFk_2#f0NcCdc!Tc<oqh7>?)<YRtAo|I(*NZ2T+E9_{{GkYe4HOpr5X|
z*Vd_W-jDdmpp*IuUqzpef-;}q<ofqq*evwAJ8teC9&{DAPwMn%8sRl(Z0YSU;JVlC
zeBJ*~WE*ty-S9O34rulD%uZM1+}H4O_8sItLR}<f(Pjcp-Wdm?0k-t9t;8UKTcKBa
zgaNzVE80(@F5#*EjuC*Z^}MU0|GO0RfBw~hdo8c?b#s{aB^C-<eqYJfe?JSUYNY#8
z1~DsI>GlF%(ky<F0l?+z<Ns!XKt&(f=`i4otuA9xWM*nUTes|C*a?J)=Hez3rZ%)G
zMs?uoK>*2gtC@R^Oso{MH?n%v3niDnF(4nC|14^<?N9#PO8oy^az7X_+1c8<S+%Si
z6X{C!_G{-<*|DqEL2wC~3SDld2_l&<M^BKgf}Dq&V(`+V2m7_{@$*|7^)3Ax+)Te9
z%pZ#s@Ef~=gnap#>g72cobSe&Yw$15e3$@MS#3}KLr7<Y`H>l?AQV(!jTD9!jq!lV
z*46&au2k$?NOY@@UTF0rlsVth74RX+Sr`1=<HM8RhN=8gvd7kYr%>)W_O7FDxuAQ4
z0!)Av>y(56C*-RK^L|1d9%%>+^rqExbx506goC08Qev%7=qtvz8m{|xbi9zQf3(vp
zP!)6v1%t9Li-)v3+D8^|8B40wNT#@W#R4rh==*SB-b*MM#R@I(IgzLt)XbH8NPMen
z!!*;NLZJf5kX2x=<qXY+XmG2U`}zk1r_ZeCclv16`UfephAOrtYjvS2W_7}BM#q=B
z<xEZZbJD>06xq8cve+H;+O6&#>Uc(wu3c($Idm#L2<uNHGh_)@ork4q&5$9ku(7lC
z{DJ@V-4ybnYgQxZHzH6qxnc(|qpa}_$he1EKbG1Re_dE;0*(W!k!|sGpGv1rP;rHL
z-{**(#(qK5ufz57g)@K{2~@KvCj(0uREB<COZBo3UaOg#;|vgl3X*7_xrs(n6<Tvv
zYmzS^AEG}opxDRf1tz8lJ^Ra-o?yX2h=NT|fJZ*qpZ)W(hjn}5NA0<g45N<*+KoWK
zR^V`GJUf~d9M8*dIXttg(VsiCw$#$6-y<C^3=*MXU?_X8KqM7Vf8Q8H`&t%8?h_se
z)GFY2gv$dR)LBJHV7}uWX}=5!QiFL+*ofdX&FMViChG?crDdwpT`)9_9nrBs)Npqe
z<=6@u8Z7-`H%S=SL4j2WDk68YhII=BiDPP*NyuX22pVTnTt+|<3^=D{f;6Y!VR1t?
z^9wukhk>OH5*V0XKYX^0rBY;M74H5JZHWBFgMGjG3G63<^8+=eu0VNX33zup&GY1`
zc8Zx(@;NeEfSqhg$^#_K6+cl;hG#Vfqj>8<sy|SnFeSa=<9<n74)BzXHl!6cw|c#e
zqA0trs4_rn93te4_N1`!s<5c&FRMYS%CDf27-uUmMyLc?qC1`r&d67yjI5Lqa~@Iy
zDEM0nQ03wdKVnrsuFe})?4=zksX3QExpz^B;4~!V^NfXsF^m>VC$<ar#E|8C@?tMR
zC?t^h(&`AzW4|FfB6<T<0~rXYfc+L>BWKudRVdi_sqNH;6=f&sGfCOBn=+*hv9-XP
zxN!^VmoMhCu#;c@gtTyde+gPMCBJ#Y3BK_^ZY0h5cjm=dDDbx`wrcpshYaW?*gN4N
z8L~VR51F|H5|wo}RnR)uNSY|$Umyg@MNOj4*C#5VXhFylpwlEU>RqcxuT)7j63@kH
zOUyQUla+xGAdoT2Em1<B{|rq_(YSvW1<V7$GDZjv7nfEyO}u$W0FKOdKeZYNR8`BX
zqyHPIFaYA!=`+)A<^;OiUhhvei8P&_W{z&SK4N`NkygOXJW9uckBgrDdI$6$1pRkn
z029x+Bue77`%`5?N|E~tkPIa={aPYjp4DZZppF6aw<-bpZ2>KkF|iJ?G4$W7p%0$^
zjIpQl<BKd1&$r#W@e^hvdCI8F0790oEB40&1SRjKghqTII0^7~XsgoI#udAfgw4Dw
zuDWQ;onY&JGJm<%WUN&Qfz`-$a$LakRh|y)ZJ0i7XEv(k@X3?>6J~4IG&dFf`?t<(
ztUCknobGrD4AqV_m5$ulh;i~wcCPi$>DjdxXPHYnMlk@#lsG{M7}0=RN~0dyK)o`n
z19arDg=J_FHQ9MU7P5D<ruXV9d{3F%!QRTd+&n@E^U*Ks#}9qe$_?Yn4O8Q`(4D8O
zj>ga(STmMv=U)Zf7Y&<e6O}kDgL3uy1~nYI^#Z(NoSx@J&p0&il{NUi%t(e%`8}+Y
zlW%E5Yl`v>G9(u{)6(Pb0jcoixAA|=PCgnxZ{?z(98DSNm#*G=0;a&AMy`kSDUzM(
z?+Hnt)%WIiF1Uug?z?ciuPkdzEheGTZMK)=b77D3iSQ$Twafj0ZyEZTexLXXFAp!G
zv--tEcxuEH+l-UJi)IW9+tkbdHFfF=NXiVII2a6F2W~}PS>_1z{(3~>Qj-CJrI&DW
z{GQnHYi%#W0<OLavh!%5O=_H_eSI*N<WdKqwEzCOXq55E%WA+QZUMW=_B6e$h0nm(
z^VGMM1yn$^8cDW`74r*D%oU6T^~n2mfjbsSZ<58kp*ugR8(!8npSc4r0-hQ1jk<cv
z4`TC=83*b<P|ukwB*OY%iaqz%NZGM2v_9RL2yV6ab?&|>rnbHeerTX8O%vc9dHC+S
z;PJeIA^jeV7ZDgwk3b1#h-43Mz1!dfDD__XSUUeV6d*l>HQ<`z=SxTNJ|mOG@Zs2I
zSAo}3)F*K1-!ZAW)ZWZgt|S)>=(5i*-_YAK-NVq}4{^W)(v<%tCR%ou<aF?}=1&R1
z->i6CuI<46CrnaQ3TFT~JJoflVzG~J4Ru9Rd4Sl(%@bL3c1hYvJ150ek+D%^;J1U2
z8-rZKslw&I0BX#Rm1<Zn-8keD(I9x(DMAb}Cg9@J8@!g>5NQc4kT+`(gy5hn47j)G
zLCjD@XcHmuc<-q~6BuRrS_E5FzEu?6J41h7DfsaptyH*wHj7Y_E!3}{K@G886i*q@
zo1`<XkcNzpDv(YgBf^{iSuHj)CP)OmuWnAH-C1bgb%txJiZ$OOBppG;XFJ2UnZ#0=
zH&@Rs!ko8;<H3=jQ88KLr@0UOO-I`s-~JF0MoUN^s6bsdi!Q|PL@vc00S)(`ABgY{
z4;*e44WbVp4jfKtk)2pAAY2Sj45vqnKp2tNv6zqo7#h&9YcC!E`?Y)y>h^3aGH~2F
ze-FeNK+PfoRSSwVRqHvxhaq;&ov1Z;lZgq;IFLRJR4f-fwdT(-3H%X<aw5R45yY<u
zz{(&A+4|pCOGk1dS!Hr64Drd=%(wXR@){`>d6bA)>t!*_^l7T0(YE>FNCg*LrIi5$
z(>x(^v7hp-IaidIWSaoHs9(~rU9Dsq=f%8n1UPA|tel?w{?^CkR1l(z>A)6ma%a<t
z2ln1yziOwVU~y@?u921A{V)~!$UycR@io@Ib<Nml9bQXWk4lwoehmbBpRNyCWQ2R%
zg?*wKrR=soSs)<GrEfp)ae6R*NDvljO)=>%aG_*>j@6fK-bW4#KJ}r@$z}Z8vS1UN
z$@*~k(Od&6-mv$lRWz2EU3bJpPtb3OoVCc78pV`^@2As8TSemdgkKa@tlP5-%8`#K
z@apL*OQg_9fb$5(bWtmA{F-;3(4_jDa@zcAMHxRq1PsES``VtVtwPi2=!0Qx!ORou
z$g4$JVr4D<=l=IVGM~mnO~(wFdP&l>B}l+ntaCI^tPQwDRY+zAhBshV>#7;jt7U!1
zE~)`^bF`kFj^<z+`Wzwsd-KS(bnjN`jyE=`_-1}mmJxXJU~AW?(^@~W?~T0v+3N=T
zI{Fjd-CAzN2$0O*0opbmU6``OT6#lVD)l?+2Zps{ufk&rhGG15WBq{mKsWwH&$HMY
zk}38hac}_@2WQ64Lpg)5*zVL@U!|>`zNK67ukTWY0561yxG;eRG-s9DyRoArPx)?v
z<UT2#>G(56ez>D(^0nz2NJvaflAAkFtUZ9N|1F9dHdg9b{)De+7SYyM2+%!k{%$q|
zP*YtZNS437rSts-61ID4J6cZ<bU+Du(dW<;cOC*r17to=6v=g@ZwoDnM{fwgJ0OiA
z1JWs2aBcPUkHIc2mB-T7v*QGsM=ZJn?TA}Y$KMkWPR!chsgjRa<Q5Mw{`yk)rZTcF
zbP3t)Ayhm7UXB07`gJhmKcfp^6)qg2`@Lp6_w^3APDEbG-^K2J8JtZ6V#Oy&O<%)+
z=L01On*?*`M*?0aMMw4rY-sy-+u}tR2`kF$s6se<9)eLz8(ou?=Z2-r?pE$kjUB9;
zFI%vq=WH%k&AmHxrD4I_y!*6~z{lRh@JTe3*5!B@W-(U4LHCUL;(Chg0LV`STurph
z!amajyfm6ps@L`nbFxY3xX6<(u>6J`_rF_&Fb1$!1~Avvuq^>3QO_%1PLcXJMPxbW
z==F!U8@A1&x!Z?%HS6O_Py|U@CA;d#)$jClS1QUP=L=w!kZDDS=A`KBxbb9Gj*8KK
z5xSR-!W@j9-X_nFCAX0Bkq<pr19Fcqma(O5rQb7Z;-`wh-rJ~C+0<dO=^4z9`@1*=
zN!{}qc416fd^(#}A}?qpDBFKch`wDt_FOY(d#8%MW!DzNY?5wNo4Vj`)9(+61;hZX
z?0{D7bh$^w4uO+gL<+?>`;z`WH6!n6z_$``_3wdbC|9&MVF=yvZBNnltAYQ&o@Z(b
zQi7@MoVLpJ#yKY)&u77N(SYywM(xr)JI=4K8XGT@K1sC5I73&$Zy|C&u4n_}8BuFH
zy<#^1{U1r!7#&yJwc8|(8YgXRn~l-fwj0}S+}O4nt1%`{8{3}Pp4j-#^Sx{3SJs+I
z=FE+~uYCdX7T&5ln@oi$M?g@#c<gl9L@y>BY;@v!tPi97UE_-ebJeVsYkBpY=l-Z7
z8z5Y=9R?<`FOS_%RC$l%ifp{zmCH|X{|01&Y_J!IxX+xZvBXV%7!*kzoKJ^vfMN)V
zDzPNLq&&Qkme$;?k@O!`I2Q+h<;i#>gR~TNdl*WrvBhlttMhQlO=Ad6glPlpqh4sC
z<iLz077m81G*lZ?Qs40Rh$K3muU|o-i|ISC;ZTQdk!DthnLYoY$$Nj`vLc^T0iL^2
ztg*CMZ1LagexUSf`S|~ij2Cz20oY93&xfbAitf2_R%HOK(<E-9M9c-qK}nz(W+G++
z&qVA51GwXNgaoRg%9Wt*HZjs$&9h*;UrVBLFu(dl(ZtviW5~*2>Ll6A&<98jcDE&b
zq5hQ~X(oKam8~Bh;xtN3g#|kkiLy;m2r%lxa!iwu>r(VR)X9=O?WSPh4wsb0P9a)1
z_Hv$)<YT)heBz;8O+quq){dXv<!{awM_0FgqjK{HeARp6^q-Vbwc}aMKI^lo8Y?Ry
z6n+p_7?zQpD2RfsCz(aba_#+k_B)V)&XnS_x)Q=p0HX);2lcs7u+%R(IUoruAU-i^
zCXPCvCbFm6Bb@z$*{+$8LA5x3^fdF3e<&HE0A7W>0e$1jy!^^MN}$I*OC;(qZ(8B@
z45a|RJXIO2ecG&cYWdWXb<Of~z=y;@$F8<{x@g*c$O4&a5b=*g6F}Z~9#)VAO9PCA
zY+<Rvy%6~x78&daMBEZ;fMg<r7M$JPD5%$R(<`i$Ld+(hO<{8+I-`R1sp6LDwJR>4
zzWf)fg6Glgr>APghO>*lLYFc5v}wP-K-hW)V{<jX9gtuILqx}$vkueKTRXi~>q)?O
z&nrMYq44GLWiqcsX%%cT&Vlu|;2_jn{Mn}C?MnUlmdK_OStCtVyr8-=+xO}Nxd~5f
zUhX!k|NEzPe-E!oUxZ(OSO1~s0*>W?PZLL$FDIPIH(|6X4qWL}Kw8S)%?-$Ga{)qw
z2ouQT_-6&woY%`Rw3<ZyfA7AqsPm_aLkqYR_M%Qio4O060Et^jqBv8Y@S;P`*d*Z}
zK*yGj8#7<bi@mP9_tZoOI0byLl8P}q%J$v<fT{W^*YA#H8Qf^sGAUa4vf|*6I17BC
zpOi_mfUvR@pJ}=IT4lMq#Mk$R`wih{(??(82c9GLnr={s@A|Ec!@%>u571))q8KDi
zFsTJCFs-|6jg|T`_;oAr;)ikSe~R=&uoB(Vu!d7;V4GlsKLnGr{Qc2kwei}P=dpJN
zJoIIus|8>6nv>3ogUWV@hp~bB#>iMw2G=;x#`UXjcUeWxSOWS06(WHUdte34p#)nX
zo40Fleu5rzE#1HgEO6^8sfP?_s0i7P53ka7%ULkW$sW*m-!M1<DO(}7f+0rMK1bMj
zXK-%We&(4p(b8srsI4WF6m)%4j5`;$t{%+*o>H)VS)cOQl4q`kVS1-YE95I+O#z(h
zb8->x;GGw5*^cW0c@$#8y~BuU)Oa%$s-#_EH02sMDGU1)IUy#THktBdb3k+mNV>BC
z5f4L7-6j87NtD$Q|8oz6$<AZDJ#|(SkF!tmk*KKa3K8}sGdq7OxuKlP)fmhj6NLr=
z_27o3t1uPaROb&J-r_AJ{1as0Uf#b&25JW4T2W7obexIHVnrgwYA^Lx0Ah7vCfr+A
zO@dM0#yy8aZ!R{mq-(Z|m-n4I(NM?q@2ks4G7;4dmCZm^Q-%L%(yLu>6_s%*0(nj3
zcd?^arZJ!OxSJ;Y5kMXCF`xUdukb*kb(Ls)$^#}*F0QdVl`>_E!S~9&8C$O<jneMe
z0*bxJjOhLceYpe>3vZ%{tEoRTj=H)O&pt}XP7V;vo7OaJW;fu?T+0&O;_ecZGB3$@
zLM}BDpsJlUE!tb;jB=FSyVWqO=Wh{vY>kZDFP#BNP(Ic7(N$^1YRyL~|C3Xea!iOs
zPg*{f9C4Ix*)}kAg9ZpxL+x0cTp37@tE<Uiimp*alOk41>h++%v#WK)hNUz+vT?Sm
zv_Znk$`CX2l{0C6<KhJp|48R8{}W?{FGXvmp}T~erM4g`GU+i*C6rj)MQW)IZaFLB
zFXd1s(UnOW;d!WzQ-X0{5dpa(flnu4EuwH`c0Ng%hw-Rc)d3%*^*RbweY`>a*TNr<
zGJB4Q9k`9=0vhhvK;N*5O0-|LkoFXnbDG;UHUt<NO&u6vm0x+2rL}S~T2z#tu_o~{
zYbq~1%^!Unl|aBe<pegFzUuA!()F*mztSTV0c2Uy@c&S&{bifziu;z$n!UZl+SOz*
z2d|(9$q6ufr-sbW48rVWGp_%=ekD^LJ-vH;{i|k6_D$pqU8pf>V_%dKI$g6d<_O>~
z79Kto99zZR`2+KlC@ZTvzOI|&oNJs?@=`@m@roE*Pn-Zu1grZtU)gp)QQ!?NUhk4M
zo}}z_%*w+Ib)+a#KSe2acmfTLR^-~XN264^w1^>tiCVr94Xg-FdgQz&Hq~>o$XQdd
z7#%As?YE#Rs%PS%4?vWPF{-3|AwrB)sB0k#6QS#TpPC$-PM6_N!eMw(Rw*l7wfsxr
zk)zEYvQ<R)L)X9xTST_J<#*kAyKQT)SusePU8@EGF~HEwKU`WxKxdTyu;bvL*FbBN
z!{;aVzPW5jDg&?G?8KnN(i7OZET%ncdfL4PBs_WS(Yc?P_#irFz-$hc3~$_CaV?X^
zu$Lutov(2I5_4mjX5boQKL6koQpyZ>voM<2Yd2_x=qxtO%34fW4oyPM+HQp~&wRB1
zx<@~6G469D+0Z_L#Nf3nui&6!Y@roh%ukSFfXFr^O+gnhESLaJf$|Kp5hlMF5sC#S
zpk^fdX;ya4#c9RS)|jbJFi4To%<XKP95D<vs1WV+a0q{vD$4{}O=ZaH@CcQx&*o>3
zu(#yEXS&rX)$E~vE*@$1iBz?q!pUP`1AJWEHWFVk58EWHxMg{5W{)0BU8ED8+V^J8
z9){V)HKmFf2B@y0qxT&NOctji<OZlx*mz#&D3<@ox1TAm+s@cirhYh*Q-Sh320~Oz
z5rKx_KD$HS!fpnXpc<N=e?k|U5*$*#QgyT7Iv`Raf5q11w($KsuSwFe{KV~i_;xDX
zuKm<)QTDQXBp;Tw2>d{){iE+jwVbaC@Y{M5PmZVqSO!K8?>;xS;mlD!K%)o2!yya)
zE1j|XnbsT?)#VyUBN+WwZKy3eBKEJ;T3TvWqud^A&{c=1i+J1JH<-pJKxtJa^r!t4
zNFcthXx{a*^EX!nqf@(JPP1g?(cOgGOq$xaz3MNxkrjZ{>QN+eMk%v0O#`s7X7P6c
zY$|{b1n|39UR{e&Seu%1O&KnSYLdyiU(c{GD<4VuJZj4JwLChcx?G@20>kvkn{>^-
zfPoV!X2#Kc(xcq$1PR#!c!$5J8SP!U1cS}Bl(?f5-}DsW+Xio|9c>F2^SbyX!s??@
z%<lE<`S^wUZbf85utKtfI-@qq(4Yp{92tW0MSiALA+h}Z*B78fu-QdI>AF_LUS)F}
ziw(fYW@c5fX4dT(C~#ln3YnSzD(Ldx@0EJ(Ut1{M7O{K2JoXZJpDQ^~X;BJg?!3PU
zy+Pc+5lyDfm`2jRp}s@9*X{#XRyg6YzFqP^$GpERJ`*mKWA4Zi5g#lwXG?dWfBA>)
zcdN=L^Mk}I-@)$s)IxzOuN+Zhq|aH-?@Z`TcIsr8!0Qf;O+n4=RsYcA7e?ZcOvcO8
z`z<pyp-SB>O(%!JW{RQb+XAaCUpyn*Nl2b|3B=p|s<<%Q^AbMqHL8X}FbNew8E4kY
z8vy3Da+!td8|Pm|!u!&WmZp{M^^=Fa7*l3mHz3%l#V-4ERch0A%~_}&XKRk29WRV@
zc|zIMkKV#!5k1cI^V|t0_FnMzua!3(nmc!L4z0THBe{KS$sa%GoV=2xW*bmApe9Uv
zC`5)E@M(AcJwwf@thx?%`WrDeOCz#2jq<lhpxtC6u{-jO`in!3n?tdrWv1LpSR#gb
z|7rpYW3zHl{k_mMxFN^R{<#Z<C8LEfmw3wB+vlD-4U@QOm<*z?2lz_8X>R=VG7JhC
z40P`t?O&``g=qgox;Wfg;(h!RgND%R`F4f4Q@ETPB09;e1|J!MMWSV(3wa!;bJZj6
zP7~}FH;9Wd%`jwWXw)f;Kasz1^P%fh`m@)BXN0B9P^6{r0MIk3W25U0>{Y6prHkd9
zwee>Oj<tLFdEAV7O)mHHghsLb&uL9-h{*!--uGR6&hRIxy1Z5Hq${dC9@nH;Nii@0
zLzfcn*Ev(6Pp=B#$1MN*(IKsZvUZ32n`LQ*+zcuH#orEvP@o}p;Tel%vWdH2CA5~A
z!v|fiZ9=UrC+^<9S!ak(s6;h@77almJ9qQ5A<rzeL9@cZgfG}-@oovyj%m_v#0+(9
z0P+B42Y8d6o;aj1i#64kD~dIgUGZ%rfc0HzUQTPJ|Mu6bek}i2uCBkJ_Y3{E(~aDn
zd%tI7TkwykDYRa4?HQ{m?${%D-^^R4Yc8$?sa)?%mb}LvTHs*fYsS7;X=d)|4hG+P
z@0x6n@_6_r0Zcst*=jw#d}W9VBZx%~S$|QgSUyyOZH!>0o$TPE4jrK1U4?wvx3`@t
zqn17c3~F-y++nGkx;-|SeXhL}@^XyriU*3XM?0SP2{xW5yqq7gOm@7si88d-Y?Wz2
zTH4jlcgwi3xi~vZ!>q{yr{Tcq?Xw?M+Tv=Ik+rz+`2N-laXuVkX$T9$3>0Ai{`Xiy
zViV(vzb?!~Z6<8DVF=hYHJ9rtW(HnAQw!NqK|R(1A9FbbUpx*!D8f|GrRUOZ!=ZES
zb3G2*EP6qDFydhpUE2gL6ckwM!usBJLaSmkDk2F9Rj03yR6&du>FwiBQE!T7Y26Nk
zci0zI?haKhlYm&q4$KKj9cUq3A>@UsC^&CL1;5js_l^Q-jCy%{t@11K_xVW?&qv`K
z+Mi%R*f8rhgMQ2*)34S3Lg1w{&vQ2*!-q2-%>?0J=k3-+=Sr%0)M`iz7#Sl17Atzo
zU<nbp;7bl)(UQQ7Cn@01qLfIug<=Af+Y4Ri3kzq@$!NbeEfKbmhF{I-Q8K5z&DK2(
zJcI@xi~@<pfKT(79aLRDrtrn8S+C+UHEb!TvzCZ@H5O1;f8!lLPg+ljLze01D9PV?
zA{9p4f+NjH4ymsE^M~sRQ@5fZUIv$d&u0{y8=lNn->h&|Mnx~=@6<P{!E3B5S_1H2
zH)z*R8B$36_!7VG&qUWa4t_VEXqw33TOTuafyq8bXSN)+JWF0{jAW7)fh8U94>j9_
zuPMH+*!Ilt?M*pVc_UrTF3d~o)ZRGYm8zQCS|=gM-ZOIAGmEhL7vS2d>(G*b7j8c?
z(!m47<B|PXq4{Sg>2tX&kc<NhR{5Cw4gI1u=c7h})csMur!KbC-6+}_+^9n80h(07
zGP<aqboWu9oa0e!-vi<pjL>$xKGMso>o8)|QUYt7Hcgj-SzSr}i@I#Cs6}4ZGIl;U
ze_}ECQu*7b4S=A<ixp`FbO<;l%@7;5oVxUErmI^+zud=G`BZFrPkX7R)dFqE9iN=;
z?)#iv0{NgsdIsa!$xDd}mFldx!P_n?P!_Cq)G1URIlms`Ra8(^$f+9{7ieC!*K`Vc
zhMNrcSf|J^BG_jbmQy61H1tNNp3ARs|NQ_*2rc3i@cgTSZcHJqY#x|wja546QNxo1
zSOF$}=s?X&NLu;}8hWHiKt*^Llu`E*9o+I&+Y+7ONyODp@YnDzUex%TBoa{c#TW5Y
znHjr``_bIRY^9&05cWV%dSpl07#bMqA0zq;8wNiqy^HH~gD$H~z#{&b1qbs@@=cC4
zgfnLci3S<l8V<%F&XAU3q9wuSuB^%NuiIs524KDtjb5{@72Y$zRh&(lHVh4I%}m2^
zEmiNu=)^}9(lMlKwo&hqU<dh28FXrQJoC)G?rmjpLWB;U`-6)AOeG2l{Gc8pF-*|<
zZihgVQFz~^sGC>Z*ayD!TX-!afhTJ-_+B1Qc9t%uh^4Jlweu9AxRpeK^*l-H6{U2_
zxkg>jOe~4?Wftj+N9d8%Z}4raqgOGp0lQ!#Iq;h3y=MwT0$EOa#{I9O-&HVp1rv+4
zXyTpaV5V$a#hm2o;;GV_xj6*p{DrWZANTg^-G!oIJ%9hmJTqI-g&e;%sGkesbl?7w
z_oD-^7p@-o`DjfG`Cm4>G~ad|zjE2m25(^4IlNCpl24VM?$sjhuO|pL*Yhh7*~3Cx
z{LH@0&H?jgQELKTei0`cmqq6TFbIe>;D3EV8dQii;-mWPl9lc65OHPxdGS`c$-vWK
zWqWGc2ry~S_Oo`@ME%DSdDtl6_tZ<zah#*CBZpO5N&ii&^)>?y3Orp$n3VVYwEir>
zpBS$eYXS%ht54Y3IRDMLBCILhQ$j7#J##YV7``lg1_0urX9&~9x$gCxjh%H0XJlrw
z(ZMxsq^K3(cAo8Hop?Fi(^c(6ZDz~|oA)s0G*F7z2xbCGuDyObCxXHgJfM92oo3+I
z?IF)VSr@I`$LMg?dB^NUz53Ih&ZAap8MP>x;g4D?FX*3#zk5c4N^0E}gQR)rJz>Qa
zi>)6l&Zg7%Ayi$B=MQjDx`a+ZQ^1*|aB~;CkgAwpU4Ab&C4gZ2$-Kots(nY9uE^tI
zWequyc-zg_;CY=g)!yFu_LXvl5gW8)l8&daV(ilfM6RK*x|ybnQV(kB{&C)_;^}%1
zgUnQTa9__D8N8e#<i6k3q1txOA6~`1H30sLtrAVEyAP_WV+8nn%&*>gYiT1&GQ&cT
z%x~eN5XPCZ#tcE;v3$&(m+kIrgsb+k68kDlan`lw!4#J$fV7~cUslUzSTgHw^{vhK
zTb>mzH*S&->v)3dPPD=o&o}l#Orcb7HDN#|1qti8Eu{a$sNU*i6rxisUb=VpVwIR^
zPi<zz2P?Yc6*}mG6nDV$`ofTr9hAiBL5Wq!QlNZxvE$IKShZSUU{}|yR;UiCuTv@1
zhHSbe1rMt&6mTT2UAMj7`oAAM^rb0K?-{|p05%J3sehR5>p2bg&j9n=y(hf+7}#-Z
zd|~DvW;CKydD|DuRw#Kn`%|j3yXW~XD8oN|_6B%QuCqFxUqAnuuu}rt&irY{2#Kvu
z7+L1V%{l@KP(osht0kO<QfgLIsfgnbsIe^YkDdMx7JC1M2fvQzowvR)zg96{$8_I*
zDT$3UIxSQ~KEyA2KRv_e$YiR<jvwXSW#eSd&5`i`bzc#U>Cn{_!UniQB)q>7zpz7b
zksv}&!B2Cg3KwGs3fI_g=bE&qv#Oo}uSR^h2lk%_roA!6L22Qk%08oT8Wa=(1>uB6
zCW$Rs4}a|LVZc>uU?-tPGlG7#Mf~J6dImjhqstMx7@4RmXJpXXcC&yFvsVpm#V?~H
zoDu~qe#MgX67JNU3)NWwU>?iOJ=HGYZ*`0rM6NlRwQ|?)sF(3=7#@jn%S`z?Zk;7j
zobl4Rg%JX<+A*J$*+?tP4?{yMXb($bbJ*%;zdmj;XpB&3jwlg~CNY*|@Uq6HusOM3
z_7QDv8QJvI&%2gu=tyNGdx2wx>C6&jHgtb4E$mtVtqyz}MVVDQc5y*?--)8ClZtsw
zutBFCAFB~gLz`av!IY3VdJ+5A;{48Dg=SC#rAF=9t{*d&>ivz+GH+Tg{$|@p`$g)=
zM5liX=5s`KWhZ#eCcjUPyEbZ6sK9qY;TjFHSOcIQ4)ICsZfprtzWalG&*Ih*Mb4TF
z<1H3)jaX9l&I5PA`PStOIko*8lK4*Lj)ijns{m?oGEn(W##wrF?5-%OM|#1T<t6R8
zbq8UGA!Qu-6%T)aCJ;lyiiBRpZpI+JxB1~cl~4q8oL-_}pNC+l%iK5eGpPRrU(d%P
zH|3Fyi@9dT%ByAVL+@OzDpi#Pc0PROEsFbysY&s`lXFUl%?ZZ|p#;@uSDkix^=%q+
zx4NDyy^QgB-i$w@R2DAGsvq$y-M-d1C}}(VzMFYEpQ~HOI~_CBw{U5i*z>^F(yahC
zgo$0b3}|QCs_iwc+vtd!Hc4)s^g^^EOFp}?|IjpW>yrOi5Ppw46~=GLrf{Gibf9fm
z&gyR#Bhe%eI@|L4Sa5)DRVpVp`dh<FdD&9Qz$SizCt6|GX{Nohuek%GrmI^F*n!HB
z+E$gpGtWl6HNu02HOHg7u{lVnMsH^+WXq`c9!kT(e#*+-$z$12U6bc&3@Nm@@Q9E2
zzDg&{ylK3ctGdD2Bxlq?&%(|x>1V5S`}#+WFE-8TR4EOYdU^KXVs(fk!1!Ye;aHx@
z;j`4Gi<4*)2iD<#F9gu1QHS*(zIAeiGX?4=ziED3<0%aEDCoLoGR4Sbt^5pP38#rR
z#m!|XutXJ{N>RahB3(-zjk(9ZN9wJep;|W1oblX>K+9rFwPn(@<Z7E+!1rbn;!rpB
ztPi(8zCTO5H3};!hZm1`m-|Ihuy!lWCovPz4gK%B7EMwbv2F1Za3%Ts`BFcRCH#Vy
z2*?5P{CE;&R^81Pw|IHq0SmrGv2nrgc;6W<x{hP|@NZbBs2+uUR`ifhq+l1C_RzgI
zb){3=&Sht{M|63A?Z*-?zz%Lzf%Vpf?{^np_j_V(D=FA8OO#XZua+(Y?Fdhr050f+
zc~9m+8dbd`w{9c!>Zvs~4bCn(=1uZ$Rk4egPm5$ySn9%DuCA(uZ5q@$9z$`aM;!W*
z<UA|4C>bJc_g>XPR*hg7ebC;FRU3o8cIytG(!9F4qWllu{lIjb#LkL%_fApJ*)$E8
z)nfbHC@8$I>5&civNSqHD^~_QeA^h)Xyg*(3x7l@sZHGkE6pJxkFwUOz%CoZj<OD8
zsq9MDn_kh<*?h~6mZ!_>8P>u{6{dpxSb{AvJ5>rpaeQB*15fS|IzP5kTSDM;4K`8R
zs*0@Xl@$eL_{ZFvC-yX!rh7xtphh`sZJ+YJQSmdC9Mz!ZmGAAS(MQ7F50$UM=@qf7
zOqAV{@T5}9RJ8b!-V|*cv05@@xXO1r9KB4R$omHyWx4)_!TeVUemuu?!fL2fIk4E^
zne2X}-YC_EVBF1p);$bGUu%{$>-<;j@fFyE<3H1AqG@WrUA$hP==#^k*X@Gd!XQrP
zP58Fe3y@5~Wjk+IFwx#EEU<M8@bQEmXYU_Fx~~w0?$Zp&Qkw2>s3Qx)kIj<+?^^K7
zkwdp|t0dJ~y@eP$j33-#ZJi2q;_}$f;_(b@^9;c@zI>bq^d{#hV*h6WsP~2D9d2C9
z{^_bjdv*1@;=ii%)Ywc=N*lIUHSbwM+cQ~QEl&1t(EgLDY%d#r_d=$oZDP%hE}_o@
z&ru!EL7!jVgq~2EVg{;*mq}~u)Qn6J>~jsb2fOcKLyNDgy6>;EeE<;SrT75S=I=z{
zayehw@k9-|>h!;5&rDe$OqG)o4Ctq?{9aJvb$4CLb9<%Sb$j0xnpDU72QDwaDot0<
z-vg)*YF-zEy;uFi08`$X#oVnE|DDfr1k3FNk48WMl;4fR`clbZJKy6C@E5<m^}OF5
z;AGO}`@qPJL9ipyvUzzW+D{sk?b&#<DbwnR%WH5cV7eD?wcF}t>^lDqsDz~8pUjQQ
zr&d?1=vS(OEzusfx{`7nat(L)AH}<_nf+g+qGlDlT$9=JxCd(9;JU?}7`k^HjIavf
z1Mkp$Z3{`Zw<{MP6yHYt`wMeZGPv1BH2u#Se6Fzb4u)pg;~J|5KZ4HcJk3&wU$Yil
zZ&todyq{V-%bz(B6|zuWh*(|)vXIDY(njxdUq|fl-<I$AyfOR#vSsxhWE(E7tkm;*
zrg~p{zsy7b)Gj2+9>VcHE%e6sUj^`Tk#j~uguP8OaPp+*^NPo{VYplB|L`?yRDA(^
z<Q1Xz^}7TDE3W7BX*WWx>epqJOiX41b659ti*Cov2=c<{ag;)9=)LI=(EPRpGRQ78
zw_8X;2xemJhgS-Au_+2MI~lAua2E~0EJ89S4iat>0N0Z`Ddyn!4n6Qje7n5BEi-4o
z@m95%h;d+EpeB1@JJIEuzEwxipTLk=4HyzvNu*_^X_o)t@&fD<F&*MqXlVt*WynZj
zcGxM8=Q(rnl?W!3@W$CV_4^buOzSyC(4`Qneu|uq>uZ~s<^MW>RpZjt^Kyvrp&h60
z@(H~mVvj!y9lZx|5T-76#li*QS+!6JmuxSq)NLhLYCE9jRL0rzCOs>W1s-_4Qc3;#
zZ|xK3?F?F!9GrF&{E{kmR=&QCw{9PHWzD;(vgTH2`vh45N~*uZ7Nw6@hMxH~?roR~
zLPF0&(vh7c#leh_KVUR*)-2gCr;YQ}SbXD5kk<z`2mgD12;j3@_0vL=&55f|IT`}n
z@#L^!<eMLDgipZBE^XCO>*60^Ufh50fAEdz?UXKUy(QKg?$bFTIMQUFnQ5z8-<06`
z$f0W}q10kJ8jevr<!>tUA(8BQFUj@v_q%z$XD4c}?RM`En{W|s{a^?)8Vq`@Nv)F=
z?x%mHhP=Nn<HHw#rNN-DYvNK4IL6$iblQUp^&y+>AJ>{?K}Xx|f@c!gH7A&`&(xS6
zo9O-^T^X?e3Gm+Wwz+>jMI@zYD^}P*6lzUp6({6CZ`DTkxx*iYZJUM)iR`~wKZCyh
zUMI1k`RzVzQ;dYOyujwAxRG4L%=Qfa;<8pnEiY*JCc??!F~mapKvio(Aw|WlP}r;~
zHhPCoP!i;ml}7<&XdsC&0aW~^EFg303=co*3tpD|!dK4AmG#1ISjq?c@13jLS6N&@
zc{ehCkDbmdI59SiAo!kUNUFND=4T%85e2b%9o<3mK<ku(!iW5@{^(nVYh<(zk077(
zFPm|<YR<)r?cb%1Q9Mam#xqRu>;xKXc-Z)(jZkSMvG8VnTXXPXDxw^sX+Nj7By6C?
z;VGsN^(3kYs2g^oS9k!a0hk`LZAoRdR)E`b7&#K2VMO&!P6EWOnPbsk#lEq=dre-N
zUi%p<T5OAWG`({C8)qlg^%+|v+M$RUulh0dw1cO7Tf$_w_D^UbM1<{l?8vZ$zapj4
zOo@J$;|_%gpH$~B3*(dRullFi$3R@I(<{Gm-4S-ul_at!6xgiyEJO8245IoKfRqAb
zTB{JIFqPi1l28`)oQjR@su6;;Ec!Vh<hb^Qv)4S8m2a?7m8@96XZ{e_tnjeG+aK;@
zSnkk8gumd`MPrid;^xDD`4Xe6vExWDd$TaP>!4fGN{1-(UQ=+-HT;i)CWxd6=&<e-
ztLwYedhbQD8>RD;w~o@{SiF6b%X>uuhB+i8dGQ!1)oid+y`Bd(Ba9<T${*|l_V^!F
zexEJL6cJ{O&Dy({Yl7v7@XYrQ;RkawDKzDj35E-3q;>4Qn*NQC(g*xjmWQ1=D;d2S
zmuK1oXu3B}OF>Gm?Sha__n>0@EZ`n{RLM*jhGO>Fhrw*1L@Y+qn6zvI-z6sQS%-}t
zeAVix`#0d6vs_pht?<=-tqTomZHflP;^ElP$7yh5;VV5nsg^bkK>xg4ChdB`HfSj|
z?FfR$?Vsb!!WwJ`jdbGaPrUE4VH<Rgq=4+#!FQ%?7ae!!1UVXj^-kfgjMY`|G9jsO
z7rqkM^5O}!VRrt4F}k>LZgP+hsAJX+XY5+#^0I%px<6E#EkGlo1*5N3Pxd%}p`{Ef
zm1U?|IBFBD;rEAsB@L;!Wl(RqXsBG}2S}R@!z(XT<JO;Rc7%cpJ?kA`143?fghG~3
zMX>&fQewd^5jRWmfRfPWA+Nh^i|ZLXRgjK%C218}O8Y?zV2=UCTC!#Zf%hHSY$+9v
zP%?#bCHQ4pXPz_0`8onK)T2iOCkK3I$;GSZ_sYAto^wF$e?b-K;ju9z3DEY#b(H;$
z&j!5zGik7zU-8*KnM_#jJh{>$F^i@U`Ar5ZXvbFz7Pw=nB0didT9{0rFkQV};Du-$
z)T!mTfhOkn=`5~i3FPChoR8o~*XSS%`@khYVe*TctV&xeGPV#mxswXA_|+-|A%7_b
zV|!Wy8BaLu8)%|(&t|D2kP3^l0~T1kMI1>T2?dxxUp#jZdo@y>_!O5NjLLb92v}{+
zq^)3O*XXd1WjhR7C#G*`c-E*KioVN`(Pr2<)Gw7gwzfu6VKInHq9ewd|DeMg|1I0E
zNN25+FUxg9n}JJ)du?Es&}d(PkkWbwTT-FQp`zBw=|$de5vo|fQgv<Mo1ih(A4lH7
z-KUXMXFz_)vbesRbIflgP`A0{h~J_dK&2M?hr_I<zjy$Vehn{YXvf(kr1>l#@n3oh
z^naTP?(_dccOo><OrQy)O4`tIrw=bn7R7vu!vtnS1eD=PXvm_hmt<)qcb6u4Qm`;H
zl9;dwNZQw_I1ME@?4_2WZZJP8Q0k)NRkkgUpwq;D-oBbucXjuT_=LDK7hlVEzd%s~
zE&i;bFXEb#^0y|*C=n;_-qTA~ycEv&!}qsm27`?smjeTVXVK6;$CVadkJqIS^b}SD
znYqAthEn=!owr$!wSTM*UGQ>`{RJ3Rp|)Hs@XNXYkzncwz3`y+`ww6b=<1GcsrI9S
z3dFp}$A)a5pP7?BXAIVp6b3Xmvn7KTGJSQskCOz7yvNFNbS7u?Mf*F!fay_NvqV?g
z8_3Zs<m6!gG06Yr;1y%%x&O&0W8=-?9cPx4#WrZTu<-TzeOAaPN*3^20oHFE1QvBJ
z7JRAI($SOm$}D8Qb%ppoA@s11LfrTfb}6<RU&+Run?s*$FFjk3Qvyd?W8uWNc%>Jo
zOkW7}*W)dXSQRXHio4BnT!}Au3e53#R7H`nXAUz*^17W;Se`5iz+uQv3`ZR8FPnzl
zBdC7Q>eXHBlAt|7mHy)7+B&WLuI1ekU9N{m|NGCr&j_8R7y5=Y4ZI+yA1QfV__dB!
z8F_D8x-X|2UA@QSZXL042TyPk0|H*Q$=Kaj91EC!d7qp<ai#aN#ui4LVy>kHg)@FS
zS*uVdvIK*?EC&+AXcQL|EVy8t#MT^Uk$3}k9f)3`WOERORyxLt^eL*eJJdU+mu(Vf
z3A<Py`BSZx0Ba@B9X1Db`>WfC1Fiex7UjR75(DGDk-BqEPY~x|x6T7@9s}VCdRk&l
zY|dW!3s%$_;-aq2%kql19PcN!{M!8mo|LRj7jkM~(Yxjs&?2@?DFtsH4CI*)jVYn(
z5uBx3_C|^71dgIEGAFPTycN!F9Ksa=_tC74b750#Ibd=s{&siCJbTd&Y}pNcAw~L|
zso;^i8=PK^(0+vstI{EC35DzSC<i6fHa+`4^~VbcJK=_WFWLn2KYDGhX2<C}RC9J_
zMX7(fv0YS^r=`0hGPu*}l`&tg-Cn;q#QG%|u}763W>+#RUGu#>ZB526FmU7}$>hOt
z$K#;=2SHFIDlAbYlV-9E9ect2Qi27DY+Tk2M^&U~rZ)se1ZczIIMNK{WVpswD2TsE
zP%Oic>5PLkmOfCl8ACyd(;P+ymROc;Z|YS84Ua4r7s3mgIQn79#7%;cd0dQf=@@D<
ztAp1S!beF3#m!dI&x>5SQ|l1aW|IID3dGL#^w3J{L~9EjUQrV-nZj?W2O~h8(XcK*
zv;Q+FRsim*Gu98QuTRBT=ShE&mC<)FVE^~{p`g`}mdb|hj1>i9e-?z<`Efj}5kDgC
zAczE!d?f}YN>c+TlYxbkPmDko7{J`ReAe^!AgXEiIP6=8ODH2-+~=G|2KwNT0y?;!
zUH^a}IMqcd9xD7j&Yal6RpSgT8E4#fhx&IGG+0vm!CsFbUtL(Abdq2oT<RCgF=b{w
zfE9i~jb;@0s$AbXgXA2{oGfa$wWad6d)#9CwS*T^=#}9uw7v|u#V6)RKrI{NQQOQ`
zxLKxx;X<>)zmgNLWKu?~V-~x8V`Xa$E$r-rH0<6Nh~fyKTt&%+vQ4%RE%S<eRp1K|
z8Q=Bg><Hu^4>2Qk?==z`2nzA>*c33L)#X2uhWE4(Z>#IqkYfQ&^Y0_PNWcMb*=Y6p
zN#PGZpuKXA?h^Q`!RM6yqObg^J`JPF8c{i&qEVL?n$Ijhix+TO)UE>HwmKCF5&r&R
zcQr;_(csP>B;u`2d71eFR|oZEFrgLs@F7YAW1!LGS1Lb(L@t7v%zhw`DmC$sebO|e
zN@hp};Ly@nvRH)ISpH;3=NHv_M^!adc<x~dYfnai{u?o*(L7;+u|89N-H`<=#(fig
zxFxNPp;kSpAc3lI*%I{WZn+|`{P-}kO*DRcko0Uw6dg)+dI)zS_Aje|)DW*E`_z}1
zXme62e&kM?BK*f9_0OvFjvSckG&qq88Xi9nC=0#<f0}W`AStWrHuq|#82=Hpf=*{O
zPFARE>e`OoRxpJk00X5zUF&TvEjle_0}$uE0-$4pdZ&;s@`10yelDM|=}^p0Wn~s8
zGUEH@Akppbk^X(YfFG;bBI=20@l0a|B8?<fl!VxygvV=??kiiIKnLSAQz3!*Iz@9F
zUr{Qac9|EeKF*K$WY9yHF+$PX$`i)<2)wO-?O0GlTB?DHXwLJpf%>BDqr=<9)y~S9
zcPN^%VLk;oO)@ZI86!p~?B1X|@ZggYgrZp7o1z#&{D%&#0oUKp<Rd4@)>+c6|IQG@
z!F=*T|ITvIC0Vng%<%TUvL$xBl^$^47s`rF_u|HnXgMD>*|gZjrFGxgCdzcEZRJ3y
zp*O>h<eOaGQZ$;zpG0ugRpEe(vz;ud+0ix#sG*k18a)qsFd9_F2SOVxD}Is)*r4K>
zGF%3QH#sMfL@EV;S5NLF+JWY$u<g8t5;Aou?{Rn&dJl-{M{J7eOj;+t^Mf%MI@$0`
z11=bgyK-7{MTJdM+X@>1Y?>#0TUNx=Jvduwzt;1+hJC+!zkG&S4|<jrv<1`%In6j(
zgxgCE4Q2OJi!03M?qee1g#I4ApXhRg$ZWcT^J5)!?QL{D9Be94oAa)HyutTR_s{)z
zeg)B#!0@730Lb{&cZ7e12b~#}0ucb4?!FuX<s5C7Z)6qK&JSZ0<$r>zX*~6bK}nuF
zWSDIAv#tQNw@!xTefH3a;XOMO(E~q;40PClY4+n;R<zt#+#K43dG(bTrnHT=;px&+
z+)M_F``^S{9=<Bt_@ppEZziufjr64k^Y;;5M#0_G+`Y%I5}Mtgy9Q`sFVk0iFl?mD
zUHq9PrX{VbTK^W1LdTIZm8OG5ggxNR#O56uj=lj=2I)2qSA+Brz<xD=J##!hLmZP%
zB@mr2s`!}XuUe9`DKkohnS)OmMX=s<2Ny({>#F>j&^c6eU5*mcps%34E@f1KM=}*0
zS$-VMMiy<N^iPR{L0wW+4N1IL16eH}Z8*Jt(X?21$J{$;L-!}9zVtw~mw@>25RhD)
z`7b<2T$2L}rlf*;=YWP^X>ty@^O<w`McMy`0UgN&8Q}K!9TQI-ASN&MDajWBY&ZFJ
z8s)o1r$VMMRq6}lv`oW&YgeKO3Mz^C<S9B4d4ouJ5nPee0{BlML3<}EVB7j;CDK@m
z41k=Nw6j#+X%VNUZnQmx)}LUDVSR;zbVN*jnk-G1gEo58kyk*|_3hdlPOJGJ0MhiN
z+<$HLvPuE^iLw-3S3V-@2?bU`UE`;rArj<EB6M-q%IhqkZXbFU>P(~<uU>enz##o$
zY98)7k<XH;xPU<Zm5FiIs?9ZXO#rNw1ExSC8<AD#Or!sAkI*n{3jKy<Wz12VFnSq+
z2k42j-vHwpV4`Eg#TDLTIT;uQ`P6a!`uV}WmK+}FVw**kVJ34kdQiz;NP3!G<#u|{
z!k)PEX%J(}XH!`dun2PKl!v%cQ{>dtLxAJm@MT_c+wIjfV8a>Vg(XAl*t1i(TXr)9
z#?R9c%RKI*icHsYmeAgRcSKiLEC}@^9-J`3Q{;lux`k9?w`odf%8=kBSGos`<l5xZ
zu4KN{>}(_qMHHmFclJVFK>lMchCd@~URMs5^v=<<;mSTY2paAm^Km^Uy+6W@8S1TT
zUfp(){AF?D(C?R_{4dlECRtqAb<%9kePnleGVi|+Jwkps3otl6h5A3I9l<UpP~68<
zW7XbhN8T;M@6Z|P6|cMsGQJb6ZBkWM`N!tRLd7=-N>4n&kX#ggp<5H8jJEEpmu2wf
zXbLD-NCXK*<x@$wAwx<zRyFHxdZlo;BxS{%;7DBu*x#8d5<iwJANk=k>yd<yNQqFe
zHoGIqW>H!AW`^F=**gZM2hddSNa8O&vBKaHzC+ROFj!sV+P<<Fw2VkRgIMRC)F@-{
zC#ausJaDDo=~6kP(D<l{@#i_Q4Z9VZ(?z&A*58l*+ou4|oWx8h!R5x(=@cX<C|(j@
z&}KlLqj<ZB9iW5-K+gb3s1+MgKqvi8!RG{b&->$E3f|(n?(Ys2@+8H4T)MXEz{5|Z
z>fl}PK(DE+u}i3ZCdLLIlN|R>0E?RW<2Hn)0xv%Gr?F0z%6$c3hh6pJDgd3N`l8aj
zq|hFwYy_2B7tbTVdrh`y4=tMPa9Iv;@g*f1;-U|QOH7Gl(^0aIho?}cCeoG;EmG&2
z^h`kiM))F5^T*w0?uFBP9wYpjffKk2ffj7#v+6QNt<R6=+LHrsVN5!5^Vo{Dk}qvO
zHpi4#q0j;AmG!zu8dkT>{-s}GZV*OD)-5t$09Zj73BLd1`DYP$0!DE(xK{w^ETH8T
zp^ynpPW`8>%B_=Wu0@?pnrcm+P$tqJ=lk85mNOwb!ZiFag(oXgS}dB5L+$c+c{M7w
z6V@znFq&FK7+GP3vK>CHQ^JYBtKfd-OG(C%y!wF}Z|boB?Sfnc$PW|Qrg@Yb0ApHy
zq%GH6aa~!j>S{{vdzPC0CYK{hJpk<AKa3idYJ7m>Zgu657C>24lkcxbmXjTHMpBa(
zUi%8e_7{${__Xq=x|>VUw;=);&SM4U)JdD!q2y$c>5j1Qr@$})uP&fd)3Eu&oP5;0
z+K#f@&X~3$5p>(n23%Z#cygRjtjPX2z4_miSm29e>T;E~pJ<_heSKXr#afDHMGN73
zwVk+f-&NB$35!sob!og!@{n4tzyxV+c=6xmh`GcVx7C$l#oGYqxi|u<#AKCyx+x`f
z{ZI3~o(30(tEyr$dz@pf7S3?O1P@KcuY!PT`b~r)xn$akE5`^_QkWxva>`8HZ|D7B
z@V#`o-vfHJIS%aX;q$cxFqx#>3re6s66ql+FtGRArP}W?cvx!k*l)R7i0Lxx_xn*S
z=c+m=tqY7lcEcKy2d=eflUxPonOkk`WGO(iRKQ&Wuy+N6^!-aIL*?#{o?5-?i#Y(Q
zRlc$nrP#{HfKzR||FDdgC*<lp-5<Vw*SXDgd&qVxu$lP<M|5rFg=I1Y;UHI6(cXy_
z5=@cllZRkoG0@&!XSS#i1)>R*(BZq^^R+OSo4JAlg^@YxW7moZS9&479%cA~_h}St
zpQRHUI(0;Nu_9U;!VX@-DTde=F^4O`NWNFQ{u%1<5g6qZt>%bgS-_yU01@|^M=9yP
zj<|aIY6Ch^u$|Zrt=|sIh{P<}73Nd06SNQ=rr3!Tlrb*GpkQJ=LEb>z!cpkrNB9CZ
zgO;Vw(bK?rq@2PK%KNKW9<yJ5<&DR9O<Yq3W*Ro(6s@1o_~;hCFlUL5p3@E*fZS{5
zEWhzK;_F+V$a9FA?d`*^<(sngo_T8BG5!mnK<Kz`6TEdc{#TI2n~!}C|16!W$jJGX
z9#}<}621)JzcRWJ>JpF@c+i>+xC+IT!AfnV^G80D{on~bmOTBDX7M#jWC?}Y+_R^I
z6zx%PmKYlemDm@m3YOaW)%8Gr3^H18((L%@q<T~JGJxSiLLMoRsc|@crN`O%RpU_k
z7JOI%?0~}GrH+LG+2=|uDp)aMMrE{g6-rC4m|vQgvQ$=YYn&Y3GxKHH54XiX0<ej|
zVd7`Z4M$1Y9s?-cy7O;JXf!l96`}Y7=?5S>7_VN^($c5FmK3HcdOVEbOx+X0e>rvP
ziHwvj%HNk|Wk%)2d)00YmhXX)GQs~&gEkh={EG}fW0wLFtY}^K&e9^7jC91$SfS&r
z6d0er#7BeK!9*p$_Rjg~*Sttb$xurbjA^Jc3ksbbkt_>o2JEN_?Kfo2V;I1{IWpHk
zsIdTlFIBiXzMwAd<6e>&)_@vk=9r<b$<{Hii{_%`0-xGKR!feU`gW`EOacm-4>JW~
zp*PVF3un&m3wq`xdTyMO0bQXsk@h3!%N#GJZcumyZL&nY+!%_}RfbjW`<Rmi)fH0A
z9?^7yKL?44bm!`BC$awa3ZF}(wH=l^X^P9ki=j`(<ZHhs_tPmus>v#yE*UPr!GFAo
z=c>HRW8!X6vtsu}_tn@*;<s6$(t4F00A=t<RwL$RA3oBIy_EGo83lL>TCvOY#WFK}
zd@)S(x4iE+LXYxH-CjY*I<K*3!G3*@c?L$F6*rsI76EY-6@ar{3TI|Xyfe~(q_bXI
z+rZD(;s0=avtv~8{>!ULf!@<{gkL0W79y3}R!(O*Ja2pcw{YG}d``B}<iKp=hRcv5
z#pT??<6ex;B58uBsGhS94W}&?O_4Az%H@P0hk;d3N{Az+KnaGNowDl^-%wgGzEh-T
zT}anthmlNPCSvjOVl7^waP)YUm!6CBf%tuP<L72Tc~EFd7Ctb_i|Tmoyk^idSmw&0
z!TQ%=$laUIuIjU&W?00MNY0g<yhM3ts;g{$%H5q~o(7E1pM_e-+J#z%yoK7tyqcPO
zE0tvqIrI(Q?|9bVhrj6DP6R4b!vcYIz@xtv@=6nWq4r<DZffURvWk);?N`m?pLp0p
zA3#BMxyjI;dBj>4;YHX*16v_2--BHEh+>?Rp3IYqZEVyQtXF*;5<*7llQnHPMym)n
z@{^h#=eP_G6}JTt8(%;dz3L^-{=}mAgGwN(EetXdO_@WPgz{C=ku#x!6GJ1iXRhJ&
zNoW$K<pO>NyUgL!4cKG@X=kz4YX|MJ*F_|r?(iz&mFZ?OSKC*3%;oO>)Qy<$5C?~)
zN7#DJjAS+1Rz02fXR-Qzt*4sXl|{#B)xH_>$O^F;QFK_$*6s-G>ZzM`Dm%e72i4yN
z<z5o({$Iq?Nhn1QUw78({40K0okT070og=aZC%2C+(AZ19F=x$jHta+nB8LHn{Ka!
zyRFeCcqw1^=J9}{6d1_um@-u7WkKLJg`K+roFUhKw6{?{l3e?=F(j!;JCAwR3A&9i
zZmPTZJEq7@&lyEo`~)ACM8i^S1XvXvO#9z+``IcEuqXhWL9u#}ZBz2(9r+6c_RKK|
z{h5RE8izUMO#tbe+oBt2F4T`;I>zU%6kq5Nt}I%cXW)##oBx#zfJbFqQvBU_!Xji?
zBOkU8t-4s8BWX*+r<GclS2pjzZuCWALOHC^vhHCKFHuj$_}~erZD@PuWSt>bb7(q|
z=aI7aF28V;x?uhXDo5m-Fu0Dqq#e9}&{wX*%3*J%oymOs{``Z6caY7bQ8exwXrR00
z(F7`kKQ6Xd61T3tsIgNtT~6I%hL$XW!K3oUzxoB2y_|GnztoeCYfV!Ch2^jCzyFc_
zgTIS|w{B~TnNIzitFD_|VwG-ad#bvr^O?|w(M0QNvDzW+ExxVP$bhb3+6DYUMOlp5
z(G23ds#DTE@$u$*MTO9SuX}93I!6{VrmF3rvSthXYyo4m*ti13<lM!A5^DB`ihWGa
zEdh_i5Hc2q9P&~sK+`5dJHD^;AFoD@>%XxEFjD7E^|b$PRw!*mGY)ht(UZwIIdq#v
ziS<bz?StfC0WSi|NMm5B=e^6;T-;bFusOM6QQPI)k@prSTLOIV1Z9KA#{;ddHi^S9
zj*%)pPV^A;YwWZm&b6+3aW1!#*qBS;RadLnc?I05gGZE3kQU8)X}EVla$u|lEA+Gm
z99f2ZD8*bR8x>7JNHfwXPI4W}hnr+V6_s+gmabZ9g8uZ90e}nythH+F^>2E|1_?~u
zG{^8x1d#H-U3QY?W_BZ$O}>owI=mSonRTMQrl6Do0o%ipP$O%aOhgsqEM8@Tolm48
z(ef*Po}m}I8-Zw0{Yx9KS^Q}nf7F6g*brVm)L`<f%<u1nCSz<MYh{5q0i;;c*Tw%>
zwwDt_sOtdb65x}u^74%hsUh&$ogICnH%p|c#0M0~LeWWe8G@`6d>h?=fuVdceI;Ki
z>PvjfG$jhEgj>ksrInga$K4>r@ivDC%Kv>YFtj|0c$m%4Gq~5H6d0bT^YhA-q*Lk2
zsp2vJSdnl>fn1!%*PY%6W=F>)xgBz}%MlV50&-M!hlZanNfO1<X2qe4x40Qh$~faj
zXT4MhehI9GeVUqwFq%%iJi#oEH<*VqMEZnh>KM{kNWoJ-2TQ3<R~PD}5&B@9LQ*|Y
z!o4GfLKGY`q}=1hItAYsTG0=W(c0L8|1LRA6h$ZWHNIZMI5kPqAySYU>4~R#9Ug2T
zs%?=dMTA5}{z8L|to`swy4K_+pVmvx4NF{$rl+OyWmF;Kzxi=Vya+o7K#d7VF3Zf+
zVt623YmVEa*m$*^6<7XZjW54~4B!U|->n!XmlcUDOe@0etpVDc*er${c>wqlM~Gu=
zDc=Z-bSQPE^WcvH?*W=8X%{|FC|2Mj^D?GQ#o^@A8Lvo3_+m+`0hApM5g{>W*(RdF
z#LM1ZEJ<gYX9_GzH0eC0w%{4cNMGYtA$0@3n-(oYszP1<q&%b5339Oloem{K<N2z>
z-z+;wq_Ug+!iLkH4D2$~QiX^qr1Ybo`$ajR(`qG~_gup|wtmp@21e6lSVc-82L7E!
zLMaV<Y^`g+is5K0xQZD*;7P!J|0{SLDI>$~)yx7W-z*tE=A<1rof}c+n4uBblHy&?
zLuU`8!{QJ(nj5*t3c$l%lfXob{7pP@m9drNsT@#@C&wdR-!^U$rpRV$&Y~7$;oQI>
zkanN8@Lko5ic6IG4E?@(HZg+=7-&_*;+x?%TuC2Bp%tkmskS1h2#BZ(|3(NQpTJ3A
zrUA8?79fc;21VyDxV5%wn{nqDb0>)qtJxr51hbN0!FiILo(t4<Pd1a6Vh<g`ZD7jF
zEHk&Si1<rf66Nkil1()ZK0+-W7oEj$r-~VkJ%aXIZYH3FUJ5;uFf1}oK}s;0C5gje
zoMvG<yF1=Fym6f@h0($_XNYuX?H4GQhdJ&BYKaUU!I7ROWWN_`AX-vn@_Re})R~&L
zewpKW(+Rg#l!XCLPgI^j;2sW6No@5hUKxtxXD6&3Nmdbg-X_CWn>;gD^Y9tZH|SBs
z1Pc7v2^3Z~{q1o`cA>J>%%8?{scb+_yS<k}n5P~4Z#XUX0ytE*F%A9CW1r2_rD>NN
z@`U8+Y_5|w{DZjHbK+A~W-6Mj=6PMSm@-RHfFAKF+(f!*eSg1)DyKTGfTl>5$|)Po
zG!hM!F_|*OP09?SPf21DVQ#rA^UR*KINs;&>RBOWw986czk>tj2seo!mWck!W~#b?
znX`aNM%oFq7S3|3fZl9jxm^w-3PVe|);v1X^v&RX*5%=R9ojb^=pM5QCnv6MyD!CK
z`2_$d!*2361VAZ}R1dTS`+-^oK<CsoTVM8(HL9!54k1HY=Spe<R<1e`aJ!0co8#Vy
zRmy6gs7+V_p#ygJ6Gz@l{{e0;osrg)z%6kw*_1rtnq2rhc>dZ5&3UKu)7P46=e_YP
zfEIMss|~d39Iw;J|E?A+E_%#3SGr|!G$Xb-Mavz2oJdZ23r2uQJRW^zk<hloPSo1{
z7szwTf>|zpc@?<^hM$#tLj~r?7F4z`C-zC<PF<}3#@C}BP?X6)4^|G*%377cK*Z`-
zpvy5PB%RCMX5q0=3FW)f)%=We?AdMlY!7sll6kpD@AnC%B^Xz(2l@BV#@kXeWz8*q
z_8&iptK#GlntN8vZNw%gz9^*vwH$+?AzY&1)Yz~STmMZp(TOhDptbd%PL0@xOhz;@
z9+j%p?cxyx%;;ph(R)27D=B4m8pf;bPTdHdc701}u0jc1!8}QMB3}^eqInDrjc0A3
z9BBl`@^3B(LF~q6xOI1VRJjWb3Z{cR37z63ZzE&$?M#*Qcx?rj<y$)*Yx{L$XZL?|
zj4BXIDlYfxN(Fy^eV;kZc!My1iB+=qc$odX$j!&vbDb1c=g`ozBHZclnO(*TV3w+8
zkIUbtsfYBi+C=N|j`B5q2{lVaCy$H%eeUk%Yah{oNxn<?xhhSntEtnw|Hl}|-yq}f
zG(agJ@Ld@TNfo?B{pCJ!^?Z-COMGQ5t8woQ{Q<oTBs9O-bL+PLbgAC;?67X^)g^}`
z0Z<Dv(itx!m~%=vQq4>Y0!k_cx*4a*^Ebzd4YmgQzbyEjeA_;Ji~T>2t~of4zK<7i
z)0mCZIBC?Fjcpqj+eRDPW`m1u+qTiz#>IK}d1vlsGW*9~W@mq2ejo$ay_;hYGzh@h
zOws^^c;3p^E4xjV8z|oLg5ke1p@Daz-6OM^*3t_C+1#&uhvlE#wF=!HdgG=cV$bk-
z#2L)WG`^pMDyVgptdWOe@Om@{NY!7G)m$DvuYXMfF*E<{V}GAe!%bV-6z(1?hW~K=
zoilBoO?R+$r{+vFxWBX%pOZV%=J<K#?E{gwSxFCo+Cofbh7t%UDBi7M6A#UW8}nXK
z^jfQCts5$!(+2z&XDF%@@YARWV>JInQ@q%8LEh#k-7dtEFI(QSj)g^3#19C3Uisg!
zf+wWycT+W_Pr9>$OA3JG&~a~>y|WuG#weY6!{6RxA?NHoby>^r5#HG8nI#IYx6Q5P
zNHR668Pa=>_DS73A_ZT40tVwIJYJpzDoUw*oZUdunecfcv&YG?u&6A%n-)+DEAj{`
zUfU#()5&e>Hhg^#ES8C5%j&c?m!R{G;T{%<ae5hb@;?c%k0&|6mPnOD9VDOuwyn3D
z%ibI6RE?y$jU*wZPX2g6|6XGFGxd@Cmo!GB*^_PUGu^FEHV3IWM8Gb%07E5axRB%Z
zI`(aO`s?fGV>1!V2x)BU2nz41e6*u;1N~=RQ`1;%^k6ZZEGqrN@@E9fW+Ee}bO5pA
zUdT0Qxp(qX=ar}~*~VeiGx5`KPo8hPPZ?*hj)#apB4is!N2S^+vd;V;4wtT(evzc%
zG-^;vOVB4_`!UTtk<lA!F1Ci8_-a7xI>b=*czm~24NB<9NU-SavCYFV_9PusHzU=E
zG@INytw<0>s@anJ!^t?C^(LjQmU>H2`3VbebQL8clQX8$?4jGoFjDb!&uC~E9DN2v
zkHybk`2d0$-k*wzW<&N#gvn;{f)<}Rb?eJ3oXTeBh`E$Rp_!!bJ#&~L5Brju`3%+(
z&fpcSWFh2B^SGV`|5<-58A2|BkGQL*s$`Mcinh0HY-A!ApnZ_Z44eS_<7V6_eqIrC
zve7AZq-twXE6djtY*jmEEG;Hp$Y&B^Lk{aBBL}2r#Wb7M?{I=MoUpTV>TS&uc`GKM
z=AZ)@7E6Ntin3huk>B!dUqk^Hdwha^$y84yvxbU`*i^Jg$uA-bAxlI#DL=rtX;h5N
znF;G>ut}h}krg8;^G^&-v^h9#B;^*K!KsfQh-|HR!xbAsOK4bD>HWwOpbx3h`B(fi
z&te*ReJ}di$f}vzjFr*)uX-g$3I0U^^7UO`Qd+Bq1_a&pUPE8(f?|(IqB1fKj7;E6
zvnN+t1>pXaARy#%e&XMq8x>pDE}5cYKUxFrb>|7=2sc?LC!U;)>8MMN2tbzDRg|jm
z<B#HZfEsFh=;u$P@FVZeymMe?Nk=KMGtQGlnz2jfHZ93updlpLi7k&tu|=izyzs2n
z{Y&ZEZ41qsKd?(!E!<49qp?3l-6hm0nByD;o$LhOGyTu>8|n_KRJOW{M3(Z$Fh<t|
zE!)lB!9U#8bq#!SC3dI0i<^qi8&c_><+ZCFcT!hG-w{<neIts@vreSQO4HBXap<yt
zm}p(~Pm2jL+Zc_&8~P_Jw>>erpdB0u=zx;jfgrMtxR{7YKdM|jD8SA=>3}IgHkR!x
zm(Q<3<Rz<mrn-O(x`K=>3-*E|kGWRDh8)n*x3stfgNubIq9EWxeTCE@<j9SWbI^pR
zRKeW!=;0$EvR*GeQy@@&Vra4QU!Rqu4@BC_*q#?KCXJ=D?$fab;tiGr&I1V$%BUj`
zaK6cTIRC*`Ts4dPQE<PWqpUnF^=)BF26Iz}N4^A4=96#suIS`!#r)}gycnb>=@Uv^
zT%KF@(Ud)zrw=3HdMgTxR!C3C{3A2}<NY(>-e6#X&&fK0-T8>G_qY(=D#La03q=^R
zYfwj|-VkMc;`LN2clS!L`MT`<AI7Hh;iA+30H#ih-uHghwyHyU@Ajq^x&Ad8O}4`=
zppegfJFATwIWr3?)vZiKp^jni=n5Oj@f!S{0~b$awbP=j>MIgIs|beh9DBN}_QaVR
zfTMzI^H=g<@9O?tQA$<vZ=i>wydl|*@>5X7_3!~Q2vIrAQ;5PpAqsoy+#|t(nmOtb
zm57E<Bfv+vbb2e2-#dDQ@0B(Cxd%7v^~F4j@2CG2+)&_FG3n+@WaX4~bAZnfnBDf2
zlj*T(%G{~xX#yYE6L#M@-aKm#4lm)mdj#3Ou2){IVNdE85@xrYT#=f9A1BS8FDT(h
zd3AIK+`bKRxUbeoggQ*Tke!tKiqP>QS_j14e3hJ7WV*xkYm&uLTQ+-V+nXTDp%o!r
z?prW*A^CWLC^Kw$A{NV>i>D3hxYzp|#u8Sg5a^#1#WPpS*wq^dK9uGbDahQ0-N)pM
zYn-O1YUFwuek_&7a>$qQZ^TyRVC52~&g^ON4-~)|WYH#Kh%oc~=<9LyZBjOpNo&k8
zPun<e*`!*tFu?(5B0ptJN}1fA4wEz$gO$Zu%y`YFsIJxPV&rR0Ltp__hL+~up<U=C
z5qBSVIBgl5rW0T<<dqbv9R${lS6ne*=0`C=y!?lATL#Nvcd5<K#9!eG?;n$sHK_&6
z3>S_8v2h=cRW<o}_H=RTY3IoCJsO+ALIA-R#_g1*Gs79o7_y{Zrq2ljp5{rs<4T<8
z!rp9}s5Ujl$;2hq8#$$&6Qc67;_II>i<%Ea03eGq<6n6eFG@MiSyrh*5<nlHw?c9W
zNkv+@iCR%ia9$zIEO`D1Jz{fMr_H8%?Dl+V7^gU6-t4r>*Fi)P=OF}oI;46u^w8S?
z&5u*;-3<u+*z0)JMj%PyWA-a3<$)CEjp=BZy4%D@&T}P3npB!M`^v@eX|&2%<4WZ+
z3iA1(6;Xa9LEFrp5&n}?yv_RvE=mhC$3v9CDlS_vo9FVZ_~~MnG7JI{$yaZ<zkASp
zkO6b(c6BtkEba;M=c`=Ye%43&l%D{_>pM>s=4swTMBv+q{H5hTrKD;NbM(Qu96?3C
zd~?{JP$vo`Nldn?di~1MSrfdSpuWaqdPlHxXkqPSEIS`ndKkFx?lYYbh$`EJDw#CB
z0ftX18pZM^olaX*cBqwCoLfby`X^TKq^#p{BFHT0ey9U42Tr!lj-&XOo9$K?O4yx4
z_<wMeaqw|R5<7uE0KI&9(R=6lkFG}dTKzD=iwhT&Q5j#$w=AV7t6xOU0<Hpaeo)Fb
zpt_R^uqUAYj?q7`fb{V%0-hNEi158F$rMTvRhR_bXT#<Gxq_!viS$We*k*MGS8^>7
zt^OydBp*l8JD#zEWJ)0*3gw%^ny?ZA9LCJRtojOK5LXac-%LR~A6R}mfu%*UYg#Th
zjHRG}IqA)r&b#1XmBa0TkH)G~jW5h~+@}f*hd-W=Gijo3TUYfpQ*=>8%>|--?-#SD
z=`YzTR3Bdi`>MO?%n~oEgn?D+d|VMu6qtce&@+cPW0FfIoeq<i%EGzYQd;yqgtR1+
zz83rmxKJ;PEw)JA$lX^htfs;um9ynh$CJG!9hUKWIJf-StBnz8D>(rCfpBJBvv&W<
zLrT=22y&ZM(9y~_0~FK;g=>fSxbZ|9dyG5_noJYLxY@D>K>ypN-M^&RyMJ~_88sAe
z`m1SH+&gZ)*$rkkLNIseZ<o1l)Ga#7kTIa@eNz0|xKrD#S-5%+=MN{-`4b)!0@rWS
zF4bo1Y?zBQ>k*K<dUaICvn`HR>Y$cu8@_Z}$E%7>3(Nt!Z$5ePAA0T;r%9T#glBd<
z(>dWwZBrHK+9<5HIl2vI-aB%iFLZA{tpX*4iV}yHLxyO5@AVo5VAierojRvE`8?_`
zHe0PVChj0mwLYR!-=K&26<8XDo7X%e`v1;iR>eFl5cT1ZDm*$5m#2&TuPZw*Hftvc
zD~b65uFh!Hvo%1Owr+-{Fjtn8z?afyCk`|0;SlYFr49T@NXWyVzwA)V-U2APSszWM
z@4a(;^~;ZFo@o=;93=}NZ5;Vq>Jtb#xp3fcj^JrU4>Q2Yv!tP3)%T(be+%K=<U?4J
z{D!=fQdC&5dG^(?h$g7z#w$s!gicqd-_@V@8Q6iv;f(-8ri9|1o#!;Tb|R~G+r||}
zYmnYXR5Y5Rq)|qIqYkh;xVz3wJoSbXKTwPy__p6)$rl-4O=M0y5--9Wnq2RKT)y-*
zh$|xJoG_P!k+I%h`piGHrLlJb8FUhS(Pk<rB0_HJZ8&+h=Iv_>ZBev@k->1*Z2KAU
zvWl2IUnX9WOJt&kQ5lmRF8;vh;@torT^LnS@`WmQ?O6WArP!6Xjrd9rYDm-M9nx?x
zd+h~09~BIIq3#)HD;>%Ub&jCv#)6gdOmWFI;=Tn|N%P<~5U7ZTfM0y38xvYcW!bF$
zxo;;adIwknQ}LD9&VA(TLuuF8>5`Ik{;KpJKMvySk=P@SwLYcZR5!zb4G16diZz~H
z9cO0<sX&WA+-$z!icQGggzC9bT+JRomiOCdkS$Fh{y~u@&@sL~qyqgEg3M9#I~gK2
z?l_*kFlU`8>3-pa96R?gZa2#j3Kg{?>v%K#d-i=mN}l|2-ugpC0Vk7gs;Eu_0EF*b
z5X>%UWUc0N#F48l@lG>^8SVp08Dj69+2keNyu?uINq;)Z^9V$k>c_Ec20Kq$A}!K^
zpnlQGIS4>OE{1Js5l9WGU7^}eVeRSAZTodY>r0A@N<1dR0DG3<-OP?gieIH$HFnmS
z-zf*D9f{rs^W&>=vgizfR)MscMaS64BSf^he_wI0VibV{7_as0PFFua&|^4&$Feql
zX%U9OisUSvKh$v(9?<{DvqWf)h%`RLAzBtV>F!sRbg!Q#LCkye>|tRwq4;73*?PQF
z@W=L?d!aFCdlrr_pvt$3PcKzbrIk@-$CE}n;BYp3A5I|>bLx$mSB=l6qq8el%sF-m
z-9e5E>vVg8>a_DRML2p1B;R=60((P;Bg$YrJigx@q;N60$R(jc!e`tF$K^S%ZxN*y
zRe_ZO|25kM96W$mkWyQ00wyFq`WH7~bDGVENCwC4z+R(!4Qr;Z51$dM@B&cU+N*j3
z6P;}mN_klMdfe!R>Sv9?8@t;p6p6CQ^B&<0Ssc=X$m-T?p)S>>nwAYqR^;)w)(ltb
z5%(!o8nzAUC9Hf?QN`vwyqp8`cL*1BWmOwijt*8K*d`R}mUVD>DQ%$Y>2rBkUJ6HC
z3WroNmn@hEHv`5M+<#pL;o*uHe`daaZm)=Lh`h9C#sUbnmx5{aNI?5>`RS1Q(E-d-
zQXsEW3M%~3VjT?-18Wy@bS~}%sS`Q||6V{Zl{DKLtO6PRC=aOZ;;AGt;uq=ZzJv2Q
zGRWg=?PpXwzixghvT2~IWN&hJPaF|Nmr;X=ga9ITOGbYp_r84q934ws-46;EQ+WAC
z=C%v~%z}uFw8wfy^x{|btkvC_)-PrBsv$jaDoW>RGqmE8r9TD%iBvmoz8s<&=FZ_`
z!@$VIZ_S1XGIHXrj3I!1+O>y2K)O|%0Ep`i7t3v(v-f7KE!v%Rf;85#6DvS-6;y1n
z3{z4-i~)^182UsTQk1w_#-Ikg_5!sF0&oELVF<7wxzi1yTbHLsG<C@bEsXr2Z(|LP
zXU0WvTq@S8byJAW2ckNqwY8SqwSe<(H%`-GkStfW;QV=}U7+yRp%I<a&3PrFiV_nY
z!6?%Ot+g^0LX!2G%HEgu5B|CuZvtHl)YkR9PC5d!b8lrgAEL2KNT=$_UKtTVEvs|O
zu)7ZKMj=MRlvcBFC%`+4*(uF!abxpZ?jx;A2U1-(#vd2JY~3`quk_MeRK{1LJT10?
z)Z9Ka<!!aJHPi_=&kCUW<yv2Oj4wZxo9-lSS2Qde0nFL9=!2ldniO7E0j>j{qzh8_
z3Opcm7OWrgC<rP@4i6ZnUOTWJ-JE?~pOY{?^O?DBm)1nOyo@b!0g>WPAuU|(unDY@
zgtYbvOPEEVz+qtI<RB2pq@-BD$SiSaeiSjI+MWP-0add7t+G@)$_9*9nSyFoEC$m^
z>{mNjnN`wMyoR`+(4fDnFjdX-1jUh-N0Xq0cvFZ`PKt&SH3GM{QT`sm`_d#tCuEpQ
zc39$Sm1dX&k1jP1D%Ox@4gb|#XsIMAAuW#LY7TAbW*^T8bbh2CPyh(Cf5lS%odRP2
zQDQkQGDg<6h>Ty85ce8!2yai5lyr!2?%!O5&niszbEH9WJ=0-U)TS5E)e*7G`Ir?u
zg9I-{62v<Bh@sDmp}$bM5Wck-8c<QQ^bbsjQ3;B*k2*WN#~A&HZv*9((x5-mwUp>v
zeB)f*F1|voNs=Hj2HhsS{tV=)PLN=(%XKJ9P=--&5nW(QrQZj_OdIiO<!8pM(ZAFq
zNbkZzN*7a6`pnt=3#^(I0t3vrlg5m!k=5F15yo-M&SWvQ($`V-dF3Br+))0*0w58S
z0Rj_RT%st|Ufu-1V~a^`R)s#Hi-{H6vH_oFpo`I69EAA!XiTK4MFAw=w)fdmX+k{m
zOF@8*xGQB2aDfZtB1k|It<yOT(`1=)1``SLiLboch0%!d!^;?AHSK7pNR{3fq-vXb
zf+{LV+22g>AE=V70lkdGNDAB62ZY552FLSxKt7PknxL^A0;e{QDa-Q{*u;TOZslnk
z9~R$lVcQ;-(f|975fb&+Ib*08csCF11O7^H<7yf@WmPru-8IgLQiZE6j*Q`ezTgO%
zmN*l0tSP`ZT)lIL%%1>Qx@EyIQ(Znm8q1uc|GEl|lglRvz5Ui1r_cQXHk#lJv)SXi
zccz$l)ZPGC<!#IN-V?wdFacDmcsaRvBFUdz8eOufhe1jCTrOS!yZ%78ed49wdE;do
zP=FUzfEJULVf4P;kZJ!hsDHmim6{Qm3%9La;|B5v{>eqgAHa%nAeDzDLcFgMAe3j}
zO<6dla&q}iQ!bOC#JfF&SZA-}MqBEG0L83Wx)pB^!IBcef|QNfhs`P{2O-?DgwT%3
z{N6Kpj6d=95N-CT?fhFCqK{0`pVJC*PiQKL{sohgU?2~5c(4662b3xQ(uBIETm(xv
zl;?Ww!uK;GsXHe(Pq{^hk3%$^)j~p>r#oQCK2OQRB#ap#fur=PS~n*ZFlLWEj0n(2
zr<RHuraTU8yZYB~N5?7NXSr=}LWilNu%+<nv8G&@X0nIY6a&SnLwiyp`<cHaCtq+K
zH3m9OZ0(MUNf=*ba6MN64|!0JL%48x?;4MtP^-1^dlWf9ax#6}p6N)EJHQt;k;M0O
zNxJHV<-gszhhL6Hdu(>Lsz$WW<N9)zt#D-{e{*04MH^5fMa2t6BUq#^i6u22Hxo>q
zIyij1BhAHNP*U8A7It#(uDkv~WEOm~q!~LI{gyq1JDbnq{}u8HSdV|n%$`PKyUfLk
z!_l#~t0P69aKwlZ!XE`pFL7QqidwyqwZ849gqT!`&UX%591v)3!QAPiGFYJW(Z|6-
zf0bd9u>8)U8EXHmA$s~VLcLHvaN2X={58`ybCl7={6R|F(kEEv0%2S~(MBBxgQcIi
zP%eIYkTdBO!5tKoz~+a7u#FTi;aLwmg{WHm9KL4t`dhV1lvkZ1WVNr)tOtk^z}?Lc
zjIZ}e3g(j)0#<zA&z-$iE8~f6YL|Q>)A%O~JOfpmf`|ZsaHCjPNs1(vkVO2n7<EeU
z5bzAREA@+Tm7U+Q_#uArpxz8zA^|&Emf8dtDlkD*WCCB+i#VGM{-F3T)W)ItSn0GJ
zr?6r#BpHP%n^IyA8;`>I-za{DBRMH6?U`+$vz3Y2c+jhH!#iKs2ju@Vr#{2ZvH`^B
z9sobb7~+y(2FR<R{4=r^EewB6SRB#JbmZ^oxjHbxO(!5#vIFeUtCvYmm9Kxl?rlDx
z6_*JW#1x%|<#BdgtMN$`qzuSvL6on{%xH=;#`RwCvUk=1di5JoNB9NI9If@+3uI&4
z)Ys=Dw>7|XvZsS@i}3)9pa=s)A=5(_FE-VavN7xP<)o4lX#(8+Ime%E*ZoS`UY=Pd
z?LzG{`@o2Q|0&S;G+|kZ3LqFi*bEIwM&?xG^S{$FK>YMqv^`7>ChrTP5pV7~pWuDo
zv)=>2>FI!!lV|0ozI(-3_DkvFloO_m(p7s*7jm%;TPSFFNchjB_p3RE$d=xVt8c>v
zl%=?!JlBtCU@>4tx7hTsz|)drup&_vC@<{$4>J%o(jr)P^?Q_IO&|t1mM;6f-!z5O
z<>E7pjN0%newN1(qX5d)3WOd&AtXk^yx+6ykta4(dB7LO3FlB53*x>VZ@!TRZXu$e
zh@=Nh^OSJ?A+`D?0QZ^1DgV~hX($d!JZ%uH&mx^^MeV)Wp&*EwGO;lt&^tpNvFlP4
zdQnV3GKFY8>B$sDu7I*$`|VzV1ehQ5=Po+{C}G*f!A&vhjSt8~1vxn-ewAML7z!8=
z?!%H2{Zso_pQRjXuAO@_+#jREr??%RR|L}iyZt>s_*vlrx<ej#=!oc64r+=u(Qshv
zc!uI+9?Jj&Re1Wh^x7BFR9P-wp0UCLQ#&W`Mas7JGtN_IuZ8{5Itzka{b<($Afcf3
zDv>K{m`)yC^#+s_1JhW;$K&<SwS=rjbg7+9eKUmJI$9|lTs=Rtxg!&ws@wu4$ZA~I
z;gBQ~dwYM8dA~G`_dgNIUsWjG+58(M0CFzXx^S#$05J^iOd{(`lL+@({{9brOX#(t
z?vz)Sy!%w|dfd?%mnMN;y@7Box;i~Dp2}g6ir^6hGmJS3?sN3tc>@*i=o;5Z>H~5L
zMTWm$!nwVX0bI}w61#ip3;!&_;!%L{T9E)*d)76x@JJJ6e4tN3T!?-aiQOEAmd<sP
zqEznEX-mznj)Y~5SE7;FW=GU{V%{gbrBi%euPb_$H_&hf5|S5_mQjdVF$<T3Q$5LO
zltr9`nzrOi^OA&CgIng1_vp>GKFZ>c$)%9Wc<-^P6CjK>LSJr2z+N)_m3GPE&)!5j
zzNBvw$;|_Szm$uYX~2U*yyf^s&AIO1Z5_FUY=w0B7I9ou^v_I!qD}25eUT+|FYeN;
z{@C?64YJIM9_E{a%|yV2uNFNILx~M?oDox`<obv|HSeiZxFN?4bfHxLExtMI0C`UU
z8jasC4j)GI6gr_O8FM=eYJ7Jsh%t1l=~_CSs#qQ0z-loBO9N2QHMN=STsTCbgSpyS
z03f5bp_N;+(RBtxH<^sSna@FO3#6x#(v&1wVE6ZOL`{PyqZxVLAucU~3RJ~;O3*-F
zmoaYt_-PFQ)wB-}Nb+(blLB&8te7fFc8XX+AkK+4#?iZQT6m_$=-x3*r3^Qduq&dZ
z!+VTBK>K$rDu|Cj631-x0ieHd^>5KB1qXB9^pNBOu}SjuJo;3D6?1(qj`^fQu6?GU
zZR6K~#8f|Q2#3gDb4j#+3gS#$8b*c<eL3i$2<ctO{QksEslGY_dT@|gqjrUkdcnHg
zRr~KiOT3|SZxjiQrd$dHmQ|)_5=Q$qvar#BE#|)@iHL$raHJTdxd41tckVYFN>K?C
z8GLXwU_fpNrc2;<^E`(pfl8~$J<V-cMv_^yV}=~erm!SH)t;sf(4u4B2#{bj#`UYH
zkVF6$<78ob4Y-e#&8|cYR>i0{8tFw4q>p@9;HVOL2}|4=&7d5&0L${xrIOyG)8#j2
zQunR(`dyh@L8}*l_<i?50;iwo@dol&9tEdFbfX5x1wX>u?Fq(5+`1jmZn^i$f+rbD
zWCr-rPB+u!+!rt+s2F07`8U*0wU*JiHITK+vV|h+^Rq8sV~B>CJT106FmB{N#lca>
z$LRxwcFM0c$_g^H{8Q@N1~{>0Eq0Sp5AyR^$&xDMG4EEDwAK~g!2(Zc_L3Zg&oWHF
zdh%A%-uNAd)R0v0XbXB=xA>Yupv{$W4a*RB1_3Ru61PkNf*oS?yCCIo>9@EzA1<0?
zv`LjD?OInfm%2q(8>f&cp4fWcEoTDZ$vO1O7KM$nn36QcT>hAPQTu`QOi}{VpVRF@
z>lTGXS@j&;GCQhQP8Ne)b61Ma#w=8uxxeQORWt7CqE&(@u2TVlG-JAtPBXgF!gNA3
z8_ogpo`cKAkftK;-pFH?7xE--TcE_43LQBNi}VXB-uEz`yB%2;GQ?H9IWVWTY*L6U
z<NH&-Ka8vN+hY+Thv8Z0=e)4~g|2?{FW$Vou;Ppr&9cw%{r!pXeFZwd)pTS@U9XJ8
z)h;i=j*q_iH=u-%0!+8PoeTE@QHqeS2zjX>&mV{w{$Fv^1zdNlMWJl_qX&L+03$MZ
z@6jE-Y}D#CR(f{ID|atB#WMKpaOyss+WTCJ9i+6j3<R<t0CGZ3+<ZaBKz}Jcmh_+G
z8K;*;Mxic8-^pfYUpjxAAV&W)g&tBiz9~TCr_4?@xq5=(f4=#Wu=q`xJ*`QHNCXqm
z0hm4_{k{X;@epZ>n@tTUxZ#MX#O)4wx0%&EVgQQan=i0>rp`G4_4hpeKiM_CiW&2!
z(4PJoYDD89OeLQ8Vh}#>&+gf54nJdD;LKA;85JjM1$1u^#(qb4KTR0cd*Aep3_QW3
zTVFFW_K62DFn~M`6skQ2C0Ru=ptlG5DI)n@BkOsW3Fre3rmhqar8d(;TD|~R6l8h1
zd;6S1@sd^DF7AMzPXdOQZGh=F^<j``LkwxWYYGpGusK<HU*XB?2i(S(Cbu^j!6lq0
zjex1p-%-z$#6m32aa8o*;qA*R|CZ#L9d8_kA|tF%p&6fhKY`(59~jS_%fBVbHY5nN
z%k4!FlUPDX>37u8?h|rhKeklFNN9NN_vcxuYSEQ1Ou@oW%0Uq<7EYgDdv5X#0z}Z0
zKyl);l$Y1eE9e<dvJhY8zi@#EHw<|QnBDC<;kqa_y4Gj`Olc)GiWN#jYdfuXAULf>
zPHifA2oHTSJ0~kkM8(Fd#$kibK0Vz`$%RZD90|wm9EK7l;Vbu!3sp(a;n@EL*uelQ
z5hUjs)q}Hnr_t6jvhuPq56n#&y$v&xJMIx(Ry+_rAO3}G(+jNSp6hif1`nrE!tWqe
z-+J=%8Xm>Zn92t%-#o;_OJK4C=zKCA%{Q3<d0fX1I9Rffl2e_%*OiN^Bi)|Jw8OC8
z{F_hl#n@E1gN(|sGSydkNCu}fQEcXSk|FFZ*i#tky{QZ_(-6IyBhjxDi$0B&qC9br
zq(E(Je}F4Z9!Z1PqL2v`sTL5OeJy@4dSWr`7j0XgWRI#Y%AhwS^F5n+hEF=xsdia;
z+d74Wbj(|AzclecLp)*Sn4W#Pz&Sk<Wwl}HlpD_m)jt#Ju901~YFod-=PhW+?seEN
zg2LcaE#Cva+->G<F`$lqfQ~$xqm5W9OtI4y#>Og{G7rS7^LMUbd5aLO>Jxz=%Lhay
zJXaEj!Mj&JX<0QTtDm=h{avwyFXJ29#?%|*jIZ^BIKU5YzWDKr@~e9VTSp}D_Y*s(
z-ZKFZ53U}o-%*s>J)LF0t8bN$@SFCw3$vHx(jxUPNFagvrKWizijAgJS`Ri4fl2`=
z5!l*kmD@_8sz-BfO^0xiv*o2zVG0L>6kzh#KYTvz`ftS=n>%xUIWa?n-i#<RSdic#
zpU}tX+rC_|^UT7VJuRI!eJTsRbyiE)I^JUCU0`9cxoX?#Hl>kK&Z00oGmJU=&<mpw
zv%S1En?i*{W!3^n>+Ob{7epZ{eH*_ItvowUef@O?CYBpRiXBl;X^?F_0#x7v1h&x&
z(lw(|>QXt`Bq?n3j%aEJ#q1R+f{GRJCzyF+2OV4(+)=`Q#l{eg08GW~ml51=^GM?!
zu$|a;e=TTaSNdF}f#3MalGg7cjUf^<&i&F;*&*1d7MH;QJ}-$-Qi0|+w%fgh0tA6-
zDF@7yH6L_C7QX_f)#?M@cgBLpocYXHO2KiC7AphZ)H1H8!3BmZjGl%GP7@|(bYgi6
z5|XX{C@K=lu`VNhb@3NYW<1G5vqk}Aza+7zPy~fkf<tx?6zX7RD5?Ljd5-jdp#B^a
zT}Y=oov`8T+BqUH&A{7<r~KoJu^s#QcjlQ@aWq6-c0~B{k<5s>6%Z`t;s2$ADJ}GU
zFXi<>+kwu1;$TM*B>+(0?FF;6R4A5H(ipC?p+SpG;=Jb}{UOdXejfB-7%YSPQ+$F^
ziv(22mVSmVzo^aw8Kcaf2rKF79ehBUy^kultB7|Wv%V2-jRB1SuoP}z>)RCT3PJIc
zW|E<S7<GIRk;u9LMBtuGYHc}hn*O=8`LtdUCei%2^C$qQOVWccQz#$8807;46VUi8
zrY|eW1jvWp<bKOGWdta|#dElXUJ3Y>sN+Zyk|b<g!@~Nk<pA$}AAK4lPPHtPVYbN<
zkBB6mpbDaLPF^@hH6r6Y3w61$C{dn1z98l|b890#<65nlz6bmC1U6|+BG8Qcp9nrt
zQ6e#PiZJ<Uj4vuUK(@nUEqZjEdw~YhXo+jQOVghM^%Ti{|DCvvRvm0M(EZQd2x_4C
z-AEZw1|Zu8i1QLJIH)+14%)NDYD0%0pki$+5+UO~eq)Ye^IF^q&ELGq&@Mnv3N;QX
zHo>iy{kg>>Hq0Zci6?-`g+LQF#gvFB#{6+~y)l%FZ@p+it?C?_-D2u%sdC#1i=QzW
zDga*R1cepPNpY;8nDai$0z_<kj~ptnF8uW;ymM$S1x)g(;zviLTYJTo^F*VVBHoj3
zQlB+ZxImH<j_(WRqGbSy4PHi_Dl94|K$uxv(5cP<zg&EnN09Dw%@aq^_2n!2g@_D}
z)bNNXfr<*w51-4GWj~?-I$O4(LhI|)%#NlCBEWh!%K0K}2$+gx{HJ)pqgd9s@{;a|
z{W!N}E*pgy>w4OuYS_G?U%qTuz3?v(NGvE}kWVT~Sxbm@1(f6ik#S*`Twaf3_5}!>
z6b{SW72iRrWIUUBeUfn9eO93Wg}X32dmZ92I3ewDI!2cLbgc9Y7?ijU?GsR(%M1EY
z0+Y12k<GX5j#bo>E*I%2-n&av^b5?i0>E4;VtMB|`(rdX9Y<R#W=0GZD@;76IR4>^
z!k`Wg4#OaiYM7Pe=<)v2E$+99N`D<<0<65<d7+W=G=}tn!0K{#@|Xa%E6k;TNCh6*
z-dma=g>mi%phfZl8D=y3(CIUhT(X&~x9Y;TKKqF2o4c1Ll&}v`NyqOS>@Ae%&$Xf4
zWVR(GexRe27D=4`-5D(0LHvB4i$9D}#m)4#l@*F7F4T7;S&^&CVZN`+2TuWp|AGO9
z(AVJ>0IoBHr3BFpy+Wx{AuwEl35>-*^MF*NhpiV#8Q06=1b9x6o2N+{u!zwl_dLWT
zaDS%i5mt(8oeeK>>LJIF2ByE%Y+;NFQ}+IxzXa539uxw_U6>N^qxeFLk#gX^li+f4
zOtul*%)%vy=0}6~Q|z)pV?Jr9&$m%~w;RMH{i>Tc_YBXvQ6fOCS;p5beH=fQ&mRij
zx3Qe;o|a4)%X8{sZZQPvQv1AbK5GSAm49ierN27{v!V5GI2{`Y$SVlPHF*}+=t^Wo
z@X7Y-8FsuXk<mH{0x3?M3+L>|cUK*L>hg~N+P?6(8egp+4rDj|ggMQ%MCGMO)ZQt%
z&Nw1wPQ5fXjem@Mjc%|~)$c2SQS}F$>Iud~kI>Y)!YP|C_ssK%=H6t~YRM#}>yB1U
z*q6C5)e%c}l^?dx0}M~6;gUkPKgi%jEX(~g$u!<Y>PV&j0Z)m$#ll^gNa;B~s_p=4
z_A@t&z+hhUA+Qb1aQ7M7dvuPHMv85<#$R>z*5>bHW@*?5dmwSYhC=-9Y>^rNpPWLs
z`i4+~rJ!G^NR3Z7iQNEgE;J~Zq(^sRVKmYyal&$h7MD*lnSvuI0e&c0x5_Yr>Tp+X
zFkB^1zel>g8}lg6)+*7ig~IAUxy1--wl*jM3ennxZj^lRyN+y0;MsFGmQ}!zV%n_v
zL(wx?DL+C;=;QQ0q)ItF86n%KR|_<|`Y$+rlRVEf)fwqV`5yOr0M=jQ{{|!bs<a6w
z)|xuesnw)HkGH=pJ+a4j9bR75`2Jvv2G~bzv~JjR?jjx7X5MstS<)`qu5WM0L-Fe|
z%hEoY=o`ojGQh(Sbu1gVp79>DZnUso*k`*p2Ir=Kn;je+P9&5WImr`5S-i~qmT87c
zO<qzJYX1>kiZ_60@hW#b>q74ryY_&h7~?!zrv68Uk|~7!&~5s(II35S97mLqEX<so
zFX<`58mh=x)S_a9_NAXx4l%~Rj}`FO7Pi=P-62G2?t1Ka3O|VB*6w!%V=zJQ*u+2N
z779xHY)<-^hm99G!%%<cGQef9+J-0=UKlB%_UR;X+0G!Ueqfx(2clu>93_N<O<<S{
zNl@|57A5Gp)zk6~pIwXp*qtSfV}%iPuR)P<pm4GM{zD$eHA?^uH1{*WK3N^6%xU91
zHoz26lpw`$GWaecEiL?A9T-=fTKXcRkpZi`okx=LC^4pkm>L=U(Z3tVH8sonbt$5f
zW(_*W<@EC=$qwa_31~uU?vP`I^m;Zuw=Jrq;yk$S7Yj^&L|g`A>U~B3<3Asfp#IZW
zLjEd%p<v^B*@MCmF@+JB=m97~gfte1t`Yw|dSuaw7MH}=*}Q`MP+lR>%!(!=H?N56
z%Nv?u4N{c##j8#bwvWII;%JE~pkdKLUY(*|0uYzLT5sljJBY+5Wvs-qBn)(D^aEXL
z_7LVH0sr4Ek47}_9UKt_;J2={3oe3{FIt?uvKz38p^C!(9=QihchfN8{+kwpgI4)b
zV;t1Mo2n3kQ3Xcxa1gT3A=}%IPTN9juepW2s(F#mb!{@h*m*{+j&SuZ_<DJm1L5J=
z;ebbzxWlN``lvyK{olGOs8P10P_Yb}b)j8_6n6%GwX8`BUoN|?cO{gqU<YPSQ-@3U
zSKgVTrStF-#gn&3wa?tvA=h9Sm^XRUD*abvZi>w)IU?ko8xF82Q7@)EfGxWF+(G!B
zAA12^hqul<n)wk!hMYa4`-#z`00CM@!jHZ|TmVSZ78TgXsHF0tSFz%VtkD(u@Y^t2
zBOE%zxzw(Z63;bpxMEVkvHDY^pY!n>nu;xw)_5KbOj?yoHGK0s2!(fhLb;Yh6V({m
za9%YWNa8I0!UIfkDK6>-c&Zm0QA@t0kfdvQfqq3tGty>JP>;{?EvzY-CxRo;sV@RM
zGGfMg#D=s%MMqbp*TZ_#VorxAr)d2S?uOt_7C&-Q+*||#F<Qf7ce=X?O!anArg_Aq
zG!Zo`L)=@mM)s@ReH}HGfT+C05dRqB^BE*IGpJGJ_H=a%B$brIFmG7yRDZ{If3h&c
zTn=~^OBWt(eq7&%R=)9u@B#`0HUpelv*xk{JSw<3U80pcKV3%6>x#?V6xG4ryU$K4
z{mgg&`Dgw4e+0_`KsPTF+}KSD6;<-(O46Ktii#I4535|G;q@^5t<6Kx6_eBV-V;&L
z*UNdeUdNYXQD@%o$1)r0>L$etUD2d|RNJQyaAHAWFZ0;hTkBvIA1`kthKQn8`b9Px
zU{@~4w0F64;+TPpx0Rg5HC$Y6(8ICsI;r!|q<O@!9O+kgwY!T$#v}oEUyfncNxI60
zmc|b3;=a7_wy(lTlaX}1;mH2x`*z{8@v`k0!`1l=jqMNmJZc2o)%*?nVU2~4_Re_!
zhW`;eo7f0YA*5X$DhXhcOZdMv#jt4|I(elLAg|8YxBmuY#rff$Z?8W@BTEQYcd@YK
z*Wu8MU^q}KMqO2t_K?Mys0ZsFt&QKa+SFBE(<*fiXdiI#ue~^~Ev-B2h)7K60p>vM
zzp3KN)HK_Ce6q0RWRyn0E;<)GNJ1*OKnG4rk4OsWaBumH1PA_Qj3a-BQgH>CShV1a
z;mRk2Zc9qSuxAnsXCct`5L_xih|ru*<Y|ecOw2m>ZAcuVl@~Xk<;JjT^ugX8D_qjB
z@T}V4qqa_=J}_=OoHP%#<OS<o-?-f$4B;vvrVhHNJeR{|W&rb*J%~vDQCK9{c=!-h
z*YkC)NcN{XNnSKxo%f0#3a_BTavE_A@1A)8sS86&6j-ho7_M@|K|zC(%9w_ICQ{4y
zrvsP2GeV*)lKX%}j`_|Nds{t^4^)%|EqZ}<zc4Axy#vIb+8vvv*;}|dEsHq|GLlnm
z-xErF{S(i*f%21WEgWCMH`b4HG{pJaIg{1tmC#=R=;4$$$?uzx-R9|k5}vLe6oe8Z
zwOXc<<|YtQK&7p*^l!a%^ks#iO`Iv6Gzyf&j%SuOvTGMrfnB9&qpuYTcK}SuqpTTO
z<9ugexd03XAR7!DoDf%VPz|6aj6w0shJOHrWJIwgo$|@cdFuiEj#j|7{K!_|5qyh4
zmr3jT>Hut`r-@g9;z$lUlyEg!1jxtfl_Gh8Efg$#-=eY8j0jHfFSj)M@kK}B;dEMP
zsb!$v0eX-n#CS}we!_}r@*s-f)8B<N2Ond9A@HZ90@UG@3Zg1a+v{;tS*FxcG+|V1
zRraO^1%ujkQ5C2#lra?xy2W&_ljWa4Jgz8yxnDgvg6b9+4#oLb4QfPM?>?NO)ykoX
z_HYe&cqm5y*gI9#6C(Ok;hXU+R!a$CjP3glG=GSlPPQupJvtO%j>pufE<oic*KP+T
zw8+N>KKvwr13Twu^x>e0nr>cD?c9bbHzYuwhmEyQoCL5mXelxL_AQFFin1BKhofNc
zIYUbeRJ{D_lh_w%-PDYpuR<*bLxSxCW?bXyT(}8?3K6UK_l5EpfAP3l-gaBg0T(Ov
zfmc{B-Va_3e`ilo2A}1rXg&cNR=Cmk+7h_vQrRWGp)IbFN4IKB_lmab(2W#3aoI$-
zGw31KG_C7Co$;=l@uHGMCS0%ZX<OgYOcibpfQnFsf7@Xvx_Z7(i!m>H$BaB|0M)5~
zK>kAS54rplCalUSfyFd(m0-W}&n5*@KDcc*fwoSxt*T@m?JroDd06X3VMMMWhS}mC
zeE>-abu>iYL!v9Jv+lqJ9H0&pP%VZ5+ulV0tt0`WdM@=trGm@JrDaQFgx@<ym$aiD
zqllqb!2f{8U{k%~jm=(SU#_vX_;?tAnf506{t`IzJ<b&pUO$IFdnEU7@J9fOayw^R
zk;HuKu*#$9QYH^jMF35pBvFArez&}0JK34P^I5Qhbo-ve+W?I<!>>hF)lr#%!#&P{
z8o9G5te+f76W5~t4S0;aaf8U;S1RP{m%+>S8k&_P#x?8y&iS9c*8b0vqcU^nOOy@X
z^N5$jPuo9{%l!4pmY(h=-8Soclx?+@`yhp>mNGX%(lNzN;!~8hwZxg}e;rY(kDwtL
z`DTY(ph{!?I6k51j5)?fYNf%mV!tc`f`YXp2j{#oJFdWlxN(<sH6)p<FQ&2|?0k$f
z`8&P*>rKMjtVurbhZVW%OhiOpzRYo?<xbswp7>D-g!`0|AW|sHajbcpWCj9$!39~g
z#}4l;njf}AeB#et3s=^e_2t-unHX}b$*Yl*82CIp8~JoBf@mZkp`pRHW`L)(@!Cld
ze@daIAy4K*8(GT-Xq6&3`z{mNL?hydqRNleiFMvp^z~v$I!cUAiK?q2Z~|P$_i$^`
z%b^?};Qab34*?g0Tq+Zf+%7;=bQ0P9F;xiXX;6rrMm(!HHlpYu9S+L;hkp)EQTx<y
zZUF_Tuw0}BWC$F8*wSI0yQOm=WN{JDl%1R;+)f;(e&HzCa?jXY`h{u;n{(Lw)}ieB
z0nqH=`{?`+3r$eL_wT>*XOY8TCoMwe4bKHts!y{_({*CJW3hcubM2*cjh%xjH^s1|
z7`B4~<ggd84Vqn5Ggj)@p5Q(_;h92AD_|9^5EupC1(s4V?50c@uv$L=btaL+c1L^L
z224RXCxe`|UOP27Xq|ld00Fe)ZM5O_=ljN<EwWg|t6Ylpq5)9|DZo1iIv{rG9vxsG
zM<+xoxXtkk4PBzM^4I#8Sm`#(?>)NjtndlbiLV;Oa3m;-0_YTJjQ7MC<OZkr_YA40
zaN9`67c|Bf#~mxHcQ}T=lL6*J5<e}nbIuvihUm}q<K<iGdYQ}ZK0`xG{g7vlmamJ-
zHP|vESJn{`IH7ex7JQdNMIhKTH7JMq4SIWDe!d`<sNv~Ee{O?l2StfzYG`QIpC6s4
zW)W8BxwyER+!?x7%R@Es)aEhvxQX`2UPk}qo{13SUis73i#r+7_mM;VQ)Ac1FQ@b-
zE@G!egwwOUKT1obMiXLlbUFw5d6;QROKE<Va!Wb6dYP^;)AX!ow+074du~DiyHpq5
zV=D<B%ErT$)1PwlQe!fzO?7nwX~w77#Rk&4Z0lcgW6we^xZp_a=)RnM-&f-s=nZGe
z;TXu$Zzq~U61-n5o%`}OBvPTjdTOgo-O{SYisQgP!0-8tZ~LPhrBLI1oC4ZZb&<N6
zUNfDi8A)Jy)VAW443ZEd_)oo=i)xrTiA%={%)vaZpZhO*g_?s+tdJsPHenRc`hK1!
zfj7BV$$6yWXNy8>gUI}iII|2TA}$%V$e>BJYQHKPJPt_;b#hR^$VP_J*E;{-R5HaL
zd@DG)EdBKul9E<n@p_6;hj(#ms19p%GI)ukb+;)vfn{gWw`k-qY}+T=gl*m6ZoGUh
z6TL06=a={~?DO4|de_4OnHGt7^NSA+ZWn}7YB09d-*k4hFEGPY6R9B|C}|kvt1swr
zpLK;Ur<IX57=-Ob`9qFwdtVyOOLdCP29`XHR$`2U@?Z-tdDGFwOdpR<lGSxua}eC%
z25=$xg5p>R&l*UTHw=|;?+<RT@jP0-gw(rs`e}U15=TTZ+7^wE7e2Q_veL5Gsh?pV
zdK=}Y<s4XLhwaT^KEGX_DXA-7_l?oT!2S~!kWM;3_c7qcO1k-%wKvkj|52||D9$Lr
z|F8i5m|H;nkD3F~Ve_{g6F3Lvli1@*`}`M?g^`P@Z&`-qJpC3ASfNNbMl$pe-@f^7
zInMPbbjf=}^bORgq)y@fWif#>SzOmVnLkY@61sol?#&#yXNMa~xco`P**Vr9(N%jI
z)x%|xg~T1mNp~S2HPtHPk9sZQ1_v}<Wl|~5p?CKkejm~TBGMt>DK#%ls2JpD1SBbm
zjMlFHI{6@a9Na#({vm;Y*L;wn5rXsf7##jSd=eYgGvwtOy!(f_&@(GE(=c5Bchunl
z=Ay1sw%da7jKAk?`-`-j7<Ex7tn2_S^~3cI<<vj~#VYjLwBD*B8aa6_I_7Rw{Phb6
z)@^^66natAvUk{DOY-6?2eO@mc?45~p)^%gHD#5N&-aL#2&Yl$R;D11@pGEL#1cQ#
z{6AX0@|6?sP6-o`lMmpOZEcow@lf|2^8b8k<@{+p<Q+*z4Ih_aG}>Xz#bA#Gx0chG
zgz?E#T++ryC@%dG4|J_TLO$#ydv48Jrff=<x)C3Cz$l|}wg={2!Ff_J#o)`!7nTs{
zcELgPH+oWti1SOk$TP~K!R>=DUg%2&UTN?y7e+?rDBn3Y-Ijb^2}h4mJeslh41pxc
zJwki_u!CDt5O?snCnd%W?k!D{9iu4v(Oc1H&H*vl0i1}BgAMYMhQ4rq=4}2||ALav
z44Pfnkjx9rT|cp{c&C+r6iE3SY2aQighP=x@gn2}=ZWw~e<8g$skz2<B(uO`F@~zd
zB{C0;j!{;f`mAfHl=EQk`seffN@RClQ|$7J6xw$AmNkVM^||ml0+Vto|G#_(5@A^i
zzTY~Gng@L+^jsQ(a8`qY8ms6M3Jav-$-#R)&EI7H#`FlLV`yPfFF)hvFNV~xA;P0t
zD@xvzE?CDoD-odN)8Zg1iX$w1Dn3UyY9^gTr2WY=-=*@EZY%zfFLM_^2_Siq{zOH?
zlft^3gOc?5&}+OAIDWFALJmA5SLFT8c)EYZ%mxc2Lu_!fSk;7#QzvHEF>!ttj6-Rs
zv^>G&+H*(^U(*?d^m^7yJ~UP|y65aoMse$jts8~PIwU4u{?NRFej299DgkaIVu_%I
zRh1u3J4$7c7Z8cTmKti_k8R$c>?%UFaT@IolDk+iJ=%XNJhQuLA3!5C_QaB#x6AJw
z_iz=YXHB(>w(6X#k`cqK&KDcU|Al}@P1aF@Zc?t$B$aRn=M+B|KxJSs`blBIp!y+n
z+TB+kMNs}WQ$f$d61;S_vD&9vX}Vc|#g<$P6{Wy_H%hqAw~RydBLcpk=^jdD6U<`Q
zv~e^OnmhfKK~hPz#oNyaJ7`Dfb|+<)_N43{1_!b8c?`WN$q<F|<uUb(QxEs(t!;3q
z;d!aOd!C5pXp2FdgLz(m^%1<u2zc%N>mQ8ksGnL5amqZ&#1iVq_u|g7#NR+mfY!&e
zKkt>i6)XvVn_X(4MPS^?<^IeF<G36uxY^)FIH${^a#FHV%n{|ECf1jEX4r4eC0V1X
z_0B5-!j34H#l6oOMXDSe3ch9tW+f9Cn4V~$zwu>g#~a?3p5!fETA3GiO}B_|6<-T%
z`y*UK;9dVHiv?&zFP%=99(3${*9`OGCkgzk`-2$#SNpb#@VB37WpyzWn%{K9V{aIh
zB!{<6DtMla_T;g>52shlG^r{fU)_$M%Zk*!c>ep|;Eit^t=ohC791=>@SuMzZxCA=
zvBZ*E@#XH=SdpauY#14XP^UYJSp<nxEdjhpF-8L@l7fbC&XqF%mxk;4_jRd5>3E7(
zr3ITLo>GDriq<P=`nxwADJ(|OS-DDs;ZI3aF^7aI2aJ>!zL|Ufg3DkSK;q)g;ubLY
zr7z?(6R6rMt>)<l3%kev(sAN*0tUB6Y^S9FHq-mp9;-;{1M<4rx0^AHtU{xUylmaQ
zxq<gz(^-Q_n0`*UV)N9i&#AOtFnY4>*-DTp0g2#}_GsYqxnB<5n84$RX3;O(q5Pd0
z?@FX)*xAp@pLkWDmrH7XS*#zppUlohoO}Qe?s7_NF%F|yW&}kr*e+&!VsW~@TZ#_W
z)}b2Gt{^Vk%i9y+8PK~osbs%@Wt8aZ+C{p)C4C?_O_3LWdYVU7Z9~1jKtYg5c5%NH
zG3>%eB$%7;7%yhpo%YY{@j!!$PikCa&18?;2IE70xLt;fcuvvMjq<7cJ!aPT1zx|p
z{=IHw4fqX1Rvr;{4blbPq+WK7@CkYOuOs(#n4W|uBoFH$2IhSWp7&=PtvgR^O`EnA
zupnmph~O_ELHh_^f%bpsU|h-qN_SJ^$oB*G4zYQN87v7p_|wMJpeSDNQ6j4@k8kSF
z(vv#Bm`H(Nlo1?_4HJb(L|u*6_v{ugx7Vymt=@0l$a({{KdiuvI0d8R=Rvrs<q228
zd*c^nWmlU%C(k&aQ>XDWt?b-#yAAUO>Qzk#t%0#fgW~q3k-tF3rEBLqy4PyK;l4$8
z+QkLD`S*aXxMqkbv+_?fYdEKkAae3@Vqt`C<>Dcy<^)(<@nI`)pHcOYrtR-vq+p!1
zo6T&rG37z4KB+QMY>lrBUx_@LJIAiBDO0bI^7<x1dqa_q3Qp*t58!I(<rX>ueynGZ
z9ePDmom8uPMdYgVCyLPD>w(i*%*jWskTwxi1F2p4pTEd44y_>0uwg${+M8c~8-Mu5
z!1_+G5hKr|=@VssLHyxlT7@2>XBy)yA#?tySZ9$?4v&<~7gXwie)_WIa{%Jle8x?N
zwY|35p*4%QuXtx(F;ef@H`<#m1H@nopM|oDyhB@lKEKJm;UFWf;HakS)QtUW{v1V+
z<}=mG;>Q*wfDw%`e?NsrN~rmriaK=G>2Nd;ZYP0k)LWp{pwFUk@Xs(;7U*Y)q4sJ|
zJ?52sEFl^E$@)iyxU1Vg&9HF=r!826$a1y5IRZHAWlj_E*^b$x(TbEWvV&=dDe}P&
zHNVLR*Sp&NP(G<?7_Fe>A01BXM{H>}jwZUmifO1{&~&bi<L9IB*fFEBNr@AU?arBm
zblVUIC6c#ts=x^KbNc<7k*ic{fG9ae0SC_1hyn&`_KmWLbC3xKID9q^p;W7X2|9c0
z-q#K@$^sd_2OSRtJyStjMiJ{!45?02nB+W&;A@bKEWp>WR@`<>#2#P#m61-V_<6)D
z)a!{s?v-FyZS+y>Jd<*#H=x|&hZYvqYVBz<1LGO5U`oBlx3&QfrzA`N<Y@|nm<q?1
zSISd{_O9H!P@Vc58PODH@r!?d+zS6YxXQu5y9i)>+VD&cv)j=+`V}9(!T1+iV3bP`
zmcMeTm>Lwx--^X+Xob3g5K|?lTFIai>#Fm^(e4=&`caGta;;qBuhJEgLXjHo<O0@w
z7Zb^?j!5KjuCLF`it_6=;|1-}U0rXMJTldpAyR94FJ!YDdBPg$;D28=uYh-}Bbq5q
z-qpSE#(DqCq}|-x_Vdyt1RgYWGQ#ek=wLf2a~dYyHqJ~0<{QHy!jJHb1GU+P<hbh1
z-*B)f97vXqFV|DV_kRNN_<V^n54P#y)?&CJy=|R2EUG}9K4YDK3{b&8*+-aa{g0)u
zj*7B<{uV^(4(V=53F)q-LplVO?p_+DJC<%~>5?vKmJaD|knR$A@8|n_&*2>YTW<Eg
zu9^A7%y6TK;IH>K*|Rk*d8SCi+|w8dN<Xv<g-qA|^kmD)PSkj}Ozy3@LpS;kSVxs{
zrshHhU<!jJD_4&K<o9KrgAwVV;t^?^oRQWdMgiWKz<|WoA&A}IcN7ziPWDmx+Z@_V
zGsFn(Ex#fQXf@Xhj$4w1Ki~1KbXWJ^kkMN(KZwn1efcYG@H$YDjRVc!j)u36jFrs4
z>h>ACQ|-lZ06rzD2V%z&$^l>pa!t`!6?DX@9Q(Y}3rQ;tp7@O5n|qY<O**ZDC?ItY
z2`WFK#+@DH)<ujKBIu^h9^kB+We=9;2AOzW>bXT2wRRUah12+v>KgO3OMTQWPOR89
z*OkCNd@o(jyJ93!h-lY0e^^8ky!b7~4Egg&#EzV(fQ{fBT%}pMQLA`9jXLg(LZ+K$
zV*eJn+0KKlNwnm|EMz3;vuFP8J9V;pyeuj%qS$LbE&m*&r5*KG^w?C<mM2`{f!?r9
z^B+8YAbA1WC0^uq#MM`>fk||lX_h8cMhvBnHgT!$h70@5IZ81UahNNS)Pq#$*}`>i
zT9HTGp*%9vyGn76)(->LGR5en<2onThq9b1$GPTrk3k(lMR>S3({HUFg2HqLe{G}N
z&36++-rk`#e);2<OR1!Dco$wD?N3@iede0i(B0q=*1EslrNDD1PD1W){Qeh2jdiQ^
zz01!m7qb|s-<$8G*q^J)z$5CXXY>Z@WLOrq2P`Aj#EGfmkS$l8x^Nt}P990v+Mvue
zz4IJ34_uCoYK?_jk9j=Xj1pU(QXpr>pJ2W+37Aozwnq39mg*gc7*awiJb1edrzTEu
zkkJKy%iArK@d$bV_i<AnfC?=<b?3JWiXX?_xWDYK@>hUoltG!?UkCfd$bC&C^pUx_
z3>s6bCP|dd1ncA$b4-Q>L5n#p=Gl<y+yke<c<5Mf5@TUaZEzF;(^8>SZ%yhLs{=&j
z((N#Kw9ibik*TIIh)#&*aQFMCLMdHDa2-j+*4>2>Ww4k@K~hWs$`?+n0=1t06cL4P
z+ukz)Ggbkm#T@gddD!Y!=*?WVDMwgtdUVzo#i2oV-gpML{nx|Ix=ipu<+{nsV;-s(
zDL8uBcqNe(JfZs0^WScqXvmy})Uo}VR%PB<E?ywRzNMF$1xk#`{i_-%yAluTTYOh7
za);M-cZ^#=)M0R#J#o#KvbEUnm7|x|3vFQ^)XE)Dn&{0H^hS~eVFj-HK63uzEZ9Zx
znv9~OQ%8zbR&uh+@BW}dO60{1@4GhyC*tLV?W16GRDyA~{}2>qCgZp_9uo`ZBD4?`
zx;g|4y{vR^N;0ui)iwTFWPJ49yr;T^d2+4zlS>s8l6rHYe;`1!?73X@q@$JiUH|kU
z^oZj+xSitd2T9Sz4Z)AENr}lSSN-W-;@xGGVcD2;CsRkl_On)O7)FxFnZQPwph)46
zY8Ser;#!Zzj2~9B=`NV(iF;k<@s0P#f4=6Qj_y7+7NLO$1m$|uWp}h`2CR&h?rDr{
z1A^ja1K>hwca>{`V;G_e1?Z>W23ExJddYIY;5pu_;GZef-4NbkNPIhD6uCJznfv@`
zpl@w*rUt7YM-%V~5J3T@Tuir=bNjs23yOc6=$?et?(Ub2>#9MTnZ2R!nDchyU=%?e
zB(%KMB8iINOny&WNIAy6ug!aaK=sU6d?28xtsvy;lryWGOW7$({uA6TYJggGx%CLS
ze@L(Xv_Bzwu=+4*oTt7S@K9@czqAOs4-@qXaUG){=^$q}Y?EP+1%_VUuZzBdZnet`
z+%G}WsM*$a_J1JO8Q5VkNvuLJut-^suGX%h9GSS1r<;;G22%QhLoUz9XaWXN=o7$2
zP|@(bWxMMfka0s%Ab`1vWx1bMGWmXFh%sHwOEsXCOD%0-@G5+v*eC}@!wyOm+@Mjv
z@|*axp9|XCiDT$|Bj*fq6hG3+H+z<SuP%Prm>Ts#Wg^{+nlLVhf8X13`uVV^oV(x(
z;c%d;sX$4dp=E&57Mk`(|K1Mb0A8gT;ys|9hbcyjsW#l9!%8y~(!)7y6V1BAeOVS~
z6n)}MPN<LB?^N5x(i%LxxT)`Q+%P7UtEN@77sJOl%ZUXOBHozH<)yM=&J;uZwNP0i
zZ}Ae>IJJT_q;yklgS2&6L`0cS{3o&G_E1#RYlwl|rtnNrhyB%<ruBEy-H@;ye|H)l
zQgiwjJfuxy#XzDQaOJWYY+2_P6r9zQh91mFy^Ek%{T-B07fZGI{^Do16p~u#a{MAV
z`l80<KbF99;S2gHf<lDhLsUy+gFP?>0#8tL&K~{ulJ$BL79;X_8xp&IsXh+$>aNkz
zM^LA+XUXENI#Qv!{?G(z6W4_wWZ(aaOJVgD!@3NNgKILmFkNJ<>0B7Maz)fQrXC0|
zLAUtII7i_YZZQsZp>&4y*?yj7Qr*MPwuRUW)6&SOSPMP<32QNx87sfrQX6&Rs%qRl
z>XTV;kKV+PV|NRp+mRk>)Rdvs@v0F}CU7W{9v3UAC#u%{?R_TN4hkLPNICjwKbP_B
zOZ`@|=)mLz>wV1=@3rBh=qkp8@O&d)Y>^dapxTheXCz&RyYLyj`Nng@%v(w`tbVtk
zaAmA%;$R>{EU4REzx`BMo7CrO2UT?Sw$8q#yc?fg`q3aRf{@3(Oq6>T3_*+#J|>68
zf5fat)P|r@HWL`+5mm1@VO7MT2#uJ2E$ZQNz2f%G?Y((#qtm^~7!`U}U#*_EwRW(G
z#Cc7-a`;G`^7QvhqPe%u_|qF-v<9k}8N*caGrB@NMuijkOZ#Z52%I`QNbnX%UBuYh
z++MJ!1@$9L^AoNKa$KvcsT{dcCrn!fg+xCk{XC~n6Me2HHT^PYpvj_E8csH)#yq{%
z2S<CixVYtUL>B#t^1;OK9uJiH%-rmp)70e=mbk6sm3z2XxoUqTsSb&0I7ic1L$=#o
zbv}%_#~C{~mP=<={gUM+-=s;h=hdh0B?P{XH)y}|CkBVRh55Hi2zJURosbUIF;%Gc
z<o!Knm==CKWUdA13?;n_I+VE`)lDy-o&62&(zTX<K37jnI*E#{gVv$@;qJL|ki~Fz
zRkY%?OO<>N5DlR#4WaDHCUHRZe8g|!GOwoSD31p1GqM2$t5rG$mA5EVsD#3AK4GEM
zU@tJ*I?J{1$xDBy8kxg3eOoXO_m1(GbwNG;r;b3pqRpot70+^DIKgG97|wy9K2JQs
z0YXg9HR14%)$JV<@1Z_=>Zz&tpI6R~7uhXd^o~Au&nwYAj>d^*i}`ZWE_IjIa|PvD
ze|_V`=LQISaU0k_ZL**t_b-EO84z7wvtsUv9UHn7EO5|%6q@q1%av`b4O)FJzRqD*
zuPr&CKk5_s4ds0wf)^QcFHj2lDKMjBdiQ=CEF{FS(>L>=aFo^2JlxqL@NPZNh}BrP
zO=J2Pq4MU5yd4!zdP15+RlRQd6q}x@5qh1UR!%~O<(0o-)-t5mq*DK(W{qU>7+vS=
z)*4fSRDbFilhKE5Hea^m0JjgBJ-ba}%Jt_x`65TU(Hf@kHHJLX+d{p9zExYMQ39Se
zyshr}$}@O1f=i2io?lbTA|JF0%z2^o5#+d$KFITR3)+>R^qH|Oi9YDFeo91aIw}9c
zxHLZWXpU<t2R)(3Un7*vurRX@bt6~2GqlX$ljpdDC3<~y3CV9L7mS*UM?luSe7WVC
zeJcRtkA|IBfc7Fq2PqBV5o#S`QtE@_O6d7jAAzIc)cPEEVMeB+v{5FIlaX&c#-aU>
z6#r=>g`khjD4_WVsM`(-LK#KBydCGTN=*3c^fMe+&IBDfV>S0<P%-Y;-K7n4oAE8)
zzv8_%=L930B%i}ssY=_zehNG}=<5AY?P&p(re=gQ9_1~vS-~b1w5|G67sJ`&YoDHK
zplpe2&fbS8M^i+mt0k!wbpZOPctwb1S*sm$aESrH3*=g5B{EWY(09{%9MYv!DCl($
zI)6W4MSMzCxH1MY3Eig=Em8j|SVr=>I#JDi%Fuwp>%lXnI*J%Nb+`Aq$o)e$D|X1b
zI1;A$7}R{k7(RMRZdPm<mZgd}Zk6<X^1u!m3{NSp7lxgWpevTqE}qdI8;^^$No7t%
z6(!dK;_&x8!vy=DbJF7t5`v?JgFgC^9%3KD<(*>xC9h(kT$4<%7c)gp9i<J{%~evt
zi7C$H1<<s95?^4xW^eL4;&CB>2OJV;Z@#VO)A5B8y`C%S^ICmMT-)0J3Db!kugCt%
zFa@Xbr&DS+oob3o)YdOM=Kj%e%$J~o8TS-E^|6}foAn(fv62N2P>U4UDSg_f=uUy;
za8hh<hP+9_6Y{o;4Ot}CEq1nxGVShOje_g?{*wat-Nn;VbS0k3NiN+?3p1y3{Ypw;
zmT?j_rhQ#f;ZBQU3Tk0`vHE#hWimgnAPDA~Ai<%*8dpKhLN~Q^-nYdfzn7=_Zobpe
zrt^>07E3{@6yaO^K^mTnFP2ts%f;h9RDa#u=6d2&EyX?(3LZ!%5YPC*d7q+GcIECn
zGC(L<adm}jJGM9{pyB_0`vx(Wpaqwj%(?iEH}RCael1%eo$N6G-s;_-6%|INi{K68
z4iRentUP@AEOSPt+R%L?U8s7c94Q^`)VPt2a~iv)D5V6a(x*Tpxs=raiKz?H;Tvj~
z5BO{{w(p<gY1cwTS9xp963SeYlzqQ@xP>Z)5u%kM$Lr|WB>sl=o*B#no5uKcUU*tz
z@0KozFtq&>NBi6oqYVDOTv)jPCtmfJMf$nOZRhQUNf=cD?pI5G&!DRgN3KosA}b|T
z2*y?!N)<C$f#SPZX0#3_5GrRkShaeaTK)tia2y$f;=EoDms2R#iCRR#TmmZWy5foI
z^><t+*?nr#Ni`95<f}UZwo`&xC;o{JE@VN)W@D=E1lD|EjJi#s6-*{nUlQtgBquV8
zf#N@w9oO8Dz61PcHHdqqR}K$eys+&WYMycNZXEKOrR;)FXUGvPUknLk^&^PN{gKL6
zPu?jR-*7-b|Db!7TdUSOlmy9QI>Tm32x|(~&7`z<=DBAY=_aWNEpa)b-8?QE%jXH9
ziDDthwG{Ra0|;k8I<aEVCNw+xlI5q^EPJj=W}6n8jqXQ`Xr0J-G_6!Mqs*3=k!DF8
z5R=an;W+C!lacqKdNO*#x$ODuC;t<Z?#!Q6$>y@?5*xm0NlIA+(|knWk6Fp=w@f~<
zC7k95_Zw`2Y{p*<vuEz$vkhsKCMbg?hNvax5(bPFF%u2@58y({1@ybqzOl4Lf5ClN
zplO4bpq74Dpid}3xGHgk{#$YwxsZj*9RGXF6z3Lio)}OSar{>maSjmryl28|bYoh?
zH4`vlZ4G3IlB43}P&B)R1LY&4)v-Oh(Xb=Wy=}El)M^*{f=5hxNTo)|J$C=-WGI<W
z<Dex-+zP_ApZ3+#kVAm#AQtKiDp8-^>i2Xfi&UDu3lc|;3M?}Pk=VP`adLW*n0gw>
z>*(|lG2x<ziZ9X230}_-B#_6a#VglE;(c1rabo<*yy`}#z{j$L9zE43upx2DWuW`x
zr_DBWACr+6Io$;&&D5<|uTspTmX&{lUR`@9zd}eEp)qX+G53K4;sr+LCeAHKJn}+j
zNJ3?hhI%VeJ|msw-<|)oj`==H*y=2mWge`Xk?KMcL&NIrJnGG7On0!YM-ar_tr-bD
z`4P7Jca@Ktqzv0OmYyfWf>706I4S;D!MDI0N>ht9L7`oZ23yF#_EZn&B%e%|9?mt)
zd~S0;jvsqZc=nk+9A8*fT*ne~*_)OX2~ZUAU8&{eBen$@8?Fj7Ipd{}t+U=>THwgr
zD&dr1_Q_7w;X8CMCTD2aN=~AJAe4BlK>fE@V+O}$7kMibTSl#lcg)YSxjjT&WdkIZ
z_d$3BRTX)`VIOVf@|-kdpdAznfVd&sFCtZj*r$uC@Yr0YJe9#PIyV#=(K}#Q)`*sJ
z&a@m>WA4SSJS!Puz(hW!qOFUuM#;q~Z3~q`Y%Yr|ALgqAnud>YE&Tvm7Z64O0Wrzx
z+$<#22VvdjxYa(QM}y}V2)M2{=V;DzvcCx=YE=Mepm)y;=q(&aKY|rtIVRJ>k>$)f
zms*+ySUA=QbUrCAt@5IVG*fU(W)-q$@fq=>v|hS3SU^qhP^ZWxkcu1ED!a-r#%`FG
zTXlTt$>LkC4Dj8j<h1B22?y~Wz9Bc~*(RlpzXANSfS?;iX<v)eE*{V88mGDozz)jg
zbk$#lQFxKacSxbp4t3mLq^oLha;QfI%mj*!c`jdSYbNQbW;uiGvKfyiK~+<+)jwdN
z`}^Zvus>30)AS?VnSHu(-#cV%Bn))B>unaMWn+>0zv*D=ps(kXeKn7-1f(Jw1%70^
zb$R$RGM3=;1RHXuk8=DGzx&hJWE|1fZP8Ne6Y?W}6XC>b2G?A6dG1UbeqcIkSyCIL
zmZH*TM8O=GIOG(0Ll|fJe+f@a{TFdN$Hj+cZqIB-w%4~TCg=*1Tp}VD<)kbk5n|3f
zo|*Id>-otn*hk++%_@RF@X!0CTatV&vQbg5w`5#K&$!Thv3oc}msCb6q|dWcsv~+z
z%t$(`df^g)Epcr0QHE?8Uw|w+3Yv~B$I{KeZen+KJx+)tMV1ZJ$5hvKof86i@Wd=#
zd~S2_C?K4U%(q-Z)LzYXPqjyaB!+(b%f64nX%~pAQ^o>^J435oaW#E^aX`DKNVYe-
zgvby8I_WnU1yg9#1m&C3%yW3Sry?v5=keU&_76y(?3>*xVU*z!TS@Hxe-UylySk|H
z--@%-9-ke1{Yt(6aWEG=)V4JLWSD{|oDw9GQ^%;oJ7|+=g@!oHGu|-oWq%?t5+q_i
zXws;<XJrphhfrN%IH*a`Y3^EMP(l{g-s~2!&i9Woj=MOaH@+MbUTF8i>INBuAlB)p
z=T7Vh{+I8`PRRQHHR01?WZHscFH_~B+w&?pJBN!cnIcC6*dKU#@7cSq$X<F1;x5|a
zL@~bA;U{}1%(?jNzmLwVpDSvcD*1F_9A3f#Lu#cG=y*kuu0BxDt~ieLRoYG}x+*^w
zZK*kN(cI_5-#_??a5eQ9z<22=sP;tC>yx)*wcFIPIn;VXp3dH;`Vao9e<H3?1EQi1
zQ9+xJPdW)oI(cs5^n=Y;^T|HkUkALXA{efGG^3}Q6Rtuxf^%3HU3rNBH-7m+$b3tR
zdx}k7{`x+)y<TOb4Nw*l<#XxBy@Pe5j=CqBS6-<cFRRZcjjGnl7oYgPJhBXa?D|&F
z_*zNE7LZd`|69*9@=sqO{mxBH0KWh)|MeXgJsFwCtdZH0Pp~D!i-2RpYy4;Zv$b47
zNt61ndm;CI%5}q+<zI>Aw5=1#-3kU||L}O%{6wz6`iw%od6yGY3R*x`Z25G5QMH82
zsH_!`uJsQg#i`|!XM~n-f`wa(g<EV?$5~9uirv|2Wl(o=vc5<gSu`x%J$3h72?!|s
z^Ut?!jR9A4j)WhGBIodUEE8n^c7;|ulmxDjER4@A2sP|x=S}{0!|IXIm94G7wS#_7
zdB)4^a_@5T91%EE_Uf#y)c+dC`Tt!igy3Uj8553aiyp(@Pz;UJm%Im;s<{l8J4{PX
zI&{k%*|J=!;m6)fa1g7o!J$SieT_K)8#i(b?Ub;Nu$b^tY9<NoHdPxeoy_5w@Zz*Y
z6_U_po~YuJD&Ctv4cOgUAbLz2N+D<Vb5ry!P8V5BKoJ`}M?J&58ecREYg}fFoa7W0
zi*bF+p^0cn1pjaWK}KSg!t0}VSujJ?eVNcF``5m{YB1=7N-|s!tAPm5L))Kh-K1Zl
ze}cl};CbJwZ1K^7KGi9@x|d3mmawpKueqj98XrL3qj|U82`wSFQ4NYP7S(`?59v6M
zOvD6Z8TEMIjpXg@7`c}c;Ms?b5+=ppHwLlNR;epKNZT=$@|}jO8W6i34q&Szy|=D%
zFhG5J;Qci|Q$?}mx-FLqsQ+Iomm0-&fRb_IkErru*|GPsNyc;(jcK+|kgobv42?Hv
zR533YFHp+zk8o~&wo1HJBEtt+U2>-ly}6op1F%AJYAnXrk5u7xXiNx=Nm9Bpye!r#
zVVzksAzQ3))|j|xEdsYO$@r~meOFHeAa|LMXb*D_S1dQ)zIF~d55wqzJ$3lIGRVuT
zErJf;PGxfa8JfdnYlWeFMe7(t<Oq2>PNm8z32jL2@`=&2<x1}bv&w~hcL#XfOXh!g
zG{<!<Yd);@ZI3Tw-8soMmNF`7C}BzQ#fGRuX<?V9_Do1Ygm07N$@Of1@$$tcmkS3W
zO}N&4o;`v%li(pmY6UT!5y}pK{gGOM)+?oFMlX{YZ1+<S7b(dpzGtAx#<NTwmSM3J
zkQ6B#M-%lqWb=4y2+(?Z1SMb@#a2qO|4?yPDYR+`0huU7r9ZvIO6k*A&rr}E;am-#
zk07A#yaDbjLFN6Y?0e#8w~*1k-a69=u}xicAx)s{<=hvQ?$`ZcrL<Yf9LoYd$PSp#
zoB+r?re&_Iif5FQ|D*{0>lvQ>3Wc(_yb+3k_dqiQcwh}+|JNyY6{Zo@Tt^#Um{+oL
zcgBwKAy?9|ZYzvuuAm;^%s6aglF~C+?%44NVp&WTDAvm~eibw7&LkZZk-9VF$^sm$
z1_TqZ2=z~01nb)B$dKhJ@m_MI_Q)XHdPbWw-wNTLs+Eny=TzkPb!2jkbcHQrZ;7Pb
zEU4Q5bhzT@Xsx!R!)c<KA0*t~986OMsB6w!Jb9fzSwuGDC+ZgtKlVn|T|I7l(r@B8
zj@EVU>m$IsD#zXwN8_aKmZy!mi_{DfB`ev_+7{0RqmNC@l<P4if4_DfuIDgctn{&;
zIam%ZfR6`uo(vaE)D4*;%uAKnos*yyJU&+TI$70SC1Su3T*3nge2*|Ko~YtbG`$?|
zqqSmE(J20K5@{;*WP=%%j@x`tn(~}AD*t4sGs=1(`0H=Y$kwB6U4ooC{#Ct#+`ju1
z$qFt3XF2u=<ocbQ5}DI?q=!yFoRAh2M@e5C3DN2z>NNK}AFzcQp6V7E6?8G*z6V9~
zhUVM5cC4G1=B8rmsdLJiwr_g9musLJ#(57CkYB-=N#alf8bk)f(u(j{K7JLAQIqWX
zET^%>0*)U5?g!MI+n3@=`2J#z9SI>;J!^TvxO9HI_K>KDdsDuo7s76sPa^$qwj{@*
z(>G|S!7j?Bqxqu*Hu#|7Nf2swhhv>J?TG1-oztG`go**&oCZ|PewHySHhYeP_h-xA
zTfKqYvr=jjO(g2)hIabcp`7aSEDF;Oh=le|WKp!R@a-h^MVb-rRflkO8!5&$bOfCB
zGR{qM@yzJtbG#t87@)qA!jy9p6R1m5TbLe95z(|vD65YH-SJ(8l!SKrn92q^esqC~
z7XLj42V5jFn$%+(_7N(H8ZyiYqrI0UIM<BPeMPnz_s2*T6{Y2E>RLylI<F*-WpQf1
zjAD6LT}x~9)+D^1yq5e&a10Ixolj_F$8P{qy)F8{sHcI1*IA}fLr+*ZW)BZ`2xS#!
z*>oxV_f7x?1X!z3%Yz8~Ks%Z^I&5A|OA2$J6q;RjH8Pwu0R073M6mud0o9Lr_~k2I
zjy9FC=uD`)6A%^JW}W$kIn+rpbV|fGz!as5aSMOd1`ARv*q*`_uYe`t-Cgu07Bn<%
z#;Fk%a`T9?3o==zlrN8H#~;n;$=_egu^gJ9=9aa^L3w&BUTJ4uV0nXktA-4axMfFu
zqz@x&UW!g&5{eU_X+jF}|I9lB0ExjV@+n^Zc=!*6OIMBC2Y-{;%9^CXR8d#xnAqM}
zJoHW|oaaY<bj&VqWy847@<14=^m4ZbL6`Rdt@lrfBniq8F=T#H#l3FAvlk5E5gC;G
zmCjzt+%Mf=TrNrY@eL+aIy%?>OF8j7@xX2;)@H?z*3PWW61-nL?EFK&?=y&u6}Gk2
zqyu&|%*QugUY-r&Y33}LkH7M<^yPUqCO$iN%x~@{AC0CCBOy5QXdg;Zt<suKvv27V
z&@EHV5`%v?U46^qP~iJgx~<O(_%|P*5_U(g4;;p|db<HvD-8Gbu9kosIJxUN=xho@
zGUdt7|D=zG)Rx=R&6^k!H9UP`XK|~tg%6>J#Bf%8T{Z@<vke!VVLxVnE4NHthp7JX
z5qHlY-Qo;th!V@7Rc>~%h`7~DWtshH_>)+4baLtZQic6TgN1i%Pf^s7TN_nu<<Hs3
z(Q(Zd?;;R%=Pm+uf4<q%B<3MRAh~St+U?!52o%_vLFYrTo?)DK&XR#<58doIkZHM~
z$EFP){U}wVI!%OQf3{0*Hz@!Ij@LQ<C^BfUX&tK_fUWet7e+uuixWW{n!aN1qrUJZ
z>mAA*El^ugbHSXbW#eL*sy%B}d&om4ckaG}li6K=T*EI}v26b6J7sku)h*m4%`?ay
zS*DdH5uP4&XtW-YAg2!65xdX;{Ah#Q4eJufmd&DVxdzN=$tmVOF9Uac6_bmPWP8@*
zEqZDo#E5=nxEOfpZkw8}Yk1TUOHMP%n=*1G=&Elv5^e7l^Xg{Hld*6)5NLb9{b$7`
zJj4FaU#KXEq<eD1FTf+dxV(D2r7Tw;EuK{~eS%xa#9&E(R`$o%bz?RT%=`E@Bj_97
z7{@nTCg0^fv4T+W?y~Ra!;91II|sRhF?WY%v{ij+u?%ZHaj~SmzsV0a=59hw%T2Z?
zY!TyWY`f;JXCk@I8L10iDGeo0l`$rzGesZzxu4z=9PtoK2TUvzfg!3XOE(+SR+1UV
zii{{!s`9E!@0e=zX`Oq1kl+9;8HV{ojReZ~_A$o?kA*Ko$PS(C$)Pp^lFFYPOkI(+
z{W#h{?|WxAP&$6eiqs^1erk%)kK%3$!h@I9y@rOfa8{ssUx%9I($P{PO{ck`9>x<Z
zrP1>ZOCXD96<MLBBwZ(_@r_IhVD@qL?tUK0A}eA<Lmr@1lKC!(Ndh$i-O{5pj=9xJ
z2}XO`+9y*g0X&@Ac{($JBS@@?H0rMz(co%}&;+4X_1%HP_1!-{4~OM=dLrjEtZQ;b
zSpCV;y*Xyrfoa=ZW9fn(NxryZ(`-q@bTO}Ce;tL9`_Z!)9(`dtJrYi!xFSb*IIsZE
zDM3EJfhtymm-o?40Pfje3af7+mKq7V3F&+wS$XaNU-_5UTz&fUl%>;F`iDTmI0~Nk
z+fv7BZ{srWdr1^C<4-JbDNYIb?<JR!3nbB)Bo=ne&j?x|Mxo+h<Ot}yB$ggk>{9n|
zPGlSssZQm!Sn-WF#FC+6dBGB;)A3oeRuTxj>i2|~K5m_{aGzKXjkmW-mwf&PIY5(|
zP|LhTn@zOMHj$1xzcK)EYQSd@vA#qI5DVZwRkkeHU0m+k`kqvB{bT65=O@ox&iqnK
z3F7bS?55~)&HzjvFOFR=s0%NvkkINz0pGLZcbx&JIOVG%>Aa&_@+@=Z|H4G?kc&r(
z1U*o1RBh-W2|t_Nv&T*?PCt9hx3${_TlbXDr|6!#Eh0(ypQSTc=|E1u{byeUyj@>?
zcNk+#zc00oTYg3XoVP9VUMjP4dL*5$d+?5|)t9S4i~F;R$cSYesaa=h(@Au#AYV?5
zhLZ;m=`b|9h9a;2N!0VS0kOish~Ze)3^13e)N}+a`VcXTwol4jO%KGWN?a_$*iAu4
z^zdp(->W@DjjvcU4<!<28$?Ldey3~U(jmlt`C=F+WohuYF}#k1HVy}8zD}1>(<y07
z(KcJRw5Djw*C$BI@;Z@lzOE+NES{E;>YO$6K|Lf?+t_PzTfL;;n}d?;?iJFE`yM3m
zxl^|iVrLrYH_L3>{Vnutdy!WoggPaOJLp^FQLLQPJS0u@lVo1IV93^Ny@KNC>}h}A
z@q))B`XS^!=4kJf2dn%n^-Vf6NjX`@ygtNeK@6v;!oXnrT4CSw@hZ+_@x^a>J`8(U
zy$>W)zc|u?8$yW&{xyY%f)Q&wbtY@j+N@mtVT%uEM9a$Fiq}U`ImID|^X1!yk&2|%
zs%&Qbs2eOo!l^=<mW>kRmZ;dIRu>7CPWovY&Pgww8P08+kj~cWN6N2wqjbYu>R=M_
zUj30#jhf4=D3Fd}ie4h~4IPT4LNZz<_*X<k{gF;xDENeChKz$)L23U4`z;YXD$_vl
zDv%9pKNI3c0>3Oh@BiS&s{iqgTld;Swo68gX!o~IZ%WnX?`W67Dk07Kx$3csI-gN!
zJ<#okOQR_rfR$HR_+^C!krTLLBW^F+BwMt*OY)f!dI`XfIM)8(%D_R&aL_awM5oT|
zSNENL#hul!T%WlUWy`CcO=+kimm%Ahof=tDI=!5!QCDM+Ue^S>s0TdVU6qi$d^ZE;
zNr};UOY>CzK{ReQ1+CqDkGuWCJ2mn_rtFxtw`xcZ6>iPvd-zbsmNWYR!deo#foEcd
zs5T@B=Ya8=WNDsQjj9gqu!L6rQS)>!bWTY@v2FQj#UaF!iT)qFit<=&pl&dh9GvE$
zEQ!+WO*q$B=F!IjKT$o~4Sj;xI!_0W^#jr{>p&<Jd;?-hPpv-O<W0u<Vu-0APcKBF
z&2*d0d_UKlD*v2ltNk$W;QG0P0n1F!wRCkLK6UHsna6p>zkdOT=h&T|j4F@UC>U2^
zmW*1cNK71$<IhM1=p!HIb@}5}xPfcZ8pIq>oluma;P}=2<nMr=^_d42H74dF#21*3
zZm+_K;r!f#BKkDWr0l=N7&0uIs+y$kbbQaEn}Qpmn-W%az|H<(`1L4{OR4nuVyFPs
z40s=PdET5|Up1Lu5MveFDGmlisg$e1iqUu?@&rR}6yJHMUw$Ej>QbF5pOaQBLGFp%
zwo`Fm`=RK-i*GB`4Wslzl?>%X?$}}An*&}5llN5lx8l8kbUuA*dG@X4K`h2kGYpF3
z@n%W}M{nf!cyYyD-dDbruaZnMq*1O`b0QaqAtvI80_B!3-~VYxA2<eftP_D(4Q-b!
z<}rcBugG-ZVWRJDbCV=fpeB^x%I64PJ_NSY@`AYXS!k3sg0axHf;m7#YdrDX16cG-
zrQ<>GF46b>g!GvrV-r*B(3?*5A~Vje?t9R9)_c_>W5j<?R2f(nEtl-HLTK?m3-|>x
znt102lj7I~aSW)VtV3khxSXLl{Y=l41MVzawBVM-?neA%sB9BOKF|#SDxtuUVR|<~
zP8Mfhj{UvKJ-&m#VtB%t_p-Q`(07o2rX^Lrm<N<H6+;coi36XrqUtjx;XSkre_}Qw
zAK%c^I<2-qOXo!Z_1HN64%vG@zih~h5th_207a4A1r<K?5hW{{qRGqq4t9$FlDYV4
zhl!?+gwmM!bc5XeT_%PS^z-3`)qD|vRq+hzYkV&2jcOA4JH6Q~PvSv!c*9yln_jC`
zS^TR|EAOtDXCD&36t=3Ek!(>rtcMMwW0&b3!o>3aGnY<zB*rr80YY!<I7Rb?y*(J3
zy+?q(uKF%$vFP90^XarR7!7}Z+qVtGH7XfA96R!dBYjaVvfqV=J$p6-)D>>4OIrR}
zW*Aoa_f`qd4spGX6O$>mmK-6=nzzZ2o{LCZ;Ipr)DDP)cZ~H|rSpC<_8pBLaM8}>r
znOx=ii611C$<2<z`QzLlQ|AvWAZH2ywU5Qoz|sBKFjtl0Snbj5_Lo^)lv;tS(3_&O
zk-`{>DlLN<^VzIvCz$BK4PHx20Pt@#;iEqNm1B|}u`}E+@I3X9$TFf+oCx9s;uz;m
z-ZYl_s`w8MvtXE4u+t<x^^7o1hj^ON?<TxPp0`N9kdYEyb;`bD5tw+x1=G$9M%0%R
zCZ=Xvwkl*94ys)tne4wRS0|X2d)|J})6S!uG5oYjH_HmW7EtqsTVLbfaRO2=;kE<E
z|1{4JlLO~}XX)0A^tLg-3Wiwfdp7oW%Vc|a+QJ{%&Zj)U`pf^_Z{fecsEHnFEdAj3
zviHI0htW9`TCxq`U7p^x{dfM)+~4Jb85rEO({fy{sdIYmuz34fId?ld+1=mwVmN$-
znGb`(g8qSoT}X1O);Ux@JY7Blrfy`@u!zaxgQ2lYt(NgA{H(%1GBH}~^G5$XTObV4
z^~vH0&ku1H|2im*5rmDz#_o8&Bsl*N!!87>+@cBFM3VSDJIf0keZpQ!#qjNDK2R-d
z$l0RM(*ZT^?3P@EXWO>l$=^>MeDpIJUu^xaN@dg8@VozOC?J{F);Yc5cn=t^s)f9x
z89wYSXqP+HE^hUsraqjuL@`p`XXZZP%@k431`f`8WV+gt{DbM2w9K7O$AKR~qn&!m
z+cSwm4IHv%Jg>mFW`V^ZWi6l2MPRGx{|uA0#&hZKU4Pvi0j#N%W3UOC?)|$QFQ|8S
z$=@@B;akVA0hw1vByI&(a;hZ$yBCSTcgDZ)^Q8HO5Q11r>pvxFX`%nlxO#SfT3;La
z=}y%A;qM}y|6@rtPBd<gsGCz1Mpc(!gCTJV!n2c^c&)w_V73-iFg1-$rD(B-UHRl4
zH0nztcjwsz1tmZJME4@8mQj!w;cRl`BWg6yT?4ma;&gdz(RR6+HI?S@8ypSPE6aV~
zUK}OM*qa1D@m&o|*IkcGRnKMI>V;`{KGVmE1Vpz;`he@}aG`v=vu8P5Tcx&lMID0T
z^00yl3L1q^ombWVzqT*S0aF_HlY!?piaLq~<|$k7L2q;>pE%rZq)P1$y5?Y0Qwz~m
zI3yIu+>ZY{9(ioTw}L%T9i4iIczo6%lqc!BW)@FAg>%P*Tm3#MtK{Oi!1Fd?g<*;X
z*Ib*4FK&A=3{>ZCx7e&y-tu)zt9cHN)Rsbe|Bxz=iLqrO;jjDBCS=GB5lo%LQqZUK
zA6fw)lMMuK5n{e;q=(pd)~9dX{KyMKX-;J~wCoVw07tnd8GcxXR@?;Ye+hnrKVe>L
z1oW(Cn9EV={JjRercq<OrM$=0%U0lnP;B;`HmPFt36^n<kDg|F^_)mBhk~38W_%D=
z43}aVKF3P&-oK^yi1ap!XoxH=pPW2N2jVS=vN=pUC{)?+xg#NLa7(047U|^4Cc7xo
z5zJ2uDbzEe$v12#4ssb52qw|?pw{Pje=O`^<P!%m!jk63<kUsNpd#AX%5zfG%B#9V
z$g-d;XxOGpg*_S@o;){`o-0E<%gMZ8Os_i5ak;nV4J_gih}bL;?-r_;OO*O#9P^3Y
zNvUk@YPMA*xZjlD^0y}$A4#qL4E@R@krv|p-0N1_r`RIJfOZ(lpTMudrq2F&oli)I
zz;4(&oEIS=Jx>MuWb-Z#cNgTXhVXktyXtD__)lZ-)}Ch9pTpWUiu3z_X!1LUzh`!-
z=^zH=9jS!ry&pm5`BE8X%Q%s`WypxwC&2%ALp~cZExbO+4YR6t*Xf!wefB>39!wGK
z46G|4m{X-|!&M^;Lw>&9sKV8HxABo;S;upDFabke=d)i`-)iY{qXvV$zs1RKAv-q6
zXDTpeJ@asVg&Nb9PxoH!tYz7M=k}j%Y7-qE+~WzH<Lf;Os;ottFh??O{oOe!otnfX
zs;)qnyw6QH{WvOBT3R({t!jx5D;9dbz2=IZEtGLHh9ZkzNxk?3gUijTp{Ha(np4}+
zjxz0*$5C`Ger6&U&UYR(LpUl@Qd@Gc>92^;TOk5<Poy1=q6HZwRHox8fyNB#S*1We
zdRR(A?+KHd4DMvyR~p4}AOw3Yp!UK_O(I=8l|ne*)1g{%QO=Md;Lwpgh(vbO-@wZK
z<|bREp`DT<9`&^+U^zAM;iVd4TAGoRN&4SuZ<YmulZsfEr)UqoeyvfCRTb<YsLwea
zZzDM$32PmZFI}s-Y&GUu_MQ|T@=!{b^0V+n6?r(`{6_;FWBk|Q682UGJlTs_OH`D)
z3TSCExt5NCqUpTB&cmNoatro+{*`oH^V3JZLpy(cIE`z`E|~Ofkm%UBx-vR_8}cpS
zb--GgwbJG9Bl7?u;FSkFC5sg2vejK<jzTw#UC*Q2qhI6=92y@=M7?f`e|%FS&CS_3
z_!3mMPlHgXcctQgjgrl=WvN}IabZ9o`FS)&_Hbl?BOF(&&5w;oe^hgLRQoK;jUmi@
zSmGP~-SQ#2gq_0X0)e`GVG>KF`@uClslpV=4oX{tR<6rbf!^)n0h&usjg|yTMCI>0
zJKy=@FHYEE-kES;L}U3Ie#ytv{y`P#y6vMO1Y2Re|F@mnK0H9V5jBXp%_!Xuc?e0A
zWop6rkjdKVdJAtkH}^2Q`F1o(K`}KFu=GpRQ$$zcQXwQ3QOBB_3@JosK7ae_cT6ii
z-%Z%7!v1yJyClj|7l`?TSBQ7DD<{t0<}m?})3!owd=nCtft7eb6Vby1uB^_{T}%7a
zX25;70-wCIi-o0hpG%Vh1KPu7L;=wK7FbVb@3E4;?#igo$^VssRO(s}qO3TZPLE=$
zRc%+}ZJsS(;5pG5H@0q#!(bp>-!~nCKUXEp*Hy=PiXM!$P!)5sAV<e3<EZaJfkC}w
zySj2@cfi>^lJZj!T|H4vRa$7*1U0jALe@P~e1Y(cOt7fivA?ZrF#Q>q)Z30i^j|?L
z)sp|Ja{Zvn%Qa8V{V^!k?-)z{gpA)w5NPskTHL-|p0^UVl2AhdNVGbD@d6hQKdMJ@
zFN)C8D{yt*g|Sbq9$fv?&KdAvDQup#FpuV36KvF**+D44p);^dpyXGAR#Jw<VezUb
z5u$g6m>mi0qEM`hNTg*kfKriXP=`zcCe?9UmN@R;m#$IH_(g-n?msuQnWthkBW=c~
zlgDOst38EU&-g@fx5;H?6)(RsNcPl872T)SRQAg0E*nJh@hcT;!>&=(=Nzc<#Bu4^
zaTy%3gVzUYb9-u4jP()E#0Yso_2qJHzE2bN<~;{KXn~G-V{g`<(K_!A|Hoq8z1d#d
z0n!5W7{%KA-Mkl?y+r;!x*bsI^L`_d7vfC1Aelilp$U$edW(eu+RaHacPj|rRgTL)
z;!tDeFl00N2+FX|Nz3hqwmdq0Oc4|wud2KnXu!|s?ybf9kV)d!6V9+_88Iz{>{=;m
z>=$4DjzM0!SYA3Q31~BqI~hsUKf`obx@~DduWArzclP6Fcn;q9bIBZQ?rdrS-Qkrd
z02^0+-U#r$DEYRLN+CM#TUl2Lf0`i4MQhC)Das@1C^n+r92@f1v#P%&M?|ss$~Z+H
zCMhpop!XYMFEqHdFX|Pj#jtUl?2cfp3r!5OV7$k8H_^SimDh}~mQlBIxVc0SlOKl%
zzpSp99EkuLmBBLp76|6j9UW;UGw0M`ORxxy@&9e8g}fHHNBM&+cvN#Fslz~Wk@5aM
zc1*8pP`)Y5QeQDO>JLf_PVL{PUqRtF-QUFPIw%NsO71>T@Q=@GWd_`Dr#b@y$oBc{
zVC)RzeRB#A`Smd;>Ab}&?45Td+{e^8h=ISxs>}UF|Jd@B@b_`<%4Ce!)7K~T@eYr}
zH6HGPw_$)BE)!woBSyNWOSfz^B7F3I^&2;=#;)P$={uc$KKGWl6F$?<SY!Z|6(7(}
z>^!}1L`CwrnPUVDMwu_jrA=E_j1mzM?gh_$PGzR>G^2>!Kd*jW|H=>xwNHjQr`32j
z!1P6h6!MO*c7R>-ZFg)nd$VVqW0~xol3lpRKXcl@T8(NwtT>8J+`XQc2(EpM`M!69
zuH5Ao8*sDk7qcI5XpJG<c(z$tK(YNcr0kXGS47xfu@6iJq_!Aus8|eao$p&DBB<d*
zY*~%d0G~LM!xt1L-QokG5KA%|E<=HCi1QzA2_%&90<VokuHW%+?`6l}QU2gr97KF{
zAYQT+qfzCv`9A%V)Y}nTx;oxs{wLlmvHaMN9blFedF&#u$+mzBSnfBi9M45nC8O`1
z>%w0wiRNQqLm<o+tw*%Kid4$w$aPfxiOIVw`ZwL|$jZ$4G5}lq{)4TajK<gBzEqo-
zlK_cntcph3<OrUyZYoGMlU(Ay*IXTeEnKktWDOIlh+Ax}tfPxEuimRlAUS&{V-)`2
zziZxK-XUVCo%t*9jXhd=Ehv;}sC2GZEWyN6A;Sc->1gReWm*fW*FCtXPSAKr;aN1h
zr(Q4pIl3mPhZveEzXuv=(g1NI!U0ecXy^j?<Zjp^Q)E?)JED0IR-pXhp7LNZC*;Me
zGdckZ^R~WTqmO)vfwx$9b+U^}jv<e*%?tivba5e!II-xDRT$H~6$<Ji?Bv}GB{s7)
z{cCZq)X8>C4>NXEo=<D<fKb%)M*pLfJ)xTH-Hm}oXz`O~4{d((9(h=*vVRMdMNTaJ
z0IWTsEX0+mxOvo3|D;L0UVKM9tj=v=dtbEbUXjXPsaA#$=zjn5+xCO*#%#U7MPt(;
znr!V}A#;C&&_xNi*8oMi$UA{C94JQ;8QHxYsv)IK<zE;e`+ju6KTI{7SZ&Ewz8td#
z(r%iT_ZKN=78%9O`io+o*RcfBiofkNukF(7Fkdxo5Cd1qnAa(Cv$%HQM)UTG_uROS
zWcf4<PnBS*W5GXRi1eM|TSKuisH<{xxBeZag0|cSEtj4Hzh3fP_xZ2+UZACb69x_&
zM+QxL2IMoF0(?^*BxjP!L}FS5<b|6r_bdGxE*vj{kf{(FTN_ZM)kr&dlbRO?KtK9U
z7+eZ#67oZ#=D$j}bgp#j&=^^Cr8i7rXz_xntR$hxGuSB=CNP1NvbSfVLrh&BiM~&*
zl2AkHkvXUAlKA}aB)VW0>Y+hdy*mzisZ6#XSUuA1Q5(1t#-&Ug$iM`&qc!_wZhG+}
z0&DLaTCXtLj<k<FaC9Vc>A5~ks7RXye^^5CDuIcabFG3by`9bz_&pTRUQNoekvVq~
zN%=L`31may`NGv3HbpGVyvY=KY5itQ;$vlonbq;I@@q=y_W$z`8VjkDZRdTX>Q93c
z|3?!Y0dq@ajKC@l;>2D;n`{l@L=Hs*n<i!bR-b9U1+nmiK<~!0e5DHQy;Q<i3Y=`I
z%`>d4Ag%45FE|00dxHP8yKe9?cx^lz$3Cx#3@(q9e}15LaF1>GT839xt&jpHD;zz;
zef7B_dvxvzxXJ92>UNKpI7ejfQm&_1nRCV7h%*xHf4CvwO2$!PAHO)HL3CI;Tixoo
z^|Ce3RT1?&7^popm8>$aRV{aFnJvZ*wE`nSlVT`;Z1DX-eTOg^WeT+6t5-%$Cmm(8
zHPWTC;Cr}7OYBg=EpniH9}#7-;DbJm0iE%;vsdEA^`gdDgNpc3qnaNTQx&p|bPIT|
z<yVj-1jL8TYUQRDvk|vmyp#LAllKWecs@VkII>j!2jxe#KmO~1wQ>EU09*3qjO7h}
zfK<Z!?(bf?WeTr7P7x8PjB<4iiX#mWx)nb>iaugEzMP|_u64$CDtZ3{6v%tJxL%cG
z1{BlBY{67Ji&FXn*?-p)MkVVQ_kXHI>dQ|QXeU&B9~)6xDo3JgA<dIE7q9m(5M4%X
zMm`MD4*!@#(}=;668^SY@uXrQenB67_3;Zk<`|p_-$Q30<mSwG-QC8XJntM;JMUS3
z;D5Y^+lw3Js1I;ai7RQF+K!=U?^Wr1VXpSy|0C(HQl_kRzr!v(R!Wg=a@fPH@If20
z(gjF;A71axGe%f3ggb}U?<WE>)hnC#rH&0v%H8h?Db(9j->^jV^*6;)g#_WuvJUsI
z;s%<yq>NsdK7RcTjcL<^_*hNbr8D}6h~M+%?`TGo#~&Uc2^F$vRR7DZ`6Cj19<ikz
zp7{A7?5iY<xY0e@<>IcUG6*tjlfjx;oO+1<@=ooN9^{>(wcjNZo+VY0;!m;u#0_!n
z3_6g`zt_y)DZ=JF<exCsmu15Dk5a6L7Hc11yu3?a6Qgvko1ta2eLwNcoxF7h=SAdE
za(6f6h6}VCd3(vV-ZJ9*<E}p-<UE0lkK;rJ{;$bB451~@8G|QllbOb8$}OHS{)aoo
zck$8(-%y2S9UEf0BmKturgQsD?`{S~903z4hUjy9z!TfBF$XmRqnSYS(HGRWmghL8
zrqDWWmPWrgc!mOnY~9f$>h@G)RBZM~vJBS8ix}vlqHPZ?*?2fW0FEnEH|*JzOA3ak
zv8)OmwM?Hldo;j+hV@F?Tz;4MAl!!K6vDG$!E~=PkJYy9@9Yb_VGJY{w~s*F^?m-6
zuEsd>qL<u@dy}WfsU6~fcMMccEReP&1E6@yq?rkg8Y9@B%gE9-EWwp&_uTx1+JJI3
z`$?9bp(dHw%aj)pxQ9n%Kr8-Ux%uCa_CJrn<h(UKJ(J4$5)v7+fpb?`Ocytsz`Fg*
zy=j#Fxy*l4Bt)x>)Uz2X6l)U(4T_&5J-3%WomEuT|2e!|YM}F08@)J0{`)Q$W}1*|
z&<cQx-|EmJ<<w+{IH1f+XIg*4ijSkV8#LV<LW^l3_FtqqmMz%GTkf`!gcMBVzIMm`
zr<mj?0XsE9Z$uFDWk`A`O@RY>*6#a#zAGT3+%n}<;2Su)trxxFrjmKzex9gv?WAzX
z!^tmfF-XI}^9rCb|0-S$M3um%qj4w5iobl^z+WQ+yL0g-{{gRvn#s&WfiY%}NUP@g
zmksvCDu+>{qK>QQfH6L6I)+6g>oy@&p(wqBqV9oKSXXnH6Y=JYjnq%vpu>ho-zQA}
zp$kjQi_s4hB_f9XH|y)hnzm!fkd*(3%=O0)qC1Z*$zhR-!JENVMSK^>Cew_&aW5}T
z5$^@lRG{mw+HBQ{eM|w@kS^H21R@Nf*0`1+4NqxE^GV0ks$CgYueg*W`1fVMrob5a
z{CKs~{e^U_kk>c$%5QbIkq1Ntr=(l3fio;izhJ<U$p3e|8?jOJY*&N@i;%W4Ylt;F
zSfNV3z0H2nh9HWNPC*iLu%or{ow}COF)otH?qA8(9#>J}FUY*1CQOpAvbLfU3x(eA
z6y>YV+kE77yXy#;?z_H;Cz_AowX+xexvt56d+b5_Q%NqRGQlEs(mN*q^<(ch5=m$d
zz0yRYg*GSs8*bgkKrA-tSAbJBRs2o)NT64pXkja-Hjws>k3R;S+Xo52sLZ5Yq<i1p
zH3*&QeI|LG8@xaN&$51@O36+*hQ1xbL1<E7hE64<m_ijC#PLpyDxU8)!IvIp#`s^J
zDPAG^4PmjNS1~%3<pi?Ejl`*!OT(-Q*h$jRbO<*p#P~~R7O_%>MTLitfo)Sd^EzV)
zV+))41l_PYa6#)u#UiLXIQA}OGX34a8+kDRO~XRRsY7@ffCw6H@CXynibm=m>ppWS
z8I0Oz2Z$QgE597wtU+}sqY^e!Ar_<8o!R>HxBUe`^tyU%Fwdvm_1R~O9qtc!Ivh-^
zOlqD!HAYuRF>3XVF-tRj{ur0N0ejH>#cALOx!(*KF|c<BGLv>S>l6z7quQuxhdj*P
z8V^-R{!=)()92JQ=h1G@)5Sj}9~|`k%9i9maGhm?!EN(zP9yG<8gq1{PE}JIaCsSE
z+%Xd0yDnD}@koJZKCdrV$kKP5MwT3};5`h+hS#akW@=*-?Q{!4J!17;riOj`^_@MJ
zkyD=t7nmuY0_OB_ii}t!-qlOsQyjX!C0h}<{Ehi?qEc&^340LekBnnLkcYL&>+<w|
z@+v^rEj#3W$_hC7wEmK7v~!X=K4rhgPrDZssBiaSR5hk@Y_iI@iNw^cDw?+`8h35N
z&vvHjx3Q{3-3)0ITpd-ZDN~F6n?bFncg|t9y%%H_n93TA4^6%vBe%acflvGXeK)FH
zjz1ew;pZJWi}TD&mjc~QjWFg~NA>&3rDFkv{@+9NlD66FwT`agXLrpFyi(S~dEVLk
zdmru#Aj<VRrI#y!YBy%X*0k*VwAG(UkJ8jr$4dUtr>4bTz5R%>Nx76VG_!<tP4hnx
z?ua;goZE9_m_(N#f11Ha(J}Y%0NRd5bu`$kq{!X`cF9gl%F_3ox8XQlmj-!C$2q>J
zutWQhy-ChsN_H$w*46GrZtwv3r?iHuvG~Z*$<j?qglEd<ow<=a3Iz0`+Pn6cUKv$$
zDOq+54j1tly}npi<$m2v77a*bf9Y4@?BEm6JN9El>R(NATEEQ1_Ypl&gJ1$<l8!I5
z&P0RbdvSK}T04K&o+`bGz`~&`W7O?$jK%J+PB_H(y{p%mgHOrmu=ZMBic_C4TSO@}
zq8dqAlgxytE0a`rj-~Ao!|Rahe!^+=yRT}pRFujvq#LO!P|D1I9r=GGU2|NW|J&bp
z%UbrbJIm&3*_~R(vTe6)o@_6>mTfKDwyo#h^ZTQE#nU;j`@TNc^}gPqQ3ntivHcE0
zuS5)Am~u@u^H{%otbnS&g(D;{N-V2XfJSk6tT9EW+eJ`z@|{KFK4dEkzy|<$%<|aZ
zM;j29oc>#V0JG1scvYE~<{C2`CW+Wy&rc??&$Fa+g$+B#m3<x`q@|=PdUQSSB*)7+
zA3NSAIRWqpdO)vQv2Sq-%@Gt%9*>cpVQLQ?Z12Zug5ThOS<vz=@5MHy@ZGxAwF34o
zdx8%$4z0D#<35+->)Cs55Wb`)b3Exi1QFk`{Z08rLdzNM7T~*gl^s!EDI36SVbI2O
zoOj;|dNgc0=>fELLf1VbRR345#WnH!1Od6zSXU?y;92)jPc6STeSPnJ`DhUQu#?m0
z`GFg>QR>Q&2mu<ne`|?!W4P)=|KGsfQ(=^ozcCcZ4e0Gr3!C2K%dZ@a=|v~2(RR$I
z);+Hjy$@pz+#bTgt_^`E>bRde-n(lLa<a&9EemK`tmXR29xSpRa8u^;CK6(ly<GCq
zpE67`0RuC@_703LEycIo9oOWtx9<9ex5YMsmDEGua^$vf&((IFhg3`vOr*P0+wo}E
z{ubRXU9`CD>{gEKuhZ%BejDv}+EN6xW`bkC#IarPq~#S#u<a0Al%Pe0WUk%A9V)fA
zjuwsD?`^z=E$Y8}luHw?N&Q<SGY3&Dt&yMTi4aodONz0DNNxp~qE2d9TOEIH#9CE}
zKHg8NCJfZQvE?Hes8?+0zFf<SHWG|Dghty>oKsK!UBjeK8G;^w>gs&vmSl`SuR>wg
zPa>tZbU=p6*X%=eAHyERBo_nTXhG3SN2OMO;~WWzi+ELH4_hmr7b{TQGSGE}sJ7q2
zn0PzuX%dV2Qb=)MABn!*y`P<50g%|<18cAw@N71)((lV4fZk6Q+&o5<XrRZ99T*p^
z@EIrP_p~RN0bd08=LxAm+FC}BQ%e<t6>M^5<#p;!tx>8swqCHyiVK;M+dO%azwQyg
zpT(91W4H^&u}CQSQFP%6M8nw0*ar_Gl0wghq7P*8_o{loJG?v+zl6-vkDV^h1OZ#h
zte3;m*4HU@fy;3D>h~Q!pm~Nb!7v)W-D)`gp6N$;N6yghl+fs7AJwSKGjN!d3AD~F
zlmVjZ2m|$@-48h=_|*687b8TvkH=ZtGxFn?SDfn$v+g|8W!hF#>gQK`;U>v~e6n7J
z!$8}>+Q!v&vjqh}?zZ6!<0zR;Jkv<c|M|;(b7+#S<o|iP1T%u8vZ!X}a5%&6XFZrr
zfC|klnU0P^=BM)qr)VSR7wNf2NruG9rqA};8185EeyIFI%6u9<P4NZ@1QDX~fkM*V
z?)M*%o_e^Nx!&*Q(UFCMGBP{gp9h;d-A-8)a`M${Z;YL|0T)2?`)PUUy)()wg87X7
ze|w*NTOmu`Zl_N!_C&3mgC>0x!BodIv}%WUmmtLTYV|VJVq|}HtzwBdq<NLmc{)C3
z!4Y>K->wasKIJBf#WBgkP_Ui^$1fYr^yCzL_YcOHU(&+P?Xnen;^JI?ODTiN3N{XA
z03vPKXP6$t?N<H)FdUTVyby^3m_-qEvGBr%(f2Xa$_kznZ3cm;&kCGL%*N5NShEk_
zyPFTP=#uLx@FS-^L4ErOtcYfs+B8gS>b&SN`c5TJ#q>O|rsR&Js~Z=T<=Ko&2t6%{
z14|~dan4LnZ0d66k1%e8*W4aIzB>Ct;*Jbcgck?s{|tUTB9ReLn^({DBSI#FX^W{Z
zCD0P^icF9`20mn%qOP;pCQ0e@VvA?;e8cQbe_ibJa2BxkDEn?SmQ66Fa~xyDqsnB&
zLw#RQC4Fn!G<JX8fuDgF$3-g5x<x`7s<cJ33EY?(^rzaVJx}$>Yi~o`sUuce6J2&+
zK_(J3&Di>`@{ptc^|5<Mf)6Zs^+6y%4wGJBws@Gv)C`r%^2Wa9m+Qk9OZRQ5lx67v
zJF!xnzlXuTKkHWkj!K-FyFVN)H08PxYJaa;kcDQCFN4>>mD7j{gn*K2&s>IKM!mV}
z6SpzR(EvzWZFiI&M=}?)0JE<|K4)wD&)tC<r|RGDM*DN;)Us1A?lLS}G?bxAPvrvf
zh{%O^?6&+KBOG@qW^pyuE2N<qQ(SG2?#+iwcsiPz0`k+K^>tfUeo?nhF^A&%(wR+~
z!HMN%L2hY>;=pZgU}5k4)p9_LHs#&gs6uX8xp;Se_M**2TRyS;x15TtmIdaNA$^}=
z4%5|61`Q@$JcL-gEzCyK5{k3|>{3UFCY%it^=cjtH9@)F`+Q}%+r>eY#zaxa^Pj(U
z=b|d()Hza2&*==+2vFnxQ6ch3sz5_x`wi>k%YUxMoyI%7Q?6~ajGff5Td}~B_^dzf
zzNBqus51Pu;CE%OKUKpVCK|}(7QyY+@_xoYtv~zv?9B_*m{dcgW<77Oin__Af18B@
zMD|3+imfMxD4XaC=;9rTz~8kwxvWEQ?xaGDqY2TgzL5zW766(z@2(}-C`{PbD1&fl
zd5&Ry6*|%C4t-@Yg|xn$elr@;Ut2aA;G|O=ch4TltOnjgkRCnI7z-MK2avV-IVLvS
z+BWB8*x|9n5jB8~2=GH_ubl!0OZAuZM2y)e2aIUg#+I4gM5Di6J0Kf)3^6zOcV#y*
zQw6lN=u-$UG%0lTYBu~Aqc4Hl{gHI2bYCmLHmI`C){gzg8(*L$@B=8I>iPrrA*m?V
zvOo}|F~|;Z9SDa0x9$2&b7sT&9nRI!I#qnX@UdVZYTY@dK2o53-1jh)W#TMrfARIY
zWvRhLldp|yU^?7^_Z-%*Qo#H9Zap$IcS4njcU<+Xsw2-zz;M^fAi}Pr%GNP)$uXhw
zefu2khHR;{QU1Rbggj)k^s8E%j=qWZS8Sh``*u--2H<qizw9N{ne1cSqqGD#vgQ9x
zl8~K<YjM|#bnq`IBExTB5z=88d7s<7(gCmW3#ZTZ`FR)GIy91q-e@3a<wc(0Bc7h%
zXaf6d2$xJqkL!rXrGi^Lsv~(E7iDOic2fQtyv@tTm$ip3-o{tU_!&Ds*vbQaUWCd6
z<R2y+-a~y2UswFn=%=&@Di7>W4*fl^N{RChmPo!yb?we#pKEFM)RwO-k;!l|X`3{w
z<ZE2uiZCasF87)VY`h&VmID48-ni9EXXJs|8W#sJO&v!L19zLe*cDc*)vcOzk~wS?
z!cS<r@6_w$DAu|NyiZa=QnSEWNLA_iEc>=Y?3woDn9$@u-9&6U`Q@?GilOB(BhdfF
z<Cx7O;5EeC<6Gk_b)-@Rhv(CL);7=;z#mP|^2;;B0;)E_$EQ-ZB+WV%-hejK{FyMn
zbW3;-y$VC*xXF5~8?w5&W%u;6fN}R|VxQ9=-Y@m4HjkFIb+fk_llAes^4P#@erstt
z&`<BN5EXdL{ikPrkJ|f^mTK>q&G_n<{_O3;L$^R!gKTmkA1CL8d{V`=&s%>MxXLQ5
zVeCyKatcLHyA~D*kml^t6yyOs7t-Axx6Zt!Vg6yLHtnuKHZQfr3TbpoX(cRef{dl*
zY{N{-SNEEq{5G9zA5SfAmOpKo5+sy;n0Ii!3EX}O?0Cd_8-L$CcX%q=cUdcX{;*vC
z2%ulmPPsCFksl{J-too?=CrNy+U5${=5~j9Ig|7eXsb?S1MB=%9qq|DhC=+3*@h}7
zWi5hWBb6=uD0038;eNt^&Y~Fk=YN%sT7c(Ip{H9fJbMpV07Zc@3Db;yzLl_JO;8T8
z6_1zl+t*w9<zXgbBE>;X)cgjFG-NC|{9=+Sb++qwjl5qc<00CB3um!AL#7e41iEFh
z?bmQ6`ci<`1<(g(Vhlk%a&N5>1|^xn=MlHz29~h!V*a6xF<~y8iLu>%4cMV^^ODo_
zJ?2~=zNc!Fe|civ8}8#%_ZZ-i37Y%jc@OP*&Z=fky!|1OSpeZ5_0sc$-8+2MsYD~i
zSV(RFr@St;EUUnK_hoB<`R4|&VD>Zn$A5GrX9Z`St;d3n2U@w;2hjT)F_1im-ZEmR
zS2+s+iZE>-jA%j9r1_o6tt%|jtTk+m;meZH@J;TgvGRnwhZBPRZy47HGD>9+0f1L=
zD<|u9OJG+_0Q~&K*Xuk%H%e6vbBFjX`x~BF@`A-Z`|~8375F9=I7jT*UU;z7jF?Y8
ziBcjy9oFpEbN=h==xKTVC81ua(j-_u8p-6H^+*GHs#0j<BO@3);ZmHMr6a`)LQ8s8
z#^wfLxFo4Af~O}ud?Vr!@aUYhh@@04K?FqjynoN@{U9C|0CAE!Zea-MzxbUojF8Cc
zz^rPVqQbhtSJmtchFisN{QXXOxaWc;{&<_*PrDc+<2i494&N=*OCZQKHoSWqTVs3e
zK0Kv0ltQ^EQT(T=gJ=5wMq`Oj-Yz-*`y`3}Uu5fc=X{aHo?}VL`~qNE#eFgOQD^82
zS{RU<sViU~P%IpqYjs`S#BD4^i86m|8m~%6XvU^ic9N}(MgrMU>bN7U4K7?%8y+$3
zc^l6m*PJ{Lps*9GoFy)CcgS6^-EN2U<GqgivNc_MNy7b7b$q<ieMAb*T8KVg=6pmH
zFtvP3#Eu%fLi9PUm7okJiZNNguQ#Z}qeaalG5-65lh3x+@`j+rL@<3BFjy#kJ)f4Y
zoI;Xk-4&GU6X=AzQ~15S)y)zAg(sIQugDGh!I5bdIX;_4UkXgf8b05EB^@2s!2tXc
zuIF;@4j1N^;OjADaK^LW=PiKz23-9q_Mv%+3G^htxJCdNa}k{4XBBVOGwTfeT*RoU
zWw98-!0nqa*T}*j#}tYY3Dz;oCXq?N91xR+i$lPLvlvitOYydMYCQ0WS_DbH+fl8=
z|1mE^@Q4{4BWBZk__TGyX7_@><T%;vk1EjMggW8%A1MMH2xfC$a!R^)hyWMkR}36!
zb$Q;O@puWv@gM$h5cc40J~5YziJ067$iH!SVNMZ=S<*d<=80MHiYH~QGuc<hCMMtH
za&>~l2v7P;Zv%>fj0^zg{$XyP;+jLVJVw=UnRNHsH(-ZP)jGtbtc*2Qjm-@Z`aqlc
z{4vT2la>IEnQC<4!S?@Qr<@?>Ak*5`VM~FPPNy<Oc)N7Nd@~NISGKgQ(pCd(YCOC2
zC<)<mWT{Zk7*c4V<iBS~e_V|+D8>$u$q0GxrKN)XNlBsHlf|kQb68>cCd3egxRkFg
z@!jYt?a~P-hy6)l{*ywuvHkE{tnfI7VzFu)B=*I0zRfN|4}$UuI>_ony9IdyuG1B8
zALqdoP;}S2-NX+t^<TXDJfr(tOVnh5_c;c!JccUT{%c$<(xW~3C4PT-vrk;WtZ8s7
zh0(DSPqpYpj>+sM`O~AkrIcdp8Ko!0R_c7~nCEKeZH0B*w3~}^j4d->Q>|Ar2=(K9
z!*5K!64B@a<0Q6e!~UO|2rjNRjbB6Og1}wSpM(gvmpC#F6d51uo=8)OP6k<JzRLY<
z;+PJP&kr5<nst_xJCNBw>S>`!C4vGdZBLI_6}oChuS@;@YZ+;JxN#LN_fUk6pLoXB
zWJ{*vwl5B5ZVuL;zXS)Jv#K%x_U?%gLUT5;iCbP$A0mP%0ViMK#qEjr-DuRLxsaZn
z3Qxp%8q(0UcdsG(KQo1Ne2)&%Ow5`sdWRP=IUGN7c+~fXd8H*Nn>?R*Hve|qzM^`I
zrD-Q9tP7fQY_XOF+t?PoYqQakq}&ko#K4L<b%!K)XYKur(Y#RuOev%J>n7BXoXt=^
z&OLn^t{5Sal&C>sy$Q+unq&tGFU>%)OWdRpbwEX>palqwnF+9iR*51O20)QdJ=c>I
zO)dmxmAal7nz7$V2~lnbT4(G_p=8}`l#;C7Y(_O|*+*_}S&s}85{ym5<_~l@&ANd3
zL7$3f$z4}8TTXItlo=Afm44mOl~39W5g95RDH;vLG1&0N0}(c^#+P|Fr(;8<2E-^X
zS8LHbL<??<U`FfT3CLoGuXx3jK!oZ&RG+#bOR?6MKodi!wjsB*JJ}`)vyAhWlG9rr
zkObgVANh?Xd8FmBzs-`6R>{<_dZQn{3#V#BvuN$pQc&hw{w#*BvqtM<+}F$UJ?4ut
zIu#$1ys}e*rImuS>v@wPiLK%DoDjy)A0_#0IceoM2Zb4wEaReJ4ns*DThqTF<QVap
z;NNga?C$x>Yh!n~1OupKQq7Tq7=7;0_6kcuqjL{u(G#{uqb#q$Nn&KUbRnJP19=5z
z2z*NKi}>1?$LR4YpY~r}e=U*KlFOOZ8SQ_rL*Z1iJx<c^H+fopvO+4C>wJ6UabRVa
z%hIHhWCe&yi)R=C@Uvm^iRRs0n=U@P>U5M@KKGIHrY^$nuOT#&DQOi~yAzp)HJL>(
zZvfF?LNU?MxMtMd!WYxl^&Jy>9bj~OzYL4Q=tY3z#{V8XCv`k<U9+-d8(X|=X0;C&
zl*-n~V2HUbblSXMv5v~BrkF>>2MjzM2*Y)CPvU8<1DILXYwfwi(SV6d0mX_1u-*g4
zcAs6rS7d;`Ft`=U4Jo(?V+g0-`|~jOBlpX&{=fpBFdWs0Xd!_S$~fBs((7zL60Ev@
zzDT+iB&8(5_2^>7^rH#A_5O+>?T}?#_vGVHnsAFX?0ix1tip%?K75cA5mI(ZPA|Re
zc<OjzV0@dTe<^*xTgQM|E_#l->=Np-yRh<b%vc#?nqqVZ5oPTQKJj);aK1l&ez+rk
zi75!TxIbO1Q$KqSTz{pIe_J8vyY3r+e<lT#1<t$Lk0c}k8`mAzl9`WN287<8vBW;F
zKfIqJIYay(GD{1IVSv-)iDW~g=sP_UAh;4Y@5$XpEu@|2)wV1Kk{r0yDkER8V0S1W
zHp`<4(uA3&wsv`<kiwhX5I-xWTR!7qN`UPjQ^=(vaH(zg1twEEz0h$xSq1gqa(2%{
z1`Cl50U9uA0qB@9g}4U4pNS~v3k;V<)cXNz=F6c_UiXM7yL-4PCzwNoq^I@VB&~uZ
zE%M<dT%<%>nngs+ay*nD-l4hwEJ!ncOt&b~z6oTbbyLcVt_6I+?CY*nyy>vdD_g)t
zMfinZ5%05KKlP43*Z^T>1#ve7y#;bsAOkN-=Jlv)+GFi9F<@<!9=*LJ-#%iZNEQRP
z8F@GDqTA^p5Jmfz@YTcWmx8az5G^D<TZh|Q=~)=lO!*BP*vcEDzTufQ1Xu_L8VE*h
z^TB*e)ye04$YQ1<kz4Pt!ES`=1c>6npSJ1UBR+rSc#fjC;7=v+0xX(|5<u+c(2zJ#
zrPJZPL+I1wr+C0ZSqxs9-fD}>C|4&Rrxy@Q|Ff>r?=q^<$yKBWGq^#*80t$VP8<{7
zNcukvpvW>W(kPWa0Ofo#)xEycy;L5Tijbd6wuSYlTe)=Umu%MWjW~+5ZlF=+!y9rC
zrQ31FF`u3NFR3Ae^2IzI`oF&uenY%Klqo4?5yR!rLIH7c+rfoq4X^=<-MhzMEv2h%
zD*6H2w@iz?`ocy0zh^LIoX=bh`2RZ6{A#=ag%T{TmtOC=N-Kr3ht^B~=>Y$ScBHkh
z1Ksq0(p~RRfja?cqy&ywe}H&>M3$re&F{C@^!J{+0(3DfpRpE@u$g)c*JSl=m3|cj
ze3RVZ=-p_U|3x4t2S)DUcV37dJGL>;=>qr~7u}Vf5lVvG;uZz6KEX^;%tQ<~TgfA*
z*tG>LKPE;hKau_k3|xcmWh(D>2I1GT%kjA+bIDvyJ?wHE&ue<LziVz{X_v$sMe%#Z
zh-V581DGk$Q&wdqy&VO2GG44Myo@!se{WLUx`=<4jDrX-?w^$69I|<^onN{wf3-&p
z(i<EhD&hZ1OUr{2jPC@a$%mvp(ybUqF%pzR?dBAgr(9uta*OI)fa$Qyf;G_-8~0jo
ze%AB*x(ZX8jxIAC(@zBzwSYEJnFiolqa;F<wQwk*sEdk#Pcjpd6oSp9#;ySi1}4|U
zK$At+M6$Wmn)u3hrV?F2Qy_!k)iJbwL)QJ!X|9Jev=*iM4EeYUsru|Qd_RhFhsY{7
z0-WdUx1rS_LliI5zEgkbz6*Go0NC#3z6NKxf{yAkRtmiHfDD24Q~NO4sf)ckN@2*a
zRz?ydtm2m5L#zNUe^O{*V;9BD42D$Cu<4h{5pI7E`N#4L#_#VO)=08u+zQX)5o+4m
zLiP&KIQ5-hZx=)DQyvk}1?mRwr}8^rpGWG-i}A-F0+%;J-Ap;F$Xs<kaj)0NR0Mr#
zJbalJ+f5wcz2U@4?@M?PrQ}ouj*mN0fh7?)U=&j;-iUKmJ%G*aVwW(zucD@N%mN3*
z_3a)G++Ds*2dk+c+n!C~`#cm?GV`nFDBqYmeKIa8<@46h91^p0L`tgQXmU0BV(`;G
zx3|*!QBoz1UuC}K<+!pftek?_!!s5qlbda6JzO<a>rc&i{Vqq!Tsj|%hffEDx!)B|
zu?(B*@sj*shjDj^0n*hndUX#!^CH1~%^jH$_Sby@;M;`(6c!iTC#vWg+1;(CdB)Xi
zugBlQaMk3GjcHDR0iX?_IJiy0m-o6uyUR-6&w5*bM=tVl&lKWpJufM_RCsI4!$W%5
zd%X5M+aMkO4&HqgrjxAJ*hpa%7zeoj-zB<IR2f#3gcae00DSyl8uoGZeY=tg*vuV?
z2-wQSM`RP{t``An$cp35$F^1VI|PPk&n=o~d4`LjO794t>-BfqeVvxxektC2WG`RO
z-!b~hOxAjf=8TUbp3D7>R)x}y)W#9agqeTr#*u&$-Dh73`;kx6&ePs6cblYOXQ*jW
zlS&S$YUb45xE$U$4>P=;&S||!3-F=-l482j@LFDSR$e(EvbC0z1+r^;|1$3MmaOBB
z%(PGwKrRhA;jWtuSi}dc2WGT@JQ%>tY+J3{WXT7Cn_{7VedtV26ZXS*n+w?9p|tNG
zSw4aCK{+!>QLi+d^j!Z$(ZBw8p$T{H>u~i?Nu>do665v)HuU-?A|oMnn3BpI@1H2q
za_~2)&;p7`_gE5{gU@6ULtb-)%Ro_7C_mxrxw8gts|SuKD?LrO=cxGi8;#TdUWIxe
zM=YT9x({pV0jKR$^Fr#8hl)tlpUYwTU3xW&z123}xbXkQN1{iXul;hg3_M<<kQBo$
zf>P{u@o@~QH~u_dZRYZ6Y1KFPT%mH!Tg47A1t|GFp-c<me`|cdefK*yN#ee)4R5_`
zYjm);!#Nyn5iM59)?(c4qNm>fx8&bLkyipeH%7#0uj`#%um#q1n4CsmUUbnn%P_D#
zly^Kzm+6>YO=Y$B_bI71z1%r1S!A?aJ+u%=&<4Zz-?@Hx6!?omuG4BCNNsF<7a+5O
zU_}2?Gr;(IJ5l|HD1UjW>l!!jbAh5Nr@Mc3czoU>q62_TTea`Ke6U2?8yFoIm`cx7
zfJD{*cvWG~P_jRp0EItgowr6W#VTJ3stL>>ql8`#KOLZKp`XEgh*MpVpC$sa49?xH
zLJOp!{ms1=btF)^@pJJ<`_r>-cJ12k{)AU5t6<CEtph!`**YS;M+=g$d$dAgzB2t(
za=F9J;j7G7Hm<i5J?yAag|w3FnO92OHU2|pO@_-u|L4hml0ZUQ)J9E{T!qf8u}VZz
zs7x!p(;DT+HksxKJC{KT3CGWxkIK73D2eSNLps@p6QqHNxOJg`QGc(PV^AqzRuDFB
zU-CLZyD-gF5`l}M>jF(ljq3bM>{ie~BDPk&mLwn$%nHZXulkBhEcVaLL7)zmOqJ#=
zt8$wsOnN@`<_WD_?py8b1O^qWzY#oS1+t3>8I>*Ply(mo<Xx^X*j#9QAA%zl%VB7I
zmMPW?4aHRJnP-xrlO>H}^&=@<p5SeWvSJog>bbvG7p8?uED#&+b*cB=Um}kKOEDwa
zO!nGIHR9NNHI13q4%~>Oypiam_PR#Z7ab*e?k&coBwN=6RGL4iSWPs%TO0n19Wa0=
z)_kJ5oFqWfOw`w}7+=|ZYxvZf@*4j@d0sI!&?rnRS*&B|Zs+$Y8nj~9)bxE?nR-O+
z&V&69o2z}SSIcYJ`Dhxe@LoO&EPan&alYZo@vl5Y9@0gfquvMuHjn^T3Sbeb`FXwp
zps{!X&T~BDWcRwm#zuC%1?R7j0$aY|&?bC9rwpi+Ag|Q>+;5|#0j*x&;!YQV3ssGa
zrPiub*q|`XO4FmzRWUJ_MRDz}<sn<ozCAMuPaq)UX-s+ZQ}l^}eTC3pL_0*3M5}5~
zy9AmL$y_%1gE2O<xHZR9W~4j6&0Fg0jx@<WFgzpyHi}kSpZoFl;0Xn|MrmdddK_x+
ztG<M%_$$$9Dn6mg7|s^bLoA@vzZz=hvU2$O(u`Tt2Kscwu)L$-M2&;fDz=ierYL%D
zEhCuS9wd@c#U(S>`06w#mm=a?ua7L4Z^Y_ir1TdN23&0U)B3eC$mP%W50qeCfuWja
zHjL(Y4_&#O-7LNRy#0F#yIx`y(awEs?rDs*`y(ZD^*DeMhHdLd<YK|(Ys8y>7mT#a
z_tREprIXG9^|c$+_J;reHpDAfDo-TU&@q+2dF+hll`nKE4gJ{Wep&yT59RzaZ+&6T
z(M?ltvFYO^qnk4IFfc)13{poiIsA+h&k_vUUL@BHe-2#c*X8&T=~5fT3(8vyzZ+Qa
zpxNB`O=skRMhhx@EfNpVk9yG`mx(|PJMM}ObxKlkOk}c%O@#w&8Ac6O!d{x46}v^b
z>tWk?0knPnA0zqUuYq?%|B6fkHSyxWvPq)r^9n*`W^<T@CNR`AwNK?PBTi~yh^0DH
zXKyU4B@#x$H5`AG{4WtbU!CLTb=6C}MUh^ShU+A&^165*1$c{!5Wv{+53v?Bq$Vij
z^;)yMb-OLMP)pqU3rOIuuH}J~A4@JnJ$HK5!>2+SwrpVk(M9zQLtyTKKQrT@)MKrm
z>gkYYUH#2QjfQVb|B}1pPM}QtvB1++A+6#f>3v&QJdMD=e_4nw<+*9-elCSk*;C-Q
zbmD4A*V|Z=G6KRm7=Hh8xt{ysK;VuzYybXju5!(;X-ufP<}3pz@>C5(m}c}gh?MnK
zzYhnCmL#VQY=wCMZamlhk`b^z25`e%ArV4Kq~<PDrgK-01_Q-1tlu2Nz>NgTOf~^-
zy2&CGCLhC~C1pIL;>pVucz`e;?X}6A`E)X5)iwg5bf_O8idYQ51b*Y?MfZ&@>perh
z{T*3=LP08bjeOIqBO4@XRMR{0I!FC5YQra<Xgc2R9(sFBpvC8uu!~q~S>~wLRwIYm
z3kXCOq9x)XY(w_BgJ57+wY>;27nPd*=sjd$uIq1~Cj#t*PrA&2Wixj4#MT4g1kkbX
z(JPmnZgWBWnz25R%unay)j8P4XwzP#0R}s3qxx};*q+B;l_}hDUCsOlFft`l4a>AN
z3=X&O_jNl)`#3A7G^}bJ?IN>r&~Jpdn7V!{NbO-zwfEe#!^{pLC_Up7J};00(k-sb
zQ9TeRb=R2)$fTGGU*zEA)hie<mT~*LYk@NngEuBzJS<!-+-G-4?RGIk^$0nNa5$x^
zo&&^_V2i&OXPGB}%y;M!ChKVyzaO_oW?K8a+TJKb+D6*|AbIaj&)dh@<;hzVd?)OM
zdJO>$4c1sH*XLRWZZFYjZenWzFG7LTuYS)+{n;XBO_RF~%*YgcSmM>-?d63AVI+*2
zUH+$xNM@LCW8A{C+!DDC-D|PC%kKAM4-*PbDE95o?7*BDd-gYyak~@-`JU_Zb}vBE
zkGT9Ftt>}0(JYQ)yIx7v%;h^sx~6qW&#7%7l$>>@1iFxVxUBJsP4iRx{dO%dg+Vbp
zOtaHbo+s8sFL&W3%9s=z=kaeWGq(2_=84pw#8Ti@IP7Psx2a@n+|eZQC93dv-iw=j
zumzsISm@%=)iV!lrUmOPjon^1!idEe?}sZlAkZyCN5WZNW)>M&)?B}?sgX9O0%TwJ
z;s*EvwwI9hy;8&HmWi7SZ&~{0g<+P5J}<SSezZtCwqRUVOl;nVW=bphd^iaEWV=K-
zh(OBJy)mfe#o}R`3NG(G`6US~Ge<(xbtK{po0=)*nAIx~me^KY_y{UDwy?BHl#CFJ
zvO=49cHPmI>ut<!T3!`<Vxpe|6={YPHd*^$yXGu})Dg@mhFL}llk=x&z*!Z4z4Qfz
z1asGkBH&Kg#uI*|%t?^OfOFs8PhMSOjMTl?VZFz>=LKx0OpM&t+lyKTKErf&eiriG
zm<q{Ow=YN-L}n4zkSc`}m9Wr%R}%%*FKLG&#FEj5BE||K!+rPN=(L6DMCx~zUoK%d
zpE7CpynAxEi+;XJ7y;>Ov(KKhPBN>XuX>y{?E&xZU%WdiGsI<@bcmcRny~w%{+oBX
zkR}42PUFT_(koxs8?%nC+v*>2V#OCW#kwz1vNE>q^^&|u3%aES^lq9@*M`--%9m?n
zu+~P7S%hmzN7Fwn=L^-oR_zZW=?Uhxu#<$w@ufQ9GSeD)6E|9lR)ag~n=wnFQyrY7
zu!t*n$aXWRGe_@sX1|AZXVC0uR7#t(q5nenD>(+*CbPi*Rw;6^pl^b<w%oZo<Iu%5
z9Jg^*)!i_EGv8a9*H}5`<paX|G`rbwI9g!p%*Ls{e^_yfZO4f%>{(Bob7Nz2>kq+|
zn~Kck<0lw!qEY4p{yBv^+WByR46fftAWAF<zXhZ;T2*sBV4$zUBFWx!504Xt&E3cv
z6!A@q)Z(`enO|^FdPL>&_dxE^L(kBT1qe1_dz+=pT5#h(ew23q7Yc#T)`p>Wb$3PB
zZ;F(vQzKHgd=p2BzDhm$i3P)eNrEErMzK53a$-v}9&*b6-DFMN;RXB!-8ii*@O(=8
z>dBANBeT%M&yPKn(uK|nqI>>o7|3KX8N~>sw}hS<Fu_qY&~26SWSWCrKIa5*p4^Yk
z7cmE^HNpc9$u}KhLbBjG6SF_!Lo(eeo{2)ua%C;~Jh;s`^n5=CVt=HrF<YwlCbonh
z2}=Z^<r!I@58UC3lLkhX()Fqb2YAY)r4DGqY)I+_#r7}9_8Ig?xUoe*_c2d^)C=MB
z0?ykUQbxkRw(4mM86agn@8}s9mB?^Nr3-WjqZW8xKjTQ$Mu28LAEg;<d~&#DloA)_
z&S>o`3=}J|nL1TWI*GlXLBaR(_CIq{=JW9induVdO#@Cb_g1W$0o<kh0aV`bxN*Yr
zVK!{y@;fW0XRy>{U(F27*JrVSpF3LRVv2f?cOYp+y5>=tAGlCx^NEcT;7E2tI2^D2
zVE4q8A4X9>e6B+8NT;;@EW>qb<Q7w(2BG_+SsTT;`763MBdts0fmwO)=$p6C(5mM^
z1;pTt7zmP@Ox}FA79~*-CL7EWdUR4X*<4r=UteUt7wKx?p0m7~yJGQ~I=>v^M|^0A
z^pftqLsa5}WV@1srG{_Ocilr5KPg4$kMZgcPX8vZNwG$+T{$NU?EQftug=Dol_CuP
zpNP5?W2pFK*eO@8Wy?dNVN5TSO6JjP_Wj!FZ3DGOYVB?CN?uX)3!a(S$A#i@pMDZ;
zXo>*~9~4?lXp6WsSu&)ch=MK`*UDQ#=IxGt$UBSDS~%bXtkc|Eum)T;iH8N@hCCu9
zfSqxwM@Wzdq@>ozL<mjRSbymfx_Jmo#g7v&zZ7W-S$`E839RN?5=CD+im6kunc3Nx
zs@A>V3_a(caecZSd*mzUnR1=6ZcO<=M3VBgHHw`6Pl;cjlaQTbLE6h7$M{mqzWt`D
zXMCZCE)wk?+(=xakyHoZ5tIGce-%+kx$^21>CG9_^9(E#yvG!}04DQ45auvL&+N+I
zWjXSufjgnQEI|-4U$#%+Tc1wn53H~|q{PAKOSz8!V)u9R&cHa|cFMO0?Y+lY05b{J
z$xmOlpLZ2SOV>@$9H_zNLv>w>M?v*xqpqHu#-povh+zhq>L5);6{7bvMjt;4Ni=W-
z)oiH|@p2s8e_7tQA1e7eeCK#RSAC+R{Opm8ecvblWfOz(#HdDn$&MEY=G460Z-1e)
ziz5x}v;z@p+Pz$Wq~N8Xld_&-F@QO>O=BZrABU^eC(gY*q<}*A?Gk5@g}=nVQM-1M
zxLN#N{QWHHqIEfsw~(5i&0JKDDCJ9m54IQVME%44+tfaw{Q^(!R=!LXNlYP)fXO-e
zX`zAc;UH%rtfC4}S0vZ=oJo^!@A9wpZoR^B%L@lFtYjP-472WIR=Z?@$_CE+RBb#8
z-(H>p_sWiih0Ue+^GE5;eyer)KkRQuZ&}8}<<qwG^4Y-#XGtWoT<hj~^nH%S0MMHy
zUb|Yek|}i?dUI~JrRL?=wu_%KL~U$YeDRfl7AoF5Huc!9YN?Z8?l6t<M+_OxBB?xM
zM-oz8G^-o`@rc&Zt3Z;w&$k$Bg$5ih@GErTOVZVoyNfF_8?OE;VC`Imma%8~Jg<iA
z{Y@+aodL^34_6x(E&mv}CPnU<PPDKKvMQ>G+6PkZDyKpj<BvX2UN<}ZFcJLtivwP7
zj!Xtf$&tn^KL<h^kuyu*S=jG8zZ0Q-r*0Y*d-(6X;Z3~T5rdNN-*=GjY2x3)X*SQA
z*MPqTSj>wvs*7M4zymIWh;VFpKz&QLipu4sZjDd>{a(=8e*Y!P0b(@?)Q`P>AL%j=
z%RrN=A7_In#rUB_sK#F#wrcCP5zB%BV%$so3FA8yv<H4)kC^wd9-ARig6R-hgC`pX
zkxS19$yBrgTDw%m8^Q=?C_AaH>S~C7?fQU9Sllrn3a?{!Z4ga0ivy8MfaBQ6C6o$>
zMWrgF1;b*5f6|LGh7HyASAUgbEVpxZ@+aoC3(@EzPAK@>U&Rhrm5{r^BO)1ws&IS0
z9^x>X98GQ@WH-thj`<Oit=@6%U#)fZM@iqV;6$m(zvbxe<VUS{%Wp-H7IFFv-8?k)
z2$<8$g|l&Y@i0U88{xBaUh?V8;9=-7V@~{7uyjV$tuGe=(;&xRsxRY%d#q`q79TaA
zxHyr%LHViOANEQIG)Hpa!T492|EUQnDuIhlTZdXy$vo3%VZ%$2l)U+1a3y5cm(rv9
z11fBkf`aE~j8)uG%!~-8vcKPKXCm|tGA;9RF>f^ys-b4DI<YK5&mzG2Jv-@%WB4dp
z=0U-eon`&=Z=M&V8*qKy82p%c@i!m%B9NwmmSIBQ9uda?!<w4V7$7~(&*TWBKXdNg
zEM^=x>ARdLPyyO5rIYe*JrWc^(y*veu5DiuHA&UTyBUm-I16H?TECOp&&iM*@br|F
z88%+o)TkQY?HaaP4_23n5zUWoa_p7cxt9}*m%kS-VHZl>kO+)(OFiEXIaw&SQB0kZ
z*B_1we?{ZnTMH=#?G3x&_>7!A=$xx_WU_-EZAV-hz-r(v^}7SU=N_ZRiFc0egPi4|
zye#tEvN4SZqVfa6SHqMz{_kV_BGdf98LNMeD(XsK3=cPj%+Y-x>Ih3oNH?xSsNNmR
z&Vmtl7z4!L3}yB-QlaVNTnkf3aY=0c93d0+z*bGPQ^pfl5%<#<)CQt?7sDo|<rA5y
zfLJIRL#2h9hi?;4qZEcbhO9heVvb=tH6b?av}#Iht$9GJz*~e$0Hh;0#?e~_6#?5C
zBwF@;)QXa=VxEto9Pn+9DMHOsF%{EMjJW~Q)a^1unO#3x<jE-9J4v)f(~y1vD34-Q
zk)08c+W=mjfbKgWj6DNdhABygX-S4{b!3REt&n0G1hBq#_vK*z82B}u>nblLe~jgy
zX9rR0;%zSA9(VwSR__;Vv)ro=LjhRE$f4#$<{a?s$j!PDq)hgj^%p{*zE9H(3}=b1
zGLa3j{U8PSg+l3nk6>{P0NI>fYOEpNDT#<=sD=8?Hm;^rScN~nyiNq3gKEFuRx-1}
z89;6rHg`>(&R8dv&@`kH0%S@bsgDIG0z5*@&Ub7NTh~U!9Dhw`RN5E6%jTAaQ|<md
zL>zsXsIGiCjQusdwehuih$R#rz7|DqPVehW%uE0-Qdar{0U?bSiYhjI4fgRSx4?;a
zLiqvu=?=a)z2MO0k^H3NXY#(W+R&6xwa*i_fMlU8fEd-#s!p;RFt87QIT&3pFhB1~
z6d;&%o6B=ZH-F~<JXwRE)vEB*f4>sOuPLUE3+0yexI0EQYU<{E(WM-0Pyqaa2}(0;
zI?T^Ei}v2H6`Lhv>K8)BFURLPC?q&ToqSQ_f*gDUx2P9%UyvxdA7e8nh@IoO^41X_
zyIdGzDDYsT$4GX$mYheE#ee<BlINg!K{So%PqFFQ(ifncz4Zt4%YHTFdcD}@xXV|G
zz@n9fU%JP~K6VS(i}>8`CS@($WwATAc#DNrZYRBH1NN@K!R>1C+Ck3V#5@o?%=q^r
zigmNiHo6?w4-lIkSK)aLW^V1P|MrP$D<J+Nb``n_#<QCfO@oqcuyEAuO6~o@4#tQv
z{A7%1vr$3^Xi2+0Vk)MjD=r7<-%Yy9MCk>j>7P(FF-_g6U1K2oG#1nHNp3FJK7~nI
z-{V<yA3zR)@+_xqVJo5#RzuKT$B@PY1O4WGF*mFk&wy*eBj;rq&)i>lZb2A+hCA;h
z>D5Z0W*GCkN3&+=?kYU)C*QaT?g=%>#Q@y_0>+x8j`iC!<|&?*`j>``xWi;(%eQ-=
zfd<Z;31dfm-)4`8sCvwEvE1i?MXFcB1d)5isT|V@g}Up(kpWpjxrhFy5w>vXRM9MA
zE$zbD&uZtNlgkrRXt21rdHXaPCk_*w<~+PutbXJ0No7h8IsL}*B$VD<#3rsN!=R#t
zrN*BL7oeQiD_ABEQPNt@J>VHt8PU?R+0?)WY?!2q#5qR;huKC#rXnKW009NFZY9{(
zGTn}2KAG9Y5JVG&cO5Xf6qApqUO1T|rcURQj)D;ejkBx*z@}0NTJvOK*E}&%2HK1u
zOOk0IPD!%1RZN1g2<V61Pd9a|_<rP^o$NLpW%b9928!kap%q#5uQqwI_Ws$XOjO?y
z0_mk&)!qv>ksQ*-9?15abq%KYgKU0O2YvjR`w83MCHVrSy72+#SvpIYK-QS7ux)#x
zr>nGxPR2F3s$fLLGmumB9ZA}qS4DV8W;Ae(^Pqo(f(HmWmIks_P|?ekkWzEmxx<h^
zzhPv>uk~LiK9U5I0rvXMJ&$Meirs~WguSt%_~YI>zhB9co_vJq+eL)fX_i@K{xnH9
z<^d}_GTGt9apIVR{{ZjUK5QbenjuwAJjkKx-3pk|0mrmZZQZyjw(a3QCyse{kgi2e
z8DF=<-|z(=*D$Z(Lbc{4vJtil3+9%;*&6iO^_$%(Sncm)wJ(G6{PH;mm*tgN<CUBS
zYVAvazMb{jDbvG^5km=U?di_#sV(LwYJ4Gn$Hv9fF|5QE;9hR~Hp*g`o|{hsrw?_p
zWdZwpHhhL!s`d8t+Oq66WShd}6V}Br0qhWXY*9(NX}JKiuJMVc0DwBVq-e1D1zz(8
znw-u2M{wp2oO)Iq$z}<;nFnSpu?&z#<~7pYd}5W(b%0}R{WY@DR8GZICQ*H1-O!?T
zg0sUpRjS-~f6;OIKkvz$HJa-83(S7p_Q(2ZLo@4abii3nEHp_+@LTao4rJ#g1&d?8
z8N>)A*>C;9c0fcv8bj}!8tc9dWTh{wbpE@<#I3#A8EfW!k%4Ggb|2F1x)b7lwHx??
z%Pt+gWAxB(n(-V;^{i*iZCZ<UuO8kk<AD{WVoYrIoH8{1yS>&eGa-8{>AuykC{u?u
zmSO~M8ltw3QkRGctVv5j=;cE}jFPVuRI{mvU^klnU16;_BM2eRJeUiNmJbiqAL24l
ztwJ%2It_~wD96ydV-fCC9H^%e#5dCaBTU3%3q(H70_Db2@?lGFeJY2yvP%JAv^slF
zAWuVXg@^&>IPHR4vt|i<@f?N5bf_?0h4kWWi1VQ)V^q_^ntr>M5W$%lZ#3oBP7sHS
zxtGWK)y%5Nd!sw`S;KwH>WBc!{h#Muv7R{P;NIquz_SiLRvuY%n3;?ow$^Q#Cq{5x
z;kDBl_Z3&?j~^xD|53H>Ctv7%L-6?XR)tJnZA3b8(n;b{Z8JiSX+^cNKba3qM{(m;
zUUomAzl%-tOY$~-<87CSv1S>ZGy8cav^UJEfa(UN1F@=Rd*BH7w*k6d*OGqAO($c-
zO28_fJYeb46*oRMC3*G&wl0?y4s-ggbQD`>;0HUzwz86w4@UN$>*oQLYG^G(Y1i`T
zQx?TEJXozocOHmr%*sE^$Tpq$8QzU-MGtXIxzZJbPl~+2RGce}*CJ&d(vI%WFcmdf
z3=#O2hO0XJo9Efq=r*eOA{w2vvl{bOm|;zO$<jblvR1iM1wm7CNk}4>9ZL`gm2~18
zeKU&aeBn+rpuatWHPqN%!gi>?V&Y*ouEhZs<`v+FDA^%ED;eNT2;>Govh#XU(Jgn^
zejUz~p1rp{%{ZQq#$(+x{{LfI9@h#92m=ofD=t*9m6(ojrv3)^tH|o<6>cQ1=>e_4
zZPBv)TEUZcu#QTWT_|QJDl5epwHMcbC^Xv?o>+I*;Xk>Bg(;I5t0`F(SCeC1aE&zs
zj13cw-gYs|b6A!zLb!Kx|587mO3!qFI)SFU8Xb-?3wUXWz3>%7#%<vDf&&~W(5q^?
zl21-x3pCu&E(3P`W@|R@rP|Z{Eb%qyt@35Ca8TEQNyXeAirqxb*U+vd5rl>N3pL-m
zQnM{5b|!<S@{%eh!x*pb_EeK^b)mk&C&lrL4rS&hRm7$yr}9q(xFomraawaXrjF)=
zpwF`d#<Vt#hVR&-K*-NbKgoH-In{@vE6r<`OB3gU>UU9+CMxZoR!bqnL~sjg$NwqN
zJ%h9tDWa4>(%@pO-*X5QlEcIL;pg7hAjS?mRMghjws1F|#<<q|Jxap)tpkVa(XVVY
zs$S!n8oAR%s7U&`G&#z5$(p7yy?FlKy)Ek<$%t!|(c^O;%8|#0=rjnzu%Z!7RGOUK
z$T_*C*!pqzu<?8KhCOVw3)Sou6Ss!@*tI5d=4htYPL#?4+XM%3HEnB$r&Ws^4^qiE
z^g#H`^K3}(Eoe@aC!N2(cgdc>VB@5i(oaaBDsx$>sEvJN+2@87@tNxPT)1V0OYsas
zuLsx|2Ormf%fmdBVm$Dre2fSvu6IPKy$x7V7Iu#>bU?+^YO0E=!3xwr^EKzi?%S-M
zUqTh9{rC0uszd@t^|(*sh1~a>2&xPfIjpQKwkfMh19nzN(SKX0=V<$Zg*e%~wF~A#
zqu|6B+CJHl)#fNX?D$ph9OgV0z;}gd&s`H7GRgC}&TI3o81mn#VJEn%uW5~L=|G%;
z2H!wJroZ?Oo!B|)p|}Yr(_Dyon57}tmutG`8p>&6KoQ$65zPqim8+0IJfFv)Mhyxo
zg`=+fMU;LvHSAcgDUN1j0T;>D!U+Bo4Xwkc*qp&eESLbZFq_30e*ZjAmU2l)v1AIv
z9)WKRG}fYBzfrx*l&D_G+Ku85w05*U!(b`}`(+e$8jE3|JQEtxrs?^{0W6=hrA8(o
z4guz|MtE)7nJD-}mKi|q|C8txk2cb9kwx4QlWV2q*l#xB(w&TJAY9Q=XlSWvD51E~
z94q0+OdA9_ZAtEgAw}EqlRrDb|KP4>z4K%*tQMlz5WtMrkMx22g^{4bAZYQkb2~p0
zZX_y${y~hTj34umZ3}vpAj_r0vRcniiCbUqnqH|3FO5k&3Jxq2VuwIZpmdzIaAZ;m
z!HF*FWb2<7Y=KtVy+~b(`CXswKQ<W<aOz7E<H#;9e$VHvYmzAQ=vCj(d`d?wGgq^w
zDg?sb(Ap>T-_vl}+Uq;DHkH^`@-R<Rw3mmZF9Lu8`v$N_w*B1{oP4F*pBR{?Rdj8z
zq2Roy$U-a#vq+Wkz@pd?$Z`2s*26`p`tVE9A<;m>Y+A(^QVLw5F>YTD_>V%luuz9E
zd;dx6<K|5o{u_A$ivAk@DG^@fj{pKjxP1iW@=*akb=dhN&C?7bQKk`~|4>ZbJLga*
ziq*O1_oS|@#iyc$Uha3X@?55pLFaJN`7~Mk^++^}Vr(Jg8lH(?<`=^P2j#>V^^zmt
zqHtjeSja}8El6$gVnYw)Y`HB+MNVf7L^Q$vujD0r3vM0zc;eGKuqNTijmI0ON~>~k
z`Ivp7h4R=l2l}>B3vJ`V617A_uiD`KCD)3vCu1C6;jX?03i}6^>)+<BqRrC0P5qB+
z#OOw=E3INXQC>oGWV4gD&QCn-CZ7@e=Bo>`K9ilQo8J+^3{hzg?P`I(%q3I@j6hr>
z;O|k{P2>eykp9&4`WI@O##dpsicj+ohAvG+0ugo=I2uy~C@&6vWwN|Y!$21%Da*Dr
z0K@}2CXMbqyKeKikWT_h&!WKNldNWA=?<IppnX^55=)B^Y8WEX9{2-$-rNY@qxvRz
z8(zu6uC#kp;Kbnhr~CYEPxEDzv0bVW<6^nv$!qVPJtei=?rerdGVb!~7}kOMN+rvi
zaZ5>;YnUKQaJb{~mQ!*IQryI22eH3Ap?mf2?aE{Id<q{})H<$dnA&V?zv90mN;cGc
zhg#}f5snwU9?3E`C?DC=ND_Q|{rtzXTE-$zJk@yg)as%j%OmtB>a^MChqm>X|6Z*_
zwiizTDW^fr=vIR4-rdaO4UYT;Z^xZi^QrGOF+**`6qPLN+bE+C{<_P8+WA$RP3Csb
zedVR<`(Csnjhixo=-S(vXn?QoLwHuVofRZ*p@A$4JeSDpd37!Bc3A%j==;>9NE3SP
zFkv3(0V9lG%mANuEiLJw?$g@S9CW6S6XUE#tl*o!5+OhH!1|NCHwr1V@Ls(<ppRGd
zQ}zQYV#oWk&GdN?4dvrhl5VboBXhs)?G}Fdt$@#~jZdil5TO29(IY0Nv?*s~k-*5b
z7zGk4#Ob<0LhBa>m>)e8!s&$)6_nkSC1NNSg!KUibioHM@Ram5j~I}6Ih#r&{hNy@
zF(yD=Dw#4sU8iyU2X<{BOB);2WGZ~6gz*g%S*P#^p+s<1g?L1yo1@m5<>hnIcx@y2
zJA$i=RRZVU-Nn-h-+c3z3a1uNk3)okwD=R+eW&3HXP(w3An4srvVQNLA!B>@P+cc8
z^-E~XD%UXirqLN&+rshH_>z>)J%{Xrt%Lu($-bMH^XH0!14`y~O?8o>mjcTvM*HI0
zK4LANiI=L14c=0EPj~NM{~od2LN%l&0$`^5&r-rjb~6(3OPV94b@>Xaw+bg0w(_tB
z6Co@;*1LMFH>jUDsU6+}y&l$l-cLb|oCm3vu@2XFe($|Ow9Ks3_QMuAO#6b>z4u#c
zpYALk=LkWsmtOMKyIL_^uO#bt)qif2dKg7Tlg*#0a&%thtIPP|wEPYTL@qsghn8`#
zBq`^;(Uy6>0ZRL(i{z=p_vrjXAQw1{nVG~cBgr-+iN;kB;ag&P)#4)~K+sD}rIeG)
zlZ7qkRhII>ns-ZJdck0s7C!ze^)_Lk?(rdHixYnPJa-2(F}24*@HO@eJuM-`7H--p
z(f|CiYfjK4rVK!RsPTP%!Jl*EpIyRM)bE$VJWJ{38wxHBrSXzqDtjrX@v@>7!=IbU
zl42%aggOQ5G!MGWy%7PxrZJh^%-ctxTXg7?KTq9jm5s6f8(E23U<Kt@(vs!J&Mh;!
z=9a%Vj4<3#9S|*&BN@z&TL~<MPI<gByY;6$ew8@b&cC^;U<jr`kxIyh3@&{J(eyWq
z(+l*}zY*86JupZuu&rzpmcOAxACudL6N4SUwA=1<4jLZD!(v;z$D{gkEMvrR%KIT)
z@w5r={KBK&D~#!ZmlH46(sHyc93J==mH|{$FAVkwygA*O)O#FNwUs0ELfZIUGHT<Z
zD>jn?fxFlpgZ>rze;{Wvbp&&e5Gr{fi7XI1i9X;Kpigv}j|&B_2Z=Mr%gma;210kZ
z<PPtygc3P|0JdYO82o&-smrG=F0X@jv-rPJmB421zxEQa0y1bb7syA;D(K?v2`Nb1
zj-x=3=9wpcQj^Gu5k{8Ps0h#a7%NVOV1mi~=XI<nTNY{O<JOqj*LmIVk&~wJHF&x|
z`T4#NWs2zM1h5h!HK^gY0!gQ{t4ztBx{>{{lzRw_=W6j~n<qs-+0V^v5-2YbQ2OG;
zo3^IY%WQ$lrkUnNIMFYAwYb1GDWcasyoC*zjuNHkD__F-zZ8@L{Sz>~`gup3YRHT!
zOU6fxt7Mf&61AWI``tFVZzdL<$nbKQVJHPP(#0pSy?BxkbSUOFxz0Ib;^iUoCtw*m
zUt0|lt;Co*g<{i2oUf(9T-BqimTlT1Eg%_V%P9ZvbW8yFi>eG|+m9TpauQrGk!n(U
zyf70kL1yoM`inhFIsLLZ2Vg5q+61rsQSu*-iAflLJiV=yS$;aS4P+CeiPH)R_S=CV
z5Z89urX&A9L}Qqu@Byed2JWlAwZtIiMg<f5LaCesJzfM>Osy~Tdq;gvFMj^IwhJD%
z=*5<2j@m^$d1)x7ecDTsL|#WyY0XMG=1DYaoZ<kWlw3~pvwFSIvIP?qT>AR8j`=}F
z=Pw^CzN-44sqRM5lA?q$Tk()mJ8OK=i)-RoooYUYIFy<2r1Jqa+K4}cL!W1gbld;2
zbd_OIwcT2f?q=xjZlpuHJEgl*8kCgoj-e6hZjf$}?(RmqIotO;*TtW4a8UN%>sf2v
z1(4g+Y<d~TDZYI(zyLDVo@4|fawnn&kSK^sUN9<EX~{0|TM`eG=Bnjr;18*`E}^^g
zZEz1u(D8dU1vX^^f||Hl(2ua>r0;NOXmwF?T$*PMX{1fXfHZ7+vPHv;J}vIbdYxGB
zo0+&<T5wdnn5qYY=Sbd92cdy%N+YIIqoIqs8pU`qQgkRC|5)cj3BK|(k8<{~SM<3X
z`38%)z9b@8DV=6|mUKXyh*5zKiO?uMerxq4qzaeMXifoQRbz}DV_~;H9Qex`I0>+r
zYj>2LJM^&>F*TpQ2#k^w{hC__sTTaLQ5K8ISG&E`i9>$Ybk-*<l8nhH7!oJ@r0w_z
z;hJ{90K-(iQ>n7Hy3nkLMY;O=hnSWQ{~Z%*CfDqj_nf93+FJnR9JBIv?hDaGq@t9{
z7~f)(_H?xlw_QU~=n~ly3ch{rAQ4~ynba?dWkSf#I+gE$F!!jm%pl}Lxd{rF$kPqF
zYhu}c9a(x89+}s#i~L|0TU@k3RrRzIj3(<&OQRHwRK>I##R^5LX!?`?Bc83%{eyVK
z)W;;deN)gJrJU|R(_eVW6ASM|%8nmrL?R=x^Zj~o-?`}+x-;#9Nm!+|=oS-`%DwQ<
z*&^mSQ+zK^J|iG1aVc+a(F8Xlo3dlFNiRsdi<m&NXM^?ZucT+xrR*e0*rgX57uvVF
z`0HMQAQUBZvlFCgY&(_0-LYw>SQY2H^{mQv#8MRaIwnrKbeZrvVum1qw|!2uFhfn&
z*?p#)nP#Vr=}SY2lj2lU7%+HES>pgAA-G{me7G0$e-Vc{q8|<Vhn`;DxLiOVpOXn_
zbeSW)dB%%vt{E{NEzc_q=y`#!19tH+9=S-bM3<}t?4!Ch>E9PF^GMOO#Y{deNURco
zM^;wSf9+BUCdki#=D)ZxA%2o~Cr;G?aqOS}gU(HJSO-K>_E;>IK`^3XXajb3cRw`{
z7gO?Q;D^|wP4(ot<#=QI)33|y8enf=(Fai`fyH1dvm+~)N}lRnOY3aDx^HtTau78e
zL}WLrXV+_{ul1d9!4YwxnL<JuM2A^2D*yXF@!jA3U|ENRl2B~NLJnCHZ#Ph1G+oaA
z-Bv0!1sg=_^TxK#yMn*Xn{bKABv3z1)+{Ob221a{{5Q`CK={?CJFaT)Va9wDx1xVu
zw|Q}rbs<I*Xysy#|GKYyWYpVwM9DdbGtV&K*#*{ZKp*IJs}@F^BB*=vr4Zxa1i5$Z
zmE9Baig_x?+TAiU3T&l-*)(Xbh>6*72=+Rq$VxHgZ=^$x>JqI=>0bQD6}lelgsBUO
zdTwv^6X@e;6J|(HZdKVQKz_|q_(@}+kx5{3pq8r9b_<)ZFu|<U!nI=*D6&Ag`|Ifc
zs$fSGAg^HyjgM*GXMbzwARH=&U?-*W>tWWx*()|ND!PHW>oxge4?Q|2e+}P=KO+1H
zp~JY|xIiag{jbODTh#Y?$=JPqrj#ms=gUJ&-n&(SkrCKRvEL_P!GGOl=M#aWu?|Al
z;g#k4m1SC1WiCQnR~i-do=ZST)5?Kol^?{nV!f^8W%Qgf;${UApbfG$2Gh!=Uq;Rn
zfvcFZr3l7-Yep=1bHUWSs_cg4F8M<Jj}z3dlmm5)z)V`fYc|cowv$@QPfTD823}Qa
z=V8OPujt}+wEEs2<Dn!G5dPZrTFI%6gVR;{-QXW)Kp0I9l>+-kwIcmSF6*a~io1ZX
z+`0<yWcCK;y2F?K-U*BY@3KWz6_1Fl@(Hy@KO}&~i(HAq%{!-KB6zG)tM6}padOI}
z$a<#ZYkGzx*Nt<clB!+OJiX0w{*E-`A40dVukR5O`O5WXcE$(*<E5UZovDH$)K#<h
zYqKSLMv=k>uV~R^Q+O54u?$Rh)-|B|4?jOiz*q;DF}~f^49ChVkIj5CHY}2yyVgE-
zcS<s07(0={X3R8=hL7Q<mW&Ss%zV+I#*#-lJ0L4af2Ty;ih_4A6V<<@*6zgEU_svO
zq?N6qU>ZP3(Pj7>(=zWD@emgMY+YAi9$oR{S9b&=q$|JjKQxY$%2<U!AXoh!-lx<l
z);V@xLg-cTUdnO7)}o8y%=l?+W8ClVak_FRxar?$DtD`mq>ps@S|l-HXII_y#Alr0
z(lE0R?s!J2VBM|id_jOczV&gq@V|ha#D@$~O~iT?cAt45ov}|i6=Oa%x1D8pN0-%P
z9r$znvJpPRL3t#>XbV9Fm=p_3_;YA|lRQCAnSUpjRb0D+LKh<sma4fdQLg2FS_K6i
zw2P%wpwnEK$~!(F;hHV+IlF|~9BuSA-U+>Zbo~e;ZUZ^d7!XbRg=R{Sx`V{D$0vvG
zeeZeX*CIUKX<qI_+|KZpC(YCsm?J)|=Z)M{#{J5PBm8uD83mDI%=+O!l&g{7nn&lG
zXP-NaN1QXgw`c)~h3$*yZDZ2*nzS33R8J~1X)G8Rp4+=_l`h(7(!;~1lKC$p6PO$6
z3xa(Hf69=}GBqGyTrAp=yaNyrcJ@y1-Mei5$D~VM?KeD|b237WPC17A!JsJTt$pK#
z=n`2ZIW&+6D7<BBnV8Aq11G7&lYi6MspI_8M*C}y01gH)Fnj#}j!;e}<Ca`a4cnsF
zl}*{U_r?r*MU~dw^mA;U{vF^pdMxK7Gu>`rQhI1ozxC(4%m@`A1n`{Oh&&O}hYH1;
zz#>Q_Lu>x^gTpOJ4|TEz$FJE|<xsJ<uc2FS4BJ35AFh^(Z<xKq&5v?XP_a;%v!fS;
zWZCwfVww!jHJKz=?!8F|$$5g<F^Ei}BoV@CMi<$u&YCegCv80OO}{D<H3dgg*#QG{
z7P7<hdWsNqndp>FzQRDu`9j*AqO$YVY+fG}ln#NRMoqAf(#LmN`9=Mc_`VjM;Q?J-
zQ=~ab_#(>WUz25EzR#>bKHW}eBp567t1b~B7zA<-|0^ggK%NR2ROf{<qt9$6RX(fv
zSEV4JKKfoEN`3b=GUvxx`zq4L1u9BkjW}45SJbkyznS7AxdB|InuwI?+dPQ$>E+nj
zG|bDmayMchjto7MZ3Mg48Rd-mabj%IrQlN%3XdiZ%=w8dXe#x!P3>D0Ds*-?<MHlD
za<(fj^m8|mWoDvGhKuxXm$WZf*DB9eJHP32@Z>(O0v374MaXY+T@TD%H>2P@?THg{
z#qoJy(<eWnuG8K=eAR$M(&-Tm)JR;zm97&uxVkitm4nAz*Km%GvJY-EFg}Pg!B2M^
zx^vDl?%y*`X5>sXgI=f>)VR3@rARMlf<^JwoCQ!cGZ<05k*0(FGmK>V3$@IaSyZa+
z=X->J{_bS!gPb&bfpzP@7b+<x@DlxZX_pcDhYkscQK2Vwe1|pchg*8w%b*0#JhL`!
zRkpp<%Or`UB2Pf;85#DnM=^%MolhK4e@8aCaCf;=H(3z;I|YYo)Rbz~gzI#hJ~OC@
z&fo0`N=`Jh!t-|%_e2dgDzAP{acZc1t9hruJ9{=|ZX%Sg-z`>{teUU?G04&Wiv`2^
z^#bZUT*}Z1rG_1e-hMAR9aQ?%zjCRPl7QE1JN}WD>``lB-DJM1M%fOq<|)V}?Bw+e
zbgTda85RC!NU?h!sa1JEd$JG1wP4z+y=~K!D7Cd-3y97>O=az7&tY#f?#PymN2+l!
zs@p88M(0BbFKQQH4z>&NE7d7)&K-Ti@yX5;sc=e`=yzU%gV8^0{4}FWGoq^LE!bII
z4gP%b@|+~*R6S2BtLA@wYOVP!h*9C?;1V%w#U1p4?yG;^N~vR;bIF;ypyR?VaS~uK
zVCesss?+_J9=ECS0e0h^Ih)p`XyKsY(QBUpTZoNc>PYCAX8q!IQ>V8Ur@G>G)f<}t
zGog3^utu)Fiy0~WCQ`c8ZejivnNC((rGVsxTGtW9mWe(JeyCO<DtyS6$^e(4DC>7k
zEa~Er03BdWY}+N9QStGDJUA8&r_v9SF2Z-VO0%q6uf71$Ez#DD8q%c>nT+yzJoU<|
z{Y#YUIrR4)z)Vl+0i~8}dCKb_^y}b~Ou8n5fJjF;az~uxRufw6K47&xED`7y<lpLM
zxN_8&`f1@&f$uMsNw(DOT_TlcP?I*TAA}xGyoE<ll07G0Y0MB!F%zLqpT_O;R}E&}
znU>*^%3I7i)~D;g2-+D*>aYNa@2a~MM!ED2;Hb6w{E&H<5YX^p)Z^+iN?0vdc>)!%
z0jp6&C=e0gtdDkA?Lhx6JC&6cpAND2sTe(Xike)3C3hCEH5bivAQogSv*G}35-0`3
zu&^1qVv|<fgY@9G$U?%{ww&|>Oo`+PhFGaZN7%i_XW4*Z81esyVbwtIj-lDl=}YO$
zKec@uwm&Wu2z*n46Z*aT`LS{Kn|BBA(+Uts(yN>s97zGt{Zjo~6)D?prZt|9V0ieD
z3=G%Fr^wdKk{xQJM5dL1rC%_Wpnyhy%A4Ok<s4c3d4YnY@VI4+>6&Gn!?czyZ!Iq)
ztvy+A{yrmGp`Kd;)$%a;3QBNk_>jE(+&V{;0hac3Z;Fs;BlI^66yRe;Tf?zzq-rKp
zp!IboY)LIL>v#H%ogE?rZOB7Hm;^`e7;DaFBAB;JuW0Ql<{^w5L(W=h%{LNr(~2`h
zg-y!l2A!ESQyW=fsEbF$2hAcMJCK<TwM|VMBFz~H7Y1stp8|AJN?Q0TCA>fo49P}+
zBAo~$Z8}6+j@1CjgzM^1hzzRIHn9)yZ2qk0h`Z8K%`rvW@aWG)uwA7)d}yFagXZV6
zxD;Os**y#PWZm^J-2z?=Ec=z7TGuU_st_w6gAJnu_*N;pKNDXnpLyl4>m5H<TB=k&
z0fV<pLc$%p-C)o4^^aj*dEjG73x{m8T5(poxEC7ek_8nz>r;Ua5vR(owsV<mhU(WX
zIS{LCo-yz_{cBmQdO|lTIovis*f6^W%b}XseoE%)16HzBTE7`T+=>Q`(sMa4aXQ;g
zLRza{uF+Bf)*n^{>p?R2g%Z0qb)r~axp22oDykTD&Q*b{u@5Qgyt3#gjPDZ+e`3Tj
zn9^?|y!c}xDX!JEqKDP`!XOjb;_#!(T&7BourDio+DQ8OiolX~1A-ALqr=B9hdFR9
zbdetf%sIAFKB?y9nRzk7Fuj?*GP;*Y_cBe%k=sd4xyjLzvHiAL%-hF;t4*tDR*It{
zEF0SzI@v>;HqIU%+ijqj{Hk@C9OU?E?4dy*P*G&+F71k5TWp&yQ!oTZSUL5Y^TKC&
zM(PI|(liv6nE}s8tz_wFIvW;Iw0n?@ba!JqLo#5U{3mkfWmN~qoW?`AF*$$h`Ecvj
zEGo~8|CCM(uaHfXFt!o!dnmrPOe(u_YfwS=Ew%C#Y8+Er8;yw+=44D~PFjo*1Dd?T
z0VCvSEsSjBnFf2iQU@P+faX$ZzIOjr;MOX%Yw1rnzKdz$#|FLw9zDQ_IcsgT5K{sO
z#smWfGC)T;>-XMy?6UT+riqV`tDa(UnY*Y!!Z(Gp;Xon+p*Zk=ilq{ABu;R|utbOQ
zc+nFh!@Yb8>=97u%9`M<Rwf2iH31K7t2Ht<HrbR9A?9a9_zeQfd@UXn(mc|ig>iSP
zr2&EwPKOylxC$*fZvJ)k`wUe|x(&g^gMy^QBKU}!V2Tc?Nk=84ytToO3d+iu>Y<@*
zm5dZ2L86K2X!hIBI9R4@1(=2~P>qb_^`vva5Em}m%FT(_j%&%u@e7$bq({Y^egbk`
zu)-%BSoCrBE=ee3nW*bMJ68+F6IcT5=IH24KOn?B$*Gjr$J(3bQUg;?=t%}gT&$R<
z8>v7cy895$o)2y-ks-p_A&N3fUzrmoxCd!w0~tMyvC5BLKMH>M245A2O+ME>(^pI+
zUxCE*>Cr5R5D7U;RRnO|Cc}t=3tO481Mlc_HcGwY^bj@D4a7$P)$8N`SFa2Hc7TE!
zA9<{}dgMiYzI6dBkx#3uVDXX&pzuu#@960<D%0l6{NEkt=yWkXub#dcB1A?AhEaX#
zDIZ_Zd}A<K6VFWY>sP9+dXu5QyZKl&SuSbGyY@!peS~1VT%5>={*|8*+5cOK&Fq>V
zVbvQFwhxX{idWtpVmVX^@5U=2bb25B+zKmM5FA++0UY8N$~6bHx|n0Q24V=q3tDds
zE~z%Dk3DjW(<NpKG2|SMW+VJDj&l$5%fe<{58piW-ZAuWettrHSv(EMS}^I`o*U@u
zwebC}b`~(c*X{A6mN*ni3g>SHUlq?gzJktfqun|YKpIi>`R({x<u&5aHg_<mM6^xg
z|AsA#jk=;q$j8_FEZp4FU&qk?)>1IWygQW}WFXx|K>Dqz%jX{zghK9?w)Rp@*d^;V
zti<zvoL!5h;u`gBo$A9&;Al85?xiom==y7oierlBTe6?NKwD38B*9C;`^7~()g$7{
z<jb^epGptd_w1(fgg>VLJH-sr6Z*-hz5gxPKhdrE?X7nPz>yzzabr|yTX}ts`<zGi
zu5DjX-!C@yHmC4Vh_bhKM?DmIGWD#CSYIZp{J{MTnZEa#2XU%Kbm1o}z$&mqXE%D1
zXm5EB`7QH(&~dAkJ0yQ}E3xiWn6v*h2PSa!bLl6Iec)Tn0TAc?D&P?(EOz{|AMF3#
z@U>)P7x;UGlhk+-k;3n|Lc^yo*)v2GM6SPl(#H?i37HHXCZega8^Z=cq4CxW6q(4?
z*>*1j>IM(`1VNwm4Zk)&gfH(RV`7`k1`fXuNqiwoyOJdpfgje-^X`yL8s5PuTueD>
z*?B#a)O7|cVz3@8lrD!5EyRnlAIw?vwrrl!!D@Z_%xBDSUI(&sX>5}>VQ0Qskc^pg
zFZsq`ui1m5u~K4#`xV=Rdxsd;+m;bV&)0jKHNat`<R_od8f9#5by2>NmzSW7wOXw}
zc`WU?7mZMxB?)4(P0lPGr41;%N$|+6K+SvxpwIalWMvG~=!A|svTztyUh)7!Z9%MZ
z!Xl?6rMX*PA-423nZ!0m2C_7|<TPd+FLMiS;SESeveIVeK^p2BGylEUn{J8%TjO8K
zBetwI*@iS?Mx*)<_788;8!fk|r?X83(bTZE(a*~h1^Hk~w}Qjs$(+m#lYov1t@VJ|
zVKH=%X_Hp%o|J?Je{k)Is`JI!qes_$kY%jEueU~}kXZXO8bzf<i^$#~@qg}TWTTpw
z9VFdoX#K*ZqukZypMLFiaYZTW7n8iqGrONbts1*b*50Wy&K};q<4)hut0n`G2wkgi
zWKz+W1)nVK+TYjFU1Ov==2V`E<A>q^>($HhnxwAkrhqZ2^YZf(wAWD<=@&~tH*n$b
zhRKe(RSGl7^@f0X4u5<epU3L^8lHIgO}i=l_QS*F8xQ@a_H8PlRv7IN&LuD`A~M_!
znin=535ZW@2so%zkXAQ{fc?&dIGZg_So(%n{F-`E#ZUl$L_;HQty+28)g5wvQH`E6
zkOI9Q3Enb#ED5vz8+)*nY+iN)+x0yTy7025{A1w~SN?-SlHD$PP%RR5KM-d#3c^f0
zaxW|=4Gx>yVhybMcGAv?^<4QbnRvrKa5D@og2-yNgs<B)bTjfNeyz6#uuD0Rt}AN)
zl9;c6Ywu0*U1fw_R$;3R+^;(GyY7ps2|&*5*H$Lv*oUVG7AakW#rMb{@`+35;K-tq
zAOCiCC~i8vRh|VskUK01-K<8WT$_1H*C{(?lN&vd0F9uDEVl?JBsG^qGd5pi9-j|H
z${bH_l^!2<&F)%LAX^Gk`FMjw(=yF~`uCt2?cE5@=<s>M7a0b!+aK^%=Bc>QRpv$E
zVX5pGx3=_d^Q`5GYmDT;zc?m4r%SAg!$Qx;@#z?ooc?OqANtZ-HN)1JfBz*Y9A#Gj
zlg}qkY`Y9!ZQa>{2#xQTbhvelx__2>m>IPMJi*4Vz4**sYUrF_s;+k~)i++`YXmJO
zdOh7K&=H!LUa?1?a~wH7sck)6BPKBr8>dxQI|h0ec&>?R!%cH4h3BlPl?X*~wtw|X
zY)IyoQkqct^^{Zw?N)5<h|K%kO}<4s;LHT{S0Y`wY=;LdBaIblITgTID=QOWp4w9_
zRI;<L5)FRbcBZy0qm^^HY4Iwyu>GtOfrrmKHnuRNI&KU8G<GT$<kEitl%XOv6#&IB
z@PGYaosh>kJm!mRdN)Hfj{<GQDW`4&T{t2EF{;`AG5~Q$lF?IpjUPKc%$`DJt*G%Z
zEc}Xajo4H&_bd@snoe){a)j%Yr7w~sn{T#mVVWOo&VWKZp8fLx2fx?tq<z4oKxg2Z
zNa!)7;2~s{sbzg^K_($;A4o-S@On$`U_1qjEFlQ4h8?xw_g_t@d>8<U5zWYb<dXqQ
zZ+uE%6CU5D7CqhP-C9!-BaQBclk6ECN8Xrj(re;By@*zE<azTm-Mx8TFA&(<l#O)2
zKr<hX;U_nuL|I!l)LK?Qh2$#vR%R!}<?Pw~BiF1AtKy}LRZd#LAlACX-gBgQE5)<I
zIj;8XYW$YN*Z6pGLWQ!)V~3&uXuYatX;&PGt>Jr3Zlm5hlkKmQ&b-5#a%e=EXRRru
z0wd8L8EX7ST`2Oj;bxi0qcC{7igkIgdq=9e?VWX3NvWNJnmg1s9M3YbFb+bI*G9h*
zW0x!}Je+TDD}dpz>QCj)Rtbj_A_9E=_R!8f-adL6WVT(`or|8sk}w2E7VTHh5=!15
z!FDB=FyenaJlRNxB5MVi02L-^)9@pPDGZP!81anz0U8Kl3!VC5qm3~jF@i5ZZM?6T
zbmsMILiBjTSazPV@)!CE@vB?9rdw!&U=Yw$xuOWA(AKvZ|GAl#fH{Im4|g(42V{A{
zK7sjyZKmMDA2ROWxTjE<*720)tUU)y+ob-66}hLtY>*SX9Z{xM2lskE5S#lDPcHif
zD#@TKX`)NBW1=6Uz(jk)1!cyjoMj~Y0XS|gPNz6aOGJrHQa1D*R+q?dj!!u?BV-7g
zzd?pbv)K|k-^x%ICW<OnTz)Y37bFN>)NfGYQEc6;5pl-#CM5RWaDW^@q0oWU9k+t#
z>Ti7()eKYA(SbQ!A-`Q)G#k9G#~*4+C0mqGzsoo?5ENjy2jaq_aU6Ta=K%CgAVA+V
z;JXS!2z8zxFOW$B6{nbqJF`)6u$iQhW1etJ%;nllvYmiQt4h?!N0tlua*vpE73AY8
zj7Ec!PGt;!zHeK(BK9ktE@P8HDco-gdUOEW{~F5+FRu{s@g?BPb-|owRb0L~?CXnz
z<KJi^VGlD1z~{X3uH>t|){pkP!m^0j>=2)m2ck<vW)4?(gXhz&%>1=RwH<d0K<vjk
z%sRl@R3ciMfVx;^pj*-~b+Cx&leRWv<lQJ)%w@T5xJ%IW4k3zWx`M;f-ufQnw>Y|c
z=(telESSmic7s?j2^0dKq|KN0lOr+k^WVgRF2ncJ_^FLLAN;ZN7P)AJQqLV%DUTN$
zo8pnl_s5mVbTr7W&23zL|GUZduY>!jL~Q^I?GfzhaN|*-QaDdrTOD9>vvksSbEb$i
z9j7>5l8Gd(@bw<sVaq?X>mHx2S+C6_^U(88o@ckqU#74Mv)`nV((c^!a->iNSEz0F
zy;>;9B}2hl7Sk1%Md@ePlyQ(I*;7gsfsABBCaQ^K^`M59>}q{=W;KHlaCSgAD!<&z
zegn@Z&77ihA#aM<u)O0|!b%?6#XAL+A09gf6Y*FSI#)RhEhG-ueHUSR&v(s@t~`nr
zRoAv9Ld_>GxVo7IT?~~zTB7L0Z~m9P(WC(qOOFC_TVxepcD5|Kj#H@q6iVSx`Ug~Y
zw!$eHgK@ib@zfM^ayKxBq9X`K1!k_akOmvYXgF;W5-}+l|ID&JZlPQ#5X%aA>i+Fj
zcD`fV>-s$R=^I)^t4|U@N(D4p6%T~|e}2bP$<CkBa_kn!?{HEVWa?84xoiP6RoOd6
z<ckL<vHSTw<N**Mi2c<|q}$HXIcK&UklyMF+Q`T~JtdnL)Sdd|{g*3hSR1}GmP$}x
z!@Q|pQ}4-B^W2;8gt%K7ZB3EPe_73V{7)9;JQ4H#+c%(Xcsim7l#85en5RsBe{*PR
zNkGPV>VBXWTlB#aRtwg0b8U$c1lc)Ov$)&uyWYR*WJIM4X^~Et2S97Rq*LA;9%c)I
z_3L7AxJCG8-pTTg#-%!ij7Sv3y}*Ez-OgN4&B`YR=VP_IoBuC1<)9mzn%Jg>#QrFd
z&D1~bpIUIhckGZl^>85dvVyK&MjLele+~hm4!N+pM#A7i0zNEXP)WE=GN~c1X8_pp
zbT<_{n}vVAm*SEpUX6Dg>jiez9VGe|M>dhD>zyMvcF{`yZ=g!cSeQ;&z=?&n@!?5p
zqnCvjD}vY<ZL7J3)U(NLl`S@PG)RN_Ce=fx_t{gqp0Kzb0Sp!xm=leBKY)G5m(o?Y
zi}mXdZ!5;;S;Yt&ooQd_lw>%*e*g5UK^mJYV32OAl-Ip=#aYFD=jvWP9N>3c27r%p
z{dredY6i)sdpcK(2*bg8J*8)&@WV|!6H{`%CBMFY8Na4oOl*$*Nxhl&yki+lxTofG
z?wJ4cXhZLHGxqxRx2r*a<(c>hj7!pX^Nfq*<|2zS{mV8jwxKkMsKG}CQk7bnjwkSM
z<y;`i(?VVVi|@)OqNvzP{k={gLpG&3lP-wu3u(7&0F<8Ki`iCzh>7ti`QWdvzQTJ*
zNBb8)?)({G;fGc6$>tn_{;so)=SG^%j8763`Q@KXYVQk`p1mr@nk9#j_=V63&3c50
zNjM~8$fQc+zNhO>7u6W|r;b~e58t`*-0#s$!WN8`xX>#@C>Vgd*T3~Mz{u`jlIve@
z0}=%Zw4MwtDFphrH}$l8iq46*TLujCj!%8c<HJ{Imww;-yCq$nEl(m}SmJ;GC`P8t
z`!(l^k=4vQk<}k_LFl_`UGI*7zNNOuR3qvEdXJ~}aq5u77G%nD5ZSmbJNb2E#lh8W
zh*?|AP9q{`4`cz`XQ=#ds)@XJ!+CAbGXegCQC_;Bcin-g$F%tLAKD&H^66uJeXWA{
zAgb0#3}V$KGd?kR0xcc@k<o5)6`caHV;YZ6(|%dZo#G=#h%_aJ6@weWCMiG`+rNcz
zl#mU#KNw(4oWTYdy%ecV0MwxSol>TBE|OMmn-`(Negqrb0ZUDnBJ||;lWk!sqRnm~
zTLo)<5Sa`L;d>P!N>Xt%_afySUQBIuQAk2Upi51m*+7|ULs+Pwm`Xh%N(y!Q)d*J7
zXqI7be8erQ$76kAAAZJHTC()(6KSYd&XF0bq8^Oiiz2gus)R!<rM>uoXE{tesur@T
z!aZe=h~{Y%r99E$D<C#tPeaBn^a)M@kFhkz>TDpEe_ZUl#n#`?75-Tlu&OCxie(;p
zm4Um8@!!2FxK>(S?bm!&U{{vE*l|b}xFgy>c|8>plR5$Y!8Y;JlL~3@2MW5SYpX<6
zpkhgDf(py*Bumi6lxtn$_iLm|zFc6-E>b`+aQsy^k`JS+d3<GONzQ|>b@v|T%D0PD
zhed5NCqttZD3d`Jom)a>1MWRQ@#LhDTnnrmURR*Fsq6@K@~xB-4~aY6;tgu08Tc|Y
z)8GIuo;xIuxLWN8Q$PdRNPAknx<fTbR&!p9mz{^5O*Ml~Wf}8NP~CxRxTixM%RizD
zM?huM8-Qoj*7sX+Wer7ES=+|{a9hBux3)lxUfO|C!)d2^uFJY5b7h{#x6@B;{M}wY
z%A6_JY$w!SXbt_R>41R3f5ZSG3ph$u+I%}ig$OhoN|@H#7$!O1Uy??ef2hgExTO_7
zNUIW&hQ>#hP8e3o-5KPU_mk=oj*G;4-Ds!mJ|MQ048zm$K2Af@80v0H`5%W6Mf+x`
znFC)jIb$nJ#G2t}0a0H0`pEOmH*C?;t?_{_52t21kO4dK&3`fciu_;uyUbdW%4Od6
zr@$b<dU}TDqWKN6L9ktUr8m_Ayz%#$WwJ})$^Ky^&jy#*AieE~3u+U9i*Ky5!RbEE
z`d-#!6sEqyo~^8XP*WtBR2LYM8^0T4ceKL*BA$SKm0G8bNelDj+&cztTi56w5W;Qz
zY{-h&CB62EU4HM?YJ>-lQo<HrNfY9*NRIXhXz*gNw8?RUT`UiNl)Va@d0h$u=f$!>
z#&TW^qba{cjAlUi+$Phy{VOKmbTA<KKn$pZC4h*zUu)BjAyfi55yF8b_*rK!`2Q*b
zAOaCpP^mqj9VsPhEVdp@m3B+j_ONcHp&RyLnY*Svq>?L#+SpOO_W-oWN#%HV$pKN~
zdn`LYT?}@fOXZhvq?dks2zTvx+%FGIoT{69Kfl`x9H`wdz5zl-hrJ_j$QVEoQM03`
zM!QA+*<jWn6UwwUZ>1yzi(9rCtNf__Lxa;F>fShH%Oq$qT1p(T-6PUQ#_gX7cbG1`
zFT74o-5UzU2>g$dr&q5tyoE2#@lqBb%>ta!t${%Uk>)wl-JFHC!O8R6XQ{RIG`9Pm
z2mebq@@l7S-0E3@%2y28xww2;1Es%5k9&^y5;C!&K3Sr*l3DIcQHnFsRZhj%Wv5K9
zwC?wZPK5W(1+!S#mMnW_5E~hk!%sJfRO@RmgAenRIll@NWNjb;i23Y6z_@id>YX0&
zm#cVKr8pEPZqac?F_Is#+d>AgmL9vv>$QOX!h3eaA{J7|A8D%wmeT>mR7AjgPe<&p
zZXu|R{?HpXs@27zfj>#PAkt%`6@~!mDMDmEm)z3w$9t9MXJb}LObdH}hR*yoAeMB6
zvWmp64nUm+x}ve}CiYEuHh&@b$O+&5DA2w*J9>0V-Em;pcz*C21OEGy|IOK^p=CC_
zzedK%-WT3GopX&P>EL*Z30FH~6yRg2V|Uz_K|$Q1tO_cCmUm}mzQE|Yh>HWroRx}Q
z^=dLS8b@yV%ELD>vgMT`7G=?z4AQaO9gT&xx{vCPJC3SomSQ*;Iyx6%U0IM5QZfG1
zYb%Rd#Z~8Lo}NjSKtSYAh4K0Ay@jJ{>~$KvdF!_0C_#|@ZZUL!y}$7TbmzC|NTw_n
z?a!k01ZWv^zyvK`B)3DudXC^ay>n|5&y8gv!vp~;|7VpuD|@SRXOf)w=kB^tG#r3S
zwZeB<*yf@{Ypm9I08A=ybxeS7L!ezE@Dvp96X%;<bSIk=-*f&D0e-u*x*SR6pZNAM
zYR+9s?|rb!@c@H`<vz+*B_5s6q}7E0FFYLMfFwK@?$NQsYBE=0r0||xWuAIWml35i
z8jG1DMC)2ri05-HJQ*MY_#isNFM|*D**Vkp)zPR7qjLn=Q3UOTIQ%^EP$)h8QsbkJ
zlQhZi(kD?iK>1&ksc*{Vi^wV+U!v!cSOz5?w%4XozrU#WM6T4+;0s(QVc)2YvB9Xv
zMe?tY&jzV&?%9JJw8+y*<D{Dxe%G;HUKXKUFVhUM=KLf)Pu9{rL{6On(a}G9i{9AJ
z3YCN-L4{;Bia$b`n~kcAqM5K8tAFyFBa9U6C#AXB&StX%$g}zx2ByQU%*8S)k)BMf
zZ4ejt4vOgAREMtsifZCiM4LY1d<(aBLH3Of0*_16vYSYn1SKEU?C{T=JO+C^>n-{)
znI_4ltMpsyv}>BQ>r8nc<kQ&PZ!Zpge0ku|_7$N?+2-N&b*^O@up%H*3ZZ~lPXxGw
zX?OVY&0Kd6iS5dQ(!Hh1^$wLv8FGKGC{oLE`mgISN4KaWyZJ5}SgP?nv=Mj?sUVDT
zFf*~JC>xd4voRz_Evtn4#mL?-jI2?#{OY+T9d>nENus>2<UJ=<-0uLf>{0{(QX6jS
zA2cmSO#BtwsWJ_qES*fSe%GL%5Mut?_0RX+!Yu+2dGoYHPzey~So8=E>;F}oUF*dv
zmtns32SlJ%g3~#GC^lx{jqrmkFTkLyU3`ZrC3b4RI|u{#ufRZUVD-Xv_ZbXa$Sv86
zSh!mEK(}cBR!C6NWp#+sa7Nxaah~0Uaq%U-x#c9q*?Tt7vXOG2uOz-L_to!=77Qo)
z<Q=<R4X2iv=2!ujTj`V10-V!Wnq}4*T(!I{Mz&O&73myaWi5bU|Kboa8g8ep9s+jY
z4P;X~#0n-zrBl7`SdcYDYLdUMc`>EvIYZTL35y)q5t<i7`xAdmG-K020m+T4R_tot
zd<fuoR+Ff_R2Zb%xPGH-&DA1o4=Ix#*~NS?OfVnWn2BmO`ia@0m92{!5?M`fej?Ik
zk^<Y6PGlpkj*wh840aoEq5e2ABr$@$0x-Nt;^jnfoPW87lSYQ$oHZm8T3_qF^2Yey
zSnIxWZXO#&R}>DCB04^=YcbO>JpU~WDmXuVYZ?D)rdO_pk<C6NhLIg}$1+bB#F?Lc
zqm9gCJ=j5%ND#!hZ4!W|^+_METwvB80g6Q(Rn>I_6<eo~DW8h3C=;qak@%I<h~oTD
z%yYQ}(|kTR@QUM{bw~`x`g1v^Y9jgxXRHl2hLpCps<B+81AA_+K6gIK=oU;Wtj7MU
zjLp~ZPXUk{F3!6hMDJmu1mZTe@zr%$<*uDweHN?6Y}%6na@Nv?n4B$b<rMaW*63za
zhxc64;`k0BuOWEHis>0@#3??wi&uY(WQ7n9EaO7kH(I1Qu^=3Gm7Q~BnnFvm;*ZpY
z5sym9QlCZ{LkJkd2=q@`W)xuT2JB(1nNz3%Me%nktToQxS}4Z&Q?jj$VVQOVUx3et
z4!}@qS-hG;N(S#ecc;ZB2)Jv(6Hp0IcO1~IT>tnot(NSDF2;7&B|nu>ynR}*eVS)A
zPTo8xLJvOv*%r2>^@Q=k{r>W@)w9~x^f{xpP)byuZ7aJ^3)$B;@ZT;{3?5exhgNrn
zbCm*cKV{U(-6u2&IFbV%8MVgy(?1(o`GTXtpTgPjBz!_6I&kIA?bvC8dsL`0&i}5i
z_vR2})Q!a+e_Hnx_)u8wq(NmU`Bcb9KGFzRr|{2-NxMfJ9#`&3{Z!CXGcjMVLp<|8
zkA@7tJrXH+Tq%v}-R!juXbh=j;2-K-FQd{kpxM8YQmYZ(>SN{hMjV{aB`Et!46JF=
z+Q`PDA4&e1C6$9rrR%AsF<YHK7jh&p7NqvcKS@x(LS|D+LPC#9j+}8af(qgFi~(I{
z>BM0PJf{D5nJ!)od-e+W+9Y*bn@XvC4j60MwOc3R-qDktW<R@o=cY!-wXi{V#1(%T
zzqC$4YlpLgrFD%;B+bY1e#cruhiV*q!RfP>>0+x#-+ccl@ggsO<H-Z%dzBzdHtmBh
zfm;SfXac*wvz5-OC91bK+kn(oH8G*>?(_aPcEgq@uJv`k(FUW}#*2d&__rC%uCXMo
zlC9NY4NlAF#S)9O)-<;kzJK);sA}5CdUpMSl~A^y+u(l2M!ugQzVjPY5_Kovef(0#
zW1w|bKbd~6@$UnHdVWzqc@S7XOe|vv9q1Q=hmySiaJ6cg#<IJOEs(RZa@T1tIin=*
zf3{5G^2;au!qGpi1a8C9M^@VAYdQ(|4XSEB_Dc1PRaQEs2l>tD_W5ONc_r)QOPhTM
zUR8I1=jkNJg%bPT9ElalX4vzKK0*240H1d-@Y|SDeB$xD=RxsJXOZvhtKR_idl?+E
zI9pfuROvs_6R3nKE^m}BwVh9{_i##$_&oGKPIBz<(CLMQt%EK1{GI-Gl=;5jZ|w2B
zJ#U!)UCr(vbLkig08lhPoR|rAA0wLU2omD2_=u<6LZIuUYPq9OfYlL&cWs3y^-tQ5
zo?tb;aso)^dqK**m*N%3seDWm4LoU=ks#B<0d(jUQTXnWT&XFSv`fUBL{HF~RrCCb
zQ^iX0ZgU@>Y0-x1FXg@_yUs4}Xa~ZX7%_jB4fK84Jt=1TVqI5n)9mXC9LFlg19T8|
z?75fu*Ay)ai*&lwZct-SoN&8KIPkW@2930;uJJdv(AI<N>%myHd*6{tL=pZ7-iFSB
zFaiQb_qO_;ZwveTk99QQwo=p%%3`9>m-%!KC>gPScWY>fAkI81enN2C=C#lL))Mys
zh&vEMSleJ9ATZhFNM%^h!}tk|7H_w{q+`<j3vN`+(ls<~*f{Vl>mTK)YiG~Iou3~-
zGsiQ0-1M7paJcjky0xZ{$plZ9M3F{*+A!Sp$t>ZW=>Tk8jHy;BXJgmn`C~)zfs#m0
zWGYmg(lh|7ga*Jlf|t8#Fq#E=jUs&Qk3KW;Zc;o+8VRccuv_Xyq$tj`%+t%nm4`M8
zk2cc$_00w+{`q79=A)}?gu;`~Z=2a|%xF_W=J9LUSI~s1blsd)595C9{Kl600lTAP
zc2VLDiL^Y_AITYo=a;Fc6@6mHYl{<ce~0s#LcW4rfpRI`8=(UoA>ozXsbB(mZ!TS#
z*vMCN|A0Loed6+33<r#poAc<?-;H>(aUtb{_ChnhIi`CZgiI^~mo47&7qBF-+}l9q
z@4-k2+*7SX^!?K!nXjg(d7m5XOV7?XfW!uK!+yy1qYL?tVbgb8=H3Q4PEB)U{$o#)
zkiqn7VxgIP9lOjq*A!AtWhfF(%bD0zDiw2;1rc}JQ-tj5HYv<7D1Xfo5Sy}6tpMm1
zqJYZ{W)Guz=>l-|ct=cX7K$*X+_vLL6^M`IcDd8p^jDX+PxoOgxw%6FGf3w$1d|a&
zGh!m%V68`BZEbx6tm6-;O8~8wCfXk*ljEF8+chsnI>4&t7Z*SpD_z<1wM|5wU-*gA
z)dqM39QLzq80wnEQ4%_E0>art8aBx91(Y<@)alI0ajLA+7!wWLj|0gJz-{!wRGVlw
zo{?(B*!@B%_`?FrA0-Un7V7M(A5yOwlH=g$y}538Ea92=@-YWeZ*ur(CdSMt`An&n
zcf}mzdGsus7Y*~f#Q81?#7sj=c`@{KNlq5Z95AX09WKwt?`7PclD-h3N?C9kr(7C5
zLu$b=*!5)(wswf(unm#V=QH{4<wtK>d9i4(Q^-}V#c)T|1}9hdA5ED1SG$MW2DxAL
zV4*HDqn#uHO$KS?VpLnZx^NWD_3Wk;ku~Dv{$q=MrnLye5r!H1iApAFo0eynYkZN>
z4n)z$36u_VyF(vQh9b0{_9>nG_Vwn`<m45=Jh6E0{1XFf_gOG0PTig)+=$L9{xE7M
z*=u+3(fGdJ<SBQ7%nNq*CGmV5xatD}b^lukh$W$o;WFqSHGEprJ>aPGp<6_`sAT!*
zm2ur|lP#LzRMXbK=a5M%^RtyWenOl0CXGb{{kIPRLqTf7Oof0%oe99S(E$FidDfb3
z3)d;RztFHxB~}Q7T3*fnb(ZdK&gSJz$v?uc0l(86(;P2Gl~>kSP9|-Ciac_SIkmCz
zVIyGM9cA|9v{e1E375sGWo>^!3A{asN@!M@Rg%c<3np0$_@-rPsdIk&ApDjY&|xcF
z&z7~antO!%;5sR&G{Zs~vZ=N1muZl7$#BsLWYTUyTa0=k4*(!F2f@h;Y*j~hyhUQE
zN&E(XK#ban?aT6!T05s;?<Dc3o@=!kEW6CE_qB`5o*Pclgv}LhJ>ww~!%q1n=ZC&i
zLg<ywQpvp;5r*>`{KkiiiFf=m<H+%!*MC@+??({l#M_nmA8IPQ6VsBkODLo^EyDw^
zeq;CXQH>G%6`o{27@TmHv}vU|{UT%>cP+2I99oWXA6Z)GdfR&3Fk{m$$-W^u`rHk4
znTa=#BoprpK(Fsx`?zY_;wVsda3DEfz>WJPr`@x?b_eZm`!|!4+OP0{fg_`;qO(7<
zf&+^w_O%~i?(Y--tgw9azhpEWstR&lGgoxSIVwSqsimchT`Zi<CYKd}_bK}Cyx`bB
zGWyR82Aw<@6!8T^Nk<-6mRHufd7cm_Jk^sPw<Kmh<0g^4W`b55B}TP*B>(&gZqunE
zy<`zCjV?(<L==#wllUwavl+?AbT?k`Zq89da}Jon<;88U6EZW=@hVrv<Momlw#f5G
zq|xInsg>pjH#0#m65pA3su}~{;7yDfok}zjo|asM@Ud~3HPQfi!ClGZr{xk5Umq?O
zU%O-U?R5_Sph*`f@HDbj3rKaz`9}Plh(gF4gH4PUvgWPMV@;I?MH<MGuT0A*K4luf
z-Qd{3J8cITZV9bwmu$E8`XwtV_~ndQZ5z8ymrj^#_TqGKHW#E>$wfwJ<eK2p(Z(k1
znaYGv&C&+a6X0_JQ&{T0L+M%JpwS@$;-++D;8mJa*=*Q8CW#i{UY9I4Q<|_=Wbnly
zCy8ySCl7vNTpFs<#i=m*HV!fg4N__u)!m^GZE@Pf(KzBWP1ezuj*707dMiG2-#wKE
zxrda<Di>Tcxt}Wb3Z_W$F~GrMfZ@cXUy_P+SQtdql#QnlC(*tp6qb<CyZ0z%LT${N
zb#Ab)et^MX97!7a6|00Yq4sRXiJmhX0l6fwz>d)RAXH~}>U%fqnJ3+9AsFUn+K5uI
zT*@A>h#M)o1?9tn`>$OYGM#bDx_UHM4|J;~?Oe9hNu3IlGsQn)XE;D>8Eml7L4_-Z
zyNSj1mxpG$O+(0a55yesbKwDF34dnE5BHIB;qMd`&oPXCDS%9YJ@CbI66Y8MVVto^
z9|`>O{$M3VVwrMemf)DOQhzQaF%g4>gMjxmB9R)R`@<Av5N3y-m5N>)UzL#)c7vfE
z29aH&On_{b%Oip%!cC?JLH64p;xpB|fER&0tedbQu82ZVme|h@qej+N#3MY=nn%9z
z#*6U=wd3Im_Ep)`w{Q_&Qh{pW?{O>4Ydf~U^v9+YT9eCbF(&l`BcW6*T&8O%-rM!&
z0el(Ra(&>Wd~E!8diRu8!HYNQ_wS({hgxOAiY`IImYV2;j2Q~8BLd;B_%k<RQ`P$L
zDQZcXdm$)^|N4lQ_CCifq48y--$3|y#zBET?qusD&W;|p#-wSde%|>rkY(dV%r#j+
zGT65iga-{rM*E2wczN^;M<!hx6?6+@8w8=npPkt!yHNYnn;3bcgk8QMhb|d-bA#6}
zLKBTNG|&pL_+(=XVY_@=rU&j{ASTDhw(O;^TRbZ*?RSEb5QZb*PQ>AT^zFjV|2NP4
zMo}utIS9QVxG-0L{{{XI+Y(qzj6Grkk1L4K8X}N3@(?8?9ymzGn|mMEF>I%B1O-J*
zFOx?L^-QNL))JkE>!K*^Wm5*THda-zn&bP-f_3CE3eEPva=^&ZkEAH|GjEmoJlmg#
zqM7VQJ?Bc3)r4$odwm}>qv*C-=~#^Ch8{H!a89ACn)trWs8Aw1Q!(u{(mXPtWpM7|
z$O&vj#((zC8AUsmcL7cPSq!;nzFKG7BZT?r0b*j+Zi6w&w)qH1+=A1wVZy1^$6QK0
z7ob?Cxt$PJo$h&>lMIgf(5*<&Ykr?KE2J(Uy4Q|wZ06M7Z_6yvM&Je&ZdnC1CJ=XU
z8VTB9noWJY_u<KD0G1yoQ#fn&O7EfY$U_&FRHFwX&M7;|9a-h)B{r#6yx0Oqxxx8h
zXtx9*0_U&`$DI8uqvQswNc9W-R`O~1fciIXS!n}DLaC(?fEfu+fByb~3|dwu$^F2T
zlquZvhyEsidd{g?)E)2Vjx*=q->0!${j<lc1oo6`E>4G@8J$+xa9+^n!)J|P(ssW{
zPX;+aAbdt9L)hdLWf8p+>I+CJkwk@-NI)fhqJId$mxmel=%xe&kQ=3R)rull9qr>L
z=y`WRSEO$+W~pR)-Dx1S&Gz7GLx=_*T*{eIG+*cs6qJWdzadpf?kd<$SK87pZQ+cK
z{}?TkM!>1Sp1^^?Tf=z&20@yh|FMC{faRCs=xO6b_5ixa(?ndtG4t!LfOBJb0e-U$
zf?Uc)^}IV_(Zfv-Bn@@R!*q8qaD*BaZR~VCG<6MH;@n-ebUZI<Rm7w;CHJjSEngbT
z3E<zvumH}DXpc}=xAu5riY)GdD=2Qm&JW>1u#b1!T%G=p<SgT3)p$_lch8)@V2W}0
zSv68xvCgW6K(0=gTU!8C6cI-Dz{aFm!{;yvB1!iSv96jZU+7EbPN~0wBZRsN9RfVe
zSPP{4XU#tAh|wI)D8K@{f*%x2Hod9$vHaI>l!*?}ANyO{ij5rxi2e<rb7h7HHq~EO
z?ls!_Xfh}N+Pu;thJ<;@WxJhdqgtnth3w7^urXTyl{&d#J>W@qvTaut9tl=6pSRuA
zBW|pB0#<ypw8t7qYEVVWATn!SY<kW3PXU3L$$mgb?eFo}=DXN267sffzrqb_wf>#l
zjlZ!WFg|?jZ=-nh{k|v>W%0+dZ;5+ES<u{<RG%8}AAbFK{x)}sNlf6ttIOm_40a_S
zEJy;x!MdNH%z<asv*>FQ@L+a*@kyM?9;J{vm^Hhp+pNKJ5|BHvq<PXAGO{wNeLdmR
z&N9to?FVN(BWbjK9%kNTz?B=?@`r~C%-`Fh3u{#~p2*D2L;)x_S^uiSy<Q1?-EQNC
zT~a?VpYHJByr+S)yn=MPybNFcG|ypy$kv~nvh6n^n0-^(Ge^m)W5iiKe~H^;_U}0S
zXlhtzEN=8uV?T-g(L%|oX9H0x4PL($h`RcX=w9`f=pq-uuYn~!g)=>b1;g-O-miZ2
z+M%D9NLDU?%!hNqV14{O{VXH0mtT14sxtiyO$x&qh~x%4^Xvms5os0{vSS=DOGQ6d
zB5wyztl;0;!`GI!I~J!#CKh#tRL2COr5)O)9TNPoW7}xV@=b!Z|2Ku4NB&pNF*kt~
zKgrjD*YlGDI`7hR3`+uOJ4UYyleiBNjX^x}Ut*?%fv8FllJ*Iz_Q`!ZOR7|mA6Xx(
z;9>W@b<-<QWobv@rm>{xkp6^=t5(n<uhljU*H5G>sOE271ySY^NMJD%D1GVT(p6>G
zV>Xo=)&$kAo=l;L0|~fO&a`}}xMWwf)--;aJvf#=3s$Jv){ayx^oGF6o*`cJDJJ!v
zeM{4tHyO5d9mYCM$`CII!{w&-&Dnzgm?qYYZr$C>uq9Zhy=*Ip3QMDHC~CvZ(0O0Q
z<NiCE$T&0G0naCcrO_;&?n12tPcIUMrk*4{@m29(Wgvuw#`;UApS%(yU*mU@{cdJh
zJytu&S{*Y1iM91_)#iz<t6uC?M;bxk30V5Ed^5e-c)=83QbtTW?p)X&_OU-ba|B|w
znI-OhfY4fvm6@wedYrBX7#IuDGo5MP?eYB<q#MGvbohk%op)+hgw~%UIS850ww$a{
zD@SOgzKX?{xbXwq953}+a$xk{K>@m4xgcy4zdG$=HajZ8iLX^xrTea&YpdnvO*^TG
z#$Nuv6I)5_ENKhVC)7NOKwk>Htx}4kVLqxP<VSa_V(8JaSD?csjXi^vdcM0b$zqz*
zC+-P^7-qH$grk}93DdZMl4*xR?1RV@>s~SzLRl3ri82Fyo?T5=`o`1RV_#_pK;px$
zQl_wEP`U^91J>&o5f@~iJJ0VtDaJWf_x)BT?&4OS*<bkIkx#SsoNc>Q3zmMgn)MEI
z4N;^VygYFvUI}2dDTI;{D7ITzVUkL~(-9(hyAk1Cm1BJGzw?|<Gi!E;N}wvd%o&@A
zsz$4gslJ228GwpX4QqN|Pu45oM1<3U#r){J9-0LSRj73x5PKE=LH!L}?P9Fv;b?96
zt(>g<)#E(#!z@w{UtAN-#>8YYeCUcV-%_WeRR!B}ZW7_E-mi8vwTvTy+}~*@_h@84
zc91H#l5LFLl>Sxjnc@GzOVOXV^Ar*yBYOJh8+;7(OaVQDei1D{GkC2nwqP7y^GQ(O
z+}Xl4C^0dysYpoJChGe*sR+XGUImlIs5v8@m#tU&SCC8nQlXJyfEOMmyzQ%y7Qg*S
zOs{WIPk#l@MP+4mm8NN{n_$L3LPDuY_^*Q<>3)(goxx>Tz>i2h+Fmn65vJ$N;L#(w
zGB_Z&3{z3&S5X%-%<>Ic$Q<-)@W07ZOY_~^W=Ne>=!AQ@>}QGca`N4~(!V8r@4pWC
zsQ0ry<&dHo5;(xY*{@hRZgB2>ZD)wVOJ}8EprsC5WAM#)e#vX}Xmw5B`0~iS_T?CI
zKASyE_WI@K6mUtMSWATn5>c)}c-b8z0Pq&zEZ?Z?Y&mHprkWgiY$2c;wVZdny1oYQ
zSXo2Jt%D)bDVR`F_MMW)ySEA7$CnJvxop-NS9R<AC1<y;)mYRT<m7#B`5SGe@ifcZ
ztKJ0Y>)8s^Eo|dbFKNBb4^O46C6fw~ws~=J+?m%EQX=J(BHeo7sHhrx+}UU+Tp(Da
zRqcuZ@h!X<LQHmMGBg>aq*&gEh)VG+bENHH1JD$r=>%hytBZd`;`L0^?a~M11eB)a
zzugTQ37k729URRmA*OV8Mbgtz^Q4<2130g=`_bY)=)0265<Ia#^iOX75)o|Fz$apn
z{cf_)r=*&}->6Yx$5n1%gZr(@FGX@U^CSA_sBqVfLaQ||JAcNl?MwEKa3m9P$I)7%
zcw#zp`uPX$^m8;y5>=<1UX?m4%ny)sjMH|AtlBmh;-8B@PTNJRH-*>PCao!LFTsLW
zE8$>`&!FcvpBSp3Yi0dI)@7nNR&hFLebLP0h*-Hdk>5wZQR3n&eAv<=)q}=_<PL?Z
z9nX8<iFyLg?{Ez5=l^5sE5o8{zpn+6mhNtbkPxK1yE~;pa_AwYySt@DTDm2NZV4&r
z?(YBb`Mn?BbMbBBT+G?`zSmxR-D_VC$~0DU;8QZ)bG1CLKGuImHP0xSN0Hr#c3z}b
z<mjQu*Kx*Fo3ueFl9fs{hYJE#A0Fs28`)yQAsOFIZ8o0-N%Q`*@;m3i!vXqq1ZE0S
zmR`MseOP4<N&7E?)#Rmw#)2NPek4iz0z?#Y9Kgv#z<Ourey9uq4_o^|uoJwEe9UG}
zO;Cdy+TPVTAnf~y0Kkn<<G<JU0vD2RK21my_i|SoQF3I`j5OCY^c%E{5?^|Mhs+yC
z`|xvDL#*6Fm~yzv=9t~QgKdW6j@Bk#^z7@8+_$=ccLHS4KOPGBHbAgceDbIq^3^hw
zqpj3IrffMv@P)=3SshU9^X@!FJXXDJ#9o5#+VG&63Gp>fv~i-UZ*7a0lE(H`nN(KY
z_x$6J!BuU|g`aWFF_}yb8?AqOOQOG*0P1+{poXk3=l0Z?0C4v)xu898-}b7%7Bo2L
zmimD7IiD?rJ+w*BD%@3}z4wL;ccSOMMZ2T}KF_98q_-@3Sb15wZ{g<WCwkUva1Cb|
zR${T!W~0TYOr{`QM)v@QYWEqpcuP|FA>GlvI#hi{m6}`Og;+tF!xfnF95S2KC@Qh9
zwz~xe-L?B6?1w8tvG$Y!8n!I<c3=m$q_LN;UbVkU(LMmjF}Ol!<Za==V#$`woIiBr
zeomjTYcg!`a{-@GO*H)~ii2GWOg&YrjF^euy-`rVAUR1ch_}r2sA5h!5cmO{a;Kij
ztYae9Q7b6=w%2+G%y#>0#vq$$v)a|@{H#kufK&v@<gX8M0{!4ykTa2u01l)T1BrkC
zOGaQ_n>D66yGg23(MP~q#Tp7(`CFn7i#m{QMJ1<t7*BEkhLWVnsa6wLCT#6mMkk-V
zE2y%BVS!%uiZ0`X`X_DjRYH&SFxGURd8;ta?>x?4jbr^2=zJ|q(A3*LP(Q!&C$2@l
zo+9oFu)Jcn{zS`a;E@_x1Zd>*D_lIKD>1fz(o!Mi>0Hwjc5Sb-Fe+S7c)2#$(8rj$
z(CvP_MzeL`@P4Hb-%OFsi@r4CPtIOo{xdc$*PM57_olCVG!WfWZ2v{K4&cK{LC!Ob
zEb4_j)*<{0yAon$k&$8)r$tau1XvKXo~pYUqHz-e=kKftVVzQXnvS!KdWr@SZaVGP
z%pIoDs5^a+8TCa)=p!fLwGeze{r0K6%Rk*{+4`6|0EZb7hpT!iWO?{2HWy+{8LLL7
zERz5_o`G*1^kJfonK5^yK`D&s81Qb*S-xImJ$u^1dH;G7cnAzTmnKs5yS%btb1IrD
z+7Q~;$R)AotW|26G~W30_a;+69$jtsSvEHL=FI2%udnoZG+`aK7$P&-L<8sk9IxuQ
zB8GeG2T48?YKK!0+$zc+>xX{~<xiqjvIO|gvQZ38<4o7o$;Un7l6Q)&pCVJ0#~A8T
zuE@*3HIJcR-nZbx1tOIWk2LgZko{ubmXb@2W3s=&D?zNYmKMeQ%&-jbGLT9?63WrN
z%)!yGe$IFSuyB9+aO|G@;QEy?oGX757C#Nx$W6Hc@sjZ+!-$}El~m<}=YpK+*A(}-
z6s5SBldpm?$ay?$amf(A%k66*@v_>gT^qLNhwHeKX3|<;zil;<NG`IwdFy2&AScTO
zA3Ls~;+m6BN9A4-m;Pm}<+tLr!scS6JBCTLN$u~UnH<by-!#jzU#`W`7%ksCP28{<
z-o+M&Cq^sSel!E}I{-wF-eZWVFf?lj0Db`&hz9biPNYBHp|34Ir+}syB8GTWvI}xh
zbu{hO3d<HkR09vu(`M^91|;BybnSQpDoZejCI7w&9le^;RS@<gUK5h)7LxtZBvbdE
zld>^$K$S!1X8;aMD5BXFDCS{^uyt84;3@SqSe)f(+hzdrr*<HnWe*J^u`akOu1Nk9
zaKxh6;^e8`RgLh%t?|HsJDqKM)ZN*qiBwC)YXYXLb=>k%0tNzrgf!-w1)ROp5Jrju
zRV8?vYo*TIy3j~OT4g0!L(Z|IYw;gP$S#FQEIn774g2S)zv;%L{EuL@u`|ibiIuQ)
z$@`2Jvb6l7UrlxbBVxz_wz`1H#?#omuxtUxF!!v|ALH`cQnmHseM01$Ys7%J4MhI8
z9C@@e@IjPAoND2!<^i<Zif)+2@g(0r-JuIVFRJ=}KeorW=dT_rXgYk}>e)5+zQ^4e
zP7xq7-P_T*ZYQONG)hj~e+dbZOA$;NRyP~?iR0j0)-~$fEK1)Z*fWcVtlZ*bvxA*o
zK_Vg;IM~N-M#k+{8eK~A!#$$1$Rmr|xdNMS|LdqgI{y<z)ZNLBP1XB3kEc~UJl1(M
zmx^|gm9k~+AD2oxVyY@E)t_PkKa<YdmlN@Z+ak#F?yiFjoVrm^$OdQF@TE>1#jys`
z&@P=(5fHPshexp^*#`zxQw;uIFD~DSQTdXY)m&rEMu=dC{`@UB-#IUBJeBIdO|MLW
z><)j-nA1QZo99|8`tw&Oa?I%0?=dcp1_8d)(P4P_bVmF|_3Dqh3>%AcH9`fVa<V@@
zb+DC?O2C18evhG5*{}0+MOC6@aE;E&ffyJdXqA2<i!K>Il6l&Gidv3>3WSC@Z_pS9
zY*I0c3CqU6-?8M{Pl0elC%n6X+sKw=FyrffanrGL170bclQ0S8SBS#X+w{Uq#RBp@
z0fj8baA%a&5{O|B9&<$BFgGi&XR)6R?elQCnunb0%p2C9Q&M$=x0eqI=)P8-kr=QH
zcJ)XyKP`f523@m29TElem<x#cU!ye~F|4AByioL&Hon{VJhF*8$4WTHM>#Fo^eP{w
zi|^1eet9SHmg7$Pt5`T=I@<Sl7l;Gi6&_4kpGiZ{=Go8n!;fA+Drn+;qZ3sU=rn{N
zgAJn=TZqzFDyIG%saNBdaYr5r^F$mj0$x7ZFP{@aIuz;X53_~adLH!BP<H15lOubk
zX$>=7_~P6Q<HdCL36lR#kj4py&cd0uDqDJiHrFnrf8qp&8aE%}!BJ?EwRq0#ihVBk
zIXhkAE+t-+TTx%)uBNuRds(si7#6a^R3%;K<hZmag(<(n!cmOn(n}PhJQ8igy<bOA
zfo(Blzk~Ru^CJD6h%<-rw>R56z=_F*f_te3P=$0lJ7QNvvlsD^DpDL-ey<@e8v^==
z`^Rb%D#$|>^F=2bWD$t0!6H=YHwP8c`sgdGNju=Yyf(@Z^XW>pI$$Ki)a(KlVy1W!
zqx2uht7A*)&2+r`H2vtt`d0EM1MPeXOncL4S(Sn_iT4aX&;r$~jB4${==>wzWPvp1
z8I5P34d$_rM3Ut5jp<dXp;C;d$;itG2rb~i@%hD)zYEQcrl%4y5o$1NwZI42eo3^5
zq;Fm0(aT99S1ESv&Ac~NtGq-KrCmHiS5ZT&PI|he8JQ_!>IL=r@Z-@=(8{R=^5h@!
z;}{}LG^YQ+sZB20<7Km>kBc6~pi>4{;R(p~%8v5P+%<+2)2vYRG<;xuhb~{nZ<Lj)
zg2(^@;U8}$Wp{4xY{T^h8P5+8^oUA$cR*V_Sb|_iR7rfV-}p`SGc}{no&-5af8PAg
zD?$|<k}UMusnS<w9Tu5Ze&Gu;g8<2=FxqmRpRu%uh$P9(0kZ6KFv-l9eFcY&E9u8+
zBC9IZ>Zz9#vjX9af4^o+@KkT9Mo0xQQ-)&Jf0w<$*(>~JDKaZUz^41sVz+asBP}`>
z$Q*F(!y<!BU)>g-LfonoHiYo4*!zgMrLO*2?PZ1Q3;YrOC0E}Je@UI4WP{#k=O2N)
zyc%DG8h|luTFE111ieRgF;aCBwMSFwAZ$q_n-V}D$b;M<Z#eU>_a^wi-rJltCwtHq
zl}W2a$zyUhHBL^@Q%$i>`r%9PZTr)+Q`yQ+mUi{o!?FOvp$E&rt7;vdJs3FGYMrKM
z0gwkH*VLTZjIs53M3k=o1R)rl%g9->VPnlMGaf|Z73yj^{DZ62d-#XJF3*yB=au7G
zys7adEdPWDWX-QlR2WB03Uv)5T>cB5*+7QV5d(kcoT$G=oQT6vX#E7(WLmU|uo5o2
z8y}a#=!4_5mL++(5hKM+%0I5`2^QGlPGt6~Dzi|P9knD2rrk@iC?GljjPmET>+Rix
zl&Rf61dZ@8<jgy?oXI#xc@-St*j!$3Eq~AscaETVSG6fj{C2<)a9AHm{`}Tpbzx)F
zIae*Wh;Ri2Og2~$Puus!b`yeFua~F}ri^htgDhVqf+F*z1(h`Axb6SJ{Rtz>${G40
zPW2QlX-hg#YYWVXySHo!<nV&ZV$Gt;DBm;eA%cyWl!C@$U$xeE=ZVh?^hsEOv6{W6
zWqAhyF!q0a5Pr&o0nJA}<-K%wjXdSsSl$RRik`1F7McenKEluEMACxJj?MTR^)=`F
zYkUk$oPHarpx}6#ByT(>l=7p%IKxv~vCUm_&(~>svxRhlJEUQQeR0f4S8CG=59hqj
zLv8QQj@OnZ42`?)x>g!;3>vzioiJj@P@cRN$g*V@@=ZB+{k?1KzQMeuSL5*2s0zsn
zOD_}LwG>%pv&UNB-lbQE=ZrI;^tfODU*C?MrrOY4#x2g_iBh#uspKu^zKS)m@K_8x
z&@Hp7U0T=IuAYve&VCj4ekC;5^~&=I?79_vdGMaG(z1libWXje=M?!0C-^QNhvCcC
zr$jAmY8wwLdQ;0QldjQ|fdQqy@nBO+cS{NTL8qde6kWLjOom7}hIlr($(R$VtP8G=
z7Ra;Ujqh!53xuieV;y5T<A_@xIjo50ipzxeli)7z#Oo^oJgc(8M|DQQ{r)9UrjwtO
z#<X+Zw~XbBv_@swMW0E3bz~%*C$Gz)?6RP7hEPG?bTeupmA}yCG<WUphO(uPD1JOh
zKDF)i5T_vUD39jDMFp(aVdVF7P04=0wBV~1IZXW2Y`*OSST)!QC!W--4KI%bisk15
zx;Z2!KT>@?oXQVrZ4w*bB2<6KGiU0wI)5K=7e-9D`LIN(w0wS#=b=Q8P&T<+G5|jl
zXtk7_Vp<eW-24=6c)1wWk!n(rUix>T%&vGQm98XN1_lcKVpHAEpXyQ{Pwl9$Q&PLT
z;5E6kwLD7zh5n$CQ+Kj+zENUVMb#_KCL))8wUasW4u;x?8n)Ide>Vl1F6rtU9RmXS
zk@phU1n|nr{XM-v>visX(QBI_GMSQF+UeT;eUdZC;lryD`7x%i^J!12;H%H%#BJu?
zuMzjJHo02Uo3f{Ok7sKQs~)|A@`vdO=U{ql9FC7djn>Jr5s6xQ1tD@HT$2JVJBzn*
zII!|^QXM3kw<p^cfmfmh)=Sa5m;7R%Zwg4^E3Ul^fClMNYxM4n^X}B!R9WFK^>ZN3
z4xVqA?l(B}aDjpQ?8h-H*ZIQKn>PK4JBE*&Wsg_%wmC}Vhr#Z%OB^AdhkB~DC|fZr
zl#1x$-B+M=mJ-fM#t#U7sk}$eE-Jwo$rS>;n@$D>OSMHq;p(PCYi(U6(~*|57IxCD
z*T-jYiix2*d!Hvxg;~%ZR66HfV{JBY$Y0n^sv)~M^>+7ugS=cVZ9Y~Y0lZT~SjOUS
zT0D2Bp79d(W_el*;<f~}QOvi*cd~uuzYA}3yEz6{Z@(h&rsn2&L!+TkzxjLx&e6d;
z>v*I{LPBzVni6J}`iZ~Ls9@O~zxHsy0TK>cXt6c_ld=ES$Ssc82ZjuW)VoX8jvm&I
zv*}oj^bSw^FPYkOboWVC<7nRUye0Ru%OC0WrXpMILhTPsyywN+-Z+<t_p`7a#|Ws4
zfu#oULgT|u91hVQ{x)o!<TCW-uB&{!+(O0ICp)Q36!|NYrP|hGxloWMpgXm10>OFQ
zrI4Y)Ryv*}jeHYZpYCjHu+MyS4=FO;@wSa_Yg#h4CdK^mzR0O28Z*!nbA*8R%3{Rx
zi6=B7DSi3K0pmw{W>P7cE1A5Sx75FDU`BxsWNGe$N|;JwjjfKyW`S8u&8#~RA9gqZ
znU$dwL3F-YbqK4Zu@aX%*|w4OrYmMC?!E0IK|_}0KUpt#QbvduQTvI!rHGzE%Wox6
zN79LLQvTHs3-yoi(ZHvpZU{BnZ^_zEtm1N!CDQyS-5e|+AqMS44A^<6P(f65Y;^*h
zF@ZUuart80l_LMJZ!~J`s<9LyF~5E#hRv_B18#CeT$1vtje@2rPL*|1i{tAuE>7qd
zMQLo*|E|rU|2-+QU>S7=MO_Ko5H2%?7Jswr=+Y<&CL$AJf9b^)`y!0!KeUlMGpYqS
z=jSG@`ATcsj*t0Qg$!xO1Kph+*f7qa;)}!7<Oyn@k%JO*tOV_Z67ScdN_}5R-~xVe
z9E;0)uEsK;GP;|rLFldjfc>Rg+A-)t2dM#@W$9Y;_rS<VYGm3?LTX38h3U^dl{IAb
zcQw2dDBHRN%UCw<-i?mJXm(u=Xx?v5dN&z&fq9fS54ZgKg;vD_goK1)vj07TiYaT;
z)+tS|DMjYO;L1D$MvH;x{Q8nKIPX+DF-A~oWe@c}dujrhRZlg|XrqpZ(^}F{PnGpp
z_dE3y4UGn7f*hho__U3abOo*)6IIGLSFr+Yyyy21=j*L^Vz`(zQ=Mw*W(!*iw+Vut
zvXtQBpzb6WG~qEIpb&qhjOV8ni62m0qav8)3AO1lJ<(8T4K?~}g2W!CKJ}RA=rj!J
zLY+pzAKA|rp&0O`@<}AxX2FbfRy;b>gEvP|#7bA97qjI~7Em$L10^?WWjqrfjvQIB
z9?Z;gSM`y}wEcAp*d`;x%uGYdg9!G?NTzggv*XlYeJ}!PM@jiJ@7xR#a!x|Rd354`
zE6;Yieplk2rZuepxfq|Ra$gE2L5`fQJT}aJxwFE$a({p_K`mHTVaWY_^m&D*R*qcn
zgH4fzL|E`#rqtdh6tj{Im^P(BaykixJXurW7Tz3tGdLB6FpwX|92+_A*Kz+PXEja1
zI1C>D)v!%Zd0it(e^PhgSn`Zq$WqzN{Um@}VG4_zXosXFm%qTG!(f`T><x30<k}wm
zob4GJA9vM`iKt*gL8i_WXl4IO5?ucw#E0gXWLkynZA;wWa@nS`=`Wto>U>mMiUsCL
zphXH*K`b+We7k|V5S+k3$nD>zXz4JuOi(z68b$Fhw)gdOG_^f!G-Ak!62((8YN-9f
z#qgp*unHptt635z3W*>Eb*dtX;aTwaYl<@#EgHFX9z4VVwMh3u={;#2CSK-|zWVnY
zAi6W^CnFI830HmJ3rR;1C{$DetMt}7l#;zdBY0JgXH6(J9`>ryq7JnPM@GB=t6}#c
zSakG{X^>o{NY!2-yp0ShM~6FYLP6)B0zNIOSS;oxiPEN*TM{djk&iPLBZGs33qgQq
z=HTG3<af-vy@|M};IoSb8QS)S#$R8$M%1duCh|N37R4;?TBb8SxKnkG-I^C2F3jpm
zAyr(Rr%!yUGE7$)!?+0p>q4Wi>(ifvzE@wgHL;xk-ki9sgXUQ=YWE0jfywCQY#(Gr
z>L=cIP`K&o#!;^D5(;RbbW<~7k9m68NRe{&a;@q3$LV+AvbgOmqAmq95+SpAq|OQr
z*=@4Pl14t7AikB?5n!~+z`=snu#qL5y;L0Md7B_cFrXHBa%vMt{8~MTYeLYoeWF>W
zD`7PKT|n9{UhxOCT`2oTaz|-&(9?5+&2s&LDAsI!$8MNfQlr4yuAU*)WuZ#4bP>u1
z2M~I<;v1mu(~z=wE4d$Lv<gfeyXDpOd-Yx#Qc=ykSq9y-$YvWdnDD?vusEX;tCLZh
zP|AHbV2m^Z`A=8h7-gRqX0sVwI!kG52iHB1x5yT8C~I9qDd>22m#@0-q4JMj)vTXv
z=J*jQj4!^&q^WhQ*V&RR$@X{t4&ght%sbFYFz7DU8Jar03l?p+^?g|RdPvTq27(}F
zAP3$j@*7mw?0wdy)3fcN=owr5_Ks22J9g&yF4#|D58aQLGn%~2bTPv`J|Ur&d+|3V
z^`==Y9i^5%l_u1}?#yvtd{XoQmO&(6HHbLQ@NzzAVzFyJbvn|I#HGV<SI;(ym7F)i
zZBT5@B?U}kb8#|&)za2XlSj*$snY+p^tTZrvyCZYMkj>c&C;z9V~MS%NHo1K=!UQ9
zwt@0ptr}d=MEx8bWB%tqTOYF6WHDfwZ7|*&6zkdYsfq~hxm4&Bf3~ogBe$qmitCV?
z-4T1Fn{OSdc*q*P)v}Q^Br*x3h)@y8DLZc>jr2}J){0Xi!Y}fD=%Z$Y_|4r;bS%8c
zUx1b;%O0l|Zn;$oBiw$Dk+QH!=C-?~8o6euR8!X`^w9kSKx8D9pQ7gH_c^^?Gl3s)
z7U}MQ*s8`Z2o&AoW|88@`mJHn%%`;{V%Mq}0?tq>SFX)2oH>{|ylcM+sY9gHX>Cy=
zp#{v1Hm=>I=toHW9YSv`)0E05u2JN-kkLY%9|8^E%4TCcV2ZMe$?>|T?aGtIS|#-X
z5%b<4z9V*G`r6HF<xLlHjjLHsnOR}9lBPAcm+LKoG(*f93Q}+SH}Z>dZdP_*yJ&o2
z-#}vgR2y#ZwmJG()A~^NLg;~5PKv%8-LBMNTKjB53-nr=mT@K4JKE*4=i{+doX=um
z!(#E$(dGWeCC+dQDcVFdaDDhF$__m2v2R<t9ub;RL0lVapYSVXRe~A2l}#s!#0S@1
zW>e#F%V==R>H!N<23niNsshYA14nz{DO2SU2?yGy%TUfFYpQV<t?G%5sZ9Q9ZHSoV
z8gf2sVX*kaVu+}uEj6UiwP_TP-N28@r-c;J`RqGsGn7RjQ?9(Om^|mD;?;cXCohS@
zdo+V*E16DHPerb+>lrG`kE~*?KpEz}_DSIhP<I#mPR)LE6?AtdP@9et3&!v)2_cv6
zlcNmzOuYxLG_>krG7sF4CJ;p2*z5DfdnER;efAZyHnb}10xKIYQ5gF<DX~8-jZZW^
z%ZhvyxJ94fC{>~Hz?`9>>IfACAawGqP~hRPw8`so))MRY`nkBR2j<grwGUIs{c{Vj
z;yXjS^x?C73128eqA=S0ZG|GOE0LZNi*c-LNU(d^M2e^)<YsG<)tCf%e5R*0Dc^-s
zsweDxwMda;NYqK_L(;QV7$HfubNHZ)Mf+WJ@$k5jWFPz?SVS&@b9#C)sA5eEQmI8$
ztf9v>{8#da%x+r)S||f%ST=?~y_`)Vk8D%-HvzZu+23r@;!LW(@!(MVH;Fk*^5xwS
z{$)~Aoq~2Z61x;~N2~iC_$=EGMadN(9DcUU?aZP`52guf6zI0sjvw^Ut!R<MWcxu<
z`wtIiwe?AaxyPo*+~)9zvwg2YjH(6@$AD=WvXPH158be;7#wbP$?kR1z772$O^$5d
z&VfD*2>O((L1v7xSg11uC!0P~@*}mq;RXPq!h=Y8=1tjDRbfhy$fMK@1`{qds5hA{
zS(z2L*pj4x9!T>*G9jJlYwfXGng60U#MaikN|~gXbpY6+T*RHWpCR>g**@opp|!V;
z3xZHxn~&a>iN%Ne?!N0Y^iG%KlPehsKz7Rcx8K|mP_wa1B8?Dq%MtYrOYg@&x@p+K
z3!OSv{M^5-E$+5l*sa5M@%iGDDnskq6MuVHUU3cB_-A=d?%p5p2=jSIO4x7(33d5B
zi|@24YCV#gK0_6D<=Rz<cNHw61GmqVS=uEzuFjJ@7pl+kl{zJUpATl>y)G3u>F#^%
zK{0E!ctX2bbG$-Sxs}JxPg>B7v$}d7v&!qK^K^<kdi<^i8DjCuNmzg9%Ed)sl)VLa
zk(uhF4OISYZ<^b+k%W=HuweN#ue0|__t1mA*t~~nIs!I%u3gAI7^KSCBLtZtL+o;@
zZIQC_CDYHO(VL2R>s+F^S`TUA3ZZmBX`Ub=5_HlN+NXs)?9&O2)$~>yyxKe5Xz3nR
zV}8F|1(1wJB`oiZMITEN2Z^0c0=FTMf8}lWzBd$qazaGzY&j<@_Y1P{-<+K5#(*zb
zc*O&)4_(9i=m;S{?iztA!^Zcd1LiVippSe!?_if|*!pe|?B0Wzc_Xbv3m#;^r)#-!
zu&M-?YcG}lgHI{APfEY?9$EcDm0uU+b*jdmiY->32i~!?yX6dgiQ17O?oCcl9U2`%
zqKk{Yh+q|h9_`Eiz}|iv)5O&^#O=5FVfEz!GKY8Yw2=3Vo$YlGV(kEj8nsRAe2H>=
z8CYUA(l@!^;j4^6le1A6`KB|b4%+3peLzxb=NzH$yjvE89(wrjjghTAjWy}Ew2VJ(
z<7N_*7Ep-wBUk^8XM$vVf>ZaCHhnInjlOAo_`5^C64h|sulRD;w6;E0-7ztSB2V#m
zOWwt2hu&zTf!r_P4@}c`A%Qe4au>eyb%#E)q4DPQZS~B;9zgUIEuCOPW&ddXs&jHd
zQ-?wcgw-}fCUST778$-IrI23g>o1$TnIv7vz|4FkAdI%jgimszZokc8s#yN>w_iEW
zd_x9sIgqolgKo4ala{KSI~ip8(SKXouj^d?+lRsd%wCkj>07AkKX{^JROPAa&(Mzj
z=<y|caRytbG2{(np`=`cK&4b%#%7^SR}Tz;C8}QsZV7WL&cux&F+M}I$fk6=Uko7r
z0Wrn!*wSC36;j!bHJ(;&v)v0v#zvSp4@v)Il|`|mPEU3`&y~&`6gF6%T+whqp?mcY
z$zR@ik&-VhK5|#Bp_~ZCT3rtBDyje2sTGW(Q9^v6thzn-6irM>0Q;K<no12o)2|G{
zfs_Ucx)S>zM9*J#i|R{0V%(ZmT8F`CXEu?t%h}2`_J(KCt3^`CHqS16Zd4gySGY)3
z9IppfQ=vmFCb#rz{XP`a4{HY17lSRAX);QT*~ZDlC8o?LLX}&Z<4QK!R6zSz+|1S7
zNX+{JQ)g{a@FCc>VQt;gJE_IgVo!llXIy>7OqJq<kh!jdc|zILOI3yyZJ(Z96pK1U
z1UX>(%ii>n1f?ie9pTkb2A7%)04adi2Pgx=W$R1u!)W+cZh_k?Q?-IcDjbCOggG`g
zQbo=+JYv0nTIV#f=$sz{CACvw)94StzWgZXEQ{NKq_^Y?{y8ebgwyv0n*+~9#=k^d
zsch${#OlBtdIH2PSoO^G9+5&wms^h3EdQ+ABBRY}T>fXb?}ZNH=-Iwupm5*hn+Z{w
zd2Tl(GWWSEIycwTHh;JvvRG57N4=7aYaEYFzU$ZNIN|39*>4S&_TZ%LL))uALWlD2
zxwJB8)3TOZ>qqZT4YvovqUyQ$U5NyXC}%{FgbOrJDc;NONh^4~rQ4A@*(ZwLOa~B1
z!~Ofzs_NR>+0S+*Qq{*U=a1Yvot*<AO;xpAUEL3AK}vODb40zIgZPFQ+a%iwRE0CY
z+hVap*mI=fvheYAJ6pzqn^~BZbq`m%@x=(K5)`KNoZGbriYJ0HiS3J$NxU6GYcm*s
z*G|W3{0)<27(1wRb1)>ao4<^z_%O@s?3HLRRje|O{+5^QmPa3LcEBqOy~`zq82Ik2
zYM0F?*c>U=W9|hM6>#EeS2JFt?bPW5=bRo*Efq3V2|tWFR4NP_kmhlAftH_l)A30m
z!lpEzxpIsp)n2U%FT986JrN;~b`ni~%T&qC5%wKrC<E9a%4dptFKkwO>B<|X#QtwH
zUO--GXLD}I<|5CDJ<M1<yqMf%rc_4|d}IpASPUBRh~gX`cdcEL+6QF;Cn!;gC{Ev1
zD@=%-(EBfhJcGAH^bxo@mX0bnB=1QZ^^Y2aN>WbVF0q4MxEjq&39u?TMTHCI&uzFL
zIp_H8G%}kZfVA$Gl-|wIn->9E7fQ*ZXK^b9RQKLV{}r@m^|29}DC&4lqeu@^Zl)_H
zD!nd$?{%iXne+QxFSv~2G8zD9&N>?2`5o@OTTK^;WOzrrv_2xObpB@nHI3-dN5y!X
z+cA6BvGb0eN3-f;6R4=VI(t%f;Qeo|%A;E#Z&s_ToeJwB?9&B|Nq3=E%5^&)Ex#Sk
zZiVmAc7K><m&a1WW&eo2h@v+tBD>N#_P8@%eKa#7&RP%o(<eA@Qaf+ixwPf~dO;lR
z4Y}AkCLSu)#K9IrC40E_yPFn?myqD|y==#QQ#*B9&``3omBFNufS5eT6Ds-LR8Lie
z=}LFMiC32>|MTMV-mGkW4@RJ0B64F%a@pHY$P0+A6*v6MS9*7{!D7Pd>&(cCMFnj%
zmR5VBKkl-wQJw}ixOGv8JlxI|y$cl})IJVZw3aTLqn>7-p}yZ%EA;#L*5l?@EvT(Y
zdWe<>66sQF{aJrY(DyO!h%SjNqZH!?M9QF@dp?4W^MbJ6dkvDgL%cH0N$c{8m@$Fb
zJ<H%@O%RpWx@POtyCNqxi*=Q>LtPUfyo;M0&kp@xZ7WzmEg0AzXH&>MP8q&B1ptNA
z+0OjxE{E_v@`V2bjq&r^GvX@DaD3CG-i$+0@ed~M`TMlj-czUj<HP!c9K#tY(df1J
z*1y}Lm9#SiIUw^84}D)?Ka5#>Lh%2E-U-3%B0qu1h8GI0Xysk^!;2yMy&C(4k-xe)
zo*kg)Y}Nrcx-mhHjM&icx<=dW@<@3-D_@h85zRk3r++<2<GH^e*)<Y=k$^_@q%#RO
z_pdz*znDE4u`v&=L^UT(p5AfJFTL^E_3-;e-}MB$D+CENzS9?u)s~41YMDveLT1_R
z@_*Z#EW`R<Ro1lsajiqnqDaQAq7PxME%aDtG$;2><#`*-+WpGyjM3NQuiSnIxQvDG
zT0i6gu+8Ue=ab$wS*dZZg|kC&G4Y{I;+3C?f*j@@=Bdvmmh^<e#YU;J^Lb7dvw^;u
zeZJ^qly!v%P_ow8VW(I>`2l9KsJn!~CYl<ya+|73P}ed?R*$r>m}Y=@W01F0a58>?
zQK@dy)cI#)ZW|Za*kfYQw)Ot~V*KMb=O?>O6adk;DgPf!7LD1{hapLDwZODs1s-EK
zY1&$3SCCpJN#$fKG9MkGerE>{xXafRb%$@R6O^@C%#N86!)J-c>8x}vE(;yZ#i%k}
zls)<mER)dke_&_OMSHiDPj;ny=^cI5reW{6C&8?PCYm^j=-YbUO_G+EkzTyx`Lsm5
zTU#tTUVry=1*U6<tuhfxDJY=9#ZhdzEjF-KWZg%fv71PNA|bPjh0o^vP)`7R7V_^w
zt>uEOC(&I-$IRqp9kPBAp-W&y$aseX4i;qUEm+Vf>gd*cD>;SWO26bs6hy+w7~dDq
z&9^M|jz0+-ZgF}QOq@7{hssmb1+@7F04994tjK}KX2oB4TDqR!&c+nQWeuT3rvHx7
z%UoJKut&M44Ze4omAv@br6&JVKxDXPpzomUjhwAlZP(_l4L@vvOV~G1yv+LFOm)yP
zHeLB!=;iT?FFF1{FjnQ?EK<G6;o+W1{?b3e#?Bq6?ZmDaWVBSevUkz3<{bxsixKX*
zmZ$Oedc>sTz87#w($X2}q`Z?lvIV;O-)HP^nt>?c($3O=%KO}u8WAR!m00|gE!b=D
z1%TdN$5(9D@sBRfr)e>IHgjoQEf+!hPvx)M9vNNr3Rp~Zy94RGyyF@3vFv=B-RE|}
z7_Lh~IZ|mJuY0hEQ9xK3ZXZ|s4-Ut;eZjUEu#yHq82{PLQnmN)?^_4(eh#tECikkT
zeP^r*;Xl;(ca%Q%{9<=Pjf`P+{{9g(z-}MpT=@(5`YGFMS*-qZ{8*JL-0w=sLumr2
zGZe8{f3ir44((s=);i?PDkV#&HV?cnUG;^G?+y;56*LFaT%r}VL7JBUw!)-3R?T2)
zwyxy8{iBM?@gAitCT$RR#kET&Aj`w^Icg$-#-?jb?NeBC;^u@R2fIEssv5UhZDMb|
z;y{VIv<=R{7V=4zoA=4}=4fu_FL&mP;w!()Efnc=A+F&?Ws?4%igwTf1E$G^J*V|!
zViG})p_cjBpFV|31br2(+zh`j0CuTufMNc^=OQdmoJlbeWb`zP#Aw#PzUy77+_`np
zU)?!yr|@ou3$o8q%4Q$r!*I;13);OqFusRvG~3uBiTq7+U(j~SQ|)ttDw{}AYz{1H
zvBg3Srq5Ok6Tpu37;i}W@uScHB2B0(;3!8RfT;V^Yt51NJ*AU*CLKK{&`fyKLt{VZ
zh!|j>UgjC{i+x6|mST|*^i$jHRfa(fSN*4fU4~G*ZfF4Q78@L$jH%pB<3w>EmzpZG
znuo_5`^x=u)A!n$PY*HZNQngEGUFNpgIQcv=dMPKAs9T<tMfU9Q&)*!Rf-*#q3u22
z6r9f7vvcBFA3Ia#GYhuSnttD$9zFTR?l1RN&nJnzUpCAT2XpHes{};ytaWxLb_L`e
z;T^mSEJ)duamb#xwc^#!E;Qdpw|MHEs~i=*Kk<{`qg26+`%$)|g?wp(xIo_j?D7q4
zA|1ETOEZOR9P-E~6S8oS-~9Y1>jhSB-(;97|Igh5pHFI4<<CwXtA{%tX(h$8hq(4%
zQ!X?A$X6(U!)jXo6x7c3)GGkt4gj{RHkc+Bmi6YjfOnFWIAhmbSxkx#EAeU{CiWCk
z(pGtT?-Ga#)p6~h0LiMCW$0k2SE6~!=4O|jP&T}JIhzU8D-K2m8y${@azU1M)VSEf
z;ArL7J$Z#Z5-3xv45f{|>w<yphDV^Na3>$IGHt4wTEKq)YLG11k#cmZyJBA94fp1V
z=_`JrCYBGEt4%E6=b(3D!T_(k@o#wy<BtQp66&RpWL__sG-7}W!PW>FG*4Kp>9;gf
zzr16%g=_0@-!dp=3bw=^>m57s$osh+Zk^`#z&Cs`WY;Nl;N+T?xgMrg97dao5g%D~
z(r_cHh6&2x&ptbiD*D8%?{D)g^nr~>S}7L&twv*~zRL$j>UZ_<Hp_kyKWVW}pnVBM
zn;e>nI>n+N#n?XT!n@xl*i|$ETwJynI5c7r^ML8N{!0<LD(Q!f<0<2rG2YSKYyvof
z6{E(=zxmH|yIUw6y%2@*V*$qtNss20#w4cJwgDJm9r0zCXpE`<5PEWy06JXKS*4c@
zyuc2^PKlv|bL{e!>N<PH-$scwR_CAzNmHQ+Cu#*xuUDcfoPov<t8UqLCQiNEvSo=<
z28+%`@+jcWT8?+Gzp1WTXKaW)g9+SHs|5M0vV8T(DV7K3o=~XjQ^+4p*%_!QY9f5F
zyK0N(;T=X$AkH01OCQFEfXx%jEBPF&#xDJQL;4+}ssZTCb6ScdE+ch>#cOt(<tjrS
ziT`jo+j|r1zjlx4!`27$^2Cf?o<3HS6DdR3rULo{j&pSM5n(zw;f=9fcq*ed-ckUk
zrVZ1dAXa!fiQ!`ZxKr6_kQ^FT?~F>Hi*2nyh>_mWiE$I-KfxrO_VS$tN{>msT1?I%
z!ts2>!X+flz8_r?)i>_V#61LX^UIw#U$C%NpmBJ6lJm7=><W-uGGB5{jl>(=C)?L+
z){ky>(Np^e6y4m<{h$~ekk;i>f7hj^(9?<L!N_~ARN~<0__gO(zbHTG?lQeHiFE~y
zmcgr2f+;O@P$Q)4&ZBd<OnV2Ed|9SKwSBfdzmR|#E9?(fdCj&BIfc+Y-Ml_X8$fR9
zWRq30KpYU)<kzd$b8=NeruCg{QYr<Db{R<huPcA{ZXneMU>H1ie>h-L^t<+dG4$KB
z5+2&ujyvXG%^^swrOt1vo!eM@>R8(h0y;|@x7B8u@K#2G1FX+^evyT{C4?Ew<e<t2
za16k6MGL<g`&yidNqyEEU<0gT3D^{a_BS^bMq^Zd;CkK?<KJ(;UJ4^jPp`>4u1UxZ
z-6br+E<V#}llwb(#Sb#y;($YZoLXKf1R2ZCB>nc7s(*U==JX4<%9JIV0Sjlj?A-fi
zcG-6Eq(KP1r`Im%|D#?<&))Bf8zFOMN-(UJSJzD1v#;3z?i*1JNCq=Sc|{#PEL`(v
zN#R+?bhUDx5c9;q6uu+I#xP2_9MIpk@=JxCNZ`-2q~Eo(FYFrE!7cM?YT7L`Us*Wz
zu5W=88u`f*1($_;4j``X3X2cx3%~l2oQv59Qipte=GpLS8^3lBas$p;YUKo4%*2Qd
zH;#m-?K-;%Dhl8wruc<z8-;E5GipM;zi4tq6n%zxh6d4&npF2KSwDb9SkL$AVH(?K
zR9)D}tXe$uoLgRZzc7K;<MC|d+gGtXZ<xSO%`>r&oV{o(3v23db-}XTS3C)MfG_RJ
z?`IETYl_+PZ+YwM>oQT<>!$J?$JB0N*dJu5ykyy|-+sGMRP$E>$OOq1acmsnFF<D!
z^bPy=7WbJfRENI)gzAn+Osx@_XW(R3oq-v3-y~c>Z9$+xm?AD7pt`wKE$vF=AVpu@
z!U`1;1Mo5prV9B~ckWQ65ud{wLihj}VOQ07<_(i-c8t+}BTgGREt7yR<Pv#K{VDQy
z{U~JKF%3q?1HTVQk@F{YUbaCGa@b!ZT2z%fIpuANzG^#pd`QB8rSU8gwJ#XG%o7?K
zPzwT3QA~sTL7)D2^&HSK;==+8<*)it4cBR>?GF7>W4)c8toa2UhtKJW%0B13O6>w8
z3F_E5Ob~^`mx*0z-dN79$$+NQ=b$&@$VHR{89zRL%t(!wHi@1qQ~!A8*!8z<?J<7X
z8YTr4ywDcY8?-u4a^+oOp;m<(-V+RzyT%tFEoTHQ^IM`#qr*!IftX64j~_qg3jU+`
zsW<a6mR@cTqqJ4^)Ndc3&PHW{u}|6e4oPF*(0_So@7}K-2)K1klo!rC9i8u%@sWil
zM|;0xwwXkIcp8YgRM`GEoq}LO6PhuIdzX`i-?Ct^d3^m&teC*f<tfD_&wO?ysmadI
zfBoZS4m|msc6f3R$A^~(m%M_bX4itRj?626#mr(tl#)QQI)@(C(bv3*)n}15=hywV
z?Jccet#te3FzMKVhC)w-+Hu(jeU74{FZc|4WK||feM4x{Deztq%Je5Qv0fTSJ^5ky
zBy_L=lv{>PP1E{iRbf!A{VmJcA-I0u1ysF?ckiEQ7V7$DKiLgy<<=E1in~M=n^q4f
z_lUd2B2x}#us~+|KarSLBA#O4_~K5-JOm}`h4{+sj-`GjElc-W;H$rW07}P4!Y*95
z{r<4DqIS)8((<jUSPON6Xg&+)9S4MVN)#Qb_v&~FrjECF(m4m78T;6q8qkrgNbj@+
zWJ-+CZw5?f7sOV&9Ss0!@_r7VyR4cM*vpb_L*61qz5&qk{gbw_m3eEc{I7O$fB`qF
z><4_$^S^l>-P;(wJn0%twCr9aOGo+aK#g~vJgS|ySF&8Q1iA3ITOcOv$EP0XqL`G^
zMMmlc$s7Mj%&@hNo_}>E{VtHO?jpMGAUoqq9PHc|e+wq5Np}58D`V5X#{$??u(guR
zTCwX8`yINwAttcX*0!PEgH83|`{i;?x7VwilzSh{f$K>6Ux8&Vz?RDC>E@crk;2}|
z=?hCajhv>#z!)pve@<|HA)rmV%dzQVGeJDv8UAjBEVRxpMZh1t1IHSxP$Gz5EV~FE
z$|x&8naK4^vBn@OnADm6{876v5ldXg@8vEE5Dcgi#YiD{Yg7d@s0SQa#pZ5?St(5m
zVSko=3uXJ~7-6DTW9N5sclk6p$`CF3Ibu2!iPcR;D93rj9yn&(vJ98Tf9WmsrW!$U
z^-ud?>6cvsaPDf>bmi<9m$lh1ipC+qj6$4YxWDvjhNLE`w1%q4a^p~H9lf7QgOrv_
zaj$Pygv^ve3h#%+nF>QR1kjSgW4_5!|H)Z+sL`1=AFixDnqNfp$m6b6YMwKsnnL1e
zsTC(~B6PEnvVV|uvKHhQjszHU8oqTY$B-W#ZNdw^(=m?*UnXW&OMRA;;b&G6X)oPp
zbOIt6Mv}9&Rrw?ku^G_joHvznZw|XVzDMH$MU&*PcT|AV>iXcmtn<>t{PiCp`T2RU
z3tFnn=`YfmkHDLFUwSaxpL!#j0pQ5Z%7Xc>X{F4J<I~Q#BKh~(-{*F8aWSf741ag*
z03k)&)aJmwWULUkc$xd{mLrT#Y=5Qvh|k$Elh5Y-nyG!hl0`*dss9tL(6t$>%foN8
z+oM|#R<d~>g#H>-pccp{$ATg;s($yr`ZW&p_Xj;M{&Brh18=EAzHNAFWIsFd2y*xm
zqz|q<=PSPf+InEe)2!nb)9tD?VYTKq6|NN4mFvq4AHv+))fs*CY~EgrSq7KNHn<}^
zDL!x>afgKwa~=U-QSN{mz9^&GDf!2@epqCB8P<HtW0ni~gl@SN>7H@V`BQPs6k8NU
zz85zhQJy8@Q=^pVs)ztS<5n8EKIOUzGDVdA%`&wt%_&!JDrl`zdpYXF6IcNM2b|_U
zyT*OCDS8Jw$@9*yx1_e7j(rUCFr2YzR%Au8mRb??7AF$hkcleDSV~~|An_+ihbSdX
zFW73`%Zb%)o=)3|H@tS9(}HO3=a?peG&{i1&<OqFrBV}}I=4gKUiQ6ST#EXo{O;GW
zX{xppgVrSiUuU#vOZDcWPORi)TzFu(R);v&$`VX<L&?hCPaoeH^e&H(l&nKQg)w0H
zC3+&(>ESnT<nQITDZIibU@>8;Skos55fY{i5E)_!5ulveEBa&&5VWCkS7!#R54ZoY
zLUd`?e>#gn&jCV@asgwZ0rX7mJ=&M53GFAoHJwM8JW@ykQd4X7+cR0}ge_DL<J<h{
zNDKeB^EG7)9v%=9oZ?U9ja4o!bxxp5Z;T?Kt`a-Btofk=CwnD<{rxTOaRy0y2=xc&
z67TO-KN@Pf8^))94SC!tr^eR*tCvV`(@(399|Y!*$m^>%iMS?GVo8V7iTXosK2*8k
zqg(jt```eb_HehJ{u@Prs|({&j<M`)8W3}gQCePd$&A!AA1zaHk<-~Yb1cjY0b;+#
z5T)raiNe=9ROH_Rsdb7fsAgVcWU@YvFiMD`Rmr_${OBL(#25qJhy*p9AJcCx(E8<G
zI(JTYNRd-WR<z>S!T~KrAA(NaH}Z3Y*NZsa*3NN#|1%gp8)j&qGjn^pd}lU){N<$$
zfz|y05mOVF=j&41_v(5b<K?1;se#k5D}ET+?05+zaB@6NBwM&hP*R(;uIGO$ICb&=
za-X@tX7mEB5^iifx1gS?qc(bjOn?0b*{(h}#;>UDO=SyS!vg}Q4MOiUBs#s?1>;il
zZQj&8pS^ReN<_`Rh7+pG=igzuYe7G^J^!$p2x{2`IyOr?wnIZ0qT5n4pp29X1>#_c
z!<bo1S2uqQlLziF8N7aGHb}w6jU3E6g*49>1?Z-|YU9in(0>PM9M-4wG>l_4d9}S8
z4O=g4_DB0k(n0fC(Av47Zm^y^vPoLG_fgbltp8@rHxB8mjbrlSGF)P>y#C5~os(cQ
z{X^r-5rx2!77kU;P@(Ip@Le`SPRUGa;Vn(9snFA^W&uTsfZDhD^C`I*14r<Sw>B^@
zKJPI@S>^i{CVK67oGGA=cy{<TFim&*vi@$Tx}qq6^V03fD0~eiUX7v%kflruWqx$q
zdg%Ci9WwSdqACun_)~slgoaoV7IJFP90m=0qlqbUKwck#n5pbrVcC^M-Wh-n2&5s?
z+Ub)s8Jxu>D~D5;BiUS~eFBIF!U?R5Z|Q&tOaZ(rJ{+{FKtAV_3;)9%bG`<o$9rI6
zJO3V1fxXc@5i+MJ;!?#E#=v{E^(V}N$$Vginip3sY(va32VCj}qK!?6+^2=%Ze?P=
z<|gwLLXV<ECFxzAPrx}$x16O_o5E(&Z7PCjcQa122SiR5?aqmR$Ww}2r1cNF)z>DM
zjbtqf+^Bt`(QFHsC|KCPldIpbbPO?j!O3Y3gQPh>1$}FvQ)B1$Vq(6TCwD*hI8$8~
zMgS-UVv{JQ97)EdDpK^HesX}Zs8boo#P!KV=ZvB^_2|yPNv6~*n*hpukas>O$n966
zW`{JS9D|}ipt1Hd#+kD<>k!<95`Dp{?}QU;J$xlWY6%J@T9F)G?ZyKF3Xbi&f!Nsv
z9lOa>cusCU1J6UEj>ZX;Ji(YOkJ=-IYA#QjP3t|*)@6aNKF8N2#~NpsoH<K`8BR8Z
zw=-M-8>^0BP8)WduG1J{lU09U2((N!UWev*Z8`Jh_M~7sc>0pz^~9Mj7_5oqi2zB4
zJkge7m=ei1w?9?I_+hS_7z`3bk@#T?QV(tGP|PY56ZEPX<t5%MphtiH?SESa$KYJ~
zOBi<Fm59i~1ky#tXT%6I9-p6Hu>~2Maoj=+F0I_e_&{D!BjzEB!!IGbOk4%T)+8g!
z;96hXi3xGsOUq5zT$@X;W9D}=-ro~@(e=4KZ7-?hpWl0(pQxQfLu?nKd2tPTSJf8|
z288hSxOLGp;TU@o;?~wx8ZQ8#*ol73^g<WPCZo~QE9KO*L1wHENjm*K;Zok@^<9vo
z$qX?l)6jH)cvHe8Gpl3UQ1Fr}$EihdLbwaCYFr-0=efYxZkYETF>qjYDs1bMTJTxu
zU+b0zzmg<pb>RB>o)arHYYG6NwC=;I^~`tq{K;>!dH847Eebp(+^(E7q}FF6;o0H8
zXN-CE)~oU*K%$vO$=cpMqGt)3U_*#A%!_(?-n8rF!qtB;?z(RTEd@k6d|F}z2-txS
zhI#IVQFBB~4WK#XbOasprMkQ63I9xvYSK+?W1rZO)734Y1Ne0L`qHFp{AF_W=)$(^
z>C<?pUpDJ&#)QzBmrx{lgJ)g))wrv7+rtqIblO5~0B&X7>SY)|Lx^{Ld69u+UWy3I
zW-$L!6|o!W2-bPpr|jq*M%1e;h`qrAgcMetbwgw0bYh4_7_&iS$Aea5r)sr^md>~&
z)Ex-tN#T(>g{IzcvVC5Y+ikYo3_57JChHk^(igb7)e0K~bOY)-v_Qu=;hf_C#e{S`
z=Om5J&tQT+R1hf)toVX;;+3f7(sO2?1nRP+927)46Q!Nd)5if-lYd7M3}aodwBQgY
zLrx~iDE1|UN)+8oNB1Ll_HB{~VnD!_j$fi5*4g-u1r_NjvhQBM5OKi}!kDdi+H|ve
zcOqR08`<#jetA3v5}=c4tgi`{UF6fje*Az+S+>}(0ZOK;jr2&@;>>iPHCwE9$@fj-
z=+~9ABoim8xKcUfgb`3<2f_zP!v-g#Guki*Nbde?jNnm1;D4OyC`7j`!0qU>>aPZ(
zY54p}qjfy)Jb=ck6=#ejG@gcUv7zCKrU=(f_dOR3Xz@19Dfxt02c3xd(QUlR;pc{<
zkXo%AVgLiGR1OwB@(lAMv3ICbeF2#^f7J3`)n~*Yq$aO#f1^K`rc6fjEgw~$nH=)1
zEC|nv;N4lD<ONMD!)iS#vUuRJ1#fAbBbKnSZFl#5mtgX$o$&FGLD!oHRFQ##VwMKI
zCFa|Nwerb;UYP$e_utNY)&|H1PDKJuNoea2NPFzdhEwg);QFDjZ3muQ+X=82N}}LG
zaY((VG9hmScA%fkBuYde$gP@}t~dd<#O>5<nhn)bNzrL*7ET>H5WWf5n@l3e-w*VW
zwK{qm(06J{lJJGSBQLBmtDS(15+(?U;_g<yhA@>guj$ZVQJ2JOrwj1?V}a5IxCUlx
z*->W}*59n~Ndd|RK2>D_TN&GM4KZ%yMbt-)91?3q*4RA>7(eGnp5NAb331bzI<z{|
zzf$27<h~;qW}1-mI!*9}$`;_(sx9mvoBtEBO9%dkl{|O8hv7$P#$oQhL$#r1LrkJm
zBjAyWk$41=_BMw3$>XuZ$HCTKAZbSF=Tw^v!McR7qOU}jjOM#a6g(m}N^k|>;K91E
zoyN;thij6@l<Z{tZm>v4{GDmo9V8}OTlLI~`PN`1BF}ViPAtE+;q!=RwN&>sRK`u<
z!kApK{5Gz#-gL~dX3}_5%_^6@v?ttfBdNjV_B!4cDM{Bc8>vaEpHT%}zb!aTMbf}}
z1qhY<a;SgkObGSXXppc%zn&`k($mg#lV=ws2IV*l;pL=I4Dd!DN>?{ou5|8btCyE~
zuhEy4g>NG%_;PWcM?-)53Ugrs-2KXwTw8Bne2VmW$tz;Q>)XB2GwiOMOZ%6+&gy$x
z&Im0Z?@izFCdUhe^0l??Q7?^bMv`t0l2v<y66{+K-%i4YMY~1@{deOxyLajw!odt<
zZ^;)sks+nv3}FNBG)Mb(k3CZ=pLziCA!<r|r}A?-&uY)h+p5mHL$=_LW9WG6|ElK^
z@$bFDI=)daLV}dgY~*SUB`^)Q)MBf!=#8HzUKPSEz>r&R@4(ACpPKcZ!UF_J{(P(N
z3FKYcP+{T1$tL<PC=M@!H2kZ61?y}J1RRl(gzbc$W-^Jc+uE2KS>(s4fIrN;Gp?|{
zb#k2h=|hk@Ybk7Yd|(TQx&~AZ*c5#p*E+{M{BH$UALnSfwDtcrqYj`(8w)NRw;j1a
zV0LY)8$0}TvPik^zv}Nt$>Z%W7j})+?sWP;p58gE?*IQEAF}OQwrkmT3u|ea%l2u@
zC);+*w%rNKww7)Eo_oDN-`{ohN2hC7ot@_c_xnwEl;!rYI1O<kYUfnJE!qK|pXZOo
zGIhE5w_11nW!K9@Ofzs_NBj2(u$PTT$DHcEP}nWS+axt|;{Zz)Qx9Dj{O{kves6II
zu}O}%P67_eJ$K;#6zOkT+A(CX24ETXOq~DWGAR@qKF=m`Qug5V&ynVlQ(^Nm&Ogz(
zr$N%JXm8{g#9v&-w+O!K8bd{h9pDX?`Ds`~osqGk!(kXP9&8S=gH&lWe8hl=s*!~n
z3I0@Rgt#_dFu5oSQH1ixLe7*+sr$px{fC!?#-=|V&6V!eTk{ujKcyCcX&5ONQur?P
z@uNhN3`w^pn0sHMBfcu|+}rUVPJJUAD;5{Do(6kb2QUG~BZkw<gC!@PDbMV3@<5X%
z!rj?J%Z}z(l2t*dOxvy61^xYX#%FY(+hzHx#BP*SvLqQ=7)*wgk0wD+Hpf<83=Acx
zLFa6q$u$3LVc+56FSUR_J{?PqT?)Y1=mLA0_F`~=_>XoJtvG~mbyu*LW6!J9d0QyZ
zBZ^`TZ}3troX1qxvdAX|Dtme@+HyldA-l)0a!B(Z<L?ei^>bmZHbn%Jn)3jS(Rjou
zLfGpm$<JS*_q{i6nwP*y_<bD999Yi4MLj*XPeTU6a4c=?sR3fY+`x$Cgk`W}#746r
z-=!@3&1O0(O@(MB83xe@c)tmRQZU(GYuu)v8a?3<ipJ?3b8JTdekS&l2te^uv6)>j
zW~rzT?Yt#)lRb8Gig6_B|B15__=JOp+jLOYTvwK-k=;7I<L@T)06h?bZ2s0}a}9a}
zuyTakUhPsKimYjb=3LyOYtD2jyw;ZFfkf0sZn-2ty#Z*O+h&`FjO={=m^<Dz@5_WO
zuJGvN`J{w?^{(6eG|_dlp~pG5jF;GbSdLsb75^jf`?N*53OKiUaxbGYtEgj2LarNN
zmL?An9%38wj_(~d-MI?1GZ&}hC>?r6#*iyIxKX<R@f=Z*<?%uKisRDfxh3x-V7DxZ
z5tDT>cmmR69#>le7GIHH&i3v$#O8Wyn+X$HRM!;oQ*Cd9NsGERmp8sIg4Pq%vRKj+
zN}q<_KNJthZUwN0xHhTU4EBui_SWpR|B-V71atuW|10}bY~LXmArwFrTcGuR;}bE=
z;kh7E%CQ|{*&|`f%OR1m!P-hpRDsp~%(X4s!_lDVsWn1b!GLC~!O%dSBV(<O6@{#T
z|DVanlI)*Yn>~{^9tAkwGxfUTNg`Fqz9^E<l1&Q5UZ2>Nwe<0kYJAr<#-d}?&67I3
z__9zVlJDufO+|@A3U)@FC^ppc0QMZI<y6$XeFS}^N)EbScdUnivB~)tV3Jn}s<QSi
zWAOsCUTNm0>Jg6oi%Y7CoidFI|LJ7p^yOymt^=oVe>(Sgh??09ov}Qkw019AC@C;$
zLPi*V0WP&}Td1^~8Yoi<4AWd!2yKIF`<r1gWE)6$re+TD*Vfu3gm2vvD5U8NON`cR
zb+@GK@YPaB-Se*F(0?ew%O@v`ZPAoCSqfU$kZ>lSm0#@bLC^Waj1}{zXVD>D20;RJ
zs0aj{h2aa^(3kwrqhzRBBg>>_axm{6Y+nQjA8<%RT*TI{&tVL)2o#egBmgP57=WHe
z2XJna#DoHTPd>k+{)e79P&ING=7Z&uN)(l^&%8sHMSsDqz^~A%e93WV_^$$tKI@+8
zD+n+LeS!dRBY)yi;fnk33V0O3@~gX^#-PTuP52@irBHQ=1S_9RG^UJE9Iew{FF27h
zYY;b9rO0x@tCmiDy*h(6N(2oNw+x)J{9q?&T|2YBkuhMZ@yz#)53%>e6i#;B8AwO%
zd)di>?vHwWT||^mU6|^LA2>Ia{zotfMci<e1}YM$q)9LU*)(0un{u$?c-NT1*xtQ3
z!WMd_IgJB%Tr5caYy2^Aa;}-OZUNK%i?FAY?wtbV^Zx$-6T>j->ko1wucZ4M7O;4t
zm4xKS7tS97hri=?5BaJYs-?_;`48aI;91*tqY=}#RqQrByywX<%bL|8{OIrnU~|Rb
z07jp6bh(_XVU7k!y&uF~Ymsuw^N)@lv4}a8NCAl2k9PreL}3&~)Bx6NY3B+MurUML
zVE|#Y(HB-5|J$PwMyWR#-SCqcQ9HJ7ts=L&9H0xQSD`J4{z#^16`_&JBPTgTxR0yV
z)FOvLqujQ$hz8_tf2p#~0xT8-?OTynl=-FF4egs*jV)ew(9kw7|6F?m(kcHdcc>?6
z$yce=ZT#{jS@g&!$r6X+(B2sknlffY4}A~|5yj`k>lsLtB+`<KMo<Q$OwuZBZlvU?
zr>pg~2>+d=h5woca>xFoNgidc^e565gF1q9<btl*%DG@HoO|S(xzGe8A?`WPs#B5S
z6yuaa8wj~YceRxM_E6>F^XE+Zw23TeS#U-q52hV1L4%SH+Z^=@e*@^NWE%%sBN%k!
zV8Wg#S>3jU+Icp<*}cH#NB8Q5^4mVTv^ZP(m6Fe0L<XH<bcgL?0{!3RVhry6ej_NW
zk&A_BYl$d*Uw)7_g}0;Ok{URMHCC2CE0$q0*V{P&z=yBqi;(J&VH9-}lU-3xiRZmr
z!RJWB7;fEhoP9hehP!reNsd8f1)m@pnw7sy)2rggvlg~D8d|4z=Uxo!y@@y!uJH3!
z4oFrT1d4zAONzH?fZ;7L?FC!JSNxe-d)5w-pHkc-blShZp7#5K)*;?skjNem4kjGS
zc!wj_5Yi0OKp4lV%u{TQz%1qmLLi16b!si|Sm0a3c$9Mn#!N#!2AmSM8IMZxCJnXl
zm~i{W8L&%x#kGQ?E?=ADE<}0HhkK9!Kg;vQz?1)td`2?v5_j{I*2Z1py23~7=-$L8
z9lsK>q9aZ;zdJF~p%fC|*S}Ft?81s`*CfjYua=!8D}bUH0A_^mJD=$RsaHC8$0Y%c
zerlfjm~ku4$ry85DbwqT@FVI!8n)obind?~SFq#R{1u8uFO`30w^<)a?Gn>>6WL5D
z(rI^<u#UU+ddcUt=<U#V`}k<^;aItCbhHG%%`YrIc26pJ;745LOPKK9zytK!LoZ^V
zgI|){{bJ{ZsZu+;8*N4FzL1Nb@x<7l-)>ESs>l02gW-9z^MT~d_X(pO%>JKbn*CB@
zfKJ^}Mto!UJL57X!gigBXL<jm6UPiSM7-z+21Du*6LY6iT$r8y{@t7JdQSah_b{(S
zcQ1d#C+Mx8z92bUXy5{1Cn5YFKs2gSWmaYK{*U_rT!Tus$tUR}JT-S(3=!kd=j=9K
zF*w=Wr|Y=Scu>tvdvJ;L1`zgCya+J_!U;T4gAM#Vyq^BgKl)mf%N~DrvB?29#W)eo
z<SQn!Npsvxi3RIn{QLXSp{td{a{GeTkSxG|DPrZU{pu>cUQZK9r{Gu!k>AB^3Q}Y^
zL=KEN$+vwM`1UihCw)`3#<5M8ci5WwWHp(C2x<#_uViBh5SDFvf{@^HLfyj^f_Uds
z%1L@A!<|=>HjE5|kkyiE*nYIw*o1v|P^hx{#QDpZyz}-e^Q4@mWHumbjE3?zyP;0x
z41$mphZscpAXxIAE7->W0~$)a{eY1`G^c8;?SfJMz2tW8|AdpSJ05FRdd4}8QY;s4
zHok%6>IhApA{Z0)w8<nuIqt+LJlv#1W!K_Qnh<;@eXp`E>{j6~VqeG;Mq$I{2ZQ)>
zlLIH98}%e0-2eoQ?a?G(4Dck%L%_Qfj4mB<MK7NA+<^QFU>yNjIZkB-APw`0dXR^>
zL*q`fAGmq9jFBX*xAzY?eoUYRpl^UpXZ11*U6MHXlXL(Aa*l{uIJ`V#=Y4mefqG<O
zz|kLAopA5@RDfl$ptr=Fy?%R8=c()c#CKBw<ABBC;+<Y%Y)s^97z79qa^i>65@joB
zJuYgCs=tT*6G*qdkErKbfAdHE+YqT%wo@(ml#?Ec${uMb1E}p6t~e;cTLZy}0M@lr
z|M~Ur{Cd7RLp00&A35~FP^CP`<&8_CU75;n9NKtCQiF#_zF%)9zoBloRT_By<3Z*C
zdJzEP%@N3;@=n7(cGEC1qr+Y9?bs6tdW#S=an>1e@F*8+16+5cN;lhYta7b<RyQAW
z$f`=6d1FM|3mfyx3LAv~^_7!tE52kw5;Qz|(LQ#?iQ8Is?-J|t0XCC5A5Am)`Ml2x
zcyxg1yo!YL4r$aK515`~{2<#Q@cQ^CCys+SAB{4q`BV-`R}#Cm>zmnHS3K~XJ}<T0
z$%qM%K+#cpOz-ZF$Vz3f19&HtzexDY7g}uxxAloTa&tcK8rMkW+05<wL;QDhelQeD
zDL2`oM4vhgr~<m!ri45?IiD!tKv^J+jk{j)<yY*|E^FKLtmJ1-Ok3oC03fc8wpR<;
zS<-(;mx!bU{od?|W#I}sXR2@K^Y>>;f%v5NAAZpx>y@VOVa{@-GmjfUS_9;W*e7~!
zHf+;9JtBb$6cFdF8*Pptd;;Aa3U)eO7HDNYUCS!93k0Y63YhLbkp*P4YwrMtjOP{K
z%e?0_{a3-I2xhA*7Y#d`^V|7}_1#ud<l%qK8YD{?vN#|4N&BGz?L%*T+eN}Wo-lh4
zAme5Abx0YIN?U(S5YDe&+XU`kbsD*$?u$oKqXqwP3S{t!w)d9&1mNYgP1n!<dIp?U
z_cU)~mB!jIk>;4vmhjG4DD+Ya{#maOVTtNQ8WiJ>Y2Ty*!d9;?fD{F2(Tx9tvqnMO
zBU_Q3vZ1#s*MNr(0TJvW&3@${;-{Py-9!vF=%c#;E;B&$u=g_Og7awQ-3ZFGT@l7Y
zH|B?)HXbdp7ZC18w>!>hRGJ)hsBn(&^f=uASH%IfQQLZ(R1;IkCa5}J7Fa6>OIPU(
zV-5{G(qnYUUXmK+<Uswk3wnu0Y(@<tLjv?e!UC@ZMF`UOZjg1uVSV$C#@mG?Q(=0I
z_w!W`41>O*r5Td11}9HXg`uCYbhLMnqlDQWKMY=C{#z9_F8o7e<}K+=;~3QFtM}c5
z&A5fE0L%_@yyR%p<{g{YSl`jGODN6ghvg$dBBM*?)vL_dZJuHqPl#mS)2Pb-CGw?K
zPNDfT&@iEVZF(*~&0_k1Jt_ZzGZi2rSd`m@uv9ubZn-jG+dAL@PdtDG4B$%XZ>k#x
zIWz{*Wh%(@0VKr&qNPk|y@2ma=j${87Hz-S>F+%PTNdy*a82uh0q~NIzh^-qVqe%P
z)~WK7IZ&g`txo;?#G%){yMV~?ytV!c-*N7gwKKNvl?C`><>xhkLJZu4SI%iWKETuj
zXe>><8wLQBd<@X)0Zq<yW_WP8ApsGuV7LA~OXrB)+sOPwH#f`FZ#VZdouvE0w>#h7
ztVd<v_~u$QH)RbF)V2(r$BF#Jzk{p9c>5ph4zRTgnm^E>(N)k4d2w8aO|1(DCTpjO
z1i8olby#wAfSR_;YrVr8FOBxUkOH=te;xq*3Cb;I$JvSrs0AapksZ-}?(|_F-~Hj(
zmI~{E{DediL|Pq>Ls4Kj1aP&W|7KOBm{D1JQaq~LPg`5WS0N2*Z$=^u7DQw+G?D>R
zF#Xnup|cAB?tp&gOIE*9G^6MMoekXsypyJ2GD=`9Aj|2rvX~e)^3%+LO*`?KuAY2q
zGP$A_qn5`HrIh`VK^`@p9&pdKy}(b0#u4x{QiZcCoWQoNskF>ko*2sQVjZ{K;)qjw
zYk>Izr5yV25ShUM*>G|uCxs``LmR!-nUaQ^H=U=ESZdzh9BXWnB}-F6oJ3Auoz&jX
z)_YH-?m^-d#~U>7FS5Ux=DK~7)}c!dicaq7LW8L=RAUtc&N!gP<Kd&_NLX&Dr?H9L
zqqdZ8Cx);<^|IgeiXecQC^?$hfatZrSH6b2sXtK*G*f`Z2N|N!Sh+gaqSXVi6^X2L
z+PuGAWA^0+d34gZ)eX&fh*{A#ir!amyAwK%G)WPVJO0;=<5a8mUaqGfY~iDT*zyhb
z{!tL9+MK!LRZ#pI7Zsq&<w{e_52aux8zn4ifYIA3xRm{&6w~I>^o#1Q_rGOI)>WhM
z4`)Ag2U9AsGWid90zNm`URL1Sf3h(m;@$p<jLo58_}|;G3@#0faU+^BCEME;*#g@6
zj$LPK^PV!l>J+8+r0f}Z0sUmc1-afDU|%6a$W{Ns$g>m5JeZkgc(}mB(&-R%DT7|Q
zfwEsvPaTf&hhUj2_ywf6od0Fm>00+uC!WQ_-NSsnZ;z9WH{<l0!AaNKGE%8_;?anh
zW*=yM{O#jTI@hBtiRkcB$~HW?EP~cqW)Yy;-*w_{>{zd)_g-H({4>&lan1kvbh1B9
zS>EzGI;PWx6f4FLW3LJ(G5xn@4@50q@~`Ut0axrKR60oyOp{ELp`HsS0R5Qb6Lyo`
z4FDh~zrM^zcm>es3e!d<iWwjR!aOd<A4=f1O}4}MWJhUymyvY3aaC3)03O|VuW^h}
z>Yi-+%>pCi3+fW%;}M{n0E7ZVW(#JEmD@C%tYE&AEK7iUbqwlNunh;6W%UXr%Qq#J
zTKOF$b7}YPImbdWf>eHAf<ObbE;15%;ezrD%<{ifLSZk+%nf!xPSExbbFk}59=_{e
zs%}zFif#-udaUH}E|op@t#~>u53_a$V7<UM4qWtL1qNfuHk{!WU~_vhl-;MbwR?c;
zv%8IaGt6elzD)k1qYmgwK&hxJS@57<A^6-ngt&{T&`d$ZpkRb()uexl1T9y$<g{+x
z{L(PMgVbR62EzCg+Ung20#o^BAeN_b=AuLt%d^}D3;q@8?dPxtTK9nrdTFP)HVyvX
zVzok(y*q)m*zSu$ln21Ka-0>oM)1~%`pRbImR}>jH0UrxcO~3*o2Al#=>MnqS~x}y
zzy%y@8%F>cfF^1x<Mo_HKXCt2&alB?$m9JR*2pnf?M+WkGNJ5P$P;YNBTjZ|`8Vsf
zP9ODy@Xi@<vkpd};sR>?wfnfri!F2I3pL+|;3`4H1dBS=-fYGOVpOrhaV|1cP?=SM
zEX;7X_R%$TEZH6QAW6Jb?I0{}l4hk_2xdQ^WAh+_$V|*{8VYHCih0#Qpqt_}uI67j
z2E_RQ^)w2G&&N6d%~}#%YLveF)m0bX-LUBEg%kyL-**-HX-Uv~hH!B|u=tu$zGEfm
zt};xDXK~aj2Df97WjAJQ)%l|!Cdm8m%;A3;2x;ZLe_0bl_aU_|c`Psv6hYDP<sS+;
z*$QM?Zh5~ZlYL=}0qAB<do~+E_xu94plG}vJfZA8q~O>D8grhRV~hrc43#LOMdYdD
zgV+RVIC~h&xfjZ8;yduyN3{0(QPmJ<j{s3XIm;?Y?;4Z(y^kZ^ko-C$`Eod(Yi)S0
zCZ(rKoh?!`$6A-F1}A0>rokb=@2WrNN-ihpX^?;iVx1DS%rjLeu%PTQy}T<kr9Bz-
zO^v3Kkt|T~n29g>!%xkJx*o{=1s|y9y+0boU~w#mSu!NTST@dfrHJ?jfRD;BjM}mF
z$g2W=(T(LCjd2iBuh2_!1XG+4pSJTi4sJ8@uXenAx6VgPXBq>LNJma?U^3mktVDip
zP6Z&Ea@vq%OeO)!wq!Lj^QI>fyC6<?EUWsLHnsqh8Rl)dCyH9%hPEK_#!Zo(8SQPE
z;bJwwKIJi8K=@Rb%lxY)L$iHX=^6<Z80UUW{<T$RmVN{OR?Ufc!RYDY?<VW1dbAjj
zRODD=A3zEZ`*gKg2^-wHQKCspWgjBl5^Yo!MREdiB#KKZL70_8Dd3DWHcCYm+AAn!
zxPA$l9vn10(#7yU>hc+Pb63#3TSJMmN<Udg5841J=Uwxs`~<lEm<z`LU5@ylC>lsm
z91G>go$;OMm0f?Gek6n9ohCEqQ)sHEY3GST7X3LBhPCsR)lT)2Kw&@XqGt&8(-d5)
zZCiAUHzR;3qP5zgVw|Ym`HE09i7>PwQ6{r1ucdBVTreoO4+4!$CW7?5VJtOiS~@d{
z$5hy5SNzEb)7CBp+vCjXQ+qrVeJO$Oe}7$FDm6s5hkgf=IeAmFRz8o_Mp7vPM_THY
zNnEt>h($(AkPXDdGuLlnuXy><n<t~ir(=b==u;CjEKMYVg4^pQdxlb%^2<<IvUU;6
zQ3Je%_Bx4ISozdnChn}ck}$iY+GT9GgD_6I{y*?7^EJrd<NX8G<l<;QKYJbCDzdpT
zrb$`3vMeWZI8`yqA(LO7(l+C$8sv{$+UvPhFc2VZ-^wEj+JCj>_CH<2U2zp%t42lp
zAdaAVk@&woBl15f3sAE51LRl9a}q88#AH}f)0ekh@r+KX>ZK<f)g_)iIGEE+A*^4&
zjMY;ZUO6LqLnWpnE1b$7SS+CS(cyldhQVcKehCbR6=y?xpLy*E{JQt?Q{MYe^C|jE
zJ1>Y~3d$PEcnlYq`ko~7vXypW42l}_+RvMA%tfYMVt)=`@Pe|{&+j+6#~p!Nt(1_d
zVtr{N<Ie8l<<55V3H@zb_}M2PE4grI;^o;KuVfFsE06)QqP?=Sin<5hf-3mzH2t}7
z0P=iJXwHTtnoj$AQ2ELxipIgMW^7unSi73Hdf{=gf+T!Vu&?#qu2%2teC$k*INnG+
zZ+6g$DUuj}^X6Nm<Mj~SyEA>wops-rkC7z!-JD3a%yS1%WU^)VVZM*G;Za!CjQ)-5
zS^G<4F3kG+R3vbzMUfF4f+~AXS$yDsw(XAB6M4o;u4Xp<Pqs<gpC_D(XdZgZl|G^c
zu+0PANq4`bP+MDiXto>>(I|YC$8s^%jBmZXb9wW%<6)IyhVc6{DR7HZO97u({&FuT
zGENd<+siA{UJ`)}T}W;~$0t>KPlfQr`@k#@<ldnQlYcUpsL=nDeu>>XNbn=jEi*U7
z$nmVw=6{k_Cqh+QbA_cXKj=p<jBeWV*KcWTMKvfgurI2$uEc3=Y}G&6%iB|sR~IP*
zNcs$kqIUcQ1eE}Qf2Ts+8Rh))ku&B8dI?F+j}HXp*wu%Ia=7B|SY=uPtSWpx%5&ha
zus|RyU`P(Zf(f!8*5QCd>dOvLN5EXB&2tW)LSLc6ld@7Q<CAC!{#038KZvwxfG-I!
zRlnX_U=U-JP=i#9Fjqwo(lqSx*EI)YJ&5u`$s8A?9GZwKc!SK9Hd5kbkc?Jg$z<!4
zi<eN-J6=?bj|9SC1qWTzA^E52nl`-0oYhmBs$0o>=j%*#!4+9EF@sgQ-;nm0Bo7}K
z2?iIqBCBU{)k|jr^RZWHdp;|UjGtEdmpk-GOd@>HohD*#B!en!``+Ng-z95|0EWRR
zV9h6DPD3j}q}TZIS4{PzbgX%*__t{sW%<sYa3rXOhF_L)xjZ?m7Y^1=gLXz({m!26
zfd|W~&A=*@sz>8bYGh~`XI83=CM82w#ps`Ij_S*g$O~%;ry#zDGrbisd&7k&pXOc>
zk%z4<-aaX5rPzqO)k6KD+q2#OOj;enn~$~QgkoV&j7SD$82{%0dPTR4LxX{pOPf+j
z)qMNr0a=NN(AcOfz&P#tC3?3Wryy6FY(IKpF*%4da{7u_CA2DudHM1O=0tt)a`u{x
zSDI_<`--&NZ|(J(=Iv{e1Rs_;*_ixw#|PFLUi?V+dJ?d?(tLE6dm19HJ@KhD6WQ8^
zS&_g;+Q7R=w9G%6MQ#EFirhjz2xQQrc(pZiTXRMk95mEbOdorrtx+0u)=?dZ88Ynt
zlf~uy=Uv9fR}M+gOKO}?x?h<gGS(ycsdGY|lt$?7u*W00jIWet(O<tuZ8~UJq3KcV
z(3m9pzBjf&u!vaToeUWadC&Nn^-G#VQsL<Yy{Kvtdb)YeQ|tAXDJR>DJG8K#`HWWt
z`rX%YjaLHIWLgZam%BwIA(Q$yCM<aH;WQG9THPM)Vv)PU&f8Ba2-NTKh`GvY{I+28
zaLf{}b`xlw#Gy0}0sSW(&6;x&_|9yLpd^bR+~&zwmur!qBRU-6o|PQmp7D`3b5!n!
z`54;mYJlVKX5;(2rOD5fIEB~ABR(-TPKhdKpWh(?HETzQF(){}Dm?d>jN9~MZPZ$h
z{W@(qI3XARo>E(_u2JkKsf<w%We#zW_^)zI81?T_DMnydAOslw%=L>@GG&0=WElDA
zFSPk<AEMrTgXLZaghWBC-OI$lsZ>|2DP-{$m7#|Sm&inVZ!@#A%M(^v&9fVKV1Q(b
z5iqwdM;5xP=BRM@9H>fS1HMpU!E8I{g|wL(;=`o92o=Wj1j%xo!^c4(-#etrdAF(d
ze`c~4uW{k6F`46M+CC6L=(b`Ra{$gf-U&0CJPt;VH6<)6MrQ8&>(aq{HQ^U{h3Spw
zUDMYh-)q=1o4Unfw`9O_Af&xByKmm?>g2D{I-&nmYj=#+<i~1eTnl-CKvt3~uiRd5
zl~sp|I^O_8%qyyHXMOirARneN6@9^V3n>iBAWMg9YI8~klSn=mWwlY>+NM*MK=(J_
zE$nwfO-+5iZ*Krd5v9zk%ET(DLIN7(q|Bp$?znEQ<p)jhuc~vlyE<jmdj`Kf+dbn2
zw)xMUL*A~BbUPYGBBs?8B9mxw1=sjHLyk0`1NHBbfIllIiTl}}UhEOGdhz&T;&sgJ
z;ew^3OaF1&*H3P7Sw*kCzj_hftf&+(i0D@4#k})Y5OlKM-kbG0a>V2Mh}XJ!JZXLV
z5SRsukXsa&8-BY-?T~7pH1;U(w<s5>Pxs0;Ci|}eI{gpuks2Vwq=si`M>(O*CJang
zH3AaED5nF-p&^?;YR8Ql`#n1$tyU0qq9k;dLEz<&%3ht)uz2g>)T5YMRp~CH#=t3P
zGepx0&ZD|sgL4r(z%zkF23GGe+u+#p#9|8meMAP!T%?CKc?$cy@rV&OOCC3iVKs&l
zY0A#6L8dg5Z5Iz*e}1%P&1+JYV=<H0-Qsj(Q)Y<M(F*FJx_T?wizioLHI8J}!c&T6
z0wE#+NMxR^bJ)XpXWm}NsL3fJ-jree8!^|T9s6O2(ju=Q97_!Cta0_zXU4ptiz#6A
zrFb!cuFWgQ$hg+;arxvLR%c)g1k8(j!eWoI;fTNof2s5LU=+>M7j*1>Ui$IHC+#(f
zV9MWvs&}YgB+_Z$@R6p1r(B%_HC<B9o|)sCx$PrVi1K=p?_@9cu)58N>8#BVgoAA2
zt0XehKL;`~^gf&^-5|q#jdOL62z82#b@6TjeRAXS$<ir@0n2^&CbdWUIL|qx#U)Bq
zyI={pxA(dXoBr536sVX_-#IA8eG+uVSY}20Fm6{ijq>rC$FNW{-+-UdWl3E(D)y*q
z@(dYz1cWsiW*qRY0Q-e!GjNhks-4r)Q@HzE4sU1mxKyV!0}|dh53JN(CBpZ~>@Ly_
z<yxoCfBVs2c+A+diVT+3SBb3JnX6SP<y2h17a~Y<J+|j?uq&p_>;ASgK-%NZoKUNA
z<EQ3e&&1+SuXTGs=1}y%m?ZD_3$rW~#6%X4y|U&+lN#PQ#)YeHzuOppkW%UKZ0|M8
z8ywM&^L<&iGhU|7*3z;gE1(QFif>{1(bCW#Q$qicUVF5JWXaO=gEx48sTVgW(uQ4|
z0njP~`*P;~L?|8DH`D`it?9iwkUc(}?Yw^V70iRj8G4UciE6#GFN{s<3?3cNfli#u
zK5LKNW8GY_ZSJ-~+Efz@GQT=LZ9Sn!8plj5VqGd7T6bLCQK>L8a^G)kVSrV$r#s?t
zE6dOVE?7kgvemEgi0KTp2CCc&wlx<TWU&UkLc9OfCHTSrCzB>(2WynwwgP5HYZxCQ
z3MS&Zfc)boz>+3bH2kAeo*zl`wEjS%gh%tvtFHGa;Cghmz${K?tNh7?d<cr#64BK?
zYyg6gCM`k}#fM#iX9^+$Ja9SA(7%Ax#$JO!(ojoRpYe6=kJ;&Wnrqf^PK?y0k}aY#
z>9nDl;#f4!FVX#;VLY<5yF{bE<PAJ(BTVtI1e0`*kQ0w=l$0WjQh*f2-3*<v%`DUB
zd?i8m;O4D~FHZUcu~bI01-N5sb;{8k=0C4RWzf}7*UV>LpthSQjE2cy+#?E3eX|Y5
zRBDtBLY8x7^IQ6Uiw_G)j;D6Ve8o7K2HV!)w?$cncljWM%1KN77N_8eGLB?Tc@jt*
zD%!1C{i#>i7xachamwJn$CF5Fun2v*hcvJAh9JI&cO?{P9%(q-)3J@DeTrFvlk)?u
zgsX6LI|UPtJqce#7)9&2F1R99gvvb#Y_6q%9eVFD>RBmoX)g%KkWTMX>^=jr1tXF2
z@stP60R}m%M$>28gYdkNp6J*J5URLb-5lqKtO&g*QdtWap)pcYnXR0UmzpJ`CLKJ-
zVNExr9am(T#M=^b1(4Y@Wcg$p3ZF&$_GVe`P+$o1Dy_jNM6HU5>&b^tCApB+PN%^Y
z?aP&8Z&i@lMqd2@7ZO6EqGcK(KgG6IceI}>kOJldi=so<FM>pQ^11ltoZFp&-Q-AM
zf$t5Y;O~vNCrGA<5U7p&i4B<ofmJQ|(-eP({$W$ojXb~Wim}Y5WITu{Btsh$>Y{4v
z9ndEfW3_*0A!<k*<D`P_HEfMpaAMLO%w0wV=R(mzvk3bJ1QsZET&yy1rutwM4DA!u
zO@&8bg&0X<(Igl4H6Rl$ub?N_)GHXqCu(&*ZGKQiB1#GBK9owMl?&QrdB;0nsD91b
zAU9M$z>dtw(XO|ul>l^}K&+Ab|9{3)!C#$F%P|n82(bps_5eAS!|s$W_t$*Rd1!;I
z_n2x<!0NX9-YJuhApqHumyVo{GVX9aLeNjXNFKrt0@Oz>>%G8_JhzBG*;Y6JVLQ!B
z3sv5#q~{7wgT12KuEi<D3>+M)X1S_610&R;@l~337vr;%iG()e3Q>k>FscX|1U5ai
zIk*Gq>1Ax(dXgxfg%2tURA)Kydl^<?lyaCf@RgbAW_9sJ>0S-rr3oZ+jnN#_u9T3x
z(ALJ|h!o0=ISGCZ&jl$LtumEqOTo_*(U>c3BkBG$-Dgzg(Y1V4`#p|$*WM=DCd%Iu
zX|5DqTWD{BAN|v4^a%-ac(ii-3={KX{jTjy0^OnHLOH}G$+#dZ&nT-m(X_^MKfcYB
zLx=wA^blc{HGj{8@hKz6m^Z}Owjs5RFD7r#BYj<yLN)Y4H*-;y*XP1OOMJePj8a>i
z2FU_iC<txkM`K8W8E2At&T1hx)M&!ULXhZMP08I;Q(?Dt$*5yvZ@DX?478t2Ngd4=
zF{J&o5;uZdI56cV^4kx_I_>N2kYO?Oe<6~TG8j@$9^;YWH4B!tb4QnRm*mw-#VyQX
zCtN@>rL9SLf^G1uUJ_;kJ@67_9DzAY5E-)?X(r$wQhvSbrND*OxAiO8)!fTyupv3K
zj8#ZAe;N6H`RxK#jW&N=yns{e=aF`D(62S>NO-#2_N{>!BZp?$(rwhiBUtn+`Lwpn
z9&{;b1b)3o`1i+b!t>QU?B93iwy3QLZMHQ1;}Coy42p9{#Cl$qkw%k}@9O0;<%YLc
zN@P7j5<ayM-@7|dl5)FaJkUfA?^`?arrC05&)!<rKVc!BMsCE@s_M42^o;fMt?CVB
zJschprBqBE1wS9!fwBm%TpHe9*A4(;`kzJ1+r-WO-+>(Uj*e78HFzQ<Mj8Q(72C2-
z2vZh7FKRVr_NVBRbZ>C11RdA2kYOyT<WglBZXl<4mf7EFxMxFBf2+cXKY2FYu!)>N
zx?P%RR%#mI4}rq?g+kGB+3%4rthw8;65t+oN*iI)a0~?srtafgF(?Bam_#x#hGfyF
zKNlaZIhbahZ7?Sq{syCq5^V>wIpp3VIeW}iMX;MbA)TBPfDa7`u^%r8f}9<~2^!kI
zGgGtDEz-R2mOD#ZkV?_K0kS1xC3W+H&|tJ_{12f0)QhpmT^wac>pta0POkWZ6Qy!o
z(#PZKu=tU0WW==sqG^e1jx2A54h9*nb0q=CIu`H9I4@D2Uz5D%s9=&0ni09d-#v6M
z?~a%CtUXwnLCz8n5@`tbGf(bL({(PKa3tQ1qlBCTwQTYbZgCScM?Z#~)lL_*g}i?R
zh{c5`myRFB^E}JXRISQd>8lk`PPCai)Ts|B8x1&m<VpZ$)eP?tQ@rq9N9WuSR$10S
zO1tH<n-)B={C1YFeq^fO92Om_kcKUoC)9I9)@pdZ66Y8I+38cU2eh(5M!95EhOu92
zh!yBymBh!uauGF0v5nSyBiKd>UtCu?`y>f^yAsh^f~``O$2!`Gf98Rm{ipyz<-Kft
zi{LK_Dmb#CG?Z9%h0p}K&fozeZyHs2fOw^x+-P$%d5ksp#ka7_r6iLv0xac!qA2QM
zAkj@h{iS(ongiRGpMjrf8v^gCs^Hh>g`}YP|3Xs!He2?9hEkM?_J>Nq#LTVc(B+@y
zEGu;NjZNG8BOZ{s(gXqRpBu;luPc`F&W#vbq&}7=9HZmv#i}VX&^Rrfm+cq8-gyKM
zUtstM?>v?xTQ5t<$;1!1FlO=#g3<W(jaRKi=%7oFnARQ)KxleX`P$<u%$``6<G;rF
zA?$c1h2(~%)B72ywgoSrTn@V!u?3}mdkD;n(TxFk^SM9Vbaa4<SR*b_+3Yx$AbLQk
zJWgjQRnpJrP;Fx;_<QFVoj54s<w-Kr_^N?7uqQ?=9HMG&il;KfFE0J}_T-;6CFbJ(
ze>8r$xD?zkE6uuIbtnNfV);OE$evm2FwnRH#%(w1pQv0K4hnH?rg5~Ngq7UQec<H@
zu&jeYMAcJARSTAeaNXWTU~(qh6%b}Sl?*WOy=6TQH<*awD;un7afK<yG8gnbwG!4*
zIZ9~+3J7cZ6!zXQz!*O~@p5KaFp+y1_-5z3)rN#R<E&1ZwJYsDF%g7xUlaK6CHED}
zOrz!nGqZSVvRzj7f!la{6*i@{{yw9K*8DP8G8`dFWK^lzJ0GpytP842q4$nad=nhE
zdll4m`XIkoZ30f`m7Nqq5fMPcsq0vMv)q3?1jMVZRd%X(8IdDT=2m)R8y_I;!V*Tn
zZ^3gCcA2mNRr>sH_IVC1KXDw~2dnl{ZoG&Eps>&B5jA8dG+H|X*#czP8Pi1eLB2R*
z=TrAk(adKO9jwm^mWnh8z%Vio+M4mik?`G1ESumG@0ie|%jboAdw!s3@nRlC$#Jbh
zf@E+daUJ<f*h_LC0nvXR5Tge5LW||zwNf!SrFp5~D}JqZ;@7I155``6PP13QZmcap
zhz`;T-?vMeh}ylR)V>%WVJGELBP@81zflgaCs&0(87i`91`Nd<f6)&DWT>v=;Kbqf
zE-5t0PokE?#Er`TX&{|}pkanXV}y?rReuNG6I5k9f6Q2a;W6qxyFy)i(_50qRUCE&
z4DCER#6H%3Mil4GGn)Gr)ndc0#XOcGA(m;+4{w(YQKtALpS6p?kj^{l{bm4YacNgX
z8?eY;M)Uxp6YabYfkkNjG`D(pF!$hK4P<yK-6!~7FkSKn%kd7bKST75yz6AjW0m_Q
zr#JN9Ztvjppm;3^S=ltUb|zJH2l@U+1L3K<VE|bTfT<?Nwen=<PJ4Y&)0n0|5}toG
z1Rv$M6PTN;25)pek8y+Zt^?<rr{jnORkw%KvB{tfv97E-uTU7Qm>8!;=proTGKKla
zsuyEK&m@6n8FUC?xdb-IC5!JBlLAM(v<i3+_ie|j?RJVN&e+tJ*?Q^}=J~18H^ewC
zK8!g+BkLl@XsPy64>7AG{J%RT{eS2qj|q8!=HG^59%ha}jCpOB(8OLsH7D^+O4UY4
zW|`=OD47I-MfPl!TPm96K@AzD??Lmty<*(&ZMMT*S%!G1q7e!Ocj!xvCAe3MYCobT
zDMpVc(dqhWkle%~CLa6CGo&(8iY|g|y88W(Kq3wbsz~KIdq#?k2~wgD1~uA!oJb?Q
zxbrn3QW&|EIcuj5R_)+@O;oBs5_0HN@T;UiQcpST?vgggcV=`3N#RfjMNIL~Ur!vX
zIBuA!r%9T32ZNBAl_WOPOqILO`Bl+9eOx2_g|oEJ?%47;DRj>~K$XrTh5ZX`9C@7C
zc!=VsmDn}2P$S0QCP&jE+szkBQ3_N`kt&jTaIt(JMDw-rraqQ0p088O5X7H2C0|C?
z$&*F*h#CP^d}PHj@0*N^=D`bk#$Re}no%s@)O22#Y}4gK{JC=<sOU!G9!gQVK;x7d
zFCW{_1PV!VJJwe2$95-5<<mc73S5IhSQjHRJ00YqbM_Z|^bkUuwbq(Gvr_4KR9Mu%
zA0Vu>*hIhkiLyY3kq6c6aTEoD`!`h~KCj-52l;3_jA6Kg)G$=nALcnHEq>^s%yX(H
zt$$<|AA?-vrmVeMX0#k3(XmPp#MaDyyaDZb{h5HW)VeuXg3~UtmE30o8^Vg_JnS8Q
z<?=&GGmK&@5?Q=Wz8(QWXq9_JYufiR#&i~@`mkbmL5Tl^mKep!U#K{HNO*hyg#g-z
z#WO~so4>8)yBSx{@AW>?=jlaa?h@!{3I<Y9H5kTnlzUBVL~9;5+_wW9@^GGcRXBaZ
zAlK!#INUE&{O9W={XSHq9@Z1dP?(8Y+8v_b2}H8FDR@lmT&gDdo;vAinY33)uh-@!
z@dA#S{wsS^-rH(49yk43p6zJ8(VB^(&CdK|FAFQQ05UY5nZ961>1K^NUp?hv`492Z
zrk{(#sV;Ay_|%IQA4bB`X&>-SKba~N14%q~Vv)bEkAsHhzVvO9Fgyz9Lf32k<nsA|
zZqH2W{+LD?2~vURVg5&$U2vOedIO*-ir{<Q?NOs|!Hhe^2+P{pJPpGK+nE2r`{yF1
zlcsUy$fV#Lt}GyYwgl|>$S?di2X7D_tQxL?h*xN0TPRiX7hQ_2!s|)*{(?nF8ILMF
z5-Z5^&%Z5)AFS*eI0h7UJSI>E@Uq=C_zr?|FU*DU3Ofj`x^ixbj;D8a@A_@Jp_kuu
zU3Ev4JZmfJsjD--Z>6Grm_|zu>Z`WZf4r(_-|pVMjc8Y_PhMtwwQqYqfhF}?Zd2$5
zN;utRPg+A|E5&r$RFH@OEelfa44JC4IMA*Ik%4WDWn^=)cp>EGpHBVj=h!Z?XBJ~6
z0T3rq9ivo8n-Z^wFh0l9XjcBa48S8mG;5G7{)EyV9HU)wB1kF->%Hf!KAsLsf>ZZz
zbAf_1G1*h`Q7RBX4O5G%N*{!1x&RfMj3HSSpx6{|TBr%96XXoF6^Np{{8>mimglT6
z$(I=#?gj{#>y-XVLu3>%hz-C%w2O>ko@~h1;IR!s@>$UXG&)AkP`$PQENWHFg_<_=
z11CJ1>+NLQ<iyEAIm`igum(@{uvFuqT&uq+-i{a|C-AAn$C_;DIwSc@truZJiMy?2
zK&dDQhcwkxb>H;!*@4`{Zh*9Q7Sd3)%~4L|5$IsBc1)bKR7s+v*Z7ekZ*eg&T_%yW
z*rWAM?Ntc%qJ8fqmAc~LywUfme0_CJCuAn8(WTvU>5q0TNuAcsGH35A=@*(p>;0h9
zNg1j>xk-63sQ2$6AbQ$8#WX#lEgH6y1sd~(J~@?or`{7swBTHlfP+5mNw~+AAKXoI
zzvC<v$7_<ulkCImb~I7OxdrVTf@BYKSHxlyC%+Nf1-Ejm!W+i^0e>K`uk9C`y{IzL
zp3AgQ%*7t-GVhq)adh&3P{Nca`1>p55YLPNhf_0=6bv61pz#+~E%G}B^7?sPa_%mY
zZ!bo92!<p#!Zaz_^|`6mqH8rW=62-HrZgC!5#b_97GKCMxKU>L(?JjEy(yTOUgK_#
zZEZ*EjcW8w@d(VA#%><nWE*`ee_yjuY2<qi2c&^pe*z~#HFD&A#jja8(0t1pK%Esu
zMXfvO1(5+8m%d<izUd@<4k3K*l(|O-+TX}<|3(6?JLcfYmoDkQM*QvnHR5WnM4;Ol
zr#k<iu2}!ZMmWI8hIt8M5MQsOggVHe>fP}tX?N$vx&`NU_l7e-jdG_3$clAW2UF$Q
zt!c}AS5n>5!l~BKU0>KqIFQxL%=8XXaf=HDp)<4#Q_At_+PxfR!{(Y5o*T!XOe^dN
z`FeR~{E4iXMyYftebKQL_aRnw(aYcK=yQIB$i&c#MXL0({bqFbP13wMpgBtJp)yx;
zs(Cc8YJ?BXIETR{e2e~4AEF*?%c-2}bsZ}iI_GdX$0!{p9EQc!pt9+HkYo{<<nH$J
z1|*2lIz*sLt$gEAd4w+GUrE65FL}nbgu&(Me7KvgvCSJ&cpao&q$%NJL8C?n*olhz
zSM0=5W5Ta%T5om+UzD;M&4$vXd30W)*!oX{r%P}6a5d(6g;c2&FqrME4Ip*%x->}m
zct4vaEw%>PY=pBDuZlfMZa`VT_b*bKDa3zy2v;y!pTEwUf_Aw(Axmbk1)Po>1Lat&
zGcie&Wpn%%1rFAjS9Fd;rUF_}e!nw%W2lS5wgFepWNJjV_~K=<y}YhPIoj_4wSG1n
z&$N|8Ta1#r=X%269i*_(jP3Y@Ad^7Z(Mj(Jl}2~{`F>X{)^*EE$eB-Yfo)nnC`pq+
zw|6Tl$<CpIZ{R{TLZ9b`e66eC-m9^~9^{l@$FeRF_lg5dgV-<Kex_mZNo+Gk{%Akv
z`CVv5cXz%5)aBhMn~M+i4*vBPlC^EpJTPe#DD}s@etq|o?>+T50>X5=vg*ydAswy?
zL&plf@vC|Vko756f#}2I?f}fUR2R_hvks*;;8bRbQZkbFcbiMPf52opccPizDAB`m
zsMp$WwAI~ckHCJW?1_iTw7f{l@`|WUV54?I-8=rT>jwJny8pLKYj+2_U?8kPz~IW|
z_Sz(#OID?D*oRX+eUGY#5OH*lJc&tU3II-n@*7r-F<T#uBEM`<WI@t8yDr{qSNAqC
zN9_ofJP6Qh3;9%;<1!j>$BT48#yZ(YOFRX(ea9N}BmioQ%qolf`?KvcB;;v?6iYJh
zZ#3zmLHnBzwPO|`LZ}}nt?B3sC!A<LA6`#)qN#OW09K>?1aN4ZoL*7#$*hL1Q3qYy
zn@}MKv(Z})g`s6bdsq>OFDy5Ncf~?G?r|0}k~XV}U}BXmirR+(&etG&VEH*j%)lGV
zL;)c#2P66-2!v|x)?jcnACa2d)><QWYF&CAW`KmOpDJ3hdiv~&D;>USbR%PEr1&`d
zg#w~*BwK(%?R?SN5hk5v?o`b*f7En;J<htYuyW~<aSDuD9@RJrvAJWu4CsqgQGDSt
z>TolT^Z*3QX`Dp<c~aa;Q8=WS+iSFvi-(OvjP7h}L0Or0Bu)yhySfK1MvgU5v~0SH
zK}}AeH`k(>h#`D~21su>M@l=;4IHZqrcf+&G6iB$Wk2c^njV5xcbN7&DitFQ*$;Og
zVkl_-75Z|uO4%4cA_uLuIe?JkAGWsl%O6;E6x2EfodP!(eGQ$E12%g0=xHDn;i!Gh
zz@j~?7<J0m+|z89>UWie8DFOe#E@hVWD%G)>KnTdpB@}e!9iTbsf<wM$Y4=%5g2fS
zrgoIHw#<gH9k@GUXshk$Gp8{JhG9@G8@8|Kp<lztCTo`FAUc(=@1o*Vd~tGm{%fuM
zx)dP>%q9Rro&m5tOUU!~k6yeFQE{RZp6dC7a+Z<p9;p%}nC9fWm-*n_;6CHOLSe|A
z{r@dRihwRG80h8fu0ioK9tD7$#0}tl63R3MxC<^XA5WE0=VpmyO6zOSrbMs}0Z$<q
z%Se;psmg+Q8oqKm>f0ASvzGI`_+!j>y^h;<OmF*?^h|EYG^NfxX_WNYhnbt22c`ZG
zv>3$p%@1#e)laZ}BZCCg;)qC_><MpM6`*jptyJSt9N$L~2y+0Xxl#;AQE@X1@jbuC
z5ghQ9w`S#~WDFKa%-DZeS{L{uaMp)rdDdf#1>~eg{h^gz)o(CFl9R>uSO&=aflEuv
zRn~iPk-YVyNoCCOS&`@kPt8>XBP~s<%e@DWXVP5lk&BgT_}3lW%>4qjY0W}5Yr2hK
zbUA-xg4QW9;or0w2qp80T=#qY^TW+tiIyfW{S9P+8zv6k-;&2P@GC^V)ChPw40(+~
zUlxvq#0>(kb@fV#iS_)i8$8xnEYEZiC+hB-<5<qy6FlS^<hc=2m^AMD)mTpHX3}X3
zDtcnK$<Zk3H@}VhX1U^>zYZW!*uFMo|8;vfJrwZWJf`9KM!fB8O37rW@#BkJ#<;NE
zB5<Z<@q$pq<vQ9O!zPqJZ5PDInj!2GA0^RBCg<lEt?P9RufOzsOQy^3*%sz~^U?4;
zA%+lI_5bMXJzHt(TX(<Uc>Z(kaG5v;&?~51i4VQ~N4j>lmvK(!uI(@$u`4JuM()H*
zhZOGn&Ii8J!t!*%EaxN%f2aepHHOtncX+wH&ZhpJ93x%$o%m%-ty9c1h#o<al{x<)
zrU(GfJ?ZOnR0DZ&6x)k5tzrMe7k|^XpztnlF|Y^)WBIk&s6agW<Tkaaon{eO6e72i
zVLtqt@(f12W({%qBpKedGI_-)lX|^Pg|umef8gIdMFu{l2&m5U&7S(#5P?yuBHBF>
zg>(-uYx}ByBn%s+N|a6dM`K4&GgYf=$I${k;7?*>$YdBP{<T}2DjF5SANRTOjVuXE
zf)k+|jU=g7<y_9~*$=``1-L00#YU<8yKsXwe~2RAy_BI1hTc^&U+e{6d7rf6dhA|v
zQtT2XY^^>e`{*vB$Jd_N`OVbdshYxwF2&i?f9r0lwL96?nIQvq+ln>!{p%w+AQ}|2
zFR6~S(gvo1&}cNqfupcSo_8i|y=`9EJDsk`v(oqmQbuTt=s#Qcx@SA}DjV(bE9OT7
znd{V7frj|kDTjEfauxO5zpf7(7i^qLS52yy_k0E4d_YeFlKE(ssjft1Xrnl%uRXi6
z4mXc{X=&dR6A9CK1&0@>TXk#$3`gfX9b$B@00q+bU0l$uOC&LIfrg-F&*iohCOQ>_
zmN?rb+$uu^Nk8;Zlw}ne3MXhZFFuO;J=V)#@#nu7l6T1Qw+D~wRA(TVK>-*(F*rmz
z0gPE_&Y&`Z>YM)_D38E@)^p$)m-NJ2;sw_-@$_(o=NJ!t#=rgQO^E_aR%HS&Zk;Rp
zSE3OR|A=hRyuIC?at_s8b(}rjd5nWjmm2Rfefp7L-o1||l?lz~8i{A@ufZ;<(X7Ux
zDd8!hWZ7zy+uD)*9orVBme2;S9om&6VgQ@AG7fN=4r9ooQ@%$#diQa3jzh5hZZ)Y^
zNLep^S#Xs@(4WNMC;q#Mq94B-ohAhDR!kpXAK#we6t}#?{$x_%Df2W){G?#8z>;0d
zCD#8C`U>`UE-C)us2rX|<}36N8DXyD6@=UkLfp9pf&M&wV^G8@qO|P56!8S6lBh@g
zaXTaUqVE0h0FRjiXFs3jGpFOD-Hz^%nlrN|Cy;k88pV$&I^6Ny=Ts+aC4cwDL@wrc
z`cXR$w<obRnFFKMejb&C%3|wL6yE3geQTf4T~M$q(PVfK<E?g|$H2n?(yl{PA8bw?
z^+>G|>!Q0wI1`npfI{JMlNX7Vte!$2&IbWV?haOE%zKot^F_x^jPbvtOsRCR3a+2f
z$277gX`2T%`q7Fhhc)%j*oml3v_MfdpI}3EZzlPq;_~X3JRF9;q80=JxhWL!B-t(w
zt$|f4zxA#2DB=lX4w$t%esxJ6y%%%W%#|o?g|qh7g0VTd3g+r%McSV3g9;5Y#2YB`
zYZ}}~P3top@kLP_H@jv(b9+URD}tl^fJmo1KI5Af>jd>P)C*%h)x_oAXHHspZ*C(i
zs+53Abzw9}e_P?j&EC{UfO7ZB>It;0=jmPfbS-+eu50y}mrOb4+OfZY6Y---?d0Ag
zX*cxF*1D=?(Pt*uNWdhI(bTxj**&@7IZF5mmv)g^4DNO9$*zi*Ao{4iQqajTrMYU<
zX&R9;kIdKk3c=U&hyXY3=(%XZ*T43LPH9%i`>mZnt9MRF(Dn0%%&_y9J-2b;iN?ru
z-aj2eOuF-1`yCfh^*_2ErBK&>>$<OCC;4d96yHJNw3hyr9_FW9RQ#~dnDPVNd>*|=
zI`rK<A5>G*ZA|WO{rjdlmE3E3|9fQB`baG1#IopJ8*44|LPt0{aj2|y;X3>vLvNg9
zkx5phUiV|4DQtSN1@+Z9qRM9~M`GLrf^CrMhp<qu57IdDnN&Cpj81iz`@`x1Q<l}J
zP;gr69NHXkh7^C?Yq~ctvyAb4!H_fS$)%?L5!Eot@!~l#p!n_xF+KU@XIT!;izl4t
za^Frk^1jl+O-`xw6*J$>;~f&oMU}TwOx@c#yd^Xcot!^rW3+wjqbrb^4lk(Z(#hz~
z6G|V9okNHqSG#b(SCtb2F~i<sX*0wtRhj;58$8dErkW0=od_MVg$y(v=Suz@X`Zv0
z0_U|-Qx(af@6rKdL$Ad<_<XS>R7@AbgUX^F-JnAg(e4w!UN?_TwMO>F;7o(y3qF_g
z<Pu9aZG*=eAHUmPFIzVrV0PtyQoZudWi<8S+0f|h6)Vxc{!ILh|3|r7p{CvPsl&r<
zzYb$%-K6&PnY8t1*wKmE<jmjaTZlBx*RKR;?VWOYDlnY>qN5V+67`2pk2{Q|R>W(d
zeH=N<OI`GSe3~d_hv&aot9lZR+(ri)PDOW{27u)A+xE($#}p^cm}BBMKHB=BksoQ@
zq&cb=yl;I1aS`kVQ|(@~R>&R|?gxWO2RFv?s+6*k@qW1aJm5K20xHI}6%!tXXjL>C
ze9P3U(Lf3Xg@FIBwZDvtYiqhd;T#}Hg1bv_(nxT(AVC7b9fCt}cXua9<8A@cxCRXx
z+=4qD=-@Q&e4BHg_kKU_-^=I$V*tB*kG*QGsyS;`m7=l+<=*}`Y{Dkn#O;rqs|fa5
zYOm<1ht$bRA_74yBw=AG^dQbp0;(z4Z+<43i_?UL*v&3f2{mscfxpv+@vW5^6NkgC
zFFhY*%!q+)mayP%)grR;=S5mKq3F!dG^~bz`3g<~VP%k76-0mQHq~v-3(9b~6PVFT
zy8d_pJHlg<1aE(bG<aReYIz-vFpBX6ZS~fOY*5Qji}Yg3$jNwM<1jYA#pf#div{&t
zcT`}mDemi<2sH&#Gz7_3XZM$8yN4Wz1F34zH7_v!2WF>(2gV=A0TeGXL0Zz^3ZfG{
z3<obc?U<wY6IDO!-5E_>p099^c*Kj1;2%ClUT7v9Q6m7v2e6ITsF$v^?G#MpqV~0Y
z{5$<@<ubn(3#j4)^NM)C_>ND5*uBk;bX8dgU@J-eoRh1w6?Zt2*h`|@!Y!3Q#&HSh
zg*?9*M^BSvD1Fc%DyfIRC`FAM0MqEgiobkd%67V#gL0`$+8ChoCuzd(iP`Dn>tZjA
z^Nhi31WW^71Df20JKp@$TaK**U!CJpB@$F}r<AW=qtlxYnx~gEKye<p2fh-56Zz||
zwa$EPnTHxoOu4&pgMSd!i0;*klIDA8bZ8hPL_>`g<hUrE>(>i}A9WE`z(?ob+mlr@
zZDPpU{osW0ruDUp(4`BETwjx*WX4jj%^1d()`tGPhrgVb$`b@3IfCyo$CNp^)VBY?
zNtO<2h}Lx&MhJAkGxk_2@+uHyTf0l0<-eyh^A6bIm|*(FCBS-rgVd4<rnzY+cp!6u
z{Bnz5E*DowITo4JDv^<beAdOC?)=+)-EtrhQJt#4SG2_`*@Ev7#hdxI;+nx$9^omH
zX^+$v-16mG?;GZx4f6h{GZn&Xy}4h&V>D?{nu30!Fs2C$nU;I^S>~F_MBHQuSNb}g
z);w^I7yLceha3eE_0EyVCjhQnK@+D(B686Bcl@(m8vl2CaZvs<-{=M3xAZ#Apl!eA
zvb^!>y7N1|e|%^R4XpVC@0lMz`Ry{u6flnbrO#TaOl&LQA%cBs4|6xc<VQ$4liV&A
zp3Kytp@oB?;ST##T$jtdC{i%=HHH#J?jNyxh{Fm`jk#VGHz556&n@fgu58?%66QQc
z#?1vPGCP-`>PJj^q*tX0_}GTi*5mm;EaG`q`OTk>`^ZgaYprz*ZOO-YR9DxwFB)^m
z6HCcWMT|Fn1N#majMx_Sl=rHQD$jcEoD1jLKv$gZJB$^9`@;%wjheMcm>r|k%lT(j
zqEE&ra5%>C$l)P`YHNWP-1y|w>G;T`OrEznA8=`naO|F6)L_A(cnuWL^8f?dJ(GL6
z+;T<hyN&MRs%snOEWC<FJOX^9#x$p@-%SvJ=`-w71pLf0xnxUkmbe(1BG&vWWi8v$
z9?uw`<Z)EjaG30|-j^?69mCgS*G;*+V^o^LOv4mCEx#@VTGU<{;Lb9R3uRY4vJk+q
z!6#HpZUO2%6J>u|vcK`P{9f9q4mieg1ihZGOGlU7*<MY6H)q-013qywR)&sckPt!P
zgYU@B1eH%PZE9OY0eLm=b)1^=*@S)j#FNi9>z-kE*Z?{a1ME7ZwJ3!=t=s*2+tgCP
zFlWP|^U^OgunzhT4__m=t#x`UD$4qC;C0t8EX}I3=C#LnH~bAK*E>CEO7o02I|X>!
zZG@s_z<LW6&c{rW`rjEnu#CL5^S?ix&3PqF^D;z2vYuz7C;2sKbRMuxkb;R0?tG)?
z)&cooyi#G%CdUpWrkOY%*Z=l5E@w|{8GL^*KjCzF4&t-7uWeY_5_&p!8yBk$#79{7
zxE@YZf~OKG*Vav2m^T6%%ngxY^J7HB=c{&%?x&U5XWnYf>#YAh9WNp1nKUmnM2f&`
zOk97Q@06+5I=8*wOsJaNL-*P`SPl6sN=i1E+22HpbW85!O;BR`0;EIhn)kDg!9#<P
zF!fIL+R6s=6KXW`L_7}$^rxQ3#Sj4kWo7H?a~Kq1jvx($MW%!9vs$@tPeFrDF;5Ih
z{JnKCd?q*ii8Y`o)mM<1^7iFaeXs@y1Kj34j|RV1KQq%&Y7@wBoGojd9c*INpD0zu
zAVxP)ukzd~??qKvIkHKc|J1tEQ!kqc{Ri>EurHsewrP6j7o3?C$`{{p6bZRtJDf}8
z9*VBuR4`d4WE>yG4P^t<4-!}+h&c|qNUOdbKYl>ySMur3rvk>}(8xJY(?N$U<3BC)
zyi;c$8&*x`R~q8#&!<X;32?c%CGnRmlNjqHQM(FU^a-m*=Zu^}70+M1;LDSfl2Av#
z#mSkg@vP?arxlrE;tD8!hq=l<#boZ%q2N*<u`j?>5-EcQ*2wNnw%l>l-_NC4l`R=e
zsC9SvP|5cuS}j~fGIQGuTG6r!d-L&1EKdiV47-i@gf;=Xb+Uo>^PM+uvncGV8g*9p
z-bI?+_IkFb=D&TTzg)-{DOZ;rcNyrsQO98by_SR`I!r(=cx}cg*^SzVhAkq<Dp{8v
zfT;UecmkO0a!czwU$9CxMK$o9?=D+F&`&EJRl2&*IHhiiv}THQl0*u<D20D42DV>y
zNG)6bke9Zsk?cXD{PzgMbgs!e@N*$)UBlW=+{lQ&!P3^=G((56Q&kf8d(@vyN^)G%
z4%lk1^mod>WD5%GoKLS*ORDN}uk4}Z_C`pnfxMcEBUlk^catmA_4}D}Xs{PJrC#mh
z8C5KvyjPlKh&qcMqHf=ZseT}5_H;H0kA_Y~hfBMaH>9&`09!XGe`gI-qB)|@H91|K
z8ANje%1VNAP=MW$iw`v2M1VK&vZxrGvx;<BCNKY;agG2I@Har*Q6NC7;XMF!boF*X
zw|ypMuda@lE00gq4HQc1WZY1ipu@y(zGco=pIYU6Uk{2{JK#xf#J;sW)35!pR4_}K
zXdbQ0T0F&c+^Pt{<xqLeoc56O2=S`=d+|ndUT6VKr^G3^iX)fw)%+ENTlH0NcY*%t
zH%-LSQkL%yuGYLL#nwt2Z7Cz7snN=fq(DH_AoTt=B%Qk>pi3V@pi`=Cu%B2e0H(KY
zLU#4RDN+eO#80U0_NcLo`O-g_giwO-l#L^OMT&H`NpKZ4*78+WMUEd6-%jU!G`0c~
z^`ELUy}r<`_~sM@pKQu6?$S|hY`qlgT<E<VqH&7(RzP%g@D&!#Bu|2A^5p`X1_|($
z)Q)Hf5mQXk@+ZO(bj-mC)Q%r!vYF)JekjY}h4I5D6I-D8ELHuSderkNhrsY=)7<cG
zNTa82u+J=mF;}>6YZfDkZoB$PD*%TE2?(mzpTvybM5&F7TvSu9zWJozF}t<2?e_Rr
zsQOGVVB69ip}%pPSL{C7!|QBTdI|Cmm>&4xnm=b+Pf&+<0an2$h~S^ABhy=iF<Nss
zk78XP+IaG3NKf+~n!DU&^S^m+N2Dz-{e4H?2Qpm#ypV7cX5^m<iK9I3Yz(FP0V20Q
zIeuWQM^y>!sqS<Qv(cLK+AoXgcmAw^9WFZ2;hALgFh<0bDx5NBYj^IstIQ6E9(N7?
zc1;CPpMgD2INQY#XTXKnE&X2H^dKRVq)JE1+c-P9;R0EK^H1{cqPcjN{h9>d=X=un
z`xewXXuDaJj;nY0P9(N1Qq;9f{|UI0WuIC`!;bm9;$n+1@zcdlumh)qzi5`Mwq>cO
zmK6*%`g&MQCeO+vHrhGbU#RN#zR4lGzdj_p-&L+ojO|rkZ*<BoWO=8=Sx9GI$t7ho
zHtn6&T>X9eTbS?NTNtVV*~IEyrGDlPx-1&xG153?qm9?TLyGlm7o*TA5moJib9=Ji
z<<jU<L`bK=5baX&SLfYYpr*&KxLHCm|2yRMo1fBaKk9-_^{%Vl3plFiCKr>u%`(vB
zZEL?h!X3$?$QAL4#ET%kT76<1A{5QlC^{I0{^Bg)QQ$M8QxPH88A!vh-G%D%6yKXg
z*kpg_;n!*N5bx*!JuVN9Q+npX$hfi{MujJxxbG9gsZK|KKfHy;YcTL@W^DAg7Ky_>
zyQUYnbeo41D)}yL$rdmNE8OBW_EAJJmz%z6yccf14uIu7Zt4~5j5EpK49ri|aTv*>
z)_{WcwSRx1Ni~>V(S1*Dso(iyoazxS9h~1Hww!|lAWta~aho_(z27!8RW>xm`G#1v
z6j|<;Qeb9~9;b)~1A5HvY%c6T(M@yjF~|hW99|T9{5T~I>{R28X)>u|>+v3aj8vj0
zW#B`OT6jY2^gKJ?XTqq6wf*rC&?L8n%CH(PP@e9`?I;sq?ayJ|RK~xcbm6Oc^wpXH
z&6x9KW=WQwwyJ7n1YlY2-omX_(j}xdu0?WXTxJ%f^4h0NT7KX(-9N28SmdN}oOsFf
z4d4V{{_wd>(1^9&#r6356WXBC_(|H+YM!Y{om3YY{3uJo?CP79(6{mo7NgrG>)e}Z
zrv?_5>MA2c*gzxDMXq_+DiMepWyOAXCQ#;?I9K$X>&NjKwT_EDjgwuiXzB)2J9=%}
zSk{1sD%lM-7s{>uVPe-W0lm3V!3-rQDZ@2%?K4rX$nX&3&h-GhXjEb__mJleN}7uN
z+3m=@=gy63=yu_c@)^=P-})i;`%^B(2@NNah$}X>`qs5=Szr_yUYVumWmq!R9<M+4
ze3SKW`Fp*m=@=mb-%lX2&c>-7WkX;xf?*eO_t!<V$A|U%+fD}qzX_TX^5T^z2?3qA
zG@%=<E)g;G5vhrI5e((2eqXj<C=iO^715biifjNQQ`;XOS?%pyJ&y+jx$w-Z)|O0+
zE95uU4R#621c1QP!N>r5aph3ZxHE)Te?MB!C?F^#A#h&9+B&0ED;B$p`NsZxV^lKw
zM5Fa@N#Wz8&y|{JC;C|dP_0gN;e;S=wFV#B$E>G^wsTo&@mm)o;jzV{nNe<*yWArA
zp)&jys_Vf(?vd8Usm-gWYmA+;iu-|yfFRfe1;YtB`SP0)m)oMyX13~+xm1F+*3N-D
zKHkahR=#SN%MVWI3A&3q-Sriy#st000CDE$oD+*k7$m+m%*lZ5<+$wj1uI##-}zST
z3iA3I3hU|VL6WGs6Y#k5ONB*`Xw6$UqHvSacb?xn`A%#$&O0P--zaV5l?v#M{o|Bf
zpfSb%PQis?&sc>9O=xxp>x)a}#I$n^wPQvm=<MEQ(DV3#XKt>|hh?_EMYa+!S!3b&
z|G5BQY$6%^ohme{r^#*;g>CgHax9Lr$_Dy_*BWp@)-$%3I0&Q_lC4`@!~=aQ@?Gq3
zzlZ^|-CD1^oDzW$|K}rrT-YnJELUh4a00+_er%x6COMICQZ;{JyBEjVWPm=7t$Kvy
zI5zf3;owT8SVE{;aeW;$a_fB8xh&6I>lYJ7ixCX8EPlG?QOeHP212%*qT_anG7-9u
zTq`RBO)pb*#mf(j7YS8g6*6s)X%WgL$6loJ%K1hfW?))pz9VHArO4d4-X&pR7?COp
z<sNGB0*1<ML-$!Nb&|T1gx$Uz*JLv(p&>>9GqDeRt8u-3H%EISyz8kvF)y6EfhAr5
z_q%rVB{RaTeoO9cZ(P>Nm1sL$;z&B$6!q%X%eL{E)N_3<nzgJjH0fds(8-;lkg|1)
zHXq70<y!uB(vvJJ;AR!=tgX(7rXtLE*PE{C&}ZfsqLT6^l=>t)=O?J`rYi1u>9>c5
zS-;$Xj8BavQ2gySPL;PkY5PF?l2G0TC_@2eDl6yY!WQczu9vt5;j3?IW=U_0hzFBg
zBXIcUmt2u?DzgmMj8;BZsd#}9q~}?n+Vt-1gAFCkXI{oWUNGos^raUMWjeQEl2LUU
zQ(AkDv8G(MaRhXJ$?u2-5)(DyluZ+suZzYM){mXK$wVU;EkW0+iXQ$h$55(L<g;m!
zY?6iIN3h2d#>#$q(Lg{qDJC9rZ#wrF5LVwlq&t^iuYJY_LM1mlQatmDS<DB2scNyM
z#RRWnfR`gq;KE}f1%3(@<ByKc0fyspI4p<<-LBNj5|JrFVwQ#@TVvPH9^gqc1IFcr
z87C73Wh_IJOw+XKE{PdY98>qW<q*Ye;=SW;M*htxuc)Mvo?S)w9<f4HIRH*vWIVbf
zbM^kXt8o^V!)Jdw@OFN;0mZXZp;@GOJ*MU4K!sFo8*6Ro{YDG#g-leG49P@uMrQe^
z@|Pc&;qTL!<fCNeYNaM>TkeluDa`W$;l@6HE+WF5L!-5#7QdIfyE4ybVsFK9^^A;a
z6$kug*e^IR7ka00{eg0(-UG|!n){VsM8Mg6^w6rb@?_iFFc5P_*7sAJ^_FhHKmv$e
z?7U*^1N!dx`1pC(^EEq#R7W|b%lO{N#fTSaUJ7ul!FJWo?leDw-zTVU)N*L7MzvkO
z#-mF0rr(Hx#h*Zk#!tiQBQD9au%%n>#$ZaD3xq+ilL)aNeKM639{!GBf%6amz_&P*
z4>^4zqU*;tP?cYG*@o<INSYU~+q$lBUwBnz<dk#p=|QyuZeCxtx0}l;<))X;P{1#R
znys3Ukvc=L5#}3Dgni~OVy}C}yt9s<7JV9)-skdjjZ{CL5?M7yoZn4}RMV1{*xFuR
zGp_r^^pj=j>#h803-JBAJH)A+YxLQ@bf6q>#`hQ{&GV{*pvrJvJl+Q*Vl(2YH~INg
z@lB%4^YD6xb+n8n`Jy;)O1fR_dg@~A^t8d!;BB+r%afSGVcL%|+r}5(AN&eKQ-Zn2
zROGot)JoJ(DYJ}0FLbSm*`>j%2cdk+59NJT9I`8Lr)FU-p&91_;uoCcecwTio@Zq-
zAaZNR+ZAEM4M&^Wp;Of}yhGa7RWZe1CIY$ULk7m_#99jy<Uqb*pv_?wnB$lGG;FOu
z0aWSfRkLk*W8RKOf2{SRXr9O;Xa8qz?=o~wS%?Oy%H`N7xru6CGBAa(q`OF$C0z6m
zP~5R7G7)B~r>NeWV?N)@zda|Dm8akSGb&7uh2B9}M`y)NB%!GL?X8C9$j{CYll;Fv
zd>X(omlOPe+dYDC75Pd&0EH39;`TV@pD|?&_a;n)66Let-S5F&vLVWT#eNtOXld0|
zYHVKFJ|?+~87v4ARrp#}RrO6k$?{lvGS|IH71R1uvnHxU>mR4BYkaY*F_#nt(Rfqi
zArs<MbGd2tO@3a0?^2@7vv95(Ws=XxDxbDW0Rri7l&UN~ipoR;O`Wi3!yq#f8Yu`v
zlQ(wqb*bl3%F8q_q{I!Ubg9?)G8@Qoem(rUEHXLPd1(1YY{<<nxVuCb4YjxMu=|oa
z)A=vF=ZsPD?=xx;Cj6i4NK~Cp2XRd?IUQX8R`M*qs46k=LFSGYQRr-#6T%C}qO$%3
zIc(lIn_3i5S8+XG!t_PzCu<e)3U7J1aAzxSM8>dAI^J#m)>yhs=?uL^u5Nb?>v}YL
z6olmo1jB^d;lpm(T6U)gMHiO7*v&pZcIzo^cfQuqESV-=XKtkymG`M#muD@x?=%0z
zhNBf3*D>;k!Rb!m4I77NT8b$1P_!wkyRkc|15Cu`vhjGamB+`bL%)eqPRz;FX=wTI
z9ZGbS>ARV4pD=;4Y!i;yR%e&w<Hx_a>yLY0@#C{j6lBZ;3br0OGqMyv4jE4j0Cueq
zcP(IJ@?0vaUe?l)A_k=8ih`3PA>}{}_2Hc}^;{MmJ3?=unl+V0{i*)RgoO#-*C$&o
zbBJZK*4i*y5QfaCtmtwSbpuB-8{4kj2lm+%DO<K!U)Wj1(U10&VCO{`K&X%B<aF)B
z0M`64F6+8CJ?uu%$orAMOnK~R(W21s$G)@iU)*qvc=ApWaag61sN4GTDXjD2w}iu`
zQrp+Or=3<rqX8gC!Xc`}@QEAvdD+a^xA1g#C*bUgTfz;dr^?zLU*1bL|FMd5xRbbJ
zkvFHArz>JMnb2}Rhnq9!XsI_?%cO<4#b2^c0br|8dMuik$6YQldVHBe%U>W-GHANi
zJ(K-s2ITV$BhH#>%k5_aALDa;v%zkJb=-`U^eu)eIM5q=C%wW@k9A!D>Fi*BJZK%Y
zN}pWXtM{&y#^&cPWdW@&Y%TfNfXFk<zWlh2v>)qDD;C&?h|b&F)wWC*uTs@cQ39C(
zxlEig5_#)7{n|y!*fJ)V)sa!TwO*3^U-)Yy!7<yS(e)?j{Nf(^&6<st*Z%OU)TD`B
z+8Od3h>NRx@awW2rk6(|l~0sB9{PTNeXgDw>&U%FKWfxMmYa)&A{T70GQNii%T%_A
zaUpx51kp86`sEErl&HeJcFK#|AI4b?1J01EJDVa^`?=x3<|JZxdqv*zZ)Rbj*YscJ
z3d%;+lq8J`|B9U8yP`kA0P<2)(u$N})?$N9r?bph6Zm0zXi?a+i&XwbNaBa?-BpIt
zQ!Rr5O2|6%(Dp5MOKu!Y2&rIj#~bCTB1ARQ-KNH&B?T4@gi;TNQe`}!`6FX~GR*VA
z-xGPPpiEIle1JgwYwdi*UFwx{x4*MCm(RTi=r4UZ{JyR1aV^1o<c%V_NXi_@&_LFP
z7}Mlb@lgNDUJ?~MIIa;h-gL?uOGoF+^q0#FF>VRdy%{R~J~<phwkmF&wZG2h*2(>|
z4671S9@xpSXxn?`eG~pZYWWXI2S@Z<ci57j^@87Xxut}k&1)_mpj&%He7C>QcDRU2
zj<pvnTuu<j_j^^gN6%8Ays=2-{o`QJxJ^2k{x}bH2^@C3<m0VUn(;=d?oNOBnj=M%
zDQD_qb4}P;#w&b-K@0CXMF=U-yVggSeROOtntl?+)BeEAV9lPD<FP^Ad8jUtdjw8(
z;x_xQVYB~t0{PnW$M>HrrmkPlcMU5C_@+MHbUl@+SBR#5=`Ju;^XZ|smJ?PuEve4k
z87|QP+Nd63If_K&AHaXt%a*Gn&S?ok?Owi?CAF<`%MjxJDR$eDmsm<7vB4=|usPa#
zBl18}@a_B#;O0d#v;1y5a7Oqttspl>j}ZX_qrN$<VQBu_>>|o`h1$ATy<%Qze1@$`
zE=95~mCDsbaIDAbG$4X;{BzAc(dC&`mMeBC4lB~d%E*P(ITrtfkm=ozJ>61mdh>Q3
zJ0AQ&2fKLWYqQ-ce$?{3D5-4!&Q{;F(u1YHhez*!*xWfP1wASW%;U9zQ1WRl-;Z_O
zv0J%^pUb{O2!d&oXF|AC&;W+Mr@Ob7F5c7$SjJfhWn~r$)t-w<!Oz-Ov|K@f!R?Zd
z{->81hTi*vHe;g4tW{@gTYx0Ncf#1eVwf*iWQZ?UXb9Ll*9lWKv@}TLxuQ9D^~K$8
zpuQ@gTc-0Cx7a6a8*=?p(?Z|wyN)!pLzbDfud;q0u;O5g<bvEk0m$M*hSi<Jif|-b
zFVcJ$uOckzczb?uxyI2S55xrFwOxa-W)*<!?Y$<p)B4_$J2q7BlJZs*mMa(wB`na%
zeT)1MX>Zw5-!YfT1tUt&g*ct}af4ZFDPjQ7D{nn6<`>#KSmxd&=IWXR=tYT$G4M|H
zjfIk^&!a0o{<9t3<sw{Vc{XO`9c`5YFlQl#NV;lSOgLZ>d3vk>twz{QSpo+S(6E~T
zFB2ssUAH5YieJ6rAFeaEVtjqiBVsQw6oqX&I>B77^I?C2OMsI6q%luOmb~ou9!=Hp
zXPu<#`vbi5Hk>J@fjT-cYx$hKkRN?zqvL!O(n!<w>HNf}a%6NA8~{h%ur)@V)MoBI
z<fqL2Y2BLj0DA&M1G(GY7pIVCR-J9B4W?&(=ipKqaIw=L9H@nu{2lW|aLwHQ&gX;D
z*=bUPk%Ev0J;U&w-}${Mx72|%uci0h&P~VWQfKj?Zt>`>sF`RN!&C|M9S%gGfyaUg
z{nJVi9&7jG+^@?i)5YaWc$B)}zS`}e_xTBL)X=nUs|!A9_b?3KF#(-(m8)FDoqn83
zbEZ1loiOOW#gA6+|Gi2=7(5fmFfOZ4)js6w7%lKbM+OJ99=|?ZWSl8u>uRuF8PRB<
z$-_J~U!cn9Bvf$8&1MwmHNw9qzI@`&P>MXG(Yh5Y*%@~R`6k(f@cp%9P0{=#C|$s>
zbBoaA8g)hkF^e-^lYS*v#i>f*!X*6ON~<<(#G<`V#x-R2FKI41-0TDJj%FGe=a@A8
zy*i@R4M4ocp@0);qZ0}D%u;9OOiljwhC@>~`CDuqRK-c8@O!#5<-+CozFjGPhGuaq
z3$loH<SDwAE<e~TrIfmx0*eV(azmG}b(+pgDccf|h1@!J`<9RT-W(C4FVD{?y_rMy
zD-Fh8Z>kOJOOod3T(G0XR(weV2H8(>d?YDGgLw93L@`$!J@|w_Lz@B1)v~K*|9|Zl
zn|$74^Fv4&Z8I6{$_GawCQIMn!<_L`=+@ZYrl}gaC~v>ogrDQZI>5o~wk`$5_qy42
zUZ>vi9jqVrW#|An_o4exDJQ3G-^b`?2Tv$Z?5rQ^@o>M3xYA_S4s!DeJ`b}@sH?HL
z?zRll%%mIhg58pe`JM?r7>~Mkj83(p`NPBNvqd?jAqU58*{7$|3;;;PYDf2KLzucE
zw;(mo737&<QfdWe2r0zu11Z4#WvVG4SKwk7=kC$>%>O-=aPc=?Xe;__$|su%>>&=L
zyOeyWYfo<ywa~-8!rQ~h*pDUajbX}x4kv2<kf~B*aSxG_{=>3uwTs{+YUXspD-Zi)
zhF*{P`X@=nI6k<B*vxM2xFeR8oT1~r?SKM$9dAgxLcjfne8PT6GhhIuABU<6gDl!d
z0rT?m3y!;HAh4`M#n%{SIzID%BEXD*@ss9Svi=yCX_u<v!sP)B7sG>6IUM~AlP{de
zn!eIg^Fzg(a2+Z=pz)YXsC(SlH6dR_nib<d|8y@U|LE=D(24-V%1s0zlZE`(9f1xy
znHThf60f4f6aSDrC$Dk2`#BFJG80iq_2dPeVrl7v?1(~gn0k8oCrHehJI#xxT(=^V
zpsGD36tXXn;tkMWBT5d^kGUZ0$Y-0QPlqauVUROlVc`$X&yZuZE?K_`jNUhv3$i5m
zxiw};#!Odbeu(~>v=oi3h$d#0H)2@hKS-SC^IsT-&Y{4DW#yBxVLA0V<>YZ1xl+%-
zJA@drc^{?onA3Hwf%$PB^=L-Hj+ovRx#$klQ~;IvWx?_3XvWL&ymVSQt}2k->E*1(
z<E7Xm+SpMdlibaeUJPIZ{jE?ca?XI2ByLl;dW9lV)#??WIv)@0`X96Ot2_ejx~Cbr
zOaUgTVA7BM8Gk-_#y1PD)2g8<&vy=Oo!EiHkAvqFy<gw=92g-}&oJ{L6GhEN+C1>_
zYx#YZyTX?3W!$yUyLUXJsv}{4w>f^g^~dOQ%9VD4eZJfH<_QQ0LCv{3rG*U2NZ8LL
zCUQ+~ARDbw4qx}*^sPsyEy{xzBhzZaKK8Q(`)b|#y4*H@(w$OhZV~j%vHvkNq4+ei
z&|}<_u{pfqHte1QW9STHB`>b2>Fd3_c(SPOZB)V&sNzse0Y=v%HT9ZdPe;*$?+oOt
zVp!>|JWX9v$EFhFjPu@avjps(zZ70(P>ViZ*ELHorDK8h{6X)ub17N<V^yNG=+rv3
zKdE4nBwR$0KwQk6q59`pP-Y}{L8m5x#>{(6a>VF0e&xVAtzZ(aBfq#?&-?dmZ{QUM
zdp-`*c@puuJ1Qtk0m6DKH|ijE1EOwO+>f>4z<AbkosIpg=L&}>{xvWTT7cDKH7a)q
z^^jp<dMbuH;g7s?z^cPR#n04-E%eB|c*SFg!2HWK{ssANeuHFD%pqm+a`M}L4tcqH
zUq)hdVGqlUGynIpfas=-q(kDJ_;yIe`H|(FFzP>@`x|ZfjS9e!l4h!RDri=25r8xR
zpr(jRP?oCkp`wm$N-p3^k)La_IE(@#Sq4hvneE5!9TI(~G7+GWuZ6_k>aX-A*B_7&
zN#p1NMcM!^uRN1vTQsdcH>tEzc7j#e{s&OXc+}}XQPIC#5%49}QUXF#rwHbXr1ePv
z2Y^sHN^OI)jYz(`If7fDQDSx#IeXGM*zmAa;O2zh@m;#&4IN=`yFxaW+;3FYm?pF)
z$CK}glNIr0(Qln|zV4GNEb#aA)=QFaZpr6O3NGX)p)^tix^HdOvWHTSbCFx)2rAV|
z@kd9Ct9<abR?IdxV;OAxZW47q?qpr)6t>BvKw`lxZ?iNN8BWD9%q0lLo+3=rw{|We
zHfL5v^<6H_kt)_D2)HI@A7n#@9CRM`Ur0f>rw+gIUrHox=n+cnU~fzJAI@2Q;EN(I
zMtd7VxysK*$#}KW{4aCi|9{eqOrOS^r*C&FnEptPPjWx<iuK=y-&nzH^t9<%%u{65
z4{*UXks87DAP~)N2_lH5T#!K3AoQhq+xdbz;9upYZOe%AUjR)qR8Nm}B+@LNiD_Ut
z0NPr#CSfB4SCV7qo1>?DA3O|M4m?9O(BMsrTy!md2jn&E4*gc7oQ9c{9K`g+g4dX~
zfJ~~e*XiSI5|EWK^l`{w8ge9$8T#^}h;+?`<YurRm$2%*HY|it8cSM%--=p;`N1|L
zkGm^`R=Bu^*n&cz<dYM_q?JC2W5qprWs%JavHqX^nXVyyN8Bj7A=%hdQD9t&0|8<*
zLZze?#_<jReA}LX>bTr#dQ1-0q@pI=OuP_KKolO09;g$AyT6pZL!}v{>FAnqfG4ZF
z8(8$<&j0wxSptaG=89<Ks?tvoGp8bFjT2_@FoxqtE|h@IYRUe;rsQ*WYeFq`KG6IE
z*!+NR#1_mCbPQk;U<J(Qi}t*~W8PYASe1lh_fNwhQ;|PlF5mRcYnR^)#nf<8UCFy%
z-n{R=yojxfE%7IU@Wj*Cmh|CbTavto{2h3wVwgPxZ1_HsE9X%+6$0ykZZnsE9W;n5
zs1R6Jcq{A<Ga{b%y2Qu_Y?ZQccZ6bOl~(wqC6mNQV%~gmNCLun<CxeZgPNs}f!))C
zyA6L4oK3ebxr<bSC+tJYtnW-gOJXE5m`^||oee2EkBs*C=VwRSn!moS-ZM<dTK~}<
z#!hZtsA7?V)jHiZ%tZCorhn=LHDmZM3=tgOJZVL4J>^LDdsT3(L7>V+eTAIu-LD8=
zx6_f9t)JspgZ(bHJER&2)%;zg+BTP-yJPzRVeLQRY*@mruy04Gm3a>zN%MLd7zmmV
z_PC{GW39rYC$ZvpvH~Em3hSK@OYZL$g#9JwWRI$9K+;9{U>utg+&c8C@w6k2=on~~
z+XO28LVv3N?EK-6oYtlMqU+r*hiwRh`UJgdAZAgHgMBPKHbaB$2nT&j{1RXI3Xbsn
z8k%v0({S7T-1XFQ43LqOmT~GagY?bki3}+gonEVZTKCKNB0_k~+r~FH$TiA-HvY^q
zW06P*dC<maUGX6ZWUOGXBQ#=Ugnn{F*1Nsd%mCc|R|9o=nVUeBwf99|wY7U_W=JyR
zJ^a@umaHHoJ0hBeKq=ysBTPWeD;MIK0XX+e-}#?wV&O!R)M3&}o%OD_&`)lD!Xpf>
z(XW)(>!ME4OL#EE=*lg!bJ9%&QEQ8fx4eZCoS2cyRoj<W78cjxdw}^xL9BlHmP-yf
zWw2{7wXvBGZl}fP$RHL#6W>Z#5jf>SKSVhQ(LskLX{d*s*?9P(YgG4hI%DHg$g7nc
zD|n+=V>r~*gy)+o8Hzw;mWL+#A2D(@)D0A9tgbgZ2}YiA4cyD*KPJFs!W~r6=y=Qx
zMJXKm9Vo>URc8*`EHHyJtl^4+QGcmp(ddIJg*!tT)I^*qzE+|#3xjsQmZLJ;{&CMo
z{a~v)`$kP<SXZQdYY>IHgbw6IE+o)fo6Pkhc1tv;Sb=XpX+JicOQMwPhfab7uekNc
zAxzZofk`YgBeyRWrj2RWiqkGW-EM-~{D^H8R4b8E5U?hId{?Zy!>@juN=5beNpMvI
z2#-!xi?>b8TcBwQU=T(8CHO7p5mfp-{LyOm-<zy1WQwhEa6hUeGC*;`DMB6&Rnfac
zX%6;|c0j)sJtXx47^lu#6*Mefd|(cbIa(>>Fgi44jl;sa1IW3899&U-EiE~sONo`B
z{De*P<)M!#N}o050S)PVS{9IKSusnU^l-F&UE=oclLdJs8>HC@6cZ)?s})-Rd-(Ce
z;}MM|+zlQ30}^3@LBXCPuD1CbWV$b*(<DI5$@(MSAypey$;I!4q4#?)$3AsfUm8t$
zbky%a<2Ca{H{$JnQ=?a}^}PSE(5tAx&)P>g_6e)e1X+7zA+;q6vl(y3BhKr2r#z{e
zSMTDPgB8e1V$ddg+l7t_tW00S3c^}C?Vvh@sqjGDpKHh%ZPl_i9e^HG1!pCSR`a&s
z%vAvuQ==k<94LPO=JTjzzIEwevG$mdc38mHOr+ckF^sU_mPE`L-Yr9;U#6+a$=P2N
zI68DkY`biH;MsC2FW?2(xY)rMH2i-f2U=CZ0)bmD&Q;mnbpE&hWNO}X=JLciOwfkL
z*?ip6;aX06Go;6)iWKaA&KZrwEbPo9xr?f&=>(BuIeHmgGQRaSH0sJkE-M=799*Z(
zl6gg9L91(>m8sU>?EA(2B{nydAq&m`97J>!GB>DtzNe|+D`+e4Yc+ygfsSq_dCy&l
z^jcTz(8V_4)1Qg80{j+rg?}DY6dj0Xj^Y4z^QN3-B2P?_{`|V@>7)^>J(qg~V12IZ
z=c`>V<`}>!3joAqt#~H0tV&4enN^Z-`k8gAK1^r33|a!oifAA)D(aZu;<xO-Z8;8L
zRziSca@?LHoY&I5|8qzd3Kb2{P&LyT|4e)q2UCXsF8Atun02{6dN?jylnFEPhLf{*
zxaClF`Go)+A0Mi4g!A8b(YRZnBEHC&+&I!_ghMpWb`oR6#-Jg_h7@f5#L@eGaR1O_
zx0LK!lO%}g7FRyaq7EH(X%|@;iP5w06anuDbm*ExW&0?qJl{1G8xR}QK~=}y-Zy=M
zn@f;Cm^xtY6Rh(@?BM<wI=0EmTS(TT8Hi6P|5mbcSl=<Y@?qY(%%&k(qwl))csOKz
zJ;-1ni8m_RilNdL0&?N^4Q4*ZmhCyidT3=lg5NweB};y~LhR&jt~r}I?0(dCEBt$R
z^Mc*egR)n$WZ1VAAvVO>;GB^Fy5G9KMpcxi^X$4jZU0jfa8M$Aj0aStgLD--AdNWz
z$pvjr>Y?UDA27>n5J{m%f})#BF;h-~Yy2EDfW*9|sv`b)i<kZ=t`IUrfKbJl7go7u
zz{}(`<f~lBH<Mb>@D`B@C^kMsh<i)-r(u)N$i^HNe=MAK`gBJ8Qoc}o&FAtjHyGcn
z^*PyDKWj-$u(|d*B|hSF_tc`G8lHKlqeajc0qTj_Ag}~-ZZG@>d1SvoFiF!vDsww_
z;AcUKiDiE1+$S^<$#v5vm7Sh)FC`E+sxZpU3k5bi1?SUAx+12MRWd-`St=Gy5{o-6
zY>7?(3x3!PirQbeuJX%&1RHNSUoLPvWdiz^6@9y}76K3e<%~`0LVYmLW)p{Wqw>6V
z_!$WqoG9+_Fzi9bF5JFJlNDRKq7fmCzudxU^-CXU`;n}CaFxLTc)^)?RU4+KC_|}r
zKbvj+LMb)ReA=L!5Yx?rPz#yAr^t5Rsd%vV1R*0{MNpPHYBo{nM-V=)UQ0HU$j5A~
z+RzYM10=%aBLp{(@a_u7_H+E+d!`@_3F^T#7e_NEid=$1*Z5-3#}@F!)O0daPTVn9
zt&50?Xdf;w-Vr$<BV?vLQe6${Bs^?3s105C;nEx7j6N4}k2nfFS^5IxQHb-9{{x1x
z5#rPmHYrLUPB9uZQ8z!2ysFAJOVpQ+UB4&73w;@{0hH>iyA3=nBFPW-uNB8lGiQ({
zm1A13u{6yHL`HDPncDhf!gH6MyZL?xZM$#_I}eKXiJS%M1nk7iEnr>6-MJg_euhCK
z;G-E{<K#I#E_T4S|7ml~T02FGO-}->i|T2)7J^}mW9*D<>2)i6t_7gCn3DliU(nA-
zYj^Asl*&1ojL}>bC4m5&0O$mDJ8)Ez3f13<%w5?^u5T{*hJ@{s8VLrZyk>-Hr&q-}
z9RGAkw$sTL5qwX7{wxHENn3{ve2D?rW$V&NS+pP+wkM|A1@6oRF5c`(Zm-qlN^Uo_
zXGp+;jDT0y?{Nc#NN0Jk_Q$L=bC{jp=toU{4`1*ZAWXSo&n?wmT4p~@{;ZJZGFyG%
z>(_MKGY*sOaUn;WIP?|Sr)oRyw0M9D<?*cukRFjo^wtZlw|%-J{UqG=X0|N#yA$LI
z86k?+Ah*H~+Ibi7<8cgewbYIm6XvnX`+`|Nx9aHt@o?~&W=4nRhprvxgg)Z~VwBRx
zHyVe9l3#5ZnPzm2hh8xIa?a9g(Q>Ym7|Cx9BTFts9=@U&^E?R_r=I*)*rS5<=SwKV
zV14OlefX7Qe8;!o5EInMlr3?ZY5zNHD1G#mP(uRkCv|x|dS<<xO{Kh_&VQXu3g89f
zGwyDm%cyYrtyTKd2zn`BfS7ARa`fjXB3Zfu)XzLDY(O4wur_+5igc^h<LOY7SvvFW
zZErf$IB`F-SJkfpMEa(QMErigO(EVYQ#H&Er><U;JgOa<#Nz%7w_6+_qe8!^G{Mh|
z1O_3u{2mq!I{x&kU1am%@>5#Z1B%$r)Af_#KO3(t39s274;=u_rme#C9){dZHr<E^
zB~g_rjyD@{$y*d{=-`572dS+`{&m@Y*I?MvJQY9aIpG8xV&oaGo@Kqg*O8%#Et;m}
zU;?Mf!<z5fonLe)GyZ-pJ%pQcOY&=T_JQdy<M9?AylN9nvJy&BAGzgsMK(7-Cnj!3
z3y+`yIS=6iEt`Qsf1&P`HI$V{!FaVg#mzf5KntAF0c*V_CTx{wMtvy6+W5M7E4!A5
zji7)^Ivawu>oi!f9;SBY)0qd0{>cFlt?lr0D`xuK6wgNG$N8E=sPNy=zai7Q&^GD6
ztv;leWrO|!MnqUAXFkW3-{jA&T3nEz1&UW)M-%S9{@twumLdQ1+XX+gh^cGM<1(+p
zuof=!p%|js{No>zV(mSo%KzXXVG^ykN;eA?uEz-YxW~7)vXmsr=Dtm$E7QLO)O^vL
zBhf!8mj5YI&8*bo1F8+OMYv?k|ERD~_<HtPt^$eMJ!K*Rch@Am!7{3gO<zzn@xx5#
zhBV?b-r&oA>|&vSPKsixKVBKfzB@xNCPYS?cl=?LLAN1C%m3Nz)PKmwSeWjrqI0?J
z``Hu<vRBo@%E62+W}@okZY(jN>j+72Y{Znyd?%t&Iuoa@WBn`=vf_>&u5kD1-m#z(
zbNt0A-ON=uLy=_uW!*nEPiEELNfc1Xy?9n=qWmM>Sa6K5kU)_|H?&}TS)SsnKX1Vi
z3#g`Z-?9+o(G6KQ#+;E$GtYhrRL%TJ&G0dXe%yFt<Bl!0Zem9>Pk5qyRx+s=HJ}~@
zNVkX0^K^NrQCDPrf<<NeO_`wX-K7$h@T>gmSspfI$|1-5GxWae?7uAwG7I9b1mEvB
zT$9Ho;st6P=rQ8c6p{ywPTjDeVi{AggHsX`WGgY{AvD|gs9g&YH3N5~D8YhV4+5_s
zcUH4fy0Q{Ts5yZ(lS@l(KIE>Q(Q|&qJRWxo?(3ABZ~ELnJpDBi``3Coy8lP%2+;m=
z`B*PN{V}G7Maemdjy772xA``<5T6<8xjxFzBaCr;{17R6)xK{ULYNvYOK$lc;)Wx+
z;l-QxRrsr+n2Am0#Hl<PO?MM(Md}MA?kvAAje)wXbSDPD61<(C%gFtX9Zsn?Ci*Pt
zjxH~MrEBfo5h<*O9`SBQP2*I*wsw)0^h)Xb{CkEy`i8lcmR9L(GxE%8U>e0a$~ztK
zW-DfLvN?d)@R-&}w)`2qarZ(Cd#X{_8kAy=(a@0c+pM<U9L&6OjU{fznEVom&9)Il
zStvL41=SnL3R~3VZr(_Q97}*y3;9dfFd<G|a7{c>R=&ibRb!ZZH8nX#AwrMD2EurY
zAQyX2*WulJ?Z3XSbBx}{kV*#6^}@}C8;*!VvZVsYwI;vdvFb+~jlGmik@&TB`Rf&+
zKDBv1HwU2o|MxICiKQBJ5j8cJJq>Y`q*dfI2?^8y@mlK6?ZwCNBBc37oVM@=Cdg1-
zw#_{6lrB_|P!1>uwJejYogt~KUF>b52U06{(%S`qv?VXIMDsOMnjctei3##;UNZA=
zD|@GP=hr5(vWQz`no;Y(fCUu|(jZW`b~#Ee=6^#PB7y!Rz1>!iP%a4&Ar&#vpvTml
z49~iq!W&@K0f*=+0E=EZUp|Y#z;Jmvvm&CtT`z7<G*uCTt<j(>vHkYLqWCZ7&@+5p
zNd6f{%3fe1sy?@XWXp#;ey=&HN(M=OD2pVKBT(&QsipEGW_+F*VT3%#f%;JG!yTQE
zPdWnKpP?&>3vsMp$*kQhEEE^mkO*q|d|LI+(1smsXXIT!g3yS$L`HT*{6X4ERGh-5
zE=vl@{eS*Of_@l=rg?`p5MtNGHz)@-1r0NLpgcd?aAWeo{~bv#eNC*v-NyD+;V^;_
zNqPDNVYNT<fQSf8Uu!3qgs<Rmra1KlE1JUUBZP2+pHMRJSfJQCKC!=U;|{~@reX5O
zUyO{>8~#tOQH3U?&e;5(xgq=7=*aIvB!U4=sv4cOQZ6$fQgcj9j86+vU_Q~0-~ipK
zTIj@!P`c8FzJSOj#VT1g)T0Z^#jp&TWVlIYS}>JdK@jXPW&g;lyao^?LJ&Se9D|m3
zSyuroy{?Tj#HskAd!}9NoghmE_5~_rN%|MBVG`&Z8}h?y7GV{Ub*cvuiBu)jhg$+`
zQadmKn?@)#zBoTTKLT1Irs1oc5dE+xYL&JeqRRaZM>k<$q})ZEa0Gnu0&+_|aQE3~
zsGihlF#np*aP5074$FHk@k&f;3G_fz2o(MpGj#M9A5y<{iAq%ed-3_$j2(>ozb7e)
z`p&S5%<<Y0n!9|60pU(t(=)g0crD&R=nNE=;o;FV+4;4j+(+`qhwU%f+Fv*sWa;wc
zuP02B>d*gdqLc51Y!mhxOKu2#)2G4ilN;XCjbLJvELI&d<(5Cj)P0HS)wXZZMKxuM
zf$EDw6D`g$L?D+0pX=A-kC!h0bLca^Zm{|}y;#`A3Ui{?iS_kh-6wf2MK#V6ahu^z
zS@2r`{}5icoH}(pspBy0Xi21CYa-HEieLZrHEoyj#HhjUVeuv!Uh*tIMGGa(KhuMn
zkF)h;O2Yu&SRy5;0TmdBk%+4B;#F#O{+W5x9rMvSmsETg+ocvLfiiy<^}~xeY>6ok
z6{QeR(HTLCu5_h&B3?hIjfi+9rEWq*7i!r;vr-_j6amc$stQUW+)nK0Dx%4M$0nu7
ze;JPf*smOs%S*k|b`QMgw6Kn@B4ibF`A8$`TIcWP{GoKi5@I}M2Hga~v5_J4Pn0#F
zKayYUtz#|5_TAj2HOuHp3f8yY;)gcQ6J=zBT!0-c8Cm#-Lkm!3tD@$5?Q!UoVw)Vd
zPU{w>tO-<mRkb()>Xc^P>;RKo)pFFjy~dL&C`BJyRtOD|)_iSfcT!Rv49EzPb^H@=
zXRJ_L4_X2zsm&z+M#$@~rE0rVT!7VnH-+YgxZ|`(CBD&4)}F)Hz4){!)L-{`|C*or
z{6$nl!W*-=Le5EvUxG^&33nWVLLr*bKUwkL8w}jZhy^joTBb!u%Ze`ye%+$$uSq*h
z#F-Qz1>~5VN4-qK`KYg0I|7>~VtoW(MT^FKa<v$B_hyn*1&(SGqX@P0aC}~B;5PmX
zIuZZVHW268prF0|GP{AtpENk={%a{6b@$>;Q>F;;taf+zau0W4dp-z@bVDuPb~yu5
zQGiOw@#-cguQFic!k#P+_s44F;v!3GUDxsB3)Pay>DaMHY#Q-5e_PR<z_rtdID(k*
z^m3=<%XO&aSvR_=lWwTlC{G%nUI9aJ({q`SFBH`gK>M3WMv|zZJiUk3L(qKt1i5q1
zPti4{U&k{#mZQ)@zq|M>)`=gSQ?ED#EJyGEu85Ogr*N>R`3@9dv4s~M=wBKR0`qd3
zE$@ik1JpfyAM)>>2@oJC{DbzOvzu@K?;!@qmQs<-HfvaZFFaA8i+0lfP|4}>L<;aj
zBFksC!&hi8j<?5+hQfP8H#v+=-mJ79J+LSSIJ$kE`z$4bUL#c-d+S|4#v~VYM$U|+
z`pS2inT4iti>xexOAqqNIR`~l2BS|-Mws%Cse;^w(67VXM6CWJ7pE)H7?)I4^%I>t
zTaPXyhhrip`(vT?3qQGcUS3@zA|LWSt4G%MwLkt_C<A!05%qudtw7Pt7QeJ-y5+0E
zM)-pd`|HlLyON}<g361d_Sk*G`M28-SA0eg)z`j~K$$EZ`c~+W>aSlPcjHY;hv|nq
zV{CN#e_=zu-HMJ!5a-hl1etFLAmyHQrv(Js+;&5mZb|%GM%Irx`#Y)J*L&_L63{T8
zsiNNN^LGT#T?2qu9u8looqeO=@7_TEk(Svb_-KI+=EvVhhM#P_&z_~Yz>6yBztarR
zfYBCm(~fi6GEeE^Sqjik^e<ZqHvHcoW3fj5^UeQW^zWtQ3%&N(rvEO?|NU~nGX4K9
z_-~t|_wsZ6x6%LmwCC?mpZ}NSe7@U%U(oLV8S?-0PXj^!V>bTpZ8%~P{}-(O|347L
t;$JTH|9P8U4$RU2*G>L^c0&(OuUmLDzVS7&ya2xBq?M$qBtHlL{{XfYJVO8g

diff --git a/communities/microgalaxy/resources/tutorials.html b/communities/microgalaxy/resources/tutorials.html
index 44aa545c..eb1038d1 100644
--- a/communities/microgalaxy/resources/tutorials.html
+++ b/communities/microgalaxy/resources/tutorials.html
@@ -84,25 +84,25 @@
     <tr>
       <td></td>
       <td>Assembly</td>
-      <td>Assembly of metagenomic sequencing data</td>
-      <td>https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html</td>
-      <td>Metagenomics, Sequence assembly</td>
-      <td>Visualisation, Sequencing quality control, Primer removal, Sequence file editing, Formatting, Read mapping, Sequence assembly validation, Sequence composition calculation, Sequence assembly visualisation, Local alignment, Genome assembly, Sequence trimming, Statistical calculation, Sequence contamination filtering, Sequence alignment analysis, Read pre-processing, Data handling, Variant calling</td>
-      <td>2024-08-18</td>
-      <td>2024-08-18</td>
-      <td>0</td>
+      <td>Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data</td>
+      <td>https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html</td>
+      <td>Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology</td>
+      <td>Sequence assembly validation, Statistical calculation, Sequence assembly visualisation, Visualisation, Genome assembly, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering</td>
+      <td>2021-03-24</td>
+      <td>2024-09-18</td>
+      <td>15</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>bg_uniq, megahit_contig2fastg, ngsutils_bam_filter, megahit, bowtie2, tp_cat, quast, random_lines1, collection_column_join, filter_tabular, seqtk_subseq, fastqc, bandage_info, coverm_contig, bandage_image, bamtools, cutadapt, metaspades</td>
-      <td></td>
-      <td>UseGalaxy.cz, UseGalaxy.eu</td>
+      <td>fastp, bandage_image, upload1, bandage_info, quast, fastqc, shovill</td>
+      <td>UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)</td>
+      <td>Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.no</td>
       <td>0</td>
       <td></td>
-      <td>2</td>
-      <td>2</td>
-      <td>0.100000</td>
+      <td>6735</td>
+      <td>10837</td>
+      <td>3.783333</td>
       <td>0</td>
     </tr>
     <tr>
@@ -111,7 +111,7 @@
       <td>Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)</td>
       <td>https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html</td>
       <td>Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial Resistance</td>
-      <td>Visualisation, Sequencing quality control, Sequence contamination filtering, Genome assembly, De-novo assembly, Sequence alignment, Box-Whisker plot plotting, Sequence assembly validation, Sequence composition calculation, Read mapping, Scatter plot plotting, Mapping assembly, Sequencing error detection, Sequence assembly visualisation, Cross-assembly, Filtering, Statistical calculation</td>
+      <td>Scatter plot plotting, Sequencing error detection, Sequence alignment, Visualisation, Cross-assembly, Read mapping, Sequencing quality control, Genome assembly, De-novo assembly, Box-Whisker plot plotting, Sequence contamination filtering, Sequence assembly validation, Mapping assembly, Statistical calculation, Sequence assembly visualisation, Filtering, Sequence composition calculation</td>
       <td>2021-03-24</td>
       <td>2024-03-13</td>
       <td>14</td>
@@ -119,86 +119,86 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>nanoplot, fastp, CONVERTER_bz2_to_uncompressed, filtlong, flye, bwa_mem2, quast, fastqc, polypolish, bandage_image, upload1, porechop</td>
+      <td>CONVERTER_bz2_to_uncompressed, fastp, filtlong, bandage_image, porechop, upload1, quast, flye, nanoplot, bwa_mem2, polypolish, fastqc</td>
       <td>UseGalaxy.eu</td>
       <td>UseGalaxy.cz</td>
       <td>0</td>
       <td></td>
-      <td>6851</td>
-      <td>10571</td>
-      <td>3.433333</td>
+      <td>7147</td>
+      <td>10976</td>
+      <td>3.400000</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>Assembly</td>
-      <td>Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data</td>
-      <td>https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html</td>
-      <td>Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology</td>
-      <td>Visualisation, Sequencing quality control, Sequence contamination filtering, Sequence assembly validation, Sequence composition calculation, Sequence assembly visualisation, Genome assembly, Statistical calculation</td>
-      <td>2021-03-24</td>
-      <td>2024-03-13</td>
-      <td>14</td>
+      <td>Assembly of metagenomic sequencing data</td>
+      <td>https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html</td>
+      <td>Metagenomics, Sequence assembly</td>
+      <td>Data handling, Visualisation, Sequence trimming, Read mapping, Sequencing quality control, Genome assembly, Sequence alignment analysis, Sequence contamination filtering, Sequence assembly validation, Variant calling, Statistical calculation, Sequence assembly visualisation, Sequence file editing, Local alignment, Sequence composition calculation, Read pre-processing, Primer removal, Formatting</td>
+      <td>2024-10-02</td>
+      <td>2024-10-02</td>
+      <td>0</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>fastp, shovill, quast, fastqc, bandage_info, bandage_image, upload1</td>
-      <td>UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)</td>
-      <td>Galaxy@AuBi, GalaxyTrakr, UseGalaxy.no</td>
+      <td>ngsutils_bam_filter, tp_cat, bamtools, bandage_image, filter_tabular, megahit_contig2fastg, bandage_info, bg_uniq, quast, seqtk_subseq, cutadapt, random_lines1, collection_column_join, megahit, coverm_contig, fastqc, metaspades, bowtie2</td>
+      <td></td>
+      <td>UseGalaxy.cz, UseGalaxy.eu</td>
       <td>0</td>
       <td></td>
-      <td>6432</td>
-      <td>10369</td>
-      <td>3.750000</td>
+      <td>6</td>
+      <td>7</td>
+      <td>0.383333</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>Assembly</td>
-      <td>Making sense of a newly assembled genome</td>
-      <td>https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html</td>
+      <td>Unicycler Assembly</td>
+      <td>https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html</td>
       <td>Sequence assembly, Genomics, Microbiology</td>
-      <td>Genome visualisation, Sequence alignment, Mapping, Read mapping, Sequence visualisation</td>
-      <td>2018-06-14</td>
-      <td>2024-06-24</td>
-      <td>29</td>
+      <td>Genome annotation, Visualisation, Genome assembly, Sequencing quality control, Sequence assembly validation, Gene prediction, Statistical calculation, Aggregation, Validation, Sequence composition calculation, Coding region prediction</td>
+      <td>2017-10-11</td>
+      <td>2024-03-13</td>
+      <td>23</td>
+      <td>True</td>
       <td>True</td>
-      <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>circos, lastz_wrapper_2, random_lines1, Cut1, circos_interval_to_tiles, addValue, collapse_dataset, Grep1, datamash_ops, bedtools_sortbed, tp_sort_header_tool, bedtools_complementbed, tp_replace_in_column, circos_aln_to_links, cat1, tp_cat, fasta_filter_by_length, Filter1, tp_sed_tool, fasta_compute_length, tp_replace_in_line, join1, upload1, jbrowse, bedtools_intersectbed, tp_grep_tool, mergeCols1</td>
-      <td></td>
-      <td></td>
+      <td>prokka, unicycler, quast, multiqc, fastqc</td>
+      <td>UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au</td>
+      <td>GalaxyTrakr, HyPhy HIV NGS Tools, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no</td>
       <td>0</td>
       <td></td>
-      <td>5938</td>
-      <td>12067</td>
-      <td>3.033333</td>
+      <td>2144791</td>
+      <td>5917098</td>
+      <td>4.566667</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>Assembly</td>
-      <td>Unicycler Assembly</td>
-      <td>https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html</td>
+      <td>Making sense of a newly assembled genome</td>
+      <td>https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html</td>
       <td>Sequence assembly, Genomics, Microbiology</td>
-      <td>Visualisation, Sequencing quality control, Genome annotation, Sequence assembly validation, Sequence composition calculation, Coding region prediction, Validation, Genome assembly, Gene prediction, Statistical calculation, Aggregation</td>
-      <td>2017-10-11</td>
-      <td>2024-03-13</td>
-      <td>23</td>
-      <td>True</td>
+      <td>Sequence alignment, Sequence visualisation, Read mapping, Genome visualisation, Mapping</td>
+      <td>2018-06-14</td>
+      <td>2024-06-24</td>
+      <td>29</td>
       <td>True</td>
       <td>False</td>
+      <td>False</td>
       <td>True</td>
-      <td>multiqc, quast, prokka, fastqc, unicycler</td>
-      <td>UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au</td>
-      <td>GalaxyTrakr, HyPhy HIV NGS Tools, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no</td>
+      <td>join1, tp_sed_tool, lastz_wrapper_2, upload1, fasta_filter_by_length, bedtools_intersectbed, datamash_ops, circos_interval_to_tiles, jbrowse, tp_cat, mergeCols1, Filter1, bedtools_sortbed, tp_sort_header_tool, Grep1, Cut1, collapse_dataset, cat1, tp_replace_in_column, addValue, circos_aln_to_links, fasta_compute_length, circos, tp_grep_tool, tp_replace_in_line, random_lines1, bedtools_complementbed</td>
+      <td></td>
+      <td></td>
       <td>0</td>
       <td></td>
-      <td>2074750</td>
-      <td>5746521</td>
-      <td>4.550000</td>
+      <td>6026</td>
+      <td>12166</td>
+      <td>3.016667</td>
       <td>0</td>
     </tr>
     <tr>
@@ -207,7 +207,7 @@
       <td>Checking expected species and contamination in bacterial isolate</td>
       <td>https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html</td>
       <td>Whole genome sequencing, Genomics, Microbiology, Microbial ecology</td>
-      <td>Cross-assembly, Taxonomic classification, Expression analysis, Statistical calculation</td>
+      <td>Statistical calculation, Taxonomic classification, Cross-assembly, Expression analysis</td>
       <td>2024-03-04</td>
       <td>2024-06-27</td>
       <td>4</td>
@@ -215,62 +215,62 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>est_abundance, upload1, kraken2, recentrifuge</td>
+      <td>recentrifuge, kraken2, upload1, est_abundance</td>
       <td>UseGalaxy.eu, UseGalaxy.fr</td>
       <td>Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>229</td>
-      <td>302</td>
-      <td>3.950000</td>
+      <td>260</td>
+      <td>343</td>
+      <td>3.533333</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>Evolution</td>
-      <td>Identifying tuberculosis transmission links: from SNPs to transmission clusters</td>
-      <td>https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html</td>
-      <td>Genomics, Microbiology, Infectious disease, DNA polymorphism</td>
-      <td>Variant calling, Phylogenetic tree visualisation, Phylogenetic tree generation, Antimicrobial resistance prediction</td>
+      <td>Tree thinking for tuberculosis evolution and epidemiology</td>
+      <td>https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html</td>
+      <td>Genomics, Microbiology, Phylogeny, Infectious disease</td>
+      <td>Phylogenetic tree analysis, Sequence analysis</td>
       <td>2022-03-16</td>
-      <td>2024-07-12</td>
-      <td>12</td>
+      <td>2024-03-12</td>
+      <td>11</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>Grep1, bcftools_consensus, tb_variant_filter, upload1, samtools_view, snp_sites, tb_profiler_profile, tp_grep_tool, tp_cat, snippy, tp_easyjoin_tool, addName, tp_sed_tool, tp_replace_in_line, snp_dists, collapse_dataset, __MERGE_COLLECTION__, trimmomatic</td>
+      <td>upload1, interactive_tool_rstudio, raxml</td>
       <td>UseGalaxy.eu</td>
-      <td>UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main)</td>
+      <td>UseGalaxy.fr, UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>1533</td>
-      <td>2414</td>
-      <td>3.133333</td>
+      <td>1373</td>
+      <td>2071</td>
+      <td>2.233333</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>Evolution</td>
-      <td>Tree thinking for tuberculosis evolution and epidemiology</td>
-      <td>https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html</td>
-      <td>Genomics, Microbiology, Phylogeny, Infectious disease</td>
-      <td>Sequence analysis, Phylogenetic tree analysis</td>
+      <td>Identifying tuberculosis transmission links: from SNPs to transmission clusters</td>
+      <td>https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html</td>
+      <td>Genomics, Microbiology, Infectious disease, DNA polymorphism</td>
+      <td>Phylogenetic tree visualisation, Variant calling, Antimicrobial resistance prediction, Phylogenetic tree generation</td>
       <td>2022-03-16</td>
-      <td>2024-03-12</td>
-      <td>11</td>
+      <td>2024-07-12</td>
+      <td>12</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>interactive_tool_rstudio, upload1, raxml</td>
+      <td>tp_sed_tool, tp_easyjoin_tool, tp_cat, bcftools_consensus, samtools_view, upload1, snippy, tp_grep_tool, tp_replace_in_line, snp_dists, Grep1, tb_variant_filter, tb_profiler_profile, collapse_dataset, snp_sites, trimmomatic, __MERGE_COLLECTION__, addName</td>
       <td>UseGalaxy.eu</td>
-      <td>UseGalaxy.fr, UseGalaxy.org (Main)</td>
+      <td>UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>1308</td>
-      <td>1983</td>
-      <td>2.183333</td>
+      <td>1605</td>
+      <td>2499</td>
+      <td>3.050000</td>
       <td>0</td>
     </tr>
     <tr>
@@ -279,7 +279,7 @@
       <td>Genome annotation with Prokka</td>
       <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html</td>
       <td>Genomics, Microbiology, Gene and protein families, Sequence analysis</td>
-      <td>Genome visualisation, Genome annotation, Gene prediction, Coding region prediction</td>
+      <td>Genome visualisation, Gene prediction, Genome annotation, Coding region prediction</td>
       <td>2018-03-06</td>
       <td>2024-08-08</td>
       <td>25</td>
@@ -287,14 +287,38 @@
       <td>True</td>
       <td>True</td>
       <td>True</td>
-      <td>prokka, jbrowse</td>
+      <td>jbrowse, prokka</td>
       <td>UseGalaxy.eu, UseGalaxy.org (Main)</td>
-      <td>Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au</td>
+      <td>Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au</td>
+      <td>0</td>
+      <td></td>
+      <td>2149523</td>
+      <td>5925124</td>
+      <td>4.316667</td>
       <td>0</td>
+    </tr>
+    <tr>
       <td></td>
-      <td>2079352</td>
-      <td>5754405</td>
-      <td>4.333333</td>
+      <td>Genome Annotation</td>
+      <td>Identification of AMR genes in an assembled bacterial genome</td>
+      <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html</td>
+      <td>Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance</td>
+      <td>Genome visualisation, Genome annotation, Read mapping</td>
+      <td>2024-01-23</td>
+      <td>2024-09-27</td>
+      <td>6</td>
+      <td>True</td>
+      <td>False</td>
+      <td>False</td>
+      <td>True</td>
+      <td>jbrowse, tbl2gff3, upload1, Grep1, staramr_search, bakta, bowtie2</td>
+      <td>UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr</td>
+      <td>Galaxy@AuBi, UseGalaxy.org (Main)</td>
+      <td>0</td>
+      <td></td>
+      <td>1138</td>
+      <td>1576</td>
+      <td>2.750000</td>
       <td>0</td>
     </tr>
     <tr>
@@ -311,38 +335,14 @@
       <td>True</td>
       <td>True</td>
       <td>True</td>
-      <td>jbrowse, create_or_update, list_organism, iframe, create_account</td>
+      <td>jbrowse, create_or_update, iframe, list_organism, create_account</td>
       <td></td>
       <td>UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no</td>
       <td>0</td>
       <td></td>
-      <td>1836817</td>
-      <td>4949160</td>
-      <td>4.950000</td>
-      <td>0</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>Genome Annotation</td>
-      <td>Identification of AMR genes in an assembled bacterial genome</td>
-      <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html</td>
-      <td>Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance</td>
-      <td>Genome visualisation, Genome annotation, Read mapping</td>
-      <td>2024-01-23</td>
-      <td>2024-03-13</td>
-      <td>5</td>
-      <td>True</td>
-      <td>False</td>
-      <td>False</td>
-      <td>True</td>
-      <td>Grep1, jbrowse, bowtie2, tbl2gff3, bakta, staramr_search, upload1</td>
-      <td>UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr</td>
-      <td>Galaxy@AuBi</td>
-      <td>0</td>
-      <td></td>
-      <td>967</td>
-      <td>1368</td>
-      <td>2.933333</td>
+      <td>1906178</td>
+      <td>5119567</td>
+      <td>4.983333</td>
       <td>0</td>
     </tr>
     <tr>
@@ -351,21 +351,21 @@
       <td>Bacterial Genome Annotation</td>
       <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html</td>
       <td>Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements</td>
-      <td>Genome assembly, Sequence motif recognition, Genome annotation, Nucleic acid feature detection, Structural variation detection, Multilocus sequence typing, Genome visualisation, Protein feature detection, Scaffolding</td>
+      <td>Genome annotation, Nucleic acid feature detection, Multilocus sequence typing, Genome visualisation, Genome assembly, Sequence motif recognition, Structural variation detection, Scaffolding, Protein feature detection</td>
       <td>2024-02-01</td>
-      <td>2024-08-01</td>
-      <td>4</td>
+      <td>2024-09-08</td>
+      <td>5</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>Grouping1, jbrowse, upload1, integron_finder, isescan, tp_tail_tool, plasmidfinder, tbl2gff3, bakta, tp_replace_in_column</td>
+      <td>jbrowse, tbl2gff3, plasmidfinder, integron_finder, upload1, isescan, tp_tail_tool, bakta, tp_replace_in_column, Grouping1</td>
       <td>UseGalaxy.eu, UseGalaxy.fr</td>
-      <td>Galaxy@AuBi, UseGalaxy.cz</td>
+      <td>Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>1800</td>
-      <td>2378</td>
+      <td>2243</td>
+      <td>2969</td>
       <td>2.333333</td>
       <td>0</td>
     </tr>
@@ -375,7 +375,7 @@
       <td>Comparative gene analysis in unannotated genomes</td>
       <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html</td>
       <td>Genomics, Gene and protein families, Sequence analysis, Phylogeny</td>
-      <td>Multiple sequence alignment, Database search, Transcriptome assembly, Coding region prediction, De-novo assembly, Sequence alignment analysis, Phylogenetic tree generation</td>
+      <td>Database search, Transcriptome assembly, Phylogenetic tree generation, De-novo assembly, Sequence alignment analysis, Multiple sequence alignment, Coding region prediction</td>
       <td>2022-09-08</td>
       <td>2024-03-18</td>
       <td>8</td>
@@ -383,14 +383,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>tab2fasta, cat1, orfipy, Add_a_column1, rbc_mafft, rapidnj, bg_diamond_view, regexColumn1, Cut1, bg_diamond_makedb, Filter1, bg_diamond, tp_split_on_column, join1, gops_intersect_1, collapse_dataset</td>
+      <td>orfipy, rapidnj, join1, bg_diamond_makedb, Filter1, tp_split_on_column, tab2fasta, collapse_dataset, rbc_mafft, bg_diamond_view, Cut1, Add_a_column1, bg_diamond, regexColumn1, gops_intersect_1, cat1</td>
       <td>UseGalaxy.eu, UseGalaxy.org (Main)</td>
       <td>UseGalaxy.cz</td>
       <td>0</td>
       <td></td>
-      <td>974</td>
-      <td>1476</td>
-      <td>3.100000</td>
+      <td>1045</td>
+      <td>1602</td>
+      <td>3.583333</td>
       <td>0</td>
     </tr>
     <tr>
@@ -399,7 +399,7 @@
       <td>Essential genes detection with Transposon insertion sequencing</td>
       <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html</td>
       <td>Genomics, Microbiology, Sequence analysis, Mobile genetic elements</td>
-      <td>Transposon prediction, Primer removal, Sequence trimming, Read pre-processing</td>
+      <td>Sequence trimming, Transposon prediction, Read pre-processing, Primer removal</td>
       <td>2019-07-02</td>
       <td>2024-03-18</td>
       <td>12</td>
@@ -407,14 +407,14 @@
       <td>True</td>
       <td>False</td>
       <td>True</td>
-      <td>transit_gumbel, Add_a_column1, deeptools_bam_coverage, tp_easyjoin_tool, bg_find_subsequences, Cut1, Filter1, tp_sort_header_tool, bowtie_wrapper, gff_to_prot, cutadapt, __EXTRACT_DATASET__</td>
-      <td>UseGalaxy.no, UseGalaxy.org.au</td>
+      <td>__EXTRACT_DATASET__, bowtie_wrapper, gff_to_prot, tp_easyjoin_tool, Filter1, transit_gumbel, bg_find_subsequences, tp_sort_header_tool, cutadapt, Cut1, Add_a_column1, deeptools_bam_coverage</td>
+      <td>UseGalaxy.be, UseGalaxy.no, UseGalaxy.org.au</td>
       <td>UseGalaxy.cz, UseGalaxy.eu</td>
       <td>0</td>
       <td></td>
-      <td>2070408</td>
-      <td>5739476</td>
-      <td>4.250000</td>
+      <td>2140389</td>
+      <td>5910080</td>
+      <td>4.266667</td>
       <td>0</td>
     </tr>
     <tr>
@@ -423,7 +423,7 @@
       <td>Genome annotation with Prokka</td>
       <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html</td>
       <td>Genomics, Microbiology, Gene and protein families, Sequence analysis</td>
-      <td>Genome visualisation, Genome annotation, Gene prediction, Coding region prediction</td>
+      <td>Genome visualisation, Gene prediction, Genome annotation, Coding region prediction</td>
       <td>2018-03-06</td>
       <td>2024-08-08</td>
       <td>25</td>
@@ -431,62 +431,86 @@
       <td>True</td>
       <td>True</td>
       <td>True</td>
-      <td>prokka, jbrowse</td>
+      <td>jbrowse, prokka</td>
       <td>UseGalaxy.eu, UseGalaxy.org (Main)</td>
-      <td>Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au</td>
+      <td>Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>2079352</td>
-      <td>5754405</td>
-      <td>4.333333</td>
+      <td>2149523</td>
+      <td>5925127</td>
+      <td>4.316667</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
-      <td>Assembly</td>
-      <td>Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)</td>
-      <td>https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html</td>
-      <td>Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial Resistance</td>
-      <td>Visualisation, Sequencing quality control, Sequence contamination filtering, Genome assembly, De-novo assembly, Sequence alignment, Box-Whisker plot plotting, Sequence assembly validation, Sequence composition calculation, Read mapping, Scatter plot plotting, Mapping assembly, Sequencing error detection, Sequence assembly visualisation, Cross-assembly, Filtering, Statistical calculation</td>
-      <td>2021-03-24</td>
-      <td>2024-03-13</td>
-      <td>14</td>
+      <td>Genome Annotation</td>
+      <td>Identification of AMR genes in an assembled bacterial genome</td>
+      <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html</td>
+      <td>Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance</td>
+      <td>Genome visualisation, Genome annotation, Read mapping</td>
+      <td>2024-01-23</td>
+      <td>2024-09-27</td>
+      <td>6</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>nanoplot, fastp, CONVERTER_bz2_to_uncompressed, filtlong, flye, bwa_mem2, quast, fastqc, polypolish, bandage_image, upload1, porechop</td>
-      <td>UseGalaxy.eu</td>
-      <td>UseGalaxy.cz</td>
+      <td>jbrowse, tbl2gff3, upload1, Grep1, staramr_search, bakta, bowtie2</td>
+      <td>UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr</td>
+      <td>Galaxy@AuBi, UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>6851</td>
-      <td>10571</td>
-      <td>3.433333</td>
+      <td>1138</td>
+      <td>1576</td>
+      <td>2.750000</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
-      <td>Assembly</td>
-      <td>Making sense of a newly assembled genome</td>
-      <td>https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html</td>
-      <td>Sequence assembly, Genomics, Microbiology</td>
-      <td>Genome visualisation, Sequence alignment, Mapping, Read mapping, Sequence visualisation</td>
-      <td>2018-06-14</td>
-      <td>2024-06-24</td>
-      <td>29</td>
+      <td>Genome Annotation</td>
+      <td>Refining Genome Annotations with Apollo (prokaryotes)</td>
+      <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html</td>
+      <td>Genomics, Microbiology, Gene and protein families, Sequence analysis</td>
+      <td>Genome visualisation</td>
+      <td>2021-06-04</td>
+      <td>2024-08-08</td>
+      <td>20</td>
       <td>True</td>
-      <td>False</td>
-      <td>False</td>
       <td>True</td>
-      <td>circos, lastz_wrapper_2, random_lines1, Cut1, circos_interval_to_tiles, addValue, collapse_dataset, Grep1, datamash_ops, bedtools_sortbed, tp_sort_header_tool, bedtools_complementbed, tp_replace_in_column, circos_aln_to_links, cat1, tp_cat, fasta_filter_by_length, Filter1, tp_sed_tool, fasta_compute_length, tp_replace_in_line, join1, upload1, jbrowse, bedtools_intersectbed, tp_grep_tool, mergeCols1</td>
+      <td>True</td>
+      <td>True</td>
+      <td>jbrowse, create_or_update, iframe, list_organism, create_account</td>
       <td></td>
+      <td>UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no</td>
+      <td>0</td>
       <td></td>
+      <td>1906178</td>
+      <td>5119570</td>
+      <td>4.983333</td>
       <td>0</td>
+    </tr>
+    <tr>
       <td></td>
-      <td>5938</td>
-      <td>12067</td>
-      <td>3.033333</td>
+      <td>Genome Annotation</td>
+      <td>Bacterial Genome Annotation</td>
+      <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html</td>
+      <td>Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements</td>
+      <td>Genome annotation, Nucleic acid feature detection, Multilocus sequence typing, Genome visualisation, Genome assembly, Sequence motif recognition, Structural variation detection, Scaffolding, Protein feature detection</td>
+      <td>2024-02-01</td>
+      <td>2024-09-08</td>
+      <td>5</td>
+      <td>True</td>
+      <td>False</td>
+      <td>False</td>
+      <td>True</td>
+      <td>jbrowse, tbl2gff3, plasmidfinder, integron_finder, upload1, isescan, tp_tail_tool, bakta, tp_replace_in_column, Grouping1</td>
+      <td>UseGalaxy.eu, UseGalaxy.fr</td>
+      <td>Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main)</td>
+      <td>0</td>
+      <td></td>
+      <td>2243</td>
+      <td>2969</td>
+      <td>2.333333</td>
       <td>0</td>
     </tr>
     <tr>
@@ -495,7 +519,7 @@
       <td>Microbial Variant Calling</td>
       <td>https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html</td>
       <td>Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation</td>
-      <td>Genome visualisation, Variant calling, Phylogenetic tree generation, Phylogenetic tree visualisation</td>
+      <td>Genome visualisation, Variant calling, Phylogenetic tree visualisation, Phylogenetic tree generation</td>
       <td>2018-02-26</td>
       <td>2024-03-15</td>
       <td>23</td>
@@ -504,133 +528,157 @@
       <td>False</td>
       <td>True</td>
       <td>jbrowse, snippy</td>
-      <td>UseGalaxy.eu, UseGalaxy.org (Main)</td>
+      <td>UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main)</td>
       <td>GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>12166</td>
-      <td>20322</td>
-      <td>2.000000</td>
+      <td>12475</td>
+      <td>20692</td>
+      <td>1.983333</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
-      <td>Genome Annotation</td>
-      <td>Refining Genome Annotations with Apollo (prokaryotes)</td>
-      <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html</td>
-      <td>Genomics, Microbiology, Gene and protein families, Sequence analysis</td>
-      <td>Genome visualisation</td>
-      <td>2021-06-04</td>
-      <td>2024-08-08</td>
-      <td>20</td>
-      <td>True</td>
-      <td>True</td>
+      <td>Assembly</td>
+      <td>Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)</td>
+      <td>https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html</td>
+      <td>Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial Resistance</td>
+      <td>Scatter plot plotting, Sequencing error detection, Sequence alignment, Visualisation, Cross-assembly, Read mapping, Sequencing quality control, Genome assembly, De-novo assembly, Box-Whisker plot plotting, Sequence contamination filtering, Sequence assembly validation, Mapping assembly, Statistical calculation, Sequence assembly visualisation, Filtering, Sequence composition calculation</td>
+      <td>2021-03-24</td>
+      <td>2024-03-13</td>
+      <td>14</td>
       <td>True</td>
+      <td>False</td>
+      <td>False</td>
       <td>True</td>
-      <td>jbrowse, create_or_update, list_organism, iframe, create_account</td>
-      <td></td>
-      <td>UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no</td>
+      <td>CONVERTER_bz2_to_uncompressed, fastp, filtlong, bandage_image, porechop, upload1, quast, flye, nanoplot, bwa_mem2, polypolish, fastqc</td>
+      <td>UseGalaxy.eu</td>
+      <td>UseGalaxy.cz</td>
       <td>0</td>
       <td></td>
-      <td>1836817</td>
-      <td>4949160</td>
-      <td>4.950000</td>
+      <td>7148</td>
+      <td>10977</td>
+      <td>3.400000</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
-      <td>Genome Annotation</td>
-      <td>Identification of AMR genes in an assembled bacterial genome</td>
-      <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html</td>
-      <td>Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance</td>
-      <td>Genome visualisation, Genome annotation, Read mapping</td>
-      <td>2024-01-23</td>
-      <td>2024-03-13</td>
-      <td>5</td>
+      <td>Assembly</td>
+      <td>Making sense of a newly assembled genome</td>
+      <td>https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html</td>
+      <td>Sequence assembly, Genomics, Microbiology</td>
+      <td>Sequence alignment, Sequence visualisation, Read mapping, Genome visualisation, Mapping</td>
+      <td>2018-06-14</td>
+      <td>2024-06-24</td>
+      <td>29</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>Grep1, jbrowse, bowtie2, tbl2gff3, bakta, staramr_search, upload1</td>
-      <td>UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr</td>
-      <td>Galaxy@AuBi</td>
+      <td>join1, tp_sed_tool, lastz_wrapper_2, upload1, fasta_filter_by_length, bedtools_intersectbed, datamash_ops, circos_interval_to_tiles, jbrowse, tp_cat, mergeCols1, Filter1, bedtools_sortbed, tp_sort_header_tool, Grep1, Cut1, collapse_dataset, cat1, tp_replace_in_column, addValue, circos_aln_to_links, fasta_compute_length, circos, tp_grep_tool, tp_replace_in_line, random_lines1, bedtools_complementbed</td>
+      <td></td>
+      <td></td>
       <td>0</td>
       <td></td>
-      <td>967</td>
-      <td>1368</td>
-      <td>2.933333</td>
+      <td>6026</td>
+      <td>12166</td>
+      <td>3.016667</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
-      <td>Genome Annotation</td>
-      <td>Bacterial Genome Annotation</td>
-      <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html</td>
-      <td>Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements</td>
-      <td>Genome assembly, Sequence motif recognition, Genome annotation, Nucleic acid feature detection, Structural variation detection, Multilocus sequence typing, Genome visualisation, Protein feature detection, Scaffolding</td>
-      <td>2024-02-01</td>
-      <td>2024-08-01</td>
+      <td>Microbiome</td>
+      <td>Analyses of metagenomics data - The global picture</td>
+      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html</td>
+      <td>Metagenomics, Microbial ecology, Taxonomy, Sequence analysis</td>
+      <td>DNA barcoding, Visualisation, Phylogenetic analysis, Sequencing quality control, Taxonomic classification, Sequence read processing, Sequence clustering</td>
+      <td>2017-06-22</td>
+      <td>2024-08-09</td>
       <td>4</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>Grouping1, jbrowse, upload1, integron_finder, isescan, tp_tail_tool, plasmidfinder, tbl2gff3, bakta, tp_replace_in_column</td>
-      <td>UseGalaxy.eu, UseGalaxy.fr</td>
-      <td>Galaxy@AuBi, UseGalaxy.cz</td>
+      <td>humann2_regroup_table, mothur_summary_seqs, humann2_renorm_table, mothur_make_biom, mothur_count_seqs, mothur_classify_seqs, mothur_make_group, mothur_make_shared, mothur_filter_seqs, mothur_merge_files, mothur_classify_otu, mothur_align_seqs, humann2, mothur_cluster_split, mothur_screen_seqs, metaphlan2, mothur_pre_cluster, mothur_unique_seqs, taxonomy_krona_chart, krona-text, metaphlan2krona</td>
+      <td>UseGalaxy.be</td>
+      <td>UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>1800</td>
-      <td>2378</td>
-      <td>2.333333</td>
+      <td>3586</td>
+      <td>4852</td>
+      <td>2.783333</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>Microbiome</td>
-      <td>Analyses of metagenomics data - The global picture</td>
-      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html</td>
+      <td>Identification of the micro-organisms in a beer using Nanopore sequencing</td>
+      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html</td>
       <td>Metagenomics, Microbial ecology, Taxonomy, Sequence analysis</td>
-      <td>Visualisation, Sequencing quality control, Phylogenetic analysis, Taxonomic classification, Sequence read processing, DNA barcoding, Sequence clustering</td>
-      <td>2017-06-22</td>
-      <td>2024-08-09</td>
+      <td>Taxonomic classification, Statistical calculation, Aggregation, Visualisation, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering</td>
+      <td>2022-09-29</td>
+      <td>2024-06-14</td>
       <td>4</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>mothur_cluster_split, mothur_count_seqs, mothur_classify_otu, mothur_merge_files, mothur_pre_cluster, humann2_regroup_table, mothur_make_biom, mothur_make_group, mothur_screen_seqs, mothur_unique_seqs, mothur_summary_seqs, metaphlan2, humann2, krona-text, mothur_make_shared, taxonomy_krona_chart, mothur_align_seqs, humann2_renorm_table, mothur_classify_seqs, mothur_filter_seqs, metaphlan2krona</td>
+      <td>porechop, fastp, Filter1, taxonomy_krona_chart, kraken2, krakentools_kreport2krona, fastqc</td>
+      <td>GalaxyTrakr, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au</td>
+      <td>UseGalaxy.cz</td>
+      <td>0</td>
       <td></td>
-      <td>UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au</td>
+      <td>1239</td>
+      <td>1942</td>
+      <td>2.966667</td>
       <td>0</td>
+    </tr>
+    <tr>
       <td></td>
-      <td>3013</td>
-      <td>4081</td>
-      <td>2.750000</td>
+      <td>Microbiome</td>
+      <td>Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition</td>
+      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html</td>
+      <td>Metagenomics, Public health and epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis</td>
+      <td>Scatter plot plotting, Visualisation, Cross-assembly, Phylogenetic tree generation, Genome assembly, Sequencing quality control, Box-Whisker plot plotting, Multiple sequence alignment, Mapping assembly, Base-calling, Aggregation, Statistical calculation, Pairwise sequence alignment, Validation, Taxonomic classification, Sequence composition calculation, Mapping, Antimicrobial resistance prediction, Phylogenetic tree analysis, Data handling, Multilocus sequence typing, De-novo assembly, Sequence alignment analysis, Phylogenetic tree reconstruction, Sequence contamination filtering, Sequence assembly, Variant calling, Sequence assembly visualisation, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)</td>
+      <td>2023-01-26</td>
+      <td>2024-09-27</td>
+      <td>11</td>
+      <td>True</td>
+      <td>False</td>
+      <td>False</td>
+      <td>True</td>
+      <td>__FILTER_FAILED_DATASETS__, Count1, minimap2, snpSift_filter, compose_text_param, tab2fasta, tp_find_and_replace, tp_head_tool, tp_multijoin_tool, param_value_from_file, collection_column_join, collection_element_identifiers, bcftools_norm, krakentools_kreport2krona, krakentools_extract_kraken_reads, ggplot2_heatmap, bamtools_split_mapped, fasta_merge_files_and_filter_unique_sequences, barchart_gnuplot, samtools_fastx, flye, medaka_consensus_pipeline, tp_cut_tool, fastqc, snpSift_extractFields, regex1, Grouping1, tp_sorted_uniq, porechop, table_compute, bcftools_consensus, split_file_to_collection, bandage_image, abricate, Paste1, add_line_to_file, tp_split_on_column, multiqc, Grep1, Cut1, collapse_dataset, Remove beginning1, clustalw, bedtools_getfastabed, tp_replace_in_column, fasttree, newick_display, fastp, samtools_coverage, samtools_depth, clair3, taxonomy_krona_chart, __FILTER_EMPTY_DATASETS__, kraken2, __BUILD_LIST__, Add_a_column1, mlst, nanoplot, regexColumn1, CONVERTER_gz_to_uncompressed, fasta2tab</td>
+      <td>UseGalaxy.eu</td>
+      <td>UseGalaxy.org.au</td>
+      <td>0</td>
+      <td></td>
+      <td>1964</td>
+      <td>2918</td>
+      <td>3.000000</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>Microbiome</td>
-      <td>Antibiotic resistance detection</td>
-      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html</td>
-      <td>Metagenomic sequencing, Public health and epidemiology, Metagenomics, Microbiology, Infectious disease, Sequence analysis, Antimicrobial Resistance</td>
-      <td>De-novo assembly, Sequence analysis, Box-Whisker plot plotting, Pairwise sequence alignment, Scatter plot plotting, Mapping assembly, Sequence assembly visualisation, Genome assembly, Aggregation</td>
-      <td>2019-06-25</td>
+      <td>Metatranscriptomics analysis using microbiome RNA-seq data</td>
+      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html</td>
+      <td>Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis</td>
+      <td>Visualisation, Sequencing quality control, Phylogenetic inference, Phylogenetic tree editing, Statistical calculation, Taxonomic classification, Validation, Sequence composition calculation, Sequence comparison, Sequence similarity search, Phylogenetic tree analysis, Sequence trimming, Phylogenetic analysis, Phylogenetic tree visualisation, Sequence alignment analysis, Species frequency estimation, Conversion, Nucleic acid sequence analysis, Read pre-processing, Primer removal</td>
+      <td>2019-11-21</td>
       <td>2024-06-14</td>
       <td>4</td>
       <td>True</td>
-      <td>False</td>
+      <td>True</td>
       <td>False</td>
       <td>True</td>
-      <td>nanoplot, gfa_to_fa, racon, PlasFlow, miniasm, minimap2, staramr_search, bandage_image, unicycler</td>
-      <td>UseGalaxy.eu</td>
-      <td>UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au</td>
+      <td>fastq_paired_end_interlacer, tp_find_and_replace, metaphlan, fastqc, humann, graphlan_annotate, graphlan, humann_split_stratified_table, humann_renorm_table, humann_regroup_table, humann_rename_table, cutadapt, combine_metaphlan2_humann2, multiqc, bg_sortmerna, Grep1, Cut1, export2graphlan, humann_unpack_pathways, taxonomy_krona_chart</td>
+      <td>UseGalaxy.org (Main), UseGalaxy.org.au</td>
+      <td>UseGalaxy.cz, UseGalaxy.no</td>
       <td>0</td>
       <td></td>
-      <td>1130</td>
-      <td>1752</td>
-      <td>4.016667</td>
+      <td>2136358</td>
+      <td>5901051</td>
+      <td>4.266667</td>
       <td>0</td>
     </tr>
     <tr>
@@ -639,7 +687,7 @@
       <td>Taxonomic Profiling and Visualization of Metagenomic Data</td>
       <td>https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html</td>
       <td>Metagenomics, Microbial ecology, Taxonomy, Sequence analysis</td>
-      <td>Visualisation, Nucleic acid sequence analysis, Taxonomic classification, Phylogenetic tree analysis, Statistical calculation, Aggregation</td>
+      <td>Phylogenetic tree analysis, Statistical calculation, Taxonomic classification, Aggregation, Visualisation, Nucleic acid sequence analysis</td>
       <td>2023-05-03</td>
       <td>2024-06-14</td>
       <td>4</td>
@@ -647,86 +695,62 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>est_abundance, krakentools_kreport2krona, __UNZIP_COLLECTION__, interactive_tool_phinch, taxonomy_krona_chart, interactive_tool_pavian, kraken2, metaphlan, kraken_biom</td>
+      <td>interactive_tool_phinch, est_abundance, taxonomy_krona_chart, interactive_tool_pavian, kraken2, kraken_biom, __UNZIP_COLLECTION__, krakentools_kreport2krona, metaphlan</td>
       <td>UseGalaxy.eu</td>
       <td>UseGalaxy.fr, UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>3655</td>
-      <td>4993</td>
-      <td>1.950000</td>
+      <td>4443</td>
+      <td>6096</td>
+      <td>1.966667</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>Microbiome</td>
-      <td>Assembly of metagenomic sequencing data</td>
-      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html</td>
-      <td>Metagenomics, Sequence assembly</td>
-      <td>Visualisation, Sequencing quality control, Primer removal, Sequence file editing, Formatting, Read mapping, Sequence assembly validation, Sequence composition calculation, Sequence assembly visualisation, Local alignment, Genome assembly, Sequence trimming, Statistical calculation, Sequence contamination filtering, Sequence alignment analysis, Read pre-processing, Data handling, Variant calling</td>
-      <td>2022-12-05</td>
+      <td>Metatranscriptomics analysis using microbiome RNA-seq data (short)</td>
+      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html</td>
+      <td>Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis</td>
+      <td>Visualisation, Sequencing quality control, Phylogenetic inference, Phylogenetic tree editing, Statistical calculation, Taxonomic classification, Validation, Sequence composition calculation, Sequence comparison, Sequence similarity search, Phylogenetic tree analysis, Sequence trimming, Phylogenetic analysis, Phylogenetic tree visualisation, Sequence alignment analysis, Species frequency estimation, Conversion, Nucleic acid sequence analysis, Read pre-processing, Primer removal</td>
+      <td>2020-02-13</td>
       <td>2024-06-14</td>
       <td>4</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>bg_uniq, megahit_contig2fastg, ngsutils_bam_filter, megahit, bowtie2, tp_cat, quast, random_lines1, collection_column_join, filter_tabular, seqtk_subseq, fastqc, bandage_info, coverm_contig, bandage_image, bamtools, cutadapt, metaspades</td>
-      <td></td>
-      <td>UseGalaxy.cz, UseGalaxy.eu</td>
-      <td>0</td>
-      <td></td>
-      <td>1376</td>
-      <td>1931</td>
-      <td>2.533333</td>
-      <td>0</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>Microbiome</td>
-      <td>Building an amplicon sequence variant (ASV) table from 16S data using DADA2</td>
-      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html</td>
-      <td>Microbial ecology, Taxonomy, Sequence analysis</td>
-      <td>Visualisation, Analysis, Variant calling, DNA barcoding, Deposition</td>
-      <td>2024-06-05</td>
-      <td>2024-08-09</td>
-      <td>7</td>
-      <td>True</td>
-      <td>False</td>
-      <td>False</td>
-      <td>True</td>
-      <td>__UNZIP_COLLECTION__, phyloseq_from_dada2, interactive_tool_phyloseq, dada2_filterAndTrim, Grouping1, __SORTLIST__, dada2_learnErrors, dada2_dada, dada2_plotQualityProfile, tp_replace_in_column, dada2_removeBimeraDenovo, cat1, dada2_assignTaxonomyAddspecies, dada2_mergePairs, dada2_makeSequenceTable, collection_element_identifiers, dada2_seqCounts, tp_replace_in_line, Add_a_column1, tp_head_tool</td>
-      <td>UseGalaxy.eu</td>
-      <td></td>
+      <td>fastq_paired_end_interlacer, tp_find_and_replace, metaphlan, fastqc, humann, graphlan_annotate, graphlan, humann_split_stratified_table, humann_renorm_table, humann_regroup_table, humann_rename_table, cutadapt, combine_metaphlan2_humann2, multiqc, bg_sortmerna, Grep1, Cut1, export2graphlan, humann_unpack_pathways, taxonomy_krona_chart</td>
+      <td>UseGalaxy.org (Main), UseGalaxy.org.au</td>
+      <td>UseGalaxy.cz, UseGalaxy.no</td>
       <td>0</td>
       <td></td>
-      <td>614</td>
-      <td>840</td>
-      <td>2.066667</td>
+      <td>274</td>
+      <td>351</td>
+      <td>1.433333</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>Microbiome</td>
-      <td>Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition</td>
-      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html</td>
-      <td>Metagenomics, Public health and epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis</td>
-      <td>Visualisation, Sequencing quality control, Sequence composition calculation, Taxonomic classification, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree generation, Phylogenetic tree generation (from molecular sequences), Pairwise sequence alignment, Sequence assembly visualisation, Multilocus sequence typing, Cross-assembly, Genome assembly, Base-calling, Validation, Sequence assembly, Statistical calculation, Phylogenetic tree reconstruction, Sequence contamination filtering, De-novo assembly, Mapping, Box-Whisker plot plotting, Phylogenetic tree analysis, Sequence alignment analysis, Scatter plot plotting, Mapping assembly, Multiple sequence alignment, Data handling, Variant calling, Antimicrobial resistance prediction, Aggregation</td>
-      <td>2023-01-26</td>
-      <td>2024-07-26</td>
-      <td>9</td>
+      <td>Antibiotic resistance detection</td>
+      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html</td>
+      <td>Metagenomic sequencing, Public health and epidemiology, Metagenomics, Microbiology, Infectious disease, Sequence analysis, Antimicrobial Resistance</td>
+      <td>Scatter plot plotting, Genome assembly, Box-Whisker plot plotting, De-novo assembly, Sequence analysis, Mapping assembly, Aggregation, Sequence assembly visualisation, Pairwise sequence alignment</td>
+      <td>2019-06-25</td>
+      <td>2024-06-14</td>
+      <td>4</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>__BUILD_LIST__, __FILTER_FAILED_DATASETS__, abricate, newick_display, krakentools_extract_kraken_reads, Count1, Cut1, snpSift_extractFields, kraken2, table_compute, fasta2tab, Remove beginning1, fasttree, add_line_to_file, collapse_dataset, Grep1, Grouping1, bcftools_consensus, bcftools_norm, ggplot2_heatmap, collection_column_join, clair3, tp_sorted_uniq, fasta_merge_files_and_filter_unique_sequences, tp_replace_in_column, CONVERTER_gz_to_uncompressed, regex1, porechop, tab2fasta, __FILTER_EMPTY_DATASETS__, taxonomy_krona_chart, tp_find_and_replace, tp_cut_tool, Paste1, flye, mlst, bedtools_getfastabed, collection_element_identifiers, bandage_image, tp_split_on_column, clustalw, regexColumn1, medaka_consensus_pipeline, samtools_coverage, krakentools_kreport2krona, barchart_gnuplot, nanoplot, param_value_from_file, compose_text_param, fastp, tp_multijoin_tool, multiqc, samtools_fastx, bamtools_split_mapped, snpSift_filter, samtools_depth, fastqc, minimap2, split_file_to_collection, Add_a_column1, tp_head_tool</td>
+      <td>unicycler, minimap2, bandage_image, PlasFlow, racon, nanoplot, gfa_to_fa, staramr_search, miniasm</td>
       <td>UseGalaxy.eu</td>
-      <td></td>
+      <td>UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>1680</td>
-      <td>2521</td>
-      <td>3.016667</td>
+      <td>1281</td>
+      <td>1950</td>
+      <td>4.033333</td>
       <td>0</td>
     </tr>
     <tr>
@@ -735,7 +759,7 @@
       <td>16S Microbial analysis with Nanopore data</td>
       <td>https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html</td>
       <td>Microbial ecology, Taxonomy, Sequence analysis</td>
-      <td>Visualisation, Sequencing quality control, Sequence contamination filtering, Validation, Sequence composition calculation, Taxonomic classification, Statistical calculation</td>
+      <td>Taxonomic classification, Statistical calculation, Visualisation, Validation, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering</td>
       <td>2020-11-24</td>
       <td>2024-07-31</td>
       <td>5</td>
@@ -743,86 +767,86 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>fastp, multiqc, taxonomy_krona_chart, fastqc, kraken2, tp_replace_in_line, Remove beginning1, datamash_reverse, porechop</td>
+      <td>porechop, fastp, tp_replace_in_line, taxonomy_krona_chart, multiqc, kraken2, datamash_reverse, fastqc, Remove beginning1</td>
       <td>UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au</td>
-      <td>GalaxyTrakr, UseGalaxy.cz</td>
+      <td>GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz</td>
       <td>0</td>
       <td></td>
-      <td>2344</td>
-      <td>3314</td>
-      <td>2.800000</td>
+      <td>2758</td>
+      <td>3844</td>
+      <td>2.716667</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>Microbiome</td>
-      <td>Identification of the micro-organisms in a beer using Nanopore sequencing</td>
-      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html</td>
-      <td>Metagenomics, Microbial ecology, Taxonomy, Sequence analysis</td>
-      <td>Visualisation, Sequencing quality control, Sequence contamination filtering, Sequence composition calculation, Taxonomic classification, Statistical calculation, Aggregation</td>
-      <td>2022-09-29</td>
-      <td>2024-06-14</td>
-      <td>4</td>
+      <td>Building an amplicon sequence variant (ASV) table from 16S data using DADA2</td>
+      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html</td>
+      <td>Microbial ecology, Taxonomy, Sequence analysis</td>
+      <td>Variant calling, DNA barcoding, Visualisation, Analysis, Deposition</td>
+      <td>2024-06-05</td>
+      <td>2024-09-26</td>
+      <td>8</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>fastp, taxonomy_krona_chart, fastqc, kraken2, Filter1, porechop, krakentools_kreport2krona</td>
-      <td>GalaxyTrakr, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au</td>
-      <td>UseGalaxy.cz</td>
+      <td>tp_head_tool, collection_element_identifiers, __UNZIP_COLLECTION__, interactive_tool_phyloseq, dada2_mergePairs, dada2_removeBimeraDenovo, dada2_assignTaxonomyAddspecies, Grouping1, dada2_plotQualityProfile, dada2_filterAndTrim, cat1, tp_replace_in_column, dada2_seqCounts, dada2_makeSequenceTable, tp_replace_in_line, Add_a_column1, dada2_dada, __SORTLIST__, dada2_learnErrors, phyloseq_from_dada2</td>
+      <td>UseGalaxy.eu</td>
+      <td></td>
       <td>0</td>
       <td></td>
-      <td>1103</td>
-      <td>1743</td>
-      <td>2.816667</td>
+      <td>1089</td>
+      <td>1460</td>
+      <td>1.833333</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>Microbiome</td>
-      <td>Metatranscriptomics analysis using microbiome RNA-seq data</td>
-      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html</td>
-      <td>Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis</td>
-      <td>Visualisation, Primer removal, Sequencing quality control, Sequence similarity search, Phylogenetic analysis, Taxonomic classification, Nucleic acid sequence analysis, Sequence composition calculation, Phylogenetic inference, Validation, Sequence trimming, Conversion, Statistical calculation, Species frequency estimation, Phylogenetic tree editing, Sequence comparison, Phylogenetic tree analysis, Sequence alignment analysis, Read pre-processing, Phylogenetic tree visualisation</td>
-      <td>2019-11-21</td>
+      <td>Assembly of metagenomic sequencing data</td>
+      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html</td>
+      <td>Metagenomics, Sequence assembly</td>
+      <td>Data handling, Visualisation, Sequence trimming, Read mapping, Sequencing quality control, Genome assembly, Sequence alignment analysis, Sequence contamination filtering, Sequence assembly validation, Variant calling, Statistical calculation, Sequence assembly visualisation, Sequence file editing, Local alignment, Sequence composition calculation, Read pre-processing, Primer removal, Formatting</td>
+      <td>2022-12-05</td>
       <td>2024-06-14</td>
       <td>4</td>
       <td>True</td>
-      <td>True</td>
+      <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>humann_rename_table, Cut1, graphlan_annotate, humann_regroup_table, metaphlan, Grep1, export2graphlan, bg_sortmerna, humann_split_stratified_table, graphlan, fastq_paired_end_interlacer, combine_metaphlan2_humann2, taxonomy_krona_chart, tp_find_and_replace, humann_unpack_pathways, cutadapt, humann, multiqc, fastqc, humann_renorm_table</td>
-      <td>UseGalaxy.org (Main)</td>
-      <td>UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au</td>
+      <td>ngsutils_bam_filter, tp_cat, bamtools, bandage_image, filter_tabular, megahit_contig2fastg, bandage_info, bg_uniq, quast, seqtk_subseq, cutadapt, random_lines1, collection_column_join, megahit, coverm_contig, fastqc, metaspades, bowtie2</td>
+      <td></td>
+      <td>UseGalaxy.cz, UseGalaxy.eu</td>
       <td>0</td>
       <td></td>
-      <td>2066154</td>
-      <td>5729924</td>
-      <td>4.133333</td>
+      <td>1613</td>
+      <td>2258</td>
+      <td>2.950000</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>Microbiome</td>
-      <td>Metatranscriptomics analysis using microbiome RNA-seq data (short)</td>
-      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html</td>
-      <td>Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis</td>
-      <td>Visualisation, Primer removal, Sequencing quality control, Sequence similarity search, Phylogenetic analysis, Taxonomic classification, Nucleic acid sequence analysis, Sequence composition calculation, Phylogenetic inference, Validation, Sequence trimming, Conversion, Statistical calculation, Species frequency estimation, Phylogenetic tree editing, Sequence comparison, Phylogenetic tree analysis, Sequence alignment analysis, Read pre-processing, Phylogenetic tree visualisation</td>
-      <td>2020-02-13</td>
-      <td>2024-06-14</td>
-      <td>4</td>
-      <td>True</td>
+      <td>QIIME 2 Moving Pictures</td>
+      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html</td>
+      <td>Microbial ecology, Taxonomy, Sequence analysis</td>
+      <td></td>
+      <td>2024-03-14</td>
+      <td>2024-03-14</td>
+      <td>1</td>
+      <td>external</td>
       <td>False</td>
       <td>False</td>
-      <td>True</td>
-      <td>humann_rename_table, Cut1, graphlan_annotate, humann_regroup_table, metaphlan, Grep1, export2graphlan, bg_sortmerna, humann_split_stratified_table, graphlan, fastq_paired_end_interlacer, combine_metaphlan2_humann2, taxonomy_krona_chart, tp_find_and_replace, humann_unpack_pathways, cutadapt, humann, multiqc, fastqc, humann_renorm_table</td>
-      <td>UseGalaxy.org (Main)</td>
-      <td>UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au</td>
+      <td>False</td>
+      <td></td>
+      <td></td>
+      <td>UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr</td>
       <td>0</td>
       <td></td>
-      <td>234</td>
-      <td>297</td>
-      <td>1.666667</td>
+      <td>131</td>
+      <td>195</td>
+      <td>3.383333</td>
       <td>0</td>
     </tr>
     <tr>
@@ -831,34 +855,34 @@
       <td>Binning of metagenomic sequencing data</td>
       <td>https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html</td>
       <td>Metagenomics, Sequence assembly</td>
-      <td>Sequencing quality control, Validation, Genome assembly, Sequence assembly validation, Statistical calculation, Sequence composition calculation</td>
+      <td>Sequence assembly validation, Statistical calculation, Sequencing quality control, Validation, Genome assembly, Sequence composition calculation</td>
       <td>2023-12-05</td>
-      <td>2024-03-14</td>
-      <td>3</td>
+      <td>2024-09-12</td>
+      <td>4</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>False</td>
       <td>megahit, checkm_lineage_wf</td>
       <td>GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr</td>
-      <td></td>
+      <td>UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>1648</td>
-      <td>1997</td>
-      <td>1.483333</td>
+      <td>2076</td>
+      <td>2537</td>
+      <td>1.416667</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>Microbiome</td>
-      <td>QIIME 2 Moving Pictures</td>
-      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html</td>
+      <td>QIIME 2 Cancer Microbiome Intervention</td>
+      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html</td>
       <td>Microbial ecology, Taxonomy, Sequence analysis</td>
       <td></td>
+      <td>2024-02-12</td>
       <td>2024-03-14</td>
-      <td>2024-03-14</td>
-      <td>1</td>
+      <td>3</td>
       <td>external</td>
       <td>False</td>
       <td>False</td>
@@ -868,33 +892,33 @@
       <td>UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr</td>
       <td>0</td>
       <td></td>
-      <td>112</td>
-      <td>171</td>
-      <td>3.816667</td>
+      <td>153</td>
+      <td>281</td>
+      <td>3.483333</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>Microbiome</td>
-      <td>QIIME 2 Cancer Microbiome Intervention</td>
-      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html</td>
+      <td>16S Microbial Analysis with mothur (extended)</td>
+      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html</td>
       <td>Microbial ecology, Taxonomy, Sequence analysis</td>
-      <td></td>
-      <td>2024-02-12</td>
+      <td>Phylogenetic tree analysis, DNA barcoding, Visualisation, Phylogenetic analysis, Sequencing quality control, Phylogenetic tree generation, Phylogenetic tree reconstruction, Taxonomic classification, Sequence read processing, Sequence clustering</td>
+      <td>2017-02-12</td>
       <td>2024-03-14</td>
-      <td>3</td>
-      <td>external</td>
-      <td>False</td>
+      <td>4</td>
+      <td>True</td>
       <td>False</td>
       <td>False</td>
-      <td></td>
-      <td></td>
-      <td>UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr</td>
+      <td>True</td>
+      <td>mothur_dist_shared, mothur_seq_error, mothur_summary_seqs, mothur_remove_lineage, mothur_make_biom, mothur_count_seqs, mothur_get_groups, mothur_classify_seqs, mothur_remove_groups, mothur_make_shared, mothur_filter_seqs, mothur_dist_seqs, mothur_remove_seqs, mothur_rarefaction_single, mothur_venn, mothur_classify_otu, mothur_count_groups, mothur_align_seqs, mothur_taxonomy_to_krona, mothur_heatmap_sim, mothur_chimera_vsearch, mothur_cluster_split, mothur_screen_seqs, newick_display, mothur_pre_cluster, mothur_make_contigs, mothur_unique_seqs, XY_Plot_1, taxonomy_krona_chart, mothur_cluster, mothur_tree_shared, mothur_summary_single, mothur_sub_sample</td>
+      <td>UseGalaxy.be, UseGalaxy.eu</td>
+      <td>UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>119</td>
-      <td>220</td>
-      <td>2.716667</td>
+      <td>5448</td>
+      <td>8271</td>
+      <td>2.983333</td>
       <td>0</td>
     </tr>
     <tr>
@@ -903,7 +927,7 @@
       <td>16S Microbial Analysis with mothur (short)</td>
       <td>https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html</td>
       <td>Microbial ecology, Taxonomy, Sequence analysis</td>
-      <td>Visualisation, Sequencing quality control, Phylogenetic analysis, Taxonomic classification, Phylogenetic tree analysis, Phylogenetic tree generation, Sequence read processing, DNA barcoding, Sequence clustering, Phylogenetic tree reconstruction</td>
+      <td>Phylogenetic tree analysis, DNA barcoding, Visualisation, Phylogenetic analysis, Sequencing quality control, Phylogenetic tree generation, Phylogenetic tree reconstruction, Taxonomic classification, Sequence read processing, Sequence clustering</td>
       <td>2019-05-13</td>
       <td>2024-06-14</td>
       <td>5</td>
@@ -911,62 +935,62 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>mothur_remove_lineage, mothur_cluster_split, mothur_count_seqs, mothur_dist_shared, mothur_sub_sample, mothur_classify_otu, newick_display, mothur_chimera_vsearch, mothur_venn, mothur_pre_cluster, XY_Plot_1, mothur_rarefaction_single, collapse_dataset, mothur_screen_seqs, mothur_unique_seqs, mothur_count_groups, mothur_heatmap_sim, mothur_summary_seqs, mothur_tree_shared, mothur_remove_groups, mothur_make_shared, mothur_summary_single, mothur_cluster, mothur_classify_seqs, mothur_dist_seqs, mothur_filter_seqs, mothur_remove_seqs</td>
+      <td>mothur_dist_shared, mothur_summary_seqs, mothur_remove_lineage, mothur_count_seqs, mothur_classify_seqs, mothur_remove_groups, mothur_make_shared, mothur_filter_seqs, mothur_dist_seqs, mothur_remove_seqs, mothur_rarefaction_single, mothur_venn, mothur_classify_otu, mothur_count_groups, mothur_heatmap_sim, mothur_chimera_vsearch, mothur_cluster_split, mothur_screen_seqs, collapse_dataset, newick_display, mothur_pre_cluster, mothur_unique_seqs, XY_Plot_1, mothur_cluster, mothur_tree_shared, mothur_summary_single, mothur_sub_sample</td>
       <td>UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au</td>
-      <td>UseGalaxy.cz, UseGalaxy.fr</td>
+      <td>UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr</td>
       <td>0</td>
       <td></td>
-      <td>1744</td>
-      <td>3211</td>
-      <td>5.733333</td>
+      <td>1985</td>
+      <td>3572</td>
+      <td>5.616667</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
-      <td>Microbiome</td>
-      <td>16S Microbial Analysis with mothur (extended)</td>
-      <td>https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html</td>
-      <td>Microbial ecology, Taxonomy, Sequence analysis</td>
-      <td>Visualisation, Sequencing quality control, Phylogenetic analysis, Taxonomic classification, Phylogenetic tree analysis, Phylogenetic tree generation, Sequence read processing, DNA barcoding, Sequence clustering, Phylogenetic tree reconstruction</td>
-      <td>2017-02-12</td>
-      <td>2024-03-14</td>
-      <td>4</td>
+      <td>Evolution</td>
+      <td>Tree thinking for tuberculosis evolution and epidemiology</td>
+      <td>https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html</td>
+      <td>Genomics, Microbiology, Phylogeny, Infectious disease</td>
+      <td>Phylogenetic tree analysis, Sequence analysis</td>
+      <td>2022-03-16</td>
+      <td>2024-03-12</td>
+      <td>11</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>mothur_remove_lineage, mothur_cluster_split, mothur_count_seqs, mothur_dist_shared, mothur_make_contigs, mothur_classify_otu, mothur_sub_sample, mothur_taxonomy_to_krona, mothur_chimera_vsearch, newick_display, mothur_venn, mothur_pre_cluster, XY_Plot_1, mothur_rarefaction_single, mothur_make_biom, mothur_screen_seqs, mothur_unique_seqs, mothur_count_groups, mothur_heatmap_sim, mothur_summary_seqs, mothur_tree_shared, mothur_remove_groups, mothur_make_shared, taxonomy_krona_chart, mothur_summary_single, mothur_cluster, mothur_seq_error, mothur_align_seqs, mothur_classify_seqs, mothur_get_groups, mothur_dist_seqs, mothur_filter_seqs, mothur_remove_seqs</td>
+      <td>upload1, interactive_tool_rstudio, raxml</td>
       <td>UseGalaxy.eu</td>
-      <td>UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au</td>
+      <td>UseGalaxy.fr, UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>4695</td>
-      <td>7229</td>
-      <td>2.983333</td>
+      <td>1374</td>
+      <td>2072</td>
+      <td>2.216667</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
-      <td>Variant Analysis</td>
-      <td>M. tuberculosis Variant Analysis</td>
-      <td>https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html</td>
-      <td>Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease</td>
-      <td>Global alignment, Sequencing quality control, Sequence contamination filtering, Sequence alignment, Sequence analysis, Sequence composition calculation, Sequence alignment analysis, Taxonomic classification, Phylogenetic tree generation, Variant calling, Local alignment, Phylogenetic tree visualisation, Validation, Genome visualisation, Statistical calculation, Antimicrobial resistance prediction</td>
-      <td>2020-07-25</td>
-      <td>2024-07-26</td>
-      <td>30</td>
+      <td>Evolution</td>
+      <td>Identifying tuberculosis transmission links: from SNPs to transmission clusters</td>
+      <td>https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html</td>
+      <td>Genomics, Microbiology, Infectious disease, DNA polymorphism</td>
+      <td>Phylogenetic tree visualisation, Variant calling, Antimicrobial resistance prediction, Phylogenetic tree generation</td>
+      <td>2022-03-16</td>
+      <td>2024-07-12</td>
+      <td>12</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>tp_awk_tool, kraken2, bcftools_consensus, mosdepth, EMBOSS: seqret84, tb_profiler_profile, qualimap_bamqc, samtools_stats, tb_variant_filter, tp_sed_tool, EMBOSS:%20seqret84, upload1, tbvcfreport, fastp, jbrowse, multiqc, jvarkit_wgscoverageplotter, snippy, fastqc, __FLATTEN__</td>
-      <td></td>
-      <td></td>
+      <td>tp_sed_tool, tp_easyjoin_tool, tp_cat, bcftools_consensus, samtools_view, upload1, snippy, tp_grep_tool, tp_replace_in_line, snp_dists, Grep1, tb_variant_filter, tb_profiler_profile, collapse_dataset, snp_sites, trimmomatic, __MERGE_COLLECTION__, addName</td>
+      <td>UseGalaxy.eu</td>
+      <td>UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>5641</td>
-      <td>8997</td>
-      <td>2.950000</td>
+      <td>1605</td>
+      <td>2499</td>
+      <td>3.050000</td>
       <td>0</td>
     </tr>
     <tr>
@@ -977,68 +1001,44 @@
       <td>Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance</td>
       <td>Genome visualisation, Genome annotation, Read mapping</td>
       <td>2024-01-23</td>
-      <td>2024-03-13</td>
-      <td>5</td>
+      <td>2024-09-27</td>
+      <td>6</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>Grep1, jbrowse, bowtie2, tbl2gff3, bakta, staramr_search, upload1</td>
+      <td>jbrowse, tbl2gff3, upload1, Grep1, staramr_search, bakta, bowtie2</td>
       <td>UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr</td>
-      <td>Galaxy@AuBi</td>
+      <td>Galaxy@AuBi, UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>967</td>
-      <td>1368</td>
-      <td>2.933333</td>
+      <td>1138</td>
+      <td>1576</td>
+      <td>2.750000</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
-      <td>Evolution</td>
-      <td>Identifying tuberculosis transmission links: from SNPs to transmission clusters</td>
-      <td>https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html</td>
-      <td>Genomics, Microbiology, Infectious disease, DNA polymorphism</td>
-      <td>Variant calling, Phylogenetic tree visualisation, Phylogenetic tree generation, Antimicrobial resistance prediction</td>
-      <td>2022-03-16</td>
-      <td>2024-07-12</td>
-      <td>12</td>
+      <td>Variant Analysis</td>
+      <td>M. tuberculosis Variant Analysis</td>
+      <td>https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html</td>
+      <td>Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease</td>
+      <td>Sequence alignment, Phylogenetic tree generation, Phylogenetic tree visualisation, Sequencing quality control, Sequence alignment analysis, Genome visualisation, Sequence analysis, Sequence contamination filtering, Variant calling, Global alignment, Statistical calculation, Taxonomic classification, Validation, Local alignment, Sequence composition calculation, Antimicrobial resistance prediction</td>
+      <td>2020-07-25</td>
+      <td>2024-07-26</td>
+      <td>30</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>Grep1, bcftools_consensus, tb_variant_filter, upload1, samtools_view, snp_sites, tb_profiler_profile, tp_grep_tool, tp_cat, snippy, tp_easyjoin_tool, addName, tp_sed_tool, tp_replace_in_line, snp_dists, collapse_dataset, __MERGE_COLLECTION__, trimmomatic</td>
-      <td>UseGalaxy.eu</td>
-      <td>UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main)</td>
-      <td>0</td>
+      <td>tp_sed_tool, upload1, snippy, qualimap_bamqc, tb_variant_filter, EMBOSS: seqret84, tb_profiler_profile, mosdepth, jvarkit_wgscoverageplotter, tbvcfreport, tp_awk_tool, fastqc, jbrowse, samtools_stats, bcftools_consensus, multiqc, fastp, kraken2, EMBOSS:%20seqret84, __FLATTEN__</td>
       <td></td>
-      <td>1533</td>
-      <td>2414</td>
-      <td>3.133333</td>
-      <td>0</td>
-    </tr>
-    <tr>
       <td></td>
-      <td>Evolution</td>
-      <td>Tree thinking for tuberculosis evolution and epidemiology</td>
-      <td>https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html</td>
-      <td>Genomics, Microbiology, Phylogeny, Infectious disease</td>
-      <td>Sequence analysis, Phylogenetic tree analysis</td>
-      <td>2022-03-16</td>
-      <td>2024-03-12</td>
-      <td>11</td>
-      <td>True</td>
-      <td>False</td>
-      <td>False</td>
-      <td>True</td>
-      <td>interactive_tool_rstudio, upload1, raxml</td>
-      <td>UseGalaxy.eu</td>
-      <td>UseGalaxy.fr, UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>1308</td>
-      <td>1983</td>
-      <td>2.183333</td>
+      <td>5788</td>
+      <td>9172</td>
+      <td>2.950000</td>
       <td>0</td>
     </tr>
     <tr>
@@ -1047,7 +1047,7 @@
       <td>16S Microbial analysis with Nanopore data</td>
       <td>https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html</td>
       <td>Microbial ecology, Taxonomy, Sequence analysis</td>
-      <td>Visualisation, Sequencing quality control, Sequence contamination filtering, Validation, Sequence composition calculation, Taxonomic classification, Statistical calculation</td>
+      <td>Taxonomic classification, Statistical calculation, Visualisation, Validation, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering</td>
       <td>2020-11-24</td>
       <td>2024-07-31</td>
       <td>5</td>
@@ -1055,38 +1055,38 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>fastp, multiqc, taxonomy_krona_chart, fastqc, kraken2, tp_replace_in_line, Remove beginning1, datamash_reverse, porechop</td>
+      <td>porechop, fastp, tp_replace_in_line, taxonomy_krona_chart, multiqc, kraken2, datamash_reverse, fastqc, Remove beginning1</td>
       <td>UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au</td>
-      <td>GalaxyTrakr, UseGalaxy.cz</td>
+      <td>GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz</td>
       <td>0</td>
       <td></td>
-      <td>2344</td>
-      <td>3314</td>
-      <td>2.800000</td>
+      <td>2758</td>
+      <td>3844</td>
+      <td>2.716667</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>Proteomics</td>
-      <td>metaQuantome 2: Function</td>
-      <td>https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html</td>
-      <td>Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics</td>
-      <td>Visualisation, Differential protein expression analysis, Functional clustering, Query and retrieval, Indexing, Filtering, Heat map generation, Statistical inference, Principal component visualisation, Quantification</td>
-      <td>2020-10-29</td>
-      <td>2024-03-15</td>
-      <td>14</td>
+      <td>Metaproteomics tutorial</td>
+      <td>https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html</td>
+      <td>Proteomics, Proteogenomics, Biodiversity, Taxonomy</td>
+      <td>Prediction and recognition, Visualisation</td>
+      <td>2017-06-28</td>
+      <td>2024-06-14</td>
+      <td>41</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>metaquantome_db, metaquantome_sample, metaquantome_stat, metaquantome_expand, metaquantome_filter, metaquantome_viz</td>
-      <td>UseGalaxy.eu</td>
-      <td>UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au</td>
+      <td>query_tabular, peptide_shaker, search_gui, unipept, sqlite_to_tabular</td>
+      <td>UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au</td>
+      <td>UseGalaxy.be, UseGalaxy.cz</td>
       <td>0</td>
       <td></td>
-      <td>348</td>
-      <td>504</td>
-      <td>3.800000</td>
+      <td>2310</td>
+      <td>3828</td>
+      <td>2.633333</td>
       <td>0</td>
     </tr>
     <tr>
@@ -1095,7 +1095,7 @@
       <td>metaQuantome 3: Taxonomy</td>
       <td>https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html</td>
       <td>Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy</td>
-      <td>Visualisation, Differential protein expression analysis, Functional clustering, Query and retrieval, Indexing, Filtering, Heat map generation, Statistical inference, Principal component visualisation, Quantification</td>
+      <td>Visualisation, Indexing, Differential protein expression analysis, Functional clustering, Statistical inference, Principal component visualisation, Query and retrieval, Heat map generation, Quantification, Filtering</td>
       <td>2020-10-29</td>
       <td>2024-03-15</td>
       <td>14</td>
@@ -1103,62 +1103,62 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>metaquantome_db, metaquantome_sample, metaquantome_stat, metaquantome_expand, metaquantome_filter, metaquantome_viz</td>
-      <td>UseGalaxy.eu</td>
+      <td>metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_expand, metaquantome_viz, metaquantome_db</td>
+      <td>UseGalaxy.be, UseGalaxy.eu</td>
       <td>UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>371</td>
-      <td>502</td>
-      <td>2.633333</td>
+      <td>377</td>
+      <td>509</td>
+      <td>2.733333</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>Proteomics</td>
-      <td>metaQuantome 1: Data creation</td>
-      <td>https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html</td>
-      <td>Proteomics, Proteogenomics, Biodiversity, Taxonomy</td>
-      <td>Visualisation, Label-free quantification, Filtering, Formatting, Prediction and recognition</td>
-      <td>2020-10-16</td>
-      <td>2024-03-14</td>
-      <td>20</td>
+      <td>metaQuantome 2: Function</td>
+      <td>https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html</td>
+      <td>Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics</td>
+      <td>Visualisation, Indexing, Differential protein expression analysis, Functional clustering, Statistical inference, Principal component visualisation, Query and retrieval, Heat map generation, Quantification, Filtering</td>
+      <td>2020-10-29</td>
+      <td>2024-03-15</td>
+      <td>14</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>Grep1, msconvert, peptide_shaker, search_gui, Cut1, unipept, Filter1, query_tabular, tp_replace_in_line, Remove beginning1, regex1, flashlfq, tp_replace_in_column</td>
+      <td>metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_expand, metaquantome_viz, metaquantome_db</td>
       <td>UseGalaxy.eu</td>
-      <td>UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au</td>
+      <td>UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>773</td>
-      <td>1343</td>
-      <td>3.800000</td>
+      <td>352</td>
+      <td>508</td>
+      <td>3.766667</td>
       <td>0</td>
     </tr>
     <tr>
       <td></td>
       <td>Proteomics</td>
-      <td>Metaproteomics tutorial</td>
-      <td>https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html</td>
+      <td>metaQuantome 1: Data creation</td>
+      <td>https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html</td>
       <td>Proteomics, Proteogenomics, Biodiversity, Taxonomy</td>
-      <td>Visualisation, Prediction and recognition</td>
-      <td>2017-06-28</td>
-      <td>2024-06-14</td>
-      <td>41</td>
+      <td>Prediction and recognition, Visualisation, Filtering, Label-free quantification, Formatting</td>
+      <td>2020-10-16</td>
+      <td>2024-03-14</td>
+      <td>20</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>sqlite_to_tabular, peptide_shaker, search_gui, unipept, query_tabular</td>
-      <td>UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au</td>
-      <td>UseGalaxy.cz</td>
+      <td>query_tabular, flashlfq, Filter1, peptide_shaker, regex1, tp_replace_in_line, msconvert, search_gui, unipept, Grep1, Cut1, Remove beginning1, tp_replace_in_column</td>
+      <td>UseGalaxy.eu</td>
+      <td>UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>2256</td>
-      <td>3750</td>
-      <td>2.616667</td>
+      <td>781</td>
+      <td>1353</td>
+      <td>3.816667</td>
       <td>0</td>
     </tr>
     <tr>
@@ -1167,22 +1167,22 @@
       <td>Quality and contamination control in bacterial isolate using Illumina MiSeq Data</td>
       <td>https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html</td>
       <td>Whole genome sequencing, Genomics, Microbiology, Microbial ecology</td>
-      <td>Sequencing quality control, Sequence contamination filtering, Cross-assembly, Sequence composition calculation, Taxonomic classification, Expression analysis, Statistical calculation</td>
-      <td>2024-07-15</td>
+      <td>Cross-assembly, Sequencing quality control, Sequence contamination filtering, Statistical calculation, Taxonomic classification, Expression analysis, Sequence composition calculation</td>
       <td>2024-07-15</td>
-      <td>1</td>
+      <td>2024-09-02</td>
+      <td>2</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>fastp, est_abundance, fastqc, kraken2, recentrifuge, upload1</td>
+      <td>fastp, est_abundance, recentrifuge, upload1, kraken2, fastqc</td>
       <td>UseGalaxy.eu, UseGalaxy.fr</td>
       <td>Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>61</td>
-      <td>76</td>
-      <td>3.883333</td>
+      <td>185</td>
+      <td>225</td>
+      <td>2.516667</td>
       <td>0</td>
     </tr>
     <tr>
@@ -1191,7 +1191,7 @@
       <td>Calling variants in non-diploid systems</td>
       <td>https://training.galaxyproject.org//topics/variant-analysis/tutorials/non-dip/tutorial.html</td>
       <td>Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation</td>
-      <td>Sequencing quality control, Genome indexing, Sequence alignment, Formatting, Sequence composition calculation, Sequence alignment analysis, Read mapping, Generation, Data handling, Variant calling, Statistical calculation</td>
+      <td>Data handling, Sequence alignment, Read mapping, Sequencing quality control, Sequence alignment analysis, Generation, Statistical calculation, Variant calling, Sequence composition calculation, Formatting, Genome indexing</td>
       <td>2017-02-16</td>
       <td>2024-03-15</td>
       <td>23</td>
@@ -1199,13 +1199,13 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>picard_MarkDuplicates, freebayes, vcf2tsv, picard_MergeSamFiles, vcffilter2, bamFilter, Cut1, fastqc, bamleftalign, bwa_mem</td>
-      <td>UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main)</td>
+      <td>bwa_mem, picard_MarkDuplicates, vcffilter2, bamFilter, picard_MergeSamFiles, Cut1, bamleftalign, fastqc, vcf2tsv, freebayes</td>
+      <td>UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main)</td>
       <td>UseGalaxy.cz, UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>7035</td>
-      <td>13427</td>
+      <td>7149</td>
+      <td>13577</td>
       <td>2.050000</td>
       <td>0</td>
     </tr>
@@ -1215,7 +1215,7 @@
       <td>M. tuberculosis Variant Analysis</td>
       <td>https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html</td>
       <td>Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease</td>
-      <td>Global alignment, Sequencing quality control, Sequence contamination filtering, Sequence alignment, Sequence analysis, Sequence composition calculation, Sequence alignment analysis, Taxonomic classification, Phylogenetic tree generation, Variant calling, Local alignment, Phylogenetic tree visualisation, Validation, Genome visualisation, Statistical calculation, Antimicrobial resistance prediction</td>
+      <td>Sequence alignment, Phylogenetic tree generation, Phylogenetic tree visualisation, Sequencing quality control, Sequence alignment analysis, Genome visualisation, Sequence analysis, Sequence contamination filtering, Variant calling, Global alignment, Statistical calculation, Taxonomic classification, Validation, Local alignment, Sequence composition calculation, Antimicrobial resistance prediction</td>
       <td>2020-07-25</td>
       <td>2024-07-26</td>
       <td>30</td>
@@ -1223,13 +1223,13 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>tp_awk_tool, kraken2, bcftools_consensus, mosdepth, EMBOSS: seqret84, tb_profiler_profile, qualimap_bamqc, samtools_stats, tb_variant_filter, tp_sed_tool, EMBOSS:%20seqret84, upload1, tbvcfreport, fastp, jbrowse, multiqc, jvarkit_wgscoverageplotter, snippy, fastqc, __FLATTEN__</td>
+      <td>tp_sed_tool, upload1, snippy, qualimap_bamqc, tb_variant_filter, EMBOSS: seqret84, tb_profiler_profile, mosdepth, jvarkit_wgscoverageplotter, tbvcfreport, tp_awk_tool, fastqc, jbrowse, samtools_stats, bcftools_consensus, multiqc, fastp, kraken2, EMBOSS:%20seqret84, __FLATTEN__</td>
       <td></td>
       <td></td>
       <td>0</td>
       <td></td>
-      <td>5641</td>
-      <td>8997</td>
+      <td>5788</td>
+      <td>9172</td>
       <td>2.950000</td>
       <td>0</td>
     </tr>
@@ -1239,7 +1239,7 @@
       <td>Microbial Variant Calling</td>
       <td>https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html</td>
       <td>Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation</td>
-      <td>Genome visualisation, Variant calling, Phylogenetic tree generation, Phylogenetic tree visualisation</td>
+      <td>Genome visualisation, Variant calling, Phylogenetic tree visualisation, Phylogenetic tree generation</td>
       <td>2018-02-26</td>
       <td>2024-03-15</td>
       <td>23</td>
@@ -1248,13 +1248,13 @@
       <td>False</td>
       <td>True</td>
       <td>jbrowse, snippy</td>
-      <td>UseGalaxy.eu, UseGalaxy.org (Main)</td>
+      <td>UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main)</td>
       <td>GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>12166</td>
-      <td>20322</td>
-      <td>2.000000</td>
+      <td>12476</td>
+      <td>20693</td>
+      <td>1.983333</td>
       <td>0</td>
     </tr>
   </tbody>
diff --git a/communities/microgalaxy/resources/tutorials.tsv b/communities/microgalaxy/resources/tutorials.tsv
index 3b1e593f..ef7358df 100644
--- a/communities/microgalaxy/resources/tutorials.tsv
+++ b/communities/microgalaxy/resources/tutorials.tsv
@@ -1,50 +1,50 @@
 Topic	Title	Link	EDAM topic	EDAM operation	Creation	Last modification	Version	Tutorial	Slides	Video	Workflows	Tools	Servers with precise tool versions	Servers with tool but different versions	Feedback number	Feedback mean note	Visitors	Page views	Visit duration	Video views
-Assembly	Assembly of metagenomic sequencing data	https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html	Metagenomics, Sequence assembly	Visualisation, Sequencing quality control, Primer removal, Sequence file editing, Formatting, Read mapping, Sequence assembly validation, Sequence composition calculation, Sequence assembly visualisation, Local alignment, Genome assembly, Sequence trimming, Statistical calculation, Sequence contamination filtering, Sequence alignment analysis, Read pre-processing, Data handling, Variant calling	2024-08-18	2024-08-18	0	True	False	False	True	bg_uniq, megahit_contig2fastg, ngsutils_bam_filter, megahit, bowtie2, tp_cat, quast, random_lines1, collection_column_join, filter_tabular, seqtk_subseq, fastqc, bandage_info, coverm_contig, bandage_image, bamtools, cutadapt, metaspades		UseGalaxy.cz, UseGalaxy.eu	0		2	2	0.1	0
-Assembly	Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)	https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html	Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial Resistance	Visualisation, Sequencing quality control, Sequence contamination filtering, Genome assembly, De-novo assembly, Sequence alignment, Box-Whisker plot plotting, Sequence assembly validation, Sequence composition calculation, Read mapping, Scatter plot plotting, Mapping assembly, Sequencing error detection, Sequence assembly visualisation, Cross-assembly, Filtering, Statistical calculation	2021-03-24	2024-03-13	14	True	False	False	True	nanoplot, fastp, CONVERTER_bz2_to_uncompressed, filtlong, flye, bwa_mem2, quast, fastqc, polypolish, bandage_image, upload1, porechop	UseGalaxy.eu	UseGalaxy.cz	0		6851	10571	3.433333333333333	0
-Assembly	Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data	https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html	Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology	Visualisation, Sequencing quality control, Sequence contamination filtering, Sequence assembly validation, Sequence composition calculation, Sequence assembly visualisation, Genome assembly, Statistical calculation	2021-03-24	2024-03-13	14	True	False	False	True	fastp, shovill, quast, fastqc, bandage_info, bandage_image, upload1	UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)	Galaxy@AuBi, GalaxyTrakr, UseGalaxy.no	0		6432	10369	3.75	0
-Assembly	Making sense of a newly assembled genome	https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html	Sequence assembly, Genomics, Microbiology	Genome visualisation, Sequence alignment, Mapping, Read mapping, Sequence visualisation	2018-06-14	2024-06-24	29	True	False	False	True	circos, lastz_wrapper_2, random_lines1, Cut1, circos_interval_to_tiles, addValue, collapse_dataset, Grep1, datamash_ops, bedtools_sortbed, tp_sort_header_tool, bedtools_complementbed, tp_replace_in_column, circos_aln_to_links, cat1, tp_cat, fasta_filter_by_length, Filter1, tp_sed_tool, fasta_compute_length, tp_replace_in_line, join1, upload1, jbrowse, bedtools_intersectbed, tp_grep_tool, mergeCols1			0		5938	12067	3.033333333333333	0
-Assembly	Unicycler Assembly	https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html	Sequence assembly, Genomics, Microbiology	Visualisation, Sequencing quality control, Genome annotation, Sequence assembly validation, Sequence composition calculation, Coding region prediction, Validation, Genome assembly, Gene prediction, Statistical calculation, Aggregation	2017-10-11	2024-03-13	23	True	True	False	True	multiqc, quast, prokka, fastqc, unicycler	UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au	GalaxyTrakr, HyPhy HIV NGS Tools, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	0		2074750	5746521	4.55	0
-Ecology	Checking expected species and contamination in bacterial isolate	https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html	Whole genome sequencing, Genomics, Microbiology, Microbial ecology	Cross-assembly, Taxonomic classification, Expression analysis, Statistical calculation	2024-03-04	2024-06-27	4	True	False	False	True	est_abundance, upload1, kraken2, recentrifuge	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main)	0		229	302	3.95	0
-Evolution	Identifying tuberculosis transmission links: from SNPs to transmission clusters	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html	Genomics, Microbiology, Infectious disease, DNA polymorphism	Variant calling, Phylogenetic tree visualisation, Phylogenetic tree generation, Antimicrobial resistance prediction	2022-03-16	2024-07-12	12	True	False	False	True	Grep1, bcftools_consensus, tb_variant_filter, upload1, samtools_view, snp_sites, tb_profiler_profile, tp_grep_tool, tp_cat, snippy, tp_easyjoin_tool, addName, tp_sed_tool, tp_replace_in_line, snp_dists, collapse_dataset, __MERGE_COLLECTION__, trimmomatic	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main)	0		1533	2414	3.1333333333333333	0
-Evolution	Tree thinking for tuberculosis evolution and epidemiology	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html	Genomics, Microbiology, Phylogeny, Infectious disease	Sequence analysis, Phylogenetic tree analysis	2022-03-16	2024-03-12	11	True	False	False	True	interactive_tool_rstudio, upload1, raxml	UseGalaxy.eu	UseGalaxy.fr, UseGalaxy.org (Main)	0		1308	1983	2.183333333333333	0
-Genome Annotation	Genome annotation with Prokka	https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis	Genome visualisation, Genome annotation, Gene prediction, Coding region prediction	2018-03-06	2024-08-08	25	True	True	True	True	prokka, jbrowse	UseGalaxy.eu, UseGalaxy.org (Main)	Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		2079352	5754405	4.333333333333333	0
-Genome Annotation	Refining Genome Annotations with Apollo (prokaryotes)	https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis	Genome visualisation	2021-06-04	2024-08-08	20	True	True	True	True	jbrowse, create_or_update, list_organism, iframe, create_account		UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no	0		1836817	4949160	4.95	0
-Genome Annotation	Identification of AMR genes in an assembled bacterial genome	https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html	Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance	Genome visualisation, Genome annotation, Read mapping	2024-01-23	2024-03-13	5	True	False	False	True	Grep1, jbrowse, bowtie2, tbl2gff3, bakta, staramr_search, upload1	UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi	0		967	1368	2.933333333333333	0
-Genome Annotation	Bacterial Genome Annotation	https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements	Genome assembly, Sequence motif recognition, Genome annotation, Nucleic acid feature detection, Structural variation detection, Multilocus sequence typing, Genome visualisation, Protein feature detection, Scaffolding	2024-02-01	2024-08-01	4	True	False	False	True	Grouping1, jbrowse, upload1, integron_finder, isescan, tp_tail_tool, plasmidfinder, tbl2gff3, bakta, tp_replace_in_column	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, UseGalaxy.cz	0		1800	2378	2.3333333333333335	0
-Genome Annotation	Comparative gene analysis in unannotated genomes	https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html	Genomics, Gene and protein families, Sequence analysis, Phylogeny	Multiple sequence alignment, Database search, Transcriptome assembly, Coding region prediction, De-novo assembly, Sequence alignment analysis, Phylogenetic tree generation	2022-09-08	2024-03-18	8	True	False	False	True	tab2fasta, cat1, orfipy, Add_a_column1, rbc_mafft, rapidnj, bg_diamond_view, regexColumn1, Cut1, bg_diamond_makedb, Filter1, bg_diamond, tp_split_on_column, join1, gops_intersect_1, collapse_dataset	UseGalaxy.eu, UseGalaxy.org (Main)	UseGalaxy.cz	0		974	1476	3.1	0
-Genome Annotation	Essential genes detection with Transposon insertion sequencing	https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html	Genomics, Microbiology, Sequence analysis, Mobile genetic elements	Transposon prediction, Primer removal, Sequence trimming, Read pre-processing	2019-07-02	2024-03-18	12	True	True	False	True	transit_gumbel, Add_a_column1, deeptools_bam_coverage, tp_easyjoin_tool, bg_find_subsequences, Cut1, Filter1, tp_sort_header_tool, bowtie_wrapper, gff_to_prot, cutadapt, __EXTRACT_DATASET__	UseGalaxy.no, UseGalaxy.org.au	UseGalaxy.cz, UseGalaxy.eu	0		2070408	5739476	4.25	0
-Genome Annotation	Genome annotation with Prokka	https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis	Genome visualisation, Genome annotation, Gene prediction, Coding region prediction	2018-03-06	2024-08-08	25	True	True	True	True	prokka, jbrowse	UseGalaxy.eu, UseGalaxy.org (Main)	Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		2079352	5754405	4.333333333333333	0
-Assembly	Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)	https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html	Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial Resistance	Visualisation, Sequencing quality control, Sequence contamination filtering, Genome assembly, De-novo assembly, Sequence alignment, Box-Whisker plot plotting, Sequence assembly validation, Sequence composition calculation, Read mapping, Scatter plot plotting, Mapping assembly, Sequencing error detection, Sequence assembly visualisation, Cross-assembly, Filtering, Statistical calculation	2021-03-24	2024-03-13	14	True	False	False	True	nanoplot, fastp, CONVERTER_bz2_to_uncompressed, filtlong, flye, bwa_mem2, quast, fastqc, polypolish, bandage_image, upload1, porechop	UseGalaxy.eu	UseGalaxy.cz	0		6851	10571	3.433333333333333	0
-Assembly	Making sense of a newly assembled genome	https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html	Sequence assembly, Genomics, Microbiology	Genome visualisation, Sequence alignment, Mapping, Read mapping, Sequence visualisation	2018-06-14	2024-06-24	29	True	False	False	True	circos, lastz_wrapper_2, random_lines1, Cut1, circos_interval_to_tiles, addValue, collapse_dataset, Grep1, datamash_ops, bedtools_sortbed, tp_sort_header_tool, bedtools_complementbed, tp_replace_in_column, circos_aln_to_links, cat1, tp_cat, fasta_filter_by_length, Filter1, tp_sed_tool, fasta_compute_length, tp_replace_in_line, join1, upload1, jbrowse, bedtools_intersectbed, tp_grep_tool, mergeCols1			0		5938	12067	3.033333333333333	0
-Variant Analysis	Microbial Variant Calling	https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html	Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation	Genome visualisation, Variant calling, Phylogenetic tree generation, Phylogenetic tree visualisation	2018-02-26	2024-03-15	23	True	False	False	True	jbrowse, snippy	UseGalaxy.eu, UseGalaxy.org (Main)	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		12166	20322	2.0	0
-Genome Annotation	Refining Genome Annotations with Apollo (prokaryotes)	https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis	Genome visualisation	2021-06-04	2024-08-08	20	True	True	True	True	jbrowse, create_or_update, list_organism, iframe, create_account		UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no	0		1836817	4949160	4.95	0
-Genome Annotation	Identification of AMR genes in an assembled bacterial genome	https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html	Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance	Genome visualisation, Genome annotation, Read mapping	2024-01-23	2024-03-13	5	True	False	False	True	Grep1, jbrowse, bowtie2, tbl2gff3, bakta, staramr_search, upload1	UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi	0		967	1368	2.933333333333333	0
-Genome Annotation	Bacterial Genome Annotation	https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements	Genome assembly, Sequence motif recognition, Genome annotation, Nucleic acid feature detection, Structural variation detection, Multilocus sequence typing, Genome visualisation, Protein feature detection, Scaffolding	2024-02-01	2024-08-01	4	True	False	False	True	Grouping1, jbrowse, upload1, integron_finder, isescan, tp_tail_tool, plasmidfinder, tbl2gff3, bakta, tp_replace_in_column	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, UseGalaxy.cz	0		1800	2378	2.3333333333333335	0
-Microbiome	Analyses of metagenomics data - The global picture	https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html	Metagenomics, Microbial ecology, Taxonomy, Sequence analysis	Visualisation, Sequencing quality control, Phylogenetic analysis, Taxonomic classification, Sequence read processing, DNA barcoding, Sequence clustering	2017-06-22	2024-08-09	4	True	False	False	True	mothur_cluster_split, mothur_count_seqs, mothur_classify_otu, mothur_merge_files, mothur_pre_cluster, humann2_regroup_table, mothur_make_biom, mothur_make_group, mothur_screen_seqs, mothur_unique_seqs, mothur_summary_seqs, metaphlan2, humann2, krona-text, mothur_make_shared, taxonomy_krona_chart, mothur_align_seqs, humann2_renorm_table, mothur_classify_seqs, mothur_filter_seqs, metaphlan2krona		UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		3013	4081	2.75	0
-Microbiome	Antibiotic resistance detection	https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html	Metagenomic sequencing, Public health and epidemiology, Metagenomics, Microbiology, Infectious disease, Sequence analysis, Antimicrobial Resistance	De-novo assembly, Sequence analysis, Box-Whisker plot plotting, Pairwise sequence alignment, Scatter plot plotting, Mapping assembly, Sequence assembly visualisation, Genome assembly, Aggregation	2019-06-25	2024-06-14	4	True	False	False	True	nanoplot, gfa_to_fa, racon, PlasFlow, miniasm, minimap2, staramr_search, bandage_image, unicycler	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	0		1130	1752	4.016666666666667	0
-Microbiome	Taxonomic Profiling and Visualization of Metagenomic Data	https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html	Metagenomics, Microbial ecology, Taxonomy, Sequence analysis	Visualisation, Nucleic acid sequence analysis, Taxonomic classification, Phylogenetic tree analysis, Statistical calculation, Aggregation	2023-05-03	2024-06-14	4	True	False	False	True	est_abundance, krakentools_kreport2krona, __UNZIP_COLLECTION__, interactive_tool_phinch, taxonomy_krona_chart, interactive_tool_pavian, kraken2, metaphlan, kraken_biom	UseGalaxy.eu	UseGalaxy.fr, UseGalaxy.org.au	0		3655	4993	1.95	0
-Microbiome	Assembly of metagenomic sequencing data	https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html	Metagenomics, Sequence assembly	Visualisation, Sequencing quality control, Primer removal, Sequence file editing, Formatting, Read mapping, Sequence assembly validation, Sequence composition calculation, Sequence assembly visualisation, Local alignment, Genome assembly, Sequence trimming, Statistical calculation, Sequence contamination filtering, Sequence alignment analysis, Read pre-processing, Data handling, Variant calling	2022-12-05	2024-06-14	4	True	False	False	True	bg_uniq, megahit_contig2fastg, ngsutils_bam_filter, megahit, bowtie2, tp_cat, quast, random_lines1, collection_column_join, filter_tabular, seqtk_subseq, fastqc, bandage_info, coverm_contig, bandage_image, bamtools, cutadapt, metaspades		UseGalaxy.cz, UseGalaxy.eu	0		1376	1931	2.533333333333333	0
-Microbiome	Building an amplicon sequence variant (ASV) table from 16S data using DADA2	https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Visualisation, Analysis, Variant calling, DNA barcoding, Deposition	2024-06-05	2024-08-09	7	True	False	False	True	__UNZIP_COLLECTION__, phyloseq_from_dada2, interactive_tool_phyloseq, dada2_filterAndTrim, Grouping1, __SORTLIST__, dada2_learnErrors, dada2_dada, dada2_plotQualityProfile, tp_replace_in_column, dada2_removeBimeraDenovo, cat1, dada2_assignTaxonomyAddspecies, dada2_mergePairs, dada2_makeSequenceTable, collection_element_identifiers, dada2_seqCounts, tp_replace_in_line, Add_a_column1, tp_head_tool	UseGalaxy.eu		0		614	840	2.066666666666667	0
-Microbiome	Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition	https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html	Metagenomics, Public health and epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis	Visualisation, Sequencing quality control, Sequence composition calculation, Taxonomic classification, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree generation, Phylogenetic tree generation (from molecular sequences), Pairwise sequence alignment, Sequence assembly visualisation, Multilocus sequence typing, Cross-assembly, Genome assembly, Base-calling, Validation, Sequence assembly, Statistical calculation, Phylogenetic tree reconstruction, Sequence contamination filtering, De-novo assembly, Mapping, Box-Whisker plot plotting, Phylogenetic tree analysis, Sequence alignment analysis, Scatter plot plotting, Mapping assembly, Multiple sequence alignment, Data handling, Variant calling, Antimicrobial resistance prediction, Aggregation	2023-01-26	2024-07-26	9	True	False	False	True	__BUILD_LIST__, __FILTER_FAILED_DATASETS__, abricate, newick_display, krakentools_extract_kraken_reads, Count1, Cut1, snpSift_extractFields, kraken2, table_compute, fasta2tab, Remove beginning1, fasttree, add_line_to_file, collapse_dataset, Grep1, Grouping1, bcftools_consensus, bcftools_norm, ggplot2_heatmap, collection_column_join, clair3, tp_sorted_uniq, fasta_merge_files_and_filter_unique_sequences, tp_replace_in_column, CONVERTER_gz_to_uncompressed, regex1, porechop, tab2fasta, __FILTER_EMPTY_DATASETS__, taxonomy_krona_chart, tp_find_and_replace, tp_cut_tool, Paste1, flye, mlst, bedtools_getfastabed, collection_element_identifiers, bandage_image, tp_split_on_column, clustalw, regexColumn1, medaka_consensus_pipeline, samtools_coverage, krakentools_kreport2krona, barchart_gnuplot, nanoplot, param_value_from_file, compose_text_param, fastp, tp_multijoin_tool, multiqc, samtools_fastx, bamtools_split_mapped, snpSift_filter, samtools_depth, fastqc, minimap2, split_file_to_collection, Add_a_column1, tp_head_tool	UseGalaxy.eu		0		1680	2521	3.0166666666666666	0
-Microbiome	16S Microbial analysis with Nanopore data	https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Visualisation, Sequencing quality control, Sequence contamination filtering, Validation, Sequence composition calculation, Taxonomic classification, Statistical calculation	2020-11-24	2024-07-31	5	True	False	False	True	fastp, multiqc, taxonomy_krona_chart, fastqc, kraken2, tp_replace_in_line, Remove beginning1, datamash_reverse, porechop	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	GalaxyTrakr, UseGalaxy.cz	0		2344	3314	2.8	0
-Microbiome	Identification of the micro-organisms in a beer using Nanopore sequencing	https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html	Metagenomics, Microbial ecology, Taxonomy, Sequence analysis	Visualisation, Sequencing quality control, Sequence contamination filtering, Sequence composition calculation, Taxonomic classification, Statistical calculation, Aggregation	2022-09-29	2024-06-14	4	True	False	False	True	fastp, taxonomy_krona_chart, fastqc, kraken2, Filter1, porechop, krakentools_kreport2krona	GalaxyTrakr, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.cz	0		1103	1743	2.816666666666667	0
-Microbiome	Metatranscriptomics analysis using microbiome RNA-seq data	https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html	Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis	Visualisation, Primer removal, Sequencing quality control, Sequence similarity search, Phylogenetic analysis, Taxonomic classification, Nucleic acid sequence analysis, Sequence composition calculation, Phylogenetic inference, Validation, Sequence trimming, Conversion, Statistical calculation, Species frequency estimation, Phylogenetic tree editing, Sequence comparison, Phylogenetic tree analysis, Sequence alignment analysis, Read pre-processing, Phylogenetic tree visualisation	2019-11-21	2024-06-14	4	True	True	False	True	humann_rename_table, Cut1, graphlan_annotate, humann_regroup_table, metaphlan, Grep1, export2graphlan, bg_sortmerna, humann_split_stratified_table, graphlan, fastq_paired_end_interlacer, combine_metaphlan2_humann2, taxonomy_krona_chart, tp_find_and_replace, humann_unpack_pathways, cutadapt, humann, multiqc, fastqc, humann_renorm_table	UseGalaxy.org (Main)	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		2066154	5729924	4.133333333333334	0
-Microbiome	Metatranscriptomics analysis using microbiome RNA-seq data (short)	https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html	Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis	Visualisation, Primer removal, Sequencing quality control, Sequence similarity search, Phylogenetic analysis, Taxonomic classification, Nucleic acid sequence analysis, Sequence composition calculation, Phylogenetic inference, Validation, Sequence trimming, Conversion, Statistical calculation, Species frequency estimation, Phylogenetic tree editing, Sequence comparison, Phylogenetic tree analysis, Sequence alignment analysis, Read pre-processing, Phylogenetic tree visualisation	2020-02-13	2024-06-14	4	True	False	False	True	humann_rename_table, Cut1, graphlan_annotate, humann_regroup_table, metaphlan, Grep1, export2graphlan, bg_sortmerna, humann_split_stratified_table, graphlan, fastq_paired_end_interlacer, combine_metaphlan2_humann2, taxonomy_krona_chart, tp_find_and_replace, humann_unpack_pathways, cutadapt, humann, multiqc, fastqc, humann_renorm_table	UseGalaxy.org (Main)	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		234	297	1.6666666666666667	0
-Microbiome	Binning of metagenomic sequencing data	https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html	Metagenomics, Sequence assembly	Sequencing quality control, Validation, Genome assembly, Sequence assembly validation, Statistical calculation, Sequence composition calculation	2023-12-05	2024-03-14	3	True	False	False	False	megahit, checkm_lineage_wf	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr		0		1648	1997	1.4833333333333334	0
-Microbiome	QIIME 2 Moving Pictures	https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis		2024-03-14	2024-03-14	1	external	False	False	False			UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr	0		112	171	3.816666666666667	0
-Microbiome	QIIME 2 Cancer Microbiome Intervention	https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis		2024-02-12	2024-03-14	3	external	False	False	False			UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr	0		119	220	2.716666666666667	0
-Microbiome	16S Microbial Analysis with mothur (short)	https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Visualisation, Sequencing quality control, Phylogenetic analysis, Taxonomic classification, Phylogenetic tree analysis, Phylogenetic tree generation, Sequence read processing, DNA barcoding, Sequence clustering, Phylogenetic tree reconstruction	2019-05-13	2024-06-14	5	True	False	False	True	mothur_remove_lineage, mothur_cluster_split, mothur_count_seqs, mothur_dist_shared, mothur_sub_sample, mothur_classify_otu, newick_display, mothur_chimera_vsearch, mothur_venn, mothur_pre_cluster, XY_Plot_1, mothur_rarefaction_single, collapse_dataset, mothur_screen_seqs, mothur_unique_seqs, mothur_count_groups, mothur_heatmap_sim, mothur_summary_seqs, mothur_tree_shared, mothur_remove_groups, mothur_make_shared, mothur_summary_single, mothur_cluster, mothur_classify_seqs, mothur_dist_seqs, mothur_filter_seqs, mothur_remove_seqs	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.cz, UseGalaxy.fr	0		1744	3211	5.733333333333333	0
-Microbiome	16S Microbial Analysis with mothur (extended)	https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Visualisation, Sequencing quality control, Phylogenetic analysis, Taxonomic classification, Phylogenetic tree analysis, Phylogenetic tree generation, Sequence read processing, DNA barcoding, Sequence clustering, Phylogenetic tree reconstruction	2017-02-12	2024-03-14	4	True	False	False	True	mothur_remove_lineage, mothur_cluster_split, mothur_count_seqs, mothur_dist_shared, mothur_make_contigs, mothur_classify_otu, mothur_sub_sample, mothur_taxonomy_to_krona, mothur_chimera_vsearch, newick_display, mothur_venn, mothur_pre_cluster, XY_Plot_1, mothur_rarefaction_single, mothur_make_biom, mothur_screen_seqs, mothur_unique_seqs, mothur_count_groups, mothur_heatmap_sim, mothur_summary_seqs, mothur_tree_shared, mothur_remove_groups, mothur_make_shared, taxonomy_krona_chart, mothur_summary_single, mothur_cluster, mothur_seq_error, mothur_align_seqs, mothur_classify_seqs, mothur_get_groups, mothur_dist_seqs, mothur_filter_seqs, mothur_remove_seqs	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	0		4695	7229	2.9833333333333334	0
-Variant Analysis	M. tuberculosis Variant Analysis	https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html	Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease	Global alignment, Sequencing quality control, Sequence contamination filtering, Sequence alignment, Sequence analysis, Sequence composition calculation, Sequence alignment analysis, Taxonomic classification, Phylogenetic tree generation, Variant calling, Local alignment, Phylogenetic tree visualisation, Validation, Genome visualisation, Statistical calculation, Antimicrobial resistance prediction	2020-07-25	2024-07-26	30	True	False	False	True	tp_awk_tool, kraken2, bcftools_consensus, mosdepth, EMBOSS: seqret84, tb_profiler_profile, qualimap_bamqc, samtools_stats, tb_variant_filter, tp_sed_tool, EMBOSS:%20seqret84, upload1, tbvcfreport, fastp, jbrowse, multiqc, jvarkit_wgscoverageplotter, snippy, fastqc, __FLATTEN__			0		5641	8997	2.95	0
-Genome Annotation	Identification of AMR genes in an assembled bacterial genome	https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html	Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance	Genome visualisation, Genome annotation, Read mapping	2024-01-23	2024-03-13	5	True	False	False	True	Grep1, jbrowse, bowtie2, tbl2gff3, bakta, staramr_search, upload1	UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi	0		967	1368	2.933333333333333	0
-Evolution	Identifying tuberculosis transmission links: from SNPs to transmission clusters	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html	Genomics, Microbiology, Infectious disease, DNA polymorphism	Variant calling, Phylogenetic tree visualisation, Phylogenetic tree generation, Antimicrobial resistance prediction	2022-03-16	2024-07-12	12	True	False	False	True	Grep1, bcftools_consensus, tb_variant_filter, upload1, samtools_view, snp_sites, tb_profiler_profile, tp_grep_tool, tp_cat, snippy, tp_easyjoin_tool, addName, tp_sed_tool, tp_replace_in_line, snp_dists, collapse_dataset, __MERGE_COLLECTION__, trimmomatic	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main)	0		1533	2414	3.1333333333333333	0
-Evolution	Tree thinking for tuberculosis evolution and epidemiology	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html	Genomics, Microbiology, Phylogeny, Infectious disease	Sequence analysis, Phylogenetic tree analysis	2022-03-16	2024-03-12	11	True	False	False	True	interactive_tool_rstudio, upload1, raxml	UseGalaxy.eu	UseGalaxy.fr, UseGalaxy.org (Main)	0		1308	1983	2.183333333333333	0
-Microbiome	16S Microbial analysis with Nanopore data	https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Visualisation, Sequencing quality control, Sequence contamination filtering, Validation, Sequence composition calculation, Taxonomic classification, Statistical calculation	2020-11-24	2024-07-31	5	True	False	False	True	fastp, multiqc, taxonomy_krona_chart, fastqc, kraken2, tp_replace_in_line, Remove beginning1, datamash_reverse, porechop	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	GalaxyTrakr, UseGalaxy.cz	0		2344	3314	2.8	0
-Proteomics	metaQuantome 2: Function	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html	Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics	Visualisation, Differential protein expression analysis, Functional clustering, Query and retrieval, Indexing, Filtering, Heat map generation, Statistical inference, Principal component visualisation, Quantification	2020-10-29	2024-03-15	14	True	False	False	True	metaquantome_db, metaquantome_sample, metaquantome_stat, metaquantome_expand, metaquantome_filter, metaquantome_viz	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		348	504	3.8	0
-Proteomics	metaQuantome 3: Taxonomy	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html	Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy	Visualisation, Differential protein expression analysis, Functional clustering, Query and retrieval, Indexing, Filtering, Heat map generation, Statistical inference, Principal component visualisation, Quantification	2020-10-29	2024-03-15	14	True	False	False	True	metaquantome_db, metaquantome_sample, metaquantome_stat, metaquantome_expand, metaquantome_filter, metaquantome_viz	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		371	502	2.6333333333333333	0
-Proteomics	metaQuantome 1: Data creation	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html	Proteomics, Proteogenomics, Biodiversity, Taxonomy	Visualisation, Label-free quantification, Filtering, Formatting, Prediction and recognition	2020-10-16	2024-03-14	20	True	False	False	True	Grep1, msconvert, peptide_shaker, search_gui, Cut1, unipept, Filter1, query_tabular, tp_replace_in_line, Remove beginning1, regex1, flashlfq, tp_replace_in_column	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		773	1343	3.8	0
-Proteomics	Metaproteomics tutorial	https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html	Proteomics, Proteogenomics, Biodiversity, Taxonomy	Visualisation, Prediction and recognition	2017-06-28	2024-06-14	41	True	False	False	True	sqlite_to_tabular, peptide_shaker, search_gui, unipept, query_tabular	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.cz	0		2256	3750	2.6166666666666667	0
-Sequence analysis	Quality and contamination control in bacterial isolate using Illumina MiSeq Data	https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html	Whole genome sequencing, Genomics, Microbiology, Microbial ecology	Sequencing quality control, Sequence contamination filtering, Cross-assembly, Sequence composition calculation, Taxonomic classification, Expression analysis, Statistical calculation	2024-07-15	2024-07-15	1	True	False	False	True	fastp, est_abundance, fastqc, kraken2, recentrifuge, upload1	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main)	0		61	76	3.8833333333333333	0
-Variant Analysis	Calling variants in non-diploid systems	https://training.galaxyproject.org//topics/variant-analysis/tutorials/non-dip/tutorial.html	Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation	Sequencing quality control, Genome indexing, Sequence alignment, Formatting, Sequence composition calculation, Sequence alignment analysis, Read mapping, Generation, Data handling, Variant calling, Statistical calculation	2017-02-16	2024-03-15	23	True	False	False	True	picard_MarkDuplicates, freebayes, vcf2tsv, picard_MergeSamFiles, vcffilter2, bamFilter, Cut1, fastqc, bamleftalign, bwa_mem	UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main)	UseGalaxy.cz, UseGalaxy.org.au	0		7035	13427	2.05	0
-Variant Analysis	M. tuberculosis Variant Analysis	https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html	Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease	Global alignment, Sequencing quality control, Sequence contamination filtering, Sequence alignment, Sequence analysis, Sequence composition calculation, Sequence alignment analysis, Taxonomic classification, Phylogenetic tree generation, Variant calling, Local alignment, Phylogenetic tree visualisation, Validation, Genome visualisation, Statistical calculation, Antimicrobial resistance prediction	2020-07-25	2024-07-26	30	True	False	False	True	tp_awk_tool, kraken2, bcftools_consensus, mosdepth, EMBOSS: seqret84, tb_profiler_profile, qualimap_bamqc, samtools_stats, tb_variant_filter, tp_sed_tool, EMBOSS:%20seqret84, upload1, tbvcfreport, fastp, jbrowse, multiqc, jvarkit_wgscoverageplotter, snippy, fastqc, __FLATTEN__			0		5641	8997	2.95	0
-Variant Analysis	Microbial Variant Calling	https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html	Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation	Genome visualisation, Variant calling, Phylogenetic tree generation, Phylogenetic tree visualisation	2018-02-26	2024-03-15	23	True	False	False	True	jbrowse, snippy	UseGalaxy.eu, UseGalaxy.org (Main)	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		12166	20322	2.0	0
+Assembly	Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data	https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html	Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology	Sequence assembly validation, Statistical calculation, Sequence assembly visualisation, Visualisation, Genome assembly, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering	2021-03-24	2024-09-18	15	True	False	False	True	fastp, bandage_image, upload1, bandage_info, quast, fastqc, shovill	UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)	Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.no	0		6735	10837	3.783333333333333	0
+Assembly	Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)	https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html	Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial Resistance	Scatter plot plotting, Sequencing error detection, Sequence alignment, Visualisation, Cross-assembly, Read mapping, Sequencing quality control, Genome assembly, De-novo assembly, Box-Whisker plot plotting, Sequence contamination filtering, Sequence assembly validation, Mapping assembly, Statistical calculation, Sequence assembly visualisation, Filtering, Sequence composition calculation	2021-03-24	2024-03-13	14	True	False	False	True	CONVERTER_bz2_to_uncompressed, fastp, filtlong, bandage_image, porechop, upload1, quast, flye, nanoplot, bwa_mem2, polypolish, fastqc	UseGalaxy.eu	UseGalaxy.cz	0		7147	10976	3.4	0
+Assembly	Assembly of metagenomic sequencing data	https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html	Metagenomics, Sequence assembly	Data handling, Visualisation, Sequence trimming, Read mapping, Sequencing quality control, Genome assembly, Sequence alignment analysis, Sequence contamination filtering, Sequence assembly validation, Variant calling, Statistical calculation, Sequence assembly visualisation, Sequence file editing, Local alignment, Sequence composition calculation, Read pre-processing, Primer removal, Formatting	2024-10-02	2024-10-02	0	True	False	False	True	ngsutils_bam_filter, tp_cat, bamtools, bandage_image, filter_tabular, megahit_contig2fastg, bandage_info, bg_uniq, quast, seqtk_subseq, cutadapt, random_lines1, collection_column_join, megahit, coverm_contig, fastqc, metaspades, bowtie2		UseGalaxy.cz, UseGalaxy.eu	0		6	7	0.38333333333333336	0
+Assembly	Unicycler Assembly	https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html	Sequence assembly, Genomics, Microbiology	Genome annotation, Visualisation, Genome assembly, Sequencing quality control, Sequence assembly validation, Gene prediction, Statistical calculation, Aggregation, Validation, Sequence composition calculation, Coding region prediction	2017-10-11	2024-03-13	23	True	True	False	True	prokka, unicycler, quast, multiqc, fastqc	UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au	GalaxyTrakr, HyPhy HIV NGS Tools, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	0		2144791	5917098	4.566666666666666	0
+Assembly	Making sense of a newly assembled genome	https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html	Sequence assembly, Genomics, Microbiology	Sequence alignment, Sequence visualisation, Read mapping, Genome visualisation, Mapping	2018-06-14	2024-06-24	29	True	False	False	True	join1, tp_sed_tool, lastz_wrapper_2, upload1, fasta_filter_by_length, bedtools_intersectbed, datamash_ops, circos_interval_to_tiles, jbrowse, tp_cat, mergeCols1, Filter1, bedtools_sortbed, tp_sort_header_tool, Grep1, Cut1, collapse_dataset, cat1, tp_replace_in_column, addValue, circos_aln_to_links, fasta_compute_length, circos, tp_grep_tool, tp_replace_in_line, random_lines1, bedtools_complementbed			0		6026	12166	3.0166666666666666	0
+Ecology	Checking expected species and contamination in bacterial isolate	https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html	Whole genome sequencing, Genomics, Microbiology, Microbial ecology	Statistical calculation, Taxonomic classification, Cross-assembly, Expression analysis	2024-03-04	2024-06-27	4	True	False	False	True	recentrifuge, kraken2, upload1, est_abundance	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main)	0		260	343	3.533333333333333	0
+Evolution	Tree thinking for tuberculosis evolution and epidemiology	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html	Genomics, Microbiology, Phylogeny, Infectious disease	Phylogenetic tree analysis, Sequence analysis	2022-03-16	2024-03-12	11	True	False	False	True	upload1, interactive_tool_rstudio, raxml	UseGalaxy.eu	UseGalaxy.fr, UseGalaxy.org (Main)	0		1373	2071	2.2333333333333334	0
+Evolution	Identifying tuberculosis transmission links: from SNPs to transmission clusters	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html	Genomics, Microbiology, Infectious disease, DNA polymorphism	Phylogenetic tree visualisation, Variant calling, Antimicrobial resistance prediction, Phylogenetic tree generation	2022-03-16	2024-07-12	12	True	False	False	True	tp_sed_tool, tp_easyjoin_tool, tp_cat, bcftools_consensus, samtools_view, upload1, snippy, tp_grep_tool, tp_replace_in_line, snp_dists, Grep1, tb_variant_filter, tb_profiler_profile, collapse_dataset, snp_sites, trimmomatic, __MERGE_COLLECTION__, addName	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main)	0		1605	2499	3.05	0
+Genome Annotation	Genome annotation with Prokka	https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis	Genome visualisation, Gene prediction, Genome annotation, Coding region prediction	2018-03-06	2024-08-08	25	True	True	True	True	jbrowse, prokka	UseGalaxy.eu, UseGalaxy.org (Main)	Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		2149523	5925124	4.316666666666666	0
+Genome Annotation	Identification of AMR genes in an assembled bacterial genome	https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html	Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance	Genome visualisation, Genome annotation, Read mapping	2024-01-23	2024-09-27	6	True	False	False	True	jbrowse, tbl2gff3, upload1, Grep1, staramr_search, bakta, bowtie2	UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, UseGalaxy.org (Main)	0		1138	1576	2.75	0
+Genome Annotation	Refining Genome Annotations with Apollo (prokaryotes)	https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis	Genome visualisation	2021-06-04	2024-08-08	20	True	True	True	True	jbrowse, create_or_update, iframe, list_organism, create_account		UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no	0		1906178	5119567	4.983333333333333	0
+Genome Annotation	Bacterial Genome Annotation	https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements	Genome annotation, Nucleic acid feature detection, Multilocus sequence typing, Genome visualisation, Genome assembly, Sequence motif recognition, Structural variation detection, Scaffolding, Protein feature detection	2024-02-01	2024-09-08	5	True	False	False	True	jbrowse, tbl2gff3, plasmidfinder, integron_finder, upload1, isescan, tp_tail_tool, bakta, tp_replace_in_column, Grouping1	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main)	0		2243	2969	2.3333333333333335	0
+Genome Annotation	Comparative gene analysis in unannotated genomes	https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html	Genomics, Gene and protein families, Sequence analysis, Phylogeny	Database search, Transcriptome assembly, Phylogenetic tree generation, De-novo assembly, Sequence alignment analysis, Multiple sequence alignment, Coding region prediction	2022-09-08	2024-03-18	8	True	False	False	True	orfipy, rapidnj, join1, bg_diamond_makedb, Filter1, tp_split_on_column, tab2fasta, collapse_dataset, rbc_mafft, bg_diamond_view, Cut1, Add_a_column1, bg_diamond, regexColumn1, gops_intersect_1, cat1	UseGalaxy.eu, UseGalaxy.org (Main)	UseGalaxy.cz	0		1045	1602	3.5833333333333335	0
+Genome Annotation	Essential genes detection with Transposon insertion sequencing	https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html	Genomics, Microbiology, Sequence analysis, Mobile genetic elements	Sequence trimming, Transposon prediction, Read pre-processing, Primer removal	2019-07-02	2024-03-18	12	True	True	False	True	__EXTRACT_DATASET__, bowtie_wrapper, gff_to_prot, tp_easyjoin_tool, Filter1, transit_gumbel, bg_find_subsequences, tp_sort_header_tool, cutadapt, Cut1, Add_a_column1, deeptools_bam_coverage	UseGalaxy.be, UseGalaxy.no, UseGalaxy.org.au	UseGalaxy.cz, UseGalaxy.eu	0		2140389	5910080	4.266666666666667	0
+Genome Annotation	Genome annotation with Prokka	https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis	Genome visualisation, Gene prediction, Genome annotation, Coding region prediction	2018-03-06	2024-08-08	25	True	True	True	True	jbrowse, prokka	UseGalaxy.eu, UseGalaxy.org (Main)	Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		2149523	5925127	4.316666666666666	0
+Genome Annotation	Identification of AMR genes in an assembled bacterial genome	https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html	Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance	Genome visualisation, Genome annotation, Read mapping	2024-01-23	2024-09-27	6	True	False	False	True	jbrowse, tbl2gff3, upload1, Grep1, staramr_search, bakta, bowtie2	UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, UseGalaxy.org (Main)	0		1138	1576	2.75	0
+Genome Annotation	Refining Genome Annotations with Apollo (prokaryotes)	https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis	Genome visualisation	2021-06-04	2024-08-08	20	True	True	True	True	jbrowse, create_or_update, iframe, list_organism, create_account		UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no	0		1906178	5119570	4.983333333333333	0
+Genome Annotation	Bacterial Genome Annotation	https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements	Genome annotation, Nucleic acid feature detection, Multilocus sequence typing, Genome visualisation, Genome assembly, Sequence motif recognition, Structural variation detection, Scaffolding, Protein feature detection	2024-02-01	2024-09-08	5	True	False	False	True	jbrowse, tbl2gff3, plasmidfinder, integron_finder, upload1, isescan, tp_tail_tool, bakta, tp_replace_in_column, Grouping1	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main)	0		2243	2969	2.3333333333333335	0
+Variant Analysis	Microbial Variant Calling	https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html	Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation	Genome visualisation, Variant calling, Phylogenetic tree visualisation, Phylogenetic tree generation	2018-02-26	2024-03-15	23	True	False	False	True	jbrowse, snippy	UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main)	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		12475	20692	1.9833333333333334	0
+Assembly	Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)	https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html	Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial Resistance	Scatter plot plotting, Sequencing error detection, Sequence alignment, Visualisation, Cross-assembly, Read mapping, Sequencing quality control, Genome assembly, De-novo assembly, Box-Whisker plot plotting, Sequence contamination filtering, Sequence assembly validation, Mapping assembly, Statistical calculation, Sequence assembly visualisation, Filtering, Sequence composition calculation	2021-03-24	2024-03-13	14	True	False	False	True	CONVERTER_bz2_to_uncompressed, fastp, filtlong, bandage_image, porechop, upload1, quast, flye, nanoplot, bwa_mem2, polypolish, fastqc	UseGalaxy.eu	UseGalaxy.cz	0		7148	10977	3.4	0
+Assembly	Making sense of a newly assembled genome	https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html	Sequence assembly, Genomics, Microbiology	Sequence alignment, Sequence visualisation, Read mapping, Genome visualisation, Mapping	2018-06-14	2024-06-24	29	True	False	False	True	join1, tp_sed_tool, lastz_wrapper_2, upload1, fasta_filter_by_length, bedtools_intersectbed, datamash_ops, circos_interval_to_tiles, jbrowse, tp_cat, mergeCols1, Filter1, bedtools_sortbed, tp_sort_header_tool, Grep1, Cut1, collapse_dataset, cat1, tp_replace_in_column, addValue, circos_aln_to_links, fasta_compute_length, circos, tp_grep_tool, tp_replace_in_line, random_lines1, bedtools_complementbed			0		6026	12166	3.0166666666666666	0
+Microbiome	Analyses of metagenomics data - The global picture	https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html	Metagenomics, Microbial ecology, Taxonomy, Sequence analysis	DNA barcoding, Visualisation, Phylogenetic analysis, Sequencing quality control, Taxonomic classification, Sequence read processing, Sequence clustering	2017-06-22	2024-08-09	4	True	False	False	True	humann2_regroup_table, mothur_summary_seqs, humann2_renorm_table, mothur_make_biom, mothur_count_seqs, mothur_classify_seqs, mothur_make_group, mothur_make_shared, mothur_filter_seqs, mothur_merge_files, mothur_classify_otu, mothur_align_seqs, humann2, mothur_cluster_split, mothur_screen_seqs, metaphlan2, mothur_pre_cluster, mothur_unique_seqs, taxonomy_krona_chart, krona-text, metaphlan2krona	UseGalaxy.be	UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		3586	4852	2.783333333333333	0
+Microbiome	Identification of the micro-organisms in a beer using Nanopore sequencing	https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html	Metagenomics, Microbial ecology, Taxonomy, Sequence analysis	Taxonomic classification, Statistical calculation, Aggregation, Visualisation, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering	2022-09-29	2024-06-14	4	True	False	False	True	porechop, fastp, Filter1, taxonomy_krona_chart, kraken2, krakentools_kreport2krona, fastqc	GalaxyTrakr, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.cz	0		1239	1942	2.966666666666667	0
+Microbiome	Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition	https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html	Metagenomics, Public health and epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis	Scatter plot plotting, Visualisation, Cross-assembly, Phylogenetic tree generation, Genome assembly, Sequencing quality control, Box-Whisker plot plotting, Multiple sequence alignment, Mapping assembly, Base-calling, Aggregation, Statistical calculation, Pairwise sequence alignment, Validation, Taxonomic classification, Sequence composition calculation, Mapping, Antimicrobial resistance prediction, Phylogenetic tree analysis, Data handling, Multilocus sequence typing, De-novo assembly, Sequence alignment analysis, Phylogenetic tree reconstruction, Sequence contamination filtering, Sequence assembly, Variant calling, Sequence assembly visualisation, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	2023-01-26	2024-09-27	11	True	False	False	True	__FILTER_FAILED_DATASETS__, Count1, minimap2, snpSift_filter, compose_text_param, tab2fasta, tp_find_and_replace, tp_head_tool, tp_multijoin_tool, param_value_from_file, collection_column_join, collection_element_identifiers, bcftools_norm, krakentools_kreport2krona, krakentools_extract_kraken_reads, ggplot2_heatmap, bamtools_split_mapped, fasta_merge_files_and_filter_unique_sequences, barchart_gnuplot, samtools_fastx, flye, medaka_consensus_pipeline, tp_cut_tool, fastqc, snpSift_extractFields, regex1, Grouping1, tp_sorted_uniq, porechop, table_compute, bcftools_consensus, split_file_to_collection, bandage_image, abricate, Paste1, add_line_to_file, tp_split_on_column, multiqc, Grep1, Cut1, collapse_dataset, Remove beginning1, clustalw, bedtools_getfastabed, tp_replace_in_column, fasttree, newick_display, fastp, samtools_coverage, samtools_depth, clair3, taxonomy_krona_chart, __FILTER_EMPTY_DATASETS__, kraken2, __BUILD_LIST__, Add_a_column1, mlst, nanoplot, regexColumn1, CONVERTER_gz_to_uncompressed, fasta2tab	UseGalaxy.eu	UseGalaxy.org.au	0		1964	2918	3.0	0
+Microbiome	Metatranscriptomics analysis using microbiome RNA-seq data	https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html	Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis	Visualisation, Sequencing quality control, Phylogenetic inference, Phylogenetic tree editing, Statistical calculation, Taxonomic classification, Validation, Sequence composition calculation, Sequence comparison, Sequence similarity search, Phylogenetic tree analysis, Sequence trimming, Phylogenetic analysis, Phylogenetic tree visualisation, Sequence alignment analysis, Species frequency estimation, Conversion, Nucleic acid sequence analysis, Read pre-processing, Primer removal	2019-11-21	2024-06-14	4	True	True	False	True	fastq_paired_end_interlacer, tp_find_and_replace, metaphlan, fastqc, humann, graphlan_annotate, graphlan, humann_split_stratified_table, humann_renorm_table, humann_regroup_table, humann_rename_table, cutadapt, combine_metaphlan2_humann2, multiqc, bg_sortmerna, Grep1, Cut1, export2graphlan, humann_unpack_pathways, taxonomy_krona_chart	UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.cz, UseGalaxy.no	0		2136358	5901051	4.266666666666667	0
+Microbiome	Taxonomic Profiling and Visualization of Metagenomic Data	https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html	Metagenomics, Microbial ecology, Taxonomy, Sequence analysis	Phylogenetic tree analysis, Statistical calculation, Taxonomic classification, Aggregation, Visualisation, Nucleic acid sequence analysis	2023-05-03	2024-06-14	4	True	False	False	True	interactive_tool_phinch, est_abundance, taxonomy_krona_chart, interactive_tool_pavian, kraken2, kraken_biom, __UNZIP_COLLECTION__, krakentools_kreport2krona, metaphlan	UseGalaxy.eu	UseGalaxy.fr, UseGalaxy.org.au	0		4443	6096	1.9666666666666666	0
+Microbiome	Metatranscriptomics analysis using microbiome RNA-seq data (short)	https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html	Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis	Visualisation, Sequencing quality control, Phylogenetic inference, Phylogenetic tree editing, Statistical calculation, Taxonomic classification, Validation, Sequence composition calculation, Sequence comparison, Sequence similarity search, Phylogenetic tree analysis, Sequence trimming, Phylogenetic analysis, Phylogenetic tree visualisation, Sequence alignment analysis, Species frequency estimation, Conversion, Nucleic acid sequence analysis, Read pre-processing, Primer removal	2020-02-13	2024-06-14	4	True	False	False	True	fastq_paired_end_interlacer, tp_find_and_replace, metaphlan, fastqc, humann, graphlan_annotate, graphlan, humann_split_stratified_table, humann_renorm_table, humann_regroup_table, humann_rename_table, cutadapt, combine_metaphlan2_humann2, multiqc, bg_sortmerna, Grep1, Cut1, export2graphlan, humann_unpack_pathways, taxonomy_krona_chart	UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.cz, UseGalaxy.no	0		274	351	1.4333333333333333	0
+Microbiome	Antibiotic resistance detection	https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html	Metagenomic sequencing, Public health and epidemiology, Metagenomics, Microbiology, Infectious disease, Sequence analysis, Antimicrobial Resistance	Scatter plot plotting, Genome assembly, Box-Whisker plot plotting, De-novo assembly, Sequence analysis, Mapping assembly, Aggregation, Sequence assembly visualisation, Pairwise sequence alignment	2019-06-25	2024-06-14	4	True	False	False	True	unicycler, minimap2, bandage_image, PlasFlow, racon, nanoplot, gfa_to_fa, staramr_search, miniasm	UseGalaxy.eu	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	0		1281	1950	4.033333333333333	0
+Microbiome	16S Microbial analysis with Nanopore data	https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Taxonomic classification, Statistical calculation, Visualisation, Validation, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering	2020-11-24	2024-07-31	5	True	False	False	True	porechop, fastp, tp_replace_in_line, taxonomy_krona_chart, multiqc, kraken2, datamash_reverse, fastqc, Remove beginning1	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz	0		2758	3844	2.716666666666667	0
+Microbiome	Building an amplicon sequence variant (ASV) table from 16S data using DADA2	https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Variant calling, DNA barcoding, Visualisation, Analysis, Deposition	2024-06-05	2024-09-26	8	True	False	False	True	tp_head_tool, collection_element_identifiers, __UNZIP_COLLECTION__, interactive_tool_phyloseq, dada2_mergePairs, dada2_removeBimeraDenovo, dada2_assignTaxonomyAddspecies, Grouping1, dada2_plotQualityProfile, dada2_filterAndTrim, cat1, tp_replace_in_column, dada2_seqCounts, dada2_makeSequenceTable, tp_replace_in_line, Add_a_column1, dada2_dada, __SORTLIST__, dada2_learnErrors, phyloseq_from_dada2	UseGalaxy.eu		0		1089	1460	1.8333333333333333	0
+Microbiome	Assembly of metagenomic sequencing data	https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html	Metagenomics, Sequence assembly	Data handling, Visualisation, Sequence trimming, Read mapping, Sequencing quality control, Genome assembly, Sequence alignment analysis, Sequence contamination filtering, Sequence assembly validation, Variant calling, Statistical calculation, Sequence assembly visualisation, Sequence file editing, Local alignment, Sequence composition calculation, Read pre-processing, Primer removal, Formatting	2022-12-05	2024-06-14	4	True	False	False	True	ngsutils_bam_filter, tp_cat, bamtools, bandage_image, filter_tabular, megahit_contig2fastg, bandage_info, bg_uniq, quast, seqtk_subseq, cutadapt, random_lines1, collection_column_join, megahit, coverm_contig, fastqc, metaspades, bowtie2		UseGalaxy.cz, UseGalaxy.eu	0		1613	2258	2.95	0
+Microbiome	QIIME 2 Moving Pictures	https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis		2024-03-14	2024-03-14	1	external	False	False	False			UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr	0		131	195	3.3833333333333333	0
+Microbiome	Binning of metagenomic sequencing data	https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html	Metagenomics, Sequence assembly	Sequence assembly validation, Statistical calculation, Sequencing quality control, Validation, Genome assembly, Sequence composition calculation	2023-12-05	2024-09-12	4	True	False	False	False	megahit, checkm_lineage_wf	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	UseGalaxy.org.au	0		2076	2537	1.4166666666666667	0
+Microbiome	QIIME 2 Cancer Microbiome Intervention	https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis		2024-02-12	2024-03-14	3	external	False	False	False			UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr	0		153	281	3.4833333333333334	0
+Microbiome	16S Microbial Analysis with mothur (extended)	https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Phylogenetic tree analysis, DNA barcoding, Visualisation, Phylogenetic analysis, Sequencing quality control, Phylogenetic tree generation, Phylogenetic tree reconstruction, Taxonomic classification, Sequence read processing, Sequence clustering	2017-02-12	2024-03-14	4	True	False	False	True	mothur_dist_shared, mothur_seq_error, mothur_summary_seqs, mothur_remove_lineage, mothur_make_biom, mothur_count_seqs, mothur_get_groups, mothur_classify_seqs, mothur_remove_groups, mothur_make_shared, mothur_filter_seqs, mothur_dist_seqs, mothur_remove_seqs, mothur_rarefaction_single, mothur_venn, mothur_classify_otu, mothur_count_groups, mothur_align_seqs, mothur_taxonomy_to_krona, mothur_heatmap_sim, mothur_chimera_vsearch, mothur_cluster_split, mothur_screen_seqs, newick_display, mothur_pre_cluster, mothur_make_contigs, mothur_unique_seqs, XY_Plot_1, taxonomy_krona_chart, mothur_cluster, mothur_tree_shared, mothur_summary_single, mothur_sub_sample	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	0		5448	8271	2.9833333333333334	0
+Microbiome	16S Microbial Analysis with mothur (short)	https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Phylogenetic tree analysis, DNA barcoding, Visualisation, Phylogenetic analysis, Sequencing quality control, Phylogenetic tree generation, Phylogenetic tree reconstruction, Taxonomic classification, Sequence read processing, Sequence clustering	2019-05-13	2024-06-14	5	True	False	False	True	mothur_dist_shared, mothur_summary_seqs, mothur_remove_lineage, mothur_count_seqs, mothur_classify_seqs, mothur_remove_groups, mothur_make_shared, mothur_filter_seqs, mothur_dist_seqs, mothur_remove_seqs, mothur_rarefaction_single, mothur_venn, mothur_classify_otu, mothur_count_groups, mothur_heatmap_sim, mothur_chimera_vsearch, mothur_cluster_split, mothur_screen_seqs, collapse_dataset, newick_display, mothur_pre_cluster, mothur_unique_seqs, XY_Plot_1, mothur_cluster, mothur_tree_shared, mothur_summary_single, mothur_sub_sample	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr	0		1985	3572	5.616666666666666	0
+Evolution	Tree thinking for tuberculosis evolution and epidemiology	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html	Genomics, Microbiology, Phylogeny, Infectious disease	Phylogenetic tree analysis, Sequence analysis	2022-03-16	2024-03-12	11	True	False	False	True	upload1, interactive_tool_rstudio, raxml	UseGalaxy.eu	UseGalaxy.fr, UseGalaxy.org (Main)	0		1374	2072	2.216666666666667	0
+Evolution	Identifying tuberculosis transmission links: from SNPs to transmission clusters	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html	Genomics, Microbiology, Infectious disease, DNA polymorphism	Phylogenetic tree visualisation, Variant calling, Antimicrobial resistance prediction, Phylogenetic tree generation	2022-03-16	2024-07-12	12	True	False	False	True	tp_sed_tool, tp_easyjoin_tool, tp_cat, bcftools_consensus, samtools_view, upload1, snippy, tp_grep_tool, tp_replace_in_line, snp_dists, Grep1, tb_variant_filter, tb_profiler_profile, collapse_dataset, snp_sites, trimmomatic, __MERGE_COLLECTION__, addName	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main)	0		1605	2499	3.05	0
+Genome Annotation	Identification of AMR genes in an assembled bacterial genome	https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html	Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance	Genome visualisation, Genome annotation, Read mapping	2024-01-23	2024-09-27	6	True	False	False	True	jbrowse, tbl2gff3, upload1, Grep1, staramr_search, bakta, bowtie2	UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, UseGalaxy.org (Main)	0		1138	1576	2.75	0
+Variant Analysis	M. tuberculosis Variant Analysis	https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html	Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease	Sequence alignment, Phylogenetic tree generation, Phylogenetic tree visualisation, Sequencing quality control, Sequence alignment analysis, Genome visualisation, Sequence analysis, Sequence contamination filtering, Variant calling, Global alignment, Statistical calculation, Taxonomic classification, Validation, Local alignment, Sequence composition calculation, Antimicrobial resistance prediction	2020-07-25	2024-07-26	30	True	False	False	True	tp_sed_tool, upload1, snippy, qualimap_bamqc, tb_variant_filter, EMBOSS: seqret84, tb_profiler_profile, mosdepth, jvarkit_wgscoverageplotter, tbvcfreport, tp_awk_tool, fastqc, jbrowse, samtools_stats, bcftools_consensus, multiqc, fastp, kraken2, EMBOSS:%20seqret84, __FLATTEN__			0		5788	9172	2.95	0
+Microbiome	16S Microbial analysis with Nanopore data	https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Taxonomic classification, Statistical calculation, Visualisation, Validation, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering	2020-11-24	2024-07-31	5	True	False	False	True	porechop, fastp, tp_replace_in_line, taxonomy_krona_chart, multiqc, kraken2, datamash_reverse, fastqc, Remove beginning1	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz	0		2758	3844	2.716666666666667	0
+Proteomics	Metaproteomics tutorial	https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html	Proteomics, Proteogenomics, Biodiversity, Taxonomy	Prediction and recognition, Visualisation	2017-06-28	2024-06-14	41	True	False	False	True	query_tabular, peptide_shaker, search_gui, unipept, sqlite_to_tabular	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.be, UseGalaxy.cz	0		2310	3828	2.6333333333333333	0
+Proteomics	metaQuantome 3: Taxonomy	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html	Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy	Visualisation, Indexing, Differential protein expression analysis, Functional clustering, Statistical inference, Principal component visualisation, Query and retrieval, Heat map generation, Quantification, Filtering	2020-10-29	2024-03-15	14	True	False	False	True	metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_expand, metaquantome_viz, metaquantome_db	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		377	509	2.7333333333333334	0
+Proteomics	metaQuantome 2: Function	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html	Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics	Visualisation, Indexing, Differential protein expression analysis, Functional clustering, Statistical inference, Principal component visualisation, Query and retrieval, Heat map generation, Quantification, Filtering	2020-10-29	2024-03-15	14	True	False	False	True	metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_expand, metaquantome_viz, metaquantome_db	UseGalaxy.eu	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		352	508	3.7666666666666666	0
+Proteomics	metaQuantome 1: Data creation	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html	Proteomics, Proteogenomics, Biodiversity, Taxonomy	Prediction and recognition, Visualisation, Filtering, Label-free quantification, Formatting	2020-10-16	2024-03-14	20	True	False	False	True	query_tabular, flashlfq, Filter1, peptide_shaker, regex1, tp_replace_in_line, msconvert, search_gui, unipept, Grep1, Cut1, Remove beginning1, tp_replace_in_column	UseGalaxy.eu	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		781	1353	3.816666666666667	0
+Sequence analysis	Quality and contamination control in bacterial isolate using Illumina MiSeq Data	https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html	Whole genome sequencing, Genomics, Microbiology, Microbial ecology	Cross-assembly, Sequencing quality control, Sequence contamination filtering, Statistical calculation, Taxonomic classification, Expression analysis, Sequence composition calculation	2024-07-15	2024-09-02	2	True	False	False	True	fastp, est_abundance, recentrifuge, upload1, kraken2, fastqc	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main)	0		185	225	2.5166666666666666	0
+Variant Analysis	Calling variants in non-diploid systems	https://training.galaxyproject.org//topics/variant-analysis/tutorials/non-dip/tutorial.html	Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation	Data handling, Sequence alignment, Read mapping, Sequencing quality control, Sequence alignment analysis, Generation, Statistical calculation, Variant calling, Sequence composition calculation, Formatting, Genome indexing	2017-02-16	2024-03-15	23	True	False	False	True	bwa_mem, picard_MarkDuplicates, vcffilter2, bamFilter, picard_MergeSamFiles, Cut1, bamleftalign, fastqc, vcf2tsv, freebayes	UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main)	UseGalaxy.cz, UseGalaxy.org.au	0		7149	13577	2.05	0
+Variant Analysis	M. tuberculosis Variant Analysis	https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html	Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease	Sequence alignment, Phylogenetic tree generation, Phylogenetic tree visualisation, Sequencing quality control, Sequence alignment analysis, Genome visualisation, Sequence analysis, Sequence contamination filtering, Variant calling, Global alignment, Statistical calculation, Taxonomic classification, Validation, Local alignment, Sequence composition calculation, Antimicrobial resistance prediction	2020-07-25	2024-07-26	30	True	False	False	True	tp_sed_tool, upload1, snippy, qualimap_bamqc, tb_variant_filter, EMBOSS: seqret84, tb_profiler_profile, mosdepth, jvarkit_wgscoverageplotter, tbvcfreport, tp_awk_tool, fastqc, jbrowse, samtools_stats, bcftools_consensus, multiqc, fastp, kraken2, EMBOSS:%20seqret84, __FLATTEN__			0		5788	9172	2.95	0
+Variant Analysis	Microbial Variant Calling	https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html	Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation	Genome visualisation, Variant calling, Phylogenetic tree visualisation, Phylogenetic tree generation	2018-02-26	2024-03-15	23	True	False	False	True	jbrowse, snippy	UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main)	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		12476	20693	1.9833333333333334	0
diff --git a/communities/spoc/resources/tools.html b/communities/spoc/resources/tools.html
index e65fd810..2a0f5c66 100644
--- a/communities/spoc/resources/tools.html
+++ b/communities/spoc/resources/tools.html
@@ -87,16 +87,12 @@
       <th>Tools available on UseGalaxy.org.au</th>
       <th>Tools available on UseGalaxy.eu</th>
       <th>Tools available on UseGalaxy.fr</th>
-      <th>Tools available on ANASTASIA</th>
       <th>Tools available on APOSTL</th>
       <th>Tools available on ARGs-OAP</th>
-      <th>Tools available on BF2I-MAP</th>
-      <th>Tools available on BioBix</th>
       <th>Tools available on CIRM-CFBP</th>
-      <th>Tools available on Center for Phage Technology (CPT)</th>
       <th>Tools available on ChemFlow</th>
       <th>Tools available on Coloc-stats</th>
-      <th>Tools available on CorGAT</th>
+      <th>Tools available on CoralSNP</th>
       <th>Tools available on CropGalaxy</th>
       <th>Tools available on Dintor</th>
       <th>Tools available on FreeBioinfo</th>
@@ -116,87 +112,16 @@
       <th>Tools available on Oqtans</th>
       <th>Tools available on Palfinder</th>
       <th>Tools available on PepSimili</th>
-      <th>Tools available on PhagePromotor</th>
-      <th>Tools available on Protologger</th>
       <th>Tools available on UseGalaxy.be</th>
       <th>Tools available on UseGalaxy.cz</th>
       <th>Tools available on UseGalaxy.no</th>
+      <th>Tools available on Viral Variant Visualizer (VVV)</th>
       <th>No. of tool users (2022-2023) (usegalaxy.eu)</th>
       <th>Total tool usage (usegalaxy.eu)</th>
       <th>Deprecated</th>
     </tr>
   </thead>
   <tbody>
-    <tr>
-      <td></td>
-      <td>aegean</td>
-      <td>aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval</td>
-      <td>AEGeAn toolkit wrappers</td>
-      <td>gaeval</td>
-      <td>gaeval</td>
-      <td></td>
-      <td>GAEVAL</td>
-      <td>Gene Annotation EVAluation.</td>
-      <td>Sequence annotation</td>
-      <td>Sequence analysis, Gene structure</td>
-      <td>Up-to-date</td>
-      <td>https://github.com/BrendelGroup/AEGeAn</td>
-      <td>Transcriptomics, Sequence Analysis</td>
-      <td>aegean</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean</td>
-      <td>0.16.0</td>
-      <td>aegean</td>
-      <td>0.16.0</td>
-      <td>Sequence annotation</td>
-      <td>Sequence analysis, Gene structure</td>
-      <td>1</td>
-      <td>4</td>
-      <td>4</td>
-      <td>4</td>
-      <td>1</td>
-      <td>4</td>
-      <td>4</td>
-      <td>4</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>4</td>
-      <td>0</td>
-      <td>47</td>
-      <td>168</td>
-      <td></td>
-    </tr>
     <tr>
       <td></td>
       <td>anndata</td>
@@ -211,30 +136,23 @@
       <td></td>
       <td>To update</td>
       <td>https://anndata.readthedocs.io</td>
-      <td>Transcriptomics, Sequence Analysis</td>
+      <td>Single Cell, Spatial Omics</td>
       <td>anndata</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata</td>
-      <td>0.10.3</td>
+      <td>0.10.9</td>
       <td>anndata</td>
       <td>0.6.22.post1</td>
       <td></td>
       <td></td>
       <td>5</td>
-      <td>4</td>
+      <td>5</td>
       <td>5</td>
       <td>0</td>
       <td>5</td>
-      <td>4</td>
       <td>5</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -263,118 +181,43 @@
       <td>0</td>
       <td>5</td>
       <td>5</td>
+      <td>5</td>
+      <td>0</td>
       <td>625</td>
       <td>35620</td>
       <td></td>
     </tr>
     <tr>
       <td></td>
-      <td>arriba</td>
-      <td>arriba, arriba_draw_fusions, arriba_get_filters</td>
-      <td>Arriba detects fusion genes in RNA-Seq data after running RNA-STAR</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>baredsc</td>
+      <td>baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d</td>
+      <td>baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.</td>
+      <td>baredsc</td>
+      <td>baredsc</td>
       <td></td>
+      <td>baredSC</td>
+      <td>The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.</td>
+      <td>Data retrieval, Expression correlation analysis, Differential gene expression profiling</td>
+      <td>RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability</td>
       <td>Up-to-date</td>
-      <td>https://github.com/suhrig/arriba</td>
-      <td>Sequence Analysis, Transcriptomics</td>
-      <td>arriba</td>
+      <td>https://github.com/lldelisle/baredSC</td>
+      <td>Single Cell, Transcriptomics, Visualization</td>
+      <td>baredsc</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba</td>
-      <td>2.4.0</td>
-      <td>arriba</td>
-      <td>2.4.0</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>3</td>
-      <td>3</td>
-      <td>0</td>
-      <td>0</td>
-      <td>3</td>
-      <td>3</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>3</td>
-      <td>0</td>
-      <td>38</td>
-      <td>3528</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>askor</td>
-      <td>askor_de</td>
-      <td>AskoR links EdgeR and AskOmics</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://github.com/askomics/askoR</td>
-      <td>Transcriptomics</td>
-      <td>askor_de</td>
-      <td>genouest</td>
-      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/askor</td>
-      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/askor</td>
-      <td>0.2</td>
-      <td>bioconductor-limma</td>
-      <td>3.58.1</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc</td>
+      <td>1.1.3</td>
+      <td>baredsc</td>
+      <td>1.1.3</td>
+      <td>Data retrieval, Expression correlation analysis, Differential gene expression profiling</td>
+      <td>RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
       <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -402,39 +245,44 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>4</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>71</td>
       <td></td>
     </tr>
     <tr>
       <td></td>
-      <td>bamparse</td>
-      <td>bamparse</td>
-      <td>Generates hit count lists from bam alignments.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>cite_seq_count</td>
+      <td>cite_seq_count</td>
+      <td>Count CMO/HTO</td>
+      <td>CITE-seq-Count</td>
+      <td>CITE-seq-Count</td>
       <td></td>
+      <td>CITE-seq-Count</td>
+      <td>Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.</td>
+      <td>RNA-Seq quantification</td>
+      <td>Transcriptomics, Immunoproteins and antigens</td>
       <td>To update</td>
-      <td>http://artbio.fr</td>
-      <td>RNA, Transcriptomics</td>
-      <td>bamparse</td>
-      <td>artbio</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse</td>
-      <td>4.1.1</td>
-      <td>pysam</td>
-      <td>0.22.1</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>https://github.com/Hoohm/CITE-seq-Count</td>
+      <td>Single Cell, Transcriptomics, Proteomics</td>
+      <td>cite_seq_count</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count</td>
+      <td>1.4.4</td>
+      <td>cite-seq-count</td>
+      <td>1.4.5</td>
+      <td>RNA-Seq quantification</td>
+      <td>Transcriptomics, Immunoproteins and antigens</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -465,5512 +313,41 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>18</td>
       <td></td>
     </tr>
     <tr>
       <td></td>
-      <td>baredsc</td>
-      <td>baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d</td>
-      <td>baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.</td>
-      <td>baredsc</td>
-      <td>baredsc</td>
-      <td></td>
-      <td>baredSC</td>
-      <td>The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.</td>
-      <td>Data retrieval, Expression correlation analysis, Differential gene expression profiling</td>
-      <td>RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability</td>
-      <td>Up-to-date</td>
-      <td>https://github.com/lldelisle/baredSC</td>
-      <td>Transcriptomics, Visualization</td>
-      <td>baredsc</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc</td>
-      <td>1.1.3</td>
-      <td>baredsc</td>
-      <td>1.1.3</td>
-      <td>Data retrieval, Expression correlation analysis, Differential gene expression profiling</td>
-      <td>RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability</td>
-      <td>4</td>
-      <td>0</td>
-      <td>4</td>
-      <td>0</td>
-      <td>4</td>
-      <td>0</td>
-      <td>4</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>4</td>
-      <td>0</td>
-      <td>0</td>
-      <td>71</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>bctools</td>
-      <td>bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events</td>
-      <td>bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>Up-to-date</td>
-      <td>https://github.com/dmaticzka/bctools</td>
-      <td>Sequence Analysis, Transcriptomics</td>
-      <td></td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools</td>
-      <td>0.2.2</td>
-      <td>bctools</td>
-      <td>0.2.2</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>7</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>7</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>7</td>
-      <td>7</td>
-      <td>87</td>
-      <td>2895</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>brew3r_r</td>
-      <td>brew3r_r</td>
-      <td>Extend 3' end of a GTF using another GTF as a template</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html</td>
-      <td>Transcriptomics, RNA</td>
-      <td>brew3r_r</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r</td>
-      <td>1.0.2</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>cell-types-analysis</td>
-      <td>ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals</td>
-      <td>Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td></td>
-      <td>Transcriptomics, RNA, Statistics</td>
-      <td>suite_cell_types_analysis</td>
-      <td>ebi-gxa</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis</td>
-      <td>1.1.1</td>
-      <td>cell-types-analysis</td>
-      <td>0.1.11</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>6</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>6</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
-      <td>6</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>cemitool</td>
-      <td>cemitool</td>
-      <td>Gene co-expression network analysis tool</td>
-      <td>cemitool</td>
-      <td>cemitool</td>
-      <td></td>
-      <td>CEMiTool</td>
-      <td>It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.</td>
-      <td>Enrichment analysis, Pathway or network analysis</td>
-      <td>Gene expression, Transcriptomics, Microarray experiment</td>
-      <td>To update</td>
-      <td>https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html</td>
-      <td>Transcriptomics, RNA, Statistics</td>
-      <td>cemitool</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool</td>
-      <td>1.18.1</td>
-      <td>bioconductor-cemitool</td>
-      <td>1.26.0</td>
-      <td>Enrichment analysis, Pathway or network analysis</td>
-      <td>Transcriptomics, Microarray experiment</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>9</td>
-      <td>98</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>cherri</td>
-      <td>cherri_eval, cherri_train</td>
-      <td>Computational Help Evaluating RNA-RNA interactions</td>
-      <td>cherri</td>
-      <td>cherri</td>
-      <td></td>
-      <td>cherri</td>
-      <td>CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.</td>
-      <td></td>
-      <td>Molecular interactions, pathways and networks, Structure analysis, Machine learning</td>
-      <td>To update</td>
-      <td>https://github.com/BackofenLab/Cherri</td>
-      <td>Transcriptomics, RNA</td>
-      <td></td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri</td>
-      <td>0.7</td>
-      <td>cherri</td>
-      <td>0.8</td>
-      <td></td>
-      <td>Molecular interactions, pathways and networks, Structure analysis, Machine learning</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>1</td>
-      <td>207</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>chira</td>
-      <td>chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify</td>
-      <td>Chimeric Read Annotator for RNA-RNA interactome data</td>
-      <td>chira</td>
-      <td>chira</td>
-      <td></td>
-      <td>ChiRA</td>
-      <td>ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.</td>
-      <td></td>
-      <td>RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA</td>
-      <td>Up-to-date</td>
-      <td>https://github.com/pavanvidem/chira</td>
-      <td>RNA, Transcriptomics, Sequence Analysis</td>
-      <td>chira</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira</td>
-      <td>1.4.3</td>
-      <td>chira</td>
-      <td>1.4.3</td>
-      <td></td>
-      <td>Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA</td>
-      <td>5</td>
-      <td>0</td>
-      <td>5</td>
-      <td>0</td>
-      <td>5</td>
-      <td>0</td>
-      <td>5</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>5</td>
-      <td>5</td>
-      <td>97</td>
-      <td>6418</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>cite_seq_count</td>
-      <td>cite_seq_count</td>
-      <td>Count CMO/HTO</td>
-      <td>CITE-seq-Count</td>
-      <td>CITE-seq-Count</td>
-      <td></td>
-      <td>CITE-seq-Count</td>
-      <td>Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.</td>
-      <td>RNA-Seq quantification</td>
-      <td>Transcriptomics, Immunoproteins and antigens</td>
-      <td>Up-to-date</td>
-      <td>https://github.com/Hoohm/CITE-seq-Count</td>
-      <td>Transcriptomics</td>
-      <td>cite_seq_count</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count</td>
-      <td>1.4.4</td>
-      <td>cite-seq-count</td>
-      <td>1.4.4</td>
-      <td>RNA-Seq quantification</td>
-      <td>Transcriptomics, Immunoproteins and antigens</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>18</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>cosg</td>
-      <td>cosg</td>
-      <td>Marker gene identification for single-cell sequencing data using COSG.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>Up-to-date</td>
-      <td>https://github.com/genecell/COSG</td>
-      <td>Transcriptomics, Sequence Analysis</td>
-      <td>cosg</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg</td>
-      <td>1.0.1</td>
-      <td>cosg</td>
-      <td>1.0.1</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>cpat</td>
-      <td>cpat</td>
-      <td>Coding-potential assessment tool using an alignment-free logistic regression model.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>Up-to-date</td>
-      <td>https://github.com/liguowang/cpat</td>
-      <td>Transcriptomics</td>
-      <td>cpat</td>
-      <td>bgruening</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/cpat</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/cpat</td>
-      <td>3.0.5</td>
-      <td>cpat</td>
-      <td>3.0.5</td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>21</td>
-      <td>134</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>cpm_tpm_rpk</td>
-      <td>cpm_tpm_rpk</td>
-      <td>Generate CPM,TPM or RPK from raw counts</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>http://artbio.fr</td>
-      <td>Transcriptomics</td>
-      <td>cpm_tpm_rpk</td>
-      <td>artbio</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk</td>
-      <td>0.5.2</td>
-      <td>r-optparse</td>
-      <td>1.3.2</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>crosscontamination_barcode_filter</td>
-      <td>crosscontamination_barcode_filter</td>
-      <td>Barcode contamination discovery tool</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td></td>
-      <td>Transcriptomics, Visualization</td>
-      <td>crosscontamination_barcode_filter</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter</td>
-      <td>0.3</td>
-      <td>r-ggplot2</td>
-      <td>2.2.1</td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>17</td>
-      <td>347</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>cuffcompare</td>
-      <td>cuffcompare</td>
-      <td>Galaxy wrappers for the Cuffcompare tool.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>Up-to-date</td>
-      <td>http://cole-trapnell-lab.github.io/cufflinks/</td>
-      <td>Transcriptomics</td>
-      <td>cuffcompare</td>
-      <td>devteam</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare</td>
-      <td>2.2.1</td>
-      <td>cufflinks</td>
-      <td>2.2.1</td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>65</td>
-      <td>1130</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>cuffdiff</td>
-      <td>cuffdiff</td>
-      <td>Galaxy wrappers for the Cuffdiff tool.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>Up-to-date</td>
-      <td>http://cole-trapnell-lab.github.io/cufflinks/</td>
-      <td>Transcriptomics</td>
-      <td>cuffdiff</td>
-      <td>devteam</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff</td>
-      <td>2.2.1</td>
-      <td>cufflinks</td>
-      <td>2.2.1</td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>228</td>
-      <td>5831</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>cufflinks</td>
-      <td>cufflinks</td>
-      <td>Galaxy wrappers for the Cufflinks tool.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>Up-to-date</td>
-      <td>http://cole-trapnell-lab.github.io/cufflinks/</td>
-      <td>Transcriptomics</td>
-      <td>cufflinks</td>
-      <td>devteam</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks</td>
-      <td>2.2.1</td>
-      <td>cufflinks</td>
-      <td>2.2.1</td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>319</td>
-      <td>32218</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>cuffmerge</td>
-      <td>cuffmerge</td>
-      <td>Galaxy wrappers for the Cuffmerge tool.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>Up-to-date</td>
-      <td>http://cole-trapnell-lab.github.io/cufflinks/</td>
-      <td>Transcriptomics</td>
-      <td>cuffmerge</td>
-      <td>devteam</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge</td>
-      <td>2.2.1</td>
-      <td>cufflinks</td>
-      <td>2.2.1</td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>122</td>
-      <td>3292</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>cuffnorm</td>
-      <td>cuffnorm</td>
-      <td>The Cuffnorm tool</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>Up-to-date</td>
-      <td>http://cole-trapnell-lab.github.io/cufflinks/</td>
-      <td>Transcriptomics</td>
-      <td>cuffnorm</td>
-      <td>devteam</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm</td>
-      <td>2.2.1</td>
-      <td>cufflinks</td>
-      <td>2.2.1</td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>27</td>
-      <td>660</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>cuffquant</td>
-      <td>cuffquant</td>
-      <td>The Cuffquant tool</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>Up-to-date</td>
-      <td>http://cole-trapnell-lab.github.io/cufflinks/</td>
-      <td>Transcriptomics</td>
-      <td>cuffquant</td>
-      <td>devteam</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant</td>
-      <td>2.2.1</td>
-      <td>cufflinks</td>
-      <td>2.2.1</td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>18</td>
-      <td>688</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>data-hca</td>
-      <td>hca_matrix_downloader</td>
-      <td>Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td></td>
-      <td>Transcriptomics, Sequence Analysis</td>
-      <td>suite_human_cell_atlas_tools</td>
-      <td>ebi-gxa</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca</td>
-      <td>v0.0.4+galaxy0</td>
-      <td>hca-matrix-downloader</td>
-      <td>0.0.4</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>34</td>
-      <td>439</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>data-scxa</td>
-      <td>retrieve_scxa</td>
-      <td>Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td></td>
-      <td>Transcriptomics, Sequence Analysis</td>
-      <td>suite_ebi_expression_atlas</td>
-      <td>ebi-gxa</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa</td>
-      <td>v0.0.2+galaxy2</td>
-      <td>wget</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>99</td>
-      <td>799</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>decoupler</td>
-      <td>score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk</td>
-      <td>decoupler - Ensemble of methods to infer biological activities</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://decoupler-py.readthedocs.io/en/latest/</td>
-      <td>Transcriptomics</td>
-      <td>suite_decoupler</td>
-      <td>ebi-gxa</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler</td>
-      <td>1.4.0+galaxy3</td>
-      <td>decoupler</td>
-      <td>1.5.0</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>6</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>deg_annotate</td>
-      <td>deg_annotate</td>
-      <td>Annotate DESeq2/DEXSeq output tables</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td></td>
-      <td>Transcriptomics</td>
-      <td>deg_annotate</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate</td>
-      <td>1.1.0</td>
-      <td>bedtools</td>
-      <td>2.31.1</td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1774</td>
-      <td>19910</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>deseq2</td>
-      <td>deseq2</td>
-      <td>Differential gene expression analysis based on the negative binomial distribution</td>
-      <td>DESeq2</td>
-      <td>DESeq2</td>
-      <td></td>
-      <td>DESeq2</td>
-      <td>R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.</td>
-      <td>Differential gene expression analysis, RNA-Seq analysis</td>
-      <td>RNA-Seq</td>
-      <td>To update</td>
-      <td>https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html</td>
-      <td>Transcriptomics, RNA, Statistics</td>
-      <td>deseq2</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2</td>
-      <td>2.11.40.8</td>
-      <td>bioconductor-deseq2</td>
-      <td>1.42.0</td>
-      <td>Differential gene expression analysis, RNA-Seq analysis</td>
-      <td>RNA-Seq</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>4990</td>
-      <td>95752</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>deseq2_normalization</td>
-      <td>deseq2_normalization</td>
-      <td>Normalizes gene hitlists</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>http://artbio.fr</td>
-      <td>RNA, Transcriptomics, Sequence Analysis, Statistics</td>
-      <td>deseq2_normalization</td>
-      <td>artbio</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization</td>
-      <td>1.40.2+galaxy0</td>
-      <td>bioconductor-deseq2</td>
-      <td>1.42.0</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>dexseq</td>
-      <td>dexseq, dexseq_count, plotdexseq</td>
-      <td>Inference of differential exon usage in RNA-Seq</td>
-      <td>dexseq</td>
-      <td>dexseq</td>
-      <td></td>
-      <td>DEXSeq</td>
-      <td>The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.</td>
-      <td>Enrichment analysis, Exonic splicing enhancer prediction</td>
-      <td>RNA-Seq</td>
-      <td>Up-to-date</td>
-      <td>https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html</td>
-      <td>Transcriptomics, RNA, Statistics</td>
-      <td>dexseq</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq</td>
-      <td>1.48.0</td>
-      <td>bioconductor-dexseq</td>
-      <td>1.48.0</td>
-      <td>Enrichment analysis, Exonic splicing enhancer prediction</td>
-      <td>RNA-Seq</td>
-      <td>3</td>
-      <td>3</td>
-      <td>3</td>
-      <td>3</td>
-      <td>3</td>
-      <td>3</td>
-      <td>3</td>
-      <td>3</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>3</td>
-      <td>3</td>
-      <td>218</td>
-      <td>16064</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>dropletutils</td>
-      <td>dropletutils_empty_drops, dropletutils_read_10x</td>
-      <td>De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td></td>
-      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
-      <td>suite_dropletutils</td>
-      <td>ebi-gxa</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils</td>
-      <td>1.0.4</td>
-      <td>dropletutils-scripts</td>
-      <td>0.0.5</td>
-      <td></td>
-      <td></td>
-      <td>2</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>201</td>
-      <td>1599</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>dropletutils</td>
-      <td>dropletutils</td>
-      <td>DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data</td>
-      <td>dropletutils</td>
-      <td>dropletutils</td>
-      <td></td>
-      <td>DropletUtils</td>
-      <td>Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.</td>
-      <td>Loading, Community profiling</td>
-      <td>Gene expression, RNA-seq, Sequencing, Transcriptomics</td>
-      <td>To update</td>
-      <td>https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html</td>
-      <td>Transcriptomics, Sequence Analysis</td>
-      <td>dropletutils</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils</td>
-      <td>1.10.0</td>
-      <td>bioconductor-dropletutils</td>
-      <td>1.22.0</td>
-      <td></td>
-      <td>Sequencing, Transcriptomics</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>126</td>
-      <td>3934</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>edger</td>
-      <td>edger</td>
-      <td>Perform RNA-Seq differential expression analysis using edgeR pipeline</td>
-      <td>edger</td>
-      <td>edger</td>
-      <td></td>
-      <td>edgeR</td>
-      <td>Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.</td>
-      <td>Differential gene expression analysis</td>
-      <td>Genetics, RNA-Seq, ChIP-seq</td>
-      <td>To update</td>
-      <td>http://bioconductor.org/packages/release/bioc/html/edgeR.html</td>
-      <td>Transcriptomics, RNA, Statistics</td>
-      <td>edger</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger</td>
-      <td>3.36.0</td>
-      <td>bioconductor-edger</td>
-      <td>4.0.16</td>
-      <td>Differential gene expression analysis</td>
-      <td>Genetics, RNA-Seq, ChIP-seq</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>945</td>
-      <td>18117</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>egsea</td>
-      <td>egsea</td>
-      <td>This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing</td>
-      <td>egsea</td>
-      <td>egsea</td>
-      <td></td>
-      <td>EGSEA</td>
-      <td>This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.</td>
-      <td>Gene set testing</td>
-      <td>Systems biology</td>
-      <td>To update</td>
-      <td>https://bioconductor.org/packages/release/bioc/html/EGSEA.html</td>
-      <td>Transcriptomics, RNA, Statistics</td>
-      <td>egsea</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea</td>
-      <td>1.20.0</td>
-      <td>bioconductor-egsea</td>
-      <td>1.28.0</td>
-      <td>Gene set testing</td>
-      <td>Systems biology</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>177</td>
-      <td>2524</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>fastq_provider</td>
-      <td>fastq_provider</td>
-      <td>Retrieval and download of FASTQ files from ENA and other repositories such as HCA.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://github.com/ebi-gene-expression-group/atlas-fastq-provider</td>
-      <td>Data Source, RNA, Transcriptomics</td>
-      <td>atlas_fastq_provider</td>
-      <td>ebi-gxa</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider</td>
-      <td>0.4.4</td>
-      <td>atlas-fastq-provider</td>
-      <td>0.4.7</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>fastq_utils</td>
-      <td>fastq_filter_n, fastq_trim_poly_at</td>
-      <td>Set of tools for handling fastq files</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://github.com/nunofonseca/fastq_utils</td>
-      <td>Transcriptomics, RNA</td>
-      <td>fastq_utils</td>
-      <td>ebi-gxa</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils</td>
-      <td>0.25.1+galaxy0</td>
-      <td>fastq_utils</td>
-      <td>0.25.2</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>featurecounts</td>
-      <td>featurecounts</td>
-      <td>featureCounts counts the number of reads aligned to defined masked regions in a reference genome</td>
-      <td>featurecounts</td>
-      <td>featurecounts</td>
-      <td></td>
-      <td>FeatureCounts</td>
-      <td>featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.</td>
-      <td>Read summarisation, RNA-Seq quantification</td>
-      <td>RNA-Seq</td>
-      <td>To update</td>
-      <td>http://bioinf.wehi.edu.au/featureCounts</td>
-      <td>RNA, Transcriptomics, Sequence Analysis</td>
-      <td>featurecounts</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts</td>
-      <td>2.0.3</td>
-      <td>subread</td>
-      <td>2.0.6</td>
-      <td>Read summarisation, RNA-Seq quantification</td>
-      <td>RNA-Seq</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>4679</td>
-      <td>696399</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>fgsea</td>
-      <td>fgsea</td>
-      <td>Perform gene set testing using fgsea</td>
-      <td>fgsea</td>
-      <td>fgsea</td>
-      <td></td>
-      <td>fgsea</td>
-      <td>The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.</td>
-      <td>Gene-set enrichment analysis</td>
-      <td>Genetics</td>
-      <td>To update</td>
-      <td>https://bioconductor.org/packages/release/bioc/html/fgsea.html</td>
-      <td>Visualization, Transcriptomics, Statistics</td>
-      <td>fgsea</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea</td>
-      <td>1.8.0+galaxy1</td>
-      <td>bioconductor-fgsea</td>
-      <td>1.28.0</td>
-      <td>Gene-set enrichment analysis</td>
-      <td>Genetics</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>307</td>
-      <td>5240</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>garnett</td>
-      <td>garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file</td>
-      <td>De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td></td>
-      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
-      <td>suite_garnett</td>
-      <td>ebi-gxa</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett</td>
-      <td>0.2.8</td>
-      <td>garnett-cli</td>
-      <td>0.0.5</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>7</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>7</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>3</td>
-      <td>27</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>genomic_super_signature</td>
-      <td>genomic_super_signature</td>
-      <td>Interpretation of RNAseq experiments through robust, efficient comparison to public databases</td>
-      <td>genomicsupersignature</td>
-      <td>genomicsupersignature</td>
-      <td></td>
-      <td>GenomicSuperSignature</td>
-      <td>GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.</td>
-      <td>Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction</td>
-      <td>RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment</td>
-      <td>To update</td>
-      <td>https://github.com/shbrief/GenomicSuperSignature</td>
-      <td>Sequence Analysis, RNA, Transcriptomics</td>
-      <td>genomic_super_signature</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature</td>
-      <td>1.2.0</td>
-      <td>bioconductor-genomicsupersignature</td>
-      <td>1.10.0</td>
-      <td>Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction</td>
-      <td>RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>11</td>
-      <td>46</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>gffcompare</td>
-      <td>gffcompare</td>
-      <td>Galaxy wrappers for Geo Pertea's GffCompare package.</td>
-      <td>gffcompare</td>
-      <td>gffcompare</td>
-      <td></td>
-      <td>gffcompare</td>
-      <td>Program for comparing, annotating, merging and tracking transcripts in GFF files.</td>
-      <td>Sequence annotation</td>
-      <td>Nucleic acids, Sequence analysis</td>
-      <td>Up-to-date</td>
-      <td>https://github.com/gpertea/gffcompare/</td>
-      <td>Transcriptomics</td>
-      <td>gffcompare</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare</td>
-      <td>0.12.6</td>
-      <td>gffcompare</td>
-      <td>0.12.6</td>
-      <td>Sequence annotation</td>
-      <td>Nucleic acids, Sequence analysis</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>381</td>
-      <td>3477</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>gsc_filter_cells</td>
-      <td>filter_cells</td>
-      <td>Filter single cell RNAseq data on libray depth and number of detected genes</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>http://artbio.fr</td>
-      <td>Transcriptomics</td>
-      <td>gsc_filter_cells</td>
-      <td>artbio</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells</td>
-      <td>4.3.1+galaxy0</td>
-      <td>r-optparse</td>
-      <td>1.3.2</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>gsc_filter_genes</td>
-      <td>filter_genes</td>
-      <td>Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>http://artbio.fr</td>
-      <td>Transcriptomics</td>
-      <td>gsc_filter_genes</td>
-      <td>artbio</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes</td>
-      <td>4.3.1+galaxy0</td>
-      <td>r-optparse</td>
-      <td>1.3.2</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>gsc_gene_expression_correlations</td>
-      <td>single_cell_gene_expression_correlations</td>
-      <td>Compute single-cell paire-wise gene expressions correlations</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>http://artbio.fr</td>
-      <td>Transcriptomics</td>
-      <td>gsc_gene_expression_correlations</td>
-      <td>artbio</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations</td>
-      <td>4.3.1+galaxy0</td>
-      <td>r-optparse</td>
-      <td>1.3.2</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>gsc_high_dimensions_visualisation</td>
-      <td>high_dimensions_visualisation</td>
-      <td>Generates PCA, t-SNE and HCPC visualisation</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>http://artbio.fr</td>
-      <td>Transcriptomics, Visualization</td>
-      <td>gsc_high_dimensions_visualisation</td>
-      <td>artbio</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation</td>
-      <td>4.3+galaxy0</td>
-      <td>r-optparse</td>
-      <td>1.3.2</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>gsc_mannwhitney_de</td>
-      <td>mannwhitney_de</td>
-      <td>Perform a mann-whitney differential testing between two sets of gene expression data</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>http://artbio.fr</td>
-      <td>Transcriptomics</td>
-      <td>gsc_mannwhitney_de</td>
-      <td>artbio</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de</td>
-      <td>4.1.3+galaxy0</td>
-      <td>r-optparse</td>
-      <td>1.3.2</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>gsc_scran_normalize</td>
-      <td>scran_normalize</td>
-      <td>Normalize raw counts using scran</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>http://artbio.fr</td>
-      <td>Transcriptomics</td>
-      <td>gsc_scran_normalize</td>
-      <td>artbio</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize</td>
-      <td>1.28.1+galaxy0</td>
-      <td>bioconductor-scran</td>
-      <td>1.30.0</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>14</td>
-      <td>78</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>gsc_signature_score</td>
-      <td>signature_score</td>
-      <td>Compute signature scores from single cell RNAseq data</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>http://artbio.fr</td>
-      <td>Transcriptomics</td>
-      <td>gsc_signature_score</td>
-      <td>artbio</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score</td>
-      <td>2.3.9+galaxy0</td>
-      <td>r-optparse</td>
-      <td>1.3.2</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>heinz</td>
-      <td>heinz_bum, heinz, heinz_scoring, heinz_visualization</td>
-      <td>An algorithm for identification of the optimal scoring subnetwork.</td>
-      <td>heinz</td>
-      <td>heinz, bionet</td>
-      <td></td>
-      <td>Heinz</td>
-      <td>Tool for single-species active module discovery.</td>
-      <td>Pathway or network analysis</td>
-      <td>Genetics, Gene expression, Molecular interactions, pathways and networks</td>
-      <td>To update</td>
-      <td>https://github.com/ls-cwi/heinz</td>
-      <td>Transcriptomics, Visualization, Statistics</td>
-      <td>heinz</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz</td>
-      <td>1.0</td>
-      <td>bioconductor-bionet</td>
-      <td>1.62.0</td>
-      <td>Pathway or network analysis</td>
-      <td>Genetics, Gene expression, Molecular interactions, pathways and networks</td>
-      <td>4</td>
-      <td>4</td>
-      <td>4</td>
-      <td>0</td>
-      <td>4</td>
-      <td>4</td>
-      <td>4</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>4</td>
-      <td>4</td>
-      <td>242</td>
-      <td>1186</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>isoformswitchanalyzer</td>
-      <td>isoformswitchanalyzer</td>
-      <td>Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.</td>
-      <td>IsoformSwitchAnalyzeR</td>
-      <td>IsoformSwitchAnalyzeR</td>
-      <td></td>
-      <td>IsoformSwitchAnalyzeR</td>
-      <td>Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.</td>
-      <td>Sequence comparison, Sequence analysis</td>
-      <td>Computational biology, Gene transcripts</td>
-      <td>To update</td>
-      <td>https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html</td>
-      <td>Transcriptomics, RNA, Statistics</td>
-      <td>isoformswitchanalyzer</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer</td>
-      <td>1.20.0</td>
-      <td>bioconductor-isoformswitchanalyzer</td>
-      <td>2.2.0</td>
-      <td>Sequence comparison, Sequence analysis</td>
-      <td>Computational biology, Gene transcripts</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>29</td>
-      <td>822</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>kallisto</td>
-      <td>kallisto_pseudo, kallisto_quant</td>
-      <td>kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment.</td>
-      <td>kallisto</td>
-      <td>kallisto</td>
-      <td></td>
-      <td>kallisto</td>
-      <td>A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.</td>
-      <td>Gene expression profiling</td>
-      <td>Transcriptomics, RNA-seq, Gene expression</td>
-      <td>To update</td>
-      <td>https://pachterlab.github.io/kallisto/</td>
-      <td>Transcriptomics</td>
-      <td></td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto</td>
-      <td>0.48.0</td>
-      <td>kallisto</td>
-      <td>0.50.1</td>
-      <td>Gene expression profiling</td>
-      <td>Transcriptomics</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
-      <td>2</td>
-      <td>299</td>
-      <td>24155</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>limma_voom</td>
-      <td>limma_voom</td>
-      <td>Perform RNA-Seq differential expression analysis using limma voom pipeline</td>
-      <td>limma</td>
-      <td>limma</td>
-      <td></td>
-      <td>limma</td>
-      <td>Data analysis, linear models and differential expression for microarray data.</td>
-      <td>RNA-Seq analysis</td>
-      <td>Molecular biology, Genetics</td>
-      <td>Up-to-date</td>
-      <td>http://bioconductor.org/packages/release/bioc/html/limma.html</td>
-      <td>Transcriptomics, RNA, Statistics</td>
-      <td>limma_voom</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom</td>
-      <td>3.58.1</td>
-      <td>bioconductor-limma</td>
-      <td>3.58.1</td>
-      <td>RNA-Seq analysis</td>
-      <td>Molecular biology, Genetics</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1012</td>
-      <td>20344</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>masigpro</td>
-      <td>masigpro</td>
-      <td>Identify significantly differential expression profiles in time-course microarray experiments</td>
-      <td>masigpro</td>
-      <td>masigpro</td>
-      <td></td>
-      <td>maSigPro</td>
-      <td>Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.</td>
-      <td>Regression analysis</td>
-      <td>Gene expression, Molecular genetics, Microarray experiment, RNA-Seq</td>
-      <td>To update</td>
-      <td>https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html</td>
-      <td>Transcriptomics, RNA, Statistics</td>
-      <td>masigpro</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro</td>
-      <td>1.49.3</td>
-      <td>coreutils</td>
-      <td>8.25</td>
-      <td>Regression analysis</td>
-      <td>Gene expression, Microarray experiment, RNA-Seq</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>13</td>
-      <td>576</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>mircounts</td>
-      <td>mircounts</td>
-      <td>Generates miRNA count lists from read alignments to mirBase.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>http://artbio.fr</td>
-      <td>RNA, Transcriptomics</td>
-      <td>mircounts</td>
-      <td>artbio</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts</td>
-      <td>1.6</td>
-      <td>tar</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>monocle3</td>
-      <td>monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers</td>
-      <td>De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td></td>
-      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
-      <td>suite_monocle3</td>
-      <td>ebi-gxa</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3</td>
-      <td>0.1.4</td>
-      <td>monocle3-cli</td>
-      <td>0.0.9</td>
-      <td></td>
-      <td></td>
-      <td>9</td>
-      <td>0</td>
-      <td>9</td>
-      <td>0</td>
-      <td>9</td>
-      <td>0</td>
-      <td>9</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>264</td>
-      <td>3266</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>multigsea</td>
-      <td>multigsea</td>
-      <td>GSEA-based pathway enrichment analysis for multi-omics data</td>
-      <td>multiGSEA</td>
-      <td>multiGSEA</td>
-      <td></td>
-      <td>multiGSEA</td>
-      <td>A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.</td>
-      <td>Gene-set enrichment analysis, Aggregation, Pathway analysis</td>
-      <td>Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules</td>
-      <td>Up-to-date</td>
-      <td>https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html</td>
-      <td>Transcriptomics, Proteomics, Statistics</td>
-      <td>multigsea</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea</td>
-      <td>1.12.0</td>
-      <td>bioconductor-multigsea</td>
-      <td>1.12.0</td>
-      <td>Gene-set enrichment analysis, Aggregation, Pathway analysis</td>
-      <td>Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>2</td>
-      <td>53</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>music_deconvolution</td>
-      <td>music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution</td>
-      <td>Multi-subject Single Cell deconvolution (MuSiC)</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>Up-to-date</td>
-      <td>https://github.com/xuranw/MuSiC</td>
-      <td>Transcriptomics</td>
-      <td>music</td>
-      <td>bgruening</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution</td>
-      <td>0.1.1</td>
-      <td>music-deconvolution</td>
-      <td>0.1.1</td>
-      <td></td>
-      <td></td>
-      <td>5</td>
-      <td>5</td>
-      <td>4</td>
-      <td>0</td>
-      <td>5</td>
-      <td>5</td>
-      <td>4</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>5</td>
-      <td>0</td>
-      <td>240</td>
-      <td>1872</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>nugen_nudup</td>
-      <td>nugen_nudup</td>
-      <td>Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.</td>
-      <td>nudup</td>
-      <td>nudup</td>
-      <td></td>
-      <td>NuDup</td>
-      <td>Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.</td>
-      <td>Duplication detection</td>
-      <td>Sequencing</td>
-      <td>Up-to-date</td>
-      <td>https://github.com/tecangenomics/nudup</td>
-      <td>SAM, Metagenomics, Sequence Analysis, Transcriptomics</td>
-      <td>nugen_nudup</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup</td>
-      <td>2.3.3</td>
-      <td>nudup</td>
-      <td>2.3.3</td>
-      <td>Duplication detection</td>
-      <td>Sequencing</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>pathifier</td>
-      <td>pathifier</td>
-      <td>pathifier</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>Up-to-date</td>
-      <td>https://</td>
-      <td>Transcriptomics, Statistics</td>
-      <td>pathifier</td>
-      <td>artbio</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier</td>
-      <td>1.40.0</td>
-      <td>bioconductor-pathifier</td>
-      <td>1.40.0</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>10</td>
-      <td>228</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>pizzly</td>
-      <td>pizzly</td>
-      <td>Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://github.com/pmelsted/pizzly/</td>
-      <td>Transcriptomics</td>
-      <td></td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly</td>
-      <td>0.37.3.1</td>
-      <td>pizzly</td>
-      <td>0.37.3</td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>16</td>
-      <td>208</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>psiclass</td>
-      <td>psiclass</td>
-      <td>PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.</td>
-      <td>psiclass</td>
-      <td>psiclass</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>Up-to-date</td>
-      <td>https://github.com/splicebox/PsiCLASS</td>
-      <td>Transcriptomics</td>
-      <td>psiclass</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass</td>
-      <td>1.0.3</td>
-      <td>psiclass</td>
-      <td>1.0.3</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>15</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>qualimap</td>
-      <td>qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq</td>
-      <td></td>
-      <td>qualimap</td>
-      <td>qualimap</td>
-      <td></td>
-      <td>QualiMap</td>
-      <td>Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.</td>
-      <td>Sequencing quality control</td>
-      <td>Data quality management</td>
-      <td>To update</td>
-      <td>http://qualimap.bioinfo.cipf.es/</td>
-      <td>Sequence Analysis, Transcriptomics, SAM</td>
-      <td>qualimap</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap</td>
-      <td>2.2.2d</td>
-      <td>qualimap</td>
-      <td>2.3</td>
-      <td>Sequencing quality control</td>
-      <td>Data quality management</td>
-      <td>4</td>
-      <td>4</td>
-      <td>4</td>
-      <td>1</td>
-      <td>4</td>
-      <td>4</td>
-      <td>4</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>4</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>4</td>
-      <td>4</td>
-      <td>1328</td>
-      <td>664470</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>raceid</td>
-      <td>raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory</td>
-      <td>RaceID3, StemID2, FateID - scRNA analysis</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://github.com/dgrun/RaceID3_StemID2_package/</td>
-      <td>Transcriptomics</td>
-      <td></td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid</td>
-      <td>0.2.3</td>
-      <td>r-raceid</td>
-      <td>0.1.3</td>
-      <td></td>
-      <td></td>
-      <td>5</td>
-      <td>5</td>
-      <td>5</td>
-      <td>1</td>
-      <td>5</td>
-      <td>5</td>
-      <td>5</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>5</td>
-      <td>5</td>
-      <td>82</td>
-      <td>4569</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>repenrich</td>
-      <td>edger-repenrich, repenrich</td>
-      <td>Repeat element profiling</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich</td>
-      <td>Transcriptomics</td>
-      <td>repenrich</td>
-      <td>artbio</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich</td>
-      <td>2.31.1</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>repenrich2</td>
-      <td>edger-repenrich2, repenrich2</td>
-      <td>Repeat element profiling using bowtie2 aligner</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2</td>
-      <td>Transcriptomics</td>
-      <td>repenrich2</td>
-      <td>artbio</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2</td>
-      <td>2.31.1</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>rgrnastar</td>
-      <td>rna_star, rna_starsolo</td>
-      <td>RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper</td>
-      <td>star</td>
-      <td>star</td>
-      <td></td>
-      <td>STAR</td>
-      <td>Ultrafast universal RNA-seq data aligner</td>
-      <td>Sequence alignment</td>
-      <td>RNA-Seq, Transcriptomics</td>
-      <td>To update</td>
-      <td>https://github.com/alexdobin/STAR</td>
-      <td>Next Gen Mappers, Transcriptomics</td>
-      <td>rgrnastar</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar</td>
-      <td>2.7.11a</td>
-      <td>star</td>
-      <td>2.7.11b</td>
-      <td>Sequence alignment</td>
-      <td>RNA-Seq, Transcriptomics</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
-      <td>2</td>
-      <td>4015</td>
-      <td>425658</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>ribowaltz</td>
-      <td>ribowaltz_process, ribowaltz_plot</td>
-      <td>Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data</td>
-      <td>riboWaltz</td>
-      <td>riboWaltz</td>
-      <td></td>
-      <td>riboWaltz</td>
-      <td>riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.</td>
-      <td></td>
-      <td>Computational biology</td>
-      <td>To update</td>
-      <td>https://github.com/LabTranslationalArchitectomics/riboWaltz</td>
-      <td>Transcriptomics, RNA</td>
-      <td></td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz</td>
-      <td>1.2.0</td>
-      <td>ribowaltz</td>
-      <td>2.0</td>
-      <td></td>
-      <td>Computational biology</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>14</td>
-      <td>161</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>rsem</td>
-      <td>extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie</td>
-      <td>transcript quantification from RNA-Seq data</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://github.com/deweylab/RSEM</td>
-      <td>Transcriptomics, RNA</td>
-      <td>rsem</td>
-      <td>artbio</td>
-      <td>https://github.com/artbio/tools-artbio/tree/master/tools/rsem</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem</td>
-      <td></td>
-      <td>rsem</td>
-      <td>1.3.3</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>4</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>67</td>
-      <td>377</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>rseqc</td>
-      <td>rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin</td>
-      <td>an RNA-seq quality control package</td>
-      <td>rseqc</td>
-      <td>rseqc</td>
-      <td></td>
-      <td>RSeQC</td>
-      <td>Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.</td>
-      <td>Data handling</td>
-      <td>Sequencing</td>
-      <td>Up-to-date</td>
-      <td>https://code.google.com/p/rseqc/</td>
-      <td>Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization</td>
-      <td>rseqc</td>
-      <td>nilesh</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc</td>
-      <td>5.0.3</td>
-      <td>rseqc</td>
-      <td>5.0.3</td>
-      <td>Data handling</td>
-      <td>Sequencing</td>
-      <td>22</td>
-      <td>22</td>
-      <td>22</td>
-      <td>22</td>
-      <td>22</td>
-      <td>22</td>
-      <td>22</td>
-      <td>22</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>22</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>22</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>22</td>
-      <td>22</td>
-      <td>3206</td>
-      <td>133498</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>ruvseq</td>
-      <td>ruvseq</td>
-      <td>Remove Unwanted Variation from RNA-Seq Data</td>
-      <td>ruvseq</td>
-      <td>ruvseq</td>
-      <td></td>
-      <td>RUVSeq</td>
-      <td>This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.</td>
-      <td>Differential gene expression analysis</td>
-      <td>Gene expression, RNA-seq</td>
-      <td>To update</td>
-      <td>https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html</td>
-      <td>Transcriptomics, RNA, Statistics</td>
-      <td>ruvseq</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq</td>
-      <td>1.26.0</td>
-      <td>bioconductor-ruvseq</td>
-      <td>1.36.0</td>
-      <td>Differential gene expression analysis</td>
-      <td>Gene expression</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>76</td>
-      <td>1236</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>salmon</td>
-      <td>alevin, salmon, salmonquantmerge</td>
-      <td>Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.</td>
-      <td>salmon</td>
-      <td>salmon</td>
-      <td></td>
-      <td>Salmon</td>
-      <td>A tool for transcript expression quantification from RNA-seq data</td>
-      <td>Sequence composition calculation, RNA-Seq quantification, Gene expression analysis</td>
-      <td>RNA-Seq, Gene expression, Transcriptomics</td>
-      <td>To update</td>
-      <td>https://github.com/COMBINE-lab/salmon</td>
-      <td>Sequence Analysis, RNA, Transcriptomics</td>
-      <td></td>
-      <td>bgruening</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/salmon</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/salmon</td>
-      <td>1.10.1</td>
-      <td>salmon</td>
-      <td>1.10.3</td>
-      <td>Sequence composition calculation, RNA-Seq quantification, Gene expression analysis</td>
-      <td>RNA-Seq, Transcriptomics</td>
-      <td>2</td>
-      <td>1</td>
-      <td>3</td>
-      <td>1</td>
-      <td>2</td>
-      <td>1</td>
-      <td>3</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>3</td>
-      <td>3</td>
-      <td>969</td>
-      <td>61937</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>sashimi_plot</td>
-      <td>sashimi_plot</td>
-      <td>Generates a sashimi plot from bam files.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>http://artbio.fr</td>
-      <td>RNA, Transcriptomics, Graphics, Visualization</td>
-      <td>sashimi_plot</td>
-      <td>artbio</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot</td>
-      <td>0.1.1</td>
-      <td>python</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>sc3</td>
-      <td>sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare</td>
-      <td>De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td></td>
-      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
-      <td>suite_sc3</td>
-      <td>ebi-gxa</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3</td>
-      <td>1.8.0</td>
-      <td>sc3-scripts</td>
-      <td>0.0.6</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>7</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>7</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>9</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>scanpy</td>
-      <td>scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders</td>
-      <td>Scanpy – Single-Cell Analysis in Python</td>
-      <td>scanpy</td>
-      <td>scanpy</td>
-      <td></td>
-      <td>SCANPY</td>
-      <td>Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.</td>
-      <td>Differential gene expression analysis</td>
-      <td>Gene expression, Cell biology, Genetics</td>
-      <td>To update</td>
-      <td>https://scanpy.readthedocs.io</td>
-      <td>Transcriptomics, Sequence Analysis</td>
-      <td>scanpy</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy</td>
-      <td>1.9.6</td>
-      <td>scanpy</td>
-      <td>1.7.2</td>
-      <td>Differential gene expression analysis</td>
-      <td>Gene expression, Cell biology, Genetics</td>
-      <td>6</td>
-      <td>6</td>
-      <td>6</td>
-      <td>0</td>
-      <td>6</td>
-      <td>6</td>
-      <td>6</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>6</td>
-      <td>6</td>
-      <td>766</td>
-      <td>51978</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>scanpy</td>
-      <td>anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data</td>
-      <td>scanpy-scripts, command-line wrapper scripts around Scanpy.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://scanpy.readthedocs.io</td>
-      <td>Transcriptomics, Sequence Analysis, RNA</td>
-      <td>scanpy_scripts</td>
-      <td>ebi-gxa</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy</td>
-      <td>1.9.3</td>
-      <td>scanpy-scripts</td>
-      <td>1.9.301</td>
-      <td></td>
-      <td></td>
-      <td>22</td>
-      <td>27</td>
-      <td>27</td>
-      <td>0</td>
-      <td>22</td>
-      <td>27</td>
-      <td>27</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>14</td>
-      <td>13</td>
-      <td>2185</td>
-      <td>39356</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>scater</td>
-      <td>scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results</td>
-      <td>De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td></td>
-      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
-      <td>suite_scater</td>
-      <td>ebi-gxa</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater</td>
-      <td>1.10.0</td>
-      <td>scater-scripts</td>
-      <td>0.0.5</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>1</td>
-      <td>6</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>6</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
-      <td>2</td>
-      <td>16</td>
-      <td>387</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>scater</td>
-      <td>scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne</td>
-      <td>Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.</td>
-      <td>scater</td>
-      <td>scater</td>
-      <td></td>
-      <td>scater</td>
-      <td>Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.</td>
-      <td>Read pre-processing, Sequencing quality control, Sequence visualisation</td>
-      <td>RNA-seq, Quality affairs, Molecular genetics</td>
-      <td>To update</td>
-      <td>http://bioconductor.org/packages/scater/</td>
-      <td>Transcriptomics, RNA, Visualization</td>
-      <td></td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater</td>
-      <td>1.22.0</td>
-      <td>bioconductor-scater</td>
-      <td>1.30.1</td>
-      <td>Read pre-processing, Sequence visualisation</td>
-      <td>Quality affairs, Molecular genetics</td>
-      <td>0</td>
-      <td>5</td>
-      <td>5</td>
-      <td>0</td>
-      <td>0</td>
-      <td>5</td>
-      <td>5</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>5</td>
-      <td>5</td>
-      <td>77</td>
-      <td>1365</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>sccaf</td>
-      <td>run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out</td>
-      <td>SCCAF: Single Cell Clustering Assessment Framework.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://github.com/sccaf/sccaf</td>
-      <td>Transcriptomics</td>
-      <td>SCCAF</td>
-      <td>ebi-gxa</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf</td>
-      <td>0.0.9</td>
-      <td>sccaf</td>
-      <td>0.0.10</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>4</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>4</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>2</td>
-      <td>110</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>sceasy</td>
-      <td>sceasy_convert</td>
-      <td>Converter between difference single-cell formats</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>Up-to-date</td>
-      <td>https://github.com/cellgeni/sceasy/</td>
-      <td>Transcriptomics</td>
-      <td>sceasy_convert</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy</td>
-      <td>0.0.7</td>
-      <td>r-sceasy</td>
-      <td>0.0.7</td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>90</td>
-      <td>721</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>sceasy</td>
-      <td>sceasy_convert</td>
-      <td>Convert scRNA data object between popular formats</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td></td>
-      <td>Transcriptomics</td>
-      <td>sceasy</td>
-      <td>ebi-gxa</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy</td>
-      <td>0.0.5</td>
-      <td>r-sceasy</td>
-      <td>0.0.7</td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>90</td>
-      <td>721</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>schicexplorer</td>
-      <td>schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol</td>
-      <td>scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://github.com/joachimwolff/schicexplorer</td>
-      <td>Sequence Analysis, Transcriptomics, Visualization</td>
-      <td>schicexplorer</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer</td>
-      <td>4</td>
-      <td>schicexplorer</td>
-      <td>7</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>16</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>16</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>16</td>
-      <td>16</td>
-      <td>23</td>
-      <td>779</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>scmap</td>
-      <td>scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features</td>
-      <td>De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td></td>
-      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
-      <td>suite_scmap</td>
-      <td>ebi-gxa</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap</td>
-      <td>1.6.4</td>
-      <td>scmap-cli</td>
-      <td>0.1.0</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>7</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>7</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>13</td>
-      <td>83</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>scpipe</td>
-      <td>scpipe</td>
-      <td>A flexible preprocessing pipeline for single-cell RNA-sequencing data</td>
-      <td>scpipe</td>
-      <td>scpipe</td>
-      <td></td>
-      <td>scPipe</td>
-      <td>A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.</td>
-      <td>Genome annotation, Validation, Alignment, Visualisation</td>
-      <td>Gene expression, RNA-Seq, Sequencing</td>
-      <td>To update</td>
-      <td>http://bioconductor.org/packages/release/bioc/html/scPipe.html</td>
-      <td>Transcriptomics, RNA, Statistics</td>
-      <td>scpipe</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe</td>
-      <td>1.0.0+galaxy2</td>
-      <td>bioconductor-scpipe</td>
-      <td>2.2.0</td>
-      <td>Genome annotation, Validation, Alignment, Visualisation</td>
-      <td>Gene expression, RNA-Seq</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>11</td>
-      <td>628</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>scpred</td>
-      <td>scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model</td>
-      <td>De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0</td>
-      <td></td>
+      <td>cosg</td>
+      <td>cosg</td>
+      <td>Marker gene identification for single-cell sequencing data using COSG.</td>
       <td></td>
       <td></td>
       <td></td>
       <td></td>
       <td></td>
       <td></td>
-      <td>To update</td>
       <td></td>
-      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
-      <td>suite_scpred</td>
-      <td>ebi-gxa</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred</td>
-      <td>1.0.2</td>
-      <td>scpred-cli</td>
-      <td>0.1.0</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/genecell/COSG</td>
+      <td>Transcriptomics, Sequence Analysis, Single Cell</td>
+      <td>cosg</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg</td>
+      <td>1.0.1</td>
+      <td>cosg</td>
+      <td>1.0.1</td>
       <td></td>
       <td></td>
       <td>0</td>
       <td>0</td>
-      <td>4</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>4</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6003,34 +380,32 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>4</td>
-      <td>25</td>
       <td></td>
     </tr>
     <tr>
       <td></td>
-      <td>seurat</td>
-      <td>seurat</td>
-      <td>A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>dropletutils</td>
+      <td>dropletutils</td>
+      <td>DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data</td>
+      <td>dropletutils</td>
+      <td>dropletutils</td>
       <td></td>
+      <td>DropletUtils</td>
+      <td>Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.</td>
+      <td>Loading, Community profiling</td>
+      <td>Gene expression, RNA-seq, Sequencing, Transcriptomics</td>
       <td>To update</td>
-      <td>https://github.com/satijalab/seurat</td>
-      <td>Transcriptomics, RNA, Statistics</td>
-      <td>seurat</td>
+      <td>https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html</td>
+      <td>Single Cell, Sequence Analysis</td>
+      <td>dropletutils</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat</td>
-      <td>4.3.0.1</td>
-      <td>r-seurat</td>
-      <td>3.0.2</td>
-      <td></td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils</td>
+      <td>1.10.0</td>
+      <td>bioconductor-dropletutils</td>
+      <td>1.22.0</td>
       <td></td>
+      <td>Sequencing, Transcriptomics</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -6054,14 +429,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6071,48 +438,46 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>66</td>
-      <td>1543</td>
+      <td>0</td>
+      <td>126</td>
+      <td>3934</td>
       <td></td>
     </tr>
     <tr>
       <td></td>
-      <td>seurat</td>
-      <td>seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features</td>
-      <td>De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1</td>
-      <td></td>
-      <td></td>
+      <td>episcanpy</td>
+      <td>episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess</td>
+      <td>EpiScanpy – Epigenomics single cell analysis in python</td>
+      <td>episcanpy</td>
+      <td>episcanpy</td>
       <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>Up-to-date</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
-      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
-      <td>suite_seurat</td>
-      <td>ebi-gxa</td>
-      <td></td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat</td>
-      <td>4.0.0</td>
-      <td>seurat-scripts</td>
-      <td>4.0.0</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>14</td>
-      <td>11</td>
-      <td>0</td>
-      <td>0</td>
-      <td>14</td>
-      <td>11</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>epiScanpy</td>
+      <td>Epigenomics Single Cell Analysis in Python.</td>
+      <td>Enrichment analysis, Imputation</td>
+      <td>Epigenomics, Cell biology, DNA</td>
+      <td>To update</td>
+      <td>https://github.com/colomemaria/epiScanpy</td>
+      <td>Single Cell, Epigenetics</td>
+      <td>episcanpy</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy</td>
+      <td>0.3.2</td>
+      <td>episcanpy</td>
+      <td>0.4.0</td>
+      <td>Enrichment analysis, Imputation</td>
+      <td>Epigenomics, Cell biology, DNA</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
       <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6132,7 +497,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>19</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6141,17 +505,18 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>3</td>
       <td>0</td>
       <td>0</td>
-      <td>181</td>
-      <td>1966</td>
+      <td>20</td>
+      <td>736</td>
       <td></td>
     </tr>
     <tr>
       <td></td>
-      <td>slamdunk</td>
-      <td>alleyoop, slamdunk</td>
-      <td>Slamdunk maps and quantifies SLAMseq reads</td>
+      <td>raceid</td>
+      <td>raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory</td>
+      <td>RaceID3, StemID2, FateID - scRNA analysis</td>
       <td></td>
       <td></td>
       <td></td>
@@ -6159,32 +524,26 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
-      <td>http://t-neumann.github.io/slamdunk</td>
-      <td>RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers</td>
-      <td>slamdunk</td>
+      <td>To update</td>
+      <td>https://github.com/dgrun/RaceID3_StemID2_package/</td>
+      <td>Single Cell, Transcriptomics</td>
+      <td></td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk</td>
-      <td>0.4.3</td>
-      <td>slamdunk</td>
-      <td>0.4.3</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid</td>
+      <td>0.2.3</td>
+      <td>r-raceid</td>
+      <td>0.1.3</td>
       <td></td>
       <td></td>
-      <td>2</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6210,51 +569,45 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
       <td>0</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2</td>
-      <td>361</td>
+      <td>82</td>
+      <td>4569</td>
       <td></td>
     </tr>
     <tr>
       <td></td>
-      <td>sleuth</td>
-      <td>sleuth</td>
-      <td>Sleuth is a program for differential analysis of RNA-Seq data.</td>
-      <td>sleuth</td>
-      <td>sleuth</td>
+      <td>scanpy</td>
+      <td>scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders</td>
+      <td>Scanpy – Single-Cell Analysis in Python</td>
+      <td>scanpy</td>
+      <td>scanpy</td>
       <td></td>
-      <td>sleuth</td>
-      <td>A statistical model and software application for RNA-seq differential expression analysis.</td>
-      <td>Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation</td>
-      <td>RNA-seq, Gene expression, Statistics and probability</td>
-      <td>Up-to-date</td>
-      <td>https://github.com/pachterlab/sleuth</td>
-      <td>Transcriptomics, RNA, Statistics</td>
-      <td>sleuth</td>
+      <td>SCANPY</td>
+      <td>Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.</td>
+      <td>Differential gene expression analysis</td>
+      <td>Gene expression, Cell biology, Genetics</td>
+      <td>To update</td>
+      <td>https://scanpy.readthedocs.io</td>
+      <td>Single Cell, Spatial Omics, Transcriptomics</td>
+      <td>scanpy</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth</td>
-      <td>0.30.1</td>
-      <td>r-sleuth</td>
-      <td>0.30.1</td>
-      <td>Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation</td>
-      <td>Gene expression, Statistics and probability</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy</td>
+      <td>1.10.2</td>
+      <td>scanpy</td>
+      <td>1.7.2</td>
+      <td>Differential gene expression analysis</td>
+      <td>Gene expression, Cell biology, Genetics</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
       <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6281,48 +634,45 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
       <td>0</td>
-      <td>8</td>
-      <td>64</td>
+      <td>766</td>
+      <td>51978</td>
       <td></td>
     </tr>
     <tr>
       <td></td>
-      <td>star_fusion</td>
-      <td>star_fusion</td>
-      <td>STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>scater</td>
+      <td>scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne</td>
+      <td>Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.</td>
+      <td>scater</td>
+      <td>scater</td>
       <td></td>
+      <td>scater</td>
+      <td>Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.</td>
+      <td>Read pre-processing, Sequencing quality control, Sequence visualisation</td>
+      <td>RNA-seq, Quality affairs, Molecular genetics</td>
       <td>To update</td>
+      <td>http://bioconductor.org/packages/scater/</td>
+      <td>Single Cell, Transcriptomics, Visualization</td>
       <td></td>
-      <td>Sequence Analysis, Transcriptomics</td>
-      <td>star_fusion</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion</td>
-      <td>0.5.4-3+galaxy1</td>
-      <td>star-fusion</td>
-      <td>1.13.0</td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater</td>
+      <td>1.22.0</td>
+      <td>bioconductor-scater</td>
+      <td>1.30.1</td>
+      <td>Read pre-processing, Sequence visualisation</td>
+      <td>Quality affairs, Molecular genetics</td>
       <td>0</td>
+      <td>5</td>
+      <td>5</td>
       <td>0</td>
       <td>0</td>
+      <td>5</td>
+      <td>5</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6333,7 +683,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6350,46 +699,45 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>35</td>
-      <td>1212</td>
+      <td>77</td>
+      <td>1365</td>
       <td></td>
     </tr>
     <tr>
       <td></td>
-      <td>stringtie</td>
-      <td>stringtie, stringtie_merge</td>
-      <td>StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.</td>
-      <td>stringtie</td>
-      <td>stringtie</td>
+      <td>sceasy</td>
+      <td>sceasy_convert</td>
+      <td>Converter between difference single-cell formats</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
       <td></td>
-      <td>StringTie</td>
-      <td>Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.</td>
-      <td>Transcriptome assembly, RNA-Seq analysis</td>
-      <td>Transcriptomics, RNA-seq</td>
       <td>Up-to-date</td>
-      <td>http://ccb.jhu.edu/software/stringtie/</td>
-      <td>Transcriptomics</td>
-      <td>stringtie</td>
+      <td>https://github.com/cellgeni/sceasy/</td>
+      <td>Single Cell, Spatial Omics, Convert Formats</td>
+      <td>sceasy_convert</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie</td>
-      <td>2.2.3</td>
-      <td>stringtie</td>
-      <td>2.2.3</td>
-      <td>Transcriptome assembly, RNA-Seq analysis</td>
-      <td>Transcriptomics</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy</td>
+      <td>0.0.7</td>
+      <td>r-sceasy</td>
+      <td>0.0.7</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6403,7 +751,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6411,6 +758,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6418,20 +766,17 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>2</td>
-      <td>2165</td>
-      <td>167659</td>
+      <td>90</td>
+      <td>721</td>
       <td></td>
     </tr>
     <tr>
       <td></td>
-      <td>tophat_fusion_post</td>
-      <td>tophat_fusion_post</td>
-      <td>Wrapper for Tophat-Fusion post step</td>
+      <td>schicexplorer</td>
+      <td>schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol</td>
+      <td>scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.</td>
       <td></td>
       <td></td>
       <td></td>
@@ -6440,30 +785,24 @@
       <td></td>
       <td></td>
       <td>To update</td>
-      <td></td>
-      <td>Transcriptomics</td>
-      <td>tophat_fusion_post</td>
-      <td>devteam</td>
-      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post</td>
-      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post</td>
-      <td>0.1</td>
-      <td>blast+</td>
-      <td></td>
+      <td>https://github.com/joachimwolff/schicexplorer</td>
+      <td>Sequence Analysis, Transcriptomics, Visualization, Single Cell</td>
+      <td>schicexplorer</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer</td>
+      <td>4</td>
+      <td>schicexplorer</td>
+      <td>7</td>
       <td></td>
       <td></td>
+      <td>16</td>
+      <td>16</td>
+      <td>16</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>16</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6490,48 +829,45 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>16</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>15</td>
-      <td>216</td>
+      <td>23</td>
+      <td>779</td>
       <td></td>
     </tr>
     <tr>
       <td></td>
-      <td>transdecoder</td>
-      <td>transdecoder</td>
-      <td>TransDecoder finds coding regions within transcripts</td>
-      <td>TransDecoder</td>
-      <td>TransDecoder</td>
+      <td>scpipe</td>
+      <td>scpipe</td>
+      <td>A flexible preprocessing pipeline for single-cell RNA-sequencing data</td>
+      <td>scpipe</td>
+      <td>scpipe</td>
       <td></td>
-      <td>TransDecoder</td>
-      <td>TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.</td>
-      <td>Coding region prediction, de Novo sequencing, De-novo assembly</td>
-      <td>Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing</td>
+      <td>scPipe</td>
+      <td>A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.</td>
+      <td>Genome annotation, Validation, Alignment, Visualisation</td>
+      <td>Gene expression, RNA-Seq, Sequencing</td>
       <td>To update</td>
-      <td>https://transdecoder.github.io/</td>
-      <td>Transcriptomics, RNA</td>
-      <td>transdecoder</td>
+      <td>http://bioconductor.org/packages/release/bioc/html/scPipe.html</td>
+      <td>Transcriptomics, Single Cell</td>
+      <td>scpipe</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder</td>
-      <td>5.5.0</td>
-      <td>transdecoder</td>
-      <td>5.7.1</td>
-      <td>Coding region prediction, de Novo sequencing, De-novo assembly</td>
-      <td>Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe</td>
+      <td>1.0.0+galaxy2</td>
+      <td>bioconductor-scpipe</td>
+      <td>2.2.0</td>
+      <td>Genome annotation, Validation, Alignment, Visualisation</td>
+      <td>Gene expression, RNA-Seq</td>
       <td>1</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6541,11 +877,8 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6563,42 +896,45 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>348</td>
-      <td>5468</td>
+      <td>1</td>
+      <td>0</td>
+      <td>11</td>
+      <td>628</td>
       <td></td>
     </tr>
     <tr>
       <td></td>
-      <td>trinity</td>
-      <td>trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats</td>
-      <td>Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq</td>
-      <td>trinity</td>
-      <td>trinity</td>
+      <td>seurat</td>
+      <td>seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension</td>
+      <td>Seurat - R toolkit for single cell genomics</td>
       <td></td>
-      <td>Trinity</td>
-      <td>Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.</td>
-      <td>Transcriptome assembly</td>
-      <td>Transcriptomics, Gene expression, Gene transcripts</td>
-      <td>Up-to-date</td>
-      <td>https://github.com/trinityrnaseq/trinityrnaseq</td>
-      <td>Transcriptomics, RNA</td>
       <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://satijalab.org/seurat/</td>
+      <td>Single Cell, Transcriptomics, Sequence Analysis</td>
+      <td>seurat</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity</td>
-      <td>2.15.1</td>
-      <td>trinity</td>
-      <td>2.15.1</td>
-      <td>Transcriptome assembly</td>
-      <td>Transcriptomics, Gene transcripts</td>
-      <td>9</td>
-      <td>13</td>
-      <td>13</td>
-      <td>13</td>
-      <td>9</td>
-      <td>13</td>
-      <td>13</td>
-      <td>13</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat</td>
+      <td>5.0</td>
+      <td>r-seurat</td>
+      <td>3.0.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>7</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>7</td>
+      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6613,64 +949,55 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>2</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>11</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>13</td>
-      <td>12</td>
-      <td>1762</td>
-      <td>31951</td>
       <td></td>
     </tr>
     <tr>
       <td></td>
-      <td>trinotate</td>
-      <td>trinotate</td>
-      <td>Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.</td>
-      <td>trinotate</td>
-      <td>trinotate</td>
+      <td>sinto</td>
+      <td>sinto_barcode, sinto_fragments</td>
+      <td>Sinto single-cell analysis tools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/timoast/sinto</td>
+      <td>Single Cell, Epigenetics</td>
       <td></td>
-      <td>Trinotate</td>
-      <td>Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.</td>
-      <td>Gene functional annotation</td>
-      <td>Gene expression, Transcriptomics</td>
-      <td>To update</td>
-      <td>https://trinotate.github.io/</td>
-      <td>Transcriptomics, RNA</td>
-      <td>trinotate</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate</td>
-      <td>3.2.2</td>
-      <td>trinotate</td>
-      <td>4.0.2</td>
-      <td>Gene functional annotation</td>
-      <td>Transcriptomics</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto</td>
+      <td>0.10.1</td>
+      <td>sinto</td>
+      <td>0.10.1</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
       <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6685,7 +1012,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6699,46 +1025,44 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>151</td>
-      <td>1796</td>
+      <td>17</td>
+      <td>91</td>
       <td></td>
     </tr>
     <tr>
       <td></td>
-      <td>tximport</td>
-      <td>tximport</td>
-      <td>Wrapper for the Bioconductor package tximport</td>
-      <td>tximport</td>
-      <td>tximport</td>
+      <td>snapatac2</td>
+      <td>snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing</td>
+      <td>SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
       <td></td>
-      <td>tximport</td>
-      <td>An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.</td>
-      <td>Pathway or network analysis, Formatting, RNA-Seq analysis</td>
-      <td>Transcriptomics, Gene transcripts, Workflows</td>
       <td>To update</td>
-      <td>http://bioconductor.org/packages/tximport/</td>
-      <td>Transcriptomics</td>
-      <td>tximport</td>
+      <td>https://kzhang.org/SnapATAC2/</td>
+      <td>Single Cell, Epigenetics</td>
+      <td>snapatac2</td>
       <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport</td>
-      <td>1.22.0</td>
-      <td>bioconductor-tximport</td>
-      <td>1.30.0</td>
-      <td>Pathway or network analysis, Formatting, RNA-Seq analysis</td>
-      <td>Transcriptomics, Gene transcripts, Workflows</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2</td>
+      <td>2.6.4</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
       <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6771,17 +1095,13 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>88</td>
-      <td>1408</td>
       <td></td>
     </tr>
     <tr>
       <td></td>
-      <td>ucsc-cell-browser</td>
-      <td>ucsc_cell_browser</td>
-      <td>Python pipeline and Javascript scatter plot library for single-cell datasets</td>
+      <td>spapros</td>
+      <td>spapros_evaluation, spapros_selection</td>
+      <td>Select and evaluate probe sets for targeted spatial transcriptomics.</td>
       <td></td>
       <td></td>
       <td></td>
@@ -6789,26 +1109,25 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>To update</td>
-      <td>https://cells.ucsc.edu/</td>
-      <td>Transcriptomics</td>
-      <td>ucsc_cell_browser</td>
-      <td>ebi-gxa</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml</td>
-      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser</td>
-      <td>1.0.0+galaxy1</td>
-      <td>ucsc-cell-browser</td>
-      <td>1.2.6</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/theislab/spapros</td>
+      <td>Single Cell, Transcriptomics, Sequence Analysis</td>
+      <td>spapros</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros</td>
+      <td>0.1.5</td>
+      <td>spapros</td>
+      <td>0.1.5</td>
       <td></td>
       <td></td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
+      <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
+      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6841,10 +1160,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>78</td>
-      <td>941</td>
       <td></td>
     </tr>
     <tr>
@@ -6859,14 +1174,14 @@
       <td>Tools for handling Unique Molecular Identifiers in NGS data sets.</td>
       <td>Sequencing quality control</td>
       <td>NGS, Sequence sites, features and motifs, Quality affairs</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/CGATOxford/UMI-tools</td>
-      <td>Sequence Analysis, Transcriptomics</td>
+      <td>Sequence Analysis, Transcriptomics, Single Cell</td>
       <td></td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools</td>
-      <td>1.1.2</td>
+      <td>1.1.5</td>
       <td>umi_tools</td>
       <td>1.1.5</td>
       <td>Sequencing quality control</td>
@@ -6891,10 +1206,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6908,11 +1219,10 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>3</td>
       <td>5</td>
       <td>5</td>
+      <td>0</td>
       <td>379</td>
       <td>61618</td>
       <td></td>
@@ -6931,7 +1241,7 @@
       <td></td>
       <td>Up-to-date</td>
       <td>http://velocyto.org/</td>
-      <td>Transcriptomics</td>
+      <td>Transcriptomics, Single Cell</td>
       <td>velocyto</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto</td>
@@ -6942,80 +1252,9 @@
       <td></td>
       <td></td>
       <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
-      <td>0</td>
-      <td>2</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>volcanoplot</td>
-      <td>volcanoplot</td>
-      <td>Tool to create a Volcano Plot</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://ggplot2.tidyverse.org/</td>
-      <td>Visualization, Transcriptomics, Statistics</td>
-      <td>volcanoplot</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot</td>
-      <td>0.0.6</td>
-      <td>r-ggplot2</td>
-      <td>2.2.1</td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -7033,28 +1272,24 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1749</td>
-      <td>30946</td>
+      <td>2</td>
       <td></td>
     </tr>
   </tbody>
diff --git a/communities/spoc/resources/tools.tsv b/communities/spoc/resources/tools.tsv
index b1844867..c72a3466 100644
--- a/communities/spoc/resources/tools.tsv
+++ b/communities/spoc/resources/tools.tsv
@@ -1,100 +1,19 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on ANASTASIA	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on BF2I-MAP	Tools available on BioBix	Tools available on CIRM-CFBP	Tools available on Center for Phage Technology (CPT)	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CorGAT	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on Protologger	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-aegean	aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval	AEGeAn toolkit wrappers	gaeval	gaeval		GAEVAL	Gene Annotation EVAluation.	Sequence annotation	Sequence analysis, Gene structure	Up-to-date	https://github.com/BrendelGroup/AEGeAn	Transcriptomics, Sequence Analysis	aegean	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean	0.16.0	aegean	0.16.0	Sequence annotation	Sequence analysis, Gene structure	1	4	4	4	1	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	47	168	False		
-anndata	anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Transcriptomics, Sequence Analysis	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.3	anndata	0.6.22.post1			5	4	5	0	5	4	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	625	35620	False		
-arriba	arriba, arriba_draw_fusions, arriba_get_filters	Arriba detects fusion genes in RNA-Seq data after running RNA-STAR								Up-to-date	https://github.com/suhrig/arriba	Sequence Analysis, Transcriptomics	arriba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba	2.4.0	arriba	2.4.0			0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	38	3528	False		
-askor	askor_de	AskoR links EdgeR and AskOmics								To update	https://github.com/askomics/askoR	Transcriptomics	askor_de	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	0.2	bioconductor-limma	3.58.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bamparse	bamparse	Generates hit count lists from bam alignments.								To update	http://artbio.fr	RNA, Transcriptomics	bamparse	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	4.1.1	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	71	False		
-bctools	bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events	bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0								Up-to-date	https://github.com/dmaticzka/bctools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools	0.2.2	bctools	0.2.2			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	87	2895	False		
-brew3r_r	brew3r_r	Extend 3' end of a GTF using another GTF as a template								To update	https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html	Transcriptomics, RNA	brew3r_r	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r	https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r	1.0.2					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-cell-types-analysis	ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals	Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis								To update		Transcriptomics, RNA, Statistics	suite_cell_types_analysis	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis	1.1.1	cell-types-analysis	0.1.11			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	6	False		
-cemitool	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	To update	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.18.1	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	9	98	False		
-cherri	cherri_eval, cherri_train	Computational Help Evaluating RNA-RNA interactions	cherri	cherri		cherri	CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.		Molecular interactions, pathways and networks, Structure analysis, Machine learning	To update	https://github.com/BackofenLab/Cherri	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri	0.7	cherri	0.8		Molecular interactions, pathways and networks, Structure analysis, Machine learning	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	1	207	False		
-chira	chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify	Chimeric Read Annotator for RNA-RNA interactome data	chira	chira		ChiRA	ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.		RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	Up-to-date	https://github.com/pavanvidem/chira	RNA, Transcriptomics, Sequence Analysis	chira	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira	1.4.3	chira	1.4.3		Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	97	6418	False		
-cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	Up-to-date	https://github.com/Hoohm/CITE-seq-Count	Transcriptomics	cite_seq_count	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	1.4.4	cite-seq-count	1.4.4	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	18	False		
-cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-cpat	cpat	Coding-potential assessment tool using an alignment-free logistic regression model.								Up-to-date	https://github.com/liguowang/cpat	Transcriptomics	cpat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	3.0.5	cpat	3.0.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	21	134	False		
-cpm_tpm_rpk	cpm_tpm_rpk	Generate CPM,TPM or RPK from raw counts								To update	http://artbio.fr	Transcriptomics	cpm_tpm_rpk	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	0.5.2	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-crosscontamination_barcode_filter	crosscontamination_barcode_filter	Barcode contamination discovery tool								To update		Transcriptomics, Visualization	crosscontamination_barcode_filter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter	0.3	r-ggplot2	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	17	347	False		
-cuffcompare	cuffcompare	Galaxy wrappers for the Cuffcompare tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffcompare	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare	2.2.1	cufflinks	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	1	1	65	1130	False		
-cuffdiff	cuffdiff	Galaxy wrappers for the Cuffdiff tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffdiff	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff	2.2.1	cufflinks	2.2.1			1	0	1	0	1	0	1	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	228	5831	False		
-cufflinks	cufflinks	Galaxy wrappers for the Cufflinks tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cufflinks	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks	2.2.1	cufflinks	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	1	0	0	0	0	0	1	1	319	32218	False		
-cuffmerge	cuffmerge	Galaxy wrappers for the Cuffmerge tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffmerge	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge	2.2.1	cufflinks	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	1	1	122	3292	False		
-cuffnorm	cuffnorm	The Cuffnorm tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffnorm	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	27	660	False		
-cuffquant	cuffquant	The Cuffquant tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffquant	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	18	688	False		
-data-hca	hca_matrix_downloader	Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects								To update		Transcriptomics, Sequence Analysis	suite_human_cell_atlas_tools	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca	v0.0.4+galaxy0	hca-matrix-downloader	0.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	34	439	False		
-data-scxa	retrieve_scxa	Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home								To update		Transcriptomics, Sequence Analysis	suite_ebi_expression_atlas	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa	v0.0.2+galaxy2	wget				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	99	799	False		
-decoupler	score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk	decoupler - Ensemble of methods to infer biological activities								To update	https://decoupler-py.readthedocs.io/en/latest/	Transcriptomics	suite_decoupler	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler	1.4.0+galaxy3	decoupler	1.5.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	False		
-deg_annotate	deg_annotate	Annotate DESeq2/DEXSeq output tables								To update		Transcriptomics	deg_annotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate	1.1.0	bedtools	2.31.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1774	19910	False		
-deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	0	0	1	1	4990	95752	False		
-deseq2_normalization	deseq2_normalization	Normalizes gene hitlists								To update	http://artbio.fr	RNA, Transcriptomics, Sequence Analysis, Statistics	deseq2_normalization	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	1.40.2+galaxy0	bioconductor-deseq2	1.42.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-dexseq	dexseq, dexseq_count, plotdexseq	Inference of differential exon usage in RNA-Seq	dexseq	dexseq		DEXSeq	The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html	Transcriptomics, RNA, Statistics	dexseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq	1.48.0	bioconductor-dexseq	1.48.0	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	218	16064	False		
-dropletutils	dropletutils_empty_drops, dropletutils_read_10x	De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_dropletutils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils	1.0.4	dropletutils-scripts	0.0.5			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	201	1599	False		
-dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Transcriptomics, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	126	3934	False		
-edger	edger	Perform RNA-Seq differential expression analysis using edgeR pipeline	edger	edger		edgeR	Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	To update	http://bioconductor.org/packages/release/bioc/html/edgeR.html	Transcriptomics, RNA, Statistics	edger	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger	https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger	3.36.0	bioconductor-edger	4.0.16	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	1	945	18117	False		
-egsea	egsea	This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing	egsea	egsea		EGSEA	This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.	Gene set testing	Systems biology	To update	https://bioconductor.org/packages/release/bioc/html/EGSEA.html	Transcriptomics, RNA, Statistics	egsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea	1.20.0	bioconductor-egsea	1.28.0	Gene set testing	Systems biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	177	2524	False		
-fastq_provider	fastq_provider	Retrieval and download of FASTQ files from ENA and other repositories such as HCA.								To update	https://github.com/ebi-gene-expression-group/atlas-fastq-provider	Data Source, RNA, Transcriptomics	atlas_fastq_provider	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider	0.4.4	atlas-fastq-provider	0.4.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastq_utils	fastq_filter_n, fastq_trim_poly_at	Set of tools for handling fastq files								To update	https://github.com/nunofonseca/fastq_utils	Transcriptomics, RNA	fastq_utils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils	0.25.1+galaxy0	fastq_utils	0.25.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	0	0	1	1	4679	696399	False		
-fgsea	fgsea	Perform gene set testing using fgsea	fgsea	fgsea		fgsea	The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.	Gene-set enrichment analysis	Genetics	To update	https://bioconductor.org/packages/release/bioc/html/fgsea.html	Visualization, Transcriptomics, Statistics	fgsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea	1.8.0+galaxy1	bioconductor-fgsea	1.28.0	Gene-set enrichment analysis	Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	307	5240	False		
-garnett	garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file	De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_garnett	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett	0.2.8	garnett-cli	0.0.5			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	27	False		
-genomic_super_signature	genomic_super_signature	Interpretation of RNAseq experiments through robust, efficient comparison to public databases	genomicsupersignature	genomicsupersignature		GenomicSuperSignature	GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	To update	https://github.com/shbrief/GenomicSuperSignature	Sequence Analysis, RNA, Transcriptomics	genomic_super_signature	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature	1.2.0	bioconductor-genomicsupersignature	1.10.0	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	11	46	False		
-gffcompare	gffcompare	Galaxy wrappers for Geo Pertea's GffCompare package.	gffcompare	gffcompare		gffcompare	Program for comparing, annotating, merging and tracking transcripts in GFF files.	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	https://github.com/gpertea/gffcompare/	Transcriptomics	gffcompare	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare	0.12.6	gffcompare	0.12.6	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	381	3477	False		
-gsc_filter_cells	filter_cells	Filter single cell RNAseq data on libray depth and number of detected genes								To update	http://artbio.fr	Transcriptomics	gsc_filter_cells	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-gsc_filter_genes	filter_genes	Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_filter_genes	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-gsc_gene_expression_correlations	single_cell_gene_expression_correlations	Compute single-cell paire-wise gene expressions correlations								To update	http://artbio.fr	Transcriptomics	gsc_gene_expression_correlations	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-gsc_high_dimensions_visualisation	high_dimensions_visualisation	Generates PCA, t-SNE and HCPC visualisation								To update	http://artbio.fr	Transcriptomics, Visualization	gsc_high_dimensions_visualisation	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation	4.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-gsc_mannwhitney_de	mannwhitney_de	Perform a mann-whitney differential testing between two sets of gene expression data								To update	http://artbio.fr	Transcriptomics	gsc_mannwhitney_de	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	4.1.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-gsc_scran_normalize	scran_normalize	Normalize raw counts using scran								To update	http://artbio.fr	Transcriptomics	gsc_scran_normalize	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	1.28.1+galaxy0	bioconductor-scran	1.30.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	14	78	False		
-gsc_signature_score	signature_score	Compute signature scores from single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_signature_score	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	2.3.9+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-heinz	heinz_bum, heinz, heinz_scoring, heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	heinz	heinz, bionet		Heinz	Tool for single-species active module discovery.	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	To update	https://github.com/ls-cwi/heinz	Transcriptomics, Visualization, Statistics	heinz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz	1.0	bioconductor-bionet	1.62.0	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	242	1186	False		
-isoformswitchanalyzer	isoformswitchanalyzer	Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.	IsoformSwitchAnalyzeR	IsoformSwitchAnalyzeR		IsoformSwitchAnalyzeR	Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	To update	https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html	Transcriptomics, RNA, Statistics	isoformswitchanalyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer	1.20.0	bioconductor-isoformswitchanalyzer	2.2.0	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	29	822	False		
-kallisto	kallisto_pseudo, kallisto_quant	kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment.	kallisto	kallisto		kallisto	A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.	Gene expression profiling	Transcriptomics, RNA-seq, Gene expression	To update	https://pachterlab.github.io/kallisto/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto	0.48.0	kallisto	0.50.1	Gene expression profiling	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	299	24155	False		
-limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1012	20344	False		
-masigpro	masigpro	Identify significantly differential expression profiles in time-course microarray experiments	masigpro	masigpro		maSigPro	Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.	Regression analysis	Gene expression, Molecular genetics, Microarray experiment, RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html	Transcriptomics, RNA, Statistics	masigpro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro	1.49.3	coreutils	8.25	Regression analysis	Gene expression, Microarray experiment, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	13	576	False		
-mircounts	mircounts	Generates miRNA count lists from read alignments to mirBase.								To update	http://artbio.fr	RNA, Transcriptomics	mircounts	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts	https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts	1.6	tar				0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-monocle3	monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers	De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_monocle3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3	0.1.4	monocle3-cli	0.0.9			9	0	9	0	9	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	264	3266	False		
-multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	2	53	False		
-music_deconvolution	music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution	Multi-subject Single Cell deconvolution (MuSiC)								Up-to-date	https://github.com/xuranw/MuSiC	Transcriptomics	music	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/	https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution	0.1.1	music-deconvolution	0.1.1			5	5	4	0	5	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	240	1872	False		
-nugen_nudup	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-pathifier	pathifier	pathifier								Up-to-date	https://	Transcriptomics, Statistics	pathifier	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	1.40.0	bioconductor-pathifier	1.40.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	10	228	False		
-pizzly	pizzly	Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.								To update	https://github.com/pmelsted/pizzly/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly	0.37.3.1	pizzly	0.37.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	16	208	False		
-psiclass	psiclass	PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.	psiclass	psiclass						Up-to-date	https://github.com/splicebox/PsiCLASS	Transcriptomics	psiclass	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass	https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass	1.0.3	psiclass	1.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	15	False		
-qualimap	qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq		qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	To update	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.2.2d	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	1	4	4	4	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	4	4	1328	664470	False		
-raceid	raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory	RaceID3, StemID2, FateID - scRNA analysis								To update	https://github.com/dgrun/RaceID3_StemID2_package/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid	0.2.3	r-raceid	0.1.3			5	5	5	1	5	5	5	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	82	4569	False		
-repenrich	edger-repenrich, repenrich	Repeat element profiling								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	Transcriptomics	repenrich	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	2.31.1					0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	False		
-repenrich2	edger-repenrich2, repenrich2	Repeat element profiling using bowtie2 aligner								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	Transcriptomics	repenrich2	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	2.31.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	False		
-rgrnastar	rna_star, rna_starsolo	RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper	star	star		STAR	Ultrafast universal RNA-seq data aligner	Sequence alignment	RNA-Seq, Transcriptomics	To update	https://github.com/alexdobin/STAR	Next Gen Mappers, Transcriptomics	rgrnastar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar	2.7.11a	star	2.7.11b	Sequence alignment	RNA-Seq, Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	2	0	0	0	1	0	0	0	0	0	1	0	0	2	2	4015	425658	False		
-ribowaltz	ribowaltz_process, ribowaltz_plot	Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data	riboWaltz	riboWaltz		riboWaltz	riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.		Computational biology	To update	https://github.com/LabTranslationalArchitectomics/riboWaltz	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz	1.2.0	ribowaltz	2.0		Computational biology	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	14	161	False		
-rsem	extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie	transcript quantification from RNA-Seq data								To update	https://github.com/deweylab/RSEM	Transcriptomics, RNA	rsem	artbio	https://github.com/artbio/tools-artbio/tree/master/tools/rsem	https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem		rsem	1.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	1	1	67	377	False		
-rseqc	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	22	22	22	22	22	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	22	0	0	0	22	0	0	0	0	0	0	0	0	22	22	3206	133498	False		
-ruvseq	ruvseq	Remove Unwanted Variation from RNA-Seq Data	ruvseq	ruvseq		RUVSeq	This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.	Differential gene expression analysis	Gene expression, RNA-seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	ruvseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq	1.26.0	bioconductor-ruvseq	1.36.0	Differential gene expression analysis	Gene expression	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	76	1236	False		
-salmon	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	1	3	1	2	1	3	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	3	3	969	61937	False		
-sashimi_plot	sashimi_plot	Generates a sashimi plot from bam files.								To update	http://artbio.fr	RNA, Transcriptomics, Graphics, Visualization	sashimi_plot	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot	https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot	0.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-sc3	sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare	De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_sc3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3	1.8.0	sc3-scripts	0.0.6			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	9	False		
-scanpy	scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	scanpy	scanpy		SCANPY	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.9.6	scanpy	1.7.2	Differential gene expression analysis	Gene expression, Cell biology, Genetics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	766	51978	False		
-scanpy	anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data	scanpy-scripts, command-line wrapper scripts around Scanpy.								To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis, RNA	scanpy_scripts	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy	1.9.3	scanpy-scripts	1.9.301			22	27	27	0	22	27	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	13	2185	39356	False		
-scater	scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results	De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scater	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater	1.10.0	scater-scripts	0.0.5			0	1	6	0	0	1	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	16	387	False		
-scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Transcriptomics, RNA, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	77	1365	False		
-sccaf	run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out	SCCAF: Single Cell Clustering Assessment Framework.								To update	https://github.com/sccaf/sccaf	Transcriptomics	SCCAF	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf	0.0.9	sccaf	0.0.10			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	110	False		
-sceasy	sceasy_convert	Converter between difference single-cell formats								Up-to-date	https://github.com/cellgeni/sceasy/	Transcriptomics	sceasy_convert	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy	0.0.7	r-sceasy	0.0.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	90	721	False		
-sceasy	sceasy_convert	Convert scRNA data object between popular formats								To update		Transcriptomics	sceasy	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy	0.0.5	r-sceasy	0.0.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	90	721	False		
-schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			0	0	16	0	0	0	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	23	779	False		
-scmap	scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features	De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scmap	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap	1.6.4	scmap-cli	0.1.0			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	13	83	False		
-scpipe	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	scpipe	scpipe		scPipe	A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, RNA, Statistics	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	11	628	False		
-scpred	scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model	De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scpred	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred	1.0.2	scpred-cli	0.1.0			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	25	False		
-seurat	seurat	A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data								To update	https://github.com/satijalab/seurat	Transcriptomics, RNA, Statistics	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	4.3.0.1	r-seurat	3.0.2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	66	1543	False		
-seurat	seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features	De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1								Up-to-date	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	Transcriptomics, RNA, Statistics, Sequence Analysis	suite_seurat	ebi-gxa		https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat	4.0.0	seurat-scripts	4.0.0			0	0	14	11	0	0	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	0	0	0	0	0	0	0	0	181	1966	False		
-slamdunk	alleyoop, slamdunk	Slamdunk maps and quantifies SLAMseq reads								Up-to-date	http://t-neumann.github.io/slamdunk	RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers	slamdunk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk	0.4.3	slamdunk	0.4.3			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	361	False		
-sleuth	sleuth	Sleuth is a program for differential analysis of RNA-Seq data.	sleuth	sleuth		sleuth	A statistical model and software application for RNA-seq differential expression analysis.	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	RNA-seq, Gene expression, Statistics and probability	Up-to-date	https://github.com/pachterlab/sleuth	Transcriptomics, RNA, Statistics	sleuth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth	0.30.1	r-sleuth	0.30.1	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	8	64	False		
-star_fusion	star_fusion	STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR								To update		Sequence Analysis, Transcriptomics	star_fusion	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion	https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion	0.5.4-3+galaxy1	star-fusion	1.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	35	1212	False		
-stringtie	stringtie, stringtie_merge	StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.	stringtie	stringtie		StringTie	Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.	Transcriptome assembly, RNA-Seq analysis	Transcriptomics, RNA-seq	Up-to-date	http://ccb.jhu.edu/software/stringtie/	Transcriptomics	stringtie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie	2.2.3	stringtie	2.2.3	Transcriptome assembly, RNA-Seq analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	2	2	2165	167659	False		
-tophat_fusion_post	tophat_fusion_post	Wrapper for Tophat-Fusion post step								To update		Transcriptomics	tophat_fusion_post	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post	0.1	blast+				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	15	216	False		
-transdecoder	transdecoder	TransDecoder finds coding regions within transcripts	TransDecoder	TransDecoder		TransDecoder	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	To update	https://transdecoder.github.io/	Transcriptomics, RNA	transdecoder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder	5.5.0	transdecoder	5.7.1	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	348	5468	False		
-trinity	trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats	Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq	trinity	trinity		Trinity	Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.	Transcriptome assembly	Transcriptomics, Gene expression, Gene transcripts	Up-to-date	https://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity	2.15.1	trinity	2.15.1	Transcriptome assembly	Transcriptomics, Gene transcripts	9	13	13	13	9	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	1	0	0	0	0	0	0	11	0	0	1	0	0	0	0	0	13	12	1762	31951	False		
-trinotate	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	trinotate	trinotate		Trinotate	Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.	Gene functional annotation	Gene expression, Transcriptomics	To update	https://trinotate.github.io/	Transcriptomics, RNA	trinotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate	3.2.2	trinotate	4.0.2	Gene functional annotation	Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	151	1796	False		
-tximport	tximport	Wrapper for the Bioconductor package tximport	tximport	tximport		tximport	An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	To update	http://bioconductor.org/packages/tximport/	Transcriptomics	tximport	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport	1.22.0	bioconductor-tximport	1.30.0	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	88	1408	False		
-ucsc-cell-browser	ucsc_cell_browser	Python pipeline and Javascript scatter plot library for single-cell datasets								To update	https://cells.ucsc.edu/	Transcriptomics	ucsc_cell_browser	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser	1.0.0+galaxy1	ucsc-cell-browser	1.2.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	78	941	False		
-umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	To update	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.2	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	5	5	379	61618	False		
-velocyto	velocyto_cli	Velocyto is a library for the analysis of RNA velocity.								Up-to-date	http://velocyto.org/	Transcriptomics	velocyto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto	0.17.17	velocyto.py	0.17.17			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	False		
-volcanoplot	volcanoplot	Tool to create a Volcano Plot								To update	https://ggplot2.tidyverse.org/	Visualization, Transcriptomics, Statistics	volcanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot	0.0.6	r-ggplot2	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	1749	30946	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
+anndata	anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Single Cell, Spatial Omics	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.9	anndata	0.6.22.post1			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	625	35620	False		
+baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Single Cell, Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	71	False		
+cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	To update	https://github.com/Hoohm/CITE-seq-Count	Single Cell, Transcriptomics, Proteomics	cite_seq_count	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	1.4.4	cite-seq-count	1.4.5	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	18	False		
+cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis, Single Cell	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Single Cell, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	126	3934	False		
+episcanpy	episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess	EpiScanpy – Epigenomics single cell analysis in python	episcanpy	episcanpy		epiScanpy	Epigenomics Single Cell Analysis in Python.	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	To update	https://github.com/colomemaria/epiScanpy	Single Cell, Epigenetics	episcanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy	0.3.2	episcanpy	0.4.0	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	20	736	False		
+raceid	raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory	RaceID3, StemID2, FateID - scRNA analysis								To update	https://github.com/dgrun/RaceID3_StemID2_package/	Single Cell, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid	0.2.3	r-raceid	0.1.3			5	5	5	1	5	5	5	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	82	4569	False		
+scanpy	scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	scanpy	scanpy		SCANPY	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Single Cell, Spatial Omics, Transcriptomics	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.10.2	scanpy	1.7.2	Differential gene expression analysis	Gene expression, Cell biology, Genetics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	766	51978	False		
+scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Single Cell, Transcriptomics, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	77	1365	False		
+sceasy	sceasy_convert	Converter between difference single-cell formats								Up-to-date	https://github.com/cellgeni/sceasy/	Single Cell, Spatial Omics, Convert Formats	sceasy_convert	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy	0.0.7	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	90	721	False		
+schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization, Single Cell	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	16	0	23	779	False		
+scpipe	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	scpipe	scpipe		scPipe	A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, Single Cell	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	11	628	False		
+seurat	seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension	Seurat - R toolkit for single cell genomics								To update	https://satijalab.org/seurat/	Single Cell, Transcriptomics, Sequence Analysis	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	5.0	r-seurat	3.0.2			1	1	7	1	1	1	7	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	False		
+sinto	sinto_barcode, sinto_fragments	Sinto single-cell analysis tools								Up-to-date	https://github.com/timoast/sinto	Single Cell, Epigenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto	0.10.1	sinto	0.10.1			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	17	91	False		
+snapatac2	snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing	SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis								To update	https://kzhang.org/SnapATAC2/	Single Cell, Epigenetics	snapatac2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2	2.6.4					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spapros	spapros_evaluation, spapros_selection	Select and evaluate probe sets for targeted spatial transcriptomics.								Up-to-date	https://github.com/theislab/spapros	Single Cell, Transcriptomics, Sequence Analysis	spapros	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros	0.1.5	spapros	0.1.5			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	Up-to-date	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics, Single Cell		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.5	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	3	5	5	0	379	61618	False		
+velocyto	velocyto_cli	Velocyto is a library for the analysis of RNA velocity.								Up-to-date	http://velocyto.org/	Transcriptomics, Single Cell	velocyto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto	0.17.17	velocyto.py	0.17.17			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	2	False		
diff --git a/communities/spoc/resources/tools_filtered_by_ts_categories.tsv b/communities/spoc/resources/tools_filtered_by_ts_categories.tsv
index b1844867..c72a3466 100644
--- a/communities/spoc/resources/tools_filtered_by_ts_categories.tsv
+++ b/communities/spoc/resources/tools_filtered_by_ts_categories.tsv
@@ -1,100 +1,19 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on ANASTASIA	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on BF2I-MAP	Tools available on BioBix	Tools available on CIRM-CFBP	Tools available on Center for Phage Technology (CPT)	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CorGAT	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on Protologger	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-aegean	aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval	AEGeAn toolkit wrappers	gaeval	gaeval		GAEVAL	Gene Annotation EVAluation.	Sequence annotation	Sequence analysis, Gene structure	Up-to-date	https://github.com/BrendelGroup/AEGeAn	Transcriptomics, Sequence Analysis	aegean	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean	0.16.0	aegean	0.16.0	Sequence annotation	Sequence analysis, Gene structure	1	4	4	4	1	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	47	168	False		
-anndata	anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Transcriptomics, Sequence Analysis	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.3	anndata	0.6.22.post1			5	4	5	0	5	4	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	625	35620	False		
-arriba	arriba, arriba_draw_fusions, arriba_get_filters	Arriba detects fusion genes in RNA-Seq data after running RNA-STAR								Up-to-date	https://github.com/suhrig/arriba	Sequence Analysis, Transcriptomics	arriba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba	2.4.0	arriba	2.4.0			0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	38	3528	False		
-askor	askor_de	AskoR links EdgeR and AskOmics								To update	https://github.com/askomics/askoR	Transcriptomics	askor_de	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	0.2	bioconductor-limma	3.58.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bamparse	bamparse	Generates hit count lists from bam alignments.								To update	http://artbio.fr	RNA, Transcriptomics	bamparse	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	4.1.1	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	71	False		
-bctools	bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events	bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0								Up-to-date	https://github.com/dmaticzka/bctools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools	0.2.2	bctools	0.2.2			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	87	2895	False		
-brew3r_r	brew3r_r	Extend 3' end of a GTF using another GTF as a template								To update	https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html	Transcriptomics, RNA	brew3r_r	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r	https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r	1.0.2					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-cell-types-analysis	ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals	Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis								To update		Transcriptomics, RNA, Statistics	suite_cell_types_analysis	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis	1.1.1	cell-types-analysis	0.1.11			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	6	False		
-cemitool	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	To update	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.18.1	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	9	98	False		
-cherri	cherri_eval, cherri_train	Computational Help Evaluating RNA-RNA interactions	cherri	cherri		cherri	CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.		Molecular interactions, pathways and networks, Structure analysis, Machine learning	To update	https://github.com/BackofenLab/Cherri	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri	0.7	cherri	0.8		Molecular interactions, pathways and networks, Structure analysis, Machine learning	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	1	207	False		
-chira	chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify	Chimeric Read Annotator for RNA-RNA interactome data	chira	chira		ChiRA	ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.		RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	Up-to-date	https://github.com/pavanvidem/chira	RNA, Transcriptomics, Sequence Analysis	chira	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira	1.4.3	chira	1.4.3		Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	97	6418	False		
-cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	Up-to-date	https://github.com/Hoohm/CITE-seq-Count	Transcriptomics	cite_seq_count	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	1.4.4	cite-seq-count	1.4.4	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	18	False		
-cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-cpat	cpat	Coding-potential assessment tool using an alignment-free logistic regression model.								Up-to-date	https://github.com/liguowang/cpat	Transcriptomics	cpat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	3.0.5	cpat	3.0.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	21	134	False		
-cpm_tpm_rpk	cpm_tpm_rpk	Generate CPM,TPM or RPK from raw counts								To update	http://artbio.fr	Transcriptomics	cpm_tpm_rpk	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	0.5.2	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-crosscontamination_barcode_filter	crosscontamination_barcode_filter	Barcode contamination discovery tool								To update		Transcriptomics, Visualization	crosscontamination_barcode_filter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter	0.3	r-ggplot2	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	17	347	False		
-cuffcompare	cuffcompare	Galaxy wrappers for the Cuffcompare tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffcompare	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare	2.2.1	cufflinks	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	1	1	65	1130	False		
-cuffdiff	cuffdiff	Galaxy wrappers for the Cuffdiff tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffdiff	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff	2.2.1	cufflinks	2.2.1			1	0	1	0	1	0	1	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	228	5831	False		
-cufflinks	cufflinks	Galaxy wrappers for the Cufflinks tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cufflinks	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks	2.2.1	cufflinks	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	1	0	0	0	0	0	1	1	319	32218	False		
-cuffmerge	cuffmerge	Galaxy wrappers for the Cuffmerge tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffmerge	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge	2.2.1	cufflinks	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	1	1	122	3292	False		
-cuffnorm	cuffnorm	The Cuffnorm tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffnorm	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	27	660	False		
-cuffquant	cuffquant	The Cuffquant tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffquant	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	18	688	False		
-data-hca	hca_matrix_downloader	Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects								To update		Transcriptomics, Sequence Analysis	suite_human_cell_atlas_tools	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca	v0.0.4+galaxy0	hca-matrix-downloader	0.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	34	439	False		
-data-scxa	retrieve_scxa	Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home								To update		Transcriptomics, Sequence Analysis	suite_ebi_expression_atlas	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa	v0.0.2+galaxy2	wget				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	99	799	False		
-decoupler	score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk	decoupler - Ensemble of methods to infer biological activities								To update	https://decoupler-py.readthedocs.io/en/latest/	Transcriptomics	suite_decoupler	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler	1.4.0+galaxy3	decoupler	1.5.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	False		
-deg_annotate	deg_annotate	Annotate DESeq2/DEXSeq output tables								To update		Transcriptomics	deg_annotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate	1.1.0	bedtools	2.31.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1774	19910	False		
-deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	0	0	1	1	4990	95752	False		
-deseq2_normalization	deseq2_normalization	Normalizes gene hitlists								To update	http://artbio.fr	RNA, Transcriptomics, Sequence Analysis, Statistics	deseq2_normalization	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	1.40.2+galaxy0	bioconductor-deseq2	1.42.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-dexseq	dexseq, dexseq_count, plotdexseq	Inference of differential exon usage in RNA-Seq	dexseq	dexseq		DEXSeq	The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html	Transcriptomics, RNA, Statistics	dexseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq	1.48.0	bioconductor-dexseq	1.48.0	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	218	16064	False		
-dropletutils	dropletutils_empty_drops, dropletutils_read_10x	De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_dropletutils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils	1.0.4	dropletutils-scripts	0.0.5			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	201	1599	False		
-dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Transcriptomics, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	126	3934	False		
-edger	edger	Perform RNA-Seq differential expression analysis using edgeR pipeline	edger	edger		edgeR	Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	To update	http://bioconductor.org/packages/release/bioc/html/edgeR.html	Transcriptomics, RNA, Statistics	edger	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger	https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger	3.36.0	bioconductor-edger	4.0.16	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	1	945	18117	False		
-egsea	egsea	This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing	egsea	egsea		EGSEA	This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.	Gene set testing	Systems biology	To update	https://bioconductor.org/packages/release/bioc/html/EGSEA.html	Transcriptomics, RNA, Statistics	egsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea	1.20.0	bioconductor-egsea	1.28.0	Gene set testing	Systems biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	177	2524	False		
-fastq_provider	fastq_provider	Retrieval and download of FASTQ files from ENA and other repositories such as HCA.								To update	https://github.com/ebi-gene-expression-group/atlas-fastq-provider	Data Source, RNA, Transcriptomics	atlas_fastq_provider	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider	0.4.4	atlas-fastq-provider	0.4.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastq_utils	fastq_filter_n, fastq_trim_poly_at	Set of tools for handling fastq files								To update	https://github.com/nunofonseca/fastq_utils	Transcriptomics, RNA	fastq_utils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils	0.25.1+galaxy0	fastq_utils	0.25.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	0	0	1	1	4679	696399	False		
-fgsea	fgsea	Perform gene set testing using fgsea	fgsea	fgsea		fgsea	The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.	Gene-set enrichment analysis	Genetics	To update	https://bioconductor.org/packages/release/bioc/html/fgsea.html	Visualization, Transcriptomics, Statistics	fgsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea	1.8.0+galaxy1	bioconductor-fgsea	1.28.0	Gene-set enrichment analysis	Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	307	5240	False		
-garnett	garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file	De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_garnett	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett	0.2.8	garnett-cli	0.0.5			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	27	False		
-genomic_super_signature	genomic_super_signature	Interpretation of RNAseq experiments through robust, efficient comparison to public databases	genomicsupersignature	genomicsupersignature		GenomicSuperSignature	GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	To update	https://github.com/shbrief/GenomicSuperSignature	Sequence Analysis, RNA, Transcriptomics	genomic_super_signature	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature	1.2.0	bioconductor-genomicsupersignature	1.10.0	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	11	46	False		
-gffcompare	gffcompare	Galaxy wrappers for Geo Pertea's GffCompare package.	gffcompare	gffcompare		gffcompare	Program for comparing, annotating, merging and tracking transcripts in GFF files.	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	https://github.com/gpertea/gffcompare/	Transcriptomics	gffcompare	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare	0.12.6	gffcompare	0.12.6	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	381	3477	False		
-gsc_filter_cells	filter_cells	Filter single cell RNAseq data on libray depth and number of detected genes								To update	http://artbio.fr	Transcriptomics	gsc_filter_cells	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-gsc_filter_genes	filter_genes	Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_filter_genes	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-gsc_gene_expression_correlations	single_cell_gene_expression_correlations	Compute single-cell paire-wise gene expressions correlations								To update	http://artbio.fr	Transcriptomics	gsc_gene_expression_correlations	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-gsc_high_dimensions_visualisation	high_dimensions_visualisation	Generates PCA, t-SNE and HCPC visualisation								To update	http://artbio.fr	Transcriptomics, Visualization	gsc_high_dimensions_visualisation	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation	4.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-gsc_mannwhitney_de	mannwhitney_de	Perform a mann-whitney differential testing between two sets of gene expression data								To update	http://artbio.fr	Transcriptomics	gsc_mannwhitney_de	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	4.1.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-gsc_scran_normalize	scran_normalize	Normalize raw counts using scran								To update	http://artbio.fr	Transcriptomics	gsc_scran_normalize	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	1.28.1+galaxy0	bioconductor-scran	1.30.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	14	78	False		
-gsc_signature_score	signature_score	Compute signature scores from single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_signature_score	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	2.3.9+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-heinz	heinz_bum, heinz, heinz_scoring, heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	heinz	heinz, bionet		Heinz	Tool for single-species active module discovery.	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	To update	https://github.com/ls-cwi/heinz	Transcriptomics, Visualization, Statistics	heinz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz	1.0	bioconductor-bionet	1.62.0	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	242	1186	False		
-isoformswitchanalyzer	isoformswitchanalyzer	Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.	IsoformSwitchAnalyzeR	IsoformSwitchAnalyzeR		IsoformSwitchAnalyzeR	Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	To update	https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html	Transcriptomics, RNA, Statistics	isoformswitchanalyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer	1.20.0	bioconductor-isoformswitchanalyzer	2.2.0	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	29	822	False		
-kallisto	kallisto_pseudo, kallisto_quant	kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment.	kallisto	kallisto		kallisto	A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.	Gene expression profiling	Transcriptomics, RNA-seq, Gene expression	To update	https://pachterlab.github.io/kallisto/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto	0.48.0	kallisto	0.50.1	Gene expression profiling	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	299	24155	False		
-limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1012	20344	False		
-masigpro	masigpro	Identify significantly differential expression profiles in time-course microarray experiments	masigpro	masigpro		maSigPro	Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.	Regression analysis	Gene expression, Molecular genetics, Microarray experiment, RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html	Transcriptomics, RNA, Statistics	masigpro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro	1.49.3	coreutils	8.25	Regression analysis	Gene expression, Microarray experiment, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	13	576	False		
-mircounts	mircounts	Generates miRNA count lists from read alignments to mirBase.								To update	http://artbio.fr	RNA, Transcriptomics	mircounts	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts	https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts	1.6	tar				0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	False		
-monocle3	monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers	De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_monocle3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3	0.1.4	monocle3-cli	0.0.9			9	0	9	0	9	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	264	3266	False		
-multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	2	53	False		
-music_deconvolution	music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution	Multi-subject Single Cell deconvolution (MuSiC)								Up-to-date	https://github.com/xuranw/MuSiC	Transcriptomics	music	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/	https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution	0.1.1	music-deconvolution	0.1.1			5	5	4	0	5	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	240	1872	False		
-nugen_nudup	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-pathifier	pathifier	pathifier								Up-to-date	https://	Transcriptomics, Statistics	pathifier	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	1.40.0	bioconductor-pathifier	1.40.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	10	228	False		
-pizzly	pizzly	Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.								To update	https://github.com/pmelsted/pizzly/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly	0.37.3.1	pizzly	0.37.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	16	208	False		
-psiclass	psiclass	PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.	psiclass	psiclass						Up-to-date	https://github.com/splicebox/PsiCLASS	Transcriptomics	psiclass	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass	https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass	1.0.3	psiclass	1.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	15	False		
-qualimap	qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq		qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	To update	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.2.2d	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	1	4	4	4	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	4	4	1328	664470	False		
-raceid	raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory	RaceID3, StemID2, FateID - scRNA analysis								To update	https://github.com/dgrun/RaceID3_StemID2_package/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid	0.2.3	r-raceid	0.1.3			5	5	5	1	5	5	5	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	82	4569	False		
-repenrich	edger-repenrich, repenrich	Repeat element profiling								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	Transcriptomics	repenrich	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	2.31.1					0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	False		
-repenrich2	edger-repenrich2, repenrich2	Repeat element profiling using bowtie2 aligner								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	Transcriptomics	repenrich2	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	2.31.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	False		
-rgrnastar	rna_star, rna_starsolo	RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper	star	star		STAR	Ultrafast universal RNA-seq data aligner	Sequence alignment	RNA-Seq, Transcriptomics	To update	https://github.com/alexdobin/STAR	Next Gen Mappers, Transcriptomics	rgrnastar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar	2.7.11a	star	2.7.11b	Sequence alignment	RNA-Seq, Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	2	0	0	0	1	0	0	0	0	0	1	0	0	2	2	4015	425658	False		
-ribowaltz	ribowaltz_process, ribowaltz_plot	Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data	riboWaltz	riboWaltz		riboWaltz	riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.		Computational biology	To update	https://github.com/LabTranslationalArchitectomics/riboWaltz	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz	1.2.0	ribowaltz	2.0		Computational biology	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	14	161	False		
-rsem	extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie	transcript quantification from RNA-Seq data								To update	https://github.com/deweylab/RSEM	Transcriptomics, RNA	rsem	artbio	https://github.com/artbio/tools-artbio/tree/master/tools/rsem	https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem		rsem	1.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	1	1	67	377	False		
-rseqc	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	22	22	22	22	22	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	22	0	0	0	22	0	0	0	0	0	0	0	0	22	22	3206	133498	False		
-ruvseq	ruvseq	Remove Unwanted Variation from RNA-Seq Data	ruvseq	ruvseq		RUVSeq	This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.	Differential gene expression analysis	Gene expression, RNA-seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	ruvseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq	1.26.0	bioconductor-ruvseq	1.36.0	Differential gene expression analysis	Gene expression	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	76	1236	False		
-salmon	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	1	3	1	2	1	3	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	3	3	969	61937	False		
-sashimi_plot	sashimi_plot	Generates a sashimi plot from bam files.								To update	http://artbio.fr	RNA, Transcriptomics, Graphics, Visualization	sashimi_plot	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot	https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot	0.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-sc3	sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare	De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_sc3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3	1.8.0	sc3-scripts	0.0.6			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	9	False		
-scanpy	scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	scanpy	scanpy		SCANPY	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.9.6	scanpy	1.7.2	Differential gene expression analysis	Gene expression, Cell biology, Genetics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	766	51978	False		
-scanpy	anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data	scanpy-scripts, command-line wrapper scripts around Scanpy.								To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis, RNA	scanpy_scripts	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy	1.9.3	scanpy-scripts	1.9.301			22	27	27	0	22	27	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	13	2185	39356	False		
-scater	scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results	De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scater	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater	1.10.0	scater-scripts	0.0.5			0	1	6	0	0	1	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	16	387	False		
-scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Transcriptomics, RNA, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	77	1365	False		
-sccaf	run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out	SCCAF: Single Cell Clustering Assessment Framework.								To update	https://github.com/sccaf/sccaf	Transcriptomics	SCCAF	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf	0.0.9	sccaf	0.0.10			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	110	False		
-sceasy	sceasy_convert	Converter between difference single-cell formats								Up-to-date	https://github.com/cellgeni/sceasy/	Transcriptomics	sceasy_convert	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy	0.0.7	r-sceasy	0.0.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	90	721	False		
-sceasy	sceasy_convert	Convert scRNA data object between popular formats								To update		Transcriptomics	sceasy	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy	0.0.5	r-sceasy	0.0.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	90	721	False		
-schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			0	0	16	0	0	0	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	23	779	False		
-scmap	scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features	De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scmap	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap	1.6.4	scmap-cli	0.1.0			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	13	83	False		
-scpipe	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	scpipe	scpipe		scPipe	A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, RNA, Statistics	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	11	628	False		
-scpred	scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model	De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scpred	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred	1.0.2	scpred-cli	0.1.0			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	25	False		
-seurat	seurat	A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data								To update	https://github.com/satijalab/seurat	Transcriptomics, RNA, Statistics	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	4.3.0.1	r-seurat	3.0.2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	66	1543	False		
-seurat	seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features	De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1								Up-to-date	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	Transcriptomics, RNA, Statistics, Sequence Analysis	suite_seurat	ebi-gxa		https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat	4.0.0	seurat-scripts	4.0.0			0	0	14	11	0	0	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	0	0	0	0	0	0	0	0	181	1966	False		
-slamdunk	alleyoop, slamdunk	Slamdunk maps and quantifies SLAMseq reads								Up-to-date	http://t-neumann.github.io/slamdunk	RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers	slamdunk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk	0.4.3	slamdunk	0.4.3			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	361	False		
-sleuth	sleuth	Sleuth is a program for differential analysis of RNA-Seq data.	sleuth	sleuth		sleuth	A statistical model and software application for RNA-seq differential expression analysis.	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	RNA-seq, Gene expression, Statistics and probability	Up-to-date	https://github.com/pachterlab/sleuth	Transcriptomics, RNA, Statistics	sleuth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth	0.30.1	r-sleuth	0.30.1	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	8	64	False		
-star_fusion	star_fusion	STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR								To update		Sequence Analysis, Transcriptomics	star_fusion	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion	https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion	0.5.4-3+galaxy1	star-fusion	1.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	35	1212	False		
-stringtie	stringtie, stringtie_merge	StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.	stringtie	stringtie		StringTie	Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.	Transcriptome assembly, RNA-Seq analysis	Transcriptomics, RNA-seq	Up-to-date	http://ccb.jhu.edu/software/stringtie/	Transcriptomics	stringtie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie	2.2.3	stringtie	2.2.3	Transcriptome assembly, RNA-Seq analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	2	2	2165	167659	False		
-tophat_fusion_post	tophat_fusion_post	Wrapper for Tophat-Fusion post step								To update		Transcriptomics	tophat_fusion_post	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post	0.1	blast+				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	15	216	False		
-transdecoder	transdecoder	TransDecoder finds coding regions within transcripts	TransDecoder	TransDecoder		TransDecoder	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	To update	https://transdecoder.github.io/	Transcriptomics, RNA	transdecoder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder	5.5.0	transdecoder	5.7.1	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	348	5468	False		
-trinity	trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats	Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq	trinity	trinity		Trinity	Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.	Transcriptome assembly	Transcriptomics, Gene expression, Gene transcripts	Up-to-date	https://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity	2.15.1	trinity	2.15.1	Transcriptome assembly	Transcriptomics, Gene transcripts	9	13	13	13	9	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	1	0	0	0	0	0	0	11	0	0	1	0	0	0	0	0	13	12	1762	31951	False		
-trinotate	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	trinotate	trinotate		Trinotate	Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.	Gene functional annotation	Gene expression, Transcriptomics	To update	https://trinotate.github.io/	Transcriptomics, RNA	trinotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate	3.2.2	trinotate	4.0.2	Gene functional annotation	Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	151	1796	False		
-tximport	tximport	Wrapper for the Bioconductor package tximport	tximport	tximport		tximport	An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	To update	http://bioconductor.org/packages/tximport/	Transcriptomics	tximport	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport	1.22.0	bioconductor-tximport	1.30.0	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	88	1408	False		
-ucsc-cell-browser	ucsc_cell_browser	Python pipeline and Javascript scatter plot library for single-cell datasets								To update	https://cells.ucsc.edu/	Transcriptomics	ucsc_cell_browser	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser	1.0.0+galaxy1	ucsc-cell-browser	1.2.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	78	941	False		
-umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	To update	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.2	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	5	5	379	61618	False		
-velocyto	velocyto_cli	Velocyto is a library for the analysis of RNA velocity.								Up-to-date	http://velocyto.org/	Transcriptomics	velocyto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto	0.17.17	velocyto.py	0.17.17			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	False		
-volcanoplot	volcanoplot	Tool to create a Volcano Plot								To update	https://ggplot2.tidyverse.org/	Visualization, Transcriptomics, Statistics	volcanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot	0.0.6	r-ggplot2	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	1749	30946	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
+anndata	anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Single Cell, Spatial Omics	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.9	anndata	0.6.22.post1			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	625	35620	False		
+baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Single Cell, Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	71	False		
+cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	To update	https://github.com/Hoohm/CITE-seq-Count	Single Cell, Transcriptomics, Proteomics	cite_seq_count	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	1.4.4	cite-seq-count	1.4.5	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	18	False		
+cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis, Single Cell	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Single Cell, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	126	3934	False		
+episcanpy	episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess	EpiScanpy – Epigenomics single cell analysis in python	episcanpy	episcanpy		epiScanpy	Epigenomics Single Cell Analysis in Python.	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	To update	https://github.com/colomemaria/epiScanpy	Single Cell, Epigenetics	episcanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy	0.3.2	episcanpy	0.4.0	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	20	736	False		
+raceid	raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory	RaceID3, StemID2, FateID - scRNA analysis								To update	https://github.com/dgrun/RaceID3_StemID2_package/	Single Cell, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid	0.2.3	r-raceid	0.1.3			5	5	5	1	5	5	5	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	82	4569	False		
+scanpy	scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	scanpy	scanpy		SCANPY	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Single Cell, Spatial Omics, Transcriptomics	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.10.2	scanpy	1.7.2	Differential gene expression analysis	Gene expression, Cell biology, Genetics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	766	51978	False		
+scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Single Cell, Transcriptomics, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	77	1365	False		
+sceasy	sceasy_convert	Converter between difference single-cell formats								Up-to-date	https://github.com/cellgeni/sceasy/	Single Cell, Spatial Omics, Convert Formats	sceasy_convert	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy	0.0.7	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	90	721	False		
+schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization, Single Cell	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	16	0	23	779	False		
+scpipe	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	scpipe	scpipe		scPipe	A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, Single Cell	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	11	628	False		
+seurat	seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension	Seurat - R toolkit for single cell genomics								To update	https://satijalab.org/seurat/	Single Cell, Transcriptomics, Sequence Analysis	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	5.0	r-seurat	3.0.2			1	1	7	1	1	1	7	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	False		
+sinto	sinto_barcode, sinto_fragments	Sinto single-cell analysis tools								Up-to-date	https://github.com/timoast/sinto	Single Cell, Epigenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto	0.10.1	sinto	0.10.1			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	17	91	False		
+snapatac2	snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing	SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis								To update	https://kzhang.org/SnapATAC2/	Single Cell, Epigenetics	snapatac2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2	2.6.4					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spapros	spapros_evaluation, spapros_selection	Select and evaluate probe sets for targeted spatial transcriptomics.								Up-to-date	https://github.com/theislab/spapros	Single Cell, Transcriptomics, Sequence Analysis	spapros	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros	0.1.5	spapros	0.1.5			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	Up-to-date	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics, Single Cell		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.5	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	3	5	5	0	379	61618	False		
+velocyto	velocyto_cli	Velocyto is a library for the analysis of RNA velocity.								Up-to-date	http://velocyto.org/	Transcriptomics, Single Cell	velocyto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto	0.17.17	velocyto.py	0.17.17			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	2	False		
diff --git a/communities/spoc/resources/tools_wordcloud.png b/communities/spoc/resources/tools_wordcloud.png
index b931241508cc257303771d981dbb0286e7374b91..1952d0d0e0d19d15ce1df45abdda8c0eb9ec5f56 100644
GIT binary patch
literal 119799
zcmeFYbyQU0_daSOAR#G@NQdOmB_JT(2-1uU-Q6lBAdC{ypmcYqNJ+=g-ObP){$BL+
z`Tf4@uDkA9_s_f5T?>VQIq#YCp1q&_?C04hSXogT6P*P8&Ye4$GOu5$-nsJ-|IVGe
zN2n;^H}X3_+`%_~CrK?QHCvdItC54r9R(vNJ1bi!D|6##E+!6+=C(Fmto*E;EYHlG
zoa`J0*x0Q9_ZwJk9ZcD%6z@-fMbPYCYdhY#gKc#C?{2nemie8#ckal%5>t0e+`c}I
zq%lvPb8Xb~H2eBCny?@<OS&Jq-Lrisbfyh?j}P^pG)0&Ybw8GrV0_a4qghcg!KI0b
zxFq6Et}iIKLQn1lw;}J=jW;8+$!8GY_#7^Y$746s*f?=|8gbf5#Bmyoo0k?_h1($*
z{T(eW)SMzW-pNIoQL3m^{!hgJ^IxmTdWZ0x|M`mzst>9E`_KMQjOS>S@&Eg7aNKsn
zgOLC6@{@PuOO^kzV2Ld*1N#41?nL39<o|ft+9>m#;s2c7f1DQ$Kj43y?UL^QKl$I?
z{r}dsui9h3ybXdy28N6~uT|cAEE8gqTkl0@3jg_lMx`vvarQ`gv#inEmc&fw&+l^<
z5CLSQ|L(j!9V88_;(KS4&L94Y?=tjA)lziz{O3(v*O*K$A0qVlkVfeH;+w6)KGplo
zHm;NoMOB;!E_5^K26>Hr-EE=rrtNS$|Jyy|L;cT+xtNy8X8tdbM}##KHT|n;A5!&}
zGj1eRGijCa7h`FdjHu1_ikrH6k=I|V5OP9=EB$!sgE--ew^#6p_Fn+@`MW0Yo~Nzs
zs$uK2GTk+#HXA^ly2@MGJ+y=tIWmg+_N4vGip8V<BtTZYDmok5IxR&~wsh)HhmDeY
z7i{1=-f?9fG55P2ZmMK9{w;9bpUPhS%ZNma9MuQr{xJ{S%!`*?0#XTF*6C+CJ|nlM
zECLVLeJL^F>Gpwl2JYxo*<l2IUa;adJuepyo%F$Cd{`o@OqS{%dYd=NjQ_o8^A_I}
zsWGP<xQ7&eh!*V;6mC~tn3SRO4)c**)w2E5JNWrRzR(li^E@?!tdz4OJUBzx{^A``
zOjJay&mvwXl@Hn8br`QU_GX8$)osddi~Z+=+QbKDB=FS+r0MvZA8F}D21+$|edU;j
zk}hf!W^x=Cw_VS29v46S8LJ1Q66~#3Yv<U8QvBdU!%(2NHL=GGO6|f+ziS`=B%R8L
z1SbQ{hvZ2HhZyd`;l-m4;di%Z5(@Z-DSRVN3e=|W7_|6hH9x!^e@@I}@<HqiM@n4k
zX4D<+&YkSzMG?x1-My?l(bcpQ@;my>dJ9!qzDfBTvfmjfpk@MrnM>=Vg;mVYG#Gu$
zuddew*>9I8`}CjXuOZd?)vpEe&TcN)a)PWqWKu#j(l?{dED;8#RDv&z7P;nW@4D88
zI;Gv%V@oF9OR30Q9gR=?8(b6rV6Zi(k^omxK%+dhy<wJ98<9cm9P5-TUklY`PRx3@
z0(Vb0?bdAh%pRtNy;;Z8it{&_O(XyF0q{UbmnN-=c3*o(sWRY`kkn=x$vJ*8%_Q}l
zUZ2h)l?(U_y{)0*|Ji!9+RXc3I6gxuIv<OR@opf(Jl%r-jMqm0U3Ssxzt~F_D?W%J
z2ubD9e~w7{i>LZD7yrpg@k9}HaEH*lufvuoLjGc{Ti<^%{ZS@9<QGptw&%3OzmM7<
z_aAs){D~jpd2K@2Q1O3r6mABGK5jA2u(|)v5=Hob)=Xyv5&7w9vMT!f*KKt!xg!JY
z+<1D3N<lQrwtjgT8TDFeS6xh<s)0e2KUwB=HuM@H3}MPGz9^@|9NbGK`%K)`!YYh8
zvXtjG1A&*>mf&ut39p!DGSO;;yrN}rTQ<e2{9#TaAW&P$ebCTxqg_dnrp{<g051<)
zKxGevayoC^xrR*jqqm(n$_k$x&nt<dZM1q@h=rc8swJyM<7VRc;Lg+D{9fYV##19D
zD^p34u5))1MM$48YivNPL_NYWZpgecECnw1&Kr;GeP>;e5+NTK&acN^@4$CkMysp(
z5KEImWrkbV(7h`a!M^BbYe7r{lSlABqlc&i6#R5{<^7%@;uabHR=LH1r+NN9+lNY&
zH)u`yzQs!?A$p6xyr<-SE3nvZd5VdCuO{cnQ=O{wh4utNn<}TsKU)=lzSQ*4Xt&Hb
z3RV<%{&CxdgM=LZNOuQ;<ZI$TC(virH>TsldLMHJNn;hA^-7?%P4a9oF(!!2jVjf9
z*TcH6x__^Tu!ub&ZW_xzxqP|c@O#rQwoOV^Y#p#nAP*{gM<OR!EXLumUcXVcjn&4N
zfg(VB-)D=bN&x!|F+y2(*>TVh+n_7@R=D?e1AQ+3Z0Prr`&Xw$iiUA$Z_!||=Wq)T
zshFS5v}teNpq!9LiL|g4&Mxk!xlNIG6H`A23nT*ens^TtZZ3Lk4L3%ql4U#}4}EI8
zVY2iItN7l2J<D{x(0DHM5`t0sqL&6*z1)kz&(+d4O@@fG&zxy)`sU)*q*|56YAKd<
z*<iA16nc40P*3wy>E1<&Qr9yYXXi&9#f)0oxtd?&dLDr5P~XNyAjeC>{*+Il+wY!!
z%L!0Go_sU&w-&HZ@fd$D3;hLoF8ipTR&9&}f~UsI5UZ`*l3_)VJt-NY8UA>JzsuzV
zN7iSm$WDM2iH869%S%~VYOAtETV%DhrH5%EMW!s$UPnW}AiHd<zZ??D9$d+sc@mNB
z|90HCx2OaM66l+!@;Ls1`RiQ#>sIK<)UxL3U0%Uc?Z=xeo?ER<VvLgXNZU7Y8$?IO
z@a}U*t=bYjay&Ym?pc&7&(P@&k!2g(uP(zG#4eT0q;)0Iu0*YTfo<i2edp6GwIl^y
zQg?lD2f{t`&(d6RD<P5Ky06Dc-AUQdMX|InE%H4QAT2xzMxpxKgW+``p|8iY2zmA+
z-#-gGnO2OI@>i<yZW6G!)mq7z|Ma|#J#4*0gj6g^b9f5t<EB_BfiE80{(j))Q&C)o
z$y$X`r{5&3Vk9b$6Y|};Nosf`nfue#nn!omR3A>ky{{mKBU9-VmD<O=+9#vtl6sm~
z3Lj}`h%`UhJPZl9fo>7<BQlIC&87VYs;vmjS2G!PBxN-z#){$jxR)%GxdQS-{!+s~
z2wcpi$SF?VfV=eV3Ug8=#%Fsl#G}<*KHvCx^m|pJ+7CZAh~mXY?d&lUQsYb!U0->*
z%F`$$nWaZqRZ7v{Va9~$wT`}E(G#gf1ErsTSx@Gc0zgwC#?)pQzaB&vZx<XMPF`Lu
z92j7TchNIllNcpPjj!t4#=$3D<GSS!QVgz78MV)MWZPV(m*C%;I(qx=BadS!|9ogc
z=VqHQY@3_E9#yb$LOSv{{rq!&FxNI(Afdq&vSteCLs5+H@4DUumdmXU;Y8C^a_5>c
zomHhbzQ6o#(3xj1Oh+4~T95EjR@tc=M!ZomGBfm<6W1JkKFr14IMXGfKNLQ-a=oL4
zZNcJUd9|>3I*v**{A<;8)-+GNkfQRv66r>DZSTl0_eNdsXf{oKV;-*H7atZ)4<g>X
zl29JH9HQ)U+YW^Y(xlkmMSZ3KtxP?cJ&_FWASI29{{S8LDs+nu*v6lWJ$nvy2`<&+
zn@qZeXsmzreDQOzy1ccP_Gs|sRcDt0;8XIk?Sj8r>A735a%9hCcF0-RR^4mdg5iR$
zw^wyNx}!JNJ=N=>{AfO_;<P#{VM*5pmhL@B6XJzLA+SzUU=z(z%|IRcl48}^0<J&B
z30bmeJ)~4Gv6CZSvTZ#O?2&)YJ<DLQX6%#vCL|`jJl@Juxbf}4;+rt|S+!#ffH3g&
z3=_Lzhds=Fz#!wPr`JGj8!vrht1j##^SNWG&m5jAx7O*2X~n7AfWZPd4#Z8Z%pb12
zPVDC@j6S#yWtZ<2r<YcSOiBagi2qWeM6!RGY$~5f2e50VT8Vk{K;;taxL7iGs3X2G
zooNP#{lfeuNd_pr)KET9z}LilqjhG2^3N-FHX;LIR*$?pi#xm1YV9d8!$^}Z@e9Zv
zPngfotEE`aJh!Y?-x+erK6sb*B(V31arBdn{qT}c*9ZuvT$LSWP><Ru@|_#TN67T?
z{^%gPGamW1@{gzt9qPHKBG$1Bv?2xB-9bB3(>pKh(;R*KFU{DkG&#@K5Z_2G#?Z?Z
zr_=CGwN7}8og&p4`%JQ`vdSn%M@5{VaDbn61qoh5joojRJ-bBA*5d<tthUNWUYh3(
z4yLK9zEug*99|If4M5A1O>FOh(b+paR?D2Q2_1^nU)+~jqu>=dtr@IoTHET4>`!|E
z=dqsHy4OEn^Gz9BCpKOzv0X4c0R)Tv^fK>*+e-EsZRiuXZ)8<GWyyMh>SLV;GX6Ql
zJtlOWL?Bpl0$x}cS$15vKo-HBxf7Omet2cJ^akuFJ*}j4%K#=Jr`mY!L$myggz_|G
zICe)v>rxP@Ehp@$dx6u+&oE{u2%vDQ9{WPR&YPBQGB0DLj*M;V{Om;cgD4NYMa<_`
zBKxivw3b^=8PH+jV{&7$4(;o&8ibqJG|>Qq^y}r_Xul?}g7cfOuCB&9bl5qYF7NBI
z=@JEwQM;g<K8d|<yXbeX+eh22w80h0NL7+<;U;TO<Rorsqd@UDA{kV=+NqE^J?Or8
z<TczVA&5M1*vB;>y_|l%<l{w&BKpVIeJ^Wz<HdpfC9*Kgj$$S#H9E^|r87?3NkM{9
zQgk0+EM}8pX~#KEp1-KhCE9L<O)<sr`NjB_ZdX602W4MKT>~xXT<Ape8v0@5<6QFP
z5Ii|vVpk@<S_N1&>&ob4&2=lF<K@5l)ZixVPT2yq`pgDYj-L)+13Ysh{72OKV%0O;
zWPY~XF!dJurA_tJ;_3GEbFFCFJ3W%@sx>g}Ejkpt<k4Rgtqgk>rnS#=CVB16^ASab
zM6LXw$CNIvTajZY+{m1cgrxfhB|*&3HJ+Ekvh|0$tmwXZhcG}!jyiw$_sS{=h<tCW
zGRilTuN=C@(aOaRH0I)b+sX0S{?9PY1FR{I-mJHi<lr-gw{lp)xbX0M$!^p>mWe^}
z;3*?>CRH+f+SDz&un4*HhX*j1<$Za95eaV84SI@GPv+?jRuDlrGz(Cpvi9%j4n3?K
zt5I=Ixd6!{^nQ-Mkner@;}gQ4Jq%>FM=-Be6}uU7-GMyMUtcKOu*^C1d>ens<y<*B
zBta~az&8?5Q_bs1m$i)-0s@&f?4U(3TZy$}TJB}x=L&_6ubWN%co!=*{E={`TGZ^>
zVgW+QD?<9js5pgO#A425lAIpO2S_^++g@!*j;dR5ztq4y?3600x+?80w<(Mv-p^t?
zHJaYE8Z=GcYz)mupN&i6WN<X^X*s1)_>c^RT{tb?xR{Y=;(QGO7Xk9D*qKz%^Q6}Y
zaEMQSU;b($d{9-C4~xBh67s!<JY3DB(J^NUj!iPnJ=R4#m7CV3>jhv(aA}&M1c5oS
zk7jKB=nAq!GtK1%G<>|T9(y@1hDPO+weQ_WhEz2h`z8SdYBet<A7?;Wc*V6{yg7!V
zpf7bc0)4_l0(a`4Y1n9ss8Y;yR@2lI^8dVGN5y*?H@DX2_kCP@T9|=ZOPh6d?cD2}
zgrLrCxaCS-2jQP!6qGVLJE8BmCsUgl$*osN*mrn-;M}O(sMy@KuznJrGbzjH5v(M*
zxd*$Zo;CLtFIxH9egj=o%*UOzoe{sQh9ok`u7~8W3XezqDe!h%FF1f*OCX&nhbA&e
zhKDg7V1aC!2CJ$z$-G@-_86X*rXoxlj5FiV37xgbKH(eV>$R2&8p@)GtybY#8=szZ
zo#r70ke&jQkLxm1p940ebufCK?QPnzLqY;d+2b01AJdC5P`y=4Lj5}XJcVEuTIZ9&
zmqOb`4oyux@disttAI?vU4~b@T)xTGxXUX@`-)NCa&r2Zzl}{Rafb4EZQES@CDxiF
z7k-bD#LM@&dcU}>L<}1HW{}T$Yq2Tnd}F1`Q(4j5s`VCpeUZ0pL6yC1eI0JyF^r-A
zLT|yyH#+Egq@xlMQhR%5M&2OH-{r#l+l=^f*Uloy=@mBKxy**{qn!}FckSeByFGsh
zmlWed^k{5hRe}k-bkK3Fw{Zrfe}u-+*UnE`W6qvpH+6d`&*7X1ufI4f`qm`f+2u&v
z^s-YxOCpRRO#5imEz8~ylvjyA!A!>FVfI-)%o*KRtF19{eez$pINxEo_V39^P+L|f
zb}Morqxe&jj5>AJ3|M?(6o)&M{5l%{6ts8byCo#{_bFG%Ef);tDJYfkDV(J{#;oXx
zn@d-9#u4A#{Ms%4k^~#dStL4XWVO<&mFetSTJA6TlJs1jx{>Q#<E>Fp#rHmOm-teR
zmrHF0SOlO>IQ-M|5>+x`R&Np&YDdWROs!kQ$DA@}_Qg(D>F>4SOXeDbKq%FlH?|4?
z7(G=&-cj6{gAu71tvNiwfhCG&E-jdaioT!EV91>f=t40u#5LbJ>jywAdn(=zxq!!h
z$GBlxyzd7gnD_6uu%q<5BQh+W@~0$7Hiy3~dFttZ%{_WWqEYvHkclkYg-4Y`ZdSnZ
zhAzSAFnHfDC!xnQt0qxr-eci8aZB?+ipYx-gvFfLUNu4Bi+5St2c!Gf9rxR$#_3eh
zwtO(<cn!v1a!3w-ngoTY!@AN&1#+0!-^-a0N5t~51a2X&fC%h$bYhuF|Ct517Tn|@
zRA;c!=%(11y%mq7C0Jbn8+~G`KEevN&3KYL%WT#4nnDi&bcdg9)3aeuS(jI<HTjg<
zSQj_zl<c`7ejujlk~YJq>RYoYcqnzU6h4_UYA}M%E|iy)5{Zh3snEe~b<@6Gb$+?#
zlaLxchZC_Il!qN(b>-*S)V<s5gLfFb%E1`&EDV7DeIHfNn4|X}Jm`^!GZiTgd6#w_
z)|oKX%7ZKEr#C3RCYyQ7Jw2~26;^v$)*Q>OvSMzq3<~Q%?zc+&Y0(0Dv1?u58B`~K
z?5)BOt%@z^<cfyhv5or%{V{&e_6Jg>oeV=*&6fm|9#%ldrArlV8AA4dBj6$6=8S2U
z7ivr}2xzHND?H~>{jhuR6d&qMc?z>DAQ)mN^s*p976VkLovZ`mLXY*gfx4D|!M$1M
z#8HG%7p}yo;n4mppV-9uX90RyM6~H7`BKKBq-<THboZ<PC?ZD@H&BJplhmkG^5g7B
z3Yzs{dUa;~CiJ&-HA3SjcVe>^RyDTHDF?(aM8gn>QOAo96X{3w<<);R%;JJ(t6|)e
ziVY)s=MT~gQ%+qx)}LYcb%zmee5Q5NEX4>9kWN0O{ga^WrB-@bH0q9q+pf63o2@Vk
znJ_`ym^fiEL30gbE|3ElYz)1fPhl^@unzQ%{X?2r)0j<S%##y-wZ;VQ8BXrif!U7P
z#Zm|e2!8vlU&p_Y9~R>cOgnYbNRNY0a2W16r6LU}KemTg;N4y2RI697e?8lSob+0G
zhM|yUxDwkd?@(ZO_cGX#PlYk`HpCTb?NeyH_rI|Y7;1Uf9@gOI#QNYq$%|6YI1r!*
zHzMGlaBnX~P(Ze%cwU0SR0q<!G_cMT?*oUa@{hCfaY=v?SflSeRa0?OA(I@(>Yq%F
zdW-h;w^qYZsCDS3nG6aVr3NP(bj}#MG(Qx<y~EM6N|!35qV%`-ZMNw0e5?(o>SlD7
zBaz-i!oPCl&iNaa-O;wVM&*S*fsW($Xjlx>l7Ce1_fElHC6^tD_vl7^U%J{1H~TC`
zyw^}oN7#uT;iY8<yTEPixV=^*y#4;U6oU8W&*#D}5~6jY`0zsWbPLn%HIhE|cW$x)
zsXSWJ_EpZ)su}52p>8%F!5y%H@nilN4&4LTw^EItLaE0{!+`?V9@a=wO$-tK3VuyA
zQXjwbp5eyIF$}?$jY)V)n1J6gWhg8;HCl8C*+krO8^Ij9EWI?U`_L*+nV*4k<F3&w
z+NqWTP(}AKS)>*%-~?fP_di0!5h#dxu0TPpH)@&8k3ox>mM(s4c<`m^wos^3AoG^i
zzaz3M<(|cI>pH+rxCF!EJs*aox0*j!yW8dnR5_vbA|z_#XQSu|f3+WmtL#!{#-&f?
zxQJc5K2OkgY2LjKE~Ax)0%~Q39D3-@yX6x`U<;M5-X$UgDh)uj*|TlOgJ-3I-PJlq
zJ*=wit|+E6)&18u=sqMA3rfP|^1T4t?m5PFl6MfI{8*%9^G*4)ve2{wy3w8;<nx*F
z$lO~w*EC-JuQ6j9l@Z4m*s!J!GrZ&p6FWxO%$aYEhD%}A*_y*s(!T_<EY@tadjmw>
z$Lp1Fa%xY+b?5S2)`03vb?f*!%UK#drZ_*hCn;Opoi#M!JudEr4NT*_o~UiBR%_;8
zo`lx{oK`Rgn#^&rg0O|Ci>K(m_6aYl{?C{8#Zp$^&U^3;a_fI}BzZb5&O+xRBZfi*
zu5$Nrus!plcJ9R-K9=VrSS^i|=hM(_nVn6(?L{X4i!gyO!yV7JS(P&tCo-8f#+xY(
zNev>;nekscr@FOQG8taeq>~@J$h*&OzDnkBDLiyn=M0o<?%Lsl<3<mC7JzfpPri7f
zF8f3I2-kLOZ*UkRL=(%Ca&0Laq-cKJ#Qv!m$q>d=tNGQiH(w}3p@n<f=rHMV{#nAA
z%-(ppU7O+CGeE)RuDPvdQVE>3e)oOJ#@9nI#`3fDwho6ibK<SD^+18WwYdHD9|26m
z=>0hyCh?{P1hu<=FC`%K_#w|Q(GX@G7ru7{NHjb_TIS<Z?Bw6P4or>!wDN(>C-EJ3
zMLH&0dFo$~NfjeBzY3C$q=Uj<c=*RasWw)C5HzyTTJsbJh2&an(}|jG2%up(nbm_e
z{Rzj|u1TYbse6bofZ@9}IVXtfT%*zEy_{g(^EhXE>gcHZyO(o89oueD`Zk2Mm&xV-
zhB72fZww-|=W>$V!_pf3L)qV4zEtiB?{}jOy1<j|U-lBb#m<gnWwer*g2^3PwG|zw
z828$o;B-<X0+lvc_qt76hkAwCo~1Jw6X0c`jdJBj2<2e(K7+37cBjx=R?{$<v=jlT
z_uE9!|7z2sZDpb|d_s6>{vJ^Y*gk-R9us=Tcz(J-@^n4Nfmd?+wg89|QP^f}?*ZMS
z^|3gqi;W129wNN_L%@^%kE$Wh&|C|){ltFSY>aYY;w$w29C~r`_Rcd^;4NUqJQ+V1
zmWh8tL$yI6_W<<A8QSap#YL$Zah@(eXVI<wARbir+X_sm8r8i6VwU6pcXuzlp|a%`
znJmk73Qa*dGh*MK6-LEmTZP5-EAAg}Zt1>AoYOzl{PB*d925w=-L^}GTf56m3`68X
z_6dVNhF>xBWQogS8p{sx8wRYg7c<Q0vg+br0+-ccV?7+SwCaP&GatAiEHeTTT}v}n
zqPkqijBu4GDSxJWE`?=h&+RcnEdvha>!4oHD@@R!7`4qUr;U=6s3iC-iXPvfw}mvx
z2wNR~uj=yGF_~sO4BKa8-%yY3lo!epzSZresQ<cF_VUBYCC!5aMCvAJ`^N4U+Q%$P
z!Tpn!;+U6sJ0eotSIG@FV<-DuSX*U2fr|(fJ~mDXE(UG)5Lh^|E7|*qX!_UpG`(Xq
zhuh>nirq<&s&lD5jkv>xW+p{$VH8=aVc11X{rVou4Cu8g$F!nCZk=8Fuz$RoLs=Fl
zC#&F;4)}1G<YUFBiG`1!<ecRoRI!;g(Y}V9e1_bLz2lyN5}C01&Aw!{c!Uwbs=g%)
z#W&*tFWT9RoL)j{UVG=QxT`Bf*T5~&UX322z3Cbr(>k=Y3RLjX_k;&sYuLC@%x5*L
z<(UfFr`SxdQO^B=!lvyDpR(=on)*ftY#*sHOWoG-rRV?IlSPR8<|BEk)*Ew@@!E<t
zj}%$4tKrNSK{46>d|?xLzXk>{tY#+5HUbMbfXP+4CW68GYFl&1MSU^LzmS9^6NWVw
zjK62TGC#_}4PlsiXf?Aa7yYI>(O`aLhyax3w<<AhH<K=IXEbf|{KKCGrja7cPmi(3
zF-W{}F3<&PA(r44*{8n#YkZU4Z=3h415j)afk3Qge7Z=2LzLV4A+1X4;@OLOOO0Yg
zr^FwggS6V6kY^<4k#yH22-!PgQnVgtyp**1?eN5%OK!G@b3;=`LpG6adVAJ%Vro9C
zzPq$a?2A7Q6FIB*{ux)MAO@LrZz>_=+-pUEFkar1@b(k@w!MFwP8`Y%0xFcEXmC#k
z@kBJgmxHa`R=O=zuYYxXjK`N0HX91_?6<;5%2pCK+tGq5OH*6Il1b?90SJR>RR;q3
z;lajI5w;2th)D!*Zn7Eh!-^G{w~^Jo!}6SgfN-lay57;D+FrT3w^qspJO(MQZ6GdP
zt*lM~DSUccWc;}C^rG9%{HM+_oIfT3#=~`<D9r}?=Iwv80>+f#wI4!MLx3qMl4khw
z)6=j_%!_!zT7~8w+zgyf>gHtC5Swjb#FII>d$sny9Z~P}5S<CyiCOt6)fL#aAM+O?
zxb!~m?U%GO{lGg79%>ll6Ux`$-kJO{KBRyS!&2i)S4G~bq+lMi147-$Xlh#+qxM4(
z;Pr8!5L+1efyG_sfJpvI7zosi6Yl@yM20%Hf#={;*1v=VMvHl>&tQyJ$igA2@-h<`
zB;{$QZ(h*0hGttm)%vXnHHQ}+#(XKI7&ey_%-ao@W!?loyUNQ{I)MO%NHRAS?a0??
zz@~%Ai)6$|N;b##BIbX$Uoiv#@p=e#O3<b|ftb(%!54Tf?{gALV_6N}?c=+ubIbW#
zntYMKfv$Sr*zNfx=0W|$*%uSrB_b)N|FeT^LJCuFtE}KssOe`i>{gX_ZnBIK5ThC2
z%7wru{e7JU%FMC+K);E-Sh8ef$}oFiO=1+}GEA)qx49l_R$m4>garNOZuOa=IUN_0
z?;%%R(N5R|0o}}IxHP{k)Iuy0HVn2_W@J!r8CVHGQ5D=ozWo6h5NyVtOz&P>%Mir+
zaxQ<tA*1*wbB0{KZf$v5nq$5(U=<B|@znr3pLEFlwK&;?ysO(s^k<CJGWHOL{ZbDf
zMP~yM2$%yG`+e9*@kFQi%8?P5T|<?eG(9@QCQzx-vTCVgRTyezQh-cK?h4=b3KSa{
z`!wmabW^xRN>bbGuSR8BeL1P$#tNEU!AwH>+c;Q%<>w1Oz&VL{FEviV+V*6pS{O(`
zd>U5fza7%aT3}t|P|z>bZ1;pe)(MsczQz>|S)!UW(R0B0o&^1)*3Hk<%bi0%FKk!8
zQ02hBw3OCVsNNi_p7G>6`w}aXkP|8{Bo_#qUq4Cien7)S^;%+>Yg?*52Dml0>V=V9
zGkP6W$g#7H)w*(cu|PGk^Evp@>MTspwtpQfh1tM_ldH05NAE@ATC`Ecqz!zp04Xt>
z@9UOs$;f*0=3IM6xL%mmL4Aj_=uP3*In(G2zF3*8u7K(7LcOjk0b6>ZKZmy_$av^q
zMAmoHQS0XnlmJZyD%B#m`$dDqijia$;;%6OXdhcnBUvdX@GYp4dG!z+5NLmebPFVt
zoZOmV-iN<dVX%h_sm`DiKwedqN>NpdZ7!80M!znh?!}m~7x5l8zUt!owT~5{DyR9u
zK1+PCYYFLCYd2~K@`x^xNt>%|>4dwfeP$N-x>e9AJ2p4UXS<AIxMoW4xtFo$t&|g&
ztCsq1)fKb8bs<CcYdYh$s<VX!%7xnKIS>`7!u|f$6y-q@|0ha{{Ercz1ZO09{OG=h
zU<>uyF~5F=dGAv~(&bg^iOAQ8mnw;hftk<^lvQ?huZWlj`463cK|GKMh+a$PyOo-#
z1XB^gilvj@@6Bvml*OxK>vVpFwP~Miw?uZb0c<u;^}=(43drYpQ{tA5eZoUDT4yru
zUC6{|e&ym)-@$$Jc#Wv6Td;9W-!{04gc5-|<rXY@0L_mA#zR<kZ_+I8E<|)fh1=Q!
zCFbCe<y{si5&2K8x(-L7m&;Ak4c?;UPN=>PQvxJ~3x?P+D_^jtz$Gf8|3#HgKR|0J
z?&2Z+G8K@n){dmQtEmx6L|DVu$|fAh*%-6vV#BC{<`rfHG!~1gRb>zo##q%=tu||~
zLv3{^wnYeRJbli|a|fcp%)^z<JOH;mi9A>4sF4u>D}5_3@NUdDJj>H&Uu*b?kqm+n
zmW83yGuJKAsX;XT`xs98Yz9l9m<?bPJy`jSF-P|2IUtFGqki)0vh>LPe##qS(MdO8
zEAFhbTx&<E0!ypyhUCxTwQoyZFKN1xe9p*#9cF?7sb`Yq`Qf9<8||+Vi?kx5(`N)=
zQ-0u7z{?L@im%_3CV5`vp5qMSO#uW1{`NyhU-DnKMS5+et+w@cAWTTIvx{p(-L;@v
zR>kTJ6G;C{pt|CRBrc>{UKGy!sLGYcjee5nZ?jzjj6M5H)-50JG1gr1M4)K{g4^6v
zBD+&E^^qo>uw3idGHU0!Ba$Z5#%tASV&|nIW*<N1&QG!F(Q&{O;#Gn|^wRN;_bAQ3
zMWj~G8BpCSMnD#Q4Z;|suEDZ64cBVmoz&M{d{IpEK)`%L!N&*UnIKaP@O?~SalP`K
zOW~AmwYeDy;C9EkbTCXwk{DTDKKB>L$-n^yOD7R4Xk<PM5`cPWi7{F^T@YbyNeMin
zOdLy}B(Q^&Rl7sMo`M!dWr1>SOr>9vGA&}TAU9>=jFPeK)0-kda1bMvzuQm5Q)y#l
zK?nMtO_Ym0B415{AF3hvlCgn)Fg~#a6I(wGUq@+nD>D>4#puMEra+O~`hNJ2_;5J!
zH@$4`+VAL|qkk<vL@%Px=3xn(m<Q&+SFVKS;;xuX@?OH=*dAz%TVj41wvoGq*HOTS
zyS!f6!TyYL@$5U_H~ngHvhcw6=qrBXXuGn@`I0GB)sK*61J;{|hZET6kJfyGfIzUT
z%tVzz>B(0c2Hm!uX{Hb3C(yrlgS@icU)vI0lUlohR*kg~f@JeO-uLZa>w0spyTN1|
zWsquUVt=BwHJ~I8{NJjClsy|@Y*yI}hI`V~spkWA?)<of*Dc5GgN&(fuNH-g1xh3k
zoO2q%_|ZNag-?vs@NA>7WC_mj`QU1iTirRw?SKR@g51))fW}zDZP~#?FaY-k1~qVT
z4;zjRiWhAMX49ZYYu#h+6;8p2HN?8tWm%RflIQ^`54>!bVw}=MYBRZR=Z)}dfMO>P
z`^adTIMMSU+-Ap8)-B!miUxSX*2v>;XU**iQ{<H?QQUfsJSUTdh||B6ljbkw<X9&0
zgJHcnSOe;{);=#~owxD?*ZSGCl2<*=cPoO<IM%|2?_64QOtR4D1c<Q9@?Wew*)3q4
zXs22(RTY8~Mh$%503e~zCwX?1HqmS6s;Y8lr^{;8>TSg39(`?+qr9x+ZVF6!CHN61
zAeHo3`)~_*ZgVzv#m8CuzsGcZH{-)Ih|OB2+7xRu?L~MccsGDAZ%?v|+A#&ls)(2C
zP8M)4pS|bR#ZZut0A?MdWO_t1ha&VN<T<$_rB8)h+#A^#Y#|;6(&787Js3cz1|oDY
z!XE@j$2Srpd2*y<R^6wV2Q2Pe%RLyh%<vp+rhcMAE~30x*!Yj9o-9}flpev-7q4Qo
z)3_4i<{fUxilTsMSeB-tjdf}?&FC0**mA7}?bMmOp=dJ<8&e!!@*B0*Y)}9~$Zule
zQW%O(Rpr)mYS2%D2{Q#ipm2u4B+L=iw}XFa6D!gt8Z=D0%(_2^dcKY#r``(ks4z16
z9RjT^M>cp!x_|B6rI(_*Y*f3arhSlktH;2+m~R|I7%*b>5bWc*xWkWpEd<(6#z+ET
zsk<sQ=SSW|uZP|hBMUzE7K@4QqegtHYcL6c*=Q|TfHI)fvKF30Jk`NL+z5Lp^HLOT
zon9pGh7No%uI(q8gW)N{$f&q}d3#ntiOvYd{#$$}{D<#UI#mo>+WM?|;t0c$xoMTM
zwD$zQe&7p?{eaF3C|J3Atwe<*qe}O{WJPZg4zQ6oX(hOR6SK}GpK*d|x7Xj#J{9CF
zmdJh@B4R_Ul*oLB89YQJiW!WEWyjo){PLRiOy*~4)rXh|g7GBjvS5k=+!WxShe5Tp
z;)Bx!#{+{i5~^$cGKl#C{W7p`SfPA=FJD%<Cf&PCMGWwzBxK;7cE%$O$(!g$pKsGr
zG_*oZO#JHOG7MLU%H*^rzc;^1RW(+<qIvdOynZ|@;Rp<JU7x{m8Ek;M2rQ$r%`s&r
zleW2^O22mQDEt6(0AO4PdHSZ3)DWYVxz5jmiyO71zSUINY@WV3IV=tW+TdkXpX9B8
z$3Y~Q-#D`5JDK(@HaNf8lrCC}RE{n@%SJyh_9i8Q>@#RT4AD&f7){R7`TZxU{sS;`
z;+lVYwk!fBhTa^m0ciNT)%KVguE(g{Vlm?8mMmpn?rkH@ME6=8jQl9#)kB`igOL7S
zCD&m^B%ful&uixtDmC8BO~x|wbMS?g_g-SBRZ>TMu;pYd*edKy2GSPVWo$>0s#Mm3
z?7F4Y$h4`bf_vJCw!xi+06I(sQYR7kP%I$7q{ka{b-Q!l3d}D-!A$J#Gu#}~(*fYy
z`44>eQKhTS@*)jPrdbhT!pPHaDYdgkyhsH6b{wsFP0hNlmPyvt#h+*3{CJ<&t->uh
zCN##ZLm0T+K8rGugeYQ*9?EM$q)m$*3AWgja+PC+YVRj+)G(Q*1AW)%seDMj2n}jI
zr#0!FOXtwtRU|F^TBV^PfciMdH*3T1c#Y@**6sM#8~Ubp;K%0Y8&&$H=>YNPfHL{d
z{hOJ|{<Cy%*M7#U>+udHaS|iXOO9Cq(V+q;e?AIXM(VD4qq0vhu+K`R0uyE))z4hH
zjqS<>A#~ncg>~dkR3=-h#0yn)UoyAJ0U!FX4l(!L_-VM+72qIAokeyHc3(N_dWuLW
z_Xl)l94RO5WAqnG2-l|wLg1R$NJ;56OK8dx7>2P`@`;Ox796e~^Aot8J)6B?(|T-?
z4lMc+YTr!w)t@wjsx)Nb)OH&M$O8ueI6p9Rv8zTulNI{ZEbUe{-aLBT)bb{`$aq6A
z%a1aEJuEvwf#mDW@5433nnx~vXL0U@dF5!q6{+Lgs<@42Zu+gP^!nde2z+25dt7pr
z6R%#q`gPQ;Q{0<fX8Gkyc9g#pI{}grXv5H2`ALGp<)_uLDfG55FchVYpnWZYhJRje
zY{g|}S5@WoZYoS&KC1N*l26DcW*=cFeX3K!P5TBIak^c-j=WW$V$Q&9)+?sjeJ@2~
zdFQameq?q&*7(omvgHDnN+bIUJFNGL!x<En`v@SjBok##I$vz)S27KPIZ@^SN3aMN
z@a;)QKaiGeOCo@)g7ffp&XoL=o!c+0SS(gbu)U7E!Np*T!o{I4K^u&-0aU#8t5(#-
zmXt4_WDFWkUgD`$U_<k^N_oYhd5Y75d+`+{B!QV~&a&wY7bRd2q*=3tRBHWRL&cH!
z2rI{uq8(`3ykH^rbzbw<w{BMdf7m!41On3ib{Z<B=ucuo3wi>3m^At~h+z+-J!8|)
zx%g`Z7+2)fmQhV$Z@StK(o<}FV^n)pVDK}aKP(MwiODV6gYRB*RD72doNf5EU9A=0
zIo6@S7CmGF{O-f6&P{kVLT6EPZ9y#$D@95I3OsW#6zFSxvDIUe$)F?sChjb~RAW8?
z&tTbO|K65Q(jV)MIp7$QG38Hf(p|T8b$k8b%wBeKN}%p@QhFhQ=!|DIp!7_dnhEk6
zujR`27g>D#Qkz<$jdky`Y;F<Qk(L3E*Bzb!`uX3nKlr%*8#&BT0WV-EnY$)}p#yN5
zu<y-ak{iruq*0WF1Zx1!*|Om*0Ng|lt6Z0_xq7J<Piqnlz&3D2#yx}bO^J34S~I!e
z<Tbf`_I%O0UYXo&QuirC=c?hnsa<NoaAL~vMfPCmC77Z#BC#$?dE~dT;<rj5aAN0O
zm%pG|egJli(e-m^%{eutDXdy*v5LO&*P85D^_amAoLj+k^jg4&#HQ%@DRu%wTzqgr
zLUoIy=TMGnB|6}}PaU|_x1X2A$&?0O%8yM>Pr3~D7@5fX*sdlF|Dt1_1tw0I;xJS=
z+xE>18|S>SfnrK+Qiv%mN9!To42P^{GGIlZhXbyi9A&}XZf$P2ZL3CA@7viPuZ#;4
zQlBJ1!8yFx_V7~lw=wH@gIdgcEr<lL7A@4c*aQ3B$LxL+v6?U|_4RPBXo5KxAnHFY
zb;K{2J}Li`mh14hy^H_X-mzASD6;_q4V*3x-VQKCetN+?z4c=7vq1jk@s1Rg7|D+`
zBQq4*+r`*Zl8i;T&Q3FiBsl}Q#!sjzpODW0*39^pe^EM9K_@<dL$`m|yz*X8V%!AB
z!-3I)1%VGK4NZZWkz8D{@iGVFM?1|TJ3*Nn<F%5rJwhj^{9F?4)4l`7W&+_xyW@TK
zc9^aP9by>aj-z(ODGX&ekm@m=1<f^)isFC*Y{9gSyJ95w&?UI+Fi7QiJ4yU5zvT<5
zA^B*TJ3y{%^qhT#BSv3XO)WZ}X#9dKCi1qZ`hux8a_K5yrU=+$v!S6PP?MSu1)zNR
z`7G{S-5JwD;3mO1@jwevoH7{i<=Gj_N{q<Zj53oJ=J7)TZNvmBiI$$@c))BH>2cNl
zw$BTTB!rU8N+3yN;+AE7KIH1bL<F6ew={pvADi2G&EVOK=+wH;J8B~!EWOKb7q0A>
z+<zJShJmq18{0U|;UDDA=Ke3PXwrcyhKO|=C)UM$^P$3-RE-PhV84o)kK|#A9CfWg
zxI@J4?{qo4H{1%BBxakPnx6or@ptRdjC@}p+p0yIy+C5J`PHZ7ehSY6BK35P8*=q)
zEANghO2Ra!ffdN>w2n+Q%a@&9wyxo`%%6eL%DZV>v~rf6zp%JIYDk)bL+Ee*N^rB8
zHBwYg^M>nwWI-l@819Z%mNI3bm}ap<3bA6Y5#k;j+8$yrXYNwS>Y+>~45M}>Bx~}b
zf|Hh35$`#HEpO_$P3!*en$nR{V@qKvFlnB0m?@IIK56@1c+(9p`U$pQDqk3-B?c$a
zR@TxmH>P#<Xc9+0AJ?h9kFeavUIhb1p$;)NX@?cJkdY@P%1og1(N4$2ki3%urT=Qb
zA!TLqef`ChPu#|bFv2%g9|miML?;78G&c4cURoDn=Ni^6bS>>Z-djHO-m;%V*P|3h
z`CD4}F#kJUf4gb7PfY1rJpK3Me_sC$fAE*TFaKXZK^6C(2ev*TUNN?fie@iS^ir99
z|B-e#K9l^^?C-LzjQ?l|RqI_AcgyMBqP>}sl%Wt0Fs%ADdgmS(&L#zr8r%7q^3?AC
zdcc{?Yvygcx~kXIR^YEvJT@`r(!z9!d(}a=>L*~f#M%=7&rf`13f*dE;$-hL&DZ0@
z3*xjUH?B3hh7`ceoCHbfzl-)8j8e_25&dzyVymOZ?Ql9FWx34)ZL>YL={s%2%JC34
zlgn2yyoy}-cZAyVk-p~NedI$av{9=(0Mr97WAOIvU`(Ujfv?v2zYj5Feg5Zlij)1+
zz8sN3yz46ayV-n1Iscwz<GX`4|L?j(6>nuozI!?ZawW1dQGhh6X1tCD(vB>nDt^wr
z0OP%#5b3SN@&#XR%*sg`42RI>G4Nc1IjEr4zSb5b7sX<&^Ov;id`z;8_#u2V0-21A
z8z=S(K^^Mkd$Fk>!YjR5xKVB!vO@2R3J#%fY?~b9LN^!`rwi`U*+&RR^h$V(K3r7D
z9U~A^BM{ysay2;s!O)YIZW#_+;6FANLH19Mg7u0b_xED4`q;qmYQJ03)sdD>19GEf
z?3Es(*lDR`={z-ARN7=K@o}X8a`55apyTdfTDtH-e3dh+w}+P#hC)Zw5;eHwM337T
zZN&lCsLF^ffVnA_QkO&$HjqW^mVYdGwDd(0e;`caBTXiyv>&#qxooQH%a&10K$kf&
zbX!`7oxp!Q@>Vm3J)Nq>dhLlAY7@^NP8rdurEkAum}2GcZvSFaAWbKWcOlbyy#sxl
zMc`JR_C9_tjZ%8}KDH<tTBJX_!Y4!&gTiYK^!PyQSS`@0lJd1cH;L%95p>Xac@y;I
z7eOIOMnaL)wv+NO^v`wt?b9sZZWbv9Uooaa7HqN<x%RY>RTF!)<<u!7K0&j4i55X3
zVz^7R`|MZb555TD;*-ROa|xknBQgyI-(f`NMv^CrDt?=g{}2+nBK|{sqVo&)&XNym
zUp{-Vc_0OEd;-gH!tj-dTmw(RKpMr7x%6El5<D6-qlhONXz}grUpVcZ?(2-@@M$}I
zQy6rJ>m*>DVtx8p16E24E0vV33}yT<@&j@oE;YYz;~f`2XWF|}JZ*^xzQ^MyVuXvA
zfu@i9BT5{4R+~loP9gN;3On!>yYLyNh*=3bw0_5E|BhZcyAAQI#QYyX3VVc~1qPbS
zHeAgEL@f1VZ14wAg)DsF`edaGt{WXV`ec~*;E;AW^rO=g5C18G&wjGlchnG7E!dV?
zv?dz@nLsNN;77D`D;#7hG`n;X5z<c4T26v9cd<Xn;Un&H2~0HMLar7&-=F%jC0#d>
z`wcxZR%%`4^wKHyJ-6)>tqSp!__?g7K~@*S^$Q$3ZFh|#212P*A#|D>#SutEi24A#
zvv*ypQ{F-EurrzW-iJCf!RkQC(emFqScOK)#k%N~63q_T0@|gS3Y{*DlYllG_jDR<
zpi~->owm4|>1ce{CmRgE$I~!-0-Xt!s8#tHIF?2k1d)I%;xD%06#S-_2TDtODD@(Q
zY7!k!Ws0EXf;u{7wV0`EwAV=4_6upUpbp%=ubkM?F^W8<euMpMr&>9PMi!_IVF$aC
zwT4DSCd=s*%kf*Up|^8m-cC+*ocx3bCi(^PlxL<kDF)^}7ELXgb5KVj*@_l1_G#41
zqtq|3`2|{>8HQG+)E!5QJaM-?rojOWd2c(Rvdl1O>^u3$h$Je@w;&$D7Dgl)(dm3Q
ztdloIm&b%>6p+&2oH1s&4Oka%oSuCzsg#@9v4OzKB->}mQYaJ1bAGwlQP58B@|dGg
zFkkbK`oJ~UOUA7S!|qQSz2rLDi;T6w|B}vFqWa3bXI=wazW3*Vvz51<y%qCOZ#*Gh
zoR9{++(;*9<O}6euAUWH`D%XjN<aSmM$w$fAN_%IOAQz31p|V6*O=gmJN|mz<Yf={
z1LDtn?}8CgK@D`>4TM#b3Dnlq&~f!7jJdeFQoU&K2<GCuFG{iEs3q7scLR)-YerEo
z>kSN66tnvJ$0&=3Y#o~r&t}FRHO)ve(aH{eMdsa&jJt;yN5&RSU!zI}<<VI@gqGp6
zJdzlzqMNq)!|4+tS}rUH*Oykq$UJghdM~&mK*^(7GiSXQ8WuEsEmHB_H#X%}EFJZX
zqvhsd#v&1(O>%b|N8cK=yy;`FLIH_c2X<%7O8Dka8IepS{U-Hd;f#75x9Ocx_oB*Q
z4n@75VFaTMtO-8w<tJmpj}TmsI-c?Uyhi^fG3au(cqRlgQa?xjux1lO!}Q6?;qO?*
z1L#e*R>riM_1@F&sx$hk*~u|)7QMB{P{*s$s|xQ&Axg;x_VEK@_h$2o_H3*JPD%2-
z#<emirKg^%om9;<rv!(f1+hi$nC+(J-j4}^_N;YzIUkT2#1WCnA^N_H9(dCqpLvh#
zE+tK(|4D)SR_;2^CvZJ=ZxCp)95Hv=DP!Xka?b}?N*ZwGb$yptC*jKM80k{&`y@Do
zDq!bLzn%jxX0<BWn%9qCRWR1WfD&z%2Jz9-0m_M)NEa^v&8}O_S52a4`>*fD6_Bzl
zcVBgkHTF~tJ+M1C*=J}o|8;q+;ZyAp<m+=f^R<#AuJh2rJ;Jt6_ZQDmf1}^6ye@TH
z-Nu73o4RG2T25nZ%f>D3(<;Px(f0y1NQ~minB;|6fFZ3&f1tflao#!UZRM@}L8F))
z#4TG)R%|cf`C_XO?No*#e+SR(QWS%v;6cqyu6<cUv(gxa@?#GxtSpX4El`rIw17Hk
zDh)rTx<^SM-gtQ90jQh%yLV@9zKiRQcB|p+REIIYD_6RL%&0R?s{BlH2_r4Q{C4qT
zwx|f}+kMpg9`>(e=|KHqP{1Ofqmc5ghBU)9cMrP5g5LGQW9<$<*YG!rxQE9uN9r;w
zeBmhIYUp{HijVF2!s4d+<1xP0Huw4W#x874Wbv?N$+RsZRN}(kX`bC4-;bkQ>(pb~
z%6d=wR5abH&I`KwoGqH}{Ge4x8}Vyede7x;{%Ku4U()><dU-sO4;?8lX6BdL1$f_*
zP7$0Wu|HEy)5AY!L3bOsEJeDWr&oxL^r<?RU7cKU7e=*%o6V)gd=__gG^k*Lel@x5
zezP)j3hL8($KVGfWd@pD1EK4rvrQ#0e@fAO;sWslqxe0<@#QpGi2%<0;fS_~C{I~K
zVKKN_kxSc+erQy!R16uPhN9TRCiXmpwz+HO3Jx``gERC)r*<Ye+Jovs0}&$^_D5R$
znxo|aWIxitX10ts1wc0CCS;iL^99QEl~*OGCraw5eNFfv&5Q2FhY?^~&f}I>`HE`~
zOE=&!pYf;M^Vi=GU(<d=iAuuQ(vNu-9M?yv{L`zj)vA(DOHNIYSc7cCj=UA<jyi}g
zaPV1rMYC#Ao98jX70q*j_B*FCI?-W9d*<dN7EKbMpmJasb8E3VQW;SApM1L?@3Qy{
z-l8fy7$#m%^ISG^r=7$TEi#r}L2JXcdZuvS#X7FaQZD~U5H1{)^3<2_MI-rnz8kr2
z3ym$mzl?l4gg>T8xfrGUabf^d2`GT!S38e!m8P=TW%eRJt>`DL_#{;E#+;|u^c9@Y
z0Vyixw5nhUf$lwegyr51<BaT3GA5gON2l}5a<V$m-8dW$ja8pvS+WTaiOis^!gBI$
zGi=%tgSXj4PFU^tpoGZ8<I<poQtL*!4eJ*E7H>Q-hjM{}Oy54?^$1V=6SeZ8C&2DA
zTagP!S3ze&&t9W9-3Sw9oMGdfF>#3{$~mvdII9omy1{da4Zkve5g8=u{^ZW*Dq)?o
z`9+h7_wcIQbNA2(8okRpOU9$5((zVX0R1849vn8mZ|_JRIHUfjy(Z?|@381#r1Rkc
zefkANQEl{s9Kh0nzIU8&l~-uIXm<JxGTeLGZ#qk#Y$#OXW~^@au!zz}e%9d(yU^>y
z8)k%;=}A}I)%U#jipvOep|?Mj1|3o^NJ@~-?&FpR;7L+xmSdg#ld1lCT>B=~jP(wj
zIlbCuY|Y(0xNUu>uhWiPy$DY?z@emIS%h<wbjBPNaify3HJs;~f|7Uad{^|GALN7;
z%JmL68(bomZumaj*X5G@pyk;2&q8-o`&urSF0)c%Y+BmgZ<&YfXJqJF#QXd{b$Uzv
zF}C{_&KIrq`jiz&JK<?;(!61541DhSuzmhUff_p)n;YPy=6?rog^XIZ9EuS0Y-31=
zCd9m^XQbvj<<wDkT4@E0Ty_vuXc4jk*0XOK_{ptM_^lmKsc_F&X(`OSrP(~}QOT?9
zn)XM>BRgG<2tpbW^DQ?EbPT<$?RWe!Y}lh`f>I3(-$gJ4$Lg^tc}KNRYx6Jlc<L#9
zaFaG286`23MP>I}qU)yge$Ekr$J`pdnBslNqGDd<d+Kp|>N>5zx_c_%>{IUohbL?a
zt@Er)H3y^NQD(enkXdJJ!+x`S@O`QkPF?tou3DW;V(F;RJSIEpSy;{^Z>E-ZT_yBL
ze-QRw)4FR}mZvp{9E6Bi2a_Zq9iXQ99_~R!ED8_DR*URe4PdNq1dt2hVP{#!!svFi
zh*;6aKMSvSX-W0raFQ*jU++UA+XNPR&7?}EE%#+CBN>Pb7M-84tPwjpux;bM0A2gg
z-<e6TT0ZYsx_l4v*=gP7KdyhMk*=hzo6GWTLQFa%ntA#`@pDUW-4i#g7UUm<=xFc^
z78AGXB*@ik=qz3`SM3Lh4QQvDlMp+yW7_h(5vY8r!YG-GUofzypVfEz&DJrmp)-Lr
zG)tu3TQwD52KR7v^|`A6w}n_rqPbd$9+M(r5`t8Ar(MaI=Zb=B;(3kqjXtBKkgn`}
z!v&LXqf@A>MK?7swTJ$YQA@gkHLHD{25J6CmN{TJej8aWW1kQ%7-|`)k^WKxbI8K0
zYzBq(HY!^i)`Qjd=e~_zTd`6XPAc)Z8FxjsYFdKAxMjmbQ2;gSk-m4iBqZ?kK%<`T
z*N}6>@_doq@pq*!t)LTm7F?ouc2Sjf3q&KcMDF~d^(%HF20s?xDPCRt6i3}p1>*#$
zR7C0pPHA6!k2?F$i%YuLc%MEB<L@(!J!6m?i|biFXLfv(BQUW<(f9S!kiX{oAt)@<
zH}lh>67_rn(2~)YedXt?N3@0b9VnJz<On|F=mQmK7-jzSLdvv9=qy-K`!Qb1FuJ!-
z$;}t3fwek0-ZM7QKjcg<C}ZW}o@UapynFj^&B=aS{qau4|8uf{Ia|PX*fisr(pM}t
zVm=gn?`C<SLui}ld}I~(&&F{P=hx1ZSjNgn1Q}?jf|#6vZPf{$+m*iHfpT8nr{_zT
zl!I8;P?Ck43<e7^_@9MHg99J$XxFXBS2J=&DW6Vrf%;bC6)=`t2G-O%#u~+-*JRYk
z-9J2jbY|aLq>$t*MJ+5s$vt+~9bNZ|x{<EOMDD8MyzH<p7&MfUw+*GfnT|>aC=kX)
zZI@vhNasxmg?YQ3ruoZ}PL74uoN?l9Xfl(hmMmkf{p;S{eL%JVwE@fwP>3v#kR8(!
zOh4uf`}V}`l0uG*yM;zSi2SX@JWg`OTqARv@p}R0zhay%D6q@XT9LIU<MY<AsY8os
zhD=KPeQ;SvpbFh?kP0+Op~>|#HJM)5yfd_9taZT2rh+$Eqsyw&ZCZj<CRLT>Lr_ZV
zl<yc^{M&`Kh*kc+n0J`RfS`)Pmt;DX5ZJnXky^(nrpTKlBPx)BI{r|BDli2+3@OcQ
zTQQEdS*GMu_HS;S*&QYpgnrOY%si9%Up!p}P?YQUzKVpTO1A>il1n3~lysMrl!)Zg
zNGKv*!qOeGNOzai(z%3mNq0B=-}N{1pK<0g-nrcUzV|)nJm-0yb5^o{uXOQD`ZFyT
zBrIyjp;YC$X-}snAQW={62HTG_I0m#W>qHN^<uFnMP1vNmsJtzR>{-RyCUmg@m@Ic
zK1sde+>FlOX74-9<IH_O!B`>WssNmWCry0rqytxRP0lhIpd>htyH?|XX$C@98|M-<
zy?49IX$N|a6ClZ~nH^7wH5d|={jqr>>L9x3OwnMVw`4ST1;!FRLbF6D<Zt-%4dZIB
zq?!c92IrfPFP3RW-ey9~ODC2bpw?G=T8;R3+XEt=UoQ9srjt4a>xO4-0n?njyv}Hp
z9KUvFzk<{GlEDGqUk&FR#(oJ>6z%yf7!zJurHi%QKjUb;#g%pw1t6q${zK`6N$tGY
z{!KN9QomV912@0xholYwXmp<fS$xS)>&T;_wzf-oeD?^P|9P~A4HY_d7-#6<ft)$E
z;B1Tr03w>j{daC)g4A|mU1|{r%HEmG?l}2m?Qn&#^kX9iNDS98wfWac0kq{jtpVLg
zb|v*)r%%_P93#J6mGo&dk&=0sOl??>Mo7eZ*nDGnM&*w#Zdl)&CVKtd#py6-U{^a&
z&AaaOt2fmF=o88(>CBmqCS65eXF`m#=Q9b>f3mJLPO<KdYoCX#=oNV6h@30NEX5@e
zY#{Ef9X>CLV@&9wnXhXuGCp|coLFtuOT?aJNJRZH2ooKUC+w&1M7Jx+9LwtYM}%xZ
zW5zj78>(Mvy@^pA(QjX>(lL&AtX}`04~QABe=+k`F1JM^@Aq<H|8v`FD|$uUsgQ90
z46A<w5bLPPUbyAQkJG%B6*AtcGzvHr5TeOX>`|;zV7tt%Xt3;03W_RY`)5W%k5hPM
zVpye;89|v6v$Wj@aSO1O<mQD2<EM}7Q{!oES-D=HHDV~JhM6KZhN+|gYy@{o&Smva
zzF^h;jXc;&<t9Y@U1KjR)dqI3-da?~*7RDmm}pKF&0Px@hN<c=<1ctp!lEQWazV(J
zTBlK~pRDPR-9QC&vvLgDT6x&x^5JSmys!!`8epmLgJEV1a$Zy0a&<y1?e)MJL=cL9
z8iF_}${;a{Q|hVPTGD(cb|kYI+8png(~MBiI;zqd1Z%e*{_|;cr9t#K$?Q>Iv01m0
z)Rq2mMv!^{Y@~M6(_2gA7S)>C_e2iA^0>aS+7blrvAk#^sc1%qwhxLjukVF4k^mJF
z+^;-X*5-%m&eMj3x&f!EuJ1`%W)}NPzMMyZ-U6M~n0HcvamwZ^Xnw5$Cw}eN)K5Zm
zdNAJy;ULLV_;5&eshfL50+#ilT#D^DviIa08SQL14#a1#$4u2P@Oy_KJxczQ){zO;
zksAs=4J%x`tIRt1;l@j382(^h)Ym9hJsVUjKua-k8&WOeO+0;fR0kkmz$``zbNb6A
z&W#9G5f1ePI!;ZvU|KQNXOGSfWfN3R3OJivi=g#<D}bFk{W%B@x5LC2>V;cdlsHkV
z^OpG2e*5O6GEDsQ;f=9r{O5&XT7Gt+f?@@ZeZK>tP(mV?zSUrWb?+`)WC}c}6J<uP
zUt==Ph?+CCy(yCH9snQn7rw|>Tfe+2+xHt7a(KcQpJgTE8Jw2CYOR;g?coaZUU}`h
zZ2H<C1X6a+Y>et`RJ)sc#wJ_xCUnzooTgRVQaw3M1P^jGD|~n2F>jGQPa~w@ga-rJ
zuT~J@S=1K~GiTL%YB33@0X>20G$eQh+1#^S>9jI{Py&^qz@6H*f*&jD``<v{Ma&e8
zyTLQ>_AdvQ0-&<mA0v;p90YMa_gpDvY$h&f?HaphU2c9)mpc2F?Kp548PmbmOrW9P
zR#d7C00okj^e4he|1@Av*LmKwZBLEh5>Ob%$i33f?J<!djf{8wGUDhMq>n)4a#b$Z
zrki}E(C%5j9-q;?U1>a%`P?{t>~Y=Q7IC3RYG^9zSjUz~?7KpHYqG-6*DOB5Z{7BH
znm4XiR6jrqCG9(Z_Lg`8+JR`+4$Lq<G25c$4$LI@F@rjiWeOkkU$y!{nLAtwEGnhE
zpsjj7-NDC>9qVfquT$rfyERQL%=HoX5yL~(#78+S#uVZt-;T3>yc^1)4e(Xr#@&x<
z3D{C18w$EF9NE0bWi!(cZG<R|S16gIf2F`E0jY8C#rzU%9AO_kKO7Jw1h~?7;GP1m
zw87Gj7TLg8)6cEo01p!@sN$(;VJKu)3=ANKzNP^5<1F(}Qa@0tn6R;;;sNu9dwIMZ
z_-<&vNP0E|V?A*IlzyCx&7izg9tiaWSFO%3HIS$c^u&fH%|B8|Sv`73#2yC~kRPvL
zp5!q1;CgP~*B!-Y14zDsic)7-fw_$~h_P@At*6qKZ=&H3WEI52KazTK#344mi{;<o
zQ+nGyQghyNgE}#6i6JcIjHFO?zk~|GD-^0OYNN~|6%7Zx2nTvE$iW$uepgM+85^NO
zx`2XMPMBG69&tz*SOsv)m@BP?8<)r5FL%pV&K6@$<(JwwLAtku!p6Tl-o$9FA6))n
zcW&+k#9pJVuPqT(_d&>r8JRvmDsx!9cUEBuRwCN>_9Dg$tMm@=e&V%y14*~G_$5d_
zu)-E?9hYDYwSQ)PejCgEq73e56(6rh+U`I0Q}qcU{9&W@Tam*Jsb_0P#2|Hm{~WXJ
z)unN@`}%+4<W09<{^-+NO(pkgci|hkrsWh)%*qN3_QtRPkjC`81+Bx7>QL6oS9*v^
zNj+3ue^~#>!}_y9VunmS&9#0X8Hu?_n?lvwNoZON7O*E!JxBS5IH~xOqfXk!>OEDA
zUXBJ(;@K;}YV{L1BL<IBCVK%9#Qqm7Wm&e3W&{9jRw;$AxOckpIS4M0d9j2azkWgh
zpYTSwtd>1*f|R~Ol!SYR0u`YmPkI5GW3YDTab;6C$gDu+)H=WeNTacCM_<z<Hpgs;
z^qf;y;`m$I>pIm}oY;W7Q#rZ<-2<rlrBizg6WaSx@%C=)u31(TRYi{3f{2sD_MqTA
z4D|?S!$Kv({Ad8`uJG%eF=A95YoDy)5OWaa0T|G$!8q9QhS-A4jLHw}F@W}6oxGOW
zN3}GOd{L^e3e@KEUPS(iE>=#Fkx7~Q@rpZM?rLzi!Pj4!bM8w#)&eftDheea&e@F;
zbe`G?1tjLxY5IK5F<2(0BtXGi&?x@##uE+I$p+{Mv}Qy$aq@npEmGgq?XT7Nu!!y)
zc4)-)zI;uSOuKOVi2G)KQa@6=NBw%YHZFcJrdFSdk^{+Ir$kn=;d+7WpadNnNNdlO
zU=jhr*ykMxI&h1dJ$9c{&Hm;JUt9X4U-aEH-uDa*zo}0G&?`AreRcEn3WPj}jcd2q
zOu$6xZu40NWcB|96#<qYdQ>}-tJkc7^~_K*=ZIP!EMmzZL<hN0>|=pLwc~#7d%abM
z=itw+FPqVOVfFVsupAQ$d)%W0bWxyQbK3x!Abv2e)-d(AvdOivxgPy~&2$ko|7E<x
z1=K2q`NAoMJFKNnIWAbUiQ74~!2J@8W|1*mBd6_-##f)DFh3Q`v>l-E-Cqt_cGPDN
zKlp6!?`PZw`?j-0!5D5F#oZ^N*=B}|qbJZ6PcmFWccRA|hXspQA_8ZR`jnQ1<x_k6
z#-?Ff>&tj-VW5~y^b&&9!^BT?yYz=jw{0nH-kp>)+{K`HXb3W}(%WYiqR$bIq9Q?G
zp#gt|fK=zdvY7>p2tD2gA4I?H?@A95&IPtnieTrBt*^Mj^><e*Hb71U+>+CdgRU>y
zWgSM#;cA~q&0y_}2m7|N@3CgM`U#pm7}2j*lJYvHc!f%qFCm)}#N01I-8r%(^X&OW
zg1yGUuyG7m{DY~cm6RzS(59Y|8hXQvw+4Y@W1FcesW%3k_PGeDc&C0<yG9l0O=u=>
zKPZH3SVuOy-x4>ybPTc^)L&w<I=k4o^wPRYktj5s!hWd|EM9kauUOmSyfPO@hHJ^U
zH<6!^qd`C64YC5QSUZ8)FRgvX+IBy`j}Arri1`&0=c)lr8gxc!MQ^v9eaK)JI%q;Y
z>_-ncrNQwHk7`gvBsTGLdic@ye#h{0VZGLGTY8hxBcJ`S2_mKp=rrE68<R~vMdriH
z^enrv?)$!<Qf#S4a79^xc!Sc9RGB}kzU2&G?|hc429zCcrcO!52zTrp5xc^yQ&~sf
zq@8|x-4GR88e}jm!`k9p-`PJO{Bkb-PN%9@tAW1S5)<4*uAUz?<RW>J`B%@n5=nX!
zNGK?_yyHMS752^eKLP0h2c_-k6L5q8J;f(wubyp4-V>&XErOL}jHT!zmp)m3^V1Kq
zT9Gx(SKwX!z%rd+VTcE}oO=Jca!0L%3eMwuLayD2Kg;}7i-pqgOeIF6aL59=H;i=|
zpXj}b)^Ve8&*~MTBEcTm=i)9}|4?bmFY9wE)7U%}ElBRw<p-+KOh0$b3*7Mz4Hkfz
zXxswc8I{r;mpb`^n@GVpsXofJj3hCtFL&}Su!MqaG&Uk=lp3G2X~r@sqeuK<)Au<R
z&xatWfbxLDI*^ryn8*xYkyo+`Dyi2&y8vGR-X^Cq!*tkCDw8@`PZ0tLJn13Y+<QuS
zL{^4zSF;#KiSb`BvOKFsOD+aLXZz{PF@`G$Xi{uV+#5*88K4W6glC&40e6K(<3w@o
zwnKAsUOo{s1ysTd@XGI&Pm1@q)Jdx-?Ww98EMWpRs}534LXJTi*%hr{F=sLM1hme(
zr_eyFpiuRDW#o_J!&hm3NriZ~`?r{$LptWjJ?d_LoY*$D7|Yw$3+;=gb1KjZ?QFyk
zUYYi%U%a)g8CYp|;VSuKQ@ZMW-qJ%2P`x2#lCd=zbDCt4F`xyGK${3Mn8aM}3mC5r
zkSm+Gy?i*8+3j-$5f`5BB_HOrFpo_sip2_Iua%3w#Gvx5v1!cRmB@UKNUK!9i&6>=
zrdzX{dq!kQS;zMk7I~e01rQ$qy&-kmvLeuxcxtcMZUN9R<E-diPFxd0FUj%RWck_M
zI)YQ$7WbZS2q|B4r(WfALssQOIrB{{8P5hFi#0*G2fsMnuz@^bx-sY-qbxrGWYBYu
zIK#E#wEBTBC#PrUze*7vVPlci<P6+^0%6ig91yVJu+i2Qv-2-H=--eR^zV+C*age~
z&M4X3WV>jSzxd%Yl^=R?>S@LTs1C>}?h$?`49(Q}_`0tzh{4iYC@X3P&utM1jaMm%
zw=p(wIB&{}!z++n-ei<fGt!(*y^FZ@#KSW{%Z6abws|&vHzflSG=MbTg65Ysot`SP
ziDf+7+n4$MQo=GrJ3y%i$!8gat^l0Vp;5Huds5p-*qY(WePtRMj28+4K)Eh5J}gX-
z|I42AP$0tN4clDRDZSM@Pxl(FHBc4hS7Z^hK)E6YCj;oRX|9Ns(m9)k|KRY_A8e){
zDU6bY2WMS&RFD?F42v%LE_wC2dtkN3Z>Or?^MZG*AY!JCm&(POM8b`lLgAL6y>17>
z%GE5QYdT!B2V_I3>6e5)nHiS)%o?Z=Yc97>$yG2GQShYEY~jKpafG+o^&6NA>!p+6
z$8POQH*}F^v-IBZiyJm}g11dAuk9Sxf*zz<EHUh`zZAIsb*wb(w`uN#334yf%J*y!
znMrf3yUDj9EoSVnKVJx#C+i~6YSCK=b-G!CS)}&Y$$iRnAWm@kB+@V&SKs<%+Qj#n
z;Q;o?%1rS}GQc4bzL>~Zr2C##eW7v_R}PP{C1pl+?}aK0LA@dnO)eH5SwU>L17-u8
zMY#vJ#&o?c7B5RR7<RRXQOYuJ?Glv0d>)jPqcL*1*tS~F1iOBHxLLi<Ww)(8cghQu
z3hE|)cYLsbV>&lN^gu{~aM$G%<lAKDIL}Kf2n56<&<qdiaVA)F21?O8d~;8Q42uW;
z+fSb+yEyN#>;cUuDBms;zhKuhH|(*t_Jxp^IL1{J1L(7M=LvyO8%&&!_dRD-iZ!wp
zWsr-CMC%~x02owxeDCP;4=$lCzFSkLEZPUh=c}J><Xk=s8H<VOr2oObX*nb@j0?3)
z%X?Kya$GZ3G#t_vIo{EiNCN6OVrDy6e_9tH291A2fnee9W#h92;@~>?L3WUkn7Ein
z0c|Y7mQy%I1H)?CoOg(FVwPgg=jd>Roq`dnXE`6(CT6ug9TnqXO32*^t<}Y@>IIOr
z3?2rR8=#yhIiDsKlbIZ_FIKlGou0A{c6{{u$&s;RiXF}H@imOu0>Ih0i!+Yq7CQxl
zr*>1F-eTm51I?}*&K$(~o}>C%#OL(X&4P+3b~I+`Pi`YwdA3<S>R{Wny~Ap^4~*hV
zoP6`Mp|`z*Ujpt<v(gUQ#zc-Y-~Zfq&7NPq>aD);b>sxW7bWih{3YbQC~UcUt@z+3
zMr7ub9gQ2MF~w2i%Cx6Bo!RLFs;ry33Cn%o7?ERXT)%wV*!jdpL?6qP1*oRJD`4tz
z$uAxFcGSN?5FuG!d}MCXi1hm1c$m~gg}QEbCSIr46k_fn8h--^;6^_M;C@Ip_8S22
z0w7ji;2S7OCNxNKduN&GFJyhIQZcJMAt#DHD2@jjgAZlsfWwt3N(7^}oY?D9&kU(-
zv};p{g(;p-uK@8|pIsxNk4UL~D+`g%J!D<g<@YA$IuK8jDEMC^2QailaKt?L`;!p{
zz%@OerdDtigO^%2;+rXiI9~98lLl-9z3Ux5^1I7=`N&?$_#Rbe%*e;8QznZkAakme
z0a=$Y2PHa<H*n;tG2Nbk38834K#dT{BwrYR6h`kQPtD26VO0kP5|ro3@F@$nc+mb5
zmfiQFC|?$@=WrfB3ohXU2+%D+!|GVCp5xI~Nyw%Ydv|^rhf=ELSGwsbGQhfn1^uSh
zy)=)6=^cv7g#|n@q6H@I!XeYPEiTv#V@ivh#jiGG`s`X40i0h_xCLA@SygOi-wW&g
zbzLn!;>-#Rd(0utoSr5*`b~`Bvm(b|w!bGx^3T^(qv%b%9)6iC;Z!r!eCkL*1$&!r
z-hbY^qEs&}`i7nXU6K`r)+l_P=^{)?UUziwgLHXqf5IU=<x}4-W7!Ja2s}wI9_Kp^
zQEiiloiKwDhcFazDppV&2ALJIm{O=i2U)m7@R{N+FgR^TG<?E&W=JN72d51`#Nouf
zG&REu2`$(=n(-RdUz4$N4U)$CMtkzfJkf~Kg)Ft3L|L&i+3mI}m6DhV==S7rUO$OK
z%ki)`;FXsOyP*%tW?NC9u&OqKl+4jl5D1C`xrI>BGJ<xDH>TfCV3<Nm92@B8GM@yY
zGx}|2&$L%RStf(qk9%WAMSp%QXaG=mc91(Le8B;NgD9ED&<p)!#)=42!64^jJxI<q
zhN*(~_WA#D2I-tkHE8Pz9ivxR^vlzMx?MhE2MgV=j|oSx#pEid#SOj>1)jN7>VJJA
zt{<J&Mh5&5Xu#dyu!<Ny&_j-rdME-GFq8_T?df%mKGkw%4+J!>JxZ%sGOPo6fXRt_
zq2|mJ@Gh=jneJW2mxXK+B_0W+d#-5r*vJFm92!wJT*<c50iO!+ggpLy4(}f`aHIH;
z=z--`GRE>+I^^ViSi*Hsu9D|yP13SwQ!4<|(Dsei|JZIw2t0iGq9T^{c_AsGmLLP$
zH>r^4nh40Dl=Yp{)wf&TV#>x*xOvq#w{IU8!BLe7bT>nSLa(cV27V*t-VF4YcHYbk
zU>Ld#q=iRQXpo21t=9+&a)tw58d_f24Sr46R-8F*NUnlUv-_gv?P&*?AF5D*9&RKe
zvPZ}!dSIc#_ez1~>>HSS6lID8@-J1~ykQLjlxeCn`%|-z6y!*7M&ASwYg{t8FGW;;
z&nn%tV~W-%*dJZr)@ti?#enH}kCCsTmIs&s9)Qk?-Y#eLOn0}kb~+b{)sRKGaL>!z
z8swsSf78&ay3saUn7I4-L%zF(UUpICS-}O5-s;+k+z6*H63FwDTpUlR=WU=2Bgj_n
zsO4}6twWWsCBoY@$oTI^xVU-Jsu@BW1^<4qf_+%0&LeNFNm{{Kc2qDw{2QKel_S_#
z#rgq}OhssG`<H`6HE}2ce-3x^XPz)Q2ML0CI)She_dD=fw&e~I+Is(WKFNe+5MJbP
zJQ^SF(&N_-UJghsyDI=0E@J}#E?(G+aDA!T$`2d9wy<&TChZ6zp;bq7z*O<JCgy?<
zVO%ZCyASC1AgckeXo)tUO<K@Km|mgZ1rHVs0|Z=-NpI*qAaR7DY_1Jl5R4esSldty
z^XN=K7V4bU{l~ORdR_jD`10Cw`B_rH_IAUM;(hQIKM1S;9>Gh{dX8_+s`s8>AU;+g
z_-W9FWJ|(BB8zgsREQ}LyC`=EX*!qntpw9+Ghtf3p+62BK@u}3)+tR6?ALBWh?zWQ
z+T2;?!Tg?Z|HT{PPA(bzFTM<`zL%S)9w*TF9+Db;3R5~5ZLTAf3A<)Cw{)}8(x0hZ
zu9W%`u;VnR?<!=lh(cm}K?kS+I>7$a^NB~Gkcgn<Qnw6TxMl*8&Dw8Tt!T9dZKD-m
z1jWvfxHB!ga+b^ABj80DmBuA<hQN7Ih2dhP{XV+Yab<0Lh|NepC}yDz7)Av|ub((d
zA4+l%v0fvNrOKFUgb!4KYijK<CX#I)xB<xB+H=;OjnFuV5rRg)s94iIQh}Y46}E=D
zW7-;*vVEX4;lEzSAu{HoU!qhetuaiba;MxI)jD56ECn?@IsirjAU)7W>;T&kxX?dh
zbirB&=%;^AU~KISbHasX?$FezN!>g7Z3?`If2@WhFp)ogsvWGe05vrps72#@OC4Fx
zuH$@RAcQuoeV_sXe66Fr&;BceO95LQA54|?x#~u#bJ|N*3P2MRGxd5FInjY36h;f-
z=$*bUVtA?CK~&%|k)r!JBrHfFoSP|xJNeQp%0^L{QwJaCf@e2yivVHSlQ@x0NImaS
zff1iLu(CvkOc>^rWIs&=G}T)W=~nD#Q$TW*@m9<i*5x4WEK%;Z3Itgo<=@S+2UG(v
zn?a9#zvw(f#_R1++!YhtMiEe2<%m)U))JMBqU=nnIG-PEeDujQjlVu^<ujyB5}LXf
zOsa&a@E>!_l0pko`!4ISX~e5A`<_GFOibGZ=-7M)du&SnK=f9zVy=?7Q%PA(6QB-@
z>w)RBhEt!Z;G50#A7qyfvk|pHR+T(piSzWrh-Gt1jQPac_WUsx1)B;NCD36Um7icr
zGVNC`bB)2^a7Q3b3Vh%I>#BghW0JF6{R)K0o9EN!&$MZ3r!B;>Ylo*6P*ULTk|J;>
z<-uE0FyvTbKfeGxL!`K*C9c?z0ZX`@c3|@MB^5MkvX0xKQ|qe+a3Lqx=q$Xqo?UnY
zwsm)>6XZ83qsfDI)$#8H_}5F2mzwJ1e0YpAul<%RqXcXQh*@h8ACVixkFr^Ix-8nZ
zX!NiOG9r0xz}wW8Tc+pZJd6tbu#Q)+l@?k_bOr5_YgX*v8xFoko1Y)Y;~?pb?;`?j
zT~Ki{7}Y5K_w^i{$z`xb{U)A62qk9_0MbVQ%Uy3Qb%H+XX%HroTp5|uPpFWgvt6lk
zB1~^5F##5vEI2?za}^e`WS9&kt85q65nVpfZ}4(N(`>73?K4!eJ$vfP66?Zk$O7Wa
z#Ny>V65$0_9~I0FHD*D$ud)aD&8(}Z8V^Yp5@Hm%r<m3+<XBP^S#s~LqQW8f3Fljr
zcNv2_E@7YTJq_|{$3j{cw|&HBA19WAwh-_D>ItGn#{Vo3Ie*soMnQbYrS!&i$CKP4
z3k58{-$W+m&wQHD*{syvadj&cewjQ4@!Ayom?oL~O=O3Hpe`)3nmdinF;`G}vO83R
zoUT2~x=mEWZ%KENjB!GqFtomQnWo1_C($P>>7QJOnF>$H1FmMJF)4byFhC@1sJp!G
z;8w`9jpY`Q=@=NolEE1P74SyMm#qWJLpAU5`%P2dUTXb-Og|sL%tx;Au=}^x8yMln
z_LUHnq{_v1!#}TA`_kcTBiS59`U0>S;bw-a`~nyKI-r0+@j`%2npHiW__Dw~%lR8_
zR6Mh6&E(vFHv94p1!~~90ac-kq~lF4bAAU$Po)a}FqA`0<0(8A8@0m|(`~xpukk8S
z0x9?s>5=waVuF0|uhMLtg&v-`0&t%%r&neMw+P4QJXeB1@TR%C;>UAwTAfkT!gfMH
zb@;Fzc3g8ME6IB-8}2^an`~MBqZpV|f&1(Sm9^pmvm)@q0s`@Ytf%#!rJnI;5o}Zk
zHp<>VdfZ7v05WdQ^u{Hg1laZPwU83<wZ%%QZQKguv9{q2g+v|jc?)Fopz_47V<{H`
zG<B%XqbLUDs)0FQN&mPHTGTCi|Hl6S%RC`Rm;<*2zt5+TQlA}nTt(Cd@_XzB`|MLC
zd=efO=Q?;ny}#5XFhcv@ybLow2VJ*9(Qm-!Fk3~qWPKg;zWOsE$T7(wHNB#r(V920
zXj~0VZ#;m-6Hr(I?`iJEOGX}dryVz8dM3Hj@jaBd>eTA1>^h*wPiPxH!HNt>9O3w9
zrqy-;N}&uA;sj~pDg7Fbh|u19{IfeFpNyzv(e)te#}|jK7w~fQ4?I#JOBu83EqsDf
z=?QQ-J*-IuhWQ4;OyWzYEc?GZz+ntnRJ9c5_Q%8I1@d*8md>n}p$*|6yt!ZGDUnD_
zD4WM)`JRO5E0HLg{`?@=C<yv-Y5=nNXMEy%VQ$balVbOU+@oAI_Oo{=A`-Bgtz~In
z(&K+c>lIP}iL{ZKY6IH%E^%R{XWgI}H5JL8b6ouzWGpJ`FaTVEd90%wsA+DP1v-<8
zOxVEq#CC&^-V1y(2gpEhgL|sv=bY?u38%>vba{S$whdrbJXi|!rh5DnGfk~B+u8zT
z5s<`}0^{q#3xVz3>MvZYb4SXZ&)x|T&kl*ENe$-e6*G}%3rLnhrmUi4&!#tQ$I^)o
z1SN|n=fK!Ekuw0J-9;YZh7kU<Rqr}KM4J7yVgD-+0zp|bzztj>57gIR9JI1dk^^J+
zL0a=A-tFY9>-pH~NTh8uB|0#Z-d&9A{i&0kt3bhp4wIN>9uGfI?k@B%-hNrt9m4kl
z`8V^ic!@Q+V|m}2{F5ncsAQf}?12J}#J8`6b}AY1LSw`S#3CZwDuvuV(QBY|Za7DH
z^&G`=h7U%TTi*_MHUlr^5}MZe>?gaCAT$&d#f(WB{Fsa~Jkl1;tz@lUc1@p;oQr}M
zf{FAJ+?3FN0PxKS1P>25<^h?m|3XoPK$OOXQbw!4q%!b}c=&!G=r%#=Q6fqQu4_?n
z&0)4a-&VL{s3DI^l`K~VRY5_trJ||9*&<0%PI?Snj=@`w?Y32LYy{XG_oNlVsHENs
zd8VXp!gtO~UF06e%y<1RgUmBU?66WT_;|QD;I6o8k2l_yEc;<^<9OF#Z~1S&Dhfqe
z=V4ik4KUj%JVqQ$j%2XXq2GHQ4F`fDY($R9^d0DWE<90u5WS$z*(c7R+$*o~8=%=|
zUs6qQD~=F}E4ux$QKQUIugs$S%N_u@*N*PwC5voO)Mfq$v50Nr0P1!dvI5=fomI1<
z!*Bf1tBkL2p99Ya${V^|=|RLE(5;Yar(^^yDxveqwF<*7+=VH`&pAf|&YlKY2HbYF
zgyn8Uv&SV{F5}l*hagSGtwNs5Ep|Na|DE;tGdOqY1<)e`M=@tGYG^(jYXnT40Fym~
zVvzq`+OL+0VXnZ?5i^mWp(EcJ6ssq+s6CD3qTuw3nxbqDu~KtoMuB`-$|9Xy-FgGL
zMGtzD@TI1yFK&$~kYTMmA?TeKVtJMn;l^rJyg=RR6scT6!wi1?1gQ}`U8tzv=2_%p
z0<6rLUzHQLtT8YNh>l|0F5bj|dzY8wfk6+xHV8`fZ$fOr3WlTKr46=T1I?;I&&YjM
zyqs31;CT9aas=<zp?}Fp{5lZ03xLf4yt4QKqMCP!zlZojN!LF&k#<7R?Ed;4zW}2+
zU<VESF{fZhI=3?Y{>KO4Qro<X1VX3;fbocDe9bak1xnya!T5~XquY+Qy!OJP2EDOB
z-{xgxPrEVkk{0^X!rf$%lE!pQaKzkNM=YO>L#)?K+oLOh{dAFHW29O7j`?&h5HJXW
z{I(Npp0eC57*}rH^wJ{;=&r_&JHOAAHG4SuNo0KnwJjpNzj}aV@0e8^9@kE9u$?qO
zat`?7p3{vje6Z%r#O}}%h+tm<^2}U0yeQQr3g#=8U^{*Y`<tN2@SHW9Hs^Sm<iF~7
zNeUJreIG*B6Q${m5Tkg9v0)+w{M-=gBckG<N?OnbDYr(_I)f=+U4D2$irbQnB6m1g
zy2tRK`{~nd$$OOEad^d@Kpd4G0vwkK@A@#l7nmP7;9@5ljL4?UsUq(Uk)D9CFGG~w
zXvF4mO;sL?wC1K}25Mefrn}v5)zlNHQTfG#nw0Scrt}Icxfammfm4*sUSA(HZ|1+|
zIICAQaV|M%eUILkiLyUPBclId@z{U6-Xs9^3k*`IRCd&#(0ffF;N4O<&R96~g+tuv
zUj7Zgm0<u7Om*s%fM4+X4?93-*K@7%00e;{s6lhl&JKADbzRtF(vfPXl(Li-eui_w
z4I*DgQNXXDtifQ|D8@Spz~S$*K;ZhxRlsmv@lM60eR(l)HGOlZ29r(<mJ3$exo;D@
z2Sk#K&Eun1*5d=*{%x0PxJ%k%3qw2DRG%XZz#K%1%g!rmm^#tkm^KiDPJU;76sj3~
z_Vemj>3~tu>~jVDIrjc>MbIaDn_kkn=h_2r46hVwxPT1gF?n9#deY}qM0I(Kz#9sT
zPi4E#GVcV|(~0yn_1Z89Eqj1dyWhS<Z009e#{^b_8;9n>%=v-Qi_1}q;Zupr?61<u
zq75@e`8ts_6>q9i@?(%l$`;Rn)LFi91{zD<jcPEMmBRJMHj_>XUjmukcEpll1$MvN
zC(cug*{HeHc#*OD+Vcp%B$zAa105Qu3FR|Z)Xc!L=V2y-4Gc+$laaq*UF0&PL!NHD
z5x=+b)F;0cPjSs8qZRamh>D>VFTlAD5TTfrrH4|esRsp%L!f^H%kjSnn`wNZRGB{1
zdd${FC0~yejOG~~&@4bpRaO9f=~xLFaAOR}-B_oH08>N#nk=$;STJAZ{3&2NAx8=y
zskbS^WF}a*5%*lD_`EAVM?@rUHPjybcuM~A70F;kIHS*R7UPc;vEDs7qE>o7ON-Xd
zpT%W?GyrA<dV#xmDEu4RtZRPR)$AoUs0y&jmI6NuXn|?W5Vn^Vc%GY6pFO)xVQo1=
zV3aE>Dg|Zz^<fVHCmvnz_;I8Y?zUr$0C~S^T-{A8e*ObY231d2nv$#Y?w>z3TmfzW
zoCCP=hrrqfV2!7{iSdxniH@|3Q&rvOZqD?c?Xj_d;zKc|@GxWaC0bxH3~0ote#cj*
z`ZcZnfh@b~5{vP=Fudr%Iui#vs&u6~!nZR-T#6kSkTRnjb##I4-V6M%m&Ap?ncgm=
z%{G%9pMzG&kVP5VD0&hq{V?qJGA3KK?v|@`U2`F&rz4osh-3O6<W;(lIuaAoME>;x
zYck>T+9%}5OzV0e8Ed4l$HI|VUZ`A;ovQcrNq)4T5}1;M&u5Va`~-tbPpI0=`uce`
zR=agia|<!v2F$w4cq#B<j0rtqqDd>n?>3Gq*>tX%x3sTTUjv8S+m_qEbWAQ8l=Bk)
zB*zbKDWhhSmYJ&SSgC5R5Q0q(VD(A*VBN&ap_^($y)7RZChRWptnj%T!6iUwu6@;v
z=F;ipHGKz8KqGlOGC~oMSqCC1X<)VVk`UW8YW(g_-ZB}aO(4_mam@Y&|4+NI*zoMj
zXIdMlb&m6TP5sSvcVgfWuV+KjmQOZu!A^chTBItN*c5J$wopXPdrCSTdq(=n_JN_E
zFIU6L?!`^5GW{onr;&zK(cY5xA|72C<FXMET!n@pVdefyBoasv)IiPb9C5y#sdrAl
z3b1Ugn^<x2fGH;u1M*aABE0FbF1QE7o3m(`ssBk$8w;y10Oguk#PP2wA*fi_sEQTn
z_2=?Y;XPgCs!2wVk&#;vr()kxCBhwy@z_@L1G)>;$2CK|$jo1uG-;5Di=68D)txCG
zz&?UfkuYMf*oAy!qY0xj>1V@Bh;`Qon3o#;dUA;gOy?W|^LUc?-RSoq@SSM*NfGgN
z+*o{0Xw-o*nU9YnJObZr_gV_AojPc+k)*Y|-d98p#UQrE$iFeH4#p9XFxvuN?r30@
zr&tRfZr0fS0$3~6hz*nYibLY4tmXKB1Cx_BE7BL*?FX20LD;{iL36-`<y!lIKZ1&2
zq-||^RXE&sB!b?lFd$Bnp)D_P?Ifd!G~jsY$I9*d#!g2+Y}C}Jqtv!>bstitGUpYA
zQ}UZnf6mh>(NUv@UoP-z`L%V)p*w}XLu6Wm+`rP1_aHVN!9`VBmXAd*1@z)@AT~oW
zqujV)z>iyzU9po#0rES-G_hslp-e}})<q?Ohd+iLhD;eL(?N<d5(2~)VB!N`qes1X
z<_A2`l;arC#LQ^nGHer+frP(-qi~4Uk`h?!ff5)$wPB0TfU2+mCVZcfB_jOZ_|@u1
z&c`<a&o!_qpU)lI0P-2!yp+!iFV8l#!1NTz8(=Q2K`UWNq+A=N8o~W%pDLHV_KW8}
z#H8<dFMKY$wdp?oTn^eiy@1K)dd?*9r6X^mMLE;r*3qD?osS);ByukPnL9j-tH3}a
zHT}#^xW-?0ysXp-4Xks;HNCO|-@E0EHo+Az7I>L+Z+U?L0s$i>0(z9!^WLYOl1v3H
zzK@jUh#59E!ifm810xokXGSndv6LwA;`?K3bf}hB4vB!5uYX8nh#z=FK@~VjkI3Bu
z`r%td?62swLh*&2{*}n;gHPtc05pn@^vHtdfa%{BL?~7w+}P6Bp3an+sts6&DmuM@
zCcAcMPUDnRA(7@>EH83+u(Y1=rAuBzF6yVXn}IDQqkC`0`~Q*hiINi)gnEU)9BT$r
zQ7bfG-i!(5y#3J*h6B<HX4ht?ctD%(O+l;sEB_wcR;A1U@Mj$Z3yCCP_V}X^P<gnS
z<Oj;S69GbQ;Z^|iu!xe9Fyr^XwtywDkdiF1=_V(`>Q9|efrFV$d|~t(mX5>~2Og`G
z?`}~Psb6x=oVheN-x^9NZC<6oE#niVhaGC(QRGm&W8xFFF=UXUv%4h4Co1uOIR`%0
zscYlvmP0JO3ijD_GojF0Ay%bRNwHJF7=-(y77joqA&S7KW~P|5v3;^*+W{CXXpZ_C
z>P*v1dmM_T4wLiNOky0s-+>uWwdQ^+;5rDIXa-)mX?dd53Pv16Np8=tEVWnBjA|L@
zRKFHYMdMdzR-3QZEv(NC8t97@AdnO=PSFTyseO|mfLH~H6;Pa9i>pvYoFBiG17G-_
zr6Ij^pR2NLJj=i0`#p3*Nc|}$1-F^oF%lFbg1UaRSplg<Chq1b{WmR<5K~Hx3pU`A
zg63C37p^Q6Lx6_`C6tFlOdkVlt^x{vxJg4WUUvb;2NVTRFD8%c!B`SNRqQ7iVfy1Y
zG%Z*-skEbEs~BPFU<%9=NKZydqONq}W*coirK-LIlG(@0>+Q}bqWMo^4%g(X&$}<d
zilzvzmx*hK-;+#%ES(Sg2fZ~4)G7=d;EKa8P&`<u&@VBfH=-O`EU%x~1>EMS{$M<p
z?K942f1%hpdXhyx%BxbL4+!l+f>^tw49npN0+-i}3WVNOw_h7p_WKj$18Bh5u6gcs
z=IYrxwLSZP#3F5g%H;wc+t2La#FY5|VG#0Re<Tyo>VnaZYM<N){v<^Q>=sZqW!gp*
zh1+t6j1wPack|}5f+_abPY%jYu7E8IB^$c%#51vL%xo5kZ2kh@%oP>S@UoHir*a6h
z;)bMH8W;u4sR~V#49II5<HM5&=2echBVYI%qZFO@&x}^zx!?Et<0OT3;FPO2xZU{I
z9jtxhQpB%*tVme^%S)MgHO#F5XbccWcVA9#dEdfB#ka4UHh5|6dZu?j*}*&awhPi`
z{R|#G{qM<x?&ZjwM?r#Wb?@I|cSx;MOE5BQ5<y9^S)HIiC1)4^d*Y8%j>BFOa`K^J
zFZFa~Ry{&sgZG3kEpIo~QeD$v)?n=BPV&ELbxq|DVi%&ytFY$lga+HC2lqtC2cIAw
z<IG}gDPaoW4w;c(h^5-~I_j+RZ=j2{;M?`dzIulgN~C<6Lta0J@%qt&#rKcyNxgpb
zJ)lbsq9C;#$Ea)@BRN>L#qO$i-G6A#F*;E@TCnh)06v&WjnSZPARS|trxbU0eU5`0
zzkyi-2fSoVf$jF?H|D@Mo2iW!2@b6(h11kcmFJJ`v`FG@Cid#>%qQP+C$Q`fDtRTg
zO+JBbv})C6#uKt)O|SVsOZokBsE~I1cMhrB%%J*@tHQVZ({$T1Ph?3}CP$d5=a-dN
z#b#8;-Vk-NJ16N|X<n2x^_0&1r#m}ya;k4Nc7EHVS?5!|+?g1RD2Z8FiIj*BuIVFs
z@Y-!Ah`#YDR;xrsLM8JVlM({j7Z}r_25A*s`e^%g#V{nl5HC+DVp0i@3Ckt<xxGMl
zhfGK{f9&~om+?1dlRrJ%Nqw9KT5t0&i+W4j1mRmA4@{oyp%Hd+1F~b$#ofls$2rHt
zsHHtRPj%=;lb~>0<n@0tj%d-LqfPktv0A-J5YKGMXx0}sY>DQyMILF!ULmJfyu2h#
zj%Gw62ORSR`vlfF7k2H*xm6rJl8cMEV|#X3)5$uyUsIJXI@ONn?Fx!$+=ug^Bajz`
zHyl{so{G*%zETAz_Be_mC@LY-3@(_=w&;J)W#K4grPp&*Cuc`wv}EIQE?h2s*F1N^
zY}WF~*o#>An=zXNRp%AmuaC^Ey8VAn(BBVnww+|z=YRR*?PeH3$#kr{Q+a+cwe5BG
zU%w@zjDxxN^1ga9E3RqoRFg+PzO9b5+mj2`@6_j*^#LYi#~#eP;f!oLH%aPOJ8ljl
z0X!Xg{!u%}G5NwT=jL>lvNKrxU7@=nvT*6*X&Vj!HaC%(voZ!KMEv)n^+U}lf_5>|
z2d^LPMqn{xe|x%3pIDIok*7G6W+gkr(%a^eopxNicCP54up?yDASrfjySwfi^Qy9i
zxLM`IYOPO@7px^xjZaP*+dNM3c$WG7m@N`dG*fUc&esCJjye2da!S<BhJEq-ZBZ{P
zv8)M?!C%L$fb%PvRC79m-zsNo+AzWJGsrJaEP^QN%hAR;uM>#ZXkx13Y^Cc>E-!IR
z!v~sph1v$=$4?yV1Y50h5Ng%6S)Ikx)ZSJ6opw~-!QD>xOaq>GHvV4j@1b){kruCa
zwlI@jRrgg-ei634ANdVjy4RKB&6POd#4^le-|SkvAX$zd*1(sF>e^zoa!DF9Oadde
ziO3GTwkvG=c82W1kQ5Bf9C;<)GpV3lMz)`PUK95Q`ZL&-?(WpC7KC2f(wVG^ILFrY
zUu_P<yRn(DeUrNgxM6Hr-91fs|H-u9tbMjegS5ihBHny%+4a4-YWYCWG3&kRr28!U
z)75GGAvCezJqv|;!hP!bS?H@_JhV?mienq9XV%gM+u<~OGS3`Sgq^Fam-k458BAGN
zvvR3?uL?NJpJIL6UkLn~37$xd5se8)BAFTYpy!Wj5g2@)yrcrNu{VXc!Dm^UF16!D
z2fi^|4T6H*PE|Dml-{&Fi38~|lg|Eh3|>TAMg57hfRg{?3M(K0hvc4B*5!woDvHZ^
z`$VY!uPew4K?*bmTBr6nXQ}gPzd5ilUvuu~3K_J%+-|-q;S*hJ;vquj4g81^<023K
zQE`1f@(1@3m}YU8i3kgXW_>;T#P+MKk5eJ})nrR;@z&L~n{%w6lBoqH-d~7sq(*Gk
z1<&%vbvP|2h$1Ql%r#s#@MPa3FTK+EF>61Twf>4(MoJ*B+p-1^2*O1>by#KIjqO>z
zd@;D#A10M&>uSe;Ev6eREnCfHzS6|;z{)ma#SpgspOMO*j4j#FAr-4qfWOt=XQ2R|
z=cz0a+#k)~<|D>EyqXVN&AR-aQa!MJG<2+g&CC#*g*GW)x;QmDGgk!rrk<zN{Wh!X
z>a6Av8qDCxF3@ELfBSCCmFUroQ+8#GOxTHy1vvs5N_bh}8DLe&T4_KvA)}@{5Yt&g
zWHV3Oiw@FuBRvlh_$U6?{&bUW1yu;UbOC$$j_}%6exEDFAD`x}!!@M^XhxHCTjg2D
zBSHz)?oAB;%naGXB3^5X)c(3zv7zT*t|BQhD!k(St&k5J3^*<5U<!~I>m=j%nB~th
zA8}$ovSV6&x}W*AXz%&G4rXbwSFbA-ZRRsJChJo*Z1Py8+JsfegM%5kBU!jUnRi=C
zi$85BrzAg0!65H{8frRfgRkd!KP`3*EFf6)zYVYU80xVv<NDsz))a<{l@=HKffCdY
zvEOW=d4lcDpASec`rDL&M<R2l%&cO~L;sVOPPK>=nw^nTpgKcBkV5L>=)mV!v(}}^
zg*RR)ugsWtbAyp9SqNcUr!Om~$}!Rxhv%wJ=3nB3?LHlQz#g`~euVa#s%*qc9V#60
z+0n&3d*Vax^wfzEOL0PI&e6xSVX<XZ6^5X0YoD|vQE(_b=LaAp<C2I;gq;(osg_O+
zZDIrjNU$;ua82)poAr7^kGs6I6~Jx6!t8AkZUc!7>uuC`y59I3jCCe#2~lyb*K%Vn
zd<X_Q#8zDCxLuE$rv`sHH;%uQl7MSta-Bu_h}C0h%<>t#<}$RjIx9ly`so~=C;kO$
z5H;My1T<c*3`#dAPgkP{Gw8-5Cg~eO6<%kmc0J+es&57M*U`mXN{*~+6=U;MdDJjj
zC7|W{g2j3uDMXID(4^xm1sX2!&RbfGq}PmCl@3|%3Q}ssm|+w^R=iKzZRILZ7sq#N
zA=w!9gI-sZg52==@et&$BZ!oo%VpkE?7r3x|HQj7ui<v1C<cU@kbhxcQC#V$jYFw!
zOUN75(}n=yrrx~SIp@_J)?Okfm@!*hNsJH|=@nnK%-9AUSagLcrO@}OSg~W0_6Azr
z`_OZI2VZdzF(-Ag15dW)P94bFJ@Qem<~1?Dxb8B>uB*(a^aFKl>aw+pNy^At<2=2o
zZrL$A<5w~VK5rz;4`k>S1)LETy`oDXcYm}0DjOv!jU<;fcZYtALUt?~aOUsSqr%FA
zd-wUnpakonZUy6s-ak|{4!OF<W43#<h?k4WLpd8$_4uNc!98xmX=bA|>DIA)_5Eta
zET5UNF{P>6JaYyP`F-WCq>!$)GgE(@T{0i6m%SM-A(LMj#_v)LNg@xH>sEk5j6N`G
z&p}m&@kPOy>f3PLnG60vQVht;06$ybY+J`pi@WH&gOLRYfI2?Hsh|*Gc`Pra{O@(I
z2g^zG3MRkcjvN3P!<LNUCDGaI-;z=9yLx!u!(C%i?ma?qgPDsV%VXZ&?~MyGk6qUH
z>O%El#Mu6R9JHaUH&80V4(^lN_Q_fNKmgocFv6FdV6xqqZ#lsNs4AD)9L*>Oc1`-i
zO*7}^-xZoQ39P+3!3Z7JK{w%miZ<R1QYm&9ictefPTXC$hSSU+{ub)49u-x(G>x+N
z0R((oq%d6Ka;$>_hX+sZ2ZK)^aZfkO&D;K4d3K}$XB)oPR8u|YeMX)q;Hpz~<E3|F
zA9Az>+mh{Ths3#6*OhhZo&P<|dL%M)qXAWnWl6FOMdQI6ji3|u>8;d?$uFD|J9olr
zJ#B~fbs&VnJ(Fo<5m74@X{ZxZ?wvN+labI8N~JX$0!xW-QsVsK=ht0*;l7#1RI1Rr
zzA7t#bUJbDXp;@fMXsG}!u_|l=|og5hI;mwh8UL5puFmj9=sN;!M}9Z0zW)udCaj+
zqHA*|p>WOIis$PUnSu458CzG;0s_!rrNImO(5#<-izj~Wp6+MaM^qnn6A}_44vO?1
z%Dw$n=J~#78QgTw`qxbRSnXFbg0D=Xv`FwK;G3uRdyh1xIF|%>E&7D|TsH;lx6^)g
zV-s%Ncb}c1aBxrw`&kAo(q<5^PGp{G`sQ)Xc;3?N;-9fos-mjA`b|xt*a6-cmiJwo
zJ{x|Z8a>^90X+t|$PIV9L&HoQ7wY@o$c$Mo>N_Kw86PY`KcV2m_9r1@D#t<t(<%eg
z$_WIH)T?!GDemsS+XiBWQ4AWgVq8YAKuY&R)Wz?!Q@ypB&)z%*_hB7<E^98iK3KM_
z$4V(Kzkl{jWt7-2tCr_EePuP}IhMjtoIW!U#5n4c7h#poIc=CHe92rj*>NURo$XMC
z+45QyqpYpH>qaPp_L8JG0I~#Ty0rir*x%vzoVlZJ360s$t4p=wE}p!C?HX;QuLh4=
z1CL8|q{eAetYdC%OLOxv23zAejm;!XK9a#nYSwvNnMmgNzTJd+CT$hKLd`lguf~LQ
zyw)EWtIt+mEN=3RZx3Y6Mb{r@{-7;1T=O(dc{+Ea7!sZLlHa`M$&WGICWuRP+vG?%
zZS$z*;Ro|Y!j?(0bqt#PM*g)et9opHaRZ8FzZO}u$P{K!>f4`K{0CB9r{p7<@58&k
zkl^U(%w49~JgA@^U2)QxrrOxPwb-YE@(->bKMxdP24g*y=gF&>E{c8B!EH$PWant&
zX|U<LREdsVu6fJtx@)yZG?j)6(Cpes1&fGGFZb(^<@l%AwNq2?D<|fhxm01qBPg`;
ztZ>7lE{tIMLv2;YFREUGZPw*7N;m6226aAh(G6!tSAyY|pFv*C*r^w(Ysq^1BsP=V
z%$&T6=W3ngCklL(>=d)ffH!QcZ4$*E4R0=I2@~KYiiyrEPh*Wctm_W(Raf{BZ02k_
zLCWDgv3fIw4W^X`thSEoX_)E0a`gVx@S2z`c}+BYI_ot*I1=&3FrR(j#W`VXhhji%
zPn-$MRn5`E(_@1NK!(QO({VD*%;8{pr5&dM_+7gJAH#IW8F|qGq_8}Bk4Yqu&6lE$
z2zOx6o;&!;BXT@xU$1Ycsk_Tx?M>7En08b<VQ<vcQ>^b3MnJg~{#tN^6v;2}6eS*X
z>8L{>3k=e&p0*a8HQ)rfi3rbef-r{m!9x}E1ke<&$z}a2E88;f_`Mb5-qh?613+?k
zbN$0iWnq9>ED=TXOrY<Yvf8T?pK4q1d-h^*1(Qu1TuqPBBzml~=fS2kTni@Ut(24@
zR}M8p);R+rW9IzZyIv=sMWZMe%#5)vz7m+$CeU>QL^$jeo^^5Wm^u~H6aZ_ySi4Ub
zk0l?M7gB81Gy8IqvjBwE^$Foa`<WgD<_zs)6;wZo+s<7uNu75_t}>GxTx;}JZG_YT
z&>+@Ovrcsm@m=uliwg(K|5%P3>SubJem1_sm3p2}UO%7$6i??IU+T*%+dDgaR{J+;
zb<@jZC++}5)0}*G*y<G|%QI3`#qZ`}`cPm>`~~KcAY-uU>J;Bxe&Nvmwt)qj{O?8m
zpsZRSuQ8l+@9ro`IV5>iS>Io|^`3$I!K%0+vl#g|UrlhoL)$%bO7oL`NYQsBEMZwX
zyS9yhM(cZLz`ssQ6a%!ro%s_0e3xvQ<LX$#c{;8(HP6!lSZU!@PR+E2yYg)~z-U2r
zNV?9iz6};nxcTa*gmx!(sU#NUkl3vw98uM4ttuY;(TyMMP79euG(EJo4)$r*KM(xk
zc#CS#>l3|Mv95-bDCMs&X3#nK$8}v#JHL`}V(V^IUL>vLUmu*DLBGwS6B5fJG$4j#
z@e4=^^@x?x#pR28-o{H05~wi_mjqYaE-B)Y1Z)A?Y4@lkUKI(Wejy)ehCsT5K3k&Y
z|BF-kT@eL<Ff@+@aBHUW%4}Ur(7w#0^SI=1OtL${9N>vod*=sF0IK>irf^tSS^SyV
zRxV%IoVP=vsxLjJso31zxXYxv`vO5xthuUNK3(DEYGmHCV*y|lzxo-mTliAEbA6kB
zy;2PU{H5IoMwj~$I467@kn!4)so!`K!*=Q*n0;jWcMe^ggSHA;4ar2yj^0yseup|Z
zE~aeq9Hj{JRab8f>b)ByQ(j|9uq?Y=P7sQlcmcn>`R=NAN=2yd=rQ^-i7UJWEuv~~
z<S>OAFDWXLj7vQ_j0nB$&1`@GEefIq$R|GpH_)U)G@y8}X%Os|0Z69_%WT^(zmRoa
zx2|tY%UOFxK9OC0=!JhFZkyHzqZ5^xpFKQ6vwzo^!jGIRx0_;#A0tl<n#!I0?p7Q3
zj^3H4UMP7*R2?5^L)hWv&nu{7XT4?uD*3!i9PsSYjvYgMvTb2szFgonReQ!9ot$*8
zl0C!v(a<T<)CrhPzNSk1$k@FnqOG_#oVc}fc?Wk*`|4r^g^cQfu9gfj%Q#uQxVq#{
zy0hAaBBwp+39A}V&;r}aO!{z_%-EDpSuOkD+j2qSCD7vkYS51{A0U#6?~akp7w$2w
zi9kJdiYo011_(e=_LSetc3^A!=H>n8ZA)gxfyQjT2iH%*+P#ij>N8)5XC|0paf!rD
z&7LuPMf%x|z0c@%`xiD2$)xBj?b7NQWI>0Q699*{em%45EtpKXN^IDYxu?jvdRElX
zpJ5$27}2+{VHq9dEwtx7LkiGU`(wO`57`r|a#m=ZxZvc#5-_k%iT0eIELiTf067mY
zL_f*D`lvwXtJMyxEg7f@T!}pZxqCEZPZLT$HYC~)yTH-^ReZ2HC93Iq*7z3PSUe;U
zr21lQlJmW}yJyWpj^PrMbV56eCxdvISOU1`%admp>9GnFyK|jC7!9=I2S_ezgG{4O
z58St#PCT&1)oCQ8r-om}1jZXKa8Klxe{$8?<bUW&rZ8^iw}#0G@Z`&;D;)rM{yavd
ztHq$j6ZzCeX30o~aSv*c!@n_4C4Ng7#?{c3hW#x}k9u&m+Up1kJVQ&nzlCE)6XN2M
zf^^gBdp)~>e6FyJ1DaXojR7P4?GyD$x&V>qa9*jzR1c$j9bDlL+rGN;$LefVaubJD
z<YjeZgNq6ycG7h>E52JT`4$-eG#D%M$J6ljOPYL_HN;mxu7!j{GND;d=6h0#T3j*l
zWs#uf*5fm4rO+4?aZeOwb@K@Id;WsyW(hI|z7cMcZz~7vT53o?HqI<ULbv&;D65kA
zkNK0A12Hn(M8q$$(z|<#JhE&%KO{I#yXMyO7Z-Bc*Xm|03e_9JLnW02$V<zp1_>h7
zT<1+)n_+KL_Y|rWW-BA#%b+jWl9lZ`fn20pE%IH&twQoi&C6sqUNdu-niT+ZTbJb?
zfNt82&JWs$d7?QWFn&I8Xs(v0^bY9`wU5emid^=4JwOz|LP0X_g?n$(%8+OT$Fqt1
zODe&Zm8awFeI>GO;dm@r^05iHGEZ#J-eRm68IOGtq~~sRhV(+)?uKt~LhE3!+>HOe
z)@PgB^~)<y*9&ZO`u+*H5;T*m{RnMYColXm@O}?*j(q<Pv{G|L&e1p9&{u#}-pPxA
z>G)yhkEn$IW9lt{qU_%PVT)2gDFNy3?iK+7$)#jTk(TZTC8c3$q`N`7QM$Wp>F!4A
ze|WyXcjld09cP?{-TOZ0I-k0(d&R_aDLt0C7uIg)v)WzWKF{3Oq5oB*xvj<XvccWu
z7Vn`iiUmjksO!t_Twv9oo^v%fxF;O4=o*%c)s{Y~A|<3;_yb`4{dogipFDZf%VtFx
zNIO8HJNh%ZEh+sl+oI9fUK7V`m;XDg$%ojpMxU0xh2J9)7b&-UcSG2G`gaYs^a=;X
zm=xx1K;a=Jk9Z9}Ugh&}P>xRb`2o}m1A5J)0JH&az2WJILDVA$y7^D?J8FNqg1ka0
zwdqF&G&I29&pr8u*NyxdE!j<sy1yaf%jKG6m8pc9i$ooZ%8M`de>A^g7J}>7O?_?K
zE*}SmXeW8_0yR*w&byIO;-xkddf(!6a>T!;i>T22m0(7vs?Qm-nsCBfPI;_mxZR9o
zEKZ4E;4syRCI-+?*|-J!TnQVj7dC<FUxaF^N|U`~z^Py8HEzkiv*NjtPITq0_mk+~
z*|XO?sHU#mMDWbrh9UuNaCPe!^opl)HZJm}i5h9=cMdltF>I1vY!Sc34+Qu;aZc>R
z?0J1AuTk5!O>=W6&&JT{{GS&TYOw$Y|1hAR{h`oj7r#56&#S#SqrT$q5gMaIATYm}
zMlAvRso!4qcKJ{6O4cp(!-^ZjXXq9;IM8fqHFr{PMy2l9=N15+qCr*P;>_bES}bNh
z)p79auzY?4dOovNLdz32K(QN3SkdR3xpo{a5bb%C+siDSsuvF0!^w9_l9Lqn2E!0f
zP@zzCLz(!XfA3o^L16{j#eK8uBeszO6C;qxLFbU=oop<nQbFhO?VG4=K_D3B22-GF
zn1Xj@sh~+W+dQp^i(_Z|wXVmu+w_P5M6{X)0fz%h|8d4msxX5LW^Pd1BWE9Ou@*#@
zRc%vLX%_U17G)T4n=ouNvGNv>$6NA!3fFG-o<E#(uI6oZ<{t|7i3-WK3(?@C=6LC!
zK`t{|k|QQ*1F*VEGO^r{UfVuUZXiyNQZl1sA^;gGm)l3AP#CW!Vfs2BEleEmkU0zQ
zdGeq2;!p`@?x|~<F5M+9(-2VxpZ<Lj<xAJp#qIN-(uf?|W>Z(4w+P_pG(w>B5LT5~
zN>quC@DCY6u0trTnQIbcyYc}d_4mSJYW}}f!gK}fV*yQaSrCshoL<i>$r6%$4~}}D
z7&9%CqSNAz@T0b5?72lKq$XY#_p1Mh?B&0UfM`Mk7^U9%^L*oAibfn}3xPC{SR}Y3
z$mwg^2peP?OLzw4sS%v@K$Q7M(dd%;KYs1>rsH^WDXPv9O&N0C*Acu`?wxP4<`5N<
z!(m|5W5VyUKyDQu4}^mWHf%I8)e$NL37F#AT8XD@2(G{H9msUytw=l#^)%7|1(9D!
zBc<(YjcAwCjSv=*>yH+izv9|zU}u4@*@2$cVV%8_fCE_@Us&YV=7lBT)dI%kR)0$?
zuagUEZpHq)!wEH30|add_{BLHkz=Uri9ho5;)DFjWi)39YzS8+$V9Q1!NldQRY?rc
z(RV_$_ooZZXYCU5lfdr<r1sqIGKaDKj<!@&))=P8jr-25Xm($lr7!%$Y)T)AmRop>
zPGf)SVDhF^Nxy7KyR1kV+ZSrl&i$<`;^aSu6P6Y8rb;&T?&`XkJN5vSsVopXE*;Xw
zU!5Fr>gN-JS82%*z%P1E3TkhNNgqY^w^-YPZECTpMFXQ~jTS=H2eW7H;SYx$Q{Wp=
zadZGV7wm`_X4nX-ZM~=($4HE4I27f5>n=&fY>L=GmFYEi+%MGvdE1Jtoijj}Q(j<E
zy^l0#X7>yk3L~U0##hjaC^XNy>b+u9bKSSN^eC<q0tMAi=Yg;yYHC^B^QXdVIgw%F
zUynz~UyA?TQH)MDBKW#v1-4zHsKyxnZ(9Q{A8);LH|BynQe{j<P6Hfp3l06^of(F)
zEfEr7-@h(^4}xwnl)YjP>dvcVL{H!wL8tezQG)|jQUFDw$lpt0zR`=I3~aQ->|#@h
z>oU1U2ZUE{XmQK~#||{r*EbcX7M6#Q6@sNxWb`HfU2I0W)Jf<caL+#SAfUEA5&6{n
z>sLxJ))i8<xf+bpo(f+F7*Xv73ttxw_WoVBQ$kxoX$2NV&gSqL;q2WP*S}?W)vkBk
z&oS9YC;w!{YjU`@@n%eT?b()gxHk;eFDx(2zLXovscU=s26znl?|>rIZy<vTo`6(k
z*5I1reUv6Gg;(C{Oh2@}!U{mzSDKufP`X}E>=j9}<gkGGhmi2x6I499Z}Q<qmP*5N
z<@JGNg<GGzOmHwQv6uXxGJ*ZSJ$gh4*txQuYmvZQ>c>VR{|t5mL*7J^C2_qsa<JF3
z{&zaRRYJvPFaZ>a!)dfQ!@S6h2&$++xhRirOa;1UX8s-)ZY|EE?Iizr!oP9MUvH>%
zj{_ug4fZm^l6fq;T9x`O{H(P0!Dpa99|^+}_G1X0WMv9HdEL6j{wA$=m%7E}iteKl
z)W4X~%l+<7TY+dX&|s%rlIKYH;+@wm&chmmGppFo8lJ@7<M1${p@IdY^tmiI5+Na;
zYe@Ttn!idlJ(r(LNXgD+LUGCy6HpbExW@0XEk(kRGm&Y|Om7a<-mnK*xd$EOZZ4b9
z_l>RF+#mFh5e~-YH3;bx_ro_Uuzits>;Br@{~g)Pa}yHID?Z@O<POqLB3;rb?ByzG
zZ2n#AVBav8z|>54$g^n3;Ohop>s2m|?#lIFY3eaQq%!|Img1eq`WywCIG}pz%J5SH
z5VGZiG1$>6f8~ssJ6(S~sgZvDM;YgHi_<znA8OZmZlu*XfHMj@eG|d_*iY=T=+>P-
zD5Ys(?ZDH+4@{g}1)spJDkh*B?O6MM*CzK9J9J^G?uX4S>ssksmX*cL@qIZ6CKTyw
z7G5had5C^}v!s~(KWDmfaqKQ}wil3iRP~@|w?gsG#Q<_9kPk(7U0nxafpx?Qr7px@
z<BUo&8bz5WLgRkpi^N2p0|MhVA<PW!p7#FUmSAGIlG8qsf@(7#?^RE#uogS!W^X2N
z<E*PWKaEHcZJkctP4^F{fY^m5p<ebJWys~mv|B}p(Ie`I=?VS5(Ez}?mg9ds|AR^S
zhaRcpiR0BIx-iyAI>8;eS?~axXTTIAkPj#_vi|*Be)#o!l-FV8eOU&{xib3k<(;oT
zm#*FnrXbCHg<U+Cp4k|DM&3Y1k={oyX=j*1fVau8+NGG4)z808VXVZ;xHpXTR6<WT
z@TSS@j#fODQs-SFdGXGzfkjvvyzN|1-WSfmE{$?g@qATKn|RgPQ}IRZ_a6HnV;y>+
z>=+JNZp<?lZYME?DYB-7r1Lyhox%UPbo$IFVYIiCk-07foV{^fVPA=s*f#|rlz}Ya
zB&+78(NTVS&2`p4F3lJ!g*Kn)2$L{Mo;*j@z`qy0fiC7VpGH;9NH$4duG`zh>-#<R
z+#K&iO~j85M_>l5(m1GXe4g2}vgrq|_YrG**+j(z%5!^(Wfi@jUgxbWM{b|t8^&gK
zTHh@9c7e2is^St2h{@GH#Sp8xA@TXf9sz&`YxaOs9-kX@PZ2kl)EBXu7+uW+{olXN
zxbJay5|jL&R3wxC4xnOj{vqXTh&(o8&-RA?jJh_A(zZU3QaXtat>RnFu%X|p^D2X~
zUT&J?mjcH0^jp;6Xg$u1ShtK)Z3x9e40j!KY*$k8FJd&7p?JKPDTDfSvo!4K?1_KN
zVkBbP+m-bm0;T^oy6SyjB%$YwlpcHv0R6G{ySu*<HwiDcf_e@3hk%j-DlJ|$yMY77
z{A{!u*C+puh?tIWif=q<uNz1(71@<g<4sTe1F3^$KI*w;@EWDpd}OiTMnpFhl2ns{
zj8=5RZWXKl2D`id=*!Sf$EED5!>H&kgMNsb=sFQ71MFsH?@{ZESE5W9QAq(O&Pt6@
z3TO%y9Dc4|&5*exs7knOozv|<xB77XH@tSd=t$3FA7VADKM;ZA>AAuS)+R7fUzarX
zxz`-$@tDmSe4&h4pUN3JnFw4>VnkiAIcxu(u;J|aMjHbxJ1^U|@70H}QF|3w{#lEl
zLlCHQAA^?L{?S`~jw3lYT8ts@LB%t@uh1Vl-TT7}a7?&s)CG~8yuYfD2=5Oa<qPIC
zT5u20?SP4wEqD(n@NL5CB=agi(=Tz1t(%9g^ob3f*e@gN;<>*QbK!m3ku$aK>g4yZ
zJj+u%D;;Ln!gq||sekecb<4%ThC}hqMaW~ZIco1VLDVG{=>!hJwLB3IDsh97I`ork
zOEM!WTQc2A?=%KA$U=<rg*+GjZrH$`nwkF%^^>XRO?L&OBLT1ouV!Wm8Jf6v<u@^`
z))ymc+3-3PiTCL|>{`OJZKa1qp&LpStxmDbtG-X~pKl#j;mS%-flW6$E*-Yk>;BC;
z2*?w=*YgKh%Ir%0YrR|LwX_%)G%PQ-5v9Wwq~#Yo=-Hv#n^UhvI%Y<Z0YSdC_XrDG
z_&X<=s-O(%F{1{3EQ7yqpQPdoi_f^*B9+aD0^uR36@c5bXW_s+yfmm|$27iCMf<gj
z;p-N-f-LefVYlS>bm5ZZQwI4MbD9ogBv3YZnUKQ?{zu{U=-v&Xg#cL?c+5xUx3ulA
z#9Ddz%l=9PuJtvO6#_9rhlfv_aKqdt9_(+BZNa`?p2t~K;Dm}s;eblLR;Fygt_-|G
zlX7od1ZT)k5{VZO=QJHRfIKMi0T;)PfhCZaYK9A@)#iUuUvt2sc}a^;2WS8U_(2}H
zRwM|=hSIGnDna!f?^_h6BefC|%&${$hw$Z$d1FN5R4G#`XBL6E+J5(xkp~U!)8gs7
zA@mSsc1C-sVcisYkp7NkIBC#DB@$eI;Yv0KxM+{*8hIRl&;=zPxT2j0YmanKkQsOx
zM2WSqd5Qn11%shezg0X-xs{!twZA8nth@!FkUEH>{)ZUH7IC+pA`oQf?rZ;ng6)j_
z(!WE5_a9@6=N2Of3elKVXjx4;1L?p|-lyJJWJhj3rm`SvOil-1pcmX3UA$zn++XTJ
z{^@y6jC1a==n%>+#|&2SE~m!_DFA-5SX%NZj_WKD{Vc5qes&C<EwAQ^mP>RTVlJMv
zVU(xm4WlMN&hh$nPjv{BmW+2#Z_O>jNQ!ha*XzP>Tfvn=?B{G@cStlw>I4-SXhk(m
zuayhJ7^P7)@!#o$C%UnQ6Sc1P?ZyehO-Jv<>;HhrlHXsHSU0BorP&4$0<!rHS%%E(
zRH%eDTAmODq^<y*j*CPMaBO1HPrGR$T3A2OF2R@SIxz&wH30X!>p+!%N-?m#f*eqh
zEi|vRY(qnlPWLX?Rv8p9bK@BO1e6r!{<Kfzpvr_(9QV8h;t-h(CY`EeoT^g6;C3tP
zbE8CXh|ZdUJP7w5^TMCZeSu0rT%MN)yTR8w%2fEus&x2tz|csG(fcFC_Qi--^PL`N
zjDGhg_S|tAR)%AF1L=>kup$X<HQq#qOlfxT^M2c>_-~di+nd%3@i$8@>|=BuQ`D9D
zuQ{k0CS>U8(e?N_s`2#X@duPs0X!8@E|J47aZ;b~BJ2`^7!LLg%$r;quvK}S07WW%
znTcuZddAB{b6)VnZWIw~x?$pwn(l3CLy8VSAJbx%um7R|iW)tDT|jB&M$&u7IP#QZ
zpgsx{lsh=e3Nj1oAztHW1AHh9cG=8$ny@Sul4A>u%d%k$5Z;*F<F*v>@hX*mFVE9s
zf|#im3;Y35jyAjJSh6{%*l4eyu!{*BixwCqNH2l?5w;mHZS8t_-jr>S1rk^wjdU#Z
zVH!gkrWnEdnYT4hb;a4po8wwcHpgF)c=Y{SaI7)^Z$oGHN|$YH|6qIKX}QA7G?cwB
z0EnnT{@l{H!rlqBn8dj@ltgL#uFM5<(w-GO*0Cgp(8q^Y<fqet7#Q`aU-78%@&T&E
zx|HR2in^yOyg3ImMRP=pv+65tv-Ci02I7)+>r&)74hObhh!F@`fXLgrxLyQB9eZXz
zqjJLNkGk$Cs)Wj%Q(2cJyKFXL9@luVR}PD{9;vg@oP%JljC}xOfzS*hr9D&+3^4&w
zxlKgstMOq<F(X8oyR{da7A&7(@%?N0ZbBth1($-tQc`;X;klK4?xh}O+iqgB>voYa
zAt%KPu{RRa=|c;`8h{Sx^T#HhsR9{CZfIFE7`JY|=xB8U3W|eHS<O>W&FuIRdu?cy
z*JSi1U5vhj^vFI{Uex80M2Cqow8@AmgJF+`ZQBQ~e1Q86p~+HW9b8)9_|o{0)44mW
zT}w9M1C5ySKj82Ls1(`|XBX#pJcJ-nIQ=7>z^_t}=2`@v{?!QtAm!j7$H%MpzR&I`
z;|UF_HDE+R)@|Qe0R*pwr?M@+Ol+s5`Xn72RXMTCl1)w3o09?Hno`im5h)0#5^#=s
zWPeoVL`|TU14?XiH);f#bQb~tCZlPh5#izuB>D#=`szbqsui7SR0_rgEr1xu*|SuC
z<5hp4c2WHN(8}8h1P5N1CPV2@&!9m;<UO>unBz*6_#kSS&z}SG9E_s{@@hP^TRkmE
z{hTffl)1mMxQN8mr1Ldk+J%%*FQiCu*fmVa0jO6kyf!e)C3d*!*`?htt_Ha-ry1*d
z@TG~a&OW5F0vUF|eFU$#g+-NbCN(i5VhnZ{qvp_S6qIDdKFfl{g7;Q}LPBGr`x~{(
zLgV2N`XI_vC!>@NTpEQ@-u3y@u(l23nl#PJs>Ov-13%;5RaxVp+t&8LWR~}zax{&(
zR{u03RV4O2oGZ6@6Cj9>40=z)qF;3L1gPve0e<)5KCHZmNkWVR$J1uzg)SanzZEgR
zWXJaK5n%}@kBKYye_4?cG{M9auvV^YMuU07Rw)Ibu@EW*8P(taQtQeS$P4jhvrbVp
z0qH{ZQS+}XQ09ce1IZ*Wjk|k~fF9t*@05~liRBbG10PEue>{3W;XLPjG`$)C!WNy*
zW(~<J;TqwLv7Z#5z*&0^<Dztj(f8$b$E$6`rb^oQ620IQ`sHs{G5ea{0zILu##=_(
zv~n)h$P7vPJ=;%;)~%24Z7OaVQD~`uP>ZRJ82E+c=+nOgtAbnk?vGUBQwq7oGN8SG
zJ%29Kx;V`^Fk#?V8M`-CtGko*qS_V2EI=kCMkiQ)Y2;XYrz8~XpZzUmS}jxuuLDDm
zkmhN}eHx)^Eacx07F8G<c1(zox#2G(5Ei$Da4Yqcy=IUBMe<uG#iD?l42%+Wy>p3F
zsywe#$pz%ifNKtbZtP)sGk)W_Q2h_dH<DL+FWO0e<0LK2r`BgEvML#<CWjcYni$e<
zQ3H$!Hjm%^aAH%xJB%t&3@NW=+Q`Lh283Bej`DamBZqN-k3a()NkMD~;U!X$xky^A
z3o)Sr9IqYX;0mr%qotCQn@W=9$@Q7`H%s<u^HXXK*^u!eWKhzh3nJAVPW(H*Jbdg)
zmyHC~e?)~DMLzgY&aD$XxO)IKC*y#Ai{(5H!afG1K9iLyj7Kgm3b?pl++J8)%bmy_
z9aaF+^*oD6Tem$v!<{q26W=UB*6eTU1)Wm#U4gB`YO&)Rh8i$uXNsF6qhpKvs=76W
zd$UtG&nJrPfoBqQbQoB~==gz2Mz9IktEH^9riXWzx`%EplQk^NP1iATS(>_b+sxr^
zgmkcWgPcF&)I%KW$G<L)i*GKYQcDyLGUxUsp{}rt9MbtWV?$vrLzcj8$}mxvH4HK*
zzO-~gZ9K+bxIJ4ST{x?gy=M}Rc^%|Vax<yIIT-yhp(hrPo#WE;`y-HV|8MD04GcS9
z<ED`7%0`iNr+v#%*|e!l7@=Ia`b#nQc6qs$FPI5sBWUVYv<^dk+CpCdTn+;kjVMdc
zkA^mc^Orzx{+cV@=XB&W@-U^M0!#<|a`uey>_<PH>9N)|7{tHR{Wq}*?%1Q03t-X8
zM!(B)&#*P<WhojvBfK@)^s$#!U6-Xpp%wo0%R&<N5E>B)GLL~g7WcyU>N!P~=Pjd?
z`UlvAp;kL)MDWVSfz*YP+4moIkfyS=5oWBkjbWnhyLMLwv4;cDrcv#bq5a9{H3x;7
zslU#C7wMTww%u{-=H|g^ZslQ9;l)!nJeGSknsZ1UByPkJmDre)!lKU3|3#KTgyAtK
z@<elo`+B!S2Dq1DBxbbqz^Dek935V`k@Yw=&&l=R>@O`-mSfM;cc}z|U9zqrL+B|T
z;m=&t`xJPDzjTz?6jyxUsXWen0(J|IPl%BXCC6aA>c%S{h0J-Xy9IQi$p!u?0S2wz
zlHsG-B7TSY;kHnB%J(rij2&r3n{+$S6b54bX-2jf;@OE)GbEvRIsr91aq4zED)We3
zrJ(>LM}{*On!rANtm^(ohZrIlFqVn>4ncl1w`QS}B7}nf$AIR!4C5I+;~W8ai_Y4r
zBw0>|J{{uNHb#zeThgEchk0yS^#1v_j>9+i@x;wJGpq8Q@q;U;%@Yp7o{-~-NL<#M
zy1luXqeSysInT!9r@QjW1#?-r^-?fd4K}<QM0{=;chfD?TiW+=sv{@jZ-}1(=x|ZR
z8}!?ac_CJ=X_OijM(1sVYV@f~79TYfcjRoXm{0;k?+pZ6vN|j5IJHn;m`%%`y)2l$
zOxQkbCcvnzOB1D#zD+-%5kM<@uoB~MtB&uZ#pcnsQ2FQeRy9##6|-a4-ztxCKWv{>
ziK6JR3~Iw6NW6L1ZHy|2B4|pDS<KXiDG+vKu_M+g`J0nfRqg*E!Mq~dmEqFr>bmsK
z>X(Y7L*I}xL}kAoZ}WKic&kAL_FxDDnT)jM89>h(5)ZV7nLr)jTWF6U*<aTq?BZ-<
zHj_`@T~G}(qV6`s-y1eu$geQ?TsNF(Jdn=;*UrSP2hWbBr^5@9*Wh9^KvPwMnSGyY
zkIn!Gs5^7zhPq8bzr$4gVadpufXY0z<=V1D&!x455-Uz}{UTXu_K0DO+OSw8CAf>7
z+&%`5TcZ~iMhy($w&7~nfj6j@O0?|)>g9=@)<d6I1XDsS{}xm*_u(UX2!;H5?qOXD
zKm{4!{dD|-=9b*eVhtO53$!ygssL~hL1!~0QXa9PNYz<-(@EyZoR+moyFKG(gynDJ
zOM*~&%gj|HhZmrUAFP9IZis<SAkq8rpadG?wCXS1G`wu<7D?si6I_f?07BqXo#@&I
z(ydCUu0LeJNVzX-Qgn!kMF+0Q-lXQKfEV9r;C*BqvOKyk{Cs`j<?3VEM|~vLN@}n(
zjU1p5e){WS59gB@-;-x7S!0#geefH)SDz>A?nl_uNxUibvQa&c54{poZ;Io7X2ypv
zrmVI+e0~V5U?I}8uKc5LzvGdVB8e@2I}g9ZmK>BnT4BhIh$f&Jm+xC%5wN>G(>%1h
zzC(yD{p@`3ismZR>)*>UnvXqeu!i~+f??Cy+lGhJRE!s7EbiObB#n-t>oYHZ;M$($
zqv+gU=Q>~5b<thaG)>u<nA>0ZJWRpM*lR=`iUS#C)J=Upd)^_033L4&V<B<7V)?Ir
zfx^ZjVbh;Drq?_Ml04;whM)z(rbIBPst;x4wGxlLiL-^;9=%t^#ap<JTT~95D#VIu
z_hR*pz=_Efk*&r%nYz=oc2@L!H=_GF884{`i)Haeq6hAu6!YD=+fGlNb8Y<Ewjnx<
z$xEL*b&LeLYKu32Z;ZPXItGg9Uen1mp?P0jcrY(?cZIrxjb1<Z-Lm|(hG;konvmU)
zXPf2L$PxeT{jJkg9@kKTa*M^6VqE^S4*`i&D@~oM_qGx%X8J64{2~LN{Zm`ajA*`R
zZ-LSgW=PXxYRdm36w7rwU9!Vs368DONa9dBkbUv2Mc@*w$imclD>i4y`>{jY-%WoA
z&V!SBNLFNghL$7+UYES`F5>{je$T8K_h?a}bhyNc@2*vkIvhQ!H~xj^Ps?w2j2#3{
zh%C(lL$~Xy8t25yUH;d5EXiWAR4aIdbF1A6D5x@R``0f#-+N@D*~sdV_F3J<>Hc+a
z=MN>06H!kqSK7Q9QwBTRKc<KxhMU*jHbkX!Z7<j8D*RzXKs{f;Lod*DqJi{B0{c~K
zsi02=Jtwz@N-Tl<<*pSwCq$fsYZO09=5XM2Fr3+LZSRG#j$lXvJF?H4+|A>`a25>b
zr){fLL1KKU%5KPRy8oR5qSHgSv}?(sR7P`7%mPhu|5@siFdf$$#<c09*?w}!sYcPX
zDk>E8H{zeTCO#DkC#RFbw0|B@4bR-EikA;(wM3gguA_y8<Zltmhr^~u&z{8vj+44D
z4WvQ;sMw=IL8(p}279%3I8lG5Wc0)h6x+o-?Uk7ow$TC!9T~WdwkNiAT~m9&!0v6@
z3A1XAgsiMu6<!76<BR<jo^APH79}4_1lK?OD1~)n-e}_HT{F=7<4I_nUD19y1z-JS
zoDd6dQ?f_TmVEp~U*EDB5XnJ+>bLM`W1&;^n`N*=&EJO5!to~VsC+X2e+hn0Ff}IX
zF)??j%Uc2K<5fU9ti@8{zaG$c<$ZLv_VzlOrLnv0pZ$_ambm|V&P8we{5vegkXooy
zmYVMQXG6cA@%~fk+fFXIo_>jQ8{lM7I-PCMX(2_P1CCQ`^IJa*20H@Ug8n7-NIMo1
z!!KD+Fl(y=HeYOYhAz#nR5>s=as^XLhseJ^x-J#+$te_v$m(ax(d%by)2HlXA!0OD
zgS(5}i?4IrYwFIEre=EFdC5{XUTMnXnwMCPqc|=Xntn_!wknYm9(okla>;Qf@Zxd>
zZ!aY{r!cF6IyXh6f7tm)RmVG#>q)oU36jR%&Tmoa$Cx?!752rg0wT@bR`-K(_#&L$
z-75G~$0jPX?yFw^*o=D9su#&Mr2-$@Odh3dEHL}nn|H<5&L>94tScOzv?P?k%$iJh
z(3fJjpB8|Npta4Y*ZodHsIRUSmBJ_?e;hbZ<kFaEAZ>0@KCEdx%?M$)b#mt}r_Ai5
zAKTVD(MYshvZnU>NmkLl+>eaUC85D~oblcAONGg2P|bN>ZoS~%Pm`o6%jcE*IKa-w
z<T2+!RjSZEF^EZ0waEuh6#MugjtepLnIy+*Qoo!HFUKbhE@?Vy$E_7#Vl(+ruG~R$
zr<lwHwvWXp+PcZ{@j6>&!-Yo`J1*aJ0H?v@4kjE3IW<4VldM?H!p4%}%5$^W(fOsb
zWvi``4i@xb@yIJ8BZ0!L@{iI(&uU1<ztT(hoPCdMS>M#zIxU`<GI1ty6(HgE96Jp(
z`A78Db+=Ku<-;%w5(#@SfE=eEj$Z_fW`bC`cz=+#;Xr<c(UiK)H}~O2dFKE|MbS4G
zVUOoXqETMs)%uv0^C>_4-e)Slp|<tNAi-F~De1@WXX}xI<?gGLHO>ynW+cqVy0=p;
zt<&j$i@&6j%U}oC)(DXi3-fi3r3(2M<mV;!=4EquI!E*>CD#QrNMRbhYB<!6XUK6m
zj!}*`eGZMpPoZUVG>HgIAbYpVw82u0DT!eg%(cN%dff03-XhMSf-ONE7S$Y)oFiAN
zU(u|hZ(lE)C^^Tf`M>($TnWy2baxO$3w_Mehbt8F14Ri01kpD?-LNJh_c`KdPvWu3
zxEo&aHFKUZ@-g|*)6tHG_WY$1>PtVP9l{Ae_hN=~z5hm!*ur(*JNd#uPAQTKUp00n
z$;F(G-#;UAiUa$ck>x`Es8r;i2mcQ-*?ui6z`odH-z_;-b?aacgHpde8Xk3G_@$eX
zJ^9^+Q`kK{lu6<f8*G1HL6f<?Cwf1BoE1Wd(N30FWO+A`><syHIk~tDj)KW#ei(>-
zBzU>(9kQC^(CuDprp%>5004~_6l^c7dUXZ)^T8@P7QQaRbQhr;D$*wFYJbTx?*VlA
z!{VlafMUMJZpkRskHzc{6TjhU=4(A>+mr%T50_Yzq?ty6bY?$EEE|Uo2R#S`?1drk
zSdd#6AB8SmW$c8=9?X(`JtwV@XnDdeEmx}_I~q|Z)+q@btMPZJtz{z9?UnZSVog-v
z^UmDJEYVG8{?*ZEZqviWTgJscLU0TusF6QpY~9O?mnSjm#zwKc3@S*Y1%JKy$R_#*
z(;owZCyLsYnnJED<*~xh)~%B8_cwVWSveMPQ~~5mu?K05s;QjinX?aGUExDJ)Esr}
z_yg~wVvx%GE?Gh-u%$Pg9lZm`-%wG^y}n=gCkKsOyKkw!6oSG?ixYcV4l(nTBNQnU
zV2`L@7TOitSZuqcv$c5qo2jL*elBg>$)+_+VKw~>xvK)J=RGb|?C#3*&?=~RP$!%e
z{ZUOn;Qsj&Z}>DMkqTTsurSi+>vg$P<ERT!FKDDc&r_q7icMHRE(I#@h)oB8M%;l!
z79#d`AFV(K=At=Xj`~Xiap0M0hxpC(5vi(@;@5<XNW)>Nl$#9gzs-HS6v(Z2|2cP2
zI0-$OZL<BS$D^Nztd|F%Z%d0$??gOajj?yfjNV2)+)Y(K3$h`ksp^#aeipd2ybqG}
z*qv|eGF^@ag6kAO#!#ZiU`MlhbHl4snpK%c<$kf{iats*AoAbS?tMX||07I2k9jBX
z{5F5%!*BJcAVt}cPG?(x{iNFR&_E^lvww;qJC`rn;Xvqla;(#4B`1V13c}=?E>o(T
zXpY1@uXoj5puGCcI8bNH5)I2G-QGL*ghM^(I52I?vcpF9jbD=0K>5b_(|Gw%Ye9jY
z?~xA%!zcOxF@r5+lg=eMU^a3j0M5?Id4A=fu#9dek6Rs(bY~5#orTW!?j^~h0R|>7
zF9$!q2Hj8jTc`;L^6NQymo%cUK;xj`e5McSo+5Tf(cqMcihxvkdwNu+;7uLYZSlkH
zX|$xRmZuf*RGp2aqd|FpdnDQ7)uIb?lYrzK-@EeVc*o3uu~TH9qu8<g+jTBs_q%tZ
zUQc@eDJ4&IJW`qCHlMYigd11%{g2^Jp6-FOuED%P`6b*?&7$A+id4FTtd7nRqhDf2
z6~kKJ$2xi1CcM^ZaqJUT*DV;!b42#pl7~b8kEqaecNqDlmJBQh2$beTQU#8vgbksR
zkhg?C2Tg5JN~qw7r`@`|OuqF5Jx3Z<tTB|4WaM;l&0|id1ycsUKa&Mfs7RA#YJ_O4
zyIqLQ(+Swu_}7}Ff57Js4oO(IK$~GRNG^|TpxQ0Pnl9oy7m&~NjA*1yBjB&}SyVIH
zEQ5X-XSCS8&Wg@Ly<3GQfL0Kp$aH}DAb1dMi!_s$3)P_+-M*sY)K=-gTt$KpJK=GX
zCn3b|vg#)d9GZK3=Mf7E-bk<kcBn@xqemK*bag{D2rf&nZSsU4ee*9_&#+cxj_fEF
zL)Ib!8VdL;6CPJzQK`bkj!XBw5*dpo34Y_{S>lAom}r(LM)>73dImJx4$dFAWzAZ-
zs=H~w-p#lNX_5KqZDS)<0Q{f`wM_f=(kBz)Nh|AD{cO?ZB(h|#NE}mL?t!=eyQIX8
zd8vP^Ce1je@(*hjlEg<vew(O=<l5o&-ZxRI{CloqtMSq!yd2Bw?ME_C!W9W&J;G&4
zGBylIOU+kzWdvoKGLh=i)rQ5*Lj-1~7D?GgE+~JdhGzDp8>kCO!yRaM#rv-S@VAHV
zsU9St%v`u}-W@RgZ5v2i%*=~^x$=hP3=E$FmlQiHq`ryx1kgKGWuBP7U{$8=!7Bnt
zBVHWoJRBf^Bgyuzl|6`_f`Pq0-FBz0?RHY+fxd1uv>}G2(Kbk5LE)I@;ozq6vV!4u
z{qP}#HYCCjpF#g92JRlo^6>9fyG;nAw26PvAripExA2Gc!<AWLJ-lN-U6<H|F@4mK
zwMeT^r@AQ%OA7Z3ucy^5h6^0kYs&{`KO~!N#&y3PMGeEfp76SLImza%Pf!2$5)v;P
zb)Wfg-%!M)f^r)nM$>iW_HbKBC?o(bv-v}CY0?J3^!I!4hX|5~jt2KTuPgBTD5NpP
zRuNJjR-`}XBL3{ieQbOJa!cU)W5)W|t5B}R(&9IJtZAS@3Fzm*7Z8WQ;Xe0_9e<Q$
zvyiX}zg-b+xb1404^=Ezt5@@Ey+CjJ^A|<io3}L__D5}$XM}3js4jxYwbF+eR2Vfh
z#52Lf%1hlfx8=}3>p51XO+E0Urcm4cUzhIgBKAQf3&^zpz=M*ke>z`@$t4ZTcqj1O
zF=oHZQnk~h!zn0=P-DV2^}0a7@$CvkmP5WtET9uSAH|?HLgYK{w`ZRgk5%OIi_B-w
zR5r9<?VMBR;k50*9`d+<F~G6P$<5zxgBd-B8k1>E10&5?#p-&4h><z=Jjuh<-<?lx
ziH2%aGBq(xFi8@&uBo(Z*TFgDc@G9f`;48M@YHt)h3I|T%8{qGg1j39q6p*-h98?+
z=i2yb03Ke?*tavllfi+RzuK0?-Z^<PP$_Rp+x1G9U!rg^dtnPxLV9dVR=A_R|4k6R
z6~n~;5gKQ~D!~9Ao>+A!egSmqXP^@~VTCm+p|$xzr;hJV-CJl*jpyvQSls`#CdOGD
zdU+qqtzneCtQx+wUix>KbRAD%n41o{VI%?KbJK^?{`!sQf)@qGEBlkD$E3!1lD^_s
zNad<Zw}JiL_X1xu!(+iI2^pe7e(m!gw6ip6JnGH2cxWo1%S-IYZMNMA^8#$;2LUCT
zm(L>(OSx&427h|om|J+`*H3lbHd4IeUJ$tX>PhjNotznmEu6|k=<VR;3>teL&kMyp
z_DO@6Ae7sO5p8HA*UYYHZb6$#G7e`j=3~Mj_J#E>amao^Wc3g_cuX)gT+1cK5X?8v
z4GZz5>;d^1HMvMtWdqJv+Dag=sH%h<XmYK+GTb(2LwdRV@dBGp`a^^hAG>HwwB+2^
zZSKOwgGs4juSN1KTIAP>;2Zs)9zaU?gsZ0O+%fd9R4aS`(A|4KEy0K#wA`5bmM3^V
z(X4&A1LVzWlG&!NNeV9@OEs9~wNRVAt1s3Jojp_{O4T5rBo+p{U*G?;(enG@`L5-2
zmXpIeV&#!2c5Ug_P<MdONf)m<58O(-NHaBRUOe$K+%pU_=;Vt{e!nR3g$XQK?5H#D
zo3{s4Vw2K6HL*N%={JGwTLLI65tdtTguQJoM4d<fi{AY2Bex3UVt~e5&=4?eEh0>6
z;0F9)kY>Ukn4W4=C-%(~u{WH^=a|#Z#^p7r#HKKc%$%_?8r3Hp2uqjhr9pHB^<>@Y
z21jzPkDJrbgJBrA9W;OH1rW<`>2=Sh#8~f^2W4+*iVo9;Nik3x3U!V2<DEPukk9D-
z1jC^(?3NO5Kl>1;vt+(|EQ(EiM?&(~_Z#?tf>2|O{{adh%RQ$J`Fd}E(58*{b>^)9
z4{s_7-)%br7FmLp*6A$cCAWGd!xPyY#Ou0cT<3guz`nhvx<DA0r_APqmF6x1>xpcZ
zKS&P<*qeTQS|}e%R`JJ|tI`;u&a@*7s9+|hjorE6n5*Xsa=ak615iM0vODiBbfOhS
z8_2lz%DH*QQRNSAd$pEZ<px$u{+EN~I4_p(1zn6WMW3L`Y<AC}+;==2A6lQ(Z42o(
z=P($YynQ&*y(iBP`MufqI5+~lQV0ng<AALKg6)sJK_WU)hM+xZL@PnrPjCErY*jVx
z*RPG;E!o&=G1#&l@0SmJUVq-Bf92?>vt%g{FJJ(|%1^{5ttnDz!<=(H5oql3i5W6_
zcWBtjoWwvUC3IQb@?}+~ZGO|As==4-M+k?e>;-=LTXPy}gfv*GJORssFJYAFQtW_S
ze*My1)A_a3o7oId_vo)_46`)ExQ{bDlui>tK^=SLw21j0^s<2D&2nG`A86+oexe^B
zeEEJdJ?~{~!BH>V^Zp0p|5r$Esh$!~gRVMD)%ZisX=_K}5Q#Wd#A4Ld?PpjCt;~`R
zgyuGcm$@A9?%Cj*2NCk?1tU@myOu5xmJVPPP%Uv%tA6G)2N~z^wUPQ*Wu1{Ve*MWf
zkQM#9b!iMxPqC4IW2sT-KYwYy?c%8pyti_IHt9zwL>d^4W`d8;urHyu|1OBK0-)#>
zJbaWokvu~?6gHk`KiSyy2rY!HwADtkBys5hLboxCh=uEeukJt9UXHe-Ltr04bshU<
zZ=?Ael2CzVaEFfJTtXIrGAaMR?Yt-UINIdw3OE3_BUP7qbq&Av1QUBtUWW_!jc8p5
zqEbJ@15;d}<b^rIhBz!Q)j@aK<jyYk8DlvmWV~F{3x3j2#OJVBq`MY6E3x5f_NEI2
z1zJMy-TjM{N9}G$w`2h89aJbJDL1!Lyqvw&9eiM>v5g`ek_VDM&{$=mZGnRG!@0{2
z`L0Z{$!OlRX=#R6bE~Ohk<kK0GOIFeLtp6mE0R^|Eq(kJ`5$UtwRGjrbJEx;0|pO}
zHG4rIE&}Ml7uXs>F@LA?OJ*OTK3(ji+_BO&HcPC+!AvupPJ7bXa0?37kk5w0Ev>=K
z%u-9knPj6P|6jZ8RoPts5yQ~<c!ylk4vVAE_0)2c&;Nw5I~3oFIu8S<WEw{Vxz5%h
z)UhjjLHgaAMowpsK7~3RQQy3dM$?grIHX-NPR-Pbkbl7~?m6}eU63C(mcE3&HX*k!
z5(DxFL6No57*$uH*CNRH#QhN3EIdYINOV&jwuX*HS@~?%f(>$8gV**rm)}U_vvsA!
zugg72L3EFWUJyitB{7)b%b+olnVZ3!SKHfUQxpd5LjyxT9X#^fU*Sd3=a8rfAgk+D
zw1XOJmTU+#`-%KxwL44(#~AO}q*aQq{GQ>7@C_xiNK$mVT|P?fjCCid6TzicDnLo)
zy}$QfSguv<s6cJLP2UlF!6-*w3C8ZDp-RlXv;}y9rp)wOs6YoxhWlqxgOgZv1SlM<
z`JyQdM4QR~48Q683Yz<~xAg)dwP2=C&mRlBb$SDOh>--&wh)Eh?!6SnX17FJ60aFL
z2wwRa+k)@A2ef&JNCR6C1wh-|PRBQ6MZ2EAu66u)zTvXr5G7DnSXUI)6#?nK?*4rO
z!J!NkM!OBAE)tdB$cf)C0pd=de9Wt27jIsJ>WU!h!uEE~TXeb7K5uPNiH-bL4B>AB
zW9Y7Po?bw?wj*aJ-3!{iy6xeCFYi>nj4LU5%F3U#>2=d`??T-rL!MSUgrL_x)pE=o
zS6X6cQEfZa;`MLu#gMSj0Q`RTQREf04%;0wxwu+*xZ-#lx5KH)t$V#<n&SBlHsrN2
zoq~W3cd<%ox!S#~b2dbqLOb|Z<JZ{1@^H(i<9-kUc3HdTXNMY{MWKA$ZLsf(YrP_V
zi-m)92N;A{SahLr=E!F7fxJgv5XNwN`==etBMC-@0#)Km{`K)0kd%7PzRazQ40_?>
zqsXxRT=~fwcC`9sm-b=iM+G5W*s{da&jNjOFKIt0@!z^{^SUsFhP2mA>KJ#FD4lDl
zG`&6KE?Kn0?_yugQavqsu0|>SA&yhtfCirj33=r^xP~Q8kIBF_TVor|xnF9s{sSwM
zZbz%FykFC627%6IHC4JKPArQ3B|zFJ8yCUcS?-qhT8C>+Tfe8oHeV>5*$gizjLs}i
zi9O+;@_H25P12%$r0{4DIvI8eioX0?&Nrtwr*OmShF<?UgEotkv7La_d8GHB*j#?w
zd+QQB5I$`5PMJDAnvukm82E2|X`&frx=*5RvX!P=)TT7F8q0f6K1FFX1(Wz{)mD1%
z|8xJ>fgd9D@|z6Im$A={+YsVh?yJ|Wdw-7P3u#{#^N|h1l_-P0@f8|*<qo>;NwmE{
zZ>R&97qWMBz|(vn9%JC?azeS;tH0tt<-{p4m=@Wk$obY4hq(sV)R}0$yDjt?Ht2!1
zr#=%!3~_HUa84AZ7>XHG8tt+Q_*jIg`_9w<c>IZ(rO#<7v_L1g9-gy*iM$fQ8U#wC
zsv0={p-dg$BRBI~QGqOU!i`vKQvOLz=D1Klb)93q0@T6IAZ7iI5{S(%Z+bX^3sB1$
zd$Mq_WJaV5-zsmD0XcIBJB-aJ#;W0#HZ0$T34FA{nhkL0fBwvar?Lm>-_lOM^aR@y
zFTlK(43phfgabl;4L=?yH5Q9gZ@9az$TD`Rx5k!+LCYB$wHst79>s#%bdcUsFaKMn
zYB1b=x_x5WSuC0}))pN?NSFJG#oF=K6~((u=+VDcAVmrMDm<|CK30B;Ds06wb0?nk
z=Mf0D9S3GK;CvPY!Pd@8F?W%68xK@5F;zp<yFs}!5*i>w`C>Gs1Y}5UB?grgy2WDD
zYB#0yb$<LMKh?2qj6S)eEvrm1E0I5yoTbG7d>yr|&4sW_;a#L;&*mSSXSby7r;bif
zX#^KDXj{)e4C-o8ztmTX9ehtG_WLNWMi$IPp${Q%<;}r$27M=B1`OzIs+%qvK5^nH
zR*S;{LydY`-vm@pefJ<yiKYw;F@ms{ha?)FXato<&W$+$RT0YNM{vDX1*8~=&9Ad(
z0hV7fd+Gf%*!0lYzs0&#JBI+L0)HX{#~z<O7`*ePMr`HRR_<mBBb7puMvgoeiwxSY
z1NlJ60;bk2E$Pn>s1hKkS6(0i8Djq$!<UF}JWNY!u{xnli4TqCh2iUu(`R<G`yIS9
z?Pyi9-y6=xtq1p-p3Yzb+jN35H<vFK-?*F6mQx^%4qi7a`{6?jHtO}g7)sBV7y*&e
zteULBgj+KIkY^Tf>do=|TC}}ku~^E{pdJI)pOA`vyN*?ZDs0mZgLX#9B|lKj_?Vh#
zu&NM5YhyskX~mLKHN5Zfx_~|t$=bY{26h92JwJ1Bp98a&)^cvCZnnlQh|hcEwX&}K
zyG4v+E<M>Hm~vU3F{P&dB<N(h6NpS(qN-6;Tyxb~v#6hzwA`O>Gnkx^7NH=t#uO?1
zyM+qnf<OHN7?$hVo5oug@CTu}j%ts3qPWy1n^1<SNteU6{TO5vg;=9Lqo&c7rq^#H
z4FmIgFvA*7mBazsl>@^Sb}p_qZV^DL^`xSTFNu}3G5jxP*U9t8XuXz8h#o^lfac8-
zUU?@=XmdMDNTU><q%@bP$oHx^AXl0=dMEVbm7)sCRPr72g-JIDQ2wZ(%#_!wNLe<&
zXU(-8yPaH%gQZ^9ST%fd4a-PbS9D$L^j+s&Oyp)F6ZKlal>V-|Jh|OJ7o&ul!UUe&
z+&V((6M?)!Fu<R6|1hT&=dQf5l)P2mYm7K}qIAvqaCOA8XB{jo9fPAHT?Za+-c8GD
zg3X(fJfHZf2^zyBO?ufPu-I4x=Q}ABr;I9$I?uZiP6Gq8LjQL^KukzmLK#Oz?k_u+
zH!Ecv*RfAT)j4%yb&c*kx;JZxx<&~{jiSC~dT;vn)0ckOP9_wm)A^J2{Y)went3ZX
zWLT?I-b;(hsFxbTR%~3592F_5=NgUQ^8+!v!ca5m-7cF|R1qX1BXJT~L!_Ym%_O6J
zuF;?HN6iL=G~<q(0XR`p`&DcCJ-x68VGGMP36xrG!mfVD9gvKxHv{d${uvQU4xkM=
z4#$9wZeNAU)a*)pyz~VK?vn-`Wkkeo4!;rv1r-brn%IAAr2JGW!E<yt%W-IFK&g~C
zI5Phvl{k?)b7zh|Zs9dJXrhR3slH+6HMkw^IbvgDON+);X%};#nC!bZ31|=HG@-X!
zBJQhTf7!hGQnNchZzqtS$QB(?;o*Hm`54r3_U^I8RBx=K(XQD9h)Hq6=eWa;#ZRw)
zPb+5E4rc?`Y<!1^Ke>siVrFQPfvH5hl(j`sEY?ti=@;pA1Lo@fJ6c0U9KYpsLeDp&
z+q_A<{H+|DIf_+H9$<97ZwcM->!RnpVG6$^$YU_uvVAoz7PU;c-541skM698TwPy!
zTU%?H7uhvwuPWL3fZ^X$av<0jTM!9BvzHK!F+_z*#29iy|AuGWt7wO(9FC!B8O?zw
zw8nw)g&+V7CN9#<<#w}!zIf2H!4gVDmL2pb=rJU8*<SMnY=CA`)H+*><cX?DFiu7C
zt3z>5%<k@s<+j)4i~XEjh+KYN_X@gyPd{YPlBdc<%5S?Rrh{ye>dcn)@#wcveGUu3
zodJv&%Vc1<ANakVm9}V7&zuvJqC4pCirNQkRr7U)f6YhyM7c=_f)Ik9ejw-hKeepo
z!FgIv$!3s!jcY92HM7DRn_*FSnewP9>_z{_2qK~dZak%mN3!SUv`<fc=!5h#STh!E
z@_1bD?nT3a)=V4JKi<AigZk3V*bW&|VX^A=w1nWz$C1hR)X-Q(1AK`X2o8SVC>ttT
zo8m}imeaUnhfT;Xg65ruHj5PEQv{5&8%etI5K5W6f_ajcSrG$?c?I4D-Kkr}_<)|_
zf!IQFSnwu-v(C>=B=I{v<zbfeF>Fro^iLIA=qqi7Pm71+BwPot^KA)JK|JPC%$v2{
zL2P5Au*j-1>fz$qB!fkXj&7G@qk!<k-ye+6*Ud-ccA0lWG7Opq)Lu`a!S2=qG_%8l
zV0*##vwzAtM}aZ+&j3Cmu<fY56H2_0^615)Z`SB2Orcq8r>f2UJ%83pN*?l0sQ(}S
zetn4&W7aSyf-25a&*h#qNixSbikIdY9+S9+!~MVuwJBh2Pm2+aOl=IpdQ|$B|C{0Y
z;?K6Ocxe&03Fl?b+EyB}&rkU&!=_OqhvMt@vk>gGk-gv5iz{v-_1(RneCn?0_e*?s
z5v9KCnHY>Bc6<nOUtAgQVMAAV%_;;nGGPs9^wBA_K`k_6ijCd9-K#QVWS+>IY~XyS
z?d`clAH~gz7OF%yuqE~5_sFwUmu=*AC4VJ0kGXYjP3|h!xG8vT=ZccgdJH0i85&_%
zm*XuZUVblXYy~R1K|&(qY4#9_v3=J2-`1Ny#B2!1zRhUW*LN0{>gu~xi541G)Xx90
z^AHs2p)N45ydJY^ZcDxEXmIklf7q(g-5|MdQh-;86t5zV?`SulE}ZrcT9uWlXDaQR
zpK~y6L`|(+8^5->-C`XQaYGjS42j-Hz-H0aUi}4k4X;^DmYh<#|J-tFn3LNZ5{9j=
zk<Y=SyN)DM-@am-?3yW4vzu=EGB%ryO~=5!vb*$lbPRmt!>dG)?Ay9sSwnej=Q7Yk
zUPr;BrFo=I{EukH`-!=V0NB*T(nEhF2OI^BHhH$}i7;f{Kk$YPRn5F4(NSNym1JOK
zoY->I)?hMb5Mv9|C-0I$oZuxUs6r3Tk*k_bUvRwY&n<RC?Bb^R%*;3$|Eu(*Q?tTc
zWv-}*8`M>B6&;>u@IrNScfSe<1F~Q~3;yGP*L408%=g^X^tyXGwaKjxwHV&6wQpcv
zNRh$rkb;R1549Gl%-Op!SGfil6?U~dN0#2*@+p~up7)L7xxq<C#!}9$Gc9jY6j#R|
zq_P)Lj56^#{w4XePTN9eP=2RE{z{8*wYiM|k-GlYuc3XPCrzq}W-XB5@Oeq;CsoF7
zjrSW48*dA=n(GHQMchIn(*+YMZH8n!c>QUEqKeGvvc?>sIu^s`=T{d_EM<+eU-W)|
z%w1jK750oUF#0Fj-TF1T_900k>BF0gI5LJdP~ch6<ZJ{*YBT!{ALX8DGz>-eR*P64
z1W{W(Yzd5>vR=;wJWQ#yZp?DV%f7a)hp+}6!UeOY6cWsHmTpQuy4+DN9B6FyJ#d+o
z#^)>u&fLJDf^u=M8_KNv@ydPAfY}{WENa|JJ!}lgW1`6kT?H?<Y$A8)tJa^iAxA!}
z35fJROig%%;A?zVLh!2`+opRgkp7p5i~y%q@676vAzK*FrH9f1t{(>5ypn6fjE~e#
z+?U?FsVCK5dJT19&K&BP9qp74P1TDAdifunl^^~9aNGFZa;V9;CxVftG_ZhPvvhmk
zR}U7rezQEOqOKYfX^5}dWOu#3FAj0ftUS%ZRMq}mvzW>wa=Ep!x$xjF0g=r#1xq!1
z%*IN?@nqhuTC&D19Md{qgbjRG?Pqlks6WXwjus)ZbzZ2W4(q?2hv4R?9>nMH2R&?y
zCSlFgANOp}EeV6U`xFi7W_X+!vhS|ywWc;#)>U=9>|&?j_08uAN-FqbpCb(uSYOsW
zQ&=dG$z3heF{O~fjLkn@ISr^ep8s?D{Owz_#^Xsw_}yR0N&)mw52xgPm<2iJ$)C94
zsrz9vh5KcY{iXW97S9(%@$>|QOIsY0U$Zb`b=i1%b$18(mh|8y`tKsW5cS<fJaZ*B
z+huwiw+rZ$%l35}YVYX&^Puk}zO^X|Qx_4GC~f1cvS^gnLL~6l5LG|(PRd_wQSb#(
zYP*{+@C~!keHX@3?yC_67Q1x~gt-gYU1m3)zdxmPJDAMiY!NQ=c{2VGiI|4wlX}ia
ze#0ln)glxS?6GbB+7bmkiQBWP!ttGj;>+m`Z2Ny*TSgU<{1$2S<+PdDz8;|I|6>s&
z3%a~@4sWYL4#-GLgSF`V?C19tEN0{nu0r7?O|E{~>xdP01mio&o+QP1eWTr3s9_`o
zdS8pWgNKO7<Emh!t3uCcE>B4Ax44+KG?xGEA!bq_<WPUQ&4ha<{IErQG9~wnue8}F
zIeVRd%7}qegWIxYyq{HtQCZ)FR5Cx_Xk(akb5NF5SZ)5e`pUB#X){h;!_?ZMx^?AK
zvOG=Q_r*q&p-sjUzF;w6f$;HlUa3cpEZ<i5^)EhHNA`W5x;nLL0;n9Ere1d}UV&pY
zT@i+XA1frQCLi&+p+!^2{D&CJp|;CsvdRj*=)tCgDa6L^m499h$yy=cyyl0$hH9JH
zSd_GaBKEnoc<i9Qa+X^!{spW8-^YFMs|jgWg0g-H>L#DtH}7PvG5)Y2$+*u@O)JQZ
zNk!vq+Jd8cVI{06H6>v6pQhJ?4~gzdZmIVA<-^svTjyXdb)TS{We|(kF(rlAwZQ$t
zb$D!@tw(a{!}T0**lSq(rm#nJrlkMX_2)tJo4Xf^#ST}OEtgntW4{%Za6jdBHTdau
zdnwY_tr(^?SigQ)I-r(kURftxBib~Qxwu6I)z*#!-*u>Y<YE7xR!mG4HT<gZ@&KQg
z6*cs;u$MQu8qV8(2^JO&`&YMrr{GJo=PyaLHR?9uB+2+I!{bjLjt)H%qtBh?bQe(x
zJ+DUC3(e$&8_Q&i7qdt9Mh<vih>E}QH!1MWp<A<iI};-PJKo5(y!}02UqX~Vpr5fW
zhaRifWV-|w_p2mL@)d@_s7t**gP@bVTUy8ce=J>PSd?AYeN+@h5Co({8tIY_k?!u2
z&Y?S%lopWgmX@JgItCc&7(yCEa_IaH@Adul8ku|UbI#stueJ6*vELMlt<u0?YZ>LH
zE%pZGLfyT?l@N2l_yk&xD#R`I;r;_*7Yx-AbZF!3Z#iK7Bp^H&H5ivFnk6hSIBAx8
zRQ))u^erRyUcFfHE(eGVbI@u?Y-)Fq-d0FDVRMA0JaRHs#<>aCTF%n9^;eH}+)=fO
zh^;b!dv=Jm5sxk20OQo`R_~`X7}^H5N7;8bkoLp5HQ&v`{A}%ZO1Y@mH-sbu$8$={
zSJw{yyMA}8Rm;WDu_AqW<OXZjI!LnY?{%8j+J7>Uo^tp9;|+E1Ux{w8xV#ndjy^rb
zV`nc`j5;1}dY9#86CbxiQd)Wf>q{@M;JNIs>JY710?=d=^X|eeW)%I%2)Gg@W~Ly^
zW=<s89?M1r;A@~`CN|EW@v{YnU&2ZA)MXQ(Cj}zrGlhl+;J5a&srN~~JRepB>cI-z
zn?$25!NEu|wTA>f{&&qS223@<I%5Ti<70?%@Y>bzh?b5H<hb*a1^_orP2$>lcM%`9
zJ}z~6Il5;=x5gM!uQ1~jclCmB+{>oie@ye2SMnspvx`yv<C!^_Bb%}0(blm&zPprQ
zNaU7d#F$_7H@$f)KB10opupmKg>d)u{)E_#&3g{V)G@SHp4(oi&Ef~kZincu7y1^D
zo?`){P2hIaCx^cT`Punz4}GsmM5i-eqmTQyUD}}M)6;s5m9b26wE}~^E-h=I!Z3Gl
z9}0<N1ONxHQ=opp3I%+J`Oajz5cLag?)e`P!`qHoxt$9!oQSiak@Ad<DcV!-<XDy}
zXrsQRSK;WmGu2?!Zd0%^dJh*9fHhKOi713x(`hK8J%`FMonQXdKNI&f{555}3j!$k
zZ7LOR0GZfCvt$wbnlx809&}FI2%P&0@6?L6tYIzXo6Vm-=3iX*`y?Q92pz+;*jFcz
zoFo?F<_2$yE}<l{_e9fcy`PzR22_zwmw$;W>cv_n;Qt}xp%dveVk}*HP`ra4E-u}@
z0$;b5Rr;bu@RD2f5dJ*9AJa@I+7iPrdB3g^G%T|^I5mxi$T6xjKq^Nxtm;VlAz@j2
z5c9fHSq>7g!DV##0bbgR5u<PzvqzAm5`qZ%Uz+zhlj6+j&RNhvCH`AEY_OQl{|4A_
z)+8RNqYY{?IHuFJ-*Z%1LRW*0->#|7?_6fq?k#8yTJ{dd3g0AYCBRQU@O6VXx|N-}
zxjoEA)jhc7!KqiBjQmN8DK@ix79WprmF?JT=7!nFk`m@=OB)k01O>@t_vCiksRou0
zfJB}-yF&|0&qRFk%a7iA%EU5bU1z_{sS#g5{k4qYcDREWlmJcSR$92J>axY(l-PfZ
z;QtdRkQ`=J*U>JmHne{I<WfHZ9DJwai|1+yG_t*1vH@L9MehpK__szCoxwY;yTVS4
z=1wZCF|<};Dj2jFfm9$cKZ4ziVk}MzalTroPgtV?`28C!mEaZ$h4|ni-!aK470uZU
zO(XG9R>r=?5y)*3R6_-McsoH4sn=rj`I86hmT~MuR<m(o*m!{1t!LA2rFHudx|S<Z
z>6Ts9IV&m{b^x+F_9D@Uw|{Ug9|XM0y%D{E)5r6R1s=(37oak@yy98f9P!w+s@p>(
zw>*{kRRyXI8}5=R0TAKQW(}Ka$i-`QUj>}<kRSIUYV^|=8w(ds-4WVl9;rs<NAv06
zn!M<2pA9a!@cZ6m;Q(i;+k$x2{S=FU=L6SU$)2at0CSxEBh9vjpMm2!JPP@=&EU|^
z+0W{`fi7}hI8iXs7sG)#i=>aZoFks$y&vOPzV4LDe!jg}zIZ@W51n7{j@4vyP3#V<
zJep$7Tup>$7kpEqDDzlGUCio_^><GNxqO#+ug#zTddY{J<#-7-QopIaUBsJ4wq-x<
zP+NLv1VG(sx4R4Yl8IZJ+e}V5x%h=>@S1DA{~3te|KUokHUzAxp<`|in2)rOVS=4&
z0qetzkGIg!^4#eq1S@k=gSd)~Hg#1Ho%vqz-xP>z^SYyL_9k}EMgvYJV4jAbndCC~
z-jB{rtleaG+}=RQ^LH7Zs)915zK%>L{^ABG^{40Qk2)-~v%1*S=OJO_ck9m1f|&|X
zH*y*{=EV`b@^Gy84L~Qkog`t!s28XK=QQYR(`Qee&>sXJie87?zDVD#Yy68pH`u3=
zm=bY-LX%J=BVTm?Fot~0VxY4&JjkBKFVI<aU$JE`@PpQT=er!?t5b)0(pqBez{AG4
zI52qujzPYu)-7X^M-d6*|6c`)ZJ9+UPtreoYjG2Bamv%=%si+bu|^;fH}*bcr-Y-a
zT!O_CJCywkIkY*6>vxs9K<m|}8;gNKH^=+5inb;!m&MPTh$7uxXzTbN%=>kPN;u>b
zf^6rzC@n;lp^zN|Lq?Wp!=uGsq@`Snq0r@K`*~A_8~m3cNk6D{X12<1c7XCSRObdb
znmqq!-|T<L$0QG!D>&=emQ|V5O&3np>*(6sohJLNRp^vXu@FzaGP+rK5gO(!;JtLv
z$^$>0LvsM;v$iEMwKqj{Ff$I?kdJ6GvMg`Qre1-1HnHxRF~J(DjKxN*zjtc1O;`ug
z7Ve;c5TwWV2342mUd8Us`cxSx$X?_>2R~XpRZQ&(_#;i_py5F;==tAh7RE9K5*|X_
zpSAj14>kCWN%ZpFh!VT@XpXhV=;)9cdi!zVM6E7&X6)%xeIVGWfZ)`dSn+E!&c9@1
zIJeVhf5!RU$fReuyoC?`acmb7PG;g;J|J1qt*|EwXazu30T!=hs^!1$5!L`>$}1&`
z#ATj3m6kdl&mJ<1=J>FqCmP)h=?LF;$&1Kwygd{nnJJ#$R;_UN+#A_-^@wZo!U|Rq
zZ`e8xGYSYQt4XYg;?qeQC{TDNYdutmUNU0msIzY=6{c<r(S?NRR>%=ZSfzDMigUQ}
zWsV=rMNnq4gP`Oesw0jo(R$uVSxM};{}07!xc-WL33l3q0alv|oytt6k4;_pdMBSG
zlkoA`zP4M{#=_0DeBb)-lmDtZ-h-l*S8@C!6?(qX38^2!g9`9*G@y3)SoX>1gnp^`
zboaF5a7g^sNTfL-+9j^o6FyoxS((iie8;0>h9?{UriI(_OP23Xw&N(;FPd-))ULkp
zg+1>|kbZ38Y!1d4w)1)iCxlRdK@wb-N4u;{50q2@WzI!#_!kS#7ZGi@OZwyaa7>jq
zsjl-m>hdnG7GIs;i8ZD4VNwc;yv-b+`{C}m@Oelw{ZuycsCu<6?7f{D7PU|%*mr=}
zIq>`Wl}WBZ^;ysp9T35(#Q0R-J&_5_+8ejy14~<4s!U&yLc(faR;)!LR<~sCpF6bc
zU{s87J8H!e({h+YEi_4UW>=Ub{|<%Do8?b;A|HcNyZ=<jP+`bEpLcV(gxy&OXJWGc
zw$R?cI<)fL@Ti7Np=;<fmthjJ0&Qtd-fyBw=6UoM=5?Jzx;P@wt+{+W4W$935HRX>
z_iaD!RV!d3MY243bQU?1b9QVK)Uc%RxOA^RsFWrM!&xVRic<_^jiExWcu=shPw9r$
zo#Mq)R~yO<g&;`7c3p_Mh=dF;yJY0W^3`w5+(&4|wD_Ft2xc%2TMv_#4S;l3`A)wX
zigs&+kyHbApx0fh*g5*Rc9Nv9tufK{`A`1$DtYSC%j1l%b2JaId)X6hd>C_56bS*?
z^!huDQuq<vw~}Zc{zWxZesljze|kx2*H|h=Akb|R;2m2bC*CY_Wf)+qw<7PlOo^3G
zZVOl!eYWs*^lZm=y?&HNS=-1*y&)ie$HpH|mtLc+L8uY8bLvadZ|OCXr+JWP%TT|U
zyMqQ)bD*6!`yZTV=av<e7qHr*J`eh~TSNS#v}@Mtk%88j`qOUZ2JeCWKFPX~D{scZ
zK=n7EDDy5Ip0zU8f+1dp=BhFjja_vIafg{h6m9)yyVztIo=qnRSN_*6#@8qH(gVX$
zR+U4CKY^Y8&G@8^LEu{xNQFeP%K;t+xzXsa4@un<=Cwkl{2=`v3`i41L{!qJL_Ex?
zC`Rk{b+QYE#?e-UXN5nsMC4Pn^9dUR5k+tL@^dV>+{})quqT3vUD$A44Nkr}({aYs
zlo8^umZXI)ZY-WZw{}zb=I(}dX`>AjKQ$B42uVG$Z#4Yyd;3V_zOziG<0sqd%WR=e
zwPL!9lVS@t3}!;~>i1|TeO$k%PH9z0OjC(^eNcqs{jmNQ2;{V8uKXwxvecEbGylvL
z7hg27W>c8c=!hOGT)&Np|1jGp8F_ya-QcyG={3zzLH&GUn?qRh6DTe5MLbLp8~ymK
z6*<;u;6$`v6{`7OMivunTh1*mV6sJ+=t9y@qq*<T?$5<oj12M@ol1C`U7J}%E(U2p
zPTJVOZ{WdNQ#o$^On!U9@sRF`9Y(N2UIVkHt3?W{-#%}4z$I@}h8OG(_3J9N-n5hN
z-Ij=N;>%>sCP$}K`<Y%hzq^0w2aabayd6gkSuJbLZU!3zxw+JQ2c`!GGYWz4Wu`T;
zRhZsPfL+7q;r@7otTQy7?qFZbG(V&QK02Z~qo>Xd<YC{nJZf`mz}WKn`MT<*HpDa0
zsI7QNtC%rK^l@>$rH!f4>n0=H%Egp}xq;O6vvs^+LgDcTkb-%gJ--H=DYbvK{y~4c
z^n-`=EGJ;$WtW-iMK7!j@E?GA9fLgki!NrKld(|-44$``_~79~90JY-MZ8YY0xtJ3
zc|Cv*we!f(bDu4>R@8==$Hv~$oF+Actp7G@W)K@J{?YTGeeVFun!Kg$`vyMqI~BmB
zmzTfanHwAt`aBjVxVF{{A(eZe73g6g^SJjLyHzw*v=^syF%L$N)0?wJ-3ExsVr6kP
zKMYHL7#^c<{oMr&U&0HOE+I<Gdn+;)Ee2|;U?~L@-0Zia-?(P7^?pEG=Vv2|x0{Dv
z!bw&qk5nQ;xI%N6>L2;bJ9qj31m2d_zhS#8?!)z#LPt@&Zki&y<^otPz5bq{NLhvs
zm@}(yoQX-T@>)2)ZAmn6uF8tZtdy&nGc6JMN)yw`1*rH){A`io>Qv)notLMtaLV6E
zNX9#72ylKWV({G+AYW}17R7Qp)qScFcR4I46-Qk^^;0;?M74Pc30Hgw-CtBK7*j4^
z+?r?cy$7NKfRH4>dyhf^xRwI7XRIB(H5!$T<Ps`TyCE4Jjl*54(QHx58mS+Jdo2z5
zyN>d^anatP8?^1+VQM@z(0T|^&6Q3Y^ZfoD`cC$_vci_e2;t_+oYHJ`Nt)Y9`wkZ~
zox2`od>KXP!Q?f`hgx#ri+2v=k>tQyGfk$s9p;jVb7)~bcW${VGeyRHDIYjT|3l_l
zzc*nopr<zcC=}HN?88BeC;_q{Zb10qO2{jIKV10lfmu4pq-bvHV3u1;bxDv(M>SZv
z(tiWknX1~0?Nzj?=vM&IgnZ<1wXrMzCZEJoP*2L`aV6^gmEAQ_e*VMU8gzB!L(V~%
zdMSjTG+A*b7oqUjHN8KKUKWbgB9yG#CWm}|uCTD~^{9Stkwbh3D5)iy0<G6~T|#0{
zLB)%Qx64}znt*xjKVXHPdro3NnT%8C4fG@cEiNO4G{=<zeY4(R-o}-yFXqG0Br<;j
z?4H-ahM33#It`?51Ei#-2e5%OO*u#qF%JKz4n`)u)1WF#2Q%KlBzyVFVbGNC$)Kdk
z^LxGjJTx6>MUIXSWl0a_$7Z2q+nP6cNq;{$zjjC?GP(msXDKv~5phrra!v$2><4O@
z;Zdyv{vNYpZd6=!471C5){M1*713v?`@-yMU~t&no>HwXH)Ipv22?90)A60pc4|98
zDO}~h!*!YAHuEd4=pArW8G8GNmV|SN-0W;r-09)7RQ%x;uH4P1AFrqTWHJ5>SaRMy
z#CAx50})YZ<?*UZ*x(k^lD9_|n>;j8xVct#X#BdfC*_v^FXdm%MGzAC7>Eb&X56B`
zI43>u?&I%nD{0cx6F!NY-k=9P;cGwAI-r@;z0I-VHXXMSSa+Fzf)V(l>-O*5lIH!q
zf@!`4KytUl_#XG@FlaCnUEyd;92DK~Zc+uni=ZH#=EZYBd0BJ&a9wrQAKYup&a;sa
z{Xu36jZTWE`i`z{iXqyHWE@_lj=3e;^(~w^ISFu|8xTmI*u^qx%{)||wSX^Zl9_Se
zag9f}SjK!2_>E0oS9`%8?JEC|H`oo!@ocwk<c14VP&1t_w_DQ8WH1v78eg*1bq7sF
zGRtu|wIUC6p|vgLPR2gq_9GW2k%90oEHK?;WT$%4cI=o$)0=s|J(BcdHaC_$#M5~8
z-Xj?Q>3}pnG^*ss!w{<)`cyo=MKD(o+`7h*$n4zACNIh(5exKt6k{XoN4<0dSKjGm
zHE+D@8xnPRIWjDrTYCl^vlh6EKayn<c5%Ibc!?{G9$C`OYVjzXVbA#7Ouhqd?<d&@
zkzXMjL{;rx(OE9}tcV?){0t$XFXlFg{oKTnG;yb4HA~u*%rXvvjxSr!xYC3k783Ah
z@=8euO&K3YP0Z-w!zceubHmVLNyx<G5<b{8Y^{1dI+ct)l}#^9<S#V2$`a!uOAIOG
zcR><!rJYUtY)u}$RwN;&NE~kf!$mL>KQ68Ij2Zurv8?-QYUN?@zypKNFfrc0&5n4x
zknB2?^R2<Y=|iiqmgvkIVdS{V8QZ?QmRf@OGgN2>Kj<o)URh1lsMOc9bgLV@`53KR
zA=a>a#`#%I#`ddak=JI4jJigXEw`($n%C_J;SV2RkRW1CcevST86LI&`BT07^syl8
z2aPwbLQRhftkFur^<HSASgVbXz$0Jhi)=x3u~I@KS|g*ZB;sUrt~3J%_ToJ+x~+nJ
ze5|b^Y6?}rw4#fC0arUYL!QB1T0%&GKRNF<lZ2R-Iv9<O1xCIG&)ge{puM=B`>H~M
zgR^|%@by}4ES{;C`mk(>qx8GkR(eDzEgfOxI}Nco@m~*S*V%0G4@WP?_nOqX=TSPN
z1s0pi2S4xynOh;+pAVjq=i8!1P`(cJN!X!~!3HKCfE}QOYhU#L)FNKN$}j@|NXlq8
zeFr>yV?}w6LTTxzG$KGCSJ-9I$2hfp20X7=kO#bc;kzvHI+V8Ld-aIF6E-L%SuEpV
zX@ehLvP!eWlV(d!08UP3*^6b6s%{Q-9NArw<KFZgJxAqwF6<ntQ(ta7$d)Br*LEtf
z{PM?iLU?E3&+I}~@9|Ml1*l?tr<g&~wI6B?VS>7BKgaumyWVv}GHjmYL}<JlAcHHu
zFhwxrTccg-qX7VVCdhA)43PAcF1|wIJG=>iBM1pcsg?`>u?*(P*9%2}$<qtB*{s}8
z94lhFK`BaZpl@#PAEen&k-!boWJE9SJGo+IX;UJGw4xkahM2X9zvn~?n2#iM6rtbk
zxj6vV<yLubF2&kRDWjdFSnYXW*u~?6Z5nP2l<wDMyCW4$^Lyj9W}n7prB}W@HKCEo
zvnrq`VvED$=|4*!!J|Zzi4}Vg+dNgnLCh@}gQgmlLf-qM5|9mXx_CND-L9x6DN<zT
zY0Cpbd++RwPIf7pNhU*(y9-pNLOM%(>b9hnhE)q3D;{>W1L65p0xXxRZ$d!DW>p7S
z@(Oq)Jv75&q-Sd4>tp^EltqBN6==`lbWNlRL;aHC9*|eOcLnrQdOTI!m)D$mjm=A|
z^Z)voX}qYqpVIcp3M`>UP;x2{{j6P>y-MAER$k7vo#}b<<*{gE`q+wKTIn~q&V~Qy
zy$k*H3gC3j(RDx$tEmb4xyP%~NmdV|igc=}n1Q#*D(sPhpCu$tAYo_c+UV_<$+Mib
zL04s12p!u5VEO3gn{45T!~LR?3XA!Eqx{79HH53+4g-u%So|FEC6<K+d4EYBFsxfB
zK_Ceh@p1vyfAJ62&&y@d_j^hS#h1I3)MAUf(HR1<&AZG8BU*N%oM1->2e*C20K>)S
zcK%}t^lQl;x}^q8y-h`T$DKn*FW`9vy#LKweF4SS4f&mikxx0Q)QkUh6f8tOrxzC0
zZxBIw+x&VMq`S-Vy8M=ZgIs#y`h5jc&~v7ouPB%Le=Ge^JQxWLu~!;}0fNGnkRFf5
zu0CPmpfuOX`=+$0YDg0Ly3QLPv1IrG#^I(qeHQdIJ^cqg_NDLNq>>C{tZ^Ge14`6+
zy8TS<*!Gg@>iM*Q%P^~^7c#Sn)Ibms0|!{OT+7~!-u}$0^-_rC`E^|BkQwK*Y@bVd
zeAcStebmTc<KV3@CT5=JfnP&<i9jJNUH$FBh7Th3$5F~ejx#PRS7fzA4VO+l&9PTx
zs#uVAks?7K(C!ZbEniyqN~^MB+1Yf{J>n9#(1b|F#P)GDg50E#zJ;|WdMyPY6u{zW
z9;{v)2N;p94evNfhPnW)&pVyiTm^Tn@h%G;7qOsqUQ-}HpQA0EyUPI0sHL*5gXmU}
z<x_dRCh`5%#WwH6y8Sll>)FqM+6ONRxTullafA{U{N;}Oq8>{D6K5)V^TaN{jI6AK
zg6Y8(iLA64N8gj3d;I>v@3wG^`k{0)op}a>B^hOh1ZtX%<s>&#a!_%VnXfe?7@OXs
zznPfy(08GQam+=9J5BtT@HT4uY(a0R={((#l~CLX>2nzLQqHITW(10~iiPH&tcU_p
zQ(bmT4NfZgaTTyvB>i;HskloAgExR;%BeicCYZ7|=b{EULCHx6cuwh{nY~wRF|9-V
zb^nFy&?mdv4>jhd1Ps7luy08udEx(a3bE&&t~{Xk{c58D_#!0}E844g$ay>%B20*)
z%{+%KLhH?US`QZ}`uZapM$#4*M&C-02AvBi+addOk84fywk3^fGl8)yL>~<{xnsjp
znSRn!F&$6LI+(-!TKz#*c~DlsojAUMD578YJbQSay0{wjLQhDIeoAA@JR2}n98Zi_
zHN1WF9ZN!m<LP9}J0GPubJe8!eCLC7&_OxW?8e}P+dKHQrlak1US)}l&JxQsB<(Nr
zwMc}C9fE4MKNTkn|96d$`;@Ui@oI|S`%Vq4eMyZsirFNlcD27E;pD3=A{So)7m;yq
zmHIOvqjIJNh?2<2_jktv<eyTB=wf5<?&q%IZ~2gd)yQjM;Wk!>6`}d-BLU8q8acSo
zl|a15qzt9f>eB;7eDB<EEV#MKJ-~n9U=^rKHfVm>s2^VgTb$eQteG&K_vmi<=#{=C
zV#t~`ES~%2St<5Yb-cs-o|Bvw<<!gdgv-WdBqs?UR}a#%I3;TcJ6iZI_vMayupKRs
zp&Mhutoa3*1`pPc*wrOAG4C%-?fMJHeqJnLRykg+^8z?I*q+>b9(0C%R-aA>B|-T>
z?tU{nTYh}TYOhjKd*$!<oI}2w0z>AN{q)Am_rquVJ`F?8KUo8IE(z@y=Kl=Uy<hS=
z;O<oo!q3VEyqdbi_o@GHp9+!!g&IZs!CC;rG__1;aFag@#`!t7%SUhdIqna1jP{5(
zKPN{xcJBGiclI|<1*&S+Jg2Ez>w{g-*KQRv>_3}YXC170Eg3|n$Vj~i;o?&8S||KD
zD4vq5ANB1BeQ%y0hdLyPu8}<_E<RAE$5JsSK|UCuOq&XYilriT`#-$Eagwe}sxBcp
zF{wyfDb;2j2kT4805@J@lH09c`?Hz1K_;wfUxc}Jt>l~r<_-PGTv1>A$BS^cs<WHs
zVYIWKI`qr_mK*mqOoi-N_sH|B9e3Y=W4vmUXpOm(4@GR=fV^UX3{6nyyWDTn2z-H<
z$X)MRfw}b}>x7Y>-xzf>IP8tNg-cT%l>(orNT#K!yFK>OnPHt!Qq38L;gPMm+44_9
ztAC2V<zmN%fyPdlv-a{2Rr=`?b={sdkA~md76XhCzHkgC88nU!008sG*qZnnWD4ia
z-0Fry<Y4PiCytWmabLgW0b2v^0+*AYU4L)A!TjD^q+UFA5iN&RGjvx5{t#z^AWZlr
zxWu)3csu$TB~;x$$F1#KYP03z<#q4uHB$LG<h|*aV8Qrg<(k$U0T9wM$eJs*6g3~g
zAJ2aaxZwt`7;sRGJ+gAk>{tA+gydxorG<V9Uwakyb31crPeb5sT8|o~JX^QC{LZhD
ze)sz`!vAfNw8MpT6t)zV*o2e*CQ1rNI7*w+;|Ki7`C2?!`DC{11INi*?Xxl?p~$^P
zJ3GxLkPU&O_To~YfnF<}O8_UFbjH-)KeFkP+5h;=ElWUPu$qeM20!3bq087$3P-AH
zS>MvUuIH3^S6;y)HFeb4lUs_3sJSexV%O_CgF;eL#Lar~OlmrO%}aR4_50k89V_ts
zwb;qTOVf5m#TI()C5q`cwszI+?)n~%J#N51wzJpp+6mEl1>a0b8_1z|u9`8av94}5
zH1;a&xsnWF1udZ6Vos7$fz}OBCeH7XV8g`~eCimtO1U}N;`xt&P-e+3C~w*-0X}oN
z=+NH3s`@3Q_i@a%RRu+SI1tqcE0-5?bZwDibde-kBd?>0GWdkXd~WThT`QLMpW2Hk
z%)DtooOb$8_{J<wwoaj<epKYvD4+|uRqS<lgDZuJi4(p}5Gq+?ZJfrvAshLzdh}Q}
z?qzb4%KMOx)0t(;gqS$_VDg>YhurOPy>VW3IEI+f(HTH)&cKg(?pqxG4I;g>`sq3v
z2P@<lTW|LwZz}FrX1tKQmSe6?rdD)G4v^#6`{HF&mpbt_H9yd1EvdbBf2VZEy=5o>
zh06ikJP(Mxz*rSk$>{O)5u|^QQLUSf9!a$B?}r$4R?aG4)S&!loaVmVR_mJsnLq!&
z7$SBRQv(cQ-A)Sz{nWRLRloK&MxfNj1h>hKA}`X4usE6%w1PZ@gp*c#s#RXW(J6#h
z^BAE~##TKhu^lL`SgswYm7I;{`(53TWxBEmd2Z5;g`F2gbetfKaBVmz^cFsLdFjQ?
z4aAQ`Z$D}Lq=?DCv=m}%h4>a;D>trNd?MGU`u+KaJWY<)A;b;b;gT46V>$Y>Y_&P8
zRH8ag2v;j^uv_G6b@9SIzt$A@dm-!cG50zcWkih@j4sEmv5(lAiyUvkUG?7SFfA>e
z<sVp)p<l&MmOcYdkrN3pr{&E-e?pS+v(npbo!h9N3gOVvjkg~CeGTNS!Z9xJy{RJ=
zL=N|>7FYzQLB?jMp)z1!wW}E0aSiGPY`C?bcf-md>W)_n?zG@PZjx?x$Kq8pp(5Nb
z=YSx+*T=u(imUO$Tc00TMlU_v;Xt4aWcA<g@taZOGI89TL<v}9?HKh4@Jy{c<seSi
zSn_g++2!H++K;X-v13l}j(VY;BvxasQpq)FZkm}yyZS2V0eoy+lVxo^0=+>vrW1U3
zeF4{H>M#tOLfV77ZHB@MhTf6C{;X+l1#v*FM2L-oJJrJSA8CI#G^3?xe?Ryj$Xp<H
zVfIcYj{1dy8h;Ra!P3(#NDFUfWQ_qP=;3y$N5!R)p)|Al@pqKcw0`ZWTB?WF?bfw$
z(#BHVow-gI+vJxlv{JXnc!*>+Jd8LQiPSWCDp(LP`l6iA>5Ih!pSL7-P$ryk0&&V`
zRNXIP$jFLRA?$+RKg?)+d^iN-b~+&KZpbER!dBa2@dyYN9XHoKzmcAQ_Df}gNq?xD
zrZp;GYZhgEEQ5BZxbyF&!o;JU(f=65v<S&!T&yg<CiM5Sx&PMv^;;u`lrUG{TD20T
zThgYEJJBZ6q~!I#$c92@54p5AI+7~XQQty$mlkP7!JQQfG|AyEe|va|_1-UF#D2^b
zt)5)J8gT;$Tv)iGC}hp^;-Vnob*QtGq2CS`xj$4oclMW4dAo42D?<bmEDD{DjX6xU
z38*9Cg^4D`q|!ghNa?hzB&FASs>iN{lc{9@ow+TIZJ^f3*ATwuSzeJm$1n-@+^Y9d
zJq7cBs#SYm^9HPJ4pU)JCfRiWhF;;m5Gue44;w`99TW56IXu?+CN1T8<kD~5z*JiJ
ztPJTTIP>PgY5wtl>ljV2&QaaMF<V-Pr`Ow88K!;Fu2eXlH}>zq#7^Xg4I7~sJ@J9Q
zI4U98l&+(3`iQuP8^xx#Ffs8PhD3`4%QOZ~{xoX5mqLHyJk(1SWH)GAqUrf#`YqaJ
z^R1V>APO|;;d?vldu>Vb!Gxo|P5!2&{7$nKzR}SY43@Xyw+4-L>+M2Lg7=liG6EaC
zWO|qLU*=zhEP}oXb&jq`xPr^wKa`>!$DJXD1AksPx!)EJ6Rfv3WAsBT35cM8m8T)O
z`Zst=7ZdvpCdn?~_jHDb!EVDgrAVO+jIkv9gM(%*p8qV>_4``CWGac$(IrnTPHfm$
zNq6C4ITdO{f8!*iCGF(`alf`9^HHbN%koMM`eb7D(uyU83aiPtxPa<3m5(Y08Nl)1
z!1Eo~^{g!+u5?pp%8_cSZYC!Di$Ns^<r0*HY*->~1QQ72Ao~!I%N^Mo2}!XKQze8u
zgRSMgxIVo%(k`6rsNKy5hN}eJzQIdIyE#;<gx2a)8`&wBJw51`qD(~x5q((RoRCyT
z@Q^S6b*3Zz$o*Z%6?UO>f>EnWWJuv-Ihe%s^iZurdc8Fcxa#az{1MxZYjAZOb+J-3
zCwH2eui*RNI)5K>{Gyq}YF$;v>IQ4ZANbu!16vpWUsD3*%i4G|utD+&86p^P6oMs`
zHL<eZJ_PY#F`^yyb+t#m+#w(LD$(P@oEF}eRcks-*dt<1RnGO#yLgD+6Abmf(@JkE
zuXHZ#wP=^*e`Cz^!Z~ZJx>}>fR`*991Nz3QI90YEdxt^Ye4f7bs>c<d@V~28pRv70
zmdlTAGg=sd|2pLPBZPlFkpYh`Hg{p5^ZoK;bo9vI${MrtG}r92%tg34>pLi}*-!uG
z)6Z?lagXJ5>vZmsBAGJCVj>L!GkkP);q=aro!KYb?OacEGY9zHw$p}A%tB2{I*+KR
zhMCu`xrTF;jPe!Ql>@B$Y<LS26s7n)EaC^l<yoIwddOO}khc^u5QNHd*|2e^QD;WP
z%Sb6}nD@{1ES~=!!6GM@d%a(qO|O;4MTA#TKZUppGG=6`{xRm&Mt|hFUHOQ~AOhPg
zLrJk92x?88HuC4v4uL^SPfRpt7p2b7wJjYeEiR>DmL<R=!$Q0UdWgU-MYvgbe8YI2
zD*yZXv@RLb<>Zj9u34r9GB)xSosc0kH*TaSg+S?Gn=fDGi9{T)n@Lozeufw)-%uiL
z{ho;cOIm48DO%i5MXtOAdC8O%>A0w{Ah+XhPaeJjWHzuaPWrK_B}{AiB?fH)4^*WC
z;QEWotoVP8R+0w`><eq5m68+${nj?b%EAsJ_QE>T=dxfE%xEklY0$R+*=*S7669Q(
zX_moTFNZ*v-AiLe=5~lks}8cM;aG3tBSrbhML*a&H4Ti3iDh>FhiQZguzWLFq@2WY
zi1)!(S}7Y}7VYb09kH8_C8DLu%iLeQ>8eOis`Pc3)ykG%SP+3Q<`{VR-*V!vp*jo^
zIL}x{LuuTG(~6k$ICT2ftk%(R%S0c&jBqy5(D==DS~+8#?v9nwQC4u&`PVJMxlkhC
z`fL%^zC{U>`S^DK7yfH?5^6xgyid)A%zq!kIPT?-mi$RxIimnlKjw|FE1g`}$9Wub
zLuwi9d@4ZD#{=@R-V)Bo7ia8D*?n1~Cg8vD;OtQ{6d-%~IyNLFbyWBm>6WdgL2WXI
z1<yoWUe86B45F(gr1l>#fD;uvapn>a=NF3ezMr{tu)b~@S;U+lbn%_`vi9IzEzVw@
z=<x68U%u78&sq+cZ8{X%vN+d?QDTJ`XCsYwRlNuJ{|RqSbe!wJec*b3?=nwzmfKu}
zPIO@H$@{v=+0|s^wIqm{euIG9&j)=$!jWNq#lp6P`yRK4J8(C;Wn0l%=7)2NzJ)D~
zGWRZivgh1ydWMm=9%j+rhlRB)TC%^;g~#InSxN-R3q&E$+bOEn`?1HTqY@X1yS4z&
zIJ7zwXlN*Z4?Fm@d&-@DNrcbBT9a7yNc5Q^$Lq~Y<b;_AZ*}8bEj{io@EY}9SVgSl
zUWk#qAkS!d>><ik4L{4@axy1Ga0udB+EIrWVeVT9@x@6_sH=uQuiQ0F<F+M!L#?x!
z5DAl)FCZXQ+=oGT(uhz@8~kpjbR(S$>xxC|w3+BB7PDU0wdzumj2{UqyK8SauZ(kO
zRaTv9Fx*;4P~yBmP1Q4iOcW`Xi#VU<A9?~)svutTE@y)I3yrv5zyDqFT%ul8`vaHw
zX4MCOuu5xI|DCZOOV;k|@Q|;?lx9*1tyhH!=t>1LX8SI}``yuzu=3HZri&$#I_F5;
z!f+J&Qh7l_<JI3-YEq$IM@YJ_eFyE_s<^2(C7p?wc%J7{4}Vc*Xl4wfUIEhh-+vR@
zGUB4@iOS+zJ(t$BuP}~Qw_>RnkNq65lk07Kk=eJw6;m9&6)iruw}toJTAr7Y0*yNx
zVol0h$JfYV0|Rs0I&r76X#v(Kny#LS*Q4#eU%@DyR6c(X@@4n#0x;WfLgX%ZWQt=~
z?x`J2R0S8BFB6lQ`e%Di#zHa5#7<7riif%Vv?^e9Q#L$0k+S2m<C>#}PBNTkpIWW4
zvVS!i<8H0v;$8a|PE5#!?fr;WIPJ%Qh+z-^b5d?C+2H(VO=Gw_xx6Cx`x3I3L{laS
zR+JY^M)!XS`-*Dh$w|E~uC^1lF6}CkbXuD_dp$O_jTpvlQarPyC`oBDBav5HN}OC-
zCaw%V%O4gx?(c6?ZfsIb;R@_rX_Sf4M+pvoJ=40WH{PHTkG+e3%TQ=IH(@QqXYbG;
zmPe1f!aKd8!!HgzH_Rn{Hq*9s!79EapDM%e5-UL}^x#tXG1JoQA22$WPM(z1!is5R
z_((<5-r?v7ZvV4RvyY3EOT&2e5Nkq8%5zr>jxD!@kd?%`VsDH?HHL?D>sI+P=}+?)
z8b9E)!VO9&uKdTl@)hdEtRP$4H}<TX2Wf1+$~|kwef_G`*v6%q@q5lqgAt`a>kT`J
zk7bIw2C|(zej@{idq#Y}O=&Z|x2g|>u89kZ)8f#i$6&uWC^zeL6G~HvY(k`Or+s7~
zyc_<4R=K;vO9o@4!Ap*qtw#)QzZ}|!rV`|S<NocDL1~=n%FuPFOoDKl<ABT;i8YO{
z_f<qMaqV06Y(HHfbG2*~(C)7f>ZC5E#EB;It9W9d^&;$G|D{%0U5TqK293;o!jf6;
zH%UPYSEzANOW0|%Ovyryw*9xSVPqG#)l6ZU2n!I0$DN&&0<WM<uV3wYn6suAiB(VL
zEY>@bc=XS;bd7SQ(I#!=m2lV;e{V{sxqiF&&kE-J!$UT+g-e41clz5iPqu^yO_K+H
zex#2%;Y#L-!)k^yw*k+ymo&02>+6bkvj+}{T8(^NdlS7^S-Zx;TnxQfb+QSZtRt&S
zmIk^-Vl+mUck@KZnHinNcF{89aeH0S!E#EqcU-?+6FoTscbBe7vbNOTai_FEhyMCz
z-FS!Cl)Oe?8^@)lW}4VM+;K7)WXrwInDEL{s<Brs<9fHXJ2|8<T(3}Od|bEeYc920
z(5PYVS3Pj5gr}2+C}`BlSAjge^utz{!@y2_zQ)NXS$v@W{nDQe9b((o)#n_So~%g^
znWD$H;mt%Yde^<l2$TCp7Ly<?@mpYqpdGU!ba2xqyo{U$>S-DzJ>1CnTVr%a$6x@A
z750jsBM>t!8D0PTtIs+7($@Aznrz|hTb?8nzb5HI<zijCJbQ*<O8&Vx>Z~nJuB4Bc
z);>#Av(*N}Nxe5<?n_lAyN6ezb8d|Jyl1;o#X^Dp5AdmiMX0oe$#$r_QY<X7i8;w0
zVj}LU3rY%;jJn>(A<+yWBMjI%VO)KdF6c@N)&b+UOhcDMyK<eDaYn3avp-O#Xob0K
zAS8%hHZGGvN4B5)YBP+W>?Fodaw1LE?Ed(8Iti_u_02mw&FXn>=}wNGgx3o~KkTrB
z!4)6Ap#;ql@y}iEhN*!xJQhOZyIj1)b_sgTUK$3RJ`Xs8w@P!_<dmEj$<)o`y_9?E
ze_UhRdcGo<wDGUI#gnT<JjF_TD+H+~-o>A-uUn*RJHZXP+vvC?WEByCRr&3aP>8iT
z6y-q#aAh&tPcvV(UUv%CdAH0294F#qI$iZ>|Gu}u$3Foj+5O&fNB2yJbEtIBCts%U
z%EcCIZauuqkC`HO`%gjRV)tHaB@?Xm>^N75k-|3v4CKV)yy%-5JzA1N`ktdEKcY`e
zzd;7va#wXYr|=jGbrDyQQQ%<+{XCgL`hnKh#3^iW8f6n{#pVc%Ja;{fU`d1Ggbszu
z^{1gN{<cB&)*#KrDL(DIkV=I0e4`21o&;<}N|9LMya_l;4eht=tU@9%BqqJv!fd(o
z$}xwC|25G|xe%cp7XmbEc_oXll2J?W;}CwpA+iSCQSX?2*WVvZ>KEP<ZfYD}RgD`P
zqt5SsVPWZP^|w2yzWqS0tPYTKgXaOhAtslj%0B=u{O9^=Pxu=10h_V$)dTrpb3Xb#
zHyK;%*<?7oVkSXApd9xHUq_PU?0^HxdocC%d-V>9>4XlDlMSU*%zb_9H5u$GleAmw
zzF7PS&O6VlsbI#t*mSrJh8@7cW;y(;rO3&hX?(T)JfifI-YYpC9%*w^>KgX%N{P`Z
zqD9Y=m&#mj*Jy;#qmdbY8*Fo9)Vp#Lnp+JQ2_jd)>B(B(G*Y$NT_fg{%%43r3k8<n
z``zrksamT^UElNNHrT?3#?t*@9cjg@ey7XsfKwNHef`b+1_#H#z)YM?w6*?{69^#X
zL*>Je6@C^#EGl1&US{rk))LVMoPgXVAkrF0EknZ3*N1<1f()j5W&vC6Zm4p(4D#|n
zygr~}#FkP-os0M{_v>i(JtBL{a=B@stIn<c-siw&tqVKgAmHldkLJK#&zr;Z<*mLD
z^ZIF+?<tSb=BW{%nBbeHvW>VoXye@=b^{ADPITDCYPSCub?#6LD}Db1?noY<3y=Ht
zFv0t2_PlDWFs0}{FHM6cWmCWEUm|ze{+Q$g=rk7#RoRwST;X|)O!}CCGxwmi^K<wd
zNx<F#j07m(?(0i73^foJWEV&F%_<&v{L`wel@qzJff(u^xPJkgdZhmCXm-O(ctkfn
z+jrOWZldFsCZ3v|BXtFSGXj5&Mtso@zYcJY-azQxT<DP>@!WS-Ib9X%D7Le?EF*hQ
z3$Z~=aJVm4BFG**S|FAhjHZs$0EsnKS(^^~W&SJ2_vwy@UmYemsjV(pkPCC~0E_?k
z^gR;-V_$W{*4NkgH5{3eHH;M-@>MeWEfpL|pO^-)vHjwbiE+v2gYFCMG)-8Zw#~nD
zJw&yA(i{v9$Brgos=&483M6wyMm`0^n5r#1dlDrc#_Q;%ojt9J`XB0gpv-M@H4jlO
z`EqbAPQ?$3>6&6XUMJUe&Klway3B~2A84n|gHrfOKX~M0NXcmNUILQ*n?Rd110WSb
z_~qmzk~AY~`MVvPF)o$J$W1L68uDk*SCv55=!zSZj1>6dg6ukca}}G$Tgx!ht@+e#
znYkNmw38xBpFP3Dm5@|>V@9K0g^fA-6YVN!kVJ(4V~u%rt19?W9{~HQ^Qyt#!8i>_
z@ic&&OI1fvP*cHe@<3g7*C)bAsJB*QdS9ZcH~AN$S~5_H%4mll3%p*Y>(FXLkT4C7
zd!H@eOoz!w6@s$+1WM<}svTCjJ7zQ2llQDiKPqlz{mHfV&;tPp3W(9YOJ@5Khex8n
zE`nn5OQz?USl$qj$>!_=gTQ&HInW5Sm&+Y}D3l84``7}@*KFz}>ZbRv+jcWwtTfq0
z$ur27jQ1b|nHsZO{W1|Ry<*5oDM-eDyVXq?jdeTe%X3=!v9V{-ran)A?K2(Dj?}ss
zU=|~VTn#W0?sG#k^ti;0`<b6g%mqMx-%ZyrQF)?~7=-r}8eIC09=ZU#^7T|^xtKr-
z>chLM4fI(r?gT2O%FI<*cn*lX*S&>7^!ixcc_mpmK_)7xX8s)lJNgO9DO0y+>qyx;
zuG655%Rv`T566DBOT9|r%Di3o4%R9B%SoR|AySjGv6{0(J4f5*6N06bf%AJbr*InD
zJlPMEp{fV+aLh($c*Nmor9X0*bzKB`Zc_c56Zl~TV=dYgYNm^(*iutQ*nOO%<`O(Y
zZ7`w>Q%j<qZ<^kP(v4ePWq!&zxc-iGo5p*oe{UA<$uN8&pTyJQpXACS$$=xLN-fxL
zYQ-c$U;a9RXgm8=>xHP--vRZ|nktgb8)B(}XzCaJ=+5~sXfZb${f!9`uG+2DojdrJ
z2iN{!AOjDVnS`W<Ib}6g->b58qB`y=lT5v2tsl5H8D3sV$sLaIa|x#C(KITPIpgmH
zGJYWiR|lV$K(;JSZ6X0w_}Q-AV}tNLWo_?TU!eeTPHIYBzn>-x4H<c0RHSL+c-k!?
z7;E@JCH~j*T>xNLA_K0xgzqkyleX#`5BEuq%m@^;nvOdk1B3QVyK~yynrVTH6SYoz
zS-%O7T#epi-@m;&;NeOcaO8qh`Gkj#7x3zw6Ji7W!L;(pEL2?l$|{$=H5w9x`Q`<E
z_I;m=JUKBf5hfL5Cw~SXzpPhT%x>e&u}^Y%Z}&L{J%4@om1<mfaUZX<MW7n%Ft%JM
zcsax2Trq2T9#Hfa09QbXqn(8)(6L2sh@4ZZg@y4QEpU|<{kg`9A=LM^j2TJ9cF~&t
z5YG$#d0|VvO7%zn4~{CoQ!W6wEMlUu!$ZEAg|CFWI^GsBp8HolU3vWwktCC7Ml*=|
zk%A`GSf}3U^*hR?TqQj6o0|>19<(X`eBYx{3*BO1Hy^Wn+eb&56wt+JaK}?fl+@^_
zG1Wi34s<(QXnMzGu(5TpV6un=C#$?N5$yOzXTNC9V%h<VJaqFl(LdctZ5`$WR+QUU
z1~c7AUo#!b*O;7~nQN0r?4XNrUgI7r&mUSexWL2%Ob^kvJkxv#uf3ycbyml^R!uN@
zU^rTjxUq7^wl)20SSo>>)5+msj1MM%W#pP?iiPsfJebFq6m8xDyz#r~iH13OWsqlu
zM`gR_X$mi?3SN(Ea4EcyHGdDhm%raX)$w*zmeP3h3jS)$2EkO71TacU5zdL84hv{{
zTOXg&h!1DuR0B^)s-Si#NDgzhY6yzz)Lk_5%MaW_&F)5S6_HyHh;!Ne@g}1Zdm+zB
zPj@Pq4T=*$ay|~T4CCcWr%DdbW#Gudm)EVg3v+Jj-FA!z78V&=O3WAZvfIsFJ2<AZ
z^{~BO!K^LQv{%6S0IHgm`DiyqQgSLHb~f}x$%%rw+D2bUqH2>&yD}Zo`>*{U0h-a)
zWf4~WP%S{=OOJ0!k6*0ou)-@GvvySDVIS8B{n)Nd^%@f=lF-v0OCHj|Y~zNr9HwO?
z*mI(8A@xY2|Ap)%q9_Q`0ytJgZ8d4E=7fn~O_xP`XidfB02ir^TS8(TcD2<H9-#)k
z%`)50bETOnLqsTQB1}(HS=T~<WiKfj(o)M$m_L#vldE1l)~ZIi-b4oKw+i2i8Kmk2
z?#Iwj;~ziLKGGNDx(EKld})`&$eg4lr{7*5v2_WWhfma#06To49dD&gM}k(*3`bfu
zK+r<?3uP1JlC`Y$xMS8RWJDRi42GkxnZ64R!*01)2c2cXx6?L=g{<Y(uEIB!i`w_Y
z%K{!2$1hl>J{<{WyLWflA$aTi56wcu=O`qLIogCnFa`GU8%ph%-lTNY_YoTjbf+d`
z9{o*LdL8l47YaSN)-Dorr|#72@J<3J?f}hMr>Oh9{Zg11Mgt1iv70CtPH+vM`invr
z7h&9KkA){~Iu12;nifZW-pYk1i4(0CA!{UjLPsUbB+UnF#8Y@$!up?VE20iATQAEj
z2~(vL{$+?=x5NL1tDq5U*c)nZZuTZFLEXaWY?_C9>|z@H_XP2m+eW5sQX>zB<46^-
zl|q}`yb`r3hk5S)f@nlYo7K#NwS6sY0W(=uj)C9KdxiF?waujRa)}qt{t>wyWwqv(
zXK5Gc2S2VR|FniUl83wLWJwUp#O`MnTy@iguj2N!Nv(p*%?t(M>Uq$wrIUqN56aeG
zYvPH0=Eor7mbEocc3H<!bvtA&e7_5K3!KNilOIVMNsPtQ)?+Y9Rs1&QZNl~ZmwRB<
zgjCoONit@DcV;g!F>j{X+e_gfrm_tSEajUaLdhZyGxy)=Mp$HEl#_7KYBg4|QVbIF
zZfWK+|G>ZNp$F5J83@`CZ{LeS%2I5SKm3Ds+VxNTm5DAHjRbqc*YZ8H`oYH*G7t*~
z4YjtRxlXII^!MG%_wU=UyJ29A+HhSuahstpxgYc^Q1=njU)E6O<Q6}qS2DKVbWx0E
zr~Y~Akoh(}eBYa(tBDgQ3Y~`6$?kjE%uJ)dOAzCXrpouX*QE$kxRbtJ|E@X4-?XlE
z@lc?<@fvv|d7I?zq!PY7y4yx%AEE}_uorFoxfE{SI)}2gDbjwo2JJTP2keYx=JkLv
za&`j4vb=Rt;!#xTJV7_({l@YI30+Jy2mj4sPG6juSkx=Jlr(9NA)YD|9nnt@B)r`-
znx#%8YPP6HMCw{|=8Ituj@geCZ`NKPG=_-rgJ$}+K7oVfO_95!{x&kVB5N00`v)Zy
zaQwr8XGhJuBc~6)C0E~0N=zQzVC@0t+tJFlK%6$NbXnhOS8|n1ff)AP`%Cp77qlxz
zz#y{RZrx431j0D5KiDBmtqV`24@kiqBDHkqhl$)&kONc!{7iO;Ty^_nI+2#wzGqN$
zyX#R;VG1!*cYZnAni_%rj`Ipk(9!2LJ<Z6Q`2yLFD%^R_eo@&n`PW0SXNHGyJ<<(u
z%jf>60{4}`X|TcCK9rkE(jVjN{^S5?m-q1dOH7|z3ZeVa>z(#uO+<THg;<R_atRd)
z)-$TItZingodn8sH2$*Y=2GO8vb*WxiI2h4U5;5RA$UJhAE+$l<w=e1rWiVZ@B9u0
z+5_myX1Ow#JnnxFW7SOP++7)YXD;Am%|A3=2{wCouLBFqP~v8Hz$Ia!4O(g(N<vsz
zst|kMdB>$N`OV;aQ1h(LHoXJkL4J5sd4B@>;@7z^U`kAPG#y8rPySJZ=>h8oI#B|^
zDe5gv#S_1NacS);c00K&=FTfxGmjQ19-Awq?q4x{s+7cr;5JngP1^YFd9{N1&uVgB
z|JL!5P8>n@2s@Yi{cy*yW8fT)sqe)Z1~-4VgSv*~-`d~^+AjGpxAv<oqs`62H|@xl
zgPfhtPXJcrlL&EkG8zd>(EHxIQ0OFu112;S8$G&se_xLNOA#Z95YOOog+h|O{kXl(
zxnGu4b-Vhfl|CXVxFUy>C;jvP{JmuxC{Jah0!~oL<BiIc7fPRrc0l&3)eVeYX<^&0
zv;)s3$?g_85O_1fx&RZ&y9!6H`#tla9anjkO}5p=x}~kh^hxIxlyZ3@i!n3uwOlA+
zs%(OMWG-V@0>$G9cuLN?7A4VpUakbt)cL|p#>Brwy3BgqN@q4H$oknMaf!H~aLa0}
z>K~m0j)5T0@d*luH;q%{y(hcNds5_cME=SeC~<sVzFZfnOe$6Ble>^K$jb>=D_4%s
z)PV_v3L4V1l+>%w!aY-5Kz-uv863C58_{~5`=+@FrCXn0Ex=r-NZal=H$<12aUl4_
z&y0^g93(_)9OKm^EHE9w2`GH|RD+6#PL@>$``;mmv(aK#57ca~v}`}N<bqFEb&wWO
zvF$KH%Yol)4_?twU@$T%k!cz)(6t2*G#i6>$>t8DYNpw3F3KqtbvNTJc>Q9RL_iSa
zDjQ3OZBF`#9>A(og@t+T|HEaprTL2ihCD{Ep%nfUeM|TJ3>YaW<$^yFg}%P2Nr3Je
zy6<?VAuZ{Sd^@yk>~&rxk$!i({>&6qibAuQD*s(va9EkUFFZeg9m)<w4{_l&Ge`qR
z3H^m5pnQPr&)rbkHh!Rq=t2hmN}`mL&O9ind`A!(Vf^EKugzNo@G?_%9CD0>hM41F
zPW+ER`}5uKvWiBkF7rUMKNiegNB5O3svWt_@!R%;2|JxO3i)hv3x-H@KFmD`A4kTY
z**IfR7+Amn%f&9ReC`h0N8!6Q<c2cIv~ldp)5;F~{wjf?NJ4Jz%>kR0#_m@3@HKt#
z>&+T1x)8(Ab<=7`;KJ=MI=wEoT|+smNLH`tBL8DrobPcH1g!P<mu}c4&jD*a=6O;1
zIY#N*+>8xMBI=muS2OPE87$64W%iF(mKLCi5j4Cv#vsxgTa%e4at$FXUc#l7@k9~%
z2PWFFYmJkP%uKMpb3c}LPN@sw85gA1%#TFk6y}!*S4TU1ojC8r`Upx8gaH=~6!Nq>
z?yLiF2MN5xsg@`1qNY-bn(z6jO{ljLt<iZi6A>nulUz|0zKb$tEMN^mvMmx1SRjfP
zYrpn&2UA}8bzov+$pt?LlaUd<HhL+{kxBtj(3%pA5oKVO?p>*rKc6>M^0nz|<uNg=
z*T>)CsPEa7YLNQ`CGHE*fY;^|I=M{|?Z`wwbzlCc`R%{=fW?y}Y#y4mitjkIG|U_0
zg*~`BKwzJ7s7PR)WLF@Dzw|!oHK71w3fF(T#=twgqQnKGiUvVlD*dnXTf{9GhO_dm
zFIglY9^U2@6`8D=V#MTlG=v8HP3pFyM$Ps`%KUFAG9#R8aqQAkhuAnX{R+ZOArqn+
zZ`#i`CR!c+(@vw&M6Pz;Yt9TU7!Ig8qyX~>Z~4<N1^OBI+36M*46yVn^1V~$h3L0W
zV2FgBUmhY3#XO5FS=#Z`qnTNMh6kO5@2}V^7xlLQGzG5fe07_j)f)Lz&_Hz1kC-CH
z4=Q6b!QtFF3X38RfKGYc%?faockZdd^lRuGfkV4@@D^O*2;`W~8`Z4;W9mJivF_ja
z@rI-_GO{-z6d`10kIb?&!fmhYO_?EkWQ5F&$etl9n<RU$&~0zs#_zg&zW@L4cTT5s
zp7V&0&;1_P^;*}h_Zk36{Ib0NxgSGFLKEaWfVhW*@W|ld02xS!Shucbm3y_n{c77=
zfUkX5KBU^$KCI6x-YY}8;ko>0OD@n1O0xGlt}s7#aSMRofGHYl(b)srmL_+X1<rv|
zt+!1m*T&wB!22^7=5HXh2D)zR<w7yyawH*_nv)&_F*j*{d)Km&g0hL+>`L*UvttpV
zAV=%h`Xj5Yz5}y^TN@)v>AOXv5xXrX77;YHeG}4wK;6TR{1fi-W%;#DeM5|o-Yr|x
zHY2)!;<DaXe~w8zA|q}`QcazeKsR09>wKo)LpLen){2{6K{6xIU#p3?x3{IcbXe&;
zbJBcg=3?iOj$&+xgv19A!yu>wDVft!m`cw+v;}JnwXILZVN2mG0NOD?c2}D|0n1pD
z`t~=Z(6TXq`=xJXl*tFYjVoD}Tp>;snwj;4#fyV^mH9--iWK4t$akrxIVT;>ndb8U
zQ>1*YKuL&Cir?~fC^=8T{oaJWuyoPpj95Hs;(M^J@^+G%`Q&2WN`kH^cN#QL*GHYV
z+|PWD8zYf!V;Z+vaAa`a4czROCzv;XtFodyX)VZuG`-C}Q^it7PpB--`7ZUkt1!ng
z8uSj=Nx4|Q*cHU{R-h+rx7J=gy3rOyFHkCZ9DTLeuY>|T(eM6jn)9eL5kGR<SeE!8
z{HTA$QU;U(X%xEFh3L?m>}UAE+=fV!Dn18@HzNZh-FJ_F(O4|mn?Kv$oT++o?)w**
z4agxPs#r-L_o%z9ZO52_(P%zc$idEfcDx|8x7R5FM4eE8{i3k>+<(p6wbQS-aJ5dJ
zo|-;2lpu_}(;IQuc9cr?^8UyMx|!D)${gYJcj#5}t+Z{bvSyk{Vm#ZXV>#NZ9gTd*
z8{@&=9LN3XyWA%i&A(J}Pp>cU2b($|xF3RaxTAt{;=Ulu-ugakw4j9EJCz^Y9K^Tq
z!$>8w#6;_5gkQVRd;!A$ZS$>_Pmf&?0q@h(+smeBwj(}%Ro}$Mj1CEK2CQpbfk?vl
zIHc`xdEXllL!LFYxWReEr^xhawxahYpu_s17Ox=ibIq9aX7`Q>T9$%r@`zXwh|P!%
z;UqM+pck~>^xkqf0fc|(x%NNWJGF%;^<~rCHB{hSvC|JWPNJJ0WD$|MSX-RWcf;&b
z=ax!UlkZz8E7#nW1A!hs!Orz935Rjgi|JXEz@{<QXFR;Sq|~8VqS?QsRQ<O4#)k+g
zML><bl56fPU!vFpwinco+Uv!gT*=f3xeg<`OniSeE(QMVFhUt<(5`kK89EkrYcvv1
zJ@L?Wok+Vfz4!qxy!;PdhCyAetslI6g8GIDa*D|LM6`{(^E>%2#+8rDeUW<r(0>2n
zR&b=%S`+)&w9*FF_@JAcX3|-+J74MuA4)>~j(DoEFCRZ?1nE(nfiJOCG?tVT;x09I
z!RdlrMX->IHS1FrqmNT&tCKRK^=L(;TbeRIu{fWa&(7IXBECYe4L*a*C+DNAjVs1g
z)|9C8B0peMhPmu@@ffm?f_OFqZQEmW3xPPQw=jfcFTk`al1;xX>F}ww;2SIVH!wav
zW(S&S$0-0U*z1&taekJhW#-mrmTDI2C_di>-ZHZfKiA^j%uUS*{i?${#M_KBt{<|Z
z*kc&&{~Y^o=?cr0v4fbn)6@u5Lg{13zxqEY@cdp|^Ajm-cz>wVw)fAbDCsj<Tq;A&
zKB=kK0~G)@$_iBO0(b7FhH}-0QS<BNBLbjzt{w6m`rLrhMjVii?=P-(xk7?PN93kY
zQ>iAjUIu5oYu=vTHG5Q^zqq{N&Yu6cdoO`Jj;)WXde&{k`2}CNl8GVfYG6&R4pWnU
z?z22@Uw~U^ICgePl%xB<cZJ{e{}zdnQ8Lp*ZN+z=e3&>|>#g4Pmvs$MhatK50x~gU
zC^3kT%S_3+>--;C*tnt-BXZeD4Z}%9ef{9xx?Cp9{)@t6bh(Z?V#5Ksdy|jjK4Aog
z$=rNi^HjV#Li@MlEPo{ah)SjB`@TJIc5W<|x`^P<Q)C50_vLIKvFncBB^psxbJt8t
z#DiIUG4vT^tkSYs!<?lPBYO7}>gtwvHxdG;ycM)2V~M#zRT%LH!|v%qEnh?onY>U5
zkpZ3sDV@!LU!mW29y+A^Q1y#~7TRe5jwDmJv;n}ch>35Z8d$FD*fNR<kQf{BcHsGJ
zT`l%5Yx{Fb9O4wfVCLV|0hyzYMsb#A+kJguJ;1^noP}{@?W+!!rvD@OQ(8EAx&sA(
zmA|Wh@>9+<B64$er&Ka=h@;<Or(rVg7LGL25Y+H^A6)LsiP1XLpXwyNc&~9hUd^Eb
zK3g{5qr&Xq1t29awl8)RA2hh8h#qT-E`sQ*(e9*t#X~I&XP4p*uSO_#c+O@rlT8XP
zY?>BpK|m>)_DMxP0kr`<h~wS@SL>q1=PLhPHdmY%JHqLOH0&i#R<Tp&q41}7+uz?u
z&?JCIse!Zg;8qX&fK3dQ9GAOWqU`$RVIKneL>6o!7z+HK69e9lpBK&U33<DNaTAHj
z9PnJVDxaQxe$K`xXJQPaiEPaqeB53Xn(QL)MEPZ~l}gsUmt~P7NXo!y1)zrcCsDPf
z?)l3!xY!tfsv3p7bbGtvUO{eZM?2A$LAS5B-{zTUi}_*8A6es8OoF}0ZSz41PqEx&
zD6i6Q{z2Kh&z-I&TT+X3LEoQ&{v%KGh3?7AG;?~%Lc^He?|!pVe{i^(kL2*~%HmzS
z^90r;Ozi<?Ia9-Ow~NE}p+LN$6RW?ixola0@nfKKOnamUi86O?0}00{*K*`FaX;)J
zho0u*)RdFmjJ35lM0FvAv!M9Z>Jn*=S2!CDJEyxjRHxFcs5Sjaf-=_fDwVl28iU1O
zPq`bO%`BM4_YJ@Np~OnDGFB_sl76%7U?hjc>%5r4%cW|0j=%YJr%O+!s#TWdZmRRW
zS?%}6+>ayDY(Re>evoqoM7TErfNgnrRXZV1J^4ShoIj!`pTtyl#pnn_6O|Lp6Y(Jl
zSaRd#L*n<d>7Slib2>97^5183FuVN@NcGG-F^#pQ`FSdwH$(x<=xOKZ1&#ib7G*29
z(yfyOGCUuS{%_^%!GTC5K=IKpG&LTBGdRR4PVGSu(k=0R3f@d(|Ifbgj{_*T<mi0t
z={hyJ1kxmh=U;dqd)WG=kZ9Jp+mlJDlBRTVc{`D6C)isD!#hh`$>;<YtSt?b=<>Gz
z`d62s7B2sLt>HTLe4M$eHmXyf@k6d%eG0l-ru>G_wUPqz{FbkddolPp9zfZn2XCeP
zmA8K^hr;zYEZRnnIg<4z^PVDR2EtRfSfKyZ|Jx#0>{HPR{q6ajL1W+gj%u1Ok~H5M
zTPoh-*Tm9jHxcwlMs%RvdB~fJgDLn|B>tH{1<Cu98DF>bl^LP#L2g2rYW1dowI-qm
zX&~IUe6(`nKYLCFn3bHVQCqAb<A&00g@n8BqWWPkf9{94uO!%-0mgLDS9F{nINzkW
zlN*7(H=(ICD~$M5&nisQ;o?7MHkqqod*~Mm?uz@5?yXogZ<9zMak$nJ*k}X=<>>Fs
z2RB`aIBIIJEL(j&IVcya%Fb{={ULXJubEU|_kGMMf#dYMWAl+^B%B^-qzMSy2Th^_
zt{2nw?-a7#7m;Sr=9AKedsIr*s+f7_Kj9~)=ZirY@m?=WTwuq>{C_v5IAuo`#16gS
z06)T^r#)s`K_?s^=0Vc+7CVR49CI!~hxy5nNo*eU{n$D}v&kXZ@e7ryn~=A1dVT2{
zyYIo4cRU1B#kM0UKyrY_0Rej)>v|cB73iEB8Numj<TSuFSXJ-r9=Keq*m!0)ixb3A
zM-7Z-ku+!au3!@ix9PMw{-ycbjN1{Ur{Ncenp><C8ft+C7gly99-d*YjlO{`rtuW%
z?Di*Tlc|Qm1k$n$3GcRn2;EG6`I&_aPXAG#y*vF49*G7%7dI;%{Ao^SP-6*UTd36Y
zP=V;Y=3WwMGHT_^Vo5$(6ALL#2gVw<D{_d;uLp%I{PsRKb7H;WvRN?@6o=&n=iaEO
zzL8Dox9zrcrlb%<C(Pq}1quM@_U_=rFZ61;^;+^UZ+IOUHs&zV`7ht|#}Vl%OWXPO
zEra#kM8X3ri|Nyd`M&~9$1`_z2at$@1OW*RYoDX^(<pPHfX|(hi*zw-EEgxD$B!Jc
z<Ss4bV-*zdR-dB`%yxcbj*94Gr}gY?XN;!o4xE#u8-v8@lR@&v{`3^ZwA`qj&lx*+
zhcsG?2FvDj?r5f?R8NTSn0-G=8lL_90F6)^k*0I1pzo*u9lrB7O09!ETC)c$%u^20
z8#$IJ#9T;$l>%@m#PrRwpOigf35+U;XXB&*Yw@GH>B<<oJg=zSMg&j^JXR_<CAhf;
zO#p~|bZYVA9`}gR-cP{RxAOc_2bA0ox0^KSYKP|%NJcsO)UYATME(fRS$#K`PakTY
zeLf1>AvMHd_#EARO*<f5=N8r#9SzisTxSdbXhB#qP6h2u)epXul<H>IsJ9;pd5Mxz
z6NHduJM7f|WsolmU}aOFBnK@SU{VO1(kF#var~ZX!MTM2Edn75@77-}D7k#xI+9Nd
zFZmAYu-r&o*D|r{BL55w<LBBDX{iXS%6C?tZpE`~&o|H0Z1Vv1dhFogH+&*gR2Q=1
z*7nShAc^IZ{s+U|AGdeZmKu?hmXkabOz}pko7^&lhM6I+%<R4Y48PQ?i=c?Bw4-?a
z>pq*vK?^q23>vm&Le+9vwhQjm^X38jDj(nw;^vCKn-o6Hm-wDa?#Jiq5M~BR8m^p^
z%>h;MVIpa!pNv28t46v%2l4>hm_Qb1YZc^YYYz7rS8K?e;BLMNr#QJWH=6W=1Ii*Y
zXcVhONw$$gS{!nrw!>UkYP_7|XHS0DR|uNm%pU)F4DG@qpU=Tp^Aa|+OH}zu!wiTc
z_b$#2&J)2R<#I4qT1wP`i?`>CqPYNKSiV2toSmJx=226-=-*GG2&-VSP+yeY*Y?>{
zq@D2ZyA%qITi0`1^rPZy8b~rQXq}mkT*~&cZM=6k-KqVaX@4Q4M2hgGuDlT(C~cTc
zL%O-81#kI(md*RqFzH*JZd{$Mry5`1zf~`K1gD()F=A`e^ZBFY;&cCoo}>Da8?MS8
z>z@g=qdk$!K1d_fu8)VXQ*bE;^042SYI36?uAr;IxxzcuGc6K1bt0_z+(WEm_WZ&N
zt!nE0qIn$Nbci{7Y-KlBJCkZsV>Mp8<zzN{<bSkrBA6WWz<DM%_ns?`+M0K@*Ttqu
z&4550<K~IJ%|$PrmO*_(F4CJgb@Zs=x;L?FBT_GIWqv~6%-tVbBf6bM=pMbq|Fc)n
z9Ai;D46vGSV#jF4zd@uuuiA3l@a;W)>Ez@w*yV+mRHxsSUq5SLl%u^amhN-lCly(u
zR5!5marumW+M*W^u$5hJpRHnDCQ&WioJd;TZT=f^=QFK`D`Ho!<$qa<2=@LhsE=7=
z7v;f>(3a+vGzu*dZR1n^zxy?RSO@UwQmH4ZZb3H6m_!)!FJXA@|9341FeBIu7XO4l
zQWzTFlEQ~w9?%#PWA^|5?~dL*FEDV<@PI|oEv<8a0KNhjlwbe180*y?0JKGgedHby
z64k&DtH*C!7JXu*MYWbc{+W-Jl_jUkoY?m0Q8ZoZySH+XyZvv8J)U&X)@4;Gt~m5m
z#W0-xdS1!>!N(%OWyt97YNroJ1gN2(K>aX(gN$09Qz&i@%qnO4ME^b5{0&FS_XmA9
z4?H}ZNThBb27>5El&^9&j1H@X8eignb57w=smrU@UO{@z3wPB`H2zNM_3!hUzc+^x
z$z21PL3r*s>Im>lAY3NfU37IvJM4wM20D)XeQ9fq+2shzFv{p*+DIsUmSuA~orJ^?
z5!i7E1_6{cmy}5`L1@RVZzZg_L%MS1Nal2vMHTym4MoQeaD}>~tp`Hz*OCA1mbbLS
zb|hSTb)f~FXzaDvh?IOs3rkNEE0AYUY5ua;Y{#CL&iydR1JtlG9>;}8)4`2cTo|KH
z+nV?Au}g_Y+^F5th8W7s&gQC&LeMMoWTI^+Edm)O5e08Os~c(7UD4m5CsW7DSo?v^
z(Dy%|tws;Fg_`)X#bcgCFTeE7mW3akOz!n13*TQwmLVD|3*yAT_Bc<SoTgRwfywG6
zt?YE$rq}3XZumxxR<8ddCW^9S$753F)!S`P<kJ{NBB@QU3;#v`%udo&;{e0FfOju_
ziNXS-?%Xh`P9J!lTmN9vCPhA{>$@qi!c$xA1Ok*D?PYq&iiABk`%}PFQ%1$!15#IO
zL4My|p)b{uyJs)!pImWAm1?Vl8&xrW(D{yf{Ea{-Cq<B~yp_b^Q5Q?NYyXZIWBwa@
zas@Q+*%X()9<8VpRpzUuu-_+vHK$f+qcPgUL(T;HZveV21bC81Qg6A9;wc4znj7az
zNJdmpaUr~^!8|ek&ky6mV-+N2nOdQ5mHk8ye{(wBk*hm0+M)fx=sQw3m7m(!v3c#p
zC1MfeK8}0tRlDj5n(|=x`GsTxcx}QarHbrys39?0@C~8fbAae&+i0V)@IzLC%Y&vF
zaB{GX(Zz>ylK<RvkMuvR6&fFajC9;ayo8N1^}O;b{olWf6uXC+PP|f$^2Hi#pV?KE
z+K>$0ys{5R<{KAvF?Ga3sS0z+9WYnMfP^5emoqMm`(c`?HBSh^&%gSc{;NL7i9J6G
zY9xia#;E*MO{G}v6oT8}(=YAOzJ!p)n#6=K#y9Le0q<yKZAn?dnE>rJxJYw9mA%7m
ze{AoC4f7*JDn)3jeD2;LlEO@D9GDlIR0FeKVRdaoiB#>+OqIOyQuUlcPH4z^1TW8S
zK5VfU`r5A;Zu?SY14E8Sk&gHgR<Qr2zbd>+?50sY-^r+yqQL*clhVq`gV>lkIOVaq
ziZ>bQo(AAJ(M@N7bwRO{&-eEhi^v}lDEZ<BcEpf<WxCz*b5r@c7G+iX|IBba@bfAr
zh(V29Xks|tjHC0#F?LPqwyN~drZq`W20=JE_}q+2Z!@&Y{mhrOySNiZ7VxfFRQeVW
zYw!LI*`TD2So~=#2y(M~@hR*Nh*{$NF3HyZY$>CJZQ0`@AjVez-hQD*pM$$NC3O|`
z+Lzg1JjPG(po|^7=PE>G+R=$ayXFNyYln(6tXStuq<JYA;@<((%h?LjOD1mcc@-3_
z9~F483^{=k?R?zsBF-zLDy!q`-=B2)?rXP=v*es?R)SRqf^%}Nq`Xjn0KA<|gF^lk
z&^LxUxTb=gp`f=Ka`4c;orav3V1C}&;e0l;#gj~&;{dLlBm<U@u4PN~;LDO_jt$}B
zjyFWGbd8r2wq?>8sb&pS9=IKg04as`>)LsvVyT3g2u4nNe0S8r{^u}027x5cY)VVD
zmv`fVo3ZTW_-(;^U&kiQbm%5mrGU1styxNKZ2lc<jz$`Uy>?81iC|}$LZgbYMeW-H
z7BuT!mrHQd0>P~c!V*A>xgI5flSPUiUrasiJnTC-vcQxK^}yIv0hg;MTW8xNn`9iq
z$sIpuo9ldhaM(>IJld#hK5Ck-ioTO%SrlH-O<Fh6)2YbVvc&a}sblDa$Rni(BxXkJ
z2R}@nFVV6b@|bG6mfKd}bcTlhR#>1?RJKA9$h;@PN>a6WP)6iQrltQXHXqfnMa6Jw
z_Q1ahY0VJB4lC7DI~%^9b}TP{vdkF=K=pBjxbY-P!1)O~q;CZK(Jl?Ol<6uAF&X3y
znI{s-J9ozuhl4m<BPv|0sL~VJsA0FrKT~Y5A}CtZn^RaAIZw6T|LQ?AAhTZ&zCR2K
zUVzI?aKu^%-gbh9{AW8gmIQM4FCb&Q|0mU^)n!UQP^P*LeZ({8k*`wU!a5J$I;lw`
zq9n8?k&7|sQ9x*mt1jyk*JrpE2sz#D)W=(U7tTaRro;)fR@;v1!r&Zc1{Nz!!-@Jg
zPPOIrAN^kEtCZ7W(Uz5W5LI_9r@$!jT_e0mJY2eUJ$_;RymHKiZfkS(Aps{35lAA9
zv~lAtZ_VxjO#r7`sW}UOKJ||n<<SH46y9`QEhG2JimVRAvq4%nfw<Sfx_D3w*$9H{
zC_J})YU94fh&+fnLzd&|+Z_l;r%$9z_=X;0vHFGIN{?R3%)bfY1E3RHa`QLu1-(K{
z&-W1NeI>aO+PD`dT2(z09)Yei^$l4vZN~o+!szk6WiGdG1{&r}zzZ)eNrV{-cQgdG
zL#CgMM7$q6s`e&sUOCd<(^=fP-6csn>0*&W9D(E#`HeZ=grB9^a$ZqlL(<`#uQA#1
zdZWFE4XUPEA1kWS>Av%>4twucmj%ZzypuCKv6qdA!f@0SGxYfe)dF8>F;M<gRX=H*
zwbxGg!DDi%@gg!8rH3ugyET=_5>E~vn$~3AtHs}#fkvtA%k)K6;Wk^=7d~57Z)QU>
zYZ?}N{nMY)k72^z0hTd(9s^8r@&R&;EuhN`E%=Dt*0`$g8WEz;(evZrw7)NCZkB2i
zVs&9ljqtI8*b~@KqEMWIN@6Q36QEfga=NmZNQyrvXpPU8{;^L^>!s}>;Ar41pAB;`
znBHjFJN=kF>r%r0{#m|Q{?yXpDe+S_sjA&apq<SeuG*^i9Ur&4d|V^aoGRhA%FA@Q
zu9!<C&B#GWvGjxVs5-E&VE&Wk&m&l?B8Kvg6!C8i3+G3_Si@kDp@HCPcLufh*-k@S
z|K6b=?KHI}N)>bY>WdTd7bgPMzj>qMKT>Y4uiY^H<aql1ODe1&uzRE*mkB?J*9ikT
zl?*OUs|1%dd(ZsuDW)bby9n3WroNx@H+r02H7McrbkuyPT71U-$PKg>BFAoTME`DH
zL+@x|;bt^X5wgS6)z*9p6_lBCg91Iiktr+c$E?9@UP+zCZ`boPL2GOE@u`A??qL@~
z*>#zskz9Q{xD3TkRByL=EXFfX3JSDnHhI-OCqLRpSlU>t1B$S><+Fu0pnWcWPlK#;
z(Tfc4o8$JrSiII^m>Sz5?S8P_`gM1~I!f;ItY<+X+PwH?mk1GBrI-T3j#1msdtHGh
z@JZ=5)!Khz&e=NfV^dC6{t=p`!Ixyf4xi1%;cQb62)!iAn;#k>_{AQS*DEYCckOw}
z=g_8jS=?m_neHCde(?p$4bTK0c+9yRAzjOow)%I8(kQ{}GBW9PJb1-%@5NNwfFrE3
zqN+OxQCE?avxx@^J%&CR-xiE6%OxD2i5^Ee33LNb@%7-ZY6KM(oasAi>sf$g)`h&z
z1TyZDMJ0Rk{X)&$s;@ex-dW=LQ!m|XC5x!z6mhx_<c>DIqU4qgCkeorOO8WGlMW`#
zp;&FOkZ;D<P%Q~=79~iP{%SkeOxGT3cv9<PoC<U*_`qS#4BcwjSXq_Hp%B?L9ZAGu
zsd^q{Ig*3)3bGHtK@lx4g{%8=aL>DYnJGNTdA4awzfF_%K7>Zh0gnoDIOrTah4IrF
zXFomvNwMGm)!CD6EJ88mIrDdrHgXHZkd7(LTwlX{3VXn@x*9Er%!#Le`t+LR0dskA
z{Tqq_#~trjuuMUqZml|mo0@`>8Tj98o7jdoJXkO#oYkbhk4xol`;^;2BI7jMxULrK
zGxlM~DJiScK-)nqUtGP@RyR~kH--tjZ7d?}@a*ZkaK^{Z4)5|qu#=pK#x9HlfCZW0
z1-rP<Vb2RF1dIBg#6u-L!wIbq*qG&W0;kvb?ybWpf}jua-C*8iMN26)liAttun<$g
zdGZJDF!wUl#r2&t!KCnFB%~J9+OyS=y;>Z>97s<wa^vs%B}qPZu^|pLh0i}U#E{0B
z`&K;}BgmbLyi)(?oTf3*{a*ILyEbeFZ}te*4O%J*+WG#pw53|d*mn_(gB2g&tJrZZ
zT>fP_4nKEFSx?B8BOHGBND*xaLsFkPZ|{3^vd$V$94{Yb!p-%8HvXN%5&#N`gDJG$
zw~y15!GUF;o`E?%&|Id+yZ6ZFbO`C?Wp6>-jX^i|-Hu~PTlay($pm@Rp*kVz>r-9|
z;aAH8)6O=N%_Sk}O^&gyv*~6&r6qPfOZ?PUsn2HdMD#&>4bBi_BO!0iZ@gNgkXxIa
zi|zHKw7yt);L~swT=lzy%ulD1Czn$3Y=<nhuQPpIMl~P4V1JZoFlOY$C|5KiJ*oyw
zVSxZ?$6M2(h2K-e7pDdd)5v@GuoE^W0~c$cdhVT`S!h)zK3R>u8=8X&_Mg3HoA0)+
z&(==vxdYD;&`MsE(1%vU;WC3fWb<R;*$glAZ&m-5{oWcZJY&6@Co^~t%D?Iu6%7S<
zl~F1TQRgYdPQxrQB;TliqcWQb2tk$y&cE;F6*#=?aVr@9xO6h44V8CzZWr7sUKcW&
z5P%l$Q2Us(xozX0r-!TQfWx=t)_~&P&pqz1huwxogFk#YCL(ImM#(IPYF4&B_m?Ek
zp15v-;C^730$HJRG=P{=2JyamqSsdNd-sd1Yd6~k;OMmf{i_ZAFCRz96x!@Goox!D
zRiJ;uos;{{nMOsRo7;t1F!L=rCSXQd=`rB%+A+>D|C9R7hy^X+srb8|ewh8s(gxhv
zFlNX^L*pr^4710}I2D7X%P(eXQGL$dP|=<4xN^L5w2d8K1J8)4XSkO2#dS~j;$S4E
zuo&K-hsPFX$+&RY!R6f7SBnD?ik}8~1mmd>BT!;^$uCP{`i^{^0-tJXxL>qhJD*DT
zcmww1WZvVeTW}av{a1*HKyNMGicXjq;VW1QJ2=zN79O&^*4J;>Zv$`y>~m5I#b^ag
zld9_*N}iJyV0>tpiNCFIR%!DdqI1w8P2c;_^_-0(CpQDMwq=x{&C8B)2N8t?w}ji{
zbT@XM?evf>l$f@em1l`C%SJ!RAJ~#`<NJfnYWR;?_|tJ;@b$5R`j5TXMSf65CWdig
z{!ODfcDJT5+?XT0tPLrc%MOlBBpVMJX%v!OC}C(tVsh_ow37;^6JC?MqNqOT^03Ie
zsU|JbLSRaN%*e3x+t2Qoh^ftMlP>q-VfPc4C<MRw_uFvsCSx3Kk<Jfo_}6f7aIC-H
zLV@V{k4}gcAFq}c>$>HSaoRl)PUnnUyjZZevb`l2172?Wp6gpva<>CMjn1V@K?07@
zGD51wMHf!bZyqgY(`gv9%&W#AM5$C?<hU^VvfCXNjEhJxDzaTT8Lsze9j|%{K_2NB
zhcN9d9=6%WBEe>Vyp<I+baFhFuXc|~!HVYAM6#9vcdBu@e60iX>t&S4MpfT{uX`BU
z)&`art&!%jgo)f%8gFJT)7d@uvq}a~v7;Ka(%~9|nnd(u+_~|rAq<3<m>x~)c8M_e
zSG>V+cU~s!H2r+@OVqny6~Up84ER)X<m=y}*{{XsqfZe%wymQDA!2BFVRc_1q08Yj
z5bZYjd+Uo6)8N)o%ng5eG#p^+UEW<ZnR2xO=co|mX+@RCsTbQ1U~J~z(Z$Rtr<1xh
zi61TYJO9zkx^QydBa95}G+Crf?u%BE0(yWN5+=$kbYM&c$q8gIr5(R|*DzN{ov^G@
zSn26+CUWW)Vh27o(6Cun0@l1xTwC11F<aj!xHXNwBpok34G`_Cg5h#u@|Do`LeOvH
z!G`kj_97Hjl~;$9ZR<gN2Ep3uwtY5b@n3Ls2dZpMjiB;+agkqMeCy!Nmgtx|%Si2`
zrmpHH*XT%&2aBke0X*XK&FN)SH<8&xs;0SRaB3gHqf(3>Xlt`MF8^T_bw^F;@!??1
z52>j$rG|o+#?*t=^P|U)%@K`8cpEQHyC4Eds~27%08aaFvC+7NH$()?mw*M{)RHUA
zLLlz2#z`e+6=yn%F)HdK-^PCbjpNkI4}I)pd-X9NSx@GuSigb{p1Hl#lY5}aOu*}J
zxIc@R+%%eEL#{|D6<h1#h~DCg8Dp!3Q}QuS5*Qh^#s4T}Hn5$2e6GK7-NX$NF20D6
z&mN)EP(o<)a*(X^m(x2p>ZonFvDUlGBy%Q~NVa;fne=;Of-#E4V)F1x15RK^lQ+>*
z9O#tLCP+yk1zv7aLc40K6yA0tPB4jPm3_LrzxnsQ$vrLP(Ih5T(5~D0X7w8#;Y6R)
zepEFCsz3&<syfV5yCJgDd~?p$Y?T!V>W68$gPd?3uAf+0U!2bh<9kl7%%P5*ssj6Y
z=Qief0gKCV@IT49LgVxG+x$2rSG}?u$1oIBSAW}1Bppns5b+5X<f6N$XVx=ZrDTuh
z?#+{-X;fZ^=R3^2k%?mwul+9i!MvGUA4B1W4me}F5(*gORa$Diox&yuOfO&MPuZ-Y
zk~~IHN>Z|)vYK!EMMdNmt|rSfX426)U*X|R*!W?trB-+!PL`XIhVl#XRxtE3&V6w>
z3$)3Q^0U6SCu-ZcRo<wdF<f@<eF}s`+rTlm%9faye-jd%bRQ@&Q2{FG8LM<h>idxw
z<><yirgbIsjSviF!y4a!#9MV2f$Gf%X>cCbbpGC8W%xZ_2CF~Sstu0<@%yki4qj+f
z;NrG4m{pfbP*D%uDJ24xm;#eHI{`fc<LsdBa-2p_OO<~H2PEH#mx?u(xQ<6P(qPD6
ztO}CUz`=QOesKyqqEN0UB=2U=&hG;7u>7|#+!K@V;Az5L@V8sCN^ns##YO;%(r}}<
zm;@nRHOULYLS2g(j$Z&&6Fm*ryXH*Qu?WxsNDG~XpeFo#c{Ky8x$$(*j+!|dYj3B0
zS=dt_S}o_md0js@c1d>A+qg*c0x(e+l9DI0E;=!dRV${L4naGkrG4*tQDxq&*}~r}
zEj>2y;5>FWqLfR3l$*B%%JbZ*qJmOF)W5SJ9a7_jR_-GUSF6O%93?B&-E1rKWCClN
zI`K{wdn&w+1M^Du2~$p4JCjO<B5JrLpEV5r4)%43f2C!H;P2W;VCspIqBwwI);Ho{
z#PZ|3q^54_#3T2Bgc%=C)o$I(!R&{OEPWCdAr}w81c2d=s%NVD%W5%G<AI0p$D=#b
zDlq#%U7ZvAPRPf#CL6)Ah^O^bx}0DLfl>whBl*9wpIJQ1uQC^1ShDDG$RAZKo}GA-
zkaLw(CE%p}N`}fKtU6+(AZ{^fojmIuI`~Q9<cMdgnGZpBBu-BaV{0<;uSz9E->KC!
zwbaJVT?Pg7&~vhXkt5){&mQD~u%$Wv8HPvMeD{L^*0w^T+m?5cxtMhWCOH!eaGk=^
z1Q%iM+B!=Oqg<4{Gzj7xl1K;hlptRwE{qV|bX7K@(;o}AP>Biti#3oMJPc8UMeQ1m
zFof;dgKEgz_=Vh%*<{vYeWYdZrKC)U>3w*#{H8BO0AR)%R@{8(!tgZ&Y*pX^w71sX
zDsclapi=X<U^^asi~so|Dzt!wC7BY@Tq}~W0p4GT6w8@_fWR)2KR^f#>!f%!N*CIQ
z@_YnT9U9K}Uy28<lTu%f&6zSE$`VM_@-w75k63F9;-<+G0O-VSc^lUP(h{)s+OaIa
z@d>TBoD{HlEp$|^SR+lvZ05<KnVoLM!HacZ(zF;)%xztFO4a#a)Z#O{M9@oWC7@(c
z^woqPlMFfu!%5+s7*D$oV^@Q|ugb;%mwlXOn*1n*iN@>e*eGH%X^oxx`FO*NL=l|j
zh2H)p$WsGC;ZjT&XBNW^2%$+sZdh8@XLbg>o725Vean!vxv`5=O`I-VVMW?nh**3`
zU_}uCeAd-uKcu@GR236iRiIP`nUp7Anq?(1;3|KmuMIg+-<w-QHGizH48J*QXAN-A
zzfrY^sbjaGM!>$L_dF@Nlk-uuDMZ8+)hhN<nZC#`Q0V-@?}Gp_IfhK+J5GTQSRS_&
z5i07})Th0xlD1Gh0wh~BFq<{7rw2xjw0t)`h%PTv=$U7>Gw3+->Q7I_z$~oT6B8O(
zOg&oJ)=l>+ZCt!%rkx<m*z!S8xVe@)wpYOnkY6Ij=dP(ZW4tzCT1B@UhvI2lUKd6x
zKga)EIF{PHH~PdVOfUi=TG#8cEo~Zl@nD;IWz5`g*kVs)>EQy$7+8O||60j_&hMc>
zjHLRKUW4ZBQNEi0$Au1(gyZ)5>csj6SkoTa&sHsq`T#A&6V;zvUz3XoIZJsv<4pr0
zf=Ip*bUxkWt;mt4r!lm#Xq0h2EM2g<YcUJT{~Li7dJQt82P{PBnh;vb_-ZgJR)%*+
z=tx6cB47w2-IHz$pzXKj0a^S@ORm;kd5aEVOcU)tiZ#>}axfMQ1HeFdmjHdY7*eTE
zPaicE4p*7;-WNGFkN%hLSdMHC&-<NqV07SpJhvzXezIzP(NK1j@+*ocQ20Z>eiuBA
z=ilDFF!u+ikr$XlQ{KD>E3-o14KAL3*;?D(&l1FzB8y@_gw)gAdkTsOzmJo+*Gc3E
zNQ1gn9`wU427Nx=`|yXrdc}ssC`qAa9>Bd0(R?o6sSwdPdwwnzn)5xaq9UojA<(Aw
z>+va1Y2L$<4s$rjaQ;Jfp5%TiM<WI!BRycdbm{qFYF38$`4G2nsngULF{B#PCA+2M
z+4;lcu7BjuJRzc=Dr!lZ`pL`3rT9L}Pd~XGow<WK1>zRG4733;x(ffnu4D>{pHXrh
zobUYYWp}-y|2@XoS~M)pvSxzkZbs{XAzTW;9B??uYDtX#Y80VSR0jvc2T{SU=+=Ll
z*h&hdZbNCmOgj6ZM?f<x04)&U<+a&od^Pp#hvlU8Z!4{Yy&qc{nVqmVz+utmxB}s3
zvXF_^neDeum@^=fHu(09K*8<sRkY8#^w%7$V>A2wZ+*3WjcJ4*2P=-(2J8qT17XgN
zlR=NL;(v(LMG+pHHQu5yHIPzRs28F+(G6Q!5=*W12d&;!q$g7kK^KB_T7`@{)Dfa)
z1C9Kl-Cg-Tg$Y7*@2zx9ZGk(>aFZ=w7j1NyeVxhv6dm&i>6$@=a2m*d$`q6H{Y6WO
zTUO+x2*Vb!B|NjgMZr|yhe<0iqi(;GlcSNdb-Az*8V5Jj3g5$`bMA@Jk)GA$7Fgy^
ztm5p%e>@+fGFS*=DymUWHt^-w??_Q6dhe$Cr1*=CszD$IXHbUsZ^nIDNoF#%rPRcW
zU5bgy*n?F9$h<Ie$t*f2VHS&#N6XPwx1^#yI|92vavq6W{`DDP1CM6BMOSO5w!%L>
zt9`RrBQ{{HNS7KB`VrtGlqqL~JXAbaE+whO0p|+nn0#g6%1MKd$9xp^huh5blt=_a
z8d%G>RX*tQ&eR@{*T>4s#R!at-<*%??|gNo<A77~daFv3K`-3d7F(HL^LmalG;Vb-
z-3;{j^lNpFGG;=s^Fj3TN8jZ!*-(Jl0o81UZ>Gkz+nN5HPY}UE!o1RvNcz+`fG3I(
z_%fm}XL4^-tUEVxh_rLZD?D?W{8?DSyxgQs^PZ2myScm_`t;rXAV(tmd9;j=K@8)8
z-{F6r9Mc|pgFFVglK3ysVS6izRoMiC6(P`wYN+BNwvEAq8DWmj7TwvrS7#%bMI)Ql
z&Z`Q>iZY3*{q~3Z7=YE#6W=<(oZAOkKQ_ba&U;7%q>_Wa1ol1@W%2U@5%r($7NYJ`
zjy!fSPdpOUd7_HY9hKPJzl`I2C7@Q}T~`;+b3!rzL>S(OgVtXxAxAhpU~-ZK=Nc+=
zZH+w{7A@&iO|4k|&vj2X<sTkd;CXHRG0aS?@^vph?(pk||1K8NU=x9P^9a(Opi3{b
zivK7%d+V@1IXBblW?gX%T3c(3j*(yQ1tRMPczX}}OAnuw6y;|RiKWDX&Y~7HWzpJt
z_ZQupFJ<~1D(0@uxr?QQD+tI7P)!e+kbu1<y!op<V8CwD;Sss8a>26%p*@h!3eF$6
zuhC|~=dl(Ml;qMI2x``{Q%UY?5aZA{8UbU0Fa}an7G^JIP+rG7;<Mh1P+9ow%-C=x
zjS&urxKF`F==+;5ZRK?QUjGM58FiZbFZRXM)PJ8Q$w9`PG31Blu(6$<)A;-vb$pb}
zbduQy)iUfKuv|?}270%kGbmwx?=~c6JZ1cx#j<NWt`8n+;z!5jO*=vZ>FEpmUG|M9
z*J(<=KASjjtSwds^3pK>8&EJX%~y&4bO{x&ozQyZ<CYW#HjGge#n+7dn{bk!BQJJu
zL32+=qj)gvHxF~M>ElDU!@s02wy&50Ji8O=i<E&()4z3V5A%TWgdg>L8qc=8LKop!
zD9=iUj$}iAp@aqulG$R-Eu#$YvT^M)VA#4oy#ff`-0>hjZXfPWkE`uYpXl+W`hjn@
zg(f@wsJ*Yd1lTksKJ_iJSp{5X%F54JcuA?`plAjMfU%4W+VlvN(_>$k7_DEcRAKec
zm(wwBfbE={H)dgb{WjkU?}^OCesE%L_@oR|<;n@#o7r)Ym^5?Im<*sn{eO7k>(12A
zpTL9i@Nrs81?6|?X9zA;V3MK3ydAQdO1luNsQsrgtpM|GTI`|)+6M0|EK*l8rfJab
z(TcFBm7VnRcyN3f=5T-&s<n0~7OF>1?2Xa}jUz`@q8k!1{9J+oi#6zj6WDnj@1t=s
zfP*0!lKK|a*lQztYIGECny6^|PF9vAee=>pM-J*S$P9Q1mzQ<`vnGQe(ge-WdfeRO
zC-8yUmwtm7#DG@Mrd~Xw@#af$NQh|C<2X7KGE<7YF3k3+Ec-b=kIj~-|7P9$OWMz6
z@3zVkeBGJAhgN)N^Lq7;_eFlE+B)vMfCspK?H?+Bip@wufTa^u<m3+zb1v2ny`zf@
z-$gP#b^$HBe&X`(usZATv~q5>^?Tr~z{$FPuy9j3{$)LU7TbT>f+4(CJsvWdA98(o
z2~a*gzVzrXneKO+R$X-{W;yW~FJSaQ%ldR+;FagY*-=GiKxilPpmyGZ?*kL@LjUo{
z*tg|w%DbYE>S82*IB6<vX6bC03rXt_D0p^S9L1h*gGtx^!}R;H5u^<<@m|FwL`_ic
z>pzKM+&MjgQPSiqka4G6A*q;fH-ZwEOUrI%YDw6$@yqK>WE}v4^zXxkgL1r18Sk0@
zy2u$w2VD3$M0%&MB0oJ>eb$AwqVxrPVr+#ujekw<JVmFfEZnl&@Oj;u#ibZ*S=0`@
zBo0N%2!r6iG(vK)857*A3`gUI4%I-5gOx+G$tih$iVJ|~mNFOKYhFK`T_Yi<{NbZC
zh&y^Kjq@|VnblK`C}}X7F=7z{#;lObjaNdeHp)u0KI&SCJnFzQ+;VOrSTwdkR}gPq
zm=f@C+OPjXfx>+pOud>XEh`a=7jcbOLkkP<N(U`8Tu^5p-2*p~#6PJo<~zpbHZAh>
zIX|x`PbR9zJPL5-u58U1L7er3hlysST^0L3>TE;b?z_LW7khhB?4s9spE2y~G_A+O
zpK$Q*9y|K}mLk6&W?8A2Gcl#^lCbCoh*;MW;`h$|C1U^}zchHg1p>l-?;uN(LAg<_
z2I*)=ZEQr}2La{Y2NXcrTyhcG@#dJWscjxcTJgNlFz}}B=y>)4#*E$?Q0C^2pANQu
zOiH6Xzqm(o-Wzs$nhFGtZ^eyaf5!LWu}V_@Wxu^A2G(J0@P|=@$GvdgK_0-=>Bxg4
zsRtA(cc3rcI6OZfyn`F$)=SG1i`?g=oO1jms|8Ixu4+DJ!)?3inU;xmpP3^%gS=Rd
z5sOM|C*f7s`yh<U#@S5M04R*?t{eg6ukjOMw~;QrHe$?#9}8LfF&hjieS2OCJ%BUd
zdZlygX+nz32cd`G;ZY=ozS@yp4JzgmAc%8cb|}>|&^l>EtBwXaU3sM3Rain5ShDSx
zwmE~%9J6EQy{T9sk`!(~E}=MD;%V;$dq8T{UL+<Akv-Tw77hN$GiJtZU~HH_rpb0y
zJ-RD5>jOWpG%q0o0c^ihUW7Sxuu9Z;n6Z@m6vUHjb>s?J!^3ZI8NsT=MP_Ow)HkMO
zIXZiF_WF<mShSPxBfqVO1)OCRG{>2?{s1oaW%(gwY$ZW66NB(z^`DVp!|HK)IEmY5
z>f71`$o^r=oPG{$Jgn>BfAZStTl^sMaAtJTo2F{lnYXIodR0df`%`SZyZo-Eexe8A
zE1f1s)nB3+ueEZ*HMCf%iMv&2m%1fU$sJe^c`<@#IMePwja2<Z28qB~VxjMO02(sf
z0(uBccSnY2DI7#^SR~`d%WspZp+3Y-;tlN8+B^CmiPVHQ^t=ISQ?zUVzmIjC!NuRl
zWl3lEQ<QV)(K3Mln30B+=bnM7?mH)BGj7XR4(XTEptt#>L$>mIJq*K;8Lsdhh`^<v
z=)hsdvK1)$9B;wvI_n?}DO?=?AaxML5lI<&3AKai*iGn{rnE`9g-dQHb?@8E;(Neg
zvUfzh`&bZZ7P@Wg6nqG6EWf*TMQna4Y6ZM!C*t0tVmW7A!twK!ns@-AsvOo%6`{zW
z(SXeZs-wT%2|I5fe4{e*-0=*!e@HzA+~Odp7Wr9LF&6HnPzmnGPG>ucyt9vQXvgqF
zK@R!um;xzV7Q7$AxJ43fVjAy9KeA5d9k#qRN|>b8GQ^OC#r-&%DgNE<8(WRS!HaGX
zR(#bFt;1Sl_y?}FFhrXq>GGmsFMPa=LwptMN<W7x|HKRyIkAM_<J_^Zp;Zy?FS|bj
zw+<+3YF9$N0aK3?1ejc>XOoR#{4V`m$kioOR%`bCz3QVZD^|2^jcc&cZv%qOAQ6hM
zx1+@As7wK-ao&W-g7#}mT3sD|*MbkTpzh*saI>T)j8<^`b3A68x_^Hvoly?Vd0-O@
zam)Mi(-B}AJ_XfXb|Ey@Gq3vr!KF|W>C+T}1P?X3yJ~5~|0jYpR0eA{TyJz!9eRg4
zS&Eg12(FSt9f3P0mRvn2@Ovm?kK86~{qeS=72=!zCSRGfd;y~aT!z_wM9m9Y+T21H
zWu#%y4MFRVL(garsC3950mhB~T2@gGB4k{5ct=HmYvIU**Y?hpz@M82%IbIEtVRQ@
z#xg-Ptv?U!;KGJCmYNoU;>%mn&PB4yL}JIv9aVF%swcZ;YJS*`i)IV~&X>?QUr%(T
zN>4r>GeLOlU#F=5uT!L5ztO7FWolH9n|Ns~!t>=;iP=w8rti-KT0IQ5&g^5*sityw
z8N3w*T_8KYr^WfYAe-zE5wQ1&pQ_?Pyq8R>TxFke+VBvJfF{m6-l%%g#bDg;j1x_y
z-z*aGaA-HigyPsuNYebZU)^mlnHIw$Zq9oZvtfG*&(xC?m_{@$J|R8Esyv^h7-6-T
z#b$pTwW7zLIWYE~6;<&cf=c!8e><Us88&Ht7f*&r_qa6(0zX`JFLg6#>HzoNk6+C~
z+1;USV_GpzG}>ZS8_$X=?Wdb@4})6C(b0KYG@!c&pQJ*adZnI^vRArvYxcMYm*NqH
zVi@Qj^7o@33W+2y97h|%v<BKwL&$;_=;7g$IPz3YlY{i&N70*XuNLa4p`H%=7V__{
z!aXQaJB{bKCqy&k^h)Y?F?3Ui?fyeJpaQPS4gGpaDoyj|QOCh6-K{762r?RF`_t9V
zCzvXi5OQ#p6Gm=`u=PN86^`Q^HxZ7+;;#_ZAP1D7>aiHCx(r=P^>LFf?jM%g6_baH
z+9jLFV{|;0e5F**&-KDyZ)^6hK?a7r?zw&ZjTpuop#DnjddO4J^n5H`y^J0|GKljp
zY4<{1W2XvHnoj9kCB_QWXWQAMQYuXZ%T2!$I~QL`=ml;Epj3$RpWD`<z9p}?U*E*7
zXS{aTYYh>g`(S1i<wL*-#rGhpo6@;K>GAL-<sQ{LNh-1?Zv0|AkkPi_#iXYhA{E})
zU3!1A-Tlh_%gKsi@Ls3Q+?}Chc4B;3GU><OgN@TJcNk5_EF_>E1CrHWBDMnVV8C^+
zPZM~6byfL_geEH4XA>n-%vN;^j`o3<X*=kN5Z5CLSS7PE8a>+F(`IX1eO@VrO3;O`
zb+H2)2>8O~r=5SIqp*Sx8Xsr~eHp5@eqBxz6uhVqVJ3T*;p%9$ouJ}#ESbN^tyO;8
zsAd$Yd)ffZw-~N;m>qb?o4n9D-`qE%PL#w@E&-<?>5smHe5Nig7*3LVfX~0<^)O1x
zjaBXmi}me4Y!dir#j>FR&Tq1GP#?dV>nwwD5@$GV{92`wmz)$$pnoNT+zfw>h4H&`
zVw{EPpJ`{AJ8zQD;V~z@1!*JZU+zmPh#Pv(Q8y8_`cbI|HSuhHjk!f^p$dS3hpYxj
zOw3`9=FmRpp&SWm7r#nz?4{#;BqiS@5sT@{#|Tp9Ka^Q0%0Ep1-cK}tELul>7?3Hu
zS|{*BEVTha%4%$Uuf<zI+2^N|-UiaBeGex18b`&_ltE}{Ee5t*e^LP}X<bmo<V$(x
ztL>h>-t6A9pH!?>ig{emv>=w^Q)XMHSVG^&&8rYdHstr(h?Q)Ot@FXYGIYXv8-)YK
zv_gH<_u%C7D~W8w*MsJ9j6p1D?DcnoLtU0^G)zTKHr43;qxLP|uX8S<9sl!?tCT8~
z{q1BFa=52QN~#DaiE-zWKIT=LqZ*XfUlF2EXZhu6GZylo?qjV`S+{L}<fZ7h{l{7b
zU*>7WFBtvKqIu?;eZ|~<E}5<Vqe)@17y82Y6gT?e*mjsuzye3Flg)PdO~0`CbNNAk
z{*gIpA`mBQ{USXMdnlLL<Z@|SQllwSx!eMx-|Brn7j!c&(p6k7x&I_el`M=bb4mMl
zz#F<N8=&i!Tu?wa#JB%`L^dPlRaRdjOoWS`<wF|!J2SQqXQWPCL_N#X?}d=)Q3o;G
zm%CK31Jyt<`R2xJ^fLi4OaGs!JwU{%ybM=7XklpmBZ382fW{BI-9?lv6a;Zt8?W~-
z-Qpr@S0Vl<Ll2OlOYVSwDwK0-BRuML(eFEZQoiRpHO(;4gu191@SSm=s!Fe(-~~1I
z9%i+W3rBvaf)Fu5_^%^v#?Sb|m;CK90o;XY2rx$=88Xzruy75UV;#K47*z*}?VY;=
zN0bZ#9e&C*4BwipIET!r88*)cg*(uNlp;lk_bFk|wRzR42At!4og1ig|LQP7yuZH&
zM9w^2`|H6sJY7|~4nr-#f_Iqm@6`*n>yCmyD}O`>$gT+(Xx^Y$Z!={30@O1gcZTqf
zjfEQOs*Sl?2<lqkr!HPGoP1Eca^SOB2Qi8mzFU7&J8HEO6ia`NZB?I1<`uA)eK<^F
z1XVR5{^fQV^vP;rtc_c>xcPUdIc}x%4Vgn`zWgihC)V{q!rRox$>WeK#sWK}VFyuS
z;ieQrPNh^NaPCr)Ou7hmT*8~gjli=#s+qsmab<Mv^z)u)G158W4s}tLRD<p2(Ij!e
z^<6I-K!)SVD|DJ4gJOA*m+H@f1~dQWOYH{{6sMj?^)tc-4wM{Y8Uh!awLW(B+a8m_
za86acXg*0qM+iD{_Mf7UOi!n+k1rq+<}nCwtCsi6-hsyf5aMbyFzzu82HP}?aV^tr
z{*Il^Mp-9ap@FSb%6k3VlKVoU$F+;|?)tChS3MfSWWP8Xo+Jhj;$lcetEgR*!jC08
z3S+z`rY990ZGungK~#)1)P9gQYVbRe{V8eC$i<H&W(C+uic$i!J(FM1x@uvaqB$*i
z{Jw-h8$pPRg}5{8_wqU8wS$Nua~;URD710D!bA=3%^Fuf#+j-`agLV@*Z2}QDM_aE
zZ?_+OoiR=eG!Eb#tJ5Bz-tvIY({ggm<<$()6s<FaSTs21(T4p1+}YlmqzCuPIy{i`
z`M$@bICITrooj!zF3rG!$I4S^22akbHpHz-VJ`{&D=J>SJ`srnwN$kwXn(R*EK2}L
z@h%sKAR3iCQEstD<}OYiI9co*%1W5kr05XlkSxPUClV%u{$+9lM^_@mRT=3GH@?MP
zz$wZ9IYa2`8}r#<jUFTW{7%Ts@XGi;<&_5W6uz4V0;Fjnus}*D^xTUEjy>oWH5$Kn
zTZVvU6XsInEMEb7NxId`RHp__sXzVKYvR7%oZh#r?E9?|KY6S9+B|$q9bx{RqTxxc
z1VU^LP8;i<JI!q!z)|Sumt!F|@Z>-udQC2-&20NED3vSz;<18=2*VXm_Ir9}=XKUB
z2j){HJHDYZkWZo~<rtTD?>a>5v}WsCU}}fvN@N)tfqt9WSe23?;8W7<Jp+CHd#Y#=
zRA+gqcFr>!RhAKp6kL$vWm&jzxhYyt-f5PEl}7cC{Ry}{-0);Qfr0M@G3YTN2>F4o
zE@&894j?XU*L1$?Mz?i(+RHXEM!B~!d%_DRVsiRTcU@yJl5;5&ZNw88)zn3{;qBpl
zPpe6-x&s>`%Mb+EVJCq?d$-(+r>8y+@}S787_hFZx{CgG7s*}5urX9fIcXOHD)E87
zj-g?`Y=#zz_boUJsH6X#1=uVDd+@yJy1GW2hfJb>W3AK*&@p_jFVZFK@y@zpO-_<n
z-cusV7&BP9-{9TE@q1|=<T${1lp4dBPpBe9IvK$DG_PP+4I>LoA0Y7~d2oNH+@Qa-
zR5e4*VrK0PTiLHbvnU8!WxWrwHjpCefz8Mnn&+y;nPEa5G<wPNKc2%&w5GnXQ8h!$
z@)h!sxO$~pYmx;F2wBrWO|NsvT}ktM+4hDhWWB9n0VR@#Jo0uFk6}c}32?$Q40h!T
z(cb#1$j7h6GICEdS+~Bie?mG5-VC59Gq-Puxg|JNhk0ZvmX6JVt`*+?`{K`_NzGNk
zD#LG|BZQBr0Y)Oi9dPxdXABZ0R`uh6f<m{U@jH$0k+>QCCoFngg28IL3pppz;4}Rg
z|1XoqpJ&y0LujA4s)*dYaYIT(Yc_S`&23QpFVn*egY7Nf3-5yA1eR%{H0{ZO^w4%p
zc*(yb8_#Zl-1iTTWBPj~KmgYMr&9QaPL~dg<Y3<cl^t4<?NBS%V7TBu<HL~#M!ZrP
zrHM7AaS>YlI)8yXU&qVPNaq=i-ZJF9>oe6OLyZHr*8v;SY3QSYU^b96!Vn+1(y?zm
zQc-Zp&)fe`K=-Q;+cE|BR@gPPwiAZyg61x9WYH>fwr}&98ku%X)bbpS9IiY`&Wz~P
z%B;Ux)H3bR^?R#kD;{tc0QW5^okL4W`;+?DHcf?ii$9U_`k^??-LQwx3!MpBrURo`
zL`FvA@7~ak77#YBrlLXQYyS2bwHJ$t67-c%?I_=H-G(`IP+pq$czo`8Aaqveoz1uR
z2(8bptLy%wlQdkpYwWF;@7SLWz9a%{*Jn$DD~e@aD_`?G8!Nm8Pxfo?V6+|qHlkxA
zJn|0(xB9n!N(NYmdBdJwJ8!yJtq1uEh=q*pGQSjX0oX3r0p+UELw|EgW`ucwxB$$O
zMY0AJXR>ewWn>m`6_B6ms+(XdiVgjm8L&J+>z#bI@I(>rIs0z2uc1_tPVmp~IFlZ)
zD<b!LxHMO4Ud1k-!*sEfewGNd#EJM>DGdYke26?o0(_9SNzzL~B9*igwghB>0QIP-
z?zi{`pOVc<PimM*O^OMTmlyg|Fl{WN2gazSH*t5=Z_WCAwR__BXS@o+^_N6X&rx6Z
z&M7HUDw$)7D7e(X2m&%3cGH)n<RNIk*dR~5ik1Y@`c`u8et)%^y4Wz0crpwUB=snv
z>I!Xx11rTb<@CH-#ACgO14_O3|AEWt{1IU$wWsSOd}yhNQR$!s`T6QV5sTQi9SaEq
z@go>d$GBh!RJSDkyNp7ZTEm}xq~ucBFZJ@3AKUeT3=G#FckU)yviG=_k^861$vSM;
z=adCm2;_zCuG&4h9l)GhAAXclxdMa0f1P*K32BSGx-B3F;U<$6=u~H*nvI-`6pCy&
zyB>-s_zwuBgn(gcNx)Z{9+K3sKrR&QjLpE$OPcyx_K2UZhpQkLLt7_x<tEp(3DMnS
z?W3bQQEtUxk7-7PdE_}}fLQ{_9CBM>pcT#eF`9pTUR<$#$dZ_6adSuOt(y>$HH~37
zyf+?l47@CSD!u1FaB%cARqo`t?x|}q@~DqjDR!n$h}2ECr#4+T=T*oY{E^1q1oc5I
z<G+(YS*!X@jZHnILHg`$Qi75JI#HT6_j(haP<C+L1+<Wtb3X=P0~%-$2>mzP&#%cB
zo5Xq9flw;?=+yn1n48z8g79W69?Wt&{9FqMm)Put*s!p4O&Vz5e}l#bJ%TN+yHBS3
z+n)q&2!Dp$G`etL{6OTN6&wUp(}3aq-Z2Eq*yxhRPYp~dieVt@4tiiKaN}&vmf|3&
z>!(Aso$m$xunxtLR|WCI-KuYHjF})Be(A*1KG-S&03M($;Fy5P6h^9xgNN_a!C?$b
zoSqKfoCITj?jHgY;5~Qs{g<MhU<j1d{PN|wdt2jU$bvat<y_3V2ZTW15+VqK*0N*Y
z<T=aR5NV66$6tLM^?$f}3#h2xFKpBTl$I_*I;EsjK)SoTJEaFy8l)Sf1*A(rq=W&6
z9s%iYkY=Rod-3<b_kQcH<zg|&4CkD^-@Tvx>;f`}N$e$Uo-`Y~2m?xi%JU7UgAg2A
zOV;v`b>#E|NJTl{M2Rj>%uP_E;6A*6P%$+3_4**epO&V8i@9x6`l%9$SZjXQQ+JLK
z2RX^I`Fa-A4o*5dsjzTU__!F-y|A>S8bX5)f&EEqTk)po63}0o9<RPm{n98*wPaAr
z0XS~|Kj%shnp8oZVwpXy6MWN_Yp9LYfi^;kqKjc#;S*qrL59F>cMFW&lf{W}sZ#w8
z1Z@olZRY+yXzM(KunY*Z<8HSOKVS@eUk8E&I?z@JK87*r4+I7GogppB2r;Q5hhU<m
z15F>;@@!GZAti;wP|FhYyz_&qb6OI!A{Z|TcBX*@KWJB+#HXX@1S{7-M$+y0oB;&7
zW9rjNjP2p2|6h}ukZHr}@j@6Hu=eQ}-TsU40wz?6X+GogIoJDTj9|h)(T}MLw2#$-
zKPpAkh;w!>x%3H!af!mK356!1TquGPM<5$=Uq*Z?-gb~1@dQXZhJtjt>UyKBwSn-X
zi^{92r0?L|Wj6AFjyi~_vJiopH^cDag}yP^jnF-1<A#;02Asn*Wu*{61lcd|hub;?
zT<p(LBjHL*;{aJ*fYk^bp!>^#CWKBd9Z75pdMdkL%d#i%YvTv`Nod3>*{ApUd)}b(
zXa9kfhHrN4rqBKOQ!pGAVht%uxF_P;PwU;ms5Ou|+4E6;3-)Y-Qs8%x4Z`D=o2blt
zRvwOvX?w30tK-yUqCEY(3Mn#O*s~!opNfNB>7a{x`B|-Fs?-?RYo>S{a#=~S_#&H~
zCt+=C+4O$7#Bz0LB}UKw+~VmSz^v$Ei$YDjkZ(Ef&B`p7zwevtb+)eilJ7ML#}P*Y
z(3=4~gd`|{fMEOpWr_*{onQuNRU6m9p~@rZR{Ix76~=-dA+jO+^t2TKexNRg#r{k}
z=bp~v0F}PSa~F(Y&KwQdM3*Nepz)s~ucB&z3naexe;~mJnhgQPQ%OM)K?KrvxBbp-
zJ$<+ZV6@T)TkQR-`8JEIRvM6F%Af%SXMi3^8W=JZ{@q}R+I>l_tOrqZxc6xo7E<c~
z^@0Lm(86QGHDoAiq>c|%&Hsei`n(5hrHKtwN$S`_+FS*FYj2R<LOMV-)%`vUcQi0~
ze$Oz+S_bETeEHpK;0Z02s=0|?*ZC7(9Apl20JoM+k<FEvz{P(8!{$I=hs#w<+>oXD
z{q#LhDgz2KXgJutCc#M4cf$UzIfmGnWY5Cif^w|rV^)ft@8tEqq_ZMK#E}iFs?Hg)
zLfjXwp#Kq+E`p)6#=O>@V6IYjrj@6_EE*kVKgT1{^Gft%b~01;>4t$(w+OkyaqEf7
zLBLmk77~#XA}9a8*ZEFZNc+A#_<!NX;S&$GTmS|@u<^&<`vZ$Cs2#Z&Tl9`uUVZ{v
zE>FxvaNr2gBxY=p^R)8=wQQWs+i;jfd4;y;i4Lge25O#6xsL*xay0b#hL@haX@-S^
zPGqpE6><`uNCRy2b<ZRmYmEb(c+lyM{{h#O@S~e`7%49=1KyQAK1l5vUtT|pAtRU4
zL}5sqG8NqaU`q^SU7ht`=u9aB1`1jRxSpvC;!A=X9RLbsUQqIZaeR8X!H{Wu;zRmh
zrl*}e32%9DO_?dCPb3rvtQ=cM&vJw5E9M*e2<;xHs%}39tyZAq+~%Z)l^!;BzeE{u
zCoVdRS4jSED>p&$1^du^;}v$cVjIP8p|lj}+%-Yr@jksE;B$MV5<sS~&nn-qJ<c!J
zh}V_}tLIi7<QSSenyK&snnt}4;j5Idvjxt|%kY?X00&eTfa;j|-X%kZM|?5Tb(Rse
zFU0uX)4T+m7xv8WK!l$xhc@7LC={5h$1xY{h$4)KQn5DeY5<y?<?5%k17Qku{f91K
z)f~n5-M0@G5uh4>_hCOeK61{Eub7r={kV3{gf~mqmQ8{VSFou~tm!j~=mQj9{uz`n
zC>6lUdIpUY>H^JUw4P-R5fAd6-z{TN8N)O34hWr|&I1I$A7CS<W=c(`SH9?AW0J@w
zfQ??Doft4$W8XkJS+$}8>+Q6Aqq3=JPz^aD90AJqLA$rY*mfCwsc+RB^q%oocNoCl
zfhq1bT%Mv1Qr@29rH*pzbXK$bJ9Iz0-e#m43%z9!^6q&1G!!3S{vA{DJO&hSZ$wZ2
zLC3=<;EA;^><hk@NTI#Y9q8D^raByao8<wmyX6m=sll{_WtwMzgDd&HFP{yeFqkX`
z^|J6uWY5T|%?r>P3itx8*`61<_tWt}g!<*BH4`yqVhpC!n~|fb!O6F_#nsG1DUx-z
zC&GuXNI1X}JyjHonG0cmh9r_CFp~k$%r<Y%%0c*{OgQ<hC|3Z2JPWwx%$Vn-Ki}v7
zBZul7K`bPQO)U5ErGF$%{7{d~*>jcPmpa;&T+>q|bN9ccVej|{qwav^Ck$-X9_%}%
z{!6Gp2L&m3<X72K!crjby`dHDt8T$?dPV$ha=q@$c&!bW;^ilLoaimkn49zvo#C=A
zcJm5!Gs;=s^I*$M#4W;QK!obO2>%&K%FY9s+P7dtq0oC;!8R-~M&18DK3C<MBMg2l
z^9U@a0{#mixr$hF|EK{;RwG^FuiJgI{4oO{0Smet00Y1OT%or9s%`s;7~RCn1&@y}
zb@W)cb#-5<mDPh*fYW4_KAByS{4Jl`pC>o|I4rXroO=PQ5n%T))pPRR_hz%-K;1R)
zvb}_M{|%XF=JEE^0>N8xTrBWC5NiS%nfvhy=tcz)u#*IjRD(&8Wni6HJ{$ZB*a`Em
zNEx&pj9jJB7&GyLBDkgRHwQc9^l$`dHp6tN;)Ej($xT~rGd>n!EO0!^RkH;FJt!(T
z(<PsymF=zltsR=bdBGQRHu%C^7#{eg+*&ez<lVa^POpa~7+|V=wAR4BJvLZ))fsRf
za-H8bo-K+cRBS^QFCej^+jX@q+jh=XysPX#2Om6<dGGRsGJa)LW}vW3g@I?n20t=-
zK3tQX$Ma7032iqk?>9<USq_`WG;gLl1|Ot#48HJd-JV@YZrpwy3ptBT1ZAPKnwn>O
zm2EfvPJgqSG?O<!3r(jdZ>GYpgv5oA^&}Gh2pd0TK+3i@7rZ(!<A_mTxB>*VlY`K<
z#B*_>Fa8VbzayUYTLw-xwz`@JVZn!SgOA$&fRT$a>casoy>tFIvK0M>v{=NS`C>vg
z_u82}--ET!{C-aHe|0f&`<OmB&i-Wg%yE)*6|W-PAE>?^ODej|Gg5Y#?K&%mOzV5N
zmJACX7%pl*&JV^m<E2r-6Ay>IVGOZM|0-<o_6>ndsA<bV3Qm!&oM^cBK@flCyiVX~
z7<I6>%*AJD4YhevWV5jVsnoMQ&!0^Qc^1}jiklAMU?*Oax`pMQYh=>QJ$eYAmt{I#
zQPbHk>c|AhB-GPBeZL7!-v94Wr-Y_S00D!<@)W@axfW@#m_qYBy<$#<9M2e6b$P3C
zZI7!QcF$F5t@_Tc4@bMo=H8jpuf#X1Pmhukz*kE0$Av#@(LV_XidRPDdoR9<cm@qt
zqQ74~uQmDQE*4u^aI!u<yD|aZ+`NCBLc@3y&@~R+c4foq_=5-~UW<YSQ%HegbKPC&
zM+T%KOA{h2+|M*`u||T9#^PugTaCKruIYF;cuzIIB4`+p8qD_?`7jI8lz68aC1OQh
z71^3(Y>@v@vPz(N@y&c%bn}%WcdJovzg;4;wsu7R&5781Z1LTsCz0Y$kBD@N#3&C;
z_iEZTGwgVF<{d_tMUEFx-2D;CqGp!$vR*kaGO^9hP<>*-h6`efSMdY<&28aWo#D>c
zePJNdjE0OK?9HD!9}bD$guk51A>5Z^MD-zr&tE01Ta_snG_@mV&!sIcVcnfWDh-Vb
zrgufRp*|}L&|JN~WuM_n=jNK}<<VsBPM5%to*bUV#=Z+oKSeyh*0>>GYh#RWwvAW*
zH<=WNx6<wo6U}f>V^zv7b;U=Ll)>KU3S%#GyiQvj=*KgnhcL5FZ=dev^W`mUxt&}x
zZL+dFm*o5;84iC0Rq?JIa;fO;@<uXGO;l|Zxz^FMa{-MwU<fSZi|yeqSMj=W^8nMt
zvdM`v&95%Zg?Rjn9j;!Y=+^Re(*+A#`%#lCT;p7s!UP06pyo}e!n3-HsVf@~%FeK6
z_*wX`gj4<1^sfTQ#O2!9MiWn4`&n-5ESm1(6vc=9i40GA6UWve=}iJ%VhuMm%C0fF
z|E`{8c95=k#;;jN0cQw^bB9#9;cRjOrze+!qrJKhv?wiwi8cWhpMFMp+QVKOP*sOw
z2P#nNcd*31fnCxtfb&|8pz>T9t@O2jeXi=6KIs~Op<64Q6p)rTEm-0q&8l*$tXFGp
z%~b}owJkHC<m$HTF=_?3ZAR_)xusP^l>gZkp$*sBro|p?hzp~1T&S)63g!bTfQAe(
zKT*BzqF9BMs2nojLw=LX<B>*#(5f6)c=@I04u`(J^L-oe;#CJyrTl>{5Q)<NL;`)8
z>dt^K9ElV=-=OwsHTX<4ZI&=GiI+#v-^1xc;3a%<sk3n1x-usb8~(8%Od4#o*EN96
zob2HL>|CK+ygZc#i|zd<1P?|iRvsgn4gxCex@__Cd1_Vp{>~&*;mb`yJOpcDLTuAO
zzsh?w!aCW0WdR4f`m1{-GrrEGIPSq>O(^m;)==C>X>erc2c+QC&98!!XdXhgS9R4Y
zpb_q>i((Vjjc_>jNp+is%}XF1bgBh`Zm6R!dd9P>=geiV0Ee@<?iFyiCuR(z_mu(X
z<kx9irTA0It{CFbPId*iHi^8Y(d~Vw3+;?AEU$QVjGf2!kiS>97NZS^J(qlDiuW4G
zaGlxyvv8wK6-6JZ8Kp>2X|j-Nk_yXZuxjm2)R7YJm&w@s%`pbUreCzW8bG|@46*Q{
zR;)v9sz2cYr~CZ;8s`Kup?{c|)XyX#3@_3+e0n)jnQBw%?4hG)JGvdZ=1=Mui+|*o
zjL{yhYh=sG+ujG;BrM_eJr-OcD6(bO7}~Ra=8WA%BiryvD95Wr%k90?p3l_mZE;d3
zCw`2h8jJT6)0Q2PuN7K3-Gu@bo;hlL6#g>D=fmj}83EXJst4@gHZGzD4BCD)REaKO
zi-%|ZXWt5rYB;4aqiY)$=oG!$uIXe?mO8!TDcXHP2(xqY^!frLrG1MF*O37sa0I_y
zKLe`y%Rx2>LMc*)ibPl_=YNEd=JN`OI1~Lmd%`oSfw-T%C+dS>3TYYW@(vk^A1!wI
z))<wa=1ISlbBo~p?r)jgU3jUEYnLo90_KX0Y$HEe-v5}mo{X$#A8<T@4{-PT(uZZ`
zZH9x&@qPExIjX?F(PyAZmH$t4b}(Jek^ljCoBQc%xA44(EY9uxL0dPV23!u`U<`1c
zadBMQuKpkZRWuKE-+U)MkxF&qU8?Y^9NB&%6lirh#@FQ+xe|;enz32oRdobgynZiL
z#^z`ijGaS_!+=WJWzHpJU}EJPp40L!Iefk~@3#QjN!wYFeA0l=w@^FUvl7T?Wj&p&
znr~}3f-v>Fi){$-g}S<qBRj&=g%aZ7%BgCovo+qgfAPdbS9Y6_5-iTtGq1$DX7n<h
zZ?|<pQRe2<2#1xm-K;zz#rlpm9&LF=<9A=jXfXNv{?XK*oT}r}iBGWYFYU5h!w*DU
zMo9#+-tz`{NAM~2ZPqe1DAzG@$*Qf;tY3%FZV>LYT%2-)-rj=wXEX{eXk%PoH4#Yz
z{Kr0FPP{YYc1RU<a=!<(wJ%P+;O@ugU_P~_!|b(!Hq%T)_wEN0X8R%V5S7#x0?q{H
zoqEr8($z*_h*OcRb+J({zdH|zQ&!<Ro%8h}6|fj%b|_s(x4WxM!PtJ3AM&xqg`^6o
zX)(#4vcGzK%3keb+XQxfh2g?_j)bDrMxgAU_Q<WV{KRVBnHHSv4R|b^FVl($3BqBU
zspNK7;^D<%j_ECjbLga`FN7wGCedU)(}!tg`=wf;fW5vdFK^gF;ebjYDU5wDsI}v*
zGHwiIpRLlq2?sqR7q_vj_sqAIxqG03=X|u<$m(HUyfDVzgDsE8ZC5==Zf(#m?{xp+
z8;t<zHv}2MstQ$vM;n5Ze1WFv;87msHQec1>(WU`AeAPQ73M2rcXb`@XR8Bk`D@od
z*?vM<X|Kw3fv12aanwt``6>rpuzsT<yEK-$%Y!TtiV_BxOiSfPW%VKDg&$I7_=hV9
zu#E7->KwW$Mfc5=fVRG=nP~X=`5X?#=d4ZrK+hDHRD2k)JzR1BFh#+3A5*sdYoR1*
zd&Nf5{XeI&rLxepKrrK?)2mH;ZL`fY!(6(D&)>yDCGXG$R?N+%FTAnAdk?w1M89|Z
zv5Q(yrfa>ui5=&{Z*VlzCm^wDw3PjZt^B$$SLZL^JGYPRm-bc1C(aPCx7A#EHZn2k
zOf+K^OcekJOtXlNspa^X1qJIjQ6;|1=lOQpJrs@|Qr(;`VB*bPOFBZL2ENTe1m>5r
zP4jI@_&l}h8&5j=0#qy3e1Kl#np;jx=yPQ@`@I+^>15bwUTps<O~H0Z2(CJ)?tTi#
z2k8c(hWTe-C!4RghM0lH>Az<(%DJ|MbKym5(+S1{oE!>4p3QfIS{&qQl}CkeignV!
z<K^s`uy2A7twoJ;N4D-S{wLgjoA33Q1gKQLlqtinpLnY(-i-U}K>9bSuv?pAVM4Kr
zOAUpDvc>~=J-@qeq&s0MFpOLo&BjU;-5emdbBJ|kyts6tjRiPNBEYFV_lF12Xtvx0
zye%d@UgfQFF%JNBe`)6CbrJv-M(*E{tO@{YYcfkWZ^R&<AA+rn@eD5ndxgWzFw<<r
z+^j_$uecc#kJ2xwy>{XYMew~(;37&>saSI%Lxb1VEu$2Duq9zAR0(~Qr8uK7ikD?K
zs(}l8=9(~iApOKtfv5)@_H^T^wYd=5`>bEx0%VDP2Nn2bx}N?nSvl-34}qIvyOKQY
z6;J)g&w-nP#YP`ZG*8x6SJs6c+vUz;Y<o(48@}B0$yO{LE7oFGVY<{wiEvC$EBatM
zS57iYqE;~yG+EA|6uz2dRR+J5I`us{x{%b;(jR1V5OK-(sEIpq-}QLpdlMJ%Yhmo>
zf@`WF!q)dw3?A_d)=|5?+jkoFUwM5!1Rhct>*P<Oxn`B;&m*$-9&|S-DnQ>5n-KM!
z9)xo#%Dy`lq>4~a;IfARCn-i$Q!{N^x3Iq3BnhD5CP3w4hf5C)E6v?)8l+0=`o{y<
zXyzo@mf;C@w6KoH+(Ph$vExIoaSuOAH2HTK739!*sv)hM08y$OFINXNSUr0Z33^B~
zF}oc`#_mOu-7nh=3{H}7{IZRU6kle8JO$=iR2;bcKA{ux+ohjp-%LG{gsQB$v)1Pc
z;jUW#n0J{JmZ}dmVq5FErc0K~=96W_hsa6BijP3u>o!Anbcl*(M7;DH=Y28ckT;nl
z>X^E~g0mCqnLUvqt=L!*Ba?udVK64*t*S!8++7VfdiP%qd>BszE|`HM0pL-W`u*2n
z?@vjO;B^=Msmg~Ff|EKr<p;Kcwxz&nUoTU%$F8OUu*%Ff#L1&(=INPM6Hf&UP2SQn
zA6<-jJbEWo3Dg3aeSB%=UMJByvi|4foztLWb;E+0lW8K~f?*Zc7#H6=vwsH}05m3m
zBAPhbYswZ>#KUiFJ-+nzy2RIQ5^!Jyd5Na^ece3$qZc(^Pe75C1tZcxBNyURC`>Z{
zt_942%L_DEO#?JK0DA<BiX@uV9xxR{<OuyL&5{6<aPP8JY1nzRF(kTiv9%|<31ebX
z@XOU!eLp+ieQ~w;0<an<!mnm0^l+t~E#4yBb&5LLZ_b?ER;He)Cu+u!6Ptg{F!%T_
zBXVFiOOS1CX)2pAx*Za1+K|*V{b$7K4D|PfjE@tzqmi<(a&MhTj2e=q*b<>nqF%!S
zcLvG<0MaR~`>{afuzRpQo0IbRwS-0)f56?&0eJ8Behu4^mdqVUqrOm(FwLNQJ*LUD
zP6qz25WL5|4vQpNO&2?*h$e!LDA@GoW&UF9Q)rqNGum`>Yn)b@G!dOwxf0mk5Cmo%
zwPhgv&M~9tROUqQu7R2d8_VkG-F8$ymVBT{VAYOTc((w#Lk_$i!b&5ma#@)oLa~<q
zs^vbYpmiifFX)vWO)^(B8T%AOX7og#b40W&D{I<DHURz=`?VleynBAq%Z^uRew5jM
zOVaci3e4U01u3DYu(#Ax%51#<Y>1kisV-fyveKx-8Q4+9&%-MijCEw|L00_Nqw4}q
zelBfxX|CJStu1<02b@V$qO{PNTMyw#^--?*{Ucmtjv=kU>Mx9Q@6xt@5QyFst_pei
zMuMl+C95Ttq)E7!6XikKwcsF}Dtb0!YA1n2kV^VZ5AvgRUR!5TE>RO25^n`edyiCD
zNVh=DYwvkZjK5lz?-E+AkW5=%1iV%KQD!pMpaA%|48Yzl|LQO$NZt7+D5hoBs%%u6
zq-ImW?{7l{)%X;fT*CXquM#z+oT-(f%b>Yt_);np)Lgn6GMBN}y+W5Top-A&;G3>A
z!GZ=e#MpBA{`Gynr<C(D+zX%XQOoHcG0@6l=~=|Hweyu+|J`hWg)Uvw=K*j~)Owq*
z*Y@nOT8C)HZL+F=fO7U-@RU2a@PSEANB)|5Bh{F#u77j8LPIHAyFR4POqkD3?tnPG
z5sKJ_l<9#&>0nO0u|&;p6Cl9!TPT{yco`0$8IBYOU^|w65QMZu*<xz>=t!N`mCz~G
zf<iVA#I=KF2v3Ia<&DiGJPJfHVBgcn0%<7@#UMV}zRlAKQB5GhC;v(CHAeT~AT}^q
zbo5Lf&C3!<k-A9Aot>i#zL~=4vpkFh21XFu6lj<f@T)dnmmr=C+uvjeo-$S<dr=VQ
zb#a=LBVn&t)!zK9-YXG_G~-g@$zws&4CFRv_l-3g09iQ%)V^p9)u|nyuG^1K>7;8w
z*WRXc$x<+>{1&)cvIW8Cj4!E9pa;t3gQ9edc0PBvgfV)0;unnh=#oU;Ie-3c-wbnM
z7{FH6j$8pi%sO-4wT--_FVu5Bvlt}bfv3pPO0yoY^Xul#q5&yly&GPkvCpbb6-mL8
zU<}#RBNI|t1>TZ_UzJjkJIm?)foNN)GO%+x|DZ8$?)x!%y7Mcr2;e&Kwpes^E~HTS
zMBP6DUE*jwN2DVP4nI^k=KCR>>;XKbXt?VOv@9taxXl=d73|4iW^VbNfk$V7F#rck
zUvGPf080EuLqSahSUK?EFOrRYBh*G7n^=75vMPw0QKpT2j7mh_kI1>DH(rjtJ%_a2
zR$y(Pb{5-(N0>4wWu-0I8}s*p>Dq%b72#@;d1CF0{=*$48kWLQ;DW#g8}*8{CO1m}
zthIF)&v!%K$7VR{UY{&plN|)|!SBvR12Y#)EW5|V8M|F7eg+<D8-beLXQ2KY>dNwM
z0`T#2g`c4f3i&#hATBr+U6rK(T#Jx>k{UzdAtbD31jkxQ(QRXG%_MzMgeCdn2~;IX
zUWDy)`UdzEupN{#)x8=;UENV|XIqDL-No?Yi(xqYW5wjFSxz7@U_SYPeT|z@S*|%%
zoqaV~pO#$;vV@=`FFRl3xY0Nj6)9D11U}jfvDh)tPwCroi71fn@xJJO98{QgwQF)9
zUQ*6Bw=Jf*0vIw4Igv{HJdKG>Hd36`M0m6ErArP`AzrriYXj!PetDF%^h!0R%d1*5
z&-UJIQk60SK6c@*d)FkO)>(UcM_Zw$YxyT$g8JU1m`lTmUNA2EoSrU`!D<-Rgym@O
z;uZf8fY2sU<32*dtsP%IBn-UuxsPQ=lksP=-m}jw=E%)9bpQR0eYfn~GCV?E@F^y#
zp&bOLWGw6H+2sj#H@_eg!Pr+}wj@cBA~}IK?7$LMs~)(V%#cJW=dO1uY4r1p+|8H<
z?3aO-2mh6Z15IWhJBbjnkd<5W4CM7%_@<Fy*RDe}2t^TSnSSI;N8fc)#A>z>JAoIL
zm@mjSdY4CL+nk9|2RMl+n8)m_UvXwznitRptWFxyM%HF0Z?Zm7mK;Aw%umV(7}?Vz
zsr`fk5+8V575D~lLy1q6zqGF^5d##jbG@sr<a)VA!zRR=tf)<)B4?T&IivES?+7(o
zD)sy!E&zrrviBSzWp;I5o=}71@jo3M@~S)<Zl0X}>UB1cB$>CQ%6N6X0vCnvDnuv3
z=zBr$lh9nvE6iccF}pKey@edHAZ)V(16U`+=J`(h1^+#85?mB)7e4wc`x-sOT>pA7
zHP-!n>1mGN3Fr>(77Q46ud{6I&gVU6w?0!hrwB9afHo-JY6tG2fqZKx@9mmI#t`|9
zN#KjB9UXLx^^29w7~snI;G(>W%jEdsq5a7A0N1k`8TkxK|7f=u|B5V%P>1pRdM7Pj
z1bOM`e04Vu0BSzdw(*?@1d6xE#{M4wS9p=N=odERo2um(s3^mO4mwxjL3DE7xf90k
zZWozncbknLP7OuE97K1$T^W5ni}~j1(cgc8PWH<}ytYjfT{^aQ@ArTVH7`(1u=8z=
zGrH^3%4bN1lx7d`14T(AV?&Ihp`;P9fg`(r5jyn^Jv0n$%|b5^J4d$2)<XC=Mp=c)
zm!*meWh_vACd<U{<L>Ggyr2bt*7XE<y1F`<2;X2{5Y($h%kdRs!;2{Y1xoZ)2q}Y;
zW}T>)FDi%*yaM98K_d)c0}hr^R)tsqTD)dS%MxZEbT2OE1Gllf{HVw^w(zT*YQ+Xa
z>NU)-`s$aK<=tP6WIJxyG(tYDNUV9Rcnl)~MZK|mk7X=3&g=fc0XW-yFh8{~Ikh9L
zd@V6u(ZQVU>~8X-r*Cz&<?>i8wA9DoY$0_CK)(vDH^NA-T!OL1@3G?)3d@*@#rH1b
z+bFif`W$|+hIbV*Y^=B8x7dFEmUXZZfJYT>INS9c@$l!2wXTR~{%{|YD(T4@(3^Cf
zUM2K=rEa)E5fBO2S?x#vjd+=(yW3xE@B5>-Q=^=IA{0hAtN>O+VIIveqX3h$Jav{s
z<DgGBmMB3}Q*?u!m_!klXZJzd_>>>wmT+*lg+r00zjPn08Xfe7(8oBgfDH<V?$&(1
z7D;T7TZT$=Q{4@S-$N2qaN2x!$KIXQRd_xM+^Guu03PioE9()8abV7l`;LQyNA}<4
zJ^jK20C$f9FBfk>u%ow(BHGmDwfG&7*HP!sFnBl=A1~HjT-%57x%z+1x%tC*%#Siz
zLor3|?q9Be-J`Q{dw|9mjQ!8^h*Xc;2$2r1xNZE#tJnKr#}A7Cvj9<yh<ew_P8TWC
z%G)bvnG=&LCsLnRzI_4AIglz)r$o}=2rN4SCtW(~`bXU#f$>ppQ3Kk!<=BeJQ0PJy
z6u(T>;COT&xh9X_)9|_m<zo(K(^EF0$G28Rrg3mVbWMbUvL<mU0WeCRryoPXYrYtt
z1JtGp$28<|x$O1vjRN8C(hfUb!D;}<fKG&Xu{WkQKPIdI9Wv?`<itjEo|Gz1h|0>p
zXlmBd2@cOlJQX}A+sxw2+hH%2&`$542Tu#}B*ul3-7p8ZWJW!V&)WUS8nTsR%z-ZQ
zx!D9)-3-d6Xp<PU)%N#Tg+=?OURrI|u!Rg=U;>(gaWgHWT!qOeZQ=%c36o?DF@1j^
zsGy|bz22?s4>x^R(LHW&@8IM)?cnk3<Cgl3;D*oXl8<VU+Azm!;VxkG6+Wc`<l<m&
z9ds5c8LL<E-Z7I%E?#6u8J)7LjqaZ3*`?MUa|$BN$ywIm>ab^{SOa{T>(Mdlypc@Z
zIJIm8YfCL}x*w#fq~Y!zLcE6)LrOZ5EUg5XP!L0K4)nS_U##=ucKub0E+s8L{Z<o3
z^=ajbWk5YG=vi27a{qptX{n*2lIGXF^=xH~<X7@@d%;tCR~L**nHmm??Q=IZ=|vrF
zq$7S<awU81g3V1;p`7gKt0igYx};2i8Fk-UVjo~u1huU|$J)9;45K$hE}K81S8#Sd
z^A3T>fS#=ALSBN;AK>sQ=XTV!sHk*M0b}n^lP$)~YdnIM7ecJcTlIe?sEJs{MSQ(K
zK~bdnAa;>ulUhDktvlCi6=k}bT1mO4S7%+&wdeYq1{g-{_~7rp7BE;rR8ef4k8l9a
zl6G^p5hHC1EP@k~knk~>q>D65_`5)vZu`~R?wL)=mO6_!nGm}|Gwxv`ARhKtI5*i?
z#|}dNUOg|Fh+X3don6GL<}R{19Cc=pY}!?4+ywMbFu0VjT8ODDo7&?EgqeT&;FJxR
zt3{`~=zy>e42S^?q%2r-k^Uui|7NUW)9&yt3MqDEnJOo6j~&Iz4j3SoY<qLjT)E3c
zIa<&acO;bQ#Ma`RTxeTbym1zUy;3K;O+W7~3D|JM!V)@J^&eU9L6~TV#FZheHCfxA
z1CkTRazUPgxns|4>L2GbEbN=7*hS~z^}O`1d4)T`*}Go*C&7O>Pj5)I*Y8twG9VGu
zSg+8r@DGJZ7rlBn4OnJ>s$f;hwP+HM{JiwdJlX62;)fCmfcU|*?qV+NZx0`_fdL48
zUVidaA4%l?1>ZEF>lwJZjlR|rEzv52_iXH^<m#nF?96<^Bs>zjQs-~rleOjXE8ndZ
zA7rm>pG?HXce}kk7$=s}jcqF|q*HBaZg+0W(QE_UKu%=4^8?k-zYbvE1R<9<;lN^)
z*}u}7)B_oYFZ26#P1AYf`(rzjKnAV}=%wj(sJycru4HI14shOkH_7bAAFZ0xf^15d
zRaoDq0Z1~KjX-Paau$d9BUgigM^xg?Z48R|+u*p|#G{^=On<9mQz4s>^fG+g<1v6m
zPP`T%7X?xPWjn7@QZqe%h)p=xkm7`L00Jt(Zj@%I^jS2^CtwH%290J7Ci}%J@})%%
z*tt~;)%rL%4J^JUzz~l2DY&{L13&5Hog5)g;6+UW+C;u~{y3wJ*yKOY2I;W(^~y}E
zB98i-46@u=N^jaJMs~t}^EPwo32zYa=z@HP!>Nv;^T?j02XY`vZNx~>*`pFE404Kr
zej{E*=ud<Lz#wOP9p+Bztkz;yHCw7>8-1IGc0p%PV$7EX2(nX!PbV;$_sMxd!l^W3
zC0MIWxeELZOL!D`1Q#KS6TG#P+0oIMH!n#vPOT~)C-4o4JmCC((Ne8&-EqN`>K>Gx
z#|rR-oMg^+2~+n+X#kCSt>HQT!}BKyvz_x*zV(@tcPlha&aoN;oQ!M2{g!tn=fVuZ
z=ezO$K-MGus^1`j1mbf?WO9)hrf6r*elTmswaAmib`C_X`o!X0Q@)FFG|_Fwx*3Of
z!IVta{SgL^N__l^r)F0`iwpqnSqWT)lTkYQ&iA(2DImy`ehL$>E|;b`Eq3*Zq*n9>
z-^5EAt`aAdNS~gb+B_9Nk5)U{tCU<i%wE2DF3BO!j4^S)!lO~wsP9pCkI8#^&;k+^
z&NUL0%UHHwyXWBZ-F6;_0rO*_|FET7e(ei}4aD@Z;?cQn#r6r+OxCTZ%beYbE)WFi
zlgKP589e&8rV1HWv4|n26BaHW#mDe^R|B-gI`HTX=+W@dkYdd`3V4#}bKHqa2^xZW
zi{mGzef0I5e%W}YXI9nKOb<Wm9&$Rpbhpn<+baK~VoC9mD73R-aPI*R8lEGt<TWFl
z03H3dz+bErO~zUPsdv%;FzX{;<C2r1z@6rsv*EcP2AijM3zuymg&Z!un&`~!3=y8)
zZvNH$ilgO1*r)Y!?I2t^z_GENx*>&k;2`{FJpf)fd*`?56v%LJ>uqi9CqRKvu8i~M
zf=6ZEx$fxt=)vQG%SgV@NmBx_^Y2Ue3qJw-$&mlOy8n@K@c-`@{$1Pu^ZQS0%<mol
z|ND~CbI^Ab<>kNET}lwYBPzm7dpw6!>TXjb(sZBEFq-@SIvV_^FW_4t?#g;zA3sQT
zMkb8c@y$Kp0vRuuVu}#jzwe4er5=;WGb$7Upz`kmg%ZDr13drltxCzT-gHdKS<507
z@X6HwK3PFc&;I5M*8g=&Pmes}XyO0Y55iw0{_pil+qa3gw&HPg<!6GywhBpf40r%b
zymn-YiFM{rlgo43b|j+XaGytxF<l`cAW=-C`<DN{B80QeQoY)MsWP?%{gb{^j@?lG
zDe?^sof7VYBsIKOsrh@HYwHx=*Ecj&3OEx%n5r2##m`7o-aDpw7lk<UYmiY4e82E%
zp3sH$7~zbdUU{s<F(`(=ixf9~5M#TX$pbZdIG{q*KP9rSQT!V!azm3(8b%XTMcn^W
z13B9kV>mOq@RQ*1tbgMN$27jsXAJpVdH5%?D4RnZ3T_P&)2BxYXznh%q++SQzo@MR
zi5R#tl<;uAaFi(3AjfuBr^1~;&BDaA`B;R+hTyx<Rw1NWYG?jNVLJUk;4Nt{Vx6Zy
zU3Jgy2i+@yNb`La$o=!i`u5x2y|uMNwDsKF>Dvy=yUesuv)&<unPY-+IzJRmLOqEr
zR-d|X-6-mAqe9e7z}U2b{cSle!4Ji@R+o4qoV@ph_KE%hYcJacuE;cDFb?N7$>`DG
zyDP!PB?I%2aU;?Pli$vdr%VH^uAc_(^$uVOoi-^2?d&PuUUc*7{^8c$ub27O!-+0+
z^Qf44RY*H)NgL~P-pYnkvtwM3zk%_FG9l~n>i7=JnO-@{3kPTy_baPo{A|*UrGu<<
zDoYr(HU9%3WkJ;Q8&d10Upni1C;TL)v7UHwjbx=xG3M*f1AI2n*)SD>_*5D{H?13G
z1|FVLypCt)NUX|LVL8dT-tLtA;VM(gUDwUTHd%Dhovu#C9IfIe^x)QFS*RVd_t=Ou
zyQ9%zg=-y!S-WXYub4FKlQ&XKQs{*s%xF``HaM>XG7$vZ31gl-ZwCW)uCvUm5U*FI
zeIOPa4KRxVuM}2<AFs$4Qt8hnF$iOT>IE;#?vG43{J}l71tifWj3leTi+OQ5r_0(n
zA^UB^!ZHaSP4;qxah}htZEOji%KCcI@o=Y(ZAt(1bdMXmm~nC@6Nu~6r6d`2jZG=%
zOU~QBiQ#1xiVL$kFC`HJuZz?BwHutBnS$Eg4v{7<Uyz8!QdAh4SB||YkZlTNKIBu}
zrhmR@+|)U{gIIG2d%eJCOeQGvxrjz@Oqr?&8TLg)m3Ug7D&XKU%)qYlXn6ytAmGE}
z5GJ2lF?&UU?>E(%^v?WKp-m9K$03ese^=t(7PqKnE>yPd(m${G3NPFsaV|G7rQSMb
zMj2kxZS<rb?XvAZIi-u5N2Z;Ha=&Wh@nI<=8h@6WVQ*ktfza1pTy>^^V8FjsV<dX0
zs9p|V3h@sVZLITakt}=r1S{dGVfld@zV7Qps%+%Fhz?>iD`6Qf=M&*(gQpo=)GsbW
zFR9qDl$Yn+EJ`Mx$PUW2caKjX1Bs?Lt#jbsKV<8i|5?42?2j~7)LVyHh4KbY6$mxQ
z$gyPC>?);S%4U_{CioY1mWNLGD;sz(<j0C#6nA21YX|1(qO0M|P`a=v?f|Qmr(!tj
zSbhdJ*KzVg+#AgpZS0%_-j%^(4IVRG=mEAHT&@|vqN%B}e#z%Ivv%Bkd0PzZLF2^6
z`S2+1?eQRSOmdh{o`7tc)ojzu%ufy$w-kteh)HRkW#?j=C``Pu&#HaEy$+Y`)i|F4
z37rD&rE6DH4{CwYQH*6rsG3gy%W)DIyH693;`j;UG`V~$!6pgwwadDIa}~VqxyMD+
z82wT8!FQ~IR)S2i)ae!Muqdd%<;v3-Q(!X6T6xgs=?<J&4$%_n(}uMhB!)EXhq<*F
zbTG4RkDB6jt<W@oxONGWBJSlLlw1am-u0hdcOpGg2Fbo7qSIrAO=gEsVepoSF}#Ws
z&!r4IMS4u#123H|p7Z+YO}@CQ{q2L)d%ez9`kx~S_xmxbw~4hWQuO>ZZ8-IUE$2?R
zKPJq1#)b>lPpz;qa2+M@43v!Opd9Z0UB|qE&tujzNsX_lFVO!QLB=}4FvFTrK02g^
z476&!v8ok5eaXo`uq<PH-cUG}!pSg&S!rv^oS5}AF|E)k(GxFM#sA$3LtO~d*oB;y
zY4}EW9wVOagEY`BbL?gx9W}%)GG(v^&hFjG5&Y=SAv)BEe3pHLgexP}ek?82Rr;qb
z)8j?Ab5dy|+6l&mmloVfD?kg={X?XtR_CLUM4Zaww*FS0QI0T{OkCe28n1xQdfxtC
z{P|As=k3Fa5X5yNn&^tJb)stf&%XYtQ%8(KK8^CDK>u57#wpC<+^}_pyv{tcXz+uu
z&-Udmp6=--{^_diPk&ZtZi4f?7P}#`QBltiPOgGwTw|R;w-ecMPd|R8*B_n!rSWCr
zm{e)cziIbIe5Fq8KNtJdRe6tZP0#P~EPF|lPtWzEeUmtp_Y*E(`GT$W{w9Q<<U+%Z
zzncrjn3~P7QX6Gc@-_;$bn_@+;@g8uaL{Jq=_E(*DRO{$$eHFh+)Y1|AU;otcAlOJ
z?EuaYwHiH$k~hqL=DY~ZL7_Uyg{d`4rqSRzrsA%vO0_&fnr+?NbUX9rt!PNWZobW0
z<jPy~{^YI8_kA4qXoBfy=H^hoNwdP5+^0*VmX4#Il0NUsx6?<m--<}XJXTy>7HU7d
z<{!x0_5O4jG8;ON?&lMOXRp(rOMIq_C7|KF{bF062b@0tF*+G40zXBAu^CJ}C|8*R
zMq-+2)tl*~MnCC$%(60VB6Kc&4;v`E>PpE^`6hMpfECdwHzlR(dG#UNd3ul_lwpds
zWMa^Z)ZxjzV1v4+e-T1cXspc<=UX8<u<OJK`3L2vvn(fiTUU+JbMY1CnS;rFx|ny1
zvF&hCkvr;Jmwoff`kin2OWBQvf9k)_=|OqWd#<VAn)JP*oxcV-6r`>n6{-DQO?z9s
z)%-V@MUWf?RkJ^){RN%47DVUW^`7~kF3LT=sfCYfk<Z$@(u@b`WEOuY&Te}9Bz<1T
zE_{Z_5~%pveshzsdas<gO;n+3E%ly30~Pgq2VSe;6jcWFBN>}vbYJ;IDoy)>t?zG~
zm<k`DKCo7lWhBE1&m?n#y4400dlu_{rt`>;tIHfPaCYXLELkKcvsFZGX%tZ|<sPb5
zW{cUMig8Q>f_9Zp``*oozT1&=Yw~oEx)-;x?0KN;B_91i!L`Xc$w@V=k&x|pVg{qX
z0fr`#__;F1y;ewouWc7``Z8jhmP2y3)f#{G#^F`Tt&4lax>2Hgw5EWn3|q_=tuFVn
zT2=SS=>~+E^#zp5d3siuR@4WjvF*!<S8#Q<t)sGa+et%DF6VD@mT@N-rC7q;wFoMV
zo!@}Os&H{*{sc*`0hS8G9E*88arFXNX73W7?lS0WKLJr7=V0$2U~F+PwgtvUBA5Nb
z0n{@$%}z1R>ZY|J<*ZL~taZD?LRC=<^4P5{*n7ry$mFFQ&x>=X@i6_+xj9dn6IsA)
zOpYjX_WGicFyLh2EEeP}IhAy9ZYL&l6d~|uRDU-0FuBhQOwMKkeI%6D2^AX};z(y+
zO`GPR6QGq<XR$ORX*T|ii#a^qy}_idN9wO(T=W9Tqae-+$0@L#R65DwAbYk3{V}Y?
z?_|-@cx3i&#)_n;6@HPMQ$Up&n&pQ0Y#p0yHpk}n(s<o(AQhmZ@X;hIFc@lA4a;|p
zB@Eh464O+dopOJ-=ez&t-S;}hf5*b5eoG`8;z>++-@@!C`BaEjO!DX;RGv#gmsF-C
z2)n%p8}#>;kJ%zArYhBjnCPMD*Zm(}pJ9}Qwq6@PuC>9=-EJ<oj2R7Pmwh@G+_J7x
z+bVrIvrI&%$qREP_l=M#4wfBMo~U%stLblVI%Y*{MRsN}Ucb8@H8!ErM*hkDN@y&f
z_+-0hx$^A76_PIcS#W@KKzl?FLGc0-Qeu#PWDt?CR|A~V@*mBBvzag!kIb_<B_4Jw
z=d)%)>A#7BWs+kZVWOZr)uy%e^JQW-MMkbk^Yw83S<}n{z>w*PA<fDLp59s3ut;tr
z;_M!dwS<2%pXhZC1U`LXqT60HqG?KR=u*RWC@z!UnjgK1pP(6I;v)d*7V7NvMffP?
zC$lZ>O>dY{x4NHm^M*O|CppHxwa@3;P_xg{p|`0ZK9gU&$M_5N88k}jom?B@?jd}N
zrYa8;8V%fvhV*_})i2VGFJ%&#2Qcba7I711ls(`pipWDZfSNV1drZpZ>K~j*O<A_7
z(~mF~nX<2~_2~m|>R#9?71#CPldt4)gFN$}RU$ecX8jGq?O^7Lla6D)L?<#3MBLB-
zl*2ef&dn>GROGSp9x-I8r~2O6D(_8)XNiDF3MD>^xKOlP%8)nfj&qvbkVo4`NbF`E
z)sDV*<NFfQFaZ156=mwB;x#)9_3B2Q$HFgda&7#QUc^eLGdN+$9I=pU+pCRj$k-AM
zu=BUoyb<1YZEclJTPPo8<|l_5Wy{cm00=nE(o86~*Xd~!@k!H^0rd5&Ql*&Hb=A;$
zA$(p^6C4^2F`UHRuexjd%Ape(L)FsMyNPzu9Yc{vMmRMK2iQd%MVv%#kn83rk+ies
zznN9uxpxVytGQ<Zgan)z02Ovlm@xMBAnJd%iUv@dE9to(w0>{GQ-*PAI2bctuglW8
z(*olH&Jdx#y~3sCu@+B<JN1@JMQg{Ib`|@gWA$%)w;!CtX~th1{JLyC<1ez-qdZpM
zzqN1U@(nLB2>A$B-aTTL!_83r$xApqB2R^0cs{yiN_WG#8W4eq)?6@XSISopZGB`+
z#Q(PY2xw_^NUSOose=h4@NMu9{wG$CE1G5Mt=iN#mBD2dab%mi|KRMfs2r?L-2?}7
z3cap$a5Bs~eOUARs8NB%)!<s0PPQ0;?hE~v$0-scr#jo*wlGRkv9QguL^77&z(CLQ
zS>(+wfw)BLa(eVTfDqf@Lf1v&-yBWIeRVL}RjkF+56=P`0K6M3_oR&!M5@K1AK{cE
zR#7eb6yMw|%Z&MP1$T{7)5MHL#iG<hZeG}-$t8!&WMog~-xrJRCryy5SrR$dFMNY>
znbwu_AY5QOI=v)w^{tCts?M~gGp3YN19lU9IG=jfl+&gQoBmZ*7z7|VZ(Ey4;J%H>
zGP-^g*1nd*B@k5f_4^ty_Y9-_uO2uyZw0!0rYdWlLm{k<JX_ry4W{hb%<~+rB(;mY
zdQgS7M?bGf(F`0a0q)r>UHx=bxR;&y?|3%I0F&%ZXJA)RL;j7}HEM8;c@VF3O_31B
zRfC>bQ20DD$fV|V+9m&fYOUR8gOJHk>+_XfO4No%2!~H)(_r)|ozFngpL2jOym&X7
zei^JgQ<Ru}6=V|#;wr*L@>q?FFo?L9#GvLcJw#7GZHDTbp#k-G{=Tw<2MgXg!1P2W
zu8z;3OU@Sj**IUlsGAGtJrH>AAz!X8;>1!%?m>iz{9K~IzGgKZL8xEmU;XW;`?&0J
zihSRZw>2cj`FAQZVRGcl2;_kkwG>}Pxd!Qc^&WT2$cBM5?Uk%({(u(GX!T@Q)P{i$
z@#t;;<b=H=5H9rT@0&3EOe|CSG@3+Vl(X8naP!`n-#q~;Au))l`6XW}{6)qqjSB#i
z&jSPh3RiMXUQmc!V#4I80mwa6$kZw3DiE2}BL#5HnBOH7D0EFQkK~xV*=;JolQOnx
zlhRfZ$P|Ou2zlpPVh?^J@^u@Z;Kw0<9N{Ax_BdIXrI%DxS=bm%g@Uf(<~nIX+3y?e
zq#&$ZTDpJgw|XeUkYT&}JQWNkO_OWNglyO}&*}RM8a1`ZnI?L5F{M$0WN*V_Z$BG<
z7U_0y4S&}Dw!AJ9QC5Kw*#Ikpj;*m+H-F@?p80eoNzkmQR&j4AxLME(0mxbwcTc9M
znl};NG6|HE4>iwnYpNd(JnP6gTKR>Sc)@9!aM-ay6<F)?a7=}aIo9nPmmA#FBF6T3
z{RnE{P=2&=NjA_*hffb9gkieos@!PA=--3etNWNO+*+LZ&sgLmw-ji#_R^bxt%d_a
zmeikprB-HH`AMCx9o<qShTXmj@YA`i&lWlGKt=4uP+(kr`bt`TVmw{zMtCMnlHEt(
zh{dEE8X(((*id+?O0w@%_3yJW@8*v#MFO(peH?2WvLjfZKZ0;Zco)+*p-Ew_9|Zaj
zR;2pfs`?PgvcPUgIK@y@8Jd?&TJ(IyDVA;EB2z3?_mvGdPYbpc?{F(=Lb5`WXlac%
zL@(AeC#6f_>`mt>sYpMRp9+fFq-Pw@I8h4oB1k#E-bFX>?kxTxTEV@Y%VcMtUZ^1v
zS*$za$*)5MSQY?r?|FdwqMR=8BFTJpJ=LG$#qlTf3W?2H$TOjm!)`kJph{1y<MioR
znid}WqHSEAgA#fQl5>cDYsasI@qn<G5nJ@r_LjVuHOYNujeXK5mIl;2UVMKD4;4w_
z{hfmq=FKCObp#$;v>a`=%ju_{h3}aEsJkN+Hu}Fe`k%*BT(|M560iIEC0-~6MGb+F
zuve;GUR*ATZt&e7Ksy-yN^FGms#hC=8#b_a{`J%kur&*qB30jbb#}Z!JhszOjQ9{m
zg~t8R$>Yx&3;hmC`deTqYNqVnzOr}4t3?BM>rUKUf{sZLs<U0Mdtkj;U24K)T(mZ)
zI}Xqskb2O6vXAR}D=R+Y={0wU>ckq~s!xVj1iWVcmiPA}Fi<kUYL|h3plK7QI$<xq
z(ctz^M=JlK!E$3&I}9yZR%omU7X{A&3+~~9p4exQ4lOhVW^W4p$M?`^YpXy7%Uzpv
zUACBCdg|ZiXH#an1!!ez1L7-9P2)~DqTWSP=`*FqA(=ByKiS2L7FTsMkZTa!$}HS}
z$~`VTJeipP?i8h#ebN_w0CDN6kWe&L6k$m;#raTEs9Ok(nsU5Fj2T;1s&5(_1w>I)
z8m%rGK~i7JRws!~pYZFEZJ4+|g?+!$SOY#Ga+PBjf9k2gH598&G43q`5{M<vueVs*
zJ(qm!i~_EBK!o4Y<Qa6gctHWA_QpOzKZU=&J|O6BeI@o`_gC$ugPco7V8_=y-jO|!
zw}k5OK*=ebSdXRMt+%mC$>bZPr;mJGZ4z=w1iJ{OvDAps*FHMvdQ2akS7qPnE-V_X
zWuk2Y!<Q{;*wSnD3(E1ze{4mirUxMXss1UWA`F*O&Ynfl6WZIp3kvs!wn0(vt5{XQ
zf3^s4LTg5!-VHIg_ljOG&9*ex9QIQ1N-!FgDymk$2%QtU2aI-pK}KYpyZ3?EQDbcD
z@X>KE#F+2}bPZ8Z$8x6sZS{TW>g&WRmoI$RKi3!kgSq!D5=RO|XYy(NOIgvRzoFz&
z^K=qUn2X=QN!Fg(8GOgnG&0@Ai4M+6+TlQ2zsYa5S^|&r{bO1ygan>rEF~|@qEaDp
z!^}N7bh=<?jpzvVY!81b=COcl??n$Mq7`|>gztlS+Gmzn0Gv1`r)d<-fPD|wHkld%
zWbnd#8ntut?>V80uYqvJGJS<YzBmfAHjsmKPiIj4%Eu27%`7{gF8Qj1c|1ZfXfBsz
z%f>a>wf$|J)V0eAlY0}YYla!aWB2B(lpj7L{;6x#D;weU8-C2G#I9)Qe$zRAn(h8G
z4$!5)Qw)J;h^phcE+S~ibuqbjn{c~K-QwnwO7e(!_OkzN2QQ9Uj+$IvebLG}k=&8|
z>tfp{!WpXU-jH6Vvaq?i)1UFp?IN}+k=mif97!t{mY?_(RZ&4ms@{ZZ32S~eM{*_)
z=(!F)(_c{spSAqUTGkK!-<dVzkk-l$;WptIr}K68^)p0QOP7PP;%@GW-K&6zbpMH~
z(}_sCLOdJ50+6v_9=RvN_zj7RNu~cLJXI$KaS*VY8-$0it{Tj}6r)V5ej29<49nLu
z@_b~CLxLnWadNZ4z8kMiVu`?kSx;!3pMBI<yNbvRGwM=7o#bK+$cN=UB7?51&v4y^
zZMO9@L&pGw$ZVy5sL0cCF<>4B)I}A`w@YA}T*kAS&jaRp(9^Q+_0z#LoVw5yz3|JW
z-hKENdLRCI(|x+2<;vK}QUvsTR4biyBsY_iRy612^crA%#se}xud`29yk6S?1S3a#
zmsC5{pg5)wz2^o881-lE!R9*G7JCArYF)MhI#iB{TS*#=K6&F2kHDv;>e+wGe~?(d
znQA?)u+H=?|JH>41C<;u2uiCn4ax3IPEZ>-OMH9)jof$i-a*#cH+4OPB&}atXRq=5
z#6m7^NYabItAHGa*kcrTiqV)yWYlG~fY{92@&+8+@$JSV`y0##)0K3d7+X`49+PRW
z1}t^rshqEGN!$<s2{cY@@)>;1`%s$bNA)3J4Rt`{GtrBUuC2r3w)TqB5--9O9XqQ5
z0mA`sVuVgWzQQ5(;~r-^^MNfX<NFCA<E*J{lAD*SO*r5mphypFb1H3t+=vlTem`2(
zP+{Ky4VXrbPB%T&W;nLOj4OR`<=)QaepzYE#!n8I{W(bN5cex1qKvhWyuRjJg?w(w
z*;RLH6mq8Pv7kV_$p08dqN`E@!+W0{oB7Xff3((9*krnPR)*mB+U*JrkUTM?6BYG|
zWRH#*eKN~_^a{nfn(LB~P6?;zS&b5d9`BU`zGLj?^~1B6KwE4YMh9qaPLIFe_KKlj
z_|O_Nx*t-2<;F#anrSp3p8J1tDzx#qerEebCZ5NR@fhAR9dsxvcr?cFlN0^+B$>BP
zw#2r7d{{txmegx^fKvhFmH2dt0l|V7(y4;nW^2muSc36(BOV^Vh3DaUWKT>Nsz%22
z8(`49J@VKRat+4P-L!_%*nof)8e?KXx#1uD{>vxJk6V(I<|oPqFOrZkccn`v4D=RF
z+7_1N!>n>ZGOH$V>nb`PCnr+hPh?j$jqcj}L|~J&46xDi5{WIRaSsdsv7!O+Vf<_m
z{?v050Xr*oLsc?-={*0#V8C<VP*~foMXWooN3G}7QK68XgNO%hcJ}xC$j2;}aiz@|
zwCs&xtzX3o7b}8{9H3uJnr89C^kHA?t^TH1`b*A2RVd{w&kme!`Ug8E5h+2=GhR-(
zM4T0St32QNg}S&|B2zN6nmZ=<J-5GW()#Q)4ePV&*&k~);2n#}*Bum7beDTI|Mr9Y
zFqMg;`Pu<FbRb=9NGnNlRY1gugb+?n=-PULA{jw2ud_nsSg1eSZ!&6`nKbjapKuQ<
z(h650sU+9cL)C;=1AiSeKRdowXI$2sIBoir5R53Z_b5mUz^nOXQ#-Nk=IIln)eiSB
zc=p~}H;DEZKkELFWvHJ0grMR7sqU-aqWZ#bO;8#clt!fn1PKX=5m6jk8U+ODMmmR*
zp^@%EatJ{X3F(mTmKH`Dq(NGky8%D<KF{~wf8g@lJj|T4&)#pWwcdB{Gp^famM!y<
zvB@;ZT>ZdNZTj_|h;68QD>wd@eT3we%|tgPhKh}xnAxmVD3i?Jt-PYiwNF>%mBDDI
zvW-ZN{8?oy+2%}lP8LKYRGJgSGH)0p*3MfO@i>m)HG8kkp!TlfA}!WdhG(lCHqags
z9=G&aK}aZvk?uxKK*y&XZ@3n~rYr+G(DAZ=p?)bA_El~x4Te+Yu1WY{D@}=zx+r(&
z%+qgOX=!Yp8~6p>k-f^@hh>v{DK&==>yD>eOOQIp-bbF;7|yNVe;5no<n79;_BW=E
z12(j3TC7AoQAQ-zF78nRi?>Ht_rA&^$IN^gzTG=5=B({;F7&c8zWkQu!@&mjFYX&m
zUU8pUf0&+9{-K1`-=)&EUX_l&+c{)^GoxA`!=AWK>`#5v{I%M_=4rhrva6lqNW!Jj
zWoP}V<E@a*hu+>EYm-k$eTynL?yYC1Gy!p;Svwd$s-KUUF8fj~Gt|BHEl?k*`4IMm
zb#{QbL{`oUgCcf&x1wQ7{F>yRmu}-2PE@V*g2ujD4FAU7u4Y}<w}pxh#=<EoKkEW7
z9!>9>p;T<t#N=rK?y40h-QFJ1RRvIPB_$0Tp7x<=@Sd6{c0tv%;XsdL<UMki{vtDG
zXOl1dK-Tl5Lb+N9CdC<auodFsaf~b`W*_P|AVXm{XYp0sQv#LVW89_*vUK}yKL3(u
zW&6%BWaCX`$5ubp+mEnIURIiaLtbg8l3y$F4)^?vE*o9iJCI=s<5pwmitKfDSfKR>
zlNvbC?eVTNpa0GX|3Or6ocfCWA!xLnqs7IPe%e3gb#?c^uDZA?b{&bw-C=1pG%F#Q
zQBHdg|1tYaKgQE;UMrpVo|H0B0AIdpJsb<v|M9b$-RbrjHaV*!ZGE!P(q_%v+)&~^
zXxn=fPg2>eut1iW`ZuQ^)%`B40v<&i8|&g?<{g*K9G`EboGq-|bU4Hp?fr4~C!Y?&
z)XW>)bGemUG1B1u3{jI*N9zM~8v2~AzfBYcFXffC-|$zuYlyWWf@R#QD}(eCCf=v(
zqufrv^Gcz7ldz|aVaqQ_3%X@(+{#<(#SGKZzVi}vX+CTbsDeFtt+6mOjuZIu@Ih~q
zUb;#~Y^RN>J2Fg7?GVgD0+hT^4*6&neG3|t9h5`R5gKNWf>><S4o%JU0|pv2OYC~G
z{zdg!JR?9{^doVXeD&k2pV)c<odDEb4^~fVNx>X6C7%&|5<N`+Q<7F6smNVJds;tR
z!Iq%wV5gFKci}YErBK7Evbd4_8Xl(x9s(jl)q{chtAD#+y=~wxW|}R2j)K?8Q?PUi
zP^<iHu`ILW2o^Udcy75d$lbm6Bw*hbjM#Ix2jQl>cZmh=cQ~f+U)Y@&>5%@$AWI|b
zj$d_MdBglSLXX2gfoqw=&qN4Y>|UIv6kvJ6Ve}_jIB)d!J#>$*0bCQ5<~ZW<EP{}j
zx|jTLd5dA<Z80HPCzmy&>{+B}@;Y0~dwaB*kZ*3G?Me~IAw0WX98bq(yqyqcRg8Xl
zxN%8%YjK{$z{ZwZiw<V!qh~7#1XJ23%&+^Aq-o2t6+gA4Rz0Vq8*5iKJBZAjn1t#T
zk7Tb_e7L<+9{UYu(8^1I7uqOZ(S!)@wAeecM+bbI{UsTb?kpYOQLgV5bztw36=J;p
zq+C_nl9*<qbM34oymcY+Hr1lNkk3^kRd&X^AfnYzS~pT)y;~7f68`4EdD`QM=ybs7
zxaCTQ!`M}L37QQm#E14b4w5ZV2c<8fGsJDS6^{F#3VblZy|;GP0J``{8~W2mw7Q<r
zyiq|tti|K$f2AYPS$-zTJqvJ`x~x2Z-*aUs?w~^7AGnNQSy78wcB7T2b?k<AMT=}j
z7v|*e=Q%ChURU0_0SJI`g(3baO75Z>Ku~3RIhgpiYLVF3GrHrM+=}uOet-wgJf@uf
zywtratf}fM*gD;|Ny6YOlJD`9=acvwvu_pUl`m^XjPobDv$RChpOQLaoVKDIZDn2z
zoA>jA_6-tdR<TI0;WD|Ym&$UY9kH)8{Xm}tMb%Ou^Tp*!!cZ6MSd+e@U`^`*f(zh`
zqM?U%f9nM*6s<OsWL~*g8U>lH_b_#YB`V=Ha+O|fW|ZqcT6gf5u2<+WhQ^^+E7{A&
z!7Gh+j=CUaExt+6nZHL=tO}ir&~l<LOr1&pI%woWFK(5jV!rU3(EBm7v{F!Vu$B5~
zmLP@R0Gbx3$@E#j!v^(Nu=B&;l{MU~ZJ0!~QtYATnF>+g?MjpURx5j{;>Wfi1n>Im
ztoP=qcq9HK*OKtX-K)y%e40RTw<AMG!@@q!e(hhg)wN72TfCj)O4n-kd_p<<-ymkB
z&bw`ZeSBMRtr4pk$tLrWjSf<Ar^ghU{5fXl)hI!d5USYG)mma4C&bMM>Qg*u$Ow-h
za4D3W$;(?^D#$An&i0p+l<=-XkLhalZQePAOuK~!Dv|m&@DtdEhD=wyMy9c$eMR2J
zCry`49fwng;1tN_bE&iOeC)NeaYq(+ey%PnZz}lsq}}|{;3zmG;tc!&)Ac#8#^}8*
zimr#3bqe&nO{a!mv-yBSGuTvSnVd+WU#c;Uk8AV}A95#=qt<1b$7(8maoi~BZlLL(
ztCvpaCpNZ(>D|QZ9dZun8V_l(Ln9ujK&7n+y5j;-C)8p~>p>E6@3!WKXIq`e{?+Z!
zZu`tGP8!jU9Ws5{m}33poamf+TTnXA+$Ho_ISE^mAl3aC?gXOK6VIKPxPyeoVj617
z*t6!g^WipK3>O2AdDzo}@3;`Dbnqg*JRm^cHdlve`75Itx>PzKZ*X^Fb6Wj$!;39D
zY9%=S1V%<ryCpMxOS70Tc>YQ{S!Qg9%PQxkhyuqB2;sQ7<bLY|QH66A;I|?Iq+H4m
zF*^s@9Zb<mAE{_F`!@!Op1DmJJ&t2o1aImzb>zTr<rNfq(^x3Wk8mFsd&(IE9$w$~
zO0V1pZbdf5?Vl3Xj{hzFG}OJ|-PT#~BHM0%E9Z3l!eQn9yk;Cb#&rVs#CxK0Xn0Mu
z0we#>*Q0Nr-kxAzXhG9zr(M4mWBJcpW~9zbNdG=P0}Wp-NKf&L`M7Xcp8wGSCi}0%
zeDU9=(Dvx_nj`DpCyjd>M!z~|rxvyM%c9mqgN}<PbOlou4yzVRhla5tD7%MOz0Yry
zY<Y1_c|N&Z2916Pjeb6=X(sOssc?(%r5keI4NWTiS=*a=RH2F)CcTkm%xz<2qi{Ok
z3ZM&KlS*>64t3;}7gf)u=8RhM68DD^MDrA?5_PueQo980vDfm+j=_TRx8pk|`)kun
zo<FFRW+)dI&`u}gj9hvWNW>M5%%Ksn^YMmBO`*~kVE%@4PpO4()G8_6qN;!4+Afs8
ziC5#C1hpi~;^4g*t_OAcnnERL{^28E&)5C?rHbFbj~jl^l5&uQRZFsHq|#~Ml?9%P
z6!$k7sMlZ6qkNbw_(4CKb#xH2cJ*MGt2DyD$_HtFQl`FKBL{oz&)m$9NAvK6s_`_~
z>EsX*=n&^o)Q-D?4S-r+<w`!j{{j)a^>fkb8^?uBjxn4C;~QI$0S&a2l*3aNjSNz4
zgGY~h;hUslMN*vF-3_d?=&xLaxSeg&n&@(P0@O6B{GMM?p#|{|(3_~znjw@Gmp2fi
zHoD{~{-{z~Ks$@JJ8J2P4OMFN`!se7w3j}_`on$Qf%GMsyH@ggsE5q^pd%AcP%iw(
zGLyLl&f@55N+#`OD!CTRFl?qI%=B@52ZM3QV3_gEB<3&b&BbQU3nV7KN=}Z>{RZUD
zy5o$J{5k%M%i=OW8h7l`h7B2F;rx9<Vo`cj4`a7C^A+*-c&{U9dubZV;G6mVw7zj;
z`mrS0FxM@f-CrWzOKdAA#5W^_#EQi7uJ$3H_HTYANcqU;XG}!OObEftgv3TvnP=Q#
z<`C)!I&n&PhWnf1hIp(H`Tn)oZKsb{;imrD)eTDf{ywH;eUR0wU~p6%HfM8quj$eG
zp(-RZtmMoNsA<(Hjbp2ukq!+Rfy}f%h5~VUX3qwAX?(=Zp^(l=dY-wYv;|miU<am2
zz)X1DSad9vjAOgLMKqnZyFW~zFT;Rzviro0Fo!5$@F7f10Xlp{udws-(OgnT?(KGr
zohZsjeE-mSC*><;vT;6^PJ_j1mE|R(>CcTw9Ppsh30)4S(Wre9W4}`Y;!i$5-dMQ<
zc@>jR%@Oh2#QJn#ZNn;X@FBO>(V4|x&Lmh6#u$wv-rq69UXSh2Wm|l|$SKLMzTpY#
zF4zE%YO!d?(q7D3m^zPhm&Tu2)u)ARPL$m>J>iI;sG&M!nyr&X-71|JYt;Ode89l%
z8iNp5=ZH64@NNVt+41|<8w$id#Z#Us;{IN6U9MGFZvYlgTEqIhPg7*)qD?Sa2?Wtm
zf+txi215bT>OX!eKQ_AFo0lFP*l@T1at=}8;FA-B5H8EXkhsk*DyBt}ELZEc=-)n2
z%R+GFn5o1Pv<vWZX&<Z5U-5?9!`HH=39nQ~t7JD-%0!pk7`&}GUjN8{tDBU4e$vS^
zf0Jr=^9pr+tNqM%CEAEG=B+%c>*luxt+``l@~%df$OB8J=IjrCwcPyR2NM6MiDxi3
zmM^GB?AQ9qRZH~K9vWH|?EL1M%^S40<($ojE6}UH_ob_vO#NM*1G#d@vgD4ogz}eg
zKG&4xRA#qP&+gaAqoRkVgf0GvX51-=_)Rfrol{|K-E}`y5zcCEUE64J=uFiY@~X(1
zOPk3!M6tw}d%aM6l3RLijrEOP0GB0cHmy*<NMgN<-_J*1k*!pzV0bq;(*g@s=zz8J
zJs53Cx|ekhf}HoxG4nH#%;BSrqG3<}yQVs9cP7}mBCxkW04PFSQ+9!V5Q`sSmi%pj
zW4tUL%qWz)M5EINt3hk~X|(>C;Zt+9vdcU~Fjf+Ky-(WRvooUHecR04S#Fe|!jd7B
zL0>Q!x?tM6^JhjC_?w{lOmZi(ELLcwF&Io#RQE4^y~#!ue#1pB^8LrN6}{6GhBU>p
z;k-8ng+A9fy<V$%5pFRc&o5=)He@8;LxtAqHGqL`4a3_H*+k3(iV!|`$C`LW;D6(w
zWByzD+<1FUj?jtVk)@W-zSHMa^@a^4Qt|xD;ydh4o<3HDQDyWHC^P%MN0-qix8isM
zk1ZHx`(JtDp6Sc7^Jtwu<wB`&-q9OV*|Z$tOW~1r0lA1<4q;5cL)9Bp9)f@#ZgDG{
zR->OLYdZ4xTQPHYOy-#8VjUTW0`bFC2XB3Hs35LQx7l!_(s}0kKlYlxBowlVmzq=F
zO1Y)2$A(oEDfTlhpGZs4hv1&vCiD9ll_7NhWz}P&o2^jY)l@SM$=`0(hrOTt7jbmc
z)8}aBOqL6jY{H_7TfTmv@#87Otv2Bu50tW(%tfySRUb>)r*!|K0S5GXxkf7Q7_w?g
zMDCfOi)9MhBZ!S?{odtQOYwr246>%4yKZB4vRLusfCJ17Lv@qchNbL0&rIEi_9U4|
z|DVc`RaT-HkL$jHhI3po!D;LShE}im#^LY1VRB=zhHu04HZ{8rLj6~C2MoSp`DZIQ
zMGh_xqKuq<9i6Xw>F&Sqt9~RqUl*hg;UX|bc!nz8|JKqkq}wL^B9|eu#NV6<W*rc!
z#0-9?L+$eA+ig<`0m*?UH3o#41Qre(nG1#M1A(_qB<z5-@Untj7x-6xI({A(BXN<0
zWG_I1v$Wwot!rNIeGTVuVi3&}o(hvkE4APAYmVr6Gr<wq_if_&P5t7QS*X2Q9+`tj
z%AGRB+XH8=yF;7;Rs2gD%#nt*;JIfKo)fraL&qN-47XW|S`n-#TFwOwsw>gzQ@ViZ
zNk9HGLq6V5(>N9ERP!0kBd;4|A=OrX(!sPO&4QO|qARM58RU`5Exer2vIqCeaB6<8
z?P=bkjl5+%K||1C)6Ek*jX6aIt+n-~wY{TzqyQG?XzOS%a-Yi*#ET+nwb`lndXYHl
z3aC=aK!y0na8`U<`meI*n&mSQ;s2st?6fW=ozwt>EC^hJO6d}{DcVKS4=TkNs>^A4
z<mPIhb|aEehz0NtBWYoF`&xiB@SwKCj|~^0`lpL73gK#Bv$yheMLxsh`2z;{LpFI*
zA1fSO|JCzUR(DEm&8d#ddWFSyn1XMEH{{oq_v@t0yJACG9>2IXkaSUj>x1&c%S}5b
zk+`dNP7oZ1DH#)5eJVOBs_-SR%ynYQt*dx@b1*CF42RnYO!l3EOKgcemhxPyHRWh&
zwTor5_;1-_R*~1FkTFy8ON6=e4+T8^(_zn>VehSoX5)S9<uO#?CAYj)S_0Z>)Ew{R
zMb)5e>o(FoX{&V`gHcx5rLOx-LK)<}q|9=VplTTRCutSpsW2sq@g}~GQTThPrE#Nj
z<Tp)b0ncq_VbQ((ul*`SdpbJ!UtyFQD}O?@L&~har_RtkUy1*Aim*?=9?APlZx*9e
zlFcgU-=;qM+OMppRdc_V+ONo_8}Io#C2AT#hI%;ms))IX^}}}sO<g^n($OWOODRl}
zR1~jOCdnYHIbuvpjiNngeDZ&HJ<hPIe$Bo)fU|P4k29?v+}z`|{1~_R)Ds!|-mgfp
z<NIBFUq|XoI9tp$1}6)5qQyM8-png@9EtdWWSL%qYfytP*T^KBDEx`8D;7fCF-6Bq
zmQCxO(X%GwCt8RRi_hsdp(Vc3z^?PWxF*_V1xiLcRVbLxhx&6`L#PNzQco{|-B{xf
zjAX`7vQoAQLtlO_SYGL)w8wD*b=r?-%~W_j3XcdveDJ7-11LeMl}VLycZd{+-%T$u
zkm%;%?fgxlz;%6SaJoAQhNfnbgyP>Ko}Ulq<18(=;E4i(*P}>`p<MDoB^*}%l%cvo
zZ;|j#agezhMR(21c0uuOSQ4SdSiQ=k=5^B~ojzf1{4!Z!VzsJ>jD40w@yWZxmtFge
zt<!e2Vk<@G+)mzpMdJzP-yB?Uv}%7$7%;HT@~mEXHwvUis+D?w``H)X8811t?+ss;
z8fO{0$J(y*SUTnPe&9gQm-Uo}xu?^MU=afbh!X47E4O&4>(zhPzj#+to4_%~?@zJ&
z7Cl3UUZtro^HW^)s3<fZj%WQV0@8Z-5}w#VD!I1tw|#!qeaO1yb2X)5B=Ojdo?9zK
zsoXKW;-|sUtH`RUvh!qlU~#c2#aUV%PSi`I+vQ0J(kZdTauYr>x4K1#LW1mb3K}H5
zuo37uu5~xti^WTRwp>nqcQ}W1)nX)uQ+mHQDBPBYjhB(;gcjdbzz|?>O|ta6r<Z&i
z$xq)+g5mAz&;#V6T@8m-KjqX$Q))2<j1*fxvLt#}rCNVuDOy~@B+0few-r$sa>d2`
zBRAH81}({=ol4tHmPzYfB6dqc+!SBA;#xa%l1Xy9-HqP7$g*s%m||GKf|%@lcrhH{
zp-@F;*+k%maO;S4_s!C$ifB`RJ9{)!5m$dRzx2TZG*o?j_vB(bM#_H-DJ|bHzgBhD
z<WOK4-U)!vm(o)&5cRoEyud0%fimcZVOhP-C?cW=5v@O8=Vz?OO<;~d>_;wztKcG;
zDwzFj6)1!?ysN3(9jz;lQ`fbNe7lxm{0T|`?v1*G{TEgwjD+QxBk5GKJ&xVC0J4Nq
zKNn=Il=$elEI$3k@0SJ4=sE(WAA=2dbVk0cZi^Y-7$7K6BIYE?rkyEyE}+e<$!N)g
zLd4`Ef*PCOHWuejbmr2R5RCJ_v2CHaZtSOL?-g>Y?z+X+Swqi_I;IhX`6-zpD)x*v
zNkca8Ujox&91>N=BC6PaR_g~IeJ-jr8GD<@aubH3=doT~mIEPiroOM1;WBx<7zSxg
zAJbsCvkRAjVPN3jxP&gxo4t9HPEz?ft9ir>sSeMM0-o1#wCIRx$|REGkX59l>&OFC
zJ~gX0lsf*<bK(`cr1{xmRo)+uF6j-9^pX(EIaa}9l}Tkt9;@wMQ|kS``tR2=6)1Qc
zJAX6=16ZEKHF>OJ*-O>Jk540j#nBzehy%sQo<SfaZ+Je9F9k3i0QyOjKqKpfu>nq=
zRalr6QKS12-&F1l4U-h&2Qt{l6xsbtq{buxFd6-5N!%JT>S@FAenKyc!0P>vvX19s
zGKmw@1=*w2p`v4^`=ZV~q&ST3&Fe4vLbl9b<4j1-NycQEUIMV$jAmnW67n(pu(m#;
zq2+GkW+WlI6i#Q9K4gI*VVgh)`aqZ{6UQa<zOlT5P1vIZ>^5B)O778ArKhG$lK!MI
z!$AN*!7r=1;)C9#&w%&bAQB?&oWHXF6xVgr3&znMcU@w_#7^r^&!SW#dG8LuXwXlE
zQ4G?;03jT0fhp*^(&`)&goyqq=xt0i>2#?p-*y-pVMn4ohI|r}_$P|6A>+M1B+wy+
z%aVjK(Z`hf5{9aK9ZR%-9@Xw8b6iLODcpGYt<Xom>skQc@DHk!6-F7Ov7~pXut7%7
zF|VD}*H3)3t9u?WV3|Npw?l-gx9~kMh(WUEgf2IKE{9Y0Qn?tku2EcngZ2rmfkiV(
zQ#F|q%gm4VE5y?FHTg&-QLkAMUEzH(CfE?L&(k|{x}*6_eD+J3JV0^Z(Rl;B(a6s<
z%(kMw%=41V1${R-6^S2OJMN?q;56AMY`7&l^0t2N@eI*l&vX4cN7KUH;jBhT%OY;-
z|LwHO<kt2cWNit@yk;Ngxe>1pm}%|>&zEffw(@A5%Sq4NS}arv*w~*Ui?;GfbJuU?
zuCqdL5~p1nGNfK{g#V6DoE}X|OEOm5%AZbr+s6v7R~q4&@jkubJMSAe^JtHvm+_^`
zO)_(lfx_z(jgkXikJm_7=rkmtKXlA?p;@-{<zbK42Es-*gjNj;*7xG)^K70fI>_s?
zg&El=+|2=Gtf)2|nKMEBlOHE*TG27|QV_Hn%yT0@-cyv^&9H}2OC-uJ2Wo1U6FA5`
zOWb+R)upEMo*TfKmEkMG4`$bCy$#<wb>oF90uD-=N$`96dU}bRz{`GO3icUIhHLFO
zcvt1T;e$6g0fsZ1+A%rV6npE4AXBb@d^8>4x_<_tsOR#ym1v2xs5dM`_k|@2*U2)q
z26&%ErE|4wM$P5*(^@`~*0i6^6eFp6gmCF{Gru;H2OzRfTG!gseudkpB>x0y%J>eW
zHke%cbAS>wruhiwfxB~RXVQIS=)YVVkqwf~BlG=y4f1nj&|6wnFn?a6coG|Vi?E^Q
zPrax|u=u{zz>{#*FNW@yHn5I&t>hGJi4^UPY(DUye0+OS9$^jvRJ)=${&R)40%-|}
z@4;S|?$Nyjh$};NTXRcY8l~1`b1W|^-hOjYEz6cG#%^Myp+qdYbiJxs#s5bmKH!gf
zHQ396>l-sBdq?r6k)RPuk5D>+Vzesxt0mNb>u21jN|sB=yJunT^-5i@k##6Ab`^<o
zqnN;-@-VJ9|Ax<>bG|z-nTM6zW*kjjknZ549}DOK_l=IC)ILW1p+7oa(vl!hH$V6j
zCC5wExoI8Jp;O*Ed6g}*G>b6~D(v4cbPpt*v$Pbtd+IO#k{Cl(&%X`r61%Qd$|x{&
zGbdEiLHwg5cXWs`kuKG`*6|KyN7@|CU3%GHC~{z-XRPc=Q?Z{Slm^Wkf5W|4kDD42
zmFggyhhP+9l-3xtNnj#y*m=Tcs7pnZHJzqRnDJ+p&~=MScl^83DaT+IAL~uU0cKfh
zFe&M@93<H_TGx>|p#ctI?@9=~^l#&aB_weaw>)LN8iJEw{3OIQ1-b?(_Khf<OQjvN
z@rFet&WmZl70Ud!x~M=vl+^&P2X_wCu9i(dhRRyRpqILSa+9BT2tEtYyzn>?!}N^j
z!l+qf2sQ#_tWQ|B7YM&<*o*q)1~oy8Vy+uIdfo;}z_a0-+;(fCY1EvTQQolTa0E{0
zCSAGwNS<}|wm|vMzh{h-m3w#dmR0^q83BS*$&u(0ut)u9>#kd1;_Sr%M+Tg?`Ewrb
z#!Mobh6Ae#^v7h?Dt*x`TT0vBzTgpn`*)J80F<woI%Q6*f3dyCIOtpOD}m3gxOCEv
zYXAVumn0)+a#@p%#h&Pl!R`iE0+uHhR!m!`-qFh40jLW=R$@i<(i?KX%GzP#LxN&G
zbgkd-^<NenFv#532h!<70S{_$0PVK8sa<QDUOewo(@u5G9wy><fG#lJy?X!wUPl1)
zC=8(q43%;K;|76l@Ww-1^a)1;FFr)3M=W<eM=ZXQTAf6*#Fzqb<!@Lb#qk-lmHnk=
z^D!6h?So+`-~J)Y;_U^)mYJJ8mnEZv9K!C7=>U1Fdy@xfqx?Y>9StguYAK(T0mPEk
zytaiSrX-;|qX}xJi}7t(pxz;V)e;y+l(A5Bx)Wu}-X6yQ>tGa0C)Z+-{0(@P?7TtE
zp(L=|egWK6kZlNB;pXnWhi#hf*E@Si2@FZIwSZ&{9{Q-ADsbJdhFp);s&AI__>lcO
z0nX)L%!=dpq^q3%Q2iYDC@nbxd)7R<%nIH!r;%~mWF8)~qpSb}2KWCR{~8y7uk;e6
zx$39Kt*pZS6{80n-u8B_VR3M>Y%OntsBcrkyp0dk4}_h&O4)?Jy*x{1pdH0QuSRuD
zUBAgQffPHhCI5D+5|ga1KkAtP^fWHhzL3~J2YN2xdaOdl$lq#|E%(n+&HDKf+axol
zXoxf=^ltyX{7p8^&cq6HmF!C~CumuA28sUUwBN}FO`bPpVCBz1z)L=Z^C9{W(`$?U
z5%6q)$#L9=O?>Wb6nXM3?Z>SN_v<?TB_4fSpM2jqWFY8^9@PJ3NxW~AP1w6?k<s3o
zy%-Mqo*u=$#VGbh;~$<$+SM&a*2#=(fXKyGVlY$ddrgMCcx0WMKpvskdTY>yr5PE2
z%ObhrBp6zyV0QdiZxUUBY+W7RS)gFT+aq|sZfZ7VM}cs|UyLWuU6%sVF`PJ*9>UDD
zc<DOA?CW2R|8}2Q{nPg;TcLVF{*Tp8S4z+;dHbS38D7c;dMo#*Vf-=#s}THhD|A|&
zfdJ7PRhCWJSre)c`Kl5+se(QnhJF!jT7+Y*>}Q$OTt(9;0XHq^3%LU%#y}z*7?C9n
z!^+_z1-aQ2Wl#^h;o_!F-9DNtx-o60fI9|Dg&SNKt*QqfF}ZdJmpp(&DM{{ADFHF!
z>(5F9dPd`rGimpC@?GN)3@IC`BlCCickW=>xw@v1JpogRosx#nO_dV4vtk=<B41R~
z7M{rWC+p^J^3kBZl$ZtWe7H>CaZ1$EkL2mFrYH~9$qA#f={}<4@+>hP=7Hr6G$KYW
zZ|qE}*a~%e31Xv-Ywql8h%KSWEg0n6lbIy>aXT@^Qhf}k=EyXT^ECDB=f!qZkZN^x
z*y17|1zSS6V&vob0|$U2N=Kj@IF|dPn2^4+Z5Bn|(L?HHcMU^Bsj|7|sPWae0X&W#
z6;a{(G)fiNtVi|BXOg+kA!E0+We!2jWP%-Jx7ozT*B$iipKE&EX;j(_8)ays(UMZ2
zz9MMOs|inX>=#P>WkK<<G@_AbdoKT`h+ROW9ZBn_pWo<Hm2k3b0eA5$qTJI?*O5~$
zF_yHKl>QKiG(C6>2c&}nL(^Oa=i=&T{BTeJIM0nieiy{{mzeO0MM8W6-~~X82~}j2
zTtVuTgwXw|`k9+sLg3jKRwUaj7-|*rE3pwN-CFaCn5v`e^pv7!?-%9su~GPC3{?wX
zCt|AfLM(NJ=I;^>FP}voJyDmXx0oP*yev9LY?YQ$)yN6VL=-W$KFq)2IDuH(h^U@)
zZ38x|?_#%$tp_q2s-I7!7(SK!3tu1WRn5oxuX@{bRm%6Gu;Mz9);l|e&Hh&BKeqnv
z-7%0(Ikr+?8L(()P#0W6Rm0i?KtSH!>$W*R2_fKQZOYv4+^3t2r9bX1Gl8xy<ZGwP
zIGv5ey3oa&^hp<^){s2E0jN5pQ*-i+oIV1}lSiE`*Dly5z8?JA51T<Oe-TWX{_Vm)
z_%NsuwL~}R><d&yoAG89{ujq2wR}ODw)?bf=LaC%Ys&xM-z^{6ydx(KRMsXtz>1iL
zE|)4Aj3Pq4`FstX!ww}cP~70Za$P`gfcSpEARU!lX~tM;T;5qm8b5MJO_SfE)nUWM
zP#Ko~k(tX6WN{z85LH+&>P}!^m3Vw9kac~e@Ff-F|3vZu(HyY-qb=s}nM4N2n(6j1
z1mM*He~ydN-hbsnH@L;0-m|B^U4>zio+xvZKucZrO=BmDJ>_Yf!gn^hp5b&}l<^s5
z`nUJ}34`qXulVaA66QX?MVrdS9qnrs5?<T_BnFU?0ExSdBc1dA7@&{gLAen*2DJZy
zZ0lFV9V5{$C_4mecU}*U{;010`>de}G<L`?BSNlT&};da$7@kbI$ZHgVo~V|UJWWl
zezsqu{nIR>BQq~VB|WQu^L)OR;2@27H{OdUJinOFDEGfXUwkAHK0l%9d^yj}wDo`f
z{G8PO`|>kzM#X<c=W{yre;u>&KZ~pvxaPmh|9^e+W9(JMKX)Q{_ms>pfj_AiFU7w+
H)A9aaof~?Y

literal 238932
zcmeFZ^;=YJ8!l`hp&$q-DV@?OjdZsnHQ>;Vbc0HFcZrmUba#W~(A@(JNJ%&B8=vQW
zzxVrT{{#Ct#u;E{*37!^E6%u<LCT6!7>@}b-@A7YLq=L$_1?WlxcBbeKSD(Yf05tG
zbOjH*4iXv;YBt6W&QLp}dkRp8kCrwLmS*~7PDXb2W;WIw%)HF(jAW(`4j=9LSXiw7
z`vPVgI};Xi#fQ`2AZQ<@HSO=+!-U@byZ>D{&+Oj)d-r6-Mc%rkZeP2GQfa17oqJ|L
ztiAMX7hO$^jOWK85XdNk(}V}5hn#nAnOOpxN}5UB{1H}&AJv-&NK7SPkVF_5(L}JQ
zl*u|Rcvk-;FCP&L&O<!MhQ}QZ)z{JpPS>7!)u+s!9|gF&7^@qLOR7s4N~$+vM#gDA
z+ck#u56sPZ-CQ<iM5@Z-N~rwr?L@?V<e~Ea{snh!GxI@k@He{uxoxLBrhD~2ztaVm
z*}VGt{eNFV*V~l;>D&MBU38bZ|L;Km*EKR0*u4Lr7ag4Ws`#>qHLy}eW0R9*5>3^e
zX9wioJ=?1$`Uv;=KYO?KBzu>a(UEY@^sVVRb23(ga{B7|K}QTp^55lGLVK?K_V13m
zqG!ii)<YaJRZ1+m)40=G3~1CkhJ<DrIio^1kcDO&nH^!v@?Q9}f#n0KEwqu(%-Th9
zR>-&|Tzik(J}Kn+(IC;ccSKMi?Xx{58?*g;^j@*=|88@DqO1%Rwdw+zmO$hOEFE_(
zA3{~xUCT@)qz8eKmV8!>3V9!<e>xF?AG_3QFCTbfPkT@Jc+*_SEu3p&$?!FG@2JP6
z3|JYnKf<p2jKud@iUnQz_xgvR0~`Z)t<&TA>{#C@aSCX$m^`Y30{YFh#Hz25b|d#A
z28o#p(@T=N+~Ww;zbg_Opmty4?@v!5_!3tIq+TtB$FE44e(qh=1lgtE&g)%Ej8sXq
zdGHD6jtK<BDf*Zfhr~uly^RlrLWyXe6uu(hXbsXyO5Q3N`f*4*?0BFaP0sIk?}|=;
zz)ZCy8W%^V?sEjr+1q($2?m)Nd1dLTF-X9gqR;-@@CGA}xWO3qT_lXO7L&@^)%jlb
z6vY(1bRjX(*H{nYXEEkj$*i>Ga}U8y$u8k#pm{-Gvm5-Ob@6-6A7jp*b1bRCU5i(p
z2{JT{=+_|xLJZWZ0@{SMffRL_Fv)5^QomP;e-o{@NiZ#A>~9FT{*Xq4Oy&)5mTKDI
zNZNLNBlSmuiepLMtMQV?@^?33BeB)RS9X3m$NC13Fc}N=naKk_=%@V6d%mjJzfd8g
zf4+gueQDA!6U5A!+R_~&+Q9l1$K|J^)>%)aD6YO4-+W8nPQB$RpE$cdv$iOXbDUxb
z&qG+)3gY2)>6<=h+XopHNoR9NQ55u>M*`+n0by<_tigd4L8OvrP-)!G?y>!SyVRaD
zTvCIKIA$cY`4+SlIPTe;;g7#X<iO?s3!zb@JR1KJCY-*Z%{n2$MU(R3%wgLpYp0AO
zEKGS8^eLzM)c$z-8Tu|YUL>qu)a=k(Wc17^Hf#@rE1oBXgu)v2e&k5h{GAyYjV<ol
z3|Af&ezDLIv=zJcH<D*6;u96m-n7b=%~+|P66?|_EpUWqTeGLom!#6`qlRtD-`9>1
zzJL^2Q}`}<*y74fk{*)q5u=SR&Gpl5iho)5@UMc8I0{y2L#ha0&Is<wVDA6=lNA_`
zuq&@sp#Aep`-E($@Ne#xk^Wl_doyuFKbqSG?yH8Y;fNtY1Mz(4w2JM_yu$YM8jiCA
zT$a!w-6IZ2Ll_>(UJ;IY61~+LJKS)_)*-mQV_MZ-G&iHXf|%IH(mKg``(Mc~(puWb
zICUA7mV8C#GOHnCI27qpDzc*V`A0LBd`#S_FSh1iMEUAd1Q8)uct#ZJ1}IC8=>#Mr
z?nVEY&G|5$I5A2pU&a*kq}-rC9M_DW#0zWWcP-<)-yVC{L^_asflYF+SE^lV$R2w>
zMB=LK96BGqrDjDcdi^%y`wTNK9@xBM6-BkKu8Qi=On;@Oa@RXzua*CkZD}+}F>CIK
z%|o9^Rc?ubS$EMaKH_AoL@i=@&I?UFUEGlq_&VJ^jAAJ|N~AC2iVqb`R~d=aMzLCC
z^FH4@h!4ZL$VLz0@Pk@&6<8kgaeCs(jh15I$W5~OO7=N#o)DFAdM1P>eT@zDQG6Dy
zxHOC*pw6doB{E$hRkw(7VP-<WS5DdK?lrM-RFl5A;-g(qa^Q=6LLfuG?-N;F%=Ap+
znX2po{iWI?T%+dxCL$M*!Fa(2Q*}Ls6DN3eNIHMdM=I|>Z3@MdBF^O3;0JR;H{nqR
z6Y5`yFT4@k1*l}1Dg8zvpc)0%Odbp_M%NHk-NWM7G<cvk%9BPKbbE_~X87Q9&X#=k
zfrrTfr%b!}9xU(d3B23I(IGw-iY?PK-6k#Uf-8)Od6^rRm9t<w^}X`^Jj{rbJduEY
z#pNbXD<03Up|<u-&SdU7pNGwH*9XOcY59G7j*Q&DWj8?SKjr^vWTqK@vJ(vEfK<1X
zKBE8RB|WvR>7HWJrjHl5%OE7K2h(lNXT4SKH%--ocWSPvq*6*1yiCPr*wK?wj24|z
z$cjCa2I&z4Nd6Ijzf3c6)#xDwRsS5>w7<n=`t^U?hp1DXu<*9YrRT1RYpPwvHWEg)
zHl(Q7YWWd){QmTM9j9-Xea^nS*Sh5W>f~AU=_FW%<=-;gr1AF6-&g_R68>E_tG#mV
zaS>@`X(6oQr?RX%pCh4H#E)6(*l67)`+|3CeeE2fRPU7kjV_gcqKj9bPcTA}WmmPp
z?7=L%G&Ljk`VI4}s%&=b7{6d$5vDYDuE<PyLZ<gO;!|rV{xivEkV#rp$}7-2qtj-z
zAfqd6NyxcH2HN|H;pX{<LyIKc$7tUI$wEP$qFSIKUn#Xn_Af${htNWQ<JW~31)*5K
z$Ca=p>w1EEc}W*a@r^Eh4{K%Zcd|bXQhcUC5;B^Y)T~jGGl=y8Nq5$!We;S?WFUnM
z>~Q}}jhGW|Ppe0;C@MN6WYTD3DmUl^b!|XZwvDb0lhUmyVsX(%rGg{LK&Q9Rg0RZy
z!^tF$&6dw3WsYINbnCI0?<buRnwSbyN*OGF2S{`C9#vU$x{EhKqQ4{`l$_Icb=@Ua
z72EfjF4oG$eO)Yy9O7*Tkt?n329heHZ>M@8jVJG@sCBVM4!_*k5;l_*jMHq5zYxJE
zZ62_W2y+WD)IUA-u^gdEkQMll7OjgvbONbzhZx@85*7IndDXcR{N4C-ebxW0eA8(w
z#tmGX)ZV}`#Ikq2(!}_@k|k|zx^_Q6m;m{HtM?J9cRy*fw+|V*>-j3K_j2W7gM)sw
zDtG0UeZdZMoMeFT+4MX0Dk4V92~!6*Bo*KME!=V$*=bxoUjDxQVQlc=Q)G6^g~t2p
zRTy_l*we+!C1i_n8o4;WFhxw3Kp*ZZqsR(**=f!k%V<zY1-w1JBrQ`=`W=1E@136!
zjBv~APD#MiEaa|fQq3IM9&*sB6C@>X8RP1m<~*+$;NZv-@U~2SVh@jHmqGX3ORKDS
zhiJYDxJ4EYl-5ALg*D$M;IkN+Ik+|K4_h&_SlQWnr8&WJ;4X>&iX-faB+MVJjbjhX
zvphDBI0^Vm_pYfvA8Unl%BGQexP+XC5yly(Xw8bCe$KZDeNm2%81-1|XG9oF@^Wwq
zpvLa3-=4v46Hl#+B4stM!t^|nnokPxrp+BSroQjbI~UuzXUXOaXYROY_$$&REnRKX
z*=I@ITooXGO`$~xWsUpIV2Y|&rRb#U!B?*M5)!!0oZLC<1<@hxoai)tyvCBjsTl-o
z1+ad$RHePzVvrFtPv0jnTpb-e=$pkLd>ODN>r=F~>~cRU_UCx=)!|+<3_uPa!H0$3
zTQHBH=KT;B1HuczwcWZQo+MIz_Fo(+n<^#I(o}tE$YM?x_fDh#)|?FIf18?=JaZiA
z3-E&xnsKKD3x?;q!mp+9B`<qF+BbYU4|}CO@bqQ3#3UDXe5*KpwMD!^9-_429in~K
zqTgoX%oOV5)}1+H_s6GX(Tr!1&VrvL8H>?s;(O)GL0CAuW_ZGNHpg=#VX>0w9a~Sw
zls>r>Mw{{4I@QeSO%)q{o^&NFnQwI85RV+tBZ}~pt(?uAAYF32G_tjq@h>Hwh2#Bc
z-QilOuWj2oes!!EA=@ZXj~G7m;gQ4GI4Pe>o+t6bSGC~>k$5)vB#+KWEgO5i=<-!`
zbkWvn`Qiih0tNGz0nWuN_Kvk}=9Mxz!{Hpyud$ZT9Ux)SU+{b_CuU7W4b16a`=ujd
zdNGB@0RwI+q}~EB^U9v%I3|D%_`*Z*d{09QrX7PQdfW<ot|a5$!v-T2XiCtpKW}ZG
z-%m@&izpa2E>%SYBv_Ze&9`?oi_x0RguB(~zJcNJq{GII!gkbAKHmibOg=19QOn(U
zLg=ZgY<xAL<(T%>D*RD=)$gCyuQiJ+Kl)$^qhg_Q4oJz$<RQTFIJl9hiMi?ua`+hi
zPQ182B$NG$cr-Tqv`-u3ciI`x_3Ak@)`nZ^aoyz26w@yj-#1cNGBPYj!{XR#90XOP
zRAE`qYu??lg*DTEK{T(v<YP^+GyCueM1EDB4x~ug%5lFv()Z+#oO2$+*0ol&a0eWu
zmlMA?mzS5#LGN_A{^7^Hd7ZUWFQ+8A!>u>O4OkDbb3f;sxrj*j*@7(lY57`u_5~@E
z^`FV6W9;*aFeCg=9xEc9%Cc3-kej3S6cD=t)e{B#CxQI4744XS0%eaLMzw&oWJyb>
zLA^9u$k4E!wRPS4O>w(&xi?R5v&*7}0~!O`H&hs=sS|{7p2VW^1u2VlWF<~&GJe|-
zm+IxOx)6X#eHpDMO!-M}SKaqkE^Li+GA(S^zh+|e8osY00^e(8#7YcNTWcF05f^#T
zTHG^e(X3^4&|3J;>oN>;%G?Qg7S|?1WDGN09l*d8$olIaI$9bg4Y3Ap*)9Da@AnNk
z>tWh{EmyU%w{i{fzJ$wNlj#g$hN3wrU`g6y?as*hrC5An2uZo}D^4}x$!M(#6_H$s
z;b~eiLt47{4c4USQ0evv@`W|H+vm+Bm!(?wUIMkv#4Ol(9o?DLuHP?cY5jTl1x1C7
zFb7-ftHpYGzD{k|{hZYHS;V`X?f^Xjg}kmPN`dAV6^^^&=SUeXcW(Ipw@Cj<gQ>v}
zTVGW5Pk$Qy!;?_{+gm{yvFuyYyCHjKGFB^8JyBg-Q!@CZn}(HiWV3R@>1<!>5JY~W
z|6m_&9uJ#JxQ}v%%g@-4jyY{P=Ug|Nrwcg~POOe;#i?n_t7lj&sflC>Wo(!BXI5jg
zKi{QX<yEtkk8gi;&+6T~S*1u=pFDGKK6%I9(}Ba}{gko?w2rh0JnpmI`uC>1B>qLV
z#^#B&QP_Cvk^~Iv(pofiMawlLkVzA0xn#js+5GQ=?QMLVoNZ5gEW%_-`jnNU4lK|?
z<X%Bl`l)!icsrzp#JH2lpuc^iI*uPQGyN<t(S)Ba)MA@3@G*P;*?pHT%spsx(`J7;
zlTH?TX0qsw2?_CuTy)*XHOZCa5mebtD1Tg){BpvA>83q}v{c2W9DL?Arp?F(Ps2$+
zdTnf&)jVm-w(I>#^;cKJ?vv*+m_=$9{J0$Sx&lJ2a<sHbFX>gKX+=6(2S7OlsdqCv
zo3L3&@_MrByxaTiDeNT?qS*U#jVHxA!pimVH^roS)vsLa)HIUy6j<8V*r0N*oY20V
z1O^PRy|g|?D=t$$X5kB$bik`_*I60{P024i>fXKAhP-&ab+xO+Z0A@jiX~1=#9(Wu
zA84b)qe!1Zkx&(-B7nIPHqHdv*+ER-e!>IN1zkAlbvNl@2rOfj2$o(`e5E;wq$bAu
zI7zL+&h2;l;x!@zvMhYN{TQ_DOv_*!LGS1UB}Fz4)hWk@97}T;dY9r->6}$0H;#i?
zhHtLHR&KBAUv0r?@n3`&o|tW<+Dk=mtZG?ZH#RE>m=Y*k0{r~`Jw6YERb{VOzs=i&
zKD|*VRF?}5{DCK-$!3s?9?m{-e*6k75O_{Ti)KwH*q*~6HHmn=Z5w~u@PXK5B)0z(
zD}OtB>mnO__r~7Nb4PGoaaC0_r#FEj9D&_Tp%e{dOEbMMCe^D!n##<+$dQje<S-y6
zWwC{><J^~kWx+32Rk;hTBX-mimPP%29dD(wc_@`Z?!rO7N275(rBg&_o5Q3__Lsz$
zxni{zkFJnkXsQy=8f~}re8J%8e|Wi<&G7lyJVcbHCn+B~I1p+FU_lJrNFE}E3Ro&Z
zZ%%DfnFJN}xO##)L;4f@`teToF!u++*B#<>H%-Zl-^+9@qDpZ>@yZ3<0URlZ0~Yox
z$I>@2Bc_z;@g@~G|JvH70o9zrfl4d(9wcxaomcxUEo<TNaFEuE$-J$b`Ox&VmsycA
z(G@F$os~`r`g}c=<4jZ^UCn%CvtHg7twqYsT=s4YNb_I*SlF}$DXO2->Qo@dY{kK^
zx;kBJo1R9Ll_(P>(>1${@=T`h%_tJ+;vv<Oro7DW<GFbS!4k|Z@F(PMm{iZi_bBf!
z)S@r;<e=D-C;Kb%rsx~jwB!e6!fLFd;}<ETpT*~@$!7n%`LUk=?HMc48X<sXnu`88
zsiZC{wx;~N*YNSNdjdk{>&)*Gbt}8_+cTZsbp{jT#Fz9!e|Sak_b-L(+bZK8tF{I0
zvzz2eo>?q<e0E^BRgz4^V%7S^8VzGr89XfC>eJCaHvnw{(18qH%{y++l9nhi^|DMU
zeCsYx^GFvy*p?%+qPAU6HXp>*Sp1<?ox?Vc7Ugp_8SL;fS!-;tGY?KsIw}8!bZRuv
zN!=isD#5K|=vvU~UafuyPqZz@r5@9X3Z&N#Q{3+8UGTNnawe@d-k-H&mJqT!boO3*
zcQc)FlbT{Ndj=IR-#S>{akT6U<-icmT-e>8wefh9Gb~BwvV6t^3gIe9^qk8tFwvIM
zQf#&MM~aG1_gR{6g_^IsP(Wt0Vx*CJ3c&iVe|F7J<%)n}R(!kC2f_jc^355SL*{W3
zRlM0pBiESQ8@($wfM>$D4);fBRNHEkqNHY=QP$RHxNi>v_R3W(qT~}B+>HJ8+%`EE
zy>?eUyF<)OK}mrcXaBM=F*z5$Di>Y>7!2qS2RA$Kf~Rp8-FA6u$E-~bmH|1;>S0V#
zBw`6h^a!MoW`38=_=o-F(el?<{)K<1&nT=rKDyZj)(&H1IWwd$ejj$y(Ghl8I?Rrp
z)0j7gX89wHRCOvd4`|R!33+<|`L<T`b5hHai=VTe84CqhkB>LVsLOsL2<7IpC3~wh
zdHZxe^dKL}3x9uqg{DtCOl+0~Q_akwrmP_dej!bOVhkGyJ-Fbor;;}qT3QkDu1FKU
zG<BoAh#2K8?G_5Y)yN$@`uN#H*k$!XNVnOwZ;;sEz4%FPz!R`~^oS8E#>3BB!(3rH
zuSCexvJ+*#S$rW2HFa3Y<vWcAwaIc!3*0-**PM5kchm6jbCn^u36dp+j5xSr5&dJV
zXkvM5H2`vFO*oy*#oI9t<o7^Fs{Aq+lcbabZ?596d2b~j6Xf=~_D<u1B$ABo93U(h
z@AkHoVAs!D&@W#wt|x#QB$qKZdAKF#+j+qZdf6Qh2vXp1>hQ4V&mM4_GYM&FEFKek
z>G%f9okf`R>ClDSX7Y4N9}GX3|0}M0l>RHB6N@Bc^@qnM682L1eqFHDD6Rwzp;7Qb
z@RJlS^(uIa9Cy;!R5_Kw+}%ENpBmRb<E)nna5tfQYHJTbBAujqE1<H`oeB!+QpCt(
z`9A~gefnqhB?co22_wHLNdDQaaUKoI7Ip^!dR$JXrpP`W*AOIknX++A-Fo3;)EV!Y
z;Gu~(Z#l&4G^ZT+m?o3OmHeV&D$7Tz%LPPxCp}=%hQzMgZT60OZJ+%4f~A0}s4$22
zVNY@t$!u0XI}&PL5oosI;7&66zS`7rUQq8+pQdL{`q?b!1tf3}bM7%YopChaO}ORs
zmVM$B0NH-$<ilKqqA&(iX%EymG_2KtW?qFp2n%IXo#MY|@|$ndxAQG8X+}3Hz}(h9
zt(MQ1arl+KE=r@ey1eS%w@iXhvrBB<FslCpb>{!o7>PwhTY7@nfy#(apDmM!Ttxb3
zJ?>Fav8CW2UMQ98>BVC_#Or$iU$t!^)}1g!-)X<JF0#gWAX{a`sw&OF8{1rL*5Q+F
z6~YlixjM=%g3H#dVwAN&=pgJh2jHOfQ8jH^2@eNX8^9pFW$79mn2^z5$0?QDksXJE
zy-HP4UiZk60KKCLIJnfxuu57TmElyt>ZuWt#+@fs)|s|0snHaZ4a&5j!l8*-6QI0g
z>?Y~W;T7Z+Z5soU=xeZi4ryTd()zmsxSl^Kk@tZcPzNVbMfp~m#|*f+>lyG%Lvd{_
z8heeK56g@;3@x|Pe~tzukubBq){+dYsqHJQv~p{@?f4RO&uY=A6k<?0`(fTp)xMr5
z^R}Za>#w;mDm9S#S7eroZed3+>p@am6Y#<s-f?BL9K-i~WBe9&2uRnDYx!6ALsvOK
zx;bM!brX^9J`T(lA4NhNZQ*o~zh1si8t7w`WT^kg1%|nQ1$YV@#>;EAYWI^bpPXQn
z!Bp`%F>=!y{<eD6>o9ZL@}Cn<9~(Z!kGAjFRFnFPM^SAjaMpXZ9H{#o&&;=$T%$z$
zell#EE1&KWj6iX)&6_>27AZ(aV3w&mDo{dyC)QQ%$t(7a^-wW!W<HY%BJy<+X~4u@
z_Yu}5^!K+Sz+|Ei;1PSBR&vq$Q3m$pPx_mrlGvdg*BUP!Zfiomc(V_Lgfk?X4bE~j
z@*`+CSiUNpQ}0FacNl8i@Hxp@xzcj?R;0*tb2%(cqzNW)2qOL#MJ3XI)UjAf)4XzP
z&>VX6&9uV%2EyAft0zb_%r!0efx2qRJp=eUCpizd)@rQ*9KRk3wUG=Enji`S6cj59
ztfeU>#-Sm2_+aic6m^O_v9f3@W}K76Ij$5DP?5&-#{4&5Cm=~A9xalxGFTEinnfjb
z^Q#9V$VA5=Hzqb$&dCK?S}-ZU(NUmg!D1_u6g8+$36vX5Qh#~<IlNiq)qOL09QCGc
ztY<1nWXV;y*t0FvXP&=xhAz5B_Y?eF!+*cU2)|BpgniHA?0_seP_96s{T>0z8)t@N
zVR>ws$zx=D5*ntM3ah8<UULy|+o-I%F+Lk2LGhPs?h6XL=--#neoas|3OoXzT*e2j
zk!fDPIQ}*e75)E+2C-PS3G43_6>M$2!nO*u0iXG)o&s*M<@qAqQ-D5$?rSTMQDMc#
zuVYw|NNupVIPD_5HIGMtBAD@EZC#M+s4viH&hz{e2aXS`Vg2}8V+uoqvwfVl#cYKe
zNuf1nU|&pmRap82t0RU2jx_ydtx%kCK%w!eTA_2ESwFP)lFK7@^5z*f6UtW5>Wyq8
zHNU|O!4zfaPNd+$J~OH7`<Hx$iyyktJor8b+-unA;ST=mjjnBe`$rJA^PP@wJ^GmL
zG1E2X2;hg?EVO)q#{GRvxYq3QiR5!()KUcl*6vyBwY(MxBn<wuzDC~pwl#;}{{BMg
zXyK_0))%iOrl+eC!>zuyPQCt(WQIlst(~)54Yr%yvxUr}9riNo(cJX2h82<2P(muE
zhkZjqk(@KO@E9dhWnZ6kB)hzVO0tC}>E8M;E|}gsl=Se)o1%>wvOl$b_Ris@*AkOd
znW0mzXwG~}!f44u$oJ>zqJ1pY=uh!h(VfFP>rV=EZNH1G1WdbLixNCLLQJ9WnPVSj
zpZwF|l`#Jk%>C>Rk_Vcg8)zo~v^UCcb1Up5O0e#nPq7MNjRySLb*q;m9KoU6yFY+X
zWL59qt+kwGr^~hCBu8xvG|oGfJ{)@l6>o$uJ=(W-Q23C9Je^&+cfR&iwT<=HQQyaF
zvTrlnOKvDJj?|xl8hpFsy!fGU;@iwFyL!K^v0Y&EMHpTpBZ5AAM}+<-+0&oAMKGz5
zt*eFEgxXqN!N^i#U&|4SgkXN9dapO-qai+?mt%(yf6tRd#iFk4!g|t179i>H3-UrQ
znTvMcs8D|8Q+}sB%Minr;l3te1_ji|W+`vI=U+}{?YR7sZWAhqn-xrm9~Hw!!Esaw
z>6^-EIoUQn7qqUd>Ph0(<PhmTE#VX-f#VRx{gd-J<7=9CkrB>145J`sFy`e}mz;bw
zP}CPzX+;d{#-s$j-F$}`GAT9533_BX<)e|FMk2;+oEKuX=>A3IIUSf{cbaAQ^m`O7
z7St(AhYi>JqNt#X6U-7CHVIny_{#96v<-1KkbTG+&V{=nL64I7e^;f}EDsoGDb(Y=
zZgjP_4#f*sVinZ+8mka3Lj%;5e6JEZvm}k&1(-R1qLl!hp92tJ{oY_nVzZzF$)$oA
z=xSI_ZX|J%?n4^cu?kS_u5?XjL0H~`?aA{R^eo^+%1s_)q1w@>gr>Q~DhObSqW0Eu
zPJ8{~LZ#FZ{yJg1;d;3htYdTfy{hgLl~Gb`89ln#qVtO-a;oq8TQrnT{;6?f`6*{A
zXB~Cr40j0Tz(JMZ@94k*ZX!wV=x*(u%{0dU^iIO$CrKw|Z`L%p6TBaS7Skyo9fM;O
z8eoXFuF4%F#w$-bD1Xo%s8!ETmp9>rX0VNfaMNwE%TcUGWLkWQ5{(z7ITtU(xewk7
z?<Dpw8g>)}gwQr#8_VNIE{$_R<;u0Hl_QEsg&vP^cT)bdu8`@=FJk<qNp#WsTe!X%
zX4fcIbQ#7KaT0+pp}JVAW)<{CF@~q8;(HAzKqikXr18SnPeO+05a)L+B;}{2OXVyy
z(YCnXdWCrJqCDHGd;wq&mhxaOU3N@{V>xM3ky&U$8IS<To;vWQ!z2s+7GS+|1A|p>
z39Tk9tg?OOU$ttmg&1u_XdDm=pQO8r3j6#_TGA*A#W}0+#C!c1HESa%9xBYVdt<k<
z!18LBldJBsCf+&j*P`n@$<-8!Fap{)=l&z8vCIAR@Z^%`4%bZoJDLI3mxv*%1bw7R
zrg0P?R*k8j6gjJi*Y7n7s)l@*&fz$zDFmHE#{tG%Yopw`nQR<7Er(*<L{>r#jsCH$
zf~nm@&X|nj{I>5mor{=M_Ktv-!;+D-zIry)YJEltfG3X3*>wgacL4;!eH%RpMJQGC
zNly7x2Ko05lxMpT5s~{;Od;8or&9TfFa&J^0+`vt$90(P(&S>3$4LbAW#bz|yR~<P
z4lHica$6DX38hRH{G+F12oPIG?H_i@X#yF!Tl(f^7w)V*ZM_sg?tOl2(v!2>e|s(i
zjDXkb)!=M4T!lnY2NlCU>Ngx|a-XXWbG5E2rzb5x;Anruy=65M-sim7*fq&aY~T`M
z<#hci9uCabG`S~Rf8ESg1``ux>aj~GAs@i(sGmuF-zLw)=JxrFG~_qj1QNc5^29Sm
zv7Zc@s_&Xsx?8GiUF~{b@j`Ds$z!UL(&!Jjnh&l7BaRzBId!j{HeZr6SU4I|mEzEB
zI(%8Y3Mp28wXmpJKkqa>W4#Z5Z9|r`+I+=OtUu@2Bp#JLd3e5n$z0x`3b(nboRrCN
z^1e=12=L3Xx;Z4(4fXMRP_{{hNKabQ))Rhmlt*C7ceUN<>UDGTKvfnULYY=}e)1Y-
zcXD(lvdwp=&)SRsV*#$wM=EN7xC2a4Q26V#<FvJ7DY`*q5UuZrAE_ok6T|wbNTXHs
z!5K3GZdCCyVn8wl2uWiz+y%1=z=8ql3ZyxvU;~A`2qdJ60T9_LckTh%5a2q3-bHWw
zs~W>?q%1%5HOpY*$(*$sMw{2tH1g>wM0t^=GSokL_~q+k;&3Ffg;Dq019h9_oZ3QD
zer#`xK_*#uXE0S|wG>&>m5MW5D-NevgF%1L>Vwv*n&jMG5I+}11+E=)+|rb35a4FK
z%pq}nwQs*vnul1v`fNpTYFK-6^~o9r2cjo~HU=oEK-ZL;1v*!h!Y(9w&e0PfZlKGc
zLkxZ<c8(p3s2gDU*LbyD8HWKzBSP=_3d*kfOSw1qsbjN1Al4VdX8CjQNxATq^ZP()
z0Z|DsadxDP{%^iIC)$u9ThAYb%zfI9+`p}~APK%^tf@*IueI9ds1q;9;xjSVk&nMb
z$~G#13>!U^rs;QY;)#4S2IHJ#&>kD&46Qd7>P<eO+)ZMsQZMK}aY`8<=c}@cRMZ63
zyG2sDh)B7>QFGC>q;@)6SsIE@2*ux-VHZFZs|)Y$HOHV|^TZ5EG3gxe`tosaa8p$@
zYqO+s-q@&6kvoPgsRC7)ZGkoP`#8U)HMgdAff{3W3pZN(pJD!#yF#mn`Y*^*x-T{f
zS^*G5Rsc98ozn$N$Gug_y*ICsyXIn=ytJkklbTMvaBIian&Ev+9J5B8@M5yIvT5MA
zlh50>J8<f;(`FlN=C1sraoDuHMiW7LJA4OW!Ln+wwI3;eo`emkcswx5=VzCBGRy9A
zeZ_W=L}jB>H_$n2p`%@-Y{7pgW6I^_CNUypsO34Cn8S8Y1mdfS-V(lKX0bl#-K19x
zjRSn-!-j2*F<pXjMP$&!DCpd?Q<Ma2P<axGm_V$$34h(F5dxT~`7%aM2ePnwp!!Hy
zK#LlN1<N|q^E`ZXGp{79U#bdkKYz#lo2h{e=$Rydwxh0DzG4oEj|Q@9^~8@WxUd@l
zfG8~JNd(MxKvXVH6Rxu8T7Jrcn(s_}vrpPMz%iP2way~Yt-&V8O@LDV!zy5QYxXJx
zSY(xPOl@@fJQ>Eo>6+_Djaj>bPcdOS*nR82-JWGpId>KY0G!4~PcM6??#@jLn`CAM
z(I!2+KXzZ_*Z7)(my>7G;_dWvAR|*nPcJ`!4TK$D)Yb;<7SzX;(F1T*Q>B`@;B?lr
z=4vbzJeAvO-`&NA(YRR1pAIjb-ieY;%(jfPb<wb1_)$`(Zs1hck)X#rn9%Ida7#US
z9Wh^2b-uJhvHA83UV7Skwb$W0bjqjeyB?+c-yI;4inM3;%@+cyyN$&3)bEQ5%QemH
zEOYxa&QDwi)6;5f8XD7K0eA`fbDv_m1I`N<J>u->2V0(J*rnc0mm&Tg@at6rMKa$4
z>}cln&OY$ffZd_tFEYE&iV^lL%`iJMGjZBmSt+n)xo>*&+0AyJNexePmt^69R0t6u
zJz%0FvXsd|fijc|$gXbH-Ksf?uqSjTY94FbjCku^(zGkxo+Ij6VmSmbO2ox|FDzhc
zdtsGn<l9^2u)A26&%zg*&)Ljo+qlDcl=INgA*4uFxdD$iF0Qwx%|0BijgGFWanBAg
zGt6QD)^$A21QNJ<vcNDVsD?_16<?~)7I0=@M{-a;0!qzpdfp(nBY;^f>4}EW@<F%C
zp0M$|RF}+?;)8;y6J+_i<;M9kL3?Y~H*=N617t_S>)M7287#?&lQvR{(V;}*-oud|
znK`nhyaYVcQyrn2M%lt0<-vIp!<YUl9qQ$B;5Rb|tOx#w1ULO5c`n9oNNV0LF;UY|
z6re-JSN{f*QXb+F5TdJ$$czNK^()7rUgffrhtktDz%X__2KGXB<JOfIu=}bAIr*Lf
zpy7r8>_l%ee5<r-UcYdLP{0eC)dhSMY_Kk@4vb=Albq-f6LUHxA*;pLEXG}m02MCb
z4U%T1${nt+J>s^oT6pr_^i-hi+Fw9LnBTE{*tl>;zkZt9taIRt*Y&u)00+mH{5@{|
zO&^6=yF26lbur`01-Td2!C)n|dI5&l)xLm#Q6}1FQb}<YaeUb(H|zM~^b~jBN{<^C
z-A`K=4Y$kK1My<jM9%n=Tww<GVxj1W#AL>i9k;RH5U+y?jKQ?DrM6m`dpeVOT3hVR
z%9+!@_kSmZmqV=Vce;=hSc+8(oi{2VzF2Rov_m7->EqZ_dALKjE_lLW^?R_pmN~KW
zIIT#I0(#)Sc>PJ0O`$Y$y+5BVJNBmyXDwHA&x8|EA1AW?3%>9Gt3~>V2#TJO1MYFH
zfSk2g;qa_2!sZ(WnD>h9GZ6JxE8K@qv^`wRg47G7^0xM~UfX<hw+#s@ebA|&JRC)g
z$HG)zr;b>W>f;Fy*bBJY&+wA3jfEQW^z}QqV(Hx39kDO}Q*Y5AqddGSz{?dw)mShm
z^ZmMYj!rv@j^KzbH?zyXPGH$}D1CG`VNYx7<PO}B7u*(e3*QeW;v^V3p1#=O9F1g8
z*JifT4vj0j6Q$q7`XehsQH*<mGO43Cz2bAuH3PxyKD52Q2gCgC>~<Rau$nkQ`0AX?
zvX2Z9L>!u25*Ybu{}CMrr35g*QIK)(bCSC_S*M1kEp^Rsr;`pHdZ<^Y{IujcTblUo
z+4-4&ZCSJf7Qz2)5$y_%9H>Vgz3YB(9A9XMQ+Ye+0hK#6q)e8Pa@5j^$OA<oct|c@
z(tKuYKoU*R6Y@c_F0$GyXy1qHZ}4ULF~SDJz#Pov`>Lt$)wPxCYoOQMLn{}C=~AIU
zJ~?Kx#VWC>_a9U~=}shI{${a~dA~D1Q=m9CS>LQ+a73M0dV&jsTwJG#o*IguY4&ZA
zm+x*)!{fTmcBHBjaRBVtyTP=N?iiC#fTGxays~+pk6F8LaH;gpQCpg4pt@Y!>+ub`
zo3H6%$jbwt!m8W9P=00D29!czfr|;nt&Uvr?WD_9?f|Ru%iZ7(=7}0^&zZ{zXYQfv
zdRMRq;#_T&<K&^wt~&v}ArRv;J-{qg*6=3Kq>+IaYhX&4oSSK}e-(@kR%A`*chtk+
z&!pJMP=W3R#qx-oEpwXC?wMFISzbE$^T1ZNgPx3?9K^-g7R2jhL4YU)gAgNtHI!B1
zC5-<O(7<0tgbg4!-_B#QVR&LGA6-Qj?!4IZEcrF#mS%54s{tuIoS1#B2`LzL6lhZ(
zu@#7aZ=u8Ux@T@1i#8miTTj)&?P?owXlcnk{gX3@BB;oMM=)Zu2b*J*dfhkx^-JXJ
z;qwJI#EWXYs$bdIhW0Z4vSx0Ax9M-7#2%I<B{c*5!p#afBa*K<Z~9r%n_qvWgYRVM
zO|29<TbEX-b~--%CcWZzA7qDsyI1sd68S+bRRVMI$1Nv6kVh)`<ey(J)^;lMwoj`W
z;65??M=aRQ`bQi&h-GyM1EV?pHg5@-4D+kgM6x1lqbTlt*_j)MFev~}^*oKkK^@#W
ze&KzvfB`027~h#!)G>?T9{ZT1J>KL|vvI1pvnl|i%Eqoo@c?+9d9e5}OYX2Db>YJe
zi;S?c<NL?~%$1^Xei5NUy@WjSjdR<t8*yrC+wc1GExt?xza~V_GYr)4yO8f$^W(Aj
zIT2c&mqDM%iecIJHB|wK<UCvi2@*=Nho&nFElT7utHoZ|k9382JIB`^3tw$;Yll6Z
zEqn_2-mI+*Ee_yx@|cM8lSA4&2x0lNW8l~-oGA|Zb6u99TTP28dAlKRw|>rGgmAJ+
z<|1#yw5<p#qnZg-MsBRkep?V)dJ@Un_84pX`B4+%VLuH{e<<#`-tBrdNSU)yOq;T|
z`D#{<ph=;PlEsw*-MFLw<7eT^UQNjZg5KIOG5&a1@%!3}l0i(Cd74m)?9jdnl+V5O
z4?38-bGFV+R}??U2A*BX(x4;#Y1<D%DMDQJ({)SArKS_EWcgtT>CP?vw)0c>9#n)(
zN*^HtQt1#pT)h2Y9)(@KmpxS}D@1DVQ@X5%MsBP3C0_I3PS`6jc|{WvM>uYrkPF9_
zz*Y!66R2P^mU<kTU?0(t{@VLi(CdJ7F-O-7>ump0)|Lu3Bp%g#(tM4fI^E5m)@tXR
zqAb~;E431B{UKAk6_+oj=Rhpu_68;7>TG~WJ`|6~*%$zp43aCw$x8PJA2BI8MVJ#-
z*AmuU*0*_tT@R6oQWV?-GoB!5Yd=~)?qg>iIMb1)X2M2`X}+v(YTY@1yysmbU5tns
zn7JBZ(ItZt;QNQ0{hq69>=C|B5MEC3-hbeIGpTF%Jr(K&4XO5a+G?@|$hX!ckJr&I
zG(k6Ut@?HcR^#e^*wnq5OqL<HAEw9C&cHITe@&{Jxv()}@7Z*agF~D`L=zRr(ZbZX
zRD9LN@YdpG({0x~ok`kY3a?Fmm?~p-i99^&<W3Sg==={2kDW5hWdkndxQQ{4TwJbe
z&j%GE?9BC1`_3E^oFE|xQ(_h)U`=ax^UKHD$z!Z-9_h3x>*Es=%u=M3@dDSug{{wp
zK7hGG5b>us&kEqehK~(WlZV3NXZIAtG1+u`pC;=G{8CgNWq0VU#TCJiu3{o)`8u;(
zHXiEZ&3|8_ZwQzgeiefF2x)R3K%oW#axDn`<fB35O~!J7WPs7DiQN?x+Y{rNDqy*U
zJ}*xtCJjz7BJ4-UI~&<F>k8Hk4~rk-EVY=n;Dhd8aFo}G1kwNl;DKNLdTy-h$|ZUD
z*63~x`twn$3y4q1CRMl83Nn3?;g=X3u~k*~*K(!kFV!Z&#N3Az<oR@%Dce(xYGOPQ
z;!pI((ZDbPeiT6XAo}!=IM7eUMpw$N)5=zitGmVNrLsn|5RdTvfeH;b!Yc<~NLtI*
z|95*RZW*z?=Zv6Dq|Etu2Xf#SKV^3kmO=e&m4sh6SUQZYLIutl=tqh$K+G<3MhV4g
zIotglbk+s2o4qc3Ry?p2a1uog%2K5!xqk1EfXR`sY)?A6jbA~5!QUk}eaX&vN<kU4
z_sFtPz1Gn-O1)44zXKsvy@`eVY}kNtJmGq>c-i?+R%FuAN8vZbDw|x=8#FjQ*uPL-
zr_Z>0H4Yn@)%M!s<t8P+VrNe!GUU4uISV|*d+eYPDXT?g6=T_zJ8wJ8DMFs1@3OIQ
z{Zgs<UXFgUTca3X+?z>G_D!UAF--@En5<0sbk^+ghLd2KW=c=cgL9o=r+TT<L}U8`
z$3?rCD!*aakRlbyl^2UIet&tQbO-$SnpG&`$!Wyv3?=f<@_e6*o_v#5W$rYZz7yZd
zi2hY`^ZG-&X<cj+(0{;Q8PI~6!kZNfyr-5)pndOe&*A@B`OIYB47^Nm1J#PR#3=lE
zIf#n}2Rl2x2t3h0zmo_+GcDg+yUn;gDHi<5i)FIFH6s{5X|B`MG+3=C+&=Y@SXqEW
zs6R4ob*di=&El5y&=(7LR3><Hm6Ge&6<0-=s4`Xopa|iTNpaNH>I~ugsXUQuJB;?P
z>u8V(3iX5p8@J#jMoE{h)=i{GLiR1iO8Al$=2jC3hPkE+2iP9E8f}~$#utYOIVwu^
zv{#Ko2vO(@Ur9R3qDpn?EpC`$9xG?seA|HvRsIAYBlCM#P)y24PmMW+WD|DUDX8CC
zSk1gl@DP$HP0Wpq;7>vv(hsJSn7HPg_)6v9d0zGZPA<6i60hqR2b6A0Y3A+)SXx(_
zIz#v%udS1zzYWW|3!N|*F$rGwW}eow6kBqFjys&mSSufGxxR2txup=GIGLlh7hR?h
z?04ore<&8OZehs5UHemEDFEQ8`ccZ5Dw!D?w7#$Nw$nc<>7S3_*C`gvQ=*EsNvrne
zN$269C$OJd8dNSojT*!Ex)1NiKhAI6D>xn`lcPglStk#R7i(kxm2LHVfVl{7$?ZN`
zA6XPDKC|&3pU7j`7!PI%J~Ng6JRnVoyfDI-bRdq{(MkbN0ECcCI%3K@MhHnwk4R%h
zUJHra0rS9YZ~G%*)IBCK5k}z+X(eMK#ap(6d#5~;$2=2T^+Hb)-kZKn4k){ldUwkI
z)1kU{MkkkmN1UCIb9LBHazQ?G@0q+Wk4CkD$%Sw0?c%Ww{n|r*4zbkQP1jbzwF4A|
zh2zEg?iVKbLT;`Ncgned;y<w2!yL?KOYC16CS#di@8<YKmwC}!3gl_d^&6Pz3P2{2
z74TQO&^s^~F0Su6K)xQ^{74_eXgE0YgNhdpXHI-Ht$NAWM`o5n_O)!jZS&l4)M+l0
z7j?R*3au^Bl22r$$=kRyeQVT|_ovkaI6EqA8WF6OBY~<POcVqOcGdjMMO&km$H++z
zB3P;x4x00(9n_0;T~3WS30me9yWfc<(7nHDicIcnKy2Q4>o(B^uNY{&DIAuV<fI^Y
zhHNXf<kn6e7mWBiH)lS)TLVmOnOTaoGJp?@@Ji~2TaHB^*HTf6O}BbjVP$ZDD=c=-
zIcKk}BBRssO5SY^nexRxrk5A%-T)(<Ac9<qL`KJYgxAmaW3wp#JmgNO+T={56~w*Q
zFqF6Kyy45d(*m8ImZWTQlF#w~l|*0R$!RpqiP1jv=L!pkiA+$R(O)&U`Lvm1aa~a?
zjWzfp?EO=guQh7Oq!QN_X3g|bp)1U5wk>Lq+dJZtCG%G_j8(F-s8;}m%c@+2+kk^R
z8s+QcVU3+<njM=$ej?PdF?{rJ^F#oYrp@fmqqjklqfn!qt}_ji(Xr_w$Nk1nWTE(^
z11i7r64Mz4mkZyL&<dk#&RSy21eyJ|wSUN99lPvGt_bVqbgcSeRkWakIA%%vP?IV#
zS|Rdcbl%Bp#L;6!hKL{fXCaKMjdev^PtYfGOPXrWqvRg8A}MLkTj>~Se8!(|pNT5}
z%F&p$1hL+PXSckKWTF&)&|YmlWdBgHe?j}p?;{WHYHg3h%27~eUoSMVq2hYL8S*yx
zgoMwh6-MYo-m<suPm|jvQFVGm%T_9k?M79=x7*W+mTLAJV*GT1%^TaD3I}>>-6sKj
z)MxJe@s891uBd^GL+Q%Rog%K%u?f#&ESzw;Y;^UPB>=z<YL*gf#kL^q9LGXZy=8lx
zmhv{fK*^2n9{Q|na1bM<Q##q>B$<e>$1p<$fir<yDhOVzoY}f@?;YVZ?puz-Lm)Tr
z)q>%-&ONq#q$;anOTLO(!Mbp{S7yVOCoX%}kA93lt<PoiLKbcLqZ~h8$v18uu(NYV
zX6@(|3K!P0BHnK}=#*(*E<aJb+fv#$|86N$bTnCLIS=+V&5O7l?sNnPn>txasZ1W@
z6)PBn{6^Py_`o4^x$Zs`pPW;qarx6Hr&;O@Iri8}vnsbwAKbi0$LKR~9(>L<I|C!u
z{<a@s?2+t)JR@9ILxr4Ctod*GK@Ag1p)yN3HKOl&nFHq?{Q_**iB0F@=ZuBpGPD4r
z`H%&&qBHG!n0FDBSGonH6CKH=!qF)*J2lI5%{mAahOh1W(1vZYp&MYX9$zBROMTag
ziKH01F=T@U><dP@h;mz$z73NPGBS<J9Rx{Go?nlxopq9#0wiyh*rDIdzNpXUENqXM
z@|}4}PwtyKx}AxL!!ROMqh+;xj#uq^AVmChdgx80B~8kiqZ<O7nfGjmhC-jj-4{`<
z-rcHcN=OTB>ItG?5fYYbT>f}G!?)vPQ*vd;E0&*V?7<iTHO*FgK^q<clJsgRtRQ<7
zEww1Xj1a)b`+4V|SrvTr$p`%GV=S$z&w5f`)4fowm}x|L;UJ~b5m#WrsVzvT5O5rZ
zoEF~4zqgR9EFC4Q)vuT!lXq&}k$u->P((bx-025GT*J)>`}t3-!5qC46I+0Nvv^-V
zsAEQ@405u<$fklOk+otz5Ma5t!W<h{_`+Ivij5z#o-}H3)tceqiwID1!-?ybN0rv#
z1DZ$yTpyM=h4v7J$)@nKk6ojHbC^pcKXUzK<%KA!A_<XkMQZ1+GyejZi4fPHr2+C<
zgKjrFhN$35qg+TRx)A}r30ixg?{nDXcQf0B(Ms7Ex>#^HLt-jU^qqy;feYtr=L8k=
zWPhXI+Z}I^I&x;wLe6uns3HfZeC#Ag$50^J&b=&LJA-^66-`AWD+X$ON<W!rwW}Al
zt5+%*)%$^~YDPcQ&*YZP8{60WK}~<!aBn)m2fM@KePUTv2S;|CQPS}T7GLjWA9R-3
z_g`4Ij2t^^ji2C<3^($LV6r?GIzCh)A%(io^$FkZRM(WLATEU)<f-8H`^WE<>`wZ5
zaNv*R#b^`c4%Xg>AMVG!yCcD%?bgOF&rPG5A3rT}-sADbLhTU3!R!3c>r<amV!s;^
zzIrxTJ-F{f3Rw#fZsPuRBJ5>Zb4%Txh5+JUSca~NW2I!_f{|6BNZ!_gyZ4{_IjYH}
z!vg0X2MeF{y&Iin^GF3Y(v~~*j0F~G1ny+hQJG)e^HmDKm^+`-fE240I)ZzH4Zi$X
zKQQcZVgKsI6Enc6-`f<y>+UB{WPBv~JmkbaxbpKA?8(NlfPX+4dK?E}8nS+z#Z7iP
z1LVh#RBiaKhA~;xeo@n}s=fWe1SZJv29@CF%U>N_XnkOZ4<jQh6spXvsw_^8HNzrS
zdyIBO?(utBr&iXCo^`N03J8OV9Qs*8PLKSFdY`X)RF^UCkELmuRAoYTv;v$ajka(;
zCpx?W0rM?UF4OFbRu+*7cd*NXat+RVEK%TIY-kBAnwF2ZW45{Po;#P3Ro?K3d%qN%
z%p2cT`IS?`_>x>);Px9F;0~-WtwJ$xXyV9%shUW!eQhTUN4VJrTu6yI>8WoIz0Yi1
z5L$D*XRsy@e?8YVMj!-HTz@)ej_a0_m2u1(+zFApI`!TmUEy8uB&cpzqoz>|-EY1%
zxs@yH>}QtaOD*+uzDDq5c4uUGJimU%j_d3TE^_s?e5++^A4evRogr1L6aBWAVlsoD
z6IJv_<<t2hsmXoTBmT9a#&jhrY7RAO0J2ZY{RLSD>tKf4f<6b~@ZsMuiyvErVr%Xx
zJm+50d0VPB4z|RkVw2#+W~(-wAPx`%^D@q}Zw8)OpSRADM0^ol3I?h&PqJ?P<Z2UX
zY$x#;RJ&dl`;butQyiT0#O%j>A<I_Z>aZtxxMsI5?a;0c@;#h6?(aO6hq-^I0j>PO
zG}SZPk5mbjLEqAd62YZova}^Q>yXzf*pp9&95MRXhd41NkHPo~lxp86P={Ma(n!&B
z+4RA-uLxfpSwdw#7azW)K!W~A{PhTeC$VO917#(}xH0n?(kZtxt3n#s&fY5IX>b0B
zh!mt_A2&?=K4p3w;qXiTPFZ^Tb@-=cw;WgJEOpS%YEoYcfV;->!5agi+J=|sb3Q3q
z0;a_I*%J95_kIZ{W!7$$T|Atg_F4<c2jFGO{FzJZ!@koDs@DgbNP^sMj_AM`Q>@_h
z`MLk6Xtj>S1P3NB=s}{}K14t;xMQIs8YohIb}dcA6pe|xv;)4JsE`Et?H?oa<PZ7{
zC3}uy0t<GV%dH>4>lYA0fB)x!e=a9o<G^P&!GC3xn8u8`9u^`-!p`jY;z1@__`uWo
zQ=RGC2yu!)j`EwMFox7bqV?^~QW2S?gU)D~Sr5dPiCHyd29lt6HiE{;aZ`hBLcMT#
zR?l&rOB*cjxnk^2yFpfg!f82;SgxFH=TuPc&pSIfEI(y(sYZCjQ(ln4ke`day%%3x
z#CAJ;;F%T?@x|A;j9}utyZR<DHi|5#+o(Y;pWMswDvnm*&Wn{$`DXz7d~D@|f=-vC
zb8bxRhoe48cx@I5abuv3K74Vys&&5>+M9!3=VT(pyA~pWT7vH5@M>_bRNjC!V~I8*
z0Ocj=rJ%9U7JT>ST%`E$YleGbpIhRh%Z>n`M;I+&C>o3nzLRwIwJdx)tuZ4?Qo1ev
zsrCrfl|zAHymJg)o=M31@dTWq@h;+UjsCq@%Yz1UkkI|;UI<|L1F<r5YJ`Oz!>Hs#
zjv_yVl`;>Guton^=((-SV2Ziko6f*-uqc!?a!sL3{QAqmJdv&5MakfW0;;^iJV3#q
zz^QyK`gQjh_0{Z)WtV!ZIKUrbG&xj9V(QjE%Uz6)rQ-#h#S)mRdx%m<pZ&u6^yFMq
za_2$q_6>sd?{xxeAOFr__Tqht#jf63t`*wRLMcYTYlYI`&-|aM;5&Oa)GzzxTHwcj
zwl<}*eA35VY8msEIS5Lqanfpxy=#~&7)%$s;Rw;`Zg&(&RgY-F{Nv{3ok9i0I&prm
zksF>Ha&yLnEfZtO=3|sHwb}83SdU6o*6k%;F=DjH`J+3@XQHLu?e-f|ncJx$q~u&E
z4Z4F^w`?Mn>I?O6-j*836GDVO0%%aI75DpTl6UX2;yu%Sv-Ai_ckYd}B=*JHWnE^L
z*?#SZ=@<SvF}*Z0*^JmdXD~(H6O|V(_W{wUa68leG<o>3p5!y>UPRi?Q=dOg#$3ro
zo%2%|7#z@VL~ae&RY6AD+4eG=Vnhz}UWD702Gwgz^+JmE0ei^%O|}BxScAc}JeSnL
zD}yuq-Ax;$ICYtwh)-7fiG0RwR8bYIOg@I(yoq8bbkjZZ4)r93pps|F6>kY{LIst_
ztyGR@RtGqr?Yk?F?&)vYt{*6(ocLf#M7JE<x(n&Tx_9cpH{5bT^1>p;5xI3i&8n}f
z><&xkRQQ^*e>_rw-tTpK^p=@GPfr!i_v9#*GNTJ`Q|pevb^HzUwI})(m0c(1VVK?y
zNriE*v<tYnUsQeMV^%B(KwS7j@fXpl<*}<Ipj1+P35JGs{eRvjMQyUv>Luo|rW&~X
zxXONww)jM&zOm=R!|&MdaWxC`@RYfVX8y=l-I-v9;;6`pPfn6(u=p#HqFAVdap3SY
zRQIfl16?UTk&ol1wrP4cEH-)|#|m(z+N%jiAQFsmr~G7j3zobwJY@DTGO9y<j+Z;w
zz?J=+N(_g(D<XoGQ+IVt&VDt(F19;F$*r8^7x1PS6quXseZYaNy=tUA%Vi7-z|C*3
ztCd?}atJ-lftd>xIkZ2v2Xl>Qe~uBSJAfdA2x@7K&t!Y_FnB&*tbSp6qSMGc1>;rU
z?9YX{ukW^$0af7xOWbaDih3PMh6?|XRAgX+O%?qj-!ghc<Fh<@=UM49Nn?NfG=i0*
zkZx&XEA+$7|3lSR21MC*-991`k^)LfOE)9kAl;})gS1F@2qN9x-6GN=4bsgJ>d-NC
zcMr_Dc;5H>&N=f(f50$vT|3uWd*5lq8j1=eGHgbArrzbfoqepY`L|#5lYM0Sxa?+-
z>4sOifrnBhHOZx%B{R{<<+}Srg(ZbPL5W*Li$P1CTSVi%i(BY~mA@%*@rp#4+v&Ly
z(W~El+xmX?zGKT*Oigq8`Q%NAwNe=O%Pe)pyFYL|Ofz|UwcM}(;fs9gLPKj!or;=9
zee<hpvZ!(fn|eO$x55Hh3rj*<ZU$edQ5D2vDbVq2d$3C*Rjj{Dc;?HSFb#!mSdyku
zzP~;d2ri|gJW{GH8TcO?2^0x`i3@^+k$T0-xUC=}1G$Cw)s}DnrgZ^IhKTS(rlg69
zwr$j)h?{L~vy|2IH5}ccl+|B92#gYHtsq{6xa)UPgNV|}C8ZcvZ0&d+Re{4}zxyL9
zOVzl9z)Z<{qLF?rjG)9Y(-bj<!I+)V!G(7r%)<PFC;oSR`gf?k<KDa;K=O2&eg;o&
zFaPlV@!`1-tOVwY86ZGTdl=AxFfKOFB_&IKYDv$)%hxk5;wB_1lp<2~w?5gN2l579
ze>ZC+UL~PaIa$y+zg~~*TkP6uxVT;5f*beQ-@5xnAHOq!nm0!G9oM~lR`I>c!#rut
z#^wjP!FCcut12Gs$Wcf%pE?{E9SWut@#gJHm!fWJvMOyFby6L=|BNyX@C@h`OqEwi
zYkewcOD(I17>!2!w)Ns&P9+y|oFE7Bi}o{dn<JRGED$-_2B>~X^`Ct3Q8pHv<;@!h
zXZBRUUsCNWdb6{1CW6S0*+2`xCd=zdlMA-S<{960K^gkl|7?<;mv2iy-gKjcG>sI#
z%i71RMl?V)k@G<qPqSpY$l#y`d~UCzj_nbZpRf-<cCzlyuTO>csfC>xGx)LTq{Ksc
ztFF_Gj>N`RKCWdMr<=zPPti~ExiLt3ewXlN8XBHfh!z(f>3^Lzr+(gVZs(SPn`My_
zA>K6j_d`_O)#E>PWU9@?mRf>hcF+RY{@KMV55^%u?3LTRu!aYJRC|l9u@|UthJLB)
zfDamGhA>wyjxC1h8XvDR1;vRtZxq8N!d*QMk~D~x&wPZUII@DJ0a#JL*1aKFr&3Rf
z{H}GNx%k0p2TqVB>keCcp?P$5i-2W!$WtI1oQtr5d90*y=9nR-`j<8|74L2b^?p1I
zF{1QK3$*wgxTtf-ElAg6l<teuQ8IKH(HS};8!%%La2CY=*4}Px&aS#my~Dcsw25QB
zIAG&ifE|4?ir2?II*cn4P35DExUj~gJI@|A$TKo5{z+T|$vlNMe2q@Y)3t=yD#-%K
z8Rm&bqJhXy#y3YAK2IuN+~>??^?$XHa`H>)0_-6<h>)CWC+C&6#e+oHrxnij!QZ9a
zOA7?^l7f2TvsTN;k6{a~J<z*LT5>GC)253>5uXWF^%vA_I-xHQJR{9Bh-95)OahB-
zD1^mvLf)kjy?Ua-v;`5m9j<w_aMgvU1H$Xzi0gg?WbeJDH-#7Er`|uqel0#rD|K3!
z(FUpOm52bNN4N~Ro8AvbbTbZ+qk2ES?cMm=r=o57#2X=-+vTkxcp{fmAlJ^E;hs>j
zJ0CG>Uu~Aa-Zj^Swa2i%AeE=3UD`KYF$5;jmiZ!0A=jE#j8CkHDSi%NY~p||9-77#
zmLFPcB!o*A(72S(h5H>;E;>e2WE7l3Fc?+Sf=3gd0?FKTuiNcHZp0WW_@c@=Y1C;7
z)GjzGu<FS$Z=r0e;w)PnL@X1=k$%p$SHQMc){y<8v8hSK&cVEeP2Eq+F{^rWC3-^=
z9N+VSPyZZwO9DoUxAO1G#w#9<H$T{iegD~3FuPm$M9~o4ckY$7t(%3n*w8sq_tMTl
zw-DwSwm;Jr!mcJ8&(v_@VR=}2(~jV_4d_&lu5NrX+TxR0-Dom#MFjllHN)K(*-3Fd
z2N}g_<OF@U`>g;zS)fY>F2Gl>EfRpik9^1&>0$r*)+XSW&Qj3Lj9dK<+|8g3DQxds
zT)l5$)}%}%tDH^J%$SQ|Y>gH?W_|sf&7^nZsU!8{&~^=v(5w{+*%~7_RSKl?oOjmV
zK!0_nxqjNPteUUA@xW%l_$rV7@dNShohv+_Vb!Xmxw4W}F;P`(Hu3%zCHitn9mI-|
zT3aZL;9eW}-zrOs9$U(5Uibu!L2UdH|6@84*v1X=T1D)7;N`uII0_vhj5U6=lW*J}
zdWq=`y~#|LCJGceHkhK@hERMU$GP)EmMogD^`e#W!_Z01Lt3^=WS7uS!R(Q${x|FC
z3t5jY>Q47hz6Zz?(TZE2Y<J`(ts!T&oPE1w((R_JzDOSxstxYV+Vs1*e6GyqdZqHf
zs37+HBRQ@WZ|m<|dpZ|QZrMkHPpV+&_oEyB=gq?1KDx+7U2Ue1Z}K7-5?1E15kL0H
z&G~?ROAV{bnKxToM-#t_IjCu?dS%`ylzPE_D82e1`zB}g%m-v)kTnszF=F%yYDZbf
zZP!tsE!0Y%jYdYH5aZ2|?+Xj7|9<_;W%K09@*eYf$*CO9<HNsu7briqZGQ8S>EB$H
z-_0dpMrY-~SDkASMaXri<}SL8SUFSVeZ6vavEjMVOjT2@o@a0Xay@PhYk@DHLFOCx
z4NJ8ESn#O&*-T5L>m$y`p`VE(`bbq*pWK8ooWC-WF)i!)lQX~C#a~h7;2D%b#nC(I
zvuj2vdpuV0LW5-4O_byAl7*_>HH+$QwqEdJTVd4i46=B|X~f8%D5^PW>!b0XAX4xz
zO_5kKtQzpNeg_vNT(ftY_-q6%WwEKF&wgR)TuuqlCY?(Tc9aG3y)Qnkyy~V&qPa4Z
zsNZr}%gO)|V7PNF$rsb;K>hE<j|hN=*9tEzF{mplEIs<jX6Ja)^{S%9IbqFa$AxUZ
zYipN9QufJ}Q*x*Le(tw^_dgZxR&Qsi*QiZ*W}x=99-culi%r}ZH59$`RwUg~WG&fH
z;8`f*tMlTG{l7~cL7Wjfm3>hcg{B1idwCee`h9W1>}Z>8WbbWDYm5ew0xgX35XFao
z>3EhOGa%HAVW9d%E2fo51X~Kc$qIjEt%qw8>%p8^YfkBfK!CLdeOSH+8$P-`$Om>%
z@mOczxNZeQe-)Evso2NALRMTMSs~(ArPLVaGL!Cyv{aav8WKzeclK1ib_4QGx3`{u
z?d+Y7qRQCxbu4Te6`h-(qCcT3Xt*N0yuHApL0##SO%>oCoNFxY6G{%bqBR7Slt$uz
z_W`MqW2(;PO}g|a)%5!o7Q$S08fpgH@7j@fOY2u$m^38mEZoj+DDwhSpW&k;VH+Nx
zBE3xTJ2G9kO^9$I8(p4j@UfE@8sSiFmiw8y?_QfE@I0mLU;*xq9Cz1gYm1%~TmAeU
zKk_-b$@c10p5+3lPrvQB(!1Mv_#Fz{JKo;T>R%t#NgG_u1M98!^-fSN7_w<Ue~)Y#
z!#iW}0B-7cskXQTsstI^mAjhRJ{85V9gmh9#*``Ge}>jaDR<g_$u44#D0~$*=3gv<
zbS-|#D871L^x_$=iEe-z-QxmD?b!eUu6+54IlJ2Gs-AK@Vm#wOIVJv6s~b^WNj&k#
z|0s;uBuo(gx@!^%G3i#j>uLs0W4mxO8AI9im5L*r9^CZ1#zy}!$Y{G;c%!ox`b^z*
z?G4=E|2xV&(5{sIHTkGYD;>6RiJ0}fM4v-A_^<8kG_;~a6<pK_m?M@;d5Wr0w)D5v
z#Ww574eUNO^tazp`Naecu?p-hNC$)ko5v2$M2_HUQH&%EzECK##mBY__5%9mBKGYJ
zob9A_e@lnQDzVIk1J5R7)Dzvg3IpGk6GBt?4H&R#h0ZvT$H;4{23PB_B=Vi+QEgXs
zP*@fnq4dO2l<FU=!yY+GIC_@{!%lQAJ<{&)2^?(qx$fQ=>{h`9zuLj`k#G`qlG1UK
z(Wkh)u!+2Kd#jp$)<w@`@&hPU*k|}W3+tQvC`*#Y?0j8h+H$&w6;sqz9!Y=ThooD$
z4!F3w9I=7a<6T4~$-VS+O4M#UVH;3}E8wm5-!xQ9OdcE)GZ?)hMhRQZ+5_r!Cl2v|
zpE2(5R0uQu_8^*0W+>sp`CRY`wTg*v^~_Pk0yl%0z3ag_r&XUh*Xv{eDB<byFWq)b
zG{fvED^)UH)U>d)4YjLragDOu=~%PNUku|h(X*1B>(QC~;gRpHLT*MaWAdAGEt2ti
zF)d=p?ro=;RldAXhDc&`k)|Sx(kz>S!5VOU&=Py2-4QTj2`A+Wq%&%da(()cdF(Og
z%Ace{iz=gu+a$T6M9NY&`?375)oa~`==w@!tobptC`X7v9~T57EjRfnIIn<ID7aLM
zl9R{r{b|@R)yDY-4Att*>_-k;=c~O85RCS8St_hiM#icM7@D5AFZ_n!<n_F04hSZ?
zEygp!?{$7B>)w>LFJDNQ$QbUpF)O`~z*!O$1AUomD`iT3+oyy<#iad*gJMDWR!yPJ
zPcvla@Fihr2D*<N&3{DFYY_F!8{A~Ywq{?95hyUf$dXL~y{Ps=<G{4GYAm}&)yEU{
zFZ)~i;R6Y#g(u9zf&K^k^Vnd;k6m{bTxCdt-vxV!<YRj=CjLd+`q9pFob@+Yh|4p-
z)JxI9mA^f&h66jCjf5j;BBl2x$bz1ff5<4ZvC;S4L92^mXuDaGB^3^QMuk^wZv3t{
zx2&$h=E#QOpZ(pKEKdygb7_*^lYt;fnJPKn$28r!X@92X4m&c*X~o=KrTdgc-fOdw
zx}QX!bEg#IqjXJ7YZE8RnE@O_%WuisT-aeVn4`e$fzo7H>?v)I+tQNUgY>bnLJ8uT
zij9;p)B;{<aKv%)x|fDk?$gZ;C%RxUMGj*zW&6dB*W80Pzj@Rr?dZWyV+P(EB8|<2
zr-q=}_-mVBbFlFKqg(27sV2hE1-0g=&FVj;#(1f_B?yuw>dgy9jq|c72goH;-$VNa
z_@FTVMW!%oTJ^xHR;G_*w2z=tMIudB#KR|ULjJH5KqCHi%dh|hLEYeSU7fJbV|UP=
zWFogoAJa8TPq&TXUAZG;#8-RKPaOHzTla@hK}`^iRhhFq>vvX`D0@QBd%hHWuzyo?
z*{efK=OBc;=aq7Bmq6uo63}3C+O?{vGr00dRYY8=A~O$?&M2NpXCUAA;IB`(k6?h^
zX#hcQhl|GoKWU1@zRSw(c)MT7ef7dGuK#P6t}1@;#Q=`EpqoiBTs~TvV_(*0h9Rsl
zXvgEyPNHn4_~&$P)3`CH(dUz$jg~3|;x{_Aq1c1^co~WDy>BCsr^q|PidOFokh<nx
z8XHeD05pTwNT_4;6yMTNOjRg{K20T_y?7iF#T4l<Bbuoi)5BW!eMGzAlVcpH4MeJj
zjsm{V&lsELb(RuG`{Psixm~NHpf)-MD|3%jV`;gN89b}}zDr3#VElqzvA~ldI)=;9
zCsAK;XtlJu;lzPYfrWUnAtO0#_T<o;vTlUoPZS#H>#q)@hF-t@_OWtb{N`lu!1vd+
zRFFMlUHiUSoILONh<Ny82W;P|_Zx&FR|)Dl*~NXlP@lM)iJu%h0x+J(_hVpnBMs<m
zu9iPiC{MTs7B720s91sjc<%K)Wu(XULxu_nyw55sG#5YCc-ff3sN>BuDE#b#(|8j=
zoTifhsEXmA^^-YrHC06LS{{l680;{k#nvwsO;6DO$XX2MG_sxrB=&_91v|aN!w9vA
zBFal-bK~a@^2cA2qcJ3^+TyE%Jk;7GDj%*mVSY@L>S^)CZph?3Z6HJy{XL0LvaKUx
z+WIk_VDE-3X&OfYt0fcmhCICr!4_)q)0leL*0{A0I6FHdU5ih7ojp_rc^cMmm$^@S
z0p&?#$SdT{?H#v(^3O!i;|D#QOaFfm-FCePjO<$Yp(A+DQjs2{u%iRa7VD<o!`ESX
zVYCU1eI(gzaU6vt=}bMOp9WAZ#3O!HVFM)NF|B@I0nBxa@A<Z#N>e$d9_yQJa8OBT
zto;0NwqKK`h0f?m$#wu9&3~=+vI*F$yUy<DcHtPnS`>m#Ye$3Ru@YdMZ?cWoPD7~R
zBE8XLpJi#q!=cpbYHbZQ4#PjfIS+zCxgZ+!Nh<G42;cowV9DsNVF&S9MR?AFqB)MB
zX^-;H85wLbV`Dueg3VATDnn|njtWQ1((2pr)Gj^<36aCtaRVhx=NCEV8MoMk&*y(*
z-b}v}PRj(vO8G?L>~2l#TTAacS?A`F<0#i~I?rOYDASVf^XOi`<|_Ku>g}rPbelO-
zzmk)II{?`(augdBLtmD+c+#ZOmj?*mc6KY1yi>4=l_YEcRDSGeQL2#WXxN5@z!8Ei
zBSNnQ84%;xOnFB+ZKc_}20fwTG_{0}woypE&&Eel321bl6tGPJ0kr?_yl)MuAZr=S
z6txEOdgLf>!azwso;hg2r%Hi`SXAK+2MYF&VqH&5Prnb&8z5Ne3nmrkQ?@PW_~UM0
z?ei(CZkAkTc|lTm5y$F}(0xSi<5cGTWC8zm(Uo;I@8xs4?#lP9{v4ZuLGu}Si<8Q%
z_W;D)omOyK^T;v7Vpg8*R(%0y>$z*B2!4`B1@{*7C)OlmKP^$;bUYtoMAxYSJ)vsr
z(2P$IP?EV8ND>9UQ;5*wq%0885UCnASAmhFaX2oQS@y3|l^?0p&b)WF&Zuv{dGM$1
zx*|r&f&ieDh+`w9P}uK|6l=y>K2zte)sO?E6HBR{K;Do=r9THMwY(J?O2_*Wsop9D
zQp{tE^m(@}Rnx+c%p(9;n%rp!_?!<w^y1OYU3~Br;((NQjqNHATbl4yymiJ$W@(|E
zPF0;LYj20v->x|Lmxkd8^~|13R&znajP=VP>t`I5Rn_Xt1@#px%^lg(U=Dg&$gv<9
zR6*-K_Sw=(6ow23zW>{k{JTXeu_ShKUt`t^v>D`cm&S3Rg}6W%PQGNDHQW9z0K(pA
zir<xIF*F(v<?{`u+umGk^M4RDj(gCHr?o=P`unfb(j)0K*w^a$_gB|KJ12U-`7;14
zJ_)Jm!8QWQ-u25`-r>woKO};tId6QH$v09(xWn<kxD}A|Urw#9s}Z0-&AB>OV2F;&
zC6z0H?BOcZle&M}I~!8bwzHc%!BBx!@$&InGI;FUSbCnH@eXI@khx&{C7Kq@y1Z+x
z8>q`!w78lf%PQ^yqSmd+m4G!-+=>;)Gs}9)OJUY0=rM+OJ(hxJ6BJOt+cZhcg)U%z
z501_`40X(xk9kf~QcCUlF0h&Q8*ax5f{RY}7Oz=mX!!I6d`;5F@H|)C7t!E6(ARte
z;N2|^MF;LdRB^uHw3O(xb{UVr;b~tuNFW>S=hy(yKlbpyw~1Msm->CP!tV%VUC42%
zZcl~Me74n5!UN7A&&7OCuBCYuCZ_=r-sJ<tv4cmJC8XJGe(TgmOChI1qRAB%HPsD0
zH{uP$gCjVZ02)7&H@8)7cZodqIN~keuxqN|<`M1gKgEZ(`L4%hH;Wl9gYwRKZ7%~4
zlW7JZS(j_=SFV75wWK&IsCLED;{DnX)!`joM2bQ4Zp%*NM-9<;2+!@|1Y8;DB4AL5
zoe2UZ7;FsUpT?z7Y#VKqYJ%uyB5w0a4>P3$A)&{7D#oKtHH(Zq@znRSfOXEpFZ*g}
z=*P}{YYAPf<J-H5KQBRgx&JidN>g}q#3%pK4kBd#Dj7W=kAU{|y7SqYV!*na<)O1m
z#KW+~%MoqCizF@m%WVJ*6AgU7Ewxt%Hg`RY3f!jUvit-wv3N;VY_3khZk&p4G~s;`
z@aVoi$)DWZy=t&*cMDE{LXRfup{9PlJcDqn>`G)2=j5E7NvaTNs-IZC_mKjkh1s*q
zs~r9Ot4_9!Hm7ag@{8P8aiBE8nrmv1F>Q8LlX%My84et%yxX&PgkR~5`mKSF5|tIs
z%O)OW)@!j21}JN#FDsyxh;n-nqgO*}LU`)e3&sFh%QsMo*t0+Ggyop*BOn8jx1~dT
zeKAq$6eFNGJ}zm$)w%~vCaeX#NBi7vCJ6kgG!4q)Sk2`v@JgzG0UJ`-(7OMgfY^u}
z#c^J)n>35Ct_gy?o#?LGH#70ob?nL`szhFC-$&g0oYIbHN1*?N?RZ-d2tQA`@H;%B
zL%*f!fhWBIJcvZu-|3egK$H!<F~xUF(0AqFmY^%)#qMjk#9)l8G+mmC)9y5BF;v+B
zM6gX)(I)l~(C|DwoT%rF9ei#$aIvBC$EJF`Y$cHLxZ>f*VUFYSILq;%XbuSW(czBz
z&(!50`%F`S{JRapSFxNUsmRx-uB>@_Aj!5SCEq*d@^ga5Q18RV>6YVhm*4{Ot`Bh}
zjvQama{mV?5)WHHw_jfPZSj^PslVEU-RoSbwx8<)%!~Q=oZY0g5P)$|Z_zND^5U2a
z(}ekZN>ifmZ=`o!R?KzGp7D@cX6^@d+>cmI+;x>X<`=?D!Z;@Bv+RHEY~kMC5MO*Q
z&-anj&IyGlrBI)TR;g%>n!#Z!1)!5@IN#p`12zEha@9|^|DM2J9HTD*h?~|48QJ*j
zw-IA84_TY?Kr_ng=@bc~z3D!J2wZwjlVtDG)YyS2UpU>>WrGLGh?SUNo3dC>De?L}
ztyH^F42l#nS1!k~!j7?2LEesG-h|=otkvtAlZN?u;jHr}4$zxiTM$n2;j!mhl@JgG
zJ7;>I5dq?&YtnpuR3(0RYO}Y%QdhKpl*dJyQE!lokN?XUMAk9{^Gm3#`Nc;#7siU_
zk_8|$O?7+yspvp-0aYqjs2jWcU)QMdG@9O+9%uRVWJlu@l*fP?_Rm(7V3912Wx($2
zxRKWv%a#=n<TMeh%=cX(G1xtIjz(tuW<R#Lj*GULACupR9~R>c!~fEVr4^~1lqMuf
z$qyIIwU87xRkVO}9)Tc`*YwuX;~Rw~-vKw$xPEKwE5z}6j2VMRew6(0e~YZ?|16&H
zd~7RfoZW6Vvks`SOJQV}JvT%{=ttP_0WO4+o>T$AOMqJd{eQE2{8LAU^^--9;0@p9
zU4OpE9_vGl{mB!ECHDmimwH4YQ=-phSImQfdf%P8hk6(Ou~m%?pP(^;_yDKp^gW^Q
zTcbj-(D6z;zWqxhz{2krT*T{c7v6p%j`-uTKlV_F7-B%DrF_!KKN?3h2ylW$1lF9L
z>jh(f1I5jH&#TBlN$VdD)GG}c_$Ue#o5(Wce2(|h0U*&^Bmg_6?R)mB;%=8g{0{G6
z|9Xlk@?kWPg@Ld&@$P}N@Kj9hpEDsn);iG*RR|%2(RI;=!0qvoT9(2Y6U3lv;-zY<
zfcxgowMY#lATjP2k&vu7`IB5TbMbkUM=j?&oJTX2?Jl1S=CbUpKx05wxdF27VSyhK
zH)(Btk+X@tWO1`343H8@;%jb{sIKhy`h;`Ie?@{~=%9W)Yd=)<i>@FDdkt4d!3+^J
z$~}1WeNMlm@y|?cBqT{ilWatbV)VI(Rw`&HLU*)CMuF(Heo-x6v!+hh)VoNwek)d9
zmqf0Co;B{r<+|Sy*@mI0f@e#pb(-3I^$`<9<vujr-w0_sQ@lLoTw_&j=7d$IC@(~#
z5Vo}^Xlb<c=sQ$9RpiLZz(ahbfs&C1HNC=dpS2{kGc@O}<RUbG9;z4G%w^B^5d=Cs
zk(<G-1{b|%_r{RRDW<4r{i|9r<~h%koZ;4gFb(F$EE$Bs*1p~wUK_FNo4W)dxqpHg
z6kARsh%XQ2v?<9>qdP+ZGEcy~Gk``!wG`p@?}<?EZ!SDw4$t3}9K<*bRmz3H>uWI%
zZ;+h-tY95=yyl1OCiZ|@${F5B$`jP*T<bF?C2nR@BwMnz>)B;q!Zx__3NQm<5BKj<
zho=JUDzl1Deto9x_KyQCZT(s<`E?u)6Irn;OUCL|rFhryG$v1w+z#puWCA;j5IW+3
z=!B$o79_pe*9N7Saw?JB3E;53@576kcdM#<is_a$1Ek|L%@II=*h-9tQ@md{UA%tt
zkq0hQPLld48bW7ZmU)DXp_b}vzV!4^1VAUXw5BYI^yV&+7~>Dd`Kr}%z?DW{RE{*2
z67K$?5exsSou0^uTj2?nyc97~f<wul98PC^S746oK9EMi8GG{H?+ww>#!Qx@$TY_y
zV61LjAqSs<?NG|{9eMi&jy<-T!B6*mM*0$Cjw;u>0HZa~Lgb-{0Y7C<@9!-~RWbe{
z0C)@?nr$iIZD^f{=B$zLK+4KRsZu~77Ud7h63f(NHGl!~H~Ih#MCoR+QR|C_Pu6KG
zP*tj#cVcCPP^c4Pnl$^<?eNAnngjpa33@&G6Rh^57Z#(cl-o@%()Wy>%p`>G84LJj
z_lKaqnV6cnY4Fuu3s3Xq|BK0&{L>2NW?#H2M7gJH3B_JjQv%FRd{tk{6U{HPt{0ho
zs)9n{7HEuzm&?5`AS&dEB5EbUsj4`l%j0`Sw50srq~c<O=ek)*J2uUf#c_#%)b)CP
zafEwJBL;=V%L@f+JeTIAyZjD2jx9bBEyS*h#AGwY)#5yGrg+|BOsSRAITrI)0xX9y
z=fB6^2IFXouqLEsXFsFqJ}bnN59C9gcr}O?D=~=1qyNZdOtJrKP~^|B&NqSm)MmJ(
z6|@f&0`ZymTh@AZB+VqOsHI~$@W04Ee9%v+*~_0LMUSsbnYTuTRGkhveiui`IUG0o
zBIaZ9obUZ|3C9b&UX;{i$@PE8s&{3r9Cci28{N5tu%(2ea6wzepf<BPjNg}&)uGCW
zTSRxEk-%O^n)RGPZ`hd1;e31Ejf~)_-0|vQnkW_dE5|K_p^kzYD-Eg?@w=a|9NE-b
zCkjXQAM|jA0;1@6X(cQ*8PJ{*7;ZKt<Uvo8l31kW*lv_OtE$c70`21KC#*jI#bZh)
zlq(~;G;u3N?@!`c9nt|3p##dx<fStNI^QGj`0R6=u*7)vpRp4!;tgElBr&j<rN4ar
zvI9-{F`94VDS`j$Iqg=iH7P1tJO;BtA@=wWNP5+Ho%iBR!B;tY;mZyo4F4Vhlh^1d
z*tXyYzI^p(V54{ZM}v?rU7mIfvw+X{og^$cmWMWy?DlAZRF1w`o;G&em?FJjEa?q!
zd>=89R`+c1?|%Q+h{&Iqx9$%fjtF4ZJmQg3BZ||AVrl@g2lEgneHoY{^+&VUG>?<x
zmT5I}r1J@{h~sL|J*;MkLW!v1pNqcJMy`A&MaL_!jTH?Pdsw4FWcPV@k;KN_<s|J6
zeWbt=aN2-|(%Fr?EettM>zChWJ$%og>{K+IH~$-h=6db7w<QazuYB!{*u;aL73k<;
zCqL9gtjB*{jvJx_A7<@SFyE8L62Qag7&8l-0P2H~S8?524RY54SKkQ~B0zEdaaeoG
zaQ4>GpLlGi>2{(mz`TTzp6ZyA1dXO%OutYdol3bZ*RDH;fd<vmS?dC^yI;zc-3u!h
zd28(PEzrZeKGwY@$_^&%bU>_ztdoJG+XQMn71!_Ju^6u-&~)4KgjqF<%VInqN<}SQ
z2~xUTevG*yfD(a`!!^ecFUn?$rbX4rnM)$8f^fj$)R!T&M&<Ku2&M`w+=F4{lZhft
zA>~t4P}*X#VCzV_D$INq!-h!n;eTiht7PzPp9GSp_OeO6LtTEXu}X^xceLuFA1-12
zRRI<e3{85yQ3uOT<YmhO@1DAxyb4T~4kgM%it)^#&=$IccH+3Kppr?;TvMcTM-)R(
zQ*sL))!yc);9pWv|9IlEqa%eR;EAk7fiLFJo%&H)GK3RJvC_yq%TuH6dWxYPI#l#%
z2}N$FOZ0OZ7fA-W1-L4@$+Z$5n<YEY^#1U|YmJ-0c`j_5XC1=Z7mNQzhUI9Cyo4(f
z$eos-4AJ`wH1O~kSRgJjy0nU<XSL-<fR_;)3g3<yA4=kPI~Rz44*+0uE7Up|jywNb
zfmjo7Bo-I(PsvVi(E$2Kk8jGhwT+g!0~aV_*IWPTl}Y+W)%^Ac`Ng61@v~Vt*m=AO
zWWL*9!UrN%crxgHFFXzfsf!BT0|$@A)nEkv|Il`ReTV^xlbKWsoan%|tcqmDwj~kQ
ze}(Z-WoQ{q2?GLQ52{G1`oWeg7RC^N!EOXQ!7%CRP>f?R8J%z~yS#-~#km}I;SkV9
z{h|&Rk{6XSF0i@sMKjY+qB9RApX(e8H`}!zI}_VQhcwd<YfY_V3N75olg4wYiLZ--
z;VGw(`=>!UnaNK}%c=xctq_=-_(#Sz^nb;viHa1$U>l3aU?)U>P<J`2^TZrqm+vl3
zo~|eapFt|)pQ{Hl>~Oqelsxm;i3ig!vj3TtwE{PMkfN`I?}hLnt@ak{NGKo|TB}BB
z)I85i6I6T1yh45#GE&I^8FRtGJu=jsd;~Y)SLNYYo-6YoPI%9N4N%{j9>~Dyq~FI~
z?c!Jq7mLj!RM;aRCS<L4w{D4~ZzIPK9^c?&RRzO`mMV)knPIdFn{pw?Zt3jipcEg&
ziDJU0dZ)oc2UN)&+vNcBYnNciVF;(+@*z;M!q_`GYZ9@A*Zjr^qu)jfOA(y$>e7)`
zPs}rz)2Axnh%b+e37M9#`Ee3_0pMRuuj|^08+)8%HMb_3yc8r(mUzo|+7X2YA~h{J
zSVeVeQ#*-({<g&~53N{x0>86~WFWv$k%RGA(MB=w9LdRV5y;whetkva8XJh=VkYju
zbad09szC28Gx36!BPV%vyzXNQ_Oz@bo=PFtnPZ_(MCd&E7ZBb=aQ~ZuWN=le=p6h$
z<1<56=rz4QD{Qv;C)(y>?Q+tw;VLh@j7cApT#Xwi^KZsYrFQzfiB4(jh7#@GB!`#n
zLp|#e%Qg$|K5@olZ}j;fuRtW*A7aKiAb<YQGlV~J3@hwQYYcB5=5XNA81-O6>>z{S
zRVTMoPwU3TjmVSqT&{T2>s{3KF1s1L_n$C!UEq1o1BwzGqTN^5WrXF^E8>(HDGe<+
z%-gZHJ2Hd>Wj902u&ig!IPB~%qM_Q0tvw?VSUzVkqjk_JA|{NGWCK9l^maZcrw{}1
zkSj8jS-;F@Z6|QNUbni5U(z;C=$bIR93JXPQ1fbtVKd19!aKZMF-a%0wy)PB21;;=
z>|loD%VmbVk0#r6@}&5(FA)w&TpyM^sAvMi7zn7{nqCG3hcUQ`G497Od_-j^U%(5?
zccY+Be4we6Ytwjl&GCe^52I5>1j$z+hRH*LXxl<y;+t5#>iimpzkO~12CSr8>6n2t
zV3Y@1Wd0+For+;gqEdK`qeV}ER~Rtn^f|~vEM!dXz{~g9h!17nQ_0lL^+$nk|B>KT
zrCwu_qR(6Wwl*3f6*d+u*<B<r#hRZ+e7#5#aaR*#D5uc%8^AkpgY!mSClCTDz$-Kz
z#j=$+lvH=oxVYs~{j)79@=xIwnH!70FY3eaWLqAdH$pY@C3xw@Hh{v4w<hm`Q0k%O
zR@hiwcfnq`qgclw^es9tpI9=BeXJkq@Waiv+bld$P;GUI>|tg7zA!U)R(<3x-@T^<
zR0YrV`%Hlt6DT=(Eg9u4c72yNPA+txo1;id@vm5jV<a~}ZOR);HIVs-=7~)!nZoTB
zHsZ0$?m?;$S+&g4i3|G^5-(B}Fk_&Ds*8BVBNQyAEOf+DEC$lH=HJ@xBvx6ZlC3`j
z0m+O*`)?fr8P_j|3l}8PtOYiYKAy0phw{Q!%o%PTIL64I14D<H<b}OPIu{4$C5_2^
z`FN~HA1UZk9*U0%=NzMxI87Pv`rY@>UiKMKt%@-J#}o3l%*T|vsj{g@@#oTP<QL9r
zQ%zcZpeI4eeN~2}h<3YHhmFPcv}Q_AcZs7rybCGLK2t$Bww9$wld@3#1%;g&Rvsom
z)o*FmzM0@J3x)9Fk#`rtDpr=gy`d&WJ7fU689NfgOt$6b;XM^>z?{p;!u=Lg_pmfn
zY2_j-kE}=Xl_P3xmU#0gG(}vSJ*iysF8~a@s?071VuIGzMt5V`PN0c-R#|a;lmQbw
zgHu=<3PxwCs#9{lPen^-fMXZk{Ve@wWtl)iv%V_O{{?mn)2|pQi%B{wDQv}T=k-a?
z5yHd6-EO+|6DRg3Qr**`GTk}cb&~6O=8>kPrn^22kSIsDn@o}o?T|o|sBFKpY}cuE
zYwT9}K_PLEXmjNU2|mZX-(}wO_(BDY69YZr6)#kGg>XM7x-L)d;{uxR;lJA+C?xTk
zB*iz?mer<9uF(OA1;9$P^Q{~h#xE`$+2TPqk-~vjC0kWq&V;b(*21G&(AS;KX54o;
zVxv{qfZ(IkVX$VvR$K|{o5);c0?O97G@i5&3gN*Gz2aE-EV9Q2)$Z5&1RtOV@J1lX
z8gr;C*WM>=h6ZcpNQ79>G6m3muKkX1R?Z|@>vpbnOeiiv);O+`N`Vn?<@u$$V;x%N
zf%E}iVVr@owc2;-O`kmV#r$9d4@5SVO3<_BnzIgtfa%#0A6#uMtc~GaU-`BpH0{9@
z4~4;Y_;;qkCnro)+qh28)u>c32o!co5B6K6`60*B(;*8D4bgI7Lh|4mePNXrn+}CD
zw|c(U`poT9CjJp3tWk5ldKh-`6|%RPY)XZuG6{FG+&OXNpeSaF#JHJ63zQ5!xDJ$*
zA(BP)4F!)Ck|%gIo~x{<c<ndT?8_i2MgOACw}7yu^+xbSU^7@1$k|p)xm8=az&QGt
zwF}jZprI^5$vhAk17;m`QQ)0O0wF(j0Wm3*LZ74-&t6#lk&xHqTV&5ezJAnK-P0|!
zqZ=<FqIaan)n=Cp%$NbOpo-Ve`GtiM5c(@7BREJBBA{kQ#2;(2anK>yndKaGdC*g4
z1Bk*9A>@JNO^bmNWhPA<5}G9pC8m7>t!{wU?b}n_cvsvH1UQ}Uf4LXQe0rj*?_{H!
z6I1WRYr^B~7LOSFBT5DP{<Gnz0|nq$Op&-hn8P<bevmzXYj3N*NGCmB<-!vLskLN`
zF_X~XkG2y$HyMMBixdC$(ZpM676TyszXVFxdgn8sRI!`PtDf)NyK2aywBy7rY`Fbp
zx*2qN`#JpJ8dT1kA(w{u=nSn(c{oXw=p$nuYr;^c?I4}Iaq-I%U^RI)`tuhjMTsDa
z-Pc)SUMFC!OB|~u;30bfF+0HOw+;}(V3LgI8W-0gyC0k%@gHAmZb6DIzzRPn=deUO
z-VCuh4k-8{ZmmNAg04FgD)$Njpj^p(!Tj#TP6MhTK5{PvNb234@j5$@A(EksCpR7a
zmlR?9+vj&+fat#h80Y^zuk>Gvx_AfQuM_XBe+y_`MAF`;+ZEjW@+5f3Sva{{<6xcy
zVD-7H(uYGtx@~Q}APRd#*V{ON33^au0!$WrNWw~v(^+~F0xZ-y;mt9Z6yZC}hkG<Q
zpW2w*cnSdR2mA-jrvm%<&iQe|RtWIBP3-7U90y(8He!4a$;>(u*+5@;l3*E=IZx5i
z?j}|`)<`&ZZ<ccJ9W>`h*2M!>YXE>9mHFLd0N!wIPaN_2PX;-7znGsAq?Rr~^jpTy
z@1QH1Tv>U4oMOBkQ*&IVwOz_Nq>LtdH}*|=yF*o31>1F33%%%}cOqG&bP9rTqOofS
z6zxFo2`RIEYi9=lLF<q8U+wt-ENC~>vDfRo-DF^oPl6p#l~Yb~&g->u0v{E8f)u7e
zu!)6a=f9&p>}gI0k)0_<_Fq^lTT|+@HEB);-gQ%60@Yxz-ykVqq&FWFh5xIqdkfH7
zPRmq5u=VJpZ}5I2Xr=>fPM+Es>UX;b7}UxKeg+KX+7U`q-t&QfzKo#)dHC}V<BdEZ
zuHeCi=$%>DI=Ad6erPgC@hTbsw*XcWbORfJ`T9n<wJMd2f9fm{)dxzBRG~`5gfkFu
z6&qT^1q~5>XXyUpx5r*$hLw_lek_lOc=vN)mp38PcZ;ONNKE!;D$wuu`4dZ%Q-sJJ
zwJux7zl?W5Nx>sOk<kRtBdo+TqPFz8Zq#%iJb%bZeJItE-3Q25KH~bz%@J}SbguzJ
zt{T<^XyaYPmx32T|2>lbtcA>eE7eVPEN;nP4y4p~$lY7_?=LLV7clSI4*O<z47`+h
zwp6NHDnBsleJCwT)7fLAmrwUc#gTo-R@MCLJ#p%E&;EPasW=F4ysoIG(uWeaH-Fw3
z1b=7oN>DDYhuwI$U?TUZ9QQ|B(qLxs)&rMM%na9YPF`gSY{-Z#p0wfR+(tl8TK%rH
z$ZTeX!+o!t?H%?`vC(s8lzt}CB&qnUewwijDcX9oa5;J5af4psu(wB;{ZwVS$jCD|
zKyB};|E3uhs<v5I{ha((Mx4fOKITgzLCK2K)+#;mV(TEe-?iAEHK8a)tVJBkZ#Ano
zLDr<o6wlY}Z*%Twd5MWr+na{nk$=?QrRkV@TI|u;!(2rwveHb>Cs4$1)a<n=Id~fC
zV>a3yznF4Tnt9lZ&oCA~?FlH{{#n|@&h|%w@NsZ{?K&UV>nPFEyO<v;(4$R=t?yCD
zfy3D;wxwaSe8EI_U29bQnyb6raLGY4Jp*{HkA@z&y$3H!4VeS+oF6v`xN-JvOiaQk
z;})d(au$^Z#GmA1n8yWF+zh^nL5CjFpETkA8im8#pMcf*sTiW?(K-j`c!m2<S4IX+
zhBVFKyw*>N!H@MgPR6J&PftAvHPpt{3h0!<s*s6%9UznnU@jgV<?(cjZXAmEK|b%D
z9DG+r7x+0lLXWeUbPnu&hj{MWs8tEnb<VB5NVa^t1!;nm?Fr8|MCx*alu`fmY|Pm<
z#%v~kwkB<M5}IvF2MWcSp3_#rUuu}a`Hlj-1V!RlLF$9T7(W`KcRV1h>=qmxRU);$
zTQJTVhnG%tLIx>Zq4S}$$C%d~;6b2GFpH*E#rd5Y#y1R>g-nY@JlCn<rAA(zOF{@<
zC+gfS^*K^T(c*VGelmb;`dhR)Lm8pPiuj9M!SlG%&RJVC@=i8|QvFh#_qBdYqF9lg
zy*!tZauwirZ7E=2*~e4gDUp3tK({N%r-*!a6&=IAzCa@;iPu^`)O0B7?ip5AQgXG2
zyo&)+)hXMJ2Qj<L1p=ut46NBCmgW_mtJ6A$S6Te2LgI2etphPn6UVJxz^M!y>Mlhc
zWEXP9u5sQ5*w-8!Ir0Sk?sdwM?YLRVWq$mMZUn2Si%AN<KNjzsHg}RRmQlRsgtbef
zk5jn#O}Vz<$;_*5n-R4nJ${D#z1hri=+ObA(Te`3<i)8Q9ZG17)_%mJp8KPSkz!-&
z?FKKA*G%c*X^_ipBfm6fd&Bh`<oeU8^+rx?>6tp*1H>T_Och#nQO*7Mp`h$JUM#1j
zf(6@fVdFB~rHMne&)l_ba9ckpsqr!RF?9nwWA{v31D5b_u^fdS#}R$^CrP6fY9Pmr
zm%WzuvciX}N6l{o2V9=I5n#GHp4-b!zHyPJ6OZjuOfRg#j12U*u%eG=NYBeBCDX06
zEGxG8njZd*c{5nHY{BGs7+Y&&{VUtwgO0cb1JGWhtM2BFr4(scb32=4r$t2EAKx*$
zmW$r`&(Y2K&7Zc2#?Rt+#NzL*jKtA%=DLR3&)FWDzK9Hb5)tm+y{?1u;N7>dyt%s-
zCHz32%UWlBQPHll_KRmqlVx#Ow{)Rl7M;{_Kl_O^3!M~Pl=>9YNs5E*wn>tszm-}w
zg?}si`r))q6Y}VdR->C&@Sn!V#0!nr@-IaD?$5RRqul>J;c$t`H|II2zqXoI6-k9u
z$f48um3gSpGo5r@b5F0N8N~p&adhv8gb8&pob`&<)E47@va8;_*26aFs%(f&U(dqY
z!d31_f(a<?NHaH0f#0HM&jpywr%3~kw*vy!dB=BY1}g|*Z2{!@)8t}pdmDo{T4UHa
zU6I{*^S`+X<G3^_+2e=lfy^pZfv{^r!JN%SORnC<g_nQ;M{5yZ1zW46=5^ne02}o6
z=MW=x2qBt9XYN=|kF&_NoYLxz6aB<9Fja0^{;GMQqfXQZ+UIO%q>tV5`4?8h^)jUH
z589qr$Pr!F*YwU`9#r8h@Xrwj?}%p+V|`c;C1}kdl|=oYCBmcD+z6~h`?~fU^aWpz
z^juUp-tDp0v#*v%1T>Wvkh6ehe2_tYEq?W;mi!=2hQU8=jGO%-tNHog@%&#9l~xWO
zG8Pkj+RqUOhM!g^vQ6*f-20!j&xrp0AEi(r?bOAkz?MG2BG%=WpHEiAfx)cfb7qs}
z8J>s))=a;f$5Nq&RCPPg>&*^IA=q6^(^q^Gh6&aYaSsC!t;h}gF>yl%?LnVyMH^E}
z4iVVOyf`w}-OneT>h3SpZZU}|SKyuT!I1{8XmiY6HGy3Ayc#HY(^RMv7rf1HTf4lN
z8{Zk-_98!GoMFL|(?mpX<R9;)=W)0AeeP)e)N(nbW>VkQGb0tnTWPeqOP-S22!a05
z;zhm75*9Cuc==%nC)x7vl=H{H_6y{-9*BYj);p9G1B?;s!OHd8Rnjri(@$RKErmQN
z+0iO|ozPnP0P<?SItM;n^ok=Va}^Icol`5M-Du0LF;0XlUK`^dCWb3o8xlrWkSG^U
zgjU1!&8f>BYy9pJY?0rg>mp$4_ln0koVIRF_8^LoHJtnY6(jaPQF4qXP~y!aARDBE
z?v=F7P-m$*o{uOs{H(XNuEBmmpy06qy{k7aQU(>Yn$JE4p`6?%6{~$H2RAp~W7s)}
zd@abyTKyXbv;#gx=h`A{@J?OOy#l|&?!&tWXuU&)Sj^!8o&dI~?v{A<hL-#I3ERd~
zDeBk$`7B@4W!?}4ewJ1{c%h~2Xyu59t~#t`P*Ka%+&l4`Wj?vpwDON@Au4I$Z*B5n
zgK>|Q<^$);>01g9CwLRnQ)evOMT-$@u1SNUwds~xH_TT|@=}GUS})ZDJKcDN!CbA2
zLGkFw(SD5T<hP%0PXk{X6bZaGwz8*^_P&`$cB5W71-Bg$^!STx`GlLzT=(Z7?;ld{
z1DE>!uf>VYcYk@W3|_<1N<umC%Lw#wNYZla!(si@5)JF+seRFx9vH7;M@vYAA>FXM
zb<63CDUxYThG+l0rxbAO%WIkgVZN2BG0RO7L(;S1*VMAf9efdqwzf>$<3IO_WUC+q
zA83yIlX=XPNO8rR!GQ6*RDF}}UA7WmH%izY80xH^9SvUb<OeWSTXScO?+vk4)8Im1
z@7U?AS^@IM_-V7gEhqQ1Ve$6QO;p@)d?qQbxLw8qMvb2H(tQ(>iEpkAK2Gs4<f_5k
z{<A$EJDJZWq>)sV>y7rAOVgENqrW^b=Y38o>SM@uDl{<V^Dh!wmQ`Nxv0zttYt(zq
z^Z$+0vsXHu%RlC`r?8`dUF(h;?X}&x!Pc+&y3WcMmQq{yUFLTi=k0{!`+HaeB^phl
z*z4zoL&z<8+G4`O!Wtv~_XMGraVFP&irC7Djh72A7q0Kn^}zzC=7q+x8)n>fX6#ju
zJ90HHH>=bDwf#JZ{x9WpcUN(4ZmOhOdwuwBMv65|2z6m}zgyoZ*p!oE^~CSU^WOB~
z4iDxV(4~^~{rYcLlN?#TNg=J`^qEKe87~ft4qD`08%LYPg+`L_ib3>7YhKx%5$gE2
zJX;IUh9(R%c%GNV07d`7q=txY;xL;UF<$JSgoeC6j~YK|B5tBjF!f}xTSV<{Wk+93
zFwDlgIa!FxdzsohI_lWQ@51JOMD&XOo9_ix9KB=S$%wr1x7JSmlFp2>ly^1ckXDX1
z?5fuR-?NvF5CU`qw46zJ`QceNF{7@mnWZDgzOM0ank7eejG2WLMpjGVhE85zept-E
zg~dw*w`e!^ezc5A_+w3G7-F{sN1es`-IRai_X%DJ9*ePX+}s2+Db-s!`=d1MUN-E;
zf@&fkT4+_g#mh?pjXLu1ja)V}nRU7=D>vtONqo65rx2X*=&mEre&VqC_Z*-2JAs~W
z^Ts`43>lC-%^DsNy}3T#o=>MbIxbJtEI?kH6MZkq{coX}#~AmMi!E!y!GE}J?fK9s
z(VN^4WG48stpw7fBZvqlY)K}RS5K`#0=IcLz%=q#F%{e~a}1Hd@vbl0#W}B=hllBW
zYAX6b6H^V3p2;<WqHW`VWH&cM2n_plLHA9eM;gHwcyqNjI$$ygor+oT!bA?kAM9F8
zmK4gNT}&y`x0$qa0eh%aV5#jj@+Ibz)-Lt)(bzBCW=*WUlFCYoJ>j)-@)m2oV(%+V
znaG;dNmUXt%=*>yJ@huLZbjiUl(5lZb%SpQ9x5y!5;esfT>?SGF+Uxn{#LwD3!}sC
zoMlNu{usm27i#MYx)zztdIQeP+QVS?7hNn(dVbA1L?Z~)nLL^OS`gmVD0whL=YUmY
z_Q#rMT6fvSHaH^c(FeN>2{e-M=%VeyjAxJNdUBKc79@#Kt*-fA){ivyQaEQlcFuY^
z$Mq}afx%)Cc>{T82@8>;1;b2;#XK!ph~~s;)3EEe%rdA`b@i_rgA({pOm9MNm3F0h
zTRQ*1Z-lg@3PkFGP7zg8IQoAxpAnOtfbQ+vtVMC{pj3UYi+57`?EZ6a42-{X&%Cuh
z?T8J<AUk{R?@{7^>JtKw3TPUP!|A#%Lf_|tW&c?z^jonp1NQN)AQ-w-h4s{l2GXj(
z36c>~{H{{W?zD#8*v584NmU^7+8DaBf*qLziVAX^3)A<M3}#GeBD`It+R(jBWsY1C
z{iS~Ao2wz@QpVR{H?_(QYK$$2?Uz}c5YIqvU^&LwoX9%p;c=xHXkgdek?o5sgQd)3
z9%pkEJ4V9KF%67v$vJ_58lL@Kc+7t7z~ecoBAB{5Kwe_+^^W46%gp41Kf&sEYaT7q
zjQ6Iwew4j=<-L2RcT<d9Sfgst$(iR}&zgA2vMX~2DQ+S9R(%c0x8C&0_f4&X&=e?*
zzf#nrHg2CUmAImALq9Wrtu#9yoJhKc!`^c6#P)0O@rY>6MX){um+$?@#=}J7tx^@B
z_9<qkuh}Xq^_QAY7{>z#fp<`h;*MLITYK^mXGFBLImLy~(w6HW){cm$61Gi6-V`qm
z+sz~sU$^Kr_5%OEESPp@${>9#8xB2vE~WjNh-j35UB{ISG5VX_=Uv9Ku|=$($Esdo
zQr5%Fbi)*_I_5Uv3$YFI6Om*pQ`$G{X>c*!HkGa&hi`lVv_y|(KWK+o-shq$0<3>C
zc#dXaq6<n$u_f=Mj;Vc9PEA^4fvt-Vu@PF~%ZOl@Nk;`Q0PrXFRl^ROR#xH7+G%3q
zP$=>cbcJsZ4g9o7^=NJ5248qC>#1py4NiiG4><dvh*M*9e)Wr`1%%g|H)GgO=}dry
z08<EiP0z)^`z)Mn(V<Vor{SlZZINW{-`=ez;U>bMe22^FPrH8aDc)#%o8VulHarf%
zFIn+{&ujB%OVgl&sePv}P{bfF_5l?&wv+`2`|i~2gsX^d9Utq-Q_U;-pu2{gwYNUM
zck0^y7S_D(+81ap&PhQ#5jkq411bR=?jyrCHIcrqy{6sE^;;tRL43wTL8F|FzK9Zq
zZw!Q`JVxYRU-IJ^O4GhdO*=feGhQY-$zsvgRnoWPsN$UOdsh>gCmT}@{0{!pv)(Dn
zyjitF{%9nRa98DmH=c<AA0G4oy;geohxXOg@gsz7{A^(&Dvw!(*0Pyvdf*4Hxb2l$
zIyDV0P5PG)IkB1abdF`?51={SxFSOS5qTd@(@0;hU5f^iUqV`NE7`J4^7KrZG?vJ_
z7)jKUfi1>8)c9q3#a%31hPdjqZffi5=|#~_SHfn*I@O!?ll|Vv?%UuH{(!YFZx=si
ztxw*X0rSr<oQHE`D~-nwa4pcrpW61lKK*~&IiJVx4(y-3JWkdiw142Xq~WNSX)~+^
znMjO;&^VcTj^D`9YRH_Pc!fpdfB9)Yi6cVrO|ompsk}~V94u6r={+9o^N>i$>%Ktr
z-<}K#0#Bq^P#KjeBF^RE(pawr{S(~{`W6*uk9i<>4ii{t(4=27`@{VyD2}QwE}2Y2
zLJCmVy%B~O0r<@;_^3HPA@HdC4z5(>Zn}#I&52E=a^ibkX(gn7Z<g5Of!l0e)9Vs}
z*qBE>&C0bi#cea)&LW-0mj1#p;ztLC&I30*ajP>N6??wh5vtP6);D|!<>m`z`fJ8+
zsa?}g+C&jV;p%+zyz<Ox2Y)fZvu1`i(yS}FCk;)x;`%m4d)>Uv+d)7CPvNSs@hLvw
z>T@a}QGDIWQM9V=20Cahgv%BMjgwaDK<{0s7h}Z~4hKImsai6)9gk8Uhsh1Aad|DS
z_<N6zHY!*VX2PiHU2prUx~bvb46<-A3sJA8x!9s#qVzNk5ue(rzBLCoi2G))@zbMZ
zlY4KJ-z;jVfAla|C{sP=KW`bf91IbNCzsT&5VqxiG}rwel#s)s)c<K-#9j=$+dx`4
zBIe0n@TyD?Yw}IHxVo?K@y62BW<9o1jR>-fT9%=d{<C?>K{tRR9VTMAU3<wxU#8Qd
zon<y{cX*c9r{kK==2F&Dy`At^IrzKCr?<&stj#M8Ztp>t4zMc9%DawPeJ><gcC(K1
zZ<VaL+lM~Ol`X$EkP|0~!B`}YJeI?Z_<e3VnYu-@Kiv)9GCc-R*-*A=!G($064+$R
z!MQgjeV71>!?bpUkzaz{P_d4Umd;n(*>=vv_{JfnLT6@%=;*nPINzF5jz2nCl?%z3
zRa~(fM=3FL^$wYT8d;PkZF0Oq-ZMIQI-fmG*n6r^dg!!B6TL25&)z4RP4()@7o+d`
z#vK)oHGDlQL5`ZbuW^0KTZbF3DeRVbvsq4xI!raDf7CPvik2~wDkWd)FPbb==$rJk
z{ZXLkkNq}VyeAACR6xU+I<DQk@rMO>-1h(B=_{kEV7hP>kuK?!kVYEmknRp?q@=rB
zTDm(A-AH$rbeEKfba%rY-tXS~%e7p<I&03JnP)$-r$-6d6Yr<xyxDz2VvU{|gIznb
z{B#3XI?+~I57iE9jaF!i+lN7uI~3OW@@fN)+n?<I#e0OKR?m1b(-`U0GPYy_UF!!-
zn%Yx@7#I#&A^#C5I(9^;^T-mE5sicw?<k{5<^D{bH0OOnjE*7rzF%oZO@X+AFWV7@
z0W@Lu)Jg-`_oA#3<f-pqcUY$h<e-En6#|8TQ!Z6f>63<oR^CO%{j+6oJo@-m5&b;Z
z^%a)dxA~t-4Xb5ZH2%4agkQ(26o)>DB1wxY{<UD+iWA2T;5=NSqf^5aWJx25c``lj
zSP~ujC1~kFh;JdwYqCAFE6<V&0pTthWSkuW1|=<XG)rZ*5a^b}KaMN+JipQ!+p;m<
z)4U$3<I`R;Za9G_?PRK>p1gg3Er;ZXwsvVY`@7csP<+>M72|>FYhUs78Icf8%C1WE
z=Oq{Gm__o~-7$QCThK!=T-o^2{shG>ToD1B6CE9Z&2=ZE+L15n8``OYJfsGryy*T{
z@zowOgQQ+in{C`^KpV^6r4-5~rO75Ya^-Nz3Q066_;+@W1rp!p@pH8Hq3BU&djHB#
z^FXJ^5J@z5d?a?RJOce>bO56T9d!9e^#66IHFTpvvgK0-mhyNXurY}>=4|K=J4MNu
zRSpxiWc6Uui^sERXuZBAeku%HYe{*Jf*?Ut>~0lX(xs5oX`A!iulp-m6p=f%knKkv
zAtlzErw5udvAtYmHL-k)nj~zu%j-3=6B{okoKTW4V`p?e+okcr2+8mt7#t#Rd(m%5
zSLTkozzlAMPk~01z6s4dZ89!7)3wEwpENQxTDI@qlivwt7a@SNlJjClw<05R@yvlv
zXv*rhmR#&IW6tTS*iC$V0L0U%TR)>BY-LraNLA%+&(v`k&!meNz+4uHpGu@JJ=!~h
ziR57bga_A$FVZc54b~ny92aID?CZ#6dOiEqdu;Ie<i)8-R0zpKb5V^2In2q_(G%hH
zK9z8Snhi{<L~jFA=OODW_(z7Y?=9po7%vn9NOGx|>K9D<teDrz(WM4Ax5$#x!Wx{?
zn{%eFtkQL$MWtu)WU(bz^V?@%*Z>!)|6t<5(6UUR1M!&B(YUpi9BsbQ-EUej;L-$4
zVn==bqsc*t98SU<n|^Iw)8Z}9dX)i(#?D;w@f;}g#Ub<nQtO>*6VZGw)rQf~l};4x
zJ!{xe6~%z+bysaWd`C}M<;kO={r5qnIBPBav#5pe4_}9;y8eES^gU(ST!$L0#nQ83
z&N2-^i@A4B+SjH=D5+RYy7<EsukC(}A7}FI=(hd++W@qe@isO0+c67|`K^UT&3*}N
zF6G=O+Rrh2_l4Aa5Jwyp*)|(2oP>OQK;8pFv7PbWV<AQfY|eHhMKoTGWnnS-uf;75
zbO0>Elo2Mn>!4lqyrTNCJXxZ^<P1lw7|?m3s$v=V`71U4#vsc$=CwUInu_<3d|0mE
z_k=)c@c9zC%hap6cDP4;DijryKM~q}l{+{^zjQ7{%ySVf0sbgJ6Y3@H7Qd@0F|P{l
z@Z=L*wB@i6XhuV&GeB{_$NgV%!_(w`j<n`5H?5%dtDB`fuffuuA8_y@T>20{*%NKN
zJBg}P&8gRC_aNcQ#-<`GIG?LTh9^ZhKX46|7Y`aPeN*ZZzv@1J8#WYMOGX3|wCoau
zW=KwnIa_~Z%jAvjG2iE~Rdw>oGkt3K2eh6U1x#Ng3NXz1QprzMwTsDV#;X5RQfPn0
z)Wiu9ZNWDf<K~9tGX`xt(n<IC*qAPOzU9u`uXz)JQY6CUvCT_@IOgPpP^mcv)U>)g
z9|A~90W9_-!&FLbD(1S$Affm;S|--^vwl}N5%7<gO608Yjvt=5!)}c}Km)qadOSkt
zVrcouPA5M;mI*GUt@YR6nLWOh`P=}7geCM^OjWmRdJ#-f!G>C$j%z?X*5%&6#v8gP
zQ}H3RzHSxstNf9kbiETjcWjuNfDOvwebI+Y{SWb^N@DBQ9!g#pT8mmxvh`%S6u)*u
zWFOxN)4*>=tbbU-NT9OOgKO2rUs;ouZU3!lFluI7%`Mrpuf#G9S||(9AG2Wt?ZumQ
zAk&ffmcE}jf*u;4i*FDzg2wfsX}>MTPbez^VrlHGEk`nuVCu*5qP_^C3HXBc$`Z`E
zJ*XIv_qI))-GpiKjMbz_Rkdj#G@nJWX?1_M<gADpIPSHH+gyPTP1@nQ2{l`X9d`Z+
zCdeKMX=}mb>nl;!om#6^pMCu4c{Q^JA~7l{-qRWAM`14X5G`r>?#~8G?`<9q$mSUs
zNdvx`)^^4i_8_6)*b+tw+;7A+R><Q@p%CJer?6LjBw9m_Mjv|Az^_9&uTjl(_htki
zN3CY~cKTeKlSjPpP>HtC?T8hY=GsKU<jAU{3U<^sr!zaj#K-;X2OWiXetgv<8@J4C
z5V7a1qp)5mAvOq<pYS3i;-AUa+%FS|`ELM65H*S67PT!l84&uao%x}+qUL0YG~dY1
z9!LX2^~36BVMdhiT;M`)RkF=#frCwF?RIYT8mv&5g~v@rlyg+C^BUp~Tg$@(cy4*`
z;DB#&AXlPg6;eO7pc3nbC<NvwNEl;W+kEAK;NcI-7<@S`2ghwW`%Zl`;H9^)*XB_%
zLgFP^h-6a_1E!tqJdQC|X3!c)q1Kqumn(+<EpmCEXbI%D&$Zs)yF$N%Lr?WBpr(cc
ziijN(Pj9Bm^U>ON8+;rAky~?)!POnCyZ-0thK2(VIK})RI)7QHe`+s4fQeONW#6``
zsrPzY0Bna;1&Lis4L-?^lnnss7vhc#<x6a&6~`6WK7KMEm@+YTYp=~}+kK+<pkB2v
zYV)XlLF&ON>I&f@A&Vj{W~>~_q%mx`gk#FICMS>I-OD2iN|O`Ee!0f%X(A4sYG@WI
zQWxwHkHpB}yH@n|uJWG+k}rDN_xOT<YkoTt806imPK6}2^^Nu)f+Uh~u0zjATLKe+
z-e7E}Ga=!U;WI?=4%WfQ9v(k};V?0xqVyjk4NDXBqdymtvhchrWo3nejzv}T6nP38
zF7A*%uI5a@%ET`mWuz!<4GrsTYQNh>gu(dJ5NymqG?8bC_{*$$8<n@F+FA5pM8`GW
z4Mq|S4`!Y#+qR{2R1}%+`?x6MhLZBHei>=ja^?Yh5on{ppJ3GA{qy}1EMR(~{7Y!S
z*Ol7dvi~KBv@QWA(3h~U>p_QT;LgK-eGeUwF-kgRePeX)SzjP|%_=7P_JK?bx(b*g
zC>HzggSQR>3QB<#!=@7kQ#&eNjzr;$14O`}0*i}?Rn56uCVk3?B9|Sj9VX`ieXA;|
z;(7mTYqI=a2R^yS2i`CI$vLXW2fv>$ru|B&F~iy5XGNf#DutI^m@qFt)G<gF!Qk=v
z`gJ0EnOno^S$kDHGG(tjpVlMF?5zj9N3QHCnHC{)D`<?WP6@fAqvfU<B`Ks@%sMJG
z`lb+Ay}6*=EDD~JN8|Jr@3X2(dZK@$@<J8A7yT<=1HN|InGzy~%nXxpU+=R%%*Que
zn)GSA7Ieu4V(dx(ZbF#13h2tp*;CSVdze)2VEU;qjU~usGCi$Po4woOrKBXu^qJZl
zq6}yv^v&7!bto%8)?9bK8qAX{pIW8%p-IHbi|4El-WSOq9LOU4peGSCrk*aqDqc55
znI>QTJn`xt1;v^>sHX5+le<}n^}yy0h9U3cLwgaqCR|xS*DrNnONOr5urN0F4N#8L
z0?8g|g%9o33?IGYH+!*-g|r@5R)iFtGc)wGiVX5)OQb&qP-o-a)$<MheF|lc;*Jq!
zcG8LzrqMTcj?m_En1}8o=z9d$^Q~>_7oTI<Ic$r@tFf-v*Rhv&qCUU0R`;*>+ZgkE
zuZ4jQoy^VA;eg+OW)x~Rbxn$9!~=pRUxu;?6xWtAC~Z6$zixFy1sN;6r-4E}HZdo2
zx*xlgs~PUDGoHGg(ZRs1)QduI*#MKAT*FF<<py%@k#~fQnPRBQH6+N-UwSFpL!A!P
z)|B#!@ypGrX3<Fr(g1)!)DB>*aV^UnHZBhXUjt;svwX{1y6%*`TV_{YC!<+&lOI#)
z$}7;Xkn_`QttDnU?m~+TlhpK<9kg|k+hQCMRt<(;>T4D+5DD!++J)m?Pz<ZWw8}?i
zFmT?Hp4NlU!5n*f#&o7d9iC`-3cg1dikwfl6Z@Jk!aYfP8{71g6?n%bfqlX;fhpX5
zhcj{@L0UQhvTVy*Fh$vCpSsQO@O{WUtU<3uhCRv1F-M|&s^8^JteL~`s$26rE}D#r
z;2bzM`n^i<HpG}Wr+AC;^kHM3`#!8-<3^9l$fG#iuY?+-&|Ryf)0OY}gIG@kJ~wHE
zoXlPARFptriU&et1tZ2~|I94)FEYxlcLP!>;Y9dkU&gZ2@H01TS}bt`TF-k>ck2mJ
zc$>B>A_RkC?=<7Gp2i3~PxiRvp8rD0ZFeD1yi5SJIPZ5^E1W(!TQETZbP?d>8co_x
z>kW+SyBVKOh#1;E61FrQmR2i49&&^-nUlMFqTTnNqccrG6^oU0hk$-kK+V9+-AOAc
z$HJra?%rnIQ3oY`!N0`ju-_ebhk$O<+L0LpMv0pTp#{izFF!HKp-I-#<1(6o4nunU
zxWo2>9Pb6Vglq7FtCl5%SY0b>qjs+ls7m8no9sjCk53%!7&Z8+Xl#u$&?J{?CNZ&e
zCfO5sqo|}wx)fBf5AiD*vNlg2aNYQtXm<KgcoPq}Z7OuW%~~ID_G7gS-uCl4S0*`j
zB=o3U@>n-D39x?8-+MT^AShcve)3!wjx-VnY`$O2Z+jx1lauaO(qY|NGmTZ!FA9;&
ze*oH2Xj&zfCeC^QqNX~5j686PCNyFF+i}THDqprLxx4lvBGVm>kGi;i;I~wq(NwRD
zh+p0@EZZItKnxZ8klm)tA2{Vy0iWk*kp&eMMP}&u;(-QjU8JI>1uZDio-Cq@#gvm7
zd8rv}R2`zPE02Q>hYn9f8dsDmRQ{VXO&Se4R;*k&cQt>dUQso$GfF!8y&Uvy`#~hC
z+dfJ(pvvL>(Z)~hS{T5n1Z^L3YV&4i@h;f?-G8AaB$&P>Gz8swW`KB)wBC(jJty_b
zj=VL>DWMGs7X@(ukk(rhtkpag)Z7_Y)F|_^gjM?k3+B}tSM{G=&~C4_1K&qqun;x8
zA6nsjVMVpND2LOYg>339_Mj!y%1l+P*s&L3U3;U}@k%Eu+{5=hd;b)~b8Xjc+Jt;f
zO!9hUwITAgB#I1q(flS<I0zgjB$_^dFrnt7e5KVLe@6@xoJP8~{?QQn`IjV6O$HRB
z`+}yZ?|^!rQYEn&2iE704Wnzr9?>_3ks1~)(l1hR^v3*Wry>+%{Bld+s_5TDEocPd
z6VP9IT|7>or+>Uq@Iiuf;}X@KsVfG6@DuXNd=iN)%LMm+EVX4HB4FW6X3eH-jPZWj
z7nQUtipI=+l=_yMlTxs`_|efq+oBwF383jGK_{n^OG~+;r62EKDj;_!5`|NNWdA4%
zcW>9~L-v}|^!jik^{PZ+5-Tt~lLUfKUc2LPb+;gMH-eNqNG81kBkk-zJSxg2YWz_{
z<nXcr#R!+E6sf4is+H-_S7$Wo5TQ4qaWHtV_Ma;A4FjAURN(pELIF-;<MO^vg-E&K
zMG32`*6#p@u0;Bq?WMgR1E2sJ@=xCTS*QOxezB%9stpz<M}<!nvQk~Fy3`oiK}txA
zkT*ri==H?3Zx<%?eZ@&5xzzr287k~t^`JtWlHk$XK#$mYe$&N!|5L1qZ1pYqhKCex
z+v$yW=N|>%t{7fWhs0jTn0hzA?WXV$RaJMKiPVw^8Y80$Xxa>2qfPj>zG14`KIHq~
zWR73^oF`Z%#X<6xoL|ffV;v5c%|)#lI?g=q^HnKKAPOP!n=FPMB+SDJ3G*hBjE_&5
z#ZZx%?Z2X}EVs9EQ*LFF<Wz63w>=(s7^Eu;@I-Y)D3A&dZYnD~E}?A3kTH7hOJ4D_
zU&XkrSn;S}TRe0LJn|>W%h})hn|0d;$FAQ0h>s<K11_4_a~r+&O98Je6$YvA0;jiz
zNJqOHoys1#Je(pBfne*^Hmx<e>4N&HKR{|neUUnL=NYW&&MH`IE3<(52)4pO>Q7IB
zWKI?^>uU3CP}1mUTXrK`+YpZcuc%d1m&?;BW7YP;jxgRtP7y+gj2{p+jn57~IwavV
z=+xIQXSYxNn_csX+e}eyf8r1bE;(Gyb)?G+|81*%`!!VHA<Mh-pii`9IHK`R9}yFp
zX7*oxyKsE@$L9`2fj^#Jk<Y`y9mA)~)Sz}KSp9MCYQ2IfTI6QU9NL-3T_|<`@nA6K
z&}q!A@dK<=LhWhxhgoj^o2$hk%kzE$u`&xQug)??9niLpD|GsjNJT#YnZW?|sNOJL
zA^`v-0nLZ#lq>w_22>xL4Hqbd06$91P_fkNgmuKn0ZzsAKUEJ~;~L77G%0vbbF1U$
zcY731(<4g{rKJKCrBrSZ&+p-hB>8xN=A>WywrI_?s7V@4`h0BigzX=~+mFmJ{2xM&
z_#Z+JFx$lpHOut&CSIwKrnOr4;BO}etqS}@v~L$-L2>Rb0-PWOH^D0W_%L@S39|Te
z5GVE@VllM@iSf_tKd<`i@muy|B=8A@j40D~n%e$|y_T5%gwTfxi-OF=8Q*i5z=<PG
zGo=wGBDC$G#}!l{$}r?f8d4$}NScXrIR^YO2>ERJ_VItp2=F~nFO-kQC(IYg(Z$A*
zX{ZxfQ2%)jSVo}52-~@?y^3n{{IM7oHltS0s2Iy~H|~s*wj>&aK7MLzmE<g(TQvt<
za{83A72ce}5CLg@k^vypQ%7NXZ2FiVko;)cE(_ZP%(*E?bGp~YRJ|YBEA+im<khDx
zSjSYI7tfS$;gtyeYpIl-b9+QVx|25tk-}d2lBILsuFl9x9k2i|Yq!2qs*<$V038Wj
zRQ-`iHMUlPcjksmQ;Qyh?myy?$XC=<_S}!khk-+3`)rWr%nMHm3@~1Y3egqvEQs!x
z!Edug$5K_EL`D{k&>qq!iP8VDeb*QnJnd{Y_j|!AEnyJ>kWzElB`*qL-RvPzE*clq
zXh2tQ%)88|GedQnbBOJ=EFnRcgO~RMv2G8d3u3pq!{G>$&sC+KzO6j*eP%L=mQ)<*
z;|l0iWJM=2jcj;)anPVi+X?<~GqmIUaa`VEojcuSZ&9ZKZk)$|LmIIuQAzG?-u&h9
zgBV#nLJd~O)YL+bD=#jdx=k1sIK1U0`DfRZGlkbH;e<yV9db%iV7$n*6X2bdG)lll
zWVh*01N<~V8<uIAY}?e1B*qh)RRvzfL)_ozk|vLy*b!{OEW!_a3#=nfw1B;zJS779
zZqt<Z9zD`8>R+2FQ@Z^gLTeF^34v(1q5aZcur#=mj-tlJT7|$}S0)ER#L`g&Bo0lg
zS>!kI+nz<2#%1kBV@qEopam9Mu%?&Dtp}4Dvr1<r2x9Ds#hy2NRBtXV_zsMJVfYj9
zUP%hYIGBB?9?XUd9a?o1Ko5Zw0cC3HjHse6Q6p+t_@V*}eq)!#jZYFVQ`D!q?f_5p
z$Ue|uVPMpN=Tc&0i9PHI8;>qDJ6sTj2Qx{+-#1$C$#Sr$g@5yF+qvE+3o9rNKc>M5
z$BKc7%sL-;<n7Zo357bc`y%C1t_bN*^XuIlbVa<6EOGb9|6=Gd6d;IO?m)2d!;J}!
z^cUt7Qg{;A(_hkN*)+BCHba{Am9K39r~T0(v$uQw<ITnT6tbDmTkycy_SH6r5#iO(
z3-C@C<5t`Nu=f~IGk<(jxPL@#P-jjg*Wnx^mfr_lk1DeIUvp4ZRhd8XnZw!&cUJ<^
z`_xQDb3{ki$jv$8+Q&ZVmQGrmhp%RnA5)c7S<2yG)0+jWV70o(PAy456&&BmWTvd#
z@W@6*x;^}Y1JlT+6f&Pq`B`o;Hz&Krq~Fk)<?O}$1OtUZ3iXiFF--^Gf*#Q6Mdj>`
z7pvsbtfgfmYR*m+P(>v|AeVP=!Ze`A{UgQGc5{q_#oZQ=-^_6^`e;WtcuQu^z%V=W
zB@Oegy7lA`8(4#Ild0p5hxL>3n~TNQssw*nc(_&sPurPsv;g4~m|>@DcWW)phn>#6
zG}wf@WRi)s6toAVa0$J<1pqJQ-hDFmcjaG-1~%1~9rhMNuk}~rnM+X>;&M(sQ<dXR
zLlP1~Lb?B0YA<`tD8ciXPR@zIC<bh?HjC|OP@>8JI{U>iCAZZ6n3sP0%ofK=HhEy-
zAH_PW`}S)|U3bY!_AZxcsE|+?q4!(9K8!$kN+siuvyBvNa>^=ln3TUv747dV=x{U+
z=90}SV-;jsn)^0x?XFB<T&p~P#LY@>aa-(!2Du9h^phYJH`0&IZQm@Oxv7v+Q=Rc<
z5)Y_2u~FFnykqG^_5?ziM*V)PUQ-aHD32{HL}jgjKe|K#R}y=02R;bnt#_?!>fjXu
z&fdA>8yu<=$vsNR*=(bN#jN*Vc~vQMHFmV%LPODZLZyUQf4Uon7P7stpP2t+KPi?9
zH~mTuJ@<2VwVrhqp_lbT=B@YPUYEF=EMbOz_JWfdHE=HUX&uqKt85=UY4;v$^9uap
zeN3ModEU89l(~=L`nvLY(8Kd&h|BvbYju5i%`N1`VGU#yw#VFr;lAEwhDSq+vb@1K
zJ<g$-CNAIwJ8T|%NT5h8oPWWAj>5tmpMa|^DBqA0$y1=y#S54=*DkAgP}&JB8?hQN
zz@+Pwi=;?UoR1GfYqzwi*dZK1Hz4MQO+0=J?fnao*orD|RaM!A(&ng=*eT!6>71W6
zpEDy-=%b<EbOotn-*j1p2!+y8qio&oKOa`w@9efslJ^Rq5ycNt;wA5FAo|?C9qVuk
z943}IY?dor?AzshSnP0nD?4A&Qai7ey-cDooN0@Fr5&cv2u+Vf0U>7bHcIxAmto?x
zyN>O48vc50Xb4J-By74g-Q)bMf@WB5U=#R5o7~-lz<l2<LvkdUVG?BtNSY!s&w$-&
z`p)Bet<H<D)01~TOuKBQJPK^pk#&<R5WKjyFbx{IxaCs&MmLk_f&z2PM)JK&#J4(S
z)6^Q85sCc{zT%ozCD4x+Q%1E%;etrV!?2jeOD&QSl|P6$2%1IY9h4{>dWmm^DY;5U
zhtJLa!{Hk}@>~k0+5M%`M*64AgfF1=o;uZe8Z_+aS1%C}t0805Ki*OwDtg}y&s*@D
z?jcLyCaP>fc2%RL8wWNrW@8Tey7rqv{*b51Uy27^y<a~Y==0~3G_ZhYJ_kM_?^}-L
zWV5l4`}ZoNkfeK*+|VMQTs$7Umoh^;EtCfbDgD8}>ffWjmv(b)OZP2l`@Oul0Y8+Q
z%T@mAGRq*3pT195Cnb%Km7DIb0xH=?H_sPAA&7uDZBnPZM7lV0mJFEA5>v%_w(Ol3
zkg)jaAhKn{qx(8X0jnkH*GHhtO^a}_AxTFGeR+7*awsOSCiX)FyqKUR^HMYi0?dM7
zA|z*gA!oeF(;oV|aIy<U{_;Qm_U#`Mjzm0cBMT7HD?;LYrs$U3>>`g4G$;rHx>*=-
zMHOn8)v&cmwM?#@y2nC#QQv6RjSal_U$G<8zhbz;SHT1ZDWt=QJJm5g4Y44n^rI`j
zbHEPixESJr0Vfb(0S2yMQN<H&)U`{GF=?MK%o>W&eGn)NaWT%PDN>mJT!fG_+Zg9I
z0>sb@p<8!~!F^v!Vly7T^-%>jB+(D0#|O^zDOwFpr`_LouV^zmNg;Sh>RdqEXjW+W
z=#|tgx)e24$hSLvW+~Kk=^_3OAxMEKJnH(!s)W0sByMpN7kmc>N3j3jWct^UaI2DG
zQr!YPz@j$PyPv?yZwlgUie{%n$L(E%V6ba#Wz?j<Fw)_n&xCN;ZGa(#O#5R)hlm~1
z_(A?#><aqhz0T%$cv8PFqo`ma2yy@HAi{F=zn&0K`v!LWSeqSQR<MF%>o|3&pS8K?
zB?td-6%LB+zr{z?2-Z_E;L_8(y&Ok_Ax-E5!ca%h^rEh(hYIK2gEtuAW_vlqHb2(+
z_ur6JWsB~Uo=YmR+jDC1`Akye`3z3fDR2@7C_n=^0{l?G`pN8Ly!*k1XKVFOAb(s2
z*3h@0Q=^dhZ`L%F-A)`8WSA<LLNvQU4D0@;WCSlcgzrE8XU9(t4i(E6waV`TZ9?DK
z1^)E*Hb~ZiDUo}0vb@J#VIdrU?_ZajgR#<j-XpAfZs9gh+j^g;>w^0OG0)+Fd2^T0
z-JP-HY3%_4jQgo%cChokEtS4zLlafRVhO|?_dX0MnqRKD2ho25zO6g4P~i1kt)uVP
zA&SfSnvDOAY|qzKkLbrzgrq9&Do1DUq<*B&784b}PyCtfI^?K^7PIR#2_=TU;P$D*
z8(7k%N3>f%)&5l!npFWql5L)kJ9=l8ryu^gfcMHO?7yTZERjM}rw&zZqcYi9#xp+6
z;_MR8Tf+@D=htj6P%E35xGXA-_<x2I6k@i0lZ90ng5e$@f$3)96c!&lIER3fhB)(x
zA{+vhJBZ%=gSZk@3_o9Qmg@`K#*F$_AI-ppP;HxTL{H=IBXQQZr#+UMq<XnsQ2Pp4
zY_butoF1tA98^Iz@_DV6D!&J*>tarVyv^EdeTf>-#q#Y<bV2cu$d}HMDogbF8I14=
z!}*pJUqmEIY%9y?C9lDS+FIePAs?A*0T~AHbB_FyZjHY-viL?Ih1b>3AtAEE#-V0I
zJ))S0PnYPbs=n5Hz}o^8;u$)6PsTl`z56aN>2z%1`p<oeSL^=zaKa>>$<v9r#w+NS
zccaiCgx2<C<?k`{@18~b=_|UZauEZEEm2hGIs8L#Db>~?kdB+lIIp^2$Kr)qn0$-&
zB}XEcn-5WHJvJz=TSd&5+>QkYNY^B&;+vE<+__67UD+>Sfx*C7j<;leyo5zUq@`3l
zFbv3*!hL2jQy<Yw><rmaA>ntda`j)5EzAD|@zabNQ7e8{{(JlcdM<g?|F;_zCd%q>
z&V8;CU#vfcdM!VuSDF~L^_k@BlfQws+kTTR#Q>kq7-Ei)+I~Nu7LT5{3}^8}h^84}
zv>~MokYoUzE3LFstB$t3l9c8wdy+u%KiG~-TD`k5X(XA8l~b-CAx#*L%EGKl53@cu
zR(o{F-cRDkwpXLWfbc<>&F|Nd)KXIk1n&C#Ox*34tGh}V?0td-mhVMAwLc186a?p`
zewSmf#hMr<>SS)8>yCTm5;~{V$Mb2Kj11$wWkRrh><%*GejdY=6vWaL07p0HfG%(6
zP0Twv;8XuLCBoqt&x3^Gp<vo9Mq7BA;d3!uHui<<c1UCO{uCguk!oA3+f0DI;Z#(c
z3dcr4Ksv_cx(1lIseGIx=?V*Oc8^;Hz3L=Oe?KiO;Rt2#(MEY~F?kRZZ%F%WiUP03
zR3PS^?Bf}dw8@&GVZ3;bk=^{&QArWr`Kg2j_8K977w`ePb#M<pZ!f#xNnvs-{!q$P
zg-o1T(aMD_z8Dv|Qrl(a<j(+Y*}-ylQSnIda%%ER_WtKP9}y0yupqCIY`@7!Dk?u%
z{@KQvEY49ITpw`c9HYbn(l8)3;&~H>2of>bD?7`7m%%G~LlgjP;BhhiI%$7h-G{ju
zgFYB8N@fM_|MQ0>C-A;YWDtb><jrzL@V0yHKGE+8h6t&!{9;veI%I}6fsmE@2KwT7
zr73j_yUiXm-G{4b;_KRFKkFS3X?dY48s1e@5g7&txufp7c;Q}SiM}KB{ziP;{_%}R
zJ&q~HE_GfWn@VF;?i-NIt@in@cgNV#x?dffx#%&!R=U4bqeL0KdBS=RwqW>s-0)TL
zOO#99mRE%sZ{=S2J5dy|kZ`3))wiO`KVvDIA^Q3BN{i4TwW4bhF(BWz{`eS9OaxiT
z>iKy=A0;}gqSRDGtXH_$);G)ESQxeL^(Hwa>V5mqO)doz9SH~?El6&Nn^BM7OuhrA
z$KCp7Hae?jdV&FGj@UAtr5=Y?Q<koC4(&mfcnPB!0$Ejs_+QA)nMhWYvX06h5~K|%
zkjwI#n46eeZNA66c>}_6AgVEQzcbTHP{z|*9xn+I81|*2nsEF?JITi(4yK-~T1=NX
z0Xo2%2SEk?;l%xCX!vq!C>gklLDP+d#rjT1E2K6sfsHBdWlS@q?eWDD8B=w%$V~cq
zRyB4J8m#P3^q8fxY84aXZxMHzh=m&yMYSh70(;X-9#H{;jdr{x6_9<}=KMGbE!;%8
z|6-kS^!YEzgU1cyyMbYHR_vf+8?N`G6PynR-tCti_hjwc4!M~{yZE3D0X>_qhduwF
z>02H97WI;`(+6tjKcv3af2z0GZ?m}rOQ_+Xy>b5p@Dr^;ObhU2FgeqS{<>Pnx5fy)
zs}cr=@U3b8=+j#D|56ce3?5%!cs$<~zVzw>4-Eoqb8mCa5prRJT@N;UJZ~$#g7^l+
z!7+C2>FJP!o!tJjv*Z5wDH@2yk%Q@KQzT&OozKI(PZU7y(0^4<qlWGd2P0f)I5LNB
zTCHVqg95yNEpjkcv1qLi1y6s})+qos!e;G(I-P_1u>D2}_~v&BW~qsCc1-fzSvfYf
zzd%EJCl;1|v#c1qNIvL6ezQymJhEEs;JFmQGy{KvqMq4L&L$x+K3vgis;m}F0nSjv
z84u~sB=Z#)+wPxnr#YWA0`X2vm~)U?5xYiJARJM~AF;b>dd#y2DV=i+H=VnRalj+1
zXKEO3{e@!1*($DNS5GMw5vn^hXvoMUAxO9^X_lf*>y*LItCl=_!=<!H{$_&$Bw#|{
za9t4+0De1$KL2>%El!C{cyLHNu(+n?B_*}znJ~!8N)RWR@eN!`wnR1?uHeo!>L=40
z0T2fWHb1XVnfp;uS>0`aIP%~A3i-vX<p8|mK(i3g;2u?K81pO)rScM@sZ#N;{ievK
z3}OJxF|_BG>loy!Z<O0qMIu2U<CYxbf9_#s)bKm=I1q~U-hT#B41O+2<Er{idqAVU
z*)V?U7r6a&*B=V*Izahk3babn0LdUDaTIj5FTBro!kPz0!@jjfLH&`z?ZERv$G_7g
zRAqbyPqMc`_gzEgaeevR9oNCfN{4~e55F1t29>G$2aV&XQS~*CdODjW)~p>*2(zrm
zRa=f)V<F)p1G;!Wf$c|%8meuZdRmr<6=HMYudH&}4pY92Jhw97OAO#6c!uv9N_%O)
zY0vLhF`ljqjkr+GvaPtdm&S)e1INtx%ze2o8Qd6L3sdrHcokJqMdH<ogeZR`ij2gF
zZC6emoWhMi9<MVuM7J4{;QfmN1OB<oi>ZbYW`-8z>`uC|$`F;itmcf{zExe~7QN0S
zl0U9la_|H!T!S&dtj^<hP2MYIh*3fpt5kecm2)0ZK$%IX|A`LsZL0Bj;GM(q&J9XN
zXZ}{boiH)S3CC0#7IcZi1ZG0~H-lpCw;v*CMGoYEC*XGGT@o({4|@K6F(rNSG{Xo$
zNlYD>Izx3=Xa3x>8nP^`Ot%yo0tYmXY7ogp;ji0nZ~hF7Pm&m;Gh8SCpn=pPRG(Z>
zt-e$(po1$VG?2UULz|%w(p^}fa$vo|$sZw>RI|OUp=$<pl7e%!;r5zu@oyK(38`^g
zFKdSUYXy?)@8TC<)ln-HKVkKR>If6VLg2tTdos9#+`w>$m)NdYPv~G1twaWI*UdoG
zA*lw~WK@Q1>Uh$2M>{_h--};+#+Y{dk0MH}lIE1gtmm)9+@4Q`Q8{YudKi2!Vgkr#
zKT6WyS2Y|4GC+_fFo}Gtb9aEmUHb^r?l@?5eg}dHyu7{B)BxvYAuw>XkMqzyhZB!H
zH)xwZod}{*6%1Six;<U^+%lIsB+&aX27qKG|1(b3_WbiHW1RQr-N8_@7ZgWGwBCyo
zdF4K5CGS++_1n|Qq0Rc`Xp$KzL<qrfZkpmABp!WMR?Ap~<;LeYsJ4_p@BdAF>fg84
zi+l*nof#aM+AtEhmG)q}%W*63@cic4ZmVP4as$W3cnQlT#_gWPs-u1X76txi56ZDh
z$9NX~LnWvFbwxNSI0;wZ@w@~Q`LQIR$ochcwk|Udgrz?Jl@1Q#5f-A0of*0|(u?8-
zDXa>oqK~uc>6$C-JH1kANXG=(yh=ZMMNYp;A<SQ=3{irxOoL2g+q(vWw_khh|Ccx`
z#POv>x*N629P$aQb@uVEsTV^ZijH<_@Q_g&WidT`lfB1aUvUZpY2~>dQgz8xHOZ`1
z`;5WU()SjjnQ0--J)PeHNp`vIRV4s^9>V_%fh>y(LACzuNp<ig3pNn6BQT;iQ_-49
zBq*a-Y0zPasRqQ8kUoh#+2bE!Qgpnqzn`t=z3suwnS~=SeASmlO<_WU_q)tYzEE-_
zUP*kFRlCuYRhAT9foMGWJRHHIOd~wEBwF<M&hRVAV?+mrkfluYQ07em9G0*8bK0u2
z`#m%!Bs=@nJk=wapcEMzW`rO@|DOV{im0g7Od-4r?@+WhD;m$*)p(9fkcEUJiGB}R
z{zzVtm3#T9CvHgy!i;XOB^&KL(*|0+-@BX0uYT0DUfsIGL;5#LuQFHpyua<_)uD*c
zCbHY6wm<Odk96g=W>MQ?1@ZjlV`bL#r6H7rIUc%sYJ8&MY|5tR#;Dd9g~)ZIQc#i5
z+7`DW8V8{d^&8qTD8!Xv8S<zc#5W&m(a5Amu&D`_Gz8dvzmnU*y)NQ_kKV7G9i9I(
zx1Ep~@~0o0W?qk8wP@M34MeRy+5VTC+5-G8c2SG6cF{9)uziQjBKJdf@Pz{U&1=vW
zX{3O>YLgLr7ictM>G%lwD%f=Tq*8zA;8))3em{n>8*~7x&A0u~C+dB7j)*1|8i?t$
z$;cO6z~78I__FG2+LrCIqdHy4JTq;dG`$o2Q%vCV1}wM9nhl~=SUoF_dEj0Xbqo?%
z_=Gd+w12wr`7HW|oNnx+#St$~n$4-olLZnL3e$YsuN=NXqx&9YW}5id_fzuKj9z{@
z%(d%6TGdp=jpy2C8F?6NRsPs(xDQK66jwI*HXNqaTVv<?hpNqj7#y|m#-CSrOgQbn
zzu7Gu-09=tN7XfDop0-P+$OA93BwHygs2<ULdhQAwTW|>PM)Z7PP;~=wt$bM0x_h<
z9>?yGlw*uj$<_5km*g;IS!?U=+v0Kb!}s0+wa#x5{@MXJ(6$A;t6BRJ<|NfJ@PufX
zRm1X9H$<MKF(XJF`+DKQkHgrMd*M(WL{FX7KG4cd2uck~{3RK%&mt{Nf-~wgx)<JC
zMX>4^JI~i6TiJ&_l1{4E+ipR8POtj+PM7u>zx3*(s!PapM3!hyPC&SBo@JyR*|R8H
z-%i_H%Z79m_+kIwQ5sI)Zu8eW!t%wu-06;>KG~$OUh3IWpYsN@j!&MImNlKHmv;19
zUXvl)AoCm;P{X7$;Yt(bn<7;)IvEHTWtwN@|7BpB<r3yF%|Xb}Be<=UD4IWh=H2}{
z(Kckc&Fiod7NC?v2V+J*9&-?eq<PPTi75Zu@qzOAi;u*L7DYME&W$WsavBN>hvY&;
zJ&JNHrrCc)dRpKFo&TR#T^`=={@vfNu&TeG5S$eTP&0tBSR4yaO0y2d*<;%wZ<jVj
z2w~KfQwXbD;jc$ak|g}Q{H>Sa0LyeaD&|ET&D!m)0cLy9`ZvGij6A0zw*~cKV<a|%
zR;ZDLam%<_sf+Szd68}2@|bQ&<GfAye8=|qsdXYkMCjdZW6nt|yORypm)`-<A9+~8
z*U)SLL44y&63t(b+Sun+bSc6mEjxK;p|bq8)wae#?<!!pq~!+{5mH~b3Pu16!dqrc
zi+T9gG!2(3F370%HCaZsZ+@Ockr^iB&xN1(T+$)5(^kuuR}$tLLU<xw<Sa(BDHQSi
zgCgYAK`dVfGjp~W)}>*kB|l)o!Aln5IrfPRMO#l8)H}QraFi&*!-N2T7@}3lDms*4
z$EWv!y#en_$B^1DBrV>4q==w&Ow|pvo_P6_kOIZPNJ=Db?>J)*1V%^qF=;^#)9DMk
z1wjH(>_$KBbm=MT)-#ceKXaJ={5zt+1S4tIK=7La{?zPN)qM4=z}{5Pol`%lxgivz
z-uG8k31VDcqA&(Gl%SHVA$7=3s)Evvfdiwt4zv5bG<WlRA(Ng!>U?tYPI&GS7sg3s
zP4bzM{<`%bu$XUks&Ic&!sU~LjQ|SHC8bukS0%1UD0laZtshG17-1^Y%Sp3k_<!SI
zE-}qK(z7W6I?#pkJo?nYq`q70Y&}uFOS`B9)8on6Ua?#O-oc_oaz3KZ)6$IpNRTx3
z^5qNrkr-K(_oX<Theu!!8e>G&K3z%jWWoafGc9}&`u(7p*MsTqS~LgD4dRFA=&Xtd
zo&uh2+ir$CqKl$);V8ri4w^K>R)q)Sp)ICngY{r*l~lT!2z$Nn)m&18g!<HW-_IlF
zHEJtYt49@JJQeQYb$6IzIe$G}#Kn(J?zlihL!t_n-H6*H$jeXEHe1qv`GnxWdIyH9
z<?PX)$!*@xUq_9{^7Spv9-m(NKKrfrzDA<x3S}Jy|JS#*gc<%?3_bY!FVbu4&2gp~
zX#Y9gNFzP+(ggNMifH~!M-97gZl!01o{-~8JL-Ev$xp+ftUa@Hl9Wrt)kWI*mJwHC
zq{WS4>gK872%}E<fE(JEayMS=L6>gTDmICmV-(4h$vxzGjUINTdXU{VnPfYfVz`*{
zt@F3A?(qO3;TXGaE<x?f(tLvd<X^CpUeO^ns<Ym<hw4WAoWO&Ic^saX`XS{Pb2{e)
zhRs{Xc<+?-)dpkY(My(XK?`CJrKr>C1fOy3?Y{-a%M%4#4Cl_99=s{fER2ahfdQ$I
zT~*FCPk+&Se8iQ~_&Xmj!;I7xnWf4qflFvn!{l1sf0mEiGp)wpWArFZ{|j&Tutx!q
zgr1jB-V_`S*H|<Zkc%pRe2Xzr%~dF8g+3H~Mb{7{=Gl)0srhT}>9zb4n#2pW5w}-7
zGs`sKR4#U#x_cG2qU`vfnw}k5f?L#`_x0#QF7i~CYwJ86Me|}A_q_T}YcLs`BZc4?
zZsC@kqC=srANQ-~Sdv`SxT!llIevfIdWKI4EP02F(`VQkJMB@^4zT8-qEh=*CNh75
ztO6P@KgbV7f4-Ypwy1p&H6Q!b`qQ7FKBmo^sUY=3X;chrKTYcWWc+^H!^4Dr$t5k3
zPeOf%Okb18eB}gk34n;-Kbf2(D-QBXh!Go;-+nAHxcH{y1%OScS7LpG43&BpJicNU
zG2YiAGbD=9&wt^SGzByaFSdGI$xn&0I$N4-CcXurDL$74_a4q$J8GnqA8;QzvP)8C
zwW4M&ybxt{g48K`MOA8M>$hEESvBGb^1n}cB`_fd#Wd(rFw(LyGu7(m2&6gDm^#VO
zQ^N0fV8d5_(6aR_5A56^ua<jeP5#rj7b6D6=%`O-?OvvR9MQ0H{ik`qY>z>o7XGRr
zi=-Tf-TgO>k|6aRz1OLAu=PYQN-Fsbo8%{HrBMhRma-(v*TX(!D{k+Mf-m{I<&$S6
z>1B_}bmei>LVYN|7X*1|`BrglB+%}_-2?9OpB$H*@SnWATB*PHr}9J*)&AOl%&R3V
zh!r7`u;3Dl6IWMn5lXwG+%7LBm#}b?+B)e!!)ueEGW`l`1qB5SrMlBry{TAoL>8*B
z!$DQli1=|aE}RlIMx{ojO;m=WX&r4A6XZ-@J1{CqF|e-{EIDATTGby*QrAB|_OA`<
z1`c3baI_(mXN$=lf5_itP9R4>NK7?gvrASUqXWmjP<I4>WKim7bS1Xn58@yEYIQqN
zmK^=(f|Nf2D4qLXSDK|n{#tIqXtwF|Xp_{EUcpA?WvVJ{vUy^FrU({g=!AqhMK5wh
zmBkTe*vhrygv9QntA1MFk!0#BuZ|CvD6VN}AjXW{=o`$DM^h=Nx@(HH%X#&K_NdQ&
z3Q7S}CbL}Qp<a=Z9S9O^6oOp~;$yhEM(?{--li@Pj#RDwYTBh&aAIJcc1NZvT9+me
z9*kxdI~6A2FeS4wb8lOf;?CY3t=ZBxYPu(tTj+&PmDv5D@N<TcVjr&E@z)L**Ry6y
zPV`sVsdCb`u(&A>Y@i1wTI3S0dDCWxv@4veZ{`&8Yqm(Fx(oWV?Vo!x3U)^)Pw4`t
zK9F}RC?%U?t0o701DkRALX)=y7(_396^HhXZBfx_C?tSo9@svhpT<!7fJZ7tayg3j
z{-sQ5^l_`3=kg|NbH}G)`Ld%1sSaJ=lSBEEenjdM`62_H(-p~zNI?pUf%VL0O&A>Q
zFeM7R90Mt+jI2vsYx}PkDDpQY&A3!lg>CPlj4?IQr!EOho8=a97vZ8_yLS;0BZH1k
z7*;2lz<35NL4W&#C9FGqD94{&ZlMd=N-Z4^e|4*U44iwDEywX96@!s$pGm0GatXR;
zBR1-KurnPc%okVPq6ia%V)L?5|45m{DZoSNFoWWt`4okwh}V>#HxUp?l{=+J3QbE3
zN?(^ad-ux(mOsBkc%okZQTa*ZlUo2<?IU-yK@LLQbzx9^Y?*Gs7CpF<U8B^s-cud?
z2_Ql@$CsAPp;H{Jr9?vLCn0@J-|?I0%jA9zB9Z&Hs<NXHo&l|-qyAs%r09&wXRvN7
z{{bd>n$U@p9){r+R7s0B|IiKdBGy+&fq4Chn0f?tT=^)C@~tDHg8bKBZV^ZPfC$;2
zw|SroG7T@#H6l6Xgs+nr*2~!(WnBR&pnEbBTuFZM)#aM1_W0OTm$!@uOlw|A)lSK6
zyNm{Aq7OfXXWROfwlSqwly}G^vz)@$XKK<Sdy?4Y6t>&yo>S^O!XbHh<DQx6%#oib
zF19od+U1w@`jZ+G=f&_G@MT>hL%l+(-EfshV<v{a_rep%eA3gea)?d2vdF7tdFw!I
zW(D_3Hu+%KGlj(QB)@02KTFxAu*ie;V9+y$Z<o>XcUJKhb3EG+@}N_w0(}0s)HPdT
zsv*-U`EI5yd~DyC$IP;%oT_)&<V+ZOEfk&?oDOfZmmYY+;+zIhpd0p?`@m?!+G_K4
zVDsn`OZ);+@Ghc5>+=v^^WmX%T_D;;1UBBn^!2Z>c2smbpWm7Ny}Z>ofW13M92rw3
zzEC(q09}h)G~A?g+aWyN-=K>XWb%U<z28ZIE?|Gs!{UaWl4s83?T@>yWLgOkVtcYZ
z^7*5%rGa9SSvXGElFzX!C$T_Yw$g_BI662q@1rRn(Vi(%MnkF5*82tK3A<-*t26mh
z>4-=0;;9LP4U$XKaILP(A|5R<_DQ#Jy?oL}b^;#X6(XDUDF{c*Z}YJ`>HU*z8}l)i
zi@UBW<U@k1IdDho{)eTqG@%nyO*n5q!q@#ME|4_cj9|3ju+*pJDv2mv5R9nr5Yi+T
z*=)|Hj&ao|kfu{&yH>78iJO99nn8ju|13pUGs7n<@p&bqV4T}|n7Vc1D1U<}$LM{5
z5mCPa3-nZ<N=<DmMfy+4>9h~!sH@f9^OXuNg}ZlHn2z9iph*)VigMB6RC5$rb(uQd
zu1l?k_<s`?Dj6KtWC2o|#0OkZ4&Qr`ml_4*`o<*H4zakOXyMBnNvRPq(aql#!vwI{
zJDW>EiJGdLXNI>o@oHdf1@)ZX!C@j%^eLR-AyGu+Z%LR^V7{ZE51Q&xU<J4SLAKnI
z9%XTY8>fL3KN(b6e2Dd-C#Lnhp`CroqkQ;Up|4fMiXG>9KLrqQH)=DiG7^IF<3`9O
zzF{PX@EqS?NQy~G7H&+LFMa$tXI4jK33xgoOwnvJgeL7+#~~xjyzj&TMWOZsIhOxS
z6C7LK50}dBU7}<}N*C^f&>+i;!?~jPUo||!E%~iysN;}`s!hjjM|><8p|j$wu5CVH
z&chiQybnWQxPUx8BS9&X>1Gbq<NC9~NJ;8}q_>K1uEZ*Jlp&)+yyfu4YDSFarR!Hw
zs$LLjynAtNB1wUK*7UEUa&~qQt3tNoZ!`a`XDmik1Y{RMA~~aS%6xH#K!<RE3Qj05
z{3?H+wofQl=C^?@Q&a&hPrKT+g#ZWmlpu!F{5xmzK&iamuI<(MIlPClX8|Ne3O`SY
zvPanMqx1k<t<Lz;-ECG%skQcS{o#~3PkKvZ=al^nW!_?KN=D_`qkupJ@L0jAs^SvS
zD9{$*5iYd*XyQuwkz}hKgVj?hAtD^;spsRhX(QCgE}8V;NT`+oB+w9EHC|XRN|p~Q
zVB&ch1mM&UykKVciJI$!kHKi&A0@P=sZ#8QF>+c+S0<9=;jm9ntzY0U*+f4?zxLh{
zF`i&)-b&LAOw?Pd^(61y%}d}lcEA*+9&u(s3*eWn6dJ^B_xC~sZtEGAA~IU6vAw>C
zi$4lM65W}vTus*AfL4x<(t1b4x-UDdAo*r$$#xqax*$~ur~i@!n;iZVhFNrMX12T6
z8Un2(y}wBH-bftB9Xnw-1PR{wdw#(rR#+rp+ge;9VU&*P;2_iz!J$kouu1Gc`U*o2
zDHz=K;)KZVlvn*7$wr81T_t`C5=rriJxL7KxFT{Q6z=5&tF$ZGqGEK`oDbHpf-1C(
z@TWZzrYJ_={e*@qr!MF$=XtbuL#ll*a%y*@e&iQ`>t!W7kjU{w2v&CIW(qXk+1b%^
z2x*!h;7LFCv&I2f94o)oU<fFdNRdZLmFj*tc}$;;#5HLe$=x?9>BHLAp2R#wleQ+*
zTH@?s>PmkH8N7az1Uqy{4f6gd{>I@=6u>ZDK5u#(rjjn*xNc&-_=UuZE#}YHqoiL1
z8%7rdHe$quM`NHBH$R$5Y<rWoN_f8Fa?;K2=D;{`?o&s#C(7YUfyb2U>8pCrYvp6S
z<iMQijpynXc6w_Rq1gI!xY{eIpy7M|7EPMC$37i-?caVk))}@`1JZy{h>`U!U(@W9
zVDv;NukORX7DL=zu&G;^w%Nlg4$CRqLK@ur&utu|wa2i4Bi%%A;l|_{Wk`~fJG(K7
zvV>#19=>$RC7CI4x|y_j_M;<~**KmMV2-KBU0xC|h+e&1;Fm2+D*sYqRq$=@X0UWS
zB~`=Fs$90kDtDi@IDT;5-#<J8>o&hqz<2v?(eI2x521gKB{RQU&sWK}85x*56b!u~
zLHjT_-k-UxVkOfEmjyZv2gJC%9dRvM19E;WHMh@2nUqg`b1&#F?P%;Au?(z}3Ugnf
zgoE<4brGymmtf|N-@ch#hox07%i<U~RWGmQbTdz-n^#lUE@5TWf-GTR2cloHjpoS?
z<s*4*B4xRqzRK-+d)8z$!)O(Jem%!Cf0H5Lnx@&-bNb=K0Ul$FR7wEkU%5*K^QX3<
zK<ThD)g{izC?tyFcuC5*KOq|*4wkgG!WN+i^Fneg*P`~l54ZaraBfJ;6GwwhOqx86
zQ&7i8rc4)R2#C5BfSnth4>1s^+z)TtuQm-YE{&Oyt>(|S++Jry_Uzl}>U&r9cN;`(
zZc<)~CCSY%n!;CA|28tN8{DmNSh5~wacY0O9N;?bT}XslzB>)jmzck5bhk>`T|_7Z
zxwzt5z}iokbKQ8uL7{`7GlZ32)4;W;(_#Ez{m;|uvQ?u=wE-uAsO_x{1V6NveY>+6
zq_}Ad?Z#Sg()e4?_c(cdl%`6V;i~nC4yi)V^0+1Of5YXdvvTG7-dF_!p;HtPr8@W<
z<owT4M87Wuvd3WkkuGLIAM6x$snD2SL3{TUV-I{;=AvflaEd5xy>^$e+&LBw%gvx;
zwYLfBtKuYl1;0%e(!2?kLrNICGhL0Tw}=vy-T=lQ;6S4K9T;S8!MN}V_x#c61wlk#
zAu&1wYIxpV1(z=prEX;+_@s*xp=tqsw6#0(qPf|qB*woSw?8J{9Rz(~jep(#qAcLA
z;v@S60tyR-CvWB>VD2opq2TEw^7HuZO|?{{tkwhB4}T6B?IQ)ne&tjYdPkc&L4zyY
zsGn4^mP1hM(Ooqb>ktvtAeHs$eZ+dfy!qp&=G)^y1?E|D2oi@>uWX9QI~XhzUo4NH
z!&J;7Az|fO3GIX<`Z%loHum{zFNd_W%QfR#GPw!JZlzWFd|ql7%I^^;#vEF13J2)7
z6xK;-7!Jh$<J{;0rYeXPea8(!vh5iwk0f}<b%d@N66=Ph(^L%o1rA)vU{78paU_hD
z<-!pO%PO;=8c^@j_s5Vzu+7}hUDwNv3*;uUcgOUL-zxonm6*DO*-oaQ5Fn>XoJUYL
zdG+OZhnJdKUFyA#Bm|B~p!Rh0@sKB%j^^X1V6q%E9F83l;?s7<k^&Yx$M|9g2Lie8
z<)-sIFM2GPQYlrC{9=t_dmMZJk)M_&9yk{F!F-S}a<X=Nv*)!0JW1~^BND;fHL73O
zHf@OlqaQ2TlJ$ztVSOGL5T%jl<}@8W<O)gPK%i$H@#bWN@Jj`Q!|7kLU=$=4W?ixc
z3dMV|X5ff52ETFfzQ#edpkUtAg={-}<0gP_`)dt|sx{aCW=N{|c)syv{Irgd$iyJ0
z7h^!&1q&G)dw*o?%WbXz-ykU5I&%xd^fzxbjHpj}vov#C*44EOqvc~|@G%i-U|{W$
zQ2re)eQG1pr>?S!@;PPH)Bjd6q?s>Txc`@%zkUM)hExz&h#Jl>T9Yqt+D=2ggq2TA
z-;`;<By(*%PClHKU9+{^%h@WbIOP+AuBL%=`_OF|V(k(`Mx_5XY}@-%G<GX6T6TVk
z-2_Yve1c{5JhzBCU8qu=qH&lvIrC^ErkN*-p?ml<V4_i4Yg%_8;keIrng_iOTUJqL
z%5Ftj_@&9!ET*aoUGJ$|@k%b9CaL~;<fN6v{#Ym3#ID$P!`;>U`~M;7Dx<3WzNR8S
z36Tcryrf8Xcek{Jq;xk3NOyO4cQ;5QBF&|{yHnsj{$CcKSc}UAo^$rzGka#Ni}yMk
z&xw?Q%!(R<zR1&6k@>3l)OPgVtGnRi$lqC;F8PMp!ewXEMnYbOZYQWtMvO?!vRw`E
zsfHTbyGKmz?zlemal+l+UIvU24Y1k}jy&-by&6LS@4)M!?p=CYb@z7Jh$9H6jtn~#
zhq_WzWK{Oq@$vKW41%w>yO@XWX3Y=gym`a>c$KM;{#gkPvDKiK!O2(kTcW_1zv>;G
zVc3PS-O7`!A=2X=jMAJZ52NqbmC!d}2`QBaQzZEU?L<tM3ubxf7NDkXY-$-?N7<u1
z38xMPPO;@mCUe}~J`F)s@AL`}=$U8udwsv-{_quzop=`?F+p7}HnKWlS0YTFhvimz
zX9XAw;!jW5;Kr!LQA!R{1f2pcE5PyY3|6b^j1&Nc;J;9Yj3%tl>lW_I)NQ)K_^OrB
zt?}y9Y&w?-&u+@8t}sco;7^=vQ>0psYgl84_zyB&ze-sE10q~SD~674&-jES=3x4n
z>?VWEzX$LEAO9fjrrDf1t{=+gN9G|`Kp%OA&yT*9w1)k)+;*AWRD?$uGN;I-_q2*j
zbDZcL0MH^BJCC#FN2=^Q@3G%k3ID_)vAL?Fy5=+-&V$c6o7!F#$Kozb?NgMEHBSuG
zo3}6T4e=`$-hDcVQVI}PmSaif6$a!8pp1TyK(>soC1N!8pee_?+54)l#@hnXvljqQ
zf1FZ?<#=%Iyc=PCLKM(^Xo8NFA*DzX7LDPFd`4=2RPiMQ3xxkD`z&R5WLVs_03De9
zD`_-O2<eb1e@or^-a8L{GLABS7_q%QX@fYh>B!nIDnuSlue?HwR4gokL0K3pq-y;s
zMmc~eAV!k7MGP;EfpDohgi_WKZ8UL(`mN|TGGc42u=-^8g4~zjNE+IXo3oxj;*4^R
z^tqbm9F{lM?#?y_Uf;^Qu$35PNWjluxzOSi@&l%8s4p=JU6{Z;MH&PnS1VImL&=wf
zIWIbV2DHNFN5X*HQ2bkvosKPDm40H~CdU5D_zSZ0Vj(b-KJTyqOAkO|5xDfzsSp<r
zIB|yL<!O}6Wxzv6Ox4xCXt%fjn;umx2r<Q?<x{|PfFu&uhlfzPy9q}MZj_uuyuciB
z`QpX7sCdOPC(y^+KO7NUhOr$qAcMlrY^FR^gc>S{1|tA}_7rV0QaE3m@}-!WTU%6m
z_(#W6a$#WMGOeN{4T8w<fmU2t5;m8Mex`Wu03#dV+ET*Byt({<X5pQNrWI)9%gb5G
zg^-8xKS>v`KHl6+{PQG~T~#W%?)duDY+_O-J6b+*+zM=i^-YZ?u|spSi(|q>1JR-H
z_8fJ90$i&?q|P{QL<0cq<UdpvJ5-h%b--20>23D|l>Lmzuu|H1X)_fHZek&v4Nm^Z
zO{J2?k{KTGyGIh?n%I&^Fq>6>vFz<wiaLdB*6rS!rUjjr{lOJo3@Yi637w-{L?!uz
z2g4m{<MD(!mr5BSo?KeYI!sEv6s_4;&4<}tIngYq;d~)_i`Oxx7_hPT{dhoY1uXP%
z@P_?=&Y8wo(fTtXMJUtAnZv;~#E<VcYj-rZD<P*#?tz_yPf4Px{efjex8xJ`D|?eC
z&E@3)Ds}W_+`9jEn^Q`=Fe<<K=*oMT^?tc>WcoMWE<L?v^Cu@AiUignV~pZbUou!B
zoRE~!M7aX&ke!tJ09a&VJV-_@<7m+1`LOb5*vVdHfQle)f%B)VwY4T&s%h`ulJvJM
zH(QZC4>9^<1<F}L7%3m(11OI@3Gxcm@vb?3gwEA|lrUJT#gKYdvkpNuJ)0Ty^#J+!
zcmii|`X+G5NV4%+nfy${IReuFwPFZ&Jk%d3svd52O6WpX%8LeYesC+WWL)CQ%LpaL
z#tb6x+)avL(VFp%nO-om*#yXscO&rlh?2nPH_a>2s6134!0gv;{2oV0#V?o~CW#<+
zSHf*d)#tPWL{t6=JqG#>deRhNBf#6dlI~;^qpG@%14Booh`KDgIVG)e=lV0}!J86A
zb_w_bh2<}#72Csm1uKwN-*{iZ)T{2%%|YF7&!Q*oAq|$(hZljdyMpeHe%RJ?V!xu>
zC!#1>TZQ6`lKW9~Ffl_1NID&xmpqAWb7_ez7*b0OgEHhQ2c2r&Qv@HtShp6yPKdh^
z$o@<j_oMGUPlwSlJpx+<Eo*vq-Ff<}ue4Hu7;wq^>3JK!G0<}nGV&A2zg;OY2j*F5
z1+O>()ahhkxAc``f4B1It?Oqw7*{YTNo=k^i-YBrmLf+#+RNi6&4#gwvmG<HcXyKm
zNzMx0@6HNDhGsb&lwMMhQe)@bBsv%_Dt?hVQiS9by3jwNawPrMrh>Oh&kiZr8Fy)B
z8ppI4T&<e_P|^ZTw&{}ND4s-^C9{i>9BTLa>}KQ7%U}tB*oab(fKrEu#I9iC1=ow#
z?){)Y;%?V@z|>BbX|!83#gFRdpGE%h!_7(8KLY~!=Pjhn<J!{@J7A{ky=W|e%nUZ-
zlTdWIMgm+aFJ@8XYdBlNmup=xF|br~yzBd(F)(;vMln#9>~5;p9!V_{u)AEJ(7msg
zQP}-UpX~#yKzKqFA-?`gCr~K~1v2t={Q9k(AaJ*N+wAESa?79G<7AT|*^Em=(YSee
z31v7h@^%gl2*5)hGQsd%uM6UGHcBQBdMgDq7@xlxH~gGb_B(w#6QL~1{r)^3CGTKt
zpJKo?3Mw+v)hf3XdSFc3`SC5~{gZ$@sQDCGG8bDIo1RY}2f3Ub;YY?fw3}o;z6Te_
z9r4S2lqqXo=68>Q5ds1B9=(T|A~ZgIv3dDVEehbo8SfJaaLd+2=dK*t-mRgM_x^``
zbVwD~IAntEnyCPFZeefv_2pE1^Z2&1rhYP8+3dVGE8W<$UA81%-<2__^u$y4GR*0D
z6tpC${y2fZ7`%b9_L#=uY8*917KSui%fjJV7_#(yuP`=Yxd85|70*Y+8LhOJ4V(7x
z#HAMX{f;GtiWPmkl0Ppur>nuz2YgxUKMDN&xSo3$1p3DXBY*zn4Mla;?fz>J@ww>R
z-P#o$mBJ_^i~2gpOH<aA`8@B-5kHXtdu_oKeFn1>h1~P7z{6~za<}u~y5957ShJ&3
z%H@X-xL`H!>*}kQy;E-|86i(XvHAPdDW?Qwrv51f`EgURkdZO|hM?z8I&u*=!~o3J
z!VNcm06t+S0Z~73`v@4*W~9Sdc6U<JsxAt~h>cwtCH5%?Z$Mi$c>Qng^L`lf{{2fU
zPJWOgt%lRyG<dAbGx+K80nnt7xVK=-O1fe6*6WV+^OQw8Usw0yshs`u23fBk*Uj<q
z=GrqHK6)d55c3%Ny@Wm=*_O;3Z^O-71?)~3=A(cJQJG@}f#J?8gv^g#hYzWTx7Nxx
zzq0?+Bf5+DM8%r$3B(qd=xs>e^hbD5wJ_lc21jgvHjgx79+BKwE4&T}E|s-Lh-;BU
z>Nik0umk;>NAA``C%HPlvNe2mV#?OLC-37#!!YF{j-b~38D0Rdf=z^t!t=_(8qrNc
zDFP$T8t*Cg|CH{}+`H^QO96zulkdufU5=7kG-ToX4$fdLL*5D|61k!)-7S~VNu8(A
zv(vP0%0oo_D4O&RBj{UJnB}(%(J$8fgaXT-@Ld+r-JTxMpduy%u@bm)MC&Dgq3l*D
zvsH0l^vY_PWQTDU96NKPvkw<l72P_oMkX@1AK=}gVa=Vgtg~;xZppd!`Ql=xx{k({
zV^|gP^S6n^cDr`pS|;gXoOQv66dvTIe}2*l|3t(0m}CV;{rn=M83u(<c&XKrX5Y6W
z`0%BCgyD~}2MQi;ozK0O+)|f!8aP(VmjTQ_jv1!-fX`C>1x?y!B-Vn*wAw_^DCd&i
z$>yzyoW9wA4}CSdhP!(vCM6!B2`BSWynl|P(Pz`&u`Y2HE(%DX;Yn3s7O31>qXwYf
z<&5?}WG!7k2~f}4pvv@$Wj<WksqK8^K@82@oG5Q_dulsnakGvDRtx`xtA){pz{^@1
zR|5gV4xjG~Y+kex$wPY^bW&&7GYaLLTI8)-<ntyCF0SZC>MY7f)ookp*O3i!6=BtW
zZ3Wl>7piYJxn?dag3ocGo38169AkeC{<%toW_L04Lc2WE4J86`ap^_BAGli={rpLg
zSa8|EK)kyg_c@)H?faL<8p14x-QAQ-%{*l*jKElM6aXZE8bwHGVw7J^>T8-R+!8+k
zFp0kb<n7mg*jghc8WwW2j?Zp9pw!s0SGUGKqx2eM?~>E105nl^Y#K|NrEoF%?h%)e
zKDr)BMRnfR2J1qKU~sp_kX*a7_4n0pJcoCx4-d?I(8Rl9tNIh#!`z*JhtYDLGg6`@
zois^Gk*<*G{rjnKg1o>SCMMk;yYJ=xe{Q|bNC93#60K5Zm6&)4fJ`M9H~DwHsDtO6
z&E7sW6J!c}OyYVpBK%2xtPLw7bOcMQ3fxxq*9(ZC=TlSrQeNID38BTW9D{4fn!l$#
z%}OtvID(1wr2omHaJ;^^PI@DM6(f}fajz8V9mm-lySO`73hj4f_+9kpLK^gcNs5?1
z*WbMP(#jJMT#2z=h^Ya6M|NA>O#iARR1n&rBjW>{U{(QeoTSGaym?PTK`!#2vRRxZ
zrBDyEqUsO*;wy}6CC~eUH=uFti_+tgm~*J1r=O9c4F3Y#|LDf6EM2LsvvV<HJX`un
zo1+{2$?xs~@H91;<L4J2N<+s&o2G{O-_-Q|kqjK}(O6CEZ0^J!aQ`~ZN)@N}ee?Lh
zkx>>Da@{%3k+*U-RFvEE2_~WSxfdJ1!;GiNZ4TdH)QYZ)XxyGfSsG^F@bOb+y};Z|
zg()?*)Tdsbh9v*gljSVhHX?P$w~d-70|o5q)(4da(~*yz2y&M6hkB<~pT3SfE!}b3
zu({MNK5*p07f{uo{2q9ER$E-!;mq3&%@`#0Z}y5fxxrid>DF=Y-Z6EF4)n=9|0E?2
z7#x2fzZg?V<CLxAJ1g<0D;XM}d!2Zm29lDRpSSV92ZgMJm(6MH2rWfR3uCtxX*7(n
zOnF6|Pk*CHhQpCf?^c||F~?Kgn_f1nWc3=7UtJ)UkZs3bRP_H*2m!$9Yx={wG>$*X
zFn2j&#48Jr;|K@88&-`vAK9&JQhM+8$cq#d8E+-l>3amRxQp_Q3Or64BX_u)c1^S!
z#_BAy^uayxCIkbCA~RRu9I!jRDs|Mtz3=g~t)2lQ>F4fGjq<_uVI=B&_EzAln@NOi
z+QlqmJP^Ayb-ug?oBBYe0#s7rIp3cMyqp<Y?6E_$_ZOUgm^=mHuTBZ#_yhfMY6J49
zblSaz3~-(RVF-aGmkvN|VpiE;-Bzy6!8+LjVR)MS3=}ScZeUDD!D!q(U!T_mFvy)y
zu<<@XIPM12iOJ&{*?sY6X_A;RFK8Yf9qM_MqS&Cz9et~fV2)=QypjztnG%PpynU$i
zJUop0OkW_is^XhDLJ5|u!;wDhIrEw9l(MF=gVN-(lD4&vf#DD80sbMVv`5+r<`s1l
zn-$UE0AD`VSkuN~3rEXqUL{Z{@UlzS8MCl;4E(lC_|Zw111qL|i^gY)DYjmMfr0<h
zHKQI^Dt^*nG)WS}h=ce0@_>O}*~am8@hmspCpP$~fNGgw-}o56Yk*K@dbp!d5#hHL
z2<UJVQXEG{V!G{i3`bntH%Pw|!@}?Q>-<2}@!?Uki|E_8vi9o}wgoFV)v#a1Sso@R
z4E#;RI;*@j*`<ITp~0FW;AR{u7?F7eU@1_ILrm&M^qw2ORnvV}ciDX+$&xw0kclz0
zY?~@8MGVY|8KH2yFDUlEr>aU9K~G>{_%uU<ZT;y-dlmqHdq8l8j&ANm^@K`*(ZI$>
zJ>JF!59QBNMY4ch2@PO9%}npP%#A&XD>9+RREEu2Vt0Co>v{OjP_2~fMRgdM(|#h_
z-g|9B8O>jjJ+Qw}2FoK$AcJ7Wr!Y@IT6Ake+qG=|a`=g$S%&`n@Q3(B&FUZ6|Cx2?
z$^YBDwfr&Vv|mp^3I1%FrFD&yMpilEO~>QKPSrg0nTKGxTpwqdv!v8Fmv*l;RDT~h
zTv8@=%i<Va0tW}P$rji*d1ChctlK}er+JQE^Kwe!)|%^OZ!;(}qcF!j!}Jb+n@A8H
zLn|7;NZh-#ki@l4Te@NVTEb=jK+SRtHFbYCC-h!N%IfON{x<C7#g3V~!xG&E7a$N%
z;HZ1DEeY4Z-Xv8|^OiEA3X{h3f3kT^Whue;-i1^eW*S~N=#1UtlUn-6>2xW?9j^gp
zh8l)THr9S&Au;%XNaBED%jLm~36L$OPw~GTpaNEvwQB)47YPm$!L|uwAdvuJQ;s6N
zvN*-9fxy?zL5fwRx0)4`%{}|J!-o<6Z21-R{7i=!_(<Q8g2av%{vX6^3q+Y9=n_b$
zLxe@wnf3mbG5jMhs!u}@(Ctq9<Q%P{K+~wHW06Dc3+f-2yKAr~f6GMIi3z|8r11dc
zfBriJVa0Qo_V~}A_p>}YNgOMkJ(Kot#L#%XJpBiwqQncD+8|=5Db$zuNhnNRig{WV
zw=hPfzsJ;ZiD)g+U3?kywGO{7PPhW*O`Bb)XR_%#$qZ}2bLUZD@%}x(&S2h5trWx&
z>1m=JYs3U&uT`2qDPQdrOwMzSGIhod_^+YhYxHSra}%VQUiJoq?5~C4Z%z*foq7MH
zrw!WWPVZM9$H?OFyft15djiU*f&~+k${s*aYL9)ZuNva$yudLe@7Gy&ETz5c*+q^U
zqvCRMPgGkJ(zLJxE#_uk{~~gun+7TjxCy}B0p<<I))Vo&nC0))>+t&2T!1kdQBQh3
z*H#qu-Q!pIjl24ZXifBnOcqZMikD}gc||WkJ^K5(>*}!HzO99nXN(*Z8|V863}dP2
z7_T8$4IW6xp#c444ucGPmeJqwwMdG?HoyZ?82a0wybw0F!6E*QZn5~7-+=k1pBaHo
zY%K_=BGGB$j2>naIXXYsK2(%#jhNjK;jS2zxdblT0mp<toemM;@a>Ng0yQ0&B}3fi
z+*nTy3=K}0!A1ceTFpO~Y3uQFmz0)vQKtqes|qpWmLJP@W^AoMyfOBkEQc)KUmph{
zG}O1SOo_z<NVMd>YQ5dp_SI$*qcyB)RiyeNsYEcOOl>S_{3&oiI{1-)@so#v{uK*q
z!g~zVKq5Am&{mGR5|>}S!6iFjvBReu0k3@FgXE!~hB-2-t3Di0@rM7k?whkuzS!;^
zj$}U>A6Vk~h4#SG+HCsBoX~aSFLG9jkV*(bK@g#eS##Z<G$JWxe!LP)mg0oJ)AI4;
zB2`Bx(}V@a+9sMmy^~8|D}I8P*R-xM%E!_|KplbD5Y)TZ0Dzw;uHU;NQ22uOmed+`
zV}T>S`j!B-L>5LBIxdIhq@#HC#&@MFa}&cgruxnfSR)zH{{(tIV9^%T5fu?5`2`#U
zqC;e?vG>I@dG<m+%A{hXS;C*2P>xZBvrA*zs<h?vPR>YLi5@oQl#<0=z6<m_s%(^>
z>Uw1!w8Z>t+v*w?ks|^}$JhS+nrl7r{C1MDsC(6EUnGuKu`6FE`(6aPw}uX@#Qbnf
zkPpcDOR3s@*b*IoSJK>0k73=jz<AV~n}$W$zK%JCc*o_O8E4z{AtqxjJTPl21JwKw
zB;I&))u9bx1Wxn~0H{7EddY72u|Go_MHn7Q=P+U5aDpplY4*^8A!Ks%dnqWMh3^H~
zEheBz^X#ts;z%L|Rp~zuC{!Q4B%2PEt6Zp$qklaWW89H;?tZRnWRlJJp=4``vU+J}
zg`yfp`KOm8HQvDzMGiXt9_ux$1!1B|9)iF}{c*E-65v%M3oNyBE%?vCu4^|V$P<Ew
z^vvhOjw(*5V2vtrbRJ@q2-imvueI<C!#k2MR3TAF*ZEoJOO<dDEcRNvB)2sR*9hP*
zkI?#dzuT)Pl$D`EqL@hl_93yOMU1lV#Xc)Gm}XUO>Qf*=*4kd{S6%-w+o$Hk5NbLm
z=|!DlCi|9)T5sL#4UT{(14)L=MjQWfqu<IqU^GD=N`@+JBo5yL@)B}yE9Gb?gitp;
zCb%XYu|AshRStq>rJ&G%BM+&42Ayn`-ToEb>EA8h-IcU_U9-){rmP+OJJQz^B0^1s
z3A2@S(@olH)Jl5UgL=H(KL*9`$DSuR#^WEUMd5{{PX`eW%DF#i)QsgIX5`NX;WzHz
zeUxp~&DkH#qoF*I>(C*hyci&&V;d_NxHW5bXm7h2!<G3S=-YzwUqUKRzrig;&PHEG
zU*)rG?EoXzE}~9TkMivsbS+$&(Fw;7fD8xC6g-EeB`2o~S;cz;3$~@|UgcZNSKmVh
z$Ni;9bO2?QV>E<o7`!53tNbx$9FfjRq0U?nQgR(L{R?)oVEYp@)Ge*lfel@YXal;D
zN9MowFQ%wF&SS69@}ITm?n=AoH~g5G=IMnTluaEG!N&CU@hOk{>zAD*+=WGj#`u=o
z$M1b0;;*7nByYa|5{6Y(-<5hyaCJ81j3aJX0|^Cd+{F&3aZx`0*O%k9dyb=TVTuVA
z!S3w^>=d7%2ReyrsRW#i)%)U7O0fI&E$b?Wj-ZQ4VnkBHG?qc5L^7&^`vT!bKuZWs
zEo`iixl|H*H5@NRmh-u+>fLZt(om}8-ccHL+)58uJ=T7`*g@b|%#d)(ca4%kUC>9n
z4xjxL#OnvAb&?duxvr+D-&Q9@Rp~iZ>7@GmbCD9L(uLn<skexch0gPUku$)cn+`WB
z6q@-3|66Y4Gry*9(1JX}#LJk8ON2J5)|MaQ6)2m3E_En6tgW8@dWGf?vw|QGEm+>G
zWo!`VPW$?Dj#m2dz4=Eu>_X_!RveOCJa_<Gt%3qd*bui_13KwKX*Dv-m_3{VeoT<H
z<}iC(C75*dE*NC2hcKJ;bUX2aj`mnQ=|>IO58`TG_5PD)STDiKbkaB(W$JGlnH3~4
zvIInhQ?+I@JmvJWN^Aiaf{_N^*vsQ7X<8KVjLu(uW&-eJ>ae_SiimCRhV3HxJK*Hh
z&D40bA8Z4`&lnEx|K%C+OWAL`h4xL}f3YdBCFT8-vH{!ow0VyYG0Mt1X5u}C{yBWc
z<@rAnSexCQk)b!Z%c}~jikY5ztXvIVZCnB^(qMNzBnkQN%lzZmSD8uHE|kZDG2WGB
zhmMant)(6KQ-;pYgXKTzuwmK1!lQmf%=JYQXUzYqn4>6}12372`4c5rFj@l@@(SIj
zzHLtDD0!KQXNqNUndP{xw6(ouh3NDm9~#8FtD@>M!#3k|m^iE_>$2Lyak-V|#=Ppe
zy8AuzCCj{IxFISD7jJ|Fp3&QlP%LiZeE@J1Xfmv`HICTONE99DzJ=kgpue^c%Q>gp
zw@gnlG(-tFu@(g%S=8A$=Y5lU_icYC$ikrPcWV(N@lbrr%4t(JSzepnpM5&SizsKl
zwh2?gB`Dg$GJ-~AH;7CnJ{XQAnjEIwA0>T#si`G>e?@!6`Z|Zt{An{)e)!35`#~}{
zR6e!0#74<whsKGaW@RcUUhIwLxK!B`B!S7Ys^9%~$?6ebIdZ<Qisao}Hjl`box@<?
zNfwWZ=>PouhV=?e#*~^qpf(}w8Bd!*g!IXtX){-i>pU_`zvroU(y<uu%86%C6v!jp
z;Id`*M%&NnhDEjwgUv&7MDw|~LgWRqv8pJwlWuTw3!2eeN+PJR8#I1nFSGBE<hGJI
zd3%Bc_!K}G$l`PT&9+y)!VH%9x3F+Rf}MGWtgl9mLqoD?<T(<!Z(O<?30e~!STyBc
z>8M+$rP~DLO7<ZcFIrfnI%^orkJR6IW^t@`4&2LpY(Jk(u!@>G=600z$bJK#qn2yT
zmG!IsGgitQ7LoL>W?$;S1@~>~G!AdK1o9wpYV6N^O~d2y{k7V(4eY0#0)xNIv4ng=
z&gt^V_s83JNvHK$<kBKWDe=?f4n`RjE#{GzE5kOM?{s|*AAw5Rw9VbhZvY#&-$f)=
zbi=OWo4kX~k!YkLLnOxC>kN4u*0v|kg-B_h$6H5l;-;dBxsy4+@WG&fPMYBj`vB*`
z-1#GeROHA*{Z+EZjYs}%^R&^?w>l$k)V|w|o0HaGnvA8qJoN*vuip}9=q#}p?=|xu
z17m!LG{03hT|ub*4cn!Cm6B7+t2fOpg5!G84YENRlM-qG1$nPMxOwL=rNW*{w>-Di
zcgX@P)IF|2iBydhtB+tSyu0<Tj!tJazg<^?1(Q{TA|nilg(naGV-y3pAi8^p*i&a@
zWv(=5qDaM(fniH%xg>S1s24<zw<Mr-x8tVJ0l{;uh%vR0F_w}ierpo$k_0~8>l*bu
zUmn#55@r;nOu)}K{3}9^y8<sXRU%$Aym??p`aSfTaZ$%4GCcMVl}3AQWX$*w)>LuF
z@4kc<IY$u+o~!+SvDHgW9qI`)=X1U+QSLx$M9xMTXKE=s-jQvVFpa{9(&738LhfVw
z(!%TmL_-!4O!28cbazbI@ZezAy<nJ7GzEe;amYXo%i3~t&P?3p;n(DKcm9puZ^??s
zQKUcE0;N4$Ll9C$D1@$3dgFw5LndeOAIb+g*%-x8*#UtdTFSj<3KgawbO%kwcT%~b
zWCJ3b=;tT6xV5I)p?0iH0g$EN52*j)s)pvhmBKtf$vuuO4tQMM=8VlI2}L(N-(@PN
z`}8fMu`T4dNwFUm*C{pL9!Yb&`U%_V+d1}kF~xp}*e0fx3kE|qwF|@Mf5`kqG{)ii
z%zsRexG*R7tg@Pqd9B+jVfqqCMTPX|IK}!~rDs~@r!-%~V*Vtl0B=*gS5WNK-lX9T
zwL$vmiCgL)L^ca#ViZkQNg6{We1$l*qP^y{4wAeThitF*aRWRFJx(7YsHDlJC0+cy
z2Hj_!s?FAw?Dhj8(qNca2pJ7}C|TSPWimh0pYsnW7cHyqKO9Lz+Wle|sIUgFZPOQ>
z1hB*wYQB`wg%pRjA73{RqKtIn`Xj)+4g7E$y8Fmkd0S$eKqnK9R5Wb7(T5ZuKbSMY
z%H?1kA}Tz{=uSW8FH|g^H}W9v_Ypc<GRrNQJ2YpSxNd;BPl|qYnpEu4hTIT1yd<20
zf0<@!$*Q4Q_MVxkqSEj1zPU1L_wlYX%F5#wQyWbTO()J~1Znx*%?76z>eqStlTS}E
z)QI}C`}B@6z27k*6Fqjlk8|^4#(lb|usJm;yZ4Ttf<SJ%#o>GY&T3h(SD|e-Vd(_6
zN35YgFQ2NXm*3TKTJczR<sZNB{Bru<s<YcjH(anyD>I_X&)epzkhTBlmHhp_+Wf;3
zoT!wrlArE=9S0)?;@30!x27C&o($QXnR&WqpFgsR5bD34oaZdDOn3d2t$F$t;uuI}
zug%jXTd_oz09y6Iq4!0@m^~!vr*OfsJ|w}ex>ee`dkKHwUJIdq{X%~nC{;8gmPoN6
zhXE6<iVNMBLUZG<@n8AK#vWXR6y7Xeu_Vl)B3{(vle6rEN)cl;@b%(rOu$DAR`X*a
zMa3CRcJ<OZwc@(;KNL6_^tS6yT)boNDAe2w#<s7y|Ct+H_BOUXcQ?ym{>PqF=Bf)0
zXt9<l(JnVpYGw2=RdLc64V|={2_$D||KZ&o6ER<5Ai7ilB=!8x+*w>yl($v%b$>7w
zI`q8R%MLJKr!TSiAJl0oW{6E0YsP+0pdn`vtR~T6$w@OCrIVD6ZosW{+lmS{mz)O)
z>IzIgW(3nMA?*=LdPSu4C7r!N(QL1yPYC`!e6$LI=l$C)f@YIwA27%-=o94=?3#39
z%6^VjxS`jLq76B>_M`a`&MhLH@|E{_vRksyn_fS~ma|_V{$a=Jhm=w@Q$CW!WY?dZ
z>8f?O6B2xi-?Z`3Vj1<^{gxN%J&o3R1;sLEk>9*{rt{mkFJWOJLL!)3i_C<oO!8`J
z>jgP4yzOePS$FiTutH>c@+h6}q+C5m1qM(e7<qNpw#p<l^r$aSqW;+4KjD`z&waff
z*m;9M`zutmFxkMda41AQijkYAZ=ZpHJdt&L6R$L9<%9YVRRp6?W8EPoyl`@bJxY=$
z&fmk8mN=#;2!he%+c5zSKS;>meHVeRb<<mI-d=%vogRLU3tufc-}t|t=`TQx2$X7B
z7#PP242<=B<j6EOp?#UhbIICI2E);C*F%#{ZMBBJeogq|R2PQmI0&T?rpl7Zre;p1
zM}f&rsw|(_*U-2*fzf}OJncX(J?XdeU)f!WQb2mc_T<vnyMC`@ldRp=`IGp0xQ(uA
zws?lyPq2tYkP=G-idnml6H0c?+%KB?DeRDg-T6BMucW`iQ}xJGfC49pKwv!{p?Lwe
z43uO1eL{#||9Cl4aFJtqW$%oGOwR8&um24tnTK)1RQy=YAO8DcL<w?N)|0&5I*ZhC
zBL6eiJTRjTbn#lnYI!Ms>n|kES83p)Q<<fgqh>y7ot*A<Pg1#A<7(wMI)fK^T;urt
z4b*NpDjzomymEwj(1p97N~3sdbf2Zu{dt#nQcMYNjZv`&-Ks&ju?r!183Z;0k1)Mj
zbaR5xCL=D6QbMf=`ck6EZBeBoW6ea3mYNVEs77a_kTbOyW!9SBi;MT4qjM&&?Iyjo
zU-M$6X>xQ^$cs&CR06Sui#2<x>;W-IHU9E$6@iejy};1s!FLR3;Nw;rQ!(6i1K!sM
zoPZX4=a_)9!|7iYi=%`@uY6G}UwuQAsudZAvv!}%nwANcoSda-M|VNq2*C9iXdF}u
z;Q2-@?HdZQ>RO-;<7WP1p&T&4l+$+MytslleRR4wMznO`>0GEojl};M&44un`xCTq
zXWGthoQsnZe=qk>F;n<7OR(mlwShZjqs``9dh50I2l~K#7V~h_Bv>P%e50m4cOC9b
z1X%ds;#_In(HLm$D~(LCnUV=dEywR+B=Cx2SR#|Svq9qpXAdgnv{-GS+h1J$=i!)!
zyQ9Oat#}x-=RX>W3CD`%8{jFS|1$(tZh_sN!7GDuFn-Zlh(KO$3@~g-uAr~nykVwk
zS5)qPFT?Cdf+=;H)+l))cL^!shyjU#nh7Fu`OSf)W%-u~u`RIo6LeF91H;HgG~vcE
zs%|oI(ZOkwu~#J*3WMjiF4R=(x6<ZKGO)^9)khUkB=7`0%;?;VMW=F6Cw(<al!Fdg
zw2MeoZ8<puHF<e}U;<=KLO=mxf^=9UuE{wmFsl))o2P(>DWtSVLMg%_9%W{aB~4gr
zJ@p(fub64}w906?M+g1e@5<gi$y7_qKZ>M3a>^hZc&UXXBOSvH5Fp66IJ~YF{Y&I0
ziE?o4A`nFm50gr}x<hjEs2|dnO><Pg0KN4a5AH!hg_jfLmod9}>b`wLudTIxF~f$P
zNXwc^S$XL2wNQ{5jsJ5=eq`w{oK#;(&{G3lNO|RqhHlA9VoOVwB;RKC7sKJtaa=&;
zFmL%c6FXo)oLN?3XX1KLVXQfdP6o#=V&2e@x-=XO>i$-YueZSGr?4w3?49m7J{0WU
zE-R++YCsaF(I{fpL$t@HAvoHXK0c28KW5_^#*qTf=W|wEu&fRHRM0!t@+>?+sX>Dd
zAya@ewAn(G3yGzHgix>|XQY#4L}AG6t-Dmw{3akQV2l-yDnW`c0S`Th@K9loBzm`)
za=ib5Jy^TPgay-c{)5iIX?cYcW@GrwVengE&(Y&6OgVAE?plJ{0EoEux0^nk(o%om
zfYF>86*C^vf32J1g5w%d6mFa4|7XYudC}gEF36GohjsB#s3fo161rnVFzD9q{@1Nx
z3ZcHmTe%AZ{x@wy8#58#&4Q={DNuShH9-kQk&qVd`<|CIUvHMsJe#>``DDmlDJ9rl
z%>TPuH$VIPe>EJ3ysOPawJp-%8F%KXUuG}-#+>`%e&I|#IZ^?g>QBnUV7U`ilL-oc
z76TiS9=jQ^RJS#a^y*X7==}giWn*RC#3wY=XeH%vJo0w6I|40+G{?%iZnzni_#@`V
z(=}LRi~*dy2gx~hsU>xn(@qaVFIE{ZR-{Dt%E1TWl+gmjuq1U*CMKwxG}>z9%d97@
z9jj$|9CKL-2^RZZo-*<CP`N+j(T3u2R|jnzz6D1iL^gfHC=+~w1(u`FamB5kUv`B1
zPR8rU&z)?E|I5+MY3Q}Ig}#@eJ&mVv{n$!rh(r4nsS*q8b*wILzjek)6&ZOf^>%5_
zG%#kJb-A*)<#L3MPL;6@Iq?`MQ_#d-YbFY-A6mv1DahGBlpx3x5mT8^`+f87+SgmW
zOj5i1b30~h*y+D}-?xd!z$Y*=RRj`{_h}sE?p16#;b8~{H#<;v%$kmW?Dxm{PzTa)
z9ejH7+r6*X(lL@+YAo;aUgjGsnrXBpMA3{19_-0J_L_huKCc72!kI(-^77enrvO>*
zfu>Hc)cJjwAQWWsTWk~SWt6q0dt<NrKkw;yrWclMFvZA-+W6A`_V0dkyAOE7>)?(~
zaj<$SNtXj2P0#JcvDKSL5_p`H-zdI8PpfE*8uf3+krH;h96hU7W2Qd4ES;z+&vTA>
zo}3kV5yJ{`$|LV3h^%&==6sIx%jzxfOQTNx{h{mrYArb+#xWUf$-xj?^hd~>{<LFH
z_k$g~M`mOf)6=OA=as|~_Yr43LT~+QE4MtMI%{Sp(_}E9*OD=LcpiP;)g&16Dz!4K
z6UkbjCnF=<&?k3~6X#V@;YhPApXR&_vnXF8tL?xSRe~f$==U`+)=8noV5M}UjPwGl
zq66+X86TkMwnvL%vvKn{n=B%I?qwNhQ6KpE<%;@qTYk^XvUO^CM)(s1z2Yy=GMv{o
zu4t1Nmx@tDr*ly+;c@aZygF>|lo@2Xe_lY5qM<>iG+~0gS!`;VYnIiLI#0-9h*n}T
z%?+jdWfVWoTD0G&(ZtTR+T2%ig#cdny-&a&^luisn#Yyo@MQn74gR=8;$jQ?;IF0V
zwRWzyO-Rp5f1a@MVd5k<r8O%!R?-?GM}}eO=xmD0Tkl>Oor!PW`X8U4k5?d>KZS}f
zwLgVcF5^&Xj1hwB=V(j>RrT>J#xF`NnEpYKy~|>QJ;ab^ak88V^DjA!Pwo-gCnu>T
zO_P>RnmScBWi&~W2SzMRlQbD>BR$uiYS06tNhW!M4&rYYX51O$ecMF>U44`G0ha6o
z>UunXz)cU?#51UJR8TU;)FexomZEfWwDO2cfeYFF4~Q^kXYuJise=rx4aHa}zqfyq
z9%uKDc~ZyYlh=v@@TM+w+&Yi1n>@XhR8mTY2~w^`Wv3#|9KKift^4)s`gmBdOUr@J
z*2J*WN7LNjeHw|{&fmrcUkR<5MC^@T?0fuVB|LZ^x1B(nRzUfxNIufxXoz|&Gm|WV
zIeMEXDGJWt_<7VB{A*A6OudN52FJ06`Xq~xN@tJ>rwUc9YwDG^r-u>Z2RVjq$58uu
zrXNo0W!eTSPg#t2m-V59!$`|T4zZ9J4eibOF=B*kil)bAY78duc%hLaQiI2fwbUxH
z(x$paIZx^M$TX{yMufK{ub8>DG8R`FRp9`~?!9IL_|>whNURo-6Zgm22vZx_ouLJb
zHNr6_V}mt1_WhW7pSc`GBHp4zk$SC7IrB_sa2vM?%ZA1%F|RkXko*?DTEK~wC;O^+
zkggmHE9A3|o4<ugLm?(DPX-UuNGw06szgzdKTK=pC?%1^x~0q2xbI}fEhnvpAcYDy
zsQrP%%!7l4_zjGT5@`tpb>A2lb?t#3t0<88&QI1i2tf#S+z`)Q7C7h~xj2wD3ZnKP
z@yR7fQNAaD7ERR@t1L{LXJl%0xDJLGtYYRaH&Q2kas3jnfavQ}I)u|I%#Hz6EU6Xr
z1@>{$YypQ4Ii}CZkMm#ZNShG<Ht=BMrvdT6$TU7>fTwSsgt+T^irFL|+?d1<68H!W
zZo)8Usv|>39es1=u`^rqk+sBQ*Lof`Q^*Eyd#anq4+tW7_RtaD%f;1LeHgLV)Gc9V
zPsLr5a6xMSZ{3L@AvONv`qQ$v?nMjiaNle#VHN~QH%P!EGivvtV-vOwS+}h+XuiR$
z=~F8oO)}UnnHJTcY)=sJShZTN)#eqLvzx!w%>?BfY}RlSlE;|7Us~c|$D4}`%a!EO
z1?vr~XPi?>DEHH+&aI~%M3+P@Q=PYU9X#{miDD`uq#1ISkGihPr)7@;iw+s;^~a-2
z;Nm$URuW{|2-&zu5%anWIvqDZqDzL4{zQqJGIX9`BQSO+`vbHNL#3>?7k^d83-n%3
zIP^KtC7CqHnRUolESa24(w<r1$h~^~>XnqJkV;7X&mp78X=D~BGNMmQ-G)=NHD(F(
zd)600GTxzNLw;Q)xxU+6%|C)5lHvP#ba1a<y7~o9`p;p(4TQ@U2$y9h$=$_r{)Nst
z(XH$+`}?L4O7r$q?-(Y-_*}JY1NFIj>G)$>0d4P$Ch5~x`U4Oj!e))mh{HB*Q{5fQ
zCtmP?;Ta2UXg$77g!Xs!Pg9a@)MXzc7AZtJtY6SVD_!pIdJtnF%4KN~bi4<`Up#)V
z=th97>UZ1en11SFlH{NPUY7SZ<EeLj_k2{6>*F%MBR6|hyQ_~Sr8r%q14bT6a|#JC
z;?>sKty*dAF=>%v$JkZxvXAYB3mP^$k*l-oI`i|X++J(t@N2Av#0Fbr(b_#j!0b=2
zr&FY5W#~=z?!`_bR@A<Qb1Kd)k{Ew;qd--<fYST9*8%Cn=kN#<#U^SG=VhO)zengv
zRh6$%qe`|M>>`N>DcZt3BvE_5mFv0dl%=VdAKNMgFH2kzK=Uk?PeRMh5Nnbfw^`O7
zUw`}a>HItZOO^#m_Tz0fn@86eT+gfRcVoX%r&PWEJ_P)9x!z_VGHy;@nPFM%qEjj-
zGbrl&{PsM^_Q#E#kwXc{9npW-+Ui!MA|o?64fzLt!DjAGStkSRxST=N&Lvtd$DBD1
zE{MzCJ+`-qiu3O@Y>9TdhH{&Q$!Nx2mCwgi*}`Z@Mnv8o^ROcwrgx<45h_~nh@F9Q
zcrxZ@$(3EKJ<RJLKCh&rab|;hm`%IiX+wmzz8YZ5O^=HvkX8sPx1<D6kwmL0!;1Tm
z{bF4PG{bh@1DB{!b}<%XJ`NLCB>e$_^lxVU@ClbDWcXy(fshd<Y3G2}sqPE9NC-+^
z7%dUM#d3u1+s&16D1PhI?mL$WRrln51^UAVc9TKzlNKh*&jVK8Hf(ZQqt?kK*);i+
z1LQ81x1oi@>AXzx1+(h|+6aqwnv14qn^~E=b1_N-;*&<Tc6}??rmS*!@8hBv%5Cot
zxJ{rdY9eUDA2#9!2WeEb=;#vnwU9rSv30)m))AzBQl=}!p@k@6B8bJDX%mm#*3czY
zZjT>xTUxT8wZ9UJ0gIo>1`5S5^8WK~&I})yjScIh^7IW-<;TkPZ|7AW!JPuZ;BL(!
zk=hWPI{n+PY7gKb|46jYX#asbNlt>haJ0uDB`gWrY-@(Kc=Ps=pXRD-@w|qPftROu
zQaQk+Or~IA;|XPVUyGjVAG>Sn7cR1jV%pGFZpEshQ(?Eg@DIrHQA|4<XAG?L`~`3N
zQB)~AS|)mrFwcTZrPONW@oVP!1YN%Yx}2)};B5^d%GkR)=j}}W;R;he4ja`N&={_w
z{ClbWUw9HIQA>^RYmfXU&>U^+nwt5o3O!vzyAofzFxT7SEZ45FqL-8)6s#J;q+9;<
z-dY_{42hqvVB#>ikbfh^jP*~j{wEiA{-h`|S*uMjSg>4EqOzC_(Ai(%n4bx_IscYy
z@*>YAjx5**s8Gu9V7yzY2n?}mGqOK_EPag+`x=xivoDtAvp5+;F<#-=i>L83EgyIf
zHb1W3YPQyf&eYg_f>TvjVogyY4VbAhjZcHrAsDHOqyASO8DYF&6sXKs#~brt;%Cy(
zKYec3YL%o0)Tt{!o%kS{M-e}NI%q>Q$uc7YCON$X+su%Wf>B|4p+%||d4p`>{_@;e
zqM^R=XlO2wf3+6PwNjyCDYsqsn?plm-uJ8IfsoyAuKQ(!ZqE&h!H2rKL$P#dGSYpq
z>#y7n#y7c8Bbq}XlKBakQd~mH@)rg-nuuCNN~m!2-nAqs%&)9gg#_0`52(#3#DqIL
z(mCLJEQNF?ao7S=f+O_Zb<}>VdNto*1U8T<6e+~SZ{}}75V-z?Y$?fqlP4p&=?TdR
z3EN)OwgP?ytadO-MU#V)A8BOAHo%p6xcq3NGK~WNpBJO8_}{H;b){{gkfmP!vkobr
zQ<0YGTrF#T9K?A~160MMmk!<I>Q?3cz5nn(?+1;nyD%_027IO(Y;iVxBNkI_l>~6n
z)yJQjmQ;@X(D!U~JV;*+>xRKxE$}kICB2PZd3Z{fT|AP`&Gn~8IptlFnx<A|ZLQj-
zLf7SM27ZB&b-&(pPIhtLO7t)@4V@2*c4n-y=GVwGT0tzkiMBdXM#@wPtc^(2?wwJ`
z&3>`#{o9CX+t~d%n7$B_ke(tIPmjxA<1`OD-#fEz+o(hHr<gXF-m50;I}?JM510-k
zcUlF~EWyNrpD<c=GX>gamp5%3cXvI^9~i0vD#vQCME}Ell$GCNL`ukd{!3QTC{|&8
zapU1YN3R-;k4R2#7Qb@sKoA9Zn}2ug#QcAt4ip(K1m||gh>*A6{iRE#JT2AM#S{w_
zk(%t_2kg(U1a_OJ3%s%P%pOKe$v}|t{86ci(B`Yr)$ptI%AoC^t(Do-=!x64)ha)o
zzVqK+kopL9PhEQ+IK=^Qq}kRkfWzA^L2Xg^GZvl4w*eWC@BFCzdJ@PHYpwhN!m$w%
zZz~%6Z@q03-_(h;pB*7dAP3C%m*fLk;9R3b-o(BXK5L8ncR%G8F-ohmqp7JVZ9%&;
zWaN==J)Qf7vfCt|78?nywRH^-1Y=YNva1A;z~-1~Lu)=W6D(=-v4hP^`xkBL2Z3ex
z^2L?sb>AYhg?M(nbPsQ2zQWjF1N=1|<BRsT;(n{7OZUl76^~XPjv(yL@ax%@t83>N
zm0prBb$00mpVV7kNf?2zCrf14%5MOu5)*=<fG<m!mEAf2^?VZ15H64@_H8Vk5(ArQ
z{FmREsXdZ=#jV0lb@F-BeYbB~kLlCi8P8&~S97zc=1g{F990IGn*yp2ftPsfnz}-T
zG4^dsjI0fQ(Dl9CqzH|DFYd;^20+w;o8SGfyXj`O;`iEpi$BspXqClKn9R-lTkjE0
z58xH`3uMlq7crVa3PP`ghxvQ|5OwZpQ_Wo}gV)7&Bj+gfPKWJHRO{3hPnm!qHUt7m
z?>5#T-Utg&mm0DIx%VhZ&#)s+XfbC9U=wtNf3%qiQBX^Y2@QX{f2mH}QfKFB0k?03
ziF6Gr-YKp0k<lc)c1b7aWcq$;`!q)eueEr}c@gs(CfD|5RMK;7cTytk?=!I9Z<aUB
zoRkn;6S%MH>R&ISl;jtt$g2=fI#h?wYm`l~5z6!O{U}_eTR(Ottkl*h&^A}Da_00h
zhuK6Jkxn!YF(B>V)#Vo@tGp~)1+lQpMotX_S%2r@{`N=x$tk(`I<P-SU%6|ji9E)~
zGFlRc@pt6qTJBfEY~mmq>}$EW`@bK9k~4@lR-e}yKo?uvIkA>;yTb{%m(%Bd+`ddE
zh1Kf8%kR8ngV&z2Q=|#gTwX?wizGYKqM2hL$f^v=4glcvC)bes0Q+Qp%8;f}i~nFD
znh+D}K0`b>6wDNyk&BH>7MzC+KN1u~A$Xb33IzC@&@Qi3;=gwU;DP>Y5aRu0v$7TS
zEJ`uKg1-07kvmeNZpPT1b`08egPFNor)dt(CCAM%?+r-bl9)1jUODaj)h|=_H|X@c
zWW{Wu+Uc2s_Y2ifN4Umo{k72L{e@(cJ$Qch)b$ZP-d`UX2)EXLk2f0cWQoR5$P2JZ
zm08)HY#Ptb9@Z~n3wUfYpSBAG=`a0uMe=>MilV5RQssRN2|`A8c-ZQ*%AyK^X{EeO
zU?AM==~vZ#DU*r+^$Aom@4qk4$f<>2aioi__5e$i1PCEJ?ac4)cp@k-Hxn&lzqW5G
zt9GCGv-nGC9nJ(}UN(q<GV^XEip#|-C1D0ny|S{dU0G}j(@07*zArP-!e=*NN4FCH
zM#7iG7C<h4B^YgqV5=Kda%PT{Ke5q-=Svkj3TA6r*R*Qr8<9z%!h+go)<ma<Jpyvi
z!keXOF$}F*r0Z7ncfO(x-k8qv{MK9UZqykly6h<L_u0O;Pd4LD@2TPQeHEIA+gd1B
zvDDK@s15BsXkCZ-LOC$xnkafv=v;hyPdAoi#x84~z%D{gqaydSMh9#hWHieC3ym~}
zXc{<F$QKza5sZ+8!u%jstZF>>^ATneYmA0GHb-vzRU;n0Jg&Y_oc_Hct2|!8t|cTI
zJI{L3>w1z@5p%P~L7mxrAaQ6|Y(#^NaU|`3FhG!sO?ER!A9QB=LRm|u4{?f3;jATF
zZy|zxouQW05FqC{Cc%aoo)6RwxjGzf_i1BaQ`kWygCJcAD8+>eveCaOhcKtwUpDJB
z3P(p)-4pNMjcDJmap%E>n({C%h6cN$|9@KxxPcZeK<c{Gf4AoBA5zKe(ReEs()XR*
zIfw+F+E-Rwj%6om(tgpg1{EG|skE4c<f{k!r=|$VP~R3#YB6$cs<~Q5Yu<$I7t`E8
zNNBM^a}O;UI!RtAqTv8FE(Kxe!#id>nt^7f&<}Ub9V8~iXs?w}L!`Lf*anlCd})iR
zbA4$`!Vkzh#$uXR*|<#>3v1`s7VfdM2g%QDQ0D3nb~=qXuir>CZY!5H_BtcLh|9ib
zA@hBuib9oEOEzKl#c_eXrdc{qzqVa5XPy<|F9`wCEsQF#h_QCo)GZ&kcHVaeA+f!u
z87>{OIg2&tey=oR##wRY)Zt-@RTum$eZAQ8=3832awTDfioJ_y(S1qQnu)x|aA*_Q
z6)|ze5_&H9phap{K?91N3bceGO2$T-eMfW2g!ro{a>}eaLQpJGseCQ#_1iyGG1E$_
zxK2q1yS}I<5=bZoobImvU@V%SGgYhzm=|bphXdb315xT@R6!EaHzynWIZp;~JdCiC
z>4Psx(}9}aF!QnmstH`ca6nX8L<s@_9O~Q^#&ZwkwWnhWDbd7U`(YJjpx$R>Pi-la
zu@RUfks)ivHt#?X-g{WuUs~SRh!sT=AvG!17p$D8NSRJap^YBv7m-`}?mBi=M-k*+
z$P5Meho-r*g<~-rw~D#d))(22`6~|5QiI7jV|GVF@Ymnnor&Lq1Bi)fQuGd_QHFr@
zg<qdQ|1hHk2fc)Qi1!_5F;z5nlryn}^lrH(Zc0et5=o=2{&;glg$64LVHKB{1j4yc
zNZ7PF;eu6|^B7WP6Gbd0UKgMS8jq2G%Ui#+pK+yU(66=dhshY@jnV_K^}wCaQ$Vsu
z@S933#DFOQun9SSVn{kU^LzH7MK^XPR%~D0of4oD^3jm}cMVSTlHYmxKtde3u`?p&
z%CNi|cOS3nE*?@^Ldo>^)(yJ%Bm-q1CN!^Fu@;?~c(5C!(?k~pp;)Q!G3pG-um8;4
z!lY*sl~RYWniKMlk!M6~auexHk-}#$j!<8DdfR4z1Ac6hBwpc19U`ereNH+|7RJGj
z+FxB|H7iFjNRAB!d7MkiaWNruxsXX>7vRZKG1=3&^poFrJYc1*!NzEdlPF;nyTKg4
z>@eG$ITu0(zkVN@8*CdkJhmAONc2=4wH;|dW`|p>((fC&5NZ#$S)twLP{8-lJ+JT#
z-g+)vvwNLBHnt(>;=C>Cwe;?p+>I2Y%Q1Aa{B81~Zl<5ziWk~@n80HZ7%13w`#63y
z+(1b1MSKFw0KrdVQZUK_71lL!ktN{5*3v~H0UZrZf%gBqfqxy3R)LoJiRt516~PAB
zW*Mrz(m)X<yGhiq7^+s=O1Uagz`B1$m+~>)BAtqK5O*fXjpmj&mt^BVA_46eghZP<
zOL~kXq|gi0E}nZHm%r&>q=pdWi?TKxA4(Jwux^{wApsxi#?FOr=HU$5(P3YYIHUn1
zY}@jn@pe+5Nq0Zu?=MJ^n*kKTR0F86uc7D3=`_*O_*+4-+Fh+b1L|bbIr)StCU-jY
zbiq1t9|m57G`^1d5DEp24ZEgJ<;BlMXiS3bq)u7=1Z&EMZ79p>sKfCEc)DUo22+yh
z8QH#o9Xqe94wg3`w#K~gaXL>Owm0w^%+su)lvxTJx3&GD<Yq>i`O4N4)=vAW$XPEJ
zOo4$@NKu6~t;i9r!%>|sfogSOGYxLnGJ`m{BhkYH&5m9HBfIL1Jm9_=*pmH`@<s%_
zFM)@Z6rt+#`6OgU=2U%8W*3E;otg=xJaRMfz$q{c-w%(`gVr`j+iYrIqc~KQuJGR(
z`yA)y^@Lvp%(E~xAz2Zht6WT3+ZKsH8E2K-Iel3k`&`lZuOvF`s%vOhGIDf<n1Q{k
zwxR;+IC<Rs*taS5Kc^JrnAsE8x6bW0T!y#ceH8_mrbjF=!pi#OGPJ&1<S~q0nl;dA
zRaE;cs~USf?-)P-T)pSb^4LZ#$*-w8O-<Q{0q+9L^h?PM0V!q$YQ<*rtT7Y_I_lsa
zU}BElQP<@e*b<EdR0wgVX0}HZMP<|*U(`hYs7NE%oh!`KPH(Vy!Va8E{*R=q0E&8R
z`w9q%ASqoU(jwhmf`EW@3rlx*DBTE1EC>i(y1PTdm2QcpySriGJG|e_opG)M>+b%~
zdCv3v>L8sP$O(%RM-7@mqGC+IZ=Wz53Vd>8kalFahQ_>)KvGI4-u#<|dw*h1)F4vd
zi$?Ws#3F?&O+R3v(pB<xa<uB-9ukV)mwge3XP%F|N#&b2<iZ@C@I!;mopY=tO)F%2
zb4l!IoxJ>$pF$!-y%5Obj5Ou+IJbmjyKkzsCU1^^NRk?33^aWBW9fHZOz-g!=($1I
z2Xtwj#!AT5lXW;fY|7A2B%u8Q$R?=CBvk!JbDZPd?nXyvY_HL?=<;SNadB{@;v&rn
zNitcFg3HsN{4%h8BS(`^ElKY06`$$%fLXWibhph&d%cnUsdi#*?$+67dpDmU#_Y+}
z644aj=>d68f;Q5yxn<kHHj$Z}`RZN5!)+$`6*<4#L*JP5Nz$^_;}xP<hvNa7<RMna
zt*dEU+jF7J9<sMGbWSa2ja_$pXy#yr%b6QvM*qi%nNLD0SKX$wx+!{<BEc@ll2zTL
z_MGz{W@7Km>#-TW;J7o0a11Y;&^dXkKyx+|gHFT>FzD16$TMh*=h_VwQ6;ilj?o?1
zI3`EJ*xHGs_^9%ln&I}ueEOlaySpWNhUNgWXxjuW0}o-JZ2aGEs*F}-SOa;z(5c}!
z#T>^9LK7MUC<KzyJL)gGKeMxpZv;|hJ`<--SE5-6>{XNMPLOz{?P(nJGf#9Vs%>qX
zOR3SLKCMIfl*vshrKILw)Gr9SH$|>EML9yEUPSi;%Fxo=NG6mD<;Ok;BY*D?b~(M6
z#R=WpC|HXv9L+?K7%;{!UIEz+_L@iYYxFOsg%Y`Q81m(RH~{p-F~hh1Iib;-OiLe)
zml8E)AV#rtj4m-I%MwGiTJpbf)ZUukYYIlnb%{gWM?#ssP^8L~j~upa+^S+KrW^J)
zKnHl8g))v764v92CzqZZ%wYywxhj0FrYNIgVh0A<`6>%8g^&ojm1Ch&GotYtN1J4~
z;z+v!%viG#muJ$6DeWrRD!e3=ihwfc{V^1-im%3O%alu(_!)odSeDjRz&6sWwChDV
zB~1cAnsz3bY&DXY3R0s$I!#FDT`kr}GAtSTD%nei#k0eH3D$3UechOeX7J7(0lu=(
ziL`EWPJo`LD=-aI5lDY)KZd^t`(!!>rV4|}(w=<_?@y1xM|qk}{XJ}#T!c$OB>C55
zodu7g9xsbMp?3nIdK~CJ6cc+l@xdyu)KVHhuDhk}a1;jQ$s;6@q*+u_IwkkkRVH*C
z>{HYx=ao{LyH<tI^+Z7>yr4tyryQ@b<Z9N-WR4sB<9QF=_GR@Y#E~YZ==~mMy;kMe
zq>l!_sGuOKOdf>FT67ze;zP9Y9I;dgQc?%-W35d%9YZ1+oo4v@^lS1m{M}L&W;?3%
zjYImbw34!#Q6>U9U@vS)he)x!v3OOD_JRf%5v?S~P8lhbIaz*EQ+Ucg;Uxmmta&5<
zp;Xf&x6$=$CCLa-t`<TuXIcV?_-s;=9qwMbjflU3pvzu;lhjG4E{)>kj(fAv-xOG(
z$CD{PcYeFQ2#=@5i7X@+6zBuzKR)bF1t22ax(3MDS^8sPTzHPr$D=j{&(SZ1hPDpr
zBWQ{+@;@oCaYHu?S68R&LRTA%cw!lX@>GOZ<Di9|zkVR>GA*~508Z_qxV){Z3TC6S
z-Q_0ADwfy%c)kC9VkM(bj?O8<i>Gzi5{p~BzBmPb{XBYSf)hdPl!KmYpPlNb($D38
zg@$}47f}9h=3s@75}bO&67Q>ZlB6dLLX1V_Rn$d&?d#L@!Q!zIIUZ^1zo=etmCVvU
zT$(oOb*zV+j>4yUvEFta)|t~zx4)r)<?7g}ELbS(6jwKDbk*rqHKLqq@=og&s}g?#
z%j4QO9&C8-@VH}^(h#}k$@R7B@&BA1%M5j1a1z+Y%9|&5O7ltPYV%r72mmDG$3L=y
z)BrOE7eT`0p?AyPPi5YJXTBJ4znT3SygWfYtxev$<SA0OPR)#0#UzXuLYo<E2QxdK
z71;kX#8g44fugc>bc*KSb%NxpH}zssv?^@Z0}!4}ncb9*70o=^wAlq5l|O!0w>w3=
z0oR9~iNy`}aDYj#F%GkeiQV5X4gicSrVd9?5@R{YuTn-inqC|7+$oq6C5fp8$AqR7
z4$j+S9{w~SY=A#bEV0}O0@ua!0!_HfU~}?+PpN~7SFe{RAnipYl@D9-pH#?JO8hgb
z^s~0>(9sncjN`u*Z2(=4a?l5FYJ3#%rK!x%X@?vkzeQ(APURxg$74+2MwX0HTzkUi
ztz#au`m)B?rax<P2QRXim_2btHdRlA((Ds~YGAL4P}b`0)1El4@c%y1k(pc2Do)iv
zo7=?2#02nHr+e8vh*6$Wweo%_wmj)0ij7y;wn*)~ZEyLMJBFb-js1#*q~8ItgX+@7
z5@R<dp7hq~8YS2`UXAY0hr=NwsL`JkhM;dvqv0$7>PA;)49+#l;Ek|tOvxMkCMk{4
zGZJKCTG)4D{7gMDyoY;ihM20&IZ&qc6x!#9B2Eo`WO4s^X}=R(2E}LL+>x3q<x#F9
zk~%+m?+%7po20b6vrQtP5(O`4ohjNm;PP!V6G{i=8sUB>*Q9L>dgm%R3II@AlVOz^
zz&q+F6vmBQTmRfi1ekwPnos8OBLqP+D4}`z7=jD-1>a2yzOPNkjoQ`=`#7X@33An-
zqaPuK=2ia*aeew4S6QKl-^n9Bisu^*@y}8OyW*7i2?5alQoleCka8Sboq0`y^i+S0
zgxzE%B8<vIZI8^QRUm0fB3U&|cDgN`WyfS9Tt9udG%PzTFG3+^GlhI{vMdwICdSGx
zoY-!kSy*(kq_an$odjwVn?U@v0&F4jbbI_goRZ`vXI_2hrLP_kDq|wYc$NQmk>H}E
z-$$nS89FUVrc4mThE5i_o25~@8>avRy<8;kN24#&aU&3`Lvob0jQ?cvZAZB&O3EaQ
zM|-f5#v1u1KS%211{Vc$kjzLRRYSlPT*1Z>UZsll5a*?7^o(6q9s3dPF1)$gb*2Dn
z9HlLAHdRBGr?cSB`IB!6r;hY8&l5@GS@4v$#J*<#%^H7?6v320_R-jtB7mCsPOrG8
zb3fy22}kj6MV;1f8+*=n&%e0RamSKx-0yT3f8S_0Q!HY?HS5-0lZc;56M&w7#xI7%
zi3o&b_vv{)2m~;EmxU1v@{!wlCx3A^qVb18fUtB9`sjO@e!L8HD%ZfuNLM%6)Uru}
z18}B1YzN}Q3^c~PTiGFbg?F{b_RDDXyKr>$zu7@_A~%;tOK5Wq4Sg%Mw};dS?dMPW
zU5@lKr9QXYau6p42b&rjD0vTGcKVB`E44`ip)S0#3y)H=)poSgRY(tZXxh{p7LU`!
zbMrKU6{{*hO<gAGzi(+d)aZeD2HHE@bQfpwW%?lUGFPVcpZNF><uJo9zt#)Ln1E=j
zE=maI2G}7jy<O9fA6xE%yS74R@fZ9#JRfpAfxj5yS}Mb2$tI$+=I+1wR^|g|fmI5W
zVJ<ZtJ@A$m9VtSR@#PTVBe|(rUh2F&#xy9C{JBx?h+#`t*a4}fBX^hEqS-W~7ooWF
znNsC@1>&WCdCaPNXG!N3bN3p#!57X&zZdT-!sWFw`9t?>8<ZbdVdIOm`9ota|3-2#
zIm5@feyX#yhm&bt{m#*6C3bu`Mm&LIoIBX|zvlh1_DL8xORRm4{;5YmprITIayVan
zm|{20yI9_<keeJ_3qzQsvCbW_$w{7bmcIR_+2(=?aEPl}d*R5<o2?LuC&KefM^F_n
z*3NpXiM}eXk)?e!6M#e{mm79gksEmKGZ>f8sl`jvnPHHNu*Vej%2xedv-#H14%MDH
z)XdEg$)U#hkCWZt>TY@AmIadsRh-x+J~8d!ES7UWueS%As6exxht+%Sx?7VGgn_zT
z9=hL+pf@gK4(b#{Bbfa!Bl(gdt(yb)y5}i5fm~wfQJD;*1W&}4UT<)g4jm|AkAEC@
zV}cnmxh>5}BIeLp{^I5EsUvx^PNTFlS$ZP^ND)rfs4c47G(L<I2)v8*km#x-AF~WR
zF-tJ(>aNq<;XdU&$BJNz8>DBj=dqkn+$gg*?pAZre;qdlly}!;X<JPJC9<@5S@0}~
zx9}?`kykZN`mvyG-cJg~oeG0-kCEhD@=_J=Dwn&Vl0;-|Vsr3Hy>=09J3sxrO?)j8
zFOw6v>xCmGKqeWVIroJIs26iJ4gpUPPm32@NSkm|mz(5!Gm|cEkA!^|^;Uut2_OT_
zJjvxH<2JVCMAzETpMT>%kzl@x$96=O0djKLfGDOv%DENgXUN#nQE}?|-=zbA0f8Zi
zB&=>q0*BT_T$<1Y2N~}~`HB-~=?w-=1hFLEk8j%lgv;@ygm7+9pQl;7k~4EDuo;sU
zu_h>xx#$p1el9leqy|voFDs*@**;?uxYP5yuUdMNoN64`eAG+cB4owfP2l?CUmr=j
z69l{zfc8YYsWKeWEX*G~!q9o@^Dn6g6dCD6hH~Cc1S0g55-*4iu8h$=;(ABOpV>C5
z_TXNhbg^5XqUy^5e~*r|Wjb|v*?L}m14FEdTrU&E>}SKcq_zpQUkAejEBn$p$L$2)
z%Zc$$D5ZBLh~Wf<SkK2On&z+<eDol1Ty<|Byeui;Fs9>a;9V)yvLF4|`mWfK7Y2MG
z4V;f~LS;U@a=Wh7HZc52YSwqMkJ${PIk>ovqCm!0ZChRWIp+i?N$5pD$Jzi+8`V)l
zJ0I*sBG{zw%Z=F6H+k$lP%zzyD1ppc6CwGj8c9Un!kT40F?+P+hYyX8uIXUn*3vDE
z8-$UN46^aW<-lF9dJTU{6G-a+%7K08-B{IYZt<HM=28reT}Z<o{y@NYKf(8A)d*@Y
zYF%bvJ#H0JHUy?t<i+UlZK30!A@_Skb6B<*9T`3KmMQy%nY$9TFP0Q~zxb*!)^FXz
zKtaV{_V;tn?@Qe+E-=l2cLq9wivna%8XDGj_w9Ei$>np1+cv|y!S;I^B?_uHnex=O
zaod%Pe*;43=x`fIMwGjWs|q;N?r1=k`^K#O=ZV-Hbka{F(yvxzvq@2D){!h-1A;!I
zph&GPh=P>Sd-7-aRDOD}9vj`3OHIuJO&zVgt}V3~ANHOs{8g5P=`{pz*_S#=*wlO9
zU9QF~+VCI0n?;)yYV#=s*#*0gv_e$hQ;6Z90J(Umy}qe$W5njo042q8N2LmwDb?iP
zEg-H<If7B3dI24mj=oQ;A;%ZHM8IPpx4FV)osO0#cc<N;+OcmC=-`e)dazb)_LA^8
zaOvX9iUw?2d_3bnv6WIS{ZNg06WhuYiv~VXF)2CB{v-Q1?(Zhg2OFxFb)=-aTk)k8
zX(+vIm?wN^o`aT;<l~QYVqC|}g2YFURQG{M%M4j69VdJGru+Q`v#b+?Y^LmvZ0pnQ
za>O6b>AFbV@uODdRSqZzI=aU}?o0)WcAQ9VsVOnja2sDFZ6rg45Zm5}3pBaiAt*sf
zDfsO`YLpQJXj>0&?{4hdadsLpkb2b$dOWVCi3_8?l`;Rv=|~RisncWiYmu0$;Xk|X
zB6fWBhR}?D$BWN`GP5s^nKp%=j{ueN)pM|QXcKw(+^l}~LM4<knP>^8lnKJ^5f{!`
zf~71W+QO-KQlDmTf?}$&WK<i+z%l1{eSigkQF0+=piNxUMRFF$S>mHi+OKNTFt^L<
zj&8)$EVoxKP6K|NGn0%2`af}|&qp0qOu`ieWL{@B=yD#Ag&WA-=3FJ}7$EoCS1q)P
z!QX|h_lbXH*^VMnQmrOp)aBjk!{TC>`^>oVj9=<C>4iuUir?4Wn~6R}HO1w~MZRFW
zf`U{Dp+Zh}Rk3(!4I(Ch@+UgWn}o*y=ltB*F<OCj2-ruWQbO{W!9lTMm0rA=48mU(
zUW;?Q%2C-p+K3%GEp0!?E3}D97#>zOC?79z2Y7fAsou2*6ig2IoX<|WELnZnh7)6x
zpJ#WR)oq24>gV2qg~qZt4VD7=M>8oRZlI3I43p8ojTO$=3^nx@6eD<M^429bGA!(B
zuO?0ZqcykQ=JEvni}N&;c*a1JzK&A~OBB#<cD_=w2weQ;p!>wk<ApP>b{s>DkItDP
z;aeG4wNY<85j8p{7iQp-_`+%G>ithI6A?>>;2$1J{`M6#$b|}9V=NK8)!g7Er9RVZ
z%3{u8+5^hyB$G`a{haviOLEc!OXFvOyT`O3TkP+pUXd+4SI^e*d{&@r7eEC~gs4eq
zsKZZP-l2`xKn+=(w@*lk%1cy=gTICA@wiA+vgQFrha3R_7Dt!4%9`tE=mMTV6{55h
zR+k6)UUm9NsC-C>NADc;o`Q9q+uF2CihX6Ji<71RC&c$qwpP-B@nK4=C+rhauTZ!c
z!<mBDha!Hh%CWnM2Hz2HO^OVGMp~`rU9y&h`OV1Duh@gsm+>@lLp|)egwd&DmZc&i
zH>zAv1rhe?{MeZ~EyJ?c%rr6zZxUj`Gb+%OoacU*r%e1wmATfUz6r<+XDVm(3LTfG
z8K6D^z-shj>YpS<J3~SBTg2FI*zhMDG1F=Qq|T~5(*S<hZUfwB1aBz40dcvwyrvK@
z#ijo^RN-ERkLg7BQ@uOjllN$ERCPNsFk@LPop8yoY_?&IDPy(>smi_BrAH1Ie2eKO
zgLvJ+nNLT;MC-AM;MbV40_;HBEs;5nG_D-MNX?Pp2*LAVY#>$u?BBTrgkty-v`UJJ
z&~(P5DgRymPvm3}4~AfBF`+Wt$ilnBhw<_y(XS-gEOM<&rx{c`88|qjxm@^_<|Mos
zjqjRAzH@ASPW?eDz>fA*Haltr+zLf20&}@DMe+$Uu&f@ze=VGN&4Uh<e2lJKQBR+V
z1mHXqpmald`Wea>{vZ2QI;7d>XycU*R>G%o8cl`lZKJw+NVAI~ns8n=OhkWY%Tq*u
zoDR~BW~TMwlcK}PHOUI&YK-=I8_~|#$A}<128$*<v&=|A=HckD2CB2cgCt6c>Si#G
z(nmfv*;lJ*&04MaUJsEn!QgugG<!F3>8Zs@AljRLmP<KN*|~`2H#=%h5W)D!8H}SE
z-wN^%nOm+VL}beX#H8&e7c%fZNn59=s%@r&%XXF`vTXh9`j-gMBFKq}snf1FMoa0@
zLr0*g1MGmi?XZbc8*6xn&H{WC7ba<oXCxLiuNQwWs|Hbv;i=jA+FxGA;XMDo^v^!~
zfp^*Li`<s?g-reRo4^sy{HDYXY_APfTPc2*r!qLQ|6xWzNXiVgat-WOJw=XzrfQra
zDleQKEAJ)Yj9%%erR(vX@(@iN&sI%S3PoCDzjX;~B3Pu>@~_BYral70f1DCeywbA<
z=@JL&;#p)MurM?kK){ww6xeWGG&2HMj}qVi8U%Xu=|;~^3UakKG&F8X4^V40ILji#
z@@%Y(*s+QP4vNelj@$Vt`hW^OJ?gaZ<FrMe5NlqZ2B6x&7WtX4W?9*!0W>DyoUpwG
z)(e_Y)_HbGQy1DnAk?oMWhrlQ`RdZwF_Ose<(32oWtk@@Nf06I1r?P+Uv5WHxl*I6
zqm2Z~jMYW~BhDVLq&copR>z+$+>Cn80vT+r0B}S&bul{i&~EERb<xALo7%)JTfafP
zJ<4MLljYi_t96R(r+TkqV81lWD$mQ)yM_nO*LC_u#P>e4gcU8qYTK*=4v88<oZ}||
zg^w`tE$rN|@@-GU$HhGk!Ux+8EKQmNL7*Qjs3|PrEwGtzY<*lg9@KIGf#(ki{Ve2c
zg*SCxL4m!9jUK@ErmftUF#;)@A)5&=f+>rMBRnX?C-&{uBYgvmHJfkSZpenI`*<^{
zwBz`%?^r@JQ^6Rf!sUtMz-3IDnst=szo{-XEJ^T;OJ7=L{o7MbJBHr!`-@X>%?C9`
zK~dCf!g~hHeBc0B7N8Wz`QF$4o%XpL;q{+I58SC^Wv<{3>{@qK=#`&-Mi@PMwe4s@
z9b-AKg&O>J{^#Se{|Vmwqh-r+@mN38i=Uv%J$tV^3>M@kla*CW-1LzSAHGQ_EhR(}
z79YkCz7|mk_kWK;JC52`zIrPX&*1kFt(h-r8~WusEZajqB<Cymnb7h2J7GN(bd|7k
zg$g_1IKp^iiB3$;+{Y8+q3oiVrqdW~I_u$Wv-Ar5yOk7RQ9XXAD{T;0in5=&c~z9#
zx1hL5N$tJM`Zn<o+MaoSSWopn9u_`L)n|=WmZATrZVqAh@$p9<@#;JDfG0?u99;cb
zDz@V#u5M*HS3!6vSp}ZWMxU9v!H4aviqJvpuc=f(gSj08iOp%3lZd$3PU4AW$VZ{9
z91<qbhXK8(36Bg<rj!Py@1;U9nL(gVBR2!D<)mU0McSw0$laTUm`H1Hj|{5R@95MR
zNXF$gA16&7p=Q$+Mr7eUJS9?-P`qwDfkxw^&8C~Jq0cv$Dmg%Pnft0Jcf*gDk;eGQ
zfDKM~Zj~0j&IFi9uiW67x^1_T3V&w+wMi0mZYqDKC6JbwG%;pGR@9V8o~aS%z<(q9
zQ$odbt(ka5h=mXA7=9ZTP0RC|WgRU1ewQt-L4$|&^D2EL6cyqhZlsP_ikfUIq~PSx
z`fP5&A}M5vqvR*xz3T{+>R`Cn0R}=h%YU;I{kA|F(LB>rN4|G3=$><UV>Ba3-Jf+@
z&Jg*xDhSxCo@31`kGceF^@;JS0nDV(2J=l`mc@yrFV*}<Ls+T$;Yf)qL+RvpO{aU#
zOkKshP&-)LeiJqN->R^Zpu^vQnB^n@ga%Y1UTXG>1y>+#WWCArgQ)#7xH;ms)sF0V
z20XH<<BBGuhslDvE`KYEy)wysl9+aIkU0xWsYu25R2U|`B~bhmRtUUacMho@9OTwL
z@dBx3dzah$7>n5Yy}X*m1NsI%bw3eyV{d-b-xh(nwH`8F;I_r3SW*^fd%nR7?!oaw
z5tdYvd&!w&DlLU44J>=Hg$$_xIg#Wf018JY{I0NKlNWM9@Ty;LXej-&zZ!Q-%8Ndk
z&P2bcEu?O+tQmVi(AV$s-@EGQgQ$R=#D9v_u+o_AP-G&olkD6MZ~31i6*QfM$EPCR
z{A4*tGZq=tNgLA%T;C-d(AUn_u&S!m%hf&{u}ev@B?F(>mPii6Fr}#M7fcP0F%V=i
zaZo^jM|ruI{7nM5TTEtr^0&OUPgs8-s`%!UyM@|g#8ErIeXIW&dD<m_dm?U(gMsmL
z&??lbFx<8g%#Fp6<ulZFUo38EEP5pwy|+mtqgaWZ79napGG!^oD`Igrufxq4{#Hdz
zq<zIO9`;yz-KbG7k{~W--|-3))f!=5uFhL%GXctEBgB`gdG|{li<)}d<jz&wn{#rp
zL-!{PN5}&)wWT>NVp=p)*b@6hZB$FsFWZRx+~HX}9PzXVGl=QKc3?!`oNo;(rm|3;
z*l%yYN9=ftv=M<4JNY>wF_=Shm{n!QqJqPaQbBpJE_k(JI*)U!SWRDiTzy3@+J;?P
z$drvE0|M5pBUc~;2G~Y2db^1x7=gPrnV1=Jq8+Znj{+UD<i^Nio3ek}(D(n7xv&-5
za8)$hSujBOmuWxl%;yv-&}C9*jLB`{MGa%dk$qfgq6}W<%4Wc9!!OLYu3y}|*WS7`
z^21qbG@>4;)c;4wti}s&bXI?iQYZ?ZDxKd8vFosX0jx+i?ngqw!wq5Ce=V8<vU`n2
zN;YYJGUv&f8ApBE08T;B;f23Fub|b$kav_8_bB*ib&F`7da*Q}ByU+dbmNprMx;@g
z2uSiDg_^T9x*)@JXsHRs4=3gu*E0~N1Yrsu<?2<4iaRD>MGIkwGJAv+9+i{vG_Nl>
zo?f2bm6qYN;@JgK2Mq@{#eQ3+Mt_WOx^!22$=pj*#Pnt^v}b@Ceamg{-6G@X@=Udf
zX2YC&;v7+teJ({E*92g@)zU4gXj3!wEtF`U$!(g!47_Q*Rfz9q3nQLVR)cCu&;!T)
z(AyMY0f{n@%`9~C#xmeXOv&GR62u<t(#^V4(jk(td~tkZ?_tPQ806dR%Bv^Y*&O`c
z8@deqW;tT8p^lCu3(7^L?8!Yn?%W<s(iZ}E0%c)FtE|cgk|0yt1zL(enLv%M|HfYu
zy-F{OH08g_P+CH3z5GRB)xd-YT=fIpox!!EnBgu_3L?LcOp<`DGP^g>(Z|q0{73h<
zGAF6-)i4|>OI=)S#+dyTKGtX}u;N1l$3Z=JvG_L&HdQrbw8ZWIJ(+IRk*2d;)^r(D
z{RGv*05hIss~0x&SLe)_xLgY+R@%N>@JEnE4H6Ki_bpxyFTN`c>0Oz09cuGUzh>Um
zySMme2RqRBwr5Lu0dz;xS2#Fxgg^JOC2rp<st|l%XRDUhpvA}`34v7$oi+j%*)9aw
zt7j#5?7WIOkN-GD7jGs_YZW>j2R_?LB#hQU8*b!RK15^c6kja;cCb|UO}Cw^NR%Iw
z0wNt`a3r486|PES%Lb<YwQn@<{r6F>m$?81Ea_Z&x8SR+Q#xMcKCM@ZCG~rXu%D|a
z-N8WvThm7u3xD{y4io1b%=-+fRr$qD0Z)egmeJ8-qK`}45q-YCe|8fIACmpAM8^v1
z>VGN}Hc0><w>`q#a6R}vMYBC@@!k44s{hrksL}n2KtC@}{hS64%Kh($<ur0%uZXzb
zx%{)<1GJd^v3)JTcb`%@Zs+tg+g+Y9qw#w<{VabdO&-N^?H@i9rh*+e9Nm)xvf5*H
zczCR!#`2$_(Gu*`QQyD9!2xDozu5j9DVvu149Ps6_5umbD5-NTiw2efHCySx$v5N=
z%RV^tDm}b?#Hai8!Y}>Y!h?&+)Obi;6v>9qQ4yL;w;l`nL#<Qx=g9wM6I|?P6QH^z
zK>4=yeiF6&MD+$re`@zauQhi&E?Bt*G_&cyWG0`hf9f0W%T;trRha9$cK`K@VBb9%
zK5QpDbVED|O2e1?_FM2|<MuN-3w3XVf+J1Wh-^qWvLrdbu$&+5;M%tp-{%)|*f;7g
zfJq+-IQaQ4hp+?&S<UD%3tnav>Xr?HMLgn7bWt8U(ZBTLRh$beFz#jq(!)HDnPH4E
zrr@dEdfh+VJseX!dUcUc69r$RBZ2k;mYKQif4X@0rwx_hp{w01kl8%>>MDH~&Ppu&
zFsssrz;2Uu6pEyTHz~~nBk)x_!v4WrV}s|=Lr?rG{_rq|x6P0Cd++l3+VUge%oCZw
zYXDDQZKw~m^M0tE0B(OYUrkZv397V<1gy^0GnkIAa|v4*BlFl7@k+i7;9cIRHS`ZT
zh9Yr(_;C5oVczgbl|ovdOu~swx>;@4j&Z}1I;hW$0IZh_b*AjcgzdlwSKeyVs>&V!
z$qbF@(U@k;=^jyx!%bqKx7*Kju(-gSdOWJD2}-BqJ;GC<)Gmd4-uo~V;^AL$Md(9g
z^vny<Fw&fiV|Srne`aWGFGSsoSJ@x~zUL9yRAl-;3^AtsHv<IWKfcusro5$DQF+@3
znz^kbAu5<t!_D!@FP6ar0njaeVrI$N=4v+L(VEH{NAHgT#Ht;vvrcayiCb$1K3S<x
zHC(&xwkOPAFV#PN{PEIYd73q5y~+iW0LGbJB8>(&zu@zQBKyTbhx{|c&Nj5U<rW(_
zmgWa;XxTPfm9p8*U-a-F;!MpCF<}VIZm(R$X3HudqBO9pZ2Sy4zCoQFBm`MgsM-vd
z68;V=!4F7F3BiCI8Yv2WDi5XwD~{kwOwJE7UFsuI$6}nB12NLo|FY)2+XiBy=dt>4
zi*o7GlcY;0KnmTsWhx+OT~g=S#)~1VhaljD`MfXCk*OqErzUMaotEVgv^HSVt1#Er
z`S_{n|E|?%akjrnNgr$9?B89EK)9uV!)d<RuUIsz$cCrhW_ZKu@${_dq2)(Mnr-!V
zT<#Ol9Ad2mA3k?CEoGlIsqvJfQv3nc0j;s<xAX4xf7Omr4RtwD!>t{czAWQeRWrX@
z7MA*;(*Kf+^x7-%%u=TWnyuhsBHiuRt-AGRdg&U|A80w*L7+w5K062WO@h+*_jx!}
zxb)VGr`t7M_a#j;Cif?#X~nLfbvL%nBJb04DWOp3pX)1q^$L+*-$#rujSF|Pm{gb@
zWP{LYDvTDnGsJ8XlMc?UlKAo5h)+yj<E=-d7QZlMZ4rfm69fEz-THx*0%uCa?eBL}
zIqrtfmwioL_4THxQ2ZV<k$UMnJ61$cG|47;cI6Y_-BO?&3B?|xow33r+FS;2oLqN#
zkk6g0r&imVaZvymX74$-ryL>GcQtX<;(xbe##h$h;}*BRo2DmR-wi5{Mou*ZIi4CF
zy+s%MX#2K0)8hL(y%$7SOz-kuMt_$j^G-D)MR|JuQOgNllE$Z@We2y^)uKoPL5(?M
zdE<MZ4eUqkQYVUSt<v5#<+biQ7Hr=9nA-7nVy)-+F1vHEI8FEC!U41_Dm&53<r(_f
zH3sIcZBdZJvhn}}(S_n5_{CdlG08YK_;T~;jzGyf4Zwy6MxAv!kiN-^Q}_^KhZ~Fi
zICy8hVUf2!hCQrowp<gLUpDi{QkcQBn`YKxA9{wh8mflQUod-nwV2gPR?ixNg<yZ*
z!~c1PuN~oC?zpwaM{k%iKMpxW0ng3NhSj&G1N?Z)y*ZFK2Q{T(gU?@~5SqJdw6u!I
zG^7*#39`k=H<<nR`D27RgK@_xQ_y`}b9#fZHy-y>pBG4?Q!L8;_vHjka8v+KF!SB*
z&;q#iJB^03Q6&GXVL#HHxAUvU9d0P%V)>@*?v{xPufI`Fxlt&z8v-klY0mHWes}Ec
zccY%Hnfi0;M=td)g3Bv#GJiip?W8coXmiU2*|5V&Fp0=zu~L=@%~NS`znx*p(ZO!A
z$DujV<z3S}*5c*k1YW}1;Aa$Uc()}aqqka^Y<9g<pSjuJe!Yimj~@i7GMiuf;D5%d
zIrPr)V1K`Q;Q&hAQVyh=B?E~b51Yxdn|MCg^%?8HV7zhG-@3PmQ2H0u@BwuDAFa=u
zQQ6*uZwh?s>-%=ZGqe6#mEf*c<?<TP)Ug=MQ$xeqxssL-?~@HTj|!ikbQSK4E^#`n
zb}})azGcnS&Tdi3uNnpTYSg?d&D6%QSUbwS;KL3UkZZ2@&E%rNzdj*{=hSHA*Jy0c
z!urLuw%I%@{(=+bz0WDvcxb3xM$Dr|;{TsM<X5Q2qH|b=%|P9&mlF$_t1D<P2K062
z@zej7Ry1c7_F~^J*$%Y}cISe8?saQ=64F8HLoxh)KX8$Q{lk^e<6H8r5i`vJ(?nLw
zLPsUl%gq+E(k`f>UXJ$u(fzmA;1n`^1NCDw#ZR;5UhqZWoofEG_&1<zSZ1yR9<yPJ
zZR9^fI$f|;lQwy-m#JF1b|j!WN{eUWY#ecri|H*f`6F>)xX>JaSIuF#V!n9&^*om;
zxAq2kA0{-MKfZIauuIhFXcSx<jDe;Ub9}}e`dxiHYXr0H)gtyflZekL1}L;1hv)J?
zcy~Z@0Jh=-_OERWfQZnF{`6ad9k|&540_?d_gPtn?nd8CkG^@Mp9aWRQ$IZFr}7`@
zOmuyG*X=jF2ERbwTH^d7$5xnkj*6}7J8nmBuh0MnK*xbL_VH-;xjVp0vbVXYA*LGe
z=(5oTKF}-dhm-OYA+5Dt|J}C$FXy=K&LBS=gFXXKa^+9(E0%GR6v6!|<B6P4hHcyF
znFedK*QTJ`7`L-~?|l9X{qF0SRWwl3*yM?^WI3*#t@-gX161P?qNSm9zM+``vk*A;
z`7ST8hCs=T*%dxYDc!vG$QwLAW#(eC9Z2d~`%P0t6GtWY24gQ=1fC9Fvd5b2G4TT~
z+WOVn`&OgKgZHMaWIkpP6n@P%xA-qK9}HA4^p+aOtF*vS)TWg+KAW~z78W*dtozao
zey=7rdMR<)U)zJBImF_4vA+vX%3Rb8Qbw!cOY;5oyIR?M%<R68bV|fvqczj;U|UjT
zx~=4}yQxXp%(*rs`|nj7RcZr4LV@u79OC7Zb4AUjR)wj4bHe|H#<h5^XZ;*tP92z5
z_-3;4+q4?s*S3wolfO|OMA}cZkd~v;>P_u`IEz%bUgeV`)jDV9nl%uoijQLOm2w<4
z)dM#cnDW2Wy<_Q@e#AcVRCX(>lve_I%Rn+@bf3)Xx4K?eiPG~(sv*@G8;89aMnKU(
zdAveMFY6bX%6YZY-v^tXVNX?@#sP!_KnSgKE8vlUe*O{s7O9Z#o*%K)2F0eno{tLm
znD2j2BIAkQeQWGvkrKTg$F3+1&G|38WdVRApBF6Hyj^}Q-rD;GYJL7No{07jb@9?s
zAG`V1p?yvgpC-~DbapS_`=6sM-Yd0*6*0?x{*jJ*Yyv{~3N>{y$2P6Fn_G?%oGpli
z7cCE($&OxjKy#u(pbVIYZKP@#l}*UXT(0`U-EaQ;9dC0$1&Dylb*7H_Zil!*iowxn
zn&y?@!}=7zhcWOT!w>VoRvOd^#a?LWbblC31NG+D{Fca%-%{!cpwAS#4eshr_=7B1
zc8K=VdsBc&G-XriK0gxzeOXrBdfjC(Zj}n8GJX$K4<ul-ol+ryp$M$6#;mn_9u{NG
zvp_LW5ddZ!4<+_LyA@sEX*3;bb@nyP>;Y@|`VZa19hHBm{oO&o55hhK8c}t!MXD$~
zbaq>GdN_P~_yC)7ED3FnkQp^GxSxGahfQ$#h!I~VKEjE|#H#Z)RYIC8cizsRMCHP-
zUCf5vf)Y%hsVAtYc`p4WPKvtbs|$rRYc;b>0W4@3i=lifjy4VyamY(y?%&^5bG)l)
z?&MHjPjFfO6F?6*f^xhETvUM?SL0>?6E*V*HQ66mA#xZ+L;wDTmiUvh-N$AP?5fR$
z#-Y*td`b*epfN)O7>Ns9!y;+SI|dYVFz$n%`4!mq#_m)l_vzV;n9-&no9hP}*Rcyl
zY%$e)=j|>}(1v^{ott%Kt32ef?^dVP#z=R26-SNE38KuqoP`B!t(O8CRe?`-l1*E`
z;Aojl)8d~%%UR;8Y(#_o`f%MkSaWwPp_^cd(O9?c?Y44}-LMeIa7HO?j6!yhUs!+*
zVzo|4bvOCSPERjueCOh4s{18>72bkU5$ok#+FO(k?2gKx3xcC?{Uy;SqUfEsR&4{i
zqI{vJ>kyQCh8c;KIQFLz=*8+*xpXnFl7tt*05xmu`QbOUIKg)*+)3q5$7H70a(DsL
z{ah}-dhk|y=LSDGU`zlg;CXo->9d@cFK1?qEgj<8tq737{F(KE_hpXftLq~Qr<5Vb
z5u`DT=P4l!=jmzEI2}}c5x0DGfx9=CLTzj-OxusN)By4zUu>8M&ZDX%H0fyF*I&fC
zzB0R&l=BSjjkhq}wo=VhGE>WSAh`DYv>yOAZs#P3cpdFTxjd}TP~yrT-?IBaTG)IV
zK@BP0eu!M{T<3n`>^|KWjq;!w_eBJ+{qcGGHE`rd6ofQvPRag2i4oycoN~c=`*aw7
z{U4)^?qM^*vzn9$+;Q1Ftf-WT>|PLVX-~Z}YN-u08Gr?F8(tUu;+{~`feqM;1}{Gn
z;W7@PI5NzS7slV2JH9;eEvI^@5OS|4&vJ(xo;!k+*nZ4Fi9qVmCty>Q{nTF>r1}Ym
z8hw8v@jy3yV9?N$b!m55O{w}AECr2u-Rn(twQYXYaytG(&&NL_cA=@R7;%e8E|D!r
zRq&&Y27GQv1g>fq$9P%bOl5@vnSCRV18h#QeUcksuY<#Fx44mDx<vGeyNFB9c|V_q
zZ?(q`)F}e!$o)Q<_mQtD@Z(u6)m=muY>w@u3V`1~%#&nN7~gE67v=4FYTG}MCi0T%
z-FiSXeJ{I4_#nI-)QB>591!XKXk_gHAfT4S2b|6?ir}yxuL5bJr0VTNQW$P`Z4MN%
zlRX@ZxApc}Bp6L)-~0Yt^dR_G7Qo*FXp#BUbQUYYn(Dpk;t)mils$7qP<EdQhTK`o
zM<Gja7{{}WS-N(Kspdr18^Cr1vLp}f{?Ldsyah19Gcf7o8;F2tqQ$9SZC@SazdBv2
zRD{~wxH=Ef3H^Gikw0k)$^DZC)bEqQV`Z#4I4>PQi389wO#P(CC511GF)L3HoE2YO
zC4KufS|#fts?IIC2ZiaEn*bmJX_-BhHjjY+-eV#bHboT+(EMH9O)2?q)Es@ycyeZz
zQ2%gpS4Zj@UL$TqJ9xZlCVMD;kzB;AFz_;NV9(YJ3i1Al=;0Re+GQ$#m_g$zf@4m2
zg~k6Ju}FmilY$7h95BsI58$NI<ybf|{CbBTmi=|nJL{$_79f_urEd(~F-tf-90aj@
z36s}jF)q(3;E?MZI(x(s%b-=7JtAH6QUUW;17PNm@n;!+>p0HvtqXu)dwkqn3U>rl
z)f-jMDoHs2{mv;@B`@Qb*@Q4}b#{FDdx_*T46D-v-{ASjH0MJ-h-q2(`HNz{y5`kz
zUCZ1*&7!S;`wfNVn8@hU;c4EMHhCT8_t8X!$+~=(zdnFc-*S2Lmb8{<|IfvSXy$D#
zurZjAV!A4Y=BS2-Fh=F!QhnDj??wPFX3jtv2r9|@*KZ#Vk^$z0Yagk=DVIc?$@rb(
z<L94$Ie7G`<2V4$Y2lUft#s#O3f5l3G?0or0g(xaub$|8Ox#gsuGNAvFMINGM&mQ4
zuMU4o@O$D**a7;O0YmLo(D;4dF?0TKi=O?psQ0IjQBqtl`FQ9DVrU--ts-WBrGkee
z<#?nAL=cC!9tL9d0Kx-&!oLO=v$*J7rp?97uFE?LMH>L|^TqU2A?}qt4<bK+-I6uz
zbkqFjvg^s7;eD_7BiN%s)Mxa|C>h|8dHqp}M6#Rs3Y1J>LIhns2>$^>P-CVDrZ;j(
zb^FWwl%JGhM{IOKZ;9+a1E8iFGP=RpbmTNxX4=NuDJS-S<xV!S=eZd6ch}l}_w%t5
zh*65Rgfp!xJE8Njry+kh1}I713jP4Wa%hKADtON&>7QnhY4CbvfGIp(r?7W!ox9Ax
zWdLBmR)vlGmB^wUwZf0D)8J(n{&4nimIjEiQ7Hs&);!nswfpdwx~7^`eVu4QGK;h7
zf>=>rMG)TmJO2;xiS%OSD|0_nA?WfhsaM{*UDoQq^dYT%S=!Wle%k-I>34}V!J`*+
zi?-7c<V))RU~iDCe&}%52)%W?A8vIEI!2b9_&Dg@SJdoi36N+_#`3B9!5sxNW1nr_
zO!4to1g3|1h}0}LXO|zN+jkihs~W7n6&+-veBk7pbA&n@(LTNz)%Qd3RC1gmoI#YT
zD%>R6ab3R(7^pEY5Au)ni9xb$Oz2D{cpIRGTSvYsN;3+6oTlB1y{C>(vJzH*die3U
z6oO-7Anaf#EHtK#a`I{qN9L~Dnl(|wy5vvoLj1%(dpmVi@T|!Bcs?3&okC*~awgI=
zaqP;qt=?xq^JAl{C)_@8mzW-|%bXfj)Jp)X27Z*s1}R4=bSNI=8p~ESn1)F49iR0Q
z;;Hd;CO3o9TQu<J<E!H2M0ef*>R;BgCGRyxxPq;=83CXYR_LANNDcI*ObN1N3REOn
zH5ycU%z!pEiSzi3U5&LW&}$Rr!ZVbWPxqHFK1yM;_Z%q#Dq#%gXagO9H#oP?Ka#=R
z!rr<Bd>y&^&vw7yN4Ebv`C@J+vYCwWb>BwXdQg;7L^vcaDdmx@*9k#e2HV>k7%>Gq
zc3@OxMb38$Hp>|BWF`wBU&kF9qi+sGvkGOdT7K}7vKYX>?7v*Oh-WeG=EAcCU8woR
zG;yPG{Bk%sezhd+SUoBMxO3zwh@R`>=_&~ttR*dNlB=DdNg63g)B*dd8Zy2=U6V!!
zswMap85?`mLr_*6g_1Tu0<2?T!wRc^u4x#YqKcZ}>jI&ZF+Vd*Tm*&(;zrqi5l?+z
zYnE3C8Y3`zQqL8S3VcEGAbn(_{~hV1TLX1fPjRjNk>mOv4X9yev9Y-FTi62%T^zRm
z2>U>fxBe$MF~fUr$m|$EzH)c~r1j{dPLJed7nI8TZnAU429*d<5dBrqx7GSJo8ft2
z$&jB|<#-iC=@jUl0V8>qA_GpUrWx?O_>$zCXDCp{F}f@<a-hQd#R1eM3>8g0ysV{F
z4yNhrjbll_uSMcn;s?6_VgpZAufy3kW5lYqS!^`e`E?ZS&&0*R0xq2ZVZbJGv~fHs
z?JY9RrlXdrx(k}(I6>MENnLmA+yPHk7$L)0{WKziW%#HSfR>s`P;0<?8kHg=R0!f(
z`FyP6LEQ>fQu<EyDS_hSOTvajDI63q1iMv}p<bCjS9vL443B0_|927jvuxMMjRh1&
z02e*-0@UaS{jJ;_ac`1F*mY;T$LRJ`0agX}2o0q!+PIqja>p_IiX4SHTrk>6Iu3k_
z@cavn!^ulzazVYlwDy`NM1%Gd>F1os^k$(cd~DsL<{%UFKWGYx#AG6cdFD+<tZlQA
zSfw3^ss!+d?D`6jmJWI~h?%(Vf4lyEc#VRC%4Qx)V;K?#i+>a+jJys*N-cA^Dh&7I
zxHdOF-a)MlqBNVd<&^mcVUmQ9d}{Ui-Ye<-I@SB3ui;Q;@%i!a{iLC-p~M)(L#Q8Y
z+lOQSb1bKxiFaP?f`WOEOm8>%Td@Cr`Zy+;l>&Wf@59-mUose1!6aRe_?dXk0Wd*;
z(1%GXDIQHkRts8pm{S`n98cPd!cOMsUT97|9dQYknq304#3KbdUQS7?D+>b8J9m*<
zox=4g6{vrHCB##pU>dX3<tn1MpBF{2gCUl~-_!L&p#1RZHIQfnVlD3__M3>y_5qIZ
z7h*ws_xyT>MJJkzqLS5an*)JLPDg8e`Gz9IW_bt8oHUp_Cp47mK8yKPGbY<NsOA2f
zl1cVIjt(lm#0_-wAJ1`>`+!u0jMOhabzf=ac{2?gx>~7!S<>j(uOw1^!tV1y?tC6R
zQ~8Ls&E;}0T=#l{W%o%)RFS3?TzsoBW#rq~H{AY!3*Z){x>^L16iXH-D6#f;rOBQ<
zxyWk~a<rAaxQolq)V;>j_UriMLhLb+W*abL-R%idotz%}b@%yr>LUKw!8X7Y47>oK
zPZzpv?CQR7I9}2K^UGbc{|$uIzvl18M_bKXQpa?_KukSs$b(lJ>LoIdGcD9Kc%j=m
zuKo^FErEJZ9+}Unzf}t7iz@|aEdVZ4>66p#E!rGp8uD})Feozl7b0*FgU6Fpe7E~>
z@V>y7$DKd{xYbPP{v<!l0-kHf=u@l5lSyS9cWpPofBwbFO%dklvu;1;0?7qb_rII<
zuD-;$`*}I)4jRGS3KMni${*H3eU{1cp?qvLreB3tmOGq%AEC5+{iL@qGc%SZ<k7BA
z>_sH~_@e(gM=V;ln|5=9>~254o)?B95%aEBf&Le&K;*H~nyC+@R#zFrf<QH2r{8v#
zHau5<YjyMY?=O=J0}C}lV73lmP_LW+7gi{Q=mQbFe3jh>q>z2Y9cm{=Ky5Gwz^_2>
z?+KS@=*I)A{Qe#+;=I@xHg;VpoI_id>C8+*STzBxYJido>-O}C-f#}Q?h#7_+-)QH
zBi7F`8gPn-o{!%ySf4&$1p0AtvHyQZv3nRTqP>f`x5}>QkAE#raG}U|Z?KKsRQ^+Y
z?e5muMdx3g>66N!KVX}H6ZuCV{hwa!e0JlVGR_Zn6ej2N+A@0dqAVwqi+&lqo0?ZM
z?xNW$wxON9x=W3e=6;S?02jF5b5Wx9Jd|OKpi?E5b6%UEjoFW<_!#$&mKge%T|l2Y
zF<gbXH>mR}Q=Do)0a-;H!!-{@e95`pExxi)$p4}}X#ICm<2g4HU?qd|SiDVIJ-x*|
zFQ-I>7Sj)>{6D>+C<)uIc$duU?+^nT+ri0M+utmJ=~NHjZ1?z434INgHYbB?(kstP
z-(LC!$!uaP*62^`>?;DGn0rXjXK-B%@Z~JlYsxDwT%A^z3?)0Jmm+%vP_wyuqySpY
z=U_LV&%-!MjgAnt%k9`_zRvbg=Wmfh-S@R^O>D5`u9m6VBrR(}?%wQ%&=;^HA89uL
z_lZRoHop|xM+G@tZIz(sVFuL1$Lcoc!ET_kTv@^a9h=cf2TtgxPv1#CW*42bUaGhg
zk6VC@Zd*r|5*&xUkwO;>u2Zp_&VKVGfLBAk8iOb2@8<)b0N$}1u#oTl*HOCg`PKAi
zI3Rm5RHxyU87yKfWzIK~fhHKw!9qH0^$S0df%M~90F2p=M;q*TG<&_}Y0fyKnH&Ys
z8;w|mlp`))L|s;WQ&(J2H=EjrjAa;Pu^x3=e*pGAOEoxv!Vj2uN9fUisaUEQ6jwJX
z)9K3M$@|m=e}~sj9PVE)loGh`<$IoOaJzR_>JygR1|6nRVEQWwiFScb0UWX5G>cpF
zZbx<ZqLR3Z(U5xnnsTTRTnqv>Zj6wyT>h(%AqpTB(;?^Cei$t7f51x$j)1cl*cY9l
z_IkhTe!kPZc&0)f7X#2p+V{TKd>=BQP2~yAZLBlJ?KcFHZ%DvC>#Uu(MUH5raySn3
zR8#y@_cP<u&_e0fc~2|$Phv?8(>!c!PN6u{o1?!OX!R2G3UTJ5{z1#fEbUjvFcd%6
z4^Mjl&*s8PY1J~9&jBQ5AD+V8JOQv?(e$$PW}l=Yf(~CPWTvMY2IIRJn6MoNqQZK9
z!pqy1bXI}$Ts#1@g8yD-5I6hN*FDQ1LRDNqY(L}Cw9-x5!;nZ(=W{j*S{)udnk^Tl
z*qNTs4<?brllu=dMnt%0BFm`kr*`LM0C@jTtRqba>U!+&VVU&l^1pVxIWe&UzII${
zx77WPmM;b}=egrH&@=S)@ZFrz8s2SKg5C#HKjQLNY@$iH#~5`6W<LsO!UH!$Ucw`q
z>Y*&l+!zhuY7Ef8<<GO#zk5dX_NjIpDC62O!h(a_$=D0^cp@qUDz0%kN=k85pW@!p
zfmQOU+RpC!6DE?yq$0q``EMhwqlO7&^B}_5Wm~OR4B(nTpz{Iu0Bkz9U#MAZI8)uc
z6GvAp$nZLTQmF9rx_>vt)*AkmMhr+cbgTfJOF@jej|w|JLd-WS27WC%P;5VCSe>Tq
zKh34^bq{#*;ggcnN+VRc%`&zx`c~Xp9iK5KcqTGSFD!JXZbqvR_)_*}vLRC4e*aT0
zQsRTFbcsZDmR3Sf!JxLtA*h0blJ^qJ`L5B@?^5)EH2g=Ux%Ss0LJaPQz=zfPtH6h4
z`W86z_H2Yq?cho+)+2KMIL}pXcV^V=Yh+x{89l!BDw^N~7@EawR#BGU`r`fjwm*jV
z$G0u_>Dcx2`2c=5uveb3i0?aaWt5ld?vh+WQ<E=+6Dpv*W|6*GssD5eF7F)#u(12j
zEAAp&o+PG{cS*;sUwb9HOd=Vpg4Y6tg7tB)o^CFtuiiC3l0Bxn^t*cOJx5Y8_77cC
z#A!o^GqfKyXjkOYA31WzgL$&M$cL#*2NrYrapY>-)g~;!3($bc8Z2E8rP+;JBmQIX
z4x9Db8=6)TQgUmLJl9K6?%zcIi0#{hgQjX8^n&b`O(+Yn&Q$+fZk>AXv>bR%vHfv~
zl45neJbmfKBH!SVl-=+`!i+?L(%qE*p}Zb{eK!@NI@8WNuaZM^<wLGJ|NR_SWyXa;
zca9_wdU(4;*(3HfJpqHBg}O;OXV8_PeV^lhW@-cfpKuYX%i1Qn#o%+k`WC2Hub0ot
zVlG>$el8CHo}-?Va_Z{C!%=_tVPMkTY7nHkWNupI7Xy$2<pGXNJHu<cqmB4D_=Su>
z0$SwX%-5V8AcC15<n~Dkt(>7rq$l;9$0iphrNVc#!{h({#)pvevCGtbpR2B__M0g&
zW586}AWk3R6o5jOXHoA76OcisB5(76zTV@$_qCr&Z=gaIyOc1*mz^Z|V-5sMd2;_j
zTvBz-Bf$+nw!z58gUXNMIs6{_TWs}Yeg~f@Xikm-1@K9dxx3WVfV)dR<5#~TeLC?`
z5uEiSFGPfFW~dQSeLdD$+99pct4-A4(w!v8@Fz}?5g*6n)xMZ^um3{|sBL8EPostj
zr?ragv~|c)o`QfQ0KTZ19rk^OD<%L1!{DSqG=<f3So}?g2Qy2o{9Zqzf-JpZSOT#4
z9=7Q~6_{UJ>zPCyWV+OIj0rU1pl2Sv90`(*e=8+t0;DK0tKdu>vr5s`-~)H)0HvL2
zn-sW7M}WwGD`PWE@C~@2;{0xaHb>QStg$=8G=-^1!HwaSS$wp)C2zCG!9PGux&e{t
zK`+I^F4VHIEVQT(nCT^k#T#b!Ue>IP7f#zoin2ov6`oU>B8hU%&DdqU>BaL>c$+kF
zY3d`&V4I9G@i*-43j6;*E;=<Hvb()zs>((UxRW4Y57eQCh;$+-zrcx@#y-Hndxfq$
zS+W^`zci~^G0C`fY-2xDZ)q(OjnB!;X&BzH_&1^(5Hf|}9#JaFjUAXgT%e(;4t5f)
z$R+7nz*#~=bCIe>H)Ma;I_$XAP282x*lagtsSV;>Mj#kfEL8%UG#MNhT=1Rh6;H~;
zHorJBqPpQ4eCaq~EjiNle|YhqbGSI;KLa3a0qM9`fHpjeR?Wg4=g|rNcIbStzYCHl
zc>ONdg)OIce4sB5hpQhGspb|&UrFR&LxvTOgY7fucz^ip(Vqg?0FW`9YCLIhGYhaT
z!P^GK^ms)xM)<omxLaWSgAACoLA~t(?RHYxVylZVdgs#M2YY?M*gamH1feFmlmcFM
zFp~Nq4qF7!=?-2QSr!fa#$N>tJs3vdJJIgI6+HFNeJ**f&w+jLH?nl9VnUWg1ah^}
zw(XP?pT7~w)G02?|NPTt1<2ZB+DXcnS{F+y-Iu<zg9mj_r4_MZJ*jQp)dfH<J&)UJ
z1=u{tfG1$=1q?C}YZ$rKy_9%GUj;xSmg~5)4pZlH!y1I#K4>%O4N{~h*KA`!I$dHk
zY8tqwM$=l?j7#L@S-FZEL+@Ut3W4kGIpyNzc1<0X77$qvfr|!~*Isavdz(dc%6j!v
z>i|=bh+xo69q6nJngXgm+<06D0v+gBEf!Cb^+bJd%{YWfsnzANSpEmnT=i2;=9mL;
z1nvR&NDXR8U8I`$6CimX(@6)iV>9pFy#{Y1K*E8qa9*RDsPl`qK=M+zGpElrZ|2*K
z398xKWj`DgBR6k=L<e7PTJR3qUaD{hzrVj32XpPsHv=+p9Ke{go#=wab48q8gQ(nO
zEq7Yq!!xtKWyuRed?0uRiqRAL%uFm-b??=#)~4Z`Okok#rN83|f*kPbrk5ZPWZ>Tc
zas(NfD{$epTm<K|oQ#RT9C*pjslW91w^7^4tRqO22AQ)Ud}4J~o6hSYD&{|`7x;;{
zu_L++(>M1(A_R9jLdZgdXpGClIUea%*MP6!>XR`Y-w(z4Gd}U#Id5n`%WVB0OV=Hb
zW&8FUDrJV0JwwP2*&{1^M6x&8dsEqjkR7sD$ll7{ZW-BRZ@0b2dw72D=kxsC!{xfp
z^Ekef`|w65ek3UWAwa9M3ICmL!}6e+I+U-z&s2SzaDl@3w=L?fC@-Eh<|hSOi`wCX
zz`*u+*!h(Kt0Y8N@xD}f5f6$)>JZel>nJwUF44rKQL8u$#u12~n=p3FPw3f?c=#ZF
zmH)X!JucvBoV>5ta77gtEv0YQk|e6~GfMx(IB1B@@Dn)}_@9i(2~Q!?DB|2EIB1Ll
z<^T!T-^kW`ve&Re;<db2>5;oe5Z=uxg_j=hKSku8-%j~vUeg7MiB;Q;d<lj9n--Sb
zYE!15HV4!V#J8rlO!`;YEeeC~Fc!OQG)A9f?cMk1eVIXmf(OmJ+Li_rTmPmf%y<(E
zn9AJ(ay$8QGXzj^?g|TW5-p#%K3a3cZB~%V)<5zRkw^U`gfO&N-~11W=4)@>JExOo
zrPRj?nl5?xFq|9Qo_~NQI_YT&t4I-GYkJ(^<u)SccyybpFrtq(?j>i}fMd|`$!^6N
z^rbB{-P;2sR^TC~8SDzH%~ZVI3j4P}O4r9(^B(>+hEL?%O|fBnL(-+ZT}#^+H`;Aa
z&bd<B0?lVz7AWwgb!r+qCj_fMREM^a2r-&%w^}C~8?s&9c<00muzy#}e_Tih>PR26
zb#4EjAI{uohp<GxJ{2G^1w3?DGYACOu#Y$yazLu*Nx`oxSIm@zSHomTT}odi0u$)K
zn`|8>F>89{KL~ozxR-3N>G%HKCWQeJ08e`dUtE|tciinYjFa7x<)NQv3fTV9(m|jI
zc5Y}86>GdwT!=@I&HXMezUMZnLgT;e)}qX#HP|*ir;hr#s#fnq*PgSHgONH@L5x`L
zkjRaJ)op@ZzLeMHvIWzrV{2PEMZu`ZSVOln-$1MOwhCfSRdaM}4!X}9eKOY})yvn+
zTA)On!p|8KgIp1_f`-Kkz%tkLoaBIAD#MC01;~;*VnZSFKb##(T)WmCKhYZg%%o!z
z*PM!|FnU|FWVP-^0IYXfy9#)x{37tcGnzzA26tTkbYlgviY(0+;q5yv9e?Rh)mcK{
zCq@IVHa3ZEOxuP-2q#Cw6OIFnDnKDO6ioNa9YdP`>6n!_SS~GEL7M>R2}0kQNZ>k%
zZC2Zm5_;*&@bMu`EQ>{8llyZB*k=0R9lST<llSbQxeJ^6qk}->aU*3cg2_^&YipDV
zWTym)&-uQqicg}|q(=6%bu8etC}TNAXkh#G`*9h8TwdcY-c8is_MqYwi*!o9DZmq%
z`fh#uuy#a>x{L))@y5sj9q6jZ@gbr4yI6b~FLdz?oV0|MY<n{QJ3Wb3khi4^+W%lE
zL`j*<kv0uFjEC(<w_zk#*ZE;lokZuy<OZm&j@sHQMMF~#Q8UN&8>T64)vaxI2gM@_
z8&vtJ>{D{DS#Aq5x;j<f=Y(>vFlwc{Q2`-9<ns2}l*$CGiAO=B%(9zlz1>6r>lx_p
z0AT^Z!Dgd?wpLt|>UuYqMVbeh&=W!b->OlF)fBV3R=_Z%6rBm&#j^}J>CPYO;??*$
zpid9xlQDyIQ+XjLeaLuAM$DCmT0W*YLzg#vX=7obgHK`oR7b{sWdX(7<7%T~Vq7a0
zFnu^7^hciNJ;Vxg;o)fM!o#^%1MoY|WC}z{_vbm9s#J1DePXE{*{aD&D49Q7?MT&A
z5u4MwOymOHHnjuFP0f*PC9}OX>3heM3;`^pKV@3egQ=zQ+Dcj?&3VT!(<=-6tsGn~
z%hP9_r`OxkF3Bn9F8?QH(E~YnbSMpovF#HdxxZ2724%1&>%oV2&L-4Sx_}sVX_`q)
zjC9HFKYfJo7P%E1>`OX`?aVTIA62a<<?BXoV4#N7GA^;Vae|B8a{O}`hPWcLYW`%D
zObdNQX@hP{GM8-}Yz=TUC0;}87+`mqnK&gt^0pw4sGlWCD-a{LI{2E`#(yw<-RfNV
zXEmx73-rD6nCXV;nL&0ow}%_f2?gg;^-NV*`(*1INTA{!_wsNGOh;_=)af%5K>cVw
zj<~#uH3Ny*gi~B?ow)0@NsKPIEW5Aq;gPr=ckiq+?itMsa@1K~z3iIYibW7aw<z;s
zdC7fV?pVf!2BlR8#&Js`-y2eR5d3CW&0TFle8D<mRj*@O(*)a$rr@u-^vzgni-EjE
z$fHFZy}Z~JmTO><=CdT<{6_-br($-PnP0U~eKr~&VkqeEv`9o3kiv%>3rq9IRTM;j
zMf5v;!x(r$GTzJdkqjFp{Fg=|H2KkVU?SL2$;q!%xm{OS!R>KZZ0h8d4E7y7F~YC>
z_q>F>xJ#Ww>m)#PrELWl9xt2LYh(QkyB$xg1XF(z#=^~<t6j|$)v1>1d+9#%12Z#@
z{PaYjB)k&K5(9cSR9x6z&w>-DSc|ayFsv|w+#hp#EOjW%koyp4N&%!Nrv8xYph38G
ztSwZl2k0!+O;WE*o?Y0y@^}D}MFyIPjEnoKXucs;yu+_RC_XYaHRr^brT^qXr>|VC
zrD9Pc3Q9-tD~ebl#SBlZzk;tNOC$^9sH1~Y+f^9t&7){wWpkGW9Y(lSP74kp40pf|
z@a0myo@+R=gv*2H+A%iwFiX{{*v80GB8#|$Qjr)DIojH_rcEArtJt?;{*f8@bACA5
zSb_;J`NJErn-mGhuU=V5vysgIE@u6F-1k_DZzLU(4mf0bU}G*ONFo?-R-GmS;V{(D
zp2|6HJ&*!9pC^(R(qSb{c^~vuhe@Q5r<(iA9UP@+{4Lf5;CN+&W!-l79}8%zAChY8
zB%i&mwNjcg?YHv1i>pELniBjCowOZTNNc0pz8_Jh6oA&tRpb4tYOZ00bQOT93^bI+
z;bD{nic+i1;%v|;llLKQOIb)3yC2=Cz1>-h8QswO;qMxvV9JQjmJUOGl#R1-1Xain
zNzjtS!xaoH8*H7vMpn=7LjVoP)c&=#K596#o|y}o;p_c4Z%}udFaJ<})zoc>>(wg{
z{QtdfG7xP$X1dk!6{=X3>W42bz{9qnB}3{d_<Q4ROAU|sc_R@fc<cByfxm@jER1ZY
zOoAu!1Tw_ex8tCdQ+#dJr@St#q`rh@H|R~}?JEn(cEDL3Z9pi2&Fak}2^SSdj2#Ov
z{!T{mV9N$CC<e@4$Pjl=MJyGPqh{>c!cH%`SC4$LnFZ|Cc)VUHWyCXTr_9HdvA%7B
zw}3k`93SQUjtUGZ*a2in2&d2Pif<5775dT0o#`G9N(hY(dJS?|LRmn73BKFXyIYX8
zF3O49UP271#m1%GLx!ZXAz6zPe~=+<CIK#6<>_Eh)pJg=G^i8CPH;MT9uh*vcx{e3
z5f3U}y;VJn$KEau4qB!7<J;U|cW)2LS%yqqUshhuVI^~kr?$}PV@!tn_UO+W`^u`Y
z%Jt!?-&iY77Q_>tbhm<ic7wI6ZLx0%7j0MRd?KE#@kC-(dUjY|5m=aNU{)+zsW*Xl
zGy}2+Yf`^Fr*<;b9iqh_`C|a0Vz73Zfy}Ox&*B+X@-oO2D~H=QA(JSN#=tqr^Z888
z<GmjWu{|`&{U?k%BH2cMuxw5#{)SH-guSchQS2WrxN70-AX(jlx<#54p<%MZToHQQ
z8QW`jVU7i-GlzJv%Qob1$WT<zN6tg8<GH!}ErAzbC&HZCvsB*iwlNpN7wqEoJN33G
zw7o!ih-LkCaa_c#1D?X<9r*SD9-;N#73g&{ky!HmNcQiPbcFc_xu!4HOkGpNV3Z6g
zF{z5}YE3X*5b7--p`+%X-*F!9u;3nO!k5aDlm)+F@VeC%Wq}pvNy^m(GBsznq2_}>
z!LzL}c563xJ?E)_wqEY-+hEsGwHmZa_&Nd@Scp@)G!zo_A&Q$hHKr8i2ORk!j?BA)
zAC9H#nV@~o18SqnwJau#>@zE7vSH3qphVSkN;BT*!MISRPsE5REL3K$y!$le)6Yr*
z`XiB<ubG38ihOZ&*~@&qL-y;jb`-zWgerHvz>m_9%PGe?mgWU^(ptrftJ0$s;g}z*
zNo0ragJjm-iCgcjiz?Zjw~lY#y{-FEOIJ#_KBoK8Q@dD0mJEd-lr311A~=sI#iS-N
z5{BKL|HMSOYy4qnsqY}GzK97aM`AsYEwGTgw&h-1E9V@$*`+htFs$Xc`;7}EvU}cF
zh`q9$m<0Y!wN@OSG4M-v2~9|}VuORL>oxAL07?@#86%q?KN&c8{$h*tbA2^(%&mMd
zTmVnCczlrfnf_VO(-*s*&la+|1O91P&-@#Rc1?cC-!&-`E#HUuFDgfp#-OM7&2eLR
z(e~WlJt=;XkHr^qoGIk^Bgbvl4L#-d?B@&Nef$GE!q`hY^{!^gt3=Ws`=#cvO$PfA
z^woI;HtyUq(MkR-x$;D@#y2o90OvkL47fkZuC-ZjwS>&yeChf(4U?8A!YiYzt&SzG
zDFj|IP=iK9V?5EeF<M5Xx0UNOc<p|$N>EWFf<;GeFm37)PH#o%x|>T_fMo!MOES@e
z053JZ{fn(5O|luZrV)362BbuEB5ZcPH{PgyA<Jg7#{PG9^PP;?A3Wb1vT9CAw;PXq
zwz6JXi%8ZFe3}kE+~V<I-nb&AWgeS)n>FY-bF|bToq>+`W?Jq3$w=PNVcPWT65!)D
znTjPoJXCX+o0=O1L!q^OM&PCx>PO1%97qPq#dP955D$1=-rBDa<J8`^cWy<&|B(^R
zqCNc&hda&*)fPDeo12Wy$^uKnV-{DVkGrpZoYE`LtIbEVd@Om&)?g$`6fX}=qyHMa
zUR5DYlR_OG67`&#Ri7}ZtT@?=0&LFIIIyoCvZ%JFDsJw76}2rYUD}wC15R?Vq{>z=
zY)qrOM~=yUzKIyr!kN`wZi}k`J8X)getbCihqT$OfPk?2lH+!|tD%^_S(Xfa<(Y`K
zC*1Rv2Ju+(oL3w_m!`c2lFO!8%nnyphA^Tnblyu$o$?Ap4qA@mw)>MxLv_mOM_SHk
zpZc}N^9?%Q^A0g=da_E4OQSwq(ujU^U&^h9f%0Wo$g&%Rv-&!wh)9a0t(S$P<VlD{
zq9A_RevSwdz>{5)n7NEwUp66gzujmt5ohVnF9Lv?e;e9onf;wLHF;Jx#f62vdyu%j
zGxRv{bKpwS#fvC7QoB$|f|o8wJ+UgZ>(I1>X&BI6WEDQQJ6pRIeO+$Pvj20K!%Ss-
zG=^x42I<pH`mlHc`xf9<)Tzx!o-lQma>Z8fUq1J53!zJpF{<vHWjD~HbSieYdwSv}
zlx^n!NG!#!39n3kI{saj&#;r5{me7HJM$74@iXgSpEerjuNHnPB{Ddywe$~<?%j&q
z)}4|2`8CLpmjk3Cs2{WPJGu<2dXAoyFs9S7Rcua0RkYh`#l)<YCEzFI@eMQe7U*wI
zgS)iuc*zzr+}XKeUDkOYL&^__dA%hIKkBt1VW^mg^Wb%e3XS-cWLR<Y?fq~=0D`%p
zC6%$keLw_k?I;nTku46`nY7x<_52r!Rv}rhQR@W$#!;qBKf=M0$JN_gvVHZQA-i@-
z#uuG5Pr)Xi7?Rc%u1dghW5U5q<sGAJ5#{}l#yK2$n=B{}vBjzvqZ5y-XGqfr8a-j=
zX?JpWqm_yT4Ut(&!5lwVkL_6Z3mnQH`*ry!VmC`D4>Vhv_iBz>1mdVRpZN+YMrTha
zq3S-N->H%-_?tRb($ouUYvzElap7mP>I|i}hAMmwNUFB~w?ZziX<*8S=s9>AvxEnS
zF(-)!k`?2=@Y{|2sWQ6ff4@8mdVAfOe($A?!v`4(sfsTxh<o6mrIwad!owsfz6wNv
z#g_l``iY|0KUxTS;~QC?PtjUFJyCDCawqHm;rx>aGi?6hD_2VhmmnFST4KS8B%etU
z;bRwv$~{Qsd@F*r=aRcy7{ZD63F7S16?!FpJJuzmIX|27o23dGkiVI{9#A+!YEQT3
z?@x_P{$g@NOU<1rW4-_pQBkG%Fx;0K#Z5+7G39a@8U2{{32E1^;AJ`)RMDBZW;S|X
zVR`#zJ>y8EDf(p>_v?6_Icl}o&b7to8K!aPQRWHaD&IS$T7yCJbemJ~B;B5|?}rjY
zW%BU_gvx^p;SZwF_Hr}P<7lQ1@$c=&bj0V~Hm(#s(>ftrmeTtsI1h^}|Mvi7{@v62
zv}{^(-tps2VqpPiwUd{>G;+rHv<+u*(Tyv^b&oj@JC$8r@|HU0uh)^j)FIpMQzUET
zsHQ{Xda0k_NI2W2Bm9niivkT#OnexRz8mAc60Q{fHDS^^6jQ!ui+U?<P9{7MdB(py
z7EOI$Y|69MrGjt<%Z+TpS4fH4DPEYhr*_2Pvg9{bO)FE{vZ-2e$bhuP3y8+~@L@1p
z{7IhSvsevi6${4k7a`;2>G&-~DCT<FI$R*W#e)(R|KuY5B{8i7T~Uu(d`*L-Yo;(*
z+y-6GIZ%bMYi70hEV_jyXV0~U@lGY|z+Wk%$0C|4NV4>9QkKN@RSW*Z|6L+8Scg)Q
zlS?H_D;6(gthChsIbU63z5S-1sc30EX7YgI3-!l52D-eG<lAzams+ZZ4q6x_QOWYl
z!J(V{7k3CKDJ!DLQNa<Z@p##Em={&bW-aqRn;-Sh5d3Pb<$WjBikbD}h8ahP!!KkC
z_<Dik0va248WX-(?ZD^YV7FCqr}#%l2Y(ICNb-^CpyLsRudX09W{>e4WVwj@+i?)m
zWDe8ZyqQPO&i7T+(--?PFjPJNx8{?MFGzX&wN@XFyyw#=(@&Y|xH=cHtPK!qwimQI
zyl@m5WeOW*Hb#eMOB&64Y!R8b&W0Ma=m^SCl88QV`cnrGPssm&3D~Lm1+hQ5dld)-
zc_2~J-D)>dk}zYymc!G&h7nB8!?Ksdg2w`tMbFu|s?XmJt2}z)z>7gf2e?+}qbN}3
z>fZ<U_2Wb3Kj;`#g@qvj=C$#W)D$R3=US1}gu|TC(RZ&_t}feuB$Ug(oCyp>;Owi!
z&6=f8v8Y#RH3gbOcWwUs_ng-`MH^W!e_^ldP1R?VJ>egc;4}K3=WhLOMDQDg<EOa%
zdFor0|8A|hC?0vQs$xR9d_Eg$ExtU8*S0$Rjb&qDtrj$XQ?J3GvORQY+avShyN1|?
z5|l1L(c@dm2${7f{#^rhq2hyco6goOY~KtFxg~lOsAkR3z8D1=()3B|@N@<(WA*2h
zgFz@JbL>H^;5TDir)am#gBF^l-&pV*rq3FUXdnkYO7J`mlE%8xLm$J>`S`+$D*654
zbPwbl>L(rCQNgk|f1~_FknICd60&g<O#kV*0?@8#buIO@i^|@9duG2FWrm;ix-7B&
zu@ST{=FxyEwI%8<#K|51xd|fOlaJ^p4R|{l!i8}yf$N|nO(&X8druTF8Xdb1C{SKS
z?XIdApO$a5<Ct@r{*7Z{AwK*EZ^JgXUKa}saaFrp|4O_3!`Iq~zEjmu>-&e4Za@1E
z`aw|QbLw1^c1Yx`D*T1q@|MD>*GVU5oGY1V+TusF@44aP`C(6C4DlZ-@KFeF$BEHV
zawZMD_W{h1DOTu>k%M}gDpKK{Wr@;z-?U0bR?bL?!Nb4CS5~wRjsEK?bGrUbLWDC%
zFl+dIe4{xb8lDS7NEs1{MRzM(v%YEg-myzz`<hayaY65{rr+)MyAX%%z$DC=dhqS+
z1pw*Al`4L4uDE|${Hc_=d`cuoI#|v9YgbJ`-j+p_CS^1W-wIO%mD<%_^KSC;-eq{<
zuF2IYzm<;G@3s9c8NA4UqhpHVSVwyUkHgu$96oq>-+dE3Ld#_SN$*%}<8?75w0vkf
zJ6DHS_<+^F*rcskCP1#+(9G!t<3jO7vNDAN$DK~69e32;({tu;i#^@A=wXizHB(Ae
z3HGEE@p6}CX-5uL%bwSH#$>CiQme>rt&;9|3TkR1OPYkjR{y=Tk}ry0DA$bFn9R`<
zr>og2oSE=i%(m77m|Go_WR1!=CoZcQdG)8gr&rB&YlEA;)M%U}@#?_)_|fUv0Poaf
zHmOu307t%}v=S~C>n5hE6JY9u&s)q&M`NKYVDJaiNO3{C{7b`la4l^!U)3U6+5WV1
zdF>f#d+c%F3&XUUi-+5tlv4N_HK$^Ld;_R)X}oLRN3L6cD=TjkAu+SYJz2-sK2$Ci
zvrJ!g*oNjv0hiI@?>{#&iOJ?#?C0@L2VsJOZ5Wh7ZhbL<f%PIk<?Z)RfMk8CB8@RF
zYtP?fR>}V>^7}-kH2)i>LrpBi9$0E-7Vl^R@9<OK8S6MX+~6h3<t2`mimWi#P_o^K
z9|b}~`TIuk{ol5AF!kLIruQ@07jUP6fq5qV9S3hX8Okxl)k(o|7p45vZVaW<w=o1k
z_HVM4Ag1u|j?<w1;a5A8W}OcxY&bg(=weYX_qr&=F%RrF;%%3*Uk|Bj^i01?Q+ltY
zVJV<0xWYpk9nFKhTA}ZBK&L>Vx)(B42H{EaSZB&_pw9aBTU@+m;oVsut$+94lDO;O
z+p61JCy*p|lT8}0jZ?zyC*KacEF13pkTkBxY;5vke-OofTt#$mXy7P*o#%?ez9uA5
zDnB1y<tSkJ;qo{bLj-5V|8@3LgW_W4reaNtLA|4=K9d4X-zx0nO_1&a73JM6C6+?N
zhWl}U2VXq6PM&d!Um>i>9U%@5&imfZk)c(g_jA}KxsrL=tu~_klSc_7U{spbHA3Dx
z3D8?A%}i{lm)jLUCcjxTbnEO6gyUdDD>KX8(EG*ZXc?3_#%Aq(L>Z;_m}P>qV$mVL
zO>i8Ut8KRTN51Hf;5RWYmAm5hQ-S#x!?a?2Q?EV&<VV^TXl97^?ERu@710GY4FBp#
zhsQ~0Scrq%0?w05r04H7C2M_s2!}DP`>k`v+|c>&ZE}<DUB?jn?<hA>YRxY2cU0!w
zZ*KYr864sB9GCT5#WTtk+3mL8AE;(IXttUp{{jhx0zqRHW-od$bY{%dkGPqRs5%`$
zj5QsV{9XgIe3(WXYYUNmt$m4-Kcr5p4U;GsXxnP+{H28=l&?3i%8D$0IM}feCF%YH
zdn!u5oTR6sw_yw0>3$@tSYCBC+lV#O&emDwardu-mtiCXLXjvR<>k#nC@aEeeeRq}
zlmJ;GQ#zfhZMHKjU&v~2?<YUq@Nu}<J(##E(Ye7ps52i8bl;MC<f8OMGiiS%URenK
zZ!iYJ5zH%+MDj77g5L*AY!1h6y$@AQ7j-P}T(e7(%dc$hfXCs}{@;-KipIYfqX{%6
zRnzlNeZvA*qRCPJMuj73ZwWdeAs+-Pm<{hkS%PzoUWy2G(MXYGw(sM`RMU`e=x~UN
zg&$PRLRCybO;D|>!>f&kpGO5k>_awv{ms>Gh4R;3iB5mAM6rXH>!;Vv?+hJk5Z-_k
z-RE49xXw4@WxnZCbPn~<N54-r9DuB|C>g@_J=-@^Rk}JYhvdFOgKs#ro+fjED`DZ@
z0FX4WG9)i6zWebfr|hj(VL<h3cb9&+qD6jBE&%f`_DR1*S&SMq8yk9XsaxpeX|!(7
z{&+)X&UIFiYE&D(O4L1B$03n#Wwo-TIUlOy=0C_R3zLYo#@mefDo_r^`o)X!Szd>u
zRa_BwM>3|a(x=opl8iV3*hH(%-4XN{bIW0HOIVfK&hwe-V{`uc230dfEz7O-(7;zb
z;%r1nGregm^|ycNlPW@&Pdd6TZGJvwx3#;-O-A9IuzQ=FuUp|1u0VovGqaUGTFF`w
zWW;iXg7rwd7{_<`n{Ag)j7a>xZ-f*{Y{%)yZzj6ry(7Qu5>gw{6X=x-9KRR}3y>kr
zNXd#XAnh~nS>0tQJIFgLz0Mq`uXY|4da^Y;Uk=xnC9293l_swb0&cz^j@W5>9L5fy
z8PPkkhsFH=`+R7U*;a^pzUL6hztWsAu+8e3RZg-r9osT+E$nI9e=m==1^G5n@+@A4
zA7*{Te9Jt=)HG=w<WJ7j2}bX23|T|nB(YH8{D6hSPxl`&r)576@s>}OB$ZZhO#e=J
zY^QgBbJ0s%pB{IuOi1g%yT{%$!*sBJx~r5lAQGxe#(=tN@y#N9whquR=RsXKmmm1V
zTbj=HMfJ5k!!&fm!6TV4a;zrB_ndgj)JOhd?R|(_=G5T&{4<|9U1MdG`B3&ZNIu9>
zawi1@w6@$f&o{8Z<U7cSQ==rGwCK~fiUdOmTqJem{Uj4a7%SV?r%7y1HMtLuX14_7
zBdJwHXII7)gMHLXTJgA;`gX6+nIF!a91K;3h=aXS^v{dM&$BgNZFZi5QrpHe#ovJS
zO;O|v^vFDMx$x2fGuzUduDr1}T3zxOL&j)5YG}OKyKrq86#f5q&o<Pexbj@6a9vS*
zjeqjUEFF$^?YzN|G}D$B!J_K$->&DXrRfw2U~n7UilnXlfkNahZIz>P%&+-Jnv18}
zyKa|_sN+uROWp1T!T^U6@uQ?f!Dz09r6zUjL1n@Z$%Wu&pIxlY@Yfb0LD^v0x{!oA
zrXOT|cw%k#oJ`ycXEy;!aVr<|A|I5Vo#&Tl%#G@M`sI;pb3+&OT_12(tZqDjh)NU)
z7XaJ9lsRT=m0ZOa5B;N&q}HRmt;kzWPyy;e)_(X?=AL;<HNu$zK2{l;z7Cr$c0qRZ
zXrFm8%&^DK-;ExI2Y*2cre^0>{cg=IQOGRDn9FW&4=K*8RanSa4}=N4Tx&`s-41Y`
z(hlL?H08l(NWve<dwO?H%1#_zR_U!3SG9t+e(~^cv|DY;v&KrQ;kas#+!*xm9~QIz
z?>qxW=QA0B&^iSo#-Lh8J1JY~y@hDE6Ip)93)Q83{+D=Yx6P8T&i}A9UU3eZ#lzTk
z##A|_ErGqX9%*!c#(NvtcjN($t}_Os7pe;H@=E!1T8|D>P8Z;ATgAo(mM*TLM#z?~
z8wTisoN`Epol|hiP7KO>_L+?2-x}>8f4!GpmTyG=p`*UHSTyS#A?$8l(vF0~p;{L9
zm1^K0fP=WjD<{nI31P0xXSiq(dt`2*w*-H4YIQMS#4IzQe_o1MOsW+RoBw0>4t~I)
zu3iisW~omW6pbsdikCGrutZc1@!nwWW%38!ARcTS6CQESH!ES&Y26q-bF-(Q)X$Hg
z7M@XvL3mzpNFY9M&s?Qkepp{N=EU3ON5BKI*_=d|K!injHE9MHBKN|XygNMd<pym{
zUvdg#Z=d#aKW{fKRG)uafu$aKoKe={klyAVVt;<PWAdyejW6tBVsoE$vjmV9oW&W!
z4T7P@IYc#h&1sCB@E*O+Ek=T##9+`&W1p@2uS2v2t6!Rx_jIO{bK`!$pLENXXdsJ+
zk&mVpe9&*V{I_xoGC;GdVYw;2Bc=EVXZ48)>McQ`VLS+H&^DuBz*)n6fR*S6Z}Hh6
zwNi2NH$CX-wTe?wB|IDOV|o=A1Cf2fw+ZGtr@J;7d*8hMrai@l`1A#(1V=kvo2%!2
zK4?Sfk9qlM%GXI$@$=ThIs>481e~?6=<)l)ll#5s86YasdPU!n7|Z$IvMOMOb(-yC
zV$sz{y!LyK3bl1wO0>>v?F{Y-f7q<*=~FviI7c^Lpqo-grTFsbnGFAnZw4DS-f@(<
z0flXxTJIN^vheC2puT<2Rm>N@eCE%cgk09;X+L-$6t=!?VH-GqLfLLFmb^|R9{Y%9
z-Do4g!b9Q}AN~JcUMZt_bkOlhKgl5q)Dgzkt+0F@^1|4P5m|fR1WYwn@8JDCh!am0
ztS^{rddIC+FsXmI#1>Zn%Wh)R5k>FLaA>k9Y$d#$$;$;-eU*vBt%Tk7(VnZi>e43P
z=^ltY5aTViv_0G96PKZl2-|eP{n($%?eSBxBJS1TFor$JSeA79U%k^MoN_yJNRB*H
zc;UCxd||lTnXE17>iW@q+2sCtk}JORE%k^eg5&bGIhA!0A?!w0S_#PNxG_~l?Lzy#
zIYw2iEncxG0z&4<XAUVTw2XOKIcznlB@yp*HJpiqd2I#DiD>pJrAL#dlqF4m*>5$W
z&s;P<eFtefdn4_hGgvDQ!~z0by}wRU1ix#~q@45~K^7tCv$^+nQB1U7`mRv;kFAaV
zV6qC^Cc6O#gss@3b&^;7FWWUSuZ!(xebM+g8+Bfu+|nWC?|CdibG%Ngqe~sX^e)qP
zQ_TExV6TC*MeFt3iyui1f<G8-b~M8^Vwbu2j1T{^AuqRa3<A#F`w#~l|7yJug))!;
zkP&K$AXuysh+e!q$Q5%~_ni)fE_g_J*Bez-(U}eXIOyRms>1X&EHYIea=sDc-V9Z%
zh`s~WXeajg>hhjVbF{OPZFx!(gZ=Fr7wN7RgYb$O*wlg6=1U)~6QBI#lw{;9I8q|m
z(=~aya34Iw0^6eN(Y@G*sCV0UCx*JF{H#ogU-EX%$y8^Ls7YhQ7<b9&=%lg4QE05l
z22OT&1o!+YH5g*B1R&GCc?2O_2s*u)<B%c?(RI?E0Zl(?vdK0MF8po>(Zx}A1H5~j
zwD(G~@>gt0ipM>2Vpd%RVpbK@&A<aA^3aYbH(CRJj6wUb&cFg%{6Wa{_THEG?n?FX
ztlQnCfFL7Hvz;k2P0DBvZbuJPPoL`MDe#0&`WWChy$o2k`lie|*ZCxVC4I2O{WPg6
zOd?;;Dq&qigxpct$<X0;`;nCSU5N3+(dUm3phhXd)@nZ-Oqrw7KO5y|UxuYvLLAWX
zohN;fNZUD04NF#ggLt{_CdWF@`7Rf{zaq;O$}9K9vVIB)rH@bVY?si|q8GU13EMIU
zxT4)mDEw}Ly^B7JGGn2^v7Ti4ya9S=plC$fYG3pFiW$f#ExK3nQ}071)f+V%##omw
z-4&sSvT703W@;(|n(GsTW89+ie#ryO+!fsbymm1-5>HIUde)|O?PD!V8qf0|@Pj(x
zhjUzQy$JmOSx2^=D7$eysa~@A8Pa{XwuxVhR*j1-vP5=>t6`(SFAtxnUd^O3#WS%t
zPY9X6OlI(Pl+dTHcKKt9eNtdF9pagAEBHkI+g>z6->l-3rPyp~t)I&Ed|O(gWa8A&
zG&DpHdtz3Wn!2_bc{dJKbG5|lVldgN$GAoL)*OldLr$FxYeP6r)S9i&=+TAEMY$AZ
z5fej4<f{qCFTSrthM!0q(>>WyP}rz=_LhO5d{6mXVD{&ZR6xbsBdCLx1)TB3B3!Qm
z)HppZ1}x&=S9fj{JW`QeeYs&)1aYkisW*uNZr}C#U~XMBI{rSc?jQ+GMqAy5K9Bu%
z33<$ryPUtZ6TlRWZRQnIfnQKM9e$XMSeq5MZG;+~2G~z51(!Y#P%UU)h`vKp#I!-n
z{}6EyUtRplsJgMsg8+dMG7tOg(r{6Vo=vRk7%}f;IP%^#C053X8pO`a3Be`{|8^+k
z1e`y7EIu#nykD(l>fcpt(hhNW)VUVl#0yGimt@ihmar~YH9Y3Ibc`L+khwY*oxv@C
zl&N~;V>%8pVa+3>_j;q62qRl4TIpw!Efd2uYa$Jz2M!D&*OZ9uLDXvKUfBJ>Y;<k6
zJ?^o&C2lzb+ayCCe`*w>PBsv94-Jcbj(csFs6>b2B~(ADZ(GwcET46x6}B<eV~_X@
z&AzDF@?qQ4_oB|#u6oH*^B#!$s9(<ix_GpELcQvMe)6zs_l+z?@{s$3qJxVMPJ@)u
zQxl5JwIs4?6;l!Dsk}QvJkmEje)6^NXh!HWHqN*&c0buo+L@vKzQ|qG5biq~wYL#C
zCA|Q>)T8sL6f0z%Y%B>>NzxWoANFg-D8OY;2<C~F8QSV}_}lTIb9xo5yOkyWt*Aml
zI^k=c>qah~bj5ftIl-m`I0do$jb68G4O<86>5xcjct(;Lp~>1h?|!h_o4aZx<p3Yn
zO*WmSXo)oATA9aI^^jF0?qcCq{r4}30yBkRaiw$~@2(Rv>oq-*$+6H!3koTVbP+0H
zx^Hq?It!aft+Y4De`l8sD>Eb5l<2F^_rahh;QQC-`x-ZsG~5?DS_?2KjmkIr_lZje
zzbcGd7#;f)iZ+V!?=4eGou|*l2!7>M>zLVu$L?RprEFD^?BTm)TEsmp+%dHAp{c8h
zrN8Af3>Hq6_!spz$}FvPbiP-IzTD9qnIAtPSh9-U*7Vk~#NTuxZciU$t9CF-29|N#
zCQOs*V_Ju19Uo#qsUZ98)CwYM*;QU)<+~vEatk?E%hKx-G=he0S={T|fRt)a=Bs4z
z)$3u#_`Iuhg-R8~VJjvo^5w6CewWsT&JC}B_AE*B-RS|6bZ4}SZ(9DA{;DXXqD&S?
zfs=wR^l!&O_6~j?k^eX#f$oBJpT;U&FU+$QRqo{GpKbWt{DRdN&p}l9XR+bpC~2?w
zJ?9Yn(}L$+F!m@~+V4zBtqo_Ve}_TFO-4-BeWEf?ZG1>I(cOuHS_;SSBZqWpz2E3_
zgqmaqh9;LolhvYqrBh0DthvW-pDZYew1+Lph@@iZ(2XTC45-;{2To9K_%$-FYU&4Q
z9O;6d0lHCGzND&}{TU<YdWVeyU-b837T1$*TCf_><<%`7jamt#eq;<`Ia(NF1+L)t
zB>7Rs^63vom1;+`WDAPUe=axQs6CupCB_=*do~d}Hxz<9*-%rZM?u!^bh1r55=e`#
zeb)7i+I3!GmG&tfQ|i>p_B0j~ySsU2HlGb}s^VA&5t6N>&pz+#Ww6;kxL8eYTH%$A
zf{WO7X}Eda6RCQH4BNC@^_hSJVp@#|)%~ODL>j0l8rzj~f_rw-eTLRaEGFiC!mZMC
z*?evj44B1hlhKPs|1o$ce-yp!29xtXhDplCD@xMWwPs*C;OF-)p?nx(-mx2XRzpqU
z;;4&`vL4oQL!mZ=XXGftkNn0t`9Db-gbk&bQYcVoy;RrqaWc-Sf2qfMrOvYZ)s|<W
z7vDwy$laTa2-Pa;sU@8&EWw5HqNJt%pxJDmA%^InfM`L#Q5I*-`T>ZsQV$d4z3Z9#
z+!F4B|9C1ODRRCNR>@1{M5g&Za+nXom}J(16DV!{L6O%1heaQujYfn~&<@pYy@LhP
zxI{+13d<N{2KYUsOt@%AMlOJUImvy)<jK;CxIFftquWyUKs0lbfYm5$p4Hj>j_nh+
z+Nvi3X&oLru_@`+blqg<gDIBBr$Ces+a9NT@8GwmkSt68Iz3l@_L={45Ux)K8!LeQ
zPkCg~Oww7@LC;ALv)r`+v7OukEwjqa6a5281~wcBB1o1G_i_tedmrUA=<&~-A7P^B
z79Bz+vpY3&_91qfPgpPNK{DTGqQ}P7j;_feNcjP?169+7MdoW4Dz4=2($t=(C_!5o
z`u^ACG<BrSPW?pPcAG7{22n_93eMu^DaMYueFHM_m6!Xs78l!MJmp&EcT8q}byTC3
z)?MyW_y?3gaY)PFt%T=MSc1uOT?b-bhld!KQCBPG==(>9GN9@>xx}->dPuI?KD!&B
z3>yQGVW%0{xH~tjw7<=-wJY=A4=&E=`~8-*ca)f*4Z=Ad3iWcTzu-OJI<R;6)^B+=
zB46L(LLUMpo4uHO1w84U=x)@v#Vm0CB;mn*sjflShQo6&97~C~gC&Y%rK~4l%{XjR
ziGi!y$;$uZA5e|6aU@H`EXo$o3O+Eu{nPU0sBs*%&M@AC+pDq~sI-HuO7Sl8n5}Z%
z`nFl14V$kfjjXHoBmCP}IaQWZz!_i1hS)#I%+8Yxqn0+@y}$p~y7v3xB2PEk3rM*9
zSYg%|xhW#~31TSI+P|sCm<{Gs03jF%N%X$$mKECu8hTIqLPP9(CN<Mkt+v+Rhr<r}
z-eIMzIZZ{iy<xd}!m=q5c+C6anD}twNo5(tO>qjMA`VzR6Fc)mV2n(SqQbj7Ks_LS
z>^0#MW<D|uRm#uN@+}QCm^_=up7$c3$P?n-y?yF$Uq*<Z*}CT6UY3XtpXtRpWAZYn
zFC>lUp70;)B}##@;oT>4AqTWO2k-vnsd0!tRg+=kjxlkpZW}6Z4L}eu#tyggs0k(;
zZ`cUJ0;V4A29@m-oRvk4HtTc5y{B!D6kljjB(ptv(mN>lZEDEr=>V%;E1nY8%k}F#
zsFj~A^<Dd+Pa*y#uj~Yow0ts})eO*Hlp21{5BSTFGCq*lK+mIxcFoVBO9aFn{WFh)
z{R=7@U*`(vTPo&OkeUh305ELVnM`aIHebx4kySC?v@tq0XHaYYZQT!m%@C;s5+W*S
z+E|~^7TOuC3JWkAXY7kn|Mu(%&nO+5*YqEVdG4|*OulI)&@G-a%+t=)n^5_I`66F*
z!V&uerPPpRRId1=c5j{@w1>4ml5lssyas>bH&@qB`DC(+MP*gze}?>ru_3ww>2<}n
zxOn%TJo*mT71yt8XG28AFLMZ`i$0-;WeG+iIL(YsAgXC8tNv=cQ6Rywly}GFIPh1E
zO1iq`Ug(TVd}A?j&=5YgDwgi)DW%|Lv%Cv3K<%x1j@6~f26;lE-S#o|<C$Loj#=wy
zv=sB>8>_Ao^+Zm!h83StFtEYaQ|%=X!YDm8>4^1`997g1VgSxrQ_k85+QKm%7|^Y)
zYC(35ru_7B%=?0bKC`U>ANMBcL<UFj%_?P3MN)qs-S%J}RgoApru6;SF{XIyA3$eW
zg-`%dD7YW@8;kquP!_h?Vs4Ekjb8^mCOR*D^N=z#Ruz_oNr|(E(RYC0I6w5>J$T-$
zmHYlduFNO3Uv810XFs}{x<^#Wjtc(inJZdBgM9_EUble9Gkkp?(|t7l_67X0igQU0
zzfMlMV;0qJB!wec(`2s0E9*tx+tX`QhcVy*mx!^I9bnzdAeC{sATs$<`L7zjfof03
zkJeXvm2q_?{mO-7O}a5r%*48L3)mM_)v}gA$JMDd&-je~B*QrW;N0LI0h%FVo|iK8
z4A!TPB|MyH%K7J=$hzixf(>xVY>s`UkY}Gc?lNoG_ro=0KT=JG=2UI(MHbp{3`J{)
z4gry`B8AMYjkrGi2g|DMO9KJQGT#W77B+-I&Z8%=!`}fvF6{hS){GD%$`T-l5yg<<
z<Z!!2(VX48wuKfLwo|`q3<j?55>Oy6^arIrANz4SyYYNlBVjS|Ubua}>QX>y^iS*%
z?2H#ax#FQn8LfGZd-7knDwx=4^u3F@+`qz#h4@(^>b#cev%(r0pV$qH5{8%<>Rz=v
zN#e}KJwaVVC|itbhB=uwIoQ&TG#7x)q@So#j^!}214-Q46KX`yfI**+k;fn#CQw?P
zO5oY74vUZc@|^o@)9wYCR;r@;UZ#%cO|dcJ*fh(Ra7I{rF7v^+S#^B5piJ;7j}8YY
z+f@r<Sv6aW<<yWQ$PQC`cfN|O>)x{_o{t~F#FbysD=g&yfSqdoojY#n`bDy46y)&5
zZaTAYEo}00wt}0yZZ}#P?_O!n_&l<z=w%Zq`Nlep1YFneRx<S}GjJ6bWd9m%5eLGm
zP*8Rpj6Zrz^i+kLYrz5LM<ROUy=qtI(&uBpyuytOLM<(c+a|2uPS$WEQZCky;LF5A
z)VT%D>BcnfoX1o>(rQP`-(^yPuIR67Ydur%Qb7<6g+*afK+jL4pirPhLj7nF&hm7F
zRQh<+n#DOfz@;E^k-s`7hL;4LjLz<GxOw3;QiJAGMIxjW_cry=4`1uB9sq)}AJ@g@
zy$<E1C~GuT>RaNV>p=NTMkLhn>9)i@b*((hIC)moTLNC|Jkq5`Fy;b@DNb{$I7}O2
zwe1NR&eiba!qbHaZCOA$iGsg5oJ|9AQ@7J=0?|5&UOM>+B9ulpD?=>yQ4EZIU%B`|
z(2av~(|ecK+J0f5&P0bF5`XxsiOC>!1;y((kfz48YA#1-v7nQ~EVUGT@drbm$m_;t
zMK5BeI%rVVY_H8+;u#)JT$X6&xN+vt_abK5qFp6EGX>%vY-wN2`p~5lD2~5~B4|jj
zYrbY3b}v@9swzY7HJs@>T6A?gPG4LaF?qWrT2QneN8AJ#E)}k4Dy|?dZ3V{i5)Y{|
zD6?E`!?3*VLKmy)KVEG&faw^Mm<T<+3B5d<ekwe8)0Mjc5u`~LvpiiaKRItWsqyP5
za7z9fSLZVV4468C<2e0F2kK!=|8f>`yk)M0A{KZP1LQHTOMAXTIt{KFh2N~|Iwn2E
zR_zU}<x=5e9j??G<UMSZ<EfyZ$TNooe2~hWtiAz+%fz*z>7>#c=13sAdKI3bTUmK!
zX|hV`k%y*rx-?w%Yqh|4q7}}NB4aSY#O%3>Qe4%rCFk-rsOz1W%na5xakzMas8MDg
z@64~3NyDJ(&ge5z+E*hI)e<A9k&F?YPay}aC6dQ#m}>O5(STJ#-Bo&ihTVM_kSH*W
z6&#J~mG;x+ut)IU3RgzDV*93cnp2(_%W?Z*=hTQ~eOdTjEF80(PxK&I7+ZlEj<cE%
z>s6mg*Ce=9fC+=r<<7Khr@QM2)nkvB6%z1c^rG2&91ogn3JT(?x||QyQ)ehBjOHJW
z&VMJMj~B7yKlq5e2h7pBTdHnp$nw~##iwOK=daRaGHmwt@qqHC5;av2#~62))%sC7
zh&Hk%^#>JpU3U~nPc5gNS&$33ll--cA}9a1WkO#y*nTGbcD2NS-P0gw@r1s#G6s}|
zmhcv=MRNwz<I1m9@h@<ADEVT;-|e@>1R&rxB#*lt+-hbt4lqHTl2)bw!>lwLZga&c
zv^PXD`pwT~7ZOdHXl`g%Zofn;QvAs&aO!mwj{yQ-@EpQ@qIc;Olo-1d2Ur6<onC8x
z3BErX2ged(sKQq^D@#PY1L5l~pvS~$&4ryqT|FmKrkxyB(g+t+Cnc1iC{W^3xzhVF
zCHRrd-+2OJlJx8r)1MW3@b$u3KdyYBA%!|H#@&1m?VIZ=dGYfqRdX?xwwfbl=1=;y
zW_lV-*Ef3DCM&2j07uB9@5mc+pP449<r@J}H6+3vmWvgpB+eE<)~pdv%0sP@X)YWB
zXVPxFoDp6R532;#i6%$SYkDt5UU!1D+%0i2`jl!B!Kpt>^On*Kh;&U8A6Ks%rBMu^
zmt^*sJwCOkXV|SV-&I^LpB>>nqWdWzI8D!rsL)I(=Nv&GKsy}CXuH2bCu-ozV~I9F
z_?=~CZn@cJ`@pMaf-I=^FH?QR&fuOTVsA&2EZ@Lc_GYE)@>%T9-T><a(G@vj{vr7p
z1>-@kz`xtK$ON|uWV7PUhPDJA){&Ewuk?MaT$raie0Ggu?|cOl1l{|OzfM!Uqp-X@
z`~**8k-pV&oaEcL=@}daE?pC)$)=aEAV(YepkP4n`fVC^89{v8z*XNi>8++{xLN9N
z8Z-~)-?ktx&_d9Hr3aKXa4ABn=B}O3@FHQkUDQ}2!)T0;L4XxL0*$s)<K>C$G7fNY
zFVDL4jIEds%E;qtYC5_!qrql|1{X>-g3QSD$99LF&wona2W009^sxeQhF&GF%7^NZ
zC`yWkc(UTdk6^N#8m)a9;Y-bJWAWvhKM_2cw<ijo04qG7&aC|9;zZrvl(fg<NV3U!
z2PB*%3k?oSV4B-nIP<HSW}88eL<d#|aBC&41<xwjJ-&CSd0&WGX?~kvVRQ@~e;)-I
z&@)%e-r;i!{#;%=Fj!%*IOU``2oy8r2*4Z;Om!)ThMt*mw6iz1e?MXd6YW=3*crh?
zF;&9{7iRB5F$?%T!udh%@p&}+!JS_DLKaYwvlo%jBu^5~8nZ+Etqg1Di1+-Xuw;To
zvP+$-K-Kg?<tOgf#2v>;(yy!AkcTKkfnH6IZpiIm7YLgK2&a?Lx#aZkdwQmtX)sx-
zbpVeyVFw=)gr@>yp4mzm`Ytj0<UzN6D*K;`Z(B{>%@va*XyrN#G5ciaNUwPBGr`Ni
z>yz4PZ}!9wY3x`n4zohfm212qjd%l$JM*H~yBLg3JSpT!LAcUuISH>BQwyx?3Us)5
z@w%?VICI5I@wF>k<JpFl*fm#1c;AxTYq#Ce6g*!$)}tu4Bv+H!QM(+}SwLL&x|dyT
zo~gVJ4dA`)vz>hUr&4e!Jw=OFLuR)tR*sEB`+D@e#uIisRaFVUsu98w*Bu>h1<-@v
zm<9s~)|DOnus^-xY128aozb0Z!47h;=x#ypRdCshO%_(9W@-=|8)Pk<x1DcdgsZ#m
zBKxt+fq6Co?<68#4KqTLi2r`;@bI>JE!<CV!c+ku0#g*+EXHS-dVOOeI8r!24!Q4&
zS&#^xoj5XSCojjBrh^dbWPARZ=7>ZjO77Rj4NX7f#Wovrz0DVgqE$zfj=UZ;9d2<-
z%k8ZrW@{J8d@KD5i_1pu6Zg+Dcqiw~$=A3&9E+@T;iPWnPLNA3oBt<O+e#E$fw(VH
zvQ;vp!i4yMKPB<;aurOp@ZCKUd!yj!7vUoY6tXz&=@a7asIJykvc8C}HrV^ZH!?6`
zxA21zBr1131iC8|syiRShy{SdkFfgLI7(mgnEsRT6z`xvK@GIr>jCMn*=m0DI}tM?
z``VILt2Oh#<|L5l2M3S#)@DC+5BqPs>4G}6H&Fy2Xv`e?*RppnuBJjV|Ie7s?>#7d
zcKBJ#JKg)<MaC?*?R*mll=TUPX+#ea3JZ}|r(RVC%cD%m%SE&*Toat-c4(y}_}_EX
z63P;2GEeA}D}}?VWnZCw{Bozbs_#!}dRd~e{HL^am$F0}cCMIy1Nw?p7Q3AA>u4D^
zP-2VSClL_7;e}m;%|Fx5s?`%Fn{8QK^ESIqbNN4jus}h(aGobc>&N|@z|O+x?J%yo
zLO7MKk8q1K_D*Qdmbl)WOo!d8?(wIHzd&EEJD<hNmv*Gjyc^_zKBb`OXf*Y_cI(qY
zja*9MhgnyFLfi)gAaTe`e4FJnR>2LDEx^7FALKqCOAT#xJoPVuKOIzr{$R4K`wq`y
z#z|ePP%j?y@l1-LQE?Z{)1VRIkiFk}R=8)<8&pNZ2gd3(JAN60pPD9Xr;w(y!qY$o
zaJLF)-;PQ9_0H1CfR^Y<;PgC_(Ua!00P3f$PrA;vuD;kEB`_{iY<ohSRNwjL8`!9b
zD)>SA&4ud6Fo-!-DlBAHEM7lA86Q+2Xb?=FPPFD$;@p0)J-Hokw_!7AD*N4{k`a^w
zNvbP6MFpI-)ss$_?+OouYf=XUBj@4Ef=ZA*<YZIDB*s({cGlBveynyY14j$Mj}QkV
z%8u9C&WtcCU%w0vDn=KZBgZ{ZkZF9*(l!J7(&61KjRwe+$`o4HxR0FaEC-FgJ__>i
z4i3T<<=Y$A6FBdDkx<?zs-<jR&FYD0he*l`mjrlA^Sd443E@n!D#biCe1oagcoQ1p
zpeC+R!ZlZ}en8*J&M$slTC1^qaPNYhJK4mg?l;IwVdSKJKs${p6$wCSQ}6H};^=5`
z`P8#85&`ClMZ1G20$5`paPhb&Qy;1-dHf!kO_^;?J0ew7o6Zcq@>-fUarOrDRn!uX
z9(lZgK4VU9J7YWwltnVltyO{WQJ!~}iQ<EXhIA6y^A22Ux5z)A+w!M`otVytW8adJ
z1VO-ebtJiz8fV}7SZE!L@sPl~JX0^0IYd2^LNhp3g|4-JOZZ9sPki-->dVt_2Ak7m
zJfLdpH=6)QPfhCX<Z?J=_in}gU>n-rws$;eQkW^}<rqbo)oeS4RYBh**WhUbJ{-At
zAo=A5EtSx}0E#(~y6`ZCk%YN}7#R}HK`;l-3A*S0s}ydY4d61m+m5!6Wg=x<NzUvZ
z8)2A`XSqAu#iz!=P)3r7rM3jbb(L0;?ip$J-tCp$X?l+*#kE1#K7#Bo<+mON6Jl=s
zIy?G>7<!RUn>|MeWh>c62OA~hXfQQdpU<i1W!?oIV#BN$M)*DD{2uv&U62s_7B^ok
zfZCFb0OW7j(rYdH@H+d-eT@OM9nhM$3D4oyOD%ibyiV~=ERtI87YC#RoxHrB;?~A*
z!57Xo+v6MtW*A5do4GWx1{u|)n&bt?EJ|@RqQPF^-2cOz5Y({AWnnMjD8G36?VsDt
zutk57s>OaQ|2e&M{H6D2`_vkdMnWu3RVf95)}c=wKl`@rEVn`Q(Qa2}GVM3j_QtiL
zW4KE&e^GqzCtH&0T9|(_73>fH%<^~%q>e-H#_3&G#Fp`j&_}>$J=U4)`<%U&r#zq1
z31EP1DZ}2j;Y6co2h3k392#wVoR}C|&E@<FP61%usjNt?MR}v#0j`E?!7a?{Ryyjy
z63>o?<2zYuFjWj^)QnH2#cUBrQbX7$-%&NyHBDtz;=BH%|A+NAwx@MWOvsCsuG6Er
z`y~8@AX;V7=YbE6S_+f|oA6h#RAhKTW~Ob&C4!pldccD4yrc_|Lr*7IGpLs@>L_`2
zWfSJpe)n2Tdi{}Yz<1DIQy4I@f4ohrHu5W0vK@da$V}XaobQnxVrH2)%1DPP9q?Gy
z(pJ(4@jPAz7OvrRSqH-Z1&(*#Oy(r4hvC$O@q-xg`)~#FRBBXjrc?RSbnl@Q{x{D9
z7D%uNxY~HG*}mR+-^$4X&Y>RpXp!u6N_IX~^5h{YL;dwP-$yu&Avgn6hm5gu695Y9
z#$)znx9r1kG^dL{)lY|RVbzr;(Rkzm%8hI4!Pa&wIi*u;R$wGnoJ-|%m6HkX^TL9V
z?6CQ{ai)X!0mcQ8Ak}7DM?3!S<zdg0Y@Gxb3klPrx_&O1KY@E!mkY~`6^UPaIIoTe
z0&*f>bvqtM2SuG%i_%J&*K!e3=_CJhO31TT>j#6{Z@b(3#D21d58({+26xQaDDH86
z7!bkXOV^JPrqLrWhs6lu55huE4u6h=L+o>!(_Vkat{W5G$lgvZQ?CMf$xeNM{K``)
z@Ft&h71jTS`2lbpn>b{?f#7~s{f8`ujMDql=YLCqaBrTNso!6*#_4xFj05>|^OPY)
z(>cHIBR8K~P4{FnIbY|2_?>YzId<-Mx@+&~v@O2M?=+w&6jhkM-~owHzZPxF>DI}(
z@2}VgIXA%NA04!}sN?yO%0wLMK%xB2E$<y+ajgPg{5&EIMEHh#QeOK3Wbom+8b*K`
z6e*wH&f&E#ctQw+@!Y0h?T4|7qfHkV!MRQrthu7AUao2{FMq)^HRK;N4erDAAf=d9
zDDPHn->O0WB@Pzm>J1{h9Qz*Fc!9bnVC;I3pY5_LO&iC}T37H!yB!m2yI{sE3C8i>
z5c{w0c#i}_$0}?rV^!0As0+k+P>!^zMrNw$F!bCaG+8_2V`+|0t?POK<^<(rM~Uz9
zX>Aj0ozDFv?+00n{%I<Y+jru0at2J_t|aWfeTWNgg3(j~ubmn9=x{Hmr1-?}s+%Mq
zkZxb`^PP873SS=k+z`~|Z#Vn7rGP#a?EVmObpP9j_qn$6m;W3C^tos=kTb5B&^X|D
z(T<O+9M269!QS|Yob6g>kc3?Pe$IX?4z)_?)&2=WnUj~XJkhk|GfnqGC^v9|RGl1a
z_%+p3hh+aPKX?W$FZSaInfT@jA5Yhcl_wVUI;L1uS~631;z0fUb|WQiGTHKYbvz5l
z-;MfH%WR`Tv#}wDdfp~df9y{xoWkH^8)TMeamu)E90wmy))&-}(v8`fs2?4sA~pck
zgl*bhCTYZxWYe}UP5r3W{XL%GZ^b5h?*Xb53!CCAXcnr?_M6SNWqf>(WkQ~YsXO=;
zkhBZBWC8M6?6&%-|3}hU09DzoQ5X>A(4Ep88YGqOZloJ2k?t;uL$}h>-6fq8(yfAY
zr;^fjH~*b+#&L!Lgl~WQjkTV&G|9eh@=9Z2o;UYurd!WQM5;sG&TTBSCWXlexHdaQ
zTmxmr9S?>Ds}Aa0b$ZVPeH|$7I4Kfz3}j~T#@n4imy*`nICyG6>$)N-&LYYa6E+&L
zGw>EK0`*7<h|qx5QgHgU9xfWsSt|;>c;etDE*cqw<MtNv_c%0F(#7=Q1x)Is7+i(u
zr_SenC2s55lFUlC9xiI7OlrU)rd%=rNavnVBgLXS|4ZX=H7s1>o^maGnMZPtBp@YN
zl^{=2QT3+u=RA<!g3*&z%Qz4PH~vi=35Cs(Kc_-0D*}g&?|NMf?16zvZue`YO!@*6
zyvbDKy(rJ?sZYW#9XKlcV9D_$sJWVY8ocU1rj<!6zLmR-Q*C0E&wK+9pU%RSIG7`g
zBM+sMw&na!oQ28j=^GCOu7I8h(suYJ^aH#DLD`>;tUJd>%EvVfhFDrDFBf@5Mg|-V
zR}$O@BSVVH?^?PZUeIT~+!+P&J4rRvOLMvKT7(BC&*#Y{blsT~p`H(@0}L3JRzK!_
z@9Gamms<ne4vL>kB@q*ioisfxSD*HZT!m8v+~R^si%?jV9Y~AjU{Bw9+Nx<k?(Ym?
zzMpJc3*0jZ`gS6C)}(z2D*<V7I_X9h{|4bA>=Et&g6l@+v}Arc0|(Zxf%7kBGqt0k
zN8~Z!fpO#vpDAuH-FrU4JYp)?5ASCB$!Ynp^!U%L3MA;wxBMRLZwUR^nacuTHWJ0s
zPuoM6|AwnoqaweG2H)orGYx4(cm2!u502OXxqe)cP=`mlk5E)@-8JpUo0o!*Fta<A
z#}tQZZH^V>IvDgB4d27X<AXLMhGp;YLP+etz!QYR>wR_NqAqREYZ!89m^1kJs{xi2
zl8VnHcbJbW6!~SGmC5~t!XBSj?#@$u*alC5=ME248eD*_(<#y)_prK=<?JJEOND@^
zxrW*WK<3$G8_Zo72$78)e5jg?uF&m&bKV&RC0Gi51htp%CxE{*u1`-4M^hVg>U{Up
zU`z+-Tl9>q8fl%iA!e84Z(5T2)L#sJ{x&xSANz%Pscs^{0(nf;>!P6-yfb}QEHAcE
zlGM!f36jJiz`zu2<^?`#3;0REW1hpnDUR~Vgt;s_VG?|Lpgh_8dU1$RhlL=OFodt(
zehf2%Pz@5OgV%kq*`*e#30v*9>!-FI-~E1MbKUi&Bjcwf=)RiW!h9lyELe=5oTjKa
zgHxX-jsqM%3q%ULAQjra`A_3(n}Hgo6fjW$9Xu8mf#yD4{z{aKog5CLICZ81J16$>
zmdGV2ol>5D-<wG=!;MbVY#0>w4GsJjqMJKU#Pqx8Jxd0->k<JKn$*mZMWu>uY+W&J
z>w2=b`Q;5%D(S6T;X%<-XNEdt%1xvcY$LP${z8Cn-u2bDQ*juqR8z3&@=K;lWEnGB
z3_g+2;=t7!JVrK2E_=MuitmDb2xMRv^edBr)W#1kY>r?<2&VEtPW!u2iH4>Mm^C(l
zb@ge?0^C%d;$4<^Lxk$wHg-Bo$#hbSVTyFISV6PKLW(WZMFwEjUtSU!UBpZ(!YLbI
z47`zovpPBj%I`t*URDGm!gRkFS#19ru1cMCpaV&-icM_RJfn6lBo~ntvcRSZ&Nvzc
zOH~}3&9z}ud6(WTDfYugR`yuaK6sgb89c{UZ+vrP+xI~ApI;mqP_M@6JTJ~^z-SK(
zEUl}IQw!S{bACcTu^jbL%R{gazW_C^Fwj6`&33w{1K+X!O-mii$u!}U3LZ`>;kx#W
zBStUv&X-wAib^td#EEx+tD0hs@L`=9ym)p)-6w3!X)EM~c+&^=d42R$4QTXbPj6<&
z<7G)eqnMh3_UWOmvCR*^>$mWdY;rIAhNZE{C}{jZ8Tw>ODAb@o?!AlCPjY|9I(2*O
znIKUddcD<k#|Pqt(%p{`ITN@UFwDvM7OksIGcZ7hZ)=P@aXEz^<EbXI)Qda}!-A@r
zG^`olmuG`@l5Ukhr&9iW(N~>=q9#bAPyt{*gj|<Krw$)WCYV_c@ZO9PootR9IY^;P
zZO(T2hic{bcIyO!c@O@Gv*Ta(SzRpKrL${ML<pid@BxO?_OSm|(WYC$0O<l*+@2?6
z8(;jrf^?==r;(aUE4X_WKk0wTP=R38NeY&_-2LV-x|v1>ifj%*h#$CRrb0X^2*jSf
zO6t1t@_#5M1Y{oXLa7n1ri*24lk{NVUaZ~ue!X5TJOM5pj%c5mHw=-ICX`B6PPcDr
zsD%~i$Y?S-iFN~GrF#p$&Z9}FzD`@qHAppc!adxfDV8A?_z}0`2{N4M6kPC0NBS@C
z?e=f`g^U}66ouuS*cF`EdznIBPJjC~Ug%9#QA#t3o&?_cM%UAFMtAE@U~NA2Z;5t(
zsY?6momcFM#vAa!yoq_5eawXc6l8t2!0^+zw+L$dUxi-4_Xxfc!B)}>uqjW*7+2H&
z0IbbK0*fkO`4q8(5zk6DwD}3jReK&kT1hvXvOZ?)pB(W?f@Lhp>vrN*-P4BqyiiH$
zSM^J#>p<>e;3@%KZC1br5r`ePrMm78IX(IO4Jbb~<j0DcLQV$L-iBfl5U1^0Zhyzo
z7EWK^Zz0~_+NPm@Ji@1fy^<3u3cdXGhD0Av_X%>+@YtUL>=blh;eK*22d1V#ySrG#
zuLsp-ck)fmefHews;Bmx)NIdoy)#deiO}-uos&xFtuThPK|cHE+;)xPuR0PqK~uf=
z(d5f*LF+;gB7tczB>r!K3f^Kr<BFTToU;0VbAp|dK1m}Juon-bsr*YgQUF1IJA=PD
zPVcQ=$ea;HusZ<Vb&D@3=*R1;$+nM6P5vw8$|+Rp!KxT2IatO%mujZ#lkb;5DTz5j
zaRjs$K!)LT^@APu!0jiYyJ^S5e@ZOL>+c6R*kB4w)%ieZw7$_~&mQ0d1M`Z!CC*y@
zj2*mbGbXTj+>m+Ud3YuRE?F+n51RA;swC*}spu1jxEgNt^QbufN#g)#-U4h8p2|ru
z7%MAOLVJA}nui&^`Bd2gCFj#FZO;JVUN{d{#uQEZ$IOJkj{fiko)leX1oqK|pE%Bk
z{SACGFRZev<LMM-@Zk^u!p5U`{KpUO>E?fHb_NRzbqE?JH{>ud^j_-eEMt$S12ud0
z{mO%o);1Fmvp+2%fo}n9(5LP77Se~U?2JUbOR~)-qQTp9>#BYOTJMy|_zc+1&&t$_
z#~Q4W7Z$DuVd2GLOCH6*;>DSsn>bF(`>=Qw8Wq%;iw26sgNuK~39n_|@uvXEsQRu-
z7;dHk!or1)VOhd~0vI`x4)h+*HQVcKu~d9H*l;V~ulkEp)sh>67b;(=srU(u_tb&v
z9c^XW9Q;rJb6eqs)kTx-=d;IeKYc^f-x~$AHI%4kQ-DkbRIm*{pqWwmZlBT@lB0gt
zI+5{Iw9mO&RA>g$td4u323ELF=qJ7922o`IbPnocU^T;?h<o~_0MD$d=2k8hR&De5
zxdeDHs4<P02!+rkuK84LDb6#4$%nM!#vrknU~aX|EZEX{7si;iEiuiGdl!y$V;%>8
zT&-HVVCRlI?4awBPqUddMrCHM+A96w`W#$7JfCS3Vrw%a^MFwR%Eg{YlNkfFu2}~O
zvc$6DKz7f<Tmd=cCwHIKT=g;8+OG+6bBx=tsT9wh_A82R4t-w&a)xM%CB9ue*+|3c
z3OG-Y8d;N&doMtMr*wz+Bk4PYL4r?fd2Ug!^mm7ocpY6Gd;Rs2X{G5R!37Wp-qfVa
zm}7dL*?SyzDm(NY8RzU5&9T@sz#X!A+hbE;4a6mpp3~j?b6}uo$KPBPX4Y~rk#^*E
z+tfy?rPdUH>)~gJil35HV{CkD-NzlB`h76h|Mb4}{3`~yp>3&Jm{C_M_#!^-5rM-2
z>1j7d1T>@`@%QH#Rewzu4sXu&%4<3=qF*eb<T}o#&UF|i{^+nTi)IP?sWJOqdPy~c
z9^KT*&rnqm+|OV*2i{RNIC~gIO%3cPwj2$@mb+hBfQk@EpQ^ut+7&QKItJ4YmP^%0
z5x;r=lhDzj{ZmdWm-9hBHAqr>5)EHTeGo4Z=vRmZ_`6Rmdxcq6Qs$E`$LAY{HgN&`
z=Be{hF1ARJB>|$n1I;?S5#272o?E)zi@$5BjashKkY7i*Qs_M2z>~G?c7Yi~*y`s4
z^j3Gzs-yCT&|-H$N)6<UD(GlXlEPbY2`^U*@(m~$`qaNm&=}!KQGZfNJW>!ku@nYZ
zI|r{(_vKxdL3MvFnx5jlBGKN`m4A1SDgMHqVGXu8yI`u6Pfv`H97=Wh`x59h2ftF3
z#;e#JZ?I;2KhncZCP?2-A;i;;d6Z>Y(Ikhm^Hm&W;JqBq!DRu9LP=}g^3ed!3-GD;
zd`(A2;lv@_LcRnzdtzW!*wTq7hE>z5LzDFb5bMDx^lH0>T)9cU{^%MUxC)lt@ycJ{
zTU6R2W`D6~AGW<V1gYiRcs6Gvz&H-BrQJ2**i5o~_EeKUgWZkx-dAGXm3qYGGJ(hL
z9X-x%ur?WHH<>@ml2{hGv7V8-T^(&n9dBHhB76uDR0KRk9>lO7COFB!)B<cf!ExvE
z^NRpdD7ywZua?*+=c*Fvg8oE4bY!}<*VGPyR0WJ+Krd>}FYUx20Zi#&hYB=~hkfr@
z9ny5Nv;Y2ZGj1aQ78N(r^mB~aiLshGoegm1X{A_$Um^Da8R<yjOye(lv$aie=^4$s
zYiMnOGWay$id}I8?CI!4)}q!=k3JJ8COa=HV2r{H22PkO)tAdY@L;A0AfWs7Twvk@
z*0LPn8wL4f9n(GgymO6FzZ+YlE_2!_Q#jU{o-i-DAU!6cxQBh&Hy|Aprr@Up8jb#3
zmPi(=)=wRo&F?)9xqxWWy7b$=T4u`vGZ3lD0$Rl4-y~IY08DBXID9{#XB_g9BU48l
z)v!}S7Z5FEl+n4sHUV7xKyWr}=!N6cGC)p}H;Z0thMGNfez1OtmEQL2^I_lP+mebO
zY1sxQ?#{$3XKB2A;w!4LJ#Vxlm#h!d=G`QEeA&>3SXh678hjK8dqAQQP(Op@uu8qK
z_xZT?&@_)S|LXIDGJ=bfvL}bj(`j%)ej)8#P<NvGhgTJZwB+qEi3hday3e&dbPyi$
zkk7j}=emMgdaIB>s=gdZIY4A1FhhZPab_~?C;pVdg1&Kxbtnl+n00e$!GH!>gsHZV
z_U%z%WG~gyJo|?k*3-qJa9}d=r{}=^@{6^dnVm)MFn|;Qe;9+uZS}CcS;vvPEx_8$
z67HAf;zWh5ErO;2m@q+4o{#H?7sg5I_a042`>jUlPOUS~@t)00g&RQhE;jRy42#FK
z4B<r0&^|3Hy;C2@I5XKTEwMr_qsfJh0p<Z<_YJ_Xe?tO%mM^|*l%Q0XoYtY}UHvv|
z(R<x{b7DK6+U%}UVHk!Kusd%l;!V++hUkGT-%%0TtCV!OLg83xJFxY5vf>}sU+6vY
zcTywm@$TpjA^2Ga7lxmA7Kj~UQLN?^=@<qA7N)}Ysm?{ezS-*M)=#+C&N|~nPOg>h
zgN0N4a6ce7fTr1iqn!t7;Ot=ian&;r6vqi$hwZKh{>9nJtiJ*RL@O8bbZxkR>s+q|
zn4x2UCDpwb%xMc|8aWmSGT(o|VOIkG?eo?=fYW+yN>T>=?Hb%P(bmMIBVij$I<cL(
zq`yrQd+B8+qwS6Re~l-QhitXnRr?={aQ!T~_;=H4Vd_Kvc%vT>LG!z^nxCvzB%Cx7
zTjljZW-FZ6OHw(ocFlhLEmc<N$az0%6UK;PK`g>q!%W|Msr(DR$B>uGl$4iW_E9!#
zDnb}6Er<Fq>Gr<bMK^y3W5!C%s)OJfC`@j;?O9zJ6W}jNYrHOGzWT5$O>{^%G99}K
z^TzUsVk@fxqrp^OzESWK08{$ZrHF8|wksp7LvMHbe84st0#1|Gs3Z1&G|4|^ql|Vr
z?EGfW-p+r$@bQ|z`sX%@j{XF4unx(6CdJPhRbNf|L<JbpT`|Py4Q?A()z$NWRc%Sm
zpyO+zAMwys0hjcUE!xs#PacoH;P0hyflFct6$}HaNtg8oC_T;G{!F6(bnE3`T5_8>
z5!G`!9V(G;Rwq{>`4B4Kh{YfKX-}sqT*6`Emwn5?uj&y3ZM)YCZ$OQNn7aTpBD7iT
zKz4so!2U>i$QO6s?klz%nM7+UmzjHl@MIedQMMg$Z@bTk+qpjQ{>Y-B$fj|1wNE-g
zceBS_!0VfXDO8mEGB>rFnCYZInUhRnMibg{Y15)pre4+9>}eJ#y^#02@oKnyfaq`{
zUSZ(qRyfWD?V}Z+@8yp6P~irtz?=*nzQjRj;gW-(#_Q*DIME(bT_-g6fFB+Ew@Tm?
zczE4<zeIHsR<M<99d5%|kT<I~SO{iYqg<18)PPh6+^Huav3a)lrgw5JKFU&Xb$G33
zKMr*q+;7>+?ZOaXTNP|`d)vhN3m-K;*Bqx7l|yG<47q{`+kx=X18fYRh_>n&(RWa8
zbItAJJ?v0SJV37XykBlvz;Az3gzPlnW#89x+ZP^2t=z1e3^^Jg-%%2nY6`o&KkNt)
z8PocAod`Yo^P2;Md>5|ft48rM<S|Q;1n*2P1PY{0{e>in(A)!*vO2Hap370Lcy=8A
zdm29A*#t9%(b)RKX^&Y$U-&E!`g?ia>ZJH2)!pPaDRWRT6_tXKiZ@6st7=C#U0>R9
z?+Tz-`|b_>Y{8#uhg!cts9RLOtlbtHc7&A6xPGXlh|Pa$A!YQ)G_p2Nm%uss@3?&f
zS%~y;ourP%y}f!GnpSHbIve(#$M<i`H1#YKGlNe>K+N3#fe&;wjb^{>Q}6Cn*w}em
zdiK@ObrZlkfMG+Xv9WvbeI3E~_kCvvI}L)ywC`}r%|4Cxf%G3<fLn7NK`s7+7m1@R
zYq}wz9^u+mt5qWXcI!6OU8E91#lFrjEr^%N_jQKV`v&k_fTX@Gtfd?{Oh-+azw-Ra
zbUQYqlGIt!i37NaAsPOQ$~b$c{yoRz!eGT{0?)P0-6Gb!vU3csD9z=Y4~a0f%<C-@
zq_DFB03&q0>+DJ%;Cs>SB(&VcJ~pSC{LM5{(m=*XHY95i-xJ&jn7(7_BUWR3ZQD@)
zd0qX%YAG6^d=yy7F_ccVmY_}WmOrgOr0QuoNav+<D6e5c{&r#}G3QPc<o(dY0@qqK
zxstNI8c1EoVxo(Yh=usEEW`?{5rGQ!k_J?owjBL~k}Ju+<MyIQt;iI~+lAV{#PepS
ziO;<i!E)me34Z@gVR?8tNxx2zF>rpWztkQhsC$Ac{of<;26^Jl>X(3l=OsaABgnA@
zHix$wX+XT|U7T?_2e80B|3K1Y2h6NZwyux<XmPXq<Xf>8=$gYl`GIAflwYVPDXs|A
zlrN;uN?N^DASQhm&L1iUuN-4j#-q>jFRRYt0**2#E1QM};Gm}b0hiUj$RN3%nCX-*
zJP)3|%OD?6`+qEulCw=`ul!zg#KyiQo8Xhdnq!!c`Z(&294X#CH<*cjeF-!_Ek9O8
z9u|zLG9z;taGr#gUj#WupM*-;U4FsU{(DeC!!(`??#2TS-7;0h?~Fw_LS!4)@IT$d
z^qDQ*YuWhz9mVFXtz1%#hxP4*eve>g>K%$XlgI4)1U3TB+&d9-lK)X@K4FE}hk6co
zg8<M4nzT3Jw3m$=)~v)%)E1K!ZeYgk`li#NtVbFcQH3gC(bdHv25foQN>v^xN=Z{1
zY0bF_@<g(UU)QD|oniyozpyqTA11XS2YpPE|KvTB_p`Q^r`Fm>vTsHa%kyK{kuvVP
zXOsn`;!rGVIjkQi9Twe4P$=WG9#II{N(McI1!4eg3CCi@a_Xjq%zGXxA#_E=*FhLz
zSWY3~xQGOuO`^^ClvG3a5DhHrD_yZLI7}+EkZ`I31o3~uEBNAz>U(o;ek?O$dj#yd
z3bm`ZCi?^v=N}p?*e87Y8r5wwzS<$JT)s6&Hq@NNBOW=?v1^R5u}<AtaB?z;OSTJR
z%nIpN#V4I8-r!|WOAV4qfEr8`Tm8QB|M<66V}Z^}LPp(uxDq3s`qMHr_br4sbv$<j
zC30>Kn=gIz*ms4U<9d%(n56bzGE!8skFF;9mM)o_*W3Lwpu>G8upt!^`2NjILSU(V
z;5{p*1}HG|Ev26v8Q{6zOQ9PSG95GkjNLwEU<Qr-n`gz8HC1^>q$v>XiGU!oy6qa_
zJtC=|bgnu8q|xXQgP<Ikg?~o3@pCBNUt04m_Bv<8m5vw-e<VlIU4~(<!C`js{ocbn
z<jyVxF;vZ4ggS2oxim^hy5}KU<GDIQ0I^6374yd6DN!P4;1R2d#{--rJo?Wo{>0A`
z;b>Lo>Vgg!A83XoWKS8&F1)bfj(FWk;{YI5%`TUTQ}2y|w@;@^!>^)ccB_U;A0`$V
zTZ$$H{P!cT=Nl#FCy584L-ZTGSp$kK(sV_*@g@yZd5imwZ5mWnr9@>t@93l|%{aA7
zKTT?Kas(4%#+rWEzbUfl{o2Cb);F{!d^*HSxRbo6K+F5OjxQ*W1!}bW@`d*TkzZ{<
z2;r?vp3;wSC0a1kau1<|0NUb?Zdx@qmgDL5voD?x-O4-%5m?lU$`6DO!E9C9exyQ+
zDx72sdqqOn;t;U22fE5w@KVH{A>!A8W-bY)$N&>m7>MZ0+MyZ2F~0e^Be&y?$`Kwu
z$Ju%qQ9}|b*;Lj|;HL$rvu25ctSb7ak!<s$z|ad3H?mgcgqpvc5WCxq*=O&cZuYG~
zE;HH0cc-TYIvWFB>WVaZJWS_r%6}4w_+Iiyq<&8^;*$qgucrB{Wu15KwZrG776v>O
zIgCR=68TaXG5EZ~9HNRVS+{LJ8&h>FoUgYLTt;5Y|0Iz4e(Sl>-;0K)cKNjz6Cqjq
z<tW>%=j|ss#f5%1Ki?Jllvpm#_^k#@%tVC&t47vWD|(yLF;c?q+!6!Mz#08=hS@xE
ztvTRk7t7e^FR%E=gX@aV83t(v>+^pt(pga<OUah8=v=~|H&$igEeP?Mqr&I(Y=d&7
zuw1dIVR?S!y2N6#R)RbHoyOA1NbyOyxh`*qL#o7bbN8#)ZfONQNJL6-cnPOIbA-rJ
zGb6=sz4c9y<m!x#pN5!vj??;fk+u>@;ZWg`9)t}Jn`r!Xx$-A=oHXtFb?=4N_X$~~
zSOo*DP#*VJ+QY!ES)Btb*QM6LK2f><>NJC1w(ruNd&a2HPT;F;SPDjL$lCCT#f=)W
ztHi+NJ$oFrsw~~{9o&c$F`GH@C{%8rzv{@0@0AP^3Z6Q$un<h=cE`CxD&K6wbJ>zf
zQ-m>2?+<`+)jz34>?~QmuE!M4K(`fMAPdwHK1QmDK)6e9%-cLOHs=b|QU5SScp2|E
z>fV&N>k&L%4o84p*>kYMTfdi$k9|^tIJe3p+SeP;@U?OV7ygdmUC`0T&r;!kXgY_|
zS9fsVXsmP9FNBddU05oK-v1l%g^*DGbIf&{nBd3y+GeLhDS0wA->C!?Ld8}IvI9UA
zHi25BnBhKy#$4-Bjw|!&@RkO0Yd7MqTiKXuRN`o64fA~yYsClM;ID(et!hX!u5$i+
z!C6H}z$z9Z^%kssOuyFH0nOPp_X5EgvzxtQwd2V)b@E^5i#c|fBEq53fJbjiF(H#d
zd+o=A=U4tZ=dEmnt*5LDw3LD=&Xr^T#M26YzDVB4E9Hzmz~xGZ`?vMU#v#hCO_5Ej
z`L+7`{w7XkEV>v214(G)5fa*^C6@T_&x^6x*lpR4?Ruze$(s-CuEft*jCBb~EVi%`
z7b(cG=dgGojA0>^@e5Z*r2;RmAwzH)A)m#?DVf8t#c3eEz7EJM)gBUQE|A=H0YWVQ
z1i0*vs+%cExZz6klP^hz*S&=)`~_i0w?rK1V!NugKa`AoA1LW#(en<b5`F1w3<*cv
zhUn1d8<i@})^RD31Gie|s=_v|57ZfF&p7a4pG_zuY8*U-vYU$%CSMz@44n6v{fgz%
zfawhsOz-E&PAA)wq*VpKyz0Zlj}UN4YY5_q-C4UL=g^Ensh6}Rd3%Ik`xhirA9#cA
zaRA_vqsjILI5RWtwfZpDT7)aT!(5IQp_wr=BIyH{d02hnh97-UM~?z8I0q#t<LV0|
zmNH!smz8Q(q=>o@YK^`6cxqaezrD!`(%8M9%s~%CcNN`iZ7C6k83&Gc!JXqz8n<0q
z9%>@&FwHpxUocUh%#zpsT?nQg0pq+lf8XZ-0r{FAa3+hYUL7yK9FW~f?8`5!z?4ix
zY}_~*`spRyDcIZp67{aZ*e7P{8;jpHG!Y97kETw9V`DE*n2m)M7AL{vu~02o<a*EI
zp`W62f_Z{e$K%BAb!ovj7kX)47uRt4j<LtJ$Mdj)PnVBmKK|WtD_vr3W@j+MxZ}m4
zx6(*;VA{9k`Bf>y_e~%R@@X2PvCloPL%U;Yz(1d($wM79yqR|A3pga1Q&G<@WcbDn
zjxGb>G^ZC?h0Sc-!5jn!A|l|SR63On*V+N6R1SWwQ3-))&tTlwO5<n1_0NpW2;~bT
zzeV?Tcu{`e#;}hJZONuA!EIgQTI?`5Uz8KPwBF^Gl#;y{P5T(5j*b|J9QcenMpPyo
z(fiLVHZ|S@Y%r+i_o&kY*aA%@kXow5P1~kxl-W^=zBLDQzdkhlUeyE|%hT9*ZRF>T
zLn>9vFDP+&N*a~G%<XRyiku;RuFYt&4L9q{88^nJc?eaiUgab^tKzIh;qRVvKPXk|
zE6p^$Qg&S?u2i{`^>5hzmrG{`hB|9Uz8fy)>-szco(^8IE$?HD1s$WC^KyqwgeTy3
zn=uHrQ=0WyPndD(2lsshf?k<kVgc~!LM#Z*PSOWT(b&H@R|j4vG#6Co)=|UOxC^d5
zlg$iqihauKO%f^MlL%ds4AU)Gu2P3N&jN`bULWh=u7=<tN%GKtCg#6}h%!+Iy`Ei7
zKd41k!=Xa!Zr-5&9EPQX_-z6rQ7Izz4t9vvMbe5`h?fJ)j*?hq4QhhSEwQt5*=B@S
zHt`wIyRqtu;l@KC;wRi6o?*z|W0{MRh(Z|uWZ!EZk5J-^wZ_d+om1g`>V6<z_eX8(
zMyZZ6Mtw=O4q-$#_33R7fvRc{0~^WWF^T1=Tqp)!1T8wA+lKtN+cfL^;EfxWsvn@J
zOqn2mSHh;mZ$;^rnJKn9!$DRyh5@e0bS7LxRR{M}<Em*}eNUSzsYYQ$1snvqgtvHU
zsku~gIG9Y1jELYGWT}4B{92#d{=-*+H^KdQWqF{_eQRENVESB1t%n*dG6c}OBNY|3
z<@yd6XT`84Kcs2ABr}+$PnsltIhvqMvUUsXsr<^+MfL6T-IG6LRohVka%SU>1+*Ey
z0U%dk3Q$M=?L)m=A`U!B0}kN;ipOB(yQVUYJ1(8r<oC<%R+!qTy;Cxr97)gR$kj5d
zfsE8CC{-0!wR@a?RpU@nQ9XOJu1=kUMU1evI!{4afROlEEHMlsNn9<U97zd-Vt#C%
zA$<OA8^s6MUgUx_rbX2)Tn(Qi02+5@B-O~YIx}5*QLlW9m~ck3gKX2$ZE8_)-ZG<B
zJ$B<p-PdW#OwPfAECVcc^R(15&P0WL_x>hd>d+&kcHa-txwetEi;&FgssT`H1@McB
z&p6(LR>7o&{Js>CLrIE~_eb`CD*lbSoN1Xn$S$`+ftiy^XsR|&1`5wsI2G3Qutify
z-29j;lf@~2pTWFk(FrUfBlB4Qr#0IFGPzEwQQ=J8u|c+djd7oFVY`N<MOBblTLKq{
z>CSHCOEFc<=K=u<-TEjJC5QX@2wlXHHjr*ahvz?Vv4}n{;*V*4%Ya8vbw#+d7nT;m
zJ8375mw{{|K+v&Wna@h;Aq7zJI|0#Fl?A=k*>4^2YRMlt;+-Lzs=KZZ!7f!9>+HlR
zDf@B=xhvSb&)^er9y&4*MWUtdd3_z=2lI1FO7J1i6}mIRaxhL!u(I8RQMRxGHFg{C
zU%j=j{Od1(2kp>b+mU;QXo^=m7L*5702ZRW;lapgs2o}>A>Y~l+Oc4s>P}c4cskB(
z+Rvw;0c!^nCp(>|ibUIshFE~I1iaS=c2&x+PL^RHyB(oNP~&XG&32*p%+FUu)H}Ye
zNdoAT{)mbIFlw+z6`0Hr?@t_G@6Z$NkFY0?oqv{Eo%w8IH{9^1j7fczj*tC|@uTi5
zGRqRSG3(0yMdu_>MKjZX*o*xte3hX?z(sEsE9CQ0olPlc9|a7OI&Z6&O-@fq{}%N-
z+-DlEPVP;~sxF!#`lGHGe|H)8I3uhYgU1J5LEy}v2ixaVb%Vp$l04N;SU;$aA;%D&
z(!;SfRynDloM1aY3SCfRlcJ(_c)IXjv>}S&%9&%Sk$y`zv$Z*eR%`leX{K#HTbxoE
z7V^68E8hC~cjM3<R2SOzEY3G`>?d=UXG}guqLourY3!;=NDkXeLa!DYM;i1MNJ*Im
zC#@dXg@wK!L@M$ZxmXuaNN65muYE`Pecpv>A+pef_WsDYqL?jn6&6e*nwsxa`it^q
z9F+o2dR+q}tNm>G7dF<wRq{1890WrxoxQKT+IoGi`Gej6Z|EB{txJbMNB)6lG}B(b
z?-lS9<1|&VNWS_RPWBza0sl|-M}g<_QMom{z6krj1=#9WsMsG7bGzm%?-*9FQSV`@
zf9i!HQqois2LXs)a0Q){&l#eREq`H3z_VRbxUcM(^w#3?-&SM?@u2T>tttmy4`AIY
z#mn@lT8<uOOX}cBg;3KsuNoZ^_`dDgfUn37`I{JJ*p&CI55D7owB2T%)if8*%J1dB
z>LAYP4L5Z0+8HkoAyN`-%%yBG<G7<*FTlJrWm8$5C$E$aLj^Si!R+CW^axJ|kUS6V
zS!YrxNAJAvMfE+1vK(}eiqmZzv925wxz1iOaitt_2sog1PMiEWdpLLZfcfgUBinds
zt=^Me9D)%?NW8D$ax;iEQmzD^uz-tSnyyMz*%4=BJSrU1*?yas_y|Ehjr7#sfYfi`
zc}w>!|9RqXUeqRq(Pf>y*7?;jpvVMcVTb!6FfhB<*j!&$fiMQMtjkIly{!8KTN~&R
z4d;!#K&W&6=t%krTTPoA%@^-4AEk~*3u=K6=~3hZr?X=+<p&x`1UaZE1B6jUksQ9@
zn23>hTb6(%{bcM|=(msZc^fC?5krz*2H>8km5S9{)V9y(q*mi1!Z%rJbGRlM(8aPS
zfG6$9mwjk0*pD=AS0)+pZ|v9~aZm({F<G(mf0jr-LK_DXKsD=04m*NmYf!E3w#qN6
zrs<bWf6$A@u$a<#E|rjKSOPSl_kLEVzY$whTDs!?5fY6TO`2OM6u~9JX(sb=@dF?H
z0o9;Bj0G_=p4|JDDKjdX^dAK<Au&~e1i`If0_`to8aJ9ja-bO>=oh;GjNy;QO03?x
z>b(JGS0F|6TD`Rjm8Z6dAE%unPi$^}Yh%`EYrRDWw%dvWfcec(7QJ)hI!^!=AiwKQ
z1le3=-RW<DwZR$%<eiPvsx}}6D7RUex&zlKI>Mt^6~7oi;XwF7fy>E&b7#e<HdtVK
zR>^SU7W1ZxCDQs%fD~PToZ``#JNTsui3ceS$sic>iEM2_=^^ozJoM-m;6>+^K1ny+
zch54Gi8H;VNsBOBv>Z6`M-=;bbj^K0muv-q30Vhg^W^G0$vWwb;3r?TF=d~wXk?gU
zWF>Tb4?LM5w@hDl*~RGn0MLBJ{;WL_r0DR$+`Oe2YnZgs1>P&LSj*bUXTW(H(3!AK
zD05?p*dYeapdZ+Utbfr#9q5>qB13$A{60{-EhrNnY_GzX<r&0HVF+L1CA62*QQ1pi
z{mKQdL_vS5Ltr{kA-o&%xi<oMt9P*D`XmWNf8<3uNmVMyX$UGM?Hx_D>eo+dOY&1<
zyIOtEe^kMdgxKLaQ4*4~{is<|%VTy9y=;MtUq|f3SXLv#c=({r(_Xb~da2W(|J)lX
ziv|ci<2NZ?nfICM>Sh#bI)bYh`&^U6Uqx7e{zgNmlsg_OON(YO0b+yR6O{kkQjf;m
zVcf=%6=!eKkO&xTZq-*cPt)k3%!tGVAXm-p`M<Pf=Wn74`Hg+A2Q6b0LVi>(?ys#_
zdMK(}a4UVo^krEn{MiTwfRv6xaj{$P(lIy;C5|}$IdrZ12*>EXoIO|7g#9ce0pSql
z{NLx+;6cH3-5YSDPJ)@nCHY6Wr-vRzywm0tBlMR!2Nfsf^rF)%chs2Y@bPP6{R86g
zA`5OKEgwU$oG&e<J<u)={Zs(TqRW=n2BQ=1m&@Uh`0AB#(4;1T<G^3m5K-|}x0$Mn
zmT`oho>vHgP(-_dZzn?Q=>(DT0vdCrOSQU{Umc&|(N3g<GtO2S80Vo8R{U4~qI6`v
zZhqD=7)4vai(RxewLkacB^@Q0v_F_ec4P3Ao3=)7c!Q<qLD?0U2`!6h+VY3a`#EG&
z?h;Tq36UtFj<~CuN9bsewr3RNntVV>{QA0o4oWqtnO0DhU#?H1w;aPX1cdJWe<)ES
z3P^<Yjj&Xklx!y?{%&6Y!ZS;ru0mh(l$9<(uAbyO1oQ!WKj6Cny$i6H6<btemNmVa
zaJn59d^~+TTSDrb?Tes#!f$sS6B?U*xcl}~Vxq(E6NpmSR`I_i1M=SE7KbluK*SWg
zE}AY~IaYY--~yyYU^OMzF`cJnmCL{x$)rxC$i<t!GZ|shd1u20kRSo8I|g0sBLJp)
zHy&^)#Ls%rS)G8NR{d}j^~KZwOZ6ix#i!l+^3>;Xm;UYwQzW->e)Fu$Gr8-**!L4K
z7`B<51g|{CFK82_cGmU*e(1o(@w04K@E&`)F**|VG$sV32xV%E9NQXMCzceC0LL_y
z<<@VQ{*S##o%Zhl+otOun(<Y?C2;qAEj|O4m;1~*0NkyA@8{dLuT(X(Q`4)Mwoh%2
zRl!08+id^<xTAPXdAthL3l=>FdD^{zM|PbA^mm(WJ<#_KmB$kg86p;^!-9bO3=j@y
zH?tGR83DH=LJcl4z_)d`dMWZG^~`IWht8&K&OUt4xZ5}OqnZEVqlZkgnuXLt@tGz^
zh)^rk)l$OAiHxj(^n)=<W}qkofqPGlNdn>qp(r1UXKwyvbzm3b{t5dR9j_NZ3RN}E
z2wSf+$P>9(OM=h7W!9M8-m88=+ebXK-Q87HhM5eXs_H~b?IUfu&b>KYk%1}kh?<L$
z!1>0X=8!(K+FhQN>!n08q&j{}z_cFQ%vjjn0)I-hYkc?$uPJ3%K6q%v<#Wn@bF2bO
zZdlaNZp&fB2JSOb(s36s`wF<JXMS3OT|X?$@(LPlmRFMvI0>-`jOLb>bEXx5$R7|j
zE#m+9Lj7!uOgK0U7m>ZmKq8qo^mdw*l$Blhi=`*!2xx@Ai97~herOcA6(nvIFQ?I|
zZ2UFxX#XOTQE}v(lL3L2wLxpk;9fqc09DJrK21%2*+v9BrWlzspe%GCQS}JAMpDy2
zzrj2lK)#Fd)vq&BA9qrks*O4Fala~`J|h#F*<bhHzZhj2VW!_6E=ngJ-135xHA9ta
z1?7%WD~D0b;o(NuTbKZFPQ}iZjh;!Dx@_M`Fl7afogRcL+=gUUOTMCU;S2d6`oe>P
ze}9$e>!e$zO`Ti&csgCv!4&sS3w7eG)-J_$I%n!@vzJdAkFkI>Rf@SQ@4%pHa&916
zlcknKEeC$SnoVupd``TITBTd_Ys2-;gh02oqty?AGXr7Q%M(?q<sQd^aoX7;eSMzT
zR5^M_HO&U}?@JKHy2na!YE!=-zq`n~`2KaQbo-uCL$@eZ(e|!Ki8_C;z%BS_Y<b<h
zDoz_|0Ip<#U?sEjn`xUE2SFT@pp5MkXtdU1u1KPCadW%SYhDSrd;<${Z9Er>D#!-0
zAqZ!ed+0@E(*)~%i{7RDZcHTIiSru%H^50|T`E>=_1|j(&<kLDn)0ZcEHmFY$w-H!
z5}$V-(I7{d^T(Qr2sTNwQ~^;2k+5pPPj)9e!Ubm#Vye}Ph8hLFPU|D0l(a9KAR(YK
z@F)T_tMBnfIT+!83AiKxr=>wYN_j?aC8->Vb+oY`{2FTowN19SIUOEOUC?5I`*r?V
zb#6Q&&=K5;rUO41P;j~l+0K0X6QVpw2|*>k%6gPF(eK<bYqTRM8Ua)@$Wl^fO=4C&
zScY_;1vwhBA!|q=lTlpSF_fe`8*9G>P>l5!C;2E%;4lJW3f-*onpOk)%ovd$ZYVa&
z!vH7!2@tJ-#sa820UK%ab~<7A7>;FTZ70Ax3ml45dB5J-Y=5VqDT#Za|6Zhl9I*sB
z2G(tV*ySe(8Ck-RqJkpievHTRSjt~}2uG1M!5=!O;9a7S&!wT>-S+7@cz8SKX#(w;
z9ilM_ue-5Lm0|ku(U}?#e%2uVa<RZhinICbtYMwgCU=mxqD}Bu=R~plet&VNFiPI7
z$d(R+^b5KxGK8}Q$bA$gnNKv2pD(u|Ri*-#!Y&ZVcP#F=>gI*D5r$yNCW@-#E0dxS
zdVmII!&{i<nJySD{dSF34@2UxO9{A^p)lRey`_OeGo(%8jz1dC^n92XtXIG%VU1#L
zO8(%+vMlV8QF_hkcZ~-|Po$)b@pApDtt})JTd8{ay#pzhU^-qFgTb6cmvwXoO6Dzb
zrz~;0Z}s%j;NmxJ9Uj}m2Nm;JV+0f$Lg|X7hvCra8)Ca}bYhGXl#g@+q#T!Q%4e1i
zhHJr5Gat%&a%-vCvWaC9ES%GLSMGYOYzH<nUDUsHbz&u}I}0T`Wlo3$gm?NTO2&;p
z-Und;0IRyLmE%_L!l;2Ub!L>y>XWY<ZT1AxUXrtrWs%=`=`V6r+vWeEt25Z|!M0L)
zrqM|dbBfGiqfA_U7OPvMVc5AI2G#MPEJDu=DS8XHZS7W6rU|xEkt|awvZ~e%H9`&p
zGf0fU*TJYbk;Ku4t&ybnask6Iyozu<5Xy+w{#q&Q{Y;+TLCsgS0Rw%TEBHh#=sJIB
zmFcehEb&oJnKO|WZ3Me!14}~m0ZY<8n6UJVCwh1E_NW1le&z<IY5Bmz-z@zvj2Na2
zOxoqlqpxl5Tp!*b1cs@A^vo#Q>v^4(Ru?d1=XzSbR#L$YTzueRl}Bwj-|}R!0?1c?
zpvSTW^kglIb;jT;i88lB7bjC>vOR33+!p0jn(}rH@K)};bP&l|;s#uOMMO5ypPP<`
zWQb2`YLXxn8+IVr&MON<Rm??C%KY~oz|CyM!~azu>~&)%dgB5}=UJnGN&hK>!KFz7
z6whr4UqUKm2W1aTdK<S?nVV8uT1EjH6UYuiG<X!R#2}1lQ->5oPRD&%nbMw>>F27S
zD|uf9-g<K3i$H*si>_SZ{BTDOI{hN>$V_3i!4E1Yu4Tb_z4;7A2M^?T(Wwt<$R^;J
z-nDRyclqE3eFUd&+B62Bjcc15b8{djJv%_214v-N<qd3#K=p9?Y){tJ6E1e^c>I#h
z3B;WNrkL&BO&5XI`AedaqdY~ar8|W{q*ScAk4yMS!9GUx@z>F<bdo%Xdiz>IjgY9C
z)TND|$3B5xJATiKUna8PA_}jHtzxaxIQFVqezsqTo|Izv!QPdx<CFaJd_OrbUS}dL
z9Gw?Ytf^9b&wqQ~%gaP_=k<xYtYIyOuhP|Trl6Xf@4@qp?)W`DT*{u~o=e#yCb3LG
zlSvGiu;*4^nBVzPeBQ{hug)nc;T&>B)6}lD1I*MJe8Z;V^<yKcWLj4xv4p~!>}15S
zfk-rhnRXxh$VOc=?@mR2D=?qq^ZF34Ur*b4d&bNVsYqvW{QWFUjvoESdB~?MefbOH
z$=Vh%*lhhEAq%2h9j>G;+F=HwgGMf~SGZtqm+Q0GuxBCM%qvm4Sg_1Z^|8Du`N&7H
z!|L>*-%4v(2^{LNSlEWQt74eO^t+sRQ&;w=yusb{o*wy_j2YTji#npoh>7v+XfSY$
zukOymgw=I5WP>865E?h8KcxFQI+4tt$@RH*u6jPrts_|mp=Q2&N%`&fLw3u29vMI7
zqdtC2tvcOSkl}SRj~Ay4B+(@4LXu0CeZLN7@%CRbfM1+8d6GzY4hf;+CxLim)>3#!
zuUfra%aRxl!pM1zP)aXMuoY+g?al#uRf?9}hupUD^JlU6s0W(iDI`kcY%I0Y*11C{
z`Dxt#SUE$^9_`C~+?rJ6Gdg-zCVb?18H7`Ag6oFr!DXS(r?6JNg^RW(Kcs8e*pUv<
z5X{6EI#$T_aRVb-H5P$r>1%$XP!j&+y;!9s)ots_Uis2MXvFztRKIwFmgW{KYiON5
zZ!&Wt&w6_YcdtfAk46W|$6N-|5dyxfgN>Nn;J%-gZttc4uswCaHdv}evS+729)9=x
z#0R)ZHyHi@AyK#h=q0cl1HZ1<nf}D-wXyGZphNKoAbk&Avl5yv^LRRBl_RLY1D`i6
zczK=wL{Yg)@Q<$Q{!tO;^~}K_l_r66mtrhoTx2mzm^Zl?fFRe@X>z$HF<qozDOR5v
zKRN`Yfa7jwZ~wd!Fe9#ZP&M_=F=|7`*&eqhoIv(me%LK=1Rr>XzVdU-D78^&KQG>?
zWeu|)+Mo~khYT8X|Gy5tYk}gKd4r_<uX}(*+vsuL%2$LE^0ZS|@!uiqJZn4pFQsPT
zwV}m3?tv%T#wyQ4Z(DENv(Ed8<@FmF-*}e`FsDR*s}&5m@4BLm3{FGpT$w*QoWU2z
z-6NvU66prEI#5xo>Xp>-)(^)$9-H~^H5t)&ib?SfTr`8}Ft9I7TIo?zrp2BB$EG@w
zr=t&b7D55bhib8%1rvB&2a-E^o}(2B@zB{R(OZOO!tNU*ozdrfqkatMfd+6p2+gy-
zJ**FEy9S?S;Arof?lA&=P#1|24vHaN@Hg6`@}Wm|4;;KH-#UKZD-xOp2;&{7iWlbz
z!fzkJlh5sl1>k;;n55eEMf>IPEdy;~oAskJ1dEaa(%(7W1QIwJnI8_86pzqr0+d&m
z?=%)Vi5giQd-kUf(Gfgw5ME+KCc7qCuS^47gxlYg<d!hSef+noR8X0xYsckfL0)ba
zhRV)5+PmokpGb;~gSnozK|@NyI(Z^!&gc3A%;EV>j<fF@YE<HgnOe&z<#4(l&Mh5D
zF&9p*%<Zw+j=eT^zp)o5AG{r;`*nL%-QoX*$A~v%=k}{&hJ2d@RT|J_K&jYWlTxel
z7PsV&UXD199(!`7K`G+6z9>`6;Uq$ZT}F3Ble^9{vQc{v4dQG@$_v~w*KC>aWGo^y
zn$#LtkRKMckG}e$m$pG-_x3GMMNx9tQlOtAolYlLy+QRO$)jQ#UNjtyxwSh{e08%E
zTd(E-)(zK^ETcb57%#t=Ny-9gG0#JOHK&(F))4cV?>Udrd(S*fO-%+?EnUM3=XDq|
zpoac&Ri~l$&SOjX2sh693P)QLC;hv1d5kC+`L13ISM5xFMR1j($}J@wwAfRi!xA-6
z2Y(Tb6(A$j2*!n4tX;(s2z|wmj@u?C83YCId-GK!kG=;1f%pUQm1@5;K5i*#b^IHY
zAs^>Sls?O7xS^2o*-l3UP4ro~Y@a<<-lW9mRWGHj_gaIFZodc%gRlx~AIh+!Pl+0@
zP3wkNeD)OPI>UatS;~vQV?aUHq^%0^dP76~CaU;xC~^+F&zq?Jju_k0swx_LHvSg@
zZL2tcw(p1Wo&iumGcm`Uuag3^`V)%=*j_n#jYMbh@sx6BP*58f%7TiRf%gt=V@-gk
ztSHCY_xp*ZK1SVi!<qx9)<9AF9}Ym(1b|jx4<i=VF@MJ`BWSgHD_jZEihPKiG69b4
zEg+xqumS@qP!)%TibJR-(eam5sr-(_MbaW*RNv#g^b(=*&@=-Mw~5POaFim#vgMj*
zO7@t5_w9u=#l1gB2E?9Wz_0+m7eG##0r>OITFG*&^%nAJ36vioR%Y=ph*GSfHe|vz
zX8V51?qS)tER*w57I!fJBmOoOo)Z>w{H<u@GlYU~HT(6GB5uAqwzTm#5>Co}@Qip&
zZ4o=zrIU;dTdnre4Y!)2IYEPz1@H)erQ*Zds@1VSP?jQ|I_~=8y~v&3dFBzB0l}t^
zM_t?5a23&SE4O=Q;xAi@8G`oZg%=(bEmb(IO56gWfLb=K<{kmkV{-;7n2Io)D03dt
z+v{VO!aG9|?N$*s_k{zRg3e>1Mq(;tb6Uk(Y%IXk`aFo;NEJzK()W5>-a>GNo(yxq
zO$6e&#m+s3t6I+j7TjmOrdr4nGBM1au?jQwQ~0pdDia@ayMbJ*-$Z3WB<hpcsXe{i
ze$gTF^X%b%Og|$IZe4A|Vvp8kg<EXDD6)hmOv(<RL8(gI6$P;;Pe}QTqF4}5QX`>=
zRY$lsHU+pGFQTmGV}t*Ce-<FqkdppHThTp`@+=;)H7{ovN6t{DwT&!Gre*0HYEMj4
zDoJNo!eosBCfjjDDU&#4zX-M$@-kY^P(qCsO}E$f%_N=}r$r9Hg55H#8)+z+c;<y4
zG=rI&ziqsD0NrRo&Tt>ji-9aM%j53gGaDJnKXhuXu{*bD#WQ^xu#hsCNt-wCgoZ_0
zbD5eV9XlSaZ%k38HbnX53viQ$R;=Q_<A0^3k2xdHFdU0-4zeUlm`+=37~ct@P&OZ|
zU{%3$md@Q=YG`&I9UMw0LlYwe4u&P~#tm2?LH5?HSmL??)olwWKX5}foPTm!@x5^q
zSj5tXifP4Bg@dqM0P_2<T|M~$n0r7$3*1Yf!#aL)MT71pTUYRXt9>8vrd;}D7zQ69
zT_ukk7>kUR5@MW!3w4>sU|7~1RStOAH~@rs988y<X3Lc$XMl|>y@&DRHn6u?8jN~u
zvK7_ABVE#1$}(GvK|rzZ>_(b$=CEQ8(m~+>5|z)@I@R?Rwq}sueu6mm<W>J+*X$|7
z@=s$3{CxRZ_AQlZ?p#S0?WhtYCp1>(5~XAUCSG`B%fPangl8nnANWvse1vJ8_po)0
z`TlaQZCL_B852K)81X3L^GIwVlU3wl+I5UQ+xCwjt>*b>9>XF(mCNQVVkf@dwTfmv
z=M+5}vV@%q*KxHwhDzZI*Mg*2cQ091smKxC#NOI3Yoo3zmx|iAW&3puo|Fm8%k9e{
zag$-qX)ww62!vK}c>52nZ(*%;hawL=_NnyCmtGHV7CbN!`SkMQW0=@~YF|M)&Z^Ym
zthh-QE>1Vc=YIIaDZ%}i6;MBZc`KOx+{l#Ki3^8-LfG3N-+{N@&jcHhsy3vve7<Es
zIlZyhx#4>TkEN4fTyxoa7<}VVy-roGEVbEh?n14M(7)j6kTW!+B(`kWApG^!?(~G{
z+B5od)l`jLRV5*@JpB;Si#kg7dfn~H7Fz$cMMgRo-S5tOWD8%myje64MpMdJX7}59
z--ypN>Q?>qvUi1OCSG}3WTsM^m7qi=k+iaKBu(TFbNUn2=#)y2ux#p7@-Q^avn1PW
z;!e$J*`Tw`_MQs9NOW?pCE9s$i*<x`r#QRO(T}e<+kf`#yNeY!ACAcEzS4YbuZD0K
zi<B0Wxq;sVQhba0wyb{VWa*$u_5=7LT&eOoL_#260)#+&*0EVTbv_fr%6sV#gKiWf
zQB3W6|MO%=6w6^F&u1ey<Ij!~^u69JVS!^*GGj<uk5b2-^53emh%QtIe+2sK1Rfts
zup2)$dqjHr#8fT}v_Ag1joXm>j_k|S*x%K1g3Z-{Gs~O-*Jlpfxe2?T9z^bB_YL}5
zb}rdZE+eg?`sbwY?CxbT@9iQ0!^e~%i4+Q`YJQ5Kbyd!yu(-Kn2x<<9{|Jo&P}v+^
z2bbG@l*TR7Mi5IWhV^`NfDW?p;dgr66t16aqAW`(pkQWgaJg7K2j=#hB*qXSy_aJ}
zN^bQ->!aTrCpP|FV~-09_)oMPo`g(Z`#<0P@=;!Z{BhIb))uL4nXTR}lEOYBAP5iH
zH;7adeYxY$ExMD>Z!!*h0lfF+nGF111o4MDsg474;t(l!-|0;HTPiYm=j`*=mAS*~
zc1Uh_tofMCaR%o)2}s=d3m-=HV}!LTfPEsOICRQ8kjMu|9Y1u2F?2@GcEXH3>0PIR
zMXlP#;ya4i9hZ8Yo{K!DI>PUvrD+89g(zAwAMX}7i4J1u6p~0bTF}IZ40*K|2$V+F
zwob4WXU%vs%^8vk;=}*WSGnq%f`36jiNi@xGs;)KX;J_$dKnx<`AUL5vp$XI3sFpX
zulY~}A-(ZAXGrfVmvgKH+POJ;^g4zVYbAT#2Z{Krm1FHtQ!HP&Yjs_Vi8k1ArYmu!
z%eh$CJsWXLkW7d$2>qP3Gra%8Ni$a@t^2}PTr>%alP<6Iam_Wcxrj4W*>sWS^Pw1W
z5MZK}CZ%gADE&%#!pFtPXSnzF)REfG^k4e=vL$i=f~;B|2E3*^p!|dV6J0jtLN-8W
zaB#m3_Z=iZz3%OZ?daHWj#Hu0$M^Bj5?b*Z@#f4hVNVlHDiC5mXj~51$?q|o5V5`>
zIlDKiUok_vAMJg0G&8th6J=0so2cdX^l%wxct>J6KFe;<3Wj+nt=RaDR%f@0D#tB(
zcnNvCN<2Mtk~9#64SJ+hexB%xKNpL)+_|7nRgCV;9R<O_RMz)n=f$$FdMSQv-EM+{
zJn|p5k@4}GKoTFKm@Kv3y9VGoi)w)30E`4GTXwi|-y#3dhb9)V!Alx@@qR@5v*ZgI
z7c><-atoq&aWa9FjwL>u9$m(&`M<2h{(hA|BEY4v{e5|LzwGh{VWD&c^KQ8p8!^F?
zJ~Hm2Xgv9yGyT>%Nq-WGSuxV?a^Yn?nBf+<#uOCg$x?@wt%kv)k5E@0e9auZWrs*`
z>rzw1nY6ybpXtHO8~9#lRaPYTlbey(Nm5KS$zs3qjTlk<q()-8ytrmWDas8wbq0%E
z0eZyOswr-6wNUA$I(9?M88_sf_~gIwKe&6a?kM|?AmOGzkir&D)cys1EZTb4Lhg6M
z`|_M1sS&nuyJ`Aj<2QFy5|i7={My0uw+gxoPH$-=#HpnhoIdEhNo2?y;cQ72TdMPD
z_dkfEQ`n6Z7oQ0)MX8NF+7z4H=RdxOn>cr}!<;<_cw{{7GCXaj(Ip*_5TR~V{g%0j
zJ%gaK2(}~5v+&XGmRP7LZy;~7#dA0(fVX#2GH_88MK_s!odgiVe&R#r+KXX>Z?QwE
zIte9zG5R2$!A!!<TEY|OG>`S-$m5<}-Yl7$U0xDCR3KXjwVG8KtvOp|ro50&mEYpc
zj%&AgSv96#j=ETu-26Y5zA`Gx?t5Dik(4fx9zwc7Qo6yRTj_4;?vj=+>F#c%hE8da
zl9Gq+eh>fOyVfi|0K?49oco-;_f?B@r=!@Wq$g4y{L<%9Z33AZVo)%0>Myt>6yiKC
z#t#CB_w<fr3v$7Nj8(^3y*^^pK{lae)~AOikmm&y>%(6JVUf{z&DWQx_^YYen%p;w
zUwrJxBjU7^lA3QH`6~{x{{i>!@A3E&$=()CE*rC(c2d|-KGv$*x9hdfBdJEKnwws1
zZSn^QC5D?ir*%?^akWnQ=IzT5D{Jk2#@!g;u<0|2NHsruNUMF3=R`d0<WhGK)HPy)
zB#pz0Lnwrp!(j~VMS~kE7_?~jBSS<jjK4!OC(2j8aItqIW=1rdfBSKj1_H@0aTV^$
zuXhSol2(y6Xi)ie;e`-~WCRt#dez}$nMj66Nj}lg*gkYgiJ054v%jBK#;t{jn1}XC
zJg%u-Q@=q4v?RT%L1d_5ACMDw?2Www;)D3Hn^B#H3l5sVDTjl_inaLbuhlAw#uqxr
z{ZlN`PR^cN1K?bn)M!g~tB0X#f&l$0Jb&WV#@GJq%(JW^fQ(~7gNYKcyCIY&oWfnl
z*p6X*5GA+m@d5=1VfRQsdXuWmooHk%K{6C$KK%EGL}zKUox3uYRK{_;In0n$F`7ic
zoxkFTb$r~+Ha@jN{LJ?Qqx~NxC#A}YCw$yYr-%J)de?uypj^7Tp2PQ%C^8t(tcj{^
z(QLq}K|!Ramm;ebGyHl5*UE8}kRp$E_9x|?;Nry8V=j(=)^vRcX_lN*&G08iM*rGW
z*P%MaHFl0@tLRcY8*=F+WSJZ>?tW+jZ^Ou>mTOCnS!qy38HW3+1%~pegR_AdWWnB=
z$IA}VpG0)wbU>Zaur+C=(Tfd4Kjes29csBvdOPRM`dCP4lm(Z8w~CnBjLtO3nsP9z
z>|#Vj0vSlMb^Vr`@TYuhwjT;MA;9G%`VW%&hu+Qf!|25jap6xucCadm18)R{5V5<u
zyT*9(2Qwfus95mzXVbGigz*FvLt1jkA}B!FLYGAe=|vY|W6khnkYKVQL!$5|AVY=&
zN(DUeOj2SBB6calce#0Xo<1<%<O*4t=-zfe6*zG$%~EcRAjPP5v|))@G4Sk3ISUUj
zh%nhM{L9d#^4UoqUGNTGE4kwwJCq1TLqdBwaW((*e!>U~AkVLVcD4=D-nXhy(`?Z-
zvNy@lDwfWjqCh0M|JsRb(M57p&**Z;`Qky8Pyy)7pQIAIKO^iVm*9>TjNS<~^`8ep
zLCPxokAv{Bi+r~H8M-;4bkiZ?J*02}_w#EjY#Z@QFNgR31G((~-B(IR=N8b=Ub-3p
zcN<DPszPGPf2TbXYLE@2cKo+fR5cX#kA2eNrK<4IpQ??t*1t8|>iz7L=J9aITRv%}
zEdA|=$pQza2Ij$=B*hrui8`4piT-n;sz^;sr@c<DgIPM8d9dFdZRrx2_KSRp6B{Cn
zohbg1$}pBhKr)I2Qdr^!E=uW_TdEc4tS5w$`(4F~_wEpsFT8hjPrBz>FjN^XX@sN?
zm)*<sm#+1@rh8uPX8hgcBOERu9F|BV_Q-dO%2P%yR1Vaa>Zx(_F?W(|wI?UZ#fWCr
z9kA}CA&riWAoM5*f195Z&UF$+WYx3x`|>n++9TR9V$U-w_FFjVs$SR0!vXAptn0H;
zf30~YA>rc5pYoH#_mWM9@AU~z7sF17D_cpmmuv_ET`R`_s|PmVdK=77Yo?%5(L&qr
z80JCk*a15+csL#exB>T-N}mTfX0My~#X9eG)%k4RO5SN(%r1Ifxvc)G)<J-s(OSF{
z4&64m9Ae`Z)LQEy)s>u#I*QvqeCQWu9z4oSk#zH}UhOz0+ix(f>Srxqf_mbkJGQ-9
z|G9tNR6Zv>yJ@c-qDYiOMg}Jj`xW!!px0Ii5ny}@Ym@>n=XwQ5nBDyiqG|BKk?f_!
zgaeLd0W6XT)J7O76ldU^iZJEB&E+#}aDwz$X|-J>C1HyBWry*<I4Bq$TBf#?HU76{
z@-3S`eLbH!gDPc@5btXDB@17zaI5v%za7PFbL1Qdn^0?5j!fHa{|B2D4MY8gfv`P5
zdLc{TqP6)w=@f*omzkqxIc@V1^{wfE(MGhDz#>|NOtpeOPXsM;8FM1Y#@+dnB69S)
zW;yAO%0U6&0kt5mXzI{t>WyY586t!uL7iH{g}+d0gDLh@Z+P*jex)sGjE6&WyYD2H
z7$4@1@tKqH^kn51>q^w7aP(h&0yYopguWECKeuDBGR7ZZA5sZ-;y+q%s0<PYCc39%
zUv%{k``-!OT*B@bS8w2eTyd)TIu`jwv5x<jJH?LPMT0P(i>G@oz$WmH>_T@v@=(`I
z*MwOu-j_c;Fk6#ON5A4bW)(=1-BRT$$J;+Z*f)t!-2d#txJ=fC;&o3}@=X<(V*L0l
z7FLEwSy5!9lJQF;?z@E@MFLIkzdV(Pjx4YA`3}iGR!!@<6iXFaZR<oWRR$rMkG39f
zZPp}#%`OEJMJgm)md#$AGWQ<@Co<bL+@GZIXCI-W$)p%k>?WqaR;Fl=Q<LV>PlL3w
zdLk<=#&;F+J=ONFNcoPDco{QVAi3W<BK%1xv(3(lq$M`Zk=@gk_XK~ua!)3~FF2ZV
zApWzeW71<)wOj(N(@NGmzgD|QA^!k)A#!SjELcXI0pPcT4L%gaHCJ5uz=E)^f4`5|
zpFvC1=CqlW;n0aFu{O9N5hloyWeYC*I)EG?5$7Mfrc;o0VicT?CyGZ>d9-c6v*ibk
zE9v*S`V}2INEdJd|03$BcA|(abLe=VCX4(b^h!V=li_)Jl4Mc93%eed#*EYYll`<n
z-qT5+EEb%_ldXHlCEFOG!c7FIV33Gs2V9Xbkj$`i3taKR#|5g*isN7s0l`whh_QA9
zu7D89^2n%7@^H9tI-u-I+?%pkfcFli4b#ZLlkWLE!9gVxn$RoxF3MP&DZv1^UWY+s
z!Ri2UPC#VeD=@X{;VHt6l=?xp=QEBNw5c-Lu5)Wp3Fpv3#n2<>>d#F&1o7`7vh;BP
zAhJyw?{%0Lgb*$zuIje}oA0#cj+zm$BQSOH$>uKhbFEY)I=;Ww`_w$&^$#K=^w4bX
z$xMbf7sK0mk^5=JxL_<AxKt&#w{%aHJL$j-AGhE6k;aUOKTd^Fw!LghKsbaKRE6ak
zq^VfPN93!9tHmd%Wz0Bd6zqR?WLWNkp?I}L{VbBfDxu8{$NDHBp)@&QhCo@3qsb_-
z<T$v`>Y(*KFegWb4M|fJ>vf(X&gX6x<PR2ZT-M|HW?Tz(S`76T%O%!IHH#zM^vRhK
zTOM`GQJ;1^266&vLwDl>$>||D)*kn{Cc)m6!dbCh=Q>y=5;Bug#k|3u$7e-9Yah4;
zh?cI*TewtVIR=f*TAGDcjhf~&3oL2BbuC-rhTnSLvwV8-O<EX}N<}(HF*;t!2_X_<
zTq^IwfTbN*q5%FDExL)&1e)amFQ=(#l`>>x=sOi#Xhyj4wV3Y`OWKbzJbYRDvIZgs
zE_$nEd96&@>3T|GR@AV;3~Na!AxGTb3xa|jXtn%38CfNa#VDxB(={Ttz_Rvt*<leI
z&g++&F$7VC4V^pXs|pKT#eCEeqjX91`wU#AI;A$?e@NF5w$~b{A4)yg`@`(JXf?-!
z1RV1*t5=dR<=|I_FzP|Gsb5qmuq#b&A~44#x^@vDTCo03!$zCa)U&uzv~ZibUojfI
z(2E|RtD0UzixsaLYzU=#2=KP;If3Y{olVcYPVZXAOK9&Z-1?ZOn!&!%?d9d~aqf!o
ze@k8<(+mOT_?*cFOfrmzh|nt9xQF*lVMSJ4AfMy+ko=#UQhFS9OTaQ%*r7@0XP2V8
z+bt;qvxVh>Z7g{20PaqYpbkHr8<9AGFza!<?Mrea^<b=gPRUvkOBDO2OOBeOVhY8w
ze;@5$E^ptifDwpudq~<~{~quNw=2roIG~><jZ7*lfI;1>+-6C(Od2#%D2w2$D}6Cx
zvT{-%YFC2b`GVm$LM^{qZS}UwkMs&OZLzPTqtVqsnn44@<HFO$s^eud5{TQnO~XN$
zhD=FP9v7!}|Gt5$=w|ycz-*s{9^WrH5Tuc;;Xfr+I<7m?Orl;4q(QYZM-SXngwor4
zTl>Vf-{Gc{A>V~Pc6Jh_?7XfE>;02610UKV%X=008Xl}Vt(lvt2^<>b*Bw0k@*T>f
zt~##zpQh_?e*Lp%N>sa<4l3nXkt%C-Z2#)wQG$K#8@<)4LX6_qpSh2#t^zhOL7{K{
zwoyWT>^Ir3qUR1&f;*add*sS{(ba5$*lOv_Cz@4q_!?sE)xJVli*a!)<uCOs^i0ks
zG>b@JbmxuYge~MP|DX12n7a2+)`)KQ*2ksI;UZpBwuk#^<_81|N!qh+-#(KBA8wa0
z(uy&M+6F>v+x5pW7qmHqxdNkl4Ko!CjO)t{CxaRpHTLV#y&aw`qQ8;9r1M18C_PoQ
z)`jjKk2Y5I9b-SMAiMiNT{?F5ItIlaTvYKVt)|?>$Zm0Vbh@JmAvTInw9fUMy$73r
zEZ$j$)AiMv`hYpYgGAiZ%Cs#@!iXcAF3<5icNxOd=-sM*0f@zJo=#H7f(N_*)2jL-
z^(%=}4Idv2>s%p?l=Y{}$ut$K+OyVh3}1iDota0Z$EERyQ$IR68YRvCIKr{5+YhOX
zcxjws@Ti*W-?$WYpkad+m0bC-*ePrr5B_iP4RrYMIqZJpQc6<MUJLeLm&P~$^X-j8
zprk?m`$h>zy_CbkTE>#ogo*j=w`@G%z&dizn$5^VG&g<+L4*6x1jZ9d1P;G`Wszqy
zp5TrF4rBl^){qlVgcK-V+G@)-Rp19HOHpLv|15$Mz>cNxq_IAn=d)}?SJd+){w7Ri
zsN&a#9KQl|232+U&MV4|TDE9ddnQyhM;wf-6gwTwTiGW6Q+Xj|6G*PX7?RLTv3k?)
z0+OB-*`2)MS6r)xXjjiPGng^2TeX{r>bZaukV8(i^R&nhv4078mMCdpCdN-pDHJ1k
z-ol}qmTGuX-e);7I}AQE{c`0MocC)woXd|_8H0=DjB~$G;Qr7vO@1R*FurAhY-zwp
zlA)$p{?N3TakccyOmPpZcg|?RRy}|HhUaL}wtX=(V6Qo2s5HR3R1bq?j+R}S`DA^Y
zjXe^}xO7yeRbk2LZTja{f$gzdglxqbu4XmH4R}E(m;qhF4p=#2!u(j1eJF70T`;u!
zgYn8%E>2k9`XWJw)6L<Oyv+>P&E73P{lV=kTiZ!1$<@Bu`=_rLTxXHUFKFUE_G6{I
zs)VWa+1Q29&N~oyS4mGhf~AIW-PATDnUCw;A_%i+joQ4^t?Z-O$C$FSzGwLxZNhBN
zH9b!Mu$eym_I;76I==Ck@tdM~>c;&o;&Hc(izdAlGQ?L31$QK_H!E0y<fR9^mL`U+
zGG}9}nY4&<5MYlx^+vEil(?F|*g`5Nl$;(hgKp%<yVvmo|J1HY6iEbxt6`M-`-f!Y
zU_?X^xb)_FeCV}wbZAi|-|bkBou&5LKtqTIzs!$Okfvd}36|E-z7tql?Dp<4fLMBJ
z1x%_#`#1~6(AZf{uhr<SSIQs7l2^?=AIQqTy&#_)EbBUfe7n3p2ZJlGhvEZx4dKws
zrLe##8`@ag9M`$adFkePcPl%dp0&>=FvDnn4G~kboUWNG6LW5c+hBI6lk#|88_ckK
z_NYwHyq2T&*O&W4K2SWQa-Mw}#^%$Tf)epoIsMn<0ip;$UfN{D3rH!|?YmkrsJos;
zubR5nbb*jTd1VZeE*X%DmS~!jxZR2=h6zuQ$uLor0upLU`VfZMiC%!r5_BqB8&$;_
z;s~&-2&J}<h}2@K`mKcU%~dTCI`UCWZw>JZ6V#YD5QOC)KJ~xpMSrzSwx(tsk1j)h
zKTLFFa0it=wqHYd=}qunrs=rHx7j2pt8Dzl*48VO2p*kb+s5m({SPjj^|)~b)T9Dh
zaL}SNfOe|1N|4%HU7xkoAvx_-#D}Mc@sYyY<AisvRNRJJ=E~ESdw(nFrTqB%LF8+j
zSuT*-Oaa$Z{X5FHqzA0cC__+HE@nm$U3*qFkC2Y)88kruK)qb9c$bfs>O9ehudZh|
zobXar{aK7y5+UTJ=xuLP%k0Sc2IQ=-mV=*H5F=L7j3F-01B+3!YV^Ijfa%;B1svG-
zsj-_YdRh)mEQP3%D5S-y?B~$J$xy4k(8YhacN;`g<~}#AyHYiwB+8gnFUL`6%je9w
z4-QZ!NU|6?<b}C$;B$O`j7IWy?33PH9{*=aGigXi|D+6JhvaqU3T=6Yx3zGW9Hb$j
z4rEVvb556AH`CUO!eTd5a*;KfdC5V3df@<vO;Z&*_#uzUW#8tj{%dNK1NvQq?|Z#x
zu#f+dC?aa_WaW_AJ*Kciq?fh7w|;SlQFezG7g1`0nAL{8s%9l|AF;4$0r&rctXnuN
ztsi%u<{FzHC*k%Zj6H3SP|iHa2PsNQ?Ea;&p1%6fU+`uCEe~)ljP8_aO9FESt}{Ud
zGDugP8AaGK2uK;01&gZb@)v(c<I;|$5V!_4i<1YTN8kJuil<4R3zS~06?L4C4KT&W
z4a3FA_Fm=evv)~d=pZ^!_GrZJAmHPROpi^}!c5|$+uFl^lvhK}Y2ffm5lU_CHK+~V
zJi_BT62pO43J<1}_(l5ir5?uDTc*SvCspaB7|!5Lb3LMTGA7c8j@`|vcSp8NCmxN=
zH8xy1|LQ59eq{W;;8`UQ=&}3nD_kWcRIcz8jFs1dRwBZ*g?WM*azojmeMaZH^S|0V
zWxuw*bD~ZB8`J^K97QKJyI)zmCgHYB8{wo|F2cRhw2w`#^-=PWQ-g|!HI;$otgr@k
zIk;0xntdO?nsF0qB1z!W!Q${&wF+gF&YR%)pl^S<3^&F4$JH?%<WvNQa$HOZ@wnU9
z9roo^&yrPn$*6p~;!(~!lo?G?=rf9ooSJLCPx^2IXHAL1L4{kbSM*WkABiMfP-d)L
zIFRDd9A6LKGH{m=c?dEi!&SZ&OGtiWJZ({H-f(?+k7f}iKV0v^>HQ(6ch%?73Be$`
z-@O19FZnzipMY|vs89z(WCMkL7ivC~&uO%^3$K1f5RZ>FvcF?$-np?_fhGY-JFBeW
zzCF+PJPCetUkp_qF!3KgO9S!8-emQR8eks;sbhLo*4NDRt!O7#h5*RVot1z>tfuqZ
zpr&pOQXsSgRYa*79<;FE1A}u&Rx2h^bnYj5PSZmDzf+X>ev<OVPL}fj4xw%GlP5rc
zhY$4+3=E|1t9syKtdx-%#14F^@O9EomZKf{p&P#DCkEEW>$fjomRt|^Ehi?$P*{NS
zIMnx`(PMC3pk-rhRZB{Wt=Kjq%tg>886$iXy!av`(cFn0LkJ5z%mG|yC{^?-3Ya6=
zU;@)QOrUOfo>R9lc_^z80&``Tz#icK8|K&pP}pGV)4VgJ4e5YyOnzljwBdmOuI-3k
za45Pe97swvYY|zs!xK;VPyyogv^Yw(AA<T=O4yb)iYe%^5)2@4-{|RNa=O+u-qyCa
zy6<@Bp}SE|TnbdEa`6gUs#>isu^zz1eCCJ?mr!GuqJ5VNiC5ylfr{W!iNLjymAtU<
z7<1;WJMc)(l<ldn_Ofl|m40y>$@5CWKQD*aTs)oV8fO%b+frPRp&WF`E47Pk<fUdc
za$1v<#;@h$pn*k0pRxK5d~s+HLGl&fv03xmhNDTlgM*=7+Ooc{T~ay2Z}^hJ1GO^B
zOg>L+^0jS?<(%ZH66?lE(*gJ}H=NC0Q#>Kh?7tkG`lnka(2*T{RI!RLuvD%~b^T>y
zDl+ZzL7R~&QJpY6pC^g%6J~UwN6)DMllp9mtxA*X>as!+!h{&1d>p}daeW#jO{xmB
zBG9pYaLxF8P-1A{&ZN4OXVhrkGFCC9EQDIjOYL~UhA&&1K6>f0_%-^liC=j&&!`@p
z*gwtc?chlLXoFh5_DX+v$ErzH{;w$RJNe+XekeWy$NPu^q8r+ZhJBClPUkhlCF=^6
z*;x2k{JZ`J?21<5|6D!r&Ur*nI1U!6ov*{z2r+8(x#sIqe-lR}mr;<O)SF-ggHgF>
z?NGtY;)Q1&^W+BtB({=j7*>m6HFVRt{Jk}burGy-2Xc7(*&~Uh^#9#DVTGvu3TVJK
z&7Uj}dOOKK{Nm+{7ogx#u|7NDYdm@IwY|Tk2jyk2GB04yH49$I5DCMJ$4Z+Rgjy(m
z_KX8L=t}hUIlncA^Z(tp-M~og{_R0K&PR7bX`FE6`|Aa)hO<}dpg2h43DR3F=n5%<
zLO_lR<_YC3($(hnC*_3iY1kBm?43i;n6r4)STVbhQ|sDzBMwS;4bs!O;1ON3dr~<i
zMHH};*i=@W(!08m7{0OkG4&C06__^}4~-#vEz)-URC1oxu=rv++A_)>x~qiB{H?f^
zD!nV`XCxUJM&L_Tmw*`GHeL~M3&u~wQqATz2m5zbE(I*AtB5>>zB*M%x#f=aE2*3q
zr!mPk&S3_c67YSzE()2?eS;AcQ<T~b#`{eTlJ@yi^)OvJqCy{@;W;3Vk;@`AK0ROa
z5)h%%{9Z!H8T5^5Z2p@NzFtbV6F*4sS$%kL0T2tLptlFY_(6q|gIBR!t&PJ)z(<92
zVw2nA*or@eFwV#A)w`PtJ&)gD^6+%CeYad@ZEyfhp$(&$-s8uw3GlQx3oopBWyJYP
zcabls=s=QU)~bC(tM%7`dsxJl>g*z#jS4qnXkab=twd7{k(l6yq5ZVe^`9Zej@EDS
zN0npCR~OiW?<r4km@gyQ-i@<hDaJ#c>J-AOu&;siV$eppUVe5IVXlM-jJ7<Rn&s*#
zQ8T2rlNE3Yc*QQ_U;O0=08eMWiaeQ)bdymddZ8K~*n@v3K`5K&M$J89Mj<a8!QM18
z<uP{(I;EBBo5_D*<<8w)ok0mk^%$Gc=C+q2<_N<I-HLs_f43kb?P0C>mwaEEc4Ui^
z=@K_*hze7>zdf%_m)hou-=n0a=Y!wDD4MrcTXOPl;Tr$KwEEY=DWJge$n9x8_Y@f%
zK0@5?;onP0i(MZ~QRXl(i(0c(G=_3|zcLJtM`x@Dbt8hRn>ubmcOM*ZjYP&azr*j-
z(nza*msC$x9Nm2MsrQUnx?uZ4C^-0;Us~_q<GW8{Unx>HL7@*`)9NmsZg*g*>X%6F
z(1AqCo=Rq(YaREy0G8f!UBN{i{S~YK+&g~4QslM?*y8e3AG&r_SG7~uCF#%Zr~aBF
z7)T=+w%XQ(`hQY7Sdlug|MraFpl1MM%stb70)a`%QX8mNWi{`YZmY$zv80J_uQd}8
z0|q)_PW+%nOZT!#KVw#m9TaMDR;jgC{y*?0W6B*3D5}~45Sbf)BonXI9AwxGFFa6>
zjz6yxF{=orf_%X0hG>dGsWQDTAi$?uLc}8ve=GmuUA<C-CFz)<_TlC2wH}D0)Oj+C
zH5r8*i@sBhkM`yjb*h#2CW~AwrcKx~TLIH^X76>>XRz{!^y(wmj3PlGYSdP7BJj4v
zQ(w(8bZZ!xx!Q@vMS@}>-m{eC*?EDw20|I{#ecUrSn-fzqzQ?gYCb+iGN~-D`PMox
z)J?6A0pe<MmA$})!D$|L{5v62Nk{v4NNreMTa@ER{cfb5dHV9-fWQBycGE8e0JgCV
z_#+3xXNNHLSM^d0@4E0S8BNJ#1}k-)Tju@XCx5wr@Y><ui&Pxbl~e%u(X9%4;Xq^N
ztF~jsQj$GgU)_;p$qS-UY-EJSeR?vBavcI(x@;H+Fpt?4BkiGy8fPz-jD91I0pHE?
zw~skJ8<@E|dB;ylWVpMzsG|4+BmJl?9yk3Tg?jwLtDl3{2jK?gtoU&D$U4<E6Qzs{
zJP$1uS?x_QRFySS=m8<trS;EBQv(cOKMDj>^*>!J?NjB`oQHE(su2CZs?V5EfPVIR
z4OYkUebGSHIgO~E!nn14pK~(|HTQ($X}uVqAUvOdBQB4#eOj&cs)-XSqQp@U=LW_o
z3I!-_%R&;<P8x@y)Z(>+L;*C(a(@q7AJJ<Bsai*Ma!0bpzUX&oE}S`0z`0S5eWM$f
z^~z0`zKWkVT#}w<)fC1x2ADdgIDkr%L^z}ie!>Xl^FF39eRXH*<Z({SnK78Qh@C<0
z-$)THAD_Jo-uTeL?+~X}*mAsgkI_@jAzF>&C6Vq*Gs;s@WR_8l?12~#4)#fSy**M>
z&=wn&bTuYcI2O0b^elYnvUdB&$W_{=uCoE|A}mP;CSeE*r!LV^RN8CJ(Y1wpmdZ;-
zJ38I3YzdUbW&|}@LA}c#v-G7zCJDk!ucxX;KJ)j1O|7%-=8yCISjK#Z;!1s!k|qtj
z0x1ROjSa*23P~D;OfMv;ll6f?xtM>)G2m|<fwcIFBQXxtfG3e6y9i<wnO0BX!{!r|
zpkOu;^^r1fJNbU_{<*yDBMMkS3fIp1_)hW6VU@s#*CzqF)f$(pjQYrmVWJQwO(%Jm
zQCasqYv2&@7<WF7)qrdhovw>)z{7J$ZzTA!I<)waA9)cMgs!N%T<%VyJ$KKdu+Y*X
z_r&ZlIDi>CPj_1_fRPId`~DJ57!>215yX3Y!T$8&gU(X>PE9lsXn1u>?Eyx$ZChbj
z5BxfMs&oE*ggNBm^p6c5E*hlBRR3BuKvGrzj02)Bpg)Qj&CkVz!s`5DUF%%J-*LuY
zY_XBv?^2fs0}sFXf`}b=jRH}SQJC^pp8$N3ZR9G#+20KgCsB^YB~*={L=6IV<2#vI
zpVaay;QOq;z`>jeQy9p?;W~&u>y+12>#X<p^&QNK<BOBYP&7Y6By{!{-+%%bUiwpX
zv0Nr$PRoMPo^z~wa}X`ES&JO7%b##1f%5(d7Z|pkI<-g-6^f+z7wSLnRwkph*Mlx_
z-xZ+{`ue4G3=$F&VhlXt%a=muh$7K37@{&?rR+IAL{Ss+_yz6FL3@#~91=f18MaM`
zi;3ZH4&=xTm#$xfTixgM4Jj)QraNwgK;|bgC?p}$b_oJ(ucdw@Q7J9J=Gg0Drb#Et
zuRvsWweqWL?}_H(D`~!5+OUCeu?ptF`N5aZyB`Q*MQwik9Tk%oKp{iXf=SH&M#6DK
z_X`!Os2aY^b!KO2<e?4V4qq-J_r!aFPLGzj%!vaL4ixz{3qQ5Wri<!9B3bL3386&3
zn4gGH7D*r;=1!aUP@#F-9|xu}$2Y&QAvoowEUz?w#KcZSX6y)qZR=*G%$iM`*^zoh
zQ7@X<Z21n#p*_M)r^8TwsA>HH87`HU9W1_YHZfU5ANy436gNmHhGt)Hdc*a#EaaJS
z@s+PjZcZja(K3hL+Lbm)uT)=eOmHX<zTX^Vpjbgkl!0m6vn3ePW*RWW>Q`u*l<O95
z@m{-F%RbK~>XVC;T$^oC4}IwFx&p<@+q8>v#Pp)iJoS^u(KFWM3Z63eX%R*KO4AMk
zq$!=mkUw^vIk93h<YiR5GRs-di)lwqGqpjp{#fL2z3Z?p(s<n43-~VtsRq0mrV~IQ
zPYlrWTtYBYe<>i{iMgZY6wt6U@$Em|#}vl#t@cr>0;P}3U6LKzd2Me#GWLV3(@~3k
zZJz`)A8i0t@7i$Bv?K{mi+KYj{p<0i`gY;JeC~9rpK#G>Mx_kubiYHCKy6cOiaonY
zKJmXvr|_plD(_99C${{0-qpL!D}a3enmVA^G9aG2Kni%V5=ysxi!cpVsgYTYZ;6oB
znJ3Ia6R<ZPa$i??HNDXPOC@nFU8CkINta_SL19??=cKrma$N=Ewcb<z>s!fMBNBTu
z`SxW4<BncQ+ZAx<F74w6e~TmSIdHt{LT8aD8g^(97o3-|3|<d|>%7*k%!YBcd=$qM
zk9}Nc@Hu)q-PdvRiK0ImwZAc~{XN7;m*0Qs*^dR{;1qaCO~18db*wX>yQfFfpmkgi
zk1MTMIqa=yc9TI;!t5^>!VbctHksPOrOn?jY{)#&^ycAcI=#@9A*0v`=0f@?Dkr1t
ztac*mva|z1ePv-2TT|O#P%j77r9kv@_=lmlJ8}6>C4<8M1?xxgNlk-kO$ls6Gm&p|
z4t*^%grdmI=d^sKKhjlIpr+G$)cJo|^D>*JHV5<dY#cT>C_46?JT*lN#-rm7_EX}o
zT-z|jV>_}re6F6ZOFeh4{;UIRU6(77e#sg}2@*>){%zXc<A0%?%c97L&ZRw_q)9}9
z(w|m7z_LvLijj`C4BlU;YDGT0f{@h^YJd-EV}!R9#TZ%C{M+WQ@pUlOUA@U@Y`*;U
zo;@jX;4+_=8^O8baH}$7=WkH;8$H1;gW7JZ_CV7Ah;vT+yO6x~|3hWf6gV$Vg@odq
z^Jvbj^>v%kSYO1Tv_}YKb^`Q*ieYt$eZmNmX+jaZMcQ%9d3(-NOljuFxXbF0is^Pn
zJc(p2Gb2s=?rG`F76T(E94n5@Avv}rM+`s=rPw<kGY)q;-JbY3R#q}I0F<0GT&fYj
zgMMPZLJmd_=nAJI`hlH}+qfLk?rTmX<_N)g$BpA{Bhho)*SXEIt$NrPr}pNcC%vAU
z_&tgG$kf5Z(N`(Q-#2}e{RS^lReIxFLA1~Dz4{F)(?fEnR!3j(!g4j5cE@nv6tXG1
zSNia!BkxK`NA!RfcUaWw-t-MQ1iGeG-?VuHpvI%h`TP38Lc(a%$(D1o|AI?roV@F}
zT1y>N$Vz@@DD1cy+WBiF?bnckV|iUHE^P*jG7M*Pa3ni%E?1KKe|2WLbEfOmr%!A5
zvNXWV*?wc0Wz^k+5BeEuj3XY-?<WCbP>rDV9=0_AgR-V{6n;TjL2MpTXHtZ!czLpc
zKhDDMHs9(2CyMR%y{Vxx*>$_w9s_=)KwO`;C#+U<a{nlRHVh}2E!{&Ou26XfBz|VY
zR3L6wFWI!ESiBv4nZ3`NMb-UGPNm~g=Dj-Uuf=o{Ah9Z-EjoXZLkp}xfDA$l%~5;c
zHwWOnhEh3EE2768DGD4*my&^F#y`)~p~R$@lX@I2cBCIO`nJp)eZv7+_{B;@whThc
z4>A<jng}AErI}zjxR;NYyvY8c)O}L)uO$pkrRYAYOum4}a)=T(L>5(`Ad68BkiwuA
z+f7eIuG(bP{hlqu+jGkiSM*bs6_V{DwR>W;*&<lpawF{&PbP-D1sGWpR>VZ&A9&xS
z@^Z^vM3`QmGz#{gdESQ9rhC}Og((N1em4O$-#WvV^>>j}V$qf$D5&Xp2q&#{<_<X=
zBP_hUWe{)~RJfeUgeR-{ZNBJ<Oyg#HZE`d}M*Vc1+wVtT4`@k>Ude!{My8Xj+7t_*
z`je57lM#z@2Of9;z+=lKGC|ENDVY{SRUvcu{LIQb`6XpFW6gU!X^g!ozXD58&H?Jw
z$!^0z`OOh`9H^4CChY^hsvBDjJI>c>d8ow`Qz;cr9j7c~?9{yKeLH_jhfGldu?KZm
z1ynfR=>6&{AwRarq{YF)tdE9~Fr*MhAZrBZg{+`y5c|icT~J%{ONDOSqE%tR<_K%O
zjpggKg?+1@30sQjQB5GnVxkz>>fcq=%YHuZ{>t~>WVDPubAUwaU39mGC)Wr-d_h==
zG-iI(8#9I$efxojh|Rm-R%u6!qhfmLC%-Em5+R6ff*g})(Esd>&MQbf_^}$W+?AVo
zDj%08S04B-&S?uXNw$VNPw!(H&lEsEGTy;ET3e|=I(&Mx{rqjeSs=v(&GSa@0?5Mb
zbUo>)B<1_q1<roG$J2!X)Uyf19N(Ow=ab=dgf)axto?lHDMbqAdh4icgr0)2z(`o1
z^=-b<D-J&>2lX4Bj%c7lj+?@Y2Z@r5U+nxIarDKW;rSlaIN0}-8u7e6)(5ixWZ0Ln
z=%!OLeRQJ7-)3%3mZX>k`$LW@9R5vi+Kc?R4BvWuiUW4bW;gS&E_Anpef;a?xlHg5
z*F)H%7)kp<5Ao$@2EXY#UfZfnr9~#ILVfX>y8tEy#a373$lCJ-qgyVvXOXL(kza1L
zZDYpzuG(1L2}Tr<kG)H=lT_I<{<XqV3ihk!%UD;-YFZ?#f&gpHD2N$V{^TszRI2pW
zlq=bqB~c8Q>NXO-;phkpC#|AKtJSYDWOW6a6N)9Rxj9TZoi0aQ@mUy8Y-|UiS(Q2V
zGlxZXn2Y3`%BO)6P17DLIH>6iwEo;CECoOS1xh!sm?g1tVu}hKMG^hG_=qArf_DHp
z;2A%?_$3{OUPVFyH~u%c+AHgbVP*M52SWnsfc*l?T-B5zcD?GrP`Gf$vsiOW&Dv2N
zxshoQ03K{Oin%f&Nye!aJr1?~E_gQJoqbRhO)~1`)5_wM-jHjk1i%6h+yCHtL3S{m
zJ-VM!O|-H7ga{Zaev=F|<I&$#Z`^+Tr>g6wVl4tFb@N2hiM)@c<iZ$Y1|D{8xU>T9
z@9_jGCJUwR3!m1~d_U>4$n#zuAAI<p+}|bj8)^Vt32Z7>=43%lM>%fp=%Q`TjhGXP
zIo<FoA*yFb1CQ#jhil}_`-q%{yz$W5R<6?%{btq8)?x0;@=yERSoinygkvVR(#5x?
zkLjX#;ssNHbYMFDhtM5I)q_`;ri}DQwOBBi*5K4#cZ98@`-gs#;N(dea;&dW5U6tD
z|5DHRFG~DVsB7S=kDQttn1@gHP6j??$l-?$B7acrLAuu!rXDVT2gd824#ddr?^|$i
z#f8_3t%T6#D9ZoU3B0+gU<!(sp@-KWP?u03Y5CW%t?>*1wJa=eEg)j3s|X75^tn<v
zHlhDJ-ipOeANgzE{1y%>zP&QI6GukUY-<@k&IP&`$!HQqetiPBd`;_+X3J8Q2(%X<
zwd3Yd1;%%>o}qDcp&26Y)VgYzb%7E>BJjdUyj#i)>Y7L@=5pX+94<iOXrw6;Ck8l>
zQ7@MEM$x_AhX+C;z?kqa!W6@@)+%n419#LGD159ugam2hAaP?fv5;8j9*V@NSl*Y+
zl4`nCGG=jYN6;F;VzHSSFlQAz*)3^_N^P;UF9k%A13cT;Wce0g)l3z_pwSbghtuI?
zh)W+PU9bbm71ppZNZdZbGC&JR6X%Ai*<4t(f~LJWO_h?4w^W<3g60W;S`;`OD1VKk
zsQ8a$DI@99{#XX)e6uDA{~tNi-!gRl4W{cC%utd$0DxA6KGBdhi+bvw?oVRcgKB?-
zr8~EXR+H+tc^8Tpg3JZDXA2T3!IlRlzKQUdqG~BpMuYDs+t8?#z)l`+y|D~+qeq5o
zDZ@y@-3Sl&hM$QMaJQOVN_9WqJxTeg%B}gO<TzKTQ>xUQTn3KW=i<F-Cb5qd^IPz9
z`?}tEUP@)J<&L)R*6tut=@he3@p9K*r|93N{i2|=gRk@Sc5c@4vT>n3x5==HVY9y>
z@krLk#0j?xB1O<g0*SBf*$wdfkrVWDej(KVKoCkryAa!XqE~v>GqZ$KPCZ@B|3THm
z%61~5oQu?^Vq%`sNG!n!;X4G(zub1$LTG}DQWa^Kj>u`THiBM89c?=IHg0|eEy9H#
zaJ~G#{*$1l`zu4eElN2le4S1jaQh^N_EnM(@+Xl}yND&&=8*lAWdr@VRL(%c&~4OC
zMpxmwR$2YN5l03&<;+73<}UC=T^{(*(a0v6+b}I_pRFm31&^n#itrs?^I&aXrCQ#*
z$~~>#*>TQMbMz}DbEEjb7mJuko`C6gN8-clk+D?I#?31j%c{AR(m@W|`9Y$d`1buw
z63L-Wdy}bLu#_b~t-WcAil#+cdP(1~HC2|T<7pYZU|E`MO{9s(iiI$(7|FsrgZ_Rz
zW9ONAtv8=22^b3lVcz~Md2M<jh83UoCO2ta(;G%X(oX~Pf~tMx&MgqUb@)^rQ^K56
zn(L%$Z8kJW06!Q^$JCtvASQRP^p}3=wEH<eP{Mk94*x;5aBqIzMOCysO<rUz+C*qu
zjBb2Sj`Sm=vk^s?KF})wxWR=XHM4!VQ2s@*;Ri6`LDl@I(l-+y_@XGsbNpr=xt5O!
zE4=>`gWK-EUcOj(O!+v>s~bNAU*c;5$=_q;p;*CXF`qeAPRzWqMQCD7X%h{~SLV++
zUw&?ow`iED|JhVeDo@8d{x{^NsIF$8lN|baI$`J?T)-PFoE|W})S+t_6seW5j4oLZ
zGfLc3d8vsLZS~|`-}cL@+@EQfKjCO6rDGu4Ynarber9bnf9ZaCp5ueOP~7-`lba_z
zSYYmv3&UKydkF*&3=yF@p=2WMi(o}|Yp=FH6Y<_JQDw-+>?^W5*(9%r1*Ay|MOh(H
z>SJWUNj}=GJF9D*A7%J4YWLy!V>}30P~H9Q-M4Rv5n$@(Qz+}HI$PD}uq9u={NZ(4
zQ{IWl$5i4nLJnP<xZG4ETUyfQfM(c{H#`9?Lk5lS0rh=r!B)IA({0Ga4Z86B&Asq~
zMQ8f$6m4q7=RZY~o5(KFTRcr3d`o}&57Q-cP6D-kULIyLXP=RFUmjglte#-^&NkpK
z-=ww80qoJ^o?&FNhdLu7o)OZTDmi{;#>oID#1mt8q`}0lo>*+nWj4de)X84Ev)}Q^
zE$H%9m^GL1d=JS%3zZqMDkH;xqhKb-BJKXqL9|=7Esn0*gqRy&kVaFk$qCd-Tc1G5
zk>OuOyQx+^8RGZeY1BUDqMYALkBt}<q<tRwn6|ICiQnXq0r>3pd+#eMiq&Y^k6Md!
zl&pxN?^lIt;4S5UutE|7%Sg=W+i62l-$}DAdLML=17_b$v(Lu;3PdHL@J#gYIZqtf
zf2k<LXV*=25?PsR-*}OkJttP>r=1!Our5zG_+v*v9XMb8#KVvzyWiGW-93HtvS9jS
z<^d4}{JW@8^d!@iQuXGh=KfMq!{_l<>?G*L!4B42)$(~m@v)G!mZw(On7t*J@cL!u
zzH(*Vi4MBFy4&8c=}kAYfUGx}69d9gG#2c#$c9TJld+~*&G2NFH!@YaeK}8)+nyMG
z?y^A~*ct(g+~=717%-S+bu$U={u~^O{rY?Itawg=FC>gl>91h<k6BC5RBzjsDbaH-
z=#(ncbFwaRMarOzM>No^o(W@s5gC}1siepW3iAU`!al-GhUdg#dm94E0upnNKbwL3
z*TA;|^s#`-3TiGh6?wWew0ARjQCr|9uGk00)=|VaH-N#ABPCT6STZ<J^1Wa%?@ao8
zphO3=IE6KaA`u8wmC8e{c^DLp<_69eskC-mrj7Q*m9;C#=;Cs1*w4fHikb$E93`tN
zwnphveUSQVKD)@%5VGkC@BIlQaLF;B2sumzl`<PjFcQNA*(Dugv$yayqE_I)_^V3>
z=mnz|X(_|QDqKWmBlyJ$S|Hvm(t>F9;^aN4Fgz3s>J+3QLX$bQM>Ga<sR)EV4h$Ii
zJyRu&g-Ul>%lFA@yU^`>%(MkV?Y<C<9s67#J>qrjU|-*%kfn70x<ZG8-mTjz2*J|m
z+3(G)o#!k;HD3TV$k*MuD`ig~J!elHIL^;Dr;gK<*f1xV!JI&OW%4hr>_~Z#ii{<3
zfCXp2gRu^FLV-d7+ReHWNs1#(=BGb?^xCR7l9aUD7X;wjxq>k={#~CKq$O7Fn(%_F
zrYa_F`CUIH&<&vyAdThSX;`Q=D`~D`rcRx|2b{XJL8GWS1nO9l&vNHIF<H3y%^F%O
z%5pfq_{fxC*4<%CwI@uwL=6~Ob1+2!4DAwo1mxwMjAHLx_oNK#EbH{3yj5fUlMB;(
zZg#;&&gyCdu>r(4z|R2ii0}(24lCBX6BU0DHuSvZbIm*rd_RbOx8wkVdZ*koOv*=Z
zl~QK<uo5B>=pDtioFd%I#as2)c}X%ieJE%x*uo29p8YHhfftU+G&OfjP8$@^(Ll-~
z;D>z1aZ^ttd?E6UymQ9n(VYC*Wh1X;Ar!vHB5gw^0XX1nj37kHL^xCngQPSr;#5xT
z@w1cmuiBq~;3BCefHW2rt|*{AH{Jwmd#agdG*z07h%zB8_5)-R4VN<8i>|Si1r_Q3
zMXm9)jl|iEjTX2KfDWZtUCXLs#%xv|WS5NsTg6K|EA;UQc=1N%8%k*doMW;uTCF<W
zVl9pkcR9n_7)avpFe)c5bxVj6!p$#^mh2o0w(7hnlcL^@cR9bkT4QL#Xv4qH)UYnS
z1=FfEQriI$f?!~T*s4EiqXB5Jshsik`B+55la~!08U-tL;DxoEu;)(fiJ2EA0x&dV
zWB4{K`ON`fJVfNA)XbAVwp>_aj~rkQ{El3eXfoMi1cSKcx><Uy7QleoEmxs_{%6g?
z*TY*a4s{@JNB|Lj1*+U9I;7)h7=1+)8Z$WGpEKm3D^_ts5}iFjsnEbI4e~?4-%5z2
z9Gnuk(gqHaYCSnkO62o2XgV11!89n~TB`FNi|?(4Xlob_y%^@BS^oa)`y5Wk&O6gt
zc@89YYD*F`Z>e!?y}qPE9I2<rttd~4=@$-k%X=D*^zTSiVes&DQPLulv|94BOK7L=
z-;>K?plCQyceC<7eF8wjlk>67l6fgr$}64Ehk0#pT52(YB4V}LcbNA=J2Qk70YLVo
z2=FfVd~}HDh+%Z+;EGQLw%-{K&HgE#hlSB164Zp#$w<=C3LtYxi*!mBO$uZB29_PB
zc@twzUFwv1HQae%s^ZI{_F~CFYIQ1Y)>f+HPkMagW^#<`0s2{^g?jU{qcA20aMEU+
zz2+QCXffk)L5-Sj@_w)FM!0SihJ*VM^)rhFHH;oPj%*|74a&g3NkgIk&vqujQKf#?
zs+NM_(mD$hl^Ja16nBec!1I5$Z=qaDf~0(Wx48@R1NX(&5|QWKYDdqhPHgjjsqU)l
zr4DH-SN#-C@Z@s`2DF87;!JI9qrH2=-jCd0sI;Zx#`;_sMKL~2C%kFx@<g>GCM`8S
zn?BMpIJ~6;C<X6~5=7;jWa#FbCH+_0s?|$~v0bbjsn4W5b?<}M5(T#(A4cXUD+WXX
zr^RY`>v9IyMo;JO1L?}oCMDyO%iCA@ykg#ke=2~f8TXZEd(IHJBMqltoktt-T-`%J
zv(0mJPSBG54Jy8*8NvcV^xu`CLN%X}e}DH?A9Do@o?LAh;2Yu<?Lx36AGZ{TYK7+c
zUH3mad?gHA+FbPxD85VTLMPr>VlOER>~B+8Gu=<%72A0Rm6<bkTf+adH{82KkYy*j
z?>l<<K64|_rABv^QCjYgGIwImnS<99l$J$sL!T<gP;v5aj@j<=21)N`NEyP;+Uo(I
z0WelSOVW|Ekf+rn!-lIr%(USns}CWa&m;mcH#_y4J(~_MlThu`rTouI+y?__j3W-1
z@ox3HhOA=6cw5MwKO59^@4v!M&J5W1@U%QZaB_K48wxTB0*@?fhBy@trIIoAkiw4%
zhnpy(%76iebh56}gAk}<9WhIy&ww$y{+Yq;r%VM57j|Xd#1&CaM_>Mqs&v$|R%Xf3
ztmUozT>qu+yNXC6_$FcBO-cV;B0vOKMbbTS#i`c<rHIlwtUu(8WjD^BoL*9I53sR-
z;K3jo=aBK4MtdNbw43Od^77M~2YsWnYas%0tak-;y=Mx!5=|}!qg5yqL4P15-?&1J
z%UJ+G8U@p@gAI!*WnKOl4Etvv&hN&_DMj}G7xGedsT-+{(z^0!^40%TDHi@LU1&Ow
zb~nsLJgrCm!jQ}RsR?xgRs@WXO(#c*AtS-68#HN0hOfEe$WAZ(#<7zOi#Bo<(MB$*
zZZ?<&hS{^y`mGi~BS0qBtpPlNGuc1_{AZ^vWnFQsU~<rpR@S-hR8~~+)MD!Tt};pB
zPf1SnfyI)IUuEYQ3AP@$_OZVy<kaJDPtJD=!l=%P{}`oa=kQY_<=tUAml%yC_SK_r
zYc@5Hb(ild=1%2kSrC^u;fU;pfE4HVOIu4%m)132AD-t^%MmmLDGVU-m2|)1PRbW0
zrL|$GUnVHp+aZ3#qFy;cqsL-Na)#4Mk$=2UwNay`{nxfu!psd;Se<Y|jFFYQug;ga
z;zEf59IQOYyDuC|1+svl(z{1~9wlX;tTy;CpW3KR%3RZ-vb~|r4o-;$ol2-q#aGS4
z*fDL$CGTW|j-}(-rZ^DC3{M#O?dS=KgPb6}Rah(wYPDR*){;1oKfo@~cR+askb0?B
zH;y}w@e6ZqYo@3FxJu8cD!f?6QL==9h&glbjM77k3)E9Gmi4rsjj~v+-1xl{?La}d
zXY=KQ3`IDd_?d@q&*4MVOw_^Ybmw()*t95W6zMXy+rA@UEdxRrpbE6=ZLDli=wV<i
zZ_09c;jg~E-n)fUrz2{st?m+I8~z#lH>I1!%RT*<p%wRA(JD`T?)lEsftUovde?eY
z`KGCo+QkY$+McwtwrG$ZcC7M>Hj(5%_m|>W#zGHZfspZ<zU@Aa7Yd9PlM5_D(~Zxg
z5m|<cBdPL75e>nWKn{pBK+_a-w}$J|bAt1doN%TK1&+a|kf(XM;zZ9rZ0EEG(o%M8
z-NFT`4~tgeg+ICvS`(XX8U$3u@4Xs_f^>x7j+f>H$%@U+VL22pfKJ6?7KmUfqqABH
zrIvDG0jGNcHRrpNlomILUVln;3>I`&y%|s`$8#73lRTox+tE*0XqYnW!b`Mw4o*Wj
zmhnnx&nzC@RG@AQ@O@%Kt{e1X{$vnTIB-OkMo|5^`GbpRYYl2|-qUg9fEch#gGZk>
z(KF3|pBgYK5d9~Ly~CMmRIIa{cVU5`bO?xX9xhO_vb%Wr`24xoqvKV{o2vT`K&NaZ
z7`uTg*Z?VVYk?x}ef`}#do)##`x3q$1=-~NYYpo(u<wuPX|Lb;oW49rY}ZY=ndrw3
z1pbw7l()+X&7%i&i|pg_Ed0<<(Lf>dO;H%wwP`uU$B%!HJ&+}TF@-tyFzdX{OH#1M
z;%J<*q^<@y*g{<m=|vRR$;a)!rxF?9vDA&cKMaIekrP63#;*LJU60Nm6<vD+s*n2l
zua~#TwohBe;2g+<@-1@pmLC}d{COq_i(5!f3~D^mFghWoFPU&L``)^~DCDk=&qwWK
zIm$@_KQza;WC$_NZq=H(Mir5=6l*UY7%?n;xvZ8?A|hq_X(8$OmJLgh{VSw+ky={Z
zumO6g((1-@hlsBy+1sM}l-GT0L^rNM5kNPXJjf7SmgBVe(|CPXNw=}e3*CkEOI<m~
z<|d|BR5auI_^Ix{sL@D^Sj!o-3iSvu4Bb;9_2ymTe(k5AeZN^RB#0PCOF`PxK=oqC
zOT-b##`t=<VrITeeg2KAm02tMdAUvtaBZtSqsdTntJ?4GowX}OC#{qYLRVbkXTOaZ
z-G&ke6mh2vVPTvq3O*8s)3RYijD@6=Vc~T0IQZ|}1vj?idYtnB*~+tu&j21CM|gez
zRaW7~Y_%uKbfdYOwYOSFlc)+mGQ(>2KaON;MxYI_U--JRD24~wIE|kcx#yX-Nw%t(
zyUBQ3=UZ;6>+N@VeMEw<EeX<}mhW9-Z-`1qbTqgBJHx)e^|{2YQ>ZtkF#jpkum47E
zDO=C_?9J1;ya^K{tA`h-1*KDah?cHVgVi(Nr$GZ4W1N-x+@YlN3k}^QDe$)me-kDM
z{!MSq)WO-~;(bI6Iy%rLRWn{yW2%F-Zs+;D%K#;TFb)P)Y%I3dU58|xIEU`mN@t7A
z+MA-5?qbt^aL`ZIWrqk$HP5eYXg6LTlHPysOWWtLq;A-HKQDUtX%kU2(KMorS+(hU
zTD$EeV*L1bM10$0WFhndwl9*SV^syX4p|S4J|gz{GWqj7YU{WZCo`wk9d~y^n;D%g
z-T%$t>fN4dW<K4g5NC$xM<NV6ra^-YqOGl_!^+58<_lEi$rI$sT=Zozu3yqSruAa+
zg2EajpMU(zm!+!$#Znsy!6sd8)n!s?jO){54(6-qvtjHVS4ZPuAXx=%4^b;6!*cY3
zL=Y(DuEK}^It5I+27e(Df(?En9mfrhuH*YQEIW32CA2e5b)&4FJ#S|XYEp00ZORH&
z?j|kGRlJyVGM<L>tq?z7UphfT-0(O%+sUJ!h;T)5HJuuS5;MPCB7D)$2@wh6x|2c*
zZhqE1BbLtmor@)4<^(uxfSBu^<(te0$l5n2i_4h?Ipo7Y{MRPP<Hn%sPcx+{5ofMo
zf(%VCD)pm9G>aPvQ%S5Vh*xv^K|>~14cqJ~+#h%zv=JjBO8F1CdIkzIhhR5p_{pzW
zpL%bd#-fDBk>!N4v3>}~cQ?xkXELXa7IxZ*2O2oQ9E)Hl(z#t=Kxv%)VEemK*^v|h
z5J}wxOV841OGW^3Y7Epxc{Qv*U{ynJbJh|}Mva_0dLtuHo-q=Dr#Tz?*p_WVP=6iO
z9l1x1Z)J@dq`eKNW96MuWH{MXcGrc0qtx>_mq_Q%E;E0L=yy~L@jc>+P8JK|AUZh2
z4_D$K!&tyQNzZ!SO;DQB*$6lMpg_D-|KtyPh2z-<+;C&WZ@O|?)dx(Bpf?|z8io((
zhp#&ny;<a+>=OMZmnjLSGk_j;p@y$>7<U#=hQo3@^G_;Fm_UO29bl2o=2HQn%3W^r
z?+p|f|02Qxw6xZQ#Pao7A!e=lw2hW75^p#ih&XLI{dl311y1cL?zj~^oYBNlpz{-t
zgEun1GM2?jp6M6peuyVS+^v}^Zo_h;77~-0`7E9yUkVr^Uwf<!+z+FS=J~?9g}dH*
zwoSm0JpX{4y&0>ocT7De90ApkA<Q6$>x`dq5A&yLcO1ZV#dz4L0lM+9!Im^^$xvUC
z!IIvNi4jVVoJyNJj2sN1j4)7nJ&)N2fqoMEgd+wh9%M%Kx`ig%KQ7JW1)K$mzrehZ
zny(sMj<=joQbl<c5dD1_Leu5&HP~GW^E~u@w^|uEE%R_5GW|DZd4Qy0=>kik>P&+g
z2@Z%mz1;nq%HBsH(nnzBki|`-L4<eTx8}^A{3yu|rTBj=on=&3+uQXIiim*H-HntW
zDH77%+;m8HcT0CS2na}*ba%IOcjqnL@Gkz(JBH(o^GWoaz1LpXHRt?I?KSeS>roi!
z_$L3}3mL&96crXYhd9%IE_e+ia?{F0@TuOhE893YAMG!Fl<H>=jPP2>2%-IWVfrQZ
z?BrJ@k!YWCw2*DhU=Ux!0QAutaQ~d(iG-)6;PHnr@ut~<^U-^=?S@v?+Y0m@{W6Q1
z1^Y5jE6a-Rv6bdQ;^#18Fcn=}WV$EoS4jmCKkWw%ud3!YYwxB#kK-?r;zeaMI7+fs
zEXccGL7$^mbLthcv|VAb)scgVCS7)><B%d(76qlp4HV{aE+xSKGaTM=QCjp>?Q6f`
z`x*D*wD;gddKl%qV+08jWq0Tg{~&1;e@!pvM2)0G_~swRI()*<VpuNKiz)g|C7%*p
z!N+n9;OM(72qRQB{PfZolUCDnr~jyG(6jv0F_gbks4oLiggkXKZgxmR6k?5C*nv@1
zF;p_D5NPpQgv11ko1)%VsIn~%zKG>gqL~o0v-{_pPat<QFnsa?|0uASirT);3kLe!
z#<?H0OR2YSCO+>-%>o>scG~va;yRFxH$6f3x1)Y>$2UCa9-_Td+g5N*uny1IDJIVs
zD;7}!K@TzsrVr4M9*9Bky{^e1tgvcI><x~&)z(uYCmU#y989#Z4-C1uOc*ncB=h%f
zP|W&KxGy^AFN#*Eg0<sEv*#<{A8o3QqX~m>xf`3_KixIw&7}E0bguC(UZVDIh0>gY
zP!x!=Ws@AKWAnk^);EVzg#H}3Koxgzf6pEZQBijU8G-N1m{{atXxMgsQdCt1eM$_?
zY$~x}fvU9SvbBtdW|cpM=-d8-f)pW22lZQ&EOpfEv<^V75V?zl!#r&cJpadcfr>If
zYidwYNB2dhq*kzWYRmcgR0nWU2%C<D#B1JuL-{sNb}Bn=0N-)`s-!jodIzhe&AFI3
zv>*_|@x1jKeD8qU0cAUwyCgCc827;4-TQIXI|)P{kMlfjP?i5vi;;)C6OKVOjA=)%
zpnp4d`hilx3PjTmza{}5&?L5q%kiNsxp>sh;3p)3mAex|##YC$%iOap#)%#o#7a~Z
zR7&PMa(Gy;t)M-po#Q{pzf%NaJ5C7z11fkmzq4w&T1|t-u``uId6#|MA;3ZhZT*L~
za_v4?yKXmm|6@#AX^;jVJEfX<3Q4f%v?>UW{XqktZ25NV92s)F$3+BvS_7;T#32Wl
z+o4@BCLuRBcl|X}9oE)bM}FD|;rd2jORl$A=)&T_ig%G5N)v`6qL-`BlbqWDc4*37
zTle0d+y5E(#GpSWOE*zdo$#Bs$N+;pWZQ^7i<vb8I=J~a*!*E;^&T$df*Omql5CtW
zbu;%<=BB+)+n+<8<G`M_hqh<jfuqxvIgB?xC075cS-VZRM^pl36)L28X-k<jKCvv)
zRLvEw%ubF0@AZ;qmPHyE7y4Jf+#_^VV3<Pq{uI!l)F>29JiY2@;U*!b#(PPKZ+SQ0
zVVy?|w(98#DB}iGzNoB)N*OR9S5G8*T<x^FuhIaCp;<W<{nmb_HBscl$fLc>n907h
zX464)kLHUmG_d4O_Je952y3@?;<qR|E->YRKMd4F<*F<Cnms96I7TPM#Y_ig@}0*H
zJ|>_^3_7{b)<fhsrk`wOauI{@pe;9}oeYc#Ga&d65AP1Q(4XD!?X`}1r!OmW;2tF^
zDf<S9DWWPC%df+Sm}RJmKeg3SCzOWOl>V29Ps||4$WA2oBgOz#IAI(K6QT(A-Q-zW
z`-8Pf>hWG?pwcD-dkyR?4>!4pYWLUfJIcZifNM>I9g$-e{BvKE4DAik>rRp)8(=y8
z?5rOFe#^fFwWlp7GA?iAzi}uT2nzr|5M<?QMbQx#q8M!u(~f9Tmy@V4c4}*Z4Yrm9
z#FN#hEz9S%*vg9?W-r%7*mjo8uOUQ=QS=7CG(0~2TCPrRtLOy?DPpl7%Lv=!4w&Lt
zz!<I;LKH^r2(0Mw<ox5;f&`Nt6+GNyeHAS<$zA8C%|F_o4e&2o?!%UVpbz>3gciQd
z=TM%>bdoGx?IONoPN#YQ1k5;pU`hiA9!A)#wA43da&zC_5rQ0knv&xiwZv$M>DS-X
zShHlP${0DT`G@*xqqUbm^o6ra^c%F6;o*IwN2c*o%VLLnlX*D==(BSArh=3U>mkAr
z_2LR(Nv}cPHRUKNt7GB+PdxT7(i`Ep@e3L)Z4M<6=%NtCmaX0Yp2k?ay>SndvAOP0
zTeufEd{Ts6WeCcII6g6qTg{7A3f;qd-e$no?v%(|0s>g$gc+L_<!q9GJXGgBIo$*!
z-=vt_u-!%>Dx-&$+pIfY0#=Fu8o5_9QL8{-kW`$3U22ERXUWM55VQN8ohAO+7lpF9
zmZvVRvDv)|JYccQy&t#%=tPGgLj+A|qDTfO@a-J~0zA#elWBds)7|N&%)D9E-x8aK
zW|1Cd=a7&}lp5wJ>Pm1Hf@yW#!s$m=B+Wg^@g{?c0H)y<H3`nP{6^4vYw2?kslgD}
z_h-W)!tom>@HJ-~Fo5`l2qjJ{dj|c&L93jx`eVh;?1?QMfBjI};4>ysEYid7e48SX
z{@CY2CaKNWnnsKmK}(!8gMunY@lI>SQ|5Q@L<J=N>c-+Fq7J6tP3GOc)yDppuWYZx
zwof;*JO&MtQ8Fh>KiJLeTvVZN-NkOfDahX|?mFu35@#IhYB1Kl3=eX8CkwR1Z7eSv
z<Kosj=W%e-Mr<R1fbLvWNMFXG+Y~Ls)5B_W&*Ex}RO!@F<C#LN5Ub#J&!==l6SA@H
zLVmDy0RsrS>;cJ<MftlBf6m#{7urX!L<-<JHD5ozFr7?!eyD8T1HuCEDf(@?%JA^?
zPBpB*)i@PYn706|`ZAmCmM>Vw?2T6u=)yh&EP_a~Sis`N8qk3xxCyW|u%T4s5=|{`
zwY3c-NT$k*Q^l5p=4>-6gD-Mbc{%uN7+DrdHR-OL-@5~z<7g{W$XvjH%V+e>ZbfoX
zD;?-G2?&-yiU!`6$&{!pYI=HSc%OOS3F6hT*Um3nlN3c`e7U^9$x(ddzTANI>{1hv
zxj>cN>#wZN;bHzw9`6oQjF<-0fcmF(ZV>LTKRY>kU2|4GY+2c=N~I`fcXBHZ7Li~4
zgH%xu8+g4RK6&+*4oNCWF4v4$Wtkx~_^^((I>n+J2e};NepE=oDYWpI^*{~etQD=A
zG14{in=hsVnG~1jpjlHk`jRWF3Z{Rry&g)V#0~Xdk|Vh(mxATcI1!vc`X$ZXtLcO?
zt7HR&ccZPG{Pd;-d*^5=IDF3<<;+~mZM)}yRK%G<9w$p=a{E>oRj4wx0~l7$a@S2C
zn7(HLE}Q&LlO)HjjeSaw5vDUS^Y4AGYMvx-huc1nGVh<>HxIL1twwKAFx~_Y(H`(F
zlaYRR`;hqTLXZRP(J5Wp7)j7jA~ctUsa_RhiWxrB;k$<PqT!;2;z0<n2-b;kt=2Yg
z`s5$+^xW=MW)Oam4wzgQ411!8pqqMm9U*a;_h@CLQWp0J<aG9oKxFdHFL0ZR@72q?
z0HlItw&2K(F$WK5wczRzH~pdZ(-GX_bu?_u^SQYWb?LtQ6C>=mFWFxX|8H+8%dEY&
z8OT_d7RK64MVTK;d<Skur27;Juy5Fgf|<XG_4h0|9$2AI*4@~x?uva3>30`If$#j$
zxM(o1xvQ=ZCpa-c^N}~n+e&A039ND8ldT!f`7aUvGo>6*xziC|=t?4kf8G4oc$s$M
zpSn^yoOF2rem$qpBC3m!US%Zd{?;_oYd4?xSRnxq3T+j~x&h=+=vsh#9f3*qAbtRL
zh&WuT!}Gz9YuY4L=2_gZ_c8J42Gba`_*GL&aDaWKIJs4gq<G2<`)g}T)udd`smLWu
zR3K7Ou1bosSL|qgvHmhWJ{|9U-9VsL?-|2FYY4sztbZ_kL3Svu$Ws*fQ;J#GEEe2b
zHMi%V03#Yh#b4kU<dsmCX3;~c)GJeTDzccPTx#z^<WZ6r#%6=Nc;%@c*__DFy>@L}
zYoUzI4mPU2gAY5eYo;S*E+_eZZttt)@8b_LajX5ZrtypUJ08(O7wf@S)Cw49qFnfZ
zrQh|}C1b)ZVhB2-pk6G$Qn1Rl8}n<%A~~ve(zZ{P%=rXd$^eie1#Akc@sw5cvWXON
zaR!*Z+<y4PXkxI(y-587m-$?n8D|;iSg@o;R4m+TBne@PK&m~IR8%jvJMMY|w*K)m
zX4iyZMa61H1@(N!E25p`i(M{L_$pKD-v!h}FpMgEWN$=6ucLjP>9!9Ggb8q!!XX$!
zm&FBYKscaEi<2Bdk+A}G<G&Tq0of|06;^ps*P<xXEmyc@BClFISB(P%c|Vo{g>L~k
z-bhFW$-02^I_(5HNIdMwqh7-vA{DNxK&>bSRwoTl9o%uoL2{0m>qMI^_Dik1=TFGx
z_K#g}@M@e?^x8<;|GEI^WGGnKhRa;W5sR@f#ZqRl1I@9ZsCn0!$h9!=;=N%l9inLd
zeG1pt;ZjLSdEt}G>H9qKAl=|y;r+R?P1}=zcj5I{a<qDMJ#hGRnBX{^(=2slpbE`y
zzqpl$6RG;?YUK+wd%H(dV8S;6k&{Kw2Y|v+ONcQHLGf`>Fn-wj?{&@>z>^x**3mVz
zLa%C2RK4KIbn05D72i93m$?78pt=yEp1!))65@fZ4_G!@5So*K?7{GK0+Je8$*Syu
z=9}onYv>YRe|lR`mRMWNw|$BUncTCIS~Cwhb=^s`3SD+*25NXg;5r3?K#*Mo>kNaM
zxw6@1XKo<9RhIvPCuQr)UgvIItil#r$EGXg0$0K^dl?ux$`t!~m{ukS-wxH!XTj(n
z?7av!0(ia3)eq&838VhzWb~4RtFJ+?$ePi$lq2a|xO4Y@N@4b!F*}H_#1IjpL5Ot<
zOXQjKzQXqW*-SUNeaX<rm&}wIBKJ-Hl)26#l82x4Lh6o1>PvgrUjl4;0V!o?aj+pd
z%N<9jn061EyWAURc(GXIN0uULaoCu;S@M=>8y2<<j?B>4Lf6ovRjR^q{C-Nx#3`Zq
z!!|dZvP<sJ8s-mH?N?E3&DH+H_9w-x>+M;9cv<gjY)#Y0oyu#E^4O1Il#w9S&;Q)i
zVR&HvPrpL9b?$mF!#A54PPKJJ%033uJbiwK%v?DpaW-!|g)j;`<Yy{rxe;eNcgOks
zIZkXOg_*xUGEY|d3HwdgHuU=)mDQS+&b?)B1LZd7uEL~P>Qut78>fB26<Y6hY=lqX
z^|mA9?Y$0z{`sq&w_ckp6K+rSr6+pjZM%Sb3b9q|&`2+V<*I=gbXU_XwK<WJst06{
z-ul=3^c6L9#5VNi-Z_F<U%E+Ph~-p}SS?<>pE=gf_q;GJyibJ2<O{3(y!K4``B4xr
zWqzl|HnNNTre!PpKd#AB+cUF7jS*KX_MLjAHkly~X3wzSKS^>ZTp7<Xb`|r*KH4hD
zFSpv9>~uSu<6E=QmwDH>Ka4oCCpxX3E+GP+Kq3I?4l91jSUYSxwcBEt5xz{M2oa0z
z2ggd*Dey&}EtyjTNrg1{l?q>Sj<VIsM++y76vrh{HNIn(0DWw_R@I<cSG^`qB0&Js
zWPS$j_IcY4J#a5mDvCL=8UH;+P%?xQu}4Dj^xoCU$gY$Zjd~1^TFuB(C_%ru=38V>
zV~2V`5gy6aM!ETX^62^)X(n*(a~5_czOt}3!t2f#dGVYtae6;Oy;2-_D+p=MNx+Sb
zC=52s0Tg>Ym&&F0EWX@m8lKi)&GKq~ceG-W;J_xU&;_9}Ae3r7))EZmsGG$O_JZk9
zinL=;Gv=}ffTzA-K=zB&!ORJmq{mS0^{eUavRZHc;0ILdQ6#&AedgAu!%uNyeSafP
z)Y;zfe~X3v96$j^Pq3X`g!HUF$066>o}x+Car|5QMaO@0aBmOrRzMWy4I&BcqouKm
zFt#rpyo|yEiWYxv{a1PWPp~iCE1(|tfc)$2!zUg;n$Y0uLRw5%QZsT{2@nJ)k9*Te
zvUSTLW4pO2>~)8Y2V5|VcJEFW@-1DvujWGL!Kh2CNXNkpo&3NU{HnrVgchGKelFh(
z0sKYpdCLnvXWlm~uY@Aw^P_;bv{F4BOnXI^AQ!dP+oV}4lwssvgR5*22ez+KgT>vL
z$3J|@x(yt4bSaT?w&oXj6k>_lyl~{4Ex@7_OQXrUJ;e8$rm_naM?Xk*2uqB|G;)hT
zMa7h~u1!tec>gqYXJi<I>wH~z3>6j=Tdpy2zn>3=U)237%Kwr)p>^dE(Uf<F2Z4Yz
z?4e@Ke&k~WyYsFewYzpXAlEhTS!GC{u~T@|&SUv5(l^T`Hg<Z$*-BFgP3X+6WE1!9
z9aw^RJj;P>KCs9GmrEwsD*>t1t^8c%8`J&Qi3`P?K9XW$$|K*!fJyj|S($xPLwjsP
zC{<C(VvNgmL9#gm^Q!i`ta7X5r1>W7hsJ`eFs@sdND`!ff>D)<`4ff1P4mh6tnB@(
z1ou>d9?(BNn<Rx4H@R7##?Ka#eImBil$P*R4q2`*SR1hUasF5(%>5Z^R(yh|`!g<-
zV5Yk3WbcD%pB^6D`N3j^zBPg(m?9o0(YnG4^WzsxxawD>25E62A%q(`%a(SzUU9_M
zt$n3C+<Dfdh-j$=p9`)@-=SIUO`J(7m%bmANvO6<FOJagD1CMu&2zeESr!-TZ>$mT
zvb3vkieM`i>#~edi0j_Q;m47)D=JYFelpw4*R)<TYW_T|gMSOB#`gHl_s^~iz)s$r
zdp}|wN^YO5P=Kuj@#;;43g`3xZ24EEB1c%$a)48CHv2UB$##A7<I8bS_cWq0Mb`vv
z=QZ;s*)j&iHSjEhEnt`93GsK*k7zHJ{bXLgPIH~MZ=kr6&~B9E41*rY@MgR1k}E%x
zaI-T=(c{p0B~RIGMezuH{`$^tZjNy^`!+eAIrv1&_#6u=mZF&aYkEEdIhD4j*ON|H
z|6K%#!g$|Yw{_eMz?}J+{?<q15f=Y$()?{zF0s&_++%xIyZf^x7T0t>2$O(-K<di!
z8{xIL@_$0U0|Z>6H3$b#b6yT}j<}_fAT^~z=MRftL>rAHtofttI}Di77A8Q0mHF3W
z%`02RCrpd~wOW;a08K<{D?-O5@PDCZn?Pi5J5U+A)N1{;XxAlvrs!du?-{1t^YK-=
z$7P{l#CC?iJk2l=x^Kh0@7YH@=`oy0+wHA?Zh*Y>dO~>yb(}1Ll?HmY(7(yCaF);W
zeK&>tRyt}s8g1uS<mG>!SpNW3ntHWSthBjl;lv6<cxQfAhS}C_Pqh!@h7^Cu@FH2H
z7VtrNR>S<Wb^8&Xw-w86ThzCx5A7f3JK2;MFSW``=cxEJ(+#;&jJX`4zwcV2g<^nr
z>~MM`V=TxYteuf?qQ)MUq(Mv)3=owq*RF1w%C{gfna}b_k?{6h;^n`5;Qju~`&!6p
z37`dhNHO!&Ft`5!-@IEBza_HIhi@3)DH8S8f;)v_!TMX9Cj8Z_RrTiDO{#Ar6)x`j
zKIKT6-Gi=s&hR&NW|V-$QP2b+ugB^q^GE-IpqP~k6EQZiW!c%)0@?E+;-|Q2B!!~h
z<<)*=cxm8A7JgxC6m}tUE02(c9Ye4d=r~)$NX^4>UK=EUh+E$~%>%2rY)GC-(z|!y
z^S|_O?OjR`NTvUlF&EKf?+;U}G(*su5Tkwf@V5{ACd2O!wEfts`YRiNz{1*$1=JRC
z<ZG)~T3V@|J|<5@I-5TpY2dBIkC=are+Q>4HeH$%icm?y{9CkD?A0sGe370)`=**d
zkE(6TB&2<EZvu)m@=cOHav9pm1jb1nsn-4{CNL#Kf=K4)MqD9tf3GZDgx{$2HT$@-
zArikH9-cd?aN<fzFV=RfDl1hZ|2PE}mL|LN*LWR+vOs?-<o6D{8vCqj9sB94Oz9?H
zvO$V%Mp-w3f&`5h4;#J8)y3UHn5K6qh{EJ&;u@Q9%TjsQ$I<f#)59o9{|0w_OD=!@
zeo?*_5H^l^p4abGj_zB!guG1R2))7i4uH9n&lqk8(rl09^W+Uxt!&oWw6Vlu`c48Q
zyf>%sJDGkvWx67EMcY+$99=?ygbplk;G=5djsl@(H#<IVk9Cg`>%+kt0|qf!fVxqO
zi8Qp(7@Bf;BdtP)ESa6C1W^Ipu~f%6m%%;t<Twgch)Om-r}mHCTjY3F!Wu47$e%i1
z?QD4#D4nKcrH~a#4|wWjK&=T7rQNkYgpt6*$D-UqiavwCUw*T;v168yVUCxqEhkdW
z;0AD_15^mWpfr{ldC39Chh|At17K+@^g#8#E@srl$qO5=%Hi=i)$6a#c=VugiD>E{
zEHU|#FfqCLxiwsV%gE29>|~NKDo;!W=?W<AqgHH>jHLI0DuV_f8vvUvNIdIP(hOz?
zhxglXM_|KMa|bzxg-sE})z&GtS9(TGE5ASg(V6&?MyY*-h4S(t3WC6xl7;=E&V~Hk
z-V!1Q{1sBwoB%3i;HLb)L3xO4fWN%tF>mI4&evv=_7B{EG)578Ersum0xa`-X<uI{
zIFUswIK~c+YvO|%1>JrVZs`Ftax#>q^`Uh*7(h}rs3}yn1UQV}qfiq-zFjEVeCymw
zj({5KTttMJZq~8cjhu~==ARv-#1>oBdKfFRN0ENLXRGvoAH7uVFlfnhaLNuhB!5&%
z?`PG3sh9mxlAN%k#++$A1N#wL8_%=ok`=?>s~p5P5RdwSLJg_z!2L<P>Sio8wh;#p
z-;z`TRLok8lIUniasTuk!&A=^RMGZO)n~-QJVstWczkY6kg$r;j5}#wt;Vj<$&c8w
zHH?^OIIIuZ(?}!ir?kxZZKq^&a?20eqGpxb<jh3gt>r;s@X;FyX6_$D_VCG{G~S!E
z(=5^2eH^5G(t8Y|Pch$%?H!souCF>|D5P*<wEw{WgJs}jh9sY`gm|>lhDSD9Aeg$-
zWCFY$4(rsaLWk>;QY;x_RakyXNRc7l<E8}-*Qo@Ha|ycfwQ=51W{mu#WbFGo9W-8<
zG|cuiFx-~6!(LFm<63SP61M{T$vAW0ED}@-Ze}j;47yiosl1Yi?FXN%_W4~Z*Q?7o
zt(IMW+%MyOYpNLsMsY8$v}L}V`3jFwejAG<fbolZejo!rH?0=qgC+Q}7TZt|;QTUi
z+g+jcJwgf#BuFc{+6FF>v2WHhJsnoBU+ky}slX^Aj3V4CdqOB?g8|-Kpa+aho2is%
za`N;S>wJ~1jb55nIpahHn*Kni&x$z(E8uQ}-UNRiQJ|=r6%O>;fo|!ypP+}6wLQv3
z=YT14Tg>NyT#UHR6~lgWP~Osip2;`DQohoJaL0sW8-d;CLe=>07w9*>_7=%;gBE!#
z+JTEN7=_^gPH1pyp0t`#;}0=xmErjbav6)e<#wz7!p5kpyIYjQYR($)G9X3lnkp?e
zKX)B!dK?0;#AtqcJ2Dt+nVmfoz~}J%Nta$A{`=EJ(&z+V>ercy`Mj>o$E&C>&u3F*
z{(F4^6)u55vv&@Y<n$S<8SMQq-f^L2#WBdb<d?1z;@d99Eex2w(HQir%j<|ZD0Zcd
z{4!zdaJ-c?WIRTsV2o0<TbR3twJC@l-gj7yq1w9B1<_};n!IaHCVm_}ccP&YJi${8
z&)#tlQEeQX;?@CmcWZYf7y#7WTO}viX5!Yt;ZMSRn!j}ZcTzu(gSK(Q3wT+8p`}Co
z)lZ1R3QVNux~7In$(eGjj9YLx5%~iJeb~K~Jz``d)zdp>uE0kfGpQf!d@CU7+it_{
zYOoRq;&ZjXi86tP{aMz^&C)0p5o~#~NzU}HUQM39W0e=i=pNO=h7p|EryiT1!l<M<
zmA_o5y<W}vhDL!TzPo>ct0YgEOA#aNDvBb8BcLq)xd59pCHZ?rODG{{{1Gkgw#y>X
zwVrI&TJR{pqJ(c;h`3&*PjJ7gMRM_F%H9AI1>-(=$zqga`?I@$WKfq1O~17qJE|^+
zKJW^|V#phPW*_{aOj4XH|7N@F52jDDft;K!EpH%A@Ni9{Nj<}$Qv%7jFit@1#${(1
zn3wky;<KsXU+Ib&&wtS#<Qb{CLt+6lBHOOK@HPx=Pc%?LnA{z6i)Rl5CCDuQ4Hr|V
zaHH2G5vueg)4coXeG8jS@o!z$%ECRG#|)q%hBdV#JDHo^Rrm%%g#ZesYE1SYcs_I~
zF7z>b$e>?ijJ0_}vIjLi=p=AjbqqC7U^VZ*6Ro+t5eDK2b5jA=E07<!6NxPUeCkE8
z!xG`&+pe0S#K^z)w!bpivY|dwl-qKtE`7%0tH;G;8vPiit;Kb#b^xIFfGv{CE!{47
z`v~uy;Fv&QoZ=mLY?Vd-Yw@05UJytL<7?^pC-kHWD?H>-|1gSlsO8qts|W{%N$rOT
z+`!(mK6M!LZZ_?k2UAe-GE{}H#F3_@QsSj-Lm1`U>Kp)6=tc>r6Z~N&R(TRdG2ZAp
zGjPYGQNqrw5UyGQ_H5#?&A(n25Z?EF3gJC0n&nu|M_)Uc&}hM@0NJ<y{0OGbRUSo*
z7B6mq-X3gKiWrBkY35&WWgr?y+?3b{Xp!95-o$)@^1%;h@#IA^7VaM)eR`7?JTtm%
znOH~dn?|1K(uq+*au;2|N|$V{bdBMGDNmMVVla&(zHP#gg%&EpAH|YBST$pHWY(o)
z25C@VUIRijd=CmA5};K8)T^_Wah_7dE+YBX<(%Lboe7GN<Ps8+wHsc{p(RXJ>M*jW
z*GKy97xl#dTeToi+nC;CnJc4G+sF&0OopIKb&Ev%r(@R@6#ybLdIjpw_HDh(J9116
zVSXV@A*zj>`&KHmpvV|VHpY6aVo#+do_4&<<8QzdOF{yE1SNS=*t;5T<}Z!z)bOtY
ze}iQRiL(OYq(rRCuIpkQ^W!r0kC%8i^RLw=H}N<n3Vs7QX#RdpiaCSs9hM_><;h8d
zVw)3NA)m%%o)EJffY`-pO({DXwpi1gQqo4gD3>^%nNck~b-E*x@uN`wVH~k=AVm1p
z$7c8V@rAm|db;)`iR=q9MVSQc77G|~ES!<oVxP8n-?<mqZf?9X8fq=aPAw5b3g1oP
z=IJg(%n>!du}6mGUjy0c;Y4Yw%y#=05M0+q0TN+?(88SIe_p@+*OEV2C9URQDT?o+
zAyd-t6aZyUT7|ft&CdMEa&rAnGz=W%S|KtGPcM;Y&c_R!GZ;lH;`q+*fd;f9x+Ky$
z3nvnC^rf@)j;8MxJ=VqQYF?a)D8<K2peEqJ$eEvhzyZ`2AyH=%34h(WFomeROj#q6
zAUrz3T4W?E*Zg|*9E1~8R@3zNot&pv8+<T;+p$|wWcDc!CBV!QL_K)g4v)*HnV8d*
zw<7M6<0g?1+&pGUsVUIpe3?i{ggn~)CT27#F%rgw0;iqylYZ^N@v`-88I_8Ou=Jbt
zMqcxp2?#8;Q_t;kYyGDr-)Jni;rG{xkk%=!NS~;Fy19?KzI9BXs?&tblcEoW1K#AG
z5r1ce=!JfCP<@GaHcm+HA8C`W>_~-%3&=zO9-Az^gSRasP#=ze1JLO+!#icA9AyO{
zWD}=M9EsdYO85KZhW-=MNm<L@Z-r|x)r<a*TUn^LykgL!*@wu3q()u*8{8#+Pd|S8
z(5KhsqPx3wp;-AGFB}pcD}at6AV9y`@t){8Zrch47DjN2nSxL{oK`p6Uw{x2eo{oa
z4g2m(Bt7k7{xlf)9n@o5B3HLaMFomBOX1hxh@94zu1Si65yUA+T|8V?XH29OzNDq@
zsBg0WN7*!(r<k=}GfwI0&U2NmY*tyJ5W)SoQHq}jr13NF7hDw@ZYpjvmm^3JE+PzW
z0#@A;te;00r-q{bXwksVUcP8-QEivZ$Bf-^fHukTJaZ_o+Ai3f7;6v$vR$7Z&g>ty
z7O@*VGZCgp;2TcYUp1CZ6s7GkzZd4o=yF04!mi@E>T~u4xIDhw^RTJLYBHC{-B16f
zBo)QZy3lomnay0i_J?-Ge(OH~;)na{H7KzF(i<QF$Kr1O)eiWY*rKUxYvfncgBCfx
z>~)_|o(?KD;tB@4ObfAvd=$sR(c%7;KdpN6yXH_cS%5Zb1p8U#TQIBR)i5qhf92;Y
z_d0%f9TM^%uq1dtBYV9aatL<ZXF0fsF}F|q>A8L?&9u__&f}<k(J>KFLQ*LJQ1Xlv
zwyHuX@x{bv(b8;OKVVnf%h&eAvQgRlD?=!WICJQmI7;xq0YKpTlUk1TEay|+@w?X5
z1B6MBCl9_mHx9$tI<U{<gi^XTSReh(R|Y06&9V|j=VP9>^8um6U4*V~!%J0}O^^uX
z5E)wwAg#my>W7M*3ZY-kG16EZ*b*)daZL)g7JDg!0HLZ7!mK^lPuj$Ipa$X*QKdHc
zV^r@`abMiPrai^}cn+e}YW8-Tzkh+RlqS2J&~1h@y?!jeR45OY6*B-xy&ZL8(_E~w
zd5z6sbNUXx6Ld)zG`<Jhrs{`1*e_cH4QUkrg_2mlo%&Yor8mVH{^JK(f4{)iKlB>3
zphbS{_ABmVQPzASpnef@s(QsYV)?^p@1diKXh)6+hdQ~sBQ3*@6lD9-7WH>NVK=@a
z3;dlGLK{l58AxQcHhyJkAkW{>S5~J6qSCZLY3Ijgco$0_3!<d9ZYU6*(Y46n((OZl
zecFcsj;mPu6%O2+`hVP+K<WnutC2?WKeA0zVB`a-LIaoVZ=Wr>s}I7zF49qtA=#ZC
zpENHJEapx#0jv8sNBkEee)-^TnL<f&$G-3fT0Zl_`f0m3pe2cvM(D3<*eEEas0!qG
zvx2LtQQy;HJ#eP+W4!pg46FF_7tb<WGJ;IG;=|rg1Z)9ZQbGh*S}}xsw$1uYJ&DNG
ze}ek1Af5!jaXPj*bH>uZnKSt)&lCYrV71Vu)5rg2onEA_Y2+P~x}*D(T{giN{+tcH
ztS*fo4ey*Yb|7ilVa#wh=i`!#3e?sj%B{iGf<q(Hw}6aB!k$s>Sc{|1ke?!}fF|3e
z;F!nEbrkU1ki_R9uDdt#l%NP5?hVhVeSj{AG10%mqu{4tEWU>;yV3pDW2NsFgnqva
zqS<pxR`Ctm3?i7CJRc&kVKGLi=#IH0M`-;jrhGcpe3`nDUty(UmMPDiUZF<YyMbLQ
z5riuvO{R#3Ib~4(@1{w%Kl;rgp9aTEb%S)VFiIfs7OJj{;=g&tgd)lGoq{~;fpqEU
z?O(%yAVtLaoIYyqR?$@=o~vKmDXcA6y6}y^<CGPgZ#R#rsPNNit3};AF#<_pNP%ow
z*)Uquiv-ps2UdQe8huxUKihi{dB6q)`L#f&4CZPaDU}F3O}4LtXhO!{TdV9aD>)%t
z;drRqEVaLoz3X*}g;q%|PgvvZTKXAy>QW%~eyNM?2f+>6C?ltd^*1El6t4v*YJ0|7
zP~N~m<i;s61t(5h*tPfMo$+yE18t+KPbSnOz%I?U(S#3E7=|bBGi%1~kv%$c4FYZA
zUl3Ws0k^Z%EIszp`%tVtAIpZN=IZ`CyWHY0hd{05n(o_k;0rzbhwL*@-7yLL4x-*(
zz}tLshzS(N(!ieMV!A!%1fjb<&vIBY(r?pEX;EMV14f5Q*(l4f$ILeXbpgJTm_rUH
zbR~ed3ixE<(w8ipPR;DF?x15OKa(hTnF&=WhG}m3%7I!Jr>2&1)Z%+L8=Od`D0?FC
zzJmSbq1iKuIGLN2;n@+B;;snML2UxQ7`iMTkRu22FUw-XGnGJ8&E6BF38Byb;P@U#
zbMHg<P$1rI{{mQExNl6!u4`kMlrf!hsrfoQ1J;j^I(r8^AcI#EAdQyd2gSceZ$xf-
zTyB_RLQ1h#uGji>%moGIJG=~$jD%%oH2(vIjk~07D@OqOM;|qSDgJ(FNzf>%J^U$w
zEw&u<%02m#=ZJvzg;ACh;!Yg2)NWiRuS=G~V<TxfS7_I~Oal@bF?H-a&i=C(oSfQV
z2@Qb!^J~T-!d_Mv7q1aP=@6PfjOEyR&IH1$PD;n=H5NvY{ztIG`%a+vC-{G~k+YdQ
zz&!vZDRp%T(PBT_v_9#+<+YDEV+@0lN8!vQTytoI{^dY;>GybP=i-IjWYu}rNuUW~
z@UN&$%?n^rV4SYIs4Rz3+9$9T_g}NGyiDFrAR@?*irK3tC=bcNf$XTYj-=KAUA*&s
zM)M3EKZ<h-?CRyK4`lywv|v@0Qt}pP8<o`v%ol#6E}$$o92a^cJ&}DN2CK{^uvs*n
z{we-j^>T;<^-@SMO*R1p9(4om#B))CF75qJS^3JW4l)_E9PC&pIpSUSyqtVdv>x6^
zZYOhn?FP|~e<$dHb_8>IU0`~qaY~Wn_A-kG8|0`GGQoI?@Olvtu;z;f`f^iw!JL))
z|L4sJE@K{Z<M@8di*B~=JbiIylfZLd-+jDDzU%K)BVs@2m`QG^T!MTTqRQM_LX7K<
z>&rZ-Cw7w}A3r54Nl3fK?Dr*kX+<+wSeu`XWc=vmSkZlUB%*SjI0`ybctF=A_l0LF
z4FYIU0hS!@KI5IiGr`A)z5s9u^o<5dx~E6$XMZq%WT&xR-`)Y^G%z&Y9O$^mWS#nj
z>=jX+56+IVcx2zB(1N}!3_u-zTRilxE1EB*4Pc8tV~sH-20!6c+8K!VS4Dh=VkOn9
z&;K&1b&}pzw&{|G&4q7I3X+YT)O$ETgsvTvCNr=W13a>~!#1^M|A(`MHCVOjZ#@2-
z=x7^nNkR96)f)Jg`&AgsuGlgQZ#y*pfgWmP49U*!f&to<{rTA#+U7?wFnKQZ&-R!|
zJ%1+G(YYpLpD3gQ=|{&86v0;%9oxsgZ;Nt{SLSU;tj3NaB~MmxXCv#Xa|!D)NZ!4o
zfCK4h8GR+$>*|aX#?s14g~PuSmyhc)^AIhvoTATFm5rOY_|q{bPxh!pCs649O5Jno
zSk&(Q@Jy)Y$I{cqS-v$p)0&*Jc*g6#hEB9MRs0f&EJTvb1mX@C9-w2~sp<1++T^aQ
zx2I3`bn}R!Vw?e$p6Lfr{~)4BgDm%E{v+8d@)(M-%kY1XJ%@F_|1`DsDdm0}VNNN-
zGFjr6<4(Zc5-T$9>z&OV($1ozadIvB=V_HPe=LN7640a)%k$v!z@Sm@vD$aZqpa>q
zWnT63lTOE}7OQ;jY(J_B84?Z;(2W_*OkxG5tpIHov+3>>17kg7cgt%`S?+OP-X2eC
z+PFcrVbsBsNN^(fBdVT+zc!Dc>Ic+>E}HD{;Ci*Jxx!!dU#>p%ps(+kL&;}P(yw4%
zAs0SK<dWOUC>yxJDGF_5-CHrZtFjk~>leZU2Sw-nmpNg&?1;^6RmP#JH)iQB?lAiq
zIP*`i*UHt-ALKDmASpIV)Og79nx$)2r+HRsA3(L5`bc^MHvBgVD+hWnNT}og{9394
z$b}Rv@+jAl4bM)SZ~3^lRA@^W61a-05rtXrf+h>D_etxt-~~t`O#=n!ar5NOEwyZS
z?=fbJ;_C*`9XGElGz%0p%g4oYJ!wkDzs8G9PK(;h#`#NUJ;zDaOno<OZSQfmmQyXY
zz*QiJ@31|@A7!d+!-ly3nMD+j#rZNPOE&3h5=#?$fs_}VPljAA{iArhrrr6^^sjYQ
z&Q?(g#H>)XA_^d$#gdTJE&4$(k8qXL-oTJYLgnii@@U_zXk;RL%<xVG61a#Jhxbef
z#Rpa4p}@BqqF1oi?xLx@H>(Y~jj0_kvYc?RSkX@Jxze-~@$V4(`KKgX+$SP>sWunY
zf6djBTxryNu?y5S9yZh;d)9C#C7RpkGEC)OGQER9Rppd~LrPFdvrP()u_n_hc#>|_
zQySbt0^Cx3YzU-dIr?0w!6Rat|As>=XuvKbtOs*NN9Wi2+zo8@cwe8=-gwoF%t))I
zI*bQdXdvSNO*RgOGdwZxqcwNmd`8f51I93%Vgk2y`Dn#d!P5Au0=nT<&%{NLUY&oG
z1qc4Dk~(q~U&i+3_Pz%1wMXW(azc?|<wU`Xg80W;L|nKoTQ`Ag?Ek<cyeXz4cXXyo
z8a81>SF-DV{43U-4~|p&??U79&5!M`8fA-T7GP~OJF~id+=(kSw(;HJXHuoCJ*}<3
zP?KfT@&#hMgn2~XqFzId#I&ow4|WtPW$|Fm0#X~xweehQ1Z~m7a62|GBC<Ub*NPX+
zjog~OC-!8O4Nnpsp;Z?(y!AdSO0TJPmo@d*;%v7uEYCitk7bbLrq&7hfNUcg0`4zT
zc^oV2L>7E4f**UMkp9g$GoH8&8buSC+Z`X#*GL!#KIFW;OXlRd>F3Fr;IW14V;Pn$
zwYsfbF-rvy)2#7z-jz?jG)&FqNu6eF{~{N&d1~b?b=m2?&NIEkx@05IE_EJXrDh$O
zB3A`<A`6)BP^o|ueM%n9<1_wdzv3pcCR>db4r#>t;}^4Sxao-&VdvFrwTuyKji#zq
znG&58x<9N<D={eevZ9<f-SF!lUVo{@mq!6ls$|Q;hA7|OMbi3az@f{-t+!WPv9VD~
zL*rCTQhAAl$FX&5fA=`dMf6?!Vj?62eGJ-EKJbn_`&8w5@e`kt@S#~%Z@>n^s#ZPN
z;L&9FKe;5X$i?Rr5(ScrSGpyyo5V(!ptS`3Gj<23NYCXUmwgSIH<x|Nty@TnI_mBR
zqBc@BLz>vNA;BOqlSTVwsH}mQ2^SxSmv5bl@hyqB`+v!s?wa&vHZ|3~-YHyTiu3$%
z-~=&*+hfb#3WsNg2%;LYiuXFDw|oC(E>xuoQ1<I_3-Fx>2W&!sNDBD(Kz(Km@qhOE
z)cc6S`&lgf!kCocU3m;as;VIx#ZI(7<+$+3tX$rZHDa`7Z|h#=x%=3w_Ytnk+54%2
zCu-X$0C@)6#oE)SExAo(+~ThpA_SBoIMR>h?s(WSd>~4c_KE&xV^z=o{IFDf5un#R
z$1$qdKnl+5t3H<g&Qi>PNGP)w1CyHeu5;cflL}%h9gs>AU}H*9ciO%@(0gXhjY4s%
zEn!%_o_p00jP%dP`%k$UF;xoZsfHpB7-r3+ruUi2j-rfl5U8CDe`+;yOYr8&K5Oxo
znPdktnt@YnYC3%<kpVH!Sl10p<6YD%;@WvPi*%QR%}EChRShK+P!uL%o?fKbcS^7!
z5wFeDCFJ6tOu*lklbP{th|RXiXq<3;Gp;Taql7HcSXYee9b2!eOR_ePd!IhNOGiV+
z!+r6cnJZSFvGwT8>V6M(frMiP4}S4uT`UP|Y{Vi_9=nZJlvxFTmF~uZm1u2BC4J0E
zg!9k926X=%xDbb}7^VE_V(GyiuF|}Ss(}1-aFHmIVnroOh37GogoOVQp&%03`-L!M
z<(`sagfc}Azo_%R-~eH~zN1|=@j=3MsM=!oTs7qrNhsMT?@fk4<crv2$-jK5{IR)O
z<&2Bs^pknYrT`C>OnBo!TSQP@li$@pm{YSDZ4jdRc_L=+@ZN{dsC2>YdsJmw1$~fu
zL&$XH*AJExg0v|sH#z9}Z+u*6rC3k*)TfCldukBCN2M%1UEj;BhMbvsG4q!-Mc0~3
zqyr<0Gtouksb<vnJhz)Fc>*Hr>(y)KH1<le<<mwK*!3(rpO#u@4Y`3`y~bDPm!N@4
zxW~#iw^~F<Ufhh-L7bF=E=`xJk^~OZiWe{dwi|(tcWIQKJ#SEyny**$2TDQ(s4M$N
z|4~mqTArS)L$O~LjVSW086)rY8$Pft>eVVYmmZ9rd(yA=Tyf_WxrQ3~`OZ`1nFwLN
z*HUJuW6>Jxy5vy@S$<A%JF1+|URR~(D2^}1GAzbaqHAQ#fG#JMSN<*2ObgEaXq2YO
zP`-TX++vpIBlp!kBttGfOYCQKNp|SxY!cXY_YBdIcSTG|_>i3g!yR)<2_yTe0|pAZ
zZjAI#?+L%>sc+S6<7@Htyxp>?e5)0kQixUf6${jNU1**e`Beo_N+`#%i1=%hhti4{
zWMc$JwaRu?s9MjcSx(o>Gst~TbLK(rQ)nTO+3Lqd6*%*g)m%buq==gm0AGhG%di?{
zxvlkE-osL^yu-DdI(8%D3#PZ|Uy#&Xx8i2C8js+#_$!9=g~cY|hu}!QyJ11{BM+Od
zJ#I~1siXm!q0jeQlY|Yq@LZR<3egIKL;JPoflLmA@(ST3i<(KPoHHKDH+5;I?-!MP
zTyA}i0&+Ymjt9g;P5^S&XPld0yiC8bjvmvsRn3YX6XQfOCi>KxUa#t$s-cZfoV%S`
z&5b^GjS}$n>&?xLYKCWAGNFsB$ZwQ0Eu=oJK2W8cE6?)PE#!4HW{8FN2G}OV)brC~
zyHmVUXpqaV*6#Uy%z&;&sV2aIp*Mh15yS*tWeoo#Lyvp1r#o4pDRBrH&WqS}6<a(4
zM#xu1wCIxlxO_`d)0K4?7^k|H6+*V9gGV)n8TS?X1a5l%N{m=aGy`?DSv;f1e@pX(
zy>bO|tTyJZ%fzt#f7x*oOhSt-?epa@LR@HlCv*|bYNmcETdg(lW>av-v;3H@{#f>A
zbxh^~owT4}_&o)2z2TKED(uOS?8RnhZ&e>C3YCP)+V4M_hMG@DCKBQdopt9UGqJ|F
z7u4$i*LRxSSpO~W6F)8fYZ&gA{v?#pgC;6g_nQ({bMQ+_dB*xy3Qb5!o@`0Rke!0k
z<oS{Z6h>}yrD57!3t+%1iSP8Z+D1~|!w((Qu26SX4oW_5s%A(|v#Xg;|0(^7Z*g-o
zJR>ozupy;uy4d@V1UxW*DN^{FZHXowt<aMIbP;$(dZ%y&Dh0f0L}r4~6j?FE5f;)2
z({e=uLJcbyik5A^+Cq%M2d4alZ^T?uvAKpT4BA-ddgVBuO3mW;`vRrbIbvJH@%*lQ
zfy($S?5C+pzgf0FBb|@|+uqHoR;UsB?BZQPm~Xp%gKkDYQuIuxSW|K;J;JM;ag3U@
zH^L7i&yVtMg7T61_kW#fnDQi(T12iTpl7NvlM?_35KA)dpiz?IdZuhTi4T>bXH`zN
zq+gjN75+v-for0`v^i~qr<Bf>XiOTsKv+DexoTL+K4NEnoS}c^K|ECR&jT68CzwD0
z8_HX?bHj+))T`tfsb06-pieNiVj(<3nGj6SXpWk?>#kbXqp2U0yVEkZYPonyXy%0S
zG?8N*{IRa>TS`XH_5sGB5$cclRFYgu_@S((TJEOWp#=q7bJF|>iZGKvfjsI+A~(*}
z+#u3KB>h?oA=B$OIS+Oz(*b&-3<Zr@vHQ|TDYcry?_oz}=qNqM^5xCt8Q6mJJHL|s
z&2`iBINi<2RxhfmRXq}$b0SDGYv{oDw#{I%*4%vS{lNQ}qjr^vv$40&96L`Vax<=#
zxyYZhpl9p$zW6n=q&$ZBww{n)ly-F>38y%6p_rX<f^6%qzQ%`by$G@4Z<EB$2*2l<
z)HLYz98Cg9=+LqXWb$^$Av9JlFeh)AT{r;xqT!J4;h%=F>#^*Z#XJ!*KjeI_gE!-L
z303=HAZ`)un?VhI>*H5zTflew!1D#+n{MuK+a2-q583CfkG$uTvb-1UL|C)eOv~*Y
zawzQFH@pue=*OC<K&gL!?lA_hgEJ>9vWg3%A+$EX#PoIp7p~Kmv39ZX+72pdO(P<v
ze0%s-=KSgIRXM%%@};##WS3^kuw7LnZtZRz4-vyyPm3U=fb`=<Kn_5SzRMVR&w>&O
ze%Z554^2-jFm&K+adn+)#TIq&abLP>XS59t*{i5pPg|S5hWo>f-FIce*<oE6<t>W;
zBg&2>V?7{)x%IP0aEzGUZ1Iy2|JLn_Jb0CkuzZ`~!-W-_=f2jOL*l_j!R)Fx4U)u2
zm@SDHQ|qE?e~_HfV`u(eaN<?PP9B!htg|h562v}zduHZII<??eC<55su7gWNaVhsl
z27W0dp_~W=k)bNEAHhnc!zgi2t3wp{KH5Y|F`wbLEK{6l^*L_Eq(RMmTaD#h=@_qe
zcWKhTd?*OC-%eR!+buq&c67DWxgz-u3T1{Wl3ORzEKc8-$-$a5G8o|_;>5~`O~m+<
zY&+#lH>|^ECY2z(di9ZwUm;}Gu9Yuz*A<lc(N|R!DG4XYv%LX%wk=WT2%6Mzs{*l!
zpuX>QCR6G@&U)0x>qSDGMb7jkN35~*q;zMV@BC`Fzt_@xcpGc;vI*vTQwWZI3ssU0
ze~>Ud9Q@2zP{y!pu7pt2UR=J^ZSN;B=pg%3%9?<@Br8biBDz*><gQ+cVIfg4R~1S_
zBMurxPzgs|Sas=%g;CyMTt2D)<>||r{=-CMm)%*Rb&#-=NR)-51ZTB0rc`R5<w*^i
zU!+yI&d@!VPCeT^Gw`G`()6zuKGU7|d~bt-jxHfRxckWWo^uDy?{|moJ!g`JfaJkF
zD;O_iF{Jx+hmg>jPB&8P7mr0|E<}_3o_@AP8ot5ur{(y8S9wHmiC#a#<2q-bV#`ml
z>zGM$|M+8UBKDK=cOxW4CIqsVS;1&@BeZX-#FsxbqtrE#$;KHVsgafx^drj&=ZSx2
zhU}^qVNW_H7bmD%&X_cgTC#s5;>|n!?({v5ktBKw>9bq1exY{cZ?`$@F~I+nhvf5N
z=;x^)A%r6T*mMo{ZTE3W1moehNPuJygx2XVT$>N_vDwN8fwuu9-MM@i+cw!jiYZ=q
z0?Zo=CyVmIuaE*a>8I&vvV-lDLM7x;f<NMY<f+f>U%swm%tUGQ)l2F_fGCB~$w&5H
z+2`=~dDy2wOPWWs=3qVDK0uT>ir;CJiFeSSTCEer)!;U}4-dd4`01iag#X6NH&H2=
zV{5It<I0cg<4oYT8(J+-69&&|bL$fk=I#n|Ls3EW^u%6l;Gz34M-r~p<)lrTKLw#0
zd~0ACbiz*Kq36I{YI=u#w)ovLZdvIZ$}yV6T0?wY=*<l{kV8rI`}rmRL`ChZf!)Y<
zdZ${VdNC`}H#tof#E1QfYd?0QFG5lw7NH}M{0=?y0PFH*nfWp@1TyN4xAVlfExTNV
zeK~)WbJd{3INW&1ZxYO+=89z!DOt7nk<Dppu$12t*)Iy)mf{6#rz_K39j7A*U-Hsn
zzyQoZ%LK(_+FT5?DX4D~3(N;CadJ|-QQn(D$=5OT$M<p!Y=wzC$=n=cLv8o$G07bv
zyH^#@Hz?q-visL<^B3*W#U$iEK$9s(?1}95;zwJ+40Z4FlSO+I9_^$P_aSmqfsTX7
zjTrnSubK(@_V^dC`#MSY4yq1*C~Xcdt;kD@y+&;V-%0!#B(I$QocL)z6ObWmG0<Va
zm4*DR`)zL9v;LyjXtPs-MU_=HRKf8)%u|0$02M^7ByuD=mKp`ly-?tbetw{K=R_Gh
z<M_ZUtd5MXa;ep@1h~icukT&TjQz`zh&L9`Rc=Yz`su=EO&dmQ#Y12HC5~jqlKzY;
zxysVKqg{~QZG3-S0k#A}MVUHnXY8|s<`|{--r9b@6ciIEcsZCl1|0bKIGkPyBgHns
zOt=LrrofD1CaSeb;+rQmP1?|_mq`mu-U6x2!}i~QZMK(MVC1_U?W}p**s50~5{0@=
zOyC_;p_&?^dKdG^3J*^peI-{Xt)L!UIo+63>ccny-YRB1>Dajr*aJqbD?Injks`^Y
z4|B<uY!rU^iq!v3Kh7D>l)l2IB^ti(PM~QlSifO}<cqA(Z`={7F$8SS&poB<Sg_Be
zkH`L$A=(5B3R<U#umo{hnRN3SQ?ld4gNVVNN-fI#{Bg?&Ur6@$iW>Zca72gPCp89X
z&5#KP4b5Wd^LxbAY|)`#;$~|pCbNZHY-LK;Yj=$KXrjrc^nYzmGLBN~Brr<Q^31_c
zkA!}AcamFnnQYZA(#&74{VRkijsgx^hOcBnxU6p0#TaLvnV2lHU8V}oc=fGel5&?E
zi>mEc1RmT3tJ|8l2=6FGgg%fX0>lFuA{s7(u(~wtO8i&N5DJp$NfwL}1aL?Xv3*>G
zJQ?h}|DNJBWeYiMQq7QFp{<<KG;F9D6*BN|oHQunT|BKtlR$zf*?1<^As9C(r{#*u
zlGg+rLF_%N?&Q%iC(L|bk2AwXthkrWUVEfoV%09Ix&I<kVD9XAJ(N>&f%YQOF?G@w
zQ9+A-&6T9Fnx(gV2ghYudfG02+ZCZ+h$u8lS+!J-aq5H)chQlXz<rlCkG(8s+|P55
zG@%eNjDBPrY(ZA98^Io{Mhl=q<92rkJ|#6gJRw0Nv`J$^K_5)6GmSJEI=J?bp2QMQ
z_<h&l*KnrpAOn%9%`>!1^{{z!x+bPZ_enGL5(X^jA;F!OoYq_+bbZ-|AjxQXX<`+_
z*ZdR4d-W3H%SWVdAg+h{zR!uT);C+fNi}Z-|5N7fLW3*#(W6*xeAzVM`ZDJ6MDtb#
z2{rWKTFcb)6NQ?=^C{`UG*#Q}*i*O-y-?0Vc6|A1jtb-IB$~ld|9@j1>wB*)ow*Y~
z6k%L49gc9hR&^-k2#nPB*B!7D;DeUg1*+QJjq2AD&9%<iH1NT`pbn76*Prw)#EDdx
zGGA2ekn~Q#R)kC(9PcHl{7G9{=F3a)+~X7>;Y2$DEAmtuxZw6mlPW!v%9e-^DXJA8
zxA^YLSi7soCDW8WEQ$sTSb><7tjq-h;k0-FSIk02!Rq(hhzU(RmW?c2Bu<D(PHqXu
zT7iW#e)x3u!%w3^`E>!?0FPps*6BH<ZYC|`bIpFee-DM?pKT%36ktuFe}N}|Cm<i0
z>$d;yO$P~C=Z<6AG&y$~K2@Gcozj%Jub2*}*DO<u%uUF87lG84O|!-$9j1IX2ZkY8
zqSu<^Y6RFafeOXF_rg$B+j)H<@qN;%CKtEWPkDz{fy@1X0ITd$X#Ml`DZOYc&+zO}
zN!`Klv;-?*TAul&!_kO+UTs{rqI$4@9t)cIX9DR7b0N-nu=>6fC9(pCxb5_sQe&ol
zfFTxs!s1hJG=|LY`+c_TDCxH%NsNp9FYCy;EJ<2Xy?a%wQri|@$rXA9d%TkB8L?vV
zP6ha(y27uHp~@*ar>{W>)7;2w2s_OmZBxvGPo<cnV8L+*PqHNCO_>q^aJ(Ziab{4%
z)Lh-1zYs?f&)={8)AE(?|FQIy0a12c*NQ0JB@F}84FZzVT}n$xhjceL&47S(ceiwd
zl%$Sy44ncZ&Cq<u=ly>8L(v&Vu5<R@Yp;lO)MVOeBqU`YF))J;?ywwa$FKi-5?*BH
z%m1oFas)jfk4HbMzs^7Da9{NKV1m|;tbb0F;oxP~58N-|Q%mOr$gM`X#pXKP^jI=U
zA=Hi<rE;((t>5~fQ)`K;%9OE#eZREV&jGC0jVtV&qfIYtoeF`-VOq(AAQqP4;Lw%J
z0%fK;!%qvU<!CNGQB^6XP06J@)878~a`ZETT|U@=3S}5wJj>F3M27}pB#0;%x`=%)
z^E4<8U&2Nw*{D**%!l~i2U`L6X;ASjI#x^Ak(6Q#@5gg43No6)S4V9QurqFQ?Jvhm
zPk|F(#B>C@$~*@$vYV95^7ej@_EdqEfbitp{tWSjZS-~d3?=oP>bf_T1B!hMj?$`A
zh8N5DL!uO_>6(e9_<!HFZi58i8|OmNQxab#M2KjoQrE7gHq+Gf1+_u==@%k21$?|>
z97dYU(PwRD!h99gvHG5(b7o-QHJI)$cC`+W)8)&}Td|r=(MJCuxI^||O?5uWMLG<#
zYo-EvFk*wlOWpEfIOfbYoj=($o7Yj<<vJuiwj$m_i-BV1&57Nba~ZI4&>m5W8kmoN
zT9cE$p6u8yM^D^`$Tza#@pg!93fnMDb*DfCA<IbMI-E?fW?)5GCSnW{&3<sVtdNPa
zq(kMmnYC#PYPI%ufE&H~S{olmlP8mEZknO$$fT%<0ZO2WV8WJseMDM?qf)|I2qYSx
zTWdqNB95*bRzCiOHHHO1?Wu~aRj)sd&y4;H9sTsaL78H;|FSc$K#dS>44oDvoW48{
zg$!tA`=4Nj#0!S33qH#i+~*I|kS2`zS~W=>t5K)y^O;;(2SZsWdZ}!ud||d^_~2Ts
zf+=5#$3&)(laQ{Q6ck7ons|#qHYr7cFGo&yiT2#*^7U39zWeiXp2wa_9{p~vMHm%b
zaM_5Cmyds|v4a6y)aH*Y7?1>d7Z%>PWA1|Se>d$+pnJA>T1ksGYbq><pFYv8F|mEZ
zluN)2H4{mu+<Ggb#6j4ICBAPJgcT%QRrW{CJiVMquTu)I0aRo~bI);tCNOA^u6Vf|
zOm2(e;z3#P#4>$THlZPYffwv48I{U&yLtlART?xk(t8sPBDnzxR_{x>M57T(Bu;)-
z4TD#z=8g2uucBC3Ky&EL`zU77p*T}M<&?oxpsXBwY<~JOB;QCZ+dFD(=728?z)F8>
zDIrM4zpn|^7~)QrXXf-AsvG7FOiH@{JG!+_P<$8T%EkXvDZNwx?pgZDmF=}o+XwN9
znSH*%?z?9!9<Sv)9OPhE-JVKe8-t^->G=bao+BgEOKj=hJ%N>|t~f6rrE<Cy3k~|2
zk**^6=MHZ;RN;>Umy|z~IB01at#Cr94JB}|M!I3#g!^*%ul{C*b#_Ifehz(cB}@<)
zgNWKquYfss@k{-vab4*QW~cy!buX_psR?In*&+D~v>GkP<NFx_;g#6`zFB*H$=!cM
zIwIlZ(#kcf=cg<Z?;sAZnkd~B#D~My=aC}{HiN#l4{{%i#OXIJ)J2%8=a-!f-#&Xf
zK+~i<<2ff#V`TG=T|jJ>%1VGhlc~L9<GoGj>wpIxv7zxMi=SQI*+>3oa)A5#x3b_=
zRa40w6gMT_1HZ?(6{#5_S?o(-B(wRe+yq<vjiLypg!X0l+$-b)>o>-?^V${uNiiQ&
zRHt^1!tL9pg)Y?zQDyiV4Z9<juoUpQAurxNY%V-lH&OiTa?cjO{vpun;gO<fb8t^6
z9VAsMdo{@^(qCuAC~sK^e>f}LV==zDY3MxO9Ad80Dof6&`bl!NY<!EY*6kKKl`HBu
zXW{$eJ)9>zt%5)!*h2}1aPq^ML%^v<sDj)#BDe#)kEA|0&3irI;eC<DQ^5TqgQkZo
zP`Po5{%-?NQ2$+?ex%fQ$O(SiQ5R=)+wvW8ucBd9Sg%GHnrB;Qn9dBId8WUSj#+Gx
z^nBTzn16;&L@8i{m%$1+j++LJL#@u(<`S3*jWWz-6hy^xM%$OpgBP8`FV?IJq<==9
zzRT^!5Tydmt;lh7&)(vqpfQqUN1vv2;?@WKNoo|y1WDPrV`bRzvz8mrz0=l7BEk+4
z4<IL<z7$D%o*pv64f?Cb6wud+tkM;Pj+809h%w^PPe?HAy*;kmtdS261q;eOpvNuV
zYc3OV-&cJ`O|AC@I!qfb=?}0^v{#BfEB$p>5-vU&krc99vk~Pn5nszFWbw?wGc{t(
z?9+&e)dJo1wJuOpj!95A#U$&J-r~wAa^~WXWgGn*dZSQr0{@;li%;=6wrS2amou<i
ztv2mdkES%QCZU!DhX1_7Y^9|&Gy76|NY(SFG#UAjrKZ;tL$(WEIdKJ}=E-?jS35&N
zC&RexFnYG<L&t^S9Yhj^WF(>7ck!_2$S(Tf;84q#JG=P!oUJ>VjYpMznMn8?7V+y<
zOc@0bLpK@_XleeEPR`0P;S+hA8!tuj+9!qroHrgk(vsC-dp(W4O}c0vJ@ye@FI<&(
zXbM7LhvLg0UPO?B^}Vkjyd8bgyruP+_HKWj;S#p-hJ~Kw3f)sWB&2$L&D2AN=0npD
z9Jz!t6OKL8fBAxOJGo>DXnj!LH>&Cq&a#-_&ZcJ@fC?~KC9b=ivU}}i^h<WJ>^XZ<
z0h1}evfUKeJA*u|VJv#+tA6Q?7f}%LceUzs7hjc8dY(A~L$Kba%dZE=PIjdYquR7(
z0R)IqQ5Cz@DXKcTLl01|nzvmJ?<f*Uh|_ZQi!}sJme_M*%;WR@ML$#iwc7f~xn9;y
z_pjx|jU|<s*U>H1uz@Hb0qm@u@#mWK-<mOpR7abS82xnB^h;R$ImNHgG;NOl9+Y4`
zMOvpst=+2^UE0ION9{nWzw*j$iP^15Irys1>R6(=s{9>wiaZKGMJq|vZhf+NO!e2l
zN3WR)q@|B_rg`7w1nzF41Q+xqXT79BMY@-b4WJvUy9#1|5X2q%-Y?a{7RbntB+^WF
z^y5x*b@%A{dTN9~BwJ+S<i_E99pz{xQB9|)f+d%V2mu|~y(a{p1d82@xEJ?^vFb#A
z;!YSrUg$j+WsNwEmZ5;tro<Llqu0Ate!1Kf<vanumff#OCe=<QZ$^GR2D%;;h7Obu
zn5e$OUcJ12kw61{ZHG2cn#DZrv883NdnoRbJ8I4fTe~s3<2Y<7;;6U0?$%P^zl#j}
z5g~jFs*BHP<=M6QywwPqAYT{i+cW1&LM#?@ao=!%B#~--I(+_09`QY0kmuW|WRUpX
zg-&{V<5&BK|8jO4L{hE1IbaI{wPvBO6VjP-Z${B#v#7S$%JEF0zbu1q3%|LF>Z=^&
zvtCj$Hg5`@E#*zt5#SlTeLG`rZsFJ&i5C1{ftWt6FXQq3w@O6Z<0ejeTm8V~xR2ae
zc}CxEk4HubV+45Tubb?V6(xCPJay(TB?uLY3btOn$2^2Tq)c-F1du|E`q9P^hp9QE
zvzy018n*KS1z#_=*jGcQ&OT_mc#JWkCU1Vbu9!EzWVxp9*+I8^5T&jaW2XN%_nYoG
zdc{Z=_4qcPF4=(mw-o|)%;?aBNc!iwBq>T;B+&y?8icRi=G=c88s+KP^90x?$@93t
zR~=rj`1-Hxb^k4y8})D)8ya%$iuK=@){suR{5e*`1nqb@J#06UlOQ#u%5hS*dOLF5
z)N>6PbA6s-b=LW~s0AP~Hq}~txJOlrib-`J7@#&MeW&OfG-Aa&;vV8L<y7MeY<VU*
zbn3i~;O~zK=$RZ)x>vhP-T4wpmZUBf1><Ot?O}0?9iKYpy@+qtBIa5>9CBEx$KNq~
z%>L{;nx~<=^%cBNmnw3pGZbbZheJ#I?v`o;a#rHchj#qj_9nMadQobU=UTP(3hkP{
zcES(UV(EPa<M$6%3fui4d+1SyVwZoWS@Vu=(^OcG<28`he<1ubnuw!H@~nA&*z$Vi
zL##E3EI>B8vmHtUUXdh5!GD%zk*5)y?`t++m=JWwJsHjjo;JEv-E2MJNr)_xZ`|Lp
zObe+R9<HE3ritvGA3Gp280so6R<mZj0XmgxU0_yVM~bR3qEo(AS@hx^Fs?lEv8HuD
zlbNtxkif_~qKkq6^s|x&m!bvh{0lJ~9dy1V=2M4!ROk`PjAZc3Msr0VPZ1K-UOQk=
zgjCctesFxQf3ah!6<<-AnU4by)6B~f&M#HNOqA$E!u$jWD19=e?A5`oo|3FUNE>QM
z9d~pcG(0uq?Li2VI{x9Yf^ICz09oy=qX0p<>e54Y`f2RsLoQq&E~T0*I%*=|U%|a(
z=FG6#y^A(IiUnv78|7TGx>CGJh8-*XVReQJi$f@@h!9`>2sw_{+N0w<A!%HG{YUBx
z`DT>46YJ>@ORbH=VV)(r#w_-GXe?2^hyW+ZQ15%X^Ek_2G0TpI(~>N5Ib^H6GnIzz
zZrA4Pw_+GgJW3bn><DdYo4UjMdFm+cm$5C`TOHu56X1?=^L}eLwLXsE_$ck}BU?}J
z>I^`K)%$8{m*YLOOYt{9Jp&G2D^|Xu7&CDS6i@FZBq;q3B7ufJ1fEg_qpo|Um3F%&
zxCKU;t5NvrX6x<x_S}=jZqq12ZdGF@glGHbPu7KTb~wh&QKrt14mM|20~2Q!UQ@s=
z{>*ck4TbMz{+5{_N)UD4FBXc~mzykl{zWrgnnShH;T`KL?c^V9J{FagyFyQa!J*xN
zeddHV!3np}hFSyjzoU?9pJ-hM#Utz3iNgNYnlZ$~)Th>(2&O0z#QRbO#47~^W82*&
z{g{CE-s)WR0vB_&HtHbe`BzmBn!zSSY1-XKGKv2*9TO6B-$+78<OpTD@2QRRL4b>4
z+<WjxmNY65lHEn$_XfU>QQFG`k^7i`kE~V+%(lXLaa<Kd_z=bYf9j|R*6}o%d>*o6
zzIFUzJ8=uu<r!Zah?}ZP2T>=2XW!}HrxIUJ;Bc7nSKFg;ofzOW*qnSH+r64#O}(CV
z>=`WWaS8rMW;x%*F0}0+SX*xyd@wu`czn5bi=e$aD)-HBQrfuM{0Z(-$H%|IooDw-
z%Eo&8W%a^2QBHRYXaRqAb9a8fH|x0czhwf-ny^b*UA0sWLox5x?xD)D_gS25tCxD3
zGrw^L0e;Ozq2jSUz>zEe4`$}Ti9GV2R=oJOwbXcWm&aby`p(o}OihG93YR7Y8vj=*
z;SZDm8sW?qq1`3ZWngvw8+R{=u+EL}hk9?s#URr51v*F(As@w62p_?+fHL%F5`A&F
zwJ@9@G}kI<HR#^t=|19hb*2JgV3p|LL9xyMp6tn>fGBma<?gs(Jl;uV(&%hDwJW?~
zLe)UE+(!}@e{Ef?O+V?cpeZFYLzGgYU6x8t5viumI$KWk>5sUmDjz9r3bela3piNk
zF$fw~iNTGHEpWXgx&<a!R?B#IMcJ0km#B12=V>{bNMlXjD}W2LaMFBZ3pG86Z^A9<
z)F;`eJm`o3`KL8{^qfxF)~BqialHLxhT<9Y+Z+nIlvwbg3+2u!yG@&S3WsitylPf8
zeD;UZ^A0;2Du_T<jV792JT*KIWO_csnUWLn(;$3H_+=|^e-4pI5nvjs?3ks=p=i_f
z{l*1469xgZx=(T2h2l|=S%+6m#IBFQ^~V%IwxB^h$1WvZnImW{`MdUp2pP#Y2)idU
zqlRX5BL_{T-B?nCQZJtB!54xYBuu$Hb(c39Q0erA0}-+7J+4~gvN;J!UCAu@s=uJG
zOh}U*&D~fVQ7Yz}w$giE1BKRX*7F#@#j%ly;_Ky&n5jQnES@M<O63rinW`(-Ww-qF
zDusLoE~ZxT0^mRcgk1;O^V<YUh}1TvRFnb03n&&UpkLDkOp=4vB<(Rawb}wQ79U;4
z1p<H*=DY>!zd5=d^>23i^C|sTBi!NGmjp0bARbsf)9dV(Y*MF-k8#}!lfwLSu)LIW
zbgPN+dR+F)S2ER5G#M;nhSc)p{T6m!|A1I<ilq}|Hujj(d->*I%C09rDn(8P2|~?0
zFQxuiua05uA6CfF6%eRIUxD728IzidUO0&%KIRPmc#gvb5h5s+El(xq`^27ebMija
zjMi^;cl+_!-*!+4cE4p)P>!0Bf13NSyIT5{aDB@vZnC1KjJU$9Ci>{P2~W)?eryD;
znwlLILJIbW5xj0nERU~qP}>-Wb+{rEF(fDEq%als-;;=3aruVDBK<1odc&qx65P<+
z%1CEB0o)Yv-lNq5dgPp3qz_amGV!QGm|!cmN7XAC7aA9P&yo68&^E8)G`4AasaosW
zXs)PWw8(|~UE51wWOWxuX|euYD0L-wXIY1%K_s(OPvE4>W9;~uQEkpH09CUBt)f`1
zESYO`yf>y$ev>K|9PC>P-KuIPK}|o_{u-%x&MjXw<Mv#%%Klc@BScy#xP%#poylQo
zN~psC&Wy-CR!BHBFVuS6=n!Z<U*WS_N&92{25{S6jyYeAXow+r)jT-R9iPQ+I^Xw+
zq^}^4C=-T$Jgw5UHI=>q%@2533{5sQiY+tQ1Xz@{PTBZbTJ8;JBaiJI($a3c9#%Z}
z>M7j<(?Rk07|cR>_m&Bh#oEANXpqN#JRC|jJJC<A-3={xThI72-|8}P{8d`F;84sN
zFNK#&)*tn7P%0{IHkzI{#EFUAcEdKd@CTE5p7;}Voqx9EKByMv*c9TZ4p(3!l6b9Y
zu4Va1V5Xc!@rnXRwDsk7|L8f{*i_{c^B3=!GVmMOFpw(p^Q_SmAnVJ7StbLR1$)2Q
zIV)oK*5*~!70N~<6JB1GH5s!#3zRBew*O5BLgDEPY|-}~=o!U*lY;L3vjXpVDoVHl
z{6g<cpElUw!v@r`h-4Dq+!rSvUSRw-iSc3xXF8-bQNW#FdQ^3?BZ0d#KlB@ZW0Wsj
zIsA`MFGZcOoIo@_C!es?NbuYH!;e8-p?m4m*&t6DOi@uzyS91KLXu1sbR)t77=JhF
z7xfEwrWGm`+!PquB7{HaK4CB77L2D`Cf}XLxV4$q2OP+z$F9+BL@BThOH(-r8u~qt
zO%mu9(q|jC$ExIa*y95T<V&$=g9S_l71>(N6&2&Wx#E3S>rZ3FUN_TiF4*u%(I!WW
zx@iG&I-uclZLjc9X0iMEcw(&L;8#%Znjc-4zqYL5I5`zqG4<~LHNgW_4plY|&b>{B
z@$kjNF>T=NRVjm>0SNn8G0~s-jB-zzs#2~69<Ok&r`57HifhH{DmVAQjKi3Tm?QD_
zen5Y9Hmi#9H1g96K*i17r=+VPi?jR>aFU+>|1v}KAJy!MNZg$%uz3yn7~jlQ6!Ch0
z`$dx}`&B39O@8Aujq@+EP3nbupWcxl(B{N6bp<!(#k4FIHR{VI6u-@TzfGenjg8Fz
zM1dF&J|-CJ3+Jghz*h}*GQ?>xF>MxoCZ+KVcJVcXc-t@8r%e?oX;lD`#;~`}a6DY$
zm2shV#Z(oajb;W@MzCd>e3aXiV3CTHKkN*Ym*J?-7K=;*TKn?#t)%r|gYaHE*+p#F
z0^46{5bR^POlT@_NgljUtrrhB4Smv0{im|#ojyAqD^FWKW&xY2G#1;GtZiCayCgl4
z1kS->MS5P7kJ_~v8d4O5);(?MPdn95qw<}TXH$WWsY7(E?|vaIJ*_CgRSP3sOfB@Z
zcGN6(P;aUPWEgx~B*SSg`mRmF+Y}OHZqj$h{tL06gm48v0qQ{9YF!=^DpCUd$I#b+
z8^}V^-%J5H;fnW)bW$F2HW<AoE52Zf(Z>Mpt^9|#WVuID)l25-BA^g(HHG8N{w9?_
zloxJgLSv#_0WMWE8K{Zm$~?|)A8%34Ue@95&)5k2{5tIv_-oU>yD9kBjG3vu2KZ!}
z+E`{+TJ7p){BTVF&4wBjrdT6Bauxqn_7aisH>O1#-nFU#yU;Uc)A%`eVo*ytz5_Hp
z>1Nk(I93N387vr`L{j}Kd)=zPB~Oy=$R%XIqD3{`!;(=rpfz_sB4l#gtB1QiALKBk
z!c|ClDaQBh0;k0LKJ(}oZ-R`5g}F?LV`oH&+R<jq;~w>786WTfb@!2Tp?Bft31ObK
zJTve;dXa1jOoRDj4xVd#+?ZzKCE4-1K&)=vq}!O5qxMHc{3eHSgQ9H4Nwvr}wCMF~
z^>O-&GF8FcOyq2v@#?2zmm(PAEb}CNXk<#n!wPnpYm&TgVJn5L27RugFD?<2J+*Q1
zbRmQ~qg9++;47=8o!TV;ybxIF|Mp;XDf;GT(3HfnvM&wlfAlB?`@XAU(VsfJx?w?6
z1mJ@56pfY35g*?FBeZ&Rar8pWGh?*-ec}0M^QV#YbVWV{NwX|qC8sMidV0>1VpHd4
z7Iw|5G;WYlYE(g>B75wgd$LIvnJ}DtSK0G6Ng7y=K0~<y-#fj_Np>e2)k_Tk0}46r
zEy`D{V2HxV#R}kf1J2?vO=8qFOA~Xf;4Wn;<Q+yb3uv!8#%K1m7$BSU(*q@f^Ju&m
zdUmTjPUkcU$HzF0rnkmaVsn-6&&mDG8&Pmr6NsQeb(r^sHaQPVCfzq<xh1XI+Z%BX
zPCFN$K<jC`Ke_QNJ5|3;p=)yM!>U(w`B?Pb<m%&OtjIKLg)%+fKHKw^vvQqG9Ic>h
zX9;ckK8>zI76CvDrS28oasV*aOe5m+H*awe3uv{Pv5_nukPDXS>9O4(>REWXGS(Z6
zeG@qE{!E1y-q4+8xOe3VHR=gae}Mn@Z+2e+)Xg4V_wc#Y(l%X#?nAWqspbJbTTG0T
z{!E74bz_WK|7Lfyxc}b1gP!R`1d@^9DBuFjO$AnsB9kQTB4uMP14)6t;LJ*hT&Ulp
z{9z*PmU9nftkdV$m#53XER1+9sqyT`FRp?Y%|tI_5SUib63COXc0~vJF{_>jqzWqJ
zD0&xX2$U<>$=5pK=+@KF(#%)Q??EuemO!)!FN!qOl=gFEEFQPlC1XyJ7EVQ0I1U!B
z%8Sj&0jbD>Z@k9d5Y&%#6yey|xGK+Q6oZ+THnw+e#Woq`ev^)T<Yxy(6yeYFZ0|?K
z@V#0r@7JCq;t944Ou7*W%>SYsd<-{Z9_x`8F8!pE+#%Y_(%STVbn`kIgz^^*@mn;|
zMILrODXeCa2|Veb-N2i@A7*4~aufYz>uJ5eCuld)nPgEU*b->sXW#vU|DP5{L{cym
zE*sMLt4nj2{Ygmv=`dDZqR`-Qn7+24-M@H2Y)4mwhyIDuo9V^jBk>BAO4#Lzo-KQw
z!*)86l|ni5JH>=Z{QPykG>7rEYa=J|_ldwO6~d%EQ)(@Ug-ipHiyQ{j6eJDYI?>F*
zS$vBQOfl(XCO!6O$mo2|kC+=iF)<`ah^%<H`A7K|6=e=l8Dc@6l?NSs%M6K42Uk~-
z!ScB)a`HTp!|@&3-1c{_61c&>$t(nFVGDtFU%;$&V#Scw-Z{K48Q(TSq)ify(5m}=
z%jM}$gdB8Tt_Aw7I`atjMM_A^y@0UIYlKZ8$#|EE+%Xey@TRMBH{ZlXj!jRizOB?=
zW)_(%T;Os>$YXdg{tLw@9zQh*Itn}!Eva>5n2snE0&<*x&^d+3>(6-aj#z2zgyYTQ
zp@kvSl_~+ZfxhWrP2DwFlvR83@JZ*$+y67={_eRI&e4W7xC~DPfrKe`_xaJwL!`(L
zeGKr&Wj8h!?Px$5vb2>kGR!dTHtIe+;mO}Wf2jc$tE92?m)b4wQ#s=P``-f{^Xp+<
zzDy&)XDu4u?x2CMaPdmve1KGx|1%R>OQ*=QteYin5tw7kU(`csi^$?aiRU>^zAqyH
zVtf<AA~|;fj07lAoe(6K)hTao`g-3II*CYYTpd5>#ONwq5UvrxrHb*@CJAt(=#LPy
zJ2~t8NFi_ppRZeor=Sf<Wy0Iq-np8kkH6i|G5h!8s4=)~o((~Fdz?An&P0GF_!XMR
z@muN;lpCQ%PQ4_6KEJcgVoa11*53hf<#?i1kjm^IZW$_>+QL~wh<mxqw+(p2)3$%R
z^U5MLKYyK#2ip~|#*En<mG}$)+)ll3CzKScCc`hKG106OWPg-9R|^45Ju-OM+KW(%
z2UXz(#t)fM4^k<fVQU)$b}8l9^-VxzV&fyxv*n<DqQ^c*jDeNm5IwT!E+U?0&P|_P
zlwpSvh2CDa?4t6fTWY!7wax`i0{6>vQp0Hptk7{);4~nC&f*+_K=5?-kboHE)>&AS
z>se&MTfpCMbEklJeUcxS(@W=E^A>Y`U)hTcYsQFj>6okuL6=!w#azBAq8q{Y8488~
zicyM<V-7;jSq(nleBj+kHfu(J4}fWaezxmweBYK?dHDOh3R~J<;y*8;zHhqWB!Q>&
z>t!eMA!_t8rgy)e=)lHL4_Ey&<=F^zDKs+-?mvcar(bk%-1h0Hdi*Pv?Mvaiw|vVn
zBdAXma2IJmk@s+mb>qlXj=byYt5gzb)i&DfYI@!&EMi#Fh}$1ek3yigVY^HD%COzf
z;2%!cE<z7T^dp{uCwRyXm3Da2Ps>B_y*2DmdX`WS`j(9S6k?;{UQRt@OSLGA+Cwgt
zXAL@E%;U}Z!zWClb!@t1O{$}MP(-@HanZK5L(l4v;URyuOn}pE{y{zpxY;jC;*Bkl
z6R87oAo2^TXVP1!Z`j8!76~19R(IaIiGz%kcke%k%Ylq=LJe75X=!Ai3kvQxqZsKV
zfRv+`q>dccnY_Ea;d_4Ik69WKIjTXN5q;-$?+$SZ{YtUpc8Z3{9139pjJ6keZ^o_a
zIhURNN~|WFG8;t_p~r$KkXw1%k&YL`Zc+5nn5yT$c$0R@VN{m;8xYs`tam4lovOv^
zARx!RF-O0xcdX~0*!XIp^d$vMbUF=uZt=nj`}^UoHnHn%o|$)MABK(v3-%;hqbGx4
z<-0yroT=r+<h?rAc&qi4W5D24oIkmw$t48Di1r|Q0^>$p&ve<Xlq8IJH4B_WjIU;3
zuE$$kCz|H2lV=+Fdo1FY7gpX6N<++dr=Y$6-|FrD@!nVDWJ5wVaOZEZ3GCOUC-(o)
z)>7NdPLaT5&)J=;kN!bvAWH_nf@$+v&XESshqM~0sirbGamwxr14C3W$ZxnC7&Z}u
z3rOf{P+zD4cB^mjzbS4^s$Pp|Fk9@X@pMCig|FFGbcy}1l`jr&Gs>F>Upx&$=)ifb
zG{%!5=Q<Vg2Ak*WC~;*Kzz~aVs<(OB5W$EkhXpyo&CW7~+hHK5gzWmXX!iak;;%q4
zQ^ftH>3IMy>58%f1u_$6Y0c}eWWNyp<`NQklzlF!dRJT;a~FpDs+0;}Km{mpAyoKM
z_U82ya|sAr1eyYn?E@o@FUuVm;`KE7N<yOgfY?~p=I%E4jl>^wuXhRy__59qYO2r@
zPSmlZ{7@IX=o161J8t1N#fI5M9*X{E%9Necq|+uEOvQL%>}Lz;S{RFs!e~zbi_5lL
zqQUY-Il}i?2+mHZ^|w`v0tpXhyE;W^xF?ur+fk>?D4*4g2w)nMmH9L37a#r4BtPag
zAoH^iO6$cBpMPKQwEME|FKT{EAVKs<*R3t1K|_X<-*kj>p-7;Yf-2+oPp*czSaM&G
zw?n+w4ng-n7R7;KNNzZYg_38}1~b|DK*jdWI_GTo+4R|?!`hHeq$7LRzx8`EV#9x|
zCU&_Qv5ocGEhwwhAj7n4BG{mzePk$cm?AuZQ$s{B1PE`djA5CYK{An%Auei0<o8^+
zZF&nnWapYarz!bOp=`cDGRB1qZDFPC*ey^>{lAHw!}p0Eu>xWMEll`R?y&*Rm>bjf
zC)9$sTX<+uz&N6Knt0#idRuszfDvxoH8^(W0Gz%pdDRLR0cSS}I}E-oO>9mmv4E-L
z>`yY*0PaSq=_3uO@9l$cciiCuAW*SX*ss!1<KPUrI{A~xXoAfz-cuOjxOFU~kp?$G
z(z@U~M*426cJ|itMw}q-f|{%nFFx5q$~_5kP);vlTM+$i9L~w%s&B;6U8-lBvp3o&
z3`fx+^vRq#;%LBN!%zR+{Jb#~B6MF!s_B1Vs|>pU`X+UQ+BIF(FWC2yp>=XGmSyHX
zo0KiT+8usb8jQ}#@0e1Cwf#YEQVh{AZnHu%{TsIHv!yfYcidlj_p|4Y>cZA_3`!|M
z7&(9yD=yqS7kGgIP#Ddw2Ewyt$q92p6^0aaIz`BdTT)IwU;ph92a_0!2&~_3VZKC)
z-oehOC1=->!C|a|;_BXGA>pD49mDl`z}cMf_Bk)XT};o#LiY07ceAmTw!3oej4HO|
ztKG+QHD==d#ti=TuixjTV*^hguVn`0td))hH=ouVy|4S*lPOCqEnBD%a4~!aNL<5v
z*?L`|KTyc?mD`^Lz>DaAMe;#;FJ}avu{DFA46sK5!muJr(}sUOFte$naYYG?$<gub
z^j`>>kFmRkxG_Y&2RDz-3__k2E{I+rJ>^<8_*mXFV16%DbHqbTWkxR|Ic4Kg=MrC_
zMPDJUP_AIA__;BIp=RLZ*qikc+lF01Q6*kuDs-DGq5wrt0E4YLWkMQj&XW`;jzGs0
zHL~-A7mgmL^mt<m1B)E<f`uhnLsdp4n}Cj!Uql+dRH_>V%%ojRYGriu+6Z^P{>RYA
zDJAX1H<#nc@vXgqcaH(lO~voz4okQFVnB=5r}3;UL~}<KFc^FyCNrPXeR%cglOtC>
z36u}nE9-7U{4b~l&c7(O3&d8iQm#&sH4!T{c=vHXtA6&>v*W}+w@)$5rMvk6-favl
zEM4-y2VM(^uYKQsMb<P6%)Sdo!O~d#Ou*Q5WB3VF8Cfs+GARwUMLT-%oyo&wtzXK+
z#CQ&A=@H7x{NM!{C$RSkEflKLOnWvI0T4WhMz%nYZ#-Z(g0pXai;o$*3*;Pe(}kzb
zl7xelwF94k{1nl$V(!J(uaqn9H?-C-CqZ99H)ity(to(MQ<TP4YhBmJmkOz78S$mw
zMOKiBi@Jn{Kq(>;-xNf3Gu9*mzAXB(aT6%xZVS&qe<4^>7!mxD7@$hZWX=?+cZzS0
z@%*IuY}r}D7U@o0FlF4q6`WDCCiFLjNG50Z{pcK1jZR4FlxP8yVsI#fE#Hz57OeM@
zl1D$Bsw*NXqd-2s1YTgC`c(u&M*Y{o+oC9D4ZBs#Wqmo~SAfYD5y4P#zTcH(tD`G$
z#uO}R0G+Bt;Om&`<_yN%#CUv*>T|M=jHLK}%9i1f*go~mMn`@&TL|gnEw)x^)UNOE
zf*?qMu1Z@rpj5Caonw_k2e5#ArOBm`PNGhOm$^#2<+ZYuhDE^$m#n;$mIYYm<^=ZO
zan&~)Ff5Zl4xmTXL-3%aWf{Rmk%F_cM1lWPXN?aBtr)&sKfDstRFVkWFtVUStpvWI
zBB{IM<cWYZ@Iglt9T!RtekNId0pe{z17^<lw&A1sjIv({_j0IO3+O#WpkF5{{&*Yx
zN?5`kP9$QsHd(=ZVaqt}+sjSDFUsIQUZV2GcysB)+{h&(>B})Lt_+z38G4P6H>da{
zfqXvz$n`&I8a~_uZ{VXpc{4dVyl3HE@0s77M_3_SbY@@&?YM8vP`KEUZ}0TaAClWY
z#vK1d&_gr*`&VSWa`7Wae9ObM6Qnh@7}7BbVy%TI_c439c~mkzSJDQWDUI%y)+yn$
z_XRfS870SmN-rC@bZ7`CTe;hA$|5f2A*gw%5Wpyl!mpwBv+{eKRnU0)RO1O?C?n&^
zB*@#)0&y;h&(O>0lHvXMnlw<^<$nL`<N$zz0$NuU9R*7>%+Hp3t#!>7@2VEQwjTc^
zgt~>E(A{_NO@06(A#Q*7=X1;Vm*22@H@-n>cS^MN(pl}=#%CHDo=^n1B*|roe^rRf
zp(`vFpmq>QNPQ(CNhl3*Ni%+V)AqyX+c#G3mv{NUB}7E*V6w#K<{Gln$WL8-Qj$^z
zE<}(02QG!4OMF9l@%iCnw%BmNQa~E9LixxKV(a+KloNlSi=5_P?0J#Yv1W`QhDagG
z>84mpdXskL?lO!$)rMag{S%Ra)oqO&Sgy##uiuLTa#T%LI=p_-!M}VU&ZtfKQQims
zzLc7TUO{@A$mc~u6?Tzsni1S3p$H%o;Ai^A$t6vbqgnV_7uxDsdPn!@q;kMq%QAD#
z=0sJ?)!F0uizB~Bo-tSNEcO~t4MKJIFi!t_(wv)dT3MWn{4%&W=~sgJk{{>E#q2$<
z<p!U7q1Yb^{H<TJf$xmiv8s?X$ZB&wUko_ORhm49NOu%87?e%frP05`^ZVv*P?M8w
z=FJ~h!U{?g=Ft%?z5w`_99;rZ#q%_TGhoLf^=KV#XPot}JA9$h=C!gU9wl8Bcc2;8
zvO1~wBsHpU0B*ZB%QQ&9<Kdf-;-dl*U=fHvwKhpqCJZI{-LoN&H|GPWQ7m*(lDL>!
z4)yKo(n-jKS_Pg=4a`C{9K_bM%Cb0@cv04&5MRdf=2A|HX2zerboX#=ivUJ4_e9hD
zpQA2N7Xj%5vlte|&)?rwWx6ZRS=IrH(>xyq#+190KebHKuUF|`3%JNs;&~w=@l>cH
z1e>IN^-+x>Fkvt-{QMtE*S<tF=AoxotIjmTtd%L^ZkOg{eWb(ZM+ju~tkY!xyXH)N
zNh!}Qlol}E-yRl23X@l6gr@>$h_A(Y)^HARk5_EVs?#$4>8|r)Ha2tb{%`lML)gZT
z>bhrUdZS@Ja={y5<aV0=X1jnYBrkl`H_4npW3PR4eVFbV^x;D-y+Yro%&^tFbhhCu
zK*UhU3|@PIgcOyRceT{4N=>aWxrUv)tU`Z&GJ#y(W$8e^>Cq5Rm^(TcSt@+S>S9My
zY2i6-<SV}UB-hS37_=lhu%C4^`<2@-rgT!uk~8O1LaP3BHBV++ngtT1Gl2(TaPNXW
zb4vhd#Y-;a0XTXD#C%0y>DFZL5p{$@WED1pZnc_a4rYt%?RRVGUUB^_QAkj`q{7mn
zc~7@5;4PvcqNmcksvu*CquX~g#p5r{pMgQU1+N-4z&M(Ze~3kv0puoqe(KHutT|^q
z8NA&Rv^t+A1(V`nCMYOPKqnhetPCcuD*554P$tw?RooO>1$>}Mu^qL1U1-)JF_X`h
zZ_5MF=13$Af!XpDvQP+_QUgdyAx@yMlf!vl4lkg0-X3S`-leO=e@{aEONxatXO%>g
z`$lYcwJXT}&DKrge99Ct1U@w2(dKLc1^qL<1Mu+x3IgbWBx>-tNjtH56os`uVS!;R
zh6PWzCkiS2tVFfOhCAOcw7w${xN#Bk77o>;8M!}PAI8}TP<)`$ZWKes3z(tvvi$?i
zh8Zf+6DMp?>9q0@qVbd%i#7_8Ni_%&gHK{tw9O*n>1&Rx>>>AHE_w~ZmlUe5f3}XB
z4dj9jp=#y2yL}7Zqs2mDelgl(mL5LY;`bp42eeZmr?R;Fh#LoesubcVLX6kiDWigi
zXVlT8|D<Ht=YR`i`=N2UEVwJzg39BOVrcXG1rf_O!=RtPYk`CY{RR{lbmZ|TY#APp
z9{B$GFMC>#pn1UvI)N;xZg`LrrgNN|zaODq(o57KXVJJu;u7=Mbp|9;u1+F2Fhu-w
zJQ>0X`t;9u3?;t-)BilYU_i@%DA%*y%{%LV6ZX<TwvnXxh&WA&h3oYVx>XIElf6$e
zF!UaJr;ePa$HetIcb7B33tAiSaFs(qC=mIoAM>+C+g<N?O5mqV{)R+WU?vXi*IJ`#
zUy!dRUlijv%;_{Y4W0*py9-+QjLnmV0cl*Nh6XjriB@qV2ba)M7B{q`*>qLqHv#ff
zsPIw5f4Gr6)Ox!+k3IcX2r~F`bHjVo;J59JvJis9-$#Z+#WRhqO6r?ZAgZuf+lDsM
z$|Rcj(IsEDYq0>RwPzY5nL2XccIeFGnsRpXHWlN3U=;uc7|IQn8`lq(w$~0{ClouK
z%(9cOyR`CKoqL*8A_mi6cV8bFTX@&JZ3-D>QHcLdu6Xu7@cuof%K4XZk4wWvR?yb0
zJY0HH-1ejK&z*2(5`!MBdE4o(&7Ub_Jdu-f(Z#=JQ=^ve`sY!PQaj^!=q_TSLJ#-%
zoF=+E@QEs5;wjI03C06rtA8v)+IT4PMs7ZmMCI2ac_u{~^y>hpPq^^%pY?3{WurSs
z<4vxvAaeALlWF7_^|;f;ABs}3rd+U%YjEJ<N|Bk;0#M8=9)IUpkc|dkZ3{iRr4W4c
z8BhDE*CFhu2^<?1@E6rb{uKpQ&Y0a;zP_!~-|7QE+7UxEO&NU1*u4{e|3{eTKa0iA
zlT+_lQC`&&f$x=p9w}0#;iMVECZWjID0=t551Aj<JXdyh15dmeE)icwmxS_N_wGa<
zPjeri8$W*H<Pyv(Spe~;%nj}DOx)X)n-<OOi~Do}FPSf?_cw96Px!&JZ(BUV`8aCz
z#?9?NdFfR<?wUDe2B1MZc<ecvuuGfw;6ghy6L)rjBg>%bFOlq^-(3QjBcMyNYq5`y
zk|R5JcXTl9!^36m1GSOqYOh%6+sZ+A(HaB&t&O%fD>v(}$=nIX++Jq>Ht}MU;-REX
zM=xX|PYglyj7xPnUVUt`TM6(_DF4K2(Ejypp+oQyK}=ZM{Az!<RM(czCJsH*-)O5V
zIkmv+-XR1kI2TZ$9GhS9`+GFG?OY0smiAl-a(2z&9JQUUSYsa7P#A^GO(=t#hc_R%
zdMLz1M?VDyc#NgWz|Q{dKaGsn|A3P2W@|ntQU^+IK->7FT@DZnq?kMr4s$5W^75bt
z_w@v3v0=6cqQ{dm)usC<&chX^TrSz>TKS=`-d;WL)x-BdyBL~g|7nl4W>IHwW#M!8
zkyW=tUE}x+VHb7&5eVZB#RiAd^jfhK=si2>oB0U)H-1MrfsMtu2lE^;w$YWlJ72V*
zQfi<7EEX97hk&p8Cf*!sCe`h%@IQpBXTUQ9a2u()yiIbh%bR>}&?IS8nJNZ!0<Wk3
z2=fnL#RtjZyPbV4^4+{U47@vQxjApX#~~@5W3Ea99ZD3{J7Ile05JoW$b^(XW~{}V
zhjGE213E=hF6NfOi;^<*I`g#dc)ohbKi}?^ctW#?TMbRHmF%mdR16a;VB_{EbL72W
zK=^5@><pX{%r}E}<Ktr;t+|Y;d)@G#CL%xavV?PyxU+vq_UD38wx3mr2Wt2#p^NsT
z&SDpvL%~pP1?d^W3@n1V6ZO}mbOnj>a;QUYnkv9ylya;Q^ktSc?EmVWeg&|7su%3~
zx#pFkzSYb4IfYosK&a;%%<tX?WPr#ysyXl6lm5(2-!A5)$TzTcGII&r1L&4Y^m;sI
zBP)`ba|nUj=VS4^#9Xrge%PdBy!h?TEsjV^2PkBlw?0=WkH?I<Mr?JRx?2K|hm{n<
zug5v>CS5a)lAnlno%~Ru?J?RuoMUYBa)|BoiRrnU6PID4@Y*-(YL&0k-CeyOJ35)%
zjXR#)#RhlbGxjqs<yBoX6MonN!t(c_+HvLM+7KY;ts=^kGMJ)5OIVlH^T7CJC%oLD
zn93nwBFxbgKC<M3H|EjOWM89{stN|ddVe%N!#yUAS@&S#*7VA;&(x&ze&vgMsZNzP
z|M(j3%FLSo-kWwLf{aWE`K$Dp1bMk(PMyDdj61gy$Nd)=XXZCZtE@lNsWLBn)F6OL
z=tv|uA)6p=uC)?>AP%&zb9xMlBUWQ;*nl<DS_gKtK)U@q{08cmu4E1=^4VaD`n<b<
zz;r@iyfjF$oQ0M`fThxB&Z`ax%j~EMKn12Nf5amF=MfTP^+mr}0gysxTwQ@(J>ajk
z81Pf@%3DJIh>Hyj2O0HE4DqIGPHA0IlDBVK0jOhU5D8Qmi33j*-IADvMzpZk5a$rD
z{n>rt{CjHhd@Nk$l{SZ8`W#UbUeW)Ahh$MKW}%vpy5^z$UA(B@*6qO+Bbh`o<Wy}1
z^x$(xewWI$|M?_#`<GqIwrzMl^TR)gMa8ne%9QTgAnGS@1X{A*YY@T@$0a^A+rI$|
zO1nTLxJMm3iD=aevnitbdj(VI;fYrhTZC+Xks}QtM~(m3YV&gr@~IwNbIQ<NLiNKq
zb3b))Z?M<KMJAMCh)+_W@3+qQ%oYt7drA<xh>SLhf_;Gp{cW8QOdnk|i5Dx*9n7?{
zINR?0aL`1o!^!@xviX-=7-$(Hhp^nFuvj+yb6u&&U5?eoXKbV8HG7UM3b;4(FWZbh
zX$;RXC6i&sSk8Oq#mOtnJvsgK+HPp@Ok~UOkNN*t4<TwRiT0@+h&)Yu7ki(W?Iv5U
z%)2s_>1_fz2*E4DS%4sxCub&MG_j|qiwLNJ>~26Ol%}`*qiAXdj(khtBPA$co_-$?
zlDL4`{2lw^<SsS#EPFN3b8PgdPw@!i@yefG1_B6vYg@SA%@#)=ore&9fCEe@T=jAa
zGuexUf<D86x1I%0P0njwX-E(;>(0^D(!}12Qfq8s!vU+a`c9fPJRxvC@~Lf~Tyb-e
z12nVmx@8Mz7hTd@dOV>Q+dP~PTMC*QOUdUm2P7n37iwa8MhiZE9nhoee}v<J<5Fs;
z%NT`yN(ymg!HaT#zZ+J@H}@M7eG_q3WBxF8bkQOnf15h956F7h`bi(K4r2RGWIIk}
zF+~1bXe`&!hx3oHMICNga(^wF_nJ=vdAZ4Nu9uMS=}56fx$z0DFb*w3^P+UL>CLY%
zeY2?Ef%IRQWF|f~j!xkpzocW|bN<=gZ+kNyE(5CSI-}ekx$5TaA^m~<Rcu&4*+P!s
z{WE4wEmQv{$vSnq9u97vl;T+jP9wwgA_H4DeYb~UXUe#X8T8f1=rh0VPim(FQ)ZuI
zcKM}Z#Lfl_$A46vbvYV;bnwVVtakM#s>Q7$cwizuamP}jn}V?s7H`&W<r5-H#$JX;
z7063F+&qYfyQ2R?Y&QQ5Lb+aS@ZyDfugws0wrZ_3LpC1Ko>&^xyB&d53Bu>n5+7IP
zQ|ws!uGC*h;5r$^g>6HM6%(6GW0ZM<k8TaxyFVX#dF2c}#8b4nh29swL6-RDE}AmS
zQngd5%(+!ApiD6*MJThOk!{X4kSG^{O3o5Yb37`XIL@}^y)(cBUW@$9n@yN&P4&Cv
zXB>-{l*(q-r<P&K79EYsnVvA%yBhv-U<1*U!-S7!^BKG3B``&eCd=eaE&(T0uhZ8d
z#id%Ncy{2I7QMzdcYl3P>uMK6oGBMUUyC5gHi>Rc6lzTw(>#G*C*y>moB?~@?$}Ki
zGclNc{`WgYsO8uSg|Q>QY#{&7hY7YQh>0G@oTav&QRP?tvJGFFNF=E)v`Hve1cOh!
zgZ|_9G!C`uudVtF##PU8v@3!SyfqJY>~}7V;J+Vk>}cpYYf=R6pWM1QPeO5ru+QnB
z8zt&<)_QEUTDq*7HhlIjdrX5aA?briDTf6t__uNmn3wdwj}(^XE|^dyW|rsk11N?L
z<kjt7D@Pq@adZoS0iD~~ZLPc6Tl^{qw&()ACjX>tXi%gb(6|>#zT54|^y9>e(QCJZ
z1k^W*gB2qCoPUyLNbSQO$^bqsXa*rCzjDgg+O7xP8HXA_z`b#UD`-*yZkZxPSR;iO
z1GZpp5vhj}CY$qsy0HmU{bF41bl->6yuEZbIPdCTQT(FzevdTg>insjsCDWR>q>Tq
z^8<*Y#<BS$&OI<)EJK#~0mJkHJP?EUyDROWsK$1$XA_v(kD1t)5B%9e7vSKuUr_7>
z!fpnumDcZVEj7IU-ppk$RwX0RWZYE6dg2IRhh}$9;u-lX`1~i%A2-{p3HL#t3%F^k
z2UU{X8JL^iV$~&sAXUgH@S36<M^<+e5QKjpqIKb{q?ucE|7Z4wZAlldEpg&teuEDt
zCNO-)_%z8>PY$??eE#|!+#ZfywaeQ{H{Ego!{{;ij%p(qE7hh>w@gr4!{6p(NxT{Y
zIAjJxbOK*Kg72hHO0`eEK6FtvomiR{wMfIlP4vo&T(WxCyY=s;t0@0I!$mvPqAj$a
zY|jl@1E2qy1weANEbyVY-MjB~aXKMKR_UhQ55L5w+j3q4TWDoDT|Jf)-<}HwsY23s
zd#IbYzLC;yk{#yIDFBeG5&v_#Vx$^!FXvY_^7l*_oZ%Te&|;f<`n3BxyW#CGS;Qa-
zw#&!Hh?9KGCpib)Et;l2w6N`RBJ5biny*;kLr65AK5_HG$-lqmRgenK;1dIwm3MXD
z;K-|hs};h7L9&u<nlXs~f}m8F0)uS5b;W0hQs+Y<^S`&V*0nMz9ymB!&Rc23g%>O;
zsU6W}qZYE5@C)&)!1Hx&ju$%;*=n?P^;ugIQDy2!P&viA;>`J^>8m7epVrURkED`y
zo?g;Nf3irKV=3C8HPr~|-xTFL`Za0$hGRxH+VkfRt`6O;?|xLP2sBa_MjV`tTd@UA
zLX~6zD``>KP`zP|YVE(ugTwLTeFc9VC5a628;`u)L=+U#ziJS4q^9<fuun=^J?+CY
zd#^=SrSN5P1Vx7D)ic0<NCo71j?I6YKAN`dKMgW=L&h+aVYP)!JSUO8;5^r}EvKmN
zdQ+)P?Tk*d?AEfo{N2ZoC1~uR7XAeTFK|!yhEGM-jy$DBpPv`wIfpVwol%wZ-CJ?+
zn-w8ml`b1RY#YCmun?yD^C!WkU+jc^%Hk~hH~NI%f8a1n$F6z5d+N)();piy{R2Jn
z(45Y~&6^*#w1o~D5_tPV1T8$5hHwH}N|%J;Zador*PunUX0Fi&l|zhPhMw>>?sKY<
zF~s-iiX-5b5x46NV4wmPVSSCYTXJYQRq(f+v9<8lb0+EUF=p%S5>W?t7epz$LKq`l
zePrc!ZgMPyw8wu$?gp5^k{xt1nu=I=>_*7sGsKPow@CSsva9lBqDA>=EmXV9=5+qk
z2oVtI?kY<EM!t60f&WsCmk>MaB{mYLP^%-@^M}pwSgm%(R>^O@NN7<}6=fqI>gBQD
zajfDNXzRP1-fymcG(r9QjB3Uuqy;P${t@Z2R`fMf&Es`>1{#b7`yL3SFx|iSbk3cK
zP~Xx)YH@yDk{G13u088Bl&lm}<a20bR1(!Dj;dl$273>4{?Q-;sh1|nZjM<15ctt9
z1Hj0F;!Vj8d*a2OnZwK75A3|5mjiiT@PTmp=*(4K1$=R3_@zI+9z8r01pc0OiTlNY
zf600#V>d>d4t2R2iC4)L)r<ct$h_W0)qJR4+gO%DrWy5`?1K1H^s9h7PVs1(zI{`u
zZ5y;;82B~-!2PA@e8kr#|1HsY`lnjS!BKLwxHv=?{m5n#PwKLR58as_#BBYj$*`g=
z`}^EQKYvja!CS<PUbHSuv4HAALUEFmuxw{${W;IR2AlGeNKFyex4m@bJ;?HQ%#e~p
zdHGTibecXl_+=TN>7l+3r(XeUJx<{N&by)3Zw0w)@%z)=G`(Thol_*86765F!ya!)
zjOMF0Fe3OGg*%;+SyVVwIlx2s`MmTBob+7edAnC=q|{_#(FJcANOz!gQlGIbh8g;q
z>ZPk~PWC$zJH0J4Jb(V=;?7#X3JUP^(@*KIJTlrH?iPDE3fvu&ua_@hTJwCodsd@T
z`>wp{YJoEwLW=X$>0wmzgI|bRHr4J_DdX`|xQDI*^HgedqKce@_j<r#7xPa;J!#x^
zUcg@rV;r(c=dZkG>A99W+VG~Ta5*^K_<?YAvawC~EB|>Ca(`Fdb7uo2sm4`j9jiD0
zwZO)|X4IYzs!>9y&=%PltmXh{bR4nzW(d^eo@-awL?Sew3I8G-3Q;JF3e9I8XD7L?
z7WX01OZh!Aa8)UO&zC?C2AjZ}dyK4(dVm{Jfb$#g@Bf6YCgnO?+&8zxCSFPID!CSA
z7uHA-fcQYo)nd?T|1Qv`sV}$NCCIcb2sAV}fww~%M5M5@s~u06tA%Z{_`}1SSn8K+
zzaP3kq!=17^S*9TWguPuri){IyMbl^!<mFUmlw|yh^LRr3fQ9o9@qQ1-Ej+zE$0y~
zhH*NNThE9cs_<dJyieq9Gv~=$cn|sD1<OJ7tB13mtIHhkla;p`=3p4%e7NH^2yo0u
z4ct9sPX*jOklj)HI3;fKM_pX}L<z?0^EJ**&5uOZPq^4G#-;oFf&gPW5LVgO4X-`~
z-m$d>ZN=I*XgjFu*Pi}(JSKZ0rxwQ@VE&(7AU<8uU-?#rQUgE43+lULvWCP;%_u}o
zD3SEjAL=9LuU?A%iY_=D-vk*TU{2YDsURn+K0dr2z4q0?^R1DqURt{iJQoA!{-^Pc
zqgekiAc0bnFU4~^fYYeKJkxgdmk;b20Q&!9xBHSFgo^A@!Y!F9&dNEdOIx*fPSZ*C
zu?}*KqMm?TA+_g(xXI<&oX4A+^Q-0v)#~wWfNHI;K5_=i1{8Nz9|Y(IT<z`xrC#iu
zv6x(?gL~t6wDFq}aBqk_7H?8UB>izuDVe)s?749~GH~bkuY|Spe1=ibiQ48HsQDxh
zv%5|dB(RJ4t-Jyb!r5d0WT)x1RA5oN=`EoPR1kQ-B;1{k|0In|LtjarH^XZL0J;b;
z>k~I**vYTYI3Z2}cO*HzXGkZ<1Fi%Vg51(&%R53oWjLZm5CurjIU*2q?qtz4kVdki
z9fb2l77TDcEOV}K510XQgVjpb*0~aj*Ip$fDHV*{-#!d%RY8{$$sh^b0T0wR+Nipz
zBQt#D+m1$%VP|z!aW|h=Ij%4yZ^fzJ-`l!g9p0letT}MvuN=ddL@03T$E6^w_$TIR
zkNb~TZ=%A;#-d*VWXsCEt?%*X@rD4KntJQ198c_GAw*idgcucc>)w3-*R2O@WBxy?
zzA-wlsN1?oqc*nF*lBFrww*LK8nm%(qp=!0X&T$M8r%MM-}~M>#&>=^W3+vGo`by?
z=9+7+kW8m|(Jm4s7U+Gdz=|*PY5WVhEF<<jskCXr!`bv0Mn&{re)a|xSga5&hrAOO
z#7?C`2|F;3LqgTaov3bP#|jQh&<q=t!I$tw3{Ke>PR@BD38g`TvG|E>VAW^f-sZdI
zeV1*`g-<(Fuv!b|b=ZlMVo#o*D;S5EtBY9&p<8i(s`y(vOpC@2^o(=bNxGgXQ_J;_
zVxlE43l6@+8J*|X!Lt3m1Xc@kPvXmRR`(^hlgwu%Ci7HQ@YfCglx1jNhw0GdO+u83
zhWGeWtvG#4#5>(qen&4~`$~2VEU?JpW9u6e_SoscN}yL+Cuwtrns7;vmQ5su*`A2y
zSuk+4^zMPq#7qeA)5a1%O(1v8@`#*__}(1Igi(VQxdGvQIjCJZrS}31ai6BFG^FWK
zF^}4GrmL)=N_jG0GPD0ole^8^q_8&Md=E(#M0^u7+JgnA=5eddPhudx+j>d3C&E~5
zLaN=-f?s$ciG9*%n#AeruhIdLIS?RcbaYPX*>{#a)M_w1B@=AP`0A#I0AMy_GRd~Z
zPbCqjzNb(x;+9gRBof<COG?1Mwh37<0vJYU!Ns-*PLHm}!YG9`;wzxIPnD&W(V>G;
z@{JdrpQtZCNZw=D*VSwwW*!=(z&pm3CewcWvCcVoMcRKwHZJs)OF>yo!LKAaqr~RS
zi=fYeK?@yhQJ|M(cJag=p=mi}N2HP1e?tl?{d<Acj>j#>u$w^tE`<0!DCjlTx0vvU
z?cOVg!fC>VNuA1o>CETceBuTX2LjGVtg5{>twqg|Ql$oyR_f}sX#j~SpC;_kGytbQ
zlp-~)pix>BMD<c9ks!&0jXRc_<cl@1aoEXRlYw6Bq3+>yoKtH&%Y&W}P6lFpPI6C)
zNl%XkTbZ+8)&CViL1FP>5cunRF>E?#rU=b2hn!IWEopZ&@|Q0!D|(`lBIO^SW6AiN
z&&p_yj0*RQ{Xm)o^_}YK>u2Fu(#fVfysr9xB&sPau4TD;zKMx?w)U<8D`xW!=XV13
zMz}!C>VbDZ^X~7nX5+wx@p}!J5)YOw)eTjU#;UZ_eg{&2h64!XSVBl%O41NENTf<l
zn3;zg?D!YGr?)b5o>UkuTkZFE>vdUqxFF2?!)gsw`xHzBkusd*fNePAA&`hUxzhof
zRT7{4l~2ifhHm|8?U!7ZRIb=)9UHd1l6=}R?(7=ao*4NUHQ!F(G{uu3ExDMpmdiMw
z{T<I#og#~YApV(aIp{^37c@Nr+Y7aZ@m2%9-#8C5P_SR#g2kFy$H1gmJb!xqU`Hg=
z+xs174bJgD8cpPX3gp}*yu1~smq#HAvUvEd`6j|Dej2~imY}8vmP%(0kuut?($71Y
zBMRKZvWut~=`%C+J=ukR(%J}jVfWqK+M9R;Ec6hK%FI|A5F;XDs7daX3<s1-0cR>k
zgl=ec=0ZR<cA26_>0tDE%;)(d{g?4L{uq(?;K<!aZZAXs!<s{y`cgJlh??RiXAqWL
z&UrsrJUGHAi@YOIJVzYMz};&5Sd-q;EPhy!)O%QC34C=w6S){W^J<sfYY>qR&C`aT
zbGxz`sou`w6*k{xPaKG?h5WDh)2CEY%;X}YW&Q8wIxablaA@~3<??4iGbA!SH$!ij
zoD3r4I|6YbHFoc80wJ}#iTkFJ<Hk(6s>$^XN2aI2IlXlz(DsHr$*PANNw7!$v-D}=
zcC5;W#5Kqfp_=HTXBQzhIKYPE_CZKhytr9#Og?nX^IAgpKJS(j8TGB|-;YnL9S^)r
zbBO?`_pf}pmNW2oCb{p#SLGQi)V01Cb)~<^Q>#4dM5z1#6QI?)&I=2nu-?B9`g}lZ
zlUbvOOX3Vb^oKYShn}XfU+?ui({j8x9>f?ucQEv_eVDt(yN`FD4d%@Oq(kwmUHk7r
z3P<AZ#jv&(*ghsqzXaoj!=oR@t>v{Mq0T&`0QqUC#=XMxOBfB%Z5;&Sf1s@OFIae#
z`-Ch9g~q`pQKxL?Uh(_%x%89)SfT*<MeeuZzXnmVIQd`2P1TTF9s{QU;Rg`MEcXHj
z16*ybn!<NIK#PLULz*q3j6Wvd@|dF@cQ5e00EhLbusJ18IfM}0T{f1_scn|u-uyPT
zoivn2yN#1sZfa!KLoNVKB~Bg*cVXDIiSTkvt!`>Y^tZ>g5G2o$U;>k0Vc`8AJ&%JQ
z<PwC9h2@}A`0+0Z(DAlLFPJkwK6_b10CsKFYlpG&Wnm$*O^8M4b4+A57FFW@*$H)$
zt6Mxm9{|a6Lhua-#uL4B0k`h;Oz$aTi4W0tP2&DD832{|RZps|w9HZPV@Sw?|Ck1g
z6#~u$;5(dm;>3Y++SM;?C$>9Y9=|?`hJgNZZc`HtPz?Y;XOo5E{H5n$Pj>#Cb1U9$
z{IUeAC*DQ@mEh}5{i!;UFt<&13FC}p*vt;&^Lq&rU!y&D@Aa-`%^X`ofeJQRDii?M
zAA6=`&euO21pdL!`6c=)AL=n;>_pRNS*iUu;Z%Fu%zFcC5)Ts78NjJh<p1Fo;Kybk
z$XSjNLA@T?AOO}~O{=bfMcwfB5$Cn(dKD4$ml}C}?|fnAGJ8iye?n+sV(dU~$C-$6
z8&@Pdp3_9t&<W7q8!X#qp<tQZdf&->nwdq4tH|N4|2^h~#IH>P;<I_2b^Vcy03+_?
zILm!OipLLeam%oPw-tv9w#n-CLU|VFT0U2FpFzjhxK*D~xqP0s^(1447Cw6#Fza0;
z=o2ve2Y69&yZ6&L=(JO!){m!FwW+qsDuLnIzO@sz<{I!7yAzCf(nGzsUd%uPYw{gm
z>kVUI1;kRTg;qp?NR7_Gy`L*tO1dtwaZ%c?eVcmW>=z5xW33W?wsDmvTK-T3Z3ahj
z)>#ypK=+HD_n^&JesB&5^PO=bUT}{Y9sGG0kN^uvbXGpGKdNYiP&fcFY(jW1a%<&G
zX{a*381)d)larg81p&sqeeZrTWI{95E+dU9@?)7l7W8tQOBQ~ss^VK%h0uGU9wQnM
z2<Ul`Y%+Sw+@YAG!E{gmdV>bU2#U4St$cjNmkH;xgqZ*XS76GIl|e)anDVvDU$hu=
z*LHXqOHRLNgCqgXb`?yC2EPlOHE6s89YHl928MVoQ?)RxzX>ebXvR04G6bIR<CLYg
zw@)B}H?=fHZrrgPvRnXAcOhX!3Xc}$Mk7N;$ibpIkhzU&0eWVU#}j3B=B(1Q=u+{Q
zEVD_V+g%6rIU4{+cuiaK!YV&aSpK*_hG(iz(?b0skArWJ^%4>XQgCqdlo(&}J}Qkg
z4*(bqe15Cc$+2a}Q(oUO1fCr8xI|t92HC>TrEi_<VBSW)&6o>dy+$0$Lo&mrc04Qx
zWFx7djv`%Sqe#nAq~>d+GdgF^Vq3z#R{Z`7iFH)sRUA?z!TmNt3KY`qy$-Kz)@}h~
zuf|pu6vuj>u2mrW9F09t!f}t_bTf$`XwkHBhVDW3Q%zY8H3xX}z0*A(z+Hg`&+2OV
zR-?&Ee8qh%>6&)!gFDV;y4fVjr@e$B<*@6>q^iZoyBk+}Ui9+OG4Blu5FOY_uPKTz
zG>Y0@!dbaaLaqh;CV%iQhd*(tod1aLh`<<VH>_{REk;pdlqP$IGk?+`^OIPdjYn!F
zOnjPf4#nuJ!-u(RcDqJ`H(+qE->L34C<t5MGOt*J44no^Fj0hR2QrDC<_mLd?-ym7
zA%U6gk?0g*#$hJ<qr6|bJJ$r-pXYGMk!L2D1Eetirle>Jp+Z#i*u&$Wh_OvS>WWSg
zoFsUf6ocyZCttfy0pcwWb*k3Yjfigcy<0hWml!Aix<&uPQyvl`3L$DPAq=^#NIrYc
zPH^>Z>YiTa+^wLSoJU3d5Sjov(;RZ>-q5-O^KLKI_aP?eB;p48mH317zHzd-FmXpm
z6bN>C8*6`iRE5$=iRT6vh^HA)wj<OZ+Jq{X&{%tjLN1}p8)NMkgc5Y%m2JB7)^9nu
ze<c;?f9Y=@suu5-x3xfVz{OZ{Q9yHN65o-Xj||)L5YI(?dL%~RuSSKanwKS92eL#S
zCqVhmSi-8I<YNO(UjHO59<A&*F2Di$rA?$)MjY~ob_m8${`y`4K?1tlSSJRlC&T?M
zgCJGc<2S%C1ZzUnqAhez;$s=Y;gAVzDH>J4KV~!dT#p;<0U{_0U$bg%ezE=Gw^}kV
z@UXrNcm#1Ta3TQiIccQShynGg)g0!Y>jN;Tl?}QN4z%~;2WL~84EA_L_b&Y?nlGw1
zSJnc{e!?jLynZ(y`eN<)nD<`(L>`1U{&oCE@D|5*AEQ*Kdh2womU4hTa~kV?0&;?(
z-`A?qMa2}&{LV!~hO@p!Kb1^GWefIW)w47OmVng_)P;5u(CgIZCqWc~2qp~`TZP+A
z^CL89HQ2z?L(?((IIe(DyUq#>uK>jB6zZWeI#f{8{<9tMp(MZ8OXYVU5$Awa{CSs`
zzv~2!Bw~OJLHEnVr;07Zl+ncFh4FeM^-@LcQX=Sg=gL5<UlIuV0)Zv~zvmWzNv+7X
zfCYjmh!EWL<_fO=I9ovT+;phmmuilJMRmRM*B}OF)+M)w3%wPY&3$N5;XEG_sTzD~
zekaA9?QgtcQ~#`>Mh3n8+4L8`Ee>VC@cx7%6~KqezL>Nm8mydWTFp%WAyGbx;r<$=
zM!9<!|IxKwtvFSh89&#DL?&-`*;$}U)dr+1_wAaAV0OWNGH7~S?2NG{058^Jc4U;S
zUpoqLq}WXnC*rmKgyV9VchFYOfv_9qI8Mhsf4|dMjq%a0?=$kuz;&-iGBt3Q)I%l^
z*)!G2soJC+sv;H*QhYS+r&C|o3IR(>(^|n+4+q?#dXX(;;J)ZOLla(Za>0;)7u7~^
zpb5uvV>`CzZ60UhezbVt#9}>5Ownjg-g|9!uD;<27WCbZ;K6+o+Ig5ULH`>H!2A@e
z_{?_Uv!};5Lst6rM<csCU-KpMY-|EQBuYlyRAG$6nOwRl55lRcQ3VtE|KS`kM!Zuj
zW~SUO{SovC519y@@=lx-Q1hJJG4;<#vv=l+Qmh+zy}_v*Pl`C-oO)!pH~(%-WB&Q6
zlWWfHSWL<M;8<@cd$QuvnzFik-$*E(le>Se-OjhCj?qy{#Cr>2HCNG6!8)1yn?rmw
zeyy0TGGU^n43R;ET}$2KC3ng7Y{4lZgsw?Q@{fXnZX(XthK}d0?MVe>SGO39MYKp9
ze<AFuVA<m3>_o;>b{Eh$HBD$}4r*Pd)OQUzK6_&7#dSrq(uM{Z(G}UXJwx(ZzpZMm
zsOr$Gf=2@lXU#RH)Be(C@`31pr0lZ<5#MV9`5lnFXB-gMQf_sYf500ZvLOt8mvvvP
z1S;nJuMcZJev=+`MwRqqml}F>3hJeH_s>`_+YP!15Sk)jiq_s|G?5rT$(d#>?(Ri8
zo28;vYc+wD!~D~;eFad=z1%KDu=^V!0b1;B=PLNV<Wgi~!RkE(n7IKhhr2qTD=450
zL%D3W=etl1SR|5Fkrc3iLUfO?wC?XhoNiaDUVqNVIvK}PY2CUiTYt6mq8de<Xu-r+
z*SmS;K`7p!)yw+S1Hk~z8jVI-w8<P#xUU=wyfPqEX}PRZs<8PDj=Fqo-1Rs<7=5(O
zd)yr38QGZ1>sE}>@zGFZNeLl-erkI?-@WVdxurU7^GN7PxsDX>f%9A|)Gkt>o%u(g
zjq<j0XA)qA{xFaD!WLhRpk%}L^6j4>7eZx2l&tLW2Z+z?rhJdoSsQ;^*zT@hZwaQp
zsyEcCtbQyt0ex<S9jbuq@N%~Hs(%^4iOUqNf~69}AcHehYd%}PzUbh4NG;y!d`hJr
z7TaH=$1ORgAG-0}79Zve{Ns`vMDsE|NS<F7Uhmo5Uxvut&kJQ^#KqWzgf-#PHope=
zTt~fr2c@^Ok3PF$QEs&a2$8r1KO2A`$5S7hdh*C+)XSqS5dRVt-%-lq2{$OZ^N#j-
z{nc2}m*sWoRZuwF=;jhB+V#h3VcL>b_kL7l)yEZECuzXg=qbPBiAIRn;-UU?k@OU*
z;ywl6tJIj|@gSqmSwusXH53@jU`FJ5Un+N&pT!NsPlmBY&G!sZB^*qRfqr+b_lOUs
z`B=AHU6b$OiJ!T?wh$B+vb9rw;_YX|X}uXVp-WHM`qRXL%@QZtq9pp}rA6=ARRGOU
ze5dm1T8@D^*1(v?&th?Vj@t89Yqz+bdXiKF)X5y$U}SkX{tS?dNfhAI(EP*1bxuV8
zvqQ;96!_;*rI$J{y{wi*P<@mBMz}6RSzBLo6ZFCS5e4Pb0rg-vVREY?<wLTFM46_=
zpY-3zYmP@7)XE!v(O`7R%ag$9#0|_F99;ANb_5j1Pnv!o-jYZV;<JeN2muTznlwh4
z$bZXi8XNsms%J^i5I`9j!Q*KWHL;b*jLHv=_Qn!_progI?fpv1(<I3MT$vgT)1X6R
zQ9X)Q`wLOUQfxNbjJNMLo0kYPBm2*y4m$s<Ub*FBD4?EcM=kWc3o9iJe2D8_5-gyA
zO$%8`(2Og-cXmjjs6O3l#2>Om14XjsGK$b#esMLd11ZA=Iv@lF`3?CW)dMy;(XZzG
z-2=4lFk3~9IFWEv+UEA<V{&_S_jW))<cE)Am*=hZ2#S|o*HoJN%ydJB(evhu?8k{K
zvhpk`p#Sp42&8i?(jdLv%g?x;JB*LmLXX6{`wfIJhe55DuI-zjL)B`P+gkyX_^mq7
z%7Pdo_YNQ+O}}*_b0{EPK2;Ot6kQaYVbWkI|8A~u?PHyKB+Z1K;)*wY>VNazsHy(?
z_etHlwUv~D333WWkX#he0J7~<k9$cz=e49|7>lR4ybMP0-OcKr=Nb}gqy{67i5+(z
zN*3>L(0&U1>gj2wDd#eGIdGOEfpwJnT#<f8P3m~6Wbgm=tr#Z*=_q755trqTS}C)}
zNHL4HKqHQ#W7r-zR$m3Gd+h74yK4<}x1wxdEkl!M;TqVni+Hz%l1Q0155K%`n}$L*
zc2E%Qs}ar<9VaRq1av;k<DUnsFA#mQ@KZ%;fP{oJ2{=@C7grRUGN0Le3BP<vhJERk
z|8?xL8*&KLRH|umDUc`Jf|WU;R~F&ly-J6id-3cw`y#<UiG2_t#GcyU53_wa7Ioe}
z6DK>voJEx$>U7p-T%ahH25yRd<JU`$Np!y#eT_f`d89ibw6aC5^g%(0f8zoY=@4=W
zRos9mOn?fvXLz!xDd8xJT-1bBSamK5m}9>$9e?h{QO#3D`^@xDZDPm!f2g;@(b;8_
z<{Ed$@umvM<HA^Tmx${>sP$PDZ>{D;5=D^hjcTl2?OBQl({=lq7}DK~ywvGuDOItr
zOtu90!^%D+1aJIqkWYN~7Us1}vUF8CzH=3VKs&YT*6Sw9)Pk87c83$xMK>N_Obx3D
zp~ZcF+xf&g)D38v6@Y&X^oYasAZ$%6kx8ZfIOTvzpvW4vpl|DII<(pG)T6<@w!7|z
z0BXw2v}ZzPY_yuRX#fjO5l#--p!qmNs#!21?gJ~5_=Ps8Mh#tEo7VA3pRa9U{;xMc
zq``Iq43XAv-ib;<kkKZ9h+*nr8Zod?H<EY~@f<7$CyR@#Z_*~2v%LP>JhBlHdT6Fu
zVyYH+#_HmJT9w!q3HIDP3&wxB-#M7Y_r=kACsH>s1C*9khk8ANm6eEdYfkqF<-GnP
z_GP90u3Pz?rhs}QtshoGNixN#_n1b1(P^m$L{zl7_}1)y%OpMSn!f#3=tt)f#MF8f
zSIB-d%--}8RH^PRPohDD8sqlT7iqtJg=rZkVoI)dA|?Ms@)`PFm2h&Ekk``{y-(`e
z;~bD?((Lqr23>?+sn=X;ZLX437)Dq61Y<t??0083w{)AUpEVkXPLS{PAr0-Xh;!sq
zbHF$y0cS6A7eXCQ!Krtp0R*oH#ZbC^ASA-&<otF2>a6oQ6WaQL!G=(RXw3WTYvN%`
zlf$#YAAKA2Q$VXZs}g`Gz}fz&*M7_B`vxlN%JEE`FAEHg!n5A>PFh&MD>jJC!iLQL
znzpUwyjk*tOae33VTjia^guR|JmmU+6Xbq8;w8zU#&!V;C%6AW8JC3_@i*sRyhn94
zj7_V4zdl*g=TUS@uNP)wn*Czy+z45P(rm~T?>6Gp^FD{ZSIqFajF@9^LX%05s3(Z!
zyBvNih_E17ty;vuQPX?sb@<+j-26CJ_^kr!{zxxJb!F64U!W~gUnU2`Aitb1pU*W>
zWd~o+;i(J~e6e}SAICybfI(K>AlbGSM#3{qW^F>*>TUIEXTI*Nc|r}r<L|MEm|9VE
zb=w8T{FwgBh|;Ao83LXEHOw#{^ymFuVs}BLA`W?%=V#Fy$arOJc(t?nR9DH<l`?b*
zN)GphuMbOi5NNR*(Y>AL`0ZE4LO(YN+V!tYb3LD_<t}DZEDA6#p5!`i7)yu@_Na=5
zgUN}7(mU$ihP*)(=Y1nZe!o7+?HDHFecYhi<HBRrC!%DWYmiYG6@}>CEqa?v!q8d?
zC4mllm|CAA8bD`HUn@dZ`7uA@yR}9yF{rx>dS1CPedOZfKFr7iV~@@F3znm{3kUM=
z1*NzgJfijV|K=+F*e@Ld;&@?=H(MEs_Yy!C1EA1julazD%h~@={rD$wl!y8oico1H
zv<-~c)u?}y4E_;p9xHY7f2nplw#+SvF$iMkK|S6L>bYkE;pBS|Aie*Z@V8#Maup#p
zry8ha%K6+N7V2>d1Cn%yCQz~6RM!zWS0IM|F%x>~XT;GT+PY9%g(Q2`2<7jzfIW6u
zJg50|mN3+MelYW>>EcAx*ZqQ@>EYsQ$5pm%Z_uW)`+WTYj70o-jo2$j#muwTccBfY
znC^2LU!6TOv;4!yhJ>d6i8MCB$RvPb(#8u3$YytXsdC?xP)#vfAElL`K?o2U7Xcax
z<Tn)8E8bQt3DgPYfG(6a>CuX+#7e_OI#A1s!ZMCU+C+Na=N#<+eyvlQ@eeRGI&rqe
z;qk&h#MJ?R1yp<*K&A(gGMz>?lDGmd5Ce@PaILFH=ba{}PlqR>Vq9HJL4Am(dZEI-
zCKf~58^kEkFTn+E;wQ~0-7mjC)MK9%3V2(-gR+F^K<o)YBoWcZqdFweSy{yN)jSb!
z)@DDlfT+CUFsFpEU<V@6>7Bn*0+@oOdWi=9TJ2JWdrT}=IPg*F(=931Ueiqf;umGI
zKt@nA1Kmc$G^p~ZFk?aBAuFpCs9PX@^tt1=Fo(^1PYF&74CkaK$C-7lRqnCBr3N~Z
zZR&XfNzAXDSQ#kDx!lIfn$G`7{$9c7BZ-8RnwbGUMgD?kG+k>~0<-TM4+?Q5JOJ>v
z8~KG3oQTEyvMLE6gY?^+QMi10p2<2*0K1Z(8xM@bP*N|=#fFt)vIL+JP{1!Qs52{}
zdjBehMqGv@<9~vsTdT7aX9AQ(a<E`cFFQ+BU6CcwCxoy;GoCVQZ_Jd@r-<FX1xWhx
zW5M|DSH5pP*hU(uS+0g1w@14tT1Qf*+q#dFDmp#7^D?Y012Mu5wF<-tG@Y!Xf5HuZ
z|DOM4F#jEH{)I7_9-sdEmvPM4;R)zOX-VZc)PWPzn%k3uMe19go8WI-CuV$=eCgk8
zMNLJGg-u0;>72a-2FpU(Z!>q=Z)wIJpR)LxiPYKIB23NQZ1}y(BMkPL*;*vZehbAf
z5wI4N=iy-AD<(?6>=9J6=#Z)n+dUnjy3B4r6X+TnHA#4t%dCG0%4DGuc95l2aZLAi
zPmH4<ad<kKE@G-Ug|t|>RQfI-FEF?HJtBcDUz3-E9(J$(fq8Z*IWh7)8ZT2RlV?+X
z^7Nh=zxrOwnI>xLHY95jrhB8?6j7}9y)B{y$rqJ~`cuW*hxirzs`w&`<dVRg67WF~
zG`+%`@tZW%Xq#e613Auk-{pPQHXE|i#5n2)p^3d9UR_jVVg}TNaMNt+11}kLB}GL=
zeE;ZT9%53H?z2Ngxc4Ve2+R^e946zqq$w~-4!?%=Ib>8$56oMa9{bKS=02@Go<JfD
zZ0F_%3&0x?9a)drEUzAYPRzD+t?tTYU%h$cIz;zXz~8o8I6ftp_*1o$og+L6MX14x
z|77*(al)h8HD|4tBrkk%yT|fosp0v=S{ZW4mM^kvi*(Bv=R^3a>o>?TuO();m0wAn
z@>gM7m?}+Eq;_|y8=RZpZr&sRP_@!pyBT|4-Ex@!6m>l-nzobX?ETtt&y-kc`>Vay
z+58aKl&<~Zgi`l)(!%@Lb?vA6K&}-v0o2`@SknEC&#Mvd!+8Rf%eR*mpF6bGhlh`?
zH~CY0V$(;aR~&t@zdx#LEp8_HIEUQ&*u}_syBt>yks`bkQRx3mtLtg`W2$o4;b2EY
z*L{~HMaW4Rtd5SYi^taypY=tvp>&_uUM1p+NJRMzii_SPxyzk3j|3(9F@=)9^2+uk
zhA&-TaLp9Sc2h?Z$VwY<o|b%W-rMMCn(ROHqOAVO>94T6xppsznseL5p|?M}BB>$o
z%j&=BXCH`M*0#Jjm#eridtJ+NJbt>!aZyuM{;)EB*SqE!HdQ%#ZrSljmg>EW?frPb
z>2o#a)BniV+Pyh*4b`4hQ2J!{+OoDWO$}u2|DN}?qkG;WtZrpJWxYn*EV-9J?D=hL
zb=<;t+<!Z@+w9rr!TC0=ru9_%+LyJ#$!kw@AJK8i8sGr`c^zYoXKW;_6y)PiClc-8
z>-ZD+KXF;|9$N$)!4$wIGiCYd!l?nyR;Z4dmCd!)J5)Z|izU4Z=}rH)ma<7U>l=Na
zby4k`)wi7N!yS7VSeNnF+PyMMQu4o=+$~N^NUI1*O3+^wxA43;ofFAoBK9XU1u*m;
z;}(Xoc>nUq7&?||{?QlWnc&*Dn=+Evzb98uL{3V&vp|$FDkZVddnPKRblbjx2^$9c
zn^#6ysA1ZhN9=*_<mblYkw2&BZ*OR$Dfw|_7mYPpKCfgW=UtXJEw+!5hu*<k&U38C
zH@V*!zXVk(1bp}UiqiGeLu^CArOC$6n$?Kban818c)rLfH8<Pj;+-Nplv6Xq_5GRz
zVI|H{MY4|DOgCd|K1JfMoLuaPRuNY?+7xS1I7XB-i6^FLRt?qfX(+meEmUd^@P+ES
zRnzka$m=@vwnV>g{rTHKiQ9r|CWL6gH-i~7rBac`EQN<d);U+)IoEElkJ0`GtM%EE
zzS_<vm8o*1s%rV?%wARdboQF_etib<F?t!rJ1#SYk{yb<i(y=XJWh@EX{nmwj8sCk
zT7@Y2ZXe7O>DljyumKL}A_{klYi@pZJ&=b|a5lP{`77W=ts?6|!W$b+>#@D>!I$Vl
zNRp`(%eIST&{KGMMXOScPPW;5$mj2sDBht32vQCWB$>wi&PT8X7lI2D2KD*wBdNuo
zFEw9!@0?Pa;<j3^W?_2Gh9utSSfgk-j29gk1cb%=^$lXTz9cX$x7H4B&NzENm}P}m
z@U_+Zl~A`{oJjnYmEqo?mEn*Uy>(564LVxp`%3a_*|KW?rvCtv{D_-$%Jk1@)q#_S
z>$mA6nu1(KMn<Q1Q6EQGWdBkRT-;N&jTbW6vB6^{3fVUE{B<CW+@+o#rqNjWt?CT^
zq%2}kwFI&LwMBMju)x<)QgTq}{EFu~|0g)O5kEty_I3{@KlQG8ge|GfH9EUTP=sqV
zsr2nP6ZaLxOT5QVc{=}oEB%7W$*-a!!ln|Lk+OZaK-qrZutugg8ja^PvkF6P^o3QW
zdo&dR^^dYlTdC5nLSBhP<LkmCSQjZ<`3>mmO-%!1?cXwo2-ZxGUHmBU8wt1ZZr|i}
z+*Tnogfk!uZP{P&GuvUOB}Qhjr10@{c3TBBDQ&er^~5Rne%yw=i3u@DO%%rRJfGA3
zefuu;nht}nvFEt-(DP}ETH=16|EifOv2j;@`IvbX;}$<l;CmZCD2L{2W(L&6(WIws
ze(dmw9CZ7!sJvf{isUK;EkI@#GoTSZ7H?sDZEoXo*Gb^hy;<k1Jy$sAaJH<!{Tm;D
zD~PkeZ;O?)U@0=cgi>9@ulOF;NXcZhop)?Fgh950QH<4=)ZIz$tsqh!dq9Ar(lA|k
zm76nO;b~3#JRzo&Wn$MB(Je3UZRV7dP}g8`y0;0Cv>my;nbXTw9x_P2Wm^i}!d&xW
z^xYiiDaKi3Vp%1Clu<$)yy1^usbV6l^tq?8C(+Pb2G-d9ZQ<_c7+gNCk)r{7-N%cR
zN9=lBGGcPZSn*!JS4b6#0k^Gvr$70)G*B$?B(eG4VTq@TtW2$nDVyrNA(z2Fx8HrS
z*e%x37)>C%TfIPAUDMvyVlo@RAv2TO@~p0toN_#A<_U>`u$P{4bT3WZEsY}=UBV;g
zNTgO`WrEJ$Y0*ApcFSjUwu7Po_QtVu%APzW791D-(!;97;TY`K7c^~PI;x>x&*34k
zp3CjcvJEqZGkX(<>=54K>j5FuDiZ#*U5pg*jPZRJ+d~@Yqp}RFI)<hO;fgFl2@EJ|
z^Z1Fw`&%r7M(*u*hxEL^l<D;bqX$xhG7%c-A(Y8rQ3o}^Mp<uqo4MuqxX3v&LWeUX
zGmC-av;;rm0abXoamB4oP8b<$)B9<8upmF@D^+uafjV|`u~OM~KZdnK&!>bCVVW`-
zv|<_b0SqQ}EEE|vD8rztyvxg?ai@qu^&e~<4uNXzZoYc2D{SYjZyHXk>gThkoYeIe
zbC(XLths8jdAR!u=j_jMvwkDk<7H8Vhx{=|wI&pfohsUg4YbJq3LBVjU`9)`r0-cT
z-JTrYah}2m;-q~e6=^9kHfKhS%Mkn|KO(JPRg93Y6R&$}u|_ku8hWd_O$#RH2b{;E
zNe>=rs%>FYxBFJtXV1~&2rzyW9EqX)Q!LCfonNkvkCL&09pkc8#G;R-U)T<1MPWj_
z$o~XBKS_x(DN7IWvnfkU5s093N2I&i2R6l_0Q*9jii3xZgID2Q-#=>_lz`)`8DX=T
zX?+djxBZO*a->gMO3r_|wP)Tb#gJuaIpn<io=f*9cV=HT93zM2oTDbLR4aLW&Rsxd
z##Z;osc!qHGr?yjK^r^SX;(zYQxS@HQ?u^R)Mo6Dy;asJ4ah6f4*X#W%P~>Avh!v$
z7H5wQFTOT=h~1ypQa!_r79@13aQP;!CEOiw``M${13w$!DvirH?Ytc7$g)vlqZgFq
z!ZHj>E`L;^P%isa@3Px6d-mX|u2+EP=B6OLP&<y6Al@sc5grW|UwSlbC?z<?*aM3V
zlCc+BBX%K;KeDEzOBhv)x5wwt+3ztwUbWB}AR^yQP{d7rasH%4u2xH_>bM<>^;b4h
z36K5@hg#3CYo35^uBDh(wW<pzr<D~1L1-r(p*fbLvXFR*%rt}jS{xoKBlnW64-Yy?
zs>Dbh%k6yT^N2_v>^J=tAp&EdLsKgZlNXCNMC$cpMwa6H9E=^%6VBi5Xl6=}N@{b;
zg~W*{K!oPz?z?IiP4F|1pjkCrCppl{HEfOBwm7BoaMO41H-k`WJt$8UT}XgIAlpKc
zh$Pj6s5zA?F@xE+SSGO_E%sb3gC=%}Joj+QK^q=cMW$K{PKkg+tJ*zmR5;6OG<WK#
zs%|1@<!Fn8H$ydRJPO)3nj%<K=Y&N^Dso4^bw5zFBEGX4Zm`aiaTS)eZh)xCSH?N_
zPC25c4N*{k0W#4#n%<-zfs9L8X8h|F#T+cSvh+-`%45U;Bm+bQh@S0qQ!|;PG70Bu
z@tky%1NDUBd+Z)bbZVm`FPfhuk(uGyN!0V(uq|Aje72v`yiGo`E)?!HGC$Lm+W3{O
zkb2}u5fWFpBu${vqM`DMf!B{1Jq7m;YvSyojNO_DD{jKc!vMJ>7uICm6O|AG`D_yr
z33@gIUQ0JC^0aE_IwW7ll#meiZEEiFj5%p+tn51YpX>_Xb4u>cFH`1HV`Clee*SZC
zl7o)^248`3$IPN!c@AsC56^-t-w>Bq3D`GcDTtamdEM!P{xsIfpo03LOF5aBH}PqG
zrYQr%6Ln*UgPk`@%A}Rwr1f_dQ{3(A#b?RPEHm(otyT>UD;#d=;m^|(nP+0S8_+xB
z`~FJ0hFl(Nl{IMzGm5_9E6pMg7Ha1>pN(5>jVInD?ET@pZe@`^R4()KTz;wj)kdD#
zN*1HfE?2*APCWbM=6o}{L%V5Evcr!cDE+IlM!y<|7VeU>m#?t#5d@ucgB&8Mj6P~r
z2c~a4IFA4K=DI6J)2`_3^^W$nAJXyqyjm7{&H8ri7v}6`q9~&?r!rZ8#!o-9%5)6%
zm0L~^6QQUE7^T2SJD(!|-G%8~X|Bh7igRcbr(8Howeqm0tF>i}D^_3$#T}E)J(j2Q
zoX72E2MJb_cE}pnId))f4mFj@6j?ljE~+9!T(!yDR^`-etNGy_$!^BpR4y^TPr)X`
zRoW@7HgEMyIZ<39ZAa1#mPeyz6Q*Qzi=`QoXg7r4VvUG15(H!$^YYNGgIh84Q<j&O
z_`hQT16-@24;Z@VJvgw;921^WRhsPS4Iv^kF^&d@_8~<0P2yL5imWW7v!Bu82i`$A
zZ7SZ4_b`<SvenTaQ^q3Si&0bHce5i3W`9gbO~^Mj3E6ZTUpCn-3SH0+S<tq)dR^-I
za||-X;;*fmZCWI?EE)IODJjx1m?32GW@O03z^UznI{LqS@W01R&(0_j#$v<WPiH(}
ziXw<|xE~-{<zg{lFO5~=2<G_maX9_$yV=NAx1GFiBy1NQ<!DHEwb&ZRn|cb%ag@Wk
zMR=s1Ac$b$jc_T%NKPmPvwub|f_v{H`Tu`Mr0ew82Fv+Yw7h6{cUDX5K-pIYn}mCZ
zW0U26@>qt#i<)q)9r8AdF&^ZBg1Ow2Iv8VdiY;;?vOgQ)et8Zb3o5$7S^WtAd)7>k
z?a$ma+#zZEUGq`L+|~%tV?(?3dhlO;vi^E4hjrm^31#jWU6nCDS*fi+N{y05%|`4m
zh(Qa8*7TdBzt*7mJWJS)?!r=%A`isY45Ti(<u1iW`hlN_|L;3<hlDl`#<<r$EFV8x
z1WVuQ173Q69!9f2BT+08>^l((%urcTrYcmwPzAzDvm(q7rbpNuv_cAFyfM#qMp<x`
z1I;ZWOncS)b$dZ{8Nc}K*o5!w#c8$#>SIEwl$}I+<ei*y6d0@LOGIRAic>`#Qb)pd
zx|G8UD=2*-eA%UM7M2Vb7Ji~!EnIM25n<3@oNpm=+=*der{>1aSULFl6qaL~5RX+2
zLnN9S1{dDWiV%TsT0PJvKH!u!!ZqgzO`Wdyy%oSEl4$n84i#0csbUF}C>5Nc_+mYm
zTwOX}a{tqHr^=2v%XHjiWW}&+DHnqiY?S5st`N`Ve&Se$oN&kwu0#W$QD9T$2P{|%
zO5)}ix0%z*OqncH`Yo}(nj*<e$WJM@5tGLw*=!?V8`km`Iv5Vdkpv4h=X8O)?>gn)
zANjZZ@0TyHRuc;U6N_Kg`r;pFyRMC)L1>Kpk^jWF_`EqV4udinth+Y}^UcYZH;JoZ
z0qB@=q*=MiJj94`?I8^Ye}Px<_oYIWo*^t;FjkIB)yOs8#$+3EQ;2?QP{D^rlVI!a
z+8gFrhT?+<29?}l9|B%#6ufsx=Z=xosce)Riw`>K{lIQLu@lBJ#Dp`T!l@`Q_y-na
zCx?pmP(;sIg?dCXlnN`1A@w3@j1c8%s+U9-n5&0I5}~5z;NG?K1glFLVogPHKg}0n
zU8&n2&~T+K@0E|kdw{Ft6d)kKIVa+aLCKdERuUntG^5<pfb|HJ9nUjOd?PW?AE!cF
zof<)gI!!)4aj9!a8Di{@;?5q^2dn{0L+AA>Y{TPWtsj1x_eXkI=*{oylBhZQC7d64
zgjDN_&3aRQ4L152DU8=_*L_NrKRwjM9!RE$oIlg*=GvZJDEX0}YOH+O&-*Ce3t=CO
zbAM;gKLubTEt(rPb^F8GE_};T^yhxOr$eOP0aw-FpTs2<<^wOV3BH*<s&JB`k*$g0
ze!A=O%ns}^LFFl!p^^ERd!d0G=HH{6(Gije;lZ<f9`A{GCU4`Q%o1v4&qm?AB0`{t
z&%FBk?~Qt%NPOt|w{hZywxSZf`#V~%F>arimEpV{FRXQ`GS{W*l3YEl35gRkWZD~E
zcnMhP9a}nN`7WXrkr4(nF`qa{5|MJkV}l~I5q{U5zzUM&<`6*?7~0V=b=u0b4K)<3
z^7^;63y~OAI3=;KwGZf7dy22v*6cJuE%Bk^xh}>*(8CkL@4Y8_g9vV!p9HxG^C=Hn
zKw(UQ(V<nBv!{$_)N)5D{t7qchq;F`csguOcSF~=O|v?G&9pGih_b%Ghs20CJ>r8|
zeK<mFP8!Y!-`A5Oq@X{`2mC2s{^Xbf^YSoVDbEz9JhB;cvLp*m(Pev{bVzWa@d$MK
zDkHU%y6inpGesH6poKhgKK`y-z1VY1ueOw4VtM&{rIu1}DLtRiqPqn1P}T(ZBA4~z
zn#a(d(LiN(Z+QKoUGZB)YbHl4-kK<%QzN*jB(0>TS*^cQv)4bSSczh|ce0i3&(@ao
zxYN0Vb0?xw1zfkaalKuG`oz#+nNk>fM;I%UWUHbxHuEQ8lp|HyU%4mGxI7n|1<0K;
zuL^#8%4#?^G)^}~;JC|q{Ez7u|KArz5<d|siyrb5?aI!@jpB@mfc)a#ed}G=C?~kB
zs!e9m{E^2Ux_iM$?_hr1uf>`1v9e(KJKgJ3BMD+W;*>SRJ;a0&1V!Dn`|+7n$3A*5
zz<S)-|0XX#1aG2oMsI6oQsOTYiu9t&w2(__fPHsv&8VVJ9QBF_or{gqt)`P7Z%nu=
zs<f++&EwUk@Hdh-s>_fz+m{6XgVLtqQ%xG^)k?-JIP981nlz-;vKcB3qmLs)+9x#C
z2ebA>QEpj}oXbPzckYtrZq|R;x9Mlswv258<C?H!cg?Dl-+$NL`?W*9^TOrT@Wf6M
zZUoP@HX8MQxqr9j25xp4QjJrJc-NZGAp}3~@bqTvwPFR+(}!)D%x2q&G6d(+M3(pO
zD))*wWk^gJr!%Jku<0W7PUnUM^stbEZMYn@v@@8vIDVlq<b?~<WyrmRiu#q#<=<o;
za-^8{CUF{(xV(L~IjujeOk9A_5X`log3Fk|T!B-X(CC+C07ke~jAAXqX8o+D*PT-!
z%X=F*L}1fewYB-7f5ap6!HbRVvbb7qqeuP}MmD1049tz0ppo<d`*p+31zAM_e^1u-
zK?gj@suR|I|J$(JB_wFFa#$nPkR;eXf_rV$UL>|}rDe@p%SV;(d}A|r(&B7$LVu2T
zpl~{M@k%|*XbMDmZ^JK-yaCWL18PQWOra@y5w=LEhs)U5i-0gAQE=XmLk~nPBu)rM
zlHj}`&JF~Qw5%;@@5pe|6=$zd<6&Ur>76WsyqXON=q1TufU7OF*{b*!r1i}51nk7k
z?Q$P*7g<=l>ZZP-8uN25ydn0#P-4ROAiS`>g96tIPU_A#-`K8u26gY)!cj4kl`*>0
zcKNH|b9DY&sqm@)b;cYHh9oQFoe?L{L|w=m-rEYdnokP{V~xjUHT!k&PAj2^$-rC}
zL3#V}d<wU{v$nZXy=MzsD@1eJ$N!Pn7v|N<K2U*!-2d~F=P(sPXg2%PFbR0TU{{QY
zjg)%&Jo{~b-u*68-uy4}__qhaDsrh4Tj)0`CM%JTR>Th}qJT0P1&`Bnw!M>p<`u1z
z@bSWa-`@)?3sSSVB-oEu_jm=zR3MJb9*4m@c%O6_r@zPSL=;8a(RDk!wrgseK)sTm
zr@<F%I-ZYr6$4JG{_+#kyCaZvXYLy{@OEIw4m3BggvLWdnVbctLYtBDfD2Gyy+|J%
z`C_5+ML8okQzT)aYVr6RGO>mWtA=Ys<E$3eP8;0~s~y<6?SKukP+W5~eXp_gC-YHh
zy2jJ;!n$3Zqrq073gzZLE+MOGeoep2^5W}0NoAt!nS;FnN$m}Bl1alT*sz|<t*K6L
zZnz-q#Yu=SGy}nVvq?|~3pK8oA+0#)LjP^;zUzHyMAUteyYslesVgdkUQzl^!sa`A
zw8&G-H5a0IBn+;w)(+>8)3S~zemicifw^AYF6Fo}t0CK(ZL5o^2eaj)@~Zs?iw7M;
zEaLp1`o<uvAa|Tf9~yJ4_`(;=kLl(`u!-wV-b`$-?6cV13EU&~ipeZwobhx2x1Ww{
zYpKsvN-k(pEGH<awzq8Rm)OfEw!bz>{_HFIpqK?I?t+N<->a8+uHl*Euu!>MoVPSq
zIn06R$-{>dI%)0|{fwg<Hk2Vk=Nc=~;u0-f@QM5w+-r4=*<{I?<~<3MOGKy!|I*(L
z*}TvH)?e)Zt-qh~wZ3$~i$2rDBjM=A5m<S4Be3!PHT6NG=e!FiQDShbvP);EaauoJ
z`P2+zgQv8fQ^&T3;pPSr)YCN;cX<jw>E?xDb`a>A2hlV>)p}=!9j86*^g;o@Z-dJn
zYh=>VEpBr?SM*4$n$Ah?F!j{O)Dh|pO>`~`_OE?;%kZo1`6KWjPkVMZw_jaDR2qH|
zK&20iom+0%PM&GeaN$4^>GHzb962`C^wVQwxY-^OmD;?g=X~Ji5t?voxp-ITz$Dgw
zl1CKFpyi#E#WH$%`S8K!O3hvnfn1i6B1ogOt7=!QlVZqW$}$%=K`wO;>V!M()%a!Z
z-f#yOYh>|S3wbD+z}ou{@X~A^rFnsB5-^W()?Gvr%kEu8-{C5Inj3mf*Pa|%+t6h?
z!cg2L3QqX7jR^T&|L~^i#x>6wE)<_%SIsfpG9HC=4a|9AlEf0iYuv^yFF02Y5YWHI
z%T$VxA8qx#RY*TNJwub}5aQZXxLx#|ZWUFnyPKWXO7EAwRNXleDqjnGf8ZU)r{@(V
zr^%*%V7uP?*82#hd!p#ad{;JMzXfak*W8fDu?26`v$pG74JTIc9prvHk`lfchCBa0
zf$;6eLjnizP@@jA$WE^M`yxCyCpg{&8nxkYmNhy9qZ%_~CA(vK2kzWfWi)2$xHd-x
zq})GZ{|Aeq6pIwz{KWMnDM4cN5HkdlD79}=%edU^e0u^S0$3&`aJB`+ShhoI%UCiB
zDZi+;Ax)~Gs`(U=2ZICG{u(}_vptrUv0w8@)uMH0ht&kKnrBx(cajp}H*NT`yZ>4n
z>q;vykB{K~Kr1C%hj47rANHQLjcl%2O8a2dbjJFqX-wihJemxNj#mShk|7q#=kq*$
zFdAd?%@{)Cs@CVk*q#?ol^XGZe!TgY6)6&<^nRm-g>A!KvY}Bj&{<O;bW5avhDA<V
zI7o={g@_EFn*yN)-?lHp%ad<i(iKKV!M%q|qU&@V)&uI~W%(neiJ}dj69)*sc20<Z
z70hex4>Cv&YV>ODdv9RXkw00I`y~x4&+ur><cfyDiPXJnEa60PQ~ZDq<Uhg2;bh7*
zGng4{fji+b(!!#A@F16AbJ*X^hDos6KGwQpLCpyNsyJQa`pg|Hl-^&6awBFmqxi`R
zMEgq=-?r8NUJw6Pc+xjpKM`+b{~ZCWx&Fk$x~6MN>B`Q}C)UVc%J098GjJ!yCU3h5
z+e`D^oKTIe9JZQMa@M3^KlkSsnTgFMC1a9HVoT0E-w>Y+y}%f=+eNTy9N60BHAu2K
zjia$xNdGLR5X9U5*mp(5W|7Tg$HgY!INu(@ZwE{hHWz~7Uj1nxe9~eVh(5q>l&0PT
z>=%t0!{J(}m4%rfjd&9<xUKUYV+mO^G$o>MwPdiVc39FVTS9a8md%n;B-}kk>rQa|
zRtdl6;9Z44!IWdo;3nLkT&K(q6PXZ4<s3Y6-ElA2kHg^|{4-HY+WT~lr5%~<=TH&H
zP9klGHJ>2YyvQ&10_bEqg5nu~b5IzwuV9ZVPaR;PaHcBw`4jg|adz@QxY}Vm95?iR
zp#+~p(~911mhR&%^Qk@Ei9ZplRZlmF^HXJ{F9>H~9wF@SexF1o8lDMmu%i+C*gg7z
zbo0K^J;KNPl5hQpSV$HC5{lzY$`QiQOe%Ovn0bk$67ETI<a;&y4Y8yBkI;Ga=2)u~
z83uo-jE>IN@7Vu^xBB~!p1+&}M9hrzDj6U%N-Rxd(lb9-F7U?&%tmQH<n+b12(a1R
z;6l9teh(y1s5xh)MwRC~RciQ-l`efz@9A98?>l?No_Zd>J-Wb@2<Cr9FHRvH^spf*
zx`EQLJ+$$2nJ?UTJ^f}KzTNc~?LapzHgng*H9)1|MHn|UskxzPSz|kE<xa_03=ugf
z*>7?={41Qp283)nwC?lxiV}^A|8GS&UHYtC(|CLfoJ<!(teXA$yTZA4nHAd!SmcdG
zd1jCe#x+^=Lg}os<bYM`GB4N8H%exCf{t^7{^Qd?5m})l04(wq%pO-jk}%h&SBOED
zU$%s0YVuNM|D%_mKV@K=Jt1vpWYB`~z;6v`H}?)BlRi%f`@n#h7nomX*DyYfdrH2A
zr*Q9WLkbCr+p1v_knqVioNspb)NL}GLwU`%(H0zIn_W0Q4x*(0qIz0guH5L62)eP^
z+w6HOyXVl<(p|pF>C<@C74yqk-RXT$hq_l52)%#{j1gxn87SlFtvZ4LW<a$DW;5D*
z??U2{GfmeL6$2URG6{#EdUIBzUj`%&x%E+js=BClz#Q^5J&3*Ebte*!N+Z>!qdRlC
z#x*hx$;|{XP^}+thq?B;scnRwl}_tn+vxW0UB*7WJu9EsL_e9}Cf#OMF(wE(!q}@^
z)o5Tz+(X!!OP`8f2KtMeL2}~e5=*Z<dO{hmSt2__p}1n!!~~YRU4Bb<ht>-cfwhi_
zC8AmGM>L@c_ohbvo_-L0DEJd5#sVNERB2bzj1no)q<`dv6Ru;3zMk%^!)t@jgq0~U
zpSz?e>))DZ`@hBC-LEk3BRxEZz1uY1BtyNoX^Zmy!#kmg<hs7%)DHzm*zO|*KX=E`
z0N~{Z1<lca{t-MKo4xU?IK~DOvp4{UbXgiwLy{89DU2ENR!jZ$_GRD3i1?^|u#6r5
z`Isg+IaGFr#({`!<fn?kVhL#^_Dr{O+_Qp$Smco1Iy)?6<a<7N^ABwTU%sU|)5C=5
z;Wd5^A~Kb2aBp(*t&ZVC#So-1qI0%!EOtzbN}HR9<!qrVg$;nI8TMD%u`-DC&CF-)
z=a~)&tT2a0t|AN<62zMLr~`s^)A5~}S?2@qw0tP&M4N5LDo4j{UXGYF?@t)h&!1`*
z7X_kD%R9zE_WAw;kHBWSSCw13ea-N|@+Wt&uxc34@I)vmf(0y0{ZTxego4VmyAno`
zfn%m_%a2il%f@oL>-;Mw;TU>$o|?%`(>9*7;d(dmmt1?F2KhutTG`*1jyckVoMN8?
zWEmfLq;!Wq^)_=lSibXTBnv0@WzWXDu_um_=@1z@oq%ojn>_f=9~houVtT|-UE)>b
zdmm>!va(rUBhY0FU=#=t(xwcBU)G(^QDAW}zHgZOf<q6|ujU*ndZ)cW_^@X<<{U<Y
zgyNKZo-wF*osAkqUveLDYntUP+^n7K#lmY;;!0vbUST*^u?Y)X4}jB0*PxX!oO_yU
zw!51_xuzLCF%?wrx(n<$Rni4WV!xcdy--#Ms~e#t-M#7!mXzue02-&xYsur{Q|lBJ
zl`uMN26(uP({#%$I|o^z-)w#dR@g}hL#C)z$?JzjOK;O3Zub#<4tOIhl>T6h(7ySz
z)Tf?B`h_b^tNVfbrk&e6_vd%+v^9m<n8Z!<5@d*+22uQh=7Rs;spGwoXYmd4ma4@%
zyENGim1t)8R|l?^NMVP(22O{QYr!B9Ge4z!ET<fvFGC7wz7j31d6rz^LW|xA&P%&V
zGgc+0F#$*0nWI7~6zZWr?h%d7B*Og&;lT<YDJ(zKKA@Ql;|34RCc!=D%UIJB_mm5q
z7RxUd$8jsV;-@`GFR*F|Y`p(e*9=rE^+j-Fdn3#JLkX%JPS#mj{}nq&F5NK_|9Ov#
z=`9gno9&4xZeB~Bf0^<_3|BMx9AwQINX-OoLbp;RM$sY_Si+<=(WV88*V+Ia!X@tC
zEmPTZe*>48!6|?nJ7rZOY9LSL^d*U(lJrM7`&v`y@e60pa#L6h6>4?rh?QwNo1__g
zM%Iq83n!AwO^Q9{P;%g!>6E2?OULNU2{MkZ<2cq5j+1A^fTf14aUpzd*|+{*!q33x
zOJyv9fcUsEoe(JjfTm8S;WhW}-p)rXRH8p}Ggp-6%^!5?pWqdH0X#Q(ws^-luOR->
zq#K~T5v#B$ssInSUjNR~_{IZlQb-<NE8U#?H*ZybQ`DSTy<mb6xmATDDE|NfRWVS<
zxu&ECfOFI~UhBaUy-EN#DswifeKIgrj+|vcWNyhB%B|@HFu3+9-RV9d*s=N8#w=j~
zegK)EnS*1vmI<)>5Bv}<NpA9zjr(=xK|D6sY8v*j6%_)w6L5GQF<p%srnC56iZZpk
z%JNosc(W_CoCcGmIs#v85;)?rc5qN^bK!}QU5wa~?AyKKC?fm!u_SNfqfY!0eK+Z<
z-ae0$7A_PGW?Tb=S9k1-O`?m}ioj;yTae~tvCxep=zxcfvon=GEORNiF>g+A(i7o%
zpvz_NNOd5@a-o2Rh9)}qiIP-=hs{onfHx;x-Q{pkut!x!mpWrp**j1TGNYn_7%IQ<
zP&e*y1?>+zHcV(+|Bm1zI>`O-yc%4&_#{)dr&mwNN8AWg5V;c4Hu5*^fookncivJ>
z0eRKR5~v4?`R0OT;FCCR&dCP6ioc+H60EOG1Hiq-P>?`~AwT~AXgUj^Dz~?bUjYS?
zQo0)sh;*mKp}PbLrID0wke2T5E@^2Hq&uagIdpUA(r<I`|C_lpcgDG)yyxBfdDi-^
zb=ZOUkC-9doRmj|+=T)*W!eg-cR*zQ$5=f~+asJuw&(^v_uBY)H&TcuoEm{p^-4hc
z<Mb!2{;!bF*WaBGp(x80=}%L*&4JkL=9xLxQuVJO3DDyKFq;2;7!ldVj|j7J9f^_8
zp>S=urJ{GJm64Jh=~c&`4e^6_1dHmS!4WUes^eSr_<}|H^(>w(-PzxfB}q%3izi_s
zFF{?zC|s+nI$i`C-5<_ZS`UdVEYLa}-^E8DK!y6M4`_}xKLB4qaRW0QC2eu9lGY~U
zU?az|{Saf(!lxCkW+SlQ!kje4E<dmF=jZ8)ac8MAhg>q^yIpU{4xxQ&&q~_gXHJzp
z$Rn>kT^^EjtyZXh7koc}&2WK@kT)jHK$yDU64O~;2o1Pz+hW^z`^$K1%n{Dr+4CJ~
z2^{yA=SkT38Kwrp*{!x;3sS>h^S5(dFt?4bW$cA{`iy5o!u?eU?^R$DWLe)UPFZXp
zo|f5o%^Hbx1C`eL9$j(U)UC}iwKel6!G_e)#gbflh96s*v<6=CP<RwklxvLA(6N18
zgM`eO+ITJICcFEL`Lm@METjSdzj8gWbcW%>{ni``R@@9AJjJjMrg_bTAgf@>J)nDA
z?vXA-verl7DMEoXY7;=o_HPwF?M^EfL^XSH)~d-rkkqIDTjR5T_w)B$sP_*ywkODP
zK0PDL7L(`#j!nPy3U^(A55w&2gBFh%y#6Sxnib|g-Wn<OWtfYjsoEPrA6|2}O(^r9
zwY||3wp__>h$09Z6FBYAxGO3XF&mjjctw9=Wg70|x!1rz>}H=@w@;u*M~wET_g71+
zI&W{!<s0A(#J(i2tDuT`luY2MUfBsmz;Mq}QWa&R1&1RaZDMR8%&?e|?`*gAlhsop
zaC@)d!as0@hU<VaDf6SSz|TevN#cNmV`NGsMi;V7APqW-g;!}{hX{@b%kaQ=F=~eH
z^=gQ5DZx~@rfy?;PH_zx{c?C$nCF|?NNE2)oDs)rnx@hWvNNCWu|?U433ljr&0(DP
z+={M$yVk~2T<Jvm#GFH$hLN5M-HqGGn5=dTV#?+!ZJNfJ3dQu5|M?xM2xWnPLMQqT
z<`dzoYd^#F)G%-h!rWa_KI^CjdraU);D_}A1<$Ov0+<PR%mWIk@iZnK&AE0=90Mty
z{^g>1Sq9$oDqu-X15@PH?EHBub;E`t1O<$tz+O!XeK9-_3&&&^yxQ*|jeLiTs}UV;
z_pIXeG?}N*&zWJ--RoL<)I)G%Uhy^E=7eEm*rQ*~U944mCU0Sn0T-!%UmKi^eeBrA
z>JDS_5|rKIN~?kj5R~3ws-m;njqk%1Hrs346*;PGXE+xm+9QSd{N4S=_HQsg=l!EF
z<xDEsrMqgNnB(_WjT7jg2V~kQsky4-wRy~=YuR$H0z1e2gmL!4iaS+oJMV>uUse!3
zr7IsSt{(9pEfGVBw#Q;o&9=ZXzqaPj@yCC9E*7j%8B$UF@7xHV`+wV6mY`49)=H)R
zjlJn6um~eL?=K;X<gsQOwKse})I9=OX7%YBr08b72}9Lz&sNDRbPS@LDnsz^TDE>O
zh^@V|V5yDHK)|RUHowjmv`HXr7;No7Mf5m6M3dV9Sitq@Z;$UTyPV%p0IGWv5z^q=
z)YuWA;dbyavP-DX{AN6gB-A}IVZn*Yt-S+}`qa2Tc;q#bU3bZ%{N&3swi)sv0v1$o
z<V8fK&N|~_<027GZ!{GB=ms}xs<!)v6H#cdr!xX2Qk-Vs-=s6-#^njrP*qtl!1i4z
zHIDyq`!G9mh=P=w3wH*>M&cOUbo0R1lo&OJ7oUS(0Oy~7@-t*4MAgq^O~=xIYzKy$
zF4K0(F*E^5p>km$|0|A5Z|+=+(dk)0`Fo(n*fH{eiC_=>m~yD4k+zzKdBL^N^E;U1
z9ifC(d^lJgK1ClAN2Z5nWQ&-O*Xj&7u&>QNzhl*E=Q8(<o0l>o*Wv0frXw85$L96#
z|4Nf|W;Zr4Ch*!Oqio3pm})+(Ar4eLJx!guRFg+}Inh`MYSRPzgpu2HAuX|rI}|bJ
zx!onHQ|vh8)uO78L`3v|dYzl%X=k)Z+vgN~x?WxtFaD=Jhrl$Pl`8^%3lyA3y{aSh
zZ8CSAA)d`S4(|{n4$Z}A^WNi}4`-5UW|@i+R<Ch2P3UaOx_mm%c3|PSB(RNFs*O&|
zb^Ma?ozjj0@0>|w?mD@7<+sX4EITl2oYZqpB6bwepgv4ylZh*9?`;D$$6G2zJDj&_
zv4_p*_!2V&tC*TnwY!xaM>ovaa3W~U&fYG&h`8Fl<=BD$nK7AJ>_to><&g7qJHTBo
zY3&!YK|SPylzUAA3#k=CQS|$q8qAWq$K@D*1l9xZ*?`&XkaD`68-HWa{|S!;FG^)m
zif-fVONIHcX)gouQ+cQd<aAEi(LOby(G5ANm;&R}P^8IJXtg{jrLcp-er-)T(9iju
zcAc?niafMuiO`hBHY=N?VNhPUb0eJ*XV9HYr##AgON!Fc275b``REZqiV|al0G%O!
z(VtwB*WfJ{w7a@BPNV=OG?5E6-^D+gBJ#687DL=7ng&!2*FH#;hE|1S>dZ?Wn)5Lg
zh4QP>Kq4%g0X4BAr;M>W-s&PQt0Xk`n~tm@!$2BcVrD$ujf%t==GXNN$qxw4x#2Sm
z0TkgzixeMgw?BU}!j_ww+qwKl88@&d<Li5+sgYK{4$U`U2jxwa8BEW@&E@Tk>eM5z
z#{uiQNi_A<LE<9%)1Ky)TtY_|T}e@8Hh8NtujG6`x$9f+`TjiAK=3dk9x|RnKTg?#
z$Gsbf5n7Rby3^N&-^6q|Ye#kLOBe(;Ul=0WgfIo0rxrV}b<_m<5}+sUVx*>yYqq$-
zhNqXr5l>SKl0pczDQt|AYyI`$`wfcbfo{iD%XvFm=TBxpLhBbRPZUp38dN}&5f{8v
zn}F;%?nMUFe7myn2R?>bd5N6-vWDB}Su736&ehlG)9mUQ{jb*AarP%l@~@tpX2<Hd
zC801#9T%W%I&9>5IlAY>andX}w*e0s9~l@^-Qw~T-|v}o!X-OTPTHDt;u5of(@ui&
z-#%=QIZKTGXYaSdXr=AAy-<EU4pW@P%ocgu9kkaW<n=minv2=m3ZA#$aMBsAB|92E
z&8yFF>Z0$FGNK=qpcyQ3dq9PKL-KdN#rDbgnb#j%p9`ZxRJR|Fo|)Lw?ABwj_S+-O
z<bJc1!R@BTYMH*XPkhXOPY!vm6O0_@nn%qniSH-O@U@Q}cafjy6R^Kyv~N{iKmKva
zo>*ABcyy99TXD9#$DdVEQ9F6`+4}YK%S`5t8<zG<6SRxnSM{jwkvGFg?Hp$bh}cGv
zp=<s#HUaFN5r|@h*wk*C<R$JoL%<F0A6eduY{#crGQh8y@@%?g407jfAP6cwQ@ns4
zY)$KBIEa$eY`R<*yCvX<y^uegkXRM{)}r7&!>e@nB$ue83^YnP9n>K^+k4}HH+j1H
z9mAeBSPb~aue`C|@rR|`u5>&XTG#7F_Fa|t&U_b2f3144>19S+co0#tBmW!sPv47`
zM?o3x9}xw(6`;FKYHzr^5GqU%G{_GBHfmK)-j0BO>K&eRVA&%I9gWv;+p55g3Z+vA
zhF6o+=f<djR_mk;2?Ecm6=f8#52Jbqd2i6oRs$*Yyc!4QYcduqQFRdDl`4uKBF}DJ
zH(V@kKX_z?PG?^q_T{h5ZXaa52=h>q%sG778w1lsp2d-Dr%?$E!}Bb=+Cq;b3|T!%
z(%1}7^58bFcDZsDla(H|(av16Btg$PVwR4Mf(?&OtA{5B6eT}?(TY>sqHccYa_8<z
zOuVZ~0QpjrUECLZNoxFDnt|8$UC|VwqA1JhDUt|^Sgbls+2}|e@436uYSqpKvnV1@
z^S%~nrj5;TpLBlxW}y0AUY~%xYm#%hrLEhlq`xwg7vt>&yA;MyQONu-!HXsa`Dxd!
z!7DUqpK8QX*I@xoD79wBGs0=(MNj9&q>c`+*QbVAX>HSbOChDo$<=`LTK9@f_7_9r
zpH|e?upzd@)SU@KoN0Z7m%A(Ve)dH48}X&K6On66ysM=cZKVl>P-c70f7#YI+cX}S
zoAOZluU$etU;IB#S=#Ss*0gx21gtvRBnBSf>``((xfNu$D9+s>8InH<9Mra&29o(B
zVOF?8mG}~TU+2|t8T<oY@UN<I!-q|J2|47#wV{LV-XBsd$6lcVjY)(Dq5kbh$Zzo$
zY;u<jm}yAiiis1e9iUq*mv9Xk$dmQvqXccPW<DW5#OSc)Y0EEYplK+LVS8W=qOhPI
zrxv4`AR*KJL+5wwPbc<hfnLh}@5~jSvg2#79|b?ZUb#3JQ~XdK@kc1iBCB!P@#nVc
zo)O77pYx*yoNwI>rysnokeTWPzBx7v4(3HtAte@`j&Kw~e!GzT)0GC_70ax)dZwWA
z5`l{0#^>*SlIIniYmv2E8P{SSZ905p_kDuT#ZUTl(#lhh%C`HtzD-uXn2dFKZ#)gi
z*kV^u$&Rsx<?LZ1P3NzXWyZo>4x7ZRru$-o5aJtfKaH>C)N;`Ht)C9#U~AqeLoGER
z!^RfzEtt**ZYmw2YChl6i$9L1IL<G%{Q~z>@3&X9)Gp@e;ufYc;6&CO5yj~|T1q5O
zT5B>LSy-2}HNg~BdE6-#w@fjtJ%q>5($2u~%7Pbp7Az;S3g-Uu>@?Tm{Cr}5plJ2{
zdDgy4Rc`?oTO)XMIA!g8t%L{0h*6iuCf&?<a45%d51WqQZKRY)&AH^e#%XU^jb_cC
zdI?*v{6i5=4VDK9HFY3yIj0K}ItTyBcglFv&T;FeU(1)7alaT}B7z~B9?xT&bk|)k
zLXPh{msddr-Yt{A|C=3!TG_dN`rKSpem1Ec?YU66_3oHICED)ob2TtT<3Z83s?+}D
z(zrag-u`D9lT{t}`M2)^#%QEGC}hf-Oj4NsSE@s%d>}hDe&l0~)u*ewvWh%w^Qv3s
z=361;-rg?7J9>jr*ivjdnj_FnpNUB@ZnFco_H8&=;?nyURKA25cl&5P%xBA420bs6
zUn8`DRBdr<IRbOoXO^8op&0CGLYi);-pa}Z9CGmyB+a=mdnY2JBp>=W?OkG6o>mG@
zx>FI>uK)UE;{jO?NjE(+T;nYeKT1rQjt!r%Tr%N)n8_&zn^If9(bAIPv^7?3ZFcf3
zyZQ)~!<g3AZmqN=2fzs01+E@p3EZO5o>A+>baY`G{k{;vR^ER)!aM<mX;;?Xdo?4n
zS~n>Jp6T_)DNp3$W}^LP5+~+DDx4q6d|^2|_uo$m^>J2vo~(TM`-RrbA4p3;e8Z(y
z5*=HE3M+2d<#>hdw`u%n`SV9wnG-hy29g?lH+Tt%Hoq<e*+W(4owYsM979vJNfvno
zmwCa6Ipv(dR(tJA4Di|5|DR%{CTe&EH1j6*VSz98#>~p6pt8Iw<rGLRPZM6mEbhGc
zSg1u|n*tsX6r~eF7iyI2ilxd-Ta84Iatga6|AnqVE8u$QOf!Be$nD`}!=<Cn&K*>U
zzN{44Eitgvkg7_jha0@UIYr0Kh{6fYD>loTkIV?ljZ;yOb;l4v-3fTOON{AgZU`(O
zl3~`{K$oZ%OjXXhjqP?GFWS8NYJA?Y#bH9Nq*;sU<pEAdfD1z9WE-5Zw!3(9aUD-#
zs};Tf+(D^6Aq(Al@RB$|0cysIIpD@|Ke`8yw*J~;GAl_~TL60@_PHGurVoYcp@e2_
zaSF61)oHaUhQTEd6<0$e<@;;(T)=RKQQ-hyjWsg%*laux`|=d_1;m!4boca$<=DQi
zC&$e*6do`>rREzWlcW(HT(kQ%Ya=>|WZ78(D6N4|og&h6^J~)KKhO9^B&irMbIDpE
z9U+3u^|sYJRy9X9lraRMqq?T);J^oBtkAmy#HTTfh^Uge>&Y6X!W^TI`;To!&JI`^
z2rt$+_#O|wBijE^&!e9+TxeWFE8Z8hh77yz!hhG>Ft2TWZeRTP&N^l++$YaA=E^*z
zThjj*ZuueCSQ{nwmGM6sC`6H6k_}R0m^;YA(T?xXa>1PxobKk6-TH-8&)opW!Okl#
zO-G^m$C!xc9lE0CYeyk+k??EBi%h|$pIyP^w0t^Os1Zspfd2({(eDQw#8s6PRbYpZ
zEqa7T=*ukyn74bLB(;R;wzUpFiXi<8XXFZPay<}b??FA{GQ|uNGk;RYmY1Pe@+lg!
zw`<2?1jfai(`W`H>&L68=*H4r$E!VmsLKIp3HF`x)t?wpIj-cf@HnB3U=DGhlrYXM
z6^QFaVY>mf^Jq@gLjVYB_%B{0%f9b)jo%6FP1eo@aN)p8`UB&>O&nO5yuaT(Z@41{
zHU(KzI<uoq^@f%G!u+a8%3r7DicGJ`mS}i*^pq7?KyI=!uipTpF8I-?1B}#$Rn37F
zJfrUFxTSJ#d466~fzdtF=kvV|xZ|>J_ZO%9a`xs*-DayZ#=_5JPmx$~qDcFVJEmMk
zfZqtW`kyC`7=+ROIt|_16-Ia4!39=_H?y#d6b2>*@ptNjDQITB7GGAQgxkK9LLg#T
zeKJxzwi!Z!<-5OXv{4hmY5*VeK7CSH_^Ovpdy2yB;IF8z3KEz+!^*iy$6x|Um8WZP
z#^&6riG8-jk);G3`hWB^_&7B4U^n+uSr4)42FfFI_qV&)N(x4Ja$LoPv}jO|y~VgY
z+JOeuM{!G868vDO<_gg8Dd<cASc~5bE{s%d!`=!zK>?`t7=W*kBWH`YUB7oNztviB
z%Tmwz2;r|cH6*de9}{pZL@g|(_FL++XEN%1Ts4ea$kwBKRe^?neu*{Xn4|j3A^50u
zB0zScpY-+=eLcE)wlmDxg&x6JBh9Yte3(nceTFd7M|5&n4x5pdx({%LVC`LV0z3IY
z0iXw(<?@bNfntW2;Z%610baH}4)-4ld_+O8VO4Zf4j9lSrSykRGU`4=!XJM9bYhHu
zS*ko9Agfpl7#i@&fX&Mkeq#jV6#V^GN?R{E7vZ$LZa+%U6Y7jArPl{fJZ);k!E2R?
z{y#~JOp~AVhtJ`&)ZFmSGP6*qeoAV`BqygvPIf9uW&Cqk^08i%A{I0x`>Qcy*7mGY
zM)xEannFQpb<>j7X<ONBe+pe;p-Q#2>?JFc2pi7(=AepFm!~_JDgoJvBhftAFX3_1
zT=E)u<~qEh{f=x=KlGGw5cE`d^~$Q|tj;oqW{XX&A~j?^AATVy$@!L-?8HYbs(paB
z;HN4B-P>qsfvRlY(eF=%w*Nm)?ZB6HC~p`});6RRfMNv?&lznv5-XTP#6)oi`>Sth
z$a?|qOur*iwWy8D7!wZ8M&E)OWbjWy43B?}C`%%-OGtS@LY&)a$4YZ!XE}C)na)3j
z%IXj0hIHvEL8$BRk213iBsogZWG}NM^Wy{jwVs>kF!fw!q5F8VgqD8%&F?%z6X#Lo
z@E&B8#Gx7q6Yjy0CtZI=G3d#Hs7B=rgRtG?wM?iC@iNc>{zoCs{eV}d=+EWy`ct~&
z7qQR37uRl}_(Uc`V*va|xc+k+96%+8ZLyw<jUa+Cfr~4?1B682U)0`c>%Yk`X68@?
z$G$d_$B*~n;JuUjLVBQShGhxDK(X-eG5--L3s@ZjXSJ=oY~D%N*^H>oxzTJ#jnVq)
z1Te?)!OD#Hjb%9M8aOqD!h3^PA~);!u_RCimF}u8GJ;ZeEQkh^-nP%*h)N@K3wW&u
zNdQ7W@v{#C)gAbzX3ElJbhwmX^Ce_u+$fYWs?jriPG*P$>|$ZX5Y*qRD@9KgijCFp
zQe60+BY_Vxa2Jw8N85iq0Bd8`#oD|&qj{x}^c;My155V8Q)na2ig+_KHo*D=B)fG=
zp8L75!j*!x<0ECX^=Ne4u)lEszjrZB^sSI=VtxrsESun=3o#dE)xTJTp{kS5?;0ok
z<q8#OZ-&ps@p_zcRJhKPgVS?%`Y6%c>&!}AMaS4JqeSZBo>a$s{+)E{<Tb5{Hmgvj
zF(UB1>eK+A*u*jWTun;bB^H9w43ce;zaoF$bW%`7UjD(@mLud8;={0>?Rp_@F;5Tc
zXUFx&N9{W?B$wm5sZGe5BHL)Taeo7JP}dUIbSXk80vp!p@xeQ$O~hIawM=U;<h;(H
z{bPR9=lQESh#pa&iEMkeZ)GE}Q}C&fe|%Rwt}lNw%2Z%bj)l3HkaA@kRydtuaJTBK
zL)iPfZ>-kufaoByc#nkgq;XPDjN*E$8$a{rt^ha}+hPCdScI&e*R@WhIxBZ}L%%rX
z(e1bV<&xwsm**`)vD9l*kZsbi{KD-TikoIV@UE(l=tHRD^A~Rz7>~Vh0<elvLf=2G
zH7t1eRT^>oZMX=8M{_rB(o9BzgaEOUEe7d;nDAXG=9q8@p&Q*WJ5)$Yvlc9$IPuiD
zuK{PXAg&c=JRCGDn2PR>LPhwp2NRFfMU3h>47puXG&?(+fzhwat6wePEk6GsWhH&$
zX~oiDL*5JEJE}yUtZ|1LwNm86Zmv}%mN}zo2y1(O1`KMh$j~VueXDOld17=!qKE|!
z``3pUPls~TN5(Ha{UEu=$kctgxhQBFdFmsy`_ILh^!hNx-G3-a@+jl@;s<p57iv{}
zRiO%5mt0)7m~a+y)aaRUVtO#Qt;3~c)yVi}sy6B1;w8++wnmn<?~f&h)_a@bFjkd+
z>t_G8U@?c7|B>IUsg<GM0S4yq9GBu|Autl8CIc)5P(z3_t!LYTQkI#=rZwpxuZ1fQ
zC11h>$u0o=HP04ioAsM3UA5@}opC$(e_)`SVR5Km0ihJ5ED0TyT1s@xkdYstarZ7f
zKNN<JC&L!K+Jxx}anH?xXW(pe3RtuOOG3qs!p9p4d;ZgMaeA+^BgV|t=|>PQA$J?w
zfW3zpArR8}I$*l>3la)eIqKmursigo`F5mn=1yP;-7&|$TpFkR+J($)1|i}bS*{NG
zWv~|fl6XlNf0o<)oMcpS1|=`KV*Bj&0H?VSzB@>y-PJMaWMf^|PZUx->nubfvZ|Ta
zqe~l-taa>Y=l4bDg08vL(3~i-LS@9%)!I3>pd4>MgN&m9;X*&lG7TM^(gdl4?^}Y&
zg922Bbql_hSnh;&MpdquHceBS5y@{jXessUS)oJ>3;9+0!L?}jN|mc{V9fY6*lwH;
zN0|tYgS8;iv%c_Jq+s((IiT~!jS*m+R|7k%>DN1^aUO9_{^N71q{0<(;bO}<j_!E9
z9(8n7;KkQ18F{g4y8z=8yXjM8!N0L?wf~Lp`GRanR4<J(?Sj|a!nJ9wM%Kx*u1SHy
z-uPQ*3m9kaIcMXT%V1XkfY;P9Jk!~id|JeGu)>~QplkP@1dP0l81KeW*HL^heRp>^
zC*XB}2u4LAqk!y%x*HSvg<^pa1h4U_P~s~Q#YLBv91M1jD0ixCn44!~W2bIGf71XP
zm|Ik9M<Q<Vym4|Mej_$nVk3t2x*zM+DU5c86HzIUBFS0R7+KY1y|2P_<aoV11YS4*
zb){+E9C%5$6qwa8_g@}fjPu=r8dXd)0&Ov6b~&0`S_Q*5(@qD<+tVq}O+%j|v1;@m
zYbmyo=f`_aHY@Tt0sw>2)FA#{)9jV!j?EA7$K8&2!Mnizc1SW)rUl-gr6b7&=6V+{
zir*)x-KsTf+-$fR>83>^Jei0=+r!F|j(*<k42S?ZmOp<4kHIQfn45QGq)UdwH)1+j
zy6Cj5=gb{qJX|<ih-#c=SFM1Hsy(s}Ag#~fNqn%;dzMXle$!Pz4wt;a0pT<|IuU`d
z@HwGMu0%F(64k5Uz_e-`2O${O)924Sfo?oT{y#Pc-pw1@`&23d%kP`1Q5l|zkep%z
zn|cNSLtpQVKTlU7obnE+P?iLwZFzRs+o~Na)~u9{D6yJUD1|ucdptcA%yKqq8kkTm
zYL=83;Y*RX|7Zr<8|S9J&9=6jbkLHf$yscZYx)R*gi;@K6G^av4=}b7F5^5}b1AqY
zZLrpno>YhLx(SQDUFICnq0<(pw@t~D)Ob3S|B<#`P9I-&z*Nh|>GS;;tvFt9xVMl<
z_WsTJ{TE0in|h$>%FpKrU=K7R7>-A6_3<EtqM+78XE^(bp4C@G1Pn+S49pvMS*n7A
z1IjE)Vp!5k%7)K2SdJJHkM)vXula!+%;vxue%Won?u-M%HwA_p<Zft$p^5|j5%pjT
z06(%=Hjq?H&1Ewf5Ty}^6Uk6T_eyuK3UTHL*UhIb5b`evslAfvBIUb|47h4aG9ttz
zQVYyG4q8<d&pyO98=G{pougw;1cW&VbOG%o!CR|SQ^C=xDCnJ`qt~ni`)TfLkaQH9
z;hR#8$X{qHjq3d<utSXnJ_8c$xfXaw7IU;FaKc_`oY)XTJ(al0U9Zo-U~gZd295K^
zWdQ^X2%()}o~?7+005}Bh*o(6cE;93LV3<5x7jsrjLL<!ag(0%+C9$CR9P}*!(o9&
zn0CJ&mpNzp|4##AJbAJcIvN)EbaZR`=5`K5)ttOl|HcCjDi-709aA6~RSbCiS@n0i
zJBu4*v)-eP;CnL^yh7BP2=VOIf@@e}!i8OEBVNg1t$;F1QU!CVEoB@r&><s^e@Y`0
z7vcI&ROKT>?+@}`%vWkt$!~BQ8=HR?4OymVkmMcTY{>gZC21mWj*+bi6P3J;_1S+$
z>EpJ`uj7TxgTgS+t%!A!@nUxF;8FSn$0@4@uG-Ys0*R%Zp9vIpG5n%$^Ny>2S*VSe
z7H`%>eXne|vjo)s&xE5_rOLq6F-nmMm5h8|CZSo!ssVm$K&lQy;BI|Wf6ts%XS*)3
z3|U|;nrAXD;?+rpN!Sowyma7oNL7&JNEr*CLTv_-nO9QAJMh1)aAYtzfk7}o->h20
zUz*M@3?E?P!p*s-?@wvY=AWB#7)5<Ymy!|WMMldQR0PA-t&QU>;3e{GLudww7f({b
zuG6dT<VZU}I1Q!BPeG)-1lI~#Qf}sE`JndWZn$Mry<2zvh*^IB!(iA*e|0cg1@D-V
zXPREsGEE0AGuZJ?fs6)ynD~J`aJd0S2%{9cPF};Fa!mdym+MNFdrTl+j^b{W5V$$g
z-u$>_2X88X)LLyGWh21RgliXgm7mFkBkE1K7Tr?uy#evx`)}Tv%`0@#l*iV3>s?zK
ze?IR9<6JN~q}Z{ihOjNJ@ODQCa<_3WjT`ioM^&tVWC3;(9@)+HV{~xwKP6P~0_0Ig
z{=7QO7Vom94Cqh?UmI)&vEYL%H6q%`4l1H$Ag3y;6o^gq`(gpUK%oZ$a;JcU1+gVS
zYMqO1`>s!84UDrTZ@lSMg`f4h0j}Co-ya{|H(<W?W03l)jm6_$pBRPA$aJ@4sEdj4
zCST$#Cki?_aVd)F#dhbALWbnB*c$vs@@owBC!SpD#pA=d=3dV_iP^K~dC3;Ng&$Kl
zo{ebdYN?Kx5R93rAf*>;uznZlEGlG7&n#9Qq@f)KcPn&=h*XsxCAku(8abk}v<XcV
z$Do+8G&j2p)tlg@TnLt5weHrBi{T`>xn{+Qda^P~Ii|SdCgP`Wzr02Q5Vwy1el{T5
z#Go%3tHY5CN`xMhk_Xs5Aw%CSaFXjS0d2+(1lVf+Zd6L;eD=YyG7sxk--TxU=C^TS
zhdOf$-4R;7NWe=GtSKEi9j4L85rlJ-JdFu|%zr7g%L(iN&01O#$!_xF>u_=IRy-Zi
zE9R@;z}y6yYy09gE8j6@Y9zW|L33`*G?P9<W_GdJz<vvlp~ocJ*gt$DTLtR~I^My~
z;~-56j%rEFADRp(i*r)%I6;!4OBlUfoaZx0p#o=wym620$g>cQB&srA(XjLxdb<La
zRCl*yr?90B`;XexKsxpHpGYzg>hy7tPfDrlyTV;NrRnp<LeMh@JJ)h)dQX@q9?(6G
z%drLtl%8=uVAyP6_kUi!*LbEk8@IS>v%1<V+%_(XA&gDwT8MNA2JE7&f9E&1(iqiO
z{a-M3wt>UFVR%OriWPs30MHpOMdNL-C~uZXq4*XMX_dwZQgoXExG{@c7-r#;0=##v
zy-I8-CjBp0yD!@f*GIQ3P3E&ez2R_f?anU-O+WS&o`RQ`#}i$1>W=pAK>(cy)^vU-
z216xNkL!+9vB9Tff27I$?}s}9b$MFTZM1Gz)`$Z%N=%zOl()r$Jhg>C=R?@md2bRS
zRN5}8e#uorl55lR11<WMWsJ6?W8r`PZfH53|JIWIUD4MxU>8~+(z@LiG<1kFRplkL
zUD(UpH)qtxht`AaOW<gh_{~jc^$>i&4TrZGyAhyXMn9yvBddWHmC8$SAOP|G11GcC
zcoDgqzj;u8&MzDF2!szPW2=2iE!hO8hnrdUbuHbc3v*ZdGi`K$1v@)TYheb$|Fsmo
zPa1a9Zjq*PD|MtO5GXV^(E!#B0?4h9x#_mn41yHhto1K8JD+RYd+&4&Myx*rj%D{A
zjsG|GNEAeDZKy7ZVUJIEv004X@nl^>edS!o>b6|(g8+WSnT4zUhd39dE?)3K0kEMu
z4zm-UwjFU}j1ojVeXcLWtKM%kb0MC$7#FSQ?MkBWqqqxi6x4Hh07D1E)v5$DdV9~<
z9yxnb%DRu;E%`^rUW%cTF9m|{cf4c=<0P;d38&Y~;V)Ws1%KMgxAugp6&=-G7du4&
z9|62#`Ul549~aM4K_vO_`EC2Q?izuQ$E9UnYfay>J`}3PIR`~y)d2aw?S`UudCgjK
z4=-dH#oB5z6=^mNm@mR73TiPo&Jl~)&kw7<DUsko7>6Iy<;%v#HXDqt$C($?bU*NS
z!>j`T*?LWjnkdsd?(Eh6@C}w7*=wuVHiFM+=IXQ04t5WaidnLRN$5`odSHoD6iB>8
z1sU*JEB4Z!cnt$Oj^1!Rn65!)O-$F!FroupLb#xrhX3E`ruM$+BYU{5S&GeE5tpNs
zYzSNbaIJb=srJWVMz*Y!?2m%(1N$nJm=l2l((3~8SHdVkc9=dtF3EU2EJ5U^7sT+%
zn*hTI@&W*aF5B{ooRvsd8r3+gQett`KC*oklimQXk_lAz^w+}<f&w?v1;+@*sZSq)
zFQ13bl}C2;@x9z-nn2fUjuGemOhFVHR6?LtsyM>LmPTmA%<<#6_l?pJuWPwyEP!7D
zH@E@t^8X0-U8In+sW5+EX~uD6Ttr%Gu$uy87rgLv<?P$2eGtN38c(o^{rpc3QR4C@
zS(jiwtO{dxR5Xn;D7{sCr<oE9XMGIu@;6qGQ5NK9o6NHdT(i@Zy$6tH^GaugXR`tP
z%Q=PFSMuO%yZ*W(_U7E04J%dy4G1La?};$lv=0^|D$v$CjW&#g6u$oSpZ6c-iV2rO
zSP^X!bup?mWk3!jaE#L=Ta`)ZSAqHF4Ms1Hw)NfEMc$p%X^Ts##nQ0|w5@p0+9?}-
zG^AJrAKdBJHGEjO8U1<KpjLqj(krbV<YyT4&4S(JUCKx}n^6=HBf)ogrc=wH_)^Bg
zN2YG(RTh1j)%ktJUmt*IdMttX1lzM4I{@|f^sBMGm@BP5zSs@zwK7H1n}A>h^fwJ(
zLxPW3u}})jiK^qH60RDsfr+3$wm8k;A%N<an`r`8AUcs3Zxx3?pxO9WaMs&5JA|f(
zY>T35m|se@<#iWY(54kvt2SL4e*qKQHW0v=V9aBy?FQ_xUuF(xKYJ^WoRh1~2`t(f
zcm@0@NQc={An^J^4=~0$4^D%Unc8HcK<yLX0hw#F7Y^O*fQcv;1M_3vegV?3wI5LZ
z4Hucz2zx&s)Me81VjTU(poHvbgU^}hSTx}xd2%Tzo6#qBp@5*qT76KP0P;jlYR`8)
zqsda%PYHk;HzHZRp#aX?e-=TeMS6b@w(~$KH{VjPcL4DoXx{Km)y_A?<4eh+jD6`%
z0zbQTtGLp<KHZ`R1qsbLwcB^#@41@YAgspW?E(sg^@Shi781c%zosg1>>OQtu)uer
zM`{O6Zmvi)Hs+`Q1RIjj-RQ9kpUXr_%chHd+BL|1?ljJK{!`2VEBKr`DLqlt3xmB$
zUZLw(X6AySo;moVAFF@(=b12FQ$u<>=Rjk7+JR^uMSlr53%(MFUQ+J5-F=B5cFy<K
zN-~~?oQQ}#kgr@U%U~?7d985fz@ro&E{o5vvgen5uk{_FFu;|;Z4RN2@aW=YYVa6w
zK)&F^iv$iA()PCH{kR#>oOjA5QsE=ZBTp3URd9)FtEu?NKcGR4eDoK)NAC4uuS6_$
zS65j668uAd{)nn`)%FA90<%p?Ts<dR%^F;!uovk|XLoEkcUJ<>vNm|<p8Hbdy-$BL
z>`>3zu+1lGbqA{&Lk34{)`!eYfg*5^;=D=%@+pyb9A+AR@tqE*KOP7b6pW((IfQ2+
zMo-nWs(GQSv5f~va+pt@=;$8lD#_Y>{dAKd%8=YEW*QW#vaaR)>@n2jCH(0F=%2W@
z`y!Ex`ZJyjSVBgW0xq-8ZZT2B9$@d4pg)+1O851b0lzFY&BXR8A|g@GQB%u-NBfFM
z!e8463K{;b7M_A@$`PlOFK010HQ@X%j^7-7Lntc9T>ct<1uQ^7H3Gm|*ha7GxzM8T
zf-(JVOkdqHYS`$rxJQ5RT+0Sv`LWYXNQP3ux)kD|nS`Ip?ob+wYB#qfxC(FZtIZBg
z1f+Y7PsETA2K|%cvY;6#W-~s%Dhj$B5@+YD4^Fi=itQ<`x-PAo<d9t5x$VA3Ec_J=
zKg1Tx&L!LZLBGG4Q}KrqB^QMU)y>u^g+lS@NhJPIJX2U`!kT2uK)Gg|bZ>HLuPe9I
zbPbz&1m^6!6J!%uUzkZ~A+)FF`8t6AZX6vl^jBe0FTt-`I0vO0RL$($H>pU0yC_0!
z6LqPhXdgKpl2FY>s;AQU+iLt=SD!dd;@z?57&Rd*fNV%HLoNfl2<cFDqAO=Cf^(z~
zk9>sOihHe~L#v|G)-`=d^(G`oe}l;_!nr-@F!-)_^+{BWKLIlGfQr{PSmsp8g8rMH
z_P!d&Z_wFzNek?ZW0C?nRObN~B*DM1)pnK@)E0|DaT(Fu2f(Z@Qu>$O4bu?M<F(AE
za6=IHvUQ*m=<{?2kW1B;HN3W0it`?%?q3cOfZ$=%=OF1`YEe5#W}{u~=C$Y<2Y2hU
zk?aVHUGBraC-j?wFjHJ#ifGD)yE5G!-A(%|e$ja28;IEE#U!8N##TyApPDF}$vYfM
z<$%HeJV%x!yvD_*k@7!80Gm$Jf3fl+WL{erzWxQIeL#4duR(MgBAB>iR7R)mbTwQ;
z5qW}4`)<O43WD09igu37i$lrx!ATrhZ{kwp$7OMMccWBvPBCi2H&gnQ6incA*85>#
z*Vq>?#KppyUJWLLuiBg1TyRzSS^=RxWwuRbs@J(UbPAD{MGYF5=M{U2pfi25`J4TL
zm4Fw9#BqaQGDH_{luofaHNwSxE5!dpiGY3^Q9(s(@B7Wqbp=O_9OL)k19IUV1^!C4
z&O`An-B~o}(Y9)EE#dc0$_B{^VBsCv*yXjOzEvFHNFp>7=J=^=dY=>J&xiv+L9SYW
z1^Tl;@D4oj8caKT?Ci)tQ1}-s5p*I5{TZ@I^7kg>Z@h+!KbLKsPs2T_K4bd2i<vi~
zG@1L0_he8Y{+?xAWMK_Pe<1(+_<|Wvqmgrt)vi}K)HZadZ6;~=kLFS|PUvj3l`HYa
zWWX{8Ey0Ybz=<UW>Q*Y3vJ%cj&jdw&dq!3MS}rtAEFszy-EmD?X}<}!x_J}&KJ$4?
zP|i+z{|LDJhHOvEv`S^Lf~}rfgSHT(Kdu)Ztt#%j%00pH+fl&i2XUfD>7dam<M>+}
zm~bW$hq75*Y^c9XHO=?!{SY)wOs*P4agK~854v7Cs-!M3?)1Kd(m^4hgkq+x92wZQ
zl$OhQi59W*X5)YJR;4J3k7kTo+%G%ToeID0Wx839WcPts9lZm`Cmg8kpirZMG|$P-
zQ{l6~SMB^R=^<7a&s*D@#b&QkUgNmAxJUXKfW?jcTjl4LC8{FgaFd#N`LHX^q-$fN
zggDzD{so_QN;@k@va*lPo50)nnZ$dI`81))$PqEio8V-2d+hT!EmOv%BJ=kf=y8}c
z@7OdVU_GyF2tF2HwFr0d8qSwbk;yM2XqEn~KHzQYv#Kx1&dyt}c7Z*fzu>0(Pl<Lb
z#qvL(S0hL+^u@nxj7f6rnYQX3-t(#qF_xg;p$ed=+=lG;Y}n?#6*$O6#ns`eM#gxp
z0QzlYe4@wZqDa_FBg)@P(-hj%v+B!+kRyZVl9=H%vpAyiLk|lX)J0@e@!Yo14Hb*g
zCbB7Rtn~<+ZoI;%uO@Ufza=$X7q?xHhI_IyxpCr<>Y48(O7b|m7P$Hat@K7A-n(uq
zcD-pIYHqpcFlD}@eC|I+2XjgiEI}DaT*)!sNOt{JCqxQCL4E(~%U_C405_atELnr?
z(|LU1qE;9Jyj6C%fBN?&V3(wMpN-2^si|f{IiWu%9k*W4q6W!KISuR#&=}I6L`$=$
ziq3x@NDHAjmU?Nu(lx`$q(GfVj3dwS@-NmoLRQ7`)C;hU#!aK&iej>aPT&T{esXBl
zqKapGGe&DmU>+(qUEid<@)n_#3KZ~xC%u_@7iEBab-410@>SAW-f~&D>LjM#t^XYb
zL!5Pg@mA*1@xM=@DC=B46D%LY)G}oC8aSLeRL^RcOUIS55KoUr;c=P~#jdG7ZRbS+
z>>JKLf%vFJ$#wJqs%k02;Y(yI&lX>@tXa1?Ih;N|)G9sbW{$`nuo4WRQs46in^u|b
zo-T2M!V4t1QN~!BGHI%*=!5uRNqi6tJp)>jwmr8UHK-<Og4Gb~W3zoe6~-{qOfjAF
zSY@vc2f=qRSOLz4%+gB<F;qGEJEMp5)wy97t{ISXx)M|#ct4ITbVjrS(4d3}pu?Ar
zI^6f%?^@)pKg}D;4ti}k`iB>uEzpmhYI|jfG<k>2_7y=0=oASIA&i82EporkV1Qd=
zNTn+*1#dw+yO5IRtV+Pg>ZNs0FaI}VKb18KYi=g?Uuy=1ns6ksoE%!>-+cB8Y@jpa
z(`VwyVmY<Vc)_U~JZ%$PImYt2UbUt2G?wP&KMmU(vJ9trCoy?=RD^a5+GZn5x%jl`
z`kXl&rnm!Sxp@MQ)8D4~e?>NCWEzlG4YxpWfQe{7$n}m8f#|>y7sC$UkM|yFu_^>_
zKCq*LgKj0`!4lETAPLtjgSc%0{8&MJFzB7EnXiFc5s5L|-u+?9O0GrXF*d@Pdt$1J
z7&cLwjlXTBXVlFw&Pww2tEX>}X_}l@^l!+*Mh9P#ro?YYs3gfgZ_c%66cNV?{?#@U
z$t=Nw0s6kG!$S&M$6{(efTSeoPEvMk?O(CeGa#}5;blb8(RL!e@0JRjkYtVDYRZmc
zQ2^f1XJjVXyKIaZGxYH~SN7H-2$h_MC{H?o!Y%!sgB@GzXL{?I##5FtDsSvlGx#gi
zRG)npOiJ87o#<sOYr`-|PxnVxfCY-hoL!&`YwP8$T{5KN8KscmPHjzBKllF89FSw7
zE}yomOD3ag!xZpV1xd%o9s>nNK#!&p__2Jp0F<9DSd4#O%HO~I%&vxFYA+LMv$P99
z>2RAxo{W+g2{L8!`a|K~GtWr@8oLR?VE{5y96Gq;2O+y(58OWA&y6asjux+yOMlAs
zJnb!?%p-p+!2@E8-+$x6)=QeD6c2-}{Wd7@$VDHUwzz6LOYTow2JsYn-p+CX6{!H*
zv1z7#Bxv^I$dYl_f*9_ev@(ganP#9LxFAMYSkqEE)zJd5KqrrJ`r;1t4isalYOH6J
zYl~eiec+8U$LntPLc;II%_>SVZt4M85LJU=CY6TYGJ3x;3i{Ww1w|5LCCGd@f6_mK
zp>9^wBqkBdpdLYUk^e%Ju%7Oh89%k0Xf)WZ{UiHg!kuwuK-IvA^*CnSmLh^(c4umQ
zEI|l9@~<{-eaFVg4g<Bs^hC-clbztB$c(n7e)`Bb_N$s0pM&r^VB$U(2?bs3PDN4p
zP-Aos2BR5Ax>~*p?tMqks05o}Z>;da=-2flW14u+bGyq4tOY9fOT{FoCU62Fk<X1n
z{;hf^4s;ZZYF?01!$H&NQRY&o<-^BS2-C+J|C}*#d<=bw3flKHYpZY&SujA68<=HG
ziblWdiNDW&&c)!r>?}l>Nllf~-4wtMXuT?c_{i+@>v$te>!)eF0kupx7mEhoNRL_x
zgVfvq=7BS58YkN@NTh4qIn{^Kwt;~IK?Gl_c$)h(flf(a(xCFogPfLo<ZLJltC2$0
zmJM8~0=#j<0_e2rAhsj>YZ%oeub-t}*kH;QuDHoXvD@0bXY;Y-8MN&S`BNmj=#96G
z&z=eeGva`yf!z8>U-LVWy{<SoXh*F9za2yqu@DK_5Kl*;ml}`_t~3z*Yns&CF!ee7
zVPZ&QspwDKhCA9|YfmMhpzl-v)KRAnAiW?Ss_i(ld#r48AVD_kJ_Je#fDWCTDRcty
z4_YxCu?Bq8(eL@YY(R15gYv3ncaPbcEoI63k1(*h1g~WNnT)Y|Cp%dC_Dx)Yp;__>
zK6bSNs=NkNBla%#Lzc+TcV?0F6ZBLAT<XsVC;#>kAJc7Hy?uwHPJ456DwfjZ8RKHM
zg@wXN+f+&T=PJZ7WtN^UMl~CSby|RSTI{8|RoabMOvu5gSSBM5s9T%5(Oxe3(J@Ah
z54`vC?7sHq2faV8n`VIUksD!Rw@Iw#LezkCvk&N>!@dCNhhxV+uVoN;)*L%@ahQld
zPeGh`s)-Pgl5yOHa*u&WjQ@_oZNFp!o=dGO?wfC3fkCqpvBN>cp`!zfY^d%SdgkB#
zFnB!VboZB^Jz+!zH@F0IUu~_tR-J$?Q|wUy#|%<sl74rHuFbg(tY>*ONW>09K^uni
zT@Vn9Q?<h;h33el-s*p86AfQ=18iUdmsF>2@}N5&(O{0moadF9HC*|oxUeZ_VN~5w
zansBk>5%j(R9d13pqqC(NyS7@t)@M{z5Po+@Hy?Qc?8rFq<K3?iK+ma;45weNc^$`
zBay6_gG16D1c2c$Lqq<7nWliK@h{|qFbVtGc1g)vkhjJ;XG*j<X!ZmSd|(c5^2B+I
z4>xZm2v<}rp8i2SN_SunjpdC)X2b2uDih0=_T|TVmEf^B9y&+Ijxn<W*R9tLt~drw
zpJ#zo+FoXqEN&4Wdn-;&Z_t3I2^tvyxq{ye!d3;N)}VvusgS_VFQ(}JZZ-yLu-t&u
zI7sk5)(A?8f`b`2G|Nm`29yFJIXjqw4gXHng2exlz=Iq=Pb9DOH?m2jWkHlZiJu3|
z#$vdPs<KSe`Ptjo9u7XF;wj>@oZM}1MqMgSKJBwBZsef)R_uVmdL{Lq@hoLmV4w8c
znfeidk!gZY0~~*GhXvjikwsT9iqc!oXq%|NuKNdxa3q&1tW}G5Bx0GWeeo7YjjcG<
zME`Z$Tg?%gr3^LE(<V`y*D?Z(YgUblk4yHEO$4Z=B~{~6!QHHeGRtwf);Wd(#by;=
zG4w_t&C~25sr5ZSbebs_6(%i^N`AhrGI^H%ngr%~M~BWYP>DV8uSRxixHgx~_X}1j
z@DkVXk?1XNxSu<|VjVW_RR%B!5rzPdUyO8xBmT>dkw1(t=06Sl?(b;h#HeL{ki0_0
z)G}=;cEJL=9Qld2_{6b+{_B9ZOPd;@Sc?J<-<OZ=N~&eL?2?DK_%texnxb9+^7N1h
zZ0Je289^&_v0(T-)xO(8{NS;235K)?nX*ou1P)J!^%wH<)8}NMw;RMYDgSjFGc8Ib
zLs}Cz0T*z$;oMIS8a%;3rL>R)!Z&|MntVLzTNFBTYX^%ChZdbRPhekI;y-LzdHa6y
zNVg65;oH@P#HM&di`B!a3JsSV$aLz)aWhs@{yfu9kLSW{d;0id#Lm0>QWTloY<0i;
zOpVENsVqHM;qX3)N0#N)0OZrh=w)RQe6+6PhNNlor>Ad+o5q`(jCx7miVm@w;$a#u
zI6{qP$Y3CSkQNBjJ!D=xT#Y=Z%4(k7QhMh-2!7T+Mz?Z1q4oRXCkCucm1-NX7f86Z
z9s31S;86)BE{%wiZ9eGkznQ@B@N9atdjbdRC6%K<pUoU<bL(tlf4QD+PB3&bToP_?
z=L=+2yo?CFBt5(R`#&QhFrBy$8=LFT3lD$CcrP<Bc&NDC-5VOkw7+lqnJ}}Z*RF;I
z%5U#KEZ-=clh!=VGBG`amO4KZ33VP;SbPpz2ugn*%lm{huWSKB1RTr27#MosSKI)x
zcCnO=GrIMnP&yp@)QIv_!0Ut9eW(h^&P3M4<eB1?5Zs(EgKu;IPm1b)PfC8eLmeI7
z;`si;FiUZ+0N0t|U0M227D-^B9E~p;-%3*`vD-N{{_~9slAB;OL=Zj2P59(tIA-FM
zv!ut}7V-Pxy~!YlB4{j%(q-!DP<8};L-B;<tsT6M^FVeLIEWaWaK^>~Zmaef`PY5P
zm#BmzhKr1#{KRl#z9XvZZibW^K+nVv8Z_Xx04Dy%1={TszN;WK;zTe~kh{6YC}9Q9
zrGl5;xPi;aU0ohpWQYUVb%Vc8)Er;3YqHt-2UH26qQKuj(<qMmrR_2ID|?N8a}y{I
zhuK%WEvMr<p^}nyyonjzA%cnNBYJ%)*lxhG`drrntOHOelOk$_%*#7F%WB#gCEm%4
z5aU?LHO0OkFZ4CP`#IvCP1L4-n(N8mj1Fp$MczJ`Yx|>3pSN%9%wV@1k@LcyUoFoV
zn6%hBT*Zw~Yf2SF?016{?f)dP8ICt9s;PsLGtjWah6?iM7N)+Sjl!7otRzgFKwk+a
z>d<E3)<lw+N-h061$}VrB?STBQGzck|Gk%B|7$V@bMzx|%BINtibvyYJLbPxt`PjN
z^yj2Rv)K>$lNZ0cRfC$=n!Rrvwn{4FHM^~@gT80<uSM3{%ELhX5&WSy3OYeX&aUP+
zEKFN~G6sBT&j1SrE-HVpx$M{U)x@>x^7}Glj5?jE8u&7_^ahT;0W<SN0m|pLmf_Ia
zfuNS2B#X+E*L6uCL%y^A(N<`&AJqHZY|el(x5UQz53t$Z6<}Ta0YaPX?tv>O_Y)&1
z?gC=oAI}SX0aVQDcu<hz;|x=B1M&aBrb;!A&?p+`Kz73^%SSBhrgl0@?P@_u;s97W
z?c5j4z`_K_o;S%sBPpQd0+~UIAKSa?=B1C><$n6$*oplq(%??@-Ra}k2|RiSKv#mI
z(0xM%L1yIdLGjxOHJ?rsN?=Slj8<+KhaIr45!^rLGf*O%zcRMVYGLK6fEWjvQiRwo
z{T2l#G(vu?VA>_6T57g<wukXN!t()3yi#Qplkjq)xl%=}U?e*U7C0*|sRE=?<x9!l
z24|cy-F(baM^6~2w9UtNM*+7%M+8ECeEJ*t9MV-M-pAML)Bg^_Phesr^oWhs&&KDw
zze_ldG))u-oicaw+AwglC)f04l@japo$fm7$@ZWH#biciX@LJIHoxw{A{p0KGN>=(
z0uZyj%9!eS4Pf+xaz(zYQQ9d<fX+iOX~|{ifT|7nr~TW0To;x>iUy0{6*bWrVnQ9r
zgyLL~7}((;A7DSP>Y0xk(`op)0q&l~Gg`aH6+6iz)YqtylW#U)j@LZyEJP;WAVm;-
zj?8Stf(l~V?m6NdJE~U;0My1UQtYyvdVc2ueI>{&-ZxmX$b|4yiCd&AL=b^+xxp$t
zpZKzAuBnHd`QgiKXc3TrhE3?k1N=%4{_q9ZNniyt@$Xx?zj@qTRJZYfgGF=9X+%g?
zk{6Bt)UP#jQ_DHl#ggUp=Zr~e3oqxBPTqWCUO+|=0+tV;6sDtOMaA@+k)Rlu<8#E(
zc?$i~=bsVSMW1*acLFh%#tYW!cAzq~!ObhZVV;lGqtm}GGirEBmHYSTrsffFUo$*e
zwkNex@S(v!-3}Dsi}E)*Cm}7B?$zD@HiaI?w9e21`aH@qoD{eE_+p4bV&7j`5+s&4
zKfd5WRSp!J9yTy7)jj$)f#z;?BLq){>NmuVF1;n`rrw5~ZF?zzAy7s->*FKe{R#da
zL$11*fHpDxF&~5d%K#CdGP%kkeU#LUo1-ULn{V7njxV`9DK`Jr)@X(^(<Wq9Z#k}s
z?ir~IDbGivJaIas+<iv7*0vNRwByC#O8f!hLQD}Q!klohVW5LL(q+b7K2-NaK*}ap
z_W{y?Bn}%?wC0#SgE`o42hlL}z^StS6IMlZ9-adG(#h6xcDBTysZ6G9(9?AN?NB8;
zR2&x-q|X5?NzPUIYS3Kj2}>;7znu4(-9Ay-CjXRk1o$5SE=G-#E^m1NyX^y09Fjk5
z;Y5eC72~j~FJhT-{|FE8H^6C5w_Zx(%2}rEAjJX01}8xAYrDIV)*k$*Xd(wdYzY9o
zV9Eplk*uUJL!i_`QxncB@LgPi82Aef!1rHcneq0;M-E^|h^@9SdR<B*7~s{44@Ci%
z6KD<=NWgEJ*C`;qj60Yo{Tkz1J%&6oG*>E9k^+0NSqswHAc9<+3dIpe>ou~cIU?hd
zk#P{%0p&TsXy9(81AlzW3|e4}rL}2@5rW1zH=(Y4r>gCX_-$+rm43*eo?cRA-M&_7
zqQ064kcYM;ZR0?_m*kV6TuNWe2AkMvdAu5<#l2a8<9QYi9_sry&r%lYNYh|z##k;n
zCElWgp7<O2h#M<(afLk-gjk1$!eWvU9OcI}{6yTpsQ4JCAI<(g4}E)TeBt6I(JON?
zAV{#6dadp+FCI)<2z;~sKCmg@+Z$VDH;dkA?-XIrC)X5TP(9sqChp0SuR9t$q#Z9u
z$jvRVsQZnBO-16RpOUan_nCMutEp$}7Xx$i)Xv}TY5HSE?lsa)@g|13uB&&k_Emsb
z0v%FE4HJQ(g~dB!;_o=ErgN<}`YpJ%rzPISW?{<tA`-sDkSzlG`2(w+iCeV@q{v>9
zYRU#s5`TKnlX%}H)8}a;+c2tN0f!kBno6*5Nu^~S%m?zuKh|{sHRZ90GoZr!F~6T8
z!(#y@7jnJvXRlQb;*C+Fq3+}bU6<A2px*2A`IUcEk0^Kmz|RF`D^8$TpG~C1r+L37
zCOjnX%W=iu*vDqecI{hXjl8$hkmy+s^Uxq>bzqc4A%Z#~;BhY5(jWElW|O<QgnTyw
z#6-!D;n>=rfNZU=^@eorDguN*v{%mR>0>4D>AQXM18u)UNnv8UxMS<qC}vJHsNAKF
zN;NWUS#wxLjamc)W&N|GJQX2**4?VD2nG;pDZ0)l1i`Ug{gNgQ)Xt6vbjH>~38Z#H
zLkl4kvClcxCU{e_Izl`HzT{?7mi-@5Zvhln*F=kkgrLC*5Evl1OK>M4!3KA?;O;&^
zaCaCSf`#Dj?he7-WrDlgJ^8<T->W)PR8b?RPOsg2_3GZ;8gBLyven5oQX|I25h?EU
zCQ$$&oU*H8hzu*&e!k~v=DGm?iw<Z1YtL<(YQQV|Wt{Y`shhU%=IbIcq9|5RW!{R*
zY0Il6E>;<086`7U?M)u)q*}Y>SHdB`6WAo^&X!|%px^9ARI8)S&D5c?#WTUa@s%qs
zXHPMGs=`c>-eMu4p;YiU36u;-?|OgknO4?P{?*0Vm(ceA=7zfUjR!cL2J~~>bB%qF
zn84|1P}u++ZT#H_ptv`!_-Gv%$bsQ^GrkK`cdZXG0$MalQs(N^PenqsA$++<?+M;~
znUTMos6!9zk`QyVKkXsy3xa)6ngHT>qssPw-C<Sg+lqhE#R3}yGy3RH;0Q?dj_ZK=
z^-qeTFklp%y#&J{AlGU(bLavGx`AvL3vSdzICl0u?T4swoCP{~yWHluke?gJk-$7>
z!;~ZAyKVtaCC)$Z-#h-P5e0{`bo<6+hJ@~I-Be2ryY9UeB9g@rjzY?bF_T9qLVo{M
z1<>ll%ndF1M7x{H;dRkde>EsbtQ>8915Ubc_D}qU=>G;zEGgEqZ9B(TrAUKF#4b?j
zsJ?)zcY!|N7IszYy^5T`aI~k6{!o$gCdp3Ll<}l_2Vy?oehXpVCG)T$NSTBz_n;Yn
zzitgA$$P!}`0_LdlSP(VLIu9gM4p2wOzgb;*Rqf9$y*_<%x;JBNX%2PGYZY=9)b{&
z4Tf;o=@ycVBz%pZfdZ?vg$texZI)$$iGvKgJg0BAMZ)E~*S`sQ---4rbI^-Tj<6JK
z7;)n0{GJ{GI<IsnJD)cJ4Vq|)G@P>IrWnJ-5GbT|DgdQuoMkWG{GWHBApfS=v)KUG
zs2!1Qx!h7KiQD@)%dPiC0bT+3;;cZ*hz;SS#mg`2@sU0}98K5D9B+6!G>0JOn}T%p
z46N62s>RMFO!)3X&WyvO!RB)*lp^huhKA+$WI~$E%cueYwolmH*LH#!Ev-pD>Ohl7
z;8;FyQWmUsbBmjDAsnb=%-EOOzG5_Oc6_`bdhtCL0wsK<#AZQ9h}3Zz^M|Ce;${Gi
z!GM7)bJovSN9{%oe-H1PB>I5j<VbPM*TFV_l2B-FYtOhFC$)0$8*fDEKwKh7Ku8aC
z=RtVe33LwxxMhCuP!Y&Q+L;`K=Cwqcfk3pj`E29-^7>LebH#?!f}KZ$0umB9sJ9`*
zkS%`efSra{;rHqF?U;<S>OC>E$@<x9kFB0x2CtcEc7^#%g0$vz38M=CFt@4P8Q3|l
zT$Tx>*^~8c@>=J4dzR|C{KPBxrCV!FpG$3fiJQf)Q3WPu8a`*K1j**=_BlH*KYiZC
zCY@EgBW3mp!Sn+NX0)D1QW8UaI=!mv@)$!YUs5X3V>1y<<H%L)dtSapI-|0?B?MYe
zvwORF3*y~*HjxW&#S>O<8*6X46bh5S#cw~mX;>_}kTi@GZuAOuE*So`l>1W)_gy%5
z|1Wn(tDv=1VJTg1d7)sLuiNV-@OE{qy~!yw<!k1@uN~+<q=_KmIT$jsy38E}w?`vp
zWWAMVk4LtFQyu|*%qn_3{-^%>|KC9%B(dt$`5tw~nDAKPQfSg&DZ&iB&z{l3-lkd2
z_Sg#uu&i&%;qBc(7^Mmp4l64c46Ji|_ce)@X3tuF>?BevPy#2*V(JHAOv)-`Vc&mI
zhb2g*(6lbm-F(bE&Gq{XNQ^+wWS~{{dH()zgvQRcYw%$hLEB4&4n@I2zy+3?=P=OW
zT5QF3>tqt{{!d*nrSPO8+B?xT$Gc$fmx<>ngJNnxj03v8o!IJ-3&E?c<f#DtCHv~B
z+XjH*8Zvlq+|7X1ugLC*ftatg*zZJk7>(J-3m+MQ4xRx(28Umww{x5yt$rNw%DAoC
zEfG~qlKo#&|64Yn8T0!oj5i*><5y#NfaGv~e=OrHG_So|UFy8Lq~4{-LCxkKg+GJ@
zADdv+B-qr}pS9f7b7X_V{qCRfikutfB#|G@uBZ)Npz7eEUy-kDTvFi`s>both)S-S
zTU66>j;|Y6tj}TfEY-`Fjyb1eI-4s&Q#%Eg^>>{^Xk|6~mm<+Q2KJ0<BCmllRIZ+n
zMn`yA9J6Nb%rvO)bqi%zy`qv_pDjGlU$Ue~E2e=Sd`o%y$;#41GATdz8ZSk%^lTU_
zkAae}+Ph{Ny&d&7r{DcY=3kYRb(zPohkC9wIUUt499HJ{7Vm!U8Y~fqEG1#zJW>9O
zK<@qv@D)k0M3FdD$kIN=V0#E+EOCWwCD+zocX%Ng5a0}lM0y|wd`$ZkFWvi*GK#Y7
z;0<PfobGt;>fi6Fe07Nl(w@2@3G#*81IDF@)`~+o9jd_T5Ma0lO$;zr>nNA!?hFeF
zD0N0+B662~dRcln`N%u<SaI<vG=4B;Y78wG$zE@sSRIibf7c&v!r_!d9LuMuSR%_;
z3S~H2F+af&UA9gqcX6)AYPQEJaMqNp_nhAU#-K<U403qK8#HCI_!I5VDebEr8P)qa
z!SSav6Ds-NBHT?xX6#Q8YRt$%$OWgI>ihGjnQ>ebw-%4|?m%;g>*fb%Mf-3K+s_6H
zb`Bglc!jDp@y9=JGMY@`SS3}9>ZiilDg@3|f7l+4t~YAY+xX_hZ)Fb|2<+Jvwo0&|
zg&vE@^=E7_WbUxOpXSjO=y<d9RT*K&B~&(4`7tvQzIoDsS@_G?^@l5Z#_QQiPp(i!
zN<K0Ll-|~ZBU*%3d#~Z%c;-3|QsXriP5XgiqT!YbmyC-gA^|qOUgff$>`5dMr0<DU
zi`I^{)iUK%<Y1-m&JQO^SKdj9HfgdT#leRWT(I;ucwQu@X7h5EevWUcWmTPGCafrJ
z%gy*Q6A_n;=<j62J&1Ykj4`d~;NqxP>M}0*gjpv$KESNh{ks)ZYE*`~mW#Kw7F@(x
zIIHgeZcCYg>s}{Qw{_^ka;|aF#;!)ulw56FqA&=dNwP=k0846xtDswDS4t&ec3GH>
z>+#ODSQh)Nb!XUVGsFh_tTL2WtOcYp4g(i=D%STp7OR<yl0{bZ!+v3~XRv%nb|3e_
zy7D$a9#k&7kGi=q&|v9ijd)6yGYB#uu$?k%m1tGfKmLs7`+3O9frW5VnT!dUkXcWo
z|AtuTe%l~#KnS7<HFC)5%EcJp;KM6*8E8Zu1_=rDo#o<i%fOAjjwH0R3XR$IKX@2b
zqt4naTzmtu-7*H`2i_^|pIEgvA26L<-6zRx9|W{{yL^}7vxq$t{D?8<g~mLU>!@R;
z;W_tpQ=(^N&-btY^*6j5yQfoq(7MSx$@<KS6(R3BETApemHmi|c!4wBa&9*;+DeWk
zpei_awh2d4P6BH_C~#|S>`0mI;zyy6YUtgN&uDyvukIws+<E1v%#dRcdh1!d3;oUW
z_IaXGPhW6(H^0wamUGN8zq;#c^<EH}ezA+(_5s8~qR+)WX4*%Rf1G%HZy!-_TD`WF
zHplWO<X(D5>M@D*fsIo*nEy5<Z;<Vw+80cxh@|cQkfr8h{Y>d|)nU&_cFIU}0u3Em
zq5Ph|v`Y$s-OT@Wy^Aj{zfeO5?R-2DkhnBqBug21f7c%kL7{_R;o0rFwzV&;9n@pg
z-4^!xivuy(MVh)}V<}<T)a3GMbV>=F#WP6NNAtkTTwC2vnX!DFy;G9jm4Y}uzIxdX
z9sjhsb6R?6s$TRygJ)A%TWFM2n-_QqjppxCW6aVdBcUWLx3+&qnF?T!<n%TH?i0Az
z;9-h|d$cNkB86z5`(^Hi`H|Nd1@)?QJj~)l&hc`l1VIMNpK#<k-gUdBF-n=_GqVwK
zenjjPD&?%RCi~`c!6BsD=gcH9J{E-i&L)IW3O%^QO?PP8DA9r{_~3X|)-rNdW4sSz
z(Y7lZ*YtL>N8IM&u|c?NqYIb!;M&;s#PzN-Ch`I7IK9Fa?;SbXS+i=gJm>-c3oAQJ
zQklz$lA%(Owp4+(rtOnMFSbLn^LJEKt;JiY)JGld;cO!q9UrfSO>E;MrE~d6h}IB-
zX-ntmT`P4!hsZ}JL^ZyV-M)bZA-dE^yR^vPgR0Zy(iDr5(RQpe+(b<|2sq)KA7ez8
zs}S(ob~Ypt#TPYBryc0#;hf7w1_vEkg$End@^=%@^88y6yUlD`b=Bte9{_xkFp}o%
z;}yCaYf2^^HGE|_#x8W@DfEC5zI{!%Ei)HSVd|N1C@|H?m#Z6i_ejZEF0F66MpURu
zN$)<6IDHr+LXL@hXocA~vH7m7CS_R8uC-o_X3zAic^pYB_-{VhpuU4^ku7BOq~;y)
z-oTM6_I!UPMghQAp||ZQIyr1JMu#aG@u?N;LJK{q9H4`X-ojWR27g!;P(nY#4#)6T
z&GF;tM~R-|RUHHqT<ndmoefslLV9W$u}cZgUaKk(sm@cV?p3t^ZGF6{`g^O~3KE^`
z#>N)c#MO@OaM{cM^qxguK#lUG0hc(b2>)Z?$JsDenKQ<>5@j`Y4U0B^q;P&+7?YI9
zu<qm2@*LZphD{Q#IV7`0o^}ktt7)MD?rV&5c2Hxi4Ng>CQ+hXS1a}BTn?TnnG{*EI
z1fo?o3-B7VHC=#?{(h;Oqfq@+83weA_+jb}8Y68kJ}9rHo<O$Tpii416i4YlD_t);
zT4M#^=PCVpg7w`NF{a4j-5*ATsT4R$J2P)wy56#n8>Nu(jh;$L$l8KZo72VfDw8YQ
z>4vNgo{)l1jNCM7OYT!U5x4J+pDC{!v^$>S25!OGs#hk}KFP7va)C9fVo+>4FaB~N
zBCY#;UcJ|!=p^791H6W$IoH)Zwdvh9W7enkp=7lWP_Af?_a+V+j<+{U9!ExVW7~bn
zgOO);J4mGsQVe^iL)TQZ-3X{FDqLOG060b~MDwcm+Q0{$g!A)VV>XjVKhk%UZmJJh
zczMxxsR^!%Km*YmQYV6Fc}<hq$BBi}Lf?v%@S6Xf(y*`dN|ZVht;@k<F!1*##4aKz
zRl$?4(WaO6&B-tn5*{>?he;Tu=JtLFlRfU!L^mr9aq^qIDNDaC9SXuk0?TG14h6gY
zgoG$Fs6M2X1ORoVjMaZMjQMS<C)e^aF8}`Wx|fs)Bd6{qN5yNL?1Q3bIuY211K4U(
z%ic{Su$KbSjmSHrMtD*@JTG&ude-3rXn6lKtw-D1dJAkRm(`Q;s_F`1txhDwAZRs8
z>t&@Pkg@{Q=TBZrYt%SJscLa*8R}`tF~A<n@Xnj}V?}=6=Dl+3E0)?qk50S&8p{P`
zZBi*s+R{BLEMIGi{Po09V_n;lH+Bw25pr^)@%0%xO6mES4ba|+FW2k!_$-r14+7Oy
z9ZqdM(%CJrN67GQ_9DDEn3MY4v)av?j#u@AacPo_#Txp9RbZ=C<XYd2YMw}{y}z)|
z9fjC3Vem!&>bcNrh!|F3%v@UexyTkTHM(rtj~oMnzK0*kw1j}8GrUV5PFq=(prhSx
zHGpn;T3_Ac;p?`JVYEH79Y{qI$su8iI9zsqc;5AS-m-o8)wULSyZCbLHH$}7!oqo*
z(thz_H%cak;n~cH=>3s^?~YQ9V-G#qEZy19B>fU>T#MxVT-Rs*0eM{ik(LZy4~>f6
z5AfPn4p3J)gs5dH-<=JKwEp7$P-PL}$Pj0dqG}QgaIuaT&CW+#nGhn&bqPdq&F*LS
zGN;r0aOY@ttTmKSBVgv1128`|da5|MyJR}8+@9tq;3K8f;i2KCjoXYTbst;_kIh+z
znnlS0qv9Tdl)N+g=_e{q40Eczs|v@ci&xXLX<e!mvF6#d@Lm7lPhrhgq_4qaueAfV
z6n4G+;(gIYr>m*A+3vN+FTEWOVxDpP&DCktHZT~A3?i#s-S(RHXY6+Yopsk*GP<NP
zx@uWnHV2rC2+M@1fRlfvFKFiD^mo&3-s>b65vg<e);_>03^i{3KW95ief|?0mm#iL
ziny?s+AAAB)5!r-5FYmx*{REVL$BMRT^UBfRM#zppO#jWW4C5aJp8>(KL7CO<>K4N
zfhFe5j1`pYsQ}&c)q2GSV&9%5Aq+KAnEVD3m8mV}%s;1blkz_U3sMGj)U644f{}c;
zT3j_$>%p4|HpTrzwK7nAE_vYSbHHU2mga%$^6)2__o${xjV|_y2T8NH%i}^{;##T=
z@J{eWkU$1oF=$Ais?1ZlW(A28&b?!dRT_b<D5Xnhtv%?5GW~b0Nc_hNEL-f3_aa95
zL;h?#X;ejDi#+FZeqeI>dE$JW<`d0DfIVE_lsmH_$+lKMLDaWFNn42uQ3?CNGh=j4
z<Jb~Pdm;e?6!5*k@UQJ#V9n(mV7v+EE-xp6Uxqd_sWw>yw)oz-^u2U0`@>DB3OM1H
zzivdBEcOZE@wp8oTHV1G`Ff1S7c`hz*sf@lvXr`#0zKl%;YZqjTlcl|DyAMe=)O*7
zaCnw+hHgnA>o3<=Yeq8K#??&5@ie(1l7zVKpZQ%n76q6G0b(tIljgHhD*l%4+a&_f
zil8If$xh5_*+sEECjumBSB@EeY?lamsIo)}&b|4y^R`x_pk-by^$cAs%HA*Hk}qpx
z-wF;dBj^^XtPBj1!)+GH6gOl_xvDrZks!nU@j{t*H%ov|m-(NSf-1$Wb4GHr_&R%h
z2{TNhWsAqd*93>d*Z8FjTfNkxvN<K_>;<`r^bKw1(YCzkW^^{4Q0EAHv2BIJ-S{D~
zrO(w7yKO&ABR4d1UC$V8C6v>?)t(;O!`lj{am&^#G)0@ry*kO#yKT|iu?_~Fy7y7G
z-0AR>`0WuYi=&BUB>o(}yS3wofS-pR0z!P<;(aE!g?I7Ft@?7ejH-04l)Eoa=Qr-&
zM|??IS|jg^NASgOmoKsCSAW*bSA|X{yo{&78dlA#<{KaUvuwmsDs8h=zs&A$%d%5G
zn2Y31Zmg$hRg>86q7C(1(<x|9NmiAtJ*kT*p1p=Vtc;q>b!hqo3Tp#>*>hx?%<)U#
zi=)!G6+P2g*r3_Q1g=D+S&1D$Jg>&*qlhT^`eK>gn>*B~y;G}{^7Zi>rdvB4d_tA9
z#;0U8d-yg_NT0_EE@*7{%D(fjZdyIO16r{%8yEO}uD~lpUzApV?3o^C-IZb8oOLre
z;2o<SuOQ|QO4%B1@TCBelmTRZ^9jV1>83U}23W^`03H_&2oeOX`pMN!39?GDf<GxF
z+dXa4>#naRN=}toUQDnEeQut}Upf3FC>#d!sTguY+Y;A-(#_^(F;0bzv2OajlWKeV
z@m+uX2S%n!KeUnCr&BAhR%B18b(?<0&9~{wP~vRXr_3xP$4P>w?OPsKq1Kf_U%b7i
zhMWv74>J@KVquX9n2dxpV^`5KeAGJ_byNm#5zRw#BqYnQO?j&`_Dttt;qML4k~*+E
zg{y)b9E|+L50nHnv%Zt-jSNLvBWg+TNk(`MU&3w{wFXU`^Lp^G(Yp8M>e1yEV$DQ_
zM-kXVI|Hl^&|W8<xTuyQc$nk+>Q81FP$z%QZCGs%!i_^cs@@)oUI$|Yes63axVt_W
z!H?39MXR#xWg>s?Q0JAprw=s@eE8ky4BE)4-Gv;yQ)^1P85Nl^^DqYl<G=;|D6I0a
zjV^_{94266>RokK%m7S~JV^Yp;?2Ez*0=s|^qb0C?g_Ia+vxHR^e6j^AA$@Z^8a^r
z1Y2v(*NMh7E1X{}R^y*RZpxPP8rr)1+iP6a!wm>dFf=qwz&VSTah4qSEb>lr>wkyF
zw0Eue6<w&+PL{VZn#j?IbF01RAf6~|ncwuQr_@w2!04Qw?4|It`oi2}dwnk49#JN+
zoC!+GB2k*QE*H13uonVF_=n6B@BW2sC+U*Znyrh=cu}#(X!4rcaqk9mz3+C+Ci)S!
z3%Afw8XB0SG9IO;%N0G0@W3ia5ZY|5yQZ1D4>RkX5Q6JPA1`NdD4n8|R{Cc}_Nn08
z%E3FGCG%4AZ%<zqju9P41&8}8t0KB-W%de?>z0M32^d6KLM5HApYYVLGpi16G+B<~
z>QP2^U>`21Pnn`gZ3IWf8pZ<04nTCE+`|M(l_3Y8*tt}ei<yP?!Qb3LG=gPLES1Z8
zn>$DNuXuD@vJ`C7vFgWubBocK+vj`U)%8bD#*~`H16G;nvj63;f!CDOxZK!rwW^{>
z>{xZlig*#6JZ!8d=QWf2fg6~G`B9k+_!m;iV{@f85HFLuQU5dpA|&8C#Lhnm*dt`f
zD4&ojn+h*?s4YA_LIxkd*-n4sb`76Y|ME6;AA5ePr^t8m(_0u4uW3}AEB23XwdyC{
zX{wKWE4L_)JMA+1<LerRPFus5aa48pav1j<nmraoQt%P5b^#=jD7ZgTWtGc!6bbv;
zP7&nU>!5r*$ZOGW={A*<cQ_t{oLxqd437*D%Q!#JbU#mcsa<umXTH$=pU&W-#d+1x
zz0L8hA^JMTNkBuSMlEq|7v<LdsLE6$i+o7uFh&MmeKNyk$Pgx%t(R0L5)H7GG09&B
zCS)u>J*SW=Lop?WcPl48$VNq63>Lb3KWs8QuJ)?An;64oZ`gvojOHvCC3|LE{8=Rj
z7SQD)N%iaG7piRosa5HuR;VK@9*(vD=ulz;e$z_ai<z@teXq7*dU5-CpT{99Vjft~
z;iF7B99l`;JByjfizl@$i3R&ntVEy=D7vPl#W6uf-dBF}*uMea3QEL_OM)#+uGH>Y
z588cc1OsBe(UZ?0D-H-MwVnh}5Tm%nO8SJ^`#7*detljcf_;YxwAR#HJ}4JxTj;HO
z9<1%U(V^<%l}xtn90IoM)BVqg%SxJ-nvu*ICS2Rb!WTC(3be2ohnK@l4$0820Mv4A
z3bo4*X(ZW=3%}OF&A2@qGW|&#q{n9dbX<$2?V1F8vvk=rqU?Yuwx|TwL^b^=Wi?vc
zdhZ?l7rM8Q;Fi*eJu+e_We4%S!V*EXp=^;?T&=PLyB0X+#$R2i(Wg(};Lo|bWY}WU
z1Uv<(=6;<H-*XX}q@<Fm?z>b(0gY4Zy*qVeo~fL)F2A#p2V;pN!}J=1RM#8u*n|5A
z+Xp$0C}kU+JYspmB(Zxtx8iZZaGOxa$lQQymn79(sdgf)>l}kND2yNQ7z1X=EU-;P
zTY(r+OBv5*@pht#c{AV}CDV<4HK09L#NZi$MnCbkge6X76-%%2)hP@nvg%H{E|KpP
z0g+U%8Dqs!l1d7G{=(P$x)+iz=uZWqWL9)TvfrZkh54G!D<LXm5>0XD>jC@^<zT>-
z2<!CW!L<pB7I~U+062#ZY-ku#TBJ!>W96sKlLs?hP&SDd@jGo^01HJ#ec=uTk<N-S
zwm+`1^9~G;t+o9*jPd7hep+H|>S2lg&R<AfLqWao$}~_AwN~fliXLcJ3bIPb1A3r=
zjK6<><vV-Jxc7Y+L+!IY%v0A~G@U*@4FS5WjgV1Id>$n}I=rDC=Yl&SnZvzYfctu`
z>Lz2i?ftd-A;(_NgmrLyOO_;@(j7K~KixRP3RhBU8i;AGG5`d%KY3TEapDT(H9o4+
z@h<Irt`u2y_d#o_%8#TV*4`rv_&9+a<rE_lSH#G#o*U{MAwm{FX^Ve~Sc-eDN<s$j
zo0z*lyLx^W7{k-mnaEr=GAl-IpT}+%YDa;inXQhNR1L>QTO=E)VEb-ZI-dJocZ1>o
zgC*Ep*XInST*xtY?e?V2x2<+r9_hLKWm9-FyC4d4`)0iEuPenYUj1!>&xxM>W~Kk*
z<JtpA?qz|2F<omT(Uh6(6MNT4?5F2hAZp1g+<fqPWE+QUso;&3va)GzXGfE6ltZoz
zyLBUvj+lKe57xGXAIsNvNS}qD`4mwypZkin-FEmQukdaJU1Iu$z5G~S&imcYJWY9D
zhB%)OxwAUQ8xzFNA5WgE+lLNg?SG-qx@MR*FPOR;_`_Zv--WBqHl7Y~YA)&Um6B+h
zw{+xl>Fz$$?DD#O4`X>e#BuZW951@sq%}6o9~6F&dsds|$>-DD6n-*oA2<`=T|ISP
zQO$bUXa@$r;1SiN={yhmywtm|Qv};Tt&kFFYU$|SKlAE7u4*u6>1^KjssNhhk3#=k
z>5+f@U2xDhcWVSh=s9)K3fu(V7}G_DFeElI(YkK7n&?Qo)6}ADEIz9>ivnZpe7zr?
z0&o~Piq8Kq&!85yK7ei5$nqzY<$Ey8C!NQ)4r84gTpB;@aJ2A#-^*<*a57fbEC0cM
z+vlM7?W24VH`3_}SivruUFneuaL4z9&UjkwkyMVj%M={B>;ZcybtCN12lBT!1O`na
zxi7EhG}}8j_RAIQqC|A3P{x7ZVbi*&TGm2nAAx!spK{AkKzzNcMqF;OMdoj3aoae3
znJy$YDv8@ZC)n8kd@Sxh*zbYuQAy=BiLbm+)~?52##1d$@Rrs4plUs%v<bQ=tp;L1
zX=N7vx)yrCxi{Vj;=N<T6UAFyLFQT=s<skqd8Gx$&YwqWmZt0#TxxBo8^D+=tNw6}
zG<Eq#?UFHYJJ+z<tn_Y0s{H(M(V0*otDp~7AsEV^{HMfMBEO}ovFk)nNQMC=WiaXP
za+-|V;UsIl_LbF!ez=zn%hj>i8%;}rJq73D$LZ;D_Wjnob_`dM?;GmJKc6}>mFAt%
zV^Qvo@9XXJx}Wk9Q$~q@9x9&<xdXc?L_PUm+!kanhfJ27T1*k}F$z0}HG3`6?QZX)
zrry&jwUv7f**^`gRHLnG%=LL)wCRW>%97oyLbe^>{&~j|@^F)hxPDkzjLX0qCG7BH
zxSYlQIq^XKy83au+&eDxP3^|><hQfsdO1^HX|$OM@-oXxJMRzX$c$PJ*ZFT#wTO>B
zA(@do2wIj*Z8!Y|JkJBZf}I6d`3U1Lz!`k6WAak5B!|+^);SSJ>c5qzPQ<NBxp*(S
zjLUS?^W{;J1=+?n;-_342ZI69JkSUd5E|UCm6?Ussp~D8Kz@lfs?Kwx<~Gh4INOJh
zCQ?JGcpxtvfet^8mT5bslzOGs_=gj#hXtMr$|nzkC?$s~gJCfuKPPI4bX3c1&x2pq
zP8?ovE|y<<$Ycfh>TUnH-R&d5WOa5BeeO|;=eYK2?v=%*q=`YJRT#Mmvo1-d?N@~5
z?QVhIEZ;r66B-S1ny(#M{$ZR9-jg1^cl8T~LrmjeO$z^!o>o02Tj&u*Ku@Bxl?LJA
z)K{b=WpT3%qYp9`;mTL12=Tw(VvDO{c2R@tgFZwz=U#BLStLeDsw7>l>iu*M!$fa2
z@>RZyAs^Ny%q&=S&zP?zE#<Utl1VQ46JB27n<tFK{Hw^{awc~3NyYEJ><?k!?sv!d
zm$MmC)>sC`tJh-wBC~Q6E+JD1x`d96jhye&1vRrapSA93UQf4xqGt<kk0*`s_+_5g
z&&|u~2(_)b0ck0z2ap|FYT9~4nmdik23)31tJ~`jH7sR{-nViXw9b*Kh5_O~$Bv?7
z{Mb(#0~Q%Kb1&qzy2|{XL=Dn`FxZv`5YrE+<8-K(byN<~>ZJ<y0jjxao$4K_o>yw9
zcI+VJ`U&$FG9W|%s2{1l=8BFUJ(ahPOM#@MKRpl0x8Oi4e)Fh+_OJ^>BF)gm`IOV?
zLk<PQl|yjxj@#NHZZOq*DXVV>d3^c1)4ZAjUswmC08yRwIQ@Up6TwXaraUpj##?mn
zvD`H@bIv9WF0J%c`_J~`hPk6D_{{8r!r;odZf9%e*0zDo9cS66b%7|usYRgv`FofM
z@A_m4)hs^IWiwXR-CqBPb~=fi#NA2Dxx(piY2p$?{`Vd`KVWTMgr%G!D2tKIb(W4V
zTNioeLqk_gV*);J`zsMO@IBmcCM|C?G}Q|#C&)wJJN8r4s$Ad>@lGmNwoXtV1~BR^
zZQtiR??%b#^Un&R(jF(E$Pt%JSzl@J)OXElh95<8<;T8$SmCd&Z?-D20`5(bn2F8P
zC|$d=zp6R{Bhkco`X2_X3(C%is_{Q$6|%AEZk|3(sk^A6cs?gu0v~eRXBp2`j5O97
zAx`VK$S~NenN8(T0mL<)EB}j@^O3gzL#r0=`;b<~_DPEfI-=*cLpaA=h6R9qG@2Y9
zaP*>@&Fl)t*Pa&3w9U&WAAC7!QCEdOdlmHC86iu-f5ywhRX2;<z=SGaO;GaW@X!|E
zb$5JMCHJx%JUG5k;iFWQA$-Dz3uFop*yH<oS`sR_v^L*=+^@7kGhv-m1E)=<l5v=x
zA8Z=ko=Z1RYDB1h;(B{O<JkRUQyZWJXS94IPaMC9#apT>M_i`GKk_ILZ`rxqYFG|l
z@o1MR+&GrJdmTKe|1s231IX6_K`fMyiBGb}sx5-52hhuZe52D;7zo@&Fi6ENPSC}!
z{<BJg&I^P?<u+w8jv$bEY&9{sEE-pZKC`Fl_&LFr4BmLolv;0-!m!%vx|z`>4RUb*
zmfAsdcbM}}sxJ1$`7T>2EhQL7HcA?h=Xq3EZa+V#$4Q*Kkm%jdcbPD(_9T*&UCz^m
zMkxo-2!b{+4?@&?FQ-T<!zO6EYQ$NN$YSRwy@wYH4>kzrJW(m>`>@cdnx%_yJj}zW
zN;*j$)2s-B&P+z+z}<jUkcsL*qPwnG_CC1vyzQn|sU}TO|AFa93dMJ8{&7a{nFrw2
z*!^@b&w9_i45(@8-p6eHB)lCyk8(ayz})uc+$H3HB=(}9Y|{K%V$*2unQ>{eBi7z~
zhtwyKL(;sYp7-WlrH*@1;03?@;^sL#Yoo0nosCOpC&ji+EIWNGu-z@A_CTvg!EZ-h
zUDbu(@$dFKpQpJY4eE3%<a6&?3I&uu8n#`s&He3nwl4wy+~T<R0mqkBSiGM5ZCS~M
zH)wA6OfKW23~srgYbZO5HUbAgus<KSO19lDl9vlO`cldgq!pb{uw>?OIOIk+JC+U(
z&B(MpJ+S;)+_$^T*6`j`6CUiABkmmc?EYw6PF&Se(b;})`r^A&Or-rhCj}DX?d~+h
znJ%FJ43%-)ImBl1J^}e$r;W4P|Lg<!&h64mQr5=-PoB&-W|QA04gwy7Uv~IgZda-w
z2irYUOKSnf-$#&9wAs*HzGc%^Kx*@v3>Zf7S@xhcJ{il;i(<-lOTE7M2_FgKna-+_
zpT;OJ-~UQ9xeSOIZ6hh{ZTa*>i@J1<-t(PNHJ!cA<P=#I9FaIh=4x6alZJ*mTaKS~
zi0$F#Q`n%>d(6^;Zw8x#f4|MjBYB*cks=dL{}5(GH4=Y^-EMdLg}Js){lFP;$nUWe
z<19p1uTQPhnzCSnXBz*)#J$3=$}6pK^Kl39uG-Jfg9SXztz+%&mncbE8bO&%Oel53
zz9K1leD|!uL!5vs7pQLPxI2mze3<MIYaeDWR=aB#zCoM*$eL-~O5ert#eCGFeAMS+
z(zS{O)~VJ3F%KvwaSw@(BGoTbZ#1>!j%7Fx7bn?tb56KeI)GSjIL~_OjB(6j{$OCD
zzM#q^6z=e^MHb?84jB?Uxc>4TH5id0n(bKbd}Q~=o%s$9%)mh?&Lg1d?pLTE<bT%<
zaXngMye^-JsMkPMGwWsY_BpGkYkt3fOn{L{YRs10)J<UuH=I<jw|-Y@TG+%n+ohtr
zAoLbUWR1Y0?0(w?_}_iKv4I1ey!W^NM`uD0(b2*g2N2fXK0&Em&}JKyqD+-ac4-s*
z4R-aiao6z$x@-bq{1GxLgYUiKc=DA;H}23S(@p$^a?;pR;DM;F*CJDd?sFld+k0Hd
z{YnTA`1fr1G|kX9icp|plp<A9qEH{Q0>PFPod3Z&BpBQpvZd~SzPK{FqEd9~fWD*Y
z3;Fc3dL?%aIe0<uhJ5LpW?W?omRKJchzsu({qr^9N}ZsUu1Z@z99E3B)o$*@OO<r0
z7t$lsc3!3p?MI{NYAhvx7LLF3<B5}|8lQiT1b)JJ*kCss)=U|?Iq-%(-F*Xvh+&CQ
zSCc~R)CL|`srO3CvV_TI;zSGxmwBDmI4BIMKyxG}r1bfxjwFCL2bMJ;xJQo8P@}@s
zXjLzGZ0!E=Z+71f=vzvz!u^Rb+4$dFZGxGC%<0^a)>%Rszez8?v-eGB?{l2uWg))G
zt`n5q@7lTfamES1?j^fGqFf-p>a`&%{>sj@?ilabD5>gb(W~(IIl7aOr#=Z-;@0%x
z@siJUfT4fC;Y&<kf7Ew7n6LtAyyh7ESUgc{(V+TX3ZX%jSPM^5Iot(;_bN2pPz51>
z&9;sCi8g!T*wNkIUssq~RxuAZ0R?W0LbOi|<#u)TDX)+`0;i0Ld)~^$%(ePQ0jA$x
zCCX0D__xx_W0Nv84>DElESi4P6gnUWDoAJ${mqoBuWjd@2gPnOgDP+pHVL)0-Vo+v
zB2iZNvXvQ6M0jxI#<*Y`AWQ1=OT)iCE{^(?!h)rK&5Fr`higOUfw)$cGLm>ZGM(*p
zA#ZCcpr+5KM{UY)r035iKJ>pNe{`fQyIKjl;hrK=CMaz~-W|S_6Q_|#kW{K{d;*-o
zG6wpJLd!!kCeuDrnMcW@V}fcdFr0(a&yho-Wx#@JEfrq*alCUA>7tiDaj9fU)&z!c
z8XZU5>njo%SM9Stf$cX4i3Nn#%lPEr10^8OyLLSn$z=7Kp+9s|66HG55?>^y9!2_A
z2@q*aR|bs6wBGi$*rV@aOvvz2`q#aMR(v?K*gibO*Wk3pC4;B10Ycz(-NpRfS>!_y
zRda;t-NFNfSKkvd3B7RL0Z3pt*C>fckw<KmnH+Nj9x+5&dV!82kTZS%5GgoSji$oE
z){+=laza-BOBZ+FenvhQ!l|w;aZ)wH@$hdEcc+vaucnLK4t|20`li4LLvqlaO)4bC
zxi)k`2tpzIEe9=(GT|nLQrT;#DRO4XK#%(q#LsaV79u0@d2kur^QaUGbJij&bUbgP
z3yq~50#`nOxs$?B=<Ec8!KEDo>Y=s02v52R`4h{z4?e?jARe}{-UY%y#g5wWVx(BK
z;Yu6cGR3goVM`#YCj7FRFQl>CF%hb>RHD1IJ!8r|dD06owu>_s!GRv%#WIp`5hSbr
z9Dz8Pp&lgW+9evbTo-ngRQAz&@JVju&4TjblyJ+)Rk-D=bjUd-24ovE%9LU!@<(O@
z_FO#3=k}HN`ni93`$(UIs;r=^mEU*XdFR9CyG-wf!4lK#cM_Le#TmkVm14gUv#3u<
zs2lt@D8Rv&Q!3CUpU*UH5-g2j$L0{r^glYi(0m=7?3<yXE!1NJ_=@ZYtIIb2fzJ`Z
z`eM_#wbw2V>gcQQ$LgY1)ncsm!5Gif@9_!i$n0?a^|!9<PdNVH9{iyAbf!wria=cE
zwv4N5)G5xgdhhsj$C$7eTH_M~#+3d<mBonzt1F*ZKPZY5mJxp=$SqGKz)YIQ50cdG
z>h(OM@@uW@mb|q4H+vr8v%EKvvLKg#+TeP5Bo~&C&m#-;V0Y|ljZW6=!~0cC-j7N&
zjkex?m9d+Gdv~t<{NjYDD38;f4<}<nfxwPoT&BK5u~lu`aAcJ|f@8@3I5{DHy&}gn
zpoDr3vD)n5=PSrLI9u53hPd3HX2L+`XWViEZ6^o6&Z&S)h}&x$?M7JZH>=j~)7!rz
zOMLBvkWk<nKXmkd$T<00D@jr$^KU=$(CTkaF}-txjwjK0JIrlCD+n(7KV0-Twm+_y
z!OmSWTQXpd&&RqA^&So9^TZinC+O_6E?(UvlFVPZbuuefgi9lEYlcG{F022&Tx<0H
zF|F$nnDM{AZ+cxQzpO6J@Q+vR{1o6C#$G0apLc;WA!%STsi1gbmSF$DZ)j#aeFd89
zLe*wmTJ!?ZRT87ZbwB%Pt{@TYf8knQP(m$Xv8}eVNdacf))Ql2kxwdPiPMEA&CP3C
z#!=I0S|&_(JGS5l;7(Hy30zKN>ALTdrxi0XXJ~x4Y7%jlCtS6>Y4moFtj%W}xa%>M
zW%V?I$o;II`3q2=FW5A0zQfaxe=|Ssqc2q^^Qjl`47}2AtQ(xa95{7Pv`{UxscMZ)
zOrND0ijY;aO`}pO#NWI5o=3G;<DuPNBQ_uIs>k4ZBluK-GoR2JY*+k(<ogW;vA@V5
z{FQHa=lNRe==5#`u2382pwk(?gfo8rgF5+V6qaFn%7b8ar)Yyg#sSOW*Y2j7UlU(=
zhM7U9hms~??E%!p33{fjn1aPZJczy>zwjV_ex6o;)+V|u>DB!ex4UQbhQXSF{Ipi1
zLwUp+3(hmI)6O1~J|GJPb#%qSMKPlJ1*V2}smb$+?77)xpw}^O4xFcznHO=ad2W!S
zN@+=u-4>1u3@mRWp~%p|*!dKHCNBwBTjfq{$hG?f<zG?vrjNgzsR@T4sGI2*>HgAw
z7em_7=JCH|0_5~RzHsJCp4a2xl7x*Kn<%#w#YuqTaB;l}ty)d<6D2>WcRjGoOHhY`
zYJzc^>yi}T`CIWX1Z$e^bOU->=@lNnUh~-bj7(XkUiKVvwc-*hwak0T^vTuZe^PLY
zeI3rRBy_W)r39DN(I}mL9C#NRAX!V6{Y85dW*}^0Y!H9#f}cqL3q6XBt*+jQZNJ|s
zRj_7qzAjPbhs(_i4;hnWHpr+`5N*XIOSf4VA_QbN4OqmGzQ~^ryti2+8X0#7_=*Th
z9Bux}-#F^}cUuioCxw;Ovft&8n_b-yJ`Xl~iKSv{=*yy{`917vD0R<mkTc=;^EDpW
zYwglC*rxBieZ7|1QGYY;LGOui{BT<)_^yl}HuCzxw0|ePk$YwQ$gEUD+q$A|rt1b2
z1tQqlFr1<U8w-ACLhWDhL6TsJXl!ZtLO_M<ND`f%Om+%NP~@qLv<6=R=}e$FAnE^m
z%HLG`n)FU(Q0}1Bj(N-NNx6WGy`6EDF!|@?o4^gM;4b53Pm7VsiX1-O%_{2ajohbC
zTDjT`>mKO3>!&Ni9--ANOci!EJ4_h|{GWhmBsWWVklp8+9#}(e$4dqFUcn398s@NT
zlVH<!_teOIYtZ;^r5v%TLs^@tuw>lii6|189Vq<csSOcQqGAlgeM2T1_I+zeg%3rp
zyroP#ek>&&l<ExPsur|YDzHXI>n1@bv6-OT91XrfM`>g@DKuE7(6r>LYwnR83ca(Z
zwx9yrVoJ1Y;L?;>)$#DC7@D+*<P%^XDiK=$FJEO}{$EnjpyjJ%oWsV9rMA0QN^L$u
zZoIJtj<L{PqWJG=6x?EWzw}^Z)1BI0uuU@4jm_EX;MhuRKrPcM24JO?edZR<p~5;)
z*5Y9E0e-p<3}{XdCa9W<n>-8KYsz$+Je_q+JwjAVnqNWGd7-Z}5<f3-8>6H2*xiOr
zrc%mEZaS$6_oY!ua;b|SFkVc%99j9*8MK7EEaGZwS=(9XcP^Tw(aMHwB{;Dj4%AWQ
zi*(FO_~HQFbjWVUFj)Q^iC^Ah;g^-+P$56DX3y*?5nWyi@Njk+-i%`3GGDKI?q5kU
zw0IjQ%5s0Vw@%x+!n04Ws#~Crz_!vN$Ap|ue2th3+kWlpmPr(eo;J!1eAU!3(7)dg
zbDfXN7j`=DRXt7bzWim@6>5z(Dw}nIYFT1aXXbKG8A^T%0>90AK$nqcLfC$tG-{GG
zDwb5Ln#3BmcS+v#L;xpn)&ZAVDwKrJy%+qc4R*Ty29b7KK)ZkUU`-fk?GAj>&MUuj
z*CqH!mbAZW;12zUG&4_iP=Oh~*&7+N7kQ~v2vsVrgqx2;Q&2Jg4`G;lwBjnvmm+@q
zO;X4BEP0et>WYvlb7@86%1&W0dey?AgSSD3NwatkZkwT_lTAdfWA1HP^+6IgU|$=9
z$Vjo^{3{c#Z{kQpfj{=nP^Jtu8XE^OIsZ{5>Hnw_>uNTotou{%Tjnf{oXXYR&S>I|
zTMES6$8n*`;!Br;bS|~iwX4s`u;zx$uhuOiK-de&>D7&kl%Y5^en6fn&~bPg!Ry^{
zZPzoL=n`Q9tLYPYw|4|mPgz?4f6Y)(I;A}dq4s#^waxusGKA;_JbIOH3L+q?dNkTT
z1(Esi2{1)|59+c`x7NF@m7knFl3jtt2ah}9Np44*Y)3W{_4pIf*udU&i;hTLEC7L|
z4o<KsB6*)^70jDCnbkcwJz#;m0T8pKH*!7hbeRe}L{L=cHbim0lWlb|4_tegrBj{L
zy6jHYC8(}j5JBp!F4u*tI$R3%h!q*5z;EdO37hnY2dw-!cq3QcvYIoqN0IjvvjG4>
zpQR`YFaFK1lSWDvD~?6TNpE<Ihj(c2jJ1b>bZvs6OOD7o??4LQm-VW)nT^98l`*E0
zs+Hr))xQ;OGYDuDi6FHkqQ_oG*n*kUZ>WQGbW#c-lM=Ip_YF}&5Y?(&J0#^oZLXnd
zx#I?8u>;bprR?ABquqJqLap)UoBhzfNqB)?Ti0Iru(s|prL1DYq;v!{`9ryU@pj7Z
zq#(FnT1ns$+|E|RcwCJm{go)RTbjn^+B{Q>8MFcvMCeW~l(M{HQqEAy3@H!`=fIX-
zJUi11qGP(c8-eU|f3FQ0=~6O&pHBquR+RFd`-XGgHriDE{8#jW@#cTUzpN3i5_G-$
zn|MoF*00dB(g9#NJ|Li}6fLY;Rkuxl&Oh;PZ^MZm_5D%)(yRh4D{;JU9R9I8v|!w&
z+p}DWEGuM>)W7gTA=0R;e?7n>r8c|g`W4uj4EFUiz@-hQOFZBP4}-v?Q7)0L9$&0J
zYKCqYlNOtoS%NON(as{Z<s7$$?)>_CXrWg%H@9kCqqlh?hl(=&TN8}vjkmv+r`%j?
zo5_66x-ZfjYq~ZUxqM!VvyAf6#b5b6u1ux3)rhplZFS}<L5_3#3!znX+b`QE-k}@{
zm$?BxXG?1Zq`jcjva`Ql)g!XXzKq>vx`T#V+^->7Ugt>BnaR|WxUllF3)|;YUXy+X
z>FIFDHATN2F%g{qE6wYtKYOCUB7NRDd8B$`-R;Rn{>MBE)lk(HC-=mxY+REwe#c?h
zyi)-u?h?thkL4c_wLn~AqXnH}x~rWX+J?_P;@Oi_@1AViM<nR_g&z~gO?;(Fd7NEh
z!JpQXUiNWX?C$9SM{+mU{=gAzdH}f^jy^kY6xGa#u@&~rEFj?<prEOe>>DPMd0xp9
z7zg6=twQnLK}6;`Rl;<>=7BkYaKPmBc1T}J$G7IMPfh)(-rjZW%y)j;pLyMWnTQg_
z6svgJiqBltw6Ht(vaZo~JB{3STDjG{+HAw}-MF>4{biT#S3mvZW)f+B%*E$!0FM-i
z`w8LCtgJ|O*XRH4?shdCKbfTX)Uy529ECTUR+h)vCKgp~&i#Jc_*u^9;sU_D4002Y
z)H%yGcpdhS=bXvzS#@2E31IZs+Ap_qCn_XY)XwJ2{5AQi;db*TELTZ|@IYhT(eyj}
zYc91kv(mySXtIEM`_c5?cV7L?4x~EEsS`16{&tbZ)B@#E)2}>1#__2Yq>e|MgrlYC
zB1ro<?~4q%Uq>r~`%J{twXA;p07A22R3Z=$pYLb%H&vRJHIr6l92zYxQQ-GqIt@2F
z1~SdZg6zwC&4&O8W#|SNY5{lvR#-*AdSWOQ7a=jIKPTpbpq=iI5O<0UPxK}u(O4a2
zEjY8W5G#s=pmk;AH?E^{81Jht9)N8O_5PTMB^O7JI40__aJkpkv#zLI>2$S5AD!lL
z&`+q0C5I-|@OjPFJu(*C#2}{_bJ8>GYMHvXO46OMvn%ZU^;J0MjTRZpC8g4CYLl%e
zt*%|k$M5?|CaY*A#m22+?4B!GOyqDqL?3Lj4@xIAXr1^ngjY<&#Mf%(mZ|wQmEK}U
z;9{!QKyJW=dwV>KUrsp8+(jge_Y`rCE}!yL2k>fOcOYRv7)22);;?g1ZIFEWm|_W_
z*(Reh;a3=s<OCsLOMfNKqWo8I2`D62U;{N)e0}5G!JUINo;uOeblAWlZEuTsa$b!m
zmXxJTS*ekw4)gtgscVSYe*_C486qg)8PFFYhH^{p=9)VGWkQx^ZQw9g`-=c7O!cpG
zj@Px*39-Ar3F}*ps=9_=hH-6pIDlj@E`2|~g{R2^PMfE_>)rcm$Wu02?{ne~z~OPv
zR#3{EQqHTYilHH?hYrY3uidY})SIe&jWq;LC%QpRJ{}E`TMGiug<F@4UjOpgkEi3~
z0K_&oqDgyEwXITC<}LF>a|6^e8#~z7Adx&^Kvq5PF+Bm$w6^q?JwmI;eyD2`&-cXc
zvV$P7qno&fE18gCYX8!G<C2rG^f~QtZ?(}4XtLRA7i&S+AG^ROd{&6)V*CU}6=L5?
z)G1d0<Mh(WWi|P2sXy+^c?WDE_6L2LaOi~1FB1T}RNvJM!gy92UvdmHuqi~$fu*C>
zcv@DzSdQ+6Gekt<@^C1bIyML6`pvPF8+{q@1^mHQ^oZm603~8U)elQD*e79~tpzna
z^#wDB>vI&u0t;!3u{mc(K#c-EeXV^%L1QxTmf7bvL(RPIrpzamJ}*E{$R*@%Z}Bww
z)z0^d6U{aU?@&|Swytr=vjM=MjZHTDnw}C1WGh-$w-?m#dFm^|68t9iS1;HArVv3Y
z`k!UrnU_i`iI(F`F79LZBh#z&7<3KQGTpCW=Hmi|n{#^FzyX*%CVOon7P~?GH!U5F
zv1d6|Lb`w~*kh26#uTEoI7$K#ri!E$b=~#`aM@oa+PCU;f!0!Ci2_lkTd?ID2g&0Q
zYb}tseo*NZmq_N;v|gsEW4<IG0V{ccK2Vlj9In-J?vMJL(imbAP}^JT`lQ|3k*_{z
zzy22<Y!2)!gKV!RfV8Wmb4>tgLp?D;JPSg^XvFD!fvnxtBg!0e$$6>Ii@?9??#t}T
z!`8Wqnu@W-O}sglQiW1{-upj{Qy00)7Th*<`9Ro9|4+2<Z?lUl##iNa-KTHATl4W>
z{FVY1L^ZlxB$GltXnDMR%cYho@OYNH{BrxH?^n?Rym_}9z6LZ8D9(2lfzH;4Zo=nR
zk@#pW=|H(Pm8E#Y+)qYbU7`WjlD4D+tkhaC3E65(xgG%($C6hLPv?zQpI8`tX7zzH
z^lhS_T=h}q#NQYUZSDR(XGReJL!+%^sI|szW+XdO4VW%QB<2^2v(n;ELoMK|1^P)y
z`s1+2odN4-T27f=?TK^y#emJbXg3~bIH7Y|jHT8%G<1?h^EOxW%g5LlQMn0=>}NV*
zjDOXJ9&8(^`MqeDR$^u%@$_DvKV%9yr&#dTTQ&nQoWw9pJrc^Wxec-e5<dn6!r+kt
zJ0O}eOyZC=w|4$lI9-v2HjUJbWf`t@iTLJI(~%IqZe!2^KTla8z8fH=v1Z7ew>Aba
z%P6XrS^qJ=4!!@RKrm%~ZN}a7&0jh(KM>7o?w35eogiX=Z3-Y4$d7q_d>sa5O5x?`
z>uP-O*V12mQEX*fL#N`nfNMzCczKTvto>m%E`kp%pZMNaR8~EeWfovADDMEp9RR)P
z9X=>ww#iBS1%Tt$H{~#W?V|(?rVX0g1X4%jdFzK#sOireQ~+c)=DQIqtWirjfyi0b
zFjuBv1_op&1x~lgfSu$#pGf1gA{Z!*Qo6_$xUHlB!oiBR`E^epNLc6s;TF5bwS4i!
z#^&BZ4WVEFX1beGlt0ZcS`5E<^SITeK+o_?R{flTNoA^!L7m};?ws>t@1B<*3A*Q&
z=c7e_A~PoW5&w`ylnd{ydzISZU}sb(Tsl*>Md%t#MMbeAP--*K2gC}h7;B^6u~jpN
zl`H$7I5mGItnp9(UBMPZF15)z^EitdrvNMRJ%#Y7_#^iTjmdOty0k?(_)4wwa`1au
zNp13JtlOD}L||%UeVwbUMEuhCg?!5n<r;k$d)x8Yj(@-}Ix6PYrf$uKg*?m_65Ve;
zq*^@O$Y7bSrM@*;>)h3ua73vRU=L2EuUTx*2fDE+cGBEXA7R&wQ7_zd2OPO%P2nd6
z`%Y-NM@6cpUUK#S%W(hyPJ=FgLEG}&U)U?<Um;WM%IzNGE9^jIdxG4AU7&8~IqBsd
z<4Xu5i2Q9o310_I+c~BjWLL;y%lISF(8TKTS@}z`u>RT5y`7H*>yui(#;cvQ_6raY
zn+?ILBHG7a9^*k?c2GI*osAni(c_33N+m?`yPhP{93h2`W}i#)VKwgC>NO8MGO9Wz
z09mHbx0F6xq~0l`wbTbvXk+ajPlCK_+MQbzS^R^p?bq1<aEl<;Hw?K%r72wF;Mj4=
zqq@6IBHirCbp*Bfq$Xvxb=0CV2wX(Y$%Dz@BO(%$0gR46t&BVTeKtoY$!f8-bKCtx
z3lJG<*uHji#gLx&lQ9%;_FobcejNdwB9}_&J`gdPpKA~(L5kMTLY_V$C6thi8#WVR
z)c6`gE@A{HU)oH$$C)=k77(4lnP3s~OKtG=4`wK5ASTIrOdhIPDeZuOkLmNp<Iu9H
zMBK$kZAJ}|A*>FOLM9Mg8LnGNuJVrr!;_8wQ{7egMHMw|K#&k51Vrg(r4eZsT)JgJ
zQlvqoyBnmWmu3Nx1&O6gNkKwFWKmeUq+6uxyP)s;{te&$?k4O#XV00LJM)~G=ZKxZ
zdPE@+urNZrd$5yhYHAY`cq(;)4<*1FdzXInA$9-!mo*&_fVP}`+a@LAATpz>3~&vZ
zp5K~0@cNl4*@BPb`<S7|zh$qgCJ#PS(`MB3(el17kaU(CxWfC?7Hf8%{v1`raUaVi
zxc?`Do9Bhm%GH5mtN+;s`J5i*XqI~9Sm)I;7Erp+>z9-f1;n2z{zn<a5>u14(Et{6
zEhWpwlGlbr5hG_u04(0oNiTJp`cfRod$7+BS)4g8k~1LdsS({<rFlQ{Q+y_^mgU+)
zE7T<E_E+`ZzXiTTL~x7|(1-{H=Qe4oi-_v3RMCsa>0}m%3csP&OYQn|&Y_fTHl9?q
z2IQ>+&z<Z=CqFbK`Vw)iA2h8^0qed%zzZN{Ppvb2#rv3X?$Xe%6u13mU|zI5e^JlN
zh+S{4Sx%8I#joVs)DPr!cFR*UVyD914r*U#BLI;Kgf&llaNpe6JKa2<rnfI<wu?mo
zFkxW9?ofJ33BR^(Yx(pXdgegfU@=DQr!((?+`I1=Bd>_eN1h9%HsB(1pB3K+0lxq&
zI=HHx@?!7std5qtzaEgOH@U8BM@%=#sl?b`IWmZs7MHCcHY)`Vm@B%$Lj7ZotM2TG
zC!5>`*x*R>lUyc`>0|^cQv|e><0qt84fYZf8xWYnc$7VCLUztfKbhmF>;~N<BZYgx
zabFE<$hVlH{tW*aK7CmJIF1DD?1!1aV284}#jVolK!LOm^C}v%m|{qP=E0cWk}Vg?
z189ZlEW)5qlY5B@w1U@s#M3lU$L-Q8Q$#<!HLKsIGg*)4hdY_{3TflsVTbj*{aYm>
zfa+d1{z-ewmf-O~*3~nWl>Cu9N+{|Fk;;}x;d~KBB`vI>&kroXw#c<ZW=cw7QNO%z
zfAli;e4?N;J)ZWX!jnzaw6nX-Gn;>8Q)5>Fd?w9ObNN>MSD!VZtSmc|Yb?C8>u;d~
zqm2@<py{{JPrM(++qOT@ZZ}aiID64{F(5t>Pv3Yv!gIBHbuxD3f0?L3vk2TLef_TS
zIQSfJNAFLq1Rg4ZuWB^5y(M~m{SN5;OlN@<LOS#1T`CR#wRirxyhMex^Z_Qzu{_pP
zn?Ap5j#}nDj-u~3(ggm(=%E+gjXMOq4I1BLj2^lG>$BiZD?e-hBVXRx$Xb>YsFTLb
zNQ2A<6~aI|3~Ko2G!QZu_+T=VIa-}4CzPcn5^9J(BrV`#kWJ+9p>x`8j!!OB`Lg%%
zGq@otd2DY=!(=idD4pe_ER|%aJ*{*f>FK;N!xA2JG%}ywO#dGG(7Avx=qPX_h&WpC
zxt*{t;LLxzNN?L))Npco9hTkZ8SB~SJG&*V#na11Sz%vSoa)l_%~A@2hczUh(7A61
zLvd9I7n6sYeyttVudEneAKv^^tQ(^zun}|Y(dFDH|6YcQwR0bsK>DuQCPn~wGw35?
zXJ@ye40@qA^Q(tW>Wczhx_JSNI@Qq8^K{&8rNLibSdlTIUXFi9iwC>R-h+x7L}chQ
z6^H)_D7vGfr~K<v0@;4|ZKj!&c#{h`IqKqcjK1UNDUQg&9GGPB8L_zfKPSECm}XQP
zVv;2VDUfu?tg$KiJOFV9LHaad4#@>+!zD7A<@wKvB{zS5s6>KjR-VEp<fAdv?jvc#
z_%OSg<nZ`ugisp_=lg+Y_m6XuiI}Tc%gy<P^%v1o92#K02y?>*S{Jv90W}>>;-USD
zz#ZIXAMkwEP_|{jC;65n1-z$C)WFWprY^ODG(f&_dp#??_Z$N!5Op8>R#?ht!`O0N
z^<O%=ETaevkv!q;i}U7MWsY?pTTc&tKRYy>NgVZIB_9an*lKYvH?~g9{rD(%Y6`gy
zq3qx&2G@ytmK<}f0dG5dPXM+4S_RObK?Xfadx+JI77kQOISvj(vm3;`y|9o^hFU*K
zH{FMVPE~)Xc*UtnDFfgS`t^Ybzm)tp&nj-4kn8ZeJ0j$7YFW3hsx4e?Bo6v;11UVf
z;=>vJ(@&?v*1>7^xj_U+T`*J)wvNG{kmB~5tTrwf%s|Q{9VxLYWb-M`GM3R2Ga>Z0
z3%<cDni2wgo##%BYzp<CT|Hp4pzD9A&_@92-PG$KjBcd%Xyr{7v@9K$<5Xi@scN2~
zX}wj?>TDOI!~Ug;wTC!Pi|2MD>eEHs4p1xK6AX&o5&QE#y+(I5$nLa;JV~cv$mhLG
z@!aA^q4H!LWdw{S2gw{{{j#OwX9_pq!SJs*+q-AErj0q#W-0TV*cCYSEd6LmE{ygN
zwg95hpG!1I_1=yJHf!FB1z#Z`AXf%OZ0L0+nGLy9l~SzrfUaZH3J2f|NUM0@Q0J9p
z*ft>Xbg5P4ee1oP!dYft-{|Ha%Avj|nH7)@tSDHOj++PgV9)w4KIH{Q^UdD-FE`eO
zaM9lc$oW}%ta3hfwL7M?(Db<OSod<scz)5?C*jlrr(XcG%QI%w2<4UmUmFlse6hlh
za!VBPwoiDHF4KpBkltY9Bd`dT?$7LY&1H%<hHTJ5utVp}8eI$g<1TrGf1M}bFNWE2
z5?z)Co)k$qxg}k#TIVhR;MFfbT!1GaV8E)T|7w?dcK)EhR1f<5V?3Stf{_2wb_#Tc
zc}M&lp6eS8V2LNoBNh9=rM_?^rm`R}{RjZ0R7X{`9Wt98ls>QINc0VlYr;?x{_6y7
zXR%s;I>TJ}O{!lmRQPW*0{F!43*3{!P_-F7WYP+t(gRDj)DmZXSOB1OTrPtk-`zL%
z3p00p-)Z-q_VFUc<&o48e(TAAe(S}QXu#DZZ}Ps;>l6v8%i?5-fLX4q!HPgm>fi47
zY2ehBz(NFhQFc>x_tl|-RKf6OQbF{KIRPOk(D*VC+_tTeJiK0<Io34$2NHqj8im4@
z<Id=E+10kyrK`Z2-3Qs8EmOZc)%!?kRxqW5<0_F#c4r*p7^(PSgw;|Vx3QHzVRwAq
z53nQQ`@vC{qUKv~?My0-)iJ*;+Fbu6-kiQOi5V}k(^V?OQtcL5510_bWJ$`XI{IT8
zWp^|_v5neNfc*vozzvkv>U;3U1RiErbG*IMrwcrU2W|iY=69axy})8wrc+=*=-^u0
z0t9cye(NF!PnUE2vjPGjk#>zg^>D`O5+UE$5Aok)Gh(-{JR9(S8%OTsh>sSH>r!Ox
zF+Um-c*zU6^1#wg@Xj;PvWUnNNFA)d@MD?_ApGX~Nquu->nT_eJn)fb*QV?!uSc2A
zmwIj}LR7-A%^5&O3bNn7z*8K7A+3nVs(Nwh6o}tKD=10KJdHcrJ%O`z^w4Km1E#Ct
zzGcN%Z(!`Zl9DO{)->rv1fHCaub?S^LfeaSMLPCQoC!pC;zHl0!o11{_d?CJqcIl`
zn5JLKmXMd5YxViUVlczABiz$M(r*;uDZ`)XlG1BDfN;@%*kEL*3rI`8&PP4vIk*x#
zo#Qfp%zP|529s#psLpva9?0!sO|&h6tL$!5cV%sN#ut1g*Rd<kG2KxgZ)SK;Z<Is0
zn#S=PSQR%g&{M@mYM^%XI^H<%czAU_>mOl!`g`#_mOjvI$YaZ)SL*7@9~U7Aq||5x
z9x_^WbM9Q?x5bBRb_D)5zGQ<E1njBAyIj4)XH)3kIj{k$=K#f}Oed7P7AY_KT?y)@
zmvd1=+32>U1ACyJCeHS<IB=&~^S1V3HVHWR3J2zZB5sQUR(Kah4jIFCXH2Bn5{_Sf
zAiwpfi^eoP1>6Q8x6HWm&NMMBnp|9tF7AlWG1leIuL{4h(@DyL`EEI14@>9qu=)1i
z0g_}3lh)IZGV?CjeVH5QtlO+9zdAUiuQ$rVaR-r!r~fpX4DyR)0e(>QcpE(H%CY3n
zrl0~W;+>S*$|^;h8x|;6)z%NL>ty*Q9Q>iKpm2sa96F10(m`LDE!6TKH+7R?iW`eV
z8}a5DoSp$?G?^BmzIJx{R_s|%bg1#T?DR1OGs8rTWNdLDCNWHqM#cH05}{&;_n1+!
ztTCb0ernm}w-|1Z*N;2Pt1j07!)59h`EO~Es@qqd!IB7MD{_cGAPsDiX7<h8!6&Tk
zV1$10WUT!6WZ)rLX%;sObqxe273qB4cLl5hfF=Ugz6H6+G0m(zHoh4UtL>>N#<)YL
zFo#Jnl+#tU?lmfM@rxjK#+V^2!u)yhX|9|yeXvE%84*`TQO=oj?OmlGLjB0V7?h+m
z6dxRCt+r^8T${gQ6D}pYhCTKWu^H$`lKq3L?ve<r5-EU1tuXpwC6Fu`WP6QA(EqFE
zqUx4>SDT-9=u{BOIcqR(Exd-(lI-(%U^sKqLxFtKQkzDUlK_U`!E^){ZkM}((2i2K
z1fit;7naKEQPEo7lV=~tw+SnzKYx+`k(VKuvCF>gburrMF7#e4+9R=@fJ59;%qBun
zPCJ`GnUjg4imW`ZZrS9L0ov<7Hi)*jR+H#i2K<VpkfB=&Y=BE!I|>j5`bV_8rsvYV
zgAvahioGT`P>@{{3wDjnb|suF0j34M`h><vVS@?-arR~HVX!M9$i;2pF}nIK_kIwa
z1w{xG+fPZ@wrM|s_Yv67mkvZTF$@AqpjF77kXWzO-X9sg@WnEu>=jk0vbd|DWAkQ+
z6v5e?JVRK|da|BICxa&<CM;h(*S6*VS1)GxFmLqY7-J%%xNw*QSzT>|?c<bOQAc<C
zu?O9(w<;l)u6X>{EM?mxU)41`j^1zP;**;a9{X1c7Cray$l%|j4S#J()K_|LIj&4O
zwB8M-$}#5M8jhp}A_@arsK5E|gTb*%R|jF^K=w6;@Gq_{^R^9(_P=#<np1|p9i<*L
zo;>uRn-tBZjZ)TI=f!+hNpM!aG&ni?sZH3R|KhL?ZdWs9T(~@18CGZ8WH_X@v6=bM
zIW&A5>)s`{Ws&Mv(6Ex2+XxS95x|=Pp{Pb1%DzkQA9`0O|L(AC61m~KU*+IQM}He|
z^Tai2)%jZ4Yaz)AC2Vm|l)na&1qHYeA;e$N<||>uqDZSI3K{nGm=t(hBW-^^(;)(J
z{bHa(x`#Z(X0+F5T%qepd;*<Dq-Eo_C*i!X4Plwir)U+C2$=CDQP6QNBdtFRRLai^
z-5GD_sb(?uT0a&yV!gHmd^0lt+*|r*gN;h!Hm)CiGpe-;H(^oFRSTFhm6DT;IvUPR
zgB-+X3b%jmSqN>uhu5yL(6WW#+nL@gP2cj$Qj}A@ovhb^MWpMi8})oZo9_uB*glL}
z50$?>`ikBDv_vEQ4YrQ-SCA=w%uCc_c=sKe0r~-f`Gh|xx|kNZM-Di~r)3Ho<Dwgp
z%_;1aSXLnq07)Lrf5LW-fBFg78AOhW0`r-xtrw~@g$MY88SUfsSf;NbS-gTT+Z+7o
ziX}prX#_L7W|-d3Z~%wx{KKsRpz`+VFbG<C2hg9y=*Z{5WN232QN<n66Haks6EkI=
z%1d_B+vL7GhDxR@oqq%`=u8)WLlUB0B$&)*U|Zrqq2Yt>SavxQprkavMDw9P(jkd!
z@KbcYJhI|8=&u$Wp;K|7{PJS0;+Zoi`PM?~N<C$H71|IWwd~dA3kO`rDYGXp5b)ZJ
zyM@k(7;byJjFwr9!2%`b*P8~y2#P3mpz#HLI*Ou@(M(x(yPnBkn>0A3?G}7doCDtz
zeV>}l>$!6!HZ47fk`Gp|QI&@Z;<vhz7*dXJUVtvX^rW(ue71H*YGT;wcawQ{-wA}j
zbP4}C>Im$$diRvwqtfCo2rJBKZ}UNSbeptPt7^WXUWW`p;BIsHclvUM>T63%<@?W)
z`bpcfPr4=D#c7iM);F)5=7D0<*{d8tC*IAPXT!j0O28?Wjc<k*Rh$CCtjtNSk5Qa^
zxK;`_um$FpeQgd8clI#i%#q#RuV3N)cy#@0p^+J_mPg;Xch}^PsfkK$eS#=v8VChh
zX}We1(2oCbQQD!R8>GyPg$!ho8XLi;<18c(VHaFv^A?Y1mo!j{K}Un0QMG!oXYpGv
zy~%KmbE-s062`HLVLD(#_dRm7i|pjHYLh5aD>)|Q%qT|QW~rWr=B=xd6DWw0Z(?l~
zsBu6ZIaoGc$xlf~Z;D}K8BTbi`a_y+?ipKctSZIJPvxZ@_UeC}H+b}8w<Y?yD*IOD
z1A8Wt@hc6nyr*YAy5Y6bbIP8_?AA+o7D23KrU_)#sxrk(eAHy^WR&G@p2$i0=0u}h
z0!<EVEYWl!dlm7f+x?Su^otJn_^3i$7D;gpQ<YG+i`VmS%ji^l_Q)+TR(=<w!^Yp&
z6Ce&k@hcwznY-Fgl>P`QdnR^t)OBlqQpkUZH*XRp5l8d6{t=$#h(@_tzddwXwwPpO
zW8_*@2_J*MUq6HMQhij)!fhp<1q7X(OSo5n2{F_Fs;%3}Kc>ZOhaW=lwt1&Dgtw|u
z#+X#8ZQB-Q_=zbXg-0E!LesVVfI6{-Ds6L4_oSy;{zM+?X7ms7Z^yeLJ!21?;DCO5
z&5JN^;{hrWOu@Gv3*CSHW9s4a1~I}H%Ww%~L6=LT1fiQZO6J`&14~vEiY`@@{ZW53
z^?tXAfk>ZDtsHZo0D)wGXR46O1uGN|JzDRS0#3);B>S!JUG2lvy=`m~4Ve0za+>Y5
zt(}}99yYrQdsSGMPc4{>ewL90jaK!#H>LY2-fGH1@&&u9jGgJCzJB3?PouiHjh6Ex
zRU9qV(`0~%z-2{X{{-M%j0cPXSs`QAFq^_11(3L9`N6ds76A3|ZEjM49j2tbGmVpa
zs?vx;016*J8WG$>TVGrJv2Jr>dh@i@A*C5U6cXKF7g&>>GFjsg+xQvrjg`wZ@dMYH
zv-k|#D1Y)Li`FIi;*3a~+xEm*&E7KC0}_#lRn|20YCvr4H+mGlu^a)htkBYURd+&%
z!Ujh_2g^oO#)sRcJ}Fkmf-T21gvy18Ud`X&5OVPJF;~kmmZ?h$%XD`Q+gH(^SAQ<E
zW511|SI_yYCOW1d*LwNJRN$J?0?3{$F}eReYI&)<pB&EQEv}JIMzaR6>_o}pJ^j`<
ztZ|lYpDXtcuM8u$n~XB&kKUcJHyQTzwa&Gj%7Ni}J=#+Qx}S9Qwt2OV)@8+*DsPp$
zRV1v#n&Irw;T+XgcxzZotpcY_6@??<9*~sq`KsGu`=0HBkm%?J^jjhQ_)+~kW6ums
zReW`gdmJV#KekD5@y>kByN7pb6PV78M^cgy`|1{mWn=i1FLd|C*%V)AO~t8i`Ml0U
zHAu(nM&<nEO|dY#oSsVS1qR=K%EL-e3lkjJw7|;53SL<dsV8=LM+(n<vHPo~U~lo<
zgEU#EdiT`9SIOE%fZLK<2^j6+Z!^{(HKbQYU%rV_uSRXZV&-Hd9^17@ecnjw0JINC
zY=}{N@=Uq=enC&9IHUv$Bw(-WtRW;ZXyz>*q|;Z=MD4JFTpP`jd@k9Y%O+xb<boWB
zwECA6pHr()V#JQ(mp_RkzsvlQH_si511KnL)u=Bs!Ou;c+ka&y2&ykLB~s2%x$Nl`
z?IG!qBe<_ZnP`EzSk<9R3SrvQ+qpE=ak<G@>yF6$hi2ev&wL}kB@MAys*7`bb8+f{
z<pj)JnVEqS=beWHzErBJTQKb+mPd@%OS_gr_D@Fj@m;?148P5iwUHg>0r=GV5F_9O
zoF_6AcSF-sD|Zp`tXwQ)3SynVm-M;-C#W?vH3C@^ltm)kXJfRM^Z^?|L8eq@7Dn<5
zdG2I5`y04!=ihrVzknCfPT*AV_ysPAB{8~sp6}6}OAr$8d8FfsB4f>O)4VzIO6Z;0
zzH)zSB4&zdDj^xlynTd5$%yH=XNeXQ1yO(LEzaI*3Pc1m+*EovnNF@rk@<DPhp=XN
zPvTusaRuS6yJIfac*^W+3G3vuzl%jE!brkw6hHG=EPWSaQ}ZM)ahCOHhPP%AJmI3g
zA35){d9IO!)GQg1+*mdQTNX)d#(dQJ)~eOrVk|w<C|(^btp9At!;_dNvE!-1b31*e
ztm@`_=oZqcLD7h#=?Yf=+Cw}G@Z`(L&4bV}1A&P8LQ^WPfkWglc^Pi?*sDs*C~bE>
z%b{!a*_&tkGnfmz$)Y@#Mn8zFevCF}-*B+T+8M;mg`?)-?PPodAG8cCgL^)^EyGcB
zrb2lbh-!>bR^)t@XJ4?V04a_c`i$@A8s8-EC_g17wAXHS^8)Q`OWz8&*Fu>}tJ{RL
za$)PsF9e(=Lad%D(h?6@_o&OySDx#-PTHbDI8tL^;mszzIh9=IaOTd-NMQ}jnVn3J
z`pI$mwXy>0&%09&M*Z_=z9V2qI12tDY;3Y(N35ZpKtxl5{{^s%z@)d7hXB+wu4>=F
z5Z&41@Uj8ExTX4Q=44_*e}#C_ZRIFAORCk{u@l~MzX^O81HamYs|J|QnjMWbyosF|
zdsZ^^>avK`G3n<`+|eD+ll<<63xr-8g2z?eK2(k|1a`(TMEhcCx6h10gh2YM^X3K{
zrVP$2jRu=r++O>$o*{`3C9^S__m2aB#R?G1p&GrG!`-_xG+a#w64%8@O?0<B)R<;I
zc2B}1<WgJoU2Qu}xcF$?TwNLL+wv9y#_H|`HJ^w9zf^c4ZPcd`nP4{SI_W*+LAzLZ
zv}o0!Zq@2O?ZIZ%Ha?c>?Ai5*Rh7(d@~KVNfqHWE{bvUuMw4}mk&3L^Ep~W`qnY6V
zd50Q@C>_oivtyH8xa2i0ls<iz@Exq3qjO~Nc6$yGob2P=xHj|-|8Z+g^u2#&&7yax
ze@(2^HGmJTFyA!z4Kz`Od9j}bzTXNX0m=-8gwNu>S+-rweBGGYY)OK&B3zs9d7d7a
zHa~H!BjHdb6Y8WhhmsY;bcJ+949Yc~FN`Mb-xy_TrsELcj`sp}xZ{MrG+a6v+}Z%S
z2xp5>91Qm2iW}a)g%uCM`@QY&xR&`Z@V5918v&hkj=wHY*FnF}WrG>zMsFm$(tJ`H
zSX!n$V9*%eOMp~<pI8V#kOND)N4D4NZwjrkk?KxPs{SJQWtSGc;)-k;)Il%mA=JgA
z^mgh#exE9!R+!R#z^n<PzTipAG6bl(IuQ>yF7C!w4k1P<Mf=|^uiU;+tFezMR~SFY
z;MCdUa*Z*$zT9+EKhCAR=^k*&p&KXgwfiG}TrVSj7k?y7^S4`aI<gWMt3&YJ^3rM%
zzM*NnBBF7EN%fu?Lb1;5{VcNwh2>aLE}L7j7dlkSm6=*#r%?n2v0Y{5uOASgqBhM%
zIK;#TM3gV(eaDlwQFDA|WiM7reXXa?MgKB8fyTEJw>~J8K?BT|!7ufUe{~(m(b$q1
z;>kA$9lVSH=xlL`)e`dc)&+r%?-s;zvncdGp+joy<E9xitC|C^<`tDnpn}ibBnaYq
zfXcf7vd6|HX81}a6ohXuF|#LMt^oYExCGBnZ8}btZ_7<0=De~$#0e~{9Kv*N`eF*;
z{nsRWHv=L`#wquhz}x-V>87Dj>9kNP2?tWiJr%@3%7Iv8<BzS>Fc}v?bx@LtuG&x$
z^(Bw_(5Cv@>wMxa35ZKtw4CO__2>0fQsum>zvkY{O3K+nSr2=AEDA;L0yMky-!;g>
zNW63?n+21bZfsPe)_;~5OsS3(^U0@KmLaaUqVnb%1>b|AcrNuZtk|OruReUmO4t&S
zwN*12M~8wo>S1~B9vs+oGa^OI9&gSY2(k8bCXpFhE)AMyet!!wa8}IM0`?-7=(iH=
z9f@LgsqX|hgIyZJ0mt@EKlZ(wmc8zT1(YtX{G0qvFMwm_^3}Y%nDZB)ipng8Yc9=Q
zlEzLZ6`t<-B3}@ZY=J2S!ZyvE(-$hQT?O{|EUyLVIHQ!mPV&^l^dMG}6vMylJ=0In
zaWcU5$Sy*g6E@1CZ2pxiGW|mt%|wk|0ZFH-;!WK7R@nTnlXLCo&=sGEM#m`(?^T9T
zrBYbmdM@3*%Rf}@gfuxu500eXi4#6=veoyEOZJ?apXFw(3?k)hu+4&-V<|H39&UHv
zILC`||8O+mT_bMos37iA|I+97<g8oK;xnsNP5$5`m#drk_4E3d_XW)L6hHw%hWH-D
zJox?IO}_%%{`bdgSpW`C)z&fg8%_E99(e4=jrgy${QJ<k=YPWdcRb&UTm4trZ%*`I
zuG*Up-!w<K822AI>%S-W9Qcdm|NV#S$N!M6{Oizl2WTJvMMwU3s_pdu7hSr%5=~YR
Uefu-27X!E{$*IehLrg;c59AVN?EnA(